From a4bacb2474f32de98db4ad3329659849c6770a07 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Mon, 3 Apr 2017 12:54:17 -0400 Subject: [PATCH] Updated VarDict data files --- .../PoolTumor2-T_bc52_VarDict_1.4.6.vcf | 88365 +++++++--------- ...lTumor2-T_bc52_VarDict_1.4.6_STDfilter.txt | 678 +- ...lTumor2-T_bc52_VarDict_1.4.6_STDfilter.vcf | 4535 +- 3 files changed, 38842 insertions(+), 54736 deletions(-) diff --git a/data/sample_input/PoolTumor2-T_bc52_VarDict_1.4.6.vcf b/data/sample_input/PoolTumor2-T_bc52_VarDict_1.4.6.vcf index 0408595..84d97a9 100755 --- a/data/sample_input/PoolTumor2-T_bc52_VarDict_1.4.6.vcf +++ b/data/sample_input/PoolTumor2-T_bc52_VarDict_1.4.6.vcf @@ -10,33 +10,34 @@ ##INFO= ##INFO= ##INFO= -##INFO= -##INFO= +##INFO= +##INFO= ##INFO= -##FILTER= +##FILTER= ##FILTER= -##FILTER= +##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= 0.05, thus not somatic"> -##FILTER= -##FILTER= +##FILTER= +##FILTER= ##FILTER= ##FILTER= 0.05"> ##FILTER= ##FILTER= 0.01/5**vd2"> ##FILTER= -##FILTER= -##FILTER== 4, thus likely false positive"> +##FILTER= +##FILTER== 7.25, thus likely false positive"> ##FILTER= ##FILTER= -##FILTER= +##FILTER= ##FILTER==14)"> ##FORMAT= ##FORMAT= ##FORMAT= -##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= @@ -52,51687 +53,36663 @@ ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PoolTumor2-T PoolNormal-N -1 131552 . G T 24 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTCCATCATGTCTCCT;RSEQ=ACACCCAGTTGCCTCTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:13:1:24:0:1:0:20:4:0.4:0:1 0/0:2:0:0,0:0,2:0:0,0:8.5:1:32.5:1:1:0:20:4:1:0:0.5 -1 133010 . C T 80 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.37171;SOR=0.24301;LSEQ=GGGAACCCCACGGACATGGA;RSEQ=CCCACACTGGAGGACCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:6,0:6,8:0.3:2,0:19:1:31.2:1:0.0419:0:20.5:12:0.3:0:1.5 0/1:11:1:1,0:6,4:0.0909:2,0:18:0:32:0:1:0:20:2:0.1:0:1 -1 133129 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53247;SOR=0;LSEQ=GGACAGCTTCCCCTTTGCCT;RSEQ=TACAGGTGGAGAAGCCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:9,4:0.1875:2,0:25.7:1:28.3:1:0.52857:0:30.7:6:0.1875:0:1.3 0/0:6:0:0,0:3,3:0:2,0:21:1:32.3:1:1:0:31.7:12:1:0:0 -1 133238 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCCTGATCATGCAGCTCT;RSEQ=CCAGGCCCACTGCTTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:26,29:0.0351:2,2:14:0:33:1:1:1.11:45.5:4:0.0357:0:1.5 0/0:17:0:0,0:10,7:0:2,0:27.8:1:27.8:1:1:0:44.7:34:1:0:0.2 -1 133481 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGGTGCCAGTTGGGGG;RSEQ=CGGTCCAGTGGGAGGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:14,23:0.0513:2,2:16.5:1:29:1:1:1.62:21:4:0.0513:0:2 0/0:9:0:0,0:3,6:0:2,0:35.7:1:30.2:1:1:0:21.7:18:1:0:0.3 -1 133483 . G T 82 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.57733;LSEQ=AGTGGTGCCAGTTGGGGGGC;RSEQ=GTCCAGTGGGAGGAGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:7:2,5:13,19:0.1795:2,2:23.7:1:29.3:1:0.68566:1.68817:21.4:14:0.1795:0:1.3 0/1:9:1:0,1:3,5:0.1111:2,0:41:0:31:0:1:0:22:2:0.1111:0:1 -1 133826 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.06462;SOR=Inf;LSEQ=CCTGGCTGCCCTGCCACTGC;RSEQ=TCTGCCCCAGAGTTGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:4,15:0:2,0:29.2:1:32.3:1:1:0:28.8:38:1:0:0.1 0/1:7:2:1,1:1,4:0.2857:2,2:22.5:1:29:1:1:3.16:22:4:0.2857:0:1 -1 569469 . G T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19231;SOR=0;LSEQ=TAGCCCACTTCTTACCACAA;RSEQ=GCACACCTACACCCCTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:8.5:1:28.5:1:1:2.45:49:4:0.3333:0:2 0/0:7:0:0,0:3,4:0:2,0:12.4:1:31.7:1:1:0:46.9:14:1:0:0.6 -1 657788 . G C 53 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04096;SOR=18.0326;LSEQ=CAACCCCACACACTTTGGGG;RSEQ=TGGTGGAACCTGGTAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:5,4:0.1:2,0:38:0:34:0:1:0:23:2:0.1:0:1 1/0:4:3:2,1:1,0:0.75:0,2:17.7:1:33.7:1:1:0:22.3:6:0.75:0:1 -1 657892 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19346;SOR=Inf;LSEQ=CAGAGAATGACCATGATGAT;RSEQ=CTTTCCTCTCCATCATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:20,1:0:1,0:21:1:33:1:1:0:24.1:42:1:0:0 0/1:17:2:1,1:14,1:0.1176:1,2:7:1:29:1:0.22794:10.24702:25:4:0.1176:0:1 -1 657915 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23557;SOR=Inf;LSEQ=TTCCTCTCCATCATGTCTCC;RSEQ=GACACCCAGTTGCCTCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:39,5:0:2,0:21.9:1:31.8:1:1:0:29.9:88:1:0:0.1 0/1:42:2:2,0:31,9:0.0476:2,0:34.5:1:31:1:1:0:21:4:0.0476:0:1 -1 658025 . CA GG 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45902;SOR=0.67061;LSEQ=TGGACGCAGCCCCAACAAAT;RSEQ=GACAAGGACCACATCCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:10:5,5:33,54:0.1031:2,2:22:1:30.3:1:0.50671:1.63:20.7:20:0.1031:0.0309:0.8 0/1:98:7:2,5:35,56:0.0714:2,2:8.6:1:29.3:1:0.7069:1.55579:25.6:14:0.0729:0.051:0.4 -1 658026 . A G 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00318;SOR=Inf;LSEQ=GGACGCAGCCCCAACAAATC;RSEQ=GACAAGGACCACATCCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:30,55:0:2,0:26:1:29.9:1:1:0:30.4:20.25:1:0:0.1 0/1:91:8:3,5:30,51:0.0879:2,2:25.8:1:29.4:1:1:1.02:35.6:16:0.093:0:1.1 -1 658043 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50512;SOR=0;LSEQ=ATCAGACAAGGACCACATCC;RSEQ=GTGGCCCATGAGTGGCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:24,51:0.026:2,2:17:1:29:1:0.54682:2.10:22:4:0.026:0:1 0/0:59:0:0,0:17,42:0:2,0:22.6:1:29.6:1:1:0:31.2:58:1:0:0.4 -1 658095 . C T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.41121;SOR=1.93321;LSEQ=CAGGCGGCACCAGGCCCTGG;RSEQ=GGGGCGCACCAGGGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:0,5:0,23:0.1786:1,0:27.8:1:30.4:1:1:0:20.2:10:0.1786:0:1 0/1:10:3:0,3:0,7:0.3:0,0:23.3:1:29:1:1:0:21:6:0.3:0:1 -1 658096 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01422;SOR=Inf;LSEQ=AGGCGGCACCAGGCCCTGGC;RSEQ=GGGCGCACCAGGGTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:0:1,0:25.2:1:32:1:1:0:21.4:56:1:0:0.3 0/1:10:3:0,3:0,7:0.3:0,0:27:1:31.7:1:1:0:21.7:6:0.3:0:1 -1 658410 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4963;SOR=Inf;LSEQ=AGAGCTCGGATACCAAGGAG;RSEQ=AGCTTCTATGGGGCAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:38,29:0:2,0:21.1:1:31.7:1:1:0:32:66:1:0:0.1 0/1:68:2:1,1:38,28:0.0294:2,2:41.5:1:29.5:1:1:1.35095:42:4:0.0294:0:1 -1 658417 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22086;SOR=0;LSEQ=GGATACCAAGGAGCAGCTTC;RSEQ=ATGGGGCAGAACGGCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:36,29:0.0299:2,2:26:1:30.5:1:1:1.23734:26:4:0.0299:0:1 0/0:75:0:0,0:41,34:0:2,0:22.1:1:29.2:1:1:0:35.4:150:1:0:0.2 -1 658434 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50327;SOR=Inf;LSEQ=TTCTATGGGGCAGAACGGCT;RSEQ=CACACAGTCAGGGAACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:26,34:0:2,0:26.6:1:31.5:1:1:0:32.7:29:1:0:0.2 0/1:76:2:1,1:37,37:0.0263:2,2:30.5:1:26.5:1:1:1:42.5:4:0.0274:0:1.5 -1 659146 . G A 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.6868;SOR=1.78019;LSEQ=GGGGATGGGGGCCCAGGGAC;RSEQ=CCTTCCAAGGTGGCCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:16,11:0.1:2,0:12:1:29.3:1:0.27931:0:20:6:0.1:0:1 0/1:24:4:4,0:11,9:0.1667:2,0:31.3:1:30:1:0.25889:0:20:8:0.1667:0:1.3 -1 935833 . C G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCCAGGGGGCCGGGAGC;RSEQ=GGGGCTGGACGGAGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:17.7:1:32:0:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 936111 . C T 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10178;SOR=0.30593;LSEQ=CGACAGAGCCGGGGGAAGGT;RSEQ=GGCGGCCGGGTCGGCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:18:8,10:3,3:0.75:2,2:25.8:1:29.6:1:1:1.23836:60:36:0.75:0:1.3 0/1:17:8:6,2:4,4:0.4706:2,2:34.5:1:30:1:0.60839:2.79:60:16:0.5:0:1 -1 936194 . A G 129 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10145;SOR=0;LSEQ=CCCGCAGAGCAGGGCCGGTG;RSEQ=TGGCGCGGGCCGGGCCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:5,11:0,0:1:0,2:20.3:1:32.4:1:1:0:60:32:1:0:1.9 1/0:8:6:1,5:1,1:0.75:2,2:28.2:1:30.5:1:0.46429:3.87298:60:12:0.75:0:2.8 -1 936210 . C A 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGATGGCGCGGGCCGGGC;RSEQ=GGACCACGAGGAGCAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:21.6:1:31.3:1:1:0:60:16:1:0:2 1/1:6:6:1,5:0,0:1:0,2:22:1:30.2:1:1:0:60:12:1:0:2.8 -1 938116 . T G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACAACCTCTGCTTCCTG;RSEQ=ATTCAAGCGATTCTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:18:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:29:1:28.5:1:1:0:60:4:1:0:1 -1 1001177 . G C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAAGGTGAAGCAAGTCAC;RSEQ=TGATCACAGGACAGCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:10,12:0,0:1:0,2:26.4:1:30.2:1:1:0:60:21:1:0:1.1 1/1:30:30:15,15:0,0:1:0,2:25.4:1:30.3:1:1:0:60:60:1:0:1.2 -1 1001194 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50786;SOR=Inf;LSEQ=CACGTGATCACAGGACAGCG;RSEQ=GCCCTTCCCTCTTAGGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:29.9:1:30.8:1:1:0:60:38:1:0:1.1 0/1:28:2:1,1:13,13:0.0714:2,2:13:1:30.5:1:1:1:60:4:0.0714:0:1 -1 2487055 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGGTTCCTGGTGTGCA;RSEQ=CAGGCGGTGCCAGAGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:28.5:1:1:0:60:4:1:0:1 -1 2487766 . T C 33 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCCGGAGTGGACTGGAA;RSEQ=GGTGCAGGGGGAGAACTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,1:0.2857:2,0:12:1:33:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 2487987 . ATTCTCT A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=4.000;MSILEN=6;SSF=0.59641;SOR=2.35639;LSEQ=AGCTTGTCACACCGAGGCGG;RSEQ=TTCTCTTTCTCTTTCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:1:1,0:168,8:0.0056:1,0:8:1:31.6:1:1:0:60:2:0.0057:0.0056:0 0/1:151:2:2,0:133,16:0.0132:2,0:7:1:30.5:1:1:0:60:4:0.0135:0.0066:0.5 -1 2488153 . A G 274 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21719;SOR=0.88652;LSEQ=TCCCTGGAGATCCACCCCCA;RSEQ=AACCGACGTCTTGAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:414:182,232:238,295:0.4367:2,2:25.8:1:31.6:1:0.84343:1.0284:60:137:0.4368:0:1.1 0/1:874:356:166,190:238,279:0.4073:2,2:25.1:1:31.5:1:0.89021:1.02:60:355:0.4104:0:1.1 -1 2488248 . C A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09402;SOR=Inf;LSEQ=GCCTCCCACAGATCTCTTCC;RSEQ=CATGCCCCTGTCCTGGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:47,240:0:2,0:22.5:1:31.4:1:1:0:60:286:0.9931:0:0.1 0/1:242:3:2,1:59,180:0.0124:2,2:17:1:30:1:0.15741:6.05:60:6:0.0126:0:1.3 -1 2488608 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTGGGTGGGGTGGGGA;RSEQ=ACTCTCCATGCTCATGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:21:1:33:1:0.33333:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 2488930 . G A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.03875;LSEQ=GTTCCAGTTCCCAGGGCTCC;RSEQ=CGCTGCCAGGCAGCGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:10,0:12,1:0.4348:1,0:27.8:1:29.9:1:1:0:60:20:0.4545:0:1 0/1:9:4:3,1:5,0:0.4444:0,2:32.3:1:31.3:1:0.44444:0:60:8:0.4444:0:1 -1 2489756 . C T 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.728;SOR=1.5141;LSEQ=AGGGGCCTCCCGCAGACTTG;RSEQ=GAAGTTCCCACTCTCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:3:1,2:271,137:0.0073:2,2:23.7:1:29.3:1:0.26524:3.94193:60:6:0.0074:0:1 0/1:455:5:2,3:279,171:0.011:2,2:13.4:1:28.8:1:0.37527:2.44237:60:10:0.0111:0:1 -1 2489962 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04308;SOR=Inf;LSEQ=TGGGCAGCCTGGATGCCCCC;RSEQ=CACCCTGCACCCTCTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:39,197:0:2,0:23.6:1:31.6:1:1:0:60:58:1:0:0.1 0/1:199:4:3,1:43,152:0.0201:2,2:6:1:27.8:1:0.03921:10.44:60:8:0.0204:0:1.3 -1 2490048 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1087;SOR=Inf;LSEQ=CCAACCCCATCTCCATGGAT;RSEQ=CACCCTGCAGGGGACGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:19,43:0:2,0:23.5:1:31.7:1:1:0:60:30:1:0:0.1 0/1:31:2:1,1:2,27:0.0645:2,2:22.5:1:27.5:1:0.1871:11.22:60:4:0.0645:0:1 -1 2490499 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20876;SOR=Inf;LSEQ=CTCATGCCAGGCTCAGCATG;RSEQ=CCAGTGCTCCCTGCGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:40,190:0:2,0:23.3:1:32:1:1:0:60:75.667:1:0:0.1 0/1:194:2:2,0:28,163:0.0103:2,0:8.5:1:28.5:1:0.02348:0:60:4:0.0103:0:1 -1 2490898 . C A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGATGGGAAACCCGTTTG;RSEQ=GGGGTGGGTGTCTGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:0.6:2,0:17.7:1:31.3:1:0.4:0:60:6:0.6:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 2490942 . C A 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGCGAGGACCTGCCTG;RSEQ=GGGACCCTGCCCTGGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:3,3:0.3333:2,0:36.3:1:30.3:1:0.46429:0:60:6:0.375:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 2491164 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01234;SOR=Inf;LSEQ=GGGGTTCAGCCTGGCAGGGC;RSEQ=CCCTGGCAGCAGTCCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:144,13:0:2,0:23.9:1:30.1:1:1:0:60:156:1:0:0.4 0/1:80:4:4,0:64,12:0.05:2,0:28.3:1:30.3:1:1:0:60:8:0.05:0:1 -1 2491205 . C T 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59545;SOR=1.10454;LSEQ=CTGTGGATGCTGTCCTGGCC;RSEQ=GTGGATGGTGTCCCGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:138:102,36:116,42:0.4662:2,2:23.6:1:30.6:1:1:1.03:60:68:0.4674:0:1.1 0/1:224:110:76,34:78,36:0.4911:2,2:22.8:1:30.4:1:1:1.03:60:35.667:0.4886:0:1.2 -1 2491228 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.049;SOR=Inf;LSEQ=GGATGGTGTCCCGGCCTCCA;RSEQ=GTACCCCTCTCAGCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:296,130:0:2,0:24.2:1:31.2:1:1:0:60:141:1:0:0.4 0/1:380:4:1,3:242,134:0.0105:2,2:12.5:1:23.8:1:0.13555:5.39344:60:3:0.008:0:1.3 -1 2493074 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15336;SOR=Inf;LSEQ=TGAGTGAACACTGGGCGCTG;RSEQ=ACCTGCCTCTCCCACGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:229,25:0:2,0:23.4:1:32.3:1:1:0:60:83.667:1:0:0.1 0/1:164:2:1,1:138,24:0.0122:2,2:18.5:1:26.5:1:0.28243:5.65426:60:4:0.0125:0:1.5 -1 2493328 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16082;SOR=Inf;LSEQ=AGCTCTGTCACCCCAAGCCT;RSEQ=GGAGGTGGCCCCAGAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:4,170:0:1,0:23.7:1:31.4:1:1:0:60:86:1:0:0.2 0/1:117:2:0,2:8,107:0.0171:2,0:17.5:1:31:0:1:0:60:4:0.0172:0:2 -1 2494197 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.1269;SOR=Inf;LSEQ=CTTGGGGACGGTCTCCCAGG;RSEQ=AGAAGCAGGAGTTGTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:165,13:0:2,0:21.7:1:30.7:1:1:0:60:18.778:1:0:0.2 0/1:99:2:1,1:86,11:0.0202:2,2:11.5:1:27:1:0.22882:7.52868:60:4:0.0206:0:1 -1 2494214 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16928;SOR=Inf;LSEQ=AGGGAGAAGCAGGAGTTGTG;RSEQ=CTCCGCCACCGCTGTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:187,24:0:2,0:25.5:1:31.5:1:1:0:60:25.375:1:0:0.2 0/1:148:2:1,1:120,26:0.0135:2,2:18:1:25.5:1:0.3326:4.54796:60:4:0.0136:0:1 -1 2494330 . G A 187 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.55565;LSEQ=TAGTCAAGGTGATCGTCTCC;RSEQ=TCCAGGTATTGATCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:805:3:3,0:388,411:0.0037:2,0:8.7:1:24:1:0.11542:0:60:6:0.0038:0:2.7 0/1:779:80:39,41:344,352:0.1027:2,2:25.4:1:29.6:1:1:1.02736:60:160:0.1044:0:1.2 -1 2494752 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34938;SOR=3.35297;LSEQ=GACGCCAGAGATACCTGGAG;RSEQ=GACGGCTGCTGAAAGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:1:0,1:83,216:0.0033:2,0:25:0:32:0:1:0:60:2:0.0034:0:2 0/1:270:3:1,2:76,190:0.0111:2,2:40.3:1:30.3:1:1:1.25:60:6:0.0112:0:2 -1 2494772 . T A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49968;SOR=0;LSEQ=CGACGGCTGCTGAAAGAGGC;RSEQ=GTCCACCTGGCGGAACCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:33,166:0.01:2,2:15:1:26.5:1:0.3104:4.97:60:4:0.0102:0:1.5 0/0:184:0:0,0:37,147:0:2,0:21.3:1:29.6:1:1:0:60:60.333:1:0:0.4 -1 2494779 . C A 21 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22021;SOR=Inf;LSEQ=TGCTGAAAGAGGCTGTCCAC;RSEQ=TGGCGGAACCACCGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:18,159:0:2,0:24.6:1:32.1:1:1:0:59.9:176:1:0:0.5 0/1:157:2:1,1:22,132:0.0127:2,2:8:1:21.5:1:0.27395:5.89:60:4:0.013:0:1.5 -1 2494784 . GG AA 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1977;SOR=Inf;LSEQ=AAAGAGGCTGTCCACCTGGC;RSEQ=AACCACCGGAGCCCGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:13,150:0:2,0:25.4:1:31.2:1:1:0:59.9:326:1:0:0.6 0/1:131:2:1,1:13,116:0.0153:2,2:5.5:1:26.8:1:0.20305:8.64:60:4:0.0155:0.0076:0.5 -1 2494785 . G A 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33983;SOR=0.78658;LSEQ=AAGAGGCTGTCCACCTGGCG;RSEQ=AACCACCGGAGCCCGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:74:4,70:8,77:0.4654:2,2:25.3:1:29.9:1:0.38354:1.81158:60:36:0.4645:0:1.1 0/1:128:52:6,46:6,69:0.4063:2,2:22.3:1:29.9:1:0.54767:1.50:60:51:0.4048:0:1.3 -1 2496582 . G C 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14326;SOR=0;LSEQ=CTGCTCCCAGGTCTGGCCTC;RSEQ=GTCACCAGCCACCTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:55:20,35:0,0:1:0,2:27:1:29.3:1:1:0:60:54:1:0:1.3 1/1:34:32:16,16:0,0:0.9412:0,2:30.5:1:29.3:1:1:0:60:64:0.9412:0:1.2 -1 2496649 . C G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99014;LSEQ=GGAGTGGCAGGTGCAGCCCC;RSEQ=GGTACTCACTCAGCCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:1,10:2,12:0.44:2,2:17.9:1:31.5:1:1:1.63407:60:22:0.44:0:2.5 0/1:16:7:3,4:0,9:0.4375:0,2:29.6:1:25.7:1:0.0625:0:60:6:0.4:0:2.4 -1 2496653 . A G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49131;SOR=1.68671;LSEQ=TGGCAGGTGCAGCCCCCGGT;RSEQ=CTCACTCAGCCCCAGGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:2,12:0.3333:2,0:25:1:32.4:1:0.53333:0:60:14:0.3333:0:2.6 0/1:13:6:3,3:0,7:0.4615:0,2:34:1:28.5:1:0.06993:0:60:5:0.4167:0:2.5 -1 2498027 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGGCCCACCAGAACCA;RSEQ=CAGGGAGAGAGAGGCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:33.5:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:12.5:1:33.5:1:1:0:60:4:1:0:1 -1 3189588 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=GCAGTTACACTAGTGCTGTG;RSEQ=TCGAGAGGGCAGCCGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:88,68:0:2,0:25.8:1:31.4:1:1:0:60:155:1:0:0.1 0/1:169:2:1,1:96,71:0.0118:2,2:46:1:28:1:1:1.34965:60:4:0.0118:0:1 -1 3189627 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.89611;LSEQ=TCTGCGTGGGAGAGGATGTG;RSEQ=GTTCAGAACCAGAAGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:0,1:80,90:0.0058:2,0:24:0:31:0:1:0:60:2:0.0059:0:1 0/1:181:2:1,1:82,97:0.011:2,2:22:1:28.5:1:1:1.18:60:4:0.011:0:1 -1 3189714 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01886;SOR=0.14547;LSEQ=CAGGGGCAGTGGGGAGCAGG;RSEQ=GCAGGGATGAGGTGGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:0,11:0,13:0.4583:1,0:30:1:31:1:1:0:60:22:0.4583:0:2 0/1:19:2:0,2:0,17:0.1053:1,0:36:1:27.5:1:1:0:60:4:0.1053:0:3 -1 3189732 . T A 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCAGGGATGAGGTGGGC;RSEQ=CCATGGCAGAGCAGGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:0,22:0,0:1:0,1:21.9:1:28.7:1:1:0:60:21:1:0:1.5 1/1:17:17:0,17:0,0:1:0,1:25.9:1:29.4:1:1:0:60:34:1:0:1.2 -1 3625768 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCCACGGGCTCCCCCA;RSEQ=CTGCTGGCTCCGGGCTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:31.3:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 3638567 . C T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0632;SOR=Inf;LSEQ=GACCACTGGTCTCACCCGCT;RSEQ=CCTCTCCCCCACTCCAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:60,14:0:2,0:21.5:1:31.1:1:1:0:60:148:1:0:0.1 0/1:50:3:2,1:35,12:0.06:2,2:20:1:31.7:1:1:1.44652:60:6:0.06:0:1.3 -1 3638574 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.75141;LSEQ=GGTCTCACCCGCTCCCTCTC;RSEQ=CCCACTCCAGTACTCCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:68,19:0.0225:2,2:15.5:1:29.5:1:0.40092:3.51368:60:4:0.0225:0:1 0/1:59:1:0,1:41,17:0.0169:2,0:1:0:25:0:0.30508:0:60:2:0.0172:0:2 -1 3638620 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22513;SOR=Inf;LSEQ=AAGAAACTCTACTGCCAGAT;RSEQ=GCCAAGACATGCCCCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:76,63:0:2,0:29.4:1:30.2:1:1:0:60:68.5:1:0:0.4 0/1:126:2:1,1:69,55:0.0159:2,2:35.5:1:27.5:1:1:1.25226:60:4:0.016:0:1.5 -1 3638661 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19947;SOR=Inf;LSEQ=GATCAAGGTGTCCACCCCGC;RSEQ=ACCCCCAGGCACCGCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:44,83:0:2,0:23:1:31.2:1:1:0:60:41.333:1:0:0.6 0/1:103:2:1,1:43,58:0.0194:2,2:13.5:1:32:0:1:1.34:60:4:0.0196:0:2 -1 3638663 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.19457;SOR=Inf;LSEQ=TCAAGGTGTCCACCCCGCCA;RSEQ=CCCCAGGCACCGCCATCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:39,82:0:2,0:23.6:1:31:1:1:0:60:59.5:1:0:0.6 0/1:96:2:1,1:40,54:0.0208:2,2:25:1:28:1:1:1.35:60:4:0.0213:0:1 -1 3638674 . C T 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09285;SOR=1.8173;LSEQ=ACCCCGCCACCCCCAGGCAC;RSEQ=GCCATCCGGGCCATGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:64:16,48:8,23:0.6667:2,2:26.5:1:29.8:1:1:1.04299:60:31:0.6667:0:1.2 1/0:79:62:23,39:6,10:0.7848:2,2:21.1:1:29.6:1:1:1.01717:60:61:0.7922:0:1.2 -1 3638834 . C T 45 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=AGCATCCCGGACAGCACAGC;RSEQ=GGGGGCTGCCTAACTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:24.5:1:31.5:1:1:0:60:8:1:0:0 1/1:3:3:0,3:0,0:1:0,0:31.3:1:29:1:1:0:60:6:1:0:1 -1 3640535 . C G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCCCAGGAGAGGTGGCCTG;RSEQ=AGGAGGCTGAGGCTGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:30.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:16:0:27:0:1:0:60:2:1:0:0 -1 3643681 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11497;SOR=Inf;LSEQ=CTGCTCCCCCATGTGCAGGT;RSEQ=GGGACGGAATTCACCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:27,4:0:2,0:21.9:1:32.5:1:1:0:60:62:1:0:0.1 0/1:34:4:3,1:24,6:0.1176:2,2:29.8:1:29:1:1:1.32135:60:8:0.1176:0:1 -1 3643776 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49749;SOR=Inf;LSEQ=CATCCTCATCATCATCACCC;RSEQ=GGAGATGCGGGAGTGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:20,35:0:2,0:22.3:1:30.2:1:1:0:60:110:1:0:0.2 0/1:62:2:1,1:24,36:0.0323:2,2:27.5:1:26.5:1:1:1.49:60:4:0.0323:0:1 -1 4832839 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05712;SOR=0.19528;LSEQ=CCCCTGGACGTGGGCAGTGG;RSEQ=GGGAAATGCATAGTCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:12:12,0:22,2:0.3333:2,0:23.6:1:27.3:1:0.54286:0:60:11:0.3235:0:1.1 0/1:23:2:2,0:21,0:0.087:1,0:25:1:30:1:1:0:60:4:0.087:0:1 -1 4832912 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.6413;LSEQ=CAGAGCCCAAAGGCCAGCCC;RSEQ=GTGGTTATTGGCCTCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:64,47:0.0089:2,0:1:0:15:0:0.42857:0:60:0:0:0:1 0/1:137:2:1,1:87,48:0.0146:2,2:8:1:29.5:1:1:1.80409:60:4:0.0146:0:1 -1 4832916 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21418;SOR=0;LSEQ=GCCCAAAGGCCAGCCCCGTG;RSEQ=TTATTGGCCTCCTAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:71,55:0.0156:2,2:22.5:1:29:1:1:1.2883:60:4:0.0163:0:1 0/0:148:0:0,0:94,54:0:2,0:23.6:1:30.8:1:1:0:60:73:1:0:0.1 -1 4833021 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19836;SOR=0;LSEQ=GGCAAATTTAGCAAAAATAT;RSEQ=AGATACCCACCAGACTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:47,84:0.015:2,2:21:1:26.5:1:1:1.78:60:4:0.0153:0:1 0/0:165:0:0,0:56,108:0:2,0:23.1:1:31.1:1:1:0:60:40:1:0:0.2 -1 4833164 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=CCCTTGAGTCAGCTTTCAAA;RSEQ=GTTTGTCCAGAATTAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:0:0,0:30.2:1:27.9:1:1:0:60:4:1:0:0.8 0/1:6:2:1,1:0,4:0.3333:0,2:15.5:1:28.5:1:0.33333:0:60:4:0.3333:0:1 -1 4834606 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGCAGGGCAGACGCCGTG;RSEQ=GTCTGTTTCACGGTAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:14.5:1:29.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 4834641 . T A 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTACCTCTCTTTGGACAT;RSEQ=CCTGTTTTCGTTCCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:7:0:30.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 4849109 . A G 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGAGTTACTGTACATAGA;RSEQ=TCAAGAGAGCAGTTTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:22:1:32.3:1:1:0:60:6:0.3333:0:1 0/0:1:0:0,0:1,0:0:0,0:43:0:32:0:1:0:60:2:1:0:0 -1 4849384 . T C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.13615;LSEQ=GAGTTCTAAGCCAAGACATG;RSEQ=GCTTGGGACTGGATTAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:137:55,82:141,164:0.31:2,2:25.8:1:30.2:1:0.2555:1.28109:60:33.25:0.3043:0:1.1 0/1:445:218:98,120:103,124:0.4899:2,2:25.5:1:30.4:1:1:1.01708:60:108:0.4887:0:1.2 -1 4849405 . T C 133 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.95871;LSEQ=GCTTGGGACTGGATTAACTC;RSEQ=TGTCAATATCTTGGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:1:0,1:164,242:0.0025:2,0:50:0:30:0:1:0:60:2:0.0025:0:4 0/1:379:22:9,13:136,221:0.058:2,2:23.7:1:30:1:0.82339:1.12:60:21:0.0569:0:2.2 -1 4955718 . C G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48326;SOR=0.6909;LSEQ=GTGTCTGCAAGCAGGCCCCC;RSEQ=GCCCAGAGCCTTGGCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:20:18,2:23,2:0.4444:2,2:23.9:1:29.9:1:1:1.27077:60:40:0.4444:0:1.1 0/1:31:11:11,0:20,0:0.3548:1,0:18.7:1:28.2:1:1:0:60:10:0.3333:0:1 -1 4955818 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26642;SOR=Inf;LSEQ=GGCCACCATGCTGAGCAAGC;RSEQ=GCAGATAAAAAAACAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:101,80:0:2,0:26.8:1:30:1:1:0:60:44.25:0.9944:0:0.3 0/1:249:3:1,2:138,107:0.012:2,2:13:1:27:1:0.58375:2.56974:60:6:0.0122:0:1 -1 4955824 . TA T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.17308;SOR=0;LSEQ=CATGCTGAGCAAGCGGCAGA;RSEQ=AAAAAACAGACAAACCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:103,85:0.0105:2,2:49:0:31:1:1:1.21053:60:4:0.0106:0:0 0/0:266:0:0,0:148,118:0:2,0:26.8:1:28.5:1:1:0:60:65.5:1:0:0.5 -1 4955833 . A T 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAGCGGCAGATAAAAAAAC;RSEQ=GACAAACCGGAGAGCACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:18:9,9:90,91:0.0905:2,2:26.8:1:29.8:1:1:1.01:60:36:0.0914:0:1.2 0/0:278:0:0,0:147,131:0:2,0:27:1:30.1:1:1:0:60:68.5:1:0:0.5 -1 4955834 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07026;SOR=0;LSEQ=AAGCGGCAGATAAAAAAACA;RSEQ=ACAAACCGGAGAGCACGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:1,2:95,99:0.0152:2,2:27:1:29:1:1:1.91309:60:6:0.0152:0:1.7 0/0:279:0:0,0:147,131:0:2,0:27.1:1:31.2:1:1:0:60:68.5:0.9964:0:0.5 -1 4955841 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17066;SOR=0;LSEQ=AGATAAAAAAACAGACAAAC;RSEQ=GGAGAGCACGGCACTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:93,104:0.0101:2,2:29.5:1:31:1:1:1.12:60:4:0.0102:0:1 0/0:282:0:0,0:140,142:0:2,0:27.1:1:29.5:1:1:0:60:55.4:1:0:0.5 -1 4955847 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16724;SOR=0;LSEQ=AAAAACAGACAAACCGGAGA;RSEQ=CACGGCACTCAGAACGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:89,106:0.0102:2,2:19.5:1:29:1:1:1.19:60:4:0.0104:0:1.5 0/0:284:0:0,0:139,145:0:2,0:26.6:1:31.5:1:1:0:60:70:1:0:0.5 -1 4955862 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.45443;LSEQ=GGAGAGCACGGCACTCAGAA;RSEQ=GGAACAGGGGACTTTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:36:11,25:65,84:0.1946:2,2:23.3:1:30.8:1:0.1876:1.75347:60:72:0.1957:0:1.1 0/1:259:118:52,66:66,75:0.4556:2,2:24.9:1:29.6:1:0.70768:1.11644:60:58:0.4531:0:1.2 -1 4955878 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26661;SOR=Inf;LSEQ=AGAACGGAACAGGGGACTTT;RSEQ=CAGTCCCCAGGAGCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:56,100:0:2,0:25.1:1:31.6:1:1:0:60:77:0.9872:0:0.4 0/1:217:3:1,2:86,127:0.0138:2,2:15.3:1:31:1:1:1.3525:60:6:0.0141:0:1 -1 4955947 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=ACAGATTCATGTTTTCTGTT;RSEQ=CTGCTCTGCCCCACAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:7,42:0:2,0:22.6:1:30.4:1:1:0:60:98:1:0:0.1 0/1:50:2:1,1:5,43:0.04:2,2:32.5:1:29:1:0.22776:7.94:60:4:0.0417:0:1 -1 4955972 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49209;SOR=0;LSEQ=TCTGCCCCACAGAACACCAG;RSEQ=TGTTAGGGCTGAATCGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:3,26:0.0645:2,2:16.5:1:28.5:1:0.24516:7.65:60:4:0.0667:0:1 0/0:29:0:0,0:1,28:0:1,0:25.4:1:31.6:1:1:0:60:58:1:0:0.1 -1 4956070 . T C 61 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGCTGTGTTTGAAGACAG;RSEQ=GCCTTTAAAGAGGTGGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,1:0.6667:0,0:23.8:1:30.8:1:1:0:60:8:0.6667:0:1 1/1:2:2:0,2:0,0:1:0,0:43:1:27:1:1:0:60:4:1:0:1 -1 5130529 . C T 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14962;SOR=Inf;LSEQ=CCTGAACCTTCTCCTAGGCC;RSEQ=ATCTGTGCACTTCCTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:0:2,0:30:1:30.3:1:1:0:60:24:1:0:0.1 0/1:43:5:3,2:19,19:0.1163:2,2:23.8:1:30.4:1:1:1.49:60:10:0.1163:0:1.2 -1 6226463 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGGCTGCAGAAGCCCC;RSEQ=CAAGGCAGGGGCTGGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 6226476 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCCACAAGGCAGGGGC;RSEQ=GGGAGAGAAGGGCCGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:32:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 6227936 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23973;SOR=Inf;LSEQ=CACCGTGGCGACGGAATCCA;RSEQ=CCCTGTCCCTCGCACAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:12,25:0:2,0:23.1:1:31.7:1:1:0:60:74:1:0:0 0/1:36:2:1,1:13,21:0.0556:2,2:20.5:1:24.5:1:1:1.59:60:4:0.0571:0:1.5 -1 7434493 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11682;SOR=Inf;LSEQ=TAGGGCAAACGAGAAAAGAG;RSEQ=CCAGCCTGCTGCTTAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:162,90:0:2,0:25.9:1:31.3:1:1:0:60:62:1:0:0.2 0/1:242:3:1,2:136,103:0.0124:2,2:14.7:1:28.3:1:0.5807:2.63031:60:6:0.0128:0:1.3 -1 7434541 . G A 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05718;SOR=Inf;LSEQ=GGCATGGGGAGAGGAGGAGG;RSEQ=GCCGCCAACAATGACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:0:0,0:175,185:0:2,0:25.7:1:30.7:1:1:0:60:71:1:0:0.3 0/1:346:4:3,1:168,174:0.0116:2,2:13.3:1:26:1:0.36709:3.10:60:8:0.0118:0:1 -1 7434544 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.3346;LSEQ=ATGGGGAGAGGAGGAGGGGC;RSEQ=GCCAACAATGACAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:51:25,26:144,159:0.1437:2,2:26.4:1:30.5:1:0.88031:1.06:60:50:0.1433:0:1.2 1/0:341:236:115,121:53,52:0.6921:2,2:25.5:1:30.2:1:0.81482:1.07218:60:58:0.6925:0:1.2 -1 7520069 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2321;SOR=Inf;LSEQ=CACAGAGTCTGGACCAGTGG;RSEQ=GAAGGGCAGCGCCATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:73,62:0:2,0:24:1:30.5:1:1:0:60:66.5:1:0:0.4 0/1:126:2:1,1:68,56:0.0159:2,2:33.5:1:30.5:1:1:1.2124:60:4:0.016:0:1.5 -1 7520123 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49858;SOR=Inf;LSEQ=CTTCAAAGGCAAGGCCATCT;RSEQ=CCAGCCGCTCACTGTGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:86,85:0:2,0:24.6:1:32.2:1:1:0:60:170:1:0:0.7 0/1:174:2:1,1:84,88:0.0115:2,2:25.5:1:27.5:1:1:1.05:60:4:0.0118:0:2 -1 7520128 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24776;SOR=0;LSEQ=AAGGCAAGGCCATCTGCCAG;RSEQ=CGCTCACTGTGGGTCCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:81,84:0.012:2,2:26.5:1:28.5:1:1:1.04:60:4:0.012:0:1 0/0:168:0:0,0:84,84:0:2,0:25.7:1:31.1:1:1:0:60:41:1:0:0.4 -1 7520129 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22887;LSEQ=AGGCAAGGCCATCTGCCAGC;RSEQ=GCTCACTGTGGGTCCCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:167:91:45,46:35,39:0.5449:2,2:24.8:1:31:1:0.87571:1.09:60:182:0.5515:0:1.1 0/1:168:36:18,18:66,66:0.2143:2,2:26.8:1:30.5:1:1:1:60:72:0.2169:0:1.2 -1 7520187 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49844;SOR=0;LSEQ=TGTGTGTGGAGTCATGCACT;RSEQ=GGCCCCTGCAGCTTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:55,64:0.0165:2,2:29.5:1:28:1:1:1.16:60:4:0.0169:0:1 0/0:113:0:0,0:42,71:0:2,0:24.7:1:29.6:1:1:0:60:112:1:0:0.5 -1 7520247 . C G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11449;SOR=2.20392;LSEQ=GAGAGCTGGGGAGGGGCCCG;RSEQ=CGTCCTCTCCCGTGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:12:3,9:8,35:0.2105:2,2:20.8:1:28.5:1:0.68894:1.45:60:5:0.1852:0:2.4 0/1:43:16:1,15:4,23:0.3721:2,1:18:1:32.3:1:0.63536:2.55798:60:32:0.3721:0:1.8 -1 7520258 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00372;SOR=0.22692;LSEQ=AGGGGCCCGCCGTCCTCTCC;RSEQ=GTGGCGGCCCCTCTGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:36:5,31:1,8:0.8:2,2:26.8:1:30.3:1:1:1.28:60:72:0.8:0:1.5 0/1:34:16:0,16:2,16:0.4706:2,1:17.3:1:30.8:1:0.48663:0:60:32:0.4706:0:1.8 -1 7520283 . C A 83 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.66409;SOR=0.46699;LSEQ=CGGCCCCTCTGCTTTGCATC;RSEQ=CTTTTGTCCACCTGGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:2,27:0.1944:2,0:27.7:1:29.9:1:1:0:60:14:0.1944:0:3 0/1:10:1:0,1:0,9:0.1:0,0:3:0:26:0:1:0:60:2:0.1:0:3 -1 7520379 . G C 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02778;SOR=Inf;LSEQ=CTGACCTTGAATGAAAAGGG;RSEQ=ACACTTCATCCTCCGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:24.3:1:32.3:1:1:0:60:14:1:0:0.1 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30:1:1:0:60:4:1:0:1.5 -1 8074334 . C T 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.44937;LSEQ=AAAACCACATACAACTTGAT;RSEQ=CTCTTCATGTGGTCCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:217:102,115:555,591:0.1592:2,2:23.6:1:30:1:0.71166:1.05876:60:53.25:0.1594:0:1.1 0/1:1926:151:73,78:897,875:0.0784:2,2:22.8:1:28.9:1:0.61166:1.0953:60:74.5:0.0782:0:1.1 -1 8075620 . T C 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=46.91223;LSEQ=CCCATGGCTCGGCCATTATG;RSEQ=AGAAATCCAGTTTTTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1006:1:0,1:478,525:0.001:2,0:25:0:14:0:1:0:60:0:0:0:8 0/1:1322:59:23,36:595,666:0.0446:2,2:21.7:1:31.6:1:0.23195:1.398:60:58:0.0441:0:1.2 -1 8075894 . C T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.73819;LSEQ=GTAGACTTTCACTTAATTCT;RSEQ=ACAGCTCGTGAGGGTACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:15:0,15:0,22:0.4054:1,1:23.9:1:27.3:1:1:0:60:14:0.3889:0:1.1 0/1:9:3:0,3:0,6:0.3333:0,0:34.3:1:28:1:1:0:60:6:0.3333:0:1 -1 8079897 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19808;SOR=Inf;LSEQ=GCTTCAGTGGTTAACAGTGT;RSEQ=GCTTTCTAAACTGGTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:146,3:0:1,0:24.6:1:28.1:1:1:0:60:48.667:1:0:0 0/1:120:2:1,1:116,2:0.0167:1,2:26.5:1:32.5:1:0.04958:47.56167:60:4:0.0169:0:1 -1 8080236 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49645;SOR=Inf;LSEQ=TAAATCTCAGAAGCCATCCA;RSEQ=GGGAGGAGGAGGGGCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:1,70:0:1,0:25:1:30.3:1:1:0:60:142:1:0:0.1 0/1:71:2:0,2:2,67:0.0282:1,0:20:1:28.5:1:1:0:60:4:0.0282:0:1.5 -1 8084992 . T TA 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATAAGAAAAGAAATGCAGT;RSEQ=AAAAAAATAGGTACGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:800:0:0,0:519,279:0:2,0:25.3:1:29.1:1:1:0:60:48.875:1:0:0.1 0/1:996:31:20,11:587,378:0.0311:2,2:31.3:1:29.2:1:0.71348:1.17:60:62:0.0315:0:0.1 -1 8085030 . C T 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACTTGGGATGTTCAGTCT;RSEQ=AACAAATGTGTGTACCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1246:0:0,0:677,569:0:2,0:25.1:1:31.5:1:1:0:60:68.222:1:0:0.1 0/1:1616:56:31,25:821,738:0.0347:2,2:24.9:1:29.2:1:0.7856:1.11:60:55:0.0344:0:1.1 -1 8085328 . T C 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.76878;SOR=0.71574;LSEQ=AATAAAGACTTAGCAAGCAC;RSEQ=AATACAGCACCATTCACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:20:0,20:0,16:0.5556:1,1:31.2:1:32.3:1:1:0:60:40:0.5556:0:1 0/1:17:8:0,8:0,9:0.4706:0,0:27.1:1:31.3:1:1:0:60:16:0.4706:0:1.1 -1 8957947 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21587;SOR=Inf;LSEQ=TCAGGGATAGTATGAGATGC;RSEQ=GCCTGGCGTTTACAGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:13,6:0:2,0:30.1:1:31.6:1:1:0:55.8:38:1:0:0.1 0/1:17:2:1,1:10,5:0.1176:2,2:23:1:31.5:1:1:1.91491:26:4:0.1176:0:6 -1 8957951 . TG CA 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03604;SOR=Inf;LSEQ=GGATAGTATGAGATGCTGCC;RSEQ=GCGTTTACAGGAAAAGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:15,5:0:2,0:28.2:1:31.4:1:1:0:55.7:40:1:0:0.1 0/1:17:4:2,2:9,4:0.2353:2,2:32.5:1:30.6:1:0.58403:2.13794:25.5:8:0.2353:0:3.5 -1 8957975 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49291;SOR=Inf;LSEQ=GTTTACAGGAAAAGGCTTCT;RSEQ=AAATCAGACAATGCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:24.3:1:31.3:1:1:0:57.4:44:1:0:0 0/1:26:2:1,1:14,10:0.0769:2,2:36.5:1:28.5:1:1:1.38168:26:4:0.0769:0:5 -1 8958004 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51186;SOR=Inf;LSEQ=CAATGCCTTTCAAACTCTTA;RSEQ=ACCAATCTCTGGAGTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:0:2,0:27.1:1:28.8:1:1:0:57.2:23:1:0:0.1 0/1:36:2:1,1:17,17:0.0556:2,2:13.5:1:33:0:1:1:21:4:0.0556:0:4 -1 8958010 . T A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27657;SOR=Inf;LSEQ=CTTTCAAACTCTTATACCAA;RSEQ=CTCTGGAGTTGGGCAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:27.8:1:29.4:1:1:0:57.2:23:1:0:0.2 0/1:38:3:1,2:15,18:0.0789:2,2:16.3:1:30:1:1:1.64403:25.7:6:0.0833:0:4.3 -1 8958025 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50992;SOR=Inf;LSEQ=ACCAATCTCTGGAGTTGGGC;RSEQ=ACATGGCTTCTCCCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:11,15:0:2,0:26.2:1:30:1:1:0:57.4:25:1:0:0.3 0/1:38:2:0,2:15,21:0.0526:2,0:9:1:32.5:1:0.50925:0:25.5:4:0.0526:0:4 -1 8958038 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51186;SOR=Inf;LSEQ=GTTGGGCAACATGGCTTCTC;RSEQ=CCTTTCTAGGTCCCGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:25.9:1:30:1:1:0:57.2:11:1:0:0.3 0/1:36:2:1,1:14,20:0.0556:2,2:47.5:1:30.5:1:1:1.41:21:4:0.0556:0:4 -1 8958110 . A C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.45647;LSEQ=TAATTTTTAACCTCCTTGTC;RSEQ=AATTTGTTTCCTCTAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:0,6:0.25:0,2:5.5:1:29:1:0.25:0:60:4:0.25:0:1.5 0/1:6:2:1,1:1,3:0.3333:2,2:12:1:32.5:1:1:2.45:60:4:0.3333:0:1 -1 9770415 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50156;SOR=0;LSEQ=GGACCCCACTGTTTTCCAGG;RSEQ=AGTCCCTTCCAAAGGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:101,6:0.0183:2,0:23:1:28:1:1:0:60:4:0.0189:0:1 0/0:91:0:0,0:88,3:0:1,0:20.8:1:30.8:1:1:0:60:29.333:1:0:0 -1 9770714 . C G 146 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-04;SOR=4.49387;LSEQ=GAGAGAGAGAGAGAGAGAGA;RSEQ=ACAGATAGACAGACAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:7:2,5:58,210:0.0254:2,2:9.9:1:29.7:1:0.64891:1.45:58.6:14:0.026:0:1 0/1:305:32:11,21:67,206:0.1049:2,2:14:1:29.2:1:0.28302:1.61:59.1:15:0.1014:0:1.3 -1 9775554 . G T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2478;SOR=0;LSEQ=CCTCAGCCTCCCACCTCCCA;RSEQ=TGGCTGCCTTGGGTGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:1,2:125,43:0.0175:2,2:15.3:1:29.3:1:0.16967:5.74146:60:6:0.018:0:1 0/0:171:0:0,0:131,40:0:2,0:23.6:1:31.3:1:1:0:60:56:1:0:0.1 -1 9775957 . G A 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00213;SOR=Inf;LSEQ=CAGAAGTGAACGACTTTCGC;RSEQ=CCAAGATGTGCCAATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:0:0,0:273,272:0:2,0:24.5:1:30.5:1:1:0:60:44.417:1:0:0.2 0/1:607:10:6,4:312,284:0.0165:2,2:20.5:1:24.3:1:0.75492:1.36:60:2.333:0.012:0:1.5 -1 9776339 . A G 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03701;SOR=Inf;LSEQ=ATAACCAAGTGGCGTGGGGC;RSEQ=TTGGGCATCAGTTTGTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:52,20:0:2,0:24.4:1:30.4:1:1:0:60:35:1:0:0.1 0/1:37:3:2,1:28,6:0.0811:2,2:28.7:1:32:0:0.47748:2.2687:60:6:0.0811:0:1 -1 9776442 . C T 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.68708;SOR=0.52996;LSEQ=ATAGGCAACCCTGCCCTGTG;RSEQ=CCCAGAACCCCGGGGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:4:2,2:258,101:0.011:2,2:28.3:1:29.8:1:0.3194:2.54688:60:8:0.0112:0:1 0/0:341:2:1,1:229,110:0.0059:2,2:4:0:29:0:0.54571:2.07699:60:4:0.006:0:1.5 -1 9776709 . C G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2176;SOR=Inf;LSEQ=GAGGCCCTCTGCACTCTGGG;RSEQ=TCCCAACGCCCTGGATAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:47,140:0:2,0:24.1:1:31.7:1:1:0:60:22.375:1:0:0.1 0/1:164:2:1,1:41,121:0.0122:2,2:32:1:26:1:0.44778:2.93:60:4:0.0126:0:1 -1 9776738 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14906;SOR=Inf;LSEQ=CCCTGGATAGGGCCTGGGTG;RSEQ=GAGTCGGGGAGCTGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:29,99:0:2,0:22.3:1:31.2:1:1:0:60:41.667:1:0:0.2 0/1:81:2:1,1:4,75:0.0247:2,2:20:1:28.5:1:0.12037:16.88:60:4:0.0256:0:1.5 -1 9776903 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16827;SOR=Inf;LSEQ=AAACCAGCAGGAAGCCCTCC;RSEQ=CTCTCCCAAGGCCTAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:142,14:0:2,0:25.8:1:31.6:1:1:0:60:155:1:0:0.1 0/1:109:2:1,1:97,10:0.0183:2,2:24.5:1:28:1:0.19249:9.29614:60:4:0.0183:0:1 -1 9776926 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20746;SOR=Inf;LSEQ=CTCCCAAGGCCTAGGACAGG;RSEQ=AGTGGGCAGCTTGGGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:191,20:0:2,0:25.6:1:32.1:1:1:0:60:69.333:1:0:0.1 0/1:177:2:1,1:158,17:0.0113:2,2:33.5:1:29:1:0.19357:9.0608:60:4:0.0114:0:1.5 -1 9777247 . G A 29 v4;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=TCCATGTGCTACTGGCCATG;RSEQ=GTCCAGGGGCCCTTGGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:2,0:9,149:0.0125:2,0:13.5:1:29:1:0.00432:0:60:4:0.0129:0:1.5 0/0:96:0:0,0:4,92:0:1,0:22.3:1:30.4:1:1:0:60:95:1:0:0.1 -1 9777451 . G GGA 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00886;SOR=3.64216;LSEQ=ATGGCAGGTTTTCTGGGAAA;RSEQ=GATAGCATTGTGGACAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:11:11,0:34,2:0.234:2,0:20.8:1:31:1:1:0:60:22:0.234:0.0851:0.2 1/0:32:17:17,0:15,0:0.5313:1,1:18.8:1:30.5:1:1:0:60:34:0.5484:0.125:0.1 -1 9777521 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49856;SOR=0;LSEQ=CACCCGCCCCCAAGTGGTCA;RSEQ=GGGCCTCACCATAGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:139,22:0.0123:2,2:11.5:1:29.5:1:0.26305:6.2015:60:4:0.0126:0:1 0/0:158:0:0,0:122,36:0:2,0:23.5:1:29.9:1:1:0:60:30.6:1:0:0.2 -1 9777586 . G C 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTAACAGCCCTGCTTCCCC;RSEQ=GCCCCCAGCCTTCCTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:249,156:0:2,0:23.3:1:29.8:1:1:0:60:44:1:0:0.1 0/1:493:30:16,14:269,194:0.0609:2,2:29.4:1:28.7:1:0.70359:1.21279:60:29:0.0605:0:1.2 -1 9778707 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22241;SOR=Inf;LSEQ=TTAAGGGGGAGGGGAGAGGG;RSEQ=CTGGGCCTCTGCCTCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:91,16:0:2,0:23.8:1:30.4:1:1:0:60:16.833:1:0:0.1 0/1:96:2:1,1:78,15:0.0208:2,2:26.5:1:31.5:1:0.30997:5.06719:60:4:0.0215:0:1 -1 9778724 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24558;SOR=0;LSEQ=GGGGCTGGGCCTCTGCCTCC;RSEQ=CACCCATCATCCCGGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:110,28:0.0143:2,2:19.5:1:33:0:0.37256:3.87775:60:4:0.0149:0:1 0/0:142:0:0,0:110,32:0:2,0:25.5:1:30:1:1:0:59.9:16.75:1:0:0.2 -1 9778738 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.6229;SOR=2.01877;LSEQ=GCCTCCTCACCCATCATCCC;RSEQ=GCACCTTCTACAGCTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:1:0,1:132,46:0.0056:2,0:1:0:25:0:0.26257:0:60:2:0.0057:0:1 0/1:179:2:1,1:132,45:0.0112:2,2:25.5:1:28.5:1:0.449:2.91248:60:4:0.0113:0:1 -1 9778739 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12092;SOR=Inf;LSEQ=CCTCCTCACCCATCATCCCG;RSEQ=CACCTTCTACAGCTGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:136,47:0:2,0:24.3:1:31:1:1:0:60:35.6:1:0:0.2 0/1:181:3:2,1:131,47:0.0166:2,2:28.3:1:30.7:1:1:1.39088:60:6:0.0171:0:1.3 -1 9778808 . C T 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17906;SOR=0.20117;LSEQ=ATGCTGTGCAAGACGGTGTC;RSEQ=AGCTCGGAGGTGAGCGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:4:1,3:209,167:0.0105:2,2:23:1:28:1:0.3289:3.74225:60:8:0.0107:0:1 0/0:469:1:0,1:258,209:0.0021:2,0:1:0:26:0:0.44872:0:60:2:0.0022:0:1 -1 9779862 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52854;SOR=0;LSEQ=CAGGGTCTCCCAGGGGTCTG;RSEQ=TTGGGAGATGTTAGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:2,0:117,4:0.0163:1,0:25.5:1:31.5:1:1:0:60:4:0.0165:0:1.5 0/0:74:0:0,0:67,7:0:2,0:24.9:1:31.5:1:1:0:60:148:1:0:0.2 -1 9779871 . T C 137 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98739;LSEQ=CCAGGGGTCTGGTTGGGAGA;RSEQ=GTTAGCTGGGCTCTGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:21:20,1:120,5:0.1429:1,1:28.8:1:31.3:1:1:1.19839:60:20:0.1418:0:1.1 0/1:92:13:13,0:69,10:0.1413:2,1:24.5:1:31.8:1:0.34674:0:60:26:0.1413:0:1.1 -1 9780462 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10279;SOR=Inf;LSEQ=TTTGCCTGCAGGGATGCTGC;RSEQ=CAGTCTGATGACATTTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:158,61:0:2,0:24.5:1:30.2:1:1:0:60:35.5:1:0:0.1 0/1:194:3:1,2:132,59:0.0155:2,2:11:1:29.7:1:0.23318:4.43619:60:6:0.0159:0:1 -1 9780743 . TG T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.03061;SOR=0;LSEQ=AGTGGGGTGGGGGTGTGGGG;RSEQ=GGGGGCATGGAGCCGGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:5:3,2:226,256:0.0102:2,2:30.2:1:30.8:1:0.66973:1.70:60:10:0.0105:0:0.2 0/0:490:0:0,0:225,258:0:2,0:22.9:1:30:1:1:0:59.9:39.25:0.9874:0:0.8 -1 9780987 . T C 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGGTGGGGAGGCGCACC;RSEQ=GGGGGCGGAGCTGGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:112,231:0:2,0:23.3:1:30.1:1:1:0:60:56.167:1:0:0.2 0/1:304:32:6,26:86,186:0.1053:2,2:22.8:1:29.2:1:0.1575:1.99954:60:64:0.1081:0:1.2 -1 9781004 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25078;SOR=0;LSEQ=ACCTGGGGGCGGAGCTGGGG;RSEQ=CAGACCACAGCCTCTGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:2,1:70,169:0.0124:2,2:15:1:28.7:1:0.21182:4.79:60:6:0.0127:0:1 0/0:216:0:0,0:65,151:0:2,0:22.7:1:31.7:1:1:0:60:432:1:0:0.3 -1 9781106 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21702;SOR=Inf;LSEQ=GGCCACCCACCACCCTGACC;RSEQ=TGGCTGGCCATCACCCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:124,52:0:2,0:23.3:1:31.1:1:1:0:60:43:1:0:0.1 0/1:154:2:1,1:107,45:0.013:2,2:29.5:1:29:1:0.50955:2.36278:60:4:0.0131:0:1 -1 9781144 . T C 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25052;SOR=Inf;LSEQ=TACCCTGACCACCTCCACCC;RSEQ=GACCCCGGCCGCCCCCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:185,83:0:2,0:24.8:1:30.7:1:1:0:60:43.667:1:0:0.1 0/1:296:3:1,2:218,75:0.0101:2,2:16:1:22:1:0.16686:5.77128:60:2:0.0068:0:2.3 -1 9781340 . G A 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06229;SOR=Inf;LSEQ=GGGCGCTCCCCACTTCTCCA;RSEQ=AGGGCAGCTGTGTCCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:171,259:0:2,0:23.5:1:31.5:1:1:0:60:429:0.9977:0:0.2 0/1:456:5:3,2:171,279:0.011:2,2:10.6:1:24.4:1:0.37527:2.44:60:4:0.0089:0:2.2 -1 9781363 . C A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37121;SOR=3.04628;LSEQ=GGCAGCTGTGTCCTGGCTGC;RSEQ=AGGACGTGGGCTCTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:1:1,0:97,200:0.0034:2,0:1:0:25:0:0.32886:0:60:2:0.0034:0:1 0/1:295:3:1,2:76,216:0.0102:2,2:8.3:1:21:1:1:1.42:60:2:0.0069:0:3.3 -1 9781412 . C G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=3.00701;LSEQ=CCTTCCCGTGGGCTTGCTCC;RSEQ=TCCTGCCTGGCCTCCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:38:22,16:71,96:0.1854:2,2:19.8:1:30.4:1:0.10465:1.85:60:76:0.1881:0:1.1 0/1:172:70:32,38:38,64:0.407:2,2:21.9:1:30.6:1:0.27421:1.42:60:140:0.4118:0:1.1 -1 9781421 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21488;SOR=Inf;LSEQ=GGGCTTGCTCCCTCCTGCCT;RSEQ=GCCTCCCTCTGGCTGCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:103,92:0:2,0:23.2:1:31.7:1:1:0:60:47.75:1:0:0.3 0/1:169:2:1,1:78,89:0.0118:2,2:26.5:1:31:1:1:1.14:60:4:0.0119:0:1.5 -1 9781725 . C T 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67282;LSEQ=GCCACTGGGGACGTTTCCAG;RSEQ=AGGCCTGGGTGTCCTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:3:2,1:143,97:0.0123:2,2:23.7:1:30.7:1:1:1.35:55:6:0.0124:0:3.3 0/0:240:2:0,2:136,102:0.0083:2,0:19.5:1:23.5:1:0.18675:0:60:4:0.0084:0:1 -1 9781880 . A G 49 q23 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02779;SOR=0;LSEQ=TCATCCTGGAGGCCTACTGC;RSEQ=GGGGCAGCACCCACCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:5:2,3:228,253:0.0103:2,2:33.4:1:21.2:1:1:1.35095:60:1.5:0.0063:0:2 0/0:507:0:0,0:212,294:0:2,0:23.6:1:30.1:1:1:0:60:55.222:0.998:0:0.2 -1 9782386 . C T 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGCAGGCAGCGGCGGCAG;RSEQ=GTGGGCATCATCTTTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:665:0:0,0:302,363:0:2,0:25.2:1:30.6:1:1:0:60:54.417:1:0:0.1 0/1:859:30:17,13:392,435:0.0349:2,2:18.1:1:30:1:0.35547:1.45:60:60:0.0358:0:1.2 -1 9782556 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.0836;LSEQ=GAGAACCTACCAGAAACTCA;RSEQ=GCTTCTCCTCCCACCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:78:46,32:204,101:0.2037:2,2:23:1:30.8:1:0.23018:1.40374:60:77:0.2042:0:1.2 0/1:383:169:120,49:141,73:0.4413:2,2:25.9:1:30:1:0.32064:1.27:60:338:0.4436:0:1.1 -1 9782766 . C T 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGCATGACCATCTCAGC;RSEQ=GGGGAAAGGGCTTTCCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:15,215:0:2,0:25.2:1:29.8:1:1:0:60:75.667:1:0:0.1 0/1:193:17:2,15:15,161:0.0881:2,2:25.4:1:29.6:1:0.6496:1.43:60:16:0.0856:0:1 -1 9783074 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25192;SOR=0;LSEQ=GCTTTTTAGCAATGTGGGCA;RSEQ=CAGCATCTTCTGTGGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:3:2,1:123,7:0.0226:2,2:24.3:1:28.3:1:0.17103:8.45409:60:6:0.0229:0:1 0/0:113:0:0,0:108,5:0:1,0:25.3:1:32.2:1:1:0:60:112:1:0:0.2 -1 9783405 . G A 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCAAGAGGTGTGGAGTG;RSEQ=GAGGGCCTCGCCTGTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:65,210:0:2,0:22.4:1:30.9:1:1:0:60:90.667:1:0:0.1 0/1:291:35:10,25:63,193:0.1203:2,2:21.7:1:30.1:1:0.67784:1.22:60:70:0.1232:0:1.2 -1 9783923 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5061;SOR=0;LSEQ=CCATGTTCTGTTGGTCAAAG;RSEQ=AAGTCACAGGGCCAGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:133,7:0.0141:2,2:29.5:1:29.5:1:0.10988:17.83657:60:4:0.0144:0:1 0/0:110:0:0,0:102,8:0:2,0:22.6:1:31.6:1:1:0:60:54:1:0:0.2 -1 9784224 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20661;SOR=Inf;LSEQ=CTGCTGGCCCCTCTGCCTAG;RSEQ=ACACAGCTCTGTGGCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:93,126:0:2,0:24.7:1:32:1:1:0:60:53.75:1:0:0.1 0/1:183:2:1,1:74,107:0.0109:2,2:7.5:1:28:1:1:1.44:60:4:0.0111:0:1 -1 9784241 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20866;SOR=Inf;LSEQ=TAGCACACAGCTCTGTGGCA;RSEQ=GGGTCCCCCAGCCCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:93,105:0:2,0:25.3:1:31.9:1:1:0:60:197:1:0:0.1 0/1:167:2:1,1:82,83:0.012:2,2:12:1:27.5:1:1:1.01:60:4:0.0121:0:1 -1 9784247 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.21137;SOR=Inf;LSEQ=ACAGCTCTGTGGCAGGGGTC;RSEQ=CCCAGCCCTGCTGGCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:104,94:0:2,0:24.8:1:31.1:1:1:0:60:48.5:1:0:0.1 0/1:169:2:1,1:96,71:0.0118:2,2:19.5:1:28:1:1:1.34965:60:4:0.012:0:1 -1 9784279 . A G 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10244;SOR=Inf;LSEQ=TGGCTTCCTGTCTCCCCTGG;RSEQ=TTCTCTCCTGTCTGACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:181,76:0:2,0:22:1:30.1:1:1:0:60:35.714:1:0:0.1 0/1:227:3:2,1:166,58:0.0132:2,2:14.3:1:25.7:1:1:1.4286:60:2:0.009:0:1.3 -1 9784423 . C T 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=44.60602;LSEQ=GTCCCATTCATCCTCACCTA;RSEQ=GACTTTGTCCATGTGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:772:1:0,1:347,423:0.0013:2,0:46:0:14:0:1:0:60:0:0:0:1 0/1:895:49:25,24:385,460:0.0547:2,2:26.2:1:30.1:1:0.46505:1.24:59.9:98:0.055:0:1.1 -1 9786882 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=0;LSEQ=CTACTAACCATTTCATTCAG;RSEQ=GACTCTGAAGTCCCCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:160,13:0.0114:2,2:25.5:1:30.5:1:0.15402:11.89718:60:4:0.0115:0:1 0/0:170:0:0,0:142,28:0:2,0:21.2:1:29.2:1:1:0:60:55.667:1:0:0.2 -1 9787140 . C A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24909;SOR=Inf;LSEQ=CTGGGCCCAAGAGGAGGCGG;RSEQ=TGCGGGTCGTGGGGACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:53,195:0:2,0:22.3:1:31.5:1:1:0:60:26.556:0.9958:0:0.1 0/1:263:3:1,2:64,195:0.0114:2,2:19.7:1:22.7:1:1:1.52:60:2:0.0078:0:2.3 -1 9787143 . C T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10859;SOR=0;LSEQ=GGCCCAAGAGGAGGCGGCTG;RSEQ=GGGTCGTGGGGACCAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:0,3:40,187:0.013:2,0:24:1:31.7:1:1:0:60:6:0.0134:0:1 0/0:251:0:0,0:58,193:0:2,0:23.1:1:29.8:1:1:0:60:49.2:1:0:0.2 -1 10114712 . AT A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50511;SOR=Inf;LSEQ=CAAGACTGTTGCCATTGTTC;RSEQ=TTACTACAATGCCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:28,10:0:2,0:18.5:1:29.7:1:1:0:60:18:1:0:0.1 0/1:51:2:1,1:34,15:0.0392:2,2:36.5:1:29:0:0.53333:2.22676:60:4:0.0408:0:1.5 -1 10114751 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52016;SOR=Inf;LSEQ=GCATGCTGGGTAACATTGTA;RSEQ=ACTCTTCCAGTCTAGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:27,25:0:2,0:30.6:1:31.2:1:1:0:60:51:1:0:0.1 0/1:81:2:1,1:42,37:0.0247:2,2:27.5:1:25.5:1:1:1.13335:60:4:0.0247:0:1.5 -1 10114788 . AT A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.1733;SOR=0;LSEQ=CATGGTAACACTTGCGGGGC;RSEQ=TTTTTTTGGAACAGTACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:18,29:0.0408:2,2:6:1:28.5:1:1:1.59:60:4:0.0417:0.0204:2 0/0:68:0:0,0:27,41:0:2,0:24:1:29.6:1:1:0:60:136:1:0:0.3 -1 10702618 . C A 27 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGACCGGCGCTGGGCCCAGG;RSEQ=CGGGTGGGAGGCAGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:21:1:27:1:1:1:60:4:0.25:0:2.5 1/1:1:1:1,0:0,0:1:0,0:7:0:30:0:1:0:60:2:1:0:1 -1 11168371 . A G 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10344;SOR=0;LSEQ=AGGAGGAACAAAAACATTTC;RSEQ=CTCTCTTCCTGGCAATCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:64,172:0.0126:2,2:9.3:1:23.7:1:1:1.34:60:2:0.0087:0:1 0/0:269:0:0,0:78,190:0:2,0:22.8:1:28.8:1:1:0:60:52.6:1:0:0.1 -1 11169271 . G T 47 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.41438;SOR=0.3963;LSEQ=TCACTAACACCACTGGACAT;RSEQ=GGGCTGACCACCACTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:4:2,2:233,67:0.0132:2,2:19.8:1:23.8:1:0.22266:3.45938:60:3:0.0103:0:1 0/0:381:2:1,1:271,108:0.0052:2,2:17.5:1:27.5:1:0.49087:2.50234:60:4:0.0053:0:1.5 -1 11169639 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11162;SOR=Inf;LSEQ=TCTTGTTGACCCCTCTCAGG;RSEQ=TATAACACAGCTGCTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:167,98:0:2,0:24.7:1:31.2:1:1:0:60:65.25:1:0:0.1 0/1:248:3:1,2:163,82:0.0121:2,2:21.3:1:26:1:0.26557:3.9518:60:6:0.0122:0:1.3 -1 11174067 . A T 48 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.44444;SOR=Inf;LSEQ=TGCCCCCAAGTGAAGAAGGA;RSEQ=GTGTTTGCTTCCCCTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:37.7:1:30.7:1:1:0:60:6:0.375:0:1 1/1:1:1:1,0:0,0:1:0,0:49:0:30:0:1:0:60:2:1:0:3 -1 11175116 . TA T 79 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.39538;SOR=0.31116;LSEQ=CAGGGATTTGAAAGACAACT;RSEQ=AAAAAAAAAAGAAACGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:0,6:4,16:0.2308:2,0:32.3:1:30.8:1:0.54247:0:60:12:0.24:0:0.2 0/1:12:1:0,1:2,8:0.0833:2,0:30:0:32:0:1:0:60:2:0.0833:0:0 -1 11175344 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49876;SOR=Inf;LSEQ=ACAGCCTTGGTAGGGCCAGC;RSEQ=GGGGTTAAGAGTAAGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:163,28:0:2,0:22.4:1:30:1:1:0:60:46.75:1:0:0.1 0/1:195:2:1,1:171,22:0.0103:2,2:29:1:30.5:1:0.22252:7.62399:60:4:0.0105:0:1 -1 11175367 . G T 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04363;SOR=0;LSEQ=GGTTAAGAGTAAGGCAGTTT;RSEQ=GGCTTAAGTCTGCCTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:4:1,3:228,70:0.0132:2,2:12.3:1:26.5:1:0.04513:9.67759:60:8:0.0135:0:1 0/0:357:0:0,0:261,96:0:2,0:22.5:1:30.8:1:1:0:60:177.5:1:0:0.1 -1 11175384 . C T 50 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17858;SOR=0.2004;LSEQ=TTTGGGCTTAAGTCTGCCTA;RSEQ=AGTGTCAGAGGAGGGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:4:2,2:279,117:0.01:2,2:12.3:1:25:1:0.58565:2.3788:60:3:0.0076:0:2 0/0:497:1:0,1:332,164:0.002:2,0:1:0:25:0:0.33199:0:60:2:0.002:0:1 -1 11175590 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24756;SOR=Inf;LSEQ=ACGGATGAAAAAATCAATAA;RSEQ=TACGTGATACTGTAAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:12,136:0:2,0:23.2:1:31.9:1:1:0:60:36:1:0:0.1 0/1:151:3:2,1:23,125:0.0199:2,2:8.7:1:27.3:1:0.07129:10.60:60:6:0.02:0:1.3 -1 11176987 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09689;SOR=0;LSEQ=AAAAGCCATATATTTAATTG;RSEQ=AAAACCAAATGAAACCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:243,54:0.01:2,2:17:1:25.7:1:0.09057:8.90563:60:6:0.0101:0:1 0/0:352:0:0,0:274,78:0:2,0:23.9:1:30.7:1:1:0:60:87:1:0:0.1 -1 11177200 . TTATACTCTAA T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04066;SOR=0;LSEQ=AAACTTTAATTTCAACATAA;RSEQ=TAAGCTGTCTTTGGTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:4:1,3:41,232:0.0144:2,2:33.5:1:30.5:1:0.48399:1.88:60:8:0.0147:0:0 0/0:338:0:0,0:78,258:0:2,0:21.4:1:27.8:1:1:0:60:66.2:0.997:0:0.1 -1 11181327 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.24167;LSEQ=GAGCTGGGGCTTTTCAGCCA;RSEQ=AGCAGCTTGGCCAGGTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:645:286:160,126:193,166:0.4434:2,2:25.2:1:29.5:1:0.63291:1.09:60:142:0.4465:0:1.1 0/1:682:110:60,50:315,257:0.1613:2,2:24:1:28.6:1:0.91713:1.02138:60:54:0.1607:0:1.1 -1 11181963 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5041;SOR=0;LSEQ=AGTGACAGACATACAGAGAG;RSEQ=AATGAGAAAAGCAGCGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:131,32:0.0121:2,2:10:1:25.5:1:0.36098:4.0466:60:4:0.0122:0:1 0/0:133:0:0,0:109,24:0:2,0:19.5:1:30.7:1:1:0:60:132:1:0:0.1 -1 11181985 . G A 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATGAGAAAAGCAGCGCTACG;RSEQ=AGATTCCCTGCCACGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:40:30,10:156,47:0.1646:2,2:22.5:1:30:1:0.83885:1.10591:60:39:0.1632:0:1.1 0/0:211:0:0,0:162,49:0:2,0:23.1:1:30.9:1:1:0:60:51.75:1:0:0.2 -1 11181995 . G T 46 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.72244;LSEQ=CAGCGCTACGGAGATTCCCT;RSEQ=CCACGGAAGGGGCACTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:3:1,2:203,71:0.0108:2,2:12.3:1:29.3:1:0.17075:5.6748:60:6:0.011:0:1 0/0:255:2:0,2:177,76:0.0078:2,0:1:0:23:1:0.09273:0:60:4:0.008:0:1 -1 11182261 . G GT 90 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.97718;LSEQ=GCTCAGAACACAGGCAGACT;RSEQ=TTTTTTTTTTCTTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:8:0,8:8,118:0.0588:2,0:30.5:1:30.3:1:1:0:60:16:0.0625:0:0 0/1:139:8:0,8:15,116:0.0576:2,0:21.8:1:30:1:0.59891:0:58.8:16:0.0606:0:0.1 -1 11185626 . A G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGAAATCCCATCTCTACT;RSEQ=AAAATATAAAAATTAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:47:0:31:1:1:0:60:4:0.6667:0:2.5 -1 11185670 . T C 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGGCATGCGCCTGTAATC;RSEQ=CAGCTATTAGGGAGGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:6.5:1:27.5:1:1:0:60:4:0.6667:0:2.5 -1 11186291 . T TA 44 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCACAGAGACTATGATGG;RSEQ=AAAAAAAAAAAGAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:0.5:2,2:14:1:28:1:1:1:60:6:0.5:0.1667:0.3 0/0:1:0:0,0:1,0:0:0,0:50:0:29:0:1:0:60:2:1:0:0 -1 11187618 . A AT 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.63489;SOR=1.21065;LSEQ=ATAAAAACTTTTCTCATTTC;RSEQ=TTTTTTTTTAGTGGCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:17:12,5:306,92:0.0407:2,2:19.6:1:30.9:1:0.56107:1.38469:60:34:0.0413:0.0096:0.2 0/1:512:25:17,8:345,140:0.0488:2,2:24.2:1:28.6:1:0.82146:1.1593:60:24:0.0479:0.0117:0.3 -1 11187838 . G A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21832;SOR=4.72925;LSEQ=ACATCTCATGCCAGAGGATG;RSEQ=CCACTCGGATCAGCTCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:1,0:86,275:0.0028:2,0:1:0:26:0:0.24033:0:60:2:0.0028:0:1 0/1:386:5:3,2:94,285:0.013:2,2:15.4:1:25:1:0.10489:4.53:60:4:0.0106:0:1 -1 11187882 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49937;SOR=0;LSEQ=ACCTGAAGCCAAGAGAAGAA;RSEQ=GAGAGAAGCATCAAGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:37,144:0.0109:2,2:16:1:32:1:0.37309:3.85:60:4:0.0109:0:2 0/0:169:0:0,0:32,137:0:2,0:24:1:30.6:1:1:0:60:41.25:1:0:1 -1 11187893 . T C 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46562;SOR=0;LSEQ=AGAGAAGAAGGAGAGAAGCA;RSEQ=CAAGAATCAGCTAACCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:171:171:36,135:0,0:1:0,2:24:1:31.5:1:1:0:60:56:1:0:1.1 1/1:149:148:33,115:0,0:0.9933:0,2:22.6:1:31.5:1:1:0:60:147:0.9932:0:1.1 -1 11188004 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23549;SOR=0;LSEQ=GGAAGAAAAACAATCCCACT;RSEQ=GCGCCCACCAGCTAAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:123,64:0.0105:2,2:32:1:31:1:1:1.91484:60:4:0.0108:0:1 0/0:201:0:0,0:136,64:0:2,0:21.8:1:29.5:1:1:0:60:65.667:1:0:0.2 -1 11188012 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37308;SOR=3.82746;LSEQ=AACAATCCCACTTGCGCCCA;RSEQ=CAGCTAAGGGACCAGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:1:0,1:137,76:0.0047:2,0:1:0:28:0:0.35981:0:60:2:0.0047:0:1 0/1:226:4:2,2:151,71:0.0177:2,2:17.8:1:25.3:1:0.59631:2.11905:60:3:0.0136:0:1 -1 11188013 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24916;SOR=Inf;LSEQ=ACAATCCCACTTGCGCCCAC;RSEQ=AGCTAAGGGACCAGGGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:139,78:0:2,0:23.2:1:30.8:1:1:0:60:35.167:1:0:0.2 0/1:232:3:1,2:154,75:0.0129:2,2:15.3:1:26.3:1:0.25637:4.07951:60:6:0.0131:0:1 -1 11188049 . G A 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65813;SOR=0.51648;LSEQ=GTCTATGAAGCCCCACAGTG;RSEQ=CTCCGACCCACCATCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:165,126:0.0102:2,2:24.3:1:29.7:1:1:1.53:60:6:0.0103:0:1 0/0:378:2:1,1:226,150:0.0053:2,2:16.5:1:29:1:1:1.50495:60:4:0.0054:0:1 -1 11189770 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10102;SOR=0;LSEQ=CATTAACATGGCCTACCAGA;RSEQ=TTGCATCCTTCCCTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:189,108:0.01:2,2:14.7:1:29:1:0.55668:3.48476:60:6:0.0102:0:1 0/0:343:0:0,0:232,111:0:2,0:24.6:1:31.5:1:1:0:60:170.5:1:0:0.1 -1 11190646 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26781;LSEQ=TTCTCGGTGCTCTCGGCCTC;RSEQ=CTCTCACTGTTGCTGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:727:295:156,139:238,192:0.4058:2,2:23.7:1:29.9:1:0.54396:1.10435:60:294:0.4123:0:1.1 0/1:945:146:81,65:422,375:0.1545:2,2:24:1:29.6:1:0.58934:1.11:60:47.667:0.1541:0:1.2 -1 11193560 . A AGTT 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAATTTTTTGTGGGTGAC;RSEQ=GTTGAGAGTTACTTCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:17.3:1:29.7:1:1:0:60:6:1:0.3333:0 1/1:1:1:0,1:0,0:1:0,0:13:0:31.3:0:1:0:60:2:1:0:0 -1 11194368 . G T 52 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72395;SOR=0.74003;LSEQ=AGAAGCTGCTGGGATGACAG;RSEQ=GCTGGAATATGACTTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:4:1,3:249,111:0.011:2,2:10.3:1:26:1:0.09283:6.69138:60:8:0.0112:0:1 0/0:368:3:0,3:243,122:0.0082:2,0:2.3:1:21.7:1:0.03857:0:60:2:0.0056:0:1 -1 11194604 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23134;SOR=Inf;LSEQ=AGCTACCGTTCATCTGATAG;RSEQ=CATGAGTCAACCCCTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:8,108:0:2,0:24.5:1:31.6:1:1:0:60:28:1:0:0.1 0/1:108:2:1,1:11,95:0.0185:2,2:7:1:27.5:1:0.2108:8.31:60:4:0.0189:0:1 -1 11199937 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTATTTTTAGTAGAGA;RSEQ=GGGGTTTCAGCATCTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:0,11:0.1538:0,0:22:1:28:1:1:0:60:4:0.1538:0:1 0/0:3:0:0,0:1,2:0:2,0:22.7:1:32:1:1:0:60:6:1:0:0 -1 11205058 . C T 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.31724;LSEQ=CTGTAACTCTCTCCTGCCAT;RSEQ=GCAGTTAATTCAGCATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:852:451:232,219:197,204:0.5293:2,2:24.1:1:29.6:1:0.5368:1.10:60:40:0.5257:0:1.2 1/1:920:763:369,394:77,78:0.8293:2,2:24.6:1:29.7:1:0.79181:1.05403:60:189.75:0.8286:0:1.1 -1 11205273 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11688;SOR=Inf;LSEQ=CTGAATGGCTTGAGAGGAGG;RSEQ=ATTATCCAATTTCTCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:1,50:0:1,0:23:1:28.6:1:1:0:60:102:1:0:0.1 0/1:27:2:0,2:1,24:0.0741:1,0:26.5:1:32:0:1:0:60:4:0.0741:0:1 -1 11206586 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19263;SOR=Inf;LSEQ=TGCTGGCAGTCTTCTGAGTA;RSEQ=AATGAATCAAAACCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:61,1:0:1,0:25.3:1:32.5:1:1:0:60:124:1:0:0.1 0/1:49:2:1,1:47,0:0.0408:1,2:22.5:1:27:1:0.04082:0:60:4:0.0408:0:1 -1 11206670 . G A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.43982;SOR=2.11865;LSEQ=AGCTTCTTTACCAAAGCACC;RSEQ=TGGGCTTAGAAGCACTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:2:1,1:257,76:0.006:2,2:11.5:1:29:1:0.4074:3.36602:60:4:0.006:0:1 0/1:318:4:2,2:241,73:0.0126:2,2:33.3:1:25.3:1:0.23731:3.28589:60:3:0.0096:0:1 -1 11206679 . G T 45 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05242;SOR=Inf;LSEQ=ACCAAAGCACCGTGGGCTTA;RSEQ=AAGCACTACAATCTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:296,109:0:2,0:22.6:1:31.7:1:1:0:60:100.25:1:0:0.1 0/1:374:4:2,2:267,103:0.0107:2,2:9:1:22.5:1:0.31416:2.58462:60:3:0.0081:0:1 -1 11207269 . C T 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAAATTACATTTTCCTC;RSEQ=AAACAATTGAAAATAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19:1:26.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 11217114 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2385;SOR=Inf;LSEQ=AACAAAATGAGTCTGAAGTG;RSEQ=GAACTCCGTGTGGGGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:119,2:0:1,0:25.4:1:29.6:1:1:0:60:29.25:1:0:0.1 0/1:116:2:1,1:111,3:0.0172:1,2:19:1:32.5:1:0.06807:32.17955:60:4:0.0172:0:1 -1 11217138 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21311;SOR=0;LSEQ=CTCCGTGTGGGGGAAGCCTT;RSEQ=CTTTCAAATCCAAAGATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:153,23:0.0112:2,2:18.5:1:28.5:1:0.25214:6.53336:60:4:0.0114:0:1 0/0:207:0:0,0:177,30:0:2,0:21.9:1:30.4:1:1:0:60:40.4:1:0:0.1 -1 11227302 . TA T 77 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.66872;SOR=0.37675;LSEQ=CCTAGAACTTAAAGTATAAT;RSEQ=AAAAAAAAAAAGAAAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:6:6,0:52,1:0.0968:1,0:23:1:29.9:1:1:0:59.5:12:0.1:0.0323:0.2 0/1:26:1:1,0:25,0:0.0385:1,0:42:0:30:0:1:0:60:2:0.0385:0:0 -1 11227864 . C T 71 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTGGGTGTGGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:20:1:31:1:1:0:53.4:10:0.5556:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 11259250 . C T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12406;SOR=Inf;LSEQ=TGACTCCAGTGAAGTGGCAC;RSEQ=AGGCAGTGGGAGAAGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:236,36:0:2,0:22:1:30.9:1:1:0:60:89.667:1:0:0.1 0/1:285:4:1,3:224,57:0.014:2,2:10.8:1:27.5:1:0.03042:11.64694:60:8:0.0143:0:1 -1 11264299 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CCTGTGGTATTTGTAACAAA;RSEQ=AGCAATAATTAGAATACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:22:1:31:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 11269272 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22455;SOR=Inf;LSEQ=TTTCTGGAAAAAACACCTGG;RSEQ=CTGGTTTTCGGTTGCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:143,3:0:1,0:24.1:1:31.2:1:1:0:60:47.667:1:0:0.1 0/1:132:2:1,1:127,3:0.0152:1,2:5.5:1:27:1:0.05991:36.7993:60:4:0.0153:0:1.5 -1 11269281 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=AAAACACCTGGGCTGGTTTT;RSEQ=GGTTGCCCAGTTTAAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:171,9:0:2,0:22.9:1:31.4:1:1:0:60:89:1:0:0.1 0/1:153:11:11,0:132,10:0.0719:2,0:33:1:29.1:1:1:0:60:22:0.0719:0:1.1 -1 11269796 . T C 32 v4;q23;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTCGGCAATGGGAAAAG;RSEQ=GATAAAGTGTTTGGAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:33:1:20.3:1:1:0:60:2:0.25:0:4.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 11270776 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24654;SOR=Inf;LSEQ=TGCCAATCCCTAATTTACAG;RSEQ=CAAAAAGCTACACAAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:99,10:0:2,0:25.4:1:31.9:1:1:0:60:53.5:1:0:0.1 0/1:108:2:1,1:88,18:0.0185:2,2:6.5:1:27.5:1:0.32226:4.78552:60:4:0.0192:0:1 -1 11272754 . CA C 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.7361;SOR=0.66675;LSEQ=AATAATGTGAGTTGAAATAA;RSEQ=AAAAAAATAGAAAGATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:5:4,1:103,11:0.042:2,2:19:1:32.2:1:0.41793:2.31838:60:10:0.0427:0.0168:0.2 0/1:141:4:4,0:130,6:0.0284:1,0:23.5:1:30.4:1:1:0:60:8:0.0286:0.0071:0 -1 11273390 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49981;SOR=0;LSEQ=AGAATGAGGTCTCAGCTTTT;RSEQ=GCTGATCACCCAGGGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:109,21:0.0152:2,2:19.5:1:30:1:0.30662:5.09448:60:4:0.0153:0:1 0/0:117:0:0,0:88,29:0:2,0:22.6:1:27.9:1:1:0:60:28.25:1:0:0.1 -1 11273413 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23007;SOR=Inf;LSEQ=TGATCACCCAGGGACTCAGA;RSEQ=GAAATCAGAAAATCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:155,56:0:2,0:22.5:1:31.7:1:1:0:60:422:1:0:0.1 0/1:195:2:1,1:138,55:0.0103:2,2:10.5:1:29:1:0.49294:2.49559:60:4:0.0105:0:1 -1 11273442 . C T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12387;SOR=0;LSEQ=AAAATCTCTCTGGAGGATGA;RSEQ=GTAGGCTACTCACCTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:4:1,3:212,116:0.012:2,2:12.5:1:28.3:1:0.1333:5.45413:60:8:0.0121:0:1 0/0:332:0:0,0:217,115:0:2,0:24.5:1:30.4:1:1:0:60:65.4:1:0:0.2 -1 11273651 . T G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49948;SOR=Inf;LSEQ=GAGAGAAAAGTCAGAGGAGC;RSEQ=GAGTCAGGTCCCTTTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:28,144:0:2,0:23.2:1:30.2:1:1:0:60:33.4:1:0:0.1 0/1:187:2:1,1:41,144:0.0107:2,2:12:0:32:0:0.39969:3.48:60:4:0.011:0:2 -1 11287785 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTGCCAGCTAATAAAAT;RSEQ=GAGAAGGAATAGCAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 11288618 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.20084;LSEQ=TTAAGGGGGAGGAAGGCATT;RSEQ=GGCTCAGGGGCACAGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:59:59,0:75,2:0.4338:1,1:27.4:1:28.1:1:0.50512:0:60:58:0.4361:0:1.9 1/1:110:91:91,0:18,1:0.8273:1,1:24.6:1:28.1:1:0.17273:0:60:44.5:0.8241:0:2.1 -1 11288633 . G C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=6.42736;LSEQ=GCATTGGGCTCAGGGGCACA;RSEQ=AGAATGCACAATTAAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:71:66,5:94,6:0.4152:2,2:25.7:1:32.4:1:0.76414:1.18566:60:142:0.4176:0:1.8 1/1:151:124:117,7:26,1:0.8212:1,2:23.9:1:31.2:1:1:1.55156:60:123:0.82:0:1.8 -1 11288758 . G A 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.70983;LSEQ=CCATCACAGACTCGAATGAC;RSEQ=TTAAGGAACGTGGGCATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:788:319:168,151:233,234:0.4048:2,2:24.1:1:30.3:1:0.46784:1.12:60:52.167:0.4028:0:1.1 1/1:919:754:384,370:81,83:0.8205:2,2:25.3:1:29.6:1:0.73111:1.06:60:52.857:0.8204:0:1.2 -1 11289161 . G A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01084;SOR=Inf;LSEQ=AATAGCCTCTCACCATCAAG;RSEQ=AGTAAACGGTTTTTGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:0,4:0,10:0.2857:0,0:33.8:1:26:1:1:0:60:3:0.2308:0:1.3 1/1:5:5:0,5:0,0:1:0,0:13.4:1:31:1:1:0:60:10:1:0:1.2 -1 11290880 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08647;SOR=Inf;LSEQ=TTGCTACACGAGCCAATATC;RSEQ=TATAATTTCTCAGTAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:109,2:0:1,0:24.7:1:31:1:1:0:60:36:1:0:0 0/1:89:3:3,0:84,2:0.0337:1,0:24:1:31:1:1:0:60:6:0.0345:0:1 -1 11291380 . G A 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01273;SOR=0.09558;LSEQ=TCTGCGTGTACCCTGGTTCT;RSEQ=CTCAGTCTTCAGAAAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:690:8:6,2:387,295:0.0116:2,2:15.6:1:26.1:1:0.47678:2.28:60:16:0.0117:0:1 0/0:894:1:1,0:457,436:0.0011:2,0:1:0:23:0:1:0:60:2:0.0011:0:1 -1 11291598 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51538;SOR=0;LSEQ=AGTGTTAGAGGCTGTAAGAA;RSEQ=AAAAGAGGTTTCCAGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:5,86:0.0215:2,0:38:1:28.5:1:1:0:60:4:0.022:0:1 0/0:63:0:0,0:1,62:0:1,0:23.3:1:30.7:1:1:0:60:20:1:0:0.2 -1 11292666 . T A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.8093;LSEQ=TGGAGGCCGGGCACGGTGGC;RSEQ=CATGCCTGTAATCCCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:53:2,51:3,73:0.4046:1,1:23.7:1:30.2:1:1:1.04757:60:106:0.4109:0:1.2 1/1:119:98:12,86:3,16:0.8235:2,2:22:1:29.4:1:0.70898:1.3401:60:48:0.8348:0:1.2 -1 11292753 . A G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01549;SOR=5.70745;LSEQ=ACCAGCCTAGCCAACATGGT;RSEQ=AAACCCCATCTCTACTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:0,15:0,14:0.5172:1,1:15.7:1:31.5:1:1:0:60:30:0.5172:0:1.5 1/1:22:19:0,19:0,3:0.8636:0,1:24.7:1:31.7:1:1:0:60:38:0.8636:0:1.3 -1 11292881 . A G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGAGGTTGCAGTGAGCC;RSEQ=AGATCACACCACTGCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:26.3:1:30.7:1:1:0:60:6:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 11293367 . T TA 97 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.47392;SOR=0.66741;LSEQ=AATATGTGAGACCTTTCATT;RSEQ=AAAAAAAAAAATAGTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:11:10,1:161,15:0.0588:2,2:25.7:1:28.3:1:1:1.07294:58.2:22:0.0588:0.016:0 0/1:175:7:6,1:141,26:0.04:2,2:27.9:1:25.4:1:1:1.11:60:6:0.0349:0:0 -1 11293959 . C T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTCCTTTCCAAACATCTG;RSEQ=GATGATGTGCCTGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:5,2:2,0:0.7778:0,2:22:1:31.6:1:1:0:60:14:0.7778:0:1 1/1:3:3:3,0:0,0:1:0,0:16:1:27.3:1:1:0:60:6:1:0:1 -1 11294382 . T A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.51762;LSEQ=GACATTCTAGAGAGAGACTG;RSEQ=GTCCAACAGAAAAAGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:26,130:0.0127:2,2:26:1:29.5:1:0.31347:4.93:60:4:0.0127:0:1 0/0:152:1:1,0:26,116:0.0066:2,0:1:0:23:0:0.18881:0:60:2:0.0066:0:1 -1 11294474 . T A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0207;SOR=6.58532;LSEQ=ATACTCAATGAGCAACAGAC;RSEQ=TTTCTGCAACAGGCAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:0,7:0,21:0.25:1,0:23.1:1:28.4:1:1:0:60:6:0.2222:0:1.1 1/0:10:7:0,7:0,3:0.7:0,0:24.7:1:31:1:1:0:60:14:0.7:0:1 -1 11297762 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00011;SOR=8.07312;LSEQ=GCCAGGGAAACATTTGGACC;RSEQ=TTGCAGACAAATGCGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:16:15,1:23,0:0.4103:1,1:27.8:1:31.6:1:0.41026:0:60:32:0.4103:0:1.2 1/1:34:29:27,2:5,0:0.8529:0,2:22.1:1:30.7:1:1:0:60:58:0.8529:0:1.1 -1 11297771 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49451;SOR=Inf;LSEQ=ACATTTGGACCTTTGCAGAC;RSEQ=AATGCGGCTTTTACCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:0:1,0:23.4:1:30:1:1:0:60:44:1:0:0.5 0/1:46:2:1,1:42,2:0.0435:1,2:41.5:1:30:0:0.12754:17.3476:60:4:0.0435:0:2 -1 11297779 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22483;SOR=0;LSEQ=ACCTTTGCAGACAAATGCGG;RSEQ=TTTTACCAGGTACCTCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:49,0:0.0392:1,2:32.5:1:31:1:0.03922:0:60:4:0.04:0:2 0/0:56:0:0,0:53,3:0:2,0:21.9:1:32.5:1:1:0:60:112:1:0:0.6 -1 11298182 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51448;SOR=0;LSEQ=TCCCAGCTTCTACCTCCACT;RSEQ=CCATCAGCGTAGTGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:8,91:0.0196:2,2:26.5:1:27.5:1:0.17109:10.78:60:4:0.0208:0:1 0/0:70:0:0,0:6,64:0:2,0:21.4:1:32.4:1:1:0:60:140:1:0:0.1 -1 11298641 . G T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02678;SOR=0;LSEQ=CACTGTTCAGGAAATGATCC;RSEQ=CACAGTGGCGAACAAATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:4:2,2:148,232:0.0104:2,2:26:1:29.8:1:0.64544:1.57:60:8:0.0106:0:1.3 0/0:566:0:0,0:238,325:0:2,0:24.8:1:30.7:1:1:0:60:92.833:0.9946:0:0.1 -1 11298790 . T C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=18.89476;LSEQ=TAATTCTACTTTCAACTAGA;RSEQ=ATTGATCAATACGATACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:13:0,13:0,25:0.3421:1,1:26.8:1:31.1:1:1:0:60:12:0.3243:0:1.3 1/1:34:31:0,31:0,3:0.9118:0,1:21.6:1:32:1:1:0:60:30:0.9091:0:1.3 -1 11300318 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25651;SOR=Inf;LSEQ=TTCCTTTCCCAAAGTTTCCA;RSEQ=CATCTCTCACTATCTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:89,31:0:2,0:23.4:1:32.4:1:1:0:60:119:1:0:0.1 0/1:150:3:2,1:99,48:0.02:2,2:26.7:1:25.7:1:1:1.03107:53.3:2:0.0135:0:3.3 -1 11300344 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59251;SOR=0.41313;LSEQ=CTCACTATCTTGGCAAGAGC;RSEQ=GTTGTAATTTCTTACCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:134,54:0.0105:2,2:31:1:29.5:1:0.49624:2.46799:60:4:0.0106:0:1 0/0:229:1:0,1:147,81:0.0044:2,0:1:0:26:0:0.35808:0:60:2:0.0044:0:1 -1 11301714 . A G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=6.67215;LSEQ=ATGCAAGTGAAGACTGTGGC;RSEQ=TCCACCTGCATTGCCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:236:102,134:166,202:0.3907:2,2:26.2:1:30.8:1:0.67517:1.07945:60:58:0.3893:0:1.1 1/1:777:630:291,339:69,76:0.8108:2,2:25.6:1:30.1:1:0.78224:1.05754:60:104:0.8114:0:1.2 -1 11302065 . G A 51 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTGAACAATGTGTTCATCAG;RSEQ=GACAAGAAGGCAGTACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:15:1:32.3:1:1:0:60:6:1:0:1 0/0:1:0:0,0:0,1:0:0,0:21:0:32:0:1:0:60:2:1:0:0 -1 11303116 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23076;SOR=Inf;LSEQ=CGTGGATCTGAAATAGAGCG;RSEQ=CCTTCCTCTCCAACCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:172,20:0:2,0:23.4:1:30.2:1:1:0:60:191:1:0:0.1 0/1:178:2:1,1:145,31:0.0112:2,2:24:0:33.5:1:0.32806:4.61963:60:4:0.0113:0:1 -1 11303131 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06251;SOR=0;LSEQ=GAGCGTCCTTCCTCTCCAAC;RSEQ=AAATGGAGTGGAAGGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:5:1,4:204,64:0.0183:2,2:11.4:1:26:1:0.01456:12.60622:60:10:0.0187:0:1 0/0:250:0:0,0:185,65:0:2,0:23.4:1:30:1:1:0:60:40.667:1:0:0.1 -1 11303407 . T A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09405;SOR=0;LSEQ=TCCAGGTCAGGGTTAGGGTC;RSEQ=ACATATCAACAGTCAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:3:2,1:27,152:0.0165:2,2:15:1:23.3:1:0.06655:11.02:60:2:0.0114:0:1 0/0:217:0:0,0:47,170:0:2,0:23.7:1:28.2:1:1:0:60:35.167:1:0:0.1 -1 11308168 . G GA 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.24921;SOR=Inf;LSEQ=GACGCTATATATATGAGGAG;RSEQ=AAAAAAATCATCTTTACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:42,239:0:2,0:23.4:1:31.3:1:1:0:60:69.25:1:0:0.1 0/1:296:3:1,2:57,236:0.0101:2,2:32.3:1:29.7:1:0.48147:2.06:60:6:0.0103:0:0.3 -1 11313799 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24159;SOR=Inf;LSEQ=TATTTATTATGTTTCCTGCC;RSEQ=CAAAATGTCAGCTCCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:131,4:0:1,0:20.5:1:30.8:1:1:0:60:66.5:1:0:0.1 0/1:131:2:1,1:125,4:0.0153:1,2:26:1:29:1:0.07516:28.06607:60:4:0.0153:0:1 -1 11314202 . AT A 32 v4;MAF0.05;pSTD;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.13967;LSEQ=TTTTATTTAATTCAGCTTCA;RSEQ=TTTTTTTTTTTGAGATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:0,32:0.0588:1,2:50:0:32.5:1:0.05882:0:60:4:0.0625:0:0 0/1:15:1:0,1:0,14:0.0667:1,0:39:0:32:0:1:0:60:2:0.0667:0:0 -1 11315975 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10369;SOR=Inf;LSEQ=GCTCCATGGCAAGGGCTTGT;RSEQ=GCTGCCCTTTAGGCCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:130,28:0:2,0:27.5:1:31.4:1:1:0:60:38.5:1:0:0.3 0/1:141:3:2,1:98,40:0.0213:2,2:22.7:1:30.7:1:1:1.22313:60:6:0.0213:0:1 -1 11315990 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49918;SOR=Inf;LSEQ=CTTGTGGCTGCCCTTTAGGC;RSEQ=AGGTGATTCTCTACGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:146,39:0:2,0:27.3:1:30.2:1:1:0:60:15.818:1:0:0.1 0/1:197:2:1,1:124,71:0.0102:2,2:20:1:28:1:1:1.7412:60:4:0.0104:0:1 -1 11316899 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.50034;SOR=Inf;LSEQ=AGCTCTTCTAACCAGCTTTT;RSEQ=TAAGGAATGAGCCTCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:66,4:0:2,0:26.7:1:30.4:1:1:0:60:140:1:0:0.1 0/1:83:2:1,1:76,5:0.0241:2,2:19:1:31.5:1:0.14017:13.96793:60:4:0.0247:0:1 -1 11317298 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49922;SOR=0;LSEQ=TACGCAGACTTCAACTAAAA;RSEQ=CTGGTGAGTGCCGGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:8,104:0.0175:2,2:7.5:1:29:1:0.15231:12.32:60:4:0.018:0:1 0/0:102:0:0,0:11,91:0:2,0:23.3:1:32.5:1:1:0:60:204:1:0:0.5 -1 11317320 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-04;SOR=4.36754;LSEQ=TGGTGAGTGCCGGCCAGGCA;RSEQ=GGTGGCTCAAGTCTGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:31:2,29:0,28:0.5254:1,2:23.7:1:30.6:1:0.49269:0:60:62:0.5254:0:1.1 1/1:59:49:4,45:0,10:0.8305:0,2:22.8:1:30.3:1:1:0:60:98:0.8305:0:1 -1 11318548 . C T 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01714;SOR=Inf;LSEQ=GACTCTGTCCTTACCTATGG;RSEQ=CAAGATGCCACCTTTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:0:0,0:327,259:0:2,0:24.5:1:31.5:1:1:0:60:64.111:0.9983:0:0.1 0/1:680:7:3,4:367,306:0.0103:2,2:11.7:1:25.3:1:0.70787:1.598:60:6:0.009:0:1.3 -1 11318714 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50379;SOR=Inf;LSEQ=AACTGTGGTGGTGGGAGTGG;RSEQ=CTGGCATCTAAAGATTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:5,97:0:1,0:23.6:1:31.7:1:1:0:60:101:1:0:0.2 0/1:127:2:1,1:15,110:0.0157:2,2:5:0:31.5:1:0.23697:7.13:60:4:0.016:0:1.5 -1 11318763 . C G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=6e-04;SOR=5.05422;LSEQ=GCAGGAGGTATAGTTCAAAC;RSEQ=AAAGAAGACAAGTTACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:27:0,27:0,27:0.5:1,1:29:1:31:1:1:0:60:26:0.4906:0:1.1 1/1:43:36:2,34:0,7:0.8372:0,2:21.8:1:30.9:1:1:0:60:72:0.8372:0:1.1 -1 11319228 . C CA 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.48529;SOR=1.46527;LSEQ=CAAATCCTCACTTAGCTGTA;RSEQ=AAAAAAAAATGTAAACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:7:7,0:136,23:0.0419:2,0:33.6:1:30.5:1:0.59486:0:60:14:0.0432:0.006:0.1 0/1:199:12:8,4:148,38:0.0603:2,2:22.6:1:29.9:1:0.28568:1.93983:59.2:24:0.0609:0.0151:0.3 -1 11319587 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00017;SOR=5.5457;LSEQ=CCCCCTAGCCCTTGTCAGGC;RSEQ=GGGGATTCTAAAAAGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:24:0,24:0,31:0.4364:1,1:25.5:1:29.3:1:1:0:60:11:0.4231:0:1.2 1/1:43:35:0,35:1,7:0.814:2,1:22.7:1:30.7:1:0.18605:0:60:34:0.8095:0:1.1 -1 11938050 . G A 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.6749;SOR=1.80915;LSEQ=CCCCCCAAGCTGGCAGCACC;RSEQ=GGGCCAGCTGCCCCCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,1:0.2:2,0:12.5:1:31.5:1:1:0:60:4:0.2:0:1 0/1:19:6:4,2:8,4:0.3158:2,2:13:1:29.3:1:1:1:60:12:0.3158:0:1.2 -1 11938146 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=0;LSEQ=GGCCTCAGCTCTGAAGCCCT;RSEQ=AGACGGCATGACCATCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:12,16:0.0667:2,2:29:1:29.5:1:1:1.32:60:4:0.0667:0:1 0/0:26:0:0,0:11,15:0:2,0:28.6:1:31.2:1:1:0:60:25:1:0:0.3 -1 11938203 . A G 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47478;LSEQ=TTGCTGCCGCAACTAGCAGT;RSEQ=CCTCGGGCTGGGCACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:1,8:0.25:2,0:10.7:1:30.7:1:1:0:60:6:0.25:0:1.7 0/1:12:4:0,4:2,6:0.3333:2,0:30:1:31:1:0.51515:0:60:8:0.3333:0:2.8 -1 11938210 . GC AA 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=3.65648;LSEQ=CGCAACTAGCAGTACCTCGG;RSEQ=TGGGCACCCTGAGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,5:0.1667:0,0:31:0:27.5:0:1:0:60:2:0.1667:0:2 0/1:9:4:0,4:1,4:0.4444:2,0:34.3:1:29:1:1:0:60:8:0.4444:0.1111:2 -1 11938265 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=AAGCTCTTCCGCATTTCTCT;RSEQ=GACAACCGCATGTTGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:17.3:1:32.5:1:1:0:60:12:1:0:0.8 1/0:4:2:1,1:0,2:0.5:0,2:18.5:1:28:1:1:0:60:4:0.5:0:1 -1 11938340 . T C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCCCAGGGTGTCCAGGACAA;RSEQ=GCCCTGCAGTGGGTGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:7.5:1:31:0:1:0:60:4:1:0:1.5 0/0:1:0:0,0:0,1:0:0,0:3:0:30:0:1:0:60:2:1:0:1 -1 11972634 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.48617;SOR=0;LSEQ=TAGTGGCCCCGAATGGCTGG;RSEQ=CGCGCTGATATTTATTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:0.1538:2,2:32:0:31.5:1:1:1.67325:60:4:0.1538:0:1.5 0/0:10:0:0,0:7,3:0:2,0:27.1:1:30.4:1:1:0:60:20:1:0:0.3 -1 11972651 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1567;SOR=Inf;LSEQ=TGGGCGCGCTGATATTTATT;RSEQ=TATACAAGACAAGGGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:23.1:1:31:1:1:0:60:15:1:0:0.3 0/1:11:2:2,0:6,3:0.1818:2,0:25:1:29:1:1:0:60:4:0.1818:0:1 -1 11972688 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49714;SOR=Inf;LSEQ=GGCAGGCAGGGTAAGGAAGG;RSEQ=GGTCGTCCAAGTGATTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:29.3:1:30.6:1:1:0:60:21:1:0:0.4 0/1:28:2:1,1:15,11:0.0714:2,2:15:1:29.5:1:1:1.34838:60:4:0.0741:0:1 -1 12071513 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.47895;SOR=Inf;LSEQ=GTAGTCCTAATACTGCCTAT;RSEQ=ATCAGCTATCATGGTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:16.8:1:32.4:1:1:0:60:18:1:0:0 0/1:11:2:1,1:8,1:0.1818:2,2:21.5:1:29.5:1:0.34545:6:60:4:0.1818:0:1.5 -1 12071680 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.60961;LSEQ=TGCTGCCAGCCCTAAGTGCC;RSEQ=TGTGGGCTCCCCCAGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:15:5,10:9,16:0.375:2,2:21.3:1:30.1:1:1:1.12171:60:14:0.359:0:1.4 1/1:53:47:18,29:3,3:0.8868:2,2:21.6:1:30.4:1:0.67106:1.59616:60:94:0.8868:0:1.1 -1 14192526 . A G 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07736;LSEQ=AGCCAAAATCCTTCACTTTA;RSEQ=TGAGCCTCAGTTCCCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:75:71:69,2:4,0:0.9467:0,1:26.7:1:32.6:1:1:0:60:142:0.9467:0:1 1/0:61:35:32,3:24,1:0.5738:1,2:23.2:1:32.4:1:0.63395:2.22243:60:34:0.5763:0:1.2 -1 14192575 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24144;SOR=0;LSEQ=TGTCACCCTGTTAAGTGATC;RSEQ=GGACTCAAGATATTTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:109,46:0.0127:2,2:17:1:29.5:1:0.51045:2.35497:60:4:0.0128:0:1 0/0:162:0:0,0:114,47:0:2,0:23.3:1:29.8:1:1:0:60:52.667:0.9937:0:0.4 -1 14192672 . C T 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08493;LSEQ=CAAAAATCAGGAAAAATTAA;RSEQ=GTTGGACCCTCCTGGGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:315:289:135,154:13,13:0.9175:2,2:23.7:1:30.3:1:0.83839:1.14026:60:95.333:0.9167:0:1.1 0/1:392:190:86,104:102,100:0.4847:2,2:26.3:1:29.6:1:0.3132:1.23282:60:94:0.4833:0:1.1 -1 14192676 . G A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=AATCAGGAAAAATTAACGTT;RSEQ=GACCCTCCTGGGATCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:145,166:0:2,0:23.3:1:31:1:1:0:60:61.2:1:0:1 0/1:392:15:8,7:181,196:0.0383:2,2:28.5:1:29.6:1:0.79452:1.24:60:30:0.0392:0:1 -1 14192818 . G T 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00554;SOR=0;LSEQ=CTGTTCATGGCTAATTCTTG;RSEQ=GTGGCTTCCATCACAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:0,8:1,32:0.1951:1,0:11.1:1:31.4:1:1:0:60:16:0.1951:0:1 0/0:38:0:0,0:2,35:0:2,0:25.9:1:30:1:1:0:60:17.5:1:0:0.1 -1 14192919 . A G 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACCTGCTCCATGCCAC;RSEQ=TGCCCCTCCTAGCCCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:26.8:1:32.5:1:1:0:60:8:0.8:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 14321714 . CAA C 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTAGACAGTGCAATAAGG;RSEQ=AAAAAAAAAAAAAATCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45:1:31:1:1:0:60:4:1:0:0 -1 14322547 . CT C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=0;LSEQ=CATCACAACGGACTAGGAGG;RSEQ=GGCCTGATCCACGGAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:30:1:1:0:60:4:1:0:0.5 0/0:2:0:0,0:2,0:0:0,0:41.5:1:31:1:1:0:59:4:1:0:3 -1 14323295 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TCTGAGGAATCTGGGCAGCC;RSEQ=GGATGAGTGGGTTTCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:30:1:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:1,1:0:2,0:30.5:1:31.5:1:1:0:60:4:1:0:0 -1 14323668 . TCAA T 59 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.5671;SOR=3.52895;LSEQ=CAGCAAAAACAACACCATCA;RSEQ=CAACAACAACAACAACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:32:0:33:1:1:2.44949:60:4:0.3333:0:0.5 1/0:6:4:3,1:2,2:0.6667:2,2:5.5:1:29.5:1:1:2.60:60:8:0.6667:0.5:1.3 -1 14323733 . A G 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.5163;LSEQ=TGTCAGCAGCCTCAAAGATC;RSEQ=AAACTAGACAAACTCACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:9:1:32:1:1:1:60:4:0.1667:0:3 0/1:17:4:3,1:7,6:0.2353:2,2:18.5:1:30.8:1:0.60294:2.44:60:8:0.2353:0:3 -1 14323765 . A G 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48012;SOR=2.11261;LSEQ=ACTCACGAAGATGAGAAAGA;RSEQ=TCAATGAAAAAATGCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:7,9:0.2:2,2:32:1:31.8:1:1:1.27:60:8:0.2:0:2.5 0/1:20:7:4,3:6,7:0.35:2,2:27.4:1:30.1:1:1:1.52:60:14:0.3684:0:2.6 -1 14323796 . A C 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70425;SOR=1.76702;LSEQ=AATGCTGAAAACCCAAAAGG;RSEQ=CAGAGTGCCTCCTTTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:2,2:5,7:0.25:2,2:36.3:1:31.5:1:1:1.37:60:8:0.25:0:2.5 0/1:16:6:3,3:4,6:0.375:2,2:32.8:1:30.7:1:1:1.46:60:12:0.4:0:2.5 -1 15295906 . G C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0589;SOR=2.12682;LSEQ=ATACGCTTGAAGCTACTGCT;RSEQ=TTTCTTTAGCCTGGTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:12:12,0:62,6:0.15:2,0:27.4:1:31.8:1:0.58373:0:60:24:0.15:0:1.1 0/1:84:23:22,1:58,3:0.2738:1,1:23.5:1:31.8:1:1:1.14:60:46:0.2738:0:1 -1 15295949 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50114;SOR=Inf;LSEQ=GGGGCTGCTGCAGGGGGCCC;RSEQ=CCCTGAGCCAGCCCCTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:119,43:0:2,0:23.4:1:30:1:1:0:60:53:1:0:0.3 0/1:187:2:1,1:135,50:0.0107:2,2:6.5:1:29:1:0.47214:2.68328:60:4:0.0107:0:1.5 -1 15295987 . G T 43 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13259;SOR=Inf;LSEQ=GGTCCCACAGCCCTGACGTA;RSEQ=AAGACTCTTTGCTGGTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:156,120:0:2,0:24.7:1:31.7:1:1:0:60:68:1:0:0.3 0/1:343:4:1,3:196,143:0.0117:2,2:23.8:1:21.5:1:0.31608:4.09576:60:3:0.0088:0:1.3 -1 15296019 . C T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00331;SOR=1.67072;LSEQ=CTGGTAAATCTCGGAACTCA;RSEQ=TGGAAGCTTCCACAAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:67:32,35:135,141:0.1953:2,2:25.2:1:30.6:1:0.89231:1.04709:60:134:0.1976:0:1.1 0/1:433:125:58,67:156,152:0.2887:2,2:26.1:1:29.8:1:0.45842:1.1851:60:250:0.2907:0:1.1 -1 15296282 . T G 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41631;LSEQ=CCTAAAAAGAACCCATGCCC;RSEQ=AATGCACAAGTACTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:0.1875:1,0:27:1:31:1:1:0:60:6:0.1875:0:1.7 0/1:4:1:0,1:0,3:0.25:0,0:42:0:31:0:1:0:60:2:0.25:0:2 -1 15847913 . T G 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=CCTCCCTGTGGTGCTGTGCT;RSEQ=CCATGGTCACGCTCCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:12:1:30:1:1:0:60:4:0.6667:0:1 0/1:4:1:1,0:2,1:0.25:2,0:19:0:34:0:1:0:60:2:0.25:0:1 -1 16174490 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49943;SOR=Inf;LSEQ=CGCCGCCCCGGCACCCGCCT;RSEQ=CCGGCGCTGACGGTCTCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:99,8:0:2,0:13.8:1:31.7:1:1:0:60:52.5:1:0:0.2 0/1:120:2:1,1:104,14:0.0167:2,2:15:0:31.5:1:0.23529:7.21024:60:4:0.0167:0:1.5 -1 16174524 . G T 76 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.13721;SOR=4.92914;LSEQ=TCTCGTACGAAGCCGGCGAG;RSEQ=GGGAGCCAGCAGCGGCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:1:1,0:274,102:0.0027:2,0:35:0:31:0:1:0:60:2:0.0027:0:1 0/1:463:6:2,4:334,123:0.013:2,2:15.2:1:29.5:1:0.05076:5.40732:60:12:0.0131:0:1.3 -1 16174686 . C A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.65362;SOR=2.8279;LSEQ=GGCCGCGCTCGCTCCTCGGG;RSEQ=GCCGCTTCCCGCCCCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:1,0:64,193:0.0039:2,0:1:0:26:0:0.25194:0:60:2:0.004:0:1 0/1:367:4:3,1:109,254:0.0109:2,2:16:1:27.5:1:0.08651:6.95:60:8:0.011:0:1 -1 16174695 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27924;SOR=Inf;LSEQ=CGCTCCTCGGGCGCCGCTTC;RSEQ=CGCCCCGGCCCGTTGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:37,149:0:2,0:20.1:1:31.3:1:1:0:60:92:0.9946:0:0.1 0/1:282:3:1,2:69,209:0.0106:2,2:20.3:1:26:1:1:1.51:60:2:0.0072:0:1 -1 16174707 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27661;SOR=Inf;LSEQ=GCCGCTTCCCGCCCCGGCCC;RSEQ=TTGCCGGCCCCTCCCGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:12,102:0:2,0:18.5:1:32.4:1:1:0:60:228:1:0:0.1 0/1:170:3:2,1:29,138:0.0176:2,2:8.7:1:26.3:1:0.08594:9.33:60:6:0.018:0:1.3 -1 16199051 . T C 39 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTGCAGTGAGCTGAGATTG;RSEQ=GCCACTGCACTCCAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:22.7:1:25:1:1:0:50.7:2:1:0:1 1/1:1:1:1,0:0,0:1:0,0:25:0:34:0:1:0:60:2:1:0:1 -1 16199094 . C CA 72 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0.43179;LSEQ=AACAGAGCGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:3,1:0.5556:2,0:17:1:31.2:1:0.44444:0:54:10:0.5556:0:3.2 0/1:3:1:1,0:1,1:0.3333:2,0:11:0:28:0:1:0:60:2:0.5:0:7 -1 16199587 . G A 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGCTTATGGTCCCCCACC;RSEQ=TCACTTCATGCACGAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:168,236:0:2,0:25.3:1:31.1:1:1:0:60:133.667:1:0:0.1 0/1:656:32:14,18:263,361:0.0488:2,2:27.6:1:29.9:1:0.85658:1.07:60:31:0.0476:0:1.1 -1 16200163 . A G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACAAACAATACTTTAAC;RSEQ=TGGAAATGTGTACTTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 16200564 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50325;SOR=Inf;LSEQ=TGGAATTGTAGAGGATATTT;RSEQ=CTCTTCTGCCAGCTACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:113,7:0:2,0:24.5:1:31.2:1:1:0:60:39:1:0:0.1 0/1:147:2:1,1:126,19:0.0136:2,2:8.5:1:31.5:1:0.2544:6.48926:60:4:0.0138:0:1 -1 16200729 . A AT 156 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.18513;SOR=1.45604;LSEQ=TATTTTGTCTGGTCACTAAG;RSEQ=TTTTTTTTTTCTTGTGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:24:7,17:245,284:0.0429:2,2:33.3:1:30.9:1:0.14118:2.09237:60:48:0.0439:0:0 0/1:588:36:16,20:264,288:0.0612:2,2:27.6:1:30.2:1:0.73316:1.14557:60:72:0.0626:0:0.1 -1 16200909 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.97468;LSEQ=AGGTTGGTATGTCCTGACCT;RSEQ=TGTATATTAGCCCCTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:49,143:0.0103:2,2:24:1:18.5:1:0.45003:2.90:60:1:0.0052:0:1 0/1:199:2:1,1:53,144:0.0101:2,2:8.5:1:28:1:0.47008:2.70:60:4:0.0103:0:1 -1 16200933 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49828;SOR=0;LSEQ=ATATTAGCCCCTCTCCTAAC;RSEQ=CAAGTCAAACTCTCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:14,102:0.0169:2,2:9:0:31.5:1:0.23903:7.07:60:4:0.0172:0:1 0/0:111:0:0,0:19,92:0:2,0:23.9:1:30.8:1:1:0:60:54.5:1:0:0.1 -1 16202622 . T A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47687;LSEQ=AGACAAAGACAATGCTGAAG;RSEQ=GAATGTTTGCATGACTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:1,0:114,8:0.0081:2,0:35:0:14:0:1:0:60:0:0:0:3 0/1:167:2:1,1:143,22:0.012:2,2:17:1:29:1:0.2572:6.37932:60:4:0.0122:0:1 -1 16235724 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50469;SOR=Inf;LSEQ=AGAAATTCCAGTCTGAAAAT;RSEQ=TAGACCTATTAGTTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:94,7:0:2,0:22:1:30.3:1:1:0:60:202:1:0:0 0/1:129:2:1,1:117,10:0.0155:2,2:22:1:27:1:0.16388:11.20338:60:4:0.0159:0:1 -1 16237577 . G GT 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.74445;SOR=0.74202;LSEQ=TTAGAAGAATTAATAACTTG;RSEQ=TTTTTTTTGGGAATTTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:5:3,2:189,65:0.0193:2,2:22.8:1:28.7:1:0.60648:1.93294:60:10:0.0195:0.0077:0 0/1:278:4:3,1:183,81:0.0144:2,2:27.8:1:28.6:1:1:1.33:60:8:0.0148:0.0036:0 -1 16237813 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19765;SOR=0;LSEQ=CCAGGTAAGACACAAGCAAG;RSEQ=TGAGTTTGAGTTACTCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:45,144:0.0105:2,2:23.5:1:30.5:1:0.42463:3.18:60:4:0.0105:0:1 0/0:238:0:0,0:74,163:0:2,0:22.8:1:31.9:1:1:0:60:78:1:0:0.1 -1 16237846 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22504;SOR=Inf;LSEQ=ACTCATCACACACACTGTTT;RSEQ=TGTTGCAGTGTATGAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:18,100:0:2,0:23.8:1:32.3:1:1:0:60:236:1:0:0.1 0/1:107:2:0,2:16,89:0.0187:2,0:10.5:1:32:0:1:0:60:4:0.0187:0:1 -1 16242620 . C A 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCGGCCCCCATTCCACTTA;RSEQ=AGAAACAGAAAGTGAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:0:0,0:338,114:0:2,0:24.7:1:32:1:1:0:60:112:0.9978:0:0.1 0/1:543:44:29,15:328,170:0.081:2,2:22.7:1:30.3:1:1:1.00:60:88:0.0819:0:1.2 -1 16242866 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23914;SOR=0;LSEQ=TTGGAAAGGTGATATTTAAT;RSEQ=GTGTAATGAATGAACATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:0,2:0,121:0.0163:1,0:21.5:1:31.5:1:1:0:60:4:0.0164:0:1 0/0:128:0:0,0:7,121:0:2,0:20.7:1:30.5:1:1:0:60:127:1:0:0 -1 16243005 . CTT C 32 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=ACATATATATTTTCTTACCT;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,11:0:0,0:17.2:1:20.1:1:1:0:56.4:0.833:0.7143:0:1.6 0/1:6:2:0,2:0,4:0.3333:0,0:26.5:1:32:0:1:0:60:4:0.4:0:0 -1 16245362 . G A 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATACCCTATATGGACTTG;RSEQ=TTCATTCTAATTTATTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:134,39:0:2,0:23.7:1:31.4:1:1:0:60:85.5:1:0:0.1 0/1:256:30:22,8:166,59:0.1172:2,2:23.4:1:28.9:1:1:1.02302:60:60:0.119:0:1 -1 16245610 . GT G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.06745;LSEQ=TGTTTTTTAAGACTTGAAGG;RSEQ=TTTTTTTTTGCATATGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:60:5,55:16,96:0.3488:2,2:30.1:1:32:1:0.33178:1.82738:60:120:0.3529:0:0 0/1:202:7:0,7:37,158:0.0347:2,0:26.6:1:31.6:1:0.35364:0:60:14:0.0354:0:0 -1 16245803 . TA T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20918;SOR=Inf;LSEQ=CACTTGAGATGTTGATTTGA;RSEQ=AGATTACTATAGAAAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:95,10:0:2,0:21.7:1:28.6:1:1:0:60:104:1:0:0.2 0/1:89:2:1,1:83,4:0.0225:1,2:26.5:1:29:1:0.10981:18.66298:60:4:0.0227:0:0 -1 16245997 . T C 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACACGACATTTCTGCCGATA;RSEQ=GGGCCTGTGGTAAAGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:673:0:0,0:317,356:0:2,0:25.9:1:30.4:1:1:0:60:95.143:1:0:0.1 0/1:943:34:14,20:415,493:0.0361:2,2:28.6:1:29.9:1:0.72636:1.20232:60:68:0.0366:0:1.2 -1 16247227 . CT C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.07604;SOR=Inf;LSEQ=TCACTACAGTGTGCATCACA;RSEQ=TTTTTTTTTAATAGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:0:1,0:32.2:1:32.1:1:1:0:60:38:1:0:0.1 0/1:15:3:3,0:11,1:0.2:2,0:35.3:1:31.7:1:1:0:60:6:0.2:0:0 -1 16247573 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5022;SOR=Inf;LSEQ=GCTCACGCCTGTAATCCCAG;RSEQ=ACTTTGGGAGGCCAAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:1,74:0:1,0:25.9:1:32.5:1:1:0:59.9:150:1:0:0 0/1:92:2:1,1:2,87:0.0217:1,2:9:1:30.5:1:0.0652:35.71:60:4:0.022:0:2 -1 16247575 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50375;SOR=Inf;LSEQ=TCACGCCTGTAATCCCAGCA;RSEQ=TTTGGGAGGCCAAGGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:1,71:0:1,0:26.3:1:32.4:1:1:0:59.9:71:1:0:0 0/1:91:2:1,1:1,88:0.022:1,2:7:1:30.5:1:0.04371:62.58:60:4:0.0222:0:2 -1 16247587 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50035;SOR=Inf;LSEQ=TCCCAGCACTTTGGGAGGCC;RSEQ=AGGCAGGTGGATCACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:0,60:0:1,0:27.7:1:30.9:1:1:0:59.8:120:1:0:0 0/1:72:2:0,2:0,70:0.0278:1,0:21:1:31:1:1:0:50:4:0.0282:0:3 -1 16247681 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06536;SOR=Inf;LSEQ=AAATACAAGAAAAATTAGCC;RSEQ=GGCTTGGTGGCGCGTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:0:1,0:26.8:1:30.6:1:1:0:60:26:1:0:0 0/1:5:2:0,2:0,3:0.4:0,0:8.5:1:32:0:1:0:60:4:0.4:0:1 -1 16248717 . A T 35 v4;q23;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1007;SOR=0;LSEQ=CATTAAAATTTGAAACTTGC;RSEQ=TCAAACACCTCTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:3:0,3:206,51:0.0115:2,0:6:1:22.3:1:0.00857:0:60:2:0.0083:0:1 0/0:300:0:0,0:242,57:0:2,0:5:0:14:0:1:0:45:0:0:0:3 -1 16248728 . C CT 167 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00454;SOR=0.48961;LSEQ=GAAACTTGCATCAAACACCT;RSEQ=TTTTTTTTTTTAAAGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:46:34,12:188,66:0.1489:2,2:30.3:1:30.3:1:1:1.00533:60:22:0.1522:0:0.4 0/1:368:29:21,8:251,81:0.0788:2,2:26.8:1:29.5:1:0.65941:1.17989:59.3:13.5:0.0763:0:0.7 -1 16248740 . A T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.83004;SOR=1.15361;LSEQ=AAACACCTCTTTTTTTTTTT;RSEQ=AAGGTGGATTTTGCAAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:9:6,3:265,127:0.0224:2,2:21.1:1:24.9:1:1:1.04319:58.9:3.5:0.0179:0:2.4 0/1:505:13:9,4:325,166:0.0257:2,2:24.5:1:26.5:1:1:1.15:60:12:0.0245:0:1.2 -1 16248910 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18744;SOR=0;LSEQ=TAATACAGAAACTTAAGATG;RSEQ=CATTAAATTTTATTTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:15,151:0.0118:2,2:19.5:1:32:0:0.18192:9.78:60:4:0.0118:0:1 0/0:222:0:0,0:37,185:0:2,0:21.9:1:31.7:1:1:0:60:221:1:0:0.1 -1 16249125 . C CT 27 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTGATAACTTTATGTA;RSEQ=TTTTTTTTTTGAGACAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,3:0.3333:0,0:33.5:1:27.5:1:1:0:57.5:4:0.3333:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 16254571 . G A 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAAAGAACTAATATCTTT;RSEQ=TTATTTTTTGGCAGAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:0:0,0:385,210:0:2,0:25.1:1:32.1:1:1:0:60:197.333:1:0:0.1 0/1:703:37:23,14:404,259:0.0526:2,2:21.2:1:28.4:1:1:1.05:60:74:0.0531:0:1.2 -1 16255141 . GGA G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1.01012;LSEQ=ACTTTTGATCCGGAGAGAGT;RSEQ=GAGAGAGAGACGCTTAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:534:8:3,5:308,218:0.015:2,2:31.4:1:32.3:1:0.28791:2.35093:60:16:0.0154:0:0.4 0/1:727:11:5,6:388,327:0.0151:2,2:31.7:1:31.1:1:0.76219:1.42314:60:22:0.0153:0:0.2 -1 16255644 . C T 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCAAGCCTGAGCAGCCTG;RSEQ=AGATGGGGTAAGTGCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:223,268:0:2,0:26.2:1:31.8:1:1:0:60:43.636:1:0:0.2 0/1:525:42:19,23:215,268:0.08:2,2:25.2:1:27.7:1:1:1.03:60:41:0.0792:0:1.2 -1 16255972 . G T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06273;SOR=Inf;LSEQ=TCTGTTGGGTCTGGCTCAAG;RSEQ=CCCAGCTCAGACCTACAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:217,183:0:2,0:23.4:1:31.3:1:1:0:60:79:1:0:0.8 0/1:433:5:2,3:245,183:0.0115:2,2:9.4:1:23:1:0.65556:2.00496:60:4:0.0094:0:1.6 -1 16256007 . T C 276 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01878;LSEQ=ACAAGCAAGACTGGGAGAAC;RSEQ=AGCAGGTGAATCTGTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:445:441:238,203:0,2:0.991:0,2:26.2:1:31.5:1:0.21358:0:60:72.5:0.9909:0:1.1 1/0:586:395:223,172:102,88:0.6741:2,2:25.7:1:30.7:1:0.53526:1.12:60:78:0.6713:0:1.2 -1 16257858 . C T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12797;SOR=Inf;LSEQ=CCTGCCCCCAGGAGCAGACC;RSEQ=CGATAAAGAAGCTGCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:141,143:0:2,0:23.3:1:31:1:1:0:60:55.8:0.9964:0:0.1 0/1:331:4:2,2:161,166:0.0121:2,2:24.8:1:28.5:1:1:1.03:60:8:0.0122:0:0.8 -1 16258302 . A G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04699;LSEQ=GGAAAAACTCAAGCGGTCCA;RSEQ=TTCTCCTCGGGGAGAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:273:126,147:159,189:0.4382:2,2:23.1:1:32.1:1:0.93542:1.02:60:135.5:0.4399:0:1.1 0/1:765:27:15,12:353,385:0.0353:2,2:22.5:1:31.1:1:0.44122:1.36:60:54:0.0357:0:1 -1 16259335 . A G 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12528;SOR=Inf;LSEQ=GCACCAGAGGGCCTTGCCCC;RSEQ=GAGGACAGGGACAAGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:185,135:0:2,0:25.2:1:30.4:1:1:0:60:79:0.9968:0:0.1 0/1:351:4:2,2:197,148:0.0114:2,2:35.3:1:29.3:1:1:1.32996:60:8:0.0115:0:1 -1 16259465 . C A 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05301;SOR=0;LSEQ=CACCTTATCCTGGAGAATCC;RSEQ=AGACAGATCTGCAACCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:4:3,1:196,188:0.0103:2,2:16.8:1:27.3:1:0.62356:2.87:60:8:0.0105:0:1 0/0:419:0:0,0:189,230:0:2,0:25.8:1:30.7:1:1:0:60:58.857:1:0:0.1 -1 16259813 . A G 279 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00714;LSEQ=AGAGCCATGTCCCTGAATCC;RSEQ=ACCAAGCTCAAGGTGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:589:587:300,287:0,0:0.9966:0,2:25.6:1:30.4:1:1:0:60:116.4:0.9983:0:1.1 1/0:646:437:202,235:96,112:0.6765:2,2:24.2:1:29.8:1:1:1.00:60:42.7:0.6724:0:1.2 -1 16260233 . G A 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02294;SOR=Inf;LSEQ=GCCCCCCTACTAAGGTGACA;RSEQ=AGTGGATCACAAGGCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:112,118:0:2,0:23:1:31.4:1:1:0:60:56.5:1:0:0.1 0/1:206:5:3,2:105,96:0.0243:2,2:11.6:1:30.6:1:1:1.37:60:10:0.0245:0:1 -1 16260916 . C T 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCCAGGCACAGTCAATGC;RSEQ=GCTGCGAGTGCAGTGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:127,165:0:2,0:23.5:1:30.3:1:1:0:60:291:1:0:0.1 0/1:287:21:9,12:132,134:0.0732:2,2:24.5:1:29.8:1:0.6524:1.31219:60:20:0.0699:0:1.1 -1 16261327 . G A 78 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07262;SOR=6.32397;LSEQ=CCTGATTCTGTCACAGCATC;RSEQ=CAGCCTCCATCCAAAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:1:1,0:259,225:0.0021:2,0:1:0:25:0:1:0:60:2:0.0021:0:1 0/1:542:7:3,4:287,247:0.0129:2,2:8.4:1:27.9:1:0.7096:1.54799:60:14:0.0131:0:1.1 -1 16261851 . C A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05718;SOR=Inf;LSEQ=GCCATCCTCATTCCCAAGGG;RSEQ=AAGCCACCCCAGCAGTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:139,198:0:2,0:24:1:32:1:1:0:60:66.4:1:0:0.1 0/1:324:4:3,1:132,186:0.0123:2,2:16.3:1:26.8:1:0.31288:4.21:60:8:0.0127:0:1 -1 16262047 . G A 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34286;SOR=3.46261;LSEQ=GTGAGAATGAACACTCCCAC;RSEQ=CTGCCCAGTATCACCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:1,0:114,144:0.0039:2,0:1:0:24:0:0.44402:0:60:2:0.004:0:1 0/1:226:3:2,1:97,126:0.0133:2,2:9.7:1:25:1:0.58275:2.59:60:6:0.0137:0:1 -1 16262067 . G A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09495;SOR=Inf;LSEQ=GCTGCCCAGTATCACCTACA;RSEQ=CATCCGGCCAGAAGCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:96,139:0:2,0:24:1:31.7:1:1:0:60:32.571:1:0:0.1 0/1:199:3:2,1:84,112:0.0151:2,2:26.3:1:23.3:1:0.57934:2.65:60:2:0.0103:0:1.3 -1 16262075 . C A 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25132;SOR=0;LSEQ=GTATCACCTACAGCATCCGG;RSEQ=CAGAAGCGCTTCACTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:1,2:87,120:0.0142:2,2:21.7:1:23.7:1:1:1.44753:60:2:0.0099:0:2.3 0/0:186:0:0,0:82,104:0:2,0:24.8:1:31:1:1:0:60:22.25:1:0:0.2 -1 16262076 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21668;SOR=Inf;LSEQ=TATCACCTACAGCATCCGGC;RSEQ=AGAAGCGCTTCACTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:88,125:0:2,0:25.1:1:31.1:1:1:0:60:29.429:1:0:0.2 0/1:186:2:1,1:81,103:0.0108:2,2:31:1:29:1:1:1.27:60:4:0.011:0:1 -1 16262086 . T A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21726;SOR=Inf;LSEQ=AGCATCCGGCCAGAAGCGCT;RSEQ=CACTCTCCTCGGGCTCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:77,116:0:2,0:25.9:1:29.7:1:1:0:60:47.25:1:0:0.2 0/1:169:2:1,1:77,90:0.0118:2,2:16:1:25:1:1:1.17:60:4:0.0121:0:1 -1 16262194 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09437;SOR=Inf;LSEQ=GTGCCTGCACTGGCCTCCCA;RSEQ=CACCCTCCCGAGGAGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:55,79:0:2,0:25.7:1:32.2:1:1:0:60:133:1:0:0.1 0/1:113:3:1,2:50,60:0.0265:2,2:25.7:1:23:1:1:1.65945:60:2:0.0182:0:1.3 -1 16262237 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18882;SOR=Inf;LSEQ=ATTATCACCTTCCTGTCGCT;RSEQ=GAGCCACAGCCCCTGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:74,74:0:2,0:23.3:1:30.2:1:1:0:60:48.333:0.9932:0:0.1 0/1:115:2:1,1:59,54:0.0174:2,2:27:1:30.5:1:1:1.09174:60:4:0.0174:0:1 -1 16262381 . G T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.6252;SOR=2.75138;LSEQ=AGCCCAGGGCCGCGGATGGG;RSEQ=TGGTGAAGGTGCCACCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:0,1:152,107:0.0038:2,0:41:0:31:0:0.41538:0:60:2:0.004:0:4 0/1:286:3:1,2:148,135:0.0105:2,2:26:1:30:1:0.60847:2.18678:60:6:0.0107:0:1 -1 16262404 . C T 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGAAGGTGCCACCAGCCAG;RSEQ=AAGGCCCCTCAGCAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:164,112:0:2,0:25.7:1:31.4:1:1:0:59.9:26.6:1:0:0.4 0/1:295:23:10,13:146,125:0.078:2,2:31.1:1:28.4:1:0.38792:1.51622:60:46:0.0785:0:1.3 -1 16262459 . G GC 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.12789;SOR=5.362;LSEQ=AGACACCAGATGCCAAAGCT;RSEQ=CCCCCACCCCCACCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:1,0:137,121:0.0039:2,0:12:0:28:0:1:0:60:2:0.0042:0:0 0/1:294:6:6,0:144,140:0.0204:2,0:34.7:1:28:1:0.03019:0:60:5:0.0178:0.0102:1.5 -1 16262477 . G C 40 q23;Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.77807;SOR=1.22447;LSEQ=CTGCCCCCACCCCCACCCCT;RSEQ=CCCCCGTCCCTGTCCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:5:5,0:65,138:0.0233:2,0:9.6:1:22.2:1:0.00392:0:59:1.5:0.0172:0:2.8 0/1:247:7:7,0:80,156:0.0283:2,0:17:1:14.4:1:0.00064:0:58.6:0:0:0:4 -1 16262650 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02748;SOR=0;LSEQ=AGCGGGGAGCTGTTTCAAGA;RSEQ=TACCGGTACGGCGACATCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:5:4,1:186,272:0.0108:2,2:6.8:1:26.8:1:0.16424:5.83:60:10:0.011:0:1 0/0:485:0:0,0:222,263:0:2,0:24.3:1:30.9:1:1:0:60:59.625:1:0:0.2 -1 16262717 . G A 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.69904;SOR=1.58468;LSEQ=CACACACTCAGTTTCCCGCC;RSEQ=CTTCCTCTGTTGGCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:2:1,1:121,189:0.0064:2,2:21.5:1:30.5:1:1:1.56:60:4:0.0066:0:1 0/1:395:4:3,1:170,221:0.0101:2,2:16.3:1:30.8:1:0.32313:3.89:60:8:0.0103:0:1.3 -1 16262784 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=GAGCCAGCCAGGTATCTCCC;RSEQ=ACTGTCTGTTGGGCATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:39,113:0:2,0:24.1:1:31.1:1:1:0:60:29.4:1:0:0.2 0/1:161:2:1,1:44,115:0.0124:2,2:11.5:1:28.5:1:0.48214:2.60:60:4:0.0127:0:1 -1 16262806 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19727;SOR=Inf;LSEQ=CTGTCTGTTGGGCATGTGCT;RSEQ=GTGGGGCTCAGCAGGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:19,87:0:2,0:26.9:1:30:1:1:0:60:34.333:1:0:0.1 0/1:86:2:1,1:14,69:0.0233:2,2:20:1:29:1:0.32353:4.80:60:4:0.0233:0:1 -1 16263452 . A G 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGCTCTTGCTGGGTAGC;RSEQ=TCAGCAGGAGGCAGGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:26.3:1:30:1:1:0:60:22:1:0:1 1/1:3:3:3,0:0,0:1:0,0:13.7:1:31:1:1:0:60:6:1:0:1 -1 16264264 . G A 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTCCAGCATGGCTCAGC;RSEQ=AGGGGCCATGAGCTCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:243,164:0:2,0:24.7:1:30.5:1:1:0:60:406:1:0:0.1 0/1:403:42:29,13:213,147:0.1042:2,2:25.8:1:29.9:1:0.24609:1.54:60:84:0.1058:0:1.1 -1 16264391 . G A 144 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.61488;LSEQ=ACTTCGTCTCTGGCAACAAC;RSEQ=TCCTGGCCCATCGGTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:938:2:1,1:447,488:0.0021:2,2:40.5:1:31:1:1:1.09:60:4:0.0022:0:1.5 0/1:957:29:13,16:448,480:0.0303:2,2:20:1:29.7:1:0.85075:1.14855:60:58:0.0307:0:1.1 -1 16264567 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26083;SOR=0;LSEQ=GGAAGACGTAGGTAGTCCCT;RSEQ=CCAGCCCATCTCCCTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:1,2:34,174:0.0142:2,2:22:1:25.7:1:0.4213:2.54:60:2:0.0098:0:1.3 0/0:163:0:0,0:39,124:0:2,0:23.3:1:31.5:1:1:0:60:53.333:1:0:0.1 -1 16264590 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15047;SOR=Inf;LSEQ=AGCCCATCTCCCTGGCCTGT;RSEQ=ATGGAAGCATTAACTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:12,145:0:2,0:21:1:32:1:1:0:60:77.5:1:0:0.1 0/1:100:2:1,1:7,91:0.02:2,2:20:1:28:1:0.15434:12.23:60:4:0.0204:0:1 -1 16265152 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24551;SOR=0;LSEQ=TGGACCTGATACTGTGGGTT;RSEQ=GATGTGGGCTGCTGTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:170,21:0.0104:2,2:29:1:31.5:1:0.21551:7.93203:60:4:0.0105:0:1 0/0:196:0:0,0:164,32:0:2,0:8:0:15:0:1:0:60:0:0:0:2 -1 16265153 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24685;SOR=Inf;LSEQ=GGACCTGATACTGTGGGTTG;RSEQ=ATGTGGGCTGCTGTTTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:174,24:0:2,0:25.5:1:31:1:1:0:60:38.6:1:0:0.2 0/1:197:2:1,1:163,32:0.0102:2,2:23.5:1:27.5:1:0.30768:5.03149:60:4:0.0105:0:1 -1 16265186 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68671;SOR=1.9145;LSEQ=GTTTGACTAGGAGGCCCCTG;RSEQ=TCACTGGCAGCTGGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:2:2,0:249,94:0.0058:2,0:16.5:1:17.5:1:1:0:60:1:0.003:0:2 0/1:362:4:1,3:254,104:0.011:2,2:17.5:1:24.3:1:0.07926:7.28166:60:3:0.0083:0:1.5 -1 16265422 . A G 277 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01761;LSEQ=TACACCCACAGGTGGGGCTG;RSEQ=TCAGGGTAGGTGGGCCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:459:453:147,306:1,1:0.9869:2,2:23.5:1:31.5:1:0.54523:2.07803:60:74.5:0.9889:0:1.1 1/0:423:241:81,160:59,123:0.5697:2,2:22.3:1:30.9:1:0.83503:1.06:60:240:0.5701:0:1.1 -1 16265427 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0493;SOR=Inf;LSEQ=CCACAGGTGGGGCTGATCAG;RSEQ=GTAGGTGGGCCTACTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:131,296:0:2,0:22.9:1:30.6:1:1:0:60:37.818:1:0:1.1 0/1:382:4:3,1:119,259:0.0105:2,2:14.5:1:23.5:1:0.09795:6.49:60:3:0.008:0:1.8 -1 16265466 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51213;SOR=0;LSEQ=CTGGTGCCCACTAGATCTGG;RSEQ=CCCAGAGGTGGGCAAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:16,180:0.0101:2,2:5:1:28:1:0.16474:10.94:60:4:0.0102:0:1.5 0/0:142:0:0,0:8,134:0:2,0:5:0:18:0:1:0:60:0:0:0:2 -1 16265662 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1503;SOR=Inf;LSEQ=TTCCAGTAGACATAGTCCTG;RSEQ=CACATTTGCTGGTTGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:171,13:0:2,0:26:1:31.7:1:1:0:60:183:1:0:0.1 0/1:117:2:2,0:112,3:0.0171:1,0:36:1:26:1:1:0:60:4:0.0172:0:1 -1 16265904 . T A 187 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCTCTCCCCACCTCATGAT;RSEQ=GTCATTGCCTCCGTGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1036:0:0,0:409,627:0:2,0:25.1:1:30:1:1:0:60:78.692:1:0:0.2 0/1:1117:89:41,48:428,600:0.0797:2,2:24.9:1:29:1:0.43454:1.20:60:43.5:0.0788:0:1.2 -1 16265967 . C A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12533;SOR=Inf;LSEQ=TGAATCTTCCCAGGGCTCTG;RSEQ=AGTAAAAACAAAGGACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:77,291:0:2,0:23.7:1:32:1:1:0:60:45:1:0:0.2 0/1:400:4:3,1:112,284:0.01:2,2:9:1:27:1:0.07355:7.56:60:8:0.0101:0:1 -1 16458607 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49635;SOR=0;LSEQ=TCCTCCAGCACGCGGGACAG;RSEQ=CCAAAGTCAGACACCTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:49,18:0.029:2,2:36:1:31.5:1:0.47783:2.67652:60:4:0.0294:0:1 0/0:68:0:0,0:41,27:0:2,0:22.9:1:30.5:1:1:0:60:33:1:0:0.2 -1 16458654 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49678;SOR=0;LSEQ=GTTGCTGTTGACGAGGATGT;RSEQ=GCGGGCAGCCAGGTCACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:39,36:0.026:2,2:36.5:1:30.5:1:1:1.08219:60:4:0.0263:0:1 0/0:75:0:0,0:36,39:0:2,0:27.7:1:29.5:1:1:0:60:74:1:0:0.3 -1 16458660 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49807;SOR=Inf;LSEQ=GTTGACGAGGATGTTGCGGG;RSEQ=AGCCAGGTCACGGTGCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:37,33:0:2,0:25.7:1:31.6:1:1:0:60:69:1:0:0.1 0/1:78:2:1,1:38,38:0.0256:2,2:40.5:1:29:1:1:1:60:4:0.0256:0:2 -1 16458693 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50272;SOR=Inf;LSEQ=GTGCACATAGTTCATGTTGG;RSEQ=CAGGTACTTCATGCCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:25,39:0:2,0:27.7:1:31.6:1:1:0:60:128:1:0:0.1 0/1:80:2:1,1:34,44:0.025:2,2:29.5:1:28:1:1:1.29:60:4:0.025:0:1 -1 16458732 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=TGCGATGCCCCGCAGCATGC;RSEQ=CACCAGCTGCAGCACGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:17,33:0:2,0:24.4:1:30.7:1:1:0:60:49:1:0:0.1 0/1:50:2:1,1:21,27:0.04:2,2:25:1:32.5:1:1:1.28:60:4:0.0408:0:1 -1 16971069 . G C 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTGCAGGTGCCCTCGCA;RSEQ=TGGACTAAACTGGACCGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:19.8:1:31.3:1:1:0:60:8:1:0:1 1/1:3:3:1,2:0,0:1:0,2:33.3:1:32.3:1:1:0:60:6:1:0:1 -1 16971283 . T G 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01282;SOR=0;LSEQ=GGCCCGCGCCCAGCCTCCGC;RSEQ=AGGGGACCCCCTCCGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:1:29.5:1:1:0:60:4:1:0:2 0/0:11:0:0,0:6,5:0:2,0:21.3:1:28.5:1:1:0:56.3:22:1:0:0.5 -1 16971311 . G A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=CCCCTCCGTGGCTTCCCACC;RSEQ=GGTTGTTCCAGGCCTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:18:0:31:0:1:0:49:2:1:0:2 0/1:8:3:1,2:2,3:0.375:2,2:18:1:29.7:1:1:1.28664:52.3:6:0.4286:0:1.3 -1 16971371 . C T 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CCTCCGACCTCCGCCTGCCC;RSEQ=GGGGATGCTCCCAGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:28.3:1:30.7:1:1:0:49:6:1:0:1.3 0/1:3:1:0,1:1,1:0.3333:2,0:36:0:32:0:1:0:40:2:0.3333:0:2 -1 16971793 . G C 85 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50881;LSEQ=AACCCAGACCTCTGGCAGCT;RSEQ=TCACTTTCACAATGCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:7,0:20,1:0.25:1,0:33.9:1:30.3:1:1:0:33:14:0.2593:0:1 0/1:7:1:1,0:4,2:0.1429:2,0:25:0:33:0:1:0:40:2:0.1667:0:3 -1 16971804 . A T 95 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15963;SOR=0;LSEQ=CTGGCAGCTGTCACTTTCAC;RSEQ=ATGCCCTTGGGCTGACTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:8,0:18,1:0.2963:1,0:30.4:1:31.8:1:1:0:49.6:16:0.2963:0:1.1 0/0:9:0:0,0:7,2:0:2,0:24.9:1:29.6:1:1:0:54.2:18:1:0:0.3 -1 16971862 . A G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41581;SOR=1.48075;LSEQ=CCCAACCCCAGGGCACCTCA;RSEQ=GTGGCCCCACCAAACCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:26:26,0:50,0:0.3421:1,1:29:1:33.4:1:1:0:55.2:52:0.3514:0:2.2 0/1:39:17:14,3:19,3:0.4359:2,2:17.8:1:32.3:1:1:1.34641:58.8:34:0.4474:0:2.6 -1 16971866 . G T 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.40864;SOR=0.68993;LSEQ=ACCCCAGGGCACCTCAAGTG;RSEQ=CCCCACCAAACCTTCCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:57:57,0:21,0:0.7308:1,1:26.5:1:30.7:1:1:0:56.9:114:0.7308:0:1.6 1/0:43:28:25,3:12,3:0.6512:2,2:23:1:30.9:1:0.64736:2.05:58.6:56:0.6667:0:2 -1 16971948 . C G 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21447;SOR=0.81193;LSEQ=TGCTAGGCCCTTGCAACTGA;RSEQ=CTGTGGGACCTGAGGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:175:167,8:228,4:0.43:1,1:25:1:32.4:1:0.13705:2.72383:54.4:57.333:0.4289:0:1.1 0/1:237:90:86,4:142,5:0.3797:1,1:24.5:1:32:1:0.73365:1.31931:58.4:89:0.3771:0:1.3 -1 16972067 . CA TG 274 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.41664;LSEQ=AATCCCGTAGGGACAGGTTT;RSEQ=CAACTTCCCGGATGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1792:433:279,154:745,610:0.2416:2,2:28.9:1:31.3:1:0.00054:1.48:39.3:866:0.245:0.0033:1.1 0/1:1835:215:130,85:915,697:0.1172:2,2:28.3:1:30.5:1:0.34019:1.16:41.2:430:0.1191:0.0082:1 -1 16972068 . A G 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49916;SOR=0.93473;LSEQ=ATCCCGTAGGGACAGGTTTC;RSEQ=CAACTTCCCGGATGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1793:253:156,97:594,517:0.1411:2,2:25.6:1:30.3:1:0.02075:1.40:39.8:83.333:0.1855:0:1.1 0/1:1833:244:149,95:774,609:0.1331:2,2:27.8:1:30.3:1:0.14175:1.23:37:243:0.1504:0:1.1 -1 16972134 . C T 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00793;SOR=0.83157;LSEQ=CCAGAAGGATGGGGTGGCTC;RSEQ=CACTCCTGCTGCTTCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2621:589:200,389:1081,951:0.2247:2,2:28.6:1:30.6:1:0:2.21023:34.6:48.083:0.2251:0:1.4 0/1:2456:477:145,332:1026,953:0.1942:2,2:28.8:1:29.7:1:0:2.46416:34.1:118.25:0.1952:0:1.4 -1 16972189 . C A 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.49249;LSEQ=CCCTGGTGAGTGCCCCCAAC;RSEQ=TTGATCCCCATCTGCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2164:385:139,246:749,1030:0.1779:2,2:26.5:1:30.4:1:0.03007:1.28681:58.5:54:0.1767:0:1.1 0/1:2191:211:87,124:841,1138:0.0963:2,2:26.1:1:29.8:1:0.76955:1.0533:57.6:51.75:0.0955:0:1.2 -1 16972190 . T C 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00096;SOR=0.67421;LSEQ=CCTGGTGAGTGCCCCCAACC;RSEQ=TGATCCCCATCTGCCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2127:183:75,108:786,1153:0.086:2,2:18.3:1:31.4:1:0.93728:1.02:32.2:35.6:0.0847:0:2.3 0/1:2145:128:44,84:856,1159:0.0597:2,2:14.9:1:31.7:1:0.07925:1.40977:30.8:127:0.0599:0:2.2 -1 16972217 . C G 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00028;SOR=0.44145;LSEQ=CCATCTGCCTTCAGGAGGGG;RSEQ=TTGGCCCCATTCTCCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1448:64:42,22:461,921:0.0442:2,2:18.8:1:29.4:1:0:3.81:33.3:11.8:0.0417:0:3 0/1:1400:28:20,8:500,867:0.02:2,2:22.1:1:30.3:1:0.00026:4.33:31:56:0.0202:0:2.8 -1 16972221 . G A 179 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=17.6865;LSEQ=CTGCCTTCAGGAGGGGCTTG;RSEQ=CCCCATTCTCCTATTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1350:5:4,1:434,911:0.0037:2,2:7.6:1:25.4:1:0.04073:8.38:60:4:0.003:0:1.2 0/1:1280:79:28,51:433,768:0.0617:2,2:22.4:1:28.5:1:1:1.02691:60:78:0.0619:0:1.2 -1 16972239 . G A 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00867;SOR=0.57507;LSEQ=TGGCCCCATTCTCCTATTCT;RSEQ=GGATGAGAAAAAAGTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:946:68:23,45:214,664:0.0719:2,2:19.3:1:29.1:1:0.10879:1.59:36.4:33:0.0707:0:2.8 0/1:868:37:13,24:224,605:0.0426:2,2:18.6:1:27.2:1:0.34515:1.46:32.3:36:0.0421:0:2.6 -1 16972294 . T C 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01014;SOR=0.64271;LSEQ=TGGGCATGGGGCAGTGACCT;RSEQ=GGCCTCTTGAGCACAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:142:16,126:20,320:0.294:2,2:30.1:1:29.4:1:0.05572:2.03:44.4:70:0.2917:0:2.1 0/1:308:65:7,58:22,221:0.211:2,2:30.8:1:29.3:1:0.63798:1.21:37.1:31.5:0.2072:0:1.9 -1 16972300 . C T 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00123;SOR=0.40595;LSEQ=TGGGGCAGTGACCTTGGCCT;RSEQ=TTGAGCACAGCTGGGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:60:9,51:24,371:0.1319:2,2:29.9:1:29.7:1:0.0272:2.72:45.4:59:0.1326:0:2.8 0/1:293:17:2,15:25,251:0.058:2,2:29.3:1:30.5:1:0.66209:1.34:39.1:34:0.0594:0:2.8 -1 16972338 . T C 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06631;SOR=0.6344;LSEQ=GCCCTAGGAACACATAGACA;RSEQ=GGCCCACTTAGGCCTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:84:0,84:16,235:0.2507:2,1:19.9:1:30:1:0.01503:0:45.6:83:0.2554:0:1 0/1:160:28:2,26:14,118:0.175:2,2:22:1:30.6:1:0.74006:1.53863:43.3:56:0.175:0:1 -1 16972350 . G A 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01322;SOR=0.41273;LSEQ=CATAGACATGGCCCACTTAG;RSEQ=CCTCTATTAGCACGTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:46:5,41:7,209:0.1756:1,2:26.4:1:30.4:1:0.04059:3.62:43.5:92:0.1756:0:2.3 0/1:124:10:2,8:13,101:0.0806:2,2:21.1:1:27.6:1:0.34681:1.93:38.4:9:0.075:0:2.5 -1 16972467 . C T 80 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.53729;LSEQ=CCCTCTAACCTAGCGTATGC;RSEQ=TTTGTGCAGGTGAGAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:1,5:2,17:0.24:2,2:13.3:1:31.2:1:1:1.66:37:12:0.25:0:2 0/1:7:1:0,1:1,5:0.1429:2,0:8:0:31:0:1:0:60:2:0.1429:0:2 -1 16972470 . T C 48 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=TCTAACCTAGCGTATGCCTT;RSEQ=GTGCAGGTGAGAGCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:2,16:0.1429:2,0:21.7:1:30.3:1:1:0:37.3:6:0.1429:0:3 0/1:7:1:0,1:1,5:0.1429:2,0:5:0:28:0:1:0:60:2:0.1429:0:2 -1 16972476 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGCGTATGCCTTTGTGCA;RSEQ=GTGAGAGCCCAGCTTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:3,14:0.1053:2,0:25:1:31.5:1:1:0:42.5:4:0.1053:0:3.5 0/0:4:0:0,0:1,3:0:2,0:14:1:31.3:1:1:0:51.5:8:1:0:0 -1 16972489 . C A 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01099;SOR=0;LSEQ=TTGTGCAGGTGAGAGCCCAG;RSEQ=TTTGGAGTCTGAATGCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:1,1:0.8182:2,0:28.4:1:28.8:1:0.18182:0:31.6:8:1:0:2.2 0/0:4:0:0,0:2,2:0:2,0:9:1:30.8:1:1:0:44:8:1:0:0 -1 16972496 . G A 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25824;SOR=0;LSEQ=GGTGAGAGCCCAGCTTTGGA;RSEQ=TCTGAATGCCTAGCCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:1,5:0.4545:2,0:39.4:1:29:1:1:0:30.2:10:0.4545:0:2.6 0/0:3:0:0,0:2,1:0:2,0:12.7:1:30:1:1:0:50:6:1:0:0 -1 16972612 . G A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0.80505;LSEQ=CCACTGCTCTCACAGAGCGT;RSEQ=TGTGTTAGATCTGAGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:10:9,1:9,7:0.3846:2,2:26:1:29.7:1:0.09885:6.54:37.3:20:0.3846:0:1.7 0/1:9:3:3,0:5,1:0.3333:2,0:37.7:1:28:1:1:0:35.3:6:0.3333:0:1.7 -1 16972644 . C T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08746;SOR=0.29992;LSEQ=TGAGCCCGGTGCCTGGGCCA;RSEQ=TACACAGAGGCACCGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:15:15,0:22,9:0.3261:2,1:22.7:1:31.4:1:0.0212:0:51.5:30:0.3261:0:1.3 0/1:24:3:3,0:17,4:0.125:2,0:25:1:27.3:1:1:0:42.3:6:0.1304:0:1.7 -1 16972789 . TGA T 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06163;SOR=0;LSEQ=GCCTTGTAGCTTTGATCCCC;RSEQ=ATGAACAAACTGTGGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:4:4,0:294,39:0.0112:2,0:13:1:27.6:1:1:0:54:3:0.0086:0.0084:1.5 0/0:357:0:0,0:287,69:0:2,0:23.1:1:31.3:1:1:0:53.6:43.5:0.9971:0:0.1 -1 16972790 . GAAT AA 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTTGTAGCTTTGATCCCCT;RSEQ=GAACAAACTGTGGACATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:19:18,1:294,39:0.0534:2,1:27.1:1:30.4:1:0.70861:2.38:52.1:38:0.0543:0.0028:0.1 0/0:357:0:0,0:287,69:0:2,0:23.1:1:31.3:1:1:0:53.6:43.5:0.9971:0:0.1 -1 16972793 . T A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02719;SOR=0;LSEQ=TGTAGCTTTGATCCCCTGAA;RSEQ=GAACAAACTGTGGACATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:5:5,0:316,53:0.0134:2,0:9.6:1:27.2:1:1:0:55.2:4:0.011:0:1.4 0/0:393:0:0,0:311,82:0:2,0:22.3:1:29.5:1:1:0:54.3:48.125:1:0:0.1 -1 16972920 . C T 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.65913;LSEQ=GGGGCACAGAGCTACAGCGC;RSEQ=GCTACAAGCGGTGGTGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1670:496:263,233:647,527:0.297:2,2:23.7:1:30.5:1:0.45171:1.08761:58.4:81.667:0.2971:0:1.1 0/1:2057:448:239,209:854,755:0.2178:2,2:24.8:1:30.3:1:0.95732:1.01:58.6:447:0.22:0:1.2 -1 16972940 . G A 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41475;LSEQ=CGCTACAAGCGGTGGTGCCC;RSEQ=GGCCTTGGCAGGAGGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1680:908:482,426:409,362:0.5405:2,2:26.2:1:30.5:1:1:1.00:56.6:89.8:0.541:0:1.1 0/1:2117:694:353,341:715,707:0.3278:2,2:25:1:30.2:1:0.81697:1.02:56.4:98.143:0.3276:0:1.1 -1 16973028 . A C 213 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCGGTGAGTGGCCACTGGGC;RSEQ=TAGATAAGACTGGGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1659:106:49,57:785,766:0.0639:2,2:27.9:1:31.8:1:0.4222:1.19199:39.6:105:0.0642:0:1.2 0/0:1855:0:0,0:899,955:0:2,0:26:0:14:0:1:0:40:0:0:0:2 -1 16973057 . G A 186 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=25.81953;LSEQ=ACTGGGGGCAGGGGAGCCTG;RSEQ=GCCGTGGCGTTACCTTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1640:3:2,1:830,807:0.0018:2,2:11.7:1:28:1:1:1.94:55.3:6:0.0019:0:1 0/1:1792:81:42,39:865,843:0.0452:2,2:22.8:1:29.4:1:0.90955:1.05:55.2:39.5:0.0449:0:1.3 -1 16973072 . T C 140 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=21.75541;LSEQ=GCCTGGGCCGTGGCGTTACC;RSEQ=TGTGCCTTCTTCTCTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1798:1:0,1:963,833:6e-04:2,0:43:0:32:0:0.46411:0:40:2:6e-04:0:1 0/1:1922:23:18,5:998,901:0.012:2,2:22.8:1:31.1:1:0.01898:3.25:36:46:0.0121:0:1.7 -1 16973095 . G C 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.89486;LSEQ=TGCCTTCTTCTCTCCAGGGC;RSEQ=TTCCACTACAATGTGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1915:1:1,0:1015,899:5e-04:2,0:2:0:32:0:1:0:21:2:5e-04:0:4 0/1:2102:27:16,11:1105,968:0.0128:2,2:20.7:1:30.6:1:0.56674:1.27:36:26:0.0125:0:2.7 -1 16973152 . A G 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.36846;LSEQ=CTGCCATGGACTCAACACTC;RSEQ=CCCCACACGAGGCTGCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2012:1066:511,555:464,480:0.5298:2,2:25.3:1:30.7:1:0.59184:1.04985:53.8:61.706:0.5303:0:1.8 0/1:2216:650:322,328:774,786:0.2933:2,2:24.6:1:30.4:1:1:1.00308:53.6:71.222:0.2938:0:1.8 -1 16973155 . C G 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00049;SOR=2.07572;LSEQ=CCATGGACTCAACACTCACC;RSEQ=CACACGAGGCTGCGGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2005:32:29,3:953,1016:0.016:2,2:6.8:1:29.4:1:0:10.30:34.7:64:0.0163:0:3.3 0/1:2241:73:45,28:1071,1093:0.0326:2,2:15.5:1:30.9:1:0.04342:1.64:44:72:0.0325:0:3.3 -1 16973159 . A T 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1229;SOR=1.29899;LSEQ=GGACTCAACACTCACCCCAC;RSEQ=CGAGGCTGCGGCATTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2028:65:56,9:963,997:0.0321:2,2:6.2:1:31.4:1:0:6.44:38.2:130:0.0326:0:2.7 0/1:2255:93:60,33:1082,1076:0.0412:2,2:13.6:1:30.7:1:0.00782:1.81:43.7:92:0.0415:0:3.1 -1 16973184 . G A 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39038;LSEQ=GCTGCGGCATTCTGGGCGCT;RSEQ=TGACCTCTTCCAGGAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1811:884:394,490:488,437:0.4881:2,2:25.9:1:29.4:1:5e-04:1.38852:53.4:51:0.4876:0:1.9 0/1:2002:543:245,298:720,735:0.2712:2,2:25.3:1:28.8:1:0.08716:1.1914:54.6:107.6:0.2717:0:1.9 -1 16973198 . G A 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.99707;LSEQ=GGCGCTGTGACCTCTTCCAG;RSEQ=AGAAAGGCGAGTGGGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1640:193:141,52:618,829:0.1177:2,2:35.6:1:30:1:0:3.63:36.7:20.444:0.1144:0:1.6 0/1:1755:206:126,80:670,878:0.1174:2,2:32.2:1:29.3:1:0:2.06:40.8:40.2:0.1163:0:1.8 -1 16973259 . G C 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00099;SOR=0;LSEQ=AGGGGACCTCAGCCCAAGTT;RSEQ=ATCTTCTGTCTCTTGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:809:11:4,7:244,552:0.0136:2,2:26.9:1:31.4:1:0.74465:1.29:29.4:22:0.0138:0:1.2 0/0:760:0:0,0:263,497:0:2,0:23:1:31.1:1:1:0:37.9:83.444:1:0:0.2 -1 16973327 . G A 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01963;SOR=0.60194;LSEQ=CAATGGGGTTGGGTACCGGG;RSEQ=CACCATGGCCACGACCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:55:26,29:481,449:0.0558:2,2:26.3:1:30.3:1:0.57951:1.19466:28.6:110:0.0567:0:2.1 0/1:1136:39:16,23:606,488:0.0343:2,2:19.5:1:29.5:1:0.10048:1.78415:28.3:38:0.0341:0:2.1 -1 16973388 . C T 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49515;LSEQ=TGGAGCCACAAGTTCCCGAA;RSEQ=GATCACCAGTGGGACAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1321:288:152,136:510,523:0.218:2,2:20.3:1:30.8:1:0.318:1.15:30.9:143:0.2185:0:2.4 0/1:1814:220:111,109:775,819:0.1213:2,2:17:1:30.3:1:0.61535:1.08:30.1:109:0.1215:0:2.1 -1 16973400 . G A 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.33993;LSEQ=TTCCCGAACGATCACCAGTG;RSEQ=GACAAACACCTTCCCTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1251:241:148,93:456,547:0.1926:2,2:22.7:1:30.7:1:1e-05:1.91:30.6:79.333:0.1938:0:2.5 0/1:1760:132:78,54:772,854:0.075:2,2:19.3:1:30.1:1:0.01114:1.60:29.6:65:0.075:0:2.5 -1 16973419 . G A 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00141;SOR=0.59813;LSEQ=GGGACAAACACCTTCCCTCC;RSEQ=TCCCGGCCTGGGACCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1103:95:83,12:530,477:0.0861:2,2:24.9:1:30.5:1:0:6.22:30.5:190:0.0875:0:2.3 0/1:1462:78:62,16:675,709:0.0534:2,2:21.5:1:29.9:1:0:4.07:30.5:77:0.0532:0:2.3 -1 16973423 . C T 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28667;LSEQ=CAAACACCTTCCCTCCGTCC;RSEQ=GGCCTGGGACCTTCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1094:112:80,32:552,430:0.1024:2,2:20.7:1:31.3:1:0.00233:1.95:31.1:224:0.1029:0:2.3 0/1:1422:45:30,15:696,679:0.0316:2,2:22.5:1:30.6:1:0.04771:1.95:27.9:21.5:0.0305:0:2.2 -1 16973519 . G A 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.59168;LSEQ=CCTGGAAGAGAACTTCTGCC;RSEQ=TAACCCTGATGGCGACCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2545:356:275,81:1447,738:0.1399:2,2:22.3:1:30.1:1:3e-05:1.73:34.8:88:0.1401:0:1.1 0/1:2404:211:151,60:1375,812:0.0878:2,2:20.2:1:29.5:1:0.01326:1.49:37:104.5:0.088:0:1.1 -1 16973606 . G T 275 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04295;SOR=1.13765;LSEQ=CTGCGGCATCAAATCCTGCC;RSEQ=GGTGGGTAAGCGGCGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4145:561:256,305:1622,1955:0.1353:2,2:24.4:1:30.3:1:0.92734:1.01:46.2:45.75:0.1343:0:1.2 0/1:4009:606:271,335:1530,1863:0.1512:2,2:23.8:1:29.8:1:0.89424:1.0152:47.5:42.286:0.1495:0:1.2 -1 16973648 . A G 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.016;SOR=0.68075;LSEQ=CAAGCTGGGAGAGTGGAGGG;RSEQ=CAAGCCCACGCCCATCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3303:106:6,100:1465,1729:0.0321:2,2:17:1:32.5:1:0:14.11672:27.2:34.333:0.0318:0:1.1 0/1:2945:65:4,61:1318,1561:0.0221:2,2:18.3:1:32.4:1:0:12.87096:28:64:0.0223:0:1.1 -1 16973776 . C T 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GCGAGTGCCAGCGCTGGGAT;RSEQ=TTCAGCACCCGCACCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1148:0:0,0:539,608:0:2,0:27.2:1:32:1:1:0:28:87.231:1:0:0.1 0/1:686:12:2,10:292,382:0.0175:2,2:30.3:1:28.3:1:0.07974:3.81584:27.3:11:0.0162:0:1.3 -1 16973841 . G A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGCGGTATCGGCGCCCTG;RSEQ=GGGCCGGGCTAGGGAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1153:0:0,0:774,378:0:2,0:20.8:1:30.5:1:1:0:30.2:49.087:1:0:0.3 0/1:818:17:13,4:556,243:0.0208:2,2:23.6:1:28.2:1:0.79005:1.42:28.4:16:0.02:0:1.3 -1 16973855 . G A 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1445;LSEQ=GCCCTGGGGGCCGGGCTAGG;RSEQ=AAGGTCCAGGACTCCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1442:116:74,42:839,484:0.0804:2,2:20.5:1:29.5:1:1:1.02:32.7:37.667:0.0798:0:1.1 0/1:1042:13:9,4:671,358:0.0125:2,2:27:1:28.8:1:1:1.20:32.7:26:0.0128:0:1.1 -1 16973919 . A G 314 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00011;SOR=0.8092;LSEQ=GGCGGGGCCAGATAAGCCAG;RSEQ=GTCCCAGGGTCTTCTTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3124:1180:578,602:958,981:0.3777:2,2:25.1:1:30.8:1:0.82474:1.0171:36.6:77.667:0.3795:0:1.1 0/1:2784:917:478,439:966,890:0.3294:2,2:24.4:1:30.1:1:1:1.00:39:47.263:0.3285:0:1.2 -1 16973957 . G T 221 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACGCCCCATTACCGCCCCCA;RSEQ=GTTCCTCGACCAAGGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2906:168:58,110:1191,1547:0.0578:2,2:27.8:1:30:1:0.02444:1.45992:37.8:55:0.0576:0:1.9 0/0:2748:0:0,0:1321,1426:0:2,0:28.5:1:30.6:1:1:0:37.8:69.436:0.9996:0:0.6 -1 16973996 . A G 278 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0789;SOR=0.86823;LSEQ=GGACGACAACTATTGCCGGA;RSEQ=TCCTGACGGCTCCGAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2347:392:71,321:856,1096:0.167:2,2:21.7:1:32.3:1:0:3.52952:33.9:77.4:0.1667:0:2 0/1:2374:352:85,267:960,1059:0.1483:2,2:20.1:1:31.3:1:0:2.84635:36.1:69.4:0.1481:0:1.8 -1 16974010 . G C 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02326;SOR=0.79112;LSEQ=GCCGGAATCCTGACGGCTCC;RSEQ=AGCGGCCATGGTGCTACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1970:218:5,213:744,1003:0.1107:2,1:20.2:1:32.9:1:0:31.57087:30.3:217:0.1122:0:2.5 0/1:2243:201:18,183:963,1073:0.0896:2,2:16.6:1:31.8:1:0:9.11765:32.4:66:0.0894:0:2.2 -1 16974013 . C A 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAATCCTGACGGCTCCGAG;RSEQ=GGCCATGGTGCTACACTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1943:0:0,0:742,1197:0:2,0:24.5:1:30.6:1:1:0:35.8:76.56:0.9979:0:0.8 0/1:2172:41:19,22:923,1201:0.0189:2,2:24.5:1:28.7:1:0.75179:1.12:38.8:19.5:0.0182:0:1.2 -1 16974021 . G A 295 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50917;LSEQ=GACGGCTCCGAGCGGCCATG;RSEQ=TGCTACACTACGGATCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1872:855:366,489:380,636:0.4567:2,2:26.9:1:30.3:1:0.01787:1.25:36.8:41.75:0.455:0:1.2 0/1:2132:639:280,359:655,836:0.2997:2,2:27.5:1:29.2:1:1:1.00455:38.7:90.286:0.2997:0:1.2 -1 16974140 . CG C 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00024;SOR=0.37756;LSEQ=GGGGAGGGGCGTGGCTTGGC;RSEQ=GGGAGGTCAGAGGGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:56:31,25:126,292:0.1181:2,2:26.2:1:30.7:1:0.00041:2.87:28.9:112:0.1189:0.0148:1.6 0/1:395:19:7,12:86,289:0.0481:2,2:24.8:1:31.3:1:0.1713:1.96:26.9:38:0.0485:0.0051:1.4 -1 16974149 . C A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3533;LSEQ=CGTGGCTTGGCCGGGGAGGT;RSEQ=AGAGGGGCTGGGCGTGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:177:63,114:109,172:0.3856:2,2:27.2:1:29.8:1:0.55228:1.14639:28.8:87.5:0.3846:0:1.3 0/1:364:66:20,46:87,211:0.1813:2,2:23.5:1:29.4:1:0.88175:1.05:29.3:132:0.1828:0:1.3 -1 16974182 . C A 146 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01049;SOR=0.36979;LSEQ=CGTGACCTGAGAGCATATCC;RSEQ=GTGGAGTACCGTACACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:29:23,6:270,196:0.0586:2,2:32.3:1:30.2:1:0.03067:2.78:31.3:28:0.0581:0:2.4 0/1:356:8:5,3:196,143:0.0225:2,2:31.5:1:30.5:1:1:1.22:31.6:16:0.0228:0:2.3 -1 16974224 . C G 124 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23358;SOR=0.57136;LSEQ=AAAGGCGGGTTTGGTCCCAG;RSEQ=CCCAGAGGGATCTCAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:17:16,1:481,148:0.0263:2,1:26.2:1:30.4:1:0.14:4.92:35.6:34:0.0267:0:1.6 0/1:593:9:8,1:415,167:0.0152:2,2:28.6:1:29.7:1:0.45721:3.21:29.2:8:0.0138:0:2.2 -1 16974256 . G C 269 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23065;LSEQ=CTCAGCTGTCGCTCGGGGCC;RSEQ=GACCTATCTCGGTCCATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:961:402:401,1:356,201:0.4183:2,1:20.1:1:31.1:1:0:225.73:32.5:43.667:0.419:0:1.3 0/1:1048:149:149,0:551,348:0.1422:2,1:20.3:1:30.5:1:0:0:33.2:73.5:0.1434:0:1.3 -1 16974312 . G C 213 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26601;SOR=1.18783;LSEQ=GCCCCGCCAAGAGGCCACAA;RSEQ=TGTCAGCTGCTTCCGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2925:88:86,2:1785,1051:0.0301:2,1:22.5:1:32.6:1:0:25.30:33.5:87:0.0301:0:1.1 0/1:2814:100:94,6:1629,1080:0.0355:2,2:21.1:1:32.2:1:0:10.38:32.8:200:0.0359:0:1.1 -1 16974454 . T TGGGC 180 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00084;SOR=0.48655;LSEQ=AAATACGCGTGCAAGTGAGG;RSEQ=GGGGGGGCGGGCGTTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3470:63:44,19:1602,1754:0.0182:2,2:23:1:30.2:1:0.00052:2.53:33.2:62:0.0186:0.0049:0.1 0/0:3477:31:18,13:1589,1825:0.0089:2,2:16.5:1:27.4:1:0.21074:1.59:35.6:6.75:0.0081:0.0035:0.5 -1 16974458 . G C 207 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACGCGTGCAAGTGAGGTGGG;RSEQ=GGGCGGGCGTTGGGACGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3438:128:31,97:1617,1687:0.0372:2,2:5.4:1:29.7:1:0:2.99849:40.6:41.667:0.0373:0:1.6 0/0:3403:0:0,0:1549,1729:0:2,0:24.8:1:30:1:1:0:56.3:44.528:0.9994:0:0.3 -1 16974511 . G A 295 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.76693;LSEQ=GACGGGAGGAGGGTAGTCAC;RSEQ=GGCTTAGGGCTGGAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3150:850:441,409:1188,1110:0.2698:2,2:23.4:1:30.4:1:0.936:1.01:54.1:55.667:0.2695:0:1.1 0/1:2871:634:313,321:1127,1106:0.2208:2,2:22.4:1:30.1:1:0.65272:1.04504:55.4:69.444:0.2205:0:1.1 -1 16974592 . C T 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.01216;SOR=0.83101;LSEQ=GGAGAACTTCTGCCGGAACC;RSEQ=CGACGGCTCAGAGGCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4471:468:235,233:1955,2035:0.1047:2,2:25.5:1:30.2:1:0.62537:1.05:51:51:0.1044:0:1.2 0/1:4201:372:200,172:1998,1830:0.0886:2,2:24.3:1:29.7:1:0.5868:1.07:51:61:0.0884:0:1.2 -1 16974637 . T C 313 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.72135;LSEQ=CTTCACACTGCGGCCCGGCA;RSEQ=GCGCGTGGGCTTTTGCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3968:1347:491,856:1311,1301:0.3395:2,2:26.6:1:30.2:1:0:1.75656:47.9:60.227:0.3383:0:1.6 0/1:4023:1088:452,636:1437,1493:0.2704:2,2:26.9:1:29.8:1:2e-05:1.35419:48.1:89.667:0.2706:0:1.6 -1 16974662 . C A 275 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.70041;LSEQ=GTGGGCTTTTGCTACCAGAT;RSEQ=CGGCGTTGTACAGACGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3304:730:185,545:1160,1413:0.2209:2,2:20.8:1:29:1:0:2.41786:45.4:65.364:0.2223:0:2 0/1:3319:550:163,387:1248,1519:0.1657:2,2:20.3:1:28.4:1:0:1.95026:46.2:109:0.1672:0:2.1 -1 16974666 . C T 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.64435;LSEQ=GCTTTTGCTACCAGATCCGG;RSEQ=GTTGTACAGACGACGTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3176:917:379,538:893,1360:0.2887:2,2:25:1:29.3:1:0.37964:1.07:50.3:42.667:0.2875:0:1.2 0/1:3198:663:284,379:1051,1477:0.2073:2,2:25.3:1:29.3:1:0.56551:1.05:51.7:65.3:0.2074:0:1.2 -1 16974786 . G C 233 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28698;LSEQ=GCCTGATGGCTGCCCGCACC;RSEQ=GCCGCAGACTGCTACCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1056:229:22,207:313,513:0.2169:2,2:26.2:1:29.8:1:0:5.73303:34:75.333:0.2201:0:2.3 0/1:965:71:0,71:441,451:0.0736:2,1:23.8:1:30.3:1:0:0:31.1:142:0.0755:0:3.1 -1 16974817 . C G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05318;LSEQ=GCTACCACGGCGCGGGGGAG;RSEQ=AGTACCGCGGCACGGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:987:309:154,155:245,430:0.3131:2,2:24.6:1:30.9:1:7e-05:1.74:47.8:43.143:0.3149:0:1.7 0/1:1100:26:14,12:525,545:0.0236:2,2:26.8:1:30.3:1:0.6939:1.21:46.4:25:0.0232:0:1.6 -1 16974868 . G T 176 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.17855;LSEQ=AGGGTGTCCAGTGCCAGCGC;RSEQ=GGTCCGCTGAGACGCCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:959:51:10,41:472,436:0.0532:2,2:20.1:1:31.1:1:0:4.43287:28.2:102:0.0539:0:1.6 0/0:1411:14:0,14:727,668:0.0099:2,1:21.5:1:30.6:1:4e-05:0:33.3:28:0.0101:0:1.6 -1 16974869 . G C 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.2973;LSEQ=GGGTGTCCAGTGCCAGCGCG;RSEQ=GTCCGCTGAGACGCCGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:960:552:294,258:194,212:0.575:2,2:26:1:31.3:1:0.10214:1.24:55.4:275:0.5783:0:1.5 0/1:1423:408:212,196:517,496:0.2867:2,2:26.3:1:30.7:1:0.76949:1.04:56.4:135:0.2876:0:1.2 -1 16974901 . A G 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3052;LSEQ=CGCCGCACAAGCCGCAGTGA;RSEQ=TCCCTGGTGCTCCCGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:935:74:56,18:435,425:0.0791:2,2:20.6:1:32.8:1:3e-05:3.04:26.3:148:0.08:0:2.3 0/1:1370:35:31,4:636,699:0.0255:2,2:19:1:32.7:1:0:8.51:25.4:70:0.0259:0:2.7 -1 16974915 . C T 190 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00129;SOR=0.53454;LSEQ=CAGTGAATCCCTGGTGCTCC;RSEQ=GGCCCCGCCAGGGCCCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:870:65:59,6:397,406:0.0747:2,2:28:1:31.7:1:0:10.04:28.5:64:0.0749:0:2.6 0/1:1233:51:51,0:554,627:0.0414:2,1:23.8:1:31.6:1:0:0:26.8:50:0.0409:0:2.8 -1 16974955 . A G 136 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.16038;LSEQ=CCCTGGGGCGGCATGCTTTG;RSEQ=TGTCTGGGACCAGAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:938:21:10,11:589,328:0.0224:2,2:20.9:1:31:1:0.16607:1.97384:27.5:9.5:0.0208:0:2.4 0/0:1094:4:2,2:630,459:0.0037:2,2:21.5:1:31.8:1:1:1.37213:24:8:0.0037:0:2.8 -1 16974972 . C T 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.53946;LSEQ=TTGATGTCTGGGACCAGAGC;RSEQ=TGGAAATGGTTGAGACTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1088:419:328,91:383,286:0.3851:2,2:22.4:1:30.7:1:0:2.69:38.3:28.929:0.3799:0:2.2 0/1:1303:329:243,86:520,453:0.2525:2,2:21.7:1:30.1:1:0:2.46:37.9:31.9:0.2471:0:2.2 -1 16975002 . C T 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.45942;LSEQ=TTGAGACTACCCTGCCACGA;RSEQ=TTCGCTCCCGCTCCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1678:877:627,250:455,344:0.5226:2,2:24.8:1:30.4:1:0:1.90:40.4:47.722:0.5228:0:1.8 0/1:2068:692:465,227:767,607:0.3346:2,2:25:1:29.6:1:0:1.62:41.3:56.667:0.3322:0:1.8 -1 16975005 . C T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00568;SOR=0.67314;LSEQ=AGACTACCCTGCCACGACTT;RSEQ=GCTCCCGCTCCCGCCTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1791:116:103,13:1043,631:0.0648:2,2:15:1:30.4:1:0:4.79:29.6:115:0.065:0:2.6 0/1:2178:97:76,21:1213,867:0.0445:2,2:10.7:1:29.4:1:8e-05:2.59:32.9:47.5:0.0439:0:2.4 -1 16975045 . G A 301 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.69226;LSEQ=TTCACGTTTACCTCCGAACC;RSEQ=CATGCACAACTGGAGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3382:942:685,257:1443,996:0.2785:2,2:26.2:1:30.5:1:0:1.84:38.2:84.636:0.2782:0:1.3 0/1:3694:779:522,257:1542,1373:0.2109:2,2:26.6:1:30.5:1:0:1.81:39.8:110.286:0.2116:0:1.4 -1 16975084 . G A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.65652;LSEQ=AACTTCTGCCAGACCCAGAT;RSEQ=GGGATAGCCATGGGCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3565:391:215,176:2007,1166:0.1097:2,2:25.4:1:29.4:1:0.00161:1.40885:37.9:96.75:0.1105:0:1.3 0/1:3328:249:115,134:1806,1271:0.0748:2,2:23.4:1:28.8:1:0.00014:1.65539:38:82:0.0748:0:1.4 -1 16975093 . C T 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00062;SOR=0.61619;LSEQ=CAGACCCAGATGGGGATAGC;RSEQ=ATGGGCCCTGGTGCTACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3544:143:64,79:2193,1204:0.0403:2,2:23.1:1:29.3:1:0:2.2478:41.1:70.5:0.0403:0:1.1 0/1:3168:80:35,45:1838,1247:0.0253:2,2:21.7:1:29.7:1:0.00547:1.89462:41.6:160:0.0255:0:1.1 -1 16975201 . CT C 251 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCATGACCCTGCCTCAGCC;RSEQ=CACCACCAAAGGCTGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5584:255:131,124:1464,1584:0.0457:2,2:27.1:1:31.4:1:0.32794:1.14:43.3:254:0.0463:0.0061:0.8 0/0:5426:0:0,0:1751,1793:0:2,0:25.8:1:29.6:1:1:0:48.9:69.88:0.6532:0:0.7 -1 16975202 . T C 344 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.76616;LSEQ=CCATGACCCTGCCTCAGCCC;RSEQ=CACCACCAAAGGCTGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5584:2275:1071,1204:1464,1584:0.4074:2,2:27:1:30.9:1:0.50561:1.03903:42.1:60.486:0.4078:0:1.8 0/1:5426:1872:885,987:1751,1793:0.345:2,2:27:1:30.2:1:0.13729:1.08911:44.2:80.391:0.3457:0:1.7 -1 16975228 . C T 226 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01693;LSEQ=CCAAAGGCTGGCTCCCTTAA;RSEQ=CGCAGTGAACTTTGTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4642:179:89,90:2048,2408:0.0386:2,2:22.3:1:30.2:1:0.35889:1.16:58:58.667:0.0383:0:1.1 0/0:4421:3:1,2:2106,2309:7e-04:2,2:29.3:1:26.3:1:1:1.82392:44.3:6:7e-04:0:1.7 -1 16975230 . G C 371 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60044;SOR=0.96705;LSEQ=AAAGGCTGGCTCCCTTAACC;RSEQ=CAGTGAACTTTGTCTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4650:4033:1808,2225:309,278:0.8673:2,2:24.3:1:31:1:0.00045:1.36776:37.9:76.558:0.8688:0:1.5 1/1:4400:3799:1793,2006:299,283:0.8634:2,2:24.2:1:30.3:1:0.06139:1.182:38.6:74.98:0.8646:0:1.4 -1 16975289 . T A 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.67353;LSEQ=CAATCCTGGACCCCCCCAGG;RSEQ=TAGGAGTTGGGCCAGTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4801:495:193,302:1861,2440:0.1031:2,2:27.6:1:30.3:1:0.06861:1.19341:38.5:37.077:0.1029:0:1.5 0/1:4815:346:152,194:1970,2496:0.0719:2,2:30.5:1:29.2:1:0.95526:1.00735:39.7:33.6:0.0711:0:1.4 -1 16975296 . T A 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGACCCCCCCAGGTTAGGAG;RSEQ=TGGGCCAGTTATGGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4796:0:0,0:2035,2761:0:2,0:28.6:1:30:1:1:0:40.4:115.976:1:0:0.5 0/1:4780:66:31,35:2073,2639:0.0138:2,2:28.5:1:29.2:1:0.7083:1.13:40.1:65:0.0137:0:1.3 -1 16975365 . C T 117 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=10.60652;LSEQ=TGGGTTTCATCCAGCCCACC;RSEQ=CATCCTACAGACCAGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2102:2:1,1:613,1484:0.001:2,2:9:0:32:0:0.49957:2.42:49.5:4:0.001:0:1.5 0/1:1999:20:2,18:688,1289:0.01:2,2:13.9:1:27.3:1:0.01817:4.80045:39.7:19:0.0096:0:1 -1 16975429 . T C 154 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17518;LSEQ=TGGATCGGCTGGATCAGCGT;RSEQ=GTTCCAAGCTGCGCGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1214:41:12,29:514,659:0.0338:2,2:25.1:1:28.9:1:0.07741:1.88398:26.6:12.667:0.0319:0:1.5 0/0:1644:10:0,10:737,897:0.0061:2,0:22.8:1:31.4:1:0.00287:0:25.4:20:0.0062:0:1.1 -1 16975489 . C G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06995;LSEQ=CACCCTGGACAGTCAGCTTG;RSEQ=GGAATTGGTGAGGCACAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:855:345:173,172:211,298:0.4035:2,2:27.9:1:30.9:1:0.01412:1.42:32.4:85.25:0.404:0:2 0/1:687:31:15,16:255,401:0.0451:2,2:18:1:30.6:1:0.34719:1.47:32.8:62:0.0457:0:1.8 -1 16975495 . T C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32599;LSEQ=GGACAGTCAGCTTGCGGAAT;RSEQ=GGTGAGGCACAACTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:814:403:193,210:180,229:0.4951:2,2:27.2:1:30.2:1:0.29089:1.17:31.6:49.375:0.4938:0:1.9 0/1:599:145:25,120:201,251:0.2421:2,2:12.6:1:30.1:1:0:3.83592:29.4:47.333:0.2415:0:1.3 -1 16975509 . T G 136 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.87003;SOR=1.04755;LSEQ=CGGAATTGGTGAGGCACAAC;RSEQ=GCCTGTCTCCCACAGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:782:23:22,1:365,393:0.0294:2,1:16.2:1:30.1:1:0:23.63:30:22:0.0288:0:1.5 0/1:520:16:14,2:211,292:0.0308:2,2:12.3:1:29.6:1:0.00039:9.65:32.5:32:0.0313:0:1.1 -1 16975626 . G C 285 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50218;LSEQ=AGATGGCAGGTCTAGCATCT;RSEQ=TCCCAGGAGTCTGTTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2200:565:413,152:1106,526:0.2568:2,2:21.5:1:31.2:1:0.02002:1.29:38.8:69.625:0.2582:0:1.1 0/1:1887:279:194,85:1078,528:0.1479:2,2:22.4:1:31:1:0.44694:1.12:38.4:92:0.1484:0:1.2 -1 16975642 . C T 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1752;LSEQ=ATCTGTCCCAGGAGTCTGTT;RSEQ=CCTGTCCTAATTCCCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2762:265:157,108:1604,892:0.0959:2,2:31.9:1:30:1:0.10722:1.23687:30.9:52:0.0958:0:1.8 0/1:2466:45:37,8:1498,923:0.0182:2,2:19.7:1:29.4:1:0.00482:2.85:27.7:44:0.0181:0:1.4 -1 16975689 . G C 255 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.16701;LSEQ=GCAGGGCCAGCATTTCTGCG;RSEQ=GGGGTCTCTAGTGAAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3209:287:176,111:1513,1408:0.0894:2,2:20.5:1:31.3:1:0.00235:1.48:29.1:286:0.09:0:1.8 0/1:2913:47:47,0:1443,1422:0.0161:2,1:28.3:1:32.3:1:0:0:25.3:46:0.016:0:1.5 -1 16975724 . GC G 308 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.57483;LSEQ=AGGAGCAGTGGATACTGACT;RSEQ=CCGGCAGTGCTTCTCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3120:802:410,392:1128,1185:0.2571:2,2:26:1:32:1:0.25154:1.10:35.5:159.4:0.2606:0.0276:0.1 0/1:2743:455:239,216:1102,1164:0.1659:2,2:23.8:1:31.4:1:0.13629:1.17:35.8:226.5:0.1672:0.0299:0.1 -1 16975727 . C G 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.43086;LSEQ=AGCAGTGGATACTGACTGCC;RSEQ=GGCAGTGCTTCTCCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3042:130:75,55:1397,1502:0.0427:2,2:19.9:1:30.1:1:0.03886:1.47:31.3:260:0.0433:0:1.4 0/1:2756:52:31,21:1321,1370:0.0189:2,2:12.9:1:28.4:1:0.1611:1.53:36.3:25:0.0183:0:1.3 -1 16975831 . C T 254 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00653;SOR=0.76867;LSEQ=ACAAGTGAGCCTTGGGGCAA;RSEQ=GGACTGAGAGTCACAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1843:305:107,198:534,1003:0.1655:2,2:27.3:1:30.8:1:0.94755:1.02:26.3:151.5:0.1664:0:1.1 0/1:1618:214:61,153:520,883:0.1323:2,2:26.1:1:30.3:1:0.01757:1.47674:26.5:213:0.1326:0:1.1 -1 16975868 . T A 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.51097;LSEQ=ATGACCTAGCAGAGCTTCTC;RSEQ=CCCAGCCATATGCCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1311:356:51,305:348,605:0.2715:2,2:22:1:29.8:1:0:3.43708:32.9:70.2:0.2738:0:1.2 0/1:1094:175:25,150:324,595:0.16:2,2:23:1:29.3:1:0:3.26416:32.5:57.333:0.16:0:1.2 -1 16975912 . CCCTGTT C 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.48161;LSEQ=CTATGAGGTATGGTTGGGCA;RSEQ=CCAGAACCCACAACATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1076:126:0,126:422,527:0.1171:2,1:29.6:1:31.9:1:0:0:28.7:62:0.1178:0.0074:1.4 0/1:933:56:0,56:431,444:0.06:2,1:26.7:1:31.6:1:0:0:27.8:55:0.0597:0.0096:1.4 -1 16975951 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03292;LSEQ=ACATGGAGAGCCAGGCCTAC;RSEQ=GCGGGTCCCAGTAGCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1076:373:200,173:331,371:0.3467:2,2:26.5:1:29.9:1:0.04702:1.30:38.8:123.333:0.3484:0:1.4 0/1:1283:22:16,6:684,573:0.0171:2,2:27:1:28.9:1:0.12872:2.23:39.8:21:0.0167:0:1.5 -1 16975994 . T C 240 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=0.47087;LSEQ=CTGTGTGGGCCCTCAGGCTC;RSEQ=CAGCTTGTCCTGCTCAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1033:226:204,22:358,449:0.2188:2,2:25:1:30.8:1:0:11.60:30.6:74.333:0.2204:0:1.1 0/1:1554:181:173,8:687,686:0.1165:2,1:24.8:1:30.3:1:0:21.57:31.1:59.333:0.1161:0:1.1 -1 16976032 . A C 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.47901;LSEQ=GCTGGAGAGGTATGTGGACA;RSEQ=CCTGGGAGGGTGTGAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1303:417:195,222:543,341:0.32:2,2:23.4:1:31.2:1:0:1.81204:51.6:33.75:0.3174:0:1.3 0/1:1631:300:147,153:760,570:0.1839:2,2:22.9:1:30.7:1:0.01204:1.38745:52.7:59:0.1833:0:1.1 -1 16976193 . C T 256 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.46972;LSEQ=CCAAGTGTGAGATTGCAGGC;RSEQ=GGGGTGAGACCAAAGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1200:343:16,327:393,463:0.2858:2,1:23.2:1:30.4:1:0:17.31652:36.1:48:0.2872:0:1.2 0/1:1814:287:14,273:737,788:0.1582:2,1:22:1:30.1:1:0:18.22585:36.6:56.4:0.1585:0:1.2 -1 16976345 . T C 190 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06716;LSEQ=CTAAATGTGGCCTTGCTGAA;RSEQ=GTCATCTCCAACCAGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1158:64:30,34:568,525:0.0553:2,2:25.4:1:31.8:1:0.44281:1.22594:27:128:0.0559:0:1.2 0/0:1790:7:2,5:917,866:0.0039:2,2:24.6:1:27:1:0.27608:2.64589:28.9:6:0.0034:0:1.6 -1 16976436 . G C 136 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=5.70099;LSEQ=GACTGTTGGCCCCTGTGGGG;RSEQ=CCTGTGAGGTTGGTGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:4:4,0:376,288:0.006:2,0:38.3:1:28.3:1:0.13815:0:26.5:3:0.0046:0:2.3 0/1:693:23:7,16:258,409:0.0332:2,2:16:1:30.2:1:0.51636:1.44111:29.2:22:0.0322:0:1.2 -1 16976451 . G A 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07294;SOR=1.28354;LSEQ=TGGGGGCCTGTGAGGTTGGT;RSEQ=GCAGGGCCCTGGGCCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:690:120:94,26:295,274:0.1739:2,2:23.3:1:28.6:1:0:3.35:36:59:0.1735:0:1.2 0/1:658:140:98,42:172,346:0.2128:2,2:20.8:1:28.2:1:0:4.68:28.8:139:0.2135:0:1.4 -1 16976473 . G A 93 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16113;SOR=1.97959;LSEQ=CAGGGCCCTGGGCCAGCCCT;RSEQ=GAAGGGTATGGGGGGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:830:7:7,0:519,304:0.0084:2,0:20.7:1:28.3:1:0.05175:0:27:14:0.0086:0:2 0/1:664:11:8,3:332,319:0.0166:2,2:28.3:1:27.1:1:0.22457:2.56:29:10:0.0153:0:2.5 -1 16976528 . G T 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13742;SOR=0.78707;LSEQ=TCATGAAGCAGGCTAGTCAT;RSEQ=GCTGTGGCCCAGGGCCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1827:110:101,9:1182,533:0.0602:2,2:27.4:1:30.8:1:0:5.06:27.7:54:0.0601:0:1.4 0/1:1375:66:60,6:879,429:0.048:2,2:27.2:1:29.7:1:2e-05:4.88:27.5:21:0.0465:0:1.1 -1 16976539 . A G 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=1.40103;LSEQ=GCTAGTCATGGCTGTGGCCC;RSEQ=GGGCCCTCATCAGTTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1983:390:370,20:975,611:0.1967:2,2:31.4:1:29.8:1:0:11.58:26.3:42.333:0.1952:0:1.8 0/1:1429:365:339,26:634,426:0.2554:2,2:30.1:1:30:1:0:8.75:26.3:59.833:0.255:0:1.8 -1 16976569 . G A 261 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62757;SOR=0.96338;LSEQ=TCAGTTCTCCTACCTGCCAG;RSEQ=GTGACTACGGGGGCCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2673:471:365,106:1298,900:0.1762:2,2:21.5:1:29.4:1:0:2.39:30:46.1:0.1757:0:1.9 0/1:2347:401:313,88:1258,685:0.1709:2,2:19.2:1:29.2:1:0:1.94:31.7:199.5:0.173:0:2.7 -1 16976585 . C T 276 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.73409;LSEQ=CCAGGGTGACTACGGGGGCC;RSEQ=ACTTGCCTGCTTTACCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3213:282:192,90:1640,1289:0.0878:2,2:22.7:1:29.9:1:9e-05:1.68:37.7:46:0.0874:0:1.4 0/1:3159:658:427,231:1512,986:0.2083:2,2:19.2:1:29.5:1:0.0428:1.21:38.6:328:0.2103:0:2 -1 16976620 . A G 304 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=8.14636;LSEQ=CCCACAACTGCTGGGTCCTG;RSEQ=AAGGAATTAGAATCCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3945:114:46,68:1875,1955:0.0289:2,2:29.2:1:31.6:1:0.07156:1.41764:36.1:113:0.029:0:3.7 0/1:4786:934:515,419:2087,1757:0.1952:2,2:25.8:1:30.9:1:0.66033:1.03:42.4:92.4:0.1958:0:1.9 -1 16976641 . C T 310 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.862;LSEQ=AAGGAATTAGAATCCCCAAC;RSEQ=GAGTATGCGCAAGGTCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4509:588:240,348:1875,2045:0.1304:2,2:25.9:1:30.4:1:0.00164:1.32937:38.7:33.588:0.1285:0:2.8 0/1:6047:1320:683,637:2504,2221:0.2183:2,2:26.3:1:30:1:0.43572:1.05151:40.3:65:0.2184:0:3 -1 16976649 . C T 305 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.98679;LSEQ=AGAATCCCCAACCGAGTATG;RSEQ=GCAAGGTCGCGCTGGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4667:530:230,300:1926,2208:0.1136:2,2:25.3:1:30.2:1:0.17961:1.13773:37.5:105:0.1137:0:3 0/1:6343:1287:630,657:2602,2449:0.2029:2,2:26.3:1:29.6:1:0.10438:1.10799:40.3:90.929:0.2033:0:3 -1 16976679 . G A 324 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.0107;LSEQ=CGCTGGCCAGCCGTCTTCAC;RSEQ=CGTGTCTCTGTGTTTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3403:876:409,467:1024,1502:0.2574:2,2:26:1:30.3:1:0.0017:1.28:43.1:96.333:0.2578:0:1.2 0/1:4986:2048:959,1089:1259,1672:0.4108:2,2:26.7:1:29.5:1:0.00705:1.17:42:92.091:0.411:0:1.4 -1 16976681 . G T 298 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.58121;LSEQ=CTGGCCAGCCGTCTTCACGC;RSEQ=TGTCTCTGTGTTTGTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3312:285:138,147:1250,1772:0.0861:2,2:26.6:1:30.4:1:0.0237:1.33:36.4:24.909:0.0839:0:3.2 0/1:4864:951:398,553:1740,2167:0.1955:2,2:27.4:1:30.2:1:0.13557:1.11563:38.9:134.857:0.1962:0:2.8 -1 16976805 . G A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54495;SOR=1.33144;LSEQ=AGGACAAGACTTGTACTCAA;RSEQ=GCTGAGATTTAATAAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:10:9,1:29,296:0.0299:2,2:15.6:1:29.4:1:0:89.37:31.8:20:0.0302:0:2.4 0/1:381:15:7,8:47,319:0.0394:2,2:15.4:1:29.1:1:0.00205:5.89:32.9:30:0.0402:0:2.6 -1 16976807 . C T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14734;SOR=0.65035;LSEQ=GACAAGACTTGTACTCAAGG;RSEQ=TGAGATTTAATAAAATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:29:9,20:28,264:0.0901:2,2:7:1:28.3:1:0.00251:4.21:32:13.5:0.0854:0:2 0/1:364:22:7,15:45,296:0.0604:2,2:11.5:1:28.5:1:0.02523:3.06:32.8:44:0.0615:0:2.6 -1 16976810 . A T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09786;SOR=0;LSEQ=AAGACTTGTACTCAAGGCTG;RSEQ=GATTTAATAAAATTCATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:1,2:30,267:0.01:2,2:21:1:24.7:1:0.27991:4.41:45.3:2:0.0067:0:3.3 0/0:351:0:0,0:44,307:0:2,0:21.2:1:30.6:1:1:0:51.6:86.75:1:0:0.2 -1 16976825 . C A 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70248;SOR=0.88242;LSEQ=GGCTGAGATTTAATAAAATT;RSEQ=ATATTTTTACTACTTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:38:5,33:12,199:0.1526:2,2:12.9:1:28.2:1:0.15113:2.50:48.9:37:0.1504:0:1.4 0/1:248:34:10,24:16,198:0.1371:2,2:18.5:1:28.4:1:0.00071:5.10:44.1:68:0.1377:0:1.8 -1 16976896 . A G 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01706;SOR=Inf;LSEQ=CCCTACAAGTAAACAGTAAT;RSEQ=AAGAAGAGAATTATTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:7,125:0:2,0:25.5:1:30.6:1:1:0:55.9:264:1:0:0.4 0/1:107:5:2,3:12,90:0.0467:2,2:29.4:1:32.2:1:0.12662:4.88:27:10:0.0472:0:1.4 -1 16977023 . C A 115 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AATATCATCTTAGTATTACT;RSEQ=TGAAAATAGTTCTGAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:13:0,13:1,6:0.65:2,1:15.6:1:31.2:1:0.35:0:36.2:26:0.65:0:1.2 1/1:1:1:0,1:0,0:1:0,0:27:0:32:0:1:0:27:2:1:0:1 -1 16977083 . T G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGGCTCCTGCTATTCTA;RSEQ=TAGACTTATTACAATTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:17.5:1:33.5:1:1:0:33.5:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17011862 . TTG T 36 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=20.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=GGTTTTTTTTTTTTTTTTTT;RSEQ=TAATTAGTAGACATGGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:24.7:1:23:1:1:0:51.3:2:0.5:0.1667:4.3 0/0:5:0:0,0:4,1:0:2,0:19.6:1:30.8:1:1:0:35:10:1:0:0.4 -1 17012241 . G T 303 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05986;LSEQ=TGGAAGCTCGCCGTATGCCT;RSEQ=CAGACTTCTAGCTTCGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1236:1234:580,654:0,0:0.9984:0,2:23.8:1:30.1:1:1:0:59.9:111.182:0.9992:0:1.1 1/1:1289:1255:612,643:18,16:0.9736:2,2:24.7:1:29.5:1:0.7288:1.18183:59.6:155.875:0.9735:0:1.1 -1 17012645 . C T 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01244;SOR=10.51333;LSEQ=GGGCGACACGAGGGAGCGCG;RSEQ=GGGACCAAGTAGGTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:1:0,1:28,319:0.0029:2,0:13:0:25:0:1:0:27:2:0.0029:0:2 0/1:272:8:0,8:35,229:0.0294:2,0:19.5:1:28.4:1:0.60177:0:38.3:7:0.026:0:1.3 -1 17012702 . G A 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07678;SOR=0.64589;LSEQ=CGGGAGAGGCTGGCGACCCA;RSEQ=CTCTTCGGAGATCCGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:181:92:4,88:5,84:0.5083:2,1:24.1:1:29.4:1:0.74422:1.30757:49.3:45:0.5085:0:1.2 0/1:120:48:1,47:11,61:0.4:2,1:25.1:1:29.5:1:0.02645:8.36799:47:96:0.4034:0:1.5 -1 17012709 . G A 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03225;SOR=1.73499;LSEQ=GGCTGGCGACCCAGCTCTTC;RSEQ=GAGATCCGCCTGCGTCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:51:3,48:6,107:0.311:2,2:23.8:1:30.7:1:1:1.11:47.4:24.5:0.3063:0:1.4 0/1:116:51:4,47:7,58:0.4397:2,2:23.7:1:30.4:1:0.75316:1.41393:49.6:50:0.4348:0:1.8 -1 17012717 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51252;SOR=0;LSEQ=ACCCAGCTCTTCGGAGATCC;RSEQ=CCTGCGTCCACGCTCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:5,141:0.0135:1,2:16:1:29:1:0.0797:25.83:49:4:0.014:0:2 0/0:105:0:0,0:10,95:0:2,0:25.1:1:30.6:1:1:0:51.9:14:1:0:1.1 -1 17012761 . C G 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07457;SOR=2.08642;LSEQ=CAAAATGCTCTTCTGGTTTT;RSEQ=AATGTGGTGGGTGGCCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:13:0,13:2,57:0.1781:1,1:26.2:1:31.1:1:1:0:60:26:0.1806:0:1.7 0/1:64:20:1,19:3,40:0.3125:2,1:24.8:1:31.2:1:1:1.4175:59:40:0.3175:0:1.8 -1 17012936 . A T 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=12.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTATTATTATTATTATTATT;RSEQ=TTATTATTAGCAGTGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:11:1:31:0:1:0:52:4:0.4:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17013916 . GT G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTGGAGATCTTGATAGC;RSEQ=TGTTTGCATTGTGACAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:20:1:32.3:1:1:0:53.3:6:1:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17083460 . T C 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00842;SOR=6.25209;LSEQ=TACTAAGATGATATTTGCCT;RSEQ=TTCACTGTGTTGGCACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:6,1:21,2:0.2333:2,2:23.1:1:30.9:1:1:1.7138:32.1:14:0.2414:0:1.3 1/0:15:10:7,3:5,0:0.6667:0,2:24:1:29.7:1:0.50549:0:46:9:0.6429:0:1 -1 17083561 . C T 141 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00633;SOR=0.2157;LSEQ=CTAGGAATAATTCTCTTCTT;RSEQ=ATTACTGTTTACTTGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:26:26,0:180,10:0.1204:2,1:17.2:1:30.2:1:0.61318:0:34.3:25:0.1168:0:2.2 0/1:105:3:3,0:89,13:0.0286:2,0:20:1:31.3:1:1:0:43.7:6:0.0286:0:2 -1 17083577 . C T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06343;SOR=1.9522;LSEQ=TCTTCATTACTGTTTACTTG;RSEQ=AGGGGGAAAAACCATTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:19:19,0:259,12:0.0655:1,1:13.4:1:30.9:1:1:0:26.1:38:0.0669:0:3.5 0/1:141:17:14,3:112,12:0.1206:2,2:11.1:1:28.3:1:0.39286:1.98806:28.1:16:0.1151:0:2.4 -1 17083597 . G A 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=8e-05;SOR=2.43322;LSEQ=CAGGGGGAAAAACCATTTTC;RSEQ=TTTAAGAAAGTCCTTGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:433:45:45,0:376,12:0.1039:1,1:21.3:1:31.2:1:0.62299:0:27.2:90:0.1059:0:2.8 0/1:236:52:48,4:166,18:0.2203:2,2:13.7:1:31:1:0.79111:1.30:34.2:104:0.2232:0:1.9 -1 17083652 . C T 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.9582;SOR=0.99246;LSEQ=TAATTTTATTAAATCTCAAC;RSEQ=TTGAGTACAAGTCTTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1245:280:265,15:861,103:0.2249:2,2:26.6:1:31.4:1:0.00735:2.11:39.1:92.333:0.2259:0:1.3 0/1:899:201:165,36:593,105:0.2236:2,2:26:1:31.1:1:0.32342:1.23194:40.8:99.5:0.2238:0:1.2 -1 17083671 . C G 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=0.70864;LSEQ=CCTTGAGTACAAGTCTTGTC;RSEQ=TTGACTGTACTTACAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1337:463:372,91:711,162:0.3463:2,2:28:1:30:1:0.65986:1.07357:42.6:91.6:0.3488:0:2 0/1:1004:274:203,71:550,180:0.2729:2,2:29.3:1:29.3:1:0.68316:1.06862:43.5:90.333:0.2718:0:2 -1 17083685 . C A 269 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.64643;LSEQ=CTTGTCCTTGACTGTACTTA;RSEQ=AAGTTTTGTCCTCCCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1521:547:373,174:682,292:0.3596:2,2:25.5:1:29.6:1:0.48681:1.08947:40.6:67.375:0.3608:0:1.9 0/1:1119:298:185,113:532,287:0.2663:2,2:26.9:1:28.9:1:0.39734:1.1321:42:98.333:0.2665:0:2 -1 17083776 . C A 282 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.2942;LSEQ=AGTCCACAAACACAGAGACA;RSEQ=GCGTGAAGACGGCTGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2327:625:319,306:659,1039:0.2686:2,2:25.9:1:30.4:1:0:1.64:33.3:61.5:0.2683:0:3.2 0/1:1026:100:18,82:349,576:0.0975:2,2:19.8:1:31.1:1:6e-05:2.75784:31.9:200:0.0979:0:1.9 -1 17083778 . C T 297 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.10033;LSEQ=TCCACAAACACAGAGACACG;RSEQ=GTGAAGACGGCTGGCCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2341:1050:521,529:480,808:0.4485:2,2:27:1:29.6:1:0:1.66:33.9:130.25:0.4509:0:1.9 0/1:1008:76:19,57:354,577:0.0754:2,2:22.7:1:30.6:1:0.0259:1.83952:33.3:152:0.0767:0:1.9 -1 17083807 . T C 327 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14287;LSEQ=GGCTGGCCAGCGCGACCTTG;RSEQ=GCATACTCGGTTGGGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2258:1534:737,797:3,6:0.6794:2,2:25.1:1:30.9:1:0.50983:1.85:32.8:68.727:0.6771:0:1.9 0/1:986:229:82,147:336,361:0.2323:2,2:23.3:1:30.8:1:0.00128:1.6676:30:113.5:0.2321:0:1.4 -1 17083816 . G A 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1254;LSEQ=GCGCGACCTTGTGCATACTC;RSEQ=GTTGGGGATTCTAATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2187:784:319,465:692,711:0.3585:2,2:27.2:1:30.2:1:0.00012:1.41848:33.3:34.636:0.3557:0:3 0/1:932:61:33,28:406,465:0.0655:2,2:22.6:1:30.7:1:0.28926:1.35:28:122:0.0659:0:3.2 -1 17083837 . T C 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22301;LSEQ=GTTGGGGATTCTAATTCCTT;RSEQ=CAGGACCCAGCAGTTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2067:210:69,141:894,963:0.1016:2,2:28.7:1:31.1:1:3e-05:1.89648:32.9:104:0.1022:0:3.6 0/1:976:24:13,11:519,431:0.0246:2,2:26.1:1:30.1:1:1:1.0189:25.8:11:0.0229:0:3 -1 17083872 . G A 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00998;SOR=1.26349;LSEQ=TGTGGGTAAAGCAGGCAAGT;RSEQ=GGCCCCCGTAGTCACCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1725:464:217,247:512,748:0.269:2,2:23.7:1:29.2:1:0.02422:1.28:31.1:76.333:0.2696:0:2 0/1:920:292:129,163:290,337:0.3174:2,2:29.3:1:29.1:1:0.56996:1.08724:34:96.333:0.3186:0:1.6 -1 17083888 . C T 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.26493;LSEQ=AAGTGGGCCCCCGTAGTCAC;RSEQ=CTGGCAGGTAGGAGAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1515:791:318,473:297,424:0.5221:2,2:25.9:1:29.9:1:0.71384:1.04189:31.5:40.632:0.523:0:1.8 0/1:878:197:107,90:287,393:0.2244:2,2:29.8:1:29.3:1:0.00335:1.63:30.4:23.625:0.2193:0:1.9 -1 17083918 . C T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11342;LSEQ=AGGAGAACTGATGAGGGCCC;RSEQ=GGGCCACAGCAATGACTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1159:108:28,80:424,627:0.0932:2,2:29.6:1:30.7:1:0.00358:1.93107:29.2:216:0.0943:0:1.5 0/1:782:9:6,3:338,433:0.0115:2,2:17.3:1:29.6:1:0.19318:2.56:29:18:0.0117:0:1.1 -1 17083919 . G A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.44682;LSEQ=GGAGAACTGATGAGGGCCCC;RSEQ=GGCCACAGCAATGACTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1153:218:79,139:372,562:0.1891:2,2:27.6:1:31.1:1:0.35538:1.16449:33.8:217:0.1909:0:1.1 0/1:774:73:31,42:308,393:0.0943:2,2:29.5:1:30.6:1:0.90147:1.06174:35:23.333:0.092:0:1.2 -1 17083929 . A C 271 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05686;SOR=0.8081;LSEQ=TGAGGGCCCCGGGCCACAGC;RSEQ=ATGACTAGCCTGCTTCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:369:158,211:204,426:0.369:2,2:24.6:1:31.8:1:0.00106:1.56:26.9:45.125:0.3661:0:1.8 0/1:589:189:75,114:139,261:0.3209:2,2:28.9:1:31.3:1:0.27095:1.23:26.7:46.25:0.3179:0:1.6 -1 17083984 . C T 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=0.46849;LSEQ=TCTAGCCCCCCATACCCTTC;RSEQ=AGGGCTGGCCCAGGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1254:110:73,37:935,209:0.0877:2,2:22.4:1:29.9:1:0.00024:2.2657:30.7:54:0.0867:0:1.9 0/1:673:29:20,9:539,105:0.0431:2,2:21.4:1:30.2:1:0.07087:2.30639:29.9:58:0.0435:0:2 -1 17084006 . C T 307 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.49404;LSEQ=GGGCTGGCCCAGGGCCCTGC;RSEQ=ACCAACCTCACAGGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1570:1005:813,192:526,39:0.6401:2,2:26.4:1:30.8:1:0:3.18293:28.1:124.625:0.6403:0:1.4 0/1:866:405:380,25:392,69:0.4677:2,2:26.6:1:31.2:1:3e-05:2.67:27.4:201.5:0.4692:0:1.3 -1 17084021 . C G 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26602;SOR=0.85699;LSEQ=CCTGCCACCAACCTCACAGG;RSEQ=CCCCACAGGGGCCAACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1910:172:121,51:1426,310:0.0901:2,2:26.5:1:31.5:1:0.00033:1.93812:30.8:344:0.0909:0:1.8 0/1:1228:96:75,21:952,177:0.0782:2,2:24.3:1:30.6:1:0.11382:1.50542:30.1:31:0.0768:0:1.8 -1 17084078 . G A 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTCTCCCGCACATGTCCTC;RSEQ=GTGCTTGATGTTACACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4888:0:0,0:2719,2158:0:2,0:25.9:1:30.1:1:1:0:38.8:83.086:0.9981:0:0.2 0/1:4357:61:36,25:2365,1920:0.014:2,2:28.5:1:30.2:1:0.60509:1.17:41.3:122:0.0142:0:1.2 -1 17084152 . C T 241 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=389.18968;LSEQ=GGACTGTGTCATTACCCGTA;RSEQ=CTGCAGTGAGGGGAATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4824:1:0,1:2342,2478:2e-04:2,0:27:0:14:0:1:0:49:0:0:0:2 0/1:4105:308:154,154:1799,1995:0.075:2,2:25.6:1:29.2:1:0.40639:1.11:40:60.6:0.0748:0:1.1 -1 17084175 . A G 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.45393;LSEQ=GCAGTGAGGGGAATGGGGAG;RSEQ=AGGAGACGGTCCTGGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3861:212:90,122:1811,1835:0.0549:2,2:20.3:1:31:1:0.04766:1.33772:35.5:69.667:0.0553:0:1.4 0/1:3036:78:27,51:1419,1536:0.0257:2,2:21.4:1:31.2:1:0.02136:1.74469:37.9:156:0.0262:0:1.3 -1 17084234 . G A 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.51905;LSEQ=CTGGCCACCAGCAGTCCTGT;RSEQ=CACTATGCTCTTACCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4040:150:49,101:1994,1891:0.0371:2,2:30.5:1:28.9:1:1e-05:2.1731:32.8:49:0.0369:0:1.7 0/1:3211:63:28,35:1571,1574:0.0196:2,2:29.2:1:28.7:1:0.44559:1.24753:34.9:126:0.0199:0:1.6 -1 17084304 . C T 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12641;SOR=0.83664;LSEQ=GTCCCTGGAGGCACCACATA;RSEQ=CATTCAGGCGGCAGGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4576:188:10,178:2112,2272:0.0411:2,2:24.5:1:30.3:1:0:16.54268:28.1:36.6:0.0407:0:1.2 0/1:3988:138:10,128:1887,1959:0.0346:2,2:21.3:1:29.4:1:0:12.3287:28.3:33.5:0.034:0:1.2 -1 17084367 . A G 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34928;LSEQ=GTCACAGATCTTTAACAAGA;RSEQ=TGGGGGCACTCAGGGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3616:226:97,129:1630,1756:0.0625:2,2:25.3:1:31.7:1:0.13087:1.2344:48.1:74.333:0.0628:0:1.4 0/1:2901:66:25,41:1327,1506:0.0228:2,2:26.2:1:31.4:1:0.17007:1.44489:49.7:132:0.023:0:1.4 -1 17084415 . T C 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43896;SOR=0.91504;LSEQ=AGGCTCAGCCCCACCTCACA;RSEQ=CCTCCCAGGTTGTCCACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3082:211:135,76:1471,1393:0.0685:2,2:23.3:1:31.7:1:0.00044:1.68:30.4:22.444:0.0678:0:1.3 0/1:2317:146:118,28:1111,1056:0.063:2,2:20.1:1:31.6:1:0:4.00:30.8:145:0.0641:0:1.2 -1 17084510 . G A 283 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.64935;LSEQ=GGCTACTGGGACCCGCTGTA;RSEQ=GCCTGGCTCTCCATGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3418:649:213,436:1198,1570:0.1899:2,2:25.3:1:30.4:1:0:1.56173:40.3:71.111:0.1897:0:1.3 0/1:2824:373:148,225:1053,1395:0.1321:2,2:27.1:1:29.9:1:0.23799:1.1475:39.9:185.5:0.1334:0:1.3 -1 17084536 . TGGAACA T 269 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00046;SOR=0.72745;LSEQ=GCTCTCCATGTTGTGGGTTC;RSEQ=GGGTGCCCAACCATACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2425:390:63,327:685,1343:0.1608:2,2:26.9:1:31.3:1:0:2.64646:36.1:389:0.1625:0.007:1.4 0/1:1790:219:44,175:526,1037:0.1223:2,2:26.7:1:30.5:1:4e-05:2.01668:35.1:438:0.1232:0.0084:1.4 -1 17084670 . A G 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0;SOR=0.45718;LSEQ=CTTGCCTGGGGAAAGGGGAA;RSEQ=GTGGGATGAGACTGGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1599:144:101,43:720,735:0.0901:2,2:22.5:1:31.9:1:0:2.40:29.1:71:0.0907:0:1.2 0/1:1525:66:56,10:732,725:0.0433:2,2:20.9:1:31.6:1:0:5.54:30.5:65:0.0431:0:1.3 -1 17084707 . T C 144 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.0785;LSEQ=TCCCCAAACACAAGGGAGGC;RSEQ=CACCAGGAGGAGAAGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1672:4:2,2:791,877:0.0024:2,2:24.3:1:31.8:1:1:1.11:49:8:0.0024:0:1 0/1:1683:32:16,16:834,816:0.019:2,2:29.5:1:28.8:1:1:1.02205:32.8:15:0.0182:0:1.4 -1 17084732 . G A 159 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.4868;LSEQ=AGGAGGAGAAGCACTGCCGG;RSEQ=CAGTCAGTATCCACTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1597:7:5,2:713,873:0.0044:2,2:22.1:1:23.9:1:0.25456:3.06:45.4:2.5:0.0032:0:2.4 0/1:1692:47:24,23:788,855:0.0278:2,2:28.9:1:28.7:1:0.76755:1.13:50.3:94:0.0282:0:1.4 -1 17084755 . T C 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00067;SOR=0.7056;LSEQ=GTCAGTATCCACTGCTCCTT;RSEQ=ACTAGAGACCCCGCGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1522:251:47,204:611,659:0.1649:2,2:26.7:1:32:1:0:4.02095:28:49.2:0.164:0:1.5 0/1:1660:203:56,147:720,735:0.1223:2,2:25.5:1:31.6:1:0:2.57004:27:202:0.1224:0:1.5 -1 17084815 . G A 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.47241;LSEQ=GAGTGGGGAATTAGGACAGG;RSEQ=AACAGACTCCTGGGACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1193:532:252,280:355,306:0.4459:2,2:24.7:1:30.3:1:0.0312:1.28874:41:75:0.4491:0:1.3 1/0:1230:906:383,523:174,148:0.7366:2,2:26.6:1:29.4:1:0.00033:1.60476:44.3:128.429:0.7381:0:1.2 -1 17084831 . C G 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17473;SOR=0.78959;LSEQ=CAGGGAACAGACTCCTGGGA;RSEQ=AGATGCTAGACCTGCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1090:84:84,0:549,455:0.0771:2,1:27.5:1:33.1:1:0:0:29.8:83:0.0771:0:1.1 0/1:1051:65:40,25:481,501:0.0618:2,2:22.9:1:31.6:1:0.05493:1.67:41.1:64:0.0614:0:1.1 -1 17084948 . A C 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.71953;LSEQ=CCTCTCTGTGGGAGACAGGC;RSEQ=GTTGTGCCTCACCGATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3185:597:378,219:1515,1063:0.1874:2,2:24.9:1:30.2:1:0.04179:1.21:42.5:58.7:0.1869:0:1.3 0/1:3070:437:274,163:1547,1079:0.1423:2,2:24.7:1:29.4:1:0.14086:1.17:43:61.429:0.1422:0:1.3 -1 17084968 . G C 327 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.7761;LSEQ=AGTTGTGCCTCACCGATTCC;RSEQ=CAAGCTGACTGTCCAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3928:1290:744,546:1408,1223:0.3284:2,2:24.8:1:31.1:1:0.01397:1.18:46.5:214:0.3299:0:1.1 0/1:3853:1791:1025,766:1091,961:0.4648:2,2:25.2:1:30.3:1:0.01231:1.18:46.9:161.818:0.4669:0:1.1 -1 17085006 . C T 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1e-05;SOR=0.68698;LSEQ=GTGAGTTGCCCGGATGGCCC;RSEQ=CAGCCACGCGCAGCTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4900:384:188,196:2165,2349:0.0784:2,2:26.3:1:30.5:1:0.70998:1.04:45.6:75.8:0.0783:0:1.5 0/1:4838:267:133,134:2237,2334:0.0552:2,2:26.5:1:29.7:1:0.8013:1.04:47.4:88:0.0553:0:1.5 -1 17085028 . G A 195 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.51035;LSEQ=AGCCACGCGCAGCTTGGAAC;RSEQ=ACGCTGATCCAGCCGATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4937:37:7,30:2252,2647:0.0075:2,2:11.5:1:29.8:1:8e-04:3.64525:29.7:36:0.0074:0:1.4 0/1:4730:88:8,80:2165,2474:0.0186:2,2:13.4:1:30.2:1:0:8.74741:29.6:87:0.0186:0:1.2 -1 17085092 . G A 139 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=7.52971;LSEQ=TGCACCTGGTCTGTAGGATG;RSEQ=GGTGGGCTGGATGAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2188:4:3,1:637,1546:0.0018:2,2:2.5:1:27.8:1:0.07806:7.27:49.5:8:0.0019:0:1 0/1:1837:25:6,19:521,1289:0.0136:2,2:23.5:1:30:1:0.82401:1.27974:37.8:50:0.0138:0:1.2 -1 17085165 . G C 271 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15309;SOR=0.4872;LSEQ=ACCCATAACTGGCCCAACTC;RSEQ=TAACCTGGGGGGGTCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:411:404:195,209:0,1:0.983:0,2:20.9:1:31.3:1:1:0:31.8:66.333:0.9851:0:1.3 1/1:320:309:165,144:1,1:0.9656:2,2:19.5:1:30.9:1:1:1.15:31.9:102:0.9745:0:1.2 -1 17085168 . A T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99249;LSEQ=CATAACTGGCCCAACTCGTA;RSEQ=CCTGGGGGGGTCCAGGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:478:38:7,31:231,207:0.0795:2,2:21.1:1:29.4:1:6e-05:4.92772:29.2:37:0.0794:0:2.2 0/1:418:33:7,26:208,177:0.0789:2,2:11.9:1:26.7:1:4e-04:4.35068:34.7:10:0.0739:0:1.9 -1 17085171 . T TGG 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=9.000;MSILEN=1;SSF=0.01131;SOR=0.39027;LSEQ=AACTGGCCCAACTCGTAACC;RSEQ=GGGGGGGTCCAGGATTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:27:9,18:276,259:0.0479:2,2:15.6:1:30.1:1:0.07625:2.1285:33.9:54:0.0495:0.0213:1.2 0/1:520:10:2,8:267,242:0.0192:2,2:21.9:1:31:1:0.05514:4.40155:27:20:0.0194:0.0019:1.3 -1 17085227 . G C 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.14641;LSEQ=CTGAAAGACAAAGTTCACTG;RSEQ=GGTTAAGGGAGCCAGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1102:153:105,48:474,471:0.1388:2,2:27.8:1:31.4:1:2e-05:2.17:44.5:75.5:0.1389:0:2.1 0/1:1085:25:18,7:532,525:0.023:2,2:24.2:1:31.6:1:0.04162:2.54:46.8:50:0.0233:0:3.2 -1 17085253 . T C 184 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=72.00951;LSEQ=AGGGAGCCAGCCTTTGGTGG;RSEQ=GAGGGCTGAGGTAAGGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1198:1:1,0:643,551:8e-04:2,0:17:0:13:0:1:0:60:0:0:0:1 0/1:1056:60:35,25:509,477:0.0568:2,2:24.3:1:31.2:1:0.35247:1.31:52:120:0.0577:0:2.6 -1 17085254 . GA G 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=GGGAGCCAGCCTTTGGTGGT;RSEQ=GGGCTGAGGTAAGGTCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1198:19:14,5:376,365:0.0159:2,2:19.4:1:32.2:1:0.06202:2.71:33.9:38:0.0162:0.0025:1.7 0/0:1016:0:0,0:392,376:0:2,0:19.6:1:29.5:1:1:0:51.7:75.8:0.7542:0:0.4 -1 17085255 . A G 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.56861;LSEQ=GGAGCCAGCCTTTGGTGGTG;RSEQ=GGGCTGAGGTAAGGTCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1198:434:257,177:376,365:0.3623:2,2:21.1:1:31.2:1:0.00529:1.41:45.3:85.8:0.3648:0:1.8 0/1:1016:248:129,119:392,376:0.2441:2,2:17:1:30.6:1:0.8266:1.04:47:247:0.2458:0:1.9 -1 17085265 . T C 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26134;SOR=1.17147;LSEQ=TTTGGTGGTGAGGGCTGAGG;RSEQ=AAGGTCATGGGGCAAGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1048:124:86,38:492,428:0.1183:2,2:18:1:31.3:1:0.00101:1.97:31.1:23.8:0.116:0:2.2 0/1:817:111:72,39:352,352:0.1359:2,2:10.4:1:31.3:1:0.0041:1.84:32.2:222:0.1379:0:1.9 -1 17085267 . A G 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10974;SOR=0.74345;LSEQ=TGGTGGTGAGGGCTGAGGTA;RSEQ=GGTCATGGGGCAAGCGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1010:89:75,14:486,435:0.0881:2,2:26:1:32.3:1:0:4.79:30.2:178:0.09:0:2.4 0/1:761:51:47,4:358,352:0.067:2,2:24:1:32.2:1:0:11.53:31.3:50:0.0667:0:2.2 -1 17085412 . C T 303 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00131;SOR=1.17804;LSEQ=TTCTCCTCCAGTTGTGCATG;RSEQ=GGTTCGGAGGTAAATGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3345:1187:687,500:1095,1061:0.3549:2,2:25.8:1:29.9:1:9e-05:1.33:39.3:236.4:0.3568:0:2 0/1:3324:1307:741,566:1030,982:0.3932:2,2:25.5:1:29.3:1:0.00195:1.25:41:117.818:0.3957:0:2.1 -1 17085427 . T C 326 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00278;SOR=1.15505;LSEQ=GCATGCGGTTCGGAGGTAAA;RSEQ=GTGAACCGAGGCGGGAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3471:1577:800,777:887,1002:0.4543:2,2:30.6:1:31:1:0.02896:1.16:40.3:111.643:0.457:0:1.9 0/1:3539:1735:876,859:841,960:0.4903:2,2:30.8:1:30.3:1:0.02421:1.16:41.8:156.727:0.4927:0:1.9 -1 17085485 . G A 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00265;SOR=0.59719;LSEQ=GGTAGTCTCAACCATTTCCA;RSEQ=GCTCTGGTCCCAGACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2512:107:93,14:1069,1334:0.0426:2,2:28.3:1:30.7:1:0:8.28:29.9:52.5:0.0427:0:2.4 0/1:2048:53:47,6:794,1199:0.0259:2,2:26.2:1:30:1:0:11.82:31.8:52:0.0258:0:2.4 -1 17085502 . T C 306 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.38209;LSEQ=CCAGGCTCTGGTCCCAGACA;RSEQ=CAAAGCATGCCGCCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2183:861:376,485:634,682:0.3944:2,2:22:1:31.4:1:0.04319:1.199:40.3:46.833:0.3941:0:1.3 0/1:1638:776:312,464:361,496:0.4737:2,2:20.3:1:30.9:1:0.45032:1.08235:41.3:63.667:0.4757:0:1.3 -1 17085532 . T C 219 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCGCCCCAGGGTTAGGGCCC;RSEQ=GGCGGGGCCGGGAGCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2107:153:92,61:987,966:0.0726:2,2:22.1:1:30.2:1:0.02338:1.48:41.3:50:0.0719:0:1.9 0/0:1618:0:0,0:791,827:0:2,0:22.5:1:30.2:1:1:0:41.5:63.72:1:0:0.8 -1 17085542 . G A 258 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.9307;SOR=1.01046;LSEQ=GTTAGGGCCCTGGCGGGGCC;RSEQ=GGAGCACCAGGGACTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2136:359:204,155:964,811:0.1681:2,2:24.5:1:30.4:1:0.41577:1.11:32.6:118.667:0.1694:0:2 0/1:1687:286:136,150:736,663:0.1695:2,2:25.3:1:30.4:1:0.11978:1.22423:33.5:142:0.17:0:1.9 -1 17085564 . A G 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00589;SOR=0.82007;LSEQ=GAGCACCAGGGACTCACTGC;RSEQ=GCTTGTGCGGCGTCTCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2495:588:338,250:1028,875:0.2357:2,2:21.5:1:30.2:1:0.14201:1.15:31.3:52.455:0.2373:0:1.5 0/1:2091:422:235,187:902,764:0.2018:2,2:21.9:1:30.1:1:0.58454:1.06:31.3:139.667:0.2028:0:1.6 -1 17085589 . AGCGCTG A 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00103;SOR=1.49334;LSEQ=GTGCGGCGTCTCAGCGGACC;RSEQ=GCACTGGACACCCTTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3097:128:74,54:1546,1422:0.0413:2,2:23.6:1:32.1:1:0.20739:1.26:34.5:256:0.042:0.0097:1.6 0/1:2645:160:91,69:1317,1165:0.0605:2,2:23:1:31.3:1:0.36914:1.17:34.6:159:0.0611:0.014:1.6 -1 17085614 . G A 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.3146;LSEQ=TGGCACTGGACACCCTTGCG;RSEQ=GTCTTGCTGACCGTGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3176:639:303,336:1272,1260:0.2012:2,2:25.6:1:30.2:1:0.21513:1.11943:45.5:70:0.2016:0:1.2 0/1:2561:188:89,99:1221,1152:0.0734:2,2:26.1:1:29.9:1:0.28926:1.17891:47.4:376:0.0742:0:1.2 -1 17085671 . C G 303 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00585;SOR=1.17465;LSEQ=CCGTGGTAGCAGTCTGCGGC;RSEQ=GGTGCGGGCAGCCATCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2861:1081:576,505:863,908:0.3778:2,2:25.8:1:30.1:1:0.01859:1.20:38:59.056:0.379:0:2.1 0/1:2200:916:463,453:585,690:0.4164:2,2:26.5:1:29.4:1:0.03363:1.21:39.5:64.429:0.4188:0:2.2 -1 17085677 . G A 285 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00011;SOR=1.28084;LSEQ=TAGCAGTCTGCGGCCGGTGC;RSEQ=GGCAGCCATCAGGCCGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2806:725:372,353:1038,1040:0.2584:2,2:25.9:1:30:1:0.546:1.06:37.9:26.885:0.2552:0:2.7 0/1:2126:656:333,323:673,791:0.3086:2,2:27.2:1:29.6:1:0.04312:1.21:39.4:33.526:0.306:0:2.7 -1 17085712 . C T 283 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.37817;LSEQ=CGAGACCTCGCCCCGGCCCT;RSEQ=CGGTTCCAGGCTTCCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2678:720:327,393:1003,953:0.2689:2,2:24.9:1:29.9:1:0.00782:1.26477:38.5:71:0.2693:0:2.5 0/1:2096:705:322,383:700,689:0.3364:2,2:23.7:1:28.9:1:0.04194:1.20832:39.4:116.5:0.3367:0:2.4 -1 17085790 . C T 209 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03702;LSEQ=GCCGCACGTCGTCTGTACAA;RSEQ=GCCGGATCTGGTAGCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2646:123:53,70:1070,1452:0.0465:2,2:22.2:1:30.2:1:0.92565:1.03:40.8:40:0.0458:0:1.6 0/0:2221:4:0,4:1022,1192:0.0018:2,0:1:0:24.3:1:0.12928:0:57.5:8:0.0018:0:1.8 -1 17085791 . G A 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12743;SOR=0.78591;LSEQ=CCGCACGTCGTCTGTACAAC;RSEQ=CCGGATCTGGTAGCAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2633:108:20,88:1102,1419:0.041:2,2:17.8:1:30.1:1:0:3.41558:30.8:35:0.0408:0:1.3 0/1:2214:72:13,59:1011,1128:0.0325:2,2:12.2:1:28.4:1:0:4.06533:32:13.4:0.031:0:1.3 -1 17085795 . G T 248 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00098;LSEQ=ACGTCGTCTGTACAACGCCG;RSEQ=ATCTGGTAGCAAAAGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2552:412:78,334:1003,1134:0.1614:2,2:30.1:1:28.6:1:0:3.78561:33.7:44.778:0.1611:0:1.7 0/1:2160:349:91,258:887,923:0.1616:2,2:29:1:28.5:1:0:2.72339:34.4:115.333:0.1631:0:1.6 -1 17085834 . G T 316 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.46006;LSEQ=ACGCGCGTGCCGGGCCGCAG;RSEQ=GTGAAGCACCAGGGCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2411:1595:756,839:402,410:0.6616:2,2:25.8:1:29.9:1:0.34261:1.0881:47.1:105.333:0.6653:0:1.3 1/1:2074:1717:798,919:161,185:0.8279:2,2:25.3:1:29.5:1:1:1.00223:48.5:80.762:0.831:0:1.2 -1 17085872 . A G 166 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.59253;SOR=0.8748;LSEQ=CTCTGAGCCGTCGAGGTTCC;RSEQ=GCAGAAGTTCTCCCGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2324:49:49,0:1120,1154:0.0211:2,1:17.8:1:29.7:1:0:0:30.3:23.5:0.0206:0:2.4 0/1:2163:40:34,6:999,1123:0.0185:2,2:18.5:1:30.1:1:0:6.37:30.4:80:0.0187:0:2.3 -1 17085908 . C G 273 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36726;SOR=0.92447;LSEQ=AAGGTCTCTAAGCAGGCGCT;RSEQ=CACTCAGCCCTAGCCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2042:361:276,85:783,897:0.1768:2,2:22.3:1:32.2:1:0:3.72:37:44.125:0.1785:0:1.6 0/1:1787:296:213,83:698,791:0.1656:2,2:23.1:1:32.1:1:0:2.91:38.1:97.667:0.1671:0:1.6 -1 17085995 . G GC 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0048;SOR=0.68907;LSEQ=AGCAGCACGTCCCAACGCCC;RSEQ=CCCCCCCGCCCACCTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2283:171:28,143:661,1169:0.0749:2,2:31.2:1:30.3:1:0:2.88647:43.5:16.1:0.0892:0.0053:0.5 0/1:1779:94:19,75:495,921:0.0528:2,2:33.6:1:29.6:1:0.0033:2.12062:42.5:9.444:0.0611:6e-04:0.4 -1 17085999 . CCCCG C 148 Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.01291;SOR=0.39061;LSEQ=GCACGTCCCAACGCCCGCCC;RSEQ=CCCACCTCACTTGCACGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2255:29:0,29:935,1289:0.0129:2,1:24.4:1:30.6:1:0:0:29.8:28:0.0127:0.0027:0.3 0/0:1778:9:0,9:761,1004:0.0051:2,0:31.7:1:31.7:1:0.01263:0:25:18:0.0051:0:0.2 -1 17086052 . T C 303 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12694;SOR=0.43429;LSEQ=GGCGTAAATCGGTGCTGATG;RSEQ=GGGATTTGCGCGTCCCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1196:1190:448,742:1,0:0.995:0,2:22.4:1:29.7:1:0.37699:0:42.1:15.528:0.9973:0:1.3 1/1:871:861:306,555:2,1:0.9885:2,2:22:1:29.4:1:0.29041:3.62175:42.5:17.717:0.9939:0:1.3 -1 17086085 . G GC 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0374;SOR=1.41773;LSEQ=TCCCAACGCTGGCAAGGTAC;RSEQ=CCGCGGTGGTGGTATTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:936:94:10,84:416,424:0.1004:2,2:7.2:1:29.5:1:0:8.22664:35.3:46:0.1007:0.0759:1.1 0/1:578:79:12,67:237,259:0.1367:2,2:10.1:1:29.4:1:0:5.09598:35.3:38.5:0.1365:0.083:1.1 -1 17086183 . T G 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=2.5739;LSEQ=CGGGGCTGTGCCTCGGACCC;RSEQ=TAGATGGACCGAGATAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2232:30:17,13:1174,1028:0.0134:2,2:27.1:1:30.1:1:0.85424:1.14:33.9:29:0.0133:0:1.5 0/1:1505:51:29,22:788,666:0.0339:2,2:28.8:1:29.6:1:0.77565:1.11:31.5:50:0.0336:0:1.4 -1 17086217 . C G 211 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.61853;LSEQ=ATAGGTCGGGCCCCGAGCGA;RSEQ=AGCTGAGATCCCTCTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1784:29:1,28:734,1019:0.0163:2,1:18.5:1:31.9:1:0:20.15112:25:58:0.0165:0:1.4 0/1:1176:116:30,86:449,611:0.0986:2,2:15.2:1:30.8:1:0.00066:2.10532:27.3:57:0.0985:0:1.3 -1 17086236 . G C 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09678;SOR=1.31463;LSEQ=ACAGCTGAGATCCCTCTGGG;RSEQ=CTGGGACCAAACCCGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1336:91:31,60:444,799:0.0681:2,2:29.4:1:31.9:1:0.82089:1.07549:39.7:182:0.0695:0:1.2 0/1:844:74:32,42:279,490:0.0877:2,2:24.4:1:31.1:1:0.25691:1.34:37:36:0.087:0:1.2 -1 17086278 . G C 102 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00022;SOR=17.69896;LSEQ=CCAGGTGTACGGTACTCCAC;RSEQ=GGATATGCTCTCAGGTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:757:1:0,1:287,463:0.0013:2,0:40:0:8:0:1:0:25:0:0:0:3 0/1:480:11:1,10:194,266:0.0229:2,2:24.8:1:29.6:1:0.03048:7.27094:35.9:22:0.0233:0:1.4 -1 17086315 . TC T 129 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=28.18728;LSEQ=CACGCCCAGCCCCTCTGACC;RSEQ=CCCGGCCAAGCCACGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:1:1,0:340,232:0.0017:2,0:16:0:33:0:1:0:25:2:0.0018:0:1 0/1:383:18:14,4:245,119:0.047:2,2:26.7:1:31.1:1:0.44493:1.70:25.1:36:0.0477:0.0078:0.3 -1 17086398 . T A 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTACCGCAGCGGGGGAGG;RSEQ=CACAGAACTCTCGCTCGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:0:0,0:200,442:0:2,0:25.9:1:29.4:1:1:0:26:52.5:1:0:0.4 0/1:412:18:4,14:115,277:0.0437:2,2:22.8:1:29.4:1:0.60569:1.45187:25.8:36:0.0444:0:1.2 -1 17086439 . C T 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.82979;SOR=0.92985;LSEQ=TGCGGATCCGTAGTGTAGCA;RSEQ=CATGGCCGCTCGGAGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:65:15,50:118,319:0.1295:2,2:29.6:1:29.8:1:0.55016:1.23249:26.2:31.5:0.1286:0:2.6 0/1:321:39:7,32:72,210:0.1215:2,2:23.5:1:29.2:1:0.42717:1.56535:25.4:78:0.123:0:2.6 -1 17086450 . C G 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24242;SOR=1.24981;LSEQ=AGTGTAGCACCATGGCCGCT;RSEQ=GGAGCCGTCAGGATTCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:94:43,51:73,243:0.2287:2,2:27.3:1:31:1:4e-05:2.80:25.8:30.333:0.2247:0:2.6 0/1:281:76:27,49:47,158:0.2705:2,2:22.7:1:29.8:1:0.04675:1.85:25.2:152:0.2724:0:2.3 -1 17086464 . T C 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48406;SOR=1.16993;LSEQ=GCCGCTCGGAGCCGTCAGGA;RSEQ=TCCGGCAATAGTTGTCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:77:36,41:61,172:0.2476:2,2:20.4:1:31.8:1:0.00106:2.47:25.8:154:0.2525:0:2.7 0/1:223:62:22,40:44,117:0.278:2,2:24.9:1:30.3:1:0.25373:1.46:25.2:61:0.2773:0:2.4 -1 17086503 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1908;SOR=0;LSEQ=CCAGACCTTGGTCGAGGAAC;RSEQ=TGGGGGCGGTAATGGGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:0,2:3,56:0.0328:2,0:32:1:32:0:1:0:25:4:0.0333:0:3 0/0:78:0:0,0:9,69:0:2,0:33.1:1:32.7:1:1:0:29.9:156:1:0:0.8 -1 17086504 . TG T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50693;SOR=Inf;LSEQ=CAGACCTTGGTCGAGGAACC;RSEQ=GGGGCGGTAATGGGGCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:3,56:0:2,0:27.6:1:31.7:1:1:0:25.2:58:1:0:0.5 0/1:79:2:1,1:8,69:0.0253:2,2:45:1:31:1:0.21616:8.19:49:4:0.0256:0:0 -1 17086541 . T C 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00212;SOR=0.03491;LSEQ=CGTGAAGAAGACCCTGGTAC;RSEQ=CTGGCTTATCTGGCCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:1,2:0.625:2,2:8:1:29.4:1:1:1.8258:25.4:10:0.625:0:1.4 0/1:22:1:0,1:10,11:0.0455:2,0:3:0:28:0:1:0:25:2:0.0455:0:1 -1 17086870 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19498;LSEQ=CACCCGGCAGGATTTGATGC;RSEQ=GCAGCTCTGGAAGCGCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:197:108,89:231,211:0.3073:2,2:19.9:1:31:1:0.60665:1.11:29:97.5:0.3095:0:1.2 0/1:1056:84:37,47:523,448:0.0795:2,2:20.5:1:30.6:1:0.08829:1.48235:27.3:168:0.081:0:1.2 -1 17087037 . G A 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.83455;SOR=1.04757;LSEQ=CTGGGGGAAGGTCCCAGGCC;RSEQ=GGACGGAGGGAAGGTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2927:49:22,27:1587,1285:0.0167:2,2:25.2:1:31.1:1:0.15095:1.51547:25.5:98:0.0169:0:1.7 0/1:2511:44:21,23:1356,1110:0.0175:2,2:24.5:1:30.4:1:0.3617:1.3378:29.4:43:0.0173:0:2.3 -1 17087041 . C T 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66929;SOR=0.92179;LSEQ=GGGAAGGTCCCAGGCCGGGA;RSEQ=GGAGGGAAGGTGTTTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3107:79:37,42:1660,1368:0.0254:2,2:20.4:1:29.7:1:0.17046:1.37727:30.3:78:0.0254:0:1.8 0/1:2640:62:26,36:1406,1172:0.0235:2,2:20.8:1:29.7:1:0.05331:1.66072:31.6:124:0.0239:0:1.9 -1 17087065 . T G 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.73913;SOR=1.06352;LSEQ=GGGAAGGTGTTTGTCTCACT;RSEQ=GTGATCGTTCGGGAACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3881:78:28,50:1995,1800:0.0201:2,2:14.9:1:31.6:1:0.00401:1.97881:25.9:156:0.0203:0:2.4 0/1:3279:70:23,47:1657,1546:0.0213:2,2:14:1:30.4:1:0.00229:2.1897:27.5:140:0.0215:0:2.6 -1 17087072 . G A 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00134;SOR=1.2309;LSEQ=TGTTTGTCTCACTTGTGATC;RSEQ=TTCGGGAACTTGTGGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3664:575:285,290:1602,1483:0.1569:2,2:25.4:1:30.5:1:0.31741:1.09917:46.6:70.875:0.1564:0:1.3 0/1:3122:582:282,300:1300,1238:0.1864:2,2:24.8:1:29.7:1:0.23235:1.11707:47.3:82.143:0.1858:0:1.3 -1 17087244 . AC A 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.04882;SOR=0.79387;LSEQ=CTCCCACCCTGCCCCTCTCC;RSEQ=CCCCACTCGCCTTTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2184:230:130,100:1162,788:0.1053:2,2:26.4:1:31.5:1:0.39467:1.13425:52.5:460:0.107:0.0114:0.1 0/1:1533:131:73,58:848,553:0.0855:2,2:26.4:1:30.5:1:0.30503:1.21819:50.5:130:0.0858:0.0144:0.2 -1 17087262 . C T 289 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.73652;LSEQ=CCACCCCCACTCGCCTTTCT;RSEQ=CTGGAAGAGGTCACAGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2522:825:549,276:912,785:0.3271:2,2:25.3:1:29.9:1:0:1.71:49.2:50.563:0.3271:0:1.6 0/1:1851:488:306,182:763,598:0.2636:2,2:25.7:1:29.3:1:0.01201:1.32:50.5:80.333:0.2657:0:1.7 -1 17087299 . T C 262 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2005;SOR=0.89093;LSEQ=CGCCCAGAATGCCACAGCCT;RSEQ=GAGTGGGGCGAGTGTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3471:333:311,22:1553,1580:0.0959:2,2:24.7:1:31.3:1:0:14.37:33.7:65.6:0.0965:0:3.8 0/1:2767:239:215,24:1253,1272:0.0864:2,2:24.5:1:31.5:1:0:9.09:36.3:478:0.0884:0:3.6 -1 17087305 . G C 274 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00994;SOR=0.8042;LSEQ=GAATGCCACAGCCTTGAGTG;RSEQ=GGCGAGTGTTGAGTCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3506:393:351,42:1554,1554:0.1121:2,2:23.4:1:31.8:1:0:8.35:34.6:48.125:0.1123:0:3.5 0/1:2821:260:242,18:1265,1291:0.0922:2,2:23.2:1:31.9:1:0:13.71:34.9:51:0.0924:0:3.5 -1 17087322 . A G 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGGGCGAGTGTTGAGTCC;RSEQ=TGGCAGCAGTTGGCAACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3770:0:0,0:2027,1742:0:2,0:25:1:30.3:1:1:0:53.2:71.481:1:0:1 0/1:3040:49:27,22:1588,1401:0.0161:2,2:26.4:1:30.2:1:0.88547:1.08:57:98:0.0163:0:1.4 -1 17087365 . C G 366 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.70327;LSEQ=CTGCTCACATTGTAGTGGAA;RSEQ=GCCCTGGAGAGAAGAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4032:3355:1711,1644:340,334:0.8321:2,2:26.5:1:31.3:1:0.80015:1.02:51.3:61.13:0.8323:0:1.3 1/0:3283:2551:1305,1246:351,367:0.777:2,2:26:1:30.6:1:0.29098:1.10:51.3:54.457:0.7758:0:1.3 -1 17087395 . G A 158 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16586;LSEQ=AGAAGAAGGCACAGGGTAAC;RSEQ=CCACGGCCCAGGCTCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4046:45:27,18:2005,1992:0.0111:2,2:22.4:1:28.8:1:0.23039:1.49:50.8:44:0.0111:0:2.2 0/0:3223:6:4,2:1626,1588:0.0019:2,2:22.5:1:27.5:1:0.68735:1.95:49.7:5:0.0016:0:2.7 -1 17087432 . G T 247 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=225.01806;LSEQ=CCTGCCCCCAGTCTTATCTA;RSEQ=GCCCAGTGGCCACTCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3973:2:0,2:2002,1963:5e-04:2,0:1:0:27:1:0.2453:0:46.5:4:5e-04:0:1 0/1:3140:319:163,156:1439,1379:0.1016:2,2:25.4:1:29.8:1:1:1.00:38.2:62.8:0.1016:0:1.2 -1 17087459 . A G 262 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34277;SOR=0.92318;LSEQ=TGGCCACTCACCAGCAGTCC;RSEQ=TTAAGGGCCCACAGCGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3936:360:181,179:1774,1799:0.0915:2,2:25.6:1:30.9:1:0.82519:1.03:51.8:119:0.0922:0:1.6 0/1:3387:288:144,144:1578,1519:0.085:2,2:26.3:1:30.2:1:0.7585:1.03884:51.2:71:0.0851:0:1.5 -1 17087465 . G A 304 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=1.27018;LSEQ=CTCACCAGCAGTCCATTAAG;RSEQ=GCCCACAGCGACCAGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3865:1206:577,629:1318,1335:0.312:2,2:26.6:1:30.4:1:0.29748:1.07621:50.5:42.071:0.313:0:1.1 0/1:3313:1211:600,611:1071,1023:0.3655:2,2:26.6:1:29.7:1:0.38629:1.06608:49.7:49.458:0.3656:0:1.2 -1 17087521 . G A 276 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.63246;LSEQ=ACATCCTCCTGCCAAGGCCC;RSEQ=GGCACCACCGCATGTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3400:537:239,298:1343,1518:0.1579:2,2:23.7:1:30.5:1:0.32219:1.10308:39.7:47.818:0.1571:0:1.7 0/1:2914:309:146,163:1273,1326:0.106:2,2:23.5:1:30.1:1:0.5882:1.07176:38.5:50.5:0.1054:0:1.8 -1 17087530 . C T 150 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=7.4763;LSEQ=TGCCAAGGCCCGGGCACCAC;RSEQ=GCATGTAGCAGGTGCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3428:6:2,4:1558,1860:0.0018:2,2:8.3:1:25.2:1:0.69457:1.67502:49.7:5:0.0015:0:2.3 0/1:2936:38:18,20:1386,1511:0.0129:2,2:23.9:1:28.6:1:1:1.01919:37.3:18:0.0124:0:2.3 -1 17087541 . GGTGCT G 307 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=1.2455;LSEQ=GGGCACCACCGCATGTAGCA;RSEQ=GTAGCTCTGTGCCCCGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3352:919:416,503:1086,1338:0.2742:2,2:26.2:1:32.2:1:0.81536:1.02:40.9:305.333:0.2765:0.0221:1.1 0/1:3013:964:462,502:969,1075:0.3199:2,2:24.2:1:31:1:0.81445:1.02:38.4:481:0.3234:0.0617:1.2 -1 17087582 . G A 318 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00316;SOR=0.86099;LSEQ=GGAGCACCTGGAAGTCATTC;RSEQ=ATGGCGAGCGCTGCCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3380:1549:664,885:784,1041:0.4583:2,2:28:1:30.1:1:0.97216:1.00378:41.1:102.267:0.459:0:1.4 0/1:3016:1271:556,715:794,948:0.4214:2,2:27.9:1:29.6:1:0.33488:1.07704:39.4:78.438:0.4213:0:1.5 -1 17087593 . C T 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02275;SOR=1.21778;LSEQ=AAGTCATTCGATGGCGAGCG;RSEQ=TGCCCTGCAGAGTGGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3241:290:105,185:1264,1687:0.0895:2,2:27.3:1:30:1:0.02936:1.32001:42.8:95.667:0.0898:0:2 0/1:2919:312:127,185:1152,1453:0.1069:2,2:28.7:1:29.7:1:0.25153:1.15487:39.7:624:0.1081:0:2.1 -1 17087640 . A C 198 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCAGGTCAGGTGGGCATAC;RSEQ=TGTCAGTAATGTGTATTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1985:0:0,0:638,1343:0:2,0:24.6:1:30.4:1:1:0:47.3:69.75:0.9985:0:0.6 0/1:1625:82:27,55:522,1021:0.0505:2,2:23.5:1:31.3:1:0.90522:1.04144:41.1:81:0.0507:0:1.7 -1 17087682 . A G 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.40477;LSEQ=TGTCCACACTTTGTTCATTC;RSEQ=GGGGATCAAAGCTACAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:905:213:32,181:121,570:0.2354:2,2:22.6:1:30.7:1:0.46445:1.20045:40.9:105.5:0.2358:0:1.1 0/1:587:65:9,56:98,424:0.1107:2,2:19.7:1:30.1:1:0.39654:1.43731:41:130:0.1125:0:1.1 -1 17087841 . T C 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTGTAGTGGCCCAGGCAC;RSEQ=GGGCTCAGATCTAACACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:69:1,68:0,1:0.9857:0,1:20.4:1:29:1:1:0:38:33.5:1:0:1.2 1/1:10:10:0,10:0,0:1:0,0:19.2:1:25.9:1:1:0:40.4:4:1:0:1.2 -1 17087862 . C T 98 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.66;SOR=0.40933;LSEQ=GGGCTCAGATCTAACACATA;RSEQ=GCTCTGTGAGAGCAGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:0,9:1,28:0.2368:1,0:24.4:1:31:1:1:0:33.9:18:0.2432:0:1.9 0/1:9:1:0,1:1,7:0.1111:2,0:8:0:31:0:1:0:27:2:0.125:0:2 -1 17087976 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.08615;SOR=Inf;LSEQ=GCCCTGGCTAGGCATTCAGA;RSEQ=TCCAAATCTGGGCTCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:14,4:0:2,0:26.7:1:32.4:1:1:0:42.9:36:1:0:1.1 0/1:8:2:1,1:4,2:0.25:2,2:34:1:28:1:1:1.8258:37:4:0.25:0:1.5 -1 17087996 . C T 39 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57018;SOR=2.47383;LSEQ=CTCCAAATCTGGGCTCTCAC;RSEQ=TGCACAAAGGCATACGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:2,1:17,6:0.1154:2,2:36.3:1:25:1:1:1.39665:35.3:2:0.08:0:4 0/1:8:2:1,1:4,2:0.25:2,2:20:0:30:1:1:1.8258:43:4:0.2857:0:3.5 -1 17088002 . A G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20749;SOR=4.10844;LSEQ=ATCTGGGCTCTCACCTGCAC;RSEQ=AAGGCATACGCTAGGTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:20,6:0.0714:2,2:26:1:28.5:1:0.44444:3.16227:42.5:4:0.0769:0:3 0/1:8:2:1,1:4,2:0.25:2,2:14:0:30:1:1:1.8258:43:4:0.25:0:3.5 -1 17088005 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19777;SOR=4.26365;LSEQ=TGGGCTCTCACCTGCACAAA;RSEQ=GCATACGCTAGGTTAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:21,6:0.069:2,2:23:1:29:1:0.43103:3.31657:42.5:4:0.069:0:3 0/1:8:2:1,1:4,2:0.25:2,2:11:0:31.5:1:1:1.8258:43:4:0.2857:0:3.5 -1 17088052 . T G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35381;SOR=0.4339;LSEQ=CAGGCTCAGGAGGGGTCATT;RSEQ=CCTGCTGTGTGCGTGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:30:29,1:39,4:0.411:2,1:23.2:1:32.8:1:0.6426:2.94:45.9:60:0.411:0:1.1 0/1:13:3:3,0:8,2:0.2308:2,0:22.7:1:32.7:1:1:0:43:6:0.2308:0:1 -1 17088194 . GC G 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00828;SOR=Inf;LSEQ=GGCCAAGGTCACTGCCCCAT;RSEQ=CCACTGAGCCTCTGGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:534:0:0,0:477,57:0:2,0:23.8:1:31.9:1:1:0:53.4:58.333:1:0:0.4 0/1:334:5:4,1:292,37:0.015:2,2:17:1:29.9:1:0.45545:1.9679:60:10:0.0153:0.009:0 -1 17088216 . C T 70 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02238;SOR=8.56991;LSEQ=CCACTGAGCCTCTGGCTCCC;RSEQ=GACTTTTTTCTCATCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:812:1:0,1:647,164:0.0012:2,0:1:0:26:0:0.2032:0:60:2:0.0012:0:1 0/1:573:6:1,5:434,133:0.0105:2,2:8.2:1:27.3:1:0.0037:16.22015:51:12:0.0106:0:1.5 -1 17088247 . A G 295 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.65947;LSEQ=TCATCCCAGAATAGGAGAAT;RSEQ=GGGCCAACCCCCTCCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1506:650:451,199:577,274:0.4316:2,2:23:1:31.6:1:0.53754:1.08:48.3:80.25:0.4326:0:1.1 0/1:1106:369:254,115:480,253:0.3336:2,2:22.9:1:31:1:0.27932:1.16:49.3:122:0.3349:0:1.2 -1 17088264 . G C 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATAGGGCCAACCCCCTCCT;RSEQ=AAGGCAGATGGGGATCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1981:0:0,0:1223,755:0:2,0:25:1:31.6:1:1:0:56.3:55.514:0.999:0:0.4 0/1:1542:16:9,7:921,605:0.0104:2,2:21.4:1:31.2:1:0.79971:1.18388:54.1:32:0.0105:0:1.6 -1 17088343 . C A 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=16.48027;LSEQ=GAAGCAGCAGGAGTGGGAGC;RSEQ=ACTCCTCCAGGATGACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2194:2:2,0:850,1342:9e-04:2,0:1:0:28.5:1:0.15069:0:57.5:4:9e-04:0:1 0/1:1686:25:11,14:676,985:0.0148:2,2:22.6:1:28.5:1:0.83812:1.14:58.5:24:0.0144:0:1.2 -1 17088631 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATCTCATAAGCACTAAA;RSEQ=ATCTCAATGTACTGAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:0.125:1,0:31.5:1:30:0:1:0:42.5:4:0.1333:0:1 0/0:1:0:0,0:0,1:0:0,0:29:0:31:0:1:0:60:2:1:0:0 -1 17089050 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACACTTCCAGGATCTGG;RSEQ=CATCTCCTGCCCCTCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:22.5:1:31.5:1:0.33333:0:54.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17089192 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACTCTCGCTTTCACCC;RSEQ=TGCGACCTGGTTCACTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:32.5:1:1:0:38:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17345073 . G GC 79 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAACAAGCTGCAGGCCCT;RSEQ=CTGATGTCAGTTCCACGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:0.5455:0,0:20.7:1:30.6:1:1:0:60:12:0.5455:0.2727:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17345216 . C CT 51 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.33698;LSEQ=GGCAAGTAAAGGAACAGGTT;RSEQ=TTTTTTTTTTGTTAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:3,0:63,0:0.0455:1,0:32.7:1:31.7:1:1:0:60:6:0.0455:0:0 0/1:50:3:3,0:47,0:0.06:1,0:25.7:1:32.7:1:1:0:60:6:0.0612:0:0.3 -1 17345905 . A G 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAGAAACTACCCTCTCT;RSEQ=TTAACCCTTTGTAAAACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:21.8:1:32.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17350238 . A G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCAAGGCATGGTTTGC;RSEQ=CCCCTTTGGGGTGACCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:19,0:0,0:1:0,1:24.9:1:30.5:1:1:0:60:38:1:0:1.1 1/1:8:8:7,1:0,0:1:0,2:30.8:1:31.8:1:1:0:60:16:1:0:1.1 -1 17350573 . T A 42 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6876;SOR=1.85593;LSEQ=CACTCGTAGAGCCCGTCCTG;RSEQ=ATGGGGAGAAAAGAGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:2:2,0:98,228:0.0061:2,0:1:0:26:1:0.0923:0:60:4:0.0062:0:1.5 0/1:355:4:4,0:118,233:0.0113:2,0:9.8:1:21.3:1:0.0135:0:60:3:0.0086:0:1 -1 17350931 . G A 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGATTCAAAAGCCTAGGG;RSEQ=CTGAAGCAGCAAGAGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:7:1:26.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17350943 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCTAGGGGCTGAAGCAGCA;RSEQ=GAGTCTGTAGCTGCTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:35:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17353988 . T G 91 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51049;SOR=0.24443;LSEQ=CTGGTTTCTTTTGAAAAAGA;RSEQ=GGAGTAGCCACACAGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:0.7:0,0:21.9:1:32.6:1:1:0:60:14:0.7:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:31:0:34:0:1:0:60:2:0.3333:0:1 -1 17355387 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TGTTGGCTTTTCTCCCTTCC;RSEQ=TCCTTCTTCCTGCCTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:1:0,1:20.4:1:32.3:1:1:0:60:38:1:0:1 1/1:11:11:0,11:0,0:1:0,0:20.4:1:32.5:1:1:0:60:22:1:0:1 -1 17359386 . T C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.81156;SOR=1.14061;LSEQ=AGAAACCAGAACTTGCACCA;RSEQ=GGTTAGAATTTTGGATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:19:18,1:15,1:0.5429:1,1:22.4:1:31.4:1:1:1.19:60:18:0.5294:0:1.4 1/0:33:19:19,0:14,0:0.5758:1,1:28.2:1:31.7:1:1:0:60:38:0.5758:0:1.1 -1 17359676 . C A 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=ATCCAGTGGTATTTATGTAA;RSEQ=GTTCAACCTCCCTACACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:289:289:67,222:0,0:1:0,2:23.7:1:30.6:1:1:0:60:35.125:1:0:1.1 1/1:302:288:86,202:2,12:0.9536:2,2:23.8:1:30:1:0.36517:2.55:60:56.6:0.9529:0:1.1 -1 17370797 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTATTTTGGTATTATT;RSEQ=TTCTGAATCAGGTAACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:33:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17370970 . C T 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GCTGGGATTACAGGCATGAG;RSEQ=CACTATACCCAGCTAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:37.7:1:30.7:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:0:0,0:2:0:31:0:1:0:60:2:1:0:0 -1 17371152 . T C 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38303;SOR=0.75273;LSEQ=TTGTTTTAAAAACAGAGCCA;RSEQ=CGGATGATCTCAGATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:70:67,3:36,1:0.6481:1,1:24.2:1:32.3:1:1:1.60532:60:140:0.6604:0:1.1 1/0:93:54:50,4:35,4:0.5806:2,2:19.3:1:31.5:1:0.7162:1.42:60:108:0.5806:0:1.1 -1 17371221 . C T 124 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=16.20435;LSEQ=CCTAAATCAAATCAAGAACT;RSEQ=TCCTTCAATAGCTGGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:1:1,0:249,109:0.0028:2,0:23:0:13:0:1:0:60:0:0:0:7 0/1:461:20:11,9:275,166:0.0434:2,2:24.1:1:28.7:1:0.49208:1.35447:60:40:0.0436:0:1.3 -1 17371223 . C T 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATCAAATCAAGAACTCT;RSEQ=CTTCAATAGCTGGCTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:256,115:0:2,0:25.8:1:30.5:1:1:0:60:45.375:1:0:0.2 0/1:479:48:31,17:263,168:0.1002:2,2:22.5:1:29.4:1:0.75493:1.16:60:96:0.1004:0:1.1 -1 17371411 . G GA 80 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16391;SOR=0.30777;LSEQ=TTTTTAAAGTTCACAAAAAG;RSEQ=AAAAAAAAATTAGAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:6:1,5:39,159:0.0294:2,2:26.5:1:31:1:1:1.22526:60:12:0.0299:0:0 0/0:217:2:0,2:56,159:0.0092:2,0:34:1:21:1:1:0:60:1:0.0047:0:0 -1 17371494 . C T 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2505;SOR=0.57572;LSEQ=ATAAACTCACACATTACTGA;RSEQ=ACATAATCTTCTTAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:28:0,28:0,16:0.6364:1,1:25.3:1:28.2:1:1:0:60:56:0.6512:0:1.1 1/0:32:16:0,16:1,15:0.5:1,1:24.2:1:28.4:1:1:0:60:15:0.5:0:1.1 -1 17372397 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCTTGAACCACTTGCTC;RSEQ=ATCCCACTCCTACTCTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 17378188 . C G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCCTCATAAGATAACC;RSEQ=GGGGGAGGGGGGGTCAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:29.5:1:1:0:60:4:1:0:3.5 -1 17380195 . TC T 92 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.13116;SOR=0;LSEQ=TCAAGTCCCCTTTCTGAACG;RSEQ=CCCCCCCCCCGCACCCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:8,0:9,0:0.4706:0,0:34.3:1:30.8:1:1:0:60:16:0.5:0:0.6 0/0:4:0:0,0:4,0:0:0,0:15.5:1:29.3:1:1:0:60:8:1:0:3.5 -1 17380269 . G C 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.02131;SOR=Inf;LSEQ=GCTGCTGCGAGGCGCAGAAA;RSEQ=ATAACTTGACAGGGATGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:0:1,0:20.9:1:32.9:1:1:0:60:88:1:0:0 0/1:40:5:5,0:35,0:0.125:1,0:36.4:1:32.2:1:1:0:60:10:0.1429:0:1 -1 17380326 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49835;SOR=0;LSEQ=ACTGCACCAGGGGGAGGAGG;RSEQ=CCTCCATCTCCCTGAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:144,5:0.0132:1,2:19.5:1:33:0:0.07815:26.38197:60:4:0.0135:0:1 0/0:149:0:0,0:136,13:0:2,0:22.4:1:29.3:1:1:0:60:48.667:1:0:0 -1 17380497 . G T 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.13116;LSEQ=AACCGGCGCCTCAAGGAGAG;RSEQ=GCGACCACCGCCGCCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:839:835:387,448:0,0:0.9952:0,2:25.9:1:29.6:1:1:0:60:58.643:0.9988:0:1.2 1/1:879:848:392,456:15,14:0.9647:2,2:24.4:1:29.5:1:0.57572:1.24604:60:83.8:0.9654:0:1.2 -1 17380653 . C A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11654;LSEQ=ACCAAGTGGGAGGCGGCTTC;RSEQ=GGTTTCCCGGGTGGGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:45:0,45:0,57:0.4412:1,1:23.6:1:32.2:1:1:0:60:90:0.4455:0:1 0/1:60:5:1,4:2,53:0.0833:1,2:28.4:1:31.4:1:0.23334:6.24:60:10:0.0862:0:1 -1 19173167 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=TGAAGTCATCCTGGAGGAGG;RSEQ=TGGGTCCTTAATCTCATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19:0:33:0:1:0:60:4:1:0:0.5 0/1:5:2:1,1:1,2:0.4:2,2:8:1:27.5:1:1:1.73:60:4:0.4:0:1 -1 19173614 . G T 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTGCAGAACAGTATGCCCAT;RSEQ=CAACCTCTTTTCTCTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:43.5:1:30.5:1:1:0:60:4:0.3333:0:1 1/1:1:1:1,0:0,0:1:0,0:15:0:32:0:1:0:60:2:1:0:1 -1 19173895 . G T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGTCTGTGATACTTTGT;RSEQ=AGGCAGGCCTAGGAAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:45.5:1:30:0:1:0:60:4:0.3333:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 19173896 . A AT 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCTGTGATACTTTGTG;RSEQ=GGCAGGCCTAGGAAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:45.5:1:31.5:1:1:0:60:4:0.3333:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 20541290 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2436;SOR=Inf;LSEQ=TACCTAACGTGACCTACTTA;RSEQ=TTCTCAGACACAGTAATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:115,62:0:2,0:22.9:1:31.8:1:1:0:60:87.5:1:0:0.3 0/1:173:2:1,1:115,56:0.0116:2,2:42.5:1:30.5:1:0.55169:2.04436:60:4:0.0118:0:1 -1 20541370 . A G 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.82627;LSEQ=TGATTCGGCCACCCTCAGCT;RSEQ=GATCCTCCAATATCATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:327:235:122,113:49,43:0.7187:2,2:25.6:1:31.4:1:0.90211:1.05533:60:57.75:0.7174:0:1.1 1/1:321:282:135,147:18,21:0.8785:2,2:26.7:1:30.6:1:0.86584:1.07:60:93:0.8774:0:1.2 -1 20541449 . T A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58302;SOR=2.58637;LSEQ=ACGTATTGACACTTGGGCAA;RSEQ=GGAAACAGAGATTGGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:1,0:35,122:0.0063:2,0:1:0:27:0:0.22785:0:60:2:0.0064:0:1 0/1:123:2:1,1:33,88:0.0163:2,2:30:1:29.5:1:0.47808:2.64:60:4:0.0165:0:1 -1 21958587 . G A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGAAAGCTGGAGCCAACCTG;RSEQ=AGTCTGGGCCAGGCACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:19.5:1:29:1:1:0:60:4:0.4:0:1 1/1:2:2:0,2:0,0:1:0,0:17.5:1:27:1:1:0:60:4:1:0:1.5 -1 21959132 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGCTCAGTGGTTCATG;RSEQ=CTGTAATCCCAGCACTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:1:29.5:1:1:0:59:4:1:0:1 -1 22234424 . G C 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.07622;LSEQ=CTGTGCCTCCGTTTCCTCAT;RSEQ=TGTAAAATGGGCACGATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:0.3571:0,0:24.8:1:30.4:1:1:0:60:10:0.3571:0:1 0/1:8:3:3,0:5,0:0.375:0,0:16.3:1:29.3:1:1:0:60:6:0.375:0:1 -1 22234542 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50132;SOR=Inf;LSEQ=CATGGTGAATGTTCTATAAG;RSEQ=GTTTGCTGCCTTTCGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:69,43:0:2,0:23.7:1:29.6:1:1:0:60:111:1:0:0.1 0/1:132:2:1,1:69,61:0.0152:2,2:33:1:31:0:1:1.13009:60:4:0.0154:0:1 -1 22234557 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50571;SOR=Inf;LSEQ=ATAAGTGTTTGCTGCCTTTC;RSEQ=GCCGGAACCGCCATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:75,51:0:2,0:26.2:1:29.9:1:1:0:59.6:62:1:0:0.1 0/1:161:2:1,1:81,76:0.0124:2,2:14.5:1:29:1:1:1.0654:60:4:0.0126:0:1.5 -1 22234585 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25204;SOR=Inf;LSEQ=CCGCCATCTTCCAGTAATTC;RSEQ=CCAAAATGACGAACACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:69,75:0:2,0:26.7:1:30.8:1:1:0:59.6:71:1:0:0.1 0/1:168:3:1,2:74,91:0.0179:2,2:24.3:1:22.7:1:1:1.62186:60:2:0.012:0:1 -1 22234598 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20155;SOR=0;LSEQ=GTAATTCGCCAAAATGACGA;RSEQ=CACAAAGGGAAAGAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:58,79:0.0144:2,2:13.5:1:32.5:1:1:1.36:60:4:0.0145:0:2 0/0:170:0:0,0:74,96:0:2,0:25.2:1:30:1:1:0:59.4:340:1:0:0.2 -1 22234654 . C T 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCCAGGCCTTTTAGAAAA;RSEQ=ATGGAGTTGTTCCTTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:44,54:0:2,0:23.8:1:32.3:1:1:0:55.8:196:1:0:0.1 0/1:75:36:18,18:20,19:0.48:2,2:25.1:1:28.1:1:1:1.05188:55.4:35:0.473:0:1.1 -1 22234689 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4978;SOR=0;LSEQ=TTGGCCACGTATATGCGAAT;RSEQ=TATAAGAAAGGTGATATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:53,40:0.0211:2,2:15.5:1:28:1:1:1.32102:44.5:4:0.0211:0:1 0/0:89:0:0,0:57,32:0:2,0:23:1:31.4:1:1:0:49.9:88:1:0:0.3 -1 22234725 . G T 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.53255;LSEQ=ATTGTAGACATCAAGGGAAT;RSEQ=GGTACTGTTCAAAAAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:83,68:0.013:2,2:26:0:32:0:1:1.21898:42:4:0.0132:0:1 0/0:144:1:0,1:86,57:0.0069:2,0:1:0:26:0:0.40278:0:60:2:0.007:0:1 -1 22234735 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.61843;SOR=2.06801;LSEQ=TCAAGGGAATGGGTACTGTT;RSEQ=AAAAAGGAACGCCCCACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:0,1:95,77:0.0058:2,0:1:0:24:0:0.45087:0:60:2:0.0059:0:1 0/1:168:2:1,1:96,70:0.0119:2,2:24:1:28:1:1:1.36879:54.5:4:0.0121:0:1 -1 22234745 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23209;SOR=Inf;LSEQ=GGGTACTGTTCAAAAAGGAA;RSEQ=GCCCCACAAGTGTTACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:115,91:0:2,0:25.2:1:31.1:1:1:0:54.9:205:1:0:0.2 0/1:192:2:1,1:106,82:0.0104:2,2:23.5:1:31.5:1:1:1.29091:60:4:0.0105:0:1 -1 22587728 . T C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07172;SOR=Inf;LSEQ=AGGAACTTCACTCTTCATAC;RSEQ=GGTAACAATGGGGGGCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:0:1,0:23.8:1:31.4:1:1:0:60:44:1:0:0.1 0/1:33:3:2,1:27,3:0.0909:2,2:16.3:1:31:1:0.33028:4.19592:60:6:0.0938:0:1 -1 22587762 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16746;SOR=Inf;LSEQ=GGCTGTAAGACAGAGCTGTA;RSEQ=GCAGGGGAGGGCATGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:72,24:0:2,0:23:1:30.4:1:1:0:60:95:1:0:0.1 0/1:67:2:1,1:49,15:0.0299:2,2:19.5:1:28:1:0.4289:3.19504:60:4:0.0313:0:2.5 -1 22587773 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18728;SOR=Inf;LSEQ=AGAGCTGTAAGCAGGGGAGG;RSEQ=CATGGTAGGCTTGGAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:81,34:0:2,0:24.2:1:31.4:1:1:0:60:114:0.9913:0:0.1 0/1:89:2:1,1:60,27:0.0225:2,2:9.5:1:26:1:0.53269:2.20033:60:4:0.0227:0:2 -1 22587781 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20425;SOR=Inf;LSEQ=AAGCAGGGGAGGGCATGGTA;RSEQ=GCTTGGAATTTAGAAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:91,43:0:2,0:24.4:1:31.6:1:1:0:60:133:1:0:0.2 0/1:111:2:1,1:72,37:0.018:2,2:38.5:1:29:1:1:1.93352:60:4:0.0183:0:2.5 -1 22587839 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11028;SOR=Inf;LSEQ=AGAATGGGTTATTTAGATGT;RSEQ=GGCCTCGGCGAGGGCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:131,98:0:2,0:24.2:1:31.2:1:1:0:60:44.8:1:0:0.6 0/1:212:3:1,2:108,101:0.0142:2,2:22:1:31:1:0.61277:2.1312:60:6:0.0142:0:1.7 -1 22587878 . G A 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13342;SOR=0.75015;LSEQ=CCCGGGGAAGGGGCCTTTCC;RSEQ=CTGGGCCAGAAGGGGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:144:74,70:55,48:0.583:2,2:26.2:1:29.5:1:0.79679:1.08354:60:35:0.5785:0:1.2 1/0:213:109:49,60:57,47:0.5117:2,2:23:1:29.7:1:0.17136:1.48221:60:218:0.5142:0:1.2 -1 22587882 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10134;SOR=Inf;LSEQ=GGGAAGGGGCCTTTCCGCTG;RSEQ=GCCAGAAGGGGGGCATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:123,121:0:2,0:25.9:1:31:1:1:0:60:121:0.9959:0:0.8 0/1:215:3:1,2:103,109:0.014:2,2:14.7:1:30:1:1:1.88453:60:6:0.0142:0:2 -1 22587925 . T C 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09024;SOR=Inf;LSEQ=CGTGGACTTCCTGCAACCAT;RSEQ=GCCCCCCACACCTGTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:86,123:0:2,0:26.6:1:29.6:1:1:0:60:33.833:1:0:0.7 0/1:171:3:1,2:77,91:0.0175:2,2:21.7:1:22.3:1:1:1.68732:60:2:0.0118:0:2 -1 22587948 . C A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59198;SOR=2.4258;LSEQ=CCCCCACACCTGTGGCTGCC;RSEQ=TTTCCTCCCACTTGGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:1:1,0:58,105:0.0061:2,0:1:0:27:0:0.35976:0:60:2:0.0063:0:2 0/1:136:2:1,1:53,81:0.0147:2,2:38.5:1:30:1:1:1.52:60:4:0.0152:0:1.5 -1 22587949 . T C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06082;SOR=1.77884;LSEQ=CCCCACACCTGTGGCTGCCC;RSEQ=TTCCTCCCACTTGGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:27:9,18:45,87:0.1698:2,2:27.6:1:31.4:1:1:1.03427:60:26:0.1667:0:1.4 0/1:131:35:14,21:38,58:0.2672:2,2:29.2:1:31.3:1:1:1.02:60:70:0.2672:0:1.1 -1 22924270 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17273;SOR=Inf;LSEQ=CCGGCTACACGGAGAGACAG;RSEQ=GGCGGGACTTCCTGAGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:26.5:1:29.3:1:1:0:60:25:1:0:0 0/1:19:2:1,1:11,6:0.1053:2,2:34.5:1:29:1:1:1.77272:60:4:0.1053:0:1 -1 22926772 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGAAGGGAAGGAAGGAA;RSEQ=GGATGAGGAAAGGAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:28:1:1:0:60:4:1:0:1 -1 22927217 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14856;SOR=0;LSEQ=CCTTCCGCACCTTCTCCTCG;RSEQ=CCAGCGACGTGTGGAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:17,16:0.0571:2,2:31:0:31:0:1:1.06069:60:4:0.0588:0:1 0/0:55:0:0,0:25,30:0:2,0:30:1:31.5:1:1:0:60:54:1:0:0.2 -1 22927314 . A G 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0021;SOR=Inf;LSEQ=CAACCGGGATGTGAGTGCCA;RSEQ=GCCCTGGCAGGTCCGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:1,11:0:2,0:26.1:1:31.7:1:1:0:60:24:1:0:0 1/1:5:4:1,3:0,1:0.8:0,2:17.5:1:31:1:1:0:60:8:0.8:0:1.5 -1 22927326 . T G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05714;SOR=Inf;LSEQ=GAGTGCCAAGCCCTGGCAGG;RSEQ=CCGCGGGCGGTGGAGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:21.9:1:31.3:1:1:0:60:22:1:0:0 1/0:4:2:0,2:1,1:0.5:2,0:19:1:34:0:1:0:60:4:0.5:0:2 -1 23109291 . T C 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAAATTAATGCAA;RSEQ=GTAGGGAGCTTCAGAGTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19.5:1:30:1:1:0:60:4:1:0:1.5 1/0:2:1:1,0:1,0:0.5:0,0:43:0:29:0:1:0:60:2:0.5:0:1 -1 23110939 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.18937;SOR=Inf;LSEQ=ACACGATCCGCACGTACCAG;RSEQ=TGTGCAACGTGTTTGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:0:2,0:32.6:1:32:1:1:0:60:48:1:0:0.1 0/1:19:2:1,1:5,12:0.1053:2,2:36:0:29.5:1:1:2.28:60:4:0.1053:0:1 -1 23111036 . C T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00216;SOR=0;LSEQ=CCACGTGGAGATGAAGTTTT;RSEQ=GGTGCGTGACTGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:24.7:1:29.3:1:1:0:60:12:1:0:1 0/0:5:0:0,0:2,3:0:2,0:17.8:1:31.6:1:1:0:60:10:1:0:0.2 -1 23210476 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTGCCGTCCCCCCACCCACC;RSEQ=ACCTCACTGCCCACCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:1:29.5:1:1:0:60:4:1:0:1 -1 23232400 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAGTGGATTTCCCTCCA;RSEQ=GGAGGGACTGGCTCCCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:16:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 23232869 . G C 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCTGGGTCTGGAGCCCA;RSEQ=TTCTCTGGACTCTTGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:38:1:34:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 23233284 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22051;SOR=Inf;LSEQ=GGCCATCAAGACGCTCAAGT;RSEQ=GGGCTACACGGAGAAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:35,13:0:2,0:26.4:1:31.2:1:1:0:60:96:1:0:0.1 0/1:43:2:1,1:27,14:0.0465:2,2:10:0:32:0:1:1.89743:60:4:0.0465:0:1.5 -1 23233370 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19698;SOR=0;LSEQ=ATCCCAACGTCATCCACCTG;RSEQ=AGGGTGTCGTGACCAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:9,31:0.0476:2,2:16.5:1:28:1:0.42393:3.32:60:4:0.0488:0:1 0/0:52:0:0,0:21,31:0:2,0:26.2:1:29.8:1:1:0:60:25:1:0:0.1 -1 23234457 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2261;SOR=Inf;LSEQ=CTCCCAAAGCAAAACGATGG;RSEQ=CAGTTCACAGTCATCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:61,30:0:2,0:23.4:1:30.8:1:1:0:60:29.333:1:0:0.1 0/1:83:2:1,1:56,25:0.0241:2,2:47.5:1:30:1:0.531:2.21606:60:4:0.0244:0:1 -1 23234511 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4988;SOR=Inf;LSEQ=CGGGGCATCGCAGCTGGCAT;RSEQ=AAGTACCTGGCAGACATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:57,63:0:2,0:25.9:1:31.9:1:1:0:60:119:1:0:0.1 0/1:130:2:1,1:66,62:0.0154:2,2:7.5:1:27:1:1:1.06404:60:4:0.0156:0:1.5 -1 23234521 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4983;SOR=Inf;LSEQ=CAGCTGGCATGAAGTACCTG;RSEQ=CAGACATGAACTATGTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:48,65:0:2,0:26:1:31.7:1:1:0:60:55.5:1:0:0.1 0/1:120:2:1,1:52,66:0.0167:2,2:21.5:1:28.5:1:1:1.27:60:4:0.0167:0:1 -1 23234621 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49468;SOR=Inf;LSEQ=CTTTGGGCTCTCACGCTTTC;RSEQ=AGAGGACGATACCTCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:10,31:0:2,0:24:1:28.3:1:1:0:60:82:1:0:0.2 0/1:44:2:1,1:12,30:0.0455:2,2:36:1:29:1:0.50846:2.44:60:4:0.0455:0:1 -1 23235533 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49889;SOR=Inf;LSEQ=AGGGCGGAAAGATCCCCATC;RSEQ=GCTGGACAGCCCCGGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:103,66:0:2,0:24.9:1:29.8:1:1:0:60:32.8:1:0:0.3 0/1:178:2:1,1:110,66:0.0112:2,2:32:1:28:1:1:1.66161:60:4:0.0114:0:1 -1 23235598 . C A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24846;SOR=Inf;LSEQ=GCCAGTGATGTGTGGAGCTA;RSEQ=GGCATTGTCATGTGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:60,109:0:2,0:25.4:1:30.4:1:1:0:60:168:1:0:0.2 0/1:179:3:1,2:73,103:0.0168:2,2:26:1:31:1:1:1.41482:60:6:0.0169:0:1 -1 23235619 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24448;SOR=Inf;LSEQ=GGCATTGTCATGTGGGAGGT;RSEQ=ATGTCCTATGGGGAGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:29,85:0:2,0:23.9:1:31:1:1:0:60:56:1:0:0.1 0/1:112:2:1,1:28,82:0.0179:2,2:18:1:26.5:1:0.45254:2.90:60:4:0.0185:0:1 -1 23236826 . C T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22619;SOR=0.3156;LSEQ=TGGGCCTGGCAGAGGGTAGA;RSEQ=GCCCTCAGCCCATCCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:10,0:3,0:0.7692:0,0:27.2:1:31.6:1:1:0:60:20:0.7692:0:1 1/0:12:6:6,0:6,0:0.5:0,0:26.5:1:29.7:1:1:0:60:12:0.5:0:1 -1 23236849 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5122;SOR=Inf;LSEQ=CCTCAGCCCATCCACCCAAC;RSEQ=CCACTGCACTCCTGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:0:1,0:30.7:1:30.1:1:1:0:60:15:1:0:1 0/1:25:2:1,1:20,3:0.08:2,2:26:1:31:1:0.3:5.9161:60:4:0.0833:0:1 -1 23236881 . A T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24178;SOR=Inf;LSEQ=CTGCATTGTCCCAGGTAATC;RSEQ=ATGCCATTGAGCAGGACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:27,7:0:2,0:19:1:29.2:1:1:0:60:33:1:0:0.5 0/1:38:3:1,2:26,9:0.0789:2,2:19:1:26.7:1:0.19559:5.46678:60:6:0.0811:0:1.3 -1 23236925 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49656;SOR=Inf;LSEQ=CTGCCACCGCCCATGGACTG;RSEQ=CCGAGCGCCCTGCACCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:33,29:0:2,0:26.1:1:29.6:1:1:0:60:9.333:1:0:0.2 0/1:66:2:1,1:41,23:0.0303:2,2:44.5:1:29.5:1:1:1.76614:60:4:0.0308:0:2 -1 23236938 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.23497;SOR=Inf;LSEQ=TGGACTGCCCGAGCGCCCTG;RSEQ=ACCAACTCATGCTGGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:40,36:0:2,0:26:1:30.3:1:1:0:60:11.667:1:0:0.3 0/1:72:2:1,1:41,29:0.0278:2,2:19.5:1:29.5:1:1:1.40686:60:4:0.029:0:1 -1 23236979 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49731;SOR=Inf;LSEQ=TGGCAGAAGGACCGCAACCA;RSEQ=CGGCCCAAGTTCGGCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:33,43:0:2,0:26.3:1:30.6:1:1:0:60:24.333:1:0:0.3 0/1:81:2:1,1:35,44:0.0247:2,2:27.5:1:28.5:1:1:1.25:60:4:0.025:0:1 -1 23237021 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50252;SOR=Inf;LSEQ=GTCAACACGCTAGACAAGAT;RSEQ=ATCCGCAATCCCAACAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:11,26:0:2,0:22.6:1:31.6:1:1:0:60:74:1:0:0.2 0/1:48:2:1,1:12,34:0.0417:2,2:36.5:1:28:1:0.47252:2.76:60:4:0.0435:0:1 -1 23238023 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCAGCCTGAGGGGTGTTC;RSEQ=CTTGGGGACCTGGTGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 23880912 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01501;LSEQ=TGCCACTGACTGACCCCTAA;RSEQ=AGGAGAACTAATCAGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:253:181:164,17:61,10:0.7154:2,2:23.4:1:29.9:1:0.36446:1.58:60:35.2:0.7126:0:1.2 0/1:334:12:8,4:279,43:0.0359:2,2:18.5:1:29.5:1:0.07251:3.22799:60:24:0.0366:0:1.3 -1 23881005 . G A 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00735;LSEQ=GTGGGGAAGGACTTCGAGAG;RSEQ=GCAGAGGCTTCCCGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1198:904:507,397:165,128:0.7546:2,2:25.4:1:30.2:1:1:1.00938:60:44.2:0.7543:0:1.2 0/1:1542:34:16,18:788,718:0.022:2,2:25.4:1:29.8:1:0.60431:1.23451:60:68:0.0224:0:1.2 -1 23881310 . G A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGAGGCCGCGCTGCTGGC;RSEQ=GAGCGGCGGGGGCGCCGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5:1:31:1:1:0:60:4:1:0:1 1/0:2:1:0,1:0,1:0.5:0,0:10:0:33:0:1:0:60:2:0.5:0:1 -1 23881587 . G A 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCCGCCGGTGGGGAGCG;RSEQ=CTGTCTCCGGGGAGGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:30:0:1:0:60:4:1:0:1.5 -1 23884172 . T C 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=ACCAACTTGCTGGGCAAGCT;RSEQ=GCACCAGTCTCTGGTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:52,229:0:2,0:21.7:1:30.2:1:1:0:60:69.25:1:0:0.1 0/1:359:14:3,11:76,268:0.039:2,2:18:1:29.2:1:1:1.03971:60:28:0.0395:0:1.2 -1 23884206 . A AG 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37895;SOR=0.63355;LSEQ=GTTTCATCTCTGAAATAATG;RSEQ=GCAGAGCCCAGAACTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:140:6,134:2,6:0.9459:2,1:21.2:1:30.9:1:0.06097:7.23207:60:139:0.9456:0.2635:0.1 1/1:169:155:9,146:2,12:0.9172:2,2:24:1:30.5:1:0.22758:2.68124:59.9:76.5:0.9107:0.1953:0.1 -1 23885230 . C G 127 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00269;SOR=0.06591;LSEQ=GCCACTGCGGGAGGGCAGGG;RSEQ=CCAGGCGCATTTAAGGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:19:19,0:13,0:0.5938:1,1:26.3:1:30.1:1:1:0:60:18:0.6207:0:1.1 0/1:12:1:1,0:11,0:0.0833:0,0:47:0:30:0:1:0:60:2:0.0833:0:1 -1 23885431 . G A 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGGAGATACTCACCTGGA;RSEQ=GTGTCAGGACACGGCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:983:0:0,0:615,367:0:2,0:25.8:1:31.5:1:1:0:60:60.375:0.999:0:0.5 0/1:1319:55:32,23:745,516:0.0417:2,2:27.7:1:29.4:1:0.88959:1.03772:60:26.5:0.0408:0:1.5 -1 23885480 . A C 215 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGCTCCTTTTGTCGTTGG;RSEQ=GATGACAAGTTCCGGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1293:0:0,0:644,647:0:2,0:26:1:30.5:1:1:0:60:63.55:0.9992:0:0.8 0/1:1809:137:72,65:837,833:0.0757:2,2:25.4:1:30.4:1:0.59503:1.10:59.9:44.667:0.0754:0:2.2 -1 23885498 . T C 324 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.6595;LSEQ=GGAGATGACAAGTTCCGGAG;RSEQ=GAGCTCGGCTGTCTGATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1303:1024:508,516:135,144:0.7859:2,2:25.4:1:30.7:1:0.73588:1.05:60:59.235:0.7843:0:1.1 1/1:1773:1523:752,771:116,134:0.859:2,2:25.5:1:30.7:1:0.41285:1.13:60:88.588:0.8581:0:1.3 -1 23885599 . T C 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05608;LSEQ=TGCCTGGGTGTTCAGCCCTG;RSEQ=CCCGACTTCGAGGCTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1223:943:496,447:150,129:0.7711:2,2:25:1:31.2:1:0.78485:1.0479:60:33.926:0.7685:0:1.1 0/1:1437:228:120,108:617,590:0.1587:2,2:22.6:1:30.6:1:0.71805:1.06:60:27.5:0.156:0:1.2 -1 23886073 . T C 116 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0377;SOR=2.76082;LSEQ=AAAATGGCCCGCCTCGGCCC;RSEQ=GCCCCCGCCGGCCCTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:12:0,12:1,57:0.1714:1,0:19.2:1:28.8:1:1:0:60:11:0.1618:0:1 0/1:41:15:0,15:0,26:0.3659:1,1:20.9:1:29.7:1:1:0:60:30:0.3659:0:1 -1 23886299 . GC G 32 d7;v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=CCAGATCTTTGAGCTTCCCT;RSEQ=CCCCTGCCAGTCCGCCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:27:1:31.8:1:1:0:60:12:1:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:32.5:1:1:0:60:4:1:0:0.5 -1 23886338 . G GC 72 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGCCCAACACTGGTTCGA;RSEQ=CCACAGCTCCTCCGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,1:0.8333:0,2:33.4:1:31.4:1:1:0:60:10:0.8333:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 23887354 . A AG 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCACTGATTAACAGGACA;RSEQ=GGGGGCTCAGAGCCAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:15:1:32.3:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30.5:1:1:0:60:4:1:0:0 -1 23889095 . G C 220 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTGCATCGCCCCAACCGC;RSEQ=AGCGGCTTGTGAATTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1451:0:0,0:738,713:0:2,0:25.4:1:30.4:1:1:0:60:102.643:1:0:0.2 0/1:2006:138:66,72:943,919:0.0688:2,2:27.8:1:31:1:0.53787:1.11933:60:276:0.0692:0:1.2 -1 23889161 . C CT 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.59688;SOR=1.19552;LSEQ=CAATTGGGGCCCTTTAAAGT;RSEQ=TTTTTTTTTCTTTCTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:955:23:8,15:324,604:0.0241:2,2:29.7:1:30.7:1:1:1.00579:60:46:0.0245:0:0.3 0/1:1291:37:14,23:493,757:0.0287:2,2:32.8:1:29:1:1:1.06987:60:11.333:0.0268:8e-04:0.4 -1 23889378 . AT A 87 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.63781;SOR=0.39178;LSEQ=ATTCAATGTTGTGCTCTCTG;RSEQ=TTTTTTTTTTTTGAGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:0,7:0,16:0.3043:1,0:28.1:1:31:1:1:0:60:14:0.3333:0:1.4 0/1:7:1:0,1:1,5:0.1429:2,0:30:0:32:0:1:0:60:2:0.1429:0:1 -1 25228844 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49298;SOR=Inf;LSEQ=ACCATGGAGAACTGGTAGGA;RSEQ=CCAGAGGATGTCCCGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,19:0:2,0:25.1:1:32.2:1:1:0:60:66:1:0:0.2 0/1:35:2:1,1:17,16:0.0571:2,2:23.5:1:27.5:1:1:1.06069:60:4:0.0606:0:1 -1 25254127 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52159;SOR=Inf;LSEQ=CCACCTGGTTCTTCATGACG;RSEQ=CCGAGGCATTGCGCAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:26.7:1:30.5:1:1:0:60:15:1:0:0.3 0/1:27:2:1,1:15,10:0.0741:2,2:5.5:1:30:1:1:1.47706:60:4:0.0741:0:1 -1 25255982 . C T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54755;SOR=0.59302;LSEQ=TCGCCGCGGCGTCTCGGGCA;RSEQ=CTCCCATCCCCACTGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:11:11,0:33,1:0.2444:1,0:19.4:1:31.8:1:1:0:60:22:0.2558:0:1 0/1:25:4:4,0:20,1:0.16:1,0:30.8:1:30.8:1:1:0:60:8:0.16:0:1 -1 25256029 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49847;SOR=Inf;LSEQ=CTGGCTCCCGCAGCTCAGAC;RSEQ=CCCGGAGCCCCAGGGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:76,10:0:2,0:26.1:1:30.3:1:1:0:60:172:1:0:0.2 0/1:95:2:1,1:84,9:0.0211:2,2:19.5:1:27.5:1:0.20045:8.90741:60:4:0.0213:0:1 -1 25256056 . C T 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.76151;LSEQ=GCCCCAGGGCCGGCGCCCTC;RSEQ=CGCCCCGGGTCCCGCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:0,1:124,48:0.0058:2,0:1:0:24:0:0.28324:0:60:2:0.006:0:1 0/1:197:2:1,1:139,56:0.0102:2,2:9:0:32:1:0.49601:2.46912:60:4:0.0104:0:1.5 -1 25256089 . C T 82 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14739;SOR=5.49403;LSEQ=CGCACTCACCTTGAAGGCGA;RSEQ=GGGCAGCGTCTTGTTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:1:0,1:178,142:0.0031:2,0:1:0:26:0:0.44548:0:60:2:0.0031:0:1 0/1:414:7:3,4:228,178:0.0169:2,2:26.6:1:29.3:1:0.70437:1.7056:60:14:0.0172:0:1.1 -1 25256168 . G A 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06594;SOR=Inf;LSEQ=CTGTCGGTGCGCACGAGCTC;RSEQ=CCTGCGTGGTCCGCCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:112,195:0:2,0:26.4:1:30.8:1:1:0:60:50.167:1:0:0.1 0/1:363:5:3,2:126,232:0.0138:2,2:18.4:1:28:1:0.35192:2.75:60:10:0.0139:0:1.2 -1 25256181 . G A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67011;SOR=0.59096;LSEQ=CGAGCTCGCCTGCGTGGTCC;RSEQ=CCAGCACGTCCACCATCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:76,155:0.0128:2,2:6:1:27.3:1:0.2583:4.05:60:6:0.0132:0:1 0/0:264:2:2,0:87,175:0.0076:2,0:1:0:26.5:1:0.1128:0:60:4:0.0077:0:1 -1 25256191 . C A 41 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06025;SOR=Inf;LSEQ=TGCGTGGTCCGCCAGCACGT;RSEQ=CACCATCGAGCGCACCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:50,144:0:2,0:22.5:1:30.9:1:1:0:60:31.333:1:0:0.1 0/1:192:4:3,1:51,137:0.0208:2,2:11.3:1:20.5:1:0.06815:7.96:60:3:0.016:0:1.5 -1 25256202 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23182;SOR=Inf;LSEQ=CCAGCACGTCCACCATCGAG;RSEQ=GCACCTCGGGCCGGGCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:25,108:0:2,0:20.8:1:30.4:1:1:0:60:43.333:1:0:0.1 0/1:124:2:1,1:25,97:0.0161:2,2:22.5:1:32:1:0.37674:3.82:60:4:0.0164:0:1 -1 25257366 . C A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGCGCGGCTTTGGTCC;RSEQ=AGCCTCGGTGGCCCCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:28:1:1:0:60:4:1:0:2 -1 25620754 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12981;SOR=0;LSEQ=AAAGCTGAAAATGCCAAAAG;RSEQ=CCTGCCTTGGCAGCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:130,69:0.01:2,2:50:0:30:1:1:1.8778:49:4:0.0101:0:1 0/0:356:0:0,0:228,128:0:2,0:24.8:1:31.3:1:1:0:40.7:88:1:0:0.1 -1 25620841 . G A 38 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68351;SOR=0.64111;LSEQ=CAGTGACCATGAAGAGTGAG;RSEQ=GCTGCAGCCAGGGAATAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:3:2,1:102,144:0.012:2,2:11.7:1:23.3:1:0.57289:2.81:42:2:0.0083:0:1 0/0:387:3:3,0:156,228:0.0078:2,0:1.3:1:24.3:1:0.06858:0:48.3:6:0.0079:0:1 -1 25621050 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12047;SOR=0;LSEQ=AAGAAATGCTGAGATATGAG;RSEQ=AGGTCTGACCACTGGAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:52,39:0.0215:2,2:12:1:28:1:1:1.32915:38.5:4:0.0215:0:1 0/0:174:0:0,0:111,63:0:2,0:21.6:1:31.2:1:1:0:32.6:86:1:0:0.1 -1 25621130 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55452;SOR=Inf;LSEQ=CACTCAGCCTCCAGGGAACC;RSEQ=CCATCTCGTTCCTGAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:60,96:0:2,0:26.9:1:31.6:1:1:0:39.2:312:1:0:0.1 0/1:296:3:2,1:108,185:0.0101:2,2:26.3:1:28.3:1:0.55768:3.41:50:6:0.0102:0:1 -1 25724146 . T C 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGTCACTGATGATGTCAG;RSEQ=TCCTGCCCTTCAGCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:33:1:1:0:48.5:4:1:0:1 -1 25725309 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22509;SOR=0;LSEQ=CAGACCTGCTCATATCTCAG;RSEQ=ATTTCTTCAGGACCGACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:55,142:0.01:2,2:10:1:28:1:0.48465:2.57:39:4:0.0101:0:1.5 0/0:221:0:0,0:46,175:0:2,0:23.5:1:31.5:1:1:0:30.2:109.5:1:0:0.1 -1 25725485 . G T 48 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01954;SOR=Inf;LSEQ=TGAATCCTTGCTCTGCGACG;RSEQ=ACTATTCCCTGGCTGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:315,147:0:2,0:20.9:1:30.8:1:1:0:34.9:65:1:0:0.1 0/1:388:5:0,5:266,117:0.0129:2,0:6.4:1:20.8:1:0.0029:0:42:4:0.0104:0:1 -1 27022832 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19707;SOR=0;LSEQ=GGACTGGGCCCCGGGGCGGG;RSEQ=TGGGAGGGGGGGAGAAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:32,16:0.04:2,2:25:1:30:1:1:1.97043:60:4:0.0408:0:1 0/0:62:0:0,0:44,18:0:2,0:24.1:1:29.9:1:1:0:60:30:1:0:0.6 -1 27022840 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=7.000;MSILEN=1;SSF=0.15533;SOR=0;LSEQ=CCCCGGGGCGGGGTGGGAGG;RSEQ=GGGGAGAAGACGAAGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:37,22:0.0328:2,2:25.5:1:29.5:1:1:1.66686:60:4:0.0339:0:1.5 0/0:93:0:0,0:54,37:0:2,0:21:1:29.9:1:1:0:60:29.333:0.9778:0:0.5 -1 27022903 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52513;SOR=Inf;LSEQ=ACAGCGGGGATCATGGCCGC;RSEQ=CAGGTCGCCCCCGCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:48,65:0:2,0:24.9:1:30.5:1:1:0:60:27.25:1:0:0.4 0/1:181:2:1,1:83,95:0.011:2,2:28:0:32:0:1:1.14:60:4:0.0113:0:1 -1 27022905 . A C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52862;SOR=Inf;LSEQ=AGCGGGGATCATGGCCGCGC;RSEQ=GGTCGCCCCCGCCGCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:47,65:0:2,0:24.6:1:30.6:1:1:0:60:55:1:0:0.4 0/1:185:2:1,1:85,98:0.0108:2,2:25.5:1:28.5:1:1:1.15:60:4:0.0111:0:1 -1 27022910 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52344;SOR=Inf;LSEQ=GGATCATGGCCGCGCAGGTC;RSEQ=CCCCCGCCGCCGCCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:46,63:0:2,0:23.6:1:31.2:1:1:0:60:108:1:0:0.3 0/1:172:2:1,1:76,94:0.0116:2,2:25:0:32:0:1:1.24:60:4:0.0117:0:1.5 -1 27022916 . G A 25 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.53292;SOR=Inf;LSEQ=TGGCCGCGCAGGTCGCCCCC;RSEQ=CCGCCGCCAGCAGCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:40,55:0:2,0:24.1:1:30.7:1:1:0:60:30.667:1:0:0.3 0/1:163:2:1,1:70,91:0.0123:2,2:5:0:25.5:1:1:1.30:60:4:0.0124:0:1 -1 27022935 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54233;SOR=Inf;LSEQ=CGCCGCCGCCAGCAGCCTGG;RSEQ=CAACCCGCCGCCGCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:27,41:0:2,0:22.5:1:31.9:1:1:0:60:33:1:0:0.2 0/1:126:2:1,1:53,71:0.0159:2,2:7:0:27:1:1:1.34:60:4:0.0161:0:1.5 -1 27022939 . CCCG C 84 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.0881;SOR=Inf;LSEQ=GCCGCCAGCAGCCTGGGCAA;RSEQ=CCGCCGCCGCCGCCCTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:24,38:0:2,0:21:1:31.5:1:1:0:60:124:0.9841:0:0.2 0/1:111:6:2,4:46,59:0.0541:2,2:31.8:1:32.8:1:0.69666:1.55332:60:12:0.0561:0:0.2 -1 27022978 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TCGGAGCTGAAGAAAGCCGA;RSEQ=CAGCAGCAGCGGGAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:24,23:0:2,0:15.6:1:32.2:1:1:0:60:94:1:0:0.1 0/1:97:2:1,1:47,48:0.0206:2,2:12:0:30.5:1:1:1.02:60:4:0.0208:0:1.5 -1 27022998 . CG C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.15234;SOR=0;LSEQ=GCAGCAGCAGCGGGAGGAGG;RSEQ=GGGGGCGAGGCGGCGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:35,32:0.029:2,2:43:1:32:1:1:1.09232:60:4:0.0294:0:0 0/0:107:0:0,0:52,55:0:2,0:22.6:1:29.8:1:1:0:60:106:1:0:0.4 -1 27023007 . AGGC A 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.14578;SOR=0;LSEQ=GCGGGAGGAGGCGGGGGGCG;RSEQ=GGCGGCGGCGGCAGCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:39,33:0.027:2,2:40:1:33:1:1:1.17914:60:4:0.0286:0:0 0/0:119:0:0,0:61,58:0:2,0:25.3:1:30.7:1:1:0:60:58.5:1:0:0.4 -1 27023009 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.52284;SOR=Inf;LSEQ=GGGAGGAGGCGGGGGGCGAG;RSEQ=CGGCGGCGGCGGCAGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:39,33:0:2,0:26.8:1:31.5:1:1:0:60:71:1:0:0.3 0/1:117:2:1,1:61,54:0.0171:2,2:17:0:31.5:1:1:1.12845:60:4:0.0177:0:1.5 -1 27023016 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51932;SOR=Inf;LSEQ=GGCGGGGGGCGAGGCGGCGG;RSEQ=GGCGGCAGCGGCCGAGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:50,40:0:2,0:26.2:1:31.1:1:1:0:60:180:1:0:0.3 0/1:137:2:1,1:73,62:0.0146:2,2:20.5:1:27.5:1:1:1.17601:60:4:0.0149:0:1.5 -1 27023019 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.30289;SOR=0.2116;LSEQ=GGGGGGCGAGGCGGCGGCGG;RSEQ=GGCAGCGGCCGAGCGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:3:1,2:53,41:0.0309:2,2:13:1:28.3:1:0.58266:2.56048:60:6:0.0319:0:1 0/0:150:1:0,1:82,67:0.0067:2,0:1:0:26:0:0.45333:0:60:2:0.0068:0:1 -1 27023020 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51972;SOR=Inf;LSEQ=GGGGGCGAGGCGGCGGCGGC;RSEQ=GCAGCGGCCGAGCGCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:60,43:0:2,0:24.8:1:30.6:1:1:0:60:206:1:0:0.3 0/1:157:2:1,1:87,67:0.0127:2,2:23:0:32.5:1:1:1.2963:60:4:0.0129:0:1.5 -1 27023063 . G T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65471;SOR=2.44663;LSEQ=TGAAGGCAGCCGCCGGGCAG;RSEQ=AAAGCGAGGGCCCCGCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:1:0,1:123,114:0.0042:2,0:1:0:24:0:0.48319:0:60:2:0.0043:0:1 0/1:391:4:1,3:195,192:0.0102:2,2:14.3:1:25:1:0.37179:3.03909:60:8:0.0104:0:1.5 -1 27023131 . C T 51 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41431;SOR=3.14638;LSEQ=CTGCAGGACGGGGCCGAGAG;RSEQ=AATGGGGGTGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:1:0,1:107,135:0.0041:2,0:1:0:24:0:1:0:60:2:0.0042:0:1 0/1:389:5:1,4:182,198:0.0129:2,2:5.8:1:22.2:1:0.3748:3.66586:60:4:0.0108:0:1 -1 27023140 . TGGC T 81 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03138;SOR=0.17547;LSEQ=GGGGCCGAGAGCAATGGGGG;RSEQ=GGCGGCGGCGGAGCCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:7:3,4:93,125:0.0311:2,2:19.1:1:29.1:1:1:1.01:60:6:0.0271:0.0133:0.6 0/0:358:2:1,1:169,182:0.0056:2,2:15:1:32:0:1:1.08:60:4:0.0056:0:0 -1 27023143 . C T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.30299;SOR=Inf;LSEQ=GCCGAGAGCAATGGGGGTGG;RSEQ=GGCGGCGGCGGAGCCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:90,120:0:2,0:17.2:1:30.4:1:1:0:60:41:0.9903:0:0.3 0/1:355:4:1,3:170,179:0.0113:2,2:9.3:1:28:1:0.6236:2.84174:60:8:0.0117:0:1.3 -1 27023144 . GGCGGCGGCGGAGCCGGCA G 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.0237;SOR=0;LSEQ=CCGAGAGCAATGGGGGTGGC;RSEQ=GCGGCGGCGGGCCCGGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:4:2,2:98,120:0.0179:2,2:20:1:30.8:1:1:1.22:60:8:0.0183:0.0179:0 0/0:343:0:0,0:169,170:0:2,0:18.9:1:31.4:1:1:0:60:66.8:0.9882:0:0.4 -1 27023148 . G A 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.68928;SOR=0.673;LSEQ=GAGCAATGGGGGTGGCGGCG;RSEQ=CGGCGGAGCCGGCAGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:2,1:104,121:0.0129:2,2:14.3:1:27.3:1:0.59867:2.32:60:6:0.0133:0:1 0/0:345:3:1,2:171,170:0.0087:2,2:35.3:1:30.7:1:1:2.00782:60:6:0.009:0:1.3 -1 27023160 . G A 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41005;SOR=3.37848;LSEQ=TGGCGGCGGCGGCGGAGCCG;RSEQ=CAGCGGCGGCGGGCCCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:1:1,0:151,117:0.0037:2,0:1:0:14:0:1:0:60:0:0:0:1 0/1:404:5:4,1:212,183:0.0124:2,2:14:1:26.4:1:0.37991:3.44:60:10:0.0129:0:1.4 -1 27023167 . C T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.65358;SOR=2.80848;LSEQ=GGCGGCGGAGCCGGCAGCGG;RSEQ=GGCGGGCCCGGCGCGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:1:0,1:163,114:0.0036:2,0:1:0:15:0:0.41367:0:60:0:0:0:2 0/1:398:4:2,2:224,170:0.0101:2,2:14.8:1:26.3:1:1:1.31671:60:8:0.0104:0:1 -1 27023170 . C T 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08253;SOR=Inf;LSEQ=GGCGGAGCCGGCAGCGGCGG;RSEQ=GGGCCCGGCGCGGAGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:169,110:0:2,0:18.5:1:31:1:1:0:60:38.857:1:0:0.3 0/1:403:5:2,3:230,167:0.0124:2,2:22.2:1:27.2:1:0.65416:2.06212:60:4:0.0101:0:1.2 -1 27023175 . C T 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15121;SOR=4.86672;LSEQ=AGCCGGCAGCGGCGGCGGGC;RSEQ=CGGCGCGGAGCCGGACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:1:0,1:185,118:0.0033:2,0:1:0:30:0:0.39145:0:60:2:0.0034:0:1 0/1:445:7:1,6:257,180:0.0157:2,2:9:1:26.9:1:0.02337:8.53029:60:14:0.0161:0:1.1 -1 27023178 . G T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.08337;SOR=Inf;LSEQ=CGGCAGCGGCGGCGGGCCCG;RSEQ=CGCGGAGCCGGACCTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:198,123:0:2,0:21.2:1:31.5:1:1:0:60:39.125:0.9968:0:0.4 0/1:468:5:1,4:272,190:0.0107:2,2:12:1:28.4:1:0.16544:5.70691:60:10:0.011:0:1.2 -1 27023179 . C A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.08481;SOR=Inf;LSEQ=GGCAGCGGCGGCGGGCCCGG;RSEQ=GCGGAGCCGGACCTGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:203,124:0:2,0:21.5:1:31.1:1:1:0:60:45.714:0.9938:0:0.3 0/1:484:5:3,2:282,195:0.0103:2,2:15.6:1:23.4:1:1:1.04:60:4:0.0085:0:2.2 -1 27023187 . C T 52 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.496;SOR=0.52683;LSEQ=CGGCGGGCCCGGCGCGGAGC;RSEQ=GGACCTGAAGAACTCGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:5:1,4:236,147:0.0129:2,2:9.6:1:22.6:1:0.07764:6.39262:60:1.5:0.0079:0:1 0/0:586:4:0,4:340,241:0.0068:2,0:1:0:23:1:0.03033:0:60:3:0.0052:0:1.5 -1 27023252 . C T 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAACAATAACCTCACGGAG;RSEQ=CGCCCGGCGGCGGCGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:0:0,0:310,300:0:2,0:25.7:1:31.3:1:1:0:60:54.455:0.9983:0:0.3 0/1:908:96:50,46:416,393:0.1057:2,2:22.4:1:28.9:1:0.91445:1.03:60:47:0.1056:0:1.4 -1 27023312 . G A 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02403;SOR=Inf;LSEQ=GGGCGCCTCCTCACTCAGCC;RSEQ=CGGCCGCCTTGCCGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:226,261:0:2,0:22.8:1:30.8:1:1:0:60:43.273:1:0:0.3 0/1:682:8:6,2:332,342:0.0117:2,2:5.4:1:26.6:1:0.17369:3.09:60:16:0.012:0:1.5 -1 27023450 . AGCG A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.6351;SOR=0.83135;LSEQ=CTGGCCTGGCAGCGCTGCAG;RSEQ=GCGGCGGCGGGGGCCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1126:20:12,8:637,468:0.0178:2,2:22.7:1:31.8:1:1:1.10:60:40:0.0181:0.0036:0.2 0/1:1418:21:11,10:780,612:0.0148:2,2:24.2:1:30.2:1:0.82595:1.15852:60:20:0.0144:0.0035:0.2 -1 27023928 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.63889;SOR=2.25723;LSEQ=GGCTGCGGCGGCGGCAGCTG;RSEQ=GGCGGCGGCCGCCTCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:1:0,1:102,112:0.0047:2,0:1:0:26:0:1:0:60:2:0.0048:0:1 0/1:287:3:1,2:139,145:0.0105:2,2:8:1:30:1:1:1.91306:60:6:0.0108:0:1 -1 27023936 . G A 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.03548;SOR=0;LSEQ=CGGCGGCAGCTGCGGCGGCG;RSEQ=CCGCCTCGGGAGGGGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:4:3,1:112,90:0.0193:2,2:8:1:28.5:1:0.63162:2.40:60:8:0.0201:0:1.3 0/0:268:0:0,0:146,122:0:2,0:23.4:1:30.9:1:1:0:60:32.5:1:0:0.4 -1 27023944 . G T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.15144;LSEQ=GCTGCGGCGGCGGCCGCCTC;RSEQ=GGAGGGGCCCAACAAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:2:1,1:125,90:0.0092:2,2:35.5:1:32:1:1:1.38673:60:4:0.0094:0:2 0/1:283:3:1,2:158,121:0.0106:2,2:7.7:1:28.7:1:0.5822:2.60281:60:6:0.0108:0:1.7 -1 27023995 . C T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.69855;SOR=1.58811;LSEQ=CCCATGAGCCCCGGGAGCAG;RSEQ=GGCGGCGGGGGGCAGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:2:1,1:134,106:0.0083:2,2:29:1:30.5:1:1:1.26291:60:4:0.0084:0:1 0/1:306:4:2,2:168,133:0.0131:2,2:39.5:1:31:1:1:1.26217:60:8:0.0133:0:1 -1 27024022 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17951;SOR=0;LSEQ=GGGGGGCAGCCGCTCGCCCG;RSEQ=ACCCCTCAGGTACACAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:112,83:0.0101:2,2:27.5:1:30.5:1:1:1.3473:60:4:0.0102:0:1.5 0/0:270:0:0,0:145,124:0:2,0:26.1:1:30.2:1:1:0:60:25.9:0.9962:0:0.3 -1 27024030 . AG A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06729;SOR=0;LSEQ=GCCGCTCGCCCGGACCCCTC;RSEQ=GTACACAGCTGAGTGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:3:2,1:100,79:0.0165:2,2:19.3:1:28.7:1:1:1.58:60:6:0.0168:0.0055:0.3 0/0:264:0:0,0:137,127:0:2,0:21.9:1:30.6:1:1:0:60:131:1:0:0.3 -1 27024056 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51101;SOR=Inf;LSEQ=ACAGCTGAGTGGGGAGGGGG;RSEQ=TGGGGCGAGCGTGGTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:43,64:0:2,0:20.6:1:31.5:1:1:0:60:52.5:1:0:0.1 0/1:148:2:0,2:61,85:0.0135:2,0:43:1:30:1:0.51213:0:60:4:0.0141:0:1 -1 27056071 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20491;SOR=Inf;LSEQ=ACAGACTAAAAAAACCTGTG;RSEQ=ACTTGGGTTATATATTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:148,11:0:2,0:24.3:1:30.1:1:1:0:60:158:1:0:0.1 0/1:132:2:1,1:109,21:0.0152:2,2:22.5:1:26.5:1:0.30662:5.09448:60:4:0.0153:0:1 -1 27056093 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10971;SOR=Inf;LSEQ=CTTGGGTTATATATTCAGTG;RSEQ=CCAGAGGCCATCAAAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:201,44:0:2,0:23.7:1:31:1:1:0:60:34:1:0:0.1 0/1:226:3:1,2:168,55:0.0133:2,2:17.7:1:30.3:1:0.15749:6.04856:60:6:0.0135:0:1.3 -1 27056354 . G T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25349;SOR=Inf;LSEQ=GGCCTCTCTTATACACAGCA;RSEQ=GTAGATGGTGATTGTGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:62,175:0:2,0:23.3:1:31.1:1:1:0:60:117.5:0.9958:0:0.2 0/1:280:3:1,2:83,194:0.0107:2,2:30.7:1:24:1:1:1.17:60:2:0.0073:0:1.3 -1 27057621 . A C 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGAGAGTCAGTGCTAAA;RSEQ=GTATATTTTCCTTTCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:765:0:0,0:538,227:0:2,0:23.4:1:30.2:1:1:0:60:50:1:0:0.1 0/1:843:77:48,29:491,274:0.0913:2,2:23.8:1:30.4:1:0.80346:1.08254:60:154:0.0929:0:1.1 -1 27058079 . G A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33097;SOR=0.27046;LSEQ=AACTGCCTATTCCCAGCAGC;RSEQ=CTTCCCTCCACCGCAGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:2,1:40,155:0.0152:2,2:17.7:1:28:1:0.11442:7.64:60:6:0.0155:0:1 0/0:242:1:1,0:70,171:0.0041:2,0:1:0:26:0:0.29339:0:60:2:0.0042:0:1 -1 27059748 . C CT 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTGATTTTGTGTGAATA;RSEQ=TTTTTTTTTTTATTTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:13.5:1:28:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 27087177 . CA C 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.12945;SOR=Inf;LSEQ=CAACGAGTGAAACACTGTCT;RSEQ=AAAAAAAAAATTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:0:1,0:26.1:1:30:1:1:0:60:48:1:0:0.1 0/1:14:2:2,0:12,0:0.1429:0,0:8:1:31.5:1:1:0:60:4:0.1429:0.0714:0.5 -1 27087188 . A AAT 50 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0.5248;LSEQ=ACACTGTCTCAAAAAAAAAA;RSEQ=TTTTTTTTTTTAATAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:3,0:26,0:0.0968:1,0:9.7:1:31.8:1:1:0:60:6:0.1:0.0645:0.7 0/1:19:1:1,0:16,1:0.0526:1,0:13:0:29:0:1:0:60:2:0.0588:0:4 -1 27087219 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53454;SOR=0;LSEQ=TAATAAAAATAGTATCATGA;RSEQ=TAAAGAACGTGTGTGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:2,0:72,2:0.0263:1,0:21.5:1:28.5:1:1:0:50:4:0.0263:0:4 0/0:43:0:0,0:40,3:0:2,0:23.7:1:30.8:1:1:0:60:42:1:0:0.1 -1 27088546 . A T 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCCATGCAAGTGGCTGCT;RSEQ=AAGAAAATGTAGATGGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:177,7:0:1,0:21.2:1:28.3:1:1:0:60:60.333:1:0:0.1 0/1:140:26:21,5:105,9:0.1857:2,2:21.4:1:29.4:1:0.13786:2.7522:60:52:0.1857:0:1.1 -1 27089389 . G T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34183;SOR=3.47813;LSEQ=AATATTGAATGACATTGTTT;RSEQ=GTGTTCTAGAGTTGAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:1,0:151,27:0.0056:2,0:4:0:31:0:1:0:60:2:0.0057:0:1 0/1:156:3:2,1:131,22:0.0192:2,2:30.3:1:31.3:1:0.38238:2.94843:60:6:0.0195:0:1.3 -1 27089391 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20969;SOR=Inf;LSEQ=TATTGAATGACATTGTTTGG;RSEQ=GTTCTAGAGTTGAGAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:158,31:0:2,0:24.2:1:29.6:1:1:0:60:93.5:1:0:0.1 0/1:161:2:1,1:135,24:0.0124:2,2:27:1:28.5:1:0.28727:5.5318:60:4:0.013:0:1 -1 27089446 . G C 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGTGACTAACCAAGTCTT;RSEQ=TCTTCCTCCCCTCCCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:285,137:0:2,0:26.3:1:32:1:1:0:60:210:1:0:0.1 0/1:469:28:20,8:274,167:0.0597:2,2:30.6:1:31.5:1:0.4212:1.52:60:27:0.0588:0:1.4 -1 27092639 . A G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00572;SOR=Inf;LSEQ=CTAGATGATCACACAGCACT;RSEQ=TTTGGCTCCAGTTCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:186,29:0:2,0:22.9:1:28.4:1:1:0:60:106.5:1:0:0.1 0/1:201:7:5,2:150,43:0.0348:2,2:29.3:1:29.6:1:0.65592:1.39283:60:14:0.0352:0:1 -1 27092698 . A G 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTGTCTCTCTCACTTTCC;RSEQ=TCTTCTTCCTTAGGCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:319,185:0:2,0:25:1:30.2:1:1:0:60:83:0.998:0:0.1 0/1:517:42:27,15:280,195:0.0812:2,2:23.9:1:29.9:1:0.62335:1.25:60:84:0.083:0:1.1 -1 27093096 . C A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20258;SOR=4.31129;LSEQ=ACTCCTTTCAACTTTGTGTC;RSEQ=TATCTTTTTCAGTGATAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:1:1,0:88,277:0.0027:2,0:1:0:26:0:0.24317:0:60:2:0.0028:0:1 0/1:342:4:2,2:91,247:0.0117:2,2:19.8:1:25:1:0.29874:2.71:60:3:0.0088:0:1 -1 27094156 . A G 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAACCTTATGAAGGTAGG;RSEQ=CAGGTGTTAGTAACCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:0:1,0:22.4:1:30.4:1:1:0:60:44:1:0:0 0/1:39:16:15,1:23,0:0.4103:1,1:26.5:1:31.8:1:0.41026:0:60:32:0.4103:0:1.1 -1 27094234 . G T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62918;SOR=2.52397;LSEQ=TTCTGAGACCCTTAGCACAG;RSEQ=CTTTGAATCTGACCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:1,0:140,47:0.0053:2,0:22:0:32:0:1:0:60:2:0.0055:0:1 0/1:226:3:1,2:159,63:0.0133:2,2:5:1:28.7:1:0.20098:5.00567:60:6:0.0135:0:1 -1 27097515 . A G 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAAGAACTGTGGTTCTACA;RSEQ=AGATGAATACCTTACAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:149,14:0:2,0:23.7:1:30.5:1:1:0:60:326:1:0:0 0/1:140:24:22,2:103,13:0.1714:2,2:18.7:1:31.5:1:1:1.39:60:48:0.1727:0:1.1 -1 27097839 . C A 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.37589;SOR=3.67639;LSEQ=TAAGGATGGGGTCAGCGGCC;RSEQ=CACCAAGGCTGAGAGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:1:1,0:102,257:0.0028:2,0:1:0:25:0:0.28611:0:60:2:0.0029:0:1 0/1:394:4:2,2:126,264:0.0102:2,2:11:1:24.3:1:0.59853:2.09:60:3:0.0078:0:1 -1 27097856 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24907;SOR=Inf;LSEQ=GCCCCACCAAGGCTGAGAGG;RSEQ=CCTGTTGCCCTGGCCTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:56,220:0:2,0:23.4:1:31.7:1:1:0:60:54.2:1:0:0.1 0/1:290:3:2,1:63,224:0.0103:2,2:12:1:27.7:1:0.12719:7.05:60:6:0.0105:0:1 -1 27098890 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.51824;SOR=0;LSEQ=TCAGGCTTTAAAGGCCTTAG;RSEQ=AAGAACTTTCCCAAAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:2,0:79,0:0.0247:1,0:17:1:28.5:1:1:0:60:4:0.025:0:1 0/0:53:0:0,0:51,2:0:1,0:21.6:1:30.9:1:1:0:60:52:1:0:0.1 -1 27098928 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50571;SOR=0;LSEQ=GATTCTGGGTCGTTCGTGTG;RSEQ=TTGTGTGAGAGTTAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:172,23:0.0102:2,2:31:1:32:1:0.22936:7.34332:60:4:0.0102:0:1 0/0:155:0:0,0:137,18:0:2,0:20.4:1:29.5:1:1:0:60:76.5:1:0:0.1 -1 27098960 . C T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18762;SOR=4.68257;LSEQ=TTAAACACTGTCATGCCAAG;RSEQ=AAACTACTCAACTTGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:1:0,1:268,91:0.0028:2,0:1:0:23:0:0.25556:0:60:2:0.0028:0:1 0/1:310:4:2,2:225,81:0.0129:2,2:18.3:1:23:1:0.29143:2.76701:60:3:0.0099:0:1.5 -1 27099238 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.10056;SOR=Inf;LSEQ=TCCCAGCCAGTGACTCCTGC;RSEQ=TGTCCTTTGTTATATTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:155,128:0:2,0:23.1:1:30.7:1:1:0:60:55.6:1:0:0.1 0/1:247:3:0,3:150,94:0.0121:2,0:5.7:1:27.7:1:0.05942:0:60:6:0.0123:0:1 -1 27099688 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12666;SOR=Inf;LSEQ=TAATAAGTACATGCTTTTCG;RSEQ=TGGTTGGGGCCTCTTTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:44,13:0:2,0:23.8:1:32.1:1:1:0:60:56:1:0:0.1 0/1:32:2:2,0:25,5:0.0625:2,0:22:1:29:0:1:0:60:4:0.0625:0:1 -1 27099776 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24081;SOR=Inf;LSEQ=TGAAGAGGGCCTGGGTCAAA;RSEQ=GGTAGATTACCAGGCTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:162,44:0:2,0:23.1:1:32.1:1:1:0:60:102:1:0:0.1 0/1:199:2:1,1:154,43:0.0101:2,2:26.5:1:29:1:0.39419:3.55169:60:4:0.0104:0:1 -1 27100243 . C T 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTCGGTGCTGCTATGGAT;RSEQ=AGGCTTCGCCACTGCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:0:0,0:355,299:0:2,0:24.7:1:31.6:1:1:0:60:53.5:1:0:0.2 0/1:680:36:18,18:351,293:0.0529:2,2:29:1:28.3:1:0.6105:1.19763:60:35:0.0519:0:1.1 -1 27100475 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19648;SOR=Inf;LSEQ=TCTAACGTGTTGAAGTCTAA;RSEQ=AAGCTCACTTTAGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:14,170:0:2,0:20.1:1:31.2:1:1:0:60:35.8:1:0:0.1 0/1:147:2:0,2:10,135:0.0136:2,0:10:1:28.5:1:1:0:60:4:0.0138:0:1.5 -1 27102188 . A G 177 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=40.10535;LSEQ=CAACAGCATCATGACCTTCA;RSEQ=CCTCAGTCAGGTGAGTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:697:1:1,0:285,411:0.0014:2,0:30:0:14:0:0.41033:0:60:0:0:0:2 0/1:825:45:21,24:340,438:0.0545:2,2:23.8:1:32.3:1:0.75806:1.13:60:90:0.0554:0:1.1 -1 27105437 . G T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=2.00696;LSEQ=ACTGATACAGAAGACTTGGG;RSEQ=AGGTCTCTCAAGTCAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:1,0:165,26:0.0052:2,0:20:0:11:0:1:0:60:0:0:0:7 0/1:193:2:2,0:159,32:0.0104:2,0:26.5:1:31.5:1:1:0:60:4:0.0104:0:1 -1 27105469 . G A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37576;SOR=3.6842;LSEQ=GTCAATAATTCTGTTCTTAG;RSEQ=CCACTTTTCTCCCTTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:1:1,0:250,107:0.0028:2,0:15:0:25:0:1:0:60:2:0.0029:0:2 0/1:391:4:3,1:274,112:0.0102:2,2:24.8:1:24.8:1:1:1.23:60:3:0.0078:0:1.5 -1 27106967 . G A 68 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10057;SOR=0.16986;LSEQ=AGTGCAGAAGGGCAGTATCG;RSEQ=CAACCTCCTGGGCTTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:5:2,3:230,233:0.0107:2,2:19.8:1:29.4:1:1:1.47945:60:10:0.0109:0:1.2 0/0:547:1:1,0:268,278:0.0018:2,0:1:0:24:0:0.49177:0:60:2:0.0018:0:1 -1 27106978 . G A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13038;SOR=5.24175;LSEQ=GCAGTATCGGCAACCTCCTG;RSEQ=GCTTCCTAGAGGACAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:1:1,0:237,231:0.0021:2,0:1:0:28:0:1:0:60:2:0.0022:0:1 0/1:541:6:5,1:268,267:0.0111:2,2:13.3:1:25.3:1:0.21626:4.97:60:5:0.0095:0:1.2 -1 27107263 . TC T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.76894;SOR=1.11761;LSEQ=CATGACAGCCGTGGGACACC;RSEQ=CCCCCCCCGTGTGTGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:20:7,13:180,254:0.0441:2,2:28.8:1:31.3:1:0.64709:1.31531:60:40:0.0455:0.0044:0.2 0/1:592:29:13,16:247,312:0.049:2,2:29.7:1:30:1:1:1.03:60:28:0.049:0.0017:0.5 -1 27107272 . CGT C 85 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.08534;SOR=5.53791;LSEQ=CGTGGGACACCTCCCCCCCC;RSEQ=GTGTGTGTGCGTGTGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:0,1:160,242:0.0024:2,0:20:0:28:0:1:0:60:2:0.0026:0:0 0/1:522:7:4,3:215,297:0.0134:2,2:28:1:30.3:1:0.46252:1.84:60:14:0.0139:0:0.1 -1 27107313 . T A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11431;SOR=0;LSEQ=AGAACTTAGAAACTGACTGT;RSEQ=GCCCTTTATTTATGCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:3:2,1:66,180:0.012:2,2:11:1:27:1:0.18191:5.41:60:6:0.0124:0:1 0/0:263:0:0,0:71,191:0:2,0:20.2:1:29.2:1:1:0:60:31.75:1:0:0.3 -1 27107332 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49835;SOR=Inf;LSEQ=TTGCCCTTTATTTATGCAAA;RSEQ=CCACCTCAGAATCCAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:15,135:0:2,0:24.1:1:29.2:1:1:0:60:49:1:0:0.2 0/1:152:2:1,1:28,122:0.0132:2,2:20:1:29:1:0.3462:4.30:60:4:0.0135:0:1 -1 27533330 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24384;SOR=Inf;LSEQ=TTAATAGTTAATGTCTCCTG;RSEQ=TATGATTCCATCCTGAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:110,33:0:2,0:21.7:1:31:1:1:0:60:46.667:1:0:0.2 0/1:140:2:1,1:103,35:0.0143:2,2:37:1:31.5:1:0.44954:2.9155:60:4:0.0147:0:1 -1 27533356 . C T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.26459;SOR=Inf;LSEQ=TTCCATCCTGAGCGGCTGTT;RSEQ=TCTTGAGCAGCGTTCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:141,75:0:2,0:25.5:1:31.1:1:1:0:60:71:1:0:0.2 0/1:290:3:0,3:176,111:0.0103:2,0:12.7:1:21.3:1:0.05977:0:60:2:0.007:0:1.3 -1 27533368 . G T 147 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02011;LSEQ=CGGCTGTTCTCTTGAGCAGC;RSEQ=TTCATTTATCTCCGTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:31:17,14:135,83:0.1245:2,2:26.1:1:29.7:1:0.55535:1.33784:60:30:0.1215:0:1.1 0/0:352:1:0,1:203,148:0.0028:2,0:1:0:27:0:0.4233:0:60:2:0.0029:0:1 -1 27533400 . C A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06282;SOR=0;LSEQ=CCGTCTGCCTTCTGTCCCAC;RSEQ=TAAGTGTGTGCCGCCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:126,130:0.0116:2,2:30.3:1:29.3:1:0.6192:2.06:60:6:0.0117:0:1 0/0:391:0:0,0:201,190:0:2,0:28.7:1:30.8:1:1:0:60:390:1:0:0.2 -1 27533640 . G T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00062;SOR=Inf;LSEQ=ACAAAGGCAGTCCAATTAAA;RSEQ=TAACACTGGCAACTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:107,85:0:2,0:21.1:1:31.4:1:1:0:58.3:23:1:0:0.2 0/1:277:15:8,7:138,124:0.0542:2,2:26.5:1:29.2:1:1:1.03:57.1:30:0.0543:0:1.1 -1 27533788 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25557;SOR=Inf;LSEQ=AGTAGCTGTGGAGGAAGATG;RSEQ=AGAGTCAGAAGATGAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:81,142:0:2,0:24.2:1:32.1:1:1:0:48.8:446:1:0:0.1 0/1:271:3:1,2:115,153:0.0111:2,2:20:1:26.7:1:1:1.5011:60:6:0.0112:0:1.3 -1 27533842 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1831;SOR=0;LSEQ=ACTCTTAAGTATATCTGGAA;RSEQ=GCGGTCTGCCCCTGGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:79,102:0.0109:2,2:42.5:1:31:1:1:1.29:54.5:4:0.0111:0:1 0/0:244:0:0,0:116,128:0:2,0:25.3:1:30.5:1:1:0:50.4:243:1:0:0.1 -1 27533906 . AGATGAT A 175 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=12.000;MSILEN=3;SSF=0.02136;SOR=0.57047;LSEQ=GTAAAACTTGCTGTTGATGA;RSEQ=GATGATGATGATGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:51:23,28:47,47:0.3333:2,2:28.7:1:31:1:0.60507:1.21574:60:50:0.3333:0.0588:0.2 0/1:194:43:18,25:60,68:0.2216:2,2:28.4:1:30.6:1:0.5996:1.22404:59.3:42:0.2188:0.0206:0.2 -1 27533961 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52038;SOR=Inf;LSEQ=ATTTTGATGATGAGGAAGCT;RSEQ=AAGAAAAAGTGCCAGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:45,54:0:2,0:24.1:1:31.5:1:1:0:60:98:1:0:0.1 0/1:152:2:1,1:67,83:0.0132:2,2:20:1:27.5:1:1:1.24:60:4:0.0134:0:1 -1 27533979 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52744;SOR=Inf;LSEQ=CTGAAGAAAAAGTGCCAGTG;RSEQ=AGAAATCTATATGAGATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:50,52:0:2,0:20.5:1:29.9:1:1:0:59.8:101:1:0:0.1 0/1:167:2:1,1:82,83:0.012:2,2:33:1:28:1:1:1.01:60:4:0.012:0:1 -1 27534005 . CA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.53092;SOR=Inf;LSEQ=TCTATATGAGATACTCCAGC;RSEQ=AAAATGCACACAAGTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:56,46:0:2,0:24.1:1:30.4:1:1:0:59.8:101:1:0:0.1 0/1:172:2:1,1:94,76:0.0116:2,2:47:1:30.5:1:1:1.2353:60:4:0.0118:0:1.5 -1 27534028 . A G 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=Inf;LSEQ=AAATGCACACAAGTCAAATC;RSEQ=GAATGGAAAAGACTCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:66,59:0:2,0:25.1:1:30.4:1:1:0:59.6:124:1:0:0.1 0/1:201:15:9,6:99,87:0.0746:2,2:25.5:1:30.6:1:0.78905:1.32:60:30:0.0746:0:1.1 -1 27534082 . C A 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56232;SOR=0.31422;LSEQ=AAGATCAAAAGGACAAGAAT;RSEQ=CTTCAAAACACAGGAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:66,85:0.0131:2,2:14.5:1:26.5:1:1:1.29:60:4:0.0131:0:1 0/0:242:1:1,0:116,125:0.0041:2,0:1:0:27:0:0.48347:0:54:2:0.0042:0:1 -1 27534166 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52428;SOR=Inf;LSEQ=AGCAAAAATGCAAGCAAGTA;RSEQ=AGAAAAAGGGGGTTCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:28,38:0:2,0:24.6:1:29.1:1:1:0:55.1:32:1:0:0.5 0/1:106:2:1,1:40,64:0.0189:2,2:17:0:33:0:1:1.59:60:4:0.0189:0:2 -1 27534176 . G T 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.0011;LSEQ=CAAGCAAGTATAGAAAAAGG;RSEQ=GGTTCTCTTCCCAAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:40:19,21:14,20:0.5405:2,2:22.3:1:29.6:1:0.64348:1.29:52.5:39:0.5493:0:1 1/0:98:53:21,32:15,30:0.5408:2,2:21.2:1:29.5:1:0.53677:1.31:54.9:106:0.5408:0:1.1 -1 27939425 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24389;SOR=0;LSEQ=AGGGTTGATGCCCGGACAGG;RSEQ=TATGTCTGATCCCCGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:68,31:0.0198:2,2:26.5:1:29:1:0.53545:2.17486:60:4:0.02:0:1 0/0:103:0:0,0:71,32:0:2,0:21.7:1:30.8:1:1:0:60:50.5:1:0:0.2 -1 27939515 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51299;SOR=Inf;LSEQ=TACTCGAAGGTAGGCCTCTC;RSEQ=TCCGGGTCCAGACGCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:53,81:0:2,0:24.4:1:31.4:1:1:0:60:268:1:0:0.1 0/1:189:2:1,1:74,113:0.0106:2,2:26:1:28.5:1:1:1.52:60:4:0.0108:0:1 -1 27939747 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21465;SOR=0;LSEQ=AACCTGGGTAGGGGATTCGG;RSEQ=CCTTGGTGATGAGCTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:69,40:0.018:2,2:27.5:1:31.5:1:1:1.71605:60:4:0.0187:0:1 0/0:128:0:0,0:80,48:0:2,0:21.8:1:31.5:1:1:0:60:127:1:0:0.2 -1 27939759 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50384;SOR=Inf;LSEQ=GGATTCGGCCCTTGGTGATG;RSEQ=GCTCAGTGAGCAGGATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:76,56:0:2,0:25.5:1:30.2:1:1:0:60:65:1:0:0.1 0/1:163:2:1,1:99,62:0.0123:2,2:18:1:28.5:1:1:1.59197:60:4:0.0123:0:1 -1 27941982 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50328;SOR=Inf;LSEQ=GTCACGATGTAGATGGGCTC;RSEQ=TCCGACACCACGGCGTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:63,51:0:2,0:27.3:1:31:1:1:0:60:56:1:0:0.2 0/1:140:2:1,1:77,61:0.0143:2,2:13:0:32.5:1:1:1.26017:60:4:0.0149:0:1.5 -1 27941983 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50298;SOR=Inf;LSEQ=TCACGATGTAGATGGGCTCC;RSEQ=CCGACACCACGGCGTACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:62,51:0:2,0:27.6:1:30.4:1:1:0:60:112:1:0:0.2 0/1:138:2:1,1:75,61:0.0145:2,2:28.5:1:27.5:1:1:1.22765:60:4:0.0147:0:1 -1 27941986 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50328;SOR=Inf;LSEQ=CGATGTAGATGGGCTCCTCC;RSEQ=ACACCACGGCGTACAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:61,53:0:2,0:27.3:1:30.2:1:1:0:60:113:1:0:0.2 0/1:140:2:1,1:75,63:0.0143:2,2:39:0:31:1:1:1.18898:60:4:0.0146:0:1 -1 27942016 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50379;SOR=Inf;LSEQ=CGTACAGCTGCACCAGCTTG;RSEQ=CGTGCCGCAGCAGCTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:40,62:0:2,0:24.6:1:30.1:1:1:0:60:204:1:0:0.2 0/1:127:2:1,1:49,76:0.0157:2,2:37.5:1:32.5:1:1:1.55:60:4:0.0163:0:1.5 -1 27942017 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19731;SOR=0;LSEQ=GTACAGCTGCACCAGCTTGT;RSEQ=GTGCCGCAGCAGCTTCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:39,61:0.0196:2,2:32:0:31.5:1:1:1.56:60:4:0.0198:0:1.5 0/0:127:0:0,0:50,77:0:2,0:24.3:1:29.1:1:1:0:60:62.5:1:0:0.2 -1 27942263 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2066;SOR=Inf;LSEQ=CAGCGTGATGGAGCTGCGGC;RSEQ=GATCTCCCAGGCGTCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:43,32:0:2,0:26.5:1:30.5:1:1:0:60:150:1:0:0.3 0/1:63:2:1,1:38,23:0.0317:2,2:47:0:30.5:1:1:1.63846:60:4:0.0317:0:1 -1 27942345 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=ATGAGCAGGTTGCACAGCCC;RSEQ=TCATTCACCTCTAGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:13,25:0.05:2,2:16.5:1:29:1:1:1.89:60:4:0.0513:0:1 0/0:28:0:0,0:6,22:0:2,0:21.5:1:31:1:1:0:60:56:1:0:0 -1 27943453 . C A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.417;LSEQ=CCCATGTCCAGTTTGCGGAT;RSEQ=TTGTAATGCTTCACATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:0,1:49,73:0.0081:2,0:27:0:14:0:1:0:60:0:0:0:2 0/1:174:2:1,1:79,93:0.0115:2,2:27.5:1:30:0:1:1.18:60:4:0.0116:0:1 -1 27943462 . C A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51497;SOR=Inf;LSEQ=AGTTTGCGGATCTTGTAATG;RSEQ=TTCACATGATCGCCTCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:41,73:0:2,0:23.5:1:32.6:1:1:0:60:228:1:0:0.1 0/1:165:2:1,1:69,94:0.0121:2,2:21:0:29:1:1:1.36:60:4:0.0124:0:1.5 -1 28637962 . AT A 92 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=13.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=AAAAAAAATTAAAAAAAAAA;RSEQ=AATAATAATAATAATATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:0,0:0.7273:0,0:13.4:1:30.7:1:1:0:60:16:0.7273:0.2727:0.1 0/0:2:0:0,0:2,0:0:0,0:12:1:24:1:1:0:60:1:1:0:0 -1 28637963 . T A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AAAAAAATTAAAAAAAAAAA;RSEQ=AATAATAATAATAATATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:0,0:0.2727:0,0:17:1:31.3:1:1:0:60:6:0.2727:0:2.3 0/0:2:0:0,0:2,0:0:0,0:12:1:24:1:1:0:60:1:1:0:0 -1 28638126 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20986;SOR=0;LSEQ=AAACATGAATGAGTTTAAAT;RSEQ=ATATTCATTCCTAAGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:17,28:0.0426:2,2:26:0:31:1:1:1.63:60:4:0.0426:0:1 0/0:55:0:0,0:27,28:0:2,0:27:1:31.3:1:1:0:60:110:1:0:0.2 -1 28638198 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19886;SOR=Inf;LSEQ=ATGCCAATACCTTTAACTCC;RSEQ=GATATCGTGTTCTCAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:2,16:0:2,0:22.5:1:31.7:1:1:0:60:36:1:0:0.1 0/1:15:2:1,1:0,13:0.1333:1,2:13.5:1:28:1:0.13333:0:60:4:0.1333:0:1 -1 28638259 . G A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.7321;LSEQ=CCATCTTATGTATCAAGTCA;RSEQ=CATGAAATTGAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:19:0:31:0:1:0:60:2:0.5:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:15:0:32:0:1:0:60:4:0.6667:0:1 -1 29644328 . C T 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00048;SOR=0;LSEQ=GCCCTGTTGCCCCGGAACCG;RSEQ=GACAAGAACCGCAGCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:6,4:7,3:0.5:2,2:26:1:30.1:1:1:1.52135:60:20:0.5:0:1.2 0/0:18:0:0,0:11,7:0:2,0:25.2:1:30.6:1:1:0:60:36:1:0:0.1 -1 29845899 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19548;SOR=Inf;LSEQ=AGGGTGTGAGAGGGGAGTGG;RSEQ=TTGTGCCCTCCCCACGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:28,13:0:2,0:26:1:31.9:1:1:0:60:82:1:0:0 0/1:33:2:2,0:18,13:0.0606:2,0:19:0:31:1:0.50758:0:60:4:0.0606:0:1 -1 29845932 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.18242;SOR=Inf;LSEQ=CACGGCCAAGTCTACTGGGC;RSEQ=CTGGGCTCTGGTTTCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:32,25:0:2,0:27.5:1:29.8:1:1:0:60:27.5:1:0:0.1 0/1:43:2:1,1:21,20:0.0465:2,2:30:1:28.5:1:1:1.04883:60:4:0.0476:0:1 -1 30274816 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18221;SOR=Inf;LSEQ=GTGGCAGGTGACCCTAGGAC;RSEQ=CCAACCTTCCTGCTCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:41,55:0:2,0:23.5:1:30.3:1:1:0:60:47:1:0:0.1 0/1:72:2:1,1:33,37:0.0278:2,2:21.5:1:24:1:1:1.12:60:4:0.029:0:1.5 -1 30274851 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18733;SOR=Inf;LSEQ=CTGGAGCTGCTGAAGTTAGG;RSEQ=TGGGCAGAGAGGGGGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:12,45:0:2,0:21.7:1:30.7:1:1:0:60:18:1:0:0.1 0/1:44:2:1,1:11,31:0.0455:2,2:32:1:28.5:1:0.47569:2.74:60:4:0.0455:0:1 -1 30534961 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50909;SOR=0;LSEQ=TCCAAGAATGAGGTGTGTGC;RSEQ=GTGTGTGTGCTGCCCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:37,0:0.0513:1,2:28:1:29.5:1:0.05128:0:60:4:0.0541:0:2 0/0:27:0:0,0:25,2:0:2,0:22.9:1:31.1:1:1:0:60:54:1:0:0.8 -1 30534979 . G A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96466;LSEQ=GCCGTGTGTGTGCTGCCCCA;RSEQ=TGCATTTTGTAAATGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:42:40,2:12,0:0.7778:0,1:24.8:1:30.3:1:1:0:60:84:0.7778:0:1.1 1/0:35:27:26,1:8,0:0.7714:0,1:27.4:1:30.3:1:1:0:60:54:0.7714:0:1.1 -1 30535114 . G A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.55244;LSEQ=CTAGTGGAACCCAAGTCTCT;RSEQ=TACAAGTAGGGATCTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:88:44,44:62,57:0.4251:2,2:28.1:1:29:1:0.7802:1.08728:60:28.333:0.425:0:1.2 1/0:214:140:72,68:34,40:0.6542:2,2:24.7:1:28.3:1:0.47468:1.24:60:45.667:0.6493:0:1.1 -1 30535142 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4987;SOR=Inf;LSEQ=AGGGATCTTGTATGGGGCCA;RSEQ=CAGCAAGCCCCAGTAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:78,99:0:2,0:23.3:1:31.7:1:1:0:60:58:1:0:0.5 0/1:182:2:1,1:78,102:0.011:2,2:12:0:32:0:1:1.31:60:4:0.011:0:2.5 -1 30535145 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24832;SOR=Inf;LSEQ=GATCTTGTATGGGGCCAGCA;RSEQ=CAAGCCCCAGTAGGAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:74,93:0:2,0:24:1:31.3:1:1:0:60:22.857:1:0:0.5 0/1:176:3:2,1:72,101:0.017:2,2:29.7:1:28.3:1:0.57325:2.79:60:6:0.0176:0:1.7 -1 30535269 . G A 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GCATTTGAGAAATAGCTCTT;RSEQ=GCTTTCTACTGAGCCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:0,31:0:1,0:27.8:1:31.1:1:1:0:60:62:1:0:0.2 1/0:15:8:0,8:0,7:0.5333:0,0:26.9:1:30.5:1:1:0:60:7:0.5:0:1.1 -1 30535317 . G T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.21094;LSEQ=AGTGGCTTCCTTTTTTCTAA;RSEQ=AAAAAGGAAATGAGTTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:0.3529:0,0:16.8:1:29.5:1:1:0:60:12:0.3529:0:1.2 0/1:5:2:0,2:0,3:0.4:0,0:19.5:1:29.5:1:1:0:60:4:0.4:0:1.5 -1 30648945 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49789;SOR=Inf;LSEQ=ATTCATATCAAAAACACACC;RSEQ=ATAAATGTAACTGAAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:28.1:1:31.5:1:1:0:60:38:1:0:0.1 0/1:25:2:1,1:15,8:0.08:2,2:27.5:1:29.5:1:1:1.82581:60:4:0.0833:0:1 -1 30649015 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17235;SOR=0;LSEQ=CATACAATTTACCAAATAAT;RSEQ=CTAAAAATTCAATACCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:2,10:0.1429:2,2:17:1:27.5:1:0.3956:4.28:50.5:4:0.1538:0:3.5 0/0:19:0:0,0:9,10:0:2,0:15.6:1:29.7:1:1:0:60:18:1:0:0.1 -1 30792845 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGCCATGGCTCCGAGC;RSEQ=TCCTCACCCCCCCATCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:31.5:1:1:0:60:4:1:0:1.5 -1 30794414 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCCTCCCAGCACCTTCA;RSEQ=GTCTGAGTGGGTTAAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:41.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 30794719 . G C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3125;SOR=0;LSEQ=CGTATTTCCCCATTTAATTG;RSEQ=TTGTATTCTCAGTGGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:22.5:1:32.4:1:1:0:60:22:1:0:2.2 1/1:5:4:4,0:1,0:0.8:0,0:38.3:1:33.3:1:1:0:60:8:0.8:0:1.3 -1 30794788 . A G 172 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=TCGGGTTTCTCTGGAAAATA;RSEQ=TGATTCCCTGGCAGGGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:35,2:0,0:1:0,2:22.4:1:33.1:1:1:0:60:74:1:0:1.2 0/1:25:10:10,0:14,1:0.4:1,0:22.2:1:33.4:1:1:0:60:20:0.4:0:1.1 -1 30794877 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0969;SOR=Inf;LSEQ=CTGCACTGGGTCTTCCAGGA;RSEQ=ATCCCAGGGTGGCCCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:151,55:0:2,0:25.2:1:31.4:1:1:0:60:67.667:1:0:0.4 0/1:176:3:1,2:119,53:0.017:2,2:7.7:1:26.3:1:0.23285:4.44774:60:6:0.0176:0:1.7 -1 30794960 . A C 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13381;LSEQ=AGTCCCAGGGTCACCTGCTG;RSEQ=AGAAAGGAAACCAGAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:457:424:201,223:13,19:0.9278:2,2:26.3:1:31.6:1:0.58225:1.32:60:34.333:0.93:0:1.2 1/0:410:259:130,129:77,74:0.6317:2,2:27.1:1:31.5:1:0.91856:1.03247:60:63.75:0.6328:0:1.2 -1 30795039 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24904;SOR=0;LSEQ=CCATCTTCGCTCCTCAGGGG;RSEQ=CTCTCCTGAGACAGCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:1,2:53,134:0.0157:2,2:8.7:1:29:1:1:1.26:60:6:0.0161:0:2 0/0:177:0:0,0:53,124:0:2,0:22.5:1:30.5:1:1:0:60:34.4:1:0:0.5 -1 30795106 . T G 162 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.04538;LSEQ=GCTGGTGGGGAGGCTCTGAC;RSEQ=GTCACCCCAGGAAAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:40:0,40:0,1:0.9756:0,1:24.6:1:30.5:1:1:0:60:19:0.9744:0:1.3 1/0:47:30:0,30:0,17:0.6383:1,1:24.6:1:30.3:1:1:0:60:60:0.6383:0:1 -1 30795214 . G C 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTCAGGGACCCAGAAGG;RSEQ=CTGTGCGCTGGTGACCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:1:0,2:20.8:1:29:1:1:0:60:7:1:0:1.6 1/1:3:3:0,3:0,0:1:0,0:22:1:29.3:1:1:0:60:6:1:0:1 -1 31581502 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14574;SOR=0;LSEQ=TACTGGAAGACGGCAGTTCT;RSEQ=GCCAAAAGACTCTATTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:50,72:0.0161:2,2:28.5:1:28.5:1:1:1.44:60:4:0.0169:0:1 0/0:200:0:0,0:91,108:0:2,0:29.3:1:30.3:1:1:0:60:98.5:1:0:0.2 -1 31581541 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52489;SOR=Inf;LSEQ=CATTTCTCACCAATCTCTAT;RSEQ=TTCATCTGTATATTTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:16,49:0:2,0:18.6:1:30.1:1:1:0:60:130:1:0:0 0/1:105:2:1,1:29,74:0.019:2,2:25.5:1:28:1:0.49176:2.53:60:4:0.0196:0:1 -1 33132188 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGTCTCGAACTCCTGA;RSEQ=CTCAGGTGATCTGCCCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 33132857 . G C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGATTCCTCTTTGAAGTT;RSEQ=CTAGAGGATAGCAGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:1:0,2:24.4:1:32.1:1:1:0:58.6:16:1:0:1 1/1:6:6:6,0:0,0:1:0,0:15.7:1:32.3:1:1:0:60:12:1:0:1.3 -1 33133016 . CT C 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55301;SOR=Inf;LSEQ=GATCATGTGACTTGCTTGAC;RSEQ=TATCAATCACTTGGACGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:43,44:0:2,0:28.5:1:31.1:1:1:0:60:86:1:0:0.1 0/1:176:3:2,1:82,91:0.017:2,2:26:1:27.3:1:0.60633:2.21:60:6:0.0172:0.0057:0.3 -1 33133063 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15556;SOR=0;LSEQ=TCCTTACCTCGCCCCCTTGT;RSEQ=TTGTATGCAATAAATATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:19,29:0.04:2,2:35.5:1:31.5:1:1:1.51:60:4:0.04:0:1 0/0:76:0:0,0:31,45:0:2,0:20.4:1:30.6:1:1:0:60:24.333:1:0:0.1 -1 34805896 . G A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04805;SOR=0;LSEQ=CCTGGGAACCAGTGAATCCT;RSEQ=CCTCCACCCCATGTCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:24.2:1:27.8:1:1:0:60:12:0.4286:0:1.7 0/0:9:0:0,0:9,0:0:0,0:21.3:1:32.1:1:1:0:60:18:1:0:0 -1 34805927 . C T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09774;SOR=0.25186;LSEQ=ATGTCTGACTTGCACATCTC;RSEQ=GGAGGCCTCCTAATTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:8,1:21,0:0.3:1,2:26.9:1:30.6:1:0.3:0:60:18:0.3:0:1.4 0/1:21:2:2,0:19,0:0.0952:1,0:16.5:1:32:1:1:0:60:4:0.1:0:1 -1 34806052 . TTGC T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.30244;SOR=0.55985;LSEQ=TGCTGCTGTTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:9:6,3:114,115:0.0378:2,2:26.4:1:30.3:1:0.49949:2.01:60:18:0.038:0:0.3 0/1:279:6:4,2:134,138:0.0215:2,2:28.3:1:30.7:1:0.44548:2.05:60:12:0.0218:0:0.3 -1 34806066 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.25383;SOR=Inf;LSEQ=CTGCTGTTGCTGCTGCTGCT;RSEQ=CTGCAACTGCTGTGGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:96,113:0:2,0:25.7:1:32:1:1:0:60:208:1:0:0.1 0/1:248:3:2,1:114,131:0.0121:2,2:28:1:28.7:1:0.60066:2.29:60:6:0.0123:0:1.3 -1 34806090 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50156;SOR=Inf;LSEQ=CAACTGCTGTGGCTGTTGGC;RSEQ=TATGACTAGTACCTCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:52,108:0:2,0:23.4:1:31.3:1:1:0:60:159:1:0:0.1 0/1:188:2:1,1:67,119:0.0106:2,2:5.5:1:27.5:1:1:1.77:60:4:0.0109:0:1 -1 35013299 . C G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=ACAGTATCATGGAAAGAAAA;RSEQ=AGAAAAAAAAATCAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:17.8:1:32:1:1:0:60:8:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:9.5:1:30:0:1:0:60:4:0.6667:0:1.5 -1 35013586 . A G 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATTACATATAACACCAGT;RSEQ=TAACAGCCAGTATTTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:221,227:0:2,0:26.7:1:29.4:1:1:0:60:148.333:0.9955:0:0.1 0/1:512:96:47,49:198,217:0.1875:2,2:25.8:1:31.2:1:0.90981:1.05:60:95:0.1874:0:1.1 -1 35013690 . C T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08719;SOR=Inf;LSEQ=CATGAGTTTCTAGATTGAAA;RSEQ=GGCCACCAAGTGCCAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:13,110:0:2,0:25.1:1:30.4:1:1:0:60:122:1:0:0 0/1:99:3:1,2:14,82:0.0303:2,2:27:1:21.7:1:0.39251:2.89:60:2:0.0204:0:1 -1 35468329 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50241;SOR=Inf;LSEQ=GTGGTTTGGTCATCTTCATA;RSEQ=ATTTTTTATCACATCTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:97,52:0:2,0:22.5:1:31.4:1:1:0:60:148:1:0:0.1 0/1:178:2:0,2:127,49:0.0112:2,0:11.5:1:26.5:1:0.08094:0:60:4:0.0114:0:1 -1 35468380 . AT A 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.04213;SOR=Inf;LSEQ=AGTTATTAAATTTGGGGCAC;RSEQ=TTTTTTAGCACTAGCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:143,133:0:2,0:28.6:1:30.5:1:1:0:60:275:1:0:0.1 0/1:378:6:3,3:193,179:0.0159:2,2:28.5:1:31:1:1:1.07797:60:12:0.0161:0:0 -1 35468429 . A G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TATAACACTTAAATGGCATT;RSEQ=TTCTACGATATAAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:93,130:0:2,0:23.4:1:29.7:1:1:0:60:446:1:0:0.1 0/1:304:18:10,8:115,169:0.0592:2,2:24.7:1:31.9:1:0.22558:1.83:60:36:0.0598:0:1.2 -1 35468440 . TA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.17556;SOR=0;LSEQ=AATGGCATTATTCTACGATA;RSEQ=AAAAAAGAGTTTTAATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:0,2:75,111:0.0106:2,0:45:1:30.5:1:0.51786:0:60:4:0.0106:0:0 0/0:260:0:0,0:102,157:0:2,0:22.7:1:28.9:1:1:0:60:128.5:1:0:0.2 -1 35468456 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18116;SOR=0;LSEQ=GATATAAAAAAAGAGTTTTA;RSEQ=TTATATCAAGAGCAAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:49,94:0.0138:2,2:41.5:1:31:1:1:1.91:60:4:0.0141:0:2 0/0:195:0:0,0:73,120:0:2,0:23:1:29.6:1:1:0:60:192:0.9948:0:0.2 -1 35468504 . C T 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02103;SOR=Inf;LSEQ=CAGCACAAGCTGGGCACCAT;RSEQ=GGCTCATGCCTGTAATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:18,49:0:2,0:23.9:1:30.6:1:1:0:60:134:1:0:0.1 0/1:91:7:3,4:18,65:0.0769:2,2:32.4:1:30.4:1:0.34717:2.67:60:14:0.0787:0:1.3 -1 35468538 . T C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30478;LSEQ=AATCACAACAGCTTGGGAGG;RSEQ=TGAGGCGGGAGGATCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:7,34:0.0465:2,2:15:1:30.5:1:0.34109:4.61:60:4:0.0465:0:1.5 0/1:50:3:0,3:8,39:0.06:2,0:35.7:1:30.3:1:1:0:60:6:0.0612:0:1.3 -1 36411515 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21739;SOR=Inf;LSEQ=GCTATTTTTTTCCTTAGTAA;RSEQ=TATCCATGTTTATTTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:31.2:1:32:1:1:0:60:24:1:0:0 0/1:11:2:1,1:8,1:0.1818:2,2:24:1:29:1:0.34545:6:60:4:0.2:0:1 -1 36411737 . A G 133 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=19.52196;LSEQ=CTGAAATCAGGCTGCACATC;RSEQ=TGAGCACATCATTTTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:1:0,1:204,177:0.0026:2,0:13:0:14:0:0.46597:0:60:0:0:0:1 0/1:471:23:11,12:233,215:0.0488:2,2:22.2:1:29.5:1:0.83122:1.18182:60:46:0.0498:0:1.3 -1 36411799 . T C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08906;SOR=0;LSEQ=CTTGCTTTTTTCTCCTCACC;RSEQ=CTCTTATGTACCACTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:104,172:0.0107:2,2:32.7:1:32:1:0.55957:3.29:60:6:0.011:0:1 0/0:347:0:0,0:138,208:0:2,0:47:0:15:0:1:0:60:0:0:0:1 -1 36807481 . C T 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11839;LSEQ=CTTGGGTACCCAGCTCCGGG;RSEQ=GTCATGGATGGAGCTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:522:340:141,199:84,97:0.6513:2,2:25.5:1:29.5:1:0.30714:1.22172:60:84:0.6524:0:1.1 0/1:509:92:34,58:185,232:0.1807:2,2:22:1:29.2:1:0.20284:1.35948:60:91:0.1827:0:1.1 -1 36807563 . C T 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGTACTGGGAGCACTCCTC;RSEQ=GTCACCTTCGCCTTTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:132,254:0:2,0:27:1:30.3:1:1:0:60:192:0.9974:0:0.3 0/1:363:18:8,10:138,207:0.0496:2,2:22.7:1:31.1:1:0.80648:1.20:60:36:0.05:0:1.2 -1 36807628 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17827;SOR=Inf;LSEQ=ATAAACCCAGATGAAGGCAG;RSEQ=GCAGCAGACAGGAGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:19,98:0:2,0:22.7:1:29.8:1:1:0:60:38:1:0:0.1 0/1:86:2:1,1:18,66:0.0233:2,2:18:1:29:1:0.39508:3.60:60:4:0.0235:0:1 -1 36809375 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20701;SOR=Inf;LSEQ=TCTAACTGGCAGAGAAGCAG;RSEQ=CTGACTACTGGCTGCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:96,16:0:2,0:22:1:30.6:1:1:0:60:15:1:0:0.2 0/1:94:2:2,0:78,14:0.0213:2,0:36.5:1:29.5:1:1:0:60:4:0.0213:0:1 -1 36809436 . C T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05493;SOR=Inf;LSEQ=CCTGAGGACGCAGCCTTGTG;RSEQ=CCGGTCAAGTGCCTGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:215,117:0:2,0:26.8:1:31.5:1:1:0:60:40.5:1:0:0.2 0/1:314:4:2,2:186,124:0.0127:2,2:25.8:1:28.3:1:1:1.49797:60:8:0.0131:0:1 -1 36809726 . A G 151 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.79381;LSEQ=GGAGGCAGGACTCACTCAGG;RSEQ=ATGGTATACTCGGCAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:18:18,0:224,276:0.0347:2,1:26.3:1:13.9:1:0:0:60:0:0:0:5.2 0/1:558:67:42,25:220,263:0.1201:2,2:24.8:1:24.9:1:0.00911:2.01:59.7:1.913:0.0932:0:3 -1 36810011 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00149;SOR=0.18714;LSEQ=AGCTCCTGCCCGTGCTCCCC;RSEQ=CTCCCCTGTTCCTCAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:24:1,23:0,11:0.6667:0,1:26.4:1:28.7:1:1:0:60:23:0.6765:0:1.3 0/1:30:8:0,8:2,20:0.2667:2,0:23.3:1:28.8:1:1:0:60:16:0.2667:0:1.4 -1 36814216 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18614;SOR=Inf;LSEQ=GCCCCAGCACCTTGCCCAGG;RSEQ=CCTGCCCACAAATTTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:221,34:0:2,0:24.3:1:30.5:1:1:0:60:24.5:1:0:0.1 0/1:194:2:1,1:169,22:0.0103:2,2:21.5:1:27:1:0.22469:7.53511:60:4:0.011:0:1 -1 36814473 . C T 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.91021;SOR=0.96921;LSEQ=CTATAGCAACAGGCACAAGA;RSEQ=ACGCAGGCAGGACACACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:49:7,42:54,268:0.1321:2,2:24.5:1:28.3:1:0.83641:1.20836:60:23.5:0.1291:0:1.1 0/1:319:41:7,34:45,232:0.1285:2,2:22.8:1:28:1:0.82437:1.06:60:82:0.1302:0:1 -1 36819825 . C CCT 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08419;SOR=Inf;LSEQ=TTCCCATGTTCATCCCATCC;RSEQ=GAGCCCTGGGATTCCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:132,0:0:1,0:22.2:1:31.2:1:1:0:60:264:1:0:0.1 0/1:104:3:3,0:100,1:0.0288:1,0:9.7:1:30.7:1:1:0:60:6:0.03:0.0096:0 -1 36819930 . G T 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=44.56253;LSEQ=TGTAGCCTGCCCCAGCCCCG;RSEQ=GGTAACTGTATGGATGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:877:1:0,1:518,358:0.0011:2,0:1:0:26:0:0.40935:0:60:2:0.0012:0:1 0/1:908:44:26,18:485,377:0.0485:2,2:20.8:1:29.8:1:0.75722:1.12:60:88:0.0492:0:1.2 -1 36820196 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09946;SOR=Inf;LSEQ=AGTTCGCGTGACCTGCGCGT;RSEQ=TGGATGGGGAATGAATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:2,49:0:1,0:27.9:1:31.7:1:1:0:60:24.5:1:0:0.2 0/1:24:2:1,1:1,21:0.0833:1,2:31:1:28.5:1:0.16304:15.20:60:4:0.0833:0:1 -1 36820750 . C T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.25606;SOR=0;LSEQ=AGCTGCCTTCTGCTCAGCAG;RSEQ=AGCAAGAAAGGTGGCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:1,2:124,21:0.0203:2,2:20.3:1:21.3:1:0.06308:11.4846:60:2:0.0141:0:1.3 0/0:119:0:0,0:92,27:0:2,0:21.4:1:31.1:1:1:0:60:22.8:1:0:0.2 -1 36820752 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.09176;SOR=Inf;LSEQ=CTGCCTTCTGCTCAGCAGCA;RSEQ=CAAGAAAGGTGGCTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:132,25:0:2,0:23.2:1:31.5:1:1:0:59.8:38.25:1:0:0.2 0/1:130:3:3,0:98,29:0.0231:2,0:21:1:32:0:1:0:60:6:0.024:0:2 -1 36820783 . C T 114 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=19.26061;LSEQ=GGCTTTCTGTGGCCAGAAGG;RSEQ=GCAGCAGCAGGGTGTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:0,1:195,66:0.0038:2,0:1:0:26:0:0.25573:0:60:2:0.0039:0:1 0/1:232:16:12,4:148,68:0.069:2,2:18.4:1:28.5:1:0.78123:1.38:60:32:0.0693:0:1.3 -1 36820927 . G A 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43392;SOR=0.8947;LSEQ=ATGAGGTCAGCGGTCTTATC;RSEQ=CTGAAGTCATGAGCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:775:111:61,50:349,313:0.1432:2,2:23.7:1:29.2:1:0.68218:1.09:60:54.5:0.1427:0:1.2 0/1:907:118:64,54:435,353:0.1301:2,2:26.5:1:29.4:1:0.84345:1.03972:60:236:0.1314:0:1.2 -1 36821068 . G A 49 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06166;SOR=0;LSEQ=GGGTAGCGCAGGGCTTGGCT;RSEQ=TGAACTTGGCAGGGCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:4:2,2:106,259:0.0108:2,2:26.8:1:24.5:1:0.58373:2.44:60:3:0.0083:0:1.3 0/0:370:0:0,0:116,253:0:2,0:24.4:1:31:1:1:0:60:183.5:0.9973:0:0.1 -1 36821402 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCATGGCACCCAGATTCC;RSEQ=GTAATCACCAACAGAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:5.5:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 36824053 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11715;SOR=Inf;LSEQ=ACAGCAGAACAACCAGAACG;RSEQ=GGGAAGCAGGGGGCTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:22,193:0:2,0:24.4:1:31:1:1:0:60:42:1:0:0.2 0/1:207:3:1,2:18,185:0.0145:2,2:16.7:1:23.3:1:0.25308:5.07:60:2:0.01:0:1 -1 36824055 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24881;SOR=0;LSEQ=AGCAGAACAACCAGAACGGG;RSEQ=GAAGCAGGGGGCTTTTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:1,2:21,186:0.0143:2,2:22.3:1:24.3:1:0.28372:4.38:60:2:0.0096:0:2 0/0:198:0:0,0:15,183:0:2,0:22.2:1:29.9:1:1:0:60:38.6:1:0:0.1 -1 36824278 . G T 47 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02561;SOR=Inf;LSEQ=TGTGAAGGTGGAGGAGGGAG;RSEQ=AGTGGGTTGGCATGACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:332,147:0:2,0:23.8:1:31:1:1:0:60:78.833:1:0:0.4 0/1:445:5:1,4:297,143:0.0112:2,2:7.2:1:20.4:1:0.04289:8.26727:60:4:0.0091:0:1.6 -1 36824305 . C T 197 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGGCATGACAGGCCCTGTT;RSEQ=CTGAGGCACCCTCACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:105:57,48:344,246:0.1511:2,2:25.8:1:29.4:1:0.45457:1.17729:60:210:0.1537:0:2.1 0/0:691:0:0,0:409,281:0:2,0:25.9:1:30.8:1:1:0:60:68:1:0:0.4 -1 36824321 . C T 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00036;SOR=1.4849;LSEQ=TGTTCCTGAGGCACCCTCAC;RSEQ=CCCATGTCTCACTTACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:845:183:106,77:358,304:0.2166:2,2:25.3:1:30.4:1:0.40138:1.17:60:90.5:0.2178:0:1.7 0/1:907:264:151,113:362,281:0.2911:2,2:25.3:1:29.6:1:0.82519:1.04:60:65:0.2918:0:1.2 -1 36826717 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09112;SOR=Inf;LSEQ=GCAGGACCACACACTGCTGT;RSEQ=GGTGGGCCACCTCACTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:202,7:0:1,0:24.6:1:31.9:1:1:0:60:40.8:1:0:0.1 0/1:172:3:2,1:163,6:0.0174:1,2:8.3:1:30.3:1:0.11785:12.96317:60:6:0.0175:0:1 -1 36853369 . GACAC G 105 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=13.000;MSILEN=2;SSF=1;SOR=1.01034;LSEQ=TACCATGAGGAGAACGCTGG;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:10:6,4:5,5:0.3846:2,2:24.2:1:30.6:1:1:1.47:60:20:0.3846:0.1538:0 0/1:31:12:6,6:4,2:0.3871:2,2:27.7:1:29.4:1:0.63801:1.9247:60:11:0.3667:0.129:0.3 -1 36931882 . C T 158 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=48.65462;LSEQ=GGGTAGTTTTTAGTCATGGG;RSEQ=TTATGGACCCTCCCCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:718:1:0,1:386,331:0.0014:2,0:1:0:26:0:0.4624:0:60:2:0.0014:0:1 0/1:691:44:21,23:357,290:0.0637:2,2:20.1:1:29:1:0.35162:1.34768:60:43:0.063:0:1.3 -1 36933096 . T C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33047;LSEQ=AAGGGACTTAGATGGGCCCA;RSEQ=CTGGACCTGAGGTTCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:178:133,45:275,124:0.3069:2,2:23.6:1:31.6:1:0.16672:1.33:60:88:0.311:0:1.1 0/1:541:69:45,24:347,125:0.1275:2,2:23:1:30.6:1:0.1517:1.47939:60:33.5:0.1257:0:1.1 -1 36933198 . G A 206 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=134.87123;LSEQ=AGGCAGTTCCACAGAGGCAG;RSEQ=TGAGCAACAGCAGGAGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1567:1:1,0:792,773:6e-04:2,0:1:0:15:0:1:0:60:0:0:0:1 0/1:1714:136:67,69:777,797:0.0793:2,2:24.2:1:29.2:1:1:1.00401:60:135:0.0798:0:1.3 -1 36933317 . C T 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCTGGGTCTCCTCCCTC;RSEQ=GACCAGGGGATTCAAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:746:0:0,0:346,399:0:2,0:23:1:30.2:1:1:0:60:81.778:0.9986:0:0.1 0/1:683:51:20,31:285,346:0.0747:2,2:25.6:1:29.9:1:0.46547:1.27628:60:50:0.0743:0:1.1 -1 36933539 . C T 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=21.56888;LSEQ=GGCCATGGAGGACAAAGCCA;RSEQ=GGGAGGAGGCATTCAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1556:5:3,2:751,797:0.0032:2,2:19.8:1:28.8:1:0.67855:1.59:60:10:0.0033:0:1 0/1:1722:112:51,61:790,820:0.065:2,2:22:1:30.1:1:0.49476:1.15222:60:111:0.0654:0:1.3 -1 36933651 . G A 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCAGGCCTTCTGGGGCT;RSEQ=TGGGGGAACTGAGGATAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1252:0:0,0:605,646:0:2,0:25.3:1:31.9:1:1:0:60:77.188:0.9992:0:0.1 0/1:1268:44:21,23:591,630:0.0347:2,2:26.2:1:28.5:1:1:1.02742:60:88:0.035:0:1.2 -1 36934667 . T C 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTATGGTAGGAAGGCAA;RSEQ=GTTCCCTATACTTCTGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:293,22:0:2,0:22:1:31.1:1:1:0:60:104:1:0:0.1 0/1:238:32:29,3:184,22:0.1345:2,2:19:1:31.2:1:1:1.16:60:64:0.135:0:1 -1 36934976 . C T 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00048;SOR=0.26053;LSEQ=TCATGATTCAGGGTTAACCT;RSEQ=CACAATATCTTCTTTAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:40:2,38:17,101:0.2532:2,2:23.7:1:29.8:1:0.16051:3.17981:60:19:0.2452:0:1 0/1:99:8:0,8:9,82:0.0808:2,0:29.6:1:27.9:1:1:0:60:7:0.0729:0:1 -1 36935072 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGGCTATAGAAAAAGGA;RSEQ=CAGGTTAGACTGTAGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:86,28:0.0172:2,2:25:1:27.5:1:0.43913:3.03545:60:4:0.018:0:1.5 0/0:55:0:0,0:46,9:0:2,0:22.4:1:30.4:1:1:0:60:110:1:0:0.1 -1 36935128 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.36316;LSEQ=GGATATGAAATGAGAACAAC;RSEQ=AAGGATCAAGAAAGGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:220:110:103,7:107,3:0.5:1,2:22.6:1:30.9:1:0.3323:2.41468:60:220:0.5023:0:1 0/1:173:46:44,2:124,3:0.2659:1,1:24.2:1:30.6:1:0.60976:1.871:60:92:0.2674:0:1.3 -1 36936601 . A G 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=AGAGGCCGGGGATGGGAGGT;RSEQ=ACTTACTCAGGTCACACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:23:1:30.3:1:1:0:60:6:0.5:0:1 0/0:2:0:0,0:1,1:0:2,0:24:1:27.5:1:1:0:60:4:1:0:0 -1 36937059 . A G 304 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.23783;LSEQ=CTTTCTGAGAAGACCACCGG;RSEQ=GTGGGACGAGAGGTCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1298:656:368,288:355,285:0.5054:2,2:23.9:1:30.7:1:0.8232:1.03:60:33.526:0.5052:0:2 1/0:1476:1027:554,473:239,208:0.6958:2,2:24.1:1:30.4:1:0.90952:1.02:60:84.583:0.6962:0:1.5 -1 36937065 . A G 289 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.47076;LSEQ=GAGAAGACCACCGGAGTGGG;RSEQ=CGAGAGGTCCCGGCTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1313:604:332,272:394,314:0.46:2,2:24.2:1:31.3:1:0.82376:1.028:60:45.462:0.4567:0:2.1 0/1:1506:431:234,197:568,506:0.2862:2,2:24.8:1:31.2:1:0.64767:1.06:60:142.667:0.2884:0:2.1 -1 36937392 . T C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.01113;LSEQ=CCCCCCTCCCCTTTTCCCTC;RSEQ=GTTCCCTTGTGCTAGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:6:1,5:17,141:0.0366:2,2:26.3:1:31.5:1:0.50792:1.65:60:12:0.0375:0:1 0/1:87:29:2,27:3,54:0.3333:2,2:18:1:29.6:1:1:1.33:60:58:0.3372:0:1.1 -1 36937414 . G T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01588;SOR=Inf;LSEQ=TTCCCTTGTGCTAGGTTCTA;RSEQ=GAAGGAGGGCAGGAAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:31,106:0:2,0:22.7:1:31.7:1:1:0:60:67.5:1:0:0.1 0/1:47:3:0,3:12,31:0.0638:2,0:39:1:30:1:0.55652:0:60:6:0.0652:0:1 -1 36937496 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08055;SOR=Inf;LSEQ=ACACTGTGACGTGCGTTACA;RSEQ=TCTGTCCAAAAGCTAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:106,29:0:2,0:24.5:1:32:1:1:0:60:32.75:1:0:0.2 0/1:54:2:2,0:46,6:0.037:2,0:14:1:31.5:1:1:0:60:4:0.037:0:1 -1 36937614 . G A 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCCGGTTTGTAGGGATCT;RSEQ=TTTGGACTGCGGGAGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:937:0:0,0:578,358:0:2,0:25.2:1:31.8:1:1:0:60:84.091:0.9989:0:0.2 0/1:935:38:24,14:557,338:0.0406:2,2:20.6:1:27.1:1:1:1.04:60:11.667:0.0381:0:1.4 -1 36937701 . T C 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACTGTCCTGGGGTCCAGC;RSEQ=GCCTCTGCCGCCACCATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1371:0:0,0:689,682:0:2,0:24.9:1:30.6:1:1:0:60:123.636:1:0:0.2 0/1:1422:56:29,27:641,723:0.0394:2,2:27.4:1:29.5:1:0.4976:1.21:60:55:0.039:0:1.3 -1 36937878 . C T 170 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.0981;LSEQ=CTCCAGGCTGGGGCTCCAGT;RSEQ=GCTCCAGTGGCCAGGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1443:2:0,2:706,735:0.0014:2,0:1:0:25.5:1:0.49988:0:60:4:0.0014:0:1 0/1:1416:55:29,26:681,680:0.0388:2,2:27.5:1:29.5:1:0.78359:1.11:60:110:0.0395:0:1.2 -1 36938060 . A T 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAGGGCCAGCTCGAGCCCG;RSEQ=CTTACCCTGCCCCCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:860:0:0,0:407,453:0:2,0:22:1:29.6:1:1:0:60:70.667:1:0:0.1 0/1:728:49:24,25:327,352:0.0673:2,2:24.4:1:28.4:1:1:1.03:60:48:0.0667:0:1.1 -1 36938269 . A G 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGTCCATGGTCCGCAGC;RSEQ=TGGGGGGCTCCAGTTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1397:0:0,0:720,674:0:2,0:24.4:1:30.3:1:1:0:60:48.786:0.9978:0:0.2 0/1:1596:68:35,33:767,757:0.0426:2,2:24.7:1:29.9:1:0.90167:1.05:60:21.667:0.0414:0:1.2 -1 36938873 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.54978;SOR=0;LSEQ=CTGGGTCTGTGTCCCCATTT;RSEQ=TCTGTCTCCAGCTGCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:99,1:0.0196:1,2:30.5:1:29.5:1:0.03902:70.20734:60:4:0.0206:0:1 0/0:52:0:0,0:51,1:0:1,0:20.3:1:31.6:1:1:0:60:104:1:0:0 -1 36940801 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTAGTAGAGGCGGGG;RSEQ=TTCGCCTTGCTGGCCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:56,0:0.0339:1,0:8:1:33:1:1:0:60:4:0.0357:0:1 0/0:16:0:0,0:16,0:0:1,0:23.3:1:29.7:1:1:0:60:32:1:0:0.1 -1 36940811 . C T 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0409;SOR=Inf;LSEQ=AGAGGCGGGGTTTCGCCTTG;RSEQ=TGGCCAGGCTGATCATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:69,0:0:1,0:22.8:1:32.2:1:1:0:59.8:33.5:1:0:0.4 0/1:18:2:2,0:16,0:0.1111:1,0:38.5:1:29.5:1:1:0:60:4:0.1176:0:1 -1 36941374 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16613;SOR=Inf;LSEQ=GACTCAGAGGCCTCACCTTC;RSEQ=TGTCTCACCCTTCAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:5,237:0:1,0:25.2:1:32.5:1:1:0:60:59.5:1:0:0.2 0/1:167:2:1,1:4,161:0.012:1,2:16.5:1:29:1:0.05916:36.11:60:4:0.0123:0:1.5 -1 36941539 . G GT 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03612;SOR=0;LSEQ=AGTGTGTGCCTTTCCGCGGT;RSEQ=TAAGTGCTCTCACTGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:0,12:1,3:0.75:2,0:19:1:29.2:1:0.25:0:60:24:0.75:0.3125:0.2 0/0:3:0:0,0:1,2:0:2,0:42:1:31.7:1:1:0:60:6:1:0:0 -1 36944054 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGAGAATCGCTTGAACC;RSEQ=GGCAGGCGGAGGTTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:30:1:1:0:60:4:1:0:1 -1 36945307 . AG A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.37655;SOR=0.49261;LSEQ=ACACAAAATGATGCAAGTCA;RSEQ=GGCTTTTCACAGTGCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:0,17:0,29:0.3696:1,1:30.6:1:31.6:1:1:0:60:34:0.3696:0.0435:0.2 0/1:18:4:0,4:1,13:0.2222:1,0:21.5:1:32.8:1:1:0:60:8:0.2222:0.0556:0 -1 36945559 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGAAGGAGAGAAAGCCA;RSEQ=CACAAAGTTACATCATCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:25.5:1:29:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:1,0:0:0,0:31:0:34:0:1:0:60:2:1:0:0 -1 39444174 . G T 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGTTAGTTGAGCTCATTT;RSEQ=GGGTTCTATTTGTAAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:21:0:31:0:1:1.7321:46:4:0.4:0:2 0/0:2:0:0,0:1,1:0:2,0:15:1:33:1:1:0:60:4:1:0:0 -1 39444217 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGCTTGATGGCCTCGAT;RSEQ=CTAGAGGAAACAAATTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:6,1:0.2222:2,2:33.5:1:29.5:1:0.41667:4.58262:46:4:0.2222:0:2 0/0:3:0:0,0:2,1:0:2,0:41.7:1:31:1:1:0:50:6:1:0:0.3 -1 40361220 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19675;SOR=Inf;LSEQ=CTTTCAAAATAAATCAGACC;RSEQ=TTGCAACAGGAAATTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:102,4:0:1,0:24.8:1:31.5:1:1:0:60:105:1:0:0 0/1:85:2:2,0:81,2:0.0235:1,0:33:1:32:0:1:0:60:4:0.0244:0:1 -1 40361307 . TA T 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.63312;SOR=0.88191;LSEQ=AGGCATACAAAAATACAATA;RSEQ=AAAAAAAAAGACTCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:35:23,12:304,118:0.0763:2,2:22.9:1:30.7:1:0.43839:1.34324:60:70:0.0769:0.0153:0.2 0/1:619:42:29,13:376,200:0.0679:2,2:21.9:1:29.9:1:0.73723:1.19:60:84:0.068:0.0097:0.3 -1 40362978 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25206;SOR=Inf;LSEQ=AAATGTGCAAATTACTAAAG;RSEQ=GGAGAGGGAGGTTAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:160,26:0:2,0:23.4:1:31:1:1:0:60:92:1:0:0.4 0/1:215:3:1,2:165,46:0.014:2,2:11:1:24.7:1:0.127:7.08677:60:6:0.0142:0:2 -1 40363054 . G C 289 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07123;LSEQ=TTTTGGTCAGTTAGTAGCCA;RSEQ=TGAGGTATGCAATTCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:555:551:318,233:1,0:0.9928:0,2:26.9:1:31.8:1:1:0:60:109.2:0.9945:0:1.1 1/1:702:637:366,271:32,29:0.9074:2,2:24.8:1:31.1:1:0.49919:1.22:60:69.778:0.9075:0:1.2 -1 40363648 . C A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62363;SOR=2.98346;LSEQ=CAATTTCTTCATTCTCTGTC;RSEQ=GAGAAAAGAGATCAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:1,0:61,206:0.0037:2,0:1:0:26:0:0.23134:0:60:2:0.0038:0:1 0/1:271:3:1,2:78,190:0.0111:2,2:15.3:1:29:1:1:1.22:60:6:0.0112:0:1.3 -1 40364803 . C A 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07278;SOR=7.71731;LSEQ=CTGATTACGCTGTGTTTGGA;RSEQ=TTCTGTCTTACCCAGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:18,0:0.0526:1,0:45:0:30:0:1:0:60:2:0.0526:0:1 0/1:16:5:5,0:11,0:0.3125:0,0:30.2:1:31.2:1:1:0:60:10:0.3125:0:1 -1 40364939 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11525;SOR=5.29755;LSEQ=GTGAGTGAACTAGAAGCTCA;RSEQ=AAACAGGTTCAGGTTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:1:0,1:229,97:0.0031:2,0:1:0:23:0:0.29969:0:60:2:0.0031:0:1 0/1:312:5:1,4:216,91:0.016:2,2:8.2:1:25.2:1:0.03139:9.42105:60:10:0.0161:0:1.2 -1 40364988 . C T 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAATGATTCAGCAGGCTT;RSEQ=CCTACATCCCAAACCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:576:0:0,0:305,271:0:2,0:25.9:1:31.1:1:1:0:60:63:1:0:0.1 0/1:724:28:15,13:378,318:0.0387:2,2:30.7:1:30:1:1:1.03016:60:56:0.0395:0:1.3 -1 40365174 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24104;SOR=Inf;LSEQ=GTGTGCAAATGGGGAAACTG;RSEQ=GGCCCAGATCAGCGAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:40,143:0:2,0:23.3:1:30.9:1:1:0:60:60:1:0:0.1 0/1:177:2:1,1:38,137:0.0113:2,2:31:1:32:1:0.3931:3.57:60:4:0.0116:0:1 -1 40366454 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.07884;SOR=0;LSEQ=ACCAACACACCCACGTGCCA;RSEQ=ACAGACACGGTTGGGGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:191,81:0.0109:2,2:18.3:1:27.3:1:0.21738:4.68597:60:6:0.011:0:1 0/0:365:0:0,0:227,136:0:2,0:25.1:1:31.2:1:1:0:60:50.857:0.9944:0:0.1 -1 40367111 . G A 89 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14921;SOR=2.7611;LSEQ=ACGAGTCGTAGTCCATGTCC;RSEQ=CTCCCTGCGGGAGGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:691:3:1,2:263,424:0.0043:2,2:48:1:29.7:1:1:1.24016:60:6:0.0044:0:1 0/1:756:9:5,4:302,445:0.0119:2,2:11.9:1:28.1:1:0.49734:1.84:60:18:0.0121:0:1 -1 40367433 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAGGCAGCCTGCAGCCAGC;RSEQ=CGCACCGCGGGACCCGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:0:2,0:14.7:1:31.9:1:1:0:60:42:1:0:0.6 0/1:46:2:1,1:23,21:0.0435:2,2:16.5:1:28:1:1:1.09307:60:4:0.0435:0:1.5 -1 40367518 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18596;SOR=0;LSEQ=CACCTGGAGCGGACCGGCTC;RSEQ=CCGCCGGCTCGGGGCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:45,45:0.0215:2,2:45:0:30:1:1:1:60:4:0.0215:0:1 0/0:122:0:0,0:61,61:0:2,0:23.7:1:30:1:1:0:60:60:1:0:0.5 -1 40367535 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24099;SOR=Inf;LSEQ=CTCCCCGCCGGCTCGGGGCA;RSEQ=CCCGGCAGCCAGCACACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:49,49:0:2,0:25.5:1:31.9:1:1:0:60:23.5:1:0:0.5 0/1:95:2:1,1:45,48:0.0211:2,2:20.5:1:27.5:1:1:1.07:60:4:0.022:0:1.5 -1 40367541 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24599;SOR=Inf;LSEQ=GCCGGCTCGGGGCAGCCCGG;RSEQ=AGCCAGCACACACGCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:47,47:0:2,0:24.5:1:32.3:1:1:0:60:93:1:0:0.5 0/1:93:2:1,1:44,47:0.0215:2,2:29:1:30.5:1:1:1.07:60:4:0.0215:0:1 -1 40367555 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49697;SOR=Inf;LSEQ=GCCCGGCAGCCAGCACACAC;RSEQ=CACATGCGCGCCGCCGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:38,42:0:2,0:21.7:1:31:1:1:0:60:79:1:0:0.6 0/1:82:2:1,1:37,41:0.0244:2,2:36.5:1:29.5:1:1:1.11:60:4:0.025:0:1.5 -1 40367592 . A G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGCGCGGCCCGCACTCAC;RSEQ=AGCGCGCCCCCCCCGCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:22:11,11:1,0:0.9565:0,2:9.4:1:28.6:1:1:0:60:10:0.9524:0:1.5 1/1:20:20:9,11:0,0:1:0,2:14.5:1:29.9:1:1:0:60:40:1:0:1.5 -1 40367615 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGCGCCCCCCCCGCGCGCGC;RSEQ=CCCTCCCTCGCTCGCGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:8.5:1:28:1:1:1:60:4:0.3333:0:2.5 -1 40799062 . A G 69 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0666;SOR=Inf;LSEQ=TCTTCCAGTTTTGCCATGGT;RSEQ=ACACTTGTGGGACATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:90,113:0:2,0:27.5:1:29.2:1:1:0:54.9:100.5:1:0:0.2 0/1:245:5:2,3:115,125:0.0204:2,2:10.8:1:30:1:1:1.37821:42:10:0.0205:0:1.4 -1 40799094 . C T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16636;SOR=0.60213;LSEQ=ACATTCCTTTTTGAACAGTA;RSEQ=CCATTCCCTTGATGTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:22:8,14:33,71:0.1732:2,2:15.3:1:30:1:0.80269:1.23:51.5:44:0.1746:0:1.3 0/1:152:17:7,10:55,80:0.1118:2,2:18.2:1:29.5:1:1:1.02:57.8:34:0.1126:0:1.2 -1 40799145 . A G 88 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02705;SOR=0.16171;LSEQ=TCTTATAGATTCGCATATAC;RSEQ=TGGCCAAAGGAACAACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:7:2,5:7,32:0.1522:2,2:28.3:1:31.6:1:0.6091:1.80:38.7:14:0.1591:0:1.9 0/1:72:2:1,1:18,52:0.0278:2,2:10:1:30.5:1:0.46088:2.84:43.5:4:0.029:0:1.5 -1 40799163 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.5243;SOR=Inf;LSEQ=ACATGGCCAAAGGAACAACT;RSEQ=CATGTTTTCTAAAAGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:9,27:0:2,0:23.4:1:30.7:1:1:0:53.4:17:1:0:0.5 0/1:59:2:1,1:18,38:0.0339:2,2:27.5:1:28:1:1:2.08:53:4:0.0339:0:1 -1 40799200 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50158;SOR=Inf;LSEQ=CCTAGAGAACATGTATCGGG;RSEQ=GCCTCTCCTCTTTCCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:8,21:0:2,0:25.4:1:29.6:1:1:0:58.9:58:1:0:0.3 0/1:38:2:1,1:10,26:0.0526:2,2:5.5:1:26:1:0.50071:2.53:60:4:0.0571:0:1.5 -1 40799236 . C T 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12261;SOR=0.23235;LSEQ=CTTTGTGTTTGTCATTTTGG;RSEQ=GAATTACTGGAAGGTGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:0,6:8,11:0.24:2,0:26.5:1:29.8:1:0.12917:0:58.2:12:0.24:0:1.2 0/1:30:2:0,2:11,17:0.0667:2,0:23.5:1:29:1:0.51954:0:60:4:0.0667:0:1 -1 40799267 . A C 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12556;SOR=Inf;LSEQ=AAGGTGGCGTTTCTGGCCGT;RSEQ=AGGCTGATATTCTTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:6,14:0:2,0:22.4:1:29.7:1:1:0:60:40:1:0:0.3 0/1:27:4:2,2:6,17:0.1481:2,2:34:1:31.3:1:0.55829:2.71:60:8:0.1481:0:1.3 -1 41661496 . C T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08565;SOR=3.9451;LSEQ=ATGTAGGAAATTCTACAGAT;RSEQ=CCACAAAAAAGCTATTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:3,2:5,4:0.3571:2,2:13:1:30.4:1:1:1.18:60:10:0.3571:0:1 1/0:23:16:9,7:4,3:0.6957:2,2:24.4:1:29.4:1:1:1.03541:60:32:0.6957:0:1.1 -1 41827670 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24419;SOR=Inf;LSEQ=CGCGCCGCAGAGCCGGCCGC;RSEQ=CTCGTGTACCTGGCCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:29,36:0:2,0:28.8:1:31.2:1:1:0:60:31.5:1:0:0.1 0/1:64:2:1,1:28,34:0.0313:2,2:47.5:1:29.5:1:1:1.21:60:4:0.0317:0:1.5 -1 41828044 . TG T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.10594;SOR=Inf;LSEQ=CGTCCGGCTGGGGAGGGGGC;RSEQ=GGGACGCCGACTGGGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:93,229:0:2,0:23.4:1:30.8:1:1:0:60:52.667:0.9968:0:0.2 0/1:292:3:2,1:95,193:0.0103:2,2:14:1:27.3:1:0.25849:4.04:60:6:0.0104:0.0034:1 -1 41829272 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTGGAGGAGTAGACCTG;RSEQ=GTCTCTTTCCGCATCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:28.5:1:1:0:60:4:1:0:1.5 -1 43605219 . T G 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2639;SOR=Inf;LSEQ=CCTGCCTTACCCTGCCTCCT;RSEQ=GTCTTGTATGCAATAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:17,22:0:2,0:24.4:1:29.9:1:1:0:60:78:1:0:0.2 0/1:55:3:1,2:21,31:0.0545:2,2:29.3:1:29.3:1:1:1.34762:60:6:0.0556:0:1 -1 43784874 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20363;SOR=0;LSEQ=GTCCTGGGCTCCCTCATCCC;RSEQ=AGTCTCTCCTGACTTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:18,6:0.0769:2,2:22.5:1:28:1:0.47385:2.85369:60:4:0.0769:0:1.5 0/0:31:0:0,0:21,10:0:2,0:24.6:1:30.1:1:1:0:60:62:1:0:0.1 -1 43784956 . A G 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83709;SOR=0.89172;LSEQ=GTGCTGGTCGGAGAGAACCT;RSEQ=GCCTCCAAGATTGCAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:24:12,12:8,11:0.5581:2,2:25.4:1:30.6:1:0.75995:1.36:60:23:0.5476:0:1.1 1/0:51:27:11,16:9,15:0.5294:2,2:26.6:1:30.5:1:1:1.14:60:54:0.5294:0:1.1 -1 43803120 . C A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATAACAAGACTATTGTG;RSEQ=GGATTGTCTAAGTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:34:1:28.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 43803222 . G A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90381;LSEQ=TATTATACCATTCTATAATC;RSEQ=TTAGCACAGATACAGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:10,0:9,0:0.5263:0,0:20.3:1:29.6:1:1:0:60:20:0.5882:0:1.4 1/0:6:3:2,1:2,1:0.5:2,2:27:1:28:1:1:1:60:6:0.5:0:1.3 -1 43803416 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15634;SOR=Inf;LSEQ=CAGGGACAGGGACAGGACGT;RSEQ=GGGCTGTATCTGACAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:273,29:0:2,0:21.9:1:31.9:1:1:0:60:49.333:1:0:0.1 0/1:198:2:2,0:169,27:0.0101:2,0:13.5:1:31.5:1:1:0:60:4:0.0102:0:1 -1 43804069 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGCCCCAGCTCCAGCC;RSEQ=TACATAACCCCTAATCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:2,0:86,29:0.0171:2,0:18:1:28.5:1:1:0:60:4:0.0172:0:1 0/0:46:0:0,0:39,7:0:2,0:21.1:1:30.8:1:1:0:60:45:1:0:0.1 -1 43804117 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50592;SOR=0;LSEQ=AGGCAGTGAGAAGAAAAATG;RSEQ=CAGTACTAGAGACAGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:0,2:142,30:0.0115:2,0:7:1:25:0:0.03295:0:60:4:0.0118:0:1 0/0:136:0:0,0:123,13:0:2,0:25.6:1:30.9:1:1:0:60:44.333:1:0:0.1 -1 43804340 . G A 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=23.74263;LSEQ=TGCACCTCTGGGTGAAGAAT;RSEQ=TGTTCCTAAACCAGACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:754:1:1,0:332,421:0.0013:2,0:1:0:24:0:0.44164:0:60:2:0.0013:0:1 0/1:817:25:12,13:365,426:0.0306:2,2:26.2:1:28.5:1:1:1.08:60:24:0.0299:0:1.2 -1 43804433 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.12377;SOR=Inf;LSEQ=CCCTGCCCCCTCCACTTGCT;RSEQ=CCCCCAGTCCAGCTCCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:77,223:0:2,0:25.2:1:31.9:1:1:0:60:36.5:1:0:0.1 0/1:303:4:2,2:95,204:0.0132:2,2:26.5:1:24.5:1:0.59547:2.14:60:3:0.0101:0:1.5 -1 43804438 . C T 44 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06098;SOR=Inf;LSEQ=CCCCCTCCACTTGCTGCCCC;RSEQ=AGTCCAGCTCCCGGAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:71,217:0:2,0:23.7:1:31.8:1:1:0:60:95:1:0:0.1 0/1:286:4:2,2:80,200:0.014:2,2:21:1:22:1:0.58179:2.49:60:3:0.0107:0:1 -1 43805557 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22059;SOR=Inf;LSEQ=AGCTCCTCTCCACAGAGATG;RSEQ=TGTGCAAATATAAGGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:130,23:0:2,0:21.9:1:31.7:1:1:0:60:29.6:1:0:0.1 0/1:136:2:1,1:102,32:0.0147:2,2:23:1:27:1:0.42778:3.15418:60:4:0.015:0:1 -1 43805564 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4985;SOR=0;LSEQ=CTCCACAGAGATGCTGTGCA;RSEQ=ATATAAGGGTTGGAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:136,29:0.012:2,2:12.5:1:30.5:1:0.3279:4.62778:60:4:0.0124:0:1 0/0:167:0:0,0:122,45:0:2,0:21.7:1:29.6:1:1:0:60:40.75:1:0:0.1 -1 43812075 . G A 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03032;SOR=1.33499;LSEQ=AGCCTTGGGATTAGTCTCTG;RSEQ=GGCAGGCCTGATTCAATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:180:126,54:175,78:0.4147:2,2:24.3:1:30:1:0.91573:1.04:60:59:0.4165:0:1.1 0/1:508:247:171,76:166,92:0.4862:2,2:24.1:1:29:1:0.25786:1.25:60:48.4:0.4899:0:1.1 -1 43812643 . G A 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32586;LSEQ=ATGCCCACAGACCTCACTAC;RSEQ=CAGGGGATCCCTGGGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:3:3,0:95,284:0.0078:2,0:1:0:25.7:1:0.0165:0:60:6:0.008:0:1 0/1:386:4:2,2:122,260:0.0104:2,2:9.5:1:26:1:0.59652:2.13:60:8:0.0105:0:1 -1 43812663 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10963;SOR=Inf;LSEQ=GCAGGGGATCCCTGGGGTTG;RSEQ=CCATGCCTGTTAGCAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:46,222:0:2,0:25.2:1:31.6:1:1:0:60:52.6:1:0:0.1 0/1:247:3:1,2:53,189:0.0121:2,2:24.3:1:23.7:1:0.52784:1.78:60:2:0.0083:0:3.3 -1 43814730 . G A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61393;SOR=0.47162;LSEQ=GCCTGCGCCAGGGACTGGGC;RSEQ=CCGGGTGCGAGTGGGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:0,2:11,149:0.0123:2,0:31:1:31.5:1:1:0:60:4:0.0126:0:1 0/0:171:1:0,1:14,156:0.0058:2,0:22:0:32:0:1:0:60:2:0.0059:0:1 -1 43814733 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2485;SOR=Inf;LSEQ=TGCGCCAGGGACTGGGCGCC;RSEQ=GGTGCGAGTGGGGCGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:8,137:0:2,0:24.5:1:31.7:1:1:0:60:71.5:1:0:0.2 0/1:156:3:1,2:8,145:0.0192:2,2:17.7:1:26.7:1:0.16428:8.76:60:2:0.0131:0:1 -1 43814738 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49932;SOR=Inf;LSEQ=CAGGGACTGGGCGCCGGGTG;RSEQ=GAGTGGGGCGGGGCTCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:7,118:0:2,0:23.7:1:30.1:1:1:0:60:24:1:0:0.2 0/1:138:2:0,2:6,130:0.0145:1,0:10.5:1:31:1:1:0:60:4:0.0148:0:1 -1 43814864 . T C 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34368;SOR=1.23903;LSEQ=GGCGAGGGGCGGGGCCAGAG;RSEQ=AGGGGCTGGCTGGATGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:78:69,9:88,12:0.4358:2,2:25.7:1:31.9:1:1:1.05:60:25:0.431:0:1.1 0/1:184:90:75,15:78,16:0.4891:2,2:21.6:1:31.9:1:1:1.03:60:89:0.4944:0:1.2 -1 43996593 . T A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20854;SOR=0;LSEQ=GCAGAGGCGGCGGCTCCAGC;RSEQ=TCGGCTCCGGCTCGGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:26:0:30:1:1:1.11803:60:4:0.1053:0:1 0/0:22:0:0,0:12,10:0:2,0:23.1:1:30.4:1:1:0:60:44:1:0:0.7 -1 43996613 . GGGCTCC G 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=24;MSI=5.000;MSILEN=6;SSF=0.23643;SOR=Inf;LSEQ=TTCGGCTCCGGCTCGGGCTC;RSEQ=GGCTCCGGCTCCGGCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:27.8:1:31.2:1:1:0:60:50:1:0:0.3 0/1:27:3:2,1:13,11:0.1111:2,2:29.7:1:28.3:1:1:1.66:60:6:0.1154:0.037:0.3 -1 44035232 . C G 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29522;SOR=0;LSEQ=GGGGGCAGGCAGAGCCAGCC;RSEQ=TAATACACACATTGCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:4,0:18,0:0.1818:1,0:21.8:1:29:1:1:0:60:8:0.1905:0:1.3 0/0:9:0:0,0:8,1:0:2,0:26.8:1:30.7:1:1:0:60:18:1:0:0 -1 44035352 . C T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00153;SOR=0.30782;LSEQ=ACAGCCACCATGCTATGTGC;RSEQ=GCAGGCGGAAATCCAGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:32:15,17:19,24:0.4267:2,2:20.9:1:31:1:1:1.11:60:64:0.4267:0:1 0/1:81:15:7,8:36,30:0.1852:2,2:27.9:1:29.7:1:0.77529:1.36605:60:14:0.1772:0:1.1 -1 44035353 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49707;SOR=Inf;LSEQ=CAGCCACCATGCTATGTGCC;RSEQ=CAGGCGGAAATCCAGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:34,41:0:2,0:23.3:1:31.3:1:1:0:60:150:1:0:0.5 0/1:79:2:1,1:41,36:0.0253:2,2:10.5:1:32:0:1:1.13701:60:4:0.0256:0:1.5 -1 44035472 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.91073;LSEQ=GAGCAGAGGGCAGGGGTCAA;RSEQ=GGGCCATGCAGACCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:3,13:1,9:0.6154:2,2:21.8:1:30.8:1:1:2.02:60:32:0.6154:0:1 1/0:27:16:4,12:2,9:0.5926:2,2:17.3:1:31.1:1:1:1.48:60:32:0.5926:0:1 -1 44044468 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTGCCTGACCTCTCGCTT;RSEQ=GTGTACCCACAGGTGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:9,3:0.1429:2,0:11.5:1:30:1:1:0:60:4:0.1429:0:1 0/0:3:0:0,0:3,0:0:0,0:18.7:1:31.7:1:1:0:60:6:1:0:0 -1 44054486 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52809;SOR=Inf;LSEQ=CGTGAACCTGACATGCGTGG;RSEQ=AGTGGGTGCACCCATGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:0:2,0:23.8:1:31.5:1:1:0:60:24:1:0:0.2 0/1:43:2:1,1:23,18:0.0465:2,2:10.5:1:28:1:1:1.27044:60:4:0.0513:0:1.5 -1 44054524 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.5311;SOR=Inf;LSEQ=CCTACGTGAAGTGGATGATG;RSEQ=GGGCCGAGGAGCTCACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:32.2:1:30.9:1:1:0:60:56:1:0:0.3 0/1:49:2:1,1:22,25:0.0408:2,2:15:1:28.5:1:1:1.13:60:4:0.0426:0:1 -1 44054536 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15211;SOR=0;LSEQ=GGATGATGGGGGCCGAGGAG;RSEQ=TCACCAAGGAGGATGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:12,14:0.0714:2,2:34:1:30:1:1:1.16:60:4:0.0769:0:1 0/0:43:0:0,0:19,24:0:2,0:25.7:1:31.6:1:1:0:60:42:1:0:0.4 -1 44056462 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGACAGGCCTGGCCAC;RSEQ=GTCCCTCACTTGTGCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29:1:1:0:60:4:1:0:1 -1 44057128 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48;SOR=0;LSEQ=TCACGACCGTGGGCAGCCTG;RSEQ=TGCCTGGCATCACCTACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:0.1538:2,2:14:1:28:1:1:2.4495:60:4:0.1538:0:1 0/0:13:0:0,0:8,5:0:2,0:24.5:1:31.8:1:1:0:60:26:1:0:0.2 -1 44057257 . A G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.56182;SOR=0.62832;LSEQ=ATGCCGGCTGGGCAGCCAAC;RSEQ=GCAGAGAAGGGGAGGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:5,7:8,6:0.4615:2,2:25.7:1:29.2:1:0.6951:1.82171:60:11:0.44:0:1.1 0/1:23:8:3,5:7,8:0.3478:2,2:25.9:1:30.6:1:1:1.43469:60:16:0.3478:0:1.1 -1 44063224 . A G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGAGAGAGGGAAGGAGAGAG;RSEQ=GGGAGGCAGGTCAGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:37:0:33:0:1:0:60:2:1:0:1 0/1:5:2:1,1:2,1:0.4:2,2:28:1:28.5:1:1:1.7321:60:4:0.4:0:2 -1 44063250 . T C 86 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGTCAGAGGGAGTCAGG;RSEQ=GTCCTTGGCGAGAGTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:38:0:32:0:1:0:60:2:1:0:1 1/1:7:7:4,3:0,0:1:0,2:26.9:1:30.9:1:1:0:60:14:1:0:1.6 -1 44064319 . A G 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80718;LSEQ=GGTGCTGAGGCAGGACCCTC;RSEQ=AGTTTGCTGTGCCCACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:4,1:8,0:0.3846:0,2:32.6:1:28.8:1:0.38462:0:60:10:0.3846:0:1.2 0/1:12:4:4,0:8,0:0.3333:0,0:25.3:1:31.3:1:1:0:60:8:0.3636:0:1 -1 44064455 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=TCCACTGCTGTGCATGTCTA;RSEQ=TGGAAGCTGCCTGTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:74,41:0:2,0:23.9:1:31.3:1:1:0:60:56.5:1:0:0.1 0/1:124:2:1,1:71,50:0.0161:2,2:7.5:1:29:1:1:1.41585:60:4:0.0164:0:2 -1 44064473 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23111;SOR=0;LSEQ=TACTGGAAGCTGCCTGTCCC;RSEQ=AGCAAGCAGCATGGCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:98,69:0.0118:2,2:38.5:1:30:1:1:1.41726:60:4:0.012:0:1 0/0:182:0:0,0:99,81:0:2,0:25.4:1:30.8:1:1:0:60:179:0.989:0:0.2 -1 44064479 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49992;SOR=Inf;LSEQ=AAGCTGCCTGTCCCCAGCAA;RSEQ=CAGCATGGCCAGATCCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:99,82:0:2,0:23.8:1:31.9:1:1:0:60:89.5:0.9944:0:0.1 0/1:201:2:1,1:109,88:0.01:2,2:36.5:1:32:0:1:1.23729:60:4:0.0102:0:1 -1 44079139 . C T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CCACCCTCCGCCATCCCTGT;RSEQ=GCCGCATGTGCTGCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:11.8:1:30.8:1:1:0:60:8:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:35:0:31.5:1:1:0:60:4:0.6667:0:1.5 -1 44079338 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09296;SOR=Inf;LSEQ=ACCGACCTGGCGGACAACAT;RSEQ=GAGCGCCTCAAAGCCAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,21:0:2,0:28.3:1:29.8:1:1:0:60:23.5:1:0:0.4 0/1:22:2:1,1:11,9:0.0909:2,2:27:1:27:0:1:1.21106:60:4:0.0909:0:1.5 -1 44079411 . T C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49793;SOR=0.55118;LSEQ=GATGTTCCCGCCCCCTACCA;RSEQ=GTGCCTGGCCCAGGCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:26:6,20:1,4:0.8387:2,2:22.3:1:30:1:1:1.19:60:52:0.8387:0:1.2 1/0:23:17:5,12:2,3:0.7391:2,2:21.1:1:30.3:1:1:1.56456:60:34:0.7391:0:1.1 -1 44081762 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCACCAGAGCAGCCTGAGG;RSEQ=GTGGGGTGTGCTGCGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:29:1:1:0:60:4:1:0:1 -1 44083015 . G A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37479;SOR=3.35527;LSEQ=GCTGTGGCCTGTGGAGTGAA;RSEQ=GCAGGATGTGAGCATCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:12,0:6,0:0.6667:0,0:25.1:1:30.9:1:1:0:60:24:0.6667:0:1.3 1/1:8:7:7,0:1,0:0.875:0,0:16.6:1:31.6:1:1:0:60:14:0.875:0:1.3 -1 44083110 . C T 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15368;SOR=2.15728;LSEQ=CCACCCGCTTTCTCCATTCT;RSEQ=TGCAGTCCATCGACCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:72:53,19:12,1:0.8471:1,2:24:1:30.3:1:0.28395:4.24839:60:144:0.8471:0:1.1 1/1:91:84:61,23:6,1:0.9231:2,2:22:1:29.4:1:0.67068:2.24553:60:41:0.9213:0:1.1 -1 44083168 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50504;SOR=Inf;LSEQ=GAATTCAAACCTGGAGGTGA;RSEQ=CAAGCCCAAGAACCGCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:63,71:0:2,0:29.2:1:30.1:1:1:0:60:268:1:0:0.4 0/1:169:2:1,1:85,82:0.0118:2,2:28:1:31.5:1:1:1.03638:60:4:0.0119:0:3 -1 44083190 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50193;SOR=Inf;LSEQ=AAGCCCAAGAACCGCTATGC;RSEQ=AATGTCATCGCCTACGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:50,77:0:2,0:28.2:1:30.8:1:1:0:60:126:1:0:0.3 0/1:151:2:1,1:63,86:0.0132:2,2:40:0:31:1:1:1.36:60:4:0.0134:0:1 -1 44083205 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=TATGCGAATGTCATCGCCTA;RSEQ=GACCACTCTCGAGTCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:38,77:0:2,0:25.2:1:30.5:1:1:0:60:56.5:0.9912:0:0.1 0/1:127:2:0,2:45,80:0.0157:2,0:38:1:26.5:1:0.53881:0:60:4:0.016:0:2.5 -1 44083507 . T C 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42616;SOR=1.41292;LSEQ=CCCCTGCCCGAGACCATGGG;RSEQ=GATTTCTGGAGGATGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:96:80:51,29:11,5:0.8333:2,2:24.9:1:30.9:1:0.78165:1.24813:60:79:0.8316:0:2 1/1:105:92:62,30:8,5:0.8762:2,2:21.5:1:30.4:1:0.75611:1.29:60:29.667:0.8725:0:2.1 -1 44083519 . G A 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.36501;SOR=1.40129;LSEQ=ACCATGGGTGATTTCTGGAG;RSEQ=ATGGTGTGGGAACAGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:88:53,35:12,7:0.8224:2,2:26.7:1:29.4:1:1:1.13076:60:87:0.8208:0:2 1/1:120:104:61,43:8,7:0.8667:2,2:24.8:1:27.6:1:0.78243:1.24:60:25:0.8621:0:1.9 -1 44083591 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10024;SOR=0;LSEQ=GAGAAGTCCCGGGTGAGGCT;RSEQ=CAGGGCCCTGCCAGGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:2,1:49,80:0.0227:2,2:10.3:1:28:1:0.55896:3.24:60:6:0.0231:0:2.3 0/0:151:0:0,0:57,94:0:2,0:22.7:1:31.6:1:1:0:60:49.333:1:0:0.7 -1 44083874 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGTGTTCCCGGGGTATTC;RSEQ=TGTGTTCCCCAGATGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:41:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 44084739 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52381;SOR=0.2952;LSEQ=AGTGGCTCCAGTGAGAAGCG;RSEQ=GAGCTGCGTCAGTTTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:22:1:21.5:1:1:0:60:1:0.5:0:2 0/1:6:2:1,1:1,3:0.3333:2,2:37.5:1:29:1:1:2.45:60:4:0.3333:0:1 -1 44084990 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18365;SOR=Inf;LSEQ=GCCGCACCGGCTGCTTCATC;RSEQ=TGATTGATGCCATGTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:54,0:0:1,0:23.6:1:29.9:1:1:0:60:108:1:0:0.1 0/1:41:2:2,0:39,0:0.0488:1,0:26.5:1:31.5:1:1:0:60:4:0.05:0:1 -1 44085022 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50335;SOR=Inf;LSEQ=ATGTTGGAGCGGATGAAGCA;RSEQ=GAGAAGACGGTGGACATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:65,21:0:2,0:25.9:1:30.3:1:1:0:60:27.667:1:0:0.1 0/1:107:2:1,1:73,32:0.0187:2,2:10.5:1:27.5:1:0.52372:2.26178:60:4:0.0187:0:1.5 -1 44085057 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50245;SOR=Inf;LSEQ=CATCTATGGCCACGTGACCT;RSEQ=CATGCGATCACAGAGGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:84,64:0:2,0:25.8:1:31.3:1:1:0:60:28.6:1:0:0.1 0/1:177:2:1,1:103,72:0.0113:2,2:28.5:1:27.5:1:1:1.42758:60:4:0.0114:0:1 -1 44085357 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4988;SOR=Inf;LSEQ=CTGCCTCTCAATAGTTGCTG;RSEQ=CCAGCTCCAAGGCCCACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:123,70:0:2,0:23.8:1:31.1:1:1:0:60:47.25:1:0:0.2 0/1:198:2:1,1:129,66:0.0101:2,2:33.5:1:30.5:1:1:1.94747:60:4:0.0105:0:1 -1 44085473 . C A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11313;SOR=0;LSEQ=ACCCGTGTGTGTCTGCAGCC;RSEQ=ATCCGTGGTGTGGAGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:2,1:76,129:0.0144:2,2:26:1:24.7:1:0.55757:3.37:60:2:0.01:0:1.3 0/0:221:0:0,0:77,144:0:2,0:24.9:1:30.8:1:1:0:60:54.25:1:0:0.1 -1 44085483 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62214;SOR=0.49324;LSEQ=GTCTGCAGCCCATCCGTGGT;RSEQ=TGGAGGGCTCTGACTACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:68,126:0.0102:2,2:15.5:1:28.5:1:1:1.85:60:4:0.0106:0:1 0/0:198:1:1,0:69,128:0.0051:2,0:1:0:23:0:0.35354:0:60:2:0.0051:0:1 -1 44085498 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49873;SOR=0;LSEQ=GTGGTGTGGAGGGCTCTGAC;RSEQ=ACATCAATGCCAGCTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:46,114:0.0123:2,2:34.5:1:30:1:0.49735:2.46:60:4:0.0126:0:1.5 0/0:154:0:0,0:43,111:0:2,0:25.4:1:28.8:1:1:0:60:76:1:0:0.1 -1 44086080 . T C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43829;SOR=0.6082;LSEQ=GAAGCCTGGCACCCCTCCCC;RSEQ=ATTCCTTCTCACCTGATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:43:37,6:9,0:0.8113:0,2:24.7:1:31.7:1:0.57446:0:60:86:0.8113:0:1.1 1/0:36:26:25,1:8,2:0.7222:2,1:23.1:1:27.7:1:0.18067:5.87:60:7.667:0.697:0:1.2 -1 44086136 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21263;SOR=Inf;LSEQ=TGTCCACAGGAGAAATGCCA;RSEQ=CAGTACTGGCCAGCAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:113,36:0:2,0:23.8:1:31.7:1:1:0:60:298:1:0:0.3 0/1:128:2:1,1:87,39:0.0156:2,2:26.5:1:27.5:1:0.52904:2.21537:60:4:0.0157:0:1.5 -1 44086212 . C A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02094;SOR=Inf;LSEQ=TGGCTGAGTACAACATGCCC;RSEQ=AGTATATCCTGCGTGAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:201,184:0:2,0:28.1:1:31.3:1:1:0:60:76:1:0:0.1 0/1:332:5:2,3:168,158:0.0151:2,2:23.4:1:25.6:1:0.67742:1.5927:60:4:0.0123:0:1 -1 44086287 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52799;SOR=0;LSEQ=AGTGTGTCCATAACGCTGCC;RSEQ=GTCCACACGCTGGGTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:41,141:0.0109:2,2:20.5:1:32:1:0.40538:3.41:60:4:0.0111:0:1 0/0:112:0:0,0:32,80:0:2,0:20.9:1:30.2:1:1:0:60:224:1:0:0.1 -1 44086554 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19606;SOR=0;LSEQ=AGTTCCAGTTCACAGACTGG;RSEQ=CAGAGCAGGGCGTGCCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:65,67:0.0149:2,2:36.5:1:30.5:1:1:1.03:60:4:0.0152:0:1 0/0:168:0:0,0:90,78:0:2,0:29.3:1:31.1:1:1:0:60:55:1:0:0.1 -1 44086826 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49818;SOR=0;LSEQ=GCATCGTCCTGGAGCGCATG;RSEQ=GCTACGAGGGCGTGGTCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:35,17:0.037:2,2:13:1:28.5:1:1:2.02925:60:4:0.037:0:2 0/0:46:0:0,0:29,17:0:2,0:23.9:1:31.3:1:1:0:60:92:1:0:0.9 -1 44086831 . C T 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.10533;LSEQ=GTCCTGGAGCGCATGCGCTA;RSEQ=GAGGGCGTGGTCGACATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:47:30,17:10,2:0.7966:2,2:24.3:1:30.8:1:0.3034:2.7896:60:94:0.7966:0:1.2 1/1:48:39:25,14:5,4:0.8125:2,2:25.1:1:29.1:1:0.7111:1.42:60:78:0.8125:0:1.1 -1 44087496 . C T 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.86091;LSEQ=GTAGCTGCCAGGGTCCAGCA;RSEQ=CTGCTCTTGGCCAGCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:21:21,0:4,0:0.84:0,1:18.4:1:31.6:1:1:0:60:42:0.84:0:1 1/1:11:9:9,0:2,0:0.8182:0,0:21.2:1:31:1:1:0:60:18:0.8182:0:1 -1 44087693 . C A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11464;SOR=0;LSEQ=AACTACCGCTCCCCTCTCCT;RSEQ=CGCCACCCCCGCCGTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:2,1:64,122:0.0159:2,2:17:1:26.7:1:0.27957:3.78:60:6:0.016:0:1 0/0:199:0:0,0:79,120:0:2,0:22.4:1:30.4:1:1:0:60:98.5:1:0:0.2 -1 44087694 . C A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61627;SOR=0.4777;LSEQ=ACTACCGCTCCCCTCTCCTC;RSEQ=GCCACCCCCGCCGTGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:64,121:0.0107:2,2:12:1:28.5:1:1:1.88:60:4:0.0109:0:1 0/0:195:1:1,0:76,118:0.0051:2,0:1:0:24:0:0.39487:0:60:2:0.0051:0:1 -1 44087729 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49745;SOR=0;LSEQ=GGGGCTCCGGAGGGGACCCA;RSEQ=CTCCTCTGAGCCATACCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:11,65:0.0256:2,2:17:1:30.5:1:0.28571:5.70:60:4:0.026:0:1 0/0:72:0:0,0:9,63:0:2,0:23.1:1:32.1:1:1:0:60:71:1:0:0.1 -1 45795150 . A G 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11106;SOR=Inf;LSEQ=GGAGGCCTTGTAGTTGGGGG;RSEQ=GGGGGAGCAGAGAATCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:78,228:0:2,0:24.3:1:30.1:1:1:0:60:22.538:1:0:0.1 0/1:287:3:1,2:78,206:0.0105:2,2:14.7:1:22.3:1:1:1.32:60:2:0.0071:0:1.3 -1 45796269 . G C 291 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07338;LSEQ=GGTGAGGGCTGGCACTTTTT;RSEQ=CAAAAGAGATAAACCGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:662:660:223,437:0,0:0.997:0,2:25.6:1:31.1:1:1:0:60:54:0.9969:0:1.1 1/1:655:629:228,401:7,18:0.9603:2,2:26.7:1:30.5:1:0.52482:1.46:60:43.929:0.9594:0:1.2 -1 45796354 . G T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTTGGCCAGGCATGGTG;RSEQ=CTCACGCCTATAATCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:1,108:0:1,0:22.7:1:32.3:1:1:0:60:108:1:0:0.4 0/1:66:21:1,20:0,44:0.3182:1,1:20.7:1:29:1:0.32308:0:60:20:0.3077:0:1.5 -1 45797505 . C G 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=5.78333;LSEQ=GGAGGCAGGCACAGGTGGCA;RSEQ=TGTCCAGTGTTGGGAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:771:39:17,22:341,390:0.0506:2,2:29.5:1:32.8:1:0.74432:1.13134:60:78:0.0513:0:1.2 0/1:806:190:81,109:286,329:0.2357:2,2:26.2:1:31.3:1:0.36042:1.16957:60:94:0.238:0:1.2 -1 45798555 . T C 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09044;LSEQ=TCACCCGTCAGTCCCTCTAT;RSEQ=GTTCCTATTTCCCCTACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:854:851:372,479:1,1:0.9965:2,2:24.2:1:30.4:1:1:1.28724:60:84.1:0.9964:0:1.1 1/1:959:923:388,535:18,17:0.9625:2,2:24.1:1:30.2:1:0.29804:1.45936:60:114.375:0.9621:0:1.2 -1 45798717 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11149;SOR=Inf;LSEQ=ACACCCACCCCAAAGTAGAG;RSEQ=CTCTCATCTGGGGTCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:187,131:0:2,0:24.1:1:31.3:1:1:0:60:78.5:1:0:0.1 0/1:297:3:2,1:164,129:0.0101:2,2:29.7:1:25:1:1:1.57:60:2:0.0069:0:1.3 -1 45798742 . A T 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19915;SOR=4.387;LSEQ=CATCTGGGGTCTGACCCATG;RSEQ=CCCTTCCCTTCCTCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:1:0,1:246,165:0.0024:2,0:1:0:26:0:0.40291:0:60:2:0.0025:0:1 0/1:379:4:1,3:223,151:0.0106:2,2:13.5:1:26.8:1:0.30858:4.4136:60:8:0.0107:0:1.5 -1 45798981 . C A 144 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02835;LSEQ=ATATGCCCGCCTGTCCAGGT;RSEQ=CATCTCATCTTCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:32:21,11:439,410:0.0363:2,2:21.5:1:28.8:1:0.14947:1.78:60:64:0.0369:0:1.3 0/0:938:1:1,0:486,451:0.0011:2,0:1:0:21:0:1:0:60:2:0.0011:0:1 -1 45799280 . G A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09076;SOR=0;LSEQ=ATCATCCCTGCACAGGCTGT;RSEQ=CATCAGGGTCTTGGGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:3:2,1:43,177:0.0135:2,2:8.7:1:27:1:0.10442:8.12:60:6:0.0135:0:1 0/0:272:0:0,0:74,198:0:2,0:23:1:31.6:1:1:0:60:67:1:0:0.2 -1 45799302 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.99576;LSEQ=ATCAGGGTCTTGGGACACAG;RSEQ=AGCCTGTGGCAGTATGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:0,1:23,132:0.0064:2,0:28:0:11:0:1:0:60:0:0:0:5 0/1:158:2:1,1:22,134:0.0127:2,2:14:1:28.5:1:0.27074:5.98:60:4:0.0129:0:1 -1 45799337 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50437;SOR=0;LSEQ=TGCTCCCACTTAGGGCTTCC;RSEQ=CCAACTAACCCCCTTAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:5,74:0.0247:2,2:25.5:1:29:1:0.14352:13.60:60:4:0.025:0:1 0/0:63:0:0,0:4,59:0:2,0:22.1:1:30.7:1:1:0:60:62:1:0:0.1 -1 45800156 . C T 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCTGTGACCACTTCCCA;RSEQ=GGCTGCTCGTGGCTTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:913:0:0,0:382,531:0:2,0:26.1:1:30.6:1:1:0:60:227.25:1:0:0.1 0/1:958:130:56,74:366,457:0.1357:2,2:27:1:29.2:1:0.77662:1.05825:60:42.333:0.1338:0:1.1 -1 45802143 . C G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAAAATAGCCTTAACTGAT;RSEQ=ACATTCCACCACTGTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:31.5:1:1:0:60:4:1:0:1.5 -1 45805566 . G C 93 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=1;SOR=0;LSEQ=ACCCAGCCACCCCACTACCC;RSEQ=CTACCCGCGGCCCACGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:17.6:1:31:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 45805796 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24892;SOR=Inf;LSEQ=CCGGACCCGGGACGTCTGAA;RSEQ=GGAAGTTCGACCCATCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:222,43:0:2,0:23.3:1:31.4:1:1:0:60:43.167:1:0:0.1 0/1:276:3:1,2:216,57:0.0109:2,2:6.3:1:25.7:1:0.1165:7.50362:60:6:0.011:0:1 -1 45805826 . C T 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06377;SOR=Inf;LSEQ=ACCCATCGGCGACCCGACGG;RSEQ=GAGACCCCGCCCCATCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:304,137:0:2,0:24.8:1:30.9:1:1:0:60:62:1:0:0.1 0/1:493:5:1,4:322,166:0.0101:2,2:9.8:1:27.2:1:0.05031:7.72678:60:10:0.0102:0:1 -1 46509146 . G A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01087;SOR=0;LSEQ=GCTTAGTATGTCAGTGCAGC;RSEQ=GCATGGCTGAGTCCTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:0.4545:0,0:31.2:1:31:1:1:0:60:10:0.4545:0:1 0/0:13:0:0,0:12,1:0:1,0:23.5:1:30.4:1:1:0:60:26:1:0:0.2 -1 46511487 . G C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08557;SOR=1.79315;LSEQ=GGTCCGAGCCATGGGTCCTC;RSEQ=TTACTGTACATTAACTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:43:43,0:49,1:0.4574:1,1:23.6:1:30.9:1:1:0:60:20.5:0.4505:0:1.2 1/0:73:44:42,2:28,1:0.6027:1,1:19.1:1:30.9:1:1:1.32826:60:88:0.6027:0:1.1 -1 46511981 . T G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90275;LSEQ=TGAATAAAAGTGCTTTTACA;RSEQ=CCAGATTTTGGGTAGCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:20:15,5:7,2:0.6897:2,2:24.2:1:33.3:1:1:1.16055:60:40:0.6897:0:1.1 1/0:6:4:3,1:0,2:0.6667:0,2:22:1:33:1:0.4:0:60:8:0.6667:0:1 -1 46512162 . AAGGCGCATGTCTTATATTGATAACAAAGCCCTCTGACAGAAAGGTAT A 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATATTTACCACGTATAAAC;RSEQ=AGAGAGAACTTACTCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:325,124:0:2,0:23.1:1:30.1:1:1:0:60:43.9:1:0:0.1 0/1:559:41:24,17:344,174:0.0733:2,2:24.1:1:29.6:1:0.30932:1.39956:58.9:82:0.0741:0.0304:0.2 -1 46521517 . G A 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00169;SOR=1.31902;LSEQ=TGGATCAGGTCAGGTTTGAT;RSEQ=CTATTCATTTTTTTATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1011:499:254,245:256,256:0.4936:2,2:22.9:1:28.9:1:0.80142:1.04:60:70.286:0.492:0:1.7 1/0:1104:621:330,291:259,222:0.5625:2,2:26:1:28.4:1:0.85509:1.02877:60:102.5:0.5616:0:1.8 -1 46521559 . A T 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.64029;LSEQ=TCTCGGTTGTCCAAAGCTTG;RSEQ=TTCTTCAAATCCTGCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:905:446:211,235:203,256:0.4928:2,2:26.7:1:30:1:0.38568:1.13:60:445:0.4955:0:1.8 1/0:1074:660:313,347:190,221:0.6145:2,2:24.9:1:29.6:1:0.70618:1.05:60:131:0.6168:0:1.7 -1 46521724 . CT C 149 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.70688;SOR=0.81396;LSEQ=GTGAGCACGGTCCTAATATC;RSEQ=TTTTTTTTTTCCCTTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:25:1,24:1,45:0.3378:1,1:31.6:1:32.2:1:1:1.86:60:50:0.3521:0:0.2 0/1:58:17:0,17:2,37:0.2931:2,1:21.6:1:32.1:1:1:0:60:34:0.2982:0.0345:0.2 -1 46521792 . G A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71599;SOR=1.5334;LSEQ=GAGTGTAGTGGCATGATCTC;RSEQ=GCTCACTGCAACCTCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:0,9:0,10:0.4737:0,0:24.2:1:32.1:1:1:0:56.4:18:0.4737:0:1 1/0:12:7:0,7:0,5:0.5833:0,0:21.7:1:31.4:1:1:0:58.9:14:0.5833:0:1.3 -1 46527300 . G A 59 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0.17288;LSEQ=ACACTAGGGATCAGGACCAG;RSEQ=CACTGTAGGGACCCAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:27.3:1:29.5:1:1:0:60:8:0.8:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:16:0:31:0:1:0:60:2:0.3333:0:1 -1 46527505 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2496;SOR=0;LSEQ=GTTCCAATAGTAGGGCTGTG;RSEQ=AGTTTGAGGGGGTAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:3:3,0:125,10:0.0217:2,0:27.3:1:24.7:1:1:0:60:2:0.0149:0:1 0/0:123:0:0,0:115,8:0:2,0:24.6:1:31.9:1:1:0:60:60.5:1:0:0.1 -1 46531652 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49985;SOR=Inf;LSEQ=TAAAACAGCTAAAGATCATC;RSEQ=AGTGAATGATCGAAAATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:155,16:0:2,0:25.1:1:30.4:1:1:0:59.9:84.5:0.9941:0:0.1 0/1:190:2:1,1:167,21:0.0105:2,2:23.5:1:30:1:0.21871:7.79259:60:4:0.0106:0:1.5 -1 46532354 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.55944;SOR=2.75172;LSEQ=GCACCTGTGATCCCAGCTAC;RSEQ=GGGGAGGCTGAGGCAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:6,0:0.1429:0,0:15:0:32:0:1:0:60:2:0.1429:0:2 0/1:6:2:1,1:4,0:0.3333:0,2:15:1:28.5:1:0.33333:0:60:4:0.4:0:1 -1 46532407 . G A 36 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47633;LSEQ=CAGAAGGTCAAGACTGCAGT;RSEQ=AGCCATATTCATGCCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:12,0:0.2:0,0:29.7:1:29.7:1:1:0:60:6:0.2:0:1.3 0/1:11:3:3,0:8,0:0.2727:0,0:31.7:1:23:1:1:0:60:2:0.2:0:1.3 -1 46532925 . C CATATATAT 74 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=16.000;MSILEN=2;SSF=0.30246;SOR=0;LSEQ=CATGTTATTCTGTGTGTGAA;RSEQ=ATATATATATATATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:0,6:0,13:0.2143:1,0:26.7:1:28.8:1:1:0:59.2:12:0.2222:0:0.5 0/0:9:0:0,0:0,8:0:0,0:16.8:1:30.1:1:1:0:60:7:0.875:0:0 -1 46543047 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16531;SOR=Inf;LSEQ=TGTATAGAAAAAAGAATTAG;RSEQ=CAGACTGGAAATTATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:80,1:0:1,0:25.1:1:32:1:1:0:60:39.5:1:0:0.1 0/1:56:2:2,0:54,0:0.0357:1,0:18:1:32:0:1:0:60:4:0.037:0:1 -1 46546208 . T C 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00116;SOR=3.25697;LSEQ=CTCCTGAGTTGCTGGGATTA;RSEQ=AGGCATGAGCCACCATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:12:12,0:85,1:0.1224:1,0:26.6:1:32:1:1:0:60:24:0.1224:0:1 0/1:102:32:32,0:69,1:0.3137:1,1:21.2:1:31.8:1:1:0:60:64:0.3137:0:1.1 -1 46546852 . T G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTAACTATGAAATGATGG;RSEQ=TATGTTATTAATAATTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:16.7:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 46597496 . CT C 172 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.9056;SOR=0.9684;LSEQ=ATCAGACCCATCACGAGATT;RSEQ=TTTTTTTTTTCTCCCAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:35:28,7:191,63:0.1203:2,2:24.2:1:31.8:1:0.67497:1.32:60:70:0.1232:0.0206:0.3 0/1:402:47:35,12:269,86:0.1169:2,2:20.5:1:31:1:0.85719:1.07223:59.9:22.5:0.1131:0.0323:0.2 -1 46598253 . G A 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0094;SOR=Inf;LSEQ=CTTGTCTGGGCGCTCCCGCC;RSEQ=GGGTGTAAGAACCAACCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:148,22:0:2,0:22.4:1:29.5:1:1:0:60:84:1:0:0.7 0/1:147:6:4,2:119,21:0.0408:2,2:14.3:1:29.2:1:0.23951:2.8064:60:12:0.0408:0:1 -1 46598269 . C A 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=2.56069;LSEQ=CGCCGGGGTGTAAGAACCAA;RSEQ=CCGACCGCACCAACTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:34:31,3:136,36:0.165:2,2:25.3:1:29.4:1:0.14843:2.72:60:33:0.1642:0:2.1 0/1:205:69:58,11:105,31:0.3366:2,2:24.1:1:30.4:1:0.27731:1.55:60:138:0.3382:0:2 -1 46598273 . A C 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00111;SOR=1.88787;LSEQ=GGGGTGTAAGAACCAACCCG;RSEQ=CCGCACCAACTGCCCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:111:88,23:88,25:0.4955:2,2:24.1:1:31.9:1:0.8711:1.09:60:222:0.4978:0:1.4 1/0:220:143:110,33:58,19:0.65:2,2:24.3:1:32:1:0.8681:1.09:60:142:0.6514:0:1.6 -1 46598520 . TC T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12764;SOR=Inf;LSEQ=TCCATCTCGACTTTCACGTC;RSEQ=CCCACCGCTCTCTAGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:45,271:0:2,0:22.9:1:31:1:1:0:60:78:1:0:0.1 0/1:364:4:3,1:73,285:0.011:2,2:13.3:1:26.8:1:0.03039:11.60:60:8:0.0112:0.0055:0.5 -1 46641741 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=13.81375;LSEQ=GTATTTTTAGTAGAGATGGG;RSEQ=TTTCACCGTGTTAGCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:10:10,0:51,0:0.1639:1,0:20.9:1:31.4:1:1:0:49.5:20:0.1754:0:1.2 1/0:23:17:17,0:6,0:0.7391:0,1:23.9:1:31.9:1:1:0:39.5:34:0.7391:0:1.1 -1 46641827 . A G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18258;SOR=0.57085;LSEQ=AAAGTGCCGGGATTACAGGC;RSEQ=TGAGCCACCGCACCCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:21:21,0:128,6:0.1355:1,1:25.1:1:29.4:1:1:0:56.2:20:0.1325:0:1.9 0/1:122:10:9,1:107,5:0.082:1,2:21.1:1:30.5:1:0.40813:2.35473:58:20:0.0833:0:1.1 -1 46641837 . G A 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.86827;SOR=0.9288;LSEQ=GATTACAGGCATGAGCCACC;RSEQ=CACCCAGCCTAGTGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:23:23,0:144,15:0.1264:2,1:26.5:1:30:1:0.22286:0:57.7:22:0.1243:0:1.8 0/1:152:18:15,3:118,16:0.1184:2,2:20.5:1:29.2:1:0.70208:1.4708:60:17:0.1149:0:1.2 -1 46641839 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50129;SOR=0;LSEQ=TTACAGGCATGAGCCACCGC;RSEQ=CCCAGCCTAGTGGCTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:171,17:0.0105:2,2:6.5:1:30:1:0.18095:9.80398:60:4:0.0108:0:1.5 0/0:164:0:0,0:142,22:0:2,0:21.2:1:29.6:1:1:0:59.8:81:1:0:0.3 -1 46641869 . C T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21704;SOR=4.95219;LSEQ=GTGGCTCTGTTTTTTAAAAC;RSEQ=CCACCCTGGCTCACAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:1:0,1:285,96:0.0026:2,0:1:0:26:0:0.25393:0:60:2:0.0027:0:1 0/1:389:5:1,4:267,117:0.0129:2,2:5.8:1:26.8:1:0.03422:9.07337:60:10:0.0133:0:1.2 -1 46714305 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25076;SOR=Inf;LSEQ=GGACAGGGAAGGTGGGTAGA;RSEQ=CTGTTTGGACAGAAAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:84,186:0:2,0:23.3:1:31.8:1:1:0:60:66.5:1:0:0.1 0/1:300:3:1,2:102,195:0.01:2,2:18.3:1:28.3:1:1:1.046:60:6:0.0101:0:1 -1 46715874 . C CA 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90899;LSEQ=CCTGTCCCTGTACACTCCCT;RSEQ=AGTGCTTTCTAGAGTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:9:1,8:6,119:0.0672:1,2:16.7:1:28.2:1:0.39247:2.46:60:8:0.063:0.0299:0.2 0/1:114:7:0,7:5,102:0.0614:1,0:23.7:1:28.9:1:1:0:60:6:0.055:0:0 -1 46725397 . G A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.52105;SOR=0;LSEQ=GGCAGAGGTTGCAGTGAGCC;RSEQ=AGATTGTGCCACTGCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:10,0:0.2308:0,0:26.3:1:22.7:1:1:0:47.3:2:0.1667:0:2.3 0/0:7:0:0,0:7,0:0:0,0:17:1:26.6:1:1:0:50.4:6:1:0:2.4 -1 46725447 . CA C 82 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.73238;SOR=1.41827;LSEQ=AACAAAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAGCTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:7:7,0:26,0:0.2121:1,0:18.3:1:29.5:1:1:0:56.4:6:0.1875:0.0303:0.7 0/1:18:5:5,0:11,0:0.2778:0,0:23.8:1:31:1:1:0:56:10:0.2778:0.0556:1.8 -1 46725941 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8242;LSEQ=AGAGCCTGTGGTCATGTCCA;RSEQ=TGAGTGGGCATTCCTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:13:2,11:5,11:0.4483:2,2:36:1:31.2:1:0.40996:2.42412:60:26:0.4483:0:1.2 0/1:15:6:1,5:0,9:0.4:0,2:12.5:1:30.8:1:0.4:0:60:12:0.4:0:1 -1 46726057 . A C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00109;SOR=0.12427;LSEQ=GAGCTAACTTTCTAACTCCT;RSEQ=AAGTAGGAACTTGCTATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:17:14,3:16,1:0.5:1,2:28.5:1:31.5:1:0.60117:3.31312:60:34:0.5152:0:1 0/1:28:3:3,0:25,0:0.1071:1,0:27:1:32:0:1:0:60:6:0.1071:0:1 -1 46726134 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2226;SOR=Inf;LSEQ=CAGCTGCCTCTGTTGCCTCC;RSEQ=GATCAGCAGGACACAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:163,28:0:2,0:25.5:1:29.6:1:1:0:60:46.75:1:0:0.2 0/1:172:2:1,1:140,30:0.0116:2,2:43:0:31.5:1:0.32885:4.60717:60:4:0.0119:0:1.5 -1 46726747 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23912;SOR=0;LSEQ=AGCCTGCTGCTTTCTTACGT;RSEQ=TATGCTCATTTATGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:28,115:0.0138:2,2:8:1:27.5:1:0.36111:4.05:60:4:0.0142:0:1 0/0:151:0:0,0:37,114:0:2,0:21.9:1:31.2:1:1:0:60:150:1:0:0.1 -1 46726784 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60133;SOR=2.28033;LSEQ=CAGGGTGGAGGGCAATGCAG;RSEQ=GGTAGAAGAAAAGAGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:1:1,0:47,72:0.0083:2,0:14:0:32:0:0.4:0:60:2:0.0085:0:1 0/1:106:2:0,2:47,57:0.0189:2,0:17.5:1:29:1:0.50171:0:60:4:0.019:0:2.5 -1 46727122 . G A 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20508;SOR=Inf;LSEQ=AAATCTCTTCACTGAGTATT;RSEQ=CCTTCCAAGGGCTGTGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:19,186:0:2,0:21.2:1:31.8:1:1:0:60:40:0.995:0:0 0/1:171:2:2,0:18,151:0.0117:2,0:18:1:23.5:1:0.01307:0:60:4:0.0118:0:1 -1 46732948 . C G 47 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03845;SOR=11.51618;LSEQ=GTTTCACCACACTGGCCAGG;RSEQ=TGGTCTGGAACTCCTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:1,0:37,0:0.0263:1,0:3:0:29:0:1:0:60:2:0.027:0:1 0/1:12:3:3,0:9,0:0.25:0,0:39.7:1:30:1:1:0:60:6:0.25:0:1 -1 46736508 . C A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24857;SOR=0;LSEQ=GCCTCCCAAACCATCCATGG;RSEQ=CAATCCTTTGGGGGCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:2,1:30,141:0.0172:2,2:23:1:29.3:1:0.08737:9.22:60:6:0.0175:0:1.3 0/0:163:0:0,0:44,119:0:2,0:22.3:1:30.9:1:1:0:60:53.333:1:0:0.1 -1 46738046 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49846;SOR=0;LSEQ=ATTTAATACTGTAAAAGAGG;RSEQ=CTAGTCTTGGTCCTTTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:149,12:0.0123:2,2:20.5:1:25:0:0.1536:11.96969:60:4:0.0124:0:1 0/0:162:0:0,0:145,17:0:2,0:21.4:1:30.8:1:1:0:60:31.4:1:0:0.1 -1 46739188 . AT A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.62576;SOR=0.70883;LSEQ=CTCTAGGAGGAGGGTGGGAG;RSEQ=TTTTTTTTGTGCTAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:10:3,7:146,269:0.0235:2,2:30.3:1:31.4:1:1:1.26577:60:20:0.0239:0.0024:0.3 0/1:417:7:5,2:160,250:0.0168:2,2:18.4:1:30.4:1:0.11876:3.89:60:14:0.0169:0:0.1 -1 46739286 . C T 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01702;SOR=Inf;LSEQ=TAGGGGACTGCTGGTTGCTG;RSEQ=TCTTCCCAGGTAAGATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:0:0,0:291,255:0:2,0:24.9:1:31.6:1:1:0:60:48.636:1:0:0.1 0/1:630:7:2,5:350,273:0.0111:2,2:12.4:1:25.4:1:0.25013:3.19942:60:6:0.0097:0:1 -1 46739464 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.165;SOR=Inf;LSEQ=CCAAAGGGGGATATACCCCT;RSEQ=CCCTACTGTCTGTCTAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:26,156:0:2,0:23.2:1:31:1:1:0:60:59.667:1:0:0.1 0/1:125:2:1,1:13,110:0.016:2,2:10.5:1:27:1:0.21226:8.19:60:4:0.0163:0:1 -1 46739751 . A AT 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.12406;SOR=Inf;LSEQ=TAAAAAAATTTTTATTTTTA;RSEQ=TTTTTTTTCCCCCTAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:231,67:0:2,0:22.2:1:29.7:1:1:0:59.9:28.8:1:0:0.2 0/1:310:4:3,1:234,72:0.0129:2,2:13.3:1:29.5:1:1:1.08306:60:8:0.0132:0.0032:1 -1 46740131 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23898;SOR=Inf;LSEQ=TGAGTAGTATAGAGGCATGA;RSEQ=GGAGGAGCTGGTTGGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:123,49:0:2,0:23.1:1:31.7:1:1:0:60:56.333:1:0:0.1 0/1:165:2:1,1:122,40:0.0121:2,2:13:0:31.5:1:0.43865:3.02487:60:4:0.0122:0:1.5 -1 46740458 . C A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02662;SOR=Inf;LSEQ=TCTTCAGGACCATCTTGTTC;RSEQ=TTAGTGCCTCTCTTTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:25,155:0:2,0:22.7:1:31.8:1:1:0:60:89:1:0:0.2 0/1:171:5:3,2:29,137:0.0292:2,2:10:1:24.2:1:0.04594:6.97:60:4:0.0241:0:1.4 -1 46740500 . A G 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00728;SOR=0;LSEQ=TCTGCCTCTAGCAGTAGCCA;RSEQ=GCTATGGGCCCAGAAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:8:0,8:0,79:0.092:1,0:32.8:1:32.3:1:1:0:60:16:0.093:0:1 0/0:77:0:0,0:0,77:0:1,0:23.5:1:32:1:1:0:60:154:1:0:0 -1 46743451 . G A 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06118;SOR=Inf;LSEQ=TTTTATGAGGATGGCTAAGC;RSEQ=CTGTATCTTTTGACATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:183,53:0:2,0:24.5:1:30:1:1:0:60:58:1:0:0.1 0/1:237:5:3,2:159,72:0.0211:2,2:29.4:1:30.8:1:0.65004:1.46968:60:10:0.0216:0:1 -1 46743900 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38363;LSEQ=TGGGATGCTGCCTCCACTGC;RSEQ=ATCACCTTCGTCTTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:299:124,175:150,200:0.4607:2,2:26.1:1:29.4:1:0.75007:1.05835:60:148.5:0.4633:0:1.1 0/1:835:206:96,110:276,353:0.2467:2,2:24.1:1:29:1:0.51864:1.12:60:50.5:0.2469:0:1.3 -1 46743923 . G A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCTTCGTCTTCCACCAGC;RSEQ=TTCTCATGAGGAGCAGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:0:0,0:201,321:0:2,0:25.2:1:30.8:1:1:0:60:86:1:0:0.5 0/1:646:29:13,16:237,380:0.0449:2,2:22:1:30.1:1:0.55945:1.30:60:58:0.0453:0:2.2 -1 46743991 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50037;SOR=Inf;LSEQ=GTGTAGCTCTTAGAGGAAGG;RSEQ=GATAGGGAAAAGGGGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:19,146:0:2,0:21.9:1:30.6:1:1:0:60:40.25:1:0:0.2 0/1:186:2:1,1:32,152:0.0108:2,2:5.5:1:27.5:1:0.32415:4.69:60:4:0.011:0:2.5 -1 47882266 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49123;SOR=0;LSEQ=GCCCCGGGCCGCCGCCTCAC;RSEQ=CTGGCCGCCATCTACCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:25,2:0.069:2,2:26.5:1:30.5:1:0.19951:10.40842:60:4:0.0714:0:1 0/0:28:0:0,0:21,7:0:2,0:26.2:1:29.1:1:1:0:60:13:1:0:0 -1 47882385 . C A 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56875;SOR=2.92867;LSEQ=CGACTGCTTCGTCAAGGTGC;RSEQ=CCGCGAGCCGGGCAACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:1,0:72,78:0.0066:2,0:1:0:26:0:0.48344:0:60:2:0.0067:0:1 0/1:104:2:1,1:48,54:0.0192:2,2:28:1:26:1:1:1.12:60:4:0.02:0:1 -1 47882410 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51752;SOR=0;LSEQ=GAGCCGGGCAACCCGGGCAA;RSEQ=GGCAACTACTGGACGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:61,92:0.0129:2,2:31:0:32:1:1:1.50:60:4:0.0132:0:1.5 0/0:104:0:0,0:43,60:0:2,0:26.5:1:30.6:1:1:0:59.9:50.5:0.9902:0:0.2 -1 47882412 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52004;SOR=0;LSEQ=GCCGGGCAACCCGGGCAAGG;RSEQ=CAACTACTGGACGCTGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:60,94:0.0128:2,2:12:1:30:1:1:1.56:60:4:0.0132:0:1.5 0/0:102:0:0,0:42,59:0:2,0:26.6:1:31.3:1:1:0:59.9:49.5:0.99:0:0.2 -1 47882441 . G A 25 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62444;SOR=1.7482;LSEQ=GGACGCTGGACCCCGCGGCC;RSEQ=CAGACATGTTCGACAACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:34,87:0.0163:2,2:9.5:1:29.5:1:0.4898:2.54:60:4:0.0167:0:1 0/1:71:2:2,0:20,49:0.0282:2,0:1:0:25.5:1:0.09296:0:60:4:0.029:0:1 -1 47882497 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84536;LSEQ=CGCAAGCGCTTCAAGCGCGC;RSEQ=GAGCTGCCCGCGCACGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:19:0,19:1,7:0.7037:2,1:17.7:1:30.4:1:0.2963:0:60:18:0.6923:0:1.1 1/0:18:12:1,11:0,6:0.6667:0,2:19.2:1:30.4:1:1:0:60:24:0.6667:0:1 -1 47883019 . T C 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGCCGCCCTCGAGCGCCCCA;RSEQ=CTCTACCCCCCACCCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:0:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 47883024 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCGAGCGCCCCATCTCT;RSEQ=CCCCCCACCCTGGCTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:1:32.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 47903961 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCGCCCCCCGGGACGTG;RSEQ=TCCCCCACGGCCACGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29:1:1:0:60:4:1:0:1 -1 47904190 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49624;SOR=0;LSEQ=GCGGAGCCCGCTGGTGAAGC;RSEQ=GCCCTACTCGTACATCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:47,18:0.0299:2,2:23.5:1:29.5:1:0.48982:2.56837:60:4:0.0303:0:1 0/0:67:0:0,0:45,22:0:2,0:22.2:1:30:1:1:0:60:32.5:1:0:0.3 -1 47904269 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5131;SOR=0;LSEQ=CTGACGTTGAGCGAGATCTG;RSEQ=GAGTTCATCAGCGGCCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:51,28:0.0247:2,2:10:1:28.5:1:1:1.80711:53.5:4:0.0253:0:1 0/0:56:0:0,0:30,26:0:2,0:21.4:1:29.9:1:1:0:59.9:27:1:0:0.3 -1 47904339 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49825;SOR=0;LSEQ=GGCAGAACAGCATCCGCCAC;RSEQ=ACCTCTCTCTCAACGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:70,53:0.016:2,2:25.5:1:30.5:1:1:1.31777:60:4:0.0167:0:1 0/0:119:0:0,0:72,47:0:2,0:26.4:1:28.9:1:1:0:55.5:18.833:1:0:0.2 -1 47904348 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.49804;SOR=0;LSEQ=GCATCCGCCACAACCTCTCT;RSEQ=TCAACGACTGCTTCGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:68,58:0.0156:2,0:8.5:1:26.5:1:0.50049:0:56.5:4:0.0159:0:1 0/0:127:0:0,0:76,51:0:2,0:26.8:1:30.9:1:1:0:55.6:62.5:1:0:0.2 -1 47904367 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50264;SOR=Inf;LSEQ=TCTCAACGACTGCTTCGTCA;RSEQ=GATCCCCCGCGAGCCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:61,64:0:2,0:26.1:1:30.9:1:1:0:55.8:124:1:0:0.2 0/1:151:2:1,1:78,71:0.0132:2,2:17.5:1:29:1:1:1.09791:60:4:0.0137:0:1 -1 47904380 . G A 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03404;SOR=Inf;LSEQ=TTCGTCAAGATCCCCCGCGA;RSEQ=CCGGGCAACCCGGGCAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:61,62:0:2,0:26.1:1:32.2:1:1:0:57.1:122:0.9919:0:0.2 0/1:151:6:2,4:72,73:0.0397:2,2:19.7:1:30.2:1:0.68151:1.96405:53.3:12:0.0405:0:1.2 -1 47904385 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19841;SOR=0;LSEQ=CAAGATCCCCCGCGAGCCGG;RSEQ=CAACCCGGGCAAGGGCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:60,63:0.016:2,2:35:1:29:1:1:1.05:60:4:0.0164:0:1 0/0:155:0:0,0:71,83:0:2,0:26.1:1:30.5:1:1:0:57.9:37.5:1:0:0.2 -1 47904386 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50296;SOR=Inf;LSEQ=AAGATCCCCCGCGAGCCGGG;RSEQ=AACCCGGGCAAGGGCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:59,65:0:2,0:25.5:1:32.2:1:1:0:57.7:248:0.992:0:0.2 0/1:152:2:2,0:69,81:0.0132:2,0:22:1:26.5:1:0.21654:0:60:4:0.0135:0:1 -1 47904393 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25757;SOR=Inf;LSEQ=CCCGCGAGCCGGGCAACCCG;RSEQ=GCAAGGGCAACTACTGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:59,66:0:2,0:25:1:31:1:1:0:57.7:124:1:0:0.2 0/1:158:3:1,2:70,85:0.019:2,2:32.3:1:24.7:1:1:1.64208:60:2:0.0132:0:2 -1 47904651 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1746;SOR=Inf;LSEQ=CGGCCTACGGCGCACCCCCG;RSEQ=CGGGGCCGGCCCCGCATCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,8:0:2,0:24.5:1:31.4:1:1:0:60:30:0.9375:0:0.2 0/1:12:2:1,1:5,5:0.1667:2,2:5.5:1:24.5:1:1:1:60:4:0.1818:0:1 -1 47904668 . T TCCGCAC 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=4.000;MSILEN=6;SSF=0.60851;SOR=2.15523;LSEQ=CCGCCGGGGCCGGCCCCGCA;RSEQ=CCGCACCCGCACCCGCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:21:10,11:2,0:0.913:0,2:22.6:1:30.9:1:0.47826:0:59.8:42:0.913:0.3043:0.6 1/1:24:23:11,12:1,0:0.9583:0,2:16.5:1:29.7:1:1:0:59.6:46:0.9583:0.4583:0.5 -1 47904682 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.22429;SOR=0;LSEQ=CCCGCATCCGCACCCGCACC;RSEQ=GCACGCCTTCGCTTTCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:10,11:0.087:2,2:19.5:1:30.5:1:1:1.10:60:4:0.087:0:2.5 0/0:25:0:0,0:12,13:0:2,0:22.8:1:29.1:1:1:0:59.6:24:1:0:0.5 -1 47906425 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGATGGGGCTCTCCCAGAA;RSEQ=AGCTTAGCTCCCCAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 47963691 . G GT 69 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CCCAGGTACCTTTCTCTTTG;RSEQ=TTCCTTCTTTTCCTGATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:14.6:1:30:1:1:0:60:10:1:0.6:0 1/0:6:4:3,1:1,1:0.6667:2,2:26.5:1:29.3:1:1:2.45:60:8:0.6667:0:0 -1 47963973 . G A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16256;SOR=0;LSEQ=TGTTTCCTAAAAGGCCTAGA;RSEQ=AATATGTATCAGGTGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:5,12:0,0:1:0,2:25.8:1:30.1:1:1:0:60:34:1:0:1.1 1/1:12:10:4,6:1,1:0.8333:2,2:21.1:1:29.6:1:1:1.4491:60:20:0.8333:0:1.2 -1 48909300 . G A 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=GGACTTTGCACCTTCTTAGG;RSEQ=GAAGAGTGCTGCTTTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:12,2:0.125:2,2:16:0:32.5:1:0.35:5.09912:42:4:0.125:0:6 0/0:15:0:0,0:12,3:0:2,0:25.7:1:30.7:1:1:0:59.3:30:1:0:0.1 -1 48909312 . C T 60 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12293;SOR=0;LSEQ=TTCTTAGGGGAAGAGTGCTG;RSEQ=TTTTACACTAACCAGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:2,2:18,1:0.1739:1,2:19.3:1:30.3:1:0.06663:14.31264:42.8:8:0.1818:0:5.3 0/0:17:0:0,0:14,3:0:2,0:28.1:1:31.9:1:1:0:59.4:34:1:0:0.1 -1 48909329 . C G 64 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.03785;SOR=0;LSEQ=CTGCTTTTACACTAACCAGT;RSEQ=AGGGATAGTATGAGATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:2,2:21,1:0.1538:1,2:36.3:1:32.3:1:0.05231:16.65582:42.8:8:0.16:0:5.3 0/0:31:0:0,0:25,6:0:2,0:20.5:1:31:1:1:0:59.2:62:1:0:0.1 -1 48909353 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49586;SOR=Inf;LSEQ=GATAGTATGAGATGCCACCC;RSEQ=GCGTTTACAGGAAAAGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:28,13:0:2,0:22.3:1:29.9:1:1:0:58.3:40:1:0:0.6 0/1:46:2:1,1:31,13:0.0435:2,2:27.5:1:30:1:0.52077:2.33466:60:4:0.0435:0:1 -1 48909356 . G A 62 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11715;SOR=0;LSEQ=AGTATGAGATGCCACCCGGC;RSEQ=TTTACAGGAAAAGGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:2,2:29,15:0.0833:2,2:24.8:1:31.3:1:0.60728:1.90534:42.8:8:0.0833:0:5.3 0/0:47:0:0,0:33,13:0:2,0:23.8:1:30:1:1:0:59.5:45:0.9783:0:0.2 -1 48909415 . T C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4992;SOR=0;LSEQ=CAAACTCTTATAACAACCTC;RSEQ=GGAGTTGGGCGACATGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:56,60:0.0169:2,2:24:1:27.5:1:1:1.07:60:4:0.0171:0:1 0/0:106:0:0,0:52,54:0:2,0:27.8:1:29.9:1:1:0:60:34.333:1:0:0.2 -1 48909461 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49738;SOR=0;LSEQ=CTTTCTAGGTCCCGTGACAG;RSEQ=CATCTTGCTATTACTCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:29,44:0.0267:2,2:25.5:1:28.5:1:1:1.51:60:4:0.0282:0:1.5 0/0:69:0:0,0:25,44:0:2,0:21.9:1:31.1:1:1:0:59.5:68:1:0:0.1 -1 48909491 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20335;SOR=Inf;LSEQ=ATTACTCGCCTTCAGGCCCT;RSEQ=TATTTTTAACCTCCTTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:9,33:0:2,0:19.6:1:32.2:1:1:0:59:84:1:0:0.2 0/1:35:2:1,1:9,24:0.0571:2,2:22.5:1:30:1:0.4958:2.58:48.5:4:0.0571:0:1 -1 48963214 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1985;SOR=0;LSEQ=ACAGCATGCCTGGTGACACT;RSEQ=TAGACTCTTCCAGTTTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:32,34:0.0294:2,2:40.5:1:29.5:1:1:1.06:60:4:0.0294:0:1.5 0/0:84:0:0,0:47,37:0:2,0:33.3:1:31.7:1:1:0:60:168:1:0:0.9 -1 48963247 . A G 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTAGCCATGGTGACATTT;RSEQ=TGGGGCATTCCTTTTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:60:26,34:0,0:1:0,2:23.1:1:31.9:1:1:0:60:59:1:0:1 1/1:78:78:38,40:0,0:1:0,2:20.4:1:30.3:1:1:0:60:38:1:0:1.1 -1 48963298 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21168;SOR=Inf;LSEQ=CCCTTGATGTCTAGAATAGC;RSEQ=CCTTTCTTGTAGATTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:17,27:0:2,0:22.9:1:29.9:1:1:0:60:13.667:1:0:0.5 0/1:38:2:1,1:12,24:0.0526:2,2:43:1:29.5:1:1:1.96:60:4:0.0541:0:1.5 -1 48963394 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49558;SOR=Inf;LSEQ=CAGGTGCCTCTCCTCTTTCC;RSEQ=TTTGTCTGCGTCATTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:33,24:0:2,0:20.6:1:30.9:1:1:0:60:27.5:1:0:0.2 0/1:57:2:1,1:31,24:0.0351:2,2:21.5:1:28.5:1:1:1.28581:60:4:0.0351:0:1 -1 48963398 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03889;LSEQ=TGCCTCTCCTCTTTCCCTTT;RSEQ=TCTGCGTCATTTTGGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:5,2:31,21:0.1167:2,2:23.9:1:29.3:1:0.69421:1.68:60:14:0.1186:0:1 0/1:58:7:3,4:29,22:0.1207:2,2:26.3:1:28:1:0.68905:1.74032:60:14:0.1207:0:1.3 -1 48963432 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53648;LSEQ=GGCAAATTACTGGAAGATGG;RSEQ=AGTTCCAGCCAAAAGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:31,32:0.0308:2,2:41.5:1:29:1:1:1.03:60:4:0.0317:0:1 0/1:60:1:0,1:30,29:0.0167:2,0:8:0:29:0:1:0:60:2:0.0167:0:1 -1 48963511 . T C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2881;SOR=0;LSEQ=GTTCAGAACTCTACCAGGAG;RSEQ=TGTACAAGAGCTTAGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:0.1304:1,0:21.3:1:34:0:1:0:60:6:0.1364:0:1 0/0:13:0:0,0:0,13:0:1,0:21.3:1:30.9:1:1:0:60:26:1:0:0 -1 48965535 . TAAAC T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCAGATGCATTTCGCTAA;RSEQ=AAGCATTGCAGCCAGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 50870454 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAGCCGGGACCACAGGCAC;RSEQ=CGACACCACACCCGGCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:32:1:1:0:60:4:1:0:1 -1 50871167 . C T 59 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTATGGTTAGAAATGTA;RSEQ=ATGATAGGAACTCCAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:28.3:1:29.8:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 50871536 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03945;SOR=7.77576;LSEQ=TATTATATTGGAAAAATAAG;RSEQ=GGGAAGGGTGTTGGGGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:21:1,20:0,13:0.6176:1,1:27.6:1:28.8:1:1:0:56.7:20:0.6061:0:1.7 1/1:14:13:0,13:0,1:0.9286:0,1:27.8:1:27.5:1:1:0:60:12:0.9231:0:1.9 -1 50871575 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02857;SOR=9.76965;LSEQ=CTTCCCTTTCCTTTAATGTG;RSEQ=TGGGATCCTTCTTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:14:0,14:0,12:0.5385:0,1:23.4:1:33.1:1:1:0:59.4:28:0.5385:0:2.1 1/1:13:12:1,11:0,1:0.9231:0,2:22.1:1:30.9:1:1:0:60:24:0.9231:0:2.3 -1 50871649 . G C 71 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGATCTCTGAGACTAAG;RSEQ=ATTTGCTTCATGGTTGCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:14.8:1:33.8:1:1:0:57.6:10:1:0:2.2 1/1:5:5:1,4:0,0:1:0,2:27:1:30.6:1:1:0:60:10:1:0:1.6 -1 51434327 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49576;SOR=Inf;LSEQ=AGCAGGGCGGAGGGCGGGGC;RSEQ=TGGGCGGCGCCCGGCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:46,2:0:1,0:16.9:1:29.7:1:1:0:60:23:1:0:0.2 0/1:52:2:1,1:43,7:0.0385:2,2:12:1:27:0:0.28658:5.81258:60:4:0.04:0:1 -1 51434373 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18889;SOR=0;LSEQ=CCGCGGCGCTGCAACTCTGC;RSEQ=GAGCCTCCTTAAAACTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:130,43:0.0114:2,2:34:0:32:1:0.44072:3.00017:60:4:0.0115:0:1 0/0:227:0:0,0:163,64:0:2,0:24.1:1:29.6:1:1:0:60:27.375:1:0:0.2 -1 51434393 . C T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.38227;SOR=3.38626;LSEQ=CGAGCCTCCTTAAAACTCTG;RSEQ=CGTTAAAATGGGGGCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:1:0,1:185,83:0.0037:2,0:1:0:25:0:0.31227:0:60:2:0.0038:0:1 0/1:320:4:1,3:222,94:0.0125:2,2:12.5:1:27:1:0.08476:7.0371:60:8:0.0129:0:1 -1 51434469 . GA G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.78733;SOR=0.77435;LSEQ=AAAAAAAGCTGATGAGGTCG;RSEQ=AAAAAGGGAGAAGAAACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:7:4,3:214,187:0.0172:2,2:26.4:1:30.1:1:1:1.16:60:14:0.0174:0.0049:0 0/1:525:7:4,3:267,250:0.0133:2,2:31.3:1:31:1:1:1.25:60:14:0.0136:0:0 -1 51434554 . G A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13509;SOR=Inf;LSEQ=AAAAAGCAGCAAGGGAGGGA;RSEQ=TGAAGGAAAAAAGCAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:38,135:0:2,0:22.5:1:31.6:1:1:0:60:33.6:1:0:0.1 0/1:223:4:3,1:52,167:0.0179:2,2:16.3:1:27.3:1:0.04735:9.51:60:8:0.0181:0:1 -1 51434560 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.5033;SOR=Inf;LSEQ=CAGCAAGGGAGGGAGTGAAG;RSEQ=AAAAAAGCAAAAAAGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:31,127:0:2,0:22.1:1:31:1:1:0:60:30.6:1:0:0.1 0/1:192:2:1,1:44,146:0.0104:2,2:29:1:26.5:1:0.41476:3.29:60:4:0.0108:0:1 -1 51434568 . C CA 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50557;SOR=Inf;LSEQ=GAGGGAGTGAAGGAAAAAAG;RSEQ=AAAAAAGGGGGCGACACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:19,117:0:2,0:22.8:1:31.4:1:1:0:60:18.429:1:0:0.1 0/1:173:2:1,1:35,136:0.0116:2,2:30.5:1:27:0:0.37384:3.85:60:4:0.0116:0:0 -1 51436157 . G T 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=GCACAAAATGGATTTGGAAG;RSEQ=ACTGCGCTGCAGGTTGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:14:5,9:170,265:0.0312:2,2:22.3:1:29.2:1:1:1.15439:60:28:0.0314:0:1 0/0:530:0:0,0:210,320:0:2,0:26.6:1:30.8:1:1:0:60:105:1:0:0.2 -1 51437709 . GA G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.2069;SOR=Inf;LSEQ=ATATTGCTATTATTTTCTGT;RSEQ=AAAAAGGTGAATTTTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:150,4:0:1,0:24:1:30.6:1:1:0:60:153:1:0:0.1 0/1:129:2:2,0:117,10:0.0155:2,0:45.5:1:32:1:1:0:60:4:0.0159:0:0 -1 51437902 . G A 281 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2224;SOR=0;LSEQ=AAATATGACTAAATCTTTAG;RSEQ=GACAGTTGTGGTCGTATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:572:572:193,379:0,0:1:0,2:26:1:30.7:1:1:0:60:113.4:1:0:1.1 1/1:511:509:188,321:0,0:0.9961:0,2:25.3:1:29.9:1:1:0:60:100.8:1:0:1.1 -1 51437916 . G A 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00462;SOR=Inf;LSEQ=CTTTAGGGACAGTTGTGGTC;RSEQ=TATCAATTTTTAATAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:496:0:0,0:153,343:0:2,0:25.6:1:31.2:1:1:0:60:81.667:1:0:1 0/1:432:7:3,4:145,280:0.0162:2,2:29.7:1:29:1:0.69532:1.45:60:14:0.0164:0:2.3 -1 51439494 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19648;SOR=Inf;LSEQ=AGTTACATAAATGGAAGGAC;RSEQ=GGCAGATATTTTAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:165,18:0:2,0:22.1:1:30.5:1:1:0:60:182:0.9945:0:0.1 0/1:147:2:1,1:131,14:0.0136:2,2:8.5:1:27.5:1:0.1943:9.0743:60:4:0.0138:0:1 -1 51439777 . C T 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11593;LSEQ=CACTTGGCTGCCAAAGAAGG;RSEQ=CACCTCCGGGTGGTGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:80:32,48:167,202:0.1782:2,2:22:1:29.9:1:0.45661:1.23951:60:79:0.1779:0:1.1 0/1:572:14:9,5:237,320:0.0245:2,2:33.3:1:27.6:1:0.16968:2.43:60:13:0.0232:0:1.2 -1 51440064 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=TAAGCAGCTAAATTTTCTGA;RSEQ=ACTGCATAAGTGAAAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:0,27:0:1,0:29.6:1:29.4:1:1:0:60:12.5:1:0:0.1 0/1:22:2:0,2:0,20:0.0909:1,0:36:1:29:1:1:0:60:4:0.0909:0:1 -1 51440093 . C T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.52015;LSEQ=AGTGAAAATCTTACAACAGG;RSEQ=TTATGAATATATTTAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:0.0909:1,0:19.5:1:29:1:1:0:60:4:0.0952:0:1 0/1:15:2:0,2:0,13:0.1333:1,0:48:0:32:0:1:0:60:4:0.1333:0:1 -1 51441244 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24839;SOR=Inf;LSEQ=TCATCTACCACATGATCAAA;RSEQ=ATGTTTTATGTGAACGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:157,54:0:2,0:24.8:1:31.7:1:1:0:60:104.5:1:0:0.1 0/1:217:3:2,1:157,57:0.0138:2,2:24.7:1:23.7:1:1:1.37502:60:2:0.0093:0:1 -1 51441409 . A G 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03054;SOR=0;LSEQ=TTTTCAATAATTTATTTTCC;RSEQ=TGATAGTATAAAAGAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:5:2,3:100,222:0.0153:2,2:34.6:1:31.6:1:0.64904:1.48:60:10:0.0154:0:1 0/0:328:0:0,0:129,199:0:2,0:24.5:1:29.7:1:1:0:60:108.333:1:0:0.1 -1 53409305 . G T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11235;SOR=0;LSEQ=GTGTCTTCAAAAAGGCCAAC;RSEQ=AGATAGGCCTCACTTACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:3,1:14,8:0.1538:2,2:26.8:1:31:1:1:1.68:60:8:0.1538:0:1.3 0/0:23:0:0,0:15,8:0:2,0:23.7:1:30.5:1:1:0:60:46:1:0:0.1 -1 53409417 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15892;SOR=Inf;LSEQ=GACGCTGGAAGGGAGGTTTG;RSEQ=GAATCAGTTTAGTGGACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:29,17:0:2,0:24.4:1:31.8:1:1:0:60:92:1:0:0.1 0/1:31:2:1,1:14,15:0.0645:2,2:22:1:27:1:1:1.07:60:4:0.0645:0:1 -1 53569399 . A G 139 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00111;SOR=0;LSEQ=GCAGAGCAGGGATTGCTATC;RSEQ=ATATTTTACCCAAAGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:17,7:0,0:1:0,2:18.5:1:30.5:1:1:0:60:48:1:0:1.3 0/1:7:3:2,1:3,1:0.4286:2,2:33.3:1:30.7:1:1:1.41418:60:6:0.4286:0:1 -1 53569492 . T C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00082;SOR=Inf;LSEQ=CATTCCTCTTCTTACTTCTA;RSEQ=ACCTCATCACCCCATCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:12,20:0:2,0:23.1:1:29.3:1:1:0:60:64:1:0:0.2 0/1:26:8:3,5:8,10:0.3077:2,2:36.4:1:31.1:1:1:1.31876:60:16:0.3077:0:1 -1 53571288 . C G 68 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAGCATCCCACCTCCAG;RSEQ=AGACAGCGTGACTGGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:29.8:1:29.4:1:1:0:60:10:1:0:1.2 1/1:2:2:2,0:0,0:1:0,0:22:1:33:0:1:0:60:4:1:0:1 -1 53809833 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAGGTGAGTTGCTACAC;RSEQ=GAGAGGGCCTGCTGGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:16.5:1:32:0:1:1:60:4:0.5:0:2 -1 53809858 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCTGCTGGATGGGTCAG;RSEQ=GAGGAGGGAGGGTGCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:41.5:1:30.5:1:1:1:60:4:0.5:0:2 -1 53811817 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14267;SOR=Inf;LSEQ=CAGGACTTTCCCACTTTGGG;RSEQ=GAAGCCTATGCACCTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:185,28:0:2,0:25.2:1:30.1:1:1:0:60:52.25:1:0:0.1 0/1:131:2:1,1:110,19:0.0153:2,2:7.5:1:27:1:0.28303:5.66853:60:4:0.0154:0:1 -1 53811822 . C T 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.52628;LSEQ=CTTTCCCACTTTGGGAGAAG;RSEQ=CTATGCACCTGGGAGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:2,1:194,33:0.013:2,2:26:1:25:1:0.38256:2.9203:60:2:0.0089:0:3.7 0/0:145:1:0,1:117,27:0.0069:2,0:1:0:22:0:0.1931:0:60:2:0.0069:0:1 -1 53811942 . G T 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.15868;LSEQ=TTACTATGCAGGGTATGAGG;RSEQ=TCCTGAGGAGAGATTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:210:98,112:231,259:0.3:2,2:27.6:1:30.2:1:0.93425:1.01928:60:209:0.3025:0:1.2 0/1:622:299:141,158:147,176:0.4807:2,2:27.5:1:29.7:1:0.6882:1.07:60:298:0.4846:0:1.1 -1 53812211 . C T 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAACAAGGCCAAGTGAA;RSEQ=GCCTGGTGACCAGATGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:20:1:31.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 55878119 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=CAATTCAGAATACAATATGG;RSEQ=AGAGAAGGATTTACAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:5,0:0.2857:0,2:20.5:1:29.5:1:0.28571:0:60:4:0.2857:0:1.5 0/0:6:0:0,0:4,2:0:2,0:18.8:1:26.8:1:1:0:60:12:1:0:0 -1 57004147 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01919;SOR=3.95815;LSEQ=ACAAACACAAAGGGAAAGAG;RSEQ=AGAGGCACCCGATAGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:15,8:14,2:0.5897:2,2:25.3:1:29.7:1:0.15233:3.61643:59.6:22:0.5789:0:1.9 1/1:34:29:20,9:4,1:0.8529:2,2:26.8:1:29.3:1:1:1.77198:58.6:28:0.8485:0:1.9 -1 57004178 . G T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00024;SOR=5.28224;LSEQ=GATAGATGTTCTCTAGGCCT;RSEQ=TTAGAAAACATGGAGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:63:34:28,6:24,5:0.5397:2,2:23.9:1:30.6:1:1:1.02812:59.7:33:0.5323:0:1.7 1/1:51:44:31,13:7,0:0.8627:0,2:22.9:1:29.9:1:0.1695:0:59.1:88:0.8627:0:1.6 -1 57004270 . TA T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21189;SOR=Inf;LSEQ=TAAGGGAATGGGTACTGCTC;RSEQ=AAAAGAATGCCCCACAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:128,92:0:2,0:23.6:1:28.7:1:1:0:60:219:0.9955:0:0.2 0/1:189:2:1,1:106,81:0.0106:2,2:24:1:27.5:1:1:1.30675:60:4:0.0108:0.0053:0.5 -1 57004417 . A T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02382;SOR=Inf;LSEQ=GCATATTGAGCACATTAAGC;RSEQ=CTCCAAGAGCTGAGATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:4,40:0:2,0:25.6:1:30.3:1:1:0:60:88:1:0:0 0/1:30:4:1,3:4,22:0.1333:2,2:29.3:1:28.8:1:0.53841:1.79:60:8:0.1379:0:1 -1 58158530 . G A 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.84356;LSEQ=TAACCAGTCAGGGATAGTAC;RSEQ=AGATGCTACCCGGCATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:1,1:0.75:2,0:29.5:1:29.5:1:0.25:0:53.7:12:0.75:0:1 1/0:7:5:4,1:2,0:0.7143:0,2:26.4:1:30:1:1:0:50.8:10:0.7143:0:1 -1 58158593 . G C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04778;SOR=Inf;LSEQ=ACAATGCCTTTCAAACTCTT;RSEQ=TACCAACCTCTGGAGTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,15:0:2,0:29.6:1:32.9:1:1:0:58.9:58:1:0:0.3 0/1:27:4:2,2:14,9:0.1481:2,2:39.3:1:32:1:1:1.52962:60:8:0.1538:0:1.3 -1 58158647 . C G 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00516;SOR=0;LSEQ=CCCCTTTCTAGGTCCCATAA;RSEQ=AGCCATCTTGCTATTACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:2,6:8,13:0.2759:2,2:24.8:1:31.5:1:0.6749:1.80915:60:16:0.2759:0:1.1 0/0:25:0:0,0:11,13:0:2,0:19.1:1:30.5:1:1:0:60:48:0.96:0:0.3 -1 58160304 . C G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCATTATTAGGCTTTTT;RSEQ=AAACTAAGGATATTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:1:30:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 59245595 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16211;SOR=Inf;LSEQ=TGGTCAAAATCATCTCACCT;RSEQ=CCGGGTTGCTGACATCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:13,237:0:2,0:24.4:1:29.8:1:1:0:60:49:1:0:0.1 0/1:169:2:1,1:15,152:0.0118:2,2:8:1:26.5:1:0.1809:9.84:60:4:0.012:0:1 -1 59245987 . T C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTAAGTTATATCTGTAGG;RSEQ=AGAATTCAAGTTTCCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:21:1:32:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 59246115 . T G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTACTATCTTTTGAGACT;RSEQ=ATTCTATATTTAAACAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:23:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 59246773 . G A 45 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38344;SOR=0.29835;LSEQ=GAAACATCGCACTATCCTTT;RSEQ=GTAAGCAATTCCATATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:4:2,2:65,264:0.012:2,2:5.3:1:22.8:1:0.18172:4.04:60:3:0.0093:0:1 0/0:278:1:1,0:66,211:0.0036:2,0:1:0:23:0:0.24101:0:60:2:0.0037:0:1 -1 59247596 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52778;SOR=0;LSEQ=TCGTGCACACTGGGGGCGCC;RSEQ=TCAGGACGCAACCCAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:2,0:82,1:0.0235:1,0:22:1:29:1:1:0:60:4:0.0238:0:1 0/0:51:0:0,0:51,0:0:1,0:21.5:1:30.3:1:1:0:60:102:1:0:0.1 -1 59247705 . AT A 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00045;SOR=Inf;LSEQ=CAAGTCTGTCTCTCTGTGTT;RSEQ=TTTTTTTCTTCGTTGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:785:0:0,0:535,249:0:2,0:26.2:1:30.6:1:1:0:60:155.8:0.9987:0:0.2 0/1:964:13:8,5:628,323:0.0135:2,2:27.7:1:29.1:1:0.77168:1.2149:60:26:0.0136:0.001:0.2 -1 59247993 . C T 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=0.62016;LSEQ=CTCTCCGCCTTGATCCGCTC;RSEQ=TGGGACTCCATGTCGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:846:184:69,115:252,408:0.2175:2,2:21.7:1:30.5:1:0.9316:1.02938:60:91:0.2177:0:1.1 0/1:864:127:52,75:286,451:0.147:2,2:20.7:1:30.1:1:0.69394:1.09:60:254:0.1485:0:1.2 -1 59248077 . C A 53 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03325;SOR=Inf;LSEQ=GGCTCCTCCTTCAGGGCCTG;RSEQ=AGCCGCGGGTGCTGCACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:89,264:0:2,0:25.5:1:31.7:1:1:0:60:43.125:1:0:0.2 0/1:410:6:4,2:127,273:0.0146:2,2:18.2:1:20.7:1:0.08834:4.28:60:2:0.0101:0:1.3 -1 59248123 . GGCT G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.21356;SOR=0.40652;LSEQ=GCTGGGGCAGGTGGTGCGGC;RSEQ=GCTGCTGCTGCTGGGGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:7:1,6:20,135:0.0424:2,2:27.9:1:33.3:1:1:1.12:60:14:0.0427:0:0.3 0/1:170:3:1,2:42,124:0.0176:2,2:12:1:29.3:1:1:1.47:60:6:0.0178:0.0059:0.3 -1 59248124 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24184;SOR=0;LSEQ=CTGGGGCAGGTGGTGCGGCG;RSEQ=CTGCTGCTGCTGCTGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:0,2:20,135:0.0121:2,0:23:1:31.5:1:1:0:60:4:0.0122:0:1 0/0:170:0:0,0:42,124:0:2,0:22.7:1:31.7:1:1:0:60:165:0.9763:0:0.2 -1 59248128 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=1.95746;LSEQ=GGCAGGTGGTGCGGCGGCTG;RSEQ=TGCTGCTGCTGGGGTTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:19,134:0.0065:2,0:8:0:31:0:1:0:60:2:0.0066:0:1 0/1:158:2:1,1:38,118:0.0127:2,2:36.5:1:29:1:0.43393:3.08:60:4:0.013:0:1 -1 59248149 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2599;SOR=Inf;LSEQ=TGCTGCTGCTGGGGTTGCGC;RSEQ=GGAAAGGCCAGGCCGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:21,81:0:2,0:22.6:1:31.3:1:1:0:60:50:1:0:0.1 0/1:133:3:0,3:43,87:0.0226:2,0:16.3:1:26.3:1:0.55071:0:60:6:0.0231:0:1 -1 59248182 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51818;SOR=Inf;LSEQ=CCGGCCGCGCCGTAGGAGGG;RSEQ=GCCCCGCCGCCGCTGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:25,45:0:2,0:20.4:1:30.6:1:1:0:60:69:1:0:0.1 0/1:106:2:0,2:43,61:0.0189:2,0:18.5:1:30.5:1:0.51321:0:60:4:0.0194:0:1.5 -1 59248202 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.16494;SOR=0;LSEQ=CGCCCCGCCGCCGCTGCTCA;RSEQ=CGCGCCTGGGTTGAAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:30,28:0.0333:2,2:46.5:1:29.5:1:1:1.07017:60:4:0.0345:0:1 0/0:87:0:0,0:45,42:0:2,0:28.6:1:31.5:1:1:0:60:86:1:0:0.2 -1 59248221 . G A 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08076;SOR=Inf;LSEQ=AGCGCGCCTGGGTTGAAGTT;RSEQ=CTGAGGTTTGCGTAGACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:33,27:0:2,0:26:1:32.2:1:1:0:59.8:59:1:0:0.3 0/1:88:5:3,2:42,40:0.0568:2,2:23.6:1:28.4:1:1:1.42:60:10:0.0581:0:1.2 -1 59248242 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1856;SOR=0;LSEQ=CTGAGGTTTGCGTAGACCGG;RSEQ=GGCTCGCTGTGCAGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:30,23:0.0364:2,2:47:0:31.5:1:1:1.29798:60:4:0.037:0:1.5 0/0:72:0:0,0:32,40:0:2,0:24.6:1:30.9:1:1:0:60:71:1:0:0.2 -1 59248263 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22804;SOR=Inf;LSEQ=GGCTCGCTGTGCAGGCTGGC;RSEQ=CTGAAGCCGCCGCTGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:45,19:0:2,0:22.8:1:30.7:1:1:0:60:63:1:0:0.1 0/1:59:2:1,1:31,26:0.0339:2,2:38.5:1:30:1:1:1.18874:60:4:0.0345:0:1 -1 59248318 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50055;SOR=Inf;LSEQ=AGGCTACCGCGGGAGCCACC;RSEQ=TGCCTGCCCCGTTGACCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:105,24:0:2,0:25.4:1:30.4:1:1:0:60:128:1:0:0.1 0/1:148:2:1,1:118,28:0.0135:2,2:21:0:32.5:1:0.35457:4.1585:60:4:0.0135:0:1.5 -1 59248324 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50157;SOR=Inf;LSEQ=CCGCGGGAGCCACCATGCCT;RSEQ=CCCCGTTGACCGGCTGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:113,24:0:2,0:26.1:1:32.3:1:1:0:60:136:1:0:0.1 0/1:161:2:1,1:129,30:0.0124:2,2:10:1:26.5:1:0.34899:4.24644:60:4:0.0125:0:2 -1 59248813 . G C 257 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGGGGCCGCAACAGGGCT;RSEQ=TGGCAAGCGGGGGACACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:266:266:36,230:0,0:1:0,2:25.7:1:32:1:1:0:60:87.667:1:0:1.1 1/1:257:257:44,213:0,0:1:0,2:23.1:1:31.4:1:1:0:60:41.833:1:0:1.1 -1 59248835 . G GC 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50392;SOR=0;LSEQ=GGCAAGCGGGGGACACCCGC;RSEQ=CCCCCCGGAGCCTTTGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:0,2:8,175:0.0108:1,0:20.5:1:32:1:1:0:60:4:0.0112:0.0054:1.5 0/0:151:0:0,0:5,146:0:1,0:23.5:1:31.9:1:1:0:60:36.75:1:0:1.1 -1 59249031 . T G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCACTGAGCGCTCTTCG;RSEQ=GCGCAGCGGTTCCTCGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:2,7:0,0:1:0,2:30.2:1:27.2:1:1:0:58.9:3.5:1:0:1.8 1/1:2:2:0,2:0,0:1:0,0:31:1:31.5:1:1:0:60:4:1:0:1 -1 59249347 . G C 102 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAAGGCTTGCAAAAGTT;RSEQ=GCTCCGGGACTCTGCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:1:0,2:18.7:1:32.3:1:1:0:60:18:1:0:1.1 1/1:1:1:0,1:0,0:1:0,0:13:0:32:0:1:0:60:2:1:0:1 -1 59249359 . C CTG 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAAAAGTTGGCTCCGGGACT;RSEQ=TGCCACTTGTCTCCGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:19.3:1:29.2:1:1:0:60:6:0.3333:0.1111:2.3 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:60:2:1:0:1 -1 59250418 . C G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43275;SOR=0.51266;LSEQ=AGGGGCGGTCTCCCGAGAGT;RSEQ=GGCCCCCCACGTTGAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:14,0:7,0:0.6667:0,1:20.2:1:30.9:1:1:0:60:13:0.65:0:2.2 1/0:8:4:3,1:3,1:0.5:2,2:20.5:1:29.5:1:1:1:60:3:0.4286:0:2.5 -1 59250439 . C G 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04858;SOR=Inf;LSEQ=GGCCCCCCACGTTGAGAACA;RSEQ=TCCGAAGTTTGCATCTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:0:1,0:26.4:1:32.7:1:1:0:60:60:1:0:1.2 0/1:9:2:1,1:7,0:0.2222:0,2:23.5:1:32:1:0.22222:0:60:4:0.2222:0:2.5 -1 59250452 . A G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.73226;SOR=0.73534;LSEQ=GAGAACACTCCGAAGTTTGC;RSEQ=TCTCGGTCAAGTTCAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:23:23,0:14,0:0.6216:1,1:26.3:1:30:1:1:0:60:22:0.6111:0:1.7 1/0:11:6:6,0:5,0:0.5455:0,0:26:1:29.7:1:1:0:60:12:0.5455:0:1.8 -1 59250675 . C G 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10775;LSEQ=TAACAGGGTCCAGATGGGAA;RSEQ=AAGCGTGTAGGCGATCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1545:274:158,116:676,593:0.1773:2,2:28.3:1:31.7:1:0.20412:1.19:60:273:0.1795:0:1.1 0/1:1631:37:22,15:844,747:0.0227:2,2:25.7:1:31.3:1:0.5066:1.30:60:36:0.0224:0:1.2 -1 59250710 . G A 213 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=71.70235;LSEQ=TCCGAAACTCGGGGAACCCC;RSEQ=GTGTTAGTCTACTCCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1820:2:2,0:885,925:0.0011:2,0:3.5:1:29:1:0.23949:0:60:4:0.0011:0:1 0/1:1886:138:65,73:881,865:0.0732:2,2:23.8:1:30.1:1:0.47972:1.14377:60:68:0.0733:0:1.2 -1 59250778 . ACG A 147 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.58009;SOR=0.84634;LSEQ=AACACAACACGCACAACATA;RSEQ=CGCGCGCGCGCGCACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1100:28:10,18:424,644:0.0255:2,2:35.6:1:30.6:1:0.84519:1.18488:59.6:56:0.026:9e-04:0.3 0/1:1156:25:9,16:477,644:0.0216:2,2:34.4:1:29.5:1:0.5472:1.31646:59.8:50:0.0219:0:0.2 -1 59250792 . G A 135 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AACATAACGCGCGCGCGCGC;RSEQ=CACACACACACTCCATCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:912:0:0,0:311,579:0:2,0:25.8:1:30.3:1:1:0:60:25.97:1:0:0.2 0/1:937:29:16,13:348,559:0.0309:2,2:19.1:1:27.9:1:0.08146:1.98:60:58:0.0319:0:1.1 -1 59564093 . G GT 30 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=TTTTGTTTTGTTTTTTTGTT;RSEQ=TTTTTTTTTTTGAGTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,0:0.4:0,0:29.5:1:29.5:1:1:0:60:4:0.4:0:0 1/0:4:2:2,0:2,0:0.5:0,0:19:1:30.5:1:1:0:60:4:0.5:0.25:0 -1 59564208 . GA G 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.4898;SOR=0;LSEQ=AGTAAGCTCATTTTAAAGGT;RSEQ=AAAAAAAAATAAAGCTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:23,0:0.08:1,0:30:1:32:1:1:0:60:4:0.08:0:0 0/0:24:0:0,0:22,2:0:2,0:12:0:16:0:1:0:60:0:0:0:1 -1 59564276 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20892;SOR=Inf;LSEQ=CACAGAGAGTAAATTATTGC;RSEQ=TCTGATTCCAAAGAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:107,28:0:2,0:24.9:1:30.3:1:1:0:60:270:0.9926:0:0.1 0/1:115:2:1,1:82,31:0.0174:2,2:21.5:1:29:1:0.48085:2.61933:60:4:0.0174:0:1.5 -1 59564373 . C T 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.431;SOR=1.14098;LSEQ=AGTGTAGTTTTGCTAAATTA;RSEQ=CCTCTTTGGGGATTGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:158:87,71:84,94:0.4702:2,2:22.4:1:30.1:1:0.15683:1.37:60:38.5:0.4681:0:1.1 1/0:310:156:75,81:76,77:0.5032:2,2:26:1:28.5:1:0.82031:1.06575:60:25:0.4967:0:1.2 -1 59564403 . G A 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36177;SOR=3.1692;LSEQ=GGATTGAGTTGCAGCCTCAT;RSEQ=ACATAATGACTGGTGATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:1,0:136,172:0.0032:2,0:1:0:24:0:0.44337:0:60:2:0.0033:0:2 0/1:295:3:2,1:136,156:0.0102:2,2:14:1:26:1:0.60099:2.29:60:6:0.0102:0:1.7 -1 59564443 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59449;SOR=2.38739;LSEQ=CAGGTCCTTCTTAGAAACGT;RSEQ=CTGTTCATTTCTGGCTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:1,0:73,128:0.005:2,0:1:0:27:0:0.36634:0:60:2:0.005:0:1 0/1:170:2:1,1:61,107:0.0118:2,2:26.5:1:27.5:1:1:1.75:60:4:0.0118:0:1.5 -1 59564452 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50125;SOR=0;LSEQ=CTTAGAAACGTGCTGTTCAT;RSEQ=TCTGGCTAATGTTCCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:54,115:0.0116:2,2:19.5:1:30.5:1:0.54111:2.12:60:4:0.0116:0:1 0/0:148:0:0,0:49,99:0:2,0:24.2:1:29.8:1:1:0:60:296:1:0:0.3 -1 59564892 . A T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGGAAAGGTTCATTAACC;RSEQ=GGAGCTTTATAACAGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:34:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 63225823 . C T 25 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTAAATCTTAACTAATTA;RSEQ=CATACAAAGGTCCAACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:1:25:1:1:0:50:4:1:0:1.5 -1 63226645 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54146;SOR=Inf;LSEQ=GTTGGGCAACATGGCTTCTC;RSEQ=CCTTTCTAGGTCCCATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:11,16:0:2,0:32.8:1:30.8:1:1:0:53.5:54:1:0:0 0/1:51:2:1,1:23,26:0.0392:2,2:24.5:1:29:1:1:1.13:52:4:0.0408:0:1 -1 63226699 . AT A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.48276;SOR=0;LSEQ=TACTTGCCTTTGGGCCCTGT;RSEQ=TTTTAACCTTCTGGTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:2,11:0.1333:2,2:17:1:32:0:0.37143:4.69:53:4:0.1333:0:0.5 0/0:15:0:0,0:3,12:0:2,0:27:1:29.7:1:1:0:59.1:30:1:0:0.1 -1 63226758 . G A 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=GAGGCCATCAAGCTACAGAT;RSEQ=GTCTTACAAATGGAACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:4,5:0,1:0.9:0,2:34.1:1:30.7:1:1:0:52.9:18:0.9:0:1 0/0:2:0:0,0:0,2:0:0,0:7.5:1:30.5:1:1:0:53.5:4:1:0:0.5 -1 63228279 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACACTCACTGCAAGGGTC;RSEQ=GCGGCTTCATTTTTGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 63789015 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGCCGGACCGGGGGGCGAC;RSEQ=TGGGCGCGCCGGAGGCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:1:0:32.5:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:48.5:1:30:1:1:0:60:4:1:0:1 -1 63789244 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22013;SOR=Inf;LSEQ=CGGCATCTGCGAGTTCATCA;RSEQ=CAACCGCTTCCCCTACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:31,25:0:2,0:20.1:1:31.7:1:1:0:60:55:1:0:0.1 0/1:50:2:1,1:29,18:0.04:2,2:10.5:1:26:1:1:1.59489:60:4:0.0417:0:1 -1 63789293 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52999;SOR=Inf;LSEQ=TTCCCCGCCTGGCAGAACAG;RSEQ=ATCCGCCACAACCTCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:34,30:0:2,0:28:1:31.9:1:1:0:58.3:63:1:0:0.1 0/1:108:2:1,1:55,51:0.0185:2,2:27:1:27.5:1:1:1.07765:51.5:4:0.0194:0:1 -1 63789323 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53255;SOR=Inf;LSEQ=AACCTCTCACTCAACGACTG;RSEQ=TTCGTCAAGATCCCCCGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:34,34:0:2,0:23.5:1:32:1:1:0:58.4:136:1:0:0.1 0/1:117:2:1,1:53,62:0.0171:2,2:42.5:1:29.5:1:1:1.17:54.5:4:0.0174:0:1 -1 63789338 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52917;SOR=Inf;LSEQ=GACTGCTTCGTCAAGATCCC;RSEQ=CGCGAGCCGGGCAACCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:29,33:0:2,0:23.8:1:30.7:1:1:0:58.2:61:1:0:0.1 0/1:104:2:1,1:44,58:0.0192:2,2:36:1:27:1:1:1.31:56:4:0.0194:0:1 -1 63789400 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49938;SOR=0;LSEQ=GGACCCGCAGTCCGAGGACA;RSEQ=GTTCGACAACGGCAGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:9,28:0.0513:2,2:42.5:1:30:1:0.45209:3.00:60:4:0.0513:0:1 0/0:31:0:0,0:6,25:0:2,0:23:1:30.4:1:1:0:60:62:1:0:0.1 -1 65300374 . GT G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24803;SOR=Inf;LSEQ=GAAGTAACAACAGTAAAAAT;RSEQ=TAGATCTGGGAACTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:39,152:0:2,0:23:1:30.4:1:1:0:60:94.5:1:0:0.1 0/1:190:2:1,1:47,141:0.0105:2,2:21:1:30:1:0.44244:2.98:60:4:0.0106:0:0.5 -1 65300398 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22227;SOR=Inf;LSEQ=GATCTGGGAACTTTAAAAAA;RSEQ=AACAGAAATATCAAGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:10,115:0:2,0:21.2:1:28.5:1:1:0:60:61.5:1:0:0.1 0/1:112:2:1,1:15,95:0.0179:2,2:12.5:1:28:1:0.26641:6.16:60:4:0.0179:0:1 -1 65300993 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22397;SOR=Inf;LSEQ=CACTGCATCATTTCCTCGCT;RSEQ=TCCCCTCTACCCATTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:179,13:0:2,0:21.9:1:31.6:1:1:0:60:95:1:0:0.1 0/1:173:2:1,1:157,14:0.0116:2,2:19:1:27:1:0.16635:10.86873:60:4:0.0118:0:1 -1 65301238 . A G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.28435;SOR=1.51667;LSEQ=TTAACTTTGCAAGTATTTAC;RSEQ=TAAATGCCAAACAGATTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:13:3,10:22,150:0.0703:2,2:20.2:1:31.2:1:0.38969:2.04:60:26:0.071:0:1.1 0/1:204:21:3,18:25,158:0.1029:2,2:22.9:1:29.9:1:1:1.05:60:20:0.099:0:1.2 -1 65301490 . G A 65 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69008;LSEQ=ACAAGGCTGGTCCCTACCCA;RSEQ=TGCTACCCCACTTAACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:2,2:0.6:2,2:25.5:1:25.2:1:1:1:60:2:0.5714:0:1.3 1/0:2:1:0,1:0,1:0.5:0,0:46:0:28:0:1:0:60:2:0.5:0:1 -1 65301611 . T G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89139;LSEQ=TCGTTGTGAAAGCAAGACTT;RSEQ=AGAGATTCACAAATAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:7,2:23,1:0.2727:1,2:26.7:1:33:1:0.17375:6.11937:60:18:0.2727:0:1.8 0/1:8:2:2,0:5,1:0.25:2,0:22:1:32.5:1:1:0:60:4:0.25:0:2 -1 65301669 . C A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03813;LSEQ=TAATGGGAAAGTGACATTTT;RSEQ=CATTATAATACATTCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:13:13,0:51,3:0.194:2,1:17.2:1:26.9:1:1:0:60:26:0.197:0:1.5 0/1:40:8:7,1:32,0:0.2:1,2:20.6:1:28.4:1:0.2:0:60:16:0.2:0:1.3 -1 65303659 . C T 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTGACGGTGTAATACTC;RSEQ=TTATCGGTTTCAATTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:953:0:0,0:522,431:0:2,0:25.4:1:31.4:1:1:0:60:85.636:1:0:0.1 0/1:980:49:26,23:517,413:0.05:2,2:26.5:1:29.4:1:0.7691:1.10726:60:15.333:0.0474:0:1.2 -1 65304470 . A C 47 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAATGGTGTACCTACCTCAC;RSEQ=GGCATAAGCACTCACTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:1,17:0.1429:1,0:18.7:1:30:1:1:0:60:6:0.1579:0:1 0/1:7:1:0,1:0,6:0.1429:0,0:7:0:32:0:1:0:60:2:0.1429:0:1 -1 65305102 . TCA T 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.8021;SOR=1.23942;LSEQ=GAGGGGCCTGGGTGGCCTCC;RSEQ=GGAGCCCTGCAGCTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:46:46,0:16,0:0.7419:1,1:27:1:32.2:1:1:0:59.9:92:0.7419:0.0968:0.1 1/0:32:25:25,0:7,0:0.7813:0,1:20.3:1:31.1:1:1:0:59.8:50:0.7813:0.25:0.1 -1 65306996 . G GT 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.07245;SOR=0.45164;LSEQ=GGGGTCCACTTCAGTTGCTG;RSEQ=TTTTTTTTCTGAAACAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:17:9,8:326,413:0.0224:2,2:24:1:29.8:1:0.47242:1.42:60:34:0.0227:0.0013:0.1 0/1:878:9:4,5:389,479:0.0103:2,2:31.7:1:28.8:1:1:1.01512:60:18:0.0104:0:0.1 -1 65307409 . G A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10568;SOR=3.69441;LSEQ=TCCACTTACAGGTAGATTTC;RSEQ=TAAGTGTTTGTTACTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:6:0,6:0,41:0.1277:1,0:22.3:1:32:1:1:0:60:12:0.1304:0:1.3 0/1:14:5:0,5:0,9:0.3571:0,0:17.6:1:31:1:1:0:60:10:0.3571:0:1 -1 65309387 . T C 33 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGATGCCTGATACACAA;RSEQ=AGGAACTCCATACGTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:26.5:1:33.5:1:1:0:60:4:0.2:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 65309400 . C T 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACACAATAGGAACTCCATA;RSEQ=GTATTTGTGTGGTAATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:26:1:30.7:1:1:0:60:6:0.375:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 65309415 . ATTT A 63 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATACGTATTTGTGTGGTA;RSEQ=TGCTGAATAACAGGCACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:26.3:1:31.8:1:1:0:60:8:0.4444:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 65309958 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2093;SOR=Inf;LSEQ=ATCTCCTAGGGATTCAATTA;RSEQ=TGTCACTGCAGCCAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:21,180:0:2,0:22.4:1:32.2:1:1:0:60:99.5:1:0:0.1 0/1:170:2:1,1:37,131:0.0118:2,2:9.5:1:29:1:0.39812:3.51:60:4:0.0119:0:1.5 -1 65310268 . GAAGGCAGGAGATC G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.05909;SOR=Inf;LSEQ=GCTCGTTCAAGGACTTAAGA;RSEQ=AAGACCATCCTGGCCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:39,3:0:2,0:22.5:1:30.1:1:1:0:60:41:1:0:0 0/1:14:2:2,0:11,0:0.1429:0,0:22:1:33.5:1:1:0:60:4:0.1538:0:0 -1 65310328 . C CA 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.60877;SOR=0.70617;LSEQ=ACCCCGTCTCTACTAAAATA;RSEQ=AAAAAAAAAATGACTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:12:12,0:128,3:0.0833:1,0:23.6:1:31:1:1:0:60:24:0.0857:0.0069:0.7 0/1:83:5:5,0:74,4:0.0602:2,0:38.6:1:30:1:1:0:60:10:0.0625:0:0 -1 65310361 . CCCCAG C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17675;SOR=Inf;LSEQ=ACTCTCTAAAAGGAGACCAA;RSEQ=CCCAGCCCTTCTCTCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:239,25:0:2,0:24.4:1:30.9:1:1:0:60:65:1:0:0.3 0/1:192:2:1,1:170,20:0.0104:2,2:10:1:29:1:0.2073:8.31843:60:4:0.0104:0.0052:0.5 -1 65310402 . G T 68 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11016;SOR=5.47083;LSEQ=TGCTGACTTGCCCCTGACTC;RSEQ=GGGTGGGGCCAGAGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:1:0,1:330,115:0.0022:2,0:1:0:27:0:0.26009:0:60:2:0.0023:0:1 0/1:411:5:2,3:284,122:0.0122:2,2:31.8:1:29.4:1:0.1673:3.48006:60:10:0.0125:0:1 -1 65310489 . T C 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11675;SOR=1.19118;LSEQ=GGGTCACTGAGCTTGATGAA;RSEQ=GGGCCACACTCACTGTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1018:201:105,96:393,424:0.1974:2,2:26.5:1:30.8:1:0.30656:1.18:60:39.2:0.1956:0:1.2 0/1:1028:233:119,114:405,390:0.2267:2,2:25.6:1:30.2:1:1:1.01:60:232:0.2263:0:1.2 -1 65310747 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13664;SOR=Inf;LSEQ=ACAGGTGCCCCTTGGCTCCA;RSEQ=CTCCCTCATCACTGAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:0:1,0:21:1:33:1:1:0:60:46:1:0:0 0/1:14:2:1,1:0,12:0.1429:0,2:17:1:29:1:0.14286:0:60:4:0.1429:0:1 -1 65311075 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1384;SOR=Inf;LSEQ=TTTGTTCAACCACAGAGCCC;RSEQ=GGCCCCATGGAACCCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:115,4:0:1,0:24.7:1:30.9:1:1:0:60:118:1:0:0.4 0/1:71:2:2,0:66,3:0.0282:1,0:28.5:1:32:0:1:0:60:4:0.0286:0:1.5 -1 65311116 . GC CT 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18041;SOR=0.70007;LSEQ=CAGGCCCCTCTAGCTGCTTG;RSEQ=TAGCACCTCCTTCCTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:53:42,11:152,21:0.2345:2,2:22.7:1:31.1:1:0.12052:1.88975:60:106:0.2409:0.0398:0.9 0/1:187:33:28,5:137,17:0.1765:2,2:18.8:1:30.7:1:0.55154:1.43602:60:66:0.1784:0.0321:1 -1 65311214 . G C 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00219;SOR=1.7984;LSEQ=ACCAAGTAGCTCAGGGCACT;RSEQ=GCCAGCTGTTTGGCAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1028:47:25,22:558,421:0.0457:2,2:28.9:1:31:1:0.65233:1.16619:60:94:0.0464:0:1.1 0/1:983:78:41,37:486,419:0.0793:2,2:29:1:30.7:1:0.90596:1.04672:60:77:0.0791:0:1.3 -1 65311262 . G A 191 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=103.54015;LSEQ=CATGGTGTGGTAAGGACATC;RSEQ=CTTTTCCGGTGCATGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1130:1:1,0:562,566:9e-04:2,0:1:0:26:0:0.49867:0:60:2:9e-04:0:1 0/1:1094:92:47,45:492,509:0.0841:2,2:25.3:1:29.3:1:0.74471:1.08:60:29.667:0.0826:0:1.2 -1 65311684 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTCTACAACACACTGTGA;RSEQ=GCAGAGGTCAGGCCGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:15:1:32:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 65312100 . TG T 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54404;SOR=0;LSEQ=CTAGCACAGTGTAGGGTTCT;RSEQ=GCCAGCGTTGACAAGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:5,0:14,1:0.25:1,0:26:1:28.6:1:1:0:60:4:0.2:0.1:0.2 0/0:5:0:0,0:5,0:0:0,0:29.4:1:33.4:1:1:0:60:10:1:0:0 -1 65312354 . G A 95 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46655;SOR=1.57044;LSEQ=TCCACGTCGCGGACACAGAC;RSEQ=CCATAGAGGTACACGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:778:6:5,1:390,382:0.0077:2,2:9.3:1:27:1:0.21727:4.89:60:12:0.0079:0:1 0/1:912:11:8,3:454,446:0.0121:2,2:14.5:1:27.5:1:0.22425:2.62:60:10:0.0111:0:1.1 -1 65312583 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTGGCTGTCCAGAGGCACTG;RSEQ=CAAGCCTTGTTCTCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:8:1,7:1,27:0.2222:1,2:22.5:1:30.4:1:0.4:3.67:60:16:0.2222:0:1.4 0/1:18:4:1,3:1,13:0.2222:1,2:22.5:1:29.8:1:0.40523:3.89:60:8:0.2222:0:1 -1 65313414 . G A 96 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00374;SOR=11.85835;LSEQ=GTGCCCTGAAGTGATGGACC;RSEQ=TCTGGGAATGGGTCCTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:1,0:43,258:0.0033:2,0:1:0:26:0:0.1457:0:60:2:0.0034:0:1 0/1:263:10:3,7:42,211:0.038:2,2:22.1:1:29:1:0.38233:2.15:60:20:0.0386:0:1 -1 65313682 . C A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGGCCATCAACAGCCAG;RSEQ=CACATGGGTCCCACCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25:1:29:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 65316398 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50725;SOR=0;LSEQ=TTCTACTAAGATTTCCCCAA;RSEQ=CACAGCCTTCCTTCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:155,13:0.0118:2,2:29:1:30.5:1:0.15837:11.52661:60:4:0.012:0:1 0/0:130:0:0,0:110,20:0:2,0:22.2:1:29.8:1:1:0:60:129:1:0:0.1 -1 65316675 . G A 158 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66181;SOR=0.87098;LSEQ=ACGTCTGCTGAGCCGGGGCC;RSEQ=TGGGACCGGTGTGCGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:35:1,34:5,112:0.2303:1,1:25.2:1:30.9:1:1:1.51409:60:70:0.2318:0:1.1 0/1:121:25:0,25:6,90:0.2066:2,1:23.5:1:30.5:1:0.3431:0:60:24:0.2:0:1.4 -1 65319411 . C A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01126;SOR=7.09166;LSEQ=TGAGGTAGGTACATAAACTG;RSEQ=CTGGGCCACAGTAGGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:4,0:14,5:0.1739:2,0:22.5:1:31:1:0.53924:0:60:8:0.1739:0:1 1/0:13:8:6,2:4,1:0.6154:2,2:20.8:1:29.3:1:1:1.30472:60:16:0.6154:0:1.1 -1 65319455 . T TG 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12451;SOR=2.4723;LSEQ=ATCCAGCAGCTCCTGCTACC;RSEQ=GTTCACTTGACAGGCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:6,3:15,14:0.2368:2,2:29.3:1:31.4:1:0.47571:1.84:60:18:0.2368:0:0.4 0/1:32:14:7,7:12,6:0.4375:2,2:32.3:1:31.2:1:0.4727:1.95606:60:28:0.4375:0:0.5 -1 65321028 . T C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26387;SOR=0;LSEQ=AAATGCTCACACTCAAGGGA;RSEQ=TGGATGTGAGTTGGGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:3,0:19,0:0.1304:1,0:28:1:33.7:1:1:0:60:6:0.1364:0:1 0/0:15:0:0,0:14,1:0:1,0:24.3:1:29.5:1:1:0:60:14:1:0:0.1 -1 65321250 . G A 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00152;SOR=2.2921;LSEQ=CTGATGTTATCCGTGCGCAG;RSEQ=ATCTGCTTCTTGAGGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:22:13,9:337,222:0.0378:2,2:23:1:30.2:1:1:1.05082:60:44:0.0389:0:1.1 0/1:617:51:33,18:323,243:0.0827:2,2:23.8:1:29.4:1:0.30484:1.38:60:102:0.0836:0:1.1 -1 65321388 . G A 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13808;SOR=1.23799;LSEQ=GCACCCTGCACCTGCTATTC;RSEQ=GGAAATGACCAGAAATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:127:47,80:121,226:0.2674:2,2:25.7:1:30.5:1:0.66614:1.10:60:126:0.2675:0:1.2 0/1:498:155:56,99:130,212:0.3112:2,2:24.5:1:30.1:1:0.76415:1.08386:60:154:0.313:0:1.3 -1 65321419 . G A 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00085;SOR=2.97677;LSEQ=AGAAATTACATGTTTAAAAT;RSEQ=GGGTCAGGCATGGGTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:13:3,10:56,210:0.0466:2,2:22.3:1:30.1:1:0.74112:1.12:60:26:0.0473:0:1.8 0/1:283:36:8,28:71,176:0.1272:2,2:24.3:1:29.5:1:0.5511:1.41031:60:35:0.1254:0:1.9 -1 65323142 . C T 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11506;LSEQ=GGCCCTACAGGGGGAGGATG;RSEQ=AGGGGTCTGGCTACTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:0.2632:1,0:15:1:29.4:1:1:0:60:10:0.2778:0:1.6 0/1:7:2:1,1:5,0:0.2857:0,2:41.5:1:28.5:1:0.28571:0:60:4:0.2857:0:1 -1 65324068 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGTGCTGGTGAGAGAGGGC;RSEQ=GCCATGGTTCGTGTGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:21:0:31:0:1:0:60:2:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:15.5:1:29:1:1:0:60:4:0.6667:0:1 -1 65325970 . C T 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03154;SOR=1.52461;LSEQ=TGAGAGAGAAGAAATTCCCA;RSEQ=GGTTACATCATGTCTCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:58:13,45:61,152:0.2132:2,2:24.8:1:29.9:1:0.40761:1.38756:60:57:0.2135:0:1.1 0/1:335:98:27,71:74,163:0.2925:2,2:20.8:1:29.8:1:0.60082:1.1932:60:97:0.2913:0:1.1 -1 65326011 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17221;SOR=Inf;LSEQ=AGCTTAAGTGGCTGACTCTG;RSEQ=AGGGAGGTGCACAGTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:16,144:0:2,0:21.4:1:28.1:1:1:0:60:79:1:0:0.4 0/1:114:2:1,1:15,97:0.0175:2,2:18.5:1:27.5:1:0.26207:6.29:60:4:0.018:0:1 -1 65326101 . GC TT 77 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39563;SOR=0.28412;LSEQ=ACTAAATATACCCCTTGCAT;RSEQ=ATTTATTTATTTATTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:0,6:0,22:0.1935:1,0:29.8:1:30.1:1:1:0:60:12:0.2143:0:1 0/1:16:1:0,1:1,13:0.0625:1,0:15:0:31:0:1:0:50:2:0.0667:0:1 -1 65330682 . G A 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.08237;LSEQ=AGATACATAAAAGGGACAGG;RSEQ=TTAAGTTGCTTTCTTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:16:5,11:49,221:0.0559:2,2:28.1:1:30.9:1:0.19523:2.04:60:32:0.0563:0:1.1 0/1:328:64:13,51:63,200:0.1951:2,2:18.8:1:29.6:1:0.62205:1.23504:60:128:0.1988:0:1 -1 65332766 . T C 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATGCGTGGACACGCTGCTG;RSEQ=CACAAATGGTCTTGTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:25:10,15:271,336:0.0394:2,2:21.6:1:30.9:1:0.68672:1.20946:60:24:0.0385:0:1 0/0:658:0:0,0:317,341:0:2,0:24.1:1:29.2:1:1:0:60:218.333:1:0:0.1 -1 65332927 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50098;SOR=Inf;LSEQ=AAAGTACATCTCCTTTTCAT;RSEQ=TACAGGTTAGGAGAAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:32,127:0:2,0:22.8:1:31.9:1:1:0:60:78.5:0.9937:0:0.1 0/1:184:2:1,1:42,140:0.0109:2,2:7.5:1:26:1:0.41376:3.31:60:4:0.0109:0:1 -1 65335062 . A G 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGTGTGAGATGGCCAGGAC;RSEQ=GCCATCCCTAGACACTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:932:0:0,0:459,473:0:2,0:25.1:1:30.6:1:1:0:60:185.4:1:0:0.1 0/1:1013:38:15,23:499,474:0.0375:2,2:26.8:1:29.8:1:0.18592:1.61344:60:76:0.0379:0:1.2 -1 65335095 . T C 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=2.86697;LSEQ=CACTCGTTCTCAATATCATG;RSEQ=CCATCCTGCTCGGTCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:981:40:18,22:419,522:0.0408:2,2:24.3:1:31.9:1:1:1.02:60:80:0.0412:0:1.2 0/1:1095:119:52,67:454,521:0.1087:2,2:24.6:1:31.5:1:0.56094:1.12265:60:238:0.1106:0:1.2 -1 65335323 . G A 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19539;SOR=3.24178;LSEQ=AAACAGAGTTGGGTGTGAAG;RSEQ=GGCTCAGGAGATGTTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:0,3:0,30:0.0909:1,0:33.3:1:33:1:1:0:60:6:0.0938:0:1 0/1:16:4:0,4:0,12:0.25:0,0:21.8:1:32.5:1:1:0:60:8:0.25:0:1 -1 65339110 . C CT 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.7004;SOR=0.85285;LSEQ=AGAGGGGTTGCATCTGGAAT;RSEQ=TTTTTTTTCTCGTAGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:850:13:7,6:398,439:0.0153:2,2:25.2:1:31.5:1:0.78192:1.29:60:26:0.0155:0.0024:0.1 0/1:1071:14:7,7:511,543:0.0131:2,2:32.9:1:30.4:1:1:1.06:60:28:0.0132:0:0 -1 65339243 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12329;SOR=Inf;LSEQ=TGAATGCCAATTGTGGCAAA;RSEQ=GGGACCCAGATGTGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:43,154:0:2,0:23.7:1:31.4:1:1:0:60:64.667:1:0:0.1 0/1:203:4:3,1:52,147:0.0197:2,2:14.3:1:23.5:1:0.0615:8.38:60:3:0.015:0:1 -1 65339294 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21275;SOR=Inf;LSEQ=TCACCAACAGTGGTCAGTGC;RSEQ=GGAGGCTGAAGTGCCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:5,68:0:2,0:22.9:1:29.7:1:1:0:60:72:1:0:0 0/1:63:2:1,1:4,57:0.0317:2,2:17.5:1:30.5:1:0.15361:12.86:60:4:0.0328:0:1.5 -1 65342806 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49724;SOR=0;LSEQ=GAGAGATACCTGAGGATAAC;RSEQ=ATGATTACCCAACAACTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:28,61:0.022:2,2:31.5:1:30.5:1:0.53822:2.16:60:4:0.022:0:1 0/0:91:0:0,0:35,56:0:2,0:25.7:1:28.4:1:1:0:60:90:1:0:0.1 -1 65344809 . G A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01887;SOR=Inf;LSEQ=TCGTCATACAGGGCAAAGAG;RSEQ=TTGTGACAAAGAGGAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:198,348:0:2,0:24.7:1:31.6:1:1:0:60:77:0.9963:0:0.1 0/1:675:7:6,1:278,389:0.0104:2,2:10.4:1:24.9:1:0.04566:8.37:60:6:0.009:0:1.1 -1 65348485 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTCACTTCAACTCAGCACCA;RSEQ=GCATGGGAGGGCAGTCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 65348961 . G T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04286;SOR=Inf;LSEQ=GGCAGCTGCCAGTACTCACG;RSEQ=CATGCCTGTGCAGCCCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:297,142:0:2,0:25.4:1:31.2:1:1:0:60:61.714:1:0:0.1 0/1:368:4:2,2:235,128:0.0109:2,2:9.5:1:23.5:1:0.61701:1.83279:60:3:0.0083:0:1.3 -1 65349304 . G A 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00228;SOR=0;LSEQ=CCCTGCCCCTTCCCTTCCTG;RSEQ=AAACCAAACATGTCAGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:11:1,10:1,35:0.234:1,2:29.2:1:31.1:1:0.41721:3.38:60:22:0.2444:0:1.3 0/0:32:0:0,0:0,32:0:1,0:25.6:1:31.2:1:1:0:60:15:1:0:0.1 -1 65349309 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CCCCTTCCCTTCCTGGAAAC;RSEQ=AAACATGTCAGATCTCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:1,42:0.0444:1,2:13.5:1:28.5:1:0.08788:30.05:60:4:0.0455:0:2.5 0/0:33:0:0,0:0,33:0:1,0:23.3:1:30.9:1:1:0:60:10:1:0:0.1 -1 65349608 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTATGGCAAGAATCAGC;RSEQ=TTTTAATTTCATGTCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:29.5:1:33.5:1:0.33333:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 65349817 . C G 34 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGACTTTGACGCAGCA;RSEQ=CAGGAGGGCAGGAGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:26:0:34:0:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:0,1:0:0,0:8:0:31:0:1:0:60:2:1:0:0 -1 65351748 . C T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01358;SOR=0;LSEQ=CAAGGGAAGTTTAACTTTTA;RSEQ=TCTGTACCTCCTATACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:7,0:47,0:0.1296:1,0:21:1:31.4:1:1:0:60:14:0.1321:0:1 0/0:48:0:0,0:47,1:0:1,0:24.5:1:31.5:1:1:0:60:47:1:0:0 -1 65351797 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.92679;LSEQ=GGTTTTTTTTAACCAGCATA;RSEQ=TCAACATTGGGAATGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:125,15:0.0071:2,0:1:0:25:0:0.11348:0:60:2:0.0072:0:1 0/1:147:2:1,1:131,14:0.0136:2,2:8.5:1:31.5:1:0.1943:9.0743:60:4:0.0138:0:1.5 -1 66041969 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24292;SOR=Inf;LSEQ=CATGTCTGCCTGACCCATGG;RSEQ=ACTCCACGAGTTGTGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:115,45:0:2,0:26.1:1:31.9:1:1:0:60:79:1:0:0.2 0/1:156:2:1,1:106,48:0.0128:2,2:11:1:27.5:1:0.53093:2.19601:60:4:0.0131:0:1 -1 66041983 . T C 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24816;SOR=0;LSEQ=CCATGGCACTCCACGAGTTG;RSEQ=GGTGGGTCTGATGAGCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:1,2:132,63:0.0152:2,2:38.3:1:28.7:1:0.25139:4.15738:60:6:0.0155:0:1 0/0:194:0:0,0:129,65:0:2,0:26.5:1:29:1:1:0:60:96:1:0:0.2 -1 66041989 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24825;SOR=Inf;LSEQ=CACTCCACGAGTTGTGGTGG;RSEQ=TCTGATGAGCTAGTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:143,71:0:2,0:25.9:1:30.8:1:1:0:60:34.667:1:0:0.2 0/1:215:3:2,1:136,76:0.014:2,2:16:1:23.3:1:1:1.12:60:2:0.0095:0:3.3 -1 66042078 . G T 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAATCCAGATCTGATTTG;RSEQ=GTCCCCATGCTCACAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:202,192:0:2,0:26.2:1:30.9:1:1:0:60:77.8:1:0:0.1 0/1:337:88:41,47:126,123:0.2611:2,2:26.4:1:29.7:1:0.53727:1.17374:60:87:0.2613:0:1.1 -1 66042135 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25332;SOR=0;LSEQ=TCCTTTCCAACTTGGGCAGC;RSEQ=CTGAGCCACCAGACATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:84,159:0.0122:2,2:27:1:30:1:0.28035:3.76:60:6:0.0124:0:1 0/0:209:0:0,0:84,125:0:2,0:24.7:1:30.2:1:1:0:60:68.667:1:0:0.3 -1 66042192 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08857;SOR=Inf;LSEQ=GAGCCTTCCAAGTTGAAGGA;RSEQ=TTTGGGGCATTTTGGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:7,85:0:2,0:22.8:1:32:1:1:0:60:91:1:0:0 0/1:75:3:2,1:7,65:0.04:2,2:23.3:1:28.7:1:0.03643:17.13:60:6:0.0405:0:1.7 -1 66042199 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17191;SOR=Inf;LSEQ=CCAAGTTGAAGGACTTTGGG;RSEQ=CATTTTGGCCCTCTACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:7,77:0:2,0:23.1:1:31.8:1:1:0:60:83:1:0:0 0/1:60:2:1,1:4,54:0.0333:2,2:27.5:1:30:0:0.16102:12.19:60:4:0.0333:0:2 -1 66372769 . A G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01069;SOR=0.24734;LSEQ=AAAATGACCTTTCTTATTAC;RSEQ=TATACTTTTTTCCCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:16,0:7,1:0.6667:2,1:23.3:1:29.8:1:0.33333:0:60:32:0.6667:0:1 0/1:46:15:13,2:30,1:0.3261:1,2:21.6:1:28.1:1:0.2444:4.44671:60:14:0.3111:0:1.1 -1 66372835 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52894;SOR=Inf;LSEQ=CATACAACTTCAAAAATTTT;RSEQ=GGGAGGAAGCACATTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:68,29:0:2,0:27.8:1:31.7:1:1:0:60:96:1:0:0.5 0/1:161:2:1,1:100,59:0.0124:2,2:36:1:29.5:1:1:1.68904:60:4:0.0126:0:1 -1 66372906 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.31943;LSEQ=AGCAGCAATAACTGAGTGCA;RSEQ=TAGTCCTGAATTTCTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:185:142:74,68:25,18:0.7676:2,2:27.2:1:30.4:1:0.60098:1.2746:60:70:0.765:0:1.1 1/0:275:141:68,73:68,66:0.5127:2,2:23.7:1:29.1:1:0.71803:1.10565:60:140:0.5128:0:1.1 -1 67356569 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.13306;SOR=Inf;LSEQ=GGAAGAAGAAGAAGAAGAAG;RSEQ=AGAAGCAGCAGCAGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:26.6:1:31.9:1:1:0:60:19:1:0:0.2 0/1:12:2:1,1:5,5:0.1667:2,2:35:1:29:1:1:1:60:4:0.1667:0:1 -1 68598726 . A AGGCAGC 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13644;SOR=0.48112;LSEQ=AAAGAACAACTGTCATGAAA;RSEQ=GGCAGCAGCAGCAACAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:26:13,13:4,3:0.7879:2,2:27.5:1:30.6:1:1:1.32179:59.6:52:0.7879:0.0909:0.1 1/0:100:64:32,32:25,10:0.64:2,2:25.8:1:30.2:1:0.05527:2.47698:58.2:128:0.64:0.15:0.1 -1 68598728 . G GCAGCGT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05752;SOR=0;LSEQ=AGAACAACTGTCATGAAAAG;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:0.0606:2,2:49:1:31.7:1:1:1.06462:60:4:0.0645:0:0 0/0:103:0:0,0:59,44:0:2,0:25.9:1:30.4:1:1:0:58.8:24.75:1:0:0.8 -1 68598733 . A G 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00104;SOR=Inf;LSEQ=AACTGTCATGAAAAGGCAGC;RSEQ=GCAGCAACAGCAACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,15:0:2,0:28.5:1:30.8:1:1:0:59.7:62:1:0:0.1 0/1:102:23:17,6:38,37:0.2255:2,2:26:1:29:1:0.05779:2.73:60:46:0.2371:0:2.6 -1 68598743 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=6;SSF=1;SOR=Inf;LSEQ=AAAAGGCAGCAGCAGCAACA;RSEQ=CAACAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:17,17:0:2,0:27.3:1:31.6:1:1:0:59.7:33:1:0:0.3 0/1:106:2:1,1:52,48:0.0189:2,2:22.5:1:29:1:1:1.08246:60:4:0.0196:0:4.5 -1 68598746 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.06028;SOR=0;LSEQ=AGGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:16,16:0.0571:2,2:5.5:1:30.5:1:1:1:60:4:0.0625:0:3 0/0:106:0:0,0:51,51:0:2,0:26:1:29.2:1:1:0:58.8:204:1:0:0.7 -1 68598749 . G GCAA 127 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=7.000;MSILEN=3;SSF=0.00382;SOR=Inf;LSEQ=CAGCAGCAGCAACAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:17,19:0:2,0:26.3:1:31.1:1:1:0:59.7:17:1:0:0.3 0/1:109:20:12,8:42,46:0.1835:2,2:24.8:1:29.6:1:0.45808:1.64:60:40:0.1869:0.1009:2.7 -1 68840797 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAGCCTTTGGGAACTG;RSEQ=TGGTGCTACATAGGGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:18.5:1:33:0:1:0:60:4:0.2857:0:1 0/0:1:0:0,0:1,0:0:0,0:34:0:31:0:1:0:60:2:1:0:0 -1 68841023 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25297;SOR=Inf;LSEQ=ATTTAACAATCTAGGAAGTT;RSEQ=ACAGCCACCAGCAGTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:153,59:0:2,0:25.5:1:31.4:1:1:0:60:41.4:1:0:0.1 0/1:248:3:1,2:143,102:0.0121:2,2:24.3:1:27.7:1:0.57365:2.7923:60:6:0.0122:0:1 -1 68841270 . T C 100 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01164;SOR=9.54822;LSEQ=TTACAATAAATTCATGGCCA;RSEQ=CAGATGGTATCAATTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:1:0,1:227,150:0.0026:2,0:13:0:13:0:0.39947:0:60:0:0:0:2 0/1:404:10:6,4:221,171:0.0248:2,2:25.7:1:30.4:1:1:1.16:60:20:0.0253:0:1.1 -1 69777209 . C T 44 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.38437;LSEQ=CCGTCTCATCCTCTGTCCAG;RSEQ=TCTGTGCTCCGATGGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:16.3:1:28.3:1:1:0:60:6:0.6:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:48:0:32:0:1:0:60:2:0.3333:0:1 -1 69777307 . A G 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01767;SOR=0;LSEQ=ATTGATTCTTTCTCGTCATG;RSEQ=GTTTGTCTACTTTCAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:8,6:0.2632:2,2:28.2:1:30.4:1:0.62848:1.92739:60:10:0.2632:0:1.4 0/0:21:0:0,0:12,9:0:2,0:20.8:1:29.7:1:1:0:59:42:1:0:0 -1 69777322 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12338;SOR=0;LSEQ=TCATGAGTTTGTCTACTTTC;RSEQ=GTCTTTGAGGCTGCTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,7:0.1:2,2:39.5:1:30:1:1:1.53525:60:4:0.1:0:2 0/0:36:0:0,0:20,16:0:2,0:19.9:1:28.4:1:1:0:59.4:8:1:0:0.2 -1 69778029 . G T 70 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAACCCTCCAGTCTCCCC;RSEQ=GCTCCAGCAGGGGAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:5:2,3:2,2:0.5556:2,2:21.6:1:30.4:1:1:1.43328:60:10:0.5556:0:1 -1 70742002 . A T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24858;SOR=Inf;LSEQ=GTAGTCTAGCATAGGTTGAA;RSEQ=CTAAAGGATAATGACAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:143,91:0:2,0:25.7:1:30:1:1:0:60:468:1:0:0.3 0/1:241:3:0,3:145,91:0.0124:2,0:14.3:1:21.3:1:0.05966:0:60:2:0.0085:0:1.3 -1 70742063 . G C 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.08853;LSEQ=AGAAGATAAATAATGAATGG;RSEQ=CTTGCACACTATGCTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:81:42,39:102,105:0.2813:2,2:27:1:31.6:1:0.79334:1.11:60:80:0.2837:0:1.1 0/1:360:162:78,84:105,92:0.45:2,2:26.2:1:31.6:1:0.34164:1.22838:60:80:0.4533:0:1.2 -1 70742140 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50425;SOR=Inf;LSEQ=AATGGGAAATCTCAAATAAG;RSEQ=AACTGTCCTGCGCAATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:27,99:0:2,0:25.4:1:31.9:1:1:0:60:62:1:0:0.5 0/1:157:2:1,1:49,106:0.0127:2,2:40:1:27.5:1:0.53691:2.15:60:4:0.0129:0:1.5 -1 70742188 . T C 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTCCTTAGAACAGTGTC;RSEQ=TTTAGTTTTTTAGGTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:3,50:0,0:1:0,2:21.9:1:32.2:1:1:0:60:52:1:0:1 1/1:51:51:4,47:0,0:1:0,2:22.9:1:32:1:1:0:60:102:1:0:1.1 -1 71762203 . A G 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41689;LSEQ=CTTGTTTTGGATTTTGCTAT;RSEQ=GTTCTCATTTGGATTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:668:155:73,82:234,279:0.232:2,2:27.7:1:31.2:1:0.78287:1.06:60:50.667:0.2324:0:1.1 0/1:796:89:39,50:336,370:0.1118:2,2:26.6:1:30.5:1:0.57343:1.16402:60:178:0.1128:0:1.2 -1 71762268 . A G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04685;SOR=0;LSEQ=CTAAAGAGGGTGAGTATTTC;RSEQ=GGTGTTCATCGTTTGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:4:2,2:93,229:0.0123:2,2:19:1:24.5:1:0.58302:2.45:60:3:0.0093:0:1 0/0:373:0:0,0:117,256:0:2,0:24.2:1:30.4:1:1:0:60:185.5:1:0:0.2 -1 71762279 . G A 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.45119;SOR=2.39695;LSEQ=GAGTATTTCAGGTGTTCATC;RSEQ=TTTGGGAAAGGCAAGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:2:2,0:60,204:0.0075:2,0:1:0:26:0:0.05365:0:60:4:0.0076:0:1.5 0/1:281:5:1,4:73,202:0.0178:2,2:16:1:30.2:1:1:1.44376:60:10:0.018:0:1.6 -1 72058192 . C T 79 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAAACAACAAAATCTCA;RSEQ=CAAATCTACTGACTTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:19.2:1:30.7:1:1:0:60:12:1:0:1 1/1:2:2:2,0:0,0:1:0,0:33:1:30.5:1:1:0:60:4:1:0:1 -1 72058367 . C T 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCCATGTGTAAGGATTG;RSEQ=GTGATGTATAAGGAATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:120:120:118,2:0,0:1:0,1:24.7:1:30:1:1:0:60:119:1:0:1.8 1/1:71:71:69,2:0,0:1:0,1:22.7:1:30.1:1:1:0:60:142:1:0:2 -1 72058405 . T C 247 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTCACATCAGGTTGAGTTT;RSEQ=AAAATGAACGTACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:235:234:226,8:0,0:0.9957:0,1:22.9:1:31.5:1:1:0:60:233:1:0:1.4 1/1:185:185:178,7:0,0:1:0,1:24.6:1:31.5:1:1:0:60:91.5:1:0:1.4 -1 72058552 . G A 323 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20168;SOR=2.77822;LSEQ=AGCTTGTTGGCAGCCACACA;RSEQ=GTATAATTGCCGAAGTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1457:1450:745,705:1,1:0.9952:2,2:26.4:1:30.5:1:1:1.06:60:79.556:0.9965:0:1.1 1/1:1730:1727:855,872:0,0:0.9983:0,2:25.6:1:30.1:1:1:0:60:68.08:0.9982:0:1.1 -1 72058774 . CG TA 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=Inf;LSEQ=ACGCTGACGTTAGCATATAA;RSEQ=TGATAATGGTGCAATTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:1,133:0:1,0:24.9:1:32:1:1:0:60:32.5:1:0:1.1 0/1:94:8:1,7:1,85:0.0851:1,2:17.6:1:30.1:1:0.16381:11.43:60:16:0.086:0.0106:1 -1 72058775 . G A 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00172;SOR=0;LSEQ=CGCTGACGTTAGCATATAAC;RSEQ=TGATAATGGTGCAATTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:129:129:1,128:0,0:1:0,1:25.4:1:31.2:1:1:0:60:63.5:1:0:1.1 1/1:90:83:1,82:0,0:0.9222:0,1:24.2:1:30.3:1:1:0:60:166:1:0:1 -1 72058827 . G A 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03794;SOR=0;LSEQ=TTAGTAGATTTGGGGGAGGT;RSEQ=AGGTTGCATGTCAGCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:6:0,6:1,43:0.12:1,0:20:1:31:1:1:0:60:12:0.1224:0:2 0/0:36:0:0,0:2,34:0:2,0:23.9:1:31.4:1:1:0:60:35:1:0:0.6 -1 72074998 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAGGTCAGGAGATCAAG;RSEQ=CCATCCTAGCTAACATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:30:1:1:0:54.5:4:1:0:1 -1 72076617 . C G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17789;SOR=Inf;LSEQ=GCTGCTGAGAATCATTCAAG;RSEQ=CAGTTAAAGAAATTGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:228,3:0:1,0:24.1:1:32.1:1:1:0:60:56.75:1:0:0 0/1:169:2:1,1:161,6:0.0118:1,2:37.5:1:33:0:0.08136:24.92023:60:4:0.012:0:1 -1 72076795 . G T 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACTGCGTCCGGGGGTCAC;RSEQ=GTGCCAGATTTAATTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1049:0:0,0:422,623:0:2,0:24.7:1:30.3:1:1:0:60:79.385:0.9971:0:0.1 0/1:1092:51:22,29:454,586:0.0467:2,2:24.6:1:30:1:1:1.02124:60:102:0.0472:0:1.1 -1 72076894 . A T 94 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0031;SOR=12.21596;LSEQ=TAATCCTCAACAGAAATATG;RSEQ=CACACATATATTTTTATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:0,1:8,194:0.0049:1,0:30:0:14:0:1:0:60:0:0:0:1 0/1:157:9:0,9:10,138:0.0573:2,0:18.2:1:29.9:1:1:0:60:18:0.0581:0:1 -1 72241677 . AAAAT A 155 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=44;MSI=12.000;MSILEN=4;SSF=0.654;SOR=0.76401;LSEQ=CAGAGTAAGACTCTGTCTCA;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:32:32,0:28,0:0.5161:1,1:15.2:1:31.1:1:1:0:59.8:64:0.5161:0.2258:0.1 0/1:29:13:13,0:16,0:0.4483:1,1:18.2:1:31.4:1:1:0:60:26:0.4483:0.1724:0 -1 72241731 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49953;SOR=0;LSEQ=AATAAATAAATAAATGCATT;RSEQ=TGCCTACCGCATGAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:166,1:0.0118:1,2:11:1:28.5:1:0.0236:117.61658:60:4:0.0119:0:1.5 0/0:154:0:0,0:153,1:0:1,0:22.6:1:31.7:1:1:0:60:308:1:0:0.1 -1 72242039 . G A 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=2.5425;LSEQ=ATAAAGTTTTGTTGAAGTAC;RSEQ=TATGATTAATTCCATAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:213:27,186:7,52:0.7831:2,2:23.7:1:31.1:1:1:1.08:60:212:0.7823:0:1.1 1/1:316:285:33,252:8,23:0.9019:2,2:22.8:1:30.4:1:0.04291:2.64538:60:284:0.9016:0:1.1 -1 72400491 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGACTACAATACTTGCATA;RSEQ=CTTTTTTTAAATGTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:11,0:0.1538:0,2:11:1:28.5:1:0.15385:0:60:4:0.1538:0:1.5 0/0:3:0:0,0:3,0:0:0,0:12.3:1:29.7:1:1:0:60:6:1:0:0 -1 72400656 . A G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00417;SOR=Inf;LSEQ=CAACAAATATTTCAATGACA;RSEQ=CAAATATTTCAACATTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:132,1:0:1,0:24.1:1:30.5:1:1:0:60:43.333:1:0:0.1 0/1:115:7:7,0:107,1:0.0609:1,0:19.7:1:31.3:1:1:0:60:14:0.0619:0:1 -1 72401095 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23388;SOR=Inf;LSEQ=TTTTGCTGAATAATAGCACA;RSEQ=CATCAAATGCAAACATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:2,195:0:1,0:23.7:1:32.3:1:1:0:60:48.25:1:0:0.1 0/1:185:2:0,2:4,178:0.0108:1,0:11:1:30.5:1:1:0:60:4:0.0109:0:1 -1 72401185 . T C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.38192;SOR=0.5557;LSEQ=CAAATGTGAAACAATACTTG;RSEQ=GTACAGTTTTTTTAAGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:14:0,14:0,20:0.4118:1,1:18.9:1:29.9:1:1:0:60:28:0.4242:0:1.1 0/1:18:5:0,5:0,13:0.2778:1,0:23.2:1:31.2:1:1:0:60:10:0.2778:0:1 -1 72646484 . TA T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49862;SOR=Inf;LSEQ=TGGCCACTAACAAAATGTTA;RSEQ=AGAGCCCTAGGGTTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:133,33:0:2,0:21.9:1:28.2:1:1:0:60:165:1:0:0.1 0/1:171:2:1,1:137,32:0.0117:2,2:5.5:1:29.5:1:0.34964:4.23125:55.5:4:0.0118:0.0058:0.5 -1 72646511 . C T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09752;SOR=0;LSEQ=CCTAGGGTTTAAAACTGTCT;RSEQ=AGGGAGGCTCTGCTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:1,2:190,92:0.0105:2,2:13:1:26.3:1:0.25379:4.10805:60:6:0.0108:0:1.3 0/0:333:0:0,0:217,116:0:2,0:23:0:18:0:1:0:60:0:0:0:1 -1 72646585 . A AT 140 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.04681;SOR=1.92837;LSEQ=CTTGCAGCAGTTAGTTTGGG;RSEQ=TTTTTTTTTCTATAGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:15:8,7:246,247:0.0295:2,2:26.3:1:28.8:1:1:1.15:60:14:0.0282:0.0039:0 0/1:541:30:13,17:240,270:0.0555:2,2:26.8:1:28.6:1:0.71147:1.16207:59.8:29:0.0551:0.0037:0.2 -1 72646658 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11136;SOR=Inf;LSEQ=ACTGTGGTGCTGATGGTGCA;RSEQ=CATGTCTGATGGGAATACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:66,194:0:2,0:24.7:1:31.1:1:1:0:59.9:36.143:0.9961:0:0.1 0/1:243:3:1,2:62,178:0.0123:2,2:35.3:1:30:1:1:1.43:60:6:0.0128:0:1 -1 72747844 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00211;SOR=0.38772;LSEQ=CCAGCATAAACGGGCCGGGG;RSEQ=TCCGGGAAGAATCTGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:101:99,2:29,2:0.7652:2,1:26.3:1:29.8:1:0.23452:3.37:60:100:0.7634:0:1.1 1/0:79:44:44,0:32,2:0.557:2,1:22.5:1:29.9:1:0.18681:0:60:88:0.5789:0:1 -1 72748329 . TTTTC T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53802;SOR=0;LSEQ=TTGGTGGGTGGGTGGGTTTC;RSEQ=TTTCTTTCTTCCCCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:0,2:0,76:0.0256:1,0:39.5:1:28:1:1:0:60:4:0.027:0:0 0/0:43:0:0,0:0,43:0:1,0:19.2:1:28.6:1:1:0:58:7.6:1:0:0.5 -1 72748567 . G GTCCT 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.806;LSEQ=CGCCGGCGAGTGAGGGAGGA;RSEQ=GCGCGGCGGCGGGGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:5,5:4,2:0.625:2,2:28.9:1:29.8:1:0.63287:1.91506:60:20:0.625:0.1875:0 1/0:14:8:3,5:3,3:0.5714:2,2:23.1:1:28.6:1:1:1.60599:60:16:0.5714:0.1429:0 -1 72748596 . AGCG A 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.56483;SOR=0.34833;LSEQ=GCGGGGGAGGAGGCAGGGCG;RSEQ=GCGGCGGCGGCGGCTGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:32:0:33.5:1:1:1.12:60:4:0.1111:0:0.5 0/1:26:1:0,1:11,14:0.0385:2,0:50:0:31:0:1:0:60:2:0.0385:0:0 -1 72748669 . A C 100 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00167;SOR=0;LSEQ=CAGCAGCAGAAGCAGCGCGG;RSEQ=GCGCTGCGCCGGCCGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:4,5:0,0:1:0,2:20.9:1:31.6:1:1:0:60:18:1:0:1.2 0/1:13:4:2,2:4,5:0.3077:2,2:26:1:30.3:1:1:1.23:60:8:0.3077:0:1 -1 75413421 . C T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58204;SOR=2.44724;LSEQ=TTTCACTCCTATGTGAGTCT;RSEQ=ACGAGGGGAAGGGGTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:8,0:0.1:0,0:2:0:31:0:1:0:60:2:0.1:0:1 0/1:9:2:2,0:7,0:0.2222:0,0:33:1:32:0:1:0:60:4:0.2222:0:1 -1 75413501 . CTT C 104 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01038;SOR=6.3069;LSEQ=AAAGTCCTTTCGAAAAAGAA;RSEQ=ATCAATCTGTAAAGAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:2,1:29,8:0.075:2,2:27:1:33.3:1:0.54504:1.78205:60:6:0.0789:0:0.3 0/1:29:10:7,3:12,7:0.3448:2,2:28.1:1:31.5:1:1:1.35:60:20:0.3448:0:0.1 -1 75413522 . T A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49833;SOR=0;LSEQ=TTATCAATCTGTAAAGAAAC;RSEQ=GATTTACAGTTAACTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:37,11:0.04:2,2:40:0:30.5:1:0.42612:3.26364:60:4:0.0408:0:1 0/0:42:0:0,0:28,14:0:2,0:25.8:1:30.4:1:1:0:60:41:1:0:0.1 -1 75413622 . C T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12412;SOR=2.1389;LSEQ=TAGAGAGCGTGCAGAAAGTC;RSEQ=CCTGCCCTCCCAGGGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:8:3,5:62,57:0.063:2,2:29.3:1:29.9:1:0.48515:1.80449:60:16:0.0645:0:2.1 0/1:119:15:7,8:55,49:0.1261:2,2:31.5:1:29.7:1:0.78404:1.2801:60:30:0.1282:0:1.8 -1 75413644 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22667;SOR=Inf;LSEQ=CTGCCCTCCCAGGGACTCAG;RSEQ=GATGGCCCCAGACATGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:61,76:0:2,0:25.6:1:30.8:1:1:0:60:44.667:1:0:0.2 0/1:125:2:1,1:60,63:0.016:2,2:43:1:29.5:1:1:1.05:60:4:0.016:0:1 -1 75413656 . A G 129 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00944;SOR=3.44807;LSEQ=GGACTCAGGGATGGCCCCAG;RSEQ=CATGATTTTAACAGTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:6:3,3:57,70:0.0451:2,2:28.8:1:33.2:1:1:1.23:60:12:0.0455:0:2.5 0/1:128:18:6,12:53,56:0.1406:2,2:23.8:1:31:1:0.30917:1.8836:60:36:0.1452:0:1.7 -1 77900050 . G A 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCATACAATTTACTAA;RSEQ=TAAACCTAATCATTTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:16,36:0,0:1:0,2:21.5:1:30.9:1:1:0:60:104:1:0:1.1 1/1:65:65:23,42:0,0:1:0,2:24.7:1:30.5:1:1:0:60:130:1:0:1.1 -1 78414346 . C A 21 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75921;LSEQ=AAAGGAAACACTATTTTAAA;RSEQ=CAAAAACAAAATTAAGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:118,34:0.0191:2,2:9:1:22.7:1:0.53861:1.72827:60:2:0.0147:0:2.3 0/1:206:3:3,0:149,53:0.0146:2,0:14:1:13.3:1:0.57013:0:60:0:0:0:4 -1 78414402 . GT G 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00605;SOR=0;LSEQ=CATCCATATATTTAACAAAG;RSEQ=TTTTTTCCCCCACACAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:6:3,3:252,206:0.0129:2,2:29.7:1:31.3:1:1:1.22276:60:12:0.0131:0:0.2 0/0:621:0:0,0:347,274:0:2,0:27.1:1:28.6:1:1:0:60:35.529:1:0:0.2 -1 78414768 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50136;SOR=Inf;LSEQ=ATTTAAAAGGCAAACACTCC;RSEQ=AAACAGACAAACAGTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:140,21:0:2,0:22.4:1:31.1:1:1:0:60:52.667:1:0:0.1 0/1:187:2:1,1:160,24:0.0107:2,2:25:1:28.5:1:0.25138:6.55235:60:4:0.0108:0:1 -1 78415029 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22355;SOR=0;LSEQ=GCTGTAACCACAATTATAAG;RSEQ=CCAACATCTCATTTCTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:18,124:0.0139:2,2:38:1:29.5:1:0.24728:6.73:60:4:0.0139:0:1 0/0:160:0:0,0:33,126:0:2,0:23.3:1:30.9:1:1:0:60:78.5:0.9937:0:0.1 -1 78415038 . T C 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.90526;LSEQ=ACAATTATAAGCCCAACATC;RSEQ=CATTTCTAATAAAAACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:1,0:14,113:0.0078:2,0:28:0:33:0:0.11719:0:60:2:0.0078:0:1 0/1:135:2:1,1:21,112:0.0148:2,2:12.5:1:26.5:1:0.30039:5.23:60:4:0.0152:0:1.5 -1 78415120 . CA C 60 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.01033;SOR=Inf;LSEQ=TTGTGTTTGCCCTTGTTGAC;RSEQ=AAAAAAAAAACCCCTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:0:1,0:28:1:29:1:1:0:60:10:1:0:0.8 0/1:17:4:0,4:0,13:0.2353:1,0:30:1:30:1:1:0:60:8:0.2353:0:0.3 -1 78420772 . G GA 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54785;SOR=0;LSEQ=CTGGTTGACAAATGCAATTA;RSEQ=AAAAAAAAATTTCCTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:3,0:47,0:0.06:1,0:19.3:1:30:1:1:0:60:6:0.06:0:0 0/0:27:0:0,0:27,0:0:1,0:22.5:1:31.7:1:1:0:60:54:1:0:0.1 -1 78422436 . TCA T 82 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.52369;SOR=0.59489;LSEQ=GTGAAGTCTGTAATTCTCTC;RSEQ=CACACACACACACCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:6:1,5:15,74:0.0632:2,2:28:1:32:1:1:1.01337:60:12:0.0645:0:0 0/1:104:4:0,4:22,77:0.0385:2,0:32.5:1:30:1:0.57545:0:60:8:0.0388:0:0.5 -1 78425794 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51291;SOR=Inf;LSEQ=ATGCATACAAATGTAGAATC;RSEQ=ACACTAGAAAATTTAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:84,14:0:2,0:23.3:1:29.3:1:1:0:60:18.6:1:0:0.1 0/1:139:2:1,1:108,28:0.0144:2,2:17:0:32.5:1:0.37734:3.80756:60:4:0.0145:0:1.5 -1 78425801 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51096;SOR=Inf;LSEQ=CAAATGTAGAATCAACACTA;RSEQ=AAAATTTAATAATGTAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:95,18:0:2,0:23.2:1:31.5:1:1:0:60:55.5:1:0:0.1 0/1:156:2:1,1:117,36:0.0128:2,2:20.5:1:29:1:0.42162:3.21944:60:4:0.013:0:1 -1 78426184 . CA C 76 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.45029;SOR=0.40351;LSEQ=AAAGGATTTACTGGGCCCTA;RSEQ=AAAAAAAGGATGACATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:5:2,3:50,226:0.0178:2,2:27.6:1:32.8:1:0.23148:3.00:60:10:0.0181:0:1.2 0/0:276:2:0,2:81,193:0.0072:2,0:24.5:1:33:1:1:0:60:4:0.0073:0:0 -1 78426212 . GA G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49859;SOR=Inf;LSEQ=AGGATGACATAGAAAAATCA;RSEQ=AAAACACAGTAATGGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:28,150:0:2,0:22.7:1:30.2:1:1:0:60:43.5:1:0:0.2 0/1:178:2:1,1:46,130:0.0112:2,2:26:1:29.5:1:0.45947:2.81:60:4:0.0114:0:1.5 -1 78426231 . A G 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01485;SOR=Inf;LSEQ=AGAAAAACACAGTAATGGTT;RSEQ=AACAACTCTACGGCCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:19,106:0:2,0:22.8:1:29.9:1:1:0:60:124:1:0:0.1 0/1:135:7:2,5:28,100:0.0519:2,2:27.4:1:30.6:1:0.65124:1.42:60:14:0.0519:0:1.3 -1 78426284 . T C 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TACCCTCTTATAGTCACAAA;RSEQ=AACAAATTTTAGGTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:1,51:0:1,0:25.5:1:28.5:1:1:0:60:51:1:0:0 0/1:36:11:0,11:1,24:0.3056:1,0:25.5:1:31.5:1:1:0:60:10:0.2941:0:1.3 -1 78428596 . G A 105 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00755;SOR=6.16005;LSEQ=GCACCAGACTGCTGGCTTAT;RSEQ=CTTTTTATGGTTTCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:577:2:1,1:203,372:0.0035:2,2:20:0:30:0:1:1.83:60:4:0.0035:0:4.5 0/1:619:13:5,8:224,381:0.021:2,2:27.2:1:28.4:1:1:1.06:60:26:0.0212:0:1.7 -1 78428639 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25025;SOR=Inf;LSEQ=AAATCAAAAGACAGTAATTT;RSEQ=TCTAAAGGTTTCAAGGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:50,222:0:2,0:24.6:1:32.2:1:1:0:60:89.667:1:0:0.1 0/1:298:3:2,1:82,212:0.0101:2,2:18.7:1:26.7:1:0.19383:5.14:60:6:0.0101:0:1 -1 78428851 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CTTAGTATGTTTAAACATAA;RSEQ=CTTAATGTGATTATAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:10.4:1:30.4:1:1:0:60:14:1:0:0 1/0:4:2:0,2:0,2:0.5:0,0:19:1:30.5:1:1:0:60:4:0.5:0:1 -1 78429084 . C A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00285;SOR=Inf;LSEQ=ATTAAAATCCTGCTCTTTCT;RSEQ=TAAATATACATGAGATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:21,1:0:1,0:26.5:1:32.1:1:1:0:60:44:1:0:0.1 0/1:12:5:5,0:7,0:0.4167:0,0:15.4:1:29.4:1:1:0:60:10:0.4167:0:1 -1 78429215 . A G 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=GCAACAGAAAGTGTCCAGAA;RSEQ=AATGAATAATGTGTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:221,68:0:2,0:22.5:1:30:1:1:0:60:95.333:0.9965:0:0.1 0/1:291:14:11,3:215,62:0.0481:2,2:19.9:1:31.5:1:1:1.06:60:28:0.0488:0:1.1 -1 78429219 . G T 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37452;SOR=3.76064;LSEQ=CAGAAAGTGTCCAGAAAAAT;RSEQ=AATAATGTGTTAAAACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:0,1:235,73:0.0032:2,0:1:0:24:0:0.23948:0:60:2:0.0033:0:1 0/1:331:4:2,2:243,84:0.0121:2,2:12.5:1:26.5:1:0.27782:2.88181:60:8:0.0121:0:1 -1 78429408 . G C 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGGATTACCAGCCTATAGA;RSEQ=AGGGAAAGACAAGAACGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:139,350:0:2,0:25.8:1:31.3:1:1:0:60:60.125:1:0:0.1 0/1:577:44:16,28:190,343:0.0763:2,2:25.1:1:31.1:1:1:1.03:60:88:0.0768:0:1.1 -1 78430093 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24567;SOR=Inf;LSEQ=CTAGCTTCTCAGGGTTTAAA;RSEQ=TAAAAAAAAGTATTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:31,114:0:2,0:21:1:31.3:1:1:0:60:28:1:0:0.2 0/1:143:2:1,1:28,112:0.014:2,2:22:1:28.5:1:0.3679:3.95:60:4:0.0145:0:1 -1 78430094 . TA T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.62226;SOR=3.01128;LSEQ=TAGCTTCTCAGGGTTTAAAG;RSEQ=AAAAAAAGTATTTTAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:0,1:30,106:0.0073:2,0:42:0:32:0:1:0:60:2:0.0075:0:0 0/1:138:3:1,2:27,108:0.0217:2,2:19.3:1:29.7:1:0.49638:1.99:60:6:0.0224:0:0 -1 78430234 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18993;SOR=Inf;LSEQ=AAGTATAAAGGTGAAATAAA;RSEQ=GGATAACAATGTTAGAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:163,15:0:2,0:23.2:1:30.2:1:1:0:60:28.667:1:0:0.1 0/1:138:2:2,0:123,13:0.0145:2,0:16.5:1:30.5:1:1:0:60:4:0.0147:0:1 -1 78430689 . A AG 274 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19837;SOR=0.57764;LSEQ=AAATAATATATATTAACAAA;RSEQ=GAAGTGGACAAAAATGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:415:405:235,170:4,5:0.9759:2,2:25.7:1:31.5:1:0.50272:1.73:60:44:0.9778:0.0964:0.1 1/1:512:491:268,223:7,9:0.959:2,2:25.6:1:30.7:1:0.45019:1.54:60:43.636:0.9677:0.1191:0.1 -1 78432313 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24605;SOR=Inf;LSEQ=TAAAGCAGTAACAAAGAGAA;RSEQ=AGACAAAATTCAAAGAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:142,17:0:2,0:22.6:1:32.1:1:1:0:60:78.5:1:0:0.1 0/1:157:2:1,1:122,33:0.0127:2,2:16:1:27:1:0.38731:3.65744:60:4:0.013:0:1 -1 78432503 . G C 185 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCATTATTGTTACTAGAAG;RSEQ=CTTAAAAAAAAAAAAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:146,138:0:2,0:22:1:30.4:1:1:0:59.7:12.524:0.9962:0:0.5 0/1:351:81:42,39:129,134:0.2308:2,2:22:1:29.2:1:0.70381:1.12:59.5:8:0.2162:0:1.5 -1 78432647 . G GA 117 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.71193;SOR=0.82497;LSEQ=CCTCTGCCAATTACTAGTTA;RSEQ=AAAAAAAAAAATTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:15:6,9:128,171:0.0476:2,2:33.2:1:30.9:1:1:1.12236:58.3:30:0.0498:0:0.6 0/1:404:16:9,7:178,207:0.0396:2,2:34.9:1:29.4:1:0.45499:1.49:60:15:0.0403:0:0.7 -1 78432658 . AT A 176 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=5.0005;LSEQ=TACTAGTTAGAAAAAAAAAA;RSEQ=TTTTTTTTTGGTTGAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:12:6,6:128,145:0.0396:2,2:23.3:1:31.2:1:1:1.13:60:24:0.0404:0.0066:0.3 0/1:362:62:31,31:138,159:0.1713:2,2:21.5:1:29.6:1:0.67535:1.15:60:124:0.1756:0.0746:0.5 -1 78432659 . T A 125 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTAGTTAGAAAAAAAAAAA;RSEQ=TTTTTTTTTGGTTGAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:18:6,12:128,145:0.0594:2,2:13.7:1:30:1:0.33222:1.76219:60:36:0.0606:0:1.1 0/0:362:0:0,0:138,159:0:2,0:22.5:1:29.4:1:1:0:59.9:48.5:0.8244:0:0.3 -1 78432670 . G T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84681;LSEQ=AAAAAAAAATTTTTTTTTTG;RSEQ=TTGAAAGATTCTAAAGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:1,2:148,150:0.01:2,2:11.3:1:27.3:1:1:1.96904:60:6:0.0103:0:1.3 0/0:355:3:2,1:170,182:0.0085:2,2:16:1:17.3:1:0.61259:2.14:53.3:0.5:0.0029:0:2.3 -1 78432947 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19346;SOR=Inf;LSEQ=AATATGATCTTATTACTTGA;RSEQ=TAGTTAAATTAAGAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:3,18:0:2,0:24.3:1:31.8:1:1:0:60:42:1:0:0 0/1:17:2:0,2:1,14:0.1176:1,0:31.5:1:31.5:1:1:0:60:4:0.1176:0:1 -1 78433801 . T C 185 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATGAACAAAATCTTAACA;RSEQ=TGAAATTGTTACTTTAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:292,183:0:2,0:23.3:1:30.2:1:1:0:60:46.5:1:0:0.1 0/1:512:64:41,23:265,183:0.125:2,2:21:1:30.9:1:0.49744:1.23:60:128:0.126:0:1.1 -1 78434683 . A G 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12503;SOR=Inf;LSEQ=CACGTTTACATACTGAACAC;RSEQ=GGTAATAAATAAAAATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:227,138:0:2,0:24.7:1:30.3:1:1:0:60:72:1:0:0.1 0/1:393:4:2,2:216,173:0.0102:2,2:31.3:1:28.3:1:1:1.24784:60:8:0.0103:0:1 -1 78434821 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24587;SOR=Inf;LSEQ=CAACATCTGAAGCATCATTA;RSEQ=CTCATTTTTTTTCTACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:30,121:0:2,0:25.8:1:31.7:1:1:0:60:24.167:0.9932:0:0.1 0/1:150:2:1,1:37,111:0.0133:2,2:20:1:31:1:0.44376:2.97:60:4:0.0137:0:1 -1 78435700 . C A 57 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75433;SOR=0.72009;LSEQ=CCTCCAATTTTTGCTGCAAT;RSEQ=TAAAAAAAAAAAAGAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:6:5,1:94,297:0.015:2,2:5.8:1:22.2:1:0.00429:15.67:60:5:0.0143:0:1.3 0/1:368:4:4,0:120,242:0.0109:2,0:1:0:22.8:1:0.01276:0:60:8:0.012:0:1.3 -1 78435701 . TA T 177 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.3855;SOR=0.82035;LSEQ=CTCCAATTTTTGCTGCAATC;RSEQ=AAAAAAAAAAAGAAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:54:9,45:71,223:0.1488:2,2:29.5:1:30.8:1:0.29154:1.58999:60:108:0.1538:0.0055:0.3 0/1:351:44:8,36:102,192:0.1254:2,2:27:1:30.5:1:0.03739:2.38522:60:88:0.1287:0.0028:0.3 -1 78442593 . C G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCTTCTAGCGACTTCA;RSEQ=TTCTGGGTCCTTGCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:30:1:1:0:60:4:1:0:1 -1 78444734 . C T 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00354;SOR=Inf;LSEQ=CCTGTTCAGAGACTTCCTCT;RSEQ=AGCTAACAGCTAAGAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:24,157:0:2,0:24:1:32.2:1:1:0:60:89.5:0.9944:0:0.1 0/1:184:9:0,9:35,139:0.0489:2,0:15.3:1:29.2:1:0.21056:0:60:18:0.0495:0:1.1 -1 78444764 . C CGGCCG 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.07332;SOR=2.09617;LSEQ=CTAAGAAAGAAAGAAAATGG;RSEQ=GGCCGTCGAAGCTCTATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:12:0,12:10,84:0.1132:2,0:29.3:1:31.8:1:0.59929:0:60:24:0.1176:0.0094:0 0/1:85:18:2,16:6,61:0.2118:2,2:21.4:1:30.6:1:0.67473:1.27:60:36:0.2118:0.0706:0 -1 82939448 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.21048;SOR=Inf;LSEQ=TAGTCTCAAGGATCCATTTC;RSEQ=TGTTTAATAATGTTTACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:135,39:0:2,0:23.5:1:30.2:1:1:0:60:86:1:0:0.1 0/1:148:2:1,1:116,29:0.0135:2,2:25.5:1:28.5:1:0.36763:3.94968:60:4:0.0136:0:1 -1 82939464 . A T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11967;SOR=Inf;LSEQ=TTTCATGTTTAATAATGTTT;RSEQ=CATACCTGAAAAGAAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:153,58:0:2,0:26:1:28.5:1:1:0:60:210:1:0:0.2 0/1:206:3:1,2:147,56:0.0146:2,2:21:1:21.3:1:0.19188:5.20056:60:2:0.0099:0:1 -1 82939537 . C T 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.09837;LSEQ=AAGATCTGGTACTTTTGTAA;RSEQ=GGCTTCAAAGGAACTGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:95:45,50:138,154:0.2455:2,2:26.8:1:30.1:1:1:1.00:60:94:0.2442:0:1.2 0/1:473:192:97,95:134,147:0.4059:2,2:27.1:1:29.9:1:0.57468:1.12:60:191:0.4064:0:1.3 -1 82939621 . A G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.36414;LSEQ=TTAGAGGAACCAGTTCAATT;RSEQ=ACTACATTTTGTAGATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:31:6,25:29,111:0.1813:2,2:22.2:1:31.7:1:1:1.08806:60:30:0.1765:0:1.3 0/1:180:77:23,54:27,76:0.4278:2,2:21.6:1:30.6:1:0.61671:1.20:60:76:0.4246:0:1.4 -1 82939664 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50174;SOR=0;LSEQ=TCAAATTCATCTAAGAAACC;RSEQ=ATGTAACACCTACTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:0,2:3,69:0.027:1,0:16:1:32:1:1:0:60:4:0.027:0:1 0/0:60:0:0,0:4,56:0:2,0:22.4:1:28.1:1:1:0:60:59:1:0:0.4 -1 83024609 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08641;SOR=0;LSEQ=AGAACATTGCTCTTTAATTT;RSEQ=TTAAAATAAGTATGGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:3:1,2:101,23:0.0236:2,2:7.3:1:27.3:1:0.09869:8.56924:60:6:0.0236:0:1 0/0:159:0:0,0:110,49:0:2,0:24.1:1:31.6:1:1:0:60:158:1:0:0.2 -1 83024629 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18945;SOR=0;LSEQ=GTTAAAATAAGTATGGTAAA;RSEQ=ACATTGCATATTATGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:129,46:0.0113:2,2:22:1:31:1:0.46167:2.78509:60:4:0.0114:0:1 0/0:229:0:0,0:142,86:0:2,0:24.4:1:29.5:1:1:0:60:56:0.9956:0:0.4 -1 83024692 . A G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=5.37792;LSEQ=GGCAACATGAAAACTTTAGT;RSEQ=AAGAGAACTCCAGTGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:76:42,34:138,128:0.2222:2,2:25.5:1:31.4:1:0.69616:1.15:60:75:0.2226:0:1.1 1/0:343:208:95,113:67,68:0.6064:2,2:26.5:1:31.5:1:0.50735:1.17143:60:207:0.607:0:1.2 -1 83024780 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58349;SOR=2.57251;LSEQ=ACATTTTTGAAGACAGTTTT;RSEQ=TTGACTTCAATTTGGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:1,0:26,98:0.008:2,0:1:0:23:0:0.216:0:60:2:0.0082:0:2 0/1:98:2:1,1:20,76:0.0204:2,2:22:1:31:1:0.38439:3.73:60:4:0.0206:0:1 -1 84971721 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52925;SOR=Inf;LSEQ=CGGTTGAGTCCGGCCTCCAG;RSEQ=CGGAGCTGTTGAACCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:27,13:0:2,0:25.6:1:31.4:1:1:0:60:39:1:0:0.1 0/1:68:2:1,1:41,25:0.0294:2,2:45.5:1:28:1:1:1.62758:60:4:0.0303:0:1 -1 84971732 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5106;SOR=Inf;LSEQ=GGCCTCCAGCCGGAGCTGTT;RSEQ=AACCACTTTCTTCATAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:34,17:0:2,0:23.9:1:31.4:1:1:0:60:50:1:0:0.2 0/1:72:2:1,1:41,29:0.0278:2,2:9.5:1:26.5:1:1:1.40686:60:4:0.0286:0:1 -1 84971788 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52586;SOR=Inf;LSEQ=CAGACATGGTGCACGCGACG;RSEQ=CCGGGCCGATTCGTGGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:12,21:0:2,0:28:1:30.2:1:1:0:60:15.5:1:0:0.4 0/1:55:2:1,1:22,30:0.0364:2,2:15:1:29.5:1:1:1.36:60:4:0.0377:0:1.5 -1 84971819 . G A 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.0087;SOR=0;LSEQ=TCGTGGGTCGGTGGGTCGTG;RSEQ=GCCGTGGGTCGGCGGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:1,5:6,13:0.24:2,2:24:1:28.7:1:0.63715:2.23947:60:5:0.2083:0:2 0/0:27:0:0,0:5,22:0:2,0:19.1:1:29.3:1:1:0:60:26:1:0:0.2 -1 84971833 . G C 67 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.18213;SOR=0.18282;LSEQ=GTCGTGGGCCGTGGGTCGGC;RSEQ=GGGCCAGACAACTCAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:1,4:1,13:0.2632:1,2:18.2:1:29:1:0.46784:3.02:60:10:0.2632:0:2.2 0/1:17:1:0,1:1,15:0.0588:1,0:19:0:30:0:1:0:60:2:0.0625:0:1 -1 85732941 . A C 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGACTGGCAAAGACTATT;RSEQ=GACTCTTGAAAATTTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:0,1:0.8:0,0:27.5:1:29.8:1:0.2:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 85733374 . C T 217 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=62.28749;LSEQ=CACTAGAGTTTGCACAAGTT;RSEQ=CTTCTTCTTCTAACTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1732:3:1,2:898,831:0.0017:2,2:28:1:29.3:1:0.61103:2.16033:60:6:0.0018:0:1 0/1:1772:173:86,87:822,773:0.0976:2,2:23.5:1:29.2:1:0.68905:1.07569:60:85.5:0.0982:0:1.1 -1 85733670 . A G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCTACATTTTAGTCCTAC;RSEQ=ATAAAATTATTCAGATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:799:0:0,0:281,518:0:2,0:25.1:1:30:1:1:0:60:71.636:1:0:0.1 0/1:899:27:9,18:322,550:0.03:2,2:23.1:1:30.6:1:0.84024:1.17074:60:54:0.0303:0:1.2 -1 85733704 . TA T 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06218;SOR=0;LSEQ=GATGTAAATGAAAAAGTAAC;RSEQ=AAAAAATGGAGTCACTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:5:2,3:100,338:0.0113:2,2:35.6:1:30.4:1:0.32539:2.25:60:10:0.0115:0:0 0/0:421:0:0,0:97,324:0:2,0:22:1:29:1:1:0:60:59.143:1:0:0.1 -1 85733737 . TGTTAA T 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00077;SOR=Inf;LSEQ=TCACTGTCCATCTTGTGACT;RSEQ=AGATTACAAGCTAGTTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:11,206:0:2,0:24.9:1:32.2:1:1:0:60:107.5:1:0:0.1 0/1:182:9:1,8:10,163:0.0495:2,2:28.3:1:31.3:1:0.43687:2.03:60:18:0.0495:0:0 -1 85733929 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCTCATTTAAGGTACAG;RSEQ=GTACATATAAACTTAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:23.9:1:28.1:1:1:0:60:8:1:0:1 1/1:2:2:0,2:0,0:1:0,0:21.5:1:32:0:1:0:60:4:1:0:1 -1 85736510 . AT A 170 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04871;SOR=0.62092;LSEQ=CAGTGTCTTCTCTACTGAGT;RSEQ=TTTTTTTGCACGTAGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1427:45:26,19:649,731:0.0315:2,2:24.3:1:31:1:0.17339:1.54:60:90:0.0317:0.0035:0.2 0/1:1615:32:15,17:742,841:0.0198:2,2:26.8:1:29.6:1:1:1.00:59.7:64:0.0199:0.0012:0.3 -1 85739749 . T C 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5352;SOR=0;LSEQ=GAATGCTCTTCCCTCAGTTC;RSEQ=GTCAAATCTTTCAGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:3,1:13,0:0.2353:1,2:33:1:32:1:0.23529:0:60:8:0.2353:0:2 0/0:5:0:0,0:5,0:0:0,0:24.8:1:31.2:1:1:0:60:10:1:0:0 -1 85739751 . T C 89 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2719;SOR=0;LSEQ=ATGCTCTTCCCTCAGTTCTG;RSEQ=CAAATCTTTCAGGAATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:7,0:10,1:0.3889:2,0:22.4:1:31.9:1:1:0:60:14:0.3889:0:1.3 0/0:5:0:0,0:5,0:0:0,0:26:1:30.2:1:1:0:60:10:1:0:0 -1 85739778 . A G 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01124;SOR=0;LSEQ=TTTCAGGAATCAGTTTAAAT;RSEQ=TAACCTCTCCTGACCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:10,1:23,0:0.3235:1,2:22.6:1:32.8:1:0.32353:0:60:22:0.3235:0:1.7 0/0:15:0:0,0:15,0:0:1,0:18.9:1:28.5:1:1:0:60:30:1:0:0.1 -1 85739861 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=4e-05;SOR=0.13736;LSEQ=ATTCCTTCATAGTAATTGCA;RSEQ=TAATGAAAACAAAATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:31:31,0:77,0:0.287:1,1:23.2:1:32.3:1:1:0:60:62:0.2897:0:1.2 0/1:77:4:4,0:73,0:0.0519:1,0:19:1:30:1:1:0:60:8:0.0526:0:1 -1 85740024 . T C 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.6331;LSEQ=TCACTGCACTTATTTTGTGA;RSEQ=TTAAAACAATCCCCCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1159:211:100,111:461,487:0.1821:2,2:27.2:1:32:1:0.76109:1.05072:60:51.75:0.1803:0:1.2 0/1:1519:405:215,190:556,557:0.2666:2,2:27.4:1:31.4:1:0.2963:1.13:60:134:0.2659:0:1.1 -1 85741684 . T C 85 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84124;LSEQ=AAGCATCTCCAAGAACCCAG;RSEQ=TGGGGGGAAAGCATGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:10,0:0.375:0,0:16.7:1:33:1:1:0:60:12:0.375:0:1.8 0/1:3:1:1,0:1,1:0.3333:2,0:21:0:34:0:1:0:60:2:0.3333:0:1 -1 85741734 . A T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGGGCAAGAATCAAAAC;RSEQ=CCACTTGGCAACAAAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:2,0:38,0:0.05:1,0:32:1:33:0:1:0:60:4:0.0513:0:1 0/0:16:0:0,0:16,0:0:1,0:21.3:1:31.4:1:1:0:60:32:1:0:0.2 -1 85741921 . G C 304 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09623;LSEQ=GACTCCAGGCTTCCGCTTTC;RSEQ=TCTCCCGCTGGGCTGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:911:903:559,344:1,0:0.9912:0,2:24.2:1:31:1:1:0:60:59.2:0.9966:0:1.3 1/1:1114:1020:621,399:58,32:0.9156:2,2:24.7:1:30.5:1:0.57305:1.16437:60:126.5:0.9158:0:1.2 -1 85741968 . G C 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGCCCGCCCTGGGCACAGCT;RSEQ=CGTTACTCACGTCCTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1483:70:39,31:713,695:0.0472:2,2:26.2:1:31.5:1:0.46286:1.23:60:140:0.0483:0:1.6 0/0:1927:0:0,0:969,954:0:2,0:24.9:1:31.4:1:1:0:60:67.679:0.9984:0:0.8 -1 85742012 . G C 294 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.54638;LSEQ=TCAGTGAGGTCCTCCTCGGT;RSEQ=AGGGACGGTGCGGTGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1555:658:338,320:434,459:0.4232:2,2:24.3:1:31.5:1:0.30416:1.12:60:53.833:0.4211:0:1.3 0/1:1905:545:270,275:670,684:0.2861:2,2:24.8:1:31.2:1:1:1.00:60:89.833:0.2856:0:1.3 -1 85742023 . C A 224 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=36.02356;LSEQ=CTCCTCGGTGAGGGACGGTG;RSEQ=GGTGGGCTCCATGGTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1519:5:3,2:741,772:0.0033:2,2:34.6:1:24.4:1:0.68114:1.56:60:1.5:0.002:0:1.2 0/1:1852:197:99,98:816,838:0.1064:2,2:23.8:1:29.5:1:0.82144:1.04:60:48.25:0.1057:0:1.2 -1 85742157 . G C 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00185;SOR=0;LSEQ=GAGGAGGCGGAGCGGGTCGG;RSEQ=AGAAAGACGGCCGCCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:10:0,10:14,223:0.04:2,0:27.9:1:30.9:1:1:0:60:9:0.0375:0:1.1 0/0:236:0:0,0:13,223:0:2,0:24.1:1:31.4:1:1:0:60:77.667:1:0:0.2 -1 85742167 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25002;SOR=0;LSEQ=AGCGGGTCGGGAGAAAGACG;RSEQ=CCGCCCCTTCGGGAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:8,196:0.0144:1,2:16.3:1:29:1:0.12543:11.82:60:6:0.0153:0:1 0/0:188:0:0,0:11,177:0:2,0:23:1:31.6:1:1:0:60:19.889:1:0:0.2 -1 85742264 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.06144;SOR=Inf;LSEQ=GCGAATCTACGCGACGCGAC;RSEQ=CGGAGCTCGGAGCAGCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:1,45:0:1,0:24.9:1:32.8:1:1:0:60:92:0.9787:0:0.3 0/1:16:2:0,2:0,14:0.125:1,0:36.5:1:32:0:1:0:60:4:0.125:0:1 -1 85742338 . G C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCACGGCGAGGCGCGTC;RSEQ=CTTAGCAGAGCCCGCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:1,20:0,0:1:0,1:24.2:1:30.8:1:1:0:60:42:1:0:1 1/1:6:6:2,4:0,0:1:0,2:26.3:1:32.3:1:1:0:60:12:1:0:1.3 -1 85742389 . G A 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02206;SOR=Inf;LSEQ=GCCTATCGACGCCAGCCCGC;RSEQ=GGCCGATCCTGTTCCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:1,13:0:1,0:24:1:31.8:1:1:0:60:28:1:0:0.7 1/0:3:2:1,1:0,1:0.6667:0,2:38:1:29:1:1:0:60:4:0.6667:0:1.5 -1 85746410 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18396;SOR=Inf;LSEQ=GGATTGGGCGGGACTGAATG;RSEQ=GGATTCCGGGAGTTTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:232,15:0:2,0:24.4:1:30:1:1:0:60:60.75:1:0:0.1 0/1:186:2:1,1:168,15:0.0108:2,2:22:1:28.5:1:0.16592:10.87684:60:4:0.0108:0:2 -1 85746472 . A G 193 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=77.63646;LSEQ=GCTTTTCAGACCATGTGTCA;RSEQ=TGTTCCCAAGATGAATTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:862:1:1,0:598,261:0.0012:2,0:40:0:33:0:1:0:60:2:0.0012:0:1 0/1:833:69:48,21:509,255:0.0828:2,2:22.7:1:31.6:1:0.68962:1.14:60:138:0.0832:0:1.1 -1 85746754 . T C 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01043;SOR=0.07988;LSEQ=ACACAGCCTCCATACCCCCT;RSEQ=AACTTCCAGGTGCTCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:88:87:1,86:0,0:0.9886:0,1:24:1:31.9:1:1:0:60:42.5:0.9884:0:1.1 1/1:39:34:1,33:0,5:0.8718:0,1:24.6:1:32.6:1:1:0:60:68:0.8718:0:1.1 -1 85746929 . T C 67 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAGACAGTGTATTAGTTTCC;RSEQ=AGGGCCATCATACCAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:27.5:1:33.5:1:1:0:60:8:0.5:0:1 1/0:2:1:0,1:0,1:0.5:0,0:31:0:28:0:1:0:60:2:0.5:0:1 -1 87267422 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTTTCATTCTGGTGGGTT;RSEQ=GTGGTCTCACTGACTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30:1:1:0:60:4:1:0:1 -1 87268150 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TAAGCCAGTGGAAGGGCCAG;RSEQ=GGGTTGGTCCAGGGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:26:1:22.5:1:1:0:60:1:1:0:0.5 1/0:3:2:1,1:0,1:0.6667:0,2:46.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 -1 87268589 . T G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TAGAGTAAGGATAGATTTCA;RSEQ=TATTTCTTGCAAACTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:3:0:28:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:30:1:30:1:1:0:60:4:1:0:1 -1 88553551 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49392;SOR=Inf;LSEQ=TCTAGTTTCAGTCTTTGAGG;RSEQ=TGCTGACCCTTGGATGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:0:2,0:30.7:1:32.5:1:1:0:60:58:1:0:0.1 0/1:33:2:1,1:17,14:0.0606:2,2:27:1:27:1:1:1.20712:60:4:0.0606:0:1 -1 88553825 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=0;LSEQ=CAACCTGATGCCAGTAGGAT;RSEQ=GGTCCTGTATAGGGTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:0.1667:2,2:34:1:26.5:1:1:1.4491:60:4:0.1667:0:2.5 0/0:10:0:0,0:5,5:0:2,0:20.7:1:31.2:1:1:0:60:20:1:0:0.1 -1 88553882 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21212;SOR=Inf;LSEQ=GATCTCATCCAGTTGGGTGG;RSEQ=ACAAGGAGCAGGACCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:0:2,0:27.5:1:30.9:1:1:0:60:11:1:0:0.1 0/1:21:2:1,1:11,8:0.0952:2,2:30.5:1:27:1:1:1.35399:60:4:0.0952:0:1.5 -1 89294616 . G A 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30341;SOR=0.20446;LSEQ=TAACAGAAAGACTAATAAAA;RSEQ=GAATGTACTCTGTACCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:18.8:1:31.3:1:1:0:60:8:0.4:0:1 0/1:9:1:1,0:8,0:0.1111:0,0:7:0:31:0:1:0:60:2:0.125:0:1 -1 89294935 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50013;SOR=Inf;LSEQ=GCCATGTTGAGTGGCCCAGG;RSEQ=CAATTTGCTGAGAATGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:41,58:0:2,0:26.9:1:30:1:1:0:60:98:1:0:0.1 0/1:114:2:1,1:37,75:0.0175:2,2:11:1:27:1:1:2.01:60:4:0.0179:0:1 -1 89294985 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50268;SOR=Inf;LSEQ=CAATTTGAGAGAGATACCTT;RSEQ=ACATGTGCTATCAAAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:69,49:0:2,0:23.7:1:31.6:1:1:0:60:117:1:0:0.2 0/1:143:2:1,1:92,49:0.014:2,2:17.5:1:26:0:1:1.86882:60:4:0.0142:0:1 -1 89295007 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1869;SOR=0;LSEQ=CATGTGCTATCAAAAGTATT;RSEQ=GCTACACCAACAGCTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:86,76:0.0121:2,2:15:0:31.5:1:1:1.13072:60:4:0.0121:0:1.5 0/0:216:0:0,0:132,84:0:2,0:20.3:1:30.2:1:1:0:60:107:1:0:0.3 -1 89295015 . C T 141 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00202;SOR=0.37711;LSEQ=ATCAAAAGTATTCGCTACAC;RSEQ=AACAGCTCCACCGAGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:32:14,18:80,68:0.1778:2,2:25.2:1:28.3:1:0.33213:1.50909:60:31:0.1751:0:1.1 0/1:226:17:9,8:125,83:0.0752:2,2:24.7:1:29.5:1:0.61243:1.3369:60:34:0.0769:0:1.1 -1 90228194 . G GCA 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGCGTGCACACATGCACAT;RSEQ=CACACACACACACCTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:21.5:1:29.8:1:1:1.40151:60:4:0.1053:0:0 0/0:6:0:0,0:3,3:0:2,0:26.5:1:31.7:1:1:0:60:12:1:0:0 -1 90228235 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCTATTCGGCTGTGCGA;RSEQ=GTCTCTGCGGCCCCGCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:27.5:1:29.5:1:1:1.11:57.5:4:0.0952:0:1.5 0/0:10:0:0,0:5,5:0:2,0:26.4:1:31.1:1:1:0:60:20:1:0:0.3 -1 90228243 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGCTGTGCGAGGTCTCTG;RSEQ=GGCCCCGCTGTCTCCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:8,11:0.0952:2,2:15.5:1:29:1:1:1.35:60:4:0.0952:0:1 0/0:9:0:0,0:4,5:0:2,0:28.8:1:31.6:1:1:0:60:18:1:0:0.3 -1 90228266 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12121;SOR=Inf;LSEQ=CCCCGCTGTCTCCGGGCATC;RSEQ=AGGGTAACATCTCTTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:24.6:1:29.4:1:1:0:59.6:28:1:0:0.7 0/1:8:2:1,1:2,4:0.25:2,2:17.5:1:28:1:1:1.83:60:4:0.25:0:1.5 -1 90228304 . TCT GAAAAACGTAA 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.06061;SOR=0;LSEQ=CATTTCAGACCTGGGACTGG;RSEQ=GAAACTGTATAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:1,5:0,2:0.75:0,2:18.7:1:29.9:1:1:0:59.2:12:0.75:0.375:1.3 0/0:3:0:0,0:1,2:0:2,0:13:1:30:1:1:0:60:6:1:0:0.3 -1 90739719 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50174;SOR=Inf;LSEQ=GCTGCAAAGATATAACAACA;RSEQ=CAGCAGCAACAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:30,30:0:2,0:28.8:1:32.6:1:1:0:60:120:1:0:0.1 0/1:74:2:1,1:35,37:0.027:2,2:42:1:29:1:1:1.06:60:4:0.027:0:1 -1 90788757 . G C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52937;SOR=Inf;LSEQ=TGCTTTAATTCATGGTGGAA;RSEQ=TTGAAGGGGAGTCAGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:0:2,0:25.4:1:31.9:1:1:0:60:28:1:0:0.2 0/1:50:2:1,1:27,21:0.04:2,2:42:0:31.5:1:1:1.2792:60:4:0.0408:0:1 -1 90788816 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GAGAAAGACAGAGAGGAGGA;RSEQ=GTGCCAGGCTCTTCTCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:22.6:1:30.9:1:1:0:60:22:1:0:0 0/1:32:2:1,1:14,16:0.0625:2,2:42.5:1:29:1:1:1.14:60:4:0.0667:0:2 -1 90788954 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGGCCCCACCTCCAACA;RSEQ=TGGGGATCACAGTATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:20:1:30.5:1:1:0:60:4:1:0:1 -1 91182381 . GGGC G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=GCCGAGCCCAGCTGCTGGGG;RSEQ=GGCGGCGGCGGCTGCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:19.9:1:32:1:1:0:59.7:22:1:0:0.3 0/1:6:2:1,1:2,2:0.3333:2,2:10.5:1:29.5:1:1:1:60:4:0.3333:0:0.5 -1 91183109 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=6;SSF=0.18145;SOR=0;LSEQ=GGCGAAGGCGAAGGCGAAGG;RSEQ=GCAGGCGAAGGCGAAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:28,41:0.0282:2,2:26.5:1:27:1:1:1.46:60:4:0.0286:0:2 0/0:95:0:0,0:36,59:0:2,0:23.3:1:30.3:1:1:0:59.7:190:1:0:0.2 -1 91183167 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.18803;SOR=0;LSEQ=GCCAAAGCCGCCGCCGCCGC;RSEQ=GCTGCCGGGGTCTGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:4,5:0.1667:2,0:17:1:32:0:0.49091:0:55:4:0.1667:0:2 0/0:15:0:0,0:6,9:0:2,0:20:1:28.9:1:1:0:60:14:1:0:0.1 -1 91490304 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.53794;SOR=Inf;LSEQ=TGTCCCTTGCTCAGAAGAAA;RSEQ=ATTGGGTAGCTCAAAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:27,20:0:2,0:26.9:1:31.9:1:1:0:60:94:1:0:0.1 0/1:85:2:1,1:46,37:0.0235:2,2:5:1:27:1:1:1.24003:60:4:0.0238:0:1 -1 91490352 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53281;SOR=Inf;LSEQ=TCCTCAGAGCTCAGGAGCGG;RSEQ=CTGCTGAGAGCTAAACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:15,28:0:2,0:26.9:1:31.5:1:1:0:57.3:86:1:0:0.1 0/1:75:2:1,1:26,47:0.0267:2,2:27.5:1:27.5:1:1:1.79:60:4:0.0274:0:1 -1 92590826 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.37616;SOR=2.54377;LSEQ=AAGAGCAGAAGAAAGAATAG;RSEQ=GGGGACCTGAGACACTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:4,0:0.5556:0,2:21.2:1:31.4:1:1:0:60:10:0.5556:0:1.2 1/0:13:10:10,0:3,0:0.7692:0,0:27.6:1:29.5:1:1:0:60:9:0.75:0:1.1 -1 92590965 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23758;SOR=Inf;LSEQ=CACTGCTCAAAGATTCTATT;RSEQ=TGCAGTTATGTACTGCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:30,21:0:2,0:26.1:1:31:1:1:0:60:11.75:1:0:0.1 0/1:49:2:1,1:21,26:0.0408:2,2:10.5:1:24.5:1:1:1.23:60:4:0.0408:0:1.5 -1 92591472 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50077;SOR=Inf;LSEQ=GCAACCAGTGTTGAAGAAGG;RSEQ=GGGAGCTTTGGAGAATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:91,81:0:2,0:25.5:1:30.1:1:1:0:60:56.333:1:0:0.1 0/1:196:2:1,1:98,96:0.0102:2,2:24:1:29:1:1:1.02073:60:4:0.0104:0:1 -1 92591758 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58095;SOR=0.37945;LSEQ=GAGAACCAGGGGATGAGTTC;RSEQ=TTATTATTCTAGAGGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:94,89:0.0108:2,2:25.5:1:29.5:1:1:1.05589:60:4:0.011:0:1 0/0:244:1:1,0:125,118:0.0041:2,0:1:0:26:0:1:0:60:2:0.0042:0:1 -1 92591780 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25753;SOR=Inf;LSEQ=TATTATTCTAGAGGGGCCAG;RSEQ=TGCTATGCTGCAACGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:111,90:0:2,0:21.7:1:31.9:1:1:0:59.9:99.5:1:0:0.2 0/1:251:3:1,2:130,118:0.012:2,2:14:1:29:1:0.60762:2.19669:60:6:0.0121:0:1 -1 92591794 . C T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14163;SOR=Inf;LSEQ=GGCCAGCTGCTATGCTGCAA;RSEQ=GTTGATAAGAAAATGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:114,107:0:2,0:23.4:1:30.3:1:1:0:60:35.833:1:0:0.2 0/1:302:4:1,3:152,146:0.0132:2,2:6.5:1:30:1:0.36595:3.11261:60:8:0.0134:0:1.3 -1 92591916 . G A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45993;SOR=1.22295;LSEQ=GTGGTTGTACATGGCCCCTT;RSEQ=AAGTACATTAAGCTGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:81:35,46:32,15:0.6328:2,2:23.8:1:29.3:1:0.00985:2.78073:60:39.5:0.632:0:1.1 1/0:171:116:61,55:24,29:0.6784:2,2:22.4:1:28.8:1:0.41025:1.34:60:57:0.6746:0:1.2 -1 92591929 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50891;SOR=Inf;LSEQ=GCCCCTTGAAGTACATTAAG;RSEQ=TGGACCAGCCTAGATTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:76,72:0:2,0:23.2:1:31.8:1:1:0:60:36:0.9931:0:0.5 0/1:199:2:1,1:104,91:0.0101:2,2:30:1:28:1:1:1.14208:60:4:0.0102:0:2 -1 92592037 . G A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.72592;LSEQ=GTCTGAAATCTGCCTCTTGG;RSEQ=CCTCCCTTTTCTCCTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:70,98:0.0117:2,2:6.5:1:29.5:1:1:1.40:60:4:0.012:0:1.5 0/0:235:2:1,1:92,140:0.0085:2,2:27:0:31:0:1:1.52:60:4:0.0086:0:2 -1 92592064 . T GTA 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.29795;SOR=1.32104;LSEQ=TTTTCTCCTCTCCTCAATCC;RSEQ=CTTCACTCATGCAGACCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:112:70:20,50:10,30:0.625:2,2:22.2:1:29.6:1:0.82458:1.20:59.9:140:0.6481:0.1339:1.1 1/0:157:108:31,77:18,30:0.6879:2,2:21:1:28.6:1:0.35013:1.48645:59.9:107:0.6859:0.2038:1.1 -1 92592082 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50288;SOR=Inf;LSEQ=CCTCTTCACTCATGCAGACC;RSEQ=CTTTATTTTCGCTATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:12,62:0:2,0:22:1:30.6:1:1:0:59.9:17.5:1:0:0.9 0/1:92:2:1,1:18,72:0.0217:2,2:12:1:29.5:1:0.37219:3.92:60:4:0.0217:0:2 -1 92592222 . T C 91 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51049;SOR=0.24443;LSEQ=GTACACAATTAAATAGAGTT;RSEQ=TATGGAGTCTTTGCTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:1,6:0,3:0.7:0,2:20.3:1:32.7:1:1:0:60:14:0.7:0:1 0/1:3:1:0,1:0,2:0.3333:0,0:39:0:14:0:1:0:60:0:0:0:3 -1 93307302 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.48538;SOR=Inf;LSEQ=TCAGTTATAGTTTAAAAAAT;RSEQ=TATATTCCTATCTTTTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:25:1:28:1:1:0:60:16:1:0:0 0/1:11:2:2,0:6,3:0.1818:2,0:24.5:1:32.5:1:1:0:60:4:0.1818:0:1 -1 93307331 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51772;SOR=Inf;LSEQ=TATCTTTTGTAGGTGGAACC;RSEQ=TCCCAAAATGTCCCTTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:0:2,0:16.1:1:28.8:1:1:0:60:23:1:0:0 0/1:38:2:1,1:26,10:0.0526:2,2:12.5:1:32:0:0.50071:2.52623:60:4:0.0526:0:1 -1 93307334 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54651;SOR=Inf;LSEQ=CTTTTGTAGGTGGAACCGTC;RSEQ=CAAAATGTCCCTTGCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:0:2,0:17.8:1:29.5:1:1:0:60:23:1:0:0 0/1:45:3:1,2:30,12:0.0667:2,2:10.7:1:29.7:1:0.22445:4.79909:60:6:0.0667:0:1 -1 94837386 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTGAAGCCGCAGACCTTC;RSEQ=TGGTGAGTGTTACAGCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 94838188 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24547;SOR=Inf;LSEQ=TAATAGCAAGATGTCTGTCA;RSEQ=GGGACCTAGAAAGGGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:43,34:0:2,0:20.3:1:30.7:1:1:0:58.8:37.5:1:0:0.2 0/1:80:3:2,1:47,30:0.0375:2,2:22.3:1:29.3:1:1:1.27:60:6:0.038:0:1 -1 94838220 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20338;SOR=0;LSEQ=AGGGGAGAAGCCATGTCGCC;RSEQ=AACTTCAGAAGTTGGTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:41,38:0.0247:2,2:37.5:1:31:1:1:1.07791:60:4:0.025:0:1 0/0:98:0:0,0:53,45:0:2,0:30.6:1:31.3:1:1:0:60:196:1:0:0.2 -1 94838271 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84067;LSEQ=GGCATTATCTGATTTCAGAA;RSEQ=CCGTTTCCTGTAAATGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:15,32:0.0408:2,2:4.5:1:30.5:1:1:2.10:60:4:0.0417:0:1.5 0/1:58:2:1,1:20,36:0.0345:2,2:24:1:27.5:1:1:1.78:60:4:0.0351:0:1 -1 96258741 . CT C 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.78549;LSEQ=AAGTTTGAAAAATGCTTAGT;RSEQ=TTTTTTTTTATTAGATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:4,0:36,0:0.1:1,0:24.3:1:32.6:1:1:0:60:8:0.1:0.025:0 0/1:25:2:2,0:23,0:0.08:1,0:32.5:1:32:0:1:0:60:4:0.08:0:0 -1 96258846 . G T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.37664;SOR=3.60245;LSEQ=CTTTTCCATCTGTCATTCAG;RSEQ=GGAGATAGGTACCTACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:0,1:154,96:0.004:2,0:1:0:27:0:0.38645:0:60:2:0.004:0:1 0/1:281:4:1,3:170,107:0.0142:2,2:5.8:1:24.8:1:0.30309:4.74034:60:3:0.0109:0:1.3 -1 96258925 . T G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.86541;LSEQ=GAAGGACTAAGGGCTAATGA;RSEQ=TACAACATTTTTATTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:33:13,20:73,127:0.141:2,2:23.2:1:31.6:1:0.84597:1.13:60:66:0.1429:0:1 0/1:281:125:52,73:56,100:0.4448:2,2:22.8:1:30.9:1:0.3878:1.27:60:124:0.446:0:1.1 -1 96258941 . T TA 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25107;SOR=Inf;LSEQ=ATGATTACAACATTTTTATT;RSEQ=AAAAAAATGCCTTATGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:57,130:0:2,0:26.1:1:28.6:1:1:0:60:61.333:1:0:0.2 0/1:212:3:2,1:69,140:0.0142:2,2:24.3:1:23:1:0.26031:4.03:60:2:0.0096:0.0047:1 -1 99248468 . CT C 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTTTTTTTTGAGTCACC;RSEQ=TTTTTTTTTTTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:31:1:1:0:60:4:1:0:0 -1 99250254 . T TCAA 63 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=3;SSF=0.00105;SOR=Inf;LSEQ=CATCATCATCATCATCATCA;RSEQ=CAACAACAACAAATCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,6:0:2,0:18.6:1:30.5:1:1:0:60:28:0.8235:0:0.1 1/0:8:5:3,2:1,2:0.625:2,2:24.4:1:27.4:1:1:2.60:60:10:0.625:0.125:0.4 -1 99250311 . C T 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27315;SOR=2.65102;LSEQ=GGGTCAGCAGCCTCAAAGAC;RSEQ=GAAACTAGACAAACTCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:2,1:13,10:0.1154:2,2:20:1:32:1:1:1.51:50.3:6:0.125:0:1.7 0/1:23:6:4,2:10,7:0.2609:2,2:21.5:1:31.3:1:1:1.38:58.7:12:0.2609:0:1 -1 99250420 . G T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.28828;SOR=0.50512;LSEQ=CACAATGTCTTTCCATCAAG;RSEQ=GTACAGAACTGGACGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:28:14,14:5,3:0.7778:2,2:31.7:1:30.1:1:0.69515:1.64336:60:56:0.7778:0:1.2 1/0:33:21:10,11:5,7:0.6364:2,2:36.4:1:29.4:1:1:1.26:60:42:0.6364:0:1.3 -1 99250459 . A G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.8257;LSEQ=GATCAGATGGATGAACTGAC;RSEQ=GCAGTAGGCTTCAGAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:11,13:0.04:2,0:44:0:13:0:1:0:60:0:0:0:1 0/1:28:2:1,1:11,15:0.0714:2,2:22.5:1:30.5:1:1:1.35:60:4:0.0714:0:2 -1 99473971 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20789;SOR=0;LSEQ=TGTCCCTTGCTCAGAAGAAG;RSEQ=ATTGGGTAGCTCAAAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:16,11:0.069:2,2:28.5:1:30:0:1:1.43545:60:4:0.069:0:1 0/0:34:0:0,0:15,19:0:2,0:28.5:1:30.3:1:1:0:60:68:1:0:0.1 -1 99474093 . TAA T 28 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAACTGATGAACAGCAAC;RSEQ=AAAAAAAAAAAAAAACTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:30:1:28:1:1:0:60:4:0.3333:0:1.5 0/0:2:0:0,0:0,2:0:0,0:4.5:1:30.5:1:1:0:60:4:1:0:0 -1 99589292 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4974;SOR=Inf;LSEQ=TAATTCCTGCTAGCATTTTA;RSEQ=TATATATTCCTCCAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:80,6:0:2,0:27.8:1:32.6:1:1:0:60:172:1:0:0.1 0/1:90:2:1,1:73,14:0.0222:2,2:30.5:1:28:1:0.31027:5.072:60:4:0.0225:0:1.5 -1 99589379 . C T 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65328;SOR=0.92738;LSEQ=ATCTTAAGCACATGCTATCA;RSEQ=GCTATTTGGTAACTATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:344:189:117,72:92,63:0.5494:2,2:25.8:1:30.3:1:0.65803:1.11:60:46.25:0.5441:0:1.8 1/0:375:199:113,86:98,78:0.5307:2,2:23.1:1:29.5:1:0.83557:1.05:60:65.333:0.5297:0:1.7 -1 99589424 . C T 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50165;LSEQ=TTCAAGTTTTAAGGGAAAAT;RSEQ=GCTACAGGGGTTACTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:249:140,109:98,89:0.5685:2,2:26.2:1:30:1:0.43846:1.17:60:498:0.5685:0:1.6 0/1:440:175:82,93:138,126:0.3977:2,2:25.9:1:29.9:1:0.28441:1.24154:60:350:0.4014:0:1.7 -1 99589425 . G A 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01163;SOR=0.50654;LSEQ=TCAAGTTTTAAGGGAAAATC;RSEQ=CTACAGGGGTTACTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:45:20,25:215,174:0.1032:2,2:26.9:1:30:1:0.20613:1.54296:60:90:0.1044:0:1.1 0/1:436:24:14,10:205,206:0.055:2,2:28.8:1:30.3:1:0.5298:1.41:60:48:0.0554:0:1 -1 99589496 . T A 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACATGTTCCATCAGAGTCTC;RSEQ=TCCCTAACTATCCCATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:85,204:0:2,0:24.5:1:30.1:1:1:0:60:56.8:1:0:0.4 0/1:224:32:11,21:63,129:0.1429:2,2:25.7:1:30.3:1:0.84196:1.07:60:64:0.1468:0:1.1 -1 99589869 . T C 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACTGAAAAACATCTCCTTA;RSEQ=AGCTGAGGATTAGCTAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:20.5:1:33:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 99777865 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50321;SOR=Inf;LSEQ=AATTTATTTTAAAAACTGAG;RSEQ=ATACACTTAACCACACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:15,10:0:2,0:19.9:1:31.7:1:1:0:60:50:1:0:0.1 0/1:34:2:1,1:21,11:0.0588:2,2:20.5:1:28.5:1:1:1.8709:60:4:0.0606:0:1.5 -1 99780131 . T TG 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.63781;SOR=0.72041;LSEQ=TTGATACTCTTATCCAGGCT;RSEQ=GGGGCTCCCCTTATAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:23:23,0:25,2:0.46:2,1:22.8:1:32.1:1:0.49306:0:60:22:0.4583:0.12:0 0/1:29:11:11,0:18,0:0.3793:1,0:21.3:1:32.4:1:1:0:60:22:0.3793:0.069:0 -1 99780177 . T TA 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1426;SOR=0.21101;LSEQ=GGCAGTCAAGGTGAACTTCT;RSEQ=AAAAAAAAATCAGATCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:6:5,1:109,22:0.0438:2,2:31.8:1:28:1:1:1.01:57.5:12:0.0444:0:0.5 0/0:105:1:1,0:80,24:0.0095:2,0:29:0:28:0:1:0:60:2:0.0096:0:0 -1 99780188 . C A 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33699;SOR=3.56659;LSEQ=TGAACTTCTTAAAAAAAAAT;RSEQ=AGATCAGATCTCCTCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:1,0:123,31:0.0065:2,0:36:0:11:0:1:0:60:0:0:0:3 0/1:132:3:2,1:96,33:0.0227:2,2:11.7:1:24.3:1:1:1.45008:60:2:0.0155:0:2 -1 99780190 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.22607;SOR=Inf;LSEQ=AACTTCTTAAAAAAAAATCA;RSEQ=ATCAGATCTCCTCCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:124,31:0:2,0:25.5:1:32:1:1:0:59.9:50.667:1:0:0.1 0/1:141:2:1,1:102,37:0.0142:2,2:21.5:1:28:1:0.46778:2.73354:60:4:0.0143:0:1 -1 99780284 . T C 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00955;SOR=0.67198;LSEQ=TGGCTATCCAGTTTCCTTCA;RSEQ=TGGCAGATAGGTTTCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:159:70,89:76,93:0.4818:2,2:27:1:32.2:1:0.91163:1.03892:60:318:0.4818:0:1.1 0/1:372:143:70,73:105,124:0.3844:2,2:23.4:1:31.4:1:0.59411:1.13:60:142:0.3838:0:1.1 -1 99780335 . T A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62551;SOR=0.36919;LSEQ=CAATATTCAGTGATGTTATC;RSEQ=ATGAGATGCAGAAAGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:2,1:76,154:0.0128:2,2:17.3:1:29:1:0.26021:4.03:60:6:0.0131:0:1.3 0/0:210:1:1,0:74,135:0.0048:2,0:1:0:30:0:0.35714:0:60:2:0.0048:0:1 -1 99780510 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16484;SOR=Inf;LSEQ=CAAAACAATTATTTTAATTA;RSEQ=ACAATTGGTAAATAATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:1,7:0:2,0:28.8:1:26.8:1:1:0:60:16:1:0:0 0/1:6:2:0,2:0,4:0.3333:0,0:26.5:1:32:0:1:0:60:4:0.3333:0:1 -1 101971074 . T C 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTATACTGACCACTGGAGT;RSEQ=GGGCGACATGGCTTCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:13:3,10:26,23:0.2097:2,2:27.9:1:30.5:1:0.06704:3.69123:60:26:0.2167:0:1 0/0:87:0:0,0:40,47:0:2,0:29.6:1:29.8:1:1:0:60:86:1:0:0.4 -1 101971096 . T C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03848;SOR=Inf;LSEQ=GGCGACATGGCTTCTCCCCT;RSEQ=TCTAGGTCCCGTGACAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:23,36:0:2,0:23.6:1:29:1:1:0:60:28.5:1:0:0.4 0/1:80:6:2,4:32,42:0.075:2,2:23.5:1:29.3:1:1:1.51609:60:12:0.0759:0:1.3 -1 101971106 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16622;SOR=0;LSEQ=CTTCTCCCCTTTCTAGGTCC;RSEQ=GTGACAGCCATCTTGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:15,31:0.0417:2,2:34:1:29.5:1:1:2.03:60:4:0.0426:0:1 0/0:69:0:0,0:30,39:0:2,0:22.1:1:29.1:1:1:0:60:33.5:1:0:0.3 -1 101971113 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49674;SOR=Inf;LSEQ=CCTTTCTAGGTCCCGTGACA;RSEQ=CCATCTTGCCATTACTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:15,31:0:2,0:24.8:1:31.6:1:1:0:60:92:1:0:0.3 0/1:52:2:1,1:22,28:0.0385:2,2:12:1:28:1:1:1.27:60:4:0.0385:0:1 -1 102237818 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.17057;LSEQ=GGGAGCACAGGTTACTTATC;RSEQ=CTGTAAATATAATCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:212:98,114:97,135:0.4775:2,2:25.5:1:30.7:1:0.38908:1.20:60:424:0.4796:0:1.1 0/1:520:70:33,37:207,243:0.1346:2,2:26.5:1:29.5:1:0.89782:1.05:60:69:0.1353:0:1.2 -1 103210619 . A T 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05668;SOR=0.09767;LSEQ=ATCCTTTACTGGTTAGCGTA;RSEQ=AAGCAACACTCTTCCCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:0,7:1,1:0.7778:2,0:25.9:1:29.3:1:0.22222:0:60:14:0.7778:0:1 0/1:9:2:1,1:2,5:0.2222:2,2:15.5:1:31:1:1:2.24:60:4:0.25:0:1 -1 103210685 . T TTGG 76 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGAGGATATCTAGGCC;RSEQ=TGGTTTTGGAGAGTCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:34:1:32.8:1:1:0:60:4:1:0:0 1/1:6:6:3,3:0,0:1:0,2:21.3:1:29.6:1:1:0:60:12:1:0.1667:0.3 -1 105976620 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50227;SOR=Inf;LSEQ=ATCTACCCTGAACTGAGAAT;RSEQ=GCCATCTCTCAATATGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:44,24:0:2,0:24.2:1:31.7:1:1:0:60:136:1:0:0.1 0/1:84:2:1,1:48,34:0.0238:2,2:10.5:1:28:1:1:1.40585:60:4:0.0244:0:1 -1 105976654 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25203;SOR=Inf;LSEQ=ATGAGCCAGTGGCTGAAATT;RSEQ=GTGTGAGTGCCCATGGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:42,45:0:2,0:26.7:1:31.6:1:1:0:60:174:1:0:0.1 0/1:104:3:1,2:51,50:0.0288:2,2:26.7:1:30.7:1:1:2.02654:60:6:0.0297:0:1.3 -1 105976686 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49915;SOR=Inf;LSEQ=CATGGGTCGGTGTACAAGGA;RSEQ=TGTGATCCCCACAGTGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:31,48:0:2,0:26.3:1:32.3:1:1:0:60:158:1:0:0.1 0/1:90:2:1,1:44,44:0.0222:2,2:25.5:1:27.5:1:1:1:60:4:0.0227:0:1 -1 105977123 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16629;SOR=Inf;LSEQ=TGTACTGTGCTCACGAGGTT;RSEQ=TTCTGCAATCTACACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:5,48:0:2,0:26.6:1:32.2:1:1:0:60:52:1:0:0 0/1:37:2:1,1:7,28:0.0541:2,2:35:1:27.5:1:0.39039:3.81:60:4:0.0571:0:1 -1 106053681 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18638;SOR=Inf;LSEQ=ATTAAGAAAAACAACTTTGG;RSEQ=GTAACTAGAAAAAACATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:68,9:0:2,0:20.7:1:31.1:1:1:0:60:76:1:0:0 0/1:59:2:1,1:50,7:0.0339:2,2:16:1:25.5:1:0.25482:6.74709:60:4:0.0339:0:1.5 -1 106053803 . C T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42503;LSEQ=AAAAGAGAAATTCAAATTGA;RSEQ=CTGATGGTTATAAGAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:120:50,70:87,99:0.3909:2,2:27.6:1:30.2:1:0.41095:1.22946:60:59:0.3946:0:1.8 0/1:327:70:35,35:123,134:0.2141:2,2:25.8:1:29.1:1:0.7882:1.09:60:69:0.213:0:1.5 -1 106053847 . C T 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.42564;LSEQ=TTTTGCTAGGGAGATGCCTA;RSEQ=ATTTTTATCTTTAAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:96:30,66:50,104:0.384:2,2:24.4:1:29.5:1:0.88965:1.05748:60:192:0.3855:0:1.9 0/1:234:49:16,33:67,118:0.2094:2,2:25.7:1:28.3:1:0.7378:1.1703:60:98:0.2112:0:1.7 -1 106053879 . T A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24768;SOR=Inf;LSEQ=TAAAAAATAACTATTTGTCT;RSEQ=AAATTTACCTTATGGTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:29,100:0:2,0:23.5:1:28.8:1:1:0:60:128:1:0:0.5 0/1:136:3:2,1:35,98:0.0221:2,2:5.3:1:26:1:0.17975:5.52:60:6:0.0226:0:1 -1 108079754 . TA T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15986;SOR=0.41772;LSEQ=AGAAAAGATCAGAAAACTCT;RSEQ=AGTCAGTGAGGCCTGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:18:18,0:12,0:0.6:0,1:28.6:1:31.1:1:1:0:60:36:0.6:0.0667:0 0/1:21:8:8,0:13,0:0.381:1,0:22.1:1:30.8:1:1:0:60:16:0.381:0.1429:0 -1 108079857 . G T 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=0.49043;LSEQ=AATTAGAGAAATAATAAAAA;RSEQ=TATTTGTCATCACAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:212:113:87,26:77,22:0.533:2,2:21.9:1:30.9:1:1:1.04577:60:226:0.5381:0:1.4 0/1:212:76:56,20:105,31:0.3585:2,2:21.5:1:29.7:1:0.61639:1.20856:60:152:0.3602:0:1.4 -1 108079880 . G C 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03255;SOR=0.69808;LSEQ=TTTGTCATCACAAATAAAAT;RSEQ=TTTAGCGATTGAATGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:131:88,43:136,52:0.4094:2,2:25.2:1:30.9:1:0.32304:1.27696:60:42.667:0.4038:0:1.1 0/1:316:103:68,35:141,71:0.3259:2,2:24.3:1:31.4:1:1:1.0221:60:206:0.3259:0:1.1 -1 108079945 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.43446;LSEQ=GGTTACGAATACAAACATCA;RSEQ=AAGTCTTTTTCAGGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:525:302:155,147:109,114:0.5752:2,2:24.3:1:29.6:1:0.59707:1.10:60:32.556:0.5723:0:1.3 0/1:551:204:100,104:171,174:0.3702:2,2:24.6:1:29.5:1:0.92973:1.02203:60:203:0.3732:0:1.3 -1 108080040 . G T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34401;LSEQ=GTTTTGTCCTGGTGTTGCAT;RSEQ=TATTAGTTCATCACATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:189:110:24,86:20,59:0.582:2,2:25.1:1:29.9:1:0.60369:1.21342:60:35.667:0.5753:0:2.2 0/1:164:53:8,45:21,90:0.3232:2,2:22.4:1:30.2:1:0.6637:1.31039:60:52:0.319:0:2.2 -1 108080046 . G T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32733;LSEQ=TCCTGGTGTTGCATGTATTA;RSEQ=TTCATCACATCCCCTTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:170:102:19,83:13,54:0.6:2,2:24:1:30.3:1:1:1.05132:60:50:0.5952:0:2.1 0/1:137:45:7,38:13,79:0.3285:2,2:20.5:1:30.2:1:0.80228:1.12:60:44:0.3235:0:2.2 -1 108080184 . C T 44 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8918;LSEQ=CCAGCAACTTATTGGAAATA;RSEQ=AACTGCTTGGACCTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:18.3:1:28.3:1:1:0:60:6:0.3333:0:1 1/0:4:2:1,1:0,2:0.5:0,2:4.5:1:27:1:1:0:60:4:0.5:0:1 -1 108080285 . GC G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGATTCTGATGTGTTTCA;RSEQ=CCACAACTGGGATGTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:27:1:34:0:1:0:60:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 109490374 . A T 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.32228;SOR=0.2551;LSEQ=ATCAATTCAACATTAGTTAG;RSEQ=GTCAAAGTATAATATAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:1,2:165,100:0.0112:2,2:6.7:1:21.7:1:0.55966:3.28488:56:2:0.0077:0:3 0/0:348:1:0,1:228,119:0.0029:2,0:1:0:24:0:0.34483:0:60:2:0.0029:0:1 -1 109490457 . T C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08253;LSEQ=AGCTAGTTGTTTTGATCAAG;RSEQ=TTGCATTTATCAGCTATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:331:307:126,181:7,16:0.9275:2,2:25.3:1:31.9:1:0.38222:1.59:60:75.75:0.9266:0:1.1 1/0:577:296:138,158:122,156:0.513:2,2:25.3:1:31.4:1:0.55712:1.12:60:41.286:0.5115:0:1.2 -1 109491028 . T C 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAAGTCGCTGAGGGTAG;RSEQ=GGGTATTTTTCAAACATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:35.5:1:26.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 109853073 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53319;SOR=Inf;LSEQ=GACAGAACAGAAAGTCTGGC;RSEQ=CCTGCTGACTCCGGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:22,25:0:2,0:26.4:1:30.3:1:1:0:60:94:1:0:0.2 0/1:82:2:1,1:43,37:0.0244:2,2:39.5:1:30.5:1:1:1.16002:60:4:0.025:0:2 -1 109853086 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53219;SOR=Inf;LSEQ=GTCTGGCACCTGCTGACTCC;RSEQ=GCCCTCCCTGTCACTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:20,25:0:2,0:30.9:1:31.2:1:1:0:60:90:1:0:0.2 0/1:78:2:1,1:36,40:0.0256:2,2:31.5:1:29.5:1:1:1.11:60:4:0.0263:0:1.5 -1 109853098 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5107;SOR=Inf;LSEQ=CTGACTCCGGCCCTCCCTGT;RSEQ=ACTTCATCACACAGCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,26:0:2,0:28.9:1:32.4:1:1:0:60:90:1:0:0.2 0/1:64:2:1,1:27,35:0.0313:2,2:14.5:1:27:1:1:1.29:60:4:0.0317:0:2 -1 109853105 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51446;SOR=Inf;LSEQ=CGGCCCTCCCTGTCACTTCA;RSEQ=CACACAGCAAATCTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:18,23:0:2,0:29:1:31.2:1:1:0:60:82:1:0:0.2 0/1:61:2:1,1:25,34:0.0328:2,2:6.5:1:26.5:1:1:1.35:60:4:0.0328:0:1 -1 109956909 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTAAACTCAGCTCAAAAT;RSEQ=ACTTTCATGGAATCCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:13,3:0:2,0:21.9:1:31.3:1:1:0:60:32:1:0:0.1 0/1:42:2:1,1:25,15:0.0476:2,2:18.5:1:28.5:1:1:1.64563:60:4:0.05:0:1 -1 110116309 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51482;SOR=0;LSEQ=CATTCATGTTGATATTATAC;RSEQ=TTTATGTTGATTACCGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:35,10:0.0426:2,2:8.5:1:30:1:0.41721:3.38437:60:4:0.0426:0:1 0/0:31:0:0,0:27,4:0:2,0:21.1:1:30.5:1:1:0:60:30:1:0:0 -1 110116413 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50629;SOR=Inf;LSEQ=ACAGATGAAGTAAGTTGGAA;RSEQ=GTAGCGTTTTGTTAGACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:18,36:0:2,0:23.1:1:29.7:1:1:0:60:26:1:0:0.1 0/1:72:2:1,1:27,43:0.0278:2,2:25:1:28.5:1:1:1.58:60:4:0.0278:0:1 -1 113234356 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18552;SOR=Inf;LSEQ=CCACCTCCCCGCCTCAGGCA;RSEQ=CTGCTCCCCATGCTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:188,77:0:2,0:23:1:32.1:1:1:0:60:87.333:1:0:0.1 0/1:201:2:1,1:146,51:0.01:2,2:17:0:29:1:0.45531:2.84478:60:4:0.0101:0:1 -1 113234456 . G A 247 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.84898;SOR=1.03255;LSEQ=TCTGCACCCCGCACTCTCCC;RSEQ=TCTTTTACCTACTGGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:470:274:124,150:90,106:0.583:2,2:26.2:1:29.9:1:0.92526:1.02704:60:44.667:0.5852:0:1.1 1/0:562:332:150,182:106,122:0.5907:2,2:25.5:1:29.6:1:0.79582:1.05408:60:82:0.5942:0:1.2 -1 113234502 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2492;SOR=Inf;LSEQ=TTGCCCTGGCACCTCCGTCC;RSEQ=CAGCCTCCCAGGCTGTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:78,199:0:2,0:24.5:1:29.7:1:1:0:60:54.4:1:0:0.6 0/1:293:3:2,1:89,201:0.0102:2,2:18:1:28.3:1:0.22863:4.49:60:6:0.0105:0:1.7 -1 113244237 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGAGTGGCCATCTCAAACAC;RSEQ=TCCCGCACTCCCTCCTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:30:1:32:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:28:1:1:0:60:4:1:0:1.5 -1 113245320 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50016;SOR=Inf;LSEQ=TTCTCAGGAATGTTTTCTGT;RSEQ=TAGACATGCACCAACAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:41,98:0:2,0:23:1:32.1:1:1:0:60:278:1:0:0.1 0/1:157:2:1,1:47,108:0.0127:2,2:19.5:1:29:1:0.51935:2.28:60:4:0.0128:0:1 -1 113245682 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19622;SOR=0;LSEQ=ACATCAGTGTCCGGGTAGGA;RSEQ=AGAGGCCGCAGTCGATCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:47,35:0.0238:2,2:32.5:1:28.5:1:1:1.33807:60:4:0.0241:0:1.5 0/0:105:0:0,0:60,45:0:2,0:23.9:1:30.9:1:1:0:60:34:1:0:0.2 -1 113245701 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21659;SOR=0;LSEQ=AGAGAGGCCGCAGTCGATCA;RSEQ=AGTCTTCCTGCCCTGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:52,44:0.0204:2,2:42:1:30:1:1:1.17979:60:4:0.0206:0:1 0/0:112:0:0,0:62,50:0:2,0:30.4:1:28.9:1:1:0:60:111:1:0:0.2 -1 113247563 . G A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCCTCAGTCCAGCTCACCC;RSEQ=CATGCCCTGCCCACCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:12:0:28:0:1:0:60:2:1:0:0 0/1:5:2:2,0:2,1:0.4:2,0:32.5:1:30:0:1:0:60:4:0.4:0:1 -1 115251293 . G GA 45 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.6944;SOR=1.66169;LSEQ=ACCCTATAAAAGGAAAAAAT;RSEQ=AAAAAAAATGAGAGAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:2:1,1:58,238:0.0067:2,2:16.5:1:27:1:0.35731:4.08:60:4:0.0068:0.0034:0.5 0/1:360:4:1,3:94,261:0.0111:2,2:8:1:22.8:1:1:1.08023:60:3:0.0084:0.0056:1 -1 115252054 . T TA 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.25787;SOR=0;LSEQ=AGATAGAGTGAGACTCTGCC;RSEQ=AAAAAAAAATAAAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:3,0:61,2:0.0455:1,0:7:1:30.5:1:1:0:60:6:0.0469:0.0303:0.7 0/0:50:0:0,0:48,2:0:1,0:27.2:1:29.9:1:1:0:59.7:11.5:1:0:0.2 -1 115252095 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50321;SOR=0;LSEQ=AAAATAAAAATGAAAAAAAT;RSEQ=CATAACAACAAAGAATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:186,6:0.0103:1,2:23.5:1:29:1:0.07104:28.80031:60:4:0.0105:0:1 0/0:160:0:0,0:154,5:0:1,0:20.8:1:32.2:1:1:0:60:78.5:1:0:0.1 -1 115252609 . G C 52 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATCACAAGGTCAGGAGTT;RSEQ=AAGACCAGCCTGGCCAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:13.7:1:33:1:1:0:60:6:1:0:1.3 1/1:1:1:0,1:0,0:1:0,0:10:0:33:0:1:0:60:2:1:0:1 -1 115256349 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23534;SOR=0;LSEQ=AGCTCTATCTTCCCTAGTGT;RSEQ=GTAACCTCATTTCCCCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:159,27:0.0106:2,2:5:1:28:1:0.27637:5.80097:60:4:0.0108:0:1 0/0:199:0:0,0:163,36:0:2,0:22.2:1:31.1:1:1:0:60:38.8:1:0:0.1 -1 115256669 . G A 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.10595;SOR=0.60974;LSEQ=TATTAAAAACCACAGGGAAT;RSEQ=CAATGCTATTGCCAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:78:4,74:0,26:0.75:1,2:25.4:1:30.1:1:0.56983:0:60:156:0.7573:0:1.3 1/0:113:73:4,69:5,35:0.646:2,2:22.3:1:30.5:1:0.27547:2.44318:60:146:0.6518:0:1.2 -1 115258819 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0725;SOR=0;LSEQ=CTGTTGGAAACCAGTAATCA;RSEQ=GGTTAATTGGCGAGCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:3:1,2:48,176:0.0132:2,2:31:1:25.3:1:0.51962:1.83:60:2:0.0088:0:2 0/0:316:0:0,0:77,239:0:2,0:22.6:1:30.3:1:1:0:60:157:1:0:0.1 -1 116099481 . A T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24891;SOR=0;LSEQ=AAAAACCTATGGTGACTGTG;RSEQ=AGGCCCTGATGCCATGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:163,124:0.0103:2,2:9.3:1:23.7:1:1:1.52:60:2:0.0071:0:1 0/0:280:0:0,0:142,138:0:2,0:26.5:1:29.2:1:1:0:60:55:1:0:0.2 -1 116099527 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10672;SOR=Inf;LSEQ=TTGATATCATCTAGTGGTCA;RSEQ=AAAGTTATTGTAAAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:84,131:0:2,0:23.8:1:31.7:1:1:0:60:106.5:1:0:0.1 0/1:195:3:2,1:78,114:0.0154:2,2:8:1:28.7:1:0.56906:2.91:60:6:0.0156:0:1 -1 116099689 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=ATGTAAGCTGCATGCTGTGG;RSEQ=TCAAGCCTATAATCACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:3,14:0.1053:2,2:31.5:1:32:0:0.38596:4.18:60:4:0.1053:0:1 0/0:11:0:0,0:3,8:0:2,0:21.3:1:31.6:1:1:0:60:22:1:0:0.2 -1 116099916 . C T 48 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGAGCTATGATCACAC;RSEQ=ACTGCACTCTAGAGTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:34.5:1:24:1:1:0:58.5:3:1:0:3.5 1/1:2:2:2,0:0,0:1:0,0:8:0:32.5:1:1:0:60:4:1:0:1.5 -1 116099991 . T G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27931;SOR=0;LSEQ=TGCATATATGTTACATACAA;RSEQ=GGTCACTACACTAACAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:19.5:1:31.8:1:1:0:60:10:1:0:1.5 1/1:19:16:11,5:2,1:0.8421:2,2:22.6:1:30.7:1:1:1.09:60:32:0.8421:0:1.1 -1 116100046 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50786;SOR=Inf;LSEQ=AATTCCCAGCTGCACCTCAA;RSEQ=TTGCACCAGAATTGCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:33.8:1:28.4:1:1:0:60:8.5:1:0:0.8 0/1:28:2:1,1:12,14:0.0714:2,2:16:1:30:1:1:1.16:60:4:0.0714:0:1.5 -1 116107025 . G GCCA 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=1;LSEQ=GGCGCCTGATCGCCGCCGCC;RSEQ=CCGCTGCCGCCGCCGCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:39.5:1:31.7:1:1:1.40151:60:4:0.1176:0:0 0/1:19:2:1,1:10,7:0.1053:2,2:18:0:30.2:1:1:1.40151:60:4:0.1053:0:0.5 -1 116107027 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.48649;SOR=0;LSEQ=CGCCTGATCGCCGCCGCCGC;RSEQ=GCTGCCGCCGCCGCTACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:18.5:1:29.5:1:1:1.40151:60:4:0.1053:0:1.5 0/0:19:0:0,0:11,8:0:2,0:26.9:1:29.9:1:1:0:60:38:1:0:0.4 -1 116333547 . G A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00613;SOR=Inf;LSEQ=AATCTTTCGCCTGTCTTAGA;RSEQ=GGCACTCTAGCAGACGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:30,1:0:1,0:23.8:1:31.5:1:1:0:60:30:1:0:0.9 0/1:8:3:3,0:5,0:0.375:0,0:29.7:1:31.3:1:1:0:60:6:0.375:0:1.7 -1 116333581 . T G 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACGAGGTGAGCCCTGCCTTG;RSEQ=AACAGGAAGGACCTTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:39,3:0,0:1:0,2:22.7:1:31.7:1:1:0:60:84:1:0:1.3 1/1:21:20:20,0:1,0:0.9524:0,1:18.3:1:30.3:1:1:0:60:9:0.9474:0:1.9 -1 116333628 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.67613;LSEQ=AGGCCAATAATTTGTTGTGG;RSEQ=TTGCCAACTAAATTCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:20:15,5:73,29:0.1639:2,2:26:1:30.2:1:1:1.19:60:19:0.1583:0:1.5 0/1:77:37:27,10:27,13:0.4805:2,2:28.3:1:31.6:1:0.62762:1.30:60:36:0.4737:0:1.4 -1 116333734 . T C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24902;LSEQ=CCCTGCTCTACTAATAGCAA;RSEQ=GCAGCTGTGGATGGCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:237:195:90,105:19,22:0.8228:2,2:24.9:1:30.2:1:1:1.00754:60:31.5:0.8182:0:1.1 1/0:198:106:51,55:42,50:0.5354:2,2:25.6:1:30.3:1:0.77609:1.10:60:212:0.5436:0:1.2 -1 116333773 . C A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.82895;LSEQ=GCAACCAGAAGGATGCTGGC;RSEQ=TAGTACAGATAGCACATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:30:8,22:47,105:0.1648:2,2:23.3:1:30.3:1:0.82808:1.22955:60:60:0.1685:0:2.2 0/1:146:63:24,39:35,48:0.4315:2,2:22.5:1:29.8:1:0.73368:1.18352:60:126:0.4315:0:2.1 -1 116333785 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07233;SOR=Inf;LSEQ=ATGCTGGCCTAGTACAGATA;RSEQ=CACATTGAATGTATTTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:37,117:0:2,0:27.9:1:31.9:1:1:0:60:76:1:0:1 0/1:111:3:2,1:39,69:0.027:2,2:26.7:1:30:1:0.55361:3.50:60:6:0.027:0:2 -1 116333793 . A C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=4.03741;LSEQ=CTAGTACAGATAGCACATTG;RSEQ=ATGTATTTATGCTGTAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:20:2,18:26,87:0.1504:2,2:32.5:1:32.9:1:0.24422:2.67369:60:40:0.1538:0:2.7 0/1:98:41:13,28:20,37:0.4184:2,2:27.5:1:31.9:1:0.82946:1.16244:60:40:0.4124:0:2.7 -1 116333796 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1676;SOR=Inf;LSEQ=GTACAGATAGCACATTGAAT;RSEQ=TATTTATGCTGTAGTCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:27,105:0:2,0:27.7:1:32.1:1:1:0:60:65:1:0:1 0/1:92:2:1,1:29,61:0.0217:2,2:8.5:1:26:1:0.54826:2.09:60:4:0.022:0:2.5 -1 116333816 . C G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=5.27514;LSEQ=GTATTTATGCTGTAGTCCGA;RSEQ=ACATCACGCACGCTGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:17:2,15:12,70:0.1717:2,2:27.4:1:32.2:1:1:1.28263:60:34:0.1735:0:2.7 1/0:59:31:7,24:7,21:0.5254:2,2:23.6:1:31.5:1:1:1.14027:60:62:0.5254:0:2.8 -1 116334594 . C A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACCTGCAGACCATAAGC;RSEQ=TGAGTGTAAAGGCTGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:28.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 117273321 . CAAA C 89 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=17.000;MSILEN=1;SSF=0.37071;SOR=2.72696;LSEQ=AACAGAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAAAAAAGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:7,0:4,0:0.4118:0,0:15.7:1:32:1:1:0:60:14:0.4118:0.1765:1.3 1/0:6:4:4,0:0,0:0.6667:0,0:10:1:30.9:1:1:0:55:8:0.6667:0.3333:2 -1 117273456 . TA T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23205;SOR=Inf;LSEQ=CTTTGCCCCTCAGCGGCAGG;RSEQ=ACTCTTTCCCTTGCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:115,48:0:2,0:21.8:1:28.9:1:1:0:60:162:1:0:0.4 0/1:152:2:1,1:104,46:0.0132:2,2:17:1:28.5:1:0.52422:2.24745:60:4:0.0132:0:1 -1 117273500 . C T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3632;SOR=3.14974;LSEQ=TGCTTGAACAGAAGACTGTG;RSEQ=CTGGGGCAAGAAGGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:1:0,1:179,126:0.0033:2,0:46:0:32:0:0.41503:0:60:2:0.0034:0:2 0/1:293:3:0,3:168,122:0.0102:2,0:15:1:21:1:0.07658:0:60:2:0.007:0:1.7 -1 117273534 . T A 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0639;SOR=0.72539;LSEQ=GAAGAAGGGAAACCATGCAG;RSEQ=GAGATGGGCTCCCTGTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:265:136,129:40,37:0.7681:2,2:26.7:1:30.5:1:1:1.02537:60:65.25:0.7654:0:1.7 1/0:381:269:138,131:59,52:0.706:2,2:23.7:1:29.4:1:0.82146:1.07684:60:37.429:0.7005:0:1.7 -1 117273577 . G T 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00116;SOR=0.51245;LSEQ=CTCTGGTACACAGACTGGAG;RSEQ=TGAAGCAAACAACAGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:254:205:83,122:17,32:0.8071:2,2:25.9:1:29.5:1:0.51688:1.28:60:40:0.8065:0:1.8 1/0:289:197:86,111:35,56:0.6817:2,2:26.6:1:29.8:1:0.44244:1.24:60:394:0.684:0:1.9 -1 117690272 . G A 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03951;LSEQ=TTGCATGCTTTTTTGTGGCC;RSEQ=AGGCACATTATTTTAGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:475:473:300,173:0,0:0.9958:0,2:23.6:1:29.8:1:1:0:60:42:0.9957:0:1.1 1/1:475:429:279,150:28,18:0.9032:2,2:25.8:1:29.8:1:0.62715:1.20:60:60.286:0.9017:0:1.1 -1 117690445 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07948;SOR=Inf;LSEQ=TTTAGGGTCATACAGGAGAA;RSEQ=CTGGATGTCTTCTTCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:51,242:0:2,0:22.2:1:32:1:1:0:60:57.6:1:0:0.1 0/1:222:3:2,1:41,176:0.0135:2,2:15:1:27:1:0.09835:8.47:60:6:0.0136:0:1 -1 117695988 . A G 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25235;SOR=0;LSEQ=CATTCACTTCCGGCATGCTG;RSEQ=AGGCTGCAGGGTCAAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:83,202:0.0104:2,2:45:1:26.3:1:0.20901:4.84:60:2:0.0071:0:1.3 0/0:250:0:0,0:95,154:0:2,0:22:1:29.2:1:1:0:60:48.8:1:0:0.2 -1 117695994 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6644;SOR=1.78422;LSEQ=CTTCCGGCATGCTGAAGGCT;RSEQ=CAGGGTCAAAAGTCAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:2:1,1:72,189:0.0076:2,2:38:0:29:1:0.47886:2.61:60:4:0.0077:0:1 0/1:223:3:2,1:80,140:0.0135:2,2:14.3:1:27:1:0.55615:3.48:60:6:0.0137:0:1 -1 117696032 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26518;SOR=0;LSEQ=AAGGGCAGATGCCAAAGTCA;RSEQ=ACACGTAAGACAATATAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:1,2:23,123:0.0201:2,2:14.7:1:25.7:1:0.41187:2.65:60:6:0.0221:0:3.7 0/0:109:0:0,0:23,86:0:2,0:27.2:1:29.7:1:1:0:60:9.9:1:0:0.4 -1 117696034 . C A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69936;SOR=1.37683;LSEQ=GGGCAGATGCCAAAGTCAGA;RSEQ=ACGTAAGACAATATAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:0,3:21,120:0.0207:2,0:22:1:14.3:1:1:0:60:0:0:0:4.7 0/1:106:3:1,2:21,82:0.0283:2,2:8.7:1:29:1:0.5061:1.94:60:6:0.0309:0:2.7 -1 117696037 . G A 109 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=20.80138;LSEQ=CAGATGCCAAAGTCAGACAC;RSEQ=TAAGACAATATAGCCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:1:0,1:21,118:0.0071:2,0:47:0:30:0:1:0:60:2:0.0074:0:1 0/1:99:13:3,10:17,69:0.1313:2,2:23.5:1:29.7:1:0.72244:1.22:60:26:0.1398:0:1 -1 117696063 . T A 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56996;SOR=2.86935;LSEQ=CAATATAGCCTTTGAAGCGC;RSEQ=AGGCCTTAAAAATGCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:0,1:2,87:0.0109:1,0:16:0:13:0:1:0:60:0:0:0:4 0/1:65:2:0,2:9,54:0.0308:2,0:10.5:1:25.5:1:1:0:60:4:0.0345:0:2.5 -1 117712517 . AAAAT A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.56717;SOR=0;LSEQ=ACAGAGCCAGACCCTGTCTC;RSEQ=AAATAAATAAATAATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:4:3,1:50,0:0.0741:1,2:12.3:1:30.9:1:0.07407:0:60:8:0.0741:0.037:0 0/0:16:0:0,0:16,0:0:1,0:22.8:1:30.1:1:1:0:60:32:1:0:0.1 -1 117712628 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05995;SOR=Inf;LSEQ=ATGCTATACTCTGAGGTTTT;RSEQ=TGGGTCAAAGCTCTGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:324,57:0:2,0:21.1:1:31.2:1:1:0:60:126:1:0:0.1 0/1:246:3:1,2:200,43:0.0122:2,2:18.7:1:27.7:1:0.08698:9.1758:60:6:0.0123:0:1 -1 117712844 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14779;SOR=Inf;LSEQ=AGTTCTCCATTCCTCTTGAT;RSEQ=TGCTGCTTTGCAACTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:35,238:0:2,0:24.7:1:32:1:1:0:60:90:1:0:0.1 0/1:171:2:1,1:29,140:0.0117:2,2:10:1:31.5:1:0.32095:4.76:60:4:0.0118:0:1 -1 117712862 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12328;SOR=Inf;LSEQ=ATGTGCTGCTTTGCAACTGG;RSEQ=GTACAAATCTGTTGTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:11,208:0:2,0:23.6:1:30.9:1:1:0:60:35.5:1:0:0.1 0/1:119:2:0,2:11,106:0.0168:2,0:13.5:1:31.5:1:1:0:60:4:0.0169:0:1 -1 117753285 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5441;SOR=0;LSEQ=GTGGGATGTTAAGTCAAATC;RSEQ=AGTTAGGCTCTTGTCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:109,0:0.018:1,2:28:1:29:1:0.01802:0:60:4:0.0183:0:1 0/0:59:0:0,0:59,0:0:1,0:23:1:30.5:1:1:0:60:118:1:0:0.1 -1 117753455 . A G 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTATATACTACCTCCAGAAG;RSEQ=GGATCTGCCCCAGGGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1036:0:0,0:498,536:0:2,0:25.3:1:30.5:1:1:0:60:48.238:1:0:0.1 0/1:823:51:26,25:388,384:0.062:2,2:29.3:1:30.7:1:1:1.03:60:102:0.0627:0:1.2 -1 117753543 . G A 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGCCGCTGCCTTCCTTGGT;RSEQ=ACTCACAACCAGCTCCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:48:9,39:98,256:0.1194:2,2:25.4:1:30.3:1:0.22493:1.65696:60:96:0.1224:0:1 0/0:337:0:0,0:108,229:0:2,0:22.4:1:30.6:1:1:0:60:47.143:1:0:0.1 -1 118145527 . G A 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.55601;LSEQ=TAAAGACTGTTTTGTCCCTC;RSEQ=GTTTCCCTAGGTATAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:2:2,0:170,321:0.0041:2,0:11.5:1:15:1:0.12126:0:60:0:0:0:3 0/1:428:39:16,23:141,248:0.0911:2,2:19:1:30.1:1:0.60238:1.22:60:78:0.0924:0:1 -1 118155620 . G A 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=ACCCTGTGGATTACGTGTAA;RSEQ=CTGAGTCATTCTTACAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:30:1:31.3:1:1:0:60:6:0.6:0:1 0/0:2:0:0,0:1,1:0:2,0:43:1:28:1:1:0:60:4:1:0:0 -1 118155826 . T TTG 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.26142;SOR=2.22465;LSEQ=AGGATTATTTCCATTTCAAG;RSEQ=TGTGTGTGTAGCACTTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:5:5,0:59,0:0.0781:1,0:22.4:1:30.7:1:1:0:60:10:0.0806:0.0156:0 0/1:25:4:4,0:20,1:0.16:1,0:23.5:1:31.2:1:1:0:60:8:0.16:0.08:0 -1 118156053 . G A 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20685;LSEQ=ACAGCATTAGTTCTTCCAGC;RSEQ=TTATCTCTCCACCCACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1231:221:115,106:527,482:0.1795:2,2:24.3:1:30.2:1:1:1.00779:60:109.5:0.1792:0:1.1 0/1:1294:56:29,27:608,627:0.0433:2,2:24.9:1:29.7:1:0.78503:1.11:60:55:0.0429:0:1.3 -1 118156191 . T A 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16973;LSEQ=CTGTGTGTTGGCTTCTCACT;RSEQ=CTTAGTGGGAAGTGAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:53:12,41:52,257:0.1464:2,2:22.5:1:29.6:1:0.33012:1.44:60:106:0.1489:0:1.1 0/1:248:7:0,7:50,191:0.0282:2,0:15.4:1:30.1:1:0.35031:0:60:14:0.0287:0:1.3 -1 118160944 . GA G 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.60863;LSEQ=AATAGCAATTCTGTGAAACT;RSEQ=AAAAAAAAATTTCTTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:2,0:46,0:0.0417:1,0:10:1:32.3:1:1:0:60:4:0.0417:0.0208:0 0/1:39:1:1,0:38,0:0.0256:1,0:36:0:34:0:1:0:60:2:0.0256:0:0 -1 118160949 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.20746;SOR=Inf;LSEQ=CAATTCTGTGAAACTGAAAA;RSEQ=AAAAATTTCTTTTGGTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:52,0:0:1,0:24.3:1:31:1:1:0:60:104:1:0:0.2 0/1:44:2:2,0:42,0:0.0455:1,0:25.5:1:30.5:1:1:0:60:4:0.0455:0:1.5 -1 118160998 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49958;SOR=0;LSEQ=AGATGAGAGGAGATGGATTT;RSEQ=CATGAATTAGAGAGTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:124,5:0.0153:1,2:12.5:1:25.5:1:0.08984:22.73079:60:4:0.0154:0:1 0/0:117:0:0,0:113,4:0:1,0:25.6:1:32.2:1:1:0:60:234:1:0:0.1 -1 118161017 . A AG 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12465;SOR=0;LSEQ=TGCATGAATTAGAGAGTCTG;RSEQ=GGTTTTTTTTTAATGAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:4:3,1:174,29:0.0193:2,2:17.5:1:31.7:1:0.46807:1.9917:60:8:0.0195:0.0048:0.5 0/0:189:0:0,0:155,34:0:2,0:22.6:1:29:1:1:0:59.9:188:1:0:0.1 -1 118161019 . G GT 112 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.3055;SOR=1.59344;LSEQ=CATGAATTAGAGAGTCTGAG;RSEQ=TTTTTTTTTAATGAGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:10:9,1:171,30:0.0474:2,2:32.2:1:29.1:1:1:1.58:60:20:0.0481:0:0.1 0/1:204:15:14,1:150,39:0.0735:2,1:28.6:1:28.7:1:0.31195:3.62:60:30:0.0735:0.0049:0.2 -1 118161020 . T G 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00234;SOR=0.40997;LSEQ=ATGAATTAGAGAGTCTGAGG;RSEQ=TTTTTTTTAATGAGCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:43:37,6:144,29:0.1972:2,2:20.2:1:31.8:1:0.81815:1.24:60:86:0.1991:0:1.1 0/1:208:19:13,6:152,36:0.0913:2,2:18.1:1:31.2:1:0.23026:1.9415:60:38:0.0927:0:1.2 -1 118161094 . GTC G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0;SOR=0.11934;LSEQ=AGGCATTCTAAAGGAAAAGA;RSEQ=TCTCTTCCTCTGTTCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:686:130:73,57:316,240:0.1895:2,2:28.9:1:32.2:1:0.92181:1.02805:60:260:0.1917:0.0131:0.2 0/1:664:18:9,9:350,295:0.0271:2,2:20.6:1:30.8:1:0.81224:1.18613:60:36:0.0274:0.0075:0.3 -1 118161273 . T G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20391;SOR=Inf;LSEQ=TAAATAAGGCAGCAGGTGAA;RSEQ=AGAAGGCTCCTAAGGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:32,152:0:2,0:23.1:1:28.3:1:1:0:60:91:1:0:0.1 0/1:152:2:1,1:24,126:0.0132:2,2:8:0:33.5:1:0.30281:5.16:60:4:0.0132:0:2 -1 118163457 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACAGGTTCATGCTGCAAC;RSEQ=ATCATTCCCCTCTTCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 118165328 . T C 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80884;LSEQ=TTTAACTCATTGAGTCCTCA;RSEQ=GGCAACACTGAGCAGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:8,0:15,0:0.3478:1,0:32.3:1:30.4:1:1:0:60:7:0.3333:0:1 0/1:10:3:3,0:7,0:0.3:0,0:27:1:33:0:1:0:60:6:0.3:0:1 -1 118165462 . A T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07674;SOR=Inf;LSEQ=GCTTCTCACCCCTCACTTTC;RSEQ=GTTTCCCCAGCCAGAACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:244,51:0:2,0:23.8:1:30.1:1:1:0:60:58:1:0:0.1 0/1:219:3:1,2:172,44:0.0137:2,2:17.7:1:22.7:1:0.11249:7.71766:60:2:0.0093:0:2 -1 118165577 . C G 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0.56382;LSEQ=AGCCGGCTGCATGAGGTCCT;RSEQ=ACTGAAGTTGTACCTATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1010:148:73,75:445,416:0.1465:2,2:25.2:1:31.7:1:0.65637:1.09892:60:296:0.1489:0:1.2 0/1:850:75:38,37:405,369:0.0882:2,2:27:1:30.9:1:0.80953:1.06857:60:24:0.086:0:1.1 -1 118165609 . A G 179 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=66.70814;LSEQ=ACCTATCCACGGACGAGGCA;RSEQ=CTTTCCAACCTTGGAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:952:1:1,0:463,487:0.0011:2,0:24:0:13:0:0.48791:0:60:0:0:0:1 0/1:853:56:28,28:408,389:0.0657:2,2:26.2:1:30.9:1:0.89072:1.0488:60:27:0.064:0:1.2 -1 118165691 . C G 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.36862;LSEQ=GAGGCAGGCATCAAAGTGCA;RSEQ=GACGTCCGGCTGAATGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:690:105:48,57:256,328:0.1522:2,2:22:1:31.5:1:0.74938:1.08:60:210:0.1546:0:1.1 0/1:645:40:13,27:180,230:0.062:2,2:26.5:1:30.4:1:0.18331:1.62373:60:80:0.0629:0:1.1 -1 118165973 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.20799;LSEQ=ATCTCCCTCTCCAACAAGAA;RSEQ=GGGAAGAACGTGGAGCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:231:133,98:245,172:0.3559:2,2:24.3:1:30.2:1:0.80311:1.04947:60:56.75:0.353:0:1.1 0/1:505:52:26,26:258,195:0.103:2,2:16.7:1:29.4:1:0.37704:1.32232:60:51:0.102:0:1 -1 118166096 . C T 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14709;LSEQ=GACTGTTCCAATAATCCCAT;RSEQ=TCTGAGCACTTCCACCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1143:189:86,103:455,499:0.1654:2,2:25:1:29.8:1:0.63246:1.09197:60:36.8:0.1636:0:1.1 0/1:1025:29:17,12:497,497:0.0283:2,2:24.4:1:29.9:1:0.45188:1.42:60:58:0.0286:0:1.1 -1 118166195 . C T 154 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=47.77909;LSEQ=AGACTGATCGCCACCAAGAA;RSEQ=CCAGAAGAAATCAGAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:853:1:0,1:436,416:0.0012:2,0:1:0:27:0:0.48886:0:60:2:0.0012:0:1 0/1:714:38:16,22:331,344:0.0532:2,2:19.6:1:29.4:1:0.50519:1.32252:60:37:0.0527:0:1.1 -1 118166750 . A G 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00016;SOR=0;LSEQ=GCCTCCTTCTAGATGTAGGC;RSEQ=TTTGGCTTTTAAAGGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:20:1,19:0,32:0.3846:1,1:25.7:1:30.1:1:0.38462:0:60:9:0.3913:0:1.4 0/0:24:0:0,0:1,23:0:1,0:29.3:1:30:1:1:0:60:48:1:0:0.2 -1 118170155 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07746;SOR=Inf;LSEQ=GAGCAAAGTAGTTATCCAAT;RSEQ=GTGAGACGAGACCCTGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:0:0,0:70,323:0:2,0:21.8:1:31:1:1:0:60:48.125:1:0:0 0/1:293:3:2,1:66,223:0.0102:2,2:5.7:1:26.3:1:0.13645:6.70:60:6:0.0105:0:1 -1 118170173 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17145;SOR=Inf;LSEQ=ATGGTGAGACGAGACCCTGA;RSEQ=GCTCATAGAGGCCATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:22,232:0:2,0:23.8:1:30.2:1:1:0:60:126:1:0:0 0/1:180:2:1,1:17,161:0.0111:2,2:24:1:30.5:1:0.1905:9.23:60:4:0.0112:0:1 -1 118223693 . A G 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTTAACTTAGCATAGTA;RSEQ=TGAGAACAATGAATATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:11,0:0.2143:0,0:13.7:1:32.3:1:1:0:60:6:0.2143:0:1 0/0:1:0:0,0:1,0:0:0,0:49:0:31:0:1:0:60:2:1:0:0 -1 118223755 . C T 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00224;SOR=Inf;LSEQ=GATCCCTTAGAATATGTTTA;RSEQ=GGGTGGCTGTTTTGTCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:25,1:0:1,0:24.3:1:31.8:1:1:0:60:52:1:0:0.4 0/1:13:5:5,0:8,0:0.3846:0,0:26:1:31:1:1:0:60:10:0.3846:0:1 -1 118223824 . AT A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51502;SOR=0;LSEQ=TTGTGAGATGGCAGGTGGGG;RSEQ=TTTGCTCCACACTGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:2,0:72,3:0.026:1,0:33:1:32.5:1:1:0:60:4:0.0274:0:0 0/0:52:0:0,0:50,2:0:1,0:20.9:1:29.4:1:1:0:60:25:1:0:0.2 -1 118223888 . C T 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66954;SOR=1.69842;LSEQ=ACACAGTTGCTAGTATCTAC;RSEQ=TACCCAGCATAGTTCTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:2:1,1:177,52:0.0087:2,2:19.5:1:21:1:0.407:3.38102:60:1:0.0044:0:2.5 0/1:205:3:1,2:143,59:0.0146:2,2:14:1:22.3:1:0.21168:4.80494:60:2:0.0101:0:2.7 -1 118223910 . C T 45 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04702;SOR=Inf;LSEQ=ACCCAGCATAGTTCTAGAGG;RSEQ=GTGTCAGTCAGTGCCTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:241,113:0:2,0:22.5:1:30.9:1:1:0:60:34.4:1:0:0.6 0/1:310:4:1,3:208,96:0.0129:2,2:5.5:1:22.8:1:0.09939:6.45758:60:3:0.0099:0:1.5 -1 118223911 . G A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05641;SOR=0.59913;LSEQ=CCCAGCATAGTTCTAGAGGC;RSEQ=TGTCAGTCAGTGCCTAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:44:27,17:216,98:0.1229:2,2:23.6:1:30:1:0.38865:1.38647:60:43:0.1222:0:1.1 0/1:323:25:16,9:204,93:0.0774:2,2:20.6:1:29.8:1:0.65707:1.23301:60:50:0.0789:0:1.2 -1 118223984 . G A 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.5362;LSEQ=TTGACATGGCTGGGCTGAGC;RSEQ=TCTTGGGCAACAGGATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:665:405:207,198:126,134:0.609:2,2:26.1:1:30.3:1:0.52546:1.11:60:56.857:0.6076:0:1.1 0/1:611:278:147,131:162,171:0.455:2,2:27.6:1:29.7:1:0.32964:1.18:60:54.6:0.4535:0:1.2 -1 118224030 . G A 52 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10616;SOR=5.62713;LSEQ=GGTGAGGTAACTTAGGTCTT;RSEQ=GTTAAGTCTGAGTTCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:1:1,0:201,322:0.0019:2,0:1:0:24:0:0.3855:0:60:2:0.0019:0:1 0/1:469:5:4,1:189,275:0.0107:2,2:19.2:1:22.8:1:0.16452:5.80:60:4:0.0086:0:1.6 -1 118224210 . G A 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47083;LSEQ=GATTGGGACTCCCAAGGCAG;RSEQ=AGCAGCAAATGGAGTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:0,6:0,9:0.4:0,0:18:1:30:1:1:0:60:12:0.4:0:1.2 1/0:6:3:0,3:1,2:0.5:2,0:8:1:28:1:1:0:60:6:0.5:0:1.3 -1 118224274 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCCTCCGAAGCTGGAGA;RSEQ=GGGATGCCTGCCCCAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:0.2727:0,0:19.3:1:29.7:1:1:0:60:6:0.2727:0:1.3 0/0:3:0:0,0:0,3:0:0,0:18.7:1:29.7:1:1:0:60:6:1:0:1 -1 118225308 . C G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCCTGCAGCTAGGCTA;RSEQ=AGAGAGTTCTGGAAGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:33:0:33:0:1:0:60:4:0.6667:0:2 -1 118225351 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGGGGGGGTGGGGAGAA;RSEQ=TGAGCTCCAGAGAAGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29:1:1:0:60:4:1:0:2 -1 118346123 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09133;SOR=Inf;LSEQ=ATTTGACCCAGAAAGGCTTA;RSEQ=TCAGAGAGGCATCCACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:234,98:0:2,0:24.1:1:31.8:1:1:0:60:82:1:0:0.2 0/1:273:3:1,2:181,89:0.011:2,2:11:1:28.3:1:0.25844:4.04476:60:6:0.011:0:1 -1 118346219 . C T 245 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3513;SOR=1.13906;LSEQ=GAATGATCTAAGAGAGGTTT;RSEQ=CTGAAGCCAGCACTATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:485:308:129,179:71,105:0.6351:2,2:25.5:1:29.7:1:0.77387:1.07:60:76:0.6333:0:1.1 1/0:507:337:159,178:70,100:0.6647:2,2:26.5:1:29.2:1:0.21953:1.28:60:111.333:0.6653:0:1.1 -1 119721104 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.76516;SOR=1.42827;LSEQ=TGCCGCCCAGCGTTTACAGG;RSEQ=AAAGACTTCTGAAATCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:4,2:16,12:0.1765:2,2:13.2:1:30.5:1:1:1.48:60:12:0.1765:0:1 0/1:34:8:5,3:17,9:0.2353:2,2:26:1:30.8:1:1:1.12912:60:16:0.2424:0:1.3 -1 119721191 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51839;SOR=0;LSEQ=GCTTCTCCCCTTTCTAGGTC;RSEQ=CGTGACAGCCATCTTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:25,29:0.0357:2,2:26.5:1:30:1:1:1.16:60:4:0.037:0:1.5 0/0:36:0:0,0:16,20:0:2,0:25.6:1:29.7:1:1:0:59.3:17:1:0:0.3 -1 119721860 . C A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGCTGTGCTCTACTTCT;RSEQ=GCCGGGCCTTAGCTGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:31.5:1:1:0:60:4:1:0:1 -1 120199071 . G T 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40604;SOR=2.16433;LSEQ=CATTGCCTGAGACTGGAGAA;RSEQ=TAGGAACGGACCCAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:100,13:0.0174:2,2:17:1:27:1:0.2296:7.44943:60:4:0.0175:0:1 0/1:81:3:0,3:62,16:0.037:2,0:1:0:25:0:0.01136:0:60:6:0.037:0:1 -1 120199189 . C T 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.19144;LSEQ=GATAGACTAAAAGTAAATGA;RSEQ=TCCATCCCTGTAGGCTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:96:46,50:117,131:0.2791:2,2:24.3:1:30.6:1:0.90486:1.03:60:192:0.284:0:1.1 0/1:368:169:81,88:98,101:0.4592:2,2:25.7:1:29.7:1:0.83458:1.05397:60:83.5:0.4588:0:1.2 -1 120199277 . G T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10676;SOR=Inf;LSEQ=GTCTCAGTTTCATTTCCATT;RSEQ=GCATGCTAATTTTCTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:39,114:0:2,0:24.4:1:31.3:1:1:0:60:50:0.9934:0:0.2 0/1:140:3:2,1:38,99:0.0214:2,2:14:1:24.3:1:0.19634:5.14:60:2:0.0148:0:1 -1 120428796 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00416;SOR=0.04882;LSEQ=AAGGTAGGATCAGGCAAAGC;RSEQ=GAAGTTGACTATAAATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:15,1:1,0:0.9412:0,1:17.7:1:31:1:1:0:60:32:1:0:1 0/1:10:4:4,0:5,1:0.4:2,0:15.3:1:30:1:1:0:60:8:0.4:0:1 -1 120428831 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02145;SOR=Inf;LSEQ=ATCTCCATGTTGGATTTTGA;RSEQ=GAGCTGATCATGAGGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:0:1,0:26:1:31.5:1:1:0:59.9:15.5:1:0:0.6 0/1:22:4:4,0:17,1:0.1818:1,0:25.5:1:31.8:1:1:0:60:8:0.1818:0:1 -1 120428963 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04864;SOR=Inf;LSEQ=TCTGGATGATGCACGCATCA;RSEQ=CAATCCTTGCCACAAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:174,136:0:2,0:28.2:1:31.8:1:1:0:60:61:1:0:0.1 0/1:276:4:2,2:153,119:0.0145:2,2:23:1:28.3:1:1:1.28452:60:8:0.0147:0:1 -1 120429037 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22776;SOR=Inf;LSEQ=ATATTTGCACCTGCCCAGAA;RSEQ=ATGTGGACGACTGTGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:48,130:0:2,0:26.2:1:31.7:1:1:0:60:177:1:0:0.1 0/1:163:2:1,1:52,109:0.0123:2,2:12.5:1:27:1:0.54594:2.09:60:4:0.0124:0:1.5 -1 120429074 . CT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49707;SOR=0;LSEQ=CATGGGGGAGTACCCAGAAC;RSEQ=TTCCTATTCCTTGGAGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:4,73:0.0253:2,2:27.5:1:30:1:0.12334:16.43:60:4:0.026:0:0 0/0:75:0:0,0:10,65:0:2,0:19.3:1:30.1:1:1:0:60:36.5:1:0:0 -1 120429124 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49734;SOR=0;LSEQ=TCAGCAAGTGTTTAAACAGA;RSEQ=GCACATTTTACTGTTAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:0,2:2,23:0.0741:2,0:13:1:31:0:1:0:60:4:0.0741:0:1 0/0:21:0:0,0:3,18:0:2,0:32.5:1:30.3:1:1:0:60:42:1:0:0 -1 120429340 . TAC T 60 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.15548;SOR=5.79829;LSEQ=ACGCACATCTCTCTCTCTCA;RSEQ=ACACACACACACCCCTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:1,0:27,0:0.0357:1,0:13:0:32:0:1:0:60:2:0.0357:0:0 0/1:22:4:4,0:18,0:0.1818:1,0:28:1:30.4:1:1:0:60:8:0.1818:0.0455:0 -1 120429402 . A G 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07847;SOR=0;LSEQ=CTCTCTTCTAGTTAGAGGGT;RSEQ=GAATTGGAAATTAAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:5:5,0:70,3:0.0641:1,0:27:1:33:1:1:0:60:10:0.0641:0:1 0/0:54:0:0,0:51,3:0:2,0:26.4:1:28.1:1:1:0:60:108:1:0:0 -1 120429478 . C T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=0;LSEQ=GATTGATACTGATGATTGTT;RSEQ=CAGTACTCGTGTCCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:0,3:180,116:0.01:2,0:5.3:1:23.3:1:0.06208:0:60:2:0.0068:0:2.3 0/0:291:0:0,0:164,125:0:2,0:28.4:1:30.7:1:1:0:60:143.5:0.9931:0:0.2 -1 120429512 . G A 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGAATGGGGCAAAGCATACC;RSEQ=ATCACCCGAATAGCTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:0:0,0:206,187:0:2,0:26.3:1:29.9:1:1:0:60:34.727:1:0:0.1 0/1:358:15:7,8:171,172:0.0419:2,2:24.3:1:30.6:1:1:1.13581:60:30:0.0421:0:1.1 -1 120429554 . T A 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.46128;LSEQ=GCCAGTGTGCCACAGGTAAG;RSEQ=TTCTCCTCACTCTTCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:14:5,9:113,186:0.0447:2,2:28.9:1:30:1:1:1.09325:60:13:0.0421:0:1.2 0/1:262:61:23,38:76,125:0.2328:2,2:26.7:1:29.4:1:1:1.0045:60:122:0.2337:0:1.1 -1 120458004 . A T 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCGCTGACCTCCTCCAGC;RSEQ=CCCCCAGGGGTAGGGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:0:0,0:418,295:0:2,0:22.8:1:29.7:1:1:0:60:100.857:1:0:0.2 0/1:609:92:50,42:285,230:0.1511:2,2:23.6:1:29.1:1:0.90954:1.04082:60:45:0.1513:0:1.2 -1 120460984 . C T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02908;SOR=Inf;LSEQ=TCTATTCCCCTCGTCAGAGG;RSEQ=ATGCTTTGCAGGTAAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:548:0:0,0:395,153:0:2,0:25.4:1:32.1:1:1:0:60:108.6:1:0:0.1 0/1:387:4:1,3:256,127:0.0103:2,2:12.3:1:27:1:0.11226:6.01772:60:8:0.0104:0:1 -1 120461253 . C T 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=ACTCAGTGAAGAAACAAGGG;RSEQ=ATCAGAGCTGAGGCTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:2,122:0:1,0:24.3:1:32.4:1:1:0:60:248:1:0:0.1 0/1:117:12:1,11:7,98:0.1026:2,2:28:1:25.9:1:0.59113:1.27:60:5:0.0885:0:1.3 -1 120462279 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52318;SOR=0;LSEQ=AAAGTACTCAAGAAGGAGAA;RSEQ=GTAGTTAACCCTATGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:14,137:0.0131:2,2:12.5:1:29:1:0.18705:9.49:60:4:0.0135:0:1.5 0/0:97:0:0,0:10,86:0:2,0:23.8:1:30.5:1:1:0:60:95:0.9896:0:0 -1 120462777 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.19067;SOR=Inf;LSEQ=GGGGTTTATGACTGGACAGG;RSEQ=CAAACACAGGGACAACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:155,33:0:2,0:23.9:1:30.8:1:1:0:60:36.6:0.9946:0:0.1 0/1:147:2:2,0:118,26:0.0136:2,0:15.5:1:27.5:1:1:0:60:4:0.014:0:1 -1 120463044 . C T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02828;SOR=0.69704;LSEQ=AAAGGTGAAAACAATGCTCC;RSEQ=TATCAATCTGGCCACCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:129:40,89:159,324:0.2108:2,2:23.5:1:29.7:1:0.75117:1.09176:60:63.5:0.2106:0:1.1 0/1:478:75:25,50:134,267:0.1569:2,2:22.8:1:29.3:1:1:1.00374:60:17.75:0.1511:0:1.1 -1 120463056 . C T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03598;SOR=Inf;LSEQ=AATGCTCCCTATCAATCTGG;RSEQ=CACCACCAGAAACTGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:135,340:0:2,0:25.2:1:31.1:1:1:0:60:66.857:1:0:0.3 0/1:368:4:2,2:112,252:0.0109:2,2:32.5:1:27.3:1:0.59071:2.24:60:8:0.011:0:1.5 -1 120463093 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56406;SOR=3.11204;LSEQ=TAATCAGAAGGTGTCCAGAG;RSEQ=CTCCACCACCGCTGCTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:0,1:26,232:0.0038:2,0:8:0:31:0:1:0:60:2:0.004:0:1 0/1:168:2:1,1:21,145:0.0119:2,2:41.5:1:28.5:1:0.24544:6.77:60:4:0.0123:0:1 -1 120464141 . A C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.54976;SOR=0;LSEQ=GAGTTATTCTTGAAGAGCAT;RSEQ=TATAGGTAACCCAAGGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:3,0:37,0:0.0714:1,0:21:1:31:1:1:0:60:6:0.0732:0:1 0/0:17:0:0,0:17,0:0:1,0:23:1:28.2:1:1:0:60:34:1:0:0.4 -1 120464165 . C T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06701;SOR=Inf;LSEQ=AGGTAACCCAAGGTCATTTA;RSEQ=GTCCTAAGGATTCCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:56,1:0:1,0:24.2:1:31.8:1:1:0:60:56:1:0:0.3 0/1:40:3:3,0:37,0:0.075:1,0:14.3:1:31.7:1:1:0:60:6:0.075:0:1 -1 120464481 . T C 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATGGCAGTCATAAACTAA;RSEQ=ACAGTGGTTTTCAACACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:21,198:0:2,0:22.5:1:28.5:1:1:0:60:108.5:1:0:0.1 0/1:166:16:2,14:18,132:0.0964:2,2:22.6:1:32.1:1:1:1.05:60:32:0.0976:0:1 -1 120464492 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15872;SOR=Inf;LSEQ=ATAAACTAATACAGTGGTTT;RSEQ=CAACACTTTCCACCATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:18,170:0:2,0:20.4:1:30.1:1:1:0:60:187:1:0:0.1 0/1:125:2:1,1:12,111:0.016:2,2:25.5:1:27:1:0.19794:8.93:60:4:0.0161:0:1 -1 120464827 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07241;SOR=Inf;LSEQ=TAGTCATCCCTACTTATACT;RSEQ=TGAATAGTGGCTTATTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:243,83:0:2,0:25.6:1:32.3:1:1:0:60:80.5:1:0:0.1 0/1:234:3:2,1:155,76:0.0128:2,2:21:1:27:1:1:1.01966:60:6:0.013:0:1 -1 120465222 . C T 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.32183;SOR=3.9336;LSEQ=TCCCCCAATTGACACTCTTC;RSEQ=CCCGCCACCTTTCCCCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:1:1,0:256,103:0.0028:2,0:29:0:33:0:1:0:60:2:0.0028:0:1 0/1:277:3:1,2:197,77:0.0108:2,2:10:1:24:1:0.19666:5.08185:60:6:0.011:0:1.3 -1 120465443 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2199;SOR=Inf;LSEQ=GCGGAGGAGGAGAGATGGGG;RSEQ=TAAAACAGAAGAGTGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:34,184:0:2,0:24.7:1:31.5:1:1:0:60:42.6:1:0:0.1 0/1:193:2:1,1:43,148:0.0104:2,2:10.5:1:27:1:0.4049:3.41:60:4:0.0104:0:1.5 -1 120468134 . C T 224 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCTCATCACAGACGCCATC;RSEQ=CGAGCTTTGTCGGCACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:969:176:80,96:352,440:0.1816:2,2:22.2:1:30.1:1:0.86691:1.04:60:34.2:0.1806:0:1.1 0/0:804:0:0,0:358,446:0:2,0:24.8:1:30.2:1:1:0:60:72.091:1:0:0.2 -1 120468333 . G T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.03329;SOR=Inf;LSEQ=ACTCGCAGTCCCGGGGACTG;RSEQ=GGCAGAAGCAGCGGGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:517:0:0,0:252,265:0:2,0:25.7:1:31:1:1:0:60:85.167:1:0:0.1 0/1:387:4:2,2:199,184:0.0103:2,2:27.8:1:25.5:1:1:1.08128:60:3:0.0079:0:1.3 -1 120468434 . C A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03036;SOR=Inf;LSEQ=CACCTTGCCCCGGAAAATCC;RSEQ=TGTGGAAATCAGTGAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:0:0,0:142,295:0:2,0:26:1:31.8:1:1:0:60:71.833:1:0:0.2 0/1:434:5:4,1:178,249:0.0115:2,2:12:1:26.2:1:0.16691:5.58:60:10:0.0117:0:1.2 -1 120468481 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22493;SOR=0;LSEQ=TGGCATTGGTAGGAAAACAG;RSEQ=CATATTGGAAGTTTGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:28,141:0.0117:2,2:5.5:1:28:1:0.31125:4.97:60:4:0.0118:0:1 0/0:189:0:0,0:43,145:0:2,0:21.6:1:28.7:1:1:0:60:61.667:1:0:0.1 -1 120468487 . T C 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGTAGGAAAACAGTCATAT;RSEQ=GGAAGTTTGAGGTTTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:32:3,29:14,95:0.227:2,2:26.6:1:29.1:1:0.7627:1.42131:60:31:0.223:0:1.2 0/0:154:0:0,0:34,119:0:2,0:22:1:29.8:1:1:0:60:152:0.9935:0:0.1 -1 120469077 . T C 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03609;SOR=1.42694;LSEQ=AGTTCTGTTCACAGATTGTA;RSEQ=GGAAGAGACAATGCCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:72:57,15:309,98:0.1503:2,2:25.6:1:31.7:1:0.65196:1.20:60:71:0.1492:0:1.1 0/1:496:100:71,29:269,127:0.2016:2,2:26.3:1:30.1:1:0.63008:1.16:60:99:0.2004:0:1.1 -1 120469388 . ACACT A 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15209;SOR=0;LSEQ=AATCTGAGCATAGAAAGAAA;RSEQ=CACTGCATCTCAACATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:0,20:0.2:1,0:20.6:1:32:1:1:0:60:10:0.2:0:0.2 0/0:12:0:0,0:0,12:0:0,0:28:1:32.7:1:1:0:60:24:1:0:0.2 -1 120471424 . C T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAAAGGTAGACACTGAT;RSEQ=ATAACATCCATAAAGTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:42,0:0,0:1:0,1:22.4:1:29.6:1:1:0:60:20:1:0:1.1 1/1:22:22:21,1:0,0:1:0,1:23.2:1:30.5:1:1:0:60:44:1:0:1.1 -1 120471610 . C A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01062;SOR=Inf;LSEQ=GCTTCTCACCAGTAAAGGCA;RSEQ=TACGGCAAACACACAGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:0:0,0:397,271:0:2,0:26.2:1:31.9:1:1:0:60:50.385:1:0:0.2 0/1:593:6:3,3:335,252:0.0101:2,2:26:1:28.2:1:1:1.3287:60:12:0.0102:0:1 -1 120471857 . C T 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGAGGAAAGAGAAGAGGTA;RSEQ=AGAATTATGAAAATCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:0:0,0:150,438:0:2,0:23.7:1:32:1:1:0:60:57.8:1:0:0.1 0/1:480:50:10,40:131,297:0.1042:2,2:24.2:1:29:1:0.14098:1.76242:60:100:0.1057:0:1 -1 120471975 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09231;SOR=Inf;LSEQ=TGGGACCTTGTAGTTGGGCA;RSEQ=GGCAAAGCACACTCTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:0,63:0:1,0:23.3:1:31.4:1:1:0:60:62:1:0:0.1 0/1:28:2:1,1:0,26:0.0714:1,2:13:0:32.5:1:0.07143:0:60:4:0.0714:0:1.5 -1 120477998 . C A 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGGAATGAAGCTAGTCTT;RSEQ=CTATCTTTAATTTTATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:327,129:0:2,0:22.9:1:31.2:1:1:0:60:90.2:1:0:0.1 0/1:430:53:34,19:254,123:0.1233:2,2:20.6:1:28.7:1:0.6424:1.15359:60:106:0.1238:0:1.1 -1 120478285 . T C 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCATTACTGGAAACAGACCA;RSEQ=GAGAGCTAGTGAGATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:210:210:19,191:0,0:1:0,2:22.7:1:30.4:1:1:0:60:420:1:0:1.1 1/1:134:113:15,98:5,16:0.8433:2,2:25.9:1:29.6:1:0.31277:2.02892:60:55.5:0.8409:0:1.2 -1 120478807 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTGAGGTGGCTTTATTTGGA;RSEQ=ACTTTGACAGGTTTGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:25.5:1:34:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:27:1:1:0:60:4:1:0:1 -1 120479872 . G T 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05024;SOR=7.40276;LSEQ=AGTTGTACAATCTCCTGGGA;RSEQ=GTCCATGACCTCTGCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:1:0,1:465,216:0.0015:2,0:1:0:26:0:0.31818:0:60:2:0.0015:0:1 0/1:558:6:2,4:357,195:0.0108:2,2:15.7:1:25.2:1:0.19339:3.65255:60:5:0.0091:0:1.8 -1 120480394 . T C 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.56638;SOR=0.33184;LSEQ=TATCTGCCCTTCCCTCTTAT;RSEQ=CCACAAAAAAATGATACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:187:186:167,19:0,0:0.9947:0,2:21.4:1:31.2:1:1:0:60:61:0.9946:0:1.1 1/1:125:123:104,19:1,1:0.984:2,2:22.3:1:30.4:1:0.29548:5.36:60:29.75:0.9835:0:1.1 -1 120480583 . G A 166 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.9823;LSEQ=GACTCTGCTTTTTTCTGAAC;RSEQ=CAAGTACCTTTGTTTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1006:6:5,1:445,554:0.006:2,2:9.3:1:28.5:1:0.09513:6.21:60:12:0.006:0:1 0/1:884:50:24,26:378,455:0.0566:2,2:25.4:1:29.5:1:0.77077:1.11:60:24:0.0555:0:1.2 -1 120480703 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17414;SOR=Inf;LSEQ=TGAAGAAAAGAAGTTATATT;RSEQ=TGTTACAAGAAATCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:14,178:0:2,0:23.5:1:31.9:1:1:0:60:37.4:1:0:0.1 0/1:138:2:1,1:21,115:0.0145:2,2:17:1:32:0:0.2944:5.37:60:4:0.0147:0:1 -1 120482907 . A C 85 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAAAAAAACAAAAAACA;RSEQ=AAAACAAAAATCTGTGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:31.8:1:33.2:1:1:0:60:12:1:0:1 1/1:2:2:1,1:0,0:1:0,2:11:0:29.5:1:1:0:60:4:1:0:1 -1 120483137 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14643;SOR=Inf;LSEQ=GAACAGGTATAATATTCAGC;RSEQ=GCTCTAGGGGAGCTGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:222,45:0:2,0:24.8:1:31.4:1:1:0:60:266:1:0:0.1 0/1:166:2:1,1:124,40:0.012:2,2:14:1:32:0:0.4341:3.07411:60:4:0.012:0:1 -1 120484421 . G A 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCTGAAGAGTAGCATCA;RSEQ=TTTAATCTTAGATTCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:81,275:0:2,0:23.5:1:31.7:1:1:0:60:38.556:0.9971:0:0.1 0/1:286:42:9,33:65,179:0.1469:2,2:21.4:1:29.8:1:0.56944:1.33022:60:84:0.1474:0:1 -1 120490948 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14519;SOR=Inf;LSEQ=GGTATGCCCAATGTCAGGCG;RSEQ=GAAAGGCGGCAGCCTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:154,6:0:1,0:24.5:1:30.5:1:1:0:60:159:1:0:0.1 0/1:99:2:1,1:94,3:0.0202:1,2:12.5:1:33:1:0.07957:27.27949:60:4:0.0206:0:1 -1 120490993 . T C 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.31754;SOR=4.06578;LSEQ=TCTCCTCTGCTCCCTGTGTG;RSEQ=TTTCCTCTCCTCTGGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:1:1,0:270,74:0.0029:2,0:32:0:13:0:1:0:60:0:0:0:2 0/1:257:3:1,2:185,69:0.0117:2,2:9.7:1:30:1:0.18574:5.32096:60:6:0.0117:0:1 -1 120491301 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1382;SOR=Inf;LSEQ=AGCTATTCCACAGACAAACT;RSEQ=GTTGGCCCCCTGCTTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:3,106:0:1,0:23.8:1:31:1:1:0:60:53.5:1:0:0 0/1:65:2:0,2:4,59:0.0308:2,0:10.5:1:32:0:1:0:60:4:0.0317:0:1 -1 120491312 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13289;SOR=Inf;LSEQ=AGACAAACTGGTTGGCCCCC;RSEQ=GCTTTAGGAAGTTCCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:4,91:0:1,0:24.3:1:30.3:1:1:0:60:46.5:1:0:0 0/1:55:2:0,2:4,49:0.0364:2,0:12.5:1:31:1:1:0:60:4:0.0364:0:1 -1 120493101 . TA T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.81956;LSEQ=TGGTTCCAGCCACATACAAT;RSEQ=AAAAAAAATTTCTTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:6:5,1:258,47:0.0192:2,2:25.5:1:30.3:1:1:1.09756:60:12:0.0194:0.0064:0 0/1:253:4:2,2:196,53:0.0158:2,2:20.5:1:27.5:1:0.20695:3.67363:60:8:0.0159:0.004:0.3 -1 120495767 . T G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAACATGGAGAAACCCCGTC;RSEQ=CTACTAAAAATACAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:26:1:30.5:1:1:0:54.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 120496119 . A T 183 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=99.7442;LSEQ=GAGTCAAGCAGTATGCAACA;RSEQ=CAAGAAGACAAAGAGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:887:1:1,0:585,300:0.0011:2,0:17:0:27:0:1:0:60:2:0.0011:0:2 0/1:740:75:46,29:425,239:0.1014:2,2:26.8:1:29.5:1:0.70413:1.12089:60:36.5:0.1001:0:2.1 -1 120496127 . A C 204 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=58.06987;LSEQ=CAGTATGCAACAACAAGAAG;RSEQ=CAAAGAGCAGACGCAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:981:2:2,0:618,360:0.002:2,0:26.5:1:20:1:0.53472:0:60:1:0.001:0:5 0/1:847:90:54,36:470,286:0.1063:2,2:27.3:1:31.5:1:0.7308:1.09545:60:44:0.1056:0:2 -1 120497589 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17212;SOR=Inf;LSEQ=GCCCCATTTGACAACTTCAG;RSEQ=CTGTCACCAGTACTACAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:152,25:0:2,0:24.8:1:31:1:1:0:60:58:1:0:0.1 0/1:126:2:1,1:108,16:0.0159:2,2:11.5:1:27:1:0.25257:6.57871:60:4:0.016:0:1.5 -1 120497601 . A T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19766;SOR=Inf;LSEQ=AACTTCAGGCTGTCACCAGT;RSEQ=CTACAAGCCAACTGGCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:178,40:0:2,0:23.9:1:28:1:1:0:60:217:1:0:0.1 0/1:175:2:1,1:136,37:0.0114:2,2:20.5:1:25.5:1:0.38811:3.64068:60:4:0.0116:0:1 -1 120498086 . G C 94 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTAACAAAAGGCTGGAAAA;RSEQ=TGTTATAGCAATTTGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:20.1:1:33.6:1:1:0:60:14:1:0:1 1/1:1:1:0,1:0,0:1:0,0:19:0:33:0:1:0:60:2:1:0:1 -1 120501953 . G T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07903;SOR=Inf;LSEQ=TTGAAAAGCAATATTCCTTT;RSEQ=GATGCTATATTCCCAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:228,58:0:2,0:23.8:1:31.8:1:1:0:60:56.2:1:0:0.1 0/1:216:3:2,1:156,56:0.0139:2,2:10.3:1:32:0:1:1.39056:60:6:0.0142:0:1 -1 120501957 . G T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63279;SOR=0.41447;LSEQ=AAAGCAATATTCCTTTGGAT;RSEQ=CTATATTCCCAAAGTGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:233,60:0.0101:2,2:10:1:29.7:1:0.50091:1.9364:60:6:0.0102:0:1 0/0:237:1:0,1:173,61:0.0042:2,0:1:0:27:0:0.26383:0:60:2:0.0043:0:1 -1 120505803 . T TAGGAAGGAAGGA 32 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=11.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AAGGGAAGAAGGAAGGTAGG;RSEQ=AGGAAGGAAGGAAGGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:0,0:0.6667:0,0:21.5:1:32:1:1:0:60:4:0.6667:0:0 -1 120505996 . G C 121 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACACAAAATCATCAGATT;RSEQ=GCAGAGCTATTGTCTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:27.3:1:32:1:1:0:60:28:1:0:1.3 1/1:1:1:1,0:0,0:1:0,0:36:0:33:0:1:0:60:2:1:0:1 -1 120506108 . G A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0438;SOR=Inf;LSEQ=GGACTGTTTTTTAGGTATCT;RSEQ=AGCATATGCCAACAGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:42,6:0:2,0:18.8:1:31.8:1:1:0:60:47:1:0:0.1 0/1:42:4:4,0:34,3:0.0952:2,0:17.5:1:28.8:1:1:0:60:8:0.0952:0:1 -1 120506145 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2236;SOR=Inf;LSEQ=CTGAAACATCTGTGTAAACA;RSEQ=ATTTGAGAAACAGTGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:84,18:0:2,0:25.5:1:32.1:1:1:0:60:101:1:0:0.1 0/1:92:2:1,1:72,18:0.0217:2,2:37.5:1:32.5:1:0.37219:3.92026:60:4:0.0217:0:2 -1 120510372 . A AT 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1258;SOR=5.75029;LSEQ=AATATCATTCCCAATTTTCT;RSEQ=TTTTTTTTTCCTTAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:1:0,1:5,69:0.0133:2,0:39:0:29:0:1:0:60:2:0.0137:0:0 0/1:41:3:0,3:1,37:0.0732:1,0:35.7:1:31.7:1:1:0:60:6:0.0769:0:0 -1 120510572 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52985;SOR=0;LSEQ=AGGTCACTTGTAAACACTGG;RSEQ=CATGTAGCAAGAGTAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:120,4:0.0159:1,2:18:1:28.5:1:0.0781:26.94449:60:4:0.016:0:1 0/0:75:0:0,0:74,1:0:1,0:22.5:1:32.7:1:1:0:60:150:1:0:0.1 -1 120512052 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49998;SOR=0;LSEQ=ATGGTAACTCAAAGAATATG;RSEQ=TGTTTGGGATGAAAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:2,0:145,8:0.0129:2,0:26:1:27.5:1:1:0:60:4:0.0136:0:3 0/0:138:0:0,0:119,19:0:2,0:22.8:1:32.2:1:1:0:60:45:1:0:0.8 -1 120512104 . T C 262 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05216;SOR=0;LSEQ=AATGCCCCCTGCCCCTTCCC;RSEQ=GTTTCTAGATCCGTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:384:384:305,79:0,0:1:0,2:24.1:1:30.6:1:1:0:60:63:1:0:1.1 1/1:353:349:254,95:1,1:0.9887:2,2:25.5:1:29.5:1:0.47277:2.66:60:57.167:0.9885:0:1.1 -1 120512403 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49812;SOR=0;LSEQ=TACTTTTGATTAGGGCTCTT;RSEQ=AGTCTCAAAGGACTAGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:6,122:0.0154:1,2:23.5:1:30.5:1:0.10519:18.89:60:4:0.0155:0:1 0/0:127:0:0,0:22,105:0:2,0:19.8:1:31.3:1:1:0:60:62.5:1:0:0.1 -1 120512409 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23779;SOR=Inf;LSEQ=TGATTAGGGCTCTTGAGTCT;RSEQ=AAAGGACTAGTACCATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:6,108:0:2,0:23.4:1:32.1:1:1:0:60:56:1:0:0.2 0/1:109:2:1,1:18,89:0.0183:2,2:10:0:31:1:0.31957:4.84:60:4:0.0185:0:1.5 -1 120529750 . A C 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGATGAAATCTCATACAGA;RSEQ=GAAACGACCTGCTCTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:55,275:0:2,0:22.4:1:31.1:1:1:0:60:164:1:0:0.1 0/1:285:28:5,23:50,207:0.0982:2,2:24.4:1:29.9:1:1:1.11071:60:56:0.0986:0:1 -1 120529778 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50636;SOR=0;LSEQ=CCTGCTCTGTTCCCACAGAA;RSEQ=ATGGTTATTAGAATAGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:9,168:0.0112:2,2:25.5:1:29:1:0.10891:17.76:60:4:0.0112:0:1 0/0:139:0:0,0:9,130:0:2,0:22.2:1:32:1:1:0:60:45.333:1:0:0.2 -1 120540048 . G A 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13688;SOR=Inf;LSEQ=ACATCAGCGAGCTCTTGCGT;RSEQ=GAGAAGACCTCAACTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:3,146:0:1,0:25.7:1:31.4:1:1:0:31.4:73.5:1:0:0.1 0/1:88:2:0,2:6,80:0.0227:2,0:27:1:33:0:1:0:27:4:0.0233:0:1 -1 120540170 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGACACAAGGACTCAGT;RSEQ=GGTGGAGCACCTGGAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:1,20:0.087:1,2:28:1:28.5:1:0.16996:14.49:27:4:0.087:0:1 0/0:3:0:0,0:0,3:0:0,0:14.7:1:29.7:1:1:0:46:6:1:0:0.3 -1 120548095 . C A 108 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00104;SOR=6.21068;LSEQ=CTGTAAACCCTGAGGCACAT;RSEQ=GGCACGTGGCTTTCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:885:3:3,0:372,510:0.0034:2,0:1:0:23.3:1:0.07573:0:57.7:6:0.0034:0:1 0/1:821:17:9,8:344,460:0.0207:2,2:26.5:1:26.6:1:0.4621:1.50:48.4:7.5:0.0187:0:1.1 -1 120572547 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23143;SOR=0.51947;LSEQ=ACTTGCAGTATCCTGTGCCA;RSEQ=TGTGGTAGGTAACACACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:25:24,1:40,3:0.3676:2,1:27:1:32.7:1:1:1.79:29.9:50:0.3788:0:1.9 0/1:26:6:6,0:19,1:0.2308:1,0:32:1:31.3:1:1:0:27:12:0.24:0:1.8 -1 120572572 . C T 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18782;SOR=0.52036;LSEQ=GTAGGTAACACACATTCCTT;RSEQ=ATTTACACAGGGTTCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:29:29,0:43,2:0.3919:1,1:28.7:1:30.3:1:0.51685:0:29.5:58:0.4028:0:1.8 0/1:32:8:8,0:23,1:0.25:1,0:23.8:1:30:1:1:0:27:16:0.2581:0:1.6 -1 120572806 . G A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01837;SOR=0.19443;LSEQ=TATCTTCCAACAATAACCAC;RSEQ=TTTGTGGTCTTGAATGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:1,14:1,15:0.4839:1,1:24.2:1:30.9:1:1:1.07:43.9:30:0.5:0:1.1 0/1:20:3:0,3:4,13:0.15:2,0:12:1:31.3:1:1:0:33:6:0.1579:0:1 -1 120611715 . A G 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.70895;SOR=0.67574;LSEQ=CTCCTGCCGAGGAGGCGTGT;RSEQ=AGGGGTCCCGGGCCGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:10,0:10,0:0.5:0,0:25.7:1:31.2:1:1:0:56.3:9:0.4737:0:2.4 0/1:10:4:2,2:6,0:0.4:0,2:28:1:28.8:1:0.13333:0:54.5:3:0.3333:0:2.3 -1 120611758 . G A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61803;SOR=0.7368;LSEQ=CAGAGGCGGCGGGGAACCCC;RSEQ=GCGGTTGGCGGGGCACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:15:15,0:19,1:0.4286:1,1:28.3:1:30.5:1:1:0:56.1:30:0.4286:0:2.2 0/1:31:11:10,1:17,3:0.3548:2,2:14.6:1:30.5:1:1:1.73:50:22:0.3667:0:2.4 -1 120611830 . G A 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4398;SOR=1.2493;LSEQ=GGAACCCAGCGAGTGGCCTC;RSEQ=CTCCGCGCCGGCGGCCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:57:49,8:66,12:0.4222:2,2:22.5:1:30.4:1:1:1.11:39.8:114:0.4286:0:1.9 0/1:111:53:49,4:47,11:0.4775:2,2:25.3:1:29.6:1:0.099:2.84:36.8:25.5:0.4679:0:1.8 -1 120611851 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18255;SOR=Inf;LSEQ=CTCCGCGCCGGCGGCCGAGC;RSEQ=TGGCCTTCCCACACAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:157,29:0:2,0:25.1:1:30.9:1:1:0:35.8:45.5:1:0:0.8 0/1:140:2:1,1:111,27:0.0143:2,2:12.5:1:28:1:0.36115:4.05518:27:4:0.0145:0:2 -1 120611869 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1808;SOR=Inf;LSEQ=GCCTGGCCTTCCCACACAGA;RSEQ=AAGGACCGAGGGGGAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:191,53:0:2,0:24.8:1:31.9:1:1:0:35.6:80.333:1:0:0.8 0/1:181:2:1,1:129,50:0.011:2,2:13.5:1:25:1:0.48527:2.56447:47:4:0.0112:0:2 -1 120611876 . C T 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17097;SOR=1.29948;LSEQ=CTTCCCACACAGAGAAGGAC;RSEQ=GAGGGGGAGAAGGGTCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:125:99,26:107,47:0.4464:2,2:24:1:31:1:0.07553:1.67:38.3:61.5:0.4556:0:1.7 1/0:211:108:76,32:70,33:0.5118:2,2:21.4:1:30:1:0.76613:1.12:35.7:216:0.5143:0:1.7 -1 120611960 . C T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26873;SOR=0.75056;LSEQ=ATACTCACCATGCGCGGGGG;RSEQ=CGCGCAGCACAGCCAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:778:40:27,13:342,396:0.0514:2,2:24.5:1:29:1:0.01381:2.40:30:19:0.0501:0:1.6 0/1:742:29:20,9:352,360:0.0391:2,2:20.6:1:28.4:1:0.05648:2.27:34.6:13.5:0.0371:0:1.7 -1 120611964 . G C 260 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.1248;SOR=0.85294;LSEQ=TCACCATGCGCGGGGGCCGC;RSEQ=CAGCACAGCCAGAGCGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:373:173,200:192,212:0.4788:2,2:26.6:1:30.5:1:0.77374:1.04697:50.6:32.909:0.4763:0:1.9 0/1:758:333:164,169:216,206:0.4393:2,2:24.4:1:30.3:1:0.60852:1.0804:51.4:65.6:0.4397:0:2 -1 120612002 . CGG C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.17762;SOR=0.70039;LSEQ=CAGCAGCGCCCACAGCAGAG;RSEQ=GGCGCAGGGCGGGCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:731:41:19,22:329,358:0.0561:2,2:34.3:1:31.5:1:0.87352:1.06403:41.8:82:0.0566:0.0014:1.7 0/1:726:29:14,15:335,362:0.0399:2,2:32.7:1:30:1:1:1.01:44.5:58:0.0405:0:1.5 -1 120612006 . G A 245 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2677;SOR=1.1269;LSEQ=AGCGCCCACAGCAGAGCGGG;RSEQ=CGCAGGGCGGGCATCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:722:345:153,192:190,185:0.4778:2,2:24.7:1:29.6:1:0.10039:1.28835:54.9:56.5:0.4775:0:1.8 1/0:713:362:164,198:175,176:0.5077:2,2:25.6:1:28.9:1:0.23089:1.20014:54.9:89.5:0.5078:0:1.9 -1 120612031 . G GCCT 77 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.01532;SOR=Inf;LSEQ=GGGCGGGCATCTTCTCGGTC;RSEQ=CCTCCTCCTCCGCCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:544:0:0,0:229,310:0:2,0:26.5:1:31:1:1:0:54.2:66.375:0.9907:0:0.9 0/1:543:6:3,3:225,307:0.011:2,2:32:0:29.9:1:0.70179:1.36:60:12:0.0112:0:2 -1 120612034 . T G 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.36676;SOR=0.78738;LSEQ=CGGGCATCTTCTCGGTCGCC;RSEQ=CCTCCTCCGCCGCCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:527:35:13,22:209,283:0.0664:2,2:20.3:1:30.9:1:0.59793:1.24928:43.8:34:0.0667:0:1.9 0/1:528:28:12,16:210,290:0.053:2,2:22.8:1:29.9:1:1:1.04:44.8:13:0.0503:0:1.6 -1 120612037 . TCCTCCGCCG T 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=6.000;MSILEN=3;SSF=0.69818;SOR=1.09729;LSEQ=GCATCTTCTCGGTCGCCTCC;RSEQ=CCGCCGCCGCCGCCTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:59:30,29:178,264:0.1164:2,2:36:1:31.8:1:0.12463:1.53:39.4:118:0.1187:0.002:0.1 0/1:491:62:31,31:170,258:0.1263:2,2:32:1:30.7:1:0.1306:1.52:39.8:124:0.1281:0.0122:0.3 -1 120612040 . TCCG T 108 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.00626;SOR=0.09428;LSEQ=TCTTCTCGGTCGCCTCCTCC;RSEQ=CCGCCGCCGCCGCCGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:11:5,6:160,250:0.0227:2,2:38.5:1:31.4:1:0.75767:1.30:58:22:0.0266:0.0021:0.4 0/0:458:1:0,1:143,230:0.0022:2,0:32:0:27:0:1:0:60:2:0.0025:0:0 -1 120612043 . G T 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCTCGGTCGCCTCCTCCTCC;RSEQ=CCGCCGCCGCCGCCGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:130,205:0:2,0:26.2:1:30.8:1:1:0:55.5:54.833:0.988:0:0.7 0/1:418:59:21,38:111,182:0.1411:2,2:10.8:1:28.9:1:0.77037:1.10334:60:58:0.1671:0:3 -1 120612055 . G T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.0518;SOR=Inf;LSEQ=CCTCCTCCGCCGCCGCCGCC;RSEQ=CCGCCTGGGCAGATCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:154,228:0:2,0:25.4:1:30.9:1:1:0:51.9:190:1:0:0.6 0/1:350:4:2,2:128,216:0.0114:2,2:23.5:1:27:1:0.63139:1.68:58:8:0.0115:0:1 -1 120612154 . C G 39 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1767;LSEQ=GCTCAGGCCCTGGCGCTACG;RSEQ=TCCGAAGCCCAGGCGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:3:1,2:6,70:0.038:2,2:30.3:1:25:1:0.24582:5.60:53:2:0.026:0:3.7 0/1:45:2:1,1:8,35:0.0444:2,2:23:1:32.5:1:0.36364:4.18:52:4:0.0465:0:2 -1 120612163 . C A 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68089;SOR=1.54143;LSEQ=CTGGCGCTACGCTCCGAAGC;RSEQ=CAGGCGCAAATGCCTCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:3:1,2:6,59:0.0441:2,2:33.3:1:30.3:1:0.28187:4.73:53:6:0.0455:0:3.7 0/1:45:3:1,2:8,34:0.0667:2,2:23.3:1:29.3:1:0.49683:2.08:50.3:6:0.0667:0:1.7 -1 120612168 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05416;LSEQ=GCTACGCTCCGAAGCCCAGG;RSEQ=GCAAATGCCTCGACTCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:20:2,18:5,40:0.3077:2,2:24.2:1:30:1:1:1.12301:54.8:40:0.3175:0:1.2 0/1:47:15:3,12:6,26:0.3191:2,2:16.4:1:29.6:1:1:1.08:50.5:30:0.3333:0:1.2 -1 120612194 . C G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39229;SOR=0.54074;LSEQ=TGCCTCGACTCCCCGCGCCC;RSEQ=GAGTCCGCCGCTCCTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:12:0,12:2,25:0.3077:2,0:15.3:1:32.3:1:1:0:43.2:24:0.3158:0:1 0/1:26:5:0,5:6,15:0.1923:2,0:35.2:1:30.8:1:0.29811:0:45.8:10:0.2:0:1 -1 120612223 . AGCC A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.23826;SOR=Inf;LSEQ=CGCTCCTCGGCCGCCGCCTC;RSEQ=GCCGCCCGAAGTTTGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:1,16:0:1,0:19.1:1:32.4:1:1:0:53.8:34:1:0:0.5 0/1:21:3:0,3:3,15:0.1429:2,0:24.7:1:32.7:1:1:0:49.7:6:0.1429:0:1 -1 120904486 . GA G 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00867;SOR=Inf;LSEQ=CCGTGATCGATAAAATTACA;RSEQ=AAAAAATCAGGAAAGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:58,0:0:1,0:22.9:1:30.1:1:1:0:33:28:1:0:0 0/1:27:4:3,1:22,1:0.1481:1,2:33.8:1:32.3:1:0.2792:6.49359:29.3:8:0.1538:0:0 -1 120904791 . A G 283 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.003;SOR=1.29309;LSEQ=ACGGGCGGGGTGAAGAAGCC;RSEQ=CACCGCTACCGGCCGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1262:586:346,240:335,337:0.4643:2,2:23.8:1:30.8:1:0.00122:1.45:31.3:82.714:0.4628:0:1.2 1/0:946:500:275,225:220,221:0.5285:2,2:22.4:1:30.2:1:0.1324:1.23:30.3:34.714:0.5226:0:1.3 -1 120904830 . C T 213 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGTGGCTCTGCGGGAGATC;RSEQ=GGCGCTACCAGAAGTCTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1447:0:0,0:771,676:0:2,0:28.3:1:30.5:1:1:0:42.7:64.773:1:0:0.5 0/1:1173:129:82,47:560,484:0.11:2,2:29.4:1:30.4:1:0.03886:1.51:35.1:31.25:0.1082:0:1.7 -1 120905120 . A C 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.92874;SOR=1.01868;LSEQ=TTAAGTGGTCGATCTAAAGG;RSEQ=TCTTTTCAGAGCCACTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:765:75:10,65:142,548:0.098:2,2:22.7:1:32.6:1:0.16958:1.68338:32.5:74:0.0992:0:1 0/1:642:64:10,54:153,425:0.0997:2,2:17:1:32.1:1:0.06873:1.94226:33.2:128:0.1009:0:1.1 -1 120905164 . G C 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00167;SOR=Inf;LSEQ=TCATCAAGAGCAGCTGTACC;RSEQ=GCTCTCCATCTGATGTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:27,309:0:2,0:23.6:1:30.7:1:1:0:50.8:36.333:1:0:0.1 0/1:228:7:0,7:23,198:0.0307:2,0:19.6:1:30.3:1:1:0:53.6:14:0.0311:0:1 -1 120905373 . T C 53 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=ATTCTGTGGGTAAAGTTTTG;RSEQ=ATGGGGGCAAGAGACTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:15:1:33.7:1:1:0:44.7:6:0.4286:0:1 1/0:2:1:0,1:0,1:0.5:0,0:14:0:16:0:1:0:47:0:0:0:2 -1 120906101 . CG AA 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1239;SOR=2.0526;LSEQ=GGGCTCCAAAAAGGCTGTTA;RSEQ=AGAGTGCAGAAGAAGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:9:6,3:50,23:0.1098:2,2:26.3:1:29.9:1:1:1.08584:45:18:0.1098:0.0122:1.1 0/1:74:15:9,6:38,21:0.2027:2,2:22.5:1:28.4:1:0.77082:1.20324:43.3:30:0.2113:0.027:1 -1 120906120 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49818;SOR=0;LSEQ=ACGAGAGTGCAGAAGAAGGA;RSEQ=GGCGAGAAGCGCAAGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:57,33:0.0217:2,2:26:1:29.5:1:1:1.71646:39:4:0.0217:0:1 0/0:84:0:0,0:47,37:0:2,0:28.2:1:30:1:1:0:43.7:168:1:0:0.2 -1 120906121 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23222;SOR=Inf;LSEQ=CGAGAGTGCAGAAGAAGGAC;RSEQ=GCGAGAAGCGCAAGCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:59,34:0:2,0:28.4:1:30.3:1:1:0:44.3:92:1:0:0.2 0/1:87:2:1,1:48,37:0.023:2,2:26:1:31.5:1:1:1.29337:27:4:0.023:0:1 -1 120906202 . G A 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12282;SOR=Inf;LSEQ=AGCAGGTCCACCCCGACACC;RSEQ=GCATCTCGTCCAAGGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:44,59:0:2,0:28.2:1:29.6:1:1:0:42.1:24.75:1:0:0.1 0/1:112:4:2,2:55,53:0.0357:2,2:26.3:1:30.8:1:1:1.0374:41:8:0.0364:0:1 -1 120906205 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22132;SOR=0;LSEQ=AGGTCCACCCCGACACCGGC;RSEQ=TCTCGTCCAAGGCCATGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:42,56:0.02:2,2:32.5:1:30:1:1:1.33:44.5:4:0.0204:0:1 0/0:112:0:0,0:57,55:0:2,0:28:1:29.6:1:1:0:40.2:55:1:0:0.1 -1 121482188 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAATGCTTCTGTTTACT;RSEQ=TTTACGTGAAGATATTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:30.5:1:1:0:33:4:1:0:4 -1 121482193 . C A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTTCTGTTTACTTTTTA;RSEQ=GTGAAGATATTCCCGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:30:1:1:0:33:4:1:0:4 -1 121482211 . T C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACGTGAAGATATTCCCGTT;RSEQ=CCAAAGAAATCTTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:31.5:1:32.5:1:1:0:33:4:0.5:0:4 -1 121482216 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATATTCCCGTTTCCAA;RSEQ=GAAATCTTCACAGAGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:28:0:32.5:1:1:0:33:4:0.5:0:4 -1 121482244 . C A 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAGAGTTCCACCTATCC;RSEQ=TTTGCAGATGCTAGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:18:0:31:0:1:0:27:2:1:0:3 1/1:3:3:2,1:0,0:1:0,2:33.3:1:29.3:1:1:0:27:6:1:0:2 -1 121482287 . A C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTTCAAAACTGCTCTATC;RSEQ=AAAGGAATGTTCAACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:38.5:1:30:1:1:0:27:4:0.6667:0:2 0/1:8:2:1,1:3,3:0.25:2,2:10:0:33:1:1:1:40:4:0.25:0:2.5 -1 121482316 . T A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GTTCAACTCTGTGAGTTGAA;RSEQ=GCAATCATCACAGAGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22:1:32:1:1:0:38.8:8:1:0:1.3 0/1:6:2:1,1:1,3:0.3333:2,2:24.5:1:32:1:1:2.45:40:4:0.3333:0:2.5 -1 121482320 . A G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AACTCTGTGAGTTGAATGCA;RSEQ=TCATCACAGAGAAGTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:19:1:33.5:1:1:1:27:4:0.5:0:2 1/0:6:3:1,2:1,2:0.5:2,2:30:1:31.3:1:1:1:23.7:6:0.5:0:1.7 -1 121482358 . G A 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGAAGGCTTCTGTCTAG;RSEQ=TTTTATGTGAAGATATACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:16:1:32:0:1:0:22:4:1:0:1.5 -1 121482742 . A C 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCGTAGGCCTCAAAGCGTT;RSEQ=CAAATCTCCACTTGCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:26:1:27:1:1:0:29:4:1:0:1.5 -1 121482840 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGCCAACATCACAAAGAA;RSEQ=TTCTGGGAATGTTTCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:16:1:31.5:1:1:0:25:4:1:0:2 0/1:5:2:1,1:0,3:0.4:0,2:17.5:1:29:1:0.4:0:24:4:0.4:0:3 -1 121482872 . G T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTCTTCAGTTATGTGAG;RSEQ=TTTATCCCGTTTCCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:37:0:32:0:1:0:25:2:1:0:3 1/1:2:2:0,2:0,0:1:0,0:22:1:29.5:1:1:0:24.5:4:1:0:3 -1 121482997 . TG CA 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGACGTAAACTCAATCAT;RSEQ=CAAAGAATTTTCTGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:12:1:32:1:1:0:22:4:1:0:2.5 -1 121483056 . T G 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGAAGTTATTTCCTTTAC;RSEQ=ACGATAGGCCTCAAAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:2:0:29:0:1:0:24:2:1:0:2 1/1:7:6:5,1:0,0:0.8571:0,2:28.8:1:32:1:1:0:42.8:12:0.8571:0:1.3 -1 121483151 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15584;SOR=0;LSEQ=GAGAAAGGTTCAACACTGTG;RSEQ=GTTGAATGCAAGCATCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:19:1:29:1:1:1.29098:24:4:0.2222:0:1.5 0/0:13:0:0,0:4,9:0:2,0:28.5:1:30.6:1:1:0:25.8:26:1:0:0.9 -1 121483170 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48538;SOR=Inf;LSEQ=GAGTTGAATGCAAGCATCAC;RSEQ=AAGAAGGTTCTGAGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:29.9:1:31.1:1:1:0:24.8:16:1:0:0.8 0/1:11:2:1,1:3,6:0.1818:2,2:44:1:30.5:1:1:1.87:23:4:0.1818:0:2.5 -1 121483190 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=GAAGAAGGTTCTGAGAATGC;RSEQ=TCTGTTTAGATAGGTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:18.3:1:31.3:1:1:0:25.1:14:1:0:0.6 0/1:9:2:1,1:3,4:0.2222:2,2:36.5:1:30:1:1:1.29:23:4:0.2222:0:2.5 -1 121483218 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGATAGGTGAGTTTTCTCCC;RSEQ=TATCCAAAGAAATCCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:45:0:34:0:1:0:22:2:1:0:3 0/1:7:2:1,1:2,3:0.2857:2,2:8.5:1:30:1:1:1.41:23:4:0.2857:0:2.5 -1 121483221 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGGTGAGTTTTCTCCCGTA;RSEQ=CCAAAGAAATCCTCAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:42:0:32:0:1:0:22:2:1:0:3 0/1:6:2:1,1:1,3:0.3333:2,2:6:1:31:1:1:2.45:23:4:0.3333:0:2.5 -1 121483226 . A C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTTTCTCCCGTATCCAA;RSEQ=GAAATCCTCAGAAAGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:37:0:32:0:1:0:22:2:1:0:3 1/0:5:3:0,3:1,0:0.6:0,0:7.3:1:31.7:1:0.25:0:23.3:6:0.6:0:2.3 -1 121483239 . A G 61 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCCAAAGAAATCCTCAGA;RSEQ=AGGTCCAAATATCCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:33:0:1:0:26.5:4:1:0:2 1/0:6:4:4,0:1,1:0.6667:2,0:11.3:1:30.5:1:0.33333:0:29.5:8:0.6667:0:4.8 -1 121483255 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAAAGGTCCAAATATCCA;RSEQ=TTGCAGATTCTACAGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:14.8:1:31.8:1:1:0:32.8:10:1:0:2.4 0/1:18:2:1,1:9,7:0.1111:2,2:15.5:1:31:1:1:1.26772:41:4:0.1111:0:6.5 -1 121483264 . T G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAAATATCCACTTGCAGAT;RSEQ=CTACAGAAAGTGTGTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:25.5:1:30:1:1:0:35.5:8:1:0:2.3 0/1:21:2:1,1:11,8:0.0952:2,2:33.5:1:32.5:1:1:1.35399:30:4:0.1:0:4 -1 121483277 . T G 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGCAGATTCTACAGAAAGTG;RSEQ=GTTTTGAAACTGCTCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:38.3:1:30.8:1:1:0:35.5:8:1:0:2.3 0/1:23:2:1,1:11,10:0.087:2,2:38.5:1:28:1:1:1.09544:45:4:0.087:0:4.5 -1 121483282 . T G 120 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62393;SOR=2.26166;LSEQ=ATTCTACAGAAAGTGTGTTT;RSEQ=GAAACTGCTCCATCCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:29:0:33:1:1:1.7321:40:4:0.4:0:4 1/0:23:14:7,7:3,3:0.6087:2,2:34.1:1:31.7:1:1:1:31.4:28:0.6667:0:4.4 -1 121483283 . G TT 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=TTCTACAGAAAGTGTGTTTT;RSEQ=AAACTGCTCCATCCAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:38:1:32.8:1:1:0:35.5:8:1:0:2.3 0/1:23:2:1,1:11,10:0.087:2,2:14:1:31.6:1:1:1.09544:44:4:0.087:0:4 -1 121483291 . T G 113 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65134;SOR=2.12461;LSEQ=AAAGTGTGTTTTGAAACTGC;RSEQ=CCATCCAAAGGAATGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:20:0:33:1:1:1:40:4:0.3333:0:4 1/0:23:12:6,6:6,5:0.5217:2,2:25.1:1:31.7:1:1:1.19051:33.2:24:0.5217:0:4.3 -1 121483297 . C T 121 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02776;SOR=9.9182;LSEQ=TGTTTTGAAACTGCTCCATC;RSEQ=AAAGGAATGTTCAGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:14:0:31:1:1:1:40:4:0.3333:0:4 1/1:20:17:8,9:2,1:0.85:2,2:22.8:1:29.8:1:1:2.16219:34.2:34:0.85:0:4.1 -1 121483300 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.30312;SOR=0.35008;LSEQ=TTTGAAACTGCTCCATCCAA;RSEQ=GGAATGTTCAGCTCTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:11:0:33:1:1:1:40:4:0.3333:0:4 0/1:21:3:1,2:10,8:0.1429:2,2:14.3:1:31.7:1:0.58647:2.39416:37.3:6:0.1579:0:6 -1 121483305 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTGCTCCATCCAAAGGAA;RSEQ=GTTCAGCTCTGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:19.7:1:31.3:1:1:0:38.5:12:1:0:1.7 0/1:20:2:1,1:10,8:0.1:2,2:18:0:31.5:1:1:1.23603:44:4:0.1:0:4 -1 121483351 . G A 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50893;SOR=Inf;LSEQ=TCGTCACAAAGTGTTTCCTG;RSEQ=GAATGCTACTGTCTAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:29.2:1:32.6:1:1:0:44.2:10:1:0:1.8 0/1:11:3:1,2:4,4:0.2727:2,2:41:1:31.3:1:1:1.87936:49.7:6:0.2727:0:4 -1 121483392 . C G 114 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGGGCAGTTATATCCTCT;RSEQ=CTGCCAAAGGCCTCAAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:25.4:1:31.4:1:1:0:44:10:1:0:2.4 1/1:14:13:7,6:0,0:0.9286:0,2:23.7:1:31:1:1:0:42.3:26:0.9286:0:2.2 -1 121483396 . C T 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05848;SOR=0;LSEQ=GGCAGTTATATCCTCTCCTG;RSEQ=CAAAGGCCTCAAAGCGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:11.5:1:28.5:1:1:1.73:43:4:0.4:0:3 0/0:14:0:0,0:7,7:0:2,0:23.6:1:31:1:1:0:42.1:28:1:0:2.6 -1 121483399 . A T 111 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTATATCCTCTCCTGCCA;RSEQ=AGGCCTCAAAGCGGTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:24:1:28.4:1:1:0:44:10:1:0:2.4 1/1:15:15:7,8:0,0:1:0,2:21.6:1:28.6:1:1:0:38.9:30:1:0:2.5 -1 121483543 . T A 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GAATGCTTCCATGTAGCTTT;RSEQ=ATGAGCAGATATTTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:2.5:1:27.5:1:1:0:45:4:1:0:0 1/1:5:4:2,2:1,0:0.8:0,2:19:1:23.5:1:1:0:36:3:0.75:0:1.3 -1 121483725 . A T 70 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGCTTTTATGGGAAGAT;RSEQ=ATCCCTTTTCCATCGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:5,0:0,0:1:0,0:41.8:1:30.4:1:1:0:35.2:10:1:0:2 -1 121483753 . A G 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05455;SOR=0;LSEQ=TTCCATCGAAATGTTCAAAG;RSEQ=GGTCCACATATCCGCTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18:0:32.5:1:1:0:60:4:0.6667:0:3 0/0:8:0:0,0:6,2:0:2,0:20.4:1:28.6:1:1:0:40:16:1:0:1.3 -1 121483755 . G T 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05455;SOR=0;LSEQ=CCATCGAAATGTTCAAAGAG;RSEQ=TCCACATATCCGCTTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:20:0:32:0:1:0:60:4:0.6667:0:3 0/0:8:0:0,0:6,2:0:2,0:19.9:1:30:1:1:0:40:16:1:0:1.3 -1 121483777 . T C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCACATATCCGCTTGCAGAT;RSEQ=CCACCGAAAGAGTGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:36.7:1:31.3:1:1:0:59:6:1:0:2.3 0/1:8:2:2,0:4,2:0.25:2,0:18:1:33:0:1:0:40:4:0.25:0:6.5 -1 121483782 . C T 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86755;LSEQ=TATCCGCTTGCAGATTCCAC;RSEQ=GAAAGAGTGTTTCCAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:4:0:32:0:1:0:40:2:0.25:0:3 0/1:9:2:2,0:4,3:0.2222:2,0:18:1:33:0:0.5:0:40:4:0.2222:0:6.5 -1 121483803 . C T 29 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11053;SOR=0;LSEQ=GAAAGAGTGTTTCCAAACTG;RSEQ=TGTATCAAAAGGAATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:31:0:29.5:1:1:3.1622:60:4:0.3333:0:3 0/0:13:0:0,0:8,5:0:2,0:25:1:32.2:1:1:0:39.5:26:1:0:1.7 -1 121483810 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTTTCCAAACTGCTGTATC;RSEQ=AAAGGAATCTTCAACTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:23.6:1:30:1:1:0:47.1:14:1:0:2.7 0/1:16:2:1,1:8,6:0.125:2,2:14:1:32:0:1:1.30929:38.5:4:0.125:0:1.5 -1 121483818 . T C 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.36848;LSEQ=AACTGCTGTATCAAAAGGAA;RSEQ=CTTCAACTCCGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:3,3:0.25:2,0:31.5:1:34:0:0.46429:0:40:4:0.25:0:5 0/1:19:6:5,1:6,7:0.3158:2,2:22.8:1:31.8:1:0.17699:5.33:39.2:12:0.3333:0:4 -1 121483820 . T G 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09524;SOR=0;LSEQ=CTGCTGTATCAAAAGGAATC;RSEQ=TCAACTCCGTGAGTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:26:1:30:1:1:2.23609:48.5:4:0.2222:0:1 0/0:19:0:0,0:11,8:0:2,0:23.9:1:30.5:1:1:0:40.9:38:1:0:1.7 -1 121483829 . G C 29 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08867;SOR=0;LSEQ=CAAAAGGAATCTTCAACTCC;RSEQ=TGAGTTGAATGCAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:28:1:29.5:1:1:2.23609:33:4:0.2222:0:1.5 0/0:20:0:0,0:11,9:0:2,0:26:1:30.4:1:1:0:40.9:40:1:0:1.8 -1 121483842 . A C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30003;SOR=0.33093;LSEQ=CAACTCCGTGAGTTGAATGC;RSEQ=ATCATCACAAAGAAGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:26.5:1:30.5:1:1:1.8258:40:4:0.25:0:6.5 0/1:21:2:2,0:9,10:0.0952:2,0:34.5:1:32:0:0.47619:0:40:4:0.0952:0:6 -1 121483856 . A C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.58935;SOR=0.48705;LSEQ=GAATGCAATCATCACAAAGA;RSEQ=GTTTCTGACAATGCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:30:1:30:1:1:1:40:4:0.25:0:6.5 0/1:22:3:2,1:9,10:0.1364:2,2:17.7:1:30:1:1:2.14:40:6:0.1429:0:5.3 -1 121483868 . T C 77 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14123;SOR=Inf;LSEQ=CACAAAGAAGTTTCTGACAA;RSEQ=GCTTCTCTCTAGTTTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:27:1:29.5:1:1:0:37.6:16:1:0:3.1 0/1:20:6:1,5:7,7:0.3:2,2:32.8:1:30:1:0.32456:4.63479:39.2:12:0.3:0:1.2 -1 121483871 . T C 31 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07407;SOR=0;LSEQ=AAAGAAGTTTCTGACAATGC;RSEQ=TCTCTCTAGTTTTTATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:30:1:31.5:1:1:1:40:4:0.3333:0:6.5 0/0:20:0:0,0:8,12:0:2,0:29.1:1:29.8:1:1:0:37.8:40:1:0:2 -1 121483873 . C A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGAAGTTTCTGACAATGCTT;RSEQ=TCTCTAGTTTTTATGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:24.5:1:30.9:1:1:0:37.6:16:1:0:3.1 0/1:20:2:1,1:7,11:0.1:2,2:37:1:28:1:1:1.54:40:4:0.1:0:4 -1 121483885 . T G 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5453;SOR=Inf;LSEQ=CAATGCTTCTCTCTAGTTTT;RSEQ=ATGTGAAGATATTTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:22:1:28.9:1:1:0:37.3:14:1:0:3.1 0/1:20:3:1,2:7,10:0.15:2,2:19.3:1:29:1:1:1.37728:40:6:0.15:0:4.3 -1 121483887 . T G 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5799;SOR=0.45653;LSEQ=ATGCTTCTCTCTAGTTTTTA;RSEQ=GTGAAGATATTTCCTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,2:0.2857:2,2:29.5:1:32.5:1:1:1:40:4:0.2857:0:6.5 0/1:20:3:1,2:4,8:0.15:2,2:20:1:27.3:1:1:1:40:6:0.15:0:4.3 -1 121483895 . T C 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03953;SOR=0;LSEQ=CTCTAGTTTTTATGTGAAGA;RSEQ=ATTTCCTTTTCCACCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:21.5:1:31:1:0.4:0:40:4:0.4:0:6.5 0/0:18:0:0,0:6,12:0:2,0:23.7:1:27.5:1:1:0:37.2:36:1:0:1.8 -1 121483931 . A C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGGCCTGAAAGCGCTCCA;RSEQ=ATGTCCACTTGGAGACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:20:1:32:0:1:0:38.3:6:1:0:5 0/1:8:2:1,1:0,6:0.25:0,2:32:1:32:1:0.25:0:21:4:0.25:0:1.5 -1 121483933 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69289;LSEQ=AGGCCTGAAAGCGCTCCAAA;RSEQ=GTCCACTTGGAGACTCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:4:0:29:0:1:0:40:2:0.3333:0:6 0/1:8:2:0,2:1,5:0.25:2,0:27:1:31:1:1:0:40:4:0.25:0:4 -1 121483950 . A T 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGTCCACTTGGAGACTC;RSEQ=ACGAAAAGAATGTTTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:42:0:30:0:1:0:35:2:1:0:8 1/1:5:4:0,4:0,0:0.8:0,0:20:1:30:0:1:0:36.8:8:0.8:0:3.3 -1 121484065 . C A 31 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04058;SOR=0;LSEQ=TGTTTACTTTTTATGCTAGA;RSEQ=AGAAGAATTCTCAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:14,12:0.0714:2,2:8:0:31.5:1:1:1.16024:21:4:0.0714:0:4.5 0/0:109:0:0,0:63,42:0:2,0:6.9:1:31.1:1:1:0:45.1:210:0.9633:0:2.2 -1 121484069 . A T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTTTTTATGCTAGACAGA;RSEQ=GAATTCTCAGTAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:11.7:1:31:1:1:0:42.2:60:1:0:2.1 0/1:124:3:3,0:73,48:0.0242:2,0:7:1:30.3:1:0.28245:0:27:6:0.0246:0:3 -1 121484070 . G T 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58367;SOR=Inf;LSEQ=ACTTTTTATGCTAGACAGAA;RSEQ=AATTCTCAGTAACTTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:12.7:1:31.8:1:1:0:42.2:29:1:0:2.1 0/1:124:5:4,1:72,47:0.0403:2,2:15.8:1:31:1:0.6478:2.59:43:10:0.0413:0:3.4 -1 121484071 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTTATGCTAGACAGAAG;RSEQ=ATTCTCAGTAACTTCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:13.7:1:30.1:1:1:0:42.2:29:1:0:2.1 0/1:125:2:1,1:76,47:0.016:2,2:15:0:31:1:1:1.61052:53.5:4:0.0163:0:1 -1 121484072 . A C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTTATGCTAGACAGAAGA;RSEQ=TTCTCAGTAACTTCCTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:14.7:1:31.1:1:1:0:42.2:60:1:0:2.1 0/1:128:2:1,1:77,49:0.0156:2,2:9:0:33.5:1:1:1.56565:45:4:0.0157:0:2 -1 121484075 . C G 33 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03377;SOR=0;LSEQ=TTATGCTAGACAGAAGAATT;RSEQ=TCAGTAACTTCCTTGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:0.0667:2,2:18:0:33.5:1:1:1.14834:21:4:0.069:0:4.5 0/0:131:0:0,0:80,51:0:2,0:15.3:1:31.7:1:1:0:44.3:262:1:0:2.3 -1 121484076 . T C 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATGCTAGACAGAAGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:18.7:1:31:1:1:0:42.2:29:1:0:2.1 0/1:134:4:2,2:80,50:0.0299:2,2:8.3:1:29.3:1:0.64137:1.59414:45:8:0.0301:0:2.3 -1 121484079 . G A 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTAGACAGAAGAATTCTCA;RSEQ=TAACTTCCTTGTGTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:0:2,0:19.8:1:33:1:1:0:42.7:66:1:0:2.1 0/1:142:4:2,2:85,53:0.0282:2,2:19.5:1:29.5:1:0.64091:1.5982:41:8:0.0286:0:3 -1 121484080 . T A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.23571;SOR=2.18652;LSEQ=CTAGACAGAAGAATTCTCAG;RSEQ=AACTTCCTTGTGTTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:2,2:16,13:0.1212:2,2:18.3:1:31.5:1:1:1.223:34:8:0.1212:0:5.3 0/1:142:33:22,11:64,43:0.2324:2,2:17.7:1:29.7:1:0.54339:1.34:45.4:66:0.2357:0:5.1 -1 121484082 . A C 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACAGAAGAATTCTCAGTA;RSEQ=CTTCCTTGTGTTGTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:0:2,0:22.2:1:30.9:1:1:0:42.9:68:1:0:2.1 0/1:145:3:2,1:86,53:0.0207:2,2:20.7:1:33:0:1:1.23:50.3:6:0.021:0:4.7 -1 121484083 . C T 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03444;SOR=0;LSEQ=GACAGAAGAATTCTCAGTAA;RSEQ=TTCCTTGTGTTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:17,15:0.0588:2,2:26.5:1:31:1:1:1.12916:50:4:0.0588:0:2.5 0/0:147:0:0,0:90,55:0:2,0:21.5:1:31.8:1:1:0:43.6:144:0.9863:0:2.4 -1 121484084 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGAAGAATTCTCAGTAAC;RSEQ=TCCTTGTGTTGTGTGTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:0:2,0:24.2:1:30.9:1:1:0:42.9:33:1:0:2.1 0/1:148:2:1,1:90,56:0.0135:2,2:8.5:1:31.5:1:1:1.60175:29:4:0.0136:0:7 -1 121484086 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAAGAATTCTCAGTAACTT;RSEQ=CTTGTGTTGTGTGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:25.5:1:31.5:1:1:0:42.5:34:1:0:2.1 0/1:148:2:1,1:90,56:0.0135:2,2:24.5:1:32:1:1:1.60175:50:4:0.0137:0:2.5 -1 121484087 . C G 32 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03496;SOR=0;LSEQ=GAAGAATTCTCAGTAACTTC;RSEQ=TTGTGTTGTGTGTATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:17,15:0.0571:2,2:30.5:1:32.5:1:1:1.12916:47:4:0.0571:0:6 0/0:150:0:0,0:89,57:0:2,0:24.9:1:31.1:1:1:0:43.7:47.667:0.9728:0:2.5 -1 121484090 . G T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16019;SOR=0.22323;LSEQ=GAATTCTCAGTAACTTCCTT;RSEQ=TGTTGTGTGTATTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:19,15:0.0556:2,2:23:0:31:1:1:1.2583:21:4:0.0556:0:4.5 0/1:156:2:1,1:92,58:0.0128:2,2:26.5:1:29.5:1:1:1.58118:49:4:0.0131:0:2.5 -1 121484092 . G A 70 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00278;SOR=0.08162;LSEQ=ATTCTCAGTAACTTCCTTGT;RSEQ=TTGTGTGTATTCAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:3,2:17,14:0.1389:2,2:37.6:1:30.2:1:1:1.23:48.8:10:0.1389:0:1.6 0/1:157:2:1,1:95,60:0.0127:2,2:33:0:28.5:1:1:1.57849:49:4:0.0128:0:1 -1 121484097 . G C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CAGTAACTTCCTTGTGTTGT;RSEQ=TGTATTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:22,18:0:2,0:32:1:33:1:1:0:42.9:80:1:0:2.3 0/1:161:2:1,1:98,61:0.0124:2,2:20:0:33.5:1:1:1.6016:47:4:0.0126:0:7.5 -1 121484099 . G T 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.62986;SOR=0.61875;LSEQ=GTAACTTCCTTGTGTTGTGT;RSEQ=TATTCAACTCACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:21,18:0.0488:2,2:39:1:31.5:1:1:1.16227:45:4:0.05:0:3.5 0/1:163:5:2,3:97,61:0.0307:2,2:29.4:1:29.6:1:0.38186:2.3721:46.4:10:0.0313:0:2.8 -1 121484100 . T C 74 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58553;SOR=Inf;LSEQ=TAACTTCCTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:22,20:0:2,0:32:1:29.8:1:1:0:42.5:84:1:0:2.3 0/1:164:5:3,2:97,62:0.0305:2,2:34:1:32.2:1:1:1.04271:42.8:10:0.0309:0:4.2 -1 121484101 . A T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08144;SOR=2.75656;LSEQ=AACTTCCTTGTGTTGTGTGT;RSEQ=TTCAACTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:4:2,2:19,17:0.0952:2,2:39.3:1:30:1:1:1.11454:34:8:0.0952:0:5.3 0/1:164:37:24,13:73,49:0.2256:2,2:32.9:1:29.9:1:0.70107:1.24:44.6:17.5:0.2174:0:5.4 -1 121484106 . A G 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04078;SOR=0;LSEQ=CCTTGTGTTGTGTGTATTCA;RSEQ=CTCACAGAGTTGAACGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:21,19:0.0476:2,2:46.5:1:32.5:1:1:1.10263:27:4:0.0476:0:3 0/0:164:0:0,0:99,63:0:2,0:35:1:30:1:1:0:43.6:53:0.9876:0:2.5 -1 121484108 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTGTTGTGTGTATTCAAC;RSEQ=CACAGAGTTGAACGATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:0:2,0:32.1:1:30.8:1:1:0:42.7:86:1:0:2.3 0/1:166:2:1,1:100,64:0.012:2,2:19.5:1:28.5:1:1:1.55812:49:4:0.0123:0:2 -1 121484112 . A T 88 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.34911;SOR=Inf;LSEQ=GTTGTGTGTATTCAACTCAC;RSEQ=GAGTTGAACGATCCTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,21:0:2,0:30.4:1:30.1:1:1:0:42.8:21:1:0:2.3 0/1:168:7:4,3:98,63:0.0417:2,2:32.1:1:31.4:1:1:1.16558:42.4:14:0.0427:0:5.3 -1 121484113 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTGTGTATTCAACTCACA;RSEQ=AGTTGAACGATCCTTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,21:0:2,0:30:1:31.9:1:1:0:42.8:88:1:0:2.3 0/1:168:2:1,1:101,65:0.0119:2,2:28:1:30.5:1:1:1.5496:45:4:0.0119:0:1 -1 121484115 . G C 34 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0423;SOR=0;LSEQ=GTGTGTATTCAACTCACAGA;RSEQ=TTGAACGATCCTTTACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:21,19:0.0455:2,2:23:0:34:0:1:1.10263:50:4:0.0465:0:2.5 0/0:168:0:0,0:99,65:0:2,0:31.6:1:31.8:1:1:0:43.6:81:0.9759:0:2.6 -1 121484118 . G C 133 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26149;SOR=2.51124;LSEQ=TGTATTCAACTCACAGAGTT;RSEQ=AACGATCCTTTACACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:22,20:0.0455:2,2:39.5:1:31.5:1:1:1.09762:47:4:0.0465:0:6 0/1:168:18:10,8:92,58:0.1071:2,2:30.8:1:32.1:1:0.62134:1.26712:43.4:36:0.1111:0:2.1 -1 121484121 . C T 90 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04465;SOR=0.31687;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=GATCCTTTACACAGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:6:3,3:20,18:0.1364:2,2:34.2:1:30:1:1:1.10845:31:12:0.1429:0:3.7 0/1:169:8:4,4:96,61:0.0473:2,2:25:1:30.1:1:0.71326:1.56926:43.9:16:0.0479:0:3.5 -1 121484122 . GA TT 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TCCTTTACACAGAGCAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,21:0:2,0:26.8:1:30.5:1:1:0:42.8:88:1:0:2.3 0/1:169:2:2,0:100,65:0.0118:2,0:27:1:28.8:1:0.52168:0:28.5:4:0.012:0:4 -1 121484124 . T A 29 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0419;SOR=0;LSEQ=CAACTCACAGAGTTGAACGA;RSEQ=CCTTTACACAGAGCAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:22,20:0.0455:2,2:14:0:29.5:1:1:1.09762:21:4:0.0465:0:4.5 0/0:169:0:0,0:103,66:0:2,0:27:1:29.6:1:1:0:43.8:83.5:1:0:2.6 -1 121484125 . C G 164 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=AACTCACAGAGTTGAACGAT;RSEQ=CTTTACACAGAGCAGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,21:0:2,0:25.7:1:31:1:1:0:42.8:88:1:0:2.3 0/1:169:35:23,12:78,53:0.2071:2,2:33.8:1:32.1:1:0.56273:1.30:45.7:70:0.2083:0:5.7 -1 121484126 . C A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCACAGAGTTGAACGATC;RSEQ=TTTACACAGAGCAGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,21:0:2,0:25.3:1:31.4:1:1:0:42.8:88:1:0:2.3 0/1:168:3:2,1:98,62:0.0179:2,2:11.7:1:25.7:1:1:1.26:29.7:6:0.0186:0:3.3 -1 121484129 . TACACA T 66 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58122;SOR=Inf;LSEQ=CACAGAGTTGAACGATCCTT;RSEQ=GAGCAGACTTGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,21:0:2,0:23.3:1:27.9:1:1:0:42.8:21:1:0:2.3 0/1:165:4:2,2:100,61:0.0242:2,2:5.5:1:33:1:0.63668:1.63418:41:8:0.0245:0.0121:1.5 -1 121484133 . C G 85 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.99328;LSEQ=GAGTTGAACGATCCTTTACA;RSEQ=AGAGCAGACTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:22,20:0.0455:2,2:3.5:1:29.5:1:1:1.09762:51:4:0.0476:0:2 0/1:155:7:5,2:89,56:0.0452:2,2:16.4:1:30.3:1:0.70895:1.57:41.9:14:0.047:0:3 -1 121484137 . G A 28 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04134;SOR=0;LSEQ=TGAACGATCCTTTACACAGA;RSEQ=CAGACTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:18,17:0.0541:2,2:16.5:1:28:1:1:1.05721:27:4:0.0541:0:3 0/0:143:0:0,0:89,53:0:2,0:21.7:1:31.2:1:1:0:42.9:46.333:1:0:2.7 -1 121484138 . C T 140 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02924;SOR=4.52188;LSEQ=GAACGATCCTTTACACAGAG;RSEQ=AGACTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:0.0606:2,2:19.5:1:27:1:1:1.06462:47:4:0.0606:0:6 0/1:141:32:20,12:67,42:0.227:2,2:29.8:1:28.1:1:1:1.04:45.3:31:0.223:0:5.9 -1 121484139 . A G 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACGATCCTTTACACAGAGC;RSEQ=GACTTGAAACACTCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:0:2,0:24.4:1:29.5:1:1:0:42.2:32:1:0:2.5 0/1:140:4:2,2:83,51:0.0286:2,2:22.5:1:29:1:0.63806:1.62144:54.8:8:0.0296:0:1.3 -1 121484140 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGATCCTTTACACAGAGCA;RSEQ=ACTTGAAACACTCTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:0:2,0:23.8:1:31.2:1:1:0:42.2:66:1:0:2.5 0/1:138:2:1,1:83,52:0.0145:2,2:44.5:1:31.5:1:1:1.59046:48:4:0.0152:0:4 -1 121484141 . A G 88 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35885;SOR=Inf;LSEQ=CGATCCTTTACACAGAGCAG;RSEQ=CTTGAAACACTCTTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:0:2,0:23.2:1:29.5:1:1:0:42.2:66:1:0:2.5 0/1:133:8:5,3:75,49:0.0602:2,2:17:1:29.4:1:1:1.09:38.5:16:0.062:0:5.1 -1 121484142 . C T 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00838;SOR=0.31409;LSEQ=GATCCTTTACACAGAGCAGA;RSEQ=TTGAAACACTCTTTTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:13:7,6:8,9:0.4333:2,2:38:1:29.8:1:1:1.30:43.7:12:0.4138:0:2.9 0/1:130:25:15,10:64,41:0.1923:2,2:25.8:1:30:1:1:1.04036:39.2:50:0.1969:0:3 -1 121484144 . T A 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCTTTACACAGAGCAGACT;RSEQ=GAAACACTCTTTTTCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:0:2,0:23.5:1:29.6:1:1:0:40.7:60:1:0:2.6 0/1:120:2:0,2:73,41:0.0167:2,0:27.5:1:33:0:0.13538:0:43:4:0.0171:0:6 -1 121484151 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11574;SOR=0.13045;LSEQ=CACAGAGCAGACTTGAAACA;RSEQ=TCTTTTTCTGGAATTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:12,13:0.0741:2,2:20:1:29:1:1:1.08:51.5:4:0.0741:0:1 0/1:99:1:1,0:58,38:0.0101:2,0:5:0:29:0:1:0:39:2:0.0103:0:1 -1 121484153 . C G 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00691;SOR=0.27287;LSEQ=CAGAGCAGACTTGAAACACT;RSEQ=TTTTTCTGGAATTTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:14:7,7:5,7:0.5385:2,2:24.1:1:32.8:1:0.71269:1.38:41.3:28:0.5385:0:3.1 0/1:92:22:14,8:40,29:0.2391:2,2:17.3:1:31.3:1:0.80387:1.27:39.2:44:0.2472:0:2.4 -1 121484156 . T G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGACTTGAAACACTCTT;RSEQ=TTCTGGAATTTGCAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:16.8:1:30.2:1:1:0:42.3:52:1:0:2.8 0/1:75:2:1,1:45,28:0.0267:2,2:20.5:1:29:1:1:1.59658:29:4:0.0282:0:7 -1 121484159 . C G 113 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33324;SOR=2.4653;LSEQ=AGACTTGAAACACTCTTTTT;RSEQ=TGGAATTTGCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:9,9:0.1:2,0:2.5:1:31.5:1:0.47895:0:39:4:0.1053:0:3 0/1:60:13:10,3:28,18:0.2167:2,2:16.9:1:30.8:1:0.34387:2.12:43.7:26:0.2203:0:6.6 -1 121484162 . G T 122 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00407;SOR=Inf;LSEQ=CTTGAAACACTCTTTTTCTG;RSEQ=AATTTGCAAGTGGAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:0:2,0:19.2:1:29.9:1:1:0:42.6:8:1:0:2.7 0/1:59:20:15,5:23,16:0.339:2,2:17.4:1:28.3:1:0.26321:2.06:49:40:0.3448:0:6.2 -1 121484174 . G A 24 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTTCTGGAATTTGCAAGT;RSEQ=GAGATTTCAGCCGCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:17.2:1:31.4:1:1:0:41.2:26:1:0:2.8 0/1:35:2:2,0:20,12:0.0571:2,0:7:1:24.5:1:0.52941:0:43.5:4:0.0625:0:8 -1 121484188 . C T 29 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08615;SOR=0;LSEQ=GCAAGTGGAGATTTCAGCCG;RSEQ=TTTGTGGTAAATGGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:7:1:29.5:1:1:1.83:44.5:4:0.2857:0:3 0/0:18:0:0,0:9,9:0:2,0:15.3:1:32.1:1:1:0:41.1:36:1:0:4.1 -1 121484193 . T A 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.06284;LSEQ=TGGAGATTTCAGCCGCTTTG;RSEQ=GGTAAATGGTAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,0:0.6:0,2:29:1:31.7:1:1:0:40.7:6:0.75:0:3 1/0:13:8:4,4:2,2:0.6154:2,2:25.4:1:30.1:1:1:1:37.5:16:0.6154:0:4.5 -1 121484197 . A C 106 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTCAGCCGCTTTGTGGT;RSEQ=AATGGTAGAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:26.7:1:31.7:1:1:0:40.7:6:1:0:3.3 1/1:12:12:5,7:0,0:1:0,2:24:1:29.8:1:1:0:41.8:11:1:0:4.6 -1 121484201 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAGCCGCTTTGTGGTAAAT;RSEQ=GTAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.5:1:30.5:1:1:0:31:8:1:0:4.8 0/1:12:2:1,1:4,6:0.1667:2,2:36:0:30:1:1:1.45:37:4:0.1667:0:6 -1 121484211 . G T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGGTAAATGGTAGAAAAG;RSEQ=AAATATCTTCGTATAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.5:1:30.8:1:1:0:31:8:1:0:4.8 0/1:10:2:1,1:3,5:0.2:2,2:35.5:1:29:1:1:1.58:45:4:0.2222:0:4.5 -1 121484219 . T C 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09524;SOR=0;LSEQ=ATGGTAGAAAAGGAAATATC;RSEQ=TCGTATAAAAACTAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:20.5:1:32:1:1:1.7321:23:4:0.4:0:6.5 0/0:10:0:0,0:4,6:0:2,0:32:1:31.2:1:1:0:39.9:20:1:0:4.5 -1 121484221 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=GGTAGAAAAGGAAATATCTT;RSEQ=GTATAAAAACTAGATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:16.6:1:31.2:1:1:0:30.8:10:1:0:5.4 0/1:10:2:1,1:3,5:0.2:2,2:28.5:1:28:1:1:1.58:37:4:0.2:0:6 -1 121484222 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56044;SOR=0.40284;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGATAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:23.5:1:31.5:1:1:1.7321:23:4:0.4:0:6.5 0/1:10:2:1,1:3,5:0.2:2,2:39:0:31:0:1:1.58:47.5:4:0.2:0:3 -1 121484225 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGATAGAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:17.4:1:29.4:1:1:0:30.8:10:1:0:5.4 0/1:10:2:1,1:3,4:0.2:2,2:24.5:1:30.5:1:1:1.29:37:4:0.2:0:6 -1 121484229 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGGAAATATCTTCGTATAAA;RSEQ=ACTAGATAGAATGATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:2,2:0.2:2,0:17:0:34:0:1:0:30:2:0.2:0:8 0/1:10:2:1,1:3,5:0.2:2,2:32:0:33:1:1:1.58:45:4:0.2:0:4.5 -1 121484235 . A G 33 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=TATCTTCGTATAAAAACTAG;RSEQ=TAGAATGATTCTCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:35:0:33:0:1:0:23:4:0.5:0:6.5 0/0:9:0:0,0:4,5:0:2,0:20.7:1:30:1:1:0:39.4:18:1:0:4.4 -1 121484236 . T C 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=ATCTTCGTATAAAAACTAGA;RSEQ=AGAATGATTCTCAGAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:24:0:34:0:1:0:30:2:0.3333:0:8 1/0:9:7:3,4:1,1:0.7778:2,2:21.4:1:32.7:1:1:1.29098:40.1:14:0.7778:0:4 -1 121484237 . A T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTCGTATAAAAACTAGAT;RSEQ=GAATGATTCTCAGAAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:30.3:1:31.3:1:1:0:25.3:6:1:0:7 0/1:9:2:1,1:3,4:0.2222:2,2:12.5:1:27:1:1:1.29:37:4:0.25:0:6 -1 121484256 . C A 30 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TAGAATGATTCTCAGAAACT;RSEQ=CTTTATGATGTGTGCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:14:0:30:1:1:0:23:4:0.6667:0:6.5 0/0:4:0:0,0:2,2:0:2,0:5.3:1:30.8:1:1:0:46.3:8:1:0:3.8 -1 121484259 . T A 31 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=AATGATTCTCAGAAACTCCT;RSEQ=TATGATGTGTGCTTTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:11:0:31:1:1:0:23:4:0.6667:0:6.5 0/0:4:0:0,0:2,2:0:2,0:2.3:1:30:1:1:0:46.3:8:1:0:3.8 -1 121484261 . A G 52 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TGATTCTCAGAAACTCCTTT;RSEQ=TGATGTGTGCTTTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:22.3:1:33:1:1:0:25.3:6:1:0:7 0/0:1:0:0,0:1,0:0:0,0:1:0:23:0:1:0:49:2:1:0:3 -1 121484283 . T A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGTGTGCTTTCAACTCAC;RSEQ=GAGTTTAACATTTCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.3:1:30.3:1:1:0:30.7:6:1:0:7 1/1:3:3:3,0:0,0:1:0,0:8:1:30.7:1:1:0:34.3:6:1:0:5.7 -1 121484293 . A C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=TTCAACTCACTGAGTTTAAC;RSEQ=TTTCTTTTCATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:0,0:0.6:0,0:14.3:1:32.3:1:1:0:34:6:0.6:0:6.3 1/0:3:2:2,0:0,0:0.6667:0,0:21:0:31.5:1:1:0:31:4:0.6667:0:4.5 -1 121484316 . G T 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTCATAGAGCAGTTAG;RSEQ=AAACACTCTGTTTGTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:10,3:0,0:1:0,2:17.5:1:29.7:1:1:0:45.7:26:1:0:5.9 1/1:8:8:7,1:0,0:1:0,2:20.1:1:30.5:1:1:0:36.1:16:1:0:5.3 -1 121484330 . G A 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTAGGAAACACTCTGTTT;RSEQ=TAAAGTCTGCAAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:12,4:0,0:1:0,2:26.6:1:29.7:1:1:0:45.3:32:1:0:5.6 1/1:11:11:10,1:0,0:1:0,2:23.3:1:29.5:1:1:0:36.9:22:1:0:5.7 -1 121484359 . CC TT 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=GCAAGTGGATATTCAGACCC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:13,3:0.1111:2,2:37.5:1:32:1:0.40523:3.89444:50:4:0.1111:0:6 0/0:17:0:0,0:16,1:0:1,0:23.5:1:30.5:1:1:0:34.6:34:1:0:5.6 -1 121484360 . C T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22857;SOR=Inf;LSEQ=CAAGTGGATATTCAGACCCC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:15:12,3:0,0:0.8333:0,2:29.6:1:31.4:1:1:0:43.1:30:0.9375:0:5.2 1/1:17:17:16,1:0,0:1:0,1:23.8:1:31.4:1:1:0:34.6:34:1:0:5.6 -1 121484372 . G T 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29163;SOR=0.21231;LSEQ=CAGACCCCCTTGAGGCCTTC;RSEQ=TTGGAAACCGTATTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:2,1:13,2:0.1579:2,2:7.7:1:31:1:0.4424:2.98763:43.3:6:0.1579:0:4 0/1:27:1:1,0:25,1:0.037:1,0:47:0:30:0:1:0:40:2:0.0385:0:8 -1 121484381 . C G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15819;SOR=Inf;LSEQ=TTGAGGCCTTCGTTGGAAAC;RSEQ=GTATTTTTTCATATTATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:17:14,3:0,0:0.8947:0,2:20:1:29.9:1:1:0:40.5:34:0.8947:0:5.2 1/1:28:28:27,1:0,0:1:0,1:22.5:1:30.4:1:1:0:37.8:56:1:0:5.3 -1 121484383 . T G 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCCTTCGTTGGAAACCG;RSEQ=ATTTTTTCATATTATGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:17,3:0,0:1:0,2:18.4:1:31.1:1:1:0:42.2:40:1:0:5.2 1/1:35:35:30,5:0,0:1:0,2:18.9:1:30.9:1:1:0:42.2:70:1:0:4.8 -1 121484388 . T C 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.32812;SOR=Inf;LSEQ=CTTCGTTGGAAACCGTATTT;RSEQ=TTCATATTATGCTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:20:16,4:1,0:0.9524:0,2:18.5:1:31.8:1:1:0:43.1:40:0.9524:0:4.7 1/1:43:43:35,8:0,0:1:0,2:18.1:1:30.9:1:1:0:44.3:86:1:0:4.3 -1 121484397 . A C 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.15536;LSEQ=AAACCGTATTTTTTCATATT;RSEQ=TGCTAGACAGAAGAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:1,2:17,5:0.1154:2,2:9.3:1:30:1:0.17957:6.17652:59.7:6:0.1154:0:2.7 0/1:61:8:5,3:38,15:0.1311:2,2:16.4:1:31.3:1:0.68326:1.50896:48:16:0.1311:0:3.6 -1 121484398 . T G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0849;SOR=0;LSEQ=AACCGTATTTTTTCATATTA;RSEQ=GCTAGACAGAAGAATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:16,8:0.0769:2,0:8:1:33.5:1:1:0:30.5:4:0.0769:0:7 0/0:62:0:0,0:43,19:0:2,0:18.3:1:29.5:1:1:0:48.5:124:1:0:3.5 -1 121484403 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTTTTCATATTATGCTA;RSEQ=ACAGAAGAATTCTCAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:23,7:0:2,0:17.1:1:31.4:1:1:0:46:29:1:0:3.7 0/1:80:2:1,1:52,26:0.025:2,2:28.5:1:29.5:1:1:1.98146:43.5:4:0.025:0:4.5 -1 121484406 . A T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06754;SOR=0;LSEQ=TTTTTCATATTATGCTAGAC;RSEQ=GAAGAATTCTCAGTAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:22,6:0.0667:2,2:7:0:32:0:0.41839:3.47078:53:4:0.069:0:4 0/0:84:0:0,0:53,30:0:2,0:19.1:1:29.6:1:1:0:50.6:166:0.9881:0:3.2 -1 121484410 . G T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61338;SOR=0.5512;LSEQ=TCATATTATGCTAGACAGAA;RSEQ=AATTCTCAGTAATTTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:24,10:0.0556:2,2:2:0:30.5:1:0.52381:2.33552:60:4:0.0556:0:3.5 0/1:96:3:2,1:58,35:0.0313:2,2:17.7:1:28:1:1:1.20:53.3:6:0.0316:0:3.7 -1 121484416 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12509;SOR=0.23818;LSEQ=TATGCTAGACAGAAGAATTC;RSEQ=CAGTAATTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:3,0:24,12:0.0769:2,0:19.3:1:32.3:1:0.53912:0:32:6:0.0769:0:7.3 0/1:104:2:2,0:61,41:0.0192:2,0:16:1:32:0:0.51774:0:38:4:0.0194:0:7.5 -1 121484423 . T C 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.27215;SOR=Inf;LSEQ=GACAGAAGAATTCTCAGTAA;RSEQ=TTCCTTGTGTTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:42:29,13:0,1:0.9767:0,2:24.7:1:32.7:1:0.32558:0:50.6:84:0.9767:0:3.3 1/1:115:115:70,45:0,0:1:0,2:25:1:31.4:1:1:0:53.4:230:1:0:3 -1 121484427 . C T 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17372;SOR=0.17725;LSEQ=GAAGAATTCTCAGTAATTTC;RSEQ=TTGTGTTGTGTGTATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:29,13:0.0455:2,2:28:0:32:0:0.54017:2.18641:53:4:0.0455:0:4 0/0:121:1:0,1:72,48:0.0083:2,0:29:0:31:0:0.40496:0:43:2:0.0083:0:4 -1 121484430 . G C 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57395;SOR=Inf;LSEQ=GAATTCTCAGTAATTTCCTT;RSEQ=TGTTGTGTGTATTCAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:32,15:0:2,0:26.5:1:32.4:1:1:0:51.6:94:1:0:3 0/1:134:4:3,1:79,51:0.0299:2,2:26.5:1:31.8:1:1:1.93:57:8:0.0299:0:3.8 -1 121484434 . T G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.07044;SOR=0;LSEQ=TCTCAGTAATTTCCTTGTGT;RSEQ=GTGTGTATTCAACTGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:33,15:0.04:2,2:27:0:33.5:1:0.54204:2.16222:60:4:0.04:0:3.5 0/0:137:0:0,0:80,57:0:2,0:27.1:1:29.7:1:1:0:54.4:67.5:1:0:2.8 -1 121484436 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.06881;SOR=0;LSEQ=TCAGTAATTTCCTTGTGTTG;RSEQ=GTGTATTCAACTGACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:33,16:0.0392:2,2:29:0:32.5:1:1:2.03106:60:4:0.0392:0:3.5 0/0:142:0:0,0:82,60:0:2,0:27.2:1:29.8:1:1:0:54.4:284:1:0:2.8 -1 121484440 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60485;SOR=0.51165;LSEQ=TAATTTCCTTGTGTTGTGTG;RSEQ=ATTCAACTGACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:34,18:0.037:2,2:24.5:1:30.5:1:1:1.86542:60:4:0.037:0:4 0/1:156:3:2,1:88,65:0.0192:2,2:24.3:1:32.3:1:1:1.47:60:6:0.0194:0:5 -1 121484441 . A G 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.8894;LSEQ=AATTTCCTTGTGTTGTGTGT;RSEQ=TTCAACTGACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:3,0:32,19:0.0556:2,0:35.3:1:31.7:1:0.54423:0:32:6:0.0556:0:7.3 0/1:161:8:8,0:85,68:0.0497:2,0:19.5:1:33.1:1:0.02125:0:38.3:16:0.0503:0:7.1 -1 121484449 . G C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82032;SOR=0.88219;LSEQ=TGTGTTGTGTGTATTCAACT;RSEQ=ACAGAGTTGAACTTTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:8:8,0:37,25:0.1143:2,0:15.3:1:30.5:1:0.04381:0:43.1:16:0.1143:0:6.4 0/1:186:19:16,3:92,75:0.1022:2,2:15.4:1:31.9:1:0.01486:4.32:41.5:38:0.1033:0:5.7 -1 121484452 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTTGTGTGTATTCAACTGAC;RSEQ=GAGTTGAACTTTCATTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:47,27:0:2,0:23.8:1:31:1:1:0:54.4:148:1:0:2.8 0/1:201:2:1,1:115,84:0.01:2,2:19.5:1:29.5:1:1:1.36686:60:4:0.0101:0:3 -1 121484453 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTGTGTATTCAACTGACA;RSEQ=AGTTGAACTTTCATTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:48,28:0:2,0:23.5:1:32.3:1:1:0:54.6:152:1:0:2.7 0/1:201:2:1,1:115,84:0.01:2,2:43:1:29:1:1:1.36686:60:4:0.0101:0:2.5 -1 121484454 . A G 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.18788;SOR=0.18979;LSEQ=TGTGTGTATTCAACTGACAG;RSEQ=GTTGAACTTTCATTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:47,28:0.026:2,2:17.5:1:32:1:1:1.66676:60:4:0.0267:0:3.5 0/0:200:1:1,0:114,85:0.005:2,0:16:0:33:0:1:0:60:2:0.0051:0:6 -1 121484455 . G T 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1797;SOR=0.18335;LSEQ=GTGTGTATTCAACTGACAGA;RSEQ=TTGAACTTTCATTTAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:47,28:0.026:2,2:33.5:1:31:1:1:1.66676:53:4:0.026:0:4 0/0:207:1:1,0:117,88:0.0048:2,0:1:0:29:0:1:0:40:2:0.0049:0:7 -1 121484457 . T C 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57758;SOR=Inf;LSEQ=GTGTATTCAACTGACAGAGT;RSEQ=GAACTTTCATTTAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:49,29:0:2,0:24:1:30.5:1:1:0:54.7:156:1:0:2.7 0/1:208:4:2,2:116,88:0.0192:2,2:13:1:30.8:1:1:1.3164:58.8:8:0.0193:0:3.3 -1 121484461 . C A 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.57784;SOR=Inf;LSEQ=ATTCAACTGACAGAGTTGAA;RSEQ=TTTCATTTAGAGAGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:49,33:0:2,0:23.8:1:32.1:1:1:0:54.8:164:1:0:2.7 0/1:218:4:2,2:121,91:0.0183:2,2:21:1:29.8:1:1:1.32788:60:8:0.0185:0:4 -1 121484463 . T A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56531;SOR=Inf;LSEQ=TCAACTGACAGAGTTGAACT;RSEQ=TCATTTAGAGAGAGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:51,33:0:2,0:23.6:1:30.2:1:1:0:54.5:168:1:0:2.7 0/1:225:3:2,1:126,96:0.0133:2,2:19.3:1:27.3:1:1:1.52:50:6:0.0135:0:3.3 -1 121484470 . A G 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.07825;SOR=0.30569;LSEQ=ACAGAGTTGAACTTTCATTT;RSEQ=GAGAGAGCAGATTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:6:2,4:53,31:0.0667:2,2:24.5:1:30.5:1:0.20273:3.37108:60:12:0.0674:0:3 0/1:235:5:3,2:125,102:0.0213:2,2:33:1:29.8:1:1:1.22:58.6:10:0.0213:0:3 -1 121484471 . G C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.96125;LSEQ=CAGAGTTGAACTTTCATTTA;RSEQ=AGAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:10:9,1:44,33:0.1136:2,2:20.5:1:33.1:1:0.08102:6.64:41.6:20:0.1136:0:6.5 0/1:237:26:23,3:105,102:0.1097:2,2:24.8:1:32.3:1:0.00024:7.40:41.3:52:0.1111:0:6.1 -1 121484473 . G C 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.27939;SOR=0.68951;LSEQ=GAGTTGAACTTTCATTTAGA;RSEQ=AGAGCAGATTTGAAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:15:12,3:43,33:0.1648:2,2:20.1:1:32.7:1:0.14717:3.04:42.1:30:0.1648:0:6.2 0/1:234:28:24,4:100,105:0.1197:2,2:25.1:1:32.1:1:2e-04:6.26:41.3:56:0.1207:0:6.1 -1 121484477 . G T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57982;SOR=Inf;LSEQ=TGAACTTTCATTTAGAGAGA;RSEQ=CAGATTTGAAACACTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:58,39:0:2,0:21.8:1:32:1:1:0:54.7:194:1:0:2.7 0/1:249:4:2,2:132,112:0.0161:2,2:31.8:1:29.3:1:1:1.17778:60:8:0.0163:0:3.3 -1 121484480 . G C 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06261;SOR=0.1216;LSEQ=ACTTTCATTTAGAGAGAGCA;RSEQ=ATTTGAAACACTGTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:3:2,1:54,38:0.0316:2,2:14.3:1:33.3:1:1:1.40:60:6:0.0316:0:1.7 0/0:255:1:1,0:135,117:0.0039:2,0:11:0:33:0:1:0:60:2:0.004:0:2 -1 121484482 . T C 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91389;LSEQ=TTTCATTTAGAGAGAGCAGA;RSEQ=TTGAAACACTGTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:2,0:52,37:0.0215:2,0:25.5:1:33.5:1:0.51209:0:43.5:4:0.0215:0:6.5 0/1:254:5:3,2:130,111:0.0197:2,2:11.8:1:30.6:1:1:1.28:43.6:10:0.0202:0:3.6 -1 121484484 . T G 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70897;SOR=0.74466;LSEQ=TCATTTAGAGAGAGCAGATT;RSEQ=GAAACACTGTTTTTGTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:3:3,0:53,39:0.0313:2,0:17:1:33.3:1:0.26629:0:41.7:6:0.0313:0:5.7 0/1:256:6:4,2:134,116:0.0234:2,2:27.5:1:31.7:1:0.68963:1.73:41.5:12:0.0236:0:5.5 -1 121484486 . A T 99 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19285;SOR=4.19591;LSEQ=ATTTAGAGAGAGCAGATTTG;RSEQ=AACACTGTTTTTGTGGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:1,0:56,40:0.0103:2,0:16:0:26:0:1:0:60:2:0.0103:0:3 0/1:262:11:4,7:135,113:0.042:2,2:27.8:1:28.8:1:0.35529:2.08484:59.5:22:0.0425:0:3 -1 121484487 . A T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.11754;LSEQ=TTTAGAGAGAGCAGATTTGA;RSEQ=ACACTGTTTTTGTGGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:1:0,1:58,40:0.0101:2,0:1:0:24:0:0.41414:0:60:2:0.0101:0:3 0/1:266:3:1,2:141,122:0.0113:2,2:27.3:1:26:1:0.59976:2.30441:60:6:0.0114:0:2.3 -1 121484489 . C T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57623;SOR=Inf;LSEQ=TAGAGAGAGCAGATTTGAAA;RSEQ=ACTGTTTTTGTGGTATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:57,39:0:2,0:24.1:1:31.8:1:1:0:55:95:1:0:2.7 0/1:275:4:1,3:144,127:0.0145:2,2:30.3:1:28.8:1:0.34701:3.38759:60:8:0.0147:0:2.5 -1 121484490 . A T 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16387;SOR=0.17128;LSEQ=AGAGAGAGCAGATTTGAAAC;RSEQ=CTGTTTTTGTGGTATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:0,2:57,37:0.0208:2,0:16.5:1:28.5:1:0.1625:0:28.5:4:0.0208:0:4.5 0/0:277:1:0,1:143,126:0.0036:2,0:13:0:31:0:0.47037:0:60:2:0.0036:0:2 -1 121484492 . T G 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.57095;SOR=Inf;LSEQ=AGAGAGCAGATTTGAAACAC;RSEQ=GTTTTTGTGGTATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:58,39:0:2,0:24.5:1:30.7:1:1:0:55.1:194:1:0:2.8 0/1:276:3:2,1:144,129:0.0109:2,2:30:1:22.3:1:1:1.79:60:2:0.0074:0:3.7 -1 121484493 . G C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.27233;SOR=0.71217;LSEQ=GAGAGCAGATTTGAAACACT;RSEQ=TTTTTGTGGTATTTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:20:16,4:42,34:0.2083:2,2:28.1:1:31.2:1:0.07037:3.20:39.2:19:0.2:0:5.9 0/1:279:44:37,7:106,124:0.1577:2,2:23.9:1:31.7:1:0:6.15:40.9:88:0.1594:0:5.5 -1 121484499 . G A 78 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68673;SOR=2.55208;LSEQ=AGATTTGAAACACTGTTTTT;RSEQ=TGGTATTTGCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:1,0:59,39:0.01:2,0:1:0:23:0:1:0:60:2:0.01:0:4 0/1:278:7:4,3:141,128:0.0252:2,2:25.3:1:28.1:1:1:1.21:53.4:14:0.0254:0:3.7 -1 121484502 . GT CA 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.42519;LSEQ=TTTGAAACACTGTTTTTGTG;RSEQ=ATTTGCAAGTGGAGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:1:1,0:57,40:0.0102:2,0:36:0:32:0:1:0:24:2:0.0103:0:7 0/1:276:4:1,3:144,123:0.0145:2,2:16.8:1:32.6:1:0.34066:3.49709:51:8:0.0149:0:3.8 -1 121484503 . T A 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73344;SOR=0.65218;LSEQ=TTGAAACACTGTTTTTGTGG;RSEQ=ATTTGCAAGTGGAGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:101:99:58,41:0,0:0.9802:0,2:25.9:1:30:1:1:0:53.7:98:0.9899:0:2.8 1/1:266:258:137,121:1,1:0.9699:2,2:25.2:1:29.1:1:1:1.13:55:85:0.9922:0:2.6 -1 121484511 . A G 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23435;SOR=0.39592;LSEQ=CTGTTTTTGTGGTATTTGCA;RSEQ=GTGGAGATTTCAAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:4:2,2:59,48:0.036:2,2:27.5:1:30.8:1:1:1.22686:46:8:0.0367:0:4.5 0/1:275:4:2,2:141,130:0.0145:2,2:21.5:1:29.3:1:1:1.08428:44:8:0.0148:0:6.3 -1 121484512 . G T 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06996;SOR=0.12881;LSEQ=TGTTTTTGTGGTATTTGCAA;RSEQ=TGGAGATTTCAAGCGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:2,1:56,48:0.0275:2,2:36:1:32:1:1:1.71:60:6:0.0275:0:2.3 0/0:277:1:0,1:134,128:0.0036:2,0:49:0:29:0:0.49049:0:60:2:0.0037:0:3 -1 121484513 . T G 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32739;SOR=Inf;LSEQ=GTTTTTGTGGTATTTGCAAG;RSEQ=GGAGATTTCAAGCGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:59,50:0:2,0:26.1:1:29.4:1:1:0:50.7:53.5:0.9907:0:3.1 0/1:277:5:2,3:142,130:0.0181:2,2:33.2:1:31.2:1:0.67358:1.63555:60:10:0.0182:0:3 -1 121484514 . G T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56331;SOR=Inf;LSEQ=TTTTTGTGGTATTTGCAAGT;RSEQ=GAGATTTCAAGCGCTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:56,50:0:2,0:26.5:1:31.3:1:1:0:50.7:105:0.9813:0:3.2 0/1:280:3:2,1:143,132:0.0107:2,2:29.3:1:29.7:1:1:1.84:52:6:0.0109:0:5.3 -1 121484516 . A T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19848;SOR=0.19877;LSEQ=TTTGTGGTATTTGCAAGTGG;RSEQ=GATTTCAAGCGCTTTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:57,50:0.0182:2,2:29.5:1:31:1:1:1.13863:60:4:0.0183:0:2.5 0/0:274:1:0,1:142,131:0.0036:2,0:46:0:30:0:0.48175:0:60:2:0.0037:0:5 -1 121484519 . T C 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31239;SOR=0.49088;LSEQ=GTGGTATTTGCAAGTGGAGA;RSEQ=TTCAAGCGCTTTGGGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:2,3:59,50:0.0439:2,2:31.4:1:30.6:1:0.66217:1.76115:40:10:0.0446:0:4 0/1:273:6:4,2:140,127:0.022:2,2:19.5:1:30:1:0.68691:1.81:48.8:12:0.0223:0:5 -1 121484520 . T A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58371;SOR=0.40982;LSEQ=TGGTATTTGCAAGTGGAGAT;RSEQ=TCAAGCGCTTTGGGGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:60,52:0.0175:2,2:31.5:1:27.5:1:1:1.15239:54:4:0.0175:0:3.5 0/0:276:2:1,1:142,130:0.0072:2,2:39.5:1:29:1:1:1.09195:60:4:0.0073:0:3 -1 121484522 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08855;SOR=0;LSEQ=GTATTTGCAAGTGGAGATTT;RSEQ=AAGCGCTTTGGGGCCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:60,54:0.0171:2,2:41.5:1:32:1:1:1.1101:60:4:0.0172:0:2 0/0:275:0:0,0:143,132:0:2,0:25:1:31.3:1:1:0:52.3:274:1:0:2.8 -1 121484526 . C G 78 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00075;SOR=0;LSEQ=TTGCAAGTGGAGATTTCAAG;RSEQ=GCTTTGGGGCCAAAGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:6:2,4:60,56:0.0492:2,2:20:1:30.5:1:0.43555:2.12991:50.2:12:0.0492:0:4 0/0:277:0:0,0:144,131:0:2,0:24.2:1:30.7:1:1:0:51.9:90.667:0.9963:0:2.8 -1 121484531 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.55407;SOR=Inf;LSEQ=AGTGGAGATTTCAAGCGCTT;RSEQ=GGGGCCAAAGGCAGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:68,62:0:2,0:23.9:1:29.8:1:1:0:49.4:64:1:0:3.2 0/1:270:3:2,1:137,130:0.0111:2,2:14.7:1:30.7:1:1:1.89:60:6:0.0115:0:2 -1 121484532 . GG AA 22 v4;q23;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10617;SOR=0;LSEQ=GTGGAGATTTCAAGCGCTTT;RSEQ=GGCCAAAGGCAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:68,59:0.0153:2,2:23:1:22.8:1:1:1.15127:43.5:4:0.0155:0:5 0/0:270:0:0,0:140,128:0:2,0:24.7:1:30.9:1:1:0:51.5:267:0.9926:0:2.8 -1 121484533 . G A 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13018;SOR=0.69538;LSEQ=TGGAGATTTCAAGCGCTTTG;RSEQ=GGCCAAAGGCAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:46:30,16:39,45:0.3459:2,2:20.5:1:29.8:1:0.04508:2.15:39.7:92:0.3538:0:4.8 0/1:268:72:51,21:89,103:0.2687:2,2:24.2:1:29:1:0.00049:2.80:40.8:144:0.2727:0:4.6 -1 121484535 . G T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55392;SOR=Inf;LSEQ=GAGATTTCAAGCGCTTTGGG;RSEQ=CCAAAGGCAGAAAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:71,64:0:2,0:23.4:1:31.1:1:1:0:49:32.75:1:0:3.3 0/1:267:3:2,1:139,123:0.0112:2,2:24.3:1:29:1:1:1.77:46.7:6:0.0115:0:4.7 -1 121484536 . C A 27 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2631;SOR=0.25185;LSEQ=AGATTTCAAGCGCTTTGGGG;RSEQ=CAAAGGCAGAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:71,62:0.0146:2,2:25.5:1:27:1:1:1.14401:40.5:4:0.0148:0:4.5 0/0:270:1:0,1:143,124:0.0037:2,0:8:0:31:0:0.46642:0:60:2:0.0038:0:4 -1 121484537 . C A 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34269;SOR=0.3405;LSEQ=GATTTCAAGCGCTTTGGGGC;RSEQ=AAAGGCAGAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:2,1:73,62:0.0214:2,2:16.7:1:30.7:1:1:1.69:48.7:6:0.0216:0:2 0/0:271:2:1,1:143,125:0.0074:2,2:38:0:31.5:1:1:1.14343:60:4:0.0076:0:2.5 -1 121484540 . A G 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.85488;LSEQ=TTCAAGCGCTTTGGGGCCAA;RSEQ=GGCAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:1,2:74,66:0.0208:2,2:25.7:1:31:1:0.60456:2.23017:47.7:6:0.0211:0:3.7 0/1:280:5:3,2:147,127:0.0179:2,2:23:1:32:1:1:1.29:53.6:10:0.0182:0:3.4 -1 121484541 . G A 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56724;SOR=0.67457;LSEQ=TCAAGCGCTTTGGGGCCAAA;RSEQ=GCAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:6:3,3:74,64:0.0414:2,2:22:1:29.5:1:1:1.15508:40.5:12:0.0414:0:7.2 0/1:283:8:5,3:147,125:0.0283:2,2:15.1:1:31.3:1:0.73082:1.42:42:16:0.0287:0:3.8 -1 121484543 . C T 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18451;SOR=Inf;LSEQ=AAGCGCTTTGGGGCCAAAGG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:76,69:0:2,0:22.1:1:31.8:1:1:0:48.6:71.5:0.9931:0:3.3 0/1:295:6:1,5:154,135:0.0203:2,2:17.3:1:27.7:1:0.10518:5.67468:46.3:12:0.0206:0:5.5 -1 121484549 . A T 44 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33565;SOR=0.31896;LSEQ=TTTGGGGCCAAAGGCAGAAA;RSEQ=GGAAATATCTTCGTATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:1,2:76,70:0.0201:2,2:12:1:28.3:1:0.61006:2.16052:34:6:0.0205:0:4.7 0/0:308:2:0,2:163,143:0.0065:2,0:1:0:25.5:1:0.22082:0:46.5:4:0.0066:0:5 -1 121484550 . G A 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25494;SOR=0.24515;LSEQ=TTGGGGCCAAAGGCAGAAAA;RSEQ=GAAATATCTTCGTATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:0,2:79,72:0.0131:2,0:20:1:32.5:1:0.23228:0:40.5:4:0.0133:0:5 0/0:310:1:0,1:160,141:0.0032:2,0:9:0:25:0:0.4702:0:24:2:0.0033:0:6 -1 121484553 . A T 63 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.97188;LSEQ=GGGCCAAAGGCAGAAAAGGA;RSEQ=ATATCTTCGTATAAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:0,1:79,75:0.0065:2,0:1:0:30:0:0.49032:0:60:2:0.0065:0:3 0/1:316:4:3,1:164,147:0.0127:2,2:11.3:1:31.5:1:0.62536:2.68:37.3:8:0.0127:0:4 -1 121484554 . A G 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.10543;SOR=0;LSEQ=GGCCAAAGGCAGAAAAGGAA;RSEQ=TATCTTCGTATAAAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:77,71:0.0132:2,2:44:0:32.5:1:1:1.0839:39:4:0.0135:0:5.5 0/0:313:0:0,0:168,145:0:2,0:21:1:29.6:1:1:0:50.3:103.333:1:0:3.3 -1 121484556 . A C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.10968;SOR=0;LSEQ=CCAAAGGCAGAAAAGGAAAT;RSEQ=TCTTCGTATAAAAACTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:78,74:0.013:2,2:44:1:32:1:1:1.05372:39:4:0.013:0:5.5 0/0:310:0:0,0:164,142:0:2,0:21.5:1:28.6:1:1:0:50.2:101:0.9902:0:3.3 -1 121484558 . C T 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0322;LSEQ=AAAGGCAGAAAAGGAAATAT;RSEQ=TTCGTATAAAAACTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:7:4,3:75,70:0.0461:2,2:31:1:30.3:1:1:1.24:39.1:14:0.0464:0:7.1 0/1:316:15:11,4:159,141:0.0475:2,2:12.7:1:29.5:1:0.18366:2.43:41.9:30:0.0478:0:6.4 -1 121484561 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59468;SOR=0.46188;LSEQ=GGCAGAAAAGGAAATATCTT;RSEQ=GTATAAAAACTAGACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:79,68:0.0133:2,2:5:1:29.5:1:1:1.16059:60:4:0.0138:0:2 0/0:323:2:1,1:169,151:0.0062:2,2:35:1:29:1:1:1.11881:50:4:0.0062:0:3.5 -1 121484562 . G C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0989;LSEQ=GCAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:8:5,3:75,67:0.053:2,2:30.1:1:32.1:1:0.72416:1.49:40.1:16:0.0537:0:7 0/1:328:19:13,6:155,144:0.0579:2,2:13.1:1:29.8:1:0.23557:2.01:45.4:18:0.0554:0:5.9 -1 121484564 . A T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17902;SOR=1.72424;LSEQ=AGAAAAGGAAATATCTTCGT;RSEQ=TAAAAACTAGACAGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:10:8,2:74,70:0.0649:2,2:25:1:30.9:1:0.10534:3.75:47.1:20:0.0654:0:5.1 0/1:327:35:21,14:152,140:0.107:2,2:22.2:1:29.9:1:0.47403:1.38:50.9:70:0.1077:0:4.4 -1 121484565 . T G 81 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0137;SOR=0.19194;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGACAGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:7:5,2:75,69:0.0461:2,2:16:1:29.1:1:0.44805:2.29:45.3:6:0.04:0:4.1 0/0:328:3:1,2:173,152:0.0091:2,2:18:1:30.3:1:0.60226:2.27078:56:6:0.0092:0:3.7 -1 121484566 . A C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23404;SOR=1.63003;LSEQ=AAAAGGAAATATCTTCGTAT;RSEQ=AAAACTAGACAGAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:10:8,2:73,68:0.0654:2,2:25:1:31.6:1:0.10704:3.70:47.1:20:0.0658:0:5.1 0/1:332:34:20,14:153,139:0.1024:2,2:23:1:31.4:1:0.58664:1.30:51.1:68:0.1024:0:4.4 -1 121484571 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59051;SOR=0.44329;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATCATTCTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:78,72:0.0132:2,2:32.5:1:30.5:1:1:1.08274:46:4:0.0134:0:3.5 0/0:341:2:1,1:176,159:0.0059:2,2:17.5:1:29:1:1:1.10658:60:4:0.0059:0:3 -1 121484572 . TA CC 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08374;SOR=0.37696;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=GACAGAATCATTCTCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:8:3,5:76,66:0.0526:2,2:28.9:1:30.9:1:0.47729:1.91092:36.6:16:0.0537:0:3.5 0/1:342:7:4,3:173,155:0.0205:2,2:34.1:1:30.3:1:1:1.19:36.1:14:0.0207:0:4.4 -1 121484573 . A C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13572;SOR=0.49421;LSEQ=AATATCTTCGTATAAAAACT;RSEQ=GACAGAATCATTCTCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:9:4,5:75,64:0.0577:2,2:25.2:1:30.6:1:0.73405:1.46104:43.6:18:0.0616:0:6.8 0/1:341:10:7,3:169,150:0.0293:2,2:23.7:1:31.3:1:0.34844:2.07:45:20:0.0303:0:6.8 -1 121484576 . C G 33 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59053;SOR=0.44332;LSEQ=ATCTTCGTATAAAAACTAGA;RSEQ=AGAATCATTCTCAGTAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:82,72:0.0128:2,2:46.5:1:33.5:1:1:1.13794:34.5:4:0.013:0:6.5 0/0:350:2:1,1:185,163:0.0057:2,2:24.5:1:33:1:1:1.13456:50:4:0.0057:0:3 -1 121484578 . G A 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87595;LSEQ=CTTCGTATAAAAACTAGACA;RSEQ=AATCATTCTCAGTAACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:83,72:0.0127:2,2:11:1:31:0:1:1.15173:60:4:0.013:0:2.5 0/1:358:4:3,1:185,167:0.0112:2,2:18.3:1:26.8:1:0.62527:2.70:53.5:8:0.0114:0:4.5 -1 121484582 . C G 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88408;LSEQ=GTATAAAAACTAGACAGAAT;RSEQ=ATTCTCAGTAACTGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:3:3,0:82,74:0.0189:2,0:24.3:1:25.3:1:0.24887:0:46.7:2:0.0128:0:5 0/1:359:6:2,4:187,165:0.0167:2,2:23.7:1:32:1:0.42706:2.26164:47.7:12:0.0169:0:3.7 -1 121484583 . A T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55647;SOR=1.34929;LSEQ=TATAAAAACTAGACAGAATC;RSEQ=TTCTCAGTAACTGCTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:8:3,5:82,71:0.0497:2,2:24.8:1:30.9:1:0.4774:1.91712:46:16:0.05:0:6.4 0/1:364:24:14,10:178,162:0.0659:2,2:25.6:1:30.9:1:0.67397:1.27:45.4:48:0.0665:0:5.7 -1 121484588 . C G 88 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18568;SOR=4.10197;LSEQ=AAACTAGACAGAATCATTCT;RSEQ=AGTAACTGCTCTGTGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:1:1,0:87,76:0.0061:2,0:35:0:30:0:1:0:41:2:0.0062:0:5 0/1:366:9:5,4:187,170:0.0246:2,2:34.9:1:28:1:1:1.14:47.6:3.5:0.0194:0:5.4 -1 121484591 . T A 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18454;SOR=0;LSEQ=CTAGACAGAATCATTCTCAG;RSEQ=AACTGCTCTGTGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:165:165:89,76:0,0:1:0,2:27.2:1:30.3:1:1:0:48.2:81.5:1:0:3.6 1/1:374:368:193,175:0,0:0.984:0,2:27.4:1:29.4:1:1:0:51.3:183:0.9892:0:3.6 -1 121484594 . C A 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33073;SOR=Inf;LSEQ=GACAGAATCATTCTCAGTAA;RSEQ=TGCTCTGTGATGTGTGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:91,80:0:2,0:26.4:1:32.2:1:1:0:48.1:84.5:0.9941:0:3.6 0/1:383:5:2,3:195,180:0.0131:2,2:17:1:30.8:1:0.67504:1.62293:48.2:10:0.0131:0:3.6 -1 121484596 . G C 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17643;SOR=0.29744;LSEQ=CAGAATCATTCTCAGTAACT;RSEQ=CTCTGTGATGTGTGCGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:2,1:92,77:0.0173:2,2:30.7:1:31.3:1:1:1.67:53.3:6:0.0176:0:4.7 0/0:384:2:1,1:198,180:0.0052:2,2:22.5:1:33:0:1:1.09972:38:4:0.0053:0:5 -1 121484599 . CT GC 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.70068;SOR=0.92998;LSEQ=AATCATTCTCAGTAACTGCT;RSEQ=GTGATGTGTGCGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:61:27,34:64,44:0.3506:2,2:24.4:1:31.7:1:0.07717:1.82501:46.7:60:0.3571:0.0345:3.1 0/1:383:128:68,60:128,118:0.3342:2,2:28.4:1:31.6:1:0.91316:1.04:48.3:256:0.3395:0.0052:3.3 -1 121484602 . T C 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20918;SOR=1.26586;LSEQ=CATTCTCAGTAACTGCTCTG;RSEQ=GATGTGTGCGTTCAACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:72:42,30:46,53:0.3934:2,2:29.1:1:31.1:1:0.163:1.61:54.2:71:0.3944:0:3 0/1:408:184:96,88:103,98:0.451:2,2:27.3:1:30.5:1:0.91872:1.04:56:60.333:0.4536:0:3 -1 121484605 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.09005;SOR=0;LSEQ=TCTCAGTAACTGCTCTGTGA;RSEQ=GTGTGCGTTCAACTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:95,87:0.0109:2,2:35.5:1:30:1:1:1.09142:60:4:0.011:0:4 0/0:428:0:0,0:217,211:0:2,0:26.2:1:29.6:1:1:0:52.8:70.333:1:0:3.1 -1 121484608 . G A 57 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00841;SOR=0;LSEQ=CAGTAACTGCTCTGTGATGT;RSEQ=TGCGTTCAACTCTCAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:4:3,1:96,90:0.0211:2,2:16:1:28.8:1:0.62236:2.80:54.5:8:0.0213:0:6.8 0/0:434:0:0,0:218,211:0:2,0:26.3:1:31.2:1:1:0:52.9:106.25:0.9884:0:3.1 -1 121484611 . C G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9953;LSEQ=TAACTGCTCTGTGATGTGTG;RSEQ=GTTCAACTCTCAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:4:2,2:97,88:0.0208:2,2:10:1:26.8:1:1:1.1017:45.3:3:0.0161:0:4 0/1:434:9:4,5:219,202:0.0207:2,2:30:1:28.4:1:0.74361:1.35423:50.4:8:0.0185:0:4.7 -1 121484613 . T A 70 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32996;SOR=Inf;LSEQ=ACTGCTCTGTGATGTGTGCG;RSEQ=TCAACTCTCAGAGTTTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:102,92:0:2,0:24.4:1:29.9:1:1:0:51.8:96:1:0:3 0/1:442:5:2,3:222,211:0.0113:2,2:37.4:1:30.2:1:0.67917:1.57656:46.8:10:0.0115:0:4.4 -1 121484616 . A C 63 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00857;SOR=0;LSEQ=GCTCTGTGATGTGTGCGTTC;RSEQ=ACTCTCAGAGTTTAACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:4:3,1:101,92:0.0203:2,2:20:1:31.8:1:0.62353:2.72:54.5:8:0.0207:0:6.8 0/0:447:0:0,0:228,219:0:2,0:25.9:1:29.7:1:1:0:53.9:88.4:1:0:3.1 -1 121484617 . A G 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22325;SOR=0.21933;LSEQ=CTCTGTGATGTGTGCGTTCA;RSEQ=CTCTCAGAGTTTAACTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:103,93:0.0101:2,2:11.5:1:30.5:1:1:1.10695:60:4:0.0102:0:3 0/0:449:1:0,1:228,218:0.0022:2,0:19:0:33:0:0.48993:0:60:2:0.0023:0:3 -1 121484619 . T C 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22645;SOR=0.22193;LSEQ=CTGTGATGTGTGCGTTCAAC;RSEQ=CTCAGAGTTTAACTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:104,93:0.0101:2,2:13.5:1:31:1:1:1.11765:60:4:0.0102:0:1.5 0/0:446:1:0,1:226,217:0.0022:2,0:17:0:26:0:0.49099:0:60:2:0.0023:0:5 -1 121484620 . C A 57 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03395;SOR=0.11045;LSEQ=TGTGATGTGTGCGTTCAACT;RSEQ=TCAGAGTTTAACTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:4:3,1:102,91:0.0201:2,2:22:1:28.5:1:0.62447:2.66:54.5:8:0.0203:0:6.8 0/0:444:1:1,0:226,217:0.0023:2,0:42:0:28:0:1:0:47:2:0.0023:0:4 -1 121484621 . T A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17115;SOR=0.68749;LSEQ=GTGATGTGTGCGTTCAACTC;RSEQ=CAGAGTTTAACTTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:27:15,12:91,82:0.135:2,2:29.1:1:30:1:0.83765:1.13:38.8:54:0.1371:0:4 0/1:444:43:20,23:206,195:0.0968:2,2:30.4:1:28.9:1:0.63081:1.21434:43.2:42:0.0966:0:4.9 -1 121484624 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09515;SOR=0;LSEQ=ATGTGTGCGTTCAACTCTCA;RSEQ=AGTTTAACTTTTCTTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:103,92:0.0101:2,2:33:1:31:1:1:1.11892:60:4:0.0104:0:4 0/0:445:0:0,0:224,220:0:2,0:25.5:1:31.3:1:1:0:54.4:147:0.9977:0:3.1 -1 121484625 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09529;SOR=0;LSEQ=TGTGTGCGTTCAACTCTCAG;RSEQ=GTTTAACTTTTCTTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:107,92:0.01:2,2:14:1:29.5:1:1:1.16216:60:4:0.0102:0:2.5 0/0:449:0:0,0:229,219:0:2,0:25.2:1:29.4:1:1:0:54.4:36.333:0.9977:0:3.1 -1 121484626 . G T 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22462;SOR=0.22044;LSEQ=GTGTGCGTTCAACTCTCAGA;RSEQ=TTTAACTTTTCTTTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:106,89:0.0101:2,2:28:1:29:1:1:1.18995:45.5:4:0.0102:0:4 0/0:449:1:1,0:225,218:0.0022:2,0:13:0:32:0:1:0:43:2:0.0022:0:5 -1 121484629 . TAAC T 44 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.0284;SOR=0;LSEQ=TGCGTTCAACTCTCAGAGTT;RSEQ=TTTTCTTTTCATTCAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:3:1,2:105,91:0.0151:2,2:15:1:28:1:0.59995:2.29828:55.3:6:0.0152:0.0101:3.3 0/0:451:0:0,0:229,218:0:2,0:24.2:1:28.7:1:1:0:54.3:88.4:0.991:0:3.1 -1 121484633 . T C 75 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18561;SOR=Inf;LSEQ=TTCAACTCTCAGAGTTTAAC;RSEQ=TTTCTTTTCATTCAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:104,91:0:2,0:23.7:1:30.4:1:1:0:53.6:64:0.9897:0:3 0/1:455:6:3,3:226,223:0.0132:2,2:7.5:1:29.3:1:1:1.01342:47.5:12:0.0133:0:5.2 -1 121484636 . T G 82 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.01274;SOR=0.14575;LSEQ=AACTCTCAGAGTTTAACTTT;RSEQ=CTTTTCATTCAGCAGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:6:3,3:97,93:0.0306:2,2:26.2:1:31.8:1:1:1.0428:57.2:12:0.0311:0:2.5 0/0:438:2:1,1:215,219:0.0046:2,2:24:1:31.5:1:1:1.02:60:4:0.0046:0:4 -1 121484637 . C G 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22631;SOR=0.22179;LSEQ=ACTCTCAGAGTTTAACTTTT;RSEQ=TTTTCATTCAGCAGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:98,93:0.0103:2,2:15.5:1:29:0:1:1.0535:50.5:4:0.0104:0:4.5 0/0:435:1:1,0:213,219:0.0023:2,0:45:0:30:0:0.49423:0:34:2:0.0023:0:3 -1 121484641 . T A 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.18114;SOR=Inf;LSEQ=TCAGAGTTTAACTTTTCTTT;RSEQ=CATTCAGCAGTTTGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:100,98:0:2,0:23.7:1:29.7:1:1:0:53.1:65:1:0:3.1 0/1:416:5:3,2:197,212:0.012:2,2:18.4:1:26.2:1:0.676:1.61:46.4:10:0.0122:0:4.8 -1 121484643 . A T 26 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59706;SOR=0.47108;LSEQ=AGAGTTTAACTTTTCTTTTC;RSEQ=TTCAGCAGTTTGGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:98,93:0.0104:2,2:33.5:1:33:1:1:1.0535:60:4:0.0105:0:6.5 0/0:408:2:1,1:196,208:0.0049:2,2:12.5:1:26.5:1:1:1.06:60:4:0.0049:0:4.5 -1 121484650 . A G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51768;SOR=1.14097;LSEQ=AACTTTTCTTTTCATTCAGC;RSEQ=GTTTGGAAACACTCTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:66:36,30:54,58:0.3607:2,2:24.5:1:30.2:1:0.44094:1.29:52.5:132:0.3646:0:3.8 0/1:383:150:77,73:105,126:0.3916:2,2:24.6:1:29.4:1:0.29411:1.26:52.6:74:0.3905:0:3.7 -1 121484651 . G A 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.59654;SOR=0.46911;LSEQ=ACTTTTCTTTTCATTCAGCA;RSEQ=TTTGGAAACACTCTGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:2,0:90,88:0.0111:2,0:8:1:25.5:1:0.49745:0:60:4:0.0111:0:3.5 0/0:382:2:2,0:178,197:0.0052:2,0:1:0:26.5:1:0.2273:0:54:4:0.0053:0:2.5 -1 121484654 . T A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.30938;SOR=Inf;LSEQ=TTTCTTTTCATTCAGCAGTT;RSEQ=GGAAACACTCTGTTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:89,89:0:2,0:25.9:1:29.8:1:1:0:52.7:88:1:0:3.4 0/1:369:4:3,1:168,197:0.0108:2,2:8:1:25.8:1:0.34031:3.51:51.5:8:0.0111:0:3 -1 121484655 . G A 22 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59752;SOR=0.47324;LSEQ=TTCTTTTCATTCAGCAGTTT;RSEQ=GAAACACTCTGTTTGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:86,84:0.0115:2,2:6.5:1:29.5:1:1:1.02367:60:4:0.0118:0:4 0/0:366:2:2,0:167,195:0.0055:2,0:6.5:1:22.5:1:0.21488:0:54:4:0.0055:0:4 -1 121484664 . CTGTT C 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.33826;SOR=0.32709;LSEQ=TTCAGCAGTTTGGAAACACT;RSEQ=TGTAAAGTCTGCACGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:2,1:76,86:0.0182:2,2:9.7:1:30:1:0.60307:2.25:60:6:0.0186:0.0061:1.7 0/0:333:2:1,1:148,183:0.006:2,2:19.5:1:29.1:1:1:1.24:54:4:0.0061:0.003:4 -1 121484666 . G C 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.15184;LSEQ=CAGCAGTTTGGAAACACTCT;RSEQ=TTTGTAAAGTCTGCACGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:3:1,2:73,84:0.0185:2,2:29:1:31.3:1:1:1.73234:48.7:6:0.0197:0:5.7 0/1:329:7:5,2:140,178:0.0213:2,2:21:1:31:1:0.24893:3.17:45.7:14:0.0216:0:5.1 -1 121484667 . T A 45 v4;q23;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.9975;LSEQ=AGCAGTTTGGAAACACTCTG;RSEQ=TTGTAAAGTCTGCACGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:1:1,0:73,84:0.0063:2,0:49:0:14:0:0.46835:0:58:0:0:0:6 0/1:322:4:3,1:139,176:0.0124:2,2:22.8:1:22.5:1:0.32699:3.78:53.3:3:0.0095:0:5 -1 121484671 . T G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05303;SOR=0.40322;LSEQ=GTTTGGAAACACTCTGTTTG;RSEQ=AAAGTCTGCACGTAGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:11:5,6:72,78:0.0683:2,2:20.9:1:31.2:1:1:1.10698:44.2:22:0.0683:0:6.2 0/1:314:9:1,8:138,166:0.0287:2,2:17:1:31.9:1:0.04689:6.62077:52:18:0.0288:0:4.3 -1 121484674 . A T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25783;SOR=0.2476;LSEQ=TGGAAACACTCTGTTTGTAA;RSEQ=GTCTGCACGTAGATATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:72,82:0.0128:2,2:33.5:1:29.5:1:1:1.14:60:4:0.013:0:3.5 0/0:313:1:0,1:137,175:0.0032:2,0:3:0:29:0:1:0:48:2:0.0032:0:4 -1 121484675 . G C 53 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44962;SOR=0.4927;LSEQ=GGAAACACTCTGTTTGTAAA;RSEQ=TCTGCACGTAGATATTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:4:2,2:69,82:0.0256:2,2:29:1:31.5:1:1:1.19:56.3:8:0.0258:0:4.8 0/1:313:4:2,2:134,173:0.0128:2,2:31:1:26.8:1:1:1.29:43:3:0.0097:0:6.8 -1 121484676 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11015;SOR=0;LSEQ=GAAACACTCTGTTTGTAAAG;RSEQ=CTGCACGTAGATATTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:70,82:0.013:2,2:14:1:30.5:1:1:1.17:59.5:4:0.013:0:4.5 0/0:309:0:0,0:135,170:0:2,0:23.8:1:28.8:1:1:0:52.7:75.25:0.9869:0:3.7 -1 121484677 . C A 48 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03728;SOR=0;LSEQ=AAACACTCTGTTTGTAAAGT;RSEQ=TGCACGTAGATATTTTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:2,1:67,82:0.0195:2,2:14.7:1:30.3:1:0.59079:2.43:45.7:6:0.0197:0:5.3 0/0:305:0:0,0:136,167:0:2,0:23.8:1:31.3:1:1:0:52.6:74.75:0.9934:0:3.7 -1 121484681 . A C 87 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27317;SOR=3.72346;LSEQ=ACTCTGTTTGTAAAGTCTGC;RSEQ=CGTAGATATTTTGACCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:1,0:71,82:0.0065:2,0:10:0:26:0:0.46753:0:51:2:0.0065:0:7 0/1:294:7:4,3:129,158:0.0238:2,2:23.3:1:31:1:0.70516:1.63:47.6:14:0.0239:0:6 -1 121484682 . C A 49 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.59707;LSEQ=CTCTGTTTGTAAAGTCTGCA;RSEQ=GTAGATATTTTGACCACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:1,0:72,82:0.0065:2,0:2:0:26:0:0.47097:0:21:2:0.0065:0:3 0/1:292:3:1,2:131,158:0.0103:2,2:7.3:1:31:1:1:1.65547:45.7:6:0.0104:0:5 -1 121484683 . G C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11681;SOR=0;LSEQ=TCTGTTTGTAAAGTCTGCAC;RSEQ=TAGATATTTTGACCACTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:69,78:0.0134:2,2:43.5:1:31:0:1:1.13:43:4:0.0137:0:7 0/0:286:0:0,0:127,154:0:2,0:23.6:1:30.3:1:1:0:52.6:280:0.9825:0:3.9 -1 121484685 . A G 248 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80174;LSEQ=TGTTTGTAAAGTCTGCACGT;RSEQ=GATATTTTGACCACTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:149:146:70,76:0,0:0.9799:0,2:24.8:1:31:1:1:0:51.2:35.5:0.9793:0:4 1/1:280:273:123,150:0,1:0.975:0,2:23.6:1:30.7:1:1:0:52.4:135.5:0.9819:0:3.9 -1 121484688 . T A 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10308;SOR=2.05984;LSEQ=TTGTAAAGTCTGCACGTAGA;RSEQ=ATTTTGACCACTTAGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:8:5,3:65,74:0.0541:2,2:24.5:1:27.8:1:0.47871:1.89:43.4:7:0.049:0:5.3 0/1:275:29:14,15:108,135:0.1055:2,2:25.2:1:29.7:1:0.69827:1.17:51.3:58:0.1058:0:4.5 -1 121484690 . T A 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.77508;SOR=0.91436;LSEQ=GTAAAGTCTGCACGTAGATA;RSEQ=TTTGACCACTTAGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:23:10,13:59,61:0.1575:2,2:25.8:1:29.8:1:0.65511:1.25537:50.9:46:0.1597:0:4.3 0/1:274:40:13,27:107,119:0.146:2,2:22:1:30.4:1:0.0877:1.86322:52.7:80:0.1476:0:4 -1 121484691 . T C 41 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12806;SOR=0.17939;LSEQ=TAAAGTCTGCACGTAGATAT;RSEQ=TTGACCACTTAGAGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:2,1:64,74:0.0207:2,2:21.7:1:26.3:1:0.59951:2.30:47:2:0.0143:0:6 0/0:266:1:0,1:117,142:0.0038:2,0:2:0:31:0:1:0:31:2:0.0039:0:4 -1 121484697 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12723;SOR=0;LSEQ=CTGCACGTAGATATTTTGAC;RSEQ=ACTTAGAGGCCTTCTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:66,75:0.014:2,2:25:1:29:1:1:1.14:50:4:0.0144:0:8 0/0:257:0:0,0:114,141:0:2,0:22.5:1:30.7:1:1:0:51:62.75:0.9921:0:4.1 -1 121484698 . A T 37 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.79184;LSEQ=TGCACGTAGATATTTTGACC;RSEQ=CTTAGAGGCCTTCTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:2,0:60,74:0.0147:2,0:6:1:30:1:0.20599:0:34:4:0.015:0:6 0/1:257:3:1,2:113,136:0.0117:2,2:13.7:1:23.7:1:1:1.65856:44:2:0.0079:0:5.7 -1 121484704 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12983;SOR=0;LSEQ=TAGATATTTTGACCACTTAG;RSEQ=GGCCTTCTTTGGAAACGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:64,68:0.0149:2,2:22.5:1:32.5:1:1:1.06:30.5:4:0.0152:0:6 0/0:237:0:0,0:108,129:0:2,0:22.6:1:29.9:1:1:0:49.8:78:1:0:4.4 -1 121484705 . G C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12999;SOR=0;LSEQ=AGATATTTTGACCACTTAGA;RSEQ=GCCTTCTTTGGAAACGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:64,67:0.015:2,2:26:1:30.5:1:1:1.05:40:4:0.0152:0:6.5 0/0:235:0:0,0:108,125:0:2,0:22.7:1:31:1:1:0:49.5:232:0.9915:0:4.4 -1 121484707 . C T 56 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25609;SOR=0.41374;LSEQ=ATATTTTGACCACTTAGAGG;RSEQ=CTTCTTTGGAAACGGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:4:2,2:61,65:0.0308:2,2:23.5:1:28.3:1:1:1.07:44.3:8:0.031:0:6.5 0/1:232:3:1,2:109,120:0.0129:2,2:25.3:1:30:1:1:1.81218:27.3:6:0.0132:0:6.7 -1 121484711 . CT TG 61 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09919;SOR=0.2457;LSEQ=TTTGACCACTTAGAGGCCTT;RSEQ=TTGGAAACGGTTTTTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:4:2,2:57,57:0.0339:2,2:32.8:1:30.8:1:1:1:45:8:0.0342:0:4.3 0/0:235:2:1,1:107,125:0.0085:2,2:22.5:1:32.3:1:1:1.17:48:4:0.0086:0:5 -1 121484712 . T G 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01398;LSEQ=TTGACCACTTAGAGGCCTTC;RSEQ=TTGGAAACGGTTTTTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:113:107:54,53:1,0:0.9469:0,2:23.8:1:30.8:1:1:0:46.3:52.5:0.9813:0:4.8 1/1:229:217:100,117:3,3:0.9476:2,2:22:1:30.3:1:1:1.16917:47.5:107.5:0.9556:0:4.7 -1 121484716 . G A 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55354;SOR=Inf;LSEQ=CCACTTAGAGGCCTTCTTTG;RSEQ=AAACGGTTTTTTCTCATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:55,54:0:2,0:24:1:31.4:1:1:0:45:108:0.9908:0:4.8 0/1:222:3:1,2:106,113:0.0135:2,2:23.7:1:28.7:1:1:1.871:50.7:6:0.0136:0:6.3 -1 121484720 . C CG 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.95827;LSEQ=TTAGAGGCCTTCTTTGGAAA;RSEQ=GGTTTTTTCTCATGTAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:4:2,2:50,53:0.0374:2,2:34:1:30.8:1:1:1.06:40.8:8:0.0377:0:3.5 0/1:223:8:4,4:105,109:0.0359:2,2:38.4:1:29.1:1:1:1.04:46:16:0.0362:0:4.3 -1 121484722 . GT CG 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.554;SOR=Inf;LSEQ=AGAGGCCTTCTTTGGAAACG;RSEQ=TTTTTCTCATGTAAGGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:51,53:0:2,0:24.7:1:30.7:1:1:0:44.6:25:1:0:4.9 0/1:221:3:2,1:105,112:0.0136:2,2:15.7:1:30.8:1:0.61321:2.13:46.7:6:0.0138:0:4 -1 121484723 . T G 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.11008;SOR=0.45532;LSEQ=GAGGCCTTCTTTGGAAACGG;RSEQ=TTTTTCTCATGTAAGGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:102:96:49,47:2,4:0.9412:2,2:24.9:1:31.5:1:0.67793:2.07:44.5:95:0.9406:0:5 1/1:215:189:93,96:6,8:0.8791:2,2:22.5:1:31:1:0.78391:1.29:46.9:93.5:0.8947:0:4.9 -1 121484727 . T C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0.90761;LSEQ=CCTTCTTTGGAAACGGTTTT;RSEQ=TCTCATGTAAGGCTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:5:2,3:46,47:0.051:2,2:24.4:1:32.8:1:1:1.46241:50.4:10:0.0515:0:6.2 0/1:215:10:8,2:99,106:0.0465:2,2:22.3:1:31.5:1:0.05875:4.26:54.6:20:0.0465:0:6 -1 121484728 . TC T 81 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00096;SOR=0;LSEQ=CTTCTTTGGAAACGGTTTTT;RSEQ=TCATGTAAGGCTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:6:4,2:0,0:0.0594:0,2:30.3:1:31.7:1:1:0:37.3:12:0.0612:0:5.2 0/0:215:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 121484729 . C T 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00218;SOR=2.7362;LSEQ=TTCTTTGGAAACGGTTTTTT;RSEQ=TCATGTAAGGCTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:101:76:35,41:0,0:0.7525:0,2:25.7:1:30:1:1:0:44.9:37:0.7551:0:4.8 1/1:215:192:95,97:0,0:0.893:0,2:23.5:1:29.9:1:1:0:47.8:63:0.9087:0:4.6 -1 121484732 . A C 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00204;SOR=2.34305;LSEQ=TTTGGAAACGGTTTTTTCTC;RSEQ=TGTAAGGCTAGACAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:21:12,9:38,43:0.2059:2,2:26:1:32:1:0.46753:1.50:48.5:42:0.21:0:5.2 0/1:214:81:44,37:63,69:0.3785:2,2:24.1:1:30.9:1:0.39782:1.30:48.5:162:0.3839:0:5 -1 121484740 . C T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05701;SOR=0.25125;LSEQ=CGGTTTTTTCTCATGTAAGG;RSEQ=TAGACAGAAGAATTCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:5:2,3:52,52:0.0442:2,2:26.8:1:30:1:1:1.49449:35:10:0.045:0:6.4 0/1:262:3:1,2:132,124:0.0115:2,2:6.3:1:30.3:1:0.61358:2.12302:51.7:6:0.0116:0:2 -1 121484745 . C G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45219;SOR=1.6504;LSEQ=TTTTCTCATGTAAGGCTAGA;RSEQ=AGAAGAATTCCCAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:4:3,1:56,56:0.0336:2,2:21:1:32.3:1:0.61862:2.97:48:8:0.0345:0:4.3 0/1:276:15:10,5:133,127:0.0543:2,2:17.6:1:32:1:0.29421:1.91:58.7:30:0.0547:0:3.4 -1 121484746 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09023;SOR=0;LSEQ=TTTCTCATGTAAGGCTAGAC;RSEQ=GAAGAATTCCCAGTAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:0,2:60,57:0.0168:2,0:9:1:31.5:1:0.2437:0:40:4:0.0168:0:7 0/0:276:0:0,0:146,130:0:2,0:22:1:30.6:1:1:0:51.9:552:1:0:3.4 -1 121484747 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09414;SOR=0;LSEQ=TTCTCATGTAAGGCTAGACA;RSEQ=AAGAATTCCCAGTAACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:59,62:0.0161:2,2:25.5:1:33:1:1:1.05:43:4:0.0163:0:5.5 0/0:279:0:0,0:148,130:0:2,0:22.2:1:31.7:1:1:0:52.2:138:0.9964:0:3.3 -1 121484749 . A G 98 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.07804;LSEQ=CTCATGTAAGGCTAGACAGA;RSEQ=GAATTCCCAGTAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:10:5,5:55,57:0.082:2,2:27.7:1:29.8:1:1:1.04:39.7:9:0.0744:0:5.6 0/0:291:2:1,1:152,137:0.0069:2,2:18:0:33:1:1:1.10909:51:4:0.0069:0:2 -1 121484750 . G A 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55708;SOR=Inf;LSEQ=TCATGTAAGGCTAGACAGAA;RSEQ=AATTCCCAGTAACTTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:60,65:0:2,0:21.6:1:31.5:1:1:0:50.6:61.5:1:0:3.4 0/1:290:3:1,2:151,134:0.0103:2,2:19.3:1:31.7:1:0.60387:2.24757:51:6:0.0104:0:4.7 -1 121484752 . A T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56022;SOR=Inf;LSEQ=ATGTAAGGCTAGACAGAAGA;RSEQ=TTCCCAGTAACTTCCTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:59,62:0:2,0:22.4:1:30.6:1:1:0:51.6:120:0.9917:0:3.3 0/1:301:3:1,2:158,139:0.01:2,2:28.7:1:23.3:1:0.60246:2.26735:49.3:2:0.0067:0:3.3 -1 121484756 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08508;LSEQ=AAGGCTAGACAGAAGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:4:0,4:59,59:0.0328:2,0:18.3:1:31:1:0.11963:0:30.8:8:0.0336:0:7.3 0/1:310:11:2,9:164,135:0.0355:2,2:22:1:30:1:0.02708:5.43942:37.7:22:0.0359:0:5.6 -1 121484760 . T G 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32773;SOR=Inf;LSEQ=CTAGACAGAAGAATTCCCAG;RSEQ=AACTTCCTTGTGTTGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:63,64:0:2,0:23.1:1:29.2:1:1:0:52.3:254:1:0:3.1 0/1:317:5:3,2:167,145:0.0158:2,2:34.2:1:31:1:1:1.30:56:10:0.016:0:5.2 -1 121484762 . A G 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71799;SOR=0.79022;LSEQ=AGACAGAAGAATTCCCAGTA;RSEQ=CTTCCTTGTGTTGTGTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:3:2,1:61,63:0.0236:2,2:16.3:1:31.3:1:0.61902:2.05:55:6:0.0238:0:7 0/1:320:6:2,4:168,145:0.0188:2,2:26.7:1:33.2:1:0.42338:2.31131:52.8:12:0.0189:0:6 -1 121484763 . C A 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31461;SOR=0.38794;LSEQ=GACAGAAGAATTCCCAGTAA;RSEQ=TTCCTTGTGTTGTGTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:61,62:0.0157:2,2:16.5:1:29.5:1:1:1.02:50:4:0.0159:0:4 0/0:325:2:0,2:172,147:0.0062:2,0:29.5:1:32:0:0.21468:0:48:4:0.0063:0:6 -1 121484766 . CC AT 31 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20266;SOR=0.20235;LSEQ=AGAAGAATTCCCAGTAACTT;RSEQ=TTGTGTTGTGTGCATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:65,65:0.015:2,2:10:0:31.5:1:1:1:24:4:0.0153:0:5 0/0:326:1:1,0:172,152:0.0031:2,0:25:0:31:0:1:0:40:2:0.0031:0:5 -1 121484767 . C T 79 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18716;SOR=Inf;LSEQ=GAAGAATTCCCAGTAACTTC;RSEQ=TTGTGTTGTGTGCATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:65,66:0:2,0:23.9:1:31.4:1:1:0:53.7:64.5:1:0:3.1 0/1:322:6:3,3:166,147:0.0186:2,2:19.3:1:30.7:1:1:1.12882:47.3:12:0.0189:0:5.7 -1 121484769 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08317;SOR=0;LSEQ=AGAATTCCCAGTAACTTCCT;RSEQ=GTGTTGTGTGCATTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:64,65:0.0153:2,2:35:1:31:1:1:1.02:52.5:4:0.0153:0:2.5 0/0:322:0:0,0:171,148:0:2,0:26.3:1:29.9:1:1:0:54.7:78.75:0.9906:0:2.6 -1 121484771 . T C 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.32625;SOR=0.40093;LSEQ=AATTCCCAGTAACTTCCTTG;RSEQ=GTTGTGTGCATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:63,65:0.0154:2,2:7:1:32:1:1:1.03:59.5:4:0.0157:0:7 0/0:322:2:2,0:170,150:0.0062:2,0:11:1:32:1:0.50078:0:59.5:4:0.0063:0:6.5 -1 121484773 . T G 33 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20887;SOR=0.20734;LSEQ=TTCCCAGTAACTTCCTTGTG;RSEQ=TGTGTGCATTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:64,69:0.0148:2,2:16:0:33.5:1:1:1.08:24:4:0.0148:0:5 0/0:323:1:1,0:171,149:0.0031:2,0:31:0:33:0:1:0:40:2:0.0032:0:5 -1 121484775 . G T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08531;SOR=0;LSEQ=CCCAGTAACTTCCTTGTGTT;RSEQ=TGTGCATTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:63,70:0.0148:2,2:6:0:29.5:1:1:1.11:60:4:0.0149:0:2 0/0:326:0:0,0:173,153:0:2,0:26.9:1:31.4:1:1:0:55.2:162:1:0:2.5 -1 121484777 . G T 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.32797;SOR=Inf;LSEQ=CAGTAACTTCCTTGTGTTGT;RSEQ=TGCATTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:64,70:0:2,0:25.8:1:31.8:1:1:0:54.5:66:1:0:3 0/1:337:5:3,2:172,159:0.0148:2,2:16:1:27.6:1:1:1.39:60:10:0.0151:0:2.2 -1 121484779 . G A 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.91725;SOR=0.9602;LSEQ=GTAACTTCCTTGTGTTGTGT;RSEQ=CATTCAACTCACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:55:29,26:34,44:0.4074:2,2:27:1:28.6:1:0.37816:1.44:58.2:54:0.4091:0:3.6 0/1:337:134:70,64:104,98:0.3976:2,2:27.1:1:28.7:1:0.9116:1.03:55.3:268:0.3976:0:3.9 -1 121484780 . C T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53498;SOR=0.64161;LSEQ=TAACTTCCTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:5:1,4:63,68:0.0362:2,2:13.6:1:29.8:1:0.37008:3.67475:27.6:10:0.0373:0:5.8 0/1:340:8:2,6:171,158:0.0235:2,2:21.9:1:28.3:1:0.16444:3.23639:41.1:16:0.0241:0:4.9 -1 121484784 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08138;SOR=0;LSEQ=TTCCTTGTGTTGTGTGCATT;RSEQ=AACTCACAGAGTTGAACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:63,74:0.0144:2,2:17:1:31:1:1:1.17:60:4:0.0145:0:2 0/0:347:0:0,0:177,166:0:2,0:26.3:1:31:1:1:0:56:56.167:0.9883:0:2.4 -1 121484785 . A C 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31835;SOR=0.39229;LSEQ=TCCTTGTGTTGTGTGCATTC;RSEQ=ACTCACAGAGTTGAACGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:63,74:0.0144:2,2:34:1:31:1:1:1.17:60:4:0.0146:0:3 0/0:352:2:1,1:179,170:0.0057:2,2:12.5:1:30:1:1:1.05281:48.5:4:0.0057:0:5 -1 121484786 . A G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58091;SOR=Inf;LSEQ=CCTTGTGTTGTGTGCATTCA;RSEQ=CTCACAGAGTTGAACGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:64,75:0:2,0:26.3:1:29.9:1:1:0:55.6:138:1:0:2.7 0/1:354:4:2,2:180,170:0.0113:2,2:25:1:31:1:1:1.05868:60:8:0.0113:0:3.3 -1 121484787 . C G 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19281;SOR=0.19457;LSEQ=CTTGTGTTGTGTGCATTCAA;RSEQ=TCACAGAGTTGAACGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:63,74:0.0143:2,2:13.5:1:30.5:1:1:1.17:27:4:0.0145:0:4.5 0/0:357:1:0,1:184,171:0.0028:2,0:34:0:32:0:0.48315:0:40:2:0.0028:0:7 -1 121484794 . A T 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.71415;SOR=0.76963;LSEQ=TGTGTGCATTCAACTCACAG;RSEQ=GTTGAACGTTCCCTTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:0,3:65,75:0.021:2,0:25:1:32:0:0.25096:0:59:6:0.0214:0:3 0/1:370:6:1,5:192,170:0.0162:2,2:24.3:1:29.3:1:0.10635:5.62416:55.2:12:0.0164:0:1.8 -1 121484796 . T A 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.76984;SOR=1.54506;LSEQ=TGTGCATTCAACTCACAGAG;RSEQ=TGAACGTTCCCTTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:3:1,2:63,75:0.0213:2,2:23:1:30:1:1:1.67408:60:6:0.0216:0:1.3 0/1:369:12:8,4:189,168:0.0325:2,2:21.9:1:27.7:1:0.39333:1.78:57.8:11:0.03:0:2.3 -1 121484800 . A G 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02445;LSEQ=CATTCAACTCACAGAGTTGA;RSEQ=CGTTCCCTTAGACAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:1,2:59,76:0.0216:2,2:21.7:1:31.7:1:1:1.54789:60:6:0.0219:0:1.7 0/1:362:8:4,4:188,166:0.0221:2,2:33.9:1:29.3:1:1:1.13214:60:7:0.0194:0:1.9 -1 121484801 . C G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18349;SOR=0.44577;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=GTTCCCTTAGACAGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:5:2,3:56,70:0.0365:2,2:26.2:1:32:1:1:1.19835:59.8:10:0.0368:0:5.8 0/1:362:6:4,2:187,167:0.0166:2,2:19:1:31.2:1:0.68842:1.78:48:12:0.0168:0:4.7 -1 121484802 . G C 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67395;SOR=0.77477;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTCCCTTAGACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:62,77:0.0142:2,2:42:0:32.5:1:1:1.24:24:4:0.0143:0:5 0/1:363:4:1,3:185,167:0.011:2,2:25.5:1:31.8:1:0.35179:3.31303:45.8:8:0.0111:0:4.3 -1 121484803 . T A 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12381;SOR=0.29976;LSEQ=TCAACTCACAGAGTTGAACG;RSEQ=TCCCTTAGACAGAGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:5:1,4:61,75:0.0355:2,2:27.6:1:31.6:1:0.38454:3.22985:47.4:10:0.0362:0:6.6 0/1:368:4:3,1:188,176:0.0109:2,2:15.8:1:27.8:1:0.62404:2.80:40:8:0.0109:0:6.5 -1 121484804 . TC T 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18643;SOR=0.18954;LSEQ=CAACTCACAGAGTTGAACGT;RSEQ=CCTTAGACAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:61,77:0.0139:2,2:29.5:1:32:1:1:1.26:50.5:4:0.0141:0:3 0/0:377:1:1,0:193,180:0.0027:2,0:28:0:32:0:1:0:60:2:0.0027:0:1 -1 121484805 . C T 48 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0208;SOR=0;LSEQ=AACTCACAGAGTTGAACGTT;RSEQ=CCTTAGACAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:0,3:61,77:0.0208:2,0:28:1:30.3:1:0.25836:0:40:6:0.0211:0:8 0/0:377:0:0,0:193,180:0:2,0:24:1:30.6:1:1:0:57.5:73.6:0.9892:0:2.3 -1 121484807 . C T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95695;LSEQ=CTCACAGAGTTGAACGTTCC;RSEQ=TTAGACAGAGCAGATTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:4:1,3:61,80:0.0274:2,2:20:1:31.5:1:0.63574:2.27569:45:8:0.0276:0:6.5 0/1:381:10:6,4:189,179:0.0262:2,2:20.3:1:30.5:1:0.75187:1.42:41.4:20:0.0265:0:5.7 -1 121484811 . G C 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22022;SOR=0.36277;LSEQ=CAGAGTTGAACGTTCCCTTA;RSEQ=ACAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:4:1,3:59,75:0.0288:2,2:18:1:33.8:1:0.63249:2.34671:45:8:0.0292:0:6.5 0/1:377:4:3,1:191,179:0.0106:2,2:23.8:1:31.3:1:0.62404:2.80:40:8:0.0109:0:6.5 -1 121484813 . C G 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17219;SOR=0.17826;LSEQ=GAGTTGAACGTTCCCTTAGA;RSEQ=AGAGCAGATTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:58,76:0.0145:2,2:42:0:32:1:1:1.31:60:4:0.0146:0:4 0/0:384:1:1,0:191,183:0.0026:2,0:26:0:34:0:1:0:60:2:0.0026:0:6 -1 121484815 . G C 108 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19259;LSEQ=GTTGAACGTTCCCTTAGACA;RSEQ=AGCAGATTTGAAACACTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:2,1:56,79:0.0216:2,2:41:1:32.7:1:0.57231:2.80:60:6:0.0217:0:2.7 0/1:390:10:5,5:197,183:0.0256:2,2:25.3:1:32.8:1:1:1.07628:58.7:20:0.0259:0:2.2 -1 121484818 . C G 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68036;SOR=2.24124;LSEQ=GAACGTTCCCTTAGACAGAG;RSEQ=AGATTTGAAACACTCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:0,1:60,81:0.007:2,0:33:0:32:0:1:0:60:2:0.0071:0:2 0/1:383:6:3,3:193,184:0.0157:2,2:23.7:1:30.7:1:1:1.0488:60:12:0.0157:0:2.5 -1 121484823 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07429;SOR=0;LSEQ=TTCCCTTAGACAGAGCAGAT;RSEQ=TGAAACACTCTATTTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:62,80:0.0139:2,2:45.5:1:30.5:1:1:1.29:60:4:0.0141:0:5 0/0:383:0:0,0:194,189:0:2,0:23.3:1:29.7:1:1:0:58:190.5:1:0:2.2 -1 121484827 . A G 50 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02181;SOR=0;LSEQ=CTTAGACAGAGCAGATTTGA;RSEQ=ACACTCTATTTGTGCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:3:0,3:65,78:0.0205:2,0:6:1:31.7:1:0.2539:0:40:6:0.0207:0:8 0/0:374:0:0,0:183,188:0:2,0:23.8:1:29.5:1:1:0:57.9:40.222:0.9945:0:2.2 -1 121484831 . CT GC 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.31094;SOR=0.3842;LSEQ=GACAGAGCAGATTTGAAACA;RSEQ=CTATTTGTGCAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:66,77:0.0138:2,2:36:1:31.3:1:1:1.17:60:4:0.0141:0:2 0/0:375:2:1,1:181,188:0.0053:2,2:13.5:1:30.3:1:1:1.04:60:4:0.0054:0:4.5 -1 121484832 . T C 61 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0055;SOR=0;LSEQ=ACAGAGCAGATTTGAAACAC;RSEQ=CTATTTGTGCAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:4:2,2:63,74:0.028:2,2:28.8:1:30.8:1:1:1.17:42:8:0.029:0:4.8 0/0:378:0:0,0:183,193:0:2,0:23.2:1:29.5:1:1:0:57.6:33.182:1:0:2.2 -1 121484835 . A T 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10075;SOR=0.70742;LSEQ=GAGCAGATTTGAAACACTCT;RSEQ=TTTGTGCAATTTGCAAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:62:25,37:37,37:0.4559:2,2:25.1:1:29.5:1:0.30133:1.47569:56.4:19.667:0.4504:0:4 0/1:371:138:65,73:113,118:0.372:2,2:26:1:29.9:1:0.74785:1.07527:54:45:0.374:0:4 -1 121484839 . G C 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18158;SOR=0.18563;LSEQ=AGATTTGAAACACTCTATTT;RSEQ=TGCAATTTGCAAGTGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:61,71:0.0149:2,2:45.5:1:32.5:1:1:1.16:60:4:0.0149:0:4 0/0:358:1:0,1:176,180:0.0028:2,0:32:0:33:0:1:0:60:2:0.0028:0:3 -1 121484842 . C G 64 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07554;SOR=0.25376;LSEQ=TTTGAAACACTCTATTTGTG;RSEQ=AATTTGCAAGTGTAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:4:2,2:54,64:0.0328:2,2:24.3:1:32.3:1:1:1.18:40:8:0.0333:0:4.8 0/0:353:3:1,2:168,176:0.0085:2,2:10.3:1:31.7:1:1:1.90567:52.7:6:0.0086:0:4.3 -1 121484846 . T A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61073;SOR=0.5331;LSEQ=AAACACTCTATTTGTGCAAT;RSEQ=TGCAAGTGTAGATTTCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:56,65:0.0163:2,2:16:1:28.5:1:1:1.16:60:4:0.0164:0:2.5 0/0:344:3:2,1:168,173:0.0087:2,2:14.3:1:28.3:1:0.61956:2.06:60:6:0.0089:0:2.3 -1 121484847 . T G 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74094;SOR=0.91545;LSEQ=AACACTCTATTTGTGCAATT;RSEQ=GCAAGTGTAGATTTCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:46:20,26:35,37:0.3866:2,2:27.2:1:31.9:1:0.70546:1.22757:56.3:92:0.3898:0:4.3 0/1:339:124:60,64:105,110:0.3658:2,2:27.8:1:31.1:1:1:1.01813:54.5:123:0.3705:0:4 -1 121484849 . CA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06691;SOR=0;LSEQ=CACTCTATTTGTGCAATTTG;RSEQ=AGTGTAGATTTCAAGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:53,60:0.0172:2,2:45:1:30.5:1:1:1.13:60:4:0.0175:0:0.5 0/0:331:0:0,0:161,165:0:2,0:26.2:1:31.8:1:1:0:57.5:45.571:0.9876:0:2.3 -1 121484852 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.74376;SOR=0.91048;LSEQ=TCTATTTGTGCAATTTGCAA;RSEQ=TGTAGATTTCAAGCGCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:15:6,9:52,53:0.124:2,2:28.3:1:30.6:1:0.58582:1.467:53.9:30:0.124:0:4.9 0/1:333:38:20,18:142,151:0.1141:2,2:30.1:1:30.3:1:0.73069:1.18:56.6:76:0.1145:0:4.2 -1 121484855 . T G 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14895;SOR=0.71415;LSEQ=ATTTGTGCAATTTGCAAGTG;RSEQ=AGATTTCAAGCGCTTTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:51:24,27:31,33:0.4359:2,2:23.5:1:31.4:1:1:1.05628:55.3:102:0.4359:0:4.2 0/1:332:118:59,59:105,101:0.3554:2,2:27.5:1:30.7:1:0.90829:1.0395:54.8:38.333:0.3538:0:3.9 -1 121484858 . A T 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52459;SOR=1.41678;LSEQ=TGTGCAATTTGCAAGTGTAG;RSEQ=TTTCAAGCGCTTTAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:6:3,3:55,57:0.0508:2,2:28.7:1:30.3:1:1:1.04:60:12:0.0513:0:3.7 0/1:340:24:9,15:159,157:0.0706:2,2:21.7:1:29.6:1:0.29053:1.68533:60:48:0.071:0:3 -1 121484864 . AG GC 64 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04559;SOR=0.17711;LSEQ=ATTTGCAAGTGTAGATTTCA;RSEQ=CGCTTTAAGGTCAATGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:4:1,3:56,60:0.0333:2,2:9.3:1:32.1:1:0.62055:2.77796:45.5:8:0.0336:0.0083:4.5 0/0:331:2:0,2:164,163:0.006:2,0:20.5:1:33.5:0:0.49848:0:42.5:4:0.0061:0:6 -1 121484866 . C T 57 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57644;SOR=Inf;LSEQ=TTGCAAGTGTAGATTTCAAG;RSEQ=GCTTTAAGGTCAATGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:55,60:0:2,0:24.9:1:31.1:1:1:0:57.6:114:1:0:2.4 0/1:334:4:2,2:165,165:0.012:2,2:22.3:1:28.8:1:1:1:56.8:8:0.012:0:4.3 -1 121484867 . G T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.6406;SOR=1.39141;LSEQ=TGCAAGTGTAGATTTCAAGC;RSEQ=CTTTAAGGTCAATGGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:5:3,2:51,57:0.0435:2,2:30.8:1:27.4:1:0.66857:1.67:60:4:0.0354:0:4 0/1:336:20:9,11:159,155:0.0595:2,2:21.8:1:29.7:1:0.65217:1.25291:60:40:0.0597:0:3.5 -1 121484872 . A G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75135;SOR=0.80054;LSEQ=GTGTAGATTTCAAGCGCTTT;RSEQ=AGGTCAATGGCAGAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:4:1,3:57,57:0.0331:2,2:22.8:1:31.8:1:0.61873:2.97464:49.3:8:0.0331:0:5.3 0/1:338:9:3,6:163,161:0.0266:2,2:16.7:1:31.3:1:0.50182:2.0207:53.9:18:0.0268:0:4.1 -1 121484873 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06625;SOR=0;LSEQ=TGTAGATTTCAAGCGCTTTA;RSEQ=GGTCAATGGCAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:57,57:0.0169:2,2:30.5:1:30.5:1:1:1:52:4:0.0174:0:3.5 0/0:339:0:0,0:169,169:0:2,0:23.9:1:30.1:1:1:0:57:41.25:0.997:0:2.3 -1 121484875 . G T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57637;SOR=Inf;LSEQ=TAGATTTCAAGCGCTTTAAG;RSEQ=TCAATGGCAGAAAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:61,55:0:2,0:23.5:1:31.3:1:1:0:57.9:37.667:1:0:2.3 0/1:340:4:2,2:168,166:0.0118:2,2:11.8:1:28.3:1:1:1.01201:60:8:0.0121:0:1.8 -1 121484880 . T C 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.80693;SOR=1.10127;LSEQ=TTCAAGCGCTTTAAGGTCAA;RSEQ=GGCAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:29:20,9:40,47:0.2417:2,2:23.2:1:31.3:1:0.03481:2.59:59.3:58:0.2458:0:2.5 0/1:331:86:44,42:117,121:0.2598:2,2:24:1:30.6:1:0.80176:1.08:59.8:172:0.2622:0:2 -1 121484882 . G A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17319;SOR=0.17886;LSEQ=CAAGCGCTTTAAGGTCAATG;RSEQ=CAGAAAAGGAAATATCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:61,53:0.0171:2,2:34:1:28.5:1:1:1.14954:60:4:0.0177:0:5 0/0:324:1:1,0:161,162:0.0031:2,0:6:0:31:0:1:0:60:2:0.0031:0:3 -1 121484883 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06869;SOR=0;LSEQ=AAGCGCTTTAAGGTCAATGG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:60,53:0.0171:2,2:22:1:30.5:1:1:1.13085:60:4:0.0172:0:3 0/0:328:0:0,0:164,160:0:2,0:23.7:1:31.6:1:1:0:57.2:63.8:0.9876:0:2.2 -1 121484887 . A G 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.44799;LSEQ=GCTTTAAGGTCAATGGCAGA;RSEQ=AAGGAAATATCTTCGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:1:0,1:66,55:0.0082:2,0:35:0:32:0:0.45902:0:48:2:0.0083:0:4 0/1:338:4:2,2:169,165:0.0118:2,2:36.3:1:31.5:1:1:1.02417:60:8:0.012:0:2.8 -1 121484893 . A T 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34449;SOR=Inf;LSEQ=AGGTCAATGGCAGAAAAGGA;RSEQ=ATATCTTCGTTTCAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:65,52:0:2,0:22.9:1:30.1:1:1:0:58:116:1:0:2.2 0/1:348:6:2,4:168,170:0.0172:2,2:18.2:1:27.7:1:0.68487:1.97269:60:12:0.0173:0:1.7 -1 121484896 . A T 49 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01512;SOR=0;LSEQ=TCAATGGCAGAAAAGGAAAT;RSEQ=TCTTCGTTTCAAAACTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:3:1,2:62,48:0.0261:2,2:10:1:31.3:1:0.58293:2.562:60:6:0.0261:0:1.7 0/0:347:0:0,0:174,173:0:2,0:21.8:1:28.5:1:1:0:57.4:346:1:0:2.1 -1 121484898 . C T 25 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25852;SOR=0.32756;LSEQ=AATGGCAGAAAAGGAAATAT;RSEQ=TTCGTTTCAAAACTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:65,48:0.0174:2,2:44:1:30.5:1:1:1.35053:52:4:0.0174:0:3.5 0/0:348:2:0,2:171,174:0.0057:2,0:1:0:25:0:0.49866:0:60:4:0.0058:0:2 -1 121484899 . T A 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57631;SOR=Inf;LSEQ=ATGGCAGAAAAGGAAATATC;RSEQ=TCGTTTCAAAACTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:66,49:0:2,0:24:1:30.5:1:1:0:57.8:56.5:1:0:2.1 0/1:349:4:3,1:172,173:0.0115:2,2:5.3:1:25.8:1:0.62284:3.01:50.5:8:0.0116:0:5 -1 121484901 . C G 91 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45926;SOR=2.76569;LSEQ=GGCAGAAAAGGAAATATCTT;RSEQ=GTTTCAAAACTAGACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:1,0:66,49:0.0085:2,0:12:0:31:0:1:0:60:2:0.0087:0:5 0/1:343:8:3,5:165,164:0.0233:2,2:18.5:1:30.6:1:0.72327:1.6743:60:16:0.0236:0:3.4 -1 121484904 . T G 51 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05869;SOR=0.11804;LSEQ=AGAAAAGGAAATATCTTCGT;RSEQ=TCAAAACTAGACAGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:3:2,1:67,46:0.0259:2,2:24.7:1:32.3:1:1:1.37:60:6:0.0268:0:2 0/0:322:1:1,0:159,152:0.0031:2,0:6:0:33:0:1:0:60:2:0.0032:0:7 -1 121484906 . C A 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3301;SOR=Inf;LSEQ=AAAAGGAAATATCTTCGTTT;RSEQ=AAAACTAGACAGAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:69,49:0:2,0:23.8:1:31.3:1:1:0:57.8:58:0.9915:0:2.1 0/1:322:5:3,2:157,156:0.0155:2,2:14.8:1:27.4:1:1:1.49:54.4:10:0.0157:0:5.6 -1 121484907 . A G 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57802;SOR=Inf;LSEQ=AAAGGAAATATCTTCGTTTC;RSEQ=AAACTAGACAGAATCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:71,48:0:2,0:23.8:1:30:1:1:0:58.2:118:1:0:2.1 0/1:322:4:2,2:160,158:0.0124:2,2:20:1:30.5:1:1:1.01262:55.8:8:0.0125:0:1.8 -1 121484911 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16713;SOR=0.17408;LSEQ=GAAATATCTTCGTTTCAAAA;RSEQ=TAGACAGAATCATTCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:65,46:0.0172:2,2:10.5:1:31.5:1:1:1.40862:54:4:0.0174:0:3 0/0:330:1:0,1:169,159:0.003:2,0:36:0:28:0:0.48632:0:60:2:0.0031:0:5 -1 121484912 . T A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16916;SOR=0.17568;LSEQ=AAATATCTTCGTTTCAAAAC;RSEQ=AGACAGAATCATTCCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:2,0:64,48:0.0172:2,0:10.5:1:29:1:0.50815:0:60:4:0.018:0:3 0/0:327:1:1,0:167,158:0.0031:2,0:21:0:32:0:1:0:60:2:0.0031:0:3 -1 121484913 . A C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17054;SOR=0.17677;LSEQ=AATATCTTCGTTTCAAAACT;RSEQ=GACAGAATCATTCCCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:65,49:0.0172:2,2:23:1:31.5:1:1:1.32325:60:4:0.0174:0:4 0/0:325:1:0,1:165,156:0.0031:2,0:49:0:29:0:0.48758:0:60:2:0.0031:0:2 -1 121484916 . C G 51 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6062;SOR=0.51305;LSEQ=ATCTTCGTTTCAAAACTAGA;RSEQ=AGAATCATTCCCACAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:65,47:0.0175:2,2:40:0:33:1:1:1.37896:56.5:4:0.0179:0:3 0/0:331:3:1,2:162,165:0.0091:2,2:31.7:1:32.3:1:1:1.95977:60:6:0.0091:0:3.3 -1 121484930 . C A 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12368;SOR=0.24206;LSEQ=ACTAGACAGAATCATTCCCA;RSEQ=AAACTGCGTTGTGATGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:3:2,1:67,54:0.0238:2,2:20:1:31.7:1:1:1.61:52.7:6:0.024:0:4.3 0/0:342:2:1,1:163,169:0.0058:2,2:22.5:1:31:0:1:1.04:60:4:0.0059:0:3.5 -1 121484941 . G C 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17318;SOR=0.17894;LSEQ=TCATTCCCACAAACTGCGTT;RSEQ=TGATGTGTTTGTTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:69,55:0.0159:2,2:19.5:1:32:1:1:1.25226:60:4:0.0161:0:2.5 0/0:349:1:0,1:169,178:0.0029:2,0:19:0:34:0:1:0:60:2:0.0029:0:3 -1 121484942 . T C 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57783;SOR=Inf;LSEQ=CATTCCCACAAACTGCGTTG;RSEQ=GATGTGTTTGTTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:71,56:0:2,0:26.1:1:30.2:1:1:0:58.1:254:1:0:2.6 0/1:347:4:2,2:168,174:0.0115:2,2:31.5:1:30:1:1:1.04:60:8:0.0115:0:3.5 -1 121484945 . T C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.95757;LSEQ=TCCCACAAACTGCGTTGTGA;RSEQ=GTGTTTGTTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:5:2,3:69,54:0.0391:2,2:28.6:1:32:1:0.65521:1.90687:55.8:10:0.0391:0:3.8 0/1:347:13:6,7:158,175:0.0375:2,2:28.6:1:28.8:1:1:1.05319:59.6:12:0.0351:0:3.5 -1 121484946 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07303;SOR=0;LSEQ=CCCACAAACTGCGTTGTGAT;RSEQ=TGTTTGTTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:71,56:0.0155:2,2:35.5:1:30.5:1:1:1.2655:60:4:0.0157:0:2.5 0/0:347:0:0,0:165,182:0:2,0:34:0:11:0:1:0:60:0:0:0:3 -1 121484950 . TT GC 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06243;SOR=0.12179;LSEQ=CAAACTGCGTTGTGATGTGT;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:3:2,1:66,55:0.0242:2,2:32.7:1:31.5:1:1:1.66:52:6:0.025:0:2.7 0/0:334:1:1,0:159,171:0.003:2,0:10:0:33:0:0.48338:0:33:2:0.003:0:6 -1 121484951 . T C 252 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=1.37931;LSEQ=AAACTGCGTTGTGATGTGTT;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:117:64,53:0,1:0.9435:0,2:25.8:1:30.5:1:0.45763:0:58.1:57.5:0.9664:0:2.8 1/1:337:323:154,169:3,4:0.9585:2,2:26.6:1:30.3:1:1:1.21:57.8:79.75:0.9608:0:2.6 -1 121484954 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07169;SOR=0;LSEQ=CTGCGTTGTGATGTGTTTGT;RSEQ=CAACTCACAGAGTTTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:0,2:69,52:0.0163:2,0:49:1:30.5:1:0.19072:0:60:4:0.0164:0:3 0/0:335:0:0,0:160,175:0:2,0:26.3:1:29.5:1:1:0:57.5:166.5:1:0:2.7 -1 121484957 . A T 147 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00365;SOR=6.11407;LSEQ=CGTTGTGATGTGTTTGTTCA;RSEQ=CTCACAGAGTTTAACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:67,54:0.0163:2,2:20.5:1:32:0:1:1.23854:52.5:4:0.0163:0:4.5 0/1:337:31:16,15:143,163:0.092:2,2:25.9:1:29.8:1:0.70652:1.22:54.5:62:0.0923:0:4.7 -1 121484965 . A C 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16648;SOR=0.17364;LSEQ=TGTGTTTGTTCAACTCACAG;RSEQ=GTTTAACCTTTCTGTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:65,54:0.0163:2,2:38.5:1:31.5:1:1:1.20185:60:4:0.0163:0:3.5 0/0:351:1:1,0:167,181:0.0028:2,0:15:0:34:0:0.48138:0:60:2:0.0029:0:6 -1 121484972 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06401;SOR=0;LSEQ=GTTCAACTCACAGAGTTTAA;RSEQ=CTTTCTGTTCATAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:60,54:0.0172:2,2:20.5:1:29.5:1:1:1.1101:60:4:0.0174:0:3 0/0:341:0:0,0:163,173:0:2,0:23.3:1:30.8:1:1:0:57.4:111:0.9852:0:2.9 -1 121484973 . C T 95 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCTGTTCATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:8:5,3:54,50:0.069:2,2:24.1:1:31.8:1:0.71972:1.54:55.5:16:0.069:0:5 0/0:338:0:0,0:161,173:0:2,0:36:0:17:0:1:0:60:0:0:0:4 -1 121484979 . G T 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42779;SOR=1.22159;LSEQ=TCACAGAGTTTAACCTTTCT;RSEQ=TTCATAGAGCAGTTAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:40:20,20:35,31:0.3704:2,2:24.2:1:29.1:1:0.84196:1.12774:54.2:19:0.3585:0:4.5 0/1:318:133:66,67:87,97:0.4182:2,2:22.2:1:30.1:1:0.73292:1.10:56.1:266:0.4263:0:4.4 -1 121484983 . A G 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57668;SOR=Inf;LSEQ=AGAGTTTAACCTTTCTGTTC;RSEQ=TAGAGCAGTTAGGAAACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:56,53:0:2,0:24.5:1:30.4:1:1:0:57.8:108:0.9908:0:3.2 0/1:312:4:2,2:147,161:0.0128:2,2:23:1:30.5:1:1:1.09:59.3:8:0.013:0:6 -1 121484988 . G A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07414;SOR=0;LSEQ=TTAACCTTTCTGTTCATAGA;RSEQ=CAGTTAGGAAACGCTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:57,56:0.0174:2,2:34.5:1:28.5:1:1:1.0177:58:4:0.0175:0:7 0/0:306:0:0,0:142,164:0:2,0:23.8:1:31.7:1:1:0:57.5:152:1:0:3.2 -1 121484989 . C T 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07557;SOR=0;LSEQ=TAACCTTTCTGTTCATAGAG;RSEQ=AGTTAGGAAACGCTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:57,55:0.0174:2,2:12.5:1:27.5:1:1:1.03605:60:4:0.0175:0:4 0/0:302:0:0,0:139,162:0:2,0:24:1:31.5:1:1:0:57.5:74.25:0.9966:0:3.2 -1 121484991 . GT AG 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56152;SOR=Inf;LSEQ=ACCTTTCTGTTCATAGAGCA;RSEQ=TAGGAAACGCTCTGTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:57,60:0:2,0:22.9:1:32.2:1:1:0:58.4:234:1:0:3.3 0/1:295:3:2,1:138,152:0.0102:2,2:16.3:1:28.5:1:0.60768:2.20:54.7:6:0.0103:0.0034:6 -1 121484993 . T C 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56043;SOR=Inf;LSEQ=CTTTCTGTTCATAGAGCAGT;RSEQ=AGGAAACGCTCTGTTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:56,60:0:2,0:23:1:29.2:1:1:0:58.3:232:0.9915:0:3.3 0/1:290:3:1,2:133,151:0.0103:2,2:38.3:1:32.3:1:1:1.75826:60:6:0.0105:0:5 -1 121485001 . G A 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02464;SOR=0.58695;LSEQ=TCATAGAGCAGTTAGGAAAC;RSEQ=CTCTGTTTGTAAAGTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:121:87:47,40:0,0:0.719:0,2:21.1:1:30.1:1:1:0:59:86:0.7227:0:2.8 1/0:290:174:81,93:2,3:0.6:2,2:25:1:29.4:1:1:1.30:58.1:42.5:0.5965:0:2.6 -1 121485002 . C G 78 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.67918;SOR=2.56041;LSEQ=CATAGAGCAGTTAGGAAACG;RSEQ=TCTGTTTGTAAAGTCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:1,0:45,40:0.0084:2,0:36:0:14:0:1:0:40:0:0:0:6 0/1:282:6:3,3:84,97:0.0213:2,2:17.2:1:30.2:1:1:1.15:60:12:0.0328:0:4.3 -1 121485006 . GT G 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07976;SOR=0;LSEQ=GAGCAGTTAGGAAACGCTCT;RSEQ=TTGTAAAGTCTGTAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:54,59:0.0171:2,2:38:0:34:1:1:1.09:60:4:0.0175:0:1 0/0:296:0:0,0:137,159:0:2,0:24:1:29.2:1:1:0:57.5:58.2:1:0:3.3 -1 121485009 . T G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36076;SOR=0.39895;LSEQ=CAGTTAGGAAACGCTCTGTT;RSEQ=GTAAAGTCTGTAAGTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:1,2:57,58:0.0254:2,2:28:1:33:0:1:1.9547:52:6:0.0254:0:6 0/1:292:3:2,1:132,157:0.0103:2,2:46.7:1:32:1:0.59532:2.37:60:6:0.0103:0:5.7 -1 121485011 . T A 87 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00361;SOR=0.11496;LSEQ=GTTAGGAAACGCTCTGTTTG;RSEQ=AAAGTCTGTAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:7:3,4:59,57:0.0569:2,2:15.1:1:31.3:1:0.71733:1.37652:60:14:0.0569:0:3.9 0/0:292:2:2,0:132,158:0.0068:2,0:25:1:26:1:0.20974:0:60:4:0.0069:0:4 -1 121485012 . A C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1858;SOR=1.88255;LSEQ=TTAGGAAACGCTCTGTTTGT;RSEQ=AAGTCTGTAAGTGGATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:7:3,4:62,55:0.0565:2,2:30.9:1:32:1:0.70761:1.49809:48.4:14:0.0569:0:5.1 0/1:296:30:15,15:121,145:0.1014:2,2:23.3:1:31:1:0.70106:1.20:58.3:60:0.102:0:4.7 -1 121485015 . G T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01625;SOR=1.7374;LSEQ=GGAAACGCTCTGTTTGTAAA;RSEQ=TCTGTAAGTGGATATTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:37:17,20:47,40:0.296:2,2:24.2:1:30:1:0.43798:1.37871:55.8:36:0.2951:0:4.3 0/1:303:128:63,65:78,94:0.4224:2,2:25.4:1:29.7:1:0.55908:1.17:56.5:256:0.4238:0:4.4 -1 121485016 . T C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08659;SOR=0;LSEQ=GAAACGCTCTGTTTGTAAAG;RSEQ=CTGTAAGTGGATATTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:65,59:0.0159:2,2:28.5:1:33:0:1:1.10085:48:4:0.016:0:6 0/0:301:0:0,0:143,158:0:2,0:23.6:1:28.9:1:1:0:57.3:99.333:1:0:3.3 -1 121485020 . T C 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.8073;SOR=0.84465;LSEQ=CGCTCTGTTTGTAAAGTCTG;RSEQ=AAGTGGATATTCTGACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:7:6,1:62,60:0.0543:2,2:17.4:1:33.1:1:0.11864:5.74:44.1:14:0.0556:0:5.9 0/1:303:14:5,9:141,144:0.0462:2,2:12.4:1:32.1:1:0.41451:1.75923:46.6:28:0.0464:0:3.9 -1 121485023 . G C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08343;SOR=0;LSEQ=TCTGTTTGTAAAGTCTGTAA;RSEQ=TGGATATTCTGACATCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:64,59:0.0159:2,2:40:0:32.5:1:1:1.08402:60:4:0.0161:0:2.5 0/0:309:0:0,0:148,156:0:2,0:23.1:1:31.2:1:1:0:57.4:49.667:0.9835:0:3.3 -1 121485026 . G C 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58584;SOR=0.42095;LSEQ=GTTTGTAAAGTCTGTAAGTG;RSEQ=ATATTCTGACATCTTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:65,61:0.0156:2,2:25.5:1:30.5:1:1:1.06508:60:4:0.0156:0:3.5 0/0:302:2:1,1:145,154:0.0066:2,2:20:1:33:0:1:1.06:54.5:4:0.0067:0:4.5 -1 121485029 . A T 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32083;SOR=Inf;LSEQ=TGTAAAGTCTGTAAGTGGAT;RSEQ=TTCTGACATCTTGTGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:68,62:0:2,0:24:1:29.9:1:1:0:58.1:260:1:0:3.2 0/1:302:4:2,2:145,153:0.0132:2,2:30.5:1:31:1:1:1.06:55:8:0.0134:0:5 -1 121485033 . T A 103 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56402;SOR=1.66956;LSEQ=AAGTCTGTAAGTGGATATTC;RSEQ=GACATCTTGTGGCCTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:3,0:65,64:0.0227:2,0:20.7:1:31.7:1:0.24497:0:34.3:6:0.0234:0:7 0/1:294:11:6,5:138,142:0.0374:2,2:16.9:1:29.8:1:0.76812:1.23:45.7:22:0.0377:0:4.7 -1 121485035 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09383;SOR=0;LSEQ=GTCTGTAAGTGGATATTCTG;RSEQ=CATCTTGTGGCCTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:66,61:0.0155:2,2:28.5:1:31.5:1:1:1.08129:58.5:4:0.0159:0:4.5 0/0:291:0:0,0:143,148:0:2,0:25:1:29.1:1:1:0:57.8:290:1:0:3.4 -1 121485037 . A G 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32204;LSEQ=CTGTAAGTGGATATTCTGAC;RSEQ=TCTTGTGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:1,0:64,62:0.0078:2,0:45:0:32:0:1:0:52:2:0.0079:0:4 0/1:291:3:1,2:140,144:0.0103:2,2:37.3:1:30.7:1:1:1.94011:59:6:0.0105:0:3.3 -1 121485039 . C T 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.73016;SOR=1.75639;LSEQ=GTAAGTGGATATTCTGACAT;RSEQ=TTGTGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:63,61:0.015:2,2:41.5:1:30.5:1:1:1.03253:60:4:0.0153:0:5 0/1:306:8:4,4:144,145:0.0261:2,2:20.1:1:29.4:1:1:1.01:57.6:16:0.0264:0:4.9 -1 121485040 . TTGTGGCC CTTGAGGCT 51 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.16624;SOR=0.28636;LSEQ=GTAAGTGGATATTCTGACAT;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:3:3,0:62,61:0.0234:2,0:21.7:1:32.6:1:0.24476:0:35:6:0.0236:0.0078:6 0/0:294:2:2,0:142,146:0.0068:2,0:10:1:30.9:1:0.2457:0:32.5:4:0.0069:0.0034:5 -1 121485042 . GT TGA 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00242;SOR=0;LSEQ=AGTGGATATTCTGACATCTT;RSEQ=GGCCTTCGTTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:5:5,0:63,61:0.0376:2,0:11.2:1:29.4:1:0.05949:0:34.2:10:0.0382:0.0301:3.2 0/0:306:0:0,0:144,145:0:2,0:24.1:1:31.5:1:1:0:56.6:288:0.9505:0:3.3 -1 121485045 . G T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08365;SOR=0;LSEQ=GGATATTCTGACATCTTGTG;RSEQ=CCTTCGTTGGAAACGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:72,59:0.0147:2,2:14.5:1:31.5:1:1:1.2185:60:4:0.0152:0:6 0/0:333:0:0,0:184,148:0:2,0:22.4:1:31.2:1:1:0:54.1:82:1:0:3.4 -1 121485047 . C A 89 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73283;SOR=1.57057;LSEQ=ATATTCTGACATCTTGTGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:73,59:0.0147:2,2:39:1:32:0:1:1.2353:60:4:0.0152:0:4 0/1:349:8:4,4:193,146:0.0229:2,2:35.3:1:29.9:1:0.73053:1.32083:60:7:0.0208:0:3.9 -1 121485048 . T A 60 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.55624;LSEQ=TATTCTGACATCTTGTGGCC;RSEQ=TCGTTGGAAACGGGATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:1:0,1:78,61:0.0071:2,0:21:0:33:0:0.44286:0:60:2:0.0072:0:6 0/1:361:4:2,2:207,150:0.0111:2,2:27.3:1:30.3:1:1:1.37873:55:8:0.0112:0:4.3 -1 121485049 . T C 56 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5808;SOR=Inf;LSEQ=ATTCTGACATCTTGTGGCCT;RSEQ=CGTTGGAAACGGGATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:79,62:0:2,0:24.1:1:30.3:1:1:0:54.9:69.5:1:0:3.3 0/1:360:4:2,2:206,149:0.0111:2,2:15.3:1:28:1:1:1.38126:55.3:8:0.0112:0:5 -1 121485058 . A G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74857;SOR=0.78966;LSEQ=TCTTGTGGCCTTCGTTGGAA;RSEQ=CGGGATTTCTTCCTATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:4:4,0:97,66:0.024:2,0:8.8:1:32.5:1:0.15368:0:46:8:0.0245:0:5.3 0/1:421:8:8,0:255,157:0.019:2,0:10.5:1:33:1:0.02781:0:43.4:16:0.0192:0:4.5 -1 121485059 . C A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74707;SOR=0.77758;LSEQ=CTTGTGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCCTATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:4:2,2:101,60:0.0238:2,2:15:1:29.3:1:0.63172:1.67772:60:8:0.024:0:2.8 0/1:430:8:5,3:260,156:0.0186:2,2:23.5:1:27.5:1:1:1:56.3:3:0.0141:0:4 -1 121485060 . G A 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.70743;SOR=0.731;LSEQ=TTGTGGCCTTCGTTGGAAAC;RSEQ=GGATTTCTTCCTATTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:3:3,0:100,57:0.0184:2,0:7:1:31:1:0.55305:0:46.3:6:0.0185:0:2.3 0/1:444:6:3,3:275,160:0.0135:2,2:14.2:1:29.7:1:0.67434:1.71646:56.8:12:0.0137:0:3.8 -1 121485061 . G A 46 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61742;SOR=0.56015;LSEQ=TGTGGCCTTCGTTGGAAACG;RSEQ=GATTTCTTCCTATTCTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:2,0:105,59:0.0119:2,0:6.5:1:28:1:0.53903:0:49:4:0.0122:0:4 0/0:448:3:2,1:282,162:0.0067:2,2:21:1:29.3:1:1:1.15:47.7:6:0.0068:0:5.3 -1 121485071 . C A 266 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40629;SOR=0.64627;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TATTCTGCTAGACAGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:193:187:122,65:3,1:0.9689:2,2:22.1:1:30.4:1:1:1.59475:50.6:92.5:0.9737:0:3.7 1/1:486:463:292,171:13,4:0.9527:2,2:21.2:1:30.1:1:0.31359:1.90095:47.6:153.333:0.9563:0:3.8 -1 121485073 . A G 117 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3702;SOR=2.41728;LSEQ=TGGAAACGGGATTTCTTCCT;RSEQ=TTCTGCTAGACAGATGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:2,0:130,66:0.0101:2,0:22:1:34:0:0.5533:0:47:4:0.0102:0:5.5 0/1:498:12:9,3:308,178:0.0241:2,2:14.2:1:32.7:1:0.54946:1.73:39.6:24:0.0243:0:5.8 -1 121485074 . T C 89 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93436;LSEQ=GGAAACGGGATTTCTTCCTA;RSEQ=TCTGCTAGACAGATGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:3,0:131,68:0.0149:2,0:28.3:1:34:0:0.55228:0:40:6:0.0152:0:4.3 0/1:504:7:5,2:316,181:0.0139:2,2:30.4:1:32:1:1:1.43:32.3:14:0.0141:0:4.9 -1 121485076 . C A 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54752;SOR=1.19308;LSEQ=AAACGGGATTTCTTCCTATT;RSEQ=TGCTAGACAGATGAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:25:22,3:113,65:0.1225:2,2:25.2:1:28.7:1:0.01351:4.19:40.7:24:0.1188:0:4 0/1:511:73:58,15:261,170:0.1429:2,2:21.1:1:29:1:0.00161:2.51:37.9:72:0.1434:0:3.8 -1 121485078 . G C 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18971;SOR=Inf;LSEQ=ACGGGATTTCTTCCTATTCT;RSEQ=CTAGACAGATGAATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:141,67:0:2,0:22.4:1:32.3:1:1:0:49:103:1:0:3.6 0/1:514:6:3,3:325,180:0.0117:2,2:29.5:1:27.7:1:0.6716:1.80325:58:5:0.0099:0:5.2 -1 121485079 . C T 73 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69703;SOR=0.6788;LSEQ=CGGGATTTCTTCCTATTCTG;RSEQ=TAGACAGATGAATTCTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:2,1:139,66:0.0142:2,2:14.3:1:31.7:1:1:1.05277:41.7:6:0.0145:0:4 0/0:516:5:3,2:326,184:0.0097:2,2:22.8:1:31.6:1:1:1.18076:41.8:10:0.0099:0:5 -1 121485082 . G C 82 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03432;SOR=0.25667;LSEQ=GATTTCTTCCTATTCTGCTA;RSEQ=ACAGATGAATTCTCAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:6:3,3:138,60:0.0286:2,2:25.5:1:32:1:0.37546:2.28959:50.5:12:0.0288:0:4.5 0/0:535:4:3,1:330,185:0.0075:2,2:25.8:1:31.8:1:1:1.68:56.8:8:0.0075:0:5.5 -1 121485084 . C A 126 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04881;SOR=0.47764;LSEQ=TTTCTTCCTATTCTGCTAGA;RSEQ=AGATGAATTCTCAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:15:14,1:129,62:0.0708:2,1:23.3:1:31.4:1:0.04145:6.69:45:30:0.0714:0:3.7 0/1:542:19:13,6:330,180:0.0351:2,2:23:1:29.7:1:0.81176:1.18:38.9:38:0.0353:0:3.5 -1 121485088 . T A 270 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40167;SOR=0.76312;LSEQ=TTCCTATTCTGCTAGACAGA;RSEQ=GAATTCTCAGTAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:203:141,62:4,0:0.9269:0,2:24.8:1:30.4:1:0.31907:0:47:66.667:0.9302:0:3.5 1/1:566:513:337,176:14,6:0.9064:2,2:25.2:1:30.1:1:0.81263:1.21812:44.4:41.75:0.9076:0:3.5 -1 121485095 . T C 87 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01619;SOR=0.22531;LSEQ=TCTGCTAGACAGATGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:7:5,2:174,67:0.0281:2,2:23:1:31.1:1:1:1.03865:42.1:14:0.0286:0:4.3 0/0:619:4:3,1:409,205:0.0065:2,2:16.8:1:30.5:1:1:1.50:44.8:8:0.0066:0:4.5 -1 121485099 . T A 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.93012;SOR=0.98468;LSEQ=CTAGACAGATGAATTCTCAG;RSEQ=AACTTCCTTGTGTTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:59:42,17:142,55:0.2296:2,2:25.2:1:30.2:1:0.87058:1.04484:46.5:118:0.2296:0:4.8 0/1:648:147:84,63:345,151:0.2269:2,2:26.5:1:29.3:1:0.00698:1.71213:45.5:294:0.2286:0:5 -1 121485101 . A T 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5972;SOR=1.13439;LSEQ=AGACAGATGAATTCTCAGTA;RSEQ=CTTCCTTGTGTTGTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:33:22,11:165,61:0.1269:2,2:26.8:1:31.1:1:0.53263:1.35082:48.1:66:0.1274:0:4.6 0/1:671:95:47,48:399,176:0.1416:2,2:26:1:29.1:1:0.00024:2.31213:48.4:190:0.1433:0:4.6 -1 121485102 . C T 51 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06614;SOR=0.12599;LSEQ=GACAGATGAATTCTCAGTAA;RSEQ=TTCCTTGTGTTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:3:3,0:186,73:0.0115:2,0:35.7:1:32.3:1:0.56233:0:46.3:6:0.0115:0:4.3 0/0:688:1:0,1:455,230:0.0015:2,0:1:0:23:0:0.33673:0:45:2:0.0015:0:2 -1 121485104 . T G 97 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00657;LSEQ=CAGATGAATTCTCAGTAACT;RSEQ=CCTTGTGTTGTGTGTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:3,0:190,77:0.0111:2,0:36.3:1:33.7:1:0.56024:0:42.3:6:0.0113:0:3.3 0/1:718:8:5,3:466,242:0.0111:2,2:17.3:1:32.5:1:1:1.15512:43.8:16:0.0113:0:2.1 -1 121485106 . C G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74667;SOR=0.76774;LSEQ=GATGAATTCTCAGTAACTTC;RSEQ=TTGTGTTGTGTGTATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:4:3,1:194,83:0.0141:2,2:32.5:1:30.8:1:1:1.28:44.5:8:0.0143:0:6 0/1:735:8:6,2:468,241:0.0109:2,2:31:1:31.1:1:0.72318:1.54:41.1:16:0.0111:0:4.6 -1 121485111 . G A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77972;SOR=0.83839;LSEQ=ATTCTCAGTAACTTCCTTGT;RSEQ=TTGTGTGTATTCAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:5:4,1:207,94:0.0163:2,2:28.2:1:28:1:1:1.81:49.8:10:0.0166:0:3.2 0/1:801:11:8,3:513,276:0.0137:2,2:22.9:1:28.3:1:0.75575:1.43:40.3:22:0.0139:0:3.8 -1 121485114 . G T 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.22387;SOR=0.37092;LSEQ=CTCAGTAACTTCCTTGTGTT;RSEQ=TGTGTATTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:4:3,1:205,101:0.0127:2,2:19:1:29:1:1:1.48:47:8:0.0128:0:2.8 0/0:846:4:3,1:543,294:0.0047:2,2:23.5:1:31:1:1:1.62:48:8:0.0048:0:2.8 -1 121485118 . G T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.74498;SOR=0.9152;LSEQ=GTAACTTCCTTGTGTTGTGT;RSEQ=TATTCAACTCACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:14:10,4:204,111:0.0423:2,2:23.7:1:30.2:1:0.77745:1.36:46.8:28:0.0431:0:3 0/1:901:35:22,13:551,311:0.0388:2,2:26.9:1:28.5:1:1:1.04685:41.7:70:0.0392:0:3.3 -1 121485119 . T C 101 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75774;SOR=0.83523;LSEQ=TAACTTCCTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:4:4,0:216,119:0.0117:2,0:29.8:1:33:1:0.30179:0:42.5:8:0.0118:0:4.3 0/0:917:9:7,2:573,329:0.0098:2,2:24.1:1:32:1:0.49978:2.01:46.1:18:0.0099:0:3.7 -1 121485120 . A T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13609;SOR=0.70111;LSEQ=AACTTCCTTGTGTTGTGTGT;RSEQ=TTCAACTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:30:17,13:213,111:0.0845:2,2:22.7:1:29.6:1:0.32374:1.46581:45.2:60:0.0857:0:4.6 0/1:938:57:32,25:562,319:0.0608:2,2:25.1:1:29.2:1:0.2584:1.37584:43.2:114:0.0616:0:5.3 -1 121485132 . G C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9867;LSEQ=TTGTGTGTATTCAACTCACA;RSEQ=AGTTGAACGATCCTTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:423:6:3,3:256,159:0.0142:2,2:29.8:1:33:1:0.67984:1.60811:44.8:12:0.0143:0:5 0/1:1143:16:10,6:677,438:0.014:2,2:17.3:1:31.5:1:1:1.08:48.3:32:0.0141:0:3.2 -1 121485137 . G C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27643;SOR=0.73873;LSEQ=TGTATTCAACTCACAGAGTT;RSEQ=AACGATCCTTTACACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:24:14,10:263,178:0.0515:2,2:25.1:1:31.7:1:1:1.05524:49.3:48:0.0519:0:4.7 0/1:1193:46:29,17:674,454:0.0386:2,2:24:1:31.3:1:0.75943:1.15:46:92:0.0392:0:3.3 -1 121485140 . C T 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63722;SOR=1.14153;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=GATCCTTTACACAGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:24:15,9:265,181:0.0493:2,2:23.2:1:29.7:1:0.83357:1.14:51.3:23:0.0476:0:2.9 0/1:1235:69:43,26:656,465:0.0559:2,2:23:1:29.2:1:0.6147:1.17:47.2:33.5:0.055:0:2.8 -1 121485141 . G C 109 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13144;SOR=5.19284;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=ATCCTTTACACAGAGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:1:1,0:288,201:0.002:2,0:33:0:33:0:1:0:47:2:0.002:0:5 0/1:1249:13:7,6:716,499:0.0104:2,2:17.1:1:29.5:1:0.78035:1.22967:52.2:26:0.0106:0:3.3 -1 121485144 . C G 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26624;SOR=1.38588;LSEQ=AACTCACAGAGTTGAACGAT;RSEQ=CTTTACACAGAGCAGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:19:10,9:281,193:0.0375:2,2:26.2:1:31.7:1:0.63682:1.30961:49.7:38:0.0382:0:4.1 0/1:1289:66:34,32:680,484:0.0512:2,2:21.5:1:30.5:1:0.30529:1.32199:47.6:15.5:0.049:0:5 -1 121485145 . C G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24307;SOR=1.80089;LSEQ=ACTCACAGAGTTGAACGATC;RSEQ=TTTACACAGAGCAGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:6:3,3:288,214:0.0114:2,2:19.5:1:31:1:0.70401:1.34498:46.3:12:0.0118:0:3.7 0/1:1326:27:16,11:718,529:0.0204:2,2:29:1:28.8:1:1:1.07:44.2:12.5:0.0198:0:4.2 -1 121485151 . A T 76 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14788;SOR=0.45057;LSEQ=AGAGTTGAACGATCCTTTAC;RSEQ=CAGAGCAGACTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:7:4,3:303,238:0.0127:2,2:14.1:1:28.4:1:1:1.05:54.9:14:0.0129:0:4.7 0/0:1391:8:2,6:763,614:0.0058:2,2:17:1:25.5:1:0.14994:3.7247:54:7:0.0051:0:2.9 -1 121485152 . C G 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.67303;SOR=0.92335;LSEQ=GAGTTGAACGATCCTTTACA;RSEQ=AGAGCAGACTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:57:30,27:277,215:0.1025:2,2:22.9:1:31.4:1:0.67287:1.15922:52:56:0.1016:0:3 0/1:1415:135:87,48:687,581:0.0954:2,2:25.4:1:31.4:1:0.02303:1.53:50.8:270:0.0968:0:3.3 -1 121485156 . G A 120 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61642;SOR=1.52122;LSEQ=TGAACGATCCTTTACACAGA;RSEQ=CAGACTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:4:2,2:304,243:0.0072:2,2:18.5:1:30.3:1:1:1.25051:36.8:8:0.0074:0:4 0/1:1462:16:9,7:783,652:0.0109:2,2:31.7:1:30:1:1:1.07:50:32:0.0112:0:4.2 -1 121485157 . C T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80104;SOR=1.11557;LSEQ=GAACGATCCTTTACACAGAG;RSEQ=AGACTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:21:10,11:300,236:0.0374:2,2:27.3:1:27.3:1:0.50567:1.39744:52.2:20:0.0361:0:4.6 0/1:1467:61:25,36:762,633:0.0416:2,2:24.4:1:28:1:0.04818:1.73278:50.7:122:0.0427:0:4.8 -1 121485158 . A G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43978;SOR=0.76299;LSEQ=AACGATCCTTTACACAGAGC;RSEQ=GACTTGAAACACTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:566:11:7,4:307,247:0.0194:2,2:23.1:1:30:1:0.76214:1.41:51.7:22:0.0197:0:3.2 0/1:1477:22:12,10:786,667:0.0149:2,2:30.8:1:30.7:1:1:1.02:53.6:44:0.0151:0:3 -1 121485159 . G T 113 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00165;SOR=0.30521;LSEQ=ACGATCCTTTACACAGAGCA;RSEQ=ACTTGAAACACTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:17:9,8:301,243:0.0301:2,2:25.1:1:27.7:1:1:1.10086:47.6:16:0.0289:0:3.9 0/0:1491:14:8,6:797,670:0.0094:2,2:31.6:1:29.1:1:1:1.12:54.2:28:0.0095:0:3.6 -1 121485160 . A G 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0796;SOR=1.72964;LSEQ=CGATCCTTTACACAGAGCAG;RSEQ=CTTGAAACACTCTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:13:7,6:303,245:0.0228:2,2:28.2:1:30.6:1:1:1.05992:53.4:12:0.0215:0:4.8 0/1:1497:58:33,25:758,658:0.0387:2,2:28.2:1:30.9:1:0.68755:1.15:49.9:57:0.0387:0:4.5 -1 121485161 . C T 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00937;LSEQ=GATCCTTTACACAGAGCAGA;RSEQ=TTGAAACACTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:577:34:20,14:294,245:0.0589:2,2:25.4:1:31:1:0.72338:1.19:43.2:68:0.0595:0:3.9 0/1:1514:90:48,42:751,660:0.0594:2,2:24.9:1:29.8:1:1:1.00:46:89:0.0596:0:3.7 -1 121485165 . A T 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04491;SOR=1.5366;LSEQ=CTTTACACAGAGCAGACTTG;RSEQ=AACACTCTTTTTGTGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:595:30:17,13:302,262:0.0504:2,2:26.6:1:29.3:1:0.85155:1.13:50.1:60:0.0511:0:3.4 0/1:1564:118:63,55:753,680:0.0754:2,2:23.9:1:28.5:1:0.92366:1.03:49.9:236:0.0764:0:3.1 -1 121485170 . C T 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.15128;SOR=1.75839;LSEQ=CACAGAGCAGACTTGAAACA;RSEQ=TCTTTTTGTGGAATTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:9:5,4:320,278:0.0147:2,2:35.4:1:29.9:1:1:1.09:52.6:18:0.0149:0:2.6 0/1:1642:42:21,21:829,756:0.0256:2,2:26:1:30:1:0.87589:1.0965:50.7:84:0.0259:0:2.7 -1 121485171 . T A 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05762;SOR=0.51331;LSEQ=ACAGAGCAGACTTGAAACAC;RSEQ=CTTTTTGTGGAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:611:15:8,7:317,273:0.0245:2,2:30.7:1:29.6:1:1:1.016:49.3:30:0.025:0:3.3 0/1:1647:21:9,12:839,772:0.0128:2,2:28.5:1:28:1:0.51086:1.44871:54.3:20:0.0125:0:3.8 -1 121485172 . C G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07283;SOR=0.55135;LSEQ=CAGAGCAGACTTGAAACACT;RSEQ=TTTTTGTGGAATTTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:16:10,6:313,278:0.0261:2,2:28.3:1:33:1:0.61314:1.48:45.9:32:0.0266:0:3.2 0/1:1646:24:6,18:846,770:0.0146:2,2:19.8:1:31.2:1:0.01189:3.29389:47:48:0.0149:0:3.7 -1 121485173 . T C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.62932;SOR=0.90088;LSEQ=AGAGCAGACTTGAAACACTC;RSEQ=TTTTGTGGAATTTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:616:26:10,16:313,274:0.0422:2,2:24.5:1:31.1:1:0.16174:1.82593:45.8:25:0.0411:0:3.5 0/1:1650:63:35,28:813,760:0.0382:2,2:27:1:30.1:1:0.60772:1.17:54.2:30.5:0.0375:0:3 -1 121485175 . T G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.86696;SOR=0.93598;LSEQ=AGCAGACTTGAAACACTCTT;RSEQ=TTGTGGAATTTGCAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:13:7,6:314,279:0.0212:2,2:28.3:1:32.4:1:1:1.04:48.1:26:0.0215:0:3.9 0/1:1663:33:17,16:836,783:0.0198:2,2:26.9:1:30:1:1:1.00488:49.7:7.25:0.0177:0:4.3 -1 121485178 . G C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33012;SOR=0.74369;LSEQ=AGACTTGAAACACTCTTTTT;RSEQ=TGGAATTTGCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:617:16:11,5:312,286:0.0259:2,2:32.7:1:32.3:1:0.21417:2.01:46.3:32:0.0261:0:3.4 0/1:1700:33:15,18:852,803:0.0194:2,2:21.2:1:31.2:1:0.59848:1.27304:43.5:32:0.0191:0:3.8 -1 121485179 . T A 139 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-04;SOR=Inf;LSEQ=GACTTGAAACACTCTTTTTG;RSEQ=GGAATTTGCAAGTGGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:622:0:0,0:325,292:0:2,0:28.1:1:29.9:1:1:0:51.7:55.091:0.9918:0:2.5 0/1:1712:28:16,12:860,816:0.0164:2,2:24.1:1:29.1:1:0.57275:1.26:54.1:27:0.0162:0:4.3 -1 121485180 . G C 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50743;SOR=1.25434;LSEQ=ACTTGAAACACTCTTTTTGT;RSEQ=GAATTTGCAAGTGGAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:17:8,9:315,285:0.0271:2,2:31.4:1:31.3:1:0.80655:1.24298:54.9:34:0.0275:0:4.4 0/1:1717:58:33,25:835,803:0.0338:2,2:25.3:1:30.4:1:0.42347:1.27:52.3:116:0.0345:0:4.4 -1 121485181 . G T 157 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00045;SOR=5.74064;LSEQ=CTTGAAACACTCTTTTTGTG;RSEQ=AATTTGCAAGTGGAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:3:1,2:324,300:0.0048:2,2:36.7:1:29.3:1:0.6111:2.15745:32.7:6:0.0049:0:5 0/1:1720:46:19,27:847,803:0.0267:2,2:23.5:1:28.5:1:0.23132:1.49855:49.7:92:0.0272:0:4 -1 121485186 . T G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20965;SOR=1.76083;LSEQ=AACACTCTTTTTGTGGAATT;RSEQ=GCAAGTGGAGATTTCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:7:3,4:317,308:0.0111:2,2:32:1:31.4:1:0.72188:1.37161:48.3:14:0.0112:0:5.9 0/1:1706:33:18,15:846,821:0.0193:2,2:26.4:1:31.1:1:0.72695:1.16:49.8:66:0.0196:0:4.9 -1 121485190 . A GG 126 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.81327;SOR=1.32928;LSEQ=CTCTTTTTGTGGAATTTGCA;RSEQ=GTGGAGATTTCAGCCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:5:2,3:313,306:0.008:2,2:24:1:31.5:1:0.68352:1.53327:54:10:0.008:0.0032:3.4 0/1:1705:18:9,9:838,836:0.0106:2,2:28.2:1:30.4:1:1:1.00239:53.9:36:0.0108:0.0018:4.6 -1 121485191 . G T 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08059;SOR=0.55624;LSEQ=TCTTTTTGTGGAATTTGCAA;RSEQ=TGGAGATTTCAGCCGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:17:7,10:311,302:0.0268:2,2:28.2:1:30.6:1:0.4709:1.47024:55.8:34:0.0271:0:3.8 0/1:1723:26:14,12:837,837:0.0151:2,2:26.7:1:28.9:1:0.84382:1.17:53.7:25:0.0147:0:4 -1 121485202 . A T 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68626;SOR=1.3036;LSEQ=AATTTGCAAGTGGAGATTTC;RSEQ=GCCGCTTTGAGGTCAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:639:7:3,4:308,324:0.011:2,2:33.9:1:31.6:1:1:1.26702:52.4:14:0.011:0:4.3 0/1:1686:24:11,13:814,844:0.0142:2,2:24.9:1:30.4:1:0.83837:1.13972:52.2:48:0.0144:0:3.9 -1 121485204 . C A 90 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01013;SOR=0.23404;LSEQ=TTTGCAAGTGGAGATTTCAG;RSEQ=CGCTTTGAGGTCAATGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:631:8:4,4:302,316:0.0127:2,2:37.4:1:30.3:1:1:1.05:53.1:16:0.0128:0:4.3 0/0:1670:5:3,2:807,841:0.003:2,2:21.4:1:26.2:1:0.68111:1.56:44.8:4:0.0025:0:3.8 -1 121485205 . C T 147 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04913;SOR=2.80189;LSEQ=TTGCAAGTGGAGATTTCAGC;RSEQ=GCTTTGAGGTCAATGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:640:4:2,2:309,327:0.0063:2,2:32:1:31.3:1:1:1.06:54:8:0.0063:0:4.5 0/1:1674:29:11,18:804,838:0.0173:2,2:24.9:1:30.3:1:0.26498:1.56955:55.7:58:0.0176:0:4 -1 121485206 . G A 146 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01129;SOR=3.98449;LSEQ=TGCAAGTGGAGATTTCAGCC;RSEQ=CTTTGAGGTCAATGGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:3:2,1:314,321:0.0047:2,2:19:1:31.7:1:0.6209:2.04:48.3:6:0.0047:0:6 0/1:1685:31:15,16:795,844:0.0184:2,2:23.3:1:29.5:1:1:1.00474:54.6:30:0.018:0:4.2 -1 121485207 . C A 102 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19432;SOR=0.51905;LSEQ=GCAAGTGGAGATTTCAGCCG;RSEQ=TTTGAGGTCAATGGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:639:8:5,3:310,318:0.0125:2,2:25:1:30.6:1:0.50134:1.71:54.5:16:0.0127:0:3.4 0/0:1683:11:6,5:803,850:0.0065:2,2:23.4:1:29.6:1:0.76833:1.27:50.7:22:0.0066:0:3.3 -1 121485208 . T G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19528;SOR=1.71683;LSEQ=CAAGTGGAGATTTCAGCCGC;RSEQ=TTGAGGTCAATGGTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:638:9:6,3:305,318:0.0141:2,2:34.8:1:28.7:1:0.33323:2.08:43:8:0.0127:0:4.2 0/1:1668:40:20,20:777,832:0.024:2,2:18.8:1:30.1:1:0.87365:1.07:48.7:80:0.0245:0:3.2 -1 121485209 . T C 154 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00086;SOR=11.75517;LSEQ=AAGTGGAGATTTCAGCCGCT;RSEQ=TGAGGTCAATGGTAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:1:1,0:310,325:0.0016:2,0:12:0:32:0:0.48899:0:60:2:0.0016:0:4 0/1:1665:30:16,14:783,844:0.018:2,2:24.2:1:31.5:1:0.58604:1.23:56.6:60:0.0183:0:4.8 -1 121485212 . A T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.84933;SOR=0.94198;LSEQ=TGGAGATTTCAGCCGCTTTG;RSEQ=GGTCAATGGTAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:10:6,4:301,321:0.0155:2,2:30.6:1:29:1:0.53553:1.60:43.4:9:0.0141:0:4.2 0/1:1647:24:11,13:774,828:0.0146:2,2:24.7:1:29:1:0.83994:1.10466:52.1:23:0.0143:0:4.8 -1 121485213 . G A 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12031;SOR=1.37507;LSEQ=GGAGATTTCAGCCGCTTTGA;RSEQ=GTCAATGGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:36:18,18:294,311:0.0556:2,2:23.4:1:31.2:1:1:1.06:51.5:72:0.0564:0:4.3 0/1:1641:123:60,63:716,777:0.075:2,2:24.4:1:30.5:1:0.92525:1.03:51:60.5:0.0752:0:4.5 -1 121485214 . G T 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7401;SOR=0.93649;LSEQ=GAGATTTCAGCCGCTTTGAG;RSEQ=TCAATGGTAGAAAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:31:16,15:298,316:0.0479:2,2:23.5:1:29.3:1:0.85431:1.13:57.4:30:0.0469:0:3.8 0/1:1622:73:37,36:733,803:0.045:2,2:26.8:1:29.3:1:0.63347:1.13:54.1:72:0.0449:0:3.8 -1 121485217 . A C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47039;SOR=0.84595;LSEQ=ATTTCAGCCGCTTTGAGGTC;RSEQ=ATGGTAGAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:28:11,17:305,311:0.0433:2,2:21.3:1:31.1:1:0.33659:1.51467:47.8:27:0.0425:0:2.7 0/1:1601:59:25,34:731,804:0.0369:2,2:20.5:1:31.1:1:0.50689:1.23635:51.8:118:0.0374:0:2.4 -1 121485219 . T A 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49252;SOR=1.16753;LSEQ=TTCAGCCGCTTTGAGGTCAA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:35:15,20:296,305:0.054:2,2:22.3:1:30.2:1:0.49115:1.29346:51.4:16.5:0.0521:0:4.3 0/1:1584:99:44,55:693,764:0.0625:2,2:23.8:1:30.6:1:0.60337:1.13374:50:98:0.0629:0:4.6 -1 121485220 . G A 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06966;SOR=0.72967;LSEQ=TCAGCCGCTTTGAGGTCAAT;RSEQ=GTAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:56:27,29:281,297:0.0872:2,2:26.2:1:29:1:1:1.01619:49.6:27:0.0861:0:3.8 0/1:1565:102:47,55:686,753:0.0652:2,2:21.4:1:29:1:0.83755:1.06607:49.6:33:0.0642:0:3.2 -1 121485221 . G A 124 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03533;SOR=4.367;LSEQ=CAGCCGCTTTGAGGTCAATG;RSEQ=TAGAAAAGGAAATATCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:2:0,2:312,317:0.0031:2,0:22.5:1:32.5:1:0.49927:0:39:4:0.0032:0:5 0/1:1552:21:9,12:716,792:0.0135:2,2:22.6:1:28.4:1:0.82659:1.20524:53.9:42:0.0138:0:4.4 -1 121485226 . A C 116 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0082;SOR=Inf;LSEQ=GCTTTGAGGTCAATGGTAGA;RSEQ=AAGGAAATATCTTCGTATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:0:0,0:317,311:0:2,0:21.2:1:30.2:1:1:0:52.6:88.714:1:0:3.6 0/1:1480:15:6,9:702,759:0.0101:2,2:24.8:1:29.8:1:0.60994:1.38704:48.6:6.5:0.0089:0:4.6 -1 121485227 . A T 272 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59878;SOR=1.05313;LSEQ=CTTTGAGGTCAATGGTAGAA;RSEQ=AGGAAATATCTTCGTATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:292:148,144:162,162:0.4687:2,2:22:1:29.7:1:0.87214:1.03:56.6:145:0.4708:0:3.9 0/1:1468:707:354,353:349,397:0.4816:2,2:23.6:1:28.8:1:0.22711:1.14:56.7:87.375:0.4834:0:4 -1 121485230 . G T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1035;SOR=1.73996;LSEQ=TGAGGTCAATGGTAGAAAAG;RSEQ=AAATATCTTCGTATAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:11:5,6:305,303:0.0177:2,2:22:1:28.9:1:0.7722:1.20755:48.5:22:0.0179:0:4.3 0/1:1446:44:23,21:674,722:0.0304:2,2:19.2:1:28.5:1:0.64753:1.17:51.5:88:0.0307:0:3.7 -1 121485233 . A AC 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06825;SOR=0.63505;LSEQ=GGTCAATGGTAGAAAAGGAA;RSEQ=TATCTTCGTATAGAAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:29:18,11:290,290:0.0472:2,2:25.6:1:32.2:1:0.25422:1.64:46.6:58:0.0479:0.0033:4.9 0/1:1442:44:23,21:670,721:0.0305:2,2:27.1:1:30.9:1:0.64709:1.18:44.1:43:0.0301:0.0035:4.6 -1 121485236 . T C 82 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00392;SOR=0.1569;LSEQ=CAATGGTAGAAAAGGAAATA;RSEQ=CTTCGTATAGAAACAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:8:4,4:292,282:0.0137:2,2:28:1:27.6:1:1:1.03541:52.9:3:0.0103:0:6.1 0/0:1386:3:1,2:671,702:0.0022:2,2:16.3:1:32.7:1:1:1.91081:54.7:6:0.0022:0:5 -1 121485241 . G C 294 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17018;SOR=1.15245;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=TATAGAAACAAGACAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:553:284:142,142:115,111:0.5136:2,2:24.1:1:31.6:1:0.85885:1.03598:55.9:93.667:0.5165:0:4.1 1/0:1319:724:347,377:234,250:0.5489:2,2:22.6:1:31:1:0.90651:1.01691:55.8:102.429:0.5511:0:4.1 -1 121485244 . T G 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.26152;SOR=0.77933;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AGAAACAAGACAGAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:35:15,20:265,244:0.0638:2,2:25.6:1:31.9:1:0.30081:1.44709:43.3:70:0.0648:0:5 0/1:1290:65:32,33:604,604:0.0504:2,2:24:1:31.1:1:1:1.03123:44.3:64:0.0501:0:4.7 -1 121485246 . G A 265 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08984;SOR=0.83472;LSEQ=AAAGGAAATATCTTCGTATA;RSEQ=AAACAAGACAGAATGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:225:118,107:150,145:0.4237:2,2:25.4:1:30.1:1:0.72411:1.07:43.5:74:0.4229:0:4.3 0/1:1249:475:244,231:367,391:0.3803:2,2:24.2:1:29.9:1:0.32028:1.13:42:94:0.3809:0:4.3 -1 121485248 . A G 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00034;SOR=0.56592;LSEQ=AGGAAATATCTTCGTATAGA;RSEQ=ACAAGACAGAATGATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:80:43,37:229,222:0.1507:2,2:28.8:1:31.5:1:0.62998:1.13:44.8:39:0.1497:0:4.8 0/1:1272:116:62,54:570,582:0.0912:2,2:27.5:1:31.9:1:0.43679:1.17:43.7:232:0.0921:0:4.9 -1 121485250 . CA GT 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36586;SOR=0.76433;LSEQ=GAAATATCTTCGTATAGAAA;RSEQ=AGACAGAATGATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:19:12,7:253,239:0.0361:2,2:28.3:1:31.2:1:0.35667:1.62:56.6:38:0.0365:0:3.6 0/1:1293:36:14,22:631,606:0.0278:2,2:23.8:1:30.3:1:0.17702:1.63562:54.9:72:0.0281:0:3.6 -1 121485251 . A T 300 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.042;SOR=1.4556;LSEQ=AAATATCTTCGTATAGAAAC;RSEQ=AGACAGAATGATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:530:479:246,233:3,3:0.9038:2,2:25.4:1:29.6:1:1:1.06:50.6:118.75:0.9654:0:4 1/1:1306:1217:625,592:9,10:0.9319:2,2:21.9:1:29.3:1:0.81895:1.17:50.6:172.857:0.9727:0:3.9 -1 121485257 . G A 118 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30733;SOR=2.02729;LSEQ=CTTCGTATAGAAACAAGACA;RSEQ=AATGATTCTCAGAAACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:570:3:2,1:295,270:0.0053:2,2:25.7:1:31:1:1:1.83:59.3:6:0.0053:0:5.7 0/1:1413:15:5,10:712,676:0.0106:2,2:15.8:1:30.3:1:0.19922:2.10541:54:30:0.0107:0:5.3 -1 121485260 . T C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14794;SOR=1.64296;LSEQ=CGTATAGAAACAAGACAGAA;RSEQ=GATTCTCAGAAACTCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:12:4,8:297,268:0.0207:2,2:22.3:1:31.3:1:0.2461:2.21346:59.1:24:0.0209:0:3.6 0/1:1433:48:26,22:707,671:0.0335:2,2:24.9:1:30.8:1:0.7696:1.12:57.5:96:0.0338:0:3.9 -1 121485261 . G C 127 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05287;SOR=3.91575;LSEQ=GTATAGAAACAAGACAGAAT;RSEQ=ATTCTCAGAAACTCCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:2:1,1:299,279:0.0034:2,2:10:1:32:1:1:1.07153:50:4:0.0035:0:4 0/1:1428:19:11,8:717,677:0.0133:2,2:11.3:1:30.1:1:0.64832:1.30:43.5:38:0.0135:0:4.3 -1 121485265 . C G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83767;SOR=0.91056;LSEQ=AGAAACAAGACAGAATGATT;RSEQ=TCAGAAACTCCTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:590:9:5,4:303,276:0.0153:2,2:11.2:1:31.7:1:1:1.14:56.1:18:0.0155:0:3.8 0/1:1438:20:12,8:727,683:0.0139:2,2:27.1:1:32.8:1:0.50533:1.41:57.2:40:0.014:0:4.2 -1 121485266 . T C 81 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09087;SOR=0.34098;LSEQ=GAAACAAGACAGAATGATTC;RSEQ=CAGAAACTCCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:592:6:3,3:307,279:0.0101:2,2:26.3:1:31.7:1:1:1.10018:55.3:12:0.0103:0:5.7 0/0:1438:5:2,3:740,692:0.0035:2,2:15.4:1:30.4:1:0.67749:1.60351:49.4:10:0.0035:0:6.8 -1 121485267 . C G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05176;SOR=0.48869;LSEQ=AAACAAGACAGAATGATTCT;RSEQ=AGAAACTCCTTTGTGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:600:15:10,5:304,281:0.025:2,2:21.3:1:31.5:1:0.3037:1.85:52.3:30:0.0254:0:4.6 0/1:1455:18:11,7:726,698:0.0124:2,2:25.9:1:29.3:1:0.47988:1.51:55.3:8:0.0111:0:3.6 -1 121485269 . G T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16567;SOR=1.35168;LSEQ=ACAAGACAGAATGATTCTCA;RSEQ=AAACTCCTTTGTGATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:31:13,18:295,267:0.0513:2,2:22.5:1:28.9:1:0.27262:1.52871:54.4:62:0.0518:0:3.5 0/1:1482:101:48,53:706,662:0.0682:2,2:26:1:28.3:1:0.47064:1.17742:54.9:32.667:0.067:0:4 -1 121485273 . C A 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5233;SOR=0.86584;LSEQ=GACAGAATGATTCTCAGAAA;RSEQ=TCCTTTGTGATGTGTGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:617:36:18,18:293,279:0.0583:2,2:25.7:1:31.2:1:1:1.05012:46.5:72:0.0592:0:5.5 0/1:1532:78:37,41:737,704:0.0509:2,2:22.4:1:28.7:1:0.5619:1.15994:46.6:14.6:0.0483:0:5 -1 121485275 . C T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19967;SOR=1.3609;LSEQ=CAGAATGATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:617:26:9,17:290,281:0.0421:2,2:25.6:1:31.2:1:0.11362:1.94725:42.7:52:0.0428:0:3.3 0/1:1540:87:45,42:718,699:0.0565:2,2:20.9:1:29.3:1:0.91216:1.04:44.2:86:0.0565:0:3.2 -1 121485276 . C T 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53547;SOR=0.86248;LSEQ=AGAATGATTCTCAGAAACTC;RSEQ=TTTGTGATGTGTGCGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:26:12,14:291,289:0.0419:2,2:23:1:31.6:1:0.84159:1.17443:47.9:52:0.043:0:5.1 0/1:1542:56:30,26:746,715:0.0363:2,2:23.3:1:29.8:1:0.78577:1.11:47:55:0.0365:0:5 -1 121485277 . T A 117 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11844;SOR=3.29312;LSEQ=GAATGATTCTCAGAAACTCC;RSEQ=TTGTGATGTGTGCGTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:2:1,1:316,312:0.0032:2,2:34:0:32:0:1:1.0128:50:4:0.0032:0:5.5 0/1:1546:16:8,8:783,742:0.0103:2,2:19.4:1:29.3:1:1:1.05524:45.9:15:0.0099:0:4.1 -1 121485280 . G C 117 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34373;SOR=0.66229;LSEQ=TGATTCTCAGAAACTCCTTT;RSEQ=TGATGTGTGCGTTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:640:8:3,5:311,313:0.0125:2,2:24.1:1:31.9:1:0.72486:1.65471:45.9:16:0.0127:0:4.9 0/0:1564:13:6,7:790,751:0.0083:2,2:22.8:1:31.7:1:0.78531:1.22709:55.4:26:0.0084:0:3.8 -1 121485283 . A C 102 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13587;SOR=0.49428;LSEQ=TTCTCAGAAACTCCTTTGTG;RSEQ=TGTGTGCGTTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:651:9:5,4:313,324:0.0138:2,2:31.3:1:32.4:1:0.74873:1.29:54.3:18:0.014:0:4.2 0/0:1599:11:4,7:807,770:0.0069:2,2:32.2:1:29.7:1:0.37688:1.83339:59.7:10:0.0063:0:4.6 -1 121485286 . T C 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03423;SOR=0.30686;LSEQ=TCAGAAACTCCTTTGTGATG;RSEQ=GTGCGTTCAACTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:661:8:4,4:319,332:0.0121:2,2:33.5:1:30.9:1:1:1.04:42.6:16:0.0123:0:3.5 0/0:1603:6:3,3:812,780:0.0037:2,2:23.7:1:31.3:1:1:1.04101:60:12:0.0038:0:2.7 -1 121485287 . G C 126 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.82223;SOR=1.17013;LSEQ=CAGAAACTCCTTTGTGATGT;RSEQ=TGCGTTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:666:6:4,2:322,336:0.009:2,2:28.2:1:30:1:0.4432:2.08:54.7:12:0.0091:0:4.3 0/1:1615:17:10,7:811,784:0.0105:2,2:26.1:1:30.9:1:0.62825:1.38:53.5:34:0.0106:0:3.5 -1 121485288 . T G 112 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.4819;SOR=0.71859;LSEQ=AGAAACTCCTTTGTGATGTG;RSEQ=GCGTTCAACTCACAGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:8:4,4:322,334:0.012:2,2:25:1:31.4:1:1:1.04:52.6:16:0.012:0:3.6 0/0:1624:14:7,7:815,784:0.0086:2,2:22.4:1:29.6:1:1:1.03953:46.9:13:0.0081:0:3.1 -1 121485289 . G T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67196;SOR=0.82729;LSEQ=GAAACTCCTTTGTGATGTGT;RSEQ=CGTTCAACTCACAGAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:672:9:5,4:322,337:0.0134:2,2:17.1:1:31:1:0.74762:1.31:54.2:18:0.0137:0:2.9 0/1:1621:18:12,6:805,790:0.0111:2,2:14.4:1:28.6:1:0.23596:1.96:51.9:17:0.0107:0:3.3 -1 121485290 . C T 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22787;SOR=1.21618;LSEQ=AAACTCCTTTGTGATGTGTG;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:61:26,35:302,304:0.0909:2,2:25.2:1:29.4:1:0.34708:1.33671:51:19.333:0.0875:0:3.9 0/1:1623:176:91,85:723,715:0.1084:2,2:25.6:1:29.6:1:0.74969:1.06:49.3:175:0.1092:0:3.9 -1 121485291 . G A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15366;SOR=0.64785;LSEQ=AACTCCTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:19:9,10:310,328:0.0281:2,2:29.7:1:30.7:1:1:1.05007:55.3:38:0.0284:0:3.7 0/1:1634:30:14,16:787,784:0.0184:2,2:33.1:1:29.7:1:0.71744:1.14713:53.9:60:0.0185:0:3.7 -1 121485294 . C G 105 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00968;SOR=0.29734;LSEQ=TCCTTTGTGATGTGTGCGTT;RSEQ=AACTCACAGAGTTTAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:11:4,7:322,341:0.0162:2,2:19.8:1:30.6:1:0.54789:1.65129:57.2:10:0.015:0:3.7 0/0:1643:8:4,4:808,811:0.0049:2,2:34.5:1:31.4:1:1:1.00:53.4:16:0.0049:0:3.4 -1 121485297 . C A 88 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01397;SOR=0.25115;LSEQ=TTTGTGATGTGTGCGTTCAA;RSEQ=TCACAGAGTTTAACCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:8:4,4:318,338:0.0119:2,2:21.8:1:29.5:1:1:1.06:53.6:16:0.012:0:4.9 0/0:1666:5:3,2:818,831:0.003:2,2:31:1:30.8:1:0.68488:1.52:46.8:10:0.003:0:3.6 -1 121485298 . T A 125 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46785;SOR=1.71928;LSEQ=TTGTGATGTGTGCGTTCAAC;RSEQ=CACAGAGTTTAACCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:4:3,1:321,344:0.006:2,2:17.5:1:30.5:1:0.35887:3.21:57:8:0.006:0:4.3 0/1:1663:17:10,7:813,831:0.0102:2,2:27.8:1:30.7:1:0.47475:1.46:52.6:34:0.0103:0:3.9 -1 121485303 . G C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19061;SOR=1.66094;LSEQ=ATGTGTGCGTTCAACTCACA;RSEQ=AGTTTAACCTTTCTTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:681:9:5,4:312,350:0.0132:2,2:21.8:1:29.7:1:0.7418:1.40:55.8:8:0.0119:0:2.6 0/1:1700:37:22,15:811,840:0.0218:2,2:29.5:1:31.4:1:0.24591:1.52:52.2:74:0.022:0:2.8 -1 121485308 . T C 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.708;SOR=1.09579;LSEQ=TGCGTTCAACTCACAGAGTT;RSEQ=AACCTTTCTTTTCATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:40:19,21:293,342:0.0589:2,2:21:1:31.2:1:0.87177:1.06:53.2:39:0.0582:0:3.9 0/1:1698:109:51,58:777,803:0.0642:2,2:24.3:1:30.8:1:0.69215:1.10036:55.1:108:0.0646:0:3.6 -1 121485312 . C T 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.196;SOR=0.82664;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCTTTTCATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:662:75:33,42:266,309:0.1133:2,2:26.3:1:30.1:1:0.80559:1.09544:49.4:36.5:0.1128:0:3.8 0/1:1696:162:69,93:741,766:0.0955:2,2:26.3:1:30.2:1:0.11653:1.30363:50:324:0.0965:0:3.5 -1 121485318 . T G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.63906;SOR=1.11909;LSEQ=TCACAGAGTTTAACCTTTCT;RSEQ=TTCATAGAGCAGTTAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:652:39:22,17:271,335:0.0598:2,2:22.9:1:31.7:1:0.18477:1.60:53.5:38:0.059:0:2.4 0/1:1685:112:55,57:742,825:0.0665:2,2:25.3:1:31.2:1:0.76913:1.07:53.3:111:0.0665:0:2.7 -1 121485319 . T C 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.89537;SOR=0.96714;LSEQ=CACAGAGTTTAACCTTTCTT;RSEQ=TCATAGAGCAGTTAGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:21:10,11:280,344:0.0325:2,2:24.6:1:31:1:0.82676:1.12:52.8:42:0.0328:0:3.9 0/1:1684:53:21,32:770,853:0.0315:2,2:26.5:1:31.6:1:0.3278:1.37528:52.9:106:0.0318:0:4.3 -1 121485323 . T A 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13945;SOR=0.70069;LSEQ=GAGTTTAACCTTTCTTTTCA;RSEQ=AGAGCAGTTAGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:638:30:16,14:256,332:0.047:2,2:28:1:29.7:1:0.3469:1.48:42.3:60:0.0475:0:2.6 0/1:1676:56:32,24:725,824:0.0334:2,2:30.1:1:29.2:1:0.13566:1.51:49.5:27:0.0325:0:2.5 -1 121485329 . A T 113 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08507;SOR=0.4963;LSEQ=AACCTTTCTTTTCATAGAGC;RSEQ=GTTAGGAAACACTCTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:12:7,5:256,354:0.0193:2,2:26.5:1:29.6:1:0.37686:1.93:51.5:24:0.0196:0:2.7 0/0:1658:16:8,8:738,893:0.0097:2,2:30.7:1:28.3:1:0.80271:1.21:54.6:7:0.0085:0:2.4 -1 121485333 . A G 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.60277;SOR=1.11217;LSEQ=TTTCTTTTCATAGAGCAGTT;RSEQ=GGAAACACTCTGTTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:46:18,28:230,321:0.0765:2,2:26.9:1:30.9:1:0.75817:1.11434:53:22:0.0738:0:3.7 0/1:1635:138:61,77:669,807:0.0844:2,2:24.2:1:30.6:1:0.85816:1.04642:54.8:68:0.084:0:3.3 -1 121485335 . G T 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.02146;LSEQ=TCTTTTCATAGAGCAGTTAG;RSEQ=AAACACTCTGTTTGTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:596:41:13,28:234,317:0.0688:2,2:27.7:1:29.1:1:0.19279:1.58871:51.1:82:0.0697:0:4.2 0/1:1639:115:47,68:690,826:0.0702:2,2:25.3:1:28:1:0.38191:1.20845:50.4:56.5:0.0696:0:4.1 -1 121485341 . C G 84 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02748;SOR=0.24254;LSEQ=CATAGAGCAGTTAGGAAACA;RSEQ=TCTGTTTGTAAAGTCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:584:6:3,3:234,340:0.0103:2,2:9.7:1:32.5:1:0.69239:1.45:52.7:12:0.0104:0:2.3 0/0:1594:4:3,1:695,887:0.0025:2,2:10.8:1:27.3:1:0.32613:3.83:44.8:3:0.0019:0:4 -1 121485343 . CTGTT C 119 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.80034;SOR=0.85523;LSEQ=TAGAGCAGTTAGGAAACACT;RSEQ=TGTAAAGTCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:566:6:3,3:215,340:0.0106:2,2:29:1:31.2:1:0.68199:1.58:57.5:12:0.0107:0.0035:2.2 0/0:1542:14:4,10:653,867:0.0091:2,2:34.5:1:31.5:1:0.41693:1.88219:54.6:28:0.0092:0.0026:3.1 -1 121485349 . G A 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62613;SOR=1.12068;LSEQ=AGTTAGGAAACACTCTGTTT;RSEQ=TAAAGTCTGCAAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:36:10,26:192,298:0.0672:2,2:25.1:1:30.9:1:0.21474:1.67362:49.4:72:0.0677:0:3.9 0/1:1433:107:43,64:542,757:0.0747:2,2:24.4:1:28.9:1:0.83842:1.06562:49.8:106:0.0744:0:4 -1 121485350 . T A 117 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18218;SOR=3.05878;LSEQ=GTTAGGAAACACTCTGTTTG;RSEQ=AAAGTCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:2:1,1:204,333:0.0037:2,2:27.5:1:30:1:1:1.63:50:4:0.0037:0:5 0/1:1420:16:7,9:578,819:0.0113:2,2:14.4:1:29.4:1:1:1.10:57.4:32:0.0113:0:2.2 -1 121485351 . A G 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13566;SOR=1.88576;LSEQ=TTAGGAAACACTCTGTTTGT;RSEQ=AAGTCTGCAAGTGGATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:535:8:3,5:192,326:0.015:2,2:15.4:1:30.3:1:1:1.02:42:16:0.0151:0:4.6 0/1:1401:39:9,30:560,790:0.0278:2,2:24.1:1:29.8:1:0.02103:2.36154:42.8:38:0.0272:0:4.9 -1 121485354 . G C 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15938;SOR=1.46915;LSEQ=GGAAACACTCTGTTTGTAAA;RSEQ=TCTGCAAGTGGATATTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:20:5,15:177,302:0.0394:2,2:28:1:32.2:1:0.3474:1.75646:50.9:40:0.0399:0:2.6 0/1:1353:77:23,54:519,748:0.0569:2,2:25.2:1:32:1:0.05621:1.62848:48.1:154:0.0573:0:2.7 -1 121485355 . T C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37065;SOR=1.47074;LSEQ=GAAACACTCTGTTTGTAAAG;RSEQ=CTGCAAGTGGATATTCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:8:3,5:179,313:0.0159:2,2:15:1:30.4:1:1:1.05:41.5:16:0.0162:0:4.9 0/1:1335:31:4,27:527,771:0.0232:2,2:24.4:1:30.8:1:0.00134:4.60975:42.5:62:0.0235:0:5.2 -1 121485359 . C T 104 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.18072;SOR=2.82193;LSEQ=CACTCTGTTTGTAAAGTCTG;RSEQ=AAGTGGATATTCAGACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:2:0,2:162,302:0.0042:2,0:29.5:1:30:0:0.54545:0:38.5:4:0.0043:0:3 0/1:1269:15:6,9:486,756:0.0118:2,2:24.7:1:26.7:1:1:1.04:47.7:14:0.0111:0:4.3 -1 121485360 . A C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1038;SOR=2.06572;LSEQ=ACTCTGTTTGTAAAGTCTGC;RSEQ=AGTGGATATTCAGACCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:6:0,6:158,298:0.0129:2,0:24:1:32.3:1:0.0992:0:47.7:12:0.0131:0:5.3 0/1:1252:33:6,27:478,740:0.0264:2,2:26.5:1:31.2:1:0.01725:2.90465:42.3:66:0.0265:0:5.3 -1 121485361 . A T 105 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00049;SOR=0.16187;LSEQ=CTCTGTTTGTAAAGTCTGCA;RSEQ=GTGGATATTCAGACCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:452:11:3,8:150,289:0.0243:2,2:21.1:1:30.4:1:0.75642:1.38314:53.1:22:0.0246:0:4.2 0/0:1245:5:2,3:478,759:0.004:2,2:30:1:30.4:1:1:1.06:47.8:10:0.0041:0:4.2 -1 121485365 . G C 96 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04384;SOR=0.35554;LSEQ=GTTTGTAAAGTCTGCAAGTG;RSEQ=ATATTCAGACCTCCTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:8:2,6:138,281:0.0186:2,2:17.6:1:32.3:1:1:1.47207:51.5:16:0.0189:0:2.9 0/0:1193:8:3,5:447,730:0.0067:2,2:21.3:1:32.1:1:1:1.02053:51.4:16:0.0068:0:3.1 -1 121485369 . T A 106 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20433;SOR=4.40418;LSEQ=GTAAAGTCTGCAAGTGGATA;RSEQ=TCAGACCTCCTTGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:1,0:131,276:0.0024:2,0:20:0:32:0:0.32353:0:44:2:0.0025:0:2 0/1:1123:12:4,8:423,684:0.0107:2,2:22.8:1:29.8:1:1:1.23658:47.7:24:0.0108:0:4.3 -1 121485370 . T A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04395;SOR=Inf;LSEQ=TAAAGTCTGCAAGTGGATAT;RSEQ=CAGACCTCCTTGAGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:130,271:0:2,0:24.3:1:30.2:1:1:0:51.2:99.25:0.9876:0:2.4 0/1:1098:12:7,5:409,670:0.0109:2,2:13.9:1:24.8:1:0.22996:2.29:50.2:11:0.0101:0:3.6 -1 121485371 . C T 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09167;SOR=0.27786;LSEQ=AAAGTCTGCAAGTGGATATT;RSEQ=AGACCTCCTTGAGGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:4:1,3:126,262:0.01:2,2:5.5:1:28.8:1:1:1.44149:55.8:8:0.0102:0:2.5 0/0:1073:3:2,1:399,656:0.0028:2,2:11.7:1:29:1:0.56095:3.28:33:6:0.0028:0:2.7 -1 121485372 . A G 133 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50438;SOR=1.566;LSEQ=AAGTCTGCAAGTGGATATTC;RSEQ=GACCTCCTTGAGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:5:0,5:125,254:0.0128:2,0:24.6:1:31:1:0.17832:0:40.2:10:0.0131:0:5.2 0/1:1056:21:0,21:396,633:0.0199:2,1:28:1:30.5:1:5e-05:0:38.8:42:0.0202:0:5.9 -1 121485376 . C A 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.36671;SOR=1.19948;LSEQ=CTGCAAGTGGATATTCAGAC;RSEQ=TCCTTGAGGCCTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:43:15,28:87,195:0.1204:2,2:29.3:1:30.6:1:0.59993:1.20:52.2:42:0.1207:0:3.2 0/1:978:138:64,74:267,506:0.1411:2,2:28:1:30:1:0.00937:1.64:51.3:137:0.1421:0:3.2 -1 121485377 . T C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41377;SOR=1.29371;LSEQ=TGCAAGTGGATATTCAGACC;RSEQ=CCTTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:16:2,14:108,224:0.046:2,2:24.7:1:32.1:1:0.10571:3.36595:45.2:32:0.0466:0:5 0/1:954:56:14,42:327,567:0.0587:2,2:26.9:1:30.9:1:0.08594:1.72924:43.6:112:0.0595:0:4.6 -1 121485379 . C T 268 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.79738;SOR=1.04173;LSEQ=CAAGTGGATATTCAGACCTC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:331:169:39,130:64,93:0.5106:2,2:24.6:1:30.4:1:0.00081:2.28795:47.2:41.25:0.5124:0:3.2 1/0:914:476:130,346:188,235:0.5208:2,2:25.5:1:30.2:1:0:2.12741:46.9:51.889:0.5206:0:3.1 -1 121485380 . T C 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01997;SOR=0.09061;LSEQ=AAGTGGATATTCAGACCTCC;RSEQ=TGAGGCCTTCGTTGGAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:4:1,3:99,223:0.0122:2,2:18.8:1:26.3:1:1:1.33068:51.3:3:0.0093:0:2.3 0/0:897:1:1,0:314,580:0.0011:2,0:50:0:29:0:0.35196:0:23:2:0.0011:0:3 -1 121485381 . T A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.75794;SOR=0.83676;LSEQ=AGTGGATATTCAGACCTCCT;RSEQ=GAGGCCTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:4:2,2:99,222:0.0123:2,2:27.8:1:29:1:0.59093:2.24:47.3:8:0.0125:0:4 0/1:875:9:5,4:306,558:0.0103:2,2:13.9:1:27.9:1:0.29358:2.28:52.8:18:0.0104:0:2.4 -1 121485385 . G A 67 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06432;SOR=0.29102;LSEQ=GATATTCAGACCTCCTTGAG;RSEQ=CCTTCGTTGGAAACGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:5:3,2:88,200:0.0169:2,2:33:1:29.2:1:0.17556:3.39:51.2:10:0.0172:0:3.6 0/0:805:4:1,3:272,523:0.005:2,2:31:1:30.5:1:1:1.55943:50.8:8:0.0051:0:4.3 -1 121485386 . C T 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.08632;LSEQ=ATATTCAGACCTCCTTGAGG;RSEQ=CTTCGTTGGAAACGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:86,195:0.0104:2,2:28.3:1:30.3:1:1:1.13:42.7:6:0.0108:0:3.3 0/1:796:9:3,6:266,514:0.0113:2,2:29.2:1:29:1:1:1.03498:50.8:18:0.0114:0:4.3 -1 121485387 . C T 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.83692;SOR=0.95346;LSEQ=TATTCAGACCTCCTTGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:38:13,25:73,169:0.1343:2,2:28.8:1:30.9:1:0.70547:1.20:51.2:76:0.1362:0:3.4 0/1:784:101:48,53:215,459:0.1288:2,2:29.4:1:30.4:1:0.00321:1.93:51.6:100:0.1295:0:3.4 -1 121485390 . C T 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0117;SOR=0.17197;LSEQ=TCAGACCTCCTTGAGGCCTT;RSEQ=GTTGGAAACGGGATTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:6:3,3:71,181:0.023:2,2:35.2:1:29.7:1:0.35817:2.54:49:12:0.0233:0:3.3 0/0:746:3:1,2:251,486:0.004:2,2:19:1:29.3:1:1:1.03288:50.3:6:0.0041:0:2.7 -1 121485391 . G T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54575;SOR=0.79102;LSEQ=CAGACCTCCTTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:10:3,7:68,170:0.04:2,2:27.5:1:31.5:1:1:1.07:46.2:20:0.0405:0:3.3 0/1:721:23:8,15:234,453:0.0319:2,2:25.8:1:29.1:1:1:1.03:54.4:10.5:0.0295:0:3.2 -1 121485392 . T A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11292;SOR=0.23154;LSEQ=AGACCTCCTTGAGGCCTTCG;RSEQ=TGGAAACGGGATTTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:70,172:0.0122:2,2:29.3:1:28:1:0.20727:4.88:60:6:0.0123:0:3 0/0:703:2:2,0:235,457:0.0028:2,0:1:0:23.5:1:0.1163:0:49.5:4:0.0029:0:2.5 -1 121485398 . A G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19259;SOR=0.69747;LSEQ=CCTTGAGGCCTTCGTTGGAA;RSEQ=CGGGATTTCTTCATATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:22:7,15:53,143:0.1005:2,2:20.2:1:30.8:1:0.62123:1.26:50.1:10:0.093:0:4.4 0/1:623:45:14,31:197,381:0.0722:2,2:24.7:1:31.8:1:0.74588:1.1447:49.8:44:0.0712:0:4.2 -1 121485399 . C A 98 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74047;SOR=1.74325;LSEQ=CTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCATATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:2:0,2:56,152:0.0094:2,0:24.5:1:33:0:1:0:60:4:0.0096:0:3 0/1:612:10:5,5:201,395:0.0163:2,2:23.2:1:29.6:1:0.31986:1.96:49.1:20:0.0165:0:3.9 -1 121485400 . G A 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32879;SOR=0.52661;LSEQ=TTGAGGCCTTCGTTGGAAAC;RSEQ=GGATTTCTTCATATTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:5:3,2:48,142:0.0251:2,2:25.4:1:30.2:1:0.11328:4.40:57.4:10:0.0253:0:2.6 0/1:598:8:3,5:200,387:0.0134:2,2:22.3:1:30.5:1:1:1.16:52.8:16:0.0135:0:3.1 -1 121485403 . A T 130 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.8117;SOR=1.25916;LSEQ=AGGCCTTCGTTGGAAACGGG;RSEQ=TTTCTTCATATTCTGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:5:0,5:47,129:0.0275:2,0:11.2:1:31.2:1:0.32903:0:39.2:10:0.0279:0:3.8 0/1:553:19:1,18:175,349:0.0344:2,1:12.2:1:30.8:1:0.01032:9.00459:40.2:38:0.0345:0:4.2 -1 121485407 . C T 117 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.59533;SOR=0.73546;LSEQ=CTTCGTTGGAAACGGGATTT;RSEQ=TTCATATTCTGCTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:6:0,6:43,112:0.0373:2,0:7:1:31:1:0.34346:0:37.2:12:0.0385:0:4.2 0/1:506:14:0,14:167,321:0.0277:2,1:7.1:1:30.9:1:0.00669:0:39.9:28:0.0278:0:4.1 -1 121485408 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05935;SOR=0;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TCATATTCTGCTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:40,116:0.0127:2,2:23.5:1:29.5:1:0.45287:2.88:37:4:0.0128:0:4.5 0/0:489:0:0,0:161,322:0:2,0:17.4:1:30.4:1:1:0:49:240.5:0.9897:0:2.5 -1 121485411 . A C 130 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18508;SOR=3.04411;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TATTCTGCTAGACAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:0,2:41,106:0.0133:2,0:4.5:1:33.5:1:1:0:55.5:4:0.0138:0:2.5 0/1:455:18:7,11:141,293:0.0396:2,2:16.3:1:31.3:1:0.61145:1.32:46.4:36:0.0399:0:2.7 -1 121485413 . A G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38988;SOR=0.59413;LSEQ=TGGAAACGGGATTTCTTCAT;RSEQ=TTCTGCTAGACAGAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:6:2,4:34,99:0.0426:2,2:12.5:1:32.2:1:0.64904:1.45:47.5:12:0.0435:0:4.2 0/1:428:11:2,9:137,279:0.0257:2,2:18.4:1:31.2:1:0.51543:2.20619:47.1:22:0.0259:0:4.6 -1 121485414 . T C 102 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12114;SOR=Inf;LSEQ=GGAAACGGGATTTCTTCATA;RSEQ=TCTGCTAGACAGAAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:35,100:0:2,0:14.3:1:30.5:1:1:0:49.7:26:1:0:2.6 0/1:414:9:3,6:133,271:0.0217:2,2:13.1:1:32.4:1:1:1.02:40.9:18:0.022:0:4.1 -1 121485416 . C A 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48855;SOR=0.83705;LSEQ=AAACGGGATTTCTTCATATT;RSEQ=TGCTAGACAGAAGAATTCNN GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:38:5,33:28,57:0.3016:2,2:12.3:1:30.8:1:0.0273:3.21453:45.4:76:0.3089:0:3.1 0/1:373:99:22,77:101,159:0.2654:2,2:11.6:1:29.4:1:0.00286:2.2186:46.1:32:0.263:0:2.8 -1 121485420 . T C 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15756;SOR=0.16649;LSEQ=GGGATTTCTTCATATTCTGC;RSEQ=AGACAGAAGAATTCNNNNNN GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:28,78:0.0185:2,2:5.5:1:32.5:1:0.46677:2.75:37.5:4:0.0189:0:5 0/0:321:1:0,1:105,214:0.0031:2,0:15:0:31:0:1:0:40:2:0.0031:0:3 -1 121485422 . G T 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79101;SOR=1.32498;LSEQ=GATTTCTTCATATTCTGCTA;RSEQ=ACAGAAGAATTCNNNNNNNN GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:4:1,3:26,70:0.0388:2,2:10:1:29.8:1:1:1.11311:52.5:8:0.0388:0:4 0/1:295:15:6,9:83,191:0.0508:2,2:11.9:1:29.5:1:0.4059:1.53:44.4:30:0.0514:0:4.3 -1 121485424 . C A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98604;LSEQ=TTTCTTCATATTCTGCTAGA;RSEQ=AGAAGAATTCNNNNNNNNNN GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:7:3,4:21,63:0.0729:2,2:5.6:1:30.1:1:0.37477:2.23:49.4:14:0.0737:0:3.7 0/1:264:19:6,13:71,165:0.072:2,2:9.7:1:30.4:1:1:1.07:49:38:0.072:0:3.3 -1 121485426 . G T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61557;SOR=0.55438;LSEQ=TCTTCATATTCTGCTAGACA;RSEQ=AAGAATTCNNNNNNNNNNNN GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:0,2:24,66:0.0217:2,0:6.5:1:30:0:1:0:60:4:0.0222:0:1 0/1:247:3:2,1:70,174:0.0121:2,2:9.7:1:29.3:1:0.20432:4.93:22.7:6:0.0122:0:3 -1 121485429 . G T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74725;SOR=0.78041;LSEQ=TCATATTCTGCTAGACAGAA;RSEQ=AATTCNNNNNNNNNNNNNNN GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:4:0,4:19,50:0.0541:2,0:4.8:1:29.5:1:0.56701:0:42:8:0.0563:0:4 0/1:211:9:3,6:57,144:0.0427:2,2:5.7:1:29:1:0.71703:1.26:53:18:0.0433:0:2 -1 144693322 . G C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53427;SOR=0;LSEQ=CAGGGATGATAACAGGCACT;RSEQ=TACTTAACAGGAGTCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:35.3:1:31.7:1:1:0:27:6:0.1429:0:1 0/0:11:0:0,0:10,1:0:2,0:24:1:33:1:1:0:27:22:1:0:0.1 -1 144693358 . G A 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00076;SOR=0;LSEQ=AGCGTATCACAATGCTGCTC;RSEQ=GACTATGTTCAGACACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:14:9,5:14,6:0.4118:2,2:30.4:1:30.2:1:1:1.28632:29.1:28:0.4118:0:1.3 0/0:20:0:0,0:12,8:0:2,0:25.7:1:29.8:1:1:0:29.3:40:1:0:0.1 -1 144693362 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12274;SOR=Inf;LSEQ=TATCACAATGCTGCTCGGAC;RSEQ=ATGTTCAGACACTAAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:23,15:0:2,0:26.9:1:29.4:1:1:0:29.4:76:1:0:0.5 0/1:21:2:1,1:11,8:0.0952:2,2:9:1:27:1:1:1.35399:27:4:0.0952:0:1 -1 144694767 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCTGGTCTCAAACTCC;RSEQ=GACCTCAAGTGATTGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30.5:1:1:0:48.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 145177897 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05714;SOR=Inf;LSEQ=GAAAAAGTCAACTCTCTTAC;RSEQ=TCCTGTTTTTCAAAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:0:2,0:23:1:30.5:1:1:0:37.5:22:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:18.5:1:28.5:1:1:1:50:4:0.5:0:1.5 -1 145209116 . T C 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.6927;SOR=1.36342;LSEQ=GGAAGGACACACGAGGCTGC;RSEQ=TCGCTGCACACCCGAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:3,3:16,6:0.2143:2,2:19.5:1:29.3:1:0.35184:2.56516:48.7:5:0.1852:0:1.3 0/1:11:3:1,2:7,1:0.2727:2,2:12:1:29.7:1:0.15152:9.76948:43:6:0.2727:0:1 -1 145209152 . GGGC G 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.04615;SOR=Inf;LSEQ=GAAAGTTTCAGCCAAACTTC;RSEQ=GGCGGCTGAGGCGGCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:20,11:0:2,0:31.7:1:30.5:1:1:0:48.5:30:1:0:0.4 0/1:9:2:1,1:5,2:0.2222:2,2:42.5:1:31.5:1:1:2.23609:48:4:0.2222:0:1.5 -1 145209167 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTCGGGCGGCGGCTGAGG;RSEQ=GGCGGCCGAGGAGCGGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:24,11:0.0541:2,2:35:1:31.5:1:1:2.13205:54:4:0.0556:0:1 0/0:13:0:0,0:9,4:0:2,0:25.3:1:31.4:1:1:0:48.8:26:1:0:0.3 -1 145209191 . G C 32 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04887;SOR=Inf;LSEQ=GGCCGAGGAGCGGCGGACTC;RSEQ=GGGCGCGGGGAGTCGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:30,14:0:2,0:21.7:1:29.7:1:1:0:51.2:88:1:0:0.3 0/1:13:2:1,1:7,4:0.1538:2,2:11:0:32:0:1:1.67325:48:4:0.1538:0:1.5 -1 145209323 . AGGC A 100 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.11808;SOR=2.23785;LSEQ=CTCCCCATGTGGATCTGCCC;RSEQ=GGCGGCGGCGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:8:3,5:195,86:0.0271:2,2:28.3:1:29.7:1:0.11394:3.75937:46.1:16:0.0275:0.0034:0 0/1:153:9:6,3:100,35:0.0588:2,2:21.9:1:31.6:1:0.69864:1.42479:49.2:18:0.0596:0.0065:0.3 -1 145209326 . C T 28 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.60268;SOR=2.02431;LSEQ=CCCATGTGGATCTGCCCAGG;RSEQ=GGCGGCGGCGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:2:0,2:195,88:0.0068:2,0:1:0:27:1:0.09896:0:60:4:0.0072:0:1.5 0/1:146:2:1,1:100,35:0.0137:2,2:23.5:1:28.5:1:0.45792:2.83123:60:4:0.0152:0:1 -1 145209330 . G C 187 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.00976;SOR=0.49361;LSEQ=TGTGGATCTGCCCAGGCGGC;RSEQ=GCGGCGGCGGCGGCGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:71:44,27:171,86:0.2152:2,2:26.4:1:30.5:1:0.48329:1.21937:56.1:142:0.2198:0:1.1 0/1:168:20:15,5:106,41:0.119:2,2:17.7:1:28.4:1:1:1.16:52.6:9:0.1098:0:1.2 -1 145209333 . G C 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.11643;SOR=Inf;LSEQ=GGATCTGCCCAGGCGGCGGC;RSEQ=GCGGCGGCGGCGGAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:237,125:0:2,0:22.8:1:29.7:1:1:0:56.2:59.333:1:0:0.4 0/1:188:2:1,1:133,53:0.0106:2,2:31.5:1:30.5:1:0.49306:2.49543:49:4:0.0109:0:1.5 -1 145209344 . C A 64 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=3;SSF=0.72659;SOR=1.49625;LSEQ=GGCGGCGGCGGCGGCGGCGG;RSEQ=GGAGGAGGCGACCGAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:5:4,1:294,156:0.011:2,2:14.4:1:27.8:1:0.66364:2.12:24.6:4:0.009:0:2.2 0/1:245:4:3,1:163,78:0.0163:2,2:22.8:1:29.8:1:1:1.43:32.5:8:0.0165:0:1 -1 145209350 . A C 97 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57505;SOR=1.41872;LSEQ=GGCGGCGGCGGCGGCGGAGG;RSEQ=GGCGACCGAGAAGATACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:8:8,0:358,185:0.0145:2,0:5.1:1:32.6:1:0.05659:0:27.1:16:0.0149:0:2.3 0/1:294:6:6,0:192,96:0.0204:2,0:3.3:1:31.3:1:0.18232:0:27:12:0.0209:0:2 -1 145209366 . A G 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01717;SOR=1.49787;LSEQ=GAGGAGGCGACCGAGAAGAT;RSEQ=CCCGCCCTGCGCCCCGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:99:87,12:394,264:0.1308:2,2:17:1:32.6:1:0:4.85:31.5:98:0.1317:0:1.2 0/1:424:78:70,8:210,135:0.184:2,2:16.5:1:32.6:1:0:5.61:30.3:156:0.1844:0:1.2 -1 145209377 . GCC G 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.25592;SOR=1.21657;LSEQ=CGAGAAGATACCCGCCCTGC;RSEQ=CCGCTCTGCTGTGGGCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:927:89:75,14:490,344:0.096:2,2:13.8:1:31.9:1:0:3.76:34.8:88:0.0965:0.0367:0.7 0/1:568:65:53,12:307,198:0.1144:2,2:13:1:31.9:1:0.00094:2.84:36.3:130:0.1155:0.0493:0.7 -1 145209466 . C G 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCTGAGGGGCGCTGTCCG;RSEQ=GGCGCCCGGGGCTGCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1221:0:0,0:585,634:0:2,0:25.9:1:30.7:1:1:0:41.5:109.818:0.9983:0:0.1 0/1:883:23:10,13:405,455:0.026:2,2:30.9:1:31:1:0.83363:1.15695:40.4:46:0.0264:0:1.3 -1 145209538 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00604;SOR=Inf;LSEQ=TGTGTGGGAAGGCCAGGCTC;RSEQ=GCCGCCGGCGCGGAGCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:65,312:0:2,0:26.3:1:30.6:1:1:0:36.5:124.667:1:0:0.1 0/1:214:5:1,4:39,169:0.0234:2,2:18.8:1:30.4:1:1:1.08:28.2:10:0.0236:0:1 -1 145209612 . GCCCCGCCAACCGCCGGGGTT G 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=47;MSI=2.350;MSILEN=1;SSF=0.67003;SOR=1.2335;LSEQ=CCGGGGGCCCCTCCCGTGGT;RSEQ=CCCCGCCAACCGCCGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:19:2,17:8,88:0.1652:2,2:39.9:1:32.4:1:0.66952:1.29:50.3:38:0.1681:0:0.1 0/1:56:11:5,6:8,37:0.1964:2,2:15.5:1:29:1:0.10395:3.74:47.3:10:0.1852:0.0536:0 -1 145209870 . A G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CGGAGGGGCTGAGCGAAGGA;RSEQ=TGCCAGATTCTGGCGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:28:1:30:1:1:0:49:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:30:1:1:0:33:4:1:0:1.5 -1 145247137 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTAGTGGCGCGATGCCCC;RSEQ=TAAAGAGGCCACTTATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:30.5:1:1:0:54.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 145248601 . G C 76 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57466;LSEQ=ACACAGAGAAATAAGAGCAT;RSEQ=ATTCAAGACCACAAACGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:5:3,2:58,2:0.0769:1,2:25:1:33:1:0.02704:17.18057:27.2:10:0.0806:0:2 0/1:22:1:1,0:19,2:0.0455:2,0:2:0:32:0:1:0:21:2:0.0455:0:2 -1 145248605 . C G 91 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18601;LSEQ=AGAGAAATAAGAGCATGATT;RSEQ=AAGACCACAAACGTGGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:7:5,2:59,2:0.1029:1,2:19.6:1:32.7:1:0.04985:10.94217:27.1:14:0.1061:0:1.7 0/1:25:3:3,0:20,2:0.12:2,0:4:1:32:1:1:0:25:6:0.12:0:1.3 -1 145248811 . A G 153 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02928;SOR=0.40453;LSEQ=GTGCATTTGTTTTTATTTTT;RSEQ=GCATTGCAGTGTCGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:35:1,34:3,101:0.2518:1,1:26.4:1:29.9:1:1:1.00983:30.3:70:0.2536:0:1.1 0/1:67:8:0,8:0,59:0.1194:1,0:34:1:25.5:1:1:0:31.9:7:0.1061:0:1 -1 145248851 . G A 30 v4;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTATGAACCCTGTGTAAAT;RSEQ=AAGGAATGTGTGTTACCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:2,0:18,177:0.0102:2,0:26.5:1:30:0:0.00984:0:24:4:0.0103:0:2 0/0:67:0:0,0:0,67:0:1,0:30.1:1:31.4:1:1:0:28.9:66:1:0:0.1 -1 145248876 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTGTGTTACCTACCACA;RSEQ=TGGCACAGGATACTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:2,0:22,160:0.0109:2,0:26:1:30.5:1:0.01639:0:24:4:0.011:0:2 0/0:51:0:0,0:0,51:0:1,0:23.3:1:31:1:1:0:28:102:1:0:0.1 -1 145249325 . G A 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGAGTCCCAGCTACTC;RSEQ=GGAGGCTGAGGCAGGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:0,3:1,14:0.1667:1,0:43.3:1:31.3:1:1:0:44.7:6:0.1765:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 145272956 . C A 40 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23397;SOR=3.11962;LSEQ=CATGGCAGACCCTGCTAGAC;RSEQ=ATACAGCTGATACTCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:3,0:57,5:0.0462:2,0:24.3:1:25.3:1:1:0:27:2:0.0323:0:1 0/1:15:2:2,0:12,1:0.1333:1,0:17:1:30.5:1:1:0:27:4:0.1333:0:1 -1 145273007 . T C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCAAAAGGACATGGGAGTA;RSEQ=GTGGTTAAGTTCTCTAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:3,0:57,6:0.0455:2,0:21.7:1:31.3:1:1:0:33.3:6:0.0462:0:1.3 0/0:14:0:0,0:12,2:0:2,0:28.5:1:28.6:1:1:0:27:28:1:0:0.2 -1 145273064 . C A 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCAGTTTTATAGGTGGT;RSEQ=CTTGTAGGTCTGTTGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:4:4,0:58,4:0.0606:2,0:19.3:1:29:1:1:0:35:8:0.0625:0:1.3 0/0:13:0:0,0:9,4:0:2,0:28.2:1:32.2:1:1:0:29:26:1:0:0 -1 145273302 . A G 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.47388;LSEQ=CTGGGGAAAGCCACGTGCCG;RSEQ=TGTGCCTCAGGGTTTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3417:428:236,192:1719,1265:0.1253:2,2:27.1:1:31.2:1:0.34713:1.10551:42.6:60.143:0.1263:0:1.8 0/1:2473:431:241,190:1131,906:0.1743:2,2:26.3:1:30.1:1:0.91504:1.02:44:32.154:0.1731:0:1.9 -1 145273345 . T C 283 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=1.51793;LSEQ=AGGACTGCCAGTACTCGACA;RSEQ=CTCATCCATGCTTTGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4475:532:235,297:1868,2071:0.1189:2,2:23.8:1:31.5:1:0.16518:1.13991:50.4:75:0.1192:0:1.7 0/1:3300:561:258,303:1283,1451:0.17:2,2:23.9:1:31:1:0.71026:1.03844:51.2:69.125:0.1694:0:1.7 -1 145273366 . C T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51554;SOR=0.90233;LSEQ=CTCATCCATGCTTTGTGTCT;RSEQ=GACCTTGCCTGAATGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4216:120:53,67:1943,2148:0.0285:2,2:22.7:1:29.9:1:0.51652:1.14347:52.8:119:0.0286:0:1.1 0/1:3145:81:41,40:1463,1597:0.0258:2,2:26.2:1:30.3:1:0.65305:1.12:55.3:162:0.026:0:1.2 -1 145273431 . A G 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.53107;LSEQ=ACCTATGAGTGCACCTGTCA;RSEQ=GTCGGGTTTACAGGTAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3945:262:122,140:1624,2056:0.0664:2,2:27.7:1:31.3:1:0.47901:1.10:45.6:64.5:0.0664:0:1.1 0/1:2820:277:121,156:1164,1378:0.0982:2,2:25.9:1:30.4:1:0.52558:1.08897:47.6:68.25:0.098:0:1.2 -1 145273473 . T C 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.48399;LSEQ=TGAGACCAAAGCCAGTGCTT;RSEQ=CCTACCTTCAGCAGATACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2995:410:154,256:912,1672:0.1369:2,2:24.5:1:30.6:1:0.37491:1.10:44:33.167:0.1352:0:1.1 0/1:2115:403:156,247:651,1055:0.1905:2,2:25.7:1:30.8:1:0.86431:1.02:45.3:66.167:0.1899:0:1.1 -1 145273520 . G A 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.95812;SOR=1.00695;LSEQ=AGCATCTTTTAGATCATGGT;RSEQ=TCTGGCTCTTAAATGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1177:316:57,259:137,724:0.2685:2,2:21.9:1:30.3:1:0.37698:1.16:40.9:104.333:0.2687:0:1.1 0/1:756:204:39,165:106,446:0.2698:2,2:24.1:1:29.5:1:1:1.00551:42.1:67:0.2687:0:1.1 -1 145273701 . C T 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34843;SOR=0;LSEQ=GTCAGGGCCAGGTGCGGTGG;RSEQ=GCACGCTTGCAATCCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:9:1,8:3,62:0.1216:1,2:19.4:1:28.4:1:0.41159:2.54:36.1:18:0.1216:0:1.3 0/0:12:0:0,0:1,11:0:2,0:14.8:1:30.5:1:1:0:58:24:1:0:0.5 -1 145273703 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45424;SOR=1.87585;LSEQ=CAGGGCCAGGTGCGGTGGCG;RSEQ=ACGCTTGCAATCCCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:14:0,14:3,50:0.209:2,1:26:1:28.4:1:1:0:44.7:28:0.209:0:1.5 0/1:12:4:0,4:1,7:0.3333:2,0:14:1:28:1:1:0:54:8:0.3333:0:1 -1 145273705 . C T 79 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58149;SOR=0;LSEQ=GGGCCAGGTGCGGTGGCGCA;RSEQ=GCTTGCAATCCCAGCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:6:1,5:1,57:0.0938:1,2:24.5:1:30.8:1:0.18006:10.50:43.8:12:0.0952:0:1 0/0:12:0:0,0:1,11:0:2,0:11.5:1:30.1:1:1:0:58:24:1:0:0.5 -1 145281047 . CAGTG C 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGCAGCATATGCAAAGA;RSEQ=AGCTCTGAGAGAGTAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:4,0:0.4286:0,2:28.7:1:33:1:0.42857:0:27:6:0.4286:0:0.3 0/0:1:0:0,0:0,1:0:0,0:4:0:26:0:1:0:27:2:1:0:0 -1 145281203 . G A 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33685;SOR=1.49421;LSEQ=CTTGGAGAGTTACTGGAGAG;RSEQ=GCTCTGTGTCAGATGACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:23:23,0:71,4:0.2347:2,1:22.2:1:30.2:1:0.57006:0:47.5:46:0.2421:0:1 0/1:54:17:16,1:34,3:0.3148:2,1:26:1:29.2:1:1:1.40:45.1:34:0.34:0:1.1 -1 145281204 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1247;SOR=Inf;LSEQ=TTGGAGAGTTACTGGAGAGG;RSEQ=CTCTGTGTCAGATGACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:94,4:0:1,0:25.1:1:31:1:1:0:46.6:23.5:1:0:0.5 0/1:54:2:1,1:49,3:0.037:2,2:28:1:30:1:0.14396:14.2846:49:4:0.0408:0:1 -1 145281247 . T A 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.81625;SOR=0.93108;LSEQ=GAGGCTCTGATTTAGCCTTT;RSEQ=GTAAAATGCAAAGAGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:82:79,3:190,6:0.295:1,1:23.1:1:28.2:1:0.726:1.20168:35.3:26.333:0.2904:0:1.1 0/1:132:37:37,0:89,6:0.2803:2,1:26.7:1:27.1:1:0.18446:0:39.8:17.5:0.2713:0:1.2 -1 145281361 . TC T 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.34233;LSEQ=GTACTGAGTTTTGTTATCCT;RSEQ=CTTTAGGTAAGGAGTGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2849:89:53,36:1864,893:0.0312:2,2:23.4:1:30.7:1:0.13478:1.41768:45:178:0.0317:0.007:1 0/1:1986:244:156,88:1108,620:0.1229:2,2:24.9:1:30.7:1:0.94333:1.0081:44.1:80.333:0.1226:0.0252:0.9 -1 145281408 . C T 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01898;SOR=1.17311;LSEQ=CGATGCCTGCCTGTCTCATC;RSEQ=CTGTGCAAATGGAAGTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4437:562:327,235:2157,1715:0.1267:2,2:26.9:1:30.4:1:0.2754:1.11:45.7:39.143:0.1255:0:1.1 0/1:3198:465:266,199:1482,1248:0.1454:2,2:26.5:1:29.7:1:0.24685:1.13:46.1:37.75:0.1439:0:1.2 -1 145281543 . C T 291 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00555;SOR=1.19064;LSEQ=ACACTGCCAGCATGGTGGCA;RSEQ=CTGCCTCAACCTGCCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3260:797:353,444:1082,1377:0.2445:2,2:25.3:1:30.2:1:0.90201:1.01:47.7:78.7:0.2454:0:1.1 0/1:2204:613:294,319:719,870:0.2781:2,2:25:1:29.5:1:0.25281:1.12:48.6:152.25:0.2797:0:1.1 -1 145281613 . C A 252 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.40749;SOR=1.07467;LSEQ=ACAGGCCAGTACTGTGACAG;RSEQ=CTGTATGTGCCCTGTGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2742:379:169,210:1037,1322:0.1382:2,2:25.1:1:29.5:1:0.82377:1.03:51.5:93.75:0.1396:0:2.3 0/1:1782:262:118,144:683,833:0.147:2,2:24.6:1:29.1:1:1:1.00059:51.9:130:0.1478:0:2.3 -1 145281633 . C A 252 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14812;SOR=1.13557;LSEQ=CCTGTATGTGCCCTGTGCAC;RSEQ=CTCGCCTTGTGTCAATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2627:357:164,193:991,1278:0.1359:2,2:25.5:1:29.8:1:0.42275:1.10:51.1:88.25:0.1369:0:2.5 0/1:1795:272:129,143:687,831:0.1515:2,2:23.2:1:29.7:1:0.50947:1.09:50.5:135:0.1528:0:2.4 -1 145281656 . A T 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08753;SOR=1.19881;LSEQ=CGCCTTGTGTCAATGGAGGC;RSEQ=CCTGTCGGCAGACTGGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2353:225:94,131:893,1233:0.0956:2,2:26:1:30.1:1:1:1.00932:47.1:36.5:0.0944:0:2.6 0/1:1600:180:77,103:618,802:0.1125:2,2:27.1:1:29.6:1:0.87343:1.03075:46.8:179:0.1131:0:2.6 -1 145281780 . T A 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.0121;SOR=1.66355;LSEQ=AGTGGGTGTGGCTCAATTGC;RSEQ=TTTTTTAGGAAGCGCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:68:4,64:61,444:0.1187:2,2:24.2:1:31:1:0.15567:2.19577:52.3:33:0.1172:0:1.1 0/1:284:52:9,43:31,200:0.1831:2,2:26.1:1:29.8:1:0.50873:1.35:54.5:104:0.1851:0:1 -1 145281818 . T A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.84573;SOR=0.86415;LSEQ=GGAAAAAGGGAAGTGAGAAT;RSEQ=TTGTGTGGGGTGGGTTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:26:2,24:22,260:0.0844:2,2:19.6:1:30.6:1:1:1.01534:51.2:52:0.0858:0:1.3 0/1:122:9:2,7:11,102:0.0738:2,2:25.9:1:29.4:1:0.24551:2.62:54.1:18:0.0744:0:1 -1 145281824 . T G 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06993;SOR=0.53446;LSEQ=AGGGAAGTGAGAATTTTGTG;RSEQ=GGGGTGGGTTGCTAGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:53:5,48:16,214:0.1866:2,2:29:1:31.5:1:0.56126:1.39:52.3:106:0.1913:0:1.1 0/1:110:12:3,9:8,90:0.1091:2,2:18.4:1:30.2:1:0.09938:3.68:54.5:24:0.1091:0:1.1 -1 146788870 . T C 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATCTGCAGGCATAGGAG;RSEQ=GAACCAGAGGAATATGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:29:1:29.5:1:1:1.73:60:4:0.4:0:1 0/0:2:0:0,0:1,1:0:2,0:24:1:27.5:1:1:0:60:4:1:0:0.5 -1 147282258 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5312;SOR=0;LSEQ=TCCACTTGACAAGGTAAGTC;RSEQ=CATGGCCCAGCCCAAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:31,1:0.0588:1,0:19.5:1:32:1:1:0:60:4:0.0588:0:1 0/0:19:0:0,0:19,0:0:1,0:23.7:1:30.8:1:1:0:60:38:1:0:0.1 -1 147282416 . T C 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=AGTAAATATGTTCATAGATA;RSEQ=CTAGAGATGCAAGCGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:327,188:0:2,0:25.3:1:30.3:1:1:0:60:102:1:0:0.7 0/1:287:7:4,3:162,118:0.0244:2,2:20.7:1:30.4:1:1:1.02957:60:14:0.0249:0:2.3 -1 147282446 . C T 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04615;SOR=1.40176;LSEQ=CAAGCGGCCTAGGAGAAGGA;RSEQ=GGGACAGTTATGTCCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:634:479:262,217:78,75:0.7555:2,2:25.4:1:30.5:1:0.45654:1.16:60:94.8:0.7548:0:1.2 1/1:352:286:160,126:35,31:0.8125:2,2:25.3:1:29.6:1:0.68235:1.12:60:39.857:0.8087:0:1.2 -1 147282508 . C T 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.34837;LSEQ=GTGTCAAAACCTATTCCCGC;RSEQ=ACCACAAACCTCTTCTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:123:41,82:157,271:0.2232:2,2:28.1:1:29:1:0.52374:1.15836:60:29.75:0.2204:0:1.6 0/1:308:28:12,16:126,152:0.0909:2,2:28.4:1:28.1:1:0.84451:1.10488:60:56:0.0918:0:1.4 -1 147282541 . A G 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04934;SOR=Inf;LSEQ=TTCTATTGCTCCAAATTCCC;RSEQ=GCTTTGGGAAAAAATGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:90,255:0:2,0:23.7:1:30.5:1:1:0:60:33.5:1:0:0.3 0/1:202:3:1,2:62,136:0.0149:2,2:19.3:1:28.3:1:1:1.10:60:6:0.0156:0:1 -1 148873045 . A T 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=2.64575;LSEQ=AGAGTGATAGTTGTTAGAAG;RSEQ=AAAATAACCCCCCAATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:6.5:1:31:0:1:0:35.5:4:0.25:0:1 1/0:2:1:1,0:1,0:0.5:0,0:9:0:32:0:1:0:25:2:0.5:0:1 -1 148873166 . T G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.46762;SOR=1.74453;LSEQ=GATGTCATATAAACCTTAAT;RSEQ=TTTAATGTTTCATTGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:12:12,0:53,5:0.1714:2,0:17.8:1:33:1:0.57934:0:30.3:24:0.1765:0:1 0/1:15:4:3,1:9,2:0.2667:2,2:12.5:1:32.3:1:1:1.45761:31.5:8:0.2667:0:1 -1 148873205 . A T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00721;SOR=0;LSEQ=TGATGTCTCTGTAGCAGCAA;RSEQ=CATTTAAGTTATTTGTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:15:14,1:131,5:0.0993:1,1:26.6:1:31.7:1:0.47218:1.86161:33.8:30:0.1:0:1 0/0:59:0:0,0:54,5:0:2,0:25.2:1:29.6:1:1:0:30.7:13.75:1:0:0.3 -1 148873206 . CATTTAAGTT C 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.52954;SOR=1.24439;LSEQ=GATGTCTCTGTAGCAGCAAA;RSEQ=ATTTGTTATACTTAAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:47:45,2:108,4:0.2956:1,1:26.8:1:32.2:1:1:1.19855:30.6:94:0.2975:0.0314:0.2 0/1:67:23:19,4:42,2:0.3433:1,2:27.7:1:31.5:1:0.17052:4.31374:29.8:46:0.3485:0.0896:0.6 -1 148873300 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46538;SOR=1.33678;LSEQ=ATTTGTCCTAAATTTCCATA;RSEQ=GTTTGCATTTGTTTTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:27:25,2:232,26:0.0947:2,2:19.6:1:31.2:1:1:1.40:26.3:54:0.0971:0:1.3 0/1:114:14:12,2:77,23:0.1228:2,2:19.6:1:29.3:1:0.73133:1.78:26.5:28:0.125:0:1.6 -1 148873348 . G A 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07454;SOR=7.4764;LSEQ=ATTCCTTAGTTGCTGGCTTT;RSEQ=ACCTTTTATGTTGCTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:1:1,0:445,75:0.0019:2,0:12:0:11:0:1:0:25:0:0:0:3 0/1:211:3:2,1:160,48:0.0142:2,2:16:1:29.3:1:0.54938:1.66212:30.7:6:0.0142:0:1 -1 148873398 . C A 133 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45002;SOR=1.28308;LSEQ=TATTTTCTCAACTGCCATAT;RSEQ=CTAGGAGGCTTGGAGTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1133:30:29,1:963,139:0.0265:2,1:23.6:1:27.2:1:0.16326:4.18:32.9:29:0.026:0:1.3 0/1:593:20:16,4:506,67:0.0337:2,2:24.7:1:28.6:1:0.2834:1.88565:28.7:40:0.0342:0:1.3 -1 148873483 . C T 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.88544;LSEQ=GGTCGGGAAATTTTTAAACC;RSEQ=AGGCAGCTTCCTGGCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3285:71:25,46:1604,1609:0.0216:2,2:28.3:1:28.3:1:0.01607:1.83394:35.1:22.667:0.021:0:1 0/1:2207:254:103,151:1043,910:0.1151:2,2:31.4:1:27.9:1:0.00013:1.67986:36.6:41.333:0.1139:0:1.1 -1 148873574 . G T 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-04;SOR=1.37966;LSEQ=ATTTCTGTCTGATTTGTTTT;RSEQ=CCCTACTGGGTGTAAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1439:458:97,361:202,778:0.3183:2,2:25.6:1:29.7:1:0.83433:1.03:44.3:37.167:0.3156:0:1.1 0/1:855:335:76,259:121,399:0.3918:2,2:24.5:1:29.1:1:0.86814:1.03344:45.1:110.667:0.3934:0:1.1 -1 148873584 . G A 131 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.70859;SOR=0.813;LSEQ=GATTTGTTTTGCCCTACTGG;RSEQ=TGTAAAGAATTAAATCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1204:21:1,20:213,970:0.0174:2,1:13.3:1:30:1:0.1519:4.38846:32.7:20:0.0167:0:1.6 0/1:703:10:0,10:143,549:0.0142:2,0:16.6:1:28.7:1:0.22679:0:29.9:20:0.0145:0:1.3 -1 148873743 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57023;SOR=0;LSEQ=CCTTTTGTTGTGATTACTAC;RSEQ=GGTTTTATGAGGGAGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:3:0,3:7,45:0.0545:2,0:41:1:30.7:1:1:0:23.7:6:0.0545:0:1 0/0:18:0:0,0:0,18:0:1,0:25.6:1:30.4:1:1:0:44.1:36:1:0:0 -1 148874275 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACCTCATTTGACAGTTTG;RSEQ=TAATATAGACCACCAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:39:1:31:1:1:1:49:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 148876062 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05314;SOR=Inf;LSEQ=AGGCTTGCTGATAGCGTTCA;RSEQ=AGTGACAGCCCGAAAGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:31,4:0:2,0:26.2:1:30.5:1:1:0:33.6:16.5:1:0:0.1 0/1:11:2:1,1:7,2:0.1818:2,2:40.5:1:28.5:1:0.49091:3.05504:49:4:0.1818:0:2 -1 148876127 . G C 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95178;LSEQ=ATTTAGAATTTTAAGTTGTG;RSEQ=AATATACTTTTAAAGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:2,0:159,18:0.0112:2,0:6.5:1:33:0:1:0:23.5:4:0.0113:0:3 0/1:94:1:1,0:82,10:0.0106:2,0:6:0:33:0:1:0:25:2:0.0109:0:3 -1 148876241 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11479;SOR=Inf;LSEQ=GTGGCATTTGGATTTAAAAA;RSEQ=TATTTTGGGCTGTCACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:171,111:0:2,0:17.4:1:29.3:1:1:0:33.5:55.4:1:0:0.2 0/1:145:2:1,1:74,69:0.0138:2,2:16:1:28:0:1:1.07192:39:4:0.014:0:1 -1 148876254 . T A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49823;SOR=1.33885;LSEQ=TTAAAAATTATTTTGGGCTG;RSEQ=CACAGAATGTTGACTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:13:0,13:116,124:0.0514:2,1:26.8:1:28.2:1:0.00029:0:25.7:12:0.0484:0:1.9 0/1:133:9:0,9:35,89:0.0677:2,0:24.2:1:29:1:0.11126:0:24.4:18:0.0682:0:1.6 -1 148876294 . A G 119 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98667;LSEQ=CTAATCTGTTACATAGGGCC;RSEQ=TGGGTCTGGATTTCCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:13:0,13:159,198:0.0351:2,1:29.2:1:32.3:1:0.00082:0:23.6:26:0.0354:0:2.8 0/1:173:6:0,6:46,121:0.0347:2,0:27.8:1:30.3:1:0.34357:0:23.7:12:0.0353:0:2.2 -1 148876318 . G A 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33286;SOR=0;LSEQ=GTCTGGATTTCCAGGAAAGC;RSEQ=GAGACCTCGAGGTGCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:5:0,5:215,212:0.0115:2,0:28.6:1:31.6:1:0.06107:0:23.8:10:0.0117:0:3.4 0/0:201:0:0,0:79,122:0:2,0:24.9:1:30.3:1:1:0:37.2:200:1:0:0.2 -1 148876343 . G A 139 Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.30119;SOR=0.57704;LSEQ=CCTCGAGGTGCAGGACTGTC;RSEQ=GGGCGAGGTGGCCGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:22:0,22:289,155:0.0472:2,1:25.8:1:31.3:1:0:0:23.9:21:0.0457:0:2.5 0/1:216:6:0,6:125,85:0.0278:2,0:26:1:30.2:1:0.00507:0:24.3:12:0.0284:0:2.2 -1 148876363 . G A 129 Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33894;SOR=0.53761;LSEQ=GGGGCGAGGTGGCCGAGGCA;RSEQ=GTCAAAGCTGAAAAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:17:0,17:398,134:0.031:2,1:25.2:1:31.8:1:0:0:23.8:16:0.0294:0:2.5 0/1:237:4:0,4:174,59:0.0169:2,0:14.5:1:32:1:0.00465:0:24.5:8:0.0172:0:2.3 -1 148876400 . G A 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.93082;SOR=1.02496;LSEQ=GGAATCGGAGCTGTTGTATT;RSEQ=CCTGGGGTGAGGCTTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:660:119:93,26:409,132:0.1803:2,2:23.9:1:28.4:1:0.63536:1.15:37.7:238:0.1814:0:1.9 0/1:337:62:52,10:215,59:0.184:2,2:24:1:28.4:1:0.38835:1.43:37.1:124:0.1856:0:2.1 -1 148876411 . G T 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99735;LSEQ=TGTTGTATTGCCTGGGGTGA;RSEQ=GCTTGCTTCATGTATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:133:90,43:410,214:0.1757:2,2:24.2:1:30.4:1:0.68794:1.09:42:266:0.179:0:1.8 0/1:405:71:54,17:218,115:0.1753:2,2:23.8:1:29.6:1:0.09501:1.67:39.1:34.5:0.1734:0:2 -1 148876492 . A G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82583;SOR=0.87331;LSEQ=AAGTTATTTTGAACTTAAAA;RSEQ=TCATATAAATAGGTCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:741:15:5,10:102,624:0.0202:2,2:23.3:1:26.8:1:0.05183:3.05:36.9:2.75:0.0153:0:1.9 0/1:395:7:5,2:71,316:0.0177:2,2:28.3:1:25.9:1:0.00362:11.03:33.4:2.5:0.0131:0:1.3 -1 148876559 . T A 54 v4;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08359;SOR=6.18659;LSEQ=TTTTTTTTTTTTTTTGAGCC;RSEQ=CTGGTTACGTTTTCTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:1:1,0:26,170:0.005:2,0:47:0:32:0:0.13706:0:40:2:0.0056:0:3 0/1:132:4:4,0:34,94:0.0303:2,0:10.8:1:27.3:1:0.00611:0:27.8:3:0.0256:0:2 -1 148876568 . G A 62 v4;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16226;SOR=5.94666;LSEQ=TTTTTTGAGCCTCTGGTTAC;RSEQ=TTTTCTTGTATATTTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:1,0:30,136:0.006:2,0:45:0:32:0:0.18563:0:40:2:0.0062:0:3 0/1:115:4:4,0:30,81:0.0348:2,0:19.8:1:31:1:0.00671:0:27.8:8:0.036:0:2 -1 148876595 . C G 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.6291;SOR=0.81408;LSEQ=TGTATATTTACTTTCTCATC;RSEQ=TTTCTCTTTTCTTACCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:37:3,34:18,89:0.2569:2,2:28:1:29.9:1:0.28129:2.28091:32.1:11.333:0.2519:0:1.8 0/1:82:18:4,14:22,42:0.2195:2,2:32.7:1:29.9:1:0.40046:1.82069:32.3:17:0.2237:0:1.3 -1 148876598 . T TCTCTTTTCTTACCTTC 67 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00549;SOR=Inf;LSEQ=ATATTTACTTTCTCATCCTT;RSEQ=CTCTTTTCTTACCTTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:18,122:0:2,0:27.8:1:29.4:1:1:0:33.4:27:0.9926:0:0.8 0/1:79:5:5,0:19,55:0.0633:2,0:28.6:1:29.1:1:0.00189:0:28:10:0.0676:0.0253:1.8 -1 148876648 . C T 81 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.02947;SOR=5.32937;LSEQ=TATCTTTCTATGCCAACCCT;RSEQ=TCTAAAAAGTCAGTATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:3:1,2:7,65:0.04:2,2:30.3:1:27.7:1:0.29056:4.49:43:6:0.0448:0:2.7 0/1:38:7:1,6:9,22:0.1842:2,2:17.3:1:28.9:1:0.64956:2.40535:29.3:14:0.1944:0:2.9 -1 148876664 . T C 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17323;SOR=3.54789;LSEQ=CCCTCTCTAAAAAGTCAGTA;RSEQ=GTAATATAGTTGCTCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:3,50:0.0364:2,2:32.5:1:29:0:0.14141:14.58:44:4:0.0364:0:3 0/1:25:3:0,3:1,21:0.12:1,0:26.3:1:27.7:1:1:0:30:6:0.12:0:4 -1 148876674 . T C 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93377;LSEQ=AAAGTCAGTATGTAATATAG;RSEQ=TGCTCTTTTATTTAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:7:0,7:3,34:0.1591:2,0:6.6:1:28.7:1:1:0:28.7:6:0.1429:0:2 0/1:20:3:0,3:0,17:0.15:1,0:15.3:1:32.7:1:1:0:26.3:6:0.15:0:1.7 -1 148876680 . T C 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05358;SOR=4.70685;LSEQ=AGTATGTAATATAGTTGCTC;RSEQ=TTTATTTAAAAAATTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:1,2:2,32:0.0811:2,2:31:1:31:1:0.22986:7.17:43:6:0.0811:0:2.7 0/1:20:6:0,6:0,14:0.3:1,0:40.8:1:31.8:1:1:0:29.3:12:0.3:0:3.2 -1 148876694 . T A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.27404;SOR=4.00592;LSEQ=TTGCTCTTTTATTTAAAAAA;RSEQ=TTTAAGATTGATATTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:0,1:2,27:0.0333:2,0:37:0:32:0:1:0:40:2:0.0333:0:2 0/1:16:2:0,2:0,14:0.125:1,0:14:1:31:0:1:0:24.5:4:0.125:0:1 -1 148876727 . C T 63 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00465;SOR=29.09978;LSEQ=ATTTGCTTACTATCATGTTA;RSEQ=GAGGCTTTATTTATATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:2,17:0.05:2,0:4:0:32:0:1:0:40:2:0.0556:0:2 1/0:6:4:0,4:0,2:0.6667:0,0:11.8:1:31.5:1:1:0:31.8:8:0.6667:0:3.8 -1 148877598 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATGCTGGGATTACAGGC;RSEQ=TGAGTCACCATGCCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29.5:1:1:0:31:4:1:0:1 -1 148878150 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGCATGAGCCACCATGCCCA;RSEQ=GCTGGAGTGCAGTGGCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:31:0:33:0:1:0:27:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:31:1:1:0:60:4:1:0:2.5 -1 148881660 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53435;SOR=0;LSEQ=CTATAATATTATCATTTATA;RSEQ=TTTCTTGATTAGAATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:2,1:14,1:0.1667:1,2:18:1:31.3:1:0.31373:5.91609:28.3:6:0.1765:0:1.3 0/0:7:0:0,0:4,3:0:2,0:27.4:1:30.4:1:1:0:31.9:14:1:0:1.1 -1 148881726 . T C 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58403;SOR=2.13794;LSEQ=TTATTATATTTTCTCATTAC;RSEQ=TCTTGGTCCAAAGGAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:3,1:8,1:0.3077:2,2:29:1:31.8:1:1:2.4495:30:8:0.3077:0:2 1/0:4:2:1,1:1,1:0.5:2,2:24:1:32:1:1:1:33:4:0.5:0:2.5 -1 148881735 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3125;SOR=0;LSEQ=TTTCTCATTACTTCTTGGTC;RSEQ=AAAGGAATTCTACCTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:10,1:0,0:1:0,2:27.4:1:31.3:1:1:0:27:22:1:0:1.4 1/1:5:4:1,3:0,0:0.8:0,2:7.8:1:28.3:1:1:0:30:8:1:0:1.3 -1 148881879 . A G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00045;SOR=Inf;LSEQ=TTTGATTATGAATTTTCTGA;RSEQ=GCTTTCCAGTTAAGTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:253,2:0:1,0:23.2:1:30.3:1:1:0:26.2:41.5:1:0:0.2 0/1:100:6:6,0:93,1:0.06:1,0:26.7:1:32.3:1:1:0:25.3:12:0.0612:0:2 -1 148881888 . G C 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=4.26383;LSEQ=GAATTTTCTGAAGCTTTCCA;RSEQ=TTAAGTGTAAAACAAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:16:16,0:280,3:0.0535:1,1:28.4:1:32.1:1:1:0:26.5:32:0.0544:0:1.1 0/1:118:23:23,0:95,0:0.1949:1,1:23.1:1:31.8:1:1:0:26.2:46:0.1983:0:1.3 -1 148881938 . C CT 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.17655;SOR=1.88083;LSEQ=TTCGTATTTTGTGTATTTTG;RSEQ=TTTTTATAGGTGTCTACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:12:12,0:642,14:0.0179:1,0:30.8:1:31.3:1:1:0:24.1:24:0.0182:0.003:0.3 0/1:331:11:11,0:315,5:0.0332:1,0:36.5:1:31.4:1:1:0:24:22:0.0334:0:0.2 -1 148882036 . T C 243 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTTTTCTAGCAGTGACAAAT;RSEQ=CACTTTGAATCAGGTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3080:237:117,120:1373,1468:0.0769:2,2:27.6:1:30.9:1:0.78685:1.04:38.7:58.25:0.0765:0:1.2 0/0:1873:0:0,0:906,967:0:2,0:25.9:1:29.4:1:1:0:40.9:116.063:1:0:0.2 -1 148882124 . G A 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=57.46964;LSEQ=TGCTTTATCTCATATACACA;RSEQ=AAGTGATCCAATATTTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:766:1:1,0:112,652:0.0013:2,0:1:0:26:0:0.14771:0:48:2:0.0013:0:1 0/1:400:28:8,20:61,311:0.07:2,2:21.4:1:30.3:1:0.11778:2.04:27.5:56:0.0709:0:1.1 -1 148882234 . A C 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=AAAATATGTTCTGTTTTCTT;RSEQ=ACTTCAGGATACATGTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:655:0:0,0:370,284:0:2,0:23.9:1:28.7:1:1:0:39.1:80.75:0.9985:0:0.1 0/1:466:9:4,5:266,188:0.0193:2,2:19.3:1:32.6:1:0.50005:1.76635:40.1:18:0.0197:0:1.1 -1 148882293 . C T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00561;SOR=Inf;LSEQ=AAGGAGCAGAAGGAAGATTA;RSEQ=TTGCCTGTTCTCAGTGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:651:0:0,0:290,360:0:2,0:25.3:1:31.9:1:1:0:36.6:80.25:0.9984:0:0.3 0/1:477:6:2,4:208,262:0.0126:2,2:15.3:1:30.5:1:0.6985:1.58631:45.8:12:0.0127:0:1.2 -1 148882326 . C A 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.87242;SOR=0.97408;LSEQ=AGTGTGGTCAGTGTTACCAT;RSEQ=CATACTGTGTCAGTATTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:160:48,112:78,138:0.4255:2,2:21.6:1:29.4:1:0.22592:1.31787:32.2:320:0.4278:0:1.1 0/1:272:114:38,76:53,105:0.4191:2,2:18.9:1:28.9:1:1:1.00949:31.9:228:0.4207:0:1 -1 148882389 . T G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.07323;LSEQ=AACAAATATGTATTGAATTT;RSEQ=TATTTGGTTTTAGTAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:14:6,8:11,113:0.1014:2,2:13.1:1:30.3:1:0.00237:7.51:26.5:28:0.1014:0:1.1 0/1:74:8:6,2:6,60:0.1081:2,2:25.6:1:29.5:1:0.00012:27.31:27:16:0.1096:0:1 -1 148882466 . T A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.55137;SOR=0;LSEQ=ATTAAACATATGTGACAGTA;RSEQ=TTAAGTACTTTAAATACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:3:1,2:10,85:0.0306:2,2:37:1:25.7:1:0.3031:4.15:40.3:2:0.0211:0:1.3 0/0:46:0:0,0:7,39:0:2,0:24.4:1:29.7:1:1:0:33.2:45:1:0:0.1 -1 148882472 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33268;SOR=3.1164;LSEQ=CATATGTGACAGTATTTAAG;RSEQ=ACTTTAAATACTGCTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:0,2:8,78:0.0227:2,0:35.5:1:33.5:1:1:0:23:4:0.023:0:1 0/1:44:3:0,3:7,34:0.0682:2,0:33.3:1:32:1:1:0:23:6:0.0682:0:1.3 -1 148882491 . A T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54802;SOR=0;LSEQ=GTACTTTAAATACTGCTTTT;RSEQ=AGGGTTTCCTATCTCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:3:1,2:3,53:0.0508:2,2:18:1:23.3:1:0.19299:8.15:26.3:2:0.0357:0:2 0/0:28:0:0,0:5,23:0:2,0:24.6:1:28.9:1:1:0:32.2:27:1:0:0.1 -1 148882606 . A T 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATTTAATTTAAAAGACA;RSEQ=TTTATACTATTCACAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:1,2:0.5:2,2:19:1:30.3:1:1:1:41.7:6:0.5:0:1 0/0:1:0:0,0:0,1:0:0,0:17:0:32:0:1:0:24:2:1:0:0 -1 148887540 . A C 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=CCCTTTCTGCTTCTAGGTAC;RSEQ=TAAGCACCATATTAATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:531:0:0,0:474,57:0:2,0:22.1:1:30.2:1:1:0:28:74.857:1:0:0.4 0/1:179:6:6,0:147,26:0.0335:2,0:27.5:1:29.7:1:0.59489:0:24.8:12:0.0339:0:1.3 -1 148887541 . T C 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71532;SOR=0.92229;LSEQ=CCTTTCTGCTTCTAGGTACA;RSEQ=AAGCACCATATTAATTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:184:161,23:319,35:0.342:2,2:20.7:1:31.9:1:0.38045:1.30134:28.2:183:0.3421:0:1.1 0/1:179:58:51,7:102,19:0.324:2,2:20.1:1:30.9:1:0.652:1.35:27:28:0.32:0:1.1 -1 148887833 . G A 157 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.18268;LSEQ=AGGGTTTGTTTGCCTTGTTA;RSEQ=TCTTTCAAGTTCAGAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3829:4:4,0:1336,2488:0.001:2,0:1:0:25.8:1:0.01497:0:51:8:0.0011:0:1 0/1:2250:42:18,24:871,1337:0.0187:2,2:22.6:1:29.3:1:0.75037:1.15:44.8:41:0.0184:0:1.3 -1 148887854 . C T 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=43.29511;LSEQ=TCTTTCAAGTTCAGAGCTTT;RSEQ=TCATACCACTTTAGTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2800:1:0,1:722,2071:4e-04:2,0:44:0:29:0:1:0:27:2:4e-04:0:1 0/1:1509:23:6,17:434,1045:0.0152:2,2:25.1:1:30:1:0.82153:1.17658:38.2:22:0.0147:0:1.2 -1 148887908 . A C 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=CCTATTTAATTGAATAATAC;RSEQ=CATATTCTATGATAGATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:798:0:0,0:5,793:0:1,0:23:1:30.3:1:1:0:27.9:113:1:0:0 0/1:410:10:0,10:1,399:0.0244:1,0:32:1:29.9:1:1:0:29.6:20:0.0246:0:1 -1 148887982 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00408;SOR=Inf;LSEQ=TCATTTGCCCCATTATGTTC;RSEQ=TATGTAGCTTCCTGAATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:12,232:0:1,0:25.6:1:32.2:1:1:0:28:60:1:0:0.1 0/1:84:4:0,4:1,79:0.0476:1,0:11.3:1:29.3:1:1:0:27:8:0.0482:0:1 -1 148888053 . G T 81 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90553;LSEQ=AGACTTTTCGGGGGGATTTG;RSEQ=ATTTCAGGTGTGTTTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:7:3,4:48,47:0.0686:2,2:24.7:1:28.9:1:1:1.3576:27.7:14:0.0722:0:1 0/1:16:1:0,1:6,9:0.0625:2,0:9:0:29:0:1:0:27:2:0.0625:0:1 -1 148888141 . C T 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=Inf;LSEQ=CAATTACACACAGTGCGCTC;RSEQ=TTGTGCAAGTTTATCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:126,7:0:2,0:21.8:1:31:1:1:0:32.7:132:1:0:0.1 0/1:52:6:6,0:46,0:0.1154:1,0:26.3:1:32.2:1:1:0:37:12:0.1176:0:1 -1 148888186 . G A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31229;SOR=0.48822;LSEQ=AGTCTGCTATTGAAACTATA;RSEQ=AGAAGAAGATCTTATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:14:14,0:191,0:0.0683:1,1:24.5:1:30.7:1:1:0:27:28:0.0707:0:1.1 0/1:116:4:4,0:112,0:0.0345:1,0:8.3:1:31:1:1:0:36.3:8:0.0357:0:1 -1 148888234 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27623;SOR=2.54242;LSEQ=ACAATGTGATAGGTATTGTG;RSEQ=TATTTTTTCATCTTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:3:1,2:249,105:0.0084:2,2:22.7:1:24.7:1:0.21494:4.71941:23:2:0.0062:0:2.3 0/1:238:5:3,2:160,73:0.021:2,2:25.8:1:24:1:0.65154:1.45874:32:1.5:0.0134:0:2 -1 148888236 . A G 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.02668;SOR=Inf;LSEQ=AATGTGATAGGTATTGTGCT;RSEQ=TTTTTTCATCTTTTTAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:245,111:0:2,0:28.7:1:27.4:1:1:0:36.5:13.24:1:0:0.5 0/1:245:4:2,2:162,76:0.0163:2,2:11.3:1:27.5:1:0.59611:2.12433:37.8:3:0.0132:0:1.8 -1 148888289 . A T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39487;SOR=1.34108;LSEQ=AATGTAGCAAAAAAAAAAAA;RSEQ=GGAAAATAGCTTTTCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:19:9,10:99,225:0.0544:2,2:25.4:1:27.7:1:0.13373:2.04:26.7:5.333:0.0491:0:1.6 0/1:251:18:9,9:87,146:0.0717:2,2:24:1:27.8:1:0.3197:1.67:23.2:8:0.0693:0:1.6 -1 148888291 . G A 150 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.07411;LSEQ=TGTAGCAAAAAAAAAAAAAG;RSEQ=AAAATAGCTTTTCCTTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:48:15,33:78,204:0.1441:2,2:21.8:1:26.9:1:0.60591:1.19:40.2:5:0.1429:0:1.8 0/1:244:3:3,0:85,156:0.0123:2,0:9.7:1:15.3:1:0.04589:0:44.7:0:0:0:1.7 -1 148888352 . A G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66489;SOR=1.36898;LSEQ=TTTTTGCCTTGTAGATTTTT;RSEQ=GTCACCTAGAAACTTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:0,3:22,239:0.0114:2,0:9.7:1:33:0:1:0:21:6:0.0116:0:2.7 0/1:129:2:0,2:12,115:0.0155:2,0:10.5:1:30.5:1:1:0:31.5:4:0.0155:0:2.5 -1 148888410 . AGTTTTGTTTTGTTTT A 149 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=10.000;MSILEN=5;SSF=0.22325;SOR=1.52115;LSEQ=AACTCTCAACTCCAGACTAA;RSEQ=GTTTTGTTTTGTTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:29:1,28:4,83:0.2028:1,1:18.9:1:30.7:1:1:1.34613:49.9:58:0.2042:0.1329:0.2 0/1:68:19:1,18:2,41:0.2794:1,1:31.5:1:30.5:1:1:1.14:36.6:38:0.2794:0.0294:0 -1 148888506 . T G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49673;SOR=0;LSEQ=TGTCGCCAGGCTGGAGTGCA;RSEQ=CGGCGCTATCTCGGCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:0,9:0.1818:0,2:15:1:30.5:1:0.18182:0:38.5:4:0.1818:0:4.5 0/0:7:0:0,0:0,7:0:0,0:12.6:1:29.9:1:1:0:31.9:14:1:0:0 -1 148888515 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCTGGAGTGCATCGGCGCTA;RSEQ=CTCGGCTCACTGCAAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:0,6:0.25:0,2:15:1:30.5:1:0.25:0:38.5:4:0.25:0:4.5 0/0:3:0:0,0:0,3:0:0,0:11.7:1:30.7:1:1:0:26:6:1:0:0 -1 148888541 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTGCAAACTCCACCTC;RSEQ=GCCTCCTGGGTTCAAGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:25:1:27.5:1:1:0:38.5:4:0.4:0:4.5 0/0:1:0:0,0:0,1:0:0,0:1:0:30:0:1:0:27:2:1:0:0 -1 148888566 . C T 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGTTCAAGCGATTCTC;RSEQ=TGCCTCAGCCTCCAGAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:23:1:29.5:1:1:0:44:8:0.8:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 148888573 . A G 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGCGATTCTCCTGCCTC;RSEQ=GCCTCCAGAGTAGCAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:26.5:1:30.8:1:1:0:44:8:0.8:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 148889345 . A T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75293;SOR=0.7423;LSEQ=ATAAAATAATTAGCTTCCTT;RSEQ=TGTAATGTGCTTTGCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:23:22,1:33,1:0.4035:1,1:22.3:1:29.8:1:1:1.48905:35.1:22:0.4074:0:1.1 0/1:12:4:4,0:7,1:0.3333:2,0:33:1:31.3:1:1:0:28:8:0.3333:0:1.3 -1 148889543 . AT A 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.99505;LSEQ=AGCAGTTCTCAGTATATTCC;RSEQ=TTTTTTTAAAAAAATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1410:211:184,27:887,311:0.1496:2,2:22.4:1:31.2:1:2e-05:2.39:36.7:210:0.1502:0.0418:0.1 0/1:812:121:107,14:482,208:0.149:2,2:22.1:1:30.3:1:1e-05:3.29:34.8:242:0.1499:0.0419:0.1 -1 148889550 . TTA T 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.02047;SOR=1.51872;LSEQ=CTCAGTATATTCCATTTTTT;RSEQ=AAAAAATGTACAAATATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1474:72:47,25:706,230:0.0488:2,2:27.4:1:30.1:1:0.06684:1.63187:44.5:144:0.0493:0.0061:0.1 0/1:843:61:35,26:447,160:0.0724:2,2:23.8:1:29:1:0.01029:2.07286:44.9:122:0.073:0.0071:0.2 -1 148889551 . TAA T 284 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00332;SOR=1.28652;LSEQ=TCAGTATATTCCATTTTTTT;RSEQ=AAAAATGTACAAATATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1520:669:470,199:611,170:0.4401:2,2:25.8:1:30.3:1:0.00056:1.52128:53.1:333.5:0.461:0.0395:0.1 1/0:875:440:301,139:272,81:0.5029:2,2:26.9:1:29.9:1:0.00837:1.54985:53.9:439:0.54:0.0457:0.2 -1 148889639 . G A 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGAAGTGGAAAATGTAGCA;RSEQ=ACATTGGTTTTGATTGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4061:53:27,26:2134,1867:0.0131:2,2:29.5:1:30.1:1:0.78235:1.10065:39.3:52:0.0129:0:1.5 0/0:2385:0:0,0:1231,1153:0:2,0:27.1:1:31.1:1:1:0:41.6:87.296:0.9996:0:0.3 -1 148889643 . T C 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTGGAAAATGTAGCAGACA;RSEQ=TGGTTTTGATTGTAACATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4130:0:0,0:2161,1967:0:2,0:27.9:1:30.3:1:1:0:41:76.887:0.9998:0:0.3 0/1:2428:47:26,21:1217,1164:0.0194:2,2:29.1:1:31.1:1:0.659:1.18:39.8:94:0.0196:0:2.2 -1 148889678 . C T 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACATGTGCAGACCCTATATG;RSEQ=CTGCGTCTAATGGTAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3955:0:0,0:1622,2330:0:2,0:26.8:1:31.3:1:1:0:42.1:64.867:0.9995:0:0.3 0/1:2370:39:15,24:970,1359:0.0165:2,2:26.8:1:28.7:1:0.7453:1.14192:41.4:38:0.0163:0:2.6 -1 148889699 . A G 316 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00176;SOR=1.21746;LSEQ=CTGCGTCTAATGGTAAGAGA;RSEQ=TAATTTAAACTGTGAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3080:991:334,657:712,1374:0.3218:2,2:23.7:1:31.8:1:0.83868:1.01932:42.1:89.091:0.3207:0:1.2 0/1:1759:644:212,432:395,720:0.3661:2,2:24.6:1:31.2:1:0.29804:1.11785:42.7:213.667:0.3675:0:1.2 -1 148889774 . G A 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=5e-05;SOR=0;LSEQ=ATAACCAATGAATTAGCTTA;RSEQ=CTCTACTCTATTTTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:30:1,29:15,684:0.0411:1,1:22.1:1:30.1:1:0.49315:1.57:29.2:60:0.0416:0:1.3 0/0:309:0:0,0:9,300:0:1,0:24.2:1:32.2:1:1:0:28.4:60.8:1:0:0.5 -1 148889778 . T C 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=5;SSF=0.88302;SOR=0.97637;LSEQ=CCAATGAATTAGCTTAGCTC;RSEQ=ACTCTATTTTGTCTTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:245:2,243:11,436:0.354:1,1:24.5:1:32.1:1:0.15314:3.06139:30.2:60.25:0.3513:0:1.4 0/1:284:99:3,96:5,180:0.3486:1,1:23.6:1:32.1:1:1:1.12:27.6:98:0.3475:0:1.5 -1 148889823 . G A 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.19925;SOR=0;LSEQ=TACTTTGACAAGTATTTTAT;RSEQ=AAAAATATTATTGTTGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:7:0,7:3,270:0.025:1,0:30.3:1:31.1:1:1:0:34.4:14:0.0255:0:2 0/0:94:0:0,0:3,91:0:1,0:22.2:1:31.6:1:1:0:30:188:1:0:0.3 -1 148889889 . A G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.79828;SOR=1.25242;LSEQ=AAAACAATTTACATGAAACA;RSEQ=TAAAAAGCATATACTTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:34:6,28:10,54:0.3469:2,2:20.4:1:32.6:1:0.7817:1.16:35.1:68:0.3505:0:1 0/1:20:8:1,7:0,12:0.4:0,2:31.9:1:29.6:1:0.4:0:24.5:7:0.3684:0:1.6 -1 148890126 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0905;SOR=Inf;LSEQ=ATAGAAACAGAAATTTTAAT;RSEQ=ATATGTAAGTATGTAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:206,2:0:1,0:26.9:1:31.5:1:1:0:37.7:103:1:0:0.7 0/1:90:2:2,0:83,5:0.0222:2,0:20:1:26.5:1:1:0:33:4:0.0225:0:1.5 -1 148890173 . A C 258 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82429;SOR=0.85212;LSEQ=CCTTTTCTGAAAAGAATTAC;RSEQ=TGGATTTTTTTTTTTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:350:336:269,67:1,0:0.96:0,2:25:1:30.8:1:1:0:40.5:41:0.9676:0:1.2 1/1:193:184:138,46:0,0:0.9534:0,2:24.6:1:29.7:1:1:0:40.7:29.667:0.9519:0:1.2 -1 148890273 . A G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.92922;LSEQ=AAAGAGCTAGTTAAAATTTG;RSEQ=AATGCTTTACTTAATTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1346:219:118,101:646,479:0.1627:2,2:22.5:1:30.5:1:0.33362:1.15422:29.7:108.5:0.163:0:1.2 0/1:814:222:124,98:331,261:0.2727:2,2:23.2:1:30:1:1:1.00228:30.5:110:0.2747:0:1.3 -1 148890324 . G A 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00061;SOR=Inf;LSEQ=TGCTTAATTTTTACATAATT;RSEQ=GCTTACCACTTGTAAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1182:0:0,0:376,806:0:2,0:27.2:1:31.1:1:1:0:40.9:61.211:1:0:0.3 0/1:779:8:3,5:269,502:0.0103:2,2:29.6:1:28:1:1:1.12:44.6:7:0.0091:0:1.1 -1 148890360 . G T 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.80562;LSEQ=AATCTGCTTCAATCATATGG;RSEQ=TGTTCTATCCAAATTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:738:64:4,60:97,577:0.0867:2,2:16.4:1:30.7:1:0.08511:2.51934:30.9:63:0.0865:0:1.8 0/1:418:88:17,71:55,273:0.2105:2,2:14.3:1:30:1:0.63404:1.19:30.6:87:0.2096:0:1.8 -1 148890494 . A G 66 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.48898;LSEQ=TAACAGCTCTTAGAATAACC;RSEQ=TTAATGCCATACTTGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:0,4:0,27:0.129:1,0:17:1:33.3:1:1:0:27:8:0.129:0:1 0/1:15:1:0,1:1,13:0.0667:1,0:13:0:32:0:1:0:24:2:0.0667:0:1 -1 148890954 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGCATATATTTGCAGTG;RSEQ=TTCTAACTCTTTTTATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:48:1:32:0:1:0:25:4:0.6667:0:1 0/0:1:0:0,0:0,1:0:0,0:10:0:34:0:1:0:27:2:1:0:0 -1 148891116 . T C 76 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCTGCCTCAGCCTCACG;RSEQ=ACAGCTGGGATTACAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:19.2:1:33:1:1:0:34.8:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 148891287 . A G 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCATGAGCCCCCACAAC;RSEQ=GGCCCAGGAAGACCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:29:1:30.6:1:1:0:31:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 148891474 . A G 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01466;SOR=0.4596;LSEQ=GGTATTTTGGAACAGTAATC;RSEQ=GTCAAATTTAAAATGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:510:57:57,0:453,0:0.1118:1,1:26.1:1:30.5:1:1:0:27.7:56:0.1105:0:2 0/1:238:13:13,0:225,0:0.0546:1,1:20.8:1:29.8:1:1:0:26.8:26:0.0551:0:2 -1 148891481 . T C 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00848;SOR=0.4931;LSEQ=TGGAACAGTAATCAGTCAAA;RSEQ=TTAAAATGAAAGTTTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:71:71,0:517,0:0.1207:1,1:22.2:1:32.4:1:1:0:27.7:34.5:0.119:0:1.8 0/1:284:18:18,0:266,0:0.0634:1,1:19:1:31.1:1:1:0:26.7:36:0.0634:0:1.7 -1 148891643 . A G 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62737;SOR=1.07303;LSEQ=ACTGTCAAAACCAAAACTGA;RSEQ=ATTGAAGATTATAAATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2912:146:107,39:1243,1522:0.0501:2,2:25.7:1:32.3:1:0:3.36:36.4:47.667:0.0497:0:2.2 0/1:1679:90:82,8:712,873:0.0536:2,2:26.3:1:32.3:1:0:12.55:36.6:89:0.0536:0:2 -1 148891675 . A G 297 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06467;SOR=1.14293;LSEQ=TAAATCAGAATAGCGTGGCC;RSEQ=TCCTTCAGACCCCTCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2786:723:387,336:948,1115:0.2595:2,2:27.3:1:31.3:1:0.00046:1.35:36.4:119.5:0.2596:0:1.3 0/1:1486:425:249,176:492,569:0.286:2,2:27.3:1:30.4:1:2e-05:1.64:36.4:105.25:0.2872:0:1.3 -1 148891790 . T A 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.89259;SOR=0.9728;LSEQ=TGTGTGCAAGAATTACAGCA;RSEQ=ATAAAGTAACTTTTGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:864:220:23,197:69,575:0.2546:2,2:23:1:30.6:1:1:1.02781:40.9:219:0.2561:0:1.1 0/1:437:109:17,92:39,289:0.2494:2,2:26.3:1:29.8:1:0.32344:1.37:40.2:218:0.2512:0:1 -1 148893912 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CAGGAGATCAAGACCATCCT;RSEQ=GCCAACATGGTGAAACCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19.5:1:30.5:1:1:0:52.5:4:1:0:2 1/0:4:2:1,1:1,1:0.5:2,2:25.5:1:27.5:1:1:1:46:4:0.5:0:2 -1 148893919 . A G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAGACCATCCTGGCCAAC;RSEQ=TGGTGAAACCTCGTCTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:41:0:32:0:1:0:45:2:1:0:4 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:29.5:1:1:1:46:4:0.5:0:2 -1 149398791 . G A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGATCTATTGCGTCCCTT;RSEQ=CACACTCTTACTTCGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:26,0:0.0714:1,0:23.5:1:25.5:1:1:0:26:4:0.0714:0:1.5 0/0:7:0:0,0:7,0:0:0,0:26.6:1:33.6:1:1:0:25:14:1:0:0 -1 149399039 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0765;SOR=Inf;LSEQ=CCGGTGTCGGGGTGGACCTG;RSEQ=TTCAGCACCTCCTACACGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:91,96:0:2,0:24.2:1:32:1:1:0:45.1:36.4:1:0:0.1 0/1:72:2:1,1:37,33:0.0278:2,2:8.5:1:29:1:1:1.11943:48:4:0.0286:0:1 -1 149399059 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAGCACCTCCTACACGT;RSEQ=AACGGAGTAGCTCTCCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:77,98:0.0113:2,2:9.5:1:29.5:1:1:1.27:49:4:0.0113:0:1 0/0:62:0:0,0:32,30:0:2,0:22.2:1:28.2:1:1:0:42.7:124:1:0:0 -1 149399931 . G A 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCCGGAACCACAAGGACC;RSEQ=TGCCTCTGCGGCTTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:33,0:0,0:1:0,1:28.4:1:30.1:1:1:0:30:32:1:0:1.1 1/1:4:4:4,0:0,0:1:0,0:37.5:1:30.8:1:1:0:26:8:1:0:1.3 -1 149400003 . G C 48 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02593;SOR=12.54239;LSEQ=TCTGTAACGTCACCCACCAC;RSEQ=AGTGCCCCTGGCCCCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:1:1,0:216,0:0.0046:1,0:50:0:12:0:1:0:40:0:0:0:2 0/1:54:3:3,0:51,0:0.0556:1,0:20.7:1:30.7:1:1:0:33.3:6:0.0556:0:1.3 -1 149400836 . A AT 48 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATCCCATTTTAACAGAG;RSEQ=TTTTTTTTTTTCCCCGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:0,3:2,26:0.0968:2,0:12.7:1:30.3:1:1:0:43:6:0.0968:0.0323:0.7 0/0:4:0:0,0:1,3:0:2,0:22.3:1:29.5:1:1:0:41.5:8:1:0:0.3 -1 149401455 . A T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATTTCATGTGCTTTGAAG;RSEQ=ATGTATTGTTCAGAACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43:1:29:1:1:0:45:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 149783622 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55067;SOR=0;LSEQ=GGGATGTGATGGTGGAGCGC;RSEQ=TGTTGTAGTGCGCCAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:55,34:0.022:2,2:37.5:1:31:1:1:1.60874:46:4:0.0222:0:1 0/0:46:0:0,0:32,14:0:2,0:28.8:1:29.9:1:1:0:32.8:92:1:0:0.1 -1 149783655 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51906;SOR=0;LSEQ=CCAGGCGGGACGCCTCTCCC;RSEQ=CGATGCGCTCGAAGATGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:67,29:0.0204:2,2:27:1:28:1:0.52072:2.28843:24:4:0.0213:0:1 0/0:64:0:0,0:47,17:0:2,0:24.7:1:30.2:1:1:0:35.3:63:1:0:0.1 -1 149783661 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52641;SOR=0;LSEQ=GGGACGCCTCTCCCGCGATG;RSEQ=GCTCGAAGATGTCGTTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:69,37:0.0185:2,2:25.5:1:30:1:1:1.85352:31:4:0.0189:0:1 0/0:66:0:0,0:48,18:0:2,0:24.3:1:30.7:1:1:0:35.4:32:1:0:0.1 -1 149783695 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.1805;SOR=Inf;LSEQ=GTTGACGAAGGAGTTCATGA;RSEQ=GCCCATGGCCTTGGACGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:90,65:0:2,0:24:1:30.4:1:1:0:45.7:310:1:0:0 0/1:115:2:1,1:70,43:0.0174:2,2:24.5:1:30:1:1:1.62069:25:4:0.0177:0:1 -1 149783804 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23695;SOR=0;LSEQ=CGCTTGCGCTTCTTGCCGTC;RSEQ=TTCTTCTGCACTTTCGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:60,95:0.0127:2,2:7.5:1:29:1:1:1.58:47.5:4:0.0128:0:1.5 0/0:165:0:0,0:73,92:0:2,0:25.2:1:30.3:1:1:0:54.2:32:1:0:0.1 -1 149784654 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54343;SOR=0;LSEQ=CGGCTTTCTCTACTGCCGGC;RSEQ=AACTCACGGCTGGGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:119,6:0.0157:1,0:8.5:1:32:0:1:0:40:4:0.0165:0:1 0/0:68:0:0,0:63,5:0:2,0:24.5:1:30.8:1:1:0:39.3:136:1:0:0.1 -1 149784689 . CCCA C 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTGGGTTCTGTAACGTCA;RSEQ=CCACGAGTGCCCCTGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:208,5:0:1,0:23.5:1:31:1:1:0:36.8:34.5:1:0:0.1 0/1:125:12:12,0:109,4:0.096:1,0:20.3:1:32.1:1:1:0:40.4:24:0.0992:0.024:0 -1 149857769 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25875;SOR=0;LSEQ=GAGCCTTTGGAGTCAAGCAG;RSEQ=CGGCGACTCGAGCGAGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:2,1:37,14:0.0556:2,2:16.7:1:30:1:1:1.31427:60:6:0.0556:0:1.3 0/0:40:0:0,0:27,13:0:2,0:18:1:30.5:1:1:0:60:80:1:0:0.1 -1 149857790 . C T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.50826;SOR=0;LSEQ=CGGCGACTCGAGCGAGCGAG;RSEQ=GCCAGGTCCCGGCAGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:42,26:0.0286:2,2:15:1:25.5:1:1:1.60389:54.5:4:0.029:0:1.5 0/0:51:0:0,0:31,20:0:2,0:25.3:1:30.8:1:1:0:57.7:102:1:0:0.1 -1 149857797 . T C 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCGAGCGAGCGAGCGCCAGG;RSEQ=CCCGGCAGGGACTCACTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:23:14,9:38,25:0.2674:2,2:22.4:1:30.6:1:1:1.02:55:22:0.2588:0:1.1 0/0:57:0:0,0:35,22:0:2,0:27:1:29.1:1:1:0:56.2:114:1:0:0.1 -1 149857861 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22927;SOR=Inf;LSEQ=TTGGTGCCCTCGGACACGGC;RSEQ=TGCTTGGCCAGCTCGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:35,45:0:2,0:27.7:1:30.5:1:1:0:46.5:39:1:0:0.3 0/1:74:2:1,1:34,38:0.027:2,2:13.5:1:30.5:1:1:1.12:46.5:4:0.0274:0:1.5 -1 149858030 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20462;SOR=Inf;LSEQ=CCATGGCCTTGGACGAGATG;RSEQ=CGGTGTCGGGGTGGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:114,90:0:2,0:24.6:1:31.2:1:1:0:50.7:50:1:0:0.1 0/1:169:2:1,1:86,81:0.0118:2,2:8.5:1:27:1:1:1.06138:60:4:0.0121:0:1.5 -1 149858056 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49938;SOR=0;LSEQ=TCGGGGTGGACCTGCTTCAG;RSEQ=ACCTTGTACACGTAGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:0,2:77,94:0.0116:2,0:7:1:27:1:0.50316:0:38.5:4:0.0119:0:1 0/0:159:0:0,0:76,83:0:2,0:25.4:1:31.8:1:1:0:55:318:1:0:0.2 -1 149858103 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49917;SOR=0;LSEQ=CTCTTTGCGGCTGCGCTTGC;RSEQ=CTTCTTGCCGTCTTTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:38,85:0.016:2,2:16.5:1:28.5:1:0.52839:2.22:60:4:0.0164:0:1.5 0/0:113:0:0,0:41,72:0:2,0:25.7:1:31.1:1:1:0:58.8:226:1:0:0.2 -1 150546790 . A ATTT 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=7.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=TGATTTTAAAGAGGTTTTTG;RSEQ=TTTTACTTGGAGGTTTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:21.3:1:30.7:1:1:0:60:8:0.4:0:0.5 1/1:2:2:1,1:0,0:1:0,2:17:1:27.7:1:1:0:60:4:1:0.5:1 -1 150546865 . A T 93 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6605;LSEQ=AAAACCCAACACCTCTAATT;RSEQ=GAATTGAAGAAAGGAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:10,0:13,0:0.4348:1,0:19.4:1:28.1:1:1:0:60:9:0.4091:0:1.1 0/1:3:1:0,1:2,0:0.3333:0,0:25:0:32:0:0.33333:0:60:2:0.3333:0:2 -1 150547050 . A AT 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.99209;LSEQ=TGTATTTGAATAAAAGATTT;RSEQ=TTTTTTTTTCTCAGGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:566:18:13,5:380,167:0.0318:2,2:18.6:1:29.7:1:1:1.14:60:36:0.0324:0.0071:0 0/1:507:16:9,7:344,147:0.0316:2,2:22.5:1:28.5:1:0.27118:1.81766:59.7:15:0.0302:0.0039:0.2 -1 150547292 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16443;SOR=Inf;LSEQ=TCACTGGGAGCGCCATCCTT;RSEQ=TAAGCAAATCCTCCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:6,156:0:1,0:23.8:1:31.9:1:1:0:60:26:1:0:0.1 0/1:111:2:1,1:7,102:0.018:2,2:10.5:1:28.5:1:0.13956:13.70:60:4:0.0182:0:1 -1 150549754 . C T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.31402;SOR=4.1797;LSEQ=CTGGCTAGGTTGCTAGGGTG;RSEQ=AACTCTAGGAAGTTACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:1:0,1:209,37:0.004:2,0:1:0:23:0:0.15385:0:60:2:0.0041:0:1 0/1:179:3:1,2:146,30:0.0168:2,2:7.7:1:25.3:1:0.08285:9.54653:60:6:0.017:0:1 -1 150549800 . TTGG T 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.30049;SOR=1.82627;LSEQ=TCCAACTGCATAAACTGGTT;RSEQ=TGGTGGTGGTGGTTGGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:6:5,1:352,222:0.0103:2,2:19.7:1:30.7:1:0.41411:3.15:60:12:0.0105:0.0034:0.3 0/1:481:9:4,5:290,182:0.0187:2,2:20.7:1:30:1:0.31978:1.98883:60:18:0.0191:0.0062:0.2 -1 150550019 . T TA 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46971;SOR=1.59788;LSEQ=AGTATGGGTTTCTGCTCTCT;RSEQ=ACAACACTACTATCCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:147:134:10,124:6,6:0.9116:2,2:23.3:1:29.6:1:0.00042:11.97619:60:32.5:0.9155:0.1497:0.1 1/1:105:99:8,91:2,4:0.9429:2,2:25.3:1:29.4:1:0.09994:5.52341:60:32:0.9412:0.1333:0.1 -1 150551256 . G A 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCAACCCACCCTTGGCG;RSEQ=GTGAGTCCGGGGAGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1105:0:0,0:701,402:0:2,0:24.2:1:30.8:1:1:0:60:99.273:0.9982:0:0.1 0/1:829:36:25,11:501,289:0.0434:2,2:23.8:1:28.5:1:0.59543:1.31:59.6:17:0.0417:0:1.3 -1 150551295 . T C 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAAAAGGGAGTGAGGCC;RSEQ=TGGCGATTAATGAACCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1722:0:0,0:933,789:0:2,0:25.6:1:30.6:1:1:0:60:73.87:1:0:0.2 0/1:1513:119:73,46:769,625:0.0787:2,2:25.6:1:30.8:1:0.21182:1.29:60:238:0.0794:0:1.2 -1 150551491 . GTCC G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=1.03201;LSEQ=AGCGACTGCCGGTACAACTC;RSEQ=TCCTCCTCCTCTGCTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1723:22:8,14:807,889:0.0128:2,2:31.4:1:31.5:1:0.39095:1.58816:60:44:0.013:0:0.1 0/1:1898:25:14,11:919,949:0.0132:2,2:27.9:1:30.6:1:0.54987:1.31:60:50:0.0134:0.0021:0.3 -1 150551729 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.25145;SOR=0;LSEQ=CGAAGAAAAGCAGCCTCGCG;RSEQ=GGGTCGCGGTGACGTCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:100,181:0.0106:2,2:39.3:1:31.3:1:1:1.1046:60:6:0.0107:0:1 0/0:251:0:0,0:92,159:0:2,0:24.3:1:30.6:1:1:0:60:250:1:0:0.2 -1 150551732 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09679;SOR=Inf;LSEQ=AGAAAAGCAGCCTCGCGGGG;RSEQ=TCGCGGTGACGTCGGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:99,179:0:2,0:24.4:1:31.5:1:1:0:60:45.333:1:0:0.2 0/1:237:3:2,1:87,147:0.0127:2,2:9.3:1:28.7:1:0.55806:3.36:60:6:0.0129:0:1.3 -1 150551777 . G A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.69252;LSEQ=CGCCAATGGGCGGCGGCCGC;RSEQ=CGACCCTCCGGGAGTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:95,71:0.0119:2,2:44:1:31:1:1:1.33566:60:4:0.0121:0:1 0/0:121:1:1,0:64,56:0.0083:2,0:1:0:26:0:1:0:60:2:0.0085:0:1 -1 150552042 . G A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.08189;LSEQ=CCGCCTGGCTGAGAAAACTG;RSEQ=GGAAGACCCCGACTCCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:571:337:106,231:75,157:0.5902:2,2:22.1:1:30.4:1:0.85487:1.041:60:32.7:0.586:0:1.2 0/1:532:56:15,41:157,317:0.1053:2,2:20.4:1:30.2:1:0.36905:1.35298:60:55:0.1048:0:1.2 -1 150552150 . CT C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGGTGGCGCCAGCGAACT;RSEQ=TTTTTTTTAAAAAAAGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:0,2:0,92:0.0213:1,0:32:1:32:1:1:0:60:4:0.0217:0:0 0/0:45:0:0,0:1,44:0:1,0:20.4:1:31:1:1:0:60:90:1:0:0.1 -1 150552202 . C T 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04615;SOR=Inf;LSEQ=GGGAAAGGGGCGGCAGCTTC;RSEQ=GGAGGGTTGCGCACGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:1,19:0:1,0:21.5:1:29.2:1:1:0:60:40:1:0:0.3 0/1:6:2:0,2:0,4:0.3333:0,0:5.5:1:30.5:1:1:0:60:4:0.3333:0:1 -1 150552263 . GGCCGGGGCCGGGGCCTGA G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=CGGGGCGGGGCCGGGGCCGG;RSEQ=GCCGGGGCCTGAGCGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:0.4286:2,0:27.3:1:31.3:1:1:0:60:6:0.4286:0.1429:0.3 1/0:3:2:2,0:1,0:0.6667:0,0:16.5:1:31.2:1:1:0:60:4:0.6667:0.3333:0.5 -1 150552279 . T G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=CCGGGGCCGGGGCCGGGGCC;RSEQ=GAGCCGGGGCCTGAGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:0,0:0.6:0,0:17.7:1:31:0:1:0:60:6:1:0:2.3 1/0:4:2:2,0:1,0:0.5:0,0:12:1:29.5:1:1:0:60:4:0.6667:0:2.5 -1 150552281 . A G 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GGGGCCGGGGCCGGGGCCTG;RSEQ=GCCGGGGCCTGAGCGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:0,0:0.6667:0,0:15:1:31.8:1:1:0:60:8:1:0:2.3 1/0:6:4:4,0:1,0:0.6667:0,0:8:1:32.3:1:1:0:60:8:0.8:0:2 -1 150552330 . G T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98243;LSEQ=TTCGGAGGCTCTGAGTGCCG;RSEQ=TTACGTAACGGCGGCTCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:14:14,0:22,0:0.3889:1,1:20.4:1:29.1:1:1:0:60:13:0.3824:0:1.9 0/1:26:10:10,0:16,0:0.3846:1,0:25.4:1:26.3:1:1:0:60:9:0.375:0:1.9 -1 150552392 . C G 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88906;SOR=0.94832;LSEQ=CTCCTGGGCTCGAGCTCTTT;RSEQ=CATGAGCACCTCGGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:53:50,3:66,1:0.4417:1,2:23.3:1:31.5:1:0.32002:3.91708:60:16.667:0.4386:0:1.3 0/1:91:39:37,2:49,3:0.4286:2,2:21.2:1:32.3:1:1:1.13:60:78:0.4333:0:1.3 -1 150552407 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1977;SOR=Inf;LSEQ=TCTTTCCATGAGCACCTCGG;RSEQ=CCTTCTCGTGGCTACCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:148,15:0:2,0:22:1:31:1:1:0:60:31.6:1:0:0.5 0/1:131:2:1,1:112,17:0.0153:2,2:24:1:26.5:1:0.25684:6.43114:60:4:0.0155:0:1.5 -1 150552622 . T G 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=1.59911;LSEQ=TTGGGGACTTGTGGTTATTT;RSEQ=GCACAGCTCTCTACTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:273:88,185:169,286:0.374:2,2:23.4:1:31:1:0.20007:1.24188:60:67.25:0.3721:0:1.1 0/1:661:323:121,202:128,209:0.4887:2,2:26.2:1:30.4:1:0.93601:1.02239:60:106.667:0.4878:0:1.1 -1 150552718 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52143;SOR=0;LSEQ=AAGTGGACTAAGCTAAAACT;RSEQ=CCACAGCTAAACTATTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:1,114:0.0171:1,0:22:1:32:0:1:0:60:4:0.0172:0:1 0/0:75:0:0,0:2,73:0:1,0:24.7:1:32.7:1:1:0:60:150:1:0:0.2 -1 151272735 . T C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12918;SOR=Inf;LSEQ=TAACACTAGGAAAAGGTGGG;RSEQ=CACTAAACTTTGCCTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:51,39:0:2,0:23.5:1:29.5:1:1:0:60:180:1:0:0.2 0/1:51:2:1,1:28,21:0.0392:2,2:6:0:29:1:1:1.32572:60:4:0.0392:0:1 -1 151272748 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13572;SOR=Inf;LSEQ=AGGTGGGTCACTAAACTTTG;RSEQ=CTCCGCAAAATTTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:50,40:0:2,0:29.5:1:31.3:1:1:0:60:44:1:0:0.2 0/1:53:2:1,1:26,25:0.0377:2,2:6.5:1:28:1:1:1.03924:60:4:0.0385:0:1.5 -1 151678674 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCATAACGAGGGCATTC;RSEQ=TGTCTCCCAAGGCCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:15,6:0.087:2,2:31:1:29.5:1:0.52569:2.39047:60:4:0.0909:0:1 0/0:10:0:0,0:6,4:0:2,0:24.5:1:30.3:1:1:0:60:20:1:0:0.1 -1 151678707 . TTGC T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03312;SOR=Inf;LSEQ=CCCCAGCCAGCACCTTCTCT;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:22,16:0:2,0:27.3:1:30.4:1:1:0:60:76:1:0:0.3 0/1:19:3:1,2:8,8:0.1579:2,2:15.7:1:30:1:1:1.9301:60:6:0.1579:0.0526:0.7 -1 152330803 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53927;SOR=0;LSEQ=CACCGCGCCTAGCTGAGTCC;RSEQ=TTTTAAGTAGATGGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:119,20:0.0142:2,2:19:1:33.5:1:0.2766:5.83099:60:4:0.0143:0:1 0/0:78:0:0,0:65,13:0:2,0:20.9:1:30.9:1:1:0:60:77:1:0:0.1 -1 152330817 . G T 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54024;SOR=0;LSEQ=GAGTCCTTTTTAAGTAGATG;RSEQ=AATAAAATGCTGGCATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:157,35:0.0103:2,2:12:1:24.5:1:0.33748:4.43705:60:4:0.0104:0:1 0/0:107:0:0,0:87,20:0:2,0:20.9:1:30.8:1:1:0:60:106:1:0:0.1 -1 152330829 . G T 189 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTAGATGGAATAAAATGCT;RSEQ=GCATTTTATTTTTGATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:79:56,23:134,43:0.3086:2,2:21.9:1:30:1:0.44125:1.2786:60:158:0.3123:0:1.1 0/0:145:0:0,0:105,40:0:2,0:21.2:1:31.2:1:1:0:60:144:1:0:0.1 -1 152330869 . A G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TAATCATGGCTATTTTGTCA;RSEQ=CTCCCTATGTAGATGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:0:0,0:281,202:0:2,0:26.4:1:29.4:1:1:0:60:47.3:1:0:0.2 0/1:262:9:6,3:149,104:0.0344:2,2:30.3:1:31.1:1:0.74162:1.39:60:18:0.0346:0:1.6 -1 152330900 . CT C 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00667;SOR=Inf;LSEQ=AGATGATTTCCCTTTCTATA;RSEQ=TTTTTTTCCATTTGATAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:0:0,0:285,270:0:2,0:26.6:1:30.4:1:1:0:60:68.375:1:0:0.2 0/1:324:5:2,3:167,152:0.0154:2,2:36.4:1:31.8:1:0.67303:1.64549:60:10:0.0155:0:0 -1 152330945 . T C 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTATTAATTCGTGTCCTAG;RSEQ=ATAATTTTATTTTCTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:0:0,0:187,266:0:2,0:24.2:1:28.8:1:1:0:60:112.25:1:0:0.2 0/1:281:44:18,26:98,139:0.1566:2,2:25.6:1:31.8:1:1:1.01832:60:88:0.1583:0:1.2 -1 152330982 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13809;SOR=Inf;LSEQ=CTTTTTCTAAGGAAAAGCCT;RSEQ=GGTGTATGAGAAAGTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:106,206:0:2,0:25.3:1:31.3:1:1:0:60:61.4:1:0:0.2 0/1:185:2:1,1:59,123:0.0108:2,2:28.5:1:30.5:1:0.54704:2.08:60:4:0.0109:0:1 -1 152331013 . G A 142 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.06305;LSEQ=AAAGTCTGAGAGTCTATGAG;RSEQ=TAGGAGTGCATAGGTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:26:7,19:46,140:0.1226:2,2:22.5:1:30.3:1:0.81109:1.12:60:52:0.125:0:1.1 0/0:115:1:1,0:28,86:0.0087:2,0:1:0:25:0:0.25217:0:60:2:0.0087:0:1 -1 153579668 . C T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=CTGACCTTTGGAGGTCAGGA;RSEQ=GGACCCAGAATCAGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:2,7:0.1818:2,2:10:0:29:1:0.49091:3.06:60:4:0.2222:0:1 0/0:6:0:0,0:1,5:0:2,0:27.7:1:29.3:1:1:0:60:12:1:0:0 -1 153907309 . C T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.2377;SOR=Inf;LSEQ=TGCTGCTGCTGCTGCTGTTG;RSEQ=TGCTGCTGCTGCTGTTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:0:2,0:26.7:1:32.6:1:1:0:60:62:1:0:0.2 0/1:31:3:1,2:14,14:0.0968:2,2:23:1:23.7:1:1:1.9571:60:2:0.0667:0:1.3 -1 153918029 . GAC G 95 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=11.000;MSILEN=2;SSF=0.31902;SOR=0.44846;LSEQ=TCTTCATCACCTGGCCTCTG;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:8,0:18,0:0.2857:1,0:35.9:1:31.9:1:1:0:60:16:0.2857:0:0.5 0/1:20:3:3,0:14,1:0.15:1,0:21.7:1:33:0:1:0:60:6:0.1579:0:0 -1 153918113 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14709;SOR=Inf;LSEQ=AAATTTAGACTCCACTTCTG;RSEQ=GAGGTAAAGCCAGGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:75,56:0:2,0:28.4:1:30.7:1:1:0:60:31.75:1:0:0.3 0/1:82:2:1,1:42,38:0.0244:2,2:41.5:1:30.5:1:1:1.10391:60:4:0.0244:0:1 -1 153918158 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53212;SOR=0;LSEQ=AGCCTCTTGATTTAATTCTG;RSEQ=GGCACAGACCTGTCCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:55,68:0.016:2,2:8.5:1:30:1:1:1.23:60:4:0.0163:0:1 0/0:73:0:0,0:34,39:0:2,0:26.8:1:30.4:1:1:0:60:146:1:0:0.1 -1 153918414 . T G 30 v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGTGACGGGAAGTTCGGG;RSEQ=TGGGGCAGAGGGCGCGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:5:0:30:1:1:3.16:60:4:0.2857:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 154649911 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00641;SOR=Inf;LSEQ=AGGGGATAGTACGAGATGCC;RSEQ=CCCGGCATTTACAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:16,10:0:2,0:26.8:1:31.1:1:1:0:59.3:52:1:0:0.1 0/1:7:3:2,1:1,3:0.4286:2,2:20.3:1:28.7:1:0.48571:4.45:56.3:6:0.4286:0:1 -1 154842199 . G GGCTGCTGCTGCT 74 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=43;MSI=18.000;MSILEN=3;SSF=0.18015;SOR=0.18164;LSEQ=GCTGAGACAGGGGATGCGGT;RSEQ=GCTGCTGCTGCTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:4,5:0.2778:2,0:30:1:32:1:0.08591:0:58:10:0.2778:0.0556:0.4 0/1:16:1:1,0:3,1:0.0625:2,0:23:0:33.6:0:1:0:60:2:0.0625:0:0 -1 155870416 . G A 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=62.63952;LSEQ=TCTTCCTTGGTGACCTTTAA;RSEQ=GGCAAAATGTGAGAAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:702:502:153,349:54,146:0.7151:2,2:23.6:1:30.8:1:0.40933:1.19:60:124.5:0.7155:0:1.1 1/1:476:473:171,302:0,0:0.9937:0,2:26.1:1:30.1:1:1:0:60:66.571:1:0:1.1 -1 155870489 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52544;SOR=0;LSEQ=CTGAATGCACCACCACCTTA;RSEQ=CACAAAGAAAGCTTCTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:1,169:0.0116:1,2:19:1:31:1:0.02319:119.76:60:4:0.0118:0:1 0/0:107:0:0,0:4,103:0:1,0:3:0:16:0:1:0:60:0:0:0:2 -1 155873960 . A G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CCACCTTGGCCCCGCAAAGT;RSEQ=CTGGTGTGAGCCACCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:46:46,0:23,1:0.6571:1,1:24:1:31.2:1:0.34286:0:60:45:0.6618:0:1 1/1:32:32:32,0:0,0:1:0,1:23.5:1:32:1:1:0:60:31:1:0:1.1 -1 155874661 . C A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02707;SOR=Inf;LSEQ=AGAAATGCCTATTTAAAACT;RSEQ=ATCTTACAGAGTAGTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:80,331:0:2,0:23.1:1:31.8:1:1:0:60:67.5:1:0:0.1 0/1:282:4:2,2:73,205:0.0142:2,2:17.5:1:24.3:1:0.28829:2.80:60:3:0.0107:0:1.5 -1 155874765 . G GT 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.36872;SOR=2.50565;LSEQ=AAACTGAGTCTTCAACTGAA;RSEQ=TTTTTTTTTCCACATAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:0,2:1,43:0.0435:1,0:46.5:1:31:1:1:0:60:4:0.0435:0:1 0/1:29:3:0,3:1,25:0.1034:1,0:13.3:1:28.9:1:1:0:60:6:0.1034:0.069:0.3 -1 155876706 . G T 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGTTTGAGACCAGCCT;RSEQ=GGCAATAGAGCGAGACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:26.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 155880070 . G GA 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.57134;SOR=0;LSEQ=TGGCTTATGACATAAAGTCT;RSEQ=AAAAAAAAAGAAATATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:4,0:47,0:0.0784:1,0:26.8:1:29.5:1:1:0:60:8:0.0784:0:0 0/0:20:0:0,0:20,0:0:1,0:21.7:1:31.9:1:1:0:60:40:1:0:0.1 -1 155880159 . T C 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTCCAAAAAAGCCTCAAAA;RSEQ=ATAAATAGTTAGAAACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:160,29:0:2,0:22.3:1:30.3:1:1:0:60:93.5:1:0:0.1 0/1:151:33:27,6:90,28:0.2185:2,2:25.2:1:31.4:1:0.63917:1.40:60:66:0.22:0:1 -1 155880391 . T C 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGATAGCAAGTATCCCATC;RSEQ=GGTCATTTAAGTACTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:391:0:0,0:255,136:0:2,0:23.5:1:31.3:1:1:0:60:129.333:1:0:0 0/1:232:63:42,21:95,73:0.2716:2,2:25.1:1:29.3:1:0.1785:1.53:60:62:0.2696:0:1.1 -1 155880573 . C G 316 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=233.74871;LSEQ=TGTCCTCTTGGGGCCTTCCT;RSEQ=GGTTGCCCCGAGGAAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1709:1257:656,601:231,215:0.7355:2,2:25.2:1:31.4:1:0.91218:1.02:60:65.158:0.7343:0:1.1 1/1:1298:1296:622,674:0,0:0.9985:0,2:24.1:1:30.6:1:1:0:60:40.806:0.9984:0:1.1 -1 155880760 . C CA 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00015;SOR=1.43344;LSEQ=GGTGGCCCTAAGAAACCCCC;RSEQ=CATCTTCACCCTCCCTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1334:949:279,670:115,267:0.7114:2,2:25.2:1:29.2:1:0.79111:1.03427:59.9:54.824:0.7131:0.1379:0.1 1/0:1070:834:255,579:126,108:0.7794:2,2:27:1:28.6:1:0:2.6464:59.9:54.6:0.7807:0.043:0.1 -1 155880761 . CATCTTCAC ACATCTTCA 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGCCCTAAGAAACCCCCC;RSEQ=CCTCCCTCCTAGACAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1181:0:0,0:317,858:0:2,0:27.1:1:31.6:1:1:0:59.9:54.952:1:0:0.1 0/1:850:14:11,3:253,583:0.0165:2,2:5.4:1:26.9:1:0.00031:8.43:60:13:0.0155:0.0141:0.9 -1 155880952 . G A 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91838;LSEQ=CACGTCTGCGGTACCCAGAG;RSEQ=TTCCGCCCCCTCCCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:24:0,24:1,10:0.6857:2,1:21:1:31.1:1:0.31429:0:60:48:0.6857:0:1.1 1/0:12:8:0,8:0,4:0.6667:0,0:15.1:1:31.1:1:1:0:60:16:0.6667:0:1.1 -1 156267399 . AT A 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TAAGTAGTGTATCTATAGTG;RSEQ=TTTTTTTTTCCTTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:26.9:1:1:0:60:4:1:0.5:0.5 -1 156268330 . C G 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02463;SOR=Inf;LSEQ=CCAGGCTGGTCTCGAACTCC;RSEQ=GACCTCAAGTGATCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:23,0:0:1,0:23.6:1:31.3:1:1:0:60:46:0.9583:0:0 0/1:5:2:2,0:3,0:0.4:0,0:26.5:1:30.5:1:1:0:60:4:0.4:0:1 -1 156268452 . A T 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34624;SOR=3.40012;LSEQ=CAGCCGCTCCAGGTCTTTCA;RSEQ=TCACATTTGGATGATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:98,42:0.0071:2,0:1:0:25:0:0.30496:0:60:2:0.0071:0:1 0/1:126:3:1,2:75,48:0.0238:2,2:10.7:1:22.3:1:0.56221:3.09632:60:2:0.0165:0:1.3 -1 156268453 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21685;SOR=Inf;LSEQ=AGCCGCTCCAGGTCTTTCAA;RSEQ=CACATTTGGATGATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:100,44:0:2,0:24.9:1:30.8:1:1:0:60:288:1:0:0.1 0/1:126:2:1,1:75,49:0.0159:2,2:6.5:1:29:1:1:1.52525:60:4:0.0167:0:1.5 -1 156268463 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21865;SOR=Inf;LSEQ=GGTCTTTCAATCACATTTGG;RSEQ=TGATCTTCCAGATCGTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:100,52:0:2,0:26:1:29.9:1:1:0:60:29.4:1:0:0.1 0/1:134:2:1,1:76,56:0.0149:2,2:38:0:31.5:1:1:1.35399:60:4:0.0155:0:1 -1 156268473 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50066;SOR=0;LSEQ=TCACATTTGGATGATCTTCC;RSEQ=GATCGTCATAGAGTGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:108,57:0.012:2,2:42.5:1:30.5:1:1:1.88708:60:4:0.0121:0:1 0/0:146:0:0,0:85,61:0:2,0:26:1:29.9:1:1:0:59.8:47.667:1:0:0.3 -1 156268495 . C T 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=ATCGTCATAGAGTGATCTGA;RSEQ=GATGTCCAGTCTCCTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:135,66:0:2,0:25.3:1:31.3:1:1:0:60:200:1:0:0.1 0/1:164:11:7,4:86,67:0.0671:2,2:21.1:1:29.7:1:0.75821:1.36:60:22:0.0675:0:1.2 -1 156268694 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52055;SOR=0;LSEQ=CTCTGAAGAGCCAAGGGTGG;RSEQ=TTCGGAAGTTGTGGATGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:48,143:0.0104:2,2:24.5:1:29:1:0.4443:2.96:60:4:0.0106:0:1 0/0:126:0:0,0:38,88:0:2,0:20.9:1:31.3:1:1:0:60:125:1:0:0.1 -1 156268892 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21923;SOR=Inf;LSEQ=CCATCTCCTCCTCGGCGCCC;RSEQ=ACTCTTCCTGGCAGTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:6,15:0:2,0:27.4:1:30:1:1:0:60:42:1:0:0 0/1:19:2:1,1:9,8:0.1053:2,2:25:1:30:1:1:1.11803:60:4:0.1053:0:1 -1 156450873 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTTCCCCGACCTCCTTC;RSEQ=TCAGGGTTCCCAGCATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29.5:1:1:0:60:4:1:0:1 -1 156452096 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48571;SOR=0;LSEQ=GGTTTGCATGTGTGTGCGCA;RSEQ=AGGTGAGGGGCTACAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:7,0:0.2222:0,2:14.5:1:30.5:1:0.22222:0:60:4:0.2222:0:1.5 0/0:6:0:0,0:5,1:0:2,0:23:1:30.8:1:1:0:60:12:1:0:0.2 -1 156452238 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17248;SOR=Inf;LSEQ=TATGGGCCCACCTCGATGAT;RSEQ=TCGGCGTTGGTGCGGCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:96,30:0:2,0:22.8:1:31.6:1:1:0:60:62:1:0:0.1 0/1:90:2:1,1:56,32:0.0222:2,2:16:1:28:1:1:1.73851:60:4:0.0227:0:1 -1 156452293 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17839;SOR=Inf;LSEQ=ACTCCGTGTACTTGAGCAGC;RSEQ=CCTTGTCCATGTCGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:107,65:0:2,0:25.7:1:29.3:1:1:0:60:42:1:0:0.1 0/1:127:2:1,1:75,49:0.0157:2,2:23.5:1:28.5:1:1:1.52525:60:4:0.0161:0:1.5 -1 156452315 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51639;SOR=0;LSEQ=CTTGTCCATGTCGGTGCTGG;RSEQ=GTACTGGAACAGCTTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:120,72:0.0103:2,2:34.5:1:29.5:1:1:1.66202:60:4:0.0104:0:1 0/0:133:0:0,0:76,57:0:2,0:24.1:1:30.2:1:1:0:60:43.333:1:0:0.1 -1 156452435 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18334;SOR=Inf;LSEQ=CCGCTTGGTGAAAGTCACCT;RSEQ=CAGAGAAGGATGGGTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:74,134:0:2,0:23.1:1:31.7:1:1:0:60:51:1:0:0.1 0/1:157:2:1,1:56,99:0.0127:2,2:5:1:27.5:1:1:1.76:60:4:0.0129:0:1 -1 156452453 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.55455;SOR=0;LSEQ=CTGCAGAGAAGGATGGGTGG;RSEQ=CGGCCAGATCTGGCTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:2,1:39,103:0.0207:2,2:12.3:1:28:1:0.19279:5.21:60:6:0.0208:0:1 0/0:81:0:0,0:20,61:0:2,0:24.9:1:31.6:1:1:0:60:162:1:0:0.1 -1 156452783 . A T 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTATGACCTAAGGCTTGCA;RSEQ=ATGGCTCTGGGATGGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17.5:1:26.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 156468022 . GC G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGAGCCAGGATGCCCAG;RSEQ=CCTCCAGCCCAGGGGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 156785356 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGAGGATGAAGAAACATGA;RSEQ=GCAGGAAGTCACCCTAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:24,0:0,0:1:0,1:24.6:1:32.6:1:1:0:60:48:1:0:1.1 1/1:6:6:6,0:0,0:1:0,0:18.7:1:32.8:1:1:0:60:12:1:0:1 -1 156785617 . G A 293 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.76881;LSEQ=AGGGAGTGAGTGGGCAACTC;RSEQ=GCGCATGAAGGAGGTACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1268:809:408,401:211,248:0.638:2,2:25.1:1:30.4:1:0.12901:1.20:60:72.545:0.6369:0:1.2 1/0:939:711:359,352:113,113:0.7572:2,2:24.5:1:30.2:1:0.93916:1.02:60:70.1:0.7587:0:1.2 -1 156785647 . TTC T 110 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.13752;SOR=2.01552;LSEQ=GGAGGTACTCCTCATTTTCG;RSEQ=TCTCTCTCTGTGCCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1296:9:4,5:580,707:0.0069:2,2:23.7:1:29.3:1:1:1.02544:60:18:0.007:0.0015:0.8 0/1:1007:14:6,8:471,521:0.0139:2,2:29.5:1:29:1:0.79302:1.20515:60:28:0.0142:0:0.4 -1 156785653 . C G 175 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ACTCCTCATTTTCGTTCTCT;RSEQ=TCTCTGTGCCCCAGCCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1266:43:17,26:547,672:0.034:2,2:28.6:1:32.4:1:0.53505:1.24471:60:42:0.0335:0:1.9 0/0:988:0:0,0:463,524:0:2,0:25.7:1:31.4:1:1:0:60:108.667:0.999:0:0.7 -1 156785762 . AG A 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52215;SOR=1.2034;LSEQ=GAGGGTGGGAGAGATGAGGG;RSEQ=CTGCACCACGCTGCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:119:4,115:0,84:0.5862:1,1:22.5:1:32.1:1:0.1437:0:60:118:0.5842:0.1773:1.5 1/0:92:58:3,55:2,32:0.6304:2,2:23:1:30.9:1:1:1.14411:59.9:57:0.6264:0.1413:1.5 -1 156785771 . A G 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.26236;SOR=1.38598;LSEQ=AGAGATGAGGGAGCTGCACC;RSEQ=CGCTGCCGCCCCAGGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:156:87:2,85:0,69:0.5577:1,1:26.2:1:32.2:1:0.50347:0:60:42.5:0.5629:0:2 1/0:77:49:3,46:1,27:0.6364:1,2:25.1:1:30.6:1:1:1.75:60:15.333:0.6216:0:2 -1 156785779 . G A 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62103;SOR=1.22976;LSEQ=GGGAGCTGCACCACGCTGCC;RSEQ=CCCCAGGTTTCCACTCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:127:88:2,86:0,39:0.6929:1,1:27.7:1:30:1:1:0:60:87:0.696:0:1.9 1/0:68:50:2,48:1,16:0.7353:1,1:26.2:1:28.5:1:1:1.49015:60:11.5:0.7302:0:1.9 -1 156811493 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52439;SOR=0;LSEQ=TGGTGAAGATCCCATCTTTG;RSEQ=GGGACTCGGGGGCCATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:86,62:0.0133:2,2:6:1:31:1:1:1.384:60:4:0.0135:0:1 0/0:94:0:0,0:52,41:0:2,0:27.8:1:29.9:1:1:0:60:186:0.9894:0:0.2 -1 156811747 . C A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07665;SOR=Inf;LSEQ=GAACTCATCCCATCCAAACC;RSEQ=CTCTGCCCTTGGACAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:227,12:0:2,0:23.8:1:31.2:1:1:0:60:58.75:1:0:0.1 0/1:92:2:1,1:82,7:0.0217:2,2:18:0:29:1:0.16899:11.02463:60:4:0.022:0:1 -1 156830711 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09244;SOR=Inf;LSEQ=CGGCTGCCCCGCCTGAGCGA;RSEQ=GCGGGCGCCGCCGCGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:21.8:1:31.3:1:1:0:60:48:1:0:0.6 0/1:11:2:1,1:5,4:0.1818:2,2:20:0:32.5:1:1:1.22474:60:4:0.1818:0:1.5 -1 156830741 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.09315;SOR=Inf;LSEQ=GCCGCGATGCTGCGAGGCGG;RSEQ=CGGCGCGGGCAGCTTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:113,27:0:2,0:14.7:1:29.7:1:1:0:60:34:1:0:0.3 0/1:62:2:1,1:43,17:0.0323:2,2:33.5:1:31.5:1:0.49974:2.48658:60:4:0.0328:0:2 -1 156830742 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09184;LSEQ=CCGCGATGCTGCGAGGCGGA;RSEQ=GGCGCGGGCAGCTTGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:114,28:0.0139:2,2:11.5:1:29.5:1:0.36334:4.01812:60:4:0.0139:0:1 0/1:66:1:0,1:46,19:0.0152:2,0:1:0:24:0:0.30303:0:60:2:0.0154:0:1 -1 156830745 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09217;SOR=Inf;LSEQ=CGATGCTGCGAGGCGGACGG;RSEQ=GCGGGCAGCTTGGCTGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:131,33:0:2,0:15.8:1:31.8:1:1:0:60:81:1:0:0.2 0/1:72:2:1,1:50,19:0.0278:2,2:15.5:1:31:0:0.48692:2.59047:60:4:0.0294:0:1.5 -1 156830747 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.131;LSEQ=ATGCTGCGAGGCGGACGGCG;RSEQ=GGGCAGCTTGGCTGGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:137,35:0.0115:2,2:10.5:1:29.5:1:0.37194:3.8736:60:4:0.0118:0:1 0/1:77:1:0,1:53,23:0.013:2,0:1:0:24:0:0.31169:0:60:2:0.0133:0:1 -1 156830758 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.09185;SOR=Inf;LSEQ=CGGACGGCGCGGGCAGCTTG;RSEQ=CTGGCACAGCTGGGCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:186,52:0:2,0:20.8:1:31.8:1:1:0:60:78.333:1:0:0.2 0/1:104:2:1,1:72,29:0.0192:2,2:33:0:31:1:0.49971:2.45793:60:4:0.0194:0:2.5 -1 156830781 . C T 56 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.16629;LSEQ=GGCACAGCTGGGCTGCGGGG;RSEQ=CGGGCAGCCTGCTGGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:4:2,2:279,78:0.0111:2,2:27.5:1:28.3:1:0.21407:3.56044:60:8:0.0113:0:1 0/1:155:2:1,1:110,42:0.0129:2,2:28.5:1:27.5:1:0.48179:2.60016:60:4:0.0134:0:2.5 -1 156830838 . G T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00826;SOR=Inf;LSEQ=CGGGCGCCGCACCCTGCCCC;RSEQ=ATGCCTGCTGCCCCCACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:477,231:0:2,0:24.8:1:29.8:1:1:0:60:63.364:0.9971:0:0.1 0/1:443:5:2,3:276,162:0.0113:2,2:17.4:1:26.4:1:0.3661:2.54988:60:10:0.0115:0:1 -1 156830989 . G A 42 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3028;SOR=0;LSEQ=GGGGACAGGCAGGCATTGCA;RSEQ=TGCCCCGAGGGCGCGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:4:3,1:76,292:0.0108:2,2:6.5:1:21.3:1:0.03143:11.42:60:3:0.0082:0:1.5 0/0:203:0:0,0:48,155:0:2,0:21.9:1:30.9:1:1:0:60:39.6:1:0:0.1 -1 156830995 . C G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11769;SOR=Inf;LSEQ=AGGCAGGCATTGCAGTGCCC;RSEQ=GAGGGCGCGGACTCGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:52,263:0:2,0:21.7:1:29.3:1:1:0:60:25.25:1:0:0.2 0/1:165:2:1,1:31,132:0.0121:2,2:19:1:28.5:1:0.35122:4.21:60:4:0.0123:0:1 -1 156831060 . ACGCAGCCTTCGGCGCTGCCCGGGCGTTCCTC A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.01355;SOR=Inf;LSEQ=CACGGCGGAAGGCTGGCACC;RSEQ=CGCAGCCGCCGCTGCCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:0,83:0:1,0:23.3:1:30.2:1:1:0:60:166:1:0:0.1 0/1:27:3:0,3:0,24:0.1111:1,0:31.3:1:30.1:1:1:0:60:6:0.1111:0.037:0 -1 156834269 . G T 108 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=22.04299;LSEQ=AGCTCAGCATGGGCCTGGGG;RSEQ=AGACCAGAAGGTCAGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:735:1:1,0:258,473:0.0014:2,0:3:0:13:0:0.35383:0:60:0:0:0:3 0/1:445:13:3,10:157,273:0.0292:2,2:26.9:1:29.4:1:0.39252:1.91445:60:26:0.0297:0:1.1 -1 156834364 . G A 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=GGAGAAGTCAGGAAGCTCAG;RSEQ=GCTTTGAGGGGTCTAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:140,144:0:2,0:25.5:1:31.3:1:1:0:60:55.8:0.9964:0:0.2 0/1:95:7:3,4:42,46:0.0737:2,2:21.1:1:30.7:1:1:1.21489:60:14:0.0778:0:1 -1 156834656 . G A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04578;SOR=Inf;LSEQ=CAGACTTGGGCTGCTAATGG;RSEQ=CTTGGCTGTCCCCGGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:79,376:0:2,0:24.3:1:31.8:1:1:0:60:49.556:0.9978:0:0.1 0/1:255:3:2,1:57,194:0.0118:2,2:20:1:28:1:0.13566:6.74:60:6:0.012:0:1.7 -1 156834668 . C A 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.2716;SOR=3.85374;LSEQ=GCTAATGGGCTTGGCTGTCC;RSEQ=CGGGGAATGATTGCGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:1:1,0:49,320:0.0027:2,0:1:0:25:0:0.13514:0:60:2:0.0028:0:1 0/1:193:2:1,1:31,160:0.0104:2,2:5.5:1:24:0:0.30484:5.10:60:4:0.0108:0:1 -1 156834682 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11905;SOR=Inf;LSEQ=CTGTCCCCGGGGAATGATTG;RSEQ=GAGGAGGGCCCAAGCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:25,236:0:2,0:22.8:1:30.1:1:1:0:60:129.5:1:0:0.1 0/1:138:2:1,1:17,119:0.0145:2,2:6:1:28:1:0.24468:6.83:60:4:0.0147:0:1 -1 156836592 . CG C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.10105;SOR=Inf;LSEQ=TCTGGTTGCCTAGGCCGGGG;RSEQ=GGGGAGCCAGATGTCAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:330,36:0:2,0:21.8:1:29.1:1:1:0:60:25.143:0.9944:0:0.2 0/1:172:2:1,1:146,22:0.0116:2,2:29:1:29:1:0.25298:6.51268:60:4:0.0123:0:0 -1 156836805 . A AGT 95 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.55403;SOR=0.59426;LSEQ=TTCCAGGGGCAAGAGCACCA;RSEQ=GTGTGTGTGTGCCTGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:868:9:3,6:271,588:0.0104:2,2:25.1:1:30.1:1:1:1.08:60:18:0.0106:0.0023:0.1 0/0:485:3:2,1:154,327:0.0062:2,2:32.7:1:32.5:1:0.24421:4.23:60:6:0.0063:0:0.3 -1 156836817 . C T 58 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46312;SOR=1.84259;LSEQ=GAGCACCAAGTGTGTGTGTG;RSEQ=CTGTGTGCACTTGGGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:723:4:2,2:185,534:0.0055:2,2:9.5:1:29.3:1:0.27612:2.88:60:8:0.0058:0:1 0/1:394:4:2,2:108,281:0.0102:2,2:16.5:1:29.3:1:0.31269:2.59:60:8:0.0104:0:1.5 -1 156836838 . T C 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00057;SOR=Inf;LSEQ=CTGTGTGCACTTGGGTCTGT;RSEQ=GGATGACATTGGGTCACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:82,419:0:2,0:24.7:1:29.8:1:1:0:60:40.75:1:0:0.1 0/1:266:7:2,5:55,203:0.0263:2,2:32.7:1:28.9:1:0.6454:1.47:60:14:0.0266:0:1 -1 156837463 . CT C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTTTTCTTTTCTTTT;RSEQ=TTTTTTTTTTTTATGAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:37.5:1:32:1:0.33333:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 156837802 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0873;SOR=Inf;LSEQ=TGTCCTCCCTTTCACCTGTA;RSEQ=ACGGTCCTCCCTGCTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:373,55:0:2,0:24.6:1:31.9:1:1:0:60:60.143:1:0:0.1 0/1:180:2:1,1:155,23:0.0111:2,2:28.5:1:29:0:0.24953:6.61849:60:4:0.0112:0:1 -1 156838141 . T C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01163;SOR=1.93053;LSEQ=CACTGAAAAGGCCTGGGGAA;RSEQ=GGGCACTGGCAAAGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:111:39,72:48,98:0.4319:2,2:25:1:30.6:1:0.79026:1.11:60:110:0.4348:0:1.1 1/0:84:50:14,36:7,27:0.5952:2,2:22:1:29.5:1:0.60847:1.49:60:49:0.5904:0:1.1 -1 156838571 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGAGGTTGAGGGACGGACA;RSEQ=AGATGGTTTAGACCCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:0,2:5,131:0.0145:1,0:18:1:29.5:1:1:0:60:4:0.0149:0:1 0/0:35:0:0,0:0,35:0:1,0:23.3:1:31.5:1:1:0:60:70:1:0:0 -1 156838809 . TC T 75 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTACATCACTTTTCTCTC;RSEQ=CCTTCCTTCCTTCCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:1,5:0,0:0.8571:0,2:29.5:1:29.4:1:1:0:52.7:12:1:0.1429:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 156841199 . T TA 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAATAAAACATAAAA;RSEQ=AAAAAAAAAATGTGATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:0.1053:1,0:22.5:1:29.5:1:1:0:60:4:0.1053:0:1 0/0:9:0:0,0:9,0:0:0,0:21.7:1:29.8:1:1:0:60:18:1:0:1.2 -1 156841259 . A C 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTAAAGGAGGAAGGCCATT;RSEQ=TCTGCTACATTCTCTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:78:78,0:0,0:0.9873:0,1:28:1:30.9:1:1:0:60:25:1:0:1.2 1/1:29:29:28,1:0,0:1:0,1:23:1:30.6:1:1:0:60:58:1:0:1.2 -1 156841639 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.11111;SOR=Inf;LSEQ=GGGGGGCTGGAAGAAAGGGT;RSEQ=GGATGTGTGTCTCCACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:7,162:0:1,0:23.8:1:31.2:1:1:0:60:41.25:1:0:0.2 0/1:85:2:1,1:2,81:0.0235:1,2:13:1:28.5:1:0.06975:33.24:60:4:0.0244:0:1 -1 156841674 . G A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=ACAGCTGCTCCCTCCCAGCT;RSEQ=TTTCCAGATTCCCATGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:3,91:0:1,0:23.8:1:32:1:1:0:60:93:1:0:0.1 0/1:31:6:0,6:0,25:0.1935:1,0:14.5:1:26.7:1:1:0:60:5:0.1667:0:1.3 -1 156843302 . T G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAGGGCCTGCTGACCTG;RSEQ=TTCTCCCAGGCCTGCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:92,2:0.0208:1,2:6.5:1:29:1:0.06184:37.75106:60:4:0.0211:0:1.5 0/0:27:0:0,0:27,0:0:1,0:23.5:1:30.9:1:1:0:60:54:1:0:0.1 -1 156846073 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09509;SOR=Inf;LSEQ=GCTCCATCACATCAGGACAG;RSEQ=GTGGGGGGAGATGCAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:0:0,0:144,290:0:2,0:25:1:30.3:1:1:0:60:23.111:1:0:0.1 0/1:194:2:1,1:57,134:0.0103:2,2:29:1:28.5:1:0.51182:2.34:60:4:0.0108:0:1 -1 156846119 . G T 31 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.02381;SOR=Inf;LSEQ=ATGGCTGGATACCGGGGTGG;RSEQ=CGGGCTGCCCTGGGTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:261,201:0:2,0:22.2:1:30.9:1:1:0:60:24.667:1:0:0.1 0/1:188:3:1,2:108,77:0.016:2,2:7.3:1:20:1:0.57334:2.78986:60:2:0.0109:0:2 -1 156846233 . G A 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44597;SOR=1.09863;LSEQ=AGTGCTCGGCAGGACTTCCA;RSEQ=CGTGAGGCTGAGCTGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1143:263:158,105:508,371:0.2301:2,2:24.7:1:29.9:1:0.52197:1.10:60:130.5:0.2328:0:1.1 0/1:623:154:90,64:274,194:0.2472:2,2:23.2:1:29.6:1:1:1.00435:60:308:0.2492:0:1.1 -1 156848778 . C T 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.004;SOR=0;LSEQ=ACCCCTCTGGACAGCTGCCT;RSEQ=TACTGTTCTCTCAATCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:20:20,0:92,1:0.177:1,1:25.5:1:29.5:1:1:0:59.8:19:0.1712:0:3.1 0/0:38:0:0,0:37,1:0:1,0:26.5:1:30.8:1:1:0:60:37:1:0:1.6 -1 156848794 . C T 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05203;SOR=0.51035;LSEQ=GCCTCTACTGTTCTCTCAAT;RSEQ=CTCCACTTCCAGGTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:102:101,1:33,0:0.7556:1,1:26:1:30.2:1:1:0:60:101:0.7537:0:2.3 1/0:54:33:33,0:20,1:0.6111:1,1:22.7:1:29.7:1:0.38889:0:60:66:0.6226:0:2 -1 156848808 . T C 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00501;SOR=0.17843;LSEQ=CTCAATCCTCCACTTCCAGG;RSEQ=CCCCAGTCTCCTCTCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:182:178:169,9:0,0:0.978:0,2:23.4:1:31.9:1:1:0:60:43.5:0.9886:0:1.7 1/1:71:63:61,2:8,0:0.8873:0,1:23.5:1:31.3:1:1:0:60:30.5:0.8841:0:1.6 -1 156848909 . CA C 204 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCCCTCTCCTTTTCTTGTT;RSEQ=CAGATCCCATGGACCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1009:0:0,0:627,381:0:2,0:25.4:1:29.9:1:1:0:60:90.636:0.999:0:0.3 0/1:571:99:59,40:268,202:0.1734:2,2:25.7:1:30.8:1:0.65632:1.11:59.9:98:0.1738:0.021:0.2 -1 156848995 . C T 299 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.4702;LSEQ=GGTCTGGGGCAGCTGCTGGC;RSEQ=GTGGCTAGCCAGGTCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1196:888:459,429:165,142:0.7425:2,2:25.9:1:30.6:1:0.55126:1.08594:60:97.667:0.7455:0:1.2 1/0:650:374:184,190:141,134:0.5754:2,2:24.9:1:30:1:0.63386:1.08641:60:61.333:0.5759:0:1.1 -1 156849047 . G T 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=ACCTGGCGGGTCTGCATTTT;RSEQ=TGCACCGGGACCTGGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1255:27:14,13:656,570:0.0215:2,2:21.8:1:29.6:1:1:1.06859:60:26:0.021:0:1.4 0/0:678:0:0,0:369,308:0:2,0:23.4:1:31.3:1:1:0:60:60.545:0.9985:0:0.4 -1 156849505 . G A 68 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGACTCCCTGGTTCAAGC;RSEQ=ATTCTCCTGCTTCAGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:4,1:8,6:0.2632:2,2:12.4:1:29.4:1:0.60268:2.84:57.4:10:0.2632:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 156849658 . C T 107 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11847;SOR=0;LSEQ=TGATTGCCCACCTCGGCCTC;RSEQ=CAAAGTGCTGGGATTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:11:10,1:90,0:0.1089:1,2:30:1:31.1:1:0.10891:0:60:22:0.1146:0:1.1 0/0:26:0:0,0:25,1:0:1,0:28.5:1:30:1:1:0:59.3:52:1:0:0.2 -1 156849675 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCAAAGTGCTGGGATTA;RSEQ=AGGCGTGAACCACCGAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:2,0:134,2:0.0145:1,0:23:1:32:1:1:0:60:4:0.015:0:1.5 0/0:41:0:0,0:39,2:0:1,0:24:1:30.8:1:1:0:59.6:40:1:0:0.1 -1 156849744 . G A 35 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03941;SOR=Inf;LSEQ=GGTAGGCTGTGCCTTGACGG;RSEQ=CTGTCCCAGGCGCCCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:568:0:0,0:415,152:0:2,0:25.1:1:30.6:1:1:0:60:26:1:0:0.1 0/1:294:3:2,1:214,76:0.0102:2,2:36:1:22.7:1:1:1.40613:60:2:0.0069:0:2.3 -1 156849775 . T C 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCCCCTGGAATTGATGCAG;RSEQ=GTCCGCCCGTGGCAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:843:0:0,0:534,308:0:2,0:25.8:1:29.4:1:1:0:60:48.529:1:0:0.1 0/1:507:97:61,36:268,142:0.1913:2,2:26.9:1:31.1:1:0.63833:1.11359:60:47.5:0.1896:0:1.2 -1 156850104 . G C 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACTGTGTCCCCTCCACT;RSEQ=TGGCCCTTTTCTTCTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:102:102:1,101:0,0:1:0,1:24.5:1:32.7:1:1:0:60:204:1:0:2 1/1:27:27:0,27:0,0:1:0,1:20.7:1:33:1:1:0:60:54:1:0:1.8 -1 156850112 . T G 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCCTCCACTGTGGCCCT;RSEQ=TTCTTCTCTTCCTCCCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:91:91:0,91:0,0:1:0,1:22.9:1:32.3:1:1:0:60:90:1:0:2.1 1/1:21:21:0,21:0,0:1:0,1:18.9:1:31.9:1:1:0:60:42:1:0:2 -1 156850989 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCTGGCAAGTCTTCTTA;RSEQ=GATCTGATCCCAGTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:12,0:0.1429:0,2:21:1:29.5:1:0.14286:0:60:4:0.1429:0:2 0/0:3:0:0,0:3,0:0:0,0:12:1:32.7:1:1:0:60:6:1:0:1 -1 156851041 . T G 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCAGCCCAAGCTTCCCA;RSEQ=AGTCGAGCCTTAATCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:38,3:0,0:1:0,2:23.9:1:32.9:1:1:0:60:82:1:0:1.1 1/1:8:8:8,0:0,0:1:0,0:27.3:1:32:1:1:0:60:16:1:0:1 -1 156851141 . C T 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGCAGCTAAGAAGCCCAGA;RSEQ=GAGTAGTGTGAGCTGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:227,0:0:1,0:25.2:1:32.1:1:1:0:60:55.75:1:0:0 0/1:88:19:19,0:67,2:0.2159:1,1:18.4:1:28.8:1:1:0:60:18:0.2118:0:1.1 -1 156852626 . T A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGCCTCTTGTCCAGGC;RSEQ=GGTTAGTGCTAATGGAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 157474475 . G C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGAAGCAGTTAAAATG;RSEQ=GTCTTCGTCCTTATCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:32:1:1:0:60:4:1:0:1.5 -1 157474737 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGTTTGCTCCTTTTCTTC;RSEQ=TCTTTACCCAAAAAAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 157512453 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCATCAGGCAGGGGTAT;RSEQ=AGGGCACCTAGACTGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29:1:1:0:60:4:1:0:1 -1 157514097 . A G 64 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGTCAGATATGACGCTGT;RSEQ=AGGCATTGTTGCTGCCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:20.3:1:32.3:1:1:0:60:8:0.5714:0:2 1/1:1:1:1,0:0,0:1:0,0:9:0:34:0:1:0:60:2:1:0:1 -1 157514287 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74523;LSEQ=GTCAGGGTCACTGGGTTCCC;RSEQ=CTGATGGGCTGGAAGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:26,26:0.037:2,2:31:1:28.5:1:1:1:60:4:0.0377:0:1 0/1:36:1:1,0:17,18:0.0278:2,0:1:0:26:0:1:0:60:2:0.0278:0:1 -1 157516231 . C A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGTGACAGAGCGAGACT;RSEQ=CATCTCAAAAAACCAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 157550066 . T C 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.0067;LSEQ=CCCCACAGTTTTGCATATTG;RSEQ=GTACTCGGGAAACTAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:767:255:109,146:219,290:0.3325:2,2:25.7:1:30.6:1:1:1.0115:60:62.75:0.3347:0:1.1 0/1:542:181:88,93:164,196:0.3339:2,2:24.4:1:30.3:1:0.52329:1.13:60:59.333:0.3315:0:1.2 -1 157550156 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05619;SOR=Inf;LSEQ=CTCCTGCAAAATAAAGCAAA;RSEQ=ACGCATTTTTGTCAGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:54,214:0:2,0:22.9:1:31.4:1:1:0:60:133:0.9963:0:0.1 0/1:168:3:1,2:40,125:0.0179:2,2:10.7:1:27.3:1:0.57051:1.56:60:6:0.0179:0:2.3 -1 157599744 . T C 120 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.47413;LSEQ=CAGGCTCCGTTTTCTGACCG;RSEQ=GTGAGCCACAGTATCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:13,0:12,0:0.52:0,1:14.7:1:32.5:1:1:0:60:26:0.52:0:1.2 0/1:3:1:1,0:2,0:0.3333:0,0:31:0:33:0:1:0:60:2:0.3333:0:1 -1 157599795 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50674;SOR=0;LSEQ=GGACCATGAATCTTCACTCC;RSEQ=CATGGCACTGATCTGGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:55,4:0.0328:2,2:11.5:1:30:1:0.15847:12.40977:60:4:0.0328:0:1 0/0:45:0:0,0:38,7:0:2,0:21.9:1:30:1:1:0:60:44:1:0:0.5 -1 157599839 . C A 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGCTGCTCCAGCCTGAT;RSEQ=CCAGGGTCTGGCCATCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:99,41:0:2,0:23.6:1:31.2:1:1:0:60:139:1:0:1 0/1:116:16:9,7:68,31:0.1379:2,2:24.7:1:27.6:1:0.39287:1.69762:60:15:0.1316:0:1.3 -1 157599858 . C T 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=0.45935;LSEQ=TCCCAGGGTCTGGCCATCTC;RSEQ=GAAGAAGCAGAACTGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:102:63,39:52,30:0.5543:2,2:26.6:1:30.7:1:0.87872:1.07259:60:101:0.558:0:2 0/1:168:61:39,22:65,42:0.3631:2,2:24.6:1:30:1:0.74246:1.14:60:60:0.3659:0:1.9 -1 157599866 . C T 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04971;SOR=Inf;LSEQ=TCTGGCCATCTCCGAAGAAG;RSEQ=AGAACTGGAGCTGGACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:123,81:0:2,0:25.3:1:31.7:1:1:0:60:39.8:1:0:1.2 0/1:184:4:2,2:107,73:0.0217:2,2:9.5:1:26.3:1:1:1.46261:60:8:0.0219:0:1.3 -1 157599878 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20949;SOR=Inf;LSEQ=CGAAGAAGCAGAACTGGAGC;RSEQ=GGACTTCTGATCTCTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:134,100:0:2,0:25.3:1:30.3:1:1:0:60:57.5:1:0:1.3 0/1:198:2:1,1:111,85:0.0101:2,2:22:0:32:0:1:1.30409:60:4:0.0102:0:1.5 -1 157599882 . C A 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGCAGAACTGGAGCTGGA;RSEQ=TTCTGATCTCTCTAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:32:18,14:115,87:0.1368:2,2:26.6:1:30.9:1:1:1.02799:60:64:0.1379:0:3 0/0:204:0:0,0:114,87:0:2,0:26.6:1:31.2:1:1:0:60:99.5:0.9851:0:0.9 -1 157599917 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37239;LSEQ=GAGAGAGCCGGGTCTCACAG;RSEQ=TCAGGGTCACTGGGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:253:135:73,62:59,59:0.5336:2,2:27.1:1:31:1:0.53077:1.18:60:32.75:0.5413:0:2.7 0/1:238:71:36,35:83,84:0.2983:2,2:25.5:1:30.5:1:1:1.04:60:70:0.2991:0:2.5 -1 157599937 . T A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.39533;LSEQ=ATCAGGGTCACTGGGCTCCC;RSEQ=TTGGTGGGCTGGGAGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:232:122:57,65:47,63:0.5259:2,2:26.1:1:30.2:1:0.59754:1.17:59.9:60:0.5263:0:2.9 0/1:207:63:28,35:67,76:0.3043:2,2:26.3:1:29.6:1:0.76402:1.10145:60:62:0.3039:0:2.7 -1 157599988 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.30072;LSEQ=ACTGGACGTGAAAACAGCTC;RSEQ=AGAGAGAAGAATCACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:76:20,56:21,42:0.5429:2,2:25.3:1:31.6:1:0.45529:1.39656:59.9:75:0.5435:0:2.8 0/1:103:27:4,23:26,49:0.2621:2,2:22:1:31.6:1:0.08301:3.02131:60:26:0.26:0:2.8 -1 157600009 . G T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.20611;LSEQ=AGAGAGAAGAATCACAACAG;RSEQ=CCCAGAGCAATGAGGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:55:9,46:9,34:0.5612:2,2:25.8:1:29.3:1:0.60643:1.34871:59.9:26.5:0.5579:0:2.7 0/1:58:12:0,12:11,34:0.2069:2,0:25.3:1:29.6:1:0.09677:0:60:24:0.2069:0:2.6 -1 158506819 . G T 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACCTGAACAGGGAAAGA;RSEQ=AATTTGAATTGAAATTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:5,0:0.375:0,2:31:1:31:1:0.375:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 158507096 . AT A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.31412;SOR=0.38805;LSEQ=GGGAATTTGAACCAAGCAGT;RSEQ=TTTTTTTTCAGACATAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:7:5,2:174,70:0.0279:2,2:29.6:1:31.9:1:1:1.01:60:14:0.028:0:1 0/1:182:2:1,1:123,57:0.011:2,2:30:1:32:0:0.537:2.14793:60:4:0.011:0:1 -1 158507106 . C T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07243;SOR=Inf;LSEQ=ACCAAGCAGTATTTTTTTTT;RSEQ=AGACATAGACAAATTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:195,89:0:2,0:25.8:1:31.4:1:1:0:60:70:1:0:1 0/1:204:3:2,1:128,73:0.0147:2,2:26.3:1:22.3:1:1:1.14:55:2:0.0102:0:2.3 -1 158507157 . A T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23094;LSEQ=TCTGAAGGTAAAGATTCAAG;RSEQ=TGTTTTTCAAGAGCGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:442:269:153,116:93,80:0.6086:2,2:26.6:1:29.6:1:0.55656:1.13:60:88.667:0.6101:0:2.8 0/1:326:86:48,38:130,110:0.2638:2,2:27.5:1:29.4:1:0.80223:1.07:60:85:0.269:0:2.6 -1 158507160 . T G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.24851;LSEQ=GAAGGTAAAGATTCAAGATG;RSEQ=TTTTCAAGAGCGCACAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:446:268:153,115:97,80:0.6009:2,2:26.7:1:31.5:1:0.6963:1.10:60:267:0.6054:0:2.8 0/1:331:90:49,41:131,110:0.2719:2,2:27.3:1:30.9:1:1:1.00:60:89:0.2722:0:2.6 -1 158507184 . A G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16281;LSEQ=TCAAGAGCGCACAGGTATAG;RSEQ=TTATATGTCAGCATTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:499:295:154,141:98,106:0.5912:2,2:26:1:31.6:1:0.36431:1.18:60:590:0.5948:0:2.5 0/1:368:70:37,33:147,151:0.1902:2,2:25.4:1:30.7:1:0.69049:1.15:60:34:0.1889:0:2.4 -1 158507222 . GA G 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.43179;LSEQ=GAAATGGTTTCCAGGGTTAT;RSEQ=AAAAAAATCTCTGCCTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:461:249:104,145:91,119:0.5401:2,2:27.3:1:31.6:1:0.77639:1.06602:60:248:0.5415:0.0456:1.3 0/1:342:115:52,63:102,125:0.3363:2,2:28.2:1:31.7:1:1:1.01:60:230:0.3392:0.0263:0.8 -1 158507360 . G C 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00632;SOR=Inf;LSEQ=CAATCTAAGATAAAATGACA;RSEQ=GTCTAGAGAAGTGTGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:0:1,0:23.3:1:30.9:1:1:0:60:46:1:0:0.4 0/1:20:4:0,4:1,15:0.2:1,0:28.3:1:29:1:1:0:60:8:0.2:0:1.5 -1 158507398 . G T 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15723;SOR=0.22635;LSEQ=GTGGTTAGTTGTCAGGCTCT;RSEQ=AATGTAGGCATTATCTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:21:0,21:0,6:0.7778:0,1:27.6:1:28.6:1:1:0:60:42:0.7778:0:1.5 0/1:7:3:0,3:0,4:0.4286:0,0:20:1:29.7:1:1:0:60:6:0.4286:0:1.7 -1 161284075 . CAG C 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00108;SOR=Inf;LSEQ=AGAGCTGAGCGGAGAAGCTC;RSEQ=AGCCTTTTAAAGAGACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:204,5:0:1,0:25.6:1:30.1:1:1:0:60:51.25:1:0:0.2 0/1:101:6:6,0:92,3:0.0594:1,0:35.2:1:30:1:1:0:60:12:0.0612:0:0.2 -1 161284164 . T C 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCGGGTGGCGGGGCCGCC;RSEQ=GGCGTCACTTCCGTCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:928:0:0,0:589,339:0:2,0:24.9:1:30.5:1:1:0:60:91.8:1:0:0.1 0/1:736:46:25,21:402,288:0.0625:2,2:23.8:1:29.5:1:0.64483:1.17224:60:22:0.061:0:1.3 -1 161284224 . A AGT 201 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCTGTTGCTGAGGTGACTTC;RSEQ=GTGGGACTGGGAGTTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1372:0:0,0:632,737:0:2,0:25.9:1:30.5:1:1:0:60:61.227:0.9985:0:0.2 0/1:1122:107:49,58:501,513:0.0954:2,2:22.3:1:29.9:1:0.54204:1.15583:60:214:0.0968:0.0223:0.4 -1 161284297 . T C 226 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=153.91929;LSEQ=CACGTTTTGCTGATAACTGT;RSEQ=TATCCTGTGCCTGGGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:634:2:1,1:177,455:0.0032:2,2:19.5:1:20.5:1:0.48301:2.57:60:1:0.0016:0:2 0/1:478:157:47,110:101,220:0.3285:2,2:22.5:1:31.1:1:0.75318:1.07433:60:314:0.3298:0:1.1 -1 161284376 . TC T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.55368;SOR=0;LSEQ=CCTAGAGACCCCTTTTCCCG;RSEQ=CCCCCCAGCCGCTCCGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:3:0,3:1,121:0.024:1,0:30:1:26:1:1:0:60:2:0.0165:0:1.7 0/0:69:0:0,0:0,69:0:1,0:20.5:1:30.7:1:1:0:60:22:1:0:0.3 -1 161293484 . ATTTAT A 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0045;SOR=Inf;LSEQ=AGTTTCTAAGTCTGGAGATT;RSEQ=TTATTTTTTTTTTTGAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:0:0,0:192,445:0:2,0:20.7:1:30:1:1:0:59.8:44.5:0.9968:0:0.2 0/1:552:7:3,4:159,369:0.0127:2,2:7.6:1:26.9:1:0.43761:1.74:60:14:0.013:0.0091:0 -1 161293488 . A T 84 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59148;SOR=1.53378;LSEQ=TCTAAGTCTGGAGATTATTT;RSEQ=TTTATTTTTTTTTTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:6:0,6:171,409:0.0102:2,0:22.7:1:13.5:1:0.18799:0:53.3:0:0:0:3.2 0/1:512:8:0,8:145,345:0.0156:2,0:25:1:28.3:1:0.11221:0:46.8:7:0.0146:0:3.8 -1 161293492 . A AT 164 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.54308;SOR=0.84588;LSEQ=AGTCTGGAGATTATTTATTT;RSEQ=TTTTTTTTTTTGAGACGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:537:42:9,33:132,353:0.0782:2,2:28.5:1:30.5:1:0.47233:1.37038:59.8:41:0.0813:0:0.1 0/1:463:31:7,24:113,282:0.067:2,2:26.1:1:29.5:1:0.54027:1.37293:59.8:62:0.0709:0:0.2 -1 161293508 . C T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.01169;SOR=Inf;LSEQ=ATTTATTTTTTTTTTTGAGA;RSEQ=GGAGTCTCGCTCTGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:52,264:0:2,0:21.7:1:29.8:1:1:0:59.6:44.143:1:0:0.2 0/1:290:6:1,5:56,226:0.0207:2,2:25.2:1:30.5:1:1:1.23807:56.3:12:0.0214:0:2.3 -1 161293630 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTAGCTGGGACTACAGG;RSEQ=GCCCACCACCACGCCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:0,2:0,40:0.0476:1,0:24:1:31.5:1:1:0:49:4:0.05:0:1.5 0/0:19:0:0,0:0,19:0:1,0:22.4:1:29.7:1:1:0:54.3:38:1:0:0.4 -1 161298109 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15772;SOR=Inf;LSEQ=GCTTGGTATTGCAAAATATT;RSEQ=ACTTAATAAAACGTTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:235,37:0:2,0:23.7:1:31.7:1:1:0:60:67:0.9963:0:0.1 0/1:181:2:1,1:145,34:0.011:2,2:18.5:1:27.5:1:0.35021:4.21781:60:4:0.0113:0:1 -1 161310275 . G GA 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.32193;SOR=3.93097;LSEQ=CTGTCTCAAAAAAAAAAAAA;RSEQ=AAAAAAAAGTGCCTATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:1:1,0:309,41:0.0027:2,0:22:0:29:0:1:0:60:2:0.0036:0:0 0/1:281:3:2,1:219,48:0.0107:2,2:10.3:1:31.6:1:0.45297:2.27252:53.3:6:0.0144:0.0071:1.3 -1 161310519 . C T 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTCATTGGCCCTAGTCTC;RSEQ=GCCTCCTTTGAAACTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:53,255:0:2,0:22.1:1:29.8:1:1:0:60:153:1:0:0.1 0/1:223:17:5,12:41,165:0.0762:2,2:16.8:1:30:1:0.35511:1.67:60:34:0.0773:0:1.2 -1 161326293 . T C 114 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=19.38188;LSEQ=GAGCCAAGATTGCACCACTA;RSEQ=ACTCCAGCCTGGGTGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:2,0:66,1:0.029:1,0:29:0:31.5:1:1:0:60:4:0.029:0:1 0/1:32:12:12,0:20,0:0.375:1,0:25.3:1:32:1:1:0:60:24:0.3871:0:1.3 -1 161326331 . G T 94 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.01097;SOR=5.12577;LSEQ=AGAATGAGACTCTGTCTCAA;RSEQ=AAAAAAAGAAAACAAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:4:4,0:144,3:0.0265:1,0:16.5:1:32.5:1:1:0:60:8:0.0267:0:1 0/1:73:9:9,0:64,0:0.1233:1,0:20.9:1:29.8:1:1:0:60:18:0.125:0:1.3 -1 161326488 . C A 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00574;SOR=0.43179;LSEQ=GGTCTCTCTTTTTGGCATGT;RSEQ=GGCCCTGTTACTCCCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1539:41:22,19:818,676:0.0266:2,2:10.2:1:29.6:1:1:1.04504:46.9:82:0.0269:0:6 0/1:1199:14:8,6:613,569:0.0117:2,2:11.9:1:29.4:1:0.79149:1.24:46.1:28:0.0118:0:6.1 -1 161326498 . A G 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02738;SOR=0.55635;LSEQ=TTTGGCATGTCGGCCCTGTT;RSEQ=CTCCCTGGGAACTTTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1574:49:24,25:813,710:0.0311:2,2:18.5:1:31.2:1:0.56354:1.19264:46.7:15.333:0.0295:0:5.7 0/1:1196:21:11,10:603,572:0.0176:2,2:17.4:1:31:1:1:1.04:42.4:20:0.0169:0:5.8 -1 161326520 . T A 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10236;SOR=0.62998;LSEQ=TCCCTGGGAACTTTGAGTCT;RSEQ=ATTTGGAACTTGTGAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1612:46:23,23:818,747:0.0285:2,2:38:1:29.7:1:0.76712:1.09498:46.2:45:0.0284:0:6 0/1:1156:21:11,10:558,577:0.0182:2,2:33.9:1:29.3:1:0.82807:1.14:42.4:42:0.0184:0:5.8 -1 161326531 . TG CC 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0798;SOR=0.62363;LSEQ=TTTGAGTCTTATTTGGAACT;RSEQ=TGAAGTCCCTGTGTCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1588:46:23,23:783,756:0.029:2,2:33.1:1:32.2:1:1:1.0357:46.2:92:0.0292:0:5 0/1:1150:21:11,10:555,574:0.0183:2,2:31.1:1:31.4:1:0.82806:1.14:42.4:42:0.0184:0:4.8 -1 161326716 . G A 26 v4;Bias;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14136;SOR=Inf;LSEQ=CCTTCATTACTGGGTTTAGT;RSEQ=CTGTTCTTTTTTTTTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:18,260:0:2,0:22.7:1:30.1:1:1:0:59.9:9.296:1:0:0.4 0/1:168:2:2,0:11,155:0.0119:2,0:9:1:26:1:0.00556:0:60:4:0.0126:0:1 -1 161326722 . CT C 147 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.92751;LSEQ=TTACTGGGTTTAGTGCTGTT;RSEQ=TTTTTTTTTTTCCCAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:25:0,25:9,203:0.1046:1,1:24.6:1:31.7:1:0.60294:0:59.6:50:0.1096:0.0084:0.2 0/1:133:13:2,11:5,115:0.0977:1,2:29.5:1:31:1:0.14007:4.11:60:26:0.1008:0:0.5 -1 161332346 . C G 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAGATCCTTTTGTATTTT;RSEQ=AGATCTCCTTGGAGCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:591:0:0,0:227,364:0:2,0:30.2:1:31.3:1:1:0:45:97.5:1:0:0.1 0/1:527:19:6,13:205,303:0.0361:2,2:26.1:1:29.7:1:0.48597:1.46488:44.4:18:0.0346:0:1.4 -1 161332371 . C A 116 pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07138;SOR=0.39203;LSEQ=CTCCTTGGAGCAGTAGAGTA;RSEQ=CTGGTAGACCATAATAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:15:0,15:134,401:0.0272:2,1:12.7:1:29.9:1:0.02783:0:55.7:30:0.0277:0:3.1 0/1:462:5:1,4:117,340:0.0108:2,2:13:0:29:1:1:1.37557:46.2:10:0.011:0:3 -1 161332376 . T A 118 pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10977;SOR=0.40154;LSEQ=TGGAGCAGTAGAGTACCTGG;RSEQ=AGACCATAATAGTGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:15:0,15:110,428:0.0271:2,1:17.7:1:30.3:1:0.05039:0:55.7:30:0.0274:0:3.1 0/1:452:5:1,4:100,347:0.0111:2,2:18:0:29.6:1:1:1.15239:46.2:10:0.0111:0:3 -1 161332385 . A G 126 pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11059;SOR=0.41839;LSEQ=AGAGTACCTGGTAGACCATA;RSEQ=TAGTGGAAAAGGGTCTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:15:0,15:85,448:0.0274:2,1:16:0:32.5:1:0.14391:0:55.7:30:0.0278:0:3.1 0/1:430:5:1,4:70,355:0.0116:2,2:16:0:32:1:1:1.27:46.2:10:0.0118:0:3 -1 161332435 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53822;SOR=0;LSEQ=TTTCTAAAGATGAGGTGGCT;RSEQ=CAAAAACTCCCCTTTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:4,178:0.0109:1,2:20.5:1:27:1:0.05375:39.89:58.5:4:0.011:0:1 0/0:103:0:0,0:3,100:0:1,0:26.8:1:32.4:1:1:0:49.8:102:1:0:0.1 -1 161369021 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08258;SOR=Inf;LSEQ=GAGGAAACCGACCCATCGCA;RSEQ=TCTCGGCCGAAGAGGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:31.5:1:30.9:1:1:0:60:25:1:0:0.3 0/1:11:2:1,1:7,2:0.1818:2,2:22.5:1:28.5:1:0.49091:3.05504:60:4:0.1818:0:1 -1 161448241 . C G 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=AGTCAGGGATAGTATGAGAT;RSEQ=CTGCCTAGAATTTACAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:23.6:1:32.1:1:1:0:59.2:38:1:0:0.2 1/0:12:8:5,3:3,1:0.6667:2,2:16.5:1:32.6:1:1:1.71671:60:16:0.6667:0:1 -1 161448285 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22356;SOR=0;LSEQ=TCTTCTGTATCAGACAACGT;RSEQ=TTTCAAACTCTTATACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:0.0645:2,2:40.5:1:30:1:1:1.22249:60:4:0.0645:0:1 0/0:34:0:0,0:18,16:0:2,0:27.9:1:28.3:1:1:0:60:33:1:0:0.4 -1 161449051 . C CCCG 26 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATGCCCGAGCCCCCCCC;RSEQ=CCCCGGACGGTGGGCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:1,0:0.6667:0,0:11:1:26.5:1:0.33333:0:60:4:0.6667:0.3333:1 -1 161449129 . C T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATGGCACCCAGTCCTAT;RSEQ=GACCGCCCAAAGGCTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:30:1:32:0:1:0:60:4:1:0:2 -1 162039394 . G T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGGACTTTCACCTGCTC;RSEQ=GCTGGCAGCGCGGGCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:32.5:1:1:0:60:4:1:0:1.5 -1 162688638 . A T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAGAGTTTGAAAATTATT;RSEQ=TATTAGGTGATTATTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:3,0:31,0:0.0882:1,0:37.7:1:30.3:1:1:0:60:6:0.0909:0:1 0/0:5:0:0,0:5,0:0:0,0:20.4:1:28.4:1:1:0:60:10:1:0:0 -1 162722812 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.1022;SOR=Inf;LSEQ=CTTGTTCAATATTCAGTGAT;RSEQ=TTCTTCCTAGGGGGCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:269,30:0:2,0:23.5:1:28.5:1:1:0:60:98.667:1:0:1 0/1:141:2:1,1:117,22:0.0142:2,2:19.5:1:28:1:0.30061:5.22358:60:4:0.0143:0:2 -1 162722846 . C G 294 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72197;SOR=1.57504;LSEQ=GCTTGGAAATAAAAATAAAA;RSEQ=CATGTCCTCTCTTTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:600:594:472,122:1,0:0.99:0,2:24.1:1:32:1:1:0:60:53:0.9915:0:1.1 1/1:314:312:222,90:0,0:0.9936:0,2:22.6:1:31.7:1:1:0:60:77:0.9935:0:1.1 -1 162723162 . T C 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00165;SOR=Inf;LSEQ=ATGTTTTCAGGGAGAGAATT;RSEQ=AGGACTTAGCCACATGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:1,88:0:1,0:22.1:1:28.3:1:1:0:60:88:1:0:0.2 0/1:24:4:0,4:0,20:0.1667:1,0:33.5:1:33.5:1:1:0:60:8:0.1667:0:1.3 -1 162725380 . C T 35 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03964;SOR=Inf;LSEQ=ACGCTGTGCAAGCTTATACC;RSEQ=TTGAAACTCACATAGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:395,94:0:2,0:24:1:31.3:1:1:0:60:243.5:1:0:0.1 0/1:254:3:1,2:188,62:0.0118:2,2:7:1:22.3:1:0.15848:6.01116:60:2:0.0079:0:2 -1 162725655 . A C 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATAATCAATCAACCAATC;RSEQ=GTATTTATTTAGTTCTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:142:142:2,140:0,0:1:0,1:26.1:1:30.1:1:1:0:60:141:1:0:1 1/1:62:62:0,62:0,0:1:0,1:22.1:1:30.1:1:1:0:60:61:1:0:1.1 -1 162729523 . C T 22 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11315;SOR=Inf;LSEQ=ATGCCGGGTAAAAGCTCTTC;RSEQ=ACGAATGTGTGGTTAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:188,30:0:2,0:25.7:1:31.1:1:1:0:60:53.5:1:0:0.1 0/1:111:2:1,1:86,23:0.018:2,2:14:1:22.5:1:0.38722:3.6819:60:4:0.0185:0:1 -1 162729529 . T A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.11992;SOR=Inf;LSEQ=GGTAAAAGCTCTTCCACGAA;RSEQ=GTGTGGTTAACTCAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:223,46:0:2,0:23:1:30.7:1:1:0:60:268:1:0:0.1 0/1:143:2:1,1:111,30:0.014:2,2:10:0:28.5:1:0.38777:3.65654:60:4:0.0142:0:1 -1 162730148 . T TTG 49 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=23;MSI=12.000;MSILEN=2;SSF=0.46429;SOR=Inf;LSEQ=TTATCTTTTTACCAGCACAG;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:27.3:1:31.3:1:1:0:60:6:0.6:0.1667:0.7 1/1:2:2:1,1:0,0:1:0,2:2:1:32.1:1:1:0:60:6:0.8858:0.6875:1.5 -1 162730759 . T TA 29 v4;MSI6 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.01;SOR=Inf;LSEQ=TCATTTAGAAATGAGATTTC;RSEQ=AAAAAAAAAAATGAAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:20,0:0.0435:1,0:18:0:11:0:1:0:60:0:0:0:7 1/1:2:2:2,0:0,0:1:0,0:24:1:29.3:1:1:0:60:4:1:0.5:0 -1 162731291 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05426;SOR=Inf;LSEQ=AGTGGGAGCAAGGTGATGAA;RSEQ=GAGGAATGCACATGCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:74,315:0:2,0:22.6:1:31.1:1:1:0:60:388:1:0:0.1 0/1:238:3:1,2:53,182:0.0126:2,2:31.7:1:27:1:0.53963:1.71:60:2:0.0085:0:1 -1 162731404 . C T 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGTGTGACTAGTTTTAA;RSEQ=TGTGGAGGGGATGGGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:46:0,46:0,0:1:0,1:25.3:1:29.2:1:1:0:60:10.5:1:0:1.3 1/1:12:12:1,11:0,0:1:0,2:16.3:1:30.3:1:1:0:60:24:1:0:1 -1 162735473 . A G 102 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATTCTGTCTATATTTTC;RSEQ=CTGAATTTGGGTCCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:17.8:1:26.9:1:1:0:60:6:1:0:1.6 1/1:1:1:1,0:0,0:1:0,0:8:0:29:0:1:0:60:2:1:0:1 -1 162736463 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATAGAAAAACTCACCATTA;RSEQ=TCTGTCTGACACATGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:11:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162736690 . C T 88 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTAGCCGGGCGTAGTGG;RSEQ=GCATGCCTGTAATCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:2,0:0.8:0,0:28.1:1:29.5:1:1:0:55.4:16:0.8:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162736734 . G C 112 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGGCTGAGGCAGAATT;RSEQ=CTTGAACCTGGGAGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:24.1:1:29.6:1:1:0:57.8:6:1:0:1.6 1/1:1:1:1,0:0,0:1:0,0:2:0:30:0:1:0:60:2:1:0:1 -1 162736821 . G GA 158 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.10847;SOR=0.27357;LSEQ=AGAACAAGACTCTATCTCAG;RSEQ=AAAAAAAAAAAGTAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:39:39,0:11,0:0.75:0,1:24.6:1:29.9:1:1:0:57.7:38:0.76:0.0962:1.5 0/1:9:4:4,0:3,0:0.4444:0,0:27:1:29.8:1:1:0:60:8:0.4444:0:0.5 -1 162736856 . C AAAAA 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.06206;SOR=0.27327;LSEQ=AGTAATAAAACAGTAGCAAG;RSEQ=AAAACAGTAGCAAGAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:34:32,2:20,0:0.4096:1,2:25.1:1:30.8:1:0.52481:0:57.1:68:0.4595:0:2.5 0/1:19:3:2,1:3,0:0.1579:0,2:12.7:1:31.9:1:1:0:60:6:0.1667:0:1.3 -1 162736899 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCAGAAGTATTAAGGTG;RSEQ=CATCTTCCATAATTATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:2,0:192,4:0.0101:1,0:7:1:30:1:1:0:60:4:0.0111:0:1 0/0:75:0:0,0:73,2:0:1,0:20.3:1:30.7:1:1:0:59.9:24:1:0:0.5 -1 162737116 . C G 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.20758;LSEQ=GCCATCATTGTCATCATCCT;RSEQ=TGGAGGCAGTTCTGGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1193:316:119,197:356,518:0.2649:2,2:26.3:1:32:1:0.34881:1.13761:60:104.333:0.2653:0:1.1 0/1:762:53:19,34:292,415:0.0696:2,2:26.2:1:30.9:1:0.47185:1.25872:60:52:0.0692:0:1.1 -1 162737241 . A G 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00223;SOR=0;LSEQ=GTAAAAGGCAAATTGCAAAC;RSEQ=TTTATTAATGGTTGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:18:0,18:7,148:0.104:1,1:25.9:1:29.1:1:1:0:60:8:0.0982:0:1.2 0/0:71:0:0,0:3,68:0:1,0:20.3:1:30.1:1:1:0:60:142:1:0:0 -1 162737338 . G C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTCTCATTTTTAGAGTGGA;RSEQ=ATGTTGGAACCTTCCTAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:0,23:0,0:1:0,1:25:1:31.7:1:1:0:60:22:1:0:1.1 1/1:5:5:0,5:0,0:1:0,0:24:1:32.2:1:1:0:60:10:1:0:1.4 -1 162739830 . CT C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAGCAACAGGGAGATAAT;RSEQ=TTTTTTTTTAAGTGTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:11,1:0.2:2,0:29.3:1:31.4:1:1:0:60:6:0.2:0.0667:0 0/0:1:0:0,0:1,0:0:0,0:7:0:32:0:1:0:60:2:1:0:0 -1 162740009 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53535;SOR=0;LSEQ=TAAAGAGTTATTTCATTTGA;RSEQ=TGGGAGAGCTGAGTTTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:155,4:0.0124:1,2:7:1:27.5:1:0.06134:34.76925:60:4:0.0125:0:1 0/0:92:0:0,0:89,3:0:1,0:24.1:1:32:1:1:0:60:91:1:0:0 -1 162740121 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14744;LSEQ=AGGATGCTGGATGATGAAAT;RSEQ=ACAGTCAGCCTTTCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1057:262:179,83:477,317:0.2479:2,2:24.5:1:28.8:1:0.01871:1.43:60:130:0.2488:0:1.1 0/1:756:35:21,14:420,301:0.0463:2,2:27.5:1:28.1:1:0.86293:1.07:60:34:0.0452:0:1.2 -1 162740327 . T C 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10026;LSEQ=GGATGATGTGGTGGGCAGGG;RSEQ=GTCAAGGGAGAAACCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:685:681:209,472:0,1:0.9942:0,2:23.5:1:29.9:1:1:0:60:39.059:0.9955:0:1.1 1/1:469:443:146,297:9,17:0.9446:2,2:25:1:29.8:1:0.83335:1.07678:60:43.3:0.9454:0:1.2 -1 162740740 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAAGCTAAAGACATTCC;RSEQ=AAATTCCCAGTGGTGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162741494 . A G 34 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGGAAATAAGTTATTAA;RSEQ=CCTTCAACCTTTAATATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:13:1:34:0:1:0:60:4:0.1818:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162741769 . A G 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TCCTTCCTGAAGAGATCTCC;RSEQ=AAGACACTCCACGGAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:298,74:0:2,0:23.2:1:30:1:1:0:60:185:1:0:0.1 0/1:215:10:7,3:157,48:0.0465:2,2:18.8:1:29.3:1:0.70414:1.39941:60:20:0.0469:0:1 -1 162741794 . C T 89 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00122;SOR=14.5272;LSEQ=CACTCCACGGAATGAGGGCT;RSEQ=GTTGCCCTTGTCTTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:0,1:374,160:0.0019:2,0:1:0:28:0:0.30093:0:60:2:0.0019:0:1 0/1:339:9:4,5:220,109:0.0265:2,2:25.1:1:28.3:1:0.17123:2.51543:60:18:0.0269:0:1 -1 162741795 . G A 107 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=17.67208;LSEQ=ACTCCACGGAATGAGGGCTC;RSEQ=TTGCCCTTGTCTTCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:1:0,1:383,163:0.0018:2,0:41:0:32:0:0.29982:0:60:2:0.0019:0:1 0/1:350:11:6,5:224,113:0.0314:2,2:31.4:1:31:1:0.51901:1.64944:60:22:0.032:0:1.1 -1 162742117 . C T 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGAACAAAGAGTCCCTTC;RSEQ=AGAGGTGGATTCACAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:28,274:0:2,0:22.3:1:32:1:1:0:60:74.5:0.9967:0:0.2 0/1:174:23:5,18:15,136:0.1322:2,2:19.6:1:28.4:1:0.15025:2.50:60:46:0.1329:0:1.2 -1 162742180 . T C 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCATTGTCCTCTGGATT;RSEQ=CAGTATTGGGTCAACCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:79:1,78:0,0:1:0,1:23.7:1:31.7:1:1:0:60:158:1:0:1 1/1:43:43:2,41:0,0:1:0,1:20.9:1:31.8:1:1:0:60:86:1:0:1.1 -1 162742510 . A G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAATGAATCACCAACTA;RSEQ=GATAAGGAGGAGTACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:32:1:30.3:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162742843 . G C 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTTATACTGTTACTAATA;RSEQ=ACAGGAGTTTCTTATAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:12:1:30:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162743418 . G T 269 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.5722;LSEQ=ACATTTTGAATTTTCCTTTA;RSEQ=GTATTTCATCTTTAGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:482:481:123,358:0,0:0.9979:0,2:23.9:1:30.3:1:1:0:60:159.333:0.9979:0:1.1 1/1:276:275:80,195:1,0:0.9964:0,2:24.1:1:29.9:1:0.29348:0:60:274:0.9964:0:1.1 -1 162743851 . TTG CTCC 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TTATGCTCCTTTTCTTCTAT;RSEQ=AGCAACCCTCAAAATGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:26.5:1:31.1:1:1:0:60:8:1:0.25:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162745047 . T TAA 55 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGAGTGACTCCATGGCTT;RSEQ=AAAAAAAAAAAGGTAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:0,0:0.5:0,0:25.3:1:27.9:1:1:0:60:8:0.5714:0.125:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162748025 . A C 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAGATTCCTCTATCTCTA;RSEQ=CATAAAAACCATTGACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:27.8:1:31.8:1:1:0:60:8:0.8:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162748147 . G A 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCAAATAGCTTATGGCTGC;RSEQ=TTTTTTTCAGCTCTTGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:24,0:0,0:1:0,1:24.9:1:29.7:1:1:0:60:23:1:0:1 1/1:7:7:7,0:0,0:1:0,0:12.6:1:25.6:1:1:0:60:2.5:1:0:1.3 -1 162748285 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11529;SOR=Inf;LSEQ=TTGCCTGTGGTGGGGGAAGG;RSEQ=GTATAGCTGCAGATTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:232,16:0:2,0:23.5:1:31:1:1:0:60:48.6:1:0:0.1 0/1:128:2:1,1:114,12:0.0156:2,2:21:0:31:1:0.19353:9.16725:60:4:0.016:0:1.5 -1 162748518 . A T 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01907;SOR=Inf;LSEQ=CTTCCGAGACCAAGGGAGGC;RSEQ=GGTAAGAACTGTTGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:0:0,0:125,417:0:2,0:24.5:1:30.9:1:1:0:60:76.429:1:0:0.2 0/1:322:4:1,3:90,228:0.0124:2,2:22.5:1:25:1:1:1.1836:60:3:0.0094:0:3 -1 162748543 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12079;SOR=Inf;LSEQ=AGAACTGTTGGGGATGAATG;RSEQ=ATGTGGACCTGTGTACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:51,301:0:2,0:24:1:31.3:1:1:0:60:116.333:1:0:0.4 0/1:188:2:1,1:41,145:0.0106:2,2:12:1:29:1:0.39783:3.51:60:4:0.0108:0:1 -1 162748566 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.09818;SOR=Inf;LSEQ=GTGGACCTGTGTACCTTGAA;RSEQ=GATGGAGAATGGCAAGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:24,205:0:2,0:23.5:1:31.5:1:1:0:60:113.5:1:0:0.7 0/1:105:2:1,1:10,93:0.019:2,2:32.5:1:31:0:0.19945:8.92:60:4:0.0194:0:2 -1 162748588 . C A 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00264;SOR=0;LSEQ=ATGGAGAATGGCAAGTCCTG;RSEQ=CTTAGCAGGAGTGGGCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:148:4,144:0,0:1:0,1:23.4:1:30.1:1:1:0:60:48.333:1:0:1.1 1/1:67:62:4,58:0,5:0.9254:0,2:26.1:1:29.3:1:1:0:60:124:0.9254:0:1.1 -1 162749761 . T C 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGTAGGAAAAATGGACAC;RSEQ=ACACCCATTTCAGTTATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:79,3:0,0:1:0,1:22.8:1:31.4:1:1:0:60:81:1:0:1 1/1:32:32:32,0:0,0:1:0,1:25.8:1:30.9:1:1:0:60:31:1:0:1.1 -1 162750158 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12259;SOR=Inf;LSEQ=GAGAGACAGAGGCTTGTTTG;RSEQ=TTTGCCCTCTTTTCCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:0,116:0:1,0:28.8:1:31.8:1:1:0:60:22.2:1:0:0.5 0/1:63:2:1,1:3,58:0.0317:1,2:12:1:27:1:0.12391:16.89:60:4:0.0317:0:1 -1 162750208 . C T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.76854;SOR=1.30029;LSEQ=CCCTACCCCTGACTCATATA;RSEQ=ACTTTTTTTTTTTTTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:21:0,21:0,0:0.4667:0,1:13.3:1:23.3:1:1:0:60:2:0.4:0:1.8 1/0:15:8:0,8:0,1:0.5333:0,0:6.6:1:27.6:1:1:0:60:16:0.5333:0:1.3 -1 162830985 . CCCTCCCTA C 82 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTGAAAGCTCTCTTCGT;RSEQ=CCTCCCCTGGTCAGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:3,0:0.6667:0,0:25.5:1:32:1:1:0:60:12:0.6667:0.1111:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 162831191 . ATC A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.51443;SOR=0;LSEQ=AGTGTGTAACTGTGTTCTCA;RSEQ=TCTCTCTCTCCTACCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:2,0:153,9:0.0122:2,0:25.5:1:30.5:1:1:0:60:4:0.0125:0:3 0/0:114:0:0,0:106,8:0:2,0:21.6:1:29.9:1:1:0:60:27.5:1:0:0.4 -1 162831227 . ATT A 215 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0;SOR=0.38611;LSEQ=CCCTTTCCTCGTTTCTCTCC;RSEQ=TTTTTTTTTTCTCTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:127:92,35:141,40:0.3557:2,2:24.7:1:30.8:1:0.28337:1.33971:59.9:126:0.36:0.0504:0.3 0/1:245:43:30,13:131,45:0.1755:2,2:26.4:1:29.7:1:0.56507:1.26015:60:86:0.1784:0.0286:0.3 -1 162831317 . G A 265 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.99589;LSEQ=CAGCCTCAAAAGAAAGCACC;RSEQ=TTTTTTCTGTCATGACTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:651:446:195,251:93,110:0.6851:2,2:27.9:1:30.2:1:0.67016:1.08811:59.9:43.6:0.6845:0:1.2 1/0:494:338:150,188:71,83:0.6842:2,2:26.5:1:29.6:1:0.76954:1.07198:59.9:55.333:0.6888:0:1.2 -1 162831391 . G A 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22087;SOR=0.74669;LSEQ=ATTATGTGTTATTGCACACC;RSEQ=TACTGACCTTCCCCAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:72:17,55:49,148:0.2677:2,2:24.6:1:30.9:1:0.87425:1.07088:60:144:0.2677:0:1.3 0/1:182:39:8,31:43,99:0.2143:2,2:22.1:1:30.1:1:0.31499:1.67856:60:78:0.2167:0:1.6 -1 162831535 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00862;SOR=Inf;LSEQ=AACAGCTACCGTAGAAGGTT;RSEQ=AGCAGAGCTATTGTTTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:0:1,0:24.3:1:31.3:1:1:0:60:46:1:0:0 0/1:7:3:0,3:0,4:0.4286:0,0:15.3:1:29.7:1:1:0:60:6:0.5:0:1 -1 162831722 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCCTACTAACCACAATCA;RSEQ=TGCCCAGCAAATAAATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:12.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 163276396 . A G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TATGTTGAAATCCCAATCCC;RSEQ=AATACTTCAGAATGTGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:10:1:30.5:1:1:0:60:4:1:0:2.5 0/0:1:0:0,0:1,0:0:0,0:33:0:31:0:1:0:60:2:1:0:0 -1 163276534 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=AAAAGGAAATTTGGACACAA;RSEQ=AATACACACAAGAATGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:22.7:1:31.9:1:1:0:60:14:1:0:0.1 0/1:9:2:1,1:5,2:0.2222:2,2:8.5:1:29.5:1:1:2.23609:60:4:0.2222:0:1 -1 165043980 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0626;SOR=Inf;LSEQ=TAGTTGGCCTCACACTGCTA;RSEQ=GATTCTGATAATTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:0:0,0:208,161:0:2,0:25.4:1:31.4:1:1:0:60:91.25:1:0:0.1 0/1:244:3:1,2:138,103:0.0123:2,2:19:1:26.3:1:0.57889:2.6689:60:6:0.0126:0:1 -1 165044038 . C T 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=8.32981;LSEQ=AACTCTCTAATTCTTAGTTG;RSEQ=AAATGTTTCATGCCTAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:10:5,5:180,216:0.0246:2,2:17.9:1:28.1:1:1:1.20:60:20:0.0252:0:1.4 0/1:264:46:25,21:107,111:0.1742:2,2:25.8:1:28.8:1:0.62677:1.23:60:92:0.1749:0:1.1 -1 165044089 . T C 126 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02784;SOR=2.80148;LSEQ=TACTCAACAGAGATTATTAA;RSEQ=AACAGCACGATGATCCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:8:2,6:89,191:0.0278:2,2:33.4:1:32.8:1:1:1.3964:60:16:0.0284:0:1.5 0/1:202:15:6,9:74,113:0.0743:2,2:28.6:1:32.5:1:1:1.02:60:30:0.0743:0:1.5 -1 165044147 . G A 182 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTGTTTGTTTATTTTTTGG;RSEQ=AATAGCGCAAATGTTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:62:11,51:8,38:0.5741:2,2:22.3:1:30.6:1:1:1.02:60:124:0.5741:0:1.1 0/0:75:0:0,0:18,57:0:2,0:25:1:30.8:1:1:0:60:74:1:0:0.2 -1 165267008 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12795;SOR=Inf;LSEQ=GAACCAGGGAGAAGAAGGCT;RSEQ=ACTCTACTGAGCCACTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:24:1:31.2:1:1:0:60:34:1:0:0.2 0/1:20:2:1,1:10,8:0.1:2,2:22.5:1:26.5:1:1:1.23603:60:4:0.1:0:1.5 -1 165267095 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08021;SOR=Inf;LSEQ=TTATAGCTGTGGGAACTCAG;RSEQ=CAAGTCATTCAGCCTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:0:2,0:19:1:32:1:1:0:60:48:1:0:0.2 0/1:10:2:1,1:2,6:0.2:2,2:15.5:1:26.5:1:1:2.65:60:4:0.2:0:1 -1 165470814 . T C 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CCAGTCTACACCAGTCATTG;RSEQ=ACCACGAGGATCTGGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:6,6:7,7:0.4615:2,2:28.6:1:32.2:1:1:1:60:24:0.4615:0:2.2 0/1:13:6:4,2:4,3:0.4615:2,2:25:1:30.3:1:1:1.45:60:12:0.4615:0:2 -1 165470830 . C T 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTACCACGAGGATCTGG;RSEQ=AGACAGCAGGAGTCAGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:17,19:0,0:1:0,2:28.3:1:28.8:1:1:0:60:72:1:0:1.4 1/1:14:14:8,6:0,0:1:0,2:29.8:1:28.7:1:1:0:60:28:1:0:1.6 -1 165645675 . C T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50835;SOR=1.59861;LSEQ=GCAATACTGTAGACATCAAG;RSEQ=GAACGGGTACTATTCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:3,4:8,9:0.2917:2,2:16.4:1:29.6:1:1:1.17684:60:14:0.2917:0:1 0/1:15:6:3,3:5,4:0.4:2,2:17.7:1:28.8:1:1:1.23147:60:12:0.4:0:1 -1 165645833 . G T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.41203;SOR=2.12538;LSEQ=GCACATTGAGCACATTAAGC;RSEQ=CTCTAAGACCCAAGATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:1,3:7,4:0.2667:2,2:15:1:32:0:0.28205:4.676:60:8:0.2667:0:1 0/1:9:4:3,1:2,3:0.4444:2,2:35.3:1:31.8:1:0.52381:3.76:60:8:0.4444:0:1 -1 165871268 . C G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATCAGGAAGTCAGGAGAT;RSEQ=GAGACCATCCTGGCTAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19:0:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 165872043 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49333;SOR=0;LSEQ=GGAGGCAGCGTGCAGCCCAG;RSEQ=CCTCTCGGGGCCCAGATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:15,21:0.0526:2,2:25:1:29.5:1:1:1.39:60:4:0.0588:0:1 0/0:37:0:0,0:19,18:0:2,0:27.1:1:31.6:1:1:0:60:36:1:0:0.2 -1 166245037 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCATGCCCAGCCACCAC;RSEQ=GAAGCCACTTCTGTCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 166245453 . T C 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02546;SOR=0.38368;LSEQ=GTGGCATCCCTCTGCCCTCA;RSEQ=GGGGTGGCATACCACCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:109:93:58,35:12,4:0.8532:2,2:25.6:1:31.3:1:0.40653:1.80116:60:92:0.8519:0:1.1 1/0:45:31:19,12:8,6:0.6889:2,2:26.2:1:30.7:1:1:1.18:60:62:0.6889:0:1.2 -1 166245498 . C T 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TGTTCACTGGAGGCCTCTTC;RSEQ=GAGCAAGAGAGACTTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:103,56:0:2,0:25.5:1:30:1:1:0:60:30.8:1:0:0.5 0/1:85:9:6,3:50,26:0.1059:2,2:12.3:1:30.2:1:1:1.04:60:18:0.1059:0:1.4 -1 166245515 . A T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13404;SOR=Inf;LSEQ=TTCCGAGCAAGAGAGACTTT;RSEQ=AGTTTGCTCCCTTGAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:115,59:0:2,0:25.1:1:28.9:1:1:0:60:173:1:0:0.4 0/1:101:2:1,1:64,35:0.0198:2,2:8:0:26.5:1:1:1.81693:60:4:0.0202:0:1 -1 166245568 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18606;SOR=Inf;LSEQ=CCATTCCACGGCAGCTTTGG;RSEQ=AGTAGGTGAGTCTTCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:134,100:0:2,0:26.6:1:31.8:1:1:0:60:57.5:1:0:0.2 0/1:178:2:1,1:97,78:0.0112:2,2:25.5:1:27:1:1:1.24204:60:4:0.0114:0:1 -1 166245656 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14854;SOR=Inf;LSEQ=GTGTGGATCATGGGTTGCTC;RSEQ=GTTCTCTTGTTCATCTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:148,151:0:2,0:24.3:1:30.3:1:1:0:60:58.8:1:0:0.1 0/1:188:2:1,1:96,90:0.0106:2,2:36.5:1:29:1:1:1.06633:60:4:0.0109:0:1 -1 166245662 . C A 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56269;SOR=3.17568;LSEQ=ATCATGGGTTGCTCAGTTCT;RSEQ=TTGTTCATCTTAACAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:1:1,0:152,152:0.0033:2,0:39:0:11:0:1:0:60:0:0:0:4 0/1:193:2:1,1:102,89:0.0104:2,2:15:0:31:1:1:1.14525:60:4:0.0106:0:1.5 -1 166246021 . G A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAACACCCATGCTACTGG;RSEQ=GTGGTCCTGTCAGAATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:113,181:0:2,0:23.2:1:30.8:1:1:0:59.5:57.8:1:0:0.1 0/1:200:18:5,13:61,119:0.09:2,2:22.9:1:29.8:1:0.79418:1.3309:60:17:0.0863:0:1.3 -1 166246061 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.15924;SOR=Inf;LSEQ=CTCTGCTGCCCGTAGCTGCT;RSEQ=CTCTGTTAGCTATACTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:62,127:0:2,0:26.7:1:32.6:1:1:0:59.9:378:1:0:0.1 0/1:126:2:0,2:39,85:0.0159:2,0:25:1:32:0:1:0:60:4:0.0163:0:1 -1 166246069 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15759;SOR=Inf;LSEQ=CCCGTAGCTGCTGCTCTGTT;RSEQ=GCTATACTGACTTGGAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:60,120:0:2,0:26:1:30.2:1:1:0:59.9:59:1:0:0.1 0/1:119:2:1,1:36,81:0.0168:2,2:39:1:31:1:0.52699:2.23:60:4:0.0169:0:1 -1 168652905 . G C 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00445;SOR=0;LSEQ=TGTATAGGGTGTCTGACAAC;RSEQ=CCTGTTGGAGGGTCTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:5,3:5,5:0.4444:2,2:24.1:1:28.6:1:0.66406:1.62:60:7:0.4118:0:1.5 0/0:14:0:0,0:9,5:0:2,0:12.5:1:29.1:1:1:0:60:28:1:0:0.4 -1 168653061 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49673;SOR=0;LSEQ=GAACTAACAGGAGGAAAGGC;RSEQ=ATGTCTGCTGGTCTGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:3,6:0.1818:2,0:35:1:29.5:1:1:0:60:4:0.1818:0:1 0/0:7:0:0,0:1,6:0:2,0:28:1:29.1:1:1:0:60:14:1:0:0 -1 169022617 . C T 47 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTTATATCACTGAGGAAG;RSEQ=TGGGTGGGAAACTGAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:11,0:0.2143:0,0:37.7:1:29.7:1:1:0:60:6:0.2143:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 169022734 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09219;SOR=Inf;LSEQ=AATTTATTATATTAATAGTG;RSEQ=TAATCCTGATATTGTAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:46,1:0:1,0:27:1:33:1:1:0:60:94:1:0:0.1 0/1:21:2:2,0:19,0:0.0952:1,0:37:1:32:0:1:0:60:4:0.1:0:1 -1 169022820 . G T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.29083;SOR=0;LSEQ=AAAGCCTGGTGACATCATAG;RSEQ=AAATCAAATATTCCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:170,87:0.0115:2,2:17.7:1:21.7:1:0.27048:3.886:60:2:0.0078:0:2.3 0/0:160:0:0,0:99,59:0:2,0:24.7:1:30.3:1:1:0:60:51.667:1:0:0.1 -1 169022903 . A T 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATTACATAGTTTTTAGTA;RSEQ=ATGGAAGCAGGGTAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:225,207:0:2,0:25.1:1:30.2:1:1:0:60:215:1:0:0.1 0/1:338:49:31,18:157,132:0.145:2,2:25.4:1:28.8:1:0.27812:1.45:60:48:0.1463:0:1.1 -1 169022969 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1197;SOR=Inf;LSEQ=CCGCATTTGGAATAAAATCC;RSEQ=AAGTCCAAATCCTTTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:134,228:0:2,0:26.2:1:29.8:1:1:0:60:119.667:1:0:0.1 0/1:192:2:1,1:67,123:0.0104:2,2:15.5:1:30.5:1:1:1.83:60:4:0.0108:0:1.5 -1 169023065 . A AT 59 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.04995;SOR=8.08958;LSEQ=TTCTTTTTATTTATTTACTT;RSEQ=TTTTTTTTGTTACAGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:0,58:0.0169:1,0:35:0:31:0:1:0:60:2:0.0172:0:0 0/1:32:4:0,4:1,27:0.125:1,0:25.8:1:29.8:1:1:0:60:8:0.129:0:0.3 -1 169024837 . C G 30 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=13.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=CTTTCTTTCTTTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21.5:1:32.8:1:1:0:41.5:8:1:0:2 1/1:2:2:1,1:0,0:1:0,2:10:0:30:1:1:0:33:4:1:0:1.5 -1 169024855 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTTTCTTTCTCTTTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:10.5:1:30.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 169431170 . C T 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0.80411;LSEQ=AAACCTAACATTTTGAACCC;RSEQ=CTTCTGTAGTATTACTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:30:29,1:2,0:0.9375:0,1:21:1:31.1:1:1:0:60:60:0.9375:0:1.5 1/1:13:12:12,0:1,0:0.9231:0,0:20.3:1:31.5:1:1:0:60:24:0.9231:0:1.4 -1 169431218 . A C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00122;SOR=0.23212;LSEQ=GTAGAGGAACTAGTATTTCT;RSEQ=CAAGGTCCTTTTCAAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:89:58:56,2:29,2:0.6517:2,1:24.4:1:31.6:1:0.60824:1.92:60:116:0.6591:0:1.3 0/1:30:9:9,0:20,1:0.3:1,0:28.7:1:30.9:1:1:0:60:18:0.3:0:1.7 -1 169431363 . C T 263 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.09673;LSEQ=TTTCTATCATTTAAGCACAA;RSEQ=AGTACCTTGAATAAGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:530:513:245,268:7,9:0.9679:2,2:26.2:1:29.3:1:0.80421:1.18:60:84.5:0.9694:0:1.1 1/0:399:297:155,142:48,54:0.7444:2,2:25:1:28.4:1:0.42191:1.23:60:48.5:0.7405:0:1.1 -1 169431437 . CT C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.60635;SOR=1.4348;LSEQ=TAATATTTTACACTGATGTG;RSEQ=TTTTTTTTTCTGAGACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:8:3,5:62,183:0.0314:2,2:31.4:1:31.6:1:0.42712:1.77:57.5:16:0.0325:0:0.8 0/1:180:8:1,7:49,121:0.0444:2,2:22:1:33.5:1:0.44484:2.8218:60:16:0.0455:0:0.3 -1 169431460 . C G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTTTTTTCTGAGACAGTCT;RSEQ=TCTATCCCACGCAGGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:29,142:0:2,0:23.5:1:31.4:1:1:0:60:20.375:1:0:0.3 0/1:115:18:3,15:23,74:0.1565:2,2:28.6:1:31.3:1:0.75975:1.54861:58.9:36:0.1593:0:1.2 -1 169431599 . A G 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGTTTTGCCTTGTTGGCC;RSEQ=GGCTGATCTCGATCTCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:0.1875:1,0:31:1:32.7:1:1:0:60:6:0.1875:0:1.3 0/0:4:0:0,0:0,4:0:0,0:20:1:32:1:1:0:60:8:1:0:0 -1 169637303 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.083;SOR=Inf;LSEQ=AGCAGTGGAGGGAGAGGTGC;RSEQ=GGCAGGAACCGGGGCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:3,13:0:2,0:23.2:1:30.6:1:1:0:60:32:1:0:0.7 0/1:7:2:1,1:2,3:0.2857:2,2:12:1:28:1:1:1.41:60:4:0.2857:0:1 -1 169637325 . C T 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30472;LSEQ=GCAGGAACCGGGGCTGCATG;RSEQ=GGTGCTTGTGGGCCAGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:18.8:1:31.8:1:1:0:60:12:0.6:0:1.8 1/0:3:2:0,2:0,1:0.6667:0,0:20:1:27.5:1:1:0:60:4:0.6667:0:1.5 -1 169637363 . G T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAGTTCCAGGTGGCATGG;RSEQ=CTTGGTGGACCCCACACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:28:1:32:0:1:0:60:4:0.4:0:3.5 0/0:2:0:0,0:0,2:0:0,0:32.5:1:33:1:1:0:60:4:1:0:1 -1 170599573 . T C 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25075;SOR=Inf;LSEQ=TGGGCATTTAGTACTATAAA;RSEQ=TTCTCTCTTTTGGGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:4,0:0.6:0,2:18:1:31.5:1:0.2:0:60:12:0.6:0:1.3 1/1:4:4:2,2:0,0:1:0,2:27.5:1:32.3:1:1:0:60:8:1:0:1 -1 170600293 . TGTGTTGGGCTGTGGGGACAA T 61 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06061;SOR=Inf;LSEQ=TCTGACCGCAGGCCAGCTGG;RSEQ=GTGTTGGGACTGAGCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:29.6:1:32.4:1:1:0:60:10:1:0:0.2 1/0:6:4:2,2:2,0:0.6667:0,2:25.8:1:30.7:1:0.46667:0:60:8:0.6667:0.3333:0.8 -1 170600344 . G T 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=TGAGCCGTCCAGCCTCCCTG;RSEQ=CTCCAGCAGGGGAAAAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:20.8:1:31.4:1:1:0:60:10:1:0:0 0/1:10:2:1,1:4,4:0.2:2,2:31:0:29:1:1:1:60:4:0.2222:0:1 -1 170835642 . T A 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00154;SOR=Inf;LSEQ=TCCAAATCGTTTGCCTTAGA;RSEQ=TACTTGCAGCAGGTTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:156,25:0:2,0:22.5:1:30.5:1:1:0:60:44.25:1:0:0.1 0/1:122:7:7,0:93,22:0.0574:2,0:19.1:1:27.9:1:0.34885:0:60:6:0.05:0:1.3 -1 170835762 . G A 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.17661;LSEQ=GCTTAAGAAAAGGACCACTG;RSEQ=GATTTTCACCTACTGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:570:425:184,241:63,81:0.7456:2,2:27.6:1:30.5:1:0.92287:1.01869:60:84:0.7447:0:1.1 0/1:455:155:72,83:147,153:0.3407:2,2:26.5:1:29.3:1:0.62181:1.10732:60:18.375:0.3303:0:1.1 -1 170835872 . A C 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05364;SOR=0.2835;LSEQ=TAAAACTTTCATTAACTTGC;RSEQ=GAATTCTCATTCTCCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:11:0,11:2,64:0.1429:1,0:21.8:1:28.9:1:1:0:60:22:0.1447:0:1.1 0/1:67:3:0,3:4,60:0.0448:2,0:19.7:1:32:0:1:0:60:6:0.0462:0:1 -1 170987149 . T TC 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CAGACCAGACAAGTGGGCTT;RSEQ=CCCCCCAGCAAAGCACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:27.5:1:30:1:1:1.29098:60:4:0.2222:0:0 0/0:5:0:0,0:3,2:0:2,0:35.2:1:29.6:1:1:0:60:10:1:0:0.2 -1 170987152 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.52381;SOR=0;LSEQ=ACCAGACAAGTGGGCTTTCC;RSEQ=CCCAGCAAAGCACACCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:49.5:1:31:1:1:1.58108:60:4:0.2:0:1 0/0:5:0:0,0:3,2:0:2,0:37:1:29.8:1:1:0:60:10:1:0:0.2 -1 170987278 . T C 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TCAGAAACCCTATACAGGAG;RSEQ=GAGCCCACAGGCATCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:16.5:1:30.5:1:1:0:60:8:1:0:0 0/1:6:2:2,0:3,1:0.3333:2,0:16.5:1:33.5:1:1:0:60:4:0.3333:0:1 -1 170987501 . C CA 31 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAGCAACAACAGCACCAA;RSEQ=AAAAAAAAAAAAGTCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:23:1:31.5:1:1:2.45:60:4:0.4:0:0.5 0/0:1:0:0,0:0,1:0:0,0:20:0:15:0:1:0:60:0:0:0:0 -1 171001537 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23077;SOR=Inf;LSEQ=AGCATCTTTTCATTGATTCT;RSEQ=TCTCATCTTCGTGAGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:23.4:1:29:1:1:0:60:40:1:0:0.2 0/1:19:2:1,1:9,8:0.1053:2,2:12.5:1:33.5:1:1:1.11803:60:4:0.1111:0:2.5 -1 171001567 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.54774;LSEQ=CGTGAGTTTGTCTAGAGTCG;RSEQ=TCTTTGAGGCTCTGACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:11,15:0.0714:2,2:23.5:1:28.5:1:1:1.35:60:4:0.0769:0:1.5 0/1:25:1:1,0:10,14:0.04:2,0:1:0:25:0:0.44:0:60:2:0.0417:0:1 -1 171001707 . G T 68 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=CAGTTTGCTGGGGGTTCACT;RSEQ=CAGGCCCTACTCATCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15.8:1:30.5:1:1:0:60:8:1:0:0 1/1:6:5:2,3:0,1:0.8333:0,2:22.2:1:29.4:1:1:0:60:10:0.8333:0:1 -1 171002234 . A G 49 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=TGTTGGGCTGCGGAGGGACA;RSEQ=GTCTTGGGACCAAGCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:21.3:1:31:1:1:0:60:6:0.75:0:1 0/1:3:1:0,1:1,1:0.3333:2,0:3:0:29:0:1:0:60:2:0.3333:0:1 -1 171207295 . A G 97 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01282;SOR=0;LSEQ=AGCAGGCACCCATCTTTGCT;RSEQ=TTTTCCAGCCTCCTTGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:23:1:32.6:1:1:0:60:16:1:0:1.4 0/1:10:4:2,2:3,3:0.4:2,2:10.5:1:27:1:1:1:60:3:0.3333:0:1 -1 171207326 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15584;SOR=Inf;LSEQ=TCCTTGAGTGATATCTCCAG;RSEQ=CACAGGAGCGAATCAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:0:2,0:19.8:1:31.8:1:1:0:60:26:1:0:1 0/1:9:2:1,1:3,4:0.2222:2,2:29:1:28.5:1:1:1.29:60:4:0.2222:0:1 -1 171207335 . C T 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00279;SOR=0;LSEQ=GATATCTCCAGGCACAGGAG;RSEQ=GAATCAGATGAATAAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:5,4:4,2:0.6:2,2:22.7:1:28.3:1:1:1.5508:60:18:0.6:0:1.7 0/0:10:0:0,0:4,6:0:2,0:32:1:31:1:1:0:60:20:1:0:0.7 -1 171207408 . T C 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6948;LSEQ=ACAGAAGAGGAACCTGACCA;RSEQ=TGAAAGAAAAACAAACAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:8,3:2,1:0.7857:2,2:22.8:1:31:1:1:1.31:60:10:0.7692:0:1.2 1/0:7:5:2,3:1,1:0.7143:2,2:27.6:1:30.4:1:1:1.41418:60:10:0.7143:0:1 -1 171207507 . G A 74 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01562;SOR=7.13786;LSEQ=CAAGGGTCAGCGGCCTCAAA;RSEQ=ACCAAAACTAGACAAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:22,27:0.0392:2,2:41:1:30.5:1:1:1.22:60:4:0.0408:0:1 0/1:26:6:2,4:11,9:0.2308:2,2:33.8:1:28.7:1:0.64472:2.36181:57.7:12:0.2308:0:1.8 -1 171207510 . CA C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12649;SOR=Inf;LSEQ=GGGTCAGCGGCCTCAAAGAC;RSEQ=AAACTAGACAAACTCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:21,27:0:2,0:24.9:1:29.4:1:1:0:58.6:23:1:0:0.5 0/1:27:2:1,1:11,14:0.0741:2,2:20.5:1:29:1:1:1.26:60:4:0.0769:0:0 -1 171207680 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAATTAGGCTTCAGAAGA;RSEQ=GGGTAATAAAAAACTACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:41:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 171208014 . C T 89 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21569;SOR=0;LSEQ=TTATAAAAAGAGCAAAGCTA;RSEQ=AATTGATTGGAGTACCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:22.4:1:29.9:1:1:0:60:16:1:0:1.4 1/0:10:7:3,4:2,1:0.7:2,2:30.4:1:28.9:1:1:2.41422:60:14:0.7:0:1.3 -1 171208094 . C T 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGATATTATCCAGGAAAA;RSEQ=TTACCAAATCTAGCAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:13:0:31:0:1:0:60:2:1:0:2 1/0:5:3:0,3:1,1:0.6:2,0:19:1:31:1:0.4:0:60:6:0.75:0:1.7 -1 171281278 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=Inf;LSEQ=TTCGGGCCCTGTATTTTTAA;RSEQ=CTCTTTGTCAATTTGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:21:1:32.3:1:1:0:60:20:1:0:0 0/1:7:2:1,1:2,3:0.2857:2,2:17.5:1:32.5:1:1:1.41:60:4:0.3333:0:1 -1 171308832 . A G 226 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=244.65472;LSEQ=GCTGATGCCAAGGTCATGAA;RSEQ=GATGCAAAGATGAAGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:879:1:1,0:455,423:0.0011:2,0:32:0:14:0:1:0:60:0:0:0:1 0/1:701:153:81,72:272,275:0.2183:2,2:28:1:31.2:1:0.52229:1.14:59.4:306:0.2198:0:1.1 -1 171309078 . C G 199 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=148.56411;LSEQ=TTTGCCTGGGCCATTGAAAT;RSEQ=GCTGATGAAGACTACGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:1:0,1:215,349:0.0018:2,0:6:0:14:0:1:0:60:0:0:0:2 0/1:451:94:32,62:138,219:0.2084:2,2:24.9:1:30.5:1:0.47327:1.22036:59.8:93:0.2099:0:1.1 -1 171393502 . T C 75 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=TTAAAACCCTTTAATGCATT;RSEQ=CCATTTCACCCAAACATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:37.8:1:32.6:1:1:0:60:10:0.4167:0:1 1/1:1:1:1,0:0,0:1:0,0:50:0:30:0:1:0:60:2:1:0:1 -1 171393700 . C T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08985;SOR=Inf;LSEQ=TCACATTTTCTCCTCCTTGC;RSEQ=TATTCCCCATTCCCAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:162,87:0:2,0:25:1:30.6:1:1:0:60:30.125:1:0:0.3 0/1:203:3:1,2:128,72:0.0148:2,2:18.7:1:23.7:1:0.30083:3.53233:60:2:0.0101:0:1.3 -1 171393787 . T C 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.23012;LSEQ=GTTCCAGCCTCTCCTCTTTA;RSEQ=GACCTCAAGAAGCGAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:153:60,93:74,95:0.4752:2,2:24:1:30.3:1:0.4295:1.20666:60:75.5:0.4794:0:2 1/0:278:186:76,110:38,53:0.6691:2,2:24.9:1:29.7:1:0.89725:1.03762:60:92:0.6691:0:1.9 -1 171393800 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.86177;LSEQ=CTCTTTATGACCTCAAGAAG;RSEQ=GAGTGAAAACCTGTCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:86:33,53:80,113:0.3082:2,2:28.3:1:29.2:1:0.69253:1.13651:60:20.5:0.3015:0:2.8 1/0:246:138:55,83:41,67:0.561:2,2:26:1:29.3:1:0.79329:1.08:60:45:0.5556:0:2.2 -1 171393826 . G C 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22467;LSEQ=AAAACCTGTCTCCCAAGTCA;RSEQ=AGTGCCTTACACACCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:67:20,47:58,97:0.3018:2,2:23.4:1:31.9:1:0.28919:1.40304:60:66:0.307:0:2.9 0/1:170:15:4,11:53,102:0.0882:2,2:34:1:32.1:1:0.77566:1.42608:60:30:0.0898:0:3.1 -1 171393833 . T A 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58743;SOR=2.50643;LSEQ=GTCTCCCAAGTCAGAGTGCC;RSEQ=TACACACCTGAAGGCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:1,0:61,135:0.0051:2,0:1:0:25:0:0.31472:0:60:2:0.0052:0:1 0/1:158:2:1,1:50,106:0.0127:2,2:5:0:32:0:0.54277:2.11:60:4:0.0127:0:2.5 -1 171393861 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17652;SOR=Inf;LSEQ=CTGAAGGCTCGCCTAGGGCA;RSEQ=GATATGCACAGATAGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:24,94:0:2,0:23.2:1:31.1:1:1:0:60:58:1:0:0.6 0/1:86:2:1,1:19,65:0.0233:2,2:24.5:1:30.5:1:0.41313:3.36:60:4:0.0233:0:2.5 -1 171393911 . T C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29852;SOR=2.07536;LSEQ=CAAGCACAGACTAAGCAACA;RSEQ=AGCCCAGCAGTCAGGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:0,7:2,45:0.1296:1,0:20.4:1:30:1:1:0:60:6:0.1154:0:1 0/1:21:5:1,4:1,15:0.2381:1,2:23:1:33.8:1:0.42857:3.46:60:10:0.2381:0:1.6 -1 171394212 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACAAATGTTCTATTGTT;RSEQ=TACTAGCCATGATAAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 171395913 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCAGCTGTTCACCTCTTG;RSEQ=GGTGTAGCCCGGTTCCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 172415351 . GA G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31865;LSEQ=TTTTGAATATAACGAAAGCA;RSEQ=TTATCAGAGGTTCAATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:282:169:119,50:84,29:0.5993:2,2:23.7:1:31.8:1:0.50113:1.2162:60:55.333:0.595:0.1135:0.1 0/1:149:48:33,15:70,31:0.3221:2,2:26.1:1:31.7:1:1:1.02623:60:96:0.3221:0.0134:0.1 -1 172415451 . C T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43619;LSEQ=TAACACTGCATGGATCAGCA;RSEQ=GAGTAAGGACAGTCTAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:451:273:123,150:84,94:0.6053:2,2:26.3:1:30.3:1:0.69926:1.08957:60:44.5:0.6068:0:1.2 0/1:347:139:62,77:91,116:0.4006:2,2:24.9:1:29.4:1:0.91256:1.03:60:138:0.4047:0:1.2 -1 172415546 . C T 134 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00122;SOR=3.09203;LSEQ=GCATAATGAGTAAAGCTGGC;RSEQ=AAACAGGACTGCAATGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:22:4,18:28,123:0.1272:2,2:25.3:1:29.1:1:1:1.02426:60:44:0.1287:0:1.1 0/1:77:24:7,17:13,40:0.3117:2,2:23.6:1:29.3:1:0.78026:1.26:60:48:0.3243:0:1.1 -1 172772482 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1965;SOR=Inf;LSEQ=CAACATGGCTTCTTCCCTTC;RSEQ=TAGGTCCCGTGACAGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:33,48:0:2,0:25.1:1:31.7:1:1:0:60:80:1:0:0.1 0/1:65:2:1,1:31,32:0.0308:2,2:43.5:1:30:1:1:1.03:60:4:0.0308:0:1 -1 173344256 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0873;SOR=Inf;LSEQ=TTTCTAGGTCCTGTGACAGC;RSEQ=ATCTTGCTATTACTCGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:9,16:0:2,0:21:1:30.4:1:1:0:60:11.5:1:0:0.2 0/1:11:2:1,1:4,5:0.1818:2,2:13.5:1:27.5:1:1:1.22:60:4:0.1818:0:1 -1 173485336 . C T 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTTGTCCCTTGGTCTTTGG;RSEQ=TCATTTCTATTTGAATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:19:7,12:7,4:0.6333:2,2:23.4:1:29.8:1:0.25677:2.88672:60:38:0.6333:0:1.1 0/0:27:0:0,0:14,13:0:2,0:27.9:1:31.6:1:1:0:60:54:1:0:0.1 -1 173485363 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16194;SOR=Inf;LSEQ=CTATTTGAATTCCCCACACC;RSEQ=AGTGAAATGTCAGGACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:0:2,0:18.7:1:28.4:1:1:0:60:46:1:0:0.6 0/1:16:2:1,1:3,11:0.125:2,2:20.5:1:28.5:1:0.45:3.32:60:4:0.125:0:1 -1 174099191 . T C 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=GGAAGTTCTCCTGAATAGCC;RSEQ=GAAGTGTGTTTTCCAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:18.9:1:30:1:1:0:60:14:1:0:0.1 0/1:7:2:1,1:3,2:0.2857:2,2:13:0:28:1:1:1.41418:60:4:0.2857:0:1 -1 174099304 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=TCTTGGAGGCTTTGTTCATT;RSEQ=CTTTTCATTCTTTTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:0.1667:2,2:5:1:27.5:1:1:1.45:60:4:0.1667:0:1 0/0:7:0:0,0:3,4:0:2,0:20.6:1:30.1:1:1:0:60:14:1:0:0 -1 175869554 . A C 291 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02619;SOR=0.77558;LSEQ=CAGTGGGCTTGAGCTCATCT;RSEQ=ACCAGATCTTGGTGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:888:601:318,283:157,129:0.6768:2,2:26.2:1:31.6:1:0.61432:1.083:60:149.25:0.6769:0:1.1 1/0:551:341:173,168:111,94:0.6189:2,2:28:1:31.3:1:0.47936:1.14643:60:112.667:0.6179:0:1.1 -1 175869673 . AG A 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.55441;SOR=0;LSEQ=GTGGTAAAGAGTTTGGATTC;RSEQ=GGATCAAACTCACTTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:31,262:0.0101:2,2:7.7:1:26.2:1:0.03373:16.57:60:6:0.0102:0.0068:0.3 0/0:155:0:0,0:28,127:0:2,0:20.8:1:30.1:1:1:0:60:76.5:1:0:0.1 -1 175869807 . C G 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06479;SOR=0;LSEQ=ACATTGTGCAACTCAGTGAG;RSEQ=CCTCACACATTGAACACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:0.4118:0,0:22.1:1:29.4:1:1:0:60:6:0.375:0:1.3 0/0:7:0:0,0:0,7:0:0,0:19.9:1:31.4:1:1:0:60:14:1:0:0.1 -1 175914184 . T C 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AACAAATCCAAAACCCATGA;RSEQ=GACTTTGGGGAGAGACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:338,40:0:2,0:25.1:1:31.4:1:1:0:59.8:93.5:1:0:0 0/1:199:16:12,4:149,34:0.0804:2,2:23.7:1:30.2:1:0.51378:1.45773:60:32:0.0812:0:1.1 -1 175914531 . A G 137 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=TATCTCCACAGTTAACTTGG;RSEQ=AGCCTTCAAGGTAAACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:1,21:0,0:1:0,1:27.9:1:30.8:1:1:0:60:44:1:0:1 1/0:2:1:0,1:0,1:0.5:0,0:44:0:33:0:1:0:60:2:0.5:0:1 -1 175916267 . T C 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=9e-05;SOR=0.05329;LSEQ=TCAGTACAATGGTGTATTTC;RSEQ=ATAATCCTGTTTCAGTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:597:596:423,173:0,1:0.9983:0,2:24.6:1:31.3:1:0.29146:0:60:65.222:0.9983:0:1.1 1/1:425:412:279,133:7,5:0.9694:2,2:23.3:1:30.5:1:0.53745:1.50:60:102:0.9691:0:1.1 -1 175955557 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAACCCAGTAGCATAACTG;RSEQ=CTCATCAATATACTAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 175955996 . T C 223 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18093;LSEQ=ACATACCACATACCAATTTA;RSEQ=ATTTTAAAATTTAATCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:227:120:108,12:101,6:0.5286:2,2:25.3:1:32.4:1:0.32528:1.86538:60:119:0.5289:0:1.1 0/1:125:21:21,0:96,8:0.168:2,1:22:1:31.4:1:0.34979:0:60:42:0.1694:0:1 -1 175956248 . AAAT A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.00375;SOR=Inf;LSEQ=TATTTTCACTTCCTGAAAAC;RSEQ=AATAATAATAGTATTTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:0:0,0:155,367:0:2,0:22:1:29.9:1:1:0:60:73.571:1:0:0.1 0/1:342:6:2,4:101,234:0.0175:2,2:22.2:1:29.5:1:1:1.16:60:12:0.0178:0.0058:0.3 -1 175957231 . TA T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTCAGGGTTTCTACACAA;RSEQ=AAAAAGGGAAGGACTAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:2,0:64,1:0.0299:1,0:24.5:1:29.5:1:1:0:60:4:0.0308:0:0 0/0:24:0:0,0:23,1:0:1,0:18.5:1:27.9:1:1:0:60:23:1:0:0.4 -1 175957897 . G A 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAATCACTTGAACCTGGG;RSEQ=GGCAGATGCTGCAGTGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:20.3:1:30:1:1:0:41.3:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 175958358 . T TA 82 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.7589;LSEQ=CTACTTTAATTGGACAAGAT;RSEQ=AAAAAAAAAATCTACTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:7:6,1:122,0:0.0543:1,2:28.4:1:29.5:1:0.05426:0:60:14:0.0543:0.0078:0 0/1:48:2:2,0:46,0:0.0417:1,0:15:1:29:1:1:0:60:4:0.0417:0.0208:0 -1 175958420 . C T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13048;SOR=5.49833;LSEQ=AATATTATAGTTTACATACA;RSEQ=CCTCAGTGACATTACAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:0,1:371,37:0.0024:2,0:1:0:25:0:0.09291:0:60:2:0.0025:0:2 0/1:225:3:2,1:201,21:0.0133:2,2:15:1:31:1:0.26666:4.72798:60:6:0.0136:0:1.7 -1 175958637 . T A 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00047;SOR=0;LSEQ=TAAAACAAAACAAAATTAGA;RSEQ=AAATGTAGTAAATGCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:17:4,13:85,372:0.0359:2,2:19.3:1:28.4:1:0.5385:1.35:60:7.5:0.0325:0:1.3 0/0:293:0:0,0:59,233:0:2,0:23.1:1:28:1:1:0:60:72:1:0:0.1 -1 175958683 . GT G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14046;SOR=Inf;LSEQ=AGCAAAGTTAATTTTAACTG;RSEQ=TTTTGGTTTTTTCATTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:4,172:0:1,0:21.3:1:30.2:1:1:0:60:43:1:0:0 0/1:106:2:0,2:1,103:0.0189:1,0:27:1:32:1:1:0:60:4:0.0189:0:0 -1 175997035 . TA T 94 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0.89443;LSEQ=CCTGAAACTGGGTAATTTAT;RSEQ=AAAAAAAAAAAAAGAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:0,9:0,6:0.5294:0,0:24.7:1:29.7:1:1:0:59.1:8:0.5333:0.0588:1.2 1/0:2:1:0,1:0,1:0.5:0,0:49:0:29:0:1:0:60:2:0.5:0:0 -1 176012392 . C T 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGTCAACACTCCAACACCT;RSEQ=TTCTCATGCTCCTGGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1046:0:0,0:426,620:0:2,0:25.1:1:31.4:1:1:0:60:44.478:1:0:0.1 0/1:692:29:12,17:280,379:0.0419:2,2:24.3:1:29.1:1:1:1.04655:60:28:0.0415:0:1.3 -1 176012466 . G GA 155 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.88711;SOR=0.94391;LSEQ=TCTCAAAATGAATAAAGCAA;RSEQ=AAAAAAAAAAACCTGATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:38:6,32:46,243:0.1111:2,2:26.3:1:29.7:1:1:1.00957:59.7:37:0.1246:0.0058:0.3 0/1:199:21:2,19:31,133:0.1055:2,2:25.4:1:28:1:0.37751:2.2067:59.3:9.5:0.1056:0.0151:0.4 -1 176012482 . A G 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00041;SOR=Inf;LSEQ=GCAAGAAAAAAAAAAACCTG;RSEQ=TATCAATTTATTGTTACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:24,260:0:2,0:21.7:1:30.7:1:1:0:60:39.571:1:0:0.3 0/1:142:7:0,7:5,129:0.0493:1,0:28:1:28.6:1:1:0:60:6:0.0438:0:1 -1 176012495 . G A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00411;SOR=Inf;LSEQ=AAACCTGATATCAATTTATT;RSEQ=TTACGGGGAGAGGGAAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:11,185:0:2,0:24.5:1:31.5:1:1:0:59.9:20.778:1:0:0.3 0/1:100:5:0,5:2,92:0.05:1,0:20.4:1:31.2:1:1:0:60:10:0.0521:0:1 -1 176012709 . T C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00056;SOR=0.21167;LSEQ=GGAAAAAAAAGCATTTGGTA;RSEQ=TGCATAGGTGTTACACAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:53:47,6:57,6:0.4569:2,2:26.9:1:32.1:1:0.76916:1.21074:60:106:0.4569:0:1.2 0/1:40:6:5,1:34,0:0.15:1,2:32.5:1:31.2:1:0.15:0:60:12:0.1538:0:1 -1 176012807 . G A 269 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62586;LSEQ=AAAGTTTTAACAAACCAAAT;RSEQ=TATGATTCATATAACATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:674:673:496,177:0,0:0.9985:0,2:24.1:1:28.7:1:1:0:60:111.167:0.9985:0:1.1 1/1:422:421:298,123:0,0:0.9976:0,2:22.3:1:28.3:1:1:0:60:139.333:0.9976:0:1.1 -1 176014960 . G A 43 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATGTTGAGATATGTGCA;RSEQ=GCTAGGGGAAAAATTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.7:1:27.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176015104 . GA G 92 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.32842;SOR=2.89059;LSEQ=GAACTTTAATTTGGCAACCA;RSEQ=AAAAAAAAAAAGGCTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:7,0:20,0:0.25:1,0:20.7:1:33:1:1:0:60:14:0.2692:0.1071:0.1 1/0:6:3:3,0:2,1:0.5:2,0:19.3:1:33:1:1:0:60:6:0.5:0.1667:0.3 -1 176015573 . T G 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00323;SOR=Inf;LSEQ=TAAATACCTTCAAATTGTAC;RSEQ=AGACCTCATATCCAGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:2,157:0:1,0:25.1:1:28.5:1:1:0:60:318:1:0:0 0/1:76:5:0,5:0,71:0.0658:1,0:33.8:1:31.8:1:1:0:60:10:0.0667:0:1.2 -1 176050138 . G A 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAATTTGGCATATAGAA;RSEQ=CTCAGGAACTTGCCTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:51,1:0,0:1:0,1:22.4:1:30.6:1:1:0:60:51:1:0:1.1 1/1:29:29:28,1:0,0:1:0,1:22.1:1:29.5:1:1:0:60:28:1:0:1.1 -1 176050428 . A T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05403;SOR=Inf;LSEQ=GCAGTTCGACTGTCATCTAT;RSEQ=TGAAAAAAAAAAAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:102,305:0:2,0:18.4:1:27.4:1:1:0:59.4:6.679:0.9972:0:0.5 0/1:249:3:0,3:77,169:0.012:2,0:19:1:20.3:1:0.55456:0:60:2:0.0093:0:3.3 -1 176050429 . T A 30 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.71192;SOR=1.29275;LSEQ=CAGTTCGACTGTCATCTATA;RSEQ=GAAAAAAAAAAAAAAAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:4:0,4:96,289:0.0102:2,0:28:1:15:1:0.57597:0:56.3:0:0:0:3 0/1:228:3:1,2:68,157:0.0132:2,2:19.3:1:24.7:1:1:1.15:60:2:0.011:0:1.7 -1 176050446 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12749;SOR=Inf;LSEQ=ATATGAAAAAAAAAAAAAAA;RSEQ=GACAAAACAGATGAATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:50,239:0:2,0:18.8:1:29.8:1:1:0:58.7:18.267:1:0:0.6 0/1:161:2:1,1:33,126:0.0124:2,2:37:1:29.5:1:0.3788:3.78:60:4:0.0131:0:3 -1 176050447 . G A 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.38052;SOR=0.61723;LSEQ=TATGAAAAAAAAAAAAAAAA;RSEQ=ACAAAACAGATGAATTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:18:16,2:10,236:0.0682:1,2:7.5:1:19.4:1:0:175.75:55:1.571:0.0447:0:1.8 0/1:139:6:6,0:8,124:0.0432:2,0:8.7:1:22.7:1:0:0:53.3:2:0.031:0:2.5 -1 176050449 . C A 54 Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.77597;SOR=1.1534;LSEQ=TGAAAAAAAAAAAAAAAAGA;RSEQ=AAAACAGATGAATTGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:8:8,0:8,230:0.0323:1,0:7.6:1:18.3:1:0:0:52.5:1:0.0169:0:2.3 0/1:135:5:5,0:7,121:0.037:2,0:6:1:24.2:1:0:0:51:4:0.0317:0:2.6 -1 176050676 . A T 75 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATAATTCCTTGGAAAAA;RSEQ=AATAATAACAATAATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:17.3:1:29.2:1:1:0:60:12:0.8571:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176069548 . C T 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40513;SOR=2.16924;LSEQ=AAAAAAAAAAAAAAAAAAGA;RSEQ=TGGAGAGAGATAAATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:2:2,0:137,127:0.0074:2,0:10:1:15:1:0.49913:0:37.5:0:0:0:4.5 0/1:188:3:1,2:92,93:0.016:2,2:7.7:1:20.7:1:1:1.97158:60:2:0.0136:0:2 -1 176069628 . T A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34047;SOR=3.50375;LSEQ=CCTTTGTTATTTTTAAGTGT;RSEQ=TGCCTACATTTTAGACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:1:1,0:72,126:0.005:2,0:1:0:23:0:0.36683:0:60:2:0.0051:0:1 0/1:172:3:2,1:69,100:0.0174:2,2:23:1:27:1:0.56974:2.88:60:6:0.0175:0:1 -1 176069648 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22158;SOR=Inf;LSEQ=TTGCCTACATTTTAGACTAA;RSEQ=CCTGCTTGTTCCTGTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:29,84:0:2,0:20.4:1:30.9:1:1:0:60:112:1:0:0.1 0/1:101:2:1,1:33,66:0.0198:2,2:10:0:30:1:1:1.99:48.5:4:0.0202:0:1 -1 176085412 . C G 75 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAGGGCCAGCTACTTGA;RSEQ=AGGCTGAGGTAGGAGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:13.2:1:32.4:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176103954 . C T 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57425;SOR=0;LSEQ=TAACATTATAGTATTCTACT;RSEQ=GCTAACTCTTCCTGGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:8:8,0:38,1:0.1702:1,0:25.5:1:30.3:1:1:0:60:16:0.1778:0:1 0/0:6:0:0,0:6,0:0:0,0:22.3:1:32.2:1:1:0:60:12:1:0:0 -1 176104082 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55936;SOR=3.34668;LSEQ=GCATGGAAAAGGCTCCTAAA;RSEQ=GACTAGACCATATGCATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:1:1,0:244,63:0.0032:2,0:2:0:31:0:1:0:60:2:0.0033:0:1 0/1:185:2:1,1:144,39:0.0108:2,2:12.5:1:28:1:0.3866:3.65885:60:4:0.011:0:1.5 -1 176104087 . A T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05659;SOR=Inf;LSEQ=GAAAAGGCTCCTAAAGGACT;RSEQ=GACCATATGCATACTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:272,73:0:2,0:23.4:1:28.8:1:1:0:60:85.25:1:0:0.1 0/1:216:3:1,2:165,48:0.0139:2,2:19:1:30:1:0.1346:6.79546:60:6:0.014:0:1 -1 176104265 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16137;SOR=Inf;LSEQ=TATAGTAGATATTTCAAATA;RSEQ=AAGATATATAAATCAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:30,215:0:2,0:24.4:1:31.5:1:1:0:60:244:1:0:0.1 0/1:165:2:1,1:33,129:0.0121:2,2:36.5:1:28.5:1:0.37266:3.87:60:4:0.0122:0:1 -1 176105710 . CA C 198 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.20546;SOR=0.77457;LSEQ=ATTAAATAGAGAGAGAAAGA;RSEQ=AAAAAAAAAAAGCCTAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:83:15,68:90,285:0.174:2,2:31.1:1:31.2:1:0.31217:1.43053:59.9:166:0.18:0.0042:0.3 0/1:328:46:8,38:79,187:0.1402:2,2:28.9:1:29.9:1:0.10854:2.00271:60:92:0.1451:0.003:0.3 -1 176105755 . T A 24 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63702;SOR=1.63464;LSEQ=CCAAAATGGCATCACCATGA;RSEQ=CATAAAATAAATTTACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:2:2,0:8,213:0.009:1,0:12:1:14:0:0.00182:0:60:0:0:0:7 0/1:137:2:2,0:4,130:0.0146:1,0:7:1:24:1:0.00163:0:60:4:0.015:0:4.5 -1 176117805 . T G 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAAAACTATATCCTACC;RSEQ=AAGGCTTTATTATCTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:26:1:27.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176118219 . G A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07607;SOR=1.36881;LSEQ=TGCATGTGATTCCTACAATA;RSEQ=AAAATTATAATTTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:98:32,66:114,237:0.2183:2,2:20.8:1:29.8:1:1:1.01:60:97:0.219:0:1.1 0/1:282:78:27,51:74,130:0.2766:2,2:19.9:1:29.5:1:0.88972:1.07496:60:156:0.2786:0:1.1 -1 176118238 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12888;SOR=Inf;LSEQ=AGAAAATTATAATTTTTCTT;RSEQ=TAAAAAATATAACTGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:72,236:0:2,0:22:1:30.1:1:1:0:60:307:1:0:0.2 0/1:173:2:1,1:54,117:0.0116:2,2:7:0:30:1:0.53603:2.16:60:4:0.0118:0:1 -1 176131963 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0707;SOR=Inf;LSEQ=GTCTTTTTTATTGCAATAAA;RSEQ=TTCATCATTTAAAATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:317,82:0:2,0:22.9:1:31.8:1:1:0:60:65.5:0.9975:0:0.1 0/1:283:3:1,2:214,66:0.0106:2,2:8.3:1:27.3:1:0.14445:6.43049:60:6:0.0108:0:1 -1 176132292 . C T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGCTCCCTACTGTCTTA;RSEQ=AGTTATAACTTAAACACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:1,42:0,0:1:0,1:24.3:1:28.3:1:1:0:60:20.5:1:0:1.5 1/1:9:9:0,9:0,0:1:0,0:12.3:1:29.7:1:1:0:60:18:1:0:1 -1 176132602 . C T 61 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGGCTTGAGTGATCCTC;RSEQ=CACCTTGGCCTCCCAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:4,1:0.4444:2,2:28.8:1:30.5:1:1:1.29098:60:8:0.4444:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176134531 . T G 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=21.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GTGTGTGTGTGTAGGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176143045 . C T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCAGGAGAATCCTTGAA;RSEQ=CTGGGAGGCGGAGGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:1:31:1:1:0:52.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176143060 . C T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAACCTGGGAGGCGGAGG;RSEQ=TGCAGTGAGCCGAGATCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:31:1:1:0:52.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176143070 . C G 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCGGAGGCTGCAGTGAG;RSEQ=CGAGATCGTGCCACTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:33:0:1:0:52.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176143078 . G A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGCAGTGAGCCGAGATC;RSEQ=TGCCACTGCACTCTAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:32.5:1:1:0:52.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176143092 . T C 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATCGTGCCACTGCACTC;RSEQ=AGCCTGGGCAACAGAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:1:33:0:1:0:52.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176145008 . G T 45 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.41247;SOR=2.59931;LSEQ=AGCACACAATTTTGGGGATC;RSEQ=AAATATTTTTAAAATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:2:0,2:365,119:0.0041:2,0:1:0:24.5:1:0.0616:0:60:4:0.0042:0:1 0/1:376:4:1,3:271,99:0.0106:2,2:10.8:1:22.5:1:0.06351:8.15766:60:3:0.0081:0:1.8 -1 176145159 . GA G 92 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.31008;SOR=1.67135;LSEQ=TGTAGCTATTAGTAGGGGGG;RSEQ=AAAAAAAGGCTTAATTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:829:8:4,4:231,589:0.0097:2,2:24.9:1:29.5:1:0.23302:2.55:60:16:0.0099:0:0 0/1:499:8:1,7:161,329:0.016:2,2:33.1:1:30.8:1:0.44729:3.41914:60:16:0.0163:0:0.1 -1 176145277 . T C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00145;SOR=3.7918;LSEQ=AATAAATTTATTTTTGCTTA;RSEQ=ATTTTTACATTATCAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:55:0,55:1,50:0.5189:1,1:19.2:1:32:1:0.48113:0:60:26.5:0.5096:0:1.1 1/1:41:33:0,33:0,8:0.8049:0,1:22.1:1:32.7:1:1:0:60:66:0.8049:0:1 -1 176153442 . A G 50 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCCAACCTATCCCCACA;RSEQ=GTGAGTAATTAGTGCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:33.7:1:32:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 176153658 . T C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=3.08249;LSEQ=ACATGTCAAGAAAAAAAATA;RSEQ=GACTGTAACATAATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:82:78,4:84,7:0.4713:2,1:25.4:1:32:1:0.54179:1.62:60:81:0.4709:0:1 1/0:109:80:75,5:26,3:0.7339:2,2:21.3:1:31.2:1:0.43637:1.72:60:160:0.7339:0:1.1 -1 176153673 . C T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56768;SOR=2.9798;LSEQ=AAATATGACTGTAACATAAT;RSEQ=AAAGTTGGTTTAAAACACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:0,1:220,25:0.0041:2,0:1:0:24:0:0.10569:0:60:2:0.0041:0:1 0/1:166:2:1,1:141,23:0.012:2,2:25:1:25:1:0.269:6.02262:60:4:0.0121:0:1 -1 176153853 . A AT 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.76272;LSEQ=AAAGAAAAGAAAAATAATTG;RSEQ=TTTTTTTTTAAAAGTAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:6:2,4:75,294:0.016:2,2:28:1:30.5:1:0.60704:1.96:60:12:0.0162:0:0 0/1:245:3:0,3:61,181:0.0122:2,0:34:1:30.7:1:0.57581:0:60:6:0.0124:0:0 -1 176175885 . C A 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00227;SOR=0;LSEQ=TGGACACCGCCCCGCCGCCG;RSEQ=TACCCGATACGGCGGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:13:5,8:49,176:0.0546:2,2:24.8:1:31.1:1:0.17753:2.24:60:26:0.0563:0:1.3 0/0:153:0:0,0:51,102:0:2,0:20.3:1:32.3:1:1:0:60:152:1:0:0.3 -1 176175938 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.30262;SOR=4.62817;LSEQ=CGCACCGGGCCCCCGAGGCC;RSEQ=CCCGAGCCGGCGGCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:1,0:70,25:0.0104:2,0:1:0:28:0:1:0:60:2:0.011:0:1 0/1:64:3:2,1:46,15:0.0469:2,2:12.3:1:28.3:1:1:1.52217:60:6:0.0492:0:2 -1 176175999 . G T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41914;SOR=2.41212;LSEQ=CTGCCGCCGAAACCGCCACG;RSEQ=AAGGCGGCGACGGGGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:2:0,2:296,129:0.0047:2,0:1:0:27:0:0.09362:0:60:4:0.0048:0:1 0/1:356:4:2,2:233,119:0.0112:2,2:28.3:1:26:1:0.60733:1.95408:60:8:0.0113:0:1 -1 176176119 . A C 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=GGCGGCTACCAGACATCGTG;RSEQ=CTCCCTCCCCTCCAGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:219,296:0:2,0:25.3:1:29.6:1:1:0:60:84.833:1:0:0.1 0/1:433:13:5,8:173,247:0.03:2,2:25.5:1:31.5:1:1:1.12039:60:26:0.0302:0:1.4 -1 177199560 . A G 90 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03219;SOR=5.57707;LSEQ=TTGTGCTGCTTATAAGTTGA;RSEQ=GACAAATCAGGCAGCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:2,1:15,9:0.1111:2,2:20.3:1:27:1:1:1.19:60:2:0.0833:0:1.3 0/1:19:8:3,5:5,6:0.4211:2,2:35.5:1:30:1:1:1.36508:60:16:0.4211:0:1 -1 177294186 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14007;SOR=Inf;LSEQ=TGCTGCCTGGCATTTACAGG;RSEQ=AAGGACTTCTGAAATCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:35,21:0:2,0:25.1:1:28.9:1:1:0:59.7:17.667:1:0:0.1 0/1:34:2:1,1:21,11:0.0588:2,2:31:1:30.5:1:1:1.8709:60:4:0.0588:0:1 -1 177294353 . G A 94 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11326;SOR=0.16297;LSEQ=AATTTGTTTCCTCTAGGATC;RSEQ=AGGCCATCGAGCTACAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:2,7:3,11:0.3913:2,2:22.1:1:29.9:1:1:1.05:60:18:0.3913:0:1.2 0/1:11:1:1,0:5,5:0.0909:2,0:23:0:25:0:1:0:60:2:0.0909:0:1 -1 177294420 . G A 61 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24242;SOR=0.1257;LSEQ=CTCAACTCACAACTTCTACC;RSEQ=AGGACTCCTGAACTGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:1,0:0.8:0,0:36.5:1:30.8:1:0.2:0:60:8:0.8:0:1 0/1:7:2:0,2:1,4:0.2857:2,0:47.5:1:30.5:1:1:0:60:4:0.2857:0:1 -1 177295236 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGAAGTCAGCGAGACCA;RSEQ=GAACCCACTGGAAGGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:32:1:1:0:52:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 177392910 . C T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCCAGGATTTTACCTTA;RSEQ=CTGCATGCTAGCAAGTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:28.5:1:31.5:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:1,0:0:0,0:33:0:28:0:1:0:60:2:1:0:0 -1 177394601 . T C 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCATGCGCGCGCGCGCGCG;RSEQ=GTGTGTGTGTGTGTGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:30.5:1:28:1:1:0:60:4:0.6667:0:1.5 -1 178163144 . G T 60 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCAATCGTTAAACACTTG;RSEQ=ATCAAATCATAACTAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:19.8:1:30:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:1:0,0:19:0:32:0:1:0:60:2:1:0:1 -1 178163570 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1347;SOR=Inf;LSEQ=GAGTAGTGTCTTCCAACACA;RSEQ=CCACCAACTATGCCTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:12,201:0:2,0:26.4:1:30.3:1:1:0:60:105.5:1:0:0.1 0/1:124:2:1,1:11,111:0.0161:2,2:13.5:1:29.5:1:0.18489:9.70:60:4:0.0165:0:1 -1 179084149 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2042;SOR=Inf;LSEQ=CCATAGGTAGCAATTTCCCA;RSEQ=AACAATACCCCAAAAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:30.5:1:32.1:1:1:0:60:40:1:0:0 0/1:17:2:1,1:7,8:0.1176:2,2:42:0:30.5:1:1:1.13:60:4:0.1176:0:1.5 -1 179086078 . C A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGCTCAAGCAACTCCC;RSEQ=TGCCTCAGCCTTCAGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:32:0:1:0:60:4:1:0:1.5 -1 179095667 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50769;SOR=0;LSEQ=CTCAGCTGCACTGCGTGACA;RSEQ=AGGTCCATGGTACCAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:62,66:0.0154:2,2:28.5:1:29:1:1:1.06:60:4:0.0156:0:1 0/0:98:0:0,0:52,46:0:2,0:24.7:1:31:1:1:0:60:31.667:1:0:0.2 -1 180810083 . TA T 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.15958;LSEQ=TAACATGCCGTGCTAAGCAC;RSEQ=AAAAAAATAGCAACAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:4:4,0:203,12:0.0183:2,0:38:1:32.5:1:1:0:60:8:0.0186:0:0 0/1:142:3:3,0:132,7:0.0211:2,0:42.3:1:29:1:1:0:60:6:0.0213:0:0 -1 180810185 . G C 126 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=28.93615;LSEQ=GCATTAATTGGTTCTTAATA;RSEQ=TATTGTTAAGTGTACTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:872:1:0,1:418,453:0.0011:2,0:46:0:34:0:1:0:60:2:0.0012:0:2 0/1:590:19:9,10:267,303:0.0322:2,2:25.9:1:29.7:1:1:1.02:60:8.5:0.0292:0:1.5 -1 180810233 . G A 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.35456;SOR=1.1314;LSEQ=GGCTTAAAATGGTAAATTTT;RSEQ=TTTGTTTTTACCACAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:236:88,148:153,215:0.3907:2,2:23.1:1:29.7:1:0.30772:1.19647:60:77.667:0.3936:0:1.1 0/1:390:164:64,100:94,131:0.4205:2,2:24.1:1:29:1:0.60256:1.12085:60:328:0.4282:0:1.2 -1 180810249 . G GT 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.86956;LSEQ=TTTTGTTTGTTTTTACCACA;RSEQ=TTTTTTTTTAAAGGCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:11:3,8:168,305:0.0226:2,2:33.5:1:30.2:1:0.75394:1.46776:60:22:0.023:0:0.3 0/1:304:6:1,5:108,188:0.0197:2,2:27:1:30.7:1:0.42389:2.86415:60:12:0.0203:0:0.7 -1 180810259 . A T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26172;SOR=1.89574;LSEQ=TTTTACCACAGTTTTTTTTT;RSEQ=AAGGCATAAAAATAGAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:6:2,4:134,270:0.0146:2,2:18:1:27.8:1:1:1.01:60:12:0.0146:0:1.2 0/1:256:7:3,4:80,169:0.0273:2,2:26.3:1:28.6:1:0.68503:1.58:60:14:0.0275:0:1.1 -1 181474675 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCCACCATGCCTGGCTAA;RSEQ=ATTTTGTATTTTTTTTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 181475237 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.13846;SOR=Inf;LSEQ=TGTCACTGAATTCTAGAACA;RSEQ=AGAGTCAGAGTCCTGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:15.4:1:30.8:1:1:0:60:32:1:0:0.1 0/1:10:2:1,1:4,4:0.2:2,2:5.5:1:28:1:1:1:60:4:0.2:0:1 -1 181475244 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51567;SOR=0;LSEQ=GAATTCTAGAACAGAGAGTC;RSEQ=GAGTCCTGGACAGACTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:29:1:29.5:1:1:1.46:60:4:0.1176:0:1 0/0:10:0:0,0:5,5:0:2,0:16.3:1:29:1:1:0:60:20:1:0:0.1 -1 181800958 . A G 64 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12192;SOR=0;LSEQ=CAGGGATAGTATGAGATGCC;RSEQ=CCCAGTGTTTACAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:2,2:24,9:0.1081:2,2:23.8:1:32.3:1:0.56696:2.58749:31.3:8:0.1081:0:4.3 0/0:30:0:0,0:19,10:0:2,0:18.3:1:29.6:1:1:0:55.7:28:0.9655:0:0.2 -1 181800964 . T C 63 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11973;SOR=0;LSEQ=TAGTATGAGATGCCACCCAG;RSEQ=GTTTACAGGAAAAGGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:2,2:23,10:0.1081:2,2:29.8:1:31.8:1:0.5821:2.24385:31.3:8:0.1081:0:4.3 0/0:31:0:0,0:20,11:0:2,0:21.2:1:29.1:1:1:0:54.6:30:1:0:0.4 -1 181800979 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17753;SOR=Inf;LSEQ=CCCAGTGTTTACAGGAAAAG;RSEQ=CTTCTGAAATCAGACAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:28,18:0:2,0:27.3:1:30.9:1:1:0:49.5:22:1:0:0.5 0/1:34:2:1,1:21,11:0.0588:2,2:21.5:1:28:1:1:1.8709:39:4:0.0588:0:3.5 -1 181800983 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17068;SOR=Inf;LSEQ=GTGTTTACAGGAAAAGGCTT;RSEQ=TGAAATCAGACAATGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:31,18:0:2,0:26.8:1:32.1:1:1:0:48.9:98:1:0:0.5 0/1:35:2:1,1:21,11:0.0571:2,2:25.5:1:30.5:1:1:1.8709:39:4:0.0588:0:3.5 -1 181800985 . G A 57 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13549;SOR=0;LSEQ=GTTTACAGGAAAAGGCTTCT;RSEQ=AAATCAGACAATGCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:2,2:30,17:0.0784:2,2:35.5:1:28.8:1:0.62289:1.74414:31.3:8:0.08:0:4.3 0/0:37:0:0,0:23,14:0:2,0:29.2:1:31.1:1:1:0:51.5:36:1:0:0.5 -1 181801004 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14993;SOR=Inf;LSEQ=TGAAATCAGACAATGCCTTT;RSEQ=AAACTCTTATACCAACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:40,32:0:2,0:24.6:1:31.4:1:1:0:47:71:1:0:0.3 0/1:46:2:1,1:26,18:0.0435:2,2:46.5:1:31.5:1:1:1.43267:39:4:0.0455:0:3.5 -1 181801020 . C A 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27488;SOR=0;LSEQ=CTTTCAAACTCTTATACCAA;RSEQ=CTCTGGAGTTGGGCAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:3:1,2:32,36:0.0423:2,2:19.7:1:30.3:1:1:1.76398:27.3:6:0.0435:0:4.7 0/0:47:0:0,0:25,22:0:2,0:24.4:1:31:1:1:0:50.8:94:1:0:0.4 -1 181801035 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52192;SOR=0;LSEQ=ACCAACCTCTGGAGTTGGGC;RSEQ=ACATGGCTTCTCCCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:0,2:29,36:0.0299:2,0:13.5:1:32.5:1:0.50158:0:30.5:4:0.0308:0:5 0/0:42:0:0,0:21,21:0:2,0:26.8:1:29.1:1:1:0:51.1:41:1:0:0.4 -1 181801200 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CAAATGAGTTCAACTAACAA;RSEQ=TTCTACCAAGGACCCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:11:1:30.8:1:1:0:60:10:1:0:0.6 1/0:4:2:1,1:0,2:0.5:0,2:17.5:1:31.5:1:1:0:60:4:0.6667:0:1 -1 181801585 . T C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAACCAGGGCGGTGCGCAG;RSEQ=GCTTGTGGGACAGGGCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:33:1:1:0:60:4:1:0:1.5 -1 181801766 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCACGCTTGAATTCTTGC;RSEQ=GGGCTTCAGCCGCCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:1:30.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 181818020 . G A 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAGGCGCCCATTGAAAA;RSEQ=AAACCATAATAAGCGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:25,16:0,0:1:0,2:28.9:1:30.4:1:1:0:60:82:1:0:1 1/1:14:14:7,7:0,0:1:0,2:25.8:1:28.4:1:1:0:60:13:1:0:1.1 -1 181818150 . G A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGGTGCAGCGGCCCATGTGA;RSEQ=AGCCACATGGGAAAGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:3,10:0,2:0.8667:0,2:22.7:1:29.3:1:1:0:60:12:0.8571:0:1.2 1/1:3:3:0,3:0,0:1:0,0:29.3:1:29.7:1:1:0:60:6:1:0:1 -1 181818482 . C A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTAACGTGCTAAGCTCC;RSEQ=TGGGTGGGTGAAGGGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:5,3:0.2727:2,2:29:1:32:1:0.54545:2.97405:60:6:0.3:0:1 0/0:2:0:0,0:1,1:0:2,0:43.5:1:32:0:1:0:60:4:1:0:0.5 -1 181818912 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23494;SOR=Inf;LSEQ=CTCCTGGTGCCACCAAACTG;RSEQ=GTGAGACCCTCCAACACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:28,31:0:2,0:26.5:1:30.7:1:1:0:60:28.5:1:0:0.1 0/1:56:2:1,1:23,31:0.0357:2,2:21.5:1:29.5:1:1:1.34:60:4:0.0364:0:1.5 -1 181818999 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.13645;LSEQ=GCTCCTTGAGGTCAGAGGTC;RSEQ=CAGAAGCAGGAGGCATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:2,10:0.2:2,0:31.3:1:29:1:1:0:60:6:0.2:0:1.7 0/1:9:2:0,2:2,5:0.2222:2,0:9.5:1:26:1:1:0:60:4:0.2222:0:2 -1 181819067 . C T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28871;SOR=Inf;LSEQ=GACATTTCCAGGCATGGAAG;RSEQ=GAATCAGATGAATAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:6,8:3,3:0.7:2,2:23.9:1:30.1:1:1:1.31413:60:28:0.7:0:1.7 1/1:5:5:3,2:0,0:1:0,2:17.2:1:31.4:1:1:0:60:10:1:0:1.6 -1 181819068 . G A 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28871;SOR=0;LSEQ=ACATTTCCAGGCATGGAAGC;RSEQ=AATCAGATGAATAGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:3,3:6,8:0.3:2,2:33.7:1:30.5:1:1:1.31:60:12:0.3:0:1 0/0:5:0:0,0:3,2:0:2,0:17:1:33:1:1:0:60:10:1:0:1.6 -1 181819083 . G A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.21278;LSEQ=GAAGCGAATCAGATGAATAG;RSEQ=GCTGGAAGTGAATCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:3,6:7,4:0.45:2,2:24:1:31.1:1:0.36985:3.27423:60:18:0.45:0:2 1/0:6:3:3,0:2,1:0.5:2,0:26.3:1:29.3:1:1:0:60:6:0.5:0:1.7 -1 181819187 . T C 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00189;SOR=0;LSEQ=AATGACACCATCAACAAAAA;RSEQ=AACAACAAAACGGGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:46,36:0,0:1:0,2:26.6:1:32:1:1:0:60:164:1:0:2.1 1/1:47:41:24,17:3,3:0.8723:2,2:24.2:1:30.6:1:1:1.40:60:82:0.8723:0:1.9 -1 181819202 . C T 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=5e-05;SOR=0;LSEQ=AAAAATAACAACAAAACGGG;RSEQ=CCCCACAAAAACCCCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:22:11,11:42,38:0.2157:2,2:27.7:1:29:1:1:1.10418:60:44:0.2178:0:2.6 0/0:55:0:0,0:27,28:0:2,0:27.9:1:30:1:1:0:59.7:54:1:0:1.6 -1 181819206 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12126;SOR=Inf;LSEQ=ATAACAACAAAACGGGCCCC;RSEQ=ACAAAAACCCCATCTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:53,49:0:2,0:29.7:1:31.5:1:1:0:60:101:1:0:2 0/1:55:2:1,1:26,27:0.0364:2,2:32.5:1:29:1:1:1.04:60:4:0.037:0:3 -1 181819208 . CA C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54189;SOR=0;LSEQ=AACAACAAAACGGGCCCCCA;RSEQ=AAAACCCCATCTGAGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:53,47:0.0196:2,2:32.5:1:32:1:1:1.12633:60:4:0.0196:0:2 0/0:55:0:0,0:27,28:0:2,0:30.2:1:28.8:1:1:0:59.7:54:1:0:1.6 -1 181819234 . G C 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00023;SOR=0;LSEQ=CCCCATCTGAGGGTCAGCAG;RSEQ=CTCAAAGACCAAAACTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:112:54,58:0,0:1:0,2:27.1:1:31.2:1:1:0:59.3:27:1:0:1.9 1/1:64:56:24,32:3,5:0.875:2,2:26.7:1:30.9:1:1:1.25:59.7:27:0.871:0:1.7 -1 181819362 . G T 59 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57964;LSEQ=ACAACATCTCTCCATCAAGG;RSEQ=TGCAGAACTGGATGGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:1,3:0,9:0.3077:0,2:23.5:1:29.8:1:0.30769:0:60:8:0.3077:0:1 0/1:5:1:0,1:1,3:0.2:2,0:48:0:29:0:1:0:60:2:0.2:0:1 -1 182695805 . C CAA 31 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAAAGCGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAGATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:14.5:1:31:1:1:0:60:4:0.5:0.2:2 0/0:1:0:0,0:1,0:0:0,0:26:0:33:0:1:0:60:2:1:0:0 -1 182696005 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10867;SOR=Inf;LSEQ=CAGCAGGTCCCTTGTCTCAA;RSEQ=GGGCCCTGTAGCCATTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:150,32:0:2,0:23.5:1:30.1:1:1:0:60:35.4:1:0:0.2 0/1:90:2:1,1:69,19:0.0222:2,2:27:1:29:1:0.397:3.5649:60:4:0.0225:0:2 -1 182696024 . A T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55389;SOR=0;LSEQ=AAGGGCCCTGTAGCCATTAC;RSEQ=GGCATGAGGTGTTTGATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:189,68:0.0115:2,2:24.3:1:30.7:1:0.17737:5.51497:60:6:0.012:0:1.3 0/0:132:0:0,0:95,37:0:2,0:23.1:1:29.8:1:1:0:60:25.4:1:0:0.3 -1 182696047 . C CT 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=0.26078;LSEQ=CATGAGGTGTTTGATATAGA;RSEQ=TTTTTTTTATCATGGACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:176:111,65:146,80:0.4346:2,2:24.6:1:30.5:1:0.75469:1.06852:60:57.667:0.4369:0.0741:0.7 0/1:210:35:19,16:115,59:0.1667:2,2:23.7:1:30.5:1:0.2461:1.6374:60:70:0.1683:0.019:0.9 -1 182696117 . C G 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.29993;LSEQ=GGGGCCATGTACACCCGCCA;RSEQ=AGGTTGGAACAGTGAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:302:152,150:172,173:0.466:2,2:26:1:31.1:1:0.93724:1.02:60:42.143:0.4638:0:1.1 0/1:357:74:33,41:144,138:0.2073:2,2:24.7:1:31:1:0.36134:1.29549:60:73:0.2098:0:1.3 -1 182696160 . T A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01537;SOR=Inf;LSEQ=ATAACTTTTCAGCTCCTCCC;RSEQ=CTCTCATTCCAACATTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:0:0,0:194,324:0:2,0:24.2:1:29.8:1:1:0:60:42.167:1:0:0.4 0/1:283:4:3,1:115,164:0.0141:2,2:7.5:1:25:1:0.31146:4.26:60:3:0.0108:0:1.8 -1 184327212 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14296;SOR=Inf;LSEQ=TATTTATCTTTCTCACATTT;RSEQ=AGAAATAGAGCCATTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:148,65:0:2,0:23.8:1:32:1:1:0:60:70:1:0:0.4 0/1:130:2:1,1:94,34:0.0154:2,2:27:1:31:1:0.4675:2.73938:60:4:0.0156:0:1 -1 184327245 . A T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06051;SOR=Inf;LSEQ=ATTAAAATATTAAGAAAAAA;RSEQ=TTAAAGTTTTCGGCACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:202,125:0:2,0:24:1:30.3:1:1:0:60:162.5:0.9969:0:0.5 0/1:213:3:1,2:119,91:0.0141:2,2:10.3:1:29.3:1:0.58185:2.60374:60:6:0.0142:0:1 -1 184327256 . C T 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01577;SOR=0.6416;LSEQ=AAGAAAAAAATTAAAGTTTT;RSEQ=GGCACATAAAAGTTAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:139:78,61:136,83:0.3872:2,2:27.8:1:29.9:1:0.27063:1.28052:60:68.5:0.387:0:1.1 0/1:222:64:34,30:84,73:0.2883:2,2:28.5:1:29.4:1:1:1.01524:60:63:0.2903:0:1.2 -1 184327286 . T TA 68 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.66536;LSEQ=AAGTTAAATTCCTCTTCATG;RSEQ=AAAAAAAACTAAAGGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:5:2,3:194,195:0.0127:2,2:29.6:1:29.6:1:1:1.4908:60:10:0.0128:0:0.6 0/0:236:2:1,1:104,130:0.0085:2,2:25.5:1:19.5:1:1:1.25:60:1:0.0043:0.0042:1 -1 184327323 . T G 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAGAAAAAGTAAGAATATA;RSEQ=TCTTCTTAATAACCTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:76:28,48:71,145:0.2603:2,2:25.8:1:31:1:0.57385:1.19:60:24.333:0.2544:0:1.1 0/0:150:0:0,0:48,101:0:2,0:22.5:1:29.4:1:1:0:60:48.667:0.9932:0:0.3 -1 184327784 . AT A 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAAAATGTGTAGTGGAAG;RSEQ=TTTTTTTTTTTTTTTTCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:24:1:29:1:0.4:0:60:4:0.4:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 184951494 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGATGATGCTCCCCGTGGG;RSEQ=CCACAGCTACTGGGCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:13,13:0.0714:2,2:11:1:28.5:1:1:1:60:4:0.0714:0:1 0/0:13:0:0,0:8,5:0:2,0:19.5:1:30.2:1:1:0:60:26:1:0:0.2 -1 184951525 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1301;SOR=Inf;LSEQ=TGGGCAGGGTGGGAAAGAAC;RSEQ=CTGACTCCGGTCCAAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:14,17:0:2,0:29.3:1:29.6:1:1:0:60:30:1:0:0.1 0/1:18:2:1,1:9,7:0.1111:2,2:25:1:30.5:1:1:1.26772:60:4:0.1111:0:1 -1 185195864 . CT C 74 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.67277;SOR=0.49389;LSEQ=TCTCATTTAAGCTTCTGAGA;RSEQ=TTTTTTTTTTTTTTTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:5,0:0.3846:0,0:33:1:32:1:1:0:60:10:0.3846:0:1.6 0/1:13:3:3,0:5,0:0.2308:0,0:41.7:1:30:1:1:0:60:6:0.25:0:1.3 -1 185195953 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.21104;LSEQ=TGGTTTAGCTCTCAGCAGCC;RSEQ=GCTCCTGAGCTCTGAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:40:28,12:35,16:0.4396:2,2:28.8:1:31.4:1:1:1.07:57.1:80:0.4494:0:1.2 0/1:71:10:6,4:34,27:0.1408:2,2:25.3:1:29.5:1:1:1.19:58.1:20:0.1429:0:1.2 -1 185520465 . A G 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00104;SOR=0.43782;LSEQ=ACTTCTTCATTAGAAAGAAC;RSEQ=AAATAAATGCTTCTTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:86:75,11:231,42:0.2396:2,2:20.7:1:29.8:1:0.60582:1.24:60:85:0.2408:0:1.1 0/1:190:23:20,3:142,25:0.1211:2,2:26.3:1:29.8:1:1:1.17:60:46:0.1223:0:1 -1 185520600 . G A 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.19267;LSEQ=TGACCTCAACTTACCTGTTC;RSEQ=GTTGGATTTCTTGATACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:982:221:87,134:336,423:0.2251:2,2:26.8:1:30.9:1:0.21702:1.22319:60:220:0.2261:0:1.1 0/1:609:237:95,142:161,210:0.3892:2,2:24.8:1:30.3:1:0.44887:1.14571:60:78:0.3887:0:1.2 -1 185520654 . C G 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00031;SOR=0;LSEQ=TGTGAAGTTTCTGCAACAGT;RSEQ=CTATGGTCTTTCACCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:23:6,17:173,417:0.0375:2,2:22.9:1:29.9:1:0.81969:1.17515:60:10.5:0.0347:0:1 0/0:281:0:0,0:89,192:0:2,0:23.2:1:30.8:1:1:0:60:139.5:1:0:0.4 -1 185520693 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07952;SOR=Inf;LSEQ=GTGCCTTTGCTTATGCTAAC;RSEQ=CAGGGCATGCCCTCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:48,241:0:2,0:24.7:1:31.3:1:1:0:60:71.25:1:0:0.2 0/1:114:2:1,1:18,94:0.0175:2,2:25:1:28:1:0.30678:5.11:60:4:0.0179:0:1 -1 185520694 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1827;SOR=5.36893;LSEQ=TGCCTTTGCTTATGCTAACC;RSEQ=AGGGCATGCCCTCCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:1,0:47,239:0.0035:2,0:1:0:26:0:0.16725:0:60:2:0.0035:0:1 0/1:108:2:1,1:17,89:0.0185:2,2:8.5:1:28.5:1:0.30685:5.12:60:4:0.0187:0:1 -1 185520728 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGAGCCTGCTGTGATCT;RSEQ=GATGTTTGCATATCCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:8,133:0.014:2,2:23:1:29:1:0.12233:15.73:60:4:0.0143:0:1 0/0:48:0:0,0:4,44:0:2,0:24.2:1:30.6:1:1:0:60:96:1:0:0.1 -1 187529093 . G C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCCTCTTCTGTAGGGCT;RSEQ=CTGTGGATTGCTGGGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:0.5:2,2:24.3:1:31.3:1:1:1:60:6:0.5:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 187529404 . T C 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGTAAATCTGCTTGTC;RSEQ=GCAGAGACTGCGGCCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44.5:1:31:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:41:0:32:0:1:0:60:2:1:0:1 -1 188226895 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAGTGCTGATTGGTGC;RSEQ=TTTACAATCCTTTAGTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:36:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 188227425 . GC AA 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.35961;SOR=0.26738;LSEQ=AAGGAGGTTAAAAATACAGG;RSEQ=CCAAAGGTGAGTAATAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:24:17,7:2,0:0.8889:0,2:21.5:1:30:1:1:0:54.8:48:0.9231:0.1111:0.9 1/0:3:2:2,0:1,0:0.6667:0,0:26.5:1:29.8:1:1:0:54.5:4:0.6667:0:1 -1 188228294 . CC TG 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTGTCTCCTTCTCTT;RSEQ=TCTCTCTCTCTCTTCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:31:0:28:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31.8:1:1:0:59.5:4:1:0:3 -1 188228303 . C G 32 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCCTTCTCTTCCTCTCTCT;RSEQ=TCTCTTCCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:28:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:41.5:1:32:1:1:0:59.5:4:1:0:3 -1 188228305 . C T 30 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTTCTCTTCCTCTCTCTCT;RSEQ=TCTTCCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:21:0:26:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:43:1:30:1:1:0:59.5:4:1:0:3 -1 188228310 . C CCTCTCT 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=13.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TCTTCCTCTCTCTCTCTCTT;RSEQ=CTCTCTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:30:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:43:1:30.5:1:1:0:59.5:4:1:0:4 -1 188744693 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGGCTGGGGTGGTCTCA;RSEQ=ATGGAGATGAGTAACTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:31.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 188746793 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00234;SOR=0.20778;LSEQ=GACAAAAAGTTATCTCCTTG;RSEQ=GATTTTAAGTTAATTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:71:53:53,0:18,0:0.7465:1,1:20.9:1:31.3:1:1:0:60:25.5:0.7391:0:2.2 0/1:24:9:9,0:15,0:0.375:1,0:24.3:1:31:1:1:0:60:18:0.375:0:2.1 -1 188746835 . A G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25717;LSEQ=TGCAGTCTGTTTTTTAATTC;RSEQ=TTAGTTAATTTATTTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:162:116:104,12:42,3:0.716:2,2:25.5:1:29.8:1:0.56119:1.61101:60:57:0.717:0:1.4 0/1:74:29:25,4:41,4:0.3919:2,2:21:1:28.8:1:0.70379:1.62863:60:28:0.3836:0:1.4 -1 188746974 . A C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21977;LSEQ=AAACACATTTTTATTAAATT;RSEQ=ATCACTGGCTCTTAATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:475:322:125,197:58,95:0.6779:2,2:24.1:1:31.8:1:0.91968:1.04:60:160:0.678:0:1.1 0/1:285:90:42,48:80,115:0.3158:2,2:24.7:1:30.7:1:0.43983:1.26:60:89:0.3134:0:1.1 -1 188746979 . C A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05407;SOR=Inf;LSEQ=CATTTTTATTAAATTAATCA;RSEQ=TGGCTCTTAATTCATATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:162,282:0:2,0:25.2:1:32.1:1:1:0:60:221:1:0:0.8 0/1:271:3:2,1:113,154:0.0111:2,2:6.3:1:29.3:1:0.57692:2.72:60:6:0.0112:0:1 -1 188952643 . A G 24 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52723;SOR=0;LSEQ=TTAAATTTTTTCAAAAAAAC;RSEQ=GCTCCTGGATTCATTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:0,2:88,58:0.0134:2,0:19:1:24:1:0.16271:0:60:4:0.0143:0:5 0/0:91:0:0,0:57,32:0:2,0:22.2:1:30.3:1:1:0:60:88:0.9778:0:0.1 -1 188952660 . AT A 197 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=8.38249;LSEQ=AACAGCTCCTGGATTCATTG;RSEQ=TTTTTTTTTTGAGGGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:64:34,30:75,58:0.3168:2,2:26.5:1:30.9:1:0.7598:1.14021:59.7:128:0.3184:0.0396:0.3 1/0:118:94:55,39:12,7:0.7966:2,2:28.2:1:30.1:1:0.80121:1.21351:60:93:0.7949:0:0.1 -1 188952697 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16128;SOR=Inf;LSEQ=CTTTTTGTGTCTTTATCTCC;RSEQ=TCAATTCCTCTCTGATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:82,102:0:2,0:26.8:1:30.4:1:1:0:60:45:0.9836:0:0.4 0/1:126:2:1,1:60,64:0.0159:2,2:29:1:31.5:1:1:1.07:60:4:0.016:0:1 -1 188952784 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=27.88658;LSEQ=CCTCTCTAGCTCTTTTAATT;RSEQ=TGATGTTAGAGTGTCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:0,4:0,16:0.2:1,0:6.8:1:30.3:1:1:0:60:8:0.2:0:1 1/1:18:16:0,16:0,2:0.8889:0,1:21.1:1:30.7:1:1:0:60:32:0.8889:0:1.1 -1 188955252 . T C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55944;SOR=2.75172;LSEQ=TTCCTGAGATTGTCTAGTTT;RSEQ=CATCTTTGAGGCTGCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:0.1429:2,0:9:0:31:0:1:0:60:2:0.1429:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:11:1:32.5:1:1:1:60:4:0.3333:0:1 -1 188955404 . G T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14087;SOR=6.4591;LSEQ=GGCTGCTGCAGTATTCTGGA;RSEQ=GTTCACTTCAGGCCCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:4,5:0.3571:2,2:24:1:30.4:1:1:1.18452:60:10:0.3846:0:1 1/1:5:4:3,1:1,0:0.8:0,2:34.5:1:30.3:1:1:0:60:8:0.8:0:1 -1 188955897 . C T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58533;SOR=2.08426;LSEQ=GCCTGAAGAGGCACTCTGGC;RSEQ=GCAGACTGCCACAGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:2,2:7,6:0.2353:2,2:36.3:1:31.5:1:1:1.15611:60:8:0.2353:0:1.3 0/1:5:2:1,1:1,2:0.4:2,2:14.5:1:28:1:1:1.73:60:4:0.4:0:1.5 -1 188955985 . T A 31 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGCTCCAGCAGGGGAAAAG;RSEQ=ATGGCCTGGAGCTATAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:28.5:1:31.5:1:0.4:0:60:4:0.4:0:1 1/1:1:1:0,1:0,0:1:0,0:4:0:30:0:1:0:60:2:1:0:2 -1 188956278 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18357;SOR=Inf;LSEQ=ATCCGTGAGTTGCACAGTTC;RSEQ=ATGAAAAAAGCAGTTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:11,15:0:2,0:25.4:1:31.9:1:1:0:60:52:1:0:0.2 0/1:20:2:1,1:7,11:0.1:2,2:6.5:1:28:1:1:1.54:60:4:0.1053:0:1 -1 189241655 . T A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGAAATCATATTAAAAA;RSEQ=ATTCTAAGACAGAATGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:29:1:1:0:60:4:1:0:1 -1 189243366 . T A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28792;SOR=1.83934;LSEQ=GAGAAGCGAGATAGAGATAG;RSEQ=TAATTTTCAGTAACCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:17:16,1:47,2:0.2576:1,1:23.9:1:30.9:1:1:1.45952:60:34:0.2576:0:1 0/1:23:9:9,0:12,2:0.3913:2,0:15.7:1:30.6:1:0.50198:0:60:18:0.3913:0:1 -1 189243405 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTCTACTTAAGTAATAA;RSEQ=CTTTGTAATCTCTAGGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:122,25:0.0134:2,2:20:1:29:1:0.31952:4.80487:60:4:0.0135:0:1.5 0/0:68:0:0,0:55,13:0:2,0:23.2:1:32.5:1:1:0:60:136:1:0:0.3 -1 189243491 . A G 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.2334;LSEQ=ATGAATTACATCTAGCAGCT;RSEQ=TACAGTAAATAGTAAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:156:81,75:150,149:0.3429:2,2:26.9:1:31.8:1:0.76721:1.07:60:155:0.3468:0:1.1 1/0:234:126:65,61:53,55:0.5385:2,2:26.4:1:30.9:1:0.79319:1.11:60:252:0.5385:0:1.1 -1 189243520 . A C 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATAGTAAGTGGTGAGACTGG;RSEQ=TATTATTTTCGCAGGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:196,258:0:2,0:25.9:1:30.5:1:1:0:60:74.667:1:0:0.4 0/1:234:13:6,7:99,122:0.0556:2,2:25.4:1:31.7:1:1:1.06:60:26:0.0556:0:1.1 -1 189243571 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10402;SOR=Inf;LSEQ=AATATATTTCCTTCTATGGG;RSEQ=TAACTTACTATCCCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:58,151:0:2,0:24.4:1:30.5:1:1:0:60:51.25:1:0:0.2 0/1:100:2:1,1:24,74:0.02:2,2:31:0:32:0:0.43939:3.04:60:4:0.0202:0:1.5 -1 189243810 . A G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGTGAGTATATATGAAT;RSEQ=TTAATGTATATTAAATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:17.7:1:33.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 190733725 . T C 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAAATTCTGCTCTGAGC;RSEQ=TCTAGCAGATACATTATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:18.8:1:30.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 190734020 . C T 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCCTTTTGGAAAATGGTA;RSEQ=ATGAAGAAGAACATCTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:724:0:0,0:428,296:0:2,0:24.8:1:32.1:1:1:0:60:240.333:1:0:0.6 0/1:376:21:16,5:204,151:0.0559:2,2:26.7:1:29.2:1:0.11188:2.36:60:42:0.0565:0:1.7 -1 190734051 . G A 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21534;LSEQ=ACATCTAAGTAAAGAGTCCA;RSEQ=AATATTTCAAAGGTAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:767:578:312,266:98,91:0.7536:2,2:25.8:1:30:1:0.61539:1.09:60:288:0.7539:0:1.1 0/1:426:169:80,89:124,133:0.3967:2,2:26:1:29.6:1:0.92107:1.03715:60:55.333:0.399:0:1.1 -1 190734074 . A C 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTTCAAAGGTAACCTTAT;RSEQ=GGTTTCCCATAAACATCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:783:0:0,0:378,403:0:2,0:25:1:29.5:1:1:0:60:110.571:0.9974:0:0.7 0/1:400:32:18,14:168,200:0.08:2,2:22.6:1:30.7:1:0.27168:1.53:60:64:0.0806:0:1.6 -1 190734156 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08628;SOR=Inf;LSEQ=TCTCAATTTTTTGAATGACT;RSEQ=ACAGCAATGCCTATTATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:68,252:0:2,0:23.2:1:31.2:1:1:0:60:39:0.9968:0:0.1 0/1:134:2:1,1:34,96:0.0149:2,2:26.5:1:28:1:0.46149:2.80:60:4:0.0152:0:1 -1 191168873 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=AGCCTCAAAGATTGAGTTTA;RSEQ=ACAAACTTATGAAGATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:15.5:1:32.5:1:1:1:60:4:0.3333:0:1 0/0:3:0:0,0:1,2:0:2,0:19.7:1:29.7:1:1:0:60:6:1:0:0 -1 191549641 . T C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCCATTAGTTATTCTTCC;RSEQ=GATCCTCTCCCTCCTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:4,7:0,0:1:0,2:15.5:1:29.3:1:1:0:60:22:1:0:1.1 1/1:6:6:2,4:0,0:1:0,2:15.3:1:29.3:1:1:0:60:12:1:0:1 -1 192220536 . C T 101 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01471;SOR=0;LSEQ=CATTGGTCAAGTCCCTCTTC;RSEQ=GTAGGGCTGCTACAGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:6,4:0,0:1:0,2:19.9:1:30.7:1:1:0:60:20:1:0:1.1 0/1:7:3:1,2:2,2:0.4286:2,2:19.7:1:31.7:1:1:1.81007:60:6:0.4286:0:1 -1 192221363 . T G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10051;SOR=0.21865;LSEQ=TAAGAGGCTGTTGAGAATCT;RSEQ=TGCAGCTCTGGGGTTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:21:15,6:7,4:0.6563:2,2:24.6:1:32:1:0.7026:1.41:60:42:0.6563:0:1 0/1:7:2:2,0:5,0:0.2857:0,0:21.5:1:31:1:1:0:60:4:0.2857:0:1 -1 193090865 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTGCTCAGGTACGCGCG;RSEQ=ACCTGACGCCGCTTGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 193091233 . AAGG A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.2806;SOR=3.77288;LSEQ=GTTGGTTCGTCGCGGCGGCG;RSEQ=AGGAGGAGGAAGAGGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:1,0:111,5:0.0085:1,0:45:0:30:0:1:0:60:2:0.0088:0:0 0/1:63:2:1,1:55,6:0.0317:2,2:36:1:29.5:1:0.21147:8.56132:60:4:0.0323:0:0 -1 193091281 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14501;SOR=Inf;LSEQ=CAAGAGAAGAAGGAGGCAGG;RSEQ=GCGGCGGCAGCGGCGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:260,27:0:2,0:23.9:1:31.7:1:1:0:60:40:1:0:0.1 0/1:177:2:1,1:146,29:0.0113:2,2:35:1:29:1:0.31106:4.96692:60:4:0.0116:0:1 -1 193091490 . G T 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=GGCATGGCTGTGGCCCAGGG;RSEQ=TGGCAGGGCAGAGTTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:767:21:6,15:224,521:0.0274:2,2:22:1:29.8:1:1:1.07476:60:42:0.0276:0:1.2 0/0:422:0:0,0:132,290:0:2,0:22.8:1:30.5:1:1:0:60:104.5:1:0:0.1 -1 193091493 . G A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05294;SOR=7.52265;LSEQ=ATGGCTGTGGCCCAGGGGTG;RSEQ=CAGGGCAGAGTTGGGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:1:1,0:210,521:0.0014:2,0:1:0:26:0:0.28825:0:60:2:0.0014:0:1 0/1:392:4:2,2:114,274:0.0102:2,2:24.8:1:28:1:0.58501:2.40:60:8:0.0104:0:1 -1 193094120 . CT C 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49092;SOR=1.59696;LSEQ=ATTCATTATTAGATTTTATA;RSEQ=TTTTTTTTGTTAGCTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:5:4,1:165,1:0.0292:1,2:23:1:32.6:1:0.05779:36.99945:60:10:0.0296:0:0 0/1:87:4:4,0:82,1:0.046:1,0:28.8:1:31.1:1:1:0:60:8:0.046:0.0115:0 -1 193094213 . T TA 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.30296;SOR=0.58215;LSEQ=AGTTGAATTAGAATTGTCAG;RSEQ=AAAAAAAATCTTGCCTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:856:18:14,4:525,311:0.021:2,2:21.1:1:27:1:0.2256:2.07:60:17:0.0202:0.0058:0 0/1:567:7:4,3:348,212:0.0123:2,2:28.3:1:27.7:1:1:1.23066:60:14:0.0125:0:0.1 -1 193094368 . TTATC T 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=GTAAGTAGAATTCATTTTAC;RSEQ=TATCTATTTATCAGTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:0:0,0:130,453:0:2,0:25:1:28.7:1:1:0:60:582:1:0:0.9 0/1:381:45:10,35:101,235:0.1181:2,2:27.5:1:30.2:1:0.3011:1.50275:60:90:0.1206:0.0079:0.2 -1 193094375 . T C 282 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.04513;LSEQ=GAATTCATTTTACTTATCTA;RSEQ=CTATTTATCAGTTTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:532:516:105,411:3,13:0.9699:2,2:24.3:1:31.4:1:1:1.11:60:72.714:0.9714:0:1.1 1/0:348:206:62,144:36,106:0.592:2,2:25.5:1:31.2:1:0.3961:1.27:60:205:0.5959:0:1.1 -1 193098964 . A G 63 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AGAAAATTATTAAAAGTAAC;RSEQ=TGTTTAATACATTTTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:20.5:1:31.5:1:1:0:60:8:1:0:1 1/0:3:2:1,1:1,0:0.6667:0,2:18:1:32.5:1:1:0:60:4:0.6667:0:1 -1 193104168 . ATATGTGTGTG A 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAAAAAATCTTGTCCATAT;RSEQ=TATGTGTGTGTGTATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:13:1:30.3:1:1:0:60:6:0.5:0.3333:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 193104439 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.11696;SOR=Inf;LSEQ=CCATATAGAAGTATATAAAA;RSEQ=ACCTAAAGCATTTCACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:205,23:0:2,0:22.1:1:30:1:1:0:60:75:1:0:0.1 0/1:119:2:2,0:108,9:0.0168:2,0:14.5:1:32:1:1:0:60:4:0.0168:0:1 -1 193104712 . G A 212 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCAGAAGCAAAGAAACCAC;RSEQ=AATTGAGGTAAAGAAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:815:134:45,89:268,413:0.1644:2,2:28.6:1:30.1:1:0.24362:1.28301:60:66:0.1632:0:1.1 0/0:525:0:0,0:219,306:0:2,0:26.5:1:30.1:1:1:0:60:74:1:0:0.1 -1 193104827 . G A 206 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.02745;LSEQ=CCTGAGGAGCTTTTTTTCTG;RSEQ=AAAAATTTTTGTGGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:104:3,101:0,2:0.9811:0,1:26.3:1:30.8:1:1:0:60:208:0.9811:0:1.1 1/0:55:32:0,32:0,23:0.5818:1,1:26:1:30.6:1:1:0:60:64:0.5818:0:1.1 -1 193105216 . A G 74 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCCGTGTTGGCCAGGCT;RSEQ=CAGAATTCTTTCTTTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:32.8:1:32:1:1:0:58.2:10:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 193111228 . TGA T 198 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=0.74272;SOR=0.90368;LSEQ=ATTTTACTCATTCATTGGAG;RSEQ=GAGAGAGAGAGAGAGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:84:7,77:78,224:0.2024:2,2:29.6:1:31.1:1:0.00033:3.81992:59.9:83:0.2015:0.012:0.3 0/1:193:36:3,33:51,95:0.1865:2,2:31.2:1:30.5:1:0.00108:5.86175:60:35:0.1832:0.0155:0.2 -1 193119588 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29639;SOR=0;LSEQ=CAGTGTGGCCTGATGTTTAA;RSEQ=GGTAAGGGTTGGCAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:40,257:0.01:2,2:25:1:24:1:0.35754:3.19:60:2:0.0068:0:2 0/0:179:0:0,0:26,153:0:2,0:21.1:1:30.3:1:1:0:60:178:1:0:0.1 -1 193119940 . G C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATTAAAATGTTATTATA;RSEQ=TGCCTGTCTCTTACCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17:1:30:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:5:0:30:1:1:0:60:4:1:0:2.5 -1 193119992 . A G 22 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGGTTAATAAATATTGA;RSEQ=TTCCCAGAATAGTATCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12:1:33.5:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:7:0:22:1:1:0:60:1:1:0:2.5 -1 193120667 . T C 38 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTGACAGATTTTAAGGCT;RSEQ=GCAATGTGTTAAAATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:23.3:1:24.3:1:1:0:60:2:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 193121496 . C CT 109 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05924;SOR=0.2376;LSEQ=AAAATCTTAACAATAAGCCT;RSEQ=TTTTTTTTCGTAGAAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1027:13:7,6:625,389:0.0127:2,2:16.4:1:29.6:1:0.57701:1.37668:60:26:0.0128:0.0049:0.3 0/0:659:2:1,1:392,265:0.003:2,2:24:1:29.5:1:1:1.47831:60:4:0.0031:0.0015:0.5 -1 193172859 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09552;SOR=Inf;LSEQ=GAGATATGAGATTTCTTTGG;RSEQ=ATAATTAAAGTGTTTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:335,73:0:2,0:21.3:1:30.1:1:1:0:60:101:1:0:0.1 0/1:183:2:1,1:144,37:0.0109:2,2:29.5:1:27.5:1:0.37309:3.85365:60:4:0.0112:0:1 -1 193173335 . GTGTATATATA G 67 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACACACACATATATATAC;RSEQ=TGTATATATATGTATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:30.6:1:29.2:1:1:0:55.2:10:0.625:0.125:2.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 193173356 . TG CA 74 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATATATATGTATATATA;RSEQ=TATATATACACGTATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:35.4:1:32.2:1:1:0:55.2:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 193181175 . A AT 105 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24003;SOR=0.33606;LSEQ=TTTTATGACACAGAGTTGTG;RSEQ=TTTTTTTTCTTTTTCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:820:11:7,4:530,279:0.0134:2,2:20.2:1:30.4:1:1:1.0854:60:22:0.0136:0.0024:0.5 0/0:440:2:2,0:281,157:0.0045:2,0:8.5:1:31:1:0.53996:0:60:4:0.0046:0.0023:1 -1 193181412 . T G 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00028;SOR=Inf;LSEQ=TCCACTGGCTTAAAATATTT;RSEQ=TTAGATCAAAAGTTAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:183,113:0:2,0:23.2:1:30.6:1:1:0:60:97.667:1:0:0.1 0/1:104:6:4,2:70,28:0.0577:2,2:28.5:1:32.7:1:1:1.24726:60:12:0.0583:0:1 -1 193202001 . C G 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01629;LSEQ=CAAGATTGCACCACTGCACT;RSEQ=TAGCCTGGGCAATAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:80:79:79,0:1,0:0.9875:0,1:24.2:1:32.4:1:1:0:60:38.5:0.9872:0:1.2 1/0:38:21:21,0:16,1:0.5526:1,1:22.7:1:30.2:1:0.44737:0:60:9.5:0.5278:0:1.4 -1 193202032 . CA C 151 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30331;SOR=1.41834;LSEQ=AATAAGAAAAAACTCTGTCT;RSEQ=AAAAAAAAAAATATTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:26:26,0:154,4:0.1398:1,1:24.3:1:32.3:1:1:0:60:52:0.1413:0.0161:0.3 0/1:96:18:16,2:67,5:0.1875:2,2:20.1:1:32.1:1:0.62359:1.66417:60:36:0.1875:0.0521:0.3 -1 193202297 . CTA C 100 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.78095;SOR=1.14498;LSEQ=CAAGACTGGTAAGATAGTCT;RSEQ=TATATATATCTTTTCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:986:9:3,6:297,681:0.0091:2,2:27.9:1:31.6:1:1:1.15:60:18:0.0092:0.001:0.1 0/1:479:5:1,4:161,313:0.0104:2,2:26.6:1:30.9:1:0.66672:2.05483:60:10:0.0105:0.0042:0 -1 193202953 . G A 85 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACACTTTTATTGAATTTAA;RSEQ=TGTCCTTTAACAAAATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1:0,2:14.6:1:30.3:1:1:0:60:14:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 193203035 . C T 104 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26154;SOR=0;LSEQ=AATTACCTTATTTCTTTAAC;RSEQ=GGGAGTAAAAGTTGAGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:9,1:13,0:0.4348:1,2:28.5:1:31.5:1:0.43478:0:60:20:0.4348:0:1.2 0/0:3:0:0,0:3,0:0:0,0:23.3:1:30:1:1:0:60:6:1:0:0.3 -1 193203268 . C T 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0;LSEQ=CTTAAACTTATGCCTCAAGA;RSEQ=TGGTAGGATAATTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:22:7,15:224,325:0.0383:2,2:18.1:1:30.4:1:0.50837:1.47596:59.8:44:0.0411:0:1 0/0:326:0:0,0:131,194:0:2,0:23.4:1:30:1:1:0:59.5:13.773:1:0:0.5 -1 193203305 . TCACACACACACACA T 191 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=23.000;MSILEN=2;SSF=0;SOR=0.13326;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:83:9,74:53,54:0.3168:2,2:28:1:30.1:1:0:7.98056:57.3:19.75:0.3251:0.1527:0.7 0/1:138:8:0,8:36,74:0.058:2,0:33.1:1:30.4:1:0.10418:0:56.9:16:0.0606:0.0072:0.8 -1 193203368 . T G 84 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18006;SOR=0;LSEQ=CACATATATATATTTAAAAT;RSEQ=TATATATTTATTTATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:0,6:1,75:0.0732:1,0:11.8:1:32.8:1:1:0:54.8:12:0.0759:0:2 0/0:33:0:0,0:0,33:0:1,0:27.5:1:30.3:1:1:0:57.8:66:1:0:0.8 -1 193203393 . TTAAT ATA 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54499;SOR=0;LSEQ=TATTTATTTATATATATAAT;RSEQ=TATAATATATATAATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:0,3:1,30:0.0882:1,0:15:1:29.8:1:1:0:46.7:6:0.0938:0:1 0/0:19:0:0,0:0,19:0:1,0:19.1:1:30.7:1:1:0:60:38:1:0:0.4 -1 193203397 . T TTATAATATATATAATTTATTATATATATATTATA 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=4.000;MSILEN=2;SSF=0.00059;SOR=0;LSEQ=TATTTATATATATAATTTAA;RSEQ=TATAATATATATAATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:14:1,13:0,16:0.4667:1,1:20.4:1:29.4:1:0.46667:0:57.1:28:0.5185:0.3333:0.5 0/0:18:0:0,0:0,18:0:1,0:16.9:1:30.5:1:1:0:60:36:1:0:0.4 -1 193203413 . ATACA T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.00593;SOR=Inf;LSEQ=TTAATTATAATATATATAAT;RSEQ=TATTATATATATAATATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,11:0:0,0:18.2:1:31.6:1:1:0:54.1:22:1:0:0.4 1/0:10:5:0,5:0,5:0.5:0,0:10.4:1:30.2:1:1:0:60:10:0.5:0.3:0.4 -1 193203471 . AAT A 31 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATTTAAAACACACACATA;RSEQ=ATATATATATATATTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:46.5:1:31.5:1:1:0:60:4:0.2222:0:0 0/0:1:0:0,0:0,1:0:0,0:15:0:32:0:1:0:60:2:1:0:0 -1 193203491 . A AAATTAT 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATATATATATATATTTA;RSEQ=AATTATAATTCTTCTCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:34.5:1:31.2:1:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 193205272 . T A 217 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02037;LSEQ=GGAAGGATTGATAAGACTCT;RSEQ=TCACATGAATGTTTATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:200:197:196,1:3,0:0.985:0,1:25.1:1:28.5:1:1:0:60:196:0.9849:0:1.2 1/0:102:58:58,0:43,1:0.5686:1,1:23.2:1:28.3:1:0.43137:0:60:57:0.5758:0:1.1 -1 193218808 . C CT 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.73105;SOR=0.60147;LSEQ=TGGAATAAAGAAATTTTTTT;RSEQ=TTTTTTTTTATTTTGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:8:8,0:324,51:0.0209:2,0:30.9:1:32.2:1:0.60432:0:60:16:0.0211:0.0026:0.3 0/1:158:2:1,1:135,20:0.0127:2,2:6:1:30:1:0.25037:6.61168:60:4:0.0128:0.0063:0.5 -1 193218843 . C G 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAGTAAAAATGATAACTTCT;RSEQ=TCCACCCTCTCTATAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:736:0:0,0:557,177:0:2,0:24.1:1:31.2:1:1:0:60:55.462:0.9986:0:0.1 0/1:379:30:25,5:244,104:0.0792:2,2:21.2:1:31.3:1:0.1451:2.13:60:29:0.0777:0:1 -1 193219691 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGTTTTCTAGAAAACAG;RSEQ=ATTTTATTCTGTTGATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:120,5:0.0157:1,2:14:1:28.5:1:0.09261:22.00022:60:4:0.0159:0:1 0/0:49:0:0,0:45,4:0:2,0:24.3:1:31.9:1:1:0:60:48:1:0:0 -1 195109285 . A G 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGGCAGTCTTACACTGCC;RSEQ=AAGCCATCAAAAAGGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17:1:28:1:1:0:50:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:37:1:28.5:1:1:0:60:4:1:0:0 -1 195110131 . G C 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTATCTTTACTCCACAATCC;RSEQ=AAATAGACTCTTTGGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:22:1:29.5:1:1:0:60:4:0.6667:0:1 1/1:1:1:1,0:0,0:1:0,0:28:0:32:0:1:0:60:2:1:0:1 -1 195112308 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAAAGAAAGAAAGAAAGA;RSEQ=AAAGAAAGGAAGGAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:46:0:32:0:1:0:60:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:6:0:32:0:1:1:60:4:0.6667:0:1 -1 197974705 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=CCACCAGAATCTAGGGAAGA;RSEQ=GCATGGAACAGATTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:0:2,0:35.1:1:32.1:1:1:0:60:54:1:0:0.2 0/1:22:2:1,1:12,8:0.0909:2,2:35.5:1:30:1:1:1.47192:60:4:0.0909:0:1 -1 198167238 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGATAGGTGGTGGGTGGG;RSEQ=AGGATTGGAACCTCCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:23,29:0.037:2,2:22:1:28:1:1:1.26:60:4:0.037:0:1 0/0:19:0:0,0:9,10:0:2,0:30.7:1:31.2:1:1:0:60:38:1:0:0 -1 198167287 . T C 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01067;SOR=0;LSEQ=GTGGGGGGATATGGATTTGG;RSEQ=CCTGGCTGGCCGGCATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:2,10:9,16:0.3243:2,2:21.9:1:30.3:1:0.27934:2.74057:60:11:0.3235:0:1 0/0:17:0:0,0:7,10:0:2,0:23.8:1:29.5:1:1:0:60:34:1:0:0.1 -1 199066099 . G T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=Inf;LSEQ=CCTCTTCACTGCTGAGAAAG;RSEQ=AGGACTCTGCCCCTTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:17:1:29.8:1:1:0:60:8:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:26.5:1:27:1:1:1:60:4:0.5:0:1 -1 199066210 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=GGCTTCTGAAATCAGAAAAC;RSEQ=CCTTTCACACTCTTATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:22.7:1:31:1:1:0:60:48:1:0:0.2 0/1:20:2:1,1:11,7:0.1:2,2:15.5:1:27:1:1:1.53525:60:4:0.1:0:1 -1 199416906 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=CCACAGAGACTGCAACCACC;RSEQ=CTCCCACTAGGGGCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:0.1667:2,2:24.5:1:29:1:1:1.4491:60:4:0.1667:0:1 0/0:6:0:0,0:2,4:0:2,0:22.8:1:31.3:1:1:0:60:12:1:0:0.2 -1 199417365 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGGTTGGGACACTGGG;RSEQ=CCTGGTGGCATGGGTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:41,40:0.0241:2,2:20:1:29:1:1:1.0247:60:4:0.0247:0:1.5 0/0:39:0:0,0:21,18:0:2,0:23:0:14:0:1:0:60:0:0:0:4 -1 199417387 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTGGCATGGGTTTACAA;RSEQ=TGGGATCTTCCAATCCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:43,45:0.0222:2,2:15:0:32:0:1:1.05:60:4:0.0227:0:1.5 0/0:42:0:0,0:21,21:0:2,0:26.2:1:31.3:1:1:0:60:84:1:0:0.3 -1 199417587 . A G 58 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCTTCTAGTCAATTTTGATG;RSEQ=GAGAACCTGGACACCTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:17:1:29.3:1:1:0:60:8:0.6667:0:1 1/1:1:1:0,1:0,0:1:0,0:1:0:29:0:1:0:60:2:1:0:1 -1 202065925 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11931;SOR=Inf;LSEQ=ATTGTCACCATCGTCATCGT;RSEQ=ATCAGCAGCAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:29,25:0:2,0:26.5:1:31.8:1:1:0:60:108:1:0:0.9 0/1:29:2:2,0:14,13:0.069:2,0:13.5:1:32:0:0.48768:0:60:4:0.069:0:1 -1 202065930 . G T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.00071;SOR=0.18503;LSEQ=CACCATCGTCATCGTCATCA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:40:20,20:8,5:0.7547:2,2:27.7:1:30.7:1:0.53554:1.58593:60:80:0.7547:0:1.2 0/1:28:10:4,6:11,7:0.3571:2,2:30.2:1:30.2:1:0.4328:2.28381:60:20:0.3571:0:1.3 -1 202065942 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0.81247;LSEQ=CGTCATCAGCAGCAGCAGCA;RSEQ=CAGCAACAGCAGCCCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:22,25:0.0408:2,2:26:1:28.5:1:1:1.13:60:4:0.0408:0:2 0/1:30:1:0,1:14,15:0.0333:2,0:44:0:30:0:1:0:60:2:0.0333:0:2 -1 202066564 . G A 64 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCTGAAGAGTGCATGGCGGC;RSEQ=GTGGTGGGGGTGGCGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:28.8:1:32.3:1:1:1:60:8:0.6667:0:1.3 0/0:2:0:0,0:1,1:0:2,0:16.5:1:28.5:1:1:0:60:4:1:0:0 -1 202188543 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09007;SOR=Inf;LSEQ=GAGAAAGCTGCTGGTCCACT;RSEQ=CAGGAGCCAAAGGATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:199,81:0:2,0:23.5:1:31.8:1:1:0:60:55:0.9964:0:0.9 0/1:121:2:2,0:83,36:0.0165:2,0:14.5:1:32:0:1:0:60:4:0.0167:0:2.5 -1 202188549 . G T 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00676;LSEQ=GCTGCTGGTCCACTGCAGGA;RSEQ=CCAAAGGATTATTTGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:118:86,32:120,56:0.4014:2,2:24.5:1:30.4:1:0.43652:1.25:60:58:0.3986:0:1.8 0/1:134:54:40,14:52,28:0.403:2,2:25:1:29.6:1:0.34294:1.53:60:53:0.4015:0:1.9 -1 202188616 . G T 254 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00744;SOR=1.63773;LSEQ=ATGCCTAATTAAGAGAACAG;RSEQ=GAGCGCTGTGAGCAACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:539:404:219,185:71,64:0.7495:2,2:25:1:29.4:1:0.76548:1.07:60:49.5:0.7486:0:1.7 1/1:307:255:145,110:33,19:0.8306:2,2:24.6:1:29.4:1:0.44189:1.31644:60:254:0.8301:0:1.6 -1 202188641 . T C 247 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.94543;SOR=0.98475;LSEQ=GCTGTGAGCAACAGCCTTCA;RSEQ=TGATTGGGTGCCGGCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:229:113,116:184,188:0.381:2,2:25.2:1:31.6:1:1:1.0047:60:75.333:0.3831:0:1.9 0/1:363:137:68,69:118,107:0.3774:2,2:24.7:1:31.3:1:0.66471:1.11867:60:136:0.3788:0:1.9 -1 202188719 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28105;SOR=3.73937;LSEQ=ATTGTAGCAGCTGGGGGAGA;RSEQ=ATTGACACTAGGCAGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:1:1,0:95,219:0.0032:2,0:1:0:25:0:0.30476:0:60:2:0.0032:0:2 0/1:170:2:1,1:52,116:0.0118:2,2:20:1:27.5:1:0.5276:2.22:60:4:0.012:0:1 -1 202188932 . A G 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATTCTATACTAATAATT;RSEQ=TAATTCAGTTAGATGAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:1,3:0.5556:2,0:28.8:1:31.6:1:0.44444:0:60:10:0.5556:0:1 0/0:1:0:0,0:0,1:0:0,0:44:0:28:0:1:0:60:2:1:0:0 -1 202189472 . A G 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCCTGCCTCAGCCTCTC;RSEQ=AGTAACTGGGATTACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:27:1:1:0:60:4:1:0:1 -1 203027354 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAGGAGGAGGGAGAGCACG;RSEQ=GAGGAGGAGGTTGGGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 203054310 . G A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.1;SOR=0;LSEQ=TTTTAGGCTCTGACTCAGGC;RSEQ=CTGGGATTAATCCTCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:13:1:30.7:1:1:0:60:6:1:0:1 0/0:2:0:0,0:1,1:0:2,0:23:1:30:1:1:0:60:4:1:0:0 -1 203054523 . A T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CGACCCTGTCTGGCACCTGC;RSEQ=CCAACCCTCTGAGCCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:1:0,2:20.9:1:29.7:1:1:0:60:11:1:0:1.3 1/1:6:5:4,1:1,0:0.8333:0,2:16.4:1:32.4:1:1:0:60:10:0.8333:0:1.2 -1 203054782 . G A 37 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04416;SOR=Inf;LSEQ=GCAGGGTGCTTCTCTTCAGG;RSEQ=CCTCGAAGGCCTCATTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:44,95:0:2,0:24.9:1:31.7:1:1:0:60:138:1:0:0 0/1:77:3:2,1:31,43:0.039:2,2:26.7:1:23.7:1:0.57323:2.74:60:2:0.0267:0:1.3 -1 203054785 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13555;SOR=Inf;LSEQ=GGGTGCTTCTCTTCAGGGCC;RSEQ=CGAAGGCCTCATTCACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:41,92:0:2,0:24.9:1:30.2:1:1:0:60:266:1:0:0 0/1:78:2:1,1:31,45:0.0256:2,2:22.5:1:27:1:1:1.44:60:4:0.0256:0:1 -1 203224948 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49674;SOR=0;LSEQ=GATTATCACTTTAAGGTGGA;RSEQ=AATGATGAAAATGAGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:40,32:0.027:2,2:47.5:1:32:1:1:1.2462:60:4:0.0274:0:1 0/0:71:0:0,0:35,36:0:2,0:22.8:1:28.8:1:1:0:58.8:34.5:1:0:0.2 -1 203224985 . G T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0614;SOR=0;LSEQ=ACCAGTTATCTTTAATAACG;RSEQ=CCAGTTTAGGGGCTGCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:3,2:36,28:0.0725:2,2:21.8:1:26:1:1:1.16:60:4:0.0597:0:1 0/0:59:0:0,0:26,33:0:2,0:27.3:1:31:1:1:0:59.9:118:1:0:0.1 -1 203225148 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16402;SOR=Inf;LSEQ=CACACTACCAGTGGTCTTAC;RSEQ=GCTGAAGTGTGGTTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:163,111:0:2,0:26.3:1:30:1:1:0:60:67.5:1:0:0.1 0/1:187:2:1,1:114,71:0.0107:2,2:19.5:1:28.5:1:1:1.60136:60:4:0.0109:0:1 -1 203225183 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2616;SOR=0;LSEQ=CAGGGCCAGTGCATATTAGT;RSEQ=GACAGCACTTAGGACGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:2,1:134,164:0.01:2,2:24:1:23.3:1:0.59109:2.44:60:2:0.0068:0:1.3 0/0:231:0:0,0:124,107:0:2,0:28.7:1:30.7:1:1:0:59.8:114.5:1:0:0.2 -1 203225204 . T C 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2548;SOR=0;LSEQ=GACAGCACTTAGGACGAAGA;RSEQ=GCAGAGCCAGAAGATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:101,157:0.0115:2,2:29:1:23.3:1:1:1.28541:60:2:0.0078:0:1.3 0/0:217:0:0,0:100,117:0:2,0:25.5:1:29.5:1:1:0:60:107.5:1:0:0.2 -1 203225245 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50705;SOR=0;LSEQ=GGAGGAAGATGTGAAACTCT;RSEQ=AAGTATATCTGGAAAGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:78,120:0.01:2,2:22:1:30:1:1:1.54:60:4:0.0101:0:1 0/0:154:0:0,0:66,87:0:2,0:23.3:1:28.2:1:1:0:59.9:37.25:1:0:0.1 -1 203225284 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50411;SOR=0;LSEQ=GTCTGCCCCTGGAGGTGGTA;RSEQ=CAAGTTTCCAGAGGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:64,93:0.0126:2,2:24:1:29.5:1:1:1.45:60:4:0.0129:0:1 0/0:128:0:0,0:51,77:0:2,0:25.5:1:31.8:1:1:0:59.7:41.667:1:0:0.2 -1 203225306 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18927;SOR=Inf;LSEQ=AAGTTTCCAGAGGAAAAAGT;RSEQ=AAACTTGCTGCTGATGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:60,77:0:2,0:24.5:1:29.4:1:1:0:60:274:1:0:0.2 0/1:106:2:1,1:49,54:0.0189:2,2:28.5:1:31:0:1:1.10:60:4:0.0189:0:1 -1 203225322 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50522;SOR=0;LSEQ=AAGTAAAACTTGCTGCTGAT;RSEQ=CAAATGATGATGAAGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:54,68:0.0161:2,2:20.5:1:30:1:1:1.26:60:4:0.0165:0:1 0/0:97:0:0,0:44,53:0:2,0:22.2:1:31.6:1:1:0:60:96:1:0:0.1 -1 203225459 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53142;SOR=0;LSEQ=CAGAAGTCAAATCAGAATGG;RSEQ=AAGGACTCAAAACCGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:71,78:0.0132:2,2:22.5:1:29:1:1:1.10:60:4:0.0133:0:1 0/0:89:0:0,0:43,46:0:2,0:29.1:1:29.5:1:1:0:59.7:88:1:0:0.4 -1 203225539 . A C 150 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=31.000;MSILEN=1;SSF=1;SOR=0.90794;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AACCAGAAAAAAACTCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:25:1,24:6,3:0.6098:2,1:23.2:1:32.5:1:4e-04:39.05399:52.3:24:0.6857:0:1.3 1/0:29:17:1,16:11,1:0.5862:2,1:25.7:1:31.5:1:0:109.62897:56.8:34:0.6071:0:1.1 -1 203225545 . G A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.38033;SOR=2.39155;LSEQ=AAAAAAAAAAAAAAAAACCA;RSEQ=AAAAAAACTCCTAAAACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:2,0:4,30:0.0556:2,0:27.5:1:20.5:1:0.02381:0:50:1:0.0294:0:4 0/1:24:3:3,0:4,17:0.125:2,0:7.3:1:28.3:1:0.01729:0:60:6:0.1364:0:3.3 -1 204150630 . A T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07437;SOR=Inf;LSEQ=TGGCATGGTGCAGGCTGAGG;RSEQ=ACCTGGTCAGATATCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:49,43:0:2,0:29.4:1:29.6:1:1:0:60:29.667:1:0:0 0/1:35:2:1,1:17,16:0.0571:2,2:28:1:25.5:1:1:1.06069:60:4:0.0571:0:1 -1 204150667 . G T 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02365;SOR=Inf;LSEQ=AGGGTGATCAGATATTGAGG;RSEQ=TGGGGATTATTTGCTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:30,42:0:2,0:24.8:1:31.8:1:1:0:60:144:1:0:0 0/1:30:3:1,2:10,17:0.1:2,2:25:1:27:1:1:1.17019:60:6:0.1:0:1 -1 204314471 . C G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTTCCTAACAAGGAGGC;RSEQ=AGGACAGCTTGACCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38:0:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204315882 . C CT 25 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGATATTTCTCCCATTTG;RSEQ=TTTTTTTTTTTTTAACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:14:1:25.5:1:1:0:60:4:1:0.3333:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204316065 . G T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48385;SOR=0.42849;LSEQ=CTGATCATTTTCCTTCACAC;RSEQ=TTTCAGGAAGCTATCTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:10:7,3:33,3:0.2174:2,2:25.6:1:29.9:1:0.10659:4.50796:51:9:0.2045:0:1.4 0/1:19:2:1,1:14,3:0.1053:2,2:16:1:29:1:0.38596:4.1833:43:4:0.1053:0:1 -1 204316082 . C T 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00032;SOR=10.81246;LSEQ=CACGTTTCAGGAAGCTATCT;RSEQ=GGCTCTTAGAGTGCTTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:27:23,4:25,5:0.4737:2,2:25.3:1:29.4:1:1:1.15:40.3:12.5:0.463:0:1.2 1/1:22:20:18,2:1,1:0.9091:2,2:22.5:1:30.4:1:0.25974:7.55:44.2:19:0.9048:0:1.1 -1 204316213 . G A 139 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=TAGACTCTTCCAGTTTTGCC;RSEQ=TGGTAACGCGTGTGGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:25:11,14:92,123:0.1042:2,2:23.8:1:30:1:1:1.05:45.4:24:0.1004:0:1.1 0/0:104:0:0,0:45,59:0:2,0:26.6:1:30.4:1:1:0:59.6:103:1:0:0.1 -1 204316222 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09197;SOR=Inf;LSEQ=CCAGTTTTGCCGTGGTAACG;RSEQ=GTGTGGGGCATTCCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:95,129:0:2,0:24.3:1:30.7:1:1:0:58.6:111:1:0:0.2 0/1:98:2:1,1:38,58:0.0204:2,2:30.5:1:31.5:1:1:1.52:60:4:0.0206:0:1 -1 204316277 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGATGTCTACAATATCA;RSEQ=CTTTCTTATAGACTCGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:33,75:0.0182:2,2:8:0:31.5:1:0.5246:2.25:60:4:0.0189:0:1.5 0/0:35:0:0,0:10,25:0:2,0:24.6:1:30.8:1:1:0:55.9:34:1:0:0.1 -1 204316350 . A G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.00097;SOR=Inf;LSEQ=AAAAGGCCTAGAGAACATAC;RSEQ=TCGGGTGCCTCTCCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:13,38:0:2,0:25.2:1:30.7:1:1:0:59.9:50:1:0:0.1 0/1:26:6:2,4:9,11:0.2308:2,2:13:1:32.3:1:1:1.6063:57.8:12:0.2308:0:1.2 -1 204316427 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19212;SOR=Inf;LSEQ=TGGCAGTTATGGCCGAAAGG;RSEQ=TCCCATTTGCTTTTGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:3,13:0:2,0:19.4:1:32.3:1:1:0:60:32:1:0:0.1 0/1:13:2:1,1:5,6:0.1538:2,2:25:1:28.5:1:1:1.18:60:4:0.1538:0:1 -1 204316458 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=TTTTGAAAGAAGAGAAATAT;RSEQ=GCTCTGTTCTGCCTGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,6:0.2:2,2:25:1:30:1:1:2.65:60:4:0.2:0:1 0/0:11:0:0,0:2,9:0:2,0:16.3:1:30.4:1:1:0:60:22:1:0:0.1 -1 204317602 . T G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGAATGGTACCAGCTAG;RSEQ=GAACCCCACACAAACCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:31:1:1:0:60:4:1:0:1 -1 204494283 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATCTAGAGAGTGCTCTAC;RSEQ=TGATAACCATTGGGGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:12.5:1:32:0:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204494436 . C T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8367;LSEQ=TACTCTTAATTAAATCAGAA;RSEQ=TAGAAAGTAGTCAGAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:18:18,0:20,0:0.4737:1,1:26.5:1:32.1:1:1:0:60:36:0.4865:0:1 0/1:7:3:3,0:4,0:0.4286:0,0:14:1:31.3:1:1:0:60:6:0.4286:0:1 -1 204494576 . T C 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATAGGGAATTTTCTGCA;RSEQ=TAGAATAGATGTTATAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:260,55:0:2,0:24.7:1:30.4:1:1:0:60:38.375:1:0:0.1 0/1:193:14:11,3:145,34:0.0725:2,2:15.6:1:31.2:1:0.73422:1.16219:60:28:0.0737:0:1 -1 204494594 . A AT 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.99429;LSEQ=CATTAGAATAGATGTTATAA;RSEQ=TTTTTTTTTCTATTTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:8:6,2:353,110:0.0169:2,2:24.1:1:30.4:1:1:1.06955:60:16:0.0173:0.0042:0.3 0/1:356:6:5,1:255,95:0.0169:2,2:29.2:1:30.5:1:1:1.86:60:12:0.0171:0:0 -1 204494738 . G A 126 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=27.42062;LSEQ=CAATCAGGTAAATCATTTTC;RSEQ=GTATTTCTAGTTTTTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:1:1,0:252,523:0.0013:2,0:1:0:28:0:0.32603:0:60:2:0.0014:0:1 0/1:588:20:7,13:209,357:0.034:2,2:23.2:1:29.2:1:1:1.08709:60:19:0.0349:0:1.4 -1 204495253 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40523;SOR=0.25678;LSEQ=AATTACCTGGATATGGTGGC;RSEQ=TGCACCTGTAGTCCCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:13,0:1,0:0.9286:0,1:19.2:1:31.2:1:1:0:60:26:0.9286:0:1 1/0:4:3:3,0:1,0:0.75:0,0:7:1:31:1:1:0:60:6:0.75:0:1 -1 204495379 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCGACAGAGCAAGACCTT;RSEQ=CCTCAAAAAACAAAAGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:2,0:87,3:0.0217:1,0:37.5:1:30.5:1:1:0:60:4:0.0217:0:1 0/0:45:0:0,0:43,2:0:1,0:23.4:1:31.5:1:1:0:60:44:1:0:0.1 -1 204495586 . AT A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01126;SOR=Inf;LSEQ=AGCCATCAAATAAAATTCTC;RSEQ=TTTTTTTGTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:111,270:0:2,0:22:1:29.8:1:1:0:59.4:28.308:1:0:0.7 0/1:346:6:3,3:106,233:0.0173:2,2:19.2:1:29.7:1:0.38496:2.19:60:12:0.018:0.0029:0.2 -1 204495610 . G T 86 LongAT STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00176;SOR=0;LSEQ=TTTTTGTTTTTTTTTTTTTT;RSEQ=AGATGGAGTCTCCCTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:10:5,5:33,158:0.0495:2,2:6.2:1:26.1:1:0.02287:4.74:60:4:0.0457:0:1.4 0/0:195:0:0,0:39,150:0:2,0:19:1:29.1:1:1:0:58.4:8.45:0.9826:0:1.1 -1 204500257 . G A 51 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGAGTGGGTGGGATTTAGA;RSEQ=TGTTAGAGGTCAAGAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:28.3:1:32.3:1:1:0:60:6:0.6:0:1 0/0:1:0:0,0:0,1:0:0,0:29:0:33:0:1:0:60:2:1:0:0 -1 204500961 . C CA 43 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATAGCAAAACTCCGTCTC;RSEQ=AAAAAAAAAAGACTCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:8,1:0.25:2,2:8:1:27.2:1:0.45455:3.4638:60:6:0.25:0.1667:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204501383 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14226;LSEQ=CTGCTACTACAGGTATGTCA;RSEQ=ATCATATTTCTTCAGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:702:347:132,215:136,217:0.4943:2,2:25.6:1:29:1:0.93804:1.02078:60:56.833:0.4921:0:1.1 0/1:484:59:21,38:161,262:0.1219:2,2:22.4:1:28.1:1:0.77542:1.11175:60:118:0.1234:0:1.1 -1 204506107 . C T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGGGGAAAAATCCAGATTT;RSEQ=AAGATCCCATAACCCTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:14.3:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204506174 . CT C 55 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTAAAAAGCCATACACT;RSEQ=TTTCCTTTTGTTTGTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:23:1:27.8:1:1:0:60:3:0.375:0:0.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204506887 . CTG C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTTTGGGTTTGTGTGTAC;RSEQ=TGTGTGTGTGTTTGAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:1,10:0.1538:2,0:28:1:33.5:1:1:0:60:4:0.1538:0:0 0/0:3:0:0,0:2,1:0:2,0:20.3:1:32.3:1:1:0:60:6:1:0:0.3 -1 204507207 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01759;SOR=Inf;LSEQ=CTTTATTTGATGACTGTTGT;RSEQ=AACTTGAGTTCTCTTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:128,0:0:1,0:25.4:1:32.7:1:1:0:60:256:1:0:0.1 0/1:46:3:3,0:42,1:0.0652:1,0:14.7:1:29:1:1:0:60:6:0.0652:0:1 -1 204508159 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCGCACGCCACCACACCC;RSEQ=GCTAATTTTGTATTTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:29:1:1:0:59.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204511602 . C A 80 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCATTTAGAAATTCTTTTAG;RSEQ=ACAAGGTCATTGTTCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:9:1:31.3:1:1:0:60:12:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204512100 . T C 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=0.17641;LSEQ=TCACATTTGAAGGGAAGTGG;RSEQ=TTTTTTTCTTTTGAAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:329:318:64,254:2,9:0.9666:2,2:24.6:1:32:1:1:1.13:60:44.429:0.9658:0:1.1 1/1:219:183:46,137:7,29:0.8356:2,2:21.6:1:31.7:1:0.53009:1.39:60:44.75:0.8326:0:1.1 -1 204512139 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09688;SOR=Inf;LSEQ=GTAACATTCTTGGTTACTCT;RSEQ=GACCACACATTATATTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:11,145:0:2,0:23.5:1:30.2:1:1:0:60:77:1:0:1.1 0/1:71:2:1,1:1,68:0.0282:1,2:22:1:27.5:1:0.05594:48.43:60:4:0.0286:0:2 -1 204512195 . A T 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05354;SOR=0.10696;LSEQ=CTCCTATGGCGTTAAATACC;RSEQ=TCTGTATGCATGTGATACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:55:1,54:0,1:0.9821:0,1:23:1:30:1:1:0:60:54:0.9818:0:1.4 1/1:20:17:0,17:0,3:0.85:0,1:22.3:1:29.7:1:1:0:60:34:0.85:0:1.3 -1 204513256 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCATATTTCTTTAATAA;RSEQ=CATCCTTGACCATTTTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204513402 . G A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=CTTACCTTTTAAACTCTTCA;RSEQ=TACTGTTTCTTAGGTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:18.3:1:31:0:1:0:60:6:0.3:0:1 1/1:2:2:2,0:0,0:1:0,0:30.5:1:32:0:1:0:60:4:1:0:1 -1 204513647 . G GT 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.79129;SOR=1.13125;LSEQ=GAATACAGAAACTCATGTTT;RSEQ=TTTTTTTTCTGTTAGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:8:6,2:282,156:0.0179:2,2:28.5:1:30.8:1:0.71789:1.66:60:16:0.0181:0:0 0/1:297:6:4,2:170,120:0.0202:2,2:37.7:1:29.8:1:1:1.41:60:12:0.0203:0:0.2 -1 204515299 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCACGTTTAACAATTTG;RSEQ=AGCTTTTCTACTCTGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204515863 . C T 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16188;LSEQ=GCAGTTGTCTTTTTTGCTTT;RSEQ=AGTTAATTAGCCTCATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:541:520:376,144:14,5:0.9612:2,2:23.3:1:29.5:1:1:1.0722:60:103:0.9626:0:1.1 1/1:360:288:204,84:51,21:0.8:2,2:24.3:1:29.1:1:1:1:60:143:0.7989:0:1.1 -1 204516025 . A G 293 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10523;LSEQ=GGTATGAATCTTTAGCAAGA;RSEQ=CTATTTTGCACCAGCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:567:553:168,385:1,13:0.9753:1,2:24.4:1:32.2:1:0.07563:5.66:60:137.25:0.9751:0:1.1 1/1:448:361:113,248:21,66:0.8058:2,2:25.7:1:31.8:1:0.24017:1.43:60:89.25:0.8041:0:1.1 -1 204518457 . A C 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGCTCCTGTCGTTAGACCT;RSEQ=AAGATGCGTATATAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1206:0:0,0:521,685:0:2,0:24.5:1:29.3:1:1:0:60:69.941:1:0:0.1 0/1:792:40:19,21:332,420:0.0505:2,2:25.9:1:31.1:1:0.74475:1.14:60:39:0.0499:0:1.1 -1 204518820 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1331;SOR=Inf;LSEQ=TTATAGCATAATGGTAGTAC;RSEQ=AACATAAAAATGCATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:52,264:0:2,0:25.1:1:31:1:1:0:60:78:1:0:0.7 0/1:182:2:1,1:41,138:0.011:2,2:25.5:1:27.5:1:0.41123:3.34:60:4:0.011:0:1.5 -1 204518824 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12545;SOR=Inf;LSEQ=AGCATAATGGTAGTACGAAC;RSEQ=TAAAAATGCATTTATTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:46,243:0:2,0:25.7:1:31.2:1:1:0:60:578:1:0:0.8 0/1:159:2:1,1:32,125:0.0126:2,2:30:1:29.5:1:0.37306:3.86:60:4:0.0127:0:1.5 -1 204518842 . C A 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.12209;LSEQ=ACATAAAAATGCATTTATTC;RSEQ=GTTCACTTACCACATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:233:228:30,198:0,5:0.9785:0,2:22.6:1:31.1:1:1:0:60:75:0.9783:0:1.1 1/1:111:94:18,76:3,14:0.8468:2,2:20.7:1:30.4:1:1:1.10:60:188:0.8468:0:1.1 -1 204519187 . C G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAGCAATAGAATGTTT;RSEQ=TGTCACCCCAAAACACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 204700134 . A G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGAGGAAGAGAGCCCC;RSEQ=GGATGAAGCCAAATGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:0:31:1:1:0:60:4:1:0:1.5 -1 204851121 . T C 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5068;SOR=0;LSEQ=GCCAGAATCCCCCTTACTCC;RSEQ=GATGTTTCCTCTTAGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:13,14:0.069:2,2:28:0:31.5:1:1:1.07:60:4:0.069:0:1.5 0/0:20:0:0,0:10,10:0:2,0:30.3:1:29.3:1:1:0:60:9:1:0:0.2 -1 206646274 . G T 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGAGGGGCTTCAAGGGAAC;RSEQ=TGGGGAGCCAGGACAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:0.4286:2,0:16.7:1:32.3:1:1:0:60:6:0.4286:0:1 1/1:1:1:1,0:0,0:1:0,0:15:0:32:0:1:0:60:2:1:0:2 -1 206646311 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=GCAGCAGGTGGAACAGGTGC;RSEQ=GGCTGTGGGCTGAGGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:0.2222:2,0:8.5:1:32:0:1:0:60:4:0.2222:0:1 1/0:3:2:2,0:1,0:0.6667:0,0:29:1:31.5:1:1:0:60:4:0.6667:0:1.5 -1 206646427 . C A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=4.31797;LSEQ=CTCCCTTGCTTGTGGAATGG;RSEQ=CACATGGAGCCCTTCTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:24:24,0:69,1:0.2553:1,1:27.6:1:29.3:1:1:0:60:23:0.25:0:1.1 1/0:35:21:19,2:14,0:0.6:1,2:24.1:1:28.3:1:0.50588:0:60:20:0.5882:0:1 -1 206646493 . T C 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03386;SOR=Inf;LSEQ=CAGGCCACCAGCGGCCACCC;RSEQ=GTGCCAGGAATGGAATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:232,21:0:2,0:21.5:1:31.3:1:1:0:60:62.25:1:0:0.1 0/1:122:3:2,1:98,21:0.0246:2,2:18:1:25.3:1:0.45231:2.31302:57.7:2:0.0168:0:3 -1 206646723 . G A 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01987;SOR=Inf;LSEQ=CCCTCATGCCTCAGAAGCTG;RSEQ=CCCAGTCAGCCCCCAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:0:0,0:141,447:0:2,0:22.9:1:31.6:1:1:0:60:83:1:0:0.1 0/1:355:4:1,3:91,259:0.0113:2,2:37.3:1:25.8:1:1:1.05388:60:3:0.0085:0:1.3 -1 206646832 . G A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02852;SOR=Inf;LSEQ=GGCATAGGGAGCTGAAAACG;RSEQ=CTCCTTGAGAGGATGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:2,88:0:1,0:24.2:1:31.9:1:1:0:60:44:1:0:0.1 0/1:19:2:1,1:1,16:0.1053:1,2:31.5:1:28.5:1:0.20468:11.66:60:4:0.1053:0:1 -1 206647450 . A G 122 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24901;SOR=0.21587;LSEQ=CAACAAGCCATCCCCTGCAG;RSEQ=AGATCAGAGTGTCAGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:15:15,0:6,0:0.7143:0,1:21.5:1:31.4:1:1:0:60:30:0.7143:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:21:0:33:0:1:0:60:2:0.3333:0:2 -1 206647613 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.14126;SOR=Inf;LSEQ=GGAGAGGGTGGCTGCTCCCC;RSEQ=GTGGGAGTGGGACATGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:245,78:0:2,0:23.3:1:30.8:1:1:0:60:106.667:1:0:0.1 0/1:195:2:1,1:146,47:0.0103:2,2:30.5:1:29.5:1:0.43267:3.08415:60:4:0.0103:0:1 -1 206647742 . A G 316 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04335;LSEQ=CTGCGGCCCCGCGAGGTGCA;RSEQ=GTGAGGGAGTTTGAGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1091:1089:591,498:1,0:0.9982:0,2:23.7:1:31.4:1:1:0:60:82.769:0.9981:0:1.5 1/1:688:660:342,318:15,13:0.9593:2,2:24.6:1:30.8:1:1:1.0728:60:219:0.9591:0:1.7 -1 206647787 . T C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.0309;LSEQ=AAGCTGAACCACCAGAACAT;RSEQ=GTCAAGCTCTTTGCGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1045:577:241,336:203,262:0.5522:2,2:27.4:1:30.3:1:0.57072:1.08015:60:63.111:0.5536:0:1.8 1/1:681:567:243,324:53,60:0.8326:2,2:26.2:1:30:1:0.46739:1.17749:60:50.545:0.8336:0:1.7 -1 206648037 . C G 68 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03294;SOR=6.78039;LSEQ=CAGAGGGCTTCCTGGAATAA;RSEQ=TGACTTTGGATTCCAGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:2,0:62,11:0.0267:2,0:18:1:34:0:1:0:60:4:0.0267:0:1 0/1:25:4:4,0:18,2:0.16:2,0:27.5:1:34:0:1:0:60:8:0.16:0:1 -1 206648147 . T G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11969;LSEQ=GCTCCAGGCTGAGCCACTTC;RSEQ=TCCTGGTGGGTGGGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:119:89,30:214,73:0.2924:2,2:24.8:1:30.3:1:1:1.01:60:118:0.2935:0:1.1 0/1:234:11:8,3:157,66:0.047:2,2:27.8:1:29.8:1:1:1.12:60:10:0.0439:0:1.2 -1 206648378 . G A 259 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.89407;SOR=0.97777;LSEQ=GCCTCCACCCTCAGACCAGC;RSEQ=GCAGGCCTGGGACAGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:652:354:100,254:77,219:0.5429:2,2:23.8:1:30.6:1:0.53691:1.12:60:117:0.5476:0:1.1 1/0:348:187:69,118:50,111:0.5374:2,2:24.6:1:30.2:1:0.25957:1.30:60:61.333:0.5364:0:1.1 -1 206648769 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATGAGGAGTTGTTTAAT;RSEQ=AGTATGGTTTCAAGTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:35.5:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 206649372 . T C 96 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=4e-05;SOR=24.9836;LSEQ=TGCCCCCTAAGCCCCATGCA;RSEQ=GTCTCTGTCCTTCTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:2,0:53,1:0.0357:1,0:20.5:1:34:0:1:0:60:4:0.037:0:1 1/0:16:8:8,0:8,0:0.5:0,0:20.6:1:32:1:1:0:60:16:0.5333:0:1.1 -1 206649411 . C T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00756;SOR=Inf;LSEQ=GTCCCATGGCTCTGTCAGCC;RSEQ=ATGGGAACTCCTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:89,3:0:1,0:23.7:1:30.9:1:1:0:60:45:1:0:0.1 0/1:40:4:4,0:36,0:0.1:1,0:20.3:1:32.3:1:1:0:60:8:0.1026:0:1.3 -1 206649528 . C T 145 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.5938;LSEQ=CCCCGTCTGTCCCCAGTGGC;RSEQ=GGCATGAACCACCTGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:4:1,3:373,254:0.0063:2,2:17.3:1:26.3:1:0.30958:4.39551:60:3:0.0048:0:1.5 0/1:450:26:15,11:254,170:0.0578:2,2:22.3:1:31:1:0.83901:1.09546:60:52:0.0588:0:1 -1 206649720 . C A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83984;LSEQ=TACCTGGTGGGTGAGCTGCT;RSEQ=GAGACCCGCTGCCCTATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:5:4,1:160,327:0.0102:2,2:14:1:26.8:1:0.04443:8.14:60:10:0.0104:0:1.4 0/0:351:3:3,0:135,212:0.0085:2,0:1:0:23:1:0.06049:0:60:6:0.0086:0:1 -1 206649952 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.2875;SOR=1.70031;LSEQ=CACCTGCAGGCGGTGAAAGG;RSEQ=GGTCTGACAGGTCTCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:10:10,0:196,23:0.0437:2,0:22.6:1:30.9:1:0.60394:0:60:20:0.045:0:1.2 0/1:97:7:7,0:81,9:0.0722:2,0:30.3:1:26.6:1:1:0:60:6:0.0667:0:1 -1 206649975 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10286;SOR=Inf;LSEQ=TCTGACAGGTCTCAGGCCCT;RSEQ=GCCAGCCCTCCGGCTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:265,58:0:2,0:25.2:1:30.1:1:1:0:60:52.833:1:0:0.2 0/1:153:2:1,1:129,22:0.0131:2,2:26.5:1:29.5:1:0.2789:5.75698:60:4:0.0132:0:1.5 -1 206650065 . A G 256 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGCTTCGAAAGCCCCAGCA;RSEQ=AAAGCGTTCGGGGTGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1088:277:161,116:447,364:0.2546:2,2:25.7:1:31.6:1:0.40086:1.13:60:91.333:0.2537:0:1.1 0/0:817:0:0,0:422,395:0:2,0:25.1:1:29.7:1:1:0:60:101.125:1:0:0.2 -1 206650245 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07888;SOR=Inf;LSEQ=CCCTGGCCCTTCCCCCACCG;RSEQ=TCCTTGCTGTGTCTTCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:13,188:0:2,0:24:1:31.7:1:1:0:60:32.5:1:0:0.1 0/1:79:2:1,1:7,69:0.0253:2,2:17.5:1:27.5:1:0.1958:9.29:60:4:0.026:0:1 -1 206650852 . C CA 147 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGGCTGAGGGAAGTGTAG;RSEQ=GGGGGGAGAGGCAGTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:28:25,3:12,0:0.7:0,2:26.8:1:30.7:1:0.54089:0:59.8:56:0.7:0.2:0.4 1/1:1:1:1,0:0,0:1:0,0:48:0:29:0:1:0:60:2:1:0:0 -1 206651107 . G A 249 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=239.68388;LSEQ=CGCAGGTACCGGATCACCAC;RSEQ=GAGAAGCCGGCTGGGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1481:3:2,1:790,686:0.002:2,2:26:1:32.3:1:1:1.74:60:6:0.0021:0:1 0/1:958:314:155,159:349,294:0.3278:2,2:26.2:1:30.1:1:0.16794:1.21745:60:43.857:0.3266:0:1.1 -1 206651350 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCCCATCTGGTTGCTGGAA;RSEQ=GAGTTCTTCCAGCTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:37,87:0:2,0:25.3:1:30.3:1:1:0:60:30:1:0:0.2 0/1:37:10:5,5:6,21:0.2703:2,2:22.7:1:30.4:1:0.12494:3.37:60:20:0.2703:0:1 -1 206651351 . G A 85 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01979;SOR=3.83062;LSEQ=TCCCATCTGGTTGCTGGAAC;RSEQ=AGTTCTTCCAGCTCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:7:4,3:37,83:0.0551:2,2:22.6:1:28.9:1:0.21135:2.96:60:14:0.056:0:1.1 0/1:38:7:0,7:12,19:0.1842:2,0:31.6:1:30.6:1:0.07448:0:60:14:0.1892:0:1 -1 206651439 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12155;SOR=Inf;LSEQ=TCTCTTAGAACGCTCCTATT;RSEQ=CCTGCTTAAGGAGGATAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:183,44:0:2,0:22.8:1:32.1:1:1:0:60:55.75:1:0:0.1 0/1:122:2:1,1:103,17:0.0164:2,2:22:1:28.5:1:0.27435:5.91666:60:4:0.0167:0:1 -1 206651467 . C T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.40998;SOR=1.4626;LSEQ=AAGGAGGATAGGTCTGGGCC;RSEQ=CCACCCCTGACAGTCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:15:12,3:277,45:0.0445:2,2:27.4:1:31.3:1:0.45717:1.53663:60:30:0.0456:0:1.1 0/1:188:12:10,2:149,27:0.0638:2,2:29.9:1:31.3:1:1:1.10313:60:24:0.0656:0:1.1 -1 206652159 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00919;SOR=Inf;LSEQ=ATGACAGAGAAAACCACCCC;RSEQ=GTCCCTCCCTCTGCAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:191,9:0:1,0:24.7:1:30.6:1:1:0:60:24:1:0:0.2 0/1:54:3:2,1:47,4:0.0556:2,2:25:1:30:1:0.25722:5.53743:60:6:0.0556:0:1.3 -1 206652189 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0865;SOR=Inf;LSEQ=TCTGCAAAACAGAGCCCTGT;RSEQ=TATGGGCAACGCTTAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:282,24:0:2,0:24.2:1:31.2:1:1:0:60:42.714:1:0:0.2 0/1:128:2:1,1:114,11:0.0156:2,2:34:1:30.5:1:0.18073:9.96588:60:4:0.0156:0:1 -1 206652517 . AT A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.29786;SOR=0;LSEQ=TGGATCTTTCTCCTCCCCAC;RSEQ=TTTCCTCTGAGACAGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:0,3:36,240:0.0108:2,0:15:1:32:0:1:0:60:6:0.0109:0:0 0/0:165:0:0,0:26,138:0:2,0:22.7:1:29.6:1:1:0:60:53.667:1:0:0.3 -1 206652524 . T C 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=5.47993;LSEQ=TTCTCCTCCCCACATTTTCC;RSEQ=CTGAGACAGGAGTTTGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:8:0,8:24,201:0.0342:2,0:20.9:1:32:1:1:0:60:16:0.0356:0:1.1 0/1:141:23:5,18:16,101:0.1631:2,2:29.6:1:30.2:1:0.3417:1.75:60:22:0.1618:0:1.2 -1 206653097 . G T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0389;SOR=Inf;LSEQ=TGGGAGGCTCAGGGTGAGTT;RSEQ=TGAAGCCTGAGGTGGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:152,8:0:2,0:26.5:1:32.1:1:1:0:60:159:1:0:0.2 0/1:83:3:2,1:74,6:0.0361:2,2:33.3:1:30:1:0.23488:5.91375:60:6:0.0366:0:1.3 -1 206653132 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13452;SOR=Inf;LSEQ=GGAGATTGGCAGTGAGGGGT;RSEQ=AGTGTGAGCTGGAAATAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:253,50:0:2,0:22.5:1:31.8:1:1:0:60:59.6:1:0:0.1 0/1:176:2:1,1:139,35:0.0114:2,2:6:0:31:1:0.36818:3.92994:60:4:0.0116:0:1.5 -1 206653671 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55407;SOR=0;LSEQ=TGGAGGCAGGCCGGAGGGGG;RSEQ=GGCAGGCCAGAGGGGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:2,0:186,10:0.01:2,0:30:1:33:0:1:0:60:4:0.0109:0:1.5 0/0:100:0:0,0:92,8:0:2,0:23.4:1:27.5:1:1:0:60:10.111:1:0:0.3 -1 206653699 . A G 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14699;SOR=5.12456;LSEQ=CAGAGGGGGAGGCCGGCAGG;RSEQ=GGTGGAGGCCAGTATCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:1:1,0:293,36:0.003:2,0:19:0:11:0:1:0:60:0:0:0:1 0/1:195:3:2,1:155,36:0.0154:2,2:26:1:22.7:1:0.47192:2.14239:60:2:0.0108:0:1.3 -1 206653717 . TGG T 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04533;SOR=Inf;LSEQ=GGAGGTGGAGGCCAGTATCC;RSEQ=GATGCTGTCTGCATGCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:0:0,0:380,98:0:2,0:23.6:1:31.8:1:1:0:60:78.667:0.9958:0:0.1 0/1:267:3:1,2:206,57:0.0112:2,2:10.3:1:29.6:1:0.12467:7.15677:60:6:0.0117:0.0075:0.3 -1 206653753 . G T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00321;SOR=Inf;LSEQ=TGCACGGTGCTGAGTCCCCC;RSEQ=ATCAAGGCAGCTCTGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:852:0:0,0:595,257:0:2,0:24.5:1:30:1:1:0:60:64.538:1:0:0.1 0/1:534:6:2,4:358,170:0.0112:2,2:12.7:1:28:1:0.09169:4.19931:60:12:0.0115:0:1.2 -1 206658266 . G T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66392;SOR=1.79396;LSEQ=GCCCAGCATGTGCCAACAGA;RSEQ=CTCTCTGCCTCCCACCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:2:0,2:203,70:0.0073:2,0:1:0:25.5:1:0.06784:0:60:4:0.0075:0:1 0/1:231:3:1,2:155,73:0.013:2,2:27.3:1:27.7:1:0.24678:4.21742:60:6:0.0135:0:1 -1 206658275 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09501;SOR=Inf;LSEQ=GTGCCAACAGAGCTCTCTGC;RSEQ=TCCCACCTTGGCTGCTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:234,102:0:2,0:23.2:1:31.1:1:1:0:59.9:83:1:0:0.2 0/1:283:3:1,2:179,101:0.0106:2,2:5.3:1:23:1:0.3003:3.52798:60:2:0.0072:0:1.3 -1 206664396 . A T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63282;SOR=2.58851;LSEQ=CTTCTCAGATGCAATCTTGA;RSEQ=GTAACTGGATTTACTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:15:1,14:0,8:0.6522:0,1:19.9:1:30.8:1:1:0:60:30:0.6522:0:1.6 1/1:6:5:0,5:0,1:0.8333:0,0:25.6:1:30.2:1:1:0:60:10:0.8333:0:1.8 -1 206664407 . T G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60647;SOR=2.96045;LSEQ=CAATCTTGAAGTAACTGGAT;RSEQ=TACTTCTGGTATGGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:0,9:1,6:0.5625:2,0:22:1:31.6:1:0.4375:0:60:18:0.5625:0:2 1/1:5:4:0,4:0,1:0.8:0,0:30.5:1:31.5:1:1:0:60:8:0.8:0:2 -1 206664519 . T TC 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTGAACCTTCCCTGCC;RSEQ=CCCCCCGCTCCTCTGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:41.5:1:32:1:1:1.73:60:4:0.4:0:0.5 0/0:2:0:0,0:1,1:0:2,0:43.5:1:28.5:1:1:0:60:4:1:0:0 -1 206665052 . C T 207 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=96.09126;LSEQ=GTGCGTGCAGAAGTATCAAG;RSEQ=GTCCTTAGTCACACACGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1020:2:0,2:462,553:0.002:2,0:1:0:26:1:0.50369:0:60:4:0.002:0:1 0/1:792:126:58,68:303,363:0.1591:2,2:24.3:1:29.7:1:0.92258:1.02:60:125:0.1605:0:1.2 -1 206665247 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00533;SOR=Inf;LSEQ=GTGGACCAGGCAGTTGGCTG;RSEQ=GAGATTTCTGTAGCTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:0,66:0:1,0:27.1:1:31.5:1:1:0:60:65:1:0:0.1 0/1:15:3:0,3:0,12:0.2:0,0:26.7:1:28.7:1:1:0:60:6:0.2:0:1 -1 206665896 . C G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGTGTGGCGAGGGCTGA;RSEQ=CTCCAACCCCTGATTTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:20.5:1:28:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 206666734 . T G 206 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=198.77506;LSEQ=AAGTGCTGGGGAGAAAGCGG;RSEQ=TGTGTATCTGTGTGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:739:1:0,1:259,478:0.0014:2,0:19:0:33:0:1:0:60:2:0.0014:0:1 0/1:522:111:43,68:159,252:0.2126:2,2:25.9:1:30.4:1:1:1.00:60:54.5:0.2137:0:1.2 -1 206666785 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00473;SOR=Inf;LSEQ=AGCAGAGTATGCTGAGGTTA;RSEQ=AGCCTGAGGGGTTTGGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:55,269:0:2,0:23.3:1:31.1:1:1:0:60:80:1:0:0.1 0/1:171:5:0,5:28,138:0.0292:2,0:12.2:1:25:1:0.59286:0:60:1.5:0.0182:0:1.4 -1 206667175 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10464;SOR=Inf;LSEQ=TTTGGTGGGGCTGCAGAGGA;RSEQ=GGTGGGCCTCCCAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:213,16:0:2,0:27.8:1:32.5:1:1:0:59.9:113.5:1:0:0.1 0/1:110:2:2,0:100,8:0.0182:2,0:30.5:1:29.5:1:1:0:60:4:0.0183:0:1 -1 206667209 . C T 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13571;SOR=5.37488;LSEQ=GGAAAAGGGTCTGGGCAGGG;RSEQ=AACTTCCAGCCTCAGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:1,0:312,51:0.0027:2,0:49:0:32:0:1:0:60:2:0.0028:0:1 0/1:205:3:2,1:171,30:0.0146:2,2:24.3:1:23.7:1:0.39173:2.83001:60:2:0.0101:0:2.3 -1 206667268 . C T 76 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25915;SOR=2.16405;LSEQ=GGCAGCATGCAAGAGCTCTG;RSEQ=GAGGGGATGAAGCTGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:867:5:0,5:497,365:0.0058:2,0:10.6:1:27.8:1:0.01394:0:60:10:0.0059:0:1.4 0/1:645:8:2,6:377,260:0.0124:2,2:10.8:1:25.5:1:0.07058:4.34044:60:7:0.011:0:1.4 -1 206667441 . G A 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02161;SOR=1.68939;LSEQ=GATGACACGTGTCCATTTTC;RSEQ=AAGAAGCCCTGTTGAAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:122:6,116:2,107:0.5281:1,1:26.3:1:30:1:0.28679:2.76:60:29.5:0.5221:0:1.1 1/0:136:89:3,86:1,46:0.6544:1,1:24.6:1:30.1:1:1:1.60:60:28.667:0.6515:0:1.1 -1 206669136 . C A 70 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCATTTAAACTCCTTTC;RSEQ=CCTCCTAAACCTTGGCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:24.4:1:30.4:1:1:0:60:10:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 206669442 . T C 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAGCCTGTACCTTTTCTTG;RSEQ=AGGCTAAATAGAGTCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1245:0:0,0:604,641:0:2,0:25.1:1:28.7:1:1:0:60:72.235:1:0:0.2 0/1:805:52:30,22:351,402:0.0646:2,2:22.1:1:31.6:1:0.15061:1.56:60:16.333:0.0613:0:1.2 -1 206669465 . C T 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=44.041;LSEQ=GCTAAATAGAGTCCCAGCAC;RSEQ=TCCTGATGTCTGAGCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1191:2:1,1:542,646:0.0017:2,2:19.5:1:29.5:1:1:1.19:60:4:0.0017:0:1 0/1:753:52:25,27:313,387:0.0691:2,2:27.8:1:29.8:1:0.66649:1.14:60:104:0.0701:0:1.1 -1 206669607 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10903;SOR=Inf;LSEQ=ACCTCCCTCCTGGCTGCTGG;RSEQ=CAGGATGTCGCCAGCATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:5,137:0:1,0:25:1:30.9:1:1:0:60:34.5:1:0:0.1 0/1:71:2:1,1:4,65:0.0282:2,2:16:1:29:1:0.13682:14.65:60:4:0.0286:0:1 -1 206670258 . G GGGAA 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCTGTGTCTGCAAGGCA;RSEQ=GGCTCTCAGCTGGGTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:30.3:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 206941864 . A G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2041;SOR=1.63893;LSEQ=AGAGGTAATAAATATTCTAT;RSEQ=AGAGAGGTACAATAAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:33:32,1:59,0:0.3587:1,1:25.5:1:32.8:1:0.3587:0:60:66:0.3587:0:1.1 0/1:48:23:23,0:25,0:0.4792:1,1:22.1:1:32.6:1:1:0:60:46:0.4792:0:1 -1 206943297 . A G 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0219;SOR=2.57342;LSEQ=TCCAGCTCCATGTCCATCAC;RSEQ=CTTAGGGGACAAGCTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:10:2,8:58,223:0.0344:2,2:30.9:1:30.1:1:1:1.04024:60:9:0.0314:0:1.8 0/1:238:20:6,14:59,159:0.084:2,2:30.9:1:31.5:1:0.79533:1.15:60:40:0.0847:0:1.3 -1 206943351 . T C 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGATTTATCCAAATGCCT;RSEQ=GCCTCACAGCTCCCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:98:3,95:0,0:1:0,1:27.2:1:29.7:1:1:0:60:48:1:0:1.3 1/1:60:60:2,58:0,0:1:0,1:21.5:1:30:1:1:0:60:120:1:0:1.1 -1 206944077 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02369;SOR=Inf;LSEQ=TGCCTAGCAGCCACCCCCAA;RSEQ=GCCTGCTCAAAGAGAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:62,0:0:1,0:24:1:32.2:1:1:0:60:30:1:0:0.4 0/1:26:3:3,0:23,0:0.1154:1,0:14.3:1:31.3:1:1:0:60:6:0.1154:0:1 -1 206944112 . T A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23105;SOR=0.55535;LSEQ=AAATGAGCAAGAGATCTGAC;RSEQ=CCAGGAGTCTTTCCTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:35:34,1:71,0:0.3302:1,1:27.1:1:30.3:1:0.33019:0:60:34:0.3333:0:1 0/1:42:9:9,0:31,2:0.2143:2,0:30.3:1:31.4:1:1:0:60:18:0.2143:0:1 -1 206944233 . A G 285 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=1.9967;LSEQ=GGGGGCAGCTGCAAGGGAAA;RSEQ=AACTGATCTGCTACTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:735:501:348,153:151,83:0.6816:2,2:23:1:31.8:1:0.20338:1.25:60:70.571:0.6823:0:1.1 1/1:533:432:291,141:61,40:0.8105:2,2:23.7:1:31.6:1:0.19977:1.35:60:85.4:0.8102:0:1.2 -1 206944645 . T C 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.40506;LSEQ=CCTGCAATCAGGAAGCAGAG;RSEQ=CTCCCTTCCCTTAATCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:476:345:241,104:88,43:0.7248:2,2:25.5:1:31.6:1:0.58009:1.13:60:42.125:0.7216:0:1.1 1/1:345:298:205,93:29,18:0.8638:2,2:24.2:1:31.4:1:0.40086:1.37:60:41.571:0.8635:0:1.1 -1 206944830 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30668;SOR=4.5687;LSEQ=GAAATGCGGTCTTTTTGATG;RSEQ=CCTTTCATTTAGAGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:1:1,0:81,292:0.0027:2,0:1:0:26:0:0.21925:0:60:2:0.0028:0:1 0/1:248:3:2,1:58,186:0.0121:2,2:26.3:1:27:1:0.1472:6.35:60:6:0.0127:0:1 -1 206944845 . AT A 125 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.36747;SOR=0.59159;LSEQ=TGATGCCCTTTCATTTAGAG;RSEQ=TTTTTTTTTTAAATAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:16:1,15:27,192:0.0681:2,1:24.9:1:31.3:1:0.70091:2.10416:59.7:32:0.0702:0:0.9 0/1:145:6:0,6:22,116:0.0414:2,0:28.5:1:31.8:1:0.59076:0:60:12:0.0429:0:0.8 -1 206944857 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5241;SOR=0;LSEQ=ATTTAGAGATTTTTTTTTTT;RSEQ=AATAAAATTGGCTCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:0,2:9,173:0.0109:1,0:7:1:29.5:1:1:0:55:4:0.0113:0:2 0/0:116:0:0,0:11,105:0:2,0:20.8:1:29:1:1:0:60:28:1:0:0.9 -1 206944861 . A C 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.63344;SOR=1.19846;LSEQ=AGAGATTTTTTTTTTTAAAT;RSEQ=AAATTGGCTCTGGCCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:160:126:3,123:4,30:0.7875:2,1:23:1:31.8:1:0.03745:5.38787:60:30.5:0.7821:0:1.2 1/1:98:80:4,76:3,15:0.8163:2,2:23.9:1:31.1:1:0.11353:3.73018:60:79:0.8144:0:1.3 -1 206944936 . T C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGTGATGGGACCATCAC;RSEQ=TAAATCAGGTCCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:0,3:1,47:0.0588:1,0:23.7:1:33.7:1:1:0:60:6:0.06:0:1.7 0/0:16:0:0,0:1,15:0:1,0:22.7:1:29.6:1:1:0:60:15:1:0:0.6 -1 206944952 . T G 100 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.18394;SOR=0;LSEQ=TCACTTAAATCAGGTCCTCC;RSEQ=CCTCAGAGTCAAGTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:8:0,8:1,31:0.2:1,0:27.9:1:33.4:1:1:0:60:16:0.2051:0:1.3 0/0:10:0:0,0:1,9:0:2,0:22.2:1:29.8:1:1:0:60:20:1:0:0.3 -1 206945046 . C A 36 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTGCGGAGCTACATT;RSEQ=GGCTTTAAGGGACACCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:16:1:23.3:1:1:0:52:2:0.4:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 206945311 . A C 71 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTCACCTCGAATCAGAC;RSEQ=TTTCTTTACTTCTCCTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:26.3:1:32.8:1:1:0:60:8:1:0:1.3 1/1:5:5:5,0:0,0:1:0,0:21:1:30.8:1:1:0:60:10:1:0:1.4 -1 206945381 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.40032;SOR=2.3994;LSEQ=ATAAGTTTCTCAGCACGAGA;RSEQ=AGAACGCATTTACTTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:0.4:0,0:12.8:1:30.2:1:1:0:60:12:0.4:0:1.2 1/0:8:5:3,2:3,0:0.625:0,2:22.8:1:28.6:1:0.46429:0:60:10:0.625:0:1.4 -1 206945573 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00302;SOR=Inf;LSEQ=AGGAGAATGTCTAGTTCAGG;RSEQ=AGTCCCAGGAAGAGAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:0:0,0:427,194:0:2,0:22.9:1:31.8:1:1:0:60:68:1:0:0.1 0/1:484:7:2,5:307,170:0.0145:2,2:15.9:1:23.6:1:0.10447:4.50009:60:6:0.0127:0:1.1 -1 206945848 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19467;SOR=Inf;LSEQ=CCCCTGATGTGTAGACCTTC;RSEQ=CCTCTCTGTCCCCCTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:33,169:0:2,0:23.5:1:29.8:1:1:0:59.9:201:1:0:0.1 0/1:160:2:1,1:25,133:0.0125:2,2:22.5:1:32.5:1:0.29945:5.24:60:4:0.0126:0:1.5 -1 209632204 . C T 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCGCCAAGCATGAAGCA;RSEQ=GTTGGCACTAGCTCCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:31.5:1:29.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 209632430 . C T 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25602;SOR=0.66435;LSEQ=CACTGTAGGATCATGTTCGT;RSEQ=GTACTACAGAAAGCAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:55:50,5:73,5:0.4104:2,2:21.8:1:30.8:1:0.74039:1.45573:60:110:0.4167:0:1 0/1:57:18:17,1:32,7:0.3158:2,1:28.2:1:30.1:1:0.41358:3.65:60:36:0.3214:0:1.1 -1 209632472 . G T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0.55443;SOR=0;LSEQ=CTTGATTTACAGTGAGAGGA;RSEQ=CAGCAATTAGAGGGAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:225,53:0.0107:2,2:37:1:30.3:1:0.47417:2.11574:60:6:0.0108:0:1 0/0:148:0:0,0:111,37:0:2,0:21.9:1:31.4:1:1:0:60:48.333:1:0:0.3 -1 209632563 . T C 259 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.34146;SOR=1.1092;LSEQ=ATTATTTTGACTGGTGGGTC;RSEQ=CTGGCGGGTGAACATCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:969:336:185,151:354,279:0.3467:2,2:25.8:1:30.9:1:0.83855:1.03561:60:111:0.3472:0:1.1 0/1:653:242:132,110:212,199:0.3706:2,2:25.8:1:30.3:1:0.46666:1.13:60:79.667:0.3711:0:1.1 -1 209632658 . C A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06484;SOR=6.90763;LSEQ=TTTCATTGAGCATGTGCTAC;RSEQ=TATTCTTTAAGACCTAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:1:1,0:75,332:0.0025:2,0:1:0:25:0:0.18627:0:60:2:0.0025:0:1 0/1:239:4:2,2:60,175:0.0167:2,2:16.3:1:24.5:1:0.2769:2.90:60:3:0.0127:0:1 -1 209632941 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACGAATAGCATGTTAAAC;RSEQ=CCAGCATCTCAGTAATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:21.5:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 209634354 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTAGCTGGCATTACAGAC;RSEQ=TCCACCACCATGCCTAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29:1:1:0:60:4:1:0:1 -1 209744020 . TA T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGTCACAAACTGGGTGGC;RSEQ=AAATGACAGAAATTTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:7:1:31.8:1:1:0:60:4:0.6667:0.3333:0 1/1:2:2:2,0:0,0:1:0,0:3:1:27.2:1:1:0:60:4:0.9333:0.8667:0 -1 209744147 . G T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23522;SOR=0.44711;LSEQ=ATGTTTCTCTCCTAGATTTG;RSEQ=GTGATTTGCTTGCAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:14:7,7:7,9:0.4667:2,2:21.4:1:28.9:1:1:1.27:60:28:0.4828:0:1.1 0/1:18:5:2,3:6,7:0.2778:2,2:33.6:1:28:1:1:1.26799:60:10:0.2941:0:1.2 -1 209745395 . T G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTACTTACAATTCCACA;RSEQ=TCCATGCTCCACAATCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:33.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 209745400 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTACAATTCCACATTCCA;RSEQ=GCTCCACAATCCCCAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:32.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 209865797 . T A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTGGTGGATGGAAAATT;RSEQ=CTAAGAGGAAACATCAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:18:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:39.5:1:30:1:1:0:60:4:1:0:1.5 -1 209865952 . C CGGGGGT 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.6494;SOR=0.46079;LSEQ=GGAATCGGGTATTAAAATGG;RSEQ=GGGGGGGGGGGTGGGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:19.3:1:28.3:1:1:0:56.7:12:0.4286:0.1429:0.5 0/1:8:2:2,0:6,0:0.25:0,0:30.5:1:28.3:1:1:0:60:4:0.25:0:0 -1 209866075 . C A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.28371;SOR=0;LSEQ=GGAGCCTGACTAAAGTTTGG;RSEQ=CAGAAAAATCTTTGTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:3:2,1:22,30:0.0545:2,2:28.3:1:30.3:1:0.57461:2.68:60:6:0.0556:0:1 0/0:34:0:0,0:14,20:0:2,0:25.7:1:31:1:1:0:60:33:1:0:0 -1 211401831 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49753;SOR=0;LSEQ=CGCCTTTCAAACTCTTATAC;RSEQ=AACCTCTGGAGTTGTGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:23,19:0.0455:2,2:14.5:1:28.5:1:1:1.20525:60:4:0.0465:0:1 0/0:37:0:0,0:18,19:0:2,0:29.4:1:30.1:1:1:0:59.2:36:1:0:0.2 -1 211401892 . C G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19192;SOR=Inf;LSEQ=GTCCCATGACAGCCATCCTG;RSEQ=TATTACTCACCTTCGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:0:2,0:21.2:1:32.6:1:1:0:60:50:1:0:0.1 0/1:20:2:1,1:5,12:0.1:2,2:12.5:1:33:0:1:2.28:60:4:0.1:0:1 -1 212225135 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16954;SOR=Inf;LSEQ=TTTGTTTACAACAATGCCAA;RSEQ=AGCATGCTGGGTAACATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:38,47:0:2,0:25.4:1:31.8:1:1:0:25.1:84:1:0:0 0/1:60:2:1,1:23,35:0.0333:2,2:28:1:26:1:1:1.51:22:4:0.0333:0:1 -1 212225197 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52555;SOR=0;LSEQ=GGTAACACTTGTGGGGCATT;RSEQ=CTTTTTGAACAGTACCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:32,51:0.0235:2,2:35.5:1:28.5:1:1:1.58:22:4:0.0241:0:1 0/0:52:0:0,0:21,31:0:2,0:24.6:1:31:1:1:0:26.7:51:1:0:0.1 -1 212225215 . G A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23972;SOR=0.41874;LSEQ=TTCCTTTTTGAACAGTACCC;RSEQ=TTCCCTTGATGTCTACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:10:10,0:28,33:0.1408:2,0:16.4:1:30.3:1:0.00122:0:39.6:20:0.1429:0:1 0/1:47:3:3,0:23,21:0.0638:2,0:22:1:28:1:0.24237:0:38.7:6:0.0638:0:1 -1 212225343 . T C 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2266;SOR=1.70178;LSEQ=CTCCTCTTTCCCTTTGTGTT;RSEQ=GTCATTTTGGCGAATTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:138:122:74,48:0,0:0.8841:0,2:23.8:1:29.9:1:1:0:54.4:23.4:0.8797:0:1.1 1/1:154:143:86,57:0,0:0.9286:0,2:25.1:1:30.4:1:1:0:54.1:286:0.9286:0:1.1 -1 212225344 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21907;SOR=0;LSEQ=TCCTCTTTCCCTTTGTGTTT;RSEQ=TCATTTTGGCGAATTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:0,2:73,46:0.0147:2,0:29:1:28.5:1:0.15537:0:60:4:0.0169:0:2 0/0:154:0:0,0:86,58:0:2,0:25.7:1:30:1:1:0:54.2:143:1:0:1.1 -1 212225354 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49991;SOR=Inf;LSEQ=CTTTGTGTTTGTCATTTTGG;RSEQ=GAATTACTGGAAGATGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:79,65:0:2,0:29.8:1:30.6:1:1:0:55.6:47:1:0:1 0/1:161:2:1,1:91,68:0.0124:2,2:25.5:1:30.5:1:1:1.33577:60:4:0.0124:0:1.5 -1 212225370 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2307;SOR=0;LSEQ=TTGGCGAATTACTGGAAGAT;RSEQ=GCGGTTCCGGCCGAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:74,77:0.0131:2,2:39.5:1:28.5:1:1:1.04:60:4:0.0131:0:2 0/0:165:0:0,0:85,80:0:2,0:33.3:1:30.7:1:1:0:55.5:164:1:0:1 -1 212225419 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.21547;SOR=Inf;LSEQ=TGAAATTCTGGGTCAACAGC;RSEQ=TTTTTTTCCTTTCATTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:28,73:0:2,0:21.6:1:30.6:1:1:0:60:100:1:0:0.6 0/1:88:2:1,1:20,66:0.0227:2,2:11.5:1:29:1:0.42241:3.24:60:4:0.023:0:1.5 -1 212225962 . G T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTCCACACTCCAGCCTG;RSEQ=GCAACAGAGCGAGACTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:31:1:1:0:60:4:1:0:1.5 -1 214977161 . T TA 27 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.2042;SOR=Inf;LSEQ=GCGATCCTCATTTCATAAAT;RSEQ=AAAAAAAAAATTTCAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:0:1,0:17.1:1:30.5:1:1:0:60:40:1:0:0.2 0/1:17:2:2,0:14,1:0.1176:1,0:34:1:27.5:1:1:0:60:4:0.1176:0:0.5 -1 214977284 . T C 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00552;SOR=1.8901;LSEQ=CCAATAATTTTTCATGTAAT;RSEQ=GTACACAAAGAAAGTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:60:39,21:82,39:0.3315:2,2:18.8:1:30.4:1:0.73908:1.13136:60:120:0.3333:0:1.5 0/1:159:77:52,25:44,38:0.4843:2,2:22.4:1:30.4:1:0.07765:1.79:60:154:0.4904:0:1.4 -1 214977365 . A G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=2.74674;LSEQ=TAATCTATATTGGGTTTGGT;RSEQ=AAAAACAAATTATTATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:112:48,64:93,115:0.3489:2,2:24.1:1:31.6:1:0.81358:1.07799:60:224:0.3556:0:1.3 1/0:245:146:67,79:43,53:0.5959:2,2:25.8:1:31.2:1:0.89557:1.05:60:145:0.5967:0:1.3 -1 218806217 . C T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25889;SOR=0;LSEQ=GAAGAGGCACTCTGGTCACT;RSEQ=GGGTTTTCAGCATTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:2,2:5,6:0.2667:2,2:15:1:29.8:1:1:1.19:60:8:0.2667:0:1 0/0:9:0:0,0:4,5:0:2,0:24.2:1:30.1:1:1:0:60:18:1:0:0.1 -1 218807505 . G GT 59 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=1.29262;LSEQ=AGGATTCACACGCTTATTAT;RSEQ=TTTTTTTTTTTTTTATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:3,1:2,4:0.3636:2,2:39:1:29.5:1:0.52381:4.92:60:8:0.4444:0:1.3 0/1:7:3:1,2:1,3:0.4286:2,2:24:1:28.7:1:1:1.41:60:6:0.4286:0.1429:0.7 -1 219421879 . A G 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03788;LSEQ=AAGTTATCAAATTATAAAGC;RSEQ=TGCCAGGAATTAAAGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:417:416:283,133:0,0:0.9976:0,2:25:1:30.2:1:1:0:60:58.429:1:0:1.2 1/1:284:267:167,100:10,7:0.9401:2,2:24.4:1:30:1:0.79926:1.17:60:132.5:0.9397:0:1.6 -1 219421928 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.91272;LSEQ=AATTATGAAAGTTGTCAAGA;RSEQ=TGTGTCATTATGGCACTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:565:111:55,56:231,222:0.1965:2,2:25.8:1:30:1:0.83247:1.05932:60:110:0.1971:0:1.6 1/0:390:213:107,106:88,89:0.5462:2,2:26.8:1:29.2:1:1:1.02:60:29.429:0.5379:0:1.6 -1 219422204 . A G 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=AGATAAACGCAAAGAAAATA;RSEQ=ATCCTATAATCTAGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:0,7:0.4167:0,0:17.2:1:31:1:1:0:60:10:0.4167:0:1.6 1/1:1:1:0,1:0,0:1:0,0:29:0:33:0:1:0:60:2:1:0:2 -1 219991301 . AT A 90 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49523;SOR=0.446;LSEQ=TTTTTCAGTCTCTTTGCCTC;RSEQ=TTTTTTCCATTTTGTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:7:3,4:392,270:0.0104:2,2:17.6:1:32.1:1:0.45284:1.93388:60:14:0.0106:0:0.4 0/0:427:2:1,1:248,177:0.0047:2,2:15.5:1:28.8:1:1:1.39998:60:4:0.0047:0.0023:0 -1 219991332 . A G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33832;SOR=0.56535;LSEQ=TTTTGTGCCTTAATCAGAAG;RSEQ=AGGAGGAGGAGGAGAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:13:11,2:368,338:0.0178:2,2:8.7:1:31.7:1:0.02374:5.04:60:26:0.0181:0:2.2 0/1:493:5:5,0:238,240:0.0101:2,0:5.4:1:32:1:0.06123:0:60:10:0.0104:0:2.4 -1 219991341 . G GAGA 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.0232;SOR=0.50309;LSEQ=TTAATCAGAAGAAGGAGGAG;RSEQ=AGGAGAAAGTGCTTTTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:708:688:350,338:11,4:0.9718:2,2:25.6:1:30.4:1:0.11656:2.65247:59.8:136.6:0.9757:0.2006:0.2 1/1:494:467:233,234:14,11:0.9453:2,2:25.4:1:29.6:1:0.68226:1.27755:59.9:115.75:0.9449:0.1781:0.2 -1 219991450 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62878;SOR=1.71004;LSEQ=AGAATTATGCCTCAGTAAAC;RSEQ=TACTACATGACATCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:2:1,1:46,216:0.0076:2,2:13:1:26:1:0.32492:4.66:60:4:0.0076:0:1 0/1:155:2:1,1:32,121:0.0129:2,2:13:1:28.5:1:0.38157:3.74:60:4:0.0129:0:1 -1 220440200 . G A 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGGTCCCTGGCTCCCTCT;RSEQ=TTACAAAGTCAGGGAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1152:0:0,0:564,588:0:2,0:25.2:1:32:1:1:0:59.8:81.286:1:0:0.1 0/1:808:40:22,18:379,388:0.0495:2,2:23:1:28.3:1:0.52002:1.25:60:80:0.0501:0:1.1 -1 220440885 . C CT 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=4.90249;LSEQ=TCTTCCAAAGCCCATTGCCT;RSEQ=TTTTTGATTCTTCATTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:816:96:42,54:351,367:0.1176:2,2:31.2:1:30:1:0.38474:1.22935:60:47:0.1178:0.0049:0.1 0/1:589:233:111,122:179,175:0.3956:2,2:27.4:1:30.1:1:0.50069:1.124:59.3:76.667:0.3972:0.0458:0.1 -1 220440986 . T C 102 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00079;SOR=14.33783;LSEQ=CTGTTTTGGGTGTTATTCAG;RSEQ=GGCCTGGAGGCAGGATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:693:1:0,1:340,351:0.0014:2,0:3:0:27:0:1:0:60:2:0.0015:0:1 0/1:541:11:2,9:256,273:0.0203:2,2:24.3:1:29.7:1:0.0656:4.21005:60:22:0.0205:0:1.2 -1 220441229 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1245;SOR=Inf;LSEQ=GTTTTAGCCTCAACAGGCCC;RSEQ=GAAATGCAGTTTTCTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:33,166:0:2,0:21.3:1:30.3:1:1:0:60:98.5:1:0:0.1 0/1:109:2:1,1:27,80:0.0183:2,2:8:1:28:1:0.44954:2.93:60:4:0.0185:0:1 -1 220473809 . A G 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCTGTTCTGTACAAAGC;RSEQ=GCCTCTGCTTGAGGTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:110:110:74,36:0,0:1:0,2:21.7:1:29:1:1:0:60:26.5:1:0:1.1 1/1:56:56:36,20:0,0:1:0,2:24.5:1:29.8:1:1:0:60:112:1:0:1.1 -1 220473844 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.54466;SOR=0;LSEQ=TTATGGCTTACTGCTCATAG;RSEQ=AGCAGCAACAACAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:96,82:0.0111:2,2:5.5:1:30:1:1:1.1697:60:4:0.0112:0:1.5 0/0:96:0:0,0:49,47:0:2,0:25.9:1:31.6:1:1:0:60:95:1:0:0.7 -1 221053536 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49425;SOR=0;LSEQ=CTGGCTTCCCGCAGCGGCTG;RSEQ=CTCCGCTCTCAGCCGCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:28,14:0.0455:2,2:35:1:32:1:1:1.96644:60:4:0.0455:0:2 0/0:44:0:0,0:33,11:0:2,0:21.6:1:27.5:1:1:0:60:13.667:1:0:0.4 -1 221053545 . T C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13854;SOR=2.21025;LSEQ=CGCAGCGGCTGTCTCCGCTC;RSEQ=CAGCCGCCTACCACCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:7:4,3:29,13:0.1429:2,2:33.7:1:30.7:1:0.66845:1.65457:60:14:0.1458:0:1.3 0/1:48:13:10,3:24,11:0.2708:2,2:28.7:1:30.5:1:0.72786:1.51:60:26:0.2708:0:1 -1 221053572 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20918;SOR=Inf;LSEQ=CCTACCACCACCATCACCCG;RSEQ=AACAACAACAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:60,45:0:2,0:21.9:1:32:1:1:0:60:51.5:1:0:0.4 0/1:89:2:1,1:55,32:0.0225:2,2:12.5:1:29:1:1:1.70775:60:4:0.0235:0:1.5 -1 221053574 . A C 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.03088;SOR=0;LSEQ=TACCACCACCATCACCCGCA;RSEQ=CAACAACAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:5,1:54,46:0.0566:2,2:25.2:1:33:1:0.22369:4.21:60:12:0.0577:0:1 0/0:93:0:0,0:57,36:0:2,0:24.2:1:29.4:1:1:0:60:186:1:0:0.3 -1 221053589 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22709;SOR=Inf;LSEQ=CCGCAACAACAACAGCAGCA;RSEQ=CAACAGCCGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:54,52:0:2,0:28.6:1:32:1:1:0:60:34.333:1:0:0.4 0/1:97:2:1,1:54,41:0.0206:2,2:36.5:1:29:1:1:1.31328:60:4:0.0211:0:1 -1 221053641 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23412;SOR=Inf;LSEQ=CGCCCCGGGCTGGCGCCCTG;RSEQ=AGCCCCCGGCCTCGGGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:31,41:0:2,0:21.7:1:31.6:1:1:0:60:35:1:0:0.3 0/1:68:2:1,1:26,40:0.0294:2,2:12:1:27:1:1:1.53:60:4:0.0308:0:1 -1 221345640 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09667;SOR=Inf;LSEQ=TCACATCACTTCTTATTCCT;RSEQ=GAGCTTCTTCTCTGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:159,46:0:2,0:22:1:31.5:1:1:0:60:40:1:0:0 0/1:93:2:1,1:71,20:0.0215:2,2:13.5:1:28.5:1:0.40252:3.48859:60:4:0.0217:0:1 -1 221345742 . A G 274 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5845;SOR=0.91264;LSEQ=ATATCTTGTTTATGCTGTCT;RSEQ=TGACATAGTTATCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:494:371:179,192:59,64:0.751:2,2:28.1:1:32.2:1:1:1.01:60:370:0.7505:0:1.1 1/0:379:278:147,131:54,47:0.7335:2,2:25.1:1:31.2:1:1:1.02382:60:277:0.7347:0:1.2 -1 221345779 . G C 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGTCAGTGGAAATAATT;RSEQ=TTCATGACCCCTTCTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:171,270:0:2,0:24:1:31.8:1:1:0:60:87.2:0.9977:0:0.6 0/1:349:26:13,13:140,179:0.0745:2,2:29.8:1:31.7:1:0.54668:1.28:60:52:0.0751:0:1.9 -1 222474589 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1836;SOR=0;LSEQ=AAGGAAGAGTAAATGGGAAG;RSEQ=TGTTTAATGAGTACAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:12,9:0.087:2,2:27.5:1:31.5:1:1:1.31655:60:4:0.0952:0:1.5 0/0:30:0:0,0:16,14:0:2,0:28:1:29.6:1:1:0:60:60:1:0:0.2 -1 222474717 . T C 28 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTTAAAAATGGTTAAGA;RSEQ=GGTAAATTTCATGTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:38.5:1:28:0:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:3:0:26:0:1:0:60:2:1:0:1 -1 222641584 . T C 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04273;SOR=0.1394;LSEQ=GACCCCTCCCTGCAGCCACA;RSEQ=GAGGCCCAGCAACCTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:5,3:1,1:0.8:2,2:22.8:1:29.9:1:1:1.58:35.8:16:0.8:0:1 0/1:12:4:3,1:4,4:0.3333:2,2:24.5:1:32.5:1:0.57576:2.74:37.5:8:0.3333:0:1 -1 222641772 . C T 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTTGGGGGTGGTGGAAC;RSEQ=TGGTAAAAGCTCACCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:11,14:0,0:1:0,2:24.1:1:29.5:1:1:0:47.6:24:1:0:1.6 1/1:26:26:12,14:0,0:1:0,2:26.5:1:30.3:1:1:0:42.5:52:1:0:1.5 -1 222641797 . A G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.13038;LSEQ=AAAAGCTCACCTCCCACCAC;RSEQ=GAGGAGGAGCCCTGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:8:7,1:9,8:0.32:2,2:19.4:1:28.5:1:0.18219:5.82:41.9:7:0.2917:0:2.3 0/1:23:8:5,3:3,12:0.3478:2,2:29.3:1:30.3:1:0.07133:6.03:36.4:16:0.3478:0:2.5 -1 222641834 . T C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTCAGGGGAGTCCCTGC;RSEQ=GGACAGTGACACAGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:30,8:0,0:1:0,2:24.4:1:30.6:1:1:0:46.2:76:1:0:1.5 1/1:24:24:16,8:0,0:1:0,2:22.9:1:29.8:1:1:0:46.4:48:1:0:1.6 -1 222641938 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51659;SOR=0;LSEQ=GATGTCAGGCCCAGTCCCTC;RSEQ=GTGCCTGCGCAAGGAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:69,55:0.0159:2,2:29:1:29:1:1:1.25226:43.5:4:0.0163:0:1 0/0:85:0:0,0:45,40:0:2,0:27:1:29.2:1:1:0:49.5:20.25:1:0:0.1 -1 222641955 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51936;SOR=0;LSEQ=CTCAGTGCCTGCGCAAGGAA;RSEQ=AGGACTCATCTTCTGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:85,59:0.0137:2,2:14:0:31.5:1:1:1.43697:43:4:0.014:0:1.5 0/0:96:0:0,0:48,47:0:2,0:25.7:1:30.7:1:1:0:50.1:94:0.9895:0:0.1 -1 222641957 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16683;SOR=Inf;LSEQ=CAGTGCCTGCGCAAGGAACA;RSEQ=GACTCATCTTCTGAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:86,61:0:2,0:24.3:1:31.8:1:1:0:50.9:294:1:0:0.1 0/1:102:2:1,1:51,49:0.0196:2,2:30.5:1:29:1:1:1.04042:47:4:0.0202:0:1 -1 222641979 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15131;SOR=Inf;LSEQ=ACTCATCTTCTGAGAAGGAT;RSEQ=GACGCAGCCCCAACAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:88,73:0:2,0:24.3:1:31.2:1:1:0:52.9:39.25:1:0:0.2 0/1:103:2:1,1:49,51:0.0194:2,2:26:0:31.5:1:1:1.04:40:4:0.0202:0:1.5 -1 222642019 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.53391;SOR=0;LSEQ=GGACAAGGACCACATCCGGT;RSEQ=GCCCATGAGTGCCGGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:91,72:0.012:2,2:18:0:32:0:1:1.26207:50:4:0.0123:0:1 0/0:96:0:0,0:49,47:0:2,0:45:0:15:0:1:0:49:0:0:0:6 -1 222642065 . T C 33 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04528;SOR=Inf;LSEQ=CAGCAAGCGGCACCAGGCCC;RSEQ=GGCAGGGCGCACCAGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:51,79:0:2,0:24.7:1:30.3:1:1:0:46:129:1:0:0.9 0/1:73:3:1,2:29,41:0.0411:2,2:19.7:1:21.3:1:1:1.40816:39.3:2:0.0282:0:2.3 -1 222642069 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12403;SOR=Inf;LSEQ=AAGCGGCACCAGGCCCTGGC;RSEQ=GGGCGCACCAGGGTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:49,77:0:2,0:23.7:1:30.4:1:1:0:45.2:62:1:0:1 0/1:69:2:1,1:27,40:0.029:2,2:35:1:30:1:1:1.47:46.5:4:0.0299:0:2.5 -1 222642095 . CT GG 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=0.21396;LSEQ=CACCAGGGTCACCCCAACCA;RSEQ=ATAACCGGACCATCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:81:59:15,44:0,0:0.7284:0,2:21.7:1:31.4:1:1:0:37.3:118:0.7375:0.0988:1.1 0/1:36:13:0,13:0,0:0.3611:0,1:26.7:1:30.4:1:1:0:39:26:0.3611:0.0833:1.2 -1 222642096 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCAGGGTCACCCCAACCAC;RSEQ=ATAACCGGACCATCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:9,10:0.0278:2,2:19.5:1:31.5:1:1:1.11:24:4:0.0952:0:1.5 0/0:32:0:0,0:13,9:0:2,0:23.3:1:29.3:1:1:0:48.6:44:1:0:1.5 -1 222642171 . G A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06773;SOR=0.42652;LSEQ=ATGAGACGCAGAAATACCAC;RSEQ=ACCTGGCCTTCCAGGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:42:24,18:9,10:0.6885:2,2:27.4:1:30.9:1:0.58218:1.47:33.9:84:0.6885:0:1.2 0/1:29:14:10,4:6,9:0.4828:2,2:31.4:1:30.1:1:0.13942:3.57:39.4:28:0.4828:0:1.1 -1 222642304 . A G 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57406;SOR=0;LSEQ=GAGCGGAGCATATCAGAGAC;RSEQ=GGCACTGCCACTGCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:5:1,4:22,23:0.1:2,2:14:1:31.2:1:0.35734:3.73625:34.2:10:0.102:0:1 0/0:13:0:0,0:7,6:0:2,0:25.1:1:29.5:1:1:0:36:12:1:0:0.2 -1 222642681 . C T 46 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58824;SOR=0.35335;LSEQ=CATGGCCAGTGAGGACATAG;RSEQ=GAGTGACGAGGAGCACACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:5,2:0.3:2,2:8:1:29.3:1:1:1.22183:22:6:0.3:0:1 0/1:8:1:1,0:3,4:0.125:2,0:17:0:25:0:1:0:23:2:0.125:0:1 -1 222642936 . T A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71581;SOR=0.57017;LSEQ=CCAGGGTCCCCCGATCCACC;RSEQ=GCAGCTTTTGGCAAAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:5,3:9,9:0.3077:2,2:22.6:1:28.6:1:0.68284:1.63:20.9:7:0.28:0:1.1 0/1:15:3:2,1:7,5:0.2:2,2:25.3:1:30.7:1:1:1.40:20.3:6:0.2:0:1 -1 222643319 . A G 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05738;SOR=3.38718;LSEQ=GAGAAACTGACTGGGCTTTC;RSEQ=GGGTCAGGGCAGAGGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:6:2,4:22,22:0.12:2,2:10.3:1:29.5:1:0.66884:1.97318:45:12:0.1224:0:1.2 0/1:25:8:5,3:9,8:0.32:2,2:22.3:1:29.8:1:1:1.46:34.8:16:0.3333:0:1.3 -1 222643352 . AT A 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0397;SOR=0.25517;LSEQ=AGGGAACCCCACGGACATGG;RSEQ=TCCCCCACACTGGAGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:32:16,16:2,2:0.8889:2,2:19.4:1:29.3:1:1:1:35.6:15:0.8571:0.1667:0.3 1/0:33:22:11,11:8,3:0.6667:2,2:18.1:1:28.5:1:0.2783:2.5891:43.7:21:0.6563:0.2727:0.5 -1 222643388 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51234;SOR=0;LSEQ=GGACCCCACCACGCCCAGAT;RSEQ=CAAGATGAGAAGATGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:23,25:0.04:2,2:9.5:1:28.5:1:1:1.09:22:4:0.04:0:1 0/0:34:0:0,0:19,15:0:2,0:28.2:1:30.6:1:1:0:45.7:16:1:0:0.6 -1 222643441 . G C 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42787;SOR=0.63734;LSEQ=AGCCCAACACCCCCAAGTGT;RSEQ=CCATGTGTGATGGGGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:10,13:7,9:0.5897:2,2:26.1:1:30.8:1:1:1.01083:35.7:46:0.6053:0:1 0/1:21:10:5,5:3,8:0.4762:2,2:18.7:1:29:1:0.387:2.54:35.3:9:0.45:0:1.9 -1 222643712 . G C 32 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CCCTGTGGGGGTCCTGACCG;RSEQ=ACCTCACCTGGCTCAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:9,3:0.1429:2,2:7:1:32:1:0.50549:2.73861:33.5:4:0.1538:0:1.5 0/1:7:1:0,1:5,1:0.1429:2,0:38:0:33:0:0.28571:0:31:2:0.1667:0:2 -1 222643729 . A T 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12853;LSEQ=CCGGACCTCACCTGGCTCAG;RSEQ=CTCTTGACGCTGCCCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:5,0:13,4:0.2273:2,0:13.8:1:31.6:1:0.5352:0:47.2:10:0.2381:0:2.2 0/1:8:2:1,1:6,0:0.25:0,2:12:1:28.5:1:0.25:0:33:4:0.2857:0:1.5 -1 222643946 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21387;SOR=Inf;LSEQ=CGGATGCTGGTGGTGGGTGC;RSEQ=GGGCCGCTGGGGGCCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:52,59:0:2,0:26.3:1:30.3:1:1:0:44.8:26.75:1:0:0.2 0/1:96:2:1,1:46,48:0.0208:2,2:29:0:32:0:1:1.04:51:4:0.0208:0:1.5 -1 222643962 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60348;SOR=2.2492;LSEQ=GTGCAGGGCCGCTGGGGGCC;RSEQ=CTGCATGGTTCCCAGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:1:1,0:47,58:0.0094:2,0:1:0:29:0:0.45283:0:35:2:0.0094:0:1 0/1:95:2:1,1:43,50:0.0211:2,2:37:1:29.5:1:1:1.16:47:4:0.0213:0:1.5 -1 222644020 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01575;SOR=Inf;LSEQ=AACTGAAGCTGCTGGGGCAG;RSEQ=ATGGGCAGGATGTTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:11,42:0:2,0:27.9:1:32.2:1:1:0:48.1:52:1:0:0.1 0/1:43:5:1,4:9,29:0.1163:2,2:15:1:26.2:1:1:1.23542:48:10:0.122:0:1.2 -1 222644051 . GAGA G 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.44761;SOR=1.94494;LSEQ=TGTTCTGCACACAAACGTTG;RSEQ=AGAAGATGTGTGCATAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:6:2,4:14,39:0.1017:2,2:28.3:1:30.7:1:0.65818:1.38:31.2:12:0.1017:0.0169:0 0/1:22:4:1,3:2,16:0.1818:2,2:23.5:1:30.1:1:0.47013:2.52:45:8:0.1818:0.0455:0 -1 222645693 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGAGGCAGGAGGAGCTG;RSEQ=GCCTGGAGAGGCTGACTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:41.5:1:27:1:1:0:46:4:0.6667:0:1.5 -1 224135355 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6267;SOR=1.92154;LSEQ=TCCCGTGGCGTCAGCATGTT;RSEQ=GTGTGGAGGAATGTGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:7,1:0.2727:2,0:30:1:32:1:1:0:50.7:6:0.2727:0:1 0/1:7:3:2,1:1,3:0.4286:2,2:19.3:1:30:1:0.48571:4.45:42.3:6:0.4286:0:2 -1 224135520 . T C 87 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCAGCTGTTGCTCATGAG;RSEQ=GTCCACCAGGTGGGACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:30.3:1:31:1:1:0:32.3:14:1:0:1.4 1/1:1:1:1,0:0,0:1:0,0:31:0:34:0:1:0:22:2:1:0:1 -1 224135537 . A G 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50893;SOR=0;LSEQ=GAGTGTCCACCAGGTGGGAC;RSEQ=GGGAGCGTTGACCCTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:4,1:3,5:0.3846:2,2:11.6:1:30:1:0.26573:5.70:33.2:10:0.4167:0:1.4 0/0:3:0:0,0:2,1:0:2,0:6.3:1:28:1:1:0:28.7:6:1:0:0.3 -1 224135680 . G T 108 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00358;SOR=0.07228;LSEQ=GCCCTGGGCCCCTCAGGGGA;RSEQ=TCCCTGCTGGACAGTGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:11,2:15,3:0.4194:2,2:29.6:1:29.2:1:1:1.10:37.9:12:0.4:0:1.4 0/1:21:1:0,1:17,3:0.0476:2,0:33:0:27:0:0.19048:0:40:2:0.0476:0:1 -1 224135725 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50185;SOR=0;LSEQ=AATGACCATGATGATGCTTT;RSEQ=CTCTCCATCATGTCTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:44,27:0.0274:2,2:20.5:1:29.5:1:1:1.61829:45:4:0.0278:0:1 0/0:59:0:0,0:38,21:0:2,0:23.7:1:30.7:1:1:0:49.4:58:1:0:0.3 -1 224135764 . G A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00244;SOR=0.39956;LSEQ=GACACCCAGTTGCCTCTACC;RSEQ=CTCAGATGATGTCAGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:57:38,19:22,29:0.5278:2,2:25.4:1:29.6:1:0.01977:2.61:40.4:56:0.5234:0:1.2 0/1:91:28:15,13:31,32:0.3077:2,2:24.5:1:29.7:1:0.82103:1.19:40.3:56:0.3111:0:1.1 -1 224135870 . T C 111 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4253;SOR=0.5464;LSEQ=AATGGGACAAGGACCACATC;RSEQ=GGTGGCCCATGAGTGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:13:4,9:58,50:0.1074:2,2:9.8:1:30:1:0.14765:2.5899:44.7:26:0.1083:0:1.5 0/1:65:4:1,3:32,29:0.0615:2,2:4.8:1:27.3:1:0.35531:3.2541:49.3:8:0.0635:0:1 -1 224135876 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54345;SOR=0;LSEQ=ACAAGGACCACATCTGGTGG;RSEQ=CCATGAGTGGCGGTCATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:0,2:59,55:0.0172:2,0:17.5:1:31:1:0.23928:0:50.5:4:0.0174:0:1.5 0/0:62:0:0,0:33,29:0:2,0:24.7:1:31.5:1:1:0:56.1:61:1:0:0.2 -1 224135886 . G C 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59302;LSEQ=CATCTGGTGGCCCATGAGTG;RSEQ=CGGTCATGATCTTGAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:3:0,3:56,54:0.0265:2,0:14.3:1:31:1:0.24336:0:34.3:6:0.0265:0:2.7 0/1:63:1:0,1:33,29:0.0159:2,0:4:0:26:0:0.47619:0:32:2:0.0161:0:2 -1 224135887 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29376;SOR=3.61733;LSEQ=ATCTGGTGGCCCATGAGTGG;RSEQ=GGTCATGATCTTGAGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:1:0,1:56,57:0.0088:2,0:45:0:32:0:1:0:49:2:0.0088:0:2 0/1:64:2:1,1:32,30:0.0313:2,2:24.5:1:31.5:1:1:1.06563:56:4:0.0317:0:1 -1 224135900 . G C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66798;SOR=1.83491;LSEQ=TGAGTGGCGGTCATGATCTT;RSEQ=AGCAAGCGGCACCAGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:3:0,3:60,55:0.0252:2,0:19.7:1:30.7:1:0.1156:0:34.7:6:0.0259:0:1.7 0/1:66:3:1,2:34,29:0.0455:2,2:7.3:1:31:1:0.59692:2.31543:31.3:6:0.0455:0:1.7 -1 224135994 . T C 115 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=26.05725;LSEQ=GCTGAGCGAGCGGTGGTACA;RSEQ=CCTGGGGCCCAATGAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:0,1:79,37:0.0085:2,0:29:0:33:0:0.32479:0:24:2:0.0086:0:2 0/1:70:13:8,5:33,24:0.1857:2,2:29.8:1:31.2:1:1:1.16:45.8:26:0.1857:0:1.2 -1 224136044 . A T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05663;SOR=Inf;LSEQ=ATGACCTGGCCTTCCAGGTG;RSEQ=AGGTGGCCCACTTGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:94,68:0:2,0:28:1:29:1:1:0:50.9:31.4:1:0:0.1 0/1:102:3:2,1:56,43:0.0294:2,2:33:1:22.7:1:1:1.53:60:2:0.0204:0:1 -1 224136104 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11216;SOR=Inf;LSEQ=TCAGAGGCCAAGCCCACAAG;RSEQ=CAGGGGCTAGCAGGAGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:51,89:0:2,0:24.9:1:31:1:1:0:39.3:34:1:0:0.1 0/1:71:2:2,0:29,40:0.0282:2,0:14.5:1:27.5:1:0.18712:0:27.5:4:0.029:0:1 -1 224136159 . A G 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.75315;SOR=0.68857;LSEQ=GAGCGGAGCATATCAGAGAC;RSEQ=GGCACTGCCACTGCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:9:9,0:43,58:0.0818:2,0:13.2:1:29.9:1:0.00079:0:34.7:18:0.0826:0:1.1 0/1:52:3:3,0:27,22:0.0577:2,0:22.3:1:30.7:1:0.25339:0:33.3:6:0.0588:0:1 -1 224136200 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50811;SOR=0;LSEQ=GGTGTCCTCTGAACTCCTGT;RSEQ=AGTTGCAGCCCAAACACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:88,55:0.0138:2,2:20.5:1:29.5:1:1:1.59458:41.5:4:0.014:0:1.5 0/0:109:0:0,0:61,48:0:2,0:25.4:1:30.9:1:1:0:39:35.333:1:0:0.2 -1 224136257 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50016;SOR=0;LSEQ=GGAGCAGCTTCTGTGGGGCA;RSEQ=AACGGCTGCACACAGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:96,75:0.0116:2,2:37:1:29.5:1:1:1.27815:47:4:0.0118:0:1 0/0:154:0:0,0:77,77:0:2,0:24.7:1:30.7:1:1:0:40.8:50.333:1:0:0.2 -1 224136278 . A G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11544;SOR=0.49544;LSEQ=AACGGCTGCACACAGTCAGG;RSEQ=AACCTGGCTCAGCCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:20:11,9:72,62:0.1299:2,2:27.3:1:31.4:1:1:1.05:35.5:40:0.1307:0:1.6 0/1:131:9:4,5:55,67:0.0687:2,2:25.1:1:30.1:1:1:1.02592:34.6:18:0.0692:0:1.6 -1 224136315 . C T 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01487;SOR=0.40845;LSEQ=GCCCAAGCCTTCTCCCACAG;RSEQ=GGGGTACACAGCCTGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:37:19,18:49,69:0.2387:2,2:19.4:1:29.1:1:0.34409:1.48:45.6:36:0.2353:0:1.3 0/1:106:12:7,5:37,57:0.1132:2,2:25.1:1:28.6:1:0.2295:2.14:41.8:24:0.1165:0:1.6 -1 224136404 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52839;SOR=0;LSEQ=TGGCACTGCATCATACTCTG;RSEQ=CCCAAAGCCTTCTACTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:79,89:0.0118:2,2:30.5:1:30:1:1:1.13:50:4:0.012:0:1.5 0/0:103:0:0,0:47,56:0:2,0:29:1:30.9:1:1:0:45.7:24.75:1:0:0.3 -1 224136424 . T C 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98771;LSEQ=GCCCAAAGCCTTCTACTCAG;RSEQ=ATGGAGCTCCAGGCCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:8:1,7:58,70:0.0588:2,2:23.4:1:33.1:1:0.13736:5.74202:39.1:16:0.0602:0:1.1 0/1:86:5:0,5:34,47:0.0581:2,0:13:1:29.6:1:0.15186:0:34.4:4:0.0476:0:1 -1 224136470 . A C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGTGAGGGAGGTGACC;RSEQ=GTGGGCAGCCCTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:0,2:7,44:0.0377:2,0:14.5:1:30.5:1:1:0:30.5:4:0.0377:0:2 0/0:22:0:0,0:5,17:0:2,0:20.5:1:31.1:1:1:0:28.1:44:1:0:0 -1 224136611 . CACT C 65 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.22474;LSEQ=GCTGATGATGGCTTTAGCAC;RSEQ=GACACCGATCTCAAGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:3,2:0.4444:2,0:19.8:1:32.8:1:0.16667:0:25.8:8:0.4444:0:0 1/0:2:1:0,1:1,0:0.5:0,0:49:0:33:0:1:0:22:2:0.5:0:0 -1 224136748 . GC G 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCTCCTTTACTCCTGCC;RSEQ=CCCCTTGCTAGATCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:17.7:1:29.9:1:1:0:36.7:6:1:0.6667:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 224136856 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.1187;LSEQ=ACACATACTCGGATGCTTCC;RSEQ=CCTCAACCTTGGCACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:5,4:0.1818:2,0:15:1:31:0:0.49091:0:23:4:0.2:0:1 0/1:10:2:2,0:5,3:0.2:2,0:25:1:28.5:1:1:0:25:4:0.2:0:1 -1 224137174 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01991;SOR=Inf;LSEQ=GAGAAACTGACTGGGCTTTC;RSEQ=GGGTCAGGGCAGAGGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,18:0:2,0:16.8:1:30.6:1:1:0:49.6:78:1:0:0 0/1:25:4:2,2:9,12:0.16:2,2:30.8:1:29.3:1:1:1.32:47.3:8:0.16:0:1 -1 224137239 . A G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.09547;LSEQ=GGAGGACCCCACCACGCCCA;RSEQ=ATGCAAGATGAGAAGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:0,3:39,35:0.039:2,0:41.7:1:33:0:0.11532:0:21:6:0.039:0:1.3 0/1:47:2:0,2:24,21:0.0426:2,0:41:1:32:0:0.23404:0:21:4:0.0426:0:1.5 -1 224137267 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15311;SOR=Inf;LSEQ=ATGAGAAGATGCTCCAGCTG;RSEQ=AGTCCAAAGCCCAACACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:34,43:0:2,0:25.1:1:32.3:1:1:0:51.7:154:1:0:0.1 0/1:50:2:1,1:22,26:0.04:2,2:21:0:29.5:1:1:1.18:60:4:0.0417:0:1.5 -1 224137401 . T C 41 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53029;LSEQ=GCTGTCCTCTTCACTGCACG;RSEQ=GCCCTGGACCAGTGCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:2,1:0.5:2,0:33.3:1:26.3:1:0.4:0:34.3:6:0.5:0:2.7 0/1:6:2:1,1:2,2:0.3333:2,2:6.5:1:24:1:1:1:30:1:0.2:0:1 -1 224137495 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACCCTCCAGGCCCACTA;RSEQ=GCACACATCTTCCCCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:0.1818:2,2:34.5:1:31:1:1:1.87089:31:4:0.1818:0:1 0/0:5:0:0,0:2,3:0:2,0:28:1:28.4:1:1:0:33.4:10:1:0:0.2 -1 224137654 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52404;SOR=0;LSEQ=GTGAGGCTGAGAGTAGGGGC;RSEQ=GGGGCAGCAGTGGTGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:40,20:0.0323:2,2:24:1:32:1:1:1.97611:49:4:0.0328:0:1 0/0:38:0:0,0:28,10:0:2,0:25.7:1:30.4:1:1:0:42.2:76:1:0:0.1 -1 224137682 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16494;SOR=Inf;LSEQ=CAGTGGTGCCAGTCGGGGGG;RSEQ=GGTCCAGTGGGAGGAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:56,31:0:2,0:30.8:1:31:1:1:0:40.8:28:1:0:0.1 0/1:60:2:1,1:36,22:0.0333:2,2:11.5:1:28.5:1:1:1.62241:43:4:0.0339:0:1.5 -1 224137787 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17294;SOR=Inf;LSEQ=AACTGCAGGTGAAACGGATG;RSEQ=TGGTGGTGGGTGCAGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:86,65:0:2,0:23.6:1:31.7:1:1:0:39.1:36.75:1:0:0.6 0/1:108:2:1,1:54,51:0.0185:2,2:37.5:1:27.5:1:1:1.05828:42.5:4:0.0187:0:1 -1 224137835 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51265;SOR=0;LSEQ=CTGCTGCGTGGTTCCCAGAG;RSEQ=CTGGACTGGGGCAGGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:65,84:0.0132:2,2:22:1:27.5:1:1:1.29:44.5:4:0.0133:0:1 0/0:107:0:0,0:45,62:0:2,0:25.3:1:30.9:1:1:0:45.2:25.75:1:0:0.4 -1 224137839 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14618;LSEQ=TGCGTGGTTCCCAGAGGCTG;RSEQ=ACTGGGGCAGGTGCCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:149:98:41,57:23,28:0.6577:2,2:26.3:1:30:1:0.72977:1.14096:44.6:196:0.6622:0:1.1 0/1:101:22:9,13:33,46:0.2178:2,2:22.4:1:28.2:1:1:1.03587:45.3:21:0.2165:0:1.3 -1 224137863 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12445;SOR=Inf;LSEQ=GGGGCAGGTGCCAACTGAAG;RSEQ=TGCTGGGGCAGCATGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:36,86:0:2,0:23.6:1:31.8:1:1:0:47.5:39.667:1:0:0.8 0/1:67:2:1,1:21,44:0.0299:2,2:27:1:29:1:1:2.07:53.5:4:0.0308:0:1 -1 224137866 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13879;SOR=Inf;LSEQ=GCAGGTGCCAACTGAAGCTG;RSEQ=TGGGGCAGCATGGGCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:31,81:0:2,0:24.6:1:32:1:1:0:47.8:55:1:0:0.8 0/1:67:2:1,1:21,44:0.0299:2,2:9:0:32:0:1:2.07:47:4:0.0308:0:1.5 -1 224137902 . C GT 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.08202;SOR=Inf;LSEQ=AGGATGTTCTGCACACAAAC;RSEQ=TTGGAGAAGATGTGTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:13,58:0:2,0:22.6:1:31.7:1:1:0:53.5:70:1:0:0.8 0/1:29:2:1,1:6,21:0.069:2,2:39:1:28.3:1:0.43103:3.32:45:4:0.0769:0:1 -1 224137928 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04478;SOR=0.27863;LSEQ=GAAGATGTGTGCATAGCGGG;RSEQ=CCACTGCTGCTGCCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:26:5,21:1,15:0.6047:1,2:26.9:1:31.8:1:0.38046:3.48:56.7:52:0.6341:0:1.2 0/1:17:5:2,3:5,7:0.2941:2,2:15.6:1:32.2:1:1:1.06713:48.6:10:0.2941:0:1.4 -1 224139286 . C T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGACCTGCCGAAGTGGC;RSEQ=GAAAGGCAGGAGCTTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:0:30.5:1:1:0:42:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 224139955 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGTAGAGGCTGACTGGA;RSEQ=AAAGTTCTGGGCCTGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:28.5:1:1:0:23:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 224486006 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.52821;SOR=0;LSEQ=CCCACAAGTGTTACCACCAC;RSEQ=AAACTGGAAGAGTCTATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:17,11:0.0667:2,2:31:0:32.5:1:1:1.52251:60:4:0.0667:0:1 0/0:17:0:0,0:11,6:0:2,0:30.9:1:29.6:1:1:0:60:34:1:0:0.1 -1 224639577 . C T 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTAAAAATTGACAGATTA;RSEQ=ACATAGGAATCTGGACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:20.5:1:30:1:1:0:60:8:1:0:1 1/1:2:2:2,0:0,0:1:0,0:12:1:32:0:1:0:60:4:1:0:1 -1 224639728 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50311;SOR=0;LSEQ=ACGCTTTCCTATTGCCTCCC;RSEQ=GATACTGAGGTTGACTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:14,24:0.05:2,2:28:1:31:1:1:1.69:60:4:0.05:0:1 0/0:30:0:0,0:14,16:0:2,0:28.2:1:29.2:1:1:0:60:14:1:0:0.1 -1 224803669 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAAGAACCGGGAGGGG;RSEQ=GGCTGCGGCGTTTAGGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29.5:1:1:0:60:4:1:0:1.5 -1 224804029 . AGGC A 27 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.58768;SOR=2.14825;LSEQ=TACAGTTCTCGCAGTGGCAA;RSEQ=GGCGGCGGCGGCGGCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:12,10:0.0833:2,2:22.5:1:31:1:1:1.19087:60:4:0.0833:0:0.5 0/1:12:2:1,1:5,5:0.1667:2,2:41.5:1:27.5:1:1:1:60:4:0.1667:0:0 -1 226064490 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGAGTAGCCGGGATTACA;RSEQ=GCGCCGACCACCACACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:27:1:31.5:1:1:0:60:4:0.2:0:1 0/0:2:0:0,0:2,0:0:0,0:31:1:34:0:1:0:60:4:1:0:0 -1 226064639 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14;SOR=Inf;LSEQ=GATTACAGGCATGAGCCACC;RSEQ=TACCTGGCCCAGCTTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:177,57:0:2,0:23:1:30:1:1:0:60:45.8:1:0:0.1 0/1:141:2:1,1:94,45:0.0142:2,2:17:1:28.5:1:0.54762:2.07707:60:4:0.0142:0:1 -1 226064642 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1526;SOR=Inf;LSEQ=TACAGGCATGAGCCACCGTA;RSEQ=CTGGCCCAGCTTCTGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:181,60:0:2,0:24.1:1:31.6:1:1:0:60:47.2:1:0:0.1 0/1:155:2:1,1:104,49:0.0129:2,2:33.5:1:29.5:1:0.54252:2.11124:60:4:0.0131:0:1 -1 226064745 . G T 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.19277;LSEQ=ATTCTAGTCCGTACTCTCCA;RSEQ=TCACATGTCTCAACCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:244:108,136:153,185:0.4171:2,2:25:1:30.2:1:0.8659:1.04139:60:80.333:0.4162:0:1.6 1/0:347:212:102,110:60,75:0.611:2,2:23.4:1:29.1:1:0.51034:1.16:60:41.4:0.6053:0:1.3 -1 226064750 . A G 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39848;LSEQ=AGTCCGTACTCTCCAGTCAC;RSEQ=TGTCTCAACCCCTTGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:124:51,73:194,242:0.221:2,2:26:1:30.9:1:0.53901:1.14718:60:61:0.2206:0:2.2 0/1:335:34:16,18:136,164:0.1015:2,2:21.7:1:30.2:1:0.85786:1.07:60:68:0.1037:0:2.1 -1 226064797 . G T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29508;SOR=3.57568;LSEQ=CCCAAGGGCCTTAAAGATAC;RSEQ=ACAGGCTGAGAGCTCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:1:1,0:83,220:0.0033:2,0:35:0:16:0:0.27632:0:60:0:0:0:3 0/1:171:2:1,1:57,112:0.0117:2,2:31.5:1:24.5:1:1:1.96:60:4:0.012:0:1.5 -1 226064799 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13216;SOR=Inf;LSEQ=CAAGGGCCTTAAAGATACGA;RSEQ=AGGCTGAGAGCTCTGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:78,217:0:2,0:23.3:1:31.9:1:1:0:60:97.333:1:0:0.6 0/1:169:2:1,1:57,110:0.0118:2,2:10:1:31:1:1:1.92:60:4:0.0119:0:2 -1 226064846 . A G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00593;SOR=2.44936;LSEQ=GTAATCACAGGCATAGCTAT;RSEQ=TGAGTATTCTGGCCTTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:52:4,48:7,57:0.4483:2,2:27.1:1:31.7:1:0.75211:1.46887:60:51:0.4435:0:1.2 1/0:69:46:11,35:4,19:0.6667:2,2:17.5:1:30.8:1:0.75803:1.48:60:92:0.6667:0:1 -1 226252232 . C T 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCTCTCTTGTATGTATCCA;RSEQ=ATAATTTAACAAAAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:102:102:2,100:0,0:1:0,1:25:1:28.5:1:1:0:60:101:1:0:1.1 1/1:55:55:2,53:0,0:1:0,1:22.4:1:27.8:1:1:0:60:26.5:1:0:1.1 -1 226252252 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07838;SOR=Inf;LSEQ=CATAATTTAACAAAAAGATG;RSEQ=ATAACAGGAAAACTTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:2,79:0:1,0:23.7:1:31:1:1:0:60:26:1:0:1.1 0/1:32:2:0,2:0,30:0.0625:1,0:34:1:26:1:1:0:60:4:0.0625:0:2 -1 226252283 . CT C 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.56914;SOR=0;LSEQ=AACTTTTTGCTTTAGAGAAA;RSEQ=TTTTTTTTTCATTTGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:1,43:0.0833:1,0:31.8:1:33.5:1:1:0:60:8:0.0889:0:1.5 0/0:13:0:0,0:0,13:0:1,0:22.3:1:30.2:1:1:0:60:26:1:0:0.9 -1 226253127 . T G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAATAAATAGGGCTTTGA;RSEQ=GAATTTCTTGCTAAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:31,1:0,0:1:0,1:26.1:1:32.1:1:1:0:60:64:1:0:1 1/1:6:6:6,0:0,0:1:0,0:14.5:1:31.5:1:1:0:60:12:1:0:1 -1 226253316 . G T 278 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.94151;LSEQ=CCACTTACCTTTTTGTGCTA;RSEQ=TTATGTTTTTGGTAACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:565:564:381,183:0,0:0.9982:0,2:24.5:1:30.5:1:1:0:60:93:1:0:1.1 1/1:532:531:345,186:0,0:0.9981:0,2:24.4:1:29.5:1:1:0:60:87.5:1:0:1.1 -1 226253688 . T C 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00135;SOR=Inf;LSEQ=AAGGTCATACACGTAGAAAA;RSEQ=GGCAAAACCATAATTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:11,361:0:1,0:24.7:1:30.5:1:1:0:60:185:1:0:0 0/1:240:7:2,5:9,224:0.0292:1,2:21:1:29.7:1:0.03545:9.71:60:14:0.0294:0:1 -1 226253926 . T C 76 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTCAGGTCCTGAAGAAACA;RSEQ=ATAGGTAGAGAGAGCTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:18.6:1:32.8:1:1:0:60:10:0.5556:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226254036 . T C 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGATTGGATTGGCAAGAT;RSEQ=GGGGGAACGGTGCTTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:23.8:1:25.8:1:1:0:60:4:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226259230 . T A 73 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41687;SOR=0.32979;LSEQ=CTCAAAAAAAAAAAAAAAAA;RSEQ=TTCTCTTCTTCCTGTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:5:0,5:35,192:0.0216:2,0:18.6:1:31.8:1:1:0:41.6:10:0.0222:0:1 0/0:139:1:0,1:25,113:0.0072:2,0:29:0:32:0:1:0:45:2:0.0075:0:1 -1 226549058 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16465;SOR=Inf;LSEQ=TTCTGAGGTGGTTTAGTACA;RSEQ=GTACTACCCATCAGCAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:171,4:0:1,0:26.3:1:32.7:1:1:0:60:174:1:0:0.1 0/1:120:2:1,1:109,9:0.0167:2,2:11:1:28.5:1:0.16036:11.54243:60:4:0.0168:0:1 -1 226549326 . G A 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3011;SOR=3.5154;LSEQ=CTCCCCCAGGCTGGCAGGAC;RSEQ=CTCAGTGCCAGCCTGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:1:0,1:24,186:0.0047:2,0:38:0:32:0:1:0:60:2:0.0048:0:1 0/1:121:2:1,1:16,103:0.0165:2,2:12:0:32:0:0.26226:6.28:60:4:0.0167:0:1.5 -1 226549404 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCGGGGCTGGCAGGAT;RSEQ=CTCAATGCCAGCCTGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:11,54:0.0299:2,2:26:0:31:1:0.32836:4.74:60:4:0.0308:0:1.5 0/0:21:0:0,0:1,20:0:1,0:23.6:1:32.9:1:1:0:60:42:1:0:0 -1 226549498 . G A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04414;SOR=Inf;LSEQ=TGGGGGAAGGCTCATACCCT;RSEQ=TAAGCCAGGCTATGCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:52,10:0:2,0:27.3:1:32.8:1:1:0:60:124:1:0:0 0/1:17:2:2,0:13,2:0.1176:2,0:21.5:1:28.5:1:1:0:60:4:0.1176:0:2 -1 226550437 . G A 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGGTTAAAGCCGAAACCC;RSEQ=TGCATCTGGTTACTGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:24.8:1:31.3:1:1:0:60:8:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226550442 . T C 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAGCCGAAACCCGTGCA;RSEQ=CTGGTTACTGGTGCCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:29.8:1:33:1:1:0:60:8:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226550553 . ATT A 123 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.64544;SOR=0.54398;LSEQ=TCCTGCTATAGAGCTTGCCT;RSEQ=TTTTTTTTTTTTTTACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:15:15,0:6,0:0.5556:0,1:28.1:1:31.7:1:1:0:60:30:0.5769:0.037:0.4 0/1:5:2:2,0:3,0:0.4:0,0:45.5:1:29.5:1:1:0:60:4:0.4:0:0 -1 226550639 . AAAC A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AACCACCACCACCACCCCCC;RSEQ=AACAACAACAACGCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:108,5:0.0174:1,0:37.5:1:30.5:1:1:0:60:4:0.0174:0:0 0/0:46:0:0,0:43,3:0:2,0:27.9:1:29.6:1:1:0:60:45:1:0:0.2 -1 226550741 . C T 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09519;SOR=1.32248;LSEQ=TTCTCAGGACAGCAAGCCCC;RSEQ=GGCTTCTGTGCTGTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:101:61,40:318,138:0.1804:2,2:23.3:1:29.6:1:0.07706:1.50991:60:49.5:0.179:0:1.1 0/1:377:85:59,26:199,93:0.2255:2,2:20.8:1:30:1:0.89484:1.06:60:170:0.2273:0:1.2 -1 226550924 . G C 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47072;SOR=1.11923;LSEQ=GCTCTCGAAACCAACAGTTT;RSEQ=ATTAGGAGAATAAGATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:238:60,178:85,192:0.4621:2,2:23.3:1:31.8:1:0.17085:1.31267:60:78.333:0.4626:0:1.1 0/1:308:151:48,103:44,113:0.4903:2,2:25.1:1:31.7:1:0.5338:1.20:60:302:0.4903:0:1.1 -1 226551178 . A G 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGACCCCTGGCCTTTTAC;RSEQ=TGACCTTGTGCTTTTGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:1,4:2,10:0.2941:2,2:28.6:1:32.4:1:1:1.23:60:10:0.3333:0:1 0/0:1:0:0,0:0,1:0:0,0:43:0:28:0:1:0:60:2:1:0:0 -1 226551460 . T C 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.5992;SOR=1.4494;LSEQ=TTGCATTTCCTGAAGTATCC;RSEQ=TGTATCTCCCTTGTTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:55:53,2:23,2:0.6875:2,1:23.5:1:31.2:1:0.5853:2.28:60:54:0.7013:0:2 1/0:21:16:14,2:5,0:0.7619:0,2:23.8:1:29.8:1:1:0:60:15:0.75:0:2.1 -1 226551506 . T C 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26013;SOR=1.47139;LSEQ=GAATTGGATTCTGCTACTTA;RSEQ=AAGAAAAGAATCCTAATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:38:37,1:138,2:0.2135:1,1:26.5:1:31.9:1:0.5157:1.85721:60:37:0.2114:0:2.4 0/1:77:22:22,0:52,3:0.2857:2,1:22.4:1:30.7:1:0.55338:0:60:21:0.2838:0:2.1 -1 226551529 . C G 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49193;SOR=1.18371;LSEQ=GAAAAGAATCCTAATTGGTG;RSEQ=GTCCAGTAACTGCAGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:280:180:177,3:96,2:0.6429:1,1:24.4:1:31:1:1:1.23:60:44:0.6447:0:1.5 1/0:119:81:79,2:37,1:0.6807:1,1:24.2:1:30.2:1:1:1.07:60:15.2:0.6786:0:1.5 -1 226553467 . C CA 70 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.55991;SOR=0;LSEQ=GATAGAGTGAGACTCCATGT;RSEQ=AAAAAAAAAAACAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:23,1:0.1667:1,0:17.8:1:30.2:1:1:0:56:10:0.1724:0.0667:2 0/0:7:0:0,0:7,0:0:0,0:19.9:1:29.6:1:1:0:57.4:6:1:0:2 -1 226553485 . AC CA 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.45712;SOR=1.50959;LSEQ=GTCAAAAAAAAAAACAAAAA;RSEQ=AAACAAACAAAAAAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:29:29,0:29,1:0.4677:1,1:18.6:1:31.2:1:1:0:58.5:58:0.4915:0:2.4 1/0:21:12:12,0:7,0:0.5714:0,0:12:1:31.3:1:1:0:60:24:0.6:0:2.2 -1 226553490 . C A 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22428;SOR=2.03973;LSEQ=AAAAAAAAACAAAAAACAAA;RSEQ=AAACAAAAAAAAAACTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:31:31,0:30,1:0.4769:1,1:19.6:1:30.6:1:1:0:58.6:62:0.5082:0:2.4 1/0:23:15:15,0:7,0:0.6522:0,1:14.3:1:31.4:1:1:0:58.8:30:0.7143:0:2.1 -1 226553494 . C CA 151 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.48057;SOR=1.50207;LSEQ=AAAAACAAAAAACAAACAAA;RSEQ=AAAAAAAAAACTACTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:28:28,0:31,1:0.4179:1,1:23.8:1:31.5:1:1:0:59.8:56:0.4667:0:2.9 1/0:25:13:13,0:10,0:0.52:0,1:22.6:1:30.7:1:1:0:58.6:26:0.5652:0.04:2.9 -1 226553779 . G A 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48394;SOR=0.48478;LSEQ=TAAACAGAATCTTGGGATTA;RSEQ=CACAAAAGAGACCCAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:6:5,1:142,371:0.0116:2,2:8.2:1:27.8:1:0.00801:12.99:60:12:0.0117:0:1 0/0:355:2:2,0:105,248:0.0056:2,0:1:0:21:1:0.09025:0:60:1:0.0029:0:1 -1 226553934 . A C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33171;SOR=2.14972;LSEQ=CTGGGCCAGTGGCTCCACTT;RSEQ=CCTAAGCCTCCACCTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:22:0,22:0,16:0.5789:1,1:24.8:1:32.3:1:1:0:60:44:0.5789:0:1.1 1/0:12:9:0,9:0,3:0.75:0,0:22.2:1:32.3:1:1:0:60:18:0.8182:0:1 -1 226554736 . G C 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACCAGAGAAAAATGAAC;RSEQ=CAAGCATTGTGTTTTTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:21.4:1:30.5:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226554951 . T C 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAAGCTGAGGTGCTGGCT;RSEQ=GGAAGGCTGCCTTGCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:6:6,0:29,0:0.1714:1,0:23.7:1:30.3:1:1:0:60:12:0.1765:0:1 0/0:4:0:0,0:4,0:0:0,0:25:1:28.8:1:1:0:60:8:1:0:0 -1 226555302 . A G 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00289;SOR=0.71474;LSEQ=GCAGGTTGTCAAGCATTTCC;RSEQ=CCTTGGCCTGGAGGAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:330:118,212:241,434:0.328:2,2:23.3:1:31:1:1:1.00:60:164:0.331:0:1.1 0/1:638:165:62,103:179,291:0.2586:2,2:25.3:1:30.2:1:0.92598:1.02186:60:40.25:0.2593:0:1.1 -1 226555401 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07301;SOR=Inf;LSEQ=AAAACCTACATGCAGAGAAG;RSEQ=TCCAACACAGTGAATGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:7,178:0:1,0:25.6:1:32.2:1:1:0:60:91.5:1:0:0.1 0/1:69:2:1,1:1,66:0.029:1,2:13.5:1:28.5:1:0.05754:47.01:60:4:0.0299:0:1.5 -1 226555712 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09935;SOR=Inf;LSEQ=TTTCCCCAGTGGATTTGGTA;RSEQ=AACAGGGGCAGGAAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:32,6:0:2,0:23.6:1:31.3:1:1:0:60:37:1:0:0.1 0/1:18:2:2,0:15,1:0.1111:1,0:39.5:1:31.5:1:1:0:60:4:0.1176:0:1 -1 226556094 . T C 239 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGGCCAGGCTTTCTCTT;RSEQ=TAGCAGGTGGGTGCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:175:175:26,149:0,0:1:0,2:20.5:1:32.1:1:1:0:60:174:1:0:1.1 1/1:87:87:12,75:0,0:1:0,2:21.7:1:31.8:1:1:0:60:86:1:0:1.1 -1 226557669 . G GA 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCTCAAAAAAGAAAAA;RSEQ=AAAGAAAAATCCCACCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:19.3:1:29.7:1:1:0:60:6:1:0.3333:3.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226557878 . T C 113 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30609;SOR=0.24398;LSEQ=AACAGAGAGGGTAACCAACG;RSEQ=CTTCAAGTTTATGGTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:13:13,0:9,0:0.5909:0,1:24.8:1:30.8:1:1:0:60:12:0.5714:0:1.3 0/1:4:1:1,0:2,1:0.25:2,0:13:0:34:0:1:0:60:2:0.3333:0:1 -1 226558285 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13758;SOR=Inf;LSEQ=GTGATCGCAGGAGAGCTGGA;RSEQ=CGGGCAGCCCACCCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:51,267:0:2,0:22.7:1:30.8:1:1:0:60:34.333:1:0:0.1 0/1:188:2:1,1:38,148:0.0106:2,2:32:1:28.5:1:0.37274:3.86:60:4:0.0108:0:1 -1 226558301 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11365;SOR=Inf;LSEQ=TGGACCGGGCAGCCCACCCT;RSEQ=AGGCCCCCAACAGGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:25,208:0:2,0:24.2:1:31.8:1:1:0:60:37.833:1:0:0.1 0/1:119:2:1,1:13,104:0.0168:2,2:7:1:27:1:0.22233:7.75:60:4:0.0171:0:1 -1 226558318 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09615;SOR=Inf;LSEQ=CCTCAGGCCCCCAACAGGAG;RSEQ=AGTCAGGAGCCTGCTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:11,177:0:2,0:23.5:1:32.1:1:1:0:60:46:1:0:0.1 0/1:85:2:0,2:4,79:0.0235:1,0:21.5:1:30:0:1:0:60:4:0.0241:0:1 -1 226561548 . A G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGGGTGGGCCGGGCACG;RSEQ=TGGCTCACACCTATATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,1:0.5:2,0:23:1:30.7:1:1:0:60:6:0.5:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226561761 . G C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2105;SOR=2.20467;LSEQ=GCAAAAGTGCAACCACTCCA;RSEQ=GCCCCAACACTCACACAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:47:45,2:29,0:0.6184:1,1:22.9:1:31.7:1:0.52175:0:60:94:0.6184:0:1.1 1/0:23:18:18,0:5,0:0.7826:0,1:22.9:1:31.5:1:1:0:60:36:0.7826:0:1 -1 226561850 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28469;SOR=3.69339;LSEQ=TGAAACAGAAACAAGAACAG;RSEQ=CAGACAGCTCTTCACTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:0,1:314,47:0.0028:2,0:2:0:28:0:0.1326:0:60:2:0.0028:0:1 0/1:197:2:1,1:163,32:0.0102:2,2:9:1:27.5:1:0.30768:5.03149:60:4:0.0103:0:1.5 -1 226564691 . T C 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02632;SOR=1.97575;LSEQ=TGAAGGACTATTATTCTCCT;RSEQ=TCAACATTTGGTAGTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:67:66,1:80,1:0.4467:1,1:22:1:30.7:1:1:1.21053:60:21.333:0.4384:0:1.1 1/0:65:40:39,1:25,0:0.6154:1,1:25.8:1:31.2:1:1:0:60:39:0.619:0:1.1 -1 226564735 . G T 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03181;SOR=Inf;LSEQ=TATGATGCCACCTGATCCAC;RSEQ=ATGTGGATTTTCTAGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:318,55:0:2,0:23.4:1:30.3:1:1:0:60:372:1:0:0.2 0/1:174:3:1,2:142,29:0.0172:2,2:11:1:25.7:1:0.08227:9.59886:60:6:0.0174:0:1.3 -1 226564740 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10566;SOR=Inf;LSEQ=TGCCACCTGATCCACGATGT;RSEQ=GATTTTCTAGAATAAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:342,65:0:2,0:23.7:1:31.8:1:1:0:60:49.875:0.9975:0:0.2 0/1:197:2:1,1:157,38:0.0102:2,2:19.5:1:28:1:0.35756:4.09123:60:4:0.0103:0:1.5 -1 226565036 . T C 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.02588;SOR=Inf;LSEQ=AGGAGGGTGTCAGATACACA;RSEQ=GTGTGGGTCAGCTGTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:0:0,0:121,374:0:2,0:23.5:1:30:1:1:0:60:40.25:1:0:0.1 0/1:333:4:2,2:94,234:0.012:2,2:18.3:1:30.8:1:0.58231:2.48:60:8:0.0125:0:1 -1 226566726 . A C 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1895;SOR=1.46657;LSEQ=TGTTTTTGATCTCTGTGATT;RSEQ=GATTTCATTCCCCAGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:218:147:146,1:71,0:0.6743:1,1:22.3:1:31.3:1:1:0:60:294:0.6806:0:1.1 1/0:101:76:76,0:24,1:0.7525:1,1:26.3:1:30.7:1:0.24752:0:60:18:0.7423:0:1.1 -1 226567008 . C G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00024;SOR=1.68297;LSEQ=AAAAGCACCTACAGTTTTCT;RSEQ=TCCCCTTGAGGTGCTAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:835:145:39,106:189,501:0.1737:2,2:22.8:1:31.9:1:1:1.0253:60:71.5:0.174:0:1.1 0/1:463:121:41,80:104,238:0.2613:2,2:24.7:1:30.8:1:0.49504:1.17:60:120:0.2609:0:1.1 -1 226567172 . A C 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14824;LSEQ=GTGAGGACAAAGGCACGACC;RSEQ=CACTGCCCCAGGTATGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:58:47,11:138,48:0.2367:2,2:22.3:1:30.4:1:0.37984:1.48:60:18.333:0.2301:0:1 0/1:137:6:6,0:111,19:0.0438:2,0:28.5:1:30.8:1:0.59491:0:60:12:0.0451:0:1 -1 226567178 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13917;SOR=Inf;LSEQ=ACAAAGGCACGACCACACTG;RSEQ=CCCAGGTATGCTGCGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:209,54:0:2,0:23.7:1:31.9:1:1:0:60:51.6:1:0:0.3 0/1:157:2:1,1:128,27:0.0127:2,2:9.5:1:29:1:0.32582:4.6735:60:4:0.0129:0:1 -1 226567209 . G T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08633;SOR=6.0537;LSEQ=CTGCGGGCATTTGGATGTGT;RSEQ=CTCCTAGTCAGCTGGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:1:0,1:308,143:0.0022:2,0:1:0:27:0:0.31858:0:60:2:0.0022:0:1 0/1:302:4:3,1:205,93:0.0132:2,2:34:1:26:1:1:1.36:60:3:0.0101:0:1.5 -1 226567563 . C G 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57473;SOR=1.13649;LSEQ=GGGAGAGGTTCCGTGGACAA;RSEQ=AACCTGGCCACCAATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:78:67,11:249,79:0.1916:2,2:20.1:1:31.9:1:0.06819:1.93:60:38:0.1891:0:1.1 0/1:179:38:29,9:117,24:0.2123:2,2:18.8:1:30.9:1:0.35214:1.50917:60:18:0.2057:0:1.1 -1 226567882 . G GA 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.00681;LSEQ=TCCTCTGTTCAAATTGAAAG;RSEQ=AAAAAAAACCAAAATACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:5:1,4:92,350:0.0112:2,2:22.2:1:29:1:1:1.05134:60:10:0.0115:0.0022:0 0/1:267:3:1,2:61,203:0.0112:2,2:26.3:1:29:1:0.54893:1.66:60:6:0.0113:0.0037:0.3 -1 226568608 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11295;SOR=Inf;LSEQ=TACAGTACAAAGCAGCAACA;RSEQ=TGAGAGCAAATACTGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:79,1:0:1,0:26:1:32.1:1:1:0:60:79:1:0:0.1 0/1:41:2:1,1:39,0:0.0488:1,2:47:1:30.5:1:0.04878:0:60:4:0.05:0:1 -1 226568665 . T C 182 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01617;SOR=0.46971;LSEQ=CAGCGATGATGATGTTAAGA;RSEQ=CCAGTTTTTCAGCGCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:52:51,1:157,6:0.2419:1,1:25.6:1:32.1:1:1:1.94:60:51:0.2406:0:1.1 0/1:123:16:15,1:104,3:0.1301:1,1:22.3:1:30.9:1:0.43157:2.29062:60:32:0.1322:0:1.1 -1 226568972 . A G 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04236;SOR=Inf;LSEQ=TGCTGCTCCCCAGTAAGGGG;RSEQ=GGTGGAGGAGCAGGTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:40,287:0:2,0:23.9:1:30.8:1:1:0:60:53.5:1:0:0.1 0/1:176:3:1,2:29,144:0.017:2,2:23.3:1:29.3:1:0.43117:2.47:60:6:0.0174:0:1 -1 226569028 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06812;SOR=Inf;LSEQ=GGGAAAAGCCTATGAAAATA;RSEQ=ACTCGCGAGAAAACAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:1,108:0:1,0:21.7:1:32.4:1:1:0:60:218:1:0:0.1 0/1:39:2:1,1:0,37:0.0513:1,2:40:1:30:0:0.05128:0:60:4:0.0513:0:1 -1 226570786 . C T 77 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24967;SOR=2.01034;LSEQ=GGAGCCGAGGCTGTGGAGGG;RSEQ=GGAGGCGTGGCCGCCACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:788:5:0,5:410,373:0.0063:2,0:1:0:26:1:0.02505:0:60:10:0.0065:0:1.6 0/1:552:7:3,4:290,255:0.0127:2,2:22:1:27.6:1:0.71128:1.51518:60:14:0.0129:0:1.4 -1 226570840 . T C 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=1.70405;LSEQ=GGGGGGAATATACGGTCCTG;RSEQ=TTTTTAACCTTCAATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:728:446:179,267:127,153:0.6126:2,2:27.3:1:32:1:0.18931:1.23776:60:48.556:0.6146:0:1.1 1/0:584:426:190,236:74,84:0.7295:2,2:25:1:31.7:1:0.64089:1.09407:59.8:70:0.7292:0:1.2 -1 226572794 . C T 28 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTGCGATACTAGGAGATA;RSEQ=GTGAACCCTGGATCCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:31.5:1:28:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226573274 . G A 145 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=6.39995;LSEQ=CACTTGGTCCAGGCAGTGAC;RSEQ=TCCCCAGTGCAGTAATAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1403:7:6,1:645,749:0.005:2,2:6.1:1:24.6:1:0.05445:6.96:60:6:0.0043:0:1.9 0/1:932:29:13,16:438,465:0.0311:2,2:24.6:1:30:1:0.71098:1.15912:60:58:0.0315:0:1.3 -1 226573364 . A G 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80978;SOR=1.03038;LSEQ=GCACCGAACACCATGCCATC;RSEQ=GCTACTCGGTCCAAGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:683:329:112,217:108,243:0.4817:2,2:25.8:1:30.5:1:0.36822:1.16:60:64.8:0.4836:0:1.3 0/1:462:226:85,141:86,150:0.4892:2,2:24.5:1:29.1:1:0.84724:1.05:60:74.333:0.4901:0:1.4 -1 226573402 . T C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0625;SOR=1.45929;LSEQ=CTGCAGCCAGTGGAGAAACA;RSEQ=GTCAGAGGGCAAATGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:433:72:16,56:76,284:0.1663:2,2:25.7:1:29.5:1:0.87484:1.07:60:23:0.1627:0:1.9 0/1:235:53:10,43:46,136:0.2255:2,2:24.2:1:30.2:1:0.3666:1.45222:60:106:0.2265:0:1.9 -1 226573424 . T A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55575;SOR=0;LSEQ=TCAGAGGGCAAATGCGGGAC;RSEQ=ACAAAAAAGGACACTTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:43,248:0.0102:2,2:5:1:22:1:0.06219:11.38:60:2:0.007:0:3.7 0/0:163:0:0,0:32,131:0:2,0:23.3:1:28.2:1:1:0:60:53.333:1:0:0.6 -1 226573924 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12041;SOR=Inf;LSEQ=TCCTTGCAATTAATACCAGC;RSEQ=GGTGTTCACACGGAGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:220,3:0:1,0:23.5:1:30.3:1:1:0:60:73.333:1:0:0.2 0/1:119:2:1,1:114,3:0.0168:1,2:21.5:1:28.5:1:0.06637:33.03137:60:4:0.0172:0:1 -1 226574309 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGACTCCCAGTCATGCT;RSEQ=CTGTGGACACCAAATTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:0,79:0.0247:1,2:14.5:1:28:1:0.02469:0:60:4:0.0253:0:1.5 0/0:24:0:0,0:2,22:0:2,0:30.4:1:30.8:1:1:0:60:48:1:0:0.1 -1 226576127 . T C 105 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66214;SOR=0.38123;LSEQ=ACTCAGCCCTTGCTCAAGCC;RSEQ=GGCTGCAGGTCAGACACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:10,0:30,0:0.25:1,0:32.3:1:31.8:1:1:0:60:20:0.25:0:1 0/1:9:1:1,0:7,1:0.1111:2,0:49:0:29:0:1:0:60:2:0.1111:0:1 -1 226576270 . A G 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.42806;SOR=0.87822;LSEQ=TAAAGGTCTTAATAAGTGGG;RSEQ=CACAACTCCTTGAATTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:177:156,21:331,46:0.3189:2,2:24.5:1:31.3:1:1:1.03:60:58:0.3175:0:1.1 0/1:278:81:66,15:174,23:0.2914:2,2:22.4:1:30.7:1:0.17739:1.71568:60:39.5:0.2894:0:1 -1 226576296 . G A 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47527;SOR=0.89631;LSEQ=CTCCTTGAATTGTCTTCCCA;RSEQ=AATGAGAAAGAGAATCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:894:164:114,50:497,230:0.1834:2,2:23.6:1:29.8:1:0.85232:1.06:60:163:0.1844:0:1.1 0/1:537:90:61,29:290,156:0.1676:2,2:21.7:1:29.1:1:0.71554:1.13:60:29:0.1645:0:1.2 -1 226576496 . T A 33 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04588;SOR=Inf;LSEQ=TGAGAGACAGCCAGAGCCAT;RSEQ=AAAAGTCTGACACCCAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:100,386:0:2,0:23.5:1:28.5:1:1:0:60:161:1:0:0.1 0/1:272:3:2,1:67,202:0.011:2,2:11:1:21:1:0.15937:5.98:60:2:0.0074:0:3.3 -1 226576774 . TA T 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCAGACCCCGTCTGAGGT;RSEQ=AAAAAAAAAAAGAAACCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:24:1:32:0:1:0:60:4:0.3333:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226578047 . G T 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3264;SOR=0.80902;LSEQ=AGTGGTATGGAACCTGTAGG;RSEQ=CCTTTGGGCCTCCCTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:109:95,14:168,53:0.3293:2,2:23.3:1:30.4:1:0.01977:2.14:60:218:0.3344:0:1.8 0/1:190:54:37,17:102,34:0.2842:2,2:22.4:1:28.6:1:0.36965:1.37602:60:108:0.2872:0:1.9 -1 226578099 . T C 290 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03949;LSEQ=CCCCCAGGGCAACCCCGCAG;RSEQ=GCTCCACCCACCCTTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:696:692:449,243:0,3:0.9943:0,2:26:1:30.8:1:0.044:0:60:45.133:0.9956:0:1.2 1/1:469:409:253,156:32,28:0.8721:2,2:26.5:1:30.9:1:0.25718:1.42:60:408:0.8737:0:1.2 -1 226579788 . TACGTTGAGCTAGCAC T 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=TCACTTTATTTTTAATCACT;RSEQ=CCTAAAGCCCCCATTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:382,10:0:1,0:24:1:28.5:1:1:0:60:129.667:1:0:0 0/1:181:8:7,1:162,10:0.0442:2,2:28.5:1:31.8:1:0.40243:2.29927:60:16:0.0447:0:0 -1 226579812 . C T 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02026;SOR=Inf;LSEQ=TTGAGCTAGCACCCTAAAGC;RSEQ=CCCATTTCTTCTTTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:562:0:0,0:483,79:0:2,0:24.5:1:30.7:1:1:0:60:50.091:1:0:0.1 0/1:342:4:1,3:275,63:0.0117:2,2:7.8:1:26.3:1:0.02384:12.95846:60:8:0.0118:0:1 -1 226580021 . G T 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59069;SOR=0.91714;LSEQ=CATCCTGGCCTTTGCCTGGA;RSEQ=AATCAAACAGACAGCAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:725:135:33,102:152,438:0.1862:2,2:24.2:1:28.8:1:0.82697:1.07255:60:66.5:0.1847:0:1.2 0/1:467:81:20,61:123,262:0.1734:2,2:24.7:1:27.8:1:0.23333:1.43082:59.8:80:0.1751:0:1.2 -1 226580093 . C T 160 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97842;LSEQ=GGAGCCCCGTCCTCTTCTAC;RSEQ=TCCCCAGGATCCTTCCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:40:0,40:8,177:0.1778:1,1:25.3:1:30.2:1:0.35611:0:60:80:0.1794:0:1.4 0/1:126:22:1,21:9,95:0.1746:2,1:22.2:1:30.4:1:1:1.98053:60:44:0.176:0:1.5 -1 226580187 . T C 103 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67255;SOR=0.46046;LSEQ=TAACAACCGTGGTCAGCTAA;RSEQ=AGAGCTTCTTTTCTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:9:0,9:0,41:0.18:1,0:14.9:1:32.6:1:1:0:60:18:0.18:0:1.4 0/1:11:1:0,1:1,9:0.0909:2,0:26:0:34:0:1:0:60:2:0.0909:0:1 -1 226589709 . C T 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13689;LSEQ=TAAAGGCTACATTCCAAGCA;RSEQ=CTGGAAAAACAAAATACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:14:14,0:8,0:0.6364:0,1:20.1:1:29.6:1:1:0:60:13:0.619:0:1.1 1/0:3:2:2,0:1,0:0.6667:0,0:17:1:30.5:1:1:0:60:4:0.6667:0:1 -1 226589809 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08528;SOR=Inf;LSEQ=TACGCTTGATCTGCACATGT;RSEQ=GGAGAGGGCAAGCTGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:117,3:0:1,0:25:1:32.3:1:1:0:60:39:1:0:0.3 0/1:50:2:1,1:47,1:0.04:1,2:46:0:30.5:1:0.07918:33.61413:60:4:0.04:0:2.5 -1 226589833 . T C 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02595;SOR=1.94371;LSEQ=GAGGGCAAGCTGGGGGAGGT;RSEQ=TGCTTTGCTCTCTGAGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:37:34,3:150,11:0.1869:2,2:21.1:1:30.8:1:0.72835:1.20203:60:17.5:0.1823:0:1.1 0/1:97:30:27,3:63,4:0.3093:2,2:21.4:1:31:1:0.67297:1.73904:60:29:0.3053:0:1.2 -1 226589851 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27815;SOR=3.77772;LSEQ=GTTTGCTTTGCTCTCTGAGA;RSEQ=GAGGCCCTCCTGGGAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:1:0,1:236,35:0.0037:2,0:1:0:25:0:0.13235:0:60:2:0.0038:0:1 0/1:145:2:1,1:128,15:0.0138:2,2:30.5:1:29:1:0.2092:8.29356:60:4:0.0139:0:2 -1 226589958 . G A 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.56526;LSEQ=GTCTTCTTGACTTTCTGCTG;RSEQ=TCATCCCACCGAAGCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1050:366:203,163:387,296:0.3486:2,2:25.6:1:30.3:1:0.74414:1.04973:60:90.5:0.3511:0:1.1 0/1:771:179:99,80:334,255:0.2322:2,2:27.2:1:29.4:1:0.79634:1.05833:59.9:178:0.2336:0:1.2 -1 226590413 . G A 50 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACACACTGCTACATTTA;RSEQ=TGGTGAGCTGCCTCATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:1,3:0.4286:2,0:37.7:1:31.7:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 226595403 . A AGGGCCC 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=3.000;MSILEN=1;SSF=0.14987;SOR=0;LSEQ=AGGCCCCAAGTGCCGCTCCG;RSEQ=GGGCCCGGGCCCGCTCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:8,1:17,0:0.3462:1,2:15:1:31.7:1:0.34615:0:60:18:0.3462:0.0769:0 0/0:6:0:0,0:6,0:0:0,0:8.3:1:30.7:1:1:0:60:12:1:0:0 -1 226595647 . C G 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.51078;LSEQ=CCATCCTCCCCTAGCTGCCG;RSEQ=CAAAGCTCCGGAAGCCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1032:363:136,227:252,416:0.3517:2,2:25.9:1:31.4:1:0.94644:1.01109:60:44.375:0.3522:0:1.2 0/1:779:169:66,103:268,340:0.2169:2,2:24.1:1:30.7:1:0.25454:1.2298:60:27.167:0.2128:0:1.2 -1 226596686 . T A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGAAATTGTGGTAATGAC;RSEQ=GCACCTGTTGCTATCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:19:0:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 227595966 . G A 68 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0.2582;LSEQ=TTCAGTTGTCACTTGTCTGA;RSEQ=TGCTTTCCACCATCCGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:0.8333:0,2:29.8:1:29.6:1:1:0:60:10:0.8333:0:1 1/0:2:1:1,0:1,0:0.5:0,0:29:0:26:0:1:0:60:2:0.5:0:1 -1 227596235 . A T 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07687;SOR=0.68201;LSEQ=ATAGAAAACCATAAACAGTT;RSEQ=ACTTAGACAGATACATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:72:46,26:216,120:0.1765:2,2:26.4:1:29.7:1:1:1.01736:60:71:0.1762:0:1.8 0/1:306:39:19,20:158,109:0.1275:2,2:25.5:1:28.7:1:0.22864:1.52364:60:78:0.1291:0:1.6 -1 227596280 . A G 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0078;SOR=0.69012;LSEQ=GAAGCTATAAATGATACACA;RSEQ=TGTGCCTCTGGTTTTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:550:324:184,140:124,101:0.5891:2,2:24.1:1:31.7:1:0.72685:1.07:60:63.8:0.5875:0:1.3 0/1:360:179:93,86:90,91:0.4972:2,2:24.4:1:31.5:1:0.67495:1.09:60:178:0.5014:0:1.3 -1 227596405 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTCTGTCACACACATT;RSEQ=CCTATATCCCACACCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:8,143:0.0131:2,2:6.5:1:30.5:1:0.11455:16.91:60:4:0.0134:0:1 0/0:67:0:0,0:2,65:0:1,0:23.9:1:33:1:1:0:60:134:1:0:0 -1 227596565 . C A 58 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22474;LSEQ=AACGTTTTTGTTCCCCAGTG;RSEQ=ATATAAAAGTTATGTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,4:0.4444:0,0:22.3:1:29.3:1:1:0:60:8:0.4444:0:1 1/0:2:1:0,1:0,1:0.5:0,0:15:0:32:0:1:0:60:2:0.5:0:1 -1 228161888 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCTCGGCCGCTTCAGCA;RSEQ=GTCCAGCTCCTGCCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 228163299 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51401;SOR=0;LSEQ=AGAACATCCTGCCCATGCTG;RSEQ=CCCAGCAGCTTCAGTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:57,20:0.0253:2,2:26.5:1:28.5:1:0.46349:2.80561:20:4:0.0253:0:1 0/0:54:0:0,0:38,16:0:2,0:22.6:1:31.6:1:1:0:38.2:108:1:0:0.2 -1 228163355 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19938;SOR=Inf;LSEQ=CCTCTGGGAACCATGCAGCG;RSEQ=CTCCCAGCGGCCCTGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:84,79:0:2,0:29.7:1:31.1:1:1:0:38.1:39.75:1:0:0.2 0/1:132:2:1,1:68,62:0.0152:2,2:22.5:1:27:1:1:1.096:45:4:0.0152:0:1.5 -1 228163356 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50384;SOR=0;LSEQ=CTCTGGGAACCATGCAGCGG;RSEQ=TCCCAGCGGCCCTGCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:83,78:0.0123:2,2:40:1:30:1:1:1.06373:43:4:0.0126:0:1 0/0:132:0:0,0:69,63:0:2,0:30:1:31.7:1:1:0:39.5:264:1:0:0.2 -1 228163360 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50591;SOR=0;LSEQ=GGGAACCATGCAGCGGCTCC;RSEQ=AGCGGCCCTGCACCCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:83,79:0.0122:2,2:28.5:1:26:1:1:1.05034:42:4:0.0124:0:1 0/0:128:0:0,0:66,61:0:2,0:31.3:1:30.7:1:1:0:39.5:126:0.9921:0:0.2 -1 228163365 . G A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.16928;SOR=5.38297;LSEQ=CCATGCAGCGGCTCCCAGCG;RSEQ=CCCTGCACCCACCACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:1,0:85,76:0.0062:2,0:1:0:25:0:1:0:46:2:0.0065:0:1 0/1:123:4:2,2:61,58:0.0325:2,2:26.3:1:27.5:1:1:1.05131:43:8:0.0331:0:1 -1 228163393 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19733;SOR=Inf;LSEQ=CCCACCACCAGCATCCGTTT;RSEQ=ACCTGCAGTTGAAGATCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:65,72:0:2,0:24.2:1:31.7:1:1:0:34.9:33.25:1:0:0.2 0/1:110:2:1,1:47,61:0.0182:2,2:12.5:1:28:1:1:1.29:45:4:0.0183:0:1 -1 228163406 . A C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17002;SOR=Inf;LSEQ=TCCGTTTCACCTGCAGTTGA;RSEQ=GATCCGTGAGGTGCCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:54,65:0:2,0:21.9:1:30.3:1:1:0:35.9:28.75:1:0:0.2 0/1:84:2:1,1:34,48:0.0238:2,2:8:0:32:1:1:1.41:60:4:0.0238:0:1.5 -1 228163644 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGGAGTCAGGGCAGGG;RSEQ=CAGAACAAACCTTGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:12,18:0.0625:2,2:23.5:1:29.5:1:1:1.48:60:4:0.0645:0:1 0/0:14:0:0,0:8,6:0:2,0:27.2:1:30.9:1:1:0:51.7:28:1:0:0.2 -1 228163727 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACAGGAAGAAGCAGTGG;RSEQ=CCTGGAAGAGCTGCATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:0.0556:2,2:37.5:1:31.5:1:1:1.26:57:4:0.0571:0:1 0/0:14:0:0,0:7,7:0:2,0:27.5:1:31.2:1:1:0:52.4:28:1:0:0.3 -1 228163885 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22066;SOR=Inf;LSEQ=ATCACACATGGCACACTTGG;RSEQ=GGTGTTGGGCTTTGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:30,27:0:2,0:22.4:1:31.1:1:1:0:54.9:56:1:0:0.1 0/1:51:2:1,1:28,21:0.0392:2,2:22.5:1:31:1:1:1.32572:60:4:0.0392:0:1 -1 228163949 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18513;SOR=Inf;LSEQ=CATCTGGGCGTGGTGGGGTC;RSEQ=TCCAGTGTGGGATCCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:22,24:0:2,0:25.3:1:31:1:1:0:59.6:45:1:0:0.1 0/1:36:2:1,1:16,18:0.0556:2,2:45.5:1:28.5:1:1:1.12:60:4:0.0556:0:1.5 -1 228163964 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16099;SOR=Inf;LSEQ=GGGTCCTCCAGTGTGGGATC;RSEQ=ATGTCCGTGGGGTTCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:20,27:0:2,0:18.6:1:30.7:1:1:0:59.5:46:1:0:0.1 0/1:32:2:1,1:12,18:0.0625:2,2:17:1:31.5:1:1:1.48:60:4:0.0645:0:1 -1 228164114 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11485;SOR=Inf;LSEQ=GAGGAGCCTGGTAGTTCCAG;RSEQ=TCGCCCACACTTTCAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:46,33:0:2,0:21.9:1:31:1:1:0:53.1:38.5:1:0:0.2 0/1:41:2:2,0:25,14:0.0488:2,0:25:1:33:0:0.53902:0:60:4:0.0488:0:1 -1 228164149 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54537;SOR=0;LSEQ=AGGTCTCTTGCACCAGAAGG;RSEQ=GGCAGGATCCATTGGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:56,54:0.0179:2,2:26.5:1:30:1:1:1.03671:60:4:0.018:0:1 0/0:59:0:0,0:34,25:0:2,0:26.4:1:29.3:1:1:0:53.6:118:1:0:0.3 -1 228164152 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54665;SOR=0;LSEQ=TCTCTTGCACCAGAAGGTGG;RSEQ=AGGATCCATTGGGAGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:56,55:0.0177:2,2:41.5:1:29.5:1:1:1.01802:27:4:0.0177:0:1 0/0:59:0:0,0:34,25:0:2,0:26.8:1:30.6:1:1:0:53.6:18.667:1:0:0.3 -1 228164190 . G A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-04;SOR=Inf;LSEQ=AACAGATCGCCTTGGAAGGC;RSEQ=TCCCTGGGCCCCCATCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:51,53:0:2,0:23.1:1:30.5:1:1:0:57.6:33.667:1:0:0.2 0/1:56:7:2,5:25,24:0.125:2,2:29.4:1:30.3:1:0.42394:2.56188:42.6:14:0.125:0:1.1 -1 228164226 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=5.000;MSILEN=1;SSF=0.51284;SOR=0;LSEQ=CCCCAGGGGTAGGGGCCGTA;RSEQ=GGGGCCCGCTCTGCTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:39,37:0.0256:2,2:14.5:1:30:1:1:1.05337:46.5:4:0.0256:0:1 0/0:54:0:0,0:24,30:0:2,0:22.4:1:30.7:1:1:0:52.9:108:1:0:0.2 -1 228164483 . C G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54762;SOR=0;LSEQ=CCCACCAAAGCCCTTGTTGC;RSEQ=CTCTGGCTCCTCCCCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:52,20:0.027:2,2:21:1:33:1:0.48982:2.56163:20:4:0.0286:0:1 0/0:38:0:0,0:25,13:0:2,0:19.8:1:30.3:1:1:0:30.5:76:1:0:0 -1 228164584 . A G 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01071;SOR=Inf;LSEQ=AAGCCATCATCAGCAATGAC;RSEQ=TCATCACCCCCTCCTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:52,65:0:2,0:25.2:1:30.2:1:1:0:33.6:116:1:0:0.1 0/1:57:4:3,1:21,32:0.0702:2,2:27.8:1:31:1:0.29958:4.45:27:8:0.0714:0:1 -1 228164777 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGGCCAGAGTATGATG;RSEQ=AGTGCCAGACACCACCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:75,55:0.0152:2,2:23.5:1:27.5:1:1:1.36037:22:4:0.0156:0:1 0/0:56:0:0,0:38,18:0:2,0:27.6:1:31.7:1:1:0:39.7:55:1:0:0.1 -1 228164803 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACACCACCTGTGTCAGT;RSEQ=CCTGTAGTGCCTGACGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:84,68:0.013:2,2:32.5:1:30.5:1:1:1.23358:44.5:4:0.0132:0:1 0/0:75:0:0,0:49,26:0:2,0:28:1:29.4:1:1:0:46:150:1:0:0.1 -1 228164818 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=TCAGTTCCTGTAGTGCCTGA;RSEQ=GGTCTATTTCCCTGCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:82,79:0:2,0:26.2:1:30.6:1:1:0:43:52.667:1:0:0.1 0/1:89:8:3,5:56,25:0.0899:2,2:30.3:1:29.5:1:0.11316:3.67194:39.6:16:0.0899:0:1 -1 228164890 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50769;SOR=0;LSEQ=GGGCCAGGCTGAGCCAGGTT;RSEQ=CCTGACTGTGTGCAGCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:0,2:76,70:0.0135:2,0:24:1:31.5:1:0.23497:0:24.5:4:0.0138:0:1.5 0/0:112:0:0,0:47,65:0:2,0:30.3:1:28.8:1:1:0:41.8:111:1:0:0.2 -1 228165010 . A G 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=CAGGGGCAGTGGCAGTGCCC;RSEQ=TCTCTGATATGCTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:53,61:0:2,0:23.8:1:30.1:1:1:0:54.1:21.8:1:0:0.2 0/1:46:7:4,3:23,16:0.1522:2,2:16.1:1:28.9:1:1:1.07635:36.4:14:0.1522:0:1 -1 228165042 . GT G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53113;SOR=0;LSEQ=CTCCACTCCCACGAGCCCTT;RSEQ=TACACTCCTGCTAGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:67,60:0.0155:2,2:39:0:33.5:1:1:1.11571:49:4:0.016:0:0.5 0/0:76:0:0,0:49,27:0:2,0:20.4:1:29.1:1:1:0:47.9:37:1:0:0.2 -1 228165142 . C T 92 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00237;SOR=9.20201;LSEQ=CTTCACCTGGAAGGCCAGGT;RSEQ=GTATTTCTGCATCTCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:0,2:47,64:0.0175:2,0:23.5:1:32:0:0.5098:0:20:4:0.0179:0:1 0/1:56:8:1,7:16,31:0.1429:2,2:15:1:30.9:1:0.41131:3.54579:24.1:16:0.1429:0:1.8 -1 228165622 . A G 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0617;SOR=5.37175;LSEQ=GGGGGCCGCCCAGGGTCAAC;RSEQ=CTCCCCGTCCCACCTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:20,27:0.0408:2,2:35.5:1:31:0:1:1.34:25:4:0.0408:0:1 0/1:21:4:2,2:10,7:0.1905:2,2:38.3:1:29.5:1:1:1.40412:45:8:0.1905:0:1 -1 228165904 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=CCTGGCAGGGGCTCACACCT;RSEQ=CTCGCCCCCTCCTCAGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:0:2,0:14.8:1:32.4:1:1:0:39.6:16:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:12:1:29:1:1:1:40.5:4:0.5:0:1 -1 228512409 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1411;SOR=Inf;LSEQ=TGTACATCCAGTTGGCATCA;RSEQ=ATGTGTTGTGAGTGAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:47,12:0:2,0:21.3:1:31.7:1:1:0:60:118:1:0:0 0/1:36:2:1,1:24,10:0.0556:2,2:8:0:30.5:1:0.52381:2.33552:60:4:0.0556:0:1.5 -1 228512422 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13704;SOR=Inf;LSEQ=GGCATCAGATGTGTTGTGAG;RSEQ=GAAAACAGCTCAGGGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:51,23:0:2,0:21.1:1:29.4:1:1:0:60:148:1:0:0 0/1:44:2:1,1:27,15:0.0455:2,2:35.5:1:31.5:1:1:1.77473:60:4:0.0455:0:1 -1 228512513 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.146;SOR=Inf;LSEQ=ATGTGATCTGGTAGAAGTGA;RSEQ=TTTATCACTCAATGCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:41,73:0:2,0:21.9:1:31.7:1:1:0:60:56:1:0:0.1 0/1:71:2:1,1:29,40:0.0282:2,2:27.5:1:25.5:1:1:1.37:60:4:0.0282:0:1 -1 228607395 . T C 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGAATTCTTAAATTGAATTC;RSEQ=ACTTTAATAATTTAATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:336:336:334,2:0,0:1:0,1:25.3:1:31.1:1:1:0:60:55:1:0:1.1 1/1:133:122:120,2:11,0:0.9173:0,1:23.9:1:30.6:1:1:0:60:39.667:0.9154:0:1.1 -1 228607443 . G T 49 v4;q23;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04527;SOR=5.02143;LSEQ=ATACCACTGCTGTGGATTGT;RSEQ=GTTTTTTTTTTCAAATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:901:2:0,2:707,191:0.0022:2,0:13.5:1:26:1:0.0458:0:60:4:0.0023:0:1.5 0/1:452:5:0,5:318,129:0.0111:2,0:11.6:1:21.4:1:0.00217:0:60:1.5:0.0069:0:2.6 -1 228607444 . G GT 175 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.31956;SOR=1.26041;LSEQ=TACCACTGCTGTGGATTGTG;RSEQ=TTTTTTTTTTCAAATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:915:61:48,13:659,189:0.0667:2,2:26.2:1:29.6:1:1:1.06:60:19.333:0.0645:0.0077:0.5 0/1:460:38:30,8:293,128:0.0826:2,2:28.2:1:30.5:1:0.2687:1.64:60:76:0.0844:0:0.5 -1 228608991 . G T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCAGAAGGTACGCTGAG;RSEQ=GCCTCATTCCCTGGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 228612444 . A G 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00101;SOR=0.04095;LSEQ=ACAGGGTGAACACAGGATTC;RSEQ=CCAGCCTCCCACCCTAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:121:118,3:1,0:0.9918:0,1:24.1:1:29.8:1:1:0:60:120:0.9917:0:1.1 1/1:29:24:23,1:5,0:0.8276:0,1:23.3:1:31.3:1:1:0:60:48:0.8276:0:1.2 -1 228612838 . G T 331 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00215;LSEQ=CGCTGGAAGGGCAACTTGCG;RSEQ=ATTAGCAGCTCAGTGGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2828:2825:1399,1426:1,1:0.9989:2,2:25:1:28.9:1:1:1.0193:60:103.63:0.9993:0:1.2 1/0:1823:1222:571,651:299,299:0.6703:2,2:24.1:1:28.6:1:0.19427:1.14002:60:202.667:0.6722:0:1.2 -1 228612892 . G A 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27753;LSEQ=ATCTCGCGAAGCGCCACCGT;RSEQ=CCGGGCCGGTAGCGGTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2576:252:120,132:1129,1192:0.0978:2,2:24.8:1:28.7:1:0.7908:1.04186:60:41:0.0973:0:1.6 0/1:1575:46:23,23:722,805:0.0292:2,2:20.7:1:28.4:1:0.76546:1.11:60:92:0.0296:0:1.8 -1 228613052 . T C 318 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02008;LSEQ=CGAAACTGTTGGCCCCGCGG;RSEQ=GTCCTCTGCCCAGACCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1364:1360:506,854:1,1:0.9971:2,2:27.3:1:30.6:1:1:1.68699:60:79:0.997:0:1.1 1/1:868:757:305,452:42,67:0.8721:2,2:26.1:1:30.2:1:0.75476:1.08:60:74.7:0.8737:0:1.2 -1 228613129 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10721;SOR=Inf;LSEQ=ATTGGCTGGCCTCAGGTGGC;RSEQ=TGATGGCCCACTGCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:10,332:0:1,0:27:1:32.2:1:1:0:60:341:1:0:0.4 0/1:167:2:1,1:10,155:0.012:2,2:13:1:30.5:1:0.12777:14.83:60:4:0.0122:0:2 -1 228613442 . G A 72 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTCACTCTTGTTGCCCA;RSEQ=GCTGGAGTGCAATAGCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:22:1:28:1:1:0:43.8:5:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 228613471 . T C 82 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATAGCGTGATCTCTGCT;RSEQ=ACTGCAACCTCCACCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:21.8:1:31.8:1:1:0:41.2:12:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 228617063 . G A 61 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CCTCACTTTTCCAGTCATAA;RSEQ=GGCTTTTGCTTTTAGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:32:1:30.8:1:1:0:60:8:1:0:1 0/0:1:0:0,0:0,1:0:0,0:41:0:30:0:1:0:60:2:1:0:0 -1 228617397 . G A 157 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAGATTTCCTCTGCAAACT;RSEQ=AAGAGAATGTGAGATACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:46:45,1:301,8:0.1296:1,1:20.8:1:28.5:1:1:1.20:60:92:0.1311:0:1.2 0/0:120:0:0,0:119,1:0:1,0:23.6:1:31.8:1:1:0:60:39:1:0:0.3 -1 228617425 . CA TT 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGTGAGATACAAACATTCCC;RSEQ=CAAGGAACTGGTCTGTCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:501,48:0:2,0:24.6:1:31.2:1:1:0:60:77.429:1:0:0.6 0/1:246:35:30,5:200,11:0.1423:2,2:20:1:30.9:1:0.05906:3.01166:60:70:0.1458:0.0163:1.8 -1 228617431 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0931;SOR=6.63993;LSEQ=ATACAAACATTCCCCACAAG;RSEQ=AACTGGTCTGTCGAGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:1:1,0:558,70:0.0016:2,0:2:0:30:0:1:0:60:2:0.0016:0:2 0/1:287:3:2,1:258,26:0.0105:2,2:15.7:1:28.3:1:0.25732:4.91234:60:6:0.0107:0:1.7 -1 228617493 . T G 345 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01618;LSEQ=TTTTTCTCTGTCTCCTCGTT;RSEQ=TCTCTCCTTATGGTCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1839:1835:1136,699:0,4:0.9978:0,2:25.4:1:31.9:1:0.02124:0:60:75.458:0.9978:0:1.1 1/1:1129:995:601,394:77,57:0.8813:2,2:24.9:1:31.2:1:0.5125:1.13:60:98.5:0.8826:0:1.2 -1 228617641 . A T 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATCAGCAAACAATATGCT;RSEQ=TCGCTTCTCCAATTTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1334:0:0,0:400,934:0:2,0:23.5:1:29.9:1:1:0:60:165.75:1:0:0.1 0/1:742:41:10,31:228,473:0.0553:2,2:22.3:1:29.4:1:0.30703:1.49354:60:19.5:0.0532:0:1.1 -1 228618328 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTAAAAAAGAATCCTGCCA;RSEQ=GTGTTCAGTGTTTTTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 228623243 . C G 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAATACCAGCTCCTAGTGT;RSEQ=ACTGTCATTTTGTACATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:174:174:0,174:0,0:1:0,1:24.8:1:31.6:1:1:0:60:42.5:1:0:1.1 1/1:71:58:1,57:0,13:0.8169:1,1:21.4:1:31.5:1:1:0:60:116:0.8169:0:1.1 -1 228645900 . A G 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.6139;SOR=2.11838;LSEQ=AGGCTGTCACCAAGGCACAG;RSEQ=AGAAGGACGGCAAGAAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:1:1,0:69,50:0.0083:2,0:13:0:13:0:1:0:60:0:0:0:2 0/1:114:2:1,1:68,44:0.0175:2,2:40:1:31:1:1:1.53934:60:4:0.0179:0:1 -1 228646152 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51966;SOR=0;LSEQ=TGCTGCTGCCCGGCGAGCTG;RSEQ=CCAAGCACGCCGTGTCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:61,64:0.0157:2,2:33:0:31.5:1:1:1.05:60:4:0.0161:0:1.5 0/0:83:0:0,0:45,38:0:2,0:26.4:1:30.4:1:1:0:59.5:26.667:1:0:0.2 -1 228646169 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16158;SOR=Inf;LSEQ=CTGGCCAAGCACGCCGTGTC;RSEQ=GAGGGCACCAAGGCTGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:73,77:0:2,0:27.2:1:29.8:1:1:0:59:36.5:0.9932:0:0.3 0/1:102:2:1,1:55,45:0.0196:2,2:11:0:28:1:1:1.2198:60:4:0.0202:0:1 -1 228646227 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52641;SOR=0;LSEQ=AGTGAGGCGTTCCTCGGCGT;RSEQ=CTGAACCCAAAGGCTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:37,69:0.0185:2,2:14.5:1:31:1:1:1.85:60:4:0.0187:0:1 0/0:66:0:0,0:27,39:0:2,0:26.3:1:30.2:1:1:0:60:32:1:0:0.2 -1 228646356 . CGT C 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=14.000;MSILEN=2;SSF=0.47253;SOR=0;LSEQ=GGGTGCGGCCGAATCTGAGC;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:37.5:1:29.5:1:1:0:60:4:0.25:0:0 0/0:6:0:0,0:0,5:0:0,0:21:1:32:1:1:0:60:10:0.8333:0:0 -1 228652096 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16314;SOR=Inf;LSEQ=TGCGCTCGAAGATGTCATTG;RSEQ=CGAAGGAGTTCATGATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:50,26:0:2,0:26.8:1:29.7:1:1:0:46.7:75:1:0:0 0/1:52:2:1,1:27,23:0.0385:2,2:28.5:1:28:1:1:1.17028:33:4:0.0392:0:1 -1 228652200 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16033;SOR=Inf;LSEQ=GAATAGCTCTCCTTGCGGCC;RSEQ=CGCTTGCGCTTCTTGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:69,74:0:2,0:29.7:1:30.9:1:1:0:53.2:286:1:0:0.1 0/1:96:2:1,1:49,45:0.0208:2,2:44:0:31:1:1:1.08791:60:4:0.0211:0:1.5 -1 228652228 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15741;SOR=Inf;LSEQ=GCTTCTTGCCGTCCTTCTTC;RSEQ=GCGCCTTGGTAATGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:55,75:0:2,0:26.9:1:30.3:1:1:0:57.1:64:1:0:0.1 0/1:86:2:1,1:35,49:0.0233:2,2:33:1:28.5:1:1:1.39:60:4:0.0233:0:1 -1 229106423 . C CTG 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00297;SOR=0.1238;LSEQ=CAGCTGGTGAAGTAAGTACT;RSEQ=TGGATGGTGGCGACTCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:20:9,11:14,15:0.4082:2,2:27.1:1:32.1:1:1:1.13768:59.8:40:0.4082:0.0408:0.2 0/1:26:2:1,1:15,8:0.0769:2,2:26:0:31.5:1:1:1.82581:60:4:0.0769:0:0.5 -1 229223719 . G C 92 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=GGGGTTTCAAGAAAGGCTCA;RSEQ=AGTCAGCCTCACTTCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,1:0.7:2,0:39.7:1:32.9:1:0.3:0:60:14:0.7:0:1 0/0:1:0:0,0:1,0:0:0,0:24:0:34:0:1:0:60:2:1:0:0 -1 229223863 . AC A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.55426;SOR=0;LSEQ=CGGAGTCAGTGTGGGCTGTA;RSEQ=CCCCGGGGTCAGGAGTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:219,56:0.0108:2,2:32:1:31.9:1:0.49901:1.94987:60:6:0.0109:0.0036:0.3 0/0:145:0:0,0:111,34:0:2,0:24.4:1:30.9:1:1:0:60:144:1:0:0.1 -1 229223985 . G A 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GGGGTCAGGAGTCAGTGTGG;RSEQ=CTGTATCCCGGTGGCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:4:2,2:85,223:0.0128:2,2:21.8:1:29:1:0.31075:2.61:60:8:0.013:0:1 0/1:156:2:1,1:46,108:0.0128:2,2:33:1:23.5:1:0.51315:2.33:60:4:0.013:0:1 -1 229226129 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCCAGTGATCCTCCCAC;RSEQ=TCAGCCTCCCAAAGTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 230355248 . C G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22022;SOR=0.41982;LSEQ=GGTCCAGTCCCTTGTCCTCC;RSEQ=TTCTGAGTCACTGGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:14,1:17,0:0.4688:1,1:22.3:1:30.7:1:0.46875:0:60:30:0.4839:0:1 0/1:15:4:4,0:11,0:0.2667:0,0:42:1:29.8:1:1:0:60:8:0.2667:0:1.3 -1 230355372 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14682;SOR=Inf;LSEQ=TGGATCCCCCTCCTGGGCCC;RSEQ=GCATAGATGGCCTGCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:192,105:0:2,0:25.5:1:30.4:1:1:0:60:73.25:1:0:0.3 0/1:185:2:1,1:117,66:0.0108:2,2:47.5:1:30.5:1:1:1.76686:60:4:0.011:0:1 -1 230355438 . C T 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.002;SOR=0.55309;LSEQ=ACCTTTCTTGAGACTTCTGA;RSEQ=GTGGATGCATTCCAGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:111:57,54:159,164:0.2558:2,2:26.9:1:30.3:1:0.7418:1.09:60:110:0.2552:0:2.1 0/1:307:49:27,22:120,137:0.1596:2,2:22.2:1:29.8:1:0.34938:1.40:60:98:0.1612:0:1.4 -1 230355441 . G A 200 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCTTGAGACTTCTGACGT;RSEQ=GATGCATTCCAGATGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:114:56,58:154,162:0.2651:2,2:26.5:1:29.4:1:1:1.02:60:56:0.2623:0:2.1 0/0:304:0:0,0:143,161:0:2,0:25.8:1:30.3:1:1:0:60:75:1:0:0.4 -1 230355443 . A G 119 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=22.30154;LSEQ=TCTTGAGACTTCTGACGTGG;RSEQ=TGCATTCCAGATGTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:1,0:208,223:0.0023:2,0:32:0:14:0:0.4838:0:60:0:0:0:1 0/1:304:15:6,9:134,154:0.0493:2,2:10.9:1:30.7:1:0.79188:1.30406:60:30:0.0508:0:2.3 -1 230355453 . G C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-04;SOR=Inf;LSEQ=TCTGACGTGGATGCATTCCA;RSEQ=ATGTGGGGGCATTCTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:193,231:0:2,0:25.9:1:31.5:1:1:0:60:211:1:0:0.6 0/1:298:8:4,4:128,162:0.0268:2,2:17.4:1:31.3:1:0.73604:1.26:60:16:0.0271:0:2.3 -1 230355471 . G A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07843;SOR=0;LSEQ=CAGATGTGGGGGCATTCTTT;RSEQ=CAAAGTGCTTGTGGCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:5:3,2:162,221:0.0129:2,2:24.2:1:27:1:0.65449:2.04:60:10:0.0129:0:1.8 0/0:279:0:0,0:120,159:0:2,0:26.2:1:31.3:1:1:0:60:68.75:1:0:0.3 -1 230355496 . T A 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64578;SOR=0.47085;LSEQ=GTGCTTGTGGCTGTCTTCAT;RSEQ=CATGGTATTCTCCACTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:96,196:0.0102:2,2:5.3:1:22.7:1:0.25699:4.06:60:2:0.0069:0:2.3 0/0:208:1:1,0:74,133:0.0048:2,0:1:0:21:0:0.36058:0:60:2:0.0049:0:1 -1 230355501 . G A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50159;LSEQ=TGTGGCTGTCTTCATTCATG;RSEQ=TATTCTCCACTGCCCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:83,192:0.0108:2,2:24.3:1:29:1:0.22239:4.60:60:6:0.0109:0:1.3 0/0:184:1:0,1:64,119:0.0054:2,0:26:0:32:0:1:0:60:2:0.0056:0:1 -1 230355561 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13474;SOR=Inf;LSEQ=GTCCCTTAAAACACAATTTG;RSEQ=CTAGATTCTTCCAAAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:3,72:0:1,0:21.7:1:30.9:1:1:0:60:24:1:0:0.1 0/1:44:2:1,1:2,40:0.0455:1,2:7:0:31.5:1:0.13319:16.53:60:4:0.0455:0:1 -1 230459862 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCACACAGGTCACCCCTC;RSEQ=GGGAAGCCCACCCAGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9.5:1:27:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 230459926 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CACTAGCCTCAGGCCTCACT;RSEQ=ACTGCACTGTCTTCTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27.5:1:30:0:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 230723061 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACTGCTCATCCATGATT;RSEQ=CAAGTGATTGCTGTTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 230724462 . T C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.00298;SOR=0.18688;LSEQ=CAGGTAAGTAGGTAGTTGTG;RSEQ=AGGTAAGTAAGTAGGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:17:11,6:22,10:0.3469:2,2:26.9:1:30.7:1:1:1.19548:60:16:0.3404:0:1.2 0/1:45:4:2,2:27,14:0.0889:2,2:20.8:1:26.5:1:0.60761:1.89894:60:3:0.0698:0:1.3 -1 230724514 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18309;SOR=Inf;LSEQ=TAGGTGGGCAGGTAAGTAGG;RSEQ=AGATGTGCAGGTAAGTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:68,53:0:2,0:22.2:1:28.3:1:1:0:60:39.333:1:0:0.4 0/1:91:2:1,1:47,42:0.022:2,2:24:0:32:1:1:1.11766:60:4:0.0222:0:1 -1 230724517 . A G 84 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=GTGGGCAGGTAAGTAGGTAG;RSEQ=TGTGCAGGTAAGTAGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:69,53:0:2,0:22.9:1:28.3:1:1:0:60:9.167:1:0:0.4 0/1:92:8:5,3:43,41:0.087:2,2:18.3:1:28.1:1:0.71622:1.58:50.4:3:0.075:0:4.5 -1 230724522 . C T 88 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.01231;SOR=10.25936;LSEQ=CAGGTAAGTAGGTAGATGTG;RSEQ=AGGTAAGTAGGTAGGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:1:0,1:68,51:0.0083:2,0:19:0:12:0:0.43333:0:60:0:0:0:3 0/1:100:8:5,3:44,47:0.08:2,2:20.9:1:29.5:1:0.48697:1.77:50.8:16:0.0833:0:4.3 -1 230724529 . G GTAGGTAGGTGTGTGGA 93 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=1.000;MSILEN=1;SSF=0.00095;SOR=Inf;LSEQ=GTAGGTAGATGTGCAGGTAA;RSEQ=TAGGTAGGTGGGCAGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:63,56:0:2,0:26.6:1:32:1:1:0:60:58.5:1:0:0.3 0/1:106:9:6,3:47,50:0.0849:2,2:27.4:1:29.5:1:0.48822:2.11:51.8:18:0.0865:0.0189:4.9 -1 230724540 . G T 101 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=18.11827;LSEQ=TGCAGGTAAGTAGGTAGGTG;RSEQ=GCAGGTAAGTAGGTAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:1,0:68,67:0.0074:2,0:5:0:31:0:1:0:60:2:0.0075:0:4 0/1:109:13:7,6:46,50:0.1193:2,2:30:1:27.3:1:0.77229:1.27:52:12:0.1165:0:4.4 -1 230724553 . G C 39 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0.0777;SOR=Inf;LSEQ=GTAGGTGGGCAGGTAAGTAG;RSEQ=TAGGTGTGTAGGTAAGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:66,67:0:2,0:27.2:1:31.8:1:1:0:59.9:266:1:0:0.3 0/1:100:3:1,2:44,53:0.03:2,2:29.7:1:25:1:1:1.65232:51:2:0.0206:0:5.3 -1 230724570 . T C 113 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=13.11179;LSEQ=TAGGTAGGTGTGTAGGTAAG;RSEQ=AGGTAGGTGTGTGGATAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:56,63:0.0164:2,0:18:1:32:1:0.22769:0:60:4:0.0169:0:3.5 0/1:94:17:6,11:34,43:0.1809:2,2:18.3:1:27.7:1:0.59389:1.444:55.6:16:0.1798:0:3.8 -1 230724588 . G GGTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=37;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=AGTAGGTAGGTGTGTGGATA;RSEQ=GTAGGTGTGCAGGTAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:49:12,37:33,30:0.4261:2,2:23.3:1:29.9:1:0.00355:3.35363:59.8:98:0.4414:0.3391:0.1 0/0:58:0:0,0:19,28:0:2,0:18.1:1:30.3:1:1:0:59.4:22.5:0.9574:0:0.7 -1 230724609 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.07729;SOR=Inf;LSEQ=GTAGGTGTGCAGGTAAGTAG;RSEQ=TAGGTGTGTAGGTAAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:27,47:0:2,0:14.3:1:31.4:1:1:0:59.8:36:1:0:0.2 0/1:29:2:1,1:4,23:0.069:2,2:11.5:1:33.5:1:0.3202:5.25:60:4:0.0714:0:1 -1 231473151 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCCCTCCAGAGGCGGCGGCG;RSEQ=CTCCGGCGGCAGCAGCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:41,30:0.0274:2,2:30:0:31.5:1:1:1.36072:60:4:0.0274:0:1.5 0/0:35:0:0,0:14,21:0:2,0:26.9:1:32.1:1:1:0:60:70:1:0:0.3 -1 232455307 . A T 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTAAAAGAACTCAGATTGC;RSEQ=TATGAAATGCATCTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:138,40:0:2,0:23.4:1:30.1:1:1:0:60:177:1:0:0.2 0/1:97:12:9,3:63,22:0.1237:2,2:25.3:1:30.8:1:1:1.05:60:24:0.1237:0:1 -1 232455324 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14489;SOR=Inf;LSEQ=TGCATATGAAATGCATCTCT;RSEQ=TCTTCTTGCTTTTGATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:181,59:0:2,0:24.7:1:30:1:1:0:60:39:1:0:0.2 0/1:148:2:1,1:97,49:0.0135:2,2:13.5:1:27:1:1:1.96983:60:4:0.0136:0:1.5 -1 232455397 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05098;SOR=Inf;LSEQ=GAAGCTTTTCCTATGCTCTG;RSEQ=TGACACGAACAAACCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:487:0:0,0:259,227:0:2,0:26.1:1:31.9:1:1:0:60:80:0.9979:0:0.5 0/1:288:3:1,2:145,140:0.0104:2,2:19.3:1:27.3:1:0.6185:2.06637:60:6:0.0105:0:1.7 -1 232455403 . C T 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05034;SOR=1.35123;LSEQ=TTTCCTATGCTCTGCTGACA;RSEQ=GAACAAACCATCAATCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:182:95,87:158,150:0.3714:2,2:26.7:1:30.1:1:0.8522:1.04:60:59.667:0.3691:0:1.1 0/1:295:131:64,67:82,82:0.4441:2,2:24.4:1:29.3:1:0.90681:1.04674:60:25.2:0.436:0:1.1 -1 232455440 . C A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0429;SOR=Inf;LSEQ=ATTGCCTGGATTTCCTGAAC;RSEQ=TCTCAGTACAGAGGCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:178,249:0:2,0:25.7:1:31.4:1:1:0:60:46.444:1:0:0.5 0/1:231:3:2,1:97,131:0.013:2,2:22.3:1:29.7:1:0.57789:2.69:60:6:0.0132:0:1.7 -1 232455454 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11273;SOR=Inf;LSEQ=CTGAACCTCTCAGTACAGAG;RSEQ=CTTCCAGGCCAAGAAGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:143,224:0:2,0:24.6:1:31.4:1:1:0:60:35.7:1:0:0.4 0/1:186:2:0,2:73,111:0.0108:2,0:19:1:31.5:1:0.52055:0:60:4:0.0108:0:1 -1 232455466 . A G 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03537;SOR=Inf;LSEQ=GTACAGAGGCTTCCAGGCCA;RSEQ=GAAGGGTTGAGAAAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:115,193:0:2,0:24.2:1:30.2:1:1:0:60:50.333:1:0:0.4 0/1:152:3:2,1:55,94:0.0197:2,2:31.7:1:26.7:1:0.55646:3.39:60:2:0.0132:0:1.3 -1 232455500 . A G 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=0.17099;LSEQ=AGGCCTCCTTCCAGCTGAGG;RSEQ=CAGTGAAGTGTGGTAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:39:8,31:27,104:0.2294:2,2:23.7:1:31.5:1:1:1.00597:60:38:0.2289:0:1.1 0/1:83:4:0,4:20,59:0.0482:2,0:27:1:32.5:1:0.5678:0:60:8:0.0482:0:1 -1 232455839 . AAC A 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=CATGCACACACACACACACA;RSEQ=ACACACACATGCACACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:22.5:1:32:0:1:0:60:4:0.5:0:0 0/0:2:0:0,0:1,1:0:2,0:31:1:25.5:1:1:0:60:4:1:0:0.5 -1 232522227 . G T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGTCACACCTGTCCCTG;RSEQ=AGCCAAGTGCAGCTTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:27.5:1:1:0:60:4:1:0:1 -1 233163436 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53131;SOR=0;LSEQ=CAGAGAGTAAATATTTTAAG;RSEQ=ATTGTGGGCCACATGTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:31.5:1:28.5:1:1:1.07415:60:4:0.069:0:1 0/0:16:0:0,0:9,7:0:2,0:35:1:32:1:1:0:60:32:1:0:0.2 -1 234162957 . C T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00046;SOR=0.48808;LSEQ=CTCTGTCTCCCACCACCACA;RSEQ=GCTTGATGGCCTGCATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:107:54,53:121,122:0.3057:2,2:29.1:1:30.8:1:1:1.03:60:214:0.3092:0:1.1 0/1:232:41:18,23:101,90:0.1767:2,2:23.8:1:29.7:1:0.30769:1.4317:60:40:0.1762:0:1.2 -1 234162987 . T C 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15677;SOR=Inf;LSEQ=CCTGCATCTGGGCTGCTCAC;RSEQ=GGGCCACAGAGGGCAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:116,166:0:2,0:25.8:1:30.2:1:1:0:60:46:0.9964:0:0.4 0/1:186:2:1,1:79,105:0.0108:2,2:5:0:28.5:1:1:1.33:60:4:0.011:0:2.5 -1 234162998 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16786;SOR=Inf;LSEQ=GCTGCTCACTGGGCCACAGA;RSEQ=GGCAGTGGCAGCTGGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:93,144:0:2,0:24.2:1:31.2:1:1:0:60:474:1:0:0.4 0/1:165:2:1,1:65,98:0.0121:2,2:36.5:1:28:1:1:1.50:60:4:0.0123:0:1 -1 234163017 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51528;SOR=0;LSEQ=AGGGCAGTGGCAGCTGGGTG;RSEQ=TGAGATGGGAAGCTGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:45,120:0.012:2,2:7.5:1:26.5:1:0.47623:2.65:60:4:0.0122:0:1 0/0:115:0:0,0:38,77:0:2,0:20.5:1:31:1:1:0:60:37.333:1:0:0.3 -1 234164879 . G A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCCAGTGAGCTTGGGGCTGG;RSEQ=TGATAACATCGATTAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:28.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:17:0:33:0:1:0:60:2:1:0:0 -1 234271868 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTAGGAAGCCTTCCCT;RSEQ=AAACCCAAGTACAGCTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 234272690 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05411;SOR=Inf;LSEQ=TGTATCTCTAAGGGTTCCTT;RSEQ=TGTGAACCTTCTTCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:0:1,0:22.8:1:30.8:1:1:0:60:122:1:0:0.1 0/1:19:2:2,0:17,0:0.1053:1,0:19:1:32.5:1:1:0:60:4:0.1053:0:1 -1 234272887 . C G 216 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTAACAGATGCATGCACA;RSEQ=GTACCTGTCACAAAATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:0:0,0:388,402:0:2,0:25.1:1:30.6:1:1:0:60:55.429:0.9949:0:0.1 0/1:448:125:64,61:159,163:0.279:2,2:25.4:1:31.1:1:0.75266:1.08:60:250:0.2828:0:1.2 -1 234273318 . G T 46 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AACCTTGGCTTTGAATGAAA;RSEQ=GAAAGAGAGAGAGACACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:25.3:1:29.3:1:1:0:60:6:0.75:0:1.3 0/0:2:0:0,0:1,1:0:2,0:8:0:32.5:1:1:0:60:4:1:0:0.5 -1 234800899 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATAGGTACACACAGCCT;RSEQ=TCTCTCTCTCTCTCCCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 234802093 . T A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22299;SOR=1.95894;LSEQ=TCCAGATCATACCAATCACC;RSEQ=CTGAGAAGCCCAATCACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:63:38:37,1:25,0:0.6032:1,1:22.7:1:30.4:1:1:0:60:76:0.6032:0:1 1/0:24:18:18,0:6,0:0.75:0,1:18.1:1:30.2:1:1:0:60:36:0.75:0:1.2 -1 234802147 . C T 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AACATAAATCAACGTGAGGA;RSEQ=CTGAGAGCTCGCTTGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:108,18:0:2,0:20.7:1:31.7:1:1:0:60:62:1:0:0.2 0/1:63:10:8,2:47,6:0.1587:2,2:23.9:1:28.6:1:0.602:1.93392:60:20:0.1613:0:1.4 -1 234802267 . A G 260 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54399;SOR=1.11005;LSEQ=TTCCTTTTTCAAAGACTGGG;RSEQ=ACACTTAAAAATATCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:497:326:150,176:83,88:0.6559:2,2:27.6:1:31.2:1:0.63641:1.10644:60:325:0.6579:0:1.1 1/0:321:218:108,110:52,48:0.6791:2,2:28.2:1:30.4:1:0.71799:1.10305:60:23.222:0.6742:0:1.2 -1 234802365 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28983;SOR=3.64602;LSEQ=GACTCTGGCTCCTGGATGGC;RSEQ=TCAAACCTGCCCTTGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:1:0,1:41,144:0.0054:2,0:39:0:13:0:1:0:60:0:0:0:5 0/1:103:2:1,1:29,72:0.0194:2,2:26:1:28.5:1:0.49971:2.46:60:4:0.0196:0:1.5 -1 234802408 . C T 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57894;SOR=1.29715;LSEQ=CCGAGGCTGGTCTGGGAGTA;RSEQ=CATTTGCAAATGGCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:61:2,59:3,38:0.598:2,1:21.8:1:30.5:1:0.3888:2.30912:60:122:0.598:0:1.1 1/0:44:29:0,29:1,14:0.6591:1,1:21.7:1:29.4:1:0.34091:0:60:58:0.6591:0:1 -1 236306018 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05769;SOR=Inf;LSEQ=AACGACTCGCTGCCGCCCAC;RSEQ=CTGACCCCGGCCGTGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:18,12:0:2,0:22:1:29.6:1:1:0:60:29:1:0:0.4 0/1:10:2:1,1:4,4:0.2:2,2:36.5:1:31.5:1:1:1:60:4:0.2:0:1.5 -1 236306034 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGCTGACCCCGGCCGTG;RSEQ=CCCCCTACGTGAAGCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:17,11:0.0667:2,2:38:1:29.5:1:1:1.52251:60:4:0.069:0:1 0/0:10:0:0,0:5,5:0:2,0:23.6:1:31.2:1:1:0:60:20:1:0:0.7 -1 236306036 . C A 31 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.04991;SOR=Inf;LSEQ=ACGCTGACCCCGGCCGTGCC;RSEQ=CCCTACGTGAAGCTTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:16,10:0:2,0:28.8:1:28.7:1:1:0:60:7.667:1:0:0.4 0/1:8:2:1,1:3,3:0.25:2,2:28:0:31:1:1:1:60:4:0.25:0:1.5 -1 236306564 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAGAAGGCAGGGGAGGG;RSEQ=TGGAGGCCGCCGCTCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 236306825 . A G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGTTGGCAGGGTGAGACC;RSEQ=TGTTGGTTTTGATGAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:28:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:9:1:28.5:1:1:0:60:4:1:0:1 -1 240656797 . G A 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAACGAGAAAAGAGAG;RSEQ=GGCTGGCTGTGAAGGGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:33.7:1:32.7:1:1:0:60:6:0.375:0:1.3 0/0:2:0:0,0:0,2:0:0,0:8.5:1:31.5:1:1:0:60:4:1:0:0 -1 240656824 . C A 63 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGAAGGGCCGTAGAGTA;RSEQ=GGGATCAATCTTACTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:9.3:1:31.8:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 240683271 . T G 100 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.17838;LSEQ=ATGCCTGTAATCCCAGCTAC;RSEQ=CAGGAGGCTGAGGCATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:9,0:15,0:0.36:1,0:25.4:1:31.6:1:1:0:58.9:18:0.3913:0:1 0/1:5:2:2,0:3,0:0.4:0,0:4.5:1:30:1:1:0:60:4:0.4:0:1.5 -1 240683278 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCCCAGCTACTCAGGAG;RSEQ=CTGAGGCATGAGAACCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:24,0:0.0769:1,0:30:1:27:1:1:0:60:4:0.0769:0:1 0/0:6:0:0,0:6,0:0:0,0:10.5:1:31.7:1:1:0:60:12:1:0:0.7 -1 240683374 . C G 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TGGGCAACAAGAGCAAAACT;RSEQ=CATCCCAAAAAATAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:106,6:0:2,0:22.3:1:31.6:1:1:0:59.7:224:1:0:0.1 0/1:70:11:11,0:55,4:0.1571:2,0:13.4:1:32.6:1:1:0:54.5:22:0.1571:0:1 -1 240683382 . A AAAAAT 133 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=8.000;MSILEN=5;SSF=0.00364;SOR=3.05558;LSEQ=AAGAGCAAAACTCCATCCCA;RSEQ=AAAATAAAATAAAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:15:15,0:82,8:0.1181:2,1:26.9:1:29.9:1:0.59805:0:59.7:30:0.12:0:0.1 0/1:72:21:18,3:34,4:0.2917:2,2:24.9:1:30.3:1:0.69102:1.40797:60:42:0.2917:0.0139:0 -1 240683489 . G A 246 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.66739;SOR=0.95375;LSEQ=CAAACTTACTTCTTCAGTAT;RSEQ=CAATTTTTGTGTGTATGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:807:378:185,193:221,206:0.4684:2,2:26.6:1:28.8:1:0.43784:1.11905:60:188:0.4724:0:1.1 0/1:611:279:138,141:162,170:0.4566:2,2:27.3:1:28.4:1:0.87136:1.03:60:92:0.46:0:1.1 -1 240683509 . T TA 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAATTTTTGTGTGTATGAG;RSEQ=ATGCCAAGCACATGGTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:0:0,0:347,423:0:2,0:25.3:1:28.7:1:1:0:60:109:0.9987:0:0.5 0/1:572:38:18,20:240,292:0.0664:2,2:24.3:1:29:1:0.86649:1.09:60:76:0.067:0.0157:1.2 -1 240683595 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13107;SOR=Inf;LSEQ=TAGAGTTGGGATGAGCTCTG;RSEQ=TGGTCAACTAGTCCATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:27,173:0:2,0:23.2:1:31.7:1:1:0:60:49:1:0:0.2 0/1:114:2:1,1:17,95:0.0175:2,2:23:1:26:1:0.29204:5.46:60:4:0.018:0:1 -1 240683666 . C T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1256;SOR=0.40298;LSEQ=GCAGGGGGACAAATAACCAC;RSEQ=TCAACCTTTACTGTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:23:0,23:1,32:0.4107:1,1:21.8:1:30.2:1:1:0:60:22:0.4:0:1.3 0/1:23:5:0,5:0,18:0.2174:1,0:23:1:31:1:1:0:60:10:0.2273:0:1 -1 241661227 . A ATTT 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTCCTTTAAGGTTGATCC;RSEQ=TTTTTGTGTGCTGTCTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1419:0:0,0:623,795:0:2,0:26.4:1:30.5:1:1:0:59.8:127.909:0.9993:0:0.1 0/1:878:21:8,13:369,488:0.0239:2,2:24.5:1:29.7:1:0.82411:1.22846:59.8:42:0.0241:0.0057:0.1 -1 241661327 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10253;SOR=Inf;LSEQ=AGTGATATTTGGTTTCCTAA;RSEQ=GCAAAAGGTGACATAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:31,297:0:2,0:24.9:1:31.1:1:1:0:60:81:1:0:0.1 0/1:155:2:1,1:16,137:0.0129:2,2:17:1:29.5:1:0.20796:8.34:60:4:0.0132:0:1 -1 241663893 . T TTGAG 75 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=4.000;MSILEN=4;SSF=0.26846;SOR=0.28022;LSEQ=GTGTAACACATTTTTAATCT;RSEQ=TGAGTGAGTGAGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:535:6:0,6:150,369:0.0112:2,0:33.7:1:29.3:1:0.18992:0:60:12:0.0126:0:0 0/0:316:1:0,1:99,213:0.0032:2,0:40:0:22.8:0:1:0:60:2:0.0035:0:3 -1 241665510 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03095;SOR=0.21428;LSEQ=AGACAGGCTTGTAGGGAGGC;RSEQ=TTTTATTTTTCTTAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:21:21,0:16,0:0.5676:1,1:20.1:1:30.1:1:1:0:60:42:0.5676:0:1 0/1:14:3:3,0:10,1:0.2143:2,0:25.7:1:30.3:1:1:0:60:6:0.2308:0:1 -1 241666973 . G A 58 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTATCAAATGACTTGCT;RSEQ=AAATCCAGACATACACTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:7,1:0.3333:2,0:35.5:1:29:1:1:0:60:8:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 241667233 . C T 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00055;SOR=0.47056;LSEQ=TGCTGGAACAGTGCGCCTTG;RSEQ=GCATCCAGCTGCGGGATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:141:140,1:139,2:0.4965:1,1:25.2:1:30.3:1:1:2.01:60:140:0.4965:0:2 0/1:139:44:43,1:93,1:0.3165:1,1:24.4:1:31:1:0.53761:2.14958:60:88:0.3212:0:2 -1 241667244 . G T 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.8376;SOR=1.04986;LSEQ=TGCGCCTTGCGCATCCAGCT;RSEQ=CGGGATAACTTTAAACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:239:235,4:105,1:0.6928:1,1:21.9:1:30.1:1:1:1.78459:60:28.875:0.6896:0:1.7 1/0:165:116:113,3:46,3:0.703:2,1:24.1:1:30:1:0.36321:2.44:60:57:0.7037:0:1.4 -1 241667523 . C T 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAGAGCTTCAAATTTATT;RSEQ=GGAGCAGTGACAAAAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1552:0:0,0:612,939:0:2,0:24.7:1:30.2:1:1:0:59.5:85.167:0.9993:0:0.1 0/1:979:37:13,24:394,544:0.0378:2,2:22.5:1:29.8:1:0.49743:1.33672:53.2:74:0.0381:0:1.1 -1 241669668 . C T 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTATAGAACCATAAGGTA;RSEQ=GACAATGCCACTGATAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:0,5:1,21:0.1852:1,0:18.4:1:30.2:1:1:0:60:10:0.1852:0:2.2 0/0:3:0:0,0:0,3:0:0,0:18.7:1:29:1:1:0:60:6:1:0:0.3 -1 241669842 . C T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTTATTTTTTGGGATG;RSEQ=CTCAGACAACTTTGGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:20.7:1:29.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 241671638 . C T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60191;SOR=1.93443;LSEQ=GGCACAGAAAGGCTAAATGA;RSEQ=TTTCCTATGGTCCCATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:0.3333:0,0:27.5:1:30.3:1:1:0:60:12:0.3529:0:1.7 1/0:4:2:2,0:1,1:0.5:2,0:22:1:28.5:1:1:0:60:4:0.5:0:1 -1 241675074 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACATACACTAAATTCA;RSEQ=GTGTCCTAAAAATAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:50,0:0.0385:1,2:19.5:1:30.5:1:0.03846:0:60:4:0.0385:0:1.5 0/0:13:0:0,0:13,0:0:1,0:20.9:1:32.5:1:1:0:60:26:1:0:0.2 -1 241675119 . G C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00113;SOR=0.26784;LSEQ=GGATTGAAACATAAAACCAA;RSEQ=ATTCCTTCAAGAAATAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:50:50,0:32,0:0.6098:1,1:25.6:1:31.9:1:1:0:60:49:0.6049:0:1.1 0/1:41:12:12,0:29,0:0.2927:1,0:17.7:1:32.3:1:1:0:60:24:0.2927:0:1.1 -1 241676239 . A G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTGTGTGTGTGTGTGTGT;RSEQ=TATGAGAAACACACACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:11:1:31.7:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 241676255 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTATATGAGAAACACACA;RSEQ=TTTCTGTTCATTTTTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14:1:31:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 241676758 . C T 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.083;SOR=0.56112;LSEQ=TAAGCACCATATTAATATCA;RSEQ=CACTAAAAATAATGCTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:138:78:78,0:59,1:0.5652:1,1:24.2:1:31.5:1:0.43478:0:60:77:0.5662:0:1.1 0/1:57:24:24,0:33,0:0.4211:1,1:26.3:1:29.8:1:1:0:60:23:0.4107:0:1.1 -1 241677035 . T A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAAATTAATCAGAAAAATA;RSEQ=TTCAAATTTACAATTTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:157,452:0:2,0:23.4:1:30:1:1:0:60:45.846:1:0:0.1 0/1:306:22:7,15:88,196:0.0719:2,2:21.4:1:29.8:1:1:1.04:60:44:0.0719:0:1.1 -1 241680247 . G A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55518;SOR=0;LSEQ=AGGCATAAGCCACCGTGCCC;RSEQ=GCCTTAAATTTTAAAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:17,0:0.1905:1,0:10.8:1:29.8:1:1:0:60:8:0.2:0:1 0/0:5:0:0,0:5,0:0:0,0:24.4:1:26.4:1:1:0:55:4:1:0:0.6 -1 241680555 . T C 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGGGCGCCATAATACTTA;RSEQ=CATTTGGCACCTTTAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1176:0:0,0:565,610:0:2,0:25.3:1:30.2:1:1:0:60:47.958:1:0:0.1 0/1:827:28:15,13:390,409:0.0339:2,2:25.3:1:31.2:1:0.70209:1.21:60:56:0.0342:0:1.1 -1 241682757 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19935;SOR=5.16523;LSEQ=AGGCCCGCCACGCCGGCACG;RSEQ=GCGCTAAGCCCAGAGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:1:1,0:53,0:0.0185:1,0:26:0:32:0:1:0:60:2:0.0185:0:1 0/1:22:2:1,1:19,1:0.0909:1,2:25:1:28:1:0.17749:13.78761:60:4:0.0909:0:1 -1 241682821 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24863;SOR=4.16515;LSEQ=CTCTCCCGCCAAGTCGCGGG;RSEQ=GCCCAGGCCGGCAGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:1:0,1:330,48:0.0026:2,0:1:0:27:0:0.12929:0:60:2:0.0027:0:1 0/1:183:2:1,1:155,26:0.0109:2,2:7.5:1:29:1:0.274:5.86897:60:4:0.011:0:1 -1 241683101 . C A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27965;SOR=0;LSEQ=TTGTCAGAAACCGTTCCGCC;RSEQ=ACCGGCCTCCGCTCTTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:1,2:20,170:0.0155:2,2:15.7:1:28.7:1:0.29355:4.20:60:6:0.0159:0:1 0/0:127:0:0,0:24,103:0:2,0:21:1:31:1:1:0:60:62.5:1:0:0.1 -1 242373248 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGATTACAGGCACCCAA;RSEQ=ACTACATCCAGCTAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:1:29:1:1:0:60:4:1:0:1 -1 242375779 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAGACCTGGAGCCAACA;RSEQ=ATGCTCCCAGGAACTCGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:29.5:1:1:0:60:4:1:0:1 -1 242376422 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGGGCTCCCTTCCCCCGTGG;RSEQ=GATTCCTCACAATTGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:47:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 242505729 . T C 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15564;SOR=0;LSEQ=CCAATGTCTCTGCTGGTCCC;RSEQ=GAGGACATGATGTGTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:4:2,2:219,105:0.0122:2,2:25.8:1:29.3:1:0.59897:2.08067:58.5:8:0.0123:0:1 0/0:216:0:0,0:148,68:0:2,0:25.6:1:29.5:1:1:0:55.7:23:1:0:0.1 -1 242505879 . G A 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02311;SOR=0;LSEQ=AGTTTGAACTTTCCTTACCT;RSEQ=TCAGTGATGTCCCAGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:345:345:103,242:0,0:1:0,2:24.7:1:29.5:1:1:0:47.6:33.5:1:0:1.1 1/1:222:218:71,147:0,1:0.982:0,2:23.6:1:28.5:1:1:0:47.5:71.667:0.9908:0:1.2 -1 242505965 . G A 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02365;SOR=0;LSEQ=CCTCAGGTAACCAAAGTGAC;RSEQ=TGGAGATTTAAAGTTATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:72:3,69:0,0:1:0,1:24.9:1:31.4:1:1:0:56.2:144:1:0:1.3 1/1:30:27:0,27:0,3:0.9:0,1:21.3:1:31:1:1:0:58.3:54:0.9:0:1.4 -1 242506053 . CA C 126 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.42857;SOR=0.28869;LSEQ=AGAAATCCAATACAAAGAGA;RSEQ=AAAAAAAAAAGGTCATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:0,15:0,1:0.7895:0,1:29:1:32.5:1:1:0:58.5:30:0.7895:0:0.1 1/0:2:1:0,1:0,1:0.5:0,0:49:0:29:0:1:0:60:2:1:0:0 -1 242508611 . A G 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTAAGTAGTAGAATGTAG;RSEQ=TTTAAATTCAGATCTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:27:1:29.8:1:1:0:32.3:8:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 242508644 . G A 100 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCTAATTTCAAAGTCC;RSEQ=TGGTTGTTAACTGCGTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:1:0,0:18.8:1:30.2:1:1:0:40.1:20:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 242508681 . G T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGCTAGCTTGGAAATGGA;RSEQ=TTGCTTGCTGGCAGGTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:18,0:0,0:1:0,1:28.1:1:30.6:1:1:0:43.3:17:1:0:1.8 1/1:3:3:3,0:0,0:1:0,0:25:1:31.7:1:1:0:56.3:6:1:0:1 -1 242508913 . G A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03016;SOR=Inf;LSEQ=ATCCACCTGGAGTACCCTCT;RSEQ=TTGGCAGAATATGACTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:0:0,0:198,238:0:2,0:25.3:1:31.9:1:1:0:38.8:144.333:1:0:0.1 0/1:313:4:3,1:161,148:0.0128:2,2:12.8:1:26.5:1:0.62433:2.75:49.8:8:0.0129:0:1.3 -1 242508928 . C A 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00018;SOR=0;LSEQ=CCTCTGTTGGCAGAATATGA;RSEQ=TTTCAGAAGGATTCTGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:17:8,9:172,223:0.0413:2,2:19.9:1:30:1:0.80679:1.15:40.5:34:0.0415:0:1.1 0/0:286:0:0,0:146,140:0:2,0:24:1:31.3:1:1:0:35.5:285:1:0:0.1 -1 242509140 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGTGCATTGGAGAGAAG;RSEQ=GCAAAAGCAGAAACTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:1,15:0,0:1:0,1:33.5:1:31.1:1:1:0:28.7:32:1:0:1.1 1/1:5:5:1,4:0,0:1:0,2:22.4:1:29.8:1:1:0:29.6:10:1:0:1 -1 242509193 . C T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAAGCAAGATACCAGTT;RSEQ=CAGGACAGACACACAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:30.4:1:29.1:1:1:0:40.6:14:1:0:1.4 1/1:2:2:1,1:0,0:1:0,2:36:1:31.5:1:1:0:58.5:4:1:0:1 -1 242509330 . T C 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGATCTCCCCCCCCCCCATA;RSEQ=ATACAACCATATATCATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:39.5:1:33:1:1:0:33.5:8:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 242509350 . TT GTA 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TATACAACCATATATCATAT;RSEQ=ATATCACATATATATGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:30:1:31.3:1:1:0:29:6:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 243213163 . T C 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01915;SOR=Inf;LSEQ=GAATGTGGAAGTTCACTCTG;RSEQ=GGCCGTGTTCCCCTGGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:13,6:0:2,0:24.5:1:30.4:1:1:0:53.4:38:1:0:0.3 0/1:8:3:2,1:0,5:0.375:0,2:30.7:1:28.7:1:0.10714:0:49.7:6:0.375:0:1 -1 243213669 . G T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55421;SOR=0;LSEQ=CTGGTGGCCCATGAGTGGCG;RSEQ=TCATGATCTTCAGCAAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:3:1,2:67,82:0.0197:2,2:11.3:1:26.7:1:1:1.62909:60:6:0.02:0:1 0/0:68:0:0,0:32,36:0:2,0:24.8:1:30.5:1:1:0:57.3:33:1:0:0.2 -1 243213717 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGCAGGGCGCACCAGG;RSEQ=TCACCCTAACCAGGATAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:72,68:0.0141:2,2:39:1:31:1:1:1.05842:60:4:0.0144:0:1 0/0:58:0:0,0:29,29:0:2,0:23.8:1:30.1:1:1:0:57.8:57:1:0:0.6 -1 243213751 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09123;SOR=Inf;LSEQ=GATAACCAGACCATCAGCCA;RSEQ=ATGCTGAGCGAGCGGTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:63,56:0:2,0:26.8:1:31.7:1:1:0:57.4:58.5:1:0:0.2 0/1:52:2:1,1:25,25:0.0385:2,2:29.5:1:28.5:1:1:1:60:4:0.04:0:1 -1 243213760 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ACCATCAGCCAGATGCTGAG;RSEQ=GAGCGGTGGTACACCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:57,50:0.0183:2,2:40.5:1:32:1:1:1.13863:60:4:0.0185:0:1 0/0:49:0:0,0:24,24:0:2,0:26.4:1:31.5:1:1:0:55.7:96:0.9796:0:1 -1 243213761 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=55.44461;LSEQ=CCATCAGCCAGATGCTGAGC;RSEQ=AGCGGTGGTACACCCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:5:3,2:54,46:0.0476:2,2:21:1:28.2:1:1:1.27:56:4:0.0385:0:1.2 1/0:47:35:18,17:5,7:0.7447:2,2:28.1:1:30.1:1:0.73997:1.47:55.3:70:0.7778:0:1.1 -1 243214035 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14754;SOR=Inf;LSEQ=GAGCAGCTTCTGTGGGGCAG;RSEQ=ACAGCTGCACACAGTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:63,34:0:2,0:25.5:1:29.8:1:1:0:49.4:31.333:1:0:0.2 0/1:61:2:1,1:34,25:0.0328:2,2:17:1:32:1:1:1.35304:49.5:4:0.0328:0:1.5 -1 243214038 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.145;SOR=Inf;LSEQ=CAGCTTCTGTGGGGCAGAAC;RSEQ=GCTGCACACAGTCAGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:62,38:0:2,0:25.6:1:29.8:1:1:0:49.9:13.286:1:0:0.2 0/1:62:2:2,0:33,27:0.0323:2,0:27:1:30:0:0.50026:0:40:4:0.0328:0:1 -1 243214042 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51807;SOR=0;LSEQ=TTCTGTGGGGCAGAACAGCT;RSEQ=CACACAGTCAGGGAACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:60,38:0.02:2,2:24:0:31:1:1:1.57145:45:4:0.0208:0:1 0/0:66:0:0,0:35,31:0:2,0:24.5:1:31.8:1:1:0:48.7:132:1:0:0.2 -1 243214127 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57154;SOR=2.84375;LSEQ=GGACGGCAGGGAAATAGACC;RSEQ=CCAGGCACTACGGGAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:1:0,1:60,69:0.0076:2,0:12:0:31:0:1:0:60:2:0.0079:0:1 0/1:93:2:1,1:43,47:0.0215:2,2:36.5:1:31:1:1:1.09:40.5:4:0.0222:0:1.5 -1 243214253 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12867;SOR=Inf;LSEQ=TGAGGGAGGTGACCCGTGGG;RSEQ=AGCCCTGCTGCTGCCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:14,28:0:2,0:26.2:1:31.4:1:1:0:37.1:41:1:0:0.1 0/1:24:2:1,1:8,14:0.0833:2,2:39:0:30.5:1:1:1.71:45:4:0.0833:0:1.5 -1 243214297 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5338;SOR=0;LSEQ=CTGCTCATTCCCAGCACATG;RSEQ=CCGGTGAGGACACAGCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:22,25:0.04:2,2:26.5:1:31.5:1:1:1.13:49:4:0.0408:0:1 0/0:28:0:0,0:12,16:0:2,0:23.2:1:30.3:1:1:0:41.9:27:1:0:0.4 -1 243214314 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13169;SOR=Inf;LSEQ=ATGGCCGGTGAGGACACAGC;RSEQ=AGTGACGAGGAGCACACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:22,21:0:2,0:28.5:1:30.3:1:1:0:41:86:1:0:0.1 0/1:25:2:1,1:10,13:0.08:2,2:30.5:1:28.5:1:1:1.29:47:4:0.087:0:1 -1 243214331 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13379;SOR=Inf;LSEQ=AGCGAGTGACGAGGAGCACA;RSEQ=GGTCATCCATGAGGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,18:0:2,0:31.1:1:30.2:1:1:0:41.3:38:1:0:0.1 0/1:23:2:1,1:10,11:0.087:2,2:45.5:1:30.5:1:1:1.10:41:4:0.087:0:1.5 -1 243214611 . A T 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GTCCCACCCTGTCCTCCTCC;RSEQ=ACACATACTTGGATGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:25,12:0:2,0:25:1:29.9:1:1:0:57:17.5:1:0:0.1 1/0:10:6:5,1:3,1:0.6:2,2:17.2:1:30.7:1:1:1.58:32:12:0.6:0:1 -1 243214755 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52009;SOR=0;LSEQ=TGGGGATGGGGGCCCAGGGA;RSEQ=GCCTTCCAAGGTGACCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:0,2:47,59:0.0185:2,0:14:1:30.5:1:0.50381:0:22:4:0.0185:0:1 0/0:70:0:0,0:36,34:0:2,0:22.5:1:29.7:1:1:0:50.7:140:1:0:0.1 -1 243214794 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17634;SOR=Inf;LSEQ=TTTCCTCCCAATGGATCCTG;RSEQ=CACCTTCTGGTGCAAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:37,59:0:2,0:28.6:1:31.5:1:1:0:44.6:95:1:0:0.2 0/1:70:2:1,1:33,35:0.0286:2,2:26.5:1:29:1:1:1.06:46.5:4:0.029:0:1 -1 243214809 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50808;SOR=0;LSEQ=TCCTGCCACCTTCTGGTGCA;RSEQ=GAGACCTGAAAGTGTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:36,50:0.0227:2,2:23:0:33:0:1:1.38:41:4:0.023:0:1.5 0/0:65:0:0,0:30,35:0:2,0:26.9:1:30.3:1:1:0:45.4:64:1:0:0.2 -1 243215595 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCCGCTGGGAGCCGCTG;RSEQ=ATGGTTCCGAGGCTGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:77,95:0.0115:2,2:19.5:1:27.5:1:1:1.23:60:4:0.0118:0:1 0/0:33:0:0,0:15,18:0:2,0:25.7:1:31.6:1:1:0:51.4:66:1:0:0.2 -1 243217140 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=Inf;LSEQ=TGGAGAGTCCGCTGTGAGGC;RSEQ=GAGGCCGGGCCCGTGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:7:0:26:0:1:0:22:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:37:1:30.5:1:1:1:27:4:0.5:0:1.5 -1 243430907 . GA G 48 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.27218;SOR=5.05351;LSEQ=AGAGCCAAACTCCCTCTCAA;RSEQ=AAAAAAAAAAAAAAGTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:10,0:0.0833:0,0:13:0:33:0:1:0:60:2:0.0833:0:0 0/1:9:3:2,1:5,1:0.3333:2,2:17.3:1:30.3:1:1:2.23609:60:6:0.3333:0:0.7 -1 243431052 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52619;SOR=0;LSEQ=TTCAAATCTTGGATCCTTGG;RSEQ=GATCCTTAGAGCCACTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:0,2:108,52:0.0123:2,0:19:1:26.5:1:0.10973:0:60:4:0.0126:0:1 0/0:100:0:0,0:63,37:0:2,0:27.1:1:30.5:1:1:0:59.7:49:1:0:0.1 -1 243431107 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15469;SOR=Inf;LSEQ=TTCTCAATTTCAGCCATTAC;RSEQ=CAATCAGTTATACAAGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:129,134:0:2,0:27.4:1:29.8:1:1:0:59.4:64.75:1:0:0.1 0/1:171:2:1,1:81,88:0.0117:2,2:16:0:33:1:1:1.09:60:4:0.0118:0:1.5 -1 243431125 . G T 49 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16182;SOR=0;LSEQ=ACACAATCAGTTATACAAGG;RSEQ=ATACACTTGACATGCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:4:1,3:110,141:0.0157:2,2:24.8:1:24.8:1:0.63468:2.33335:60:3:0.0121:0:1.5 0/0:161:0:0,0:72,88:0:2,0:26.8:1:30.4:1:1:0:59.7:159:1:0:0.1 -1 243431146 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16391;SOR=Inf;LSEQ=ATACACTTGACATGCAGACA;RSEQ=CCCATCATTGACTGCACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:79,129:0:2,0:25.8:1:31.8:1:1:0:59.2:40.6:1:0:0.1 0/1:142:2:1,1:60,80:0.0141:2,2:30.5:1:31.5:1:1:1.33:60:4:0.0141:0:2 -1 243431159 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15811;SOR=Inf;LSEQ=GCAGACAGCCCATCATTGAC;RSEQ=GCACTAAGTCCAGTTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:60,118:0:2,0:26.2:1:30.4:1:1:0:57.9:58.333:1:0:0.1 0/1:118:2:1,1:43,73:0.0169:2,2:17.5:1:32:0:1:1.69:60:4:0.0172:0:2 -1 243431167 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51793;SOR=0;LSEQ=CCCATCATTGACTGCACTAA;RSEQ=TCCAGTTTGGCTTTTATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:46,115:0.0123:2,2:33:1:31:1:0.49481:2.48:60:4:0.0127:0:1 0/0:109:0:0,0:39,70:0:2,0:25:1:31.2:1:1:0:57.6:108:1:0:0.1 -1 243431184 . T A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52578;SOR=0;LSEQ=TAAGTCCAGTTTGGCTTTTA;RSEQ=GGAAAAGTTGATAAAGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:31,103:0.0147:2,2:5.5:1:26:0:0.41656:3.29:60:4:0.0148:0:1 0/0:84:0:0,0:23,61:0:2,0:23.4:1:29.6:1:1:0:56.9:27:1:0:0.1 -1 243662668 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGCCTACACCCTGTTTT;RSEQ=GTTCTAGAATTACCTGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:20.5:1:31:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 243662773 . T C 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51933;SOR=0;LSEQ=AAGAGATGGCTCTCTGGCCA;RSEQ=GTCCTAACACCAGACTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:0.3077:0,0:28:1:32.3:1:1:0:60:8:0.3077:0:1 0/0:4:0:0,0:4,0:0:0,0:18.5:1:30.3:1:1:0:60:8:1:0:0 -1 243662917 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51863;SOR=0;LSEQ=ATGAGGCACAAACTTTTCAT;RSEQ=TAATTTCCACATTTTTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:164,10:0.0114:2,2:23.5:1:28.5:1:0.12143:15.67998:60:4:0.0114:0:1 0/0:117:0:0,0:104,13:0:2,0:23.6:1:28.3:1:1:0:60:57.5:1:0:0.1 -1 243662942 . G GT 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTCCACATTTTTAGCAACAG;RSEQ=TTTTTTTCTCCAACAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:229,70:0:2,0:22.5:1:31.2:1:1:0:60:98.667:1:0:0.1 0/1:223:14:9,5:149,60:0.0628:2,2:23.6:1:28.3:1:0.55577:1.37754:60:13:0.0594:0.0135:0.1 -1 243663126 . G A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0285;SOR=Inf;LSEQ=AAATAAATGATTTACAAAGA;RSEQ=ATATTTACATTCATCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:0:0,0:178,326:0:2,0:26.3:1:31.6:1:1:0:60:99.8:1:0:0.1 0/1:353:4:2,2:139,210:0.0113:2,2:15:1:23.3:1:1:1.51:60:3:0.0086:0:1.5 -1 243668671 . A G 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CATCTATTTTAATTTTACAC;RSEQ=TTCATTTTTTGCAACATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:101,324:0:2,0:23.5:1:30.6:1:1:0:60:41.5:1:0:0.1 0/1:292:13:4,9:72,207:0.0445:2,2:27.6:1:31.3:1:0.74771:1.28:60:26:0.0451:0:1.1 -1 243668676 . T A 45 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1487;SOR=0;LSEQ=ATTTTAATTTTACACATTCA;RSEQ=TTTTTGCAACATTATCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:4:3,1:87,293:0.0104:2,2:12:1:22.5:1:0.04159:10.02:60:3:0.008:0:2.3 0/0:266:0:0,0:64,202:0:2,0:24.6:1:29.7:1:1:0:60:132:1:0:0.1 -1 243669012 . TCTGT CCTG 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATCCACAGCATCCAAAG;RSEQ=ATAGAATTCATCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:19.3:1:30.6:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 243675543 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15599;SOR=Inf;LSEQ=TGATCTTGAAAATATCAGAT;RSEQ=AGTTTTTAAAAGACTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:171,9:0:2,0:26:1:32.2:1:1:0:60:59:1:0:0.1 0/1:118:2:1,1:108,8:0.0169:2,2:24:1:30:0:0.14733:12.78678:60:4:0.0171:0:1 -1 243708979 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAAAAAATATTTTGTGAAA;RSEQ=TGTAATTTTCTGTGTAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:0,2:5,159:0.012:1,0:18.5:1:28.5:1:1:0:60:4:0.0123:0:1 0/0:82:0:0,0:1,81:0:1,0:23.7:1:31.5:1:1:0:60:81:1:0:0.1 -1 243709071 . G A 154 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21622;SOR=0;LSEQ=CTATTTTTCCTAATATGCTT;RSEQ=TAAGAACTAGCTTCAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:0,29:0,0:1:0,1:24.9:1:31.9:1:1:0:60:58:1:0:1 1/1:8:7:0,7:0,1:0.875:0,0:4.3:1:29.6:1:1:0:60:14:0.875:0:1 -1 243715975 . A C 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=29.47743;LSEQ=ATATTTGAATTAATTTCCAT;RSEQ=TCTCAATTTTTAACCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:1:1,0:362,80:0.0023:2,0:13:0:15:0:1:0:60:0:0:0:5 0/1:271:17:13,4:202,52:0.0627:2,2:24.5:1:31.1:1:0.7591:1.19447:60:34:0.0627:0:1.2 -1 243716481 . CA C 52 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAGGGGCAGGTCGTA;RSEQ=AAAAAAAAAAAATCCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,4:0.375:0,0:32:1:33.3:1:1:0:60:6:0.375:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 243716654 . A C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGATTATAGAGCACATAA;RSEQ=GTGCACTGTACATTCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:29.7:1:31.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 243726955 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13316;SOR=Inf;LSEQ=ACTACAGTTAACTTTTAATG;RSEQ=TTAAATGGTTTACTTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:247,47:0:2,0:23.8:1:32.2:1:1:0:60:293:0.9966:0:0 0/1:170:2:1,1:131,37:0.0118:2,2:15:1:27.5:1:0.39812:3.50677:60:4:0.0119:0:1 -1 243776811 . C A 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.58366;SOR=0;LSEQ=TAAAAACAATCATTACATCT;RSEQ=ATCAGAAATAATTTCGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:4:4,0:137,4:0.0276:1,0:34.8:1:28:1:1:0:60:8:0.028:0:1 0/0:37:0:0,0:37,0:0:1,0:23.1:1:30.6:1:1:0:60:17.5:1:0:0 -1 243777066 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.34157;LSEQ=AAATAAAAAAAAGAAAAAAT;RSEQ=TTACATTATAATCCTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:262:40,222:51,308:0.4212:2,2:21.3:1:30.6:1:0.73129:1.09:60:261:0.4244:0:1 0/1:372:74:21,53:66,232:0.1989:2,2:17.9:1:28.6:1:0.28329:1.39:60:73:0.1995:0:1.1 -1 243777087 . CTTATAA C 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.00393;SOR=Inf;LSEQ=TTACATTATAATCCTGTATT;RSEQ=TTATAATAGTACTAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:0:0,0:11,350:0:1,0:25.8:1:30.6:1:1:0:60:89.25:1:0:0.5 0/1:180:5:0,5:15,160:0.0278:2,0:27.6:1:33:1:1:0:60:10:0.0279:0:0.8 -1 243777495 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCACAACAGAACCCAACC;RSEQ=AACAGAGTTGGTTTATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 243801190 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78696;SOR=1.2142;LSEQ=GAAAAAGAATCAGACTGGCA;RSEQ=TGGCTGTCTCATTAGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:23:1,22:0,34:0.3966:1,1:23.9:1:33.1:1:0.40351:0:60:46:0.4107:0:1 0/1:18:8:0,8:0,10:0.4444:0,0:21.9:1:34:0:1:0:60:16:0.4444:0:1.1 -1 243801283 . G C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACCTAGAATTCCTCAGC;RSEQ=AAATTATCAGTTGTGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:1,13:0,0:1:0,1:24.1:1:29.7:1:1:0:60:6:1:0:1.3 1/1:2:2:0,2:0,0:1:0,0:24.5:1:33.5:1:1:0:60:4:1:0:1 -1 243809387 . T A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11302;SOR=Inf;LSEQ=AATAGAAGATGGTAAATGAT;RSEQ=TAAATATTTTCCTTTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:46,342:0:2,0:24.6:1:30.5:1:1:0:60:387:1:0:0 0/1:197:2:1,1:23,172:0.0102:2,2:37:0:27.5:1:0.22936:7.34:60:4:0.0103:0:1 -1 243809488 . C T 109 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06046;SOR=0;LSEQ=CATACACTCTCACCATCACC;RSEQ=CAAAGTGAAAATAATCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:12:1,11:0,53:0.1846:1,2:25.9:1:30.6:1:0.18462:0:60:24:0.1905:0:1.3 0/0:18:0:0,0:0,18:0:1,0:24.8:1:30.3:1:1:0:60:17:1:0:0.1 -1 243827672 . G T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCACGCCTGGCTGATTTTTT;RSEQ=TGTGTGTGTTTTTTTAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:25.3:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 243828306 . T A 201 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAACTCACAGCTTTCTATGG;RSEQ=TCTCCACTCAAGATTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:87:87:2,85:0,0:1:0,1:22.4:1:31.3:1:1:0:60:86:1:0:1 1/0:28:19:0,19:0,9:0.6786:0,1:24.2:1:29.8:1:1:0:60:38:0.6786:0:1.1 -1 245977251 . T A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTAAAATATTCATTGTAG;RSEQ=TGCTTTTAGGTGATTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29:1:1:0:60:4:1:0:1.5 -1 245977880 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15821;SOR=Inf;LSEQ=TGAAATGGATGCTGCTGCAA;RSEQ=ATTTTATTTAAACAACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:65,16:0:2,0:22.9:1:32:1:1:0:60:80:1:0:0.4 0/1:54:2:1,1:43,9:0.037:2,2:29.5:1:30.5:1:0.33892:4.58502:60:4:0.037:0:1 -1 245977881 . A G 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01166;SOR=0.29242;LSEQ=GAAATGGATGCTGCTGCAAG;RSEQ=TTTTATTTAAACAACATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:25:18,7:48,10:0.3012:2,2:21.5:1:30.8:1:0.37372:1.85169:60:50:0.3086:0:1.1 0/1:54:6:5,1:39,9:0.1111:2,2:28.3:1:30.3:1:1:1.15:60:12:0.1132:0:1 -1 245977996 . C T 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50046;SOR=1.13301;LSEQ=GCCGGCTCTGCTAAGAGCTC;RSEQ=GATGAGGAATAAACTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:396:257:147,110:81,58:0.649:2,2:24:1:30.5:1:0.9152:1.04494:60:127.5:0.6489:0:1.1 1/0:260:176:89,87:45,39:0.6769:2,2:24.2:1:29.8:1:0.69164:1.12739:60:43:0.6719:0:1.2 -1 245978063 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12089;SOR=Inf;LSEQ=TTCCCAGCAGACCTGTTTCC;RSEQ=TTGGCTTCCAGATCCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:122,211:0:2,0:25.5:1:31.3:1:1:0:60:46.571:1:0:0.5 0/1:178:2:1,1:73,103:0.0112:2,2:5:0:31:1:1:1.41:60:4:0.0114:0:1.5 -1 245978110 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55849;SOR=0;LSEQ=CTTATCCCTTATCCCACCAT;RSEQ=CACACACACACACGCACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:0,3:24,126:0.0194:2,0:26:1:29.3:1:1:0:60:6:0.0199:0:1 0/0:63:0:0,0:14,49:0:2,0:23:0:14:0:1:0:60:0:0:0:3 -1 245978150 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.51034;SOR=0.71192;LSEQ=ACACACGCACACACATGCAC;RSEQ=CACACACACGCAAGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:67:44:0,44:0,23:0.6567:1,1:20.5:1:29.2:1:1:0:59.9:21:0.6462:0:1.1 1/0:33:19:1,18:1,12:0.5758:1,1:21.6:1:28.3:1:1:1.48061:60:8.5:0.5667:0:1.5 -1 245978192 . G GCA 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.52767;SOR=0;LSEQ=ACACGCACGCACACACGCAT;RSEQ=CACACACACACACTCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:0,2:0,23:0.08:1,0:26:1:30:1:1:0:60:4:0.0909:0:0.5 0/0:14:0:0,0:1,13:0:1,0:28.8:1:31.4:1:1:0:60:13:1:0:1.1 -1 246979806 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAGAGGCGGGATTTTGTC;RSEQ=TCTTGCTCAGGCGGGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:31.5:1:1:0:60:4:1:0:1.5 -1 246981262 . C G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49568;SOR=1.93102;LSEQ=TAGGGAGTATATGGGGGGAA;RSEQ=GTATTGTGGTTGGGGAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:14:8,6:4,3:0.56:2,2:10.1:1:32.2:1:1:1:49.9:28:0.5833:0:3.1 1/0:14:10:6,4:2,0:0.7143:0,2:9.2:1:28.3:1:0.51515:0:48.6:4:0.6667:0:3.5 -1 246981266 . T C 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28293;SOR=Inf;LSEQ=GAGTATATGGGGGGAACGTA;RSEQ=TGTGGTTGGGGAGTATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:24:14,10:1,2:0.8571:2,2:12.8:1:32.2:1:0.56923:2.69:44.4:23:0.9583:0:2.7 1/1:14:14:10,4:0,0:1:0,2:13.2:1:29.8:1:1:0:49.5:6:1:0:3.1 -1 246981282 . TG T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.34844;SOR=0.48346;LSEQ=CGTATTGTGGTTGGGGAGTA;RSEQ=GGGGGGAACGTACTGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:18:10,8:5,6:0.6207:2,2:22.9:1:32.1:1:0.71038:1.48:43.8:36:0.6207:0:2.9 0/1:16:7:4,3:6,3:0.4375:2,2:12.9:1:29.4:1:1:1.46198:45.3:14:0.5:0.1875:2.9 -1 246981292 . C G 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07637;SOR=0.23323;LSEQ=TTGGGGAGTATGGGGGGGAA;RSEQ=GTACTGTGGTTGGGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:7,7:3,2:0.6667:2,2:15.4:1:30.5:1:1:1.46843:47.7:13:0.7647:0:3.1 0/1:13:4:4,0:5,3:0.3077:2,0:16.5:1:26.5:1:0.49091:0:43.8:3:0.3:0:3.8 -1 247248956 . A C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CCTCTCTACCAATGACAAGC;RSEQ=AGACCTTCAGGGTAGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:13:1:32.5:1:1:0:60:4:0.2857:0:1 1/1:3:3:2,1:0,0:1:0,2:23.3:1:31:1:1:0:60:6:1:0:1 -1 247249055 . TCCACACAGGAGGG T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=0.55204;SOR=2.84592;LSEQ=AAATTTAACCTCTGGCCCCC;RSEQ=CCACACAGGGGCCACACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:13,2:0.1176:2,0:27.5:1:33.5:1:1:0:60:4:0.1176:0:0 0/1:7:2:1,1:4,1:0.2857:2,2:23:1:29.9:1:1:3.1622:60:4:0.2857:0.1429:0.5 -1 247249155 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACACATAACCTGGGTGAG;RSEQ=CGCTGCCAGCGGCTGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:37,28:0.0299:2,2:25:1:29.5:1:1:1.31586:60:4:0.0303:0:1.5 0/0:31:0:0,0:17,14:0:2,0:25.6:1:31.3:1:1:0:60:62:1:0:0.2 -1 247249186 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10109;SOR=Inf;LSEQ=GGCTGTTGGCCTCAGCGTTC;RSEQ=CTTGCAAGGCATTCAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:42,32:0:2,0:24.8:1:30.5:1:1:0:60:73:1:0:0.2 0/1:35:2:1,1:20,13:0.0571:2,2:8:1:29:1:1:1.51907:60:4:0.0571:0:1 -1 247249268 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=AGCCCTGCCCCAACCTTGAC;RSEQ=CAGACAGTGGGTGGCATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:21,34:0:2,0:24.9:1:30.3:1:1:0:60:26.5:1:0:0.1 0/1:22:2:1,1:5,15:0.0909:2,2:27.5:1:31:1:0.48052:2.83:60:4:0.0909:0:1 -1 247250360 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGAAGGAGATGCAGGGT;RSEQ=AAGCAGCAGTGTGGATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:48.5:1:29:0:1:0:60:4:1:0:1.5 -1 247277540 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15865;SOR=Inf;LSEQ=TGAGTGCCTGCAGGGGTCAT;RSEQ=CCAGGCTGTGTGGAGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:13,24:0:2,0:23.3:1:28.6:1:1:0:60:74:1:0:0.1 0/1:25:2:1,1:8,15:0.08:2,2:24.5:1:30:1:1:1.83:60:4:0.08:0:3 -1 247277641 . C A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01282;SOR=Inf;LSEQ=GTGTGGCTGCCACAACTCTA;RSEQ=CCTGAAGGTCTTGCTTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:22.6:1:29.8:1:1:0:60:10:1:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:28:0:1:0:50:4:1:0:1 -1 247294628 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52159;SOR=0;LSEQ=CCCACGGATTGGAAGATCCC;RSEQ=CTCGCAAACCCACGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:27.5:1:29.5:1:1:1.0801:60:4:0.0741:0:1 0/0:16:0:0,0:7,9:0:2,0:29.9:1:29.3:1:1:0:60:32:1:0:0.3 -1 247294658 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12945;SOR=Inf;LSEQ=CCACGCCACCGAGGCCTGCC;RSEQ=TCCCAACCCTGGAACGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:29.3:1:30.9:1:1:0:60:48:1:0:0.3 0/1:14:2:1,1:5,7:0.1429:2,2:21.5:1:28.5:1:1:1.37:60:4:0.1429:0:1 -1 247298458 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14634;SOR=Inf;LSEQ=CAGAAAGCTAGAAGCAAGAG;RSEQ=AAACTATTCCAAAAGCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:20,5:0:2,0:18.2:1:32.4:1:1:0:60:50:1:0:0 0/1:16:2:1,1:11,3:0.125:2,2:22:1:28.5:1:0.45:3.31654:60:4:0.1333:0:1 -1 247298525 . C CA 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTGAAGAAGACAGAGACA;RSEQ=AAAAAACCCTCCAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:50,43:0:2,0:30.1:1:32.1:1:1:0:60:92:1:0:0.2 0/1:78:20:10,10:27,31:0.2564:2,2:28:1:30.9:1:0.80151:1.15:60:40:0.2632:0.0128:0.3 -1 247485932 . A G 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTCTGACTCCTCAGAGC;RSEQ=CCCGAGTAAGCAAGTCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:1:0,2:21.9:1:29.8:1:1:0:60:6.5:1:0:1.1 1/1:9:9:4,5:0,0:1:0,2:31.4:1:31.2:1:1:0:60:18:1:0:1.1 -1 247554732 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAACCATAATCAATCAC;RSEQ=ACTGCATTCCAGCCTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -1 247554949 . T G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26316;SOR=Inf;LSEQ=GACAGAGATTACTAAGAGGA;RSEQ=ATAGTAAAGGTGAAAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:9,0:3,0:0.75:0,0:28.2:1:33:1:1:0:60:18:0.75:0:1.1 1/1:7:7:7,0:0,0:1:0,0:35.9:1:32.7:1:1:0:60:14:1:0:1.1 -1 247555049 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52968;SOR=0;LSEQ=GAACCTTCTCCTAGACCCAT;RSEQ=TGTGCATTTCCTTATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:30,28:0.0333:2,2:18:1:28.5:1:1:1.07017:60:4:0.0333:0:1 0/0:35:0:0,0:16,19:0:2,0:29.6:1:31.3:1:1:0:60:70:1:0:0.1 -1 247555079 . A G 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00059;SOR=0;LSEQ=CCTTATAAAATCCAGCTTTA;RSEQ=CAAGAATCCTGCTAAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:15:6,9:9,24:0.3125:2,2:23.9:1:32.3:1:0.50411:1.76:60:30:0.3125:0:1.1 0/0:28:0:0,0:9,19:0:2,0:21.4:1:29.1:1:1:0:60:56:1:0:0.1 -1 248567495 . ACGTGTG A 30 v4;MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.03846;SOR=Inf;LSEQ=GTCCCTGTGCTATTACATAT;RSEQ=TGTGTGTGTGTATAAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:6,3:0.0909:2,0:12:0:32:0:1:0:60:2:0.0909:0:2 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30:1:1:0:60:4:1:0:2.5 -1 248567502 . T TGTGTGTGGCAGAGGCCGCTATTACATGTAC 77 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=8.000;MSILEN=2;SSF=0.28327;SOR=0;LSEQ=TGCTATTACATATACGTGTG;RSEQ=GTGTGTGTGTATAAAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:3,4:3,3:0.35:2,2:26.4:1:27.6:1:1:1.30401:60:6:0.5:0.35:1.3 0/0:4:0:0,0:2,2:0:2,0:8.3:1:30.5:1:1:0:60:8:1:0:1.8 -1 248567529 . G C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.9676;LSEQ=GTGTATAAAATGGGAGTAAG;RSEQ=GTGAACAGACAGCAGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:22:11,11:2,2:0.8462:2,2:17.4:1:31:1:1:1:57.9:44:0.8462:0:1.6 1/1:12:11:5,6:1,0:0.9167:0,2:18:0:31.5:1:1:0:60:22:0.9167:0:1.4 -1 248567539 . C G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70914;SOR=0.56443;LSEQ=TGGGAGTAAGGGTGAACAGA;RSEQ=AGCAGAGACCACTGTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:5,4:7,8:0.375:2,2:8:0:30.1:1:1:1.41:56.4:8:0.3636:0:2 0/1:12:3:1,2:5,4:0.25:2,2:8:0:33.3:1:1:2.31595:60:6:0.25:0:2.3 -10 1509949 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1901;SOR=Inf;LSEQ=AAATAAAAATAAATGTTGAT;RSEQ=CTGGTGGATTGTAAAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:103,27:0:2,0:20.2:1:32.4:1:1:0:60:129:1:0:1 0/1:101:2:1,1:79,20:0.0198:2,2:25.5:1:27.5:1:0.37426:3.87913:60:4:0.0198:0:2 -10 1509976 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=GATTGTAAAATCCCCTACCA;RSEQ=TTCCGTTATTCCATCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:142,57:0.01:2,2:24.5:1:32.5:1:0.49488:2.47835:60:4:0.0101:0:3 0/0:199:0:0,0:148,50:0:2,0:25:1:31.1:1:1:0:60:65:1:0:1.3 -10 1509981 . G C 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATCCCCTACCACTTCC;RSEQ=TTATTCCATCCTGTGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:219:157,62:0,0:1:0,2:28.5:1:31.5:1:1:0:60:108.5:1:0:1.3 1/1:211:211:157,54:0,0:1:0,2:26.4:1:30.4:1:1:0:60:51.75:1:0:1.4 -10 1510047 . G A 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00845;SOR=0.65789;LSEQ=GGGAGACTGGCTCTGACATA;RSEQ=CGCTGTGTCCCTCTTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:145:71,74:78,84:0.4693:2,2:26.1:1:29.8:1:0.9093:1.03:60:290:0.4754:0:1.3 0/1:389:143:73,70:131,114:0.3676:2,2:26.2:1:29.3:1:0.67411:1.10162:60:70.5:0.3672:0:1.4 -10 1510148 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23018;SOR=Inf;LSEQ=ATTCTAAATGCTCCCCCACC;RSEQ=CAGGGATTGAAACGTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:32,103:0:2,0:20.9:1:31:1:1:0:60:26:1:0:0.1 0/1:125:2:1,1:26,97:0.016:2,2:6:1:27.5:1:0.38671:3.68:60:4:0.0165:0:1 -10 1510172 . T G 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=GGATTGAAACGTTCTTCCTA;RSEQ=AATTATAGTGGAATCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:5,62:0:2,0:23.3:1:28.6:1:1:0:60:134:1:0:0.1 0/1:56:11:2,9:6,38:0.1964:2,2:14.1:1:30.1:1:0.6538:1.40:60:10:0.1852:0:1 -10 1510208 . C T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.378;SOR=0.50355;LSEQ=AAAAGTCTAGCCGGCTAATG;RSEQ=GTGGAGCTTCTGTGCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:0,11:0,23:0.3235:1,0:16.4:1:29.6:1:1:0:60:22:0.3235:0:1 0/1:26:5:0,5:1,20:0.1923:1,0:31:1:29.6:1:1:0:60:10:0.1923:0:1 -10 2157138 . C CA 29 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGCGAGACTCCATCT;RSEQ=AAAAAAAAAATAATAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:1:29.5:1:1:0:60:4:1:0:1 -10 2157159 . T G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAATAATAAGAAA;RSEQ=AAAGAAATCGGGCTTACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:30:1:1:0:60:4:1:0:1 -10 2158398 . T C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02485;SOR=3.53747;LSEQ=AAAAAGAGGAGAGGGGACTT;RSEQ=GCGTGGTTCCTGCCTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:16:16,0:21,1:0.4211:1,1:23.7:1:30.9:1:1:0:60:32:0.4211:0:1.1 1/0:29:21:20,1:8,0:0.7241:0,1:21.6:1:31.4:1:1:0:60:42:0.7241:0:1 -10 2158524 . C T 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTAAGAGTATTTATGCTAA;RSEQ=GATGCAAATAAAAGGTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:286:286:172,114:0,0:1:0,2:26.6:1:30.6:1:1:0:60:70.5:1:0:1.4 1/1:321:296:171,125:15,10:0.9221:2,2:26.7:1:29.5:1:1:1.09621:60:58.2:0.9209:0:1.5 -10 2158567 . C A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=14.39329;LSEQ=AAGGTGTTCTGAACTTTTAA;RSEQ=CATGTCTTGCAGACATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:19:10,9:169,183:0.0512:2,2:27.4:1:29.2:1:0.81487:1.20:60:38:0.0521:0:1.5 0/1:388:170:86,84:105,112:0.4381:2,2:24.5:1:29.6:1:0.68307:1.09:60:169:0.4424:0:1.6 -10 2158572 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14359;LSEQ=GTTCTGAACTTTTAACCATG;RSEQ=CTTGCAGACATAAATTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:173:80,93:91,102:0.4727:2,2:23.7:1:31.1:1:0.91651:1.03705:60:27.833:0.4652:0:1.5 0/1:378:43:23,20:161,174:0.1138:2,2:24.5:1:30.3:1:0.52113:1.24:60:20.5:0.1114:0:1.6 -10 2158638 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23612;SOR=0;LSEQ=AAATGGGAAAAATGACATTT;RSEQ=ATTTGGAATTTAAACACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:53,144:0.0101:2,2:25:1:28:1:0.47008:2.70:60:4:0.0103:0:1.5 0/0:210:0:0,0:66,144:0:2,0:23.9:1:31.3:1:1:0:60:69:1:0:0.4 -10 3096943 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATTTTCAGGATACAAAGAGT;RSEQ=CCCCCACCACTGCAGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:28.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:3:0:0,0:2,1:0:2,0:25.7:1:31.3:1:1:0:60:6:1:0:0.3 -10 3096948 . C A 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=0;LSEQ=CAGGATACAAAGAGTCCCCC;RSEQ=ACCACTGCAGAGTCTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:17.5:1:32:1:1:0:60:4:0.5:0:1.5 0/0:3:0:0,0:2,1:0:2,0:27.3:1:30.7:1:1:0:60:6:1:0:0.3 -10 3097046 . TA T 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51429;SOR=0;LSEQ=ATTTACAATTCAATTATGTA;RSEQ=ATGCTAAGACCTTGTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:32,0:0.0588:1,2:14:1:24.9:1:0.05882:0:60:4:0.0588:0.0294:0.5 0/0:22:0:0,0:22,0:0:1,0:22.5:1:28.5:1:1:0:60:44:1:0:0 -10 3097129 . A T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50409;SOR=Inf;LSEQ=GAAACCTAAGACCCACATGG;RSEQ=GGGGGAGGAAGTTTCTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:106,41:0:2,0:24.4:1:29.8:1:1:0:60:17.375:0.9929:0:0.4 0/1:183:2:1,1:126,55:0.0109:2,2:13:1:26:1:0.51955:2.27938:60:4:0.0111:0:4 -10 3097134 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50288;SOR=Inf;LSEQ=CTAAGACCCACATGGAGGGG;RSEQ=AGGAAGTTTCTAGCTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:117,45:0:2,0:24.9:1:31.1:1:1:0:60:31.4:1:0:0.5 0/1:195:2:1,1:133,59:0.0103:2,2:19:1:26.5:1:0.52401:2.24379:60:4:0.0105:0:1.5 -10 3097135 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20231;SOR=0;LSEQ=TAAGACCCACATGGAGGGGG;RSEQ=GGAAGTTTCTAGCTTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:117,45:0.0122:2,2:32:0:32.5:1:0.48354:2.58256:60:4:0.0128:0:1.5 0/0:200:0:0,0:137,63:0:2,0:23.8:1:28.9:1:1:0:60:65.667:1:0:0.4 -10 3097180 . G A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=Inf;LSEQ=CAATGCTGGAAGGAATTCAG;RSEQ=TGAAATATTCCATGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:146,111:0:2,0:25.3:1:31.1:1:1:0:60:50.4:1:0:0.8 0/1:314:13:7,6:167,134:0.0414:2,2:30:1:28.5:1:1:1.06799:60:26:0.0419:0:1.7 -10 3097212 . T C 244 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00452;LSEQ=ATGGCCTTCTGACTGCTCTC;RSEQ=GGTGCCTGTTGTGAAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:281:280:144,136:0,0:0.9964:0,2:25.2:1:30.1:1:1:0:60:69:0.9964:0:1.1 1/0:325:181:88,93:72,72:0.5569:2,2:27.3:1:29.7:1:0.82396:1.05661:60:89.5:0.5576:0:1.2 -10 3097396 . G C 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73188;SOR=1.52621;LSEQ=TGGCACTTGAGGTTTCCTCC;RSEQ=TGATTTTCTTCCAGACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:0,7:0,18:0.28:1,0:27:1:32.9:1:1:0:60:14:0.2917:0:1.1 0/1:16:6:1,5:0,10:0.375:0,2:18.5:1:29.5:1:0.375:0:60:5:0.3333:0:1 -10 3098086 . T C 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGAAGGCGGAGTTTGCAG;RSEQ=GAGCTGAGATTGCACCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19.5:1:26:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 3098106 . A G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGCTGAGATTGCACCACT;RSEQ=CACTCCAGCCTGGGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:1:28.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 3280406 . T C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03607;SOR=0.12775;LSEQ=ATGAGACTGATTTCAAGACA;RSEQ=GGGCCAGCCGGGCATTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:0.8333:0,0:20:1:30.2:1:1:0:60:9:0.8182:0:1.8 0/1:11:4:4,0:6,1:0.3636:2,0:34.5:1:32.3:1:1:0:60:8:0.4:0:2.3 -10 3280416 . G A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0805;SOR=0.14152;LSEQ=TTTCAAGACATGGGCCAGCC;RSEQ=GGCATTCCTCCCGGTACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:9,0:2,0:0.8182:0,0:26.7:1:30:1:1:0:60:18:0.8182:0:2 0/1:11:4:4,0:6,1:0.3636:2,0:34.5:1:30.8:1:1:0:60:8:0.4:0:2.3 -10 3280590 . A G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.02572;LSEQ=CAGAGAAGGAGATGTGGGGG;RSEQ=AAAAGCCTGTGCTAGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:375:347:212,135:15,13:0.9253:2,2:25.3:1:30.9:1:0.43019:1.36:60:68.4:0.9243:0:1.5 0/1:370:89:48,41:161,119:0.2405:2,2:27.5:1:31:1:0.62355:1.15518:60:178:0.2459:0:1.4 -10 3280619 . T C 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01242;SOR=0;LSEQ=GTGCTAGTCTGGAAGTGGAG;RSEQ=CTGGAGCTTAGATTAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:4,2:237,213:0.0131:2,2:18.3:1:32:1:0.68851:1.80:60:12:0.0135:0:1.2 0/0:490:0:0,0:252,238:0:2,0:23:0:14:0:1:0:60:0:0:0:5 -10 3280664 . C T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03768;LSEQ=TTGACAGAAGGAATTCCCCA;RSEQ=CGCAGTCCCGTTCCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:411:374:167,207:15,21:0.91:2,2:25.1:1:30:1:0.86089:1.13:60:40.556:0.9125:0:1.4 0/1:462:127:65,62:155,179:0.2749:2,2:25.8:1:29.1:1:0.40395:1.21:60:126:0.2775:0:1.3 -10 3280942 . G A 75 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGAGCTGGAGCTGGGC;RSEQ=GCCCTGCCCTGTGGCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:25.6:1:32.4:1:1:0:60:10:1:0:1.6 1/1:1:1:0,1:0,0:1:0,0:22:0:33:0:1:0:60:2:1:0:2 -10 3280961 . G A 51 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCCCTGCCCTGTGGCAGC;RSEQ=GGAATAAGAGGAGACAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:16.7:1:32.7:1:1:0:60:6:1:0:2 1/1:1:1:0,1:0,0:1:0,0:3:0:29:0:1:0:60:2:1:0:2 -10 3281573 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAGAGAGTCTGCAGGCC;RSEQ=TCAGTCAATCACACCGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 5094232 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATGAAGCCGTGGACCCT;RSEQ=GCAGTGTTACAGTTCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:30:1:1:0:60:4:1:0:1.5 -10 5096100 . G C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGATGGCCTTGATTCTA;RSEQ=AGGAAACAAATTTGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:35:0:32:1:1:2.23609:60:4:0.2222:0:1 0/0:4:0:0,0:3,1:0:2,0:34.8:1:30.8:1:1:0:45:8:1:0:0 -10 5096162 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50244;SOR=0;LSEQ=AAGGCAAGTAACAGTAAGAT;RSEQ=GCTGCCACGGGACCTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:0.0833:2,2:19:0:31.5:1:1:1:60:4:0.0833:0:1.5 0/0:17:0:0,0:12,5:0:2,0:28:1:31.9:1:1:0:56.5:34:1:0:0.2 -10 5505007 . C T 37 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCCAAACTCCCAGGCCATG;RSEQ=TCTAAATGCTGGGCTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:33:0:30:0:1:0:60:2:1:0:1 1/1:3:3:2,1:0,0:1:0,2:25:1:23.7:1:1:0:60:2:1:0:1 -10 5505165 . G C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01822;SOR=3.41754;LSEQ=CAGCTCACACAACTGCACTC;RSEQ=TGCCCAGACGTCCCTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:24:14,10:11,7:0.5714:2,2:24.9:1:30.3:1:1:1.11937:60:23:0.575:0:2.3 1/1:45:37:22,15:4,4:0.8222:2,2:31.5:1:30.4:1:0.70429:1.45:60:74:0.8222:0:1.9 -10 5505210 . T C 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCACGCTGACTCCCCAGCTT;RSEQ=CTCTAGGCCACCCCCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:24,24:0,0:1:0,2:23.5:1:30.4:1:1:0:60:23:1:0:2.1 1/1:47:47:18,29:0,0:1:0,2:21.3:1:29.6:1:1:0:60:22.5:1:0:2 -10 5505293 . G A 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63325;SOR=2.38223;LSEQ=GCAGCCGGCAGCTTCCAGGA;RSEQ=TAATTCATCAGATTCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:0,6:0,5:0.5455:0,0:25.5:1:32.7:1:1:0:60:12:0.5455:0:1.3 1/0:8:6:2,4:0,2:0.75:0,2:24.5:1:29.3:1:1:0:60:12:0.75:0:1.3 -10 5909907 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=GACTTTGCACCTTCTTAGGG;RSEQ=AAGAGTGTTGCTTTTACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:6,1:0.2222:2,2:34.5:1:28.5:1:0.41667:4.58262:60:4:0.2222:0:1 0/0:8:0:0,0:6,2:0:2,0:19.8:1:28.6:1:1:0:60:7:1:0:0 -10 5910017 . C T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49656;SOR=Inf;LSEQ=CTTTCAAACTCTTATACCAA;RSEQ=CTCTGGAGTTGGGTGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:32.9:1:32:1:1:0:57.6:56:1:0:0.1 0/1:34:2:1,1:18,14:0.0588:2,2:27:0:27.5:1:1:1.27615:60:4:0.0588:0:1 -10 6175914 . C T 33 d7;v4;MAF0.05;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=CCTGGTGTTGGGGCTCTGCC;RSEQ=CTGGTCTGGCTGAGCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:47:0:33:0:1:0:60:4:0.4:0:1 1/0:2:1:1,0:1,0:0.5:0,0:26:0:32:0:1:0:60:2:0.5:0:1 -10 6176061 . TA T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.66948;LSEQ=ATGAAGGTTCTTTGCAACAT;RSEQ=AAAAAAATAATAAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:1:1,0:53,14:0.0147:2,0:33:0:32:0:1:0:60:2:0.0149:0:0 0/1:82:2:1,1:63,17:0.0244:2,2:16:1:26.9:1:0.39295:3.63032:60:4:0.0247:0.0122:0.5 -10 6176070 . TAATAA T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=CTTTGCAACATTAAAAAAAA;RSEQ=AATAAAATAAACCTGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:69,22:0:2,0:20.2:1:28.9:1:1:0:60:182:1:0:0.7 0/1:99:2:1,1:72,25:0.0202:2,2:15.5:1:29.5:1:0.45826:2.84362:60:4:0.0206:0.0101:1 -10 6176112 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.27635;LSEQ=TGCATATTTGCCAGGGGCTG;RSEQ=GCTTTCTGAGAGTGGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:152:99,53:52,36:0.6333:2,2:25.9:1:30.4:1:0.40572:1.29:60:151:0.6371:0:1.1 0/1:214:69:41,28:85,59:0.3224:2,2:26.6:1:29.4:1:1:1.02:60:138:0.3255:0:1.2 -10 6176145 . G A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02111;SOR=Inf;LSEQ=TGGACAGGGAACAGCTGAGC;RSEQ=TGCTTGACGGCTCTGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:157,121:0:2,0:28.7:1:30.5:1:1:0:60:91.667:1:0:0.9 0/1:241:5:2,3:130,106:0.0207:2,2:21.6:1:30:1:0.66062:1.83495:60:10:0.0207:0:1.8 -10 6176166 . C T 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.0356;SOR=0.6471;LSEQ=TGCTTGACGGCTCTGGGGTC;RSEQ=TCAGGGCCTCCGTCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:88:41,47:89,88:0.3321:2,2:24.9:1:29.6:1:0.60328:1.15872:60:28.333:0.3244:0:1.1 0/1:222:54:21,33:77,89:0.2432:2,2:27.6:1:29.2:1:0.34955:1.35766:60:17:0.2339:0:1.1 -10 6176208 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49842;SOR=0;LSEQ=TGACACTGTCCTGGGCTCAG;RSEQ=GGGCTGTGGAGGCCCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:42,104:0.0135:2,2:26.5:1:29.5:1:0.49807:2.46:60:4:0.0137:0:1 0/0:143:0:0,0:49,94:0:2,0:26.7:1:29.8:1:1:0:60:46.667:1:0:0.4 -10 6176223 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1153;SOR=Inf;LSEQ=CTCAGCGGGCTGTGGAGGCC;RSEQ=CAAGTGACGCTGTGAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:28,88:0:2,0:24.8:1:30.8:1:1:0:60:57:1:0:0.4 0/1:111:3:1,2:30,78:0.027:2,2:30.3:1:26:1:1:1.30:60:2:0.0185:0:1.7 -10 6743894 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=CTTTTTGCAGGCAGGGGTAA;RSEQ=GCTATGTTCTGTGTGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:26.1:1:31.3:1:1:0:60:16:1:0:0.6 0/1:6:2:2,0:4,0:0.3333:0,0:5.5:1:30.5:1:1:0:60:4:0.3333:0:1 -10 6744002 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51158;SOR=Inf;LSEQ=AGTGATGATGATGACAATGA;RSEQ=CATGATGATGACGATGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:29,28:0:2,0:27.9:1:31.4:1:1:0:60:27.5:1:0:0.4 0/1:81:2:1,1:43,36:0.0247:2,2:43.5:1:30.5:1:1:1.19181:60:4:0.0247:0:1.5 -10 6744019 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51284;SOR=Inf;LSEQ=TGAGCATGATGATGACGATG;RSEQ=CCTTGATGGTGTTGCTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:22,32:0:2,0:26:1:29.3:1:1:0:60:53:1:0:0.3 0/1:78:2:1,1:34,42:0.0256:2,2:11.5:1:30:1:1:1.23:60:4:0.0256:0:1.5 -10 6744024 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14838;SOR=0;LSEQ=ATGATGATGACGATGACCTT;RSEQ=ATGGTGTTGCTGCTAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:17,31:0.04:2,2:19.5:1:30.5:1:1:1.80:60:4:0.04:0:1 0/0:79:0:0,0:34,45:0:2,0:24.7:1:30.8:1:1:0:60:78:1:0:0.2 -10 6744105 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48667;SOR=Inf;LSEQ=TACATGGCATGACAACATGC;RSEQ=TGAAATGTTTCATGGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:0:0,0:22.7:1:32.2:1:1:0:60:22:1:0:0 0/1:14:2:0,2:0,12:0.1429:0,0:26:1:29.5:1:1:0:60:4:0.1429:0:1 -10 8087393 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1918;SOR=0;LSEQ=CGGCGGCCACAGTGGCGAAC;RSEQ=CTGCCTGTCATTTCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:30.5:1:32.5:1:1:1.74:60:4:0.0741:0:1 0/0:34:0:0,0:17,17:0:2,0:29.1:1:28.4:1:1:0:60:33:1:0:0.4 -10 8087409 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49156;SOR=Inf;LSEQ=GAACTCTGCCTGTCATTTCT;RSEQ=CCTTCAGATCTCCGGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:9,18:0:2,0:27.1:1:32.1:1:1:0:60:26:1:0:0.2 0/1:29:2:1,1:10,16:0.069:2,2:26.5:1:28:1:1:1.57:60:4:0.069:0:1 -10 8087428 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23256;SOR=0;LSEQ=TGCCTTCAGATCTCCGGGCG;RSEQ=GTCAGGAAAAAAAATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:5,14:0.0952:2,2:23.5:1:32.5:1:0.5:2.65:60:4:0.0952:0:1 0/0:22:0:0,0:7,15:0:2,0:26:1:30.3:1:1:0:60:44:1:0:0.1 -10 8097556 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12987;SOR=Inf;LSEQ=CCCCCGACCTCCCAGGCGGA;RSEQ=CGCCCTCCCTCCCCGCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:53,10:0:2,0:17.7:1:30.7:1:1:0:60:20:1:0:0.2 0/1:36:2:1,1:28,6:0.0556:2,2:28:0:29.5:1:0.35556:4.39698:60:4:0.0571:0:1.5 -10 8097570 . C T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.05895;SOR=Inf;LSEQ=GGCGGACCGCCCTCCCTCCC;RSEQ=GCGCGCGGGTTCCGGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:84,18:0:2,0:19.5:1:30.6:1:1:0:60:50:1:0:0.2 0/1:66:3:3,0:51,12:0.0455:2,0:20.3:1:32.7:1:1:0:60:6:0.0455:0:1 -10 8097603 . G T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.65831;SOR=1.91683;LSEQ=CGGGCCCGGCGAGAGGGCGC;RSEQ=AGCACAGCCGAGGCCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:2:1,1:204,43:0.008:2,2:19.5:1:28:1:0.32277:4.70149:60:4:0.0083:0:1.5 0/1:196:3:1,2:149,44:0.0153:2,2:11.3:1:26.3:1:0.13791:6.68766:60:6:0.0155:0:1.3 -10 8098185 . A G 58 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGTCTCGGGATGTCCCCA;RSEQ=GCGCGGGGTGCCCTGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:24:1:29.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 8100125 . A G 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44795;SOR=0.52033;LSEQ=CAGGTACTCCGGGGACCGCC;RSEQ=GGATGAGAGAGTGGGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:60:59,1:4,0:0.9375:0,1:24.7:1:30.5:1:1:0:60:120:0.9375:0:4.1 1/1:35:31:31,0:4,0:0.8857:0,1:27.2:1:30.5:1:1:0:60:62:0.8857:0:3.9 -10 8100129 . TGA ATT 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12383;LSEQ=TACTCCGGGGACCGCCAGGA;RSEQ=GAGAGTGGGCCTGAGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:60:60,0:5,0:0.9091:0,1:26.8:1:31.2:1:1:0:60:120:0.9231:0.0303:2.1 1/1:49:45:45,0:4,0:0.9184:0,1:22.4:1:30.2:1:1:0:60:90:0.9184:0.3265:1.4 -10 8100647 . C T 160 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02231;LSEQ=TCCCGTGGCAGCATGACCGC;RSEQ=CTGGGTGGAGCCTCCTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:950:39:19,20:446,465:0.0411:2,2:27.3:1:30.3:1:1:1.00961:60:38:0.0409:0:1.1 0/0:1050:1:0,1:529,519:0.001:2,0:1:0:25:0:0.49571:0:60:2:0.001:0:1 -10 8100727 . TC T 94 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.03302;SOR=4.83202;LSEQ=CGAGTACAGCTCCGGACTCT;RSEQ=CCCCCCAGCAGCCTGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:2:0,2:292,411:0.0028:2,0:12.5:1:29:1:0.51404:0:60:4:0.0029:0.0014:1 0/1:663:9:5,4:278,376:0.0136:2,2:25:1:29.9:1:0.50695:1.69:60:18:0.014:0.003:0.2 -10 8100866 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18487;SOR=Inf;LSEQ=TCCCCTTTTCCTCAATCCAG;RSEQ=GCCGCACCCAGAGGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:14,102:0:2,0:22.8:1:30.2:1:1:0:60:57:1:0:0.2 0/1:88:2:1,1:18,68:0.0227:2,2:9:1:28:1:0.38715:3.70:60:4:0.0238:0:1 -10 8102887 . G A 46 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTCACAGTCGTGAAAACC;RSEQ=AGAACAGCACACCTGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:19.7:1:29.3:1:1:0:60:6:1:0:1.3 1/1:1:1:0,1:0,0:1:0,0:10:0:24:0:1:0:60:2:1:0:1 -10 8105745 . G A 48 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.01621;SOR=22.11438;LSEQ=CCCCTTCTGCGGGCGCCTCC;RSEQ=TGTGTGTCGGGGGAACGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:19,0:0.0952:1,0:15:1:32:0:1:0:60:4:0.1:0:1 1/0:4:3:3,0:1,0:0.75:0,0:7.7:1:30.7:1:1:0:60:6:0.75:0:1 -10 8106135 . A G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGGATGGATTCCATGCTG;RSEQ=CCATTCTGGGTTTCTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:53,181:0:2,0:21.8:1:29.4:1:1:0:60:57.5:1:0:0.1 0/1:231:25:5,20:59,147:0.1082:2,2:23.1:1:31.4:1:0.47994:1.60244:60:50:0.1096:0:1.2 -10 8106248 . TTTTC T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.54667;SOR=0;LSEQ=ACAGTTTTTTTTTTTTTCCT;RSEQ=TTTCTTTCTTTTCTTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:0,2:2,30:0.0588:2,0:13:1:31.7:1:1:0:60:4:0.0588:0.0294:0.5 0/0:17:0:0,0:3,14:0:2,0:14.7:1:28.4:1:1:0:57.8:16:1:0:0.9 -10 8106258 . TTCTTTTC T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.06091;SOR=Inf;LSEQ=TTTTTTTCCTTTTTCTTTCT;RSEQ=TTCTTCTTCTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:2,30:0:2,0:17.3:1:28.4:1:1:0:59.3:9.667:1:0:2.2 0/1:11:2:0,2:2,5:0.1818:2,0:14:1:28.5:1:1:0:51.5:4:0.1818:0.0909:3.5 -10 8106271 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCTTTCTTTCTTTTCTTCTT;RSEQ=TTCTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:0,16:0.0952:1,0:37:1:29:1:1:0:50:4:0.1333:0:3.5 0/0:8:0:0,0:1,4:0:2,0:11.6:1:21.6:1:1:0:56.6:0.667:1:0:2 -10 8106274 . C T 113 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=17.000;MSILEN=1;SSF=0.00021;SOR=0;LSEQ=TTCTTTCTTTTCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:0,13:0,0:0.8667:0,1:17.4:1:30.8:1:1:0:58.4:26:1:0:3.7 0/0:7:0:0,0:0,2:0:0,0:14.5:1:22:1:1:0:51.5:1:1:0:3.5 -10 8106353 . G A 48 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATCCATGTTTCTTAAGTC;RSEQ=CTTGTGAACATTTTAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:16.7:1:23:1:1:0:55:2:1:0:3 1/0:4:3:1,2:0,1:0.75:0,2:10.3:1:30.3:1:1:0:60:6:0.75:0:1 -10 8106856 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAAACTTTTTAAGCATG;RSEQ=GGGATCCTTGAGAAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:30:1:1:0:60:4:1:0:1 -10 8107572 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACATGACTTTAATCTTTG;RSEQ=CAATCCTGGATATCGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:33:1:1:0:60:4:1:0:1.5 -10 8110938 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTGGTGCTTGGCTTTGC;RSEQ=CCTCCTTTGCTGTGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:37.5:1:30.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 8111168 . C T 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGACTGCCAGGGAGGAGG;RSEQ=CCCGGCTTCCTGCTCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:21.8:1:30.6:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 8111409 . C T 250 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06811;LSEQ=TTTAACATTTGTTTTGATTT;RSEQ=ACCCTCTCCTCTCTCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:349:337:256,81:8,4:0.9656:2,2:24.4:1:29.8:1:0.49581:1.58:60:111.333:0.9653:0:1.2 1/0:407:267:188,79:99,41:0.656:2,2:21.6:1:28.4:1:1:1.01462:60:65.75:0.6641:0:1.1 -10 8111621 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03101;LSEQ=TGATGGTGACCAGCAAACAG;RSEQ=GTCACCACCACCCTCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:259:241:30,211:3,15:0.9305:2,2:23.1:1:30.3:1:0.71082:1.4046:60:119.5:0.9373:0:1.1 0/1:189:55:5,50:16,118:0.291:2,2:27:1:30.1:1:0.79924:1.35386:60:110:0.2926:0:1.1 -10 8111850 . GA G 78 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.03333;SOR=0;LSEQ=GGGCCTGTGTGGTTTATAAG;RSEQ=AAAAAAAAAAATCTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,0:0.8571:0,0:31.3:1:30.5:1:1:0:60:12:0.8571:0:0.7 0/0:3:0:0,0:1,2:0:2,0:24:1:29.3:1:1:0:60:6:1:0:1.7 -10 8115686 . A T 56 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54477;SOR=1.52329;LSEQ=AGTAAAAAAAAAAAAAAAAA;RSEQ=TTGATCTTTGTTTAGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:579:4:4,0:435,139:0.0069:2,0:19.3:1:15.5:1:0.57704:0:55:0:0:0:4.3 0/1:572:6:3,3:393,171:0.0105:2,2:7:1:22:1:0.37585:2.29453:60:2:0.0074:0:2.5 -10 8115687 . T A 84 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07123;LSEQ=GTAAAAAAAAAAAAAAAAAA;RSEQ=TGATCTTTGTTTAGATTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:13:10,3:424,138:0.0224:2,2:20.7:1:18.5:1:1:1.08:60:0.625:0.0097:0:3 0/1:584:14:10,4:387,178:0.024:2,2:16.7:1:22.1:1:1:1.15:60:1.8:0.0168:0:1.9 -10 8116079 . C T 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GCAGTATCATGAAGCCTAAA;RSEQ=GCGATGGATATATGTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:40:0,40:0,19:0.678:1,1:17.7:1:30.3:1:1:0:60:19:0.6667:0:1.1 0/0:29:0:0,0:3,26:0:2,0:23:1:29:1:1:0:60:28:1:0:0.2 -10 8116241 . G GA 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGGGTCTCTAGTGCTGT;RSEQ=AAAAAAAAAATGCTGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:16:1:31.5:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 8596688 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11791;SOR=Inf;LSEQ=TGGGAGCTCAAGGCAGTGTT;RSEQ=ACCCATCAAGGCCTGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:194,97:0:2,0:25.9:1:31.3:1:1:0:60:96:1:0:0.1 0/1:281:3:1,2:162,116:0.0107:2,2:18:1:28.3:1:0.57417:2.78293:60:6:0.0108:0:1.3 -10 8596711 . G T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02829;SOR=Inf;LSEQ=CCATCAAGGCCTGACAGTAA;RSEQ=AGGAGGATGGATGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:219,169:0:2,0:25.6:1:31.4:1:1:0:60:76.6:1:0:0.1 0/1:375:5:2,3:197,173:0.0133:2,2:25.6:1:26.4:1:0.66886:1.70565:60:10:0.0135:0:1.6 -10 8596776 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.58626;LSEQ=CCTGTTCCCTGGCCTGACCT;RSEQ=CCTCTGCACTCATTTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:16:7,9:140,213:0.0431:2,2:28:1:30.3:1:0.79695:1.18:60:32:0.044:0:1.3 0/1:317:109:49,60:96,111:0.3438:2,2:26.2:1:28.6:1:0.81362:1.05886:60:26.25:0.342:0:1.1 -10 9959556 . C T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.02718;SOR=0;LSEQ=ATGTTTTAAATATATCCTGT;RSEQ=TAAAATAGAAATCAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:6,1:13,1:0.3333:1,2:15.1:1:31.4:1:1:2.08171:60:14:0.35:0:1 0/0:14:0:0,0:13,0:0:1,0:19.5:1:32.1:1:1:0:60:26:1:0:0 -10 9959688 . A C 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00156;SOR=Inf;LSEQ=CTAGTTGATTAGTAGTAAGG;RSEQ=GCAGTGCTTCAGGGCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:120,50:0:2,0:23.3:1:30:1:1:0:60:55.667:1:0:1.2 0/1:215:12:9,3:133,70:0.0558:2,2:30.5:1:31.2:1:0.75496:1.58:60:24:0.0563:0:3.1 -10 9959704 . A G 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=5e-05;SOR=0.056;LSEQ=AAGGAGCAGTGCTTCAGGGC;RSEQ=TGCATCTCATTGTGGTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:233:232:152,80:0,0:0.9957:0,2:23.6:1:30.6:1:1:0:60:115:0.9957:0:1.3 1/1:265:246:149,97:10,9:0.9283:2,2:25.5:1:30.2:1:0.62787:1.38:60:492:0.9283:0:1.3 -10 9959736 . T C 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=Inf;LSEQ=GTGGTATTATCAAAACTGTC;RSEQ=CAACCACACATTCACATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:193,147:0:2,0:25.8:1:30.5:1:1:0:60:41.5:1:0:0.9 0/1:366:15:9,6:190,161:0.041:2,2:24.3:1:28.3:1:0.79336:1.27:60:14:0.0385:0:2.9 -10 9959785 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.30823;LSEQ=TCAGGTTTCCAAGTCGGAAA;RSEQ=GGAGTCCTGAATTTTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:137:63,74:101,114:0.3892:2,2:25.7:1:30.1:1:0.91284:1.04056:60:67.5:0.3879:0:1.3 1/0:361:215:95,120:65,81:0.5956:2,2:26.1:1:29.8:1:1:1.01361:60:214:0.5961:0:1.2 -10 9959931 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.79208;SOR=1.22335;LSEQ=TTTTCCTTTATTGGAATTTC;RSEQ=GTGACACGTAGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:0,15:0,17:0.4688:1,1:20.6:1:30.4:1:1:0:60:30:0.4688:0:2.5 1/0:25:13:0,13:0,11:0.52:0,1:26.5:1:31.1:1:1:0:60:26:0.52:0:2.4 -10 9959939 . G T 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39045;SOR=1.86462;LSEQ=TATTGGAATTTCCGTGACAC;RSEQ=TAGGAATCATCATATTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:0,12:0,17:0.4138:1,0:22.6:1:30.3:1:1:0:60:24:0.4138:0:2.9 1/0:21:12:0,12:0,9:0.5714:0,0:24.8:1:31:1:1:0:60:24:0.5714:0:2.6 -10 9959979 . C T 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00934;SOR=15.97969;LSEQ=GGGAATTTGAGGATGTCTGT;RSEQ=TCTTTGTTTTAATTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:0,5:0,13:0.2778:1,0:26.6:1:30.4:1:1:0:60:10:0.2778:0:4.2 1/1:8:7:1,6:0,1:0.875:0,2:17.6:1:26.9:1:1:0:60:6:0.8571:0:3.4 -10 9959999 . T G 70 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04076;SOR=13.80899;LSEQ=CTCTTTGTTTTAATTTCTCT;RSEQ=TAAATTTTTTTTATTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:0.2308:0,0:18:1:33.7:1:1:0:60:6:0.2308:0:5 1/1:6:5:1,4:0,1:0.8333:0,2:24.2:1:30.4:1:1:0:60:10:0.8333:0:3.6 -10 9960005 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.10577;SOR=8.9635;LSEQ=GTTTTAATTTCTCTTTAAAT;RSEQ=TTTTTTATTTCCAGAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:0.2727:0,0:12:1:33.7:1:1:0:60:6:0.2727:0:5 1/1:5:4:1,3:0,1:0.8:0,2:29.5:1:31.3:1:1:0:60:8:0.8:0:3.5 -10 9960282 . A G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGATTTCTGCAATTTTG;RSEQ=TGCACCCATCACCTGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:26.3:1:33.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 10136339 . C G 229 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAATAATACAGAAAGGCTC;RSEQ=ATAAATGTGAGTTTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:260,240:0:2,0:24.7:1:31.1:1:1:0:60:70.429:0.998:0:0.1 0/1:465:198:92,106:136,131:0.4258:2,2:24.8:1:30.1:1:0.34971:1.19568:60:197:0.4283:0:1.1 -10 10136473 . G A 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATCTGTTGATAATTCTAGC;RSEQ=TGAGAGAAAAATGTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:1,80:0:1,0:22.1:1:32.4:1:1:0:60:80:1:0:0 0/1:48:18:0,18:1,29:0.375:1,1:23.8:1:30.8:1:1:0:60:36:0.375:0:1.6 -10 10136486 . G T 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTAGCGTGAGAGAAAAAT;RSEQ=TTAAACTTCATTTATTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:1,61:0:1,0:21.8:1:32.1:1:1:0:60:61:1:0:0 0/1:34:13:0,13:0,21:0.3824:1,1:22.4:1:31.3:1:1:0:60:26:0.3939:0:1.8 -10 10216156 . T C 94 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00682;SOR=11.01537;LSEQ=CTGATGAGAAACCACTGAAG;RSEQ=TCCTGGGGAAGCAAAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:1:0,1:130,35:0.006:2,0:1:0:31:0:0.21687:0:60:2:0.0061:0:1 0/1:143:9:5,4:98,34:0.0629:2,2:24.1:1:29.7:1:0.25121:2.29026:60:18:0.0647:0:1.1 -10 10216373 . A G 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0341;SOR=0.53562;LSEQ=TGAATGAAACCAATGAGGTC;RSEQ=ATTTTAGAGAGATACCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:60:32,28:27,18:0.566:2,2:23.6:1:30:1:0.55399:1.30909:60:29:0.5631:0:1.1 0/1:95:39:25,14:34,22:0.4105:2,2:22:1:29.6:1:0.8309:1.15:60:38:0.4086:0:1.1 -10 10216430 . A G 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGCACGTATTTTATGTAT;RSEQ=AGGTTCGCTACCCTAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:73,65:0:2,0:25.7:1:28.9:1:1:0:60:137:1:0:0.4 0/1:142:24:13,11:62,54:0.169:2,2:25.8:1:30.7:1:1:1.03:60:48:0.1702:0:1 -10 10216431 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49828;SOR=Inf;LSEQ=ATGCACGTATTTTATGTATA;RSEQ=GGTTCGCTACCCTAACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:74,66:0:2,0:25.3:1:30.4:1:1:0:60:69:1:0:0.4 0/1:143:2:1,1:75,66:0.014:2,2:31:1:30.5:1:1:1.13534:60:4:0.0141:0:1.5 -10 10216438 . C A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1122;SOR=0;LSEQ=TATTTTATGTATAAGGTTCG;RSEQ=TACCCTAACAGCTCCACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:2,1:72,76:0.0199:2,2:48:1:31.3:1:0.61505:2.10:60:6:0.0207:0:1 0/0:161:0:0,0:82,79:0:2,0:23.2:1:31.3:1:1:0:60:160:1:0:0.4 -10 10216761 . TA T 50 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATAAAGATGCCAATTTG;RSEQ=AAAAAAAAAATAATAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:28.3:1:31.7:1:1:0:60:6:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 10439699 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51948;SOR=Inf;LSEQ=AGAGCCTCTGGAGGGAGTGT;RSEQ=CCCCTGCTGACTCCGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,21:0:2,0:22.8:1:31.7:1:1:0:60:23.5:1:0:0.2 0/1:76:2:1,1:39,35:0.0263:2,2:13.5:1:25.5:1:1:1.1127:60:4:0.0263:0:2 -10 10439732 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27209;SOR=Inf;LSEQ=CCGGCAGTTTGGACTTCTGG;RSEQ=CTCCAGAACTCTGAGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:0:2,0:32.4:1:31.3:1:1:0:60:42:1:0:0.2 0/1:64:3:2,1:31,30:0.0469:2,2:12:1:27.7:1:1:1.92:60:6:0.0476:0:1 -10 10439734 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16226;SOR=0;LSEQ=GGCAGTTTGGACTTCTGGCC;RSEQ=CCAGAACTCTGAGACAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:22,19:0.0465:2,2:31:0:32.5:1:1:1.15394:60:4:0.0488:0:1.5 0/0:63:0:0,0:32,31:0:2,0:28.1:1:29.5:1:1:0:60:30.5:1:0:0.2 -10 10923338 . TA T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.27044;SOR=Inf;LSEQ=ACTACCTATTTCCTTCAGAA;RSEQ=AAAATAAATTTTTAACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:72,12:0:2,0:23.9:1:28.8:1:1:0:60:168:0.9882:0:0.2 0/1:122:3:1,2:103,16:0.0246:2,2:15.7:1:25.7:1:0.05666:12.41384:60:6:0.0248:0.0164:0.7 -10 10923359 . A AT 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50799;SOR=Inf;LSEQ=AAAAATAAATTTTTAACTTC;RSEQ=TTTTTTTCCTGAAGTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:101,26:0:2,0:24.8:1:30.6:1:1:0:60:254:1:0:0.5 0/1:168:2:1,1:127,39:0.0119:2,2:17:1:27:1:0.42059:3.22807:60:4:0.0119:0:0.5 -10 10923431 . T A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00918;LSEQ=GCTGTTAGTAAAATATGAGA;RSEQ=ACTTCAAACTTAATGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:349:327:180,147:11,11:0.937:2,2:25:1:29.5:1:0.66439:1.22:60:35.333:0.9353:0:1.1 0/1:445:53:27,26:192,200:0.1191:2,2:29.5:1:29.4:1:0.8838:1.08:60:52:0.119:0:1.3 -10 10923503 . C T 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AACCCACCCTCCAGATTTAG;RSEQ=ATCCTGAAACATTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:79,158:0:2,0:24.3:1:31.9:1:1:0:60:78:1:0:0.5 0/1:264:18:7,11:86,160:0.0682:2,2:23.2:1:28.9:1:0.79996:1.18:60:36:0.0692:0:1.5 -10 10925636 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCATCTGCTGTACTGAGA;RSEQ=GGTGCGGAGTCCTGTGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29.5:1:1:0:60:4:1:0:1 -10 14379777 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCAGAAACAAGGCAAGG;RSEQ=TGACCATTCTCAGCACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17.5:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 14379945 . G A 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGATGGAATCTATTAAAT;RSEQ=CTAATAAGCAAGTTTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:18,8:0,0:1:0,2:22.5:1:28.8:1:1:0:60:52:1:0:1.1 1/1:32:32:20,12:0,0:1:0,2:26.5:1:28.8:1:1:0:60:64:1:0:1 -10 15008967 . A G 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCTTGAACTCCTGACCTC;RSEQ=AGTGATCCACGCGCCTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:13.7:1:27:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 15009109 . T C 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00879;SOR=0;LSEQ=TGGGAGAAGAGGTGGTCGTT;RSEQ=AGCTGGGCACATTCAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:11,0:1,0:0.9167:0,0:27.5:1:31.7:1:1:0:60:22:0.9167:0:2.3 0/0:3:0:0,0:2,1:0:2,0:39.3:1:28.7:1:1:0:60:6:1:0:0 -10 15009164 . G T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08123;SOR=0.16464;LSEQ=GCAACTGTGCTCTGCTAAAT;RSEQ=AATCTTTTGCGGTAGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:26:26,0:2,0:0.9286:0,1:19.6:1:29.3:1:1:0:60:12:0.9231:0:1.6 1/0:9:6:6,0:3,0:0.6667:0,0:17:1:31.2:1:1:0:60:12:0.6667:0:1.8 -10 15009184 . C CA 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.38177;SOR=0.55681;LSEQ=GAATCTTTTGCGGTAGACCA;RSEQ=AAAAAAAAAGCTTTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:24:24,0:6,0:0.7742:0,1:28.1:1:29.4:1:1:0:60:11:0.7857:0:0.9 1/0:26:17:17,0:7,0:0.6538:0,1:18.6:1:31.4:1:1:0:60:34:0.6538:0.1923:0.6 -10 15009285 . G T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12708;SOR=Inf;LSEQ=TTACTTTTTATTTTAACCAT;RSEQ=AATTAGAAAGAGGTTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:177,86:0:2,0:24.1:1:31.6:1:1:0:60:86.667:1:0:0.3 0/1:301:4:1,3:193,104:0.0133:2,2:10.8:1:26.3:1:0.13025:5.53483:60:8:0.0134:0:1.3 -10 15009339 . CA C 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCAATTATACCTTACAAA;RSEQ=AAAGTGTTAGAACAACTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:211,182:0:2,0:26.6:1:29.9:1:1:0:60:97.25:0.9974:0:0.7 0/1:499:25:12,13:239,234:0.0501:2,2:27.4:1:31.5:1:0.83994:1.10626:60:50:0.0503:0.006:0.1 -10 15009368 . A G 265 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06654;LSEQ=TAGAACAACTCGTGACTTTG;RSEQ=TAGTATATCCCAGGCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:360:172,188:4,6:0.973:2,2:24.8:1:31.3:1:0.75352:1.37:60:119:0.9728:0:1.1 1/0:444:313:145,168:57,74:0.705:2,2:25.7:1:30.8:1:0.60285:1.12:60:103.333:0.7045:0:1.2 -10 15009466 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50534;SOR=0;LSEQ=CTCCCGTTTATACAGTGTGG;RSEQ=TCTTCTTAACTTATTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:18,103:0.0163:2,2:23:1:31:1:0.28615:5.60:60:4:0.0165:0:1 0/0:96:0:0,0:15,81:0:2,0:23.1:1:29.3:1:1:0:59.8:31:1:0:0.8 -10 15009504 . T C 134 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=1;SSF=0.38117;SOR=0.65908;LSEQ=TTCTCTTGGCTACTAAGATA;RSEQ=TTTTTTTTTTTTTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:19:1,18:0,1:0.3585:0,1:7.6:1:31.6:1:1:0:60:18:0.3913:0:1.1 0/1:41:11:1,10:0,11:0.2683:0,2:8.4:1:32.7:1:1:0:60:22:0.3056:0:1.5 -10 15009535 . A G 149 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00209;SOR=0;LSEQ=TTTTTTTGAGACAGAGTCTC;RSEQ=CTCTGTCACCCAGGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:0,24:0,0:1:0,1:27.5:1:32.5:1:1:0:50.9:48:1:0:3.3 1/0:16:10:0,10:0,6:0.625:0,0:25.1:1:31.9:1:1:0:53.2:20:0.625:0:2.6 -10 15009579 . G C 124 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00957;SOR=0;LSEQ=ACTGGCGCAATCTCGGCTCA;RSEQ=TGCAACCTCCACCTCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:1:0,1:21.5:1:32.8:1:1:0:49.8:28:1:0:3.4 1/0:8:4:0,4:0,4:0.5:0,0:17.5:1:32.8:1:1:0:47.3:8:0.5:0:3.3 -10 15009590 . A G 113 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00879;SOR=0;LSEQ=CTCGGCTCAGTGCAACCTCC;RSEQ=CCTCCCGGGTTCAAGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:18.8:1:32.8:1:1:0:49.9:22:1:0:3.1 0/1:4:1:0,1:0,3:0.25:0,0:50:0:34:0:1:0:60:2:0.25:0:2 -10 15009719 . A T 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATAACTTTTGACTCCCCA;RSEQ=AACAACTACTAGTAACCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:26.7:1:28:1:1:0:60:6:1:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 15549548 . A C 142 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04435;SOR=0;LSEQ=CCATCGTTTACATCTGACCA;RSEQ=ATTCCTCCCCCGTCACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:20,0:0,0:1:0,1:34.4:1:33:1:1:0:60:40:1:0:1.1 1/0:12:9:9,0:3,0:0.75:0,0:21.2:1:31.3:1:1:0:60:18:0.75:0:1 -10 15549612 . A C 113 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00391;SOR=7.23301;LSEQ=TTGACTGCCTCAGCCTTAGC;RSEQ=GGAATCACCCCTGACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:2,0:31,23:0.0357:2,0:40:1:33:0:0.50714:0:60:4:0.0364:0:1 0/1:75:16:10,6:31,28:0.2133:2,2:25.9:1:28.4:1:0.57667:1.50:60:15:0.2027:0:1.2 -10 15549894 . A G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAAGATGCACATAAACT;RSEQ=CTTAGTGGAGGGCTTCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:26.7:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 15950149 . G A 261 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=212.02438;LSEQ=CTACGTAAAAGGGGTAGCAC;RSEQ=GGAGCCGAGAGAAATTCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:598:3:3,0:294,300:0.005:2,0:1:0:26.3:1:0.1225:0:60:6:0.0051:0:1 1/0:767:397:194,203:176,194:0.5176:2,2:25:1:30.3:1:0.77243:1.05:60:197.5:0.5211:0:1.2 -10 16154458 . A C 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00239;SOR=1.63526;LSEQ=ATAGGAGAGAAGTGATCCAG;RSEQ=TACAAATACCCAAGGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:155:88,67:93,67:0.4921:2,2:27.6:1:31.8:1:0.8206:1.05661:60:37.75:0.4887:0:1.6 1/0:318:195:116,79:71,50:0.6132:2,2:27.3:1:32.1:1:0.90668:1.03:60:390:0.6171:0:1.5 -10 16154522 . C G 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00032;SOR=1.70543;LSEQ=TTTCCAAGGCATCTTCTCAT;RSEQ=ATGTTCACTTTCAGTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:161:68,93:95,106:0.4435:2,2:23.9:1:31:1:0.39517:1.22503:60:52.667:0.4389:0:1.9 1/0:380:219:93,126:75,85:0.5763:2,2:26:1:31.3:1:0.40418:1.19487:60:438:0.5794:0:1.8 -10 16154527 . TCACTTTCAGTCCAGGCAAGCAATTGA T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00384;SOR=Inf;LSEQ=AAGGCATCTTCTCATCATGT;RSEQ=CACTATGGAATCCAAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:149,192:0:2,0:25.9:1:31.2:1:1:0:60:47.714:0.997:0:0.9 0/1:364:9:2,7:151,203:0.0247:2,2:30.9:1:31.7:1:0.31265:2.59738:60:18:0.0249:0.0027:2.3 -10 16154569 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24848;SOR=Inf;LSEQ=ATTGACACTATGGAATCCAA;RSEQ=CTGATAATGAGTTCGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:63,142:0:2,0:23.3:1:31.5:1:1:0:60:33.167:1:0:0.8 0/1:213:3:1,2:63,147:0.0141:2,2:27.7:1:28:1:1:1.17:60:6:0.0142:0:1.7 -10 16154583 . C T 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.91124;SOR=1.04483;LSEQ=ATCCAAGCTGATAATGAGTT;RSEQ=GGAGGTATAAACAGGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:161:89:20,69:20,51:0.5528:2,2:21:1:30:1:0.46417:1.35034:60:178:0.5597:0:1.7 1/0:165:93:28,65:17,55:0.5636:2,2:24.9:1:30.3:1:0.38271:1.39:60:186:0.5636:0:1.7 -10 16154624 . T A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11992;SOR=Inf;LSEQ=GAAGTACAATGTAGAATGTC;RSEQ=ACCCATCAAGAAAGGGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:5,58:0:2,0:26.5:1:28.8:1:1:0:60:62:1:0:0.5 0/1:67:4:1,3:11,52:0.0597:2,2:15.5:1:30.3:1:0.55504:1.56:60:8:0.0597:0:2.3 -10 16154704 . T C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0092;SOR=9.51066;LSEQ=AGAAAATTGGGAAAGACAGA;RSEQ=CAAGGCTAAGTCCAATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:0,7:0,15:0.3043:1,0:24:1:31.3:1:1:0:60:14:0.3182:0:1 1/1:11:9:0,9:0,2:0.8182:0,0:16:1:30.7:1:1:0:60:18:0.8182:0:1.1 -10 16762523 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.26301;LSEQ=AGGGAAGAACTCTAATTTTA;RSEQ=AGTTAAACTCAGGGTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:291:188:112,76:54,48:0.646:2,2:26.3:1:32.1:1:0.32023:1.31:60:61.667:0.6446:0:1.2 0/1:352:114:65,49:128,109:0.3239:2,2:24.2:1:31.2:1:0.64725:1.13:60:228:0.3248:0:1.1 -10 16762607 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23542;SOR=Inf;LSEQ=GAGTTTCTCATATAAATAAG;RSEQ=ATCCTACACAGAATACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:54,146:0:2,0:23.8:1:28.4:1:1:0:60:199:1:0:0.2 0/1:189:2:1,1:59,128:0.0106:2,2:31.5:1:29:1:0.53529:2.16:60:4:0.0106:0:1 -10 17054256 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23557;SOR=Inf;LSEQ=GGCTGCCATGGGACCTAGAA;RSEQ=GGGGAGAAGCCATATTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,21:0:2,0:20.7:1:30:1:1:0:57.7:21:1:0:0.1 0/1:42:2:1,1:25,15:0.0476:2,2:24.5:1:29:1:1:1.64563:60:4:0.0488:0:1.5 -10 17054570 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGCTTTGAGAGTGTGTG;RSEQ=TAGTAGGATAATGCATGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:29.5:1:1:0:60:4:1:0:1 -10 18471750 . CA C 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=GACAGAATGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAACAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:32.8:1:30.6:1:1:0:55.5:16:1:0:1 1/0:4:2:2,0:2,0:0.5:0,0:19:1:31.1:1:1:0:60:4:0.5:0.25:1.5 -10 18471794 . C T 83 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00075;SOR=25.95982;LSEQ=ATAATTTCCTTCACCTGAAG;RSEQ=GTTAACATTATTAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:1,0:25,0:0.0385:1,0:39:0:32:0:1:0:60:2:0.0435:0:1 1/0:13:7:7,0:6,0:0.5385:0,0:21.1:1:29.6:1:1:0:60:14:0.5833:0:1.1 -10 18471920 . G T 33 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67718;LSEQ=AATAGTATACAAATTGAATT;RSEQ=TAACATCTTTTTTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:0,3:186,84:0.011:2,0:13:1:21:1:0.0316:0:60:2:0.0078:0:2.7 0/0:268:2:0,2:187,79:0.0075:2,0:23:1:13:0:0.09056:0:50:0:0:0:6.5 -10 18471923 . A G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.7644;LSEQ=AGTATACAAATTGAATTGTA;RSEQ=CATCTTTTTTTTTTTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:10:5,5:190,88:0.0344:2,2:27.9:1:30.4:1:0.30105:2.15282:60:9:0.0316:0:2 0/1:278:136:99,37:80,35:0.4892:2,2:22:1:30.8:1:0.57884:1.17:60:18.429:0.4831:0:2 -10 18471927 . CT C 153 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.56606;SOR=0.83413;LSEQ=TACAAATTGAATTGTAACAT;RSEQ=TTTTTTTTTTAATTAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:30:19,11:179,92:0.099:2,2:26:1:31.2:1:0.8398:1.12597:60:60:0.1014:0.0132:0.1 0/1:274:23:14,9:170,76:0.0839:2,2:26.3:1:31:1:0.48264:1.43596:59.1:46:0.0852:0:0.6 -10 18471939 . A T 40 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01435;LSEQ=TGTAACATCTTTTTTTTTTT;RSEQ=ATTAGGAGAAGCAGAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:4:1,3:217,136:0.0112:2,2:1.8:1:28.7:1:0.3034:4.76612:60:3:0.0116:0:1.3 0/1:352:4:1,3:221,127:0.0114:2,2:13.8:1:20.3:1:0.14437:5.19584:53.3:3:0.009:0:2.3 -10 18471961 . T G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=41.31309;LSEQ=TTAGGAGAAGCAGAGGGGCA;RSEQ=TGTGGTTGAGAGATTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:18:10,8:251,195:0.0388:2,2:20.8:1:32:1:1:1.02969:60:36:0.0398:0:1.8 1/0:484:303:173,130:103,75:0.626:2,2:25.2:1:30.8:1:0.92398:1.03193:59.9:32.667:0.6242:0:1.6 -10 18472087 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21201;SOR=Inf;LSEQ=TCATCTGTAAAACGCAGATC;RSEQ=CAGTATCAACCCACACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:17,116:0:2,0:22.9:1:31.1:1:1:0:60:65.5:1:0:0.1 0/1:114:2:1,1:11,101:0.0175:2,2:30.5:1:28:1:0.20028:8.84:60:4:0.018:0:1 -10 19229312 . CA TG 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=ATGTCTTTTGCATCTGGCTT;RSEQ=TTTACTTAGTATAATGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:37,0:0:1,0:25.7:1:31.9:1:1:0:60:74:1:0:0 0/1:12:5:5,0:7,0:0.4167:0,0:21.2:1:32.2:1:1:0:60:10:0.4167:0.0833:1 -10 19229394 . A G 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTTTTTATTGCCAAATAGT;RSEQ=TTCCATTGTGTGTGTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:112,9:0:2,0:23.2:1:28.1:1:1:0:60:39.333:1:0:0.1 0/1:102:26:24,2:71,5:0.2549:2,2:24:1:32.1:1:1:1.18128:60:52:0.2574:0:1 -10 19229559 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62522;SOR=2.73415;LSEQ=TCTGACCCTGAACTCCACTG;RSEQ=AAGCAATTGCACTGTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:1:1,0:84,137:0.0045:2,0:1:0:27:0:0.38288:0:60:2:0.0046:0:1 0/1:245:3:2,1:101,141:0.0122:2,2:14.3:1:28:1:0.5741:2.78:60:6:0.0125:0:1 -10 19229606 . C T 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGAGTATACATCAACTCT;RSEQ=GACTGGCACCACTGGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:79,92:0:2,0:24.2:1:30.3:1:1:0:60:56:1:0:0.1 0/1:198:59:28,31:66,73:0.298:2,2:26.7:1:30.3:1:1:1.00097:60:118:0.298:0:2.6 -10 19229638 . G A 175 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=68.42517;LSEQ=CTGGAAGTTTGTGCACATTC;RSEQ=TTTTTTCATGAATTACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:1,0:88,78:0.006:2,0:2:0:26:0:1:0:60:2:0.0061:0:1 0/1:201:59:32,27:71,71:0.2935:2,2:22.5:1:29.8:1:0.64317:1.18:60:58:0.2915:0:3.3 -10 19229645 . C G 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGTGCACATTCGTTTTTT;RSEQ=ATGAATTACAGGATCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:90,75:0:2,0:24.6:1:31.5:1:1:0:60:164:0.9939:0:0.1 0/1:226:68:36,32:79,79:0.3009:2,2:20.5:1:31.2:1:0.77197:1.12:60:67:0.2991:0:3.1 -10 19229675 . C G 197 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGATCCAAATGTCAAACTA;RSEQ=CAAATGGGTGAGACACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:113,89:0:2,0:25.6:1:31.4:1:1:0:60:66.333:1:0:0.1 0/1:276:79:42,37:108,89:0.2862:2,2:26.3:1:31.4:1:0.89373:1.06875:60:78:0.2836:0:2.4 -10 19229823 . C G 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCACAGCAGCCACCGATG;RSEQ=TAGTGCTGGAGACCGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:125,126:0:2,0:24:1:32:1:1:0:60:61.75:1:0:0.1 0/1:322:75:41,34:112,134:0.2329:2,2:22.2:1:29.9:1:0.18736:1.44:60:17.75:0.2247:0:1.2 -10 19229864 . GC AT 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01243;SOR=0;LSEQ=AGACCAATAATGCTGTTTCT;RSEQ=ATCATCTTCCAACTTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:5:2,3:102,137:0.0205:2,2:6.4:1:30.2:1:1:1.11632:60:10:0.0207:0.0123:0.8 0/0:340:0:0,0:152,188:0:2,0:24.4:1:31.6:1:1:0:60:67:1:0:0.3 -10 19229929 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18483;SOR=0;LSEQ=CACAGGAAAAGCCACCAGTT;RSEQ=CTTGAGTCACTCAGCAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:48,133:0.0109:2,2:11.5:1:31:1:0.4649:2.75:60:4:0.011:0:1.5 0/0:242:0:0,0:87,155:0:2,0:41:0:16:0:1:0:60:0:0:0:1 -10 19229941 . C T 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCAGTTACTTGAGTCACT;RSEQ=AGCAACACTGGTCACTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:29,115:0:2,0:24.3:1:32.3:1:1:0:60:288:1:0:0.2 0/1:194:28:8,20:51,114:0.1443:2,2:21.9:1:27.8:1:1:1.1178:60:56:0.1451:0:1.2 -10 19229961 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49792;SOR=Inf;LSEQ=CAGCAACACTGGTCACTTTT;RSEQ=GAAAGAATATTAAAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:7,75:0:2,0:23.5:1:31.5:1:1:0:60:81:0.9878:0:0.1 0/1:90:2:1,1:16,72:0.0222:2,2:32.5:1:28.5:1:0.34382:4.40:60:4:0.0225:0:1 -10 19229962 . G GA 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAACACTGGTCACTTTTG;RSEQ=AAAGAATATTAAAAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:7,73:0:2,0:23.5:1:31.5:1:1:0:60:79:1:0:0.1 0/1:87:32:5,27:10,45:0.3678:2,2:28.3:1:29.2:1:1:1.19753:60:31:0.3605:0.069:0.7 -10 19229980 . G GA 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00767;SOR=Inf;LSEQ=TGGAAAGAATATTAAAAAGA;RSEQ=AAAAAAAATCTGTTAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:3,54:0:2,0:18.3:1:31.7:1:1:0:60:114:1:0:0.2 0/1:69:8:0,8:10,51:0.1159:2,0:21.5:1:30:1:0.592:0:60:16:0.1231:0.0145:0.5 -10 19230013 . GTATA G 72 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=28;MSI=16.000;MSILEN=2;SSF=0.1868;SOR=0.16952;LSEQ=TTAAAAATATATGTGTGTAT;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:0,5:0,14:0.2174:1,0:35:1:31.2:1:1:0:60:10:0.2174:0:0.2 0/1:23:1:0,1:0,22:0.0435:1,0:41:0:24:0:1:0:60:2:0.0435:0:3 -10 19230027 . ATATATATATATATATATACATATA G 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=3e-04;SOR=Inf;LSEQ=GTGTATGTATATATATATAT;RSEQ=CATACACACAATGGAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:0,16:0:1,0:28.5:1:31.4:1:1:0:60:32:1:0:0.6 1/0:17:10:0,10:0,7:0.5882:0,0:27.9:1:31.2:1:1:0:59.7:20:0.5882:0.0588:0.2 -10 19230044 . TAC T 56 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=17.000;MSILEN=2;SSF=0.17192;SOR=5.17734;LSEQ=TATATATATATATATATATA;RSEQ=ATATACATACACACAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:0,15:0.0625:1,0:12:0:32:0:1:0:60:2:0.0625:0:1 0/1:15:4:0,4:0,2:0.2667:0,0:20.8:1:28:1:1:0:60:8:0.6667:0.0667:0.5 -10 20006337 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGCAGATGGTGATGAAGAA;RSEQ=ACAGTGTATAATTTGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 20007127 . A C 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=3.000;MSILEN=3;SSF=0.01806;SOR=0;LSEQ=AAGGAAAAAGAAGACGAAGA;RSEQ=GAAGAGGAAGAAGAAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:5,3:3,2:0.6154:2,2:11.5:1:30.8:1:1:1.10:60:16:0.6154:0:1 0/0:6:0:0,0:3,3:0:2,0:25.8:1:28.8:1:1:0:60:12:1:0:0 -10 21399813 . C G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32516;SOR=2.04065;LSEQ=GTCCAATTAAAGTAACACTG;RSEQ=CAACTTTGAAAATGTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:4,4:4,3:0.5333:2,2:30.8:1:29.9:1:1:1.30792:60:7:0.5:0:1.4 1/0:27:19:10,9:4,4:0.7037:2,2:31.1:1:31.2:1:1:1.11:60:38:0.7037:0:1.3 -10 21399869 . G A 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAAATCACAAGCATTCCTAT;RSEQ=CAGCAATAACAGACAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:2,4:2,4:0.5:2,2:20.2:1:27:1:1:1:54.7:5:0.4545:0:1.5 1/0:8:4:1,3:0,4:0.5:0,2:15.8:1:28.5:1:1:0:60:8:0.5:0:2 -10 21401670 . TA T 95 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=1.02194;LSEQ=CCCTAGAACTTAAAGTATAA;RSEQ=AAAAAAAAAAAAGAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:3,1:0.4444:2,0:16.5:1:32.5:1:1:0:60:8:0.4444:0:0 0/1:20:9:5,4:7,2:0.45:2,2:27.9:1:30.2:1:0.61991:2.64037:60:18:0.4737:0:0.2 -10 21401684 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.50089;SOR=Inf;LSEQ=GTATAATAAAAAAAAAAAAA;RSEQ=AAAAAGAAAAAAATTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:11,3:0:2,0:18.6:1:29.9:1:1:0:60:6:1:0:0.6 0/1:20:2:1,1:11,7:0.1:2,2:11:1:28:1:1:1.53525:47:4:0.1053:0:1.5 -10 21401731 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49938;SOR=Inf;LSEQ=TACAGCCAGTGATTTCCCTT;RSEQ=GGGGCTTTGAAATTACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:20,11:0:2,0:27.2:1:30.9:1:1:0:60:14.5:1:0:0.6 0/1:39:2:1,1:20,17:0.0513:2,2:34:1:29.5:1:1:1.17156:60:4:0.0541:0:4 -10 21401745 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49333;SOR=Inf;LSEQ=TCCCTTGGGGGCTTTGAAAT;RSEQ=ACACCACCCAGTCTTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:24,13:0:2,0:25:1:29.6:1:1:0:60:74:1:0:0.6 0/1:38:2:1,1:18,18:0.0526:2,2:18.5:1:30.5:1:1:1:50:4:0.0541:0:1 -10 21401754 . CA AGTG 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49383;SOR=Inf;LSEQ=GGCTTTGAAATTACACCACC;RSEQ=GTCTTACAGTTGAAGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:25,15:0:2,0:23.6:1:31.1:1:1:0:60:39:1:0:0.7 0/1:41:2:1,1:19,20:0.0488:2,2:25.5:1:32.1:1:1:1.05:50:4:0.0488:0:1 -10 21401765 . T C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00027;SOR=0.14719;LSEQ=TACACCACCCAGTCTTACAG;RSEQ=TGAAGTGTGGTTCAGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:22:13,9:8,5:0.6286:2,2:26.5:1:32.3:1:1:1.10447:60:21:0.6176:0:1.1 0/1:36:7:3,4:16,13:0.1944:2,2:31.6:1:30.6:1:0.68426:1.61842:60:14:0.1944:0:1 -10 21401876 . A T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03924;SOR=Inf;LSEQ=ATGTGAAACTCTTAAGTGTA;RSEQ=CTGGAAAGTGATCTGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,19:0:2,0:26.2:1:30.1:1:1:0:60:66:1:0:0 0/1:28:4:2,2:8,16:0.1429:2,2:35.5:1:30:1:0.60147:1.95:60:8:0.1429:0:1 -10 21402110 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49126;SOR=Inf;LSEQ=AGGAAACTGAAGAAAAAGTG;RSEQ=CAGTGAAGAAATCTATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:21.8:1:32:1:1:0:60:52:1:0:0 0/1:28:2:1,1:15,11:0.0714:2,2:34.5:1:28.5:1:1:1.34838:60:4:0.0769:0:1.5 -10 22434438 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49462;SOR=Inf;LSEQ=CACCTGGCATTTACAGAAAA;RSEQ=GGCCTCTGAAATCAGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:28,19:0:2,0:19.1:1:30.1:1:1:0:60:94:1:0:0.1 0/1:47:2:1,1:27,18:0.0426:2,2:33:1:30.5:1:1:1.48675:60:4:0.0435:0:2.5 -10 22434503 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51482;SOR=0;LSEQ=TCTGGAGTTAGGCGTCATGG;RSEQ=TTCTCCCCTTTCTAGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:35,37:0.027:2,2:44.5:1:32.5:1:1:1.06:60:4:0.027:0:1 0/0:50:0:0,0:21,28:0:2,0:24.2:1:31.6:1:1:0:58.4:98:0.98:0:0.1 -10 26579975 . A G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23259;SOR=0;LSEQ=TGCAGTGCAAACTCTTCTTC;RSEQ=TGGGAAATCAGAGAGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:109,46:0.0127:2,2:9:0:31.5:1:0.51045:2.35497:60:4:0.0128:0:2.5 0/0:168:0:0,0:108,60:0:2,0:26.7:1:29.2:1:1:0:60:32.6:1:0:0.2 -10 26580036 . T G 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03685;SOR=1.93093;LSEQ=GAGTTGGCCAAAGCCATTCA;RSEQ=CTGGACAGGGTCAGAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:19:10,9:102,115:0.0805:2,2:24.7:1:31.9:1:0.6422:1.25:60:38:0.0819:0:1.2 0/1:221:32:15,17:90,99:0.1448:2,2:27.7:1:32.6:1:1:1.03017:60:64:0.1475:0:1.2 -10 26580105 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22923;SOR=Inf;LSEQ=ATGCAAAAGTTTAAACCCAA;RSEQ=TCCAGACTGGTCCAAAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:40,89:0:2,0:23.6:1:31.8:1:1:0:60:63.5:1:0:0.1 0/1:119:2:1,1:37,80:0.0168:2,2:14:1:28:1:0.53853:2.15:60:4:0.0168:0:1.5 -10 28301440 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49745;SOR=0;LSEQ=AACAATTCTTCTCTGGGTCT;RSEQ=GTCACTGGATTGAAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:44,32:0.0256:2,2:26.5:1:32:1:1:1.36929:60:4:0.0256:0:1 0/0:72:0:0,0:42,30:0:2,0:25.8:1:29.2:1:1:0:60:71:1:0:0.2 -10 29107838 . C T 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTGCCAGCCCAAGGAG;RSEQ=GTTTCTCTTACAGTTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:24.7:1:29.7:1:1:0:60:28:1:0:1.7 1/1:6:6:6,0:0,0:1:0,0:25.8:1:26.2:1:1:0:60:12:1:0:2.3 -10 29107866 . T C 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAGTTTACACAAGAAGT;RSEQ=GTTAAAAAACAAAGAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:20,0:0,0:1:0,1:23.2:1:31.6:1:1:0:60:40:1:0:2 1/1:10:10:10,0:0,0:1:0,0:23:1:28.8:1:1:0:60:4:1:0:2.2 -10 29107904 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13326;SOR=Inf;LSEQ=GAGCTGATCTGATATCCAAT;RSEQ=AAGTCACATTTGATTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:0:1,0:22.2:1:29:1:1:0:60:120:1:0:1.3 0/1:35:2:2,0:32,1:0.0571:1,0:34:0:33:1:1:0:60:4:0.0571:0:2 -10 29107937 . C G 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTACTTCCTTGTGAAAAT;RSEQ=CTTACTCAATAGGCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:100:97,3:0,0:1:0,1:26.7:1:32.7:1:1:0:60:200:1:0:1.1 1/1:77:77:72,5:0,0:1:0,2:23.2:1:31.9:1:1:0:60:76:1:0:1.1 -10 29108055 . A T 274 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00624;LSEQ=AACATGTTAAAATACCTGTT;RSEQ=TGGTTTTAGGGGATTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:564:562:267,295:2,0:0.9965:0,2:27:1:30:1:0.22704:0:60:92.667:0.9964:0:1.1 1/0:475:302:149,153:90,83:0.6358:2,2:26.7:1:29.7:1:0.63361:1.11319:60:74.5:0.6368:0:1.1 -10 29108209 . C G 180 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=AAAATTGGTATAAGTAGAGA;RSEQ=ATAATTTGGGCCAAGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:51:0,51:0,0:1:0,1:24.6:1:31.8:1:1:0:60:102:1:0:1 1/0:35:24:0,24:0,11:0.6857:0,1:23.8:1:31.3:1:1:0:60:48:0.6857:0:1.1 -10 29109847 . C CAG 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAACTTCTATTTTAGAGT;RSEQ=GGGGTGTACGTGCAGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31.3:1:1:0:60:4:1:0:0 -10 29188024 . G A 99 pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05;SOR=0;LSEQ=TCTCTGGGTGGAGCAGGCTG;RSEQ=CGCTTTAGTTGAACCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:9,3:0,0:1:0,2:16.8:1:27.7:1:1:0:44.9:11:1:0:1.6 1/0:4:2:2,0:2,0:0.5:0,0:8:0:30:0:1:0:60:4:0.5:0:1.5 -10 29188056 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.02653;SOR=0.20469;LSEQ=AACCCAGGTACCTTTCTCTT;RSEQ=GGCTTCTTTCTTTTTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:8,4:8,0:0.6:0,2:27.8:1:31.1:1:0.11662:0:54.5:24:0.6:0:1.6 0/1:22:5:5,0:16,1:0.2273:1,0:17.2:1:32.2:1:1:0:58.6:10:0.2273:0:1.2 -10 29188110 . G A 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGTTTCAGGAAGCTGTCTC;RSEQ=GCTCTTAGAGTGCTTAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:44,5:0:2,0:24.8:1:30.6:1:1:0:59.8:98:1:0:0.2 0/1:42:18:14,4:20,4:0.4286:2,2:21.4:1:29.5:1:0.70615:1.41628:56.9:36:0.4286:0:1 -10 29188207 . C A 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01496;SOR=0;LSEQ=ACAACAATGCCAACAGCATG;RSEQ=TGGGTAACATTGTAGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:7:3,4:123,97:0.0308:2,2:30.4:1:29.4:1:0.70282:1.68675:41.3:14:0.0313:0:1 0/0:221:0:0,0:113,108:0:2,0:31:1:31:1:1:0:41.2:43.2:1:0:0.1 -10 29188387 . C T 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAACATATATCGGGTGCC;RSEQ=CTCCTCTTTCTCTTTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:16,37:0,0:1:0,2:26:1:30.1:1:1:0:47.7:16.667:1:0:1.1 1/1:56:56:22,34:0,0:1:0,2:22.7:1:29.5:1:1:0:49.5:55:1:0:1.1 -10 29965811 . A T 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.10738;LSEQ=GACCCTTGGGTCTTGGAAAC;RSEQ=CCTGTGGAGATTTAGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:149:78,71:99,102:0.4257:2,2:23.9:1:30.3:1:0.58996:1.13:60:73.5:0.4224:0:1.1 1/0:341:208:105,103:65,68:0.61:2,2:26.4:1:29.5:1:0.82449:1.07:60:103:0.6077:0:1.2 -10 29965818 . G T 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGTCTTGGAAACACCTGTG;RSEQ=AGATTTAGCCTTGGTAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:166,179:0:2,0:25.8:1:30.7:1:1:0:60:42.125:1:0:0.5 0/1:349:26:11,15:160,163:0.0745:2,2:23.7:1:28.2:1:0.54388:1.33742:60:52:0.0756:0:1.2 -10 29965868 . T A 40 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32798;SOR=3.76821;LSEQ=TCCCAGGTCATCAGAACCCA;RSEQ=CTGCCTCCTAGACTAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:1:1,0:95,177:0.0037:2,0:1:0:26:0:0.35165:0:60:2:0.0037:0:1 0/1:219:3:2,1:84,132:0.0137:2,2:10.3:1:25.7:1:0.5628:3.13:60:6:0.014:0:4 -10 30692028 . G A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00606;SOR=Inf;LSEQ=AAGTGCAGGATTACAGGCGT;RSEQ=AGCCAGCATGCCAGGCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:18.9:1:29.3:1:1:0:60:7:1:0:0.9 1/1:3:3:3,0:0,0:1:0,0:15:1:28.3:1:1:0:60:6:1:0:2 -10 30692068 . C A 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTGTATTGATATAT;RSEQ=TCACATATGGTTATCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:25,0:0,0:1:0,1:23.4:1:29.1:1:1:0:60:50:1:0:1 1/1:16:16:16,0:0,0:1:0,1:19.3:1:29.2:1:1:0:60:32:1:0:1.3 -10 30692132 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22517;SOR=Inf;LSEQ=GTTTTCACAACTGGATGGTG;RSEQ=GTACATGGCAAAGGTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:74,24:0:2,0:21.6:1:30.3:1:1:0:60:31.667:1:0:0.3 0/1:89:2:1,1:70,17:0.0225:2,2:20.5:1:27.5:1:0.36542:4.03012:60:4:0.0227:0:1 -10 30692136 . C T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49756;SOR=Inf;LSEQ=TCACAACTGGATGGTGGGTA;RSEQ=ATGGCAAAGGTGTAATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:78,25:0:2,0:22.3:1:31.4:1:1:0:60:50.5:1:0:0.3 0/1:103:2:1,1:78,23:0.0194:2,2:10:1:23.5:1:0.41348:3.34106:60:4:0.0196:0:1.5 -10 30692361 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20797;SOR=Inf;LSEQ=TTTCTCAATGGTCATGGGCC;RSEQ=AGTCTTACGCAGCTTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:113,119:0:2,0:26.2:1:31.1:1:1:0:60:32.143:1:0:0.2 0/1:195:2:1,1:89,104:0.0103:2,2:19.5:1:29.5:1:1:1.17:60:4:0.0105:0:1 -10 30692382 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09128;SOR=Inf;LSEQ=AGTCTTACGCAGCTTGGAGG;RSEQ=CAGCCGCATGGAGACCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:108,102:0:2,0:25:1:30.8:1:1:0:60:20:1:0:0.2 0/1:173:3:1,2:86,84:0.0173:2,2:25:1:29.7:1:0.62063:2.03944:60:6:0.0175:0:1 -10 30692387 . C G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=TACGCAGCTTGGAGGCCAGC;RSEQ=GCATGGAGACCGCAACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:110,93:0:2,0:25:1:29.9:1:1:0:60:32.833:1:0:0.2 0/1:171:12:7,5:82,77:0.0702:2,2:25.5:1:27.4:1:0.76857:1.31:60:11:0.0647:0:1.3 -10 30692531 . A T 44 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.43597;SOR=2.1586;LSEQ=CACAGCACTGCTCCTCACAC;RSEQ=CCTCCAGCATCCAGTAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:2:0,2:126,153:0.0071:2,0:19.5:1:21:1:0.50356:0:60:1:0.0037:0:1 0/1:264:4:0,4:136,123:0.0152:2,0:6.8:1:22.3:1:0.05304:0:60:3:0.0117:0:1 -10 30692597 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=TCTCCCTTTGCACGCACTGG;RSEQ=AGTAGGCGCAGTGCACGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:66,120:0:2,0:24:1:29.9:1:1:0:60:45.5:1:0:0.1 0/1:187:2:1,1:77,108:0.0107:2,2:45:1:29.5:1:1:1.40:60:4:0.0112:0:1 -10 30692599 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=TCCCTTTGCACGCACTGGAA;RSEQ=TAGGCGCAGTGCACGCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:63,117:0:2,0:23.8:1:31.6:1:1:0:60:59:1:0:0.1 0/1:181:2:1,1:73,106:0.011:2,2:11.5:1:29:1:1:1.45:60:4:0.0112:0:1.5 -10 30692610 . G A 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0499;SOR=Inf;LSEQ=GCACTGGAAGTAGGCGCAGT;RSEQ=CACGCAGCGCTACTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:50,108:0:2,0:21.6:1:31.8:1:1:0:60:51.667:1:0:0.1 0/1:144:4:3,1:50,90:0.0278:2,2:12.3:1:25.8:1:0.14114:5.34:60:8:0.028:0:1.3 -10 30692614 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22256;SOR=Inf;LSEQ=TGGAAGTAGGCGCAGTGCAC;RSEQ=CAGCGCTACTCCAAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:44,101:0:2,0:22:1:31:1:1:0:60:47.333:1:0:0.1 0/1:130:2:1,1:46,82:0.0154:2,2:14:1:29:1:1:1.77:60:4:0.0156:0:1 -10 30692623 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22227;SOR=Inf;LSEQ=GCGCAGTGCACGCAGCGCTA;RSEQ=TCCAAGGGGAGCAAGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:37,88:0:2,0:22.4:1:32:1:1:0:60:124:1:0:0.1 0/1:112:2:1,1:36,74:0.0179:2,2:10.5:1:27:1:1:2.04:60:4:0.018:0:2 -10 30692649 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18366;SOR=Inf;LSEQ=GGGGAGCAAGCTCTGCAGGA;RSEQ=GCGCTGATCCCCTGGCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:21,61:0:2,0:26:1:30.1:1:1:0:60:81:1:0:0.1 0/1:62:2:0,2:20,40:0.0323:2,0:18.5:1:29:1:1:0:60:4:0.0323:0:2 -10 30692681 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2099;SOR=Inf;LSEQ=CTGGCGTCTGCGGGTCCTCG;RSEQ=GCCTTCGCAGCATAGCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:23,45:0:2,0:23.4:1:30.6:1:1:0:60:67:1:0:0.2 0/1:58:2:1,1:21,35:0.0345:2,2:32.5:1:30:1:1:1.65:60:4:0.0345:0:2 -10 30692717 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21957;SOR=0;LSEQ=CAGCTCCACACTCGGGCAGC;RSEQ=CACAGGCAGGGCGGGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:17,30:0.0408:2,2:43:1:30.5:1:1:1.74:60:4:0.0426:0:1 0/0:55:0:0,0:23,32:0:2,0:26.9:1:30.6:1:1:0:60:54:1:0:0.2 -10 31902215 . C A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50171;SOR=0;LSEQ=AGGCCTGGGAAGTACACTGT;RSEQ=ATTAACTGTTACATTGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:38,19:0.0339:2,2:7:0:30.5:1:1:1.9749:60:4:0.0345:0:1.5 0/0:47:0:0,0:29,18:0:2,0:27.2:1:31.5:1:1:0:60:94:1:0:0.2 -10 31902242 . T C 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.11572;LSEQ=TGTTACATTGCCATGGCCCC;RSEQ=GCTGTTGCTGTTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:40,27:0.029:2,2:11:1:30:1:1:1.47282:60:4:0.0299:0:1 0/1:62:2:1,1:36,24:0.0323:2,2:20.5:1:28.5:1:1:1.48993:60:4:0.0323:0:1 -10 31902253 . TTGC T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.11993;SOR=0;LSEQ=CATGGCCCCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGTAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:4:2,2:37,30:0.0563:2,2:33.5:1:29.8:1:1:1.22967:60:8:0.058:0:0.3 0/0:68:0:0,0:35,33:0:2,0:26.5:1:30.2:1:1:0:60:136:1:0:0.2 -10 31902801 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGTTTTGGCTGGTTCCA;RSEQ=TAGGGAGAGATTTTGTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 34717415 . A G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10769;SOR=Inf;LSEQ=ATAGTGAGATCCCATCTCTA;RSEQ=AAGAAAAAAGAGGCCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:43,1:0:1,0:23:1:30.5:1:1:0:60:43:1:0:0.2 0/1:22:2:2,0:20,0:0.0909:1,0:25:1:34:0:1:0:60:4:0.0909:0:1 -10 34717559 . C A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.67014;LSEQ=TTCACTGTTCAGAAAGAAGA;RSEQ=GACAACAGCTGTGTTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:187:119,68:123,78:0.4807:2,2:25.3:1:30.5:1:0.67509:1.11:60:186:0.4806:0:1.8 1/0:351:250:157,93:59,42:0.7123:2,2:25.1:1:30.1:1:0.46851:1.20:60:61.5:0.711:0:1.8 -10 34717596 . G C 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.85309;LSEQ=TCTCTGGAGTAAAGAGGTTA;RSEQ=AGCCCTGCCAATGGGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:236:126,110:134,124:0.4777:2,2:26.4:1:32:1:0.78689:1.06:60:117:0.4776:0:1.7 1/0:426:268:141,127:81,75:0.6291:2,2:27.1:1:31:1:0.91988:1.03:60:133:0.6318:0:1.8 -10 34717713 . T C 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50442;SOR=0;LSEQ=TTTTTTCCTACATTATAAAC;RSEQ=AAAGGAAATCATGCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:13,111:0.0159:2,2:17.5:1:26:1:0.21067:8.26:60:4:0.016:0:1 0/0:100:0:0,0:22,78:0:2,0:21.4:1:28.2:1:1:0:60:99:1:0:0.4 -10 34717740 . G A 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04871;SOR=2.10021;LSEQ=AATCATGCAGAAACACTAAC;RSEQ=CTAAATTTTATGTAAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:36:0,36:0,36:0.4932:1,1:26.9:1:30:1:1:0:60:72:0.5:0:1 1/0:55:37:3,34:0,18:0.6727:1,2:26.9:1:28.9:1:0.54305:0:60:74:0.6727:0:1.1 -10 36853842 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATGGAAGTTGTAGCTGAAAC;RSEQ=TGTCCTCTGAGAGAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:24.3:1:30.3:1:1:0:60:26:1:0:2.5 0/1:16:2:2,0:14,0:0.125:1,0:7.5:1:32:0:1:0:60:4:0.125:0:2 -10 36853858 . G C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAACGTGTCCTCTGAGAGAG;RSEQ=CTGGCGCTCTCTCCGCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:24,0:0,0:1:0,1:21:1:32.2:1:1:0:60:48:1:0:2.4 0/1:22:3:3,0:19,0:0.1364:1,0:10.7:1:33.7:1:1:0:60:6:0.15:0:2.3 -10 36853878 . T C 165 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGGCGCTCTCTCCGCCCG;RSEQ=CCTGGTACACCCTTCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:36,0:0,0:1:0,1:24.4:1:32:1:1:0:60:35:1:0:1.9 0/1:36:10:8,2:26,0:0.2778:1,2:15.1:1:32.8:1:0.07143:0:60:20:0.2941:0:1.6 -10 36853977 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51038;SOR=Inf;LSEQ=TGCACAGGGATCCTGGCTGC;RSEQ=CCCTCCATAATTTATGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:83,63:0:2,0:23.9:1:30.1:1:1:0:60:35.5:1:0:0.5 0/1:199:2:1,1:125,72:0.0101:2,2:21:1:31:0:1:1.73098:60:4:0.0103:0:2 -10 36854039 . T G 228 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCTTCCGTTACCTTGTAAC;RSEQ=GCTTAGAATCTACTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:205:205:100,105:0,0:1:0,2:25.8:1:29.7:1:1:0:59.7:19.5:1:0:1.3 0/1:397:147:69,78:122,128:0.3703:2,2:27:1:29.4:1:0.75548:1.07724:59.7:72.5:0.3737:0:1.2 -10 36854110 . C CTT 141 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0;SOR=0.1892;LSEQ=CTCCACTAGTTACTTACCTT;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:29:13,16:22,25:0.3187:2,2:20.9:1:29.2:1:1:1.08194:55.9:13.5:0.3333:0.0769:2.2 0/1:161:13:4,9:46,73:0.0807:2,2:21.6:1:28.7:1:0.76558:1.4142:51.2:26:0.0963:0.0124:2.8 -10 36854169 . T C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCCCGGCTGGAGTGCAGTGG;RSEQ=GCAATCTCGACTCACTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:0,25:0,0:1:0,1:29.7:1:28:1:1:0:55.1:24:1:0:2.4 1/1:30:30:0,30:0,0:1:0,1:28.9:1:26.6:1:1:0:51:6.5:1:0:1.9 -10 36854193 . A C 140 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTCGACTCACTGCAACCA;RSEQ=CCCCTCCCAGGTTTAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:0,21:0,0:1:0,1:29.5:1:31.9:1:1:0:58.6:42:1:0:2.5 0/1:20:5:0,5:0,15:0.25:1,0:22:1:28:1:1:0:56.4:4:0.2857:0:1.8 -10 36854328 . C T 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATTGGCCAGGCTGGTCA;RSEQ=GAACTCCTGACCTAGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20.7:1:31.7:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 37564987 . T C 61 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACAGGGTCCTCATTAGAAGT;RSEQ=GTTAATTGAACTCATTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:18:1:30.8:1:1:0:60:8:1:0:1 1/0:2:1:1,0:0,1:0.5:0,0:28:0:33:0:1:0:60:2:0.5:0:1 -10 37565327 . A G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGTGAGGAGGTCTAGGCCTC;RSEQ=GAGGTTTTGGAGAGTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:25:1:30:1:1:0:60:4:0.6667:0:1.5 1/1:3:3:2,1:0,0:1:0,2:35:0:31:1:1:0:60:6:1:0:1.7 -10 37565364 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGCTGCTAAAGAGTCTAT;RSEQ=TGGGATTGTAAAGTAAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:35:0:28:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:1:0,2:33:1:31:1:1:0:60:4:1:0:1.5 -10 38372664 . A G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.65938;LSEQ=TTCCTCACAGTGTCAGTGCT;RSEQ=TATGATTGTTTAATTAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:21:9,12:77,93:0.1099:2,2:24.5:1:31.9:1:1:1.10335:59.6:42:0.1117:0:1 0/1:190:86:40,46:49,55:0.4526:2,2:28.4:1:30.7:1:1:1.02442:59.6:172:0.455:0:1.1 -10 38378777 . A G 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAAGATTCCAAGTTGTGG;RSEQ=CCGTCCTGCCCACATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:38,4:0,0:1:0,2:24.1:1:30.9:1:1:0:60:20:1:0:1.1 1/1:43:43:38,5:0,0:1:0,2:24.3:1:31.1:1:1:0:60:42:1:0:1.4 -10 38378785 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49524;SOR=Inf;LSEQ=TCCAAGTTGTGGACCGTCCT;RSEQ=CCCACATTCTGCATCATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:46,4:0:2,0:22.9:1:32.9:1:1:0:60:100:1:0:0.9 0/1:52:2:1,1:43,7:0.0385:2,2:11:1:28.5:1:0.28658:5.81258:60:4:0.0385:0:2.5 -10 38378814 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.25896;LSEQ=CTGCATCATGATGTCAAAAT;RSEQ=GCATCTGATGTTCTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:7:6,1:65,15:0.0805:2,2:29:1:32:1:1:1.38:60:14:0.0824:0:1.4 0/1:109:46:38,8:44,19:0.422:2,2:20.8:1:31.9:1:0.1777:2.04:60:92:0.422:0:1.4 -10 38378828 . T G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50907;SOR=Inf;LSEQ=CAAAATAGCATCTGATGTTC;RSEQ=TTGCATTTTCATTGAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:82,24:0:2,0:25:1:31.3:1:1:0:60:212:1:0:0.4 0/1:143:2:1,1:98,43:0.014:2,2:9:0:32.5:1:0.52221:2.26452:60:4:0.014:0:1.5 -10 38378831 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50944;SOR=Inf;LSEQ=AATAGCATCTGATGTTCTTT;RSEQ=CATTTTCATTGAAGTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:83,27:0:2,0:25.5:1:32.6:1:1:0:60:109:1:0:0.4 0/1:149:2:2,0:100,47:0.0134:2,0:27:1:29.5:1:1:0:60:4:0.0135:0:1.5 -10 38378917 . A AT 109 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.54834;SOR=0.74849;LSEQ=AGTGATTAAAGGATTGTGTG;RSEQ=TTTTTTTTTTGGCATTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:13:6,7:103,104:0.0591:2,2:31.9:1:29.7:1:1:1.15469:60:12:0.0553:0:0.4 0/1:312:14:7,7:147,148:0.0449:2,2:27.4:1:28.7:1:1:1.01:60:28:0.0467:0:0.1 -10 38379011 . C T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.03871;LSEQ=TTGATAAAGTTGTTAGTTTA;RSEQ=GTAAAGTCTTGAAATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:6:0,6:6,63:0.08:2,0:38.8:1:31:1:1:0:60:12:0.0811:0:1.2 1/0:83:46:3,43:6,31:0.5542:2,2:22.8:1:30:1:0.17829:2.74012:60:92:0.5542:0:1 -10 38379117 . G GT 31 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.52727;SOR=4.02871;LSEQ=TTACTTGTTTTTTATTCATA;RSEQ=TTTTTTTTTTTCACTAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:1,11:0.0714:2,0:25:0:32:0:1:0:60:2:0.0714:0:0 0/1:8:2:0,2:0,5:0.25:0,0:44.5:1:31:1:1:0:60:4:0.2857:0:0 -10 38539283 . G T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=0;LSEQ=TGCACAGGATGAGGAGGTAG;RSEQ=GTTGCTGCATTACCTTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:16:15,1:19,0:0.4571:1,1:20.8:1:30.8:1:0.45714:0:49.3:32:0.4571:0:1.2 0/0:20:0:0,0:19,1:0:1,0:15.3:1:30:1:1:0:52.7:19:1:0:0 -10 38539531 . G A 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGTTCCTCAATCATTTCCC;RSEQ=GGGAGTGAGCCTTTTGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:85,127:0:2,0:26.7:1:30.5:1:1:0:46.8:424:1:0:0.1 0/1:268:21:10,11:88,159:0.0784:2,2:29.6:1:30.4:1:0.34548:1.64:44.3:42:0.0789:0:1.2 -10 38539568 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50186;SOR=Inf;LSEQ=TGCCTGGCTAACAGACCTCC;RSEQ=CCCATCCATCTCATCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:23,106:0:2,0:22.1:1:29.9:1:1:0:51.2:128:1:0:0.1 0/1:153:2:1,1:35,116:0.0131:2,2:31.5:1:32.5:1:0.41641:3.28:54.5:4:0.0132:0:1 -10 38542415 . C T 98 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00212;SOR=10.75076;LSEQ=AACTTTAAATCTCCATGTCA;RSEQ=TTTGGTTACCTGAGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:2,0:38,0:0.05:1,0:26.5:1:24:1:1:0:60:1:0.0263:0:2 0/1:27:10:10,0:17,0:0.3704:1,0:18.9:1:29.8:1:1:0:59.7:20:0.3704:0:1.2 -10 38542588 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.94603;LSEQ=TAGTGCCCCTAATCATCCTC;RSEQ=TACCTCATTCTTATGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:33:18,15:154,178:0.0904:2,2:23.3:1:30.3:1:0.46509:1.39:57.3:66:0.0919:0:1.1 0/1:439:194:88,106:113,131:0.4419:2,2:25.4:1:29.7:1:0.8476:1.03896:57.8:63.667:0.4401:0:1.1 -10 38542804 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34005;SOR=2.68912;LSEQ=CCTACACAGAGCTATCCTAC;RSEQ=TCAGTCATTTTCAGTTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:0,4:0,15:0.2105:1,0:19.8:1:32:1:1:0:42.8:8:0.2105:0:1.3 0/1:7:3:0,3:1,3:0.4286:2,0:24.7:1:31.7:1:1:0:46.3:6:0.4286:0:1 -10 38742171 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49456;SOR=0;LSEQ=GCCCATGCTGCCCCAGCAGC;RSEQ=TCAGTTGGCACCTGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:29,12:0.0465:2,2:19:1:30:1:0.51827:2.36157:60:4:0.0476:0:1 0/0:40:0:0,0:28,12:0:2,0:17:1:30.9:1:1:0:58.4:80:1:0:0.1 -10 38742272 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5183;SOR=Inf;LSEQ=TTTCACCTGCAGTTGAAGAT;RSEQ=CGTGAGGTGCCCAGAAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:23,32:0:2,0:27.6:1:31.2:1:1:0:47:110:1:0:0.1 0/1:84:2:1,1:35,47:0.0238:2,2:17.5:1:29.5:1:1:1.34:51:4:0.0241:0:1.5 -10 38742782 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20307;SOR=0;LSEQ=GCTGCAGCTGGAGCATCTTC;RSEQ=CATCTTGCGTTTGGGCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:23,28:0.0377:2,2:17:1:28:1:1:1.21:50:4:0.0377:0:1 0/0:64:0:0,0:32,32:0:2,0:26.4:1:29.2:1:1:0:55.8:63:1:0:0.2 -10 38742862 . A C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26667;SOR=Inf;LSEQ=CTCTGCCCCGACCCCGAAAG;RSEQ=CCAGTCAGTTTCTCTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:2,12:0:2,0:21.7:1:28.6:1:1:0:59.2:13:1:0:0.1 0/1:22:3:0,3:6,13:0.1364:2,0:22.7:1:31.3:1:0.53247:0:49.7:6:0.15:0:1 -10 38742968 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16585;SOR=Inf;LSEQ=GATGACTGAGGAGCCTGGTA;RSEQ=CTCCAGGTCGCCCACACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:0:2,0:21.1:1:32.2:1:1:0:46.2:48:1:0:0.2 0/1:17:2:1,1:8,7:0.1176:2,2:37.5:1:28:1:1:1.13389:50:4:0.1176:0:1 -10 38743039 . G A 77 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05051;SOR=5.54112;LSEQ=CCATTGGGAGGAAACAGGTC;RSEQ=CCTTGGAAGGCATCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:11,14:0.0741:2,2:33:1:30.5:1:1:1.26:24:4:0.0769:0:1 0/1:19:6:4,2:4,9:0.3158:2,2:28.8:1:30:1:0.31889:4.12:39:12:0.3158:0:1 -10 38743433 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49652;SOR=0;LSEQ=AGTGGTGCTAAAGCCATCAT;RSEQ=AGCAATGACATCATCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:25,16:0.0465:2,2:25.5:1:28:1:1:1.54582:60:4:0.0465:0:1 0/0:37:0:0,0:20,17:0:2,0:19.7:1:31.1:1:1:0:60:17.5:1:0:0.2 -10 38743615 . G A 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AGCTCCATACTGAGTAGAAG;RSEQ=CTTTGGGCCAGAGTATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:14:8,6:29,27:0.2:2,2:27.5:1:30.1:1:0.77241:1.24:43.6:28:0.2:0:1.1 0/0:78:0:0,0:39,39:0:2,0:28.6:1:30.5:1:1:0:46:18.5:1:0:0.1 -10 38743659 . A G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24643;SOR=Inf;LSEQ=TGCCAGACACCACCTGTGTC;RSEQ=GTTCCTGTAGTGCCTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:30,33:0:2,0:25.6:1:30.5:1:1:0:54.7:30.5:1:0:0.2 0/1:71:3:2,1:30,38:0.0423:2,2:34.3:1:31:1:0.58513:2.50:60:6:0.0423:0:1 -10 38743802 . G T 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTGCTCCTTGGTATCCGA;RSEQ=CTCTGGAGTGTTTGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:24,24:0:2,0:26.8:1:32.8:1:1:0:45.8:96:1:0:0.1 0/1:64:23:8,15:19,22:0.3594:2,2:19.2:1:28.9:1:0.43547:1.6072:47.3:46:0.377:0:1 -10 38743893 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.97128;LSEQ=CTGATATGCTCCACTCCCAC;RSEQ=AGCCCTTGTTACACTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:1,0:63,28:0.0109:2,0:27:0:32:0:1:0:49:2:0.011:0:1 0/1:94:2:1,1:62,28:0.0213:2,2:20.5:1:28:1:0.53344:2.19329:27:4:0.0217:0:1 -10 38743986 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5064;SOR=Inf;LSEQ=TTGCAAGTGGGCCACCTTCA;RSEQ=CTGGAAGGCCAGGTCGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:50,73:0:2,0:23.3:1:31:1:1:0:50.7:122:1:0:0.1 0/1:159:2:1,1:64,93:0.0126:2,2:8.5:1:27.5:1:1:1.45:40.5:4:0.0127:0:1.5 -10 38744072 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23394;SOR=0;LSEQ=GCATCTGGCTGACAGTCCGG;RSEQ=TATCCTGGTTGGGGTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:36,44:0.0244:2,2:20.5:1:31:1:1:1.22:60:4:0.025:0:1 0/0:87:0:0,0:42,44:0:2,0:23.1:1:28.5:1:1:0:60:27.667:1:0:0.2 -10 38744080 . G T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1463;SOR=0.36482;LSEQ=CTGACAGTCCGGTTATCCTG;RSEQ=TTGGGGTGACCCTGGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:9:3,6:34,37:0.1125:2,2:23.9:1:27.8:1:0.49388:1.82432:60:8:0.1039:0:1.1 0/1:91:4:0,4:47,40:0.044:2,0:19.5:1:28.5:1:0.05079:0:60:8:0.0444:0:1 -10 38744113 . T G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21582;SOR=0;LSEQ=TGGTGTGCCCTGCCAGGGCC;RSEQ=GGTGCCGCTTGCTGAAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:43,44:0.0225:2,2:40:1:30.5:1:1:1.02:60:4:0.0227:0:1 0/0:102:0:0,0:58,44:0:2,0:27:1:30.2:1:1:0:57.6:33:1:0:0.4 -10 38744198 . T G 157 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.38034;LSEQ=TGTTGGGGCTGCGTCCATCC;RSEQ=TCTCAGAAGATGAGTCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:0,2:25,29:0.0357:2,0:42.5:1:33:1:0.49675:0:54.5:4:0.0357:0:1 0/1:83:38:17,21:19,26:0.4578:2,2:28.7:1:30.1:1:0.8281:1.11:44.4:76:0.4691:0:1 -10 38744359 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4926;SOR=Inf;LSEQ=AGCAGGGACTCCCCTGAGGG;RSEQ=CCCAGGGCTCCTCCTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:6,14:0:2,0:19.1:1:32.4:1:1:0:39:40:1:0:0.3 0/1:24:2:1,1:7,15:0.0833:2,2:32:0:27:1:1:2.07:42:4:0.0833:0:1.5 -10 38744432 . C T 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04396;SOR=0;LSEQ=CCCCAAAATGTGTGGGGTTG;RSEQ=GGGCCCTGGGCTTTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:0,4:0.6:0,2:15.3:1:30.2:1:0.07619:0:50.5:12:0.6:0:1 0/0:5:0:0,0:2,3:0:2,0:23.6:1:31.8:1:1:0:49:10:1:0:1 -10 38744437 . CC AA 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13122;SOR=8.69127;LSEQ=AAATGTGTGGGGTTGCGGGC;RSEQ=TGGGCTTTCAGGGCAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:4,4:0.1111:2,0:42:0:32.5:0:1:0:60:2:0.1111:0:1 1/0:9:5:2,3:1,3:0.5556:2,2:13.6:1:31.3:1:1:1.85:52.6:10:0.5556:0.1111:1.2 -10 38744589 . G A 50 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2;SOR=Inf;LSEQ=CTGGCAGGTTGCTGGGCCTC;RSEQ=TGTGGCTGCAGGGAGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:31:1:30:1:1:0:35:8:1:0:0 1/0:6:3:0,3:2,1:0.5:2,0:33.7:1:31.7:1:0.4:0:34.7:6:0.5:0:1 -10 39004601 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACTCCTGGGTTCTAGGGA;RSEQ=CCTCTGCCTTAGCCTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:29:1:1:0:44:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 39006098 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAACAGGCAGCGAAGAGGT;RSEQ=GTGAATGATGTCCCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:9,3:0.1429:2,0:44:1:28.5:1:1:0:23:4:0.1538:0:4.5 0/0:2:0:0,0:2,0:0:0,0:32:1:30:1:1:0:47:4:1:0:0.5 -10 39006125 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48;SOR=0;LSEQ=GATGTCCCAGCAGCAGGAGA;RSEQ=AGGGAGTGTCATTATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:8,3:0.1538:2,0:30:1:28.5:1:1:0:23:4:0.1667:0:4.5 0/0:12:0:0,0:11,1:0:2,0:12.4:1:31.5:1:1:0:55.4:24:1:0:0.3 -10 39006198 . C T 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00985;SOR=Inf;LSEQ=GTGAGGAAGATTAGGGGGTC;RSEQ=TGTCTGCTGACTCCCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:31,2:0:2,0:22.5:1:30.9:1:1:0:58.5:32:1:0:0.2 0/1:50:9:9,0:38,3:0.18:2,0:18.2:1:31:1:1:0:59.2:18:0.18:0:1 -10 39006296 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19272;SOR=0;LSEQ=ACTGATAATATATTTATCCT;RSEQ=TTCACTGTGATTTGCCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:143,48:0.0104:2,2:38:1:31:1:0.4443:2.95885:47:4:0.0106:0:1 0/0:246:0:0,0:157,89:0:2,0:26.5:1:29.9:1:1:0:45.3:245:1:0:0 -10 39006437 . G A 208 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=144.80293;LSEQ=GTGTGGGACAGTGCCTGCTA;RSEQ=CATAAAATACATGGGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:1:1,0:123,195:0.0031:2,0:1:0:26:0:0.38871:0:48:2:0.0032:0:1 0/1:440:138:54,84:133,169:0.3136:2,2:25:1:29.3:1:0.35105:1.22363:44.1:276:0.3151:0:1.1 -10 39006564 . C CT 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.61798;SOR=0.35294;LSEQ=GAGGATGGGTTGCAACCTGT;RSEQ=TTTTTTTTTCTTTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:3:0,3:4,40:0.0638:2,0:33.3:1:29.7:1:1:0:55.7:6:0.0652:0:0.3 0/1:43:1:0,1:3,39:0.0233:2,0:27:0:32:0:1:0:40:2:0.0238:0:0 -10 39006616 . G T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06663;SOR=14.31264;LSEQ=TCTGTCACCCTGGCTGGAGT;RSEQ=CAGTGGCACGATCTCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:0,18:0.0526:1,0:8:0:31:0:1:0:53:2:0.0526:0:1 1/0:4:2:0,2:0,2:0.5:0,0:13:1:29.5:1:1:0:57.5:4:0.5:0:1 -10 39007146 . T G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCTGTGCTCCTGCTAGG;RSEQ=GTTGGGGCTGCCATTATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 39011138 . G A 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCATTCTAGGAGTTTGCT;RSEQ=TCCTTCAGACACAGCTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:172:172:127,45:0,0:1:0,2:26.1:1:28.6:1:1:0:53.7:85:1:0:1.2 1/1:222:222:161,61:0,0:1:0,2:24.5:1:28.2:1:1:0:51:43.4:1:0:1.2 -10 39011152 . G A 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10906;SOR=1.57974;LSEQ=TTTGCTGTCCTTCAGACACA;RSEQ=CTACTTATGTTTTTAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:22:17,5:127,58:0.1063:2,2:22.2:1:27.8:1:0.47204:1.55:50.5:10:0.0976:0:1.8 0/1:278:44:31,13:155,78:0.1583:2,2:25:1:30.3:1:0.72698:1.20:48.5:88:0.1583:0:1.9 -10 39011230 . G A 111 Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4149;SOR=0.68497;LSEQ=CTTCTGTCTGAGGAAAATGA;RSEQ=TCCACAGCTCTATCTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:13:13,0:236,238:0.0267:2,1:35.2:1:30.2:1:0.00022:0:22.4:26:0.0269:0:2 0/1:651:12:12,0:321,318:0.0184:2,0:34.8:1:27.5:1:0.00046:0:22.3:24:0.0186:0:2.3 -10 39011323 . G A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.84087;SOR=0.90428;LSEQ=AGGAGCTGATAAGCAAAGAT;RSEQ=ATGAAATTCAAGATTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:14:0,14:7,103:0.1129:2,1:28.1:1:30.5:1:1:0:22.5:28:0.1138:0:1 0/1:126:13:0,13:5,108:0.1032:1,1:33.1:1:31.3:1:1:0:22.6:26:0.1048:0:1.1 -10 39011653 . TTTG T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TTAATTCCAGTCCTGCTTTT;RSEQ=TTGTTGTTGTTGTTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:33:1:30.3:1:1:0:59.5:8:1:0:0.3 1/0:3:2:1,1:0,1:0.6667:0,2:26.5:1:29:1:1:0:60:4:0.6667:0:1.5 -10 39011707 . C A 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TTTTCCCCACTGTTTCCTCC;RSEQ=CCCCGATTTTTTTTTCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:17.3:1:30.7:1:1:0:60:6:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:21:0:30.5:1:1:0:60:4:0.6667:0:1.5 -10 39012264 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53732;SOR=Inf;LSEQ=TGTGGTGAGGACTCAGTTGT;RSEQ=ATTTTCCTTTATTTTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:77,29:0:2,0:25.5:1:30.9:1:1:0:60:25.5:1:0:0.1 0/1:188:2:1,1:124,60:0.0106:2,2:11:0:31:1:0.54955:2.05796:60:4:0.011:0:1.5 -10 39012293 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13425;SOR=0;LSEQ=TTATTTTCAGCCTTCTACTA;RSEQ=TCGAAAGCGGCCTCATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:97,64:0.0123:2,2:7:0:31:1:1:1.51161:60:4:0.0123:0:1.5 0/0:281:0:0,0:160,121:0:2,0:25.3:1:30.9:1:1:0:59.6:55.2:1:0:0.2 -10 39012324 . G T 44 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0477;SOR=0;LSEQ=CCTCATGAAGGGGAAGCCGA;RSEQ=GGTGCCGAGACCACAAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:3:1,2:101,103:0.0145:2,2:20:1:28:1:1:1.95503:60:6:0.0151:0:1 0/0:362:0:0,0:180,182:0:2,0:26.3:1:30.6:1:1:0:59.7:119.667:1:0:0.2 -10 39012451 . AT A 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTTTATAGTTTGTATTTTA;RSEQ=TATGGGAATAATTGCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:19:3,16:2,20:0.4634:2,2:27.9:1:31.2:1:0.6486:1.85:48.3:38:0.475:0.0488:0.6 0/0:52:0:0,0:10,42:0:2,0:26.7:1:30:1:1:0:55:51:1:0:0.2 -10 39012502 . A G 131 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00983;SOR=0;LSEQ=TGATGTACAATTAAAAACCT;RSEQ=ATGGAACCTGGGCTTTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:3,16:0,0:1:0,2:24.9:1:31:1:1:0:38.4:38:1:0:1.1 1/0:22:15:2,13:2,5:0.6818:2,2:25.5:1:31.4:1:0.56459:2.4775:39:30:0.6818:0:1 -10 39124008 . G A 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCATCGAATGGAATGGAAT;RSEQ=TATTGGAATGGATTGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:30:1:1:0:27:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 39124451 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCGAATGGAATGGT;RSEQ=TGGTTTGGAATGGACTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:29.5:1:1:0:51:4:1:0:7 -10 39124454 . GTT TCA 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATGGAATGGTCTG;RSEQ=TGGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:0:29.2:1:1:0:51:4:1:0:5 -10 39124469 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGGTTTGGAATGGACTC;RSEQ=AATGGAATGGACTGGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:0:30.5:1:1:0:51:4:1:0:5 -10 39124482 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCGAATGGAATGGAC;RSEQ=GGAACAAAATGGAATCGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:32:0:1:0:51:4:1:0:5 -10 39124484 . G T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCGAATGGAATGGACTG;RSEQ=AACAAAATGGAATCGAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:29:0:1:0:51:4:1:0:5 -10 39124498 . C GGAATAGGGATTG 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=GGACTGGAACAAAATGGAAT;RSEQ=GAACGGATTGGAGTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:3:1,2:0,0:1:0,2:10.7:1:30.4:1:1:0:51:6:1:1:7 -10 39125527 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=GGACTCAAATAGAATGGACT;RSEQ=GAAAGGAATGGTCTCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:4,0:0.3333:0,0:33.5:1:31.5:1:0.06667:0:41.5:4:0.3333:0:4.5 0/0:8:0:0,0:5,2:0:2,0:22.1:1:27.4:1:1:0:38.1:6:0.8571:0:6.4 -10 39125533 . G A 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53846;SOR=0.31377;LSEQ=AAATAGAATGGACTCGAAAG;RSEQ=AATGGTCTCAAATGGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:37:1:32.5:1:1:2.44949:49:4:0.3333:0:7 0/1:8:1:1,0:5,2:0.125:2,0:6:0:29:0:1:0:40:2:0.125:0:6 -10 39125542 . CA TG 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GGACTCGAAAGGAATGGTCT;RSEQ=AATGGAATTTATTCTAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:41:1:32.3:1:1:2.44949:49:4:0.3333:0:6 0/0:6:0:0,0:4,2:0:2,0:31.7:1:29.8:1:1:0:34.7:12:1:0:5.7 -10 39125543 . A G 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06061;SOR=Inf;LSEQ=GACTCGAAAGGAATGGTCTC;RSEQ=AATGGAATTTATTCTAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:1,1:0.3333:2,0:37:1:30:1:1:0:44.5:4:0.5:0:6 1/1:6:6:4,2:0,0:1:0,2:32:1:30.2:1:1:0:34.7:12:1:0:5.7 -10 39125557 . CT TG 68 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60839;SOR=2.34872;LSEQ=GGTCTCAAATGGAATTTATT;RSEQ=AATAGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:2,2:0.3333:2,0:37:1:30.5:1:0.46667:0:44.5:4:0.3333:0:5 1/0:9:5:3,2:3,1:0.5556:2,2:27.8:1:29.5:1:1:1.8525:41.4:10:0.5556:0:5.6 -10 39125558 . T G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60664;SOR=0.45308;LSEQ=GTCTCAAATGGAATTTATTC;RSEQ=AATAGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:0,1:0.5:0,0:15:1:30.7:1:0.25:0:35.7:6:0.75:0:7 0/1:10:3:3,0:0,1:0.3:0,0:8.3:1:31.3:1:0.25:0:41.3:6:0.6:0:7.7 -10 39125563 . G T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62436;SOR=0.47215;LSEQ=AAATGGAATTTATTCTAATA;RSEQ=AATGGAATCGAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:3,2:0.375:2,0:16.7:1:32.3:1:0.46429:0:35.7:6:0.375:0:7 0/1:14:3:3,0:8,3:0.2143:2,0:7.3:1:30.7:1:1:0:35.7:6:0.2143:0:7.7 -10 39125564 . A C 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.9469;LSEQ=AATGGAATTTATTCTAATAG;RSEQ=ATGGAATCGAATGGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:5,3:0.1111:2,0:5:0:34:0:1:0:24:2:0.1111:0:4 0/1:15:3:3,0:8,4:0.2:2,0:5:0:34:0:0.51648:0:42:6:0.2:0:5 -10 39125568 . G T 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67074;SOR=0.58158;LSEQ=GAATTTATTCTAATAGAATG;RSEQ=AATCGAATGGAATGCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:3,2:0.4444:2,2:15:1:29.3:1:1:1.85:35.3:8:0.4444:0:7 0/1:16:5:4,1:8,3:0.3125:2,2:8.8:1:28.4:1:1:1.46:36.8:10:0.3125:0:7.6 -10 39125573 . G C 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37037;SOR=3.53876;LSEQ=TATTCTAATAGAATGGAATC;RSEQ=AATGGAATGCAATAGTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:6,5:0.0833:2,0:14:0:33:0:1:0:24:2:0.0833:0:4 0/1:20:5:5,0:11,3:0.25:2,0:10.4:1:31.8:1:0.53044:0:39.4:10:0.25:0:6.2 -10 39125578 . G A 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91903;LSEQ=TAATAGAATGGAATCGAATG;RSEQ=AATGCAATAGTATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:5,6:0.2143:2,2:24:1:29.7:1:1:2.26:44:6:0.2143:0:6 0/1:20:4:2,2:13,3:0.2:2,2:29.3:1:29.3:1:0.24871:3.95518:41.8:8:0.2:0:6.3 -10 39125582 . G A 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGAATGGAATCGAATGGAAT;RSEQ=CAATAGTATGGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:5,7:0.2:2,2:22.7:1:28.3:1:0.56923:2.61:44:6:0.2:0:6 0/1:20:4:2,2:13,3:0.2:2,2:27.3:1:28:1:0.24871:3.95518:41.8:8:0.2:0:6.3 -10 39125586 . TA CT 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61309;SOR=2.60412;LSEQ=TGGAATCGAATGGAATGCAA;RSEQ=GTATGGAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:1,0:7,9:0.0588:2,0:28:0:33.5:0:0.47059:0:24:2:0.0625:0:3 0/1:21:3:3,0:10,7:0.1429:2,0:28:0:32:1:0.52105:0:42:6:0.1429:0:4 -10 39125595 . A G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.6624;SOR=0.59884;LSEQ=ATGGAATGCAATAGTATGGA;RSEQ=TGGAATCGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:5,8:0.1875:2,2:24:1:34:0:0.55:2.97:44:6:0.1875:0:7.3 0/1:25:3:1,2:15,7:0.12:2,2:19:1:31:1:0.53043:4.02111:48.7:6:0.12:0:6.3 -10 39125599 . A C 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6858;SOR=0.70192;LSEQ=AATGCAATAGTATGGAATGG;RSEQ=ATCGAATGGAATGGAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:4,8:0.2:2,2:25.3:1:34:0:0.52527:3.62:44:6:0.2:0:7.3 0/1:27:4:1,3:15,8:0.1481:2,2:23.5:1:31.5:1:0.27293:5.26214:46.5:8:0.1481:0:6.5 -10 39125602 . C A 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.05446;LSEQ=GCAATAGTATGGAATGGAAT;RSEQ=GAATGGAATGGAATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:1,0:5,11:0.0588:2,0:27:0:30:0:0.35294:0:24:2:0.0588:0:3 0/1:26:3:3,0:12,10:0.1154:2,0:37.7:1:27.7:1:0.25:0:44.7:6:0.1154:0:5.7 -10 39125614 . A G 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28389;SOR=Inf;LSEQ=AATGGAATCGAATGGAATGG;RSEQ=ATCAAATGGAATGGAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:28.7:1:29.1:1:1:0:38.9:38:1:0:7.2 0/1:31:4:3,1:14,13:0.129:2,2:35.8:1:30.3:1:0.60667:2.70:39.8:8:0.129:0:8 -10 39125618 . A G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04735;SOR=0.18323;LSEQ=GAATCGAATGGAATGGAATC;RSEQ=AATGGAATGGAACGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:4,12:1,1:0.8889:2,2:33.8:1:30.4:1:0.4902:2.79285:39.4:32:0.8889:0:7.4 1/0:29:17:9,8:7,5:0.5862:2,2:33.8:1:29.8:1:1:1.23509:41.9:34:0.5862:0:7.5 -10 39125621 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36547;SOR=0.3931;LSEQ=TCGAATGGAATGGAATCAAA;RSEQ=GGAATGGAACGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:4,11:0.1667:2,2:31:1:31:1:1:1.35:42:6:0.1667:0:8 0/1:28:2:0,2:14,10:0.0714:2,0:29:1:30:1:0.20308:0:49.5:4:0.0714:0:7 -10 39125625 . A T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54076;SOR=0.58386;LSEQ=ATGGAATGGAATCAAATGGA;RSEQ=TGGAACGGAATGGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:3,9:2,4:0.6667:2,2:36.8:1:30.3:1:1:1.46553:38.7:24:0.6667:0:7.6 1/0:28:15:9,6:5,7:0.5357:2,2:33.7:1:29.3:1:0.44948:2.04:40.9:30:0.5357:0:7.6 -10 39125630 . A C 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28206;SOR=0.18687;LSEQ=ATGGAATCAAATGGAATGGA;RSEQ=CGGAATGGAATGGACTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:3,10:0.1765:2,2:31.7:1:32:1:1:1.61:42:6:0.1765:0:8 0/1:27:1:0,1:13,11:0.037:2,0:10:0:33:0:0.48:0:40:2:0.037:0:7 -10 39125632 . G A 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2204;SOR=4.44094;LSEQ=GGAATCAAATGGAATGGAAC;RSEQ=GAATGGAATGGACTGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:4,12:0.0588:2,0:29:0:28:0:1:0:40:2:0.0588:0:8 0/1:27:6:3,3:11,10:0.2222:2,2:26.2:1:31:1:1:1.09612:52.3:12:0.2222:0:4.7 -10 39125633 . G A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5411;SOR=0.6502;LSEQ=GAATCAAATGGAATGGAACG;RSEQ=AATGGAATGGACTGGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:3,9:1,4:0.7059:2,2:33.5:1:30.7:1:1:1.31:38.7:24:0.7059:0:7.6 1/0:28:17:10,7:4,7:0.6071:2,2:30.4:1:29.3:1:0.44007:2.42:40.4:34:0.6071:0:7.5 -10 39125637 . G C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5411;SOR=0.6502;LSEQ=CAAATGGAATGGAACGGAAT;RSEQ=GAATGGACTGGAATAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:3,9:1,4:0.7059:2,2:30.2:1:30.6:1:1:1.31:38.7:24:0.7059:0:7.6 1/0:28:17:10,7:3,6:0.6071:2,2:27.8:1:30.4:1:0.41098:2.74:40.4:34:0.6296:0:7.5 -10 39125638 . G C 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.24395;LSEQ=AAATGGAATGGAACGGAATG;RSEQ=AATGGACTGGAATAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:4,11:0.1176:2,0:41.5:1:31:1:1:0:40:4:0.125:0:6 0/1:28:4:2,2:12,12:0.1429:2,2:18.8:1:32.3:1:1:1:48.5:8:0.1429:0:5 -10 39125640 . A T 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.28206;SOR=0.18687;LSEQ=ATGGAATGGAACGGAATGGA;RSEQ=TGGACTGGAATAGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:3,10:0.1765:2,2:28.3:1:31.3:1:1:1.61:42:6:0.1765:0:8 0/1:27:1:0,1:12,10:0.037:2,0:31:0:29:0:0.47826:0:59:2:0.037:0:7 -10 39125645 . CT AC 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1081;LSEQ=ATGGAACGGAATGGAATGGA;RSEQ=GGAATAGAATGGACTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:1,8:1,4:0.6:2,2:26.8:1:31.6:1:1:1.89743:40.2:18:0.6:0:6.7 1/0:24:15:8,7:2,4:0.625:2,2:24.3:1:30:1:0.63512:2.20:40.5:30:0.625:0:6.5 -10 39125651 . T G 57 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06853;SOR=0.13229;LSEQ=CGGAATGGAATGGACTGGAA;RSEQ=AGAATGGACTCGAATGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:2,9:0.2667:2,0:25.3:1:28.8:1:1:0:38.5:3:0.2143:0:7 0/1:23:1:0,1:10,12:0.0435:2,0:39:0:33:0:1:0:47:2:0.0435:0:6 -10 39125653 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35662;SOR=0.37765;LSEQ=GAATGGAATGGACTGGAATA;RSEQ=AATGGACTCGAATGTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:1,10:0.2143:2,2:28.3:1:30.7:1:0.3956:4.28:41:6:0.2143:0:8 0/1:22:2:0,2:9,11:0.0909:2,0:27.5:1:32:0:0.49351:0:49.5:4:0.0909:0:7.5 -10 39125656 . T C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67217;SOR=0.65561;LSEQ=TGGAATGGACTGGAATAGAA;RSEQ=GGACTCGAATGTAATGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:1,9:0.2143:2,2:25.3:1:31.7:1:0.42308:3.87:41:6:0.25:0:8 0/1:20:3:0,3:7,10:0.15:2,0:27:1:30:1:0.52105:0:47:6:0.15:0:6.3 -10 39125657 . G A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76837;LSEQ=GGAATGGACTGGAATAGAAT;RSEQ=GACTCGAATGTAATGGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:1,8:1,2:0.6923:2,2:18.6:1:32.2:1:0.45455:3.4638:40.3:18:0.75:0:6.8 1/0:19:12:5,7:1,6:0.6316:2,2:17.3:1:30.3:1:0.33308:3.99:42.4:24:0.6316:0:6.6 -10 39125659 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50968;SOR=Inf;LSEQ=AATGGACTGGAATAGAATGG;RSEQ=CTCGAATGTAATGGATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:2,10:0:2,0:20.7:1:29.8:1:1:0:41.6:11:1:0:6.8 0/1:19:2:1,1:5,12:0.1053:2,2:8:0:33:0:1:2.28:60:4:0.1053:0:4 -10 39125679 . A T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.09375;LSEQ=ACTCGAATGTAATGGATTGC;RSEQ=ATGTAATTGAAATGAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:11:0:30:0:1:0:33:2:0.25:0:7 0/1:7:3:0,3:0,4:0.4286:0,0:11:0:28.7:1:1:0:44.7:6:0.4286:0:6.7 -10 39128084 . GG TC 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAATAGAATGGAATGGA;RSEQ=GTAATGGAAAGATATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:0.6:2,2:33.3:1:30.5:1:1:1.73:28.7:6:0.6:0:6.3 -10 39128085 . G C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAATAGAATGGAATGGAG;RSEQ=GTAATGGAAAGATATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:0,0:0.4:0,2:32.5:1:29:1:1:0:39:4:1:0:6.5 -10 39128088 . A T 67 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAGAATGGAATGGAGGGT;RSEQ=ATGGAAAGATATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:35:1:29:1:1:0:32.8:10:1:0:6.4 -10 39128102 . A G 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGTAATGGAAAGATATC;RSEQ=AATGGAATAGAAAGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:0,0:0.6:0,2:39:1:28.7:1:1:0:28.7:6:0.6:0:6.3 -10 39128111 . AGAAAGGAATG GGAATT 68 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAGATATCAAATGGAAT;RSEQ=GACTCGAAAGGAATGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:34.8:1:29.4:1:1:0:32.8:10:1:0:6 -10 39128130 . A T 65 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAAAGGAATGGACTCGAA;RSEQ=GGAATGGACTGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:23:1:28.4:1:1:0:32.8:10:1:0:7 -10 39128150 . T C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAATGGACTGGAATGGAA;RSEQ=GGACTCAAATGGAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:18.5:1:32:0:1:0:33.5:4:1:0:8 -10 39128157 . A G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGGAATGGAATGGACTC;RSEQ=AATGGAATGGAAACGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:11.5:1:32.5:1:1:0:33.5:4:1:0:8 -10 39128593 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7.5:1:30.5:1:1:0:41:4:1:0:3.5 -10 39128625 . A T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAACCAAATG;RSEQ=AATGGACTCGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:31:1:1:0:41:4:1:0:3.5 -10 39128634 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAACCAAATGAAATGGACT;RSEQ=GAATGGAATGGACTCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:32:0:1:0:41:4:1:0:3.5 -10 39128796 . G A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGGACTCGAATGTAATGG;RSEQ=TTGCAATGTACTTGATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15:1:29.7:1:1:0:35:6:1:0:6.3 1/1:2:2:2,0:0,0:1:0,0:14:1:29:0:1:0:45.5:4:1:0:8 -10 39128801 . A T 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGAATGTAATGGGTTGC;RSEQ=ATGTACTTGATTCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:20:1:32:1:1:0:35:6:1:0:6.3 1/1:2:2:2,0:0,0:1:0,0:19:1:33:0:1:0:45.5:4:1:0:8 -10 39128807 . C A 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTAATGGGTTGCAATGTA;RSEQ=TTGATTCGAATGCAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:25.7:1:30:1:1:0:35:6:1:0:6.3 1/1:4:4:3,1:0,0:1:0,2:13:1:31.8:1:1:0:44.3:8:1:0:7.3 -10 39128820 . C G 81 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CAATGTACTTGATTCGAATG;RSEQ=AATGGAATCGAATGGATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:20.3:1:31.5:1:1:0:40.3:12:1:0:7 1/1:5:4:2,2:1,0:0.8:0,2:18.8:1:31:1:1:0:37:8:0.8:0:7.3 -10 39128837 . T A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=ATGCAATGGAATCGAATGGA;RSEQ=TGTAATCAAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:0,0:0.8889:0,2:25.6:1:30:1:1:0:49.6:16:1:0:7.8 1/1:15:15:9,6:0,0:1:0,2:21.1:1:30.1:1:1:0:37.2:30:1:0:7.1 -10 39128840 . T C 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62785;SOR=0.41915;LSEQ=CAATGGAATCGAATGGATTG;RSEQ=AATCAAATGGAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:0,0:0.8889:0,2:27.1:1:31.8:1:1:0:49.6:16:1:0:7.8 1/0:17:13:8,5:0,0:0.7647:0,2:17.8:1:32.1:1:1:0:38.8:26:0.7647:0:7.2 -10 39128845 . A C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04516;SOR=Inf;LSEQ=GAATCGAATGGATTGTAATC;RSEQ=AATGGAATGGAATGCAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:4,4:1,1:0.7273:2,2:29.6:1:28.6:1:1:1:49.6:7:0.7778:0:7.8 1/1:18:18:11,7:0,0:1:0,2:19.4:1:30.4:1:1:0:39.9:17:1:0:6.9 -10 39128873 . T G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53131;SOR=Inf;LSEQ=TGGAATGCAATGCAATGGAA;RSEQ=GGAATAGAATGGAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,8:0:2,0:30.3:1:30.7:1:1:0:52:30:1:0:6.7 0/1:29:2:1,1:15,12:0.069:2,2:29.5:1:31.5:1:1:1.24034:50:4:0.069:0:6.5 -10 39128879 . A C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATGCAATGGAATGGAAT;RSEQ=GAATGGAATGCAATAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:6,9:0,0:1:0,2:33.3:1:30.9:1:1:0:51.1:30:1:0:6.5 1/1:28:28:15,13:0,0:1:0,2:30.8:1:30.5:1:1:0:42.7:56:1:0:6.9 -10 39128883 . T C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7432;SOR=1.34118;LSEQ=TGCAATGGAATGGAATAGAA;RSEQ=GGAATGCAATAGAAGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:2,2:4,8:0.25:2,2:36.3:1:31.5:1:0.6044:1.91:59:8:0.25:0:8 0/1:29:9:6,3:9,11:0.3103:2,2:31.7:1:31.1:1:0.42699:2.37:40.9:18:0.3103:0:7.8 -10 39128892 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14936;SOR=Inf;LSEQ=ATGGAATAGAATGGAATGCA;RSEQ=TAGAAGGGAATGGAGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:4,9:1,1:0.8667:2,2:30.2:1:32.8:1:1:2.12136:49.7:26:0.8667:0:7 1/1:23:23:12,11:0,0:1:0,2:33.5:1:31.3:1:1:0:43.9:46:1:0:7.1 -10 39128894 . A G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATAGAATGGAATGCAAT;RSEQ=GAAGGGAATGGAGGGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:1:0,2:29.5:1:32.1:1:1:0:51.1:30:1:0:6.5 1/1:23:23:12,11:0,0:1:0,2:32:1:30.2:1:1:0:43.9:46:1:0:7.1 -10 39128908 . G T 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.73045;SOR=0.64706;LSEQ=TGCAATAGAAGGGAATGGAG;RSEQ=GGAATCAAGTGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:3,7:0,0:0.7143:0,2:17.2:1:29.3:1:1:0:50.9:20:0.7143:0:5.8 1/0:26:16:7,9:0,0:0.6154:0,2:20.3:1:27.9:1:1:0:43.9:15:0.6:0:6.5 -10 39128920 . G C 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.45458;LSEQ=GAATGGAGGGGAATCAAGTG;RSEQ=AATGGAATAGAATTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:4,6:0.1667:2,0:20:1:33.5:1:0.51515:0:50:4:0.1667:0:7.5 0/1:22:5:2,3:8,9:0.2273:2,2:11.2:1:28.6:1:1:1.31614:44.4:4:0.1905:0:7.2 -10 39128925 . G T 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.56245;LSEQ=GAGGGGAATCAAGTGGAATG;RSEQ=AATAGAATTGAATGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:18:0:31:1:1:2.24:58:4:0.2222:0:8 0/1:16:5:3,2:4,7:0.3125:2,2:16.8:1:26:1:0.59615:2.46:43:10:0.3125:0:7.2 -10 39128929 . A G 113 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCAAGTGGAATGGAAT;RSEQ=GAATTGAATGGAATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:14:1:32.5:1:1:0:45.8:8:1:0:7.3 1/1:15:14:6,8:0,0:0.9333:0,2:13.6:1:29.9:1:1:0:44.8:28:1:0:6.7 -10 39128934 . T G 99 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGTGGAATGGAATAGAAT;RSEQ=GAATGGAATTGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:13:1:33:1:1:0:52:6:1:0:7.7 1/1:11:10:3,7:0,0:0.9091:0,2:12.3:1:30.1:1:1:0:44.1:20:1:0:6.8 -10 39128943 . T TTGAATTGAAA 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATAGAATTGAATGGAA;RSEQ=TGAATGGAATGGACTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:12:0:32:0:1:0:40:2:1:0:7 0/1:6:2:1,1:0,4:0.3333:0,2:15.5:1:28.7:1:0.33333:0:35:4:0.3333:0.3333:6 -10 39128944 . T G 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATAGAATTGAATGGAAT;RSEQ=GAATGGAATGGACTGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:11:0:32:0:1:0:40:2:1:0:7 0/1:6:2:1,1:0,3:0.3333:0,2:5:0:29.5:1:0.4:0:35:4:0.3333:0:6 -10 39128948 . T A 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAATTGAATGGAATTGAA;RSEQ=GGAATGGACTGGAATGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:7:0:33:0:1:0:40:2:1:0:7 1/0:6:3:0,3:1,2:0.5:2,0:12.7:1:32.7:1:1:0:40:6:0.5:0:6.3 -10 39128957 . C A 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATTGAATGGAATGGA;RSEQ=TGGAATGGATTGTACTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:0,3:0,1:0.6:0,0:6.3:1:31.7:1:1:0:38.7:6:0.75:0.2:5 -10 39128964 . GGATTGTACTCCAATGGAATGGACTGGAACAAAACGGAATATAACGGATTGGAATCGAACTGAAAGGAATGGAATGGAGTGGATTG A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGAATGGAATGGACTGGAAT;RSEQ=GAATGGAATGGAGTGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:0,0:0.6667:0,0:58:1:30.3:1:1:0:40:4:1:0.6667:5 -10 42358760 . C T 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACTCGGGGTAATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:7:1:31:0:1:1.7321:38:4:0.5:0:4 -10 42358773 . A T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATCCCATTCCATTCC;RSEQ=TTCCATTCCATTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:10:0:32:0:1:0:23:2:1:0:1 0/1:11:2:1,1:4,5:0.1818:2,2:12:1:28.5:1:1:1.22:36:4:0.2:0:6 -10 42358777 . C T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATCCCATTCCATTCCATTC;RSEQ=ATTCCATTCCGTTCCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:14:0:33:0:1:0:23:2:1:0:1 0/1:11:2:1,1:3,4:0.1818:2,2:13:0:31.5:1:1:1.29:50:4:0.1818:0:1.5 -10 42358793 . A T 56 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCGTTCC;RSEQ=TTTGATTCCTTTCCAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:30:0:32:0:1:0:23:2:1:0:1 0/1:11:4:2,2:3,4:0.3636:2,2:39.3:1:28.3:1:1:1.30:50:8:0.3636:0:2.8 -10 42358799 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCGTTCCATTTGA;RSEQ=TCCTTTCCAGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:33:0:1:0:23:2:1:0:1 0/1:11:2:1,1:4,5:0.1818:2,2:29.5:1:31:1:1:1.22:60:4:0.1818:0:4 -10 42358810 . T A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTTGATTCCTTTCCAG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:32:0:1:0:23:2:1:0:1 0/1:11:2:1,1:4,5:0.1818:2,2:41:1:28.5:1:1:1.22:36:4:0.1818:0:6 -10 42358831 . GT TC 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCCAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:3:0:29:0:1:0:23:2:1:0:1 0/1:10:2:1,1:3,2:0.2:2,2:32:0:32:1:1:1.41418:60:4:0.2:0:3 -10 42358832 . T C 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GATTCCATTCCATTCCATTG;RSEQ=ATTCCATTCCATTCCAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:2:0:30:0:1:0:23:2:1:0:1 0/1:10:4:2,2:2,1:0.4:2,2:23:1:32:1:1:1.81007:43:8:0.5:0:4.8 -10 42358835 . T G 34 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTGTAT;RSEQ=CCATTCCATTCCAATCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:4,3:0.2:2,2:29:0:34:0:1:1.29098:60:4:0.2:0:3 -10 42358837 . C T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTGTATTC;RSEQ=ATTCCATTCCAATCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:4,3:0.2:2,2:22.5:1:30.5:1:1:1.29098:36:4:0.2:0:6 -10 42358846 . CC AA 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTGTATTCCATTCCATT;RSEQ=AATCGGGTTGATTTCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:2:1,1:2,3:0.25:2,2:30:0:28.5:1:1:1.41:42:4:0.25:0:6 -10 42358854 . G T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCAATCGG;RSEQ=TTGATTTCATTGCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:2,3:0.2857:2,2:37:0:29.5:1:1:1.41:42:4:0.2857:0:6 -10 42358859 . T G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCAATCGGGTTGA;RSEQ=TTCATTGCACTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:1,2:0.3333:2,2:39.5:1:29.5:1:1:1.73:42:4:0.3333:0:6 -10 42358861 . T C 49 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCAATCGGGTTGATT;RSEQ=CATTGCACTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:2,1:1,2:0.5:2,2:39.3:1:31.3:1:1:3.11:34.7:6:0.5:0:6 -10 42358866 . G T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAATCGGGTTGATTTCATT;RSEQ=CACTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,0:0.5:0,2:32.5:1:28.5:1:1:0:42:4:0.5:0:6 -10 42358917 . C T 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCAATCCATTCCATTC;RSEQ=ATTCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:17:0:28:1:1:1:24:4:0.5:0:2 -10 42358925 . T G 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTGCATTCCATTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:9:0:28.5:1:1:1:24:4:0.5:0:2 -10 42359119 . TTCTAATCTTGTTTAT G 30 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=13.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCAATCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:4.1:1:31.1:1:1:0:25.5:4:1:1:4 1/1:2:2:2,0:0,0:1:0,0:13.5:1:30.7:1:1:0:39:4:1:1:4 -10 42359147 . C G 57 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.51471;SOR=0.22265;LSEQ=TTGTTTATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:13:0:29:1:1:0:31:4:0.6667:0:4 0/1:14:4:2,2:6,3:0.2857:2,2:9.8:1:28.8:1:1:1.8918:39:8:0.2857:0:4 -10 42359157 . CA GGGATG 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:18.3:1:30.7:1:1:0:35:6:1:0:4.7 0/1:17:4:2,2:7,4:0.2353:2,2:20:1:30.4:1:1:1.68385:43.8:8:0.2353:0.1176:5.5 -10 42359162 . CA AT 57 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.000;MSILEN=5;SSF=0.58533;SOR=0.47979;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:29:0:29.5:1:1:1.7321:31:4:0.4:0:3 0/1:17:4:2,2:7,4:0.2353:2,2:25.8:1:28.8:1:1:1.68385:39:8:0.2353:0:3 -10 42359167 . C A 58 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.6322;SOR=0.62932;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:33:0:30:1:1:2.44949:31:4:0.3333:0:3 0/1:17:4:2,2:7,4:0.2353:2,2:29.8:1:29:1:1:1.68385:39:8:0.2353:0:3 -10 42359179 . T C 50 v4;MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.60804;SOR=0.55095;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTACATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:26:1:33.5:1:1:1.41418:51.5:4:0.2857:0:7 0/1:17:3:3,0:7,7:0.1765:2,0:41:1:31.7:1:0.22794:0:36:6:0.1765:0:6.3 -10 42359183 . A T 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTACATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:21.3:1:30.4:1:1:0:37:14:1:0:5.7 0/1:17:2:1,1:9,5:0.1176:2,2:35.5:1:30:1:1:1.73197:45.5:4:0.1176:0:2 -10 42359184 . T C 73 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.64663;SOR=0.56999;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTACATTCCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:2,2:0.4286:2,2:18.7:1:32.3:1:1:1.81:31.3:6:0.4286:0:6.7 0/1:17:5:3,2:7,5:0.2941:2,2:38.4:1:31.6:1:1:1.07:39:10:0.2941:0:5.8 -10 42359188 . A G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTACATTCCACTCGGGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:23.4:1:28.1:1:1:0:37:6:1:0:5.7 0/1:17:2:1,1:9,6:0.1176:2,2:38:0:30.5:1:1:1.46382:34:4:0.1176:0:6.5 -10 42359190 . TA GC 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62139;SOR=0.59176;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CATTCCACTCGGGTTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:38:1:32.8:1:1:1.41418:51.5:4:0.2857:0:6 0/1:16:3:3,0:6,7:0.1875:2,0:40.7:1:30.7:1:0.2125:0:36:6:0.1875:0:5.3 -10 42359191 . A C 79 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80789;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGGTTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:1,1:0.4286:2,2:25.7:1:32:1:1:1.73:31.3:6:0.6:0:6.7 0/1:16:6:3,3:2,3:0.375:2,2:34.8:1:30.8:1:1:1.45:40.5:12:0.4615:0:4.8 -10 42359196 . C G 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32783;SOR=0.34925;LSEQ=CCATTCCATTCCATTACATT;RSEQ=CACTCGGGTTTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:2,2:0.4286:2,2:29.3:1:32.7:1:1:1.81:31.3:6:0.4286:0:6.7 0/1:20:4:2,2:8,6:0.2:2,2:31.5:1:32.8:1:1:1.31198:43.8:8:0.2:0:5 -10 42359216 . C G 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCACTCGGGTTTATTCCATT;RSEQ=CATTCCATTCCACTCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:35.2:1:30.2:1:1:0:39.4:10:1:0:6.4 0/1:20:2:1,1:9,8:0.1:2,2:13:0:30.5:1:1:1.11803:60:4:0.1:0:4 -10 42359217 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CACTCGGGTTTATTCCATTC;RSEQ=ATTCCATTCCACTCTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:34.6:1:29.8:1:1:0:39.4:10:1:0:6.4 0/1:19:2:1,1:9,8:0.1053:2,2:9:0:32:0:1:1.11803:34:4:0.1053:0:6.5 -10 42359218 . A T 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.70337;LSEQ=ACTCGGGTTTATTCCATTCC;RSEQ=TTCCATTCCACTCTGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:34.5:1:30:1:1:1.7321:51.5:4:0.4:0:6 0/1:19:6:4,2:6,7:0.3158:2,2:21.3:1:28.3:1:0.62848:2.23:30.5:12:0.3158:0:5.7 -10 42359229 . C T 83 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.52381;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCTGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:25.4:1:29:1:1:0:39.4:10:1:0:6.4 1/1:10:8:4,4:1,1:0.8:2,2:27.4:1:27.9:1:1:1:34.8:16:0.8:0:5.8 -10 42359232 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52048;SOR=0.28074;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GGTTGATTCCATTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:36.5:1:29.5:1:1:1:37:4:0.5:0:8 0/1:10:2:1,1:0,1:0.2:0,2:29:0:29.5:1:1:0:60:4:0.2222:0:4 -10 42359235 . TT AA 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=TCCATTCCATTCCACTCTGG;RSEQ=GATTCCATTCCATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:29.3:1:1:1:37:4:0.5:0:7 0/0:9:0:0,0:3,4:0:2,0:28.6:1:28:1:1:0:29.1:14:0.7778:0:5.7 -10 42359239 . T A 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.22862;LSEQ=TTCCATTCCACTCTGGTTGA;RSEQ=TCCATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:29.5:1:1:1:51.5:4:0.5:0:6 1/0:9:5:2,3:2,2:0.5556:2,2:24.8:1:29:1:1:1.43328:27.6:10:0.5556:0:6.4 -10 42359251 . G C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86755;LSEQ=CTGGTTGATTCCATTCCATT;RSEQ=CATTCCATTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:11:0:32:0:1:0:60:2:0.3333:0:7 0/1:10:3:1,2:3,4:0.3:2,2:16.7:1:32.3:1:1:1.44135:25:6:0.3:0:6 -10 42359261 . G C 51 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=CCATTCCATTGCATTCCATT;RSEQ=CATTCCATTCCTTTACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:5.3:1:30:1:1:0:44.7:6:1:0:7 0/1:10:3:1,2:3,3:0.3:2,2:6.7:1:32.7:1:1:1.8525:25:6:0.3:0:6 -10 42359267 . C G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTGCATTCCATTGCATTC;RSEQ=ATTCCTTTACATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:6:0:34:0:1:0:37:2:1:0:7 0/1:8:2:1,1:1,4:0.25:2,2:24:0:32.5:1:1:3.16:22:4:0.25:0:6 -10 42359273 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTGCATTCCATTCC;RSEQ=TTACATTCCACTCGGGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:30:0:32:0:1:0:22:4:1:0:6 -10 42359276 . AC CG 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTGCATTCCATTCCTTT;RSEQ=ATTCCACTCGGGTTTATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:34:0:32:1:1:0:22:4:1:0:5 -10 42359281 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTCCATTCCTTTACATT;RSEQ=CACTCGGGTTTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:38:0:33.5:1:1:0:22:4:1:0:5 -10 42359296 . C CCATTCCATTG 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCCACTCGGGTTTATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:38:1:31:1:1:1.73:22:4:0.4:0.2:5.5 -10 42359298 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCACTCGGGTTTATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:6:0:32:1:1:1.73:21:4:0.4:0:6 -10 42359310 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTTATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:18:0:33:1:1:2.45:21:4:0.3333:0:6 -10 42359331 . C G 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCAAT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:16.5:1:33.5:1:1:2.45:22:4:0.3333:0:5.5 -10 42359343 . AT TG 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=TCCATTCCATTCATTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:31.5:1:30:1:1:1.73:21:4:0.4:0:5 -10 42359373 . G A 59 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCATTTCATTCCTTTCCA;RSEQ=TTGATTGCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:25.5:1:29.8:1:1:0:27.5:8:1:0:5.3 -10 42359380 . G C 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCCTTTCCAGTTGATT;RSEQ=CATTCCATTCCATTGTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:18.5:1:30.3:1:1:0:27.5:8:1:0:5.3 -10 42359389 . T C 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGTTGATTGCATTCCAT;RSEQ=CCATTGTATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:15.5:1:27:1:1:0:22:4:0.6667:0:5.5 -10 42359562 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTTC;RSEQ=TTCCATTCCATTCTATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:20.5:1:31.5:1:1:1.7321:29:4:0.4:0:1.5 -10 42359571 . C A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTTCATTCCATTC;RSEQ=ATTCTATTCTATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:35.5:1:29:1:1:1.7321:25:4:0.4:0:5 -10 42359576 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTTCATTCCATTCCATTC;RSEQ=ATTCTATTCCACTCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:1,1:0.2857:2,2:35.5:1:30.5:1:1:1:25:4:0.3333:0:5 -10 42359581 . T C 59 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCTATTC;RSEQ=ATTCCACTCGGGTTGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:0,0:0.6667:0,2:30.5:1:29.8:1:1:0:30.8:8:1:0:4.8 -10 42359604 . T C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACTCGGGTTGACTCCAT;RSEQ=CCATACCATTGCATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,0:0.4:0,2:24:1:32.5:1:1:0:25:4:0.6667:0:5 -10 42359641 . T A 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTGCATTCCATTCTTTCC;RSEQ=TTCCATTCCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,1:0.75:0,2:7.3:1:30:1:1:0:40:6:0.75:0:4.7 -10 42359689 . C T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCCACTCGAGTTGATT;RSEQ=CATTACATTCTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:45:1:30:1:1:1:47.5:4:0.5:0:4.5 -10 42359694 . A C 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTCGAGTTGATTCCATT;RSEQ=CATTCTATTCCATTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:0.6:2,2:35.3:1:32:1:1:1.7321:45:6:0.6:0:4.3 -10 42359701 . A C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTGATTCCATTACATTCT;RSEQ=TTCCATTCCTTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:33:1:33:0:1:1.73:47.5:4:0.4:0:4.5 -10 42359711 . TTTCCA T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTACATTCTATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:34:1:30.5:1:1:1.73:42.5:4:0.4:0:3 -10 42359745 . C G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCAATC;RSEQ=TGTTTATTACATGCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:28:1:1:0:42.5:4:1:0:3 -10 42359762 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTGTTTATTACATGCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:30:1:1:0:42.5:4:1:0:3 -10 42359776 . A G 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATGCCACTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:12:0:32.5:1:1:0:45.5:4:0.6667:0:6 -10 42359808 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCAATTGGG;RSEQ=AGATCCATTCCATTCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:29:1:1:0:45.5:4:1:0:6 -10 42359813 . CCATTCCATTCCAA TCAATTCCGTTCCAT 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TCCATTCCAATTGGGCAGAT;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:29.5:1:1:0:45.5:4:1:0:6 -10 42359923 . C A 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTAAATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:33.5:1:31.5:1:1:0:22:4:1:0:6 1/1:2:2:1,1:0,0:1:0,2:26.5:1:26.5:1:1:0:50:4:1:0:3.5 -10 42359930 . A G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTAAATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29.5:1:1:0:50:4:1:0:3.5 -10 42359958 . C CGGTTTGATTCTATTCAATTCCCTTA 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTTCATTCCATTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:16.5:1:33.5:1:1:0:22:4:1:0:6 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30.1:1:1:0:50:4:1:1:3.5 -10 42359963 . T C 32 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=CATTCCATTCCTTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:32.5:1:1:0:22:4:1:0:6 1/1:1:1:0,1:0,0:1:0,0:19:1:33:1:1:0:40:2:1:1:2 -10 42360075 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCGGGTTGATTTC;RSEQ=TTCCATTCCATTCCATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:33:0:32:0:1:1:51:4:0.5:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42360088 . C T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGATTTCATTCCATTCCATT;RSEQ=CATTCCGTTCCACTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:31:1:1:0:51:4:0.6667:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42360095 . G A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTGCATTCCACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:30.5:1:31:1:1:0:51:4:0.6667:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42360113 . G C 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTTCCACTGCATTCCACT;RSEQ=GGGTTAATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:29.5:1:1:0:51:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42360539 . T C 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=0.2;SOR=Inf;LSEQ=CACTCTTGTTTTCCATTCCA;RSEQ=TCCATTCCATTACATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:12.8:1:31.5:1:1:0:36.8:8:1:0:3.8 1/0:6:3:2,1:2,1:0.5:2,2:11.3:1:31.3:1:1:1:23:6:0.5:0:5 -10 42360543 . A G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=CTTGTTTTCCATTCCATTCC;RSEQ=TTCCATTACATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:16.8:1:31.8:1:1:0:36.8:8:1:0:3.8 0/1:6:2:1,1:3,1:0.3333:2,2:15.5:1:30:1:1:2.44949:20:4:0.3333:0:5 -10 42360544 . T C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=0.57143;SOR=0.37219;LSEQ=TTGTTTTCCATTCCATTCCA;RSEQ=TCCATTACATTCCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:9:0:33.7:1:1:0:35.7:6:0.75:0:4.7 1/0:6:3:2,1:2,1:0.5:2,2:16:0:31:1:1:1:40:6:0.5:0:6 -10 42360550 . TA GC 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CATTCCACTCGGGTTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23.8:1:31.3:1:1:0:36.8:8:1:0:3.8 0/1:7:3:2,1:3,1:0.4286:2,2:23.3:1:32.5:1:1:1.41418:23:6:0.4286:0:4 -10 42360551 . A C 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.47761;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGGTTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:16:0:33:0:1:0:35.7:6:0.75:0:4.7 1/0:7:4:3,1:0,0:0.5714:0,2:17.8:1:31:1:1:0:38.5:8:1:0:6.5 -10 42360556 . C A 30 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=CCATTCCATTCCATTACATT;RSEQ=CACTCGGGTTTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,1:0.5:0,2:21:0:30.5:1:1:0:40:4:0.5:0:4 0/0:9:0:0,0:2,1:0:2,0:28.3:1:32:1:1:0:23:6:0.3333:0:4 -10 42360577 . C A 31 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.07692;SOR=0;LSEQ=CACTCGGGTTTATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:16.5:1:31:1:1:1:40:4:0.5:0:4 0/0:9:0:0,0:4,3:0:2,0:33.4:1:31.4:1:1:0:34.1:14:1:0:5.3 -10 42360578 . A T 50 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.4965;SOR=Inf;LSEQ=ACTCGGGTTTATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22.5:1:31.3:1:1:0:36.8:8:1:0:3.8 0/1:9:3:2,1:3,3:0.3333:2,2:24.3:1:31.7:1:1:1.85:23:6:0.3333:0:4 -10 42360589 . TTCCATTCCATTCCATTCCGTTCCAC T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:10.5:1:29.5:1:1:0:36.8:8:1:0:3.8 0/1:11:2:1,1:5,4:0.1818:2,2:38:1:32:1:1:1.22474:20:4:0.1818:0.1818:5 -10 42360592 . C T 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:8.5:1:30.8:1:1:0:36.8:8:1:0:3.8 0/1:9:2:1,1:3,2:0.2222:2,2:33:0:31:1:1:1.41418:40:4:0.2857:0:7 -10 42360608 . G A 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:5:3,2:1,1:0.5556:2,2:18:1:26.8:1:1:1.41:39.8:4:0.6667:0:6 -10 42360614 . C T 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCGTTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:3:1,2:1,1:0.4286:2,2:38.7:1:30.3:1:1:1.7321:39.3:6:0.6:0:7.7 -10 42360617 . G C 71 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCGTTCCACTC;RSEQ=GGTTGATTCCATTCCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:1:0,2:24.6:1:30.8:1:1:0:39.6:10:1:0:7.4 -10 42360620 . TT AA 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCGTTCCACTCGGG;RSEQ=GATTCCATTCCATAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:0,0:0.6:0,2:31.7:1:30.2:1:1:0:39.3:6:0.6:0:6.7 -10 42360635 . A T 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGGTTGATTCCATTCCAT;RSEQ=GCATTCCATTCCATTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:17.7:1:29.7:1:1:0:39.3:6:1:0:6.7 -10 42360722 . C GGGTTA 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,17:0:2,0:21.7:1:31.5:1:1:0:35:76:0.9744:0:4.8 0/1:101:2:2,0:52,45:0.0198:2,0:27:1:31.6:1:0.49907:0:29:4:0.0198:0:6.5 -10 42360738 . A T 170 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.59397;SOR=1.24445;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:17:6,11:18,9:0.3864:2,2:37.3:1:28.6:1:0.06332:3.55202:37.8:7.5:0.3571:0:4.9 0/1:116:51:22,29:39,25:0.4397:2,2:32.7:1:30:1:0.06321:2.04322:34:50:0.4505:0:4.7 -10 42360741 . C T 29 v4;NM4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.17954;SOR=0.18178;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:22,19:0.0455:2,2:36.5:1:29.5:1:1:1.15394:33:4:0.0476:0:5.5 0/0:118:1:0,1:62,54:0.0085:2,0:29:0:26:0:0.47009:0:20:2:0.0086:0:4 -10 42360742 . C T 75 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.19105;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,20:0:2,0:34.4:1:31:1:1:0:36.2:13.333:0.9756:0:4.7 0/1:118:6:4,2:55,53:0.0508:2,2:32.5:1:29.3:1:0.6802:1.92:35.2:12:0.0522:0:4.2 -10 42360743 . A T 47 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.5633;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:24,20:0:2,0:34.5:1:30.7:1:1:0:35.8:43:1:0:4.8 0/1:118:3:1,2:61,53:0.0254:2,2:36.3:1:30:1:0.60018:2.28597:23:6:0.0268:0:5 -10 42360746 . C A 55 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.3886;SOR=0.47783;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:2,1:21,18:0.0682:2,2:26.3:1:29.3:1:1:1.69:24.7:6:0.0682:0:4.3 0/1:119:4:1,3:54,52:0.0336:2,2:26:1:27.8:1:0.61802:3.08592:32.8:8:0.0339:0:4.8 -10 42360747 . C T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.16621;SOR=0.46082;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:8:7,1:17,18:0.1818:2,2:32.8:1:31.4:1:0.05928:7.12:41.1:16:0.1951:0:5.9 0/1:119:11:10,1:52,55:0.0924:2,2:29.5:1:28.6:1:0.00929:10.42:30.5:4.5:0.0796:0:5.1 -10 42360749 . T C 63 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.49236;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:1:1,0:23,19:0.0227:2,0:33:0:34:0:1:0:20:2:0.0238:0:5 0/1:119:4:3,1:55,55:0.0336:2,2:39.5:1:31.8:1:0.61851:2.97:29.3:8:0.0345:0:4.8 -10 42360751 . CG AC 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47914;SOR=1.31033;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=GGTTGATTCCATTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:6,10:17,8:0.3636:2,2:34.1:1:29.4:1:0.10549:3.42596:37.1:15:0.3571:0:4.1 0/1:119:51:20,31:37,24:0.4286:2,2:33.2:1:29:1:0.03639:2.37048:34.8:24.5:0.4414:0:3.7 -10 42360752 . G C 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.09497;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=GGTTGATTCCATTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:10:5,5:11,4:0.2273:2,2:33.5:1:30.7:1:0.39733:2.63448:37:20:0.3704:0:4.4 0/1:119:29:15,14:20,7:0.2437:2,2:33.7:1:28.7:1:0.1037:2.61916:36.9:13.5:0.45:0:3.9 -10 42360753 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCG;RSEQ=GTTGATTCCATTCCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:0:2,0:30.2:1:30.6:1:1:0:35.7:42:1:0:4.4 0/1:119:2:2,0:58,56:0.0168:2,0:36:1:28.5:1:0.49625:0:26.5:4:0.0172:0:6.5 -10 42360754 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34491;SOR=0.35611;LSEQ=TTCCATTCCATTCCATTCGG;RSEQ=TTGATTCCATTCCATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:2,1:22,19:0.0682:2,2:17.7:1:30.7:1:1:1.71:30:6:0.075:0:4 0/1:119:3:1,2:58,54:0.0252:2,2:13:0:30.3:1:0.61193:2.13435:24.7:6:0.0265:0:3.3 -10 42360755 . T A 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36118;SOR=1.44245;LSEQ=TCCATTCCATTCCATTCGGG;RSEQ=TGATTCCATTCCATTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:25:11,14:11,4:0.5682:2,2:31.2:1:29.3:1:0.10402:3.38907:35.8:7.333:0.5366:0:3.9 1/0:119:78:36,42:21,9:0.6555:2,2:31.2:1:28.8:1:0.03216:2.69709:36.3:25:0.6696:0:3.7 -10 42360757 . G A 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05133;SOR=0.35942;LSEQ=CATTCCATTCCATTCGGGTT;RSEQ=ATTCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:9:8,1:16,19:0.2045:2,2:25.7:1:28.1:1:0.02709:9.09:40.9:18:0.2093:0:5.7 0/1:119:10:9,1:50,56:0.084:2,2:23.6:1:26:1:0.01659:9.92:30.7:9:0.0783:0:5 -10 42360759 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCGGGTTGA;RSEQ=TCCATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:24,20:0:2,0:25:1:30.4:1:1:0:35.8:43:1:0:4.3 0/1:120:2:1,1:49,31:0.0167:2,2:26.5:1:28.5:1:1:1.57149:29:4:0.0247:0:6 -10 42360761 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCGGGTTGATT;RSEQ=CATTCCATTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:24,20:0:2,0:23.3:1:31.5:1:1:0:35.8:43:1:0:4.3 0/1:120:2:2,0:48,33:0.0167:2,0:33.5:1:33:1:0.51513:0:24.5:4:0.0253:0:5.5 -10 42360762 . C T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.6112;SOR=0.54077;LSEQ=CATTCCATTCGGGTTGATTC;RSEQ=ATTCCATTGCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:23,19:0.0455:2,2:5:0:29.5:1:1:1.20525:25:4:0.0488:0:3 0/1:120:3:1,2:49,31:0.025:2,2:5:0:31:1:0.56003:3.1168:24.7:6:0.038:0:3.3 -10 42360766 . CCATTG C 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=4.000;MSILEN=5;SSF=1;SOR=0.70855;LSEQ=CCATTCGGGTTGATTCCATT;RSEQ=CATTCCATTCCATTCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:1:1,0:22,19:0.0238:2,0:44:0:30:0:1:0:40:2:0.0244:0:7 0/1:118:2:2,0:47,31:0.0169:2,0:44.5:1:31:0:0.5193:0:22.5:4:0.0256:0:7.5 -10 42360771 . G C 92 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:7,1:15,17:0.1951:2,2:16.8:1:30.9:1:0.05375:7.58:41:16:0.2051:0:5.5 0/0:115:0:0,0:45,54:0:2,0:7:1:15:1:1:0:24:0:0:0.0086:6 -10 42360773 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTGATTCCATTCCATTGC;RSEQ=TTCCATTCCATTCCAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,18:0:2,0:13.7:1:29.6:1:1:0:37:19:0.9744:0:4.4 0/1:116:2:2,0:46,31:0.0172:2,0:9.5:1:28.5:1:0.51704:0:25.5:4:0.0267:0.0172:3.5 -10 42360777 . C A 26 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.16811;SOR=0.17237;LSEQ=GATTCCATTCCATTGCATTC;RSEQ=ATTCCATTCCAATCTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:2,0:18,18:0.0526:2,0:6.5:1:26:1:0.48791:0:40:4:0.0526:0.0526:6.5 0/0:107:1:1,0:37,30:0.0093:2,0:1:1:26:1:1:0:24:2:0.0143:0.0093:6 -10 42360778 . A G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52296;SOR=0.61465;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TTCCATTCCAATCTGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:4,1:14,17:0.1316:2,2:8:0:30.4:1:0.33766:4.66:28.4:10:0.1429:0:3.2 0/1:106:9:5,4:33,26:0.0849:2,2:8.7:1:29.6:1:1:1.01516:42.6:18:0.1452:0:4 -10 42360779 . T A 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTGCATTCCA;RSEQ=TCCATTCCAATCTGGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:0:2,0:8.9:1:29.2:1:1:0:36.3:37:1:0.0526:4.4 0/1:104:2:1,1:35,28:0.0192:2,2:8:0:27:1:1:1.24568:23:4:0.0313:0:5 -10 42360781 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.9305;LSEQ=CCATTCCATTGCATTCCATT;RSEQ=CATTCCAATCTGGTTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:1,0:15,16:0.0313:2,0:5:0:24:0:1:0:40:2:0.0323:0:5 0/1:103:3:2,1:36,26:0.0291:2,2:7.3:1:27:1:1:1.44:49:6:0.0462:0.0097:3 -10 42360782 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTGCATTCCATTC;RSEQ=ATTCCAATCTGGTTGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:11,16:0:2,0:7.2:1:30.9:1:1:0:37.7:26:0.9286:0:4 0/1:95:2:2,0:31,24:0.0211:2,0:19:1:30:1:0.50376:0:24.5:4:0.0357:0.0105:4 -10 42360783 . A T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21805;SOR=0.27857;LSEQ=ATTCCATTGCATTCCATTCC;RSEQ=TTCCAATCTGGTTGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:12,13:0.0741:2,2:3:1:28.5:1:1:1.08:40:4:0.0741:0.037:6 0/1:93:2:2,0:29,23:0.0215:2,0:5:1:27.5:1:0.50175:0:28:4:0.0385:0.0108:4 -10 42360792 . TG GA 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=CATTCCATTCCATTCCAATC;RSEQ=GTTGATTTCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:22:1:28.8:1:1:0:42:6:0.6:0:4.7 1/0:4:2:2,0:0,0:0.5:0,0:25.5:1:28.5:1:1:0:22.5:4:0.6667:0:6.5 -10 42360801 . T C 45 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCATTCCAATCTGGTTGATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:14:1:28.7:1:1:0:42:6:1:0:4.7 1/0:4:2:2,0:0,0:0.5:0,0:17.5:1:30:1:1:0:22.5:4:1:0:6.5 -10 42360824 . G T 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCTA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:0,0:0.75:0,2:7.3:1:30.7:1:1:0:26:6:1:0.25:3.3 -10 42360866 . C A 101 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0.8225;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:22:1:28:1:1:1.73:30:4:0.4:0:3.5 0/1:34:12:6,6:9,11:0.3529:2,2:27.5:1:28.3:1:1:1.21:40.8:24:0.3529:0:2.6 -10 42360871 . C A 27 d7;v4;MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.0724;SOR=0.1048;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCGTTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:38:1:29.5:1:1:1.73:40:4:0.4:0:2 0/1:34:2:1,1:15,17:0.0588:2,2:40:1:27.5:1:1:1.13:35:4:0.0588:0:3 -10 42360873 . AT TC 30 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCATTCCGTTCCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:32.6:1:30.8:1:1:0:32.8:10:1:0:3.4 0/1:34:2:1,1:15,17:0.0588:2,2:26:0:30.5:1:1:1.13:49:4:0.0588:0:5 -10 42360876 . C A 29 d7;v4;MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.0383;SOR=0.05382;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCGTTCCACTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:39.5:1:29:1:1:1.73:40:4:0.4:0:2 0/1:34:1:0,1:16,17:0.0294:2,0:43:0:31:0:1:0:30:2:0.0294:0:6 -10 42360880 . T G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.34522;SOR=0.26359;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCGTTCCACTCGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:27:0:31:0:1:0:24:2:0.2:0:5 0/1:34:2:1,1:14,16:0.0588:2,2:28:0:33.5:1:1:1.14:21:4:0.0606:0:3.5 -10 42360883 . G A 93 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31776;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,1:0:2,0:42:1:30.3:1:1:0:38.7:6:0.6:0:2 0/1:34:9:4,5:10,9:0.2647:2,2:37.1:1:29.4:1:1:1.37263:39.3:18:0.2647:0:4.2 -10 42360884 . T C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCG;RSEQ=TCCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:37.5:1:29.3:1:1:0:35:8:1:0:2.8 0/1:34:2:1,1:13,13:0.0588:2,2:36:1:32:1:1:1:51:4:0.0714:0:3.5 -10 42360886 . CC GT 81 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0361;LSEQ=CCATTCCATTCCATTCCGTT;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:40:0:32:0:1:0:24:2:0.2:0:4 0/1:34:7:3,4:9,9:0.2059:2,2:36:1:29:1:1:1.31809:37.1:14:0.2188:0:3 -10 42360887 . C CATTGT 112 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63624;SOR=0.47605;LSEQ=CATTCCATTCCATTCCGTTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:0,1:0.6:0,2:41.7:1:29.8:1:1:0:38.7:6:0.75:0:2 0/1:34:14:7,7:3,4:0.4118:2,2:39.5:1:29.6:1:1:1.32:42.6:28:0.6087:0:2.1 -10 42360912 . C T 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGTTGATTCCATTCCATTG;RSEQ=ATTCCATTCCATTCCAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:13.8:1:31.5:1:1:0:35:8:1:0:2.5 0/1:32:2:1,1:14,16:0.0625:2,2:12.5:1:26.5:1:1:1.14:41.5:4:0.0645:0:3 -10 42360924 . TTCCAATCTGGTTGATTTCATTCCATTCCATTCCATTCTAG T 116 d7;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=28;MSI=11.000;MSILEN=5;SSF=0.0567;SOR=0;LSEQ=TTCCATTGCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:24:1:30.3:1:1:0:32.8:10:1:1:3.2 1/0:32:16:6,10:6,10:0.5:2,2:36.1:1:29:1:1:1:41:32:0.5333:0.5:3.1 -10 42360956 . C CCATTGCGTTCCACTCGCGATGATTCAATTA 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGATTTCATTCCATTCCATT;RSEQ=CATTCTAGTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:16:2:1,1:2,1:0.125:2,2:41.5:1:28.9:1:1:1.7321:25:4:0.4:0.125:1.5 -10 42360966 . C A 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCTAGT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:10:0:29.5:1:1:1.7321:25:4:0.4:0:1.5 -10 42360977 . C T 59 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCTAGTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:4:2,2:2,1:0.5714:2,2:24.3:1:29.5:1:1:1.81007:43:8:0.5714:0:2.5 -10 42360986 . C T 29 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:5:0:33:0:1:0:24:2:1:0:3 0/1:7:2:1,1:3,2:0.2857:2,2:40.5:1:29.5:1:1:1.41418:51:4:0.2857:0:3.5 -10 42361018 . A C 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02778;SOR=0;LSEQ=ATTCCATTCCATTCCTGTCC;RSEQ=TTCCATTCCCTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32:1:33:0:1:0:42:4:1:0:3.5 0/0:7:0:0,0:4,3:0:2,0:15.3:1:29.1:1:1:0:44:14:1:0:3.9 -10 42361020 . T G 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCTGTCCAT;RSEQ=CCATTCCCTTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:33:1:32:0:1:0:42:4:1:0:3.5 0/1:7:2:1,1:3,2:0.2857:2,2:12:1:31.5:1:1:1.41418:51:4:0.2857:0:3.5 -10 42361031 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCTGTCCATTCCATTCCCTT;RSEQ=CATTCCATTCCATTACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:33:1:33:0:1:0:42:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:17.5:1:28:1:1:1:48:4:0.5:0:6 -10 42361046 . A C 33 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCTTCCATTCCATTCCATT;RSEQ=CACTGCTGTTTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18.5:1:33:0:1:0:42:4:1:0:3.5 1/1:1:1:0,1:0,0:1:0,0:48:0:33:0:1:0:45:2:1:0:6 -10 42361069 . A C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTGTTTATTCCATTCCA;RSEQ=TCCATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:3:0:29:0:1:0:60:2:1:0:4 1/1:2:2:1,1:0,0:1:0,2:23:1:29.5:1:1:0:42.5:4:1:0:5.5 -10 42361990 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTTGATTCCATTGCATTCCA;RSEQ=GCCGTTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:30:1:1:0:41.5:4:1:0:5 0/0:2:0:0,0:1,1:0:2,0:21:0:31:0:1:0:44:4:1:0:1.5 -10 42362012 . G C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCGTTCCATTCCATTCCACT;RSEQ=CATTCCAATCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:37.5:1:31.5:1:1:0:41.5:4:1:0:5 1/1:2:2:1,1:0,0:1:0,2:38.5:1:32:1:1:0:44:4:1:0:1.5 -10 42362013 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CGTTCCATTCCATTCCACTG;RSEQ=ATTCCAATCCATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38.5:1:29:1:1:0:41.5:4:1:0:5 0/0:2:0:0,0:1,1:0:2,0:37.5:1:31.5:1:1:0:44:4:1:0:1.5 -10 42362034 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATTCCAATCCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38.5:1:31.5:1:1:0:41.5:4:1:0:5 0/0:2:0:0,0:1,1:0:2,0:16.5:1:29.5:1:1:0:44:4:1:0:1.5 -10 42362038 . G C 33 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAATCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:33:0:1:0:41.5:4:1:0:5 0/0:2:0:0,0:1,1:0:2,0:12.5:1:29.5:1:1:0:44:4:1:0:1.5 -10 42362054 . T A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:32.5:1:1:0:41.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42362283 . T A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=TTTCCATTCCTTTCCATTCC;RSEQ=TTACATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:9:1:29.7:1:1:0:24.7:6:1:0:4.7 -10 42362312 . G C 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:19:0:23:0:1:0:23:2:1:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:19:0:31:1:1:0:22:4:0.6667:0:3 -10 42362315 . T A 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCATTCGGG;RSEQ=TGATTCCATTCCATTCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:16:0:30:0:1:0:23:2:1:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:16:0:30.5:1:1:0:22:4:0.6667:0:3 -10 42363357 . C T 58 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGGTTCCATTCCATTCCA;RSEQ=TCCATTCCAATCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:3,1:0,0:0.8:0,2:14.8:1:29.3:1:1:0:35.3:8:1:0:6.8 -10 42363367 . A T 85 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCACTCCATTCCA;RSEQ=TCCATTCCACTCGAGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:7:4,3:0,0:0.7:0,2:10.7:1:30.4:1:1:0:32.4:14:0.7:0:5.9 -10 42363374 . C G 84 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTCCATTCCAATCCATT;RSEQ=CACTCGAGTTGATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:11:7:3,4:1,1:0.6364:2,2:19.6:1:30:1:1:1.29098:33.7:6:0.6:0:5.7 -10 42363377 . C A 93 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCATTCCAATCCATTCCA;RSEQ=TCGAGTTGATTCCATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:13:9:4,5:1,1:0.6923:2,2:21.2:1:29.4:1:1:1.22474:34:18:0.75:0:5.4 -10 42363381 . A C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCAATCCATTCCACTCG;RSEQ=GTTGATTCCATTGCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:15:2:1,1:6,7:0.1333:2,2:7:0:31:1:1:1.15:41:4:0.1333:0:1 -10 42363383 . T TTGATGTCCTTTCCATTCCACTTGAATACATTCCCTTCTATTCAACTCTGAA 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAATCCATTCCACTCGAG;RSEQ=TGATTCCATTGCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:16:3:2,1:6,7:0.1875:2,2:28:1:30.6:1:1:2.21:36.3:6:0.1875:0.1875:2.3 -10 42363386 . AT CA 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCATTCCACTCGAGTTG;RSEQ=TCCATTGCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:2:1,1:8,7:0.1176:2,2:34.5:1:30:1:1:1.13389:29:4:0.125:0:6 -10 42363387 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCATTCCACTCGAGTTGA;RSEQ=TCCATTGCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:2:1,1:7,6:0.1176:2,2:28:0:32:0:1:1.1547:40:4:0.1333:0:5 -10 42363419 . C G 81 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.31715;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:18.7:1:31.7:1:1:0:40.7:12:0.8571:0:4.7 0/1:29:6:3,3:10,10:0.2069:2,2:21.8:1:31.7:1:1:1:28.7:12:0.2069:0:6 -10 42363425 . C A 31 pSTD;NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.03333;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:24:0:31.5:1:1:1.41:43:4:0.2857:0:4 0/0:29:0:0,0:12,13:0:2,0:20.1:1:30.8:1:1:0:35.1:50:0.8621:0:4.8 -10 42363429 . C G 33 pSTD;NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.03743;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:28:0:33:1:1:1.41:43:4:0.2857:0:4 0/0:27:0:0,0:14,13:0:2,0:22.5:1:30.1:1:1:0:36.1:26:1:0:5 -10 42363436 . A G 29 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCTTTCCAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:37.3:1:30.3:1:1:0:39.1:14:1:0:5 0/1:25:2:1,1:11,11:0.08:2,2:7:0:29.5:1:1:1:25:4:0.087:0:6 -10 42363444 . C G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.12003;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CTTTCCAGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:2,2:0.1429:2,0:47:0:28:0:1:0:30:2:0.1429:0:7 0/1:19:3:1,2:9,7:0.1579:2,2:46:1:31.7:1:0.58204:2.44724:36.7:6:0.1579:0:6.7 -10 42363445 . CT TA 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=TTCCAGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,4:0:2,0:43:1:32.5:1:1:0:39:12:1:0:4.5 0/1:19:2:1,1:8,8:0.1053:2,2:42.5:1:28.8:1:1:1:28:4:0.1111:0:5 -10 42363446 . TT AA 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.8401;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCAGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,1:0.2857:2,0:45:1:31.5:1:1:0:35:4:0.3333:0:5 0/1:16:4:2,2:3,2:0.25:2,2:44:1:29.4:1:1:1.43328:43.8:8:0.3077:0:4 -10 42363450 . C A 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11053;SOR=0;LSEQ=CATTCCATTCCATTCCTTTC;RSEQ=AGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,1:0.2857:2,2:37.5:1:30:1:1:1:43:4:0.3333:0:4 0/0:13:0:0,0:3,2:0:2,0:38.4:1:29.2:1:1:0:44.2:10:0.4167:0:4.6 -10 42363451 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=Inf;LSEQ=ATTCCATTCCATTCCTTTCC;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,4:0:2,0:39.4:1:30.8:1:1:0:40.8:10:0.8333:0:4.4 0/1:13:2:1,1:5,4:0.1538:2,2:42:1:30.5:1:1:1.22474:39.5:4:0.1818:0:6 -10 42363500 . C G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTT;RSEQ=ATTCCTTTCCAGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14.5:1:33:0:1:0:48:4:1:0:2.5 0/1:5:2:1,1:1,2:0.4:2,2:23:1:33.5:1:1:1.73:35:4:0.4:0:3.5 -10 42363526 . A C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTTCCAGTTGATTCCATTCC;RSEQ=TTCCATTGCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:34:1:28.5:1:1:1:29:4:0.5:0:7 -10 42363534 . G C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCTTTCCATTCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,0:0.5:0,2:34:1:30.5:1:1:0:29:4:0.6667:0:7 -10 42363539 . CCT ATA 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTGCATT;RSEQ=TTCCATTCCAATCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,0:0.5:0,2:34:1:29:1:1:0:29:4:0.6667:0:5 -10 42363717 . G T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTATACCATTACATTGCA;RSEQ=TCGAATTGATTCCATTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:35:0:33:0:1:0:33:2:1:0:4 1/1:3:3:2,1:0,0:1:0,2:24.7:1:29.7:1:1:0:27.3:6:1:0:4 -10 42363723 . T A 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=ACCATTACATTGCAGTCGAA;RSEQ=TGATTCCATTCTATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29:1:1:0:33:4:1:0:3 0/0:3:0:0,0:2,1:0:2,0:26.7:1:29.3:1:1:0:27.3:6:1:0:4 -10 42363754 . C G 31 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=CTATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:31:1:1:0:33:4:1:0:3 0/0:2:0:0,0:1,1:0:2,0:29:0:30.5:1:1:0:27.5:4:1:0:3 -10 42363780 . CATGACGTTACATTTCATTCCACTTGAGTTG C 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=15.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:39:1:28.5:1:1:1:27.5:4:0.5:0.5:3 -10 42364220 . C A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCACTCGGATTGACTC;RSEQ=ATTCCATACCCGTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:28:1:1:0:50:4:1:0:3 -10 42364358 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCACTCGTATTTAT;RSEQ=CCATTCCTTTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:30:1:1:0:57:4:1:0:3.5 -10 42364365 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCGTATTTATTCCATTC;RSEQ=TTTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:27.5:1:1:0:57:4:1:0:3.5 -10 42364519 . CCATT C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCATTCCATTCATTTCCATT;RSEQ=CACTCGGGTTGATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:30:0:1:0:37:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:34:0:32.5:1:1:0:44:4:1:0:3 -10 42364533 . T G 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCATTCCATTCACTCGGGT;RSEQ=GATTCCATTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:30:0:27:0:1:0:37:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:31:0:30.5:1:1:0:44:4:1:0:3 -10 42364535 . A G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CATTCCATTCACTCGGGTTG;RSEQ=TTCCATTGCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:28:0:27:0:1:0:37:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:29:0:32:1:1:0:44:4:1:0:3 -10 42364546 . T C 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCGGGTTGATTCCATTGCA;RSEQ=TCCATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:17:0:27:0:1:0:37:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:18:0:31.5:1:1:0:44:4:1:0:3 -10 42364563 . CCACGTGGGTT C 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=GATTCCATTCCATTCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:27.5:1:1:0:44:4:1:1:3 -10 42364681 . G T 30 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TTCCGTTCCATTCCATTCCA;RSEQ=TCCATTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21:1:30.5:1:1:0:43:4:1:0:3 0/1:7:2:1,1:0,0:0.2857:0,2:32:0:30.5:1:1:0:37:4:1:0:5 -10 42364683 . C A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCGTTCCATTCCATTCCAGT;RSEQ=CATTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:38:0:31:0:1:0:54:2:1:0:5 0/1:7:2:1,1:0,0:0.2857:0,2:30:0:28:1:1:0:37:4:1:0:5 -10 42364691 . G A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCAGTCCATTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:30:0:31:0:1:0:54:2:1:0:5 0/1:7:2:1,1:0,0:0.2857:0,2:22:0:28:1:1:0:37:4:1:0:5 -10 42364699 . C T 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CAGTCCATTCGGGTTGATTC;RSEQ=ATTCCATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:10.7:1:32:1:1:0:43.7:6:1:0:6.7 0/1:13:2:1,1:9,2:0.1538:2,2:14:0:27:1:0.42308:3.87298:37:4:0.1538:0:5 -10 42364704 . C A 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCGGGTTGATTCCATTC;RSEQ=ATTCCATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:8.8:1:27:1:1:0:36.8:4:1:0:6.8 0/1:19:2:1,1:12,5:0.1053:2,2:9:0:27.5:1:1:2.28037:37:4:0.1053:0:5 -10 42364715 . T A 78 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCTTTCCATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:0,1:0.8571:0,2:12.3:1:30.5:1:0.42857:0:37.3:12:1:0:7.2 0/0:29:0:0,0:4,3:0:2,0:7.3:1:29.4:1:1:0:46.9:14:0.7:0:5.4 -10 42364720 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCTTTCC;RSEQ=TTCCTTTCCATTCATTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:11.3:1:30.9:1:1:0:37.9:22:1:0:6.8 0/1:34:2:1,1:20,10:0.0588:2,2:15.5:1:31:1:1:1.95408:26:4:0.0606:0:6.5 -10 42364723 . C T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCTTTCCATT;RSEQ=CTTTCCATTCATTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:13.2:1:29.6:1:1:0:37.3:11:1:0:6.9 0/1:36:2:1,1:20,12:0.0556:2,2:23:1:27.5:1:1:1.64076:36.5:4:0.0588:0:7 -10 42364725 . T A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32498;SOR=0.50763;LSEQ=ATTCCATTCCTTTCCATTCC;RSEQ=TTCCATTCATTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:3,3:0,0:0.5:0,2:11:1:31.2:1:1:0:40.3:12:0.5455:0:6.5 0/1:36:12:7,5:0,1:0.3333:0,2:18.9:1:28:1:0.46154:0:39.7:5:0.3125:0:6.3 -10 42364730 . A G 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67948;SOR=0.65123;LSEQ=ATTCCTTTCCATTCCTTTCC;RSEQ=TTCATTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:5,5:0.2308:2,2:19.3:1:25:1:1:1.89792:31.3:2:0.1667:0:6.3 0/1:37:6:4,2:19,11:0.1622:2,2:24.5:1:31.2:1:1:1.15:38.8:12:0.1765:0:7 -10 42364734 . AT CG 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.09794;LSEQ=CTTTCCATTCCTTTCCATTC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:4,4:1,0:0.5714:0,2:22.6:1:30.4:1:1:0:36.6:16:0.6154:0:5.8 1/0:37:22:14,8:1,1:0.5946:2,2:28.9:1:29.7:1:1:1.71:38.5:44:0.6667:0:5.9 -10 42364735 . T G 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0212;SOR=0.13551;LSEQ=TTTCCATTCCTTTCCATTCA;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:1,1:0.2778:2,2:7.6:1:30.2:1:1:1.41418:42.4:10:0.625:0.0556:3.8 0/1:42:2:0,2:3,3:0.0476:2,0:19.5:1:31:1:0.46429:0:25.5:4:0.1667:0:5 -10 42364739 . C A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.61103;SOR=0.52931;LSEQ=CATTCCTTTCCATTCATTTC;RSEQ=ATTCCATTCCATTCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:21,17:0.0476:2,2:32:1:29:1:1:1.22874:40:4:0.0476:0:5.5 0/1:78:2:1,1:41,33:0.0256:2,2:28.5:1:31.5:1:1:1.23885:60:4:0.0267:0:6 -10 42364743 . C G 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.33077;SOR=0.31287;LSEQ=CCTTTCCATTCATTTCCATT;RSEQ=CATTCCATTCCATTCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:1,2:24,23:0.06:2,2:23:1:29:1:1:2.0574:39.3:6:0.0612:0.02:5.3 0/1:103:2:0,2:55,45:0.0194:2,0:27:1:34:0:0.20986:0:22:4:0.0198:0:5 -10 42364745 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTTCCATTCATTTCCATTCC;RSEQ=TTCCATTCCATTCTATTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:25,25:0:2,0:14.9:1:29.9:1:1:0:46.2:24:1:0.02:4.3 0/1:108:2:1,1:57,49:0.0185:2,2:36.5:1:31:1:1:1.16163:40.5:4:0.0189:0:5.5 -10 42364746 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.09877;SOR=0;LSEQ=TTCCATTCATTTCCATTCCA;RSEQ=TCCATTCCATTCTATTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:24,24:0.04:2,2:7.5:1:31.5:1:1:1:54:4:0.04:0:5 0/0:108:0:0,0:58,50:0:2,0:18.1:1:29.5:1:1:0:41.6:53:1:0:4 -10 42364764 . G A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCTATTC;RSEQ=GTTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:25,27:0:2,0:28:1:30.3:1:1:0:45.4:25:0.9804:0:4.3 0/1:112:2:1,1:56,53:0.0179:2,2:23:1:32.5:1:1:1.0561:24.5:4:0.0183:0:6.5 -10 42364765 . GT AA 61 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.91924;LSEQ=ATTCCATTCCATTCTATTCG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:1:0,1:25,26:0.0189:2,0:36:0:32.5:0:1:0:22:2:0.0196:0:7 0/1:112:4:2,2:54,51:0.0357:2,2:27.8:1:30.8:1:1:1.0583:25:8:0.037:0:4.3 -10 42364766 . T G 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.73706;SOR=0.8834;LSEQ=TTCCATTCCATTCTATTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:33:15,18:6,4:0.6226:2,2:29.5:1:32:1:0.48761:1.7754:45.3:66:0.6471:0:4.2 1/0:113:67:34,33:12,10:0.5929:2,2:28.6:1:31.1:1:0.80944:1.16271:44:134:0.6321:0:4.1 -10 42364769 . G A 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08667;SOR=4.39615;LSEQ=CATTCCATTCTATTCGGTTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:50:24,26:2,2:0.9259:2,2:30.6:1:29.9:1:1:1.08171:46.1:100:0.9259:0:4.3 1/1:113:111:57,54:0,1:0.9823:0,2:29.5:1:28.7:1:0.49107:0:41.6:54.5:0.9909:0:3.9 -10 42364789 . C GATTGCAATCGAGTTG 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.02991;SOR=Inf;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:26,26:0:2,0:21.1:1:31.6:1:1:0:44.3:104:1:0.0185:4.2 0/1:108:9:4,5:51,48:0.0833:2,2:19.6:1:29.6:1:0.73956:1.32464:46.6:18:0.0857:0.0833:3.6 -10 42364799 . C T 129 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.15184;SOR=0.54428;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:16:8,8:11,10:0.381:2,2:12.1:1:30.1:1:1:1.09717:48.7:32:0.3902:0:4.2 0/1:92:23:12,11:31,32:0.25:2,2:12.1:1:28.7:1:1:1.12:39.5:22:0.2444:0:3.9 -10 42364803 . C GCAATCGAGTTGAATCCATTGCATTTCATTG 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.54997;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:21,19:0:2,0:15.6:1:29.4:1:1:0:43.4:39:1:0.05:4.4 0/1:78:3:1,2:35,38:0.0385:2,2:30:1:29.9:1:1:1.82792:33.3:6:0.0395:0.0385:3.3 -10 42364809 . C G 31 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.14007;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCACTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:15,17:0.0588:2,2:13:1:31:1:1:1.13:35:4:0.0606:0.0294:5.5 0/0:56:0:0,0:23,30:0:2,0:8.8:1:30.2:1:1:0:41.7:52:0.963:0.0179:3.7 -10 42364810 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.13483;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:15,16:0.0606:2,2:16.5:1:32:1:1:1.06:45:4:0.0606:0:7.5 0/0:56:0:0,0:23,32:0:2,0:8.1:1:29.2:1:1:0:41.3:54:0.9818:0.0179:3.8 -10 42364811 . T TTGCAATCGAGTTGAA 127 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=8.000;MSILEN=5;SSF=0.81991;SOR=0.86112;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:7,7:7,9:0.4242:2,2:19.7:1:30:1:1:1.27:46.5:28:0.4375:0.4242:4.1 0/1:49:19:9,10:10,17:0.3878:2,2:18.1:1:30:1:0.55194:1.52:40:38:0.3878:0.3878:3.6 -10 42364814 . C G 47 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=0.33209;SOR=0.27628;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ACTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:2,1:12,13:0.1034:2,2:18:1:29.7:1:1:2.11:38.3:6:0.1071:0.0345:6.7 0/1:33:1:0,1:12,19:0.0303:2,0:24:0:32:0:1:0:56:2:0.0313:0:6 -10 42364815 . AC GT 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49365;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:0:2,0:10.1:1:28.6:1:1:0:44.5:12.5:1:0.3333:4.5 0/1:31:2:1,1:10,18:0.0645:2,2:14:1:27.5:1:1:1.76:31.5:4:0.0667:0.0323:4 -10 42364816 . C T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55205;SOR=1.48639;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:7,5:1,0:0.5714:0,2:8.4:1:28.5:1:1:0:46.8:11:0.5789:0.4286:4.7 1/0:24:16:4,12:1,2:0.6667:2,2:12.6:1:30.6:1:1:1.46619:39.5:32:0.6957:0.2917:4.4 -10 42364818 . C G 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93035;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:3,3:4,4:0.3158:2,2:6.7:1:28.5:1:1:1:49.2:5:0.2778:0.3158:3.5 0/1:20:6:1,5:4,7:0.3:2,2:13.2:1:32.8:1:0.60003:2.69683:35:12:0.3:0.3:3.8 -10 42364819 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21764;SOR=0;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,8:0.1111:2,2:8:1:28.5:1:1:1.31:33.5:4:0.125:0.0556:5.5 0/0:20:0:0,0:5,12:0:2,0:12.6:1:30.4:1:1:0:38.5:16:0.8889:0.35:4.6 -10 42364820 . A T 50 v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.29942;SOR=0.23214;LSEQ=ATTCCATTCCATTCCACTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:1,2:5,7:0.2:2,2:13.3:1:31.7:1:1:1.39581:31.3:6:0.2:0:4.3 0/1:19:1:0,1:5,13:0.0526:2,0:15:1:29:1:1:0:51:2:0.0526:0.0526:2 -10 42364823 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0.61146;LSEQ=CCATTCCATTCCACTCCATT;RSEQ=CATTCCATTCCATTCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:4,5:0.1818:2,0:9.5:1:30.5:1:0.49091:0:44:4:0.1818:0.1818:4 0/1:17:2:0,2:4,9:0.1176:2,0:18:1:31:1:1:0:32.5:4:0.125:0.1176:3.5 -10 42364825 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.50769;SOR=Inf;LSEQ=ATTCCATTCCACTCCATTCC;RSEQ=TTCCATTCCATTCCACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:10:1:31:1:1:0:40.6:20:1:0.2:5.5 0/1:16:2:0,2:4,10:0.125:2,0:11:1:30.5:1:1:0:45.5:4:0.125:0.0625:3.5 -10 42364829 . C TATTAGGGTTA 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.49351;SOR=Inf;LSEQ=CATTCCACTCCATTCCATTC;RSEQ=ATTCCATTCCACCCGGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,4:0:2,0:9.7:1:31.2:1:1:0:41.7:12:0.6667:0.1111:5.8 0/1:13:2:0,2:2,7:0.1538:2,0:13:1:31.2:1:1:0:45.5:4:0.1538:0.1538:4 -10 42364830 . A T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.48571;SOR=Inf;LSEQ=ATTCCACTCCATTCCATTCC;RSEQ=TTCCATTCCACCCGGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,5:0:2,0:5.4:1:30.4:1:1:0:36:16:0.8889:0.1111:5.8 0/1:12:2:0,2:2,8:0.1667:2,0:6.5:1:30.5:1:1:0:45.5:4:0.1818:0.1667:4 -10 42364939 . C CATTA 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTTCATTT;RSEQ=TTTCCATTCCATTCCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:29.9:1:1:0:33:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:17.5:1:27.8:1:1:0:53:4:1:0.5:3.5 -10 42364953 . C G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTCTTTCCATTCCATT;RSEQ=CAGTTGATTCTTATGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45.5:1:33:1:1:0:33:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:33:1:31:1:1:0:53:4:1:0:3.5 -10 42364964 . TT CA 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCAGTTGATTC;RSEQ=ATGCCTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:32.3:1:1:0:33:4:1:0:2 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30:1:1:0:53:4:1:0:2.5 -10 42365017 . T G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=GTATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:30.5:1:1:0:60:4:1:0:3 -10 42365046 . CTCGGGATGATTGCAT C 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTGCAGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:27:0:33:1:1:1:50:4:0.5:0:0 0/0:2:0:0,0:1,1:0:2,0:33:0:29:1:1:0:60:4:1:0:3 -10 42365048 . C A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGATGATTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:25.5:1:31:1:1:0:30:4:1:0:2.5 1/1:2:2:1,1:0,0:1:0,2:33:1:29:1:1:0:60:4:1:0:3 -10 42365073 . G C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGATTGCATTCCATTCCATT;RSEQ=CAGTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:6:0:33:0:1:1.73:30:4:0.4:0:2.5 1/1:2:2:1,1:0,0:1:0,2:24.5:1:32:1:1:0:60:4:1:0:3 -10 42365154 . C T 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CACTCGAGTTGATTCCATTC;RSEQ=ATTCCGTACCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:8.7:1:31.3:1:1:0:36.3:12:1:0:2 1/1:6:5:2,3:1,0:0.8333:0,2:10:0:30.2:1:1:0:32.8:10:0.8333:0:1.2 -10 42365334 . C G 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.4697;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:27.2:1:31.2:1:1:0:36.8:10:1:0:3.4 0/1:7:2:1,1:2,3:0.2857:2,2:18.5:1:31.5:1:1:1.41:49:4:0.2857:0:6 -10 42365336 . T C 33 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.15152;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCGCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:26:0:33:1:1:1.73:49.5:4:0.4:0:2 0/0:7:0:0,0:3,4:0:2,0:16.4:1:29.1:1:1:0:42.9:14:1:0:3.7 -10 42365344 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.4697;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCGCTTGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:37.2:1:31.2:1:1:0:36.8:10:1:0:3.4 0/1:7:2:1,1:2,2:0.2857:2,2:28.5:1:31:1:1:1:49:4:0.2857:0:6 -10 42365348 . C G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.11403;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CGCTTGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:38:0:32.5:1:1:1.73:49.5:4:0.4:0:2 0/1:7:3:2,1:1,3:0.4286:2,2:31.3:1:32.7:1:0.48571:4.45:39.3:6:0.4286:0:5.3 -10 42365351 . CTTGGGT GA 30 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.15152;SOR=0;LSEQ=TTCCATTCCATTCCATTCCG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:41:0:30.6:1:1:1:30:4:0.4:0:3 0/0:7:0:0,0:2,2:0:2,0:25.3:1:31.5:1:1:0:54.5:8:0.6667:0:3 -10 42365369 . C T 28 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.44444;SOR=Inf;LSEQ=CGCTTGGGTTGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:27.4:1:31.8:1:1:0:36.8:10:1:0:3.2 0/1:5:2:1,1:1,2:0.4:2,2:31.5:1:28:1:1:1.73:49:4:0.4:0:6 -10 42365373 . C G 53 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0.4831;LSEQ=TGGGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:22.7:1:33.7:1:1:1.7321:28.3:6:0.6:0:4 0/1:5:2:1,1:1,2:0.4:2,2:27.5:1:30.5:1:1:1.73:49:4:0.4:0:6 -10 42365380 . A G 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.45455;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:16:0:32.5:1:1:1:30:4:0.3333:0:4 0/0:5:0:0,0:2,3:0:2,0:25.2:1:30.2:1:1:0:36:10:1:0:5.2 -10 42365388 . C A 30 d7;v4;MAF0.05;pSTD;NM4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0.5321;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:8:0:30.5:1:1:1:30:4:0.3333:0:4 0/1:5:1:0,1:2,2:0.2:2,0:12:0:32:0:1:0:20:2:0.2:0:2 -10 42365409 . TACTCGGGTTCATTTCATTTCATTCG C 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=GTTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:30:0:33:0:1:0:40:2:1:0:2 1/0:3:2:1,1:0,1:0.6667:0,2:39:1:30:1:1:0:30:4:0.6667:0.6667:4.5 -10 42365429 . CATTCGGTTCCA AGTTCCG 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTCGGGTTCATTTCATTT;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:30.1:1:1:0:49:4:1:0.5:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42365548 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCATTCCATTAAATTCCATT;RSEQ=CATTCCAGTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:43:0:33:0:1:0:25:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:22.5:1:30.5:1:1:0:34:4:1:0:4 -10 42365560 . A T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCCATTGCATTCCAGTTC;RSEQ=TTCCATTCCTTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:31:0:29:0:1:0:25:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30.5:1:1:0:34:4:1:0:4 -10 42365590 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:16:0:31.5:1:1:0:44.5:4:0.6667:0:5 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42365593 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCATTCCATTCCATTCCCTT;RSEQ=CATTCCATTCCGTTGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19:0:32:1:1:0:44.5:4:1:0:5 1/1:2:2:1,1:0,0:1:0,2:12:0:31:1:1:0:34:4:1:0:4 -10 42365604 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATTCCCTTCCATTCCATTC;RSEQ=GTTGCATTGCAATCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:0:32:0:1:0:44.5:4:1:0:5 0/0:2:0:0,0:1,1:0:2,0:1:0:32.5:1:1:0:34:4:1:0:4 -10 42365608 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTCCATTCCATTCCGTT;RSEQ=CATTGCAATCGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:0:31.5:1:1:0:44.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42365631 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAATCGGGTTGATTCCA;RSEQ=TCCATTCCATTACATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:0:32:1:1:0:44.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42365635 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCGGGTTGATTCCAATCC;RSEQ=TTCCATTACATCCCAGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5:0:32.5:1:1:0:44.5:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42365779 . CT GG 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCTTTCCATTCCATTC;RSEQ=TTAGTTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:30.5:1:1:0:20:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:15:0:30.3:1:1:0:49:4:1:0:3.5 -10 42365810 . AT TC 28 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCATTCCATTCCACTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:1:30.7:1:1:0:20:4:1:0.5:3 1/1:2:2:1,1:0,0:1:0,2:18:1:28.8:1:1:0:49:4:1:0:2.5 -10 42365980 . A T 30 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.16667;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCTTTCCAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:28:1:31.4:1:1:0:33.2:10:1:0:1.6 1/0:4:2:1,1:1,1:0.5:2,2:39:0:30.5:1:1:1:22:4:0.5:0:6.5 -10 42365986 . T G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.16667;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCTTTCCAGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:26.8:1:31.4:1:1:0:33.2:10:1:0:1.6 1/0:4:2:1,1:1,1:0.5:2,2:29:0:33.5:1:1:1:32:4:0.5:0:3.5 -10 42365990 . T A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCAGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,3:0:2,0:22.8:1:30.8:1:1:0:34:8:1:0:1.8 1/0:4:2:1,1:1,1:0.5:2,2:37.5:1:28.5:1:1:1:22:4:0.5:0:6.5 -10 42365993 . C A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CAGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:20.2:1:31.4:1:1:0:33.2:10:1:0:1.6 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:27:1:1:1:22:4:0.5:0:6.5 -10 42365996 . GTTGATTCCA TTCCT 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=TTCCATTCCATTCCTTTCCA;RSEQ=TTCCATTCCATTGCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:1:1:29.5:1:1:1.73:33:4:0.3888:0.4444:1 1/0:4:2:1,1:1,1:0.5:2,2:20:0:32.3:1:1:1:32:4:0.5:0:2.5 -10 42365997 . T A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TCCATTCCATTCCTTTCCAG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:27:1:31:1:1:0:33.3:6:1:0:2 1/0:4:2:1,1:0,0:0.5:0,2:30.5:1:27.5:1:1:0:22:4:1:0:6.5 -10 42366013 . C G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=CCAGTTGATTCCATTCCATT;RSEQ=CATTGCATTCCTTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:11:1:31:1:1:0:33.3:6:1:0:2 1/0:4:2:1,1:1,1:0.5:2,2:14.5:1:29.5:1:1:1:22:4:0.5:0:6.5 -10 42366018 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCTTTCCATTCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:10.5:1:33.5:1:1:0:35:4:1:0:2.5 1/0:4:2:1,1:0,0:0.5:0,2:9.5:1:30.5:1:1:0:22:4:0.5:0:6.5 -10 42366321 . C A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TGACGTTACATTTCATTCCA;RSEQ=TCGAGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:22.7:1:30.7:1:1:0:32.3:6:1:0:3.7 0/1:6:2:1,1:2,2:0.3333:2,2:9:0:32:0:1:1:26:4:0.3333:0:3 -10 42366338 . C T 28 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=0.10714;SOR=0;LSEQ=CCACTCGAGTTGATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18.5:1:28.5:1:1:0:36:4:0.6667:0:4.5 0/0:5:0:0,0:2,3:0:2,0:32.4:1:32:1:1:0:35.4:10:1:0:1.6 -10 42366348 . C G 33 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0.44721;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:23:0:34:0:1:0:36:2:0.5:0:3 0/1:7:2:1,1:2,3:0.2857:2,2:23:0:33:1:1:1.41:44.5:4:0.2857:0:1 -10 42366350 . A G 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25:1:32:1:1:0:30.5:4:1:0:2.5 0/1:7:2:1,1:2,3:0.2857:2,2:7.5:1:31.5:1:1:1.41:31:4:0.2857:0:5 -10 42366364 . C A 29 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:11:1:24:1:1:0:30.5:1:1:0:2.5 0/1:7:2:1,1:2,3:0.2857:2,2:12:0:29.5:1:1:1.41:26:4:0.2857:0:3 -10 42366374 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCGTGTTTATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:5:0:14:0:1:0:25:0:0:0:2 0/1:5:2:1,1:1,2:0.4:2,2:31.5:1:30:1:1:1.73:31:4:0.4:0:5 -10 42366378 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=GTGTTTATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:1:0:33:0:1:0:25:2:1:0:2 1/0:3:2:1,1:0,1:0.6667:0,2:34.5:1:29.5:1:1:0:31:4:0.6667:0:5 -10 42366380 . T G 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCG;RSEQ=GTTTATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:34:0:30:1:1:0:31:4:0.6667:0:5 -10 42366384 . T A 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCGTGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:30:0:29:1:1:0:31:4:0.6667:0:5 -10 42366405 . AT CC 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTGTTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:21:0:32.8:1:1:1:41.5:4:0.5:0:3.5 -10 42366408 . C G 34 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGTTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:23:0:34:0:1:1:41.5:4:0.5:0:3.5 -10 42366411 . C G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGTTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:26:0:32.5:1:1:1:41.5:4:0.5:0:3.5 -10 42366668 . C T 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCTTTTCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:31.5:1:1:0:40:4:1:0:4.5 -10 42366673 . C T 47 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:14.3:1:30:1:1:0:42.7:6:1:0:5 -10 42366680 . A T 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCACTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:27:0:32:0:1:1.7321:40:4:0.4:0:4.5 -10 42366716 . C A 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTGTTTATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:0,0:0.8:0,2:30.5:1:30:1:1:0:44:8:0.8:0:5 -10 42366737 . GG TT 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CATTCAATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:26:0:31.8:1:1:0:48:4:0.6667:0:4.5 -10 42366744 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATGGCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:20:0:33:1:1:0:48:4:0.6667:0:4.5 -10 42366814 . C CGGATG 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.1;SOR=0;LSEQ=CATTCCATTGCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:29.1:1:1:0:30:4:1:0:8 0/0:3:0:0,0:0,2:0:0,0:15.5:1:34:0:1:0:31.5:4:0.6667:0:6 -10 42366828 . C G 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.4;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCTTTCCATTACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:1:31.5:1:1:0:30:4:1:0:8 0/1:3:1:0,1:0,2:0.3333:0,0:15:0:34:0:1:0:25:2:0.3333:0:8 -10 42366850 . TT CC 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=ATTCCTTTCCATTACATTCC;RSEQ=TCCACTCGAGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:1:31.5:1:1:0:30:4:1:0:7 0/0:3:0:0,0:0,1:0:0,0:30:0:32:0:1:0:40:2:0.3333:0:4 -10 42366853 . C G 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CCTTTCCATTACATTCCTTT;RSEQ=CACTCGAGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:33:1:1:0:30:4:1:0:7 0/1:3:1:0,1:0,2:0.3333:0,0:40:0:34:0:1:0:25:2:0.3333:0:7 -10 42378258 . G C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCCAGTCCTTTCCATTCCA;RSEQ=TACATTCCACTCGGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:24.5:1:33:0:1:0:48.5:4:1:0:4 -10 42378276 . T G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAGTACATTCCACTCGGTTT;RSEQ=TTTCCATTACATTGAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:42:1:33.5:1:1:0:48.5:4:1:0:4 -10 42378356 . T C 38 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCACTCGGGTTGTTTC;RSEQ=TTTCCATTACATTCCATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:23.3:1:24:1:1:0:40:2:1:0:7 -10 42378365 . A C 46 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGTTGTTTCTTTTCCATT;RSEQ=CATTCCATTAGTATCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:26.3:1:29.3:1:1:0:40:6:1:0:7 -10 42378378 . A T 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTACATTCCATTAGT;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:23:0:28:1:1:0:40:4:0.6667:0:8 -10 42378440 . C T 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTACACTGAGGTTGATTC;RSEQ=GTTCGATTCCATTCCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:32.5:1:31:1:1:0:60:4:0.6667:0:5.5 -10 42378445 . G A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGAGGTTGATTCCGTTC;RSEQ=ATTCCATTCCAATCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:30.5:1:1:0:60:4:0.6667:0:5.5 -10 42378465 . C A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCCATTCCAATCCATTC;RSEQ=ATTCTATTCCATTCTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38.5:1:29:1:1:0:60:4:1:0:5.5 -10 42378470 . T C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCAATCCATTCCATTC;RSEQ=ATTCCATTCTAGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35:1:29.5:1:1:0:60:4:1:0:5.5 -10 42378492 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCTAGTTGATTCCA;RSEQ=TGCATTCCATGCCGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:1:31.5:1:1:0:60:4:1:0:5.5 -10 42378531 . AA GC 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCATTCCAGTCGGGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:14:0:31:0:1:0:24:2:1:0:7 0/1:5:2:1,1:1,2:0.4:2,2:18.5:1:30.5:1:1:1.73:60:4:0.4:0:2.5 -10 42378532 . A T 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCAGTCGGGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:15:0:32:0:1:0:24:2:1:0:7 1/0:5:3:1,2:0,0:0.6:0,2:15.7:1:27.3:1:1:0:25.7:6:1:0:7.3 -10 42378540 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCAATCCATTC;RSEQ=AGTCGGGATGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:23:0:32:0:1:0:24:2:1:0:7 0/1:5:2:1,1:1,2:0.4:2,2:30:1:28.5:1:1:1.73:21:4:0.4:0:7 -10 42378542 . G T 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCAATCCATTCCA;RSEQ=TCGGGATGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:25:0:33:0:1:0:24:2:1:0:7 1/1:5:5:2,3:0,0:1:0,2:26.8:1:28.4:1:1:0:39.4:10:1:0:5.4 -10 42378548 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TCCAATCCATTCCAGTCGGG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:16.5:1:30:1:1:0:24:4:1:0:6.5 0/1:5:2:1,1:1,2:0.4:2,2:38:1:29.5:1:1:1.73:21:4:0.4:0:7 -10 42378550 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAATCCATTCCAGTCGGGAT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:18.5:1:30.5:1:1:0:24:4:1:0:6.5 0/1:7:2:1,1:2,3:0.2857:2,2:40:1:28:1:1:1.41:21:4:0.2857:0:7 -10 42378560 . C G 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CAGTCGGGATGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:22.3:1:32.7:1:1:0:24:6:1:0:6.3 0/1:14:2:1,1:6,5:0.1429:2,2:11:0:28:1:1:1.18321:41:4:0.1429:0:3 -10 42378562 . T A 27 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GTCGGGATGATTCCATTCCA;RSEQ=TCCATTCCATTCCATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:24.3:1:31.7:1:1:0:24:6:1:0:6.3 0/1:17:2:1,1:7,8:0.1176:2,2:13:0:27.5:1:1:1.13:41:4:0.125:0:3 -10 42378564 . C A 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.01579;SOR=0;LSEQ=CGGGATGATTCCATTCCATT;RSEQ=CATTCCATTCCATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:32.5:1:29.5:1:1:0:24:4:0.6667:0:6.5 0/0:17:0:0,0:8,8:0:2,0:17.2:1:31.3:1:1:0:39.3:32:0.9412:0:3.9 -10 42378571 . A G 30 d7;v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.04561;SOR=0.04609;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTGCATTCCACTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:36:1:30.5:1:1:0:24:4:0.6667:0:6.5 0/1:17:1:0,1:8,8:0.0588:2,0:42:0:29:0:1:0:35:2:0.0588:0:8 -10 42378574 . C A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTGCATTCCACTCGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:24.8:1:30.8:1:1:0:24:8:1:0:6 0/1:17:2:1,1:7,8:0.1176:2,2:24:0:28.5:1:1:1.13:60:4:0.1176:0:5 -10 42378575 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTGCATTCCACTCGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:25.3:1:31.5:1:1:0:24:8:1:0:6 0/1:17:2:1,1:7,8:0.1176:2,2:18:1:28:1:1:1.13:45:4:0.1176:0:5.5 -10 42378579 . G C 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8939;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGAGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:18.5:1:32:1:1:0:24:4:0.5:0:5.5 0/1:17:8:4,4:4,4:0.4706:2,2:29.1:1:32.1:1:1:1:32:16:0.5:0:3.9 -10 42378580 . C G 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTG;RSEQ=ATTCCACTCGAGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27.8:1:32.8:1:1:0:24:8:1:0:6 0/1:17:2:1,1:7,8:0.1176:2,2:20:0:31:1:1:1.13:21:4:0.125:0:3 -10 42378584 . CC GA 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=CCATTCCATTCCATTGCATT;RSEQ=ACTCGAGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:24.5:1:31.8:1:1:0:24:4:0.5:0:4.5 0/0:17:0:0,0:5,5:0:2,0:25.2:1:31.6:1:1:0:37.8:20:0.5882:0:4.1 -10 42378587 . C A 100 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.40412;LSEQ=TTCCATTCCATTGCATTCCA;RSEQ=TCGAGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:26.5:1:31:1:1:1:24:4:0.5:0:4.5 1/0:17:10:5,5:3,4:0.5882:2,2:31.7:1:30.4:1:1:1.31:33.6:20:0.5882:0:4.1 -10 42378591 . A C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27219;SOR=0.27316;LSEQ=ATTCCATTGCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:36:1:30:1:1:1:24:4:0.5:0:6.5 0/1:15:3:1,2:6,6:0.2:2,2:34:1:30.3:1:1:1.91151:41.7:6:0.2:0:6.3 -10 42378593 . T A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTGCATTCCACTCGAG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:33.5:1:29.8:1:1:0:24:8:1:0:5.5 0/1:15:2:1,1:6,7:0.1333:2,2:36:1:28.5:1:1:1.15:45:4:0.1429:0:5.5 -10 42378600 . C A 29 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCACTCGAGTTGATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:30.5:1:30.5:1:1:0:24:8:1:0:5.5 0/1:15:2:1,1:6,7:0.1333:2,2:43:1:29.5:1:1:1.15:45:4:0.1333:0:5.5 -10 42378604 . C A 29 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCACTCGAGTTGATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:28.5:1:30.3:1:1:0:24:8:1:0:5.5 0/1:14:2:1,1:5,7:0.1429:2,2:43:0:29:1:1:1.37:45:4:0.1429:0:5.5 -10 42378609 . C CTAGTA 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CGAGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:24.5:1:30.3:1:1:0:24:8:1:0:5.5 0/1:14:2:1,1:5,7:0.1429:2,2:37:0:30.2:1:1:1.37:45:4:0.1429:0:5.5 -10 42378611 . A G 28 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=AGTTGATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22.5:1:30:1:1:0:24:8:1:0:5.5 0/1:14:2:1,1:5,7:0.1429:2,2:16.5:1:28:1:1:1.37:60:4:0.1429:0:5 -10 42378627 . T G 30 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTTCATTCCTTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:13.3:1:29.7:1:1:0:24:6:1:0:5 0/1:8:2:1,1:2,3:0.25:2,2:5:0:30:1:1:1.41:44:4:0.25:0:3 -10 42378634 . T A 27 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCTTTCCAGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:5.5:1:27:1:1:0:24:4:0.6667:0:4.5 0/0:2:0:0,0:1,1:0:2,0:8:0:31.5:1:1:0:45:4:1:0:5.5 -10 42378889 . A C 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCCATTCCATACCATTG;RSEQ=ATTCCATTGCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:29.5:1:33.5:1:1:0:41.5:4:1:0:5 1/1:1:1:1,0:0,0:1:0,0:36:0:34:0:1:0:31:2:1:0:4 -10 42378898 . G C 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CCATACCATTGAATTCCATT;RSEQ=CATTCCATTCCTTTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:25:1:29.5:1:1:0:48:4:0.6667:0:7 0/0:2:0:0,0:1,1:0:2,0:14.5:1:31.5:1:1:0:31:4:1:0:6 -10 42378902 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ACCATTGAATTCCATTGCAT;RSEQ=CCATTCCTTTCCTTTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:25:1:30.5:1:1:1:48:4:0.5:0:7 0/0:2:0:0,0:1,1:0:2,0:14.5:1:27.5:1:1:0:31:4:1:0:6 -10 42378909 . C A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=AATTCCATTGCATTCCATTC;RSEQ=TTTCCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23.5:1:28.5:1:1:0:44.8:8:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:14.5:1:27:1:1:0:31:4:1:0:6 -10 42378914 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CATTGCATTCCATTCCTTTC;RSEQ=TTTCCATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:25:0:29.5:1:1:1:48:4:0.5:0:7 0/0:2:0:0,0:1,1:0:2,0:14.5:1:29.5:1:1:0:31:4:1:0:6 -10 42378940 . T A 48 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCTTTCCATTCC;RSEQ=TTCCTTTCCACTCGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:41.7:1:30.3:1:1:0:46.3:6:1:0:5.3 1/1:1:1:0,1:0,0:1:0,0:44:0:27:0:1:0:31:2:1:0:8 -10 42378955 . A C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATTCCTTTCCTTTCCACTCG;RSEQ=GTTGATTCCATTCCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:33.7:1:31.3:1:1:0:46.3:6:1:0:5.3 1/0:3:2:1,1:0,1:0.6667:0,2:5.5:1:30.5:1:1:0:30:4:0.6667:0:2.5 -10 42378960 . A T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTTCCTTTCCACTCGAGTTG;RSEQ=TTCCATTCCATTCAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:28:1:31.5:1:1:0:41.5:4:0.6667:0:4 0/0:3:0:0,0:1,2:0:2,0:19.3:1:30:1:1:0:30.3:6:1:0:4.3 -10 42378974 . A T 47 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GAGTTGATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:14.7:1:29.7:1:1:0:46.3:6:1:0:5.3 0/1:3:1:0,1:1,1:0.3333:2,0:23:0:30:0:1:0:31:2:0.3333:0:8 -10 42378990 . AT A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCAATTCCATTCCATTCC;RSEQ=TCCATTCCCTTCCGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:10:0:31:0:1:0:40:2:1:0:4 1/0:3:2:1,1:0,1:0.6667:0,2:16:0:32:0:1:0:30:4:0.6667:0:2.5 -10 42379000 . C G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCGTTCCATTTGATACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:32:0:1:0:30:4:1:0:2.5 -10 42379132 . C T 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:28.5:1:1:0:33:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379153 . TG GT 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCTAGT;RSEQ=ATTCCATTGCATTCCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:1:28:1:1:0:33:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379158 . C T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCTAGTTGATT;RSEQ=CATTGCATTCCATGCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:1:30.5:1:1:0:33:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379173 . C T 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCCATTGCATTCCATG;RSEQ=CGTTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42.5:1:29.5:1:1:0:33:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379175 . G A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTGCATTCCATGCC;RSEQ=TTCCATTCCATTCCACTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:31.5:1:1:0:33:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379183 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCATTCCATGCCGTTCCATT;RSEQ=CATTCCACTCTATTCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31.5:1:1:0:33:4:1:0:6.5 0/0:2:0:0,0:1,0:0:0,0:4:0:32:0:1:0:25:2:1:0:5 -10 42379248 . C G 53 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CCTTGCATTCCACTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:20.3:1:33.7:1:1:0:27:6:0.75:0:1.3 -10 42379443 . G C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CATTCCTGTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42.5:1:31:1:1:0:24.5:4:1:0:6 -10 42379729 . T C 50 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATGTTGATTCCATTCCATAA;RSEQ=ATTGCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:20.3:1:31.7:1:1:0:44.7:6:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379731 . T C 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGATTCCATTCCATAATA;RSEQ=TGCATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:14.5:1:30.5:1:1:0:47:4:0.6667:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379778 . T C 48 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CATCCCATTCCTTTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:31.7:1:30.3:1:1:0:44.7:6:1:0:5 0/0:1:0:0,0:1,0:0:0,0:2:0:32:0:1:0:22:2:1:0:2 -10 42379782 . C T 46 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCTTTTCAT;RSEQ=CCATTCCTTTCCACTCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:27.7:1:29.3:1:1:0:44.7:6:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379801 . C G 34 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCATTCCTTTCCACTCGA;RSEQ=TTGATTCCATTCCATTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:34:0:1:0:47:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42379879 . T G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCGTGTTTATTTCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:9:0:32.5:1:1:0:48:4:0.6667:0:5 -10 42379892 . T TCCATTCCGGATGATTCCATTCCATTGAATTCCGTC 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCATTCTATTCCATTCCAT;RSEQ=CCATTCCATTCCCTTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:8:1:30.3:1:1:0:45.3:8:1:0:3.5 0/1:24:2:1,1:11,11:0.0833:2,2:45.5:1:29.7:1:1:1:21:4:0.0833:0.0833:1 -10 42379896 . T C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCTATTCCATTCCATTCCA;RSEQ=TCCATTCCCTTGCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:12:1:30.5:1:1:0:45.3:8:1:0:3.5 0/1:24:2:1,1:11,11:0.0833:2,2:16:0:33.5:1:1:1:53:4:0.0833:0:3.5 -10 42379898 . C T 28 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.01587;SOR=0;LSEQ=CTATTCCATTCCATTCCATT;RSEQ=CATTCCCTTGCACTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:15:0:28:1:1:1:47.5:4:0.5:0:6 0/0:24:0:0,0:10,10:0:2,0:14.4:1:32.5:1:1:0:43.6:40:0.8333:0:3.2 -10 42379899 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TATTCCATTCCATTCCATTC;RSEQ=ATTCCCTTGCACTCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15:1:31.8:1:1:0:45.3:8:1:0:3.5 0/1:24:2:1,1:11,11:0.0833:2,2:9:0:32:0:1:1:26:4:0.0833:0:4.5 -10 42379900 . A T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCCTTGCACTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:16:1:30.5:1:1:0:45.3:8:1:0:3.5 0/1:24:2:1,1:11,11:0.0833:2,2:12.5:1:30.5:1:1:1:47:4:0.0833:0:2.5 -10 42379906 . T C 140 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCC;RSEQ=TGCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:22:1:32:1:1:0:45.3:8:1:0:3.5 1/1:24:20:10,10:1,1:0.8333:2,2:22.4:1:32.5:1:1:1:43.1:40:0.8333:0:3.3 -10 42379909 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08562;SOR=0.10546;LSEQ=CATTCCATTCCATTCCCTTG;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:26:0:26.5:1:1:1:47.5:4:0.5:0:6 0/1:24:2:1,1:11,11:0.0833:2,2:28:0:31:1:1:1:34:4:0.0833:0:3.5 -10 42379915 . G C 83 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54872;SOR=Inf;LSEQ=ATTCCATTCCCTTGCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23.5:1:31.8:1:1:0:45.3:8:1:0:3.5 0/1:24:6:3,3:9,9:0.25:2,2:25.7:1:32.3:1:1:1:43.5:12:0.25:0:3.3 -10 42379929 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CACTCGGGTTGATTCCATTC;RSEQ=ATTCCATTCCATTCCGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:16.5:1:32.3:1:1:0:45.3:8:1:0:3.5 0/1:22:2:1,1:10,10:0.0909:2,2:7:0:29:1:1:1:48:4:0.0909:0:5 -10 42379935 . AT CC 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGTTGATTCCATTCCATTCC;RSEQ=TCCATTCCGCTCCATTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28:1:31:1:1:0:47.5:4:1:0:6 0/1:20:2:1,1:9,9:0.1:2,2:5:1:29.4:1:1:1:52.5:4:0.1:0.05:1.5 -10 42379936 . T C 84 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GTTGATTCCATTCCATTCCA;RSEQ=TCCATTCCGCTCCATTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:30.5:1:1:0:47.5:4:1:0:6 0/1:17:6:3,3:5,5:0.3529:2,2:10.8:1:32.5:1:1:1:39.5:12:0.375:0:3.3 -10 42379946 . C T 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCG;RSEQ=TCCATTCGGTTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:35:0:33:0:1:0:55:2:1:0:8 1/1:4:4:2,2:0,0:1:0,2:5.8:1:30.3:1:1:0:36.3:8:1:0:4 -10 42380124 . C CTTTCCATTCCATTCTGGATG 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.4;SOR=0;LSEQ=CATGCCATTTCATTCCATTC;RSEQ=ATTCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:24.5:1:31.7:1:1:0:50:4:0.6667:0.6667:2 0/0:2:0:0,0:1,1:0:2,0:12:0:32:0:1:0:52:4:1:0:6.5 -10 42380128 . C A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.06667;SOR=Inf;LSEQ=CCATTTCATTCCATTCCATT;RSEQ=CATTCCATTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:9.8:1:31.5:1:1:0:36.5:8:1:0:2.5 1/1:2:2:1,1:0,0:1:0,2:16:0:28.5:1:1:0:52:4:1:0:6.5 -10 42380160 . A C 49 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=CTCCACTCTGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:31:0:31.3:1:1:0:42:6:1:0:2.3 1/0:4:2:1,1:1,1:0.5:2,2:33.5:1:30.5:1:1:1:52:4:0.5:0:6.5 -10 42380161 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCTGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:30:0:32:1:1:0:42:6:1:0:2.3 1/0:4:2:1,1:1,1:0.5:2,2:21.5:1:28.5:1:1:1:50:4:0.5:0:4 -10 42380163 . C G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55247;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=CACTCTGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:28:0:31.5:1:1:0:50:4:0.6667:0:2 1/0:4:2:1,1:1,1:0.5:2,2:30.5:1:32:1:1:1:52:4:0.5:0:6.5 -10 42380169 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CATTCCATTCCACTCCACTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:22:0:30.7:1:1:0:42:6:1:0:2.3 1/0:4:2:1,1:1,1:0.5:2,2:24.5:1:29.5:1:1:1:52:4:0.5:0:6.5 -10 42380191 . TTCTATACAATTACATTGCACTCGAATTGATTCCATTCTAT C 29 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=17;MSI=10.000;MSILEN=5;SSF=0.06667;SOR=0;LSEQ=GTTGATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:49.5:1:29.6:1:1:0:50:4:1:1:2 0/0:4:0:0,0:2,2:0:2,0:24.5:1:28.3:1:1:0:51:8:1:0:5.3 -10 42380199 . A C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCTATAC;RSEQ=ATTACATTGCACTCGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:1:30:1:1:0:50:4:1:0:4 -10 42380218 . T TGATTCCATTCTATTCCATTCCATTCCAGGATGATTCCATTCCATTCCGTTCCATTCTGGTA 106 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00275;SOR=Inf;LSEQ=CAATTACATTGCACTCGAAT;RSEQ=GATTCCATTCTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,0:0:0,0:3:0:29:0:1:0:43:2:1:0:3 1/1:8:11:4,7:0,0:1:0,2:13.9:1:30.7:1:1:0:42.6:22:1:1:2 -10 42380229 . T C 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55122;SOR=1.69571;LSEQ=CACTCGAATTGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:3,4:3,3:0.4118:2,2:6.1:1:32.9:1:1:1.30401:51.1:14:0.5385:0.1176:3.1 1/0:33:18:11,7:4,10:0.5455:2,2:8.1:1:30.8:1:0.08697:3.75:40.7:36:0.5455:0.0303:3.7 -10 42380233 . C G 30 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=5;SSF=0.59109;SOR=0.44879;LSEQ=CGAATTGATTCCATTCTATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:40,45:0.023:2,2:9:0:33.5:1:1:1.12:58.5:4:0.0235:0:6.5 0/1:192:2:1,1:81,107:0.0104:2,2:6.5:1:30.5:1:1:1.32:37:4:0.0104:0:4 -10 42380234 . C CGGATG 28 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GAATTGATTCCATTCTATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:43,47:0:2,0:5.2:1:31.9:1:1:0:41.3:180:1:0.0222:3.2 0/1:196:2:1,1:80,109:0.0102:2,2:15:0:28.9:1:1:1.36:39:4:0.0103:0:5 -10 42380236 . T C 45 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.64225;SOR=0.65316;LSEQ=ATTGATTCCATTCTATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:42,47:0.0217:2,2:6:0:33.5:1:1:1.12:37.5:4:0.0222:0:6.5 0/1:210:3:1,2:88,115:0.0143:2,2:17:1:28.7:1:1:1.5274:42.3:6:0.0145:0:6.3 -10 42380237 . T A 30 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.58771;SOR=0.4326;LSEQ=TTGATTCCATTCTATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:44,47:0.0215:2,2:7:0:30.5:1:1:1.07:41:4:0.0215:0:4 0/0:213:2:1,1:91,118:0.0094:2,2:12.5:1:30:0:1:1.30:31.5:4:0.0095:0:3.5 -10 42380238 . C T 58 pSTD;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.00815;SOR=0;LSEQ=TGATTCCATTCTATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:4:2,2:42,43:0.043:2,2:8:0:29:1:1:1.02:49:8:0.043:0:3.3 0/0:213:0:0,0:84,112:0:2,0:8.8:1:31.2:1:1:0:40.1:392:0.9289:0.0094:2.6 -10 42380240 . A C 30 v4;NM4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.58942;SOR=0.44054;LSEQ=ATTCCATTCTATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:44,47:0.0208:2,2:11.5:1:30:1:1:1.07:31:4:0.0208:0:7.5 0/0:216:2:1,1:88,117:0.0093:2,2:10:0:30.5:1:1:1.33:60:4:0.0094:0:2 -10 42380243 . C G 116 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.60817;SOR=0.73779;LSEQ=CCATTCTATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:7:2,5:44,43:0.0729:2,2:13.9:1:31.6:1:0.43569:2.53401:33.7:14:0.0729:0:6.4 0/1:219:12:5,7:89,115:0.0548:2,2:14:0:32.6:1:1:1.0831:36.6:24:0.0548:0:4 -10 42380244 . C T 62 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.317;SOR=Inf;LSEQ=CATTCTATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:47,50:0:2,0:14.2:1:32:1:1:0:41.2:96:1:0:3.1 0/1:220:4:3,1:92,122:0.0182:2,2:14.5:1:31:1:0.31995:3.95:27.3:8:0.0183:0:3.8 -10 42380245 . A G 44 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.6438;SOR=0.65846;LSEQ=ATTCTATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:46,50:0.0204:2,2:15:0:32:1:1:1.09:37.5:4:0.0208:0:6.5 0/1:222:3:1,2:94,122:0.0135:2,2:26:1:28:1:1:1.53807:42.3:6:0.0136:0:6.3 -10 42380248 . C A 59 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.88324;LSEQ=CTATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:47,50:0.02:2,2:19.5:1:28:1:1:1.06:31:4:0.0202:0:7 0/1:226:4:1,3:96,124:0.0177:2,2:18.5:1:29.5:1:0.63519:2.31467:41.3:8:0.0178:0:3.8 -10 42380250 . A G 50 v4;NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.02826;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:3:1,2:46,48:0.03:2,2:20.7:1:32:1:1:1.90433:36.7:6:0.0306:0:4.7 0/0:226:0:0,0:94,124:0:2,0:20.1:1:30.1:1:1:0:40.1:71.667:0.9641:0:2.7 -10 42380253 . C T 90 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.97744;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:4:3,1:44,51:0.04:2,2:23:0:31.5:1:0.34329:3.44:46.8:8:0.0408:0:3.5 0/1:230:9:3,6:97,122:0.0391:2,2:20.9:1:28.4:1:0.73469:1.58705:45.6:18:0.0398:0:2.7 -10 42380254 . C G 112 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.29151;SOR=2.09166;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTGCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:3:1,2:46,50:0.03:2,2:25.3:1:31:1:1:1.82914:34:6:0.0303:0:6 0/1:230:14:7,7:93,122:0.0609:2,2:24.5:1:29.6:1:0.78216:1.31:35.3:13:0.058:0:4.1 -10 42380255 . AT TC 154 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.08151;SOR=0.58174;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCATTCCATTGCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:23:13,10:35,41:0.23:2,2:26.1:1:31.9:1:0.47665:1.52:43.1:46:0.2396:0:2.4 0/1:230:34:16,18:80,108:0.1478:2,2:25.4:1:30.4:1:0.7077:1.20:38.4:68:0.1504:0:2.2 -10 42380256 . T C 212 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.54991;SOR=0.86367;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTGCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:48:23,25:11,16:0.48:2,2:24.3:1:32.8:1:0.6323:1.33:43.2:96:0.6234:0:2.5 0/1:230:102:39,63:42,45:0.4435:2,2:24.1:1:31.9:1:0.18586:1.50435:40:101:0.526:0:2.2 -10 42380258 . C A 57 NM4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.07106;SOR=0.21166;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTGCACTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:4:1,3:45,48:0.04:2,2:29.3:1:28.8:1:0.61914:2.78548:34:8:0.04:0:7.3 0/0:230:2:2,0:95,126:0.0087:2,0:7:0:26.5:1:0.1881:0:36:4:0.0087:0:3 -10 42380259 . C T 65 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=5;SSF=0.32779;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTGCACTCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:48,52:0:2,0:28.1:1:31.7:1:1:0:41:32.333:1:0:2.9 0/1:230:5:2,3:98,126:0.0217:2,2:27.2:1:28.2:1:1:1.16588:42.2:10:0.0219:0:2.8 -10 42380260 . A T 51 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.31883;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTGCACTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:48,52:0:2,0:28.7:1:30.3:1:1:0:41:24:1:0:2.9 0/1:230:4:2,2:98,128:0.0174:2,2:30.5:1:25.8:1:1:1.30:44.5:3:0.0133:0:4 -10 42380262 . T G 50 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.29595;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTGCACTCGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:1,0:47,52:0.01:2,0:22:0:28:0:0.48:0:40:2:0.0103:0:4 0/1:232:3:2,1:99,130:0.0129:2,2:39:1:32:1:0.58137:2.62:42.7:6:0.013:0:4.3 -10 42380264 . C A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.21676;SOR=0.21325;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTGCACTCGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:46,50:0.02:2,2:26.5:1:30:1:1:1.09:60:4:0.0206:0:3 0/0:232:1:1,0:94,122:0.0043:2,0:26:0:26:0:0.43779:0:20:2:0.0043:0:3 -10 42380265 . AT CC 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.41497;SOR=0.59946;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TGCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:7:2,5:45,47:0.07:2,2:36.9:1:31.8:1:0.44034:2.3738:33.7:14:0.0714:0:5.4 0/1:232:10:4,6:96,124:0.0431:2,2:26.8:1:32.2:1:1:1.16054:36.3:20:0.0439:0:2.9 -10 42380268 . G C 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85261;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:46,51:0.02:2,2:23:1:29:1:1:1.11:32:4:0.0206:0:2.5 0/1:234:4:3,1:99,131:0.0171:2,2:27.5:1:30:1:0.32031:3.95:30.5:8:0.0176:0:4.3 -10 42380269 . C T 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06965;LSEQ=CATTCCATTCCATTCCATTG;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:46,51:0.02:2,2:38:1:29:1:1:1.11:31:4:0.0204:0:5.5 0/1:234:5:2,3:99,128:0.0214:2,2:38.8:1:28.2:1:1:1.15941:38.4:10:0.0216:0:5 -10 42380271 . C A 108 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24534;SOR=2.61552;LSEQ=TTCCATTCCATTCCATTGCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:46,49:0.0202:2,2:35:1:32:0:1:1.06:25.5:4:0.0211:0:3 0/1:234:12:5,7:93,121:0.0513:2,2:32.7:1:30.3:1:1:1.07571:42.5:24:0.0517:0:3 -10 42380272 . T A 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72911;SOR=1.71434;LSEQ=TCCATTCCATTCCATTGCAC;RSEQ=CGGGTTGATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:46,51:0.0202:2,2:36:0:30.5:1:1:1.11:30:4:0.0206:0:2 0/1:234:8:4,4:98,128:0.0342:2,2:31.1:1:28.6:1:0.73115:1.30:47.1:7:0.0303:0:2.9 -10 42380275 . G A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94018;LSEQ=ATTCCATTCCATTGCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:5:2,3:45,47:0.0505:2,2:34.6:1:29.4:1:1:1.43088:33.6:4:0.0417:0:2.6 0/1:231:11:5,6:93,122:0.0476:2,2:29.5:1:30.8:1:1:1.09:43.8:22:0.0482:0:2.9 -10 42380277 . T A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09063;SOR=0;LSEQ=TCCATTCCATTGCACTCGGG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:47,51:0.02:2,2:35:1:32.5:1:1:1.08:33.5:4:0.0202:0:4 0/0:231:0:0,0:98,130:0:2,0:22.7:1:30:1:1:0:40.1:456:0.9956:0:2.5 -10 42380279 . G T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39014;SOR=1.65301;LSEQ=CATTCCATTGCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:6:3,3:41,43:0.0606:2,2:20:1:29.7:1:1:1.05:44.3:12:0.0625:0:3 0/1:228:22:8,14:83,110:0.0965:2,2:19.5:1:28.3:1:0.6516:1.31878:40.2:21:0.0938:0:3 -10 42380281 . T A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55703;SOR=Inf;LSEQ=TTCCATTGCACTCGGGTTGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:46,50:0:2,0:21.1:1:30.6:1:1:0:41.4:192:1:0:2.8 0/1:225:3:1,2:93,126:0.0133:2,2:12.7:1:28.7:1:1:1.4737:32.7:6:0.0135:0:3 -10 42380283 . C G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.20967;SOR=0.20745;LSEQ=CCATTGCACTCGGGTTGATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:44,47:0.0213:2,2:30.5:1:32.5:1:1:1.07:58.5:4:0.0217:0:5.5 0/0:224:1:1,0:91,128:0.0045:2,0:16:0:26:0:0.41818:0:23:2:0.0045:0:3 -10 42380284 . C T 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.32757;SOR=Inf;LSEQ=CATTGCACTCGGGTTGATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:43,47:0:2,0:19.5:1:31.1:1:1:0:41.4:29:1:0:2.9 0/1:221:4:2,2:90,125:0.0181:2,2:24.3:1:30.3:1:1:1.39:45.5:8:0.0183:0:4.3 -10 42380286 . T A 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.20973;SOR=0.2074;LSEQ=TTGCACTCGGGTTGATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:40,46:0.0225:2,2:28:0:32:0:1:1.15:31:4:0.0225:0:6.5 0/0:212:1:1,0:83,122:0.0047:2,0:1:0:26:0:0.40777:0:39:2:0.0047:0:3 -10 42380289 . C T 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.07404;SOR=0.13202;LSEQ=CACTCGGGTTGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:2,1:34,39:0.0385:2,2:18.3:1:31.7:1:0.60057:2.27:41.3:6:0.04:0:3 0/0:192:1:0,1:78,109:0.0052:2,0:22:0:30:0:1:0:41:2:0.0053:0:5 -10 42380290 . A T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.06789;SOR=0.2594;LSEQ=ACTCGGGTTGATTCCATTCC;RSEQ=TTCCATTCCATTCCATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:6:3,3:33,36:0.0789:2,2:15.8:1:29.7:1:1:1.09:41:5:0.0685:0:3.2 0/1:185:4:2,2:74,103:0.0216:2,2:20.5:1:28.5:1:1:1.39:30.8:8:0.0217:0:4 -10 42380291 . T C 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.2;SOR=0.19923;LSEQ=CTCGGGTTGATTCCATTCCA;RSEQ=TCCATTCCATTCCATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:33,35:0.0278:2,2:12:1:29.5:1:1:1.06:25:4:0.0282:0:3 0/0:178:1:0,1:72,101:0.0056:2,0:9:0:30:0:1:0:44:2:0.0057:0:4 -10 42380292 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.08838;SOR=0;LSEQ=TCGGGTTGATTCCATTCCAT;RSEQ=CCATTCCATTCCATTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:34,36:0.0278:2,2:9.5:1:31.5:1:1:1.06:31:4:0.029:0:3.5 0/0:169:0:0,0:67,100:0:2,0:13.9:1:29.3:1:1:0:39.5:82.5:0.988:0:2.7 -10 42380293 . C G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.66644;SOR=0.80012;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:10:7,3:27,33:0.1408:2,2:13.1:1:25.6:1:0.18225:2.81:36.1:2.333:0.1029:0:3.4 0/1:164:19:8,11:56,85:0.1159:2,2:17.6:1:30.7:1:1:1.10:34.1:18:0.1118:0:3.4 -10 42380294 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGGTTGATTCCATTCCATTC;RSEQ=ATTCCATTCCATTACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:33,34:0:2,0:14.6:1:31.1:1:1:0:38:32.5:0.9848:0:3.2 0/1:163:2:1,1:63,95:0.0123:2,2:27:0:32:0:1:1.50:25:4:0.0126:0:2 -10 42380295 . A G 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.08055;SOR=0.13761;LSEQ=GGTTGATTCCATTCCATTCC;RSEQ=TTCCATTCCATTACATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:3:2,1:31,33:0.0441:2,2:44:1:32:0:0.61355:2.11:31.3:6:0.0462:0:4.7 0/0:160:1:0,1:62,92:0.0063:2,0:13:0:32:0:1:0:30:2:0.0063:0:3 -10 42380296 . T C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.58998;SOR=0.44551;LSEQ=GTTGATTCCATTCCATTCCA;RSEQ=TCCATTCCATTACATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:2,0:32,34:0.029:2,0:12.5:1:31:1:0.49254:0:28.5:4:0.029:0:5.5 0/1:153:2:1,1:61,87:0.0131:2,2:15:0:33:0:1:1.42:32.5:4:0.0132:0:4.5 -10 42380297 . T G 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTGATTCCATTCCATTCCAT;RSEQ=CCATTCCATTACATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:33,34:0:2,0:11.9:1:29.5:1:1:0:37.7:21.333:1:0:3.3 0/1:142:2:1,1:57,80:0.0141:2,2:14:0:34:0:1:1.40:46.5:4:0.0144:0:2 -10 42380298 . C A 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.29921;SOR=0.46404;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTACATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:5:2,3:31,30:0.0758:2,2:13.4:1:28.6:1:1:1.53983:42.8:10:0.0769:0:3 0/1:137:5:4,1:52,76:0.0365:2,2:4.4:1:25.8:1:0.16135:5.77:34.2:10:0.0368:0:4.2 -10 42380299 . C A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.4022;SOR=0.48997;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=ATTCCATTACATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:3:1,2:30,30:0.0469:2,2:10.7:1:30.7:1:1:1.97886:33.7:6:0.0476:0:4.7 0/1:128:3:1,2:50,74:0.0234:2,2:6.7:1:32:0:1:1.34826:38:6:0.0238:0:1.7 -10 42380300 . A ATTCCGGAAGATTCCATTCCATTGTATTCCG 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1e-05;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTACATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:10:4,6:27,25:0.1563:2,2:15.2:1:30.7:1:0.73149:1.60748:47.6:20:0.1639:0.1563:2.3 0/0:123:0:0,0:51,71:0:2,0:9.7:1:29.3:1:1:0:39.4:60:0.9917:0.0081:3 -10 42380301 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.54694;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTACATTCCACTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:29,31:0:2,0:9.1:1:29.9:1:1:0:38.6:29:0.9831:0:3.3 0/1:117:2:1,1:47,66:0.0171:2,2:14.5:1:30:1:1:1.40:35:4:0.0171:0:6.5 -10 42380304 . C G 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.30739;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTACATTCCACTCGGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:21,25:0:2,0:8:1:30.9:1:1:0:38:92:0.9583:0:3.5 0/1:103:4:1,3:39,57:0.0388:2,2:15:1:30.8:1:0.64792:2.03927:41.3:8:0.0392:0:4.5 -10 42380305 . A G 63 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.05499;SOR=0.2389;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTACATTCCACTCGGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:4,1:14,18:0.1316:2,2:10:1:27.4:1:0.17971:4.93:49:10:0.1389:0:5.4 0/1:87:3:2,1:33,51:0.0345:2,2:4.3:1:30.3:1:0.56215:3.05:49.3:6:0.0349:0:4.7 -10 42380308 . A C 105 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.02559;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGATTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:5,5:4,3:0.4348:2,2:15.2:1:31.8:1:1:1.31092:32:20:0.4545:0:4.5 0/1:55:1:1,0:8,10:0.0182:2,0:4:1:26:1:0.47368:0:40:2:0.0435:0.0182:2 -10 42380315 . ACTCGGAT GGA 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39865;SOR=0.3988;LSEQ=CATTCCATTCCATTACATTC;RSEQ=TGATTCCATTCCATTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:3,1:4,5:0.2353:2,2:22.5:1:31.1:1:0.55944:3.39:34.5:8:0.2353:0:4.8 0/1:28:3:1,2:5,14:0.1071:2,2:28:1:31.2:1:1:1.38:30:6:0.125:0:3.3 -10 42380324 . GATTCCATTCCATTAC G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTACATTCCACTCGGATT;RSEQ=ATTCCAGTCCATACCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,1:0:2,0:16.5:1:30:1:1:0:34.5:8:0.8:0:4.8 0/1:11:2:1,1:1,4:0.1818:2,2:7:1:29.7:1:1:3.16:59:4:0.2857:0.1818:4.5 -10 42380338 . A G 65 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=CGGATTGATTCCATTCCATT;RSEQ=CATTCCAGTCCATACCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:5.5:1:31.5:1:1:0:29.5:8:1:0.25:4 0/1:12:4:1,3:0,0:0.3333:0,2:8.8:1:32.5:1:1:0:29.8:8:0.6667:0:4 -10 42380346 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTACATTCCA;RSEQ=TCCATACCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:11:2:1,1:3,1:0.1818:2,2:7:0:30.5:1:1:2.44949:59:4:0.3333:0:4.5 -10 42380352 . A T 87 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTACATTCCAGTCCAT;RSEQ=CCATTCCATTCCATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:11:7:5,2:0,0:0.6364:0,2:12.7:1:31:1:1:0:47.6:14:1:0:4.4 -10 42380365 . A T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTCCATACCATTCCATTCC;RSEQ=TTCCACTCGGGTTTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:3.5:1:31.3:1:1:0:34:8:1:0:5 0/1:12:2:1,1:7,3:0.1667:2,2:8.5:1:32:0:1:2.16028:59:4:0.1667:0:4.5 -10 42380373 . C T 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60003;SOR=2.69683;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGTTTATTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:3,1:0.2:2,0:12:0:31:0:1:0:48:2:0.2:0:4 0/1:12:5:4,1:4,3:0.4167:2,2:18.4:1:31.2:1:0.57576:2.74:46:10:0.4167:0:4.4 -10 42380375 . G T 108 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07353;SOR=Inf;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTTATTCCACTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:13:1:29.7:1:1:0:48:6:0.6:0:4 1/1:12:12:8,4:0,0:1:0,2:25.4:1:30.4:1:1:0:50.2:24:1:0:4.4 -10 42380379 . T G 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07353;SOR=0;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCACTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:15:0:32:1:1:0:20:4:0.4:0:6 0/0:12:0:0,0:8,4:0:2,0:27.4:1:29.9:1:1:0:50.2:24:1:0:4.4 -10 42380383 . C T 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12281;SOR=0;LSEQ=CCATTCCACTCGGGTTTATT;RSEQ=CACTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:0.2857:2,0:19:0:32:1:1:0:20:4:0.2857:0:6 0/0:12:0:0,0:8,4:0:2,0:29.3:1:31.7:1:1:0:50.2:24:1:0:4.4 -10 42380400 . A G 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.06776;SOR=0;LSEQ=ATTCCACTCCATTCCATTCC;RSEQ=TTCCATGCCGTTACAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:5,2:0.3:2,2:14.7:1:31.7:1:0.5:4.17095:48.7:6:0.3:0:3.7 0/0:13:0:0,0:8,5:0:2,0:28.9:1:29.2:1:1:0:47.9:26:1:0:4.5 -10 42380405 . ATGCCG A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=5;SSF=0.5;SOR=Inf;LSEQ=ACTCCATTCCATTCCATTCC;RSEQ=TTACAGTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:31.1:1:31.1:1:1:0:44.6:20:1:0:4.5 0/1:15:2:1,1:8,5:0.1333:2,2:49.5:1:30.5:1:1:1.54914:59:4:0.1333:0:4.5 -10 42380408 . CC TT 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATG;RSEQ=GTTACAGTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,4:0:2,0:30.3:1:32.9:1:1:0:50.8:16:0.8889:0:4.1 0/1:15:2:1,1:7,4:0.1333:2,2:8:1:31.5:0:1:1.67325:42:4:0.1538:0:6 -10 42380410 . G T 62 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0166;SOR=0;LSEQ=ATTCCATTCCATTCCATGCC;RSEQ=TTACAGTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:3,1:2,3:0.4:2,2:45.5:1:31.3:1:0.52381:3.76:34:8:0.4:0:5 0/0:15:0:0,0:4,4:0:2,0:21.1:1:31.4:1:1:0:47.8:16:0.6154:0:4.8 -10 42380416 . G T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67828;LSEQ=TTCCATTCCATGCCGTTACA;RSEQ=TCCATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:4,4:0.2:2,0:49:0:29.5:1:0.46667:0:20:4:0.2:0:6 0/1:14:2:1,1:7,5:0.1429:2,2:15:1:32:0:1:1.36624:42:4:0.1429:0:6 -10 42380421 . T A 54 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.19206;SOR=0.26608;LSEQ=TTCCATGCCGTTACAGTCCA;RSEQ=TCCATTCCATTCCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:4,2:0.4:2,2:23.3:1:27.3:1:1:1.86195:55.5:3:0.3333:0:4 0/1:14:2:1,1:7,5:0.1429:2,2:9.5:1:27:1:1:1.36624:59:4:0.1429:0:4.5 -10 42380423 . C G 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.19206;SOR=0.26608;LSEQ=CCATGCCGTTACAGTCCATT;RSEQ=CATTCCATTCCACTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:4,2:0.4:2,2:37:1:33.5:1:1:1.86195:53:8:0.4:0:4.5 0/1:14:2:1,1:7,5:0.1429:2,2:33.5:1:33:0:1:1.36624:60:4:0.1429:0:5.5 -10 42380426 . T C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.9658;LSEQ=TGCCGTTACAGTCCATTCCA;RSEQ=TCCATTCCACTCGGGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:4,3:2,1:0.7:2,2:29.1:1:31.7:1:1:1.44135:52.3:14:0.7:0:4 1/0:13:9:5,4:2,2:0.6923:2,2:27.4:1:29.9:1:1:1.23:47.7:8:0.6667:0:4.9 -10 42380433 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.48052;SOR=Inf;LSEQ=ACAGTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:28.4:1:31.1:1:1:0:44.6:20:1:0:4.5 0/1:12:2:1,1:5,5:0.1667:2,2:33:0:33.5:1:1:1:30:4:0.1818:0:3 -10 42380438 . CG AT 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGTTGATTCCACTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:30.1:1:30:1:1:0:42.6:18:1:0:4.9 0/1:13:2:1,1:5,5:0.1538:2,2:17.5:1:26.5:1:1:1:60:4:0.1667:0:4.5 -10 42380439 . G C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GGTTGATTCCACTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:30:1:29.6:1:1:0:42.6:18:1:0:4.9 0/1:13:2:1,1:4,4:0.1538:2,2:32:0:31.5:1:1:1:30:4:0.2:0:3 -10 42380446 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18333;SOR=0;LSEQ=TTCCATTCCACTCGGGTTGA;RSEQ=TCCACTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:44.5:1:29:1:1:1.22474:58:4:0.1818:0:5 0/0:14:0:0,0:6,8:0:2,0:20.2:1:29.2:1:1:0:43.9:28:1:0:4.8 -10 42380451 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.33335;LSEQ=TTCCACTCGGGTTGATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:7:0:28.5:1:1:1.22474:35:4:0.1818:0:2 0/1:13:3:1,2:4,6:0.2308:2,2:15.7:1:28.7:1:1:1.30472:33.3:6:0.25:0:3.3 -10 42380458 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.91257;LSEQ=CGGGTTGATTCCACTCCATT;RSEQ=CATTCCATTCCATGCCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:4,6:0.1667:2,0:7:0:25.5:1:0.45455:0:20:4:0.1667:0:6 0/1:13:2:1,1:4,7:0.1538:2,2:44:1:29.5:1:1:1.67:42:4:0.1538:0:6 -10 42380468 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.47059;SOR=0;LSEQ=CCACTCCATTCCATTCCATT;RSEQ=CATGCCGTTACATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:22.5:1:31.5:1:1:2.24:58:4:0.2222:0:5 0/0:8:0:0,0:2,6:0:2,0:22.6:1:29.6:1:1:0:35.6:16:1:0:5.1 -10 42380472 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCGTTACATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:24.5:1:32.3:1:1:0:48.6:16:1:0:3.8 0/1:6:2:0,2:1,3:0.3333:2,0:28.5:1:28:1:1:0:30.5:4:0.3333:0:6.5 -10 42380475 . G A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24476;SOR=5.98921;LSEQ=ATTCCATTCCATTCCATGCC;RSEQ=TTACATTCCATTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:3,4:0.125:2,0:40:0:33:0:1:0:43:2:0.125:0:5 1/0:6:3:0,3:1,2:0.5:2,0:30:1:28.7:1:1:0:33.7:6:0.5:0:6.3 -10 42380478 . A C 69 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02564;SOR=22.89064;LSEQ=CCATTCCATTCCATGCCGTT;RSEQ=CATTCCATTCCATTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:3,4:0.125:2,0:43:0:34:0:1:0:43:2:0.125:0:5 1/1:6:5:1,4:0,1:0.8333:0,2:28.2:1:29.8:1:1:0:37:10:0.8333:0:6.2 -10 42380490 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=ATGCCGTTACATTCCATTCC;RSEQ=TTCCTTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:25.7:1:31:1:1:0:47.4:14:1:0:3.6 0/1:6:2:1,1:0,4:0.3333:0,2:12:1:28:1:0.33333:0:42:4:0.3333:0:6 -10 42380495 . T A 82 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTACATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:24.8:1:31.8:1:1:0:45.5:12:1:0:3.3 1/1:5:5:1,4:0,0:1:0,2:24.6:1:26.2:1:1:0:40.8:4:1:0:6 -10 42380499 . CATTCCATTCCATTCCATTCCATTCCATTCCATCCGTTTCCGTTCTATTCCACTGTGTTTGATTCT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=CATTCCATTCCATTCCTTTC;RSEQ=ATTCCATTCCATTCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:86.5:1:30.5:1:1:1.41:35:4:0.2857:0.2857:2 0/0:5:0:0,0:1,4:0:2,0:19.6:1:28.8:1:1:0:40.8:10:1:0:6 -10 42380505 . A G 31 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.5;SOR=4.17095;LSEQ=ATTCCATTCCTTTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,2:0.2857:2,2:21:0:32.5:1:1:1.73:60:4:0.4:0:3 1/0:3:2:0,2:0,1:0.6667:0,0:26:1:31:1:1:0:40:4:0.6667:0:6 -10 42380510 . A G 51 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.69379;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:1,1:0.4286:2,2:18:1:32.3:1:1:1.7321:54.3:6:0.6:0:3.7 0/1:3:1:0,1:0,2:0.3333:0,0:22:0:32:0:1:0:40:2:0.3333:0:6 -10 42380574 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGTTTGATTCTATTCCATTC;RSEQ=ATTCCATTCTATACCATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29.5:1:1:0:45:4:1:0:3.5 -10 42380590 . A T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCTATACC;RSEQ=TTACATTGCACTCGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:32:1:1:0:45:4:1:0:3.5 -10 42380619 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CACTCGAATTGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:31.5:1:1:0:45:4:1:0:3.5 -10 42380864 . CG TA 27 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCACTCCATTCCATTC;RSEQ=TTCCATTCCATTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:11.5:1:27.8:1:1:0:28:4:0.6667:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42380879 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.16484;SOR=0;LSEQ=CATTCCGTTCCATTCCATTC;RSEQ=ATTCCTTTCCGTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:24:1:30:0:1:1:41:4:0.3333:0:6.5 0/0:8:0:0,0:4,4:0:2,0:7.4:1:32.3:1:1:0:52.1:16:1:0:4.6 -10 42380880 . A C 59 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.27739;SOR=0.19316;LSEQ=ATTCCGTTCCATTCCATTCC;RSEQ=TTCCTTTCCGTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:14.5:1:29.5:1:1:1:36:8:0.6667:0:6.3 0/1:8:2:1,1:3,3:0.25:2,2:16:0:33:1:1:1:49:4:0.25:0:5.5 -10 42380885 . T G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=GTTCCATTCCATTCCATTCC;RSEQ=TTCCGTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:30:1:31.5:1:1:1:41:4:0.3333:0:6.5 0/0:8:0:0,0:4,4:0:2,0:13.4:1:31.6:1:1:0:52.1:16:1:0:4.6 -10 42380887 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=TCCATTCCATTCCATTCCTT;RSEQ=CCGTTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:32:1:29.5:1:1:1:41:4:0.3333:0:6.5 0/0:8:0:0,0:4,4:0:2,0:15.4:1:30.8:1:1:0:52.1:16:1:0:4.6 -10 42380893 . CCA GCATTCCG 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.47253;SOR=Inf;LSEQ=CCATTCCATTCCTTTCCGTT;RSEQ=TTCCATTCCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:27.2:1:29.7:1:1:0:37.7:12:1:0:6.3 0/1:8:2:1,1:3,3:0.25:2,2:14:0:32.5:0:1:1:45.5:4:0.25:0:3 -10 42380904 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.5;SOR=Inf;LSEQ=CTTTCCGTTCCATTCCATTC;RSEQ=ATTCCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:34.7:1:31.3:1:1:0:37.7:12:1:0:6.3 0/1:10:2:1,1:3,3:0.2:2,2:29:1:30.5:1:1:1:49:4:0.2:0:5.5 -10 42380906 . T A 60 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.23352;SOR=Inf;LSEQ=TTCCGTTCCATTCCATTCCA;RSEQ=TCCTTTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:34.7:1:29.7:1:1:0:37.7:12:1:0:6.3 0/1:10:4:2,2:3,3:0.4:2,2:26:1:30.3:1:1:1:49.8:8:0.4:0:3 -10 42380909 . C A 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CGTTCCATTCCATTCCATTC;RSEQ=TTTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:34.7:1:30.8:1:1:0:37.7:12:1:0:6.3 0/1:10:2:1,1:4,4:0.2:2,2:15:0:29:1:1:1:54:4:0.2:0:3 -10 42380910 . T A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6044;SOR=0.52327;LSEQ=GTTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:0.3333:2,2:39:1:31:0:1:1:28:4:0.3333:0:6.5 0/1:10:2:1,1:2,2:0.2:2,2:20:0:29:1:1:1:37:4:0.2:0:4 -10 42380912 . T G 33 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=TCCATTCCATTCCATTCCTT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,1:0.3333:2,2:37:1:33:1:1:1.7321:28:4:0.4:0:6.5 0/0:10:0:0,0:4,4:0:2,0:28.3:1:27.1:1:1:0:49.1:7:0.7778:0:4.3 -10 42380914 . C T 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.5;SOR=Inf;LSEQ=CATTCCATTCCATTCCTTTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,2:0:2,0:31.6:1:30:1:1:0:37.2:10:1:0:6 0/1:10:2:1,1:4,4:0.2:2,2:24:0:28.5:1:1:1:37:4:0.2:0:4 -10 42380915 . A G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.6044;SOR=0.52327;LSEQ=ATTCCATTCCATTCCTTTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,1:0.3333:2,2:37.5:1:30.5:1:1:1.7321:44:4:0.4:0:6 0/1:10:2:1,1:4,4:0.2:2,2:43.5:1:29.5:1:1:1:60:4:0.2:0:7 -10 42380920 . A G 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.125;SOR=0;LSEQ=ATTCCATTCCTTTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,1:0.3333:2,2:29:1:32.5:1:1:1.7321:28:4:0.4:0:6.5 0/0:10:0:0,0:5,5:0:2,0:25.5:1:28.2:1:1:0:49.1:9:1:0:4.5 -10 42380925 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.16484;SOR=0;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:24:1:32:1:1:1:28:4:0.3333:0:6.5 0/0:8:0:0,0:4,4:0:2,0:28.6:1:29.6:1:1:0:47.9:16:1:0:4.9 -10 42380932 . T G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=1.53983;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCACTCGGGTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:43:0:34:0:1:0:40:2:0.2:0:8 0/1:7:2:1,1:2,2:0.2857:2,2:37:0:31.5:1:1:1:37:4:0.2857:0:4 -10 42380939 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=5;SSF=1;SOR=0.77001;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ACTCGGGTTCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:20:0:29.5:1:1:1.73:44:4:0.4:0:6 0/1:6:2:1,1:2,2:0.3333:2,2:30:0:28:1:1:1:60:4:0.3333:0:7 -10 42380941 . C T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77001;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTCATTCCATTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:18:0:31:1:1:1.73:44:4:0.4:0:6 0/1:6:2:1,1:2,2:0.3333:2,2:28:0:27:1:1:1:60:4:0.3333:0:7 -10 42380943 . CGGGTT C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=CATTCCATTCCGTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:9.5:1:30.3:1:1:1.73:28:4:0.4:0.2:7.5 0/0:6:0:0,0:3,3:0:2,0:19.5:1:28.8:1:1:0:47.5:12:1:0:4.7 -10 42380949 . C A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCGTTCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,1:0.5:0,2:10:0:31:1:1:0:44:4:0.5:0:6 0/1:5:2:1,1:1,1:0.4:2,2:20:0:27:1:1:1:60:4:0.4:0:7 -10 42380960 . G T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCGGGTTCATTCCATTCC;RSEQ=TTCCATTCTATTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:9:0:32.5:1:1:0:37:4:0.5:0:4 -10 42381010 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCATTTCCATTCCATTCC;RSEQ=TTCCACTCCACTCGCGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:32.5:1:1:0:37:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42381015 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTTCCATTCCATTCCTTTCC;RSEQ=CTCCACTCGCGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:0:32.5:1:1:0:37:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42381018 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCTTTCCACT;RSEQ=CACTCGCGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:33.5:1:1:0:37:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42381043 . T C 30 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCTTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:0:30.5:1:1:0:37:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42381209 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATTCCAGTCCTTTCCATTA;RSEQ=ATTACATTCCACTCGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:31.5:1:1:0:50:4:1:0:2.5 -10 42381249 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTTTCCATTACATTGAATTC;RSEQ=ATTCCATTCCATTCCATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:31.5:1:1:0:50:4:1:0:2.5 -10 42381455 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTTGATTCCGTTCCATTCC;RSEQ=TTCCATTACATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10:1:30:1:1:0:50.5:4:1:0:6 0/1:7:2:1,1:4,1:0.2857:2,2:10:0:32.5:1:1:3.1622:50:4:0.2857:0:5 -10 42381463 . A C 88 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:32:1:1:0:50.5:4:1:0:6 1/1:7:7:5,2:0,0:1:0,2:15.4:1:31.4:1:1:0:47.6:14:1:0:5 -10 42381475 . A T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTACATTCCATTCC;RSEQ=TTGCATTGGAATCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:30:1:30.5:1:1:0:50.5:4:1:0:6 0/1:7:2:2,0:2,2:0.2857:2,0:31:1:31:1:0.46667:0:37:4:0.2857:0:4.5 -10 42381480 . A C 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02222;SOR=0;LSEQ=ATTACATTCCATTCCATTGC;RSEQ=TTGGAATCGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:1:31.5:1:1:0:50.5:4:1:0:6 0/0:8:0:0,0:5,1:0:2,0:26:1:29.2:1:1:0:42.8:12:0.75:0:5.2 -10 42381484 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTGCATTG;RSEQ=AATCGGGTTGATTCCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:34:1:31:1:1:0:50.5:4:1:0:6 0/1:8:2:1,1:4,1:0.25:2,2:35.5:1:32:1:1:3.1622:60:4:0.25:0:5.5 -10 42381495 . AT TC 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGCATTGGAATCGGGTTG;RSEQ=TCCAATCCATTCCATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:34:1:30:1:1:0:50.5:4:1:0:6 0/1:9:2:1,1:5,2:0.2222:2,2:37:0:30:1:1:2.23609:50:4:0.2222:0:4 -10 42381501 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGGAATCGGGTTGATTCCA;RSEQ=TCCATTCCATTACATTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:34:1:29.5:1:1:0:50.5:4:1:0:6 0/1:10:2:1,1:5,3:0.2:2,2:13.5:1:31:1:1:1.58108:24:4:0.2:0:6.5 -10 42381506 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCGGGTTGATTCCAATCCA;RSEQ=TCCATTACATTCCAGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:32.5:1:29.5:1:1:0:50.5:4:1:0:6 0/1:10:2:1,1:5,3:0.2:2,2:35:0:33:1:1:1.58108:60:4:0.2:0:5.5 -10 42381509 . C A 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01515;SOR=0;LSEQ=GGGTTGATTCCAATCCATTC;RSEQ=ATTACATTCCAGTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:28.5:1:1:0:50.5:4:1:0:6 0/0:10:0:0,0:6,4:0:2,0:24:1:29.8:1:1:0:42:20:1:0:5.3 -10 42381514 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCAATCCATTCCATTA;RSEQ=ATTCCAGTCCTTTCCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24.5:1:30.5:1:1:0:50.5:4:1:0:6 0/1:10:2:1,1:5,3:0.2:2,2:18.5:1:27:1:1:1.58108:39:4:0.2:0:6 -10 42381516 . T G 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01818;SOR=0;LSEQ=TTCCAATCCATTCCATTACA;RSEQ=TCCAGTCCTTTCCATTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:31:1:1:0:50.5:4:1:0:6 0/0:9:0:0,0:4,3:0:2,0:25:1:29.9:1:1:0:44:14:0.7778:0:5.4 -10 42381524 . C G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTACATTCCAGTC;RSEQ=TTTCCATTGTATTACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:31:0:34:0:1:0:44:2:1:0:7 0/1:9:2:1,1:4,3:0.2222:2,2:18.5:1:29:1:1:1.29098:39:4:0.2222:0:6 -10 42381529 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTACATTCCAGTCCTTTC;RSEQ=ATTGTATTACATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:26:0:34:0:1:0:44:2:1:0:7 0/1:9:2:1,1:4,3:0.2222:2,2:18.5:1:30:1:1:1.29098:39:4:0.2222:0:6 -10 42381533 . GT CC 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCCAGTCCTTTCCATT;RSEQ=ATTACATTCCACTCGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:21:0:33.5:0:1:0:44:2:1:0:6 1/0:8:6:3,3:0,0:0.75:0,2:23.7:1:30.4:1:1:0:30.5:12:0.75:0.25:5.3 -10 42381539 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTCCTTTCCATTGTATTA;RSEQ=ATTCCACTCGGTTTGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:16:0:34:0:1:0:44:2:1:0:6 0/1:8:2:1,1:3,3:0.25:2,2:39:1:31:1:1:1:24:4:0.25:0:5.5 -10 42381576 . T A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTACATTGAATTCCA;RSEQ=TCCATTCCATTCCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:1,4:0.2857:2,2:28.5:1:27.5:1:1:3.16:35:4:0.3333:0:5.5 -10 42381603 . AC CA 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCAATCCATTCCATT;RSEQ=ATTCCATACCACCCAGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:0,2:0,1:0.5:0,0:48.5:1:29.5:1:1:0:35:4:0.6667:0:6 -10 42381611 . TA CT 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCATTCCATTACATTCCA;RSEQ=CCACCCAGATTGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:40.5:1:27:1:1:0:35:4:1:0:5 -10 42381619 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTACATTCCATACCACCC;RSEQ=GATTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:33.5:1:30.5:1:1:0:35:4:1:0:5 -10 42381679 . T A 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATTCCATTCCAGTTGATTC;RSEQ=AATGCCTTTCACCCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:31:1:1:0:47:4:1:0:6 0/0:1:0:0,0:1,0:0:0,0:24:0:33:0:1:0:59:2:1:0:8 -10 42381688 . T C 51 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTTGATTCTAATGCCTT;RSEQ=CACCCCATTCCATTCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:27.3:1:32.7:1:1:0:38:6:1:0:6.7 1/1:1:1:1,0:0,0:1:0,0:33:0:32:0:1:0:59:2:1:0:8 -10 42381692 . C T 50 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTCTAATGCCTTTCAC;RSEQ=CCATTCCATTCCACTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:27.7:1:32:1:1:0:38:6:1:0:6.7 1/1:1:1:1,0:0,0:1:0,0:37:0:32:0:1:0:59:2:1:0:8 -10 42381698 . C A 49 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTAATGCCTTTCACCCCATT;RSEQ=CATTCCACTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:25.7:1:31:1:1:0:38:6:0.75:0:6.7 1/1:1:1:1,0:0,0:1:0,0:43:0:28:0:1:0:59:2:1:0:8 -10 42381706 . C T 64 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCACCCCATTCCATTCCA;RSEQ=TGCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:20.8:1:32:1:1:0:33.8:8:1:0:5.8 1/1:1:1:1,0:0,0:1:0,0:50:0:29:0:1:0:59:2:1:0:8 -10 42381720 . A C 52 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.4;SOR=0;LSEQ=ATTCCACTGCATTCCATTCC;RSEQ=TTCCATTCCACTCAGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:18.3:1:33.3:1:1:0:38:6:0.75:0:6.7 0/0:1:0:0,0:1,0:0:0,0:36:0:25:0:1:0:59:2:1:0:8 -10 42381740 . T A 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCACTCAGTTTG;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30.5:1:1:0:20.5:4:1:0:5.5 1/1:2:2:2,0:0,0:1:0,0:9.5:1:26.5:1:1:0:59.5:4:1:0:6 -10 42381743 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCATTCCACTCAGTTTGTTT;RSEQ=CATTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:16.5:1:31.5:1:1:0:40:4:0.5:0:6 0/0:2:0:0,0:2,0:0:0,0:9.5:1:29.5:1:1:0:59.5:4:1:0:6 -10 42381758 . C G 34 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.08333;SOR=Inf;LSEQ=TGTTTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:16.3:1:31.7:1:1:0:37.8:12:1:0:3.8 1/0:3:2:1,1:1,0:0.6667:0,2:15:0:34:0:1:0:47.5:4:0.6667:0:3 -10 42381763 . C A 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGTTGATTCCTTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:16.5:1:31:1:1:2.44949:40:4:0.3333:0:6 0/1:3:1:1,0:1,1:0.3333:2,0:26:0:30:0:1:0:60:2:0.3333:0:4 -10 42381769 . G T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:20.5:1:30:1:1:2.44949:43:4:0.3333:0:2.5 0/0:3:0:0,0:2,1:0:2,0:28:1:33.3:1:1:0:51.7:6:1:0:3.3 -10 42381775 . T A 76 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=ATTCCACTCGGGTTGATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:23:1:29.5:1:1:0:44.5:12:1:0:3.2 1/0:4:2:2,0:1,1:0.5:2,0:22:1:31.5:1:1:0:53:4:0.5:0:4 -10 42381793 . C G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.4697;SOR=Inf;LSEQ=CCTTTCCATTCCATTCCATT;RSEQ=CATTTCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:34:1:31.6:1:1:0:49.2:10:1:0:3.2 0/1:7:2:1,1:3,2:0.2857:2,2:13:0:33:1:1:1.41418:43:4:0.2857:0:2 -10 42381798 . T C 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:39:1:30.3:1:1:1.73:53.3:6:0.6:0:3.7 1/1:7:7:4,3:0,0:1:0,2:23:1:31.1:1:1:0:49.6:14:1:0:3 -10 42381813 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.84356;LSEQ=CCATTTCATTCCATTCCATT;RSEQ=CGTGCCTTTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,1:0.2857:2,2:28.5:1:30:1:1:2.44949:40.5:4:0.3333:0:4.5 0/1:8:2:1,1:3,3:0.25:2,2:39.5:1:29.5:1:1:1:53:4:0.25:0:3.5 -10 42381834 . C T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.55808;SOR=0.30063;LSEQ=CGTGCCTTTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:24:1:28.7:1:1:0:40.3:6:0.6:0:4 0/1:7:2:1,1:2,3:0.2857:2,2:30.5:1:28:1:1:1.41:53:4:0.2857:0:3.5 -10 42381870 . A T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCGGGTTCATTCCATTCC;RSEQ=TTCGTTTTCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,0:0.6:0,2:30.3:1:30:1:1:0:54:6:0.6:0:6 1/1:2:2:0,2:0,0:1:0,0:40:1:32:0:1:0:49.5:4:1:0:7 -10 42381874 . GT CG 61 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGTTCATTCCATTCCATTC;RSEQ=TTTCATTCCATTCCATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,0:0.8:0,2:28.8:1:30.9:1:1:0:51.8:8:0.8:0:5.3 1/1:2:2:0,2:0,0:1:0,0:36.5:1:32.5:0:1:0:49.5:4:1:0:6 -10 42381878 . T C 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATTCCATTCCATTCGTTT;RSEQ=CATTCCATTCCATTCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,0:0.8:0,2:29.8:1:32:1:1:0:45.8:8:0.8:0:5 1/1:2:2:0,2:0,0:1:0,0:33.5:1:33:0:1:0:49.5:4:1:0:6 -10 42381904 . A C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CATTCCATTCTATTCCATTC;RSEQ=TTTCCATTCAATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:36.8:1:31:1:1:0:49.3:8:1:0:5.3 1/0:4:2:1,1:1,1:0.5:2,2:7.5:1:29:1:1:1:23:4:0.5:0.5:3 -10 42381908 . C CATTTGCAGTTTATTCCATTCCATTA 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCATTCTATTCCATTCATTT;RSEQ=CATTCAATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:36:1:31.8:1:1:0:49.3:8:1:0:5.3 1/0:4:2:1,1:1,1:0.5:2,2:37.5:1:29.3:1:1:1:23:4:0.5:0.5:3 -10 42381913 . CA GC 32 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=CTATTCCATTCATTTCCATT;RSEQ=ATTCCATTCCACTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:39.5:1:32.5:1:1:0:47.5:4:0.5:0:4 0/1:4:1:1,0:1,2:0.25:2,0:36:0:32.5:0:1:0:51:2:0.25:0:3 -10 42381914 . A C 34 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=TATTCCATTCATTTCCATTC;RSEQ=ATTCCATTCCACTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,0:0.5:0,0:26.5:1:34:0:1:0:51:4:1:0:5.5 0/1:4:1:0,1:1,1:0.25:2,0:8:0:33:0:1:0:40:2:0.3333:0:6 -10 42381936 . G T 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TTCCATTCCACTCCACTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:15.5:1:29.5:1:1:0:49.3:8:1:0:4.8 1/0:3:2:1,1:1,0:0.6667:0,2:21:0:32:0:1:0:23:4:0.6667:0:3 -10 42381939 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CATTCCACTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:23.5:1:30.5:1:1:0:47.5:4:0.6667:0:4 0/0:3:0:0,0:2,1:0:2,0:20.7:1:31.7:1:1:0:32.3:6:1:0:3 -10 42381942 . T G 34 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCCACTCCACTCGGGTTGAT;RSEQ=CCATTCCATTCCATTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:14.3:1:29.3:1:1:0:46.3:6:1:0:4.7 1/0:3:2:1,1:1,0:0.6667:0,2:15:0:34:0:1:0:23:4:0.6667:0:3 -10 42381952 . T C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.4;SOR=Inf;LSEQ=TCGGGTTGATTCCATTCCAT;RSEQ=CCATTCCTTTCCATTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:29:1:1:0:47.5:4:1:0:4 1/0:3:2:1,1:1,0:0.6667:0,2:5:0:32.5:1:1:0:23:4:0.6667:0:3 -10 42382024 . TG CA 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTACTTTCCCTTCCATTC;RSEQ=TTCCCTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:1:32:1:1:0:40:4:1:0:6.5 -10 42382038 . C G 34 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCTGTTCCCTTCCATT;RSEQ=CATTCCATTCCATTCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:34:0:1:0:40:4:1:0:6.5 -10 42382057 . G T 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCGTTGCATTGGAATCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:29.3:1:29:1:1:0:42.7:6:1:0:5.7 -10 42382074 . G A 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCGTTGCATTGGAATC;RSEQ=GGTTGATTCCAATACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:35:1:30.3:1:1:0:42.7:6:1:0:5.7 -10 42382099 . C G 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCCAATACATTCCATTA;RSEQ=ATTCCATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:26.7:1:32:1:1:0:42.7:6:1:0:5.7 -10 42382106 . T G 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACATTCCATTACATTCCA;RSEQ=TCCTTTCCATTCCATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:22.7:1:32:1:1:0:42.7:6:1:0:5.7 -10 42383086 . T G 34 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCCACTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:34:0:1:0:55:4:1:0:5.5 -10 42383106 . TATTCC CA 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCATTCCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:32.3:1:1:0:55:4:1:0:4.5 -10 42383125 . C A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGTTTGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:0:30:1:1:0:55:4:1:0:5.5 -10 42383132 . A T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=CTCGGTTTGACTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38.5:1:30.5:1:1:0:55:4:1:0:5.5 -10 42383136 . G T 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GTTTGACTCCATTCCATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:31:1:1:0:55:4:1:0:5.5 -10 42383264 . T C 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.03571;SOR=0;LSEQ=GGATTCGAATGGAATCATCA;RSEQ=CAGATGGAAATGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:33:0:1:0:36:4:1:0:2 0/0:6:0:0,0:5,1:0:2,0:7.2:1:29.3:1:1:0:42.7:12:1:0:1.8 -10 42383286 . A G 63 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.46667;SOR=Inf;LSEQ=AGATGGAAATGAATGGAATC;RSEQ=TCATAGAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:34.5:1:32:1:1:0:36:4:1:0:2 1/0:8:4:4,0:2,2:0.5:2,0:28:1:31.5:1:0.42857:0:41:8:0.5:0:1.5 -10 42383303 . A C 66 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ATCATCATAGAATGGAATCG;RSEQ=ATGGATTCATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:46.5:1:29.5:1:1:0:36:4:1:0:2 1/0:8:4:2,2:4,0:0.5:0,2:41.3:1:33:1:0.42857:0:46.3:8:0.5:0:2 -10 42383344 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGATGGAATCATCGAATGG;RSEQ=CTTTAATGGAATCATTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7:1:28:1:1:0:36:4:1:0:2 0/1:7:2:1,1:4,1:0.2857:2,2:22:0:31:1:1:3.1622:60:4:0.2857:0:5 -10 42383347 . TT GG 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=ATGGAATCATCGAATGGACT;RSEQ=AATGGAATCATTAAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5:1:30.2:1:1:0:36:4:1:0.5:1.5 0/0:3:0:0,0:1,1:0:2,0:25:0:31.5:1:1:0:60:4:0.6667:0:5 -10 42383348 . T G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCATCGAATGGACTT;RSEQ=AATGGAATCATTAAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:26:0:32:0:1:0:60:4:0.6667:0:5 -10 42383381 . A T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGGACTCGAATGGAATC;RSEQ=TTATTGAATGGAATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:7.5:1:28.5:1:1:0:60:4:0.6667:0:5 -10 42383493 . C T 88 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAACAATCATCGAATGGAC;RSEQ=CAAATGGAATTATCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:40:0:32:0:1:0:40:2:1:0:4 1/1:7:7:5,2:0,0:1:0,2:20.6:1:31.4:1:1:0:50.4:14:1:0:4.1 -10 42383504 . T C 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=CGAATGGACCCAAATGGAAT;RSEQ=ATCCTCAAATGGAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:50:0:30:0:1:0:40:2:1:0:4 0/1:12:5:4,1:4,3:0.4167:2,2:29.6:1:32:1:0.57576:2.74:49.4:10:0.4167:0:4.2 -10 42383520 . A C 87 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=GAATTATCCTCAAATGGAAT;RSEQ=GAATGGAATTATCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:12:7:4,3:0,0:0.5833:0,2:29:1:31.3:1:1:0:52.1:14:0.5833:0:3.4 -10 42383561 . G A 49 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCGAATAGAATCATCGAAT;RSEQ=GACTCGAGTGGAATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:40:0:33:0:1:0:40:2:1:0:2 0/1:15:3:2,1:7,5:0.2:2,2:27:1:31:1:1:1.40:50.3:6:0.2:0:3.7 -10 42383569 . G A 102 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCGAATGGACTCGA;RSEQ=TGGAATCATCGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:48:0:33:0:1:0:40:2:1:0:2 1/0:14:11:6,5:0,0:0.7857:0,2:19.4:1:29.5:1:1:0:53.2:22:0.7857:0:3.8 -10 42383584 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CTCGAGTGGAATCATCGAAT;RSEQ=GAATGGAATGGAATAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:38:0:32:0:1:0:40:2:1:0:2 0/1:11:2:1,1:6,3:0.1818:2,2:20.5:1:28:1:1:1.87089:50:4:0.1818:0:5 -10 42383598 . T C 81 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAATGGAATGGAATGGAA;RSEQ=AGTCAATGAACTCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:24:0:34:0:1:0:40:2:1:0:2 1/0:8:6:3,3:1,0:0.75:0,2:25.7:1:31.7:1:1:0:37:12:0.75:0:3.3 -10 42383627 . TGAATGGAATC T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCGAATGGAATCATCAT;RSEQ=GAATGGAATCATTGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:4,3:0.2222:2,2:14.5:1:28:1:1:1.29098:35:4:0.2222:0.2222:4 -10 42383650 . T C 59 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCGAATGGAATCAT;RSEQ=GAGTGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:8:4:1,3:2,2:0.5:2,2:12.8:1:29.8:1:1:2.60168:40.3:8:0.5:0:4 -10 42383670 . C T 68 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTGGAATCGAATGGAAT;RSEQ=ACGATCAAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:5:3,2:2,3:0.5:2,2:30.4:1:29.6:1:1:2.07:31.2:10:0.5556:0:3.2 -10 42383672 . C T 95 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGAATCGAATGGAATCA;RSEQ=GATCAAATGGAATCGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:10:10:5,5:0,0:1:0,2:27.7:1:28.7:1:1:0:33.9:9:1:0:3.8 -10 42383686 . C T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCACGATCAAATGGAAT;RSEQ=GAATGTAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:3,5:0.2:2,2:20:1:28:1:1:1.58:40:4:0.2222:0:5 -10 42383711 . T TC 61 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAATCATCATCAAATGGAA;RSEQ=CAAAATAACCATCATCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:4:2,2:1,4:0.4444:2,2:42.5:1:30.8:1:0.52381:3.39:30.5:8:0.5:0:4 -10 42383712 . C CA 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCATCATCAAATGGAAT;RSEQ=AAAATAACCATCATCAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:0,2:3,4:0.2222:2,0:13.5:1:31.5:1:0.5:0:29:4:0.2222:0:2.5 -10 42383713 . A C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AAATAACCATCATCAATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:2,5:0.2222:2,2:33.5:1:28.5:1:1:2.24:53:4:0.2222:0:6.5 -10 42383718 . A C 78 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCAAATGGAATCAAAAT;RSEQ=ACCATCATCAATTGGTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:6:3,3:0,3:0.6667:0,2:35.5:1:30.3:1:0.46429:0:38:12:0.6667:0:4.8 -10 42383720 . C G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAAATGGAATCAAAATAA;RSEQ=CATCATCAATTGGTATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:2,4:0.2222:2,2:41.5:1:30:0:1:1.83:40:4:0.25:0:5 -10 42383733 . G C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATAACCATCATCAATTG;RSEQ=TATTGAATGGAATTGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:13.5:1:28:1:1:1:53:4:0.3333:0:6.5 -10 42383736 . T C 67 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAACCATCATCAATTGGTA;RSEQ=TGAATGGAATTGTCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:1:0,2:24:1:29:1:1:0:36.4:4:1:0:4.2 -10 42383858 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCACATGGAATCATCATC;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:29:1:1:0:50:4:1:0:5 -10 42384234 . A ATTC 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTACTCGAATGGAATAATC;RSEQ=AACGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:25.5:1:31.3:1:1:0:26:4:0.6667:0:2.5 -10 42384257 . G A 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CGGAATCGAATGGAATCATC;RSEQ=TCGAATGGAAACGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:13.3:1:31:1:1:0:51:6:1:0:2 1/1:5:4:2,2:1,0:0.8:0,2:21.5:1:32:0:1:0:37:8:0.8:0:4.5 -10 42384264 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATCATCGTCGAAT;RSEQ=GAAACGAATGGAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:20.3:1:33:1:1:0:51:6:1:0:2 0/1:7:2:1,1:3,2:0.2857:2,2:32:1:30.5:1:1:1.41418:48:4:0.2857:0:6.5 -10 42384266 . A C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATCATCGTCGAATGG;RSEQ=AACGAATGGAATCATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:22.3:1:30.7:1:1:0:51:6:1:0:2 0/1:7:2:1,1:3,2:0.2857:2,2:34:1:33:1:1:1.41418:48:4:0.2857:0:6.5 -10 42384271 . A C 34 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=ATCATCGTCGAATGGAAACG;RSEQ=ATGGAATCATCATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:28:1:34:0:1:0:54:4:0.6667:0:3 0/0:7:0:0,0:4,3:0:2,0:19:1:29.6:1:1:0:39.6:14:1:0:2.7 -10 42384302 . A G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CATCGAATGGAAATGAAAGG;RSEQ=GTCATCATCTAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:35.3:1:30.5:1:1:0:47.3:8:1:0:3.3 0/1:6:2:1,1:2,2:0.3333:2,2:31:1:29.5:1:1:1:48:4:0.3333:0:6.5 -10 42384319 . A C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGGAGTCATCATCTAATGGA;RSEQ=TCGCATGGAATCATCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:26.8:1:30.3:1:1:0:47.3:8:1:0:3.3 0/1:6:2:1,1:2,2:0.3333:2,2:14:1:29.5:1:1:1:48:4:0.3333:0:6.5 -10 42384321 . C T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=GAGTCATCATCTAATGGAAT;RSEQ=GCATGGAATCATCATCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:37:0:31:0:1:0:36:2:0.25:0:7 0/1:6:2:1,1:2,2:0.3333:2,2:12:1:27:1:1:1:48:4:0.3333:0:6.5 -10 42384325 . T C 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=CATCATCTAATGGAATCGCA;RSEQ=GGAATCATCATCAAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:19:1:28.5:1:1:1.7321:54:4:0.4:0:3 0/0:6:0:0,0:3,3:0:2,0:21.3:1:29.7:1:1:0:41.3:12:1:0:3 -10 42384341 . C T 45 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CGCATGGAATCATCATCAAA;RSEQ=GGAATCGCATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:22.7:1:29:1:1:0:41.3:6:1:0:5.3 1/0:4:2:1,1:1,1:0.5:2,2:23.5:1:30.5:1:1:1:23:4:0.5:0:2.5 -10 42384348 . GC AA 48 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AATCATCATCAAACGGAATC;RSEQ=ATGGAATCATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:30.5:1:27.5:1:1:0:38:4:1:0:6 1/1:3:3:1,2:0,0:1:0,2:13:1:30.4:1:1:0:43:6:1:0.6667:1 -10 42384349 . C A 27 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATCATCAAACGGAATCG;RSEQ=ATGGAATCATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:27.5:1:1:0:38:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42384442 . G C 50 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=2;SSF=0.25;SOR=Inf;LSEQ=GAATGCAATCATCGAATGGT;RSEQ=TCGAATGGAATCATCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:42:0:34:0:1:0:40:2:1:0:4 1/1:3:3:3,0:0,0:1:0,0:29.3:1:32:1:1:0:31.7:6:1:0:4.3 -10 42384453 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TCGAATGGTGTCGAATGGAA;RSEQ=CATCTTCAAATGGCATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:31:0:33:0:1:0:40:2:1:0:4 0/1:5:2:2,0:3,0:0.4:0,0:14.5:1:31:1:1:0:40:4:0.4:0:4 -10 42384467 . C A 98 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCATCTTCAAATGG;RSEQ=ATGGAATGGAATCATCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:13.7:1:31.3:1:1:0:36.3:6:1:0:5.3 1/1:12:11:7,4:0,0:0.9167:0,2:16.3:1:28.6:1:1:0:32.9:22:1:0:3.2 -10 42384471 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCTTCAAATGGCATG;RSEQ=AATGGAATCATCGCATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:15:1:32.7:1:1:0:36.3:6:1:0:5.3 0/1:15:2:1,1:8,5:0.1333:2,2:29:1:28:1:1:1.54914:43:4:0.1333:0:5 -10 42384481 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATGGCATGGAATGGAATC;RSEQ=TCGCATAGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:14:1:30.2:1:1:0:41:10:1:0:3.6 0/1:18:2:1,1:9,7:0.1111:2,2:27:1:32:1:1:1.26772:24:4:0.1111:0:4.5 -10 42384483 . C T 38 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGCATGGAATGGAATCAT;RSEQ=GCATAGAATCGAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:15.2:1:30.8:1:1:0:41:10:1:0:3.6 0/1:18:3:2,1:8,7:0.1667:2,2:16:1:24:1:1:1.70:22.7:2:0.1176:0:6.7 -10 42384484 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGCATGGAATGGAATCATC;RSEQ=CATAGAATCGAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:19.8:1:30.3:1:1:0:41.3:8:1:0:3.5 0/1:18:2:1,1:9,7:0.1111:2,2:33.5:1:29:1:1:1.26772:43:4:0.1111:0:5 -10 42384516 . AC CA 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATTATCATCGAATGG;RSEQ=TCAAATGGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:27.5:1:30:1:1:0:38:12:1:0:4.2 0/1:18:2:1,1:8,8:0.1111:2,2:41:1:30.5:1:1:1:22:4:0.1111:0:7 -10 42384517 . C A 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30684;SOR=0.30352;LSEQ=TGGAATTATCATCGAATGGA;RSEQ=TCAAATGGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:0.5:2,2:31.7:1:30.7:1:1:3.11:30.7:6:0.5:0:6.3 0/1:18:4:2,2:5,5:0.2222:2,2:39.5:1:29.8:1:1:1:29.5:8:0.25:0:4.3 -10 42384520 . A G 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.63491;SOR=0.51539;LSEQ=AATTATCATCGAATGGACTC;RSEQ=AATGGAATCAACATCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:0.5:2,2:30.7:1:30.3:1:1:3.11:30.7:6:0.5:0:6.3 0/1:18:6:3,3:6,6:0.3333:2,2:36:1:30.2:1:1:1:28:12:0.3333:0:5.8 -10 42384526 . A T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.72593;LSEQ=CATCGAATGGACTCAAATGG;RSEQ=ATCAACATCAAACGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:2,3:0.1667:2,0:29:0:26:0:1:0:33:2:0.1667:0:7 0/1:16:2:1,1:6,8:0.125:2,2:38.5:1:28:1:1:1.31:22:4:0.125:0:7 -10 42384538 . A T 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07895;SOR=0;LSEQ=TCAAATGGAATCAACATCAA;RSEQ=CGGAATCAAACGGAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:5:0:32.5:1:1:1:48:4:0.3333:0:1 0/0:14:0:0,0:6,8:0:2,0:23.2:1:29.9:1:1:0:31.1:28:1:0:3.9 -10 42384544 . TC AA 88 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.46372;LSEQ=GGAATCAACATCAAACGGAA;RSEQ=AAACGGAATTATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:22.3:1:29.3:1:1:0:30.7:6:0.75:0:5.3 1/0:14:8:4,4:2,4:0.5714:2,2:20.1:1:29.5:1:0.62704:1.90:27:16:0.5714:0.0714:4.6 -10 42384559 . A G 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.58108;LSEQ=CGGAATCAAACGGAATTATC;RSEQ=AATGGAATCGAAGAGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,0:0.5:0,0:42:0:32:0:1:0:23:2:1:0:6 1/0:8:5:1,4:2,1:0.625:2,2:7.6:1:30.4:1:0.46429:5.78427:34.2:10:0.625:0:4.2 -10 42384591 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=AGAGAATCATCGAATGGACT;RSEQ=GAATGGAATCATCTAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:7.3:1:31.8:1:1:0:41.5:8:1:0:2.8 0/1:7:2:1,1:2,3:0.2857:2,2:29.5:1:28:1:1:1.41:39:4:0.2857:0:5.5 -10 42384595 . T A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=AATCATCGAATGGACTCGAA;RSEQ=GGAATCATCTAATGAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:7.3:1:31.8:1:1:0:41.5:8:1:0:2.8 0/1:7:2:1,1:2,3:0.2857:2,2:33.5:1:28.5:1:1:1.41:39:4:0.2857:0:5.5 -10 42384606 . A T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGACTCGAATGGAATCATCT;RSEQ=ATGAAATAGAATGGAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19:0:30.5:1:1:0:51.5:4:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:43:1:27.5:1:1:1:39:4:0.4:0:5.5 -10 42384628 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAATAGAATGGAATAATC;RSEQ=ATGGACTCGAATGCAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:36.5:1:33:1:1:0:51.5:4:1:0:1 0/1:8:2:1,1:4,2:0.25:2,2:34.5:1:30.5:1:1:1.8258:39:4:0.2857:0:5.5 -10 42384662 . A C 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAATCATCATCAAATGGAAT;RSEQ=GAGTGGAATCGGCGAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:2.5:1:28.5:1:1:0:51.5:4:1:0:1 1/1:4:4:2,2:0,0:1:0,2:26:1:26:1:1:0:37.5:3:1:0:5.8 -10 42384665 . G A 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCATCAAATGGAATAGA;RSEQ=TGGAATCGGCGAATGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:33:1:30:1:1:0:32:6:1:0:6.7 -10 42384674 . G T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGAATAGAGTGGAATCG;RSEQ=CGAATGAACTCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:40.5:1:29.5:1:1:0:28.5:4:1:0:7 -10 42384681 . A G 71 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.52689;LSEQ=TAGAGTGGAATCGGCGAATG;RSEQ=ACTCGAATGGAATAAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,0:0.8333:0,2:4.8:1:30.2:1:1:0:27.8:10:0.8333:0:3.2 1/0:7:5:5,0:1,0:0.7143:0,0:16.2:1:30.8:1:1:0:31.4:10:0.7143:0:5.2 -10 42384686 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13846;SOR=0;LSEQ=TGGAATCGGCGAATGAACTC;RSEQ=AATGGAATAAACATTGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:7.5:1:30:1:1:2.64575:24:4:0.2:0:3 0/0:16:0:0,0:12,4:0:2,0:7.6:1:29:1:1:0:39.2:32:1:0:3.9 -10 42384688 . A G 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61945;SOR=2.96757;LSEQ=GAATCGGCGAATGAACTCGA;RSEQ=TGGAATAAACATTGAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:7,3:0.0909:2,0:12:0:33:0:1:0:59:2:0.1:0:5 0/1:17:4:3,1:9,4:0.2353:2,2:9:1:29.8:1:1:1.31:34.8:8:0.2353:0:5.8 -10 42384697 . A T 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71947;SOR=1.6144;LSEQ=AATGAACTCGAATGGAATAA;RSEQ=CATTGAACGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:3,2:1,0:0.4545:0,2:16.6:1:31:1:1:0:37.8:10:0.5:0:2.4 1/0:26:15:10,5:6,3:0.5769:2,2:13.3:1:28.8:1:1:1:42.4:30:0.5769:0:2.7 -10 42384702 . G C 69 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.76489;LSEQ=ACTCGAATGGAATAAACATT;RSEQ=AACGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:7,3:0.0909:2,0:26:0:33:0:1:0:59:2:0.0909:0:5 0/1:33:5:3,2:18,10:0.1515:2,2:12.6:1:30:1:1:1.19326:36:10:0.1515:0:5 -10 42384705 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGAATGGAATAAACATTGAA;RSEQ=GGAATCGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,4:0:2,0:22.2:1:30.6:1:1:0:38.5:12:0.8571:0:2.7 0/1:39:2:1,1:22,14:0.0513:2,2:14:0:33:1:1:1.55221:60:4:0.0513:0:2.5 -10 42384715 . TG T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28706;SOR=0.34066;LSEQ=AAACATTGAACGGAATCGAA;RSEQ=GAATCATCATCGGATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:0.125:2,2:35:0:33.5:1:1:1.73197:47:4:0.1333:0:2 0/1:44:2:1,1:23,19:0.0455:2,2:18.5:1:29.5:1:1:1.20525:53:4:0.0455:0:1.5 -10 42384717 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATTGAACGGAATCGAATG;RSEQ=AATCATCATCGGATGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:29.9:1:30.5:1:1:0:40.7:15:1:0:2.6 0/1:44:2:1,1:23,18:0.0455:2,2:26:1:30:1:1:1.27044:43:4:0.0455:0:5 -10 42384722 . A G 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.71403;SOR=1.87475;LSEQ=GAACGGAATCGAATGGAATC;RSEQ=TCATCGGATGGAAACGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:0.125:2,2:30.5:1:29.5:1:1:1.73197:54:4:0.125:0:3.5 0/1:47:10:5,5:20,17:0.2128:2,2:27.7:1:29.6:1:1:1.17239:40.5:20:0.2128:0:3.8 -10 42384726 . T C 106 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.4861;SOR=2.11614;LSEQ=GGAATCGAATGGAATCATCA;RSEQ=CGGATGGAAACGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:0.125:2,2:34.5:1:30.5:1:1:1.73197:54:4:0.1333:0:3.5 0/1:47:11:5,6:19,16:0.234:2,2:31.2:1:30.9:1:0.73431:1.414:45.8:22:0.2444:0:3.5 -10 42384727 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCGAATGGAATCATCAT;RSEQ=GGATGGAAACGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:35.7:1:29.6:1:1:0:40.7:15:1:0:2.6 0/1:47:2:1,1:23,21:0.0426:2,2:27.5:1:32:0:1:1.09307:49:4:0.0435:0:2 -10 42384737 . C T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12876;LSEQ=GAATCATCATCGGATGGAAA;RSEQ=GAATGGAATCATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:5,1:5,5:0.375:2,2:35:1:28.3:1:0.30694:4.53:42.3:5:0.3333:0:2.5 0/1:47:19:11,8:14,14:0.4043:2,2:30.5:1:31.1:1:0.76683:1.37:39.2:38:0.413:0:2.3 -10 42384747 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CGGATGGAAACGAATGGAAT;RSEQ=ATCATCGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:25.1:1:32.1:1:1:0:40.7:32:1:0:2.6 0/1:47:2:1,1:24,21:0.0426:2,2:41.5:1:29.5:1:1:1.1396:33:4:0.0426:0:2 -10 42384751 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TGGAAACGAATGGAATCATC;RSEQ=TCGAATGGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:21.6:1:29.3:1:1:0:40.7:15:1:0:2.6 0/1:47:2:1,1:24,21:0.0426:2,2:36:1:31:1:1:1.1396:45.5:4:0.0426:0:3 -10 42384758 . GG TT 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATCATCATCGAAT;RSEQ=AATCGAATGGAATCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:15.4:1:29.6:1:1:0:40.7:7:1:0:2.6 0/1:43:2:1,1:22,19:0.0465:2,2:36.5:1:29.5:1:1:1.15394:53:4:0.0465:0:4 -10 42384764 . G A 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCATCGAATGGAATC;RSEQ=AATGGAATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:8,4:0:2,0:13.1:1:27.6:1:1:0:46.4:11:1:0:2.6 0/1:38:3:2,1:19,16:0.0789:2,2:16.7:1:29.3:1:1:1.66:48.7:6:0.0789:0:4.3 -10 42384768 . G A 91 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70582;SOR=0.66284;LSEQ=ATCATCGAATGGAATCGAAT;RSEQ=GAATCATCAAATGGAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:3,1:4,3:0.3636:2,2:5:0:27.8:1:1:2.09:38:8:0.3636:0:2 0/1:33:9:6,3:12,12:0.2727:2,2:4.9:1:28.8:1:0.45849:1.96:37:18:0.2727:0:2.3 -10 42384770 . A G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69919;SOR=0.61636;LSEQ=CATCGAATGGAATCGAATGG;RSEQ=ATCATCAAATGGAATCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:5,2:0.3636:2,2:6.5:1:29:1:0.57576:2.28835:48.8:8:0.3636:0:2.3 0/1:31:8:4,4:13,10:0.2581:2,2:27.3:1:31.8:1:1:1.28895:49.4:16:0.2581:0:2 -10 42384772 . TCATCAAATGGAATCAGATGGAATCATCATCAAATGAAATCGAATAGAAC T 92 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=TCGAATGGAATCGAATGGAA;RSEQ=TATGGAATGAAATCCAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:6,3:0,0:1:0,2:36.8:1:29.2:1:1:0:45.1:18:1:1:2.8 0/1:30:8:5,3:11,11:0.2667:2,2:54.4:1:28.3:1:0.68873:1.64:35.6:16:0.2667:0.2667:2.4 -10 42384774 . A C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATCGAATGGAATC;RSEQ=TCAAATGGAATCAGATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,2:0:2,0:10.8:1:28.2:1:1:0:50.8:10:1:0:3.4 0/1:30:2:1,1:11,10:0.0667:2,2:14.5:1:33:1:1:1.09544:43:4:0.087:0:5 -10 42384777 . A AATG 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATCGAATGGAATCATC;RSEQ=AATGGAATCAGATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,2:0:2,0:13.3:1:29.7:1:1:0:50:6:1:0:2.3 0/1:26:2:1,1:8,9:0.0769:2,2:13.5:1:30.9:1:1:1.12:43:4:0.1053:0.0385:5 -10 42384905 . TATG AAT 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTAATGGAATCAAAATCG;RSEQ=GAATCGAATGGAAACACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:35:0:28:0:1:0:36:2:1:0:6 1/1:4:4:3,1:0,0:1:0,2:13:1:29.3:1:1:0:30.8:8:1:0.75:4.8 -10 42384924 . A G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=GTATGGAATCGAATGGAAAC;RSEQ=CCATCGAATTGAAACGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:8.8:1:29.5:1:1:0:31.7:12:1:0:2.7 0/1:9:2:2,0:6,1:0.2222:2,0:14.5:1:30:1:1:0:38.5:4:0.2222:0:4 -10 42384933 . TT AG 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52105;SOR=Inf;LSEQ=CGAATGGAAACACCATCGAA;RSEQ=GAAACGAATGGAATTATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:14:1:30:1:1:0:32.9:14:1:0:2.7 0/1:13:2:2,0:8,2:0.1538:2,0:24.5:1:32.3:1:1:0:38.5:4:0.1538:0:3 -10 42384951 . T C 89 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21254;SOR=5.0495;LSEQ=AATTGAAACGAATGGAATTA;RSEQ=CATGAAATTGAAATGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:11,1:0.0769:2,0:27:0:26:0:0.15385:0:40:2:0.0769:0:3 0/1:23:7:6,1:14,2:0.3043:2,2:25.6:1:32:1:1:1.15868:34.7:14:0.3043:0:4.4 -10 42384983 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12;SOR=0;LSEQ=AATGGATGGACTCATCATCG;RSEQ=ATGGATTCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:12,3:0.1111:2,0:30.5:1:33:0:1:0:27:4:0.125:0:2.5 0/0:33:0:0,0:30,3:0:2,0:29.6:1:29.7:1:1:0:36.9:66:1:0:2.8 -10 42384987 . G C 53 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54282;SOR=Inf;LSEQ=GATGGACTCATCATCGAATG;RSEQ=ATTCGAATGGAATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:14,4:0:2,0:35.8:1:31.1:1:1:0:30.9:17:1:0:2.4 0/1:35:3:2,1:30,2:0.0857:2,2:28.3:1:34:0:0.24217:6.73144:25.7:6:0.0857:0:6 -10 42384995 . T A 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14879;SOR=Inf;LSEQ=CATCATCGAATGGATTCGAA;RSEQ=GGAATCATCGAATGAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:17,6:0:2,0:29.7:1:29.6:1:1:0:31:10.5:1:0:2.6 0/1:40:5:3,2:31,3:0.125:2,2:25.4:1:31.2:1:0.11397:6.36046:27.6:10:0.125:0:5.6 -10 42385004 . C T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54749;SOR=Inf;LSEQ=ATGGATTCGAATGGAATCAT;RSEQ=GAATGAAATTGATTGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:21,6:0:2,0:25.7:1:29.8:1:1:0:31.9:26:1:0:2.9 0/1:51:3:2,1:41,7:0.0588:2,2:18.7:1:29.7:1:0.40739:2.84675:26.3:6:0.0588:0:4.7 -10 42385009 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.71375;SOR=1.52769;LSEQ=TTCGAATGGAATCATCGAAT;RSEQ=AAATTGATTGAAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:19,6:4,0:0.8621:0,2:22.7:1:28.6:1:0.55261:0:30.9:50:0.8621:0:3.3 1/1:53:48:40,8:5,0:0.9057:0,2:21.3:1:28.5:1:1:0:41:96:0.9057:0:3.3 -10 42385031 . A G 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.70027;SOR=0.81099;LSEQ=AATTGATTGAAATCATCATC;RSEQ=AATGGAATCGAATGGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:21:16,5:10,5:0.5:2,2:20.7:1:30.9:1:0.7086:1.58:30.7:42:0.5122:0:4.7 0/1:76:34:25,9:26,10:0.4474:2,2:18.6:1:30.1:1:1:1.07:48.3:68:0.4533:0:5 -10 42385035 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54409;SOR=Inf;LSEQ=GATTGAAATCATCATCAAAT;RSEQ=GAATCGAATGGCATCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:32,14:0:2,0:19.4:1:31.7:1:1:0:29.8:92:1:0:4.2 0/1:87:2:1,1:59,25:0.023:2,2:16.5:1:28.5:1:0.51573:2.33372:41:4:0.0233:0:5 -10 42385036 . G A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54434;SOR=Inf;LSEQ=ATTGAAATCATCATCAAATG;RSEQ=AATCGAATGGCATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:32,15:0:2,0:19.5:1:31:1:1:0:30:94:1:0:4.2 0/1:89:2:1,1:61,26:0.0225:2,2:18.5:1:27.5:1:0.51711:2.32112:55:4:0.023:0:6 -10 42385040 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54457;SOR=Inf;LSEQ=AAATCATCATCAAATGGAAT;RSEQ=GAATGGCATCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:31,17:0:2,0:21:1:30.5:1:1:0:29.7:96:1:0:4.3 0/1:91:2:1,1:60,28:0.022:2,2:7:0:32:0:0.54307:2.12311:49:4:0.0225:0:3 -10 42385044 . T A 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03203;LSEQ=CATCATCAAATGGAATCGAA;RSEQ=GGCATCATTGAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:1,0:31,17:0.0204:2,0:49:0:32:0:1:0:40:2:0.0208:0:4 0/1:95:2:2,0:60,33:0.0211:2,0:24.5:1:32:0:0.54177:0:32.5:4:0.0215:0:3 -10 42385046 . GC AT 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02113;LSEQ=TCATCAAATGGAATCGAATG;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:1,0:29,18:0.0204:2,0:7:0:32:0:1:0:30:2:0.0204:0:5 0/1:96:2:2,0:60,34:0.0208:2,0:21.5:1:31.5:0:0.53772:0:50:4:0.0211:0:5.5 -10 42385047 . C T 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.233;SOR=0.49463;LSEQ=CATCAAATGGAATCGAATGG;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:44:27,17:1,0:0.898:0,2:24.7:1:29.5:1:1:0:29:88:0.9565:0:4.4 1/1:96:78:49,29:0,0:0.8125:0,2:24.7:1:28.7:1:1:0:46.6:77:0.837:0:4.4 -10 42385049 . T G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5493;SOR=Inf;LSEQ=TCAAATGGAATCGAATGGCA;RSEQ=CATTGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:29,18:0:2,0:25.1:1:31:1:1:0:29.5:94:0.9792:0:4.4 0/1:94:2:1,1:58,34:0.0213:2,2:26:1:30:1:1:1.69569:55:4:0.0213:0:5.5 -10 42385060 . A G 57 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3085;SOR=Inf;LSEQ=CGAATGGCATCATTGAATGG;RSEQ=ATCGAATGGAATCATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:27,17:0:2,0:33:1:30.7:1:1:0:30:88:1:0:4.6 0/1:96:4:3,1:54,38:0.0417:2,2:35:1:28.8:1:0.64399:2.10:46.3:3:0.0326:0:5.5 -10 42385063 . C T 63 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.94844;LSEQ=ATGGCATCATTGAATGGAAT;RSEQ=GAATGGAATCATCATCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:1,0:26,19:0.0217:2,0:37:0:31:0:1:0:34:2:0.0227:0:6 0/1:96:4:3,1:54,38:0.0417:2,2:26.8:1:31.5:1:0.64399:2.10:45.3:8:0.0426:0:5.3 -10 42385074 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GAATGGAATCGAATGGAATC;RSEQ=TCATCAGATGGAAATGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:27,22:0:2,0:33.4:1:30.1:1:1:0:30.5:48:1:0:4.7 0/1:110:2:1,1:61,47:0.0182:2,2:41:1:31:1:1:1.29476:55:4:0.0187:0:5.5 -10 42385100 . A G 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12587;SOR=0.3497;LSEQ=AGATGGAAATGAATGGAATC;RSEQ=TCACTGAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:46:25,21:2,1:0.9388:2,2:24.8:1:30.7:1:1:1.66297:30.1:92:0.9388:0:5.1 1/1:114:96:53,43:8,6:0.8421:2,2:26:1:30:1:1:1.08102:43.8:95:0.8482:0:5.1 -10 42385104 . CT TA 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08366;SOR=0.33206;LSEQ=GGAAATGAATGGAATCATCA;RSEQ=GAATGGAATCGAATGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:44:24,20:1,1:0.9362:2,2:23.6:1:29.3:1:1:1.20:29.9:88:0.9362:0:4 1/1:111:92:50,42:6,6:0.8288:2,2:26.1:1:28.8:1:1:1.19:43.3:184:0.8288:0:4.1 -10 42385115 . C A 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30745;SOR=Inf;LSEQ=GAATCATCACTGAATGGAAT;RSEQ=GAATGGATTCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:33,25:0:2,0:16.9:1:30.1:1:1:0:32.3:116:1:0:4 0/1:123:4:3,1:64,54:0.0325:2,2:9:1:24.8:1:0.62619:2.51:47.5:8:0.0325:0:4.5 -10 42385121 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCACTGAATGGAATCGAATG;RSEQ=ATTCATTGAATGGAATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:34,23:0:2,0:17.6:1:31.2:1:1:0:34.8:114:0.9828:0:4 0/1:133:2:1,1:72,57:0.015:2,2:5.5:1:26.5:1:1:1.26088:49:4:0.0152:0:3 -10 42385126 . A T 60 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.73998;LSEQ=GAATGGAATCGAATGGATTC;RSEQ=TTGAATGGAATCAGATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:34,24:0.0169:2,0:1:0:25:0:0.42373:0:49:2:0.0172:0:4 0/1:137:4:3,1:73,60:0.0292:2,2:15.8:1:30.3:1:0.62863:2.45:24.8:8:0.0294:0:6 -10 42385134 . G A 37 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29911;LSEQ=TCGAATGGATTCATTGAATG;RSEQ=AATCAGATGGGATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:1:0,1:37,25:0.0159:2,0:11:0:31:0:0.4127:0:23:2:0.0159:0:4 0/1:146:3:2,1:78,65:0.0205:2,2:18.3:1:23.7:1:1:1.66:40:2:0.0139:0:5 -10 42385139 . A T 112 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01087;SOR=Inf;LSEQ=TGGATTCATTGAATGGAATC;RSEQ=GATGGGATCATCGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:39,27:0:2,0:21.7:1:30.6:1:1:0:38.8:132:1:0:4 0/1:149:13:7,6:76,60:0.0872:2,2:30.1:1:30.4:1:1:1.08511:36.9:26:0.0884:0:4 -10 42385143 . G A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20172;SOR=0.2004;LSEQ=TTCATTGAATGGAATCAGAT;RSEQ=GGATCATCGAATGGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:37,26:0.0303:2,0:40.5:1:28.5:1:0.5125:0:38:4:0.0308:0:5 0/0:162:1:1,0:93,68:0.0062:2,0:27:0:30:0:1:0:25:2:0.0062:0:6 -10 42385145 . G A 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51332;SOR=2.32382;LSEQ=CATTGAATGGAATCAGATGG;RSEQ=ATCATCGAATGGACTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:69:42,27:0,0:0.9857:0,2:23.8:1:30.4:1:1:0:41.5:138:0.9857:0:4.1 1/1:162:161:95,66:0,0:0.9938:0,2:22.7:1:29.4:1:1:0:41.8:160:1:0:4.2 -10 42385151 . C T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4334;SOR=0.66465;LSEQ=ATGGAATCAGATGGGATCAT;RSEQ=GAATGGACTTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:7:2,5:45,27:0.0886:2,2:20.9:1:30.4:1:0.11265:4.09036:37.3:14:0.0897:0:4.7 0/1:198:12:6,6:104,78:0.0606:2,2:22.4:1:29.1:1:0.7657:1.33132:48.5:24:0.0609:0:4.7 -10 42385152 . G A 60 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.69724;LSEQ=TGGAATCAGATGGGATCATC;RSEQ=AATGGACTTGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:0,1:52,33:0.0116:2,0:42:0:29:0:0.39535:0:40:2:0.0118:0:7 0/1:204:4:2,2:116,83:0.0196:2,2:12.8:1:30.3:1:1:1.39522:51:8:0.0198:0:5.3 -10 42385156 . G T 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0901;SOR=0;LSEQ=ATCAGATGGGATCATCGAAT;RSEQ=GACTTGAATGGAATCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:0,2:54,35:0.022:2,0:23.5:1:27:1:0.16264:0:50:4:0.022:0:6 0/0:211:0:0,0:123,86:0:2,0:22.6:1:31:1:1:0:43.2:68.667:0.9904:0.0047:4 -10 42385158 . A T 78 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1835;SOR=Inf;LSEQ=CAGATGGGATCATCGAATGG;RSEQ=CTTGAATGGAATCATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:55,39:0:2,0:24.4:1:30:1:1:0:44.5:46:1:0:4 0/1:218:6:4,2:122,88:0.0275:2,2:30:1:30.2:1:1:1.44:36.5:12:0.0283:0:4.7 -10 42385160 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0943;SOR=0;LSEQ=GATGGGATCATCGAATGGAC;RSEQ=TGAATGGAATCATTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:55,41:0.0204:2,2:10.5:1:28.5:1:1:1.33738:27:4:0.0206:0:3 0/0:220:0:0,0:127,91:0:2,0:23.6:1:30.2:1:1:0:43.9:42.6:0.9907:0:4 -10 42385161 . T G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01246;SOR=0.37567;LSEQ=ATGGGATCATCGAATGGACT;RSEQ=GAATGGAATCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:99:91:51,40:5,3:0.9192:2,2:25.2:1:31.5:1:1:1.30372:45.9:90:0.9184:0:4 1/1:221:179:104,75:22,13:0.81:2,2:24.8:1:30.7:1:0.70813:1.21929:45.5:58.667:0.8186:0:4.1 -10 42385172 . A G 103 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.40903;SOR=1.97933;LSEQ=GAATGGACTTGAATGGAATC;RSEQ=TTGAATGGACTCGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:3:3,0:67,44:0.0259:2,0:34:1:30.7:1:0.28272:0:40.7:6:0.0259:0:4.3 0/1:260:13:8,5:140,107:0.05:2,2:24:1:28:1:0.78236:1.22:36.2:12:0.0471:0:3.9 -10 42385173 . T C 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55619;SOR=Inf;LSEQ=AATGGACTTGAATGGAATCA;RSEQ=TGAATGGACTCGAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:70,44:0:2,0:26.5:1:30.8:1:1:0:47.1:228:1:0:3.7 0/1:262:3:2,1:148,111:0.0115:2,2:38.3:1:30.3:1:1:1.50:54:6:0.0115:0:6 -10 42385175 . G C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59011;SOR=0.44255;LSEQ=TGGACTTGAATGGAATCATT;RSEQ=AATGGACTCGAAAGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:70,46:0.0168:2,2:6:1:28:1:1:1.51614:36:4:0.0169:0:4.5 0/0:267:2:1,1:150,114:0.0075:2,2:28:1:31.5:1:1:1.3144:47.5:4:0.0075:0:5 -10 42385179 . G A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55546;SOR=Inf;LSEQ=CTTGAATGGAATCATTGAAT;RSEQ=GACTCGAAAGGAATCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:76,52:0:2,0:25.8:1:31.7:1:1:0:46.4:127:1:0:3.8 0/1:284:3:2,1:161,119:0.0106:2,2:13:1:29.7:1:1:1.48:54:6:0.0108:0:4 -10 42385183 . T A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14193;SOR=0.34891;LSEQ=AATGGAATCATTGAATGGAC;RSEQ=CGAAAGGAATCATTATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:3,2:72,52:0.0379:2,2:19.2:1:28.4:1:1:1.08:42:10:0.0379:0:5.4 0/1:296:4:2,2:162,127:0.0135:2,2:33.5:1:28.8:1:1:1.27451:30:8:0.0139:0:5.5 -10 42385184 . C G 73 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32987;SOR=Inf;LSEQ=ATGGAATCATTGAATGGACT;RSEQ=GAAAGGAATCATTATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:76,56:0:2,0:26.6:1:30.9:1:1:0:46.6:131:1:0:3.7 0/1:295:5:3,2:159,129:0.0169:2,2:39.6:1:31.8:1:1:1.22:48.8:10:0.0173:0:5.2 -10 42385187 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09841;SOR=0;LSEQ=GAATCATTGAATGGACTCGA;RSEQ=AGGAATCATTATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:76,58:0.0144:2,2:22.5:1:32:1:1:1.3077:60:4:0.0144:0:4 0/0:303:0:0,0:165,138:0:2,0:26.4:1:29.6:1:1:0:48.4:59.6:1:0:3.6 -10 42385188 . A T 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00069;SOR=3.08503;LSEQ=AATCATTGAATGGACTCGAA;RSEQ=GGAATCATTATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:10:5,5:73,56:0.0709:2,2:34.8:1:30.5:1:0.74837:1.30105:38.6:20:0.073:0:3.5 0/1:309:59:33,26:134,114:0.1909:2,2:22.1:1:29.2:1:0.88456:1.08:40.4:118:0.1928:0:3.4 -10 42385189 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09349;SOR=0;LSEQ=ATCATTGAATGGACTCGAAA;RSEQ=GAATCATTATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:77,60:0.0142:2,2:13.5:1:30:1:1:1.281:44.5:4:0.0143:0:3 0/0:319:0:0,0:172,143:0:2,0:25.5:1:30.7:1:1:0:48.6:77.75:0.9873:0:3.6 -10 42385190 . GA AG 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0504;SOR=0.2987;LSEQ=TCATTGAATGGACTCGAAAG;RSEQ=ATCATTATTGAATGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:7:4,3:75,58:0.05:2,2:20.4:1:30.5:1:1:1.03:47.3:14:0.05:0:4.4 0/1:324:5:3,2:174,144:0.0154:2,2:22.8:1:31.5:1:1:1.24:48.8:10:0.0157:0:4 -10 42385191 . A G 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03076;SOR=0.53576;LSEQ=CATTGAATGGACTCGAAAGG;RSEQ=ATCATTATTGAATGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:138:119:67,52:6,6:0.8623:2,2:26.8:1:31.6:1:0.76468:1.29:48.9:238:0.9084:0:3.5 1/0:322:248:135,113:36,31:0.7702:2,2:27:1:31:1:1:1.03:50.8:247:0.7917:0:3.6 -10 42385195 . A T 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00261;SOR=Inf;LSEQ=GAATGGACTCGAAAGGAATC;RSEQ=TTATTGAATGGAATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:77,66:0:2,0:27.2:1:30.8:1:1:0:48.1:286:1:0:3.5 0/1:344:18:9,9:175,150:0.0523:2,2:28:1:28:1:0.81102:1.16614:41.9:5:0.0445:0:3.6 -10 42385197 . T G 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05033;SOR=0.64128;LSEQ=ATGGACTCGAAAGGAATCAT;RSEQ=ATTGAATGGAATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:44:25,19:54,49:0.2973:2,2:27.2:1:31.8:1:0.71864:1.19:48.9:88:0.2973:0:4.2 0/1:347:74:35,39:147,122:0.2133:2,2:26.9:1:31.1:1:0.29355:1.34145:50.2:36:0.2105:0:4.3 -10 42385198 . A G 95 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28881;SOR=3.5281;LSEQ=TGGACTCGAAAGGAATCATT;RSEQ=TTGAATGGAATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:1:1,0:81,71:0.0065:2,0:22:0:34:0:1:0:34:2:0.0066:0:3 0/1:352:8:5,3:182,162:0.0227:2,2:27.5:1:31.8:1:0.72778:1.48:50.4:16:0.0231:0:3.5 -10 42385199 . T C 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31977;SOR=Inf;LSEQ=GGACTCGAAAGGAATCATTA;RSEQ=TGAATGGAATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:82,73:0:2,0:25.7:1:30.7:1:1:0:48.4:154:1:0:3.3 0/1:356:4:2,2:186,165:0.0112:2,2:25:1:31.3:1:1:1.12689:51.8:8:0.0114:0:4 -10 42385200 . T G 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32022;SOR=Inf;LSEQ=GACTCGAAAGGAATCATTAT;RSEQ=GAATGGAATTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:82,72:0:2,0:26.1:1:30.3:1:1:0:48.7:153:1:0.0065:3.3 0/1:355:4:2,2:184,167:0.0113:2,2:13.5:1:29.3:1:1:1.10149:42:8:0.0114:0:2.8 -10 42385202 . A C 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32134;SOR=Inf;LSEQ=CTCGAAAGGAATCATTATTG;RSEQ=ATGGAATTGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:83,73:0:2,0:25.9:1:30.2:1:1:0:48.8:77:0.9935:0.0064:3.2 0/1:365:4:2,2:187,174:0.011:2,2:19.8:1:28.8:1:1:1.07447:52.3:3:0.0085:0:3.5 -10 42385204 . T G 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08562;SOR=0.14356;LSEQ=CGAAAGGAATCATTATTGAA;RSEQ=GGAATTGAATGGAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:3:2,1:84,75:0.0184:2,2:19:1:31.3:1:1:1.78:44.7:6:0.0185:0:4.7 0/0:374:1:1,0:192,178:0.0027:2,0:50:0:34:0:1:0:60:2:0.0027:0:4 -10 42385206 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09072;SOR=0;LSEQ=AAAGGAATCATTATTGAATG;RSEQ=AATTGAATGGAATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:87,74:0.0123:2,2:22:1:31.5:1:1:1.1745:60:4:0.0124:0:2.5 0/0:377:0:0,0:193,182:0:2,0:24.8:1:30.7:1:1:0:50.6:74:1:0:3.2 -10 42385209 . T TTAAATGGAATCATCATCAAATGAAA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0894;SOR=0;LSEQ=GGAATCATTATTGAATGGAA;RSEQ=TGAATGGAATCATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:86,78:0.012:2,2:20:1:30.1:1:1:1.10191:44:4:0.0123:0.012:3 0/0:388:0:0,0:198,190:0:2,0:24.4:1:29.5:1:1:0:50.9:76.6:1:0:3.1 -10 42385211 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21311;SOR=0.21099;LSEQ=AATCATTATTGAATGGAATT;RSEQ=AATGGAATCATCGAATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:86,80:0.0118:2,2:30.5:1:29.5:1:1:1.07451:60:4:0.0121:0:3 0/0:398:1:0,1:199,191:0.0025:2,0:5:0:25:0:0.49105:0:55:2:0.0025:0:5 -10 42385215 . G A 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01588;SOR=2.87073;LSEQ=ATTATTGAATGGAATTGAAT;RSEQ=GAATCATCGAATGGTCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:6:3,3:78,82:0.0359:2,2:20.7:1:28.7:1:1:1.05:36.2:12:0.0368:0:3.8 0/1:403:39:21,18:185,178:0.0968:2,2:24.1:1:28.8:1:0.7399:1.12:46.4:38:0.0952:0:3.9 -10 42385219 . T A 47 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02193;SOR=0;LSEQ=TTGAATGGAATTGAATGGAA;RSEQ=CATCGAATGGTCTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:3:2,1:75,82:0.0188:2,2:7:1:29.7:1:0.60886:2.18:49.3:6:0.0189:0:3 0/0:409:0:0,0:206,203:0:2,0:24.3:1:29:1:1:0:51.3:57.429:1:0:2.9 -10 42385220 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07927;SOR=0;LSEQ=TGAATGGAATTGAATGGAAT;RSEQ=ATCGAATGGTCTCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:75,82:0.0125:2,2:35.5:1:30.5:1:1:1.09:60:4:0.0125:0:5 0/0:407:0:0,0:205,201:0:2,0:24.6:1:31.1:1:1:0:51.5:80.2:0.9975:0:2.9 -10 42385224 . G T 69 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19076;SOR=Inf;LSEQ=TGGAATTGAATGGAATCATC;RSEQ=AATGGTCTCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:80,83:0:2,0:25.3:1:30.5:1:1:0:48.1:53.333:0.9938:0:2.8 0/1:413:6:2,4:198,205:0.0145:2,2:20.3:1:26.7:1:0.68565:1.92871:55.7:12:0.0147:0:3.5 -10 42385226 . A G 87 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1127;SOR=Inf;LSEQ=GAATTGAATGGAATCATCGA;RSEQ=TGGTCTCGAATGGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:81,85:0:2,0:25:1:30.7:1:1:0:48.1:82:1:0:2.8 0/1:411:8:4,4:195,208:0.0195:2,2:25.8:1:29.1:1:1:1.07:47.8:7:0.0174:0:5.6 -10 42385227 . T A 78 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18935;SOR=Inf;LSEQ=AATTGAATGGAATCATCGAA;RSEQ=GGTCTCGAATGGAATCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:78,85:0:2,0:25.2:1:30.5:1:1:0:48.2:80.5:0.9938:0:2.8 0/1:406:6:3,3:192,208:0.0148:2,2:28.3:1:30.3:1:1:1.08:50.5:12:0.0151:0:5.2 -10 42385228 . G C 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08213;SOR=0;LSEQ=ATTGAATGGAATCATCGAAT;RSEQ=GTCTCGAATGGAATCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:78,84:0.0122:2,2:33:1:27:1:1:1.08:54:4:0.0125:0:4.5 0/0:407:0:0,0:195,211:0:2,0:25.2:1:30.4:1:1:0:51.8:66.667:0.9975:0:2.7 -10 42385236 . A T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26965;LSEQ=GAATCATCGAATGGTCTCGA;RSEQ=TGGAATCATTATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:164:146:69,77:7,11:0.8902:2,2:24.3:1:30.3:1:0.61895:1.41:48.8:72:0.8889:0:2.7 1/0:401:275:127,148:62,64:0.6858:2,2:25.9:1:29.3:1:0.59136:1.12859:52.9:67.75:0.6826:0:2.6 -10 42385239 . G A 55 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32792;SOR=Inf;LSEQ=TCATCGAATGGTCTCGAATG;RSEQ=AATCATTATCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:76,89:0:2,0:24:1:31.1:1:1:0:48:81.5:1:0:2.6 0/1:402:4:2,2:183,211:0.01:2,2:26.3:1:27.8:1:1:1.15:60:8:0.0102:0:4 -10 42385241 . A G 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.66533;LSEQ=ATCGAATGGTCTCGAATGGA;RSEQ=TCATTATCAAATGGAATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:1:0,1:74,90:0.006:2,0:39:0:30:0:1:0:24:2:0.0061:0:2 0/1:400:4:2,2:181,214:0.01:2,2:32:1:30.5:1:1:1.18:57.8:8:0.0102:0:3.3 -10 42385243 . C T 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58664;SOR=0.42381;LSEQ=CGAATGGTCTCGAATGGAAT;RSEQ=ATTATCAAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:75,89:0.012:2,2:12.5:1:31:1:1:1.19:60:4:0.0121:0:5 0/0:392:2:1,1:174,214:0.0051:2,2:24:1:28:1:1:1.23:60:4:0.0052:0:5 -10 42385247 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08322;SOR=0;LSEQ=TGGTCTCGAATGGAATCATT;RSEQ=TCAAATGGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:70,85:0.0127:2,2:22.5:1:32.5:1:1:1.21:48:4:0.0129:0:2.5 0/0:386:0:0,0:169,211:0:2,0:26.4:1:28.6:1:1:0:51.6:94:0.9895:0:2.4 -10 42385248 . T C 89 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00747;SOR=0.166;LSEQ=GGTCTCGAATGGAATCATTA;RSEQ=CAAATGGAATCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:7:4,3:65,81:0.0455:2,2:23.1:1:32:1:0.70161:1.66:44.7:14:0.0464:0:3.7 0/0:384:3:1,2:169,209:0.0078:2,2:24.3:1:29.7:1:1:1.61527:34:6:0.008:0:3.3 -10 42385254 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08107;SOR=0;LSEQ=GAATGGAATCATTATCAAAT;RSEQ=GAATCGAATGGAATCACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:62,81:0.0138:2,2:34:0:31.5:1:1:1.30:47:4:0.0142:0:4.5 0/0:363:0:0,0:160,202:0:2,0:26.9:1:30.5:1:1:0:51.5:71.4:0.9972:0:2.3 -10 42385255 . G A 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00378;SOR=2.95858;LSEQ=AATGGAATCATTATCAAATG;RSEQ=AATCGAATGGAATCACCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:8:2,6:60,76:0.0556:2,2:32:1:29.8:1:0.46635:2.35548:37.4:16:0.0571:0:3.1 0/1:357:53:26,27:129,170:0.1485:2,2:30.7:1:29.6:1:0.45501:1.27:49.5:106:0.1523:0:3.4 -10 42385257 . A G 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00795;SOR=2.69546;LSEQ=TGGAATCATTATCAAATGGA;RSEQ=TCGAATGGAATCACCGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:8:2,6:59,76:0.0559:2,2:32.5:1:31.9:1:0.46673:2.31639:37.4:16:0.0584:0:3.1 0/1:348:48:23,25:129,168:0.1379:2,2:31:1:31.8:1:0.63886:1.20:49.3:96:0.1416:0:3.3 -10 42385258 . T A 67 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02446;SOR=0.16024;LSEQ=GGAATCATTATCAAATGGAA;RSEQ=CGAATGGAATCACCGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:5:2,3:59,77:0.0355:2,2:9.4:1:29:1:1:1.14821:52.6:10:0.0362:0:4.2 0/0:343:2:2,0:149,190:0.0058:2,0:1:0:24.5:1:0.19536:0:60:4:0.006:0:3 -10 42385263 . T A 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04863;SOR=0.23826;LSEQ=CATTATCAAATGGAATCGAA;RSEQ=GGAATCACCGAATAGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:3,2:55,72:0.0379:2,2:21:1:30.4:1:0.65358:1.95:48.4:10:0.0394:0:3.8 0/0:324:3:1,2:137,180:0.0093:2,2:19.3:1:30.7:1:1:1.5203:50.7:6:0.0095:0:4.3 -10 42385264 . G A 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.62621;LSEQ=ATTATCAAATGGAATCGAAT;RSEQ=GAATCACCGAATAGAATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:0,1:56,73:0.0077:2,0:16:0:27:0:1:0:40:2:0.0079:0:2 0/1:321:4:2,2:135,181:0.0125:2,2:40.8:1:30.5:1:1:1.34:57:8:0.0129:0:1.3 -10 42385271 . C T 87 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11184;SOR=Inf;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=CGAATAGAATCGAATGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:46,69:0:2,0:26.5:1:31.2:1:1:0:44.9:37.333:1:0:2.2 0/1:289:8:3,5:119,160:0.0277:2,2:25.6:1:29.3:1:1:1.23867:51:16:0.028:0:4.5 -10 42385273 . G A 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69157;SOR=0.64459;LSEQ=TGGAATCGAATGGAATCACC;RSEQ=AATAGAATCGAATGGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:3:2,1:42,65:0.0273:2,2:31.3:1:28.7:1:0.56269:3.06:50.7:6:0.028:0:3.3 0/1:282:5:2,3:118,159:0.0177:2,2:13.6:1:27.2:1:1:1.11282:54.4:4:0.0144:0:3.2 -10 42385274 . A C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56167;SOR=Inf;LSEQ=GGAATCGAATGGAATCACCG;RSEQ=ATAGAATCGAATGGAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:43,66:0:2,0:26.8:1:29.5:1:1:0:44.8:20.8:1:0:2.2 0/1:276:3:1,2:115,158:0.0109:2,2:31.3:1:31.3:1:1:1.45379:36:6:0.0111:0:7 -10 42385276 . T A 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05682;SOR=0.19302;LSEQ=AATCGAATGGAATCACCGAA;RSEQ=AGAATCGAATGGAACAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:4:3,1:38,63:0.0381:2,2:25:1:29.8:1:0.29682:4.90:42.3:8:0.0388:0:3.8 0/0:265:2:1,1:109,153:0.0075:2,2:7.5:1:27.5:1:1:1.40:60:4:0.0078:0:5.5 -10 42385278 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07878;SOR=0;LSEQ=TCGAATGGAATCACCGAATA;RSEQ=AATCGAATGGAACAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:37,61:0.02:2,2:5:1:28.5:1:1:1.64:60:4:0.0208:0:1.5 0/0:255:0:0,0:104,151:0:2,0:26.4:1:30.9:1:1:0:51.4:41.5:1:0:2.1 -10 42385283 . G A 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18856;LSEQ=TGGAATCACCGAATAGAATC;RSEQ=AATGGAACAATCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:34,54:0.0222:2,2:5:0:32:0:1:1.58:47:4:0.0233:0:4.5 0/1:228:6:2,4:89,129:0.0263:2,2:25.7:1:29:1:1:1.37793:53.5:12:0.0267:0:3 -10 42385286 . T A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32631;SOR=Inf;LSEQ=AATCACCGAATAGAATCGAA;RSEQ=GGAACAATCATCGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:33,54:0:2,0:27:1:30.6:1:1:0:43.3:86:1:0:2.1 0/1:212:4:2,2:84,124:0.0189:2,2:20.5:1:30:1:1:1.47:56.8:8:0.019:0:3.3 -10 42385288 . GAACA G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCACCGAATAGAATCGAATG;RSEQ=ATCATCGAATGGACTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:32,49:0:2,0:26.8:1:30.5:1:1:0:42.9:162:1:0:2 0/1:197:2:1,1:75,120:0.0102:2,2:11.5:1:29:1:1:1.60:56:4:0.0103:0:3.5 -10 42385290 . A T 50 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02489;SOR=0;LSEQ=ACCGAATAGAATCGAATGGA;RSEQ=CAATCATCGAATGGACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:3:2,1:30,48:0.037:2,2:37.3:1:31.7:1:0.55893:3.15:36.3:6:0.0385:0:4 0/0:194:0:0,0:73,119:0:2,0:24.6:1:29.7:1:1:0:49.9:191:1:0:1.8 -10 42385291 . C T 48 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02601;SOR=0;LSEQ=CCGAATAGAATCGAATGGAA;RSEQ=AATCATCGAATGGACTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:3:1,2:31,47:0.037:2,2:29:1:30.3:1:1:1.31479:46.7:6:0.038:0:3.3 0/0:190:0:0,0:71,113:0:2,0:24.2:1:31.2:1:1:0:50:45:0.9783:0:1.7 -10 42385294 . T C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.8855;LSEQ=AATAGAATCGAATGGAACAA;RSEQ=CATCGAATGGACTCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:1:0,1:31,46:0.0128:2,0:41:0:32:0:1:0:50:2:0.0137:0:4 0/1:176:2:0,2:65,108:0.0114:2,0:28:1:32.5:1:0.53038:0:53:4:0.0116:0:2.5 -10 42385299 . G A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65158;SOR=0.68579;LSEQ=AATCGAATGGAACAATCATC;RSEQ=AATGGACTCAAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:0,2:29,39:0.0286:2,0:14:1:22.5:1:0.50766:0:44:1:0.0147:0:3.5 0/1:152:3:1,2:54,95:0.0197:2,2:32:1:30:1:1:1.13592:35.3:6:0.02:0:2.3 -10 42385304 . G A 27 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83903;LSEQ=AATGGAACAATCATCGAATG;RSEQ=ACTCAAATGGAATTATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:1:1,0:20,36:0.0172:2,0:6:0:15:0:0.36842:0:48:0:0:0:2 0/1:138:2:1,1:49,87:0.0145:2,2:7.5:1:27:1:1:1.77:39:4:0.0149:0:4 -10 42385306 . C G 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32375;SOR=Inf;LSEQ=TGGAACAATCATCGAATGGA;RSEQ=TCAAATGGAATTATCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:20,35:0:2,0:21.3:1:32.1:1:1:0:41.3:54:1:0:2 0/1:133:5:2,3:45,80:0.0376:2,2:21:1:29.4:1:1:1.18:43.8:4:0.031:0:2.4 -10 42385307 . T C 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21044;SOR=0.20678;LSEQ=GGAACAATCATCGAATGGAC;RSEQ=CAAATGGAATTATCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:0,2:20,31:0.037:2,0:17:1:32.5:1:0.52104:0:55:4:0.0377:0:3.5 0/0:128:1:0,1:44,81:0.0078:2,0:4:0:32:0:1:0:60:2:0.0079:0:3 -10 42385309 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACAATCATCGAATGGACTC;RSEQ=AATGGAATTATCCTCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:20,31:0:2,0:19.9:1:30.1:1:1:0:41.4:50:1:0:2.1 0/1:122:2:0,2:42,78:0.0164:2,0:7.5:1:32.5:1:0.54478:0:29:4:0.0165:0:4.5 -10 42385312 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCGAATGGACTCAAA;RSEQ=GGAATTATCCTCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:18,27:0:2,0:19.4:1:31:1:1:0:41.2:90:1:0:2.2 0/1:103:2:1,1:31,70:0.0194:2,2:8.5:1:32.5:1:0.52694:2.24:53:4:0.0196:0:3 -10 42385313 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCGAATGGACTCAAAT;RSEQ=GAATTATCCTCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:18,25:0:2,0:19.3:1:31.9:1:1:0:41.2:86:1:0:2.2 0/1:99:2:1,1:30,67:0.0202:2,2:14:1:28:1:0.53041:2.21:53:4:0.0204:0:3 -10 42385318 . T C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5998;SOR=0.49009;LSEQ=CGAATGGACTCAAATGGAAT;RSEQ=ATCCTCAAATGGAATCGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:16,21:0.0513:2,2:23.5:1:30.5:1:1:1.30:25:4:0.0513:0:4.5 0/1:78:2:1,1:21,55:0.0256:2,2:6:0:33.5:1:0.48718:2.58:45:4:0.0263:0:4.5 -10 42385320 . T A 45 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04353;SOR=0;LSEQ=AATGGACTCAAATGGAATTA;RSEQ=CCTCAAATGGAATCGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:2,1:15,21:0.0769:2,2:13.7:1:29:1:0.5703:2.73:36.3:6:0.0769:0:4 0/0:70:0:0,0:19,50:0:2,0:12.7:1:29.3:1:1:0:46:33.5:0.9853:0:1.8 -10 42385325 . A C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01826;SOR=0.28021;LSEQ=ACTCAAATGGAATTATCCTC;RSEQ=AATGGAATCGAAGGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:5,8:5,8:0.5:2,2:16.8:1:32:1:1:1:39.2:26:0.5:0:2.5 0/1:51:11:4,7:11,29:0.2157:2,2:13.9:1:30.6:1:0.7109:1.49:46.8:22:0.2157:0:2.3 -10 42385334 . C G 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55708;SOR=0.32284;LSEQ=GAATTATCCTCAAATGGAAT;RSEQ=GAAGGGAATTATCTAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:7,10:0.1053:2,0:25:1:31.5:1:0.50877:0:32.5:4:0.1053:0:5.5 0/1:28:1:0,1:9,18:0.0357:2,0:12:0:32:0:1:0:27:2:0.0357:0:2 -10 42385338 . G T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCCTCAAATGGAATCGAA;RSEQ=GGAATTATCTAATGCAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:5,7:0,0:1:0,2:11.8:1:30.8:1:1:0:33.7:24:1:0:3.3 1/1:21:20:6,14:1,0:0.9524:0,2:5.5:1:29.6:1:0.33333:0:41.8:19:0.95:0:2 -10 42385348 . T G 70 d7;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCGAAGGGAATTATC;RSEQ=AATGCAATCGAATAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:9.6:1:30.4:1:1:0:31:10:1:0:4.6 1/1:3:3:1,2:0,0:1:0,2:4.7:1:29.7:1:1:0:28.7:6:1:0:2.7 -10 42385396 . G A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATCGAATAGAATCATCGA;RSEQ=TGGACTCGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:26:0:32:0:1:0:22:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:32.5:1:32:0:1:0:24:4:1:0:3.5 -10 42385419 . G A 25 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCGAATGGAATCATCGA;RSEQ=TGGAATGGAATGGAATAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:49:0:32:0:1:0:22:2:1:0:3 1/0:3:2:1,1:0,1:0.6667:0,2:29:1:25.5:1:1:0:27:4:0.6667:0:4 -10 42385474 . A C 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCATTGAATGGAAT;RSEQ=GAATGGAATCATCGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:30:0:33:0:1:0:28:2:1:0:2 1/0:4:3:2,1:0,0:0.75:0,2:12.3:1:29.7:1:1:0:26.3:6:1:0:5.7 -10 42385501 . T A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCGAGTGGAATCGAA;RSEQ=GGAATCACAATCAAATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:16.3:1:32.7:1:1:0:30:6:1:0:3 0/1:22:2:1,1:19,1:0.0909:1,2:14.5:1:29:1:0.17749:13.78761:30:4:0.0909:0:3 -10 42385507 . C T 125 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14328;SOR=7.53277;LSEQ=CGAGTGGAATCGAATGGAAT;RSEQ=ACAATCAAATGGCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:33:0:32:0:1:0:40:2:0.3333:0:4 1/1:21:17:17,0:3,1:0.8095:2,1:22.9:1:30.8:1:0.19048:0:32.5:16:0.8:0:4.9 -10 42385509 . CA TG 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGAATCGAATGGAATCA;RSEQ=ATCAAATGGCATCGAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:10.3:1:31.4:1:1:0:35:24:1:0.8333:1.8 1/1:26:24:24,0:0,0:0.9231:0,1:22.1:1:31.3:1:1:0:32.8:48:1:0.1923:3.3 -10 42385520 . C A 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCACAATCAAATGG;RSEQ=ATCGAATGTAATCATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:14,1:0,0:1:0,1:12.1:1:31.1:1:1:0:38.9:30:1:0:1.9 1/1:47:46:39,7:0,0:0.9787:0,2:18.7:1:29.7:1:1:0:34.5:92:1:0:2.7 -10 42385527 . T C 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15311;SOR=0.15843;LSEQ=CACAATCAAATGGCATCGAA;RSEQ=GTAATCATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:17,4:0.087:2,2:6:1:32.5:1:0.39526:3.91152:49.5:4:0.087:0:1 0/1:69:1:1,0:51,16:0.0145:2,0:13:0:32:0:1:0:25:2:0.0149:0:4 -10 42385534 . A C 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.66004;SOR=0.73388;LSEQ=AAATGGCATCGAATGTAATC;RSEQ=TCATCAAATGGAATCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:18,6:0.0769:2,0:13:1:32.5:1:1:0:42:4:0.0769:0:2 0/1:87:5:4,1:60,21:0.0575:2,2:25.2:1:30.8:1:1:1.39:41.8:10:0.0575:0:2.6 -10 42385536 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ATGGCATCGAATGTAATCAT;RSEQ=ATCAAATGGAATCAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:22,6:0:2,0:19:1:32:1:1:0:40.5:56:1:0:1.4 0/1:93:2:1,1:67,22:0.0215:2,2:5:0:32.5:1:0.44371:3.00065:46:4:0.022:0:3.5 -10 42385538 . T C 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.56733;SOR=Inf;LSEQ=GGCATCGAATGTAATCATCA;RSEQ=CAAATGGAATCAAAAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:24,9:0:2,0:17.9:1:30.8:1:1:0:41.8:32:1:0:1.3 0/1:94:3:3,0:66,25:0.0319:2,0:22.3:1:27:1:0.56246:0:31.3:2:0.0217:0:4 -10 42385540 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCGAATGTAATCATCATC;RSEQ=AATGGAATCAAAAATAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:24,11:0:2,0:18.5:1:30:1:1:0:41.4:34:0.9714:0:1.3 0/1:99:2:1,1:71,25:0.0202:2,2:11.5:1:28.5:1:0.46223:2.80439:47:4:0.0206:0:1 -10 42385545 . G C 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGTAATCATCATCAAATG;RSEQ=AATCAAAAATAACCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:27,13:0:2,0:20.5:1:31:1:1:0:41.4:39:1:0:1.3 0/1:127:2:1,1:84,39:0.0157:2,2:12:0:34:0:0.53935:2.13942:47:4:0.016:0:2 -10 42385547 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05182;SOR=0;LSEQ=TGTAATCATCATCAAATGGA;RSEQ=TCAAAAATAACCATCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:26,12:0.05:2,2:28.5:1:29:1:1:2.12136:44.5:4:0.0513:0:1.5 0/0:134:0:0,0:89,45:0:2,0:20.5:1:29.8:1:1:0:41.6:43.667:1:0:1.8 -10 42385549 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAATCATCATCAAATGGAAT;RSEQ=AAAAATAACCATCATCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:28,13:0:2,0:23.6:1:31.5:1:1:0:41.4:40:1:0:1.2 0/1:140:2:1,1:90,46:0.0143:2,2:26:1:28.5:1:1:1.94638:43.5:4:0.0144:0:2 -10 42385550 . A C 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.57603;SOR=Inf;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AAAATAACCATCATCAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:28,12:0:2,0:24.4:1:30.4:1:1:0:41.8:39:0.975:0:1.2 0/1:141:4:3,1:87,48:0.0284:2,2:28.8:1:31.3:1:1:1.65:35.5:8:0.0284:0:4 -10 42385553 . A G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCATCAAATGGAATCAAA;RSEQ=ATAACCATCATCAATTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:28,15:0:2,0:26:1:29.9:1:1:0:41.4:42:1:0:1.2 0/1:147:2:2,0:92,53:0.0136:2,0:32:1:34:0:0.53574:0:36:4:0.0137:0:3 -10 42385554 . A G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61848;SOR=0.57136;LSEQ=ATCATCAAATGGAATCAAAA;RSEQ=TAACCATCATCAATTGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:26,15:0.0465:2,0:28.5:1:31.5:1:0.53488:0:39.5:4:0.0476:0:2.5 0/1:148:4:2,2:91,51:0.027:2,2:13.3:1:26:1:0.62136:1.77678:30.5:3:0.0204:0:2.3 -10 42385556 . A C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCAAATGGAATCAAAAAT;RSEQ=ACCATCATCAATTGGTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:28,15:0:2,0:28.6:1:28.8:1:1:0:41.4:86:1:0:1.2 0/1:150:2:2,0:93,55:0.0133:2,0:35:1:32:1:0.53244:0:40:4:0.0135:0:5 -10 42385557 . A G 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAAATGGAATCAAAAATA;RSEQ=CCATCATCAATTGGTATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:29,15:0:2,0:28.6:1:30.2:1:1:0:41:88:1:0:1.2 0/1:151:2:1,1:94,55:0.0132:2,2:26:0:34:0:1:1.70267:46:4:0.0133:0:3.5 -10 42385559 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAATGGAATCAAAAATAAC;RSEQ=ATCATCAATTGGTATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:28,16:0:2,0:29.1:1:31.3:1:1:0:40.5:88:0.9778:0:1.3 0/1:153:2:1,1:95,56:0.0131:2,2:12:1:28:1:1:1.69023:24:4:0.0134:0:1 -10 42385564 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.05448;SOR=0;LSEQ=GGAATCAAAAATAACCATCA;RSEQ=CAATTGGTATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:28,18:0.0417:2,2:29.5:1:29.5:1:1:1.54082:43.5:4:0.0417:0:1.5 0/0:156:0:0,0:97,59:0:2,0:27.5:1:29.3:1:1:0:40.1:51:1:0:1.6 -10 42385565 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCAAAAATAACCATCAT;RSEQ=AATTGGTATTGAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:29,19:0:2,0:30.5:1:31.3:1:1:0:39.9:96:1:0:1.3 0/1:158:2:1,1:95,60:0.0127:2,2:14:1:29:1:1:1.57849:22:4:0.0128:0:4.5 -10 42385566 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCAAAAATAACCATCATC;RSEQ=ATTGGTATTGAATGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:29,19:0:2,0:31:1:29.9:1:1:0:39.9:96:1:0:1.3 0/1:159:2:1,1:96,61:0.0126:2,2:24.5:1:30.5:1:1:1.56908:29:4:0.0127:0:3.5 -10 42385567 . A C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAAAAATAACCATCATCA;RSEQ=TTGGTATTGAATGGAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:29,20:0:2,0:30.8:1:30.2:1:1:0:39.5:98:1:0:1.3 0/1:159:2:1,1:95,60:0.0126:2,2:43:0:32:0:1:1.57849:31:4:0.013:0:3 -10 42385571 . G C 87 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35663;SOR=Inf;LSEQ=AAAATAACCATCATCAATTG;RSEQ=TATTGAATGGAATTGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,20:0:2,0:32.5:1:31.3:1:1:0:39.8:96:0.9796:0:1.3 0/1:163:7:5,2:92,64:0.0429:2,2:34.7:1:31.3:1:0.70215:1.73:37.9:14:0.0438:0:3.6 -10 42385574 . T C 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57558;SOR=Inf;LSEQ=ATAACCATCATCAATTGGTA;RSEQ=TGAATGGAATTGTCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:29,20:0:2,0:33:1:30.1:1:1:0:39.5:48:1:0:1.3 0/1:163:4:3,1:91,66:0.0245:2,2:35:1:32:1:0.64159:2.17:32.5:8:0.0255:0:3.5 -10 42385577 . A T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0519;SOR=0;LSEQ=ACCATCATCAATTGGTATTG;RSEQ=ATGGAATTGTCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:27,19:0.0417:2,2:20.5:1:28:1:1:1.41046:29:4:0.0426:0:4.5 0/0:161:0:0,0:93,68:0:2,0:29.2:1:28.9:1:1:0:39.8:79.5:1:0:1.6 -10 42385579 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05342;SOR=0;LSEQ=CATCATCAATTGGTATTGAA;RSEQ=GGAATTGTCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:27,19:0.0417:2,2:37:1:30.5:1:1:1.41046:50.5:4:0.0417:0:1.5 0/0:158:0:0,0:90,68:0:2,0:29.7:1:29.7:1:1:0:39.8:316:1:0:1.6 -10 42385581 . G C 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATCAATTGGTATTGAATG;RSEQ=AATTGTCATCAAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:28,20:0:2,0:32.8:1:30.7:1:1:0:39.5:47:1:0:1.3 0/1:156:2:1,1:86,67:0.0128:2,2:30:0:34:0:1:1.28149:29:4:0.0131:0:3.5 -10 42385584 . T C 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAATTGGTATTGAATGGAA;RSEQ=TGTCATCAAATGGAATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:28,20:0:2,0:32.1:1:30.5:1:1:0:39.5:96:1:0:1.3 0/1:151:3:2,1:81,63:0.0199:2,2:43.3:1:32.3:1:1:1.55:43.7:6:0.0203:0:5 -10 42385585 . TG GC 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAATTGGTATTGAATGGAAT;RSEQ=TCATCAAATGGAATTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:28,20:0:2,0:31.8:1:29.7:1:1:0:39.5:47:1:0:1.3 0/1:150:2:1,1:82,66:0.0133:2,2:31.5:1:31.8:1:1:1.24061:51.5:4:0.0134:0:1.5 -10 42385586 . G C 71 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0395;SOR=0.2378;LSEQ=AATTGGTATTGAATGGAATT;RSEQ=TCATCAAATGGAATTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:5:2,3:26,17:0.1042:2,2:31:1:30.6:1:0.63649:2.25365:31:10:0.1042:0:1.4 0/1:150:4:2,2:80,64:0.0267:2,2:36.5:1:32:1:1:1.2481:45:8:0.0272:0:2.5 -10 42385595 . T C 83 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1744;LSEQ=TGAATGGAATTGTCATCAAA;RSEQ=GGAATTCAAAGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:26,19:0.0426:2,2:13.5:1:30.5:1:1:1.35916:51:4:0.0426:0:1 0/1:141:7:3,4:68,63:0.0496:2,2:29.1:1:29.9:1:0.71272:1.43536:40.6:14:0.0507:0:2.1 -10 42385599 . ATTCAAA TTCAAAT 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATTGTCATCAAATGGA;RSEQ=GGAATCATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:26,20:0:2,0:26.9:1:29.9:1:1:0:40.1:92:1:0:1.2 0/1:140:2:1,1:69,69:0.0143:2,2:37.5:1:29.4:1:1:1:43:4:0.0144:0:6 -10 42385608 . AATC A 28 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.04234;SOR=0;LSEQ=CATCAAATGGAATTCAAAGG;RSEQ=ATCATCAAATGGAACCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:16,18:0.0556:2,2:25:1:28.5:1:1:1.12:38:4:0.0571:0.0278:4.5 0/0:137:0:0,0:66,68:0:2,0:23.2:1:29.3:1:1:0:38.5:133:0.9852:0:1.5 -10 42385610 . T A 113 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.19707;SOR=4.33334;LSEQ=TCAAATGGAATTCAAAGGAA;RSEQ=CATCATCAAATGGAACCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:1,0:15,18:0.0286:2,0:39:0:28:0:0.47059:0:42:2:0.0294:0:1 0/1:132:15:6,9:59,58:0.1136:2,2:19.7:1:29.1:1:0.58542:1.52101:44.2:30:0.1136:0:2.7 -10 42385612 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AAATGGAATTCAAAGGAATC;RSEQ=TCATCAAATGGAACCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,19:0:2,0:23.9:1:30.4:1:1:0:40.4:34:1:0:1.1 0/1:126:2:1,1:59,65:0.0159:2,2:10:0:32.5:1:1:1.10:46:4:0.0163:0:3.5 -10 42385614 . CA TT 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ATGGAATTCAAAGGAATCAT;RSEQ=TCAAATGGAACCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,19:0:2,0:22.2:1:31.7:1:1:0:40.4:70:1:0:1.1 0/1:122:2:1,1:56,64:0.0164:2,2:20.5:1:28.5:1:1:1.14:43:4:0.0169:0:5 -10 42385616 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGAATTCAAAGGAATCATCA;RSEQ=CAAATGGAACCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,18:0:2,0:21.6:1:30.6:1:1:0:40:66:1:0:1.2 0/1:118:2:1,1:51,63:0.0169:2,2:31.5:1:29:1:1:1.23:43:4:0.0175:0:3.5 -10 42385617 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATTCAAAGGAATCATCAT;RSEQ=AAATGGAACCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:15,18:0:2,0:20.7:1:31.8:1:1:0:40:66:1:0:1.2 0/1:117:2:0,2:50,63:0.0171:2,0:31:1:32:1:0.5042:0:42.5:4:0.0172:0:3.5 -10 42385618 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTCAAAGGAATCATCATC;RSEQ=AATGGAACCGAATGGAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:14,18:0:2,0:20.4:1:30.2:1:1:0:39.5:64:1:0:1.1 0/1:114:2:1,1:47,64:0.0175:2,2:17.5:1:29:1:1:1.36:43:4:0.0177:0:5 -10 42385620 . A G 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58468;SOR=Inf;LSEQ=TTCAAAGGAATCATCATCAA;RSEQ=TGGAACCGAATGGAATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:12,17:0:2,0:20.4:1:29.9:1:1:0:38.1:28:1:0:1.1 0/1:117:4:2,2:48,65:0.0342:2,2:13:1:31.5:1:1:1.35:46.8:8:0.0348:0:2.8 -10 42385621 . T G 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03776;SOR=0;LSEQ=TCAAAGGAATCATCATCAAA;RSEQ=GGAACCGAATGGAATCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:12,14:0.0714:2,2:11:1:32:1:1:1.16:49.5:4:0.0714:0:1.5 0/0:114:0:0,0:48,66:0:2,0:20.9:1:29.2:1:1:0:36.5:56:1:0:1.4 -10 42385622 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAAGGAATCATCATCAAAT;RSEQ=GAACCGAATGGAATCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:0:2,0:20.1:1:31.5:1:1:0:38.6:54:1:0:1.1 0/1:111:2:1,1:45,64:0.018:2,2:13.5:1:28:1:1:1.42:43:4:0.0182:0:5 -10 42385626 . C A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATCATCATCAAATGGAA;RSEQ=CGAATGGAATCCTCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,12:0:2,0:18.4:1:31.1:1:1:0:38.2:22:0.9565:0:0.9 0/1:111:3:2,1:43,63:0.027:2,2:7:1:29.3:1:0.56786:2.90:44.3:6:0.0273:0:2 -10 42385627 . C T 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38783;SOR=0.48834;LSEQ=GAATCATCATCAAATGGAAC;RSEQ=GAATGGAATCCTCATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:1,2:10,10:0.125:2,2:20:1:31.3:1:1:1.94223:42:6:0.1304:0:2 0/1:108:7:2,5:41,57:0.0648:2,2:19.7:1:30.3:1:0.69753:1.78883:34:14:0.0654:0:2.3 -10 42385628 . G A 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCATCAAATGGAACC;RSEQ=AATGGAATCCTCATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:19.2:1:30.9:1:1:0:37.1:44:1:0:1.2 0/1:105:4:2,2:41,59:0.0381:2,2:22:1:27.8:1:1:1.43:33.5:8:0.0385:0:2.5 -10 42385632 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCAAATGGAACCGAAT;RSEQ=GAATCCTCATTGAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:15.7:1:31.7:1:1:0:36.5:46:1:0:1.3 0/1:103:2:1,1:36,65:0.0194:2,2:6.5:1:27.5:1:1:1.79:25:4:0.0196:0:1.5 -10 42385660 . A G 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1816;SOR=2.78732;LSEQ=CATTGAATGGAAATGAAAGG;RSEQ=GTCATCATCTAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:1,3:3,4:0.3636:2,2:12.5:1:31.8:1:1:2.09375:28.5:8:0.3636:0:1.5 1/0:55:34:6,28:9,12:0.6182:2,2:27.7:1:30.4:1:0.06199:3.41356:32.1:68:0.6182:0:2.1 -10 42385661 . G T 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01843;SOR=0;LSEQ=ATTGAATGGAAATGAAAGGA;RSEQ=TCATCATCTAATGGAATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:37:1:30:1:1:1.29:24:4:0.2222:0:3.5 0/0:54:0:0,0:14,40:0:2,0:30.6:1:31.4:1:1:0:32.5:108:1:0:1.7 -10 42385663 . C A 28 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01481;SOR=0;LSEQ=TGAATGGAAATGAAAGGAGT;RSEQ=ATCATCTAATGGAATCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:37:1:28.5:1:1:1:24:4:0.25:0:3.5 0/0:54:0:0,0:14,40:0:2,0:30.5:1:31.5:1:1:0:32.5:108:1:0:1.7 -10 42385667 . A T 30 d7;v4;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.02778;SOR=0.04669;LSEQ=TGGAAATGAAAGGAGTCATC;RSEQ=TCTAATGGAATCGCATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:37:0:30.5:1:1:2.44949:24:4:0.3333:0:3.5 0/1:50:1:0,1:14,34:0.02:2,0:3:0:27:0:1:0:40:2:0.0204:0:3 -10 42385679 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTCATCATCTAATGGAAT;RSEQ=GCATGGAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:42.2:1:31.3:1:1:0:39.3:12:1:0:1.7 0/1:43:2:0,2:14,27:0.0465:2,0:25:1:31:0:1:0:23:4:0.0465:0:3.5 -10 42385706 . G C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATGGAATCATCATTAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:19.7:1:29.5:1:1:0:45.3:12:1:0:1.2 0/1:27:2:1,1:10,15:0.0741:2,2:15:0:33:1:1:1.48:30:4:0.0741:0:1.5 -10 42385721 . T C 110 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17157;SOR=6.87863;LSEQ=GAATCGAATGGAATCATCAT;RSEQ=AAATGGAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:11:1:30.7:1:1:1.7321:40.3:6:0.6:0:2 1/1:13:12:5,7:0,0:0.9231:0,2:7.8:1:30.7:1:1:0:39.8:24:0.9231:0:2 -10 42386030 . A G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GAATGCAATCATCATCGAAT;RSEQ=GAATCGAATGGAATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:47:1:32.5:1:1:0:32:4:0.6667:0:1 1/0:3:2:2,0:0,0:0.6667:0,0:39:1:29.5:1:1:0:24:4:0.6667:0:1 -10 42386048 . C A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=ATAGAATCGAATGGAATCAT;RSEQ=GAATGGACTCGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,0:0:0,0:29:1:30.5:1:1:0:32:4:0.6667:0:1 1/0:4:2:1,1:2,0:0.5:0,2:18.5:1:30:0:1:0:28:4:0.5:0:2.5 -10 42386057 . T A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AATGGAATCATCGAATGGAC;RSEQ=CGAATGGAATAATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:25.7:1:31:1:1:0:29.3:6:1:0:2 1/0:4:2:1,1:2,0:0.5:0,2:27.5:1:31:1:1:0:28:4:0.5:0:2.5 -10 42386433 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATGGAATCATCATCCAA;RSEQ=GGAAACTAATGGAATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:20:0:34:0:1:0:40:2:1:0:3 1/1:2:2:2,0:0,0:1:0,0:18.5:1:33:0:1:0:32:4:1:0:4 -10 42386438 . A G 34 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCATCATCCAATGGAA;RSEQ=CTAATGGAATCAACATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:25:0:34:0:1:0:40:2:1:0:3 1/1:2:2:2,0:0,0:1:0,0:23.5:1:34:0:1:0:32:4:1:0:4 -10 42386561 . G A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGAATGGAATCATCGAAT;RSEQ=AAATTGATTGAAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:29:0:32:0:1:0:40:2:0.5:0:3 1/1:2:2:0,2:0,0:1:0,0:35:1:32:0:1:0:32:4:1:0:4.5 -10 42386583 . T G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTGATTGAAATCATCATC;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:50:0:33:0:1:0:40:2:0.5:0:3 1/1:2:2:0,2:0,0:1:0,0:44:1:33:0:1:0:32:4:1:0:4.5 -10 42386599 . A T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCTAATGGAATCGAATGG;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:34:0:30:0:1:0:40:2:0.5:0:3 1/1:2:2:0,2:0,0:1:0,0:28:1:30:0:1:0:32:4:1:0:4.5 -10 42386956 . C A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22794;SOR=Inf;LSEQ=AAATAGAATCATCGAATGGA;RSEQ=TCGAATGGAATCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:7.9:1:32.1:1:1:0:41.4:14:1:0:2.4 0/1:10:3:2,1:7,0:0.3:0,2:6:1:29.7:1:0.3:0:32.7:6:0.3:0:5 -10 42386971 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.93674;LSEQ=ATGGACTCGAATGGAATCAT;RSEQ=GAATGGAATGGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:9,0:0.1:0,0:19:0:28:0:1:0:47:2:0.1:0:2 0/1:11:2:1,1:9,0:0.1818:0,2:20.5:1:28.5:1:0.18182:0:37:4:0.1818:0:5 -10 42386981 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.48617;SOR=Inf;LSEQ=ATGGAATCATCGAATGGAAT;RSEQ=GAATGGAATAGTCAATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:10,0:0:0,0:24.9:1:33.2:1:1:0:41.6:20:1:0:2 0/1:13:2:1,1:11,0:0.1538:0,2:30.5:1:29.5:1:0.15385:0:37:4:0.1538:0:5 -10 42386989 . ATAGTCAATGAACTCGAA TTAATCCATGGACTCGAATTCAATCACCATCGAATACAATCGAATGGAGTCATCGAATCGACTCAAG 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.19928;SOR=0;LSEQ=ATCGAATGGAATGGAATGGA;RSEQ=TGGAATCATCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:9,0:0.1818:0,2:48.5:1:29.8:1:0.18182:0:40:4:0.1818:0.1818:2 0/0:13:0:0,0:12,1:0:1,0:34.2:1:29.9:1:1:0:38.2:26:1:0:2.8 -10 42386990 . T C 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36022;SOR=0.29661;LSEQ=TCGAATGGAATGGAATGGAA;RSEQ=AGTCAATGAACTCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:0.8889:0,0:34.6:1:32.6:1:1:0:44:16:0.8889:0:1.9 1/0:13:9:9,0:1,1:0.6923:2,0:34.1:1:32.4:1:0.18182:0:38.6:18:0.6923:0:2.4 -10 42386993 . T A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=AATGGAATGGAATGGAATAG;RSEQ=CAATGAACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:37.1:1:28.2:1:1:0:41.8:8:1:0:2 0/1:13:2:1,1:11,0:0.1538:0,2:42.5:1:29.5:1:0.15385:0:37:4:0.1538:0:5 -10 42387004 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=ATGGAATAGTCAATGAACTC;RSEQ=AATGGAATCATCATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:41.6:1:30.8:1:1:0:41.8:18:1:0:1.9 0/1:13:2:1,1:10,0:0.1538:0,2:47.5:1:30.5:1:0.16667:0:37:4:0.1538:0:5 -10 42387057 . A G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATCATCGAGTGGAATCGAAT;RSEQ=GAATCATGATCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:2:0:32:0:1:0:40:2:0.5:0:2 1/1:3:3:2,1:0,0:1:0,2:17.7:1:30.3:1:1:0:27.3:6:1:0:2.7 -10 42387062 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGAGTGGAATCGAATAGAAT;RSEQ=ATGATCAAATGGAATCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:46:0:31:0:1:0:22:2:1:0:6 1/0:3:2:2,0:0,1:0.6667:0,0:16.5:1:28.5:1:0.33333:0:29.5:4:0.6667:0:3 -10 42387122 . G A 99 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAAAAATAACCATCATCA;RSEQ=TTGGTATTGAATGGAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:6,4:0,0:1:0,2:23.3:1:30.1:1:1:0:31.9:20:1:0:2.7 1/1:1:1:0,1:0,0:1:0,0:40:0:32:0:1:0:24:2:1:0:1 -10 42387141 . G C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTGGTATTGAATGGAATT;RSEQ=TCATCAAATGGAATTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:10,4:0.1765:2,2:31.3:1:32.7:1:0.51471:4.49144:28.3:6:0.1765:0:2.7 0/0:3:0:0,0:1,2:0:2,0:25:1:32.7:1:1:0:34.7:6:1:0:1.7 -10 42387215 . AA GG 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42748;SOR=0.37948;LSEQ=CATTGAATGGAAATGAAAGG;RSEQ=TCATCATCTAATGGAATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:31:15,16:2,0:0.9394:0,2:24.6:1:30.6:1:0.48485:0:26.5:62:0.9688:0:2.5 1/1:34:29:16,13:1,2:0.8529:2,2:26.8:1:30.7:1:0.58871:2.39:30.5:58:0.8529:0:2.9 -10 42387216 . A G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96919;LSEQ=ATTGAATGGAAATGAAAGGA;RSEQ=TCATCATCTAATGGAATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:2,1:0,0:0.0882:0,2:9:1:31:1:1:0:27:6:1:0:3.3 0/1:35:3:2,1:1,2:0.0857:2,2:14.7:1:32:1:1:3.11:26.7:6:0.6:0:3.7 -10 42387234 . C T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01598;LSEQ=GAATCATCATCTAATGGAAT;RSEQ=GCATGGAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:21,20:0.0455:2,2:25.5:1:31.5:1:1:1.04883:30:4:0.0465:0:3 0/1:65:3:3,0:36,24:0.0462:2,0:11.7:1:31:1:0.28111:0:38.7:6:0.0469:0:4.7 -10 42387246 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AATGGAATCGCATGGAATCA;RSEQ=CATCAAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:24,25:0:2,0:26.4:1:30.6:1:1:0:32.5:98:1:0:3 0/1:100:2:1,1:64,34:0.02:2,2:33.5:1:29.5:1:1:1.86977:32:4:0.0202:0:3.5 -10 42387250 . C A 88 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1718;SOR=4.424;LSEQ=GAATCGCATGGAATCATCAT;RSEQ=AAATGGAATCGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:1,0:24,25:0.02:2,0:21:0:29:0:1:0:39:2:0.0204:0:3 0/1:108:9:6,3:63,36:0.0833:2,2:19.1:1:27.9:1:1:1.14:29.7:18:0.0841:0:5.7 -10 42387261 . G A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55185;SOR=Inf;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATGGAATAATCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:26,27:0:2,0:28.1:1:30.5:1:1:0:33.2:52:1:0:3 0/1:112:3:2,1:67,41:0.0268:2,2:35.7:1:29.7:1:1:1.22:39:6:0.0275:0:5.7 -10 42387268 . A C 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ATCAAATGGAATCGAATGGA;RSEQ=TAATCATCGAATGGAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:0:2,0:30.1:1:30.5:1:1:0:33.6:50:1:0:3.1 0/1:112:2:1,1:68,42:0.0179:2,2:16:1:27.5:1:1:1.61177:42:4:0.018:0:5 -10 42387270 . A C 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13593;SOR=2.97702;LSEQ=CAAATGGAATCGAATGGAAT;RSEQ=ATCATCGAATGGAATCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:45:23,22:2,1:0.9:2,2:31.4:1:31.6:1:1:1.88826:32.5:44:0.898:0:3.1 1/1:112:108:67,41:2,1:0.9643:2,2:31.1:1:31.9:1:1:1.22168:34.8:216:0.9643:0:3.6 -10 42387272 . T A 101 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.51339;SOR=2.25005;LSEQ=AATGGAATCGAATGGAATAA;RSEQ=CATCGAATGGAATCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:24,23:0.0408:2,2:32:1:31.5:1:1:1.04259:45:4:0.0426:0:4 0/1:114:10:7,3:64,40:0.0877:2,2:29.4:1:30.5:1:0.7403:1.45:27.3:20:0.0877:0:5.9 -10 42387273 . C T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55499;SOR=Inf;LSEQ=ATGGAATCGAATGGAATAAT;RSEQ=ATCGAATGGAATCTAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:25,24:0:2,0:31:1:31.6:1:1:0:33.6:48:1:0:3.1 0/1:115:3:2,1:70,42:0.0261:2,2:28.7:1:30.7:1:1:1.20:39:6:0.0263:0:4.7 -10 42387277 . G A 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58253;SOR=2.42301;LSEQ=AATCGAATGGAATAATCATC;RSEQ=AATGGAATCTAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:48:22,26:0,0:0.96:0,2:29.6:1:30.1:1:1:0:32.6:96:0.9796:0:3.1 1/1:119:117:72,45:1,1:0.9832:2,2:31.7:1:30.3:1:1:1.59:35.4:234:0.9832:0:3.4 -10 42387279 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGAATGGAATAATCATCGA;RSEQ=TGGAATCTAATGGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:23,26:0:2,0:29.3:1:30.5:1:1:0:34:98:0.98:0:3 0/1:127:2:1,1:75,50:0.0157:2,2:24:1:28.5:1:1:1.49505:38.5:4:0.0159:0:3.5 -10 42387282 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08317;SOR=0;LSEQ=AATGGAATAATCATCGAATG;RSEQ=AATCTAATGGAATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:25,27:0.037:2,2:35.5:1:29.5:1:1:1.08:42.5:4:0.0385:0:4 0/0:132:0:0,0:76,56:0:2,0:38:0:13:0:1:0:33:0:0:0:8 -10 42387284 . A T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3252;SOR=0.39618;LSEQ=TGGAATAATCATCGAATGGA;RSEQ=TCTAATGGAATCATTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:24,28:0.037:2,2:48:0:31.5:1:1:1.16:45:4:0.0377:0:5 0/1:134:2:1,1:76,55:0.0149:2,2:37.5:1:31:1:1:1.37839:25.5:4:0.0154:0:5 -10 42387286 . CT GG 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATAATCATCGAATGGAAT;RSEQ=AATGGAATCATTGAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:25,30:0:2,0:25.4:1:31.5:1:1:0:35.8:110:1:0:2.8 0/1:135:2:1,1:77,56:0.0148:2,2:9.5:1:28.2:1:1:1.37169:31:4:0.0149:0.0074:1.5 -10 42387287 . T A 103 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03551;SOR=Inf;LSEQ=AATAATCATCGAATGGAATC;RSEQ=AATGGAATCATTGAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:25,31:0:2,0:24.7:1:29.2:1:1:0:36:27:1:0:2.8 0/1:135:11:8,3:69,51:0.0815:2,2:33.9:1:29.9:1:0.52394:1.96:27.5:10:0.0752:0:5.8 -10 42387288 . A G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.83085;SOR=0.86909;LSEQ=ATAATCATCGAATGGAATCT;RSEQ=ATGGAATCATTGAACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:10:4,6:21,24:0.1818:2,2:36.5:1:31.9:1:0.74114:1.30608:41.6:20:0.1852:0:3.5 0/1:136:22:14,8:65,49:0.1618:2,2:28:1:32:1:0.64169:1.32:40.5:44:0.1642:0:3.7 -10 42387290 . T G 79 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03327;SOR=0.24591;LSEQ=AATCATCGAATGGAATCTAA;RSEQ=GGAATCATTGAACAGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:6:3,3:23,26:0.1091:2,2:23.3:1:30.7:1:1:1.13:42:12:0.1132:0:2.7 0/1:138:4:2,2:79,54:0.029:2,2:25.8:1:30.8:1:1:1.45878:39:8:0.0294:0:3 -10 42387294 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07437;SOR=0;LSEQ=ATCGAATGGAATCTAATGGA;RSEQ=TCATTGAACAGAATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:24,27:0.0377:2,2:42:1:31.5:1:1:1.12:43:4:0.0385:0:4 0/0:140:0:0,0:84,56:0:2,0:27.9:1:29.6:1:1:0:36.8:139:1:0:3.2 -10 42387295 . T A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57694;SOR=Inf;LSEQ=TCGAATGGAATCTAATGGAA;RSEQ=CATTGAACAGAATTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:25,28:0:2,0:24.7:1:30.4:1:1:0:36.7:106:1:0:2.7 0/1:139:4:3,1:81,54:0.0288:2,2:38.5:1:30:1:1:1.99:30:8:0.0294:0:3.8 -10 42387298 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATCTAATGGAATCA;RSEQ=TGAACAGAATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:27,29:0:2,0:23:1:29.7:1:1:0:37.1:27:1:0:2.7 0/1:138:2:1,1:83,53:0.0145:2,2:43:1:32:1:1:1.56074:31:4:0.0148:0:4.5 -10 42387299 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08685;SOR=0;LSEQ=ATGGAATCTAATGGAATCAT;RSEQ=GAACAGAATTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:27,30:0.0339:2,2:33:0:31:1:1:1.11:45:4:0.0345:0:5 0/0:140:0:0,0:82,53:0:2,0:26.6:1:29.8:1:1:0:36.6:66.5:0.9708:0:3.1 -10 42387303 . C A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00203;SOR=0;LSEQ=AATCTAATGGAATCATTGAA;RSEQ=AGAATTGAATGGAATCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:3,2:26,28:0.0847:2,2:22:1:30.8:1:0.67075:1.60:40:10:0.0862:0:2.6 0/0:140:0:0,0:83,57:0:2,0:25.9:1:31:1:1:0:37.1:45.667:1:0:3.1 -10 42387304 . A G 128 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02559;SOR=4.76239;LSEQ=ATCTAATGGAATCATTGAAC;RSEQ=GAATTGAATGGAATCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:28,29:0.0339:2,2:25:1:31.5:1:1:1.04:23.5:4:0.0345:0:5 0/1:139:20:15,5:68,51:0.1439:2,2:33:1:29.8:1:0.14814:2.24:27.4:40:0.1449:0:4.9 -10 42387308 . T A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58288;SOR=0.41215;LSEQ=AATGGAATCATTGAACAGAA;RSEQ=TGAATGGAATCGTCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:28,29:0.0339:2,2:24:0:32.5:1:1:1.04:45:4:0.0339:0:5 0/1:141:2:1,1:82,57:0.0142:2,2:30.5:1:29:1:1:1.43478:43.5:4:0.0148:0:4 -10 42387317 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGAACAGAATTGAATGGA;RSEQ=TCGTCATCGAATGAATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:28,25:0:2,0:22.5:1:29.6:1:1:0:38:52:1:0:2.6 0/1:144:2:1,1:84,58:0.0139:2,2:36:1:31:1:1:1.44444:42:4:0.014:0:5 -10 42387319 . C G 88 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44987;SOR=2.93452;LSEQ=TGAACAGAATTGAATGGAAT;RSEQ=GTCATCGAATGAATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:0,1:27,22:0.02:2,0:31:0:28:0:0.46:0:31:2:0.0204:0:3 0/1:141:8:6,2:76,57:0.0567:2,2:20.3:1:29.4:1:0.46828:2.24:34.8:16:0.0571:0:3.5 -10 42387323 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAATTGAATGGAATCGTC;RSEQ=TCGAATGAATTGAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:24,23:0:2,0:24.7:1:30.7:1:1:0:39:94:1:0:2.6 0/1:139:2:1,1:78,59:0.0144:2,2:30:1:31.5:1:1:1.31933:42:4:0.0145:0:5 -10 42387324 . T A 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56983;SOR=Inf;LSEQ=AGAATTGAATGGAATCGTCA;RSEQ=CGAATGAATTGAATGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:24,23:0:2,0:24.6:1:30.1:1:1:0:39:22.5:1:0:2.6 0/1:135:3:2,1:74,58:0.0222:2,2:34:1:30.3:1:1:1.56:24.7:6:0.0224:0:5 -10 42387325 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57399;SOR=Inf;LSEQ=GAATTGAATGGAATCGTCAT;RSEQ=GAATGAATTGAATGCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:23,22:0:2,0:25.4:1:30:1:1:0:38.7:21.5:1:0:2.6 0/1:130:4:2,2:72,53:0.0308:2,2:31:1:29.5:1:1:1.3552:42.3:8:0.0308:0:3.8 -10 42387326 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTGAATGGAATCGTCATC;RSEQ=AATGAATTGAATGCAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:23,22:0:2,0:25.2:1:29.2:1:1:0:38.7:14:1:0:2.6 0/1:129:2:1,1:76,51:0.0155:2,2:15:1:28.5:1:1:1.48544:31:4:0.0155:0:4.5 -10 42387335 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCGTCATCGAATGAATT;RSEQ=AATGCAATCATCGAATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:16,20:0:2,0:27.5:1:32.2:1:1:0:38.4:72:1:0:2.3 0/1:123:2:1,1:70,50:0.0163:2,2:6.5:1:30.5:1:1:1.39605:23.5:4:0.0164:0:5.5 -10 42387337 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATCGTCATCGAATGAATTGA;RSEQ=TGCAATCATCGAATGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:16,20:0:2,0:27.9:1:30.9:1:1:0:37.9:72:1:0:2.4 0/1:123:2:0,2:68,51:0.0163:2,0:13:1:33:0:0.18981:0:29.5:4:0.0164:0:4.5 -10 42387342 . A T 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCGAATGAATTGAATGCA;RSEQ=TCATCGAATGGTCTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:0:2,0:29.8:1:31.1:1:1:0:36.3:62:1:0:2.5 0/1:110:3:2,1:61,46:0.0273:2,2:12.7:1:29.3:1:1:1.50:26:6:0.0275:0:5.7 -10 42387350 . A G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATTGAATGCAATCATCGA;RSEQ=TGGTCTCGAATGGCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:0:2,0:27.9:1:30.1:1:1:0:36.3:27:1:0:2.4 0/1:101:3:2,1:55,41:0.0297:2,2:22.7:1:30.3:1:1:1.49:26.7:6:0.0297:0:5.3 -10 42387364 . C A 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCGAATGGTCTCGAATGG;RSEQ=ATCATCTTCAAATGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:10,9:0,0:1:0,2:23.4:1:29.3:1:1:0:32.4:18:1:0:2.6 1/1:98:95:57,38:0,0:0.9694:0,2:24.9:1:29:1:1:0:31.7:190:0.9794:0:4.1 -10 42387370 . C T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGTCTCGAATGGCATCAT;RSEQ=TTCAAATGGAAAGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:21.4:1:30.7:1:1:0:31.4:15:1:0:2.8 0/1:93:3:2,1:53,37:0.0323:2,2:21:1:29.7:1:1:1.39:24.7:6:0.0326:0:5 -10 42387374 . A T 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02999;SOR=5.39628;LSEQ=TCTCGAATGGCATCATCTTC;RSEQ=AATGGAAAGGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:6,6:2,2:0.75:2,2:19.8:1:29:1:1:1:32.5:24:0.75:0:2.7 1/1:88:83:49,34:3,2:0.9432:2,2:28.5:1:29.5:1:1:1.04035:31:166:0.9432:0:4.3 -10 42387376 . A C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45127;SOR=0.46333;LSEQ=TCGAATGGCATCATCTTCAA;RSEQ=TGGAAAGGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:6,7:0.0714:2,0:33:0:29:0:1:0:23:2:0.0714:0:3 0/1:88:3:2,1:50,35:0.0341:2,2:15:1:30.7:1:1:1.39:24.7:6:0.0341:0:5 -10 42387397 . G A 26 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26221;SOR=0.19596;LSEQ=TGGAAAGGAATGGAATCATC;RSEQ=CATAGAATCGAATGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:2,5:0.125:2,0:10:0:25:0:0.375:0:23:2:0.1429:0:3 0/1:76:2:1,1:48,26:0.0263:2,2:29.5:1:26.5:1:1:1.83049:28:4:0.0267:0:5 -10 42387417 . G A 163 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56011;SOR=1.64332;LSEQ=GCATAGAATCGAATGGAATT;RSEQ=TCATTGAATGGACTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:35:1:31:1:1:0:31:4:0.6667:0:6.5 1/0:69:53:35,18:0,0:0.7681:0,2:22.5:1:28.5:1:1:0:26.8:106:0.7681:0:5.2 -10 42387421 . TT AC 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAATCGAATGGAATTGTCA;RSEQ=GAATGGACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:38.3:1:27:1:1:0:35.7:2:1:0:4.7 0/1:66:2:1,1:39,25:0.0303:2,2:32.5:1:30:1:1:1.54914:23:4:0.0303:0:4 -10 42387422 . T C 174 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50507;SOR=1.97609;LSEQ=GAATCGAATGGAATTGTCAT;RSEQ=GAATGGACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:35:0:29:1:1:0:31:4:0.6667:0:6.5 1/1:65:52:33,19:4,6:0.8:2,2:21.3:1:30.6:1:0.29085:2.56:27.4:104:0.8254:0:5.3 -10 42387430 . C A 150 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29362;SOR=4.78502;LSEQ=TGGAATTGTCATTGAATGGA;RSEQ=TCGAATGGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,1:0.25:2,0:27:0:30:0:1:0:40:2:0.25:0:8 1/0:58:36:22,14:9,12:0.6207:2,2:18.9:1:29.1:1:0.27049:2.07:26.3:35:0.614:0:5.9 -10 42387433 . G C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTGTCATTGAATGGACTC;RSEQ=AATGGAATCAACATCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:30.8:1:32.5:1:1:0:38.5:8:1:0:4 0/1:54:2:1,1:28,23:0.037:2,2:15:0:33:1:1:1.21285:29:4:0.037:0:2 -10 42387439 . A T 113 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.75783;LSEQ=CATTGAATGGACTCGAATGG;RSEQ=ATCAACATCAAACGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:0.25:2,0:18:0:27:0:1:0:40:2:0.25:0:8 0/1:43:16:12,4:13,14:0.3721:2,2:11.2:1:28.3:1:0.11537:3.14:25.9:32:0.3721:0:6.4 -10 42387447 . T C 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.73047;LSEQ=GGACTCGAATGGAATCAACA;RSEQ=CAAACGGAATCAAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:0.25:2,0:10:0:16:0:1:0:40:0:0:0:8 0/1:36:7:6,1:13,14:0.1944:2,2:8.9:1:30.6:1:0.10389:6.15:25.9:14:0.1944:0:6.9 -10 42387457 . TC AA 93 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27422;SOR=0.18743;LSEQ=GGAATCAACATCAAACGGAA;RSEQ=AAACGGAATTATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:21.3:1:31.3:1:1:0:36.3:6:0.75:0.25:4.3 0/1:26:9:6,3:7,9:0.3462:2,2:34:1:29.4:1:0.41098:2.47:26.6:18:0.3913:0:3.7 -10 42387461 . A G 84 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAACATCAAACGGAATCAA;RSEQ=CGGAATTATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:23:1:31.7:1:1:0:38:6:1:0:2 0/1:26:6:1,5:12,8:0.2308:2,2:25.8:1:32.5:1:0.16025:6.95307:28.5:12:0.2308:0:3.5 -10 42387472 . G A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGAATCAAACGGAATTATC;RSEQ=AATGGAATCGAAGAGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:12:1:32.7:1:1:0:38:6:1:0:2 0/1:25:2:1,1:12,11:0.08:2,2:18.5:1:27:1:1:1.0871:23:4:0.08:0:4 -10 42387475 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCAAACGGAATTATCGAA;RSEQ=GGAATCGAAGAGAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:9:1:31.7:1:1:0:38:6:1:0:2 0/1:23:2:0,2:12,9:0.087:2,0:14:1:31:1:0.21739:0:30:4:0.0909:0:5 -10 42387501 . C A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAAGAGAATCATCGAATGG;RSEQ=CTCGAATGGAATCCTCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:10.5:1:31.5:1:1:0:29.5:4:1:0:3 -10 42387693 . A T 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.26316;SOR=Inf;LSEQ=TGGAAATGAAAGGGGTCATC;RSEQ=TCCAATGGAATCGCATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:18.7:1:30.6:1:1:0:42:14:1:0:2.4 0/1:12:3:2,1:5,4:0.25:2,2:12:1:32.3:1:1:1.54:47:6:0.2727:0:5.7 -10 42387695 . CC GT 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAATGAAAGGGGTCATCAT;RSEQ=AATGGAATCGCATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:20.7:1:31.9:1:1:0:42:14:1:0:2.4 0/1:17:2:1,1:8,7:0.1176:2,2:20:1:32.3:1:1:1.13389:24:4:0.1176:0:3.5 -10 42387696 . C T 95 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26893;SOR=0;LSEQ=AAATGAAAGGGGTCATCATC;RSEQ=AATGGAATCGCATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:1:0,2:19.1:1:29.8:1:1:0:42.1:16:1:0:3 1/0:17:13:7,6:1,1:0.7647:2,2:12.9:1:25.9:1:1:1.15:42.6:5.5:0.8462:0:4.5 -10 42387697 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54023;SOR=Inf;LSEQ=AATGAAAGGGGTCATCATCC;RSEQ=ATGGAATCGCATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:16.3:1:28.9:1:1:0:42.8:20:1:0:3.4 0/1:20:2:1,1:9,9:0.1:2,2:7:1:30:1:1:1:46.5:4:0.1053:0:5.5 -10 42387704 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51652;SOR=Inf;LSEQ=GGGGTCATCATCCAATGGAA;RSEQ=CGCATGGAATCATCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:18:1:29.7:1:1:0:41.8:28:1:0:3.9 0/1:23:2:1,1:10,10:0.087:2,2:6.5:1:30:1:1:1:53:4:0.087:0:3 -10 42387705 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0326;SOR=0.19386;LSEQ=GGGTCATCATCCAATGGAAT;RSEQ=GCATGGAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:4,4:4,3:0.5333:2,2:12.6:1:29:1:1:1.30792:45.6:16:0.5714:0:5.4 0/1:23:4:3,1:8,10:0.1739:2,2:16.3:1:27.5:1:0.58647:3.54:43:8:0.2:0:5.5 -10 42387706 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52962;SOR=Inf;LSEQ=GGTCATCATCCAATGGAATC;RSEQ=CATGGAATCATCATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:18.8:1:31:1:1:0:41.9:30:1:0:4.1 0/1:27:2:1,1:12,13:0.0741:2,2:27.5:1:31.5:1:1:1.08:47:4:0.0741:0:5.5 -10 42387707 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52962;SOR=Inf;LSEQ=GTCATCATCCAATGGAATCG;RSEQ=ATGGAATCATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:19.8:1:31.5:1:1:0:41.9:30:1:0:4.1 0/1:27:2:1,1:12,13:0.0741:2,2:11:0:31.5:1:1:1.08:45.5:4:0.0769:0:5.5 -10 42387709 . T C 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54017;SOR=Inf;LSEQ=CATCATCCAATGGAATCGCA;RSEQ=GGAATCATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:21.8:1:30.3:1:1:0:41.9:30:1:0:4.1 0/1:29:3:1,2:13,13:0.1034:2,2:21.7:1:27:1:1:1.95415:49.7:6:0.1071:0:4.3 -10 42387717 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.5461;SOR=Inf;LSEQ=AATGGAATCGCATGGAATCA;RSEQ=CATCAAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:28.1:1:30.3:1:1:0:40.8:32:1:0:4.1 0/1:32:2:1,1:16,14:0.0625:2,2:21:0:31.5:1:1:1.13808:45.5:4:0.0625:0:5.5 -10 42387721 . C A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74751;SOR=0.72955;LSEQ=GAATCGCATGGAATCATCAT;RSEQ=AAATGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:5,5:0.375:2,2:21.8:1:28.8:1:1:1:44.3:12:0.375:0:6.2 0/1:33:10:6,4:11,12:0.303:2,2:20.4:1:27.9:1:0.70799:1.61:40.4:20:0.303:0:5.2 -10 42387732 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATGGAATCATCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:33.9:1:31.1:1:1:0:40.8:32:1:0:4.1 0/1:37:2:1,1:16,19:0.0541:2,2:17:1:30:0:1:1.18:60:4:0.0556:0:3 -10 42387743 . T A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=1;SOR=0.88211;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=CATCGAATGGAATCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:3,3:6,5:0.3529:2,2:39:1:31.3:1:1:1.18716:44.3:12:0.3529:0:6.2 0/1:37:12:6,6:11,14:0.3243:2,2:37.9:1:30.4:1:1:1.26:39.5:24:0.3333:0:5.4 -10 42387745 . A G 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.09158;SOR=0;LSEQ=TGGAATCGAATGGAATCATC;RSEQ=TCGAATGGAATCTAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,7:0.1176:2,2:36:0:32.5:1:1:1:44:4:0.1176:0:7 0/0:38:0:0,0:18,20:0:2,0:34.8:1:29.3:1:1:0:40.7:37:1:0:4.2 -10 42387747 . CG GA 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08081;SOR=0;LSEQ=GAATCGAATGGAATCATCAT;RSEQ=AATGGAATCTAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:33:0:32.3:1:1:1:44:4:0.125:0:6 0/0:39:0:0,0:17,20:0:2,0:33.8:1:29.7:1:1:0:41.6:17.5:0.9459:0:4.2 -10 42387748 . G A 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75376;SOR=1.34244;LSEQ=AATCGAATGGAATCATCATC;RSEQ=AATGGAATCTAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:5,5:2,2:0.625:2,2:34.8:1:30.5:1:1:1:36.4:20:0.7143:0:4.3 1/0:39:27:13,14:4,6:0.6923:2,2:33.8:1:30:1:0.72458:1.38:39:54:0.7714:0:4.5 -10 42387751 . T A 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08831;SOR=0;LSEQ=CGAATGGAATCATCATCGAA;RSEQ=GGAATCTAATGGAATCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:35:0:32:0:1:1.13389:44:4:0.1176:0:6.5 0/0:39:0:0,0:18,21:0:2,0:32.5:1:29.1:1:1:0:40.7:18.5:1:0:4.1 -10 42387752 . G T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08831;SOR=0;LSEQ=GAATGGAATCATCATCGAAT;RSEQ=GAATCTAATGGAATCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:34:1:31:1:1:1.13389:46:4:0.1176:0:4 0/0:39:0:0,0:18,21:0:2,0:32.2:1:29.5:1:1:0:40.7:12:1:0:4.1 -10 42387756 . T G 34 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATCATCATCGAATGGAA;RSEQ=CTAATGGAATCATTGAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:23:1:31.4:1:1:0:39.8:34:1:0:4.1 0/1:39:2:1,1:17,20:0.0513:2,2:25.5:1:34:0:1:1.17:36:4:0.0541:0:7 -10 42387758 . T A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.15594;LSEQ=AATCATCATCGAATGGAATC;RSEQ=AATGGAATCATTGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:3,3:5,4:0.4:2,2:24:1:31.7:1:1:1.23147:44.3:12:0.4:0:5.8 0/1:39:17:9,8:9,13:0.4359:2,2:30.1:1:30.9:1:0.52791:1.60:41.4:34:0.4474:0:4.8 -10 42387759 . A G 63 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01778;SOR=0.07692;LSEQ=ATCATCATCGAATGGAATCT;RSEQ=ATGGAATCATTGAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:2,2:6,5:0.2667:2,2:20.5:1:31.8:1:1:1.18545:36.3:8:0.2667:0:3.3 0/1:39:1:0,1:18,20:0.0256:2,0:28:0:27:0:1:0:25:2:0.0256:0:8 -10 42387761 . T C 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.58738;LSEQ=CATCATCGAATGGAATCTAA;RSEQ=GGAATCATTGAACGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:7,7:0.0667:2,0:26:0:34:0:1:0:24:2:0.0667:0:7 0/1:39:4:2,2:16,18:0.1026:2,2:24.3:1:30.3:1:1:1.12:37:8:0.1053:0:4.8 -10 42387765 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCGAATGGAATCTAATGGA;RSEQ=TCATTGAACGGAATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:19.3:1:31.2:1:1:0:38.3:30:1:0:4.5 0/1:39:2:1,1:17,20:0.0513:2,2:16.5:1:33.5:1:1:1.17:36:4:0.0513:0:7 -10 42387767 . C A 74 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17022;SOR=Inf;LSEQ=CGAATGGAATCTAATGGAAT;RSEQ=ATTGAACGGAATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:17.7:1:32:1:1:0:38.3:30:1:0:4.5 0/1:39:6:2,4:16,17:0.1538:2,2:29.5:1:29:1:0.66736:1.85284:43:12:0.1538:0:3.7 -10 42387770 . T G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATCTAATGGAATCAT;RSEQ=GAACGGAATTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:15.1:1:30.8:1:1:0:38.3:30:1:0:4.5 0/1:39:2:1,1:17,20:0.0513:2,2:46.5:1:31:1:1:1.17:22:4:0.0541:0:6.5 -10 42387775 . G A 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11008;SOR=0.1188;LSEQ=ATCTAATGGAATCATTGAAC;RSEQ=GAATTGAATGGAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:4,3:0.2:2,0:32:1:33:0:0.44444:0:23.5:4:0.2222:0:3.5 0/1:37:1:0,1:17,19:0.027:2,0:7:0:32:0:1:0:24:2:0.0286:0:3 -10 42387779 . T G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATCATTGAACGGAA;RSEQ=TGAATGGAATCATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:17:1:32.3:1:1:0:36.6:16:1:0:5.3 0/1:35:4:1,3:13,17:0.1143:2,2:32:1:31.3:1:0.62718:2.24305:42.3:8:0.1212:0:3.3 -10 42387782 . A C 40 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATCATTGAACGGAATTG;RSEQ=ATGGAATCATCATCGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:20:1:31.5:1:1:0:34.2:12:1:0:5 0/1:29:3:1,2:11,15:0.1034:2,2:27:1:25.3:1:1:1.44805:50.7:2:0.0714:0:3.7 -10 42387786 . GA TT 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATTGAACGGAATTGAATG;RSEQ=ATCATCATCGAATGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:25.8:1:32.5:1:1:0:29.3:8:1:0:4.3 0/1:26:2:1,1:10,14:0.0769:2,2:12:1:30.3:1:1:1.38:53:4:0.08:0.0385:2.5 -10 42387787 . A T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTGAACGGAATTGAATGG;RSEQ=ATCATCATCGAATGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:24.8:1:31.5:1:1:0:29.3:8:1:0:4.3 0/1:23:2:1,1:8,12:0.087:2,2:31:1:30:1:1:1.47:22:4:0.0952:0:6.5 -10 42387791 . A G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.54923;SOR=0.35488;LSEQ=GAACGGAATTGAATGGAATC;RSEQ=TCATCGAATGAATTGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:16:1:33.5:1:1:0:23.5:4:0.5:0:3.5 0/1:16:4:1,3:3,4:0.25:2,2:29:1:31:1:1:2.09375:38.8:8:0.2667:0:3 -10 42387817 . T A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=0;LSEQ=GAATGAATTGAATGCAATCA;RSEQ=CGAATGGTCTCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:19:0:32:0:1:0:24:2:1:0:7 0/1:8:2:1,1:1,5:0.25:2,2:17:1:28:1:0.46429:3.87:24.5:4:0.25:0:6 -10 42387887 . T C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGCATAGAATCGAATGGAAT;RSEQ=AACATCGAATGGACTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:5.5:1:23.5:1:1:0:23:4:1:0:5 0/1:10:2:1,1:5,3:0.2:2,2:6.5:1:29.5:1:1:1.58108:21:4:0.2:0:2.5 -10 42387889 . A T 102 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGAATCGAATGGAATTA;RSEQ=CATCGAATGGACTCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:3.8:1:28.2:1:1:0:31.6:10:1:0:6 1/1:13:11:7,4:1,1:0.8462:2,2:12:1:29.7:1:1:1.67:30.2:22:0.8462:0:2.8 -10 42387899 . G T 27 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05172;SOR=0;LSEQ=AATGGAATTAACATCGAATG;RSEQ=ACTCAAATGGAATCAACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:11:0:27.5:1:1:1.41:45:4:0.2857:0:6.5 0/0:22:0:0,0:11,11:0:2,0:15.1:1:30.8:1:1:0:34.2:44:1:0:2.9 -10 42387900 . A C 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29014;SOR=Inf;LSEQ=ATGGAATTAACATCGAATGG;RSEQ=CTCAAATGGAATCAACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:12:1:28.7:1:1:0:37.3:14:1:0:4.4 0/1:23:6:3,3:8,9:0.2609:2,2:8.8:1:25.5:1:1:1.12:40.5:2:0.1905:0:1.7 -10 42387901 . CT AA 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04234;SOR=0;LSEQ=TGGAATTAACATCGAATGGA;RSEQ=CAAATGGAATCAACATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:15.5:1:28.3:1:1:1.41:22:4:0.2857:0:6 0/0:25:0:0,0:10,10:0:2,0:15.7:1:31:1:1:0:33.9:40:0.8:0:1.8 -10 42387904 . A G 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.67692;SOR=0.67493;LSEQ=AATTAACATCGAATGGACTC;RSEQ=AATGGAATCAACATCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:1,1:0.4286:2,2:20.7:1:29:1:1:1.7321:22.7:6:0.4286:0:5 0/1:27:9:3,6:9,8:0.3333:2,2:16.9:1:29.6:1:0.42911:2.18044:37:18:0.3333:0:4.9 -10 42387907 . T A 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAACATCGAATGGACTCAAA;RSEQ=GGAATCAACATCAAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:19:1:26.1:1:1:0:37.3:2.5:1:0:4.1 0/1:31:2:1,1:14,15:0.0645:2,2:13:0:32.5:1:1:1.07:39:4:0.0645:0:7 -10 42387910 . A T 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56469;SOR=Inf;LSEQ=CATCGAATGGACTCAAATGG;RSEQ=ATCAACATCAAACGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:22:1:30.4:1:1:0:37.3:14:1:0:4.1 0/1:33:5:1,4:14,14:0.1515:2,2:13.6:1:26.6:1:0.34567:3.85035:35.2:10:0.1515:0:6.6 -10 42387918 . T C 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGACTCAAATGGAATCAACA;RSEQ=CAAACGGAATCAAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:24.2:1:29.1:1:1:0:33.7:8:1:0:4.8 0/1:46:3:1,2:21,22:0.0652:2,2:18.7:1:29:1:1:1.88337:28.7:6:0.0652:0:7 -10 42387919 . C A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACTCAAATGGAATCAACAT;RSEQ=AAACGGAATCAAACGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:25.2:1:32.9:1:1:0:33.7:18:1:0:4.8 0/1:46:2:1,1:21,23:0.0435:2,2:15.5:1:26:1:1:1.09:43:4:0.0435:0:5.5 -10 42387924 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATGGAATCAACATCAAAC;RSEQ=GAATCAAACGGAATTATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:30.2:1:28.9:1:1:0:33.7:8:1:0:4.8 0/1:47:2:1,1:21,24:0.0426:2,2:28.5:1:29.5:1:1:1.14:27:4:0.0426:0:1.5 -10 42387926 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATCAACATCAAACGG;RSEQ=ATCAAACGGAATTATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:31.4:1:30.6:1:1:0:33.7:18:1:0:4.8 0/1:47:2:1,1:21,24:0.0426:2,2:16.5:1:30.5:1:1:1.14:27:4:0.0426:0:6.5 -10 42387928 . TC AA 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71629;SOR=0.5738;LSEQ=GGAATCAACATCAAACGGAA;RSEQ=AAACGGAATTATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,2:0.6667:2,2:32.8:1:30.9:1:1:1.85:29.3:12:0.6667:0:5.5 1/0:47:25:11,14:11,11:0.5319:2,2:23.1:1:29.7:1:0.77331:1.26618:34.7:50:0.5319:0:4.2 -10 42387932 . A G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAACATCAAACGGAATCAA;RSEQ=CGGAATTATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:33.4:1:28.9:1:1:0:33.7:8:1:0:4.1 0/1:47:3:1,2:21,23:0.0638:2,2:32.3:1:31.7:1:1:1.80368:45.7:6:0.0638:0:1.7 -10 42387933 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAACATCAAACGGAATCAAA;RSEQ=GGAATTATCGAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:33.8:1:30.3:1:1:0:33.7:8:1:0:4.1 0/1:47:2:1,1:21,24:0.0426:2,2:23.5:1:30.5:1:1:1.14:27:4:0.0426:0:5.5 -10 42387934 . G A 32 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.02256;SOR=0;LSEQ=AACATCAAACGGAATCAAAC;RSEQ=GAATTATCGAATGGAATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:20:0:32.5:1:1:1.29:21:4:0.2222:0:6 0/0:48:0:0,0:22,26:0:2,0:30.4:1:30.3:1:1:0:34:96:1:0:2.8 -10 42387944 . A T 30 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02256;SOR=0;LSEQ=GGAATCAAACGGAATTATCG;RSEQ=ATGGAATCGAAGAGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:30:0:30.5:1:1:1.29:21:4:0.2222:0:6 0/0:48:0:0,0:22,26:0:2,0:32.3:1:30:1:1:0:34:96:1:0:2.8 -10 42387948 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAACGGAATTATCGAATG;RSEQ=AATCGAAGAGAATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:27:1:31.8:1:1:0:33.7:18:1:0:4.1 0/1:48:2:1,1:21,25:0.0417:2,2:36:0:30.5:1:1:1.19:43:4:0.0417:0:3.5 -10 42387962 . CA TT 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGAATGGAATCGAAGAGAAT;RSEQ=TCGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:21.6:1:32.1:1:1:0:30.4:16:1:0:4.9 0/1:47:2:1,1:21,24:0.0426:2,2:27:0:32:0:1:1.14:42:4:0.0435:0:4.5 -10 42387963 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATCGAAGAGAATC;RSEQ=TCGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:20.9:1:29.6:1:1:0:30.4:7:1:0:4.9 0/1:47:2:1,1:20,23:0.0426:2,2:46.5:1:31:1:1:1.15:29:4:0.0444:0:6 -10 42387969 . T C 108 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66183;SOR=2.37191;LSEQ=AATCGAAGAGAATCATCGAA;RSEQ=GGACTCGAATGGAATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:4,3:0.125:2,0:6:0:32:0:1:0:24:2:0.125:0:3 0/1:43:11:5,6:15,17:0.2558:2,2:21.5:1:31.3:1:1:1.05745:32.2:22:0.2558:0:4.9 -10 42387974 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.30829;LSEQ=AAGAGAATCATCGAATGGAC;RSEQ=CGAATGGAATCATCTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:2,1:0.4444:2,2:8.3:1:30.5:1:1:1.81007:33.5:8:0.4444:0:5.3 1/0:39:20:9,11:8,9:0.5128:2,2:17.6:1:31.9:1:1:1.08399:33.8:40:0.5128:0:3.8 -10 42387994 . A G 28 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58893;SOR=0.4785;LSEQ=TCGAATGGAATCATCTAATG;RSEQ=AATAGAATGGAATAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:0.25:2,2:6.5:1:30:1:0.46429:3.87298:21:4:0.25:0:5 0/1:15:2:1,1:7,6:0.1333:2,2:2.5:1:28:1:1:1.1547:22:4:0.1333:0:3 -10 42387998 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=ATGGAATCATCTAATGAAAT;RSEQ=GAATGGAATAATCCATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:16.6:1:29.6:1:1:0:38.4:16:1:0:4.5 0/1:14:2:1,1:7,5:0.1429:2,2:11.5:1:33:1:1:1.36624:29:4:0.1429:0:6 -10 42388012 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.175;SOR=0;LSEQ=TGAAATAGAATGGAATAATC;RSEQ=ATGGACTAGAATGCAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:24:1:29:1:1:3.1622:50:4:0.2857:0:6.5 0/0:9:0:0,0:5,4:0:2,0:26.1:1:32:1:1:0:37.1:18:1:0:3.7 -10 42388020 . A C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGAATAATCCATGGACT;RSEQ=GAATGCAATCATCCTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:1:0,2:32.5:1:30.4:1:1:0:43.8:16:1:0:4.9 1/1:9:9:5,4:0,0:1:0,2:25.7:1:31.6:1:1:0:40.2:18:1:0:4.3 -10 42388034 . C A 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTAGAATGCAATCATC;RSEQ=TCAAATGGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:1:0,2:34.6:1:30.1:1:1:0:43.8:16:1:0:4.9 1/1:11:11:6,5:0,0:1:0,2:24.9:1:29.9:1:1:0:42.9:22:1:0:4.5 -10 42388036 . C A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=GACTAGAATGCAATCATCCT;RSEQ=AAATGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:27.5:1:31.1:1:1:0:45.1:20:1:0:5.4 0/1:11:2:1,1:5,4:0.1818:2,2:22:1:27.5:1:1:1.22474:25:4:0.1818:0:5 -10 42388056 . C A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.70236;LSEQ=CAAATGGAATCGAATGGAAT;RSEQ=GTCGAATGGACTCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:22.5:1:29.5:1:1:1.22474:43:4:0.1818:0:4.5 0/1:15:2:1,1:6,7:0.1333:2,2:22:1:29.5:1:1:1.15:25:4:0.1333:0:5 -10 42388066 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17787;SOR=0;LSEQ=CGAATGGAATCGTCGAATGG;RSEQ=CTCGAATGGAATAAATATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:31:0:33:1:1:1:50.5:4:0.2:0:7.5 0/0:13:0:0,0:4,8:0:2,0:26.8:1:29:1:1:0:46:11:0.9167:0:5.2 -10 42388072 . A G 106 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01757;SOR=13.67234;LSEQ=GAATCGTCGAATGGACTCGA;RSEQ=TGGAATAAATATTGAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,3:0.25:2,2:13:1:31:1:1:1.41:48.5:4:0.25:0:4.5 1/1:13:11:4,7:1,1:0.8462:2,2:24.8:1:30.8:1:1:1.67325:44.9:22:0.8462:0:5.1 -10 42388075 . G C 53 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04211;SOR=0;LSEQ=TCGTCGAATGGACTCGAATG;RSEQ=AATAAATATTGAACGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:2,3:0.375:2,2:40.3:1:33.7:1:1:1.28664:48:6:0.375:0:7 0/0:13:0:0,0:5,8:0:2,0:25.8:1:30.9:1:1:0:45.8:26:1:0:5.3 -10 42388082 . T C 108 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ATGGACTCGAATGGAATAAA;RSEQ=ATTGAACGGAATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:30.5:1:33:1:1:0:44.7:12:1:0:6.5 1/1:11:11:4,7:0,0:1:0,2:26.5:1:31.5:1:1:0:44.5:22:1:0:5.8 -10 42388085 . T A 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09524;SOR=0;LSEQ=GACTCGAATGGAATAAATAT;RSEQ=GAACGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,2:0.4:0,2:41.5:1:30.5:1:1:0:50.5:4:0.4:0:7.5 0/0:10:0:0,0:4,6:0:2,0:27.7:1:29.3:1:1:0:44.2:20:1:0:6.1 -10 42388086 . G C 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6004;SOR=2.5065;LSEQ=ACTCGAATGGAATAAATATT;RSEQ=AACGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:1,3:0.2:2,0:36:0:34:0:1:0:40:2:0.2:0:6 0/1:10:4:2,2:1,3:0.4:2,2:21.8:1:30:1:1:2.60:47.3:8:0.4:0:5.8 -10 42388088 . AC GG 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=TCGAATGGAATAAATATTGA;RSEQ=GGAATCGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:32.4:1:31:1:1:0:45.2:10:1:0:6.8 0/1:10:2:1,1:3,5:0.2:2,2:44.5:1:31.5:0:1:1.58:43.5:4:0.2:0:6 -10 42388091 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=AATGGAATAAATATTGAACG;RSEQ=AATCGAATGGAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:30.6:1:32.6:1:1:0:45.2:10:1:0:6.8 0/1:10:2:1,1:3,5:0.2:2,2:17:1:30:1:1:1.58:51:4:0.2:0:6.5 -10 42388095 . C T 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=0;LSEQ=GAATAAATATTGAACGGAAT;RSEQ=GAATGGAATCATCATCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:31.5:1:29.5:1:0.4:0:50.5:4:0.4:0:7.5 0/0:9:0:0,0:2,5:0:2,0:29.9:1:30.7:1:1:0:42.3:14:0.7778:0:6 -10 42388106 . A G 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08009;SOR=13.45266;LSEQ=GAACGGAATCGAATGGAATC;RSEQ=TCATCGGATGGAAACGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:1,2:0.2:2,0:45:0:34:0:1:0:40:2:0.2:0:6 1/1:6:5:1,4:0,1:0.8333:0,2:28.4:1:31:1:1:0:43.8:10:0.8333:0:5.8 -10 42388110 . T C 81 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.13333;SOR=Inf;LSEQ=GGAATCGAATGGAATCATCA;RSEQ=CGGATGGAAACGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:23.5:1:33:0:1:0:41.5:4:0.5:0:6 1/1:6:6:1,5:0,0:1:0,2:22:1:31.5:1:1:0:46.3:12:1:0:5.8 -10 42388115 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CGAATGGAATCATCATCGGA;RSEQ=GGAAACGAATGGAATCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:11.5:1:30:1:1:0:50.5:4:0.5:0:7.5 0/0:5:0:0,0:1,4:0:2,0:21:1:30.6:1:1:0:45.6:10:1:0:5.8 -10 42388117 . G T 27 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=AATGGAATCATCATCGGATG;RSEQ=AAACGAATGGAATCATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:9.5:1:27:1:1:0:50.5:4:0.6667:0:7.5 0/0:5:0:0,0:1,4:0:2,0:19:1:30.8:1:1:0:45.6:10:1:0:5.8 -10 42388134 . T C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAAACGAATGGAATCAT;RSEQ=ATCGAATGGAATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:17:0:34:0:1:0:40:2:1:0:6 1/1:3:3:1,2:0,0:1:0,2:12.3:1:30.7:1:1:0:42:6:1:0:5.7 -10 42388249 . C T 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCATCAAATGGAATCGAA;RSEQ=GGAATCATCATCCACTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:5.5:1:32:0:1:0:29:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42388270 . A G 78 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61969;LSEQ=GGAATCATCATCCACTGGAA;RSEQ=CTAATGGAATCAACATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:13:1:33.6:1:1:0:27.8:10:0.5556:0:2.8 0/1:7:3:3,0:4,0:0.4286:0,0:2.3:1:31.7:1:1:0:37:6:0.4286:0:2.7 -10 42388291 . TG T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35474;SOR=0.49233;LSEQ=CTAATGGAATCAACATCGAA;RSEQ=GAATCGAATGGAAACACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:15:14,1:5,0:0.75:0,1:21.5:1:32.4:1:1:0:31.3:30:0.75:0.35:1.5 1/0:27:16:13,3:10,0:0.5926:0,2:18.4:1:32.5:1:0.26154:0:35.7:32:0.6154:0.2593:1.3 -10 42388308 . A G 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05453;SOR=Inf;LSEQ=GAATGGAATCGAATGGAAAC;RSEQ=CCATCGAATTGAAACGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:21,5:0:2,0:29.3:1:30.5:1:1:0:32.7:52:1:0:1.8 0/1:30:5:4,1:18,6:0.1667:2,2:33.4:1:30.4:1:1:1.32:33:10:0.1667:0:2 -10 42388311 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49499;SOR=Inf;LSEQ=TGGAATCGAATGGAAACACC;RSEQ=TCGAATTGAAACGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:21,5:0:2,0:31.6:1:29.8:1:1:0:32.7:25:1:0:1.8 0/1:31:2:1,1:22,7:0.0645:2,2:20:1:28.5:1:0.45591:3.00588:36:4:0.0645:0:2.5 -10 42388316 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49508;SOR=Inf;LSEQ=TCGAATGGAAACACCATCGA;RSEQ=TTGAAACGAATGGAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:20,7:0:2,0:32:1:30.2:1:1:0:32.9:54:0.9643:0:1.8 0/1:33:2:1,1:22,9:0.0606:2,2:25:1:28.5:1:0.52083:2.37114:36:4:0.0625:0:2.5 -10 42388319 . G C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20913;SOR=0;LSEQ=AATGGAAACACCATCGAATT;RSEQ=AAACGAATGGAATTATCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:2,0:20,8:0.0667:2,0:31.5:1:32:1:1:0:33.5:4:0.0667:0:4 0/0:35:0:0,0:23,11:0:2,0:34.4:1:30.9:1:1:0:35.4:68:0.9714:0:1.5 -10 42388322 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2028;SOR=0;LSEQ=GGAAACACCATCGAATTGAA;RSEQ=CGAATGGAATTATCATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:21,7:0.0667:2,2:28.5:1:31:1:0.46897:2.87249:24:4:0.069:0:4.5 0/0:36:0:0,0:25,11:0:2,0:35:1:28.8:1:1:0:35.5:35:1:0:1.5 -10 42388332 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49772;SOR=Inf;LSEQ=TCGAATTGAAACGAATGGAA;RSEQ=TATCATGAAATTGAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:22,11:0:2,0:30.5:1:29.8:1:1:0:32.9:66:1:0:2.1 0/1:40:2:1,1:26,12:0.05:2,2:13.5:1:26.5:1:1:2.12136:40:4:0.0513:0:3.5 -10 42388335 . T C 92 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04807;SOR=0.23656;LSEQ=AATTGAAACGAATGGAATTA;RSEQ=CATGAAATTGAAATGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:8:5,3:17,7:0.2353:2,2:27.3:1:30.9:1:0.68079:1.43951:28.4:16:0.2353:0:3.8 0/1:45:3:2,1:27,15:0.0667:2,2:42.7:1:30.3:1:1:1.11:30:6:0.0667:0:2.7 -10 42388336 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50918;SOR=Inf;LSEQ=ATTGAAACGAATGGAATTAT;RSEQ=ATGAAATTGAAATGGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:21,10:0:2,0:30.5:1:29.6:1:1:0:32.6:14.5:1:0:2 0/1:47:2:1,1:29,16:0.0426:2,2:13.5:1:29.5:1:1:1.78835:40:4:0.0426:0:3.5 -10 42388337 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51111;SOR=Inf;LSEQ=TTGAAACGAATGGAATTATC;RSEQ=TGAAATTGAAATGGATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:22,11:0:2,0:30.2:1:29.5:1:1:0:33.1:66:1:0:2 0/1:48:2:1,1:29,16:0.0417:2,2:26:1:29:1:1:1.78835:31:4:0.0417:0:3 -10 42388344 . T A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32887;LSEQ=GAATGGAATTATCATGAAAT;RSEQ=GAAATGGATGGACTCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:1:1,0:21,11:0.0303:2,0:44:0:27:0:1:0:39:2:0.0303:0:1 0/1:50:2:2,0:28,18:0.04:2,0:29:1:30:0:0.52128:0:32:4:0.04:0:1.5 -10 42388354 . G A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63981;SOR=0.62365;LSEQ=ATCATGAAATTGAAATGGAT;RSEQ=GACTCATCATCGAATGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:20,11:0.0606:2,2:28.5:1:30.5:1:1:1.78367:31.5:4:0.0606:0:2.5 0/1:52:2:1,1:30,20:0.0385:2,2:20.5:1:28:1:1:1.48801:41.5:4:0.0385:0:4 -10 42388358 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16629;SOR=0;LSEQ=TGAAATTGAAATGGATGGAC;RSEQ=CATCATCGAATGGATTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:19,16:0.0541:2,2:24:1:28:0:1:1.18197:27:4:0.0541:0:3.5 0/0:53:0:0,0:31,22:0:2,0:22.9:1:29.2:1:1:0:34.8:106:1:0:1.7 -10 42388360 . A G 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.64459;SOR=2.7189;LSEQ=AAATTGAAATGGATGGACTC;RSEQ=TCATCGAATGGATTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:1,0:17,18:0.0278:2,0:12:0:25:0:1:0:40:2:0.0278:0:3 0/1:55:4:2,2:29,22:0.0727:2,2:25:1:29.5:1:1:1.31149:40:8:0.0769:0:2 -10 42388366 . G A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51736;SOR=Inf;LSEQ=AAATGGATGGACTCATCATC;RSEQ=AATGGATTCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,19:0:2,0:21.4:1:29.4:1:1:0:34.4:70:1:0:2 0/1:54:2:1,1:28,24:0.037:2,2:21:1:27.5:1:1:1.16333:40:4:0.037:0:4 -10 42388367 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28056;SOR=Inf;LSEQ=AATGGATGGACTCATCATCG;RSEQ=ATGGATTCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,19:0:2,0:21.8:1:28.9:1:1:0:34.7:68:1:0:2 0/1:54:3:1,2:28,23:0.0556:2,2:26.3:1:30.3:1:0.59079:2.3957:34:6:0.0556:0:3 -10 42388371 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14352;SOR=0;LSEQ=GATGGACTCATCATCGAATG;RSEQ=ATTCGAATGGAATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:11,18:0.0645:2,2:23.5:1:33.5:1:1:1.61:24:4:0.0645:0:4.5 0/0:50:0:0,0:23,27:0:2,0:23.1:1:30.6:1:1:0:33.7:100:1:0:1.7 -10 42388375 . C T 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.85289;LSEQ=GACTCATCATCGAATGGATT;RSEQ=GAATGGAATCATCGAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:1,0:9,19:0.0345:2,0:43:0:29:0:0.34483:0:40:2:0.0345:0:3 0/1:48:3:2,1:19,26:0.0625:2,2:27.3:1:29.7:1:0.57383:2.68:35:6:0.0625:0:4 -10 42388387 . T C 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=2.00888;LSEQ=AATGGATTCGAATGGAATCA;RSEQ=CGAATGAAATTGATTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:1,0:3,18:0.0455:2,0:31:0:29:0:0.18182:0:40:2:0.0476:0:3 0/1:34:3:0,3:10,21:0.0882:2,0:24:1:30:1:0.53877:0:43.3:6:0.0882:0:2 -10 42388393 . G A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16606;SOR=0.44171;LSEQ=TTCGAATGGAATCATCGAAT;RSEQ=AAATTGATTGAAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:0,11:3,8:0.5:2,0:24.6:1:30.5:1:0.21429:0:31.9:22:0.5238:0:3.3 0/1:33:10:0,10:10,13:0.303:2,0:29.6:1:31.6:1:0.01478:0:38.6:20:0.303:0:2.7 -10 42388399 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.52104;SOR=Inf;LSEQ=TGGAATCATCGAATGAAATT;RSEQ=ATTGAAATCATCATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:3,17:0:2,0:26.5:1:31.6:1:1:0:35.6:40:1:0:3 0/1:33:2:1,1:9,22:0.0606:2,2:36.5:1:28:1:0.52083:2.37:24:4:0.0606:0:1 -10 42388401 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52481;SOR=Inf;LSEQ=GAATCATCGAATGAAATTGA;RSEQ=TGAAATCATCATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:3,17:0:2,0:26.1:1:29.5:1:1:0:35.6:9:1:0:3 0/1:34:2:1,1:9,23:0.0588:2,2:42.5:1:29.5:1:0.50802:2.48:35:4:0.0588:0:2.5 -10 42388402 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.29293;SOR=Inf;LSEQ=AATCATCGAATGAAATTGAT;RSEQ=GAAATCATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:3,16:0:2,0:26.9:1:30.4:1:1:0:36.2:38:0.95:0:2.8 0/1:35:3:0,3:10,22:0.0857:2,0:39:1:28.3:1:0.54163:0:43.3:6:0.0857:0:2 -10 42388403 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1195;SOR=0;LSEQ=ATCATCGAATGAAATTGATT;RSEQ=AAATCATCATCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:2,15:0.1053:2,2:38.5:1:32:1:0.29825:6.32:42:4:0.1053:0:1 0/0:35:0:0,0:10,25:0:2,0:27.9:1:31.1:1:1:0:33.1:70:1:0:1.9 -10 42388414 . CA TG 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03238;SOR=0;LSEQ=AAATTGATTGAAATCATCAT;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:2,10:0.1875:2,0:21.3:1:31.7:1:1:0:34.7:6:0.2:0.0625:2.7 0/0:32:0:0,0:10,21:0:2,0:25.4:1:30.9:1:1:0:32.7:62:1:0:2 -10 42388415 . A G 61 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03043;SOR=0.09416;LSEQ=AATTGATTGAAATCATCATC;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:1,3:1,5:0.2667:2,2:14:1:30.5:1:1:1.58:34.5:8:0.3333:0:4.5 0/1:32:1:0,1:10,20:0.0313:2,0:37:0:32:0:1:0:40:2:0.0323:0:3 -10 42388428 . T A 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72462;SOR=1.40897;LSEQ=CATCATCAAATGGAATCGAA;RSEQ=GGAATCATTGAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:1,7:0.25:2,0:30:1:32.3:1:1:0:37:6:0.2727:0:2 0/1:28:9:3,6:4,15:0.3214:2,2:21:1:29.6:1:0.64646:1.83:28.9:18:0.3214:0:1.8 -10 42388431 . A T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63422;SOR=0.63307;LSEQ=CATCAAATGGAATCGAATGG;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:1,7:0.1667:2,0:35:1:30:0:1:0:32:4:0.2:0:4 0/1:27:3:0,3:7,17:0.1111:2,0:9:1:29:1:0.5453:0:39.7:6:0.1111:0:2.7 -10 42388433 . T C 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53668;SOR=Inf;LSEQ=TCAAATGGAATCGAATGGAA;RSEQ=CATTGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:1,10:0:2,0:22.3:1:31.5:1:1:0:37.6:22:1:0:2.6 0/1:25:3:1,2:5,17:0.12:2,2:32.7:1:29:1:1:1.66:24.3:6:0.1304:0:2.7 -10 42388443 . G C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84709;LSEQ=TCGAATGGAATCATTGAATG;RSEQ=AATCGAATGGAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:0,8:0.1111:0,0:16:0:34:0:1:0:45:2:0.1111:0:2 0/1:21:2:0,2:3,16:0.0952:2,0:6.5:1:32:1:1:0:28:4:0.0952:0:1.5 -10 42388461 . ATCAGATGGAAAA CTC 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATCGAATGGAATCATC;RSEQ=GAATGGAATCATCATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:22.3:1:32.5:1:1:0:36:8:1:0:3.8 0/1:15:2:1,1:1,12:0.1333:1,2:31.5:1:31.3:1:0.25714:8.83:41.5:4:0.1333:0:3.5 -10 42388473 . A T 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCATCAGATGGAAA;RSEQ=GAATGGAATCATCATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:24.3:1:31.7:1:1:0:34.7:6:1:0:4 1/1:8:8:0,8:0,0:1:0,0:31.5:1:30.9:1:1:0:27.1:16:1:0:2.9 -10 42388484 . A G 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2528;SOR=0.15428;LSEQ=AGATGGAAAAGAATGGAATC;RSEQ=TCATAGAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:16:1:32:1:1:0:29.3:6:0.75:0:3.3 0/1:17:5:2,3:3,9:0.2941:2,2:30.6:1:30.4:1:0.60003:1.91:32.4:10:0.2941:0:3 -10 42388489 . A C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAAAGAATGGAATCATCAT;RSEQ=GAATGGAATCGAATGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:16.5:1:32.8:1:1:0:32:8:1:0:3.5 0/1:17:2:1,1:4,11:0.1176:2,2:9:0:32.5:1:0.51471:2.57:44.5:4:0.1176:0:3 -10 42388501 . A C 51 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCATAGAATGGAATCG;RSEQ=ATGGATTCATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:23.7:1:32:1:1:0:34.7:6:1:0:3 0/1:15:3:1,2:4,8:0.2:2,2:21.3:1:32.7:1:1:1:38:6:0.2:0:3 -10 42388510 . A C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATCGAATGGATTC;RSEQ=TTGAATGGAATCAGATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:36.5:1:33:0:1:0:32:4:1:0:2.5 0/1:15:2:1,1:4,9:0.1333:2,2:33.5:1:31.5:1:1:2.12:45:4:0.1333:0:3 -10 42388513 . G A 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATCGAATGGATTCATT;RSEQ=AATGGAATCAGATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:36.5:1:33.5:1:1:0:32:4:1:0:2.5 0/1:15:2:1,1:4,9:0.1333:2,2:37:0:30:0:1:2.12:24:4:0.1333:0:1 -10 42388540 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAGATGGAATCATCGAAT;RSEQ=GACTTGAATGGAATCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:17.5:1:30:1:1:0:32:4:1:0:2.5 0/1:11:2:1,1:3,6:0.1818:2,2:16.5:1:28.5:1:1:1.87:44.5:4:0.1818:0:3 -10 42388545 . T G 61 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=ATGGAATCATCGAATGGACT;RSEQ=GAATGGAATCATTGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12.5:1:31:0:1:0:32:4:1:0:2.5 0/1:10:4:1,3:2,2:0.4:2,2:12:1:30.5:1:1:2.60168:39.3:8:0.4:0:3 -10 42389152 . A G 63 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=TGGAATTATCGAATGCAATC;RSEQ=AATAGAATCATCGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:17.3:1:31.8:1:1:0:28.8:8:1:0:2.8 0/0:1:0:0,0:0,1:0:0,0:25:0:13:0:1:0:21:0:0:0:3 -10 42389206 . T C 79 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCGAATGGAATGGAATGGAA;RSEQ=AGTCAATGAACTCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:26.2:1:30.8:1:1:0:29.5:12:1:0:2.5 1/0:3:2:1,1:1,0:0.6667:0,2:26:1:29.5:1:1:0:25.5:4:0.6667:0:2.5 -10 42389218 . T A 45 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GAATGGAATAGTCAATGAAC;RSEQ=CGAATGGAATCATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:3,0:0.5:0,2:23.7:1:29:1:1:0:29:6:0.5:0:2.7 0/0:4:0:0,0:4,0:0:0,0:18.5:1:31:1:1:0:29.5:8:1:0:3.8 -10 42389231 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18182;SOR=Inf;LSEQ=AATGAACTCGAATGGAATCA;RSEQ=CATTGAATGGAATAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:8.8:1:29.7:1:1:0:26.7:12:1:0:2.7 0/1:5:2:1,1:3,0:0.4:0,2:8.5:1:30.5:1:0.4:0:49:4:0.4:0:6.5 -10 42389240 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GAATGGAATCATCATTGAAT;RSEQ=GAATAGAATGGAATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:6.5:1:32:1:1:0:27.5:8:1:0:2.5 0/1:6:2:1,1:3,0:0.3333:0,2:17.5:1:31.5:1:0.4:0:49:4:0.4:0:6.5 -10 42389245 . A C 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=GAATCATCATTGAATGGAAT;RSEQ=GAATGGAATCATCGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:18:0:30:0:1:0:23:2:0.5:0:4 1/0:7:4:4,0:1,1:0.5714:2,0:17.5:1:30.5:1:0.33333:0:30.5:8:0.6667:0:4.3 -10 42389257 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AATGGAATAGAATGGAATCA;RSEQ=CGAGTGGAATCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:30:0:32:0:1:0:23:2:1:0:4 0/1:8:2:1,1:6,0:0.25:0,2:34.5:1:32:1:0.25:0:49:4:0.25:0:6.5 -10 42389261 . G A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATAGAATGGAATCATCGA;RSEQ=TGGAATCAAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:34:0:1:0:23:2:1:0:4 0/1:8:3:2,1:5,0:0.375:0,2:30.7:1:30:1:0.375:0:46:6:0.375:0:6 -10 42389269 . A G 48 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=TGGAATCATCGAGTGGAATC;RSEQ=AATGGAATCATCATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:30.5:1:1:0:31.5:4:1:0:4.5 0/1:9:3:3,0:3,1:0.3333:2,0:28.7:1:30.3:1:1:0:30:6:0.375:0:3.7 -10 42389278 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.3956;SOR=0.23355;LSEQ=CGAGTGGAATCAAATGGAAT;RSEQ=ATCATCAAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:50:0:32:0:1:0:23:2:0.5:0:4 0/1:12:2:2,0:7,1:0.1667:2,0:31.5:1:31.5:1:1:0:26:4:0.2:0:5 -10 42389281 . C G 103 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTGGAATCAAATGGAATCAT;RSEQ=ATCAAATGGAATCGAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30:1:33.5:1:1:0:31.5:4:1:0:4.5 1/0:13:9:9,0:2,1:0.6923:2,0:21:1:32.8:1:0.25:0:33.4:18:0.75:0:3.7 -10 42389284 . C G 74 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCAAATGGAATCATCAT;RSEQ=AAATGGAATCGAATGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:30:1:33:0:1:0:31.5:4:1:0:4.5 0/1:15:5:5,0:7,2:0.3333:2,0:20:1:32:1:0.50549:0:37:10:0.3571:0:3.2 -10 42389286 . A T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAAATGGAATCATCATCA;RSEQ=ATGGAATCGAATGTAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:30:1:32:0:1:0:31.5:4:1:0:4.5 0/1:17:2:1,1:13,1:0.1176:1,2:37.5:1:28:1:0.24167:9.5394:49:4:0.125:0:6.5 -10 42389294 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCATCATCAAATGGAAT;RSEQ=GAATGTAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:30:1:33.5:1:1:0:31.5:4:1:0:4.5 0/1:19:2:1,1:13,3:0.1053:2,2:29.5:1:28.5:1:0.40523:3.89444:49:4:0.1111:0:6.5 -10 42389334 . G A 107 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCAAAAATAAACATC;RSEQ=TCAATTGGTATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:35:0:28:0:1:0:40:2:1:0:5 1/1:16:14:8,6:1,0:0.875:0,2:36.1:1:28.2:1:1:0:32.4:13:1:0:2.7 -10 42389340 . T A 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAAAATAAACATCGTCAAT;RSEQ=GGTATTGAATGGAATTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:27:0:1:0:40:2:1:0:5 0/1:17:3:2,1:7,6:0.1765:2,2:34.3:1:29.3:1:1:1.66:35:6:0.1875:0:4 -10 42389366 . T C 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12003;LSEQ=TGAATGGAATTGTCATCAAA;RSEQ=GGAATTCAAAGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:0,3:0.25:0,0:3:0:29:0:0.25:0:40:2:0.25:0:5 0/1:22:6:3,3:7,8:0.2727:2,2:17.5:1:28.3:1:1:1.14:33:12:0.2727:0:2.5 -10 42389381 . T A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0.78507;LSEQ=TCAAATGGAATTCAAAGGAA;RSEQ=CATCATCAAATGGAACCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:3,4:0.125:2,0:26:0:27:0:1:0:23:2:0.1429:0:2 0/1:20:2:2,0:6,12:0.1:2,0:28:1:31:1:0.14737:0:40:4:0.1:0:3.5 -10 42389387 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGAATTCAAAGGAATCATCA;RSEQ=CAAATGGAACCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:18.2:1:28:1:1:0:31.9:8:1:0:2 0/1:19:2:1,1:7,10:0.1053:2,2:24:1:32.5:1:1:1.40:33.5:4:0.1111:0:1.5 -10 42389431 . A G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25949;SOR=0.35007;LSEQ=CATTGAATGGAAATGAAAGG;RSEQ=GTCATCATCTAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:5,5:2,1:0.7692:2,2:33.6:1:32.3:1:1:1.89792:30:20:0.7692:0:2.7 1/0:17:9:6,3:4,4:0.5294:2,2:26.3:1:29.1:1:0.63719:1.92:35.6:8:0.5:0:2.6 -10 42389441 . T A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.62392;LSEQ=AAATGAAAGGAGTCATCATC;RSEQ=AATGGAATCGCATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:7,7:0.0667:2,0:38:0:31:0:1:0:47:2:0.0714:0:6 0/1:19:2:0,2:11,6:0.1053:2,0:5.5:1:27:1:0.16374:0:32:4:0.1053:0:3.5 -10 42389452 . C A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22813;LSEQ=GTCATCATCTAATGGAATCG;RSEQ=ATGGAATCATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:30:1:31:1:1:1:43.5:4:0.125:0:5 0/1:20:3:1,2:9,8:0.15:2,2:14:1:29:1:1:2.16219:36.7:6:0.15:0:3.7 -10 42389477 . G T 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.86095;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATGGAATCATTGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:3,2:6,2:0.3333:2,2:35.2:1:28.8:1:1:1.8918:45.6:10:0.3333:0:3.6 0/1:20:6:2,4:7,7:0.3:2,2:26:1:27.5:1:0.64241:1.93237:33.5:12:0.3:0:3.8 -10 42389480 . T G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=CATCATCAAATGGAATCGAA;RSEQ=GGAATCATTGAACGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,4:0.1667:2,2:31.5:1:30.5:1:1:1.22474:43.5:4:0.1667:0:5 0/0:21:0:0,0:9,12:0:2,0:21.7:1:29.3:1:1:0:37.4:42:1:0:2.7 -10 42389488 . T C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.63519;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=TGAACGGAATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:0.1667:2,2:24:0:33.5:1:1:1.4491:52:4:0.1667:0:1 0/1:18:2:0,2:7,9:0.1111:2,0:27.5:1:30.5:1:0.49673:0:40:4:0.1111:0:4.5 -10 42389494 . G A 74 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02809;SOR=0.11467;LSEQ=ATCGAATGGAATCATTGAAC;RSEQ=GAATTGAATGGAATCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:3,3:2,3:0.5455:2,2:28:1:28.8:1:1:1.45:41.5:12:0.5455:0:3.5 0/1:18:2:2,0:5,10:0.1111:2,0:3:1:29:0:0.15441:0:40.5:4:0.1176:0:4.5 -10 42389504 . G C 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13281;SOR=Inf;LSEQ=ATCATTGAACGGAATTGAAT;RSEQ=GAATCGTCATCGAATGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:25.3:1:30.9:1:1:0:38.6:22:1:0:2.8 0/1:20:5:2,3:4,11:0.25:2,2:37:1:30.6:1:0.61262:1.78:45.2:10:0.25:0:3.4 -10 42389507 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52688;SOR=Inf;LSEQ=ATTGAACGGAATTGAATGGA;RSEQ=TCGTCATCGAATGAATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:25:1:30.2:1:1:0:38.6:22:1:0:2.8 0/1:20:2:1,1:5,13:0.1:2,2:37.5:1:31:1:0.52105:2.46:43:4:0.1:0:4 -10 42389514 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=GGAATTGAATGGAATCGTCA;RSEQ=CGAATGAATTGAATGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:27:1:30.8:1:1:0:38.8:20:1:0:2.7 0/1:18:2:1,1:4,12:0.1111:2,2:20.5:1:31.5:1:0.4902:2.79:46:4:0.1111:0:4.5 -10 42389515 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53202;SOR=Inf;LSEQ=GAATTGAATGGAATCGTCAT;RSEQ=GAATGAATTGAATGCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:2,7:0:2,0:24.2:1:30.6:1:1:0:40.7:18:0.9:0:2.3 0/1:19:2:1,1:4,13:0.1053:2,2:26:1:29:1:0.46784:3.02:36:4:0.1053:0:2.5 -10 42389517 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53202;SOR=Inf;LSEQ=ATTGAATGGAATCGTCATCG;RSEQ=ATGAATTGAATGCAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:25.9:1:30.4:1:1:0:38.8:20:1:0:2.7 0/1:19:2:1,1:4,13:0.1053:2,2:37.5:1:30:1:0.46784:3.02:43:4:0.1053:0:4 -10 42389524 . T C 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11089;SOR=0;LSEQ=GGAATCGTCATCGAATGAAT;RSEQ=GAATGCAATCATCGAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:2,7:0.1818:2,2:21:1:28.5:1:0.49091:3.06:22:4:0.2:0:5.5 0/0:21:0:0,0:5,16:0:2,0:23.7:1:28.8:1:1:0:40:42:1:0:3.4 -10 42389536 . T A 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53202;SOR=Inf;LSEQ=GAATGAATTGAATGCAATCA;RSEQ=CGAATGGTCTGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:21.1:1:30.4:1:1:0:34:18:1:0:3.3 0/1:20:3:0,3:5,12:0.15:2,0:35.7:1:31:1:0.53947:0:36.7:6:0.1579:0:5.7 -10 42389537 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGAATTGAATGCAATCAT;RSEQ=GAATGGTCTGGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:20.8:1:30.2:1:1:0:34:18:1:0:3.3 0/1:20:2:1,1:4,14:0.1:2,2:26:0:33:1:0.44737:3.24:46:4:0.1053:0:4.5 -10 42389541 . T C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTGAATGCAATCATCGAA;RSEQ=GGTCTGGAATGGAATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:25.6:1:30.9:1:1:0:28.9:14:1:0:3.7 0/1:19:2:1,1:3,14:0.1053:2,2:22:0:32.5:1:0.38596:4.18:46:4:0.1111:0:4.5 -10 42389545 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGCAATCATCGAATGGT;RSEQ=TGGAATGGAATCATCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:28.3:1:32.3:1:1:0:27:12:1:0:3.7 0/1:15:2:1,1:1,12:0.1333:1,2:48:1:27.5:1:0.25714:8.83:51:4:0.1333:0:2 -10 42389547 . G C 89 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90475;LSEQ=ATGCAATCATCGAATGGTCT;RSEQ=GAATGGAATCATCTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,0:0.6667:0,0:31:1:31.5:1:1:0:29.5:8:0.6667:0:2.8 1/0:14:9:0,9:2,2:0.6429:2,0:28.3:1:28.3:1:0.07692:0:35.3:18:0.6429:0:3.7 -10 42389548 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCAATCATCGAATGGTCTG;RSEQ=AATGGAATCATCTTCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:27.3:1:32:1:1:0:27:12:1:0:3.7 0/1:14:2:1,1:1,11:0.1429:2,2:15:0:31:1:0.27473:8.12:46:4:0.1429:0:4.5 -10 42389556 . T C 52 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.52105;SOR=Inf;LSEQ=TCGAATGGTCTGGAATGGAA;RSEQ=CATCTTCAAATGGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:23.5:1:30.5:1:1:0:27:12:1:0:3.7 0/1:14:3:0,3:2,9:0.2143:2,0:15.7:1:33:0:1:0:36.7:6:0.2143:0:5.7 -10 42389561 . T A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGTCTGGAATGGAATCATC;RSEQ=TCAAATGGAAAGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:20.2:1:30.8:1:1:0:27:12:1:0:3.7 0/1:14:2:1,1:1,11:0.1429:2,2:33.5:1:27.5:1:0.27473:8.12:51:4:0.1429:0:2 -10 42389562 . T C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTCTGGAATGGAATCATCT;RSEQ=CAAATGGAAAGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:19.5:1:30.5:1:1:0:27:12:1:0:3.7 0/1:13:2:0,2:2,9:0.1538:2,0:14.5:1:33:0:1:0:40:4:0.1538:0:6.5 -10 42389564 . A T 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56923;SOR=0.30214;LSEQ=TCTGGAATGGAATCATCTTC;RSEQ=AATGGAAAGGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:22.3:1:30:1:1:0:26:6:0.75:0:3 0/1:11:5:0,5:1,5:0.4545:2,0:43.6:1:26.4:1:1:0:35.4:10:0.4545:0:3 -10 42389572 . A T 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.86755;LSEQ=GGAATCATCTTCAAATGGAA;RSEQ=GGAATGGAATCATCGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:50:0:32:0:1:0:22:2:0.3333:0:5 0/1:10:3:0,3:1,6:0.3:2,0:11:1:31.3:1:1:0:37:6:0.3:0:5.3 -10 42389612 . T C 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATGGAATTATCAT;RSEQ=GAATGGATTCAAATCGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:11:0:31:0:1:0:22:2:1:0:5 1/0:4:3:0,3:0,1:0.75:0,0:7:1:29:1:1:0:38.3:6:0.75:0:3.3 -10 42389619 . ATTCAAATCGAATAAACATCAAACGGAATCAAACGGAATT A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATGGAATTATCATTGAATGG;RSEQ=ATCGAATGGAATCGAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:26:1:27.2:1:1:0:37.5:4:1:1:3.5 -10 42389885 . T A 63 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAAAGGAGTCATCATCTA;RSEQ=TGGAATCGCATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:25:1:31.8:1:1:0:48.5:8:1:0:3.5 -10 42389892 . C A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTCATCATCTATTGGAAT;RSEQ=GCATGGAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:37:1:31:1:1:1:53:4:0.3333:0:3.5 -10 42389896 . T C 63 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCATCTATTGGAATCGCA;RSEQ=GGAATCATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:36:1:31.8:1:1:1:48.5:8:0.6667:0:3.5 -10 42389935 . G A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCGAATGGAATCATCATC;RSEQ=AATGGAATCTAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:45.5:1:31:1:1:1:37:4:0.3333:0:4.5 -10 42389944 . C A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCATCGAATGGAAT;RSEQ=TAATGGAATCATTGAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:46.5:1:29:1:1:1:37:4:0.3333:0:4.5 -10 42389954 . C A 43 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATGGAATCTAATGGAAT;RSEQ=ATTGAAGGGAATTGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:0.6:2,2:6.3:1:27.3:1:1:1.7321:45.3:6:0.6:0:3.7 -10 42389961 . G C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTAATGGAATCATTGAA;RSEQ=GGAATTGAAAGGAATCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:29.5:1:29.5:1:1:0:37:4:0.6667:0:4.5 -10 42390105 . T C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTCAGATGGAATCAACA;RSEQ=CAAACGGAATCAAACGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:31.5:1:1:0:46:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42390115 . TC AA 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCAACATCAAACGGAA;RSEQ=AAACGGAGTTATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:31.3:1:1:0:46:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42390150 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATCGAAGAGAATC;RSEQ=TCGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7:0:32:1:1:0:46:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42390299 . A G 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=AATCGAATGGAATCATCATC;RSEQ=GATGGAAACGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.3:1:31.3:1:1:0:33.7:6:1:0:2.7 0/1:5:1:1,0:2,2:0.2:2,0:17:0:32:0:1:0:40:2:0.2:0:3 -10 42390302 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CGAATGGAATCATCATCAGA;RSEQ=GGAAACGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:14.3:1:31.3:1:1:0:31:8:1:0:2.8 0/1:6:2:1,1:3,1:0.3333:2,2:34:0:32:0:1:2.44949:40:4:0.3333:0:5 -10 42390305 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=ATGGAATCATCATCAGATGG;RSEQ=AACGAATGGAATCATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:12.5:1:31.7:1:1:0:40.7:12:1:0:2.5 0/1:11:2:1,1:6,3:0.1818:2,2:37:0:30.5:1:1:1.87089:40:4:0.1818:0:5 -10 42390307 . A T 70 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89368;LSEQ=GGAATCATCATCAGATGGAA;RSEQ=CGAATGGAATCATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:4,0:0.4286:0,2:5.7:1:31.7:1:0.14286:0:47.7:6:0.4286:0:2.3 0/1:15:6:4,2:5,4:0.4:2,2:4.2:1:27.2:1:1:1.55:45.7:5:0.3571:0:2.7 -10 42390308 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.38286;LSEQ=GAATCATCATCAGATGGAAA;RSEQ=GAATGGAATCATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:5,2:0.125:2,0:1:0:25:0:0.375:0:50:2:0.125:0:2 0/1:18:3:1,2:9,6:0.1667:2,2:24.3:1:29:1:0.55882:2.81935:43.3:6:0.1667:0:4.3 -10 42390317 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TCAGATGGAAACGAATGGAA;RSEQ=CATCATCGAATGGAATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,5:0:2,0:15.3:1:31.1:1:1:0:46.1:28:1:0:2.7 0/1:29:2:1,1:15,12:0.069:2,2:27:0:30.5:1:1:1.24034:40:4:0.069:0:5 -10 42390320 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0.11099;SOR=0;LSEQ=GATGGAAACGAATGGAATCA;RSEQ=CATCGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:9,4:0.1333:2,2:12:0:33:0:1:2.12136:49.5:4:0.1333:0:4 0/0:29:0:0,0:16,13:0:2,0:15.5:1:29:1:1:0:42.9:58:1:0:2.8 -10 42390325 . G A 25 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87745;LSEQ=AAACGAATGGAATCATCATC;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:9,5:0.0667:2,0:45:0:30:0:1:0:24:2:0.0667:0:4 0/1:34:2:0,2:19,13:0.0588:2,0:11:0:25:0:0.18717:0:22:4:0.0588:0:4 -10 42390326 . A G 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75363;SOR=0.71259;LSEQ=AACGAATGGAATCATCATCG;RSEQ=ATGGAATCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:3,4:7,1:0.4667:2,2:19.7:1:31.7:1:0.11888:7.87634:51.7:14:0.4667:0:3.3 0/1:34:13:8,5:11,10:0.3824:2,2:18.5:1:31.6:1:0.72824:1.44:46.6:26:0.3824:0:3 -10 42390333 . T A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54338;SOR=0.64822;LSEQ=GGAATCATCATCGAATGGAA;RSEQ=CGAATGGAATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:7,2:0.4375:2,2:26.7:1:30.9:1:0.30245:4.19343:51.7:14:0.4375:0:3.3 0/1:39:13:8,5:14,12:0.3333:2,2:25.5:1:30.8:1:0.74015:1.36:46.6:26:0.3333:0:3 -10 42390339 . G A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCGAATGGAATCGAAT;RSEQ=GAATCATCAAATGGAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:29.4:1:31.9:1:1:0:45.7:36:1:0:2.6 0/1:42:2:1,1:21,18:0.0476:2,2:5:0:28.5:1:1:1.16227:40:4:0.0476:0:5 -10 42390341 . A G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56428;SOR=0.65127;LSEQ=CATCGAATGGAATCGAATGG;RSEQ=ATCATCAAATGGAATCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:5,3:5,5:0.4444:2,2:28.9:1:26.5:1:0.66406:1.62:48.8:3:0.375:0:1.8 0/1:44:15:11,4:12,15:0.3409:2,2:24.6:1:31.4:1:0.1078:3.34:44.3:30:0.3571:0:1.9 -10 42390351 . T A 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.53619;LSEQ=AATCGAATGGAATCATCAAA;RSEQ=GGAATCAGATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:9,8:0.0556:2,0:33:0:31:0:1:0:33:2:0.0556:0:4 0/1:48:4:2,2:24,18:0.0833:2,2:27.5:1:30.3:1:1:1.32491:48.8:8:0.087:0:3 -10 42390358 . A C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATCATCAAATGGAATC;RSEQ=GATGGAATCATCATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:33.9:1:30.6:1:1:0:45.1:38:1:0:2.6 0/1:49:2:1,1:25,20:0.0408:2,2:31:0:31.5:1:1:1.24403:50:4:0.0426:0:2.5 -10 42390360 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCATCAAATGGAATCAG;RSEQ=TGGAATCATCATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:33.6:1:29.7:1:1:0:45.1:18:1:0:2.6 0/1:49:2:1,1:25,20:0.0408:2,2:13.5:1:29.5:1:1:1.24403:60:4:0.0435:0:1.5 -10 42390363 . G A 69 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31158;SOR=Inf;LSEQ=TCATCAAATGGAATCAGATG;RSEQ=AATCATCATCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:32.6:1:31.5:1:1:0:45.1:38:1:0:2.6 0/1:49:5:2,3:22,18:0.102:2,2:44.8:1:29.8:1:0.65211:1.80872:30.6:10:0.1087:0:4.8 -10 42390380 . AA GT 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATCATCATCAAATGG;RSEQ=TCGAATAGAATTATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:23.3:1:30.1:1:1:0:45.1:38:1:0:2.6 0/1:53:2:0,2:28,21:0.0377:2,0:28:0:32.5:0:0.19843:0:22:4:0.0408:0:3 -10 42390381 . A T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATCATCATCAAATGGA;RSEQ=TCGAATAGAATTATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:25.2:1:30.5:1:1:0:46.6:34:1:0:2.5 0/1:53:2:2,0:26,21:0.0377:2,0:30.5:1:32:0:0.5:0:24:4:0.0408:0:3.5 -10 42390384 . G A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.08383;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATAGAATTATGGAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:8,9:0.0556:2,0:50:0:32:0:1:0:24:2:0.0556:0:2 0/1:50:3:1,2:24,21:0.06:2,2:19:1:32:0:0.60106:2.24762:44:6:0.0638:0:1.3 -10 42390388 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26482;SOR=0.31916;LSEQ=ATCATCAAATGGAATCGAAT;RSEQ=GAATTATGGAATGAAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:32:1:31:1:1:1.46:33:4:0.1176:0:3.5 0/1:50:2:1,1:24,22:0.04:2,2:30.5:1:32:1:1:1.08892:42.5:4:0.0417:0:7 -10 42390389 . G C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06964;SOR=0;LSEQ=TCATCAAATGGAATCGAATA;RSEQ=AATTATGGAATGAAATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:5.5:1:30.5:1:1:1.46:49.5:4:0.125:0:4 0/0:46:0:0,0:24,22:0:2,0:25.7:1:31.8:1:1:0:42.5:92:1:0:2.5 -10 42390390 . A T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCAAATGGAATCGAATAG;RSEQ=ATTATGGAATGAAATCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:0:2,0:18.6:1:29.9:1:1:0:46.6:34:1:0:2.5 0/1:46:2:1,1:23,21:0.0435:2,2:28.5:1:30.5:1:1:1.09307:42.5:4:0.0435:0:7 -10 42390393 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAATGGAATCGAATAGAAT;RSEQ=ATGGAATGAAATCCAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,9:0:2,0:18.7:1:27.7:1:1:0:46.1:14:1:0:2.6 0/1:42:2:1,1:20,18:0.0476:2,2:25.5:1:33:0:1:1.10818:42.5:4:0.0488:0:7 -10 42390395 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATCGAATAGAATTA;RSEQ=GGAATGAAATCCAATGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:20:1:30.7:1:1:0:45.6:26:1:0:2.4 0/1:43:2:1,1:20,21:0.0465:2,2:29:1:29:1:1:1.05:48.5:4:0.0465:0:3 -10 42390396 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATCGAATAGAATTAT;RSEQ=GAATGAAATCCAATGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:19.3:1:30.2:1:1:0:45.6:12:1:0:2.4 0/1:42:2:1,1:19,21:0.0476:2,2:22.5:1:31:1:1:1.10:42.5:4:0.0488:0:7 -10 42390397 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATCGAATAGAATTATG;RSEQ=AATGAAATCCAATGTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:0:2,0:20.2:1:31.7:1:1:0:44.4:24:1:0:2.4 0/1:43:2:1,1:19,21:0.0465:2,2:38:1:30:1:1:1.10:39:4:0.0476:0:3.5 -10 42390400 . T C 33 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03266;SOR=0;LSEQ=AATCGAATAGAATTATGGAA;RSEQ=GAAATCCAATGTGATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:13:1:33:1:1:1.58:60:4:0.2:0:4 0/0:43:0:0,0:20,23:0:2,0:20.8:1:29.1:1:1:0:40.9:42:1:0:2.5 -10 42390402 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGAATAGAATTATGGAATG;RSEQ=AATCCAATGTGATCATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:20.8:1:30.2:1:1:0:45:20:1:0:2.4 0/1:43:2:1,1:19,21:0.0465:2,2:16.5:1:33:0:1:1.10:42.5:4:0.0476:0:7 -10 42390406 . C T 27 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03191;SOR=0;LSEQ=ATAGAATTATGGAATGAAAT;RSEQ=CAATGTGATCATCATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:31.5:1:27.5:1:1:2.24:33:4:0.2222:0:3.5 0/0:39:0:0,0:19,20:0:2,0:18.9:1:30.2:1:1:0:40.4:38:1:0:2.5 -10 42390409 . A T 89 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.26511;LSEQ=GAATTATGGAATGAAATCCA;RSEQ=TGTGATCATCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:4:1:30.5:1:1:2.24:60:4:0.2222:0:4 0/1:30:8:2,6:12,10:0.2667:2,2:20.6:1:29.9:1:0.22553:3.45097:35.8:16:0.2667:0:3.3 -10 42390413 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGGAATGAAATCCAATGT;RSEQ=ATCATCATTGAATGGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:19.7:1:31:1:1:0:43.9:14:1:0:2.3 0/1:27:2:1,1:13,12:0.0741:2,2:5.5:1:28.5:1:1:1.0801:42.5:4:0.0769:0:7 -10 42390420 . A G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAATCCAATGTGATCATC;RSEQ=TTGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:22:1:31:1:1:0:42.8:10:1:0:1.6 0/1:24:2:1,1:11,11:0.0833:2,2:36.5:1:29.5:1:1:1:39:4:0.0833:0:3.5 -10 42390421 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAATCCAATGTGATCATCA;RSEQ=TGAATGGACTCGAATGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:21.4:1:30.4:1:1:0:42.8:10:1:0:1.6 0/1:22:2:1,1:10,10:0.0909:2,2:12.5:1:31:1:1:1:47.5:4:0.0909:0:3.5 -10 42390422 . T C 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31882;LSEQ=AAATCCAATGTGATCATCAT;RSEQ=GAATGGACTCGAATGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:0.2:0,0:12:0:31:0:1:0:24:2:0.2:0:2 0/1:20:5:2,3:8,7:0.25:2,2:31.8:1:30:1:1:1.66859:31:10:0.25:0:3.2 -10 42390441 . C T 98 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAATGGACTCGAATGGAA;RSEQ=CATCATCCAATGGAAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:29:1:30.5:1:1:0:35:4:1:0:2 1/1:11:11:4,7:0,0:1:0,2:26.3:1:28.5:1:1:0:37.9:22:1:0:2.6 -10 42390645 . C A 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATCGAAAGGAATC;RSEQ=TCATCAGATGGAAATGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9:1:28.5:1:1:0:24.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42390671 . A G 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AGATGGAAATGAATGGAATC;RSEQ=TCATATAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:22.5:1:31.5:1:1:0:25.5:4:1:0:4.5 1/1:1:1:1,0:0,0:1:0,0:12:0:31:0:1:0:24:2:1:0:5 -10 42390677 . T G 76 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGAATGGAATCATCATA;RSEQ=AATGGAATCGAATGGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:14.2:1:33:1:1:0:35.4:10:1:0:4.4 1/1:3:3:3,0:0,0:1:0,0:9.7:1:33.3:1:1:0:34.7:6:1:0:2.7 -10 42390710 . A T 47 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.5542;LSEQ=TGGATTCATTGAATGGAATC;RSEQ=GATGGAATCATCGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:6,7:0.1875:2,2:12:1:29.7:1:1:1.659:40.7:6:0.1875:0:3.3 0/1:9:1:0,1:4,4:0.1111:2,0:32:0:32:0:1:0:60:2:0.1111:0:2 -10 42390720 . A T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51567;SOR=0;LSEQ=GAATGGAATCAGATGGAATC;RSEQ=TCGAATGGACTTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:31.5:1:30.5:1:1:1.13:24:4:0.1176:0:4.5 0/0:10:0:0,0:4,6:0:2,0:38.4:1:30.1:1:1:0:40:20:1:0:2.4 -10 42390722 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=ATGGAATCAGATGGAATCAT;RSEQ=GAATGGACTTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:30.9:1:30.9:1:1:0:37.8:34:1:0:3.2 0/1:10:2:1,1:3,5:0.2:2,2:40.5:1:30:1:1:1.58:24:4:0.2:0:4.5 -10 42390730 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=AGATGGAATCATCGAATGGA;RSEQ=TTGAATGGAATCATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:32.2:1:32.5:1:1:0:37.8:34:1:0:3.2 0/1:10:2:1,1:3,5:0.2:2,2:45:0:29.5:1:1:1.58:48.5:4:0.2:0:3 -10 42390732 . T G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44755;SOR=0.49528;LSEQ=ATGGAATCATCGAATGGACT;RSEQ=GAATGGAATCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:4,4:4,5:0.4706:2,2:30.8:1:31.9:1:1:1.23:35.9:16:0.4706:0:4 0/1:10:3:1,2:3,4:0.3:2,2:32:1:31.7:1:1:1.44135:27.3:6:0.3:0:3.3 -10 42390743 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.53846;SOR=3.55358;LSEQ=GAATGGACTTGAATGGAATC;RSEQ=TTGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:7,8:0.0625:2,0:37:0:34:0:1:0:25:2:0.0625:0:3 0/1:10:2:1,1:2,4:0.2:2,2:33:1:32:0:1:1.83:40.5:4:0.2:0:1.5 -10 42390749 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50769;SOR=0;LSEQ=ACTTGAATGGAATCATTGAA;RSEQ=GGACTCGAATGGAATCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,8:0.125:2,2:21.5:1:30:1:1:1.31:43:4:0.125:0:3.5 0/0:10:0:0,0:4,5:0:2,0:23.7:1:30.2:1:1:0:37.8:18:0.9:0:2.2 -10 42390755 . C G 34 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52;SOR=0;LSEQ=ATGGAATCATTGAATGGACT;RSEQ=GAATGGAATCATTATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,8:0.125:2,2:19:1:34:1:1:1.31:44.5:4:0.1333:0:5.5 0/0:9:0:0,0:4,5:0:2,0:20.2:1:30.8:1:1:0:40.7:18:1:0:2.3 -10 42390756 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=0;LSEQ=TGGAATCATTGAATGGACTC;RSEQ=AATGGAATCATTATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:0.1429:2,2:14.5:1:28.5:1:1:1.37:43:4:0.1429:0:3.5 0/0:9:0:0,0:4,5:0:2,0:19.4:1:30.9:1:1:0:40.7:18:1:0:2.3 -10 42390759 . T A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.64241;SOR=0.5175;LSEQ=AATCATTGAATGGACTCGAA;RSEQ=GGAATCATTATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:1,3:3,4:0.3636:2,2:23.5:1:32.5:1:1:2.09375:35:8:0.3636:0:5 0/1:9:2:1,1:3,4:0.2222:2,2:11:1:31:1:1:1.29:24:4:0.2222:0:4.5 -10 42390762 . A G 63 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33781;SOR=0.26784;LSEQ=CATTGAATGGACTCGAATGG;RSEQ=ATCATTATTGAATGGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:1,3:3,4:0.3636:2,2:20.5:1:31.8:1:1:2.09375:35:8:0.3636:0:5 0/1:8:1:0,1:3,4:0.125:2,0:18:0:33:0:1:0:24:2:0.125:0:4 -10 42390764 . T A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49673;SOR=0;LSEQ=TTGAATGGACTCGAATGGAA;RSEQ=CATTATTGAATGGAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:0.1818:2,2:26:1:28.5:1:1:1.87:46:4:0.1818:0:4.5 0/0:7:0:0,0:3,4:0:2,0:15.4:1:29.7:1:1:0:40.3:14:1:0:2 -10 42390766 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=GAATGGACTCGAATGGAATC;RSEQ=TTATTGAATGGAATAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,6:0.2:2,2:24:1:29:1:1:2.65:46:4:0.2:0:4.5 0/0:7:0:0,0:3,4:0:2,0:13.4:1:30.7:1:1:0:40.3:14:1:0:2 -10 42390781 . A T 77 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATTATTGAATGGAAT;RSEQ=GAATGGAATCATCGAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:14.5:1:30:1:1:0:38.8:12:1:0:3.3 1/1:1:1:0,1:0,0:1:0,0:21:0:32:0:1:0:40:2:1:0:2 -10 42390898 . C A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAAAGGAATTATCCTCAA;RSEQ=TGGAATCAAATGGAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:7.5:1:31.5:1:1:0:40:4:1:0:3 -10 42390919 . A G 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCAAATGGAATTATC;RSEQ=AATGCAATCGAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:20:1:30.7:1:1:0:41:6:1:0:2.7 -10 42390954 . G A 58 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTATCGAATGCAATCGA;RSEQ=TAGAATCATCGAATGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:33:1:29:1:1:0:45:8:1:0:2.3 -10 42391006 . T C 67 d7;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06061;SOR=0;LSEQ=TCGAATGGAACGGAATGGAA;RSEQ=AGTCAATGAACTCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:6.5:1:33.5:1:1:0:36.5:8:1:0:1 0/1:8:2:1,1:3,3:0.25:2,2:11:0:33.5:1:1:1:47:4:0.25:0:2 -10 42391035 . TGAATGGAATC T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=AACTCGAATGGAATCATCAT;RSEQ=GAATGGAATCATCGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:36.5:1:24.5:1:1:0:36.5:1:1:0:1 0/1:8:2:1,1:4,2:0.25:2,2:10.5:1:29.1:1:1:1.8258:33:4:0.25:0.125:6.5 -10 42391045 . C T 59 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19394;SOR=Inf;LSEQ=GAATCATCATTGAATGGAAT;RSEQ=GAATGGAATCATCGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:31.8:1:31:1:1:0:36.5:8:1:0:1 1/0:7:4:3,1:1,1:0.5714:2,2:27.5:1:29.8:1:1:2.45:36.8:8:0.6667:0:2 -10 42391067 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AATGGAATCATCGAGTGGAA;RSEQ=CGAATGGAATCACGATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:9.8:1:29.8:1:1:0:36.5:8:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:28.5:1:30:1:1:1:33:4:0.4:0:6.5 -10 42391080 . C T 40 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGAATCGAATGGAATCA;RSEQ=GATTAAATGGAATCGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:29:1:25.7:1:1:0:35.3:2:1:0:5.3 -10 42391084 . T C 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATGGAATCACGAT;RSEQ=AAATGGAATCGAATGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:27.7:1:30.7:1:1:0:35.3:6:1:0:5.3 -10 42391098 . T A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGATTAAATGGAATCGAA;RSEQ=GTAATCATCAAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:28.5:1:1:0:33:4:1:0:6.5 -10 42391317 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTAATGGAATCATTGAAA;RSEQ=GAATTGAATGGAATCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:0:31:1:1:0:48:4:1:0:1.5 -10 42391413 . A T 44 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGAATGGAATCATCGCA;RSEQ=AGAATCGAATGGAATTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:8.3:1:28.3:1:1:0:37.3:6:1:0:6.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42391422 . A G 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58768;SOR=0.4655;LSEQ=GAATCATCGCAAAGAATCGA;RSEQ=TGGAATTATCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:0.1667:2,2:18.5:1:33.5:1:1:1.4491:42:4:0.1667:0:5.5 0/1:24:2:1,1:10,12:0.0833:2,2:5:1:29.5:1:1:1.19:60:4:0.0833:0:6 -10 42391435 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATGGAATTATCAT;RSEQ=GAATGGAGTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:8,6:0,0:1:0,2:19.4:1:31.6:1:1:0:37.3:28:1:0:5.6 1/1:32:31:15,16:0,0:0.9688:0,2:15.6:1:30.6:1:1:0:38.3:62:0.9688:0:6.2 -10 42391443 . G A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.28532;LSEQ=TGGAATTATCATTGAATGGA;RSEQ=TCGAATGGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:7,6:1,1:0.8125:2,2:22.5:1:31.2:1:1:1.15:36.5:26:0.8125:0:5.6 1/1:33:28:12,16:3,2:0.8485:2,2:23.4:1:30.3:1:0.63899:1.95797:34.1:56:0.8485:0:6.1 -10 42391452 . A T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23166;SOR=2.29479;LSEQ=CATTGAATGGAGTCGAATGG;RSEQ=ATCAACATCAAACGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:6,4:0.375:2,2:36:1:30.3:1:1:1.46198:37.7:12:0.375:0:6 1/0:36:21:12,9:3,12:0.5833:2,2:31.3:1:29.4:1:0.04073:5.08:36.5:42:0.6:0:6.9 -10 42391454 . T A 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGAATGGAGTCGAATGGAA;RSEQ=CAACATCAAACGGAATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:34.6:1:31.2:1:1:0:36.6:32:1:0:5.6 0/1:36:2:1,1:14,20:0.0556:2,2:27:0:32:0:1:1.41:28:4:0.0556:0:6 -10 42391455 . C G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.88453;LSEQ=TGAATGGAGTCGAATGGAAT;RSEQ=AACATCAAACGGAATCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:8,7:0.0625:2,0:34:0:34:0:1:0:27:2:0.0625:0:5 0/1:36:2:1,1:14,20:0.0556:2,2:38:1:31:1:1:1.41:60:4:0.0571:0:6 -10 42391460 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.77298;SOR=1.22734;LSEQ=GGAGTCGAATGGAATCAACA;RSEQ=CAAACGGAATCAAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:6,4:0.375:2,2:35.8:1:32.5:1:1:1.46198:37.7:12:0.375:0:6.7 0/1:40:17:10,7:7,15:0.425:2,2:37.3:1:31.6:1:0.11461:2.97:37.3:34:0.4359:0:7 -10 42391470 . TC AA 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14769;SOR=0.186;LSEQ=GGAATCAACATCAAACGGAA;RSEQ=AAACGGAATTATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:8,7:1,0:0.9375:0,2:29.3:1:30.5:1:1:0:37.2:30:0.9375:0:4.6 1/0:41:30:13,17:4,3:0.7317:2,2:36.8:1:30.6:1:0.68:1.71725:37.7:60:0.7692:0:5.1 -10 42391485 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGAATCAAACGGAATTATC;RSEQ=AATGGAATCGAAGAGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:20.1:1:30.3:1:1:0:36.6:32:1:0:4.6 0/1:41:2:1,1:18,21:0.0488:2,2:26:0:32:0:1:1.16:49:4:0.0488:0:2 -10 42391505 . A T 125 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.69808;SOR=1.47641;LSEQ=GAATGGAATCGAAGAGAATC;RSEQ=TCGAATGGCCACGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:3,1:0.4286:2,2:5:1:31.3:1:0.48571:4.4496:42.7:6:0.4286:0:5.7 1/0:36:19:11,8:6,11:0.5278:2,2:13.3:1:29.5:1:0.20214:2.45:40.8:38:0.5278:0:5.6 -10 42391511 . T C 66 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53044;SOR=Inf;LSEQ=AATCGAAGAGAATCATCGAA;RSEQ=GGCCACGAATGGAATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:17.3:1:28.3:1:1:0:28.3:8:1:0:4 0/1:16:5:2,3:5,6:0.3125:2,2:14.6:1:28.8:1:1:1.23276:31.6:10:0.3125:0:6.8 -10 42391514 . C A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52527;SOR=0.27609;LSEQ=CGAAGAGAATCATCGAATGG;RSEQ=CACGAATGGAATCATCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:24.5:1:26.5:1:1:0:31.5:4:0.6667:0:4 0/1:12:4:1,3:5,3:0.3333:2,2:22:1:24.8:1:0.54545:4.34109:29:3:0.2727:0:6.3 -10 42391516 . A C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24176;SOR=0.19209;LSEQ=AAGAGAATCATCGAATGGCC;RSEQ=CGAATGGAATCATCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:22.5:1:30:1:1:0:31.5:4:0.6667:0:4 0/1:12:3:0,3:6,3:0.25:2,0:26.3:1:32.7:1:0.18182:0:29.3:6:0.25:0:6.3 -10 42391559 . T A 24 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATAATCCATGG;RSEQ=CCCGAATGCAATCATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:24.5:1:1:0:33:4:1:0:2 -10 42391638 . A G 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54747;SOR=2.71347;LSEQ=AATAATCATTGAACGGAATC;RSEQ=AATGGAATCATCGTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:30:1:31:1:1:1:26:4:0.5:0:3.5 1/0:8:6:4,2:1,1:0.75:2,2:32.3:1:28.8:1:1:1.83:33.2:12:0.75:0:4.3 -10 42391651 . G A 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6871;LSEQ=CGGAATCAAATGGAATCATC;RSEQ=TCGAATGGAAACGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:17:1:29:1:1:0:26.3:6:0.75:0:4.3 1/0:9:6:5,1:1,2:0.6667:2,2:29.3:1:28.3:1:0.22619:7.11:39:12:0.6667:0:4.2 -10 42391655 . A G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29945;SOR=0.27545;LSEQ=ATCAAATGGAATCATCGTCG;RSEQ=ATGGAAACGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:0.5:2,2:15.7:1:31:1:1:3.11:26.3:6:0.5:0:4.3 0/1:10:2:2,0:4,4:0.2:2,0:24:1:26.5:1:0.46667:0:28:4:0.2:0:5.5 -10 42391663 . C A 30 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=0;LSEQ=GAATCATCGTCGAATGGAAA;RSEQ=GAATGGAATCATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:9:0:30.5:1:1:1:31:4:0.3333:0:3 0/0:11:0:0,0:5,4:0:2,0:23.6:1:26.4:1:1:0:39.6:8:0.8:0:3.6 -10 42391680 . G A 44 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50909;SOR=Inf;LSEQ=AAACGAATGGAATCATCATC;RSEQ=AATGGAAGTGAAAGGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:32:1:30.3:1:1:0:29.7:6:1:0:3.7 0/1:9:3:1,2:4,2:0.3333:2,2:29.3:1:28.3:1:0.52381:3.38757:39.7:6:0.3333:0:5.3 -10 42391688 . G A 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5;SOR=4.17095;LSEQ=GGAATCATCATCGAATGGAA;RSEQ=TGAAAGGAGTCATCATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:49:0:31:0:1:0:27:2:0.3333:0:5 1/0:7:5:2,3:1,1:0.7143:2,2:28.2:1:28.6:1:1:1.41418:40.4:10:0.7143:0:4.4 -10 42391689 . T C 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=GAATCATCATCGAATGGAAG;RSEQ=GAAAGGAGTCATCATCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:35:0:32.5:1:1:0:31:4:0.6667:0:3 0/0:7:0:0,0:2,4:0:2,0:27.7:1:27.3:1:1:0:43.5:12:0.8571:0:4.3 -10 42391715 . C T 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=2.18727;LSEQ=GAGTCATCATCTAATGGAAT;RSEQ=GCATGGAATCATCATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:1,1:0.6:2,0:15:1:27.7:1:0.4:0:26.3:6:0.6:0:5.7 1/0:9:7:2,5:0,2:0.7778:0,2:23.3:1:31:1:1:0:50.3:14:0.7778:0:4.9 -10 42391731 . G A 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGCATGGAATCATCAT;RSEQ=AAATGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20.3:1:28.7:1:1:0:26.3:6:1:0:5.7 1/1:6:5:1,4:0,0:0.8333:0,2:31:1:31.2:1:1:0:52.6:10:0.8333:0:5.4 -10 42391753 . T A 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=CATCGAATGGATTCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:47:1:29:0:1:0:26:4:1:0:6 1/1:6:5:1,4:0,1:0.8333:0,2:29.4:1:30.8:1:1:0:52.6:10:0.8333:0:5.4 -10 42391758 . G A 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCGAATGGAATCATCATC;RSEQ=AATGGATTCTAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:46.5:1:30.5:1:1:0:26:4:1:0:6 1/1:5:4:1,3:0,1:0.8:0,2:32.3:1:30:1:1:0:52:8:0.8:0:5 -10 42391765 . T A 32 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TGGAATCATCATCGAATGGA;RSEQ=TCTAATGGAATCATTGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:39.5:1:31:0:1:0:26:4:1:0:6 1/0:4:2:0,2:1,1:0.5:2,0:34.5:1:32:0:1:0:34.5:4:0.5:0:5 -10 42391768 . T A 48 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCATCATCGAATGGATTC;RSEQ=AATGGAATCATTGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:36.5:1:31.5:1:1:0:26:4:1:0:6 1/0:4:3:1,2:0,1:0.75:0,2:31.7:1:30.3:1:1:0:49.7:6:0.75:0:5.3 -10 42391857 . A C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=TCGAATGGAATCATCTTCAA;RSEQ=TGGAATGGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:23.9:1:31.8:1:1:0:47.8:16:1:0:1.5 0/1:5:2:1,1:1,2:0.4:2,2:29:0:32:0:1:1.73:46:4:0.4:0:2.5 -10 42391864 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.52381;SOR=0;LSEQ=GAATCATCTTCAAATGGAAT;RSEQ=GAATGGAATCATCGCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:26:0:32:0:1:1:47:4:0.2:0:1 0/0:5:0:0,0:2,3:0:2,0:32:1:30.4:1:1:0:46:10:1:0:1.4 -10 42391904 . A G 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52381;SOR=3.38757;LSEQ=AATCGAATGGAATTATCATC;RSEQ=AATGGACTCAAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:27:0:33:0:1:0:33:2:0.2:0:3 1/0:4:2:1,1:1,1:0.5:2,2:5.5:1:26:1:1:1:46:4:0.5:0:2.5 -10 42391911 . C A 72 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATTATCATCAAATGGA;RSEQ=TCAAATGGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:21:1:31.4:1:1:0:41.8:10:1:0:3.4 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31.5:1:1:0:44.5:4:1:0:4.5 -10 42391914 . A G 72 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTATCATCAAATGGACTC;RSEQ=AATGGAATCAACATCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:18:1:31.2:1:1:0:41.8:10:1:0:3.4 1/1:2:2:1,1:0,0:1:0,2:31:0:32:0:1:0:44.5:4:1:0:4.5 -10 42391938 . TC AA 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCAACATCAAACGGAA;RSEQ=AAACGGGATTATCAAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:5:0:32:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:6:0:32:0:1:0:44.5:4:1:0:3.5 -10 42392232 . A T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.54771;LSEQ=GAATTATGGAATGAAATCCA;RSEQ=TGTGATCATCATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:17:0:33:0:1:0:47:2:0.5:0:2 0/1:6:2:2,0:1,0:0.3333:0,0:16:1:32:0:1:0:47:4:0.3333:0:1.5 -10 42392254 . T C 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82581;LSEQ=GTGATCATCATCGAATGGAC;RSEQ=CGAATGGAATCATCATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:14:1:32:0:1:0:31:4:0.4:0:4 0/1:17:6:5,1:6,4:0.3529:2,2:20.5:1:31.8:1:0.58791:3.10:34.3:12:0.3529:0:4.3 -10 42392259 . T C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCATCGAATGGACTCGAA;RSEQ=GGAATCATCATCCAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:29:1:31.4:1:1:0:41.6:10:1:0:2.6 0/1:17:2:2,0:10,5:0.1176:2,0:38:1:33:0:1:0:31.5:4:0.1176:0:5.5 -10 42392272 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCGAATGGAATCATCATC;RSEQ=AATGGAAACTAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:34.4:1:31.6:1:1:0:41.6:10:1:0:2.6 0/1:21:2:1,1:13,6:0.0952:2,2:28:1:31.5:1:1:2.08171:46:4:0.0952:0:3 -10 42392275 . T C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23573;SOR=0.26774;LSEQ=CGAATGGAATCATCATCCAA;RSEQ=GGAAACTAATGGAATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:35:1:33:0:1:0:31:4:0.4:0:4 0/1:21:3:3,0:11,7:0.1429:2,0:42.7:1:31.7:1:0.52105:0:23:6:0.1429:0:5.3 -10 42392280 . A G 76 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5799;SOR=0.45653;LSEQ=GGAATCATCATCCAATGGAA;RSEQ=CTAATGGAATCAACATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:40:1:33:0:1:0:31:4:0.4:0:4 0/1:22:5:4,1:10,7:0.2273:2,2:42:1:32.8:1:0.61297:2.68:32.2:10:0.2381:0:4.4 -10 42392282 . T A 68 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54695;SOR=Inf;LSEQ=AATCATCATCCAATGGAAAC;RSEQ=AATGGAATCAACATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:36.4:1:29.6:1:1:0:41.6:10:1:0:2.6 0/1:22:5:3,2:11,6:0.2273:2,2:16.2:1:29.4:1:1:1.21094:36.2:10:0.2273:0:4.4 -10 42392293 . A T 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02521;SOR=0;LSEQ=AATGGAAACTAATGGAATCA;RSEQ=CATCGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:35:1:29.5:1:1:2.44949:53:4:0.3333:0:2 0/0:29:0:0,0:14,15:0:2,0:28.1:1:29.5:1:1:0:38.6:58:1:0:2.3 -10 42392312 . G T 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACATCGAATGGAATCGAAT;RSEQ=GAAACACCATCGAATTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:25.8:1:30.4:1:1:0:41.6:10:1:0:2.6 0/1:30:3:1,2:12,15:0.1:2,2:39.3:1:28.7:1:1:1.57599:42.3:6:0.1034:0:5 -10 42392318 . A G 78 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55633;SOR=Inf;LSEQ=GAATGGAATCGAATGGAAAC;RSEQ=CCATCGAATTGAAACGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:22.5:1:29:1:1:0:35.5:8:0.8:0:3 0/1:28:6:2,4:9,11:0.2143:2,2:39.7:1:30.2:1:1:1.6063:36.8:12:0.2143:0:4.3 -10 42392327 . TT AG 77 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55456;SOR=Inf;LSEQ=CGAATGGAAACACCATCGAA;RSEQ=GAAACGAATGGAATTATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:22:1:29.8:1:1:0:40.2:10:1:0:2.8 0/1:27:6:2,4:8,13:0.2222:2,2:40.2:1:29.9:1:1:1.22149:36.8:12:0.2222:0:3.3 -10 42392385 . CGAAATGT AATGG 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02222;SOR=0;LSEQ=GACTCATCATCGAATGGATT;RSEQ=AATCATCGAATGAAATTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:16.5:1:32.8:1:1:0:31:4:1:0.5:3.5 0/0:8:0:0,0:0,8:0:0,0:3.9:1:29.4:1:1:0:33.9:16:1:0:1.3 -10 42392404 . G A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAAATGTAATCATCGAAT;RSEQ=AAATTGATTGAAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:31.5:1:1:0:31:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42392654 . C G 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52941;SOR=Inf;LSEQ=GAATCCTTATCAAATGGAAT;RSEQ=GAATGGAATCACCGAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:10.5:1:29.2:1:1:0:38:12:1:0:0.7 0/1:12:2:1,1:5,5:0.1667:2,2:9:0:28.5:1:1:1:48:4:0.1667:0:1 -10 42392666 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.73242;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=CGAATAGAATCGAATGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:7,5:0.0769:2,0:1:0:25:0:0.46154:0:48:2:0.0833:0:2 0/1:35:2:2,0:17,16:0.0571:2,0:6:1:29.5:1:0.48908:0:51.5:4:0.0588:0:3.5 -10 42392669 . A C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATCGAATGGAATCACCG;RSEQ=ATAGAATCGAATGGAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:13:1:29.1:1:1:0:40.4:34:1:0:0.6 0/1:40:2:1,1:20,18:0.05:2,2:6.5:1:31:1:1:1.10818:41.5:4:0.0513:0:4 -10 42392673 . G T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGAATGGAATCACCGAATA;RSEQ=AATCGAATGGAACAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:16.2:1:31.1:1:1:0:40.8:36:1:0:0.6 0/1:48:2:1,1:23,23:0.0417:2,2:10.5:1:27.5:1:1:1:41.5:4:0.0426:0:4 -10 42392695 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCGAATGGAACAATCATCG;RSEQ=ATGGACTCAAATGGAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:0:2,0:26.8:1:30:1:1:0:43.3:68:1:0:1.1 0/1:70:2:1,1:33,35:0.0286:2,2:17.5:1:28:1:1:1.06:60:4:0.029:0:2.5 -10 42392701 . C G 88 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05101;SOR=Inf;LSEQ=TGGAACAATCATCGAATGGA;RSEQ=TCAAATGGAATTATCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:30.3:1:30.8:1:1:0:43.4:10.667:1:0:1.1 0/1:72:8:4,4:31,33:0.1111:2,2:31.8:1:29.4:1:1:1.06:54.3:7:0.1:0:1.5 -10 42392707 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCGAATGGACTCAAA;RSEQ=GGAATTATCCTCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:34:1:30.9:1:1:0:43.4:70:1:0:1.1 0/1:74:2:1,1:36,36:0.027:2,2:8.5:1:28:1:1:1:46:4:0.027:0:4.5 -10 42392708 . GGA TTC 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCGAATGGACTCAAAT;RSEQ=ATTATCCTCAAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:34.5:1:31.6:1:1:0:43.4:34:1:0:1.1 0/1:74:2:1,1:36,36:0.027:2,2:46:0:29.7:1:1:1:48:4:0.0274:0:1 -10 42392709 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATCGAATGGACTCAAATG;RSEQ=AATTATCCTCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,15:0:2,0:35.4:1:31.5:1:1:0:44:68:1:0:1 0/1:74:2:1,1:35,35:0.027:2,2:41.5:1:32:0:1:1:49:4:0.0286:0:2 -10 42392715 . T C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59063;SOR=0.45566;LSEQ=AATGGACTCAAATGGAATTA;RSEQ=CCTCAAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:18,15:0.0571:2,2:27:0:33.5:1:1:1.19373:47.5:4:0.0571:0:1.5 0/1:75:2:1,1:37,36:0.0267:2,2:40:1:31:1:1:1.02741:48:4:0.0274:0:1 -10 42392717 . C T 73 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17398;SOR=Inf;LSEQ=TGGACTCAAATGGAATTATC;RSEQ=TCAAATGGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:36.7:1:30.8:1:1:0:43.4:16.5:1:0:1.1 0/1:75:6:3,3:35,34:0.08:2,2:25.3:1:28.5:1:1:1.02902:48.2:5:0.0685:0:2 -10 42392720 . A C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.21005;LSEQ=ACTCAAATGGAATTATCCTC;RSEQ=AATGGAATCGAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:4:2,2:17,15:0.1111:2,2:29.5:1:32.8:1:1:1.12939:48.3:8:0.1176:0:1.3 0/1:76:10:6,4:31,32:0.1316:2,2:27.8:1:32.2:1:0.73552:1.54:43.7:20:0.1333:0:1.8 -10 42392722 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAATGGAATTATCCTCAA;RSEQ=TGGAATCGAATGGAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:19,17:0:2,0:34.9:1:30.9:1:1:0:43.3:72:1:0:1.1 0/1:77:2:1,1:38,37:0.026:2,2:31:0:31.5:1:1:1.02668:48:4:0.026:0:3.5 -10 42392729 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09611;SOR=0;LSEQ=GAATTATCCTCAAATGGAAT;RSEQ=GAATGGAATTATCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:18,16:0.0556:2,2:29:0:31.5:1:1:1.12132:48:4:0.0571:0:1.5 0/0:79:0:0,0:37,37:0:2,0:23:1:31.1:1:1:0:46.1:73:0.9359:0:1.1 -10 42392736 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09956;SOR=0;LSEQ=CCTCAAATGGAATCGAATGG;RSEQ=ATTATCGAATGCAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:18,16:0.0556:2,2:27.5:1:31.5:1:1:1.12132:47:4:0.0588:0:3 0/0:77:0:0,0:38,39:0:2,0:18.9:1:29.6:1:1:0:46.2:37.5:1:0:1.2 -10 42392737 . A T 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.2122;LSEQ=CTCAAATGGAATCGAATGGA;RSEQ=TTATCGAATGCAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:18,16:0.0556:2,2:17.5:1:31.5:1:1:1.12132:48:4:0.0571:0:1 0/1:75:5:2,3:35,35:0.0667:2,2:22.6:1:28:1:1:1.49199:42.6:4:0.0548:0:2.8 -10 42392742 . C T 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0682;LSEQ=ATGGAATCGAATGGAATTAT;RSEQ=GAATGCAATCGAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:16,15:0.0313:2,0:13:0:31:0:1:0:49:2:0.0333:0:3 0/1:60:2:1,1:30,28:0.0333:2,2:11:0:32:0:1:1.07017:48:4:0.0333:0:3.5 -10 42392752 . C T 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52577;SOR=Inf;LSEQ=ATGGAATTATCGAATGCAAT;RSEQ=GAATGGAATTATCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:16.9:1:29.4:1:1:0:44.2:27:1:0:1.2 0/1:47:2:1,1:23,22:0.0426:2,2:14:0:29:1:1:1.04448:46:4:0.0426:0:4.5 -10 42392753 . GA AC 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16594;SOR=0;LSEQ=TGGAATTATCGAATGCAATC;RSEQ=ATGGAATTATCGAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:13,12:0.0714:2,2:9.5:1:29.8:1:1:1.0801:47:4:0.0714:0:2 0/0:40:0:0,0:20,20:0:2,0:14.2:1:30.6:1:1:0:44.7:80:1:0:1.4 -10 42392757 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50056;SOR=Inf;LSEQ=ATTATCGAATGCAATCGAAT;RSEQ=GAATTATCGAATGCAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:13.3:1:31.1:1:1:0:44.7:52:1:0:1.1 0/1:34:2:1,1:16,16:0.0588:2,2:6.5:1:28.5:1:1:1:41.5:4:0.0588:0:4 -10 42392762 . T A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35656;SOR=3.71241;LSEQ=CGAATGCAATCGAATGGAAT;RSEQ=ATCGAATGCAATCAAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:9,11:0.0476:2,0:18:0:30:0:0.47619:0:25:2:0.0476:0:3 0/1:25:4:2,2:9,11:0.16:2,2:9:1:28.3:1:1:1.21:51.5:8:0.16:0:1 -10 42392776 . A G 74 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18333;SOR=0.11844;LSEQ=TGGAATTATCGAATGCAATC;RSEQ=AATAGAATCATCGAAAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:1,0:0.8571:0,2:11.3:1:28.8:1:1:0:45:12:0.8571:0:2.3 0/1:3:1:1,0:1,1:0.3333:2,0:20:0:32:0:1:0:43:2:0.3333:0:1 -10 42393081 . T A 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCTAATGGAATCGCATGG;RSEQ=ATCTTCATCAAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29:1:1:0:36:4:1:0:6 1/1:5:5:3,2:0,0:1:0,2:22.8:1:29.2:1:1:0:40.8:10:1:0:3 -10 42393085 . T A 78 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGGAATCGCATGGTATC;RSEQ=TCATCAAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:12.8:1:30.3:1:1:0:39.5:8:1:0:5.3 1/1:6:6:3,3:0,0:1:0,2:22.5:1:30.5:1:1:0:39.7:12:1:0:3.3 -10 42393090 . C A 83 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33484;SOR=3.23725;LSEQ=GAATCGCATGGTATCTTCAT;RSEQ=AAATGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:6:0:31:1:1:1:43:4:0.3333:0:4.5 1/0:11:7:2,5:3,1:0.6364:2,2:5.1:1:29.7:1:0.24242:6.06919:34.4:14:0.6364:0:4 -10 42393112 . T A 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0.21071;SOR=0.23276;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=CATCAAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:4,4:1,1:0.8:2,2:26.5:1:31.4:1:1:1:42.4:16:0.8:0:4.5 0/1:15:7:2,5:3,3:0.4667:2,2:25.6:1:30:1:0.59207:2.32357:34.4:14:0.4667:0:3.6 -10 42393121 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13846;SOR=0;LSEQ=GAATGGAATCATCATCAAAT;RSEQ=GAATCGAATGGAATCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:34:1:30.5:1:1:1:36:4:0.2:0:6 0/0:16:0:0,0:7,9:0:2,0:29.2:1:30.4:1:1:0:38.6:32:1:0:3.4 -10 42393125 . T A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13846;SOR=0;LSEQ=GGAATCATCATCAAATGGAA;RSEQ=CGAATGGAATCATTGAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:34.5:1:31.5:1:1:1:35:4:0.2:0:4.5 0/0:16:0:0,0:7,9:0:2,0:28.9:1:27.4:1:1:0:38.6:7:1:0:3.4 -10 42393127 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.41985;SOR=0.43047;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATGGAATCATTGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:4,4:1,1:0.8:2,2:35.8:1:31.4:1:1:1:42.1:16:0.8:0:4.1 1/0:16:10:4,6:3,3:0.625:2,2:31.3:1:30.9:1:1:1.46198:35.6:20:0.6667:0:3.7 -10 42393129 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=TCATCATCAAATGGAATCGA;RSEQ=TGGAATCATTGAACGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:34.9:1:31.6:1:1:0:40.9:20:1:0:4.5 0/1:16:2:1,1:6,8:0.125:2,2:21.5:1:28.5:1:1:1.31:42:4:0.125:0:4 -10 42393144 . G A 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15;SOR=0;LSEQ=ATCGAATGGAATCATTGAAC;RSEQ=GAATTGAATGGAATCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:22:0:32:1:1:1:35:4:0.2:0:4.5 0/0:15:0:0,0:5,9:0:2,0:18.1:1:28.9:1:1:0:39.5:28:0.9333:0:3.4 -10 42393154 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=ATCATTGAACGGAATTGAAT;RSEQ=GAATCGTCATAGAATGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:15.3:1:31.8:1:1:0:41.4:18:1:0:4.3 0/1:11:2:0,2:3,5:0.1818:2,0:44.5:1:29:1:1:0:40:4:0.1818:0:4 -10 42393165 . A C 68 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GAATTGAATGGAATCGTCAT;RSEQ=GAATGTATTGAATGCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,0:0.6:0,2:5:1:31.7:1:1:0:35.3:6:0.6:0:5 1/1:5:5:1,4:0,0:1:0,2:26.2:1:29.4:1:1:0:34:10:1:0:4.4 -10 42393171 . T A 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATCGTCATAGAATG;RSEQ=ATTGAATGCAATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:16:0:29:1:1:0:44:4:0.6667:0:5 1/1:3:3:1,2:0,0:1:0,2:36.7:1:29.3:1:1:0:33.7:6:1:0:4.7 -10 42393179 . G A 27 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=CGTCATAGAATGTATTGAAT;RSEQ=CAATCATCGAATGGTCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:27:1:1:0:44:4:1:0:5 0/0:4:0:0,0:1,3:0:2,0:22.3:1:31:1:1:0:30.5:8:1:0:4.5 -10 42393187 . C G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTATTGAATGCAATCAT;RSEQ=GAATGGTCTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:17.5:1:30:1:1:0:21:4:0.5:0:5 -10 42393261 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4;SOR=Inf;LSEQ=AGAATCGAATGGAATTATCA;RSEQ=CGAATGGACTGGAATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:31:1:1:0:44:4:1:0:3.5 1/0:3:2:1,1:0,1:0.6667:0,2:31:0:31.5:1:1:0:44:4:0.6667:0:4.5 -10 42393270 . C A 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TGGAATTATCATCGAATGGA;RSEQ=TGGAATTGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:32.5:1:33:1:1:0:44:4:1:0:3.5 1/1:3:3:1,2:0,0:1:0,2:17.3:1:31:1:1:0:36.3:6:1:0:4.3 -10 42393272 . G C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTATCATCGAATGGACT;RSEQ=GAATTGAATCAACATCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:31.5:1:1:0:44:4:1:0:3.5 1/1:3:3:1,2:0,0:1:0,2:15.3:1:30.3:1:1:0:36.3:6:1:0:4.3 -10 42393277 . T A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATCATCGAATGGACTGGAAT;RSEQ=GAATCAACATCAAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39.5:1:30.5:1:1:0:44:4:1:0:3.5 0/0:2:0:0,0:1,1:0:2,0:15.5:1:30.5:1:1:0:44:4:1:0:4.5 -10 42393279 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CATCGAATGGACTGGAATTG;RSEQ=ATCAACATCAAACGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:41:0:31.5:1:1:0:44:4:1:0:3.5 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29:0:1:0:44:4:1:0:4.5 -10 42393307 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAACGGAATCAAACGGAA;RSEQ=TATCGAATGGAATCGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:33.5:1:1:0:44:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42393383 . T C 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAGTATTCCA;RSEQ=GGACTCGAATGCAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:5:0:32:0:1:0:21:2:1:0:4 0/1:10:2:1,1:4,4:0.2:2,2:8:0:31:1:1:1:29:4:0.2:0:2.5 -10 42393415 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAATCATCATCGAATGGAAT;RSEQ=GAATGGAATCATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:37:0:32:0:1:0:21:2:1:0:4 0/1:11:2:1,1:4,4:0.1818:2,2:8:0:31.5:1:1:1:30:4:0.1818:0:4 -10 42393437 . A T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATGGAATCATCGAATGGAC;RSEQ=CGAGTGGAATAATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:42:0:30:0:1:0:21:2:1:0:4 1/0:4:2:1,1:1,1:0.5:2,2:30:0:30:1:1:1:30:4:0.5:0:4 -10 42393441 . G A 57 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCGAATGGACACGA;RSEQ=TGGAATAATCATTGAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:38:0:28:0:1:0:21:2:1:0:4 1/1:4:4:2,2:0,0:1:0,2:19.3:1:28.5:1:1:0:45:8:1:0:2.5 -10 42393487 . C A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCATCATCGAATGG;RSEQ=ATCGAATGGAATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:27:1:1:0:30:4:1:0:4 -10 42393563 . C A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAATTATGGAATGAAATC;RSEQ=AATGTCATCATCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:32:0:1:0:56:4:1:0:3.5 -10 42393569 . C G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TATGGAATGAAATCCAATGT;RSEQ=ATCATCATCGAATGGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:33.5:1:1:0:56:4:1:0:3.5 -10 42393572 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGAATGAAATCCAATGTCAT;RSEQ=ATCATCGAATGGACTCGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:31:1:1:0:56:4:1:0:3.5 -10 42393615 . T A 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCATCATCCAATGGAAAC;RSEQ=AATGGAATCAACATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:30:1:1:0:40:4:1:0:1 -10 42393745 . T A 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=1;SOR=1.31171;LSEQ=AATCATCGAATGAAATTGAT;RSEQ=GAAATCATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:2,2:0.2:2,0:6:0:30:0:1:0:46:2:0.2:0:4 0/1:12:3:2,1:6,3:0.25:2,2:15.3:1:29:1:1:1:42.7:6:0.25:0:1.7 -10 42393758 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTGATTGAAATCATCATC;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,3:0:2,0:24.6:1:30.3:1:1:0:31.3:14:0.875:0:2 0/1:27:2:0,2:13,11:0.0741:2,0:5.5:1:33:0:0.48:0:34.5:4:0.0741:0:4 -10 42393771 . TG AA 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04348;SOR=0;LSEQ=CATCATCAAATGGAATCGAA;RSEQ=GAATCATTGAATGGAATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:24.5:1:31.3:1:1:1.58:28:4:0.2:0:2.5 0/0:36:0:0,0:8,15:0:2,0:23.9:1:28.2:1:1:0:39.3:22:0.6286:0:2.7 -10 42393773 . GA AT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATCAAATGGAATCGAATG;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:27.9:1:31.6:1:1:0:34.8:20:1:0:2.2 0/1:37:2:0,2:15,20:0.0541:2,0:21.5:1:31:0:0.5045:0:34.5:4:0.0541:0:3 -10 42393774 . A T 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.41563;SOR=3.15183;LSEQ=CATCAAATGGAATCGAATGG;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:4,5:0.1:2,0:24:0:23:0:1:0:45:2:0.1:0:4 0/1:38:10:2,8:13,12:0.2632:2,2:18:1:26.5:1:0.13396:4.1609:38.5:20:0.2857:0:3.3 -10 42393776 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAATGGAATCGAATGGAA;RSEQ=CATTGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:29.7:1:30.7:1:1:0:34.8:20:1:0:2.2 0/1:38:2:1,1:14,22:0.0526:2,2:16.5:1:31:1:1:1.55:25:4:0.0571:0:3 -10 42393780 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATCGAATGGAATCAT;RSEQ=GAATGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:32.1:1:30.9:1:1:0:34.8:20:1:0:2.2 0/1:41:2:1,1:14,25:0.0488:2,2:20.5:1:28.5:1:1:1.76:31:4:0.05:0:2 -10 42393782 . A T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATCGAATGGAATCATTG;RSEQ=ATGGAATCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:33.3:1:30.7:1:1:0:34.8:20:1:0:2.2 0/1:41:2:1,1:14,25:0.0488:2,2:22.5:1:26.5:1:1:1.76:31:4:0.05:0:2 -10 42393791 . G C 33 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=TGGAATCATTGAATGGAATC;RSEQ=AATGGAATCATCATCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:0.1818:2,2:28:0:33:0:1:1.87:28:4:0.1818:0:2.5 0/0:45:0:0,0:18,27:0:2,0:29.8:1:30.2:1:1:0:41.1:90:1:0:2.2 -10 42393792 . A G 31 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GGAATCATTGAATGGAATCG;RSEQ=ATGGAATCATCATCAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:0.1818:2,2:40:1:31.5:1:1:1.87:45:4:0.1818:0:4 0/0:45:0:0,0:18,27:0:2,0:30.2:1:29:1:1:0:41.1:44:1:0:2.2 -10 42393804 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TGGAATCGAATGGAATCATC;RSEQ=TCAGATGGAAATGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:26.1:1:30.4:1:1:0:36.4:22:1:0:2.1 0/1:45:2:1,1:16,27:0.0444:2,2:42.5:1:31.5:1:1:1.67:41:4:0.0444:0:4.5 -10 42393809 . A G 31 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02922;SOR=0;LSEQ=TCGAATGGAATCATCATCAG;RSEQ=TGGAAATGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,6:0.2:2,2:40:1:31:1:1:2.65:45:4:0.2:0:4 0/0:46:0:0,0:18,28:0:2,0:29.5:1:29.5:1:1:0:41.7:45:1:0:2.2 -10 42393817 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCATCAGATGGAAAT;RSEQ=AATGGAATCATCATAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:24.6:1:31.2:1:1:0:39.3:18:1:0:2.4 0/1:48:2:1,1:17,29:0.0417:2,2:7:1:28:0:1:1.69:30:4:0.0426:0:1 -10 42393820 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCATCAGATGGAAATGAA;RSEQ=GGAATCATCATAGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:29:1:29.6:1:1:0:42.6:14:1:0:2.4 0/1:45:2:1,1:15,28:0.0444:2,2:42.5:1:30:1:1:1.84:41:4:0.0465:0:4.5 -10 42393827 . A G 133 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.42273;SOR=2.4537;LSEQ=AGATGGAAATGAATGGAATC;RSEQ=TCATAGAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:2,3:0.2857:2,0:31:1:32:1:1:0:48.5:4:0.2857:0:2.5 1/0:40:20:5,15:8,10:0.5:2,2:25.4:1:31:1:0.30712:2.34374:43.6:40:0.5128:0:2.5 -10 42393829 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ATGGAAATGAATGGAATCAT;RSEQ=ATAGAATGGAATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:22.6:1:31:1:1:0:42.6:14:1:0:2.4 0/1:38:2:1,1:11,25:0.0526:2,2:9:0:28:1:0.5377:2.22:47.5:4:0.0526:0:2.5 -10 42393832 . A T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10825;SOR=0.14902;LSEQ=GAAATGAATGGAATCATCAT;RSEQ=GAATGGAATCGAATGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:18.5:1:28.5:1:1:3.16:45:4:0.2857:0:4 0/1:38:2:1,1:11,25:0.0526:2,2:22:1:29.5:1:0.5377:2.22:43:4:0.0541:0:2.5 -10 42393843 . GA AC 56 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCATAGAATGGAATC;RSEQ=ATGGATTCATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:21.5:1:32.3:1:1:0:45.3:8:1:0:2.8 0/1:26:4:2,2:7,15:0.1538:2,2:13.5:1:28.3:1:0.59064:2.08:45.5:8:0.1538:0:2 -10 42393844 . A C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45448;SOR=0.40721;LSEQ=ATCATCATAGAATGGAATCG;RSEQ=ATGGATTCATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:24:0:34:0:1:0:40:2:0.25:0:2 0/1:26:3:1,2:6,13:0.1154:2,2:19.7:1:31:1:1:1.08:34:6:0.1364:0:2 -10 42393848 . G T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATAGAATGGAATCGAATG;RSEQ=ATTCATTGAATGGAATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:23:1:32.7:1:1:0:45.3:6:1:0:2.3 0/1:25:2:1,1:7,16:0.08:2,2:14.5:1:27:1:1:2.20:41:4:0.08:0:4.5 -10 42393888 . T G 70 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCATTGAATGGACT;RSEQ=GAATGGAAACATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:1:0,2:15.2:1:30.2:1:1:0:47:10:1:0:2.8 -10 42393897 . A T 45 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAATGGACTTGAATGGAA;RSEQ=CATTGAATGGACTCGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:14.3:1:28.7:1:1:0:45.7:6:1:0:3.3 -10 42394069 . AA TT 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAAATGGAATCGAATGGA;RSEQ=TATCGAATGCAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:32:0:1:0:31:4:1:0:1.5 -10 42394228 . T A 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATGGAATCATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:36:0:31:1:1:0:28:4:1:0:1 0/1:7:3:2,1:2,1:0.4286:2,2:18.3:1:29:1:1:1:34:6:0.4286:0:1.7 -10 42394244 . T C 31 d7;v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AATCTAATGGAATCATTGAA;RSEQ=GGAATTGAATGGAATCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31.5:1:1:0:28:4:1:0:1 0/1:7:2:2,0:1,2:0.2857:2,0:47:0:31.5:1:0.4:0:38:4:0.2857:0:2 -10 42394247 . AATTGAATGGAATCGT A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTAATGGAATCATTGAATGG;RSEQ=CATCGAATGAATTGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:29.5:1:31:1:1:0:28:4:1:0:1 0/1:6:2:1,1:3,1:0.3333:2,2:30:0:31.5:1:1:2.44949:28:4:0.3333:0:1 -10 42394278 . A G 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATCGTCATCGAATGAATTGA;RSEQ=TGCAATCATCGAATGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:2,0:2,2:0.3333:2,0:20:0:30.5:1:0.46667:0:38:4:0.3333:0:2 -10 42394330 . A G 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCAAATGGAAAGGAATG;RSEQ=AATCATCGCATAGAATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:28:1:1:0:24:4:1:0:8 -10 42394351 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCATCGCATAGAATCGAA;RSEQ=GGAATTATCATTGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:32.5:1:29:1:1:1.73:24:4:0.4:0:8 -10 42394362 . TT AC 61 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATCGAATGGAATTATCA;RSEQ=GAATGGACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:4:2,2:1,2:0.5714:2,2:16.8:1:30.5:1:1:1.81:29:8:0.5714:0.1429:2.3 -10 42394363 . T C 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATGGAATTATCAT;RSEQ=GAATGGACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:1,2:0,0:0.5:0,2:40.7:1:29:1:1:0:29.3:6:1:0:7 -10 42394371 . C A 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATTATCATTGAATGGA;RSEQ=TCGAATGGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:3:1,2:2,2:0.4286:2,2:43.7:1:29.7:1:1:1.81007:29.3:6:0.4286:0:7 -10 42394387 . ATCAAACGGAG A 62 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCGAATGGAATCAAC;RSEQ=TCAAACGGAATTATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:4:2,2:0,1:0.5714:0,2:39.8:1:31.3:1:1:0:29:8:0.5714:0:3 -10 42394398 . TC AA 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCAACATCAAACGGAG;RSEQ=AAACGGAATTATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:2:1,1:2,3:0.25:2,2:18.5:1:28:1:1:1.41:24:4:0.2857:0:7 -10 42394436 . A G 87 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCGAAGAGAATCATC;RSEQ=AATGGCCACGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:4,3:0,0:1:0,2:26.1:1:31:1:1:0:29.7:14:1:0:2.6 -10 42394484 . T C 79 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08615;SOR=0;LSEQ=GAATGGAATGGAATAATCCA;RSEQ=GGACCCGAATGCAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:31.5:1:1:0:50:4:1:0:2.5 0/1:24:6:3,3:8,10:0.25:2,2:25:1:30.8:1:1:1.24:40:12:0.2609:0:2.7 -10 42394495 . G A 27 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATAATCCATGGACCCGAAT;RSEQ=CAATCATCATCGAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:17:0:34.5:1:1:0:50:4:1:0:2.5 0/1:24:2:1,1:10,12:0.0833:2,2:13:0:27.5:1:1:1.19:25:4:0.0833:0:3.5 -10 42394504 . A T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TGGACCCGAATGCAATCATC;RSEQ=TCGAATAGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:8:0:31:0:1:0:50:4:1:0:2.5 0/1:23:2:1,1:10,11:0.087:2,2:43.5:1:30.5:1:1:1.10:43:4:0.087:0:3 -10 42394508 . A T 67 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCGAATGCAATCATCATCG;RSEQ=ATAGAATCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:4:0:31:0:1:0:50:4:1:0:2.5 0/1:21:5:2,3:7,9:0.2381:2,2:29.2:1:29.2:1:1:1.15818:37.8:10:0.2381:0:2.8 -10 42394511 . A G 31 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02372;SOR=0;LSEQ=GAATGCAATCATCATCGAAT;RSEQ=GAATCGAATGGAATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:1:0:32.5:1:1:0:50:4:1:0:2.5 0/1:21:2:1,1:7,10:0.0952:2,2:9:0:31.5:1:1:1.40:51:4:0.0952:0:2.5 -10 42394522 . G C 66 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCGAATAGAATCGAATG;RSEQ=AATCATCGAATGGACTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:19:4:2,2:6,9:0.2105:2,2:38:1:33:1:1:1.47:46.8:8:0.2105:0:2 -10 42394530 . G A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAATCGAATGGAATCATC;RSEQ=AATGGACTCGAATGGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:20:2:1,1:7,11:0.1:2,2:27:0:32:0:1:1.54:47:4:0.1:0:2.5 -10 42394538 . T A 50 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGAATCATCGAATGGAC;RSEQ=CGAATGGAATAATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:3:1,2:5,9:0.1765:2,2:26.3:1:31.7:1:1:1.10434:24:6:0.1765:0:1.7 -10 42394552 . C T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGACTCGAATGGAATAAT;RSEQ=ATTGAACGGAATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:13:2:1,1:3,8:0.1538:2,2:28.5:1:26:1:1:2.45:25:4:0.1538:0:3.5 -10 42394559 . C A 33 d7;v4;q23;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATGGAATAATCATTGAA;RSEQ=GGAATCAAATGGAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:3:2,1:1,5:0.3333:2,2:19.3:1:21.3:1:0.22619:7.11:26.7:2:0.25:0:3.3 -10 42394566 . A G 71 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAATCATTGAACGGAATC;RSEQ=AATGGAATCATCGTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:1,4:0,0:1:0,2:16.8:1:30.6:1:1:0:24.6:10:1:0:3 -10 42394745 . T G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACTGAATGGTCTCGAAT;RSEQ=TAATCATCTTCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:33:1:1:0:37:4:1:0:3 -10 42394749 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGAATGGTCTCGAATTTAA;RSEQ=CATCTTCAAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:32:0:1:0:37:4:1:0:3 -10 42394886 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATAATCATCGAATGGAC;RSEQ=CGAATGGAATCATCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:3:0:30:0:1:0:37:2:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:12.5:1:29:1:1:0:45:4:0.6667:0:2.5 -10 42394926 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAATAATCCA;RSEQ=GGACTCGAATGCAATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:41:1:31.5:1:1:0:37:4:1:0:5 0/1:5:2:1,1:2,1:0.4:2,2:36.5:1:30.5:1:1:1.7321:60:4:0.4:0:2.5 -10 42394931 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATAATCCATGGAC;RSEQ=CGAATGCAATCATCTTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:46:1:31:0:1:0:37:4:1:0:5 0/1:5:2:1,1:2,1:0.4:2,2:41.5:1:31:1:1:1.7321:60:4:0.4:0:2.5 -10 42394946 . T G 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02778;SOR=0;LSEQ=TGGACTCGAATGCAATCATC;RSEQ=TCGAATGGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:30:1:1:0:37:4:1:0:5 0/0:7:0:0,0:2,1:0:2,0:26:1:30:1:1:0:60:6:0.4286:0:2 -10 42394954 . G T 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=AATGCAATCATCTTCGAATG;RSEQ=AATCGAATGGAATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:28:1:1:0:37:4:1:0:5 0/0:6:0:0,0:3,3:0:2,0:17.7:1:32.3:1:1:0:47:12:1:0:2.3 -10 42394962 . TG GA 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=CATCTTCGAATGGAATCGAA;RSEQ=GAATCATCGAATGGACTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:29.5:1:1:0:37:4:1:0:4 0/0:6:0:0,0:3,3:0:2,0:19.2:1:30.7:1:1:0:48.3:12:1:0:2.7 -10 42394985 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCATCGAATGGACTCGAA;RSEQ=GGAATAATCATTGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:30.5:1:30:1:1:1:49:4:0.5:0:3.5 -10 42395001 . A C 60 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAAGGGAATAATCATTGAA;RSEQ=GGAATCGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:10.5:1:30:1:1:1:41:8:0.6667:0:2 -10 42395012 . G T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATTGAAAGGAATCGAAT;RSEQ=GAATCATCATTGGATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:22.5:1:31.5:1:1:1:46:4:0.5:0:2 -10 42395020 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AAGGAATCGAATGGAATCAT;RSEQ=ATTGGATGGAAACGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:13:0:31:1:1:1:49:4:0.5:0:3.5 -10 42395023 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATGGAATCATCAT;RSEQ=GGATGGAAACGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:10:0:32.5:1:1:1:49:4:0.5:0:3.5 -10 42395817 . A G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGGACTTGAATGGAATC;RSEQ=TTGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:10:1:29.5:1:1:0:31:4:0.6667:0:7 -10 42395860 . G A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTATTGAATGGAATTGAAT;RSEQ=GAATCATCGCATGGTCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:42.5:1:29.5:1:1:0:31:4:0.6667:0:7 -10 42395870 . C A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTGAATGGAATCATCG;RSEQ=ATGGTCTCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:1:0:31:0:1:0:47:2:1:0:2 1/1:3:3:3,0:0,0:1:0,0:32:1:30.7:1:1:0:29:6:1:0:5.7 -10 42395892 . ATCAAATAGAATCGAATGGAATCACCGAATAGAATCGAATGGAACAATCATCGAATGGACTCAAATGGAATTATCC A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGGTCTCGAATGGAATCATT;RSEQ=TCAAATGGAATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:12.7:1:30.7:1:1:0:49:6:1:0:1.7 1/0:3:2:2,0:1,0:0.6667:0,0:8:1:28.6:1:1:0:40:4:0.6667:0.6667:5 -10 42395928 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14444;SOR=0;LSEQ=TGGAATCACCGAATAGAATC;RSEQ=AATGGAACAATCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:40:1:30.5:1:1:1:53.5:4:0.1429:0:1.5 0/0:22:0:0,0:15,6:0:2,0:12.4:1:30.3:1:1:0:30:42:1:0:3 -10 42395967 . C T 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30751;SOR=Inf;LSEQ=TGGACTCAAATGGAATTATC;RSEQ=TCAAATGGAATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:20,13:0:2,0:26.9:1:31.6:1:1:0:30.1:66:1:0:3.5 0/1:73:4:2,2:47,21:0.0548:2,2:25:1:30.5:1:0.58811:2.21071:32.5:8:0.0556:0:3.3 -10 42395970 . A C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00251;SOR=0.27031;LSEQ=ACTCAAATGGAATTATCCTC;RSEQ=AATGGAATCAAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:19:11,8:9,5:0.5758:2,2:31.3:1:32.1:1:1:1.29846:26.5:38:0.5758:0:3.8 0/1:79:21:13,8:41,17:0.2658:2,2:31:1:31:1:0.58484:1.47655:28.3:42:0.2658:0:3.9 -10 42395974 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATGGAATTATCCTCAAAT;RSEQ=GAATCAAATGGAATTATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:0:2,0:25.6:1:31.9:1:1:0:31.5:78:1:0:3.4 0/1:89:2:1,1:60,27:0.0225:2,2:18.5:1:31.5:1:0.53269:2.20033:27:4:0.0225:0:4 -10 42395976 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATTATCCTCAAATGG;RSEQ=ATCAAATGGAATTATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:27,15:0:2,0:24.6:1:30.3:1:1:0:32.1:84:1:0:3.5 0/1:93:2:1,1:62,29:0.0215:2,2:19:1:33:0:0.54348:2.11893:49:4:0.0215:0:7 -10 42395979 . CA GG 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51612;SOR=0.60897;LSEQ=GAATTATCCTCAAATGGAAT;RSEQ=AATGGAATTATCAAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:3,2:24,14:0.1136:2,2:21.8:1:31.9:1:1:1.13926:32.4:10:0.1136:0.0227:3 0/1:97:7:5,2:61,27:0.0722:2,2:18.9:1:31.8:1:1:1.11:30.7:14:0.0722:0.0103:2.9 -10 42395980 . A G 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.64425;SOR=1.23839;LSEQ=AATTATCCTCAAATGGAATC;RSEQ=AATGGAATTATCAAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:35:22,13:2,1:0.7955:2,2:26.3:1:30.5:1:1:1.1767:29.8:70:0.8974:0:3.4 1/1:99:82:56,26:7,2:0.8283:2,2:24:1:29.9:1:0.716:1.61705:32.5:164:0.9011:0:3.6 -10 42395983 . T G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATCCTCAAATGGAATCAAA;RSEQ=GGAATTATCAAATGCAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:31,17:0:2,0:23.8:1:31:1:1:0:31.8:96:1:0:3.3 0/1:110:2:1,1:74,32:0.0182:2,2:28:1:32:1:0.51973:2.29256:25.5:4:0.0182:0:4.5 -10 42395987 . A T 115 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27961;SOR=2.14888;LSEQ=CTCAAATGGAATCAAATGGA;RSEQ=TTATCAAATGCAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:3,0:31,18:0.0577:2,0:15.3:1:30.7:1:0.54308:0:42.7:6:0.0577:0:3.3 0/1:120:14:11,3:73,33:0.1167:2,2:16.5:1:30.3:1:0.54972:1.65:31.1:28:0.1167:0:3.9 -10 42395991 . T A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATCAAATGGAATTA;RSEQ=CAAATGCAATCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:35,20:0:2,0:23.3:1:30.8:1:1:0:31.7:110:1:0:3.4 0/1:126:2:1,1:88,36:0.0159:2,2:28:1:27.5:1:0.50273:2.42486:25:4:0.0159:0:4.5 -10 42395993 . A G 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.79579;SOR=0.77594;LSEQ=TGGAATCAAATGGAATTATC;RSEQ=AATGCAATCGAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:53:32,21:2,1:0.9138:2,2:22.7:1:30.1:1:1:1.30633:30.5:106:0.9298:0:3.6 1/1:129:115:81,34:6,4:0.8915:2,2:25.2:1:30.1:1:0.49047:1.58:31.3:114:0.9048:0:3.6 -10 42396002 . C T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATTATCAAATGCAAT;RSEQ=GAATGGAATTATCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:41,21:0:2,0:24.3:1:30.7:1:1:0:32.3:61:1:0:3.4 0/1:139:2:2,0:94,43:0.0144:2,0:30.5:1:32:0:1:0:40:4:0.0146:0:5.5 -10 42396003 . G C 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9201;LSEQ=TGGAATTATCAAATGCAATC;RSEQ=AATGGAATTATCGAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:1:1,0:40,23:0.0156:2,0:2:0:32:0:1:0:25:2:0.0156:0:4 0/1:139:2:1,1:95,40:0.0144:2,2:46:1:31.5:1:0.51052:2.35819:49:4:0.0146:0:7 -10 42396004 . A C 87 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10119;SOR=Inf;LSEQ=GGAATTATCAAATGCAATCG;RSEQ=ATGGAATTATCGAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:41,23:0:2,0:24.1:1:30.2:1:1:0:32.3:128:1:0:3.4 0/1:141:7:5,2:94,40:0.0496:2,2:22.7:1:31:1:1:1.06:27.6:14:0.05:0:4.3 -10 42396008 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTATCAAATGCAATCGAATG;RSEQ=AATTATCGAATGCAATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:41,23:0:2,0:25.1:1:31.3:1:1:0:32.3:63:1:0:3.4 0/1:146:2:1,1:99,45:0.0137:2,2:26:1:29:1:0.53236:2.18696:47.5:4:0.0139:0:4.5 -10 42396012 . T A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63828;SOR=0.63994;LSEQ=CAAATGCAATCGAATGGAAT;RSEQ=ATCGAATGCAATCGAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:2,0:40,22:0.0308:2,0:41.5:1:27:1:0.54167:0:40:4:0.0313:0:5 0/1:151:3:2,1:98,50:0.0199:2,2:24.3:1:30.3:1:1:1.02:35:6:0.02:0:6 -10 42396014 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGCAATCGAATGGAATTA;RSEQ=CGAATGCAATCGAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:41,23:0:2,0:26.3:1:30.5:1:1:0:32.4:63:1:0:3.3 0/1:153:2:1,1:99,52:0.0131:2,2:44:1:31:1:1:1.89537:49:4:0.0131:0:7 -10 42396019 . T A 73 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.325;SOR=Inf;LSEQ=AATCGAATGGAATTATCGAA;RSEQ=GCAATCGAATAGAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:42,22:0:2,0:27.4:1:30.6:1:1:0:32.7:128:1:0:3.3 0/1:151:5:3,2:92,51:0.0331:2,2:34:1:31.6:1:1:1.20107:33:10:0.0331:0:4.6 -10 42396022 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGAATGGAATTATCGAATGC;RSEQ=ATCGAATAGAATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:43,20:0:2,0:28.4:1:30.1:1:1:0:33:126:1:0:3.2 0/1:149:2:1,1:91,56:0.0134:2,2:22.5:1:31.5:1:1:1.61945:40.5:4:0.0134:0:4 -10 42396024 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0822;SOR=0;LSEQ=AATGGAATTATCGAATGCAA;RSEQ=CGAATAGAATCATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:40,20:0.0323:2,2:21:1:29.5:1:1:1.97611:20.5:4:0.0323:0:4 0/0:153:0:0,0:95,58:0:2,0:29.2:1:29.4:1:1:0:33.6:75.5:1:0:3.5 -10 42396030 . A G 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57989;SOR=Inf;LSEQ=ATTATCGAATGCAATCGAAT;RSEQ=GAATCATCGAATGGACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:40,23:0:2,0:29.7:1:29.2:1:1:0:33:126:1:0:3.2 0/1:158:4:2,2:97,57:0.0253:2,2:30.8:1:30.8:1:0.62972:1.6957:44.5:8:0.0253:0:5.3 -10 42396031 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTATCGAATGCAATCGAATA;RSEQ=AATCATCGAATGGACTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:41,24:0:2,0:29:1:31.5:1:1:0:32.8:64:1:0:3.1 0/1:163:2:1,1:99,61:0.0123:2,2:30.5:1:30:1:1:1.61786:24:4:0.0123:0:5 -10 42396035 . C G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGAATGCAATCGAATAGAAT;RSEQ=ATCGAATGGACTCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:40,26:0:2,0:28.7:1:31.5:1:1:0:32.2:132:1:0:3.2 0/1:164:2:1,1:101,61:0.0122:2,2:25.5:1:29.5:1:1:1.65037:35:4:0.0123:0:4 -10 42396037 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AATGCAATCGAATAGAATCA;RSEQ=CGAATGGACTCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:40,26:0:2,0:28.7:1:30.2:1:1:0:32.2:32:1:0:3.3 0/1:163:2:1,1:99,61:0.0123:2,2:6.5:1:30.5:1:1:1.61786:24:4:0.0125:0:3 -10 42396038 . C G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55849;SOR=Inf;LSEQ=ATGCAATCGAATAGAATCAT;RSEQ=GAATGGACTCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:40,26:0:2,0:28.7:1:30.8:1:1:0:32.2:132:1:0:3.3 0/1:162:3:1,2:96,60:0.0185:2,2:41.3:1:30.7:1:0.56086:3.17611:21.7:6:0.0188:0:5 -10 42396039 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCAATCGAATAGAATCATC;RSEQ=AATGGACTCAAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:40,26:0:2,0:28.7:1:30.6:1:1:0:32.2:132:1:0:3.3 0/1:165:2:2,0:97,65:0.0121:2,0:28:1:29.5:1:0.51855:0:31:4:0.0121:0:5 -10 42396042 . T A 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.94012;LSEQ=AATCGAATAGAATCATCGAA;RSEQ=GGACTCAAATGGAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:4:2,2:40,26:0.0571:2,2:33:1:30.8:1:1:1.52871:29.5:8:0.0571:0:4.8 0/1:167:9:5,4:94,64:0.0539:2,2:29:1:28.6:1:1:1.17385:33:18:0.0539:0:4 -10 42396043 . G A 81 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10722;SOR=Inf;LSEQ=ATCGAATAGAATCATCGAAT;RSEQ=GACTCAAATGGAATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:42,30:0:2,0:26:1:31.2:1:1:0:31.9:35:1:0:3.2 0/1:170:7:3,4:96,66:0.0412:2,2:26.3:1:29:1:0.45009:1.93166:40.1:14:0.0412:0:3.4 -10 42396048 . CA TG 46 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08708;SOR=0.14357;LSEQ=ATAGAATCATCGAATGGACT;RSEQ=AATGGAATCATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:2,1:39,31:0.0411:2,2:12.7:1:29.2:1:1:1.58:40:6:0.0411:0.0137:5 0/0:165:1:1,0:91,71:0.0061:2,0:49:0:33:0:1:0:40:2:0.0061:0:6 -10 42396049 . A G 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54203;SOR=1.45895;LSEQ=TAGAATCATCGAATGGACTC;RSEQ=AATGGAATCATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:68:38,30:1,1:0.9315:2,2:25.5:1:30.4:1:1:1.26:30.6:136:0.9577:0:3 1/1:167:159:89,70:0,1:0.9521:0,2:24.6:1:29.9:1:0.44375:0:32.1:158:0.9693:0:3.4 -10 42396052 . T A 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4356;SOR=0.57058;LSEQ=AATCATCGAATGGACTCAAA;RSEQ=GGAATCATCGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:2,1:40,30:0.0411:2,2:22:1:28.3:1:1:1.49:43.7:6:0.0411:0:5 0/1:168:4:3,1:89,74:0.0238:2,2:15.5:1:30:1:0.62836:2.48:44.5:8:0.0241:0:6.8 -10 42396053 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCGAATGGACTCAAAT;RSEQ=GAATCATCGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:42,31:0:2,0:25:1:31.7:1:1:0:31.8:146:1:0:3.1 0/1:170:2:1,1:93,75:0.0118:2,2:13:1:28:1:1:1.23841:25:4:0.0119:0:4.5 -10 42396054 . G C 34 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20877;SOR=0.20621;LSEQ=TCATCGAATGGACTCAAATG;RSEQ=AATCATCGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:40,30:0.0278:2,2:37.5:1:34:1:1:1.32793:25:4:0.0282:0:5 0/0:172:1:1,0:92,78:0.0058:2,0:2:0:34:0:1:0:24:2:0.0059:0:4 -10 42396055 . A C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCGAATGGACTCAAATGG;RSEQ=ATCATCGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:41,31:0:2,0:25.1:1:29.9:1:1:0:31.9:71:0.9861:0:3.1 0/1:171:2:1,1:90,77:0.0117:2,2:44:1:31:1:1:1.16775:40.5:4:0.0118:0:4 -10 42396056 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCGAATGGACTCAAATGGA;RSEQ=TCATCGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:41,32:0:2,0:24.7:1:30.2:1:1:0:31.8:146:1:0:3.1 0/1:170:2:1,1:89,78:0.0118:2,2:26.5:1:30:1:1:1.14013:21:4:0.0118:0:5 -10 42396058 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08938;SOR=0;LSEQ=CGAATGGACTCAAATGGAAT;RSEQ=ATCGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:38,31:0.0274:2,2:30:1:29.5:1:1:1.22227:25:4:0.0274:0:3.5 0/0:170:0:0,0:88,80:0:2,0:23.2:1:30.8:1:1:0:32.9:167:0.994:0:3.4 -10 42396060 . T A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AATGGACTCAAATGGAATCA;RSEQ=CGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:39,33:0:2,0:24.7:1:30.1:1:1:0:32:71:1:0:3.1 0/1:168:2:1,1:85,80:0.0119:2,2:24.5:1:27.5:1:1:1.06214:32.5:4:0.012:0:4.5 -10 42396061 . C T 26 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85601;LSEQ=ATGGACTCAAATGGAATCAT;RSEQ=GAATGGAATGGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:1,0:38,32:0.0139:2,0:18:0:26:0:1:0:40:2:0.0141:0:5 0/1:168:2:2,0:85,80:0.0119:2,0:27.5:1:26:1:0.49787:0:42.5:4:0.0121:0:6 -10 42396062 . G C 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2209;SOR=0.21589;LSEQ=TGGACTCAAATGGAATCATC;RSEQ=AATGGAATGGAATGGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:36,32:0.0282:2,2:12.5:1:30:1:1:1.1231:48.5:4:0.029:0:3 0/0:162:1:1,0:80,74:0.0062:2,0:50:0:31:0:1:0:25:2:0.0063:0:3 -10 42396064 . A T 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37674;SOR=0.4392;LSEQ=GACTCAAATGGAATCATCGA;RSEQ=TGGAATGGAATGGAATAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:1,2:37,33:0.0411:2,2:13.7:1:30.3:1:0.6044:2.21843:40:6:0.0417:0:5 0/1:163:3:3,0:82,78:0.0184:2,0:20.7:1:31.7:1:0.24676:0:40:6:0.0185:0:5.3 -10 42396065 . T C 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ACTCAAATGGAATCATCGAA;RSEQ=GGAATGGAATGGAATAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:39,35:0:2,0:23.8:1:30.1:1:1:0:32:73:1:0:3.1 0/1:163:2:1,1:81,79:0.0123:2,2:11:1:27.5:1:1:1.02516:40:4:0.0123:0:4.5 -10 42396067 . G A 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=1.37978;LSEQ=TCAAATGGAATCATCGAATG;RSEQ=AATGGAATGGAATAGTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:38,32:0.0278:2,0:22.5:1:32:0:0.21948:0:40:4:0.0286:0:4.5 0/1:158:6:5,1:75,75:0.038:2,2:13:1:28.8:1:0.21056:4.96:36:12:0.038:0:4 -10 42396072 . G C 45 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.39112;SOR=0.4688;LSEQ=TGGAATCATCGAATGGAATG;RSEQ=AATGGAATAGTCAATGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:3:2,1:34,36:0.0405:2,2:7:0:30:1:0.61451:2.10:38:6:0.0411:0:3.3 0/1:155:3:3,0:76,76:0.0194:2,0:4:1:28.7:1:0.24541:0:29:6:0.0195:0:5 -10 42396080 . T C 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15788;SOR=0.43236;LSEQ=TCGAATGGAATGGAATGGAA;RSEQ=AGTCAATGAACTCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:64:27,37:1,1:0.9412:2,2:24.9:1:31.4:1:1:1.36372:31.7:31:0.9538:0:3 1/1:150:131:62,69:8,1:0.8733:2,2:25.4:1:30.9:1:0.03315:8.79385:34.1:64.5:0.8716:0:3.2 -10 42396083 . T A 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55246;SOR=Inf;LSEQ=AATGGAATGGAATGGAATAG;RSEQ=CAATGAACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:27,42:0:2,0:24.8:1:28.2:1:1:0:32.3:8.857:1:0:3 0/1:142:3:3,0:65,74:0.0211:2,0:19:1:27.3:1:0.10727:0:35:6:0.0216:0:5.3 -10 42396086 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54735;SOR=Inf;LSEQ=GGAATGGAATGGAATAGTCA;RSEQ=TGAACTCGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:29,44:0:2,0:23.6:1:30.1:1:1:0:33.2:72:1:0:3 0/1:140:2:1,1:65,73:0.0143:2,2:15.5:1:28.5:1:1:1.12:46:4:0.0143:0:5 -10 42396087 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54442;SOR=Inf;LSEQ=GAATGGAATGGAATAGTCAA;RSEQ=GAACTCGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:29,45:0:2,0:23.3:1:30.2:1:1:0:33.6:148:1:0:2.9 0/1:139:2:1,1:63,74:0.0144:2,2:17.5:1:29:1:1:1.17:24:4:0.0144:0:3.5 -10 42396089 . A T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55267;SOR=Inf;LSEQ=ATGGAATGGAATAGTCAATG;RSEQ=ACTCGAATGGAATCATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:30,44:0:2,0:23.5:1:29.3:1:1:0:33.9:23.667:1:0:2.9 0/1:143:3:1,2:63,77:0.021:2,2:13.7:1:26:1:1:1.63097:32.3:6:0.0211:0:3 -10 42396092 . T A 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=0.54331;SOR=0.69626;LSEQ=GAATGGAATAGTCAATGAAC;RSEQ=CGAATGGAATCATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:5:3,2:28,40:0.0658:2,2:22.2:1:29.6:1:0.6446:2.12:35.6:10:0.0658:0:4.4 0/1:150:7:3,4:64,76:0.0467:2,2:32.3:1:30.9:1:1:1.12191:29.4:14:0.0467:0:3.6 -10 42396093 . C G 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0.55265;SOR=Inf;LSEQ=AATGGAATAGTCAATGAACT;RSEQ=GAATGGAATCATCATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:33,43:0:2,0:23.3:1:29.8:1:1:0:35.2:37:1:0:2.8 0/1:153:3:1,2:66,82:0.0196:2,2:11.3:1:31.3:1:1:1.60489:39.7:6:0.02:0:5 -10 42396094 . G A 73 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=1;SOR=1.24878;LSEQ=ATGGAATAGTCAATGAACTC;RSEQ=AATGGAATCATCATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:2,0:30,43:0.0263:2,0:5:0:32:0:0.17874:0:40:4:0.0274:0:2 0/1:153:5:4,1:62,83:0.0327:2,2:4.6:1:31.6:1:0.16962:5.30:35.2:10:0.0331:0:2.6 -10 42396098 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATAGTCAATGAACTCGAAT;RSEQ=GAATCATCATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:33,44:0:2,0:23.5:1:31.1:1:1:0:34.9:76:1:0:2.8 0/1:165:2:1,1:70,92:0.0121:2,2:15:1:30:0:1:1.31:53:4:0.0122:0:3.5 -10 42396099 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAGTCAATGAACTCGAATG;RSEQ=AATCATCATTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:33,45:0:2,0:23.4:1:30.2:1:1:0:35:18.5:0.9867:0:2.8 0/1:167:2:1,1:70,94:0.012:2,2:5.5:1:30:1:1:1.34:31:4:0.0121:0:5.5 -10 42396102 . T A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GTCAATGAACTCGAATGGAA;RSEQ=CATCATTGAATGGAATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:32,49:0:2,0:22.9:1:29.8:1:1:0:36:39.5:1:0:2.8 0/1:169:2:1,1:70,96:0.0118:2,2:39.5:1:32:0:1:1.37:40:4:0.0122:0:5.5 -10 42396103 . C A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.78025;SOR=1.31312;LSEQ=TCAATGAACTCGAATGGAAT;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:4:2,2:30,45:0.05:2,2:9.3:1:28:1:1:1.49:50:8:0.0506:0:2 0/1:170:11:6,5:65,93:0.0647:2,2:10.3:1:28.1:1:0.52958:1.71:43:22:0.0655:0:3 -10 42396106 . C T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ATGAACTCGAATGGAATCAT;RSEQ=ATTGAATGGAATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:31,48:0:2,0:23.5:1:31.4:1:1:0:36:38.5:0.9872:0:2.8 0/1:175:2:1,1:72,100:0.0114:2,2:14:1:27:1:1:1.39:44:4:0.0116:0:4.5 -10 42396108 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65784;SOR=0.70688;LSEQ=GAACTCGAATGGAATCATCA;RSEQ=TGAATGGAATCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:30,48:0.0244:2,2:16.5:1:30:1:1:1.59:31:4:0.025:0:4 0/1:173:3:2,1:70,98:0.0173:2,2:31:1:32.3:1:0.57344:2.78:45.3:6:0.0176:0:4.3 -10 42396109 . TGAATGGAATC T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74334;SOR=0.78316;LSEQ=AACTCGAATGGAATCATCAT;RSEQ=GAATGGAATCATCGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:4:1,3:29,46:0.05:2,2:27:1:32.6:1:1:1.87743:41.5:8:0.0519:0.0125:3.8 0/1:177:7:4,3:68,99:0.0395:2,2:34.9:1:30.1:1:0.44999:1.93:39:14:0.04:0.0113:3.3 -10 42396113 . T A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.51522;LSEQ=CGAATGGAATCATCATTGAA;RSEQ=GGAATCGAATGGAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:1:1,0:32,50:0.0114:2,0:1:0:31:0:0.39759:0:24:2:0.0125:0:4 0/1:175:3:1,2:71,95:0.0171:2,2:11.7:1:32:1:1:1.49132:51.3:6:0.0179:0:3.3 -10 42396114 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00569;LSEQ=GAATGGAATCATCATTGAAT;RSEQ=GAATCGAATGGAATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:1,0:32,51:0.0112:2,0:29:0:29:0:0.39286:0:47:2:0.012:0:5 0/1:177:2:1,1:71,95:0.0113:2,2:17.5:1:27.5:1:1:1.34:29:4:0.0118:0:3.5 -10 42396118 . T C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24195;SOR=0.23345;LSEQ=GGAATCATCATTGAATGGAA;RSEQ=CGAATGGAATCATCGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:30,50:0.0233:2,2:43:1:31.5:1:1:1.66:43:4:0.0256:0:5 0/0:182:1:0,1:76,97:0.0055:2,0:17:0:33:0:1:0:36:2:0.0058:0:3 -10 42396119 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCATCATTGAATGGAAT;RSEQ=GAATGGAATCATCGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:31,51:0:2,0:24.4:1:30.4:1:1:0:37.2:164:1:0:3 0/1:184:2:1,1:76,100:0.0109:2,2:13:1:29.5:1:1:1.31:37.5:4:0.0114:0:2.5 -10 42396121 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCATTGAATGGAATCG;RSEQ=ATGGAATCATCGAGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:33,54:0:2,0:24.4:1:29.9:1:1:0:37.6:86:1:0:3 0/1:190:2:1,1:82,105:0.0105:2,2:27.5:1:31.5:1:1:1.28:31:4:0.0106:0:5.5 -10 42396123 . T A 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31542;SOR=Inf;LSEQ=CATCATTGAATGGAATCGAA;RSEQ=GGAATCATCGAGTGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:32,53:0:2,0:25.4:1:29.9:1:1:0:37.9:41.5:1:0:3 0/1:191:4:2,2:81,103:0.0209:2,2:30.5:1:30.8:1:1:1.27:42:8:0.0214:0:5 -10 42396128 . T A 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.8459;LSEQ=TTGAATGGAATCGAATGGAA;RSEQ=CATCGAGTGGAATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:1:1,0:29,53:0.012:2,0:46:0:32:0:0.36145:0:45:2:0.0122:0:4 0/1:196:2:1,1:80,114:0.0102:2,2:19:1:28.5:1:1:1.42:41:4:0.0103:0:4 -10 42396129 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0865;SOR=0;LSEQ=TGAATGGAATCGAATGGAAT;RSEQ=ATCGAGTGGAATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:28,52:0.0241:2,2:29:1:30.5:1:1:1.84:49:4:0.0241:0:4 0/0:198:0:0,0:80,118:0:2,0:24.3:1:31.2:1:1:0:41.5:197:1:0:3.3 -10 42396132 . C G 34 v4;q23;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55407;SOR=Inf;LSEQ=ATGGAATCGAATGGAATCAT;RSEQ=GAGTGGAATCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:30,55:0:2,0:27.4:1:30.4:1:1:0:39.5:84:0.9767:0:3.1 0/1:191:3:1,2:78,109:0.0157:2,2:23:1:22:1:1:1.4286:35.7:2:0.0106:0:4 -10 42396134 . A G 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10417;SOR=0;LSEQ=GGAATCGAATGGAATCATCG;RSEQ=GTGGAATCAAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:32,56:0.0217:2,2:17.5:1:29.5:1:1:1.74:48:4:0.0222:0:4 0/0:192:0:0,0:78,114:0:2,0:26.4:1:29.7:1:1:0:42.1:63:1:0:3.3 -10 42396135 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCGAATGGAATCATCGA;RSEQ=TGGAATCAAATGGAATCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:34,56:0:2,0:26.3:1:32.2:1:1:0:38.9:89:1:0:3.2 0/1:193:2:0,2:78,112:0.0104:2,0:10:1:28:1:0.51505:0:35:4:0.0105:0:4 -10 42396136 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCGAATGGAATCATCGAG;RSEQ=GGAATCAAATGGAATCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:33,57:0:2,0:25.9:1:30:1:1:0:38.7:89:1:0:3.2 0/1:195:2:1,1:77,115:0.0103:2,2:11.5:1:30.5:1:1:1.49:48:4:0.0103:0:3.5 -10 42396137 . G T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCGAATGGAATCATCGAGT;RSEQ=GAATCAAATGGAATCATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:34,58:0:2,0:25.9:1:31.4:1:1:0:38.8:45:1:0:3.2 0/1:195:2:1,1:79,114:0.0103:2,2:21:1:32:0:1:1.44:50:4:0.0103:0:4 -10 42396142 . CA TG 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.68421;SOR=0.62329;LSEQ=ATGGAATCATCGAGTGGAAT;RSEQ=AATGGAATCATGATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:2,1:33,55:0.0319:2,2:24.3:1:31.2:1:0.55632:3.29:32.3:6:0.033:0.0106:3 0/1:199:4:2,2:76,113:0.0201:2,2:30.3:1:29:1:1:1.48:50:8:0.0202:0.005:3 -10 42396143 . A G 230 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.98841;LSEQ=TGGAATCATCGAGTGGAATC;RSEQ=AATGGAATCATGATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:91:86:33,53:0,1:0.9451:0,2:27:1:31.1:1:1:0:39.7:172:0.9885:0:3.2 1/1:198:187:76,111:1,1:0.9444:2,2:26.9:1:30.5:1:1:1.4575:42.5:186:0.9894:0:3.3 -10 42396146 . T A 50 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02942;SOR=0;LSEQ=AATCATCGAGTGGAATCAAA;RSEQ=GGAATCATGATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:2,1:33,56:0.0323:2,2:31:1:32:0:0.55518:3.35:44.3:6:0.033:0:3.3 0/0:206:0:0,0:82,123:0:2,0:26.5:1:29.8:1:1:0:42.9:410:0.9951:0:3.3 -10 42396148 . G C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55544;SOR=Inf;LSEQ=TCATCGAGTGGAATCAAATG;RSEQ=AATCATGATCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:35,56:0:2,0:27.2:1:31:1:1:0:40.4:29.333:1:0:3.2 0/1:208:3:1,2:81,121:0.0144:2,2:26:1:33.3:1:1:1.337:45.7:6:0.0146:0:3 -10 42396152 . C T 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95654;LSEQ=CGAGTGGAATCAAATGGAAT;RSEQ=ATGATCAAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:79:27,52:6,10:0.8316:2,2:26.4:1:28.7:1:0.78142:1.15376:39.5:78:0.8298:0:3.2 1/1:206:170:67,103:16,20:0.8252:2,2:27:1:28.6:1:0.58041:1.22859:43.7:169:0.8244:0:3.3 -10 42396156 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10312;SOR=0;LSEQ=TGGAATCAAATGGAATCATG;RSEQ=TCAAATGGAATCGAATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:33,62:0.0206:2,2:20.5:1:31.5:1:1:1.87:31:4:0.0208:0:3 0/0:204:0:0,0:80,124:0:2,0:27.1:1:29.5:1:1:0:43:203:1:0:3.3 -10 42396158 . C G 106 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5582;SOR=1.6295;LSEQ=GAATCAAATGGAATCATGAT;RSEQ=AAATGGAATCGAATGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:3:0,3:34,60:0.0309:2,0:46.7:1:33:0:0.54963:0:38:6:0.0319:0:4.7 0/1:202:10:4,6:73,115:0.0495:2,2:28.2:1:32:1:1:1.05:39.2:20:0.0503:0:3.6 -10 42396161 . A C 30 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCAAATGGAATCATGATCAA;RSEQ=TGGAATCGAATGTAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:1:0,1:34,64:0.0101:2,0:11:0:14:0:1:0:40:0:0:0:4 0/1:198:2:1,1:76,120:0.0101:2,2:31.5:1:30:1:1:1.58:52.5:4:0.0103:0:4.5 -10 42396164 . G C 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30538;SOR=Inf;LSEQ=AATGGAATCATGATCAAATG;RSEQ=AATCGAATGTAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:34,62:0:2,0:25.5:1:31.1:1:1:0:40.3:31:1:0:3.1 0/1:193:4:2,2:71,118:0.0207:2,2:34.5:1:31:1:0.63411:1.66:57.3:8:0.0207:0:3.8 -10 42396168 . C T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10717;SOR=0;LSEQ=GAATCATGATCAAATGGAAT;RSEQ=GAATGTAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:32,58:0.0217:2,2:15:0:28.5:1:1:1.80:45:4:0.0217:0:3 0/0:188:0:0,0:71,116:0:2,0:27.1:1:30.3:1:1:0:43.5:92.5:0.9946:0:3.2 -10 42396169 . G C 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25525;SOR=0.2446;LSEQ=AATCATGATCAAATGGAATC;RSEQ=AATGTAATCATCATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:32,58:0.0217:2,2:25.5:1:30.5:1:1:1.80:44.5:4:0.0225:0:3 0/0:186:1:0,1:71,114:0.0054:2,0:41:0:30:0:1:0:40:2:0.0054:0:5 -10 42396172 . T A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00551;SOR=Inf;LSEQ=CATGATCAAATGGAATCGAA;RSEQ=GTAATCATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:33,58:0:2,0:25.4:1:29.9:1:1:0:40.6:21.75:1:0:3.1 0/1:179:13:5,8:58,103:0.0726:2,2:26:1:28.8:1:1:1.11:44.2:12:0.0674:0:3.5 -10 42396173 . G A 45 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11743;SOR=0.1698;LSEQ=ATGATCAAATGGAATCGAAT;RSEQ=TAATCATCATCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:1,2:32,55:0.0333:2,2:10.3:1:29:1:1:1.16175:39:6:0.0345:0:4.7 0/0:173:1:0,1:61,109:0.0058:2,0:19:0:32:0:1:0:24:2:0.0058:0:3 -10 42396174 . T G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.553;SOR=Inf;LSEQ=TGATCAAATGGAATCGAATG;RSEQ=AATCATCATCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:28,56:0:2,0:26.9:1:29:1:1:0:40.3:168:1:0:3.1 0/1:172:3:2,1:59,110:0.0174:2,2:14.3:1:30.7:1:0.28694:3.70:43.7:6:0.0178:0:3 -10 42396175 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCAAATGGAATCGAATGT;RSEQ=ATCATCATCAAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:28,56:0:2,0:26.7:1:29.4:1:1:0:40.3:27:1:0:3.1 0/1:171:2:1,1:59,110:0.0117:2,2:38.5:1:28:1:1:1.86:52.5:4:0.0118:0:4 -10 42396178 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CAAATGGAATCGAATGTAAT;RSEQ=ATCATCAAATGGAATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:28,53:0:2,0:26.7:1:31.8:1:1:0:40.4:39.5:1:0:3.1 0/1:164:2:1,1:55,107:0.0122:2,2:22.5:1:28.5:1:1:1.94:50.5:4:0.0123:0:3 -10 42396179 . A C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.37656;SOR=1.72216;LSEQ=AAATGGAATCGAATGTAATC;RSEQ=TCATCAAATGGAATCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:6:3,3:24,49:0.0759:2,2:33.2:1:31.2:1:0.40569:2.02:41.7:12:0.0759:0:4 0/1:161:20:7,13:47,94:0.1242:2,2:30.5:1:31.1:1:1:1.08:43.6:40:0.1258:0:4.1 -10 42396181 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ATGGAATCGAATGTAATCAT;RSEQ=ATCAAATGGAATCAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:26,50:0:2,0:26.9:1:31.3:1:1:0:40:24.333:1:0:3.1 0/1:155:2:1,1:50,102:0.0129:2,2:7:0:31:1:1:2.03:50.5:4:0.0129:0:2.5 -10 42396183 . T A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGAATCGAATGTAATCATCA;RSEQ=CAAATGGAATCAAAAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:24,45:0:2,0:28.4:1:29.7:1:1:0:40.2:16.25:1:0:3.2 0/1:154:2:1,1:50,102:0.013:2,2:31.5:1:29:1:1:2.03:44:4:0.0132:0:4.5 -10 42396191 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10432;SOR=0;LSEQ=ATGTAATCATCATCAAATGG;RSEQ=ATCAAAAATAACCATAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:19,42:0.0317:2,2:21.5:1:31:1:0.53763:2.18:49:4:0.0333:0:4 0/0:131:0:0,0:40,91:0:2,0:25.2:1:29.6:1:1:0:44.6:130:1:0:3.2 -10 42396202 . A G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2637;SOR=0.24997;LSEQ=ATCAAATGGAATCAAAAATA;RSEQ=CCATAATCAATTGGTATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:15,34:0.0392:2,2:13:1:32:1:0.53333:2.23:49.5:4:0.04:0:4 0/1:100:1:0,1:31,68:0.01:2,0:4:0:31:0:1:0:33:2:0.0101:0:4 -10 42396203 . C A 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33277;SOR=2.44617;LSEQ=TCAAATGGAATCAAAAATAA;RSEQ=CATAATCAATTGGTATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:0,2:15,32:0.0408:2,0:8.5:1:31:0:1:0:36:4:0.0417:0:5 0/1:95:9:2,7:26,60:0.0947:2,2:25.7:1:27.8:1:1:1.51052:34.2:8:0.0851:0:3.9 -10 42396207 . A C 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.53162;SOR=0;LSEQ=ATGGAATCAAAAATAACCAT;RSEQ=ATCAATTGGTATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:14,33:0,0:1:0,2:21.1:1:31.8:1:1:0:38.5:46:1:0:3.5 1/1:81:79:21,58:0,0:0.9753:0,2:22.1:1:31.7:1:1:0:42.8:158:0.9875:0:3.5 -10 42396210 . C G 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55246;SOR=Inf;LSEQ=GAATCAAAAATAACCATAAT;RSEQ=AATTGGTATTGAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:14,30:0:2,0:19.6:1:31.8:1:1:0:38:88:1:0:3.5 0/1:78:3:1,2:20,55:0.0385:2,2:29.3:1:31.7:1:1:1.37:47.3:6:0.039:0:4.3 -10 42396225 . G T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.54872;SOR=Inf;LSEQ=ATAATCAATTGGTATTGAAT;RSEQ=GAATTGTCATCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:4,18:0:2,0:17.2:1:32.1:1:1:0:37.7:44:1:0:3.1 0/1:44:2:0,2:6,36:0.0455:2,0:17.5:1:32:0:1:0:50:4:0.0455:0:5 -10 42396240 . T A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52941;SOR=Inf;LSEQ=TGAATGGAATTGTCATCAAA;RSEQ=GGAATTCAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,11:0:0,0:10.8:1:31.3:1:1:0:36.6:22:0.9167:0:3.2 0/1:22:2:1,1:2,16:0.0909:2,2:5:1:29.5:1:0.28421:6.73:47:4:0.0909:0:4.5 -10 42396250 . T A 69 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCATCAAATGGAATTCAA;RSEQ=GGAATCATCATCATATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:5:1:26.8:1:1:0:33.8:2:1:0:3.3 1/1:4:4:0,4:0,0:1:0,0:5.3:1:31:1:1:0:24.5:8:1:0:2.8 -10 42396380 . A G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATTAAATGGAATCTAAT;RSEQ=GAATCATTGAACGGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:8:0:33:0:1:0:25:2:1:0:5 1/1:2:2:2,0:0,0:1:0,0:8:1:32.5:1:1:0:23:4:1:0:5.5 -10 42396408 . C G 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4965;SOR=Inf;LSEQ=TGAACGGAATTGAATGGAAT;RSEQ=GTCATCGAATGAATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:17.3:1:32:1:1:0:37.5:8:1:0:4.5 0/1:9:3:2,1:3,3:0.3333:2,2:25.3:1:30.7:1:1:1.85:23.7:6:0.3333:0:5.3 -10 42396435 . T A 107 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.62139;SOR=2.30363;LSEQ=GAATGAATTGAATGCAATCA;RSEQ=CGAATGGTCTCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:0.5:2,2:32.3:1:30.7:1:1:1:24.7:6:0.5:0:4.7 1/0:17:12:7,5:3,2:0.7059:2,2:28.4:1:29.9:1:1:1.06713:41.6:24:0.7059:0:4.2 -10 42396446 . C T 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.05556;SOR=0;LSEQ=ATGCAATCATCGAATGGTCT;RSEQ=GAATGGAATCACCTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:35:1:30.5:1:1:1.41418:47:4:0.2857:0:5.5 0/0:21:0:0,0:11,10:0:2,0:27.7:1:30.6:1:1:0:44.7:42:1:0:3.5 -10 42396450 . TGGAATCACCTT GGAACCACCTC 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5453;SOR=Inf;LSEQ=AATCATCGAATGGTCTCGAA;RSEQ=CAAATGGAAAGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:33.4:1:30:1:1:0:37.6:14:1:0:4.7 0/1:21:4:2,2:9,8:0.1905:2,2:36:1:30.8:1:1:1.1187:60:8:0.1905:0:1.5 -10 42396452 . G T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55204;SOR=0.35138;LSEQ=TCATCGAATGGTCTCGAATG;RSEQ=AATCACCTTCAAATGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:31.5:1:28:1:1:1.41418:47.5:4:0.2857:0:4 0/1:17:2:1,1:8,7:0.1176:2,2:42.5:1:29.5:1:1:1.13389:60:4:0.1176:0:2.5 -10 42396455 . T C 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47478;LSEQ=TCGAATGGTCTCGAATGGAA;RSEQ=CACCTTCAAATGGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:2,2:0.4286:2,2:33.3:1:31.3:1:1:1.81:24.7:6:0.4286:0:4.7 1/0:17:9:5,4:4,4:0.5294:2,2:27.6:1:31.4:1:1:1.23:31.1:18:0.5294:0:4.7 -10 42396457 . A C 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07609;SOR=0;LSEQ=GAATGGTCTCGAATGGAATC;RSEQ=CCTTCAAATGGAAAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:35:1:30.5:1:1:1.41418:47:4:0.2857:0:5.5 0/0:17:0:0,0:9,8:0:2,0:27.2:1:30.3:1:1:0:41.1:34:1:0:3.5 -10 42396459 . C A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55204;SOR=0.35138;LSEQ=ATGGTCTCGAATGGAATCAC;RSEQ=TTCAAATGGAAAGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:35:1:29.5:1:1:1.41418:47.5:4:0.2857:0:4 0/1:17:2:1,1:8,7:0.1176:2,2:33:1:29:1:1:1.13389:44.5:4:0.1176:0:4 -10 42396461 . T C 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93603;LSEQ=GGTCTCGAATGGAATCACCT;RSEQ=CAAATGGAAAGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:2,2:0.4286:2,2:31.3:1:30.3:1:1:1.81:24.7:6:0.4286:0:4.7 0/1:17:7:4,3:4,4:0.4118:2,2:28.9:1:31.1:1:1:1.31:29.7:14:0.4118:0:5 -10 42396463 . A T 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20746;SOR=0.31464;LSEQ=TCTCGAATGGAATCACCTTC;RSEQ=AATGGAAAGGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:2,1:0.5714:2,2:35:1:28.5:1:1:1.81007:47.3:8:0.5714:0:4.8 0/1:21:6:3,3:8,7:0.2857:2,2:28.3:1:29.3:1:1:1.1356:51.5:12:0.2857:0:2.8 -10 42396471 . A T 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.23909;LSEQ=GGAATCACCTTCAAATGGAA;RSEQ=GGAATGGAATCATCGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:14:1:29:1:1:1.41418:25:4:0.2857:0:4.5 0/1:18:6:3,3:6,6:0.3333:2,2:28.8:1:31.2:1:1:1:31.2:12:0.3333:0:5 -10 42396486 . G A 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22188;SOR=0.18655;LSEQ=TGGAAAGGAATGGAATCATC;RSEQ=CATAGAATCGAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:20.5:1:29:1:1:1:47:4:0.3333:0:5.5 0/1:13:1:1,0:5,7:0.0769:2,0:1:0:25:0:0.46154:0:60:2:0.0769:0:4 -10 42396507 . T A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=CATAGAATCGAATGGAATTA;RSEQ=CATTGAATGGACTCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:21:1:31.5:1:0.33333:0:44.5:4:0.6667:0:5 0/1:5:2:1,1:1,2:0.4:2,2:20:1:31:1:1:1.73:44.5:4:0.4:0:4 -10 42396511 . T C 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=GAATCGAATGGAATTATCAT;RSEQ=GAATGGACTCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,2:0.3333:0,0:5:0:27:0:0.33333:0:24:2:0.3333:0:5 1/0:5:3:1,2:1,1:0.6:2,2:27.7:1:29.3:1:1:1.7321:27.7:6:0.6:0:6.3 -10 42396522 . A G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTATCATTGAATGGACTC;RSEQ=AATGGAATCAACGTCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:12:0:32:0:1:0:40:2:1:0:5 1/0:3:2:0,2:0,1:0.6667:0,0:19:1:32.5:1:1:0:30.5:4:0.6667:0:5.5 -10 42396535 . G A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCAAATGGAATCAAC;RSEQ=TCAAACGGAATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:0,0:0.6667:0,0:6:1:31:0:1:0:30.5:4:0.6667:0:5.5 -10 42396592 . T C 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGAATCATCGAATGGAC;RSEQ=CGAATGGAACCATCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:15.7:1:30.7:1:1:0:47:6:1:0:4.3 -10 42396602 . C T 65 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAATGGACTCGAATGGAA;RSEQ=CATCTAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:18.4:1:28.2:1:1:0:46.8:10:1:0:3.2 -10 42396625 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTAATGGAATGGAATGGAA;RSEQ=AATCCATGGACTCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:12:0:32:0:1:0:47:2:0.5:0:2 0/1:9:2:1,1:4,3:0.2222:2,2:42.5:1:29.5:1:1:1.29098:46.5:4:0.25:0:4.5 -10 42396634 . G T 32 d7;v4;q23;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATGGAATAATCCATG;RSEQ=ACTCGAATGCAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25:1:33:1:1:0:35.5:4:1:0:3.5 0/1:11:3:2,1:4,4:0.2727:2,2:28.3:1:20.3:1:1:1.88:51.3:2:0.2:0:4 -10 42396654 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACTCGAATGCAATCATCAT;RSEQ=AAATGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:31.3:1:32:0:1:0:33.7:6:1:0:3.3 0/1:12:2:1,1:6,4:0.1667:2,2:21:1:30.5:1:1:1.4491:46.5:4:0.1818:0:4.5 -10 42396655 . A G 61 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=ACTCGAATGCAATCATCATC;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:32.3:1:31:1:1:0:33.7:6:1:0:3.3 0/1:12:4:3,1:4,4:0.3333:2,2:26:1:30.8:1:0.57576:2.74:28.5:8:0.3333:0:3.5 -10 42396677 . C T 21 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59388;LSEQ=ATGGAATCGAATGGAATCAT;RSEQ=GAATGGACTCAAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:25:1:30:1:1:2.44949:46:4:0.3333:0:3 0/1:9:2:1,1:3,2:0.2222:2,2:33:1:21:1:1:1.41418:60:1:0.125:0:4 -10 42396686 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=AATGGAATCATCGAATGGAC;RSEQ=CAAATGGAATAATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:27.8:1:31.5:1:1:0:37.7:12:1:0:3.3 0/1:11:2:1,1:6,3:0.1818:2,2:24:1:31.5:1:1:1.87089:60:4:0.1818:0:4 -10 42396688 . A G 87 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.88186;LSEQ=TGGAATCATCGAATGGACTC;RSEQ=AATGGAATAATCATTGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:1,1:0.6667:2,2:30.3:1:31.8:1:1:2.45:33.5:8:0.6667:0:3.5 1/0:11:7:5,2:1,1:0.6364:2,2:19.3:1:31:1:1:2.24:35.7:14:0.6364:0:3.3 -10 42396714 . A G 80 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4965;SOR=0;LSEQ=AATAATCATTGAACGGAATC;RSEQ=AATGGAATCATCATCGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:42.8:1:30.5:1:1:0:38.8:8:1:0:3.3 1/0:9:6:5,1:2,1:0.6667:2,2:22.2:1:31:1:1:2.24:27.3:12:0.6667:0:3.8 -10 42396739 . C T 59 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19394;SOR=0;LSEQ=GAATCATCATCGGATGGAAA;RSEQ=GAATGGAATCATCATCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:18:1:29.5:1:1:0:38.8:8:1:0:3.3 0/1:7:3:3,0:3,1:0.4286:2,0:21.7:1:32:0:1:0:25.3:6:0.4286:0:4.7 -10 42396741 . AATGGAATCATCATCTAATGGAATCAAATGGAATCATCAAATGGAATCAG A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATCATCGGATGGAAACG;RSEQ=ATGGAATCATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:1:0,2:14.9:1:30.3:1:1:0:30.6:18:1:1:4.2 1/1:16:15:14,1:0,0:0.9375:0,1:17.6:1:29.7:1:1:0:27.1:30:0.9375:0.9375:4.4 -10 42396753 . ATCT A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52569;SOR=Inf;LSEQ=TGGAAACGAATGGAATCATC;RSEQ=AATGGAATCAAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,1:0:2,0:5:1:29.3:1:1:0:41.7:6:1:0:3.3 0/1:16:3:3,0:1,1:0.1875:2,0:21.3:1:26:1:0.4:0:31.3:6:0.6:0.0625:2.7 -10 42396756 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84118;LSEQ=AAACGAATGGAATCATCATC;RSEQ=AATGGAATCAAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,0:0.1667:0,0:9:0:32:0:1:0:45:2:1:0:4 0/1:14:2:2,0:0,0:0.1429:0,0:10:0:32:0:1:0:26:4:1:0:3.5 -10 42396767 . A G 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATCATCTAATGGAATCA;RSEQ=ATGGAATCATCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:11:2:2,0:0,0:0.1818:0,0:21.5:1:27:0:1:0:24:4:1:0:2.5 -10 42396805 . A G 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCAGATGGAATCATCATC;RSEQ=AATGGAATCGAGTAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:1:0,0:8.9:1:30.2:1:1:0:30.5:20:1:0:5.5 1/1:25:24:24,0:0,1:0.96:0,1:10:1:30.5:1:0.04:0:32.3:48:0.96:0:5.3 -10 42396817 . G A 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34;SOR=Inf;LSEQ=TCATCATCAAATGGAATCGA;RSEQ=TAGAATTATGGAATGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:16,0:0,0:0.9412:0,1:13.6:1:31:1:1:0:31.6:32:0.9412:0:5 1/1:33:33:31,2:0,0:1:0,2:19.2:1:30.6:1:1:0:32.9:66:1:0:5.1 -10 42396840 . A G 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68544;SOR=1.51648;LSEQ=GAATTATGGAATGAAATCCA;RSEQ=TGTGATCATCATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:33:23,10:0,0:0.9167:0,2:22.6:1:32.2:1:1:0:34.1:66:0.9167:0:4.8 1/1:71:67:43,24:0,0:0.9437:0,2:24.5:1:31:1:1:0:36.3:66:0.9429:0:4.8 -10 42396846 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TGGAATGAAATCCAATGTGA;RSEQ=CATCATCGAATGGACTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:25,13:0:2,0:25.5:1:30.6:1:1:0:34.3:76:1:0:4.8 0/1:83:2:1,1:47,32:0.0241:2,2:30:1:29:1:1:1.4616:43.5:4:0.0253:0:6 -10 42396847 . C T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGAATGAAATCCAATGTGAT;RSEQ=ATCATCGAATGGACTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:25,13:0:2,0:26.2:1:31.6:1:1:0:34.3:76:1:0:4.8 0/1:82:2:1,1:47,33:0.0244:2,2:18.5:1:26.5:1:1:1.41796:42.5:4:0.0247:0:5 -10 42396848 . A C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GAATGAAATCCAATGTGATC;RSEQ=TCATCGAATGGACTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:25,14:0:2,0:26.3:1:29.9:1:1:0:34:38:1:0:4.7 0/1:88:2:1,1:49,37:0.0227:2,2:30.5:1:32:1:1:1.32004:41.5:4:0.023:0:6 -10 42396854 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCCAATGTGATCATCATC;RSEQ=AATGGACTCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:26,20:0:2,0:26.2:1:29.5:1:1:0:33.8:45:1:0:4.6 0/1:94:2:1,1:50,42:0.0213:2,2:31.5:1:29:1:1:1.18826:45:4:0.0215:0:6 -10 42396855 . A T 23 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCCAATGTGATCATCATCG;RSEQ=ATGGACTCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:26,20:0:2,0:26.8:1:29.5:1:1:0:33.8:92:1:0:4.6 0/1:94:2:1,1:50,42:0.0213:2,2:28.5:1:23.5:1:1:1.18826:46:4:0.022:0:5.5 -10 42396858 . G T 53 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3012;SOR=Inf;LSEQ=CAATGTGATCATCATCGAAT;RSEQ=GACTCGAATGGAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:26,21:0:2,0:27.8:1:31.2:1:1:0:33.7:94:1:0:4.7 0/1:94:4:2,2:49,41:0.0426:2,2:28.5:1:26.5:1:1:1.19284:35:3:0.0326:0:5.8 -10 42396859 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10952;SOR=0;LSEQ=AATGTGATCATCATCGAATG;RSEQ=ACTCGAATGGAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:24,19:0.0426:2,2:36.5:1:31.5:1:1:1.25655:47:4:0.0435:0:4 0/0:94:0:0,0:51,43:0:2,0:28.3:1:30.3:1:1:0:36.4:93:1:0:4.5 -10 42396862 . T C 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.55087;SOR=0;LSEQ=GTGATCATCATCGAATGGAC;RSEQ=CGAATGGAATCATCATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:26,22:0,0:1:0,2:29.1:1:29.6:1:1:0:33.5:23:1:0:4.6 1/1:96:93:51,42:0,2:0.9688:0,2:28.7:1:29.6:1:0.21187:0:37.1:45.5:0.9681:0:4.5 -10 42396867 . TG AA 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCATCGAATGGACTCGAA;RSEQ=GAATCATCATCCAAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:25,23:0:2,0:30.3:1:29.6:1:1:0:33.8:47:1:0:4.6 0/1:99:2:1,1:49,48:0.0202:2,2:36.5:1:29.3:1:1:1.02062:27:4:0.0206:0:7 -10 42396868 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCGAATGGACTCGAAT;RSEQ=GAATCATCATCCAAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:24,24:0:2,0:30.6:1:30.9:1:1:0:33.9:96:1:0:4.6 0/1:99:2:1,1:48,46:0.0202:2,2:12.5:1:28:1:1:1.04303:24:4:0.0208:0:5.5 -10 42396871 . A C 86 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09632;SOR=Inf;LSEQ=ATCGAATGGACTCGAATGGA;RSEQ=TCATCATCCAAAGGAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:24,25:0:2,0:30.8:1:29.7:1:1:0:33.7:48:1:0:4.6 0/1:101:7:4,3:46,48:0.0693:2,2:29.9:1:30.7:1:0.71522:1.39:41:14:0.0722:0:5 -10 42396875 . T A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0.10674;SOR=0;LSEQ=AATGGACTCGAATGGAATCA;RSEQ=CATCCAAAGGAAGCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:23,25:0.04:2,2:30:1:27:1:1:1.09:25:4:0.0408:0:6.5 0/0:102:0:0,0:50,52:0:2,0:30.2:1:28.3:1:1:0:37.5:33:1:0:4.3 -10 42396877 . A C 38 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.55124;SOR=Inf;LSEQ=TGGACTCGAATGGAATCATC;RSEQ=TCCAAAGGAAGCTAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:24,26:0:2,0:30.7:1:29.6:1:1:0:33.6:49:1:0:4.5 0/1:103:3:1,2:49,51:0.0291:2,2:30.3:1:24.3:1:1:1.90987:36.7:2:0.0204:0:5.7 -10 42396879 . C A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACTCGAATGGAATCATCAT;RSEQ=CAAAGGAAGCTAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:23,26:0:2,0:30.7:1:30:1:1:0:33.5:23.5:0.9792:0:4.4 0/1:103:2:1,1:49,52:0.0194:2,2:31:1:27.5:1:1:1.06:41.5:4:0.0196:0:5.5 -10 42396882 . AA TC 80 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00086;SOR=0;LSEQ=TCGAATGGAATCATCATCCA;RSEQ=GGAAGCTAATGGAATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:3,3:19,23:0.125:2,2:39.2:1:31:1:1:1.21:33.3:12:0.1277:0:5.3 0/0:102:0:0,0:48,52:0:2,0:29.7:1:28.5:1:1:0:38.1:24:0.9897:0:4.3 -10 42396883 . A C 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01957;SOR=4.72464;LSEQ=CGAATGGAATCATCATCCAA;RSEQ=GGAAGCTAATGGAATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:41:18,23:0,0:0.8367:0,2:29.9:1:28.7:1:1:0:33.2:12.667:0.95:0:4.2 1/1:102:98:46,52:0,0:0.9608:0,2:29.6:1:29.4:1:1:0:38:48:0.9697:0:4.3 -10 42396885 . G T 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATCATCATCCAAAG;RSEQ=AAGCTAATGGAATCAACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:21,28:0:2,0:30.1:1:30.6:1:1:0:34.1:98:1:0:4.2 0/1:101:2:1,1:45,54:0.0198:2,2:26:0:29.5:1:1:1.20:46:4:0.02:0:5.5 -10 42396890 . T A 62 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04038;SOR=0.11539;LSEQ=AATCATCATCCAAAGGAAGC;RSEQ=AATGGAATCAACATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:4:2,2:18,25:0.0816:2,2:39:1:31.3:1:1:1.38:36.5:8:0.0816:0:4.8 0/1:100:1:0,1:44,55:0.01:2,0:25:0:25:0:1:0:24:2:0.01:0:5 -10 42396893 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11264;SOR=0;LSEQ=CATCATCCAAAGGAAGCTAA;RSEQ=GGAATCAACATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:19,26:0.0408:2,2:35.5:1:31.5:1:1:1.36:25:4:0.0417:0:7 0/0:96:0:0,0:40,54:0:2,0:26.9:1:28.9:1:1:0:38.6:22.5:0.9783:0:4.2 -10 42396901 . A T 61 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04837;SOR=0.12411;LSEQ=AAAGGAAGCTAATGGAATCA;RSEQ=CATCGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:2,2:17,26:0.0851:2,2:30:1:30.8:1:1:1.52:28.5:8:0.0889:0:5 0/1:89:1:0,1:32,54:0.0112:2,0:36:0:26:0:1:0:24:2:0.0114:0:5 -10 42396902 . C T 25 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54081;SOR=Inf;LSEQ=AAGGAAGCTAATGGAATCAA;RSEQ=ATCGAATGGAATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:18,28:0:2,0:25.2:1:32:1:1:0:33.4:92:1:0:4 0/1:85:2:1,1:29,54:0.0235:2,2:30.5:1:25.5:1:1:1.85:27:4:0.0235:0:7 -10 42396903 . A T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54081;SOR=Inf;LSEQ=AGGAAGCTAATGGAATCAAC;RSEQ=TCGAATGGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:18,28:0:2,0:24.6:1:30.2:1:1:0:33.4:45:1:0:4 0/1:85:2:1,1:29,54:0.0235:2,2:30.5:1:32:1:1:1.85:25:4:0.0238:0:5 -10 42396906 . GAATGGAATC CAATGAATA 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1129;SOR=0;LSEQ=AAGCTAATGGAATCAACATC;RSEQ=GAATGGAAACACCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:13,27:0.0476:2,2:28.5:1:31.7:1:1:2.04:25:4:0.0476:0:6 0/0:82:0:0,0:27,54:0:2,0:22.2:1:30.6:1:1:0:38.2:162:1:0:4 -10 42396909 . TG T 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00789;SOR=0;LSEQ=CTAATGGAATCAACATCGAA;RSEQ=GAATCGAATGGAAACACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:12,27:0,0:1:0,2:23.4:1:30.7:1:1:0:33:38:1:0.3333:3.9 1/1:77:65:16,49:6,5:0.8442:2,2:24.2:1:30.9:1:0.06885:3.60119:37.4:130:0.8667:0.3766:3.5 -10 42396916 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17622;SOR=0;LSEQ=AATCAACATCGAATGGAATC;RSEQ=AATGGAAACACCATCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:5,21:0.0714:2,0:26:1:31.5:1:1:0:32:4:0.0714:0:5 0/0:38:0:0,0:10,28:0:2,0:20.9:1:30.4:1:1:0:38:76:1:0:3.7 -10 42396932 . A G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07213;SOR=0;LSEQ=AATCGAATGGAAACACCATC;RSEQ=AATTGAAACGAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:1,20:0,0:1:0,1:23.6:1:32.1:1:1:0:31:42:1:0:3.7 1/1:34:28:1,27:3,1:0.8235:2,1:21.7:1:31.5:1:0.00314:52.80845:32.1:56:0.8235:0:4.5 -10 42396941 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50244;SOR=Inf;LSEQ=GAAACACCATCAAATTGAAA;RSEQ=GAATGGAATTATCATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:0:1,0:20.5:1:29.4:1:1:0:30.5:16:1:0:3.2 0/1:24:2:0,2:1,21:0.0833:1,0:5.5:1:29:1:1:0:25.5:4:0.0833:0:6.5 -10 42396944 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5045;SOR=Inf;LSEQ=ACACCATCAAATTGAAACGA;RSEQ=TGGAATTATCATGAAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:0,15:0:1,0:20.5:1:31.9:1:1:0:30.2:30:1:0:3.1 0/1:22:2:0,2:0,20:0.0909:1,0:26.5:1:32.5:1:1:0:40:4:0.0909:0:3 -10 42396953 . T C 84 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17178;SOR=6.2641;LSEQ=AATTGAAACGAATGGAATTA;RSEQ=CATGAAATTGAAATGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,9:0.1:0,0:43:0:33:0:1:0:25:2:0.1:0:3 0/1:14:6:0,6:0,7:0.4286:0,0:29.2:1:32.7:1:1:0:31.7:12:0.4286:0:4 -10 42397146 . G T 26 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCATTGTATGGAATCAGATG;RSEQ=AATCATCGAATGGACTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:6:0:33.5:1:1:0:45:4:1:0:2.5 1/1:2:2:1,1:0,0:1:0,2:5.5:1:26:1:1:0:48:4:1:0:4 -10 42397187 . A G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCGTTGAATGGACTC;RSEQ=AATGGAATCATTATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38.5:1:31.5:1:1:0:45:4:1:0:2.5 1/1:2:2:1,1:0,0:1:0,2:46.5:1:28.5:1:1:0:48:4:1:0:4 -10 42397217 . G A 25 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTATTGAATGGAATTGAAT;RSEQ=GAATCATTGAATGGTCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:28:1:1:0:45:4:1:0:2.5 1/1:2:2:1,1:0,0:1:0,2:24.5:1:25.5:1:1:0:48:1:1:0:4 -10 42397225 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATTGAATGGAATCAT;RSEQ=GAATGGTCTTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:45:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30.5:1:1:0:48:4:1:0:4 -10 42397909 . T C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTCTCAGTAACTTCTTTG;RSEQ=GTTGTGTTTAATTCAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:33:1:1:0:60:4:1:0:1.5 -10 42398132 . T A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TTTTTTTTCATAGAGCAGTT;RSEQ=GGAAACGCTCTGTTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:8.3:1:31.7:1:1:0:27.3:6:1:0:6.3 1/1:2:2:1,1:0,0:1:0,2:14:1:31.5:1:1:0:41.5:4:1:0:7.5 -10 42398138 . CG TA 49 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TTCATAGAGCAGTTTGGAAA;RSEQ=CTCTGTTTGTAAAGTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:15.3:1:31:0:1:0:27.3:6:1:0:5.3 0/0:2:0:0,0:1,1:0:2,0:20:1:33.5:1:1:0:41.5:4:1:0:7.5 -10 42398139 . G A 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATAGAGCAGTTTGGAAAC;RSEQ=CTCTGTTTGTAAAGTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:32:0:1:0:41.5:4:1:0:7.5 -10 42398141 . T A 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=ATAGAGCAGTTTGGAAACGC;RSEQ=CTGTTTGTAAAGTCTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:17.3:1:31.7:1:1:0:27.3:6:1:0:5.3 0/0:2:0:0,0:1,1:0:2,0:23:1:32:1:1:0:41.5:4:1:0:7.5 -10 42398144 . G C 52 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GAGCAGTTTGGAAACGCTCT;RSEQ=TTTGTAAAGTCTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:20.3:1:33.3:1:1:0:27.3:6:1:0:5.3 0/0:2:0:0,0:1,1:0:2,0:26:1:33:0:1:0:41.5:4:1:0:7.5 -10 42398149 . TA T 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GTTTGGAAACGCTCTGTTTG;RSEQ=AAGTCTGCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:26.3:1:31.7:1:1:0:27.3:6:1:0:6.3 0/0:2:0:0,0:1,1:0:2,0:32:1:30.5:1:1:0:41.5:4:1:0:7.5 -10 42398160 . A G 94 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGTTTGTAAAGTCTGCA;RSEQ=GTGGATATTTGGACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:22.7:1:29.7:1:1:0:32:5:1:0:5.5 1/1:8:8:4,4:0,0:1:0,2:18:1:31.4:1:1:0:36.3:16:1:0:4.6 -10 42398164 . G T 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=GTTTGTAAAGTCTGCAAGTG;RSEQ=ATATTTGGACCTCTTTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:14:0:27.5:1:1:1:42:4:0.3333:0:6 0/0:8:0:0,0:4,4:0:2,0:21.6:1:31.3:1:1:0:36.3:16:1:0:4.6 -10 42398168 . T A 71 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00966;SOR=Inf;LSEQ=GTAAAGTCTGCAAGTGGATA;RSEQ=TTGGACCTCTTTGAGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:24.8:1:30.7:1:1:0:32:12:1:0:5.5 1/0:8:6:3,3:1,1:0.75:2,2:26.8:1:27.7:1:1:1:39:5:0.7143:0:5.3 -10 42398172 . GA TC 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=Inf;LSEQ=AGTCTGCAAGTGGATATTTG;RSEQ=CCTCTTTGAGCCCTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:24.8:1:29.5:1:1:0:32:5:1:0:5.5 0/1:8:2:1,1:3,3:0.25:2,2:44.5:1:30:1:1:1:41.5:4:0.2857:0:6.5 -10 42398173 . A C 81 d7;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=GTCTGCAAGTGGATATTTGG;RSEQ=CCTCTTTGAGCCCTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:24.8:1:32.5:1:1:0:32:12:1:0:5.5 1/0:8:6:3,3:0,0:0.75:0,2:23:0:31.7:1:1:0:34.5:12:1:0:3.7 -10 42398190 . G T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=TGGACCTCTTTGAGCCCTTC;RSEQ=TTGGAAACGGGATTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:40:0:32:1:1:1:42:4:0.3333:0:6 0/0:8:0:0,0:4,4:0:2,0:23:1:30:1:1:0:36.3:16:1:0:4.4 -10 42398200 . G T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGCCCTTCGTTGGAAACG;RSEQ=GATTTCTTCATATAATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:31:0:33:1:1:0:42:4:1:0:6 0/1:8:2:1,1:3,3:0.25:2,2:13:1:32:0:1:1:44.5:4:0.25:0:5 -10 42398207 . T C 69 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TCATATAATGCTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:0:32.5:1:1:0:42:4:1:0:6 1/0:7:5:2,3:1,1:0.7143:2,2:7.4:1:29.8:1:1:1.41418:40:10:0.7143:0:5.2 -10 42398210 . A T 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04762;SOR=0;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TATAATGCTAGACAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:32:1:1:0:42:4:1:0:6 0/0:5:0:0,0:2,3:0:2,0:5.8:1:28.6:1:1:0:38.8:10:1:0:5 -10 42398453 . G T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTCGCAGAGTTTAACCT;RSEQ=TCTTTTCATAGAGCAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:7:1:29.5:1:1:0:46.5:4:1:0:5.5 -10 42398486 . T C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTTTGGAAACACTCTGT;RSEQ=TGTAAAGTCTGCAAGCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:40:1:32:1:1:0:46.5:4:1:0:5.5 -10 42398502 . C T 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTTTGTAAAGTCTGCAAG;RSEQ=GGATATTTTGACCTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:3,0:2,0:0.6:0,0:11:1:30.3:1:1:0:36.7:6:0.6:0:5.3 -10 42398503 . G A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTGTAAAGTCTGCAAGC;RSEQ=GATATTTTGACCTCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:2,0:4,0:0.3333:0,0:40:1:29.5:1:1:0:46.5:4:0.3333:0:5.5 -10 42398511 . T G 110 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCTGCAAGCGGATATTT;RSEQ=GACCTCTTTGAGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:10:10:10,0:0,0:1:0,0:15.9:1:33.2:1:1:0:39.7:20:1:0:5.1 -10 42398523 . G A 98 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATATTTTGACCTCTTTGA;RSEQ=GCCTTCGTTGGAAATGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:11:0:31:0:1:0:51:2:1:0:3 1/0:14:10:7,3:4,0:0.7143:0,2:19.9:1:29.7:1:0.50549:0:38.2:9:0.6923:0:4.3 -10 42398525 . C T 94 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTTTGACCTCTTTGAGG;RSEQ=CTTCGTTGGAAATGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:13:0:12:0:1:0:51:0:0:0:3 1/0:14:10:7,3:4,0:0.7143:0,2:21.9:1:28.4:1:0.50549:0:38.2:9:0.6923:0:4.3 -10 42398550 . A T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTTGGAAATGGGATTTCTTC;RSEQ=TATAATGCTAGACAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:22:1:31.4:1:1:0:46.6:10:1:0:3 0/1:20:2:2,0:13,5:0.1:2,0:20.5:1:31.5:1:1:0:25:4:0.1:0:7 -10 42398557 . G T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGGATTTCTTCATATAAT;RSEQ=CTAGACAGAAGAATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:22.5:1:33:1:1:0:45.5:12:1:0:3.7 0/1:21:2:2,0:14,5:0.0952:2,0:20.5:1:30.5:1:1:0:25:4:0.1:0:7 -10 42398560 . A T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGATTTCTTCATATAATGCT;RSEQ=GACAGAAGAATTCTCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:24.5:1:29.7:1:1:0:45.5:12:1:0:3.7 0/1:22:2:2,0:15,5:0.0909:2,0:20.5:1:30:1:1:0:25:4:0.0909:0:7 -10 42398565 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTCATATAATGCTAGACA;RSEQ=AAGAATTCTCAGTAACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:26.3:1:31.3:1:1:0:45.5:12:1:0:3.7 0/1:23:2:2,0:16,5:0.087:2,0:20.5:1:30:1:1:0:25:4:0.087:0:7 -10 42398570 . A C 121 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38261;SOR=0.31036;LSEQ=ATATAATGCTAGACAGAAGA;RSEQ=TTCTCAGTAACTGCTTTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:0,0:0.8333:0,2:28.2:1:32.4:1:1:0:46.6:10:0.8333:0:3 1/0:25:15:10,5:9,0:0.6:0,2:23.9:1:31.2:1:0.11808:0:37:30:0.6:0:4.3 -10 42398580 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACAGAAGAATTCTCAGTA;RSEQ=CTGCTTTGCGTTTTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:21.3:1:31.1:1:1:0:43.4:14:1:0:3.9 0/1:24:2:2,0:17,5:0.0833:2,0:26:1:33:1:1:0:31.5:4:0.0833:0:7.5 -10 42398583 . G T 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63781;SOR=2.55248;LSEQ=CAGAAGAATTCTCAGTAACT;RSEQ=CTTTGCGTTTTGTGTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:5,1:0.1429:2,0:30:0:31:0:1:0:40:2:0.1429:0:7 0/1:23:7:7,0:11,5:0.3043:2,0:26.4:1:29.1:1:0.2719:0:35.4:6:0.2857:0:6.3 -10 42398588 . GCGTTT TTCTGG 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.18424;SOR=0.16114;LSEQ=AGAATTCTCAGTAACTGCTT;RSEQ=TGTGTATTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:0.8571:0,2:18.8:1:31.8:1:1:0:44:12:0.8571:0.4286:3.3 0/1:21:10:6,4:9,0:0.4762:0,2:27.8:1:29.3:1:0.08669:0:36.8:20:0.5:0.2381:4.1 -10 42398589 . C T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52233;LSEQ=AATTCTCAGTAACTGCTTTG;RSEQ=GTTTTGTGTATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:0,0:0.25:0,0:36:0:30:0:1:0:40:2:1:0:7 0/1:14:2:2,0:0,0:0.1429:0,0:32.5:1:32:0:1:0:33.5:4:0.5:0:6 -10 42398592 . TT GG 64 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53924;SOR=Inf;LSEQ=TCTCAGTAACTGCTTTGCGT;RSEQ=TGTGTATTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,1:0:2,0:13.7:1:31:0:1:0:52.7:6:1:0:5 0/1:18:4:4,0:4,2:0.2222:2,0:35.3:1:32.4:1:0.46667:0:36.3:8:0.4:0:3.8 -10 42398593 . T G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.67055;SOR=0.5468;LSEQ=CTCAGTAACTGCTTTGCGTT;RSEQ=TGTGTATTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:0,0:0.5714:0,2:11.3:1:32.5:1:1:0:49.5:8:1:0:5.3 0/1:24:10:6,4:0,0:0.4167:0,2:5.1:1:28.7:1:1:0:48.1:9:0.9:0:3.7 -10 42398600 . T C 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10318;SOR=0.12027;LSEQ=ACTGCTTTGCGTTTTGTGTA;RSEQ=TCAACTCACAGAGTTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,8:0.08:2,2:7:0:33.5:1:1:1.82581:56:4:0.08:0:3.5 0/1:99:1:0,1:58,40:0.0101:2,0:1:0:31:0:0.41414:0:27:2:0.0101:0:2 -10 42398601 . T G 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60071;SOR=0.49304;LSEQ=CTGCTTTGCGTTTTGTGTAT;RSEQ=CAACTCACAGAGTTGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:15,9:0.0769:2,2:25.5:1:30.5:1:1:1.63293:45:4:0.0769:0:4.5 0/1:102:4:2,2:57,41:0.0392:2,2:14.3:1:31.5:1:1:1.38566:48:8:0.0392:0:3.3 -10 42398604 . A C 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTGCGTTTTGTGTATTCA;RSEQ=CTCACAGAGTTGAACCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:0:2,0:12:1:30.6:1:1:0:42.3:58:1:0:3.9 0/1:111:2:1,1:62,46:0.018:2,2:8:0:29.5:1:1:1.34411:43:4:0.0183:0:4 -10 42398605 . C A 129 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.56629;SOR=1.69961;LSEQ=TTTGCGTTTTGTGTATTCAA;RSEQ=TCACAGAGTTGAACCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:2,1:16,10:0.1:2,2:7.7:1:29.7:1:1:1.24:40.7:6:0.1:0:5 0/1:113:18:11,7:52,40:0.1593:2,2:8.9:1:31.1:1:0.79849:1.21:43.7:36:0.1607:0:4.2 -10 42398607 . C G 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15355;SOR=0.39931;LSEQ=TGCGTTTTGTGTATTCAACT;RSEQ=ACAGAGTTGAACCTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:3,2:18,9:0.1563:2,2:13.2:1:32.4:1:1:1.32099:45.8:10:0.1563:0:4 0/1:117:8:4,4:62,47:0.0684:2,2:14.5:1:31.6:1:0.72708:1.31598:53.5:16:0.069:0:4.5 -10 42398608 . A T 99 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02568;SOR=0.27327;LSEQ=GCGTTTTGTGTATTCAACTC;RSEQ=CAGAGTTGAACCTTCCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:8:6,2:15,9:0.25:2,2:16.9:1:29.6:1:0.68079:1.77:34.1:7:0.2258:0:5.3 0/1:121:10:4,6:64,47:0.0826:2,2:19.2:1:29.9:1:0.33076:2.0304:35.5:20:0.084:0:5.1 -10 42398609 . C G 144 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.41571;SOR=2.0566;LSEQ=CGTTTTGTGTATTCAACTCA;RSEQ=AGAGTTGAACCTTCCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:2,1:19,10:0.0938:2,2:11.7:1:31.7:1:1:1.05:40.7:6:0.0968:0:5 0/1:125:22:13,9:56,47:0.176:2,2:12.1:1:32.5:1:0.81443:1.21:42.8:44:0.1789:0:4.2 -10 42398612 . A G 140 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00477;SOR=Inf;LSEQ=TTTGTGTATTCAACTCACAG;RSEQ=GTTGAACCTTCCTTTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:21,11:0:2,0:17.3:1:30.8:1:1:0:41.7:31:0.9688:0:4.1 0/1:136:25:13,12:59,51:0.1838:2,2:15.6:1:30.2:1:1:1.06734:41.2:50:0.1894:0:4 -10 42398613 . G A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTGTATTCAACTCACAGA;RSEQ=TTGAACCTTCCTTTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:22,12:0:2,0:17.1:1:32.7:1:1:0:42.3:68:1:0:4 0/1:137:2:1,1:73,62:0.0146:2,2:17:0:29:1:1:1.17601:43:4:0.0147:0:4 -10 42398614 . T A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGTATTCAACTCACAGAG;RSEQ=TGAACCTTCCTTTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:22,12:0:2,0:17.9:1:30.4:1:1:0:42.3:68:1:0:4 0/1:141:4:3,1:72,65:0.0284:2,2:19.3:1:30.3:1:0.62272:2.69:36.8:8:0.0288:0:3.8 -10 42398616 . G C 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92128;LSEQ=TGTATTCAACTCACAGAGTT;RSEQ=AACCTTCCTTTAGACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:21,11:0.0588:2,2:28:1:32:1:1:1.8709:45:4:0.0606:0:4.5 0/1:147:8:4,4:74,65:0.0544:2,2:14.6:1:31.1:1:1:1.13745:41.3:16:0.0556:0:2.8 -10 42398620 . C T 96 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0052;SOR=0.21792;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTCCTTTAGACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:6,2:17,10:0.2286:2,2:22.9:1:31:1:0.68547:1.74:34.1:16:0.2353:0:5.3 0/1:150:9:4,5:75,66:0.06:2,2:19:1:30.4:1:0.736:1.41712:35.6:18:0.0616:0:5.2 -10 42398623 . C T 36 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTCACAGAGTTGAACCTT;RSEQ=CTTTAGACAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:22,13:0:2,0:24.9:1:31.3:1:1:0:41.9:34:1:0:4.1 0/1:154:3:2,1:79,72:0.0195:2,2:29:1:23.3:1:1:1.82:31.3:2:0.0132:0:6 -10 42398627 . T C 99 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21251;SOR=Inf;LSEQ=CACAGAGTTGAACCTTCCTT;RSEQ=AGACAGAGCAGATTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,13:0:2,0:28.4:1:29.6:1:1:0:42.4:68:1:0:4 0/1:154:10:7,3:74,70:0.0649:2,2:29.9:1:30:1:0.33426:2.20:37:9:0.06:0:4 -10 42398630 . A G 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGTTGAACCTTCCTTTAG;RSEQ=CAGAGCAGATTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:21,14:0:2,0:30.9:1:30.1:1:1:0:42.4:34:0.9714:0:4.1 0/1:154:2:1,1:80,72:0.013:2,2:34:0:31.5:1:1:1.11035:43:4:0.0132:0:4 -10 42398631 . C A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26283;SOR=0.52305;LSEQ=GAGTTGAACCTTCCTTTAGA;RSEQ=AGAGCAGATTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:7:4,3:18,13:0.1842:2,2:33.4:1:30.1:1:1:1.03745:33.3:14:0.1842:0:5.7 0/1:152:16:10,6:70,64:0.1053:2,2:30.2:1:28.7:1:0.59739:1.52:37.3:15:0.1:0:4.9 -10 42398633 . G C 88 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00487;SOR=0.18182;LSEQ=GTTGAACCTTCCTTTAGACA;RSEQ=AGCAGATTTGAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:7:4,3:18,13:0.1842:2,2:34.9:1:31.4:1:1:1.03745:33.3:14:0.1892:0:5.7 0/1:154:6:3,3:78,70:0.039:2,2:28.2:1:30.7:1:1:1.1135:37.8:12:0.0397:0:6.3 -10 42398634 . A T 135 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00513;SOR=Inf;LSEQ=TTGAACCTTCCTTTAGACAG;RSEQ=GCAGATTTGAAACACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:22,16:0:2,0:31.2:1:30.5:1:1:0:43.8:76:1:0:4.3 0/1:154:24:12,12:69,61:0.1558:2,2:29.5:1:29.6:1:0.82653:1.13024:41.4:48:0.1611:0:4.1 -10 42398637 . A G 145 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09687;SOR=2.9139;LSEQ=AACCTTCCTTTAGACAGAGC;RSEQ=GATTTGAAACACTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:2,1:21,15:0.0769:2,2:38.3:1:31:0:1:1.42:40.7:6:0.0789:0:5 0/1:153:30:14,16:65,58:0.1961:2,2:31.8:1:29.6:1:0.68415:1.27871:41.3:60:0.1974:0:3.8 -10 42398639 . A T 95 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.71187;SOR=0.75121;LSEQ=CCTTCCTTTAGACAGAGCAG;RSEQ=TTTGAAACACTCTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:3,0:20,16:0.0769:2,0:34.3:1:31.3:1:0.25506:0:31:6:0.0811:0:5.7 0/1:153:9:5,4:73,71:0.0588:2,2:32.3:1:30.2:1:1:1.21:34.9:18:0.0596:0:6.2 -10 42398640 . T G 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTCCTTTAGACAGAGCAGA;RSEQ=TTGAAACACTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:23,16:0:2,0:31.2:1:29.8:1:1:0:43.4:18.5:1:0:4.4 0/1:152:3:1,2:76,73:0.0197:2,2:27:1:29.7:1:0.61755:2.0725:27:6:0.0199:0:5.7 -10 42398642 . T G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10454;SOR=0.54935;LSEQ=TCCTTTAGACAGAGCAGATT;RSEQ=GAAACACTCTTTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:20:10,10:14,8:0.4545:2,2:21.6:1:31.1:1:0.53349:1.72654:50.7:40:0.4545:0:5 0/1:150:47:22,25:51,48:0.3133:2,2:28.3:1:29.8:1:0.72336:1.20582:43.3:14.667:0.2993:0:3.7 -10 42398643 . G C 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTTAGACAGAGCAGATTT;RSEQ=AAACACTCTTTTTGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:25,19:0:2,0:27.4:1:30.9:1:1:0:44.4:43:1:0:4.7 0/1:150:2:1,1:74,74:0.0133:2,2:7:0:29.5:1:1:1:40:4:0.0137:0:6.5 -10 42398645 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTAGACAGAGCAGATTTGA;RSEQ=ACACTCTTTTTGTGGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:25,19:0:2,0:26.9:1:29.1:1:1:0:44.4:21:1:0:4.7 0/1:151:2:1,1:75,74:0.0132:2,2:36:1:31:1:1:1.01342:41.5:4:0.0136:0:5 -10 42398647 . C A 97 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90889;LSEQ=TAGACAGAGCAGATTTGAAA;RSEQ=ACTCTTTTTGTGGAATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:3,0:20,20:0.0652:2,0:36.7:1:31.3:1:0.23588:0:31:6:0.0652:0:5.7 0/1:151:9:5,4:68,68:0.0596:2,2:38.3:1:30.8:1:1:1.25:34.9:18:0.0608:0:6.2 -10 42398648 . A T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.97637;LSEQ=AGACAGAGCAGATTTGAAAC;RSEQ=CTCTTTTTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:10:5,5:16,14:0.2174:2,2:30.1:1:29.5:1:1:1.13904:33.3:20:0.2326:0:5.1 0/1:150:32:15,17:57,55:0.2133:2,2:32.4:1:29.2:1:0.84139:1.17323:44.9:31:0.2168:0:3.1 -10 42398649 . C T 97 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.40199;LSEQ=GACAGAGCAGATTTGAAACA;RSEQ=TCTTTTTGTGGAATTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:2,0:23,21:0.0435:2,0:39:1:33:0:0.49275:0:26.5:4:0.0444:0:6.5 0/1:150:9:5,4:70,71:0.06:2,2:38.4:1:30.8:1:1:1.27:34.9:18:0.0612:0:6.2 -10 42398650 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05826;SOR=0;LSEQ=ACAGAGCAGATTTGAAACAC;RSEQ=CTTTTTGTGGAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:24,20:0.0435:2,2:8:0:32.5:1:1:1.19523:46.5:4:0.0444:0:2.5 0/0:143:0:0,0:68,73:0:2,0:26.6:1:29.4:1:1:0:42.5:22.5:0.9854:0:3.8 -10 42398651 . CTTTT TGTC 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0226;SOR=Inf;LSEQ=CAGAGCAGATTTGAAACACT;RSEQ=TGTGGAATTTGCAAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:25,21:0:2,0:24.2:1:31.3:1:1:0:44.2:45:1:0:4.7 0/1:137:14:5,9:58,62:0.1022:2,2:29.7:1:31:1:0.41085:1.67747:45.9:28:0.1061:0:3.1 -10 42398653 . T A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07121;SOR=0;LSEQ=GAGCAGATTTGAAACACTCT;RSEQ=TTTGTGGAATTTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:24,20:0.0435:2,2:5:0:31:1:1:1.19523:46.5:4:0.0435:0:2.5 0/0:125:0:0,0:60,64:0:2,0:24.7:1:29.4:1:1:0:42.6:40.333:0.9918:0:3.8 -10 42398655 . T C 100 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.23741;LSEQ=GCAGATTTGAAACACTCTTT;RSEQ=TGTGGAATTTGCAAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:3:3,0:21,21:0.0667:2,0:33.7:1:32:1:0.23636:0:31:6:0.0667:0:5.7 0/1:123:10:5,5:52,60:0.0813:2,2:35.8:1:30.2:1:1:1.15:37.4:9:0.0763:0:6.3 -10 42398657 . G C 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1657;LSEQ=AGATTTGAAACACTCTTTTT;RSEQ=TGGAATTTGCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:23,20:0.0444:2,2:14.5:1:31:1:1:1.14642:45:4:0.0465:0:4.5 0/1:136:7:3,4:59,69:0.0515:2,2:22.4:1:28.1:1:1:1.139:46.9:6:0.0448:0:4.3 -10 42398658 . T A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTTGAAACACTCTTTTTG;RSEQ=GGAATTTGCAAGTGGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:0:2,0:23.1:1:30:1:1:0:44.2:86:1:0:4.7 0/1:135:2:1,1:60,73:0.0148:2,2:25:1:32:1:1:1.21:43:4:0.0148:0:4 -10 42398660 . G C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63642;SOR=0.64242;LSEQ=TTTGAAACACTCTTTTTGTG;RSEQ=AATTTGCAAGTGGAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:22,19:0.0465:2,2:11.5:1:31.5:1:1:1.15394:45:4:0.0476:0:4.5 0/1:132:4:2,2:58,70:0.0303:2,2:19.5:1:31:1:1:1.21:55.5:8:0.031:0:4.5 -10 42398661 . A G 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57321;SOR=Inf;LSEQ=TTGAAACACTCTTTTTGTGG;RSEQ=ATTTGCAAGTGGAGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:0:2,0:21.9:1:29.3:1:1:0:44.2:20.5:1:0:4.7 0/1:131:4:2,2:56,69:0.0305:2,2:25.8:1:31:1:1:1.23:33:8:0.0308:0:6 -10 42398662 . A G 101 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45502;SOR=3.18222;LSEQ=TGAAACACTCTTTTTGTGGA;RSEQ=TTTGCAAGTGGAGATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:1:1,0:22,21:0.0227:2,0:32:0:34:0:1:0:25:2:0.0227:0:8 0/1:130:9:6,3:49,66:0.0692:2,2:25.2:1:32.1:1:0.18337:2.67:35.6:18:0.0698:0:6.2 -10 42398666 . G C 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57356;SOR=Inf;LSEQ=ACACTCTTTTTGTGGAATTT;RSEQ=CAAGTGGAGATTTCAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:22,21:0:2,0:19.6:1:31:1:1:0:44.4:20.5:0.9762:0:4.8 0/1:126:4:3,1:52,69:0.0317:2,2:14.3:1:30.8:1:0.31929:3.94:34.5:8:0.0325:0:6 -10 42398669 . A T 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57303;SOR=Inf;LSEQ=CTCTTTTTGTGGAATTTGCA;RSEQ=GTGGAGATTTCAAGAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:22,19:0:2,0:19.5:1:29.5:1:1:0:43.8:19.5:0.975:0:4.9 0/1:126:4:3,1:51,68:0.0317:2,2:11.3:1:29.8:1:0.31858:3.96:34.5:8:0.0325:0:6 -10 42398671 . T G 108 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29666;SOR=3.80835;LSEQ=CTTTTTGTGGAATTTGCAAG;RSEQ=GGAGATTTCAAGAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:1:1,0:20,17:0.025:2,0:9:0:26:0:1:0:60:2:0.025:0:5 0/1:123:11:3,8:52,60:0.0894:2,2:11.7:1:31.5:1:0.34229:2.2963:45.5:22:0.0909:0:5.3 -10 42398677 . T A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00227;SOR=0.22629;LSEQ=GTGGAATTTGCAAGTGGAGA;RSEQ=TTCAAGAGATTTGAGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:5,9:11,7:0.4375:2,2:32.3:1:31.1:1:0.28516:2.73451:48.6:28:0.4375:0:6.7 0/1:88:13:4,9:34,41:0.1477:2,2:32.9:1:29.2:1:0.37885:1.85317:45.1:26:0.1494:0:6.5 -10 42398681 . A T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00648;SOR=0.23686;LSEQ=AATTTGCAAGTGGAGATTTC;RSEQ=AGAGATTTGAGACCAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:12:5,7:7,2:0.4286:2,2:38.3:1:30.1:1:0.18423:4.52129:51.8:24:0.4286:0:7.2 0/1:74:11:4,7:25,35:0.1486:2,2:38.9:1:26.3:1:1:1.24614:49.1:10:0.1389:0:7.2 -10 42398682 . AGAGA GAGC 79 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01216;SOR=0.15851;LSEQ=AATTTGCAAGTGGAGATTTC;RSEQ=TTTGAGACCAATGGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:2,4:7,2:0.2143:2,2:19.8:1:30.8:1:0.13566:5.99855:31:12:0.2143:0.0357:4.8 0/1:74:3:0,3:25,35:0.0405:2,0:26.7:1:33.2:1:0.27035:0:40:6:0.0417:0:5.3 -10 42398683 . GA TC 64 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56789;SOR=Inf;LSEQ=TTTGCAAGTGGAGATTTCAA;RSEQ=GATTTGAGACCAATGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:25:1:32.6:1:1:0:45:42:1:0:5.6 0/1:61:4:4,0:20,35:0.0656:2,0:14.3:1:32.3:1:0.02335:0:39.3:8:0.0656:0:6 -10 42398684 . A C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.40944;SOR=0.3017;LSEQ=TTGCAAGTGGAGATTTCAAG;RSEQ=GATTTGAGACCAATGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:7,7:0,1:0.9333:0,2:33.8:1:31.5:1:1:0:48.2:28:1:0:7.1 1/1:36:29:12,17:0,0:0.8056:0,2:20:1:30.5:1:1:0:45.9:58:0.9063:0:5.7 -10 42398686 . A C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69592;SOR=0.53432;LSEQ=GCAAGTGGAGATTTCAAGAG;RSEQ=TTTGAGACCAATGGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:5,8:2,0:0.8667:0,2:37.5:1:32.9:1:0.2:0:50.9:26:0.8667:0:7 1/0:31:24:11,13:4,3:0.7742:2,2:23.2:1:31.9:1:0.68508:1.55268:46.4:48:0.7742:0:5.8 -10 42398692 . GA CG 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09616;SOR=0.38595;LSEQ=GGAGATTTCAAGAGATTTGA;RSEQ=CCAATGGTAGAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:4,6:2,5:0.4762:2,2:34.2:1:31.9:1:1:1.62:50.2:20:0.5:0:6.3 0/1:39:10:4,6:13,15:0.2564:2,2:37.7:1:29.7:1:1:1.2911:48:20:0.2564:0:6.2 -10 42398693 . A G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75484;SOR=0.77298;LSEQ=GAGATTTCAAGAGATTTGAG;RSEQ=CCAATGGTAGAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:1,5:3,2:0.2857:2,2:24:1:31.2:1:0.24242:6.06919:33.3:12:0.5455:0:6 0/1:34:8:0,8:11,5:0.2353:2,0:21:1:31.8:1:0.00197:0:44:16:0.3478:0:5.5 -10 42398698 . T A 110 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00549;SOR=11.76818;LSEQ=TTCAAGAGATTTGAGACCAA;RSEQ=GGTAGAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:7,13:0.0476:2,0:6:0:32:0:0.38095:0:54:2:0.0476:0:7 0/1:37:14:9,5:6,16:0.3784:2,2:15.5:1:29.1:1:0.04103:4.57:44.9:6:0.3429:0:5.1 -10 42398703 . G GA 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.58887;SOR=1.48974;LSEQ=GAGATTTGAGACCAATGGTA;RSEQ=AAAGGAAATATCTTCGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:3,5:7,8:0.3478:2,2:18.8:1:30.1:1:1:1.43469:36.6:16:0.3478:0.087:5.9 0/1:36:16:8,8:7,13:0.4444:2,2:24.8:1:30.3:1:0.49961:1.82:44.6:32:0.4444:0:5.2 -10 42398705 . A AG 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54879;SOR=Inf;LSEQ=GATTTGAGACCAATGGTAGA;RSEQ=AGGAAATATCTTCGTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:18.2:1:30.2:1:1:0:44.3:52:1:0:6 0/1:46:3:2,1:17,25:0.0652:2,2:17.7:1:31.1:1:0.56483:2.87:52:6:0.0714:0.0435:4.3 -10 42398707 . GGAAA AGGC 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52629;SOR=Inf;LSEQ=TTTGAGACCAATGGTAGAAA;RSEQ=TATCTTCGTATAAAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:18.2:1:29.6:1:1:0:44.3:12:1:0:6 0/1:44:2:0,2:18,24:0.0455:2,0:6.5:1:28.6:1:0.50529:0:33.5:4:0.0455:0.0227:7 -10 42398712 . T C 138 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00207;SOR=6.88446;LSEQ=GACCAATGGTAGAAAGGAAA;RSEQ=ATCTTCGTATAAAAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:2,1:10,15:0.1071:2,2:13.3:1:31.3:1:0.56044:2.88:44.7:6:0.1071:0:6 0/1:48:22:12,10:9,17:0.4583:2,2:22.3:1:31.1:1:0.24385:2.23:43:44:0.4583:0:5.1 -10 42398723 . AA GC 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.20614;SOR=0.4144;LSEQ=GAAAGGAAATATCTTCGTAT;RSEQ=AAACTAGACAGAATCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:2,5:9,9:0.28:2,2:23.9:1:32:1:0.40652:2.41155:35.9:14:0.28:0:5.4 0/1:51:7:3,4:16,24:0.1373:2,2:20.3:1:32.2:1:1:1.12:34.9:14:0.1373:0:5.3 -10 42398725 . A C 128 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00624;SOR=7.25575;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACTAGACAGAATCATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:10,13:0.08:2,2:28:1:31:1:1:1.29:47:4:0.0833:0:6.5 0/1:51:20:11,9:10,21:0.3922:2,2:29.4:1:29.8:1:0.14785:2.52:46.2:19:0.3878:0:5.6 -10 42398735 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53795;SOR=Inf;LSEQ=CTTCGTATAAAAACTAGACA;RSEQ=AATCATTCTCAGAAACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:22.7:1:32:1:1:0:37.3:52:1:0:5.8 0/1:48:2:2,0:18,28:0.0417:2,0:28.5:1:31:1:0.16844:0:30:4:0.0426:0:5.5 -10 42398736 . A T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18366;SOR=0.48075;LSEQ=TTCGTATAAAAACTAGACAG;RSEQ=ATCATTCTCAGAAACTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:10:5,5:9,7:0.3846:2,2:22.2:1:29.1:1:1:1.27328:39.6:20:0.3846:0:6.1 0/1:48:11:2,9:18,19:0.2292:2,2:28.5:1:29.4:1:0.09196:4.14607:36.4:22:0.2391:0:4.8 -10 42398744 . T A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04626;SOR=2.95977;LSEQ=AAAACTAGACAGAATCATTC;RSEQ=CAGAAACTACTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:5,2:8,9:0.2917:2,2:27.4:1:30.9:1:0.38644:2.69:37.3:14:0.2917:0:5.3 1/0:47:26:13,13:7,14:0.5532:2,2:31.5:1:28.7:1:0.37416:1.97:43:52:0.5652:0:5.2 -10 42398750 . A G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27353;SOR=0.42059;LSEQ=AGACAGAATCATTCTCAGAA;RSEQ=CTACTTTGTGATGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:3,2:10,7:0.2273:2,2:23.8:1:32.2:1:1:1.05:37.6:10:0.2273:0:5 0/1:46:5:1,4:18,23:0.1087:2,2:23.8:1:32:1:0.38698:3.06266:39:10:0.1087:0:4.8 -10 42398751 . CT AC 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GACAGAATCATTCTCAGAAA;RSEQ=ACTTTGTGATGTGTGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:33.3:1:32.5:1:1:0:37.2:44:1:0:5.9 0/1:45:2:2,0:17,26:0.0444:2,0:40:1:30:1:0.17273:0:30:4:0.0465:0:4.5 -10 42398753 . A G 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6806;SOR=0.6541;LSEQ=CAGAATCATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:1,2:12,7:0.1364:2,2:43:1:31.7:1:0.54416:3.23456:40:6:0.1364:0:7.7 0/1:43:4:0,4:19,20:0.093:2,0:32.5:1:33:1:0.11751:0:30:8:0.0952:0:5.5 -10 42398758 . GTG AGT 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52893;SOR=Inf;LSEQ=TCATTCTCAGAAACTACTTT;RSEQ=ATGTGTGTGTTCAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:0:2,0:30.5:1:32.7:1:1:0:37.3:46:1:0:6 0/1:40:2:1,1:16,22:0.05:2,2:23:0:32:0:1:1.36:33:4:0.05:0:3.5 -10 42398759 . TG GT 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06264;SOR=0.23572;LSEQ=CATTCTCAGAAACTACTTTG;RSEQ=ATGTGTGTGTTCAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:3,3:11,6:0.2609:2,2:31.2:1:31.5:1:0.64302:1.78394:37.8:12:0.2609:0:5.3 0/1:40:3:2,1:13,19:0.075:2,2:40:1:28.3:1:0.56455:2.83:30.3:6:0.0833:0:5.7 -10 42398762 . T C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.17553;SOR=0.38745;LSEQ=TCTCAGAAACTACTTTGTGA;RSEQ=GTGTGTGTTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:3,3:11,5:0.2727:2,2:29.8:1:32.3:1:0.62436:2.11796:37.8:12:0.2727:0:5.3 0/1:40:5:3,2:14,21:0.125:2,2:31.2:1:29.8:1:0.63396:2.20:31.4:10:0.125:0:4.8 -10 42398768 . T C 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.4375;SOR=0.50628;LSEQ=AAACTACTTTGTGATGTGTG;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:3,1:9,6:0.1905:2,2:28:1:32:1:1:1.93:32.3:8:0.1905:0:5.3 0/1:38:4:1,3:15,17:0.1053:2,2:17.5:1:30.5:1:0.61294:2.58199:40.3:8:0.1053:0:3 -10 42398772 . C A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65683;SOR=0.53773;LSEQ=TACTTTGTGATGTGTGTGTT;RSEQ=AACTCACAGAGTTTAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:12,5:0.15:2,2:37:1:28.7:1:0.27018:4.39523:40:6:0.15:0:7 0/1:35:3:0,3:15,17:0.0857:2,0:29.7:1:32:0:0.2437:0:31.7:6:0.0909:0:6 -10 42398778 . AC A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16471;SOR=0;LSEQ=GTGATGTGTGTGTTCAACTC;RSEQ=AGAGTTTAACATTTCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,6:0.0952:2,2:11:0:32.5:1:1:1.61828:33:4:0.0952:0:2.5 0/0:30:0:0,0:8,13:0:2,0:18.2:1:31.1:1:1:0:33.5:42:0.7241:0:5.1 -10 42398779 . CA AG 83 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49493;SOR=1.80541;LSEQ=TGATGTGTGTGTTCAACTCA;RSEQ=GAGTTTAACATTTCTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:10,6:0.1429:2,2:23.7:1:32:1:1:1.19:44.7:6:0.1429:0:5.7 0/1:30:7:2,5:8,13:0.2333:2,2:14:1:29.9:1:1:1.5157:46.1:14:0.2414:0:5.3 -10 42398782 . A T 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.85998;LSEQ=TGTGTGTGTTCAACTCACAG;RSEQ=GTTTAACATTTCTGTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:3,2:10,5:0.25:2,2:19.4:1:30:1:1:1.31382:39.2:10:0.25:0:5.6 0/1:27:6:3,3:7,14:0.2222:2,2:12.7:1:28.8:1:0.63819:1.95:29.7:12:0.2308:0:5.2 -10 42398786 . T G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.77721;LSEQ=TGTGTTCAACTCACAGAGTT;RSEQ=AACATTTCTGTTCATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:12,5:0.15:2,2:23:1:31:1:0.27018:4.39523:40:6:0.15:0:7 0/1:25:3:0,3:9,13:0.12:2,0:15.7:1:32:1:0.28:0:31.7:6:0.12:0:6 -10 42398790 . A C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.85329;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCTGTTCATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:16:11,5:1,2:0.8:2,2:15.5:1:30.9:1:0.52322:4.04:35.8:32:0.8:0:5.4 1/0:22:17:8,9:0,3:0.7727:0,2:12.8:1:29.5:1:0.24211:0:34.9:16:0.7619:0:5.6 -10 42398796 . G T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.72884;LSEQ=TCACAGAGTTTAACATTTCT;RSEQ=TTCATAGAGCAGTTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:7,2:0,0:0.8182:0,2:20.2:1:29.4:1:1:0:32.9:18:0.8182:0:6.4 1/1:9:8:1,7:0,0:0.8889:0,2:21.4:1:30.1:1:1:0:33.6:16:0.8889:0:6.5 -10 42398798 . T G 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60268;SOR=0.39967;LSEQ=ACAGAGTTTAACATTTCTGT;RSEQ=CATAGAGCAGTTTGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:5,2:0.2727:2,2:11:1:31.7:1:0.5:4.17095:40:6:0.2727:0:7 0/1:8:1:0,1:0,7:0.125:0,0:19:0:34:0:1:0:28:2:0.125:0:7 -10 42398799 . C G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2451;SOR=6.606;LSEQ=CAGAGTTTAACATTTCTGTT;RSEQ=ATAGAGCAGTTTGGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:5,4:0.0909:2,0:24:0:28:0:1:0:40:2:0.1:0:6 0/1:7:3:0,3:0,4:0.4286:0,0:23.3:1:30.3:1:1:0:33.3:6:0.4286:0:7 -10 42398802 . A G 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.74002;LSEQ=AGTTTAACATTTCTGTTCAT;RSEQ=GAGCAGTTTGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:5,4:0.1818:2,0:24:1:31:1:0.49091:0:30.5:4:0.1818:0:6 0/1:7:2:0,2:0,4:0.2857:0,0:13.5:1:28.5:1:1:0:34.5:4:0.2857:0:7 -10 42398822 . T A 26 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76179;LSEQ=AGAGCAGTTTGGAAACACTC;RSEQ=GTTTGTTAAGTCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:17:1:26.5:1:1:1.22474:32:4:0.1818:0:7.5 0/1:7:1:0,1:1,5:0.1429:2,0:27:0:33:0:1:0:21:2:0.1429:0:7 -10 42398823 . GTTTGT CTTTG 47 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.55233;LSEQ=GAGCAGTTTGGAAACACTCT;RSEQ=TAAGTCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:3,5:0.2727:2,2:18:1:30.2:1:0.54545:2.97:35.3:6:0.2727:0.1818:7 0/1:6:1:1,0:0,5:0.1667:0,0:35:0:27:0:0.16667:0:37:2:0.1667:0:8 -10 42398825 . T C 33 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81102;LSEQ=GCAGTTTGGAAACACTCTGT;RSEQ=TGTTAAGTCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:4,3:0.2:2,0:20.5:1:33.5:1:0.44444:0:32.5:4:0.2222:0:6 0/1:6:1:0,1:0,4:0.1667:0,0:23:0:28:0:1:0:40:2:0.2:0:5 -10 42398829 . T A 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61969;LSEQ=TTTGGAAACACTCTGTTTGT;RSEQ=AAGTCTGCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:1,1:0.5556:2,2:17.8:1:28.6:1:1:1.41418:31.8:10:0.625:0:7 0/1:7:3:0,3:1,1:0.4286:2,0:26.7:1:28:1:0.4:0:29:6:0.4286:0:6.3 -10 42398831 . A C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=2.61246;LSEQ=TGGAAACACTCTGTTTGTTA;RSEQ=GTCTGCAAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:1,5:0.125:2,0:22:0:25:0:1:0:21:2:0.125:0:3 0/1:7:2:0,2:1,3:0.2857:2,0:20.5:1:29.5:1:1:0:35.5:4:0.2857:0:5 -10 42398839 . A G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTCTGTTTGTTAAGTCTGCA;RSEQ=GTGGATATTTGGACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:14.5:1:30:1:0.46429:3.87:38:4:0.25:0:6.5 0/1:8:2:1,1:0,6:0.25:0,2:17.5:1:30:1:0.25:0:37:4:0.25:0:7 -10 42398840 . G C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.21433;LSEQ=TCTGTTTGTTAAGTCTGCAA;RSEQ=TGGATATTTGGACCTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:2,5:0.125:2,0:43:0:31:0:1:0:24:2:0.125:0:8 0/1:8:2:0,2:1,5:0.25:2,0:7:1:33.5:1:1:0:25.5:4:0.25:0:6 -10 42398852 . A C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.31595;LSEQ=GTCTGCAAGTGGATATTTGG;RSEQ=CCTCTTTGAGGCCTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:1,4:0.1667:2,0:24:0:33:0:1:0:38:2:0.1667:0:5 0/1:6:2:1,1:0,4:0.3333:0,2:17.5:1:29.5:1:0.33333:0:37:4:0.3333:0:7 -10 42398877 . T C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCATATAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:27:1:30.3:1:1:0:33.3:14:1:0:4.6 1/1:5:5:0,5:0,0:1:0,0:29.2:1:31.6:1:1:0:34.6:10:1:0:4.8 -10 42398914 . T C 34 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGCTAGACAGAAGAATTCT;RSEQ=AGTAACTTCTTTGGGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:19:0:34:0:1:0:40:2:0.5:0:2 1/1:2:2:0,2:0,0:1:0,0:16.5:1:34:0:1:0:33.5:4:1:0:5 -10 42398959 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTCGTTTAGACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:8:0:27:0:1:0:30:2:1:0:8 1/1:2:2:1,1:0,0:1:0,2:22:0:31.5:1:1:0:49:4:1:0:4 -10 42398968 . G C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAGAGTTGAACCTTCGTTTA;RSEQ=ACAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:17:0:27:0:1:0:30:2:1:0:7 1/1:2:2:1,1:0,0:1:0,2:31:0:32.5:1:1:0:49:4:1:0:4 -10 42399230 . A G 53 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.8525;LSEQ=TTGGAACGGGGTTTCTTCAT;RSEQ=TAATGCTAGACAGAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:15:0:33:0:1:0:40:2:0.3333:0:8 1/0:6:3:3,0:2,1:0.5:2,0:11.7:1:33.7:1:1:0:31.3:6:0.5:0:6 -10 42399237 . T C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=GGGGTTTCTTCATATAATGC;RSEQ=AGACAGAAGAATTCTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:22:0:32:0:1:0:40:2:0.3333:0:8 1/0:6:3:3,0:2,1:0.5:2,0:18.7:1:32:0:1:0:31.3:6:0.5:0:6 -10 42399257 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17582;SOR=0.13707;LSEQ=TAGACAGAAGAATTCTCAGT;RSEQ=ACTTCTTTGTGTTGTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:31.5:1:33:0:1:0:47.5:4:0.6667:0:2 0/1:11:2:1,1:0,0:0.1818:0,2:36.5:1:33:0:1:0:48:4:0.1818:0:2 -10 42399259 . C A 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.56749;LSEQ=GACAGAAGAATTCTCAGTTA;RSEQ=TTCTTTGTGTTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:44:0:13:0:1:0:40:0:0:0:8 0/1:14:3:3,0:7,4:0.2143:2,0:38.7:1:31.7:1:0.50549:0:31.3:6:0.2143:0:6 -10 42399262 . C A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAAGAATTCTCAGTTACTT;RSEQ=TTTGTGTTGTGTGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:30:1:31.5:1:1:0:40.5:8:1:0:4.5 0/1:17:2:2,0:10,5:0.1176:2,0:12:1:29.5:1:1:0:28:4:0.1176:0:4.5 -10 42399266 . G C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22807;SOR=0.23532;LSEQ=GAATTCTCAGTTACTTCTTT;RSEQ=TGTTGTGTGTATTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:27.5:1:32.5:1:1:0:33.5:4:0.5:0:7 0/1:17:3:3,0:9,5:0.1765:2,0:41:1:32:1:0.51471:0:31.3:6:0.1765:0:6 -10 42399267 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AATTCTCAGTTACTTCTTTG;RSEQ=GTTGTGTGTATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:28.8:1:31.3:1:1:0:40.5:8:1:0:4.5 0/1:17:2:1,1:11,4:0.1176:2,2:25:1:30.5:1:0.51471:2.56905:22:4:0.1176:0:7 -10 42399269 . T TG 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20984;SOR=0.22009;LSEQ=TTCTCAGTTACTTCTTTGTG;RSEQ=TGTGTGTATTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:27.5:1:33:1:1:0:33.5:4:0.5:0:7 0/1:18:3:3,0:3,3:0.1667:2,0:39:1:32.7:1:0.46429:0:31.3:6:0.1667:0:6 -10 42399274 . T G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.53846;SOR=Inf;LSEQ=AGTTACTTCTTTGTGTTGTG;RSEQ=GTATTCAACTCACAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:13.6:1:30.4:1:1:0:38.4:18:1:0:6.4 0/1:18:2:1,1:11,5:0.1111:2,2:25:1:30:1:1:2.09766:22:4:0.1111:0:7 -10 42399283 . C G 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94303;LSEQ=TTTGTGTTGTGTGTATTCAA;RSEQ=TCACAGAGTTGAACCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:7,1:0.2:2,2:14:0:33.5:1:0.37778:5.29155:47.5:4:0.2:0:2 0/1:21:4:2,2:12,5:0.1905:2,2:18:1:32:1:0.57427:2.29323:35:8:0.1905:0:4.5 -10 42399297 . CC AG 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=TTCCTTTAGACAGACCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:24.7:1:32.1:1:1:0:39.7:18:1:0:7.8 0/1:20:2:1,1:12,4:0.1:2,2:19:0:32.8:1:0.4902:2.79285:39:4:0.1:0:4 -10 42399298 . C G 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTCCTTTAGACAGACCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:1:0,2:25.4:1:31:1:1:0:39.7:18:1:0:7.8 0/1:19:3:3,0:9,5:0.1579:2,0:16.3:1:29.7:1:0.51471:0:36.3:6:0.1765:0:6.7 -10 42399301 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTCACAGAGTTGAACCTT;RSEQ=CTTTAGACAGACCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:27.8:1:32:1:1:0:39.7:18:1:0:7.8 0/1:20:2:1,1:12,6:0.1:2,2:41.5:1:30.5:1:1:1.92731:22:4:0.1:0:6.5 -10 42399309 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTTGAACCTTCCTTTAGA;RSEQ=AGACCAGATTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:33.3:1:32.3:1:1:0:39.7:18:1:0:7.8 0/1:19:2:1,1:11,5:0.1053:2,2:36:1:33:1:1:2.09766:22:4:0.1053:0:6.5 -10 42399313 . CC GT 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=TGAACCTTCCTTTAGACAGA;RSEQ=AGATTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:1:0,2:36.4:1:30.8:1:1:0:39.7:18:1:0.1111:6.9 0/1:17:3:2,1:0,0:0.1765:0,2:34:1:31.8:1:1:0:44.3:6:0.1875:0:4.3 -10 42399318 . T G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTCCTTTAGACAGACCAGA;RSEQ=TTGAAACACTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:43.5:1:30.8:1:1:0:39.6:16:1:0:6.8 0/1:21:2:1,1:11,8:0.0952:2,2:27:1:33.5:1:1:1.35399:22:4:0.1:0:6.5 -10 42399320 . T G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20961;SOR=0.21264;LSEQ=TCCTTTAGACAGACCAGATT;RSEQ=GAAACACTCTTTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:6,2:1,0:0.8889:0,2:44:1:32:1:1:0:39.6:16:0.8889:0:6.8 1/0:21:13:7,6:5,3:0.619:2,2:20.1:1:30.3:1:1:1.40456:41.5:12:0.6:0:5.1 -10 42399328 . TCTTTTTGTGGAATTTTCAAG CCTATTTGTGCAGTTTCCAGT 142 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0017;SOR=Inf;LSEQ=ACAGACCAGATTTGAAACAC;RSEQ=TGGAGATTTCAATCGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:37.2:1:30.9:1:1:0:39.7:18:1:0:6.1 1/0:43:26:10,16:7,8:0.6047:2,2:27.1:1:30.4:1:0.7449:1.3884:41:52:0.619:0.6047:4.2 -10 42399331 . T G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACCAGATTTGAAACACTCT;RSEQ=TTTGTGGAATTTTCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:35.4:1:30:1:1:0:39.7:18:1:0:6.1 0/1:21:2:1,1:9,9:0.0952:2,2:14:1:33.5:1:1:1:22:4:0.1053:0:6.5 -10 42399335 . G T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51337;SOR=Inf;LSEQ=AGATTTGAAACACTCTTTTT;RSEQ=TGGAATTTTCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,4:0:2,0:23.4:1:31.6:1:1:0:41.1:24:0.9231:0:6.8 0/1:21:2:1,1:9,10:0.0952:2,2:10:1:32:0:1:1.11:22:4:0.0952:0:6.5 -10 42399340 . A G 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.03725;LSEQ=TGAAACACTCTTTTTGTGGA;RSEQ=TTTTCAAGTGGAGATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:7,2:0.3077:2,2:6.5:1:33.3:1:0.53007:3.13792:44:8:0.3077:0:7 0/1:19:6:2,4:7,6:0.3158:2,2:15.8:1:29.5:1:0.62848:2.23102:50.8:5:0.2778:0:4.8 -10 42399344 . T C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19223;LSEQ=ACACTCTTTTTGTGGAATTT;RSEQ=CAAGTGGAGATTTCAATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:2,2:6,2:0.3333:2,2:10.5:1:32.3:1:0.54747:2.71347:44:8:0.3333:0:7 0/1:16:6:2,4:4,4:0.375:2,2:17.2:1:32.3:1:0.62704:1.90258:50.8:12:0.375:0:4.8 -10 42399347 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41365;SOR=0.37348;LSEQ=CTCTTTTTGTGGAATTTTCA;RSEQ=GTGGAGATTTCAATCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:6,2:0,0:0.6667:0,2:22.4:1:30.6:1:1:0:39.6:16:0.7273:0:6.8 0/1:12:5:3,2:2,0:0.4167:0,2:30.4:1:32.4:1:1:0:50.8:10:0.4545:0:5.8 -10 42399354 . A G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00951;SOR=0.15881;LSEQ=TGTGGAATTTTCAAGTGGAG;RSEQ=TTTCAATCGCTTTGAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:5,2:3,4:0.5:2,2:17.6:1:31.4:1:0.59207:3.04:41.4:14:0.5:0:7 0/1:38:5:3,2:13,20:0.1316:2,2:23.4:1:32.2:1:0.63183:2.26:50.8:10:0.1316:0:5.8 -10 42399356 . T A 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00951;SOR=0.15881;LSEQ=TGGAATTTTCAAGTGGAGAT;RSEQ=TCAATCGCTTTGAGGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:5,2:3,4:0.5:2,2:15.6:1:28.3:1:0.59207:3.04:41.4:14:0.5:0:7 0/1:38:5:3,2:13,20:0.1316:2,2:21.4:1:29.2:1:0.63183:2.26:50.8:10:0.1351:0:5.8 -10 42399361 . T G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02607;SOR=0.19516;LSEQ=TTTTCAAGTGGAGATTTCAA;RSEQ=CGCTTTGAGGCCAATTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:5,2:3,4:0.5:2,2:10.6:1:31.6:1:0.59207:3.04:41.4:14:0.5385:0:7 0/1:38:6:4,2:12,20:0.1579:2,2:17.2:1:32:1:0.21703:3.23:48.5:12:0.1622:0:6 -10 42399365 . T A 64 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00286;SOR=0;LSEQ=CAAGTGGAGATTTCAATCGC;RSEQ=TTGAGGCCAATTGTAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:5,4:0.3077:2,2:13:0:32:0:1:1.22862:44:8:0.3333:0:7 0/0:38:0:0,0:16,22:0:2,0:13.6:1:30.1:1:1:0:45.8:37:1:0:4.4 -10 42399371 . G A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66595;SOR=1.7515;LSEQ=GAGATTTCAATCGCTTTGAG;RSEQ=CCAATTGTAGGAAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:3,4:1,2:0.7:2,2:13.1:1:28.4:1:1:1.44:48.7:6:0.75:0:6.4 1/1:36:29:11,18:4,3:0.8056:2,2:16.2:1:29:1:0.41782:2.13334:45.5:13.5:0.8182:0:4.2 -10 42399376 . TT AG 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02306;SOR=0.14347;LSEQ=TTCAATCGCTTTGAGGCCAA;RSEQ=GTAGGAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:1,1:0.5556:2,2:5.6:1:31.6:1:1:1.41418:44.2:10:0.5556:0:6 0/1:28:4:3,1:4,2:0.1429:2,2:9:1:26.6:1:1:1.44:55.5:8:0.1429:0.1071:2.5 -10 42399382 . G A 129 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTTGAGGCCAATTGTAG;RSEQ=AAAGGAAATATCTTCTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:27:1:30:1:1:0:55:6:1:0:5.3 1/1:19:19:6,13:0,0:1:0,2:25.1:1:30.6:1:1:0:45.5:38:1:0:5.5 -10 42399391 . T C 136 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.25549;LSEQ=GCCAATTGTAGGAAAGGAAA;RSEQ=ATCTTCTTATAAAAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:24:1:26.7:1:1:0:55:2:0.6667:0:5.3 1/0:24:19:6,13:5,0:0.7917:0,2:20.9:1:32.1:1:0.01087:0:44.1:38:0.7917:0:5.7 -10 42399398 . T G 135 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55261;SOR=1.71194;LSEQ=GTAGGAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,1:0.8:0,2:10.8:1:20:1:0.4:0:46:1:0.6667:0:6 1/1:24:21:11,10:0,0:0.875:0,2:16.3:1:30.9:1:1:0:38.8:42:0.875:0:6.4 -10 42399402 . A T 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.75685;LSEQ=GAAAGGAAATATCTTCTTAT;RSEQ=AAAACTAGACAAAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:2,2:0.2857:2,0:15.5:1:31:1:0.46667:0:32:4:0.3333:0:7 0/1:26:6:4,2:7,8:0.2308:2,2:10.8:1:29:1:0.63512:2.20:47:12:0.2308:0:5.7 -10 42399407 . C G 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.42754;LSEQ=GAAATATCTTCTTATAAAAA;RSEQ=TAGACAAAATCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:4,4:0.1:2,0:25:0:31:0:1:0:24:2:0.1111:0:7 0/1:29:4:1,3:16,9:0.1379:2,2:9.5:1:29.3:1:0.27851:5.02619:42:8:0.1379:0:6.8 -10 42399413 . A G 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03987;SOR=0;LSEQ=TCTTCTTATAAAAACTAGAC;RSEQ=AAATCATTCTCAGAAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:6.5:1:30:1:1:1.29098:51.5:4:0.2222:0:3.5 0/0:34:0:0,0:21,13:0:2,0:14.2:1:30.8:1:1:0:40.4:68:1:0:5.4 -10 42399414 . A G 128 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.44505;SOR=2.57239;LSEQ=CTTCTTATAAAAACTAGACA;RSEQ=AATCATTCTCAGAAACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,2:0.2222:2,2:28:1:34:1:1:1.41418:42.5:4:0.2222:0:6.5 0/1:35:15:9,6:11,7:0.4286:2,2:16.7:1:32.8:1:1:1.04617:33.1:30:0.4286:0:6.4 -10 42399423 . T A 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06992;SOR=0.22966;LSEQ=AAAACTAGACAAAATCATTC;RSEQ=CAGAAACTACTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:3,2:0.4444:2,2:24:1:32:0:1:1.43328:43.8:8:0.4444:0:6.3 0/1:40:6:4,2:18,16:0.15:2,2:21:1:28.7:1:0.67261:1.75:30.3:12:0.15:0:6.8 -10 42399429 . A G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACAAAATCATTCTCAGAA;RSEQ=CTACTTTGTGATGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:27.4:1:30.8:1:1:0:42.8:18:1:0:5.8 0/1:44:3:2,1:21,20:0.0682:2,2:13:1:30.3:1:1:1.88:42.7:6:0.0682:0:4 -10 42399430 . CT AC 112 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.71301;SOR=0.80322;LSEQ=GACAAAATCATTCTCAGAAA;RSEQ=ACTTTGTGATGTGTGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:2,3:0.3:2,2:29.7:1:31.3:1:1:2.60:47.7:6:0.3:0:3.7 0/1:47:12:6,6:14,13:0.2553:2,2:25.8:1:31.5:1:1:1.07487:50.1:24:0.2609:0:2.9 -10 42399432 . A T 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1127;SOR=0.12274;LSEQ=CAAAATCATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,3:0.1667:2,2:29:0:32:0:1:1.58108:45:4:0.2:0:6 0/1:44:1:0,1:19,16:0.0227:2,0:14:0:24:0:0.47222:0:31:2:0.0263:0:6 -10 42399434 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATCATTCTCAGAAACTAC;RSEQ=TTGTGATGTGTGTGTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:23.8:1:31.5:1:1:0:41:24:1:0:4.9 0/1:47:2:1,1:24,21:0.0426:2,2:26:0:32:0:1:1.1396:60:4:0.0435:0:2.5 -10 42399437 . G T 31 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11917;SOR=0.12838;LSEQ=TCATTCTCAGAAACTACTTT;RSEQ=TGATGTGTGTGTTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:0.1538:2,2:34:0:31.5:1:1:1.18321:45:4:0.1538:0:6 0/1:46:1:0,1:25,20:0.0217:2,0:19:0:25:0:0.45652:0:31:2:0.0217:0:6 -10 42399438 . TG GT 84 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32876;SOR=Inf;LSEQ=CATTCTCAGAAACTACTTTG;RSEQ=ATGTGTGTGTTCAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:24.6:1:30.2:1:1:0:40.9:26:1:0:4.8 0/1:47:7:4,3:21,19:0.1489:2,2:34.4:1:30:1:1:1.20:33:14:0.1489:0:5.3 -10 42399441 . T C 86 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.32792;SOR=Inf;LSEQ=TCTCAGAAACTACTTTGTGA;RSEQ=GTGTGTGTTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:26.7:1:30.8:1:1:0:40.9:26:1:0:4.8 0/1:49:7:4,3:21,21:0.1429:2,2:35.3:1:30.7:1:1:1.33:33:14:0.1429:0:5.3 -10 42399446 . G T 28 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.03528;SOR=0;LSEQ=GAAACTACTTTGTGATGTGT;RSEQ=TGTTCAACTCACAGAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:0.1538:2,2:28.5:1:28.5:1:1:1.18321:40:4:0.1538:0:4.5 0/0:54:0:0,0:28,26:0:2,0:27.2:1:30.8:1:1:0:39.6:108:1:0:4.2 -10 42399447 . T C 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.67693;SOR=2.06789;LSEQ=AAACTACTTTGTGATGTGTG;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:6,6:0.0769:2,0:17:0:34:0:1:0:27:2:0.0769:0:2 0/1:54:8:5,3:23,23:0.1481:2,2:17.6:1:31:1:0.7058:1.65:42.9:16:0.1481:0:2.9 -10 42399458 . CA AG 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.38029;SOR=0.47268;LSEQ=TGATGTGTGTGTTCAACTCA;RSEQ=GAGTTTAACCTTTCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:4,6:0.2308:2,2:33:1:31.5:1:0.55944:2.75:40:6:0.2308:0:5.3 0/1:57:7:2,5:25,24:0.1228:2,2:32.1:1:28.9:1:0.42394:2.56188:32.6:14:0.1273:0:5.6 -10 42399461 . A T 98 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.1105;SOR=Inf;LSEQ=TGTGTGTGTTCAACTCACAG;RSEQ=GTTTAACCTTTCTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:24.5:1:30.2:1:1:0:40.8:26:1:0:4.6 0/1:57:11:6,5:22,24:0.193:2,2:28.7:1:28.4:1:0.74698:1.30:32.3:22:0.2:0:5.2 -10 42399467 . AC A 32 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0323;SOR=0;LSEQ=TGTTCAACTCACAGAGTTTA;RSEQ=CTTTCTTTTCATAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:0.1538:2,2:15.5:1:32:1:1:1.18:45:4:0.1538:0:6 0/0:57:0:0,0:28,29:0:2,0:27.3:1:30.3:1:1:0:39.7:56:1:0:4.1 -10 42399477 . TCATA AATC 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.45824;SOR=0.55528;LSEQ=CTCACAGAGTTTAACCTTTC;RSEQ=GAGCAGTTTGGAAACCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:4,4:0.3077:2,2:11.8:1:31.7:1:1:1:46.5:8:0.3077:0.1538:4 0/1:56:11:3,8:24,21:0.1964:2,2:21.5:1:30.1:1:0.18078:2.98899:40.6:22:0.1964:0:2.6 -10 42399478 . C G 97 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40271;SOR=0.50827;LSEQ=CAGAGTTTAACCTTTCTTTT;RSEQ=ATAGAGCAGTTTGGAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:2,3:0.375:2,2:35:1:31.3:1:1:2.60:40:6:0.375:0:5.3 0/1:39:9:3,6:14,14:0.2308:2,2:31.7:1:30.8:1:0.46239:1.96337:33.2:18:0.2432:0:5.8 -10 42399481 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24548;SOR=0.40161;LSEQ=AGTTTAACCTTTCTTTTCAT;RSEQ=GAGCAGTTTGGAAACCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:1,2:0.5:2,2:25.8:1:31:1:1:1.81:41.3:8:0.5:0:5.8 0/1:39:11:4,7:14,14:0.2821:2,2:29.1:1:30.4:1:0.49722:1.72517:33.2:22:0.2895:0:5.8 -10 42399497 . C A 116 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.13861;LSEQ=TCATAGAGCAGTTTGGAAAC;RSEQ=CTCTGTTTGTAAAGTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:0.5:2,2:16:1:28:1:1:3.11:40:6:0.6:0:5.3 1/0:30:16:3,13:7,7:0.5333:2,2:19.6:1:29.1:1:0.12164:4.11149:33.7:15:0.5357:0:5.4 -10 42399501 . T A 81 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55456;SOR=Inf;LSEQ=AGAGCAGTTTGGAAACCCTC;RSEQ=GTTTGTAAAGTCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:31.4:1:30:1:1:0:34.8:10:1:0:4.8 0/1:27:6:2,4:7,14:0.2222:2,2:21.8:1:31.7:1:1:1:29:12:0.2222:0:5.3 -10 42399504 . T C 77 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29644;SOR=0.35514;LSEQ=GCAGTTTGGAAACCCTCTGT;RSEQ=TGTAAAGTCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:16:0:31:1:1:1.73:40:4:0.4:0:5 0/1:27:5:0,5:9,13:0.1852:2,0:15:1:33.2:1:0.13579:0:34.8:10:0.1852:0:5.4 -10 42399508 . A G 110 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64544;SOR=0.54398;LSEQ=TTTGGAAACCCTCTGTTTGT;RSEQ=AAGTCTGCAAGTGGATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:35.7:1:32.3:1:1:1.7321:31.3:6:0.6:0:4.7 0/1:27:12:6,6:3,11:0.4444:2,2:22.3:1:30.7:1:0.21767:3.48:42.8:11:0.4231:0:4 -10 42399512 . T C 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACCCTCTGTTTGTAAAG;RSEQ=CTGCAAGTGGATACTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:22.2:1:29:1:1:0:34.8:10:1:0:4.8 0/1:25:2:1,1:7,16:0.08:2,2:7:0:30:1:1:2.20:56:4:0.08:0:1.5 -10 42399514 . T A 81 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55261;SOR=Inf;LSEQ=AACCCTCTGTTTGTAAAGTC;RSEQ=GCAAGTGGATACTTTGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:20.2:1:30.2:1:1:0:34.8:10:1:0:4.8 0/1:25:6:2,4:6,13:0.24:2,2:8.8:1:31.5:1:1:1.08:29:12:0.24:0:5.3 -10 42399519 . G C 66 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53216;SOR=Inf;LSEQ=TCTGTTTGTAAAGTCTGCAA;RSEQ=TGGATACTTTGACCTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:15.2:1:32:1:1:0:34.8:10:1:0:4.8 0/1:16:4:2,2:4,8:0.25:2,2:7:0:33:1:0.6044:1.91:31:8:0.25:0:5 -10 42399526 . C T 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAAGTCTGCAAGTGGATA;RSEQ=TTTGACCTCTTTGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26.5:1:31:1:1:0:33.5:4:1:0:6 1/1:6:6:2,4:0,0:1:0,2:17:1:31.3:1:1:0:40:12:1:0:5.5 -10 42399529 . TG AA 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCTGCAAGTGGATACTT;RSEQ=ACCTCTTTGAGGCCTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:27:1:1:0:33.5:4:1:0:5 1/1:4:4:1,3:0,0:1:0,2:21:1:31.5:1:1:0:40.5:8:1:0:4.8 -10 42399533 . C G 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGCAAGTGGATACTTTGAC;RSEQ=TCTTTGAGGCCTTCATTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:34:0:1:0:33.5:4:1:0:5 1/1:4:4:1,3:0,0:1:0,2:18:1:32.8:1:1:0:40.5:8:1:0:4.8 -10 42399677 . G A 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAGACACTCTTTTTGTA;RSEQ=AACTTCCAAGTGCATACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19:1:31:1:1:0:59:4:1:0:6.5 1/1:7:7:3,4:0,0:1:0,2:11.3:1:28.1:1:1:0:57.1:14:1:0:6.3 -10 42399680 . C G 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACACTCTTTTTGTAGAA;RSEQ=TTCCAAGTGCATACTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22:1:32.5:1:1:0:59:4:1:0:6.5 1/1:7:7:3,4:0,0:1:0,2:14.3:1:30.3:1:1:0:57.1:14:1:0:6.3 -10 42399690 . C A 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTAGAACTTCCAAGTG;RSEQ=ATACTTAGAGTGCTTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27.5:1:29.5:1:1:0:59:4:1:0:6.5 1/1:9:9:4,5:0,0:1:0,2:20.3:1:28.8:1:1:0:56.2:18:1:0:6.1 -10 42399697 . A T 94 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAACTTCCAAGTGCATACTT;RSEQ=GAGTGCTTTGAAGCCTACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27.5:1:29.5:1:1:0:59:4:1:0:6.5 1/1:9:9:4,5:0,0:1:0,2:26.6:1:29.8:1:1:0:56.2:18:1:0:6.1 -10 42399719 . A T 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=3.05504;LSEQ=AGTGCTTTGAAGCCTACGGT;RSEQ=GACAACTTAATATCTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:30:0:30:0:1:0:58:2:0.5:0:7 1/0:9:7:4,3:0,2:0.7778:0,2:21.4:1:31.3:1:0.44444:0:57.4:14:0.7778:0:6.1 -10 42399726 . TT GA 98 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGCCTACGGTAGACAAC;RSEQ=AATATCTTCATGTAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:13.5:1:28.2:1:1:0:59:4:1:0.5:6.5 1/1:9:9:4,5:0,0:1:0,2:15:1:31.1:1:1:0:56.2:18:1:0.2222:5.3 -10 42399832 . G A 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCATTAGAGCACTTATG;RSEQ=AACACTCTCTTTGTAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:1:0:31:0:1:0:40:2:1:0:6 1/0:4:3:2,1:1,0:0.75:0,2:7:1:28.7:1:1:0:50.7:6:0.75:0:6.7 -10 42399837 . C G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTAGAGCACTTATGGAACA;RSEQ=TCTCTTTGTAGAATTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:6:0:34:0:1:0:40:2:1:0:6 1/0:4:3:2,1:1,0:0.75:0,2:12:1:31:1:1:0:50.7:6:0.75:0:6.7 -10 42399856 . C A 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTCTTTGTAGAATTTGC;RSEQ=AGGGTGTATTTAGAGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:25:0:31:0:1:0:40:2:1:0:6 1/1:6:5:4,1:1,0:0.8333:0,2:26:1:31:1:1:0:46.2:10:0.8333:0:5.8 -10 42399875 . T A 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGTGTATTTAGAGGGC;RSEQ=TTGAGGCCTATGGTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:34:0:30:0:1:0:40:2:1:0:6 1/1:7:6:4,2:1,0:0.8571:0,2:27.3:1:30.2:1:1:0:45.5:12:0.8571:0:6.2 -10 42399880 . G A 79 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTATTTAGAGGGCTTTGA;RSEQ=GCCTATGGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:30:0:1:0:32:4:1:0:7 1/1:7:6:4,2:1,0:0.8571:0,2:24:1:30.8:1:1:0:45.5:12:0.8571:0:6.2 -10 42399886 . T C 85 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGAGGGCTTTGAGGCCTA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:28:1:1:0:32:4:1:0:7 1/0:9:7:4,3:1,1:0.7778:2,2:17.4:1:30.4:1:1:1.29:44.7:14:0.7778:0:6.1 -10 42399907 . A AC 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0.32733;LSEQ=GGTAGAAAAGGAAATATCTT;RSEQ=CATAAATACTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:29:0:28:0:1:0:24:2:0.5:0:8 0/1:9:2:0,2:4,2:0.2222:2,0:23:1:26.5:1:0.42857:0:39.5:4:0.25:0:6.5 -10 42399914 . TA AT 25 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAAATATCTTACATAAA;RSEQ=CTAGACAGAAGCGTTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:37:0:28:0:1:0:24:2:1:0:7 0/1:5:2:0,2:1,1:0.4:2,0:31:1:25.5:0:1:0:39.5:4:0.5:0:5.5 -10 42399920 . A T 42 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=ATATCTTACATAAATACTAG;RSEQ=CAGAAGCGTTCTCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:30:1:1:0:32:4:1:0:6.5 1/0:6:3:0,3:1,1:0.5:2,0:24.3:1:26.7:1:0.4:0:39.7:6:0.6:0:5.3 -10 42399928 . G A 66 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAATACTAGACAGAAGC;RSEQ=TTCTCAGAAACTAAGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30.5:1:31:1:1:0:32:4:1:0:6.5 1/0:7:5:1,4:1,1:0.7143:2,2:29:1:28.6:1:1:3.1622:42:10:0.7143:0:5.4 -10 42399936 . A C 42 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTAGACAGAAGCGTTCTCAG;RSEQ=AACTAAGTTGTGATGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:43:0:32:0:1:0:24:2:0.5:0:7 1/0:6:3:1,2:0,3:0.5:0,2:27.7:1:27:1:1:0:42.7:2:0.4:0:4.7 -10 42399941 . A G 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGCGTTCTCAGAAACT;RSEQ=AGTTGTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31:1:32.5:1:1:0:32:4:1:0:6.5 1/1:6:5:1,4:0,1:0.8333:0,2:31.6:1:31.8:1:1:0:42:10:0.8333:0:5.4 -10 42400136 . A G 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=TGTGTGTATTCAACTCACAG;RSEQ=GTTGAACCTTCCTTTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:16.5:1:31.8:1:1:0:27.8:8:1:0:5.3 0/1:6:2:2,0:4,0:0.3333:0,0:21:0:29.5:1:1:0:40:4:0.3333:0:2.5 -10 42400155 . C A 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25824;SOR=Inf;LSEQ=GAGTTGAACCTTCCTTTAGA;RSEQ=AGAGAAGATTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,0:0:0,0:19.3:1:32.8:1:1:0:31.8:8:0.8:0:4.5 0/1:9:3:3,0:4,1:0.3333:2,0:15:1:31.3:1:1:0:33.3:6:0.3333:0:8 -10 42400157 . G C 52 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25824;SOR=Inf;LSEQ=GTTGAACCTTCCTTTAGACA;RSEQ=AGAAGATTTGAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:23:1:32.8:1:1:0:30.2:10:1:0:5.2 0/1:9:3:3,0:5,1:0.3333:2,0:17:1:33:0:1:0:33.3:6:0.3333:0:8 -10 42400158 . A T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=Inf;LSEQ=TTGAACCTTCCTTTAGACAG;RSEQ=GAAGATTTGAAACACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:23.2:1:30.8:1:1:0:30.2:10:1:0:5.2 0/1:9:2:2,0:6,1:0.2222:2,0:9:1:29:1:1:0:40:4:0.2222:0:2.5 -10 42400160 . A C 93 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53846;SOR=3.18702;LSEQ=GAACCTTCCTTTAGACAGAG;RSEQ=AGATTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:0,0:0.6667:0,0:29.5:1:32.8:1:1:0:31.8:8:0.5714:0:6 1/1:8:7:7,0:0,1:0.875:0,0:23.6:1:33.3:1:0.125:0:33.4:14:0.875:0:6.7 -10 42400172 . A T 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.61816;LSEQ=AGACAGAGAAGATTTGAAAC;RSEQ=CTCTTTTTTTGGAAATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:1,0:0.6667:0,0:24.8:1:32.5:1:1:0:40:8:0.6667:0:5.8 1/0:11:6:5,1:4,1:0.5455:2,2:18.5:1:31:1:1:1.22:34.2:12:0.5455:0:7.7 -10 42400181 . T G 115 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=1.1888;LSEQ=AGATTTGAAACACTCTTTTT;RSEQ=TGGAAATTGCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:24.2:1:33.2:1:1:0:40.4:10:0.8333:0:5.6 1/1:14:12:9,3:1,1:0.8571:2,2:22.8:1:32.3:1:0.50549:2.74:35.4:24:0.8571:0:6.9 -10 42400187 . A T 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55045;SOR=0;LSEQ=GAAACACTCTTTTTTTGGAA;RSEQ=TTGCAAGTGGAGATTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:21.1:1:32:1:1:0:40.4:16:1:0:6.1 1/1:22:18:14,4:0,1:0.8182:0,2:18.6:1:29.5:1:0.26316:0:38.2:36:0.8182:0:7 -10 42400195 . T G 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.15793;LSEQ=CTTTTTTTGGAAATTGCAAG;RSEQ=GGAGATTTCAGGCGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:7,2:0.1818:2,0:13.5:1:33:0:1:0:48.5:4:0.1818:0:6.5 0/1:39:8:4,4:21,10:0.2051:2,2:11.9:1:30.4:1:0.42371:2.05797:43.9:16:0.2051:0:6.9 -10 42400206 . G A 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.08933;LSEQ=AATTGCAAGTGGAGATTTCA;RSEQ=GCGCTTTGAGGCCAATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:4,3:0,0:0.5:0,2:18.4:1:31.3:1:1:0:44.1:14:0.5:0:6.3 1/0:46:24:13,11:1,0:0.5217:0,2:20:1:30.9:1:1:0:42:48:0.5333:0:6.5 -10 42400207 . GC A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.75252;SOR=0.71529;LSEQ=AATTGCAAGTGGAGATTTCA;RSEQ=GCTTTGAGGCCAATGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:3,3:0,0:0.4286:0,2:23.3:1:30.8:1:1:0:45.2:12:0.4286:0.1429:5.2 0/1:46:16:9,7:1,0:0.3478:0,2:22.2:1:30.4:1:1:0:42.3:32:0.3556:0.0652:3.9 -10 42400209 . G A 107 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=1.33595;LSEQ=TGCAAGTGGAGATTTCAGGC;RSEQ=CTTTGAGGCCAATGGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:7,6:0.1875:2,2:22.3:1:30.7:1:1:1.66:52:6:0.1875:0:7 0/1:55:13:6,7:24,17:0.2364:2,2:18.2:1:29.1:1:0.52825:1.63161:45.5:26:0.2364:0:6.2 -10 42400213 . T C 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5559;SOR=Inf;LSEQ=AGTGGAGATTTCAGGCGCTT;RSEQ=GAGGCCAATGGTAGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:13.8:1:30.1:1:1:0:41:52:1:0:5.7 0/1:66:3:2,1:35,28:0.0455:2,2:23.7:1:28:1:1:1.59:35:6:0.0462:0:7 -10 42400214 . G T 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81442;LSEQ=GTGGAGATTTCAGGCGCTTT;RSEQ=AGGCCAATGGTAGAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:15,11:0.037:2,0:21:0:30:0:0.44444:0:23:2:0.037:0:4 0/1:66:2:1,1:36,28:0.0303:2,2:18:1:31:1:1:1.28077:37:4:0.0317:0:5 -10 42400216 . G T 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55194;SOR=Inf;LSEQ=GGAGATTTCAGGCGCTTTGA;RSEQ=GCCAATGGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:15:1:31.5:1:1:0:41:56:1:0:5.6 0/1:66:3:2,1:34,28:0.0455:2,2:22.7:1:27.7:1:1:1.63:35:6:0.0462:0:7 -10 42400217 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGATTTCAGGCGCTTTGAG;RSEQ=CCAATGGTAGAAAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:15.7:1:30.9:1:1:0:41:27:1:0:5.6 0/1:67:2:1,1:36,29:0.0299:2,2:16:1:30:1:1:1.23734:43.5:4:0.0299:0:6 -10 42400219 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08904;SOR=0;LSEQ=GATTTCAGGCGCTTTGAGGC;RSEQ=AATGGTAGAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:15,12:0.069:2,2:16.5:1:30.5:1:1:1.24034:28:4:0.069:0:7 0/0:67:0:0,0:37,30:0:2,0:22.8:1:30.5:1:1:0:43.5:32.5:1:0:5.5 -10 42400221 . A T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00868;LSEQ=TTTCAGGCGCTTTGAGGCCA;RSEQ=TGGTAGAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:4,2:12,11:0.2069:2,2:22.3:1:30.2:1:0.66284:1.80:46.3:12:0.2069:0:5.5 0/1:72:15:8,7:32,25:0.2083:2,2:27:1:29.3:1:1:1.11823:45.1:30:0.2083:0:6.1 -10 42400222 . T C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.04792;LSEQ=TTCAGGCGCTTTGAGGCCAA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:3,2:14,10:0.1667:2,2:14.8:1:30:1:1:1.07:47.4:10:0.1667:0:7.6 0/1:75:13:7,6:29,23:0.1733:2,2:26.1:1:30.8:1:1:1.07945:47:26:0.1733:0:6.8 -10 42400223 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07967;SOR=0;LSEQ=TCAGGCGCTTTGAGGCCAAT;RSEQ=GTAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,10:0.0667:2,2:11:0:31.5:1:1:1.47706:56:4:0.069:0:6.5 0/0:75:0:0,0:39,31:0:2,0:22.5:1:30.7:1:1:0:43:69:0.9718:0:5.6 -10 42400224 . G A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGCGCTTTGAGGCCAATG;RSEQ=TAGAAAAGGAAATATCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,12:0:2,0:19.8:1:31.6:1:1:0:41.4:56:1:0:5.6 0/1:78:2:2,0:42,33:0.0256:2,0:18:0:29.5:1:0.50376:0:45:4:0.026:0:6 -10 42400225 . T C 34 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18303;SOR=0.18291;LSEQ=AGGCGCTTTGAGGCCAATGG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:16,12:0.0667:2,2:15:1:34:0:1:1.32044:32:4:0.0667:0:7 0/1:79:1:1,0:44,33:0.0127:2,0:40:0:34:0:1:0:40:2:0.013:0:7 -10 42400226 . A G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04129;LSEQ=GGCGCTTTGAGGCCAATGGT;RSEQ=GAAAAGGAAATATCTTCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:4,2:14,11:0.1935:2,2:27.2:1:31.2:1:1:1.55:46.3:12:0.1935:0:5.5 0/1:80:16:8,8:37,27:0.2:2,2:29.1:1:31.4:1:0.58687:1.3649:45.3:32:0.2:0:6 -10 42400227 . G C 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.39877;SOR=0.49914;LSEQ=GCGCTTTGAGGCCAATGGTA;RSEQ=AAAAGGAAATATCTTCGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:2,1:16,13:0.0938:2,2:15:0:31:1:1:1.60:27.3:6:0.0938:0:3.3 0/1:82:4:3,1:44,34:0.0488:2,2:13.8:1:33:1:0.63226:2.30:30.3:8:0.0494:0:5.8 -10 42400231 . A C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30727;SOR=0.37266;LSEQ=TTTGAGGCCAATGGTAGAAA;RSEQ=GGAAATATCTTCGTATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:18,13:0.0606:2,2:28.5:1:30.5:1:1:1.37079:28:4:0.0606:0:6 0/1:86:2:1,1:49,35:0.0233:2,2:34:1:29.5:1:1:1.39441:44:4:0.0233:0:4 -10 42400234 . AAA C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07477;SOR=0;LSEQ=GAGGCCAATGGTAGAAAAGG;RSEQ=TATCTTCGTATAAAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:18,12:0.0588:2,2:23:0:33.3:1:1:1.48061:36:4:0.0588:0:3 0/0:89:0:0,0:52,36:0:2,0:25.7:1:29.7:1:1:0:42.8:176:0.9888:0:5.4 -10 42400237 . T C 66 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57573;SOR=Inf;LSEQ=GCCAATGGTAGAAAAGGAAA;RSEQ=ATCTTCGTATAAAAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:0:2,0:25.4:1:29.9:1:1:0:39.8:70:1:0:5.7 0/1:90:4:2,2:51,34:0.0444:2,2:26.5:1:33:1:1:1.49297:36.3:8:0.0444:0:4.8 -10 42400239 . T C 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAATGGTAGAAAAGGAAATA;RSEQ=CTTCGTATAAAAACTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:0:2,0:26.5:1:30.6:1:1:0:39.8:70:1:0:5.7 0/1:90:2:2,0:51,37:0.0222:2,0:33:0:29.5:1:0.51036:0:45:4:0.0225:0:6 -10 42400242 . TC GA 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07677;SOR=0;LSEQ=TGGTAGAAAAGGAAATATCT;RSEQ=GTATAAAAACTAGACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:20,13:0.0571:2,2:31:0:32:0:1:1.51907:56:4:0.0571:0:5.5 0/0:90:0:0,0:53,37:0:2,0:28.2:1:29.7:1:1:0:42.4:89:1:0:5.3 -10 42400244 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:22,14:0:2,0:28.1:1:30.7:1:1:0:39.8:72:1:0:5.6 0/1:90:2:1,1:51,36:0.0222:2,2:35.5:1:30:1:1:1.411:48:4:0.0225:0:6.5 -10 42400247 . T G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.41469;SOR=0.6398;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGACAGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:5,2:16,13:0.1944:2,2:28.1:1:32.1:1:0.67378:1.99:46.3:14:0.1944:0:7.3 0/1:90:12:7,5:45,33:0.1333:2,2:31.1:1:31.3:1:1:1.03:50.1:24:0.1333:0:7 -10 42400248 . AA GC 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.80379;SOR=1.28914;LSEQ=AAAAGGAAATATCTTCGTAT;RSEQ=AAACTAGACAGAATCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:6:3,3:17,12:0.1622:2,2:28.3:1:31:1:1:1.4024:45.2:12:0.1622:0:4.8 0/1:90:18:8,10:40,24:0.2:2,2:29.2:1:31.8:1:0.18713:2.0641:45.9:36:0.2:0.0222:3.1 -10 42400250 . A T 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACTAGACAGAATCATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:22,16:0:2,0:29:1:29.8:1:1:0:39.8:76:1:0:5.4 0/1:88:2:2,0:47,38:0.0227:2,0:34:0:27.5:1:0.50227:0:45:4:0.023:0:6 -10 42400253 . C A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59241;SOR=0.72372;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:7:5,2:17,15:0.1795:2,2:34:1:30.7:1:0.4383:2.16:46.3:14:0.1795:0:7.3 0/1:88:12:7,5:41,33:0.1364:2,2:30.1:1:29.1:1:1:1.13:50.1:24:0.1364:0:7 -10 42400254 . T A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3658;SOR=0.41698;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=AGACAGAATCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:2,1:20,16:0.0769:2,2:32.7:1:29.7:1:1:1.58:25.7:6:0.0769:0:5.7 0/1:90:3:1,2:50,36:0.0333:2,2:35.7:1:31:1:0.57337:2.74612:41:6:0.0341:0:5.3 -10 42400256 . G C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63586;SOR=0.63309;LSEQ=ATATCTTCGTATAAAAACTA;RSEQ=ACAGAATCATTCTCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:22,15:0.0513:2,0:35.5:1:34:0:0.18354:0:24.5:4:0.0513:0:6 0/1:91:3:2,1:50,37:0.033:2,2:24.3:1:31:1:1:1.47:30.7:6:0.0333:0:5.3 -10 42400259 . A G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05691;LSEQ=TCTTCGTATAAAAACTAGAC;RSEQ=GAATCATTCTCAGAAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:11:9,2:13,14:0.2821:2,2:34.3:1:30.6:1:0.07761:4.66:44.7:22:0.2895:0:6.5 0/1:92:27:20,7:32,32:0.2935:2,2:26:1:29.1:1:0.03937:2.82:44.7:26:0.2889:0:6.6 -10 42400261 . A T 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.89489;LSEQ=TTCGTATAAAAACTAGACAG;RSEQ=ATCATTCTCAGAAACTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:3:2,1:21,17:0.0732:2,2:29.7:1:28.3:1:1:1.60:27.3:6:0.075:0:3.3 0/1:91:6:4,2:48,37:0.0659:2,2:37.7:1:29.5:1:0.697:1.53:27.2:12:0.0667:0:6 -10 42400262 . A G 115 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5478;SOR=1.73501;LSEQ=TCGTATAAAAACTAGACAGA;RSEQ=TCATTCTCAGAAACTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:3:3,0:20,18:0.0732:2,0:27.3:1:32.7:1:0.24268:0:40:6:0.0732:0:5.7 0/1:91:11:9,2:43,37:0.1209:2,2:27.9:1:33.3:1:0.10732:3.82:39.6:22:0.1209:0:6.3 -10 42400263 . T G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTATAAAAACTAGACAGAA;RSEQ=CATTCTCAGAAACTACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:0:2,0:27.2:1:29.2:1:1:0:39.9:20.5:1:0:5.5 0/1:94:2:1,1:52,40:0.0213:2,2:39.5:1:32.5:1:1:1.29633:44:4:0.0217:0:4.5 -10 42400264 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTATAAAAACTAGACAGAAT;RSEQ=ATTCTCAGAAACTACTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:0:2,0:27.7:1:31.6:1:1:0:39.9:84:1:0:5.5 0/1:95:2:1,1:53,40:0.0211:2,2:16.5:1:33:1:1:1.32102:24:4:0.0211:0:6 -10 42400266 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAAAAACTAGACAGAATCA;RSEQ=TCTCAGAAACTACTTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:0:2,0:27.4:1:30.5:1:1:0:39.9:84:1:0:5.5 0/1:96:2:1,1:53,41:0.0208:2,2:42.5:1:31:1:1:1.28918:44:4:0.0208:0:4.5 -10 42400268 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09242;SOR=0;LSEQ=AAAAACTAGACAGAATCATT;RSEQ=TCAGAAACTACTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:21,18:0.0476:2,2:34.5:1:30:1:1:1.16227:56:4:0.0476:0:5.5 0/0:95:0:0,0:54,41:0:2,0:24.9:1:30.9:1:1:0:42.5:46.5:1:0:5.2 -10 42400269 . T A 49 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.30189;LSEQ=AAAACTAGACAGAATCATTC;RSEQ=CAGAAACTACTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:1,0:21,19:0.0244:2,0:14:0:32:0:1:0:40:2:0.0244:0:7 0/1:95:3:2,1:52,40:0.0316:2,2:15:1:31:1:1:1.53:32.7:6:0.0316:0:4.3 -10 42400272 . GA AC 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81848;LSEQ=ACTAGACAGAATCATTCTCA;RSEQ=AACTACTTTGTGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:21,17:0.05:2,0:35.5:1:32.8:1:0.21923:0:24.5:4:0.05:0:5 0/1:97:4:3,1:55,38:0.0412:2,2:23.5:1:28.9:1:0.64648:2.06:38.8:8:0.0417:0.0206:4 -10 42400273 . A G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.82324;SOR=1.15088;LSEQ=CTAGACAGAATCATTCTCAG;RSEQ=AACTACTTTGTGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:8:3,5:17,12:0.2051:2,2:28.8:1:31.3:1:0.42826:2.30587:40.8:16:0.2222:0:5.9 0/1:96:22:8,14:47,24:0.2292:2,2:27:1:31:1:0.02402:3.37839:45.5:44:0.2391:0:5.8 -10 42400278 . A G 121 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04341;SOR=0.41018;LSEQ=CAGAATCATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:14:9,5:10,15:0.35:2,2:27.3:1:32.4:1:0.19079:2.63:36.9:28:0.35:0:6.2 0/1:89:16:10,6:42,28:0.1798:2,2:23.4:1:30.3:1:1:1.11:45:15:0.1705:0:6.8 -10 42400280 . T A 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21696;SOR=0.21077;LSEQ=GAATCATTCTCAGAAACTAC;RSEQ=TTGTGATGTGTGCATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:18,19:0.0513:2,2:22.5:1:29.5:1:1:1.05:56:4:0.0513:0:5.5 0/1:90:1:1,0:52,36:0.0111:2,0:38:0:27:0:1:0:40:2:0.0111:0:6 -10 42400284 . T G 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09849;SOR=0.40351;LSEQ=CATTCTCAGAAACTACTTTG;RSEQ=GATGTGTGCATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:9:6,3:12,14:0.2432:2,2:25.4:1:30.7:1:0.44302:2.28:42.4:18:0.2432:0:7.4 0/1:79:9:4,5:41,23:0.1139:2,2:18.6:1:29.7:1:0.29078:2.20266:54.1:18:0.1139:0:7 -10 42400287 . T C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.59493;SOR=0.47159;LSEQ=TCTCAGAAACTACTTTGTGA;RSEQ=GTGTGCATTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:20,17:0.0513:2,0:19.5:1:32:0:0.23077:0:45:4:0.0513:0:5.5 0/1:81:2:0,2:46,32:0.0247:2,0:24.5:1:32:0:0.17753:0:45.5:4:0.0247:0:5.5 -10 42400288 . G A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.63786;SOR=1.35377;LSEQ=CTCAGAAACTACTTTGTGAT;RSEQ=TGTGCATTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:7:2,5:18,13:0.1842:2,2:31.4:1:31:1:0.22236:3.3501:38.4:14:0.1842:0:5.7 0/1:81:19:8,11:39,23:0.2346:2,2:24.7:1:28.4:1:0.1205:2.30628:46.4:38:0.2346:0:5.4 -10 42400290 . G T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.48703;SOR=1.4962;LSEQ=CAGAAACTACTTTGTGATGT;RSEQ=TGCATTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:7:5,2:15,16:0.1842:2,2:28.3:1:30.4:1:0.41032:2.60:51.4:14:0.1842:0:4.7 0/1:79:20:16,4:29,30:0.2532:2,2:27.1:1:28.9:1:0.01946:4.07:47.8:19:0.2436:0:5.3 -10 42400293 . CA TG 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32987;SOR=0.31463;LSEQ=AAACTACTTTGTGATGTGTG;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:0,3:18,15:0.0789:2,0:9:1:31.2:1:0.22857:0:50:6:0.0789:0.0263:4 0/1:77:2:0,2:41,28:0.026:2,0:17.5:1:31.8:1:0.17505:0:45.5:4:0.026:0:4.5 -10 42400294 . A G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07557;SOR=2.10359;LSEQ=AACTACTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:14:9,5:11,10:0.3684:2,2:20.4:1:31.1:1:0.72824:1.61:43.9:28:0.4:0:5.3 1/0:76:42:31,11:11,18:0.5526:2,2:23:1:29.6:1:0.00338:4.50:43.9:84:0.5753:0:5.5 -10 42400297 . C G 97 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01312;SOR=0.22547;LSEQ=TACTTTGTGATGTGTGCATT;RSEQ=AACTCACAGAGTTTAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:9:6,3:15,13:0.2308:2,2:18.2:1:30.9:1:0.7023:1.71:42.4:18:0.2308:0:7.4 0/1:80:5:2,3:42,30:0.0625:2,2:17.6:1:30.2:1:0.64607:2.07955:53:10:0.0625:0:7.8 -10 42400300 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGTGATGTGTGCATTCAA;RSEQ=TCACAGAGTTTAACCTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:24,16:0:2,0:19.1:1:32.1:1:1:0:41.8:80:1:0:5.8 0/1:84:2:2,0:45,36:0.0238:2,0:19:1:28.5:1:0.50279:0:40:4:0.0244:0:3 -10 42400303 . A C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37338;SOR=0.43378;LSEQ=GTGATGTGTGCATTCAACTC;RSEQ=CAGAGTTTAACCTTACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:1,2:21,13:0.0811:2,2:25.3:1:31:1:0.55405:3.12729:24.3:6:0.0811:0:5.7 0/1:82:3:0,3:46,33:0.0366:2,0:13:1:32.3:1:0.08062:0:45:6:0.0366:0:5.3 -10 42400305 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GATGTGTGCATTCAACTCAC;RSEQ=GAGTTTAACCTTACTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:22,14:0:2,0:19.5:1:30.6:1:1:0:41.2:72:1:0:5.7 0/1:81:2:1,1:44,35:0.0247:2,2:6:0:32:0:1:1.25356:44:4:0.0247:0:4.5 -10 42400307 . A T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.04685;LSEQ=TGTGTGCATTCAACTCACAG;RSEQ=GTTTAACCTTACTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:10:8,2:13,10:0.2941:2,2:17.6:1:29.6:1:0.25931:2.98:40:20:0.2941:0:7.7 0/1:79:24:13,11:30,24:0.3038:2,2:16.1:1:29.2:1:1:1.05691:46.5:48:0.3038:0:6.9 -10 42400311 . T G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCATTCAACTCACAGAGTT;RSEQ=AACCTTACTTTTCATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:20,11:0:2,0:21.8:1:29.6:1:1:0:41.1:62:1:0:5.8 0/1:75:2:1,1:43,29:0.0267:2,2:17.5:1:31.5:1:1:1.47466:20.5:4:0.027:0:8 -10 42400315 . C G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.516;SOR=1.38588;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTACTTTTCATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:11:8,3:8,5:0.3667:2,2:29.4:1:31.3:1:0.67919:1.63:50.6:22:0.3667:0:4.3 0/1:74:33:21,12:21,17:0.4459:2,2:25.9:1:29.7:1:0.62877:1.41:51.9:32:0.4384:0:4.4 -10 42400318 . A T 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCACAGAGTTTAACCTT;RSEQ=CTTTTCATAGAGCAGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:16,10:0,0:1:0,2:25.8:1:30.7:1:1:0:41.8:52:1:0:5.6 1/1:72:70:42,28:1,1:0.9722:2,2:23:1:28.8:1:1:1.49:46.4:69:0.9718:0:5.4 -10 42400324 . C G 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18921;SOR=0.1877;LSEQ=CAGAGTTTAACCTTACTTTT;RSEQ=ATAGAGCAGTTTGGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:17,11:0.0667:2,2:21.5:1:30.5:1:1:1.52251:40:4:0.0667:0:7.5 0/1:77:1:1,0:43,32:0.013:2,0:17:0:32:0:1:0:20:2:0.0132:0:8 -10 42400327 . A G 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06421;SOR=0.11968;LSEQ=AGTTTAACCTTACTTTTCAT;RSEQ=GAGCAGTTTGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:2,1:17,10:0.1:2,2:15:1:31:1:1:1.17:40:6:0.1:0:6 0/1:78:1:1,0:42,32:0.0128:2,0:9:0:34:0:1:0:40:2:0.0128:0:4 -10 42400328 . G C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06878;LSEQ=GTTTAACCTTACTTTTCATA;RSEQ=AGCAGTTTGGAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:8:6,2:13,9:0.2667:2,2:26.9:1:32.8:1:0.67219:2.03:40.5:16:0.2667:0:7.1 0/1:75:21:9,12:31,21:0.28:2,2:29.5:1:30.9:1:0.20745:1.94969:45.6:42:0.2917:0:7.3 -10 42400330 . GC TG 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46627;SOR=0.56861;LSEQ=TTAACCTTACTTTTCATAGA;RSEQ=AGTTTGGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:1,3:18,8:0.1333:2,2:11:1:31.8:1:0.12644:6.29618:32:8:0.1333:0.0333:4.8 0/1:75:6:1,5:40,27:0.08:2,2:9.7:1:31:1:0.08024:7.22375:43.3:12:0.0822:0.0133:4.2 -10 42400331 . CA TT 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00647;LSEQ=TAACCTTACTTTTCATAGAG;RSEQ=GTTTGGAAACACTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:6,3:12,5:0.3:2,2:27.2:1:30.5:1:1:1.1915:41:18:0.3333:0.0333:6.2 0/1:73:22:9,13:31,15:0.3014:2,2:31.8:1:29.6:1:0.06405:2.93428:45.6:44:0.3284:0.0137:6.4 -10 42400332 . A G 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.21409;LSEQ=AACCTTACTTTTCATAGAGC;RSEQ=GTTTGGAAACACTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:1,0:12,9:0.0323:2,0:7:0:31:0:1:0:40:2:0.0455:0:3 0/1:77:3:3,0:29,23:0.039:2,0:7.3:1:29.3:1:0.25657:0:36.7:6:0.0556:0:2.7 -10 42400333 . G C 34 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19443;SOR=0.19224;LSEQ=ACCTTACTTTTCATAGAGCA;RSEQ=TTTGGAAACACTCTTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:19,12:0.0606:2,2:14:0:34:0:1:1.56069:29:4:0.0606:0:7 0/1:83:1:0,1:43,39:0.012:2,0:11:0:34:0:0.48193:0:40:2:0.0122:0:7 -10 42400337 . G C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93557;LSEQ=TACTTTTCATAGAGCAGTTT;RSEQ=GAAACACTCTTTTTGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:11:7,4:13,10:0.3143:2,2:25.9:1:31:1:1:1.33:40.8:22:0.3143:0:6 0/1:90:27:11,16:30,25:0.3:2,2:28.9:1:29.8:1:0.3474:1.73357:45.5:54:0.3:0:5.9 -10 42400340 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTCATAGAGCAGTTTGGA;RSEQ=ACACTCTTTTTGCAGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:23,15:0:2,0:21.1:1:30.2:1:1:0:44.7:76:1:0:4.8 0/1:96:2:1,1:49,44:0.0208:2,2:7:1:30:1:1:1.11237:43.5:4:0.0211:0:6 -10 42400344 . CTCTTTTTGCAGAATCTGCAAGTG GTCAGTTTGGAAAGTCTGCAAGCA 88 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18919;SOR=Inf;LSEQ=CATAGAGCAGTTTGGAAACA;RSEQ=GATATTTGGACCTCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:24,12:0:2,0:23.5:1:32.4:1:1:0:44.9:72:0.973:0:4.8 0/1:101:7:3,4:53,41:0.0693:2,2:15.9:1:31.4:1:0.69698:1.71418:34.9:14:0.0707:0.0693:5.4 -10 42400348 . T G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCAGTTTGGAAACACTCT;RSEQ=TTTGCAGAATCTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:21,11:0:2,0:27:1:30.2:1:1:0:46.8:64:0.9697:0:4.6 0/1:99:2:2,0:49,47:0.0202:2,0:12.5:1:33:1:0.49569:0:26.5:4:0.0202:0:8 -10 42400353 . C T 48 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.37078;LSEQ=GTTTGGAAACACTCTTTTTG;RSEQ=AGAATCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:1,0:21,13:0.0286:2,0:10:0:31:0:1:0:21:2:0.0294:0:7 0/1:103:4:4,0:48,50:0.0388:2,0:12:1:24.3:1:0.1179:0:28.3:3:0.0294:0:7.3 -10 42400355 . GAA ATG 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.67537;LSEQ=TTGGAAACACTCTTTTTGCA;RSEQ=TCTGCAAGTGGATATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:0,1:21,12:0.0286:2,0:46:0:31:0:0.38235:0:40:2:0.0286:0:6 0/1:103:2:2,0:50,50:0.0194:2,0:21.5:1:28.3:1:0.49524:0:26.5:4:0.0198:0:6 -10 42400362 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTCTTTTTGCAGAATCTG;RSEQ=AAGTGGATATTTGGACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:39,18:0:2,0:18.1:1:32.1:1:1:0:43.1:56:1:0:4.4 0/1:142:2:2,0:82,58:0.0141:2,0:6:1:29:0:0.51334:0:35.5:4:0.0142:0:6 -10 42400365 . G C 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35129;SOR=0.37537;LSEQ=TCTTTTTGCAGAATCTGCAA;RSEQ=TGGATATTTGGACCTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:3:2,1:36,16:0.0536:2,2:6.7:1:33:0:1:1.12254:30:6:0.0545:0:4 0/1:145:3:2,1:84,58:0.0207:2,2:8:0:33:1:1:1.38:35:6:0.021:0:3.3 -10 42400378 . C A 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.88037;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=CTCTTTGAGGCCTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:44,18:0.0308:2,2:19:0:31:1:0.50893:2.40615:40:4:0.0308:0:1 0/1:184:5:4,1:100,73:0.0272:2,2:19:0:30.4:1:0.40368:2.90:33.4:10:0.0278:0:1.2 -10 42400381 . C T 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.69579;LSEQ=GCAAGTGGATATTTGGACCT;RSEQ=TTTGAGGCCTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:1:1,0:44,19:0.0149:2,0:24:0:31:0:1:0:40:2:0.0152:0:5 0/1:192:2:1,1:112,77:0.0104:2,2:6.5:1:28:1:1:1.4516:49.5:4:0.0105:0:7.5 -10 42400386 . A T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33327;SOR=0.73587;LSEQ=TGGATATTTGGACCTCTTTG;RSEQ=GGCCTTCGTTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:20:12,8:36,12:0.2899:2,2:30.8:1:29:1:0.25075:1.97838:47.4:19:0.2794:0:3.3 0/1:195:45:19,26:94,55:0.2308:2,2:25.9:1:29:1:0.01583:2.32811:50.4:90:0.2356:0:3.4 -10 42400387 . G A 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24745;SOR=0.57451;LSEQ=GGATATTTGGACCTCTTTGA;RSEQ=GCCTTCGTTGGAAACGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:10:5,5:44,15:0.1449:2,2:29.1:1:30.4:1:0.13993:2.88103:39.3:20:0.1471:0:6.3 0/1:192:17:5,12:106,68:0.0885:2,2:31:1:31.1:1:0.01852:3.71508:42.5:34:0.0885:0:6.2 -10 42400389 . C T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65539;SOR=0.77537;LSEQ=ATATTTGGACCTCTTTGAGG;RSEQ=CTTCGTTGGAAACGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:9:4,5:45,16:0.1286:2,2:27.9:1:29.4:1:0.11552:3.44286:39.2:18:0.1324:0:6.4 0/1:195:20:6,14:104,68:0.1026:2,2:32:1:29.5:1:0.01517:3.54474:42.8:40:0.1042:0:5.8 -10 42400390 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22971;SOR=0.50923;LSEQ=TATTTGGACCTCTTTGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:6:5,1:45,20:0.0845:2,2:24.3:1:32:1:0.66231:2.20:44.2:12:0.0845:0:2.8 0/1:201:9:6,3:107,84:0.0448:2,2:17.4:1:30.9:1:0.7342:1.57:41.6:18:0.0452:0:4.7 -10 42400396 . T A 47 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11746;SOR=0.23397;LSEQ=GACCTCTTTGAGGCCTTCGT;RSEQ=GGAAACGGGATTTCTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:2,1:46,29:0.0385:2,2:18:0:30:1:1:1.26:40:6:0.0385:0:2 0/0:217:2:0,2:123,92:0.0092:2,0:24.5:1:31:1:0.18651:0:31.5:4:0.0093:0:5 -10 42400398 . G T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.39623;SOR=0.49351;LSEQ=CCTCTTTGAGGCCTTCGTTG;RSEQ=AAACGGGATTTCTTCACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:3:2,1:48,29:0.0366:2,2:16:0:29.7:1:1:1.21:40:6:0.037:0:2 0/1:218:4:1,3:123,89:0.0183:2,2:17.8:1:24:1:0.31459:4.12005:31.8:3:0.0142:0:5 -10 42400402 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61104;SOR=0.72637;LSEQ=TTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCACATAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:7:2,5:50,28:0.0824:2,2:28.3:1:30.7:1:0.1034:4.3834:41.4:14:0.0824:0:6.3 0/1:229:14:3,11:125,89:0.0611:2,2:24:1:31.1:1:0.01031:5.11494:39.6:28:0.0619:0:6.1 -10 42400403 . G A 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.1279;LSEQ=TTGAGGCCTTCGTTGGAAAC;RSEQ=GGATTTCTTCACATAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:0,1:53,32:0.0116:2,0:20:0:27:0:0.38372:0:47:2:0.0116:0:6 0/1:229:3:1,2:126,97:0.0131:2,2:8:1:29.7:1:0.58275:2.58713:38:6:0.0135:0:6 -10 42400405 . G A 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57832;SOR=Inf;LSEQ=GAGGCCTTCGTTGGAAACGG;RSEQ=ATTTCTTCACATAATGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:54,35:0:2,0:24.1:1:30.9:1:1:0:41.5:88:1:0:4.8 0/1:235:4:2,2:129,102:0.017:2,2:17:1:30.5:1:1:1.26342:55.8:8:0.0176:0:6.3 -10 42400410 . CTTCAC TTCAT 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16559;SOR=0.63483;LSEQ=CTTCGTTGGAAACGGGATTT;RSEQ=ATAATGTTAGACAGAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:17:7,10:47,25:0.1889:2,2:24.5:1:30.3:1:0.09715:2.65424:45:34:0.191:0.0222:2.6 0/1:241:31:15,16:117,86:0.1286:2,2:24.1:1:28.9:1:0.33933:1.44879:48:62:0.1297:0.0166:2.7 -10 42400411 . T C 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5048;SOR=0.80459;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TCACATAATGTTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:17:13,4:34,21:0.2329:2,2:23.5:1:30.2:1:0.38422:1.99:39.9:16:0.2254:0:6.6 0/1:209:41:26,15:92,76:0.1962:2,2:31.3:1:29.5:1:0.38084:1.43:38:19.5:0.1902:0:6 -10 42400414 . ACA CTG 95 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20561;SOR=Inf;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TAATGTTAGACAGAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:44,22:0:2,0:26.1:1:30:1:1:0:40.6:32:0.9846:0:5.4 0/1:208:8:7,1:109,90:0.0385:2,2:28.3:1:31.9:1:0.08096:5.74:44.4:16:0.0392:0:4.6 -10 42400415 . C T 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25011;SOR=0.71428;LSEQ=TTGGAAACGGGATTTCTTCA;RSEQ=ATAATGTTAGACAGAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:31:21,10:7,3:0.4769:2,2:26.1:1:30.3:1:1:1.10832:39.2:62:0.4844:0:6.1 0/1:203:80:40,40:8,8:0.3941:2,2:27.8:1:28.4:1:1:1:39.9:79:0.4115:0:5.9 -10 42400417 . T C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19064;SOR=0.35232;LSEQ=GGAAACGGGATTTCTTCACA;RSEQ=AATGTTAGACAGAAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:3,0:49,36:0.0337:2,0:33:1:32:1:0.26646:0:33.7:6:0.0337:0:5 0/1:248:3:2,1:131,114:0.0121:2,2:49:1:30:1:1:1.74:34:6:0.0122:0:4.3 -10 42400420 . T C 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.117;SOR=0.23401;LSEQ=AACGGGATTTCTTCACATAA;RSEQ=GTTAGACAGAAGAATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:3:3,0:50,38:0.033:2,0:34:1:31.7:1:0.26227:0:33.7:6:0.0333:0:5 0/0:254:2:2,0:132,120:0.0079:2,0:46:1:29.5:1:0.49955:0:38.5:4:0.0079:0:4.5 -10 42400422 . T C 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00549;SOR=0.47638;LSEQ=CGGGATTTCTTCACATAATG;RSEQ=TAGACAGAAGAATTCTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:34:17,17:30,19:0.3778:2,2:24.1:1:31.9:1:0.37061:1.57012:40.4:68:0.3864:0:4.3 0/1:259:58:22,36:106,78:0.2239:2,2:24.6:1:31.6:1:0.01037:2.21634:42.5:57:0.2235:0:4.7 -10 42400424 . A C 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02615;SOR=1.80663;LSEQ=GGATTTCTTCACATAATGTT;RSEQ=GACAGAAGAATTCTCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:27:17,10:33,29:0.2903:2,2:23.1:1:29.9:1:0.48785:1.49:46.9:26:0.2826:0:4.2 0/1:268:114:67,47:65,74:0.4254:2,2:27.8:1:30.2:1:0.05942:1.62:46.8:113:0.428:0:3.9 -10 42400425 . G C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04838;LSEQ=GATTTCTTCACATAATGTTA;RSEQ=ACAGAAGAATTCTCAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:21:13,8:40,34:0.2165:2,2:22.6:1:32.2:1:0.62189:1.38:42.2:42:0.2234:0:6.4 0/1:276:62:35,27:105,103:0.2246:2,2:25.3:1:30.7:1:0.46972:1.27:41.5:61:0.2302:0:6 -10 42400427 . C T 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05419;LSEQ=TTTCTTCACATAATGTTAGA;RSEQ=AGAAGAATTCTCAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:3:2,1:53,43:0.03:2,2:31.7:1:31:1:1:1.62:41.3:6:0.0303:0:6 0/1:285:9:6,3:140,136:0.0316:2,2:35.4:1:28.8:1:0.502:1.94:30.3:18:0.0319:0:6 -10 42400429 . G A 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52725;SOR=0.71643;LSEQ=TCTTCACATAATGTTAGACA;RSEQ=AAGAATTCTCAGTAACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:4:2,2:55,46:0.0377:2,2:6.3:1:27.5:1:1:1.19361:41.8:3:0.0286:0:3.3 0/1:293:8:3,5:145,139:0.0273:2,2:5.3:1:28:1:0.49661:1.73536:34.4:16:0.0277:0:4 -10 42400430 . A G 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10499;LSEQ=CTTCACATAATGTTAGACAG;RSEQ=AGAATTCTCAGTAACTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:3:1,2:57,48:0.0278:2,2:30.3:1:31.3:1:0.59516:2.35649:38.7:6:0.028:0:6.7 0/1:294:9:6,3:142,142:0.0306:2,2:34.1:1:31:1:0.50118:2.00:30.3:18:0.0311:0:6 -10 42400434 . A C 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92826;LSEQ=ACATAATGTTAGACAGAAGA;RSEQ=TTCTCAGTAACTTCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:0,2:57,52:0.0177:2,0:18:0:34:0:0.2344:0:39.5:4:0.0179:0:6.5 0/1:304:5:1,4:150,148:0.0164:2,2:13.2:1:29.6:1:0.37085:4.03743:44.2:4:0.0133:0:6 -10 42400435 . T G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13368;LSEQ=CATAATGTTAGACAGAAGAA;RSEQ=TCTCAGTAACTTCTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:4:1,3:57,51:0.0351:2,2:22:1:31.3:1:0.35086:3.31952:39:8:0.0354:0:6 0/1:303:12:6,6:141,145:0.0396:2,2:23.8:1:30.1:1:1:1.03:29.7:24:0.0404:0:5.3 -10 42400436 . T A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07342;SOR=0;LSEQ=ATAATGTTAGACAGAAGAAT;RSEQ=CTCAGTAACTTCTTTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:56,53:0.0179:2,2:27.5:1:31:1:1:1.0561:24.5:4:0.0179:0:6 0/0:300:0:0,0:147,151:0:2,0:24.8:1:28.8:1:1:0:43.4:48.667:1:0:4.5 -10 42400437 . C T 30 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18375;SOR=0.18715;LSEQ=TAATGTTAGACAGAAGAATT;RSEQ=TCAGTAACTTCTTTGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:57,54:0.0177:2,2:44:0:30.5:1:1:1.05507:44:4:0.018:0:5.5 0/0:299:1:0,1:147,151:0.0033:2,0:1:0:28:0:1:0:29:2:0.0034:0:5 -10 42400443 . A G 70 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8917;LSEQ=TAGACAGAAGAATTCTCAGT;RSEQ=ACTTCTTTGTGTTGTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:55,56:0.0089:2,0:49:0:31:0:1:0:40:2:0.0089:0:6 0/1:298:5:2,3:141,150:0.0168:2,2:15.4:1:30.2:1:1:1.40838:32.4:10:0.0171:0:4.6 -10 42400444 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15652;SOR=0.47418;LSEQ=AGACAGAAGAATTCTCAGTA;RSEQ=CTTCTTTGTGTTGTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:7:2,5:52,53:0.0619:2,2:18.7:1:33.4:1:0.44016:2.43436:41.9:14:0.0619:0:3.1 0/1:297:9:2,7:143,145:0.0303:2,2:16.9:1:30.8:1:0.17411:3.4392:38.7:18:0.0306:0:3.2 -10 42400445 . C A 65 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.90466;LSEQ=GACAGAAGAATTCTCAGTAA;RSEQ=TTCTTTGTGTTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:52,58:0.0089:2,0:47:0:31:0:1:0:40:2:0.009:0:6 0/1:296:5:2,3:140,151:0.0169:2,2:14.2:1:28.4:1:1:1.3892:32.4:10:0.0174:0:4.6 -10 42400447 . T G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07561;SOR=0;LSEQ=CAGAAGAATTCTCAGTAACT;RSEQ=CTTTGTGTTGTGTGTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:0,2:52,58:0.0179:2,0:5:0:33:0:0.49807:0:39.5:4:0.0182:0:6.5 0/0:294:0:0,0:140,154:0:2,0:26.3:1:28.4:1:1:0:43.1:41:1:0:4.5 -10 42400448 . C A 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3188;SOR=1.258;LSEQ=AGAAGAATTCTCAGTAACTT;RSEQ=TTTGTGTTGTGTGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:56:31,25:22,32:0.4956:2,2:29.1:1:29.6:1:0.13287:1.79:44.9:112:0.5:0:4.9 1/0:293:162:80,82:56,67:0.5529:2,2:27.7:1:28.1:1:0.55061:1.17:43.2:31.4:0.547:0:4.8 -10 42400451 . TGT ATGG 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.57938;SOR=Inf;LSEQ=AGAATTCTCAGTAACTTCTT;RSEQ=GTTGTGTGTATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:52,56:0:2,0:25.2:1:30:1:1:0:42.3:35:0.9906:0:4.3 0/1:292:4:2,2:132,148:0.0137:2,2:25.5:1:29.1:1:1:1.12:39:8:0.0144:0:4.5 -10 42400452 . G T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65883;SOR=1.36531;LSEQ=GAATTCTCAGTAACTTCTTT;RSEQ=TGTTGTGTGTATTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:6:1,5:48,46:0.0577:2,2:32.5:1:30.7:1:0.20498:5.144:40.2:12:0.0606:0:4.7 0/1:285:22:8,14:117,129:0.0772:2,2:31:1:29.3:1:0.37589:1.58453:43.7:21:0.0789:0:4.5 -10 42400453 . T G 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.73023;SOR=0.84509;LSEQ=AATTCTCAGTAACTTCTTTG;RSEQ=GTTGTGTGTATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:3:1,2:48,50:0.0288:2,2:26:1:30.7:1:1:1.9081:24:6:0.0297:0:5.3 0/1:286:7:4,3:124,143:0.0245:2,2:26.4:1:30.6:1:0.70881:1.54:50.1:14:0.0257:0:5.9 -10 42400454 . GT G 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.13512;SOR=0.41787;LSEQ=ATTCTCAGTAACTTCTTTGT;RSEQ=TGTGTGTATTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:7:2,5:10,13:0.0673:2,2:20.1:1:32.4:1:0.66932:1.8831:34.6:14:0.07:0.0096:3.4 0/1:274:8:2,6:19,26:0.0292:2,2:26.3:1:29.8:1:0.45499:2.16226:37.3:16:0.0308:0.0036:3.5 -10 42400455 . T G 231 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10738;SOR=1.51395;LSEQ=TTCTCAGTAACTTCTTTGTG;RSEQ=TGTGTGTATTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:64:34,30:10,13:0.6154:2,2:29.7:1:31.5:1:0.47321:1.47:45.2:63:0.63:0:4.5 1/0:274:194:93,101:19,26:0.708:2,2:28.3:1:30.4:1:0.5118:1.26:45:37.8:0.7269:0:4.4 -10 42400456 . T G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.65759;SOR=1.3252;LSEQ=TCTCAGTAACTTCTTTGTGT;RSEQ=GTGTGTATTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:6:1,5:46,48:0.0583:2,2:28.5:1:31.8:1:0.20961:4.72847:40.2:12:0.06:0:4.7 0/1:277:21:7,14:113,136:0.0758:2,2:31.8:1:30.9:1:0.36273:1.65875:43.9:42:0.0784:0:4.5 -10 42400459 . G T 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.19664;SOR=0.35938;LSEQ=CAGTAACTTCTTTGTGTTGT;RSEQ=TGTATTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:3:2,1:40,53:0.0303:2,2:25:1:29.7:1:0.57935:2.62:30.3:6:0.0319:0:5.3 0/1:271:3:1,2:113,147:0.0111:2,2:18.3:1:27.7:1:1:1.535:42.7:6:0.0114:0:4.7 -10 42400460 . T G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.3158;SOR=0.49612;LSEQ=AGTAACTTCTTTGTGTTGTG;RSEQ=GTATTCAACTCACAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:5:2,3:39,54:0.051:2,2:21.4:1:30.4:1:1:1.08247:31:10:0.051:0:5.2 0/1:270:7:4,3:113,150:0.0259:2,2:29.4:1:31.1:1:0.47119:1.77:51.4:14:0.0261:0:5.9 -10 42400465 . T G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07176;SOR=0;LSEQ=CTTCTTTGTGTTGTGTGTAT;RSEQ=CAACTCACAGAGTTGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:38,56:0.0208:2,2:33.5:1:33.5:1:1:1.47:27:4:0.0208:0:7.5 0/0:261:0:0,0:109,151:0:2,0:27.5:1:28.9:1:1:0:43.3:64:0.9961:0:4.5 -10 42400469 . C A 69 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.70873;SOR=0.74354;LSEQ=TTTGTGTTGTGTGTATTCAA;RSEQ=TCACAGAGTTGAACCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:0,3:36,55:0.0319:2,0:32.7:1:32.7:1:0.28346:0:37:6:0.0319:0:6.7 0/1:251:6:2,4:99,141:0.0239:2,2:30.2:1:27:1:1:1.40239:46:5:0.0202:0:6.5 -10 42400473 . C G 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.21263;LSEQ=TGTTGTGTGTATTCAACTCA;RSEQ=AGAGTTGAACCTTCCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:0,3:34,53:0.0319:2,0:30.7:1:33:0:0.28689:0:37:6:0.0323:0:6.7 0/1:234:9:3,6:88,130:0.0385:2,2:26.3:1:28.8:1:0.74388:1.3521:45.1:8:0.0349:0:6.3 -10 42400476 . A G 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.72458;SOR=0.82462;LSEQ=TGTGTGTATTCAACTCACAG;RSEQ=GTTGAACCTTCCTTTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:3:1,2:33,56:0.0326:2,2:18.3:1:33:0:1:1.17655:38.7:6:0.033:0:7 0/1:222:6:2,4:82,133:0.027:2,2:21:0:30.2:1:1:1.23192:39.8:12:0.0276:0:3.2 -10 42400477 . G T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09089;SOR=0;LSEQ=GTGTGTATTCAACTCACAGA;RSEQ=TTGAACCTTCCTTTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:32,57:0.0217:2,2:36:1:32:1:1:1.77:34:4:0.0217:0:4.5 0/0:212:0:0,0:79,132:0:2,0:25.7:1:31.2:1:1:0:43.5:69.333:0.9952:0:4.4 -10 42400478 . T A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50576;SOR=1.44833;LSEQ=TGTGTATTCAACTCACAGAG;RSEQ=TGAACCTTCCTTTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:6:2,4:33,54:0.0645:2,2:20.3:1:31.5:1:1:1.21963:45.5:12:0.0645:0:6.7 0/1:209:19:6,13:71,118:0.0909:2,2:23.8:1:29.5:1:0.80389:1.30206:43.5:18:0.0874:0:6.6 -10 42400483 . C G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5542;SOR=0.72126;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=CTTCCTTTAGACAGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:5:1,4:32,54:0.0549:2,2:24.2:1:33.2:1:0.64967:2.35096:31.4:10:0.0549:0:6.4 0/1:199:8:4,4:65,125:0.0402:2,2:28.4:1:31.8:1:0.4531:1.92:50.1:16:0.0408:0:5.9 -10 42400484 . C T 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12519;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTCCTTTAGACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:0,2:32,53:0.0227:2,0:11:0:31:1:0.52954:0:39:4:0.023:0:4.5 0/1:196:5:1,4:68,121:0.0255:2,2:11:0:29.4:1:0.65712:2.23985:26.6:10:0.026:0:4 -10 42400487 . C T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4942;SOR=0.63482;LSEQ=AACTCACAGAGTTGAACCTT;RSEQ=CTTTAGACAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:4:1,3:28,51:0.0482:2,2:30.5:1:31.8:1:1:1.63796:37.8:8:0.0488:0:5 0/1:193:6:1,5:67,120:0.0311:2,2:33.8:1:29.5:1:0.66734:2.77949:27.7:12:0.0314:0:4.7 -10 42400488 . C T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCACAGAGTTGAACCTTC;RSEQ=TTTAGACAGAGCAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:29,54:0:2,0:19.1:1:32.2:1:1:0:41.9:166:1:0:4.4 0/1:192:2:0,2:68,122:0.0104:2,0:28.5:1:32:0:0.54014:0:32:4:0.0106:0:7 -10 42400491 . T C 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98949;LSEQ=CACAGAGTTGAACCTTCCTT;RSEQ=AGACAGAGCAGATTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:18:8,10:20,41:0.2278:2,2:14.2:1:31.1:1:0.40787:1.63:42.6:36:0.2278:0:6.9 0/1:177:40:15,25:45,92:0.226:2,2:15.9:1:30.5:1:0.57561:1.23:43.5:19:0.2184:0:6.5 -10 42400493 . G C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20601;SOR=0.20395;LSEQ=CAGAGTTGAACCTTCCTTTA;RSEQ=ACAGAGCAGATTTGAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:24,44:0.0286:2,2:20:1:31:1:1:1.82:48:4:0.0286:0:4 0/0:169:1:0,1:57,111:0.0059:2,0:28:0:32:0:1:0:40:2:0.006:0:6 -10 42400494 . A G 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30626;SOR=0.47864;LSEQ=AGAGTTGAACCTTCCTTTAG;RSEQ=CAGAGCAGATTTGAGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:5:1,4:23,39:0.0746:2,2:25.2:1:33.4:1:0.64731:2.33277:34.4:10:0.0746:0:6.2 0/1:162:6:3,3:51,104:0.037:2,2:30.3:1:31.5:1:0.40376:2.03:51.2:12:0.0377:0:6.8 -10 42400495 . C A 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.85356;SOR=1.13599;LSEQ=GAGTTGAACCTTCCTTTAGA;RSEQ=AGAGCAGATTTGAGACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:12:6,6:17,28:0.1875:2,2:15.6:1:28.9:1:0.51676:1.63:41.3:24:0.1875:0:6.8 0/1:154:32:11,21:38,74:0.2078:2,2:15.3:1:29.7:1:1:1.02:44.4:31:0.2067:0:6.6 -10 42400496 . A G 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24036;SOR=0.40733;LSEQ=AGTTGAACCTTCCTTTAGAC;RSEQ=GAGCAGATTTGAGACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:4:1,3:23,37:0.0625:2,2:28.5:1:32:1:1:1.84832:33:8:0.0625:0:6.8 0/1:152:4:2,2:46,100:0.0263:2,2:27.5:1:30.3:1:0.59321:2.16:51.5:8:0.027:0:6.8 -10 42400497 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTGAACCTTCCTTTAGACA;RSEQ=AGCAGATTTGAGACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:22,40:0:2,0:16.4:1:31.9:1:1:0:42.1:124:1:0:4.2 0/1:150:2:1,1:47,101:0.0133:2,2:8:1:32.5:1:0.53906:2.14:45:4:0.0137:0:3.5 -10 42400498 . A T 77 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.71752;SOR=0.79523;LSEQ=TTGAACCTTCCTTTAGACAG;RSEQ=GCAGATTTGAGACACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:3:1,2:20,36:0.0508:2,2:38.7:1:32:0:1:1.10917:38.7:6:0.0508:0:7 0/1:147:6:2,4:45,96:0.0408:2,2:24.8:1:30:1:1:1.07:39.8:12:0.0417:0:3.2 -10 42400499 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAACCTTCCTTTAGACAGA;RSEQ=CAGATTTGAGACACTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:21,37:0:2,0:15.5:1:32.7:1:1:0:41.9:116:0.9831:0:4.1 0/1:147:2:1,1:46,98:0.0136:2,2:11.5:1:28:1:0.54171:2.12:42.5:4:0.0138:0:6.5 -10 42400500 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAACCTTCCTTTAGACAGAG;RSEQ=AGATTTGAGACACTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:19,37:0:2,0:15.2:1:31.9:1:1:0:41.7:27:1:0:4.1 0/1:140:2:0,2:44,92:0.0143:2,0:10.5:1:30:0:1:0:30.5:4:0.0146:0:6 -10 42400501 . A G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5823;SOR=0.40992;LSEQ=AACCTTCCTTTAGACAGAGC;RSEQ=GATTTGAGACACTCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:0,2:18,35:0.0364:2,0:13:1:33:0:1:0:44:4:0.0364:0:5.5 0/1:132:2:0,2:39,90:0.0152:2,0:5:0:31:0:1:0:46:4:0.0153:0:7 -10 42400503 . A T 39 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55831;SOR=Inf;LSEQ=CCTTCCTTTAGACAGAGCAG;RSEQ=TTTGAGACACTCTTTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:17,35:0:2,0:13.5:1:31.3:1:1:0:41.2:104:1:0:4 0/1:129:3:2,1:38,88:0.0233:2,2:6:0:24.7:1:0.22689:4.57:30.3:2:0.0159:0:2.7 -10 42400504 . T G 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4049;SOR=0.51164;LSEQ=CTTCCTTTAGACAGAGCAGA;RSEQ=TTGAGACACTCTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:0,3:16,31:0.06:2,0:21.3:1:33.7:1:0.54204:0:33.7:6:0.06:0:4.7 0/1:127:4:1,3:37,82:0.0315:2,2:28.3:1:32.8:1:1:1.35056:22.5:8:0.0317:0:5.5 -10 42400506 . T G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22521;SOR=0.54427;LSEQ=TCCTTTAGACAGAGCAGATT;RSEQ=GAGACACTCTTTGTGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:10:3,7:12,24:0.2174:2,2:14.9:1:32.4:1:1:1.1628:34.7:20:0.2174:0:4.7 0/1:107:14:5,9:27,64:0.1308:2,2:17:1:31.6:1:0.75648:1.31:44.6:28:0.1308:0:5.4 -10 42400509 . G A 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.7404;SOR=1.25433;LSEQ=TTTAGACAGAGCAGATTTGA;RSEQ=ACACTCTTTGTGGAATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:30:10,20:1,3:0.8824:2,2:10.4:1:31:1:1:1.48:39.9:60:0.8824:0:4.3 1/1:73:66:15,51:2,5:0.9041:2,2:9.6:1:30:1:0.66124:1.3539:41.3:132:0.9041:0:4.5 -10 42400512 . A T 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30287;SOR=Inf;LSEQ=AGACAGAGCAGATTTGAGAC;RSEQ=CTCTTTGTGGAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:9,23:0:2,0:10.7:1:30.7:1:1:0:39.5:31:1:0:4.3 0/1:68:4:1,3:14,49:0.0588:2,2:16.5:1:31.5:1:1:1.16:44.8:8:0.0597:0:4.5 -10 42400515 . C CTT 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.50314;SOR=0.62827;LSEQ=CAGAGCAGATTTGAGACACT;RSEQ=TTTGTGGAATTTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:0,5:0,2:0.2941:0,0:13.6:1:31.7:1:1:0:35.8:10:0.3571:0.1765:6.2 0/1:34:7:0,7:4,10:0.2059:2,0:14.4:1:30.5:1:0.25497:0:36.9:14:0.2258:0.0588:5.4 -10 42400517 . TTG GTTTT 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.31793;SOR=0.29965;LSEQ=AGAGCAGATTTGAGACACTC;RSEQ=TGGAATTTGCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:0,2:0.1765:0,2:14.3:1:31.2:1:1:0:41.7:6:0.2143:0.0588:5.3 0/1:34:2:0,2:4,10:0.0588:2,0:21.5:1:31.7:1:1:0:20:4:0.0645:0:5 -10 42400532 . GTGGAGATTGA CTGCAGATTTC 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08846;SOR=Inf;LSEQ=ACTCTTTGTGGAATTTGCAA;RSEQ=AAGCGCTTTGAGGCCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:12.3:1:32.6:1:1:0:36.4:14:1:0:6.3 0/1:9:4:1,3:2,3:0.4444:2,2:12:1:30.4:1:1:1.8525:28.3:8:0.4444:0.4444:5.8 -10 42400533 . T G 51 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69183;LSEQ=CTCTTTGTGGAATTTGCAAG;RSEQ=GGAGATTGAAAGCGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:17.7:1:32.7:1:1:0:38.7:6:0.5:0:7 0/1:5:2:1,1:1,2:0.4:2,2:4.5:1:27.5:1:1:1.73:36.5:4:0.5:0:5 -10 42400541 . GA TC 65 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTTGCAAGTGGAGATT;RSEQ=AAGCGCTTTGAGGCCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:15.8:1:32.6:1:1:0:36.8:8:1:0:6.5 1/1:3:3:1,2:0,0:1:0,2:17.7:1:29.3:1:1:0:30:6:1:0:5.7 -10 42400547 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.18347;SOR=0;LSEQ=TGCAAGTGGAGATTGAAAGC;RSEQ=CTTTGAGGCCAAAGGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:7,5:0.1429:2,0:8.5:1:31.5:1:0.46154:0:33.5:4:0.1429:0:7 0/0:18:0:0,0:6,12:0:2,0:5.5:1:30.1:1:1:0:36.4:36:1:0:5.3 -10 42400552 . G T 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62827;SOR=2.81432;LSEQ=GTGGAGATTGAAAGCGCTTT;RSEQ=AGGCCAAAGGAAGAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:8,5:0.0714:2,0:37:0:30:0:0.42857:0:40:2:0.0714:0:6 0/1:22:4:2,2:7,11:0.1818:2,2:13.3:1:28.5:1:1:1.54:38.5:8:0.1905:0:4.5 -10 42400555 . G A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08881;SOR=0.23129;LSEQ=GAGATTGAAAGCGCTTTGAG;RSEQ=CCAAAGGAAGAAAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:9,4:0,2:0.8667:0,2:9.8:1:30.7:1:0.14286:0:39.1:26:0.8667:0:4.8 1/0:27:16:7,9:7,4:0.5926:2,2:9.1:1:28.5:1:0.44007:2.18206:38.7:32:0.5926:0:5.8 -10 42400558 . A T 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5415;SOR=Inf;LSEQ=ATTGAAAGCGCTTTGAGGCC;RSEQ=AAGGAAGAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:13.3:1:31.3:1:1:0:38.1:32:1:0:5 0/1:30:3:2,1:14,13:0.1:2,2:12.7:1:32:1:1:1.82:35.7:6:0.1034:0:7 -10 42400560 . A C 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28471;SOR=Inf;LSEQ=TGAAAGCGCTTTGAGGCCAA;RSEQ=GGAAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:16.1:1:31.5:1:1:0:37.9:30:1:0:4.9 0/1:30:4:2,2:13,12:0.1333:2,2:14.8:1:31.5:1:1:1.08033:27.5:8:0.1379:0:6.3 -10 42400561 . G T 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28329;SOR=0.31506;LSEQ=GAAAGCGCTTTGAGGCCAAA;RSEQ=GAAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:8,5:1,0:0.8667:0,2:17.4:1:31.8:1:1:0:37.9:26:0.8667:0:4.8 1/0:30:20:11,9:5,5:0.6667:2,2:13.9:1:29:1:1:1.21:39.2:19:0.6552:0:5 -10 42400563 . A T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53412;SOR=0;LSEQ=AAGCGCTTTGAGGCCAAAGG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:12,6:0,0:1:0,2:16.2:1:30:1:1:0:38.3:36:1:0:4.8 1/1:33:31:18,13:0,0:0.9394:0,2:15.3:1:29.1:1:1:0:39.7:62:0.9394:0:5.3 -10 42400569 . A C 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55024;SOR=Inf;LSEQ=TTTGAGGCCAAAGGAAGAAA;RSEQ=GGAAATATCTTCGTATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:20,16:0:2,0:13.4:1:30.8:1:1:0:38.5:72:0.973:0:3.6 0/1:79:3:1,2:36,39:0.038:2,2:5:1:30.3:1:1:1.83225:54:6:0.038:0:4.3 -10 42400570 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10581;SOR=0;LSEQ=TTGAGGCCAAAGGAAGAAAA;RSEQ=GAAATATCTTCGTATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:22,17:0.0488:2,2:7.5:1:29.5:1:1:1.28591:42:4:0.0488:0:4.5 0/0:84:0:0,0:40,44:0:2,0:11.5:1:30.7:1:1:0:42.6:168:1:0:3.8 -10 42400575 . T C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70824;SOR=0.80711;LSEQ=GCCAAAGGAAGAAAAGGAAA;RSEQ=ATCTTCGTATAAAAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:26:15,11:9,7:0.619:2,2:20.2:1:32.6:1:1:1.06:43.8:52:0.619:0:4.1 1/0:97:55:25,30:19,22:0.567:2,2:16:1:31.1:1:1:1.036:46.7:110:0.567:0:4.6 -10 42400579 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGAAGAAAAGGAAATATC;RSEQ=TCGTATAAAAACTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:0:2,0:20.6:1:30.8:1:1:0:40.6:86:1:0:3.6 0/1:110:2:1,1:50,58:0.0182:2,2:16:0:33:1:1:1.16:25:4:0.0183:0:2.5 -10 42400580 . T G 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57628;SOR=Inf;LSEQ=AGGAAGAAAAGGAAATATCT;RSEQ=CGTATAAAAACTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,19:0:2,0:21.5:1:30.5:1:1:0:40.8:84:0.9767:0:3.7 0/1:112:4:2,2:49,58:0.0357:2,2:21.5:1:31.5:1:1:1.18:48.3:8:0.036:0:6 -10 42400582 . G T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:26,20:0:2,0:21.6:1:31.1:1:1:0:41.4:92:1:0:3.7 0/1:118:2:1,1:56,60:0.0169:2,2:32:1:32.5:1:1:1.07:30:4:0.0169:0:6.5 -10 42400584 . A G 33 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75542;LSEQ=AGAAAAGGAAATATCTTCGT;RSEQ=TAAAAACTAGACAGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:1,0:26,20:0.0213:2,0:20:0:30:0:1:0:34:2:0.0213:0:2 0/1:124:2:2,0:60,62:0.0161:2,0:5.5:1:33:1:0.49593:0:44.5:4:0.0161:0:4 -10 42400586 . A G 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07325;SOR=0;LSEQ=AAAAGGAAATATCTTCGTAT;RSEQ=AAAACTAGACAGAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:27,19:0.0417:2,2:22:0:32.5:1:1:1.41046:32.5:4:0.0417:0:4 0/0:128:0:0,0:64,64:0:2,0:20.3:1:29.1:1:1:0:44.8:127:1:0:3.9 -10 42400588 . A C 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.57462;SOR=Inf;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACTAGACAGAATCATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:28,20:0:2,0:24.6:1:30.1:1:1:0:41.4:47:1:0:3.7 0/1:133:4:3,1:62,67:0.0301:2,2:33.5:1:32.8:1:0.35815:3.22:36:8:0.0301:0:6.5 -10 42400590 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAATATCTTCGTATAAAA;RSEQ=CTAGACAGAATCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,21:0:2,0:25.2:1:30.1:1:1:0:41.8:98:1:0:3.7 0/1:138:2:1,1:67,69:0.0145:2,2:24:1:31.5:1:1:1.03:30:4:0.0147:0:6.5 -10 42400591 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:28,22:0:2,0:24.9:1:32.2:1:1:0:41.9:100:0.9804:0:3.8 0/1:143:2:1,1:70,70:0.014:2,2:14:0:33.5:1:1:1:47:4:0.014:0:7.5 -10 42400592 . T A 88 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.45008;SOR=2.94406;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=AGACAGAATCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:28,22:0.0192:2,0:29:0:32:0:1:0:50:2:0.0192:0:2 0/1:146:8:3,5:68,69:0.0548:2,2:16.3:1:29.6:1:0.71922:1.63699:46.1:16:0.0548:0:4.5 -10 42400594 . G C 121 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56869;SOR=1.65334;LSEQ=ATATCTTCGTATAAAAACTA;RSEQ=ACAGAATCATTCTCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:1,2:29,20:0.0577:2,2:31:0:32:1:0.56697:2.84084:36:6:0.0577:0:3.3 0/1:152:14:7,7:69,68:0.0921:2,2:24.8:1:32:1:1:1.01461:44.1:28:0.0921:0:4.5 -10 42400597 . A G 77 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.34122;SOR=Inf;LSEQ=TCTTCGTATAAAAACTAGAC;RSEQ=GAATCATTCTCAGAAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:30,22:0:2,0:26.6:1:30.4:1:1:0:42:51:0.9808:0:3.8 0/1:155:6:2,4:77,72:0.0387:2,2:27.8:1:29.8:1:0.43645:2.12875:38.3:12:0.0387:0:3.7 -10 42400599 . A T 77 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69607;SOR=0.67243;LSEQ=TTCGTATAAAAACTAGACAG;RSEQ=ATCATTCTCAGAAACTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:2,1:27,23:0.0556:2,2:28:1:27.7:1:1:1.69:38:6:0.0566:0:4 0/1:158:6:4,2:74,75:0.038:2,2:24.7:1:29.8:1:0.68133:2.02:34.5:12:0.0382:0:3.2 -10 42400600 . A G 80 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68165;SOR=2.07258;LSEQ=TCGTATAAAAACTAGACAGA;RSEQ=TCATTCTCAGAAACTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:1:0,1:30,23:0.0185:2,0:2:0:28:0:0.44444:0:20:2:0.0192:0:4 0/1:159:6:2,4:79,74:0.0377:2,2:30.8:1:31.2:1:0.43687:2.1253:38.3:12:0.038:0:3.7 -10 42400601 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTATAAAAACTAGACAGAA;RSEQ=CATTCTCAGAAACTACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:31,24:0:2,0:27.4:1:30.4:1:1:0:41.8:110:1:0:3.8 0/1:164:2:1,1:82,80:0.0122:2,2:34:1:32:1:1:1.02485:60:4:0.0123:0:6 -10 42400602 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTATAAAAACTAGACAGAAT;RSEQ=ATTCTCAGAAACTACTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:31,24:0:2,0:27.6:1:31.4:1:1:0:41.8:54:1:0:3.8 0/1:165:2:1,1:82,80:0.0121:2,2:36:1:29:1:1:1.02485:53.5:4:0.0122:0:5.5 -10 42400603 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0656;SOR=0;LSEQ=TATAAAAACTAGACAGAATC;RSEQ=TTCTCAGAAACTACTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:31,25:0.0345:2,2:20.5:1:31:1:1:1.23537:48:4:0.0357:0:3 0/0:167:0:0,0:84,82:0:2,0:27.8:1:30.4:1:1:0:44.9:332:0.994:0:4.2 -10 42400604 . T C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAAAAACTAGACAGAATCA;RSEQ=TCTCAGAAACTACTTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:32,27:0:2,0:26.1:1:30.3:1:1:0:42.3:118:1:0:3.9 0/1:168:2:1,1:84,82:0.0119:2,2:41:0:31.5:1:1:1.02425:36:4:0.012:0:4 -10 42400607 . T A 109 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52337;SOR=1.96428;LSEQ=AAAACTAGACAGAATCATTC;RSEQ=CAGAAACTACTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:2,0:30,27:0.0333:2,0:29.5:1:30:1:0.49503:0:30.5:4:0.0345:0:6.5 0/1:173:11:6,5:82,78:0.0636:2,2:28.3:1:31.7:1:1:1.14:36.3:22:0.0636:0:6.8 -10 42400608 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACTAGACAGAATCATTCT;RSEQ=AGAAACTACTTTGTGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:32,28:0:2,0:25.9:1:31.5:1:1:0:42.4:120:1:0:3.9 0/1:177:2:1,1:91,83:0.0113:2,2:15:0:33.5:1:1:1.09581:59.5:4:0.0114:0:4 -10 42400609 . A C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01845;LSEQ=AACTAGACAGAATCATTCTC;RSEQ=GAAACTACTTTGTGATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:2,3:30,25:0.0833:2,2:28.6:1:30.4:1:0.65671:1.78243:43:10:0.0847:0:3.4 0/1:177:15:9,6:83,79:0.0847:2,2:33:1:30.7:1:0.59555:1.42:52.9:30:0.0857:0:4.3 -10 42400610 . GA AC 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.75242;SOR=0.81433;LSEQ=ACTAGACAGAATCATTCTCA;RSEQ=AACTACTTTGTGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:4:1,3:29,26:0.0678:2,2:25.3:1:30.5:1:0.35326:3.28286:37:8:0.0702:0.0169:3 0/1:179:10:5,5:86,80:0.0559:2,2:35.1:1:30.9:1:1:1.07453:44.6:20:0.0562:0:3.2 -10 42400611 . A G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25017;SOR=0.31649;LSEQ=CTAGACAGAATCATTCTCAG;RSEQ=AACTACTTTGTGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:28,24:0.0345:2,2:34:1:33.5:1:1:1.16333:32.5:4:0.0385:0:4 0/1:180:2:0,2:89,78:0.0111:2,0:25.5:1:33:0:0.2226:0:41:4:0.0118:0:5 -10 42400613 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.26083;SOR=0.32771;LSEQ=AGACAGAATCATTCTCAGAA;RSEQ=CTACTTTGTGATGTGTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:30,28:0.0333:2,2:37:0:32.5:1:1:1.07017:42:4:0.0333:0:4.5 0/1:180:2:1,1:93,85:0.0111:2,2:37:1:32.5:1:1:1.09357:38:4:0.0111:0:3.5 -10 42400615 . TA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06173;SOR=0;LSEQ=ACAGAATCATTCTCAGAAAC;RSEQ=CTTTGTGATGTGTGCGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:31,26:0.0328:2,2:27:1:30.8:1:1:1.18874:47:4:0.0328:0.0164:3.5 0/0:183:0:0,0:92,84:0:2,0:29.9:1:28.9:1:1:0:45.1:57.667:0.9611:0:4.1 -10 42400616 . A T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26084;SOR=0.32781;LSEQ=CAGAATCATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:31,26:0.0328:2,2:47:0:31:1:1:1.18874:60:4:0.0328:0:4 0/1:183:2:1,1:92,84:0.0109:2,2:14.5:1:31.5:1:1:1.09467:39:4:0.0111:0:7.5 -10 42400617 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAATCATTCTCAGAAACTA;RSEQ=TTTGTGATGTGTGCGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:33,29:0:2,0:25:1:32:1:1:0:43.4:124:0.9841:0:4 0/1:184:2:1,1:94,88:0.0109:2,2:20:1:33.5:1:1:1.06777:32:4:0.011:0:5.5 -10 42400620 . T G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06572;SOR=0;LSEQ=ATCATTCTCAGAAACTACTT;RSEQ=GTGATGTGTGCGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:33,31:0.0303:2,2:23:1:30.5:1:1:1.06354:54.5:4:0.0308:0:6 0/0:190:0:0,0:96,94:0:2,0:29.2:1:30.2:1:1:0:45:189:1:0:4.2 -10 42400621 . G C 74 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.78038;LSEQ=TCATTCTCAGAAACTACTTT;RSEQ=TGATGTGTGCGTTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:1:0,1:35,31:0.0149:2,0:3:0:29:0:0.47761:0:46:2:0.0149:0:8 0/1:190:5:3,2:92,92:0.0263:2,2:29:1:32:1:1:1.50:32.8:10:0.0265:0:5.2 -10 42400622 . TG GT 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CATTCTCAGAAACTACTTTG;RSEQ=ATGTGTGCGTTCAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:35,32:0:2,0:23.2:1:29.7:1:1:0:43.5:66:1:0:4.2 0/1:191:2:2,0:93,94:0.0105:2,0:32:1:32.3:1:0.49735:0:40:4:0.0105:0:6.5 -10 42400624 . A C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTCAGAAACTACTTTGTG;RSEQ=TGTGTGCGTTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:35,34:0:2,0:22.5:1:30:1:1:0:43.8:33.5:1:0:4.3 0/1:195:2:2,0:96,95:0.0103:2,0:30.5:1:33.5:1:0.49752:0:33:4:0.0103:0:5 -10 42400625 . T C 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.5719;SOR=Inf;LSEQ=TCTCAGAAACTACTTTGTGA;RSEQ=GTGTGCGTTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:34,34:0:2,0:22.9:1:30.6:1:1:0:44:136:1:0:4.3 0/1:197:3:3,0:97,96:0.0152:2,0:39:1:32.7:1:0.24647:0:34.7:6:0.0152:0:6 -10 42400626 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27364;SOR=0.34177;LSEQ=CTCAGAAACTACTTTGTGAT;RSEQ=TGTGCGTTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:33,34:0.029:2,2:22.5:1:31:1:1:1.03:32.5:4:0.0294:0:4 0/1:199:2:0,2:101,96:0.0101:2,0:25.5:1:31.5:1:0.24126:0:41:4:0.0102:0:5 -10 42400628 . G T 78 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.6812;SOR=2.11827;LSEQ=CAGAAACTACTTTGTGATGT;RSEQ=TGCGTTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:1:0,1:36,33:0.0143:2,0:30:0:27:0:0.48571:0:20:2:0.0145:0:4 0/1:201:6:2,4:99,95:0.0299:2,2:25.8:1:30.3:1:0.44247:2.07681:38.3:12:0.0303:0:3.7 -10 42400631 . C T 115 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36768;SOR=2.37614;LSEQ=AAACTACTTTGTGATGTGTG;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:2,0:34,36:0.0278:2,0:29.5:1:29:1:0.49296:0:30.5:4:0.0282:0:6.5 0/1:204:13:7,6:94,96:0.0637:2,2:24.9:1:31.3:1:0.78297:1.19:38.2:26:0.0637:0:7 -10 42400632 . G A 50 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03891;LSEQ=AACTACTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:1,0:35,36:0.0139:2,0:33:0:32:0:1:0:25:2:0.0141:0:5 0/1:208:3:2,1:100,102:0.0144:2,2:21:1:31.7:1:0.62131:2.03:51.7:6:0.0145:0:5.3 -10 42400637 . A G 64 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.57511;SOR=Inf;LSEQ=CTTTGTGATGTGTGCGTTCA;RSEQ=CTCACAGAGTTTAAGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:34,34:0:2,0:23.7:1:29.7:1:1:0:44.1:136:1:0:4.8 0/1:209:4:1,3:103,102:0.0191:2,2:24:1:32:1:0.62139:3.01488:30.5:8:0.0191:0:6.3 -10 42400638 . C T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4603;SOR=1.63101;LSEQ=TTTGTGATGTGTGCGTTCAA;RSEQ=TCACAGAGTTTAAGCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:4:3,1:31,34:0.058:2,2:17.5:1:30.8:1:0.35648:3.24:29.8:8:0.0588:0:3.3 0/1:208:19:8,11:93,93:0.0913:2,2:12.7:1:30.1:1:0.63185:1.37287:37.5:38:0.0913:0:3.7 -10 42400641 . A T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGATGTGTGCGTTCAACTC;RSEQ=CAGAGTTTAAGCTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:33,31:0:2,0:25.4:1:29.3:1:1:0:44.5:31:1:0:5 0/1:200:3:2,1:98,99:0.015:2,2:35.3:1:30:1:1:2.01:38:6:0.015:0:7 -10 42400642 . CA AG 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03814;SOR=0.51614;LSEQ=TGATGTGTGCGTTCAACTCA;RSEQ=GAGTTTAAGCTTTCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:49:25,24:5,7:0.7538:2,2:25.8:1:30.7:1:0.74904:1.45:46.2:98:0.7656:0.0615:4.2 1/0:201:123:57,66:37,33:0.6119:2,2:25.2:1:30.5:1:0.45424:1.29647:48.3:122:0.6193:0.0348:3.8 -10 42400643 . A G 123 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08234;SOR=5.83654;LSEQ=GATGTGTGCGTTCAACTCAC;RSEQ=GAGTTTAAGCTTTCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:5,7:0.0164:2,0:40:0:33:0:1:0:52:2:0.0769:0:5 0/1:191:17:12,5:26,27:0.089:2,2:33.5:1:30.3:1:0.1645:2.46:40.6:34:0.2361:0:5.4 -10 42400645 . A G 70 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.33417;SOR=Inf;LSEQ=TGTGTGCGTTCAACTCACAG;RSEQ=GTTTAAGCTTTCTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:30,34:0:2,0:25.3:1:30.3:1:1:0:44.4:63:0.9844:0:4.4 0/1:192:5:2,3:89,94:0.026:2,2:37.4:1:30.2:1:1:1.4176:42.2:10:0.0265:0:4.8 -10 42400647 . T G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGCGTTCAACTCACAGAG;RSEQ=TTAAGCTTTCTTTTCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:30,37:0:2,0:24.6:1:29.4:1:1:0:43.9:32.5:1:0:4.5 0/1:188:2:1,1:90,96:0.0106:2,2:26.5:1:30:1:1:1.07:47:4:0.0107:0:7.5 -10 42400648 . T A 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.0664;LSEQ=GTGCGTTCAACTCACAGAGT;RSEQ=TAAGCTTTCTTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:27,37:0.0303:2,0:21.5:1:30:0:0.18928:0:30.5:4:0.0313:0:5.5 0/1:186:6:2,4:86,93:0.0323:2,2:16.2:1:30.3:1:0.68462:1.84355:33.8:12:0.0326:0:4.8 -10 42400651 . AG CC 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTTCAACTCACAGAGTTTA;RSEQ=CTTTCTTTTCATAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:27,37:0:2,0:26.1:1:30.3:1:1:0:43.6:63:1:0:4.5 0/1:181:2:1,1:84,95:0.011:2,2:31.5:1:30.3:1:1:1.13:40:4:0.0112:0:3.5 -10 42400652 . G C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47533;SOR=1.38475;LSEQ=GTTCAACTCACAGAGTTTAA;RSEQ=CTTTCTTTTCATAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:11:3,8:24,28:0.1719:2,2:19.6:1:31.5:1:0.32552:2.25738:30.5:22:0.1719:0:5.6 0/1:179:40:17,23:61,67:0.2235:2,2:25.8:1:30.2:1:0.59106:1.23026:36.4:80:0.2273:0:5.2 -10 42400657 . C CT 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCACAGAGTTTAAGCTTT;RSEQ=TTTTCATAGAGCAGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:26,43:0:2,0:24.4:1:31.2:1:1:0:42.9:33.5:1:0:4.6 0/1:180:2:1,1:75,101:0.0111:2,2:38.5:1:31.5:1:1:1.34:57:4:0.0112:0:6 -10 42400662 . C G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.601;SOR=1.49294;LSEQ=CAGAGTTTAAGCTTTCTTTT;RSEQ=ATAGAGCAGTTTGGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:4:2,2:23,40:0.0597:2,2:18.5:1:31.8:1:0.62556:1.72:31.5:8:0.0597:0:6.8 0/1:173:15:3,12:70,88:0.0867:2,2:21.4:1:30.1:1:0.09954:3.16297:35.3:30:0.0872:0:6.5 -10 42400663 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGTTTAAGCTTTCTTTTC;RSEQ=TAGAGCAGTTTGGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:24,40:0:2,0:25.7:1:29.7:1:1:0:43:20.333:0.9839:0:4.8 0/1:172:2:1,1:71,99:0.0116:2,2:35.5:1:31.5:1:1:1.39:45.5:4:0.0116:0:5 -10 42400665 . A G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.2552;LSEQ=AGTTTAAGCTTTCTTTTCAT;RSEQ=GAGCAGTTTGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:4:2,2:20,36:0.0667:2,2:18.5:1:32:1:0.6194:1.78:31.5:8:0.0702:0:6.8 0/1:170:14:3,11:67,87:0.0824:2,2:22.7:1:29.4:1:0.15715:2.80819:35:28:0.0833:0:6.5 -10 42400666 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTAAGCTTTCTTTTCATA;RSEQ=AGCAGTTTGGAAACACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:21,39:0:2,0:28.3:1:31.2:1:1:0:42:59:1:0:5 0/1:171:2:1,1:68,98:0.0117:2,2:36:1:29.5:1:1:1.44:22:4:0.0118:0:6 -10 42400668 . GC TG 32 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70774;LSEQ=TTAAGCTTTCTTTTCATAGA;RSEQ=AGTTTGGAAACACTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:1:0,1:21,38:0.0167:2,0:17:0:26:0:1:0:25:2:0.0169:0:7 0/1:169:2:0,2:70,97:0.0118:2,0:20.5:1:32.5:0:0.51183:0:37.5:4:0.0119:0:6.5 -10 42400669 . C T 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01212;SOR=0.42228;LSEQ=TAAGCTTTCTTTTCATAGAG;RSEQ=AGTTTGGAAACACTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:46:19,27:1,11:0.7667:2,2:30.2:1:27.6:1:0.04219:7.53:45:14.333:0.7679:0:4.8 1/0:162:94:43,51:24,38:0.5802:2,2:25.3:1:27.7:1:0.41248:1.33:45.3:30.333:0.5796:0:4.3 -10 42400671 . G C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18956;SOR=0.19051;LSEQ=AGCTTTCTTTTCATAGAGCA;RSEQ=TTTGGAAACACTCTGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:0,2:19,37:0.0339:2,0:12.5:1:31:1:1:0:45.5:4:0.0345:0:7.5 0/0:152:1:0,1:64,87:0.0066:2,0:49:0:31:0:1:0:47:2:0.0066:0:6 -10 42400677 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTCATAGAGCAGTTTGG;RSEQ=AACACTCTGTTTGTAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:19,43:0:2,0:26.9:1:30:1:1:0:40.7:61:1:0:5.1 0/1:139:2:1,1:55,82:0.0144:2,2:42.5:1:28.5:1:1:1.49:57:4:0.0146:0:6 -10 42400678 . A G 32 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.90418;LSEQ=TTTTCATAGAGCAGTTTGGA;RSEQ=ACACTCTGTTTGTAAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:1:1,0:18,43:0.0161:2,0:4:0:29:0:0.30645:0:40:2:0.0169:0:6 0/1:137:2:0,2:55,80:0.0146:2,0:18.5:1:32:0:0.51589:0:34.5:4:0.0149:0:7.5 -10 42400680 . C A 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22303;SOR=0.21721;LSEQ=TTCATAGAGCAGTTTGGAAA;RSEQ=ACTCTGTTTGTAAAGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:18,41:0.0328:2,2:27.5:1:31:1:0.52951:2.24:56:4:0.0328:0:5 0/0:138:1:0,1:54,83:0.0072:2,0:15:0:32:0:1:0:31:2:0.0074:0:6 -10 42400682 . C G 48 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.3445;LSEQ=CATAGAGCAGTTTGGAAACA;RSEQ=TCTGTTTGTAAAGTCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:1:0,1:17,40:0.0172:2,0:30:0:28:0:1:0:25:2:0.0172:0:7 0/1:130:3:1,2:47,80:0.0231:2,2:11.3:1:30.3:1:1:1.17361:31.7:6:0.0233:0:6.3 -10 42400684 . C T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TAGAGCAGTTTGGAAACACT;RSEQ=TGTTTGTAAAGTCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:16,40:0:2,0:27.6:1:31.7:1:1:0:40.4:55:0.9821:0:5.2 0/1:124:2:1,1:41,79:0.0161:2,2:12:1:32:0:1:1.92:48.5:4:0.0161:0:7 -10 42400685 . T A 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.75538;SOR=1.40454;LSEQ=AGAGCAGTTTGGAAACACTC;RSEQ=GTTTGTAAAGTCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:3:0,3:15,38:0.0536:2,0:31:1:32:1:0.55628:0:33:6:0.0545:0:7.3 0/1:122:9:3,6:39,74:0.0738:2,2:20:1:29.6:1:1:1.05361:39.7:18:0.0744:0:6.6 -10 42400686 . G A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCAGTTTGGAAACACTCT;RSEQ=TTTGTAAAGTCTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:15,40:0:2,0:28.1:1:32.1:1:1:0:40.4:110:0.9821:0:5.3 0/1:120:2:1,1:40,78:0.0167:2,2:29.5:1:27.5:1:1:1.94:22:4:0.0168:0:6 -10 42400687 . T G 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.96514;LSEQ=AGCAGTTTGGAAACACTCTG;RSEQ=TTGTAAAGTCTGCAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:0,1:15,40:0.0179:2,0:39:0:34:0:1:0:34:2:0.0179:0:5 0/1:116:2:0,2:39,75:0.0172:2,0:14:1:31:1:0.54978:0:43.5:4:0.0175:0:4 -10 42400688 . T C 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10381;SOR=0.51722;LSEQ=GCAGTTTGGAAACACTCTGT;RSEQ=TGTAAAGTCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:45:15,30:0,11:0.8036:0,2:27.1:1:31:1:0.02608:0:41.8:44:0.8:0:5.3 1/0:115:78:27,51:11,23:0.6783:2,2:24.8:1:31.1:1:1:1.11:41.2:156:0.6783:0:5 -10 42400690 . G C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10976;SOR=0;LSEQ=AGTTTGGAAACACTCTGTTT;RSEQ=TAAAGTCTGCAAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:0,2:15,38:0.0364:2,0:25:1:31.5:1:1:0:43:4:0.0377:0:6 0/0:110:0:0,0:34,75:0:2,0:25.5:1:30.7:1:1:0:38.8:108:1:0:5.2 -10 42400691 . TAAA AAG 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTGGAAACACTCTGTTTG;RSEQ=GTCTGCAAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:13,37:0:2,0:29.4:1:28.5:1:1:0:39.8:49:1:0:5.4 0/1:105:2:1,1:30,71:0.019:2,2:19:1:28.4:1:0.51342:2.34:40:4:0.0194:0.0095:5 -10 42400692 . A G 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.77138;SOR=0.85255;LSEQ=TTTGGAAACACTCTGTTTGT;RSEQ=AAGTCTGCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:0,5:12,32:0.102:2,0:31.2:1:30.6:1:0.31545:0:33.6:10:0.102:0:6 0/1:102:9:2,7:29,63:0.0882:2,2:26.4:1:30.6:1:0.71778:1.60414:37.1:18:0.09:0:4.6 -10 42400694 . A T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.97152;LSEQ=TGGAAACACTCTGTTTGTAA;RSEQ=GTCTGCAAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:0,1:12,35:0.0204:2,0:29:0:32:0:1:0:26:2:0.0204:0:2 0/1:101:4:1,3:28,69:0.0396:2,2:36.5:1:31.5:1:1:1.2151:29:8:0.0412:0:3.5 -10 42400695 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAACACTCTGTTTGTAAA;RSEQ=TCTGCAAGTGGATATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:12,34:0:2,0:28.8:1:32.2:1:1:0:39.6:92:0.9583:0:5.5 0/1:102:2:1,1:27,71:0.0196:2,2:20.5:1:31:1:0.48364:2.60:45:4:0.0198:0:6 -10 42400697 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10074;SOR=0;LSEQ=AAACACTCTGTTTGTAAAGT;RSEQ=TGCAAGTGGATATTTGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:2,0:9,33:0.0426:2,0:21.5:1:31:1:0.05814:0:47:4:0.0435:0:6 0/0:100:0:0,0:27,73:0:2,0:25.7:1:31.4:1:1:0:37.8:99:1:0:5.2 -10 42400698 . T A 71 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66521;SOR=2.35678;LSEQ=AACACTCTGTTTGTAAAGTC;RSEQ=GCAAGTGGATATTTGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:0,1:11,33:0.0217:2,0:49:0:33:0:1:0:23:2:0.0227:0:8 0/1:100:5:1,4:26,69:0.05:2,2:39.4:1:30.8:1:1:1.50167:40.4:10:0.05:0:6.6 -10 42400703 . G C 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71149;SOR=0.77803;LSEQ=TCTGTTTGTAAAGTCTGCAA;RSEQ=TGGATATTTGGACCTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:0,3:10,31:0.0682:2,0:44.3:1:33.3:1:1:0:33:6:0.0682:0:7.3 0/1:93:5:1,4:23,65:0.0538:2,2:38.8:1:32.6:1:1:1.41047:40.4:10:0.0549:0:6.6 -10 42400704 . TG CA 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54602;SOR=0.7505;LSEQ=CTGTTTGTAAAGTCTGCAAG;RSEQ=GATATTTGGACCTCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:32:10,22:0,9:0.7442:0,2:26.7:1:31.5:1:0.08303:0:39.8:64:0.7805:0:4.8 1/0:89:61:15,46:4,22:0.6854:2,2:23.9:1:31.1:1:0.40765:1.78:37.1:122:0.6854:0.0449:4.5 -10 42400708 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTAAAGTCTGCAAGTGGA;RSEQ=ATTTGGACCTCTTTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:10,31:0:2,0:26.8:1:29:1:1:0:37.9:82:1:0:4.9 0/1:84:2:1,1:15,67:0.0238:2,2:11.5:1:29.5:1:0.34653:4.36:57:4:0.0238:0:6 -10 42400712 . TG T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18075;SOR=0.24986;LSEQ=AAAGTCTGCAAGTGGATATT;RSEQ=GACCTCTTTGAGGCCTTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:4:1,3:9,26:0.0976:2,2:26.8:1:31.9:1:1:1.03743:32.5:8:0.0976:0.0244:5.8 0/1:77:2:0,2:14,54:0.026:2,0:26.5:1:33:0:1:0:43.5:4:0.026:0:5 -10 42400713 . GG AA 79 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71208;SOR=1.64145;LSEQ=AAGTCTGCAAGTGGATATTT;RSEQ=ACCTCTTTGAGGCCTTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:9,26:0.0488:2,0:30:1:30.3:1:1:0:27:4:0.0488:0:4.5 0/1:77:6:0,6:14,54:0.0779:2,0:32.8:1:30.8:1:0.58726:0:34:12:0.0779:0:4.8 -10 42400716 . CC TG 74 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66165;SOR=2.66642;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=TCTTTGAGGCCTTCGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:1:0,1:7,29:0.027:2,0:30:0:33:0:1:0:23:2:0.027:0:7 0/1:72:5:1,4:11,55:0.0694:2,2:26.4:1:32:1:1:1.25:40.4:10:0.0704:0:5.6 -10 42400717 . C G 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.7148;SOR=1.56309;LSEQ=CTGCAAGTGGATATTTGGAC;RSEQ=TCTTTGAGGCCTTCGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:6,25:0.0556:2,0:27:1:32:1:1:0:27:4:0.0571:0:4.5 0/1:71:6:0,6:11,49:0.0845:2,0:29.8:1:31.8:1:0.57884:0:34:12:0.0923:0:4.8 -10 42400719 . C A 86 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4297;SOR=3.41211;LSEQ=GCAAGTGGATATTTGGACCT;RSEQ=TTTGAGGCCTTCGCTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:4,27:0.0313:2,0:28:0:33:0:1:0:23:2:0.0313:0:7 0/1:70:7:2,5:9,54:0.1:2,2:19.3:1:30.7:1:0.30197:2.36:42.9:14:0.1014:0:5.4 -10 42400720 . T A 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23439;SOR=0.22353;LSEQ=CAAGTGGATATTTGGACCTC;RSEQ=TTGAGGCCTTCGCTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:2,27:0.0645:2,2:13:1:32:0:0.1871:11.22:25:4:0.0645:0:6.5 0/1:67:1:0,1:11,55:0.0149:2,0:15:0:32:0:1:0:24:2:0.0152:0:4 -10 42400722 . T A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGGATATTTGGACCTCTT;RSEQ=GAGGCCTTCGCTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:3,28:0:2,0:20.1:1:30.7:1:1:0:35.8:62:1:0:5.1 0/1:64:2:1,1:9,53:0.0313:2,2:9:1:29:1:0.29018:5.64:35.5:4:0.0313:0:6.5 -10 42400724 . A G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.81133;SOR=0.86099;LSEQ=TGGATATTTGGACCTCTTTG;RSEQ=GGCCTTCGCTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:10:2,8:1,18:0.3448:1,2:14.6:1:31.2:1:0.26683:4.25:37.4:20:0.3448:0:5.2 0/1:61:19:2,17:6,36:0.3115:2,2:20.9:1:30.5:1:1:1.40901:33.4:38:0.3115:0:4.8 -10 42400733 . C T 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=2.0775;LSEQ=GGACCTCTTTGAGGCCTTCG;RSEQ=TGGAAACGGGATTTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:0,19:0,1:0.95:0,1:16.7:1:31.4:1:1:0:32.3:38:0.95:0:5.2 1/1:41:40:0,40:0,0:0.9756:0,1:17.2:1:30.5:1:1:0:33.9:39:0.975:0:4.7 -10 42401792 . G C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACAAGACCGAAGAATTCT;RSEQ=AGAAACTTCTTTGTGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:33:0:33:0:1:0:40:2:1:0:7 1/1:2:2:2,0:0,0:1:0,0:20:1:33:0:1:0:40:4:1:0:6.5 -10 42401804 . TGTG GATTGTT 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AAGAATTCTGAGAAACTTCT;RSEQ=ATGTGTGCATTCAAGTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:22:0:32.1:0:1:0:40:2:1:0:7 1/1:2:2:2,0:0,0:1:0,0:31:1:32.1:1:1:0:40:4:1:0:6.5 -10 42401822 . G C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTGATGTGTGCATTCAA;RSEQ=TCACAGAGTTGAACCTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:38.5:1:31.5:1:1:0:40:4:1:0:6.5 -10 42401845 . T G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGTTGAACCTTACTTT;RSEQ=GAAAGAGCAGTTTTCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:34:0:1:0:51.5:4:1:0:8 1/1:3:3:3,0:0,0:1:0,0:19.3:1:32:1:1:0:42.7:6:1:0:7 -10 42401861 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTGAAAGAGCAGTTTTC;RSEQ=AACACTCTTTTTGTAGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:37.5:1:32.5:1:1:0:51.5:4:1:0:8 1/1:2:2:2,0:0,0:1:0,0:24:1:29:1:1:0:44:4:1:0:7 -10 42401877 . GT AA 30 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAAACACTCTTTTTGTA;RSEQ=ACTTCCAAGTGCATACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:40:0:30.5:1:1:0:51.5:4:1:0:7 1/1:1:1:1,0:0,0:1:0,0:40:0:29:0:1:0:48:2:1:0:7 -10 42401880 . C G 32 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACACTCTTTTTGTAGTA;RSEQ=TTCCAAGTGCATACTTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:38:0:32.5:1:1:0:51.5:4:1:0:7 1/1:1:1:1,0:0,0:1:0,0:38:0:30:0:1:0:48:2:1:0:7 -10 42401890 . C A 29 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTAGTACTTCCAAGTG;RSEQ=ATACTTAAAGTGCTTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28:0:29.5:1:1:0:51.5:4:1:0:7 1/1:1:1:1,0:0,0:1:0,0:28:0:26:0:1:0:48:2:1:0:7 -10 42401897 . AA TG 30 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACTTCCAAGTGCATACTT;RSEQ=AGTGCTTTGAAGCCTACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:20:0:30.3:1:1:0:51.5:4:1:0:6 1/1:1:1:1,0:0,0:1:0,0:20:0:27:0:1:0:48:2:1:0:6 -10 42401949 . G C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCTTCATGTAAAAACTA;RSEQ=ACAGGATCATTCTCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:27:1:32.5:1:1:0:36.5:4:1:0:8 -10 42401951 . C A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTCATGTAAAAACTAGA;RSEQ=AGGATCATTCTCAGAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:29:1:30.5:1:1:0:36.5:4:1:0:8 -10 42401954 . G A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATGTAAAAACTAGACAG;RSEQ=ATCATTCTCAGAAACCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:32:1:29.5:1:1:0:36.5:4:1:0:8 -10 42401961 . CT TG 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACTAGACAGGATCATT;RSEQ=CAGAAACCACGTTGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:4,1:0.2857:2,2:6:0:32.5:1:1:3.1622:58:4:0.2857:0:6.5 -10 42401962 . T G 67 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAACTAGACAGGATCATTC;RSEQ=CAGAAACCACGTTGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:5:4,1:0,0:0.7143:0,2:20.8:1:29.2:1:1:0:50.6:10:1:0:7.6 -10 42401983 . G C 114 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAACCACGTTGTGATCT;RSEQ=TGCGTTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:12:12:7,5:0,0:1:0,2:24.8:1:31.8:1:1:0:52.1:24:1:0:7.2 -10 42401987 . G A 101 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCACGTTGTGATCTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:12:11:7,4:0,0:0.9167:0,2:27:1:29.3:1:1:0:51.4:10:0.9091:0:7.1 -10 42402004 . T C 93 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGCGTTCAACTCACAGAGTT;RSEQ=AACCTTTCTTTCCATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:14:0:28:0:1:0:40:2:0.5:0:6 1/0:18:9:3,6:0,0:0.5:0,2:25:1:29.6:1:1:0:46.4:8:0.5:0:6.4 -10 42402015 . T C 127 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGAGTTTAACCTTTCTT;RSEQ=CCATAGAGCAGTTATGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26.5:1:30.5:1:1:0:40:4:1:0:6.5 1/1:17:17:9,8:0,0:1:0,2:26.9:1:31.1:1:1:0:49.1:34:1:0:6.8 -10 42402017 . C T 117 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTTTAACCTTTCTTTC;RSEQ=ATAGAGCAGTTATGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28.5:1:27.5:1:1:0:40:4:1:0:6.5 1/1:16:16:8,8:0,0:1:0,2:28.4:1:29.4:1:1:0:49.1:32:1:0:6.8 -10 42402031 . G T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTTCCATAGAGCAGTTAT;RSEQ=AAACACTCTCTTTGTAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:42.5:1:31.5:1:1:0:40:4:1:0:6.5 0/1:14:2:1,1:6,6:0.1429:2,2:43.5:1:27:1:1:1:35:4:0.1429:0:7 -10 42402037 . C G 107 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATAGAGCAGTTATGAAACA;RSEQ=TCTCTTTGTAGTATTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:38:0:32.5:1:1:0:40:4:1:0:6.5 1/1:11:11:5,6:0,0:1:0,2:30.7:1:31.1:1:1:0:47.4:22:1:0:7.1 -10 42402049 . T A 98 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.06593;SOR=Inf;LSEQ=ATGAAACACTCTCTTTGTAG;RSEQ=ATTTGCAATGGTGTATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:26:0:31.5:1:1:0:40:4:0.5:0:6.5 1/1:10:10:5,5:0,0:1:0,2:20.9:1:29.6:1:1:0:46.1:20:1:0:7.1 -10 42402058 . T G 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2028;SOR=6.5151;LSEQ=TCTCTTTGTAGTATTTGCAA;RSEQ=GGTGTATTTAGAGGGCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:17:0:32.5:1:1:0:40:4:0.5:0:6.5 1/1:9:8:3,5:1,0:0.8889:0,2:13.8:1:30.9:1:0.44444:0:44.8:16:1:0:7 -10 42527227 . A C 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCAAAAGCGCTTGAAATCT;RSEQ=CACTTGAAATTCCACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:7:1:32:1:1:0:36.7:6:1:0:4.3 -10 42527233 . G GC 94 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCTTGAAATCTACACTT;RSEQ=AAATTCCACAAAAAGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:8:8:4,4:0,0:1:0,2:7.8:1:31.6:1:1:0:41.3:16:1:0.625:3.9 -10 42527255 . TCAAA CAAC 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTCCACAAAAAGAGAGTT;RSEQ=TCTGCTCTATCTAAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7:0:26:0:1:0:47:4:1:0:6 0/1:17:2:1,1:8,7:0.1176:2,2:19.5:1:29:1:1:1.13389:60:4:0.1176:0:3.5 -10 42527259 . A C 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53767;SOR=Inf;LSEQ=CCACAAAAAGAGAGTTTCAA;RSEQ=TCTGCTCTATCTAAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:7.3:1:29.5:1:1:0:48.5:8:1:0:4.8 0/1:16:4:2,2:6,6:0.25:2,2:14.8:1:32:1:1:1:54.8:8:0.2667:0:5 -10 42527266 . C G 129 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGAGAGTTTCAAATCTGCT;RSEQ=TATCTAAAGGAAGGTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:14.3:1:32.5:1:1:0:48.5:8:1:0:4.8 1/1:18:18:9,9:0,0:1:0,2:29.3:1:31:1:1:0:47.2:17:1:0:4.4 -10 42527268 . A T 124 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTTTCAAATCTGCTCT;RSEQ=TCTAAAGGAAGGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:16.3:1:30.8:1:1:0:48.5:8:1:0:4.8 1/1:18:18:9,9:0,0:1:0,2:30.6:1:29.8:1:1:0:47.2:36:1:0:4.4 -10 42527279 . G A 133 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCTCTATCTAAAGGAA;RSEQ=GTTCAACTCTGAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:27.3:1:30.8:1:1:0:48.5:8:1:0:4.8 1/1:20:20:10,10:0,0:1:0,2:26.8:1:30.8:1:1:0:47.5:40:1:0:4.1 -10 42527307 . AACACAAAAAAA CAGAAAAAGCAG 120 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.48872;SOR=2.37094;LSEQ=TCTGAGAGTTGAATACACAC;RSEQ=TTACTGAGAATTCTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:24.7:1:30.3:1:1:0:49:6:0.75:0.5:4 1/1:17:15:7,8:1,1:0.8824:2,2:21.8:1:30.8:1:1:1.13389:48.1:30:0.8824:0.7059:3.9 -10 42527329 . T G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAAAAAATTACTGAGAA;RSEQ=TCTTCTGTCTAGCATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:0:30.5:1:1:0:47:4:1:0:6 1/1:3:3:1,2:0,0:1:0,2:15.3:1:30.3:1:1:0:35.7:6:1:0:6.7 -10 42527396 . GA TG 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAGGAGGTCCAAATATC;RSEQ=CTTGCAGACTTTACAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:33:1:1:0:28:4:1:0:3.5 -10 42527413 . A G 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGACTTGCAGACTTTACA;RSEQ=ACAGAGTGTTTCCAAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:33.5:1:1:0:28:4:1:0:3.5 -10 42527434 . T G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGTGTTTCCAAACTAC;RSEQ=CTATGAAAAGAAAGGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:5.5:1:30:1:1:1:28:4:0.5:0:3.5 -10 42527449 . G C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTACTCTATGAAAAGAAAG;RSEQ=TTAAACTCTGTGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35:0:33.5:1:1:0:49.5:4:1:0:3.5 -10 42527458 . TG CT 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAAAAGAAAGGTTAAACTC;RSEQ=TGAGTTGAATGCACACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:31.8:1:1:0:49.5:4:1:0:2.5 -10 42527934 . A C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCACAAAAACAGTGTTTC;RSEQ=AATCTGCTCTGACTAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:9:0:31:1:1:0:24.5:4:1:0:5 -10 42527944 . T C 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTGTTTCAAATCTGCTC;RSEQ=GACTAAAGGAAGTTTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:19:0:30.5:1:1:0:24.5:4:1:0:5 -10 42527946 . A C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGTTTCAAATCTGCTCTG;RSEQ=CTAAAGGAAGTTTCAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:21:0:32.5:1:1:0:24.5:4:1:0:5 -10 42527957 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCTCTGACTAAAGGAAG;RSEQ=TTCAACTGTGTGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:0,0:0.6667:0,0:18.5:1:31.5:1:1:0:24.5:4:0.6667:0:5 -10 42527965 . G C 93 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GACTAAAGGAAGTTTCAACT;RSEQ=TGTGAGTTGAATACACGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:5:1:31.5:1:1:0:40.5:8:1:0:4.8 1/1:8:8:8,0:0,0:1:0,0:7.6:1:31:1:1:0:28.9:16:1:0:5.1 -10 42527979 . C G 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93848;LSEQ=TCAACTGTGTGAGTTGAATA;RSEQ=ACGCAACACAAAGAAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:12,2:0.25:2,2:13.4:1:32.4:1:1:1.46619:43.6:10:0.25:0:8 0/1:42:10:7,3:26,5:0.2381:2,2:12.6:1:32.1:1:0.37803:2.1799:41.7:20:0.2381:0:7.6 -10 42527981 . C G 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85922;LSEQ=AACTGTGTGAGTTGAATACA;RSEQ=GCAACACAAAGAAGTTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:10,1:0.25:2,2:15.4:1:31.8:1:1:2.34522:43.6:10:0.2632:0:8 0/1:45:10:7,3:28,6:0.2222:2,2:14.6:1:32.2:1:0.40242:1.96518:41.7:20:0.2222:0:7.6 -10 42527982 . G A 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21898;SOR=1.90868;LSEQ=ACTGTGTGAGTTGAATACAC;RSEQ=CAACACAAAGAAGTTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:12:10,2:6,2:0.48:2,2:13.3:1:31:1:1:1.62:37.9:24:0.5455:0:4 1/0:50:32:26,6:8,5:0.64:2,2:10.1:1:30.2:1:0.25102:2.64:39.8:64:0.6531:0:4.2 -10 42527985 . ACAC CACAG 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0.81215;LSEQ=GTGTGAGTTGAATACACGCA;RSEQ=AAAGAAGTTACTGAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:18,9:0.069:2,2:9:1:31:1:1:1.94942:47:4:0.0714:0.0345:6 0/1:53:3:2,1:36,11:0.0566:2,2:12.7:1:28.9:1:1:1.61856:42.3:6:0.0566:0:6 -10 42527987 . A C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.7987;LSEQ=GTGAGTTGAATACACGCAAC;RSEQ=CAAAGAAGTTACTGAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:2,0:22,11:0.0556:2,0:2:0:32:0:1:0:39.5:4:0.0571:0:3 0/1:67:3:2,1:48,13:0.0448:2,2:10:1:29.7:1:0.52957:1.82582:32.3:6:0.0484:0:4.7 -10 42527988 . C A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54996;SOR=Inf;LSEQ=TGAGTTGAATACACGCAACA;RSEQ=AAAGAAGTTACTGAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:24,12:0:2,0:13.6:1:32.1:1:1:0:38.4:72:1:0:4.7 0/1:72:3:2,1:50,15:0.0417:2,2:15.3:1:32:0:0.55902:1.6527:40:6:0.0441:0:3.7 -10 42527991 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GTTGAATACACGCAACACAA;RSEQ=GAAGTTACTGAGAATTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:30,14:0:2,0:14.5:1:29.7:1:1:0:38.9:13.667:1:0:4.5 0/1:104:2:2,0:72,30:0.0192:2,0:16:1:33.5:1:1:0:35.5:4:0.0196:0:5 -10 42527992 . G T 115 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.19019;LSEQ=TTGAATACACGCAACACAAA;RSEQ=AAGTTACTGAGAATTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:5,0:25,15:0.1111:2,0:12.6:1:31.6:1:0.15262:0:39.8:10:0.1111:0:5.8 0/1:108:14:13,1:64,30:0.1296:2,1:8.4:1:30.3:1:0.06349:6.02:37.4:28:0.1296:0:5.4 -10 42527994 . A C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.08587;SOR=0;LSEQ=GAATACACGCAACACAAAGA;RSEQ=GTTACTGAGAATTCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:31,16:0.0408:2,2:21.5:1:29.5:1:1:1.90979:41:4:0.0426:0:6 0/0:117:0:0,0:80,35:0:2,0:13.3:1:30.3:1:1:0:42.6:114:0.9828:0:4.4 -10 42527995 . G C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.601;SOR=0.73039;LSEQ=AATACACGCAACACAAAGAA;RSEQ=TTACTGAGAATTCTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:7:5,2:26,14:0.1429:2,2:25:1:33.1:1:1:1.34:43.3:14:0.1429:0:7.4 0/1:120:13:8,5:70,31:0.1083:2,2:24:1:29.5:1:0.54479:1.40687:42.1:5.5:0.0932:0:7.6 -10 42527996 . T C 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36107;SOR=0.40416;LSEQ=ATACACGCAACACAAAGAAG;RSEQ=TACTGAGAATTCTTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:2,1:29,17:0.06:2,2:14.3:1:31.7:1:1:1.17:36.7:6:0.0612:0:6.7 0/1:120:3:3,0:79,38:0.025:2,0:27:1:33.3:1:0.55064:0:27.7:6:0.0254:0:7 -10 42527997 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41597;SOR=0.53321;LSEQ=TACACGCAACACAAAGAAGT;RSEQ=ACTGAGAATTCTTCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:1,2:30,16:0.06:2,2:16.3:1:27:1:0.5457:3.64442:39:2:0.0408:0:5 0/1:122:4:2,2:80,38:0.0328:2,2:21:1:31:1:0.59669:2.09136:37.3:8:0.0328:0:5.5 -10 42527998 . A C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.55982;SOR=Inf;LSEQ=ACACGCAACACAAAGAAGTT;RSEQ=CTGAGAATTCTTCTGTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:33,19:0:2,0:18.9:1:28.5:1:1:0:38.8:25:1:0:4.6 0/1:132:3:2,1:83,43:0.0227:2,2:7.3:1:31:1:1:1.04:46.7:6:0.0231:0:4.3 -10 42528001 . G C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.61986;SOR=0.79784;LSEQ=CGCAACACAAAGAAGTTACT;RSEQ=AGAATTCTTCTGTCTAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:7:5,2:31,20:0.1207:2,2:31:1:32.1:1:0.6983:1.60:43.3:14:0.1207:0:7.4 0/1:142:14:8,6:81,47:0.0986:2,2:28.2:1:31.6:1:0.7725:1.29014:41.7:28:0.0993:0:7.5 -10 42528003 . G A 45 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02365;SOR=0;LSEQ=CAACACAAAGAAGTTACTGA;RSEQ=AATTCTTCTGTCTAGCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:1,2:35,22:0.0492:2,2:29:1:28.7:1:0.55815:3.11961:39.7:6:0.0492:0:3.7 0/0:149:0:0,0:93,56:0:2,0:18.4:1:32.1:1:1:0:41.9:298:1:0:4.5 -10 42528004 . A T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92837;LSEQ=AACACAAAGAAGTTACTGAG;RSEQ=ATTCTTCTGTCTAGCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:7:5,2:31,22:0.1148:2,2:33.9:1:30.3:1:0.6913:1.76:43.3:14:0.1207:0:7.4 0/1:149:16:10,6:83,50:0.1074:2,2:27.5:1:28.5:1:1:1.00:41.2:32:0.1081:0:7.5 -10 42528005 . A C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACAAAGAAGTTACTGAGA;RSEQ=TTCTTCTGTCTAGCATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:38,26:0:2,0:21.8:1:30:1:1:0:39.7:63:1:0:4.5 0/1:154:2:2,0:93,58:0.013:2,0:18.5:1:32.5:1:0.52614:0:40:4:0.0131:0:7 -10 42528010 . TC AT 59 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.57933;SOR=Inf;LSEQ=AAGAAGTTACTGAGAATTCT;RSEQ=TGTCTAGCATTATATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:38,30:0:2,0:24.8:1:30.2:1:1:0:39.4:136:1:0:4.5 0/1:173:4:3,1:97,70:0.0231:2,2:14:0:29.6:1:0.64231:2.16:27.3:8:0.0234:0:6.3 -10 42528011 . C T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22901;SOR=0.38544;LSEQ=AGAAGTTACTGAGAATTCTT;RSEQ=TGTCTAGCATTATATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:4:2,2:38,28:0.0571:2,2:23.5:1:30.3:1:1:1.35113:37:8:0.0571:0:6.3 0/1:176:4:3,1:97,71:0.0227:2,2:32.3:1:30.3:1:0.64065:2.19:26.5:8:0.0233:0:7.3 -10 42528013 . G T 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.69352;SOR=1.21845;LSEQ=AAGTTACTGAGAATTCTTCT;RSEQ=TCTAGCATTATATGAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:9:6,3:35,30:0.1216:2,2:30.2:1:30.4:1:0.72255:1.70:42.6:18:0.1216:0:7.6 0/1:180:26:16,10:85,67:0.1444:2,2:20.8:1:29.6:1:0.67149:1.26:40.2:25:0.1404:0:7.3 -10 42528015 . C G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.66624;SOR=1.27388;LSEQ=GTTACTGAGAATTCTTCTGT;RSEQ=TAGCATTATATGAAGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:7:5,2:36,32:0.0933:2,2:28.9:1:32.4:1:0.44561:2.20:39:14:0.0933:0:4.7 0/1:181:21:12,9:91,69:0.116:2,2:23.8:1:32.3:1:1:1.01:38.1:42:0.1167:0:4.8 -10 42528016 . T A 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48678;SOR=0.6149;LSEQ=TTACTGAGAATTCTTCTGTC;RSEQ=AGCATTATATGAAGAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:2,2:39,31:0.0526:2,2:28.5:1:30.5:1:1:1.25413:37:8:0.0541:0:6.3 0/1:182:6:5,1:89,72:0.033:2,2:33:1:29.3:1:0.23275:4.02:31:12:0.0333:0:7.2 -10 42528017 . A G 94 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11193;LSEQ=TACTGAGAATTCTTCTGTCT;RSEQ=GCATTATATGAAGAAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:1,2:41,32:0.0395:2,2:36.3:1:31:1:0.58358:2.53137:39:6:0.0395:0:5 0/1:183:8:4,4:99,76:0.0437:2,2:29.3:1:31.6:1:0.73075:1.30072:40.9:16:0.044:0:4 -10 42528018 . G A 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20303;SOR=1.72075;LSEQ=ACTGAGAATTCTTCTGTCTA;RSEQ=CATTATATGAAGAAATCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:9:6,3:35,32:0.1169:2,2:29.7:1:28.9:1:0.49382:1.81:36.6:8:0.1067:0:5 0/1:183:34:20,14:77,64:0.1858:2,2:24.4:1:30.2:1:0.70404:1.19:38.3:33:0.1844:0:5.1 -10 42528019 . C A 57 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23224;SOR=0.39195;LSEQ=CTGAGAATTCTTCTGTCTAG;RSEQ=ATTATATGAAGAAATCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:4:2,2:40,33:0.0519:2,2:31.5:1:30.5:1:1:1.20908:37:8:0.0533:0:6.3 0/1:191:4:3,1:102,83:0.0209:2,2:36.3:1:28.8:1:0.63038:2.43:26.5:8:0.0212:0:7.3 -10 42528020 . A G 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58238;SOR=1.18128;LSEQ=TGAGAATTCTTCTGTCTAGC;RSEQ=TTATATGAAGAAATCCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:28:14,14:28,21:0.3636:2,2:30.3:1:31.1:1:0.63643:1.32831:40.7:56:0.3636:0:4.1 0/1:191:77:43,34:62,50:0.4031:2,2:28.5:1:30.3:1:1:1.02:43.4:154:0.4118:0:4.5 -10 42528022 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08269;SOR=0;LSEQ=AGAATTCTTCTGTCTAGCAT;RSEQ=ATATGAAGAAATCCCGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:40,34:0.0256:2,2:21.5:1:30.5:1:1:1.17394:45.5:4:0.026:0:6 0/0:192:0:0,0:106,86:0:2,0:28.8:1:29:1:1:0:41.6:63:1:0:4.6 -10 42528023 . A C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.0179;LSEQ=GAATTCTTCTGTCTAGCATT;RSEQ=TATGAAGAAATCCCGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:10:6,4:34,30:0.1282:2,2:27.5:1:31.3:1:0.74514:1.32:42.3:20:0.1282:0:7.4 0/1:192:25:15,10:74,62:0.1302:2,2:22.7:1:31.6:1:0.66601:1.25:39.4:50:0.1309:0:7.1 -10 42528024 . T C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.80252;SOR=1.31116;LSEQ=AATTCTTCTGTCTAGCATTA;RSEQ=ATGAAGAAATCCCGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:5:2,3:40,33:0.0641:2,2:36:1:32.8:1:0.65741:1.80427:34.6:10:0.0649:0:5.4 0/1:194:16:9,7:90,77:0.0825:2,2:31.5:1:31.5:1:1:1.10:37.7:32:0.0833:0:5 -10 42528025 . A G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.03136;LSEQ=ATTCTTCTGTCTAGCATTAT;RSEQ=TGAAGAAATCCCGTTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:7:5,2:37,34:0.0897:2,2:22.4:1:32.4:1:0.44154:2.27:44.3:14:0.0909:0:5.3 0/1:195:18:11,7:88,78:0.0923:2,2:24.3:1:30.8:1:0.62168:1.39:46.7:36:0.0984:0:5.1 -10 42528026 . T A 80 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03192;SOR=0.24638;LSEQ=TTCTTCTGTCTAGCATTATA;RSEQ=GAAGAAATCCCGTTTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:6:3,3:38,32:0.0769:2,2:30.8:1:31.3:1:1:1.1848:31.7:12:0.0779:0:6.3 0/1:200:4:3,1:100,90:0.02:2,2:38.3:1:25.8:1:0.62401:2.69:26.5:3:0.0153:0:7.3 -10 42528029 . A G 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03243;SOR=0.48582;LSEQ=TTCTGTCTAGCATTATATGA;RSEQ=GAAATCCCGTTTCCAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:19:11,8:32,28:0.2405:2,2:33.3:1:31.6:1:0.79577:1.20:36.5:38:0.2405:0:4.7 0/1:203:27:14,13:92,83:0.133:2,2:34.7:1:31.4:1:1:1.02912:36.4:54:0.1337:0:4.7 -10 42528030 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07667;SOR=0;LSEQ=TCTGTCTAGCATTATATGAA;RSEQ=AAATCCCGTTTCCAACGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:41,35:0.0253:2,2:41:1:29:1:1:1.16904:50.5:4:0.0267:0:7 0/0:205:0:0,0:102,90:0:2,0:31.1:1:31.2:1:1:0:41.1:191:0.9363:0:4.8 -10 42528038 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07569;SOR=0;LSEQ=GCATTATATGAAGAAATCCC;RSEQ=TTTCCAACGAAGGCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:42,40:0.0238:2,2:34.5:1:30.5:1:1:1.04941:42.5:4:0.0238:0:4 0/0:220:0:0,0:111,106:0:2,0:31:1:30:1:1:0:41.2:107.5:0.9862:0:4.6 -10 42528042 . C A 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1942;SOR=Inf;LSEQ=TATATGAAGAAATCCCGTTT;RSEQ=CAACGAAGGCCTCAAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:41,41:0:2,0:31.8:1:31.2:1:1:0:39.7:81:1:0:4.5 0/1:221:6:4,2:109,106:0.0271:2,2:29.3:1:28:1:0.68367:1.94:32.5:12:0.0274:0:6.3 -10 42528044 . A T 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13505;LSEQ=TATGAAGAAATCCCGTTTCC;RSEQ=ACGAAGGCCTCAAAGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:41,40:0.0241:2,2:26.5:1:30:1:1:1.0247:41.5:4:0.0247:0:3.5 0/1:220:6:4,2:108,106:0.0273:2,2:27.3:1:29.7:1:0.68348:1.96:32.5:12:0.0274:0:6.3 -10 42528046 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07537;SOR=0;LSEQ=TGAAGAAATCCCGTTTCCAA;RSEQ=GAAGGCCTCAAAGAGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:40,39:0.0241:2,2:38.5:1:31:1:1:1.02533:21:4:0.0244:0:6.5 0/0:218:0:0,0:109,105:0:2,0:30.5:1:30.1:1:1:0:40.9:213:0.9816:0:4.6 -10 42528050 . G A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02362;LSEQ=GAAATCCCGTTTCCAACGAA;RSEQ=GCCTCAAAGAGGTCCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:11:6,5:36,37:0.131:2,2:28.7:1:30.3:1:1:1.23:46.2:22:0.1325:0:5.6 0/1:217:29:18,11:92,96:0.1336:2,2:23.8:1:30.1:1:0.2324:1.70:44.2:58:0.1336:0:5.8 -10 42528051 . G T 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66566;SOR=0.74607;LSEQ=AAATCCCGTTTCCAACGAAG;RSEQ=CCTCAAAGAGGTCCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:37,40:0.0247:2,2:41.5:1:30.5:1:1:1.08:21.5:4:0.0263:0:4 0/1:216:4:2,2:106,106:0.0185:2,2:34.3:1:29:1:1:1:36:8:0.0188:0:5.5 -10 42528052 . C G 105 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00049;SOR=0.13319;LSEQ=AATCCCGTTTCCAACGAAGG;RSEQ=CTCAAAGAGGTCCAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:10:5,5:33,37:0.125:2,2:24.6:1:31.9:1:1:1.12:33.9:20:0.1266:0:5.2 0/1:216:4:2,2:106,106:0.0185:2,2:15:1:30.3:1:1:1:25.5:8:0.0188:0:3.8 -10 42528053 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07105;SOR=0;LSEQ=ATCCCGTTTCCAACGAAGGC;RSEQ=TCAAAGAGGTCCAAATATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:37,40:0.0253:2,2:27:1:30:1:1:1.08:50:4:0.026:0:4.5 0/0:216:0:0,0:108,108:0:2,0:28.9:1:30.6:1:1:0:41:215:1:0:4.6 -10 42528054 . T C 130 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0989;SOR=2.89447;LSEQ=TCCCGTTTCCAACGAAGGCC;RSEQ=CAAAGAGGTCCAAATATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:3:1,2:36,39:0.038:2,2:40.7:1:30.3:1:1:1.83225:40:6:0.038:0:7.3 0/1:214:22:8,14:93,85:0.1028:2,2:31.3:1:29.2:1:0.18074:1.90855:38.9:21:0.1:0:6.5 -10 42528056 . A T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07202;SOR=0;LSEQ=CCGTTTCCAACGAAGGCCTC;RSEQ=AAGAGGTCCAAATATCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:37,40:0.0253:2,2:45.5:1:30.5:1:1:1.08:45.5:4:0.026:0:6 0/0:214:0:0,0:107,107:0:2,0:28:1:29.5:1:1:0:41:106:1:0:4.5 -10 42528057 . A G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08755;SOR=0.26804;LSEQ=CGTTTCCAACGAAGGCCTCA;RSEQ=AGAGGTCCAAATATCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:4:2,2:36,39:0.0506:2,2:27.5:1:31.5:1:1:1.08:42:8:0.0513:0:3.5 0/1:214:3:2,1:105,106:0.014:2,2:24.7:1:26.7:1:1:2.01:47:2:0.0095:0:2.7 -10 42528059 . G T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12645;LSEQ=TTTCCAACGAAGGCCTCAAA;RSEQ=AGGTCCAAATATCCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:5:2,3:35,39:0.0633:2,2:21.4:1:28.6:1:1:1.34116:47.8:10:0.0633:0:5.2 0/1:212:15:6,9:98,98:0.0708:2,2:31.8:1:27.1:1:0.59417:1.49714:43.4:14:0.0673:0:5.7 -10 42528060 . A G 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31054;SOR=0.38197;LSEQ=TTCCAACGAAGGCCTCAAAG;RSEQ=GGTCCAAATATCCACTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:36,40:0.025:2,2:24:0:33:0:1:1.11:35:4:0.0253:0:3 0/0:207:2:1,1:99,106:0.0097:2,2:34:1:32:1:1:1.07:45:4:0.0099:0:5.5 -10 42528061 . GG CA 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60375;SOR=1.4825;LSEQ=TCCAACGAAGGCCTCAAAGA;RSEQ=TCCAAATATCCACTTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:4:2,2:36,39:0.05:2,2:23.5:1:31.9:1:1:1.08:49.8:8:0.0506:0:3.8 0/1:207:15:6,9:94,98:0.0725:2,2:28.8:1:30:1:0.59672:1.43627:43.4:30:0.0725:0:4.7 -10 42528062 . G T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0986;SOR=0.28226;LSEQ=CCAACGAAGGCCTCAAAGAG;RSEQ=TCCAAATATCCACTTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:4:2,2:34,38:0.05:2,2:17.5:1:30:1:1:1.12:37:8:0.0548:0:6.3 0/1:206:3:2,1:91,97:0.0146:2,2:23.3:1:29:1:0.61332:2.12:27.7:6:0.0157:0:7.3 -10 42528063 . T G 98 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=0.07743;LSEQ=CAACGAAGGCCTCAAAGAGG;RSEQ=CCAAATATCCACTTGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:9:4,5:33,37:0.1139:2,2:16.4:1:31:1:1:1.11333:33.2:18:0.1154:0:5.1 0/0:205:2:1,1:95,105:0.0098:2,2:11.5:1:30.5:1:1:1.10:25:4:0.01:0:4 -10 42528065 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07599;SOR=0;LSEQ=ACGAAGGCCTCAAAGAGGTC;RSEQ=AAATATCCACTTGCAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:32,40:0.026:2,2:36.5:1:30.5:1:1:1.25:45.5:4:0.0263:0:6 0/0:201:0:0,0:96,105:0:2,0:25.2:1:30.4:1:1:0:41.5:99.5:1:0:4.5 -10 42528067 . A T 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5676;SOR=Inf;LSEQ=GAAGGCCTCAAAGAGGTCCA;RSEQ=ATATCCACTTGCAGACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:31,41:0:2,0:22:1:30.1:1:1:0:40.1:144:1:0:4.6 0/1:199:3:1,2:92,103:0.0151:2,2:28:1:28:1:1:1.78139:46.7:6:0.0154:0:5.3 -10 42528072 . C T 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69299;LSEQ=CCTCAAAGAGGTCCAAATAT;RSEQ=CACTTGCAGACTTTACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:1:0,1:25,39:0.0154:2,0:11:0:31:0:1:0:52:2:0.0159:0:6 0/1:187:2:1,1:84,101:0.0107:2,2:29:1:28:1:1:1.20:41.5:4:0.0109:0:6.5 -10 42528073 . CA TG 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04645;SOR=2.72903;LSEQ=CTCAAAGAGGTCCAAATATC;RSEQ=CTTGCAGACTTTACAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:5:1,4:23,35:0.0769:2,2:29.4:1:31.3:1:0.64114:2.5937:41:10:0.0769:0.0154:5.8 0/1:183:34:14,20:68,81:0.1858:2,2:31.1:1:31:1:0.70453:1.19811:36.8:68:0.1878:0:4.7 -10 42528075 . C G 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.86319;SOR=0.90213;LSEQ=CAAAGAGGTCCAAATATCCA;RSEQ=TTGCAGACTTTACAAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:16:7,9:16,29:0.2623:2,2:27.4:1:32.2:1:0.56504:1.40:47.9:32:0.2667:0:5.8 0/1:173:42:20,22:54,75:0.2428:2,2:25.7:1:31.1:1:0.59149:1.26:43.8:41:0.2384:0:5.9 -10 42528076 . T C 82 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00148;SOR=0.05433;LSEQ=AAAGAGGTCCAAATATCCAC;RSEQ=TGCAGACTTTACAAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:6:2,4:19,33:0.1:2,2:14.5:1:31.8:1:1:1.1488:31.2:12:0.1017:0:5.2 0/0:169:1:0,1:71,94:0.0059:2,0:5:0:33:0:1:0:25:2:0.006:0:4 -10 42528078 . G A 27 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72726;LSEQ=AGAGGTCCAAATATCCACTT;RSEQ=CAGACTTTACAAACAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:1:1,0:20,37:0.0172:2,0:14:0:30:0:0.36207:0:21:2:0.0172:0:5 0/1:159:2:1,1:66,91:0.0126:2,2:15:1:27:1:1:1.38:47:4:0.0127:0:4 -10 42528079 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGGTCCAAATATCCACTTG;RSEQ=AGACTTTACAAACAGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:21,37:0:2,0:17.8:1:32:1:1:0:39.9:116:1:0:4.6 0/1:156:2:1,1:63,90:0.0128:2,2:7.5:1:28.5:1:1:1.43:40:4:0.0129:0:4.5 -10 42528080 . A T 107 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35902;SOR=2.37494;LSEQ=AGGTCCAAATATCCACTTGC;RSEQ=GACTTTACAAACAGAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:20,36:0.0345:2,2:13:0:28.5:1:1:1.78:49:4:0.0351:0:4 0/1:153:12:5,7:57,84:0.0784:2,2:13.8:1:30:1:1:1.05:44.8:24:0.08:0:4.8 -10 42528083 . C A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40021;SOR=0.67053;LSEQ=TCCAAATATCCACTTGCAGA;RSEQ=TTTACAAACAGAGTGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:5,7:13,22:0.2553:2,2:32.6:1:30.8:1:1:1.20:47.3:24:0.2609:0:6.5 0/1:134:25:12,13:36,65:0.1866:2,2:31.3:1:30:1:0.26122:1.66:45.3:50:0.1894:0:6.5 -10 42528084 . T A 132 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11027;SOR=3.69627;LSEQ=CCAAATATCCACTTGCAGAC;RSEQ=TTACAAACAGAGTGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:15,25:0.0455:2,2:10.5:1:29.5:1:1:1.65:28:4:0.0455:0:6 0/1:133:20:8,12:41,70:0.1504:2,2:19.1:1:30.7:1:0.80598:1.14:36.6:40:0.155:0:3.5 -10 42528086 . T C 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13441;SOR=0.14624;LSEQ=AAATATCCACTTGCAGACTT;RSEQ=ACAAACAGAGTGTTTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:13,23:0.0526:2,2:5.5:1:29.5:1:1:1.74:59:4:0.0526:0:3 0/0:126:1:0,1:44,78:0.0079:2,0:14:0:34:0:1:0:22:2:0.0081:0:4 -10 42528090 . A G 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04374;SOR=3.13998;LSEQ=ATCCACTTGCAGACTTTACA;RSEQ=ACAGAGTGTTTCCAAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:4:1,3:11,21:0.1111:2,2:25.3:1:32.8:1:1:1.55309:40:8:0.1111:0:5.8 0/1:113:32:11,21:26,52:0.2832:2,2:21.3:1:31.5:1:1:1.05:36.7:64:0.2857:0:4.6 -10 42528092 . C G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46918;SOR=0.55943;LSEQ=CCACTTGCAGACTTTACAAA;RSEQ=AGAGTGTTTCCAAACTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:1,3:8,15:0.129:2,2:13.3:1:30.8:1:1:1.57406:30.5:8:0.129:0:5.3 0/1:105:8:1,7:30,58:0.0762:2,2:12.6:1:29.5:1:0.43035:3.58314:39.8:7:0.068:0:5.9 -10 42528093 . A T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17627;SOR=0.54734;LSEQ=CACTTGCAGACTTTACAAAC;RSEQ=GAGTGTTTCCAAACTAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:12:5,7:3,13:0.4286:2,2:29.3:1:31:1:0.23092:2.97:47.3:24:0.4286:0:6.5 0/1:100:29:11,18:18,52:0.29:2,2:27.1:1:30.2:1:0.23532:1.75:45:28:0.2857:0:6.4 -10 42528094 . G C 83 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03383;LSEQ=ACTTGCAGACTTTACAAACA;RSEQ=AGTGTTTCCAAACTAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:8,18:0.0714:2,0:15:0:34:0:1:0:40:4:0.0714:0:3.5 0/1:95:7:0,7:27,60:0.0737:2,0:12.3:1:29.9:1:0.18656:0:39.3:6:0.0645:0:5.7 -10 42528096 . G C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0588;SOR=0.42007;LSEQ=TTGCAGACTTTACAAACAGA;RSEQ=TGTTTCCAAACTAATCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:12:5,7:2,13:0.4444:2,2:28.3:1:32.4:1:0.18502:4.37:47.3:24:0.4444:0:6.5 0/1:92:23:10,13:16,52:0.25:2,2:30.5:1:31.7:1:0.10718:2.47:45.3:46:0.25:0:6.8 -10 42528100 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29059;SOR=0.38978;LSEQ=AGACTTTACAAACAGAGTGT;RSEQ=TCCAAACTAATCTATGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:4,15:0.0952:2,0:9:0:32.5:1:1:0:40:4:0.0952:0:3.5 0/1:77:3:0,3:21,53:0.039:2,0:16:1:31.7:1:0.55789:0:37.3:6:0.0395:0:6.3 -10 42528109 . A C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09271;SOR=0.22695;LSEQ=AAACAGAGTGTTTCCAAACT;RSEQ=ATCTATGAAAAGAAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:4,6:0,2:0.8333:0,2:22.3:1:32.4:1:0.51515:0:47.1:20:0.8333:0:6.6 1/0:40:21:10,11:3,13:0.525:2,2:22.6:1:30:1:0.09118:3.79:44.5:20:0.5128:0:6.9 -10 42528110 . A C 117 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30166;SOR=2.5611;LSEQ=AACAGAGTGTTTCCAAACTA;RSEQ=TCTATGAAAAGAAAGGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:4,6:0.1667:2,0:17:1:33:0:0.51515:0:40:4:0.1667:0:4.5 0/1:35:12:0,12:10,11:0.3429:2,0:14.2:1:32.7:1:0.00498:0:35.2:24:0.375:0:4.8 -10 42528126 . G C 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.90745;LSEQ=ACTAATCTATGAAAAGAAAG;RSEQ=TTAAATTCTGTGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:2,5:0.125:2,0:6:0:33:0:1:0:40:2:0.125:0:4 0/1:23:5:0,5:8,10:0.2174:2,0:5.8:1:32.6:1:0.12211:0:36.6:10:0.2174:0:5.4 -10 42528132 . T C 113 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGAAAAGAAAGGTTAAA;RSEQ=TCTGTGAGTTGAATGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:13.3:1:33.5:1:1:0:45.8:8:1:0:6.8 1/1:14:12:4,8:0,1:0.8571:0,2:10.3:1:31.7:1:1:0:42.3:24:0.8571:0:6.7 -10 42528182 . T G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTTTCTGAAAATGATTCT;RSEQ=TCTAGTTTTTATACGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:32.5:1:1:0:35.5:4:1:0:7 -10 42528204 . A T 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTTTTTATACGAAGATA;RSEQ=TTCCTTTTCTACCACTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:32:0:1:0:35.5:4:1:0:7 -10 42528222 . T G 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTCCTTTTCTACCACTG;RSEQ=CCTCAAACTGCTTGAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:33.5:1:1:0:37:4:1:0:7 -10 42528230 . CT TC 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTACCACTGTCCTCAAA;RSEQ=GCTTGAAATCTCCACCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:16.5:1:28:1:1:0:47:4:0.6667:0:6 -10 42528262 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACCTGAAAATTCCACAA;RSEQ=AAGAGAGTTTCAAATCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:1:31:1:1:0:47:4:1:0:6 -10 42528296 . G T 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCTGTGTCTAAAGGAA;RSEQ=GTTCAACTCCGTCAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:32:0:1:0:47:4:1:0:6 -10 42528306 . C T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAAAGGAAGGTTCAACTC;RSEQ=GTCAGTTGAATACACACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:30:1:1:0:47:4:1:0:6 -10 42529182 . T C 52 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATACACACATAGCAAAG;RSEQ=AGTTTCTGAGAATGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:5:0:33:0:1:0:40:6:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42529204 . CC GT 51 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCTGAGAATGATTCTGT;RSEQ=AGTTTTTACAAGAAGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:28:0:32.5:1:1:0:40:6:1:0:7 1/1:1:1:1,0:0,0:1:0,0:23:0:30:0:1:0:39:2:1:0:7 -10 42529216 . A C 52 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GATTCTGTCCAGTTTTTACA;RSEQ=GAAGATATTTCTATTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:39:0:33:1:1:0:40:6:1:0:7 1/1:1:1:1,0:0,0:1:0,0:34:0:31:0:1:0:39:2:1:0:7 -10 42529228 . T C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTACAAGAAGATATTTC;RSEQ=ATTTCAAAGACTGGCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:47.3:1:31:1:1:0:40:6:1:0:7 1/1:3:3:2,1:0,0:1:0,2:18:1:30.3:1:1:0:38.7:6:1:0:7.7 -10 42529239 . C T 84 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATATTTCTATTTCAAAGA;RSEQ=TGGCCACAAATCGCTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:29.8:1:31:1:1:0:40.5:8:1:0:7.3 1/1:7:7:6,1:0,0:1:0,2:16.1:1:30:1:1:0:37.1:14:1:0:7.9 -10 42529241 . G A 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30769;SOR=Inf;LSEQ=ATATTTCTATTTCAAAGACT;RSEQ=GCCACAAATCGCTAGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:26:1:29.7:1:1:0:40.7:6:0.75:0:7.3 1/1:9:9:6,3:0,0:1:0,2:13.9:1:29:1:1:0:42.2:18:1:0:7.9 -10 42529245 . A T 120 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTATTTCAAAGACTGGCC;RSEQ=CAAATCGCTAGAAATCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:18.3:1:30.5:1:1:0:38.8:12:1:0:7.3 1/1:16:16:12,4:0,0:1:0,2:10.8:1:30.1:1:1:0:43.7:32:1:0:7.6 -10 42529255 . A T 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.96856;LSEQ=AAGACTGGCCACAAATCGCT;RSEQ=GAAATCTCCACTTGCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:12,3:0,0:0.9375:0,2:10.9:1:30.9:1:1:0:41.5:30:0.9375:0:6.9 1/1:31:30:22,8:0,0:0.9677:0,2:13.4:1:30.7:1:1:0:42.1:60:0.9677:0:6.9 -10 42529274 . T C 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62877;SOR=1.3004;LSEQ=TAGAAATCTCCACTTGCAAA;RSEQ=TCCACAACAACGAGTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:7,5:10,1:0.5217:2,2:25.7:1:31.6:1:0.15495:6.56883:42.3:11:0.5:0:6.2 1/0:63:37:21,16:20,6:0.5873:2,2:23:1:32:1:0.11543:2.50261:45.4:74:0.5873:0:6.8 -10 42529281 . ACAACGAG GAAAGAA 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44519;SOR=0.58799;LSEQ=TCTCCACTTGCAAATTCCAC;RSEQ=TTTTTCAAAACTGCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:28:16,12:0,0:0.8485:0,2:18.5:1:30.9:1:1:0:46.7:56:0.9655:0.3939:4 1/0:77:59:33,26:6,0:0.7662:0,2:23.3:1:30.2:1:0.07335:0:46.6:118:0.8676:0.2208:3.9 -10 42529282 . CAACGA AAAGT 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08182;SOR=3.53168;LSEQ=TCCACTTGCAAATTCCACAA;RSEQ=GTTTTTCAAAACTGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:5,1:0,0:0.4615:0,2:16.5:1:31.3:1:1:0:40.3:12:0.5455:0.1538:5.5 1/0:33:25:18,7:0,0:0.7576:0,2:13.5:1:30.1:1:1:0:45.5:24:0.8:0.3939:5.4 -10 42529298 . A T 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.2129;SOR=0.20842;LSEQ=ACAACAACGAGTTTTTCAAA;RSEQ=CTGCTCTGTCTAAAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:2,0:28,17:0.0408:2,0:5.5:1:30.5:1:0.52821:0:30.5:4:0.0408:0:7 0/0:115:1:1,0:73,41:0.0087:2,0:1:0:29:0:1:0:40:2:0.0087:0:6 -10 42529301 . G A 27 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2053;SOR=0.20275;LSEQ=ACAACGAGTTTTTCAAAACT;RSEQ=CTCTGTCTAAAGGAAGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:33,19:0.0364:2,2:18:1:27.5:1:1:1.71824:50.5:4:0.0364:0:6 0/0:133:1:1,0:88,44:0.0075:2,0:14:0:30:0:1:0:55:2:0.0077:0:8 -10 42529306 . G C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30818;SOR=0.48749;LSEQ=GAGTTTTTCAAAACTGCTCT;RSEQ=TCTAAAGGAAGGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:5:5,0:33,20:0.0862:2,0:8.2:1:32.6:1:0.15311:0:34.6:10:0.0862:0:5.6 0/1:137:6:5,1:82,47:0.0438:2,2:7.3:1:32.3:1:0.4217:2.85:27.5:12:0.0438:0:5 -10 42529307 . TC AA 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31896;SOR=1.44556;LSEQ=AGTTTTTCAAAACTGCTCTG;RSEQ=TAAAGGAAGGTTCAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:15:10,5:29,18:0.2344:2,2:20:1:29.6:1:1:1.24:39.4:30:0.2381:0.0469:6.3 0/1:140:43:33,10:57,38:0.3071:2,2:26.1:1:30.3:1:0.08166:2.19:45.2:86:0.3071:0.0071:5.7 -10 42529308 . C G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09478;SOR=0;LSEQ=GTTTTTCAAAACTGCTCTGT;RSEQ=TAAAGGAAGGTTCAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:2,0:30,20:0.0308:2,0:12.5:1:33:0:0.51735:0:36:4:0.0385:0:7 0/0:145:0:0,0:61,38:0:2,0:24.6:1:31.1:1:1:0:43.9:48.5:0.9798:0:5.4 -10 42529313 . G T 48 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.02388;SOR=0;LSEQ=TCAAAACTGCTCTGTCTAAA;RSEQ=GAAGGTTCAACTCTGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:2,1:44,26:0.0411:2,2:24.7:1:30.7:1:1:1.18:45.7:6:0.0417:0:6.7 0/0:178:0:0,0:113,64:0:2,0:22.6:1:31.2:1:1:0:43.6:87.5:0.9943:0:5.4 -10 42529314 . G A 73 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0495;SOR=0.2368;LSEQ=CAAAACTGCTCTGTCTAAAG;RSEQ=AAGGTTCAACTCTGTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:5:5,0:41,26:0.0676:2,0:15.2:1:31.6:1:0.15182:0:31.8:10:0.0685:0:5.2 0/1:179:3:3,0:111,65:0.0168:2,0:13.3:1:29.7:1:0.55458:0:40:6:0.0169:0:4.3 -10 42529316 . A T 59 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.79639;LSEQ=AAACTGCTCTGTCTAAAGGA;RSEQ=GGTTCAACTCTGTGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:47,27:0.0263:2,2:4.5:1:28:1:1:1.72738:42:4:0.0267:0:8 0/1:190:4:2,2:118,68:0.0211:2,2:9.8:1:29.5:1:0.62627:1.72993:42.8:8:0.0213:0:5.5 -10 42529317 . G A 63 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.57282;LSEQ=AACTGCTCTGTCTAAAGGAA;RSEQ=GTTCAACTCTGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:0,1:49,27:0.013:2,0:11:0:27:0:0.36364:0:31:2:0.0133:0:7 0/1:197:4:2,2:124,69:0.0203:2,2:12.5:1:31.8:1:0.62028:1.79137:42:8:0.0207:0:6.3 -10 42529318 . G C 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.40918;LSEQ=ACTGCTCTGTCTAAAGGAAG;RSEQ=TTCAACTCTGTGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:2,0:46,31:0.0247:2,0:17:1:33.5:1:0.51704:0:37:4:0.025:0:6.5 0/1:203:7:6,1:123,71:0.0345:2,2:12.3:1:32.1:1:0.42522:3.45:40.9:14:0.0347:0:4.9 -10 42529322 . A C 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.127;SOR=1.61557;LSEQ=CTCTGTCTAAAGGAAGGTTC;RSEQ=ACTCTGTGAGTTGAATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:20:13,7:39,28:0.2299:2,2:23.5:1:30.3:1:0.79552:1.33:38.3:19:0.2209:0:6.2 0/1:218:71:51,20:85,60:0.3257:2,2:24.8:1:31:1:0.07195:1.80:43.1:142:0.3257:0:5.6 -10 42529324 . C A 76 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.1919;SOR=Inf;LSEQ=CTGTCTAAAGGAAGGTTCAA;RSEQ=TCTGTGAGTTGAATACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:52,36:0:2,0:24.1:1:31.9:1:1:0:42.1:87:1:0:5.5 0/1:229:6:3,3:139,82:0.0262:2,2:21.8:1:29.7:1:0.674:1.69093:30.2:12:0.0267:0:5.3 -10 42529325 . T C 49 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02151;SOR=0;LSEQ=TGTCTAAAGGAAGGTTCAAC;RSEQ=CTGTGAGTTGAATACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:1,2:53,34:0.0333:2,2:22.3:1:31:1:0.56149:3.07776:34:6:0.0341:0:5.3 0/0:231:0:0,0:144,86:0:2,0:22.3:1:30.3:1:1:0:43.3:114:0.9956:0:5.2 -10 42529329 . T A 51 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.16119;LSEQ=TAAAGGAAGGTTCAACTCTG;RSEQ=GAGTTGAATACACACAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:0,1:54,37:0.0109:2,0:23:0:29:0:0.41304:0:31:2:0.011:0:7 0/1:238:3:1,2:146,89:0.0126:2,2:14:1:32.3:1:0.55986:3.26408:27:6:0.0128:0:6.7 -10 42529331 . A T 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9723;LSEQ=AAGGAAGGTTCAACTCTGTG;RSEQ=GTTGAATACACACAACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:53,38:0.0215:2,2:13.5:1:30:1:1:1.38965:42:4:0.0215:0:7.5 0/1:239:5:3,2:140,92:0.0209:2,2:28.8:1:31:1:1:1.01444:33:10:0.0213:0:5.8 -10 42529332 . G C 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27243;SOR=0.74497;LSEQ=AGGAAGGTTCAACTCTGTGA;RSEQ=TTGAATACACACAACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:52:28,24:26,15:0.5591:2,2:27.9:1:32.6:1:0.40158:1.47937:44.9:104:0.5591:0:5.2 0/1:243:118:64,54:83,42:0.4856:2,2:24.5:1:31.5:1:0.06595:1.6639:45.5:58:0.4833:0:4.7 -10 42529335 . G C 48 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13374;LSEQ=AAGGTTCAACTCTGTGAGTT;RSEQ=AATACACACAACACAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:0,1:55,38:0.0106:2,0:27:0:34:0:0.41489:0:25:2:0.0106:0:4 0/1:249:3:2,1:147,99:0.012:2,2:28.3:1:30.7:1:1:1.35:44.3:6:0.0122:0:7 -10 42529338 . TA CG 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07311;SOR=0;LSEQ=GTTCAACTCTGTGAGTTGAA;RSEQ=CACACAACACAAAGTAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:55,38:0.0211:2,2:24.5:1:32.5:1:1:1.44159:48.5:4:0.0211:0:6 0/0:255:0:0,0:149,103:0:2,0:25:1:29.2:1:1:0:43.1:83:0.9881:0:5.1 -10 42529339 . A G 43 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12405;SOR=0.2417;LSEQ=TTCAACTCTGTGAGTTGAAT;RSEQ=CACACAACACAAAGTAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:3:2,1:53,37:0.0316:2,2:23.7:1:27.3:1:1:1.39:27.3:2:0.0217:0:5.3 0/0:257:2:1,1:149,104:0.0078:2,2:21:1:30.5:1:1:1.4306:56:4:0.0078:0:4.5 -10 42529341 . A C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.50304;SOR=0.65622;LSEQ=CAACTCTGTGAGTTGAATAC;RSEQ=CACAACACAAAGTAGTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:4:4,0:54,39:0.0408:2,0:25.5:1:32.5:1:0.14619:0:37:8:0.0412:0:5 0/1:258:7:6,1:141,104:0.0271:2,2:32.3:1:30.9:1:0.2444:4.41:44.3:14:0.0277:0:5.1 -10 42529342 . C A 70 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.93371;LSEQ=AACTCTGTGAGTTGAATACA;RSEQ=ACAACACAAAGTAGTTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:1:0,1:60,38:0.0101:2,0:12:0:25:0:0.39394:0:40:2:0.0102:0:6 0/1:258:5:3,2:146,106:0.0194:2,2:32.8:1:30.4:1:1:1.09:24.6:10:0.0195:0:5 -10 42529344 . CA C 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.26848;SOR=0.46864;LSEQ=CTCTGTGAGTTGAATACACA;RSEQ=ACACAAAGTAGTTACTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:4:3,1:56,38:0.0404:2,2:36.3:1:32.8:1:1:2.02:42.3:8:0.0417:0:7.3 0/1:259:5:3,2:144,104:0.0193:2,2:37.8:1:31.4:1:1:1.08:42.8:10:0.0194:0:6.4 -10 42529346 . A G 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.61847;SOR=0.56573;LSEQ=CTGTGAGTTGAATACACACA;RSEQ=CACAAAGTAGTTACTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:58,38:0.0204:2,2:28.5:1:33.5:1:1:1.51951:42:4:0.0206:0:7.5 0/1:258:3:2,1:146,109:0.0116:2,2:35.3:1:33.7:1:1:1.49:41.7:6:0.0118:0:6 -10 42529347 . C G 52 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.14524;LSEQ=TGTGAGTTGAATACACACAA;RSEQ=ACAAAGTAGTTACTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:1:0,1:59,38:0.0102:2,0:41:0:31:0:0.39796:0:31:2:0.0104:0:7 0/1:257:3:1,2:145,107:0.0117:2,2:32:1:33.3:1:0.57755:2.69977:27:6:0.0119:0:6.7 -10 42529348 . A C 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.02558;LSEQ=GTGAGTTGAATACACACAAC;RSEQ=CAAAGTAGTTACTGAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:3:3,0:56,39:0.0306:2,0:37.7:1:32.3:1:0.27383:0:38.3:6:0.0316:0:5.7 0/1:255:8:6,2:140,106:0.0314:2,2:36.6:1:31:1:0.47281:2.26:38.8:16:0.0316:0:4.9 -10 42529349 . C A 72 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.92465;LSEQ=TGAGTTGAATACACACAACA;RSEQ=AAAGTAGTTACTGAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:0,1:58,38:0.0103:2,0:43:0:30:0:0.40206:0:31:2:0.0104:0:7 0/1:254:5:2,3:142,106:0.0197:2,2:32.4:1:31.2:1:0.65446:2.00387:26.2:10:0.0198:0:5.6 -10 42529350 . A T 57 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57858;SOR=Inf;LSEQ=GAGTTGAATACACACAACAC;RSEQ=AAGTAGTTACTGAGAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:57,39:0:2,0:29.7:1:30.1:1:1:0:41.9:95:1:0:5.4 0/1:253:4:2,2:142,107:0.0158:2,2:31.8:1:28.8:1:1:1.32559:32.8:8:0.0161:0:5.8 -10 42529354 . T A 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00088;SOR=0.41807;LSEQ=TGAATACACACAACACAAAG;RSEQ=AGTTACTGAGAATTCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:97:73:41,32:0,0:0.7526:0,2:28.2:1:30.4:1:1:0:43.7:146:0.7604:0:5.1 1/0:245:137:73,64:0,0:0.5592:0,2:30.4:1:29.4:1:1:0:43.3:67.5:0.5602:0:4.6 -10 42529356 . G T 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00091;SOR=2.49493;LSEQ=AATACACACAACACAAAGTA;RSEQ=TTACTGAGAATTCTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:20:13,7:39,33:0.2151:2,2:34:1:30.8:1:0.45146:1.56:39.1:40:0.2151:0:6.1 0/1:241:98:61,37:76,67:0.4066:2,2:28.6:1:29.4:1:0.18613:1.45:43.3:23.5:0.4:0:5.6 -10 42529357 . T C 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27131;SOR=0.47316;LSEQ=ATACACACAACACAAAGTAG;RSEQ=TACTGAGAATTCTTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:4:3,1:51,40:0.0421:2,2:43.8:1:32.5:1:0.63141:2.33:42.3:8:0.043:0:7.3 0/1:246:5:3,2:137,104:0.0203:2,2:46.2:1:32.6:1:1:1.14:42.8:10:0.0206:0:6.4 -10 42529358 . T G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22615;SOR=0.72863;LSEQ=TACACACAACACAAAGTAGT;RSEQ=ACTGAGAATTCTTCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:50:25,25:28,16:0.5263:2,2:27.6:1:32.2:1:0.21473:1.73954:45.8:100:0.5263:0:4.9 0/1:246:110:56,54:85,51:0.4472:2,2:28.9:1:31.3:1:0.07123:1.60396:46.4:54:0.4444:0:4.6 -10 42529360 . C G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.3557;SOR=0.38491;LSEQ=CACACAACACAAAGTAGTTA;RSEQ=TGAGAATTCTTCTGTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:3:1,2:53,40:0.0309:2,2:36:1:32.7:1:0.57935:2.62347:47:6:0.0309:0:4.7 0/1:248:3:1,2:141,104:0.0121:2,2:23.3:1:31:1:0.57748:2.70072:47.7:6:0.0121:0:5.7 -10 42529364 . G C 53 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.58145;LSEQ=CAACACAAAGTAGTTACTGA;RSEQ=AATTCTTCTGTCTAGCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:1,0:53,41:0.0104:2,0:44:0:31:0:1:0:46:2:0.0104:0:4 0/1:244:4:4,0:133,105:0.0164:2,0:25.3:1:26.8:1:0.13505:0:48.8:3:0.0126:0:5.8 -10 42529367 . T G 51 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1776;LSEQ=CACAAAGTAGTTACTGAGAA;RSEQ=TCTTCTGTCTAGCATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:1:0,1:53,42:0.0102:2,0:28:0:33:0:0.44792:0:31:2:0.0102:0:7 0/1:250:3:1,2:142,105:0.012:2,2:27.3:1:32.3:1:0.57778:2.69409:27:6:0.0121:0:6.7 -10 42529372 . C T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.47775;SOR=0.58365;LSEQ=AGTAGTTACTGAGAATTCTT;RSEQ=TGTCTAGCATTATATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:4:3,1:52,42:0.0408:2,2:35.5:1:30.5:1:0.62878:2.40:42.3:8:0.0408:0:7.3 0/1:248:6:4,2:139,102:0.0242:2,2:36.8:1:31.5:1:1:1.47:42.8:12:0.0247:0:6.3 -10 42529373 . T A 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55974;SOR=Inf;LSEQ=GTAGTTACTGAGAATTCTTC;RSEQ=GTCTAGCATTATATGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:57,45:0:2,0:25.6:1:31.1:1:1:0:44.4:204:1:0:5.2 0/1:251:3:3,0:143,105:0.012:2,0:6.7:1:31:1:0.26709:0:51.7:6:0.012:0:6 -10 42529374 . G C 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55904;SOR=Inf;LSEQ=TAGTTACTGAGAATTCTTCT;RSEQ=TCTAGCATTATATGAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:56,45:0:2,0:25.5:1:32.4:1:1:0:44.2:202:0.9902:0:5.2 0/1:248:3:2,1:141,103:0.0121:2,2:18.7:1:30.7:1:1:1.46:41.7:6:0.0121:0:6.3 -10 42529377 . T A 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48081;SOR=0.5937;LSEQ=TTACTGAGAATTCTTCTGTC;RSEQ=AGCATTATATGAAGAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:4:3,1:55,43:0.0392:2,2:30.5:1:30.3:1:0.63202:2.33:42.3:8:0.0392:0:7.3 0/1:254:6:3,3:143,104:0.0236:2,2:31.2:1:31.5:1:0.6998:1.37322:42.5:12:0.0239:0:6.2 -10 42529380 . C A 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27939;SOR=0.4861;LSEQ=CTGAGAATTCTTCTGTCTAG;RSEQ=ATTATATGAAGAAATCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:4:3,1:54,42:0.0396:2,2:27.5:1:30.3:1:0.63246:2.32:42.3:8:0.0396:0:7.3 0/1:255:5:3,2:143,107:0.0196:2,2:28.4:1:31.2:1:1:1.12:42.8:10:0.0198:0:6.4 -10 42529381 . A G 108 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00761;SOR=0.29701;LSEQ=TGAGAATTCTTCTGTCTAGC;RSEQ=TTATATGAAGAAATCCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:13:8,5:49,37:0.1313:2,2:26:1:29.4:1:1:1.21:41.2:12:0.1224:0:5.1 0/1:257:11:8,3:139,106:0.0428:2,2:31.6:1:29.5:1:0.36266:2.03:43.4:22:0.0431:0:4.3 -10 42529382 . T G 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.67834;SOR=1.13891;LSEQ=GAGAATTCTTCTGTCTAGCA;RSEQ=TATATGAAGAAATCCCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:22:13,9:42,32:0.2292:2,2:24.8:1:32.5:1:1:1.10:38.7:44:0.234:0:6.2 0/1:249:63:37,26:106,80:0.253:2,2:28.7:1:30.8:1:0.88314:1.07:41.9:20:0.25:0:6 -10 42529384 . A G 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05145;SOR=0.31071;LSEQ=GAATTCTTCTGTCTAGCATT;RSEQ=TATGAAGAAATCCCGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:7:4,3:51,36:0.0745:2,2:27.9:1:31.9:1:1:1.0618:38.6:14:0.0753:0:4.7 0/1:247:6:5,1:136,105:0.0243:2,2:30.7:1:31:1:0.2414:3.84:45.5:12:0.0249:0:5 -10 42529385 . TATGA AATG 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10129;SOR=1.74339;LSEQ=AATTCTTCTGTCTAGCATTA;RSEQ=AGAAATCCCGTTTCCAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:14:10,4:47,34:0.1429:2,2:18.1:1:31.1:1:0.39265:1.80:39.8:28:0.1443:0.0306:6.2 0/1:244:55:33,22:102,79:0.2254:2,2:26.1:1:29.6:1:0.64486:1.16:41:54:0.225:0.0328:5.9 -10 42529387 . T A 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47915;SOR=0.5885;LSEQ=TTCTTCTGTCTAGCATTATA;RSEQ=GAAGAAATCCCGTTTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:4:3,1:46,34:0.0408:2,2:20.5:1:30.8:1:0.63736:2.20:42.3:8:0.0465:0:7.3 0/1:246:6:4,2:108,84:0.0244:2,2:18:1:31.5:1:0.69913:1.55:40.3:12:0.0309:0:6.5 -10 42529390 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08151;SOR=0;LSEQ=TTCTGTCTAGCATTATATGA;RSEQ=GAAATCCCGTTTCCAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:55,37:0.0204:2,2:21:0:32.5:1:1:1.48004:41:4:0.0213:0:7.5 0/0:244:0:0,0:131,106:0:2,0:23.3:1:30.1:1:1:0:47.4:117.5:1:0:4.9 -10 42529391 . G A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19392;SOR=0.19496;LSEQ=TCTGTCTAGCATTATATGAA;RSEQ=AAATCCCGTTTCCAACGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:55,39:0.0206:2,2:23:1:28.5:1:1:1.4051:42:4:0.0208:0:7.5 0/0:246:1:1,0:133,107:0.0041:2,0:17:0:32:0:1:0:44:2:0.0041:0:8 -10 42529394 . A C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35633;SOR=0.38675;LSEQ=GTCTAGCATTATATGAAGAA;RSEQ=TCCCGTTTCCAACGAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:3:2,1:55,40:0.0303:2,2:16.7:1:31:1:1:1.45:58.3:6:0.0303:0:3 0/1:252:3:2,1:136,111:0.0119:2,2:21.7:1:30.7:1:1:1.63:45:6:0.012:0:6.3 -10 42529396 . C T 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30559;SOR=0.37723;LSEQ=CTAGCATTATATGAAGAAAT;RSEQ=CCGTTTCCAACGAAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:54,39:0.0208:2,2:18:1:28.5:1:1:1.37978:42:4:0.0208:0:7.5 0/0:252:2:2,0:134,116:0.0079:2,0:7:1:30.5:1:0.50117:0:44.5:4:0.008:0:8 -10 42529399 . G A 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19172;SOR=Inf;LSEQ=GCATTATATGAAGAAATCCC;RSEQ=TTTCCAACGAAGGCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:56,40:0:2,0:21.1:1:30.7:1:1:0:47.6:192:0.9897:0:5.1 0/1:251:6:4,2:125,114:0.0239:2,2:27.3:1:28.2:1:0.68632:1.82:52.7:5:0.0202:0:4 -10 42529400 . T C 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08861;SOR=1.83043;LSEQ=CATTATATGAAGAAATCCCG;RSEQ=TTCCAACGAAGGCCTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:12:9,3:50,38:0.12:2,2:12.4:1:32.1:1:0.34996:2.26:41.5:24:0.1224:0:6.4 0/1:250:50:30,20:101,98:0.2:2,2:17.8:1:31.9:1:0.26975:1.45:42:100:0.2033:0:5.9 -10 42529407 . C T 28 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30059;SOR=0.37176;LSEQ=TGAAGAAATCCCGTTTCCAA;RSEQ=GAAGGCCTCAAAGAAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:51,42:0.0211:2,2:23:0:30:1:1:1.21179:60:4:0.0215:0:3 0/0:253:2:1,1:127,122:0.0079:2,2:25:1:28.5:1:1:1.04083:50:4:0.008:0:5.5 -10 42529410 . A T 70 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32827;SOR=Inf;LSEQ=AGAAATCCCGTTTCCAACGA;RSEQ=GGCCTCAAAGAAGTCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:50,41:0:2,0:21.8:1:30.1:1:1:0:49.3:29.333:0.9888:0:5.1 0/1:244:5:2,3:120,119:0.0205:2,2:12.8:1:30.2:1:1:1.51007:53.2:10:0.0208:0:4.8 -10 42529412 . G T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62143;SOR=0.57752;LSEQ=AAATCCCGTTTCCAACGAAG;RSEQ=CCTCAAAGAAGTCCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:49,39:0.0222:2,2:12.5:1:29:1:1:1.25319:48.5:4:0.0227:0:4.5 0/1:232:3:1,2:115,114:0.0129:2,2:21.7:1:28:1:1:2.01166:50.3:6:0.013:0:3.3 -10 42529413 . C G 34 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0815;SOR=0;LSEQ=AATCCCGTTTCCAACGAAGG;RSEQ=CTCAAAGAAGTCCAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:0,2:51,39:0.0217:2,0:9:0:34:0:0.19589:0:40:4:0.0217:0:5 0/0:229:0:0,0:114,114:0:2,0:20.6:1:30.9:1:1:0:50.4:56:0.9956:0:4.9 -10 42529419 . A T 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.49634;SOR=1.20414;LSEQ=GTTTCCAACGAAGGCCTCAA;RSEQ=GAAGTCCAAATATGCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:90:60:34,26:13,16:0.6667:2,2:25.5:1:30.3:1:0.36663:1.60:51.8:59:0.6629:0:5.2 1/0:208:147:73,74:25,33:0.7067:2,2:27.5:1:29.6:1:0.4396:1.30:54.5:146:0.7087:0:5.1 -10 42529420 . G T 40 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.6544;SOR=0.69509;LSEQ=TTTCCAACGAAGGCCTCAAA;RSEQ=AAGTCCAAATATGCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:45,41:0.0225:2,2:34:1:30.5:1:1:1.0964:39.5:4:0.0227:0:7.5 0/1:191:3:0,3:91,97:0.0157:2,0:30:1:25.3:1:0.24773:0:40:6:0.016:0:7.3 -10 42529421 . AAGTCCAAATATG GGGTCTAACTAAT 134 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01353;SOR=3.69559;LSEQ=TTCCAACGAAGGCCTCAAAG;RSEQ=CACTTGCAGACTTTACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:4:1,3:44,39:0.046:2,2:10.5:1:30.3:1:0.34931:3.34078:32.5:8:0.046:0.046:5.3 0/1:178:27:10,17:73,78:0.1517:2,2:12:1:28.2:1:0.30259:1.58693:41.2:54:0.1552:0.1517:5.3 -10 42529422 . AG CA 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.39557;SOR=0.47743;LSEQ=TCCAACGAAGGCCTCAAAGA;RSEQ=TCCAAATATGCACTTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:3:1,2:45,32:0.0366:2,2:28:1:31.3:1:0.57169:2.77635:37.3:6:0.0366:0.0122:6.7 0/1:169:3:0,3:81,80:0.0178:2,0:33:1:28.5:1:0.24551:0:40:6:0.018:0:6.3 -10 42529423 . G T 35 v4;q23;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5531;SOR=Inf;LSEQ=CCAACGAAGGCCTCAAAGAA;RSEQ=TCCAAATATGCACTTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:45,33:0:2,0:26.6:1:31.3:1:1:0:51.4:38:0.987:0:5.1 0/1:169:3:1,2:81,81:0.0178:2,2:23.7:1:22.7:1:1:1.99191:53.3:2:0.0126:0:6.7 -10 42529425 . C A 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97627;LSEQ=AACGAAGGCCTCAAAGAAGT;RSEQ=CAAATATGCACTTGCAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:1:1,0:44,38:0.012:2,0:6:0:30:0:1:0:40:2:0.0122:0:5 0/1:170:2:0,2:82,85:0.0118:2,0:36:1:31.5:1:0.49746:0:60:4:0.012:0:5.5 -10 42529426 . CA TG 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1076;SOR=0;LSEQ=ACGAAGGCCTCAAAGAAGTC;RSEQ=AATATGCACTTGCAGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:44,36:0.0241:2,2:27.5:1:31.5:1:1:1.21921:48.5:4:0.0247:0:3.5 0/0:169:0:0,0:81,88:0:2,0:27.6:1:30.2:1:1:0:53.7:27.167:1:0:5 -10 42529430 . T A 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3129;SOR=1.44939;LSEQ=AGGCCTCAAAGAAGTCCAAA;RSEQ=ATGCACTTGCAGACTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:62:36,26:9,11:0.7561:2,2:27.9:1:30:1:0.4388:1.68:51.1:124:0.7561:0:5.3 1/1:165:135:70,65:10,16:0.8182:2,2:30.1:1:29.5:1:0.28443:1.72:54.6:134:0.8272:0:5.3 -10 42529432 . T A 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.84838;SOR=0.90516;LSEQ=GCCTCAAAGAAGTCCAAATA;RSEQ=GCACTTGCAGACTTTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:74:41,33:3,8:0.8706:2,2:27.7:1:30.6:1:0.10968:3.27:51.3:148:0.8706:0:5.2 1/1:163:140:72,68:8,13:0.8589:2,2:29.7:1:29.7:1:0.34977:1.71:54.3:34:0.8718:0:5.2 -10 42529433 . G C 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19213;SOR=0.41322;LSEQ=CCTCAAAGAAGTCCAAATAT;RSEQ=CACTTGCAGACTTTACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:6:1,5:46,37:0.0674:2,2:24.2:1:31.7:1:0.09631:6.10392:33.5:12:0.0682:0:5.7 0/1:173:5:0,5:84,82:0.0289:2,0:27.6:1:29.6:1:0.05905:0:37.4:10:0.0291:0:5.6 -10 42529435 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54848;SOR=Inf;LSEQ=TCAAAGAAGTCCAAATATGC;RSEQ=CTTGCAGACTTTACAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:49,45:0:2,0:25.6:1:29.9:1:1:0:48.5:93:0.9894:0:5.1 0/1:183:2:1,1:85,95:0.0109:2,2:11:0:32:1:1:1.12:40.5:4:0.011:0:3.5 -10 42529436 . C G 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0519;SOR=0.28711;LSEQ=CAAAGAAGTCCAAATATGCA;RSEQ=TTGCAGACTTTACAAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:7:3,4:46,41:0.0737:2,2:15.7:1:31.9:1:0.70628:1.48953:36.4:14:0.0753:0:6.4 0/1:180:4:0,4:82,90:0.0222:2,0:36.3:1:26.5:1:0.12422:0:40:3:0.0169:0:6 -10 42529437 . T C 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12269;SOR=0;LSEQ=AAAGAAGTCCAAATATGCAC;RSEQ=TGCAGACTTTACAAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:49,46:0.0206:2,2:17.5:1:27.5:1:1:1.06456:47.5:4:0.0206:0:4 0/0:179:0:0,0:82,95:0:2,0:27.2:1:29.6:1:1:0:52.7:58:0.9886:0:4.8 -10 42529438 . T C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53975;SOR=Inf;LSEQ=AAGAAGTCCAAATATGCACT;RSEQ=GCAGACTTTACAAACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:51,48:0:2,0:25.2:1:29.8:1:1:0:48.3:98:1:0:5 0/1:179:2:1,1:82,95:0.0112:2,2:38:0:32:0:1:1.16:60:4:0.0113:0:7 -10 42529440 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5546;SOR=Inf;LSEQ=GAAGTCCAAATATGCACTTG;RSEQ=AGACTTTACAAACAGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:51,48:0:2,0:25.6:1:32.1:1:1:0:48.3:198:1:0:5 0/1:180:3:2,1:82,95:0.0167:2,2:15.3:1:29.3:1:0.59927:2.31:48.3:6:0.017:0:3.3 -10 42529441 . A T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0946;SOR=0.33106;LSEQ=AAGTCCAAATATGCACTTGC;RSEQ=GACTTTACAAACAGAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:6:1,5:47,42:0.0632:2,2:28:1:31:1:0.11119:5.50784:41.8:12:0.0632:0:5.8 0/1:184:4:0,4:84,96:0.0217:2,0:38.8:1:29:1:0.12659:0:40:8:0.022:0:6 -10 42529443 . A G 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09413;SOR=1.68708;LSEQ=GTCCAAATATGCACTTGCAG;RSEQ=CTTTACAAACAGAGTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:68:37,31:11,16:0.7158:2,2:27.7:1:31.5:1:0.26142:1.73:50.2:67:0.7128:0:5.1 1/1:184:149:73,76:10,23:0.8098:2,2:28:1:31:1:0.05585:2.20:53.9:48.667:0.8066:0:5 -10 42529444 . C A 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61036;SOR=0.52325;LSEQ=TCCAAATATGCACTTGCAGA;RSEQ=TTTACAAACAGAGTGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:2,0:47,48:0.0206:2,0:11:0:31:0:0.49485:0:32:4:0.0208:0:8 0/1:184:2:1,1:82,98:0.0109:2,2:5:1:32:0:1:1.19:30:4:0.0113:0:8 -10 42529445 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54631;SOR=Inf;LSEQ=CCAAATATGCACTTGCAGAC;RSEQ=TTACAAACAGAGTGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:49,48:0:2,0:26.6:1:30.6:1:1:0:48.4:194:1:0:5 0/1:184:2:1,1:82,100:0.0109:2,2:13.5:1:29:1:1:1.22:46:4:0.0109:0:2.5 -10 42529447 . T C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5283;SOR=0.81201;LSEQ=AAATATGCACTTGCAGACTT;RSEQ=ACAAACAGAGTGTTTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:21:13,8:38,41:0.21:2,2:29.5:1:31.3:1:0.32878:1.74:49.6:20:0.2041:0:5.5 0/1:186:33:18,15:65,88:0.1774:2,2:28.5:1:30.8:1:0.24795:1.62:54.8:66:0.1784:0:6 -10 42529451 . A G 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27879;SOR=0.51557;LSEQ=ATGCACTTGCAGACTTTACA;RSEQ=ACAGAGTGTTTCCAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:8:3,5:46,44:0.0816:2,2:25.8:1:32.3:1:0.71473:1.73271:48:16:0.0842:0:5.3 0/1:183:8:1,7:81,94:0.0437:2,2:17.6:1:28.4:1:0.07607:5.98621:36.8:16:0.0449:0:4.6 -10 42529452 . A C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55383;SOR=Inf;LSEQ=TGCACTTGCAGACTTTACAA;RSEQ=CAGAGTGTTTCCAAACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:49,48:0:2,0:26.6:1:29.6:1:1:0:48:47.5:0.9896:0:4.9 0/1:184:3:1,2:80,101:0.0163:2,2:33:1:31.7:1:1:1.58036:60:6:0.0165:0:3.3 -10 42529453 . C T 26 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60956;SOR=0.5204;LSEQ=GCACTTGCAGACTTTACAAA;RSEQ=AGAGTGTTTCCAAACTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:0,2:49,46:0.0206:2,0:5.5:1:27.5:1:0.24227:0:27.5:4:0.0206:0:4 0/1:185:2:0,2:81,101:0.0108:2,0:19:1:26.5:1:0.50445:0:33.5:4:0.011:0:3 -10 42529454 . A T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25062;SOR=0.50707;LSEQ=CACTTGCAGACTTTACAAAC;RSEQ=GAGTGTTTCCAAACTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:7:3,4:44,44:0.0737:2,2:27:1:31.3:1:1:1.32932:36.4:14:0.0737:0:6.4 0/1:181:7:1,6:77,96:0.0387:2,2:25.1:1:31.7:1:0.14113:4.77925:36.1:14:0.0391:0:6.9 -10 42529456 . A C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.61126;SOR=0.52643;LSEQ=CTTGCAGACTTTACAAACAG;RSEQ=GTGTTTCCAAACTGCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:47,47:0.0208:2,2:31.5:1:31:1:1:1:50:4:0.0211:0:5.5 0/1:181:2:1,1:77,102:0.011:2,2:16:1:33:1:1:1.32:60:4:0.0113:0:5.5 -10 42529457 . G C 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.80182;LSEQ=TTGCAGACTTTACAAACAGA;RSEQ=TGTTTCCAAACTGCTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:2,0:46,48:0.0208:2,0:24:0:33.5:1:0.49474:0:32:4:0.0213:0:8 0/1:179:3:1,2:76,100:0.0168:2,2:16.3:1:33.7:1:1:1.51659:31:6:0.0169:0:8 -10 42529458 . T G 78 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4275;SOR=3.28361;LSEQ=TGCAGACTTTACAAACAGAG;RSEQ=GTTTCCAAACTGCTCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:1,0:47,48:0.0104:2,0:15:0:33:0:1:0:40:2:0.0105:0:5 0/1:179:6:3,3:74,98:0.0335:2,2:28.3:1:30.3:1:1:1.32:50:12:0.0337:0:6.8 -10 42529459 . G C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30174;SOR=0.5867;LSEQ=GCAGACTTTACAAACAGAGT;RSEQ=TTTCCAAACTGCTCTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:8:3,5:45,43:0.0825:2,2:25.6:1:32.6:1:0.71447:1.73424:48:16:0.0851:0:5.3 0/1:180:9:1,8:77,93:0.05:2,2:23.7:1:30.1:1:0.07962:6.57132:37.1:18:0.0503:0:4.9 -10 42529463 . C A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28273;SOR=0.268;LSEQ=ACTTTACAAACAGAGTGTTT;RSEQ=CAAACTGCTCTATGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:47,49:0.0204:2,2:22:1:28:1:1:1.04:50:4:0.0206:0:5.5 0/0:181:1:0,1:81,99:0.0055:2,0:21:0:32:0:1:0:60:2:0.0057:0:5 -10 42529465 . A C 66 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.05412;SOR=0.1325;LSEQ=TTTACAAACAGAGTGTTTCC;RSEQ=AACTGCTCTATGAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:4:2,2:45,46:0.0421:2,2:20:1:33:1:1:1.02:54.3:8:0.043:0:3.8 0/0:174:1:1,0:78,94:0.0057:2,0:34:0:27:0:0.45665:0:60:2:0.0058:0:4 -10 42529467 . A C 45 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.70591;LSEQ=TACAAACAGAGTGTTTCCAA;RSEQ=CTGCTCTATGAAAAGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:1,0:46,47:0.0105:2,0:24:0:34:0:1:0:40:2:0.011:0:5 0/1:168:3:1,2:69,96:0.0179:2,2:15:1:29:1:1:1.43451:60:6:0.0181:0:6.3 -10 42529468 . C G 83 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02681;SOR=0.17792;LSEQ=ACAAACAGAGTGTTTCCAAA;RSEQ=TGCTCTATGAAAAGAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:6:3,3:43,45:0.0638:2,2:19.5:1:32.2:1:1:1.05:56.2:12:0.0652:0:5.5 0/1:168:2:1,1:68,97:0.0119:2,2:28:1:32.5:1:1:1.42:40.5:4:0.012:0:7.5 -10 42529470 . G T 59 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01758;SOR=0;LSEQ=AAACAGAGTGTTTCCAAACT;RSEQ=CTCTATGAAAAGAAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:4:2,2:43,44:0.0417:2,2:19.3:1:29.8:1:1:1.02:55:8:0.0426:0:4.8 0/0:165:0:0,0:66,96:0:2,0:24.6:1:31.6:1:1:0:50.1:53:0.9815:0:4.9 -10 42529473 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.53855;SOR=Inf;LSEQ=CAGAGTGTTTCCAAACTGCT;RSEQ=TATGAAAAGAAAGGTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:46,46:0:2,0:25.3:1:31.8:1:1:0:46.3:91:1:0:5 0/1:165:2:1,1:65,98:0.0121:2,2:40.5:1:32:1:1:1.50:47:4:0.0122:0:7.5 -10 42529474 . T G 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62196;SOR=0.56309;LSEQ=AGAGTGTTTCCAAACTGCTC;RSEQ=ATGAAAAGAAAGGTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:46,45:0.0215:2,2:16:1:32.5:1:1:1.02198:60:4:0.0217:0:4 0/1:164:2:1,1:64,97:0.0122:2,2:27:1:29.5:1:1:1.51:51.5:4:0.0123:0:3.5 -10 42529476 . T C 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08679;SOR=1.7182;LSEQ=AGTGTTTCCAAACTGCTCTA;RSEQ=GAAAAGAAAGGTTAAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:21:12,9:33,36:0.2283:2,2:23.4:1:30.6:1:0.61889:1.45:47.8:42:0.2283:0:5.8 0/1:163:55:25,30:39,67:0.3374:2,2:22.1:1:29.5:1:0.31157:1.43:48.7:110:0.3459:0:5.6 -10 42529477 . G T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.35473;SOR=0.37007;LSEQ=GTGTTTCCAAACTGCTCTAT;RSEQ=AAAAGAAAGGTTAAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:3:1,2:45,44:0.0326:2,2:19:1:28.7:1:1:2.03014:53.3:6:0.0333:0:5.3 0/1:163:2:1,1:65,95:0.0123:2,2:24:1:27.5:1:1:1.46:51.5:4:0.0124:0:3.5 -10 42529480 . A G 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.3017;LSEQ=TTTCCAAACTGCTCTATGAA;RSEQ=AGAAAGGTTAAACTCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:0,3:44,42:0.0337:2,0:17.3:1:32.7:1:0.24157:0:35.7:6:0.0341:0:5.7 0/1:161:7:0,7:65,89:0.0435:2,0:20:1:30.4:1:0.04215:0:36.1:14:0.0455:0:4.1 -10 42529483 . AA GT 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53993;SOR=Inf;LSEQ=CCAAACTGCTCTATGAAAAG;RSEQ=AGGTTAAACTCTGTGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:43,43:0:2,0:24.1:1:30.2:1:1:0:45.8:172:1:0:5.1 0/1:156:2:1,1:61,92:0.0128:2,2:29.5:1:29.8:1:1:1.50:47:4:0.013:0:6.5 -10 42529486 . G A 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30019;SOR=Inf;LSEQ=AACTGCTCTATGAAAAGAAA;RSEQ=GTTAAACTCTGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:39,42:0:2,0:24.4:1:31.4:1:1:0:45.4:39.5:1:0:5.1 0/1:149:4:2,2:57,87:0.0268:2,2:28.5:1:29.5:1:1:1.52:53.8:8:0.0272:0:6 -10 42529487 . G T 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28383;SOR=0.26851;LSEQ=ACTGCTCTATGAAAAGAAAG;RSEQ=TTAAACTCTGTGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:38,41:0.0247:2,2:22.5:1:29:1:1:1.08:50:4:0.0256:0:5.5 0/0:149:1:1,0:57,89:0.0067:2,0:43:0:28:0:0.39456:0:40:2:0.0068:0:4 -10 42529489 . T G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.75054;SOR=0.84373;LSEQ=TGCTCTATGAAAAGAAAGGT;RSEQ=AAACTCTGTGAGTTGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:4:1,3:37,40:0.0494:2,2:13.8:1:32.5:1:0.61844:2.74346:36.8:8:0.0506:0:5.5 0/1:143:6:0,6:57,79:0.042:2,0:10.8:1:31.3:1:0.08108:0:35.5:12:0.0438:0:4 -10 42529490 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53533;SOR=Inf;LSEQ=GCTCTATGAAAAGAAAGGTT;RSEQ=AACTCTGTGAGTTGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:38,42:0:2,0:22.8:1:29.1:1:1:0:44.5:160:0.9877:0:5.1 0/1:142:2:1,1:56,83:0.0141:2,2:20:1:30.5:1:1:1.48:43.5:4:0.0143:0:4.5 -10 42529492 . A G 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.30124;SOR=Inf;LSEQ=TCTATGAAAAGAAAGGTTAA;RSEQ=CTCTGTGAGTTGAATGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:38,41:0:2,0:22.5:1:29.5:1:1:0:44.3:38.5:0.9872:0:5.2 0/1:139:3:0,3:55,80:0.0216:2,0:20:1:27:1:0.27563:0:53.3:2:0.0149:0:4.3 -10 42529493 . C A 45 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.68789;LSEQ=CTATGAAAAGAAAGGTTAAA;RSEQ=TCTGTGAGTTGAATGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:35,40:0.0132:2,0:1:0:27:0:0.47368:0:45:2:0.0133:0:6 0/1:136:3:1,2:54,79:0.0221:2,2:10.7:1:28.7:1:1:1.36406:47.7:6:0.0224:0:4.7 -10 42529494 . T A 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18996;SOR=0.26926;LSEQ=TATGAAAAGAAAGGTTAAAC;RSEQ=CTGTGAGTTGAATGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:0,4:34,35:0.0548:2,0:11:1:31.8:1:0.11818:0:38:8:0.0571:0:5.8 0/1:131:2:0,2:53,75:0.0153:2,0:7:1:31:0:0.5133:0:40:4:0.0155:0:6 -10 42529495 . C T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.8527;LSEQ=ATGAAAAGAAAGGTTAAACT;RSEQ=TGTGAGTTGAATGCACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:0,2:34,36:0.0274:2,0:39:1:32:0:0.49452:0:40:4:0.0274:0:6 0/1:128:3:1,2:51,74:0.0234:2,2:17.3:1:28:1:1:1.37505:46.7:6:0.024:0:4.3 -10 42529496 . T C 57 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29897;SOR=Inf;LSEQ=TGAAAAGAAAGGTTAAACTC;RSEQ=GTGAGTTGAATGCACACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:33,39:0:2,0:23.7:1:30.5:1:1:0:43.4:71:1:0:5.2 0/1:129:4:2,2:51,74:0.031:2,2:18:1:28.8:1:1:1.45:53.5:8:0.0325:0:5.3 -10 42529498 . T G 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.36158;SOR=0.38449;LSEQ=AAAAGAAAGGTTAAACTCTG;RSEQ=GAGTTGAATGCACACATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:2,1:32,38:0.0411:2,2:33.3:1:29:1:0.59493:2.35:34.7:6:0.0429:0:7 0/1:124:2:1,1:50,72:0.0161:2,2:27.5:1:30:1:1:1.44:21:4:0.0167:0:7 -10 42529500 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5388;SOR=Inf;LSEQ=AAGAAAGGTTAAACTCTGTG;RSEQ=GTTGAATGCACACATCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:31,36:0:2,0:23.8:1:30.4:1:1:0:42.7:66:1:0:5.2 0/1:121:2:1,1:48,71:0.0165:2,2:14.5:1:28.5:1:1:1.47:60:4:0.0169:0:4 -10 42529503 . T C 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52801;SOR=Inf;LSEQ=AAAGGTTAAACTCTGTGAGT;RSEQ=GAATGCACACATCACAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:30,32:0:2,0:24.5:1:29.8:1:1:0:42.5:61:1:0:5.3 0/1:103:2:1,1:45,56:0.0194:2,2:10.5:1:28.5:1:1:1.24:47:4:0.0196:0:6.5 -10 42529506 . AT GC 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52874;SOR=Inf;LSEQ=GGTTAAACTCTGTGAGTTGA;RSEQ=GCACACATCACAAAGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:30,31:0:2,0:23.8:1:29.5:1:1:0:42.2:60:1:0:5.3 0/1:102:2:1,1:45,55:0.0196:2,2:20.5:1:29:1:1:1.22:50:4:0.02:0.0098:6 -10 42529507 . T C 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80584;SOR=1.17212;LSEQ=GTTAAACTCTGTGAGTTGAA;RSEQ=GCACACATCACAAAGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:50:25,25:2,1:0.8621:2,2:24.6:1:29.9:1:1:1.97488:44.1:24:0.8571:0:5.4 1/1:100:88:43,45:2,6:0.88:2,2:25.8:1:29.7:1:0.27595:2.84:44.5:43:0.8866:0:5.4 -10 42529510 . A C 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.14793;LSEQ=AAACTCTGTGAGTTGAATGC;RSEQ=CACATCACAAAGTAGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:1:0,1:28,25:0.0182:2,0:41:0:13:0:0.48148:0:40:0:0:0:8 0/1:96:2:1,1:41,51:0.0208:2,2:27.5:1:29:1:1:1.24:21:4:0.0211:0:7 -10 42529513 . C T 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.70568;SOR=0.7551;LSEQ=CTCTGTGAGTTGAATGCACA;RSEQ=ATCACAAAGTAGTTCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:3:2,1:25,27:0.0545:2,2:22.7:1:27.3:1:0.61098:2.13:34.7:6:0.0556:0:7 0/1:96:4:1,3:42,49:0.0417:2,2:26.3:1:28.8:1:0.62389:2.54819:28.5:8:0.043:0:7 -10 42529516 . C A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53377;SOR=Inf;LSEQ=TGTGAGTTGAATGCACACAT;RSEQ=ACAAAGTAGTTCTTTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:27,28:0:2,0:23.4:1:30.4:1:1:0:43.6:17.333:1:0:5.5 0/1:96:2:1,1:42,52:0.0208:2,2:21.5:1:26:1:1:1.24:40.5:4:0.0213:0:7.5 -10 42529522 . G C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.12357;SOR=0;LSEQ=TTGAATGCACACATCACAAA;RSEQ=TAGTTCTTTAGAATGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:0,2:26,24:0.0385:2,0:6:0:33:0:0.4902:0:27.5:4:0.0392:0:2.5 0/0:95:0:0,0:43,52:0:2,0:24.1:1:31:1:1:0:43.9:46.5:1:0:5.7 -10 42529528 . C G 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.74675;SOR=0.67683;LSEQ=GCACACATCACAAAGTAGTT;RSEQ=TTTAGAATGATTCTGTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:45:22,23:2,1:0.9375:2,2:23.9:1:32:1:1:2.05999:45.8:90:0.9375:0:5.9 1/1:89:81:40,41:2,4:0.9101:2,2:25:1:31.5:1:0.67741:1.94:45.2:162:0.9205:0:5.9 -10 42529529 . T C 65 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66075;SOR=2.11001;LSEQ=CACACATCACAAAGTAGTTC;RSEQ=TTAGAATGATTCTGTCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:1:0,1:21,23:0.0222:2,0:20:0:32:0:1:0:40:2:0.0227:0:6 0/1:87:4:1,3:40,43:0.046:2,2:17:1:32.8:1:0.61872:2.76101:35.8:8:0.0465:0:7.3 -10 42529531 . T G 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCACAAAGTAGTTCTT;RSEQ=AGAATGATTCTGTCTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:21,20:0,0:1:0,2:25.8:1:31.7:1:1:0:46.4:82:1:0:6 1/1:83:82:38,44:0,0:0.988:0,2:24.6:1:31.6:1:1:0:44.8:164:1:0:6 -10 42529537 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55208;SOR=Inf;LSEQ=ACAAAGTAGTTCTTTAGAAT;RSEQ=ATTCTGTCTAGTTTTTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:0:2,0:23:1:31:1:1:0:45.5:20.5:1:0:6.3 0/1:86:2:1,1:39,45:0.0233:2,2:13:1:31.5:1:1:1.15:41.5:4:0.0233:0:6 -10 42529539 . T G 54 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2997;SOR=Inf;LSEQ=AAAGTAGTTCTTTAGAATGA;RSEQ=TCTGTCTAGTTTTTATACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:0:2,0:22.5:1:30.1:1:1:0:45.5:42:1:0:6.3 0/1:85:4:2,2:36,45:0.0471:2,2:15.3:1:27:1:1:1.25:53.8:3:0.0366:0:7 -10 42529543 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGTTCTTTAGAATGATTCT;RSEQ=TCTAGTTTTTATACGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:19,22:0:2,0:22.6:1:31.6:1:1:0:45.9:40:1:0:6.5 0/1:83:2:1,1:39,42:0.0241:2,2:31.5:1:29.5:1:1:1.08:47.5:4:0.0244:0:7 -10 42529545 . C G 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16285;SOR=0.20962;LSEQ=GTTCTTTAGAATGATTCTGT;RSEQ=TAGTTTTTATACGAAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:38:19,19:0,1:0.9744:0,2:23.9:1:32.1:1:1:0:46.3:76:0.9744:0:6.6 1/1:80:71:35,36:0,1:0.8875:0,2:21.6:1:31.3:1:1:0:46.2:34.5:0.8846:0:6.4 -10 42529548 . G C 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.30882;SOR=Inf;LSEQ=CTTTAGAATGATTCTGTCTA;RSEQ=TTTTTATACGAAGATACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:24.2:1:31.6:1:1:0:45.9:36:1:0:6.6 0/1:82:4:2,2:35,37:0.0488:2,2:12.5:1:29.8:1:1:1.06:40:8:0.0541:0:7 -10 42529555 . T A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATGATTCTGTCTAGTTTTTA;RSEQ=ACGAAGATACTTCCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:23.8:1:29.1:1:1:0:46.6:36:1:0:6.7 0/1:82:2:1,1:37,43:0.0244:2,2:37:1:29:1:1:1.16:58:4:0.0244:0:8 -10 42529565 . C T 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1686;SOR=0;LSEQ=CTAGTTTTTATACGAAGATA;RSEQ=TTCCTTTTCTACAATTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:16,20:0,0:1:0,2:23.8:1:30.3:1:1:0:46.8:35:1:0:6.9 1/1:73:68:28,40:0,0:0.9315:0,2:23.3:1:30.1:1:1:0:45.9:136:0.9315:0:6.9 -10 42529576 . A G 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16495;SOR=0;LSEQ=ACGAAGATACTTCCTTTTCT;RSEQ=CAATTGGCCTAGAAGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:8,17:0,0:1:0,2:31.5:1:32.4:1:1:0:47.8:50:1:0:7.5 1/1:51:46:21,25:2,3:0.902:2,2:32.2:1:32.2:1:1:1.25:48.9:92:0.902:0:7.2 -10 42529578 . A C 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATACTTCCTTTTCTAC;RSEQ=ATTGGCCTAGAAGCGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:8,17:0,0:1:0,2:31.4:1:31.5:1:1:0:47.8:24:1:0:7.5 1/1:50:49:22,27:0,0:0.98:0,2:33.4:1:31.1:1:1:0:50.7:98:0.98:0:7.3 -10 42529581 . T A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATACTTCCTTTTCTACAAT;RSEQ=GGCCTAGAAGCGCTTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:8,16:0,0:1:0,2:32.3:1:30.6:1:1:0:47.3:48:1:0:7.5 1/1:52:51:22,29:0,1:0.9808:0,2:33:1:29.4:1:1:0:50.1:50:0.9804:0:7.2 -10 42529586 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63279;SOR=0.62437;LSEQ=TTCCTTTTCTACAATTGGCC;RSEQ=AGAAGCGCTTGAAATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:7,17:0.0769:2,2:33.5:1:32:1:0.52923:2.34:47:4:0.0769:0:7 0/1:61:3:1,2:26,32:0.0492:2,2:5:0:32:1:1:1.61261:27.3:6:0.0508:0:3.7 -10 42529588 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07731;SOR=0;LSEQ=CCTTTTCTACAATTGGCCTA;RSEQ=AAGCGCTTGAAATCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:6,16:0.0833:2,2:38.5:1:29:1:0.50725:2.54:44.5:4:0.0833:0:8 0/0:61:0:0,0:27,34:0:2,0:28.1:1:31.2:1:1:0:49.8:122:1:0:6.9 -10 42529591 . G T 48 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.1873;LSEQ=TTTCTACAATTGGCCTAGAA;RSEQ=CGCTTGAAATCTGCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:7,16:0.0417:2,0:25:0:31:0:1:0:48:2:0.0417:0:8 0/1:61:3:1,2:26,32:0.0492:2,2:32:1:30.3:1:1:1.61261:56.7:6:0.0508:0:6.7 -10 42529600 . A G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60921;SOR=0.54037;LSEQ=TTGGCCTAGAAGCGCTTGAA;RSEQ=TCTGCACTTGCAAATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:4,16:0.0909:2,2:42:0:33.5:1:0.41126:3.69:47:4:0.0909:0:7 0/1:59:3:1,2:25,31:0.0508:2,2:19:0:33:1:1:1.60039:27.3:6:0.0526:0:3.7 -10 42529619 . AC GA 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCTGCACTTGCAAATTCC;RSEQ=AAAAAGAGTGTTTCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:3,13:0:2,0:19.4:1:31:1:1:0:44.1:32:1:0:7.3 0/1:45:2:1,1:18,25:0.0444:2,2:14.5:1:28.5:1:1:1.38:49:4:0.0444:0:7 -10 42529620 . C A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.31114;SOR=0;LSEQ=ATCTGCACTTGCAAATTCCA;RSEQ=AAAAAGAGTGTTTCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:3,12:0,0:1:0,2:19.9:1:30.9:1:1:0:43.6:30:1:0:7.3 1/1:42:37:15,22:1,2:0.881:2,2:20.8:1:29.2:1:1:1.35:49.9:36:0.9231:0:6.6 -10 42529624 . A C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.66985;SOR=1.67181;LSEQ=GCACTTGCAAATTCCACAAA;RSEQ=AGAGTGTTTCAAATCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:2,9:1,2:0.7857:2,2:18.3:1:32.2:1:1:2.10574:42.3:22:0.7857:0:7.3 1/1:36:31:12,19:2,3:0.8611:2,2:20.4:1:31.4:1:1:1.05395:51.2:62:0.8611:0:6.9 -10 42529626 . G C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1223;LSEQ=ACTTGCAAATTCCACAAAAA;RSEQ=AGTGTTTCAAATCTGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:2,10:0.0769:2,0:10:0:33:0:1:0:48:2:0.0769:0:8 0/1:35:3:1,2:12,20:0.0857:2,2:6:1:30:1:1:1.19386:47.3:6:0.0857:0:7 -10 42529637 . A C 117 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.09243;SOR=7.8685;LSEQ=CCACAAAAAGAGTGTTTCAA;RSEQ=TCTGCTCTGTGTAAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:1,6:0.125:2,0:9:0:33:0:1:0:47:2:0.125:0:7 1/0:22:12:3,9:4,6:0.5455:2,2:7.4:1:32.7:1:0.6517:1.93655:47.6:24:0.5455:0:7 -10 42529646 . G C 100 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGTGTTTCAAATCTGCTCT;RSEQ=TGTAAAGGAAGTTTCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:23.7:1:33.3:1:1:0:46:6:1:0:7.3 1/1:9:9:3,6:0,0:1:0,2:21:1:31.7:1:1:0:54.6:18:1:0:6.8 -10 42529648 . G C 83 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTTTCAAATCTGCTCTGT;RSEQ=TAAAGGAAGTTTCAAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:21.7:1:33.3:1:1:0:46:6:1:0:7.3 1/1:7:6:2,4:0,0:0.8571:0,2:24.3:1:32.3:1:1:0:56:12:0.8571:0:6.2 -10 42529658 . T G 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22222;SOR=Inf;LSEQ=TCTGCTCTGTGTAAAGGAAG;RSEQ=TTCAAAACTGTGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:17:0:34:0:1:0:58:2:1:0:7 1/1:7:7:3,4:0,0:1:0,2:14.6:1:30.6:1:1:0:56.6:14:1:0:6.4 -10 42529665 . A T 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTAAAGGAAGTTTCAAA;RSEQ=CTGTGAGTTGAACAGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:11.5:1:31:0:1:0:49:4:1:0:6.5 1/1:5:4:2,2:0,0:0.8:0,2:12.5:1:29.5:1:1:0:59:8:1:0:7 -10 42529704 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACACAAAGAAGTTACTGA;RSEQ=AATTCTTCTGTCTAGCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:24:0:33:0:1:0:40:2:1:0:5 1/0:4:2:0,2:1,1:0.5:2,0:18:1:31:1:1:0:29:4:0.5:0:6 -10 42529721 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAAATTCTTCTGTCTAGC;RSEQ=TTATCTGAAGAAATCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:41:0:33:0:1:0:40:2:1:0:5 1/0:4:2:0,2:1,1:0.5:2,0:34.5:1:32:1:1:0:29:4:0.5:0:6 -10 42529724 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATTCTTCTGTCTAGCATT;RSEQ=TCTGAAGAAATCCCTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:39:0:33:0:1:0:40:2:1:0:5 1/0:4:2:0,2:1,1:0.5:2,0:34.5:1:32.5:1:1:0:29:4:0.5:0:6 -10 42529726 . C A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTTCTGTCTAGCATTAT;RSEQ=TGAAGAAATCCCTTTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:37:0:33:0:1:0:40:2:1:0:5 1/0:4:2:0,2:1,1:0.5:2,0:34.5:1:31.5:1:1:0:29:4:0.5:0:6 -10 42529763 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAACGAAGGCCTCAAAGAG;RSEQ=TCCAAATAACCACTTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:0,2:1,1:0.5:2,0:18:1:30.5:1:1:0:34.5:4:0.5:0:6.5 -10 42529780 . T C 79 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATCCAAATAACCACTTG;RSEQ=AGACTTTACAGACAGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:8:6:3,3:1,1:0.75:2,2:7.7:1:30.7:1:1:1:42.8:12:0.75:0:6.3 -10 42529814 . A C 88 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGTTTCCAAACTGCTC;RSEQ=ATTAAAAGAAAGGTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:32:1:33:1:1:0:43.5:8:1:0:5.8 1/1:7:7:3,4:0,0:1:0,2:32.7:1:31.4:1:1:0:42.7:14:1:0:6.1 -10 42529817 . T C 88 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTCCAAACTGCTCAAT;RSEQ=AAAAGAAAGGTTAAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:35:1:33:1:1:0:43.5:8:1:0:5.8 1/1:7:7:3,4:0,0:1:0,2:34:1:31.7:1:1:0:42.7:14:1:0:6.1 -10 42529819 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=GTTTCCAAACTGCTCAATTA;RSEQ=AAGAAAGGTTAAACTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:37:1:31.5:1:1:0:43.5:8:1:0:5.8 0/1:7:2:1,1:2,3:0.2857:2,2:23.5:1:31.5:1:1:1.41:57:4:0.2857:0:5.5 -10 42529836 . TG CT 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTAAAAGAAAGGTTAAACTC;RSEQ=TGAGTTGAACGCACACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:32.8:1:31.5:1:1:0:43.5:8:1:0:4.8 1/1:6:6:2,4:0,0:1:0,2:36.5:1:31:1:1:0:40.7:12:1:0:5.5 -10 42529848 . G A 78 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACTCTGTGAGTTGAAC;RSEQ=CACACATCACAAAGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:21.8:1:29.8:1:1:0:43.5:8:1:0:4.8 1/1:6:6:2,4:0,0:1:0,2:25.5:1:30.2:1:1:0:40.7:12:1:0:5.5 -10 42529872 . A T 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATCACAAAGTAGTTTCTG;RSEQ=GAATGATTCTCTGTAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:2.5:1:28.5:1:1:0:47:4:1:0:5 1/0:4:3:1,2:0,1:0.75:0,2:8.3:1:32:0:1:0:42.3:6:0.75:0:5.7 -10 42529908 . A C 136 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTTATATGAAGATATTT;RSEQ=CATTTCTAACATTGGCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:20:20:9,11:0,0:1:0,2:14.3:1:31.6:1:1:0:49.1:40:1:0:3.4 -10 42529912 . T G 138 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATATGAAGATATTTACAT;RSEQ=TCTAACATTGGCGTCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:20:20:9,11:0,0:1:0,2:18.3:1:32.1:1:1:0:49.1:40:1:0:3.4 -10 42529916 . A T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAAGATATTTACATTTCT;RSEQ=ACATTGGCGTCAAATCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:20:2:1,1:8,10:0.1:2,2:23:0:29.5:1:1:1.24:60:4:0.1:0:4 -10 42529918 . C G 138 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATATTTACATTTCTAA;RSEQ=ATTGGCGTCAAATCGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:20:20:9,11:0,0:1:0,2:24.3:1:32.1:1:1:0:49.1:40:1:0:3.4 -10 42529924 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTACATTTCTAACATTGG;RSEQ=GTCAAATCGCTTGAAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:20:2:1,1:8,10:0.1:2,2:30:0:32:0:1:1.24:47:4:0.1:0:4 -10 42529969 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCAAAAGCCACGAAAAGAG;RSEQ=GTTTCAAAACTGCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:5:0:30.5:1:1:0:44:4:1:0:5 -10 42529977 . AA CT 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGAAAAGAGAGTTTCAA;RSEQ=CTGCTCTGTCTAAAGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:14:0:32.5:1:1:0:44:4:0.6667:0:4 -10 42529985 . TG CC 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGAGTTTCAAAACTGCTC;RSEQ=TCTAAAGAAAGGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:7:0:32:0:1:0:42:2:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:6.5:1:30.8:1:1:1.73:46:4:0.4:0:2 -10 42529986 . G C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTTTCAAAACTGCTCT;RSEQ=TCTAAAGAAAGGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:8:0:34:0:1:0:42:2:1:0:2 0/1:5:2:1,1:0,1:0.4:0,2:22:0:33.5:1:1:0:44:4:0.6667:0:4 -10 42530015 . G C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGTTCAACTCTGTGAGTT;RSEQ=AATACACACAACACAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24.5:1:33.5:1:1:0:35.5:4:1:0:5 0/1:6:2:1,1:1,3:0.3333:2,2:23:0:33.5:1:1:2.45:46:4:0.3333:0:2 -10 42530023 . A C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACTCTGTGAGTTGAATACAC;RSEQ=CAACACAAAGAAGTTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24.5:1:31.5:1:1:0:35.5:4:1:0:5 0/1:5:2:1,1:1,2:0.4:2,2:9.5:1:30:1:1:1.73:44:4:0.4:0:4 -10 42530044 . A G 30 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACACAAAGAAGTTACTGA;RSEQ=AATTCTTCTGTCTAGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:30.5:1:1:0:35.5:4:1:0:5 1/1:1:1:0,1:0,0:1:0,0:17:0:33:0:1:0:21:2:1:0:1 -10 42530168 . T G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CTGCTCTATGAAAAGAAAGG;RSEQ=TAAACTCTGTGAGTTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:26:1:31.8:1:1:0:33.8:8:1:0:4.5 1/0:3:2:2,0:1,0:0.6667:0,0:18.5:1:32.5:1:1:0:32.5:4:0.6667:0:5 -10 42530174 . T A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TATGAAAAGAAAGGTTAAAC;RSEQ=CTGTGAGTTGAAAGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:32:1:32.3:1:1:0:33.8:8:1:0:4.5 1/0:4:3:2,1:1,0:0.75:0,2:17.3:1:30:1:1:0:30:6:0.75:0:5 -10 42530187 . A C 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=GTTAAACTCTGTGAGTTGAA;RSEQ=GCACACAACACAAAGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:43:1:32.3:1:1:0:34:6:0.75:0:3.3 1/1:5:4:3,1:0,1:0.8:0,2:35.3:1:32:1:0.4:0:30.3:8:1:0:5 -10 42530194 . AA CT 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TCTGTGAGTTGAAAGCACAC;RSEQ=CACAAAGTAGTTTCTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:35:1:32:1:1:0:35:10:1:0:4.6 0/1:5:2:1,1:2,1:0.4:2,2:35:1:30.5:1:1:1.7321:25:4:0.4:0:4 -10 42530195 . A T 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.77001;LSEQ=CTGTGAGTTGAAAGCACACA;RSEQ=CACAAAGTAGTTTCTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,0:0.6667:0,2:31.8:1:31.5:1:1:0:33.8:8:0.6667:0:5 1/0:5:3:2,1:0,0:0.6:0,2:31.3:1:27.7:1:1:0:34:6:1:0:4.7 -10 42530203 . T C 75 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.52862;LSEQ=TGAAAGCACACAACACAAAG;RSEQ=AGTTTCTGAGAATGATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:17:1:33.5:1:1:1.41418:31:4:0.2857:0:6 0/1:13:5:3,2:5,3:0.3846:2,2:4.4:1:32.6:1:1:1.10211:37:10:0.4545:0:3 -10 42530206 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91307;LSEQ=AAGCACACAACACAAAGTAG;RSEQ=TTCTGAGAATGATACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:36.5:1:31.5:1:1:1.41418:31:4:0.2857:0:3.5 0/1:15:4:2,2:7,4:0.2667:2,2:16.5:1:31.3:1:1:1.68385:28:8:0.2667:0:5.5 -10 42530220 . A T 48 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02767;SOR=0;LSEQ=AAGTAGTTTCTGAGAATGAT;RSEQ=CTGTCTAGTTTTTATACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:2,3:0.375:2,2:21:1:30.7:1:1:2.60:32.7:6:0.375:0:4.7 0/0:16:0:0,0:9,7:0:2,0:23.3:1:27.9:1:1:0:33.7:15:1:0:3.8 -10 42530226 . T G 32 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09333;SOR=0;LSEQ=TTTCTGAGAATGATACTGTC;RSEQ=AGTTTTTATACGAAGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:22:1:32:1:1:1:29:4:0.25:0:4 0/0:17:0:0,0:10,7:0:2,0:25.1:1:29:1:1:0:32.9:16:1:0:4 -10 42530230 . T G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGAATGATACTGTCTAGT;RSEQ=TTTATACGAAGATATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:24:1:29.9:1:1:0:34.7:14:1:0:3.9 0/1:18:2:1,1:9,7:0.1111:2,2:28:0:33.5:1:1:1.26772:25:4:0.1111:0:6.5 -10 42530234 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGATACTGTCTAGTTTTT;RSEQ=TACGAAGATATTTCCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:24.6:1:29.7:1:1:0:34.7:14:1:0:3.9 0/1:18:2:1,1:8,7:0.1111:2,2:35:0:33:0:1:1.13389:50:4:0.1176:0:3 -10 42530237 . C T 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05929;SOR=0;LSEQ=GATACTGTCTAGTTTTTATA;RSEQ=GAAGATATTTCCTTTTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:33:1:31:1:1:1:29:4:0.3333:0:4 0/0:17:0:0,0:9,8:0:2,0:26.7:1:30.6:1:1:0:32.5:34:1:0:3.8 -10 42530249 . CT C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0.70606;LSEQ=TTTTTATACGAAGATATTTC;RSEQ=TTTCTACCATTGGCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:44:0:32:0:1:0:43:2:0.25:0:4 0/1:16:3:1,2:7,6:0.1875:2,2:33.3:1:32.3:1:1:2.21433:27:6:0.1875:0:5.7 -10 42530254 . C G 108 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02601;SOR=Inf;LSEQ=ATACGAAGATATTTCCTTTT;RSEQ=TACCATTGGCCTCAAATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:39.5:1:32.3:1:1:0:35.3:8:1:0:4.5 1/0:16:11:5,6:3,2:0.6875:2,2:11.7:1:31.3:1:1:1.73457:33.4:22:0.6875:0:2.5 -10 42530265 . C G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.086;LSEQ=TTTCCTTTTCTACCATTGGC;RSEQ=TCAAATCGCTTGAAATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:30:0:33:0:1:0:43:2:0.25:0:4 0/1:15:4:2,2:5,6:0.2667:2,2:22:1:31:1:1:1.19:35.3:8:0.2857:0:6 -10 42530271 . T G 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26573;SOR=5.16556;LSEQ=TTTCTACCATTGGCCTCAAA;RSEQ=CGCTTGAAATCTCCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:24:0:33:0:1:0:43:2:0.25:0:4 1/0:9:6:3,3:2,1:0.6667:2,2:19.8:1:31.3:1:1:1.8525:31.8:12:0.75:0:6 -10 42530276 . T A 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57576;SOR=2.74155;LSEQ=ACCATTGGCCTCAAATCGCT;RSEQ=GAAATCTCCACTTGCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:19:0:33:0:1:0:43:2:0.2:0:4 0/1:7:3:2,1:3,1:0.4286:2,2:14.7:1:28:1:1:1.41418:36.7:6:0.4286:0:6.7 -10 42530280 . A T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57576;SOR=2.74155;LSEQ=TTGGCCTCAAATCGCTTGAA;RSEQ=TCTCCACTTGCAAAAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:15:0:31:0:1:0:43:2:0.2:0:4 0/1:7:3:2,1:3,1:0.4286:2,2:10.7:1:29.7:1:1:1.41418:36.7:6:0.4286:0:6.7 -10 42530304 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTTGCAAAAGCCACGAA;RSEQ=AGAGAGTTTCAAATCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:31:0:25:0:1:0:40:2:1:0:3 1/0:3:2:1,1:1,0:0.6667:0,2:40:0:29:1:1:0:59:4:0.6667:0:3 -10 42530327 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTTTCAAATCTGCTCTG;RSEQ=CTAAAGAAAGGTTCAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:17:0:31:0:1:0:40:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:17:0:33:1:1:0:59:4:1:0:3 -10 42530332 . A G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=0.33333;SOR=Inf;LSEQ=TTCAAATCTGCTCTGTCTAA;RSEQ=GAAAGGTTCAACTCTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:12:0:31:0:1:0:40:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:12:0:33:1:1:0:59:4:1:0:3 -10 42530518 . A T 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAAGAAAGGTTAAACTCTG;RSEQ=GAGTTGAACGCACACATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18.5:1:28:1:1:0:38.5:4:1:0:3.5 1/1:6:6:5,1:0,0:1:0,2:18.2:1:26.8:1:1:0:32.3:5:1:0:6 -10 42530528 . G A 68 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACTCTGAGAGTTGAAC;RSEQ=CACACATCACAAAGTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21:1:28.5:1:1:0:38.5:4:1:0:3.5 1/1:6:5:4,1:0,0:0.8333:0,2:27.8:1:29.4:1:1:0:30.6:10:1:0:6.4 -10 42530544 . A G 93 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGCACACATCACAAAGT;RSEQ=TTTTCTGAGAAAGATTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:43:0:34:0:1:0:40:2:1:0:5 1/1:9:8:6,2:0,0:0.8889:0,2:26.3:1:31.1:1:1:0:37.6:16:1:0:6.1 -10 42530556 . A T 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAAGTATTTTCTGAGAA;RSEQ=GATTTTGTCTAGTTTTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:37:0:32:0:1:0:40:2:1:0:5 1/1:10:10:8,2:0,0:1:0,2:26.4:1:27.9:1:1:0:37.8:4:1:0:6.1 -10 42530573 . A T 54 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAAGATTTTGTCTAGTTTT;RSEQ=ATACGAAGATATTTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:13:1:28.5:1:1:0:54:8:1:0:7 0/1:20:4:2,2:10,6:0.2:2,2:6.8:1:27:1:1:1.6233:50.8:8:0.2:0:7.5 -10 42530584 . A G 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTAGTTTTAATACGAAGAT;RSEQ=TTTCCTTTTCTACCATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:18.5:1:28.8:1:1:0:54:8:1:0:7 0/1:22:2:1,1:12,8:0.0909:2,2:16.5:1:28.5:1:1:1.47192:56.5:4:0.0909:0:8 -10 42530586 . T A 115 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTTTAATACGAAGATAT;RSEQ=TCCTTTTCTACCATTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:19.5:1:28.5:1:1:0:54:8:1:0:7 1/1:22:18:10,8:2,1:0.8182:2,2:20.6:1:27.8:1:1:1.56568:45.3:36:0.8571:0:7.1 -10 42530593 . T G 51 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03755;SOR=0.09865;LSEQ=AATACGAAGATATTTCCTTT;RSEQ=CTACCATTGTCCTCGAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:30.7:1:32.3:1:1:1.73:58.7:6:0.6:0:7.7 0/1:26:3:1,2:14,9:0.1154:2,2:26:1:32.3:1:0.55577:2.97549:49.3:6:0.1154:0:7.3 -10 42530596 . A G 54 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGAAGATATTTCCTTTTCT;RSEQ=CCATTGTCCTCGAAGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:23.4:1:29.2:1:1:0:59.2:10:1:0:7 0/1:25:4:3,1:11,10:0.16:2,2:19.5:1:27.3:1:0.60435:2.63:50.8:3:0.125:0:7.8 -10 42530597 . C T 122 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30406;SOR=0;LSEQ=CGAAGATATTTCCTTTTCTA;RSEQ=CATTGTCCTCGAAGCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:24.4:1:28.2:1:1:0:59.2:4:1:0:7 1/0:25:18:9,9:5,2:0.72:2,2:24.9:1:29.4:1:0.40652:2.41155:46.6:36:0.7826:0:7.2 -10 42530599 . A G 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGATATTTCCTTTTCTACC;RSEQ=TTGTCCTCGAAGCGCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:22.2:1:28.8:1:1:0:59.3:12:1:0:7 0/1:25:3:2,1:12,10:0.12:2,2:17:1:29.3:1:1:1.63:54.7:6:0.12:0:7.7 -10 42530600 . T C 125 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14222;SOR=0;LSEQ=AGATATTTCCTTTTCTACCA;RSEQ=TGTCCTCGAAGCGCTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:23.2:1:31.3:1:1:0:59.3:12:1:0:7 1/0:26:16:8,8:7,3:0.6154:2,2:26.8:1:31.3:1:0.42786:2.25819:45.6:32:0.64:0:7.3 -10 42530605 . C T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68213;SOR=0.59346;LSEQ=TTTCCTTTTCTACCATTGTC;RSEQ=TCGAAGCGCTTCAAATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:1,1:0.75:2,2:28.2:1:29.8:1:1:1:59.3:12:0.75:0:7 1/0:22:14:7,7:6,2:0.6364:2,2:34.6:1:30.5:1:0.38019:2.85423:49.1:28:0.6364:0:7.4 -10 42530607 . C G 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54483;SOR=Inf;LSEQ=TCCTTTTCTACCATTGTCCT;RSEQ=GAAGCGCTTCAAATCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:24.3:1:30:1:1:0:59.5:16:1:0:6.8 0/1:22:3:2,1:10,8:0.1364:2,2:28.3:1:33:1:1:1.57:35.3:6:0.1429:0:7.7 -10 42530614 . C T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.42118;LSEQ=CTACCATTGTCCTCGAAGCG;RSEQ=TTCAAATCTGCACTAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:1,0:0.8889:0,2:28.6:1:29.1:1:1:0:59.5:16:0.8889:0:6.8 1/1:25:23:12,11:1,1:0.92:2,2:30.4:1:29.7:1:1:1.09:50.9:46:0.92:0:7.1 -10 42530617 . C G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTGTCCTCGAAGCGCTT;RSEQ=AAATCTGCACTAGCAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:6,6:0,0:1:0,2:21.3:1:31.6:1:1:0:52.2:24:1:0:6.5 1/1:27:27:14,13:0,0:1:0,2:30:1:31.4:1:1:0:50.2:54:1:0:6.9 -10 42530619 . A T 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30236;SOR=Inf;LSEQ=ATTGTCCTCGAAGCGCTTCA;RSEQ=ATCTGCACTAGCAAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:21:1:29.3:1:1:0:52.8:26:1:0:6.4 0/1:31:4:3,1:13,14:0.129:2,2:37:1:29:1:0.59956:3.12:54.5:8:0.129:0:7.3 -10 42530624 . G A 44 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02398;SOR=0;LSEQ=CCTCGAAGCGCTTCAAATCT;RSEQ=CACTAGCAAATTCCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:5,6:0.2143:2,2:8.3:1:28:1:1:1.60839:36.7:6:0.2143:0:6 0/0:32:0:0,0:16,16:0:2,0:27:1:31.8:1:1:0:50.3:64:1:0:6.4 -10 42530627 . C T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09713;SOR=0;LSEQ=CGAAGCGCTTCAAATCTGCA;RSEQ=TAGCAAATTCCACAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:26:0:32:1:1:1.55:60:4:0.1333:0:6 0/0:32:0:0,0:16,16:0:2,0:27.4:1:31.8:1:1:0:50.3:64:1:0:6.4 -10 42530629 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09713;SOR=0;LSEQ=AAGCGCTTCAAATCTGCACT;RSEQ=GCAAATTCCACAAAAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:13:1:29.5:1:1:1.55:40:4:0.1333:0:6 0/0:32:0:0,0:15,15:0:2,0:26.6:1:29.6:1:1:0:50:60:1:0:6.4 -10 42530635 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.70533;LSEQ=TTCAAATCTGCACTAGCAAA;RSEQ=TCCACAAAAAGAGTGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:5,9:0.125:2,2:35:0:25:1:1:1.73:60:1:0.0667:0:6 0/1:33:3:2,1:14,16:0.0909:2,2:39:1:32.3:1:0.60117:2.23:54.7:6:0.0909:0:7.7 -10 42530640 . C A 44 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03691;SOR=0;LSEQ=ATCTGCACTAGCAAATTCCA;RSEQ=AAAAAGAGTGTTTCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:5,9:0.1765:2,2:18.7:1:28:1:1:1.10434:37.3:6:0.1765:0:6.3 0/0:32:0:0,0:14,16:0:2,0:26.2:1:31.4:1:1:0:49.7:60:0.9375:0:6.2 -10 42530642 . A G 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.69636;SOR=1.71269;LSEQ=CTGCACTAGCAAATTCCACA;RSEQ=AAAGAGTGTTTCAAATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:5,10:0.1176:2,2:42:0:31:1:1:1.91:60:4:0.1176:0:6 0/1:32:6:4,2:9,14:0.1875:2,2:29:1:27.7:1:0.36398:2.99:48.3:2:0.1379:0:7.2 -10 42530644 . A C 47 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03932;SOR=0;LSEQ=GCACTAGCAAATTCCACAAA;RSEQ=AGAGTGTTTCAAATCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:5,9:0.1765:2,2:22.7:1:30:1:1:1.10434:37.3:6:0.1765:0:6.3 0/0:31:0:0,0:13,17:0:2,0:27:1:29.9:1:1:0:51.4:60:1:0:6.2 -10 42530647 . A G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.94556;LSEQ=CTAGCAAATTCCACAAAAAG;RSEQ=GTGTTTCAAATCTGCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:5,12:0.1053:2,2:47:0:31.5:1:1:2.28:60:4:0.1111:0:6 0/1:30:3:2,1:11,15:0.1:2,2:27:1:32:1:0.57307:2.63:54.7:6:0.1034:0:7.7 -10 42530655 . A C 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52821;SOR=Inf;LSEQ=TTCCACAAAAAGAGTGTTTC;RSEQ=AATCTGCTCTCTCTAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,12:0:2,0:25.2:1:30:1:1:0:48.3:34:1:0:6.1 0/1:30:2:1,1:12,15:0.0667:2,2:29:1:28.5:1:1:1.24:28:4:0.069:0:6 -10 42530656 . AA CC 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65289;SOR=0.52623;LSEQ=TCCACAAAAAGAGTGTTTCA;RSEQ=TCTGCTCTCTCTAAAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:4,10:0.1765:2,2:23:1:31.8:1:1:1.23:36.7:6:0.1765:0:5 0/1:30:3:0,3:12,15:0.1:2,0:22:1:30.1:1:0.25517:0:46.7:6:0.1:0.0333:3.7 -10 42530657 . A C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.75462;SOR=0.68019;LSEQ=CCACAAAAAGAGTGTTTCAA;RSEQ=TCTGCTCTCTCTAAAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:2,7:1,2:0.5625:2,2:23.4:1:31.9:1:1:1.66417:48.9:18:0.6923:0:6.1 0/1:28:13:4,9:8,5:0.4643:2,2:28.3:1:32.3:1:0.23774:3.41534:50.2:26:0.52:0:6 -10 42530665 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.39517;SOR=0.47254;LSEQ=AGAGTGTTTCAAATCTGCTC;RSEQ=CTCTAAAGAACGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:3,10:0.1875:2,2:20.3:1:32.3:1:1:1.61:36.7:6:0.1875:0:5 0/1:31:3:0,3:13,15:0.0968:2,0:26.7:1:31:1:0.24516:0:46.7:6:0.1:0:3.7 -10 42530666 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.53623;SOR=Inf;LSEQ=GAGTGTTTCAAATCTGCTCT;RSEQ=TCTAAAGAACGTTCAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:4,12:0:2,0:27.4:1:31.4:1:1:0:46.6:32:1:0:5.8 0/1:30:2:2,0:10,18:0.0667:2,0:24:1:33.5:1:0.15172:0:52.5:4:0.0667:0:6.5 -10 42530670 . A T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53131;SOR=Inf;LSEQ=GTTTCAAATCTGCTCTCTCT;RSEQ=AAGAACGTTCAACTCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:4,11:0:2,0:27.3:1:29.3:1:1:0:47:30:0.9375:0:5.7 0/1:29:2:1,1:9,16:0.069:2,2:20:0:31:1:1:1.74:57.5:4:0.069:0:4 -10 42530676 . C AG 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.49653;SOR=1.83634;LSEQ=CAAATCTGCTCTCTCTAAAG;RSEQ=GTTCAACTCTGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:1,5:1,2:0.4615:2,2:32.8:1:30.2:1:1:2.23609:41.2:12:0.5:0:6 1/0:26:16:4,12:4,4:0.6154:2,2:24.9:1:30.5:1:0.36254:2.85349:47.1:32:0.6154:0.1154:5.6 -10 42530677 . G GT 92 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.47568;SOR=1.96404;LSEQ=ATCTGCTCTCTCTAAAGAAC;RSEQ=TTCAACTCTGTGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:1,6:0.2308:2,2:24.3:1:27.7:1:1:2.65:53.3:6:0.3:0:6.3 0/1:24:9:4,5:4,11:0.375:2,2:15.1:1:29.3:1:0.41203:2.13:48.2:18:0.375:0.0833:5.1 -10 42530698 . G A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35742;SOR=0.24093;LSEQ=TTCAACTCTGTGAGTTGAAT;RSEQ=CACACAACACAAAGAAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:0,0:0.8889:0,0:31.8:1:30.5:1:1:0:44.5:16:0.8889:0:6.1 1/0:17:11:2,9:2,4:0.6471:2,2:24.6:1:30.5:1:0.58403:2.13794:42.5:22:0.6875:0:5.1 -10 42530715 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=AATGCACACAACACAAAGAA;RSEQ=TTACTGAGAATTCTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:0:0,0:17.7:1:32.2:1:1:0:44.3:18:1:0:5.8 0/1:12:2:1,1:1,9:0.1667:2,2:11:1:30:1:0.31818:6.71:28:4:0.1667:0:6 -10 42530717 . T A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26316;SOR=Inf;LSEQ=TGCACACAACACAAAGAAGT;RSEQ=ACTGAGAATTCTTCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:20.3:1:28.6:1:1:0:42.1:14:1:0:5.6 0/1:12:3:1,2:1,8:0.25:2,2:33.3:1:30:1:0.45455:3.46:36.7:6:0.25:0:5 -10 42530719 . C A 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.11928;SOR=Inf;LSEQ=CACACAACACAAAGAAGTTA;RSEQ=TGAGAATTCTTCTGTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:18.3:1:31:1:1:0:42.1:6:1:0:5.6 0/1:11:4:1,3:1,5:0.3636:2,2:34.3:1:30.3:1:1:1.58:42.5:8:0.3636:0:4.8 -10 42530740 . A G 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAATTCTTCTGTCTAGC;RSEQ=TTATAGGAAGAAATCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:9.3:1:32:1:1:0:40:6:1:0:6.3 1/1:7:6:1,5:0,1:0.8571:0,2:14.7:1:31.8:1:1:0:39.3:12:0.8571:0:5.5 -10 42530746 . G T 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTCTGTCTAGCATTATA;RSEQ=GAAGAAATCCCATTTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:13:0:31:0:1:0:40:2:1:0:7 1/1:5:5:1,4:0,0:1:0,2:10.4:1:31.6:1:1:0:40.6:10:1:0:5.8 -10 42530758 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTATAGGAAGAAATCCC;RSEQ=TTTCCAACGAAGGGCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:40:2:1:0:7 1/1:2:2:0,2:0,0:1:0,0:5:1:31:1:1:0:52:4:1:0:5 -10 42530836 . C G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTCCCAACTGCTCTAT;RSEQ=AAAATAAAGGTTAAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30.5:1:1:0:42:4:1:0:7.5 -10 42530841 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAACTGCTCTATCAAAA;RSEQ=AAAGGTTAAACTCTGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31:1:1:0:42:4:1:0:7.5 -10 42530861 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAGGTTAAACTCTGTGAG;RSEQ=TGAACGCACACATCACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45:0:31:1:1:0:42:4:1:0:7.5 -10 42530866 . C G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAAACTCTGTGAGGTGAA;RSEQ=GCACACATCACAAACTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:0:32:1:1:0:42:4:1:0:7.5 -10 42530890 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCACAAACTAGTTTCT;RSEQ=CGAATGATTCTATGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:31:1:1:0:42:4:1:0:7.5 -10 42530898 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTAGTTTCTGCGAATGA;RSEQ=TCTATGTAGTTTTAATGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:33:0:1:0:42:4:1:0:7.5 -10 42531082 . T A 61 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=AGAATTCTTCTGTCTAGCAG;RSEQ=ATATGAAGAAATCCCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:11:1:29.5:1:1:0:60:4:1:0:1.5 1/0:8:4:2,2:1,3:0.5:2,2:14.8:1:30.8:1:1:2.60:41:8:0.5:0:1.5 -10 42531084 . TATGA AATG 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=AATTCTTCTGTCTAGCAGTA;RSEQ=AGAAATCCCTTTTCCAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:31.9:1:1:0:60:4:1:0.5:1.5 0/1:8:1:0,1:2,3:0.125:2,0:25:0:30.8:0:1:0:49:2:0.125:0:3 -10 42531090 . G A 50 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGTCTAGCAGTATATGAA;RSEQ=AAATCCCTTTTCCAATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:8:0:34:0:1:0:60:2:1:0:2 0/1:8:3:1,2:2,3:0.375:2,2:12.3:1:32:0:1:1.28664:50.3:6:0.375:0:2.3 -10 42531099 . T C 52 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTATATGAAGAAATCCCT;RSEQ=TTCCAATGAAGGCCTATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:9.3:1:33:1:1:0:56.3:6:1:0:3 -10 42531487 . A G 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTACTTGCAGACTTTACA;RSEQ=ACAGAGTGTTTCCAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:17:0:29.5:1:1:0:37:4:1:0:6.5 -10 42531495 . G C 53 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGACTTTACAAACAGAGT;RSEQ=TTTCCAAACTGCTCTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:15:1:26.8:1:1:0:30.5:3:1:0:5.8 -10 42531525 . T G 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCTATGAAGAGAAAGGT;RSEQ=AAATTCTGTGAGTTGAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:22:0:33:0:1:0:40:2:1:0:8 1/1:4:4:1,3:0,0:1:0,2:24.5:1:32.5:1:1:0:30.5:8:1:0:5.8 -10 42531529 . T C 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGAAGAGAAAGGTTAAA;RSEQ=TCTGTGAGTTGAACGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:26:0:34:0:1:0:40:2:1:0:8 1/1:4:4:1,3:0,0:1:0,2:20.5:1:33.3:1:1:0:30.5:8:1:0:5.8 -10 42531537 . GT AC 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAAGGTTAAATTCTGTGA;RSEQ=TGAACGCACACATCACAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:34:0:32.5:0:1:0:40:2:1:0:7 1/1:4:4:1,3:0,0:1:0,2:11.5:1:30.8:1:1:0:30.5:8:1:0:4.8 -10 42531902 . G T 77 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACATCACAAAGTAGTT;RSEQ=CAGAGAATGATTCTGTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:1:0,2:16.5:1:30:1:1:0:52.7:12:1:0:5.3 -10 42531904 . A T 81 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACATCACAAAGTAGTTGC;RSEQ=GAGAATGATTCTGTCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:1:0,2:18.5:1:31.7:1:1:0:52.7:12:1:0:5.3 -10 42531907 . G C 64 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCACAAAGTAGTTGCAGA;RSEQ=AATGATTCTGTCTAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:4:2,2:3,3:0.4:2,2:23.3:1:32.3:1:1:1:60:8:0.4:0:5.3 -10 42531912 . A C 53 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGTAGTTGCAGAGAATG;RSEQ=TTCTGTCTAATTTTTACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:3:2,1:3,4:0.3:2,2:8:0:33.7:1:1:2.41:50.7:6:0.3:0:4.3 -10 42531919 . C G 88 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAGAGAATGATTCTGT;RSEQ=TAATTTTTACACGAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:12:7:3,4:3,2:0.5833:2,2:13.4:1:31.4:1:1:1.88578:49.1:14:0.5833:0:4.6 -10 42531922 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGAATGATTCTGTCTA;RSEQ=TTTTTACACGAAGATATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:12:2:0,2:6,4:0.1667:2,0:21.5:1:30.5:1:0.45455:0:36:4:0.1667:0:6.5 -10 42531951 . T A 110 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAAGATATTTCCATTTCAA;RSEQ=GATTGGCCTCAAATCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19.5:1:32.5:1:1:0:60:4:1:0:2.5 1/1:12:12:6,6:0,0:1:0,2:20.7:1:30.8:1:1:0:51.3:24:1:0:4.7 -10 42531956 . G A 83 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=ATATTTCCATTTCAATGATT;RSEQ=GCCTCAAATCGCTTCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30:1:1:0:60:4:1:0:2.5 1/0:12:7:3,4:3,2:0.5833:2,2:19.9:1:29.6:1:1:1.88578:49.1:14:0.5833:0:4.6 -10 42531957 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTCCATTTCAATGATTG;RSEQ=CCTCAAATCGCTTCAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13.5:1:32.5:1:1:0:60:4:1:0:2.5 0/1:12:2:1,1:5,5:0.1667:2,2:12:1:28.5:1:1:1:60:4:0.1667:0:5.5 -10 42532372 . G T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTCTGTCTAAAGGAAGG;RSEQ=TCAACTCTGTGATTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:28:0:1:0:46:4:1:0:4.5 -10 42532385 . T C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAGGGTCAACTCTGTGA;RSEQ=TTGAATGCACACAACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:32.5:1:1:0:46:4:1:0:4.5 -10 42532392 . G A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCAACTCTGTGATTTGAAT;RSEQ=CACACAACACAAAGAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:30.5:1:1:0:46:4:1:0:4.5 -10 42532394 . A G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAACTCTGTGATTTGAATGC;RSEQ=CACAACACAAAGAAGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:32.5:1:1:0:46:4:1:0:4.5 -10 42532427 . A G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGACTGAGAATTCTTCT;RSEQ=TCTAACATTGTATGAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:0:33.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42532432 . A G 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGAGAATTCTTCTATCTA;RSEQ=CATTGTATGAAGAAATCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:34:0:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42532434 . A G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAATTCTTCTATCTAAC;RSEQ=TTGTATGAAGAAATCCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:0:33:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42532478 . C G 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGAAGGCCTCAAAGAGGT;RSEQ=CAAATATCCTCCTGCAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:33:1:33:1:1:2.44949:31:4:0.3333:0:5.5 -10 42532487 . CT TG 73 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCAAAGAGGTCCAAATATC;RSEQ=CCTGCAGACTTTACAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:5:3,2:1,0:0.8333:0,2:41.4:1:31.6:1:1:0:31.6:10:0.8333:0:5.2 -10 42532490 . C T 80 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AAAGAGGTCCAAATATCCTC;RSEQ=TGCAGACTTTACAAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:4,2:0,0:1:0,2:38:1:31.2:1:1:0:33.3:12:1:0:5.5 -10 42532498 . T A 77 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATATCCTCCTGCAGAC;RSEQ=TTACAAACAGAGTGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:12:6:3,3:4,2:0.5:2,2:7.7:1:30:1:1:1.88578:40.7:12:0.5:0:6.3 -10 42532500 . T A 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATCCTCCTGCAGACTT;RSEQ=ACAAACAGAGTGTTTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:13:2:1,1:7,4:0.1538:2,2:49:0:29.5:1:1:1.67325:28:4:0.1538:0:5 -10 42532504 . A G 90 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTCCTGCAGACTTTACA;RSEQ=ACAGAGTGTTTCCAAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:14:7:5,2:3,4:0.5:2,2:31.4:1:32.1:1:0.59207:3.04:36.9:14:0.5:0:5.6 -10 42532512 . G C 82 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGACTTTACAAACAGAGT;RSEQ=TTTCCAAACTACTCTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:16:6:4,2:4,6:0.375:2,2:18.3:1:31.8:1:0.60839:2.79:45.8:12:0.375:0:6 -10 42532523 . A G 111 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAGAGTGTTTCCAAACT;RSEQ=CTCTATGAAAAGAAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:10:0:14:0:1:0:38:0:0:0:5 1/0:17:11:6,5:3,3:0.6471:2,2:23:1:32.2:1:1:1.19:41.4:22:0.6471:0:6.8 -10 42532527 . T C 81 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGTGTTTCCAAACTACTC;RSEQ=ATGAAAAGAAAGGTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:14:0:12:0:1:0:38:0:0:0:5 0/1:18:6:2,4:8,4:0.3333:2,2:30.2:1:31.7:1:0.32127:3.68059:37:12:0.3333:0:7.5 -10 42532530 . G C 82 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGTTTCCAAACTACTCTAT;RSEQ=AAAAGAAAGGTTAAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:17:0:27:0:1:0:38:2:1:0:5 0/1:19:6:2,4:8,4:0.3158:2,2:32.2:1:32:1:0.32127:3.68059:37:12:0.3158:0:7.5 -10 42532533 . A G 71 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCCAAACTACTCTATGAA;RSEQ=AGAAAGGTTAAACTCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:20:0:27:0:1:0:38:2:1:0:5 0/1:21:5:4,1:7,9:0.2381:2,2:19.4:1:31:1:0.31078:4.77:49:10:0.2381:0:7.4 -10 42532540 . G C 53 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTACTCTATGAAAAGAAAG;RSEQ=TTAAACTCTGTGAGCTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:11:1:28.2:1:1:0:30.4:4:1:0:5 0/1:29:3:1,2:11,15:0.1034:2,2:9:0:34:0:1:1.44805:29:6:0.1034:0:5 -10 42532542 . T G 113 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06291;SOR=Inf;LSEQ=TACTCTATGAAAAGAAAGGT;RSEQ=AAACTCTGTGAGCTGAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:13:1:28.4:1:1:0:30.4:10:1:0:5 0/1:29:14:6,8:6,9:0.4828:2,2:20.4:1:29.9:1:1:1.12:51.1:28:0.4828:0:6.4 -10 42532552 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGAAAGGTTAAACTCTGT;RSEQ=AGCTGAACGCACACATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:20.3:1:31:1:1:0:31.5:12:1:0:5.5 0/1:28:2:1,1:10,16:0.0714:2,2:22.5:1:28:1:1:1.57:60:4:0.0714:0:5.5 -10 42532554 . G A 93 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64446;SOR=2.31647;LSEQ=AGAAAGGTTAAACTCTGTGA;RSEQ=CTGAACGCACACATCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:2,3:0.1667:2,0:9:0:25:0:1:0:37:2:0.1667:0:8 0/1:28:9:3,6:8,11:0.3214:2,2:23.3:1:29.4:1:1:1.43544:49.6:18:0.3214:0:7.6 -10 42532561 . G A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.69845;SOR=0.67397;LSEQ=TTAAACTCTGTGAGCTGAAC;RSEQ=CACACATCACAAAGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:1,3:0.5:2,2:24.5:1:30:1:1:2.60:28.5:8:0.5:0:5 0/1:30:12:5,7:6,12:0.4:2,2:29.2:1:30.7:1:0.71163:1.41:41.3:24:0.4:0:6.7 -10 42532564 . C G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AACTCTGTGAGCTGAACGCA;RSEQ=ACATCACAAAGTAGTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:23:1:29.5:1:1:0:36.1:7:1:0:4.6 0/1:30:2:1,1:10,18:0.0667:2,2:34.5:1:31.5:1:1:1.76:60:4:0.0667:0:5.5 -10 42532566 . C G 94 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.64871;SOR=2.60736;LSEQ=CTCTGTGAGCTGAACGCACA;RSEQ=ATCACAAAGTAGTTTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:3,4:0.125:2,0:21:0:27:0:1:0:37:2:0.125:0:8 0/1:29:8:2,6:8,13:0.2759:2,2:33.5:1:31.5:1:0.6749:1.80915:50.8:16:0.2759:0:7.8 -10 42532569 . C G 95 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16381;SOR=Inf;LSEQ=TGTGAGCTGAACGCACACAT;RSEQ=ACAAAGTAGTTTCTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,4:0:2,0:24.3:1:32.1:1:1:0:36:14:0.875:0:4.1 0/1:30:8:2,6:8,14:0.2667:2,2:35:1:31.8:1:0.68213:1.68504:50.8:16:0.2667:0:7.8 -10 42532570 . AC GA 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27931;SOR=0.34551;LSEQ=GTGAGCTGAACGCACACATC;RSEQ=AAAGTAGTTTCTGAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:38:0:25.8:1:1:1.83:27:4:0.25:0:6 0/1:30:3:1,2:9,18:0.1:2,2:32.7:1:31.8:1:1:1:45.3:6:0.1:0:6.3 -10 42532571 . C A 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.27749;LSEQ=TGAGCTGAACGCACACATCA;RSEQ=AAAGTAGTTTCTGAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,3:0.25:2,2:11:0:27.5:1:1:2.45:30:4:0.3333:0:3 0/1:30:9:4,5:5,13:0.3:2,2:23.9:1:31:1:0.42284:2.02:39.9:18:0.3333:0:6.4 -10 42532575 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CTGAACGCACACATCACAAA;RSEQ=TAGTTTCTGAGAATGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:24:1:32:1:1:0:36.1:16:1:0:4.4 0/1:29:2:1,1:8,19:0.069:2,2:24:1:30:1:0.53202:2.30:50:4:0.069:0:5 -10 42532576 . T A 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76942;LSEQ=TGAACGCACACATCACAAAG;RSEQ=AGTTTCTGAGAATGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:1,3:0.4444:2,2:20:1:27:1:1:2.60:28.5:3:0.375:0:4.5 0/1:29:11:4,7:2,6:0.3793:2,2:23.3:1:31.1:1:1:1.67:41.2:22:0.3793:0:6.4 -10 42532581 . TC GT 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.04084;SOR=0.1846;LSEQ=GCACACATCACAAAGTAGTT;RSEQ=TGAGAATGATTCTGTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:2,3:2,3:0.5:2,2:19.4:1:32.2:1:1:1:48.8:10:0.5:0:2 0/1:27:4:0,4:8,15:0.1481:2,0:24.5:1:31.6:1:0.28547:0:51:8:0.1481:0:3.3 -10 42532585 . A T 107 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68;SOR=2.02251;LSEQ=ACATCACAAAGTAGTTTCTG;RSEQ=GAATGATTCTGTGTAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:25:0:29.5:1:1:1.83:27:4:0.25:0:6 0/1:27:11:4,7:4,12:0.4074:2,2:14.3:1:31.2:1:0.67536:1.68:41.2:22:0.4074:0:6.4 -10 42532586 . G C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCACAAAGTAGTTTCTGA;RSEQ=AATGATTCTGTGTAGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:22.8:1:32.4:1:1:0:41.9:16:1:0:3.8 0/1:27:2:1,1:7,18:0.0741:2,2:13:1:32:1:0.51282:2.47:50:4:0.0741:0:5 -10 42532598 . G C 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.06872;LSEQ=GTTTCTGAGAATGATTCTGT;RSEQ=TAGTTTTTATACGAACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:12:0:31.5:1:1:1.83:27:4:0.25:0:6 0/1:19:5:3,2:3,11:0.2632:2,2:5.8:1:30.6:1:0.26213:4.93:53:10:0.2632:0:6.2 -10 42532602 . T A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.57839;SOR=0.44539;LSEQ=CTGAGAATGATTCTGTGTAG;RSEQ=TTTTATACGAACATATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:8:0:29.5:1:1:1.83:27:4:0.25:0:6 0/1:16:2:1,1:3,11:0.125:2,2:5.5:1:27:1:0.45:3.32:48:4:0.125:0:6 -10 42532608 . T C 103 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05728;SOR=9.74908;LSEQ=ATGATTCTGTGTAGTTTTTA;RSEQ=ACGAACATATTTACATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:2,3:0.1667:2,0:20:0:33:0:1:0:37:2:0.1667:0:8 1/0:13:9:3,6:0,4:0.6923:0,2:13.1:1:32.7:1:0.4965:0:53.4:18:0.6923:0:7.2 -10 42532614 . C G 102 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGTAGTTTTTATACGAA;RSEQ=ATATTTACATTTCTAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:10.7:1:32.7:1:1:0:47.7:6:1:0:4 1/1:9:9:1,8:0,0:1:0,2:8.6:1:32.3:1:1:0:50.1:18:1:0:6.4 -10 42532621 . A C 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GTTTTTATACGAACATATTT;RSEQ=CATTTCTAATATAGGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:7:0:33:0:1:0:37:2:0.3333:0:8 1/1:4:4:0,4:0,0:1:0,0:7:0:33:0:1:0:52.8:8:1:0:7.8 -10 42533585 . C T 42 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTGTGAGTGGAATGCACA;RSEQ=ATCACAAAGTAGTTTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:8:1:26.7:1:1:0:35:6:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42533600 . T C 47 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACATCACAAAGTAGTT;RSEQ=CTGAGAATGATTTTGTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:23:1:30:1:1:0:35:6:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42533613 . T C 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAGTTTCTGAGAATGATT;RSEQ=TGTCTAGTTTTCATACGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:36:1:31.3:1:1:0:35:6:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42533647 . T C 50 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACGAAGATATTTCCTTTTC;RSEQ=ACCATTGTCCTCGAAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:18.3:1:32:1:1:0:35:6:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42533652 . T A 50 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATATTTCCTTTTCTACCA;RSEQ=TGTCCTCGAAGAGCTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:13.3:1:31.7:1:1:0:35:6:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42533655 . T G 51 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTCCTTTTCTACCATTG;RSEQ=CCTCGAAGAGCTTGAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:10.3:1:32.7:1:1:0:35:6:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42534548 . C T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGACTTTACAAAGACAG;RSEQ=GTTTCCAAACTGCTCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:10.5:1:30.5:1:1:0:23:4:1:0:6.5 -10 42534576 . C G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGCTCTATGAAAAGAAA;RSEQ=GTTAAACTCTGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:10:0:33:0:1:0:23:2:1:0:5 1/1:3:3:3,0:0,0:1:0,0:28.3:1:33.3:1:1:0:23:6:1:0:7 -10 42534597 . C G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAAACTCTGTGAGTTGAA;RSEQ=GCACACATCACAAACTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:31:0:33:0:1:0:23:2:1:0:5 1/1:3:3:3,0:0,0:1:0,0:36:1:33.3:1:1:0:23:6:1:0:7 -10 42534621 . G A 58 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACATCACAAACTAGTTTCT;RSEQ=CGAATGATTCTGTGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:46:0:31:0:1:0:23:2:1:0:5 1/1:5:4:4,0:1,0:0.8:0,0:21:1:29:1:1:0:23:8:0.8:0:7.3 -10 42534629 . TTCTG CTC 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=AAACTAGTTTCTGCGAATGA;RSEQ=TGTAGTTTTAATTCGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:31.1:1:1:0:25:4:1:0.5:5.5 0/0:5:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42534638 . G C 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=TCTGCGAATGATTCTGTGTA;RSEQ=TTTTAATTCGAAGATATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:17:0:32:0:1:0:27:2:0.5:0:7 1/1:6:6:6,0:0,0:1:0,0:18:1:31.2:1:1:0:30.3:12:1:0:7.7 -10 42534646 . TC AT 106 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TGATTCTGTGTAGTTTTAAT;RSEQ=GAAGATATTTCCATTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:19.5:1:30.5:1:1:0:33.5:4:0.6667:0.3333:6 1/1:12:12:11,1:0,0:1:0,2:16.5:1:29.6:1:1:0:32.3:24:1:0.5833:6.3 -10 42534658 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTTAATTCGAAGATATTT;RSEQ=CATTTCTAAGATTGGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:11.6:1:30.4:1:1:0:32.3:14:1:0:6.1 0/1:15:2:1,1:11,2:0.1333:2,2:27.5:1:30:1:0.37143:4.69047:49:4:0.1333:0:6.5 -10 42534662 . T G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTCGAAGATATTTCCAT;RSEQ=TCTAAGATTGGCCTCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1:0,2:14.4:1:32:1:1:0:32.3:14:1:0:6.1 1/1:19:17:12,5:1,0:0.8947:0,2:16.8:1:31.3:1:1:0:34:34:0.8947:0:6.5 -10 42534667 . A T 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55034;SOR=Inf;LSEQ=CGAAGATATTTCCATTTCTA;RSEQ=GATTGGCCTCAAATCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,2:0:2,0:15.1:1:30.7:1:1:0:36.1:14:0.875:0:6 0/1:25:4:2,2:15,6:0.16:2,2:8:1:29.3:1:0.56996:2.40058:37.8:8:0.16:0:6 -10 42534673 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTCCATTTCTAAGATTG;RSEQ=CCTCAAATCCCTTGAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:15.1:1:32:1:1:0:36.6:24:1:0:6.1 0/1:29:2:1,1:20,7:0.069:2,2:26.5:1:31.5:1:0.48276:2.73861:23:4:0.069:0:5 -10 42534674 . CC TG 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24739;SOR=0.37532;LSEQ=ATTTCCATTTCTAAGATTGG;RSEQ=TCAAATCCCTTGAAATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:2,3:5,2:0.4167:2,2:12.4:1:30.7:1:0.55808:3.3264:43.4:10:0.4167:0:5.2 0/1:29:6:3,3:18,5:0.2069:2,2:26:1:29.7:1:0.30451:3.41678:32.5:12:0.2069:0:5.8 -10 42534675 . C G 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47028;SOR=1.87602;LSEQ=TTTCCATTTCTAAGATTGGC;RSEQ=TCAAATCCCTTGAAATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:6,3:0,0:0.6429:0,2:15.7:1:31.2:1:1:0:37.3:18:1:0:6.1 1/0:31:24:18,6:1,0:0.7742:0,2:16.8:1:30.5:1:1:0:32.2:48:0.96:0:5.8 -10 42534683 . C G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.79854;LSEQ=TCTAAGATTGGCCTCAAATC;RSEQ=CTTGAAATCTCCACTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:8,5:0,0:0.9286:0,2:20.7:1:28.8:1:1:0:40.8:12:0.9231:0:5.8 1/1:34:31:20,11:1,1:0.9118:2,2:23.1:1:30.6:1:1:1.78:34.3:62:0.9394:0:5.7 -10 42534707 . C A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAATCTCCACTTGCAAATT;RSEQ=CACAAAAAGAGTGTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:35.3:1:31.2:1:1:0:39.1:30:1:0:5.9 0/1:46:2:1,1:22,22:0.0435:2,2:29.5:1:28:1:1:1:22:4:0.0435:0:5.5 -10 42534710 . C T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCTCCACTTGCAAATTCCA;RSEQ=AAAAAGAGTGTTTCAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:36:1:31.7:1:1:0:39.1:30:1:0:5.9 0/1:46:2:1,1:22,22:0.0435:2,2:35.5:1:27.5:1:1:1:42.5:4:0.0435:0:6 -10 42534716 . G A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTGCAAATTCCACAAAAA;RSEQ=AGTGTTTCAAAACTGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:37.2:1:31.9:1:1:0:39.1:30:1:0:5.9 0/1:45:2:1,1:21,21:0.0444:2,2:33:1:27.5:1:1:1:42.5:4:0.0444:0:6 -10 42534717 . A T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14929;SOR=0.19666;LSEQ=CTTGCAAATTCCACAAAAAG;RSEQ=GTGTTTCAAAACTGCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:7,6:0,1:0.9286:0,2:40.2:1:30.2:1:1:0:41.2:26:0.9286:0:5.8 1/0:42:30:14,16:6,6:0.7143:2,2:37.1:1:29.4:1:1:1.13922:35.2:60:0.7143:0:5.7 -10 42534719 . TG AT 60 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00253;SOR=0;LSEQ=TGCAAATTCCACAAAAAGAG;RSEQ=TTTCAAAACTGCTCTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:5,5:0.2857:2,2:38:1:30.4:1:1:1:52.8:8:0.3077:0:5.5 0/0:43:0:0,0:19,22:0:2,0:34.2:1:29.4:1:1:0:33.4:82:0.9535:0:5.3 -10 42534720 . G T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.0364;LSEQ=GCAAATTCCACAAAAAGAGT;RSEQ=TTTCAAAACTGCTCTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:5,4:0,1:0.6429:0,2:40.3:1:29.9:1:1:0:36.1:18:0.9:0:5.6 1/0:43:28:13,15:6,7:0.6512:2,2:36.4:1:29.4:1:1:1.01:34.7:56:0.6829:0:5.6 -10 42534731 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAGAGTGTTTCAAAACT;RSEQ=CTCTGAATAAAGGAAGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:30.1:1:32.1:1:1:0:39.9:28:1:0:5.6 0/1:45:2:1,1:18,25:0.0444:2,2:39.5:1:29:1:1:1.38:43:4:0.0444:0:5.5 -10 42534737 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGTTTCAAAACTGCTCTG;RSEQ=ATAAAGGAAGGTTCAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:27.1:1:28.6:1:1:0:39.9:12:1:0:5.6 0/1:41:2:1,1:14,25:0.0488:2,2:22:1:29.5:1:1:1.76:38:4:0.0488:0:2.5 -10 42534748 . G T 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1399;LSEQ=ACTGCTCTGAATAAAGGAAG;RSEQ=TTCAACTCTGTGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:4,6:0.0909:2,0:36:0:30:0:1:0:33:2:0.0909:0:7 0/1:39:4:3,1:11,24:0.1026:2,2:16.5:1:29.5:1:0.12281:6.21:30.8:8:0.1026:0:6.5 -10 42534752 . A C 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65268;SOR=1.41111;LSEQ=CTCTGAATAAAGGAAGGTTC;RSEQ=ACTCTGTGAGTTGAATGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:4,5:0,1:0.8182:0,2:14.9:1:30.7:1:1:0:43.3:18:0.8182:0:5.3 1/1:37:32:12,20:2,3:0.8649:2,2:21.1:1:31.6:1:1:1.10792:34.5:64:0.8649:0:5.3 -10 42534761 . A T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGAAGGTTCAACTCTGTG;RSEQ=GTTGAATGCACACAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:8.8:1:29.7:1:1:0:42.6:18:1:0:5.3 0/1:31:2:1,1:9,20:0.0645:2,2:8:0:29.5:1:1:2.16:38:4:0.0667:0:2.5 -10 42534769 . G A 120 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACTCTGTGAGTTGAAT;RSEQ=CACACAACAGAAAGTAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9.5:1:30.5:1:1:0:45:4:1:0:6 1/1:17:15:1,14:0,0:0.8824:0,1:15.3:1:30.8:1:1:0:37.1:30:0.8824:0:5.2 -10 42534779 . G C 109 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTTGAATGCACACAACA;RSEQ=AAAGTAGTAACTGAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:5:0:33:0:1:0:33:2:1:0:6 1/1:10:10:0,10:0,0:1:0,0:12.1:1:33.1:1:1:0:34.7:20:1:0:5.4 -10 42534784 . T G 52 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGAATGCACACAACAGAAAG;RSEQ=AGTAACTGAGAATTCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:0,3:0,0:0.75:0,0:16:1:33:0:1:0:40.7:6:0.75:0:7 -10 42534786 . G T 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATGCACACAACAGAAAGTA;RSEQ=TAACTGAGAATTCTGCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:0,3:0,1:0.75:0,0:14:1:31.7:1:1:0:40.7:6:0.75:0:7 -10 42534788 . A T 58 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACACAACAGAAAGTAGT;RSEQ=ACTGAGAATTCTGCTGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:0,4:0,0:1:0,0:13.8:1:29.3:1:1:0:36.3:8:1:0:6.8 -10 42534956 . A T 53 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCACACATCACAAAGTAG;RSEQ=TTCTGAGAATGATTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:14.7:1:31.3:1:1:0:31.7:6:1:0:6 1/1:4:4:3,1:0,0:1:0,2:6.5:1:26.8:1:1:0:28.3:8:1:0:6.3 -10 42534975 . C G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23;SOR=Inf;LSEQ=GATTCTGAGAATGATTCTGT;RSEQ=TAGTTTTTATACGAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:19.9:1:31.7:1:1:0:34:22:1:0:5.4 0/1:14:3:1,2:6,5:0.2143:2,2:21:1:30.7:1:1:2.2554:27.3:6:0.2143:0:8 -10 42534985 . T C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23;SOR=Inf;LSEQ=ATGATTCTGTCTAGTTTTTA;RSEQ=ACGAAGATATTTCCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:29.8:1:30.7:1:1:0:34:22:1:0:5.4 0/1:14:3:1,2:6,5:0.2143:2,2:31:1:31:1:1:2.2554:27.3:6:0.2143:0:8 -10 42534994 . A G 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00794;SOR=0.09025;LSEQ=TCTAGTTTTTATACGAAGAT;RSEQ=TTTCCTTTTCTACAATTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:5,5:1,1:0.8333:2,2:36:1:33:1:1:1:33.8:20:0.8333:0:5.4 0/1:14:4:2,2:5,5:0.2857:2,2:32:1:32:1:1:1:43.5:8:0.2857:0:5.3 -10 42535000 . T A 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22462;SOR=Inf;LSEQ=TTTTATACGAAGATATTTCC;RSEQ=TTTCTACAATTGGCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:35.2:1:31.2:1:1:0:34.2:24:1:0:5.3 0/1:14:3:1,2:6,5:0.2143:2,2:44.7:1:29.3:1:1:2.2554:27.3:6:0.2143:0:8 -10 42535005 . T A 47 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22462;SOR=Inf;LSEQ=TACGAAGATATTTCCTTTTC;RSEQ=ACAATTGGCCTCAAATCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:31.8:1:30:1:1:0:34.2:24:1:0:5.3 0/1:14:3:1,2:6,5:0.2143:2,2:40:0:29.7:1:1:2.2554:27.3:6:0.2143:0:8 -10 42535007 . CA AG 47 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22462;SOR=Inf;LSEQ=CGAAGATATTTCCTTTTCTA;RSEQ=ATTGGCCTCAAATCGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:30.2:1:32.6:1:1:0:34.2:24:1:0:5.3 0/1:14:3:1,2:6,5:0.2143:2,2:37:0:30.2:1:1:2.2554:27.3:6:0.2143:0:7 -10 42535009 . A T 111 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22462;SOR=0;LSEQ=AAGATATTTCCTTTTCTACA;RSEQ=TTGGCCTCAAATCGCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:6,6:0,0:1:0,2:28.5:1:31.2:1:1:0:34.2:24:1:0:5.3 1/0:14:11:6,5:1,2:0.7857:2,2:30.3:1:30.5:1:1:2.26:41.1:22:0.7857:0:4.5 -10 42535012 . G A 45 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22462;SOR=Inf;LSEQ=ATATTTCCTTTTCTACAATT;RSEQ=GCCTCAAATCGCTTGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:26:1:31.9:1:1:0:34.2:24:1:0:5.3 0/1:14:3:1,2:6,5:0.2143:2,2:33:0:29:1:1:2.2554:27.3:6:0.2143:0:7 -10 42535014 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26706;SOR=0.38994;LSEQ=ATTTCCTTTTCTACAATTGG;RSEQ=CTCAAATCGCTTGAAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:4,4:2,2:0.6667:2,2:23:0:30.6:1:1:1:33.5:16:0.6667:0:5.1 0/1:14:6:3,3:4,4:0.4286:2,2:23:0:30:1:1:1:43:12:0.4286:0:4.8 -10 42535017 . C A 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.10662;LSEQ=TCCTTTTCTACAATTGGCCT;RSEQ=AAATCGCTTGAAATCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:2,2:4,4:0.3333:2,2:25.3:1:29.5:1:1:1:35.5:8:0.3333:0:5.5 0/1:14:5:3,2:4,5:0.3571:2,2:25:1:28.8:1:1:1.79:38.8:10:0.3571:0:4.2 -10 42535021 . T G 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74206;LSEQ=TTTCTACAATTGGCCTCAAA;RSEQ=CGCTTGAAATCTCCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:5,5:0,0:0.8333:0,2:16.5:1:32.2:1:1:0:34:20:0.8333:0:5 1/0:14:11:6,5:1,2:0.7857:2,2:18.3:1:32:1:1:2.26:41.1:22:0.7857:0:4.5 -10 42535024 . C A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26706;SOR=0.38994;LSEQ=CTACAATTGGCCTCAAATCG;RSEQ=TTGAAATCTCCACTTGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:4,4:2,2:0.6667:2,2:13:0:30.9:1:1:1:33.5:16:0.6667:0:5.1 0/1:14:6:3,3:4,4:0.4286:2,2:13:0:29.7:1:1:1:43:12:0.4286:0:4.8 -10 42535038 . T C 70 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=AAATCGCTTGAAATCTCCAC;RSEQ=TGCAAAAGCAACGAAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:6.7:1:32.7:1:1:0:35.3:6:1:0:5 1/0:8:5:3,2:1,2:0.625:2,2:4:1:30.4:1:1:2.60:38.8:10:0.625:0:4.2 -10 42535177 . C A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAGAAATCCCGTTTCCAA;RSEQ=GAAGGCCTCAAAGAGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23:0:32.5:1:1:0:28:4:1:0:0 0/1:9:2:1,1:2,3:0.2222:2,2:24:0:32.5:1:1:1.41:28:4:0.2222:0:2.5 -10 42535223 . T C 34 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCACTTGCAGACTTTACAAA;RSEQ=AGAGTGTTTCCAAACTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22.5:1:27.5:1:1:0:28:4:1:0:0 0/1:9:2:0,2:4,3:0.2222:2,0:30:1:34:0:0.44444:0:34.5:4:0.2222:0:3.5 -10 42535240 . G A 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATAGAGTGTTTCCAAACT;RSEQ=CTCTATGAAAAGAAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:5.5:1:30.5:1:1:0:28:4:1:0:0 0/1:8:2:1,1:3,3:0.25:2,2:8.5:1:26:1:1:1:34:4:0.25:0:3.5 -10 42535426 . G A 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTGCTCTTTCTAAAGGAA;RSEQ=GTTCAACTCTGTTAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:11.5:1:31:0:1:0:26:4:0.6667:0:8 1/1:1:1:1,0:0,0:1:0,0:12:0:30:0:1:0:34:2:1:0:8 -10 42535437 . G A 59 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTAAAGGAAGGTTCAACTCT;RSEQ=TTAGTTGAATACACACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:18:1:29.8:1:1:0:29.3:8:1:0:7.5 1/0:2:1:1,0:1,0:0.5:0,0:23:0:30:0:1:0:34:2:0.5:0:8 -10 42535439 . T G 77 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGAAGGTTCAACTCTGT;RSEQ=AGTTGAATACACACAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:16.4:1:33.4:1:1:0:29:10:1:0:7.2 1/1:4:4:3,1:0,0:1:0,2:9:1:32.5:1:1:0:35:8:1:0:7.3 -10 42535455 . A G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGTTAGTTGAATACACACA;RSEQ=CACAAACAAGTTACTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:7,5:0,0:1:0,2:19.3:1:31.9:1:1:0:32.8:24:1:0:6 1/1:15:14:8,6:0,0:0.9333:0,2:13.2:1:31.6:1:1:0:39.4:28:0.9333:0:6 -10 42535458 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49195;SOR=Inf;LSEQ=TTAGTTGAATACACACAACA;RSEQ=AAACAAGTTACTGAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:20.8:1:31.5:1:1:0:32.1:26:1:0:5.8 0/1:17:2:1,1:9,6:0.1176:2,2:20:0:33.5:1:1:1.46382:43:4:0.1176:0:7.5 -10 42535462 . C G 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAATACACACAACACAAA;RSEQ=AAGTTACTGAGAATTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:7,6:0,0:1:0,2:24.8:1:31.3:1:1:0:32.1:26:1:0:5.8 1/1:17:16:9,7:0,0:0.9412:0,2:17.7:1:30.8:1:1:0:39.8:15:0.9375:0:5.8 -10 42535475 . A C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59154;SOR=2.37478;LSEQ=ACACAAACAAGTTACTGAGA;RSEQ=TTCTTCTATCTAACATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:9,10:0,0:0.9048:0,2:22.6:1:31.6:1:1:0:35.7:38:0.9048:0:4.9 1/1:24:23:11,12:1,0:0.9583:0,2:23:1:32:1:1:0:37.7:46:0.9583:0:5 -10 42535480 . T C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49025;SOR=0;LSEQ=AACAAGTTACTGAGAATTCT;RSEQ=CTATCTAACATTATATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:10,13:0,0:1:0,2:25.1:1:31.3:1:1:0:34.6:46:1:0:5 1/1:25:23:11,12:1,1:0.92:2,2:26.1:1:31.3:1:1:1.0871:37.7:46:0.92:0:5 -10 42535485 . C G 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24235;SOR=Inf;LSEQ=GTTACTGAGAATTCTTCTAT;RSEQ=TAACATTATATGAAGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:27.5:1:31.3:1:1:0:34.6:22:1:0:5 0/1:28:3:2,1:12,13:0.1071:2,2:16.3:1:29.3:1:1:2.11:21.3:6:0.1111:0:3.3 -10 42535486 . T A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24235;SOR=0;LSEQ=TTACTGAGAATTCTTCTATC;RSEQ=AACATTATATGAAGAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:10,13:0,0:1:0,2:28:1:29.8:1:1:0:34.6:22:1:0:5 1/1:28:25:12,13:2,1:0.8929:2,2:27.6:1:30.1:1:1:2.10911:37.1:50:0.8929:0:4.8 -10 42535499 . A G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23959;SOR=Inf;LSEQ=TTCTATCTAACATTATATGA;RSEQ=GAAATCCCGTTTCCAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:29.8:1:31.3:1:1:0:34.6:46:1:0:5 0/1:27:3:2,1:10,12:0.1111:2,2:21:1:30:1:0.59304:2.32:21.3:6:0.1111:0:3.3 -10 42535505 . C A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49306;SOR=Inf;LSEQ=CTAACATTATATGAAGAAAT;RSEQ=CCGTTTCCAACGAAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:28.1:1:31.9:1:1:0:34.6:46:1:0:5 0/1:27:2:1,1:12,13:0.0741:2,2:32:1:28:1:1:1.08:27:4:0.0769:0:6 -10 42535543 . CTAC TGCT 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCAAAGAGGTCCAAATATC;RSEQ=TGCAGACTTTACAAAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:3,10:0,1:0.9286:0,2:11.3:1:30.8:1:1:0:34.4:26:0.9286:0.6429:4.5 1/1:10:10:3,7:0,0:1:0,2:10.5:1:29.7:1:1:0:37.1:9:1:0.9:3.9 -10 42535560 . A G 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCCTACTGCAGACTTTACA;RSEQ=AGAGAGTGTTTCCAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:18.5:1:31.5:1:1:0:30.5:4:0.6667:0:5 1/1:1:1:0,1:0,0:1:0,0:7:0:32:0:1:0:27:2:1:0:6 -10 42535562 . G C 27 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCTACTGCAGACTTTACAAA;RSEQ=AGAGTGTTTCCAAACTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:16.5:1:27:1:1:0:30.5:4:0.6667:0:5 1/1:1:1:0,1:0,0:1:0,0:5:0:31:0:1:0:27:2:1:0:6 -10 42596839 . C A 31 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTAATGGAATCATTGAA;RSEQ=AGAATTGAATTGAATCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:33:1:31.5:1:1:0:29:4:0.2222:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42596850 . T G 110 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATCATTGAACAGAATTGAAT;RSEQ=GAATCGTCATCGAATGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:1:0,0:31.8:1:33.3:1:1:0:31.6:20:1:0:3.8 1/1:1:1:1,0:0,0:1:0,0:2:0:32:0:1:0:43:2:1:0:5 -10 42596869 . C T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10632;SOR=0.12176;LSEQ=TTGAATCGTCATCGAATGAA;RSEQ=TGAATGCAATCATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:18,1:0,0:0.9048:0,1:22.4:1:31.2:1:1:0:32.3:38:0.95:0:3.2 1/0:4:2:1,1:2,0:0.5:0,2:7.5:1:28.5:1:1:0:33.5:4:0.5:0:3 -10 42596890 . TC AA 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=7;MSI=2.000;MSILEN=2;SSF=0.17749;SOR=Inf;LSEQ=TGAATGCAATCATCGAATGG;RSEQ=TCGAATGGAATCATCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:39,18:0:2,0:17:1:30:1:1:0:36.5:114:1:0:3.8 0/1:42:2:2,0:21,19:0.0476:2,0:9.5:1:30.3:1:0.49245:0:51.5:4:0.0476:0.0238:4.5 -10 42596897 . T A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.71539;LSEQ=AATCATCGAATGGTCTCGAA;RSEQ=GGAATCATCTTCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:3:2,1:42,19:0.0469:2,2:15.3:1:30:1:1:1.1035:32:6:0.0469:0:5.7 0/1:59:2:1,1:31,25:0.0339:2,2:25.5:1:31.5:1:1:1.23537:27:4:0.0339:0:4.5 -10 42596903 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49697;SOR=Inf;LSEQ=CGAATGGTCTCGAATGGAAT;RSEQ=ATCTTCAAATGGAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:51,21:0:2,0:21.6:1:31.3:1:1:0:37.9:71:1:0:4 0/1:76:2:1,1:39,34:0.0263:2,2:31.5:1:29.5:1:1:1.14495:27:4:0.0263:0:4.5 -10 42596904 . A G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22538;SOR=0;LSEQ=GAATGGTCTCGAATGGAATC;RSEQ=TCTTCAAATGGAAAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:49,20:0.0282:2,2:20.5:1:30:1:0.50704:2.41525:24:4:0.0282:0:4.5 0/0:78:0:0,0:42,36:0:2,0:16.4:1:30.5:1:1:0:40.6:156:1:0:3.6 -10 42596905 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49931;SOR=Inf;LSEQ=AATGGTCTCGAATGGAATCA;RSEQ=CTTCAAATGGAAAGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:50,21:0:2,0:23.3:1:31.1:1:1:0:38.2:142:1:0:4 0/1:82:2:2,0:42,38:0.0244:2,0:13:1:32.5:1:0.49654:0:40:4:0.0244:0:5.5 -10 42596910 . A T 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01924;SOR=0.43883;LSEQ=TCTCGAATGGAATCATCTTC;RSEQ=AATGGAAAGGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:57:36,21:13,3:0.7808:2,2:26.7:1:30.4:1:0.23442:2.49879:38.3:114:0.7917:0:4.3 1/0:92:56:20,36:27,7:0.6087:2,2:18.1:1:29:1:7e-05:6.78031:43.2:112:0.6087:0:4.1 -10 42596915 . GA G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.26068;SOR=Inf;LSEQ=AATGGAATCATCTTCAAATG;RSEQ=AAGGAATGGAATCATCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:51,29:0:2,0:27.6:1:30.5:1:1:0:37.4:160:1:0:4.4 0/1:106:3:2,1:51,52:0.0283:2,2:34.3:1:31.9:1:1:2.03:39:6:0.0283:0.0094:2.3 -10 42596918 . A T 89 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00211;SOR=0;LSEQ=GGAATCATCTTCAAATGGAA;RSEQ=GGAATGGAATCATCGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:7:7,0:44,30:0.0864:2,0:24.9:1:32:1:0.04259:0:27.4:14:0.0875:0:5.4 0/0:110:0:0,0:39,56:0:2,0:22.1:1:30.4:1:1:0:42.9:190:1:0:3.9 -10 42596919 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50896;SOR=Inf;LSEQ=GAATCATCTTCAAATGGAAA;RSEQ=GAATGGAATCATCGCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:51,30:0:2,0:29:1:32.1:1:1:0:37.4:162:1:0:4.4 0/1:110:2:1,1:52,56:0.0182:2,2:35.5:1:31.5:1:1:1.08:47:4:0.0182:0:1.5 -10 42596920 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17487;SOR=0;LSEQ=AATCATCTTCAAATGGAAAG;RSEQ=AATGGAATCATCGCATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:2,0:48,30:0.0247:2,0:22.5:1:33:0:0.52532:0:30.5:4:0.025:0:7 0/0:112:0:0,0:54,56:0:2,0:23.8:1:30.9:1:1:0:41.1:54:0.9818:0:3.9 -10 42596922 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.1794;SOR=0;LSEQ=TCATCTTCAAATGGAAAGGA;RSEQ=TGGAATCATCGCATAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:2,0:52,31:0.0235:2,0:43:1:32:1:0.53109:0:41.5:4:0.0235:0:6.5 0/0:115:0:0,0:57,58:0:2,0:24.6:1:30.2:1:1:0:41:230:1:0:3.9 -10 42596923 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17585;SOR=0;LSEQ=CATCTTCAAATGGAAAGGAA;RSEQ=GGAATCATCGCATAGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:53,30:0.0235:2,2:41:1:31:1:1:1.75417:33:4:0.0235:0:5.5 0/0:117:0:0,0:57,58:0:2,0:25:1:30:1:1:0:41.1:114:0.9828:0:3.9 -10 42596928 . T G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18596;SOR=0;LSEQ=TCAAATGGAAAGGAATGGAA;RSEQ=CATCGCATAGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:59,31:0.0215:2,2:35:0:33.5:1:1:1.88913:45.5:4:0.0215:0:4.5 0/0:122:0:0,0:59,60:0:2,0:27.4:1:29.4:1:1:0:40.8:118:0.9752:0:4 -10 42596933 . G A 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32311;LSEQ=TGGAAAGGAATGGAATCATC;RSEQ=CATAGAATCGAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:3:2,1:59,32:0.0313:2,2:36.7:1:30:1:1:1.08:30.7:6:0.0316:0:6.3 0/1:122:5:3,2:59,58:0.041:2,2:32:1:30.2:1:1:1.47:42.8:10:0.0413:0:5.4 -10 42596938 . G T 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07129;SOR=Inf;LSEQ=AGGAATGGAATCATCGCATA;RSEQ=AATCGAATGGAATTATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:61,34:0:2,0:30.9:1:31.9:1:1:0:36.7:94:1:0:4.7 0/1:125:5:3,2:58,59:0.04:2,2:30.6:1:27.2:1:1:1.52:33.4:4:0.0325:0:5.4 -10 42596941 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16955;SOR=0;LSEQ=AATGGAATCATCGCATAGAA;RSEQ=CGAATGGAATTATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:60,33:0.0211:2,2:26:1:29:1:1:1.80601:21:4:0.0211:0:5 0/0:135:0:0,0:66,68:0:2,0:30.9:1:29.5:1:1:0:40.3:268:0.9926:0:4.2 -10 42596943 . G C 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07046;SOR=0;LSEQ=TGGAATCATCGCATAGAATC;RSEQ=AATGGAATTATCATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:3:1,2:61,32:0.0313:2,2:29:1:31:1:0.28532:3.75588:38:6:0.0313:0:7 0/0:135:0:0,0:67,66:0:2,0:31.1:1:30.2:1:1:0:40.1:132:0.9851:0:4.3 -10 42596945 . A G 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26811;SOR=Inf;LSEQ=GAATCATCGCATAGAATCGA;RSEQ=TGGAATTATCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:64,35:0:2,0:29.5:1:30.4:1:1:0:36.4:98:1:0:4.7 0/1:139:3:2,1:70,66:0.0216:2,2:25:1:30:1:1:1.88:47.7:6:0.0216:0:4.7 -10 42596948 . G T 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26778;SOR=Inf;LSEQ=TCATCGCATAGAATCGAATG;RSEQ=AATTATCATTGAATGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:65,35:0:2,0:29:1:31.3:1:1:0:36.5:200:1:0:4.7 0/1:140:3:2,1:70,67:0.0214:2,2:24:1:27:1:1:1.91:47.7:6:0.0216:0:4.7 -10 42596954 . T A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=3.65167;LSEQ=CATAGAATCGAATGGAATTA;RSEQ=CATTGAATGGACTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:15:9,6:55,30:0.15:2,2:22.7:1:29.8:1:0.77459:1.21971:41.3:30:0.15:0:3.8 0/1:145:57:33,24:41,44:0.3931:2,2:27.7:1:30.1:1:0.30511:1.47:41.1:56:0.3944:0:3.9 -10 42596957 . TT AC 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51415;SOR=Inf;LSEQ=AGAATCGAATGGAATTATCA;RSEQ=GAATGGACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:62,36:0:2,0:28:1:30.6:1:1:0:36.8:196:1:0:4.8 0/1:141:2:0,2:73,66:0.0142:2,0:32:1:32:0:0.2308:0:33.5:4:0.0143:0:5.5 -10 42596958 . T C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22026;LSEQ=GAATCGAATGGAATTATCAT;RSEQ=GAATGGACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:81:51,30:11,6:0.8265:2,2:28.5:1:30.7:1:1:1.07762:35.9:162:0.8265:0:5.1 1/0:143:73:35,38:38,27:0.5105:2,2:29.5:1:30.1:1:0.2357:1.52329:37.8:72:0.5143:0:5 -10 42596963 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51841;SOR=Inf;LSEQ=GAATGGAATTATCATTGAAT;RSEQ=GACTCGAATGGAATCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:64,37:0:2,0:25.7:1:31.4:1:1:0:36.7:100:1:0:4.9 0/1:152:2:1,1:81,69:0.0132:2,2:23.5:1:32:0:1:1.17267:48:4:0.0132:0:3.5 -10 42596966 . C A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.29972;LSEQ=TGGAATTATCATTGAATGGA;RSEQ=TCGAATGGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:71:41,30:17,7:0.7396:2,2:26:1:30:1:0.33493:1.76659:36.4:70:0.7368:0:5.5 0/1:157:72:34,38:49,34:0.4586:2,2:23.4:1:29.8:1:0.15011:1.60577:35.7:35:0.4545:0:5.4 -10 42596967 . T C 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29787;SOR=Inf;LSEQ=GGAATTATCATTGAATGGAC;RSEQ=CGAATGGAATCAACATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:58,36:0:2,0:26:1:30.4:1:1:0:37:188:1:0:5.1 0/1:160:3:2,1:84,71:0.0188:2,2:35:1:29:1:1:1.69:43.7:6:0.0189:0:4 -10 42596972 . T A 74 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08735;SOR=Inf;LSEQ=TATCATTGAATGGACTCGAA;RSEQ=GGAATCAACATCAAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:61,35:0:2,0:23.5:1:30.3:1:1:0:36.5:192:0.9897:0:5.1 0/1:164:6:3,3:86,71:0.0366:2,2:24.5:1:29:1:1:1.20983:29.2:12:0.037:0:6.2 -10 42596973 . G A 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.17942;LSEQ=ATCATTGAATGGACTCGAAT;RSEQ=GAATCAACATCAAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:1,0:60,35:0.0104:2,0:10:0:11:0:1:0:50:0:0:0:5 0/1:163:2:1,1:89,72:0.0123:2,2:34.5:1:29:1:1:1.23449:41:4:0.0125:0:4 -10 42596975 . A T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=0.35459;LSEQ=CATTGAATGGACTCGAATGG;RSEQ=ATCAACATCAAACGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:49:27,22:34,9:0.5269:2,2:19.6:1:28.7:1:0.02627:3.0401:37.4:98:0.5269:0:5.9 0/1:163:46:17,29:73,40:0.2822:2,2:20.7:1:29.2:1:0.00248:3.08977:39.8:92:0.284:0:5.8 -10 42596979 . A C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13868;LSEQ=GAATGGACTCGAATGGAATC;RSEQ=ACATCAAACGGAATCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:1,0:59,31:0.011:2,0:21:0:32:0:1:0:48:2:0.011:0:4 0/1:160:2:1,1:87,71:0.0125:2,2:24.5:1:29.5:1:1:1.22378:31:4:0.0126:0:3.5 -10 42596981 . C T 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30023;SOR=Inf;LSEQ=ATGGACTCGAATGGAATCAA;RSEQ=ATCAAACGGAATCAAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:61,29:0:2,0:21.6:1:31.8:1:1:0:35.7:180:1:0:5.3 0/1:163:4:3,1:87,72:0.0245:2,2:37:1:29.5:1:0.62864:2.47:31:8:0.0248:0:6.5 -10 42596983 . T C 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01291;SOR=0.45872;LSEQ=GGACTCGAATGGAATCAACA;RSEQ=CAAACGGAATCAAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:30:16,14:39,15:0.3571:2,2:18.5:1:31.4:1:0.09732:2.25164:35.9:60:0.3571:0:6.5 0/1:158:32:10,22:78,48:0.2025:2,2:17.4:1:31.2:1:0.00255:3.54518:38.3:64:0.2051:0:6.4 -10 42596984 . C G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54539;SOR=Inf;LSEQ=GACTCGAATGGAATCAACAT;RSEQ=AAACGGAATCAAACGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:52,29:0:2,0:22.9:1:31.4:1:1:0:34.7:162:1:0:5.3 0/1:153:2:1,1:85,66:0.0131:2,2:42.5:1:31:1:1:1.28572:27:4:0.0132:0:7.5 -10 42596988 . C T 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.24108;LSEQ=CGAATGGAATCAACATCAAA;RSEQ=GGAATCAAACGGAATTAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:2,1:50,24:0.039:2,2:22.3:1:32:1:1:1.0411:40:6:0.039:0:5 0/1:146:7:3,4:81,58:0.0479:2,2:23.9:1:29.4:1:0.45823:1.85396:37:14:0.0479:0:5.7 -10 42596989 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60799;SOR=0.51575;LSEQ=GAATGGAATCAACATCAAAC;RSEQ=GAATCAAACGGAATTAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:51,22:0.0267:2,2:17.5:1:29:1:0.52216:2.28937:40:4:0.027:0:2.5 0/1:144:2:2,0:83,58:0.0139:2,0:33.5:1:31:1:0.51443:0:33.5:4:0.0141:0:3 -10 42596991 . A T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5528;SOR=Inf;LSEQ=ATGGAATCAACATCAAACGG;RSEQ=ATCAAACGGAATTAGCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:51,22:0:2,0:23.3:1:30:1:1:0:35:146:1:0:5.3 0/1:139:3:2,1:79,56:0.0216:2,2:12.7:1:29.7:1:1:1.41:42:6:0.0219:0:5.3 -10 42596992 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54241;SOR=Inf;LSEQ=TGGAATCAACATCAAACGGA;RSEQ=TCAAACGGAATTAGCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:52,22:0:2,0:22.7:1:30:1:1:0:35.1:148:1:0:5.3 0/1:137:2:1,1:79,56:0.0146:2,2:30:1:28:1:1:1.40708:40:4:0.0146:0:5.5 -10 42596993 . TC AA 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01231;SOR=0.4547;LSEQ=GGAATCAACATCAAACGGAA;RSEQ=AAACGGAATTAGCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:48:35,13:16,8:0.6575:2,2:22.9:1:29.8:1:0.59352:1.34:31.6:96:0.6575:0.0548:5.3 0/1:129:60:38,22:37,27:0.4651:2,2:25.2:1:30.7:1:0.5838:1.26:31.6:120:0.4688:0.031:5.3 -10 42596996 . AA CG 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53051;SOR=Inf;LSEQ=ATCAACATCAAACGGAATCA;RSEQ=CGGAATTAGCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:51,25:0:2,0:20.8:1:30.3:1:1:0:33.9:152:0.987:0:4.5 0/1:130:2:1,1:76,51:0.0154:2,2:8:0:32.5:0:1:1.48544:49:4:0.0154:0:2.5 -10 42596997 . A G 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26351;SOR=1.47866;LSEQ=TCAACATCAAACGGAATCAA;RSEQ=CGGAATTAGCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:18:12,6:40,18:0.2368:2,2:23.7:1:32.6:1:1:1.10955:39.2:36:0.2368:0:4.3 0/1:127:40:23,17:50,33:0.315:2,2:24.7:1:31.5:1:0.84544:1.11886:38.3:80:0.3279:0:4.4 -10 42596999 . G A 92 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02677;SOR=Inf;LSEQ=AACATCAAACGGAATCAAAC;RSEQ=GAATTAGCGAATGGAATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:51,23:0:2,0:21.2:1:29.9:1:1:0:32.9:73:1:0:4.7 0/1:125:8:4,4:70,47:0.064:2,2:32.6:1:30.8:1:0.71478:1.48447:37:16:0.064:0:5.5 -10 42597000 . G T 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.74954;SOR=1.59654;LSEQ=ACATCAAACGGAATCAAACG;RSEQ=AATTAGCGAATGGAATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:3:2,1:48,24:0.04:2,2:25:1:29:1:1:1:30:6:0.0405:0:5.3 0/1:128:8:6,2:72,48:0.0625:2,2:25:1:27.4:1:0.48081:1.99:34.8:16:0.0635:0:5.6 -10 42597001 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53997;SOR=Inf;LSEQ=CATCAAACGGAATCAAACGG;RSEQ=ATTAGCGAATGGAATCGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:48,24:0:2,0:21.6:1:30:1:1:0:31.8:144:1:0:4.6 0/1:131:2:1,1:78,49:0.0153:2,2:40:1:29.5:1:1:1.58585:27:4:0.0155:0:7.5 -10 42597005 . AG TT 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5354;SOR=Inf;LSEQ=AAACGGAATCAAACGGAATT;RSEQ=CGAATGGAATCGAAGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:51,23:0:2,0:20.8:1:28.8:1:1:0:31.5:148:1:0:4.6 0/1:130:2:1,1:79,49:0.0154:2,2:16:1:31:1:1:1.60605:32.5:4:0.0156:0:5.5 -10 42597006 . G T 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21662;SOR=0.4327;LSEQ=AACGGAATCAAACGGAATTA;RSEQ=CGAATGGAATCGAAGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:69:50,19:0,0:0.9452:0,2:20.4:1:30.5:1:1:0:30.9:138:0.9452:0:4.5 1/1:135:119:75,44:1,0:0.8815:0,2:24.1:1:29.6:1:1:0:33.2:238:0.9015:0:4.7 -10 42597008 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60596;SOR=0.50827;LSEQ=CGGAATCAAACGGAATTAGC;RSEQ=AATGGAATCGAAGAGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:2,0:53,23:0.0256:2,0:27:1:26.5:1:1:0:35:4:0.0256:0:5 0/1:152:2:0,2:94,54:0.0132:2,0:17.5:1:29:1:0.13781:0:32.5:4:0.0132:0:6.5 -10 42597009 . A T 55 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30557;SOR=Inf;LSEQ=GGAATCAAACGGAATTAGCG;RSEQ=ATGGAATCGAAGAGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:54,24:0:2,0:19.9:1:29.9:1:1:0:31.9:156:1:0:4.4 0/1:159:4:2,2:96,59:0.0252:2,2:14.5:1:27.8:1:0.63811:1.62189:36.5:8:0.0255:0:5.3 -10 42597011 . T C 95 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75725;SOR=1.41429;LSEQ=AATCAAACGGAATTAGCGAA;RSEQ=GGAATCGAAGAGAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:3:2,1:54,22:0.038:2,2:21.3:1:31:1:1:1.22393:30:6:0.0385:0:5.3 0/1:170:9:4,5:99,62:0.0529:2,2:22.9:1:30.1:1:0.31909:1.98759:39:18:0.0536:0:5.3 -10 42597013 . G A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37692;SOR=0.43948;LSEQ=TCAAACGGAATTAGCGAATG;RSEQ=AATCGAAGAGAATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:2,1:51,22:0.039:2,2:38:1:32:0:1:1.15677:40:6:0.0395:0:5 0/1:172:3:2,1:101,65:0.0174:2,2:11.7:1:28:1:1:1.29:37.7:6:0.0178:0:5.7 -10 42597017 . C T 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.37912;LSEQ=ACGGAATTAGCGAATGGAAT;RSEQ=GAAGAGAATCATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:1:1,0:56,25:0.0122:2,0:43:0:33:0:1:0:25:2:0.0122:0:5 0/1:179:3:2,1:108,67:0.0168:2,2:17:1:29.7:1:1:1.24:35:6:0.0169:0:5.7 -10 42597018 . G A 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66218;SOR=0.72157;LSEQ=CGGAATTAGCGAATGGAATC;RSEQ=AAGAGAATCATCGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:61,25:0.0227:2,2:39:1:30:1:0.50601:2.41216:47:4:0.0227:0:4 0/1:182:3:2,1:111,67:0.0165:2,2:9:1:27.7:1:1:1.21:42:6:0.0165:0:4.7 -10 42597021 . G T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.4427;LSEQ=AATTAGCGAATGGAATCGAA;RSEQ=AGAATCATCGAATGGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:1,0:65,26:0.0109:2,0:4:0:30:0:1:0:23:2:0.0109:0:4 0/1:192:3:2,1:112,74:0.0156:2,2:17.3:1:26:1:1:1.32:49.3:2:0.0105:0:3.7 -10 42597022 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATTAGCGAATGGAATCGAAG;RSEQ=GAATCATCGAATGGACTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:64,27:0:2,0:19.7:1:30:1:1:0:34:90:1:0:4 0/1:193:2:1,1:113,75:0.0104:2,2:24.5:1:30.5:1:1:1.50329:21:4:0.0106:0:3.5 -10 42597024 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGCGAATGGAATCGAAGAG;RSEQ=ATCATCGAATGGACTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:62,29:0:2,0:20.4:1:30.1:1:1:0:34.1:182:1:0:4 0/1:198:2:1,1:116,80:0.0101:2,2:17:1:33:0:1:1.44719:27:4:0.0101:0:7.5 -10 42597026 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.09459;SOR=0;LSEQ=GCGAATGGAATCGAAGAGAA;RSEQ=CATCGAATGGACTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:60,30:0.0217:2,2:18:1:30:1:1:1.98387:46.5:4:0.022:0:5 0/0:206:0:0,0:124,81:0:2,0:21.7:1:29.3:1:1:0:36.1:101.5:0.9951:0:4 -10 42597028 . A T 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.56812;SOR=0.82901;LSEQ=GAATGGAATCGAAGAGAATC;RSEQ=TCGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:26:17,9:47,20:0.2766:2,2:22.8:1:30.3:1:0.80344:1.24112:30.7:52:0.2766:0:5 0/1:212:51:30,21:93,67:0.2406:2,2:23.4:1:30.2:1:1:1.03:35.7:102:0.2417:0:5 -10 42597030 . C A 45 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.30801;LSEQ=ATGGAATCGAAGAGAATCAT;RSEQ=GAATGGACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:0,1:64,31:0.0103:2,0:15:0:33:0:0.33333:0:44:2:0.0104:0:5 0/1:223:3:2,1:127,91:0.0135:2,2:8.3:1:29:1:1:1.43:30.7:6:0.0136:0:4 -10 42597033 . A T 76 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18246;SOR=Inf;LSEQ=GAATCGAAGAGAATCATCGA;RSEQ=TGGACTCGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:67,37:0:2,0:21.6:1:30:1:1:0:33.8:51:1:0:3.8 0/1:230:6:5,1:128,96:0.0261:2,2:26.3:1:29.7:1:0.40518:3.73:31:12:0.0261:0:5.8 -10 42597034 . T C 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.79585;SOR=1.10359;LSEQ=AATCGAAGAGAATCATCGAA;RSEQ=GGACTCGAATGGAATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:29:18,11:49,26:0.2788:2,2:21.8:1:30.8:1:0.82082:1.15013:30.1:58:0.2788:0:4.7 0/1:234:70:38,32:95,67:0.2991:2,2:24.8:1:29.9:1:0.56511:1.19311:34.3:140:0.3004:0:4.8 -10 42597038 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09858;SOR=0;LSEQ=GAAGAGAATCATCGAATGGA;RSEQ=TCGAATGGAATCATCTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:69,43:0.0175:2,2:18:1:29:1:1:1.59771:46.5:4:0.0175:0:5 0/0:248:0:0,0:138,110:0:2,0:22.7:1:30.6:1:1:0:35.5:81.667:1:0:3.7 -10 42597039 . T C 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26177;SOR=0.74178;LSEQ=AAGAGAATCATCGAATGGAC;RSEQ=CGAATGGAATCATCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:113:85:51,34:17,11:0.7522:2,2:21.3:1:31:1:1:1.03004:30.4:170:0.7522:0:3.4 1/0:247:171:96,75:40,34:0.6923:2,2:23.4:1:29.9:1:0.78095:1.09:33.2:170:0.6911:0:3.7 -10 42597040 . C G 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.66951;SOR=2.32061;LSEQ=AGAGAATCATCGAATGGACT;RSEQ=GAATGGAATCATCTAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:1:1,0:68,45:0.0088:2,0:41:0:34:0:1:0:40:2:0.0088:0:3 0/1:248:5:3,2:135,107:0.0202:2,2:28.8:1:31.4:1:1:1.19:36.2:10:0.0202:0:3.6 -10 42597041 . G A 59 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.84217;LSEQ=GAGAATCATCGAATGGACTC;RSEQ=AATGGAATCATCTAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:1:1,0:68,45:0.0088:2,0:32:0:32:0:1:0:31:2:0.0088:0:3 0/1:249:4:2,2:138,107:0.0161:2,2:31:1:29.8:1:1:1.28838:38.5:8:0.0162:0:6 -10 42597047 . A G 49 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03153;SOR=0;LSEQ=CATCGAATGGACTCGAATGG;RSEQ=ATCATCTAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:3:2,1:69,49:0.0246:2,2:18.3:1:31.3:1:1:1.42:24.3:6:0.0254:0:3.3 0/0:262:0:0,0:143,118:0:2,0:25.9:1:29.1:1:1:0:35.2:129.5:0.9962:0:3.5 -10 42597050 . C A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56285;SOR=0.74319;LSEQ=CGAATGGACTCGAATGGAAT;RSEQ=ATCTAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:5:2,3:71,52:0.0391:2,2:27.6:1:29.8:1:0.6509:2.03651:45:10:0.04:0:5 0/1:273:8:3,5:144,121:0.0293:2,2:35.6:1:29.4:1:0.4772:1.97851:40.1:16:0.0297:0:3.1 -10 42597052 . T C 33 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.239;SOR=0.2317;LSEQ=AATGGACTCGAATGGAATCA;RSEQ=CTAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:70,55:0.0156:2,2:29.5:1:33:0:1:1.27028:34.5:4:0.0157:0:6 0/0:274:1:1,0:146,126:0.0036:2,0:36:0:28:0:1:0:40:2:0.0037:0:6 -10 42597053 . C G 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15273;LSEQ=ATGGACTCGAATGGAATCAT;RSEQ=TAATGGAATGGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:71,54:0.0157:2,2:26.5:1:32.5:1:1:1.31194:27:4:0.0159:0:5.5 0/1:276:5:2,3:145,125:0.0181:2,2:30.4:1:30.6:1:0.66637:1.73649:31.2:10:0.0185:0:3.8 -10 42597054 . T G 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41707;LSEQ=TGGACTCGAATGGAATCATC;RSEQ=AATGGAATGGAATGGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:1:0,1:73,57:0.0076:2,0:24:0:13:0:0.44275:0:25:0:0:0:8 0/1:278:3:2,1:141,129:0.0108:2,2:26.7:1:29.7:1:1:1.83:36:6:0.0109:0:5 -10 42597058 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.24419;SOR=0.23608;LSEQ=CTCGAATGGAATCATCTAAT;RSEQ=GAATGGAATGGAATAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:2,0:73,62:0.0146:2,0:5.5:1:30:1:0.50086:0:32.5:4:0.0146:0:2 0/0:288:1:1,0:142,142:0.0035:2,0:10:0:28:0:1:0:25:2:0.0035:0:4 -10 42597062 . T A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55407;SOR=Inf;LSEQ=AATGGAATCATCTAATGGAA;RSEQ=GGAATGGAATAATCCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:73,70:0:2,0:27.6:1:30.3:1:1:0:33.1:142:1:0:3.1 0/1:292:3:1,2:139,150:0.0103:2,2:24:1:29.7:1:1:1.84957:28.7:6:0.0103:0:3.3 -10 42597063 . G T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.54116;SOR=0.68103;LSEQ=ATGGAATCATCTAATGGAAT;RSEQ=GAATGGAATAATCCATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:5:2,3:72,67:0.0347:2,2:35.4:1:30:1:0.67454:1.60664:45:10:0.0347:0:5 0/1:293:7:2,5:136,147:0.0239:2,2:28.4:1:30.3:1:0.4513:2.30655:34.9:14:0.0241:0:4 -10 42597064 . G A 76 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.18422;SOR=Inf;LSEQ=TGGAATCATCTAATGGAATG;RSEQ=AATGGAATAATCCATGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:74,70:0:2,0:28.1:1:30.7:1:1:0:33.1:27.8:1:0:3.1 0/1:293:6:3,3:137,148:0.0205:2,2:30.7:1:29.7:1:1:1.08:36:12:0.0205:0:4 -10 42597066 . A T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.55411;SOR=Inf;LSEQ=GAATCATCTAATGGAATGGA;RSEQ=TGGAATAATCCATGGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:73,71:0:2,0:28.5:1:30.3:1:1:0:33:71:0.993:0:3.1 0/1:297:3:1,2:142,150:0.0101:2,2:38.3:1:29.7:1:1:1.8894:28:6:0.0102:0:3.3 -10 42597069 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.10862;SOR=0;LSEQ=TCATCTAATGGAATGGAATG;RSEQ=AATAATCCATGGACTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:72,73:0.0136:2,2:33.5:1:30:0:1:1.01:29:4:0.0138:0:2.5 0/0:298:0:0,0:142,156:0:2,0:28.2:1:30.7:1:1:0:34.9:148:1:0:3.2 -10 42597072 . T G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09886;LSEQ=TCTAATGGAATGGAATGGAA;RSEQ=AATCCATGGACTCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:9:4,5:67,70:0.0616:2,2:16.8:1:31.2:1:1:1.19496:36.8:18:0.0616:0:2.9 0/1:297:20:9,11:129,146:0.0673:2,2:27.9:1:30.8:1:1:1.07966:36.3:19:0.0644:0:3.5 -10 42597076 . C A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0907;LSEQ=ATGGAATGGAATGGAATAAT;RSEQ=CATGGACTCGAATGCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:4:3,1:66,78:0.027:2,2:29.8:1:27.3:1:0.33903:3.52:47:8:0.0274:0:5.8 0/1:306:9:2,7:140,157:0.0294:2,2:24.6:1:28.2:1:0.18348:3.11051:38.7:18:0.0296:0:4.7 -10 42597079 . T C 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88868;SOR=1.05958;LSEQ=GAATGGAATGGAATAATCCA;RSEQ=GGACTCGAATGCAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:21:8,13:58,65:0.1438:2,2:29:1:30:1:0.48566:1.44631:44:42:0.1458:0:4.2 0/1:311:47:20,27:124,139:0.1511:2,2:28.7:1:29.8:1:0.63483:1.2036:42.5:46:0.1494:0:3.9 -10 42597081 . G A 67 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33158;SOR=Inf;LSEQ=ATGGAATGGAATAATCCATG;RSEQ=ACTCGAATGCAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:66,80:0:2,0:30.5:1:30.8:1:1:0:33.8:35.5:1:0:2.9 0/1:318:5:2,3:143,167:0.0157:2,2:23.6:1:29:1:1:1.28342:31.6:10:0.0158:0:4 -10 42597082 . A T 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.70894;SOR=0.75178;LSEQ=TGGAATGGAATAATCCATGG;RSEQ=CTCGAATGCAATCATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:2,1:64,78:0.0207:2,2:14.7:1:29.3:1:0.59138:2.42:33.7:6:0.021:0:3.7 0/1:320:5:2,3:147,168:0.0156:2,2:38:1:29:1:1:1.3114:36.6:10:0.0157:0:3.6 -10 42597083 . C G 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59174;SOR=0.44913;LSEQ=GGAATGGAATAATCCATGGA;RSEQ=TCGAATGCAATCATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:2,0:64,78:0.0138:2,0:44.5:1:32.5:1:0.20833:0:35:4:0.014:0:3.5 0/0:321:2:0,2:149,169:0.0062:2,0:17.5:1:33:0:0.5008:0:24.5:4:0.0063:0:3 -10 42597084 . T C 96 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76248;SOR=1.3483;LSEQ=GAATGGAATAATCCATGGAC;RSEQ=CGAATGCAATCATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:3:3,0:64,79:0.0205:2,0:25.7:1:31.7:1:0.09429:0:42:6:0.0213:0:3 0/1:327:9:4,5:146,170:0.0275:2,2:30.9:1:30.6:1:1:1.07332:42.9:18:0.0279:0:3.6 -10 42597085 . C G 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09304;LSEQ=AATGGAATAATCCATGGACT;RSEQ=GAATGCAATCATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:7:2,5:66,74:0.0476:2,2:34.1:1:30:1:0.45124:2.21826:25.1:14:0.049:0:4.6 0/1:328:17:9,8:141,168:0.0518:2,2:23.5:1:30.5:1:0.62199:1.34:33.2:34:0.0528:0:4.9 -10 42597086 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.09591;SOR=0;LSEQ=ATGGAATAATCCATGGACTC;RSEQ=AATGCAATCATCATCGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:69,77:0.0134:2,2:25.5:1:30:1:1:1.12:25:4:0.0136:0:3 0/0:331:0:0,0:151,179:0:2,0:25.8:1:29.9:1:1:0:35.3:65:0.9969:0:3 -10 42597089 . T G 119 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20583;SOR=2.31406;LSEQ=GAATAATCCATGGACTCGAA;RSEQ=GCAATCATCATCGAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:0,3:68,77:0.0201:2,0:33.7:1:30.7:1:0.24986:0:22.7:6:0.0207:0:5 0/1:330:15:8,7:136,175:0.0455:2,2:26.5:1:30.7:1:0.59622:1.47:31.6:30:0.0462:0:4.9 -10 42597091 . C G 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17058;SOR=0.29114;LSEQ=ATAATCCATGGACTCGAATG;RSEQ=AATCATCATCGAATAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:2,1:66,77:0.0203:2,2:24.3:1:31.3:1:0.59809:2.32:31.7:6:0.0207:0:4.3 0/0:335:2:1,1:146,182:0.006:2,2:6.5:1:30.5:1:1:1.25:43:4:0.006:0:4.5 -10 42597095 . CATCATCGAATAGAATCGAATGGA C 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0.88646;LSEQ=TCCATGGACTCGAATGCAAT;RSEQ=ATCATCGAATGGACTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:66,82:0.0133:2,2:14:1:30.9:1:1:1.24:21:4:0.0134:0.0133:2 0/1:338:4:2,2:146,188:0.0118:2,2:22.5:1:28.5:1:1:1.29:36.8:4:0.0119:0.0118:1.5 -10 42597097 . T G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.09729;SOR=0;LSEQ=CATGGACTCGAATGCAATCA;RSEQ=CATCGAATAGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:65,80:0.0132:2,2:29:1:31.5:1:1:1.23:30:4:0.0136:0:5.5 0/0:332:0:0,0:143,188:0:2,0:25.1:1:28.7:1:1:0:35.5:40.375:0.9969:0:3.1 -10 42597098 . C T 74 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18351;SOR=Inf;LSEQ=ATGGACTCGAATGCAATCAT;RSEQ=ATCGAATAGAATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:68,82:0:2,0:27.3:1:31.4:1:1:0:34.8:49:1:0:2.8 0/1:328:6:3,3:134,184:0.0183:2,2:19:1:28.7:1:0.70033:1.37:41:12:0.0185:0:4.2 -10 42597100 . T G 101 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.76306;SOR=1.54932;LSEQ=GGACTCGAATGCAATCATCA;RSEQ=CGAATAGAATCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:3:1,2:67,77:0.02:2,2:23.7:1:29.7:1:1:1.73398:46.7:6:0.0207:0:3.3 0/1:326:10:4,6:130,181:0.0307:2,2:21.4:1:30.5:1:1:1.07712:38.8:20:0.0313:0:3.4 -10 42597102 . G A 79 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93053;LSEQ=ACTCGAATGCAATCATCATC;RSEQ=AATAGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:3:2,1:65,77:0.02:2,2:11.7:1:28:1:0.59569:2.36:25:6:0.0204:0:3 0/1:322:6:2,4:128,178:0.0186:2,2:26.7:1:30.7:1:1:1.43659:30.2:12:0.0189:0:4.2 -10 42597103 . A T 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28129;SOR=0.7176;LSEQ=CTCGAATGCAATCATCATCG;RSEQ=ATAGAATCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:21:8,13:58,67:0.1409:2,2:23.2:1:29:1:0.63649:1.40347:47.7:42:0.1438:0:3.7 0/1:323:34:13,21:115,164:0.1053:2,2:22.2:1:27.6:1:0.85397:1.13227:47.8:33:0.1065:0:3.6 -10 42597104 . A T 49 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03044;SOR=0;LSEQ=TCGAATGCAATCATCATCGA;RSEQ=TAGAATCGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:1,2:64,80:0.0201:2,2:28.3:1:31:1:1:1.5951:23:6:0.0205:0:4.3 0/0:326:0:0,0:128,195:0:2,0:25:1:29.1:1:1:0:36.2:52.833:0.9937:0:3 -10 42597106 . A G 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34036;SOR=1.31168;LSEQ=GAATGCAATCATCATCGAAT;RSEQ=GAATCGAATGGAATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:150:123:55,68:8,15:0.82:2,2:26.3:1:31.1:1:0.49267:1.51:33.3:40:0.8333:0:2.6 1/1:328:281:111,170:15,29:0.8567:2,2:25.1:1:30:1:0.61801:1.26:34.6:69.25:0.8576:0:2.8 -10 42597111 . C G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.25256;LSEQ=CAATCATCATCGAATAGAAT;RSEQ=GAATGGAATCATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:4:1,3:57,84:0.027:2,2:15:1:31:1:0.64996:2.02669:30.3:8:0.0276:0:3.3 0/1:327:11:5,6:121,193:0.0336:2,2:25.5:1:29.2:1:0.75547:1.33:33.8:10:0.031:0:3.2 -10 42597114 . A T 29 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22362;SOR=0.21934;LSEQ=TCATCATCGAATAGAATCGA;RSEQ=TGGAATCATCGAATGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:57,87:0.0135:2,2:21:0:29.5:1:1:1.52:53.5:4:0.0141:0:4.5 0/0:335:1:0,1:126,207:0.003:2,0:32:0:30:0:1:0:40:2:0.003:0:5 -10 42597124 . C T 96 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.21247;LSEQ=ATAGAATCGAATGGAATCAT;RSEQ=GAATGGACTCGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:3:0,3:46,83:0.0224:2,0:22.7:1:28.3:1:0.55125:0:34.7:6:0.0227:0:4.7 0/1:333:9:3,6:117,201:0.027:2,2:18.4:1:30.6:1:1:1.16368:41:18:0.0272:0:3.9 -10 42597125 . G C 38 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62883;SOR=0.60444;LSEQ=TAGAATCGAATGGAATCATC;RSEQ=AATGGACTCGAATGGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:45,83:0.0152:2,2:29:0:32.5:1:1:1.84:26:4:0.0155:0:3 0/0:326:3:1,2:117,203:0.0092:2,2:11.7:1:24:1:1:1.15224:29:2:0.0063:0:3.7 -10 42597127 . A G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55585;SOR=0.71712;LSEQ=GAATCGAATGGAATCATCGA;RSEQ=TGGACTCGAATGGAATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:5:2,3:43,82:0.0385:2,2:21.6:1:31:1:1:1.27:35.2:10:0.0388:0:2.8 0/1:323:9:3,6:111,201:0.0279:2,2:32.6:1:31.9:1:1:1.10415:33.9:18:0.028:0:3.9 -10 42597128 . T A 79 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67883;SOR=2.36973;LSEQ=AATCGAATGGAATCATCGAA;RSEQ=GGACTCGAATGGAATAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:1:0,1:41,84:0.0079:2,0:26:0:33:0:1:0:27:2:0.0081:0:3 0/1:322:6:1,5:111,201:0.0186:2,2:32:1:30.8:1:0.66931:2.75398:37.8:12:0.019:0:4.5 -10 42597129 . G T 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3167;SOR=0.3902;LSEQ=ATCGAATGGAATCATCGAAT;RSEQ=GACTCGAATGGAATAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:40,82:0.016:2,2:25:1:32:0:1:2.04:60:4:0.0163:0:3 0/0:318:2:1,1:110,206:0.0063:2,2:16:1:32:0:1:1.87:22:4:0.0064:0:4 -10 42597130 . G A 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19604;SOR=0.197;LSEQ=TCGAATGGAATCATCGAATG;RSEQ=ACTCGAATGGAATAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:40,81:0.0161:2,2:21.5:1:29.5:1:1:2.01:40.5:4:0.0164:0:4.5 0/0:312:1:0,1:107,195:0.0032:2,0:3:0:28:0:1:0:23:2:0.0033:0:7 -10 42597133 . T A 70 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.93343;LSEQ=AATGGAATCATCGAATGGAC;RSEQ=CGAATGGAATAATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:1:0,1:38,77:0.0086:2,0:11:0:12:0:1:0:23:0:0:0:4 0/1:302:5:1,4:102,193:0.0166:2,2:34.8:1:30.2:1:0.66338:2.10943:38:10:0.0169:0:4.4 -10 42597134 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18716;SOR=0.18986;LSEQ=ATGGAATCATCGAATGGACT;RSEQ=GAATGGAATAATCATTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:37,76:0.0174:2,2:34:1:31.5:1:1:2.04:37:4:0.0179:0:3 0/0:300:1:0,1:102,197:0.0033:2,0:1:0:29:0:1:0:24:2:0.0034:0:4 -10 42597139 . G T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61213;SOR=0.53972;LSEQ=ATCATCGAATGGACTCGAAT;RSEQ=GAATAATCATTGAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:34,67:0.0192:2,0:14.5:1:31.5:1:1:0:43:4:0.0196:0:5.5 0/1:287:3:1,2:96,185:0.0105:2,2:25.7:1:28.7:1:1:1.0377:46.7:6:0.0106:0:4.7 -10 42597140 . G T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33093;SOR=Inf;LSEQ=TCATCGAATGGACTCGAATG;RSEQ=AATAATCATTGAACGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:33,70:0:2,0:25.3:1:31.3:1:1:0:37.1:33.333:1:0:2.5 0/1:285:5:2,3:95,184:0.0175:2,2:33.2:1:28.4:1:1:1.29:41.8:10:0.0177:0:3.8 -10 42597150 . T C 99 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07145;SOR=Inf;LSEQ=GACTCGAATGGAATAATCAT;RSEQ=GAACGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:26,59:0:2,0:27.5:1:30.3:1:1:0:38:41.5:1:0:2.6 0/1:253:10:2,8:79,161:0.0395:2,2:26.3:1:29.9:1:0.50693:1.9581:35.7:20:0.04:0:4.4 -10 42597154 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11244;SOR=0.40813;LSEQ=CGAATGGAATAATCATTGAA;RSEQ=GGAATCGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:6:1,5:24,48:0.0769:2,2:35.7:1:30.7:1:0.65798:2.47544:38.3:12:0.0769:0:3.7 0/1:244:8:3,5:75,159:0.0328:2,2:26.3:1:30.5:1:0.71497:1.27:38.5:16:0.0329:0:5.1 -10 42597155 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05837;SOR=0;LSEQ=GAATGGAATAATCATTGAAC;RSEQ=GAATCGAATGGAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:0,2:25,49:0.0263:2,0:42.5:1:31.5:1:1:0:50.5:4:0.027:0:5.5 0/0:237:0:0,0:79,157:0:2,0:28.8:1:29.7:1:1:0:37.3:38.333:0.9957:0:3 -10 42597156 . G A 27 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24744;SOR=0.31476;LSEQ=AATGGAATAATCATTGAACG;RSEQ=AATCGAATGGAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:24,49:0.0267:2,2:16:1:29:1:1:2.02:25:4:0.0274:0:4 0/0:235:2:1,1:77,156:0.0085:2,2:32.5:1:27.5:1:1:2.02:25:4:0.0087:0:5.5 -10 42597159 . T A 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34021;SOR=Inf;LSEQ=GGAATAATCATTGAACGGAA;RSEQ=CGAATGGAATCATCATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:23,48:0:2,0:27.9:1:30.3:1:1:0:38.9:70:0.9859:0:2.6 0/1:224:5:3,2:72,142:0.0223:2,2:34:1:31:1:0.34134:2.94:39.4:10:0.0227:0:3.8 -10 42597164 . TG T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05131;SOR=0;LSEQ=AATCATTGAACGGAATCGAA;RSEQ=GAATCATCATCAGATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:18,40:0.0323:2,2:31.5:1:32:1:0.53672:2.19:40.5:4:0.0328:0:3 0/0:210:0:0,0:69,139:0:2,0:26.2:1:30.7:1:1:0:37.9:68.333:0.9903:0:3.1 -10 42597165 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05131;SOR=0;LSEQ=ATCATTGAACGGAATCGAAT;RSEQ=GAATCATCATCAGATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:18,40:0.0323:2,2:23.5:1:30:1:0.53672:2.19:48:4:0.0328:0:2 0/0:210:0:0,0:69,139:0:2,0:26.2:1:30.7:1:1:0:37.9:68.333:0.9903:0:3.1 -10 42597168 . A G 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGAACGGAATCGAATGGA;RSEQ=TCATCATCAGATGGAAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:19,38:0:2,0:26.7:1:30.9:1:1:0:40:114:1:0:2.8 0/1:205:3:1,2:67,134:0.0146:2,2:23:1:33:1:1:1:36.3:6:0.015:0:4 -10 42597171 . A G 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.58091;SOR=Inf;LSEQ=GAACGGAATCGAATGGAATC;RSEQ=TCATCAGATGGAAACGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:17,37:0:2,0:25.2:1:31:1:1:0:40.6:108:1:0:2.7 0/1:199:4:2,2:63,132:0.0201:2,2:31.3:1:30.3:1:0.59797:2.09:43.5:8:0.0204:0:4.8 -10 42597173 . C G 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.04301;SOR=0;LSEQ=ACGGAATCGAATGGAATCAT;RSEQ=ATCAGATGGAAACGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:15,34:0.0392:2,2:28.5:1:32.5:1:0.53333:2.23:40.5:4:0.0392:0:3 0/0:193:0:0,0:64,129:0:2,0:22.4:1:31.6:1:1:0:38.1:95.5:1:0:3.2 -10 42597174 . A T 46 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.78694;LSEQ=CGGAATCGAATGGAATCATC;RSEQ=TCAGATGGAAACGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:0,1:16,33:0.02:2,0:36:0:31:0:1:0:41:2:0.02:0:6 0/1:190:3:1,2:62,125:0.0158:2,2:14.3:1:29.3:1:1:1.01:36.7:6:0.0163:0:5 -10 42597176 . CA TG 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GAATCGAATGGAATCATCAT;RSEQ=GATGGAAACGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:16,33:0:2,0:22.7:1:29.9:1:1:0:41:23.5:1:0:2.8 0/1:182:2:0,2:58,119:0.011:2,0:37:1:31.8:1:1:0:41:4:0.0112:0:5 -10 42597177 . A G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63292;SOR=0.71891;LSEQ=AATCGAATGGAATCATCATC;RSEQ=GATGGAAACGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:43:13,30:3,2:0.8958:2,2:22.4:1:30.9:1:0.31638:3.36278:39.7:86:0.8958:0:2.8 1/1:165:142:42,100:7,7:0.8606:2,2:22.3:1:29.7:1:0.13623:2.36631:37.4:46.333:0.8797:0:3.3 -10 42597180 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05254;SOR=0;LSEQ=CGAATGGAATCATCATCAGA;RSEQ=GGAAACGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:14,30:0.0435:2,2:19.5:1:29.5:1:1:2.10:21:4:0.0444:0:2 0/0:153:0:0,0:43,109:0:2,0:21.4:1:30:1:1:0:38.3:75:0.9934:0:3.3 -10 42597186 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00056;SOR=3.84125;LSEQ=GAATCATCATCAGATGGAAA;RSEQ=GAATGGAATCATCATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:3,7:8,21:0.25:2,2:21.4:1:28.4:1:1:1.12:40.5:9:0.2308:0:3.6 1/0:126:71:19,52:15,39:0.5635:2,2:21.4:1:29.9:1:1:1.05217:38.3:70:0.56:0:4 -10 42597190 . T A 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33474;SOR=Inf;LSEQ=CATCATCAGATGGAAACGAA;RSEQ=GGAATCATCATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:10,27:0:2,0:13.6:1:30.1:1:1:0:40.6:36:1:0:3 0/1:114:5:2,3:27,82:0.0439:2,2:11:1:28:1:0.60002:2.01:29.6:4:0.0354:0:4.8 -10 42597194 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAGATGGAAACGAATGGA;RSEQ=TCATCATTGAATGGAATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:8,25:0:2,0:10.9:1:31:1:1:0:39.2:66:1:0:3 0/1:100:2:0,2:22,76:0.02:2,0:20:1:33:0:1:0:27:4:0.0202:0:6 -10 42597195 . T A 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.57356;SOR=Inf;LSEQ=TCAGATGGAAACGAATGGAA;RSEQ=CATCATTGAATGGAATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:8,23:0:2,0:10.5:1:30.2:1:1:0:38.4:30:1:0:3 0/1:94:3:0,3:20,71:0.0319:2,0:12:1:31:1:1:0:56.7:6:0.0323:0:5 -10 42597200 . ATTG A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAACGAATGGAATCATC;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:4,17:0:2,0:6.9:1:30.8:1:1:0:37.7:42:0.9545:0:3 0/1:76:2:0,2:15,59:0.0263:2,0:22:1:32:0:1:0:34:4:0.0263:0:4.5 -10 42597202 . T C 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09175;SOR=4.49421;LSEQ=GAAACGAATGGAATCATCAT;RSEQ=GAATGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:15:2,13:0,0:0.8333:0,2:7.6:1:30.1:1:1:0:39:30:0.8824:0:3.1 1/1:72:69:13,56:0,0:0.9583:0,2:11:1:30:1:1:0:35.1:138:0.9857:0:3.6 -10 42597211 . T A 49 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATCATCATTGAATGGAA;RSEQ=CGAATGGAATCATCAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:5.3:1:31.5:1:1:0:40.7:12:1:0:3.3 0/1:34:3:1,2:4,27:0.0882:2,2:6:1:31:1:0.38937:3.21:36.3:6:0.0882:0:3.7 -10 42597212 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCATCATTGAATGGAAT;RSEQ=GAATGGAATCATCAAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:4.3:1:27.3:1:1:0:40.7:5:1:0:3.3 0/1:30:2:0,2:4,24:0.0667:2,0:13:1:31.5:1:1:0:33:4:0.0667:0:6 -10 42597214 . A C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCATTGAATGGAATCG;RSEQ=ATGGAATCATCAAACGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:3:1:30.2:1:1:0:43.4:10:1:0:3.4 0/1:28:2:0,2:4,21:0.0714:2,0:11:1:33:0:1:0:33:4:0.0741:0:6 -10 42597217 . GGAATCATCAAACGGAAACAGATGGAATCATCATCAAATGGAATCGAGTA G 119 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATTGAATGGAATCGAAT;RSEQ=GAATTATGGAATGCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:39:15:1,14:2,22:0.3846:2,1:60:1:30.5:1:1:1.26509:30.3:30:0.3846:0.3846:3.5 -10 42597490 . A G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTCATCATCAAATGGAATC;RSEQ=AATGGAATCATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:26:0:32:0:1:0:22:2:0.5:0:7 1/1:2:2:2,0:0,0:1:0,0:5:1:28.5:1:1:0:26.5:4:1:0:3 -10 42597496 . A T 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=CATCAAATGGAATCAAATGG;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:5.5:1:29.5:1:1:0:31:4:0.6667:0:2 1/1:5:4:4,0:1,0:0.8:0,0:7.3:1:29.3:1:1:0:25.8:8:0.8:0:3 -10 42597533 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=GAATGGAATCATCATCAGAT;RSEQ=GAAATGAATGGAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:25.7:1:32.1:1:1:0:31.6:18:1:0:3 0/1:10:2:1,1:8,0:0.2:0,2:22:1:28:0:0.2:0:25:4:0.2:0:4.5 -10 42597541 . A T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=TCATCATCAGATGGAAATGA;RSEQ=TGGAATCATCATAGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:0:2,0:28.8:1:30.2:1:1:0:32.1:20:1:0:3 0/1:11:2:1,1:9,0:0.1818:0,2:29:1:30.5:1:0.18182:0:25:4:0.1818:0:4.5 -10 42597548 . C A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22;SOR=0;LSEQ=CAGATGGAAATGAATGGAAT;RSEQ=ATCATAGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,3:0.1667:2,2:26:1:27.5:1:1:2.16028:40:4:0.1667:0:5 0/0:13:0:0,0:10,3:0:2,0:31.8:1:29.8:1:1:0:29.1:26:1:0:3.7 -10 42597549 . A G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03021;SOR=12.55734;LSEQ=AGATGGAAATGAATGGAATC;RSEQ=TCATAGAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:4,2:3,2:0.4615:2,2:26.2:1:30:1:1:1.30:24:12:0.4615:0:3 1/1:13:12:9,3:1,0:0.9231:0,2:31:1:28.9:1:1:0:28.2:24:0.9231:0:3.8 -10 42597566 . A C 40 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36441;SOR=0.38814;LSEQ=ATCATCATAGAATGGAATCG;RSEQ=ATGGATTCATTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:5,4:0.25:2,2:40.3:1:25.7:1:1:1.54:37.3:2:0.1818:0:3.3 0/1:18:2:1,1:10,6:0.1111:2,2:21:1:29.5:1:1:1.61828:40:4:0.1111:0:2.5 -10 42597570 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14194;SOR=0;LSEQ=TCATAGAATGGAATCGAATG;RSEQ=ATTCATTGAATGGAATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:0.1667:2,2:27.5:1:28.5:1:1:1.4491:40:4:0.1818:0:5 0/0:19:0:0,0:11,8:0:2,0:23.2:1:29.4:1:1:0:29.5:38:1:0:3.7 -10 42597578 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=0;LSEQ=TGGAATCGAATGGATTCATT;RSEQ=AATGGAATCAGATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:0.1538:2,2:27.5:1:28:1:1:1.18321:40:4:0.1818:0:5 0/0:19:0:0,0:11,8:0:2,0:24.5:1:30.5:1:1:0:29.5:38:1:0:3.7 -10 42597599 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16304;SOR=0;LSEQ=AATGGAATCAGATGGAATCA;RSEQ=CCAATGGACTTGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:24:1:30.5:1:1:1.58:40:4:0.2:0:5 0/0:14:0:0,0:6,8:0:2,0:31.2:1:28.6:1:1:0:29.9:28:1:0:4 -10 42597601 . C G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.60902;SOR=2.61967;LSEQ=TGGAATCAGATGGAATCATC;RSEQ=AATGGACTTGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:2,4:0,1:0.6667:0,2:32.3:1:30.5:1:1:0:25.8:12:0.6667:0:3.2 1/1:13:11:4,7:0,0:0.8462:0,2:32.2:1:30.6:1:1:0:30.5:22:0.8462:0:4.3 -10 42597610 . T G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.64241;SOR=2.05177;LSEQ=ATGGAATCATCCAATGGACT;RSEQ=GAATGGAATCATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:1,4:2,2:0.5556:2,2:25.2:1:31.8:1:0.52381:3.38757:26.2:10:0.5556:0:3 1/0:11:8:2,6:1,1:0.7273:2,2:30.9:1:31.1:1:1:2.64575:28.8:16:0.8:0:4.6 -10 42597630 . ACTCGAATGGAATCATTATTGAATAGAATTCAATGGAATCATTGAATGGT A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAATGGAATCATTGAATGG;RSEQ=CTCGAATGGAATCATTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:15.6:1:32.8:1:1:0:29.6:10:1:0:3.8 0/1:12:2:1,1:2,7:0.1667:2,2:37:1:27.1:1:0.49091:3.06:25:4:0.1667:0.1667:1.5 -10 42597637 . T A 65 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=AATCATTGAATGGACTCGAA;RSEQ=GGAATCATTATTGAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:16.3:1:25.7:1:1:0:28.7:2:1:0:4.3 1/0:8:4:0,4:1,2:0.5:2,0:17:1:32.8:1:0.42857:0:29.8:8:0.5714:0:4.8 -10 42597640 . A G 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CATTGAATGGACTCGAATGG;RSEQ=ATCATTATTGAATAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:13.3:1:29.7:1:1:0:28.7:6:1:0:4.3 0/1:8:3:0,3:1,3:0.375:2,0:8.7:1:29.3:1:1:0:26.3:6:0.4286:0:5 -10 42597724 . C A 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATGGAATCACCGA;RSEQ=TAGAATCGAATGGAACAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:31:1:31.8:1:1:0:24:8:1:0:3.3 1/1:3:3:0,3:0,0:1:0,0:42.3:1:29.3:1:1:0:25.7:6:1:0:3 -10 42597768 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=GAATGGACTCAAATGGAATT;RSEQ=TCCTCAAATGGAATCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:10.5:1:28.5:1:1:1.41418:25:4:0.2857:0:3 0/0:7:0:0,0:2,5:0:2,0:7.4:1:28.4:1:1:0:35.9:14:1:0:2.7 -10 42597774 . A C 34 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53676;SOR=3.32592;LSEQ=ACTCAAATGGAATTATCCTC;RSEQ=AATGGAATCAAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:3,5:0.1:2,0:6:0:27:0:1:0:46:2:0.1:0:3 0/1:7:2:0,2:2,3:0.2857:2,0:9:1:34:0:1:0:45:4:0.2857:0:3 -10 42597784 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.15854;LSEQ=AATTATCCTCAAATGGAATC;RSEQ=AATGGAATTATCGAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:3,5:1,2:0.6667:2,2:21.4:1:30.8:1:1:1.18:37:16:0.7273:0:3.6 1/0:10:7:2,5:1,1:0.7:2,2:17:1:29.7:1:1:2.23609:36.7:14:0.7:0:3.1 -10 42597787 . T C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16774;SOR=0;LSEQ=TATCCTCAAATGGAATCAAA;RSEQ=GGAATTATCGAATGCAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:0.1538:2,2:26.5:1:29.5:1:1:2.45:37:4:0.1538:0:6.5 0/0:18:0:0,0:5,13:0:2,0:11.9:1:27.9:1:1:0:41.4:36:1:0:3.2 -10 42597791 . A T 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00508;SOR=Inf;LSEQ=CTCAAATGGAATCAAATGGA;RSEQ=TTATCGAATGCAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:0:2,0:20:1:31.2:1:1:0:38.4:28:1:0:3.4 0/1:21:9:3,6:2,10:0.4286:2,2:11.2:1:29:1:0.61079:2.39:43.9:18:0.4286:0:3.6 -10 42597807 . G A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53153;SOR=Inf;LSEQ=TGGAATTATCGAATGCAATC;RSEQ=AATGGAATTATCGAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:0:2,0:29.9:1:30.9:1:1:0:39.7:26:1:0:3.5 0/1:24:2:1,1:4,17:0.0833:2,2:22:0:28.5:1:0.39526:3.91:47.5:4:0.0833:0:4.5 -10 42597808 . A C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53822;SOR=Inf;LSEQ=GGAATTATCGAATGCAATCG;RSEQ=ATGGAATTATCGAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:0:2,0:30.5:1:30.4:1:1:0:39.7:26:1:0:3.5 0/1:24:3:2,1:3,17:0.125:2,2:23.7:1:32.7:1:0.10728:9.66:32.7:6:0.1304:0:2.3 -10 42597816 . T A 59 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0084;SOR=0;LSEQ=CGAATGCAATCGAATGGAAT;RSEQ=ATCGAATGCAATCGAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:2,2:1,7:0.3333:2,2:32:1:29.8:1:0.23636:5.73:40.3:8:0.3333:0:5.8 0/0:24:0:0,0:5,19:0:2,0:32.9:1:28.6:1:1:0:41.5:48:1:0:2.9 -10 42597829 . C G 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03081;SOR=0;LSEQ=ATGGAATTATCGAATGCAAT;RSEQ=GAATAGAATCATCGAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:2,7:0.25:2,2:33.7:1:31.7:1:1:1.66:44.3:6:0.25:0:5.3 0/0:24:0:0,0:5,18:0:2,0:36.1:1:31.1:1:1:0:42.4:46:0.9583:0:2.9 -10 42597834 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10476;SOR=0;LSEQ=ATTATCGAATGCAATCGAAT;RSEQ=GAATCATCGAATGGGCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:2,8:0.1667:2,2:27.5:1:32.5:1:0.45455:3.46:37:4:0.1667:0:6.5 0/0:24:0:0,0:5,19:0:2,0:35.6:1:31.4:1:1:0:41.5:48:1:0.0417:2.9 -10 42597849 . G A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30303;SOR=Inf;LSEQ=CGAATAGAATCATCGAATGG;RSEQ=CTCGAATGGAATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:1,8:0,0:0.9:0,2:20.1:1:31.1:1:1:0:41.9:18:1:0:3 1/1:23:23:3,20:0,0:1:0,2:23:1:31:1:1:0:40.9:46:1:0:3 -10 42597852 . C T 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08523;SOR=0;LSEQ=ATAGAATCATCGAATGGGCT;RSEQ=GAATGGAATCATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:0,8:0.2:0,2:19:1:30:1:0.2:0:43.5:4:0.2:0:5 0/0:23:0:0,0:3,20:0:2,0:20.3:1:30.9:1:1:0:40.9:46:1:0:3 -10 42597856 . T A 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08523;SOR=0;LSEQ=AATCATCGAATGGGCTCGAA;RSEQ=GGAATCATCGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:0,8:0.2:0,2:15:1:30:1:0.2:0:43.5:4:0.2:0:5 0/0:23:0:0,0:3,20:0:2,0:16.6:1:30.9:1:1:0:40.9:46:1:0:3 -10 42597871 . G C 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCGAATGGAATCATCGAATG;RSEQ=AATGGAATGGAATAGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,3:0:0,0:8:1:32.3:1:1:0:34:6:0.75:0:4 0/1:13:2:1,1:1,10:0.1538:2,2:12:0:30.5:1:0.29487:7.42:24:4:0.1538:0:4 -10 42597876 . G C 97 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.09091;SOR=Inf;LSEQ=TGGAATCATCGAATGGAATG;RSEQ=AATGGAATAGACAATGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:5:1:32:0:1:0:32.5:4:1:0:2 1/1:10:8:2,6:0,2:0.8:0,2:7.9:1:32.6:1:1:0:38.5:16:0.8:0:3.9 -10 42597883 . ATAGACAATGAATACG TTAATCCATGGACTCGAATTCAATCACCATCGAATTCAATCGAATGGAGTCATTGAATCGACTCA 90 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.18182;SOR=Inf;LSEQ=ATCGAATGGAATGGAATGGA;RSEQ=AATGGAATCATCATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:2:0:31:0:1:0:25:2:1:0:1 1/1:10:9:2,7:0,1:0.9:0,2:14.3:1:28.6:1:1:0:37:18:0.9:0.9:3.7 -10 42597907 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ACAATGAATACGAATGGAAT;RSEQ=ATCATTGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:8:1:29.5:1:1:0:25:4:1:0:2 -10 42597936 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCGAATGGAATCAT;RSEQ=GAGTGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:20:1:32:0:1:0:25:4:1:0:2 -10 42598056 . G T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TCATCAAATGGAATTCAAAG;RSEQ=AATCATCATCAAATGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:36.2:1:31.7:1:1:0:34.8:12:1:0:1.3 0/1:10:2:1,1:8,0:0.2:0,2:18.5:1:30.5:1:0.2:0:32:4:0.2:0:5.5 -10 42598087 . C A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATGGAACCGAATGGAATC;RSEQ=TCATTGAATGGAAATGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:30.5:1:29.8:1:1:0:34.8:12:1:0:1.3 0/1:15:2:2,0:13,0:0.1333:1,0:28:1:31:1:1:0:48:4:0.1333:0:2 -10 42598109 . A G 115 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.40917;LSEQ=CATTGAATGGAAATGAAAGG;RSEQ=GTCATCATCTAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:8.3:1:29:1:1:0:31:6:0.6:0:3 1/0:22:15:11,4:3,4:0.6818:2,2:28:1:29.6:1:0.34262:3.43:30.3:30:0.6818:0:3.2 -10 42598122 . T C 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAAGGAGTCATCATCTAA;RSEQ=GGAATCGCATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:19.3:1:30.8:1:1:0:33.3:8:1:0:2.3 0/1:27:2:1,1:12,13:0.0741:2,2:18:1:28:1:1:1.08:21:4:0.0769:0:5 -10 42598126 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGAGTCATCATCTAATGGA;RSEQ=TCGCATGGAATCATCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:13.5:1:31.2:1:1:0:38.5:12:1:0:2.2 0/1:26:2:1,1:10,14:0.0769:2,2:34:1:31:1:1:1.38:25:4:0.0769:0:4 -10 42598128 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTCATCATCTAATGGAAT;RSEQ=GCATGGAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:14.2:1:31.2:1:1:0:38.5:12:1:0:2.2 0/1:26:2:1,1:10,14:0.0769:2,2:22.5:1:28:1:1:1.38:40:4:0.0769:0:5 -10 42598138 . C A 56 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CTAATGGAATCGCATGGAAT;RSEQ=ATCATCAAATGAAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:21.6:1:33.4:1:1:0:40.2:10:1:0:2.2 0/1:24:4:2,2:7,13:0.1667:2,2:20.3:1:28:1:0.61462:1.81:30.5:8:0.1739:0:5 -10 42598149 . GA TG 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCATGGAATCATCATCAAAT;RSEQ=AATCGAATGGAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:34:1:33.3:1:1:0:40.3:8:1:0:2.8 0/1:23:2:1,1:6,14:0.087:2,2:33.5:1:30.8:1:1:2.24:24:4:0.0909:0:3.5 -10 42598173 . T A 120 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAATGGAATCATCATCAA;RSEQ=TGGAATCTAATGGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:39:1:32.3:1:1:0:40.3:8:1:0:2.8 1/1:17:15:2,13:0,0:0.8824:0,2:27.5:1:30.8:1:1:0:35.1:30:0.8824:0:3 -10 42598197 . C A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=0.42987;LSEQ=AATCTAATGGAATCATTGAA;RSEQ=AGAATTGAATGGAATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:13:0:31:0:1:0:33:2:0.3333:0:3 0/1:12:2:0,2:0,10:0.1667:0,0:9.5:1:31:0:1:0:36.5:4:0.1667:0:3.5 -10 42598214 . T G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACAGAATTGAATGGAATC;RSEQ=TCATCGAATGAATTGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:29:1:1:0:49:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42598324 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATTATCATCGAATGGA;RSEQ=TCGAATCGAATCAACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:18:0:32:0:1:1:49:4:0.5:0:4 -10 42598331 . C G 66 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATCGAATGGACTCGAAT;RSEQ=GAATCAACATCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:20.3:1:33:1:1:0:36.5:8:1:0:4.3 -10 42598351 . TC AA 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGAATCAACATCAAATGGAA;RSEQ=AAACGGAATTATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:12:0:29.5:1:1:0:47:4:1:0:3.5 0/1:6:2:1,1:2,2:0.3333:2,2:28.5:1:31:1:1:1:49:4:0.3333:0:3 -10 42598355 . A G 66 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACATCAAATGGAATCAA;RSEQ=CGGAATTATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:33.5:1:1:0:47:4:1:0:3.5 1/0:6:4:2,2:1,1:0.6667:2,2:31:1:33:1:1:1:36:8:0.6667:0:3.5 -10 42598371 . G A 59 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAACGGAATTATCGAATG;RSEQ=AATCGAAGAGAATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:0:31.5:1:1:0:47:4:1:0:3.5 1/0:6:4:2,2:1,1:0.6667:2,2:32.3:1:29.5:1:1:1:36:8:0.6667:0:3.5 -10 42598389 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TGGAATCGAAGAGAATCATC;RSEQ=AATGGACTCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24.5:1:31:1:1:0:47:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:23.5:1:28.5:1:1:1:24:4:0.5:0:4.5 -10 42598402 . T A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AATCATCGAATGGACTCGAA;RSEQ=GGAATCATCTAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:29.5:1:1:0:47:4:1:0:3.5 0/0:2:0:0,0:1,1:0:2,0:10.5:1:28:1:1:0:24:4:1:0:4.5 -10 42598524 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCGAATGGAATAATC;RSEQ=TTGAACGGAATCGATTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:32.5:1:1:0:29:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42598560 . T A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCATCATCGGATGGA;RSEQ=ACGAATGGAATCATCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30.5:1:1:0:29:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42598562 . C T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCATCGGATGGATA;RSEQ=GAATGGAATCATCATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30.5:1:1:0:29:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42598566 . T A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCATCGGATGGATACGAA;RSEQ=GGAATCATCATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:31:1:1:0:29:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42598570 . A G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGGATGGATACGAATGGA;RSEQ=TCATCATTGAATGGAATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:31.5:1:1:0:29:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42599108 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATCACCGAATAGAATC;RSEQ=AATGGAACAATCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:32:0:1:0:25:2:1:0:4 0/1:5:2:1,1:2,1:0.4:2,2:13.5:1:28:1:1:1.7321:45:4:0.4:0:6.5 -10 42599122 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AGAATCGAATGGAACAATCA;RSEQ=CGAATGGACTCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:48:0:33:0:1:0:25:2:1:0:4 0/1:6:2:1,1:2,2:0.3333:2,2:27.5:1:30.5:1:1:1:45:4:0.3333:0:6.5 -10 42599124 . G A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCGAATGGAACAATCATC;RSEQ=AATGGACTCAAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25.5:1:31:1:1:0:25:4:1:0:2.5 0/1:6:2:1,1:2,2:0.3333:2,2:22.5:1:32:0:1:1:25:4:0.3333:0:2 -10 42599139 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATCGAATGGACTCAAATG;RSEQ=AATTATCCTCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26:1:30:1:1:0:25:4:1:0:2.5 0/1:6:2:1,1:2,2:0.3333:2,2:44.5:1:30:1:1:1:45:4:0.3333:0:6.5 -10 42599150 . A C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCAAATGGAATTATCCTC;RSEQ=AATGGAATCAAATGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26:1:29.5:1:1:0:25:4:1:0:2.5 0/1:6:2:1,1:2,2:0.3333:2,2:26.5:1:31:1:1:1:30:4:0.3333:0:1.5 -10 42599161 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTATCCTCAAATGGAATCA;RSEQ=ATGGAATTATCGAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26:1:29:1:1:0:25:4:1:0:2.5 0/1:6:2:1,1:2,2:0.3333:2,2:26:0:31:1:1:1:45:4:0.3333:0:6.5 -10 42599167 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CTCAAATGGAATCAAATGGA;RSEQ=TTATCGAATGCAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:31:1:1:0:25:4:1:0:2.5 0/1:6:2:1,1:2,2:0.3333:2,2:20:0:32:0:1:1:45:4:0.3333:0:6.5 -10 42599171 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATCAAATGGAATTA;RSEQ=CGAATGCAATCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26:1:28.5:1:1:0:25:4:1:0:2.5 0/1:6:2:1,1:2,2:0.3333:2,2:16:0:33:0:1:1:45:4:0.3333:0:6.5 -10 42599184 . A T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATTATCGAATGCAATCG;RSEQ=ATGGAATTATCGAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:40:0:31:0:1:0:25:2:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:18.5:1:27.5:1:1:1:25:4:0.5:0:2 -10 42599275 . G T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATAATTGAACGGAATT;RSEQ=AATCGAATCGTCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:30:1:1:1:45:4:0.5:0:4 -10 42599318 . G T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAATGCAATCATCGAATG;RSEQ=TCTCGAATGGAATCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:44.5:1:29:1:1:1:45:4:0.5:0:4 -10 42599356 . G A 58 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAATGGAAAGGAATGGA;RSEQ=TCATCGCATAGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:5.3:1:29:1:1:0:48.5:8:1:0:2.8 -10 42599547 . CATTCAATGGACTCGAATGCAATA C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=CGAATGGTATCGAATGGAAT;RSEQ=ATCATTGAACGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:7.1:1:29.3:1:1:0:32.8:8:1:0:4.8 0/1:13:2:1,1:10,1:0.1538:2,2:7:1:28.4:1:0.29487:7.41607:60:4:0.1538:0.1538:1.5 -10 42599550 . TC CG 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69123;LSEQ=ATGGTATCGAATGGAATCAT;RSEQ=AATGGACTCGAATGCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:8,3:2,0:0.7857:0,2:7.8:1:30.9:1:1:0:36.7:22:0.8462:0.2857:3.3 1/0:14:10:10,0:1,1:0.7143:2,0:10.7:1:31.6:1:0.16667:0:37.4:20:0.8333:0:3.7 -10 42599551 . C G 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05217;SOR=0;LSEQ=TGGTATCGAATGGAATCATT;RSEQ=AATGGACTCGAATGCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:0,0:0.3:0,2:7.3:1:32:1:1:0:35:6:1:0:5.7 0/0:15:0:0,0:1,1:0:2,0:3.5:1:30:1:1:0:60:4:0.6667:0:3.5 -10 42599564 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53196;SOR=Inf;LSEQ=AATCATTCAATGGACTCGAA;RSEQ=GCAATAATCATTGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:20,9:0:2,0:13.8:1:31.1:1:1:0:43.7:58:1:0:3.5 0/1:51:2:1,1:34,12:0.0392:2,2:16.5:1:29:1:0.47252:2.76192:60:4:0.0417:0:3.5 -10 42599565 . GC TG 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01735;LSEQ=ATCATTCAATGGACTCGAAT;RSEQ=AATAATCATTGAACGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:1,0:19,10:0.0333:2,0:14:0:32:0:1:0:57:2:0.0333:0:3 0/1:59:2:1,1:38,17:0.0339:2,2:13.5:1:29:1:0.53571:2.20075:53:4:0.0357:0:3 -10 42599566 . C G 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48574;SOR=0.46036;LSEQ=TCATTCAATGGACTCGAATG;RSEQ=AATAATCATTGAACGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:29:19,10:0,0:0.9355:0,2:15.2:1:31:1:1:0:43.8:28:0.9655:0:3.6 1/1:61:53:36,17:0,0:0.8689:0,2:11.6:1:30.8:1:1:0:45.6:106:0.9298:0:3.6 -10 42599572 . T C 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21856;SOR=0.35135;LSEQ=AATGGACTCGAATGCAATAA;RSEQ=CATTGAACGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:4:2,2:26,13:0.093:2,2:12:1:32.3:1:0.60182:1.96586:48.8:8:0.0952:0:3.5 0/1:87:3:2,1:55,29:0.0345:2,2:23:1:30.7:1:1:1.05:48.7:6:0.0353:0:3.7 -10 42599576 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACTCGAATGCAATAATCAT;RSEQ=GAACGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:30,18:0:2,0:18.4:1:30.6:1:1:0:46.8:47:1:0:3.5 0/1:103:2:2,0:67,34:0.0194:2,0:24:1:30:0:1:0:56:4:0.0196:0:4.5 -10 42599577 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10264;SOR=0;LSEQ=ACTCGAATGCAATAATCATT;RSEQ=AACGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:29,19:0.04:2,2:13.5:1:30.5:1:1:1.51306:60:4:0.0408:0:4.5 0/0:105:0:0,0:71,34:0:2,0:15.8:1:31:1:1:0:49.6:104:1:0:3.2 -10 42599579 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGAATGCAATAATCATTGA;RSEQ=CGGAATCGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:31,21:0:2,0:19.9:1:30.4:1:1:0:46.9:104:0.9811:0:3.4 0/1:109:2:1,1:73,34:0.0183:2,2:15.5:1:30.5:1:0.54111:2.13066:45:4:0.0183:0:3.5 -10 42599580 . CGGAATCGAATGGAATCATCATCAGAT C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.33693;SOR=0.32978;LSEQ=CGAATGCAATAATCATTGAA;RSEQ=GGAAACGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:3:2,1:32,21:0.0508:2,2:14:1:30.8:1:1:1.31:31:6:0.0526:0.0508:3 0/1:116:2:1,1:78,35:0.0172:2,2:8:1:27.5:1:0.52998:2.21148:28:4:0.0175:0.0172:4 -10 42599581 . G A 48 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03703;SOR=0;LSEQ=GAATGCAATAATCATTGAAC;RSEQ=GAATCGAATGGAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:3:2,1:32,21:0.0508:2,2:22.7:1:30.7:1:1:1.31:49.3:6:0.0526:0:4.3 0/0:116:0:0,0:78,35:0:2,0:18.6:1:29.5:1:1:0:49.5:55.5:0.9737:0:3.2 -10 42599587 . G A 45 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03276;SOR=0;LSEQ=AATAATCATTGAACGGAATC;RSEQ=AATGGAATCATCATCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:2,1:38,21:0.0462:2,2:16.7:1:28.7:1:1:1.10:43:6:0.05:0:4.3 0/0:136:0:0,0:85,47:0:2,0:21.3:1:30:1:1:0:49.2:131:0.985:0:3.3 -10 42599589 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAATCATTGAACGGAATCGA;RSEQ=TGGAATCATCATCAGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:43,23:0:2,0:24.6:1:30.7:1:1:0:46.9:65:1:0:3.5 0/1:140:2:1,1:86,48:0.0143:2,2:28:1:31.5:1:1:1.78348:60:4:0.0147:0:3.5 -10 42599590 . T A 48 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.50797;LSEQ=AATCATTGAACGGAATCGAA;RSEQ=GGAATCATCATCAGATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:0,1:45,23:0.0139:2,0:17:0:16:0:0.34783:0:24:0:0:0:7 0/1:144:3:2,1:89,48:0.0208:2,2:15.3:1:30.3:1:1:1.08:55.7:6:0.0216:0:4 -10 42599592 . G C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10718;SOR=0;LSEQ=TCATTGAACGGAATCGAATG;RSEQ=AATCATCATCAGATGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:42,26:0.027:2,0:16.5:1:32.5:1:0.52629:0:60:4:0.0286:0:4 0/0:151:0:0,0:96,52:0:2,0:23.4:1:30.9:1:1:0:49:296:1:0:3.3 -10 42599596 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.55191;SOR=Inf;LSEQ=TGAACGGAATCGAATGGAAT;RSEQ=ATCATCAGATGGAAACGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:49,30:0:2,0:26.2:1:32:1:1:0:47.6:78:1:0:3.6 0/1:162:2:1,1:101,56:0.0123:2,2:15.5:1:29.5:1:1:1.79641:48.5:4:0.0127:0:2.5 -10 42599597 . A G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.55294;SOR=Inf;LSEQ=GAACGGAATCGAATGGAATC;RSEQ=TCATCAGATGGAAACGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:49,30:0:2,0:27:1:30.7:1:1:0:47.6:38.5:1:0:3.6 0/1:168:3:2,1:104,58:0.0179:2,2:24.3:1:29.7:1:1:1.11:57.3:6:0.0185:0:3.3 -10 42599600 . A T 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.81048;SOR=1.18055;LSEQ=CGGAATCGAATGGAATCATC;RSEQ=TCAGATGGAAACGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:6:4,2:48,30:0.069:2,2:21.3:1:29.3:1:1:1.25:34.8:5:0.061:0:5.8 0/1:174:14:8,6:99,58:0.0805:2,2:32.4:1:30.3:1:0.77475:1.27826:44.1:28:0.0833:0:5.1 -10 42599602 . CA TG 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.33788;SOR=0.32917;LSEQ=GAATCGAATGGAATCATCAT;RSEQ=GATGGAAACGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:2,1:51,33:0.0333:2,2:32:1:31.3:1:1:1.29:52:6:0.0353:0:2 0/1:179:2:1,1:108,65:0.0112:2,2:19.5:1:28.5:1:1:1.65645:55:4:0.0116:0:2 -10 42599603 . A G 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0132;SOR=2.94464;LSEQ=AATCGAATGGAATCATCATC;RSEQ=GATGGAAACGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:94:80:50,30:4,4:0.8511:2,2:27.2:1:30.4:1:0.70558:1.66:47.4:39:0.9176:0:3.7 1/1:179:169:105,64:3,1:0.9441:2,2:28.8:1:29.6:1:1:1.82277:48.9:83.5:0.9766:0:3.3 -10 42599604 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54185;SOR=Inf;LSEQ=ATCGAATGGAATCATCATCA;RSEQ=ATGGAAACGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:58,37:0:2,0:26.8:1:31.3:1:1:0:48:46.5:1:0:3.5 0/1:180:2:2,0:109,66:0.0111:2,0:11.5:1:31.5:1:0.52966:0:43:4:0.0114:0:5 -10 42599606 . T C 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55472;SOR=Inf;LSEQ=CGAATGGAATCATCATCAGA;RSEQ=GGAAACGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:63,39:0:2,0:26.1:1:30.6:1:1:0:48:50:1:0:3.5 0/1:191:3:1,2:113,69:0.0157:2,2:19.7:1:28.7:1:0.55952:3.25381:44:6:0.0167:0:5 -10 42599611 . A T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03404;LSEQ=GGAATCATCATCAGATGGAA;RSEQ=CGAATGGAATCATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:4:3,1:64,42:0.0364:2,2:5.5:1:31.8:1:1:1.96:33.8:8:0.0367:0:3.3 0/1:213:8:5,3:118,80:0.0376:2,2:14.1:1:28:1:1:1.13:43.6:16:0.0383:0:4.5 -10 42599612 . C T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82189;SOR=1.1821;LSEQ=GAATCATCATCAGATGGAAA;RSEQ=GAATGGAATCATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:7:3,4:65,39:0.0631:2,2:35.3:1:31.1:1:0.42694:2.20559:41.6:14:0.0636:0:4.6 0/1:217:16:11,5:116,81:0.0737:2,2:26.8:1:30.2:1:0.59806:1.53:49.3:32:0.0751:0:5.1 -10 42599616 . TG AA 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10729;SOR=0;LSEQ=CATCATCAGATGGAAACGAA;RSEQ=GAATCATCATCGAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:69,42:0.0175:2,2:43:0:31.3:1:1:1.6353:60:4:0.0179:0:4.5 0/0:233:0:0,0:135,96:0:2,0:27.9:1:29.7:1:1:0:48.5:76:1:0:3.5 -10 42599622 . C A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00375;SOR=0;LSEQ=CAGATGGAAACGAATGGAAT;RSEQ=ATCATCGAATGGAAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:5:2,3:72,46:0.04:2,2:32.6:1:30.6:1:0.38625:2.33106:45.8:10:0.0403:0:3.8 0/0:253:0:0,0:144,106:0:2,0:27.6:1:31:1:1:0:48.1:49:0.9959:0:3.6 -10 42599623 . A G 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.43919;LSEQ=AGATGGAAACGAATGGAATC;RSEQ=TCATCGAATGGAAATGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:72,47:0.0163:2,2:17:0:32:1:1:1.52632:34:4:0.0164:0:3.5 0/1:258:6:3,3:142,104:0.0233:2,2:33.2:1:31.3:1:0.70093:1.36365:50:12:0.0238:0:4.2 -10 42599627 . T C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.62647;SOR=1.41061;LSEQ=GGAAACGAATGGAATCATCA;RSEQ=CGAATGGAAATGAAAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:5:4,1:71,49:0.04:2,2:27.2:1:31.2:1:0.6473:2.74:51.2:10:0.0427:0:4.6 0/1:270:15:9,6:142,109:0.0556:2,2:28.6:1:30.8:1:1:1.15:50.5:30:0.057:0:3.3 -10 42599628 . C G 56 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07927;SOR=0.22255;LSEQ=GAAACGAATGGAATCATCAT;RSEQ=GAATGGAAATGAAAGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:4:2,2:71,48:0.032:2,2:30.8:1:28.3:1:1:1.47432:37.5:3:0.0242:0:4.8 0/0:275:2:1,1:152,117:0.0073:2,2:25.5:1:30.5:1:1:1.29787:43:4:0.0075:0:6.5 -10 42599629 . G C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09927;SOR=0;LSEQ=AAACGAATGGAATCATCATC;RSEQ=AATGGAAATGAAAGGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:73,52:0.0157:2,0:47.5:1:32:1:0.51256:0:48:4:0.0163:0:5 0/0:275:0:0,0:153,119:0:2,0:26.6:1:30.1:1:1:0:47.1:89.667:0.9963:0:3.7 -10 42599630 . A G 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.482;SOR=0.73919;LSEQ=AACGAATGGAATCATCATCG;RSEQ=ATGGAAATGAAAGGAGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:8:5,3:70,50:0.0625:2,2:23.8:1:32.3:1:1:1.19:37:16:0.0645:0:4.5 0/1:277:13:8,5:145,115:0.0469:2,2:16.5:1:31.4:1:0.77984:1.27:35.5:26:0.0483:0:4.7 -10 42599635 . A G 48 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.03168;SOR=0;LSEQ=ATGGAATCATCATCGAATGG;RSEQ=AATGAAAGGAGTCATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:1,2:77,52:0.0227:2,2:25.3:1:30.7:1:0.56718:2.93706:29.7:6:0.0238:0:5.3 0/0:283:0:0,0:153,130:0:2,0:24:0:14:0:1:0:44:0:0:0:6 -10 42599641 . A G 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52934;SOR=0.63347;LSEQ=TCATCATCGAATGGAAATGA;RSEQ=AGGAGTCATCATCTAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:3,2:73,52:0.0379:2,2:22.6:1:31.2:1:1:1.07:36.2:10:0.0391:0:5 0/1:288:7:4,3:151,130:0.0243:2,2:12.7:1:30.1:1:1:1.15:39.9:14:0.0246:0:5.9 -10 42599643 . G C 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33169;SOR=Inf;LSEQ=ATCATCGAATGGAAATGAAA;RSEQ=GAGTCATCATCTAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:76,56:0:2,0:26.6:1:31.4:1:1:0:46.3:65:0.9924:0:3.9 0/1:288:5:4,1:147,134:0.0174:2,2:34.2:1:26.6:1:0.37455:3.63:47.8:4:0.0141:0:7.4 -10 42599644 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10127;SOR=0;LSEQ=TCATCGAATGGAAATGAAAG;RSEQ=AGTCATCATCTAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:76,55:0.0149:2,2:27:1:30:1:1:1.37839:49:4:0.0153:0:5.5 0/0:286:0:0,0:147,132:0:2,0:26.5:1:30.7:1:1:0:46.4:68.75:0.9752:0:3.9 -10 42599645 . A G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74817;SOR=0.8067;LSEQ=CATCGAATGGAAATGAAAGG;RSEQ=GTCATCATCTAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:4:2,2:75,54:0.0301:2,2:17:1:29.3:1:1:1.38538:50:8:0.0308:0:5 0/1:287:7:4,3:145,131:0.0244:2,2:20.1:1:32.3:1:1:1.20:45:14:0.025:0:4.3 -10 42599646 . G A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18469;SOR=0.50311;LSEQ=ATCGAATGGAAATGAAAGGA;RSEQ=TCATCATCTAATGGAATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:8:5,3:71,53:0.0602:2,2:29.5:1:30.1:1:1:1.24:48.1:16:0.0615:0:5.3 0/1:289:9:5,4:140,131:0.0311:2,2:28:1:29.1:1:1:1.17:42.1:18:0.0317:0:5.4 -10 42599647 . T C 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59125;SOR=0.44731;LSEQ=TCGAATGGAAATGAAAGGAG;RSEQ=CATCATCTAATGGAATCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:72,54:0.0153:2,2:23:1:31.5:1:1:1.33029:53.5:4:0.0155:0:3.5 0/0:291:2:1,1:145,134:0.0069:2,2:1:0:29:1:1:1.08177:45.5:4:0.007:0:5 -10 42599653 . T A 55 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.30917;SOR=Inf;LSEQ=GGAAATGAAAGGAGTCATCA;RSEQ=CTAATGGAATCGCATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:67,59:0:2,0:27.2:1:30.3:1:1:0:46:125:1:0:4 0/1:263:4:4,0:133,125:0.0152:2,0:23.8:1:27.5:1:0.12371:0:41.5:8:0.0155:0:4.5 -10 42599654 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10709;SOR=0;LSEQ=GAAATGAAAGGAGTCATCAT;RSEQ=TAATGGAATCGCATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:65,58:0.0159:2,2:12:1:32:1:1:1.11967:50:4:0.0161:0:2.5 0/0:258:0:0,0:134,124:0:2,0:28.4:1:31.4:1:1:0:45.7:516:1:0:4 -10 42599655 . T G 68 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66964;SOR=2.32135;LSEQ=AAATGAAAGGAGTCATCATC;RSEQ=AATGGAATCGCATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:1:1,0:62,57:0.0083:2,0:44:0:30:0:1:0:40:2:0.0084:0:8 0/1:263:5:3,2:134,123:0.019:2,2:30.8:1:29.6:1:1:1.38:40.6:10:0.0192:0:7 -10 42599658 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09891;SOR=0;LSEQ=TGAAAGGAGTCATCATCTAA;RSEQ=GGAATCGCATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:63,58:0.0163:2,2:45.5:1:30.5:1:1:1.08546:53.5:4:0.0165:0:4.5 0/0:267:0:0,0:137,128:0:2,0:28:1:29.7:1:1:0:45.3:87.333:0.9962:0:4.1 -10 42599659 . G A 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5546;SOR=Inf;LSEQ=GAAAGGAGTCATCATCTAAT;RSEQ=GAATCGCATGGAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:66,57:0:2,0:26.1:1:31.3:1:1:0:44.6:122:1:0:4.2 0/1:265:3:1,2:135,127:0.0113:2,2:15:1:29.3:1:0.61383:2.12013:49.3:6:0.0115:0:4.3 -10 42599660 . G C 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55488;SOR=Inf;LSEQ=AAAGGAGTCATCATCTAATG;RSEQ=AATCGCATGGAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:64,56:0:2,0:26.4:1:30.7:1:1:0:44.5:39:0.9915:0:4.2 0/1:264:3:2,1:132,127:0.0114:2,2:22.7:1:30.3:1:1:1.92:51.3:6:0.0115:0:5.3 -10 42599663 . TC CT 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.41612;LSEQ=GGAGTCATCATCTAATGGAA;RSEQ=GCATGGAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:1:0,1:63,55:0.0083:2,0:35:0:33:0:0.47059:0:49:2:0.0085:0:4 0/1:257:3:2,1:127,127:0.0117:2,2:19:1:30.3:1:1:1.99:48.7:6:0.0117:0:3.3 -10 42599664 . C T 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35558;SOR=0.66438;LSEQ=GAGTCATCATCTAATGGAAT;RSEQ=GCATGGAATCATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:117:108:58,50:3,5:0.9231:2,2:25.7:1:29.4:1:0.47417:1.92:44.9:26:0.9286:0:4.3 1/1:251:223:109,114:13,10:0.8884:2,2:27.9:1:29.8:1:0.51841:1.35793:44.7:446:0.8992:0:4.4 -10 42599668 . T A 62 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09006;SOR=0.23511;LSEQ=CATCATCTAATGGAATCGCA;RSEQ=GGAATCATCATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:4:2,2:60,49:0.0351:2,2:38.8:1:31.3:1:1:1.22228:49.3:8:0.0357:0:5.8 0/0:237:2:1,1:118,117:0.0084:2,2:40:1:31:1:1:1.00851:47:4:0.0085:0:4.5 -10 42599671 . A C 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55378;SOR=Inf;LSEQ=CATCTAATGGAATCGCATGG;RSEQ=ATCATCATCAAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:60,49:0:2,0:25.5:1:29.8:1:1:0:42.8:53.5:1:0:4.4 0/1:227:3:2,1:109,115:0.0132:2,2:31:1:30.3:1:0.61516:2.10:36.3:6:0.0133:0:4.7 -10 42599674 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.11315;SOR=0;LSEQ=CTAATGGAATCGCATGGAAT;RSEQ=ATCATCAAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:60,49:0.018:2,2:6.5:1:28:1:1:1.22224:49:4:0.0182:0:3.5 0/0:218:0:0,0:103,115:0:2,0:28.2:1:31.3:1:1:0:43.2:436:1:0:4.4 -10 42599675 . A T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11179;SOR=0;LSEQ=TAATGGAATCGCATGGAATC;RSEQ=TCATCAAATGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:59,48:0.0183:2,2:17.5:1:32:1:1:1.22682:59.5:4:0.0185:0:5 0/0:216:0:0,0:101,115:0:2,0:28:1:29.9:1:1:0:43:432:1:0:4.4 -10 42599677 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0.10973;SOR=0;LSEQ=ATGGAATCGCATGGAATCAT;RSEQ=ATCAAATGGAATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:59,46:0.0187:2,2:33:1:29.5:1:1:1.27959:48:4:0.0189:0:4.5 0/0:215:0:0,0:99,116:0:2,0:27.2:1:31.3:1:1:0:42.8:214:1:0:4.5 -10 42599680 . C A 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31925;SOR=1.3252;LSEQ=GAATCGCATGGAATCATCAT;RSEQ=AAATGGAATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:107:80:44,36:15,12:0.7477:2,2:23.4:1:29.1:1:1:1.02252:43.3:160:0.7477:0:4.8 1/0:212:169:75,94:18,22:0.7972:2,2:25.6:1:28.8:1:1:1.02534:42:168:0.8:0:4.8 -10 42599686 . G C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33885;SOR=0.3313;LSEQ=CATGGAATCATCATCAAATG;RSEQ=AATCGAATGGAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:3:1,2:50,47:0.0297:2,2:22:1:32:1:0.61364:2.11215:42.7:6:0.03:0:6 0/1:200:2:1,1:87,110:0.01:2,2:32:1:32:1:1:1.26:28:4:0.01:0:6 -10 42599688 . A T 74 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01826;SOR=0.09872;LSEQ=TGGAATCATCATCAAATGGA;RSEQ=TCGAATGGAATCATCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:5:3,2:46,48:0.0505:2,2:22.4:1:32.2:1:0.67773:1.56:44.4:10:0.0521:0:5.6 0/0:193:1:1,0:84,107:0.0052:2,0:36:0:31:0:0.44271:0:52:2:0.0052:0:5 -10 42599689 . T A 24 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54726;SOR=Inf;LSEQ=GGAATCATCATCAAATGGAA;RSEQ=CGAATGGAATCATCATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:49,50:0:2,0:22.6:1:29.7:1:1:0:41.6:23.75:1:0:4.6 0/1:189:2:1,1:81,106:0.0106:2,2:16:0:24.5:1:1:1.31:48:4:0.0107:0:4.5 -10 42599690 . C A 48 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04069;SOR=0;LSEQ=GAATCATCATCAAATGGAAT;RSEQ=GAATGGAATCATCATCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:3:1,2:47,47:0.0306:2,2:34:1:30.3:1:1:1.98626:39.3:6:0.0309:0:6.7 0/0:185:0:0,0:78,107:0:2,0:23.5:1:30.2:1:1:0:42.2:370:1:0:4.7 -10 42599691 . G A 81 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10036;SOR=Inf;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATGGAATCATCATCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:47,50:0:2,0:22.4:1:30.3:1:1:0:41.5:96:1:0:4.5 0/1:180:7:4,3:72,99:0.0389:2,2:17.4:1:29:1:0.46219:1.83:45:14:0.0393:0:2.9 -10 42599696 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12529;SOR=0;LSEQ=TCATCAAATGGAATCGAATG;RSEQ=AATCATCATCAGATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:43,47:0.0217:2,2:19:1:29.5:1:1:1.09:45:4:0.022:0:6.5 0/0:167:0:0,0:66,100:0:2,0:22:1:30.6:1:1:0:41.8:82:0.9939:0:4.8 -10 42599702 . T A 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=3;SSF=0.36417;SOR=1.41436;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=CATCAGATGGAATCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:58:28,30:7,8:0.7733:2,2:23.1:1:29.7:1:1:1.07:40.7:57:0.7808:0:5.4 1/1:140:116:41,75:12,10:0.8286:2,2:21.8:1:29.7:1:0.0998:2.182:39.9:232:0.8345:0:5.5 -10 42599704 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.55122;SOR=Inf;LSEQ=TGGAATCGAATGGAATCATC;RSEQ=TCAGATGGAATCTAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:31,38:0:2,0:26.3:1:29.9:1:1:0:37.9:22:1:0:5.1 0/1:136:2:0,2:50,84:0.0147:2,0:26.5:1:33:0:0.53159:0:32.5:4:0.0148:0:7.5 -10 42599706 . C G 66 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.66021;SOR=2.15646;LSEQ=GAATCGAATGGAATCATCAT;RSEQ=AGATGGAATCTAATGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:1:0,1:29,37:0.0149:2,0:24:0:33:0:1:0:40:2:0.0152:0:8 0/1:126:4:0,4:45,77:0.0317:2,0:22:1:33:0:0.29594:0:36.3:8:0.0317:0:7 -10 42599707 . AG GA 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.10347;LSEQ=AATCGAATGGAATCATCATC;RSEQ=ATGGAATCTAATGGAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:1:1,0:28,41:0.0143:2,0:50:0:32:0:0.41429:0:25:2:0.0143:0:4 0/1:127:2:1,1:44,81:0.0157:2,2:19.5:1:29.8:1:1:1.83:36:4:0.0159:0.0079:3 -10 42599708 . G A 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72492;SOR=1.43709;LSEQ=ATCGAATGGAATCATCATCA;RSEQ=ATGGAATCTAATGGAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:65:25,40:1,1:0.942:2,2:25.6:1:29.9:1:1:1.58836:36.8:64:0.9697:0:5.1 1/1:122:117:41,76:0,0:0.959:0,2:20.4:1:29.5:1:1:0:39.5:57.5:0.9664:0:5.3 -10 42599714 . A G 32 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.14701;LSEQ=TGGAATCATCATCAGATGGA;RSEQ=TCTAATGGAAACATTGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:1:0,1:29,37:0.0149:2,0:15:0:33:0:1:0:40:2:0.0152:0:6 0/1:117:2:0,2:42,72:0.0171:2,0:17.5:1:32.5:1:0.53403:0:40:4:0.0171:0:6.5 -10 42599716 . CT GA 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53076;SOR=Inf;LSEQ=GAATCATCATCAGATGGAAT;RSEQ=AATGGAAACATTGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:27,39:0:2,0:25:1:31.3:1:1:0:35.6:32:1:0:4.8 0/1:112:2:1,1:38,70:0.0179:2,2:32:1:30:1:1:1.83:28.5:4:0.018:0:6.5 -10 42599717 . T A 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1717;SOR=1.76729;LSEQ=AATCATCATCAGATGGAATC;RSEQ=AATGGAAACATTGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:49:17,32:8,7:0.7424:2,2:23:1:29.2:1:0.23467:2.12442:36.3:23.5:0.746:0:5.2 1/1:110:92:31,61:5,7:0.8364:2,2:17.8:1:29.7:1:0.7481:1.40082:37.1:184:0.8598:0:5.5 -10 42599720 . T C 49 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.84018;LSEQ=CATCATCAGATGGAATCTAA;RSEQ=GGAAACATTGAACGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:1:1,0:27,37:0.0154:2,0:45:0:33:0:0.43077:0:40:2:0.0154:0:4 0/1:107:3:1,2:36,68:0.028:2,2:20:1:31:1:1:1.05827:33.3:6:0.0283:0:5.7 -10 42599722 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52774;SOR=Inf;LSEQ=TCATCAGATGGAATCTAATG;RSEQ=AAACATTGAACGGAATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:28,36:0:2,0:24.8:1:30.5:1:1:0:34.7:20.333:1:0:4.5 0/1:106:2:1,1:35,68:0.0189:2,2:22.5:1:28.5:1:1:1.93:35:4:0.019:0:5 -10 42599725 . A T 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79504;SOR=1.15355;LSEQ=TCAGATGGAATCTAATGGAA;RSEQ=CATTGAACGGAATTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:64:29,35:2,2:0.9014:2,2:21.7:1:29.6:1:1:1.20354:33.6:20.333:0.8971:0:4.4 1/1:104:95:32,63:5,3:0.9135:2,2:16.9:1:28.9:1:0.13204:3.24061:35.4:190:0.9135:0:5 -10 42599726 . C T 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26481;SOR=Inf;LSEQ=CAGATGGAATCTAATGGAAA;RSEQ=ATTGAACGGAATTGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:35,39:0:2,0:21.2:1:31.3:1:1:0:34.9:36:1:0:4.1 0/1:102:3:2,1:32,66:0.0294:2,2:16.3:1:31:1:0.26145:4.06:50:6:0.0297:0:5.3 -10 42599729 . T G 87 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01876;SOR=Inf;LSEQ=ATGGAATCTAATGGAAACAT;RSEQ=GAACGGAATTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:38,44:0:2,0:19.2:1:29.5:1:1:0:36.2:40:1:0:3.8 0/1:105:7:3,4:33,65:0.0667:2,2:18.9:1:31.1:1:0.68893:1.47:43.9:14:0.0673:0:5.7 -10 42599733 . CG AA 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58161;SOR=0.38367;LSEQ=AATCTAATGGAAACATTGAA;RSEQ=GAATTGAATGGAATCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:40,43:0.0233:2,2:16.5:1:30.3:1:1:1.07:45:4:0.0244:0:2.5 0/0:111:1:0,1:40,68:0.009:2,0:18:0:32.5:0:1:0:40:2:0.009:0:5 -10 42599734 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7828;LSEQ=ATCTAATGGAAACATTGAAC;RSEQ=GAATTGAATGGAATCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:38,45:0.0227:2,2:38.5:1:28.5:1:1:1.18:30:4:0.0233:0:4 0/1:112:2:1,1:42,63:0.0179:2,2:5.5:1:31.5:1:1:1.49:54:4:0.018:0:3 -10 42599736 . A T 26 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19309;SOR=0;LSEQ=CTAATGGAAACATTGAACGG;RSEQ=ATTGAATGGAATCGTCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:42,49:0.0215:2,0:7.5:1:26:1:0.4993:0:45:4:0.0222:0:4 0/0:118:0:0,0:50,68:0:2,0:16.2:1:29.1:1:1:0:37.5:117:1:0:3.7 -10 42599738 . T A 65 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.245;SOR=3.77186;LSEQ=AATGGAAACATTGAACGGAA;RSEQ=TGAATGGAATCGTCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:1,0:43,51:0.0105:2,0:4:0:32:0:0.46316:0:22:2:0.011:0:1 0/1:129:5:3,2:49,74:0.0388:2,2:19.2:1:28.4:1:0.39549:2.25:43.8:10:0.0388:0:5.6 -10 42599740 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51135;SOR=Inf;LSEQ=TGGAAACATTGAACGGAATT;RSEQ=AATGGAATCGTCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:43,51:0:2,0:18.6:1:30.5:1:1:0:37.8:17.8:1:0:3.1 0/1:131:2:2,0:53,75:0.0153:2,0:12:1:30.5:1:0.1771:0:32:4:0.0153:0:2.5 -10 42599741 . A C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6931;SOR=0.6981;LSEQ=GGAAACATTGAACGGAATTG;RSEQ=ATGGAATCGTCATCGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:3:2,1:40,52:0.0316:2,2:12.3:1:31.3:1:0.58187:2.57:45.7:6:0.0326:0:3 0/1:135:3:1,2:57,75:0.0222:2,2:19:1:32:1:1:1.51548:26:6:0.0224:0:3.3 -10 42599744 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16509;SOR=0;LSEQ=AACATTGAACGGAATTGAAT;RSEQ=GAATCGTCATCGAATGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:42,53:0.0206:2,2:9:1:28:1:1:1.26:31:4:0.0208:0:2.5 0/0:141:0:0,0:60,80:0:2,0:17.3:1:30.3:1:1:0:38.6:139:0.9929:0:3.1 -10 42599746 . A T 76 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08383;SOR=Inf;LSEQ=CATTGAACGGAATTGAATGG;RSEQ=ATCGTCATCGAATGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:43,54:0:2,0:20.1:1:29.6:1:1:0:38.2:96:1:0:3 0/1:142:6:3,3:58,78:0.0423:2,2:24.8:1:29.7:1:1:1.34:31.8:12:0.0426:0:4 -10 42599747 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16712;SOR=0;LSEQ=ATTGAACGGAATTGAATGGA;RSEQ=TCGTCATCGAATGAATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:42,54:0.0204:2,2:29:1:32:1:1:1.28:44.5:4:0.0208:0:2.5 0/0:141:0:0,0:59,82:0:2,0:19:1:29.6:1:1:0:38.8:69.5:1:0:3 -10 42599748 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51478;SOR=Inf;LSEQ=TTGAACGGAATTGAATGGAA;RSEQ=CGTCATCGAATGAATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:43,55:0:2,0:20.6:1:29.5:1:1:0:38.2:23.5:1:0:3.1 0/1:142:2:1,1:59,81:0.0141:2,2:14.5:1:28.5:1:1:1.37:48:4:0.0143:0:1.5 -10 42599749 . C A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06559;SOR=0;LSEQ=TGAACGGAATTGAATGGAAT;RSEQ=GTCATCGAATGAATTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:3:1,2:43,53:0.0303:2,2:27:1:25.3:1:1:1.61504:42.7:2:0.0206:0:3.7 0/0:145:0:0,0:58,76:0:2,0:20.2:1:29.8:1:1:0:38.3:32.5:0.922:0:2.9 -10 42599750 . G T 95 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02286;SOR=Inf;LSEQ=GAACGGAATTGAATGGAATC;RSEQ=TCATCGAATGAATTGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:45,53:0:2,0:21.4:1:30:1:1:0:37.8:31.667:0.9896:0:2.9 0/1:146:8:3,5:58,77:0.0548:2,2:27:1:31.8:1:1:1.25345:33.9:16:0.0552:0:4.6 -10 42599752 . C G 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7424;SOR=1.37856;LSEQ=ACGGAATTGAATGGAATCGT;RSEQ=ATCGAATGAATTGAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:3:1,2:46,52:0.0297:2,2:17.3:1:29.7:1:1:1.75966:42.7:6:0.0306:0:2.3 0/1:148:6:3,3:60,80:0.0405:2,2:17.8:1:29.2:1:1:1.33:41.2:5:0.0347:0:1.7 -10 42599755 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15165;SOR=0;LSEQ=GAATTGAATGGAATCGTCAT;RSEQ=GAATGAATTGAATGCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:46,52:0.02:2,2:30.5:1:30.5:1:1:1.13:22:4:0.0202:0:1.5 0/0:156:0:0,0:67,89:0:2,0:22.3:1:29.7:1:1:0:38.4:30.2:1:0:2.8 -10 42599757 . A C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51729;SOR=Inf;LSEQ=ATTGAATGGAATCGTCATCG;RSEQ=ATGAATTGAATGCAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:48,58:0:2,0:23.1:1:29.6:1:1:0:37.5:52:1:0:2.8 0/1:159:2:1,1:70,87:0.0126:2,2:31:1:31:1:1:1.24:31:4:0.0128:0:4 -10 42599758 . A G 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.56557;SOR=0.32951;LSEQ=TTGAATGGAATCGTCATCGA;RSEQ=TGAATTGAATGCAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:47,58:0.0187:2,2:19:1:30.5:1:1:1.23:27:4:0.0189:0:4 0/0:161:1:0,1:72,88:0.0062:2,0:29:0:33:0:1:0:25:2:0.0064:0:7 -10 42599759 . T A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31121;LSEQ=TGAATGGAATCGTCATCGAA;RSEQ=GAATTGAATGCAATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:1:1,0:44,60:0.0094:2,0:30:0:32:0:0.42857:0:36:2:0.0095:0:4 0/1:162:2:1,1:70,90:0.0123:2,2:17.5:1:29:1:1:1.28:48:4:0.0124:0:2.5 -10 42599760 . G A 27 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56165;SOR=0.3135;LSEQ=GAATGGAATCGTCATCGAAT;RSEQ=AATTGAATGCAATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:44,58:0.019:2,2:27:1:27:1:1:1.31:33:4:0.0196:0:4.5 0/0:166:1:0,1:71,93:0.006:2,0:49:0:29:0:1:0:23:2:0.0061:0:3 -10 42599761 . A C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28634;SOR=Inf;LSEQ=AATGGAATCGTCATCGAATG;RSEQ=ATTGAATGCAATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:45,59:0:2,0:25.4:1:29.9:1:1:0:38.3:103:0.9904:0:2.7 0/1:167:3:1,2:69,92:0.018:2,2:25.7:1:33.3:1:1:1.49644:50:6:0.0183:0:1.3 -10 42599762 . AT A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14599;SOR=0;LSEQ=ATGGAATCGTCATCGAATGA;RSEQ=TGAATGCAATCATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:44,58:0.019:2,2:29:0:32.5:1:1:1.31:50:4:0.0196:0:0 0/0:169:0:0,0:72,93:0:2,0:26.2:1:29.6:1:1:0:38.9:40.25:0.9877:0:2.7 -10 42599764 . T C 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23999;LSEQ=GGAATCGTCATCGAATGAAT;RSEQ=GAATGCAATCATCGAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:44,59:0.019:2,2:14:1:25.5:1:1:1.34:41.5:4:0.019:0:3 0/1:170:4:3,1:70,96:0.0235:2,2:29.3:1:29:1:0.31521:4.08:34.3:8:0.0237:0:4 -10 42599767 . A C 141 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.01504;SOR=0.43067;LSEQ=ATCGTCATCGAATGAATTGA;RSEQ=TGCAATCATCGAATGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:23:8,15:34,43:0.2277:2,2:25.4:1:31.3:1:0.47785:1.47682:38.9:46:0.2277:0:3.7 0/1:178:20:9,11:67,90:0.1124:2,2:28.6:1:30.9:1:1:1.10:39.1:19:0.1086:0:2.6 -10 42599769 . G A 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29757;SOR=0.28101;LSEQ=CGTCATCGAATGAATTGAAT;RSEQ=CAATCATCGAATGGTCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:40,59:0.0198:2,2:33.5:1:30:1:1:1.47:39:4:0.02:0:4.5 0/0:178:1:0,1:77,100:0.0056:2,0:37:0:31:0:1:0:49:2:0.0057:0:2 -10 42599771 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52985;SOR=Inf;LSEQ=TCATCGAATGAATTGAATGC;RSEQ=ATCATCGAATGGTCTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:43,66:0:2,0:28.9:1:29.6:1:1:0:38.2:20.8:1:0:2.6 0/1:182:2:1,1:75,105:0.011:2,2:10.5:1:30.5:1:1:1.40:45:4:0.0112:0:4.5 -10 42599772 . A G 33 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55733;SOR=0.29135;LSEQ=CATCGAATGAATTGAATGCA;RSEQ=TCATCGAATGGTCTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:40,65:0.0187:2,2:36.5:1:33:1:1:1.62:39:4:0.0189:0:4.5 0/0:182:1:0,1:77,104:0.0055:2,0:2:0:28:0:1:0:22:2:0.0056:0:4 -10 42599773 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53227;SOR=Inf;LSEQ=ATCGAATGAATTGAATGCAA;RSEQ=CATCGAATGGTCTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:41,67:0:2,0:30:1:29.7:1:1:0:37.9:26:1:0:2.6 0/1:184:2:1,1:76,106:0.0109:2,2:24:1:28.5:1:1:1.39:40:4:0.011:0:2.5 -10 42599774 . C A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16882;LSEQ=TCGAATGAATTGAATGCAAT;RSEQ=ATCGAATGGTCTCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:1:1,0:40,67:0.0093:2,0:48:0:30:0:0.37963:0:28:2:0.0095:0:3 0/1:185:2:0,2:77,104:0.0108:2,0:40.5:1:29.5:1:0.50988:0:34.5:4:0.011:0:2.5 -10 42599776 . T A 97 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.54469;SOR=1.82414;LSEQ=GAATGAATTGAATGCAATCA;RSEQ=CGAATGGTCTCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:1,2:38,64:0.0275:2,2:19:1:29.3:1:1:1.18564:25:6:0.0288:0:5 0/1:183:9:3,6:74,98:0.0492:2,2:30.4:1:30.9:1:0.7349:1.50689:40.3:18:0.0517:0:5.2 -10 42599778 . G C 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10494;SOR=0.22633;LSEQ=ATGAATTGAATGCAATCATC;RSEQ=AATGGTCTCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:5:2,3:37,65:0.0463:2,2:37:1:27.6:1:1:1.17:31:4:0.0385:0:3.2 0/1:185:2:0,2:78,103:0.0108:2,0:39:1:33.5:1:0.5082:0:44:4:0.011:0:4 -10 42599780 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53525;SOR=Inf;LSEQ=GAATTGAATGCAATCATCGA;RSEQ=TGGTCTCGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:40,66:0:2,0:32.1:1:30.1:1:1:0:38:20.2:1:0:2.5 0/1:185:2:1,1:77,106:0.0108:2,2:19:1:28:1:1:1.37:23:4:0.011:0:3.5 -10 42599781 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53525;SOR=Inf;LSEQ=AATTGAATGCAATCATCGAA;RSEQ=GGTCTCGAATGGAATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:40,66:0:2,0:32.1:1:29.5:1:1:0:37.9:16.667:1:0:2.5 0/1:185:2:1,1:77,106:0.0108:2,2:39.5:1:32:1:1:1.37:22.5:4:0.0112:0:4 -10 42599783 . G A 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02879;SOR=Inf;LSEQ=TTGAATGCAATCATCGAATG;RSEQ=TCTCGAATGGAATCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:40,66:0:2,0:32.2:1:31.5:1:1:0:37.9:52:1:0:2.5 0/1:185:9:4,5:74,102:0.0486:2,2:31:1:28.9:1:1:1.10:43.1:18:0.05:0:3.6 -10 42599787 . C T 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.1627;SOR=Inf;LSEQ=ATGCAATCATCGAATGGTCT;RSEQ=GAATGGAATCATCTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:40,65:0:2,0:32.3:1:30.2:1:1:0:38:51.5:1:0:2.5 0/1:184:5:2,3:76,102:0.0272:2,2:35:1:29.6:1:1:1.11694:44:10:0.0279:0:3 -10 42599788 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.55619;SOR=Inf;LSEQ=TGCAATCATCGAATGGTCTC;RSEQ=AATGGAATCATCTTCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:40,64:0:2,0:32:1:30.2:1:1:0:38:19.8:0.99:0:2.5 0/1:183:3:1,2:76,103:0.0164:2,2:39:1:28.3:1:1:1.4727:46:6:0.0171:0:2.7 -10 42599790 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13465;SOR=0;LSEQ=CAATCATCGAATGGTCTCGA;RSEQ=TGGAATCATCTTCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:39,65:0.0189:2,2:22:1:29:1:1:1.66:37:4:0.019:0:4.5 0/0:182:0:0,0:77,102:0:2,0:32.8:1:29.6:1:1:0:38.8:43.75:0.9887:0:2.4 -10 42599791 . T C 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67276;SOR=0.57661;LSEQ=AATCATCGAATGGTCTCGAA;RSEQ=GGAATCATCTTCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:3:2,1:38,64:0.0283:2,2:25:1:18.3:1:0.55617:3.33:33:0.5:0.0097:0:5.3 0/1:182:3:2,1:76,102:0.0165:2,2:36.3:1:30:1:0.57845:2.67:42.3:6:0.0173:0:4.7 -10 42599792 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53205;SOR=Inf;LSEQ=ATCATCGAATGGTCTCGAAT;RSEQ=GAATCATCTTCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:41,66:0:2,0:30.8:1:31.2:1:1:0:37.7:52.5:1:0:2.6 0/1:182:2:1,1:77,103:0.011:2,2:23:0:29.5:1:1:1.34:48:4:0.0114:0:2.5 -10 42599793 . G C 50 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04985;SOR=0;LSEQ=TCATCGAATGGTCTCGAATG;RSEQ=AATCATCTTCAAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:1,2:40,61:0.028:2,2:18.3:1:31.7:1:1:1.30817:38:6:0.0291:0:4.7 0/0:182:0:0,0:77,102:0:2,0:32:1:30.5:1:1:0:39.1:24.571:0.9829:0:2.4 -10 42599795 . A G 34 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13818;SOR=0;LSEQ=ATCGAATGGTCTCGAATGGA;RSEQ=TCATCTTCAAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:41,64:0.0187:2,2:45.5:1:34:0:1:1.55:39:4:0.0189:0:4.5 0/0:180:0:0,0:77,103:0:2,0:31.6:1:29.5:1:1:0:39:35:1:0:2.5 -10 42599796 . T C 113 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.14159;SOR=3.37299;LSEQ=TCGAATGGTCTCGAATGGAA;RSEQ=CATCTTCAAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:41,63:0.0189:2,2:43.5:1:32:1:1:1.53:23.5:4:0.0196:0:6 0/1:180:11:4,7:73,96:0.0611:2,2:30.9:1:32.7:1:0.76037:1.32866:38.5:22:0.0618:0:5.2 -10 42599799 . T A 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.05519;SOR=0.18838;LSEQ=AATGGTCTCGAATGGAATCA;RSEQ=CTTCAAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:3,3:38,60:0.0566:2,2:33.7:1:31:1:0.6781:1.57:38.3:12:0.0571:0:3.5 0/1:180:2:1,1:74,99:0.0111:2,2:29:1:28.5:1:1:1.34:43.5:4:0.0112:0:2.5 -10 42599801 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13751;SOR=0;LSEQ=TGGTCTCGAATGGAATCATC;RSEQ=TCAAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:41,63:0.0189:2,2:19.5:1:31.5:1:1:1.53:21:4:0.0198:0:2 0/0:179:0:0,0:76,103:0:2,0:29.1:1:30.1:1:1:0:38.9:58.667:1:0:2.5 -10 42599802 . T C 113 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14181;SOR=3.34764;LSEQ=GGTCTCGAATGGAATCATCT;RSEQ=CAAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:41,61:0.0192:2,2:48:1:31.5:1:1:1.48:23.5:4:0.0196:0:6 0/1:178:11:4,7:72,95:0.0618:2,2:27.1:1:32.8:1:0.76053:1.32426:38.5:22:0.064:0:5.1 -10 42599803 . C A 24 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.15852;LSEQ=GTCTCGAATGGAATCATCTT;RSEQ=AAATGGAATGGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:0,1:42,60:0.0097:2,0:26:0:32:0:1:0:49:2:0.0098:0:1 0/1:178:2:2,0:74,101:0.0112:2,0:24.5:1:24.5:1:0.18297:0:37:4:0.0117:0:5 -10 42599804 . A AAATGG 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=4.000;MSILEN=5;SSF=0.5357;SOR=Inf;LSEQ=TCTCGAATGGAATCATCTTC;RSEQ=AATGGAATGGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:42,58:0:2,0:27.7:1:30:1:1:0:37.7:32.333:0.9898:0:2.5 0/1:177:2:1,1:72,100:0.0113:2,2:20.5:1:29.2:1:1:1.39:47.5:4:0.0118:0.0056:1.5 -10 42599806 . A C 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71479;SOR=1.74102;LSEQ=TCGAATGGAATCATCTTCAA;RSEQ=TGGAATGGAATGGAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:41,58:0.0196:2,2:25.5:1:30.5:1:1:1.41:40:4:0.02:0:3 0/1:178:6:3,3:71,100:0.0337:2,2:27.2:1:27.7:1:0.69538:1.41:32.7:5:0.0292:0:1.8 -10 42599812 . T A 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62032;SOR=0.55754;LSEQ=GGAATCATCTTCAAATGGAA;RSEQ=GGAATGGAATCATCGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:0,2:37,55:0.0208:2,0:22.5:1:33:0:0.5175:0:33.5:4:0.0217:0:5.5 0/1:171:2:0,2:72,97:0.0117:2,0:18.5:1:33:0:0.5096:0:34.5:4:0.0121:0:4.5 -10 42599814 . G C 34 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.54032;SOR=Inf;LSEQ=AATCATCTTCAAATGGAATG;RSEQ=AATGGAATCATCGCATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:35,54:0:2,0:24.2:1:31.4:1:1:0:38:43.5:0.956:0:2.5 0/1:169:2:1,1:71,96:0.0118:2,2:11:0:34:0:1:1.35:30:4:0.012:0:5 -10 42599815 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.53535;SOR=Inf;LSEQ=ATCATCTTCAAATGGAATGG;RSEQ=ATGGAATCATCGCATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:37,55:0:2,0:23.4:1:30.3:1:1:0:38.5:91:1:0:2.5 0/1:161:2:1,1:66,92:0.0124:2,2:12:1:31:1:1:1.39:31:4:0.0126:0:4 -10 42599816 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.53735;SOR=Inf;LSEQ=TCATCTTCAAATGGAATGGA;RSEQ=TGGAATCATCGCATAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:35,54:0:2,0:23.3:1:30.9:1:1:0:38.3:178:0.9889:0:2.5 0/1:160:2:1,1:67,90:0.0125:2,2:9:0:33.5:1:1:1.34:30:4:0.0131:0:5 -10 42599819 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.53582;SOR=Inf;LSEQ=TCTTCAAATGGAATGGAATG;RSEQ=AATCATCGCATAGAATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:32,51:0:2,0:22.7:1:30.9:1:1:0:38:26.667:1:0:2.6 0/1:146:2:1,1:59,85:0.0137:2,2:32.5:1:29.5:1:1:1.44:44:4:0.014:0:5 -10 42599820 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.53897;SOR=Inf;LSEQ=CTTCAAATGGAATGGAATGG;RSEQ=ATCATCGCATAGAATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:32,49:0:2,0:22.5:1:30.3:1:1:0:38.1:162:1:0:2.6 0/1:146:2:1,1:59,85:0.0137:2,2:26:1:27:0:1:1.44:42:4:0.0141:0:3 -10 42599824 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54515;SOR=Inf;LSEQ=AAATGGAATGGAATGGAATC;RSEQ=TCGCATAGAATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:25,47:0:2,0:22:1:31:1:1:0:37.4:71:1:0:2.8 0/1:136:2:1,1:52,81:0.0147:2,2:32.5:1:29:1:1:1.55:22:4:0.015:0:3.5 -10 42599826 . C G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12058;SOR=0;LSEQ=ATGGAATGGAATGGAATCAT;RSEQ=GCATAGAATTGAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:20,45:0.0299:2,2:28.5:1:33:1:0.53189:2.22:43.5:4:0.0303:0:6 0/0:125:0:0,0:47,77:0:2,0:18.2:1:29.5:1:1:0:38.3:40.333:1:0:2.6 -10 42599836 . T C 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97842;LSEQ=ATGGAATCATCGCATAGAAT;RSEQ=GAATGGAATTATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:46:13,33:0,0:0.902:0,2:20.6:1:30.4:1:1:0:34:45:0.9184:0:3.1 1/1:80:72:21,51:1,2:0.9:2,2:17.9:1:29.2:1:1:1.211:35:23:0.8961:0:3.2 -10 42599847 . A T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50687;SOR=Inf;LSEQ=GCATAGAATTGAATGGAATT;RSEQ=TCATCGAATTGACTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:13,28:0:2,0:15.7:1:30.2:1:1:0:33:82:1:0:3.5 0/1:56:2:1,1:11,43:0.0357:2,2:10:1:32:0:0.38571:3.79:45.5:4:0.0364:0:2.5 -10 42599857 . T G 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62945;SOR=0.43214;LSEQ=GAATGGAATTATCATCGAAT;RSEQ=GACTCGAATGGAATCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:25:5,20:0,0:0.9615:0,2:16.1:1:31.2:1:1:0:32.7:50:0.9615:0:4.3 1/1:35:32:0,32:1,2:0.9143:2,1:18.7:1:30.5:1:0.08571:0:32.3:64:0.9143:0:4.8 -10 42599858 . G T 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25136;SOR=Inf;LSEQ=AATGGAATTATCATCGAATT;RSEQ=ACTCGAATGGAATCAACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:4,20:0:2,0:16.3:1:31.3:1:1:0:32.2:48:1:0:4.6 0/1:33:3:1,2:0,30:0.0909:1,2:25:1:26.7:1:0.09091:0:48.7:6:0.0909:0:4.3 -10 42599860 . C A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21799;SOR=0.23432;LSEQ=TGGAATTATCATCGAATTGA;RSEQ=TCGAATGGAATCAACATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:21:4,17:0,1:0.9545:0,2:18.2:1:31:1:1:0:33:42:0.9545:0:5 1/1:29:24:0,24:1,4:0.8276:2,1:22.1:1:30.4:1:0.17241:0:30.9:23:0.8214:0:5.3 -10 42599861 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49698;SOR=Inf;LSEQ=GGAATTATCATCGAATTGAC;RSEQ=CGAATGGAATCAACATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:4,19:0:2,0:17.3:1:29.6:1:1:0:33.2:22:1:0:4.8 0/1:29:2:1,1:0,27:0.069:1,2:30.5:1:30:1:0.06897:0:43.5:4:0.069:0:5.5 -10 42599869 . A T 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68012;SOR=2.09058;LSEQ=CATCGAATTGACTCGAATGG;RSEQ=ATCAACATCTAACGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:4,13:0.1053:2,0:7:0:29:0:1:0:38.5:4:0.1053:0:5 0/1:25:5:0,5:1,19:0.2:1,0:15.8:1:28.6:1:1:0:25.6:10:0.2:0:6.2 -10 42599879 . T A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6026;SOR=2.21548;LSEQ=ACTCGAATGGAATCAACATC;RSEQ=AACGGAATCAAACGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:15:4,11:0,1:0.8824:0,2:22.9:1:29.1:1:1:0:30:30:0.9375:0:5.2 1/1:18:17:2,15:0,0:0.9444:0,2:25.2:1:30.2:1:1:0:34.2:34:1:0:5.8 -10 42599887 . TC AA 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74523;SOR=1.31017;LSEQ=GGAATCAACATCTAACGGAA;RSEQ=AAACGGAATTATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:5,14:1,3:0.7917:2,2:16.9:1:29.4:1:1:1.07:33.6:38:0.8261:0.2083:4.6 1/1:42:35:14,21:2,4:0.8333:2,2:14.3:1:30:1:1:1.32:34.6:70:0.8537:0.3095:4.1 -10 42599891 . A G 47 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04512;SOR=0;LSEQ=TCAACATCTAACGGAATCAA;RSEQ=CGGAATTATCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:6,17:0.1111:2,2:7.3:1:30:1:1:1.40:44:6:0.1154:0:2.7 0/0:47:0:0,0:19,27:0:2,0:12.6:1:29.7:1:1:0:36.7:92:0.9787:0:3.8 -10 42599892 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52681;SOR=Inf;LSEQ=CAACATCTAACGGAATCAAA;RSEQ=GGAATTATCGAATGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:8,21:0:2,0:16.6:1:30:1:1:0:34.5:58:1:0:4 0/1:49:2:1,1:20,27:0.0408:2,2:24.5:1:28:1:1:1.34:37.5:4:0.0408:0:4 -10 42599898 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12783;SOR=0;LSEQ=CTAACGGAATCAAACGGAAT;RSEQ=ATCGAATGGAATCGAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:6,22:0.0667:2,2:7:0:30.5:1:0.41839:3.47:21:4:0.0667:0:4.5 0/0:53:0:0,0:23,30:0:2,0:14.9:1:28.8:1:1:0:37.3:106:1:0:3.5 -10 42599903 . A T 46 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13201;SOR=0.17692;LSEQ=GGAATCAAACGGAATTATCG;RSEQ=ATGGAATCGAAGAGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:1,2:6,21:0.1:2,2:23.3:1:29.3:1:1:1.71:27.3:6:0.1111:0:5 0/1:53:1:0,1:24,28:0.0189:2,0:31:0:27:0:1:0:35:2:0.0189:0:7 -10 42599905 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53782;SOR=Inf;LSEQ=AATCAAACGGAATTATCGAA;RSEQ=GGAATCGAAGAGAATCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:7,23:0:2,0:23.9:1:29.9:1:1:0:34.9:60:1:0:3.9 0/1:55:2:1,1:25,28:0.0364:2,2:11:0:32:1:1:1.12:33:4:0.0377:0:1.5 -10 42599915 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54036;SOR=Inf;LSEQ=AATTATCGAATGGAATCGAA;RSEQ=AGAATCATCGAATGGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:7,23:0:2,0:28.8:1:30.7:1:1:0:34.5:29:1:0:4 0/1:56:2:1,1:25,28:0.0357:2,2:14:1:30.5:1:1:1.12:31:4:0.037:0:4.5 -10 42599922 . A T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41076;SOR=0.61479;LSEQ=GAATGGAATCGAAGAGAATC;RSEQ=TCGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:8:3,5:4,18:0.2667:2,2:31.8:1:31.6:1:0.3446:2.60:35.4:16:0.2667:0:4.6 0/1:55:10:6,4:19,24:0.1818:2,2:31.3:1:30.9:1:0.4878:1.87:30.1:20:0.1818:0:4 -10 42599924 . C A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5451;SOR=Inf;LSEQ=ATGGAATCGAAGAGAATCAT;RSEQ=GAATGGACTCGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:7,22:0:2,0:33.7:1:30.6:1:1:0:34.7:58:1:0:3.9 0/1:56:2:1,1:26,28:0.0357:2,2:36:0:30.5:1:1:1.08:46:4:0.037:0:4.5 -10 42599925 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5502;SOR=Inf;LSEQ=TGGAATCGAAGAGAATCATC;RSEQ=AATGGACTCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:7,21:0:2,0:35.1:1:31.2:1:1:0:35.1:56:1:0:3.9 0/1:56:2:1,1:26,27:0.0357:2,2:26:1:31.5:1:1:1.04:31:4:0.0364:0:6.5 -10 42599928 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9948;LSEQ=AATCGAAGAGAATCATCGAA;RSEQ=GGACTCGAATGGAATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:10:4,6:3,15:0.3571:2,2:37.6:1:32.1:1:0.20746:3.18:32.5:20:0.3571:0:4.6 0/1:59:21:12,9:17,21:0.3559:2,2:35:1:29.4:1:0.42198:1.63:33:20:0.3509:0:4 -10 42599931 . A T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10853;SOR=0;LSEQ=CGAAGAGAATCATCGAATGG;RSEQ=CTCGAATGGAATCATCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:7,20:0.069:2,2:39:0:30.5:1:0.48276:2.74:42:4:0.0714:0:3 0/0:58:0:0,0:28,28:0:2,0:33.9:1:29:1:1:0:38.1:55:0.9649:0:3.4 -10 42599933 . T C 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78319;SOR=1.24663;LSEQ=AAGAGAATCATCGAATGGAC;RSEQ=CGAATGGAATCATCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:21:5,16:2,5:0.75:2,2:34.8:1:30.7:1:1:1.26845:36:20:0.7407:0:4.1 1/0:57:45:23,22:6,6:0.7895:2,2:37:1:29.9:1:1:1.04:36.7:21.5:0.7818:0:3.6 -10 42599935 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5429;SOR=Inf;LSEQ=GAGAATCATCGAATGGACTC;RSEQ=AATGGAATCATCTAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:9,21:0:2,0:31.8:1:30.9:1:1:0:34.8:29:1:0:3.9 0/1:57:2:1,1:28,27:0.0351:2,2:40.5:1:30.5:1:1:1.03639:46:4:0.0364:0:4.5 -10 42599945 . A ATAT 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11874;SOR=0;LSEQ=GAATGGACTCGAATGGAATC;RSEQ=TCTAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:10,19:0.0645:2,2:24:0:31.3:1:1:1.86:42:4:0.0645:0:3 0/0:58:0:0,0:29,28:0:2,0:28.9:1:29.2:1:1:0:39.1:13.25:0.9815:0:3.2 -10 42599950 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54036;SOR=Inf;LSEQ=GACTCGAATGGAATCATCTA;RSEQ=TGGAATGGAATGGAATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:10,20:0:2,0:23.4:1:31.7:1:1:0:35.5:60:1:0:3.8 0/1:56:2:1,1:28,26:0.0357:2,2:20:1:33.5:1:1:1.07547:43:4:0.0364:0:4 -10 42599951 . TG T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54036;SOR=Inf;LSEQ=ACTCGAATGGAATCATCTAA;RSEQ=GAATGGAATGGAATAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:10,20:0:2,0:22.2:1:32.3:1:1:0:35.5:60:1:0:3.8 0/1:56:2:1,1:28,26:0.0357:2,2:34.5:1:30.5:1:1:1.07547:53:4:0.0364:0:2.5 -10 42599956 . T A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10606;SOR=0;LSEQ=AATGGAATCATCTAATGGAA;RSEQ=GGAATGGAATAATCCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:9,18:0.069:2,2:11:0:32.5:1:1:1.95:42:4:0.069:0:3 0/0:59:0:0,0:30,29:0:2,0:23.5:1:29.1:1:1:0:38.9:28.5:1:0:3.3 -10 42599958 . G A 36 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.54859;SOR=Inf;LSEQ=TGGAATCATCTAATGGAATG;RSEQ=AATGGAATAATCCATGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:20.8:1:32.3:1:1:0:35:54:1:0:3.7 0/1:59:3:2,1:28,28:0.0508:2,2:17.3:1:23:1:1:1.98:38.3:2:0.0351:0:5.3 -10 42599962 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATCATCTAATGGAATGGAAT;RSEQ=GAATAATCCATGGATTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:18.3:1:32.5:1:1:0:35:54:1:0:3.7 0/1:59:2:1,1:28,28:0.0339:2,2:14:0:31.5:1:1:1:47.5:4:0.0351:0:2.5 -10 42599966 . T G 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1994;LSEQ=TCTAATGGAATGGAATGGAA;RSEQ=AATCCATGGATTCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:8.5:1:30.5:1:1:1.74:21:4:0.0741:0:4.5 0/1:57:5:3,2:26,26:0.0877:2,2:31.8:1:32.2:1:1:1.49:46.4:10:0.0943:0:3.6 -10 42599973 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAATAATCCA;RSEQ=GGATTCGAATGCAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,11:0:2,0:16.1:1:30.8:1:1:0:30.7:38:0.95:0:3.8 0/1:50:2:1,1:25,23:0.04:2,2:19.5:1:30:1:1:1.08513:53:4:0.04:0:4.5 -10 42599977 . T C 134 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00378;SOR=0;LSEQ=GGAATGGAATAATCCATGGA;RSEQ=TCGAATGCAATCATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:8,12:0,0:1:0,2:17.2:1:32.2:1:1:0:32:40:1:0:4 1/0:33:22:9,13:3,3:0.6667:2,2:18.9:1:30.2:1:1:1.42528:35.7:10:0.6897:0:3.6 -10 42599993 . A G 31 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.51952;LSEQ=TGGATTCGAATGCAATCATC;RSEQ=TCGAATGGAATCAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:11,15:0.037:2,0:41:0:28:0:0.44444:0:24:2:0.037:0:6 0/1:36:2:1,1:21,11:0.0556:2,2:35:0:31.5:1:1:1.8709:53:4:0.0571:0:4.5 -10 42599994 . T G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.24731;SOR=Inf;LSEQ=GGATTCGAATGCAATCATCA;RSEQ=CGAATGGAATCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:0:2,0:18.3:1:29.8:1:1:0:33.9:56:1:0:3.4 0/1:35:3:2,1:20,12:0.0857:2,2:23:1:31.7:1:1:1.19:44:6:0.0882:0:3.7 -10 42599995 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49821;SOR=Inf;LSEQ=GATTCGAATGCAATCATCAT;RSEQ=GAATGGAATCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:0:2,0:18.8:1:29.8:1:1:0:33.9:56:1:0:3.4 0/1:35:2:0,2:21,11:0.0571:2,0:30.5:1:31.5:1:0.13904:0:42.5:4:0.0588:0:3 -10 42599996 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49808;SOR=Inf;LSEQ=ATTCGAATGCAATCATCATC;RSEQ=AATGGAATCAAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:12,17:0:2,0:18.7:1:29.4:1:1:0:33.3:28:1:0:3.4 0/1:36:2:1,1:21,13:0.0556:2,2:32:0:31.5:1:1:1.5932:53:4:0.0556:0:4.5 -10 42600006 . A G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08159;SOR=0.23372;LSEQ=AATCATCATCGAATGGAATC;RSEQ=AATGGAATCATCGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:30:11,19:1,0:0.9375:0,2:22.5:1:30.4:1:0.3871:0:32.3:60:0.9375:0:3.5 1/0:31:24:14,10:3,3:0.7742:2,2:21.4:1:30.4:1:1:1.38:36.6:23:0.7667:0:3.4 -10 42600009 . T A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49649;SOR=Inf;LSEQ=CATCATCGAATGGAATCAAA;RSEQ=GGAATCATCGAATGGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:0:2,0:25.7:1:30:1:1:0:33.5:62:1:0:3.4 0/1:37:2:1,1:22,13:0.0541:2,2:17:1:29:1:1:1.66733:46:4:0.0541:0:4 -10 42600016 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=GAATGGAATCAAATGGAATC;RSEQ=TCGAATGGACTCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:18,20:0:2,0:25.3:1:29.8:1:1:0:33.1:37:1:0:3.4 0/1:39:2:1,1:23,14:0.0513:2,2:15.5:1:32.5:1:1:1.62122:46:4:0.0513:0:4 -10 42600018 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=0;LSEQ=ATGGAATCAAATGGAATCAT;RSEQ=GAATGGACTCGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:17,20:0.0513:2,2:8.5:1:29:1:1:1.17:24:4:0.0513:0:4 0/0:39:0:0,0:25,14:0:2,0:22.2:1:31.5:1:1:0:38.4:78:1:0:3.3 -10 42600019 . G C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23449;SOR=0;LSEQ=TGGAATCAAATGGAATCATC;RSEQ=AATGGACTCGAATGGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:18,19:0.0513:2,0:26:1:30:1:0.48988:0:28.5:4:0.0526:0:4.5 0/0:41:0:0,0:26,15:0:2,0:21.6:1:31.2:1:1:0:38:82:1:0:3.4 -10 42600021 . A G 51 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11156;SOR=0;LSEQ=GAATCAAATGGAATCATCGA;RSEQ=TGGACTCGAATGGAATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:2,1:17,20:0.075:2,2:10:1:32.7:1:0.59615:2.30:30:6:0.0769:0:4.3 0/0:42:0:0,0:26,16:0:2,0:22.2:1:30.8:1:1:0:38.2:84:1:0:3.4 -10 42600024 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49456;SOR=Inf;LSEQ=TCAAATGGAATCATCGAATG;RSEQ=ACTCGAATGGAATAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:19,21:0:2,0:29.6:1:31.1:1:1:0:32.5:80:1:0:3.5 0/1:43:2:1,1:25,15:0.0465:2,2:7.5:1:29:1:1:1.64563:46:4:0.0465:0:4 -10 42600025 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49412;SOR=Inf;LSEQ=CAAATGGAATCATCGAATGG;RSEQ=CTCGAATGGAATAATCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,23:0:2,0:28.1:1:29.6:1:1:0:32.3:42:1:0:3.5 0/1:43:2:1,1:25,16:0.0465:2,2:26.5:1:31:0:1:1.54582:27:4:0.0465:0:4.5 -10 42600026 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23557;SOR=Inf;LSEQ=AAATGGAATCATCGAATGGA;RSEQ=TCGAATGGAATAATCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:20,24:0:2,0:28:1:31.5:1:1:0:32.2:43:1:0:3.5 0/1:42:2:1,1:24,16:0.0476:2,2:26.5:1:28:1:1:1.48518:49.5:4:0.0476:0:3.5 -10 42600044 . T C 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09181;SOR=Inf;LSEQ=GACTCGAATGGAATAATCAT;RSEQ=GAACGGAATTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,24:0:2,0:30.8:1:29.9:1:1:0:31.5:42:0.9767:0:3.5 0/1:38:3:1,2:24,11:0.0789:2,2:37.3:1:28.3:1:0.26505:4.18168:23:6:0.0811:0:5.7 -10 42600050 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50096;SOR=0;LSEQ=AATGGAATAATCATTGAACG;RSEQ=AATTGAATGGAATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:19,26:0.0417:2,2:25.5:1:28:1:1:1.36:28.5:4:0.0426:0:3.5 0/0:38:0:0,0:25,13:0:2,0:31.6:1:31.2:1:1:0:37.2:76:1:0:3.3 -10 42600054 . T C 165 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02697;SOR=0.27292;LSEQ=GAATAATCATTGAACGGAAT;RSEQ=GAATGGAATCATCATCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:44:19,25:0,2:0.898:0,2:28.9:1:30.3:1:0.50435:0:31.9:43:0.9149:0:3.5 1/0:37:26:19,7:3,4:0.7027:2,2:34:1:30.6:1:0.18632:3.46:34.3:52:0.7027:0:3.4 -10 42600065 . A G 46 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.29011;SOR=0;LSEQ=GAACGGAATTGAATGGAATC;RSEQ=TCATCGGATGGAAACGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:1,2:25,29:0.0526:2,2:27.7:1:29.3:1:1:1.70837:28.3:6:0.0526:0:4 0/0:34:0:0,0:23,11:0:2,0:31:1:29.6:1:1:0:36.3:68:1:0:3.4 -10 42600080 . CGAATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG TGA 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAATCATCATCGGATGGAAA;RSEQ=ATGGAATCATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:52:21,31:1,3:0.9123:2,2:22.7:1:30.9:1:1:2.01:28.2:104:0.9123:0.2456:3.9 0/0:32:0:0,0:6,6:0:2,0:20.6:1:29.8:1:1:0:36:24:0.375:0:3.1 -10 42600082 . AATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52532;SOR=0;LSEQ=ATCATCATCGGATGGAAACG;RSEQ=ATGGAATCATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:3,6:0.04:2,2:44.5:1:31.5:1:1:1.87:26:4:0.1818:0:2.5 0/0:30:0:0,0:19,11:0:2,0:18.8:1:28.8:1:1:0:36.3:60:1:0:3.5 -10 42600090 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10784;SOR=Inf;LSEQ=CGGATGGAAACGAATGGAAT;RSEQ=GTCATCGAATGGAATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:3,2:0:2,0:25.2:1:31.4:1:1:0:35.2:10:1:0:4.6 0/1:23:2:1,1:9,7:0.087:2,2:15:0:30:1:1:1.26772:43:4:0.1111:0:2.5 -10 42600091 . GTCATCG ATCA 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04024;SOR=Inf;LSEQ=GGATGGAAACGAATGGAATC;RSEQ=AATGGAATCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:3,2:0:2,0:25.8:1:30.6:1:1:0:35.2:10:1:0:4.6 0/1:25:3:2,1:12,8:0.12:2,2:25.7:1:29.7:1:1:1.32:41.3:6:0.1304:0.04:2.3 -10 42600105 . T A 44 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06574;SOR=8.47572;LSEQ=GGAATCGTCATCGAATGGAA;RSEQ=CGAATGGAATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:1:1,0:4,2:0.0208:2,0:7:0:31:0:1:0:40:2:0.1667:0:4 0/1:19:3:0,3:9,6:0.1579:2,0:11.7:1:28.3:1:0.20588:0:38.3:6:0.1667:0:4.3 -10 42600107 . GA AG 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01557;SOR=Inf;LSEQ=AATCGTCATCGAATGGAATC;RSEQ=ATGGAATCATCAAATGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:5,2:0:2,0:11.9:1:27.7:1:1:0:35.1:6:1:0:3.9 0/1:17:3:2,1:6,6:0.1765:2,2:9.3:1:30:1:1:1.91:37.7:6:0.1875:0.0588:3.3 -10 42600111 . G A 61 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=GTCATCGAATGGAATCGAAT;RSEQ=GAATCATCAAATGGGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:3,2:0:2,0:16:1:32.8:1:1:0:33.2:10:1:0:4 0/1:13:5:3,2:3,4:0.3846:2,2:5.6:1:26.6:1:1:1.89:37.8:10:0.4167:0:4.4 -10 42600113 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCGAATGGAATCGAATGG;RSEQ=ATCATCAAATGGGATCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:2,1:0.0435:2,2:10:1:32.5:1:1:1.7321:23:4:0.4:0:3.5 0/0:13:0:0,0:6,5:0:2,0:8.5:1:28.5:1:1:0:37.8:22:0.9167:0:3.7 -10 42600126 . G A 75 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=67.97564;LSEQ=CGAATGGAATCATCAAATGG;RSEQ=ATCAGATGGAATCATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:3:3,0:0,0:0.0667:0,0:27.3:1:31.3:1:1:0:34.3:6:0.75:0:3 1/1:7:6:2,4:0,0:0.8571:0,2:22.8:1:29.2:1:1:0:40.3:12:1:0:3.5 -10 42600140 . A G 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2438;SOR=0;LSEQ=AAATGGGATCAGATGGAATC;RSEQ=TCATCAAATGGAATCGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:2,0:22,36:0.0333:2,0:15:1:29:1:0.15593:0:22:4:0.0333:0:5 0/0:61:0:0,0:25,36:0:2,0:10:1:29.5:1:1:0:39.8:29.5:1:0:3.7 -10 42600146 . A G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07438;SOR=0.40622;LSEQ=GATCAGATGGAATCATCATC;RSEQ=AATGGAATCGAATAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:53:21,32:5,2:0.8833:2,2:24.9:1:30.7:1:0.22199:3.72489:29.2:106:0.8833:0:4.2 1/0:73:55:23,32:9,9:0.7534:2,2:12.5:1:30.1:1:0.59219:1.38493:40.2:54:0.75:0:3.9 -10 42600149 . T G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51252;SOR=Inf;LSEQ=CAGATGGAATCATCATCAAA;RSEQ=GGAATCGAATAGAATTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:26,34:0:2,0:26:1:30.2:1:1:0:30.6:59:1:0:4 0/1:86:2:1,1:35,49:0.0233:2,2:18:0:30:1:1:1.39:48:4:0.0235:0:4.5 -10 42600153 . A T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1505;SOR=Inf;LSEQ=TGGAATCATCATCAAATGGA;RSEQ=TCGAATAGAATTATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:26,37:0:2,0:25.8:1:30.3:1:1:0:31.8:62:0.9841:0:4 0/1:96:4:2,2:39,53:0.0417:2,2:9:1:28.8:1:1:1.35:47:8:0.0426:0:3.8 -10 42600161 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5186;SOR=Inf;LSEQ=TCATCAAATGGAATCGAATA;RSEQ=AATTATGGAATGAAATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:29,38:0:2,0:26.4:1:31.4:1:1:0:31.7:134:1:0:4 0/1:102:2:1,1:42,58:0.0196:2,2:30.5:1:28:1:1:1.38:28:4:0.0196:0:6.5 -10 42600162 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15575;SOR=0;LSEQ=CATCAAATGGAATCGAATAG;RSEQ=ATTATGGAATGAAATCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:28,37:0.0299:2,2:30:1:30:1:1:1.32:44.5:4:0.0299:0:3 0/0:102:0:0,0:43,59:0:2,0:23.6:1:30:1:1:0:40.9:204:1:0:3.5 -10 42600163 . A T 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5186;SOR=Inf;LSEQ=ATCAAATGGAATCGAATAGA;RSEQ=TTATGGAATGAAATCCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:29,38:0:2,0:26.6:1:29.9:1:1:0:31.7:66:1:0:4 0/1:102:2:1,1:42,58:0.0196:2,2:32:0:30.5:1:1:1.38:49:4:0.02:0:4 -10 42600167 . T C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.20653;LSEQ=AATGGAATCGAATAGAATTA;RSEQ=GGAATGAAATCCAATGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:1:1,0:25,36:0.0161:2,0:28:0:34:0:0.41935:0:23:2:0.0167:0:5 0/1:103:2:1,1:42,59:0.0194:2,2:32.5:1:32:0:1:1.40:48.5:4:0.0198:0:2.5 -10 42600168 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52801;SOR=Inf;LSEQ=ATGGAATCGAATAGAATTAT;RSEQ=GAATGAAATCCAATGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:26,36:0:2,0:29:1:31.2:1:1:0:32:61:1:0:4 0/1:103:2:1,1:42,58:0.0194:2,2:22:1:28:0:1:1.38:25:4:0.0196:0:3 -10 42600169 . G A 60 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01753;SOR=0;LSEQ=TGGAATCGAATAGAATTATG;RSEQ=AATGAAATCCAATGTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:4:2,2:23,34:0.0656:2,2:24.5:1:30:1:1:1.47:28.5:8:0.0667:0:4.5 0/0:104:0:0,0:43,60:0:2,0:28.4:1:31.4:1:1:0:40.8:102:1:0:3.4 -10 42600172 . T A 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53112;SOR=Inf;LSEQ=AATCGAATAGAATTATGGAA;RSEQ=GAAATCCAATGTGATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:25,36:0:2,0:29.1:1:30.6:1:1:0:32.2:122:1:0:4 0/1:104:2:1,1:42,59:0.0192:2,2:34:0:32:1:1:1.40:48:4:0.0194:0:4 -10 42600174 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53746;SOR=Inf;LSEQ=TCGAATAGAATTATGGAATG;RSEQ=AATCCAATGTGATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:24,34:0:2,0:30.3:1:30.3:1:1:0:32.3:116:1:0:4 0/1:104:2:1,1:42,60:0.0192:2,2:28.5:1:32.5:1:1:1.42:47:4:0.0196:0:3.5 -10 42600176 . A T 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53975;SOR=Inf;LSEQ=GAATAGAATTATGGAATGAA;RSEQ=TCCAATGTGATCATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:24,33:0:2,0:30.6:1:30.7:1:1:0:32.4:114:1:0:4 0/1:104:2:1,1:42,60:0.0192:2,2:23:0:32:0:1:1.42:43:4:0.0196:0:4.5 -10 42600178 . C A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55204;SOR=Inf;LSEQ=ATAGAATTATGGAATGAAAT;RSEQ=CAATGTGATCATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:22,33:0:2,0:31.5:1:31.5:1:1:0:32.5:110:1:0:4.1 0/1:103:3:1,2:41,57:0.0291:2,2:24:1:29.7:1:1:1.43362:46:6:0.0294:0:4.7 -10 42600181 . A G 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24427;SOR=0.59712;LSEQ=GAATTATGGAATGAAATCCA;RSEQ=TGTGATCATCATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:45:16,29:2,1:0.8182:2,2:30.7:1:32.4:1:0.54729:3.5241:30.4:90:0.8182:0:4.3 1/0:103:75:30,45:6,6:0.7282:2,2:31.4:1:31.7:1:0.54245:1.49283:41.1:36.5:0.73:0:3.6 -10 42600182 . T A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55167;SOR=Inf;LSEQ=AATTATGGAATGAAATCCAA;RSEQ=GTGATCATCATCGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:22,31:0:2,0:31.1:1:30:1:1:0:32.6:52:1:0:4 0/1:103:3:1,2:41,58:0.0291:2,2:39.7:1:25.3:1:1:1.40917:56:2:0.0198:0:3.3 -10 42600189 . A C 83 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17922;SOR=Inf;LSEQ=GAATGAAATCCAATGTGATC;RSEQ=TCATCGAATGGACTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:20,31:0:2,0:30.7:1:31:1:1:0:32.9:102:1:0:4 0/1:102:6:3,3:39,57:0.0588:2,2:27.8:1:32.3:1:0.6882:1.46:52:12:0.0588:0:3.7 -10 42600190 . T C 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.55115;SOR=Inf;LSEQ=AATGAAATCCAATGTGATCA;RSEQ=CATCGAATGGACTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:20,31:0:2,0:30.2:1:30.6:1:1:0:32.9:102:1:0:4 0/1:102:3:1,2:41,58:0.0294:2,2:15.7:1:32.7:1:1:1.40917:36.7:6:0.0294:0:4.3 -10 42600196 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCCAATGTGATCATCATCG;RSEQ=ATGGACTCGAATGGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:19,31:0:2,0:26.5:1:30.3:1:1:0:33.1:100:1:0:4 0/1:101:2:1,1:40,59:0.0198:2,2:30.5:1:30:1:1:1.47:25:4:0.0202:0:3 -10 42600202 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGATCATCATCGAATGGA;RSEQ=TCGAATGGAATCATCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:14,29:0:2,0:25.6:1:31.6:1:1:0:33.6:42:1:0:4.1 0/1:87:2:1,1:33,52:0.023:2,2:9.5:1:30:1:1:1.57:48:4:0.023:0:2 -10 42600203 . T C 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.05243;SOR=0.37681;LSEQ=GTGATCATCATCGAATGGAC;RSEQ=CGAATGGAATCATCATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:37:11,26:3,3:0.8605:2,2:22.6:1:31.6:1:0.37276:2.31228:31.3:74:0.8605:0:4.4 1/0:86:60:22,38:9,10:0.6977:2,2:20:1:30.5:1:0.43032:1.5456:40.5:59:0.6941:0:3.9 -10 42600208 . T C 82 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17482;SOR=Inf;LSEQ=CATCATCGAATGGACTCGAA;RSEQ=GGAATCATCATCCAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:11,26:0:2,0:23.5:1:30.8:1:1:0:35.2:74:1:0:4.2 0/1:77:6:3,3:27,43:0.0779:2,2:25.2:1:31.8:1:0.6753:1.58:43.7:12:0.0789:0:3.7 -10 42600209 . G A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5474;SOR=Inf;LSEQ=ATCATCGAATGGACTCGAAT;RSEQ=GAATCATCATCCAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:11,26:0:2,0:22.5:1:32.1:1:1:0:35.2:74:1:0:4.2 0/1:72:2:2,0:26,44:0.0278:2,0:38.5:1:27:1:0.14789:0:31:4:0.0278:0:4.5 -10 42600210 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11744;SOR=0;LSEQ=TCATCGAATGGACTCGAATG;RSEQ=AATCATCATCCAATGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:10,25:0.0541:2,2:37.5:1:33.5:1:0.51201:2.43:22:4:0.0541:0:5.5 0/0:70:0:0,0:27,43:0:2,0:19:1:31.1:1:1:0:40:140:1:0:3.5 -10 42600212 . A C 65 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66071;SOR=2.08189;LSEQ=ATCGAATGGACTCGAATGGA;RSEQ=TCATCATCCAATGGAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:9,23:0.0294:2,0:14:0:33:0:1:0:24:2:0.0303:0:5 0/1:67:4:1,3:25,38:0.0597:2,2:12.3:1:32.5:1:1:1.95549:47.8:8:0.0597:0:4.5 -10 42600216 . T A 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0.54834;SOR=Inf;LSEQ=AATGGACTCGAATGGAATCA;RSEQ=CATCCAATGGAAACTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:8,23:0:2,0:19:1:31.1:1:1:0:37.3:62:1:0:4.2 0/1:60:3:1,2:20,36:0.05:2,2:12.7:1:31.3:1:1:1.10917:33.7:6:0.0508:0:6 -10 42600219 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.5502;SOR=Inf;LSEQ=GGACTCGAATGGAATCATCA;RSEQ=CCAATGGAAACTAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:7,21:0:2,0:17.8:1:30.5:1:1:0:38.8:27:1:0:4.2 0/1:56:2:1,1:20,34:0.0357:2,2:34.5:1:31.5:1:1:1.68:37:4:0.0357:0:4.5 -10 42600224 . T C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59249;SOR=0.66079;LSEQ=CGAATGGAATCATCATCCAA;RSEQ=GGAAACTAATGGAATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:4,12:3,4:0.6667:2,2:13.5:1:31:1:0.62584:2.16624:35.4:32:0.6957:0:4.8 1/0:37:21:6,15:6,10:0.5676:2,2:11.2:1:29.7:1:0.72582:1.48338:37.8:42:0.5676:0:4.5 -10 42600229 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76255;SOR=0.69816;LSEQ=GGAATCATCATCCAATGGAA;RSEQ=CTAATGGAATCAACATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:2,9:4,3:0.55:2,2:14.1:1:32.8:1:0.1414:5.34092:31.5:22:0.6111:0:4.9 0/1:24:11:2,9:4,8:0.4583:2,2:13.6:1:32.6:1:0.64041:2.17235:32.1:22:0.4583:0:5 -10 42600231 . T A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48791;SOR=Inf;LSEQ=AATCATCATCCAATGGAAAC;RSEQ=AATGGAATCAACATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:5,12:0:2,0:11.9:1:29.8:1:1:0:38.1:34:0.9444:0:3.9 0/1:20:2:1,1:4,14:0.1:2,2:22.5:1:32:0:0.44737:3.24:37:4:0.1053:0:4.5 -10 42600254 . T A 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGGAATCAACATCGAATGGA;RSEQ=TCGAATGGAAACACCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:2:0:28.5:1:1:0:31.5:4:0.6667:0:3 1/1:4:4:0,4:0,0:1:0,0:8.5:1:30:1:1:0:29:8:1:0:3.5 -10 42600281 . G A 25 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAACACCATCGAATTGAA;RSEQ=CGAATGGAATTATCATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:25.5:1:1:0:26:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42600307 . T A 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTATCATGAAATTGAA;RSEQ=TGGATGGACTCATCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:27.7:1:30:1:1:0:30.7:6:1:0:3 1/1:1:1:0,1:0,0:1:0,0:13:0:25:0:1:0:40:2:1:0:3 -10 42600352 . G A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=TTCGAATGGAATCATCGAAT;RSEQ=AAATTGATTGAAATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:26.5:1:29.5:1:1:0:34.5:4:0.5:0:3.5 1/0:3:2:0,2:0,1:0.6667:0,0:29.5:1:30.5:1:1:0:40:4:0.6667:0:4 -10 42600390 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.7321;LSEQ=CATCAAATGGAATCGAATGG;RSEQ=ATCATTGAATGGAGTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:30:0:29:0:1:0:40:2:0.5:0:4 1/0:3:2:0,2:0,1:0.6667:0,0:26:1:29:1:1:0:40:4:0.6667:0:4 -10 42600404 . G A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATCATTGAATGGA;RSEQ=TCGAATGGAATCATCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9.5:1:31:1:1:0:40:4:1:0:3 1/1:2:2:0,2:0,0:1:0,0:21:1:29.5:1:1:0:39.5:4:1:0:3.5 -10 42601984 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCATTGAATGGAAT;RSEQ=GAATGGAATCATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21:0:31.5:1:1:0:40:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42601993 . T A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTGAATGGAATCGAATGGAA;RSEQ=CATCAAATGGACTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:30:0:31.5:1:1:0:40:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42601996 . T A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=CAAATGGACTCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:32:0:31.5:1:1:0:40:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42602046 . T C 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCGAGTGGAATCCT;RSEQ=GAATTGAAGCAAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:29:1:1:0:60:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42602051 . T G 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGAGTGGAATCCTTGAAT;RSEQ=GAAGCAAATGGAATCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:30.5:1:1:0:60:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42602053 . A G 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGTGGAATCCTTGAATTG;RSEQ=AGCAAATGGAATCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:30:1:1:0:60:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 42602055 . G T 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGAATCCTTGAATTGAA;RSEQ=CAAATGGAATCATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:29.5:1:1:0:60:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43052740 . G GA 30 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0.64942;LSEQ=TAAAATATTTGTTTCCTAGT;RSEQ=AAAAAAAAAAAAAAAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,0:0.2857:0,0:15:1:30:1:1:0:57.5:4:0.4:0:0.5 0/1:5:1:1,0:1,0:0.2:0,0:11:0:29:0:1:0:60:2:0.25:0:5 -10 43052870 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20419;SOR=Inf;LSEQ=GACTTTACATAAACAACTTT;RSEQ=TCAACTGTGTTAGTTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:133,35:0:2,0:21.4:1:31.4:1:1:0:60:83:1:0:0.1 0/1:139:2:1,1:105,32:0.0144:2,2:18.5:1:28.5:1:0.41977:3.24648:60:4:0.0144:0:1.5 -10 43052937 . CA C 84 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.28649;SOR=3.00417;LSEQ=AAATGAAGAATATTGAATGC;RSEQ=AAAAAAATCAAACAATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:2:1,1:207,169:0.0053:2,2:18.5:1:31:1:1:1.22419:60:4:0.0053:0:5 0/1:381:6:3,3:206,168:0.0157:2,2:24:1:32.8:1:1:1.22552:60:12:0.0159:0:0.3 -10 43052980 . G A 246 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AATCACTCAATTCTAATCGT;RSEQ=TAAATGCTGAAGTAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:329:329:136,193:0,0:1:0,2:27.6:1:29.5:1:1:0:60:64.8:1:0:1.1 1/0:372:249:105,144:54,69:0.6694:2,2:24.6:1:28.7:1:0.82378:1.07309:60:248:0.6685:0:1.1 -10 43053033 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22559;SOR=0;LSEQ=AGTTACTTCAATGAAAATGC;RSEQ=AAGAACATCAGATGCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:48,143:0.0103:2,2:25.5:1:28.5:1:0.4443:2.96:60:4:0.0104:0:1.5 0/0:215:0:0,0:70,145:0:2,0:26.3:1:29.9:1:1:0:60:214:1:0:0.6 -10 43053085 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49669;SOR=Inf;LSEQ=TGCAGAATGTGGGTCGGACG;RSEQ=CCCACAAGTTGGAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:7,66:0:2,0:23.6:1:31.7:1:1:0:60:35.5:1:0:0.1 0/1:75:2:1,1:17,55:0.0267:2,2:15:1:31:0:0.42984:3.17:60:4:0.027:0:1 -10 43059566 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50051;SOR=0;LSEQ=CACTGCGGACACTCAGGTGG;RSEQ=AGCAGGAAGGAAAGTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:30,70:0.0196:2,2:13.5:1:29:1:0.51757:2.31:60:4:0.0204:0:1 0/0:87:0:0,0:27,60:0:2,0:20.5:1:31.5:1:1:0:60:174:1:0:0.1 -10 43572511 . C A 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GGCGCAGCCGGCGCTTACCT;RSEQ=GCTTCAGTCCCGCGACCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:28:1:1:0:60:4:1:0:2 0/0:3:0:0,0:3,0:0:0,0:21:1:25.7:1:1:0:60:2:1:0:2.3 -10 43572644 . G A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75056;LSEQ=CCAGACTGAGCGCCGCACCC;RSEQ=CCATCCAGACCCGCCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:2,1:122,76:0.0149:2,2:15.3:1:28.3:1:1:1.24:60:6:0.0155:0:1.3 0/1:178:2:1,1:103,72:0.0112:2,2:29:0:30.5:1:1:1.42758:60:4:0.0115:0:1 -10 43572659 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10862;SOR=Inf;LSEQ=CACCCGCCATCCAGACCCGC;RSEQ=GGCCCTAGCCGCAGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:162,101:0:2,0:26.1:1:30.8:1:1:0:60:262:1:0:0.3 0/1:241:3:1,2:141,97:0.0124:2,2:15:1:28.7:1:0.56983:2.8943:60:6:0.0128:0:1 -10 43572664 . C T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3594;SOR=3.2021;LSEQ=GCCATCCAGACCCGCCGGCC;RSEQ=TAGCCGCAGTCCCTCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:0,1:184,109:0.0034:2,0:23:0:12:0:0.37415:0:60:0:0:0:2 0/1:277:3:0,3:160,114:0.0108:2,0:6:1:22:1:0.07424:0:60:2:0.0074:0:2 -10 43572796 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3083;SOR=4.46536;LSEQ=AAAGGTGAGTTCTGCCGGCC;RSEQ=CCGGCTCCCGCAGGGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:1:1,0:149,221:0.0027:2,0:1:0:29:0:0.40431:0:60:2:0.0028:0:1 0/1:251:3:2,1:96,152:0.012:2,2:15.7:1:27.7:1:0.56241:3.15:60:6:0.0122:0:1.3 -10 43572832 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04972;LSEQ=GCCAGGGCGAAGTTGGCGCC;RSEQ=AGCAGCGGAGCGGGCGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:227:210:56,154:2,15:0.9251:2,2:23.2:1:29.8:1:0.25045:2.72:60:41:0.9234:0:1.1 0/1:135:51:12,39:21,63:0.3778:2,2:24.6:1:29.4:1:1:1.08272:60:16:0.3692:0:1.1 -10 43595781 . G T 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAATAATTGAGTGTTCAT;RSEQ=TTCTCAGGAACAGAGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:112,2:0:1,0:24.6:1:32.1:1:1:0:59.8:56:1:0:0.3 0/1:59:14:14,0:45,0:0.2373:1,1:28.1:1:29.8:1:1:0:60:13:0.2241:0:1.3 -10 43595836 . A AT 214 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.00036;SOR=0.46718;LSEQ=ATCGGAATTTTAAATTAATG;RSEQ=TTTTTTTTTTTTTTGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:111:105,6:124,15:0.3908:2,2:26.6:1:31.5:1:0.16902:2.11:60:54.5:0.4022:0:1 0/1:178:41:38,3:109,15:0.2303:2,2:29.2:1:30.7:1:0.56578:1.74:60:82:0.2356:0:1 -10 43595968 . A G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15385;LSEQ=AAGCTGTATGTGGACCAGGC;RSEQ=GCCGGCACGCCCTTGCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:984:910:401,509:28,46:0.9248:2,2:25:1:30.2:1:0.33061:1.29:60:52.529:0.9263:0:1.1 1/0:893:584:267,317:138,164:0.654:2,2:25.8:1:29.9:1:1:1.00:60:63.889:0.6534:0:1.2 -10 43596179 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02162;LSEQ=TCAGTGTCCGCAGTAAGGGA;RSEQ=CCGCCCCAACACCCACCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:544:491:176,315:18,34:0.9026:2,2:26.9:1:29.2:1:1:1.06:60:34.071:0.9034:0:1.3 0/1:482:80:34,46:160,242:0.166:2,2:24:1:28.6:1:0.70838:1.12:60:79:0.1667:0:1.3 -10 43596241 . C T 187 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAGCCGCCCTTATCACAGC;RSEQ=GCTGACACTGAAGCTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:87:7,80:9,79:0.4943:2,2:25.8:1:29.1:1:0.79406:1.30003:60:16.4:0.4881:0:1.9 0/0:137:0:0,0:17,120:0:2,0:22:1:29.2:1:1:0:59.8:33.25:1:0:0.5 -10 43596307 . G T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08002;LSEQ=GAAGGCGTCAGGGGTTAAGT;RSEQ=AGGCTGGCCTGCCTCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:52:0,52:1,5:0.8966:2,1:21.9:1:28.4:1:0.10345:0:60:25:0.8929:0:1.4 0/1:30:12:1,11:1,17:0.4:1,2:27.8:1:28.5:1:1:1.52:60:24:0.4138:0:1 -10 43597256 . C A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGGGACAGGCTAGCAAAAAG;RSEQ=AAAGAGAATGCCAGAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:3,0:0.25:0,0:23:0:13:0:1:0:60:0:0:0:2 1/1:2:2:1,1:0,0:1:0,2:33.5:1:28:1:1:0:60:4:1:0:1 -10 43597626 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGGCAGCAGGGCTGTGCAG;RSEQ=AGAGGTAAGGAGGTGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:113,3:0.0169:1,2:18:1:30:1:0.06693:32.74837:60:4:0.0172:0:1 0/0:38:0:0,0:36,2:0:2,0:22.1:1:32.5:1:1:0:60:76:1:0:0.1 -10 43597885 . G A 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=17.92408;LSEQ=AGTGGCCAGGCTGTGCCCGC;RSEQ=TATACTTCTCCTTCTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1726:1:1,0:852,869:6e-04:2,0:1:0:26:0:0.49535:0:60:2:6e-04:0:1 0/1:1361:14:9,5:664,680:0.0103:2,2:25.4:1:28.9:1:0.2953:1.84:60:13:0.0096:0:1.1 -10 43598125 . G A 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52629;LSEQ=CACAGTGCCTGCTACTGCTG;RSEQ=TCTTGCTCTGCGAGCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:45,212:0.0115:2,2:20.7:1:25:1:0.44379:2.35:58:2:0.0078:0:1.3 0/0:164:1:1,0:28,135:0.0061:2,0:1:0:23:0:0.17683:0:60:2:0.0063:0:1 -10 43598126 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14708;SOR=Inf;LSEQ=ACAGTGCCTGCTACTGCTGG;RSEQ=CTTGCTCTGCGAGCCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:45,212:0:2,0:25.1:1:29.9:1:1:0:60:127.5:1:0:0.3 0/1:161:2:1,1:27,131:0.0124:2,2:34:1:28.5:1:0.32028:4.78:60:4:0.0127:0:1 -10 43598195 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04016;LSEQ=TCATGCCATCAGTTCATTCA;RSEQ=TATTCCAGAAGTACCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:63:0,63:0,7:0.9:0,1:21.7:1:32.6:1:1:0:60:126:0.9:0:1.1 0/1:39:10:0,10:0,29:0.2564:1,0:25.6:1:32:1:1:0:60:20:0.2632:0:1 -10 43600210 . AGCACAGTCAT A 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=CTGCAAACTGCAAACTCGTA;RSEQ=CGCTGCAAACTGCAAACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:22:21,1:19,1:0.5238:1,1:21.7:1:31.5:1:1:1.10:58.9:44:0.5238:0.0952:0.3 0/0:16:0:0,0:14,2:0:2,0:20.9:1:32.5:1:1:0:60:32:1:0:0.2 -10 43600304 . C T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93469;LSEQ=CCTGGGGCCGCGGCGGTGTG;RSEQ=GCCCCGCTCTGACCGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:2,1:147,24:0.0172:2,2:15.3:1:29.7:1:0.3739:3.03484:51.7:6:0.0176:0:2.3 0/1:62:1:1,0:56,5:0.0161:2,0:10:0:32:0:1:0:60:2:0.0161:0:1 -10 43600324 . GCC G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0;SOR=0.08907;LSEQ=CGCCCCGCTCTGACCGCAGA;RSEQ=CCCTTCCCGAGGAAAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:232:204:162,42:25,3:0.8793:2,2:24.2:1:32.1:1:0.3087:2.15459:60:203:0.8788:0.1509:0.1 0/1:115:45:34,11:60,10:0.3913:2,2:22.5:1:32:1:0.21735:1.92957:59.9:90:0.3913:0.1043:0.1 -10 43600343 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13866;SOR=Inf;LSEQ=AGCCCCCTTCCCGAGGAAAG;RSEQ=GGCTGGCCCGGTCCCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:214,70:0:2,0:26.4:1:31.3:1:1:0:60:34.5:1:0:0.1 0/1:169:2:2,0:125,42:0.0118:2,0:30.5:1:28:1:1:0:60:4:0.0118:0:1.5 -10 43600689 . A G 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07622;LSEQ=CCCAGTGTCTGTCTCCGGCC;RSEQ=CAGTTCGTTTCTCGGTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:628:576:167,409:14,38:0.9172:2,2:25.2:1:31:1:0.87329:1.11:60:40.143:0.9198:0:1.2 0/1:396:181:67,114:67,148:0.4571:2,2:25.5:1:31.1:1:0.24152:1.30:60:362:0.4617:0:1.1 -10 43601325 . T TC 55 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTGGTGGGCAGAGCCA;RSEQ=CCAGGTGCCCAGCGGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:12.8:1:27.6:1:1:0:60:3:0.75:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43601415 . G C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGATGTACACCTGGCCTC;RSEQ=GAGCTCGGCTCTGCCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:18:1:31.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43601749 . T C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17886;LSEQ=CTGTGTGGGACGTGCAGCAT;RSEQ=CTAAGGTCTCTGGTTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:160:149:127,22:11,0:0.9313:0,2:22.6:1:31.6:1:0.3638:0:60:148:0.9308:0:1.1 1/0:109:77:63,14:27,5:0.7064:2,2:23.2:1:30.3:1:1:1.198:60:18.25:0.6952:0:1.1 -10 43601794 . G T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32382;SOR=3.87767;LSEQ=CTGAGGGGCCCATCTCGCCT;RSEQ=CACTGACCAACGCCCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:1:0,1:267,83:0.0028:2,0:1:0:28:0:0.23932:0:60:2:0.0029:0:1 0/1:274:3:1,2:185,86:0.0109:2,2:23.7:1:29.7:1:0.24233:4.27708:60:6:0.0111:0:1.3 -10 43603007 . TCACACACA T 32 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=21.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GACCTTTAACCCCCCATGCC;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:20.5:1:32:1:1:1:60:4:0.5:0:0.5 -10 43604148 . A C 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGCACAGACACCACACA;RSEQ=ATGCATACTACACACTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,0:0.7:0,0:27.6:1:32.7:1:1:0:60:14:0.7778:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43604390 . A T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.24799;LSEQ=TGCGTGTTTGCACCAGTGTG;RSEQ=GTGCAGGGCTGTGTCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:195:176:162,14:17,1:0.9026:1,2:21.9:1:30:1:1:1.46659:60:57.667:0.9058:0:1.1 1/0:115:80:71,9:31,4:0.6957:2,2:26.3:1:29.5:1:1:1.02:60:160:0.7018:0:1.1 -10 43604718 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55708;SOR=0;LSEQ=CTGTCTGGGGAAGATTGAAA;RSEQ=GCCAAGGGACATGGGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:65,228:0.0101:2,2:6.3:1:25.7:1:0.12953:6.96:60:2:0.0068:0:1 0/0:170:0:0,0:39,131:0:2,0:23.9:1:30.4:1:1:0:60:169:1:0:0.1 -10 43604745 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5422;SOR=0;LSEQ=GGACATGGGGGCACAGGGAG;RSEQ=CAGGTGACACTGCCTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:14,159:0.0114:2,2:9:1:29:1:0.16453:11.01:60:4:0.0117:0:1.5 0/0:95:0:0,0:10,85:0:2,0:19.8:1:31.4:1:1:0:60:46.5:1:0:0.1 -10 43604950 . A G 89 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAAAATGCAAGAGCAAT;RSEQ=CTGGGTAAATCTGCATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:19.1:1:31.9:1:1:0:60:14:0.875:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43605246 . TAAA T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAGTAATAAATATTCAT;RSEQ=GAAGATGAGGCATGAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28.5:1:30.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43605860 . T G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTTTTTGCTGTGGTCAC;RSEQ=TGTGGGCCTGGGAGAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:28.7:1:32.3:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43605902 . A G 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGCTCTGGCCCGCCCCC;RSEQ=TCTCGCCATCTGTGGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:28:1:29.3:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43606650 . C T 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=46.76776;LSEQ=AAGGTGTTCCCCTGTGCCCC;RSEQ=CTAGATCGGGAAAGTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1068:2:0,2:596,470:0.0019:2,0:5.5:1:19.5:1:0.19509:0:60:1:0.001:0:5 0/1:903:73:42,31:469,360:0.0808:2,2:26.3:1:29.9:1:0.90255:1.04:60:146:0.0822:0:1.9 -10 43606687 . A G 314 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02407;LSEQ=TGTGTGGAAAACTGCCAGGC;RSEQ=TTCAGTGGCATCAACGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1219:1212:646,566:2,0:0.9943:0,2:25.2:1:30.7:1:0.50187:0:60:70.294:0.9975:0:1.1 1/1:1105:891:457,434:113,99:0.8063:2,2:25.4:1:30.1:1:0.6465:1.08387:60:98:0.807:0:1.2 -10 43607471 . T G 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00041;SOR=0;LSEQ=GGGCAGCTCAGCTGGTGCTG;RSEQ=TCCCTGTCCTTGGGCACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:14:11,3:111,4:0.1085:1,2:27.8:1:31.1:1:0.02778:7.35353:60:28:0.1085:0:1.1 0/0:94:0:0,0:85,9:0:2,0:21.1:1:29.6:1:1:0:60:188:1:0:0.2 -10 43607503 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17387;SOR=Inf;LSEQ=GGGCACTAGCTGGACGCTGG;RSEQ=CCCAGGCCAGCCCCCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:199,35:0:2,0:23.5:1:30.8:1:1:0:60:25:1:0:0.1 0/1:170:2:1,1:139,28:0.0118:2,2:32.5:1:31:0:0.3146:4.89556:60:4:0.012:0:1 -10 43607518 . C T 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32179;SOR=3.93226;LSEQ=GCTGGGCCCAGGCCAGCCCC;RSEQ=TGTGACCCTGCTTGTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:1:1,0:261,53:0.0032:2,0:40:0:16:0:1:0:60:0:0:0:8 0/1:242:3:1,2:184,55:0.0124:2,2:17.3:1:24.3:1:0.13911:6.62346:60:6:0.0125:0:1 -10 43607540 . C T 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=29.12813;LSEQ=GTGACCCTGCTTGTCTGCCA;RSEQ=CTGCAGATGTGGCCGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:460:1:0,1:332,127:0.0022:2,0:1:0:29:0:0.27826:0:60:2:0.0022:0:1 0/1:351:21:12,9:222,108:0.0598:2,2:20.9:1:28:1:0.34746:1.5397:60:20:0.0583:0:1 -10 43607714 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05857;SOR=Inf;LSEQ=GGGAGGCCTGCAGGGGCGAT;RSEQ=GCACCGGTGGAAACGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:121,320:0:2,0:23.5:1:30.9:1:1:0:60:54.125:1:0:0.4 0/1:281:3:2,1:79,199:0.0107:2,2:21.7:1:26.3:1:0.20044:5.00:60:6:0.0109:0:1.3 -10 43607756 . GTGGC ATGG 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGGGCCCTGCCAGCCTGGG;RSEQ=TCTCCCTGCTCCAGGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:184:184:10,174:0,0:1:0,2:21.8:1:31.2:1:1:0:60:183:1:0.2717:1.1 1/0:106:78:5,73:4,24:0.7358:2,2:21:1:30:1:0.23974:2.4098:59.7:156:0.7429:0.2453:1.1 -10 43608522 . G C 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTCAGTTCTATGCATCAA;RSEQ=CTGAGCCTCCTGTGCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1986:0:0,0:979,1006:0:2,0:24.6:1:31.9:1:1:0:60:59.152:0.9995:0:0.1 0/1:1538:36:21,15:744,751:0.0234:2,2:20.2:1:30.6:1:0.31807:1.41:60:35:0.0232:0:1.1 -10 43608653 . G A 205 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=83.86245;LSEQ=CCCAGAAGTCGGCACACACA;RSEQ=ATTTCAGAAGCAGAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2137:2:2,0:1061,1069:9e-04:2,0:1:0:25.5:1:0.24848:0:60:4:9e-04:0:1 0/1:1687:123:61,62:765,795:0.0729:2,2:23.8:1:29.6:1:0.92558:1.02:60:60.5:0.0725:0:1.2 -10 43608807 . G T 198 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=150.59847;LSEQ=AAATGTTAGGAGGGGGCCTG;RSEQ=CTTCACCCATGGCTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1881:1:0,1:910,968:5e-04:2,0:1:0:25:0:1:0:60:2:5e-04:0:1 0/1:1482:110:56,54:688,683:0.0742:2,2:25.2:1:29.2:1:0.92122:1.03:60:54:0.0739:0:1.1 -10 43610119 . G A 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02017;LSEQ=CGGTCAGCTACTCCTCTTCC;RSEQ=GTGCCCGCCGGCCCTCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1334:1223:611,612:56,53:0.9168:2,2:24.2:1:30.3:1:0.84166:1.05831:60:32.972:0.9173:0:1.1 0/1:1009:183:97,86:450,373:0.1814:2,2:23.9:1:30.2:1:0.68262:1.06954:60:60:0.1816:0:1.2 -10 43610366 . G A 327 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00902;LSEQ=ACAGTCTGTGGGGTGGGACT;RSEQ=TGATGAGGTGCCGTTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2280:2272:1132,1140:2,2:0.9965:2,2:24.7:1:29.4:1:1:1.00706:60:77.345:0.9973:0:1.3 1/0:1974:1419:713,706:288,262:0.7188:2,2:23.3:1:28.7:1:0.42157:1.0884:60:58.125:0.7183:0:1.3 -10 43610455 . T C 329 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00617;LSEQ=CAGTGTGGATGGAGGGGCAC;RSEQ=GAAGTCAGAAGGGGGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2003:1996:943,1053:2,1:0.9965:2,2:24.4:1:30.1:1:0.60551:2.23244:60:59.485:0.9975:0:1.2 1/0:1783:1136:543,593:302,339:0.6371:2,2:23.1:1:29.7:1:0.80473:1.03:60:102.273:0.6381:0:1.3 -10 43610558 . C T 333 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00504;LSEQ=ATCCTGGAGCCTCCTTGTCC;RSEQ=GGCCAGGCAGGCCTCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1926:1921:946,975:1,1:0.9974:2,2:24.6:1:30.6:1:1:1.03065:60:75.84:0.9974:0:1.2 1/0:1686:1111:553,558:282,290:0.659:2,2:24.3:1:30.4:1:0.87734:1.02:60:100:0.6607:0:1.2 -10 43610671 . G T 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGAAGTAACAGAGGCTCA;RSEQ=AGCCAAGGGTGTGAGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1594:0:0,0:768,824:0:2,0:25.6:1:31.6:1:1:0:60:78.6:0.9987:0:0.1 0/1:1262:76:36,40:588,598:0.0602:2,2:24.5:1:28.3:1:0.72416:1.09244:60:75:0.0601:0:1.1 -10 43611708 . A G 337 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02004;LSEQ=TGGACACTTCCACTGTAGTC;RSEQ=GAGGTCCTGGGCTGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2260:2245:1138,1107:7,1:0.9934:2,2:24.2:1:30.3:1:0.07012:6.80477:60:82.148:0.9942:0:1.1 1/0:1791:1343:674,669:225,220:0.7499:2,2:24.5:1:29.7:1:0.91293:1.01513:60:88.533:0.749:0:1.2 -10 43611865 . T C 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.94852;LSEQ=GGGGCCTGGCTGTGGGGTCC;RSEQ=GCCCAGGGCAGAGACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1857:156:73,83:875,823:0.084:2,2:24.5:1:29.9:1:0.27696:1.2087:60:38:0.0834:0:1.2 0/1:1479:667:335,332:400,404:0.451:2,2:23.9:1:29.7:1:0.87521:1.02:60:73.111:0.451:0:1.1 -10 43612226 . C T 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGGGGGAGTCTCCGGGG;RSEQ=GGGGGGCGGGTGAGGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:34,186:0:2,0:22.5:1:24.8:1:1:0:60:3.49:1:0:0.6 0/1:145:14:2,12:18,108:0.0966:2,2:22.8:1:27.9:1:1:1:60:6:0.1062:0:2.5 -10 43612609 . C T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCACAAGTTTGGCTCT;RSEQ=GATGGGCACATGCACCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:28.3:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43613741 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1722;SOR=Inf;LSEQ=GAACTTGGGCAAGGCGATGC;RSEQ=GGTCCATCCTGACCTGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:169,46:0:2,0:21.9:1:30:1:1:0:60:106.5:1:0:0.1 0/1:153:2:1,1:119,32:0.0131:2,2:14.5:1:29:1:0.38596:3.67763:60:4:0.0131:0:1.5 -10 43613843 . G T 279 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00557;LSEQ=AACGCCTCCCCGAGTGAGCT;RSEQ=CGAGACCTGCTGTCAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:669:667:362,305:0,0:0.997:0,2:25.1:1:29.8:1:1:0:60:46.643:0.9969:0:1.1 1/0:702:456:233,223:139,107:0.6496:2,2:24:1:29.3:1:0.17856:1.24292:60:90.2:0.6508:0:1.2 -10 43614230 . G A 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGTTCGGGGCTGGGCCC;RSEQ=TGGGGCAGGGAGCTCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:31:1:29.7:1:1:0:60:6:1:0:1.7 1/1:1:1:0,1:0,0:1:0,0:15:0:25:0:1:0:60:2:1:0:1 -10 43614460 . G A 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGCGTGTGTGGGTGTGTGC;RSEQ=AGAGGGATAGGGAACCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:16.7:1:29.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43614885 . C T 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CCCCTTACTCATTGGGTGGC;RSEQ=GGGCCTGGGGACCCTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:186,8:0:1,0:24.6:1:31.2:1:1:0:60:193:1:0:0.1 0/1:132:10:8,2:105,16:0.0758:2,2:23.1:1:29.9:1:0.62741:1.63345:60:20:0.0781:0:1.2 -10 43614902 . C T 74 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02364;SOR=9.47462;LSEQ=GGCCGGGCCTGGGGACCCTG;RSEQ=GGCCTCCCACCCCTGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:1,0:224,40:0.0038:2,0:34:0:27:0:1:0:60:2:0.0038:0:1 0/1:202:7:3,4:147,47:0.0347:2,2:8.9:1:26.7:1:0.07051:4.1333:60:6:0.0309:0:1.6 -10 43614971 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00562;SOR=Inf;LSEQ=GCCCAGGGCCCCCTCTCTCC;RSEQ=CCCCCAGGCCCGCTCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:792:0:0,0:460,328:0:2,0:26.5:1:30.3:1:1:0:60:34.818:0.9961:0:0.2 0/1:580:6:4,2:311,263:0.0103:2,2:26.3:1:27.3:1:0.69287:1.69:60:12:0.0105:0:1 -10 43615094 . C T 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGCAGCCGCAACTCCAG;RSEQ=TCCCTGGACCACCCGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1195:0:0,0:582,613:0:2,0:25.6:1:31.7:1:1:0:60:41.679:1:0:0.2 0/1:924:83:40,43:424,416:0.0898:2,2:22.5:1:28.9:1:0.73066:1.09556:60:40.5:0.089:0:1.2 -10 43615212 . G T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0737;SOR=Inf;LSEQ=AGGTGCGTGCATATGGCTCT;RSEQ=CACCCAGCCAGCCCCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:109,299:0:2,0:23.4:1:31.5:1:1:0:60:44.333:0.995:0:0.2 0/1:297:3:1,2:89,204:0.0101:2,2:19:1:21.7:1:1:1.15:60:2:0.0068:0:3.3 -10 43615223 . G A 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.31385;SOR=4.19745;LSEQ=TATGGCTCTGCACCCAGCCA;RSEQ=CCCCGGCCAGGCCACACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:1:0,1:68,256:0.0031:2,0:48:0:12:0:1:0:60:0:0:0:6 0/1:234:3:1,2:58,173:0.0128:2,2:10.3:1:21.7:1:1:1.49:60:2:0.0087:0:3.3 -10 43615284 . T C 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05065;SOR=Inf;LSEQ=CCCACACCCTGGCCTGCCAC;RSEQ=CCCCCACCATGCCACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:18,107:0:2,0:25.1:1:29:1:1:0:60:16.857:1:0:0.3 0/1:75:3:2,1:11,61:0.04:2,2:16:1:26:1:0.07585:10.54:60:2:0.0282:0:1.3 -10 43615364 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09071;SOR=Inf;LSEQ=TCACCACGCCCCTGCCATGT;RSEQ=ACACCCTGACTCCACCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:52,35:0:2,0:23.5:1:30.9:1:1:0:60:13.5:1:0:1 0/1:38:2:1,1:20,16:0.0526:2,2:15.5:1:28.5:1:1:1.24262:60:4:0.0541:0:1.5 -10 43615382 . C T 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00346;LSEQ=GTCACACCCTGACTCCACCA;RSEQ=GCCCCTGCCATGCCACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:77:57,20:3,1:0.9506:2,2:28.3:1:30.3:1:1:1.05196:60:14.4:0.9474:0:1.2 0/1:37:2:1,1:24,11:0.0541:2,2:34.5:1:31:1:1:2.13205:60:4:0.0556:0:1.5 -10 43615386 . C T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=4.000;MSILEN=1;SSF=0.00229;SOR=Inf;LSEQ=CACCCTGACTCCACCACGCC;RSEQ=CTGCCATGCCACACCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:65,18:0:2,0:27.9:1:31.1:1:1:0:60:40.5:1:0:1.1 0/1:37:5:4,1:23,9:0.1351:2,2:29.6:1:27.6:1:1:1.55:60:4:0.1143:0:1.2 -10 43615505 . G A 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.60707;LSEQ=CTGCCTGGCCATGGCCTGAC;RSEQ=ACTCGTGCTATTTTTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:34:23,11:263,151:0.0757:2,2:24.1:1:29.6:1:0.71268:1.20:60:33:0.0753:0:1.1 0/1:386:68:48,20:194,123:0.1762:2,2:22.2:1:29:1:0.16746:1.52:60:21.667:0.1715:0:1.2 -10 43615633 . C G 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03112;LSEQ=GATGTTTATGAAGAGGATTC;RSEQ=TACGTGAAGAGGAGCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:562:511:207,304:21,29:0.9093:2,2:24.1:1:30.7:1:0.88056:1.06335:60:55.778:0.9078:0:1.2 0/1:591:140:58,82:186,264:0.2369:2,2:27.2:1:30.3:1:1:1.00:60:280:0.2385:0:1.1 -10 43615654 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28671;SOR=3.01821;LSEQ=TACGTGAAGAGGAGCCAGGT;RSEQ=CCCAGTCCCGGGGATGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:2:2,0:143,275:0.0048:2,0:4:1:19:1:0.11865:0:60:1:0.0024:0:3 0/1:421:6:4,2:152,263:0.0143:2,2:15.2:1:26.7:1:0.20025:3.45:60:12:0.0144:0:1.5 -10 43617517 . C A 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.30756;SOR=4.51757;LSEQ=GTTACAGAAACACCCTTATA;RSEQ=ATGTAGTGGGGCCACGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:1:1,0:105,313:0.0024:2,0:1:0:27:0:0.25298:0:60:2:0.0024:0:1 0/1:280:3:2,1:62,215:0.0107:2,2:9.7:1:23.7:1:0.13182:6.87:60:2:0.0072:0:1.3 -10 43618751 . G A 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGGCCTGCATTCTCACC;RSEQ=CTTTAAGTGTGAGAATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:13.2:1:28.6:1:1:0:60:10:0.8333:0:2.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43620134 . C T 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09804;SOR=0;LSEQ=GACCTGAGCACAGTGGCCCA;RSEQ=GGGCTGGGATCCTGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:11,1:4,0:0.75:0,2:36.1:1:32.4:1:1:0:60:24:0.75:0:1.1 0/0:2:0:0,0:2,0:0:0,0:32.5:1:29.5:1:1:0:60:4:1:0:0 -10 43620316 . T C 48 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12731;SOR=0;LSEQ=TTGGATCATATTGGCCTGTC;RSEQ=GCTCTTCCCACCAGGTACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:4:1,3:246,105:0.0113:2,2:16.3:1:24.3:1:0.08574:6.98591:60:3:0.0086:0:2 0/0:310:0:0,0:212,97:0:2,0:23:1:30.2:1:1:0:60:76.25:1:0:0.2 -10 43620497 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12677;SOR=Inf;LSEQ=GACTCCAGCCTCACCCCAGG;RSEQ=CAGTAGTTTTAGCCCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:17,172:0:2,0:22.7:1:32:1:1:0:60:46.25:1:0:0.1 0/1:105:2:1,1:15,88:0.019:2,2:26.5:1:30.5:1:0.28278:5.71:60:4:0.0192:0:1 -10 43620551 . G A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=12.37447;LSEQ=GGCCACAGTGGGATTGTGCA;RSEQ=AGAGAGAGAGTCATGCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:7:0,7:0,60:0.1029:1,0:18.9:1:30.3:1:1:0:60:14:0.1045:0:1 1/0:37:22:1,21:0,15:0.5946:1,1:17.5:1:29.8:1:1:0:60:44:0.5946:0:1.2 -10 43621712 . A G 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAGATGAGGCGTCCCCCA;RSEQ=GGCTGCCCTCCAGGCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:27.3:1:32.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 43621996 . G T 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12449;SOR=0;LSEQ=TAGTTGTGGCACATGGCTTG;RSEQ=AGTGACCGGCCATCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:4:2,2:224,94:0.0124:2,2:25.3:1:27.3:1:0.58546:2.37576:60:8:0.0126:0:1 0/0:303:0:0,0:197,106:0:2,0:25.4:1:31:1:1:0:60:59.6:1:0:0.2 -10 43622217 . T C 289 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTAGCACCGCTGTCCCCT;RSEQ=TGCACTATCCTTCCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:584:584:201,383:0,0:1:0,2:24.1:1:31.5:1:1:0:60:96.333:1:0:1.1 1/0:631:489:184,305:56,84:0.775:2,2:24.2:1:31.4:1:0.62275:1.10489:60:488:0.7783:0:1.1 -10 43622368 . T A 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00031;SOR=0;LSEQ=ACTATGTTTTTCTAAAAGGA;RSEQ=GTGAAAATAAGTGTAATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:2,46:0,0:1:0,1:24:1:31.1:1:1:0:60:96:1:0:1 1/0:14:9:0,9:1,4:0.6429:2,0:21.9:1:30.8:1:0.35714:0:60:18:0.6429:0:1 -10 43623474 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51807;SOR=0;LSEQ=CACGAGTTTGGTTTGAACAT;RSEQ=AAAGGGAGTTTTGCCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:95,3:0.02:1,2:15:1:27.5:1:0.07879:27.56815:60:4:0.0204:0:1 0/0:66:0:0,0:64,2:0:1,0:22.8:1:31.2:1:1:0:60:65:1:0:0.1 -10 43623479 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5641;SOR=3.06441;LSEQ=GTTTGGTTTGAACATCAAAG;RSEQ=GAGTTTTGCCAAGGCCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:1,0:106,5:0.0089:1,0:30:0:31:0:1:0:60:2:0.0091:0:1 0/1:74:2:1,1:70,2:0.027:1,2:19.5:1:28:1:0.07997:28.75679:60:4:0.027:0:1 -10 43623783 . G A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.5233;LSEQ=CTGAGAATGGAAAGTCTACC;RSEQ=GCCCTTTCTTTGTGAACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:26,138:0.012:2,2:18:1:31:1:0.29967:5.23:60:4:0.0121:0:1 0/0:158:1:0,1:18,139:0.0063:2,0:15:0:33:0:1:0:60:2:0.0064:0:1 -10 43623812 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45063;SOR=0.6434;LSEQ=TTTGTGAACGTCACATTGGC;RSEQ=GAGCCGTGTTCAGTTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:11:0,11:3,77:0.1209:1,0:23.3:1:29.8:1:1:0:60:22:0.1222:0:1 0/1:74:6:0,6:2,65:0.0811:1,0:23.2:1:29.8:1:1:0:60:12:0.0811:0:1 -10 43624105 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGGATTTTTCTAGTTGCC;RSEQ=CCAAACAAGGCAAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:27.3:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 44126388 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51825;SOR=Inf;LSEQ=ACCACCGTCTTCCAGTAATT;RSEQ=GACAAAATGACAAACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:52,58:0:2,0:27.9:1:30.2:1:1:0:60:109:1:0:0.1 0/1:165:2:1,1:80,83:0.0121:2,2:18.5:1:28.5:1:1:1.04:60:4:0.0124:0:1 -10 44126421 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18309;SOR=0;LSEQ=AACACAAAGGGAAAGAGGAG;RSEQ=GGCTCCTGGTAGATGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:34,55:0.022:2,2:22.5:1:29:1:1:1.61:60:4:0.022:0:1 0/0:121:0:0,0:55,66:0:2,0:21.5:1:29.6:1:1:0:60:39.333:1:0:0.1 -10 44126599 . G C 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAGAGTCTACAGTGTTAC;RSEQ=CAGCAGGCCGTCGGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:21,32:0:2,0:27.1:1:30.7:1:1:0:60:52:1:0:0.1 1/0:42:22:8,14:7,13:0.5238:2,2:24:1:30.4:1:1:1.06:59.1:44:0.5366:0:1.2 -10 44237687 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50006;SOR=0;LSEQ=TAATGCATGTTGTCTTTTTA;RSEQ=AACAAATTCATGACCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:88,26:0.0171:2,2:16:1:27:1:0.41289:3.34011:60:4:0.0175:0:2 0/0:102:0:0,0:68,34:0:2,0:19.2:1:30.8:1:1:0:60:204:1:0:0 -10 44237699 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24015;SOR=Inf;LSEQ=TCTTTTTACAACAAATTCAT;RSEQ=ACCATCAGAAGATATCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:100,41:0:2,0:21.8:1:31.4:1:1:0:60:69.5:1:0:0.1 0/1:136:2:1,1:81,53:0.0147:2,2:7:0:31:1:1:1.52336:60:4:0.0148:0:1 -10 44728442 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04784;SOR=Inf;LSEQ=GGATGGGGTTTTTGTGGGGG;RSEQ=CTTTGTTGTTGTTATTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,10:0:2,0:29.9:1:32.1:1:1:0:60:40:1:0:0.2 0/1:21:5:3,2:8,8:0.2381:2,2:21.8:1:27.4:1:1:1.47:60:10:0.2381:0:1.4 -10 44728592 . G A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09023;SOR=Inf;LSEQ=GATTCGCTCCTGTGCCTGGA;RSEQ=ATGTCATTCAAGGAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:27.2:1:30.7:1:1:0:60:20:1:0:0 0/1:11:4:2,2:1,6:0.3636:2,2:34.3:1:30:1:0.49091:4.95:60:8:0.3636:0:1.8 -10 44728597 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16374;SOR=Inf;LSEQ=GCTCCTGTGCCTGGAGATGT;RSEQ=ATTCAAGGAGGCTGGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:23.9:1:30:1:1:0:60:22:1:0:0 0/1:8:2:1,1:1,5:0.25:2,2:40.5:1:27.5:1:0.46429:3.87:60:4:0.25:0:2 -10 44728797 . T C 48 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=ATTTTGTCCCTTGGTGGTGA;RSEQ=GGTGGTGTGCTTCACTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:10:1:31:1:1:0:60:6:1:0:0 1/0:5:3:1,2:1,1:0.6:2,2:26.3:1:30.3:1:1:1.7321:60:6:0.6:0:1 -10 44728977 . G T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=TCTGGCTGGAGTTATTGGAG;RSEQ=TCCTGCAGGGAAGCCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:22:1:30.8:1:1:0:60:10:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:35:0:30:1:1:0:60:4:1:0:1 -10 44729300 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=Inf;LSEQ=TGGTCGCCCCTCCCCCTGGG;RSEQ=GTTCAGTAGGCTTAAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:33.8:1:31:1:1:0:60:16:1:0:0.1 0/1:10:2:1,1:4,4:0.2:2,2:30:0:32:1:1:1:60:4:0.25:0:2.5 -10 44729307 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49474;SOR=Inf;LSEQ=CCCTCCCCCTGGGAGTTCAG;RSEQ=AGGCTTAAGCAGATTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:35.3:1:29.3:1:1:0:60:16:1:0:0.1 0/1:12:2:1,1:5,5:0.1667:2,2:37:0:32:0:1:1:60:4:0.1667:0:2.5 -10 44729599 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12606;SOR=Inf;LSEQ=AACCTGGATACGCTGGTTGC;RSEQ=GGTGAAGGACTCACCCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:30.9:1:30.5:1:1:0:60:28:1:0:0.2 0/1:20:4:2,2:6,10:0.2:2,2:21.8:1:26.5:1:1:1.62:60:3:0.1579:0:1.5 -10 44729641 . A ATTT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.49275;SOR=Inf;LSEQ=TTATGGTTTTTTTTTTCATT;RSEQ=TTTATTATTATTATTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:24.5:1:30.4:1:1:0:60:20:1:0:0.1 0/1:14:2:0,2:5,7:0.1429:2,0:48.5:1:31.8:1:0.50549:0:60:4:0.1429:0:0 -10 44729642 . T TTTA 46 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=38;MSI=13.000;MSILEN=3;SSF=0.04743;SOR=0;LSEQ=TATGGTTTTTTTTTTCATTA;RSEQ=TTATTATTATTATTATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:2,3:0.3333:2,2:14.7:1:29.6:1:1:1.28664:60:6:0.3333:0.1111:0.3 0/0:14:0:0,0:5,9:0:2,0:29.2:1:30.7:1:1:0:60:28:1:0:0.4 -10 45071312 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAAGGGACGGCAGCTTC;RSEQ=CCCCAGGGCAGGCCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 45072488 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48649;SOR=Inf;LSEQ=GAGTGAAACAGTGCTGAGGG;RSEQ=CCCAGGCCCAGGGACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:23.3:1:31.1:1:1:0:60:38:1:0:0.4 0/1:19:2:1,1:11,6:0.1053:2,2:10.5:1:29:1:1:1.77272:60:4:0.1053:0:1 -10 45072521 . G A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01727;SOR=0.21012;LSEQ=GACAGGCAGCTCTGTGGCTC;RSEQ=CACCCTCATCCGCTGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:4,7:7,7:0.44:2,2:28.5:1:30.3:1:0.68875:1.71101:60:22:0.44:0:1.1 0/1:29:4:1,3:15,10:0.1379:2,2:27:1:30:1:0.2994:4.27461:60:8:0.1379:0:1 -10 45072584 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50202;SOR=Inf;LSEQ=TCCCACCCTTTTTCTGATCC;RSEQ=CATGAATTTGTGAGCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:18.2:1:31.1:1:1:0:60:26:1:0:0.5 0/1:19:2:1,1:6,11:0.1053:2,2:25.5:1:29:1:1:1.77:60:4:0.1053:0:1 -10 45385828 . A C 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19156;LSEQ=CCCTGGGGCCCCAGCAGCCG;RSEQ=TAGGGTGGTAGCCAGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:15:15,0:6,0:0.7143:0,1:21.5:1:32.9:1:1:0:60:30:0.7143:0:1.1 1/0:4:3:3,0:1,0:0.75:0,0:22.7:1:33:1:1:0:60:6:0.75:0:1 -10 45385937 . A G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=3.13934;LSEQ=AGGTTTTAAGCCTGAGATAC;RSEQ=GGCAGATGCCAATGGTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:51:42,9:43,10:0.4904:2,2:22.3:1:29.7:1:1:1.08:60:102:0.4904:0:1.1 1/0:105:79:61,18:21,4:0.7524:2,2:22.9:1:29.7:1:0.58155:1.54311:60:158:0.7524:0:1 -10 45386046 . T C 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68952;SOR=1.07812;LSEQ=TGTTCTGAAGCAGAAGAAAC;RSEQ=GATGGTGCCCATGAACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:147:73,74:75,76:0.4933:2,2:26:1:30.1:1:1:1.00036:60:72.5:0.4899:0:1.1 1/0:330:169:79,90:81,80:0.5121:2,2:24.7:1:29.3:1:0.58181:1.15298:60:83.5:0.5107:0:1.1 -10 45386322 . G T 62 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=GGTGTAACTGGGTCCACCAG;RSEQ=GCAGCAATTGCAGGTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:33:0:32:0:1:0:60:2:1:0:0 1/1:4:4:1,3:0,0:1:0,2:22.5:1:31.3:1:1:0:60:8:1:0:1.8 -10 45386352 . C A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GCAGGTTCAGCAAGGAGCCT;RSEQ=TGGATCTGTGGCCAGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:3:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:27.5:1:1:0:60:4:1:0:2.5 -10 46914512 . A C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.78881;SOR=0.85249;LSEQ=TATGTTGGTTGGAAATAAGA;RSEQ=AGACCTGCATATGGAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:7:7,0:92,0:0.0707:1,0:26.3:1:33.3:1:1:0:38.3:14:0.0729:0:1 0/1:115:7:7,0:108,0:0.0609:1,0:27.9:1:31.4:1:1:0:39:14:0.0609:0:1 -10 46914641 . T C 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.44165;SOR=0.86612;LSEQ=TGATGTTTTTCGAAGGATGA;RSEQ=TTTGGAGGCAGAAAAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:912:48:24,24:490,372:0.0526:2,2:25.5:1:31.5:1:0.37216:1.31679:49.8:47:0.0526:0:1.1 0/1:1612:74:37,37:846,688:0.0459:2,2:27.5:1:31.1:1:0.40408:1.22949:47.4:73:0.0461:0:1.1 -10 46914695 . C T 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=27.26241;LSEQ=ACAAGGCAAGTCTTCATGCT;RSEQ=GGTGATGTGATTCTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1071:1:0,1:496,573:9e-04:2,0:32:0:17:0:1:0:39:0:0:0:1 0/1:1609:40:16,24:700,868:0.0249:2,2:26.8:1:29.5:1:0.63042:1.20954:46.4:80:0.0252:0:1.1 -10 46915135 . CA C 52 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAAACAAAAAAACAAAA;RSEQ=AAAAAAAAGAGTAAACCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:31.7:1:33:1:1:0:24:6:0.75:0:0 1/1:1:1:0,1:0,0:1:0,0:37:0:31:0:1:0:51:2:1:0:0 -10 46915386 . A T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTGTTACCCAGGCTGG;RSEQ=GTGCAGTGGTCTGATCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18:0:31.5:1:1:0:32:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 47154319 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=57.62619;LSEQ=TGGGATTCTTGCTCAAATTG;RSEQ=ATTTTACAAGAAAGTACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:5,2:12,6:0.28:2,2:22.7:1:30.3:1:1:1.24:38:14:0.3043:0:1 1/1:26:25:15,10:1,0:0.9615:0,2:19.1:1:28.4:1:1:0:36.6:24:0.96:0:1.1 -10 47155056 . CTTTTTTT C 30 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTCTTCTTTCTTTTTT;RSEQ=TTTTTTTTTTGACAGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:30.5:1:1:0:54:4:1:0.5:0.5 -10 47396136 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23846;SOR=0;LSEQ=TGCTCTGTATGCCGCTCTCT;RSEQ=CCGGCGCGGCCGCCGCCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:23,7:0.0625:2,2:24:1:28.5:1:0.44355:3.1396:25:4:0.0625:0:1 0/0:33:0:0,0:23,10:0:2,0:25:1:29.8:1:1:0:25.3:66:1:0:0 -10 47396650 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27343;SOR=0;LSEQ=TTTGGCAGAATCTTGGAATG;RSEQ=AGCTTTTTTGGAATCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:258,21:0.0106:2,2:21.3:1:30:1:0.21697:6.06364:35.3:6:0.0108:0:1 0/0:195:0:0,0:178,17:0:2,0:23.6:1:32.1:1:1:0:39.8:96.5:1:0:0.1 -10 49842541 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16234;SOR=Inf;LSEQ=GAAACCATTGTAGGAAACTG;RSEQ=GTCTCTAAGAAGAGCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:115,28:0:2,0:21:1:31:1:1:0:60:70.5:1:0:0.1 0/1:97:2:1,1:82,13:0.0206:2,2:21.5:1:28:1:0.26912:6.11521:60:4:0.0211:0:1.5 -10 49842556 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5005;SOR=0;LSEQ=AACTGGGTCTCTAAGAAGAG;RSEQ=CGCTGACTCAGCCCTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:126,48:0.0114:2,2:34.5:1:30.5:1:0.48045:2.60837:60:4:0.0115:0:1.5 0/0:155:0:0,0:113,42:0:2,0:21.2:1:31.4:1:1:0:60:50.667:1:0:0.1 -10 49842601 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12248;SOR=Inf;LSEQ=CTGTGGCTGGGGGTGGGTGA;RSEQ=CCTGGGCTTCCGCTTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:164,134:0:2,0:26.2:1:31.4:1:1:0:60:28.8:1:0:0.5 0/1:295:3:1,2:157,135:0.0102:2,2:14:1:28:1:0.5988:2.31946:60:6:0.0103:0:1.7 -10 49842643 . C T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12057;SOR=0;LSEQ=CTAGAGGGTAGTGTGGCTGG;RSEQ=AGGGCATCTGTCTAGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:1,2:119,168:0.0103:2,2:13.7:1:26:1:1:1.41503:60:6:0.0106:0:2 0/0:296:0:0,0:131,165:0:2,0:25:1:31.8:1:1:0:60:295:1:0:0.5 -10 49842655 . C T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34347;LSEQ=GTGGCTGGCAGGGCATCTGT;RSEQ=TAGACACTCTCTGAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:271:186:75,111:31,52:0.6863:2,2:25.1:1:29.7:1:0.68665:1.13:60:36.2:0.683:0:1.1 0/1:252:108:44,64:60,84:0.4286:2,2:22.9:1:29.8:1:0.89784:1.03882:60:53:0.4274:0:1.2 -10 49843065 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGAATGGGAAAAAATAC;RSEQ=TGTATGTTGTGAAAGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:31.5:1:1:0:60:4:1:0:1.5 -10 49977719 . C G 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.35185;SOR=1.17477;LSEQ=CATATCTTGGAATGCTGAAC;RSEQ=CAACACCCATGCCTCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:113:59,54:90,93:0.3818:2,2:28.2:1:30.8:1:0.63375:1.13:60:55.5:0.3788:0:1.1 0/1:283:119:65,54:90,74:0.4205:2,2:25.9:1:30.3:1:1:1.01036:60:58.5:0.4164:0:1.2 -10 49977746 . T C 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00766;SOR=0.63335;LSEQ=CCATGCCTCTTTAGGGGACC;RSEQ=ATTGCTCCAGGACCCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:292:173:80,93:56,63:0.5925:2,2:24.5:1:31.5:1:0.90548:1.03323:60:85.5:0.5917:0:1.1 0/1:288:138:71,67:70,79:0.4792:2,2:26.7:1:30.6:1:0.4795:1.20:60:68:0.4789:0:1.1 -10 49977805 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50042;SOR=Inf;LSEQ=CATATTAATCTGGACCAAGA;RSEQ=AGAAAGTGGGGAACAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:48,100:0:2,0:23.6:1:31.4:1:1:0:60:296:1:0:0.5 0/1:168:2:1,1:54,112:0.0119:2,2:26:1:29.5:1:0.5489:2.06:60:4:0.0119:0:1.5 -10 49977882 . G A 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02325;LSEQ=AGCGTGGACTTAAAGGCTAG;RSEQ=TCGTTAAGTGAAGAATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:27:0,27:0,16:0.6279:1,1:28:1:31.3:1:1:0:60:54:0.6279:0:1 1/0:30:19:1,18:0,11:0.6333:0,1:21.1:1:29.2:1:1:0:60:18:0.6207:0:1.1 -10 49977973 . C A 59 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GGGCCCAGCCCGCTGGCCAA;RSEQ=CTGGTGACCCTGTGCTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:36:1:29.5:1:1:0:60:8:0.6667:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:35.5:1:27:1:1:0:60:4:0.6667:0:1 -10 52388952 . G A 85 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAAGGTACAGTATTTGC;RSEQ=TATAACCTCCCCATATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:21.4:1:30.6:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 52389217 . T A 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50027;SOR=0;LSEQ=ACAAAGTGAAAATGAGGAAT;RSEQ=CTCATTCTGTAAATGAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:156,21:0.0112:2,2:23:0:28:1:0.23131:7.27962:60:4:0.0113:0:1.5 0/0:159:0:0,0:131,28:0:2,0:19.6:1:29.4:1:1:0:60:38.75:1:0:0.1 -10 52389659 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09488;LSEQ=TCTGAATCACCTGCCTCAGA;RSEQ=CTGCAGCAAAGTTTCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:173:83,90:66,76:0.5492:2,2:22.9:1:29.7:1:0.82113:1.06:60:56.667:0.5502:0:1.1 0/1:281:29:15,14:124,127:0.1032:2,2:19.4:1:29.7:1:0.84665:1.10:60:58:0.1074:0:1.2 -10 52389662 . G A 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6706;SOR=1.68736;LSEQ=GAATCACCTGCCTCAGAGCT;RSEQ=CAGCAAAGTTTCTGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:2:2,0:146,166:0.0063:2,0:12:1:18.5:1:0.22136:0:60:1:0.0032:0:3.5 0/1:281:3:3,0:138,140:0.0107:2,0:8:1:24.3:1:0.24733:0:60:6:0.0109:0:1.3 -10 52390008 . C T 45 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13511;SOR=0;LSEQ=TCATCGCCAGTTTGAAATGG;RSEQ=GATAGAGCAGGTAACACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:4:1,3:149,160:0.0127:2,2:9:1:22.5:1:0.62389:2.78523:60:3:0.0097:0:1 0/0:245:0:0,0:121,124:0:2,0:25:1:31:1:1:0:60:244:1:0:0.1 -10 52390506 . A T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09543;LSEQ=AAATCTGGATCCTTAATAAC;RSEQ=TCACTCAATTCATCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:348:203:111,92:76,69:0.5833:2,2:25.1:1:30.7:1:0.74368:1.10:60:66.667:0.5831:0:1.1 0/1:383:45:26,19:202,135:0.1175:2,2:25:1:30.4:1:0.87168:1.09319:60:90:0.1194:0:1 -10 52390836 . A G 264 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01591;LSEQ=CCTTGCTCGCTTCCGTATCC;RSEQ=TATTCTACAATTCTTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:356:354:134,220:0,1:0.9944:0,2:25.2:1:31.2:1:1:0:60:353:0.9972:0:1.1 1/0:384:283:111,172:50,51:0.737:2,2:25.6:1:30.3:1:0.07879:1.51743:60:46.167:0.7387:0:1.1 -10 52390900 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25128;SOR=Inf;LSEQ=GCTTGGCATAGTAGTCTAGG;RSEQ=CGACCCCTCGAAGTAGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:108,132:0:2,0:24.4:1:31.5:1:1:0:60:79:1:0:0.5 0/1:272:3:1,2:130,139:0.011:2,2:19.7:1:26.3:1:1:1.86637:60:6:0.0114:0:1 -10 52390994 . C A 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60706;SOR=0.45326;LSEQ=GGCTCCTGGCTGAGGCTGAA;RSEQ=GCCGGGGTCAGCATCGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:50,111:0.0123:2,2:10:1:32:0:0.5292:2.21:60:4:0.0126:0:1 0/0:179:1:1,0:65,113:0.0056:2,0:1:0:23:0:0.36872:0:60:2:0.0058:0:1 -10 52391028 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24634;SOR=0;LSEQ=TCGCGGCACCAGACGCAGGG;RSEQ=CCAGCGCGGCTCGCCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:13,87:0.0196:2,2:22.5:1:29:1:0.25684:6.49:60:4:0.0202:0:1 0/0:103:0:0,0:24,79:0:2,0:24.6:1:31.5:1:1:0:60:206:1:0:0.1 -10 52391216 . A G 72 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATCAGCCCCGCCGACATG;RSEQ=CGAAACTCCGTCTCTACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:19.8:1:31.4:1:1:0:60:10:1:0:1 1/1:1:1:0,1:0,0:1:0,0:3:0:28:0:1:0:60:2:1:0:1 -10 52833765 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACGTCGCTAGGATCGTAGC;RSEQ=CAACATTCTCCAGGCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:16:1:31:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 52834254 . A C 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06797;SOR=Inf;LSEQ=AGGAAGCTTTGGCACTCGGG;RSEQ=GGCAGCGGCGACTTTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:59,27:0:2,0:23.9:1:29.6:1:1:0:60:42:1:0:0.1 0/1:109:5:2,3:60,43:0.0459:2,2:25.8:1:31.2:1:0.64884:2.07855:60:10:0.0472:0:1 -10 52834260 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.56421;LSEQ=CTTTGGCACTCGGGAGGCAG;RSEQ=GGCGACTTTGGGGAAAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:1:1,0:58,29:0.0114:2,0:27:0:12:0:1:0:60:0:0:0:3 0/1:113:2:1,1:62,49:0.0177:2,2:19:1:27.5:1:1:1.26264:60:4:0.018:0:1 -10 52834329 . GC G 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.5862;LSEQ=CGGAGCAGCGGCAGGAAGGA;RSEQ=CCCCGGCAGCCCGGAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:64,60:0.0159:2,2:35.5:1:32.5:1:1:1.06615:60:4:0.0164:0:0.5 0/0:107:1:0,1:54,51:0.0093:2,0:20:0:34:0:0.49057:0:60:2:0.0095:0:0 -10 52834362 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51092;SOR=0;LSEQ=CGGAGGAGCATGGGCACCTT;RSEQ=CGGGATTTACAGTACGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:65,66:0.015:2,2:14:0:31.5:1:1:1.02:60:4:0.015:0:1 0/0:96:0:0,0:50,46:0:2,0:25.4:1:31.6:1:1:0:60:47:1:0:0.1 -10 52834391 . A T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62634;LSEQ=ACAGTACGCGCTCCAGGAGA;RSEQ=GATCGAGGAGCTGAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:57,58:0.0171:2,2:32.5:1:29.5:1:1:1.02:60:4:0.0171:0:1 0/1:93:1:0,1:45,47:0.0108:2,0:1:0:26:0:1:0:60:2:0.011:0:1 -10 52834437 . G T 28 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12184;LSEQ=GCTCTCATCGACGAGCTGGA;RSEQ=CTGGAGTTGGATCAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:2,0:52,57:0.0179:2,0:35.5:1:23.5:1:0.2344:0:42.5:1:0.0091:0:3.5 0/1:100:2:1,1:47,51:0.02:2,2:47:0:28.5:1:1:1.08:60:4:0.0202:0:1 -10 52834447 . G T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25151;SOR=0;LSEQ=ACGAGCTGGAGCTGGAGTTG;RSEQ=ATCAGAAGGACGAACTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:3:1,2:53,55:0.027:2,2:6:1:26:1:1:1.91633:60:6:0.0278:0:1 0/0:94:0:0,0:44,50:0:2,0:26.4:1:30.9:1:1:0:60:93:1:0:0.1 -10 52834529 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12331;SOR=Inf;LSEQ=CCGACCAGCCACCCAGCAGG;RSEQ=GCAGAAGCAGAGCGCGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:53,44:0:2,0:24.5:1:30.9:1:1:0:60:96:1:0:0.2 0/1:53:2:1,1:21,30:0.0377:2,2:18.5:1:28.5:1:1:1.42:60:4:0.0377:0:1 -10 52834585 . A T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52614;SOR=0;LSEQ=CGCGCACCAAGCGGCAGGCG;RSEQ=TCTCCGCCGAGCCCACCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:50,43:0.0211:2,2:14:0:28:1:1:1.16094:60:4:0.0213:0:1 0/0:58:0:0,0:26,32:0:2,0:22.1:1:29.7:1:1:0:60:57:1:0:0.1 -10 52834616 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20617;SOR=Inf;LSEQ=GCCCACCGCCTTCGACATCC;RSEQ=GGATCTCAGCCATGTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:63,41:0:2,0:24.7:1:30.3:1:1:0:60:51:1:0:0.2 0/1:87:2:1,1:51,34:0.023:2,2:5:1:29:1:1:1.4928:60:4:0.023:0:1 -10 52834639 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49793;SOR=Inf;LSEQ=ATCTCAGCCATGTGACCCTG;RSEQ=CCTTCTACCCCAAGAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:71,47:0:2,0:23.8:1:31.2:1:1:0:60:58:1:0:0.2 0/1:120:2:1,1:77,41:0.0167:2,2:9:1:27:1:1:1.86764:60:4:0.0168:0:1 -10 52834679 . G A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24746;SOR=0;LSEQ=ACAGTAAGCAGGGGTGACGC;RSEQ=CCGGGTCCATGTGGCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:3:1,2:71,72:0.0204:2,2:25:1:27.3:1:1:1.9634:60:6:0.0208:0:2.7 0/0:145:0:0,0:89,55:0:2,0:25.3:1:30.3:1:1:0:60:288:0.9931:0:0.2 -10 52834694 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4986;SOR=0;LSEQ=GACGCGCCGGGTCCATGTGG;RSEQ=GCCCTGGCGATGGGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:81,85:0.0119:2,2:19.5:1:28:1:1:1.05:60:4:0.0123:0:1 0/0:163:0:0,0:94,69:0:2,0:23.1:1:30.1:1:1:0:60:162:1:0:0.1 -10 52834707 . G A 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.61989;SOR=0.48734;LSEQ=CATGTGGCGCCCTGGCGATG;RSEQ=GGAGCTGCGGGTCTCTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:83,95:0.011:2,2:21:1:32.5:1:1:1.14:60:4:0.0114:0:1 0/0:185:1:1,0:104,79:0.0054:2,0:2:0:23:0:1:0:60:2:0.0055:0:1 -10 52834721 . T C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.87329;LSEQ=GCGATGGGGAGCTGCGGGTC;RSEQ=CTGTATTGTCTGTCGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:1:1,0:83,98:0.0055:2,0:27:0:8:0:0.46154:0:60:0:0:0:3 0/1:196:2:1,1:103,91:0.0102:2,2:34.5:1:29:1:1:1.13115:60:4:0.0106:0:1 -10 52834808 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24894;SOR=Inf;LSEQ=ATTTTAACGGGCACTTCTTG;RSEQ=GGGGCTGTGCACGTTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:101,110:0:2,0:25.3:1:30.3:1:1:0:60:34.167:1:0:0.2 0/1:224:3:1,2:108,112:0.0134:2,2:30:1:29.7:1:1:1.92311:60:6:0.0136:0:1 -10 52834856 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4998;SOR=Inf;LSEQ=ACTCACTGCACATACGTTGC;RSEQ=TTCGTGTCTTTGTCAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:59,99:0:2,0:26.3:1:31.8:1:1:0:60:157:1:0:0.2 0/1:175:2:1,1:67,106:0.0114:2,2:34:1:29.5:1:1:1.58:60:4:0.0114:0:1 -10 52834870 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=CGTTGCCTTCGTGTCTTTGT;RSEQ=AGATGTCAAGGTATTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:47,88:0:2,0:23.5:1:31.9:1:1:0:60:134:1:0:0.2 0/1:148:2:1,1:49,97:0.0135:2,2:22.5:1:28.5:1:1:1.97:60:4:0.0139:0:1 -10 52834872 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2187;SOR=0;LSEQ=TTGCCTTCGTGTCTTTGTCA;RSEQ=ATGTCAAGGTATTATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:40,85:0.0157:2,2:24:1:29:1:0.54318:2.11:60:4:0.016:0:1 0/0:144:0:0,0:48,96:0:2,0:25.8:1:31.5:1:1:0:60:288:1:0:0.1 -10 53238115 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10966;LSEQ=TCTTTAATTGCCTTAAGGAA;RSEQ=AATCTGAATCTATAATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:383:344:153,191:13,26:0.8982:2,2:24.9:1:30:1:0.23278:1.60:60:171:0.9:0:1.1 0/1:383:188:86,102:80,115:0.4909:2,2:23:1:29.3:1:0.35571:1.21:60:93:0.4908:0:1.1 -10 53238190 . A C 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAATTTTTATAAGAATGCA;RSEQ=AAACTGGCCCCCTTGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:36,129:0:2,0:25.4:1:30:1:1:0:60:81.5:1:0:0.4 0/1:151:23:7,16:39,89:0.1523:2,2:25.9:1:31.7:1:1:1.00159:60:46:0.1523:0:1.5 -10 53238191 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23034;SOR=Inf;LSEQ=TAATTTTTATAAGAATGCAA;RSEQ=AACTGGCCCCCTTGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:35,127:0:2,0:25.5:1:29.9:1:1:0:60:53:1:0:0.4 0/1:150:2:1,1:45,103:0.0133:2,2:35:1:30.5:1:0.52072:2.27:60:4:0.0134:0:1.5 -10 53238223 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52917;SOR=0;LSEQ=TTGATGATTCAAACTACTTC;RSEQ=GGCCAAATCCTTGACCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:13,89:0.0192:2,2:11.5:1:28.5:1:0.25224:6.63:60:4:0.0194:0:1 0/0:62:0:0,0:7,55:0:2,0:21.1:1:30:1:1:0:60:30:1:0:0.4 -10 53793287 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50587;SOR=0;LSEQ=ATCACCTTTTTAGCTATTTA;RSEQ=CTATTCCCAGCCTTGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:2,0:114,18:0.0149:2,0:34.5:1:32:0:1:0:60:4:0.0155:0:2.5 0/0:104:0:0,0:88,16:0:2,0:24.9:1:32.1:1:1:0:60:208:1:0:0.1 -10 53793313 . G T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04331;SOR=Inf;LSEQ=CCCAGCCTTGGAGACAGTCT;RSEQ=TCCTCCAGTTTTATGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:147,61:0:2,0:25.1:1:32:1:1:0:60:103:1:0:0.1 0/1:176:4:2,2:125,47:0.0227:2,2:26.5:1:29.3:1:0.30962:2.64248:60:8:0.0229:0:1 -10 53793329 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25689;SOR=0;LSEQ=GTCTGTCCTCCAGTTTTATG;RSEQ=AGGTTGAGCTACTGTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:1,2:170,93:0.0113:2,2:12.7:1:28.7:1:0.2908:3.63715:60:6:0.0115:0:1 0/0:215:0:0,0:141,74:0:2,0:25.6:1:31.7:1:1:0:60:106.5:1:0:0.3 -10 53793416 . G A 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGAATTCAGAAACTCTAAA;RSEQ=TATATGTAAAGCAGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:436:436:217,219:0,0:1:0,2:24.5:1:30.3:1:1:0:60:86.2:1:0:1.1 1/1:499:416:217,199:40,43:0.8337:2,2:24.6:1:29.4:1:0.54847:1.17:60:40.6:0.8303:0:1.1 -10 53793523 . A G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.04995;LSEQ=ACAAGTGGTAAATTTCATGC;RSEQ=CGTCCGTGTGAACAGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:171:170:42,128:1,0:0.9942:0,2:22.7:1:31:1:0.25146:0:59.6:55.667:0.994:0:1.1 1/1:170:152:43,109:3,13:0.8941:2,2:23.2:1:30.4:1:0.56101:1.70:59.9:29.4:0.8963:0:1.2 -10 53793528 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22996;SOR=Inf;LSEQ=TGGTAAATTTCATGCACGTC;RSEQ=GTGTGAACAGACCACCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:32,127:0:2,0:21.7:1:29.6:1:1:0:59.3:52:1:0:1.1 0/1:147:2:1,1:31,114:0.0136:2,2:13:1:28.5:1:0.38915:3.64:60:4:0.0139:0:2 -10 54610432 . G A 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6009;LSEQ=CCCTGATGGAGAGACGTTGC;RSEQ=ATCATTGGAGAAGAGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:20:0:29:0:1:0:60:2:0.3333:0:1 0/1:9:2:1,1:5,2:0.2222:2,2:8:1:26.5:1:1:2.23609:60:4:0.2222:0:1 -10 54610457 . T C 95 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16486;SOR=6.30681;LSEQ=TTGGAGAAGAGGCACTCTGG;RSEQ=CTTTTGTGTTTTCAGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:0.1429:2,0:30:0:34:0:1:0:60:2:0.1429:0:1 1/0:15:8:5,3:4,3:0.5333:2,2:19.9:1:31.9:1:1:1.23:60:16:0.5333:0:1 -10 54610668 . C G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10922;SOR=0;LSEQ=TGCAGTTTGCTGGGGGTTCA;RSEQ=TTCAGGGCCTATTCATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:10,10:0.1304:2,2:25:1:32:1:1:1.94:60:6:0.1304:0:1.3 0/0:24:0:0,0:14,10:0:2,0:31.7:1:30.7:1:1:0:60:23:1:0:0.1 -10 54610872 . C G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CAGTTGGGTGGCATGGGGAA;RSEQ=AGAACGCATTAAATGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:12:1:33:0:1:0:60:4:1:0:0 1/0:4:2:1,1:0,2:0.5:0,2:8:0:33:1:1:0:45:4:0.5:0:1.5 -10 54611200 . T G 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00552;SOR=Inf;LSEQ=TGGGCTGTGGGGACAAGTCT;RSEQ=GGGACCAAGCCGTCCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:25.4:1:30.1:1:1:0:56.8:34:1:0:0.1 0/1:15:6:3,3:3,6:0.4:2,2:31:1:27.3:1:0.62238:1.91:60:5:0.3571:0:1.2 -10 54611217 . G GC 76 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.18424;SOR=0.16114;LSEQ=TCTTGGGACCAAGCCGTCCA;RSEQ=CCCCCCCAGCTCTAGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:2,4:4,4:0.375:2,2:27.7:1:29.7:1:0.62704:1.90258:60:12:0.375:0.0625:0.2 0/1:12:1:0,1:4,7:0.0833:2,0:12:0:32:0:1:0:60:2:0.0833:0:0 -10 54611276 . A G 51 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0119;SOR=Inf;LSEQ=CTATGGAGATGGGTGCCACC;RSEQ=TTTCCCAACCCAGTGAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:25.8:1:32.3:1:1:0:60:12:1:0:0.7 1/1:3:3:1,2:0,0:1:0,2:21:1:32.3:1:1:0:60:6:1:0:1 -10 54611291 . G A 59 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCACCATTTCCCAACCCAGT;RSEQ=AGCTTAGTGCATTAGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:21.3:1:29.5:1:1:0:60:8:0.8:0:1.3 0/0:1:0:0,0:0,1:0:0,0:22:0:33:0:1:0:60:2:1:0:1 -10 54611336 . C T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.4;SOR=0;LSEQ=AGTCCCAGTGTTGGCTGCTG;RSEQ=TCCTCTCACAAGGAGCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:20:1:28.5:1:1:0:60:4:0.6667:0:2 0/0:2:0:0,0:1,0:0:0,0:29:0:34:0:1:0:60:2:1:0:0 -10 54611395 . A G 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=AGCCACAGCCAGTGCTGGTC;RSEQ=CCCCTCACCTCAGGAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:24.8:1:28.2:1:1:0:60:4:1:0:1.2 0/0:2:0:0,0:2,0:0:0,0:27:1:27.5:1:1:0:60:4:1:0:0 -10 54611637 . G C 44 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTGCCTTATGTGGCTCTCAG;RSEQ=TGGGCCACTGCACCACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:26:1:28:1:1:0:60:2:1:0:1 0/0:1:0:0,0:0,1:0:0,0:36:0:28:0:1:0:60:2:1:0:0 -10 56058875 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGCAGCATAAGCTGCTG;RSEQ=CAGAGGCAGGGAAAGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:1:31.5:1:1:0:54.5:4:1:0:1 -10 56060068 . G A 118 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=36.178;LSEQ=TCCACTTTCTAGGTCCGGTA;RSEQ=CAGCCATTTTGCAATTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:1:1,0:14,24:0.0256:2,0:28:0:27:0:0.38462:0:60:2:0.0256:0:1 1/0:34:17:7,10:6,11:0.5:2,2:22.2:1:29.1:1:1:1.27:60:34:0.5:0:1.1 -10 56851227 . GAATTAATCC TAAA 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTATAGTAGAGGTCTAAAGT;RSEQ=TTGTGGGTAACAATTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,0:0:1,0:23.8:1:32.4:1:1:0:60:116:1:0:0.1 1/0:48:24:23,1:23,1:0.5:1,1:21.6:1:29.6:1:1:1:59.8:48:0.5:0.1042:1.1 -10 56851276 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2121;SOR=Inf;LSEQ=TAGATTAAGCACTCAGTGAT;RSEQ=CATAACTTTCAAGAGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:113,34:0:2,0:24.5:1:31.8:1:1:0:60:146:1:0:0.1 0/1:126:2:1,1:92,32:0.0159:2,2:34.5:1:30:1:0.45676:2.84645:57.5:4:0.0161:0:1.5 -10 56851396 . C A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=20.50607;LSEQ=CTTCTGTGAAAGGTAACTAT;RSEQ=ATTTAAATATGAGGAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:11:5,6:152,179:0.0322:2,2:22.9:1:29.5:1:1:1.01894:60:22:0.0326:0:1.4 0/1:283:115:48,67:78,90:0.4064:2,2:26.5:1:28.6:1:0.46636:1.2089:60:114:0.4057:0:1.1 -10 59601231 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AACACTACAACTGCAAGGCC;RSEQ=CTTCTTTGCCCTATCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:13.3:1:32.7:1:1:0:60:6:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:24:1:31.5:1:1:1:60:4:0.5:0:1 -10 60094679 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTACACTTCCCAGTGTGCC;RSEQ=GGCGGGGCGGGGCGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:28.5:1:31:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 60095105 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=GGAAGGGTGGGCCGGGGTGC;RSEQ=GGCAGGGAGCTGAAGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,16:0:2,0:23.3:1:30.5:1:1:0:60:48:1:0:0.4 0/1:20:2:0,2:5,13:0.1:2,0:28:1:31.5:1:1:0:60:4:0.1176:0:1 -10 60095143 . T C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGGCCGGGCCAGCGGGCA;RSEQ=CGGACAGGTGAGGTGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:1:0,2:21.7:1:31.2:1:1:0:60:20:1:0:1.1 1/1:9:9:0,9:0,0:1:0,0:17.8:1:31.8:1:1:0:60:18:1:0:1.1 -10 60277451 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17756;SOR=Inf;LSEQ=TAGATTTGAATCTTGATGCT;RSEQ=CATTTTAATAGGGAGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:171,59:0:2,0:24.2:1:28.6:1:1:0:60:229:1:0:0.1 0/1:168:2:1,1:113,53:0.0119:2,2:29:1:31:0:0.54085:2.12161:60:4:0.012:0:2 -10 60277489 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=44.96975;LSEQ=TGGGAGAATCCATCACTTGG;RSEQ=GACCTCATTTCTCAAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:21:14,7:205,128:0.0593:2,2:24.9:1:28.7:1:0.81754:1.25:60:20:0.0575:0:1.6 1/0:286:212:121,91:42,32:0.7413:2,2:25.5:1:29.5:1:1:1.01:60:424:0.7439:0:1.6 -10 60277549 . A C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=26.09963;LSEQ=ACCTCCTGAGGTAGTTTTGA;RSEQ=AATGAAGAGGAAAAAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:37:19,18:197,226:0.0803:2,2:27.5:1:32.3:1:0.60945:1.21:60:74:0.0811:0:1.4 1/0:398:277:137,140:53,66:0.696:2,2:25.4:1:31.5:1:0.38215:1.22:60:137.5:0.6962:0:1.5 -10 60277750 . ATAT A 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.00025;SOR=49.72797;LSEQ=GAACATGCACAGCTATCTAA;RSEQ=TATTATTGGCCTCCCTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:0,22:0.0435:1,0:42:0:31:0:1:0:60:2:0.0476:0:0 1/0:8:6:1,5:0,2:0.75:0,2:29.7:1:31:1:1:0:60:12:0.75:0:0 -10 60278140 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATAATAGTCCTACTTTA;RSEQ=GGTGATATTGTGAATGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:28:1:1:0:60:4:1:0:1 -10 63661533 . C CA 54 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04036;SOR=Inf;LSEQ=CCGATCCCGGCACCCCCCGG;RSEQ=ACCCCCCAACCCCCCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:118,270:0:2,0:23.5:1:30.3:1:1:0:59.9:10.758:0.9972:0:0.5 0/1:518:6:6,0:161,345:0.0116:2,0:8.5:1:21.2:1:0.00113:0:60:2:0.0084:0.0058:1.3 -10 63661534 . AC A 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1.1392;LSEQ=CGATCCCGGCACCCCCCGGC;RSEQ=CCCCCAACCCCCCAGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:4:2,2:109,265:0.0105:2,2:29.8:1:29:1:0.58412:2.42:60:8:0.0114:0.0026:0.3 0/1:501:6:4,2:155,339:0.012:2,2:21:1:28.8:1:0.08441:4.36:60:12:0.0132:0.004:0.3 -10 63661732 . G GT 49 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=0.08139;SOR=4.46577;LSEQ=GTGGCGGTGGGGGGCCCTGA;RSEQ=TTTTTTTTTTTTTTTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:2,1:17,11:0.0968:2,2:35:1:23.7:1:1:1.28:60:2:0.0667:0:1 0/1:12:4:2,2:6,2:0.3333:2,2:20:1:24.8:1:0.54747:2.71347:57.3:3:0.2727:0:3.5 -10 63661854 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49984;SOR=Inf;LSEQ=GTCTGTGTGTAAATGTGTCT;RSEQ=GGAATAGATGTTTGTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:124,28:0:2,0:22.4:1:31.8:1:1:0:60:75:1:0:0.2 0/1:169:2:1,1:129,38:0.0118:2,2:23:0:31.5:1:0.40934:3.36384:60:4:0.0118:0:1 -10 63661905 . T TC 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0367;SOR=Inf;LSEQ=TTATTTATTTGGTGTTTTTT;RSEQ=CCCCCCCTGCAGTGGGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:229,103:0:2,0:24.5:1:29.8:1:1:0:60:32.2:1:0:0.2 0/1:417:6:4,2:270,141:0.0144:2,2:26.5:1:30.7:1:1:1.04:60:12:0.0148:0.0024:0 -10 63662172 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09919;SOR=0;LSEQ=AGAAATAGCGACCATGGCGA;RSEQ=GTGGTAAACCTGTCTGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:74,211:0.0104:2,2:25.3:1:25:1:0.1712:5.66:60:2:0.007:0:1.7 0/0:333:0:0,0:97,236:0:2,0:25.9:1:30.4:1:1:0:60:82.25:1:0:0.2 -10 63698147 . T G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGCCAAATTCTCTCTT;RSEQ=ACTAATGTTGAGACTGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:1:31:1:1:0:60:4:1:0:1 -10 63699895 . A C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.04128;LSEQ=GAGAGTGGATCATTTCCCTC;RSEQ=AACCTATAAATAACGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:168:158:119,39:5,4:0.9405:2,2:23.3:1:30.7:1:0.23777:2.43:60:38.5:0.9448:0:1.1 0/1:181:71:51,20:81,29:0.3923:2,2:23.9:1:30.4:1:0.86434:1.09478:60:142:0.3944:0:1.2 -10 63700223 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=Inf;LSEQ=GGCGTATATAGTAACTTTTC;RSEQ=GTTGAAGATTTTTCTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:37,128:0:2,0:22.8:1:30.9:1:1:0:60:330:1:0:1 0/1:181:2:1,1:44,135:0.011:2,2:5:1:29.5:1:0.43646:3.05:60:4:0.0111:0:1 -10 63700228 . A T 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.029;SOR=0.59573;LSEQ=ATATAGTAACTTTTCGGTTG;RSEQ=AGATTTTTCTGGAAACACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:149:98:18,80:13,37:0.6577:2,2:21.4:1:28.2:1:0.2927:1.55672:60:48:0.6575:0:1.7 1/0:165:88:20,68:19,58:0.5333:2,2:22.4:1:28.1:1:0.8548:1.11306:60:43:0.5276:0:1.7 -10 63700245 . A G 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05088;SOR=0.56565;LSEQ=TTGAAGATTTTTCTGGAAAC;RSEQ=CTATCATTTATATATAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:101:65:7,58:4,32:0.6436:2,2:21.6:1:32:1:1:1.03538:60:130:0.6436:0:2 1/0:109:55:4,51:8,46:0.5046:2,2:23:1:31.8:1:0.23678:2.20158:60:26.5:0.4953:0:2 -10 63759692 . G A 94 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05956;SOR=4.13881;LSEQ=TTCTGTGGGGCTGGATGGGT;RSEQ=AAGTGGGGCTGGGAGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:3,0:47,2:0.0577:1,0:14:1:29:1:1:0:60:6:0.0577:0:1 0/1:44:9:9,0:34,1:0.2045:1,0:30.7:1:29.7:1:1:0:60:18:0.2045:0:1.1 -10 63759735 . A G 103 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0066;SOR=11.18128;LSEQ=GCATCCCCCAGACTGTAACA;RSEQ=GGATGAGAGTCTTTTTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:1,0:123,1:0.008:1,0:4:0:33:0:1:0:60:2:0.008:0:1 0/1:108:9:9,0:97,2:0.0833:1,0:19.7:1:32.8:1:1:0:60:18:0.0833:0:1 -10 63760085 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24905;SOR=0;LSEQ=ATATGCGATGAGTTTGGTGA;RSEQ=TCTTTTTTTTTTTTTCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:73,204:0.0107:2,2:7:1:22:1:0.17582:5.55:60:2:0.0079:0:1.3 0/0:268:0:0,0:88,180:0:2,0:23.8:1:30:1:1:0:59.9:21.333:1:0:0.6 -10 63760101 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.718;SOR=1.41062;LSEQ=GTGAGTCTTTTTTTTTTTTT;RSEQ=CTACCTGATTCTTGTGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:2,1:41,175:0.0137:2,2:5.7:1:23.9:1:0.09919:8.42:51.7:3:0.0089:0:2.7 0/1:208:4:2,2:49,155:0.0192:2,2:29:1:22.5:1:0.25255:3.14:60:3:0.0147:0:3.5 -10 63760113 . T C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1064;SOR=Inf;LSEQ=TTTTTTTTCCTACCTGATTC;RSEQ=TGTGCGTGTGTGCCTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:28,133:0:2,0:24.5:1:30:1:1:0:59.8:52.667:1:0:0.9 0/1:146:3:0,3:33,110:0.0205:2,0:24.3:1:32.7:1:1:0:60:6:0.0207:0:1.3 -10 63809527 . G A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51049;SOR=4.09114;LSEQ=GTGTTTGTAAAATGAGTACA;RSEQ=TGTAAAAATGTCCTAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:34.7:1:31.3:1:1:0:60:6:0.3:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:26.5:1:31:0:1:0:60:4:0.6667:0:1 -10 63810452 . C T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0337;SOR=0.18832;LSEQ=AATAGATTAGCTTTGGGAAA;RSEQ=GTGTACAGAAATGTATACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:15:15,0:6,0:0.7143:0,1:29.2:1:30.3:1:1:0:60:14:0.7:0:1.5 0/1:13:4:4,0:9,0:0.3077:0,0:30:1:30.3:1:1:0:60:8:0.3077:0:1 -10 63810458 . C A 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03797;LSEQ=TTAGCTTTGGGAAACGTGTA;RSEQ=AGAAATGTATACTCTACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:7,0:16,0:0.3043:1,0:24.3:1:30.9:1:1:0:60:14:0.3043:0:1 0/1:16:5:5,0:11,0:0.3125:0,0:22:1:28.6:1:1:0:60:10:0.3125:0:1 -10 63810562 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49754;SOR=0;LSEQ=TTCTCTGAACAATTAGAAGG;RSEQ=ATCACTGTAGTGAGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:95,4:0.0198:1,2:13.5:1:28:1:0.09703:21.35426:60:4:0.02:0:1 0/0:99:0:0,0:89,10:0:2,0:23.5:1:31.1:1:1:0:60:198:1:0:0.1 -10 63816832 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17668;SOR=Inf;LSEQ=CTATGTCTTGGTAAGCATCC;RSEQ=GGGGCTGTGCCTCGTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:147,44:0:2,0:23.7:1:30.7:1:1:0:60:62.667:1:0:0.1 0/1:139:2:1,1:105,32:0.0144:2,2:23.5:1:28.5:1:0.41977:3.24648:60:4:0.0146:0:1 -10 63816834 . G T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.65281;LSEQ=ATGTCTTGGTAAGCATCCTG;RSEQ=GGCTGTGCCTCGTCTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:147,46:0.0103:2,2:27:1:31.5:1:0.4249:3.1722:60:4:0.0105:0:1 0/0:149:1:0,1:111,37:0.0067:2,0:1:0:27:0:0.25503:0:60:2:0.0068:0:1 -10 63816842 . C T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13156;SOR=0;LSEQ=GTAAGCATCCTGGGGCTGTG;RSEQ=CTCGTCTGATGTGGTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:4:2,2:160,55:0.0183:2,2:25:1:28.3:1:0.2783:2.89236:60:8:0.0186:0:1.3 0/0:177:0:0,0:130,47:0:2,0:24.1:1:31.4:1:1:0:60:176:1:0:0.2 -10 63817096 . G A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGTGAGTATACTTGTTTTC;RSEQ=TTTCTGAATTATCAGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:108,226:0:2,0:24.7:1:31.1:1:1:0:60:166:1:0:0.1 0/1:362:30:11,19:114,218:0.0829:2,2:20.7:1:29.8:1:0.842:1.11:60:60:0.0836:0:1.2 -10 63817135 . G GA 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=TGCTCAGATTCTTTGAATTG;RSEQ=AAAAAATAATTTTGACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:18,128:0:2,0:24.1:1:31.2:1:1:0:60:47.667:1:0:0.1 0/1:154:2:1,1:28,124:0.013:2,2:17:1:25.5:1:0.34216:4.37:60:4:0.0132:0.0065:0.5 -10 63818914 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5071;SOR=0;LSEQ=GTATTTCTTTTTTTCTCTTT;RSEQ=TCGTTGAAAAAAAAAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:114,18:0.0149:2,2:31.5:1:31:1:0.26439:6.1914:60:4:0.0152:0:1 0/0:102:0:0,0:85,17:0:2,0:22.1:1:31.1:1:1:0:60:101:1:0:0.2 -10 63818920 . GA G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.3001;LSEQ=CTTTTTTTCTCTTTCTCGTT;RSEQ=AAAAAAAAATGTTTTAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:162:109:85,24:50,3:0.6728:2,2:22:1:32:1:0.00742:4.67027:60:218:0.6728:0.1235:0.1 0/1:113:43:38,5:50,14:0.3805:2,2:28.4:1:32:1:0.20535:2.11:60:86:0.3805:0:0 -10 63829539 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.13792;LSEQ=ACCAGCGCTGCCACTTGTAC;RSEQ=CGCAGACATTATGAAAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:430:252:96,156:72,106:0.586:2,2:26.9:1:30.5:1:0.68823:1.10352:60:41:0.5857:0:1.1 0/1:503:82:38,44:167,254:0.163:2,2:26:1:29.1:1:0.27096:1.31:60:40:0.1623:0:1.2 -10 63829798 . C TT 24 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.4;SOR=0;LSEQ=GACCACCTGCCTGACAATGC;RSEQ=TTTTTTTTTTTTCCCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:44:1:24:1:1:0:60:4:0.6667:0:4.5 0/0:2:0:0,0:1,1:0:2,0:16.5:1:31:1:1:0:60:4:1:0:0 -10 63829930 . A T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAAAGTAAGCACTTCTC;RSEQ=TAATATTAGCATTGAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:41:1:29.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 63844810 . G C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACATGAATGAAAATAAAAT;RSEQ=TTTTCAGATGGGCAGCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:31.5:1:32.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29.5:1:1:0:60:4:1:0:1 -10 63845705 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18589;SOR=Inf;LSEQ=ACCTCTGGAAGACATGTGCT;RSEQ=CCTCGAGGTCCTTCTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:26,100:0:2,0:25.7:1:31.5:1:1:0:60:30.5:1:0:0 0/1:96:2:1,1:18,76:0.0208:2,2:10.5:1:27.5:1:0.35833:4.14:60:4:0.0215:0:2 -10 63847565 . G A 59 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTTTTTTGTTTTTATTA;RSEQ=GTTTCATAATTATTTTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:10.8:1:29.8:1:1:0:60:8:1:0:1.5 -10 63851593 . C T 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04504;SOR=Inf;LSEQ=ACCGCTGCAGCTTCTCCAAG;RSEQ=ATCACCTTAACCCCCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:280,183:0:2,0:25.3:1:32:1:1:0:60:114.75:1:0:0.1 0/1:397:4:2,2:226,166:0.0101:2,2:17:1:27.5:1:1:1.36035:60:8:0.0102:0:1 -10 63851964 . G A 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06386;SOR=Inf;LSEQ=CTGAGCCTTCCCAAGAACCC;RSEQ=CACAAACCTACCGGCAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:203,225:0:2,0:26.3:1:31.1:1:1:0:60:106:1:0:0.1 0/1:480:5:2,3:225,250:0.0104:2,2:22.4:1:27.2:1:1:1.34917:60:4:0.0086:0:1.6 -10 63852297 . GA G 87 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.56723;SOR=1.52163;LSEQ=TTGGACCTTGTGATTGCAGG;RSEQ=AAAAGGCCCGGGCAGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:5:4,1:320,303:0.008:2,2:32.4:1:31.6:1:0.37428:3.78:60:10:0.0081:0.0016:0.2 0/1:580:7:3,4:294,277:0.0121:2,2:33.1:1:31.1:1:0.7181:1.41431:60:14:0.0123:0:0 -10 63852823 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1865;SOR=Inf;LSEQ=CAGCAGTCCAAAGCGGCATG;RSEQ=CCAACAGAGCTTCACTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:21,127:0:2,0:24:1:31.4:1:1:0:60:23.667:1:0:0.2 0/1:113:2:1,1:12,99:0.0177:2,2:6.5:1:29.5:1:0.21776:7.97:60:4:0.0182:0:1 -10 63852965 . C G 96 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTGATTTTTGTGGGACAACT;RSEQ=TAGCCCACAAACTGACTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:0,9:0,4:0.6923:0,0:21.4:1:30.6:1:1:0:60:18:0.6923:0:1.1 1/1:1:1:0,1:0,0:1:0,0:38:0:32:0:1:0:60:2:1:0:1 -10 65825669 . A AG 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.20979;SOR=0;LSEQ=TATTTAATGCATACAAGACA;RSEQ=GGGGGGGGCAGGGTAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:2,0:23,11:0.0556:2,0:26:1:32:1:1:0:60:4:0.0606:0:0.5 0/0:42:0:0,0:22,20:0:2,0:19.1:1:29.4:1:1:0:60:41:1:0:0.2 -10 65825674 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.49654;SOR=Inf;LSEQ=AATGCATACAAGACAAGGGG;RSEQ=GGGCAGGGTAAGGAGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:27,10:0:2,0:23.6:1:30.3:1:1:0:59.9:74:1:0:0.2 0/1:44:2:1,1:22,20:0.0455:2,2:11.5:1:27:1:1:1.09762:60:4:0.0465:0:1 -10 65825677 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19937;SOR=0;LSEQ=GCATACAAGACAAGGGGGGG;RSEQ=CAGGGTAAGGAGGGTGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:24,10:0.0556:2,2:34:1:29.5:1:0.52381:2.33552:60:4:0.0556:0:1 0/0:44:0:0,0:23,21:0:2,0:22.1:1:31:1:1:0:60:88:1:0:0.2 -10 65825743 . AG A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.17982;SOR=0;LSEQ=AAGTCACGTGATCATAGGAC;RSEQ=GGGGCCCTTCCCTTTTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:18,21:0.0488:2,2:27.5:1:32:1:1:1.16:60:4:0.0513:0:0.5 0/0:55:0:0,0:26,29:0:2,0:23.1:1:30:1:1:0:59.2:54:1:0:0.4 -10 65825750 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50183;SOR=Inf;LSEQ=GTGATCATAGGACAGGGGGC;RSEQ=CTTCCCTTTTAGGTAGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:17,23:0:2,0:25.6:1:29.9:1:1:0:59.3:19:1:0:0.3 0/1:51:2:1,1:23,26:0.0392:2,2:39:1:28.5:1:1:1.13:59.5:4:0.0408:0:2 -10 65825793 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=Inf;LSEQ=CAGAGAGAGAAGGCAGCATA;RSEQ=GTCAGCATTTTCTTCTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:4,19:0:2,0:25:1:29.5:1:1:0:59:22:1:0:0.3 0/1:26:2:1,1:7,17:0.0769:2,2:19:1:32:0:0.52923:2.34:59.5:4:0.08:0:2 -10 65825866 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31469;SOR=0.2763;LSEQ=TCACTATTTCTTCTACTGCT;RSEQ=TCTACTACGAACTTCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:0,3:0.5714:0,2:19.8:1:32:1:1:0:60:8:0.5714:0:1 0/1:8:2:1,1:2,4:0.25:2,2:35:0:33:1:1:1.83:49:4:0.2857:0:1 -10 66345180 . G GAA 87 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.54521;SOR=0.63157;LSEQ=AATCCAGGAGCTGTTTTTCT;RSEQ=AAAAAAAAAAAAAATTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:2,5:6,7:0.2917:2,2:25.7:1:29.9:1:0.64241:2.06372:60:14:0.3182:0:0.3 0/1:39:8:3,5:13,11:0.2051:2,2:22.8:1:29.2:1:0.68508:1.9283:58.1:16:0.2051:0:0.6 -10 68050400 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49646;SOR=0;LSEQ=CTATTTATTTTTTACAATAT;RSEQ=AGATTATCGTCTGCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:55,7:0.0313:2,2:29:1:28.5:1:0.23611:7.41617:60:4:0.0313:0:1 0/0:60:0:0,0:50,10:0:2,0:22:1:31.1:1:1:0:60:120:1:0:0.3 -10 68050444 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49793;SOR=Inf;LSEQ=AAGTACTAGAGTTTTGATTT;RSEQ=CACCTACCTGATATGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:83,34:0:2,0:27.4:1:31.5:1:1:0:60:22.4:0.9912:0:0.8 0/1:120:2:1,1:79,39:0.0167:2,2:8:0:30:1:1:2.01284:60:4:0.0169:0:1.5 -10 68050445 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24686;SOR=0;LSEQ=AGTACTAGAGTTTTGATTTG;RSEQ=ACCTACCTGATATGACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:83,34:0.0168:2,2:21:1:30:1:0.50349:2.42052:60:4:0.0172:0:2.5 0/0:120:0:0,0:79,41:0:2,0:26.9:1:31.7:1:1:0:60:59:1:0:0.4 -10 68050459 . G A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15224;LSEQ=GATTTGCACCTACCTGATAT;RSEQ=ACATACAGAAATAGGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:158:88:57,31:44,26:0.557:2,2:24.2:1:28.8:1:0.86807:1.09:60:176:0.5605:0:1.7 0/1:144:23:14,9:74,46:0.1597:2,2:26.5:1:28:1:1:1.03394:60:46:0.1608:0:1.5 -10 68050521 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1794;LSEQ=TCAATGCATAAATGAATAAA;RSEQ=GATCTCAACATGGCTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:211:107:63,44:44,60:0.5071:2,2:25.5:1:30.9:1:0.01932:1.95:60:52.5:0.5024:0:1.6 0/1:219:34:16,18:97,87:0.1553:2,2:26.8:1:30.2:1:0.5792:1.253:60:68:0.156:0:1.6 -10 68050533 . G A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.85247;SOR=0.92678;LSEQ=TGAATAAATGATCTCAACAT;RSEQ=GCTTTTGACAGAAGTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:15:9,6:100,101:0.0691:2,2:22.6:1:29.4:1:0.59415:1.51:60:30:0.0698:0:1.8 0/1:233:15:7,8:112,106:0.0644:2,2:23.9:1:30.1:1:0.79353:1.20657:60:30:0.0649:0:1.8 -10 68050569 . T A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25252;SOR=Inf;LSEQ=GAGTCACAAATTATTCGAAA;RSEQ=TGATGTCAACAGTGAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:74,106:0:2,0:27.1:1:30.3:1:1:0:60:179:1:0:0.5 0/1:210:3:2,1:94,113:0.0143:2,2:15.3:1:22:1:0.59361:2.39:60:2:0.0096:0:2.3 -10 68050758 . A G 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07619;SOR=0;LSEQ=CCTCAGATCAGGATTACAAA;RSEQ=TATGATAACCTATATGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:26.5:1:31.3:1:1:0:60:8:0.6667:0:2.8 0/0:4:0:0,0:0,4:0:0,0:29.5:1:29.3:1:1:0:60:8:1:0:0.5 -10 68821161 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGTAATTTTTAGATGTG;RSEQ=TATCAGAGTTCCTTTATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:36.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 68821307 . G T 96 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTCCCTTGTCCCTTAACA;RSEQ=GCATATCAAAAAATGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:25:1:30.3:1:1:0:60:18:1:0:1 1/1:1:1:1,0:0,0:1:0,0:12:0:31:0:1:0:60:2:1:0:1 -10 68821469 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21284;SOR=Inf;LSEQ=AAAGAGAAACGATATTTCAG;RSEQ=AGTTGTGTGCATATTCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:80,28:0:2,0:25.9:1:32:1:1:0:60:107:1:0:0.1 0/1:93:2:1,1:72,19:0.0215:2,2:36:1:28.5:1:0.38569:3.71925:60:4:0.022:0:1 -10 68821487 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4998;SOR=0;LSEQ=AGCAGTTGTGTGCATATTCT;RSEQ=ATATGTATCTTTGTTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:106,45:0.0131:2,2:8.5:1:28:1:0.5123:2.3408:60:4:0.0134:0:1.5 0/0:137:0:0,0:99,37:0:2,0:22.9:1:28.5:1:1:0:60:272:1:0:0.2 -10 68821572 . T C 251 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03156;LSEQ=TTCATTACAAAACAAATTCC;RSEQ=CATTGGCAGATAAGCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:281:272:130,142:4,5:0.968:2,2:26.1:1:31.1:1:1:1.14:60:67:0.9675:0:1.1 0/1:302:147:76,71:73,79:0.4868:2,2:26.1:1:30.2:1:0.56374:1.16:60:72.5:0.4849:0:1.1 -10 68821716 . AT A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00259;SOR=0.15692;LSEQ=GCTTATTTACTGTAAAAAAA;RSEQ=CAATCTTAGGAAATAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:36:2,34:1,2:0.878:2,2:21.6:1:31.8:1:0.21873:7.61228:60:72:0.878:0.2195:0 1/0:23:12:0,12:0,11:0.5217:0,0:22.3:1:31.9:1:1:0:60:24:0.5217:0.2174:0 -10 68821717 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.53224;SOR=0;LSEQ=CTTATTTACTGTAAAAAAAA;RSEQ=CAATCTTAGGAAATAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:1,2:0.0488:2,0:17:1:31.5:1:1:0:60:4:0.0488:0:1 0/0:23:0:0,0:0,11:0:0,0:25.3:1:30.1:1:1:0:60:22:0.4783:0:0 -10 68821956 . CAG C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAAGAACGTTAAAACCCA;RSEQ=AGAGTAAATTGTTTAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19:1:33.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 69444713 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17143;SOR=0;LSEQ=GGGCGGCATCTTGTACTATC;RSEQ=CTGACTGGTTAGTGTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:16.5:1:30:1:1:2.24:60:4:0.2222:0:1.5 0/0:12:0:0,0:4,8:0:2,0:28.8:1:31.8:1:1:0:60:24:1:0:0.2 -10 69553534 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTAATTCGCCAAAATAA;RSEQ=AAACACAAAGGGAAAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:14,4:0.1:2,2:23:1:28.5:1:0.44737:3.24034:60:4:0.1053:0:1 0/0:5:0:0,0:4,1:0:2,0:19.6:1:31.4:1:1:0:60:10:1:0:0 -10 69553736 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14101;SOR=0;LSEQ=AGTCTACAGTGTTACTGCAT;RSEQ=CTGTTGGCATTGTTATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:14,29:0.0444:2,2:23:1:29.5:1:1:2.04:60:4:0.0444:0:1 0/0:74:0:0,0:33,41:0:2,0:25.2:1:30.9:1:1:0:60:17.5:1:0:0.3 -10 69553768 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.518;SOR=Inf;LSEQ=GTTATAAACACACGAGTTAA;RSEQ=GGCAAGATTCTTGCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:4,24:0:2,0:27:1:31.1:1:1:0:60:56:1:0:0.1 0/1:44:2:1,1:14,28:0.0455:2,2:29.5:1:28:1:1:1.97:60:4:0.0465:0:1 -10 69553779 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49854;SOR=Inf;LSEQ=ACGAGTTAAGGGCAAGATTC;RSEQ=TGCCAGGAGAATTAATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:2,24:0:2,0:26.1:1:30.5:1:1:0:60:52:1:0:0 0/1:33:2:1,1:10,21:0.0606:2,2:15:1:30:1:1:2.05:60:4:0.0625:0:1 -10 69554894 . G C 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCACATTTCTGGAGACC;RSEQ=GGAAGTCCAAGATCAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 69555026 . T TA 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTCTCAATCCTCTTTCA;RSEQ=AAGAGCACTAATCCCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:30:1:1:0:60:4:1:0:0.5 -10 69760514 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.1957;SOR=0;LSEQ=TGGATGCAGACACGTACAGA;RSEQ=AGAAGGCCAAGGTCTACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:0.1429:2,2:10:0:31:1:1:1.37:60:4:0.1538:0:1 0/0:17:0:0,0:11,6:0:2,0:16:1:31.9:1:1:0:60:34:1:0:0.1 -10 70332066 . C T 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01694;SOR=0.6776;LSEQ=ACCAATGACTCTGTTTCCTG;RSEQ=GCCCTTTCATTTTTTCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:293:152:101,51:94,47:0.5188:2,2:24.7:1:29.8:1:1:1.00987:60:304:0.5223:0:1.1 0/1:346:146:96,50:119,81:0.422:2,2:24.8:1:29.9:1:0.26243:1.31:60:292:0.4269:0:1.1 -10 70332152 . C CA 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.01467;LSEQ=GTCAGGAAGGAAGATGTAAA;RSEQ=AAAAAAAAGAAAAACAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:10:6,4:406,225:0.0156:2,2:26:1:30.3:1:0.7505:1.20259:60:20:0.0158:0.0016:0.3 0/1:886:14:10,4:531,339:0.0158:2,2:12.6:1:29.4:1:0.58327:1.60:60:28:0.016:0.009:0.6 -10 70332580 . A G 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.58126;SOR=0.92308;LSEQ=TGATTCGGTTCCAATGCAAG;RSEQ=CACCCAAGTCCTTCCTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:184:105,79:135,131:0.4089:2,2:22.8:1:31.5:1:0.21166:1.29:60:91:0.4099:0:1 0/1:426:166:85,81:118,142:0.3897:2,2:23.8:1:31.5:1:0.27401:1.26:60:332:0.3915:0:1.1 -10 70332672 . T A 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23579;SOR=1.35931;LSEQ=AAGAGACAACTCAGTTTTGG;RSEQ=CCCAAAGAGTTGAGGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:30:13,17:234,239:0.0596:2,2:24.5:1:28.7:1:0.57485:1.27971:60:14:0.057:0:1.3 0/1:592:47:24,23:275,270:0.0794:2,2:28.5:1:28.9:1:1:1.02:60:46:0.0786:0:1.2 -10 70332862 . C T 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=12.18021;LSEQ=TGCTCCTTTTCCCCAAAGAG;RSEQ=AACCCCCAAAGTTACCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:893:3:1,2:494,396:0.0034:2,2:7.3:1:26.7:1:0.58862:2.49245:60:6:0.0034:0:1.3 0/1:963:38:21,17:509,413:0.0395:2,2:27.3:1:28.4:1:1:1.00:60:76:0.0399:0:1.1 -10 70333502 . G A 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGTGCTATACAGATTTT;RSEQ=CCTTTGGGCTCAGGACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:557:0:0,0:265,291:0:2,0:25.3:1:31.9:1:1:0:60:54.6:0.9982:0:0.1 0/1:626:26:13,13:289,310:0.0415:2,2:20.4:1:27.7:1:1:1.07:60:52:0.0421:0:1.1 -10 70333741 . G C 193 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGAGGGAGCTCCCAGGTCA;RSEQ=TGTAACCAGCACAGTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:962:0:0,0:497,463:0:2,0:24.3:1:31.9:1:1:0:60:59:0.9979:0:0.1 0/1:1117:69:37,32:526,521:0.0618:2,2:25.5:1:31.6:1:0.6204:1.15:60:138:0.0621:0:1.1 -10 70334006 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10534;SOR=Inf;LSEQ=CCATCTGTTGTTGTGCCTCT;RSEQ=GAGGTAAGCAAACAGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:92,164:0:2,0:25.9:1:31:1:1:0:60:63:0.996:0:0.1 0/1:231:3:1,2:78,149:0.013:2,2:25:1:30.3:1:1:1.04677:60:6:0.0131:0:1.7 -10 70334034 . G T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57864;SOR=2.68197;LSEQ=GCAAACAGTCAAGGGGCTGG;RSEQ=AGACAGCTGACACTTGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:61,134:0.0051:2,0:45:0:10:0:1:0:60:0:0:0:5 0/1:147:2:1,1:43,102:0.0136:2,2:7.5:1:25:0:0.51048:2.36:60:4:0.0136:0:1 -10 70334316 . T G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAAATTGTATGAAATGTG;RSEQ=TTTTGCAGAGATTTCCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 70360784 . T A 45 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13217;SOR=Inf;LSEQ=GAGGGAAAAGAAGCCCAAAG;RSEQ=TTTAAAGGTAATCAGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:127,185:0:2,0:27.1:1:29.6:1:1:0:60:155:1:0:0.1 0/1:385:4:4,0:149,231:0.0104:2,0:6:1:22.5:1:0.02461:0:60:3:0.008:0:1.3 -10 70404379 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18208;LSEQ=AGGGGCTTTACATTTAGTTG;RSEQ=TATTAAATTTTAATCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:63:59,4:74,4:0.4468:2,2:22.2:1:32.1:1:1:1.2522:60:126:0.4468:0:1 0/1:149:19:16,3:118,12:0.1275:2,2:22.6:1:32.4:1:0.40973:1.83485:60:38:0.1275:0:1.2 -10 70404402 . G T 41 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84646;LSEQ=TTAAATTTTAATCTTCTATG;RSEQ=CTGTTATTCAGATATTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:0,3:170,39:0.0142:2,0:1:0:26.3:1:0.00733:0:60:6:0.0144:0:1 0/1:250:3:2,1:193,54:0.012:2,2:28:1:26:1:0.52706:1.78226:60:2:0.0082:0:4 -10 70404938 . G T 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06191;SOR=0;LSEQ=TGAGTTGTGATCATCTCAAG;RSEQ=GGAGAAGTAACGTTTTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:5:0,5:246,199:0.0111:2,0:7.2:1:27.6:1:0.01863:0:60:10:0.0113:0:1 0/0:438:0:0,0:216,221:0:2,0:24.5:1:30.3:1:1:0:60:47.556:0.9977:0:0.1 -10 70405237 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09363;LSEQ=TCAAAGTCAGAGAAGGATGA;RSEQ=GAATCAGAGCAGAGAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:331:181:94,87:80,70:0.5468:2,2:23.7:1:30.6:1:0.82557:1.05755:60:362:0.5485:0:1 0/1:435:44:19,25:203,188:0.1011:2,2:23.3:1:30.4:1:0.34007:1.41962:60:88:0.1021:0:1.2 -10 70405539 . A G 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCATCCAAGATTGACACCA;RSEQ=TAAAAGTATTGCTCAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:190,198:0:2,0:25.1:1:30.7:1:1:0:60:193:1:0:0.1 0/1:432:28:15,13:194,210:0.0648:2,2:25:1:31.6:1:0.69646:1.25:60:56:0.0657:0:1 -10 70405855 . A G 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.61042;LSEQ=AATCAGGAGAAGGGCACAAT;RSEQ=CAACAGAAACCACCTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:616:281:159,122:192,143:0.4562:2,2:23.9:1:31.7:1:0.87048:1.03018:60:45.833:0.453:0:1.1 1/1:843:729:400,329:65,48:0.8648:2,2:25.1:1:31.6:1:0.61281:1.11365:60:80:0.8633:0:1.1 -10 70405901 . T C 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAATAATCATGGTTCATCA;RSEQ=TAACAAAACAAAAGAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:682:0:0,0:329,353:0:2,0:26:1:30.4:1:1:0:60:84.25:1:0:0.3 0/1:976:36:21,15:487,452:0.0369:2,2:23.3:1:31.4:1:0.49892:1.30:60:72:0.0373:0:1.1 -10 70406345 . C T 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00878;SOR=0;LSEQ=AAGCTTATAATTCTCAGGTA;RSEQ=AGTTAACGGTGAATGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:6:2,4:278,262:0.011:2,2:21.8:1:28.3:1:0.43961:2.1193:60:12:0.0111:0:1.2 0/0:653:0:0,0:324,329:0:2,0:1:0:13:0:1:0:60:0:0:0:1 -10 70406390 . C T 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01261;SOR=Inf;LSEQ=AAGCCCATCCTTTGACCCAG;RSEQ=CCTCCTCTCCACCTAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:0:0,0:290,252:0:2,0:25.9:1:31.5:1:1:0:60:66.75:1:0:0.1 0/1:751:9:3,6:384,358:0.012:2,2:18.4:1:25.2:1:0.32778:2.14313:60:8:0.0108:0:1.2 -10 70406518 . A T 249 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00445;LSEQ=CCTGGTATCTCTCATGAAAC;RSEQ=CCCTTACCGGAGTCAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:663:305:172,133:190,168:0.46:2,2:24.5:1:30.2:1:0.43392:1.14:60:37.125:0.4555:0:1.1 0/0:797:3:0,3:411,381:0.0038:2,0:1:0:24:1:0.11224:0:60:6:0.0038:0:1 -10 70406783 . G A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25163;SOR=Inf;LSEQ=GTGAGTACTTGTGTGCATGT;RSEQ=TTCTTATTTCACCTGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:59,182:0:2,0:25.9:1:31.7:1:1:0:60:47.2:1:0:0.2 0/1:274:3:1,2:80,191:0.0109:2,2:12.3:1:25:1:1:1.19:60:2:0.0074:0:2.7 -10 70406855 . AT A 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ATTCATCTTTTTTGTGTGAT;RSEQ=TTTTTCCCCATTCTTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,65:0:1,0:21:1:30:1:1:0:60:20.667:1:0:0.6 0/1:57:13:0,13:0,44:0.2281:1,1:22.5:1:30:1:1:0:59.6:12:0.2143:0.0351:0.1 -10 70406864 . C T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.05677;LSEQ=TTTTGTGTGATATTTTTTCC;RSEQ=CATTCTTATTCTAACTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:28:0,28:0,21:0.5714:1,1:21.9:1:30.3:1:1:0:60:56:0.5714:0:1.1 0/1:44:3:0,3:0,41:0.0682:1,0:28.7:1:28.3:1:1:0:60:6:0.0682:0:1.3 -10 70411536 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13059;LSEQ=GGGGAACAAAAAGTATAAAA;RSEQ=TAGCTTCTCCTGTCCCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:80:69,11:81,13:0.4598:2,2:22.9:1:30.3:1:1:1.01:60:39:0.4561:0:1.1 0/1:191:19:12,7:139,33:0.0995:2,2:13.2:1:29.6:1:0.08135:2.44315:60:38:0.1011:0:1.2 -10 70412132 . AAG A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05586;LSEQ=TTTAACAAGAGTAAATTACG;RSEQ=AGTGTCTAATTTTTGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:48:48,0:32,0:0.6:1,1:21.9:1:30.9:1:1:0:60:96:0.6076:0.1875:0 0/1:66:5:5,0:61,0:0.0758:1,0:25:1:29.6:1:1:0:60:10:0.0769:0:0.2 -10 70412165 . A G 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01377;SOR=Inf;LSEQ=TTTTGAACTTCTGTACATCT;RSEQ=TATCTTATATACATTAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:125,10:0:2,0:23.5:1:28.4:1:1:0:60:44:1:0:0 0/1:132:6:6,0:118,8:0.0455:2,0:17:1:32.8:1:1:0:60:12:0.0458:0:1 -10 70412425 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20189;SOR=0;LSEQ=ATTTATACATTTACAATAGC;RSEQ=AGAGTGATCTTTATTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:6,141:0.0134:1,2:15.5:1:31.5:1:0.09206:21.83:60:4:0.0136:0:1 0/0:182:0:0,0:14,166:0:2,0:24.4:1:32.3:1:1:0:60:360:0.9945:0:0.1 -10 70426168 . A G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCAAAGGAAAAGCCATA;RSEQ=CATTCCTCAGATGGCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:38.3:1:33.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 70427335 . A G 68 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTGGCTAATATGTCTCC;RSEQ=CTATAAATACAAAAAATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:30.8:1:34.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 70432603 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24909;SOR=0;LSEQ=ACCTGAAATGTTCTCTCTGA;RSEQ=GTATTGTAATGCTTCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:204,52:0.0116:2,2:13.3:1:24:1:0.49835:1.95559:60:2:0.0079:0:1 0/0:245:0:0,0:183,61:0:2,0:22.9:1:31:1:1:0:60:60:0.9959:0:0.1 -10 70440769 . C T 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTCTCCGTTATAGGAAC;RSEQ=TGTTACATTGTAACCAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:24.5:1:31:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 70440826 . G T 59 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCAGCAAGAACGTTGTTT;RSEQ=CATTTATTCCAAGTGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:22.8:1:29.8:1:1:0:60:8:1:0:1.8 1/1:1:1:1,0:0,0:1:0,0:48:0:29:0:1:0:60:2:1:0:1 -10 70442868 . GA G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.309;SOR=0.50379;LSEQ=AAATAAGTGGAAAATAAAGT;RSEQ=AAAAAAAGAAATAAGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:31:0,31:0,7:0.8158:0,1:29.5:1:32.1:1:1:0:60:62:0.8158:0.0263:0 1/0:16:11:0,11:0,5:0.6875:0,0:26.6:1:32:1:1:0:60:22:0.6875:0.0625:0 -10 70443936 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGAGGATTGCTTGAGCCC;RSEQ=GGGAGTTCTAGACCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29:1:1:0:60:4:1:0:2 -10 70446673 . C G 76 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTTTTGAGAGGGAGT;RSEQ=TTGCTCTGTCACCCAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:16:1:33:1:1:0:57.8:10:1:0:1.4 1/1:1:1:0,1:0,0:1:0,0:10:0:32:0:1:0:40:2:1:0:1 -10 70450264 . T C 64 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCCAGCTACTCGGGAGG;RSEQ=TGAGGCAAGAGAATGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:33.4:1:27.8:1:1:0:47.2:4:1:0:3 1/1:1:1:1,0:0,0:1:0,0:27:0:34:0:1:0:60:2:1:0:2 -10 70450272 . A G 65 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTACTCGGGAGGTTGAGGCA;RSEQ=GAGAATGGCATGAGCCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:35:1:28.2:1:1:0:47.2:4:1:0:3 1/1:2:2:2,0:0,0:1:0,0:20:1:32.5:1:1:0:60:4:1:0:1.5 -10 70450869 . G T 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17969;SOR=0.20217;LSEQ=GATGGCCCTGGCATTTCACA;RSEQ=CTTGGCGAAGTGGCTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:4:2,2:167,185:0.0112:2,2:11.8:1:29.5:1:1:1.11:60:8:0.0116:0:1.3 0/0:437:1:0,1:214,222:0.0023:2,0:1:0:27:0:1:0:60:2:0.0023:0:1 -10 70451383 . A T 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGAGGCTAAAGAAGCTAAG;RSEQ=ATAAGAAAATGAAGGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:131:61,70:435,407:0.1345:2,2:24.6:1:28.3:1:0.30183:1.22623:60:31.75:0.1333:0:1.1 0/0:1342:0:0,0:648,694:0:2,0:25.2:1:29.1:1:1:0:60:69.632:1:0:0.1 -10 70451687 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50124;SOR=0;LSEQ=TCACCCATTTCAAGTCTGAG;RSEQ=TAAAAAAATAATAATGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:0,2:1,85:0.0227:1,0:26:1:32:0:1:0:60:4:0.0233:0:1 0/0:73:0:0,0:2,71:0:1,0:23.3:1:31.7:1:1:0:60:146:1:0:0.1 -10 71539221 . T C 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGATGGAGGCTTGTCTA;RSEQ=CCCTCACAGTACCAAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:13.7:1:33.3:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 71539455 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10449;SOR=Inf;LSEQ=TGCTGCTATATAAGAGAATC;RSEQ=AGCCTGGGAGAAGAAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:118,28:0:2,0:23.5:1:31:1:1:0:60:145:1:0:0.1 0/1:131:3:1,2:99,29:0.0229:2,2:18.3:1:28.3:1:0.13928:6.69909:60:6:0.0229:0:1 -10 71539581 . G A 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17971;SOR=0.79115;LSEQ=CTTTTTCAGAGCTCAAGAGC;RSEQ=GGCTGCTGAGAGCTAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:118:56,62:95,114:0.3609:2,2:25.4:1:30.5:1:0.73066:1.08:60:58:0.358:0:1.1 0/1:311:96:38,58:92,123:0.3087:2,2:25.6:1:30.3:1:0.62052:1.14115:60:192:0.3117:0:1.1 -10 71539648 . GCAA G 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.69398;SOR=0.60678;LSEQ=AGACTGTAAACTTATTGACA;RSEQ=CAACAACAACAACAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:4:2,2:38,128:0.0235:2,2:28.5:1:31.3:1:0.2357:3.34:60:8:0.0235:0:0.3 0/1:139:2:1,1:40,97:0.0144:2,2:33:1:33.5:1:0.50443:2.41:60:4:0.0144:0:0.5 -10 71539671 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51098;SOR=0;LSEQ=ACAACAACAACAACAAAAAC;RSEQ=CAAAAATCAATAACACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:19,104:0.016:2,2:22:1:31.5:1:0.29548:5.36:60:4:0.0161:0:1 0/0:90:0:0,0:22,68:0:2,0:21.9:1:29.4:1:1:0:60:44:1:0:0.2 -10 71539687 . C T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56357;SOR=3.06389;LSEQ=AAACACAAAAATCAATAACA;RSEQ=CTGGCAGGCTACTCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:0,1:8,79:0.0112:2,0:38:0:16:0:1:0:60:0:0:0:1 0/1:59:2:1,1:11,46:0.0339:2,2:6:1:25:1:0.36821:4.05:60:4:0.0345:0:1 -10 72471033 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27273;SOR=0;LSEQ=GACTCCTATCCCCATCCATG;RSEQ=CTGGAGACAAAAGGAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:2,1:15,22:0.075:2,2:17.3:1:28.7:1:0.56468:2.85:60:6:0.0769:0:1 0/0:26:0:0,0:14,12:0:2,0:32.2:1:31.1:1:1:0:60:52:1:0:0.1 -10 72488413 . G A 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCCTGTGAGAAAAAGG;RSEQ=ATTATCTAGAGCAGTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:19.5:1:29.9:1:1:0:60:24:1:0:2 1/1:5:5:5,0:0,0:1:0,0:10.4:1:29.2:1:1:0:60:10:1:0:1.8 -10 72488445 . T C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45161;SOR=0;LSEQ=CAGTGCTCTTCAAACTTGCC;RSEQ=ATGCCTGCCAGTCAGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:15,2:0,0:1:0,2:27.6:1:31.2:1:1:0:60:34:1:0:1.8 1/1:14:13:9,4:1,0:0.9286:0,2:19.2:1:29.7:1:1:0:60:26:0.9286:0:1.4 -10 72488598 . C T 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.547;SOR=3.42051;LSEQ=TCCTGGAGGAGTGCCCACTG;RSEQ=TGCCTCCCCAGGGCCGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:3,20:0.0417:2,0:11:0:31:0:1:0:60:2:0.0435:0:1 0/1:15:2:0,2:2,11:0.1333:2,0:12.5:1:32:0:1:0:60:4:0.1333:0:1 -10 72764857 . C T 83 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15158;SOR=0.15935;LSEQ=AAATGGAACTGGCCTGGAAG;RSEQ=CCACAGACCTGGGTGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:4,3:2,3:0.5833:2,2:28.1:1:29.9:1:1:1.89:60:14:0.5833:0:1 0/1:6:1:0,1:4,1:0.1667:2,0:1:0:23:0:0.33333:0:60:2:0.1667:0:1 -10 72765013 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATCCTGTTTGCATGATCTCT;RSEQ=CCAGCCGTCAAGTGCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5:1:31:0:1:0:60:4:1:0:1 0/0:2:0:0,0:0,2:0:0,0:33:1:28.5:1:1:0:60:4:1:0:0 -10 72845178 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0.11373;SOR=Inf;LSEQ=GAGGCACAGAGCAGGGCTCT;RSEQ=TCAGGTGAGAGCTGGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:24,32:0:2,0:29:1:31.7:1:1:0:60:55:1:0:0.1 0/1:29:2:1,1:11,16:0.069:2,2:9:0:31:1:1:1.44:60:4:0.069:0:1.5 -10 74677495 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50035;SOR=Inf;LSEQ=GAACTTGGCTGCCACTTTGG;RSEQ=AAGAGAATCACCTTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:81,58:0:2,0:22.9:1:30.8:1:1:0:59.3:45.333:0.9927:0:0.1 0/1:159:2:1,1:92,65:0.0126:2,2:17.5:1:29:1:1:1.41221:60:4:0.0127:0:1.5 -10 74677694 . A G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=TTGGCTGGAGTATCTTGTAT;RSEQ=GATTTCTTCACTGGTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:48,125:0.0114:2,2:37.5:1:27:1:0.48276:2.59:60:4:0.0115:0:2 0/0:162:0:0,0:50,112:0:2,0:23.7:1:29.9:1:1:0:59.9:53:1:0:0.2 -10 74677784 . GTCA G 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.17072;SOR=0.27657;LSEQ=TCATCTTCATCTTCTTCATC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:7:5,2:55,48:0.0631:2,2:23.7:1:31.5:1:0.45199:2.17:60:14:0.0642:0.009:0 0/1:110:2:1,1:61,47:0.0182:2,2:18:1:27.9:1:1:1.29476:60:4:0.0185:0.0091:0 -10 74677787 . A G 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.49788;SOR=0;LSEQ=TCTTCATCTTCTTCATCGTC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:59,48:0.0174:2,2:26:1:29.5:1:1:1.22682:60:4:0.0194:0:1 0/0:112:0:0,0:60,51:0:2,0:22.6:1:29.1:1:1:0:60:36:1:0:0.1 -10 74677845 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.22788;SOR=0;LSEQ=TTACTTTTTTCTGTGGAACC;RSEQ=TGCTACCACCTCCAGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:91,70:0.0122:2,2:21:1:33:1:1:1.29788:60:4:0.0123:0:1 0/0:179:0:0,0:92,87:0:2,0:26.9:1:30.3:1:1:0:60:88.5:1:0:0.1 -10 74677898 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49888;SOR=Inf;LSEQ=GTTATACTTAAGAGTTTCAC;RSEQ=TCCTCCTCCTCTTCACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:70,74:0:2,0:25.1:1:30.2:1:1:0:59.4:288:1:0:0.1 0/1:154:2:1,1:74,78:0.013:2,2:11.5:1:29.5:1:1:1.05:60:4:0.0131:0:1.5 -10 74678032 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50787;SOR=0;LSEQ=TATTTCAAAGCCCCCAAGAG;RSEQ=AACCGTTGGCTATACAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:27,51:0.025:2,2:11:0:32.5:1:1:1.87:60:4:0.0267:0:1.5 0/0:59:0:0,0:19,40:0:2,0:24.9:1:29.8:1:1:0:59.9:58:1:0:0.1 -10 74678221 . C T 31 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55077;LSEQ=AAAGTGATCATCTTTGTCAG;RSEQ=CTTAATTCACAACCAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:53,15:0.0286:2,2:31:0:31.5:1:0.40745:3.45312:60:4:0.0286:0:1.5 0/1:63:1:0,1:46,16:0.0159:2,0:1:0:26:0:0.26984:0:60:2:0.0161:0:1 -10 74678247 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50695;SOR=Inf;LSEQ=TTCACAACCAAAAAGATAGT;RSEQ=CTGGGGCCTCAGGAGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:69,23:0:2,0:22.8:1:29.7:1:1:0:60:29.667:1:0:0.1 0/1:121:2:1,1:81,38:0.0165:2,2:16:1:32:1:0.54256:2.11707:60:4:0.0171:0:1 -10 74678257 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51465;SOR=Inf;LSEQ=AAAAGATAGTTCTGGGGCCT;RSEQ=AGGAGGCTCATGTCCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:80,33:0:2,0:22.1:1:31.4:1:1:0:60:226:1:0:0.1 0/1:163:2:1,1:99,62:0.0123:2,2:46:1:25.5:1:1:1.59197:60:4:0.0123:0:1 -10 74678258 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51327;SOR=Inf;LSEQ=AAAGATAGTTCTGGGGCCTC;RSEQ=GGAGGCTCATGTCCATGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:83,33:0:2,0:21.9:1:30:1:1:0:60:57:0.9913:0:0.1 0/1:166:2:1,1:101,63:0.012:2,2:35:1:29:1:1:1.5984:60:4:0.012:0:1 -10 74678300 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28132;SOR=Inf;LSEQ=TCGAATCTTCCATCGGGTGG;RSEQ=GGCACACACTTAGGTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:103,86:0:2,0:27.3:1:30.5:1:1:0:60:30.5:1:0:0.2 0/1:289:3:2,1:148,138:0.0104:2,2:12:1:26.7:1:1:1.86:60:6:0.0106:0:1.3 -10 74678348 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25472;SOR=Inf;LSEQ=GGATGGAGATAAACCACCAC;RSEQ=GCTCAAGAGAACAGCCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:54,95:0:2,0:23.6:1:29.9:1:1:0:60:36.25:1:0:0.1 0/1:182:3:3,0:64,114:0.0165:2,0:13:1:21:1:0.04929:0:60:2:0.0113:0:1.3 -10 74959528 . T A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52966;SOR=Inf;LSEQ=CAATGATTTAAAAGATTCCT;RSEQ=TGTTAAAAATAACATAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:92,19:0:2,0:25:1:29.5:1:1:0:60:36:1:0:0.1 0/1:185:2:1,1:140,43:0.0108:2,2:17:1:25.5:1:0.42009:3.23006:60:4:0.0109:0:1 -10 74959550 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15534;SOR=0;LSEQ=GTTAAAAATAACATAGGCAG;RSEQ=TTTTCAGTCGGGTGCTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:135,45:0.011:2,2:32:1:28:1:0.44266:2.97817:60:4:0.0113:0:1 0/0:279:0:0,0:188,91:0:2,0:24:1:31.4:1:1:0:60:68.75:1:0:0.1 -10 74959663 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14275;SOR=Inf;LSEQ=CCCTGATGGTGTCATCGAGA;RSEQ=CAACTGGAAGGAGGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:94,152:0:2,0:26:1:31.8:1:1:0:60:40:1:0:0.1 0/1:339:4:2,2:153,182:0.0118:2,2:31:1:25.3:1:1:1.19:60:3:0.009:0:1.3 -10 74959723 . G T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56021;SOR=0.30376;LSEQ=CTTTAAAAAGTCTCTTCTTT;RSEQ=GGGTATCTATGCTTATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:0,2:67,99:0.0119:2,0:12.5:1:30:1:0.51761:0:60:4:0.0121:0:1 0/0:275:1:0,1:126,148:0.0036:2,0:1:0:27:0:1:0:60:2:0.0037:0:1 -10 74959725 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29508;SOR=Inf;LSEQ=TTAAAAAGTCTCTTCTTTGG;RSEQ=GTATCTATGCTTATGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:68,99:0:2,0:23.5:1:31:1:1:0:60:54.667:1:0:0.1 0/1:278:3:1,2:124,151:0.0108:2,2:14.3:1:26.7:1:1:1.63957:60:6:0.0111:0:1 -10 74959806 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5114;SOR=Inf;LSEQ=TATTAAAGATCCAAAAGGTG;RSEQ=CCAGGCGCAGTGGCTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:50,83:0:2,0:24.2:1:31.5:1:1:0:59.7:65.5:1:0:0.1 0/1:184:2:1,1:67,115:0.0109:2,2:28.5:1:28.5:1:1:1.71:60:4:0.011:0:1 -10 74959829 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50689;SOR=Inf;LSEQ=AGGCGCAGTGGCTCATGCCT;RSEQ=TAATCCCAGCACTTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:26,59:0:2,0:20.2:1:32:1:1:0:58.7:170:1:0:0.1 0/1:112:2:1,1:35,75:0.0179:2,2:21:1:30:1:0.54151:2.13:60:4:0.0179:0:1.5 -10 74959834 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51146;SOR=Inf;LSEQ=CAGTGGCTCATGCCTGTAAT;RSEQ=CCAGCACTTTGGGAGGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:21,53:0:2,0:20.7:1:31:1:1:0:58.2:148:1:0:0.1 0/1:104:2:1,1:28,74:0.0192:2,2:18:0:31.5:1:0.48189:2.61:60:4:0.02:0:4.5 -10 74959839 . C G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50543;SOR=Inf;LSEQ=GCTCATGCCTGTAATCCCAG;RSEQ=ACTTTGGGAGGCCGAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:16,54:0:2,0:19.7:1:31.8:1:1:0:58.1:69:1:0:0.1 0/1:91:2:1,1:18,71:0.022:2,2:13:0:32.5:1:0.37582:3.87:60:4:0.0227:0:4.5 -10 74959846 . GG AA 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50359;SOR=Inf;LSEQ=CCTGTAATCCCAGCACTTTG;RSEQ=AGGCCGAGGCGGGTAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:8,50:0:2,0:20.8:1:30.4:1:1:0:57.7:57:1:0:0.1 0/1:74:2:1,1:10,62:0.027:2,2:5:0:31.3:1:0.27693:5.96:60:4:0.0274:0:3.5 -10 74960524 . G A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AATCGAACAGTTTTATATCA;RSEQ=TGTTGAGCAGGAGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:216,239:0:2,0:25.5:1:32:1:1:0:60:64:0.9978:0:0.1 0/1:441:17:7,10:218,206:0.0385:2,2:23.1:1:29.1:1:0.46449:1.51037:60:34:0.0391:0:1 -10 74960672 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24874;SOR=Inf;LSEQ=ACGTCACAGTTTTTGCTCTG;RSEQ=ATGGCGACATGGACCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:133,159:0:2,0:22.5:1:31.8:1:1:0:60:72:1:0:0.1 0/1:296:3:1,2:135,158:0.0101:2,2:9:1:28.7:1:1:1.7059:60:6:0.0102:0:1 -10 74960675 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24875;SOR=Inf;LSEQ=TCACAGTTTTTGCTCTGCAT;RSEQ=GCGACATGGACCAGAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:133,160:0:2,0:22.5:1:31.2:1:1:0:60:72.25:0.9966:0:0.1 0/1:297:3:2,1:132,162:0.0101:2,2:31:1:31.3:1:0.59068:2.45:60:6:0.0101:0:1 -10 74960683 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11984;SOR=Inf;LSEQ=TTTGCTCTGCATGGCGACAT;RSEQ=GACCAGAAGGAGAGAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:133,158:0:2,0:23.7:1:31.2:1:1:0:60:47.5:1:0:0.1 0/1:284:3:3,0:126,154:0.0106:2,0:13.3:1:25.3:1:0.09351:0:60:6:0.0106:0:1 -10 79127430 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4902;SOR=Inf;LSEQ=TCAAGATACAGAACAACTCT;RSEQ=CCCCAAAAACTATCTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:26:1:32.3:1:1:0:60:52:1:0:0.1 0/1:26:2:1,1:11,13:0.0769:2,2:21:1:28.5:1:1:1.17:60:4:0.08:0:1 -10 79127539 . A C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTACCTATCCAAGGAAGT;RSEQ=ACATAAATGAAATTGATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:0.9091:0,0:26.5:1:32.9:1:1:0:60:20:0.9091:0:1 1/1:2:2:0,2:0,0:1:0,0:34.5:1:31:1:1:0:60:4:1:0:1 -10 80848835 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49692;SOR=Inf;LSEQ=TGTACAAACGAGTATCCTGT;RSEQ=GACATGGTTGTCTGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:37,27:0:2,0:30.3:1:30.9:1:1:0:60:20.333:1:0:0.2 0/1:69:2:1,1:37,30:0.029:2,2:26.5:1:32:0:1:1.22956:60:4:0.029:0:1 -10 80848893 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23913;SOR=Inf;LSEQ=CGCTGAGCAGGTACCTGGGC;RSEQ=GGTGCCACACTTGGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:12,23:0:2,0:21.2:1:29.9:1:1:0:60:16.5:1:0:0.3 0/1:34:2:1,1:14,18:0.0588:2,2:35:1:29.5:1:1:1.28:60:4:0.0606:0:1 -10 81002050 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCCCGGGGCGGGGCAGG;RSEQ=CCGCGCGCAGCCGCCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:12.5:1:28:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 81003146 . A G 104 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75993;LSEQ=CATTAGCGGAGCCTCCGCCT;RSEQ=TGATTGGCTTCGCCCGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:14.5:1:31.8:1:1:0:60:8:0.8:0:1 1/0:16:12:9,3:2,1:0.75:2,2:17.6:1:29.2:1:1:1.46:60:11:0.7857:0:1.1 -10 81003154 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54023;SOR=Inf;LSEQ=GAGCCTCCGCCTATGATTGG;RSEQ=TTCGCCCGGGAAGCTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:10.4:1:31.2:1:1:0:60:20:1:0:0.4 0/1:20:2:1,1:10,7:0.1:2,2:13.5:1:26.5:1:1:1.40151:60:4:0.1053:0:1 -10 83458193 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAACCTACAATTAATTGGA;RSEQ=TACCAGAAGGAGATGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:34.4:1:32.8:1:1:0:60:16:1:0:0.1 0/1:19:2:1,1:9,8:0.1053:2,2:42.5:1:29.5:1:1:1.11803:60:4:0.1053:0:1 -10 84195177 . G C 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86037;LSEQ=CTGGACTCATTGATTTTTTG;RSEQ=AGGGCTTTTTGTGTCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:0,1:63,61:0.008:2,0:8:0:14:0:0.496:0:55:0:0:0:8 0/1:135:2:1,1:61,72:0.0148:2,2:20.5:1:31.5:1:1:1.18:60:4:0.0152:0:1.5 -10 84195201 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49862;SOR=Inf;LSEQ=GCTTTTTGTGTCTTTATCTC;RSEQ=TTCAGTTCTTCTCTGATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:52,64:0:2,0:20.5:1:31.7:1:1:0:60:37.667:1:0:0.3 0/1:125:2:1,1:49,74:0.016:2,2:18.5:1:29.5:1:1:1.51:60:4:0.0161:0:1.5 -10 84198314 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47895;SOR=0;LSEQ=ACAGGCAGCTGCAGTTGGTG;RSEQ=TGGTCACCCCTCACCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:0.1818:2,2:9:0:32:1:0.49091:3.05504:60:4:0.1818:0:1 0/0:9:0:0,0:7,2:0:2,0:23.4:1:32:1:1:0:60:18:1:0:0 -10 84198390 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49492;SOR=0;LSEQ=CTGTAACAATCTGCGCTTTC;RSEQ=GGGGTTGGGATGCTAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:15:1:29:1:1:1.07415:60:4:0.0714:0:1 0/0:24:0:0,0:15,9:0:2,0:27.5:1:28.9:1:1:0:60:23:1:0:0.1 -10 84198427 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49153;SOR=0;LSEQ=GCCCTTGGTGGCATGGGTTC;RSEQ=TGAGTGGGATCTTCCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:0.0667:2,2:41.5:1:31:1:1:1:60:4:0.0667:0:1 0/0:29:0:0,0:13,16:0:2,0:28.4:1:29:1:1:0:60:28:1:0:0.2 -10 85224770 . C A 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22619;SOR=7.11489;LSEQ=TCTACAATCCCAAATAGACT;RSEQ=TTTAGCAGCAGTGACTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:47:0:30:0:1:0:60:2:0.3333:0:1 1/1:6:5:3,2:0,1:0.8333:0,2:30.4:1:28.6:1:1:0:60:10:0.8333:0:1.2 -10 85224968 . G A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92145;LSEQ=AAACTCTTATACCAAACTCT;RSEQ=GACTTGGGCAACATGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:16:8,8:16,11:0.3721:2,2:30.9:1:28.7:1:0.75156:1.44176:60:15:0.3571:0:1.1 0/1:34:12:8,4:12,10:0.3529:2,2:30.3:1:27.1:1:0.71698:1.64:60:11:0.3438:0:1.4 -10 85225048 . T TACAC 45 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=15.000;MSILEN=2;SSF=0.08152;SOR=Inf;LSEQ=TATAGTTCATAAAAAATGTA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:3,10:0:2,0:34.5:1:28.6:1:1:0:60:26:1:0:0.4 0/1:11:3:0,3:1,7:0.2727:2,0:16.7:1:28.8:1:1:0:60:6:0.2727:0.1818:4 -10 85225073 . AC CCAT 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=1;LSEQ=CACACACACACACACACACA;RSEQ=ATTATTATATATGTATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:1,7:0.25:2,0:25.7:1:30.9:1:1:0:60:6:0.25:0:1.3 0/1:8:2:0,2:0,3:0.25:0,0:18:1:32.4:0:1:0:60:4:0.25:0:1 -10 85225074 . C T 41 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=13.000;MSILEN=2;SSF=0.26213;SOR=5.42517;LSEQ=CACACACACACACACACACA;RSEQ=ATTATTATATATGTATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:0,7:0.0909:0,0:23:0:24:0:1:0:60:2:0.125:0:4 0/1:8:3:0,3:0,3:0.375:0,0:27:1:26:1:1:0:60:6:0.5:0:5.3 -10 85225096 . C T 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.22222;SOR=7.2181;LSEQ=TTATTATATATGTATATACA;RSEQ=ACATTATATTGTATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:23:1:29:1:1:0:60:4:0.25:0:3 1/0:4:3:0,3:0,1:0.75:0,0:48.7:1:27:1:1:0:60:6:0.75:0:5.3 -10 85225107 . GTA G 63 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.04762;SOR=Inf;LSEQ=GTATATACACACATTATATT;RSEQ=TATATATATGTATATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:0.2:0,0:37:0:32:0:1:0:60:2:0.2:0:4 1/1:4:4:0,4:0,0:1:0,0:39.5:1:31.5:1:1:0:60:8:1:0:4 -10 85225139 . G A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=1;SOR=2.44949;LSEQ=GTATATACACACATTATATT;RSEQ=TATATATATAAGTCAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:8:0:32:0:1:0:60:2:0.5:0:4 1/0:4:3:0,3:0,1:0.75:0,0:9.3:1:31.3:1:1:0:60:6:0.75:0:5.3 -10 86028463 . A C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08789;SOR=0.58043;LSEQ=CTATGTGTCCATTTATTCTT;RSEQ=CGCTAACTTTATTAATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:40:35,5:43,5:0.4545:2,2:23.4:1:31.7:1:1:1.22568:60:80:0.4545:0:1 0/1:83:27:22,5:45,11:0.3253:2,2:20.6:1:31:1:1:1.07:60:54:0.3253:0:1.1 -10 86028479 . TA T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24338;SOR=Inf;LSEQ=TCTTACGCTAACTTTATTAA;RSEQ=ACTCCAAGATGGCTCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:98,35:0:2,0:22.2:1:28.5:1:1:0:60:65.5:1:0:0.3 0/1:130:2:1,1:91,37:0.0154:2,2:29:1:27.9:1:0.50078:2.44019:60:4:0.0155:0.0077:0.5 -10 86028579 . T C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=0.38599;LSEQ=CATTCCCAATAACCATAAAA;RSEQ=AAAAATCTTGAGTTGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:156:76,80:83,98:0.4629:2,2:26.4:1:31.7:1:0.66176:1.12:60:51:0.4622:0:1.8 0/1:401:100:45,55:152,149:0.2494:2,2:25.2:1:31.1:1:0.35758:1.24614:60:99:0.2506:0:1.8 -10 86028605 . C G 253 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02309;LSEQ=TCTTGAGTTGGGGCTTGATT;RSEQ=GACCACTTCTAAACAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:295:282:110,172:8,5:0.9559:2,2:26.8:1:31.2:1:0.14665:2.49381:60:93:0.9555:0:1.5 0/1:331:110:48,62:102,117:0.3323:2,2:28:1:30.6:1:0.64017:1.12566:60:54:0.3303:0:1.8 -10 86028662 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49882;SOR=0;LSEQ=TAAAATGATAGTTGGCTTAA;RSEQ=ACTCCCATTAATCCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:28,108:0.0145:2,2:26.5:1:30.5:1:0.37734:3.81:60:4:0.0146:0:1.5 0/0:128:0:0,0:33,95:0:2,0:22.8:1:27.9:1:1:0:60:63:1:0:0.4 -10 86331958 . G T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16261;SOR=0.31949;LSEQ=TGGGGTCCTTTTCCACACTG;RSEQ=GAAAAGTTTGTTCTTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:3,4:4,6:0.4118:2,2:27.6:1:31:1:1:1.12:60:14:0.4118:0:2.1 0/1:28:5:1,4:11,12:0.1786:2,2:20.6:1:28.6:1:0.35531:3.51527:60:10:0.1852:0:2 -10 86331960 . A G 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00776;SOR=0.10947;LSEQ=GGGTCCTTTTCCACACTGGG;RSEQ=AAAGTTTGTTCTTTTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:4,5:0.4375:2,2:26.1:1:33:1:1:1.06235:60:14:0.4375:0:2.1 0/1:27:2:0,2:12,13:0.0741:2,0:26.5:1:26.5:1:0.48718:0:60:4:0.0769:0:3 -10 86332020 . A G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTACAATTTTTGGGTCCAC;RSEQ=TTGCCTTTATGAGCTGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:11.5:1:30.5:1:1:0:60:4:1:0:0 0/1:9:2:0,2:0,7:0.2222:0,0:14.5:1:33:0:1:0:60:4:0.25:0:3 -10 88127039 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGCCAGAGGGGGCCGGCCGC;RSEQ=GCAAGCATCTCAGAGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 88635779 . C A 228 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACATTACAATTGAACAATG;RSEQ=CTCAGCTATACATTTACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1052:0:0,0:555,496:0:2,0:25.7:1:31.6:1:1:0:58.5:130.375:0.999:0:0.1 0/1:1179:249:138,111:492,434:0.2112:2,2:21.4:1:28.7:1:0.56698:1.10:48.4:61.25:0.2103:0:1.1 -10 88635888 . C T 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GTATGTGTGTATATAAAAAG;RSEQ=ACTATTTCTTGCTTCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:92,331:0:2,0:23:1:31.9:1:1:0:60:69.5:0.9976:0:0.1 0/1:432:14:4,10:106,309:0.0324:2,2:18.7:1:28.9:1:0.7612:1.17:60:28:0.0329:0:1.1 -10 88649763 . C T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=15.5776;LSEQ=TTTCTCATTGAAAATTGTCA;RSEQ=GAAACAATGAGCTTTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:8:8,0:107,19:0.0597:2,0:15.9:1:30.8:1:0.60048:0:60:16:0.0611:0:1 1/0:130:65:55,10:60,5:0.5:2,2:23.3:1:29.8:1:0.27195:2.16904:60:64:0.4961:0:1.1 -10 88650068 . G GT 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.47422;SOR=1.96097;LSEQ=AATTATTAAACTTGTCTGCG;RSEQ=TTTTTTTTTCATTCATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:3:0,3:5,73:0.037:2,0:35:1:30.7:1:1:0:60:6:0.037:0:0 0/1:71:5:0,5:5,61:0.0704:2,0:31.4:1:30.6:1:1:0:60:10:0.0735:0:0 -10 88652022 . G A 43 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13777;SOR=Inf;LSEQ=GGACCCATGAGACAAAGAAG;RSEQ=GAGGGGCCATATGAAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:73,213:0:2,0:23.2:1:30.7:1:1:0:60:46.667:1:0:0.1 0/1:376:4:3,1:111,261:0.0106:2,2:7:1:21.8:1:0.08501:7.01:60:3:0.0083:0:2 -10 88659494 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25331;SOR=Inf;LSEQ=TATTTTATGAATACTAAAAA;RSEQ=ACATATCAGTTTAAAATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:190,26:0:2,0:24.8:1:32.1:1:1:0:60:53:1:0:0.1 0/1:254:3:2,1:201,50:0.0118:2,2:27:1:22.7:1:0.49103:2.00347:60:2:0.0079:0:1 -10 88659758 . T A 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATTTTTTCATTTCAATTG;RSEQ=TTACATTGTTTACTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:566:0:0,0:338,228:0:2,0:24.5:1:30:1:1:0:60:187.667:1:0:0.1 0/1:805:36:19,17:446,320:0.0447:2,2:21.9:1:28.9:1:0.60487:1.24668:60:35:0.0441:0:1.2 -10 88659788 . G A 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTACTTTTATTGTCAGGTCC;RSEQ=TTTTTTGATGGCAGCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:0:0,0:394,331:0:2,0:25.9:1:30.8:1:1:0:57:180.25:0.9986:0:0.1 0/1:1056:25:12,13:560,471:0.0237:2,2:26.6:1:29.5:1:0.54894:1.28772:59.2:50:0.0239:0:1.1 -10 88660269 . CA C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTTCAGAAGACAGTTGC;RSEQ=AAAAAGAAGAGTAATAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:20.5:1:31:1:1:1:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 88661887 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGCCCTCCCAAATTGCTGG;RSEQ=ATTACAGGCGTGAGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:30:1:1:0:60:4:1:0:1 -10 88671873 . A G 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03029;SOR=Inf;LSEQ=ACAGGATATATTATCCAATG;RSEQ=TAAGACTAATTTGGATAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:64,0:0:1,0:22.4:1:30.2:1:1:0:60:128:1:0:0.1 0/1:30:3:3,0:27,0:0.1:1,0:22.7:1:30.7:1:1:0:60:6:0.1:0:1 -10 88671946 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49889;SOR=Inf;LSEQ=ACCTCAAGGTTTTTCTTAGG;RSEQ=TTTTATAGTTTTTCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:176,18:0:2,0:22.9:1:31.4:1:1:0:60:63.667:1:0:0.1 0/1:201:2:1,1:178,21:0.01:2,2:15:1:27:1:0.20741:8.30351:60:4:0.0101:0:1 -10 88672153 . G A 147 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=39.69038;LSEQ=CCTTTATTGGTAAGTTAAAC;RSEQ=TTCCTATAGACATGAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:707:1:1,0:268,437:0.0014:2,0:1:0:27:0:0.38102:0:60:2:0.0014:0:1 0/1:713:38:19,19:254,421:0.0533:2,2:26.8:1:28.2:1:0.1691:1.66:59.5:18:0.0511:0:1.3 -10 88672247 . AT A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.13131;SOR=Inf;LSEQ=CAGGGAACAATAATGGACAC;RSEQ=TTTTTTCTCCTTATTTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:0,161:0:1,0:22.9:1:30.5:1:1:0:60:79.5:1:0:0.1 0/1:92:2:0,2:2,88:0.0217:1,0:36:1:31.5:1:1:0:60:4:0.022:0:1 -10 88676749 . CA C 100 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.86092;LSEQ=GACAGAGCGAGACTCCATCT;RSEQ=AAAAAAAAAAAGTACATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:9:8,1:46,2:0.1552:1,2:25.7:1:31.8:1:0.40889:2.8045:60:18:0.1552:0:0.2 0/1:44:6:6,0:37,1:0.1364:1,0:25:1:30.4:1:1:0:60:12:0.1395:0.0227:0.3 -10 88677218 . C G 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01096;SOR=Inf;LSEQ=AGGAAACCTAGTAGAATACA;RSEQ=GGTTTGAATAAAACATAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:1,84:0:1,0:20.8:1:29.4:1:1:0:60:27.333:1:0:0.1 0/1:60:5:0,5:0,55:0.0833:1,0:23.6:1:29.8:1:1:0:60:10:0.0847:0:1 -10 88678748 . A T 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATTTATTGTAGAAGTACAG;RSEQ=TATATGTGTAAATGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:39,0:0,0:1:0,1:23.9:1:31.2:1:1:0:60:78:1:0:1.1 1/1:28:28:27,1:0,0:1:0,1:22.8:1:30.5:1:1:0:60:56:1:0:1 -10 88678807 . C T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12312;SOR=Inf;LSEQ=ATTCACGACTTGGTGTCAGG;RSEQ=GAATTAAAGTTTCACTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:92,0:0:1,0:23.4:1:32:1:1:0:60:29.667:1:0:0.4 0/1:102:4:4,0:96,2:0.0392:1,0:26.3:1:31.3:1:1:0:60:8:0.0392:0:1 -10 88678882 . G T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0237;SOR=0;LSEQ=ATGAGCATTACTTCTCCCTA;RSEQ=CCTATCTCTGATGATAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:4:1,3:248,115:0.0109:2,2:9:1:28.5:1:0.0997:6.43424:60:8:0.011:0:1 0/0:566:0:0,0:346,220:0:2,0:24.1:1:31.5:1:1:0:60:69.75:1:0:0.1 -10 88679356 . TG T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00178;SOR=Inf;LSEQ=TAGTTACATAAATGTATAGT;RSEQ=GGGGGGATTTTGTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:2,42:0:1,0:25.3:1:30.8:1:1:0:60:43:1:0:0 0/1:33:7:0,7:1,25:0.2121:1,0:19.9:1:31:1:1:0:60:14:0.2121:0:0 -10 88681458 . A G 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTGTATCACAGGAGGTGGG;RSEQ=GTTTGAGTAGTTTCTGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:648:0:0,0:254,394:0:2,0:26.2:1:30.4:1:1:0:59.6:42.2:1:0:0.1 0/1:893:39:18,21:362,492:0.0437:2,2:22.1:1:30.8:1:0.74093:1.16:58.8:38:0.0439:0:1.3 -10 88682999 . T ATGTATATA 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.03471;SOR=Inf;LSEQ=CATACATCTACTATTAAGAG;RSEQ=GAATCATAGTGTCTATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:63,1:0:1,0:22.6:1:33:1:1:0:60:128:1:0:0.1 0/1:32:3:3,0:29,0:0.0938:1,0:22.7:1:29:1:1:0:60:6:0.0938:0.0313:0.7 -10 88683122 . T C 221 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGTGCCCATGTTTTCTCA;RSEQ=TCCCTTATAGGGATCGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:266,132:0:2,0:25.4:1:30.8:1:1:0:60:198:1:0:0.1 0/1:495:134:85,49:223,138:0.2707:2,2:26.9:1:31.4:1:0.75534:1.07:60:133:0.2698:0:1.1 -10 88866050 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28483;SOR=Inf;LSEQ=GGGATTATAGGCATGAGCCA;RSEQ=TGTTCCCGGCCAGAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:46,20:0:2,0:20.9:1:31.7:1:1:0:60:65:1:0:0.1 0/1:105:3:1,2:66,36:0.0286:2,2:16:1:26:1:0.29626:3.61907:60:6:0.0286:0:1 -10 88866085 . TCA T 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGGAATAATTGTTAGACAAC;RSEQ=CAGTGTCTGCCATATTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:18:11,7:69,45:0.1364:2,2:29.6:1:32.5:1:1:1.02:60:36:0.1385:0:0.3 0/0:233:0:0,0:127,105:0:2,0:25.6:1:31:1:1:0:60:76.333:0.9957:0:0.3 -10 88866129 . C G 176 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=13.83862;LSEQ=CAGAAAATAACTGACTTGCT;RSEQ=TCTGCTGTCTTACTGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:3:1,2:83,78:0.0183:2,2:14.7:1:31.3:1:0.61361:2.11873:60:6:0.0186:0:1 0/1:248:51:22,29:90,107:0.2056:2,2:27.3:1:31.2:1:0.75535:1.10829:60:50:0.2049:0:1.1 -10 88866168 . AT A 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06326;SOR=Inf;LSEQ=TAATATATTTTTTTAACGCA;RSEQ=TTACAAAAGGGGGGGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:46,68:0:2,0:24.9:1:29.8:1:1:0:59.9:37:1:0:0.1 0/1:133:5:1,4:38,90:0.0376:2,2:16.6:1:30.2:1:1:1.68296:60:10:0.0382:0.0226:0.2 -10 88866177 . A AG 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.21645;LSEQ=TTTTTAACGCAATTTACAAA;RSEQ=GGGGGGGAACATTCTTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:97:54:16,38:18,23:0.5567:2,2:28.4:1:31.2:1:0.19564:1.84634:59.7:108:0.5567:0.0722:0.2 0/1:113:24:6,18:26,63:0.2124:2,2:30.2:1:30:1:0.80153:1.2358:59.8:23:0.213:0.0088:0.1 -10 89153971 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17576;SOR=Inf;LSEQ=TCCTCCCTTACCCTTGATGT;RSEQ=CCCTCGTAGTCATTTCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:0:2,0:31.9:1:30.2:1:1:0:60:26:1:0:0.3 0/1:20:2:1,1:10,8:0.1:2,2:34.5:1:30.5:1:1:1.23603:60:4:0.1:0:1 -10 89153995 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16944;SOR=Inf;LSEQ=TCGTAGTCATTTCCTATCTG;RSEQ=TAACCCCCATCCTCCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:26.5:1:32.3:1:1:0:60:50:1:0:0.2 0/1:18:2:1,1:6,10:0.1111:2,2:36.5:1:28.5:1:1:1.62:60:4:0.1111:0:1 -10 89623860 . CT C 83 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAACACGGCGGCGGCGGCGG;RSEQ=GGCACATCCAGGGACCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:32.3:1:32.3:1:1:0:60:12:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29:1:1:0:60:4:1:0:0 -10 89623901 . G C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCGGTTTTAAACCTCCCGT;RSEQ=CGCCGCCGCCGCACCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:6.3:1:31.7:1:1:0:58:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 89653686 . A G 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10071;SOR=0.56966;LSEQ=CTCCAGCTATAGTGGGGAAA;RSEQ=CTTTCTTTTCATAACTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:31:28,3:52,5:0.3523:2,2:24.2:1:31.7:1:1:1.1129:60:30:0.3448:0:1.1 0/1:89:21:18,3:61,7:0.236:2,2:19.8:1:32.1:1:0.69473:1.44584:60:42:0.2386:0:1.1 -10 89653834 . C T 138 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=25.60157;LSEQ=CCTGCAGAAAGACTTGAAGG;RSEQ=GTATACAGGAACAATATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:1:0,1:246,275:0.0019:2,0:1:0:27:0:1:0:60:2:0.002:0:1 0/1:598:28:11,17:257,313:0.0468:2,2:26.6:1:28.9:1:0.56711:1.26845:60:27:0.0462:0:1.1 -10 89653911 . T A 31 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24872;SOR=0;LSEQ=TCAAATATTGATGTTTATAT;RSEQ=CATGTTGTGTTTTCATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:2,1:50,161:0.014:2,2:14.7:1:20:1:0.1471:6.37:60:2:0.0096:0:1.3 0/0:203:0:0,0:52,151:0:2,0:23.5:1:29.1:1:1:0:60:202:1:0:0.1 -10 89685391 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50522;SOR=Inf;LSEQ=TGAAAGTTATCTGCTTGTTA;RSEQ=AGTGAGGTAGAGTTAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:23,87:0:2,0:22.4:1:31.4:1:1:0:60:220:1:0:0.1 0/1:140:2:1,1:37,101:0.0143:2,2:27:0:31:1:0.47061:2.71:60:4:0.0144:0:1 -10 89690770 . TA T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15663;SOR=0;LSEQ=TTCTTCCTAAGTGCAAAAGA;RSEQ=ACTTTATATCACTTTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:120,73:0.0102:2,2:29:0:30:1:1:1.63941:60:4:0.0103:0:0.5 0/0:300:0:0,0:194,106:0:2,0:24:1:28.5:1:1:0:60:600:1:0:0.1 -10 89690952 . T TTTATC 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94981;LSEQ=ATTATCGAGTGAGATACATA;RSEQ=TTAAGAATTATCTTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:14:0,14:2,50:0.2059:1,1:26.3:1:29:1:1:0:60:28:0.209:0.0588:0 0/1:81:16:0,16:2,63:0.1975:1,1:26.4:1:30.8:1:1:0:60:32:0.2078:0.037:0.1 -10 89692731 . G GT 102 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.02433;SOR=0.27549;LSEQ=TGTTAATTAAAAATTCAAGA;RSEQ=TTTTTTTTTCTTATTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:13:12,1:191,67:0.0476:2,1:24.4:1:27.8:1:0.19545:4.19:60:5.5:0.0406:0:0.2 0/1:295:4:3,1:209,80:0.0136:2,2:33.8:1:31:1:1:1.15:60:8:0.0136:0:0.3 -10 89692844 . C T 229 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTTTTGTGAAGATCTTGAC;RSEQ=AATGGCTAAGTGAAGATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:224:117,107:158,157:0.4148:2,2:22.3:1:29.4:1:0.66249:1.09:50.6:73.667:0.4139:0:1.1 0/0:619:0:0,0:313,304:0:2,0:22.3:1:30.5:1:1:0:50.3:204.667:0.9984:0:0.1 -10 89693036 . T C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12099;SOR=0;LSEQ=ATTTTTTGATGTTTTTCCTT;RSEQ=CCTCTTCCTGGATCTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:1,2:41,185:0.013:2,2:33.7:1:25.3:1:0.45709:2.25:49:2:0.0088:0:2.3 0/0:234:0:0,0:74,160:0:2,0:22.8:1:29.1:1:1:0:60:77:1:0:0.1 -10 89709901 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTGCGCGCCTGTAGTCC;RSEQ=AGCTACACGGGAGGCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:1:28:1:1:0:45.5:4:1:0:1 -10 89711813 . T A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11695;SOR=0;LSEQ=CAGTTACCATAGCAATTTAG;RSEQ=GAAATAACTATAATGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:130,24:0.0191:2,2:19.7:1:24.7:1:0.40785:2.68535:60:2:0.0132:0:1.3 0/0:163:0:0,0:129,33:0:2,0:23.4:1:29.1:1:1:0:60:161:0.9938:0:0.1 -10 89711833 . AT A 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.6922;SOR=1.70121;LSEQ=TGAAATAACTATAATGGAAC;RSEQ=TTTTTTTCAATTTGGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:2:1,1:176,59:0.0084:2,2:10.5:1:30.1:1:0.44304:2.96644:60:4:0.0085:0.0042:0 0/1:280:4:3,1:201,75:0.0143:2,2:34.3:1:31:1:1:1.12:60:8:0.0144:0:0 -10 89711855 . C CT 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.2516;LSEQ=TTTTTTTCAATTTGGCTTCT;RSEQ=TTTTTTTTCTGTCCACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:4:3,1:230,83:0.0126:2,2:30:1:30.5:1:1:1.08:60:8:0.0129:0:0 0/1:381:6:5,1:248,125:0.0157:2,2:29:1:31.2:1:0.66815:2.52:60:12:0.016:0.0026:0 -10 89717709 . AGCCGT A 237 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATGTACTTTGAGTTCCCTC;RSEQ=TACCTGTGTGTGGTGATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:215:93,122:137,172:0.4103:2,2:25.8:1:30.7:1:0.85804:1.04482:59.7:430:0.4167:0.0687:0 0/0:722:0:0,0:343,378:0:2,0:25.8:1:31.9:1:1:0:59.7:179.25:0.9986:0:0.2 -10 89717776 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07872;SOR=0;LSEQ=CAGAACAAGATGCTAAAAAA;RSEQ=GTTTGTACTTTACTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:3:1,2:69,205:0.0108:2,2:8.7:1:29:1:1:1.48:60:6:0.011:0:1 0/0:368:0:0,0:128,240:0:2,0:23:1:30.5:1:1:0:59.6:91:1:0:0.1 -10 89720251 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGTAGCTCATTTGAAATG;RSEQ=AGAAAAAATTAAATCCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 89720617 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11409;SOR=Inf;LSEQ=ATTAATTAAATATGTCATTT;RSEQ=ATTTCTTTTTCTTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:82,4:0:1,0:23.1:1:30.2:1:1:0:60:20.5:1:0:0.6 0/1:82:3:3,0:60,15:0.0366:2,0:20.3:1:28:1:1:0:57.7:6:0.0469:0:1.3 -10 89720628 . C T 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=1.01131;LSEQ=ATGTCATTTCATTTCTTTTT;RSEQ=TTTTCTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:10:0,10:84,5:0.101:2,0:9.3:1:18.8:1:0:0:56:0.667:0.0455:0:2.6 0/1:98:10:0,10:70,17:0.102:2,0:10.8:1:20.6:1:0:0:52.2:1.5:0.0811:0:3.1 -10 89720881 . T A 55 Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00921;SOR=0;LSEQ=TCTCCAAATTTTAAGGTCAG;RSEQ=TAAATTAAACATTTTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:5:5,0:194,298:0.0101:2,0:8.8:1:24:1:0.00998:0:43.8:4:0.0081:0:2.2 0/0:769:0:0,0:314,455:0:2,0:23.9:1:29.5:1:1:0:58.8:108.857:1:0:0.2 -10 89720907 . T G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29834;LSEQ=TAAACATTTTGTGGGGGTTG;RSEQ=TGACTTGTATGTATGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:135:45,90:52,139:0.4128:2,2:24.1:1:31.4:1:0.26866:1.34:50.7:134:0.4149:0:1.1 0/1:462:80:25,55:125,257:0.1732:2,2:22.4:1:30:1:0.89567:1.06989:50.8:39:0.1714:0:1.2 -10 89721094 . C T 80 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCCTTTTCCTAATTCTT;RSEQ=GTTGTTTGCTGAAATCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:18.7:1:31.2:1:1:0:60:12:1:0:1.2 1/1:1:1:0,1:0,0:1:0,0:26:0:31:0:1:0:60:2:1:0:1 -10 89725230 . A AT 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.82872;SOR=0.90754;LSEQ=CACAAATTACAAAAGTCTGA;RSEQ=TTTTTTTTTATCAAGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:10:5,5:180,262:0.0221:2,2:27.6:1:30:1:0.74684:1.45:52.3:20:0.0224:0.0022:0 0/1:548:11:5,6:250,286:0.0201:2,2:26.8:1:27.8:1:1:1.04887:54.6:10:0.0185:0:0.2 -10 89725293 . CT C 169 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.60846;SOR=1.14579;LSEQ=TGAATAAACTGAAAATGGAC;RSEQ=TTTTTTTTTTAATGGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:30:4,26:33,166:0.1293:2,2:30.2:1:32.5:1:0.79427:1.2908:59.7:60:0.1351:0:0.2 0/1:275:40:4,36:35,199:0.1455:2,2:24.8:1:31.8:1:0.62346:1.58051:58.4:80:0.1504:0:0.3 -10 90918714 . G T 195 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=95.57489;LSEQ=GCACTCCCCCCCTGCCGTGG;RSEQ=TATACATGTCATAATATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:1:1,0:188,206:0.0025:2,0:4:0:25:0:0.47848:0:60:2:0.0026:0:1 0/1:466:91:46,45:174,201:0.1953:2,2:29.1:1:30:1:0.48505:1.18:60:182:0.197:0:1.1 -10 90918802 . AAG A 92 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.79763;SOR=0.86201;LSEQ=AGTTGATATTTGAAGAAAGA;RSEQ=AGAGAGAGAGAGAAAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:8:0,8:23,105:0.0588:2,0:28.3:1:30.8:1:0.35093:0:60:16:0.0597:0:0.4 0/1:137:7:2,5:34,95:0.0511:2,2:34.4:1:30.6:1:1:1.12:60:14:0.0519:0:0 -10 90918806 . G T 27 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.49807;SOR=Inf;LSEQ=GATATTTGAAGAAAGAAAGA;RSEQ=AGAGAGAGAGAAAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:21,109:0:2,0:24.4:1:31.2:1:1:0:60:42.333:1:0:0.2 0/1:130:2:1,1:31,96:0.0154:2,2:20:1:27.5:1:0.43605:3.06:60:4:0.0155:0:1 -10 91613683 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53846;SOR=Inf;LSEQ=GGCTCTGCACCCTTCCGGCC;RSEQ=CTAAGACAAGGCCTCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:19.7:1:29.4:1:1:0:60:8:1:0:0.2 0/1:18:2:1,1:5,11:0.1111:2,2:13.5:1:28:1:1:2.10:60:4:0.125:0:1 -10 93654341 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=TTTGATCTTTCTTATAAGTG;RSEQ=ATAGAAGAAAATGCTGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:14,3:0:2,0:23.6:1:31.8:1:1:0:60:16:1:0:0.1 0/1:13:2:1,1:11,0:0.1538:0,2:32:1:28:1:0.15385:0:60:4:0.1538:0:1 -10 93654381 . C T 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45634;SOR=2.12022;LSEQ=TATGCTGCCTTCTCTCTCTC;RSEQ=TTCAGCTACATAAAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:2,1:24,12:0.0769:2,2:11.7:1:28:1:1:1:60:6:0.0811:0:1 0/1:33:5:3,2:14,14:0.1515:2,2:15.4:1:29:1:1:1.48:60:10:0.1563:0:1 -10 93654415 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49515;SOR=0;LSEQ=AAGGGAAAGCACCCCTGTCC;RSEQ=ATGATCATGTGACTTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:27,23:0.0385:2,2:45:0:33:1:1:1.17028:60:4:0.0385:0:1.5 0/0:52:0:0,0:24,28:0:2,0:27:1:28.8:1:1:0:60:51:1:0:0.3 -10 93878432 . A G 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34611;SOR=0.82596;LSEQ=ATGGCTGCACTCTTGCTGAG;RSEQ=CATGTTGGTCGACATTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:63:39,24:141,78:0.2143:2,2:29.5:1:30.7:1:0.76666:1.112:53.4:30.5:0.2096:0:6 0/1:457:84:55,29:208,134:0.1838:2,2:28.3:1:31.5:1:0.45482:1.22:54.3:168:0.1883:0:6.1 -10 93878434 . A T 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51041;SOR=0.88308;LSEQ=GGCTGCACTCTTGCTGAGAC;RSEQ=TGTTGGTCGACATTGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:62:38,24:150,82:0.2109:2,2:31.7:1:30.5:1:0.65644:1.15475:53.5:124:0.2116:0:6 0/1:440:84:55,29:214,141:0.1909:2,2:30.1:1:30.4:1:0.45502:1.25:54.3:41:0.1916:0:6.1 -10 93878441 . T C 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.64319;SOR=0.90898;LSEQ=CTCTTGCTGAGACATGTTGG;RSEQ=CGACATTGCCTCCGAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:63:38,25:156,99:0.1981:2,2:35.9:1:31.4:1:1:1.03659:53.3:62:0.1968:0:6 0/1:469:86:55,31:222,161:0.1834:2,2:34.9:1:31.5:1:0.33327:1.29:53.9:172:0.1878:0:6 -10 93878444 . A T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64494;SOR=0.90593;LSEQ=TTGCTGAGACATGTTGGTCG;RSEQ=CATTGCCTCCGAGCCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:63:38,25:162,103:0.1921:2,2:36.6:1:29.6:1:1:1.03466:53.3:126:0.1933:0:6 0/1:491:87:55,32:235,168:0.1772:2,2:35.6:1:29.2:1:0.47069:1.23:53.7:174:0.1798:0:6 -10 93878447 . T C 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58687;SOR=0.90428;LSEQ=CTGAGACATGTTGGTCGACA;RSEQ=TGCCTCCGAGCCCACTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:65:38,27:162,109:0.1935:2,2:35.5:1:31.7:1:0.88848:1.05583:52.9:130:0.1952:0:5.9 0/1:505:90:57,33:242,173:0.1782:2,2:36.3:1:31.2:1:0.40913:1.23:53.7:180:0.1807:0:5.9 -10 93878455 . G A 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56915;SOR=1.10449;LSEQ=TGTTGGTCGACATTGCCTCC;RSEQ=AGCCCACTTTAGCCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:76:42,34:180,120:0.2016:2,2:27.6:1:29.8:1:0.5141:1.21364:51.8:152:0.2038:0:5.3 0/1:564:123:68,55:247,193:0.2181:2,2:26.9:1:29.8:1:0.91825:1.03508:52.3:246:0.2216:0:4.7 -10 93878496 . C CTGATGGTTG 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44265;SOR=1.42202;LSEQ=TCTGTATCAGAAATGCTGTT;RSEQ=CTTTGGGAACCACAGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:9:1,8:164,172:0.0259:2,2:22.6:1:30:1:0.03821:7.59407:40.9:18:0.0265:0.0086:6.4 0/1:548:20:3,17:252,275:0.0365:2,2:26.3:1:29.3:1:0.00488:5.17988:39.8:40:0.037:0.0128:6.1 -10 93878509 . CA TG 120 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19863;SOR=1.9207;LSEQ=TGCTGTTCCTTTGGGAACCA;RSEQ=GGCAAACAAGAGATGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:6:0,6:149,158:0.0191:2,0:40.7:1:31.2:1:0.03082:0:39:12:0.0193:0:5.3 0/1:471:17:0,17:217,236:0.0361:2,1:30.9:1:29.4:1:2e-05:0:38.5:34:0.0365:0.0021:5 -10 93878512 . G C 125 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39131;SOR=1.57955;LSEQ=TGTTCCTTTGGGAACCACAG;RSEQ=CAAACAAGAGATGGAGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:7:0,7:149,158:0.0223:2,0:36.3:1:31.3:1:0.01542:0:38.7:14:0.0227:0:5.4 0/1:460:16:0,16:214,229:0.0348:2,1:31.8:1:31.3:1:4e-05:0:37.2:32:0.0356:0:5.3 -10 93878517 . C G 126 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39282;SOR=1.55239;LSEQ=CTTTGGGAACCACAGGCAAA;RSEQ=AAGAGATGGAGCGGTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:7:0,7:142,157:0.0229:2,0:33:1:31.7:1:0.01623:0:38.7:14:0.0233:0:5.4 0/1:456:16:0,16:210,229:0.0351:2,1:29.3:1:31.6:1:4e-05:0:37.2:32:0.0354:0:5.3 -10 93878526 . G A 123 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39237;SOR=1.55404;LSEQ=CCACAGGCAAACAAGAGATG;RSEQ=AGCGGTTCTGGAATAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:7:0,7:131,152:0.0241:2,0:26.3:1:31.3:1:0.01752:0:38.7:14:0.0245:0:5.4 0/1:432:16:0,16:206,210:0.037:2,1:24.3:1:30.9:1:3e-05:0:37.2:32:0.0375:0:5.3 -10 93878530 . G A 127 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39417;SOR=1.53216;LSEQ=AGGCAAACAAGAGATGGAGC;RSEQ=GTTCTGGAATAAGAACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:7:0,7:135,142:0.0246:2,0:22.3:1:32:1:0.01526:0:38.7:14:0.0253:0:5.4 0/1:429:16:0,16:204,209:0.0373:2,1:20.3:1:31.8:1:3e-05:0:37.2:32:0.0376:0:5.3 -10 93878609 . A G 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38976;SOR=1.15572;LSEQ=AGTTGGTCTCTTCCCATGGC;RSEQ=ATGGCCATCTGCCACCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:147:97,50:100,57:0.4836:2,2:24.7:1:30.1:1:0.71913:1.11:59.7:48:0.4816:0:1.1 1/0:354:184:119,65:108,61:0.5198:2,2:24.1:1:29.8:1:0.91171:1.03:60:60.333:0.5201:0:1.1 -10 93878628 . GAC G 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=3.45141;LSEQ=CAATGGCCATCTGCCACCAT;RSEQ=ACTGGTACTGCTTTGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:13:9,4:242,111:0.0355:2,2:29.6:1:33:1:1:1.03:60:26:0.0359:0.0027:0 0/1:434:49:35,14:247,138:0.1129:2,2:25.6:1:31.5:1:0.34429:1.40:60:98:0.1148:0.023:0 -10 93878772 . G A 159 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.00867;LSEQ=ACACAGCTAAGTTTGCACTC;RSEQ=TCTTCCCTCTCATGTATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:922:4:1,3:495,423:0.0043:2,2:20:1:30.8:1:0.34065:3.5062:39.8:8:0.0044:0:4.3 0/1:1111:42:23,19:542,526:0.0378:2,2:19.1:1:29.5:1:0.63987:1.17:57.8:41:0.0373:0:1.2 -10 93878871 . GCTGTCCTGGTTCTTAC ATTGTCTTGGCTCTTAAT 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.428;SOR=0.7691;LSEQ=AGCTATACCAGTCTGGAGTG;RSEQ=TGTGTTGTCCTCTGTAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1188:21:21,0:584,582:0.0177:2,1:25.9:1:29.4:1:0:0:37.6:42:0.0179:0.0177:3.5 0/1:1392:19:19,0:697,672:0.0136:2,1:29.7:1:28.1:1:0:0:43.4:38:0.0138:0.0136:3.9 -10 93878945 . A C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.90627;SOR=0.96354;LSEQ=ACGGAGGTTCCCAGCATCAT;RSEQ=TTCCTACACATTATTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1028:34:23,11:453,541:0.0331:2,2:14.5:1:32.2:1:0.01367:2.49:42.6:68:0.0334:0:7.4 0/1:1285:41:22,19:582,661:0.0319:2,2:14.7:1:31.4:1:0.42855:1.31:44.4:82:0.0321:0:7.3 -10 93878957 . T G 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.38978;SOR=0.85694;LSEQ=AGCATCATATTCCTACACAT;RSEQ=ATTACATTCACCCATCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1058:69:39,30:446,542:0.0652:2,2:16.9:1:31.9:1:0.07983:1.58:49.4:138:0.066:0:7.6 0/1:1365:77:42,35:605,683:0.0564:2,2:17:1:31:1:0.19891:1.35:50.9:76:0.0563:0:7.5 -10 93878970 . CA TG 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73814;SOR=0.94226;LSEQ=TACACATTATTACATTCACC;RSEQ=TCTTTCTGTTTGTCACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1119:70:39,31:479,568:0.0626:2,2:29.3:1:31.7:1:0.10926:1.49:51.5:140:0.0633:0:6.6 0/1:1420:84:45,39:637,695:0.0592:2,2:28.4:1:31.6:1:0.31342:1.26:52.6:168:0.0598:0:6.5 -10 93878975 . TT CC 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6166;SOR=0.91954;LSEQ=ATTATTACATTCACCCATCT;RSEQ=CTGTTTGTCACTCTTATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1125:71:39,32:475,577:0.0631:2,2:32.8:1:31.5:1:0.11167:1.48:51.2:142:0.0643:0:5.6 0/1:1423:83:45,38:638,698:0.0583:2,2:31.3:1:31.4:1:0.25987:1.30:52.6:166:0.0592:0:5.5 -10 93879006 . A C 239 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06708;SOR=0.807;LSEQ=ACTCTTATCTCCAGCCTGGG;RSEQ=AAAGTTCTCCTTATTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1124:177:65,112:405,540:0.1575:2,2:24.6:1:32:1:0.13573:1.29201:50.5:87.5:0.1587:0:6 0/1:1404:184:73,111:549,670:0.1311:2,2:25.2:1:31.8:1:0.17692:1.24575:53.1:91:0.1309:0:5.7 -10 93879018 . T C 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04623;SOR=0.7834;LSEQ=AGCCTGGGAAAAGTTCTCCT;RSEQ=ATTTGTTTAGATCCTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:163:50,113:327,515:0.162:2,2:27.2:1:31.6:1:0.052:1.43449:50.1:80.5:0.1628:0:6.2 0/1:1224:161:55,106:452,610:0.1315:2,2:26.8:1:31.4:1:0.04827:1.42767:53.1:322:0.1333:0:5.9 -10 93879022 . T A 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11823;SOR=0.82135;LSEQ=TGGGAAAAGTTCTCCTTATT;RSEQ=GTTTAGATCCTTTTGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:940:149:43,106:302,489:0.1585:2,2:27:1:30.2:1:0.03303:1.52177:50.5:73.5:0.1591:0:6.2 0/1:1142:153:57,96:410,579:0.134:2,2:25.2:1:29.7:1:0.33283:1.19244:53.5:306:0.135:0:5.9 -10 93879038 . CA TG 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04584;SOR=0.72594;LSEQ=TATTTGTTTAGATCCTTTTG;RSEQ=CTTTCAGATCCCCTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:95:17,78:224,406:0.1303:2,2:20.1:1:31.5:1:0.00063:2.52859:46.9:94:0.1302:0:5.9 0/1:836:82:18,64:288,466:0.0981:2,2:20.4:1:31.4:1:0.00361:2.19555:49.7:164:0.0993:0:6 -10 93879045 . A T 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08793;SOR=0.74919;LSEQ=TTAGATCCTTTTGCACTTTC;RSEQ=GATCCCCTTGGAGCAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:630:92:15,77:179,359:0.146:2,2:14.6:1:31.1:1:9e-04:2.55621:46.5:184:0.1479:0:6 0/1:731:83:18,65:230,417:0.1135:2,2:14.8:1:30.4:1:0.01344:1.99003:49.8:40.5:0.1117:0:5.9 -10 93879049 . C A 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07279;SOR=0.7403;LSEQ=ATCCTTTTGCACTTTCAGAT;RSEQ=CCCTTGGAGCAGTAGAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:600:93:16,77:162,345:0.155:2,2:10.5:1:30:1:0.00429:2.25707:46.6:45.5:0.1548:0:5.9 0/1:686:82:19,63:207,397:0.1195:2,2:10.4:1:30:1:0.0458:1.72761:49.7:164:0.1206:0:5.9 -10 93879078 . A C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.91347;LSEQ=GCAGTAGAGTACCTTGTAGA;RSEQ=CATAAGAGTGGAAAAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:278:140:23,117:22,116:0.5036:2,2:20.9:1:30.6:1:1:1.04:59.6:22.333:0.4945:0:1 1/1:282:235:38,197:10,36:0.8333:2,2:21.6:1:31.1:1:0.39179:1.43804:59.8:234:0.8327:0:1.1 -10 95374453 . T G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TTCTGCTGTTATACTTTGAT;RSEQ=AGCCCAGTTCTCTGTGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:188,178:0:2,0:25.7:1:29.1:1:1:0:60:60:1:0:0.1 0/1:488:19:11,8:232,237:0.0389:2,2:29.2:1:31.5:1:0.49349:1.40:60:38:0.0396:0:1 -10 95374469 . G A 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=30.3346;LSEQ=TGATTAGCCCAGTTCTCTGT;RSEQ=GTGAGAAGGAAATAAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:1:1,0:179,173:0.0028:2,0:1:0:25:0:1:0:60:2:0.0029:0:1 0/1:454:36:19,17:193,225:0.0793:2,2:24.5:1:29.6:1:0.48885:1.30:60:72:0.0798:0:1.1 -10 95374519 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08974;SOR=0;LSEQ=TTGGAGGTGGTTTTGGTCTG;RSEQ=GGCTGTCCATGGTGAGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:1,2:89,153:0.0122:2,2:8.7:1:28:1:1:1.16272:60:6:0.0124:0:1 0/0:301:0:0,0:116,185:0:2,0:24.3:1:30.4:1:1:0:60:99.333:1:0:0.2 -10 96163397 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49024;SOR=Inf;LSEQ=CGGGGCCGGGGCCGGAGCCG;RSEQ=GGTCTTGGTGGGAGTCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:0:2,0:32:1:29.4:1:1:0:58.2:8.5:1:0:1.1 0/1:22:2:1,1:11,9:0.0909:2,2:34:1:29.5:1:1:1.21106:60:4:0.0909:0:1 -10 96163412 . T TCGGAGC 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=5.000;MSILEN=6;SSF=0.7645;SOR=0.79536;LSEQ=AGCCGGGGTCTTGGTGGGAG;RSEQ=CGGAGCCGGAGCCGGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:9,7:4,2:0.7273:2,2:24.9:1:29.2:1:1:1.52515:57.8:15:0.75:0.1364:1.1 1/0:28:19:9,10:4,4:0.6786:2,2:24.6:1:30.3:1:1:1.10678:60:38:0.7037:0:0.3 -10 96202765 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49984;SOR=Inf;LSEQ=TCCTCAGGAAAAACAAAGTT;RSEQ=GGGACACACACTATGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:76,22:0:2,0:23.3:1:29.2:1:1:0:60:196:1:0:0.1 0/1:112:2:1,1:81,28:0.0179:2,2:10:0:33:1:0.45602:2.86004:60:4:0.0182:0:1.5 -10 96202869 . G A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25764;SOR=Inf;LSEQ=TGTTTAACCAGAACCAAGAT;RSEQ=TTCACCCCCATAGAATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:85,119:0:2,0:24.9:1:31.8:1:1:0:60:101:1:0:0.1 0/1:255:3:2,1:106,146:0.0118:2,2:29:1:22:1:0.57565:2.74:60:2:0.0079:0:1 -10 96202896 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22715;SOR=0;LSEQ=CCCATAGAATGTACATGCAC;RSEQ=GCACTAGAGGACTGCATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:40,96:0.0145:2,2:5:1:30.5:1:0.50746:2.38:60:4:0.0146:0:1 0/0:151:0:0,0:46,105:0:2,0:23.2:1:29.9:1:1:0:60:302:1:0:0.1 -10 97753910 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAGACCGGTGGTGGCCTC;RSEQ=AATGGCTGGGCGCACTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:9,2:0:2,0:22.7:1:31.3:1:1:0:60:22:1:0:0 0/1:24:2:1,1:20,2:0.0833:2,2:32:1:28.5:1:0.23913:8.36492:60:4:0.0833:0:1 -10 97754105 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54023;SOR=Inf;LSEQ=ATGCACTTGTAAGAAAGATC;RSEQ=AAGACTTTAAGACTTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:0:0,0:22.4:1:30.6:1:1:0:60:20:1:0:0.1 0/1:20:2:0,2:2,16:0.1:2,0:27:1:32.5:1:1:0:60:4:0.1:0:1 -10 97759626 . A G 47 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TCTGGGTGAAGCAGGCTGGC;RSEQ=CTTCAGTTGAACCCAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:27.3:1:30.3:1:1:0:60:6:1:0:1 1/0:6:3:2,1:3,0:0.5:0,2:22:1:30:1:1:0:60:6:0.5:0:1 -10 97759760 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49524;SOR=Inf;LSEQ=TTAATTCTCTTGGCAAGAAT;RSEQ=TTGCCCTTCTTTGTTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:36,14:0:2,0:18.7:1:31.3:1:1:0:60:100:1:0:0.1 0/1:52:2:1,1:34,16:0.0385:2,2:14:1:31:1:1:2.0917:60:4:0.0392:0:1 -10 97949207 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2006;SOR=0;LSEQ=ATAATTGATGAACTTGGCTT;RSEQ=CACTTTGGGAAGAGAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:54,24:0.025:2,2:20:1:30.5:1:0.53006:2.22489:60:4:0.0256:0:1 0/0:98:0:0,0:68,30:0:2,0:28:0:14:0:1:0:60:0:0:0:7 -10 97949368 . C A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08932;SOR=0;LSEQ=ATGATGGGTTTGAGTGTTTT;RSEQ=TATTCTGATTTGACTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:2,1:48,84:0.0221:2,2:22.7:1:26.7:1:0.55486:3.47:60:6:0.0222:0:1 0/0:167:0:0,0:71,96:0:2,0:23:1:31.1:1:1:0:60:82.5:1:0:0.1 -10 97949454 . A AATC 161 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=13.000;MSILEN=3;SSF=1e-05;SOR=0.16619;LSEQ=TTCAGTTTCCTCATCATCAA;RSEQ=ATCATCATCATCATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:38:17,21:10,11:0.6441:2,2:33.3:1:30.8:1:1:1.12078:59.1:37:0.6607:0.1017:0.1 0/1:57:13:6,7:16,26:0.2281:2,2:24.5:1:30:1:0.74805:1.38:53.8:26:0.2281:0.0526:0.5 -10 97949572 . A C 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCACTTTCCAGATATCCTTA;RSEQ=GAGTTTCACATCCTCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:69,28:0:2,0:23.2:1:30.4:1:1:0:58.2:194:1:0:0.1 0/1:183:45:30,15:87,51:0.2459:2,2:22.5:1:29.9:1:0.72291:1.17:56.4:44:0.2418:0:1.2 -10 97949707 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21311;SOR=Inf;LSEQ=TGGTGGTGTTATTTCAAAGA;RSEQ=CCCAAGGGAAACTGTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:107,100:0:2,0:26:1:31.7:1:1:0:59.9:50.75:1:0:0.1 0/1:178:2:1,1:98,78:0.0112:2,2:8.5:1:29:1:1:1.25478:60:4:0.0114:0:1 -10 97949720 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22578;SOR=Inf;LSEQ=TCAAAGACCCCAAGGGAAAC;RSEQ=GTTGGCTGTACAGACATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:104,102:0:2,0:24.3:1:30.7:1:1:0:59.9:67.667:1:0:0.1 0/1:187:2:1,1:106,79:0.0107:2,2:17:1:27.5:1:1:1.33962:60:4:0.0108:0:1 -10 97949883 . T A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3179;SOR=0.24677;LSEQ=ATTTTCATCATTATCCACCT;RSEQ=AAAGTGATCATCTTTGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:94,149:0.0122:2,2:25.7:1:27.3:1:0.5623:3.16:60:6:0.0126:0:1 0/0:330:1:1,0:139,190:0.003:2,0:1:0:24:0:0.42424:0:60:2:0.0031:0:1 -10 97949903 . G A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16713;SOR=0;LSEQ=TAAAGTGATCATCTTTGTCG;RSEQ=CCTTTAGTTCACAACTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:59,111:0.0116:2,2:22:1:25.5:1:1:1.87:60:4:0.0119:0:1 0/0:248:0:0,0:110,138:0:2,0:25:1:31.2:1:1:0:59.2:40.333:1:0:0.1 -10 98319855 . A G 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05434;SOR=Inf;LSEQ=TCTGTACATCTGCCTGGTGT;RSEQ=ATTCTGTCCTGCGTGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:31,7:0:2,0:22.1:1:28.6:1:1:0:60:76:1:0:0.2 0/1:37:4:3,1:27,6:0.1081:2,2:26.5:1:32.3:1:1:1.48199:60:8:0.1081:0:1 -10 98319912 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12974;SOR=0;LSEQ=CATTTATCTCCGTCTGCCTT;RSEQ=TTTCCCACCTAAATGCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:47,23:0.0278:2,2:19:0:31.5:1:1:2.02168:60:4:0.0286:0:1 0/0:127:0:0,0:78,49:0:2,0:27:1:31:1:1:0:60:62.5:1:0:0.1 -10 98319949 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15677;SOR=0;LSEQ=GTGCTGCCACCCCATGGAAG;RSEQ=TTCGATGGACATGGACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:68,38:0.0185:2,2:31.5:1:28:1:1:1.77923:60:4:0.0198:0:1 0/0:164:0:0,0:93,71:0:2,0:23.8:1:29.2:1:1:0:58.5:81:1:0:0.1 -10 98319957 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51357;SOR=Inf;LSEQ=ACCCCATGGAAGATTCGATG;RSEQ=ACATGGACATGAGCCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:74,38:0:2,0:27.6:1:31:1:1:0:57.9:27:1:0:0.3 0/1:161:2:2,0:92,66:0.0124:2,0:6:1:26.5:1:0.51226:0:54.5:4:0.0126:0:1 -10 98320268 . T C 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00048;SOR=0;LSEQ=AGTGTGGTTCAGGGCCAGTG;RSEQ=ATATTAGTGGACAGCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:190:190:88,102:0,0:1:0,2:23.1:1:31.9:1:1:0:55.1:62.333:1:0:1.1 1/1:209:197:87,110:5,6:0.9426:2,2:25.6:1:31.7:1:1:1.05334:53.9:97.5:0.942:0:1.1 -10 98320336 . G A 76 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12409;SOR=5.54699;LSEQ=GAAGATGAACAGGAGGAGGC;RSEQ=AAATTCTTAAGGATATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:1:1,0:56,75:0.0076:2,0:1:0:27:0:0.43182:0:52:2:0.0076:0:2 0/1:147:6:3,3:65,76:0.0408:2,2:18.7:1:29.7:1:1:1.17:60:12:0.0411:0:1.3 -10 98320393 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18367;SOR=0;LSEQ=GGAGGTGGTAGCAAGGTTCC;RSEQ=CAGAAAAAAGTAAAACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:0,2:42,63:0.0187:2,0:19.5:1:33:0:0.5186:0:60:4:0.0189:0:1 0/0:142:0:0,0:68,74:0:2,0:24.4:1:29.7:1:1:0:59.9:141:1:0:0.2 -10 98320419 . A C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26696;SOR=Inf;LSEQ=AAAAGTAAAACTTGCTGCTG;RSEQ=TGAAGATGATGATGATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:45,52:0:2,0:25.8:1:30.6:1:1:0:60:194:1:0:0.1 0/1:135:3:1,2:62,70:0.0222:2,2:21:1:30:1:1:1.76424:60:6:0.0224:0:2 -10 98320423 . AGAT A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.03083;SOR=0;LSEQ=GTAAAACTTGCTGCTGATGA;RSEQ=GATGATGATGATGATGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:4:2,2:39,53:0.0417:2,2:32:1:31.8:1:1:1.35:60:8:0.0417:0:0.5 0/0:131:0:0,0:62,69:0:2,0:25.8:1:30.9:1:1:0:59.6:64.5:1:0:0.3 -10 98320426 . T A 77 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.47259;SOR=2.23029;LSEQ=AAACTTGCTGCTGATGAAGA;RSEQ=GATGATGATGATGATGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:34,53:0.0215:2,2:13.5:1:31:1:1:1.55:60:4:0.023:0:1 0/1:128:6:3,3:58,64:0.0469:2,2:26.3:1:30:1:1:1.10:52.3:12:0.0472:0:1.3 -10 98320441 . T C 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1e-04;SOR=Inf;LSEQ=GAAGATGATGATGATGATGA;RSEQ=GACGATTTTGATGAGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:33,53:0:2,0:27.4:1:29.7:1:1:0:60:20.5:1:0:0.1 0/1:115:16:8,8:42,57:0.1391:2,2:29.8:1:30.9:1:0.59696:1.35:60:32:0.1441:0:1.1 -10 98320560 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49367;SOR=Inf;LSEQ=AGACTCAAAACTATCAACAC;RSEQ=AAGATCAAAAGGACAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:13,27:0:2,0:22.6:1:28.7:1:1:0:60:19:1:0:0.1 0/1:40:2:1,1:15,22:0.05:2,2:26.5:1:32.5:1:1:1.45:47.5:4:0.0513:0:1.5 -10 98320574 . CA C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50457;SOR=Inf;LSEQ=CAACACTAAGATCAAAAGGA;RSEQ=AAAATCCTTCAAAAACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:12,19:0:2,0:22.8:1:30.2:1:1:0:60:30:1:0:0.1 0/1:42:2:1,1:19,21:0.0476:2,2:14:0:33.5:1:1:1.10:60:4:0.0488:0:0 -10 98320668 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.49315;SOR=Inf;LSEQ=CAAAAATGCAAGCAAGTATA;RSEQ=AAAAAGTGCATTGAACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:17,19:0:2,0:29.1:1:31.3:1:1:0:60:35:1:0:0.1 0/1:37:2:1,1:20,15:0.0541:2,2:28:1:27:1:1:1.32286:60:4:0.0556:0:1 -10 98320693 . G C 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05561;SOR=Inf;LSEQ=AGTGCATTGAACAGTTCAGG;RSEQ=CACTACTGGTAAATTAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:20,22:0:2,0:30.8:1:31.1:1:1:0:60:41:1:0:0.1 0/1:44:5:3,2:19,20:0.1136:2,2:24.8:1:30.4:1:1:1.56:60:10:0.119:0:1 -10 98403534 . GA G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51163;SOR=Inf;LSEQ=TTCCATGAGTTCATGGATGG;RSEQ=AAGTCAGGCCCGCCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:56,34:0:2,0:26.5:1:29.6:1:1:0:60:89:1:0:1 0/1:126:2:1,1:76,48:0.0159:2,2:36:0:30:1:1:1.57732:60:4:0.016:0:1 -10 98403546 . C T 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGGATGGGAAAGTCAGGCC;RSEQ=GCCTCCCTGTGGGCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:103:103:60,43:0,0:1:0,2:25.2:1:30.3:1:1:0:60:102:1:0:1.1 1/0:143:86:50,36:31,26:0.6014:2,2:26.4:1:30.4:1:0.73114:1.16:60:85:0.5986:0:1.1 -10 98403616 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50321;SOR=Inf;LSEQ=TTGTAACACTCAATATAGCC;RSEQ=ATTCCAGAAATTCCCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:36,57:0:2,0:26.6:1:31.7:1:1:0:60:186:1:0:0.5 0/1:115:2:1,1:44,69:0.0174:2,2:31.5:1:29.5:1:1:1.56:60:4:0.0174:0:1 -10 98403745 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCCGCATGCTTAGCATTTG;RSEQ=TAGCGAATGATGGTAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,0:0.9286:0,1:23.6:1:31.2:1:1:0:60:26:1:0:1 1/1:4:4:0,4:0,0:1:0,0:23.5:1:31:1:1:0:60:8:1:0:1 -10 99804006 . G A 188 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCCATGCATGTGCTGTAC;RSEQ=CTAACAACAACAATAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:74:67,7:0,0:1:0,2:23.3:1:30.4:1:1:0:60:36:1:0:1.1 1/0:63:40:36,4:21,2:0.6349:2,2:23.4:1:30.3:1:1:1.16383:60:39:0.629:0:1.1 -10 99804130 . T C 102 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1244;SOR=3.56955;LSEQ=AGCAGCAACAGCAACAACAG;RSEQ=AGTGTCAACAGCAGCAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:2:1,1:139,148:0.0068:2,2:23:1:23.5:1:1:1.06:40:1:0.0036:0:7 0/1:374:9:5,4:175,186:0.0241:2,2:8.3:1:32.2:1:0.74509:1.33:60:18:0.0249:0:5 -10 99804133 . T C 100 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24486;SOR=2.38017;LSEQ=AGCAACAGCAACAACAGTAG;RSEQ=GTCAACAGCAGCAGCGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:132,149:0.0105:2,2:28.3:1:17.7:1:0.60359:2.25:43.3:0.5:0.0036:0:5.3 0/1:364:9:5,4:171,184:0.0247:2,2:11.3:1:31.6:1:0.74391:1.34:60:18:0.0253:0:5 -10 99804135 . T A 96 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04896;SOR=7.04692;LSEQ=CAACAGCAACAACAGTAGTG;RSEQ=CAACAGCAGCAGCGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:1:1,0:131,145:0.0036:2,0:17:0:32:0:0.47653:0:40:2:0.0037:0:6 0/1:362:9:5,4:169,181:0.0249:2,2:13.3:1:30.4:1:0.7443:1.34:60:18:0.0259:0:5 -10 99804141 . G A 65 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.40913;SOR=3.65037;LSEQ=CAACAACAGTAGTGTCAACA;RSEQ=CAGCAGCGACAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:1,0:124,139:0.0038:2,0:1:0:27:0:0.47348:0:60:2:0.0039:0:1 0/1:366:5:3,2:173,188:0.0137:2,2:5.4:1:28.2:1:0.67459:1.63:43.4:10:0.014:0:6.6 -10 99804142 . C CAGCAGCGACAGCAGCAACAACAGCAGCAGCGACAGCAGCAACAACAGCAGCAATAGCAGCAACAACAGACAAGAGGAGCAACAAAAGTAGCTGCAACAATAACAAAAGCAACAGCAGCAACAACAGCAGCGACAACAGCAGCAAT 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.57218;SOR=0.90198;LSEQ=AACAACAGTAGTGTCAACAG;RSEQ=AGCAGCGACAGCAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:108:69,39:73,106:0.3724:2,2:32.5:1:30.4:1:0.00016:2.56:33.4:216:0.3816:0.3724:0.7 0/1:393:137:73,64:114,132:0.3486:2,2:27.6:1:29.7:1:0.20215:1.32:32.9:136:0.3514:0.3486:0.7 -10 99804144 . G GCAGCAAAA 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=0.3823;LSEQ=CAACAGTAGTGTCAACAGCA;RSEQ=CAGCGACAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:138:65,73:78,66:0.4842:2,2:31.4:1:30.9:1:0.2836:1.32592:58.3:276:0.4894:0.0035:3 0/1:398:105:45,60:152,141:0.2638:2,2:30.7:1:30:1:0.13902:1.43602:57.8:104:0.2667:0.0151:3.3 -10 99804147 . GCGACAGCAGCAA AAACAG 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07621;SOR=0;LSEQ=CAGTAGTGTCAACAGCAGCA;RSEQ=CAACAGCAGCAGCGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:153,134:0.0103:2,2:13.3:1:24.8:1:1:1.75:45.7:2:0.0071:0.0069:2 0/0:394:0:0,0:191,202:0:2,0:19.9:1:31.3:1:1:0:56.1:42.667:1:0.0051:2.1 -10 99804149 . GACAGCAGCAACA AAAACAGCG 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0.03862;SOR=0.66096;LSEQ=GTAGTGTCAACAGCAGCAGC;RSEQ=ACAGCAGCAGCGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:66:34,32:86,90:0.2292:2,2:13.6:1:30.1:1:0.77343:1.11:58.3:132:0.2366:0.184:0.5 0/1:396:65:34,31:113,140:0.1641:2,2:16.4:1:29:1:0.32901:1.36:56.2:64:0.1671:0.1162:0.8 -10 99804153 . G A 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.73678;SOR=1.08972;LSEQ=TGTCAACAGCAGCAGCGACA;RSEQ=CAGCAACAACAGCAGCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:38:30,8:97,91:0.1564:2,2:10.9:1:30.8:1:0.0021:3.50:48.9:76:0.1735:0:3.1 0/1:357:60:39,21:119,139:0.1681:2,2:14.2:1:30.3:1:0.00979:2.16:51.4:120:0.1948:0:3.4 -10 99804159 . A G 224 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CAGCAGCAGCGACAGCAGCA;RSEQ=CAACAGCAGCAGCGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:228:136:61,75:44,19:0.5965:2,2:25.4:1:31.7:1:0.00129:2.83216:56.1:21.667:0.628:0:4 0/0:369:0:0,0:104,97:0:2,0:20.7:1:29.6:1:1:0:55.9:200:0.9091:0:1.2 -10 99804161 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25274;LSEQ=GCAGCAGCGACAGCAGCAAC;RSEQ=ACAGCAGCAGCGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:229:133:61,72:60,22:0.5808:2,2:25.6:1:29.5:1:0.00012:3.2011:56.5:15.625:0.6219:0:4.1 0/1:367:95:35,60:139,114:0.2589:2,2:25.6:1:29.3:1:0.00375:2.08578:56.9:18:0.2703:0:4.1 -10 99804163 . C T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.94391;LSEQ=AGCAGCGACAGCAGCAACAA;RSEQ=AGCAGCAGCGACAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:4:2,2:120,91:0.0175:2,2:10.3:1:26:1:1:1.31695:31.5:3:0.0144:0:7 0/1:362:6:3,3:166,170:0.0166:2,2:21.5:1:29.5:1:1:1.02:39.3:12:0.018:0:7.3 -10 99804170 . AG GA 93 NM4;Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.01632;SOR=0.1527;LSEQ=ACAGCAGCAACAACAGCAGC;RSEQ=CGACAGCAGCAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:8:0,8:123,82:0.0354:2,0:36:0:31:1:0.00084:0:37:16:0.0386:0:7 0/0:360:2:0,2:169,169:0.0056:2,0:36:0:30.8:1:0.49854:0:44:4:0.006:0:7 -10 99804171 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0;SOR=0.30305;LSEQ=CAGCAGCAACAACAGCAGCA;RSEQ=CGACAGCAGCAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:226:130:63,67:60,15:0.5752:2,2:23.7:1:30.1:1:1e-05:4.22394:53.9:260:0.6436:0.0044:4.4 0/1:358:104:38,66:130,102:0.2905:2,2:22.9:1:28.8:1:0.00138:2.20833:53.6:208:0.3161:0:4.6 -10 99804172 . C T 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15934;SOR=Inf;LSEQ=AGCAGCAACAACAGCAGCAG;RSEQ=GACAGCAGCAACAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:126,89:0:2,0:23.4:1:31.8:1:1:0:51:42:0.9953:0.0175:4.1 0/1:356:4:4,0:161,171:0.0112:2,0:28.3:1:31.5:1:0.05708:0:55.3:8:0.0123:0:4 -10 99804173 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26119;LSEQ=GCAGCAACAACAGCAGCAGC;RSEQ=ACAGCAGCAACAACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:235:146:72,74:58,15:0.6213:2,2:22.7:1:29.7:1:2e-05:3.94943:52.8:23.333:0.6667:0.017:4.7 0/1:354:106:37,69:128,98:0.2994:2,2:22.8:1:28.3:1:0.00025:2.42911:53.2:14.143:0.3113:0:4.8 -10 99804177 . G A 61 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.65311;SOR=2.62054;LSEQ=CAACAACAGCAGCAGCGACA;RSEQ=CAGCAACAACAGCAGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:1:1,0:140,105:0.004:2,0:11:1:31:1:1:0:31:2:0.0044:0.004:1 0/1:379:4:2,2:188,185:0.0106:2,2:22.5:1:30.8:1:1:1.01617:48.5:8:0.0109:0:4.3 -10 99804180 . G GCAGTAGCAACAGAAATAGCAGTAATAGCAGCAGCAGCAGTAGCAGCAATAATTA 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CAACAGCAGCAGCGACAGCA;RSEQ=CAACAACAGCAGCAATAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:20:15,5:196,145:0.0552:2,2:28.1:1:30.6:1:0.16186:2.21:39.9:40:0.058:0.0552:3.7 0/0:502:0:0,0:259,242:0:2,0:17.6:1:31.4:1:1:0:46.8:49.1:1:0:2.3 -10 99804182 . A G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37387;SOR=0.82772;LSEQ=ACAGCAGCAGCGACAGCAGC;RSEQ=ACAACAGCAGCAATAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:55:29,26:190,130:0.1459:2,2:12.5:1:28.5:1:0.37673:1.30937:51:10:0.137:0:5.8 0/1:541:67:30,37:245,226:0.1238:2,2:15:1:28.3:1:0.29708:1.33629:48.6:8.571:0.1143:0:5.2 -10 99804184 . C T 90 NM4;Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00483;SOR=0.1329;LSEQ=AGCAGCAGCGACAGCAGCAA;RSEQ=AACAGCAGCAATAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:10:0,10:219,149:0.0265:2,0:28.5:1:27.2:1:0.00015:0:40.6:9:0.0247:0:7 0/0:557:2:0,2:285,270:0.0036:2,0:37.5:1:28:1:0.23802:0:44:4:0.0036:0:7 -10 99804186 . A G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.29888;SOR=0.57582;LSEQ=CAGCAGCGACAGCAGCAACA;RSEQ=CAGCAGCAATAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:8:0,8:217,147:0.0214:2,0:33.4:1:33.5:1:0.00082:0:37:16:0.0217:0:7 0/1:562:7:2,5:287,264:0.0125:2,2:14.7:1:29.3:1:0.27055:2.71321:50.4:6:0.0109:0.0018:4.6 -10 99804187 . C T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12812;SOR=0.62797;LSEQ=AGCAGCGACAGCAGCAACAA;RSEQ=AGCAGCAATAGCAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:24:15,9:202,151:0.0637:2,2:6:1:29.3:1:0.6742:1.25:43.3:48:0.0661:0:4.2 0/1:562:23:15,8:275,264:0.0409:2,2:6.7:1:28.5:1:0.20607:1.80:49:22:0.0398:0:3.7 -10 99804192 . G A 99 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.02661;SOR=0.27244;LSEQ=CGACAGCAGCAACAACAGCA;RSEQ=CAATAGCAGCAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:10:2,8:199,153:0.0263:2,2:28.3:1:29.9:1:0.02626:5.18144:35.6:9:0.0258:0:6.8 0/0:548:4:1,3:257,258:0.0073:2,2:18:1:29:1:0.62357:2.98281:52:8:0.0079:0:5.8 -10 99804194 . AAT GACAAC 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.77019;SOR=1.39211;LSEQ=GACAGCAGCAACAACAGCAG;RSEQ=AGCAGCAACAACAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:4:4,0:199,153:0.0105:2,0:28:1:30.8:1:0.13773:0:45:8:0.0115:0.0026:3.8 0/1:548:8:8,0:257,258:0.0146:2,0:25.9:1:28.7:1:0.00744:0:38:16:0.0157:0.0055:3.3 -10 99804196 . TAGCAGCAACAACAGCAGCAATAGCAGCGACAACAGCAATAGCAGCAGCAACAACAAC T 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.00197;SOR=0.46058;LSEQ=AGCAGCAACAACAGCAGCAA;RSEQ=AGCAGCAGCAACAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:44:24,20:191,162:0.1108:2,2:13.7:1:30.5:1:1:1.02:54.2:43:0.1129:0.1108:3 0/1:553:30:20,10:253,255:0.0542:2,2:14.4:1:30.2:1:0.09046:2.01:54.5:60:0.0577:0.0542:3.6 -10 99804203 . A G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26025;SOR=0.63227;LSEQ=ACAACAGCAGCAATAGCAGC;RSEQ=ACAACAGCAGCAATAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:16:8,8:189,170:0.0394:2,2:21.5:1:26.9:1:1:1.11145:38.1:7:0.0386:0:4.5 0/1:554:14:12,2:248,257:0.0253:2,2:26.6:1:26.5:1:0.01181:6.20:45.8:13:0.0256:0:3.6 -10 99804205 . C T 71 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74075;SOR=1.47195;LSEQ=AACAGCAGCAATAGCAGCAA;RSEQ=AACAGCAGCAATAGCAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:3:3,0:192,177:0.0074:2,0:27:0:23:1:0.24974:0:53:2:0.0055:0:5 0/1:552:6:5,1:251,260:0.0109:2,2:22.2:1:27.8:1:0.11964:5.17:49.3:12:0.0118:0:5.5 -10 99804207 . A G 73 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.37295;SOR=1.95789;LSEQ=CAGCAGCAATAGCAGCAACA;RSEQ=CAGCAGCAATAGCAGCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:3:3,0:189,175:0.0075:2,0:25:0:30:1:0.24956:0:53:6:0.0083:0:5 0/1:547:8:6,2:247,256:0.0146:2,2:28.1:1:24.5:1:0.17252:3.10:51.8:1.667:0.01:0:4.6 -10 99804208 . CAGCAGCAAT C 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0106;SOR=0.67187;LSEQ=AGCAGCAATAGCAGCAACAA;RSEQ=AGCAGCGACAACAGCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:112:50,62:166,135:0.2517:2,2:16.6:1:30.3:1:0.06048:1.52314:53.8:27:0.2687:0.1191:5.5 0/1:559:103:39,64:215,207:0.1843:2,2:24:1:30.4:1:0.02072:1.7027:51:33.333:0.1953:0.034:4.8 -10 99804213 . G A 183 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CAATAGCAGCAACAACAGCA;RSEQ=CAATAGCAGCGACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:50,36:0:2,0:8.5:1:32:1:1:0:41.6:42:0.9767:0:4.2 0/1:420:80:43,37:102,111:0.1905:2,2:23:1:29.1:1:0.43162:1.26:55:39:0.2718:0:6.3 -10 99804214 . C T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61938;SOR=0.81704;LSEQ=AATAGCAGCAACAACAGCAG;RSEQ=AATAGCAGCGACAACAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:18:12,6:90,88:0.0616:2,2:16.4:1:30:1:0.22295:1.95:41.2:36:0.0933:0:4.1 0/1:432:22:13,9:129,140:0.0509:2,2:17:0:28.6:1:0.37778:1.57:49.8:44:0.0748:0:4 -10 99804215 . AATAGCAGCGACAA GACAACAG 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.0178;SOR=3.07439;LSEQ=ATAGCAGCAACAACAGCAGC;RSEQ=CAGCAATAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:5:0,5:82,75:0.0194:2,0:37.4:1:31.6:1:0.02752:0:35.4:10:0.0327:0:4 0/1:401:23:13,10:117,115:0.0574:2,2:35.1:1:30.2:1:0.66434:1.28:36.9:46:0.0927:0.0025:3.7 -10 99804216 . A ACAG 34 v4;q23;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38829;SOR=0.43254;LSEQ=TAGCAGCAACAACAGCAGCA;RSEQ=TAGCAGCGACAACAGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:1,2:33,19:0.0117:2,2:16.7:1:21.6:1:0.55094:3.39267:45:2:0.0132:0:6.7 0/0:394:2:0,2:80,85:0.0051:2,0:22.5:1:20.2:1:0.49787:0:52.5:4:0.0088:0:7.5 -10 99804217 . T CAGC 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.27609;LSEQ=AGCAGCAACAACAGCAGCAA;RSEQ=AGCAGCGACAACAGCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:99:46,53:33,19:0.3852:2,2:28.7:1:31.9:1:0.05942:1.99191:59.2:198:0.6513:0:6.5 0/1:394:58:33,25:80,85:0.1472:2,2:29.9:1:31.5:1:0.28863:1.40:58.5:57:0.2522:0:6.6 -10 99804224 . GACAACAGCAATAG AGCAA 87 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.04542;SOR=Inf;LSEQ=ACAACAGCAGCAATAGCAGC;RSEQ=CAGCAGCAACAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:129,139:0:2,0:21.6:1:30:1:1:0:54.5:32.5:0.9962:0:5.6 0/1:413:7:2,5:164,170:0.0169:2,2:14:1:31:1:0.44942:2.4061:30.3:14:0.0211:0.0145:4.3 -10 99804226 . C CAACAATAAAAGCAACAACAACAGCAATAGCAGCAGCAATCAT 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98402;LSEQ=AACAGCAGCAATAGCAGCGA;RSEQ=AACAGCAATAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:16:10,6:124,159:0.0503:2,2:33.4:1:28.9:1:0.19637:2.13:38.4:15:0.0514:0.0503:4.2 0/1:444:22:13,9:173,198:0.0495:2,2:23.3:1:28.5:1:0.27888:1.65:49.8:44:0.0571:0.0495:4 -10 99804228 . A G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22989;LSEQ=CAGCAGCAATAGCAGCGACA;RSEQ=CAGCAATAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:325:173:78,95:60,72:0.5323:2,2:25.1:1:31.1:1:1:1.01491:58.3:14.727:0.5586:0.0031:5.7 0/1:454:94:50,44:143,166:0.207:2,2:29.1:1:31:1:0.28864:1.32:58.1:22.5:0.2308:0:6 -10 99804234 . ATAGCAGCAGCAACAA GCAAAACAG 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12595;SOR=0.72716;LSEQ=GCAGCAATAGCAGCGACAAC;RSEQ=CAACAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:56:19,37:114,134:0.1718:2,2:25.4:1:30.3:1:0.1354:1.65402:52.8:55:0.1803:0.0399:4.3 0/1:458:60:18,42:183,178:0.131:2,2:31:1:31.4:1:0.00326:2.39406:46:120:0.1422:0.0131:3.8 -10 99804235 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24597;LSEQ=AATAGCAGCGACAACAGCAA;RSEQ=AGCAGCAGCAACAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:307:197:96,101:12,32:0.6417:2,2:25.3:1:31.3:1:0.0116:2.53:58.4:20.889:0.821:0:5.5 0/1:429:131:66,65:95,109:0.3054:2,2:25.3:1:30.8:1:0.50369:1.16:55.3:64.5:0.4019:0.0373:5.7 -10 99804237 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0;SOR=0.22086;LSEQ=TAGCAGCGACAACAGCAATA;RSEQ=CAGCAGCAACAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:311:194:94,100:16,35:0.6238:2,2:26.2:1:29.7:1:0.03913:2.05:58.7:47.5:0.8085:0:5.5 0/1:426:114:55,59:108,112:0.2676:2,2:28.1:1:29.2:1:0.90846:1.03432:58.6:228:0.3508:0:5.6 -10 99804238 . C CAGCAGCAACAATAAG 132 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=1e-05;SOR=Inf;LSEQ=AGCAGCGACAACAGCAATAG;RSEQ=AGCAGCAACAACAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:111,135:0:2,0:24.1:1:31.5:1:1:0:52.9:21.364:1:0.0256:5.2 0/1:434:22:13,9:151,170:0.0507:2,2:22.9:1:29.8:1:0.37802:1.62:32.5:44:0.0647:0.0507:6.2 -10 99804240 . G GCAGCAACAACAACAGCAGCAGTCACAATTAACAACAGCAACAATAACAAAAGCAACGATAGCAACAGTAT 86 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=3;SSF=0.02332;SOR=Inf;LSEQ=CAGCGACAACAGCAATAGCA;RSEQ=CAGCAACAACAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:117,140:0:2,0:23.9:1:31.3:1:1:0:51.9:18.769:0.9959:0.0278:5.3 0/1:443:7:4,3:165,181:0.0158:2,2:26.1:1:30.9:1:0.71386:1.46:36:14:0.0203:0.0158:6.6 -10 99804243 . GCAACAA G 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=3;SSF=0;SOR=0.11302;LSEQ=CGACAACAGCAATAGCAGCA;RSEQ=CAACAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:47:20,27:30,40:0.1577:2,2:15.9:1:31:1:1:1.01239:56.8:46:0.1637:0.0738:3.4 0/1:387:8:3,5:123,129:0.0207:2,2:27:1:27.8:1:0.72334:1.58637:56.3:7:0.0197:0:5.3 -10 99804244 . C CAACAACAACAGCAGCAGCAACAGCAGTCACAATTAACAACAGCAACAATAGCAGCAGTAAA 78 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=5.000;MSILEN=1;SSF=0.00659;SOR=0;LSEQ=GACAACAGCAATAGCAGCAG;RSEQ=AACAACAACAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:6:2,4:30,40:0.0201:2,2:14.7:1:30.3:1:1:1.49229:38.3:12:0.0214:0.0201:4.8 0/0:387:0:0,0:123,129:0:2,0:22.4:1:31.5:1:1:0:50.3:49.4:0.6958:0.0181:2.3 -10 99804246 . A ACAG 147 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00098;SOR=3.89635;LSEQ=CAACAGCAATAGCAGCAGCA;RSEQ=CAACAACAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:6:0,6:25,28:0.0209:2,0:35.5:1:33.2:1:0.03378:0:33.2:12:0.0667:0:6 0/1:403:31:14,17:109,105:0.0769:2,2:30.7:1:29.8:1:0.57019:1.25935:42:62:0.1206:0.0223:4.7 -10 99804247 . CAACAAC T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=3.000;MSILEN=3;SSF=0;SOR=0.29706;LSEQ=GACAACAGCAATAGCAGCAG;RSEQ=AGCAGCAGCAACAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:298:160:84,76:30,40:0.5369:2,2:29:1:31.1:1:0.19866:1.47:59.3:320:0.5694:0.0168:4.6 0/1:387:99:48,51:123,129:0.2558:2,2:29.7:1:30.3:1:1:1.01305:59:198:0.2789:0:4.7 -10 99804249 . A G 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.56631;SOR=0.83109;LSEQ=CAGCAATAGCAGCAGCAACA;RSEQ=CAACAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:25:19,6:15,43:0.0877:2,2:20:1:29:1:3e-05:8.79:36.8:5.25:0.2727:0:6.5 0/1:392:29:17,12:109,118:0.074:2,2:17.7:1:28.7:1:0.32687:1.53:45.9:4.8:0.0988:0:5.3 -10 99804250 . C T 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.70945;SOR=0.76231;LSEQ=AGCAATAGCAGCAGCAACAA;RSEQ=AACAGCAGCAGCAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:0,3:72,107:0.0148:2,0:26:0:28.7:1:0.27873:0:34.7:6:0.0174:0:7 0/1:354:4:0,4:151,183:0.0113:2,0:26.3:1:25.5:1:0.1313:0:45.3:3:0.0093:0:5.3 -10 99804253 . C T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0.16773;LSEQ=AATAGCAGCAGCAACAACAA;RSEQ=AGCAGCAGCAACAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:65:31,34:43,75:0.3095:2,2:11.6:1:25.1:1:0.15794:1.59:58:2.824:0.2807:0:2.6 0/1:373:26:7,19:147,178:0.0697:2,2:11.3:1:22:1:0.09902:2.2367:58.5:2.25:0.0523:0:2.8 -10 99804256 . C G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.21208;SOR=0.56699;LSEQ=AGCAGCAGCAACAACAACAG;RSEQ=AGCAGCAACAGCAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:14:4,10:167,202:0.0359:2,2:14.9:1:27.4:1:0.27855:2.06313:28:6:0.0322:0.0333:0.6 0/1:484:10:3,7:209,256:0.0207:2,2:11.8:1:27.6:1:0.52315:1.90249:23.3:9:0.0194:0.0207:0 -10 99804258 . G T 69 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.73852;SOR=1.62569;LSEQ=CAGCAGCAACAACAACAGCA;RSEQ=CAGCAACAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:3:3,0:173,216:0.0076:2,0:18:0:31:0:0.08965:0:35.3:6:0.0079:0:7 0/1:488:6:4,2:211,269:0.0123:2,2:23:1:27:1:0.41304:2.54:39.5:5:0.0108:0:5.8 -10 99804259 . C CAACAAAAGTAGCTGCAACAATAACAAA 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00748;SOR=0.46516;LSEQ=AGCAGCAACAACAACAGCAG;RSEQ=AGCAACAGCAGCAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:34:13,21:165,204:0.0813:2,2:27.4:1:29.6:1:0.58881:1.30571:27.7:68:0.0842:0.0813:0.5 0/1:506:20:7,13:188,249:0.0395:2,2:30.7:1:28.5:1:0.64487:1.40117:25.5:19:0.0388:0.0395:0.3 -10 99804261 . G A 85 NM4;Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.09617;SOR=0.36314;LSEQ=CAGCAACAACAACAGCAGCA;RSEQ=CAACAGCAGCAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:9:9,0:179,234:0.0213:2,0:29.1:1:27.1:1:0.00062:0:36.4:8:0.0199:0:6.2 0/0:510:4:4,0:210,283:0.0078:2,0:27.3:1:26:1:0.03383:0:32.8:3:0.0063:0:6.3 -10 99804263 . A G 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27241;SOR=1.24254;LSEQ=GCAACAACAACAGCAGCAGC;RSEQ=ACAGCAGCAACAACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:58:20,38:168,195:0.1358:2,2:29.3:1:29.4:1:0.11729:1.63505:48.9:13.5:0.132:0:6.1 0/1:514:84:31,53:184,224:0.1634:2,2:27.4:1:28.6:1:0.18498:1.40342:43.3:9.5:0.16:0:5.8 -10 99804264 . A G 142 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAACAACAACAGCAGCAGCA;RSEQ=CAGCAGCAACAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:432:20:9,11:183,222:0.0463:2,2:20.5:1:33:1:1:1.00749:34.7:40:0.0473:0:6.3 0/0:514:0:0,0:198,264:0:2,0:22.4:1:29.5:1:1:0:53.3:230:1:0:3 -10 99804267 . G A 70 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.38471;SOR=0.5549;LSEQ=CAACAACAGCAGCAGCAACA;RSEQ=CAGCAACAACAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:7:5,2:193,240:0.0159:2,2:27.9:1:25:1:0.25156:3.10:35.9:2.5:0.0118:0:6.3 0/0:564:5:4,1:223,295:0.0089:2,2:27:0:27.6:1:0.17193:5.28:35.4:10:0.0099:0:6.8 -10 99804273 . A GTAAAAACAG 82 NM4;Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.02601;SOR=0.19402;LSEQ=AACAGCAGCAGCAACAGCAG;RSEQ=CAACAGCAGCAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:8:8,0:192,248:0.0178:2,0:32:1:27.6:1:0.00146:0:34.8:16:0.0185:0.0067:6.3 0/0:571:2:2,0:231,298:0.0035:2,0:44:0:27.5:1:0.19208:0:33.5:4:0.0039:0:7 -10 99804277 . C T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.12035;LSEQ=AGCAGCAACAGCAGCAACAA;RSEQ=AGCAGCAACAACAACAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:5:3,2:193,255:0.011:2,2:17.8:1:28:1:0.65634:1.98:45.2:10:0.0112:0:4.6 0/1:568:7:5,2:222,298:0.0123:2,2:24.7:1:27.1:1:0.14632:3.35:42.4:14:0.0135:0:5.1 -10 99804284 . A G 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.72914;SOR=0.91812;LSEQ=ACAGCAGCAACAACAGCAGC;RSEQ=ACAACAACAGCAACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:39:15,24:176,187:0.0892:2,2:20.3:1:28:1:0.24345:1.50436:51.4:6.8:0.08:0:6.2 0/1:521:43:15,28:201,236:0.0825:2,2:19.9:1:28.3:1:0.19895:1.58833:47.4:6.167:0.0799:0:6.1 -10 99804285 . AC GCAATAATTATAACAGCAGCAACAACAGCAACGTCAGAAAAAGCAGCAACAGCAATAGCAACAAAAGCATCAGCAACAGCAATAGCATCACAATT 152 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=CAGCAGCAACAACAGCAGCA;RSEQ=AACAACAGCAACAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:33:12,21:176,187:0.0755:2,2:45.4:1:30.2:1:0.20549:1.64502:27.2:66:0.0776:0.0755:0 0/0:521:0:0,0:201,236:0:2,0:22.2:1:29.4:1:1:0:54.3:38.727:0.9201:0:2.2 -10 99804288 . A G 57 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.41693;SOR=0.40581;LSEQ=CAGCAACAACAGCAGCAACA;RSEQ=CAACAGCAACAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:4:0,4:182,205:0.0102:2,0:17:1:28.8:1:0.12666:0:38.8:3:0.0078:0:6.5 0/0:483:2:0,2:195,245:0.0041:2,0:9:0:32:1:0.5058:0:37.5:4:0.0046:0:6 -10 99804291 . A G 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0.97269;LSEQ=CAACAACAGCAGCAACAACA;RSEQ=CAGCAACAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:30:9,21:168,188:0.0767:2,2:21:1:30.5:1:0.0859:2.08133:52.8:9:0.0732:0:6.2 0/1:468:35:12,23:178,211:0.0748:2,2:17:1:30.3:1:0.21701:1.61512:50.1:6:0.0732:0:6.4 -10 99804292 . C A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.52025;SOR=1.2209;LSEQ=AACAACAGCAGCAACAACAA;RSEQ=AGCAACAGCAGCAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:27:12,15:166,192:0.0696:2,2:23.8:1:29.8:1:1:1.08055:34.9:26:0.0691:0:6.1 0/1:466:39:18,21:179,213:0.0837:2,2:21.7:1:30:1:1:1.02:34.9:78:0.0922:0:6 -10 99804298 . C T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67053;SOR=0.87197;LSEQ=AGCAGCAACAACAACAGCAA;RSEQ=AGCAGCAACAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:26:7,19:167,190:0.0672:2,2:16.8:1:27.9:1:0.06529:2.38053:55.1:12:0.065:0:6.7 0/1:457:27:7,20:185,216:0.0591:2,2:13.5:1:27.6:1:0.04625:2.44224:52.1:8:0.0571:0:6.9 -10 99804300 . GC AT 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.04519;LSEQ=CAGCAACAACAACAGCAACA;RSEQ=AGCAACAGCAGCAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:22:9,13:154,189:0.0582:2,2:27.1:1:30:1:0.82631:1.17643:34.8:44:0.0615:0:5.3 0/1:445:27:12,15:171,209:0.0607:2,2:25.6:1:28.7:1:1:1.02267:36.6:54:0.0672:0:5.4 -10 99804303 . G A 71 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.15076;SOR=0.27452;LSEQ=CAACAACAACAGCAACAGCA;RSEQ=CAACAGCAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:6:2,4:159,199:0.0163:2,2:12.5:1:27.8:1:0.69745:1.59601:47.5:12:0.0173:0:6.2 0/0:441:2:0,2:184,227:0.0045:2,0:24:0:31:1:0.50474:0:37.5:4:0.005:0:6 -10 99804304 . C A 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06626;SOR=Inf;LSEQ=AACAACAACAGCAACAGCAG;RSEQ=AACAGCAGCAGCAACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:158,204:0:2,0:24.7:1:31.7:1:1:0:56.2:31.909:1:0:2.5 0/1:433:5:4,1:177,222:0.0115:2,2:12.2:1:25.6:1:0.17796:5.00:53:10:0.0125:0.0023:4.2 -10 99804306 . A GCAACAACAGAAATCACAGTAACAACAGTAGCAG 67 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.02027;SOR=0;LSEQ=CAACAACAGCAACAGCAGCA;RSEQ=CAGCAGCAGCAACAACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:5:3,2:154,205:0.0136:2,2:21.6:1:29.2:1:0.65558:1.99:33.2:10:0.0139:0.0136:4.2 0/0:431:0:0,0:177,221:0:2,0:24:1:29.5:1:1:0:56.9:43.222:0.9873:0.0023:1.9 -10 99804307 . C A 61 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85766;LSEQ=AACAACAGCAACAGCAGCAA;RSEQ=AGCAGCAGCAACAACAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:4:0,4:144,195:0.0111:2,0:20.8:1:31.8:1:0.14218:0:33.8:8:0.0119:0.0028:4.5 0/0:418:4:1,3:148,174:0.0096:2,2:14:1:30.5:1:0.62826:2.54502:38.8:8:0.0108:0.0048:4.3 -10 99804309 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.61363;SOR=0.81708;LSEQ=CAACAGCAACAGCAGCAACA;RSEQ=CAGCAGCAACAACAATAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:19:4,15:140,180:0.0532:2,2:8.4:1:29.2:1:0.05827:2.90844:58.4:18:0.0554:0:7 0/1:410:18:4,14:158,188:0.0439:2,2:5.6:1:27.9:1:0.05531:2.93353:58.3:36:0.0507:0:7.1 -10 99804310 . CAG TATCAGCAA 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.85179;SOR=0.9253;LSEQ=AACAACAGCAACAGCAGCAA;RSEQ=CAGCAACAACAATAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:14:4,10:146,197:0.0387:2,2:30.6:1:31.8:1:0.41034:1.84979:36.1:28:0.0402:0.0028:5.6 0/1:418:15:3,12:169,205:0.0359:2,2:33:0:31:1:0.06499:3.28868:38.6:30:0.0392:0:5.9 -10 99804312 . G T 54 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.71385;SOR=0.67691;LSEQ=CAGCAACAGCAGCAACAGCA;RSEQ=CAGCAACAACAATAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:4:1,3:142,188:0.0113:2,2:15.8:1:27:1:0.63825:2.26093:36.3:3:0.0093:0:5.8 0/0:391:3:1,2:154,191:0.0077:2,2:15:1:30:1:1:1.61044:38.3:6:0.0088:0:5.3 -10 99804317 . A G 52 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0.88518;LSEQ=ACAGCAGCAACAGCAGCAGC;RSEQ=ACAACAATAGCAACAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:4:1,3:140,187:0.0119:2,2:6.5:1:26.5:1:0.63917:2.24102:60:3:0.0094:0:7 0/1:378:4:1,3:154,193:0.0106:2,2:4.3:1:26.3:1:0.63313:2.38837:60:3:0.0087:0:8 -10 99804318 . ACAACAATAGCAACAACAGTAGTGG A 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCAGCAACAGCAGCAGCA;RSEQ=CAATAACAGCAGCAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:21:5,16:139,190:0.0592:2,2:17.6:1:29:1:0.11251:2.33588:42.1:42:0.0625:0.0592:1.9 0/0:376:0:0,0:152,197:0:2,0:22.7:1:31.1:1:1:0:57.7:42.625:1:0:1.4 -10 99804321 . A G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.00753;LSEQ=CAGCAACAGCAGCAGCAACA;RSEQ=CAATAGCAACAACAGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:16:4,12:132,175:0.0462:2,2:12.1:1:33.3:1:0.1979:2.25762:35.9:32:0.0508:0:5.9 0/1:365:17:3,14:143,178:0.0466:2,2:12.5:1:33.1:1:0.04187:3.73662:38.5:34:0.0514:0:5.9 -10 99804322 . CAAT C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.38592;SOR=1.90712;LSEQ=AGCAACAGCAGCAGCAACAA;RSEQ=AGCAACAACAGTAGTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:4:4,0:128,183:0.0118:2,0:18.8:1:32.5:1:0.03002:0:40.8:8:0.0132:0:7 0/1:359:8:6,2:139,185:0.0223:2,2:19.1:1:31.8:1:0.08362:3.98:35.8:16:0.025:0.0028:6.5 -10 99804333 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.54588;SOR=1.70326;LSEQ=CAGCAACAACAATAGCAACA;RSEQ=CAGTAGTGGCAATAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:4:4,0:115,161:0.0131:2,0:25.8:1:33.3:1:0.03168:0:40.8:8:0.0148:0:7 0/1:316:7:5,2:117,164:0.0222:2,2:28.6:1:33.1:1:0.13806:3.49:34.1:14:0.0249:0:7 -10 99804337 . T C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57664;SOR=1.4141;LSEQ=AACAACAATAGCAACAACAG;RSEQ=AGTGGCAATAACAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:5:5,0:111,148:0.0173:2,0:24.6:1:29:1:0.01559:0:42.6:4:0.016:0:6.6 0/1:288:7:5,2:109,145:0.0243:2,2:32.6:1:33.3:1:0.24538:3.31:34.1:14:0.0281:0:7 -10 99804340 . TGG CAA 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37765;SOR=1.81245;LSEQ=AACAATAGCAACAACAGTAG;RSEQ=CAATAACAGCAGCAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:4:4,0:109,148:0.014:2,0:34.8:1:31.3:1:0.03408:0:40.8:8:0.0159:0:5 0/1:279:7:5,2:104,139:0.0251:2,2:37.6:1:31.7:1:0.24496:3.33:34.1:14:0.0287:0:5 -10 99804341 . G A 37 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6238;SOR=0.34126;LSEQ=ACAATAGCAACAACAGTAGT;RSEQ=GCAATAACAGCAGCAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:105,146:0.0107:2,2:19.7:1:23.7:1:0.57458:2.77:60:2:0.0082:0:3.3 0/0:273:1:1,0:101,137:0.0037:2,0:1:0:25:0:0.42678:0:60:2:0.0044:0:1 -10 99804349 . C G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12905;SOR=1.57674;LSEQ=AACAACAGTAGTGGCAATAA;RSEQ=AGCAGCAAAACAGCAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:23:8,15:95,149:0.0855:2,2:13:1:28.2:1:0.82401:1.19467:40.5:3.6:0.0714:0:2.5 0/1:280:36:16,20:106,137:0.1286:2,2:14.3:1:31.1:1:1:1.03:44.3:72:0.1304:0:2.6 -10 99804357 . A AC 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.70739;SOR=1.10447;LSEQ=TAGTGGCAATAACAGCAGCA;RSEQ=AACAGCAACAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:35:9,26:89,144:0.1306:2,2:16.6:1:30.3:1:0.18873:1.78188:42.4:34:0.1293:0.041:2.2 0/1:267:38:17,21:96,123:0.1423:2,2:19.6:1:31.5:1:1:1.04:45.2:76:0.1473:0.0075:2.9 -10 99804365 . ACAG A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.16248;SOR=2.4589;LSEQ=ATAACAGCAGCAAAACAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:4:2,2:94,172:0.0148:2,2:19.8:1:26:1:0.61745:1.83:60:3:0.0114:0.0037:1 0/1:252:9:4,5:98,139:0.0357:2,2:23.1:1:30.7:1:1:1.13:60:18:0.0373:0.0159:0.4 -10 99804369 . C T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.09182;SOR=1.52978;LSEQ=CAGCAGCAAAACAGCAACAG;RSEQ=AGCAGCAGCAGCAACAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:36:9,27:81,142:0.1385:2,2:20.5:1:26.5:1:0.25735:1.70795:42:11:0.1336:0:2.2 0/1:238:47:17,30:75,109:0.1975:2,2:22:1:27.6:1:0.61902:1.21324:43.1:22.5:0.1982:0:2.5 -10 99804376 . AG GA 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.12489;SOR=0;LSEQ=AAAACAGCAACAGCAGCAGC;RSEQ=CAGCAACAGCAACAATCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:4:2,2:86,158:0.0161:2,2:8:1:28.9:1:0.61676:1.83:36.5:8:0.0165:0.0081:1 0/0:227:0:0,0:88,139:0:2,0:24.9:1:30.3:1:1:0:56.5:55.75:1:0:0.7 -10 103248941 . G T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62581;SOR=2.64218;LSEQ=GAAAACATTCATTTAGACTT;RSEQ=TATGTACCAATATTTTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:1,0:90,39:0.0077:2,0:45:0:12:0:1:0:60:0:0:0:1 0/1:149:3:1,2:91,55:0.0201:2,2:24.3:1:27.3:1:0.55837:3.28179:60:6:0.0205:0:1 -10 103249002 . G A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62711;SOR=2.61826;LSEQ=AGTATCTAGGACTCCCCCCA;RSEQ=ACAACTCTTTTTTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:1,0:107,102:0.0048:2,0:1:0:26:0:1:0:60:2:0.0048:0:1 0/1:242:3:2,1:131,107:0.0124:2,2:10:1:21:1:1:1.63:60:2:0.0084:0:2.3 -10 103249009 . C CT 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.18146;SOR=0.45968;LSEQ=AGGACTCCCCCCAGACAACT;RSEQ=TTTTTTTTTCTTTCCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:9:5,4:107,101:0.0413:2,2:31.3:1:31.3:1:1:1.18:60:18:0.0425:0:0.3 0/1:258:5:3,2:140,112:0.0194:2,2:30.8:1:29:1:1:1.20:60:10:0.0196:0:0 -10 103249036 . A G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32498;LSEQ=TTTCTTTCCCAGAATCAAGA;RSEQ=TAAAAGCAACCCAGACAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:90:38,52:54,54:0.4545:2,2:27.3:1:32.5:1:0.31722:1.36623:60:180:0.4569:0:1.1 0/1:268:57:31,26:114,97:0.2127:2,2:24.4:1:30.9:1:1:1.01:60:56:0.2121:0:1.2 -10 104263913 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05921;SOR=0;LSEQ=CTGCCCTACGCACCCCGATG;RSEQ=CGGAGCTGCGGCCTAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:144,151:0.0101:2,2:42.7:1:25:1:0.61627:2.09:60:2:0.0069:0:2 0/0:465:0:0,0:210,255:0:2,0:24.8:1:31.3:1:1:0:60:65.429:1:0:0.4 -10 104263934 . GC G 77 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.07976;SOR=Inf;LSEQ=CGGAGCTGCGGCCTAGCGGC;RSEQ=CCCCGGCCCCACCGCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:178,138:0:2,0:20.2:1:30.8:1:1:0:60:18.75:0.9967:0:0.8 0/1:446:5:3,2:228,211:0.0112:2,2:23.8:1:33.4:1:1:1.39:60:10:0.0115:0:0.4 -10 104264107 . C T 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.09268;LSEQ=TACTGGTATGCTCTGGGCCG;RSEQ=GGGGAGACGGACAGGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:640:604:254,350:17,17:0.9438:2,2:25.5:1:29.1:1:0.37746:1.37723:60:34.529:0.9468:0:1.2 1/0:924:562:230,332:164,197:0.6082:2,2:25.6:1:28.8:1:0.19516:1.20143:60:61.444:0.6117:0:1.2 -10 104264280 . C T 73 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0398;SOR=6.85697;LSEQ=GGACAAAGGGGTTAACGGAG;RSEQ=CCGTGGGTACTGAGGGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:0,2:0,31:0.0606:1,0:35.5:1:31:1:1:0:60:4:0.0625:0:1 0/1:19:6:1,5:2,11:0.3158:2,2:28.8:1:28.3:1:1:1.09:60:5:0.2778:0:1 -10 104266230 . G C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAACCTCTGTCTCCCG;RSEQ=TTTCAAGCGATTCTCGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:32:1:1:0:58.5:4:1:0:1.5 -10 104268626 . T C 110 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05252;SOR=0.07721;LSEQ=ACAATCCCTGCCAATCTCAT;RSEQ=TGGGATCGGTAATTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:0.8462:0,0:23.5:1:31.8:1:1:0:60:22:0.8462:0:1.1 0/1:4:1:1,0:2,1:0.25:2,0:18:0:33:0:1:0:60:2:0.25:0:1 -10 104268800 . G C 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.61165;SOR=0.46643;LSEQ=TCTGGAGAGATGTGGCCTCT;RSEQ=TTTAGTTACCTTTCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:99:99,0:0,0:0.99:0,1:21.4:1:31.8:1:1:0:60:98:1:0:1.1 1/1:94:92:90,2:1,1:0.9787:2,1:23.3:1:31.5:1:0.06314:36.94:60:45:0.9783:0:1.3 -10 104268859 . GC A 163 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.41202;LSEQ=CTTTAGGTTTACAAAGTAGA;RSEQ=GCCTTAGCTTGACATTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:1:1,0:275,88:0.0027:2,0:13:0:31.5:0:1:0:60:2:0.0028:0:0 0/1:400:40:31,9:264,95:0.1:2,2:21.9:1:30.7:1:0.7055:1.24:60:80:0.1013:0.0225:0.5 -10 104268877 . G C 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.44371;LSEQ=GAGCGCCTTAGCTTGACATT;RSEQ=TCTGATTTCCAGGCTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:39:29,10:318,158:0.0757:2,2:25.2:1:31.1:1:0.37871:1.44:60:38:0.0747:0:1.2 0/1:563:124:81,43:289,148:0.2202:2,2:23.4:1:31.4:1:0.91457:1.03652:60:248:0.2226:0:1.2 -10 104269217 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04682;SOR=0.20699;LSEQ=CTCATGCCAAGGTGGTCCTC;RSEQ=TTAACACCTGATTCCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:36:0,36:0,3:0.9231:0,1:20.6:1:30.3:1:1:0:60:35:0.9211:0:1.2 1/0:17:12:0,12:0,5:0.7059:0,0:21.8:1:31.3:1:1:0:60:24:0.7059:0:1 -10 104309647 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18315;SOR=0;LSEQ=TACTGAGGCCACCATAAAAA;RSEQ=GGGGAGAACTTTAGACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:2,0:174,25:0.01:2,0:18:1:32.5:1:1:0:60:4:0.01:0:1 0/0:268:0:0,0:232,36:0:2,0:20.1:1:31.6:1:1:0:60:133:1:0:0.1 -10 104352124 . C CCATTT 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTAATAGCCTGTCCTTTT;RSEQ=AAGTCTGACAGAACTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:14,1:0.1176:1,0:18:1:28.7:1:1:0:60:4:0.1333:0.0588:0 0/0:1:0:0,0:1,0:0:0,0:15:0:33:0:1:0:60:2:1:0:0 -10 104353308 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22529;SOR=0;LSEQ=CTGTGGTCTCCCAACTGGAG;RSEQ=TGACTCAGAGAGCCTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:2,0:119,34:0.0129:2,0:8.5:1:29.5:1:1:0:60:4:0.0133:0:1 0/0:171:0:0,0:134,37:0:2,0:24.8:1:30.3:1:1:0:60:33.2:1:0:0.1 -10 104353345 . TG T 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1.31192;LSEQ=GGTAGCTGACCTTCTTGGGG;RSEQ=GGGGGTGGCCATTAACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:185,104:0.0103:2,2:39.7:1:32.7:1:1:1.12:60:6:0.0106:0:0 0/1:372:5:2,3:240,127:0.0134:2,2:16.4:1:27.4:1:0.34789:2.82612:60:10:0.0139:0.0081:1.2 -10 104353519 . TG T 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1089;SOR=0;LSEQ=GGAGCGCGGCTCCCTGGGCC;RSEQ=GGGGTGGGAGTCCCTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:2,1:59,141:0.0148:2,2:37:1:32.7:1:0.21537:4.74:60:6:0.0152:0:0 0/0:221:0:0,0:65,156:0:2,0:24:1:30.5:1:1:0:60:72.667:1:0:0.1 -10 104353527 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24549;SOR=0;LSEQ=GCTCCCTGGGCCTGGGGGTG;RSEQ=GAGTCCCTCCACTACCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:57,132:0.0104:2,2:15.5:1:25.5:1:0.51623:2.30:60:4:0.0106:0:2 0/0:195:0:0,0:59,135:0:2,0:23.2:1:30.4:1:1:0:60:193:0.9948:0:0.2 -10 104353681 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07583;SOR=Inf;LSEQ=GCCTGGGGCAGCAAACAGGG;RSEQ=AGGCTGTAGGCCCAGCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:248,99:0:2,0:23.9:1:31.9:1:1:0:60:48.571:1:0:0.2 0/1:469:5:2,3:307,157:0.0107:2,2:10.4:1:25.8:1:0.34333:2.92583:60:10:0.0108:0:1.2 -10 104356822 . A G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0517;SOR=0;LSEQ=TCAGTAAATACTGTAAGAGC;RSEQ=GTGGCTGAAAGGGTGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:130:130:121,9:0,0:1:0,2:23.8:1:30.3:1:1:0:60:129:1:0:1.1 1/1:120:116:106,10:4,0:0.9667:0,2:23.3:1:29.9:1:1:0:60:115:0.9664:0:1.1 -10 104359350 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49867;SOR=Inf;LSEQ=ACAAGAGGACGACTTTTTTC;RSEQ=GAAGGGCCTGTCCCTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:28,157:0:2,0:24.4:1:30.2:1:1:0:60:36:1:0:0.1 0/1:187:2:0,2:28,155:0.0107:2,0:26.5:1:32:0:1:0:60:4:0.0108:0:1.5 -10 104359359 . T G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24287;SOR=Inf;LSEQ=CGACTTTTTTCTGAAGGGCC;RSEQ=GTCCCTGTGGATTGCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:17,142:0:2,0:22.9:1:30.5:1:1:0:60:78.5:1:0:0.1 0/1:155:2:1,1:22,131:0.0129:2,2:23:1:28.5:1:0.27558:5.85:60:4:0.013:0:1 -10 104359884 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACCCTAGAGGTCAGATC;RSEQ=GCTTCCTGCCAACCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:15.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 104374618 . A G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCAGCCTGGGTAATAGA;RSEQ=CGAGACACCATCTCAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17:1:34:0:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 104374636 . TA T 30 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGAGACACCATCTCAAT;RSEQ=AAAAAAAAAAAAAAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:18.5:1:30.5:1:1:0:60:4:0.6667:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 104374815 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGTGGCAGCCACCTCTTG;RSEQ=GGGCATTGTGAGGAGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:16,0:0.1111:1,0:37.5:1:30.5:1:1:0:60:4:0.1176:0:1 0/0:3:0:0,0:3,0:0:0,0:16.3:1:32.3:1:1:0:60:6:1:0:0 -10 104374963 . C T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12293;SOR=Inf;LSEQ=GGAGCCCAGCTGGAGACTCC;RSEQ=ATCTTGCTCCTCCCTGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:153,28:0:2,0:24.3:1:30.9:1:1:0:60:59.333:1:0:0.1 0/1:180:3:1,2:138,39:0.0167:2,2:18.3:1:24.3:1:0.1304:6.97623:60:2:0.0114:0:1 -10 104375258 . G A 141 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.59131;LSEQ=AGCCCCCTCCCCCAGCAGGC;RSEQ=TCCTCCAGGGCCTCCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:0,3:0,104:0.028:1,0:13.3:1:32:1:1:0:60:6:0.0288:0:1 0/1:87:26:0,26:1,60:0.2989:1,1:20.2:1:30.2:1:1:0:60:52:0.3023:0:1.1 -10 104377762 . T C 25 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCCTTCCTTTGCTCTTC;RSEQ=GGCTGGAGCGAGCTTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:25:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 104378563 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07143;SOR=Inf;LSEQ=GCCATGTCCCGGGCTGCTGC;RSEQ=TCTGCCCCTGTGGAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:0:1,0:24.7:1:28.7:1:1:0:60:30:1:0:0.1 0/1:6:2:2,0:4,0:0.3333:0,0:35.5:1:31:0:1:0:60:4:0.4:0:1 -10 104378682 . A G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49866;SOR=0;LSEQ=CATCATTCCCAAGTGTCCTC;RSEQ=GGTAGCGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:145,4:0.0132:1,2:24.5:1:27.5:1:0.06534:32.52295:55:4:0.0144:0:2.5 0/0:143:0:0,0:137,5:0:1,0:25.4:1:29.4:1:1:0:58.7:22.667:1:0:0.7 -10 104378688 . CGT C 170 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=46;MSI=24.000;MSILEN=2;SSF=0;SOR=0.12002;LSEQ=TCCCAAGTGTCCTCAGGTAG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:39:35,4:88,1:0.2241:1,2:22.8:1:32.3:1:0.02985:9.85932:59:38:0.2275:0.0517:0.6 0/1:180:6:6,0:112,4:0.0333:1,0:27.7:1:33.7:1:1:0:60:12:0.0347:0:0.3 -10 104378750 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=11.30278;LSEQ=TGTGTGTAATGTTCAAGCAC;RSEQ=TTTTCCTGGGACAGTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:13:9,4:272,152:0.0296:2,2:22.5:1:27.1:1:0.77865:1.26:58.5:3.333:0.0256:0:1.5 0/1:471:121:69,52:198,150:0.2569:2,2:22.1:1:28.5:1:1:1.01:59.8:12.444:0.2617:0:1.3 -10 104378927 . GC G 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.25455;SOR=0;LSEQ=TCAGCAGCTCAAGAACCTTG;RSEQ=CCCCACAGGACTTCGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:50,234:0.0105:2,2:18:1:30:1:0.08559:9.25:60:6:0.0107:0.0035:0.3 0/0:240:0:0,0:53,187:0:2,0:23.3:1:31:1:1:0:60:79:1:0:0.1 -10 104385132 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTAGAACAGAGAGTTTGGT;RSEQ=AGGAGACGTGGACCAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:27.5:1:1:0:60:4:1:0:1 -10 104386854 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58698;SOR=0.39812;LSEQ=TCTCCTCCATGGTCAGAAGA;RSEQ=AGGTATAACGCTTGGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:117,10:0.0155:2,2:18:1:28:1:0.16388:11.20338:60:4:0.0155:0:1 0/0:161:1:1,0:142,18:0.0062:2,0:4:0:30:0:1:0:60:2:0.0063:0:1 -10 104386876 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26268;SOR=Inf;LSEQ=GGTATAACGCTTGGTGGTTG;RSEQ=CAAAAAGATCATACATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:145,43:0:2,0:23.3:1:31.1:1:1:0:60:187:0.9947:0:0.1 0/1:251:3:2,1:187,60:0.012:2,2:29.3:1:29:1:0.5696:1.55528:60:6:0.0121:0:1 -10 104386934 . T C 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCTTGTGCCTTCACAGAT;RSEQ=CTGTTGACCGAAGAGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:0:0,0:332,203:0:2,0:26.2:1:29.9:1:1:0:60:40.154:1:0:0.3 0/1:688:49:24,25:366,273:0.0712:2,2:27.2:1:30.9:1:0.29573:1.39581:60:48:0.0713:0:1.3 -10 104387019 . T C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09439;LSEQ=AAGTAAGCTTGTTTGACTTT;RSEQ=CCTGACAACAGGTCCCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:431:406:131,275:10,13:0.942:2,2:25.1:1:31.1:1:0.26345:1.61291:60:134.333:0.9416:0:1.1 1/0:549:332:124,208:88,129:0.6047:2,2:25.5:1:30.8:1:0.47384:1.144:60:65.4:0.6056:0:1.1 -10 104387103 . G T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17196;SOR=0.29;LSEQ=TGTGTGCGTGTGTACCTGTG;RSEQ=TGCGTGTGTGCTTGCATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:7:0,7:3,100:0.0636:1,0:16.7:1:29.7:1:1:0:60:14:0.0636:0:1 0/1:104:2:0,2:1,101:0.0192:1,0:45.5:1:31.5:1:1:0:60:4:0.0192:0:1 -10 104389928 . G A 53 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.20745;SOR=0.2375;LSEQ=ACTAGCCTGGGCTGGGCCCT;RSEQ=CAGTGGCCAGCAGGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:4:3,1:117,269:0.0103:2,2:20.8:1:26.5:1:0.08854:6.86:60:8:0.0104:0:1.5 0/0:408:1:1,0:127,280:0.0025:2,0:1:0:25:0:0.31373:0:60:2:0.0025:0:2 -10 104389932 . T G 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07118;LSEQ=GCCTGGGCTGGGCCCTGCAG;RSEQ=GGCCAGCAGGGAGCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:365:363:101,262:0,0:0.9945:0,2:24.3:1:30.7:1:1:0:60:120:0.9972:0:1.1 1/1:389:361:103,258:10,15:0.928:2,2:24.5:1:30:1:0.25637:1.6675:60:89.25:0.9273:0:1.1 -10 105362209 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTCTCCAGGCTGTCTGA;RSEQ=TTGCCTTCGTTCTGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 105363289 . T C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GGCTCTGAGTCAAAGCCGAA;RSEQ=GCAGGGATGTCATACTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:20:1:33.5:1:1:0:60:4:0.3333:0:1 0/0:5:0:0,0:5,0:0:0,0:34.4:1:30:1:1:0:60:10:1:0:0 -10 105517075 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5091;SOR=Inf;LSEQ=TGTGCCATGGTGATTAGCAT;RSEQ=GGGTGCACTAGAATCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:80,29:0:2,0:23.8:1:31.3:1:1:0:60:108:1:0:0.2 0/1:147:2:1,1:103,42:0.0136:2,2:12:0:30.5:1:0.50089:2.43545:60:4:0.0137:0:1.5 -10 105517091 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17136;SOR=0;LSEQ=GCATGGGGTGCACTAGAATC;RSEQ=AGGACTCTGGAGACCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:88,44:0.0149:2,2:37.5:1:29.5:1:1:1.98892:60:4:0.0149:0:1 0/0:189:0:0,0:125,64:0:2,0:25.2:1:30.7:1:1:0:60:188:1:0:0.4 -10 105517105 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1602;SOR=0;LSEQ=AGAATCCAGGACTCTGGAGA;RSEQ=CCAGGCCCGGGTGCATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:98,56:0.0128:2,2:37.5:1:30.5:1:1:1.74332:60:4:0.0129:0:1 0/0:233:0:0,0:144,89:0:2,0:25.1:1:30.8:1:1:0:60:76.667:1:0:0.5 -10 105517112 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28148;SOR=Inf;LSEQ=AGGACTCTGGAGACCCAGGC;RSEQ=CGGGTGCATTTTCTGCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:102,67:0:2,0:25.9:1:30.5:1:1:0:60:41.25:1:0:0.4 0/1:259:3:2,1:150,104:0.0116:2,2:46.7:1:29:1:1:1.38:60:6:0.0118:0:2 -10 105517162 . G A 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00053;SOR=1.81525;LSEQ=CAGACTGACTGAGACCATGA;RSEQ=AAGAGACAGGCTTTTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:121:62,59:66,62:0.4859:2,2:24:1:30.4:1:1:1.01296:60:242:0.4939:0:1.1 1/0:337:213:101,112:64,59:0.632:2,2:25.7:1:29.5:1:0.42981:1.20222:60:70:0.6306:0:1.2 -10 105517238 . G A 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.61885;SOR=0.48478;LSEQ=ACAATCCATCCAGGACGGAG;RSEQ=GTTGGGGGTAGGTGTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:47,100:0.0133:2,2:28.5:1:27.5:1:0.54199:2.12:60:4:0.0135:0:1 0/0:154:1:1,0:46,106:0.0065:2,0:1:0:22:0:0.30719:0:60:2:0.0066:0:1 -10 105517249 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22685;SOR=Inf;LSEQ=AGGACGGAGGGTTGGGGGTA;RSEQ=GTGTTCAGGAGCTGATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:35,92:0:2,0:22.5:1:30.7:1:1:0:60:41.333:1:0:0.3 0/1:116:2:1,1:29,84:0.0172:2,2:13.5:1:31:1:0.45538:2.86:60:4:0.0175:0:1.5 -10 108316062 . G C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.9496;LSEQ=ACTTCTGCCTCCTACTAATG;RSEQ=TCTTTGGCTTAAAAATGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:19:7,12:209,244:0.0402:2,2:23.1:1:31.6:1:0.48716:1.46721:60:38:0.0412:0:1.2 0/1:524:143:69,74:189,192:0.2729:2,2:25.7:1:31.4:1:0.84456:1.05563:60:46.667:0.2703:0:1.1 -10 108316278 . A G 48 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04096;SOR=18.0326;LSEQ=TTGAGATTAGTTAAGTGGTT;RSEQ=TTTGGCTGAAAGGGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,9:0.1:0,0:14:0:34:0:1:0:60:2:0.1111:0:1 1/0:4:3:0,3:0,1:0.75:0,0:23.7:1:30.3:1:1:0:60:6:0.75:0:1 -10 109599389 . A T 230 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68275;SOR=0.94151;LSEQ=AGAACTCTGTATGGAACCCT;RSEQ=GACTTTACATAGTAATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:199:91,108:102,107:0.4866:2,2:24.7:1:30.1:1:0.55285:1.13101:60:398:0.4901:0:1.6 0/1:456:215:103,112:114,125:0.4715:2,2:25.1:1:29.8:1:1:1.01:60:214:0.4735:0:1.5 -10 109599439 . A G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20196;LSEQ=GACTCTGTAATCTAGCTTCT;RSEQ=GAAATGTCCTTGACAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:95:27,68:62,104:0.364:2,2:25.5:1:31.1:1:0.17482:1.49911:60:94:0.3643:0:2.6 0/1:300:31:12,19:98,170:0.1033:2,2:22.8:1:30.8:1:0.84538:1.10:60:62:0.1044:0:2.5 -10 109599452 . A T 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64164;SOR=1.09358;LSEQ=AGCTTCTAGAAATGTCCTTG;RSEQ=CAACCAAGGTGCTCAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:95:23,72:42,76:0.446:2,2:25.9:1:29.7:1:0.09928:1.72553:60:30.667:0.4466:0:2.5 0/1:252:118:39,79:47,87:0.4683:2,2:23.9:1:29.3:1:0.79055:1.09392:60:236:0.4701:0:1.8 -10 109599593 . A AAG 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68079;SOR=0.4864;LSEQ=GATGGGGAGAGAGAGACAGA;RSEQ=AGAAAATGAGCAATCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:0,7:1,14:0.3182:1,0:14:1:32.1:1:1:0:60:14:0.3182:0.0455:0 0/1:11:2:0,2:0,9:0.1818:0,0:9.5:1:26.8:1:1:0:60:4:0.1818:0.0909:0.5 -10 110550348 . A C 97 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0079;SOR=0.07215;LSEQ=TAGTCCCAGGAAAAGTCAGC;RSEQ=AGGTCATCTGTGAGTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:8,1:0.5:2,2:16.8:1:30.9:1:0.57647:3.70691:60:18:0.5294:0:1 0/1:16:1:1,0:13,2:0.0625:2,0:7:0:30:0:1:0:60:2:0.0625:0:1 -10 110550481 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=TGAGAAGTGTGGTGTTAGCA;RSEQ=AAACAGAGGAATGGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:5,11:0.1111:2,2:16:1:30.5:1:1:2.10:60:4:0.1111:0:1.5 0/0:11:0:0,0:2,9:0:2,0:20.4:1:26.8:1:1:0:60:10:1:0:0 -10 110550558 . A G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GTTTAGAAGACTGCAAAGAC;RSEQ=TTCTTACGGTGCTATAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:5:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:3:0:0,0:0,3:0:0,0:17:1:31.3:1:1:0:60:6:1:0:0 -10 110806492 . A G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAAAGAGAGAAAGAGAC;RSEQ=GGAAGTCAGAGAAAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:28.5:1:1:0:60:4:1:0:1 -10 110807162 . C T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04965;SOR=Inf;LSEQ=CTAACCAGTCAGGGATAGTG;RSEQ=GAGATGGCGCCTGGAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:18,6:0:2,0:31.8:1:32.4:1:1:0:60:48:1:0:0 0/1:23:4:2,2:14,5:0.1739:2,2:17.5:1:28.3:1:0.55731:2.66173:60:8:0.1739:0:1.8 -10 110807229 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49701;SOR=Inf;LSEQ=ATGCCTTTCAAACTCTTATA;RSEQ=CAACCTCTGGAGTTGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:41,40:0:2,0:30.6:1:31.4:1:1:0:58.2:80:1:0:0.2 0/1:83:2:1,1:42,37:0.0241:2,2:35.5:1:30:1:1:1.13335:60:4:0.0241:0:1 -10 110807255 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24202;SOR=Inf;LSEQ=TCTGGAGTTGGGCAACATGG;RSEQ=TTCTCCCCTTTCTAGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:36,43:0:2,0:28.9:1:32:1:1:0:58.2:78:1:0:0.3 0/1:77:2:1,1:33,42:0.026:2,2:38.5:1:28.5:1:1:1.27:60:4:0.0263:0:1 -10 110982543 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49883;SOR=0;LSEQ=GTGAAAAATAGAAGGAATAT;RSEQ=AGAATCTAGCTCTTATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:40,1:0.0465:1,0:10:1:30.5:1:1:0:60:4:0.0476:0:1.5 0/0:35:0:0,0:35,0:0:1,0:21.6:1:28:1:1:0:60:34:1:0:0.1 -10 110982703 . C T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.14854;LSEQ=AAGCCCATTTATGCCCTTCG;RSEQ=TGCCTCAAAAAAGAGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:39:19,20:186,165:0.1:2,2:27:1:30.1:1:0.61723:1.18608:60:78:0.1013:0:1.2 1/0:500:346:165,181:73,81:0.692:2,2:27.1:1:29.7:1:1:1.01:60:172:0.6949:0:1.2 -10 110982789 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24783;SOR=0;LSEQ=GAAGCCTGCACTCAGAGACT;RSEQ=ACTGCTATTGGTCAGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:1,2:33,133:0.0176:2,2:25.3:1:22.7:1:0.49257:2.01:60:2:0.012:0:2 0/0:167:0:0,0:39,127:0:2,0:23.9:1:31.3:1:1:0:60:82:0.9939:0:0.2 -10 111440147 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16811;SOR=Inf;LSEQ=AAAATGATGGGACCCTCTTT;RSEQ=TAGCCTTGGGGAAAATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:247,29:0:2,0:23.2:1:31.6:1:1:0:60:275:0.9964:0:0 0/1:193:2:1,1:166,25:0.0104:2,2:33:0:30.5:1:0.25189:6.53064:60:4:0.0106:0:1.5 -10 111440222 . G A 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AAAGTGCTTTCACTGTGGAG;RSEQ=AGGGCTAACTGATTGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:959:0:0,0:556,402:0:2,0:25.7:1:31:1:1:0:59.2:86.091:0.9989:0:0.1 0/1:880:28:13,15:481,371:0.0318:2,2:27.5:1:28.8:1:0.33538:1.49524:60:27:0.0311:0:1.1 -10 111440605 . A G 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.56202;LSEQ=CAAGTCAGACTTCATTACAG;RSEQ=AAGAGATTAGTACTGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:520:266:135,131:130,123:0.5115:2,2:23:1:31.2:1:0.93005:1.02555:59.9:87.667:0.5137:0:1.1 0/1:486:180:82,98:160,145:0.3704:2,2:24.9:1:30.7:1:0.15874:1.31799:60:179:0.3729:0:1.1 -10 111440719 . T A 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00166;SOR=0.71383;LSEQ=CTTGTGGACATCTAGTCACT;RSEQ=GTAAACAATGTGCTGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:329:161,168:179,194:0.4673:2,2:25.7:1:29.9:1:0.82067:1.04:56.8:658:0.472:0:1.1 0/1:735:283:142,141:211,241:0.385:2,2:25.1:1:29.3:1:0.3636:1.15:56.7:566:0.3871:0:1.1 -10 111440966 . G T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCAATATAATCTTTGAAT;RSEQ=TCTGGATTTTTCAGGGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:1,25:0,0:1:0,1:24.4:1:30.9:1:1:0:55.2:52:1:0:1.1 1/1:12:12:2,10:0,0:1:0,2:22.8:1:30.2:1:1:0:56.3:24:1:0:1.1 -10 111441034 . C T 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53451;LSEQ=AATTAATTGAAACCATAGAC;RSEQ=AAGAAGCATCATATTATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:0.6667:0,0:19:1:28.7:1:1:0:59:12:0.6667:0:1.8 1/0:2:1:0,1:0,1:0.5:0,0:2:0:28:0:1:0:60:2:0.5:0:2 -10 111500499 . A T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTATGTCCATTGGAGAA;RSEQ=AAAATAAACAGATGTGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:20:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 111500571 . T G 33 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=GGAGCATGGTGGGGATTGAG;RSEQ=TTCTGGTAACATTTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:25.5:1:33:0:1:0:60:4:0.2222:0:1 1/1:1:1:1,0:0,0:1:0,0:37:0:33:0:1:0:60:2:1:0:1 -10 111500811 . A T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25178;SOR=Inf;LSEQ=TGTTTAAACCTCCTATGAAT;RSEQ=TTCATCTCATTTGAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:183,78:0:2,0:24.2:1:28.6:1:1:0:60:64.25:1:0:0.2 0/1:297:3:1,2:198,95:0.0101:2,2:22.3:1:23.7:1:0.25101:4.14647:60:2:0.007:0:2.3 -10 111500900 . T A 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00068;SOR=1.53823;LSEQ=TGGGGTACTTTGGGCAGCAA;RSEQ=CCTTATCTACATGTTATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:209:97,112:103,131:0.4718:2,2:24.1:1:29.6:1:0.63339:1.10:60:68.667:0.4747:0:1.1 1/0:596:345:160,185:111,135:0.5789:2,2:24.1:1:29.6:1:0.8018:1.05:60:85.25:0.5789:0:1.1 -10 111501026 . G A 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.85164;SOR=1.09354;LSEQ=TTAATAACTTGCAATTAGGA;RSEQ=GCATTAAGCCTACTGCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:28:0,28:0,39:0.4179:1,1:26.6:1:31.9:1:1:0:60:56:0.4179:0:1.9 0/1:50:22:1,21:1,27:0.44:1,1:22.6:1:31.3:1:1:1.28:60:21:0.4375:0:1.8 -10 111501039 . C T 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68379;SOR=0.81999;LSEQ=ATTAGGAGGCATTAAGCCTA;RSEQ=TGCTACCAAAATCACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:28:0,28:0,31:0.4746:1,1:21.3:1:29.9:1:1:0:60:56:0.4746:0:1.9 0/1:40:17:1,16:1,22:0.425:1,1:19.9:1:30:1:1:1.36:60:34:0.425:0:2 -10 111501067 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.97997;LSEQ=AAAATCACAGAATCTTAGCA;RSEQ=TAATATTGTCACTTCATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:21:0,21:0,12:0.6364:0,1:16.4:1:32.2:1:1:0:60:42:0.6364:0:1.1 1/0:19:12:1,11:0,7:0.6316:0,2:20.8:1:31:1:1:0:60:24:0.6316:0:1.1 -10 111567417 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.50089;SOR=Inf;LSEQ=TAATTTACCAAAATGACAAA;RSEQ=ACAAAGGGAAACAGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:13,1:0:1,0:20.3:1:30.9:1:1:0:60:13:1:0:0.1 0/1:20:2:1,1:11,7:0.1:2,2:6.5:1:32:0:1:1.53525:60:4:0.1053:0:1.5 -10 111567538 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24349;SOR=Inf;LSEQ=GTAATATTGTAGACATCAAG;RSEQ=GAATGAGCACTGTTCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:125,49:0:2,0:20.5:1:30.6:1:1:0:60:86:1:0:0.1 0/1:170:2:1,1:113,55:0.0118:2,2:22:1:28:1:0.55162:2.04516:60:4:0.012:0:1.5 -10 111567639 . A C 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGTTGGCATGGTTGTAAA;RSEQ=AAACAAGTTAAGGGCAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:67,123:0:2,0:24.2:1:29.9:1:1:0:60:189:1:0:0.1 0/1:243:54:19,35:77,112:0.2222:2,2:21.9:1:31.6:1:0.52905:1.26523:59.2:108:0.2241:0:1.1 -10 112948994 . G A 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.31595;LSEQ=TTTGATCATAAAGGGAATAC;RSEQ=TAATAAACTTGTAACTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:3,2:0.4444:2,2:35.3:1:30:1:1:1.85:60:8:0.4444:0:1.3 1/0:3:2:2,0:0,0:0.6667:0,0:21.5:1:31:1:1:0:60:4:0.6667:0:1 -10 112949020 . T A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=AACTTGTAACTACAATCTAT;RSEQ=GAATGCTCAGGGTGCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,3:0.1667:2,2:45:0:30.5:1:1:2.16028:60:4:0.1667:0:1.5 0/0:9:0:0,0:7,2:0:2,0:23.3:1:29.6:1:1:0:60:18:1:0:0.4 -10 114710162 . TC T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCTCCTGTATCTTCGGCT;RSEQ=CCCCCCCCTTTGCTCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:23.5:1:32:1:1:0:60:4:0.6667:0.3333:1.5 0/0:1:0:0,0:1,0:0:0,0:8:0:31:0:1:0:60:2:1:0:1 -10 114710208 . G GT 62 d7;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GACTTCTTGTTGTTGTTGGT;RSEQ=TTTTTTTTTTTTTTACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:39:1:31.3:1:1:0:60:8:1:0:2.8 0/0:1:0:0,0:1,0:0:0,0:27:0:17:0:1:0:60:0:0:0:1 -10 114710243 . A T 35 d7;v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCCTTTTTTATTTATT;RSEQ=TTTTTTTGCACATTGATCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:14.7:1:22.7:1:1:0:60:2:0.5:0:3 0/0:1:0:0,0:1,0:0:0,0:24:0:30:0:1:0:60:2:1:0:0 -10 114710450 . AT A 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.71859;SOR=1.41132;LSEQ=GGCAAAACTTTTTGGGGGTG;RSEQ=TTTTTTTGGCTTTTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:3:3,0:318,59:0.0079:2,0:8.3:1:31.3:1:1:0:60:6:0.008:0.0053:0.7 0/1:360:4:4,0:290,66:0.0111:2,0:19.3:1:30.9:1:1:0:60:8:0.0112:0.0056:0.3 -10 114710507 . G GA 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.35519;SOR=1.37044;LSEQ=CAAAATTGCTGCTGGTGGGT;RSEQ=AAAAAAAAATGCCGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:959:16:10,6:566,369:0.0167:2,2:27.4:1:29.4:1:1:1.09:60:32:0.0171:0.001:0 0/1:1188:27:12,15:689,469:0.0227:2,2:29.8:1:29.9:1:0.16433:1.83533:60:54:0.0232:0:0.3 -10 114710869 . AC A 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06951;SOR=1.31211;LSEQ=TTGTAACCCTGTTTTTTTCT;RSEQ=CCCCCCCTCGACCTCGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:161:127,34:152,47:0.4423:2,2:23.5:1:31.3:1:0.61288:1.15:59.9:79.5:0.4556:0.0852:0.4 1/0:398:203:165,38:164,31:0.5101:2,2:23.4:1:30.4:1:0.50865:1.21777:59.7:32.833:0.509:0.0955:0.3 -10 114711041 . G A 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.99744;LSEQ=GTTTGGAAGAAGGTGAGTAC;RSEQ=CCCCGCGCGCCCCGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:4:2,2:96,292:0.0102:2,2:15:1:23.5:1:0.26118:3.03:60:3:0.0077:0:1.3 0/1:591:6:5,1:203,382:0.0102:2,2:9.3:1:29.5:1:0.02233:9.38:60:12:0.0103:0:1.2 -10 114711066 . G A 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01249;SOR=5.45044;LSEQ=GCGCGCCCCGCAGCCGCCCG;RSEQ=AGCCGCCCCCCGGGCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:2,0:32,132:0.012:2,0:1:0:26.5:1:0.04096:0:60:4:0.0123:0:1 0/1:256:16:3,13:78,162:0.0625:2,2:9.3:1:27.6:1:0.40486:2.08122:60:7:0.0558:0:1.2 -10 114711399 . G A 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69085;SOR=1.71485;LSEQ=GCGCCCGGCCCCCGCCCGCT;RSEQ=CCCGCCCGCCCGCGCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:2,0:36,116:0.013:2,0:1:0:23:0:0.05967:0:60:4:0.0133:0:1 0/1:181:4:3,1:52,125:0.0221:2,2:6.5:1:25.8:1:0.08431:7.12:60:8:0.0223:0:1 -10 114711755 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATGACTCTGTGGCTCTT;RSEQ=CTTTGCTCTCTCTCCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:16:0:26:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29.5:1:1:0:60:4:1:0:1.5 -10 114712594 . G C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCCTCCCCCACCGGCCT;RSEQ=TGCCCCCTGCCCTCACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:32.5:1:1:0:60:4:1:0:1 -10 114724100 . A AAAAAAC 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1957;SOR=Inf;LSEQ=TGCTTATTGAATAGGTGCTT;RSEQ=AAAAACAAAAACAAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:17,0:0:1,0:23.9:1:28.6:1:1:0:60:34:1:0:0 0/1:14:2:2,0:12,0:0.1429:0,0:8.5:1:28.6:1:1:0:60:4:0.1429:0.0714:1 -10 114724470 . GATA G 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.63258;SOR=2.41759;LSEQ=CCGCCCCTTCCCCCAACTGA;RSEQ=ATGATGATGATGATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:0,1:32,193:0.0044:2,0:41:0:32:0:1:0:40:2:0.0046:0:6 0/1:283:3:0,3:47,233:0.0106:2,0:29.3:1:29.7:1:1:0:60:6:0.0111:0:0 -10 114724473 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=11.55473;LSEQ=CCCCTTCCCCCAACTGAGAT;RSEQ=ATGATGATGATGATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:15:2,13:31,175:0.0676:2,2:21.5:1:31.4:1:1:1.15072:60:30:0.0694:0:1.2 0/1:267:122:22,100:23,118:0.4569:2,2:25.2:1:30.5:1:0.74459:1.13:60:60:0.4669:0:1.3 -10 114724525 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.22077;SOR=Inf;LSEQ=TGGTGGTGGTGGTGATGGTG;RSEQ=TGGTGGTGGTGATGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:0,66:0:1,0:20.2:1:31.3:1:1:0:59.3:21:1:0:0.6 0/1:59:2:0,2:1,56:0.0339:1,0:10.5:1:30:1:1:0:60:4:0.0351:0:4 -10 114724537 . A ATGG 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.09387;SOR=Inf;LSEQ=TGATGGTGGTGGTGGTGGTG;RSEQ=TGGTGGTGGTGGTGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:0:1,0:21:1:27.8:1:1:0:59.1:4.333:1:0:0.8 0/1:41:3:0,3:1,36:0.0732:1,0:18.3:1:27.3:1:1:0:46.7:6:0.0833:0.0488:3 -10 114724569 . GGT G 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=0.25506;SOR=0;LSEQ=GTGATGGTGGTGGTGGTGGT;RSEQ=GGGGGGGGGTTGAATCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:0.1304:1,0:19:1:29.7:1:1:0:53.3:6:0.15:0.087:1 0/0:16:0:0,0:1,14:0:1,0:20.1:1:29.6:1:1:0:58.3:14:0.9333:0:0.7 -10 114849059 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50574;SOR=0;LSEQ=TGGAGCTTCTATAGAAATGT;RSEQ=GGTTAGGGCAGAAAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:2,0:165,4:0.0117:1,0:8:1:31.5:1:1:0:60:4:0.0119:0:1 0/0:134:0:0,0:129,4:0:1,0:23:1:32:1:1:0:60:132:0.9925:0:0.1 -10 114849353 . C T 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.02143;LSEQ=AGCTAGCTCTAAAATGAAGC;RSEQ=GCCCACCCAAAGTTTACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:22:2,20:125,349:0.0444:2,2:27:1:30.1:1:0.08122:3.57535:60:44:0.0445:0:1 0/1:578:91:23,68:143,344:0.1574:2,2:24.3:1:30:1:0.45221:1.22855:60:44.5:0.1561:0:1.1 -10 114849399 . C T 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00197;SOR=Inf;LSEQ=AGGGCAGGGCCCATCCACTG;RSEQ=GATCCCTGAATTCTTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:5,185:0:1,0:23.4:1:30:1:1:0:60:94:1:0:0.1 0/1:211:10:0,10:4,197:0.0474:1,0:29.5:1:31:1:1:0:60:20:0.0476:0:1 -10 114849463 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1816;SOR=Inf;LSEQ=GATGTCTGGGTGTGCTGACC;RSEQ=CTGATAGGGATATCATAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:3,64:0:1,0:19.5:1:32.1:1:1:0:60:66:0.9851:0:0.1 0/1:51:2:1,1:2,47:0.0392:1,2:25.5:1:27:1:0.11529:19.40:60:4:0.0392:0:1 -10 114886564 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37135;SOR=3.90498;LSEQ=GCCCGCGGCCGGCGCGGGCC;RSEQ=TGGGCAGCATCTGGGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:0,1:82,66:0.0067:2,0:1:0:25:0:0.44966:0:60:2:0.0069:0:1 0/1:155:4:1,3:86,65:0.0258:2,2:12.5:1:27.8:1:0.31995:3.93585:60:8:0.0265:0:1.3 -10 114886565 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=CCCGCGGCCGGCGCGGGCCC;RSEQ=GGGCAGCATCTGGGCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:84,71:0:2,0:18.3:1:30.1:1:1:0:60:50.667:1:0:0.2 0/1:159:2:1,1:90,67:0.0126:2,2:27:0:31:0:1:1.34074:60:4:0.0127:0:1.5 -10 114886655 . CGGCG C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=1;SSF=0.67294;SOR=0.57519;LSEQ=TAGATGGTAAGCGCGGCCGG;RSEQ=GGCGGGCGGGCAGGGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:3:2,1:51,69:0.0244:2,2:22:1:29.7:1:0.57705:2.68:60:6:0.025:0.0081:1 0/1:212:3:1,2:93,114:0.0142:2,2:8.7:1:29.8:1:1:1.62793:60:6:0.0142:0.0094:0.7 -10 114886658 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13561;SOR=0;LSEQ=ATGGTAAGCGCGGCCGGCGG;RSEQ=GGGCGGGCGGGCAGGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:50,66:0.0167:2,2:9.5:1:28:1:1:1.32:60:4:0.0174:0:1.5 0/0:205:0:0,0:90,114:0:2,0:18.6:1:30.3:1:1:0:60:50:1:0:0.3 -10 114886662 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAGCGCGGCCGGCGGCGGG;RSEQ=GGGCGGGCAGGGGTGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:37,56:0:2,0:15.5:1:30.6:1:1:0:60:92:1:0:0.4 0/1:187:2:1,1:80,103:0.0107:2,2:14:0:28:0:1:1.29:60:4:0.0108:0:1.5 -10 114886663 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55308;SOR=Inf;LSEQ=AAGCGCGGCCGGCGGCGGGC;RSEQ=GGCGGGCAGGGGTGCGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:36,51:0:2,0:15.6:1:30.3:1:1:0:60:42.5:1:0:0.4 0/1:178:3:1,2:77,97:0.0169:2,2:10:1:25.3:1:1:1.58366:60:6:0.0171:0:1.3 -10 114886843 . AT A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GGGGTGGATGCAGTAGATTT;RSEQ=TTTTTTTAGCCTCTCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:13.8:1:29.2:1:1:0:60:10:1:0:0 0/1:5:2:1,1:1,2:0.4:2,2:34.5:1:31.5:1:1:1.73:60:4:0.4:0:0 -10 114889261 . T A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGTTTTTAAAATTTTTTT;RSEQ=AAAAAATTAAATCTGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:22:1:29.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 114889436 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12342;SOR=Inf;LSEQ=ACTCGGCCAGGAATCTGGAG;RSEQ=CATTTCGATCTTTTTAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:0:1,0:22.8:1:31.1:1:1:0:60:14:1:0:0.4 0/1:33:2:1,1:29,2:0.0606:2,2:22.5:1:26:1:0.17614:12.04172:60:4:0.0645:0:1 -10 114889834 . T A 43 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05135;SOR=Inf;LSEQ=TTGACCATTAAACCTATGCT;RSEQ=TTTCCCCCCCCTTAATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:31,379:0:2,0:23.2:1:30.4:1:1:0:59.9:67.333:1:0:0.2 0/1:374:4:3,1:48,322:0.0107:2,2:12.8:1:21.8:1:0.0087:19.83:60:3:0.0081:0:1.3 -10 114889837 . TC T 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00029;SOR=0.54472;LSEQ=ACCATTAAACCTATGCTTTT;RSEQ=CCCCCCCTTAATTTAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:385:293:6,287:16,76:0.761:2,1:25.5:1:31.6:1:0:9.98964:59.9:145.5:0.7618:0.0727:0.3 1/0:328:208:7,201:21,96:0.6341:2,1:26.6:1:31.4:1:1e-05:6.2429:60:207:0.635:0.0396:0.2 -10 114889900 . GC TA 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0554;SOR=0.52974;LSEQ=AGAATAAATGGTCAACTCAA;RSEQ=TATGCCCTTTCTTTGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:107:59:0,59:0,48:0.5514:1,1:24.1:1:30.2:1:1:0:60:118:0.5566:0.0654:0.9 0/1:61:24:0,24:1,36:0.3934:1,1:18:1:29.9:1:1:0:60:48:0.3934:0.0656:1.1 -10 114890223 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGATAAGGCTTTAACAGTAG;RSEQ=AGGGCTGTGTAAACTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:2:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:27.5:1:1:0:60:4:1:0:1.5 -10 114900499 . A G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGATTTGGGCCCTGCC;RSEQ=GTTTCTTGTAAGTGGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:37.7:1:30.3:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 114900559 . A C 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAGCCTGCGTGCCTCCTGG;RSEQ=GGTGGGGCCTTGGGGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:34.8:1:31.3:1:1:0:60:8:0.6667:0:2.3 1/1:2:2:2,0:0,0:1:0,0:11.5:1:33:1:1:0:60:4:1:0:3 -10 114900595 . T C 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGGAGGTCCCCACAACATG;RSEQ=GGAAACGCAGTAGGCATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:3,0:0.625:0,2:12.2:1:30.2:1:1:0:60:10:0.625:0:2.2 1/1:2:2:2,0:0,0:1:0,0:47.5:1:32.5:1:1:0:60:4:1:0:3 -10 114900627 . T C 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.09375;LSEQ=AGGCATGGGAGATTGAAGTC;RSEQ=CCACTTCTGACTCACCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:3,0:0.5714:0,2:15:1:32:1:1:0:60:8:0.5714:0:1.8 1/0:4:3:2,1:1,0:0.75:0,2:18.7:1:29.7:1:1:0:60:6:0.75:0:2.3 -10 114901194 . TG T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.7727;SOR=0.71866;LSEQ=GGACTTTGGGGGAACGGTGG;RSEQ=GGGGGGCCCCTGTTGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:9:0,9:2,118:0.0455:1,0:17.2:1:26.9:1:1:0:59.4:8:0.0415:0.0202:2.2 0/1:121:4:0,4:2,74:0.0331:1,0:13.3:1:27.3:1:1:0:60:8:0.0333:0.0165:1.3 -10 114901200 . GG T 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.9037;SOR=0.95827;LSEQ=GACTTTGGGGGAACGGTGGT;RSEQ=CCCCTGTTGCTTTTCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:69:0,69:2,118:0.3485:1,1:27.4:1:31.8:1:0.53394:0:60:138:0.3575:0.0101:0.1 0/1:121:41:0,41:2,74:0.3388:1,1:24.9:1:30.8:1:0.54082:0:60:82:0.3417:0.0413:0.1 -10 114901201 . G T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.79031;SOR=0.74527;LSEQ=GGGGGAACGGTGGTGGGGGG;RSEQ=CCCCTGTTGCTTTTCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:12:0,12:1,99:0.1071:1,0:11.9:1:27.1:1:1:0:59.6:5:0.0926:0:1.9 0/1:61:5:0,5:2,54:0.082:1,0:13.4:1:27.4:1:1:0:60:10:0.0833:0:1.2 -10 114903850 . T TGAA 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.1002;SOR=Inf;LSEQ=CATGTTTATTATTTATTCTG;RSEQ=GTGTGTGTCTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:32,287:0:2,0:23.2:1:30.2:1:1:0:59.3:62.8:0.9968:0:0.3 0/1:282:3:2,1:32,246:0.0106:2,2:15.7:1:29.4:1:0.03951:15.09:60:6:0.0107:0.0035:1 -10 114903899 . G A 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=1;SOR=0.87217;LSEQ=GTGTGTGTGTGTGTGTGTAT;RSEQ=TGTGTGTGTTAGAAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:0,2:1,128:0.0153:1,0:43:1:32:1:1:0:50:4:0.0154:0:2 0/1:75:1:0,1:0,74:0.0133:1,0:8:0:31:0:1:0:60:2:0.0133:0:2 -10 114904036 . G A 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69008;LSEQ=ACTGGCACTTAGCATTCCGC;RSEQ=ACCATGGTCCCCAGAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:17:1:27.8:1:1:0:60:5:0.625:0:1 1/0:2:1:0,1:0,1:0.5:0,0:32:0:26:0:1:0:60:2:0.5:0:1 -10 114904534 . A T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCCCAGATTATTTGACTA;RSEQ=CTTTTGCAACTTAAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 114910412 . G C 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGGAAATTGTCTTCTTA;RSEQ=ATGCCACTAATAATGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:21:1:31.7:1:1:0:60:6:0.6:0:1.3 0/0:1:0:0,0:1,0:0:0,0:3:0:28:0:1:0:60:2:1:0:0 -10 114910586 . A G 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05707;SOR=Inf;LSEQ=GCTTTAATGACATTATGAGA;RSEQ=TCATTATGTTTAATTTATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:115,0:0:1,0:25.1:1:30.3:1:1:0:60:114:1:0:0.1 0/1:73:3:3,0:69,1:0.0411:1,0:10.7:1:27.7:1:1:0:60:2:0.0278:0:1.3 -10 114910667 . G GT 212 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.34151;LSEQ=TCATGTGAGTGTTACGTGCT;RSEQ=TTTTTTTTTTTCTTTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:128:119,9:194,20:0.3333:2,2:28.8:1:30.4:1:0.54968:1.36:60:256:0.3413:0:0.3 0/1:405:59:49,10:273,55:0.1457:2,2:25.8:1:30:1:1:1.01295:59.7:118:0.149:0:0.3 -10 114911022 . T C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08065;SOR=Inf;LSEQ=ACCCAGCCTGTGTGGGCTCT;RSEQ=CACTCCCTTACAAAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:2,161:0:1,0:24.6:1:30.4:1:1:0:60:80.5:1:0:0.4 0/1:125:3:0,3:2,120:0.024:1,0:16:1:32.3:1:1:0:60:6:0.0242:0:1 -10 114911035 . AAG A 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.08151;SOR=0;LSEQ=GGGCTCTTCACTCCCTTACA;RSEQ=AGAGAGAGAGTGCACAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:5:0,5:2,127:0.0373:1,0:30:1:32.8:1:1:0:60:10:0.0388:0:0.4 0/0:92:0:0,0:1,91:0:1,0:24.4:1:31:1:1:0:60:91:1:0:0.4 -10 114911079 . T C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.71404;SOR=1.85625;LSEQ=AGAATCTCACTGTACCACCG;RSEQ=GGGTTAGAACAGAACTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:60:1,59:0,6:0.8955:0,1:22:1:29.9:1:1:0:60:29:0.9206:0:1.1 1/1:34:32:0,32:0,2:0.9412:0,1:19.5:1:29.7:1:1:0:60:31:0.9394:0:1.1 -10 114912534 . C T 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=ACCCAAAGGACCTTATGTTC;RSEQ=GGATTAGGTTCCGCAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:22.6:1:31.4:1:1:0:60:10:0.625:0:1 0/0:2:0:0,0:0,2:0:0,0:3.5:1:26:1:1:0:60:4:1:0:0 -10 114917603 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GTGTCCCTCCAGCTGGGGTA;RSEQ=AATGCAAGGGCATTTGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:0:1,0:21.9:1:32.8:1:1:0:60:38:1:0:0.6 0/1:13:2:1,1:11,0:0.1538:0,2:25.5:1:26:1:0.15385:0:60:4:0.1538:0:1.5 -10 114917721 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19941;SOR=Inf;LSEQ=TCTCCTTCCAGGTGCGCCCA;RSEQ=ACACTCTTCTCACATCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:182,6:0:1,0:25.3:1:32.3:1:1:0:60:61.667:1:0:0.1 0/1:153:2:2,0:148,3:0.0131:1,0:39.5:1:30.5:1:1:0:60:4:0.0134:0:1 -10 114917782 . AAAG A 97 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.30683;SOR=1.83472;LSEQ=TTTCATCTCTTCATCTAGGG;RSEQ=AAGAAGAAGAGGAAAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:5:4,1:396,228:0.0079:2,2:36.8:1:31.8:1:0.65774:2.30:60:10:0.0081:0:0.2 0/1:691:10:4,6:401,280:0.0145:2,2:30.6:1:29.4:1:0.3328:2.14582:60:20:0.0146:0:0.3 -10 114917909 . G T 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06171;SOR=Inf;LSEQ=TAGGTTTCCATCTGGGGGAG;RSEQ=CAGGAGAAATTCAAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:99,289:0:2,0:24.9:1:31.5:1:1:0:60:54.429:0.9948:0:0.1 0/1:393:5:2,3:115,272:0.0127:2,2:12.8:1:27.6:1:0.6372:1.57:60:10:0.0131:0:1 -10 114917998 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54688;SOR=0;LSEQ=TAATTAATTGCTTCATGACT;RSEQ=CCCTTTTAAAGCTAGTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:2,96:0.02:1,2:24:1:26.5:1:0.05939:39.37:60:4:0.0206:0:1 0/0:52:0:0,0:0,52:0:1,0:26.6:1:32.3:1:1:0:60:51:1:0:0 -10 114918624 . A AT 55 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.70512;SOR=1.33374;LSEQ=GGTTTCGTATGTTTCAGTAG;RSEQ=TTTTTTTTTTCAGTTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:4:0,4:4,110:0.0339:1,0:23.5:1:27.8:1:1:0:60:3:0.028:0.0169:0.5 0/1:67:3:0,3:1,63:0.0448:1,0:31:1:27.7:1:1:0:60:6:0.0484:0:1.3 -10 114918646 . GT G 117 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.25744;SOR=0.43854;LSEQ=TTTTTTTTTCAGTTGCTTCT;RSEQ=TTTTTTTTTTTAATTTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:12:0,12:1,67:0.15:1,0:31:1:32.8:1:1:0:60:24:0.1538:0:0.8 0/1:42:3:0,3:2,37:0.0714:2,0:18:1:27.7:1:1:0:60:6:0.075:0.0238:0 -10 114918783 . TA T 28 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTTTAAAAGAGACTGGT;RSEQ=AAAAAAAAAATGGAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:38:1:28.5:1:1:0:60:4:0.25:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 114919469 . CT C 46 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.06294;SOR=6.98562;LSEQ=GAATAAGAATGTGACTTTTA;RSEQ=TTTTTTTTTTTAATTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:3,0:22,0:0.1154:1,0:8.3:1:26.4:1:1:0:60:2:0.08:0.0769:1 1/0:6:3:3,0:3,0:0.5:0,0:19.3:1:29.6:1:1:0:60:6:0.5:0.1667:0 -10 114919482 . A G 109 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12031;SOR=0.1637;LSEQ=ACTTTTACTTTTTTTTTTTT;RSEQ=ATTAAAGAAAGTTAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:12,0:16,0:0.4138:1,0:21.4:1:30.6:1:1:0:60:11:0.3929:0:1 0/1:10:1:1,0:9,0:0.1:0,0:10:0:32:0:1:0:60:2:0.1111:0:1 -10 114919602 . CCCTCTTTC TCTCTCTT 64 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.23179;SOR=0.24501;LSEQ=TTTCTCTTCCCCCCCCCCCC;RSEQ=TCTCTCTCTCTCTCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:5:4,1:180,35:0.0216:2,2:9.6:1:27.7:1:1:1.28412:60:10:0.0318:0.0173:1.8 0/0:186:1:0,1:153,24:0.0054:2,0:42:0:32:0:0.14045:0:60:2:0.0072:0:5 -10 114919606 . C T 68 q23;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00741;SOR=0;LSEQ=TCTTCCCCCCCCCCCCCCCT;RSEQ=TTTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:8:8,0:147,46:0.0392:2,0:24:1:22.8:1:0.20225:0:55.4:1.667:0.0407:0:4.5 0/0:194:0:0,0:132,57:0:2,0:31:0:17:0:1:0:60:0:0:0:6 -10 114919608 . T C 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00089;SOR=0;LSEQ=TTCCCCCCCCCCCCCCCTCT;RSEQ=TCTCTCTCTCTCTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:11:7,4:144,46:0.0524:2,2:20:1:28.5:1:0.47139:1.78297:58.2:4.5:0.052:0:3.3 0/0:198:0:0,0:126,62:0:2,0:10.9:1:27.1:1:1:0:59.3:6.833:1:0:1 -10 114920089 . A G 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07368;SOR=0;LSEQ=CCTAGGTAGAAGCAAATGAC;RSEQ=TCACCTTCTCCCCTCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:9,2:3,3:0.6471:2,2:25.8:1:29.9:1:0.28006:4.07:60:22:0.6471:0:1.2 0/0:3:0:0,0:1,2:0:2,0:34.7:1:31:1:1:0:60:6:1:0:0.7 -10 114920107 . C T 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01846;SOR=Inf;LSEQ=ACATCACCTTCTCCCCTCCT;RSEQ=TTCTCTCTCTCTTTTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,7:0:2,0:22.5:1:30:1:1:0:60:10:1:0:0.5 1/0:4:2:1,1:0,2:0.5:0,2:37.5:1:29.5:1:1:0:60:4:0.5:0:1 -10 114921129 . A G 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00028;SOR=Inf;LSEQ=TATGTGTGTATATATGTAGC;RSEQ=TTGGTTCCAAAAGGAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:101,1:0:1,0:18.9:1:31:1:1:0:60:204:1:0:0.1 0/1:61:8:8,0:51,2:0.1311:1,0:18.5:1:30:1:1:0:60:16:0.1379:0:1 -10 114925316 . G GA 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.02194;LSEQ=TCTCTCCCCTGTTTCTAGGA;RSEQ=AAAAAAAAAGTGCGTTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1274:40:22,18:677,556:0.0314:2,2:25.6:1:28.6:1:1:1.00:60:9:0.0288:0:0.7 0/1:1497:48:25,23:814,630:0.0321:2,2:29.4:1:28.9:1:0.55815:1.18856:60:96:0.0324:7e-04:0.2 -10 114925675 . T C 234 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=188.15296;LSEQ=CTTCCTTACATTCCCACAGC;RSEQ=CCCTGGCCGGGACCCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1917:1:0,1:914,998:5e-04:2,0:26:0:12:0:1:0:60:0:0:0:5 0/1:2326:207:102,105:1084,1032:0.089:2,2:22.7:1:30.5:1:0.61058:1.08123:60:206:0.0912:0:1.3 -10 114925758 . T C 198 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTCGTGAACCCCGCTGCTT;RSEQ=GTTTATGGTTTTGTTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1124:0:0,0:404,720:0:2,0:25.8:1:29.8:1:1:0:60:43.96:1:0:0.2 0/1:1455:103:42,61:532,813:0.0708:2,2:23.2:1:29.7:1:0.83474:1.05:60:50.5:0.071:0:1.4 -10 114925845 . T C 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02478;SOR=Inf;LSEQ=ACTCTCTTAATTTTGTGCCA;RSEQ=GTGGCTACATTAGTTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:2,217:0:1,0:25.4:1:30.4:1:1:0:60:72:1:0:0.1 0/1:202:5:0,5:1,196:0.0248:1,0:27.4:1:30.2:1:1:0:60:10:0.025:0:1 -10 116005765 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51296;SOR=Inf;LSEQ=CAGTCTGAGAATATTGGGTG;RSEQ=TCAGTACATGCTCCATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:56,47:0:2,0:27:1:30.8:1:1:0:59.3:24.75:1:0:0.3 0/1:146:2:1,1:84,60:0.0137:2,2:41.5:1:29:1:1:1.3967:60:4:0.0139:0:1 -10 116005775 . G A 22 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50738;SOR=Inf;LSEQ=ATATTGGGTGGTCAGTACAT;RSEQ=CTCCATCCTCCAGGAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:69,49:0:2,0:24.3:1:30.9:1:1:0:58.5:13.75:1:0:0.4 0/1:155:2:2,0:87,66:0.0129:2,0:8.5:1:22:1:0.50783:0:60:4:0.0131:0:1 -10 116005831 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.51012;SOR=Inf;LSEQ=CTGGACTACCTGCCCCCGCC;RSEQ=CCCGCCCAAGATGATTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:57,57:0:2,0:13.4:1:28.4:1:1:0:57.8:9.364:1:0:0.6 0/1:157:2:2,0:79,75:0.0127:2,0:19:1:29:1:0.49752:0:60:4:0.0143:0:1 -10 116006000 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13862;SOR=0;LSEQ=CTGGGCATGGTGGCTCACGC;RSEQ=TGTAATCCCAGCACTTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:36,93:0.0153:2,2:32.5:1:29:1:0.48667:2.56:60:4:0.0155:0:1 0/0:220:0:0,0:60,160:0:2,0:23.4:1:31.2:1:1:0:60:72.333:1:0:0.2 -10 116006007 . C A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05168;SOR=0;LSEQ=TGGTGGCTCACGCCTGTAAT;RSEQ=CCAGCACTTCGGGAGGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:3:2,1:23,86:0.0268:2,2:14:1:26.7:1:0.12461:7.30:57:6:0.0273:0:1 0/0:187:0:0,0:42,144:0:2,0:22.5:1:30.8:1:1:0:60:92:0.9946:0:0.2 -10 116006031 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27574;SOR=Inf;LSEQ=GCACTTCGGGAGGCCGAGGC;RSEQ=GTCGTATCACCTGAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:5,63:0:2,0:24.6:1:30:1:1:0:59.6:33:1:0:0.2 0/1:102:3:0,3:7,91:0.0294:2,0:10:1:30.7:1:1:0:60:6:0.0306:0:1 -10 116006247 . T C 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02735;SOR=Inf;LSEQ=TCCAGCCTGGGCAACAAGAG;RSEQ=GAAAGAAACTCCATCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:50,6:0:2,0:20.8:1:27.5:1:1:0:54:8.333:1:0:1 0/1:59:6:6,0:50,3:0.1017:2,0:13.2:1:28:1:1:0:43.8:5:0.0943:0:1.5 -10 116006285 . C A 81 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30189;SOR=1.77029;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=GAGTATCATGGGTTGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:6:6,0:112,35:0.0387:2,0:17.5:1:21.5:1:0.33741:0:56.7:1:0.0254:0:2.5 0/1:135:9:7,2:91,35:0.0667:2,2:18.2:1:25.6:1:1:1.34:50:3.5:0.0722:0:2.6 -10 116006436 . T C 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=2.23498;LSEQ=AGCAAATTCATCAAAACCAT;RSEQ=AAATTCCCAAAACAAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:38:16,22:207,272:0.0735:2,2:30.2:1:31.5:1:1:1.04633:47.7:37:0.073:0:1.2 0/1:730:110:47,63:282,338:0.1507:2,2:25.6:1:31.4:1:0.60494:1.11817:46.6:220:0.1526:0:1.2 -10 116006522 . C G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3224;SOR=1.52228;LSEQ=GAACCAGGGCTGCTGTATAA;RSEQ=CTTTCAGGAACATGCTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:10:1,9:68,171:0.0402:2,2:25.8:1:32.5:1:0.29199:3.56605:60:20:0.041:0:1.2 0/1:267:16:6,10:69,182:0.0599:2,2:26.3:1:31.8:1:0.3971:1.58:60:32:0.0599:0:1.3 -10 116006533 . C A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.41393;LSEQ=GCTGTATAACCTTTCAGGAA;RSEQ=ATGCTACTAAAATTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:2:1,1:47,153:0.0099:2,2:12.5:1:28.5:1:0.41968:3.23:60:4:0.01:0:1 0/1:215:3:2,1:53,159:0.014:2,2:21.7:1:29.7:1:0.16153:5.94:60:6:0.0142:0:1.7 -10 116006545 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24017;SOR=0;LSEQ=TTCAGGAACATGCTACTAAA;RSEQ=TTTATTTTACCATTGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:28,131:0.0124:2,2:11.5:1:27:1:0.32873:4.61:60:4:0.0124:0:1 0/0:167:0:0,0:33,134:0:2,0:21.8:1:30:1:1:0:60:334:1:0:0.2 -10 116007159 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCATCCCAGGTTCAAG;RSEQ=GATTCTCCTGCCTCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 116801306 . AG A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGACAGTTTGCAAAAAAG;RSEQ=ACGAAATCTGTCCTTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:22.7:1:30.7:1:1:0:40.7:6:1:0:0.7 1/1:3:3:1,2:0,0:1:0,2:33:1:31:1:1:0:58:6:1:0:0 -10 116801503 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20183;SOR=Inf;LSEQ=GTTTACAGGAAAAGGCTTCT;RSEQ=AAATCAGACAATGCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:37,20:0:2,0:27.7:1:31.9:1:1:0:49.8:56:1:0:0.2 0/1:47:2:1,1:29,15:0.0426:2,2:26:1:30:1:1:1.90401:25:4:0.0435:0:3.5 -10 116801538 . C A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05843;LSEQ=CTTTCAAACTCTTATACCAA;RSEQ=CTCTGGAGTTGGGCGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:39,33:0.027:2,2:35:1:28:1:1:1.17914:23:4:0.0274:0:2.5 0/1:70:2:1,1:38,30:0.0286:2,2:33.5:1:28.5:1:1:1.26235:25:4:0.0299:0:3.5 -10 116801545 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22505;SOR=Inf;LSEQ=ACTCTTATACCAACCTCTGG;RSEQ=GTTGGGCGACATGGCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:41,36:0:2,0:26.6:1:30.1:1:1:0:51.6:76:1:0:0.2 0/1:70:2:1,1:36,32:0.0286:2,2:35.5:1:29:1:1:1.1231:50:4:0.0299:0:1 -10 117807835 . A G 145 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01001;SOR=2.97123;LSEQ=TCAAGGTCTGAACAGAGGGA;RSEQ=GAGAGAAAAGTAAATAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:7:5,2:115,70:0.0363:2,2:34:1:29.4:1:0.71326:1.52:60:6:0.0313:0:1.9 0/1:258:26:15,11:131,100:0.1008:2,2:22.9:1:31:1:1:1.04:60:52:0.1008:0:1.7 -10 117807881 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=19.27878;LSEQ=GAGGGCAGGAATCATATTTC;RSEQ=CTGTTTCCCAAAGATAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:10:7,3:137,126:0.0366:2,2:18.4:1:31.7:1:0.34222:2.14:60:20:0.037:0:1.5 0/1:368:156:76,80:99,112:0.4239:2,2:25.8:1:29.8:1:0.752:1.07:60:77:0.4242:0:1.6 -10 117807917 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29039;LSEQ=AGCGTCCATCACATGATAGG;RSEQ=CTCCAGTGAACTTTCTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:243:131:57,74:46,66:0.5391:2,2:23.9:1:29.6:1:0.79462:1.10:60:42.667:0.5378:0:1.1 0/1:324:82:33,49:101,140:0.2531:2,2:26.6:1:28.8:1:0.89683:1.07101:60:81:0.2531:0:1.8 -10 117807951 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24889;SOR=Inf;LSEQ=TCTAATAGAGGAAGGAATGA;RSEQ=CCTGAGGGAAACCCAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:45,108:0:2,0:22.7:1:31.8:1:1:0:60:50:1:0:0.6 0/1:166:3:2,1:53,110:0.0181:2,2:17.7:1:22.3:1:0.25522:4.11:60:2:0.0123:0:1 -10 117807957 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24869;SOR=Inf;LSEQ=AGAGGAAGGAATGAGCCTGA;RSEQ=GGAAACCCAGTTCATCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:33,102:0:2,0:22.6:1:31:1:1:0:60:66.5:0.9925:0:0.6 0/1:148:3:2,1:45,99:0.0203:2,2:15:1:23.7:1:0.23968:4.35:60:2:0.0139:0:2 -10 117808099 . C T 95 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17596;SOR=0.17918;LSEQ=GACCAGCCTGGCCAACATGG;RSEQ=GAAACCCTGTCTCTACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:0.5:0,0:26.5:1:31.9:1:1:0:60:16:0.5:0:1 0/1:7:1:0,1:0,6:0.1429:0,0:30:0:32:0:1:0:60:2:0.1429:0:1 -10 117888029 . G A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GACCGATCACAAGGTCAGGA;RSEQ=ATCGAGACCACCCTGACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:32:0:1:0:60:4:1:0:1.5 -10 117888157 . A T 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGCAGGAGAATGGCGTG;RSEQ=ACCTGGGAGGCAGAGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:1,1:0.6667:2,0:15.8:1:29.8:1:0.33333:0:57:8:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 117888327 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01245;SOR=Inf;LSEQ=AGTTGTTAAAACTACATATG;RSEQ=TGTTAAGGTTTTCCTCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:86,5:0:2,0:23.3:1:31.3:1:1:0:60:17.2:1:0:0.3 0/1:87:6:5,1:71,10:0.069:2,2:25.7:1:24.2:1:0.56708:1.41361:60:2:0.0506:0:3.2 -10 117888366 . AT A 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.75593;SOR=1.08638;LSEQ=AATGTTATTAGAAAAGCAAT;RSEQ=TTTTTTTAAAAAGGCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:90:73,17:70,37:0.4569:2,2:23.7:1:31.1:1:0.01627:2.26:60:180:0.4615:0.0761:0.1 0/1:178:85:64,21:61,32:0.4775:2,2:25.2:1:30.2:1:0.18995:1.59:59.9:170:0.4775:0.0955:0.7 -10 117888425 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.23524;LSEQ=TGAATCATTTTATGTCTAAA;RSEQ=CAATTGCTCAAAGTTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:18:9,9:194,182:0.0457:2,2:26.7:1:29.9:1:1:1.06573:60:17:0.0435:0:1.8 0/1:389:158:83,75:122,109:0.4062:2,2:25.9:1:28.9:1:1:1.01136:60:51.667:0.4026:0:1.7 -10 117888438 . G C 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00041;SOR=1.65605;LSEQ=GTCTAAACCAATTGCTCAAA;RSEQ=TTTACTTCATATAGCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:160:73,87:122,116:0.402:2,2:27.9:1:32.1:1:0.30664:1.2527:60:159:0.4046:0:1.1 1/0:408:215:105,110:93,99:0.527:2,2:27:1:31.3:1:1:1.02:60:70.667:0.5274:0:1.1 -10 117888465 . C T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.8841;LSEQ=TCATATAGCAGTAGGTGTGA;RSEQ=TTAGCCTCACTTTCTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:15:7,8:141,190:0.0434:2,2:29.3:1:30:1:0.79403:1.18:60:14:0.0409:0:1.9 0/1:333:123:49,74:93,114:0.3694:2,2:27.8:1:29.7:1:0.42109:1.23123:60:60.5:0.3712:0:1.8 -10 117888566 . C G 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29905;SOR=0.67471;LSEQ=CCTGTGACAAATTCTAGAAT;RSEQ=CGCAACCTGGAATATTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:37:1,36:2,26:0.5692:2,1:24:1:32.5:1:0.57308:2.72623:60:74:0.5692:0:1.1 0/1:68:32:4,28:3,33:0.4706:2,2:21.3:1:32.2:1:0.69862:1.56:60:31:0.4697:0:1 -10 117888887 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATGCAAGGTTAGTTTAATAT;RSEQ=TAAAAATATATGTAATTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:30.5:1:1:0:60:4:1:0:2.5 -10 117888908 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAATATATGTAATTCAC;RSEQ=GCACTAACAGAATACAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:28.5:1:1:0:60:4:1:0:2.5 -10 118256959 . T C 89 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=0;LSEQ=CCAGGGGTCCTCGGTAGAAG;RSEQ=TGTTAATTGAGCTCATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:27.3:1:32:1:1:0:40:14:1:0:3.3 1/0:5:3:2,1:1,1:0.6:2,2:30:1:29.7:1:1:1.73:46.7:6:0.6:0:3 -10 118256962 . T C 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGTCCTCGGTAGAAGTTG;RSEQ=TAATTGAGCTCATTTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:25.1:1:32:1:1:0:40:14:1:0:3.3 1/1:5:5:3,2:0,0:1:0,2:26.6:1:29.4:1:1:0:44:10:1:0:2.8 -10 118256965 . A G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCTCGGTAGAAGTTGTTA;RSEQ=TTGAGCTCATTTGGGGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:23:1:31.7:1:1:0:40:14:1:0:3.3 1/1:5:5:3,2:0,0:1:0,2:24.8:1:30:1:1:0:44:10:1:0:2.8 -10 118257049 . T C 76 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=AAACAAATTTGACAAGGAGG;RSEQ=TAAAAATACAGGGCCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:30.8:1:33:1:1:0:60:10:1:0:1 1/0:5:3:0,3:1,1:0.6:2,0:19.7:1:33.7:1:0.4:0:53.3:6:0.6:0:1.7 -10 118257169 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTGAAGAGCATTGTCTG;RSEQ=TTTCAGAAGACTTTTCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:5,9:0,0:1:0,2:19.2:1:31.9:1:1:0:60:28:1:0:1.1 1/1:14:13:6,7:0,1:0.9286:0,2:17.4:1:31.2:1:1:0:60:26:0.9286:0:1.2 -10 118258803 . TG T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTTATTGGATCATCTGGT;RSEQ=GGGGCTTCTGGCCCAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29.4:1:1:0:56:4:1:0.5:2 -10 118258819 . A G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTTGGGGGCTTCTGGCCC;RSEQ=GAGAACCTTTGTCCTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:28:1:1:0:56:4:1:0:2 -10 118510678 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49661;SOR=0;LSEQ=ACTAGTAGTGGGTGACAATG;RSEQ=CAAAACTGTCCCAAAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:0.0606:2,2:33:1:29:1:1:1.06462:60:4:0.0606:0:1 0/0:27:0:0,0:16,11:0:2,0:26.7:1:31:1:1:0:60:54:1:0:0.1 -10 119379087 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05076;LSEQ=GGTAAGCGGTCTGAAGACTC;RSEQ=ATTATGGAAAAACTGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:332:304:135,169:14,14:0.9157:2,2:27.1:1:30:1:0.69196:1.25099:60:75:0.9146:0:1.1 0/1:446:158:78,80:135,152:0.3543:2,2:27.7:1:29.7:1:0.6918:1.10:60:157:0.3552:0:1.2 -10 119379171 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49977;SOR=Inf;LSEQ=TGGGGAATATTGAGATAGGT;RSEQ=GGTTAAGCCTTCTCTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:25,95:0:2,0:21.9:1:30.2:1:1:0:60:119:1:0:0.4 0/1:135:2:1,1:28,105:0.0148:2,2:10:0:32.5:1:0.38474:3.70:60:4:0.015:0:1.5 -10 119379381 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCAGCCAACAGCAAACTA;RSEQ=AGCAGCTCAGCTGGGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:13:1:33:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 121649371 . C G 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6236;SOR=2.84365;LSEQ=GAGTGTTGCTTTTACACTAA;RSEQ=CAGTCAGGGATAGGATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:9,2:0.0833:2,0:6:0:34:0:1:0:60:2:0.0909:0:1 0/1:19:4:3,1:12,3:0.2105:2,2:29:1:28.8:1:1:1.31228:60:8:0.2105:0:1.5 -10 121649420 . T G 77 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15243;SOR=Inf;LSEQ=GGTGTTTACAGGAAAAGGCT;RSEQ=CTGAAATCAGACAACGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:24,11:0:2,0:17.2:1:30:1:1:0:60:34:1:0:0.6 0/1:57:5:3,2:32,20:0.0877:2,2:24.4:1:33.4:1:1:1.06545:60:10:0.0877:0:2 -10 121649458 . C A 73 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08222;SOR=Inf;LSEQ=CTTTCAAACTCTTATATCAA;RSEQ=CTCTGGAGTTGGGCGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:37,32:0:2,0:28.7:1:31.9:1:1:0:60:138:1:0:0.9 0/1:103:6:3,3:50,47:0.0583:2,2:36.3:1:28.5:1:1:1.06322:60:12:0.0583:0:2.3 -10 121649505 . T C 182 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCTTTCTAGGTCCTGTGA;RSEQ=GGCCATCTTGCTATTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:62:25,37:0,0:1:0,2:21.6:1:30.7:1:1:0:59.6:124:1:0:1.1 1/0:72:51:21,30:7,14:0.7083:2,2:19:1:30:1:0.60265:1.39:60:102:0.7286:0:1.3 -10 121649535 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49248;SOR=Inf;LSEQ=GCTATTATTCACCTTCGGGC;RSEQ=CTGTATTTTTAACCTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:7,20:0:2,0:21.8:1:30.8:1:1:0:59.2:26:1:0:1 0/1:30:2:1,1:6,22:0.0667:2,2:19.5:1:28.5:1:0.41839:3.47:60:4:0.069:0:2 -10 121932750 . T G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=3.4267;LSEQ=GCTTCAAAAGGGCAGCATCA;RSEQ=TATGGAGAATGTTTTGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:75:58,17:40,15:0.5769:2,2:26.9:1:31.9:1:0.68066:1.28:60:150:0.5814:0:1.8 1/1:131:108:73,35:14,8:0.8244:2,2:24.6:1:31.6:1:0.80471:1.19:60:107:0.8231:0:2 -10 121932799 . A G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.31825;LSEQ=GGTGAAACATAACAACTCAC;RSEQ=GTAAACATCTGTCGTACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:109:60,49:51,39:0.5477:2,2:26.3:1:29.8:1:0.88623:1.06758:60:35.333:0.5408:0:2.2 1/1:200:168:93,75:17,15:0.84:2,2:26.8:1:29.4:1:0.84807:1.09:60:55:0.8376:0:1.9 -10 121932833 . C A 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01818;SOR=0.63381;LSEQ=GTACCTTGTATAGAGCTGAA;RSEQ=TCCAGCACACATTGATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:225:131:62,69:43,51:0.5822:2,2:25.4:1:30.6:1:0.89236:1.07:60:130:0.5856:0:1.8 0/1:224:105:52,53:57,62:0.4688:2,2:24.9:1:29.7:1:0.89352:1.07:60:51.5:0.4703:0:1.9 -10 121932919 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1936;SOR=Inf;LSEQ=ACTTTTTCTCAGTTGTCCTT;RSEQ=GGGTCCTCACTCACTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:25,93:0:2,0:25.2:1:31.1:1:1:0:60:117:0.9915:0:0.3 0/1:94:2:1,1:24,68:0.0213:2,2:24.5:1:28.5:1:0.46328:2.80:60:4:0.0215:0:1 -10 121932975 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01373;SOR=0.1611;LSEQ=ACTTTATTTTTATTTAGTCA;RSEQ=ATATAAGATAACGCCTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:18:0,18:0,13:0.5806:1,1:27.7:1:32.6:1:1:0:60:36:0.6:0:1 0/1:17:3:0,3:0,14:0.1765:1,0:17.3:1:33.7:1:1:0:60:6:0.1765:0:1 -10 122114550 . T A 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGTGGGGCATTCCTTTT;RSEQ=GAACAGTACCCATTCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:1:0,2:30.1:1:29.7:1:1:0:39.4:18:1:0:1.2 1/1:4:4:4,0:0,0:1:0,0:28.8:1:27.3:1:1:0:38.3:8:1:0:1 -10 122114675 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59963;SOR=2.30354;LSEQ=ATATATCGGGTGCCTCTCCT;RSEQ=TTTCCCTTTGTGTTCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:1,0:76,35:0.0089:2,0:2:0:29:0:1:0:60:2:0.009:0:3 0/1:98:2:1,1:70,26:0.0204:2,2:6.5:1:29:1:0.47717:2.66079:37:4:0.0206:0:2 -10 122114700 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49927;SOR=0;LSEQ=CCTTTGTGTTCGTCATTTTG;RSEQ=CGAATTACTGGAAGATGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:91,62:0.0129:2,2:25:1:29.5:1:1:1.46399:60:4:0.0134:0:2 0/0:142:0:0,0:86,56:0:2,0:29.1:1:30.8:1:1:0:55.2:34.5:1:0:0.5 -10 122114724 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=ATTACTGGAAGATGGCGGTT;RSEQ=CGGCCGAAAGGGAAAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:78,72:0:2,0:31.7:1:30.7:1:1:0:57.8:36.5:0.9932:0:0.8 0/1:155:2:1,1:78,75:0.0129:2,2:41:1:28.5:1:1:1.03975:60:4:0.0132:0:1 -10 122114727 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23783;SOR=0;LSEQ=ACTGGAAGATGGCGGTTCCG;RSEQ=CCGAAAGGGAAAGTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:76,71:0.0134:2,2:29:1:31:0:1:1.0699:60:4:0.0137:0:2 0/0:156:0:0,0:78,78:0:2,0:29.1:1:30.6:1:1:0:56.6:38:1:0:0.5 -10 122114728 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49862;SOR=Inf;LSEQ=CTGGAAGATGGCGGTTCCGG;RSEQ=CGAAAGGGAAAGTTCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:77,72:0:2,0:31.1:1:30.7:1:1:0:58:20.286:1:0:0.8 0/1:156:2:1,1:77,77:0.0128:2,2:31:0:31:1:1:1:60:4:0.0132:0:1 -10 122114730 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.26087;LSEQ=GGAAGATGGCGGTTCCGGCC;RSEQ=AAAGGGAAAGTTCATTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:102:50,52:24,22:0.6892:2,2:31.6:1:30:1:0.85917:1.13358:58.5:101:0.6871:0:1.2 0/1:156:57:29,28:48,51:0.3654:2,2:27.9:1:29.3:1:0.86816:1.10:56.5:114:0.3654:0:1.1 -10 122302038 . A G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68284;SOR=1.94945;LSEQ=CTCCTCCAAAATGTTTATGA;RSEQ=AGATGGGATTTGGAATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:9,0:9,0:0.5:0,0:16.3:1:32.9:1:1:0:60:18:0.5:0:1.1 1/0:9:6:5,1:3,0:0.6667:0,2:21.7:1:32.7:1:1:0:60:12:0.6667:0:1 -10 122302203 . G A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.77611;LSEQ=CAGTTCTTTTCTTGCACTCA;RSEQ=CCTACATTCTCAATTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:1:1,0:177,122:0.0033:2,0:1:0:25:0:1:0:60:2:0.0034:0:1 0/1:301:29:16,13:162,109:0.0963:2,2:23.3:1:29.1:1:0.69247:1.20679:60:28:0.0943:0:1.8 -10 122302242 . C T 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13305;SOR=1.27972;LSEQ=CAGGCGCTGCTGAGTAATTA;RSEQ=GTGGTAAAAGCTTTTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:293:149:77,72:80,64:0.5085:2,2:25.6:1:30.3:1:0.55837:1.1682:60:36.25:0.507:0:1.1 1/0:358:204:105,99:82,72:0.5698:2,2:25:1:29.5:1:0.74968:1.07359:60:203:0.5751:0:1.2 -10 122302313 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24834;SOR=Inf;LSEQ=GACTGTCGATGATGCTTCAT;RSEQ=GTGGGCATTTGGATCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:71,133:0:2,0:24.7:1:29.5:1:1:0:60:24.5:1:0:0.4 0/1:210:3:2,1:79,128:0.0143:2,2:19.3:1:28:1:0.56048:3.22:60:6:0.0143:0:1.3 -10 122302318 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=TCGATGATGCTTCATTGTGG;RSEQ=CATTTGGATCAGTTAGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:61,127:0:2,0:25.1:1:31.4:1:1:0:60:61.667:0.9946:0:0.4 0/1:191:2:1,1:68,120:0.0105:2,2:21:1:26.5:1:1:1.76:60:4:0.0106:0:1 -10 122302325 . G T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=TGCTTCATTGTGGGCATTTG;RSEQ=ATCAGTTAGACCCCTGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:55,121:0.0112:2,2:29:0:28.5:1:0.53145:2.19:60:4:0.0113:0:1 0/0:168:0:0,0:54,114:0:2,0:23.3:1:30.7:1:1:0:60:55:1:0:0.4 -10 122302341 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22263;SOR=Inf;LSEQ=TTTGGATCAGTTAGACCCCT;RSEQ=ATTGTGGGGCAAAAGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:30,106:0:2,0:24.6:1:31:1:1:0:60:44.333:1:0:0.4 0/1:122:2:1,1:29,91:0.0164:2,2:5.5:1:27:1:0.43287:3.10:60:4:0.0167:0:1.5 -10 122302362 . G A 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26397;SOR=0.67405;LSEQ=ATTGTGGGGCAAAAGATGGC;RSEQ=TCATCTTCCAAAATTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:38:4,34:12,48:0.3878:2,2:21.3:1:31.4:1:0.27006:2.10979:60:76:0.3878:0:1 0/1:77:23:2,21:8,46:0.2987:2,2:25.1:1:29:1:0.71409:1.81322:60:22:0.2895:0:1.2 -10 122302563 . G C 43 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCATCCCCAGGACGGTG;RSEQ=GTGAGTGTGGGTGTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:24.7:1:27.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 123239112 . G A 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.22888;LSEQ=GTCCTACTGGTCCACAGCCA;RSEQ=TACGCACGGCAGGTGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:40:20,20:399,326:0.0521:2,2:26:1:29.6:1:0.62504:1.2236:60:39:0.0512:0:1.1 1/0:865:466:235,231:211,187:0.5387:2,2:25.5:1:29.8:1:0.45342:1.109:60:154.333:0.539:0:1.2 -10 123239349 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10094;SOR=Inf;LSEQ=TTCCCAGTGCTGTCCTGTTT;RSEQ=GGGACAGGCAGACACAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:218,85:0:2,0:22.4:1:31.8:1:1:0:60:100:1:0:0.1 0/1:265:3:1,2:171,91:0.0113:2,2:5.3:1:27.7:1:0.28226:3.73856:60:6:0.0114:0:1 -10 123239751 . G A 170 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=51.02504;LSEQ=CCAGCCCACCTGACTTCCAC;RSEQ=AAGACCTCCCTGAGACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1478:1:1,0:686,790:7e-04:2,0:1:0:25:0:0.46513:0:60:2:7e-04:0:1 0/1:1706:57:29,28:769,879:0.0334:2,2:22.6:1:29.3:1:0.58987:1.18:60:18:0.0321:0:1.1 -10 123240276 . GA G 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTGAAGGTTCGAGATTCA;RSEQ=AAGTGTCCTTTGCTCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:819:0:0,0:394,424:0:2,0:23:1:29.9:1:1:0:60:61.923:1:0:1 0/1:970:49:22,27:443,478:0.0505:2,2:23:1:31.3:1:0.7695:1.13726:60:98:0.0513:0.0103:0.9 -10 123240287 . T C 307 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51277;SOR=0.55754;LSEQ=CGAGATTCAGAAAGTGTCCT;RSEQ=TGCTCCCCAAGGCATCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:805:802:392,410:0,0:0.9963:0,2:23.7:1:31.7:1:1:0:60:79.2:0.9962:0:1.1 1/1:900:894:426,468:1,1:0.9933:2,2:23.9:1:31.4:1:1:1.09848:60:110.75:0.9933:0:1.1 -10 123240429 . G GA 164 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.2045;SOR=1.36077;LSEQ=TTTAACATTGGTAAGCGGTT;RSEQ=AAAAAAAAAATCAAAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:615:33:13,20:273,303:0.0537:2,2:29:1:30.6:1:0.47372:1.3854:60:66:0.0548:0:0.1 0/1:656:47:21,26:294,310:0.0716:2,2:30:1:29.7:1:0.65094:1.1739:59.6:94:0.0748:0.0015:0.3 -10 123240625 . A G 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03825;LSEQ=ACAGAGACCACAGGGCCGGC;RSEQ=AAGCTGAAAATATTTACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:811:768:345,423:19,23:0.947:2,2:24.7:1:30.4:1:1:1.01284:60:191:0.9479:0:1.5 0/1:1006:408:188,220:277,314:0.4056:2,2:24.2:1:30.4:1:0.84655:1.0323:60:407:0.4078:0:1.3 -10 123240645 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08516;LSEQ=AAAGCTGAAAATATTTACTC;RSEQ=CTGGCCCTTTACAGAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:796:365:168,197:190,240:0.4585:2,2:24.9:1:30.4:1:0.6171:1.08:60:72:0.4609:0:1.9 0/1:938:63:31,32:402,472:0.0672:2,2:24.3:1:29.4:1:0.69505:1.14:60:14.75:0.0638:0:1.9 -10 123240667 . T C 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TGGCCCTTTACAGAAAGCAG;RSEQ=TGCCGACCCCTGTTCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:0:0,0:362,408:0:2,0:25.2:1:30.2:1:1:0:60:127.333:0.9987:0:1 0/1:892:16:9,7:406,469:0.0179:2,2:27.9:1:31.4:1:0.45933:1.48:60:32:0.018:0:1.6 -10 123240903 . GACACACACAC G 281 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=16.000;MSILEN=2;SSF=0;SOR=0.25118;LSEQ=GGCAACTAGACATTTTTAAA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:748:432:273,159:107,41:0.5775:2,2:30.7:1:32.2:1:0.04565:1.5189:59.9:864:0.583:0.008:0.1 0/1:693:177:95,82:116,63:0.2554:2,2:27.9:1:31.5:1:0.04028:1.58718:59.9:176:0.2569:0.0058:0.2 -10 123241122 . C G 203 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATTTTGTCCTAAATGGAA;RSEQ=CGTTTTTCTTGAGCATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1562:0:0,0:729,831:0:2,0:24.8:1:31.5:1:1:0:60:64:0.9987:0:0.1 0/1:1814:86:40,46:831,893:0.0474:2,2:23.5:1:31.7:1:0.82521:1.07015:60:85:0.0474:0:1.1 -10 123241211 . T C 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0;SOR=Inf;LSEQ=AATATGGCATTCTGCTTTTT;RSEQ=ATTTTAGGGTACTAGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1081:0:0,0:542,538:0:2,0:24.6:1:29.1:1:1:0:60:97.182:0.9991:0:0.1 0/1:1392:57:30,27:696,637:0.0409:2,2:25.1:1:31.7:1:1:1.02:60:114:0.0412:0:1.1 -10 123241323 . G A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04495;LSEQ=CATTAAAATAGAACTTTAGT;RSEQ=CTTTTCCCGGTTTCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:930:484:184,300:236,209:0.5204:2,2:26.9:1:29.4:1:1e-05:1.83986:59.9:241:0.5285:0:3.4 0/1:1637:76:38,38:778,781:0.0464:2,2:27:1:28:1:1:1.00:59.6:37:0.048:0:3.2 -10 123241332 . G A 308 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50696;SOR=0.68399;LSEQ=AGAACTTTAGTGCTTTTCCC;RSEQ=GTTTCTTTCTTTTTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:800:794:352,442:0,0:0.9925:0,2:22.6:1:30.2:1:1:0:59.5:38.7:0.9974:0:2.9 1/1:1464:1448:697,751:1,1:0.9891:2,2:25.4:1:29.4:1:1:1.0774:59.5:22.738:0.9957:0:1.8 -10 123241348 . A T 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.00094;SOR=0.66733;LSEQ=TCCCGGTTTCTTTCTTTTTT;RSEQ=TTTTTATTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:152:108,44:114,226:0.2957:2,2:13.8:1:28.5:1:0:4.85:56.9:49.667:0.3004:0:3.2 0/1:1083:237:171,66:327,479:0.2188:2,2:16.1:1:26.7:1:0:3.79:55.2:17.231:0.2272:0:3.3 -10 123241354 . AT TA 233 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0;SOR=0.02795;LSEQ=TTTCTTTCTTTTTTATTTTT;RSEQ=TTTTTTTTTTTTTGAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:425:250:71,179:18,22:0.5882:2,2:23.6:1:29.3:1:0.04234:2.05714:59.6:249:0.8527:0:3.8 0/1:968:37:9,28:264,377:0.0382:2,2:29.9:1:28.2:1:0.05659:2.17631:58.9:74:0.0541:0:3.6 -10 123241361 . T A 237 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0;SOR=0.02566;LSEQ=CTTTTTTATTTTTATTTTTT;RSEQ=TTTTTTTGAGACGGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:392:244:68,176:96,52:0.6224:2,2:20.8:1:30:1:0:4.75697:59.6:121:0.6237:0:3.8 0/1:867:35:11,24:374,458:0.0404:2,2:25:1:29:1:0.1218:1.78053:59:70:0.0405:0:3.7 -10 123241369 . G T 95 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0272;SOR=7.03068;LSEQ=TTTTTATTTTTTTTTTTTTT;RSEQ=AGACGGAGTCTCGCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:1,0:73,183:0.0039:2,0:14:0:10:0:0.28794:0:60:0:0:0:3 0/1:523:14:9,5:138,370:0.0268:2,2:7.8:1:25:1:0.00468:4.81:58.6:3.667:0.0239:0:3.8 -10 123241373 . C T 240 LongAT STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=41.74123;LSEQ=TATTTTTTTTTTTTTTGAGA;RSEQ=GGAGTCTCGCTCTGTCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:21:6,15:50,152:0.0938:2,2:18.7:1:29:1:0.79167:1.21:58.1:9.5:0.0896:0:2.4 1/1:434:353:95,258:11,68:0.8134:2,2:21.1:1:28.4:1:0.01414:2.27:59.5:24.214:0.8289:0:2.3 -10 123241383 . C T 159 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01227;SOR=0.52023;LSEQ=TTTTTTGAGACGGAGTCTCG;RSEQ=TCTGTCGCCAAGGCTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:36:5,31:30,107:0.2081:2,2:25:1:30.3:1:0.35634:1.73331:54.1:72:0.2182:0:3.4 0/1:333:40:0,40:61,231:0.1201:2,1:30:1:30:1:0.00029:0:49.4:39:0.1275:0:3.7 -10 123241496 . T C 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40523;SOR=0;LSEQ=GGAGTAGCTGGGATTACAGG;RSEQ=GCACACCAACACGCCCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:91:91:56,35:0,0:1:0,2:25.1:1:30.3:1:1:0:59.5:21.75:1:0:1.3 1/1:62:61:31,30:0,0:0.9839:0,2:23.8:1:28.3:1:1:0:60:7.714:0.9818:0:1.2 -10 123241587 . A AAG 48 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37186;SOR=3.03825;LSEQ=GGTCTGGAACTCCTGACCTC;RSEQ=TGATCCGCCTGCCTCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:1:1,0:269,9:0.0036:1,0:27:0:32.5:0:1:0:40:2:0.0036:0:4 0/1:278:3:2,1:260,14:0.0108:2,2:7.3:1:30.5:1:0.15434:9.09974:51.7:6:0.0109:0.0072:4.3 -10 123241593 . C T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21507;SOR=4.06876;LSEQ=GAACTCCTGACCTCATGATC;RSEQ=GCCTGCCTCGGCCTCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:1:0,1:291,27:0.0031:2,0:1:0:25:0:0.08777:0:60:2:0.0032:0:1 0/1:316:4:2,2:288,24:0.0127:2,2:5.3:1:28.3:1:0.0353:11.78286:58.8:8:0.0127:0:3.5 -10 123241603 . G A 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06188;SOR=Inf;LSEQ=CCTCATGATCCGCCTGCCTC;RSEQ=GCCTCCCAAAGTGCTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:332,61:0:2,0:22.6:1:29.6:1:1:0:59.4:64.5:0.9974:0:0.1 0/1:407:5:3,2:336,65:0.0123:2,2:17.6:1:29.6:1:0.19227:3.43145:59:10:0.0124:0:2.8 -10 123241616 . G A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCCTCGGCCTCCCAAAGT;RSEQ=CTGGGATTACAGGCATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:0:0,0:372,111:0:2,0:22.2:1:31.9:1:1:0:59.7:95.6:0.9979:0:0.1 0/1:549:22:15,7:393,132:0.0401:2,2:22.3:1:28:1:0.46103:1.3885:60:44:0.0408:0:1.2 -10 123241794 . C T 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=8.61709;LSEQ=AAGAAGAAAGTTGGTTTCTT;RSEQ=CCCCCCTTGAACCGTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1637:102:50,52:755,775:0.0623:2,2:26:1:29.8:1:1:1.01315:60:50:0.0624:0:1.2 0/1:1963:715:346,369:601,638:0.3642:2,2:23.2:1:29.3:1:0.96256:1.00462:60:101.143:0.3646:0:1.2 -10 123242026 . T C 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=5.58873;LSEQ=TTCTAAAATACTTGGGGGAC;RSEQ=TTAACTTTTTTCTTGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1272:628:350,278:361,280:0.4937:2,2:25.5:1:31.4:1:0.86529:1.02405:60:77.5:0.4917:0:1.1 1/1:1394:1178:656,522:114,98:0.8451:2,2:24.7:1:30.5:1:0.6526:1.08:60:64.444:0.8443:0:1.1 -10 123242508 . G A 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01602;SOR=Inf;LSEQ=TTTAGTAGAGACAGGGTTTC;RSEQ=CCATGTTGGCCAGGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:96,11:0:2,0:25.8:1:30.6:1:1:0:59.9:106:0.9907:0:0.1 0/1:86:5:4,1:81,0:0.0581:1,2:29.4:1:31.6:1:0.05814:0:60:10:0.0588:0:1.2 -10 123242549 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21561;SOR=Inf;LSEQ=TCGAACTCCTGGCCTCAGGT;RSEQ=ATCTGCCCTCCTCGGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:156,28:0:2,0:24.2:1:31.9:1:1:0:60:91:1:0:0.4 0/1:160:2:1,1:138,20:0.0125:2,2:14.5:1:27:1:0.24599:6.75685:60:4:0.0127:0:1 -10 123242589 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0667;LSEQ=CCAAAATGCTGGGATTACAG;RSEQ=CGAGAGCATAAATATTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:154:105,49:138,59:0.4387:2,2:23.8:1:29.9:1:0.72768:1.09125:60:153:0.4422:0:1.1 0/1:405:20:11,9:258,127:0.0494:2,2:22.9:1:28.1:1:0.33139:1.65996:60:40:0.05:0:1.1 -10 123242724 . T C 315 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=7.82236;LSEQ=GAAAGAGGCTGCAAGGCATA;RSEQ=AGCATTACCAACAGGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1145:587:309,278:294,263:0.5127:2,2:24.9:1:32:1:1:1.00572:60:116.4:0.5132:0:1.4 1/1:1210:1079:534,545:65,64:0.8917:2,2:24.9:1:31.3:1:0.8528:1.03653:60:106.9:0.8916:0:1.5 -10 123242780 . G C 314 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=8.66394;LSEQ=GGTAACAGAAGCTGGTGTTA;RSEQ=AAAACTTCATTGTATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1084:557:303,254:263,260:0.5138:2,2:23.4:1:32.1:1:0.1804:1.18:60:184.667:0.5149:0:1.5 1/1:1149:1036:538,498:58,52:0.9017:2,2:23.9:1:31.4:1:0.92019:1.03244:60:128.5:0.9025:0:1.5 -10 123242897 . A G 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTTTTTCCCATGCACACC;RSEQ=AAATGCAAGTGAATACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1471:0:0,0:738,733:0:2,0:23.8:1:30.1:1:1:0:60:104.071:1:0:0.2 0/1:1696:56:32,24:792,843:0.033:2,2:24.4:1:30.2:1:0.22219:1.42:60:112:0.0334:0:1.1 -10 123243197 . G A 290 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59581;SOR=1.03868;LSEQ=CCAAGGACAAGGGGCTTCTA;RSEQ=AAGGAAGTTCTTACCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1476:724:376,348:401,349:0.4905:2,2:24.6:1:30.1:1:0.56627:1.06338:60:102.429:0.4914:0:1.1 1/0:1742:871:448,423:445,419:0.5:2,2:23.9:1:29.7:1:1:1.00278:60:53.438:0.4985:0:1.2 -10 123244834 . C T 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACCAGGGGCCTTCAAAAA;RSEQ=GAGATACATCAGGAGAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:193,23:0:2,0:22.5:1:31.6:1:1:0:60:53:1:0:0.1 0/1:224:19:15,4:169,36:0.0848:2,2:14.3:1:28.8:1:0.75389:1.25052:60:38:0.0872:0:1.2 -10 123244842 . A T 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24919;SOR=Inf;LSEQ=GGCCTTCAAAAACGAGATAC;RSEQ=TCAGGAGAGGTATTACTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:234,31:0:2,0:22.3:1:30.3:1:1:0:60:43.167:1:0:0.1 0/1:280:3:0,3:218,59:0.0107:2,0:5.7:1:20:1:0.01045:0:60:2:0.0072:0:3.3 -10 123245077 . T C 128 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=18.09767;LSEQ=AGGAGAAAGCACGGCATTAC;RSEQ=AACCCATCCACGTTGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:1:0,1:96,281:0.0026:2,0:40:0:14:0:1:0:60:0:0:0:2 0/1:415:19:7,12:123,273:0.0458:2,2:25.3:1:30.2:1:0.61669:1.29:60:38:0.0468:0:1.1 -10 123245108 . G A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2486;SOR=0;LSEQ=CGTTGCCAAAACCTAAACAC;RSEQ=CCCAGCTGAGACATAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:3:2,1:24,195:0.0135:2,2:16.3:1:21.3:1:0.03686:15.85:60:2:0.0092:0:2.7 0/0:214:0:0,0:43,171:0:2,0:21.8:1:30.9:1:1:0:60:25.75:1:0:0.2 -10 123245179 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52674;SOR=0;LSEQ=GGCCCTCCTGCAGTTCCTCC;RSEQ=ATGTGCTCTTTCCTGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:0,55:0.0351:1,2:16.5:1:30:1:0.03509:0:60:4:0.0364:0:1 0/0:34:0:0,0:1,33:0:1,0:20.7:1:28.3:1:1:0:60:33:1:0:0.1 -10 123246612 . G A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62785;SOR=2.60278;LSEQ=AGTTGCACATCCATGAATAT;RSEQ=TTCAAGGGAAGGACTTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:13:13,0:7,0:0.65:0,1:23.7:1:28.8:1:1:0:60:26:0.65:0:1 1/1:6:5:5,0:1,0:0.8333:0,0:27.8:1:28.6:1:1:0:60:10:0.8333:0:1.6 -10 123246648 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=TCCGCTCTGGCAGGGGGAGG;RSEQ=CAGCAGTTCCACCTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:39,0:0:1,0:24.5:1:30.5:1:1:0:60:78:1:0:0.3 0/1:16:2:2,0:14,0:0.125:1,0:16.5:1:30.5:1:1:0:60:4:0.1333:0:1 -10 123246732 . TTTCTAAGGCCAGCTCCTGCACC T 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12442;SOR=1.52215;LSEQ=GCCTACCATAAAATCTGTCC;RSEQ=TTCTACGAATGTGTGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:147:80:70,10:67,0:0.5442:1,2:25.1:1:31.3:1:0.002:0:59.8:160:0.5479:0.0816:0.1 1/0:110:71:69,2:38,1:0.6455:1,1:26.6:1:32.2:1:1:1.10051:59.8:142:0.6455:0:0.1 -10 123246744 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08905;SOR=Inf;LSEQ=ATCTGTCCTTTCTAAGGCCA;RSEQ=CTCCTGCACCTTCTACGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:73,3:0:1,0:23.8:1:32.2:1:1:0:60:75:1:0:0.1 0/1:118:3:2,1:41,3:0.0254:2,2:13:1:26.7:1:0.23891:6.3241:60:6:0.0652:0:1 -10 123247037 . C T 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28544;SOR=1.48165;LSEQ=TGTTTAAGAGCTGATATTCT;RSEQ=GGTTTTTACTAGTCAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:39:3,36:1,50:0.4333:1,2:23.3:1:29.8:1:0.3124:4.10:60:18.5:0.4253:0:2 1/0:47:25:0,25:2,20:0.5319:2,1:21.5:1:30.8:1:0.21369:0:60:50:0.5319:0:1.8 -10 123247044 . T C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0.15986;LSEQ=GAGCTGATATTCTCGGTTTT;RSEQ=ACTAGTCAGTCAATAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:69:3,66:0,8:0.8961:0,1:26.3:1:32:1:1:0:60:33.5:0.8933:0:1.6 1/0:40:23:0,23:0,17:0.575:1,1:19.3:1:31.3:1:1:0:60:22:0.5641:0:1.9 -10 123247176 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTCCCTAGCACACAGATG;RSEQ=TCCTTGACCAGTTATTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:1,4:0.375:2,2:35:1:30:1:1:1.83:60:6:0.375:0:1 0/0:2:0:0,0:0,2:0:0,0:6.5:1:31:1:1:0:60:4:1:0:0 -10 123247550 . G A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATTGTTGATATCTCTGGC;RSEQ=AGTCCAAAGTCTGCTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:707:0:0,0:357,349:0:2,0:25.1:1:30.4:1:1:0:60:87.25:0.9986:0:0.1 0/1:839:34:17,17:430,374:0.0405:2,2:26.4:1:29.9:1:0.72793:1.14954:60:68:0.0409:0:1.1 -10 123247669 . AC A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.15107;LSEQ=GAGAAATAACTAATTTCAAA;RSEQ=ACCGCCAGAACAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:99:19,80:21,104:0.442:2,2:22.5:1:30:1:0.72604:1.18:60:48.5:0.4389:0.0893:0.1 0/1:263:28:9,19:47,188:0.1065:2,2:16.9:1:29.1:1:0.1467:1.89:60:56:0.1073:0.0418:0.1 -10 123247751 . T TA 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00156;SOR=6.75908;LSEQ=ATGTTAAAAACCAGTTGCGG;RSEQ=ATACTATAAGAAATACAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:0,44:0.0833:1,0:35.3:1:31.3:1:1:0:60:8:0.0851:0:0 0/1:31:12:0,12:0,19:0.3871:1,0:24.8:1:30.2:1:1:0:60:24:0.4:0.0968:0 -10 123256312 . A C 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31798;SOR=4.01741;LSEQ=CAATTCAGCAAAACATTTTT;RSEQ=GTTATTACAACCCATGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:0,1:7,124:0.0073:2,0:20:0:10:0:1:0:60:0:0:0:1 0/1:104:3:0,3:9,86:0.0288:2,0:22:1:28.3:1:1:0:60:6:0.0385:0:1.3 -10 123256346 . A T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.72254;LSEQ=ATGCTTTTTTTTTTTTTTTT;RSEQ=AAGTTTAACATACAGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:3:0,3:0,80:0.0361:1,0:20:1:23.3:1:1:0:48:2:0.0247:0:3 0/1:38:1:0,1:2,35:0.0263:2,0:17:0:30:0:1:0:60:2:0.027:0:3 -10 123258192 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17694;SOR=Inf;LSEQ=CAGCTACTGTTAGTTGCCAA;RSEQ=GACTTAGTTGAAACAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:14,174:0:2,0:24.6:1:31.4:1:1:0:60:187:1:0:0.1 0/1:137:2:1,1:10,125:0.0146:2,2:5.5:1:30:1:0.15468:11.97:60:4:0.0147:0:1 -10 123263118 . AT A 60 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.34894;SOR=0.25813;LSEQ=AGCTCTGCTTTCAAGGAGTT;RSEQ=TTTTTTTTTTAAATCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:17,0:0.1905:1,0:12.8:1:30.3:1:1:0:60:8:0.1905:0.0476:0 0/1:18:1:1,0:16,1:0.0556:1,0:21:0:29:0:1:0:60:2:0.0556:0:4 -10 123263850 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGGATCCCCTCTCAGAC;RSEQ=ACCCGGATCATGGATCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 123274653 . A G 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTACCTGTCTCCGCAGGGGG;RSEQ=TACGTTTGGTCAGCTTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:37:23,14:341,160:0.0688:2,2:25.9:1:31.8:1:0.46971:1.29658:60:74:0.0703:0:1.1 0/0:674:0:0,0:410,263:0:2,0:24:1:28.5:1:1:0:60:28.261:0.9985:0:0.2 -10 123276652 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50011;SOR=Inf;LSEQ=TGATCATAAATGTGAGTGTG;RSEQ=GATCTCACTGTGTGTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:69,6:0:2,0:24.1:1:31.8:1:1:0:60:150:1:0:0.1 0/1:88:2:1,1:79,7:0.0227:2,2:8:1:26.5:1:0.1745:10.62357:60:4:0.023:0:1 -10 123276689 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5055;SOR=Inf;LSEQ=AATTTCCAAGGCAGTTTTCT;RSEQ=ATCCCTGAGGGATCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:126,32:0:2,0:22.4:1:29.7:1:1:0:60:157:1:0:0.1 0/1:200:2:1,1:143,55:0.01:2,2:23:1:33.5:1:0.48261:2.58568:60:4:0.01:0:1 -10 123276696 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25592;SOR=Inf;LSEQ=AAGGCAGTTTTCTTATCCCT;RSEQ=AGGGATCATTTTTAACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:142,39:0:2,0:22.8:1:31.9:1:1:0:60:180:1:0:0.1 0/1:222:3:1,2:152,67:0.0135:2,2:14:1:28.7:1:0.22865:4.50281:60:6:0.0138:0:1 -10 123277742 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAACTCATAAGGATCAAC;RSEQ=ATGCAACCAAAGAAATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:47.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 123278438 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24731;SOR=Inf;LSEQ=CACACCGCAAGAAAACAAAC;RSEQ=CCATTACGTCTAAACAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:1,139:0:1,0:23.9:1:30.3:1:1:0:60:69:1:0:0.1 0/1:139:2:1,1:9,128:0.0144:2,2:8:1:27:1:0.13919:13.54:60:4:0.015:0:1 -10 123279179 . C T 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGGGGGACAGAGTATCA;RSEQ=GATCTCTACTTTTATAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1:0,2:18.3:1:27.6:1:1:0:60:6:1:0:1.4 1/1:2:2:1,1:0,0:1:0,2:8:1:29:1:1:0:60:4:1:0:1 -10 123279686 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.49888;SOR=Inf;LSEQ=GCCGGTGAGGCGATCGCTCT;RSEQ=GTGGAGAGAGGGAAGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:24,168:0:2,0:25.6:1:31.1:1:1:0:60:47:1:0:0.4 0/1:200:2:1,1:34,164:0.01:2,2:45:0:30.5:1:0.3201:4.77:60:4:0.0102:0:1 -10 123279745 . C T 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00281;SOR=0;LSEQ=ATGAGAGACCAATAAATAAG;RSEQ=TGTGTTGTCCAGAGGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:63:5,58:0,0:1:0,2:19.6:1:30.3:1:1:0:60:126:1:0:1.4 1/1:51:44:3,41:0,7:0.8627:0,2:21.6:1:29.8:1:1:0:60:88:0.8627:0:1.1 -10 123279795 . C T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01553;LSEQ=CATGCCAGAAAAGCCTCAAG;RSEQ=CTGCTGGCTGACACCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:23:0,23:0,2:0.92:0,1:21.5:1:29.3:1:1:0:60:10.5:0.913:0:1.9 0/1:16:2:0,2:0,14:0.125:1,0:11:1:27:1:1:0:60:4:0.1333:0:2 -10 123279866 . C T 79 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=ACGACTTCAAAGGAGACTGC;RSEQ=GGAGCGCGACCCTTGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:16.7:1:30.7:1:1:0:60:12:1:0:1.8 1/1:5:4:0,4:0,1:0.8:0,0:22.3:1:31.8:1:1:0:60:8:0.8:0:1.3 -10 123298158 . T C 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=55.08122;LSEQ=GACCCGTATTCATTCTCCAC;RSEQ=ACACAGGTATAATTTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:45:21,24:302,344:0.065:2,2:24.5:1:31.5:1:1:1.00332:60:90:0.066:0:1 1/0:863:685:313,372:79,95:0.7937:2,2:24.8:1:30.6:1:1:1.01:60:170.25:0.7965:0:1.2 -10 123310664 . AT GC 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00936;SOR=Inf;LSEQ=GAATCGCTTGAACCTGGGAG;RSEQ=GGAGGTTGCAGTGAACCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:63,0:0:1,0:25.1:1:30.1:1:1:0:59.4:30.5:1:0:0 0/1:56:6:6,0:50,0:0.1071:1,0:17.5:1:30.9:1:1:0:57.8:12:0.1091:0.0357:0.7 -10 123310732 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26653;SOR=Inf;LSEQ=CGACAGAGCGAGACTCCATC;RSEQ=CAAAAAAAAAATGTAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:172,38:0:2,0:21:1:29.5:1:1:0:60:51.5:1:0:0.1 0/1:287:3:2,1:223,60:0.0105:2,2:31.7:1:30:1:0.51448:1.85359:60:6:0.0106:0:1.3 -10 123310733 . CA C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.83294;SOR=0.85007;LSEQ=GACAGAGCGAGACTCCATCG;RSEQ=AAAAAAAAATGTAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:11:11,0:170,44:0.0487:2,0:27.6:1:33.1:1:0.12785:0:60:22:0.0493:0.0088:0 0/1:312:13:11,2:229,69:0.0417:2,2:16.6:1:32.3:1:0.73957:1.65:59.2:26:0.0418:0.0096:0.5 -10 123310871 . A G 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGCCACCGCATGGTTGGC;RSEQ=TTGGGTTCCCCCCGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:707:0:0,0:339,367:0:2,0:24.6:1:30.4:1:1:0:60:63.182:1:0:0.2 0/1:955:60:27,33:440,453:0.0628:2,2:26.8:1:30.2:1:0.59412:1.18693:60:59:0.0628:0:1.1 -10 123311192 . GA G 49 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATGTCTACCAACAGGAA;RSEQ=AAAAAAAAAAAGTGTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:37:1:31.3:1:1:0:60:6:0.375:0:0.3 0/0:2:0:0,0:0,1:0:0,0:23:0:32:0:1:0:60:2:0.5:0:0 -10 123323962 . A G 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAGACAGGTGACAGGCAG;RSEQ=ACTTCCCTCCATGCTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:0:0,0:342,190:0:2,0:25.4:1:29.9:1:1:0:60:87.667:1:0:0.1 0/1:658:80:49,31:354,223:0.1216:2,2:23.7:1:30.3:1:1:1.0043:60:39:0.1204:0:1.2 -10 123324186 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51432;SOR=0;LSEQ=GACCTTCTCCATAGCAAAGT;RSEQ=AACAACCCAGGAACCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:4,93:0.0202:1,0:33:0:31.5:1:1:0:60:4:0.0206:0:1 0/0:68:0:0,0:3,65:0:1,0:21.8:1:32.1:1:1:0:60:136:1:0:0.1 -10 123324410 . C T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTACCAATTGTGTAGCAC;RSEQ=CAAAGACTCTTTTTCCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:45.7:1:30.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 123325169 . C A 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCTAGCGACTCCCCTGG;RSEQ=GCAGCCACGTACACTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:0:0,0:206,340:0:2,0:23.6:1:30.6:1:1:0:59.9:135.5:0.9982:0:0.1 0/1:663:36:17,19:258,368:0.0543:2,2:19.1:1:30:1:0.49104:1.28:60:35:0.0532:0:1.2 -10 123325267 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21468;SOR=Inf;LSEQ=AGACAGATGGGAAGGAGGGA;RSEQ=AGGAGAGAACGTCCAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:23,148:0:2,0:21.3:1:31.7:1:1:0:60:170:0.9942:0:0 0/1:149:2:1,1:23,124:0.0134:2,2:30:1:27:1:0.29712:5.30:60:4:0.0135:0:1 -10 123325397 . G C 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00399;SOR=Inf;LSEQ=AAGTCAGGAAGTATCTGGAA;RSEQ=AGCAACCAGAGGATACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:0,19:0:1,0:24.9:1:31.3:1:1:0:60:38:1:0:0 1/0:8:4:0,4:0,3:0.5:0,0:17:1:30:1:1:0:60:8:0.5:0:1.3 -10 123353869 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGCAAGTTAAAAATGCT;RSEQ=GGGTTGGCATAACCAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 123488385 . C T 118 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGTGGTTGTGGGGGGATGG;RSEQ=GGGGGACTCCAGCACGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:10,8:0,0:1:0,2:24.2:1:28.4:1:1:0:60:17:1:0:1.9 0/1:19:4:2,2:9,6:0.2105:2,2:33.5:1:28.5:1:1:1.4677:60:8:0.2353:0:1.8 -10 123488416 . A G 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=AGCACGCTGCCTCCTTCTTA;RSEQ=CCAAGCTGGCCACTGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:4,6:4,5:0.5263:2,2:30.3:1:30.2:1:1:1.18851:60:9:0.5:0:2.4 0/0:22:0:0,0:12,10:0:2,0:26:1:27.6:1:1:0:60:21:1:0:1 -10 123488457 . T C 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTGATGCCGAGTCCAT;RSEQ=TGCCTTTCACCTGGTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:6,9:0,0:1:0,2:20.9:1:32.1:1:1:0:60:30:1:0:2.1 1/1:14:14:4,10:0,0:1:0,2:19:1:31.9:1:1:0:60:28:1:0:1.4 -10 124402897 . G T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGACCCCCCCACGCCGA;RSEQ=AAGAGGAGCCTCGGTAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 124403514 . TGCTGTGCTGCTGTGTTGCTGTGCG T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=2.000;MSILEN=1;SSF=0.0094;SOR=Inf;LSEQ=AGAACAGGGAGTGCATCTGC;RSEQ=GCTGTGCTGCTGTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:33.9:1:32.1:1:1:0:60:46:1:0:0.7 0/1:24:7:5,2:10,7:0.2917:2,2:36.3:1:31.9:1:0.66871:1.71:51.3:14:0.2917:0.0417:2 -10 124403545 . C A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=3;SSF=1;SOR=0.73554;LSEQ=TGTGTTGCTGTGCGGCTGTG;RSEQ=TGCTGTGTTGCTGTGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:6,13:0.0952:2,2:21.5:1:29:1:1:2.08:60:4:0.1053:0:4 0/1:28:2:1,1:12,14:0.0714:2,2:17.5:1:28.5:1:1:1.16:60:4:0.0741:0:3.5 -10 124403551 . T C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.67236;LSEQ=GCTGTGCGGCTGTGCTGCTG;RSEQ=GTTGCTGTGCGGCTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:6,12:0.1:2,2:15.5:1:29.5:1:1:1.93:60:4:0.1053:0:4 0/1:29:2:1,1:12,15:0.069:2,2:11.5:1:29:1:1:1.24:60:4:0.0714:0:3.5 -10 124403553 . T C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69775;LSEQ=TGTGCGGCTGTGCTGCTGTG;RSEQ=TGCTGTGCGGCTGTGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:6,12:0.1:2,2:13.5:1:30:1:1:1.93:60:4:0.1:0:4 0/1:28:2:1,1:11,15:0.0714:2,2:9.5:1:30:1:1:1.35:60:4:0.0714:0:3.5 -10 124403561 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=TGTGCTGCTGTGTTGCTGTG;RSEQ=GGCTGTGATGCTGCGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:22.6:1:27.6:1:1:0:59:5:1:0:1.7 0/1:26:2:1,1:10,14:0.0769:2,2:20:1:28.5:1:1:1.38:55:4:0.08:0:1 -10 124403569 . AT CG 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=TGTGTTGCTGTGCGGCTGTG;RSEQ=GCTGCGCTGCTGTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:4,9:0.125:2,2:37:1:29:1:1:2.12:55:4:0.1538:0:5 0/0:24:0:0,0:10,14:0:2,0:23.8:1:28:1:1:0:57.5:11:1:0:0.7 -10 124403575 . C T 48 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0.05856;SOR=0;LSEQ=GCTGTGCGGCTGTGATGCTG;RSEQ=GCTGCTGTGCTGCTGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:1,2:3,9:0.2:2,2:32.3:1:30.7:1:1:1.46:54:6:0.2308:0:5.7 0/0:22:0:0,0:9,13:0:2,0:22.6:1:25.7:1:1:0:57.2:3.4:1:0:0.7 -10 124403585 . C T 38 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0.08462;SOR=0;LSEQ=TGTGATGCTGCGCTGCTGTG;RSEQ=TGCTGTCATGCTGTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:3,6:0.25:2,2:22.3:1:24.3:1:1:1:54:2:0.1818:0:5.7 0/0:14:0:0,0:5,9:0:2,0:27.9:1:28.4:1:1:0:56.4:6:1:0:1 -10 124403592 . CA GC 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82581;LSEQ=CTGCGCTGCTGTGCTGCTGT;RSEQ=TGCTGTGCTGCTGTGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,4:0.25:2,0:19.5:1:32.8:1:1:0:55:4:0.3333:0:6 0/1:14:3:3,0:2,8:0.2143:2,0:15:1:29.7:1:0.03497:0:43:6:0.25:0:3 -10 124403599 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=GCTGTGCTGCTGTCATGCTG;RSEQ=GCTGCTGTGATGCTGTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:1,4:0.1667:2,0:4:0:21:0:1:0:21:2:0.1667:0:6 0/1:12:2:1,1:3,7:0.1667:2,2:8:1:30:1:1:2.16:36:4:0.1818:0:5.5 -10 124403602 . T G 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.11029;SOR=0;LSEQ=GTGCTGCTGTCATGCTGTGC;RSEQ=GCTGTGATGCTGTGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:10.5:1:30.5:1:1:0:55:4:0.4:0:6 0/0:11:0:0,0:3,8:0:2,0:24:1:27.8:1:1:0:53.3:10:1:0:1.6 -10 124403609 . A C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=1;SOR=0.5841;LSEQ=TGTCATGCTGTGCTGCTGTG;RSEQ=TGCTGTGCGGCTGTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:11:1:33.5:1:1:0:39.5:4:0.4:0:6 0/1:11:3:2,1:1,7:0.2727:2,2:17.7:1:30.3:1:0.15152:9.77:35.3:6:0.2727:0:5.7 -10 124403618 . G T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=1.53983;LSEQ=GTGCTGCTGTGATGCTGTGC;RSEQ=GCTGTGCTGCTGTCATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:23:0:30:0:1:0:21:2:0.25:0:6 0/1:7:2:1,1:1,4:0.2857:2,2:27:1:31.5:1:1:3.16:36:4:0.3333:0:5.5 -10 124403641 . A C 86 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=15;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43789;LSEQ=TGTGCTGCTGTCATGCTGTG;RSEQ=TGCTGTGCGGCTGTGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:26:1:34.5:1:1:1.41:40.5:4:0.3333:0:6.5 0/1:19:7:3,4:6,5:0.3684:2,2:11:1:30.7:1:1:1.55841:50.7:14:0.4118:0.1053:4.4 -10 124403644 . C CTGTGCGGCTGTGCGGT 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=2.000;MSILEN=1;SSF=0.52964;SOR=Inf;LSEQ=GCTGCTGTCATGCTGTGATG;RSEQ=TGTGCGGCTGTGCGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:23.4:1:31.7:1:1:0:54.4:14:1:0:1.9 0/1:17:3:0,3:9,5:0.1765:2,0:22.3:1:22.5:1:0.08235:0:51.3:6:0.1875:0.1765:2 -10 124403649 . CG TT 40 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=7;MSI=4.000;MSILEN=8;SSF=1;SOR=1.27277;LSEQ=TGTCATGCTGTGATGCTGTG;RSEQ=GCTGTGCGGCTGTGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:2,4:0.1429:2,0:15:0:31:0:0.42857:0:60:2:0.1667:0:6 0/1:17:3:1,2:8,6:0.1765:2,2:10.7:1:25.3:1:0.57647:2.51691:60:6:0.2:0:5.7 -10 124403657 . CG TT 22 v4;pSTD;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=4.000;MSILEN=8;SSF=1;SOR=Inf;LSEQ=TGTGATGCTGTGCGGCTGTG;RSEQ=GCTGTGCGGCTGTGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:19.8:1:28.6:1:1:0:55.1:7:1:0:1.5 0/1:17:2:0,2:9,5:0.1176:2,0:14:0:22.8:1:0.175:0:51.5:4:0.125:0:1 -10 124403658 . G GGTTGTGCGGCTGTGTT 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=8;SSF=1;SOR=0.65487;LSEQ=GTGATGCTGTGCGGCTGTGC;RSEQ=GCTGTGCGGCTGTGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:3,3:0.25:2,0:19:1:28.6:1:0.46429:0:40.5:6:0.2491:0.2235:3.5 0/1:17:3:2,1:7,4:0.1765:2,2:14:1:30.6:1:1:1.13:44:6:0.2308:0.1176:4.3 -10 124403674 . G T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=4.000;MSILEN=8;SSF=0.02085;SOR=0.13547;LSEQ=GTGCGGCTGTGCGGCTGTGC;RSEQ=GCTGTGCTGCTGTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:4,4:2,2:0.6154:2,2:14.5:1:30.5:1:1:1:60:16:0.6667:0:4.4 0/1:18:3:1,2:8,7:0.1667:2,2:34.7:1:29.7:1:1:2.18465:60:6:0.1765:0:5.7 -10 124403681 . C T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=3;SSF=0.02926;SOR=0.16965;LSEQ=TGTGCGGCTGTGCGGCTGTG;RSEQ=TGCTGTGTTGCTGTGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:4,5:2,2:0.6429:2,2:19.4:1:29.4:1:1:1.22862:60:18:0.75:0:4.3 0/1:18:4:2,2:7,7:0.2222:2,2:40:1:29.8:1:1:1:50.3:8:0.2222:0:5.8 -10 124403689 . T C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=15;MSI=2.000;MSILEN=1;SSF=0.01347;SOR=0.14304;LSEQ=TGTGCGGCTGTGCTGCTGTG;RSEQ=TGCTGTGCGGCTGTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:5,5:2,2:0.6667:2,2:24.8:1:32.2:1:1:1:60:20:0.7143:0:4.2 0/1:19:4:1,3:7,7:0.2105:2,2:41.3:1:28.3:1:0.58824:2.83009:60:3:0.1875:0:4.5 -10 124403716 . T G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02533;SOR=0.13559;LSEQ=GCGGCTGTGCTGCTGTGTTG;RSEQ=GGGCATGGACGAGGGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:5,7:1,2:0.8:2,2:38:1:30.8:1:1:1.40:60:24:0.8:0:3.8 0/1:15:5:1,4:5,5:0.3333:2,2:23.4:1:32.2:1:0.58042:3.65648:60:10:0.3333:0:4.2 -10 124403778 . G A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=GGATTTCTGGCCCAGTCTGG;RSEQ=GCTAGGTCAACAGATGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:0.6:0,2:8.7:1:30:1:1:0:60:6:0.6:0:3 1/0:4:2:0,2:0,2:0.5:0,0:17:1:33:0:1:0:60:4:0.5:0:2 -10 124896966 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20236;SOR=0;LSEQ=CCGGCCTGGCCGCGTCCCTG;RSEQ=ACCTCACCGAGACGCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:45,32:0.0253:2,2:38:0:30.5:1:1:1.40006:60:4:0.0253:0:1.5 0/0:96:0:0,0:55,41:0:2,0:23.2:1:31.4:1:1:0:60:192:1:0:0.2 -10 124896975 . G T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.63101;SOR=2.42188;LSEQ=CCGCGTCCCTGCACCTCACC;RSEQ=AGACGCAGGTCAAGATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:0,1:52,42:0.0105:2,0:1:0:23:0:0.45263:0:60:2:0.0105:0:1 0/1:119:3:1,2:66,50:0.0252:2,2:12.7:1:25.3:1:0.58012:2.61876:57.7:6:0.0254:0:1.7 -10 124897022 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51101;SOR=Inf;LSEQ=AACCGCCGCAACAAGTGGAA;RSEQ=CGGCAGCTGGCGGCGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:35,50:0:2,0:26.8:1:32.1:1:1:0:59.8:170:0.977:0:0.1 0/1:121:2:1,1:50,69:0.0165:2,2:20:1:27.5:1:1:1.38:60:4:0.0167:0:1.5 -10 124897048 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49652;SOR=Inf;LSEQ=GCTGGCGGCGGAGCTGGAGG;RSEQ=GGCCAACCTGAGCCATGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:18,48:0:2,0:21.8:1:30.1:1:1:0:60:132:1:0:0.1 0/1:69:2:1,1:21,46:0.029:2,2:34.5:1:31:1:0.53922:2.16:60:4:0.029:0:1.5 -10 126423706 . G A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01014;SOR=0.16719;LSEQ=CTCCCCCAACGTGAGAGGAA;RSEQ=AACAAAAAACAAAGATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:3,8:2,5:0.6111:2,2:17.8:1:30:1:1:1.06284:60:22:0.6111:0:1.4 0/1:25:5:2,3:9,11:0.2:2,2:16.4:1:29.2:1:1:1.21734:60:10:0.2:0:1 -10 126553456 . G C 90 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02424;SOR=0;LSEQ=CTGCTTGTCTGAGCCTCGGT;RSEQ=TCTCTTGCAGTCCAAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:20.9:1:32.1:1:1:0:60:14:1:0:1.1 0/1:4:1:0,1:0,3:0.25:0,0:31:0:33:0:1:0:60:2:0.25:0:1 -10 126556006 . G A 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62202;SOR=1.12277;LSEQ=CTGGTGTGATTCCATCCTGC;RSEQ=GGGCTGTTCTCTTGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:171:90:62,28:65,16:0.5263:2,2:23.5:1:30.2:1:0.11489:1.82823:60:29:0.537:0:2.2 1/0:263:146:102,44:77,39:0.5551:2,2:20.7:1:29.2:1:0.59369:1.17:59.9:17.25:0.552:0:2.2 -10 126556015 . C G 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.85438;SOR=1.04964;LSEQ=TTCCATCCTGCGGGGCTGTT;RSEQ=TCTTGAGCAGTGGTCGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:191:101:62,39:65,21:0.5288:2,2:27.7:1:30.8:1:0.0422:1.9401:60:11.625:0.5225:0:2 1/0:318:172:110,62:87,58:0.5409:2,2:22.6:1:30.8:1:0.48738:1.18:60:27.667:0.5533:0:1.9 -10 126556100 . G A 24 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56709;SOR=0.33294;LSEQ=ATGGAAGATTCGATGGACAT;RSEQ=CACATGAGTCCTCTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:59,128:0.0105:2,2:8:1:24.5:1:0.53529:2.16:60:4:0.0108:0:1 0/0:284:1:1,0:94,189:0.0035:2,0:1:0:24:0:0.33451:0:60:2:0.0036:0:1 -10 126556118 . G A 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.22886;LSEQ=ATGCACATGAGTCCTCTGAG;RSEQ=CCCCAGAACTATCTTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:40,101:0.014:2,2:11.5:1:26:0:0.49266:2.51:60:4:0.0142:0:1 0/1:175:3:3,0:48,124:0.0171:2,0:1:0:21.3:1:0.02372:0:60:2:0.0117:0:1 -10 126556124 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21119;SOR=0;LSEQ=ATGAGTCCTCTGAGGCCCCA;RSEQ=AACTATCTTTTCAGTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:36,96:0.0149:2,2:9.5:1:31.5:1:0.4775:2.64:60:4:0.0149:0:1 0/0:157:0:0,0:42,115:0:2,0:24.9:1:31.3:1:1:0:60:77.5:1:0:0.1 -10 126556186 . A G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24551;SOR=Inf;LSEQ=TCACTTTAAGGTGGATAATG;RSEQ=TGAAAATGAGCACCAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:35,47:0:2,0:22.4:1:30.6:1:1:0:60:81:0.9878:0:0.1 0/1:84:3:1,2:35,46:0.0357:2,2:21.3:1:32.7:1:1:1.51444:60:6:0.0361:0:1 -10 126556239 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24191;SOR=Inf;LSEQ=TCAGTTCATGGGCTGGTGCA;RSEQ=AGGATGATTGCACATTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:43,35:0:2,0:23.7:1:31.9:1:1:0:60:156:1:0:0.2 0/1:76:2:1,1:39,35:0.0263:2,2:9.5:1:27:1:1:1.1127:60:4:0.0267:0:1 -10 126556276 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24476;SOR=Inf;LSEQ=GTTGAAGCAGAGGCAGTGAA;RSEQ=TAGAAGGCGGTCCAATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:44,28:0:2,0:24.3:1:30.2:1:1:0:60:35:1:0:0.1 0/1:71:2:1,1:47,22:0.0282:2,2:17:1:29:1:0.54608:2.11156:60:4:0.0294:0:1 -10 126556320 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21654;SOR=0;LSEQ=ACACTGGCAACTTTGAAAAT;RSEQ=TCTGTTTAGTCAACGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:76,40:0.0169:2,2:26:1:30:1:1:1.88906:60:4:0.0174:0:1 0/0:135:0:0,0:83,52:0:2,0:23.7:1:31.2:1:1:0:60:44:1:0:0.2 -10 126556374 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21116;SOR=0;LSEQ=GAAATCACACCACCAGTGGT;RSEQ=TTACAGTTGTAGTGTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:104,79:0.0108:2,2:16:1:29.5:1:1:1.31446:60:4:0.0108:0:1 0/0:217:0:0,0:122,94:0:2,0:25:1:31.2:1:1:0:59.8:71:0.9953:0:0.1 -10 126556376 . TA T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.25416;SOR=Inf;LSEQ=AATCACACCACCAGTGGTCT;RSEQ=CAGTTGTAGTGTGGCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:104,85:0:2,0:25.6:1:28.7:1:1:0:59.9:62:1:0:0.1 0/1:226:3:1,2:121,102:0.0133:2,2:23.7:1:28.7:1:0.59565:2.36372:60:6:0.0134:0.0044:0.3 -10 126556562 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22351;SOR=0;LSEQ=AGTAAAACTTGCTGCTGATG;RSEQ=AGATGATGATGATCATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:37,44:0.0241:2,2:31:1:30:1:1:1.19:60:4:0.0247:0:1 0/0:92:0:0,0:33,59:0:2,0:24.8:1:29.9:1:1:0:59.9:184:1:0:0.1 -10 126556573 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50024;SOR=Inf;LSEQ=CTGCTGATGAAGATGATGAT;RSEQ=ATCATGATGAAGATGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:34,37:0:2,0:26.6:1:31.5:1:1:0:60:142:1:0:0.1 0/1:85:2:1,1:29,54:0.0235:2,2:24:1:27.5:1:1:1.85:60:4:0.0235:0:1 -10 126556614 . TGAA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GATGATGAAGATGAAGATGA;RSEQ=GAAGATGATGATGAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:13,25:0.05:2,2:33:1:30:1:1:1.89:60:4:0.05:0:0.5 0/0:65:0:0,0:36,29:0:2,0:23.3:1:31.6:1:1:0:60:64:1:0:0.1 -10 126556646 . G GTGA 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.67278;SOR=1.20879;LSEQ=TGATGAAGATGAAGATGGTG;RSEQ=TGATGATGAAGAAGATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:23:14,9:5,10:0.6053:2,2:22.8:1:31.6:1:0.18367:3.02:60:46:0.6216:0.1316:0 1/0:60:39:27,12:11,10:0.65:2,2:27.3:1:29.4:1:0.26335:2.02:59.9:78:0.65:0.1333:0.1 -10 126556677 . C T 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32201;SOR=Inf;LSEQ=GAAGATGATGATGAAGATGA;RSEQ=GAGGAAACTGAAGAAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:22,17:0:2,0:25.7:1:30:1:1:0:59.8:12:1:0:0.1 0/1:89:5:3,2:56,28:0.0562:2,2:13.2:1:29:1:1:1.32882:57:10:0.0562:0:1.4 -10 126556684 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGATGAAGATGACGAGGAA;RSEQ=CTGAAGAAAAAGTGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:28,17:0:2,0:23.5:1:29.6:1:1:0:59.8:21.5:1:0:0.2 0/1:96:2:1,1:60,34:0.0208:2,2:7.5:1:29.5:1:1:1.75366:46:4:0.0208:0:1.5 -10 126556741 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53298;SOR=Inf;LSEQ=ATACTTCAGCCAAAAATGCA;RSEQ=AAAAGTCAAATCAGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:51,41:0:2,0:27.7:1:31.9:1:1:0:59.3:45:1:0:0.9 0/1:158:2:1,1:85,71:0.0127:2,2:8:1:24:1:1:1.19581:60:4:0.0129:0:1.5 -10 126556775 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11953;SOR=0;LSEQ=GAATGGAAAAGACTCAAAAC;RSEQ=GTCAACACCAAGATCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:58,51:0.0179:2,2:30.5:1:30:1:1:1.13593:60:4:0.0182:0:2 0/0:211:0:0,0:117,94:0:2,0:23.7:1:29.5:1:1:0:60:69.333:1:0:1 -10 126556782 . A G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00056;SOR=0;LSEQ=AAAGACTCAAAACCGTCAAC;RSEQ=CCAAGATCAAAAAGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:114:114:62,52:0,0:1:0,2:24.8:1:30.9:1:1:0:59.6:228:1:0:1.1 1/1:221:203:113,90:8,8:0.9186:2,2:25.2:1:30.4:1:0.79525:1.25:60:66.667:0.9217:0:1.1 -10 126556846 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12146;SOR=0;LSEQ=ACTCCTAAAATACCAAAGAC;RSEQ=TAGTTCTGTAGAAGATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:44,54:0.02:2,2:5:0:31:1:1:1.22:60:4:0.0202:0:2.5 0/0:186:0:0,0:84,102:0:2,0:24.7:1:30.3:1:1:0:60:45.5:1:0:0.6 -10 126558870 . A T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGGAGGAAATGCCTGTG;RSEQ=AGGATAAGGAGAGGAAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 127191022 . C T 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08145;SOR=6.22908;LSEQ=CCCAGGCTGGAGTGCAGTGG;RSEQ=GCAGGCACACATATTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:1:0,1:264,103:0.0027:2,0:1:0:26:0:0.28261:0:60:2:0.0028:0:1 0/1:239:4:3,1:171,64:0.0167:2,2:23:1:29.8:1:1:1.12:60:8:0.0169:0:1.5 -10 127191122 . T C 275 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17646;SOR=0.84983;LSEQ=CTGTGCCCCTGCCATGCTGC;RSEQ=TAGTAATGGGGATGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:710:454:202,252:121,135:0.6394:2,2:24.3:1:31.2:1:0.48113:1.11797:60:74.667:0.6391:0:1.1 1/0:544:327:149,178:98,119:0.6011:2,2:24.4:1:30.9:1:0.93019:1.02:60:162.5:0.6052:0:1.2 -10 127191232 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14632;SOR=Inf;LSEQ=GATAATTGATGTTCTCCAGA;RSEQ=TCTTCTCTTTCTTGCCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:19,140:0:2,0:23.5:1:30:1:1:0:60:38.75:1:0:0.1 0/1:99:2:1,1:15,82:0.0202:2,2:24:0:32:0:0.2985:5.33:60:4:0.0204:0:1.5 -10 127191254 . GTT G 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=9.000;MSILEN=1;SSF=0.72646;SOR=0.83736;LSEQ=CTTCTCTTTCTTGCCATACA;RSEQ=TTTTTTTAACTTCAATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:37:1,36:8,60:0.3426:2,1:26.9:1:32.6:1:0.1549:4.74634:60:74:0.3491:0.0093:0.1 0/1:56:17:0,17:3,36:0.3036:2,1:24.5:1:31.3:1:0.54556:0:60:34:0.3091:0.0179:0.1 -10 127191355 . T C 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=ATTTAATTAATTAATTTATT;RSEQ=GTTTTTGAGACGGAGTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:0,7:0.4167:0,2:5:1:29.8:1:0.41667:0:60:10:0.4167:0:1 1/1:2:2:0,2:0,0:1:0,0:24:1:28:1:1:0:60:4:1:0:1 -10 128270435 . G T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTGGACTGATTCGGACAG;RSEQ=TGCTGTGGAAGGAGACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:15.3:1:30:1:1:0:60:6:0.75:0:1.7 1/1:2:2:1,1:0,0:1:0,2:31:1:28.5:1:1:0:60:4:1:0:2.5 -10 128270440 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GACTGATTCGGACAGGTGCT;RSEQ=TGGAAGGAGACCTGGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:23:1:30.7:1:1:0:60:6:1:0:1.3 1/1:2:2:1,1:0,0:1:0,2:26:1:27.5:1:1:0:60:4:1:0:2.5 -10 128270475 . A G 28 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCGCCTTACTGCTGCAC;RSEQ=GTGGCAGCATCTCAGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:35.5:1:28:1:1:0:60:4:1:0:2 1/1:1:1:0,1:0,0:1:0,0:4:0:30:0:1:0:60:2:1:0:3 -10 128270643 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49973;SOR=0;LSEQ=ATTCCCGGCATCCACAGCAG;RSEQ=TCCTCTCCCAGGTCACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:136,50:0.0106:2,2:8:1:27.5:1:0.47002:2.70309:60:4:0.0108:0:1.5 0/0:171:0:0,0:129,42:0:2,0:21.1:1:31.8:1:1:0:60:56:1:0:0.5 -10 128270664 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20089;SOR=4.34861;LSEQ=TCCTCTCCCAGGTCACCCTG;RSEQ=AGCTGCTGTGGGACTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:1,0:162,92:0.0039:2,0:10:0:31:0:1:0:60:2:0.004:0:1 0/1:237:4:1,3:152,81:0.0169:2,2:12.8:1:25:1:0.12881:5.58754:60:8:0.0172:0:1.5 -10 128270699 . T C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=1.90153;LSEQ=TTGTTCCTGGGGTTAGCCTA;RSEQ=AGTCTGCTGCCATGGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:148:77,71:126,89:0.4077:2,2:26.8:1:32:1:0.23724:1.30443:60:147:0.4106:0:1.2 1/0:365:207:112,95:90,68:0.5671:2,2:26.4:1:30.8:1:0.59698:1.12228:59.9:102.5:0.5742:0:1.2 -10 128270786 . C A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24942;SOR=0;LSEQ=TGTGGTATGTAACAAAGAGC;RSEQ=ATGGGTAGTACAGCACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:2,1:53,128:0.0163:2,2:10.3:1:29.3:1:0.21324:4.78:60:6:0.0169:0:1 0/0:168:0:0,0:50,118:0:2,0:24.2:1:30.8:1:1:0:60:167:1:0:0.3 -10 128271072 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGACACCAGCGTTCACTG;RSEQ=GAAAATGTCGGCTGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 129140160 . A G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAGTCAGGGGCCCATCT;RSEQ=GCATACGACCCATGTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,1:0.2857:2,0:18.5:1:34:0:1:0:60:4:0.2857:0:1 0/0:1:0:0,0:1,0:0:0,0:32:0:29:0:1:0:60:2:1:0:0 -10 129140353 . TTGTTGTTGCTGCTGCTGCTGCTGC T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=6.000;MSILEN=3;SSF=0.01954;SOR=Inf;LSEQ=TGCTGCTGTTGCTGTTGCTG;RSEQ=TGTTGTTGTTAAAGGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:63,63:0:2,0:27.6:1:29.6:1:1:0:60:30.5:1:0:0.1 0/1:163:7:3,4:74,81:0.0429:2,2:28.4:1:30.1:1:1:1.21663:60:14:0.044:0.0061:0.3 -10 129140368 . C T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.2204;SOR=0;LSEQ=TGCTGTTGTTGTTGCTGCTG;RSEQ=TGCTGCTGCTGTTGTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:52,58:0.0179:2,2:29:0:29:1:1:1.11:60:4:0.0187:0:2.5 0/0:126:0:0,0:53,67:0:2,0:25.8:1:31.3:1:1:0:60:29:1:0:0.3 -10 129140429 . C A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24051;SOR=0;LSEQ=AGATCTATTGTGAGTCCTCG;RSEQ=AGGCATGGGTCCTATTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:2,1:7,30:0.075:2,2:14:1:28:1:0.12146:7.95:60:6:0.0769:0:1 0/0:39:0:0,0:6,33:0:2,0:19.9:1:31.1:1:1:0:60:38:1:0:0.1 -10 129140507 . G A 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13484;LSEQ=TGCAGCCAGTGATTCCTGCC;RSEQ=GTGCTGTGGCAAGGCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:0.4667:0,0:26.6:1:32.6:1:1:0:60:14:0.4667:0:1 1/0:4:2:0,2:0,2:0.5:0,0:15.5:1:33:0:1:0:60:4:0.5:0:1 -10 129534864 . A C 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCCTTCCGGGTTGAGGG;RSEQ=GCGAGGACTCCAGACGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:19:0:34:0:1:0:60:2:1:0:1 1/1:3:3:2,1:0,0:1:0,2:18.3:1:29:1:1:0:60:6:1:0:1 -10 129536033 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50062;SOR=0;LSEQ=GCTTCAAGAAGGTGCCCCGC;RSEQ=ACGAGGACGACCCAGGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:18,39:0.0339:2,2:24.5:1:31.5:1:0.54413:2.14:60:4:0.0345:0:1 0/0:48:0:0,0:16,32:0:2,0:24.7:1:31:1:1:0:59.1:96:1:0:0.2 -10 129536050 . T A 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50414;SOR=0;LSEQ=CGCGACGAGGACGACCCAGG;RSEQ=AACAGCGGCGCGCCGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:12,29:0.0465:2,2:38:0:29:1:0.51827:2.36:60:4:0.0465:0:1 0/0:32:0:0,0:9,23:0:2,0:22.4:1:28.6:1:1:0:60:64:1:0:0.1 -10 129878570 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11077;SOR=Inf;LSEQ=TACAATTTTAAAGCCTGTTA;RSEQ=AATGCATCCTTTTTACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:23.6:1:31.2:1:1:0:60:34:1:0:0 0/1:9:2:1,1:5,2:0.2222:2,2:20.5:1:30.5:1:1:2.23609:60:4:0.25:0:1 -10 130262745 . CA C 58 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61462;SOR=0.35794;LSEQ=CCTCCTCCTCCCTCCTCCTC;RSEQ=CCATCCTCCCCTCTAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:3,1:5,5:0.2667:2,2:8.5:1:29.1:1:0.58042:2.78:32:8:0.3077:0.1333:2.3 0/1:9:1:1,0:3,4:0.1111:2,0:12:0:32:0:1:0:35:2:0.1429:0:1 -10 130262752 . C T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67737;SOR=1.48282;LSEQ=CTCCCTCCTCCTCCACCATC;RSEQ=TCCCCTCTAGACTTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:1,2:11,7:0.1429:2,2:10.7:1:22:1:0.55338:2.97217:39:2:0.1053:0:2.7 0/1:15:3:2,1:7,5:0.2:2,2:6.3:1:28:1:1:1.40:39.3:6:0.2:0:3 -10 130262763 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49061;SOR=0;LSEQ=TCCACCATCCTCCCCTCTAG;RSEQ=CTTCTCCTCCTCCTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:14,9:0.0769:2,2:7.5:1:31:1:1:1.52748:28:4:0.0909:0:1.5 0/0:24:0:0,0:13,11:0:2,0:15.8:1:27.3:1:1:0:37:23:1:0:1 -10 130262777 . TC T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.49661;SOR=0;LSEQ=CTCTAGACTTCTCCTCCTCC;RSEQ=CACCATCCTCCCCTCTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:0,2:17,14:0.0606:2,0:32:1:32:1:0.22727:0:38:4:0.0625:0:1.5 0/0:27:0:0,0:15,12:0:2,0:28.4:1:31.1:1:1:0:36.5:54:1:0:1 -10 130262779 . CA C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.58737;SOR=1.41276;LSEQ=CTAGACTTCTCCTCCTCCTC;RSEQ=CCATCCTCCCCTCTAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:8:4,4:13,12:0.2424:2,2:31.4:1:32.2:1:1:1.0807:34.3:16:0.2857:0.0606:0.9 0/1:32:10:5,5:10,7:0.3125:2,2:29.8:1:30.3:1:0.70633:1.40962:38.7:20:0.3333:0.0313:0.1 -10 130262786 . C T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.35987;SOR=3.93568;LSEQ=TCTCCTCCTCCTCCACCATC;RSEQ=TCCCCTCTAGACTTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:1,0:18,17:0.0278:2,0:40:0:31:0:1:0:41:2:0.0286:0:2 0/1:39:4:2,2:18,17:0.1026:2,2:29.3:1:31.8:1:1:1.0573:39.3:8:0.1053:0:2.5 -10 130262789 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.49398;SOR=Inf;LSEQ=CCTCCTCCTCCACCATCCTC;RSEQ=CCTCTAGACTTCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:21,20:0:2,0:31.8:1:31.3:1:1:0:34.3:82:1:0:1.3 0/1:42:2:1,1:21,19:0.0476:2,2:34:0:32:1:1:1.10263:40:4:0.0488:0:2.5 -10 130262811 . TC T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.49451;SOR=0;LSEQ=CTCTAGACTTCTCCTCCTCC;RSEQ=CACCATCCTCCCCTCTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:21,22:0.0444:2,2:46.5:1:32:1:1:1.05:46:4:0.0455:0:0 0/0:43:0:0,0:22,21:0:2,0:32:1:31:1:1:0:35.9:86:1:0:0.9 -10 130262813 . CA C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.79043;SOR=1.22145;LSEQ=CTAGACTTCTCCTCCTCCTC;RSEQ=CCATCCTCCCCTCTAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:8:2,6:20,16:0.1778:2,2:32.4:1:31.4:1:0.24044:3.64179:32.6:16:0.2222:0:1 0/1:43:9:4,5:18,16:0.2093:2,2:33.7:1:30.3:1:0.72051:1.39511:37.2:18:0.2308:0:0.1 -10 130262819 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49462;SOR=0;LSEQ=TTCTCCTCCTCCTCCACCAT;RSEQ=CTCCCCTCTAGACTTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:22,23:0.0426:2,2:41:1:28.5:1:1:1.04:36:4:0.0435:0:1.5 0/0:47:0:0,0:24,23:0:2,0:28.4:1:30.6:1:1:0:36.3:46:1:0:0.8 -10 130262820 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=2.02947;LSEQ=TCTCCTCCTCCTCCACCATC;RSEQ=TCCCCTCTAGACTTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:1,0:22,24:0.0213:2,0:41:0:29:0:0.48936:0:35:2:0.0222:0:2 0/1:47:2:1,1:23,22:0.0426:2,2:25:1:29.5:1:1:1.04448:38.5:4:0.0455:0:3 -10 130262880 . C CA 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.74999;LSEQ=CTAGACTTCTCCTCCTCCTC;RSEQ=CCATCCTCCTGCCTTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:6,4:0.2308:2,0:8.7:1:30.8:1:0.19231:0:33.7:6:0.2308:0.1538:2.7 0/1:11:2:0,2:5,4:0.1818:2,0:7:1:30.3:1:0.45455:0:32:4:0.2:0.0909:0 -10 130262890 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTCCTCCCCATCCTCC;RSEQ=GCCTTCCCCTCCTCATTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:27:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29.5:1:1:0:60:4:1:0:1 -10 132314567 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTCTCTGGGCTGAGGAA;RSEQ=ATGAAGGTGAAATCCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:13.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -10 132314713 . G A 84 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTAAGTTGACATAGCTT;RSEQ=TGCATCAGTTTGGGCCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:23:1:29:1:1:0:60:8:1:0:1 1/1:8:8:8,0:0,0:1:0,0:23:1:28.3:1:1:0:60:16:1:0:1 -10 132314843 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19444;SOR=Inf;LSEQ=TCAGCGTTCCCTCCAGGAAG;RSEQ=CACCAGGGCTCTCCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:21,24:0:2,0:26.5:1:31.1:1:1:0:60:44:1:0:0.2 0/1:36:2:1,1:14,20:0.0556:2,2:32.5:1:30:1:1:1.41:60:4:0.0556:0:1 -10 132314861 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGCCACCAGGGCTCTCCTTC;RSEQ=TCCCCTCCATGAAAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:12,16:0.0667:2,2:18.5:1:29.5:1:1:1.32:60:4:0.0667:0:2 0/0:14:0:0,0:6,8:0:2,0:24.7:1:30.1:1:1:0:60:28:1:0:0.3 -10 133191478 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATGGCTGTGTTCCTTCCTGC;RSEQ=GCAAATGACTGTGGAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:6:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:28.5:1:1:0:60:4:1:0:1 -10 133191575 . C T 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57576;SOR=2.74155;LSEQ=TCATGGAGATCCTTTGGGCA;RSEQ=CCCTAATGCAATTCTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:32.3:1:31:1:1:0:60:8:0.5:0:1 1/0:4:3:3,0:1,0:0.75:0,0:18:1:31.7:1:1:0:60:6:0.75:0:2 -10 133191600 . C T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=AATGCAATTCTCCCCATTTC;RSEQ=GAAGCCAAAGTGATCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:26.2:1:30.8:1:1:0:60:24:1:0:0.3 1/0:9:7:7,0:2,0:0.7778:0,0:18:1:32:1:1:0:60:14:0.7778:0:1.4 -10 133191708 . T C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=16.78459;LSEQ=CCCAAGGCCCTGCAGGTCCA;RSEQ=CCCCGCAGGTCTCTGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:9:7,2:91,9:0.0826:2,2:21.9:1:31:1:0.22487:2.84982:60:18:0.0826:0:1 1/0:114:69:47,22:34,11:0.6053:2,2:19.2:1:30.8:1:0.52662:1.44219:60:138:0.6053:0:1.1 -10 133191723 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24154;SOR=Inf;LSEQ=GTCCATCCCCGCAGGTCTCT;RSEQ=CCACCTCAGACCTGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:128,36:0:2,0:22.1:1:32:1:1:0:60:81:1:0:0.1 0/1:159:2:1,1:104,53:0.0126:2,2:23.5:1:27:1:1:1.9534:60:4:0.0127:0:1.5 -10 133191727 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24635;SOR=Inf;LSEQ=ATCCCCGCAGGTCTCTGCCA;RSEQ=CTCAGACCTGGGCCCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:134,38:0:2,0:23.2:1:31.8:1:1:0:60:85:1:0:0.1 0/1:170:2:1,1:107,61:0.0118:2,2:32.5:1:28:1:1:1.74792:60:4:0.0119:0:2 -10 133191828 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=27.89328;LSEQ=TGACCTCCAGCCTTAACATT;RSEQ=GCTGCTCTCTGGCTGAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:16:10,6:180,201:0.0403:2,2:23.9:1:28.7:1:0.30829:1.86:60:32:0.0407:0:1.9 1/0:383:207:105,102:86,89:0.5405:2,2:26.4:1:29.5:1:0.83731:1.07:60:102.5:0.5423:0:1.9 -10 133191851 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=33.18254;LSEQ=TGCTCTCTGGCTGAGACTCT;RSEQ=TCATCTCACCTCATCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:14:7,7:147,214:0.0373:2,2:24.4:1:28.4:1:0.58285:1.45:60:13:0.0357:0:2.2 1/0:360:203:93,110:70,87:0.5639:2,2:24.7:1:29.7:1:0.83163:1.05:60:66.667:0.565:0:2 -10 133191905 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2201;SOR=Inf;LSEQ=AACCCGTTACTTCCTTCTGA;RSEQ=CATCTTCCCTGACCCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:47,138:0:2,0:25.7:1:32:1:1:0:60:25.429:1:0:0.2 0/1:164:2:1,1:55,107:0.0122:2,2:14.5:1:25:0:1:1.94:60:4:0.0123:0:3 -10 133191920 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20412;SOR=Inf;LSEQ=TCTGAGCATCTTCCCTGACC;RSEQ=CACATCCACTCCAGCATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:31,114:0:2,0:21.5:1:31.2:1:1:0:60:47.333:1:0:0.2 0/1:120:2:1,1:32,86:0.0167:2,2:6.5:1:27:1:0.47605:2.66:60:4:0.0171:0:1.5 -10 133191928 . A T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.03758;LSEQ=TCTTCCCTGACCCCACATCC;RSEQ=CTCCAGCATGGGGAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:7:1,6:25,92:0.0565:2,2:22.3:1:28.1:1:1:1.62477:60:6:0.0508:0:1.4 1/0:101:61:17,44:6,34:0.604:2,2:20.7:1:27.7:1:0.15239:2.17:60:19.333:0.5979:0:1.6 -10 133191934 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50107;SOR=0;LSEQ=CTGACCCCACATCCACTCCA;RSEQ=CATGGGGAAGGAATTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:16,82:0.02:2,2:11.5:1:29:1:0.31253:5.00:60:4:0.0204:0:1 0/0:84:0:0,0:16,68:0:2,0:20.4:1:31.5:1:1:0:60:83:1:0:0.9 -10 133192043 . C CT 50 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.58204;SOR=3.61082;LSEQ=CACTGTCCCTGTTTCCATTT;RSEQ=TTTTTTTTTTTTTTTCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,8:0.1:0,0:34:0:31:0:1:0:60:2:0.1111:0:3 0/1:10:3:0,3:0,7:0.3:0,0:15.3:1:31.7:1:1:0:60:6:0.3333:0.1:0 -10 134198942 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17715;SOR=Inf;LSEQ=AATAGCGGCCTCTCCTCCAC;RSEQ=TGCTCCCTCTGTCATTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:84,11:0:2,0:23.8:1:30.3:1:1:0:60:18:1:0:0.1 0/1:71:2:1,1:60,9:0.0282:2,2:12.5:1:29:1:0.26358:6.37705:60:4:0.0282:0:1 -10 134199067 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2106;LSEQ=ACTTTTTTCTACTTCCTCTT;RSEQ=CACACTTTTCCTTTGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:314:283:128,155:15,13:0.9013:2,2:25:1:30.9:1:0.43142:1.39571:60:140.5:0.9035:0:1.3 1/0:394:259:119,140:64,71:0.6574:2,2:25.7:1:30.4:1:0.83164:1.0603:60:50.8:0.6546:0:1.3 -10 134199109 . C T 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.41085;LSEQ=AACATTCGCATCCTCTCTGT;RSEQ=GGTTCATTTGCTGATGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:96:31,65:58,92:0.3902:2,2:27.9:1:30.2:1:0.3426:1.32038:60:95:0.3942:0:1.8 0/1:303:63:20,43:93,146:0.2079:2,2:25.7:1:30.2:1:0.31025:1.36813:60:126:0.21:0:1.7 -10 134199206 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50204;SOR=0;LSEQ=GGGGTCCCCTTGGGCCCTGG;RSEQ=TGGTGCTGCTGGTGCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:1,47:0.04:1,2:24:1:28:1:0.07918:33.61:60:4:0.0408:0:1 0/0:39:0:0,0:3,36:0:2,0:24.5:1:31.5:1:1:0:60:38:1:0:0.1 -10 134913210 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08245;SOR=Inf;LSEQ=GCCTCTGTAGCCACAGCTCC;RSEQ=GGGCGGCTCCTCCCCGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:0:2,0:26.6:1:30.6:1:1:0:60:62:1:0:0.3 0/1:13:2:1,1:7,4:0.1538:2,2:8:1:28.5:1:1:1.67325:60:4:0.1538:0:2 -10 134913223 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07536;SOR=Inf;LSEQ=CAGCTCCGGGGCGGCTCCTC;RSEQ=CCGCACACCCAGCCCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:0:2,0:29.4:1:31.6:1:1:0:60:66:1:0:0.3 0/1:13:2:1,1:7,4:0.1538:2,2:36.5:1:29.5:1:1:1.67325:60:4:0.1538:0:1 -10 134913229 . C T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00438;SOR=Inf;LSEQ=CGGGGCGGCTCCTCCCCGCA;RSEQ=ACCCAGCCCAGTCCCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:0:2,0:29.4:1:32.9:1:1:0:60:66:1:0:0.3 0/1:13:4:3,1:5,4:0.3077:2,2:29.3:1:29.3:1:1:2.25:60:8:0.3077:0:1.5 -10 134913291 . C T 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04556;SOR=0;LSEQ=ACAGCCCAGTACAGTCACCT;RSEQ=CAGGGCCCAGACACAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:3,4:0.5333:2,2:19:1:26.9:1:1:1.23147:60:7:0.5:0:1 0/0:6:0:0,0:3,3:0:2,0:17.8:1:31.8:1:1:0:60:12:1:0:1.2 -10 134913358 . A G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=TTGCCAGGGGTCCACCCTGC;RSEQ=GTTTCTGGAACCCTCCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:36:0:32:0:1:0:60:2:0.3333:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:26:1:28:1:1:0:60:4:0.6667:0:1 -10 135135994 . G GC 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.50508;SOR=0;LSEQ=CGGCTACCTAAGAGGGAAGG;RSEQ=CCCCCTGTCCCATGATCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:17,11:0.0645:2,2:18:1:30.5:1:1:1.52251:48.5:4:0.0645:0:0 0/0:22:0:0,0:14,8:0:2,0:24.3:1:30.9:1:1:0:52.1:21:1:0:0 -10 135136018 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49296;SOR=0;LSEQ=CCTGTCCCATGATCACGTGA;RSEQ=TTGCTTCACCTTGTCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:0.0556:2,2:22:1:29.5:1:1:1:54.5:4:0.0556:0:1.5 0/0:36:0:0,0:18,18:0:2,0:25.2:1:31.2:1:1:0:52.8:72:1:0:0.2 -10 135181285 . G T 55 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GCAGATAGTGGAAGAAGAAA;RSEQ=AGTGAAAGTCTTAAAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:35:1:30:1:1:0:43.5:4:1:0:1 1/1:4:4:2,2:0,0:1:0,2:21.3:1:27.8:1:1:0:30.3:8:1:0:1 -10 135181336 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=TGTAAGTGCATAGAAGAAAA;RSEQ=GCTGACATATGCTGCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:15.8:1:30.8:1:1:0:56.6:24:1:0:0.2 0/1:15:2:1,1:7,6:0.1333:2,2:36.5:1:31.5:1:1:1.1547:50:4:0.1333:0:1.5 -10 135490993 . T A 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=CGGAGTCCAGGATTCAGATC;RSEQ=GGTTTCAGAATCGAAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:3,1:0.4286:2,2:16.3:1:30:1:1:1.41418:40:6:0.4286:0:7.7 0/0:4:0:0,0:2,2:0:2,0:2.8:1:29:1:1:0:39.5:8:1:0:5 -10 135491005 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=TTCAGATCTGGTTTCAGAAT;RSEQ=GAAGGGCCAGGCACCCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:23.4:1:31.8:1:1:0:40:16:1:0:6.5 0/1:6:2:1,1:2,2:0.3333:2,2:5.5:1:28.5:1:1:1:36.5:4:0.3333:0:4.5 -10 135491011 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20588;SOR=0;LSEQ=TCTGGTTTCAGAATCGAAGG;RSEQ=CCAGGCACCCGGGACAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:25:1:31.5:1:1:1.8258:40:4:0.25:0:5.5 0/0:9:0:0,0:5,4:0:2,0:13.8:1:31:1:1:0:37.4:18:1:0:5.2 -10 135491017 . C A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.52085;LSEQ=TTCAGAATCGAAGGGCCAGG;RSEQ=ACCCGGGACAGGGTGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:4,3:0.125:2,0:35:0:32:0:1:0:40:2:0.125:0:5 0/1:11:2:1,1:6,3:0.1818:2,2:28:0:31.5:1:1:1.87089:39:4:0.1818:0:5.5 -10 135491019 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16374;SOR=0;LSEQ=CAGAATCGAAGGGCCAGGCA;RSEQ=CCGGGACAGGGTGGCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:34.5:1:31.5:1:1:1.8258:40:4:0.25:0:6.5 0/0:11:0:0,0:6,3:0:2,0:17.1:1:31.4:1:1:0:37.1:18:0.8182:0:5.9 -10 135491021 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16374;SOR=0;LSEQ=GAATCGAAGGGCCAGGCACC;RSEQ=GGGACAGGGTGGCAGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:36.5:1:31.5:1:1:1.8258:40:4:0.25:0:6.5 0/0:11:0:0,0:7,4:0:2,0:21:1:28.9:1:1:0:37.6:10:1:0:5.6 -10 135491026 . C G 51 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09023;SOR=0;LSEQ=GAAGGGCCAGGCACCCGGGA;RSEQ=AGGGTGGCAGGGCGCCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:3,4:0.3:2,2:49:1:32.7:1:1:2.41:40:6:0.3:0:7.7 0/0:11:0:0,0:7,4:0:2,0:26:1:31.8:1:1:0:37.6:22:1:0:5.6 -10 135491027 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=AAGGGCCAGGCACCCGGGAC;RSEQ=GGGTGGCAGGGCGCCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:42.5:1:31.5:1:1:1:40:4:0.2:0:6.5 0/0:11:0:0,0:7,4:0:2,0:27:1:30.4:1:1:0:37.6:22:1:0:5.6 -10 135491030 . G C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAGGCACCCGGGACAGG;RSEQ=TGGCAGGGCGCCCGCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:5,5:0,0:1:0,2:36.9:1:32.5:1:1:0:40:20:1:0:6.8 1/1:12:12:7,5:0,0:1:0,2:27.8:1:30.8:1:1:0:37.8:11:1:0:5.8 -10 135491035 . A G 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48308;SOR=Inf;LSEQ=GGCACCCGGGACAGGGTGGC;RSEQ=GGGCGCCCGCGCAGGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:31.2:1:30.8:1:1:0:43.3:24:1:0:6.8 0/1:14:2:1,1:7,5:0.1429:2,2:19:1:27.5:1:1:1.36624:40:4:0.1429:0:7.5 -10 135491038 . G A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.83923;LSEQ=ACCCGGGACAGGGTGGCAGG;RSEQ=CGCCCGCGCAGGCAGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:31:1:29:1:1:1:40:4:0.1667:0:6.5 0/1:14:2:1,1:7,5:0.1429:2,2:39.5:1:30:1:1:1.36624:39:4:0.1538:0:5.5 -10 135491039 . C T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48308;SOR=Inf;LSEQ=CCCGGGACAGGGTGGCAGGG;RSEQ=GCCCGCGCAGGCAGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:31.2:1:31.3:1:1:0:43.3:24:1:0:6.8 0/1:14:2:2,0:6,6:0.1429:2,0:26.5:1:32:0:0.47253:0:38.5:4:0.1429:0:7.5 -10 135491043 . C T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23077;SOR=Inf;LSEQ=GGACAGGGTGGCAGGGCGCC;RSEQ=GCGCAGGCAGGCGGCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:30.9:1:30.6:1:1:0:43.3:24:1:0:6.8 0/1:15:3:2,1:5,4:0.2:2,2:17.7:1:29:1:1:1.54:44.7:6:0.2:0:7 -10 135491044 . G A 27 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56923;SOR=0.37108;LSEQ=GACAGGGTGGCAGGGCGCCC;RSEQ=CGCAGGCAGGCGGCCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,4:0.1667:2,2:14:0:27.5:1:1:1.22474:59.5:4:0.1667:0:7 0/1:15:1:0,1:9,5:0.0667:2,0:39:0:29:0:0.4:0:33:2:0.0667:0:8 -10 135491045 . C T 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35749;SOR=0.32196;LSEQ=ACAGGGTGGCAGGGCGCCCG;RSEQ=GCAGGCAGGCGGCCTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:2,2:4,3:0.3333:2,2:39:1:29.5:1:1:1.29868:40:8:0.3636:0:6 0/1:15:2:1,1:8,5:0.1333:2,2:29:1:26.5:1:1:1.54914:40:4:0.1333:0:7.5 -10 135491046 . GC AA 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06021;SOR=0;LSEQ=CAGGGTGGCAGGGCGCCCGC;RSEQ=AGGCAGGCGGCCTGTGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:4,5:0.25:2,2:30.7:1:31.7:1:1:2.32:40:6:0.25:0:6.7 0/0:17:0:0,0:8,8:0:2,0:23.3:1:29.8:1:1:0:40.3:15:0.9375:0:5.9 -10 135491050 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49754;SOR=Inf;LSEQ=GTGGCAGGGCGCCCGCGCAG;RSEQ=CAGGCGGCCTGTGCAACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:29.7:1:30.6:1:1:0:43.3:11:1:0:6.5 0/1:17:2:1,1:8,6:0.1176:2,2:16.5:1:31.5:1:1:1.30929:47:4:0.1176:0:7.5 -10 135491053 . G A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49677;SOR=Inf;LSEQ=GCAGGGCGCCCGCGCAGGCA;RSEQ=GCGGCCTGTGCAACGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:26.6:1:31.5:1:1:0:43:26:1:0:6.6 0/1:18:2:2,0:7,8:0.1111:2,0:39:1:32:0:0.47059:0:38.5:4:0.1111:0:7.5 -10 135491055 . C T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24516;SOR=Inf;LSEQ=AGGGCGCCCGCGCAGGCAGG;RSEQ=GGCCTGTGCAACGCGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:26.2:1:29.8:1:1:0:43:12:1:0:6.6 0/1:18:3:2,1:7,7:0.1667:2,2:11.3:1:29:1:1:1.92:35.3:6:0.1667:0:4 -10 135491059 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16774;SOR=0;LSEQ=CGCCCGCGCAGGCAGGCGGC;RSEQ=TGTGCAACGCGGCCCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:0.1538:2,2:28:1:29:1:1:1.18:40:4:0.1667:0:5.5 0/0:18:0:0,0:8,7:0:2,0:24.3:1:29.7:1:1:0:40.5:14:0.8235:0:6.3 -10 135491060 . T G 51 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28358;SOR=0.20683;LSEQ=GCCCGCGCAGGCAGGCGGCC;RSEQ=GTGCAACGCGGCCCCCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:4,5:0.2308:2,2:17.7:1:32.3:1:1:2.32:40:6:0.2308:0:6.7 0/1:18:1:1,0:7,6:0.0556:2,0:17:0:32:0:1:0:40:2:0.0625:0:6 -10 135491064 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16221;SOR=0;LSEQ=GCGCAGGCAGGCGGCCTGTG;RSEQ=AACGCGGCCCCCGGCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:23:1:28.5:1:1:1:40:4:0.1538:0:5.5 0/0:20:0:0,0:10,10:0:2,0:19.9:1:31.1:1:1:0:40.1:19:1:0:5.9 -10 135491067 . C T 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56455;SOR=0.35285;LSEQ=CAGGCAGGCGGCCTGTGCAA;RSEQ=GCGGCCCCCGGCGGGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:18.5:1:29:1:1:1.15:40:4:0.1333:0:6.5 0/1:20:1:0,1:10,9:0.05:2,0:26:0:32:0:1:0:33:2:0.0526:0:8 -10 135491068 . G A 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.67217;SOR=2.12119;LSEQ=AGGCAGGCGGCCTGTGCAAC;RSEQ=CGGCCCCCGGCGGGGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:31:1:30.5:1:1:1.15:40:4:0.1333:0:6.5 0/1:20:5:3,2:7,8:0.25:2,2:21:1:28.6:1:1:1.67:39.6:10:0.2632:0:6.4 -10 135491070 . G A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63899;SOR=0.51073;LSEQ=GCAGGCGGCCTGTGCAACGC;RSEQ=GCCCCCGGCGGGGGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:5,7:0.2:2,2:7.7:1:31.7:1:0.56923:2.61:40:6:0.2:0:6.7 0/1:18:2:1,1:8,8:0.1111:2,2:27.5:1:29.5:1:1:1:40:4:0.1111:0:5.5 -10 135491072 . C T 37 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=1.28981;LSEQ=AGGCGGCCTGTGCAACGCGG;RSEQ=CCCCGGCGGGGGTCACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:0,2:7,5:0.1333:2,0:14.5:1:29:1:0.46154:0:34:4:0.1429:0:7 0/1:18:3:1,2:7,6:0.1667:2,2:28.7:1:23.7:1:1:2.21433:46.7:2:0.1176:0:6.3 -10 135491076 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16774;SOR=0;LSEQ=GGCCTGTGCAACGCGGCCCC;RSEQ=GGCGGGGGTCACCCTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:4,7:0.1538:2,2:45:1:28:1:1:1.67:59.5:4:0.1538:0:7 0/0:18:0:0,0:9,9:0:2,0:20.3:1:29.8:1:1:0:40.9:36:1:0:6.2 -10 135491080 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.48617;SOR=Inf;LSEQ=TGTGCAACGCGGCCCCCGGC;RSEQ=GGGGTCACCCTGCTCCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:27.2:1:30.6:1:1:0:40.9:20:1:0:6.8 0/1:13:2:1,1:5,6:0.1538:2,2:36:1:29:1:1:1.18:40:4:0.1538:0:7.5 -10 135491081 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.48617;SOR=Inf;LSEQ=GTGCAACGCGGCCCCCGGCG;RSEQ=GGGTCACCCTGCTCCCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:26.8:1:31:1:1:0:40.9:20:1:0:6.8 0/1:13:2:1,1:5,6:0.1538:2,2:38.5:1:30.5:1:1:1.18:40:4:0.1538:0:5.5 -10 135491083 . G T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.40909;SOR=Inf;LSEQ=GCAACGCGGCCCCCGGCGGG;RSEQ=GTCACCCTGCTCCCTCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:2,6:0,0:0.8889:0,2:27.6:1:29.8:1:1:0:41.1:16:1:0:6.9 1/1:13:13:6,7:0,0:1:0,2:27.2:1:27.6:1:1:0:41.4:26:1:0:6.8 -10 135491089 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=CGGCCCCCGGCGGGGGTCAC;RSEQ=CTGCTCCCTCGTGGGTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:26.9:1:30.7:1:1:0:41:18:1:0:6.9 0/1:13:2:1,1:5,6:0.1538:2,2:19:0:31:1:1:1.18:47:4:0.1538:0:7.5 -10 135491090 . C G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54416;SOR=0.30916;LSEQ=GGCCCCCGGCGGGGGTCACC;RSEQ=TGCTCCCTCGTGGGTCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:2,5:0.2222:2,0:32.5:1:32:1:1:0:34:4:0.25:0:7 0/1:13:1:0,1:5,5:0.0769:2,0:45:0:32:0:1:0:60:2:0.0833:0:8 -10 135491093 . C A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68134;LSEQ=CCCCGGCGGGGGTCACCCTG;RSEQ=TCCCTCGTGGGTCGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:30:1:27.5:1:0.46429:3.87:59.5:4:0.25:0:7 0/1:11:2:1,1:3,4:0.1818:2,2:37:1:29:1:1:1.29:40:4:0.2:0:6 -10 135491097 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48538;SOR=Inf;LSEQ=GGCGGGGGTCACCCTGCTCC;RSEQ=TCGTGGGTCGCCTTCGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:1,5:0:2,0:28.2:1:32:1:1:0:35:12:0.8571:0:6.8 0/1:11:2:1,1:4,5:0.1818:2,2:39:1:30:1:1:1.22:40:4:0.2:0:6 -10 135491099 . C G 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48538;SOR=Inf;LSEQ=CGGGGGTCACCCTGCTCCCT;RSEQ=GTGGGTCGCCTTCGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,5:0:2,0:26.6:1:29.9:1:1:0:41.3:14:0.875:0:6.7 0/1:11:2:1,1:4,5:0.1818:2,2:9:0:29.5:1:1:1.22:47:4:0.2:0:7.5 -10 135491100 . G T 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52819;SOR=0.27156;LSEQ=GGGGGTCACCCTGCTCCCTC;RSEQ=TGGGTCGCCTTCGCCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:2,3:0.2857:2,0:42.5:1:30.5:1:1:0:34:4:0.2857:0:7 0/1:11:1:0,1:5,5:0.0909:2,0:37:0:26:0:1:0:60:2:0.0909:0:8 -10 135491102 . G T 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=GGGTCACCCTGCTCCCTCGT;RSEQ=GGTCGCCTTCGCCCACACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:28.9:1:31.7:1:1:0:41.3:14:1:0:7 0/1:11:2:1,1:4,5:0.1818:2,2:37:0:30:1:1:1.22:40:4:0.25:0:6 -10 135491110 . T C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=CTGCTCCCTCGTGGGTCGCC;RSEQ=TCGCCCACACCGGCGCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:13:1:29:1:1:3.16:59.5:4:0.2857:0:7 0/0:7:0:0,0:2,5:0:2,0:31:1:30.4:1:1:0:42:14:1:0:6 -10 135491113 . G A 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTCCCTCGTGGGTCGCCTTC;RSEQ=CCCACACCGGCGCGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:1,3:0.4286:2,2:35:1:29.7:1:1:1.41:30:6:0.5:0:6.7 0/1:7:3:1,2:1,3:0.4286:2,2:25.3:1:29.3:1:1:1.41:46.7:6:0.4286:0:6.7 -10 135491126 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CGCCTTCGCCCACACCGGCG;RSEQ=GTGGGGAACGGGGCTTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:23:1:32:1:1:0:30:6:1:0:6.7 0/1:7:2:1,1:1,4:0.2857:2,2:17.5:1:31.5:1:1:3.16:40:4:0.3333:0:5.5 -10 135491127 . G A 49 d7;v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03333;SOR=0;LSEQ=GCCTTCGCCCACACCGGCGC;RSEQ=TGGGGAACGGGGCTTCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:22:1:31:1:1:0:30:6:1:0:6.7 0/1:7:1:0,1:2,4:0.1429:2,0:10:0:31:0:1:0:60:2:0.1429:0:8 -11 123438 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52941;SOR=Inf;LSEQ=CATCGCCTTCCTGACCCCTC;RSEQ=CTGCAGCCACACGAGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:25.3:1:30:1:1:0:44.3:12:1:0:0 0/1:12:2:1,1:6,4:0.1667:2,2:36.5:1:29:1:1:1.4491:43:4:0.1667:0:1 -11 123505 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAACCAGAGAAAACAACCT;RSEQ=CCAAGTTGGCAGCTGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:8:1:33.5:1:1:0:43:4:1:0:0 0/1:8:2:1,1:1,5:0.25:2,2:16.5:1:27:1:0.46429:3.87:23:4:0.25:0:1 -11 123850 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1211;SOR=0;LSEQ=ATCTTCTGAGAAGGATGGAC;RSEQ=CAGCCCCAACAAATCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:19,19:0.05:2,2:20:1:30:1:1:1:44:4:0.05:0:1 0/0:74:0:0,0:36,38:0:2,0:29.2:1:29.9:1:1:0:31.3:36:1:0:0.1 -11 123906 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCCCATGAGTGGCGCTCAT;RSEQ=ATCTTCAGCAGGCGGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:9,20:0:2,0:24.5:1:31.2:1:1:0:30:58:1:0:0.1 0/1:62:2:1,1:22,38:0.0323:2,2:30.5:1:30.5:1:1:1.71:39:4:0.0333:0:1.5 -11 123919 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGCTCATGATCTTCAGCAGG;RSEQ=GGCACCAGGCCCTGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:5,18:0:2,0:22.2:1:30.2:1:1:0:30.1:46:1:0:0.1 0/1:52:2:1,1:16,34:0.0385:2,2:22:1:28:1:1:2.09:21:4:0.0392:0:1 -11 124157 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22;SOR=Inf;LSEQ=AGGGCTCGTGGGAGCGGAGC;RSEQ=TATCAGAGACGGGCACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:25.6:1:29.5:1:1:0:24.5:26:1:0:0 0/1:12:2:1,1:6,4:0.1667:2,2:16:1:29:1:1:1.4491:20:4:0.1667:0:1 -11 124288 . A T 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGGCTGCACACAGTCAGGG;RSEQ=ACCTGGCTCAGCCTGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:23:0:32:0:1:0:21:2:1:0:0 1/0:4:2:0,2:0,2:0.5:0,0:16:1:26.5:1:1:0:20.5:4:0.5:0:1 -11 125186 . G A 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CTGACTGGGCTTTCGGGGTC;RSEQ=GGGCAGAGGGAACCCCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:17.3:1:31.3:1:1:0:20:6:0.6:0:1 0/0:2:0:0,0:2,0:0:0,0:7:0:29.5:1:1:0:20:4:1:0:0 -11 125377 . G A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=GGCTCAGGGAACCGGAGACC;RSEQ=AGAAGGCGCTGTCCTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:2,6:0.2727:2,0:8.3:1:31:0:1:0:20:6:0.2727:0:1 0/1:11:3:0,3:5,3:0.2727:2,0:8:1:29:1:0.18182:0:29:6:0.2727:0:1 -11 125693 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGTTGGGGGGCGGTCCA;RSEQ=TGGGAGGAGCCTCAGCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:2:1,1:8,7:0.1176:2,2:11.5:1:28.5:1:1:1.13389:21:4:0.125:0:1 -11 324163 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGTATGGCTAGCCTCC;RSEQ=GTTGGAAAATTTTTACCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:48.5:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 324170 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCTAGCCTCCCGTTGGA;RSEQ=AATTTTTACCATCTTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45.5:1:32:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 325034 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAAGGGGGCAGGGTACGGA;RSEQ=GGTGAGTCGTCCAAGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:12,18:0:2,0:25.7:1:30.3:1:1:0:60:60:1:0:0 0/1:64:2:1,1:33,29:0.0313:2,2:29:0:32:0:1:1.13563:60:4:0.0323:0:1 -11 325114 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28361;SOR=Inf;LSEQ=CCTTTCCCTCTTAGGTAGCC;RSEQ=AGCAGAGAGAGAAGGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:0:2,0:22.4:1:30.4:1:1:0:60:46:1:0:0 0/1:38:3:2,1:15,20:0.0789:2,2:9:1:28:1:0.57681:2.60:60:6:0.0789:0:1.3 -11 353042 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTAAATCTCTTCATTCCT;RSEQ=CCTTCCTTTGTGGGTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:28.5:1:1:0:60:4:1:0:1.5 -11 353861 . G T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCATGACTTCTATCATG;RSEQ=AGGGTCCAGCCCTACGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 354119 . A G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1718;LSEQ=CAAGCAAGTCATGTGACCAT;RSEQ=GGACAGGGGCCCTTCCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:17:9,8:1,1:0.8947:2,2:30:1:30.7:1:1:1.12:60:16:0.8889:0:1.3 1/1:22:20:8,12:1,1:0.9091:2,2:27:1:30.9:1:1:1.47192:60:40:0.9091:0:1.1 -11 354508 . G GA 28 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCTGTCTCAAAAAAAAA;RSEQ=AAAAAAAAAAAGAAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:0.5:0,2:22:1:28.5:1:1:0:60:4:0.6667:0:0 0/0:1:0:0,0:1,0:0:0,0:18:0:34:0:1:0:60:2:1:0:1 -11 355039 . CTAA C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGATTAATAATGTTTATA;RSEQ=TGATTGATATGTCCATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:32.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 528208 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACGCGTGGCCTTGTGGGATC;RSEQ=CTGTGGCGGACTCTCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:1:29.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:32:0:1:0:60:4:1:0:2.5 -11 528237 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACTCTCAGCTATCAGAGGG;RSEQ=TCCATCACTCCATCGTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:44:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:30:1:1:0:60:4:1:0:2.5 -11 528575 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCCACCGAGGAAGGGGGCCA;RSEQ=CCCCCTCCCCGCGTCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21:1:32:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:21:0:28:0:1:0:60:2:1:0:0 -11 531572 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGAGCAACCAGCCATGA;RSEQ=GCAGGCGTGGGGCAAGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 532546 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51195;SOR=0;LSEQ=GGCGGGGCACAAGGGAGGCT;RSEQ=CTGACCGCAGGCCAGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:173,13:0.0106:2,2:21.5:1:28.5:1:0.14376:12.86069:60:4:0.0108:0:1 0/0:135:0:0,0:129,6:0:1,0:22.9:1:31.8:1:1:0:60:26:1:0:0.3 -11 532567 . C T 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.85228;LSEQ=CTGACCGCAGGCCAGGAGAC;RSEQ=GGCAGGGGCGGGGAGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:228,57:0.0104:2,2:25:1:24.7:1:0.49201:1.99433:60:2:0.0071:0:1 0/0:225:2:1,1:181,42:0.0089:2,2:6.5:1:21:1:0.34639:4.27087:60:1:0.0046:0:4 -11 532923 . A C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13382;SOR=0.42601;LSEQ=CTGGACTCTGGCCATCTCGA;RSEQ=GTGCCCAGGGCCACCCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:31:2,29:1,27:0.5254:1,2:27.6:1:30.5:1:1:1.84:60:62:0.5254:0:1.1 0/1:22:7:1,6:0,15:0.3182:1,2:26.4:1:30:1:0.31818:0:60:14:0.3182:0:1 -11 533223 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5038;SOR=0;LSEQ=CCCAGGACTGCAGGGCGTGA;RSEQ=CCCAGACCCCGGCCCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:2,0:142,31:0.0114:2,0:19:1:31:1:1:0:60:4:0.0116:0:1.5 0/0:143:0:0,0:111,32:0:2,0:22.3:1:31.8:1:1:0:60:46.667:1:0:0.1 -11 533308 . CG C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.7935;SOR=0.85301;LSEQ=CCGCTGGGTCACATGGGTCC;RSEQ=GGGGGTCCCAGAGGGTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:7:4,3:342,231:0.012:2,2:23:1:30.3:1:1:1.11019:60:14:0.0124:0:0.1 0/1:680:7:3,4:374,299:0.0103:2,2:30.6:1:30:1:0.70596:1.66649:60:14:0.0105:0:0.3 -11 533994 . A G 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10931;SOR=Inf;LSEQ=TCAGGACCTTCCGTGGGGGG;RSEQ=GTTCACACAGCCAGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:40,151:0:2,0:23.9:1:31:1:1:0:60:190:1:0:0.2 0/1:176:3:2,1:35,138:0.017:2,2:21.7:1:29.3:1:0.11234:7.76:60:6:0.0171:0:1 -11 534242 . A G 315 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05725;LSEQ=GGGTCGTATTCGTCCACAAA;RSEQ=TGGTTCTGGATCAGCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1057:934:455,479:51,67:0.8836:2,2:27.1:1:32:1:0.28271:1.25:60:65.714:0.8855:0:1.1 0/1:1064:322:154,168:361,378:0.3026:2,2:24.5:1:31.6:1:0.78941:1.04183:60:321:0.3057:0:1.2 -11 534287 . G A 87 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4222;SOR=0.56653;LSEQ=AGCGCACTCTTGCCCACACC;RSEQ=CCGGCGCCCACCACCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:746:9:7,2:293,444:0.0121:2,2:12.9:1:27.6:1:0.03458:5.29:60:18:0.0122:0:1.9 0/0:728:5:4,1:305,416:0.0069:2,2:19:1:27.8:1:0.1693:5.44:60:10:0.007:0:1 -11 534403 . GCCCAGGCCCAGC G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=1;SSF=0.00202;SOR=0.16303;LSEQ=GGAGGGCCCTGCTCAGCCAG;RSEQ=CCCAGGCCCCACAGGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:21:0,21:0,45:0.3182:1,1:30.2:1:33:1:1:0:59.3:42:0.3231:0:0.4 0/1:43:3:0,3:0,40:0.0698:1,0:43:1:33:1:1:0:60:6:0.0732:0:0 -11 534409 . GCCCAGC G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=4.000;MSILEN=1;SSF=0.001;SOR=0.19039;LSEQ=CCCTGCTCAGCCAGGCCCAG;RSEQ=CCCAGGCCCCACAGGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:31:0,31:0,8:0.5167:0,1:27.5:1:31.7:1:1:0:60:14.5:0.8056:0.0167:0.2 0/1:36:6:0,6:0,26:0.1667:1,0:18.7:1:34:1:1:0:60:12:0.1875:0.0278:0 -11 535026 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGCACTGGGGCTGAGG;RSEQ=CCCCGGCCTGGTCCGCGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 1782844 . G A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12119;SOR=Inf;LSEQ=CTGCCTGTCACCTGGAAACT;RSEQ=CTGGCCCAGCTCCCCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:15,25:0:2,0:29.4:1:31.5:1:1:0:60:39:1:0:0.1 0/1:47:4:3,1:18,25:0.0851:2,2:12.8:1:25.8:1:0.31124:4.05:60:8:0.0851:0:1 -11 1782850 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49333;SOR=Inf;LSEQ=GTCACCTGGAAACTGCTGGC;RSEQ=CAGCTCCCCCAAGTCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:14,24:0:2,0:27.1:1:29.8:1:1:0:60:18:1:0:0 0/1:38:2:1,1:14,22:0.0526:2,2:34.5:1:29.5:1:1:1.55:60:4:0.0541:0:1 -11 1782886 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.49245;SOR=Inf;LSEQ=AGTGAATGGCAACCCATTGC;RSEQ=CCCCGCCAGGTTGCACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:3,16:0:2,0:17.9:1:30.7:1:1:0:60:18:1:0:0.1 0/1:23:2:1,1:4,17:0.087:2,2:12.5:1:28.5:1:0.39526:3.91:60:4:0.087:0:1 -11 2154188 . G A 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGCTGCAGGATGGTGGC;RSEQ=CCGGGCTGCAGACTTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:354,78:0:2,0:25.5:1:30.1:1:1:0:60:47:1:0:0.1 0/1:364:51:32,19:232,81:0.1401:2,2:25.7:1:29.9:1:0.12668:1.69787:60:102:0.1425:0:1.1 -11 2154234 . C T 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.051;SOR=4.74185;LSEQ=TGCTCACTTCCGATTGCTGG;RSEQ=CATCTCTGGGGGGGCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:873:2:0,2:545,326:0.0023:2,0:1:0:27:1:0.14089:0:60:4:0.0024:0:1 0/1:742:8:3,5:427,307:0.0108:2,2:22.1:1:25.3:1:0.29116:2.3155:60:7:0.0096:0:1.3 -11 2154683 . G T 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6917;LSEQ=TCCCAGAGGCCACAGGAAAC;RSEQ=CTGGGCGCCCGAAGCCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:4:2,2:283,100:0.0103:2,2:24.5:1:29.3:1:0.28434:2.82099:60:8:0.0105:0:1 0/0:279:2:1,1:216,61:0.0072:2,2:42:1:29.5:1:0.39568:3.52023:60:4:0.0074:0:1 -11 2154964 . G A 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGCCCCCGGAGGCTGAAG;RSEQ=GGGAGCAAACCACCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:24,230:0:2,0:24.4:1:31.5:1:1:0:60:253:1:0:0.1 0/1:175:42:6,36:15,117:0.24:2,2:26.3:1:30.5:1:0.59432:1.30:60:41:0.2398:0:1.2 -11 2156213 . G A 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAACGCACGTCCCTTGTCA;RSEQ=AATGTCCAAAAGGTGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:24:1:31.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 2156536 . G A 230 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66574;SOR=1.08117;LSEQ=CCCCTGGCTTGAGGTTGGGC;RSEQ=TCCTCACCGGTCACTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:202:168,34:122,21:0.5855:2,2:24.8:1:30.1:1:0.6555:1.17519:60:100:0.5848:0:1.1 1/0:230:139:109,30:63,27:0.6043:2,2:22.7:1:29.7:1:0.16168:1.55:60:68.5:0.6009:0:1.1 -11 2156741 . T G 225 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACCAGCATCGACTTCCCCA;RSEQ=TGGGATTCCCATTGGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1041:131:56,75:420,490:0.1258:2,2:24.2:1:32:1:0.51171:1.14781:60:130:0.127:0:1.1 0/0:1037:0:0,0:485,552:0:2,0:24.9:1:29.4:1:1:0:60:44.087:1:0:0.2 -11 2156821 . C T 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13234;SOR=0;LSEQ=CAAGCCCCAGGCCAGAGGTG;RSEQ=CCCTCCCAAACCAAATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:4:2,2:66,300:0.0108:2,2:24.8:1:29:1:0.15552:4.52:60:8:0.011:0:1 0/0:299:0:0,0:72,226:0:2,0:22.4:1:30.6:1:1:0:60:32.111:1:0:0.1 -11 2156930 . G A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00355;SOR=0.16805;LSEQ=AACACACAGGTCATAATGCC;RSEQ=AGGTGAGGGCGCAGGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:21:0,21:2,16:0.5385:2,1:21.9:1:30.9:1:0.20648:0:60:42:0.5676:0:1 0/1:25:4:0,4:2,19:0.16:2,0:30.5:1:30.8:1:1:0:60:8:0.16:0:1 -11 2157044 . C G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65944;SOR=1.88324;LSEQ=TACACGAGGGGTGACCATCT;RSEQ=CACGGTCATTATTGCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:3,3:2,5:0.4615:2,2:17.2:1:31.2:1:0.59207:2.32:60:12:0.4615:0:1.3 1/0:8:5:2,3:1,2:0.625:2,2:26.6:1:32.6:1:1:1.29:60:10:0.625:0:1 -11 2161488 . G C 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGACGCGAGTTCGGTCTC;RSEQ=GGGGCCACCACGATAATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1107:0:0,0:502,600:0:2,0:24.5:1:29.9:1:1:0:60:49.091:0.9963:0:0.2 0/1:1017:92:40,52:410,510:0.0905:2,2:25.2:1:29.9:1:0.91249:1.04506:60:184:0.0917:0:1.2 -11 2161858 . A G 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCTCCAGCCGCTTTCCCCAC;RSEQ=AATGAGATCTTTGCAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:11:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:47:0:31:1:1:0:60:4:1:0:1 -11 2164799 . G C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36111;SOR=0;LSEQ=TCGTCTTTAAAATTAGGGAA;RSEQ=CCGGGTTAGTGGCCTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:23,0:0,0:1:0,1:25.9:1:32.4:1:1:0:60:46:1:0:1 1/1:13:12:12,0:1,0:0.9231:0,0:16.8:1:31.7:1:1:0:60:24:0.9231:0:1.3 -11 2164915 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50006;SOR=0;LSEQ=AGTGTAAGTCTGGAAAAGCC;RSEQ=GCCGGGACTGATGTGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:136,10:0.0135:2,2:24:1:27.5:1:0.14359:13.01473:60:4:0.0138:0:1.5 0/0:131:0:0,0:116,15:0:2,0:23.7:1:30.3:1:1:0:60:262:1:0:0.4 -11 2164921 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22987;SOR=Inf;LSEQ=AGTCTGGAAAAGCCCGCCGG;RSEQ=ACTGATGTGTTTTGACGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:155,16:0:2,0:22.2:1:31.4:1:1:0:60:170:1:0:0.6 0/1:158:2:1,1:133,23:0.0127:2,2:9:1:26.5:1:0.28154:5.68215:60:4:0.0127:0:2 -11 2164990 . G A 277 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGACCCGTCGAAATGGTGA;RSEQ=TATATTTAGAAGACTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:566:566:343,223:0,0:1:0,2:24.6:1:30.3:1:1:0:60:69.75:1:0:1.1 1/0:580:437:257,180:81,61:0.7534:2,2:24.5:1:29.3:1:0.76889:1.08:60:108.25:0.7544:0:1.1 -11 2165138 . G A 54 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3738;SOR=0.25904;LSEQ=TGTTGAGCTCAAGCTTCCCG;RSEQ=GCAGCGGAAGGAAGGCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:4:3,1:95,266:0.011:2,2:20:1:27.3:1:0.06079:8.34:60:8:0.0111:0:1.3 0/0:350:1:1,0:106,243:0.0029:2,0:1:0:24:0:0.30571:0:60:2:0.0029:0:1 -11 2165143 . C T 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21512;SOR=0.24583;LSEQ=AGCTCAAGCTTCCCGGGCAG;RSEQ=GGAAGGAAGGCGCTGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:4:2,2:74,242:0.0125:2,2:14.3:1:29.5:1:0.24006:3.26:60:8:0.0128:0:1.5 0/0:323:1:0,1:93,229:0.0031:2,0:36:0:27:0:1:0:60:2:0.0031:0:1 -11 2165173 . T G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.33562;LSEQ=GCGCTGCCGGGGATTCACCT;RSEQ=GGCTGGGGCGCGCGCGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:76:4,72:10,73:0.478:2,2:24.1:1:31.9:1:0.16604:2.45251:60:152:0.478:0:1 0/1:128:30:4,26:10,87:0.2344:2,2:19.6:1:30.8:1:0.73926:1.34:60:60:0.2362:0:1.1 -11 2166847 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCGCTCATGCTTGAAAA;RSEQ=GCATGCCTGGACTTTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 2582118 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATGGGGGAGGGCTTCAC;RSEQ=GCAGGGAGAGTGAGGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:20:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:25.5:1:30:1:1:0:60:4:1:0:1.5 -11 2583116 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49717;SOR=Inf;LSEQ=GTGGCCAGGGCCTCAGGAGG;RSEQ=ACACAGAGGGCCCCACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:40,38:0:2,0:26.1:1:30.8:1:1:0:60:38:1:0:0.2 0/1:82:2:1,1:43,37:0.0244:2,2:17.5:1:28.5:1:1:1.16002:60:4:0.0247:0:2.5 -11 2583141 . A G 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGGGCCCCACTCAAGGTC;RSEQ=CGGGCTGCACGTTCCATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:37,45:0:2,0:25.8:1:29.9:1:1:0:60:164:1:0:0.1 0/1:89:24:11,13:33,32:0.2697:2,2:23.5:1:31.9:1:0.81197:1.21604:60:48:0.2727:0:1.2 -11 2583173 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23238;SOR=0;LSEQ=TTCCATGGGGCCTGGGGAAG;RSEQ=AGCCGAGCAGAAGGATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:23,36:0.0328:2,2:12:0:30.5:1:1:1.55:60:4:0.0333:0:1.5 0/0:65:0:0,0:29,36:0:2,0:26.6:1:31.1:1:1:0:60:64:1:0:0.3 -11 6502636 . G C 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02876;SOR=Inf;LSEQ=AGGGCGGAGCTGACGTCGCA;RSEQ=CCAGGGCAGGGCGATACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:0:1,0:22.1:1:31.2:1:1:0:60:13:1:0:0.1 0/1:22:7:6,1:14,1:0.3182:1,2:12.6:1:31.7:1:1:2.2361:60:14:0.3333:0:1.7 -11 6502694 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15556;SOR=0;LSEQ=AGCGAGAGGTTACTTCCGGG;RSEQ=CGGCACCGAGAAGCTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:34,14:0.04:2,2:24:1:29:1:0.51429:2.38049:60:4:0.0417:0:1 0/0:76:0:0,0:54,22:0:2,0:20.4:1:30.6:1:1:0:60:75:1:0:0.6 -11 6502727 . C G 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGAAACGGAAGTGGCGTA;RSEQ=GGCATGCGCCGGTGGCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:49,38:0:2,0:25.7:1:30.5:1:1:0:60:86:0.9885:0:0.3 0/1:147:36:20,16:65,46:0.2449:2,2:23.5:1:30.5:1:0.84647:1.12948:60:72:0.2483:0:2.1 -11 6502734 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1484;SOR=0;LSEQ=CGGAAGTGGCGTACGGCATG;RSEQ=GCCGGTGGCGTGATGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:52,43:0.0206:2,2:30:1:30.5:1:1:1.20692:60:4:0.0211:0:1 0/0:154:0:0,0:86,68:0:2,0:27.6:1:30.2:1:1:0:60:50.333:1:0:0.7 -11 6502738 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52619;SOR=Inf;LSEQ=AGTGGCGTACGGCATGCGCC;RSEQ=GTGGCGTGATGGAGCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:54,45:0:2,0:26.2:1:29.6:1:1:0:60:23.75:1:0:0.2 0/1:162:2:1,1:89,71:0.0123:2,2:20:1:30.5:1:1:1.25175:60:4:0.0126:0:2.5 -11 6502744 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53678;SOR=Inf;LSEQ=GTACGGCATGCGCCGGTGGC;RSEQ=TGATGGAGCGGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:53,46:0:2,0:27.8:1:30.8:1:1:0:60:98:1:0:0.3 0/1:175:2:1,1:94,78:0.0114:2,2:16:0:32.5:1:1:1.20383:60:4:0.0116:0:2.5 -11 6502754 . GGCA G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.61415;SOR=0.53635;LSEQ=CGCCGGTGGCGTGATGGAGC;RSEQ=GCAGCAGCAGCAACAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:49,50:0.0198:2,2:30.5:1:31:1:1:1.02:60:4:0.0204:0:0 0/1:187:2:1,1:91,92:0.0107:2,2:36:1:31:1:1:1.01:60:4:0.011:0:0 -11 6502780 . C A 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAGCAGCAACAGCAACTG;RSEQ=GAAACGTAAGTGAGAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:40,49:0:2,0:26.8:1:31:1:1:0:60:178:1:0:0.3 0/1:170:46:22,24:52,72:0.2706:2,2:24.4:1:30:1:0.49291:1.27:60:92:0.2754:0:1.8 -11 6707260 . A G 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08081;SOR=0;LSEQ=TTGGCTCTCTTCTTTTTCTG;RSEQ=TCATTTTCTTTCATGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:3,0:0.5714:0,2:32.8:1:28.8:1:0.14286:0:60:3:0.5:0:1.5 0/0:5:0:0,0:4,1:0:2,0:21.6:1:27.6:1:1:0:60:10:1:0:0 -11 6707395 . C T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=TTTCCCTACAGCAATGCTAA;RSEQ=AGCATGCTGAGTAACATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:44,29:0:2,0:18.6:1:29.3:1:1:0:59.8:6.3:1:0:0.3 0/1:82:2:1,1:44,35:0.0244:2,2:15:0:26.5:1:1:1.25356:60:4:0.027:0:1 -11 7206403 . C T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0147;SOR=0.18985;LSEQ=CCAATAGCTAATTTAGAAGT;RSEQ=ACATACAATGCTGATTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:13:13,0:9,0:0.5909:0,1:25.8:1:30.8:1:1:0:60:26:0.5909:0:1 0/1:24:5:5,0:19,0:0.2083:1,0:22.6:1:30.4:1:1:0:60:10:0.2174:0:1 -11 7206465 . G C 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00067;SOR=Inf;LSEQ=AGAAAGCAGCAAAATGCTTC;RSEQ=CAATTTCATATGAATAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:69,18:0:2,0:23.1:1:30.1:1:1:0:60:86:0.9885:0:0.1 0/1:113:13:9,4:69,30:0.115:2,2:20.6:1:29.6:1:1:1.02204:60:26:0.1182:0:1.2 -11 7206563 . T C 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=6e-05;SOR=0.49199;LSEQ=TGTTATAACATGGGCAGTGC;RSEQ=AAAATGCTGGGCTACTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:234:125:65,60:53,55:0.5342:2,2:27:1:31.4:1:0.69449:1.12:60:61.5:0.5325:0:1.2 0/1:308:111:57,54:100,97:0.3604:2,2:26.5:1:30.9:1:1:1.02:60:222:0.3627:0:1.1 -11 8246137 . C T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.02427;SOR=0;LSEQ=CAGGCGGGCAGATGGACAGA;RSEQ=GGGCCTGGAGGCCAGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:5:1,4:295,194:0.0101:2,2:9:1:28.4:1:0.16276:6.06174:60:10:0.0102:0:1.2 0/0:543:0:0,0:315,227:0:2,0:23.7:1:30.1:1:1:0:60:179.667:0.9981:0:0.3 -11 8246181 . A G 202 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTTACTGAACTTGGGATTC;RSEQ=AAGGTGCCATTGAGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:751:0:0,0:392,358:0:2,0:26.1:1:30.4:1:1:0:60:186.5:0.9987:0:0.2 0/1:842:109:56,53:393,339:0.1295:2,2:24.8:1:29.9:1:0.68128:1.09707:60:108:0.13:0:1.2 -11 8246326 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=6e-05;SOR=0.39428;LSEQ=GTCCCAGTGGGTAAGGGGGG;RSEQ=GCTGCAGACAGAAGCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:86:12,74:10,101:0.4365:2,2:24.4:1:30:1:0.36215:1.63:60:13.333:0.4211:0:1.1 0/1:167:39:5,34:24,104:0.2335:2,2:24.5:1:30.3:1:0.47565:1.56534:60:38:0.2303:0:1.1 -11 8246343 . G A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15738;SOR=0.44913;LSEQ=GGGGGCTGCAGACAGAAGCC;RSEQ=GCCTGGCCTATGAGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:15:0,15:5,128:0.1014:1,1:26.1:1:32:1:1:0:60:30:0.1027:0:1 0/1:104:5:0,5:2,97:0.0481:1,0:25:1:30:1:1:0:60:10:0.049:0:1.6 -11 8246382 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.13125;SOR=Inf;LSEQ=GCTATGTGGGAGGTGGTGGG;RSEQ=GGAGTTTGTTCCTTGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:0,66:0:1,0:21.8:1:30.5:1:1:0:60:21:1:0:0.5 0/1:38:2:0,2:0,36:0.0526:1,0:25.5:1:31.5:1:1:0:60:4:0.0541:0:1.5 -11 8248426 . A T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50315;SOR=0;LSEQ=CATACACACACGCAACCCGC;RSEQ=TTTGCGTGCACGCCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:136,4:0.0141:1,2:23:1:32.5:1:0.06942:30.52118:60:4:0.0143:0:1 0/0:116:0:0,0:113,3:0:1,0:23.8:1:29.7:1:1:0:60:22.2:1:0:0.6 -11 8248440 . C G 158 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=69.51844;LSEQ=ACCCGCATTTGCGTGCACGC;RSEQ=TCCGCCGTGCTCCTGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:0,1:162,9:0.0058:2,0:2:0:13:0:0.05814:0:60:0:0:0:4 0/1:148:43:39,4:97,7:0.2905:2,2:29:1:29.3:1:0.7312:1.41765:60:20.5:0.2847:0:1.8 -11 8248457 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59524;SOR=2.37674;LSEQ=CGCCTCCGCCGTGCTCCTGG;RSEQ=CCATCCCAGCAGGCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:0,1:211,20:0.0043:2,0:19:0:14:0:0.09052:0:60:0:0:0:4 0/1:196:2:1,1:165,29:0.0102:2,2:24.5:1:28.5:1:0.28336:5.61102:60:4:0.0104:0:1 -11 8248482 . C T 172 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.84469;LSEQ=CCCAGCAGGCCTCAGGCTGG;RSEQ=GTCTGGGGAGTGTGTTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:4:0,4:272,80:0.0112:2,0:1:0:26.3:1:0.00293:0:60:8:0.0115:0:1.5 0/1:331:66:47,19:190,75:0.1994:2,2:22.6:1:28.6:1:1:1.02406:60:65:0.2006:0:1.5 -11 8248574 . G T 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGGTGATACACGTTGTCCC;RSEQ=GGCCCGCATCACCATCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:884:74:38,36:408,402:0.0837:2,2:26.6:1:30.9:1:0.90375:1.04:60:148:0.0845:0:1.2 0/0:1008:0:0,0:508,496:0:2,0:24.8:1:29.6:1:1:0:60:76.231:0.997:0:0.2 -11 8248650 . G A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10277;SOR=5.77793;LSEQ=CCTGTGGTGCCAAAGAGCCT;RSEQ=CCGAGGGAAGGGCGCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:1:1,0:169,352:0.0019:2,0:1:0:22:0:0.32567:0:60:2:0.0019:0:1 0/1:456:5:3,2:163,288:0.011:2,2:21:1:28.2:1:0.35911:2.64:60:10:0.0111:0:1.2 -11 8248698 . G A 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19447;SOR=Inf;LSEQ=AGCATTCTGGGAAGCTGGGT;RSEQ=GGCAGGGGGAAAGGAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:32,193:0:2,0:24.2:1:31.1:1:1:0:60:111.5:1:0:0.1 0/1:178:2:0,2:25,151:0.0112:2,0:29.5:1:33:0:1:0:60:4:0.0114:0:1 -11 8251654 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54545;SOR=0;LSEQ=AGTCCAAGGGCATAACGACC;RSEQ=GGGCCTTCCCCTCAGGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:28,0:0.0667:1,2:23:1:29:1:0.06667:0:60:4:0.0667:0:1 0/0:15:0:0,0:15,0:0:1,0:20:1:31.9:1:1:0:60:30:1:0:0 -11 8251803 . A G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGAGCTTTCTGAGCAGG;RSEQ=CAAGGGCTTGGGAGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:263,120:0:2,0:25.7:1:29.9:1:1:0:60:62.833:1:0:0.1 0/1:346:19:14,5:204,123:0.0549:2,2:27.5:1:30.8:1:0.46416:1.69:60:18:0.0533:0:1 -11 8251810 . C A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0262;SOR=Inf;LSEQ=CTTTCTGAGCAGGACAAGGG;RSEQ=TTGGGAGGCCAGGGTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:0:0,0:292,141:0:2,0:25.3:1:32:1:1:0:60:71.167:1:0:0.1 0/1:406:5:3,2:249,150:0.0123:2,2:18.2:1:26.4:1:1:1.10638:60:10:0.0126:0:1.4 -11 8251921 . G C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08708;LSEQ=CCCAGGCGGCAGTCACAGCA;RSEQ=GCACACTTGAGGCAGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:866:771:388,383:56,37:0.8903:2,2:25.1:1:30.6:1:0.07908:1.49331:60:63.25:0.8888:0:1.1 0/1:974:403:213,190:292,279:0.4138:2,2:24.1:1:30.2:1:0.60313:1.07:60:806:0.4172:0:1.2 -11 8284838 . A G 273 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.09586;LSEQ=GTGTGCCTGCGCGCCGCGGC;RSEQ=GGGGGCGAGGGGGTGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:560:556:391,165:0,0:0.9929:0,2:26.7:1:30:1:1:0:60:45.333:0.9927:0:1.7 1/1:460:457:301,156:0,0:0.9935:0,2:25.9:1:29.4:1:1:0:60:49.778:0.9978:0:1.5 -11 8284860 . G T 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29389;LSEQ=GGGGCGAGGGGGTGAGGGGC;RSEQ=TCGAGACCCCGGCCCGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:850:483:305,178:236,131:0.5682:2,2:25.1:1:30.7:1:0.77346:1.05135:60:79.5:0.5706:0:1.8 0/1:800:223:131,92:354,222:0.2788:2,2:23.1:1:29.8:1:0.51843:1.11971:60:43.6:0.2788:0:1.8 -11 8284981 . A C 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61321;SOR=2.13202;LSEQ=CGACTCGGGGCGCGCTTTGG;RSEQ=GGGGCGGCCGGTCTTCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:375:373:98,275:1,0:0.9947:0,2:22.9:1:29.9:1:0.26471:0:60:45.625:0.9973:0:1.8 1/1:399:398:116,282:1,0:0.9975:0,2:22.4:1:29.6:1:0.29323:0:60:55.857:0.9974:0:1.8 -11 8284995 . T C 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTTGGAGGGGCGGCCGGTC;RSEQ=TCGGGCAGCTAGCGGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:284:284:52,232:0,0:1:0,2:22.6:1:31.6:1:1:0:60:55.8:1:0:2 1/1:286:261:46,215:4,21:0.9126:2,2:24.2:1:31.1:1:1:1.12:60:86:0.9149:0:2.1 -11 8285009 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGTCTTCGGGCAGCTAGC;RSEQ=GGCTCTAATTACCCGCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:22,197:0:2,0:23.2:1:30.9:1:1:0:60:218:1:0:1.8 0/1:201:20:2,18:14,167:0.0995:2,2:27:1:31.8:1:0.66391:1.32:60:40:0.101:0:2.8 -11 8285124 . A C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69184;SOR=0.56723;LSEQ=CTCACCTACTTTTGTGCCTC;RSEQ=GAATTGGAAGGAACTACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:0,25:0,4:0.8621:0,1:24.4:1:30.5:1:1:0:60:50:0.8621:0:1.1 1/0:18:14:0,14:0,4:0.7778:0,1:23.8:1:28.9:1:1:0:60:13:0.7647:0:1.1 -11 8289880 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04833;SOR=Inf;LSEQ=GGTGCTGAGGGCTCTGCCGC;RSEQ=GCTAGCGGGGTGGACTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:70,19:0:2,0:16.4:1:30.9:1:1:0:60:178:1:0:0.1 0/1:52:3:2,1:41,8:0.0577:2,2:12.7:1:29.7:1:0.44158:2.5037:60:6:0.0577:0:1 -11 8289881 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.55937;SOR=3.23732;LSEQ=GTGCTGAGGGCTCTGCCGCC;RSEQ=CTAGCGGGGTGGACTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:1,0:73,20:0.0106:2,0:18:0:17:0:1:0:60:0:0:0:2 0/1:59:2:1,1:46,11:0.0339:2,2:7.5:1:30.5:1:0.36821:4.04707:60:4:0.0345:0:1 -11 8289932 . C T 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02711;SOR=Inf;LSEQ=CGCAGTCTCCGCCCCACGTC;RSEQ=CGCGTGCCCCCGGGCACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:235,132:0:2,0:25.7:1:30.9:1:1:0:60:90.75:1:0:0.2 0/1:349:5:2,3:222,122:0.0143:2,2:11.8:1:29:1:0.35386:2.72115:60:10:0.0143:0:1.2 -11 8289940 . C T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02867;SOR=Inf;LSEQ=CCGCCCCACGTCCCGCGTGC;RSEQ=CCCGGGCACCGGCACCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:274,173:0:2,0:24.7:1:30.9:1:1:0:60:48.667:1:0:0.2 0/1:434:5:1,4:257,172:0.0115:2,2:18.2:1:24.8:1:0.16317:5.95394:60:10:0.0116:0:1 -11 8290069 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.7823;LSEQ=TCCGACTCCCGCCGCCGGCC;RSEQ=CCTGCGCTGCTCCCGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:1:1,0:34,83:0.0085:2,0:1:0:26:0:0.29661:0:60:2:0.0087:0:1 0/1:133:2:1,1:43,88:0.015:2,2:14.5:1:27:1:1:2.03:60:4:0.0152:0:1 -11 8290075 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.09758;SOR=0;LSEQ=TCCCGCCGCCGGCCGCCTGC;RSEQ=CTGCTCCCGCCGGCCCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:2,1:22,69:0.0319:2,2:9.3:1:29:1:0.15923:6.12:60:6:0.033:0:1 0/0:109:0:0,0:33,76:0:2,0:11.7:1:31.1:1:1:0:60:218:1:0:0.3 -11 8291041 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCCAGGCTGGGCCACAGTG;RSEQ=TCTCCATCCGGTCACCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 8589648 . A G 222 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGGTACTTCCTTAGTACA;RSEQ=AATAATTGCCATCCAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:102,127:0:2,0:27.6:1:30.2:1:1:0:60:458:1:0:0.1 1/0:265:137:64,73:61,67:0.517:2,2:26.6:1:31.3:1:0.90245:1.03835:60:67.5:0.5172:0:1.1 -11 8852106 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24821;SOR=Inf;LSEQ=AATTCAGCGAGGGCTGCATT;RSEQ=CCTTACTGCCTGATGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:115,9:0:2,0:24.6:1:31.9:1:1:0:60:40.333:1:0:0.1 0/1:134:3:2,1:116,15:0.0224:2,2:30.7:1:30:0:0.31924:3.80636:60:6:0.0224:0:1 -11 8852112 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=GCGAGGGCTGCATTGCCTTA;RSEQ=TGCCTGATGGTGGAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:121,18:0:2,0:24.8:1:32.1:1:1:0:60:138:1:0:0.1 0/1:154:2:1,1:127,25:0.013:2,2:5.5:1:28.5:1:0.31008:5.00107:60:4:0.0134:0:1 -11 8852239 . C T 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14846;SOR=0.82954;LSEQ=CCCAACTCCTAAAGTATCTT;RSEQ=CCGCCTGTTCCTCCCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:457:251:108,143:100,106:0.5492:2,2:25.1:1:29.6:1:0.25786:1.2485:60:40.833:0.5469:0:1.2 1/0:571:287:123,164:128,154:0.5026:2,2:24.9:1:29.4:1:0.55542:1.10802:60:94.667:0.5081:0:1.1 -11 8852338 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=GAGGCTGAGCCTGAGCCCAT;RSEQ=AGAACAGCATGCAGACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:3,76:0:1,0:23.2:1:32.5:1:1:0:60:78:1:0:0.1 0/1:88:2:1,1:10,76:0.0227:2,2:19.5:1:31:1:0.23563:7.30:60:4:0.023:0:1 -11 9681965 . T A 32 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65206;SOR=0.46631;LSEQ=CCTTTCGGCCGGAACCGCCA;RSEQ=CTTCCAGTAATTCGCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:3:3,0:60,53:0.0259:2,0:15.7:1:20.7:1:0.2491:0:60:2:0.0196:0:3 0/1:164:2:2,0:81,79:0.0122:2,0:17.5:1:16:1:0.4972:0:47.5:1:0.007:0:5 -11 9681968 . T C 16 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6937;LSEQ=TTCGGCCGGAACCGCCATCT;RSEQ=CCAGTAATTCGCCAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:61,54:0.0171:2,2:29:1:32.5:1:1:1.12845:50:4:0.0189:0:1 0/1:168:2:2,0:83,82:0.0119:2,0:18.5:1:16.5:1:0.49715:0:60:0:0:0:3.5 -11 9682119 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.27376;SOR=Inf;LSEQ=ATTGTAGACATCAAGGGAAT;RSEQ=GGTACTGCTCAAAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:96,72:0:2,0:24.9:1:31.5:1:1:0:51.1:167:1:0:0.1 0/1:244:3:1,2:138,103:0.0123:2,2:14.7:1:26.7:1:0.57889:2.6689:49.3:6:0.0123:0:1 -11 9682126 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18129;SOR=0;LSEQ=ACATCAAGGGAATGGGTACT;RSEQ=CTCAAAAAGGAATGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:106,89:0.0102:2,2:46.5:1:29.5:1:1:1.18995:60:4:0.0104:0:1 0/0:265:0:0,0:153,112:0:2,0:24.5:1:31.6:1:1:0:48.2:530:1:0:0.1 -11 9682201 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22653;SOR=0;LSEQ=ATGTTACCCAGCATGCTGTT;RSEQ=GCATTGTTGTAAACAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:48,94:0.0139:2,2:17:1:29:1:1:1.95:41.5:4:0.0142:0:1 0/0:158:0:0,0:63,95:0:2,0:22.6:1:30.3:1:1:0:36.2:157:1:0:0.1 -11 9682401 . C T 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=GCTCCACCCAGAGAAGCACA;RSEQ=TTTGTGAGAACCAACGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:1:0:31:0:1:0:60:2:0.3333:0:1 1/0:6:3:0,3:0,3:0.5:0,0:22.7:1:31.7:1:1:0:53.3:6:0.5:0:1 -11 9846278 . C G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAATGGCAAAATACAAGAT;RSEQ=AGGTTGTGGGGTGGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 9848396 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGAGTGATCTCGGCTC;RSEQ=TTTTGCTCTTGTTGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:29.5:1:1:0:60:4:1:0:1 -11 11863712 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55002;SOR=Inf;LSEQ=CCCTCCCCCGGCAGGGCGGA;RSEQ=AGGAGCGGCCGGAGTCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:43,38:0:2,0:26:1:31.7:1:1:0:60:162:1:0:0.2 0/1:158:2:1,1:82,74:0.0127:2,2:29.5:1:28.5:1:1:1.10739:60:4:0.0129:0:1.5 -11 11863756 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53386;SOR=Inf;LSEQ=GTGCCCGGCGAGGAGAACCA;RSEQ=CTGGTCCCGAAAGAGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:39,50:0:2,0:29.4:1:29.7:1:1:0:60:43.5:1:0:0.2 0/1:154:2:1,1:68,84:0.013:2,2:42:0:32:1:1:1.23:60:4:0.0132:0:1 -11 12262281 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCTAGCCACCCTGGCC;RSEQ=GGCATGGGCTCTGGCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:22.5:1:1:0:60:1:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:6:1:30:1:1:0:60:4:1:0:1 -11 12264025 . T C 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59916;SOR=0.43406;LSEQ=TCTGTCCGTGTCTGGGTGAC;RSEQ=TCCTTTCTTCCCCTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:54,9:0.0308:2,2:7.5:1:28.5:1:0.28606:5.74461:60:4:0.0328:0:1 0/1:74:1:0,1:56,17:0.0135:2,0:1:0:29:0:0.24324:0:60:2:0.0135:0:1 -11 12264074 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23094;SOR=0;LSEQ=GGGTGGGTTCCTCCTCCCTC;RSEQ=GCCCACCCCCTGTCTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:112,41:0.0129:2,2:28.5:1:29:1:0.46979:2.71101:60:4:0.0129:0:1 0/0:167:0:0,0:102,65:0:2,0:27.4:1:30.3:1:1:0:60:54.667:1:0:0.4 -11 12264140 . A C 243 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.0047;LSEQ=GGCCCCCGGCTGCCTCCCTC;RSEQ=CCCACTTCTTGGAAGCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:248:247:124,123:1,0:0.996:0,2:26.1:1:30.6:1:1:0:60:48.4:0.9959:0:1.1 1/0:269:144:71,73:66,57:0.5353:2,2:26.6:1:30.2:1:0.53939:1.18973:60:143:0.5458:0:1.2 -11 12264214 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.88237;LSEQ=TCTCCTTTCTCACCTTCACT;RSEQ=CAGAAGAGGGCTCAGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:1:1,0:40,93:0.0075:2,0:1:0:23:0:0.30597:0:60:2:0.0076:0:3 0/1:143:2:1,1:53,88:0.014:2,2:34.5:1:29.5:1:1:1.65:60:4:0.0141:0:1.5 -11 13127828 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23874;SOR=Inf;LSEQ=CCTGAGAAATGAAGAGACTC;RSEQ=ATTTGAGAAATACACAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:108,38:0:2,0:23.7:1:30.1:1:1:0:60:72:1:0:0.1 0/1:140:2:1,1:89,49:0.0143:2,2:11.5:1:24.5:1:1:1.80805:60:4:0.0146:0:1.5 -11 13127893 . C A 206 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTCTGGAGGCCCTCACAAC;RSEQ=GAAAAGTGTGCATAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:161,145:0:2,0:27.7:1:30.2:1:1:0:60:75.5:1:0:0.1 0/1:292:108:57,51:95,89:0.3699:2,2:26:1:30.6:1:0.90361:1.05:60:107:0.3715:0:1.5 -11 13127942 . A T 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGGAACCTGTCAAGGATT;RSEQ=AAAAAGTGCTACCAGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:83,133:0:2,0:24.3:1:29:1:1:0:60:107:1:0:0.1 1/0:201:112:46,66:41,48:0.5572:2,2:25.6:1:28.5:1:0.56664:1.22429:60:224:0.5628:0:1.5 -11 13127951 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2293;SOR=Inf;LSEQ=TGTCAAGGATTAAAAAAGTG;RSEQ=TACCAGAGCACAGGAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:68,123:0:2,0:23.3:1:31.7:1:1:0:60:46.75:1:0:0.1 0/1:176:2:1,1:70,104:0.0114:2,2:34:1:27.5:1:1:1.48:60:4:0.0116:0:1.5 -11 13127964 . G A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11631;SOR=Inf;LSEQ=AAAAGTGCTACCAGAGCACA;RSEQ=GAGAGATGGCAGATGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:38,113:0:2,0:23:1:31.1:1:1:0:60:150:1:0:0.1 0/1:145:3:3,0:49,93:0.0207:2,0:13:1:20.7:1:0.04441:0:60:2:0.0139:0:1.7 -11 15511463 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20154;SOR=Inf;LSEQ=TGGAACTGTCTGATCTTTGG;RSEQ=GAAATCCACACTTGGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:116,26:0:2,0:25.2:1:31.6:1:1:0:60:141:0.993:0:0.5 0/1:117:2:1,1:85,30:0.0171:2,2:23.5:1:28.5:1:0.46139:2.80361:60:4:0.0174:0:1 -11 15511476 . T C 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00191;SOR=1.97714;LSEQ=TCTTTGGCGAAATCCACACT;RSEQ=GGGAGACATTCTGGAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:94:63,31:68,22:0.5109:2,2:23.1:1:30.2:1:0.25441:1.51743:60:93:0.5082:0:1.1 1/0:178:120:82,38:32,26:0.6742:2,2:19.7:1:29.4:1:0.09736:1.75:60:29:0.6705:0:1.2 -11 15511590 . C T 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.56919;SOR=0.91747;LSEQ=GTTCCGTTCACACTACAGCT;RSEQ=CCAGGTTAGGACCTCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:398:203:93,110:85,110:0.5101:2,2:24.6:1:29.9:1:0.68726:1.09:60:100.5:0.5128:0:1.1 0/1:391:191:88,103:105,95:0.4885:2,2:23.5:1:28.7:1:0.22511:1.29279:60:20.222:0.4789:0:1.1 -11 15511846 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=3.38757;LSEQ=CCTACATTACTCCAAAAAAC;RSEQ=CTAACAGGGCTGTATGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:36.5:1:33.5:1:1:0:60:4:0.4:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:17.5:1:31.5:1:1:0:60:4:0.6667:0:1 -11 17457039 . C G 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01428;SOR=Inf;LSEQ=CTTTAGAAACAAGGAGAAAA;RSEQ=TAGACCCTTTTCCACTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:149,5:0:1,0:24.4:1:31.8:1:1:0:59.7:37.5:1:0:0.1 0/1:117:5:5,0:106,6:0.0427:2,0:30.2:1:33.8:1:1:0:60:10:0.0427:0:1 -11 17457183 . A C 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21974;SOR=1.23816;LSEQ=GAAAGATGGGTGAATGTAAT;RSEQ=ATGTGTAGGAAGATGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1130:73:50,23:593,464:0.0646:2,2:12.8:1:32:1:0.0499:1.70:54.2:72:0.0645:0:4.9 0/1:1117:88:56,32:536,493:0.0788:2,2:12.2:1:31.5:1:0.04476:1.61:55.3:176:0.0796:0:5.2 -11 17457210 . C T 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35052;SOR=1.16976;LSEQ=AGGAAGATGATGCTGGGAAC;RSEQ=TCTGTTCTTCACATGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1116:85:61,24:555,475:0.0762:2,2:31:1:30.5:1:0.00141:2.17:51.7:20.25:0.0738:0:4.9 0/1:1080:95:59,36:517,465:0.088:2,2:32.2:1:30.2:1:0.08506:1.47:55:30.667:0.0857:0:5.1 -11 17457213 . TGT CAC 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75812;SOR=1.05709;LSEQ=AAGATGATGCTGGGAACCTC;RSEQ=TCTTCACATGGCTGCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1129:92:69,23:557,478:0.0815:2,2:26.2:1:31.3:1:7e-05:2.57:50.5:184:0.0826:0.008:2.7 0/1:1073:92:55,37:514,463:0.0857:2,2:28.1:1:30.7:1:0.19192:1.34:54.9:184:0.0865:0:3.1 -11 17457343 . C T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96891;LSEQ=TCAAGTGTCAGACCCCATTC;RSEQ=AGATATGATACATGAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:999:14:12,2:463,522:0.014:2,2:10.5:1:31.5:1:0.00518:6.75:38.7:28:0.0143:0:5.3 0/1:957:13:11,2:450,494:0.0136:2,2:7.5:1:30.2:1:0.00999:6.03:39.2:12:0.0127:0:5.1 -11 17457346 . A G 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.8874;SOR=1.07212;LSEQ=AGTGTCAGACCCCATTCCAG;RSEQ=TATGATACATGAGAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:991:25:18,7:453,512:0.0252:2,2:6.5:1:31:1:0.01479:2.90:36.2:50:0.0256:0:6.8 0/1:963:26:16,10:445,490:0.027:2,2:6.1:1:29.3:1:0.16972:1.76:38.1:12:0.0254:0:6.8 -11 17457388 . T A 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.09418;SOR=0.78756;LSEQ=TGAGTGCAAACTTAGCTGTG;RSEQ=GGATCAGTGCTGGCCCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1036:126:62,64:440,470:0.1216:2,2:33.5:1:30.5:1:0.92428:1.03:34.5:41:0.1204:0:7.2 0/1:1068:105:43,62:487,476:0.0983:2,2:32.9:1:30:1:0.06477:1.47464:39.1:210:0.0989:0:7.3 -11 17457390 . G A 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08146;SOR=0.77921;LSEQ=AGTGCAAACTTAGCTGTGTG;RSEQ=ATCAGTGCTGGCCCCGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1016:126:62,64:423,466:0.124:2,2:34.9:1:30:1:0.77524:1.07:34.5:62:0.124:0:7.2 0/1:1067:106:44,62:480,480:0.0993:2,2:34:1:29.3:1:0.10221:1.40863:39.3:212:0.1012:0:7.2 -11 17457406 . G A 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0485;SOR=0.76629;LSEQ=TGTGGATCAGTGCTGGCCCC;RSEQ=GACACAGGGACTTCACGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1023:144:80,64:413,464:0.1408:2,2:36.7:1:30.6:1:0.07169:1.40:35.1:47:0.1417:0:7.2 0/1:1085:121:60,61:483,481:0.1115:2,2:36.6:1:30.6:1:0.92349:1.02088:38.9:120:0.1124:0:7.4 -11 17457422 . C G 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11655;SOR=0.80191;LSEQ=CCCCGGACACAGGGACTTCA;RSEQ=GCATTCCAAATAAGACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1014:133:71,62:416,464:0.1312:2,2:31:1:32:1:0.19373:1.28:34.8:65.5:0.1307:0:7.5 0/1:1028:111:50,61:447,466:0.108:2,2:32.1:1:31.5:1:0.48177:1.17008:38.7:110:0.1075:0:7.6 -11 17457424 . CA AG 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2772;SOR=0.86597;LSEQ=CCGGACACAGGGACTTCACG;RSEQ=TTCCAAATAAGACTCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1012:149:86,63:413,443:0.1472:2,2:26.2:1:31.7:1:0.03353:1.46:36.9:298:0.1507:0.0208:6.8 0/1:1038:135:72,63:443,459:0.1301:2,2:26.3:1:31.3:1:0.40631:1.18:40.8:270:0.1315:0.0241:6.9 -11 17457434 . A T 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23889;SOR=0.85924;LSEQ=GGACTTCACGCATTCCAAAT;RSEQ=AGACTCAAAGTTCCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1011:161:91,70:407,442:0.1592:2,2:20.2:1:28.9:1:0.04826:1.41:37.6:22:0.1557:0:6.8 0/1:1036:145:81,64:450,440:0.14:2,2:20.4:1:29.6:1:0.24529:1.24:41:144:0.1406:0:7 -11 17457456 . T C 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44573;SOR=0.89574;LSEQ=GACTCAAAGTTCCCAGGGAG;RSEQ=AACAGGGCCAACATGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:918:122:80,42:373,423:0.1329:2,2:18.4:1:32:1:0.00014:2.16:40.9:121:0.1336:0:7.4 0/1:961:116:79,37:407,437:0.1207:2,2:19.1:1:31.9:1:7e-05:2.29:42.4:232:0.1216:0:7.4 -11 17457466 . A T 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5838;SOR=0.91716;LSEQ=TCCCAGGGAGTAACAGGGCC;RSEQ=ACATGCCAAAAAGAGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:858:92:64,28:354,412:0.1072:2,2:27.3:1:29.9:1:2e-05:2.66:44.3:91:0.1079:0:7.7 0/1:897:89:70,19:368,439:0.0992:2,2:27.6:1:30:1:0:4.39:43.2:88:0.0992:0:7.7 -11 17457479 . G A 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12863;SOR=0.80917;LSEQ=CAGGGCCAACATGCCAAAAA;RSEQ=AGAGACCCCTGCACTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:134:76,58:323,418:0.153:2,2:23.7:1:29.4:1:0.00614:1.69:46.1:133:0.1539:0:7.8 0/1:855:109:70,39:342,404:0.1275:2,2:26.5:1:29.4:1:0.00044:2.12:44.1:108:0.1269:0:7.8 -11 17457487 . CC TT 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14459;SOR=0.8135;LSEQ=ACATGCCAAAAAGAGAGACC;RSEQ=TGCACTCAAAGCAATACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:856:132:72,60:304,419:0.1542:2,2:27.1:1:29.7:1:0.00986:1.65:46.4:131:0.1561:0.0199:7.1 0/1:844:109:70,39:331,404:0.1291:2,2:28.1:1:29.5:1:2e-04:2.19:44:218:0.1304:0.0154:7 -11 17457495 . C T 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31248;SOR=0.85967;LSEQ=AAAAGAGAGACCCCTGCACT;RSEQ=AAAGCAATACCAGTGCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:120:59,61:288,399:0.1485:2,2:29.9:1:28.9:1:0.16167:1.34:48.2:240:0.1508:0:6.9 0/1:790:103:59,44:301,386:0.1304:2,2:28.6:1:28.6:1:0.01103:1.72:45.3:102:0.1306:0:6.8 -11 17457506 . C T 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33032;SOR=0.87159;LSEQ=CCCTGCACTCAAAGCAATAC;RSEQ=AGTGCCACGGTGGCAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:763:128:63,65:262,372:0.1678:2,2:28.4:1:29.1:1:0.1168:1.38:48.8:127:0.1684:0:6.7 0/1:783:117:64,53:281,383:0.1494:2,2:24.6:1:28.8:1:0.01524:1.64:46.7:57.5:0.1488:0:6.4 -11 17457532 . G A 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01486;SOR=0.68375;LSEQ=CACGGTGGCAGATGGACATC;RSEQ=CCATGGGAAGAGACCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:115:47,68:189,304:0.1891:2,2:27.4:1:29.5:1:0.67099:1.11:49.9:27.75:0.1885:0:6.7 0/1:669:92:38,54:225,352:0.1375:2,2:25.7:1:29.9:1:0.73047:1.10:47.9:184:0.1396:0:6.5 -11 17457546 . C T 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19119;SOR=0.80304;LSEQ=GACATCGCCATGGGAAGAGA;RSEQ=CAACTGTAGATAGTGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:550:96:33,63:167,287:0.1745:2,2:24.5:1:30.8:1:0.72646:1.11069:50.5:192:0.1761:0:6.8 0/1:565:82:25,57:170,312:0.1451:2,2:22.3:1:29.2:1:0.452:1.24184:49.7:164:0.1459:0:6.7 -11 17457559 . G A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13368;SOR=0.76054;LSEQ=GAAGAGACCAACTGTAGATA;RSEQ=TGATGTGGGGAGATATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:85:31,54:145,279:0.167:2,2:20.6:1:30.8:1:0.70867:1.10:51.3:170:0.168:0:6.8 0/1:499:66:21,45:155,278:0.1323:2,2:21.5:1:29.8:1:0.58182:1.19432:52.8:132:0.1336:0:6.8 -11 17457575 . TGGGACAG AAAACAC 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37422;SOR=0.78954;LSEQ=GATAGTGATGTGGGGAGATA;RSEQ=TTTGAACTTGTGTTCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:37:15,22:129,237:0.0916:2,2:27:1:30.8:1:0.58984:1.25:50.9:74:0.0925:0.0297:4.1 0/1:407:30:10,20:145,230:0.0737:2,2:30.1:1:30.2:1:0.69704:1.26017:54.3:60:0.0748:0.0147:4.4 -11 17457590 . T C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61089;SOR=0.85258;LSEQ=AGATATGGGACAGTTTGAAC;RSEQ=TGTGTTCTTATTCCAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:36:16,20:127,199:0.0992:2,2:21.1:1:31.6:1:0.59087:1.25:46.4:35:0.0992:0:7.4 0/1:373:32:10,22:144,197:0.0858:2,2:24:1:31.2:1:0.26323:1.60616:52.9:64:0.0872:0:7.6 -11 17457614 . C T 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72958;SOR=0.91601;LSEQ=GTTCTTATTCCAGAACTGCT;RSEQ=CATCTCTTCTTTGGCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:46:14,32:134,187:0.1247:2,2:20.2:1:29.7:1:0.1521:1.63578:39.8:92:0.1289:0:6 0/1:338:39:10,29:140,158:0.1154:2,2:19.6:1:29:1:0.01563:2.56301:43.9:78:0.1171:0:5.7 -11 17457630 . TG CA 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06904;SOR=0.60019;LSEQ=TGCTCCATCTCTTCTTTGGC;RSEQ=TGATTCCCAAAGGAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:43:14,29:144,194:0.1117:2,2:29.7:1:30.9:1:0.25083:1.53587:39.9:86:0.1144:0.026:5.3 0/1:328:23:5,18:144,158:0.0701:2,2:37.4:1:30.3:1:0.01715:3.27051:38.6:46:0.0721:0:4.7 -11 17457634 . A G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42915;SOR=0.79867;LSEQ=CCATCTCTTCTTTGGCTGTG;RSEQ=TTCCCAAAGGAACAGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:37:12,25:149,193:0.0976:2,2:38.6:1:31.7:1:0.22273:1.60643:38.6:74:0.0984:0:4.8 0/1:327:26:5,21:148,153:0.0795:2,2:35.7:1:31:1:0.00362:4.04787:38.7:52:0.0805:0.0092:4.6 -11 17457643 . G GCAACCATCA 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.79513;SOR=0.93258;LSEQ=CTTTGGCTGTGATTCCCAAA;RSEQ=GAACAGCATTTCTGGTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:34:11,23:148,186:0.0921:2,2:44.5:1:31:1:0.20617:1.66152:40.2:33:0.0909:0:5.7 0/1:347:30:7,23:163,154:0.0865:2,2:35.1:1:30.5:1:0.00374:3.46621:37.4:60:0.0877:0.0231:5.4 -11 17457650 . C T 51 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37396;SOR=0.26041;LSEQ=TGTGATTCCCAAAGGAACAG;RSEQ=ATTTCTGGTACAGAGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:4:2,2:161,204:0.0108:2,2:28.8:1:25.5:1:1:1.27:56.3:3:0.0083:0:2.3 0/0:352:1:0,1:172,179:0.0028:2,0:1:0:23:0:1:0:60:2:0.0029:0:3 -11 17457658 . G A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60058;SOR=0.86616;LSEQ=CCAAAGGAACAGCATTTCTG;RSEQ=TACAGAGCTGAGGGCTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:34:10,24:159,172:0.0929:2,2:25.9:1:31.1:1:0.04653:2.21401:39.2:68:0.0942:0:5.7 0/1:356:29:6,23:172,154:0.0815:2,2:21.3:1:30.8:1:0.00088:4.26546:37.3:58:0.0841:0:5.4 -11 17457685 . C T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43357;SOR=1.43534;LSEQ=GCTGAGGGCTAAAGTGGGCT;RSEQ=GGAGGCAATGACAACCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:11:4,7:135,177:0.0341:2,2:9.5:1:28.6:1:0.76297:1.33358:32.8:22:0.0344:0:6.5 0/1:332:16:3,13:145,171:0.0482:2,2:11.9:1:30.5:1:0.03924:3.66198:36.1:32:0.0492:0:5.5 -11 17457693 . A G 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41393;SOR=1.65417;LSEQ=CTAAAGTGGGCTCGGAGGCA;RSEQ=TGACAACCAACATGTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:5:2,3:126,172:0.0165:2,2:12.2:1:30.6:1:1:1.09852:32:10:0.0167:0:7 0/1:296:8:2,6:129,158:0.027:2,2:12.8:1:32.3:1:0.30719:2.44257:32.4:16:0.0274:0:5 -11 17457697 . C T 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=AGTGGGCTCGGAGGCAATGA;RSEQ=AACCAACATGTCTCAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:120,171:0:2,0:25:1:32.1:1:1:0:59.7:144.5:0.9966:0:0.2 0/1:296:13:6,7:124,159:0.0439:2,2:23.7:1:29.2:1:1:1.10:59.5:26:0.0444:0:1.3 -11 17457698 . AA GG 81 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12276;SOR=6.04773;LSEQ=GTGGGCTCGGAGGCAATGAC;RSEQ=CCAACATGTCTCAGCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:0,1:119,169:0.0034:2,0:25:0:27:0:1:0:27:2:0.0035:0:7 0/1:292:6:2,4:125,161:0.0205:2,2:11.3:1:31.6:1:0.70023:1.55055:30:12:0.0208:0:4.8 -11 17457720 . CA TG 79 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06539;SOR=0.15968;LSEQ=CCAACATGTCTCAGCAAGAG;RSEQ=CAGCCATCTTGGGTTCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:6:0,6:84,149:0.025:2,0:14.3:1:30.8:1:0.09323:0:24.3:12:0.0253:0:2.7 0/0:246:1:0,1:98,147:0.0041:2,0:17:0:29:0:1:0:25:2:0.0042:0:6 -11 17457739 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22245;SOR=0;LSEQ=GCACAGCCATCTTGGGTTCT;RSEQ=GTCTGGATGGAAGTGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:52,117:0.0117:2,2:13.5:1:28:1:0.52508:2.24:60:4:0.012:0:1.5 0/0:191:0:0,0:68,123:0:2,0:26.4:1:30.3:1:1:0:60:94.5:1:0:0.2 -11 17733984 . C A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27477;LSEQ=TTGTGTTGTTTAGTAAACAG;RSEQ=GCATGTGTATTTCAAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:777:326:186,140:245,203:0.4196:2,2:24.3:1:30:1:0.55779:1.10:60:39.75:0.4179:0:1.1 0/1:767:127:72,55:352,286:0.1656:2,2:24.9:1:29.1:1:0.77021:1.06:60:41.333:0.1645:0:1.1 -11 17734179 . G C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.31893;LSEQ=GCCTCAGCTTCCCCTACCTG;RSEQ=TGGGCAGTCTCAGCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:63:5,58:15,65:0.4406:2,2:25.2:1:32.6:1:0.08863:2.65976:60:62:0.4397:0:1.1 0/1:105:21:2,19:14,70:0.2:2,2:31.1:1:32.8:1:0.51817:1.88997:60:42:0.2:0:1 -11 17740991 . A AC 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTGCGGCCACCCCGGGG;RSEQ=CCCCCCCAAGCCCCGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:25:1:33:0:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 17741244 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.519;SOR=0;LSEQ=GCACTTTGCTATCTACAGCC;RSEQ=GGGCTCCCGAGCGGCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:130,12:0.0139:2,2:28:1:29:1:0.17298:10.44838:60:4:0.014:0:1.5 0/0:95:0:0,0:86,9:0:2,0:23.5:1:29:1:1:0:60:46.5:1:0:0.1 -11 17741265 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52235;SOR=0;LSEQ=GGGCTCCCGAGCGGCAGAAA;RSEQ=TTCCGGCCACTCTCTGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:170,29:0.01:2,2:19.5:1:27.5:1:0.27687:5.78051:60:4:0.0101:0:1 0/0:129:0:0,0:107,22:0:2,0:24.6:1:31.8:1:1:0:60:258:1:0:0.1 -11 17741542 . G A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01262;SOR=Inf;LSEQ=TTCCCCGCGGCGGTGCACCC;RSEQ=GCCCCGGGCGCACGTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:115,307:0:2,0:24.5:1:30.2:1:1:0:60:37.364:1:0:0.1 0/1:396:6:4,2:121,268:0.0152:2,2:22.5:1:28:1:0.0827:4.41:60:12:0.0154:0:1 -11 17741786 . G A 87 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05751;SOR=0.23295;LSEQ=AGGTGGAGATCCTGCGCAAC;RSEQ=CCATCCGCTATATCGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:8:5,3:253,434:0.0115:2,2:17.1:1:29:1:0.15487:2.85:60:16:0.0117:0:1.1 0/0:740:2:2,0:295,443:0.0027:2,0:1:0:25.5:1:0.16076:0:60:4:0.0028:0:1 -11 17741838 . CGC AG 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10933;SOR=Inf;LSEQ=GCTGCGCGACCAGGACGCCG;RSEQ=CCCCTGGCGCCGCAGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:48,203:0:2,0:23.7:1:30.8:1:1:0:60:502:1:0:0.1 0/1:231:3:2,1:61,167:0.013:2,2:16.7:1:30:1:0.18139:5.43:60:6:0.013:0.0043:1.3 -11 17741892 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49811;SOR=Inf;LSEQ=GGGCCCGCTGCCCCCGGGCC;RSEQ=CGGCGGCGAGCACTACAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:0:2,0:18.5:1:31.1:1:1:0:60:48:1:0:0.3 0/1:57:2:1,1:35,19:0.0351:2,2:39:1:29.5:1:1:1.821:60:4:0.0364:0:1 -11 17741955 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2181;SOR=Inf;LSEQ=GCGCTCCAACTGCTCCGACG;RSEQ=CATGGTAAGGCCGGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:58,43:0:2,0:27.3:1:30.7:1:1:0:60:15.833:1:0:0.3 0/1:89:2:1,1:47,40:0.0225:2,2:14.5:1:31.5:1:1:1.17286:60:4:0.023:0:1 -11 17742320 . C G 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00512;SOR=Inf;LSEQ=CCCACCCGTAATTACCCCCC;RSEQ=AACCAGGACAGGTCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:143,3:0:1,0:23.1:1:30.8:1:1:0:60:35.5:1:0:0.2 0/1:80:5:5,0:72,3:0.0625:1,0:29.4:1:29:1:1:0:60:10:0.0633:0:1 -11 17742398 . G C 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTACAGGAATTGGTGTTC;RSEQ=GGCCTCGAGCCGTCCCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:572:0:0,0:376,192:0:2,0:24.2:1:29.6:1:1:0:60:39.571:0.9946:0:0.1 0/1:536:22:15,7:327,185:0.041:2,2:26.9:1:29.4:1:0.82182:1.21:60:21:0.0397:0:1.3 -11 17742600 . TC T 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTGGCCTCTATCTAGGACGC;RSEQ=CCACCCCCACTCACACACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:117,309:0:2,0:24.2:1:30.6:1:1:0:60:37.727:1:0:0.2 0/1:334:14:4,10:99,221:0.0419:2,2:20:1:30.6:1:1:1.11953:60:28:0.0428:0.012:0.2 -11 17742681 . G C 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAAGTAGCTCCCTGTCTTTT;RSEQ=GATTGTCCCGGACTCTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:197:173:90,83:11,12:0.8782:2,2:22.1:1:31.1:1:0.82508:1.18:60:172:0.8866:0:1.1 1/1:116:116:76,40:0,0:1:0,2:24.5:1:31.2:1:1:0:60:232:1:0:1.1 -11 17742690 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51976;SOR=0;LSEQ=CCCTGTCTTTTGGATTGTCC;RSEQ=GGACTCTAACTAAAGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:2,0:113,72:0.0107:2,0:13.5:1:32:1:0.52389:0:60:4:0.0109:0:1.5 0/0:123:0:0,0:92,31:0:2,0:24.3:1:30.3:1:1:0:60:60.5:1:0:1 -11 17746770 . G A 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCACTCCAGCTCTGGGCA;RSEQ=TAGAGCAAGACTCCATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:33,0:0,0:1:0,1:21.8:1:30.7:1:1:0:60:66:1:0:1 1/1:11:11:11,0:0,0:1:0,0:21.1:1:29.6:1:1:0:60:10:1:0:1.1 -11 17746976 . G T 169 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01879;LSEQ=CAAGAGGGAAGGGAACAGCT;RSEQ=GAGACTGGATCACACCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1194:50:27,23:634,510:0.0419:2,2:23.4:1:30:1:0.88498:1.05889:60:100:0.0426:0:1.2 0/0:1220:1:0,1:651,568:8e-04:2,0:1:0:24:0:0.46639:0:60:2:8e-04:0:1 -11 18586080 . TA T 141 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.85704;SOR=1.12284;LSEQ=ATGTAAGAAAAGGCCATCTT;RSEQ=AAAAAAAAAAAGCCAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:13:8,5:55,25:0.1368:2,2:23.6:1:30.2:1:0.75011:1.37016:60:26:0.1413:0.0421:0.6 0/1:172:26:15,11:90,49:0.1512:2,2:23.2:1:30:1:0.51139:1.3444:60:52:0.152:0.0233:0.4 -11 18586122 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18861;LSEQ=AGAAAGAGCTAAAATTACTA;RSEQ=ATTAAATGAGTTTAATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:60:36,24:43,32:0.4348:2,2:26.7:1:28.6:1:0.8607:1.12:60:11:0.4508:0:1.3 0/1:222:28:16,12:96,96:0.1261:2,2:27.1:1:27.5:1:0.5467:1.33:60:8.333:0.1225:0:1.3 -11 18586184 . C A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13539;SOR=Inf;LSEQ=AAAAGAATTTGTGATTAAGT;RSEQ=ATATGAATGTCAAATTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:64,84:0:2,0:25.1:1:31.3:1:1:0:60:296:1:0:0.3 0/1:192:4:3,1:72,116:0.0208:2,2:18.3:1:23.5:1:0.30125:4.79:60:3:0.0159:0:1.5 -11 18586344 . C CAT 78 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33308;SOR=0.25066;LSEQ=GCCAAAATAAGGTTTTCCCA;RSEQ=GACAAAATGAAGGCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:0,6:0,7:0.4615:0,0:21.7:1:30.4:1:1:0:60:12:0.4615:0.1538:0.3 0/1:6:1:0,1:0,5:0.1667:0,0:14:0:31.5:0:1:0:60:2:0.1667:0:0 -11 19497688 . A C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCGCCACCATGTCCAGCTA;RSEQ=TTTTTGTATTTTTAGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 19498582 . T A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCTCCATCATATTGCAT;RSEQ=CCCAAGGGGTCCTTTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:1:0,1:15.1:1:28.9:1:1:0:60:32:1:0:1.8 1/1:4:4:4,0:0,0:1:0,0:18:1:29:1:1:0:60:8:1:0:1.8 -11 19498649 . G T 162 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00279;SOR=0;LSEQ=TGGCCAGTCTTGGGTCAAGC;RSEQ=AAATGATTTTTTTGGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:39,0:0,0:1:0,1:19.6:1:30.7:1:1:0:60:38:1:0:2 1/0:26:20:20,0:6,0:0.7692:0,1:21:1:31.5:1:1:0:60:40:0.7692:0:2.1 -11 19498655 . A AT 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50982;SOR=0;LSEQ=GTCTTGGGTCAAGCGAAATG;RSEQ=TTTTTTTGGATAAGACTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:2,0:44,0:0.0435:1,0:12:1:29:1:1:0:60:4:0.0455:0.0217:2 0/0:32:0:0,0:32,0:0:1,0:19.8:1:28.3:1:1:0:60:15:1:0:1.4 -11 19498686 . C T 196 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAGACTATCCAAACCCTTC;RSEQ=CAAGGTAAAGTCAGGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:71:71,0:0,0:1:0,1:26.3:1:32:1:1:0:60:70:1:0:1.5 1/0:54:29:29,0:25,0:0.537:1,1:30:1:30.9:1:1:0:60:58:0.537:0:1.6 -11 19498860 . C G 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.00759;LSEQ=TTTTGCCACTTACATTACAC;RSEQ=AAAACCTCCTAGAAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:358:355:137,218:0,1:0.9916:0,2:25.8:1:30.4:1:1:0:60:87.75:0.9943:0:1.5 0/1:414:195:92,103:93,124:0.471:2,2:24.9:1:30.2:1:0.42754:1.19:60:96.5:0.4684:0:1.7 -11 19498866 . C T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.00016;SOR=Inf;LSEQ=CACTTACATTACACCAAAAC;RSEQ=TCCTAGAAGGCAGGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:122,217:0:2,0:24.5:1:31.4:1:1:0:60:66.8:0.9911:0:1.6 0/1:392:14:6,8:167,210:0.0357:2,2:32:1:30:1:1:1.06017:60:28:0.0361:0:3 -11 19498907 . T C 237 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACTGATTTTGTTTGCATTA;RSEQ=TTATTATATTTTGTGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:167:167:36,131:0,0:1:0,2:24.2:1:32.2:1:1:0:60:82.5:1:0:2.3 1/0:219:114:37,77:26,78:0.5205:2,2:25.9:1:31.4:1:0.23556:1.44:60:113:0.5231:0:2.4 -11 19498915 . AT A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50677;SOR=Inf;LSEQ=TTGTTTGCATTATTTATTAT;RSEQ=TTTGTGCATTGAAACAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:26,120:0:2,0:24.4:1:30.1:1:1:0:60:28.2:1:0:2.3 0/1:189:2:1,1:50,137:0.0106:2,2:12:1:31.5:1:0.46792:2.72:60:4:0.0107:0.0053:4 -11 19498936 . T A 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTTGTGCATTGAAACAGTT;RSEQ=ATCAGCAAGGATTTATTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:13,93:0,0:1:0,2:24.2:1:30.3:1:1:0:60:105:1:0:2.3 1/1:124:102:21,81:4,18:0.8226:2,2:24.2:1:29.1:1:1:1.17:60:204:0.8226:0:2 -11 19499060 . G A 104 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13725;SOR=0;LSEQ=TGTGAATTTTGCATTCAGAC;RSEQ=GAACTGGGTCTATGTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:26.6:1:30.2:1:1:0:60:10:1:0:1 1/0:7:5:0,5:0,2:0.7143:0,0:29:1:32:1:1:0:60:10:0.7143:0:1 -11 19499168 . T C 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAAATTTACAACCTTCA;RSEQ=GAGGGTCCCCAGCATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:16.3:1:31.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 20245648 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGGTAAAGCATAGTGCA;RSEQ=TTGTGTTATTTTTAAGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 20245673 . TG T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTATTTTTAAGATTGCAAA;RSEQ=AGAGGAATTCAATCTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 20246591 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51603;SOR=Inf;LSEQ=CCATGGTAATGATGCTTAGT;RSEQ=CAGTCGCAAGTCATTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:36,20:0:2,0:26:1:31.4:1:1:0:60:55:0.9821:0:0.2 0/1:85:2:1,1:48,35:0.0235:2,2:20.5:1:26:1:1:1.36624:60:4:0.0238:0:1 -11 20246592 . C T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17529;SOR=0;LSEQ=CATGGTAATGATGCTTAGTG;RSEQ=AGTCGCAAGTCATTGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:38,21:0.0328:2,2:20.5:1:25.5:1:1:1.79094:60:4:0.0339:0:1.5 0/0:84:0:0,0:48,36:0:2,0:27:1:31.6:1:1:0:60:168:1:0:0.1 -11 20246597 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50714;SOR=Inf;LSEQ=TAATGATGCTTAGTGCAGTC;RSEQ=CAAGTCATTGAAAGATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:44,25:0:2,0:24.1:1:29.9:1:1:0:60:68:1:0:0.2 0/1:92:2:1,1:50,40:0.0217:2,2:19:1:28.5:1:1:1.24694:60:4:0.0217:0:1 -11 20246599 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18734;SOR=0;LSEQ=ATGATGCTTAGTGCAGTCGC;RSEQ=AGTCATTGAAAGATTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:46,25:0.0274:2,2:17.5:1:28:1:1:1.82385:60:4:0.0278:0:1 0/0:95:0:0,0:51,43:0:2,0:27.4:1:29.5:1:1:0:60:188:0.9895:0:0.1 -11 20246743 . C A 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06372;SOR=0;LSEQ=AGATTGATACTAGTGGGAAC;RSEQ=CCTTGGAGATTACTTAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:0,10:0,13:0.4348:1,0:22.7:1:31.6:1:1:0:60:20:0.4348:0:1 0/0:7:0:0,0:1,6:0:2,0:20.4:1:31.6:1:1:0:60:14:1:0:0 -11 20575654 . G C 153 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01919;LSEQ=GTGCTAGGTGTGGGGTTAGA;RSEQ=TGGGGAGCAAGATGGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:33:32,1:48,3:0.3929:2,1:30.2:1:30.5:1:1:1.99:60:10:0.3704:0:1.1 0/1:83:1:1,0:72,10:0.012:2,0:16:0:33:0:1:0:60:2:0.012:0:1 -11 20575682 . A T 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGATGGAGATGATGCTGC;RSEQ=TTATCAGAGTTTATTATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:124,38:0:2,0:21.2:1:29.7:1:1:0:60:80:1:0:0.3 0/1:155:45:30,15:79,31:0.2903:2,2:19.7:1:29.2:1:0.56373:1.27213:60:90:0.2941:0:1.1 -11 20575717 . A T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62659;SOR=2.66007;LSEQ=TATCTAGAAATTAGGTAAGC;RSEQ=TTTAAAGGGTGATAAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:1:0,1:159,103:0.0038:2,0:1:0:23:0:0.39544:0:60:2:0.0039:0:2 0/1:298:3:1,2:176,119:0.0101:2,2:16.7:1:27.7:1:0.56835:2.94715:60:6:0.0101:0:1.3 -11 20575787 . G C 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.71113;SOR=0.94317;LSEQ=AGTGTACTGGCCAGCATCCT;RSEQ=CCCACACATCCCCTCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:165:66,99:74,87:0.5061:2,2:24.5:1:30.8:1:0.31414:1.27489:60:54:0.511:0:1.2 0/1:411:202:97,105:95,111:0.4915:2,2:26.1:1:30.3:1:0.76609:1.08:60:32.667:0.4864:0:1.2 -11 20575883 . C G 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGAATATTTAAAATGAAAAC;RSEQ=TTGCAAGATGATAGTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:7,68:0:2,0:24.5:1:31.7:1:1:0:60:24:1:0:0.1 0/1:103:20:4,16:16,66:0.1942:2,2:19.5:1:29.8:1:1:1.03:60:19:0.19:0:1.4 -11 20575937 . G A 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05015;SOR=Inf;LSEQ=TCAAAGTCATATGGTTTTCA;RSEQ=TGTGAAGATGTCAGGATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:1,23:0:1,0:22.1:1:32.4:1:1:0:60:23:1:0:0 0/1:25:5:0,5:1,19:0.2:1,0:20:1:31:1:1:0:60:10:0.2174:0:2.2 -11 20575982 . CCCTT C 45 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=4;SSF=0.20879;SOR=0;LSEQ=CCCTCCCTCCCTCCCTCCCT;RSEQ=CCTTCCTTCCTTTGCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,6:0.375:0,0:24.3:1:29:1:1:0:60:6:0.375:0.25:0.7 0/0:6:0:0,0:0,6:0:0,0:24.7:1:31.5:1:1:0:60:12:1:0:0.8 -11 20576595 . T C 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGTGGGGATTATTACAA;RSEQ=TCAAGGTGAGATTTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:33.5:1:1:0:60:4:1:0:1 -11 21635224 . A T 32 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37212;SOR=0.32948;LSEQ=ATACCACCTGAGGCTTAATC;RSEQ=AATATTTTCTGATTAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:2,1:135,79:0.0138:2,2:11.3:1:20.7:1:1:1.17:60:2:0.0093:0:1 0/0:218:1:0,1:136,80:0.0046:2,0:1:0:22:0:0.37327:0:60:2:0.0047:0:1 -11 21635226 . A G 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01232;SOR=1.64241;LSEQ=ACCACCTGAGGCTTAATCAA;RSEQ=TATTTTCTGATTAGCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:83:58,25:81,56:0.3739:2,2:26.9:1:31.6:1:0.11536:1.60:60:40.5:0.3699:0:1.9 0/1:218:108:70,38:66,44:0.4954:2,2:24.7:1:31.6:1:0.48702:1.23:60:107:0.4977:0:1.7 -11 21635282 . C G 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.11883;LSEQ=TCTAATAAACTGACAATCAG;RSEQ=GGTAATGGGAGCTGCTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:101:53,48:95,101:0.3378:2,2:25.7:1:31.2:1:0.54167:1.17:60:202:0.3459:0:2.3 1/0:304:158:79,79:72,73:0.5197:2,2:24.7:1:30.2:1:1:1.01:60:157:0.5251:0:1.6 -11 21635295 . T G 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAATCAGCGGTAATGGGAGC;RSEQ=GCTAGACAGGAGGGAAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:94:47,47:88,102:0.3298:2,2:27.1:1:30.5:1:0.61402:1.16:60:188:0.3333:0:2.3 0/0:305:0:0,0:142,163:0:2,0:25:1:29.9:1:1:0:60:60:1:0:0.8 -11 21635306 . A G 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24935;SOR=Inf;LSEQ=AATGGGAGCTGCTAGACAGG;RSEQ=GGGAAGACCCTTCTTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:126,145:0:2,0:25.4:1:30:1:1:0:60:37.714:1:0:0.8 0/1:288:3:1,2:132,152:0.0104:2,2:33.7:1:25.7:1:1:1.73364:60:2:0.0071:0:2 -11 21635308 . G A 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00023;SOR=Inf;LSEQ=TGGGAGCTGCTAGACAGGAG;RSEQ=GAAGACCCTTCTTTGGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:124,142:0:2,0:25.3:1:30.5:1:1:0:60:37:1:0:0.8 0/1:286:13:7,6:126,147:0.0455:2,2:19.7:1:30.4:1:0.77727:1.36:60:26:0.0463:0:1.9 -11 21635345 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=TGTTAGGGCCACTCTGTGAC;RSEQ=AGTCATTGCTCAGGCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:65,125:0:2,0:25.3:1:31.4:1:1:0:60:380:1:0:0.5 0/1:190:2:1,1:69,119:0.0105:2,2:11.5:1:27.5:1:1:1.72:60:4:0.0107:0:2.5 -11 21635346 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49867;SOR=Inf;LSEQ=GTTAGGGCCACTCTGTGACC;RSEQ=GTCATTGCTCAGGCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:62,124:0:2,0:25.6:1:30.5:1:1:0:60:185:1:0:0.5 0/1:188:2:1,1:68,118:0.0106:2,2:9.5:1:29.5:1:1:1.73:60:4:0.0108:0:1.5 -11 23122594 . CT C 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.04448;SOR=0;LSEQ=TTGAAATAGTTTCAATAGAC;RSEQ=TTTTTGTATGTAAGCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:4:2,2:157,229:0.0102:2,2:31.5:1:31:1:1:1.46:60:8:0.0103:0:0.8 0/0:461:0:0,0:200,261:0:2,0:26.7:1:29.9:1:1:0:60:56.625:1:0:0.5 -11 23122604 . T C 218 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAATAGACCTTTTTTGTA;RSEQ=GTAAGCAAACTCAACAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:152,223:0:2,0:25.6:1:30.2:1:1:0:60:74:0.9973:0:0.1 0/1:451:165:68,97:119,167:0.3659:2,2:25.5:1:29.7:1:1:1.01643:60:164:0.3694:0:1.1 -11 23122634 . C CA 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=0.17958;LSEQ=CTCAACAAATTATTTTTAGT;RSEQ=AAAAAATTTATTTCTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:109:38,71:49,102:0.4176:2,2:27.3:1:30.4:1:0.6917:1.11:60:218:0.4325:0.0536:0.1 0/1:334:38:11,27:111,185:0.1138:2,2:24.5:1:29:1:0.37211:1.4711:60:11.667:0.107:0.006:0.2 -11 23122704 . T C 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGTAACTAGCACACAGTTA;RSEQ=CACTTAATAGATGCTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:3,61:0:1,0:24.4:1:29.8:1:1:0:60:63:1:0:0.4 0/1:70:27:4,23:6,37:0.3857:2,2:21.5:1:31.5:1:1:1.07:60:54:0.3857:0:1 -11 23122721 . A C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00121;SOR=0.18267;LSEQ=TTATCACTTAATAGATGCTT;RSEQ=AGTGAATGAATGACTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:22:0,22:2,28:0.4231:2,1:25.2:1:33:1:0.50226:0:60:44:0.4231:0:1.2 0/1:43:5:0,5:2,36:0.1163:2,0:28.2:1:32.4:1:1:0:60:10:0.1163:0:1 -11 23122852 . A C 77 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTCTCAGCAATAAATA;RSEQ=TTTTCCCAAATGTTTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:27.6:1:33.4:1:1:0:60:10:0.5556:0:1 0/0:1:0:0,0:0,1:0:0,0:29:0:18:0:1:0:60:0:0:0:1 -11 24881825 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AACCCCAGGCAGAGGCTCAG;RSEQ=GACAGAATCTGATCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,2:0.5:0,0:18:1:30:1:0.33333:0:60:4:0.5:0:1 0/0:5:0:0,0:2,3:0:2,0:32.6:1:30.4:1:1:0:60:10:1:0:0.4 -11 24882079 . T C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCACCCTATACAGGAG;RSEQ=GATCCTACTGGCAACAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:44:1:31:1:1:0:60:4:1:0:1 1/1:3:3:2,1:0,0:1:0,2:17.3:1:32.7:1:1:0:60:6:1:0:1 -11 24882340 . C A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1396;SOR=0;LSEQ=AAGGCCCCCCCAAAAACCCT;RSEQ=CCCAAGGGTCAGCAGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:19,19:0,0:1:0,2:32.5:1:28.8:1:1:0:60:76:1:0:1.1 1/1:54:50:22,28:0,0:0.9259:0,2:27.5:1:28:1:1:0:60:15.667:0.9216:0:1.3 -11 24882358 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50476;SOR=Inf;LSEQ=CTCCCCAAGGGTCAGCAGCC;RSEQ=CAAAGACCCAAGCTGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:18,21:0:2,0:30:1:29.8:1:1:0:60:38:1:0:1 0/1:52:2:1,1:21,29:0.0385:2,2:35.5:1:32:1:1:1.37:60:4:0.0392:0:2.5 -11 24882489 . T C 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCCATCAAGGGTGCAGAAC;RSEQ=GGATGGAGGATCAGATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:6.5:1:29.5:1:1:0:60:4:1:0:0 0/1:11:2:1,1:5,4:0.1818:2,2:30.5:1:28.5:1:1:1.22474:60:4:0.1818:0:1 -11 24882587 . G A 73 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATGTTCTAACCCAATGC;RSEQ=AAGAAGCTAAGAACTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:23.4:1:31.8:1:1:0:60:10:1:0:1 1/1:1:1:0,1:0,0:1:0,0:28:0:32:0:1:0:60:2:1:0:1 -11 25022127 . T C 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66023;SOR=0.51009;LSEQ=ATACAGGGCCCAAAGGTGAG;RSEQ=AACAGCAAAATAGCTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:3,1:9,5:0.2222:2,2:15.8:1:32.3:1:1:1.62:60:8:0.2353:0:2 0/1:16:2:1,1:10,4:0.125:2,2:27.5:1:33:1:1:2.34522:60:4:0.125:0:1.5 -11 25022172 . T C 94 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02526;SOR=0.09713;LSEQ=CTTAGAAAGGGGAGAAGCCA;RSEQ=GTTGCCCAACTCCAGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:5,3:12,9:0.2759:2,2:33.3:1:31.6:1:1:1.24:60:16:0.2759:0:1.9 0/1:29:1:1,0:15,13:0.0345:2,0:31:0:33:0:1:0:60:2:0.0345:0:2 -11 25023468 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTGCTTGTACTGCTGTTCTC;RSEQ=CTTCTCCTTTCCCTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:8:0:32:0:1:0:60:4:1:0:0.5 1/0:4:2:1,1:1,1:0.5:2,2:31.5:1:31:0:1:1:60:4:0.5:0:1 -11 27795538 . T C 217 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=152.34398;LSEQ=TTCTAAAGAGGTGCATTCTA;RSEQ=TGATTGTAGGATTTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:1:1,0:170,265:0.0023:2,0:31:0:13:0:0.3922:0:60:0:0:0:1 0/1:450:117:48,69:146,186:0.26:2,2:25.4:1:31.6:1:0.58951:1.12806:60:234:0.2629:0:1.1 -11 27795598 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49893;SOR=0;LSEQ=GCACATCTGCCGGTAGCACA;RSEQ=CATTGTTTTGCATAAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:37,147:0.0108:2,2:39.5:1:30:1:0.36774:3.93:60:4:0.011:0:1 0/0:177:0:0,0:37,140:0:2,0:45:0:14:0:1:0:60:0:0:0:5 -11 27795708 . T G 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01544;SOR=Inf;LSEQ=GGTGGTGGTTGGGTGAGGGA;RSEQ=CACAGTGAGAAGGGAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:2,25:0:2,0:27.4:1:28.6:1:1:0:60:12.5:1:0:0.3 0/1:10:3:0,3:1,6:0.3:2,0:43:1:32.3:1:1:0:60:6:0.3:0:1 -11 30098621 . TT A 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.43049;SOR=1.15815;LSEQ=AGAAGTTAATATAACCATAG;RSEQ=TTTTCCTTCAGAAGTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:78:44,34:105,80:0.2943:2,2:26.4:1:31:1:1:1.01415:60:156:0.2977:0.0226:1 0/1:353:115:62,53:132,103:0.3258:2,2:25.3:1:30.3:1:0.73174:1.09523:60:230:0.3276:0.0397:1.1 -11 30098622 . T A 58 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.19462;SOR=0.39324;LSEQ=GAAGTTAATATAACCATAGT;RSEQ=TTTTCCTTCAGAAGTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:6:4,2:105,81:0.0313:2,2:13:1:22.8:1:0.70002:1.54:59.2:1:0.0161:0:2.3 0/1:240:3:2,1:131,105:0.0125:2,2:12:1:25:1:1:1.60:60:2:0.0085:0:2.3 -11 30098650 . G C 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.8723;SOR=0.97437;LSEQ=TCAGAAGTTGAGTTATTTGA;RSEQ=TTTTCTAAGGCACTTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:106:51,55:90,105:0.3522:2,2:23.5:1:31.3:1:0.8091:1.08:60:34.333:0.3456:0:2.2 0/1:387:134:64,70:125,128:0.3463:2,2:27.3:1:31.3:1:0.83081:1.06791:60:268:0.3463:0:2.2 -11 30098715 . G A 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAATATAAGTTAGAAAATG;RSEQ=AAGTCTAGTTTTTGATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:162:162:48,114:0,0:1:0,2:23.4:1:30:1:1:0:60:80:1:0:1.4 1/1:210:178:61,117:11,20:0.8476:2,2:24.2:1:29.5:1:1:1.05465:60:177:0.8469:0:1.3 -11 30098849 . G T 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0033;SOR=0;LSEQ=AGACTAAAAATTGTGTAAAT;RSEQ=TAGACAGCATATACCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:0.5:0,0:22.6:1:31:1:1:0:60:16:0.5:0:1 0/0:13:0:0,0:0,13:0:1,0:22.2:1:32.5:1:1:0:60:26:1:0:0.4 -11 30254268 . T G 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GAAATAGTTTCCATGGTGCT;RSEQ=TCTTTTTTCTCTGCAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:27.6:1:32.2:1:1:0:60:10:0.5556:0:1 0/0:2:0:0,0:2,0:0:0,0:8:1:31.5:1:1:0:60:4:1:0:0 -11 30254550 . T C 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04563;SOR=0.70061;LSEQ=CTGGATTAAAAATTCTTATA;RSEQ=GCAAACTGCATATCCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:126:61,65:62,63:0.498:2,2:27.1:1:30.9:1:0.89976:1.04843:60:125:0.498:0:1.2 0/1:283:116:51,65:77,87:0.4099:2,2:26:1:30.1:1:0.62863:1.12753:60:232:0.4143:0:1.1 -11 30254607 . A G 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12064;SOR=Inf;LSEQ=AAGTATACAGCTTTCAAGGG;RSEQ=GAAAAATGTCCACAAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:84,131:0:2,0:25:1:30.4:1:1:0:60:106.5:1:0:0.5 0/1:211:3:1,2:77,131:0.0142:2,2:25.3:1:29.3:1:1:1.17473:60:6:0.0144:0:2 -11 30254683 . A C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.99107;LSEQ=CATGTTAACTTAAGCATTAA;RSEQ=ATTTAAAATTATATATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:18:0,18:1,29:0.375:1,1:25.4:1:32.8:1:1:0:60:36:0.375:0:1.2 0/1:59:22:3,19:3,34:0.3729:2,2:24.5:1:32.2:1:0.6614:1.77:60:44:0.3729:0:1 -11 32106583 . C T 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00083;SOR=Inf;LSEQ=GGTGCAATATATCAGTAGAC;RSEQ=TAACAGAATGAATATCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:0:1,0:26.7:1:31.2:1:1:0:60:62:1:0:0 0/1:31:10:10,0:21,0:0.3226:1,0:26.8:1:32.7:1:1:0:60:20:0.3226:0:1.2 -11 32106694 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0735;SOR=0;LSEQ=ACTTTGTGACTTCCACGAGA;RSEQ=ACTGACCATCACACAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:1,2:96,74:0.0172:2,2:32.3:1:24.7:1:0.58274:2.58051:60:2:0.0116:0:1.3 0/0:240:0:0,0:126,114:0:2,0:28.6:1:30.9:1:1:0:60:59:1:0:0.1 -11 32106837 . G A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03855;SOR=Inf;LSEQ=AAAAAGATGTTAGCATGAGG;RSEQ=ATTTCTGATCAGGGTCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:97,74:0:2,0:26.9:1:30.6:1:1:0:60:33.2:1:0:0.1 0/1:224:6:4,2:119,98:0.0268:2,2:27.7:1:29.7:1:0.6934:1.64:60:12:0.0273:0:1.2 -11 32106872 . TA T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18178;SOR=0;LSEQ=TCAAGCTGTGTTCTGATCAC;RSEQ=ATGACTTGTCGGCTTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:82,109:0.0104:2,2:12:1:27:1:1:1.33:60:4:0.0105:0.0052:0.5 0/0:259:0:0,0:131,128:0:2,0:27.1:1:28.7:1:1:0:60:85.333:1:0:0.2 -11 32106903 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18462;SOR=0;LSEQ=CGGCTTGTGGGATGGAGGAG;RSEQ=AATGAGTGTCTTTGGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:65,100:0.012:2,0:14:1:27:1:0.15951:0:60:4:0.0121:0:1 0/0:221:0:0,0:101,116:0:2,0:22.9:1:31.5:1:1:0:60:107.5:0.9817:0:0.1 -11 32106983 . G T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24651;SOR=Inf;LSEQ=AGGAGTCGACAGCAGCAGTT;RSEQ=ATGGCAAGATGGTACTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:65,43:0:2,0:24.6:1:31.9:1:1:0:60:53:1:0:0.1 0/1:107:2:1,1:52,53:0.0187:2,2:8:0:26.5:1:1:1.02:60:4:0.019:0:1 -11 32107011 . T C 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGGTACTCAGAAATGGCA;RSEQ=TGATGTAATTTAGGACGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:74,36:0:2,0:24.5:1:30.4:1:1:0:60:35.667:1:0:0.1 0/1:113:25:17,8:58,30:0.2212:2,2:32.4:1:31.6:1:1:1.10:60:50:0.2252:0:1.5 -11 32107062 . C T 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=72.89342;LSEQ=GAGACAGCACACAATTAGAA;RSEQ=AAAGAATTGGCAGAGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:0,1:131,100:0.0043:2,0:1:0:26:0:0.43534:0:60:2:0.0044:0:1 0/1:249:60:29,31:105,84:0.241:2,2:26.2:1:28.2:1:0.37346:1.33463:60:120:0.2459:0:1.4 -11 32107091 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2487;SOR=Inf;LSEQ=GGCAGAGGGGGTCGACTTGG;RSEQ=AAGAAAGGTGTGGATATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:149,138:0:2,0:29.1:1:31.2:1:1:0:60:56.4:1:0:0.2 0/1:289:3:1,2:142,144:0.0104:2,2:27.7:1:25:1:1:1.96776:60:6:0.0107:0:1 -11 32107172 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23182;SOR=Inf;LSEQ=GACTTTCTACGATACCATAG;RSEQ=GGAAGAGATGCCCATGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:34,99:0:2,0:25.5:1:30:1:1:0:60:65.5:1:0:0 0/1:124:2:1,1:46,76:0.0161:2,2:32.5:1:26:1:1:1.65:60:4:0.0163:0:1 -11 32409549 . AACAC A 30 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=17.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAAAAAACAAAACACAACAC;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:39:0:30:1:1:0:60:4:0.6667:0:0 -11 32410774 . A G 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGCAACAAAGAGACAGGC;RSEQ=CAAGTTCAACTATCAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:35,187:0:2,0:21.8:1:29.9:1:1:0:60:73:1:0:0.1 0/1:240:47:7,40:33,160:0.1958:2,2:19.2:1:32.1:1:0.82937:1.17778:60:94:0.1958:0:1.2 -11 32413417 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49743;SOR=0;LSEQ=TCAACTGAGTCTAAACCTTA;RSEQ=AACTTTTACACTAGTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:2,0:73,2:0.026:1,0:15.5:1:31.5:1:1:0:60:4:0.026:0:1 0/0:71:0:0,0:69,2:0:1,0:27.2:1:32:1:1:0:60:22.667:1:0:0.1 -11 32413470 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28287;SOR=Inf;LSEQ=ATCACAATTTCATTCCACAA;RSEQ=AGTTTAAAAAAATAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:126,48:0:2,0:23.1:1:29.7:1:1:0:60:57:1:0:0.1 0/1:269:3:2,1:182,83:0.0112:2,2:19.7:1:28:1:1:1.096:60:6:0.0113:0:1.3 -11 32413662 . A G 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0908;SOR=0;LSEQ=CTAACAATGTGGGCACAGTG;RSEQ=GGCCCACAAGGCTGACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:1,2:37,130:0.0176:2,2:26.3:1:29.7:1:0.53426:1.75:60:6:0.0179:0:1 0/0:207:0:0,0:48,159:0:2,0:23.6:1:30.2:1:1:0:60:102.5:1:0:0.1 -11 32414094 . T C 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61807;SOR=2.0726;LSEQ=AGATTATGGGGGGAAAATAC;RSEQ=GGAAAAACTAAACACATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:1:1,0:182,8:0.0052:1,0:9:0:32:0:1:0:60:2:0.0054:0:1 0/1:185:2:1,1:174,9:0.0108:1,2:11.5:1:28:1:0.10546:18.38814:60:4:0.011:0:1 -11 32414333 . G T 157 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=24.4646;LSEQ=CACATATTCTATTTGAAAAT;RSEQ=ATACTGGAAAAGGGGATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:2:1,1:71,183:0.0078:2,2:16.5:1:28:1:0.48419:2.57:60:4:0.0078:0:1 0/1:292:47:14,33:62,183:0.161:2,2:16.4:1:28.3:1:0.58636:1.25:60:94:0.1621:0:1.1 -11 32414518 . TA T 46 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0.84709;LSEQ=CTCACATCTAGCTCTGCCAT;RSEQ=AAAAAAAAAAAAAAGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:34.3:1:29.3:1:1:0:60:6:0.375:0:1.7 0/1:3:1:0,1:0,2:0.3333:0,0:39:0:28:0:1:0:60:2:0.3333:0:0 -11 32417796 . C T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12621;SOR=Inf;LSEQ=CCAAGACTGGACAGCGGGCA;RSEQ=ACTTACCAGTGTGCTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:247,100:0:2,0:23.9:1:32:1:1:0:60:114.667:1:0:0.1 0/1:387:4:1,3:261,122:0.0103:2,2:20.5:1:26.3:1:0.101:6.38503:60:8:0.0105:0:1 -11 32417945 . T C 193 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCTACTCCAGGCACACG;RSEQ=CGCACATCCTGCAGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:476:0:0,0:174,300:0:2,0:23.8:1:29.6:1:1:0:60:51.667:0.9979:0:0.1 0/1:576:69:28,41:175,329:0.1198:2,2:25.9:1:31.7:1:0.34979:1.28:60:138:0.1221:0:1.1 -11 32418019 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=AACATTCACGTAGGTCTTGA;RSEQ=GGAGAGTGAGCACTGGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:6,108:0:2,0:24.9:1:30.7:1:1:0:60:37:1:0:0.2 0/1:122:2:1,1:18,102:0.0164:2,2:23:1:24:1:0.28831:5.54:60:4:0.0167:0:1 -11 32421470 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26758;SOR=Inf;LSEQ=GGCAGTGCGGCCCCCTTCCC;RSEQ=CTGGGGCCTGTCTGTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:141,59:0:2,0:25.7:1:30.2:1:1:0:60:99:1:0:0.1 0/1:276:3:2,1:191,81:0.0109:2,2:27:1:31.7:1:1:1.17826:60:6:0.0112:0:1 -11 32421493 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06459;SOR=0;LSEQ=GGGGCCTGTCTGTGTGCTCA;RSEQ=CTGAATGCCTCTGAAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:162,96:0.0115:2,2:10.3:1:28:1:0.55829:3.35874:60:6:0.0118:0:1 0/0:388:0:0,0:234,154:0:2,0:25.3:1:30.6:1:1:0:60:42.111:1:0:0.2 -11 32421627 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14242;SOR=Inf;LSEQ=GGGAAAAAGGCTCAGTGTGG;RSEQ=TCACAGTCGCCATTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:62,156:0:2,0:23:1:32.1:1:1:0:60:217:1:0:0.1 0/1:300:4:2,2:94,201:0.0133:2,2:39.5:1:29.5:1:0.59595:2.13:60:8:0.0134:0:1 -11 32437699 . T C 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAGTTAAGACTGAAAGC;RSEQ=TTGACTGATCTAACAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:12:1:30.6:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 32437841 . A C 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0;LSEQ=TCCAGGGGCATGTTGATGAG;RSEQ=AATGCTACTCCCTCCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:14,0:19,0:0.4242:1,1:17.6:1:31.6:1:1:0:60:13:0.4063:0:1.1 0/0:25:0:0,0:25,0:0:1,0:26.9:1:29.2:1:1:0:60:24:1:0:0.2 -11 32437902 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=GAATAAGAAGAGGTGGGGGC;RSEQ=GGGGAGAGAGATTCTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:82,3:0:1,0:25.4:1:29.5:1:1:0:60:84:0.9882:0:0.3 0/1:84:9:9,0:71,4:0.1071:2,0:30.4:1:29.4:1:1:0:60:18:0.1084:0:2.1 -11 32437914 . T G 163 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=43.02806;LSEQ=GTGGGGGCGGGGGAGAGAGA;RSEQ=TCTTCCCATCCACCAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:1,0:116,13:0.0077:2,0:32:0:34:0:1:0:60:2:0.0079:0:2 0/1:135:34:32,2:92,9:0.2519:2,2:24.2:1:32.1:1:0.72977:1.56:60:68:0.2537:0:1.4 -11 32437946 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25612;SOR=Inf;LSEQ=ACCAAATGCTACCCTGATTA;RSEQ=CCACGTCAGTCCTAACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:174,69:0:2,0:23.1:1:31.5:1:1:0:60:80:1:0:0.1 0/1:297:3:1,2:227,67:0.0101:2,2:6:1:26:1:0.13587:6.7197:60:6:0.0101:0:1 -11 32438788 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCACTTCTTGATAAGA;RSEQ=AGTGGAATGGTTAACAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:20.5:1:31:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 32439001 . T C 170 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGAGGAAAGCGTTCTAATG;RSEQ=CACAGAGAGCTTTGCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:41:40,1:67,0:0.3796:1,1:27.2:1:31.8:1:0.37963:0:60:19.5:0.3679:0:1 0/0:85:0:0,0:85,0:0:1,0:24.4:1:30.1:1:1:0:60:170:1:0:0.1 -11 32439016 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5023;SOR=0;LSEQ=TAATGTCACAGAGAGCTTTG;RSEQ=CCTTTCTTCTAAAACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:133,8:0.014:2,2:10:1:29:1:0.12233:15.72782:60:4:0.014:0:1.5 0/0:119:0:0,0:109,10:0:2,0:23:1:31.9:1:1:0:60:118:1:0:0.1 -11 32439038 . T C 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTCTTCTAAAACTGTACT;RSEQ=TCTTCATAAGTTCTAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:188,50:0:2,0:21.3:1:30.2:1:1:0:60:237:1:0:0.2 0/1:230:26:21,5:149,55:0.113:2,2:20:1:31.1:1:0.48328:1.55:60:52:0.1156:0:1 -11 32449274 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08772;SOR=Inf;LSEQ=CGCCGCTCCTTCTTCAGCTC;RSEQ=AAAGAGTAATTGTCCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:0:1,0:20.6:1:29.8:1:1:0:60:26:1:0:0.1 0/1:6:2:2,0:4,0:0.3333:0,0:17.5:1:28.5:1:1:0:60:4:0.3333:0:1 -11 32449417 . C G 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07174;SOR=Inf;LSEQ=TGCCCGCAGTCAGGGCTGCC;RSEQ=GGCTGGGGCGTTCCCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:119,8:0:2,0:26.9:1:31:1:1:0:60:126:1:0:0.1 0/1:92:3:3,0:81,7:0.0326:2,0:35.3:1:24.7:1:1:0:60:2:0.0227:0:2 -11 32449420 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17643;SOR=Inf;LSEQ=CCGCAGTCAGGGCTGCCCGG;RSEQ=TGGGGCGTTCCCAAGTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:127,9:0:2,0:26.3:1:31.6:1:1:0:60:33:1:0:0.1 0/1:99:2:2,0:88,9:0.0202:2,0:39.5:1:31:0:1:0:60:4:0.0204:0:2 -11 32449459 . CG C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.11039;SOR=Inf;LSEQ=GCCGGCTCATGCGTCCCCTC;RSEQ=GGGTCCCAAGGACCCAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:217,65:0:2,0:21.4:1:29.4:1:1:0:60:69.5:1:0:0.2 0/1:261:3:1,2:188,69:0.0115:2,2:9.7:1:29.7:1:0.18194:5.40709:60:6:0.0118:0.0038:1.3 -11 32449486 . C T 211 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=213.25914;LSEQ=CCAAGGACCCAGACGCAGAG;RSEQ=CCAGCGCCTTCCTACCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:1:0,1:274,158:0.0023:2,0:17:0:14:0:0.36721:0:60:0:0:0:1 0/1:477:158:92,66:189,128:0.3312:2,2:23.4:1:28.9:1:0.84299:1.05913:60:38.5:0.3305:0:1.2 -11 32449661 . G A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00753;SOR=Inf;LSEQ=CCCAAGGGCTCGGGGTGCGA;RSEQ=GCTGCGGGCAGGGGTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:49,140:0:2,0:21:1:30.8:1:1:0:60:36.8:1:0:0.2 0/1:203:8:1,7:49,146:0.0394:2,2:24.5:1:31.8:1:0.68227:2.3415:60:16:0.0404:0:1 -11 32449704 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51262;SOR=0;LSEQ=GACACGAGATCCTGAGCCTG;RSEQ=GGCACTGGGGCCTGGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:5,86:0.0215:2,2:22.5:1:32.5:1:0.12553:15.79:60:4:0.0222:0:1 0/0:65:0:0,0:1,64:0:1,0:24.8:1:30.1:1:1:0:60:64:1:0:0.2 -11 32449799 . G T 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01694;SOR=Inf;LSEQ=ATTCCCCTAGCAGTCGCTGC;RSEQ=CTGTGCACCAAAAAGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:0:2,0:24.3:1:31.2:1:1:0:60:22:1:0:0.3 0/1:9:3:3,0:3,3:0.3333:2,0:21.3:1:33:0:0.46429:0:60:6:0.3333:0:1 -11 32449992 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24916;SOR=0;LSEQ=GGAATTCCTGGGGGAGAGGA;RSEQ=GATAGCACGGAAGAAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:2,1:178,53:0.0128:2,2:35.3:1:24.7:1:0.5466:1.67504:60:2:0.0087:0:1.3 0/0:219:0:0,0:159,60:0:2,0:23.5:1:31.5:1:1:0:60:438:1:0:0.1 -11 32450193 . T A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1197;SOR=0;LSEQ=AGCGGCGGAGAGAAGCACAG;RSEQ=GTCAGCGGTGCTCTCGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:3,0:74,199:0.0109:2,0:8.3:1:22.3:1:0.0211:0:60:2:0.0073:0:1.3 0/0:283:0:0,0:87,196:0:2,0:24.9:1:29.8:1:1:0:60:140.5:1:0:0.2 -11 32450199 . C T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37268;SOR=3.94235;LSEQ=GGAGAGAAGCACAGTGTCAG;RSEQ=GGTGCTCTCGCAAGACGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:0,1:67,179:0.004:2,0:33:0:32:0:1:0:60:2:0.0041:0:1 0/1:254:4:1,3:72,177:0.0157:2,2:9:1:26.3:1:1:1.21941:60:8:0.0161:0:1.3 -11 32450209 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24672;SOR=0;LSEQ=ACAGTGTCAGCGGTGCTCTC;RSEQ=CAAGACGGGGCAGTGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:43,144:0.0106:2,2:43.5:1:30.5:1:0.41236:3.32:60:4:0.0108:0:1 0/0:191:0:0,0:46,145:0:2,0:23.7:1:31.5:1:1:0:60:94.5:1:0:0.2 -11 32450244 . CG C 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGTCTGAACCAGCCACGGG;RSEQ=GGGGGGGTGTGCGCTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:40:3,37:8,47:0.4211:2,2:26.5:1:31.9:1:0.34719:2.08397:60:80:0.4255:0.0105:0.1 0/0:67:0:0,0:8,59:0:2,0:17.3:1:29.6:1:1:0:60:32.5:1:0:0.3 -11 32451920 . TG GC 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACCCACTATTGCCCGGAG;RSEQ=AAGGCCGAATTTCTGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:74,1:0:1,0:23.9:1:29.6:1:1:0:60:24:1:0:0.2 0/1:44:17:17,0:26,0:0.3864:1,1:24.5:1:31.7:1:1:0:59.7:34:0.4048:0.0682:1.1 -11 32451950 . A AAG 24 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=1.51462;LSEQ=ATTTCTGAAAGGACACTAAA;RSEQ=AGAGAGAGAGAGAAAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:2,0:128,1:0.0153:1,0:30.5:1:32:0:1:0:60:4:0.0155:0:0 0/1:87:2:1,1:83,0:0.023:1,2:4.1:1:24.6:1:0.02353:0:42.5:4:0.0125:0.0183:5 -11 32451976 . C G 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12311;SOR=Inf;LSEQ=GAGAGAGAAAGAGAGACAGA;RSEQ=ACAGAGAGAGAGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:177,22:0:2,0:24.1:1:30.7:1:1:0:59.3:10.706:1:0:0.5 0/1:198:3:2,1:176,19:0.0152:2,2:7:1:28.3:1:0.2747:4.57067:50:2:0.0107:0:3.3 -11 32451991 . AGAGAGG A 113 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0.93491;LSEQ=ACAGACACAGAGAGAGAGAG;RSEQ=GAGGGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:12:5,7:230,70:0.0383:2,2:20.8:1:30.4:1:0.01168:4.57188:60:11:0.0363:0.016:1.6 0/1:334:12:10,2:246,69:0.0359:2,2:37.4:1:31.6:1:1:1.40:58.3:24:0.0369:0:1.3 -11 32451995 . AGGGAGG GGAGGGAGAGAGAGA 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.12449;SOR=Inf;LSEQ=ACACAGAGAGAGAGAGAGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:232,70:0:2,0:21.7:1:29.5:1:1:0:59.2:29.2:1:0:0.5 0/1:325:4:4,0:244,68:0.0123:2,0:17.8:1:31.7:1:0.58103:0:51.3:8:0.0129:0:2.8 -11 32451997 . G A 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGAGAGAGAGAGAGAGAG;RSEQ=GAGGGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:225,67:0:2,0:23.6:1:28.8:1:1:0:59.1:7.111:0.9884:0:0.5 0/1:348:42:25,17:222,55:0.1207:2,2:17.3:1:26.9:1:0.00505:2.73429:53.5:5:0.1228:0:3.3 -11 32451999 . A G 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72821;SOR=1.501;LSEQ=AGAGAGAGAGAGAGAGAGGG;RSEQ=GGGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:3:3,0:234,74:0.0093:2,0:30:1:12:0:1:0:51.3:0:0:0:4.3 0/1:359:5:5,0:254,79:0.0139:2,0:41.2:1:24:1:0.59448:0:52:4:0.013:0:3.2 -11 32452001 . GGA G 206 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=34;MSI=18.000;MSILEN=2;SSF=0;SOR=0.10004;LSEQ=AGAGAGAGAGAGAGAGGGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:115:77,38:90,21:0.2987:2,2:20.8:1:30.2:1:0.02262:2.10802:59.4:13.375:0.294:0.0935:0.7 0/1:417:17:12,5:173,57:0.0408:2,2:16.1:1:30.1:1:0.77199:1.26337:60:34:0.0421:0.0192:0.3 -11 32452158 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02012;SOR=Inf;LSEQ=CCTGCTCCGCAACTGTCCGT;RSEQ=CCCGGCGAGGGCCGTGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:74,267:0:2,0:23.3:1:31.8:1:1:0:60:67.2:1:0:0.1 0/1:290:5:4,1:74,211:0.0172:2,2:9:1:24.4:1:0.01959:11.30:60:10:0.0177:0:1 -11 32452240 . GC G 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0122;SOR=Inf;LSEQ=CAGAACTCGGGCCCAAGGAT;RSEQ=CCGTGGCCCGCGAGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,64:0:1,0:23.9:1:30.1:1:1:0:60:15:0.9836:0:0.1 0/1:48:5:0,5:0,43:0.1042:1,0:19.6:1:32.4:1:1:0:60:10:0.1087:0.0208:0.2 -11 32456298 . G A 231 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=301.11095;LSEQ=CAGCTGGGCAGGTAGGGCGC;RSEQ=TTAGGAAACATCCTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:821:1:1,0:410,408:0.0012:2,0:1:0:29:0:1:0:60:2:0.0012:0:1 0/1:814:218:107,111:292,304:0.2678:2,2:25.2:1:29.8:1:1:1.00:60:108:0.2693:0:1.2 -11 32456446 . G A 44 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.3802;SOR=0.28862;LSEQ=ACTGCTCCTCGTGCGGCTCC;RSEQ=CGCCGCCCCAGCTCGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:4:3,1:96,274:0.0107:2,2:5.3:1:22.3:1:0.05846:8.50:60:3:0.0081:0:1.8 0/0:322:1:1,0:114,207:0.0031:2,0:1:0:30:0:0.35714:0:60:2:0.0032:0:1 -11 32456484 . AGGC A 83 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03632;SOR=5.15308;LSEQ=TCCTGTTTGATGAAGGAGTG;RSEQ=GGCGGCGGCGGGGGTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:0,2:31,151:0.0109:2,0:23.5:1:33:0:1:0:60:4:0.011:0:0 0/1:130:7:3,4:35,86:0.0538:2,2:24.4:1:29.7:1:0.42285:1.83:60:14:0.056:0.0077:0.4 -11 32456487 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.2725;SOR=0;LSEQ=TGTTTGATGAAGGAGTGAGG;RSEQ=GGCGGCGGCGGGGGTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:1,2:28,142:0.0171:2,2:23.3:1:30:1:0.42533:2.52:60:6:0.0176:0:1 0/0:121:0:0,0:31,83:0:2,0:21.1:1:29.1:1:1:0:60:15.286:1:0:0.3 -11 32456496 . C G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51095;SOR=0;LSEQ=AAGGAGTGAGGCGGCGGCGG;RSEQ=GGGGGTGGCGGCGGAGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:17,110:0.0155:2,2:28:0:32.5:1:0.26054:6.32:60:4:0.0157:0:1.5 0/0:93:0:0,0:21,71:0:2,0:20.5:1:29.6:1:1:0:60:22:0.9888:0:0.3 -11 32456618 . AGCC A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.18611;SOR=0;LSEQ=GCCGCTCACAGGCAGGGCAC;RSEQ=GCCGCCGCCACCCAGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:74,28:0.0183:2,0:11:1:32.8:1:1:0:60:4:0.019:0.0092:0.5 0/0:143:0:0,0:86,57:0:2,0:22.8:1:31.5:1:1:0:60:27.6:1:0:0.3 -11 32456619 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07966;SOR=0;LSEQ=CCGCTCACAGGCAGGGCACA;RSEQ=CCGCCGCCGCCACCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:2,1:74,28:0.0275:2,2:10.7:1:25.3:1:1:1.31774:60:2:0.019:0:1.7 0/0:143:0:0,0:86,57:0:2,0:22.8:1:31.5:1:1:0:60:27.6:1:0:0.3 -11 32456627 . C T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1;SOR=1.32983;LSEQ=AGGCAGGGCACAGCCGCCGC;RSEQ=GCCACCCAGGGAGGGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:98,36:0.0147:2,2:37.5:1:28:1:0.47157:2.69885:60:4:0.0147:0:2 0/1:154:3:1,2:92,59:0.0195:2,2:4:1:27.3:1:0.56281:3.09526:60:6:0.0195:0:1.7 -11 32456648 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81859;LSEQ=GCCACCCAGGGAGGGGACGG;RSEQ=GGGCAGCAGCGCGTTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:125,55:0.011:2,2:25.5:1:30:1:0.52189:2.26137:60:4:0.0112:0:1 0/0:222:2:1,1:127,93:0.009:2,2:6:1:28:1:1:1.36363:60:4:0.0093:0:1 -11 32456694 . C A 197 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGTCGGAGCCCATTTGCTG;RSEQ=GGCTCAGACCCGGACGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:196,123:0:2,0:26.3:1:30.8:1:1:0:60:52.167:0.9905:0:0.2 0/1:320:106:54,52:122,92:0.3313:2,2:24.3:1:29.3:1:0.3401:1.27598:60:34.333:0.3291:0:1.2 -11 32456809 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.99656;LSEQ=CCCGGACTCCCTGCTGCTCT;RSEQ=GCTGCTGTAGGCACCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:1,0:80,113:0.0052:2,0:1:0:14:0:0.41753:0:60:0:0:0:5 0/1:195:2:1,1:86,107:0.0103:2,2:10.5:1:28:1:1:1.24:60:4:0.0103:0:1.5 -11 32456815 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49878;SOR=0;LSEQ=CTCCCTGCTGCTCTGGCTGC;RSEQ=GTAGGCACCCAGGCCCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:75,112:0.0106:2,2:22.5:1:28:1:1:1.49:60:4:0.011:0:1 0/0:183:0:0,0:81,102:0:2,0:22.3:1:29.7:1:1:0:60:60:1:0:0.2 -11 32456820 . G A 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61085;SOR=2.15834;LSEQ=TGCTGCTCTGGCTGCTGTAG;RSEQ=CACCCAGGCCCGGAGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:1,0:73,112:0.0053:2,0:1:0:16:0:0.39785:0:60:0:0:0:1 0/1:174:2:2,0:76,96:0.0115:2,0:18.5:1:25:1:0.19952:0:60:4:0.012:0:1 -11 32456830 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21742;SOR=Inf;LSEQ=GCTGCTGTAGGCACCCAGGC;RSEQ=CGGAGCGGAGCGTGTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:64,122:0:2,0:23.1:1:30.3:1:1:0:60:36.2:1:0:0.3 0/1:163:2:0,2:67,94:0.0123:2,0:17.5:1:26:1:0.51284:0:60:4:0.0129:0:1 -11 32456836 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49949;SOR=0;LSEQ=GTAGGCACCCAGGCCCGGAG;RSEQ=GGAGCGTGTGCTGAGACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:0,2:62,115:0.011:2,0:9:1:29:1:0.54466:0:60:4:0.0115:0:1 0/0:166:0:0,0:70,96:0:2,0:23.3:1:29.7:1:1:0:60:32.2:1:0:0.2 -11 32456844 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49867;SOR=0;LSEQ=CCAGGCCCGGAGCGGAGCGT;RSEQ=TGCTGAGACGCCGGCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:63,107:0.0116:2,2:25.5:1:29:1:1:1.69:60:4:0.0119:0:1 0/0:166:0:0,0:73,93:0:2,0:23.7:1:30.4:1:1:0:60:19.75:1:0:0.2 -11 32456892 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24717;SOR=Inf;LSEQ=GTGGAAGCCGGGTCCTGCAG;RSEQ=AAGAGGAAGTCCAGGATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:52,80:0:2,0:27.3:1:32.3:1:1:0:60:264:1:0:0.2 0/1:132:2:1,1:55,75:0.0152:2,2:30.5:1:31:0:1:1.36:60:4:0.0156:0:1 -11 32548278 . T C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCTAAAATAATGCACTTAAT;RSEQ=AAATGTCAATTATGCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:20:1:31:1:1:0:60:4:1:0:0.5 1/1:2:2:2,0:0,0:1:0,0:30:1:32:1:1:0:60:4:1:0:1.5 -11 32548407 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07568;SOR=0;LSEQ=ATGTGTTGTAAAGGTGTTCT;RSEQ=AAGAGACTGAGTGTCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:0.0952:2,2:29.5:1:27.5:1:1:1.66897:60:4:0.1:0:1 0/0:54:0:0,0:30,24:0:2,0:28.4:1:31.6:1:1:0:60:53:1:0:0.2 -11 32548470 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22711;SOR=0;LSEQ=CATCCTTCTGGGAAAGATCA;RSEQ=ATGGGTCTGTTTGGAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:0.0769:2,2:41:0:31.5:1:1:1:60:4:0.0769:0:1 0/0:28:0:0,0:10,18:0:2,0:23.9:1:30.6:1:1:0:60:56:1:0:0.1 -11 35053622 . C A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00502;SOR=Inf;LSEQ=TCATGATAGGCATGTGATGA;RSEQ=GAGTGAACCAGGAAAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:35,1:0:1,0:26:1:32.2:1:1:0:60:72:1:0:0.5 0/1:28:6:6,0:22,0:0.2143:1,0:29.8:1:29.7:1:1:0:60:12:0.2222:0:2 -11 35053634 . G A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=31.3038;LSEQ=TGTGATGACGAGTGAACCAG;RSEQ=AAAAGGGCAAGAGGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:16:16,0:29,1:0.3478:1,1:24.8:1:30.7:1:1:0:60:32:0.3478:0:1.1 1/1:37:35:35,0:2,0:0.9459:0,1:26.4:1:29.3:1:1:0:60:34:0.9444:0:1.2 -11 35053783 . G A 207 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=56.62771;LSEQ=GAGGCAGAACAGAAAGCAAA;RSEQ=AAGGAGGGTCTAGGGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:2:1,1:216,176:0.0051:2,2:15.5:1:22.5:1:1:1.22663:60:1:0.0026:0:3 0/1:581:130:75,55:241,209:0.2238:2,2:25.5:1:29.6:1:0.42501:1.18:60:260:0.2257:0:1.8 -11 35053817 . A T 217 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAACTGCAAAGAGATTTCC;RSEQ=TTCTAGTGCTCACACTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:214,199:0:2,0:25.5:1:30.1:1:1:0:60:67.833:1:0:0.1 0/1:612:151:77,74:229,232:0.2467:2,2:25.6:1:30:1:0.85129:1.05:60:150:0.2467:0:1.7 -11 35053931 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=GTCTGCTCTGGATGAGGAAA;RSEQ=GAGAGTAAATGTATGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:21,122:0:2,0:23.2:1:31.3:1:1:0:60:142:1:0:0.1 0/1:152:2:1,1:27,122:0.0132:2,2:33.5:1:28.5:1:0.33748:4.46:60:4:0.0132:0:1 -11 35242375 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTGCAGTGGC;RSEQ=CGACCTCGGCCCACTGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:37:1:31.5:1:1:0:50:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 35242423 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGAGTTCAAGCGATTCT;RSEQ=CTGCCTCAGCCTCCTGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16:1:32:0:1:0:50:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 35242653 . C T 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04608;SOR=0;LSEQ=TATACCAAAATGTGATTACA;RSEQ=CTTACACGGTGTTTAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:7,0:0.4615:0,0:26.5:1:31.2:1:1:0:60:12:0.4615:0:2.2 0/0:9:0:0,0:9,0:0:0,0:17.4:1:31.1:1:1:0:60:18:1:0:0.9 -11 35242660 . C T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66564;SOR=0.49436;LSEQ=AAATGTGATTACACCTTACA;RSEQ=GGTGTTTAGCAAACATTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:14:14,0:2,0:0.8235:0,1:20.2:1:31.4:1:1:0:60:28:0.8235:0:1.6 1/0:13:9:9,0:4,0:0.6923:0,0:20.1:1:30.6:1:1:0:60:18:0.6923:0:1.2 -11 35242907 . G A 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.53683;LSEQ=TTAATAATATTATACCAAAG;RSEQ=CATCTACAAGATTCAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:162:85,77:87,88:0.4807:2,2:25.1:1:29.8:1:0.663:1.12:60:161:0.4879:0:1.1 0/1:434:144:63,81:139,150:0.3318:2,2:24.9:1:29.2:1:0.41455:1.19094:60:143:0.3357:0:1.1 -11 36128516 . C A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAAGAATATACCCTGGG;RSEQ=GCTGCTGGTCCAAGGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:28.5:1:1:0:60:4:1:0:2.5 -11 39206459 . G A 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATGTTCTTATTTGGAAACAG;RSEQ=GTTGTGGCAGATGTAATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:20:1:29.7:1:1:0:60:6:1:0:1 1/0:2:1:1,0:1,0:0.5:0,0:25:0:30:0:1:0:60:2:0.5:0:1 -11 39587051 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAATACCACCTTGTTGTCA;RSEQ=TGTAAACAAGGGCATAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:28:1:1:0:56:4:1:0:1 -11 39587547 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52192;SOR=Inf;LSEQ=TCTAAGTCCTATGACAGCCA;RSEQ=CTTGCTATTACTCGCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:13,29:0:2,0:21.9:1:29.7:1:1:0:59.7:84:1:0:0.2 0/1:67:2:1,1:29,36:0.0299:2,2:21:0:32:0:1:1.24:60:4:0.0299:0:1.5 -11 39587573 . CAT TGA 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53939;SOR=Inf;LSEQ=TATTACTCGCCTTCAGGCCC;RSEQ=ATTTTTAACCTCCTTGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:4,15:0:2,0:24.2:1:31.9:1:1:0:60:38:1:0:0 0/1:36:2:1,1:8,26:0.0556:2,2:19.5:1:29.7:1:0.44286:3.12:54:4:0.0571:0.0278:1.5 -11 39588291 . C A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCGACAATAAGGGAAT;RSEQ=AAAGCTGGCCACCCAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 39878822 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=33.03521;LSEQ=TACTAATGTAATAGAAAGAA;RSEQ=ATTGATTATTTAAACTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:23:11,12:135,118:0.0833:2,2:29.2:1:29.7:1:0.66627:1.24706:60:46:0.0842:0:1 1/0:318:239:124,115:39,40:0.7516:2,2:23.2:1:28.5:1:0.79526:1.11:60:118.5:0.7548:0:1.1 -11 39878886 . C A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12705;SOR=Inf;LSEQ=CTTTTGTCTCTCTAGATTTC;RSEQ=TAACCCCTTGTTAAGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:84,154:0:2,0:26.4:1:31.6:1:1:0:60:118:1:0:0.1 0/1:273:4:2,2:98,171:0.0147:2,2:28.5:1:28.8:1:0.6254:1.74:60:8:0.0148:0:1.3 -11 39878908 . A T 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06268;SOR=Inf;LSEQ=AACCCCTTGTTAAGAGAATG;RSEQ=TTATGTTCATGTTTACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:48,123:0:2,0:24.4:1:30.6:1:1:0:60:170:1:0:0.1 0/1:191:5:2,3:61,125:0.0262:2,2:22.8:1:29:1:0.66553:1.36:60:10:0.0265:0:1.2 -11 39878930 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49858;SOR=Inf;LSEQ=TATGTTCATGTTTACAGTTT;RSEQ=AAAGACTCAAAATTGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:22,88:0:2,0:22.7:1:31.6:1:1:0:60:220:1:0:0.1 0/1:119:2:1,1:26,90:0.0168:2,2:31:1:28.5:1:0.40678:3.42:60:4:0.0171:0:1 -11 39878942 . ATTG TTT 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=19.57387;LSEQ=GTTTACAGTTTGAAAGACTC;RSEQ=TAAAAATTTCAGTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:10:2,8:10,67:0.1149:2,2:20.8:1:31.2:1:0.62328:1.66:60:20:0.1176:0.0115:0.1 1/0:90:65:10,55:2,21:0.7222:2,2:21.5:1:30.2:1:0.72434:1.90:59.9:130:0.7386:0.1667:0.1 -11 39880947 . C T 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTGAAGGTTGCAGTGAG;RSEQ=AGAGATTGCGCCACTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35:0:29.5:1:1:0:60:4:1:0:1.5 -11 39894251 . GACCT TAC 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24627;SOR=Inf;LSEQ=CTTCCTCCAAAAATTGATCT;RSEQ=CTGTTATTTCACTAACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:86,15:0:2,0:22.6:1:31.7:1:1:0:60:32.667:1:0:0.4 0/1:100:2:1,1:81,17:0.02:2,2:35.5:1:30.7:1:0.32909:4.65899:60:4:0.02:0:1 -11 39894253 . CCT C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=60.94758;LSEQ=TCCTCCAAAAATTGATCTGA;RSEQ=CTGTTATTTCACTAACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:10:9,1:82,15:0.0935:2,2:20.4:1:32.8:1:1:1.64:60:20:0.0943:0.028:0 1/1:120:104:80,24:11,3:0.8667:2,2:23.8:1:31.1:1:1:1.09913:60:208:0.8889:0.1833:0.1 -11 39894274 . C T 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCTGTTATTTCACTAACCC;RSEQ=CTCTACTCACAAAAATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:49:37,12:67,25:0.3475:2,2:24.2:1:30.8:1:0.84148:1.15:60:98:0.3475:0:1.1 0/0:166:0:0,0:118,47:0:2,0:25.2:1:30.3:1:1:0:60:330:1:0:0.1 -11 39894277 . CTACTCACAAAAAT C 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03594;SOR=Inf;LSEQ=TGTTATTTCACTAACCCCCT;RSEQ=TTGCCTCATGCCAAGCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:103,40:0:2,0:26.6:1:30.2:1:1:0:60:286:1:0:0.4 0/1:180:6:4,2:122,51:0.0333:2,2:17.3:1:31.5:1:1:1.19482:59.2:12:0.0337:0.0111:0.2 -11 39894373 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=38.32232;LSEQ=ACCTACTATGGGTATGTTGC;RSEQ=AGAGCTTTAGAAGGATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:28:10,18:92,126:0.1138:2,2:26.2:1:30.4:1:0.54823:1.31285:60:56:0.1148:0:1.1 1/1:305:254:108,146:25,26:0.8328:2,2:26.3:1:29.7:1:0.4403:1.29871:60:126:0.8372:0:1.1 -11 39894484 . T C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.0926;LSEQ=TGATTTGATGACAAATGATA;RSEQ=AAATCATTTATCAATCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:1,22:0,11:0.6765:0,1:26.3:1:32.6:1:1:0:60:46:0.6765:0:1.1 0/1:32:5:0,5:1,26:0.1563:1,0:28.6:1:31.8:1:1:0:60:10:0.1563:0:1 -11 41939837 . T C 87 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGCTAGATAGCATGCT;RSEQ=ACTCACTGCCTGCCTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:11.3:1:33:0:1:0:60:8:1:0:1 1/0:9:7:1,6:0,2:0.7778:0,2:30.6:1:31.3:1:1:0:60:14:0.7778:0:1.1 -11 42138390 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1479;SOR=Inf;LSEQ=ACAGATTAAAGGAGAGGTGA;RSEQ=ATTGAATGAGAAGTAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:48,4:0:2,0:26.8:1:32.1:1:1:0:60:104:1:0:0.4 0/1:33:2:1,1:26,5:0.0606:2,2:18:1:26:1:0.33523:4.83744:60:4:0.069:0:1 -11 42138434 . C T 170 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01073;LSEQ=AACATATGTACAATCCTGTG;RSEQ=CTTTAGTACCCTTTTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:55:34,21:34,20:0.5046:2,2:23.7:1:29.5:1:1:1.04956:60:110:0.514:0:1 0/1:94:1:0,1:59,34:0.0106:2,0:1:0:22:0:0.37234:0:60:2:0.0108:0:2 -11 42138471 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49928;SOR=Inf;LSEQ=ATTTAGATCTATCACTTTCA;RSEQ=CTGATCTCACATGATTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:74,62:0:2,0:30.8:1:30.7:1:1:0:60:135:1:0:0.8 0/1:149:2:1,1:85,62:0.0134:2,2:40:1:28.5:1:1:1.368:60:4:0.0137:0:1 -11 42138495 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24633;SOR=Inf;LSEQ=ATCTCACATGATTATGAAAG;RSEQ=TTGCTAGGCACGCCCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:81,90:0:2,0:23.5:1:31.6:1:1:0:60:170:1:0:0.8 0/1:169:2:1,1:89,78:0.0118:2,2:27.5:1:28:1:1:1.14013:60:4:0.012:0:1 -11 42138498 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49853;SOR=0;LSEQ=TCACATGATTATGAAAGGTT;RSEQ=CTAGGCACGCCCATCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:80,88:0.0118:2,2:35.5:1:29.5:1:1:1.10:60:4:0.0119:0:2 0/0:168:0:0,0:90,78:0:2,0:24.6:1:31.7:1:1:0:60:55:1:0:0.7 -11 42138514 . C T 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0481;SOR=1.56218;LSEQ=GGTTGCTAGGCACGCCCATC;RSEQ=TCATACAACAATGGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:86:40,46:37,43:0.5119:2,2:21.8:1:30.4:1:1:1.01:60:85:0.5152:0:1.1 1/0:169:105:55,50:27,37:0.6213:2,2:23.9:1:29.9:1:0.20878:1.50:60:34:0.6145:0:1.1 -11 42138579 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=GGGATGCAGAGTCATTGGTG;RSEQ=TTTAAAATTATGCATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:45,83:0:2,0:25.1:1:31.9:1:1:0:60:41.667:1:0:0.3 0/1:137:2:1,1:54,81:0.0146:2,2:32:0:31.5:1:1:1.50:60:4:0.0148:0:1 -11 42138604 . CTT C 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03068;SOR=Inf;LSEQ=AAATTATGCATTTATTCTCT;RSEQ=AGCCATAGGTAGGATAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:29,57:0:2,0:23.5:1:30.3:1:1:0:60:172:1:0:0.1 0/1:98:6:2,4:34,58:0.0612:2,2:12.5:1:30.2:1:1:1.17059:60:12:0.0619:0.0306:0 -11 42138732 . G C 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.58042;SOR=3.65648;LSEQ=TAAGATATTATATGATGGAG;RSEQ=ATGTTATATGATGGATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:19.8:1:29.8:1:1:0:60:4:0.4444:0:2.4 1/1:5:4:0,4:0,1:0.8:0,0:20.3:1:30.8:1:1:0:60:8:0.8:0:1.3 -11 43266834 . C A 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.04777;LSEQ=CTCCAAAGGACACAACTTTA;RSEQ=AATAAAAGCAAGTACTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:191:86,105:98,118:0.467:2,2:24.3:1:29.7:1:1:1.01396:60:37.2:0.465:0:1.1 1/0:506:325:160,165:83,96:0.6423:2,2:25.5:1:29.4:1:0.57661:1.12:60:45.429:0.645:0:1.2 -11 44368381 . A G 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.16408;LSEQ=GGATTCCTGGAGCTGTCCTC;RSEQ=TAGCTGCAAGTACCTGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:174:93,81:114,100:0.4485:2,2:28.1:1:30.7:1:1:1.01:60:173:0.447:0:1.8 1/0:428:273:131,142:76,79:0.6379:2,2:26.1:1:30.2:1:0.84122:1.04273:60:135.5:0.6392:0:1.7 -11 44368416 . G T 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-04;SOR=1.7066;LSEQ=TGGCACCTTTACACATCAGT;RSEQ=CCTCCCTCCCTCTGCCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:155:66,89:91,102:0.4454:2,2:24.3:1:29.9:1:0.44819:1.20242:60:76.5:0.4513:0:1.9 1/0:351:203:80,123:64,82:0.5783:2,2:26:1:28.6:1:0.44106:1.19936:60:19.3:0.571:0:1.9 -11 44368605 . T C 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10294;SOR=0;LSEQ=TTTGTTGGCTGGCTTTGCCT;RSEQ=CGGGAGGTGTGAGCCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:0.5385:0,0:32.1:1:31.3:1:1:0:60:14:0.5385:0:1 0/0:4:0:0,0:0,4:0:0,0:20.5:1:29.8:1:1:0:60:8:1:0:0 -11 44458019 . A G 55 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGGCATGGCACATAGTA;RSEQ=CCTCCTATGAATGTTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:37:1:27.5:1:1:0:60:3:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 47286171 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21151;SOR=0;LSEQ=ATATCCTCCTTGTGGAACCC;RSEQ=GCCCAGTTCTAAGATCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:39,14:0.0364:2,2:31.5:1:31:1:0.47475:2.72554:60:4:0.037:0:1 0/0:64:0:0,0:50,14:0:2,0:26.6:1:30.7:1:1:0:60:128:1:0:0.1 -11 47286271 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19558;SOR=0;LSEQ=TTATACAAGCAGTTTTGAAG;RSEQ=AATCATGCTTGCATTTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:104,84:0.0105:2,2:12.5:1:28.5:1:1:1.23669:60:4:0.0105:0:1.5 0/0:239:0:0,0:121,118:0:2,0:24.7:1:28.3:1:1:0:60:118.5:1:0:0.3 -11 47286290 . T C 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAATCATGCTTGCATTTCT;RSEQ=ATTTCATGAGTGAGGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:95,95:0:2,0:27.1:1:29.2:1:1:0:60:94:1:0:0.1 0/1:250:26:13,13:112,112:0.104:2,2:27.7:1:31.3:1:1:1:60:52:0.1057:0:1.1 -11 47286347 . TC T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5061;SOR=Inf;LSEQ=GCTCTGCTTGTCAAGTCTCC;RSEQ=CCCTCCCTATCCGCTACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:52,86:0:2,0:24.8:1:31.2:1:1:0:59.9:68:1:0:0.2 0/1:177:2:1,1:68,107:0.0113:2,2:18.5:1:30:1:1:1.57:60:4:0.0114:0:0 -11 47286414 . G A 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03738;SOR=Inf;LSEQ=GACATGGACTGAGCACATTT;RSEQ=AGGTGTTCATTCCGTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:3,27:0:2,0:24.7:1:30.8:1:1:0:60:14:1:0:0.1 0/1:42:6:1,5:4,32:0.1429:2,2:36.2:1:30.7:1:0.55683:1.58:60:12:0.1463:0:1 -11 51578637 . A T 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTTCTGATAATGCTTC;RSEQ=GTTTAGCTTTTATGTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:1:29.5:1:1:0:23:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 51578642 . A C 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGATAATGCTTCAGTTT;RSEQ=GCTTTTATGTGAAGATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:30:1:1:0:23:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 51578649 . A C 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGCTTCAGTTTAGCTTTT;RSEQ=TGTGAAGATTATCCCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:32:1:1:0:23:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 51578660 . A C 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGCTTTTATGTGAAGATT;RSEQ=TCCCTTTTCCAACGAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:1:33:1:1:0:23:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 51578665 . T G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATGTGAAGATTATCCC;RSEQ=TTTCCAACGAAATCTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38:1:32:0:1:0:23:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 51578686 . G AT 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.33333;SOR=Inf;LSEQ=TTTCCAACGAAATCTTCAAA;RSEQ=AGGTCCAAATATCCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:0:33.5:1:1:0:23:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:17.5:1:31:1:1:0:25:4:1:0:3 -11 51578711 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATATCCACTTGCAGAT;RSEQ=CCACAGAAAGAGTGTTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:30.5:1:1:0:25:4:1:0:3 -11 51578717 . G C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCACTTGCAGATCCCACA;RSEQ=AAAGAGTGTTTAGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:32.5:1:1:0:25:4:1:0:3 -11 51578768 . T G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATCTTCAACTCTGTGAG;RSEQ=TGAATGCAATCATCACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:49.5:4:1:0:3.5 -11 51578804 . CT TA 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCAGTTTCTGAGAATG;RSEQ=TCTGTCTAGTTTTTATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:27.3:1:1:0:49.5:4:1:0:2.5 -11 51578902 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACGAAAGGAGAGTTTCA;RSEQ=AACTCCTCTATGAAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:33.5:1:1:0:60:4:1:0:2.5 -11 51578907 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAGGAGAGTTTCAAAACT;RSEQ=CTCTATGAAAAGCAATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:31:1:1:0:60:4:1:0:2.5 -11 51579291 . C A 49 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTGAGTTGAATGCAAAC;RSEQ=TCACAAAGAAGTTTCGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:17.3:1:31:1:1:0:36.3:6:1:0:7 -11 51579303 . T A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCAAACCTCACAAAGAAG;RSEQ=TTCGGAGAATGCTTCCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:5,2:0.2222:2,2:6:1:28.5:1:1:2.23609:41:4:0.2222:0:7.5 -11 51579307 . GG TC 89 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCTCACAAAGAAGTTTC;RSEQ=AGAATGCTTCCGTGTAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:10:8:5,3:0,0:0.8:0,2:19.4:1:29.7:1:1:0:39.1:16:0.8:0.1:5.5 -11 51579310 . G C 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCACAAAGAAGTTTCGGA;RSEQ=AATGCTTCCGTGTAGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:2:0:33.5:1:1:0:44:4:1:0:4 0/1:10:3:2,1:4,3:0.3:2,2:34.3:1:29.7:1:1:1.44:46.7:6:0.3:0:6 -11 51579312 . A C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCACAAAGAAGTTTCGGAGA;RSEQ=TGCTTCCGTGTAGTTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:3.3:1:31.7:1:1:0:41.3:6:1:0:5.3 0/1:12:2:1,1:6,4:0.1667:2,2:15:1:29.5:1:1:1.4491:41:4:0.1818:0:7.5 -11 51579337 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCGTGTAGTTCTGGGAAGT;RSEQ=TCTCCCGTTTCCAACGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:28.3:1:31.7:1:1:0:41.3:6:1:0:5.3 0/1:13:2:1,1:6,5:0.1538:2,2:26:0:31:1:1:1.18321:40:4:0.1538:0:7.5 -11 51579339 . C A 105 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGTAGTTCTGGGAAGTTT;RSEQ=TCCCGTTTCCAACGAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:30.3:1:30.7:1:1:0:41.3:6:1:0:5.3 1/1:13:13:7,6:0,0:1:0,2:36.2:1:28.5:1:1:0:38.8:26:1:0:5.9 -11 51579344 . G T 68 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50893;SOR=Inf;LSEQ=AGTTCTGGGAAGTTTCTCCC;RSEQ=TTTCCAACGAAATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:36:0:32.5:1:1:0:44:4:0.6667:0:4 0/1:13:5:3,2:4,4:0.3846:2,2:36.6:1:29.4:1:1:1.45:45.2:10:0.3846:0:6 -11 51579355 . A C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTCTCCCGTTTCCAACGA;RSEQ=ATTCTCAGAGAGGTCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:46.3:1:31:1:1:0:41.3:6:1:0:5.3 0/1:13:2:1,1:6,5:0.1538:2,2:44:0:32.5:1:1:1.18321:40:4:0.1667:0:7.5 -11 51579358 . T C 105 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCCCGTTTCCAACGAAAT;RSEQ=CTCAGAGAGGTCCAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:46.7:1:32.3:1:1:0:41.3:6:1:0:5.3 1/0:13:10:5,5:2,1:0.7692:2,2:40.2:1:31.8:1:1:1.89792:36.4:20:0.7692:0:5.9 -11 51579367 . G A 79 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.91151;LSEQ=TCCAACGAAATTCTCAGAGA;RSEQ=GTCCAAATATCCACTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:44:0:32:0:1:0:36:2:0.3333:0:8 1/0:12:6:3,3:3,3:0.5:2,2:27.3:1:30.7:1:1:1:44.3:12:0.5:0:7 -11 51579389 . A T 97 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAATATCCACTTGCAGA;RSEQ=TCTACAAAAAGTGTCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:17.3:1:30.3:1:1:0:41.3:6:1:0:5.3 1/1:9:9:3,6:0,0:1:0,2:10.9:1:30.9:1:1:0:40.7:18:1:0:6.2 -11 51579396 . A G 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCACTTGCAGAATCTACA;RSEQ=AAAGTGTCTTTGGAAATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:10.3:1:31:1:1:0:41.3:6:1:0:5.3 1/1:6:6:2,4:0,0:1:0,2:7:1:31.2:1:1:0:39.3:12:1:0:6.7 -11 51579458 . C G 87 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCTCTGAGATAAATACAAT;RSEQ=ATCACAAAGAATTTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:5:0:33.8:1:1:0:37.7:12:1:0:7.7 1/1:2:2:2,0:0,0:1:0,0:5:0:33:1:1:0:40:4:1:0:7.5 -11 51579464 . A T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATAAATACAATCATCAC;RSEQ=AAGAATTTTCTGTGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:10.3:1:32.7:1:1:0:38:14:1:0:7.6 1/1:2:2:2,0:0,0:1:0,0:11:0:32:1:1:0:40:4:1:0:7.5 -11 51579472 . T G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAATCATCACAAAGAATT;RSEQ=TCTGTGAATGCTTCCGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:16.6:1:33.5:1:1:0:39.1:16:1:0:7.5 1/1:3:3:2,1:0,0:1:0,2:13.3:1:30.3:1:1:0:35:6:1:0:7.7 -11 51579500 . TG GA 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.64297;LSEQ=ATGCTTCCGTTTGGTTTTTA;RSEQ=TGAAGTTATTTCCTTTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:0,0:0.8:0,0:38.4:1:31.1:1:1:0:38.6:16:0.8:0:6.6 1/0:7:5:3,2:0,0:0.7143:0,2:29:1:31.1:1:1:0:37.6:10:0.7143:0:6.4 -11 51579511 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=TGGTTTTTATGTGAAGTTAT;RSEQ=TCCTTTAATACCGTAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:8,1:0.1818:2,2:39.5:1:32.5:1:0.34545:6:47:4:0.1818:0:7 0/0:11:0:0,0:8,3:0:2,0:24.5:1:29.1:1:1:0:41:10:1:0:6.8 -11 51579516 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=TTTATGTGAAGTTATTTCCT;RSEQ=TAATACCGTAGGCCACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:9,2:0:2,0:28.7:1:29.1:1:1:0:39.9:22:1:0:6.8 0/1:11:2:1,1:7,2:0.1818:2,2:15:0:33.5:1:0.49091:3.05504:43:4:0.1818:0:6.5 -11 51579519 . A C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGAAGTTATTTCCTTTA;RSEQ=TACCGTAGGCCACAAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:9,2:0,0:1:0,2:27.6:1:31:1:1:0:39.9:22:1:0:6.8 1/1:11:11:8,3:0,0:1:0,2:29.5:1:31.6:1:1:0:41:22:1:0:6.8 -11 51579523 . C A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTATTTCCTTTAATAC;RSEQ=GTAGGCCACAAAGCAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:9,2:0,0:1:0,2:25.8:1:29:1:1:0:39.9:22:1:0:6.8 1/1:13:13:9,4:0,0:1:0,2:27:1:29.2:1:1:0:39.5:26:1:0:7 -11 51579531 . A T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68082;SOR=0.55083;LSEQ=TTCCTTTAATACCGTAGGCC;RSEQ=CAAAGCAGTCCAAATCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:11,3:1,0:0.875:0,2:16.2:1:29.5:1:1:0:39.6:28:0.9333:0:6.9 1/0:24:19:11,8:1,1:0.7917:2,2:16.4:1:27.6:1:1:1.35:43.8:18:0.8182:0:7.1 -11 51579537 . C T 27 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55428;SOR=0.30639;LSEQ=TAATACCGTAGGCCACAAAG;RSEQ=AGTCCAAATCTCCAATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:14,7:0.087:2,2:5:1:27.5:1:1:1.93655:60:4:0.0909:0:7.5 0/1:36:1:0,1:19,16:0.0278:2,0:1:0:21:0:0.47222:0:60:2:0.0286:0:7 -11 51579547 . C T 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55108;SOR=Inf;LSEQ=GGCCACAAAGCAGTCCAAAT;RSEQ=TCCAATTGCAGATTGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:14.6:1:31.5:1:1:0:51.8:50:1:0:6.8 0/1:59:3:1,2:31,25:0.0508:2,2:5.3:1:28.3:1:0.58805:2.44273:56:6:0.0536:0:7.3 -11 51579553 . TT AG 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGCAGTCCAAATCTCCAA;RSEQ=GCAGATTGTACAAAAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,12:0:2,0:18.2:1:30.2:1:1:0:51.2:24:0.96:0:6.8 0/1:70:2:1,1:36,32:0.0286:2,2:19.5:1:30.8:1:1:1.1231:43:4:0.029:0:5.5 -11 51579554 . T C 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.65639;LSEQ=AAGCAGTCCAAATCTCCAAT;RSEQ=GCAGATTGTACAAAAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:26:14,12:0,0:0.963:0,2:18.2:1:30.2:1:1:0:51.6:25:1:0:6.7 1/1:72:68:36,32:0,0:0.9444:0,2:16.6:1:29.6:1:1:0:49.9:33:0.9706:0:6.8 -11 51579562 . G C 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05242;SOR=9.19803;LSEQ=CAAATCTCCAATTGCAGATT;RSEQ=TACAAAAAGAGTGTTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:30:14,16:1,1:0.9091:2,2:21:1:31.3:1:1:1.13808:51.3:29:0.9063:0:6.6 1/1:95:94:51,43:0,1:0.9895:0,2:18.2:1:31.1:1:0.46316:0:49.2:93:0.9894:0:6.5 -11 51579573 . G T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.68474;LSEQ=TTGCAGATTGTACAAAAAGA;RSEQ=TGTTTACAAACTGCACTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:45:23,22:0,0:0.9783:0,2:22.9:1:30.3:1:1:0:51.2:90:1:0:6.2 1/1:127:123:61,62:1,1:0.9685:2,2:21.6:1:29.7:1:1:1.01626:50.5:122:0.976:0:6.1 -11 51579579 . A T 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57401;SOR=Inf;LSEQ=ATTGTACAAAAAGAGTGTTT;RSEQ=CAAACTGCACTATCCATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:24,25:0:2,0:26.3:1:28.8:1:1:0:49.3:98:1:0:6 0/1:141:4:2,2:66,71:0.0284:2,2:33.8:1:29.3:1:1:1.08:39:8:0.0286:0:7.8 -11 51579583 . A C 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60489;SOR=1.95171;LSEQ=TACAAAAAGAGTGTTTACAA;RSEQ=CTGCACTATCCATAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:49:24,25:0,0:0.9608:0,2:27.8:1:31.6:1:1:0:48.9:98:0.9608:0:5.9 1/1:147:144:69,75:1,1:0.9796:2,2:25.5:1:31.3:1:1:1.08632:50.6:143:0.9862:0:5.8 -11 51579586 . G T 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57411;SOR=Inf;LSEQ=AAAAAGAGTGTTTACAAACT;RSEQ=CACTATCCATAGGAATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,27:0:2,0:28.7:1:32:1:1:0:49.5:104:1:0:5.9 0/1:152:4:2,2:71,76:0.0263:2,2:28:1:29.8:1:1:1.07:54.8:8:0.027:0:7 -11 51579588 . A T 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0659;SOR=Inf;LSEQ=AAAGAGTGTTTACAAACTGC;RSEQ=CTATCCATAGGAATGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:51:24,27:1,1:0.9623:2,2:29.5:1:29.9:1:1:1.1225:50.2:50:0.9615:0:5.9 1/1:152:152:72,80:0,0:1:0,2:27.5:1:29.9:1:1:0:50.7:75:1:0:5.7 -11 51579594 . C T 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18732;SOR=0;LSEQ=TGTTTACAAACTGCACTATC;RSEQ=ATAGGAATGTTCAACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:28,37:0,0:1:0,2:25.8:1:29:1:1:0:50.5:64:1:0:5.3 1/1:164:158:73,85:3,2:0.9634:2,2:28.2:1:29:1:0.66483:1.74061:50.8:30.6:0.9623:0:5.5 -11 51579597 . A T 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56253;SOR=Inf;LSEQ=TTACAAACTGCACTATCCAT;RSEQ=GGAATGTTCAACTCTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:29,36:0:2,0:26.3:1:29.3:1:1:0:50.3:31.5:0.9844:0:5.2 0/1:172:3:1,2:79,89:0.0174:2,2:29:1:29.3:1:1:1.76957:47:6:0.0178:0:6.7 -11 51579598 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACAAACTGCACTATCCATA;RSEQ=GAATGTTCAACTCTGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:29,37:0:2,0:26.8:1:31.1:1:1:0:50.5:32:1:0:5.2 0/1:175:2:1,1:80,92:0.0114:2,2:39.5:1:29.5:1:1:1.15:60:4:0.0116:0:7.5 -11 51579602 . T G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56623;SOR=Inf;LSEQ=AACTGCACTATCCATAGGAA;RSEQ=GTTCAACTCTGTGAGTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:30,39:0:2,0:27.1:1:30.2:1:1:0:50.4:68:1:0:5.1 0/1:188:3:2,1:86,99:0.016:2,2:18.7:1:30.3:1:0.60031:2.29:43.3:6:0.016:0:5 -11 51579603 . G A 57 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57681;SOR=Inf;LSEQ=ACTGCACTATCCATAGGAAT;RSEQ=TTCAACTCTGTGAGTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:32,39:0:2,0:26.7:1:31.8:1:1:0:50:70:1:0:5 0/1:192:4:2,2:88,100:0.0208:2,2:17.5:1:28.8:1:1:1.14:56.3:8:0.0212:0:5.3 -11 51579605 . T G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCACTATCCATAGGAATGT;RSEQ=CAACTCTGTGAGTCGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:33,39:0:2,0:26.9:1:29.9:1:1:0:49.7:144:1:0:4.9 0/1:196:2:1,1:92,102:0.0102:2,2:20.5:1:31.5:1:1:1.11:59:4:0.0105:0:5 -11 51579606 . C G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0713;SOR=0;LSEQ=GCACTATCCATAGGAATGTT;RSEQ=AACTCTGTGAGTCGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:33,38:0.0274:2,2:29.5:1:32:1:1:1.15:48.5:4:0.0286:0:7.5 0/0:199:0:0,0:93,104:0:2,0:27.1:1:31.5:1:1:0:50.9:64.667:0.9898:0:5 -11 51579610 . T A 48 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01646;SOR=0;LSEQ=TATCCATAGGAATGTTCAAC;RSEQ=CTGTGAGTCGAATGCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:2,1:31,37:0.0411:2,2:27:1:30.7:1:0.5941:2.36:41.7:6:0.0417:0:6.3 0/0:211:0:0,0:96,115:0:2,0:26:1:29.7:1:1:0:51.4:41.2:1:0:4.7 -11 51579614 . T A 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16535;SOR=0.17199;LSEQ=CATAGGAATGTTCAACTCTG;RSEQ=GAGTCGAATGCAATCATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:33,38:0.0274:2,2:22:1:29:1:1:1.15:60:4:0.0278:0:6.5 0/0:209:1:1,0:94,113:0.0048:2,0:1:0:24:0:0.45673:0:60:2:0.0048:0:7 -11 51579620 . G C 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.576;SOR=Inf;LSEQ=AATGTTCAACTCTGTGAGTC;RSEQ=AATGCAATCATCACAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:34,40:0:2,0:28.2:1:30.5:1:1:0:49.3:73:1:0:4.6 0/1:207:4:2,2:90,112:0.0193:2,2:21:1:30.5:1:1:1.24:52.5:8:0.0195:0:5.3 -11 51579624 . G T 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56616;SOR=Inf;LSEQ=TTCAACTCTGTGAGTCGAAT;RSEQ=CAATCATCACAAAGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:34,40:0:2,0:27.8:1:31.7:1:1:0:49.3:36:1:0:4.6 0/1:201:3:2,1:85,113:0.0149:2,2:31.3:1:29.3:1:0.57971:2.65:47.3:6:0.0151:0:6 -11 51579625 . C G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.29711;SOR=0.36707;LSEQ=TCAACTCTGTGAGTCGAATG;RSEQ=AATCATCACAAAGTAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:33,39:0.027:2,2:29.5:1:31:1:1:1.18:48.5:4:0.027:0:7.5 0/1:199:2:1,1:85,109:0.0101:2,2:25:0:33:0:1:1.28:60:4:0.0103:0:3.5 -11 51579626 . A C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAACTCTGTGAGTCGAATGC;RSEQ=ATCATCACAAAGTAGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:34,40:0:2,0:27.5:1:30.1:1:1:0:49.2:148:1:0:4.6 0/1:199:2:1,1:85,112:0.0101:2,2:30.5:1:31.5:1:1:1.32:60:4:0.0101:0:3 -11 51579629 . C T 47 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01785;SOR=0;LSEQ=CTCTGTGAGTCGAATGCAAT;RSEQ=ATCACAAAGTAGTTTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:0,3:31,36:0.0429:2,0:42:1:29.7:1:0.24907:0:47.7:6:0.0441:0:4.3 0/0:195:0:0,0:83,110:0:2,0:26.5:1:31.4:1:1:0:50.8:192:0.9897:0:4.5 -11 51579632 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTGAGTCGAATGCAATCAT;RSEQ=ACAAAGTAGTTTCTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:29,39:0:2,0:28.8:1:31.8:1:1:0:49.3:136:1:0:4.4 0/1:185:2:1,1:78,104:0.0108:2,2:27.5:1:29:1:1:1.33:47:4:0.0109:0:6.5 -11 51579634 . C A 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.67536;LSEQ=TGAGTCGAATGCAATCATCA;RSEQ=AAAGTAGTTTCTGAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:25,34:0.0164:2,0:33:0:31:0:1:0:39:2:0.0167:0:8 0/1:180:2:1,1:77,101:0.0111:2,2:39.5:1:29.5:1:1:1.31:54.5:4:0.0114:0:5.5 -11 51579636 . A G 112 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04051;SOR=Inf;LSEQ=AGTCGAATGCAATCATCACA;RSEQ=AGTAGTTTCTGAGAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:25,35:0:2,0:31.8:1:30.1:1:1:0:47.9:29:1:0:4.1 0/1:178:12:5,7:72,94:0.0674:2,2:31.1:1:31.5:1:1:1.07194:47.1:24:0.0686:0:5.5 -11 51579639 . T G 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22924;LSEQ=CGAATGCAATCATCACAAAG;RSEQ=AGTTTCTGAGAATGCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:24,34:0.0333:2,2:32.5:1:32.5:1:1:1.41:60:4:0.0339:0:5.5 0/1:172:7:2,5:71,92:0.0407:2,2:27:1:32.4:1:0.70003:1.92238:47.6:14:0.0412:0:4.7 -11 51579641 . G C 34 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16744;SOR=0.17321;LSEQ=AATGCAATCATCACAAAGTA;RSEQ=TTTCTGAGAATGCTTCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:24,34:0.0333:2,2:37.5:1:34:0:1:1.41:33.5:4:0.0345:0:6 0/0:170:1:0,1:71,95:0.0059:2,0:39:0:28:0:1:0:35:2:0.0059:0:6 -11 51579642 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGCAATCATCACAAAGTAG;RSEQ=TTCTGAGAATGCTTCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:25,35:0:2,0:29.8:1:30.4:1:1:0:47.9:120:1:0:4.1 0/1:166:2:1,1:68,94:0.012:2,2:23:1:32.5:1:1:1.38:53:4:0.0122:0:6.5 -11 51579645 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAATCATCACAAAGTAGTTT;RSEQ=TGAGAATGCTTCTATCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:24,34:0:2,0:29.1:1:31.8:1:1:0:47.5:57:1:0:4.1 0/1:158:2:1,1:64,91:0.0127:2,2:25:1:28.5:1:1:1.42:44.5:4:0.0129:0:6 -11 51579649 . G A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCACAAAGTAGTTTCTGA;RSEQ=AATGCTTCTATCTAGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:24,33:0:2,0:27.1:1:32:1:1:0:47.8:114:1:0:4 0/1:145:2:1,1:58,85:0.0138:2,2:9:0:28:1:1:1.46:46:4:0.0142:0:4 -11 51579651 . A G 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75479;LSEQ=TCACAAAGTAGTTTCTGAGA;RSEQ=TGCTTCTATCTAGTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:1:0,1:22,30:0.0189:2,0:9:0:33:0:1:0:50:2:0.0192:0:8 0/1:140:2:1,1:56,82:0.0143:2,2:46.5:1:31.5:1:1:1.46:57.5:4:0.0144:0:6 -11 51579658 . T C 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.49347;SOR=2.49486;LSEQ=GTAGTTTCTGAGAATGCTTC;RSEQ=ATCTAGTTTTTATGTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:47:20,27:0,1:0.9792:0,2:23.9:1:32.1:1:1:0:47.8:94:0.9792:0:3.6 1/1:119:118:48,70:0,1:0.9916:0,2:25:1:30.9:1:1:0:50.7:117:0.9915:0:3.8 -11 51579661 . CT AA 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTCTGAGAATGCTTCTAT;RSEQ=AGTTTTTATGTGAAGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:20,26:0:2,0:22.3:1:32.2:1:1:0:48.1:92:1:0:3.6 0/1:109:2:1,1:40,66:0.0183:2,2:18:0:29:1:1:1.64:59.5:4:0.0187:0:3 -11 51579663 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTGAGAATGCTTCTATCT;RSEQ=GTTTTTATGTGAAGATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:20,25:0:2,0:21:1:30.1:1:1:0:47.8:90:1:0:3.5 0/1:108:2:1,1:39,64:0.0185:2,2:35.5:1:29.5:1:1:1.63:56.5:4:0.0187:0:2 -11 51579665 . T C 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGAGAATGCTTCTATCTAG;RSEQ=TTTTATGTGAAGATGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,22:0:2,0:19.9:1:30:1:1:0:47.4:84:0.9767:0:3.3 0/1:105:2:1,1:39,63:0.019:2,2:6:0:30:1:1:1.61:59.5:4:0.019:0:5.5 -11 51579673 . T G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62505;SOR=0.59547;LSEQ=GCTTCTATCTAGTTTTTATG;RSEQ=GAAGATGTTTCCTTTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:12,20:0.0588:2,2:26.5:1:32.5:1:1:1.64:54:4:0.0588:0:2 0/1:84:3:1,2:31,50:0.0357:2,2:17.3:1:31.7:1:1:1.23689:52:6:0.0361:0:3.7 -11 51579679 . TG T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.52465;LSEQ=ATCTAGTTTTTATGTGAAGA;RSEQ=TTTCCTTTTCCACCACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:24:9,15:0,0:0.96:0,2:16.2:1:30.7:1:1:0:48.2:48:0.96:0.2:2.5 1/1:54:50:20,30:0,1:0.9259:0,2:19.3:1:30.2:1:1:0:50:100:0.9434:0.0556:2.5 -11 51579703 . G C 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01818;SOR=0;LSEQ=TCCTTTTCCACCACAGGCCT;RSEQ=GACGCACTCCAAATGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:6.7:1:29.3:1:1:0:37.3:6:0.75:0:2.7 0/0:8:0:0,0:0,1:0:0,0:27:0:33:0:1:0:40:2:0.125:0:4 -11 51579706 . C A 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCCACCACAGGCCTGGA;RSEQ=GCACTCCAAATGTCCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17.5:1:31.5:1:1:0:40:4:1:0:4 1/1:7:7:0,7:0,0:1:0,0:19.9:1:32.9:1:1:0:31.4:14:1:0:4.3 -11 51579709 . A C 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACCACAGGCCTGGACGC;RSEQ=CTCCAAATGTCCACTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:33:0:1:0:40:4:1:0:4 1/1:7:7:0,7:0,0:1:0,0:16.9:1:32.7:1:1:0:31.4:14:1:0:4.3 -11 51580091 . C G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTACCAAAAGAGTGTCT;RSEQ=AAAGCTGAACTATGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:21:1:29.5:1:1:0:23.5:4:1:0:5.5 -11 51580110 . G C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAAGCTGAACTATGAAAG;RSEQ=AAGGTTCAACTCTGTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:21:1:31:1:1:0:23.5:4:1:0:5.5 -11 51580157 . GG TC 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATCACAAAGAAGTTTC;RSEQ=AGAATGCTTCCGTGTAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:21.7:1:29.7:1:1:0:23.3:6:1:0:5.3 -11 51580204 . C A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTATCCCGTTTCCAACA;RSEQ=AATCCTCAGAGAGGTCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:28:1:28:1:1:0:28:4:1:0:6.5 -11 51580206 . A C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTATCCCGTTTCCAACACA;RSEQ=TCCTCAGAGAGGTCCGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:30:1:30:1:1:0:28:4:0.5:0:6.5 -11 51580222 . G A 61 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAATCCTCAGAGAGGTCC;RSEQ=AATATCCACTTGCAGATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:27.3:1:30.5:1:1:0:25.8:8:1:0:5.8 -11 51580240 . C T 46 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGAATATCCACTTGCAGAT;RSEQ=CTACAAAAAGTGTGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:24.7:1:29.3:1:1:0:26.3:6:1:0:6.3 -11 51580246 . A G 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCACTTGCAGATCCTACA;RSEQ=AAAGTGTGTTTGGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:20.3:1:31.7:1:1:0:26.3:6:1:0:6.3 -11 51580423 . G T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGGCAGATTCTACAAAAAGA;RSEQ=TGTTGACAAACTGTTCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:28.5:1:1:0:31:4:1:0:7 -11 51580428 . G T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCTACAAAAAGAGTGTT;RSEQ=ACAAACTGTTCTATCCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28:1:1:0:31:4:1:0:7 -11 51580433 . A C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAAGAGTGTTGACAA;RSEQ=CTGTTCTATCCATAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29.5:1:1:0:31:4:1:0:7 -11 51580437 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGAGTGTTGACAAACTG;RSEQ=TCTATCCATAGGAATGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31.5:1:1:0:31:4:1:0:7 -11 51580444 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTGACAAACTGTTCTATC;RSEQ=ATAGGAATGTCCAACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39.5:1:29.5:1:1:0:31:4:1:0:7 -11 51580455 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTCTATCCATAGGAATGT;RSEQ=CAACTCTGTGAGTCGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:49:0:30:1:1:0:31:4:1:0:7 -11 51580508 . T C 47 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTAGTTTCTGAGAATGCTTC;RSEQ=ATCTAGTATTCATGTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:41.5:1:31:0:1:0:39.5:4:1:0:5 1/0:5:3:3,0:1,1:0.6:2,0:41.7:1:29.7:1:0.4:0:40:6:0.6:0:5.3 -11 51580516 . A T 54 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAATGCTTCTATCTAGT;RSEQ=TTCATGTGAAGATATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:46:1:20.5:1:1:0:39.5:1:1:0:5 1/1:5:5:4,1:0,0:1:0,2:47:1:23.6:1:1:0:44.2:1.5:1:0:5 -11 51580519 . C T 42 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GAATGCTTCTATCTAGTATT;RSEQ=ATGTGAAGATATTTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:46:1:30.5:1:1:0:39.5:4:1:0:5 1/0:6:3:2,1:0,0:0.5:0,2:33.3:1:26.7:1:1:0:34:6:0.5:0:5.7 -11 51580529 . TA T 41 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=ATCTAGTATTCATGTGAAGA;RSEQ=TTTCCTTTTCCACCGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:27:1:30.1:1:1:0:38.7:6:1:0.3333:5.7 1/0:5:3:2,1:1,1:0.6:2,2:29.3:1:26.3:1:1:1.73:34:6:0.6:0:5 -11 51580545 . G A 49 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AAGATATTTCCTTTTCCACC;RSEQ=CAGGCCTCAAAGCCCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:19.3:1:27.5:1:1:0:37.5:8:1:0:6.3 1/0:6:4:3,1:1,1:0.6667:2,2:24.3:1:24.8:1:1:2.45:35.5:8:1:0:5.3 -11 51580579 . C G 62 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=CCTCCAAATGTCCACTTGCA;RSEQ=ATTCTAGAAAAAGAGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:37.5:1:31.3:1:1:0:41.8:8:1:0:7 1/0:4:2:0,2:0,1:0.5:0,0:29:1:32:1:1:0:29:4:0.5:0:4.5 -11 51580589 . A T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=TCCACTTGCACATTCTAGAA;RSEQ=AAGAGTGTTTCATAGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:39:1:28.5:1:1:0:35.5:4:0.5:0:7.5 1/0:3:2:0,2:1,0:0.6667:0,0:20:1:30:0:0.33333:0:29:4:0.6667:0:4.5 -11 51580595 . T G 64 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TGCACATTCTAGAAAAAGAG;RSEQ=GTTTCATAGCTGCTCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:34.8:1:32:1:1:0:41.8:8:1:0:7 1/0:3:2:0,2:1,0:0.6667:0,0:14:1:32:0:0.33333:0:29:4:0.6667:0:4.5 -11 51580602 . T G 65 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCTAGAAAAAGAGTGTTTCA;RSEQ=AGCTGCTCTTTCCAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:31.3:1:32.5:1:1:0:41.8:8:1:0:7 1/0:3:2:0,2:1,0:0.6667:0,0:7:1:33:0:0.33333:0:29:4:0.6667:0:4.5 -11 51580612 . T G 51 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTGTTTCATAGCTGCTCT;RSEQ=TCCAGAGGAAAGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,0:0.75:0,0:26:1:32.3:1:1:0:43.7:6:0.75:0:7.7 1/1:1:1:1,0:0,0:1:0,0:38:0:29:0:1:0:60:2:1:0:7 -11 51580615 . C A 63 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTCATAGCTGCTCTTTC;RSEQ=AGAGGAAAGTTCAACTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:21:1:31.5:1:1:0:41.8:8:1:0:7 1/1:1:1:1,0:0,0:1:0,0:35:0:27:0:1:0:60:2:1:0:7 -11 51580630 . C T 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTCCAGAGGAAAGTTCAA;RSEQ=TCTGGAAGTTGAACACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:31.5:1:1:0:47:4:1:0:8 1/0:2:1:0,1:1,0:0.5:0,0:14:0:32:0:1:0:40:2:0.5:0:5 -11 51580961 . G C 69 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAAGCTGAACTATGAAAG;RSEQ=AAGGTTCAACCCTGTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:33.4:1:29.8:1:1:0:38.4:4:1:0:3 -11 51580972 . C T 72 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGAAAGGAAGGTTCAAC;RSEQ=CTGTGAGTTGAATGCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:25:1:31.4:1:1:0:38.4:10:1:0:3 -11 51580982 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGTTCAACCCTGTGAGTT;RSEQ=AATGCAAACATCACAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:12.5:1:28.5:1:1:1.7321:42:4:0.4:0:3.5 -11 51581033 . G A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTTCCGATTACTTCTGG;RSEQ=AAGTTTATACAGTTTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:25.5:1:31:1:1:0:21:4:1:0:6.5 -11 51581042 . A C 40 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACTTCTGGGAAGTTTAT;RSEQ=CAGTTTCCAACGAAATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:28.7:1:25.3:1:1:0:22:2:1:0:6.7 -11 51581044 . A C 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTCTGGGAAGTTTATAC;RSEQ=GTTTCCAACGAAATCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:30.7:1:29:1:1:0:22:6:1:0:6.7 -11 51581077 . T A 39 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTCAGAGAAGTCCAAAT;RSEQ=TCCACTTGCAGATTCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:0.6:2,2:33.3:1:25:1:1:1.7321:40:2:0.5:0:3.3 -11 51581094 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTCCACTTGCAGATTCT;RSEQ=CAAAAAGTGTGTTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:14.5:1:30:1:1:1.73:21:4:0.4:0:6.5 -11 51581097 . A G 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACTTGCAGATTCTACA;RSEQ=AAAGTGTGTTTGGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:0.6:2,2:17.3:1:30.7:1:1:1.7321:22:6:0.6:0:6.7 -11 51581102 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTGCAGATTCTACAAAAAG;RSEQ=GTGTTTGGAAACTGCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:7:1:29:1:1:0:34.5:4:0.6667:0:5 -11 51590306 . C A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCCACCTGCAGATTCTAC;RSEQ=AAAAGAGTGTCTCAAAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18.5:1:31.5:1:1:0:23.5:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 51590317 . C T 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTCTACCAAAAGAGTGT;RSEQ=TCAAAGCTGAACTATGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:29.5:1:32:0:1:0:23.5:4:1:0:7 1/1:1:1:1,0:0,0:1:0,0:11:0:32:0:1:0:24:2:1:0:6 -11 51590319 . C G 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTACCAAAAGAGTGTCT;RSEQ=AAAGCTGAACTATGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31.5:1:33:0:1:0:23.5:4:1:0:7 1/1:1:1:1,0:0,0:1:0,0:13:0:34:0:1:0:24:2:1:0:6 -11 51590338 . G C 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAAGCTGAACTATGAAAG;RSEQ=AAGGTTCAACTCTGTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:44:0:32.5:1:1:0:23.5:4:1:0:7 1/1:3:3:3,0:0,0:1:0,0:16.7:1:33.3:1:1:0:23:6:1:0:6 -11 51590360 . T A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGTTCAACTCTGTGAGTTG;RSEQ=ATGCAAACATCACAAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:20.5:1:28.5:1:1:0:23:4:0.6667:0:6.5 1/1:3:3:3,0:0,0:1:0,0:35.7:1:29.7:1:1:0:23:6:1:0:6 -11 51590385 . GG TC 65 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=AAACATCACAAAGAAGTTTC;RSEQ=AGAATGCTTCCGTGTAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:0,0:0.8:0,0:28.3:1:32.9:1:1:0:22.8:8:0.8:0:5.5 1/0:4:3:3,0:0,0:0.75:0,0:26.3:1:29.7:1:1:0:23.3:6:0.75:0:5.7 -11 51590392 . G A 27 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ACAAAGAAGTTTCGGAGAAT;RSEQ=CTTCCGTGTAGTTCTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:15.5:1:27:1:1:0:23:4:0.3333:0:6.5 0/0:4:0:0,0:4,0:0:0,0:26.5:1:31.3:1:1:0:23:8:1:0:5 -11 51590398 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.44444;SOR=0;LSEQ=AAGTTTCGGAGAATGCTTCC;RSEQ=TGTAGTTCTGGGAAGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:38:1:31.5:1:1:0:22.5:4:0.4:0:6 0/0:5:0:0,0:5,0:0:0,0:19:1:28.8:1:1:0:22.8:10:1:0:5.4 -11 51590432 . C A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47368;SOR=0;LSEQ=AGTTTATCCCGTTTCCAACG;RSEQ=AATCCTCAGAGAGGTCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:1:0,0:25.7:1:28.8:1:1:0:22.6:9:1:0:6.3 1/1:9:8:8,0:1,0:0.8889:0,0:21.8:1:29.6:1:1:0:22.5:16:0.8889:0:6.9 -11 51590445 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63719;SOR=0.42162;LSEQ=TCCAACGCAATCCTCAGAGA;RSEQ=GTCCGAATATCCACCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:3,0:0.6667:0,0:33.3:1:30.3:1:1:0:22.5:12:0.6667:0:6.5 0/1:9:4:4,0:5,0:0.4444:0,0:30.5:1:31.8:1:1:0:22.3:8:0.5:0:6.5 -11 51590450 . G A 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCAATCCTCAGAGAGGTCC;RSEQ=AATATCCACCTGCAGATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:31.3:1:28.8:1:1:0:22.6:18:1:0:6.3 1/1:9:8:8,0:1,0:0.8889:0,0:33.5:1:30.8:1:1:0:22.4:16:0.8889:0:6.9 -11 51590460 . C T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=0;LSEQ=AGAGAGGTCCGAATATCCAC;RSEQ=TGCAGATCCTACAAAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:31.4:1:30.6:1:1:0:22.4:18:1:0:6 1/1:10:8:8,0:2,0:0.8:0,0:36.8:1:32.6:1:1:0:22.3:16:0.8:0:6.8 -11 51590468 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGAATATCCACCTGCAGAT;RSEQ=CTACAAAAAGTGTGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:36.1:1:30.6:1:1:0:22.6:14:1:0:6.1 1/1:10:9:9,0:1,0:0.9:0,0:33.8:1:30.7:1:1:0:22.3:18:1:0:6.7 -11 51590474 . A G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0.68231;LSEQ=ATCCACCTGCAGATCCTACA;RSEQ=AAAGTGTGTTTGGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:33.2:1:31.7:1:1:0:22.5:12:0.8571:0:6.8 1/1:10:8:8,0:1,0:0.8:0,0:30.9:1:32.9:1:1:0:22.4:16:0.8889:0:6.5 -11 51590478 . G A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.47059;SOR=Inf;LSEQ=ACCTGCAGATCCTACAAAAA;RSEQ=TGTGTTTGGAAACTGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:25.9:1:31.8:1:1:0:22.5:16:1:0:6.4 0/1:9:2:2,0:7,0:0.2222:0,0:38.5:1:32:0:1:0:22:4:0.25:0:6.5 -11 51590495 . T G 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.15649;LSEQ=AAAGTGTGTTTGGAAACTGC;RSEQ=CCATCTAAAGGAATGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:6,0:0.1429:0,0:9:0:32:0:1:0:22:2:0.1429:0:7 0/1:11:3:3,0:6,2:0.2727:2,0:20.7:1:29:1:1:0:22.3:6:0.2727:0:6.7 -11 51590504 . A G 25 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=TTGGAAACTGCTCCATCTAA;RSEQ=GGAATGTTCAGCTCTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:12.7:1:29.5:1:1:0:22.7:12:1:0:6 0/1:11:2:2,0:6,3:0.1818:2,0:9.5:1:25:1:1:0:22.5:4:0.1818:0:7.5 -11 51590520 . CTCAGTTAAATACAATCATCGCA GTTAGTTCAATGCAATGATCACT 68 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01786;SOR=Inf;LSEQ=CTAAAGGAATGTTCAGCTCT;RSEQ=AAGAATTTTCTGTGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:2:1:29.5:1:1:0:46:4:0.6667:0:2.5 1/1:5:5:3,2:0,0:1:0,2:19:1:29.3:1:1:0:22.6:10:0.7143:1:5.8 -11 51590527 . A C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=AATGTTCAGCTCTCTCAGTT;RSEQ=AATACAATCATCGCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:48:0:33:0:1:0:22:2:0.3333:0:8 1/0:3:2:0,2:0,1:0.6667:0,0:47.5:1:30.5:1:1:0:22.5:4:0.6667:0:8 -11 51590536 . C G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=CTCTCTCAGTTAAATACAAT;RSEQ=ATCGCAAAGAATTTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:39:0:34:0:1:0:22:2:0.3333:0:8 1/0:3:2:0,2:0,1:0.6667:0,0:42:0:31:0:1:0:22.5:4:0.6667:0:8 -11 51590540 . G A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=CTCAGTTAAATACAATCATC;RSEQ=CAAAGAATTTTCTGTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:35:0:32:0:1:0:22:2:0.3333:0:8 1/0:3:2:0,2:0,1:0.6667:0,0:38:0:30:0:1:0:22.5:4:0.6667:0:8 -11 51590542 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=CAGTTAAATACAATCATCGC;RSEQ=AAGAATTTTCTGTGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:33:0:33:0:1:0:22:2:0.3333:0:8 1/0:3:2:0,2:0,1:0.6667:0,0:36:0:29:0:1:0:22.5:4:0.6667:0:8 -11 51590550 . T G 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.88119;LSEQ=TACAATCATCGCAAAGAATT;RSEQ=TCTGTGAATGCTTCCGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:2,6:1,1:0.8:2,2:8.3:1:32:1:1:2.64575:26.4:16:0.8:0:6.4 1/0:9:7:0,7:0,2:0.7778:0,0:12.1:1:30.3:1:1:0:23.6:14:0.7778:0:7 -11 51590565 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=GAATTTTCTGTGAATGCTTC;RSEQ=GTTTGGTTTTTATGTGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,6:0.2:2,2:47:1:31.5:1:1:2.65:46:4:0.2:0:2.5 0/0:11:0:0,0:0,11:0:0,0:19:1:30.5:1:1:0:24:22:1:0:6.4 -11 51590578 . TG GA 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.55338;SOR=2.97217;LSEQ=ATGCTTCCGTTTGGTTTTTA;RSEQ=TGAAGTTATTTCCTTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:1,6:1,1:0.7778:2,2:34.9:1:31.4:1:0.41667:4.58262:27:14:0.7778:0:5.1 1/1:12:11:0,11:0,1:0.9167:0,0:24.1:1:31.1:1:1:0:23.9:22:0.9167:0.25:6.2 -11 51590599 . T A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30341;SOR=4.1559;LSEQ=GTGAAGTTATTTCCTTTACT;RSEQ=CCGTAGGCCTCAAAGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:1,5:1,1:0.6667:2,2:32.7:1:30.3:1:0.46429:3.87298:27.5:12:0.75:0:5.3 1/1:10:9:0,9:0,1:0.9:0,0:33.2:1:30.8:1:1:0:24.2:18:0.9:0:5.8 -11 51590601 . C A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14087;SOR=6.4591;LSEQ=GAAGTTATTTCCTTTACTTC;RSEQ=GTAGGCCTCAAAGCCGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:1,4:1,1:0.5556:2,2:27.2:1:31.4:1:1:3.1622:28.6:10:0.625:0:5.2 1/1:10:9:0,9:0,1:0.9:0,0:32.6:1:32.4:1:1:0:24.2:18:0.9:0:5.8 -11 51590607 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=ATTTCCTTTACTTCCGTAGG;RSEQ=CTCAAAGCCGTCCAAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:1,6:0.2222:2,2:10.5:1:28:1:0.41667:4.58:46:4:0.25:0:2.5 0/0:9:0:0,0:0,9:0:0,0:30.2:1:32.7:1:1:0:24.2:18:1:0:5.8 -11 51590616 . C A 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84356;LSEQ=ACTTCCGTAGGCCTCAAAGC;RSEQ=GTCCAAATCTCCAATTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:1,5:1,1:0.75:2,2:21.7:1:31.3:1:0.46429:3.87298:25.3:12:0.75:0:5.5 1/0:7:5:0,5:0,0:0.7143:0,0:28.6:1:31.6:1:1:0:24.2:10:0.7143:0:6.2 -11 51590632 . T C 81 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCGTCCAAATCTCCAAT;RSEQ=GCAGATTCTACAAAAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:16:1:26.3:1:1:0:23:3:1:0:5.8 1/1:6:6:0,6:0,0:1:0,0:20.5:1:31.5:1:1:0:23.5:12:1:0:6.3 -11 51590651 . G T 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGCAGATTCTACAAAAAGA;RSEQ=TGTTTACAAACTGTTCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:1:0,0:7.3:1:30.7:1:1:0:22.7:6:1:0:6.7 -11 51591132 . G C 82 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAAGGCCACAAAGTGGT;RSEQ=CAAATATCCACTTGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:25.2:1:32:1:1:0:42.3:12:1:0:5 1/1:4:4:3,1:0,0:1:0,2:22.3:1:31.5:1:1:0:31:8:1:0:4.3 -11 51591158 . G A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCACTTGCAGATTCTACA;RSEQ=AAAGAGTGTTTGAAAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:1:0,2:26.8:1:29.8:1:1:0:39.5:16:1:0:5.1 1/1:4:4:3,1:0,0:1:0,2:33.3:1:31.8:1:1:0:31:8:1:0:4.3 -11 51591180 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=AAGAGTGTTTGAAAGCTGAA;RSEQ=TATGAAAGGAATGTTCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:0.25:2,2:30.5:1:31:1:0.46429:3.87298:31:4:0.25:0:5.5 0/0:4:0:0,0:3,1:0:2,0:30.5:1:32.3:1:1:0:31:8:1:0:4.3 -11 51591189 . G C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAAGCTGAACTATGAAAG;RSEQ=AATGTTCAACCCTGTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:5,2:0,0:1:0,2:30.3:1:30.4:1:1:0:39.4:14:1:0:5.6 1/1:4:4:3,1:0,0:1:0,2:21.8:1:31.3:1:1:0:31:8:1:0:4.3 -11 51591192 . T G 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGCTGAACTATGAAAGGAA;RSEQ=GTTCAACCCTGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:0,0:0.7143:0,2:28.6:1:30.6:1:1:0:36.6:10:0.7143:0:5.8 1/1:3:3:2,1:0,0:1:0,2:25:1:30:1:1:0:33.3:6:1:0:4.7 -11 51591200 . C T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTATGAAAGGAATGTTCAAC;RSEQ=CTGTGAGTTGAATGCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:26:1:30.3:1:1:0:39.3:12:0.8571:0:5.7 1/1:2:2:1,1:0,0:1:0,2:28:1:29:1:1:0:30:4:1:0:5 -11 51591215 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACCCTGTGAGTTGAATG;RSEQ=AAACATCACAAAGAAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:14:1:30:1:1:1.7321:46.5:4:0.4:0:5 0/0:2:0:0,0:1,1:0:2,0:13:1:30:1:1:0:30:4:1:0:5 -11 51591273 . C G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTCTGTGAAGTTTATCCC;RSEQ=TTTCCAACGAAATCCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:17:1:32:1:1:0:40:4:0.6667:0:5.5 1/1:3:3:2,1:0,0:1:0,2:9.3:1:32.3:1:1:0:32:6:1:0:6 -11 51591305 . T A 55 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTCAGAGAAGTCCAAAT;RSEQ=TACACTTGCAGATTCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:35.5:1:31.8:1:1:0:45:8:1:0:4.8 1/1:4:4:2,2:0,0:1:0,2:35:1:27.8:1:1:0:30:8:1:0:5.8 -11 51591307 . A C 65 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTCAGAGAAGTCCAAATTT;RSEQ=CACTTGCAGATTCTACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:35.5:1:32.5:1:1:0:45:8:1:0:4.8 1/0:4:3:1,2:0,0:0.75:0,2:34.7:1:30:1:1:0:30:6:0.75:0:5.3 -11 51591352 . A T 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTGGAAACTGCTCCATC;RSEQ=AAACGAATGTTCAGCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:11.5:1:30:0:1:0:40:4:1:0:5 1/1:6:6:2,4:0,0:1:0,2:13.7:1:27.5:1:1:0:31.7:12:1:0:4.8 -11 51591356 . C G 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAACTGCTCCATCAAAA;RSEQ=GAATGTTCAGCTCTCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:15:0:33:0:1:0:40:2:1:0:4 1/1:6:5:2,3:0,0:0.8333:0,2:8.6:1:29:1:1:0:30:10:1:0:5 -11 51592092 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATCACAAAGAAGTTTG;RSEQ=GAGAATGCTTCAGTTTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:32:0:1:0:44:4:1:0:1 -11 56503728 . C T 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1023;SOR=4.62268;LSEQ=GACCTAGCAATTCCAGCATG;RSEQ=GAATTGTGAGAGGACATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:10,0:0.2308:0,0:16.3:1:30.3:1:1:0:60:6:0.2308:0:1.3 1/0:10:6:6,0:4,0:0.6:0,0:22.5:1:28.7:1:1:0:60:12:0.6:0:1 -11 56503835 . T C 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.26039;SOR=0;LSEQ=CCTGCAGGTCCTCTTCAGTG;RSEQ=CCTCTCCATTAAACCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:107:67,40:0,0:1:0,2:27.7:1:31.4:1:1:0:60:52.5:1:0:1.5 1/1:140:137:89,48:1,2:0.9786:2,2:28.2:1:31.4:1:0.29012:3.67:60:136:0.9855:0:1.2 -11 56503851 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17081;SOR=0;LSEQ=AGTGTCCTCTCCATTAAACC;RSEQ=ATTAACATGTAGGATCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:75,51:0.0156:2,2:36:1:29.5:1:1:1.46602:60:4:0.016:0:3 0/0:181:0:0,0:110,71:0:2,0:26.3:1:30.3:1:1:0:60:89.5:1:0:1 -11 56503873 . C T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29261;LSEQ=TTAACATGTAGGATCCTCAT;RSEQ=TGCTTCACATTGGTGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:53:28,25:48,36:0.3869:2,2:25.6:1:30:1:0.72443:1.18895:60:106:0.3897:0:1.9 0/1:206:32:15,17:93,81:0.1553:2,2:30:1:29.6:1:0.56521:1.29956:60:31:0.1535:0:1.8 -11 56503910 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50706;SOR=Inf;LSEQ=CTTTACCAGATTCTCCAGCA;RSEQ=CCAGGAGTAGCAGGCGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:39,66:0:2,0:25.2:1:31.3:1:1:0:60:104:1:0:0.6 0/1:139:2:1,1:53,84:0.0144:2,2:12:1:30:1:1:1.58:60:4:0.0144:0:3 -11 56503938 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50045;SOR=Inf;LSEQ=TAGCAGGCGGTCCATGGCAC;RSEQ=GTCGATGCTTGGCTGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:20,48:0:2,0:23.6:1:29.8:1:1:0:60:21.667:1:0:0.2 0/1:81:2:1,1:19,60:0.0247:2,2:16:1:28:1:0.43519:3.10:60:4:0.0247:0:1 -11 58009466 . T C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24391;SOR=Inf;LSEQ=ATGCATGTTGTGGTTGCCTA;RSEQ=TTGGCAACAGTGAGCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:0:1,0:24.1:1:31.3:1:1:0:60:58:1:0:0.1 0/1:61:3:3,0:55,3:0.0492:2,0:31:1:32:1:1:0:60:6:0.0492:0:1 -11 58009485 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61878;SOR=2.06022;LSEQ=ATTTGGCAACAGTGAGCACT;RSEQ=CATCCTGAACTATCTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:1,0:85,6:0.0109:2,0:6:0:23:0:1:0:60:2:0.011:0:1 0/1:90:2:1,1:74,14:0.0222:2,2:24:1:27.5:1:0.30712:5.141:60:4:0.0225:0:1 -11 58009594 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.58271;LSEQ=TGTCATGAAGAATTATTTTG;RSEQ=CCTCTTCAGTAACAAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:53:34,19:103,90:0.2154:2,2:27.4:1:31.5:1:0.21152:1.56:60:52:0.214:0:1.1 0/1:288:143:76,67:80,65:0.4965:2,2:25.1:1:31.1:1:0.81308:1.08471:60:70.5:0.4947:0:1.1 -11 58009595 . C A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12827;SOR=Inf;LSEQ=GTCATGAAGAATTATTTTGT;RSEQ=CTCTTCAGTAACAAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:136,109:0:2,0:27.5:1:31:1:1:0:60:60.25:1:0:0.3 0/1:287:4:3,1:152,131:0.0139:2,2:11:1:25.8:1:0.62723:2.58:60:3:0.0108:0:1.8 -11 58010309 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.34119;LSEQ=TGAACATTTGTTCCACCAAT;RSEQ=CAGGCACGACAAGTTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:117:55,62:141,146:0.2882:2,2:24.2:1:31.9:1:0.74244:1.08844:59.9:116:0.2893:0:1.3 1/0:558:321:152,169:114,123:0.5753:2,2:25.7:1:31.4:1:0.86432:1.03045:60:79.25:0.5753:0:1.4 -11 58010357 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCCAAGTGCCAGAATTAC;RSEQ=TTTTGGATCTTTAATACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:125,203:0:2,0:24.9:1:31:1:1:0:60:64.6:1:0:0.5 0/1:430:24:10,14:156,250:0.0558:2,2:25.4:1:29.9:1:0.83002:1.14:60:48:0.0565:0:2.8 -11 58010380 . A T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.44176;LSEQ=TTGGATCTTTAATACAAGGA;RSEQ=CAATAGCTCTGGGCTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:58:22,36:61,125:0.2377:2,2:24.2:1:30.1:1:0.52618:1.25:60:57:0.2346:0:2.1 1/0:301:156:54,102:49,96:0.5183:2,2:23.2:1:29.2:1:0.9037:1.04:60:51:0.5134:0:2.2 -11 58010397 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22098;SOR=0;LSEQ=GGAACAATAGCTCTGGGCTG;RSEQ=ATAGCTGGAGGCTTCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:53,138:0.0104:2,2:25.5:1:31.5:1:0.48235:2.59:60:4:0.0105:0:3.5 0/0:217:0:0,0:65,152:0:2,0:23.9:1:29.5:1:1:0:60:107.5:1:0:1.2 -11 58010432 . A T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.16023;LSEQ=CTCAAAACCACAAACATGGA;RSEQ=TACCCCTAAAAGAGACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:28:8,20:19,78:0.224:2,2:23.5:1:30.6:1:0.30866:1.64:60:27:0.2177:0:2.9 1/0:123:92:14,78:6,25:0.748:2,2:22.3:1:29.7:1:0.58241:1.33384:60:184:0.7541:0:2.3 -11 58010439 . T C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.81004;LSEQ=CCACAAACATGGAATACCCC;RSEQ=AAAAGAGACTCCTTTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:26:8,18:21,73:0.2167:2,2:24.6:1:32.5:1:0.43884:1.54:60:52:0.2185:0:3 1/0:110:63:12,51:8,38:0.5727:2,2:22.6:1:31.4:1:1:1.12:60:126:0.5727:0:2.7 -11 58010513 . A G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00033;SOR=5.20008;LSEQ=GCTCTTGATGACAACATTGG;RSEQ=TCCATTCCCTTTGGGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:13:4,9:13,33:0.2203:2,2:23.3:1:30.8:1:1:1.13:60:12:0.2143:0:1.8 1/0:35:21:4,17:3,11:0.6:2,2:23.5:1:31.6:1:1:1.15416:60:42:0.6:0:1.8 -11 58010633 . ACTT A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATTATAGAGATCTTTC;RSEQ=CTTTGGTTAAGTTTATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:26.5:1:30.5:1:1:0:60:4:0.3333:0.1667:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 58010711 . C T 62 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCTTTCTTGATTTCTTTT;RSEQ=CAGAGCGTTTGCTATTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:30.5:1:31:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 60617646 . T C 65 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGGACCGAGGCTGCAGC;RSEQ=GCACTAATGTCCTCCCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:21.8:1:28.4:1:1:0:60:4:1:0:1.6 1/1:2:2:2,0:0,0:1:0,0:15:1:31.5:1:1:0:60:4:1:0:1.5 -11 60617834 . C A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77086;SOR=1.21665;LSEQ=AGGCCTTCCATGGCCAACAA;RSEQ=CATGTCAGACACAGCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:5,7:3,9:0.5:2,2:25.3:1:29.8:1:0.66685:2.07:60:24:0.5455:0:1.1 1/0:20:11:5,6:3,6:0.55:2,2:26.9:1:29:1:0.66992:1.62:60:22:0.55:0:1.3 -11 60617845 . A G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23077;SOR=Inf;LSEQ=GGCCAACAACCATGTCAGAC;RSEQ=CAGCACCTCAGGCCGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:7,13:0:2,0:25.1:1:30:1:1:0:60:40:1:0:0.7 0/1:19:2:1,1:7,10:0.1053:2,2:29:0:30:1:1:1.40:60:4:0.1053:0:2 -11 61197460 . GC G 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01617;SOR=0.14385;LSEQ=CGCTCTCCGCCCCAGGTCCC;RSEQ=CCCCCCCGCCGCCGGCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:59:57:57,0:1,0:0.9661:0,1:24:1:32.6:1:1:0:60:114:0.9661:0.1864:0.2 1/1:30:24:24,0:6,0:0.8:0,1:25.3:1:32.5:1:1:0:60:48:0.8:0.0667:0.1 -11 61197664 . G A 193 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTTCGTCGCTGGTGAGGAGA;RSEQ=AGAACGTTCTAGCGTCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:961:0:0,0:458,502:0:2,0:25.8:1:31.5:1:1:0:60:79:1:0:0.1 0/1:1273:91:47,44:555,627:0.0715:2,2:24.5:1:29.7:1:0.44583:1.21:60:44.5:0.0707:0:1.3 -11 61200952 . T A 148 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=23.94755;LSEQ=TTGGCTAAAATAATAAGACA;RSEQ=CCCAATTATTAGAACAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:1:0,1:266,275:0.0018:2,0:17:0:13:0:1:0:60:0:0:0:3 0/1:754:32:15,17:357,364:0.0424:2,2:30:1:29.6:1:0.85732:1.11138:60:64:0.0435:0:1.1 -11 61205337 . CT C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.07498;SOR=2.05163;LSEQ=TTAGGTATGGGACTAGGAGT;RSEQ=TTTTTTTTAAATCGGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:10:4,6:196,286:0.0203:2,2:26.3:1:32.1:1:1:1.02792:60:20:0.0205:0:0 0/1:563:23:9,14:219,321:0.0409:2,2:26.7:1:31:1:1:1.06117:60:46:0.0411:0.0053:0.1 -11 61205434 . G A 233 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTCTCTTTTATTAGACACA;RSEQ=CCTTCTCAACCTCTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:226:226:115,111:0,0:1:0,2:23.6:1:29.9:1:1:0:60:55.5:1:0:1.1 1/0:212:166:100,66:25,21:0.783:2,2:22.7:1:29.6:1:0.50109:1.27:60:82:0.781:0:1.1 -11 61205676 . C CT 164 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.07231;SOR=0.6003;LSEQ=CCTAGATAATTTTTTTCTTT;RSEQ=TTTTTTTTTTTTGAGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:44:0,44:4,39:0.44:2,1:26:1:30.2:1:0.05544:0:59.3:43:0.4479:0.02:0.5 0/1:125:40:0,40:8,59:0.32:2,1:25.6:1:29.2:1:0.02408:0:59.5:19:0.3363:0.032:0.2 -11 61213355 . C T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11851;SOR=0;LSEQ=GTTTCGAGTTTTAAGATTCT;RSEQ=ATACCTGAGCATTGACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:1,2:203,74:0.0107:2,2:9:1:21.3:1:0.18005:5.44677:60:2:0.0072:0:1.7 0/0:289:0:0,0:212,77:0:2,0:23.7:1:31:1:1:0:60:578:1:0:0.1 -11 61213555 . C T 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACGTTGAGCTGTGCTCCA;RSEQ=GGCCTGGCATGGGGGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:81,183:0:2,0:25.9:1:30.2:1:1:0:60:65:1:0:0.2 0/1:337:35:10,25:107,195:0.1039:2,2:25.2:1:29.4:1:0.4596:1.37056:60:70:0.1051:0:1.1 -11 61213559 . C A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08826;SOR=0;LSEQ=GTTGAGCTGTGCTCCACGGC;RSEQ=TGGCATGGGGGTTCAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:2,1:74,176:0.0119:2,2:28:1:29.7:1:0.21549:4.72:60:6:0.0119:0:1 0/0:314:0:0,0:108,206:0:2,0:25.8:1:31:1:1:0:60:156:1:0:0.2 -11 61213583 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20422;SOR=0;LSEQ=CATGGGGGTTCAGTCTGTGG;RSEQ=TGGTAACTACTTATGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:41,129:0.0116:2,2:26.5:1:31:1:0.42982:3.12:60:4:0.012:0:1.5 0/0:208:0:0,0:54,153:0:2,0:21.9:1:29.6:1:1:0:60:102.5:1:0:0.2 -11 61213622 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61045;SOR=2.1561;LSEQ=GACGTTAGCCTTGCTTCCGG;RSEQ=TTCTTAGATGCCCAGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:1:0,1:6,72:0.0127:2,0:1:0:31:0:1:0:60:2:0.013:0:1 0/1:74:2:1,1:7,65:0.027:2,2:27.5:1:27.5:1:0.20585:8.75:60:4:0.0274:0:1 -11 61213623 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.49722;SOR=0;LSEQ=ACGTTAGCCTTGCTTCCGGC;RSEQ=TCTTAGATGCCCAGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:5,71:0.0256:2,2:25.5:1:29:1:0.14885:13.05:60:4:0.026:0:1 0/0:73:0:0,0:8,65:0:2,0:22.6:1:30.2:1:1:0:60:72:1:0:0.1 -11 61213920 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGCTGTGCGTGCTGTA;RSEQ=GGAAAGCCTCCCGCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31.5:1:30.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31.5:1:1:0:60:4:1:0:1 -11 62098295 . T A 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00223;SOR=0.05206;LSEQ=GGAATTGTGGGTGTATACAT;RSEQ=TATCTGTAAAAGATGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:9,0:10,0:0.4737:0,0:15.1:1:28.9:1:1:0:60:18:0.4737:0:1.3 0/1:24:1:1,0:23,0:0.0417:1,0:41:0:30:0:1:0:60:2:0.0417:0:1 -11 62098371 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28439;SOR=Inf;LSEQ=TGTTCTCTTGAGCAGTGGTC;RSEQ=TTTATCTCCATCCACATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:51,32:0:2,0:24.4:1:30.2:1:1:0:59.9:40.5:1:0:1.7 0/1:131:3:2,1:75,53:0.0229:2,2:43.3:1:30:1:1:1.41:60:6:0.0236:0:3 -11 62098387 . A C 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=GGTCGTTTATCTCCATCCAC;RSEQ=TTCTCTCCCACCTAAGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:100:60,40:0,0:1:0,2:27.7:1:31.2:1:1:0:59.7:99:1:0:1.7 1/1:155:134:74,60:11,10:0.8645:2,2:26.6:1:30.4:1:0.81809:1.12:59.9:66:0.8684:0:1.3 -11 62098407 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12678;LSEQ=ATTCTCTCCCACCTAAGTGC;RSEQ=TGCCACCACCCGATGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:58:34,24:26,25:0.5321:2,2:29.9:1:30.2:1:0.44648:1.36:59.7:28:0.5333:0:2 0/1:160:20:13,7:67,73:0.125:2,2:25.6:1:29.3:1:0.23147:2.01:60:40:0.1274:0:2.1 -11 62098508 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52501;SOR=Inf;LSEQ=TAAAGGCCAACAAAGATGAT;RSEQ=ACTTTAAGGTGGATAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:52,43:0:2,0:25.3:1:31.2:1:1:0:60:46.5:0.9894:0:0.1 0/1:154:2:1,1:88,64:0.013:2,2:7.5:1:27:1:1:1.37209:60:4:0.013:0:1.5 -11 62098521 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51543;SOR=Inf;LSEQ=AGATGATCACTTTAAGGTGG;RSEQ=TAATGATGAAGATGAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:61,51:0:2,0:24.2:1:30.2:1:1:0:60:55:1:0:0.1 0/1:163:2:1,1:91,70:0.0123:2,2:17.5:1:29.5:1:1:1.29788:60:4:0.0124:0:1 -11 62098726 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11485;LSEQ=CACCAGTGTCTTACGGTTGA;RSEQ=GTGTGGCTTAGGGCTAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:227:158:73,85:35,34:0.696:2,2:26.2:1:29.9:1:0.56518:1.19767:60:30.6:0.6923:0:2 0/1:246:51:23,28:88,107:0.2073:2,2:28.2:1:30.1:1:1:1.00121:59.8:102:0.2082:0:2 -11 62098734 . TT AC 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10798;SOR=0;LSEQ=TCTTACGGTTGACGTGTGGC;RSEQ=AGGGCTAGGGCATATTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:2,1:92,106:0.0149:2,2:23.7:1:31:1:0.60018:2.30:60:6:0.0152:0.005:2 0/0:220:0:0,0:97,123:0:2,0:25.2:1:29.1:1:1:0:59.9:35.667:1:0:1.3 -11 62098735 . T C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06253;LSEQ=CTTACGGTTGACGTGTGGCT;RSEQ=AGGGCTAGGGCATATTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:197:92,105:0,0:0.9899:0,2:24.1:1:31:1:1:0:60:38.4:1:0:1.9 1/1:214:184:80,104:12,18:0.8598:2,2:24.9:1:31.1:1:0.84297:1.15:59.9:368:0.8638:0:1.5 -11 62098737 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23375;SOR=0;LSEQ=TACGGTTGACGTGTGGCTTA;RSEQ=GGCTAGGGCATATTAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:91,105:0.0101:2,2:34:1:31:1:1:1.15:60:4:0.0102:0:2 0/0:211:0:0,0:93,118:0:2,0:24.8:1:30.3:1:1:0:59.9:51.75:1:0:1.3 -11 62098753 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50032;SOR=Inf;LSEQ=CTTAGGGCTAGGGCATATTA;RSEQ=TGGACAGCACTTAGTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:66,89:0:2,0:24.1:1:31.8:1:1:0:60:76.5:1:0:1.7 0/1:175:2:1,1:74,99:0.0114:2,2:20.5:1:29:1:1:1.34:60:4:0.0116:0:2.5 -11 62098766 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49861;SOR=Inf;LSEQ=CATATTAGTGGACAGCACTT;RSEQ=GTAGCTGTGGAGGAAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:53,82:0:2,0:23:1:29.8:1:1:0:60:270:1:0:1.6 0/1:143:2:1,1:56,85:0.014:2,2:17.5:1:28:1:1:1.51:60:4:0.014:0:1 -11 62098773 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGACAGCACTTAGTAGCT;RSEQ=TGGAGGAAGATGCAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:41,74:0:2,0:24.6:1:31.7:1:1:0:60:27.75:1:0:1.4 0/1:119:23:6,17:35,61:0.1933:2,2:25.2:1:29.2:1:0.4653:1.61937:59.5:46:0.1933:0:1.7 -11 62098774 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49784;SOR=0;LSEQ=TGGACAGCACTTAGTAGCTG;RSEQ=GGAGGAAGATGCAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:39,74:0.0174:2,2:11:1:28.5:1:1:1.89:60:4:0.0177:0:2.5 0/0:113:0:0,0:38,75:0:2,0:23.1:1:29.8:1:1:0:59.8:226:1:0:1 -11 62098899 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.54933;LSEQ=AAGTAAAACTTGCTGCCGAT;RSEQ=AAGATGATGATTATGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:1:1,0:39,34:0.0135:2,0:1:0:25:0:1:0:60:2:0.0135:0:1 0/1:96:2:1,1:46,48:0.0208:2,2:39:1:28:1:1:1.04:60:4:0.0211:0:1.5 -11 62098934 . A AGAT 175 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=8.000;MSILEN=3;SSF=4e-05;SOR=0.2221;LSEQ=GAAGATGATGATGATGATGA;RSEQ=GATGATGATGATGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:69:54:37,17:6,9:0.7826:2,2:25.8:1:30.5:1:0.06936:3.20:59.7:53:0.7794:0.1884:0.1 0/1:77:34:17,17:22,20:0.4416:2,2:28:1:30.1:1:1:1.09862:60:68:0.4595:0.0519:0.1 -11 62098943 . T TGAC 92 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.00142;SOR=Inf;LSEQ=GATGATGATGAAGATGATGA;RSEQ=GATGATGATGATTTTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:49,27:0:2,0:21:1:30.4:1:1:0:59.8:75:1:0:0.1 0/1:75:9:4,5:31,33:0.12:2,2:20.4:1:29.3:1:1:1.17167:59.9:18:0.1233:0.04:0.6 -11 62099066 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18196;LSEQ=GGAAAAGACTCAAAGCCATC;RSEQ=TCAACACCAAGATCAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:282:195:104,91:49,38:0.6915:2,2:25.9:1:30.2:1:0.69845:1.12781:56.7:64:0.6931:0:1.2 0/1:263:76:44,32:103,83:0.289:2,2:26.3:1:29.1:1:0.78416:1.11:56.3:24.333:0.2852:0:1 -11 62099069 . A T 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24935;SOR=0;LSEQ=AAAGACTCAAAGCCATCGTC;RSEQ=ACACCAAGATCAAAAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:1,2:151,133:0.0105:2,2:6:1:20.7:1:0.60264:2.26439:50.3:2:0.0071:0:2 0/0:270:0:0,0:150,120:0:2,0:25.6:1:29.5:1:1:0:58.9:134:1:0:0.4 -11 62099172 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50553;SOR=Inf;LSEQ=ACGTTAAAGCAAACATGCAA;RSEQ=CAAGGATAGAAAAAGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:24,83:0:2,0:21.8:1:32.1:1:1:0:59.8:214:1:0:0.1 0/1:137:2:1,1:45,90:0.0146:2,2:8:1:30:1:1:1.99:60:4:0.0148:0:1 -11 62100880 . A C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGTGTGCCTGCCCCCTA;RSEQ=GATCTTGAGGTGTTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:32:1:1:0:60:4:1:0:1.5 -11 62789131 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03195;LSEQ=TGGGATCTCCTATCTGAGCT;RSEQ=TGAGGTCTCCTCCCTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:353:318:157,161:18,17:0.9008:2,2:25.8:1:29.2:1:0.85997:1.08553:60:317:0.9006:0:1.2 0/1:362:81:42,39:124,156:0.2238:2,2:21.6:1:29:1:0.25538:1.35:60:162:0.2244:0:1.1 -11 62789169 . T C 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGCCATCCATGCTTTGGG;RSEQ=GGAGAGCCTCGTTCCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:95,154:0:2,0:24:1:30.1:1:1:0:60:248:1:0:0.8 0/1:267:19:8,11:104,144:0.0712:2,2:24.7:1:28.7:1:1:1.01:60:18:0.0679:0:1.1 -11 63010648 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49746;SOR=0;LSEQ=CCGTGTCCTGAAGAACCTGC;RSEQ=TGCTATCAAGAAGCGCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:32,13:0.0426:2,2:30:1:33:1:0.51156:2.40879:60:4:0.0426:0:1 0/0:40:0:0,0:26,14:0:2,0:23.5:1:29.9:1:1:0:60:39:1:0:0.2 -11 63010898 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49893;SOR=Inf;LSEQ=AAAGGTTTTCCCTCTGGCCA;RSEQ=GATTTACCTGGACTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:102,55:0:2,0:23.2:1:30.8:1:1:0:60:77.5:1:0:0.1 0/1:167:2:2,0:102,63:0.012:2,0:34:1:31.5:1:0.52731:0:60:4:0.0121:0:1 -11 63011204 . A C 220 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATCTGCAAGCAAGTCCAGA;RSEQ=CTTCAATGCTCTGTATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:130:130:41,89:0,0:1:0,2:23:1:31.4:1:1:0:60:129:1:0:1.1 0/1:141:42:10,32:30,69:0.2979:2,2:20.5:1:30.5:1:0.5412:1.38814:60:84:0.3:0:1.1 -11 63011241 . G C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00201;SOR=Inf;LSEQ=GCAATGTACCCGCCATCAAT;RSEQ=GTTGCAACTGGAAGTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:51,61:0:2,0:24.7:1:32.1:1:1:0:60:224:1:0:0.6 0/1:99:8:4,4:46,45:0.0808:2,2:18.9:1:31:1:1:1.022:60:16:0.0825:0:1.6 -11 63011334 . G T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08172;SOR=0;LSEQ=AATGCCCTGACTGAGCTGCT;RSEQ=GCAAAGATCACCAACACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:2,1:69,67:0.0216:2,2:25:1:23.7:1:1:1.93:60:2:0.0152:0:2 0/0:180:0:0,0:94,84:0:2,0:24:1:30.9:1:1:0:60:177:0.9888:0:0.1 -11 63011410 . C T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.49557;LSEQ=GAGGTGGTCTTCCTCAACAG;RSEQ=CTGCAGCAGTGCCATCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:87,53:0.0071:2,0:1:0:26:0:0.38298:0:60:2:0.0071:0:1 0/1:189:2:1,1:107,80:0.0106:2,2:16.5:1:26.5:1:1:1.3354:60:4:0.0108:0:1 -11 63011423 . C T 44 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13105;SOR=Inf;LSEQ=TCAACAGCCTGCAGCAGTGC;RSEQ=ATCAGGACCAGCAGGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:94,70:0:2,0:25.9:1:31.2:1:1:0:60:53.667:1:0:0.1 0/1:202:4:0,4:112,86:0.0198:2,0:6.8:1:22:1:0.03795:0:60:3:0.015:0:1 -11 63011426 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19869;SOR=0;LSEQ=ACAGCCTGCAGCAGTGCCAT;RSEQ=AGGACCAGCAGGACAGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:94,75:0.0117:2,2:32.5:1:28:1:1:1.25166:60:4:0.0119:0:1 0/0:212:0:0,0:117,95:0:2,0:26.7:1:31.3:1:1:0:60:211:1:0:0.1 -11 63011476 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20144;SOR=0;LSEQ=GATGAACTGGGCCAAGCCAG;RSEQ=ACCCCTATAGACCTGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:83,113:0.01:2,2:21.5:1:32:0:1:1.36:60:4:0.0101:0:1 0/0:245:0:0,0:115,130:0:2,0:25.4:1:31.5:1:1:0:60:80.667:1:0:0.1 -11 63011599 . T TA 71 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.7057;SOR=0.55947;LSEQ=TTGTATCTTAGGGCGAAACT;RSEQ=AAAAAAAAAAACCTCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:0,5:1,23:0.1724:1,0:28.4:1:30.8:1:1:0:60:10:0.1724:0:0.4 0/1:29:3:1,2:0,24:0.1034:1,2:43:1:29.7:1:0.11111:0:60:6:0.1034:0:0.7 -11 63011631 . G C 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02894;SOR=Inf;LSEQ=CCTCTGCCCCCACATAGTTC;RSEQ=TGTTTAAAGATCTTTTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:0,22:0:1,0:26.3:1:32.1:1:1:0:60:21:1:0:0.6 0/1:17:4:2,2:0,13:0.2353:1,2:23.3:1:32.5:1:0.04412:0:60:8:0.2353:0:1.3 -11 63011713 . A G 53 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CTTTGGTGCTTATTTGAAGT;RSEQ=CAGCATAAGGGAATCCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:24.5:1:26.8:1:1:0:60:3:1:0:1 0/0:1:0:0,0:0,1:0:0,0:28:0:32:0:1:0:60:2:1:0:0 -11 64002177 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGGGGCCGCGGAGGAG;RSEQ=CGCCCCCCGCGCCCGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 64002405 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCCGCCCGCCCGCCGTG;RSEQ=CCTCTCTCAAGGTTGGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 64126666 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20513;SOR=Inf;LSEQ=GCCGCCATGTAACCGGCGCC;RSEQ=CCCGGAGCCCGAGCCGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:148,34:0:2,0:15.5:1:30.3:1:1:0:60:35.4:0.9944:0:0.3 0/1:152:2:1,1:114,36:0.0132:2,2:27:0:31.5:1:0.42881:3.13729:60:4:0.0136:0:1.5 -11 64126679 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09959;SOR=Inf;LSEQ=CGGCGCCGCCCGGAGCCCGA;RSEQ=CCGCGCGGGCCCCAGCGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:192,56:0:2,0:22.3:1:32:1:1:0:60:23.8:0.9917:0:0.2 0/1:217:3:2,1:156,58:0.0138:2,2:28.3:1:24:1:1:1.34288:60:2:0.0094:0:1.7 -11 64126691 . C T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.34318;SOR=3.45846;LSEQ=GAGCCCGAGCCGCGCGGGCC;RSEQ=CAGCGACCCGCCCGCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:1:0,1:246,97:0.0029:2,0:1:0:26:0:0.28488:0:60:2:0.003:0:1 0/1:300:3:0,3:206,91:0.01:2,0:10.7:1:21:1:0.03009:0:60:2:0.0068:0:1 -11 64126698 . C T 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AGCCGCGCGGGCCCCAGCGA;RSEQ=CCGCCCGCCATGGGGGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:283,109:0:2,0:26.5:1:31.9:1:1:0:60:77.4:1:0:0.2 0/1:359:12:7,5:230,115:0.0334:2,2:25.8:1:28.3:1:0.54659:1.42712:60:11:0.0312:0:1.4 -11 64126725 . C T 68 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1811;SOR=3.26216;LSEQ=GCCATGGGGGACGAGGACGA;RSEQ=GATGAGAGCTGCGCCGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:2:0,2:437,202:0.0031:2,0:1:0:27.5:1:0.10095:0:60:4:0.0032:0:1 0/1:692:7:2,5:420,265:0.0101:2,2:6.9:1:24.3:1:0.11672:3.95434:60:14:0.0102:0:1.1 -11 64126993 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20918;SOR=Inf;LSEQ=TCCTGCCTGCTCACTCTTGG;RSEQ=CCTGGGCCAGGCCACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:26,149:0:2,0:24.5:1:31.7:1:1:0:60:34:1:0:0.1 0/1:148:2:1,1:30,116:0.0135:2,2:6.5:1:27.5:1:0.37617:3.82:60:4:0.0138:0:1 -11 64127230 . G T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTCCCTTTCTTCCAATATGG;RSEQ=ATCCCCCTCCCACATTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,2:0.3333:0,0:4:0:30:0:0.33333:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:1:0,2:19.5:1:27.5:1:1:0:60:4:1:0:1 -11 64127560 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.18697;SOR=Inf;LSEQ=TGCACACCCTCCTGGGTTGG;RSEQ=ATCGCCCCCACCCCCCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:168,44:0:2,0:23.1:1:31.7:1:1:0:60:105:1:0:0.1 0/1:162:2:1,1:122,38:0.0123:2,2:12:1:31:1:0.42466:3.18205:60:4:0.0123:0:1 -11 64127565 . C T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26859;SOR=0;LSEQ=ACCCTCCTGGGTTGGCATCG;RSEQ=CCCCACCCCCCAAGCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:179,60:0.0123:2,2:15.3:1:27:1:0.16212:5.91263:60:6:0.0125:0:1 0/0:175:0:0,0:131,44:0:2,0:23.7:1:31.7:1:1:0:60:57.333:1:0:0.1 -11 64127744 . A G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=7.76476;LSEQ=GTGCAGCGCGCCAAGACGCA;RSEQ=GAGCACACGCGCACCGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:28:11,17:174,198:0.07:2,2:24.8:1:31.2:1:0.55638:1.3571:60:56:0.0702:0:1.1 0/1:322:119:44,75:84,119:0.3696:2,2:22.3:1:30.6:1:0.47976:1.20252:60:38.667:0.3671:0:1.2 -11 64127763 . C T 50 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09936;SOR=Inf;LSEQ=AAGAGCACACGCGCACCGAG;RSEQ=GCTCGGTGCTGGAGCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:152,176:0:2,0:25.2:1:30.9:1:1:0:60:81:1:0:0.2 0/1:284:3:1,2:111,170:0.0106:2,2:12:0:32:0:1:1.30469:60:6:0.0109:0:2.3 -11 64127881 . T G 278 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.68329;LSEQ=CACACCACATCCCAACGGGG;RSEQ=TGGGGTGGCTGGGGGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:496:494:313,181:0,1:0.996:0,2:24.4:1:31.1:1:0.36768:0:60:43.909:0.9959:0:1.2 1/1:417:416:261,155:0,0:0.9976:0,2:23.8:1:30.8:1:1:0:60:82.2:0.9976:0:1.2 -11 64127902 . G A 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05992;SOR=0.67302;LSEQ=TGGGGTGGCTGGGGGCAGGC;RSEQ=AGGCCACCTGACGGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:71:43,28:329,220:0.1141:2,2:24.2:1:29.7:1:1:1.03:59.8:70:0.1146:0:1.9 0/1:539:43:26,17:301,195:0.0798:2,2:25.3:1:29.3:1:1:1.00925:60:42:0.0791:0:1.9 -11 64128423 . G T 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41127;SOR=2.34849;LSEQ=CTTGGGGCCTGATCCACGGG;RSEQ=CCCTCCTTCTTTGTTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:5,0:25,2:0.1563:2,0:25.6:1:26.8:1:1:0:60:4:0.1333:0:1.2 0/1:13:4:3,1:9,0:0.3077:0,2:33.3:1:31:1:0.30769:0:60:8:0.3077:0:1.3 -11 64128494 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28736;SOR=1.92122;LSEQ=TGCCCTGGAGACCCCCTCTA;RSEQ=AGGCAGATGACTTTCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:7:7,0:94,2:0.068:1,0:29.3:1:31:1:1:0:60:14:0.0693:0:1.1 0/1:73:9:9,0:61,3:0.1233:1,0:26.6:1:30.9:1:1:0:60:18:0.125:0:1 -11 64128537 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20704;SOR=Inf;LSEQ=GGTCTCCTTATCCTGAGCAG;RSEQ=GCCAGGAGCTGGAGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:185,24:0:2,0:21.5:1:30.5:1:1:0:60:28.857:1:0:0.1 0/1:175:2:1,1:148,25:0.0114:2,2:9:1:28:1:0.2758:5.82466:60:4:0.0118:0:1 -11 64129050 . GA T 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGGAAGTGGGGCTGGGG;RSEQ=GGTGGAAAGGTGGGGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:215,274:0:2,0:24.3:1:31.4:1:1:0:60:121.25:1:0:0.1 0/1:543:23:8,15:220,291:0.0424:2,2:22.7:1:30.1:1:0.52098:1.41663:59.8:46:0.0431:0.0074:0.3 -11 64129051 . A T 51 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06212;SOR=Inf;LSEQ=CAGGGAAGTGGGGCTGGGGG;RSEQ=GGTGGAAAGGTGGGGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:0:0,0:205,270:0:2,0:23.7:1:29.8:1:1:0:60:32.929:1:0:0.1 0/1:497:5:2,3:209,280:0.0101:2,2:24:1:22:1:1:1.11943:60:1.5:0.0064:0:1.2 -11 64129075 . AG A 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.05421;SOR=0;LSEQ=GGAAAGGTGGGGTGTGAGGC;RSEQ=GGGAGATGCAGGCCCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:4:3,1:166,225:0.0101:2,2:8.5:1:28.5:1:0.31755:4.05:60:8:0.0102:0.0051:0.5 0/0:422:0:0,0:185,237:0:2,0:22.8:1:30.4:1:1:0:60:37.364:1:0:0.2 -11 64129767 . C A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGCAGGTGACCTGCCCC;RSEQ=GACGGCACAGTAAATGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:43.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 64132498 . C T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCTCCCAAAATCCTGGGAT;RSEQ=ACAGGCATGAGCCACCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:27.3:1:28.5:1:1:0:60:10:1:0:1 1/1:4:4:4,0:0,0:1:0,0:20:1:30.5:1:1:0:60:8:1:0:1 -11 64132664 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18681;SOR=Inf;LSEQ=ACAGCTGCCCACCCCAAATG;RSEQ=CAGATGGGCCCTTGCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:169,9:0:2,0:23.7:1:32.1:1:1:0:60:43.5:1:0:0.1 0/1:136:2:1,1:127,7:0.0147:2,2:16.5:1:29:1:0.1146:17.03684:60:4:0.0152:0:1 -11 64132701 . G T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0445;SOR=Inf;LSEQ=TCATGGAGGAACTGCCCAGT;RSEQ=AGGGTGGGCTGAGTGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:281,101:0:2,0:23.1:1:31.5:1:1:0:60:53.571:1:0:0.1 0/1:326:4:1,3:222,100:0.0123:2,2:15.8:1:25.5:1:0.09493:6.61804:60:8:0.0125:0:1 -11 64133166 . TC T 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAAACCTTCTGTTAATT;RSEQ=CCTTCTATTCCATCATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:0,3:0,16:0.1579:1,0:30:1:32.7:1:1:0:60:6:0.1667:0:0 0/0:5:0:0,0:0,5:0:0,0:18.6:1:30.2:1:1:0:60:10:1:0:0 -11 64135435 . G A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10951;SOR=1.99331;LSEQ=CCAAGTGATTATAAAACCAG;RSEQ=TGGAATAAAAAGTGTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:16:16,0:72,1:0.1798:1,1:23.6:1:30:1:1:0:60:32:0.1818:0:1.1 0/1:59:18:17,1:40,1:0.3051:1,1:18.9:1:29.1:1:0.52075:2.31508:60:36:0.3103:0:1.1 -11 64135477 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17046;SOR=Inf;LSEQ=ATCCTGTGTGTACCAGAATG;RSEQ=AACTGGAACACCCCCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:185,2:0:1,0:26.8:1:32:1:1:0:60:30.167:1:0:0.2 0/1:132:2:2,0:128,2:0.0152:1,0:34:1:31:1:1:0:60:4:0.0153:0:1.5 -11 64135541 . GTC G 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=2.88216;LSEQ=TTGCCTGGTTCCCCACCAGA;RSEQ=TCCTCACCCGCACCCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:501:69:46,23:318,113:0.1377:2,2:24.3:1:31.1:1:0.2438:1.40607:59.7:68:0.1396:0.0319:0.2 0/1:485:153:101,52:221,108:0.3155:2,2:21.5:1:30.9:1:0.83562:1.05342:59.8:152:0.3207:0.0701:0.2 -11 64135748 . C T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.16821;SOR=5.51142;LSEQ=TGCAGGTGGGCTGGGCTGGG;RSEQ=TGGGTTGGGGGGAAATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:1:0,1:101,265:0.0027:2,0:1:0:31:0:1:0:60:2:0.0028:0:1 0/1:269:4:2,2:72,193:0.0149:2,2:17.5:1:30:1:0.30412:2.67:60:8:0.0154:0:1.3 -11 64135780 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15051;SOR=Inf;LSEQ=GAAATTGGTTTTAGGAGAGG;RSEQ=CTAGGCCCGGGGACTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:74,165:0:2,0:22.5:1:31.6:1:1:0:60:58.75:1:0:0.1 0/1:152:2:1,1:47,103:0.0132:2,2:15:1:27.5:1:0.53329:2.18:60:4:0.0141:0:1 -11 64135837 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1582;SOR=Inf;LSEQ=GCCCGCAGCGTGAGCTCAGC;RSEQ=AGGTCCTAAGCCTCTCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:119,67:0:2,0:26.5:1:30.1:1:1:0:60:92:1:0:0.2 0/1:124:2:1,1:84,38:0.0161:2,2:18.5:1:28:1:0.53186:2.19499:60:4:0.0163:0:1 -11 64135894 . A T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06172;SOR=Inf;LSEQ=CCGCGGGGCTACCAGGTGGG;RSEQ=CCTCTGACGCGCCGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:238,154:0:2,0:24.3:1:29.7:1:1:0:60:77.4:1:0:0.2 0/1:396:5:1,4:245,146:0.0126:2,2:6.4:1:23.6:1:0.07047:6.68141:60:4:0.0104:0:1.6 -11 64135907 . C T 120 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00084;SOR=7.90894;LSEQ=AGGTGGGACCTCTGACGCGC;RSEQ=GCCTTCGCCTTCGCCTTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:2:0,2:269,181:0.0044:2,0:1:0:25.5:1:0.16338:0:60:4:0.0045:0:1.5 0/1:502:17:11,6:285,191:0.0339:2,2:26.2:1:29.6:1:0.80399:1.23:60:16:0.0326:0:1.5 -11 64136141 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10584;SOR=Inf;LSEQ=CCCGGGGGCGGGGCCGAAGC;RSEQ=CGGCGACCGTAACTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:194,99:0:2,0:23.5:1:30.7:1:1:0:60:57.6:1:0:0.1 0/1:264:3:1,2:167,94:0.0114:2,2:19.7:1:24.7:1:0.2998:3.53534:54.7:2:0.0077:0:2 -11 64136184 . C T 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3434;SOR=2.21908;LSEQ=TCCGTCCCCCAGGCTGGAGG;RSEQ=GAACACGCAGCGCGAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:3:1,2:323,190:0.0058:2,2:10.3:1:24.7:1:0.55868:3.39164:60:2:0.004:0:1 0/1:546:7:1,6:305,233:0.0128:2,2:11.6:1:24:1:0.0473:7.82859:60:6:0.0113:0:1 -11 64136592 . G T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAACATGGCGAAACCCC;RSEQ=TCTCTACGAAAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 64136667 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTACTTGGGAGGCTGAG;RSEQ=CACGAGAATCGCTTGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,1:0.2:2,0:29.5:1:30:1:1:0:60:4:0.2:0:1.5 0/0:1:0:0,0:1,0:0:0,0:37:0:33:0:1:0:60:2:1:0:0 -11 64136721 . C A 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.66423;LSEQ=TGCAGTGAGCCGAGGTGGTG;RSEQ=CACTGCATTCCAGCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:7,0:21,1:0.2333:1,0:36.4:1:30:1:1:0:60:14:0.2333:0:1.1 0/1:6:1:1,0:5,0:0.1667:0,0:50:0:26:0:1:0:60:2:0.1667:0:1 -11 64136772 . C CAAAG 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=5.000;MSILEN=4;SSF=0.20106;SOR=2.9367;LSEQ=GACTGTCTCCAAAAAAGTAA;RSEQ=AAAGAAAGAAAGAAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:47:47,0:9,0:0.8393:0,1:21.8:1:31:1:1:0:59.6:94:0.8393:0.2679:0.2 1/1:33:31:31,0:2,0:0.9394:0,1:14.7:1:30.4:1:1:0:59.2:62:0.9394:0.4545:0.2 -11 64136839 . CG C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50091;SOR=0;LSEQ=CATTGGCAGGGCCCGAAGGC;RSEQ=GGGGCGGGGCCTGGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:147,39:0.0106:2,2:23.5:1:31:1:0.38116:3.73461:60:4:0.0109:0:0.5 0/0:164:0:0,0:117,47:0:2,0:22.2:1:28.7:1:1:0:59.8:31.8:1:0:0.4 -11 64136845 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20534;SOR=Inf;LSEQ=CAGGGCCCGAAGGCCGGGGG;RSEQ=GGGGCCTGGGTGGTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:155,56:0:2,0:24.3:1:29.2:1:1:0:60:10.105:1:0:0.3 0/1:177:2:1,1:119,53:0.0113:2,2:34:1:27.5:1:0.52561:2.23376:60:4:0.0123:0:1 -11 64136877 . C G 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00723;SOR=1.97003;LSEQ=GGTGGGAGGGGGCTTGCCGC;RSEQ=GTGGGTGGGTGTTGACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:32:23,9:154,107:0.1085:2,2:25.7:1:28.6:1:0.18348:1.77:60:15:0.106:0:1.3 0/1:248:48:27,21:117,83:0.1935:2,2:29.5:1:29.3:1:0.87081:1.09598:60:47:0.1926:0:1.2 -11 64137167 . G A 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.29904;LSEQ=ACCACTACCCCGCCGCCCTC;RSEQ=CAGAACATCCTGTACGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:756:2:1,1:419,332:0.0026:2,2:41.5:1:30:1:1:1.26165:60:4:0.0027:0:1 0/1:800:65:36,29:408,322:0.0813:2,2:22.3:1:29.9:1:1:1.02068:60:64:0.0808:0:1.3 -11 64137875 . T C 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.47094;LSEQ=AGGTGCGGAGCTGGAGGTCA;RSEQ=AGACCATGGTTGGGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:786:66:27,39:304,416:0.084:2,2:25.8:1:31.6:1:0.89673:1.05549:60:32:0.0832:0:1 0/1:737:178:74,104:239,316:0.2415:2,2:25.1:1:31:1:0.79398:1.06289:60:58.333:0.241:0:1.2 -11 64138433 . G A 92 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0.2887;LSEQ=TAAAAAGAGAAAAATTAGCC;RSEQ=GGTGTGGTGGCGCGCGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:3,5:0,2:0.8:0,2:25.4:1:30.8:1:1:0:60:16:0.8889:0:1.3 1/0:2:1:0,1:0,1:0.5:0,0:1:0:20:0:1:0:60:2:0.5:0:2 -11 64138663 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19553;SOR=Inf;LSEQ=TGTCGGCCTTGACCTAGGCG;RSEQ=CTGGAGGCAAGGTCTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:206,28:0:2,0:26.6:1:30.8:1:1:0:60:38:1:0:0.3 0/1:186:2:1,1:163,21:0.0108:2,2:13.5:1:27:1:0.22313:7.6066:60:4:0.0109:0:1 -11 64138805 . T C 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.88299;LSEQ=TTCCTGAAGAGCGTGGAGAA;RSEQ=GCACCCCTGGCCAAGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:957:65:27,38:428,464:0.0679:2,2:27:1:30.5:1:0.36821:1.29786:60:130:0.0686:0:1.2 0/1:997:220:92,128:368,406:0.2207:2,2:24.8:1:29.8:1:0.14555:1.26079:60:54:0.2197:0:1.1 -11 64138905 . T G 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.3391;LSEQ=CGGGCCGAGCCCCCGTCGCC;RSEQ=CCAAAGGGGCCCCCCGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:694:57:33,24:316,320:0.0821:2,2:23:1:29:1:0.26934:1.39:60:8.5:0.0796:0:2.4 0/1:589:102:54,48:242,239:0.1732:2,2:23.9:1:29.4:1:0.66356:1.11:60:11.75:0.1688:0:2.1 -11 64138922 . C T 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20018;SOR=2.82344;LSEQ=GCCTCCAAAGGGGCCCCCCG;RSEQ=CGAGCCAACGGCCCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:3:0,3:351,355:0.0042:2,0:1:0:22.3:1:0.24901:0:60:2:0.003:0:1.3 0/1:590:7:3,4:296,287:0.0119:2,2:19.6:1:28.3:1:0.72155:1.3744:60:14:0.0127:0:1.6 -11 64139013 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08553;SOR=Inf;LSEQ=CCTGGGAGCCCGGCTCACTC;RSEQ=CGGAGGCCTCTGCCTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:57,202:0:2,0:22:1:30.7:1:1:0:60:42.167:1:0:0.1 0/1:205:3:0,3:51,150:0.0146:2,0:24.7:1:25.3:1:0.57465:0:60:2:0.01:0:2 -11 64410111 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49909;SOR=Inf;LSEQ=TGGTGGGTGGTGCTGAGGCT;RSEQ=GAGGAGACCCGGGCCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:43,41:0:2,0:21.9:1:30.3:1:1:0:60:41:1:0:0.1 0/1:95:2:1,1:48,45:0.0211:2,2:10:0:32:0:1:1.06598:60:4:0.0213:0:1.5 -11 64410135 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19103;SOR=0;LSEQ=GAGACCCGGGCCCCCTCGGC;RSEQ=GCCCCCAGCAGCAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:34,60:0.0208:2,2:27.5:1:31:1:1:1.75:60:4:0.022:0:1.5 0/0:123:0:0,0:47,76:0:2,0:28:1:29:1:1:0:60:40:1:0:0.2 -11 64410183 . TGGC T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.50086;SOR=Inf;LSEQ=GGCAACAGCGGCAGCAGAGG;RSEQ=GGCGGCGGCGGTGGAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:15,47:0:2,0:18.7:1:30.8:1:1:0:60:30:1:0:0.3 0/1:75:2:0,2:23,49:0.0267:2,0:12:1:31:1:1:0:60:4:0.0267:0.0133:0.5 -11 64410192 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=1.32974;LSEQ=GGCAGCAGAGGTGGCGGCGG;RSEQ=GGCGGTGGAGGCGGCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:1,0:8,32:0.0244:2,0:1:0:26:0:0.21951:0:60:2:0.0263:0:1 0/1:62:2:1,1:18,42:0.0323:2,2:12.5:1:28.5:1:0.52247:2.30:60:4:0.0323:0:1 -11 64571710 . C T 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01644;SOR=0;LSEQ=GGTTTGGGTAGAGGTGAGGC;RSEQ=TGTCCCCTTTGGGCTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:7:6,1:365,43:0.0169:2,2:19.7:1:28.7:1:0.54643:1.41338:60:6:0.0147:0:1 0/0:367:0:0,0:329,38:0:2,0:23.3:1:30.4:1:1:0:60:72.4:1:0:0.1 -11 64572018 . T C 321 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05025;LSEQ=CTCCGGCGGTGGTGATGCTG;RSEQ=GGGTGCTGGCACCTGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1420:1413:692,721:0,1:0.9951:0,2:24.6:1:30.8:1:1:0:60:66.286:0.9986:0:1.1 1/1:1693:1541:723,818:74,73:0.9102:2,2:24.2:1:30.4:1:0.43762:1.1468:60:58.269:0.9094:0:1.2 -11 64572403 . C G 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10042;LSEQ=GTCTCAGTCCCATCGGCACC;RSEQ=AAGGGGATGGGCAGATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:671:591:209,382:31,47:0.8808:2,2:22.8:1:30.5:1:0.45341:1.20518:60:72.875:0.8807:0:1.1 0/1:630:268:91,177:126,234:0.4254:2,2:22.2:1:30.5:1:0.79965:1.04728:60:88.333:0.426:0:1.1 -11 64572460 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.03676;SOR=Inf;LSEQ=GTCTGACAAGCCCGTGGCTG;RSEQ=TGTCACCACCTGTAGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:171,252:0:2,0:25.9:1:32.3:1:1:0:60:83.6:1:0:0.5 0/1:331:4:1,3:138,189:0.0121:2,2:10:1:30:1:0.64193:2.18578:60:8:0.0121:0:1 -11 64572557 . A G 277 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94251;LSEQ=AGAAAGGTGGCCCAGCCCAC;RSEQ=TGCAGCACAGGCGTGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:542:539:286,253:2,0:0.9945:0,2:24.8:1:30.6:1:0.50117:0:60:43.917:0.9943:0:1.2 1/1:511:508:287,221:1,0:0.9941:0,2:24.4:1:30.1:1:1:0:60:126:0.9941:0:1.4 -11 64572602 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=5.21743;LSEQ=TCCTCCCATTTGCAGATGCC;RSEQ=TCGTAGAATCGCAGCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:58:24,34:310,332:0.0829:2,2:26.3:1:31:1:0.33881:1.32226:60:116:0.0841:0:1.5 0/1:733:235:123,112:260,238:0.3206:2,2:24.7:1:29.9:1:1:1.01:60:234:0.3245:0:1.6 -11 64573311 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10916;SOR=Inf;LSEQ=GGGGGTAGCCCCAGGGACCT;RSEQ=GCGGGGGATGGAGCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:24,177:0:2,0:22.6:1:31.1:1:1:0:60:200:1:0:0.1 0/1:185:3:1,2:25,156:0.0162:2,2:9.7:1:23.7:1:0.36855:3.09:60:2:0.0112:0:1.3 -11 64573313 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23355;SOR=Inf;LSEQ=GGGTAGCCCCAGGGACCTGG;RSEQ=GGGGGATGGAGCCCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:22,170:0:2,0:22.8:1:29.7:1:1:0:60:31:0.9947:0:0.1 0/1:181:2:0,2:25,154:0.011:2,0:28.5:1:29.5:1:1:0:60:4:0.0114:0:1 -11 64573589 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17091;SOR=Inf;LSEQ=TGGCCTTGCTGCCTAGGGAC;RSEQ=GGATGGAAAGGGGATGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:77,5:0:2,0:24:1:30.9:1:1:0:60:26.333:1:0:0.1 0/1:59:2:2,0:54,2:0.0339:1,0:33.5:1:28.5:1:1:0:60:4:0.0364:0:1 -11 64573636 . G T 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.59748;SOR=2.34047;LSEQ=GCCAGGCCTCAGTCCTGGAC;RSEQ=AGGGTGGTTGGAAACTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:0,1:133,50:0.0054:2,0:1:0:25:0:0.27717:0:60:2:0.0055:0:2 0/1:158:2:1,1:115,41:0.0127:2,2:10:0:31:1:0.46223:2.78331:60:4:0.0127:0:2.5 -11 64573875 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21854;SOR=0;LSEQ=GGCAGAGGATCCTCAGGGAG;RSEQ=CAGCCCCAGCTGCCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:50,138:0.0105:2,2:15:1:28:1:0.46583:2.74:60:4:0.0108:0:2 0/0:217:0:0,0:62,155:0:2,0:23.8:1:31.3:1:1:0:60:107.5:1:0:0.1 -11 64573878 . G A 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62653;SOR=2.6356;LSEQ=AGAGGATCCTCAGGGAGGCA;RSEQ=CCCCAGCTGCCCTGCTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:1:1,0:44,133:0.0056:2,0:1:0:28:0:0.25281:0:60:2:0.0057:0:1 0/1:204:3:1,2:57,144:0.0147:2,2:31:1:22.3:1:1:1.26:60:2:0.01:0:1 -11 64574185 . TTCA T 106 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CACCAAGTGAACACCCCCTC;RSEQ=TCAGTGCTCCTGCCACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:1:0,0:30.4:1:32.2:1:1:0:60:20:1:0:1 1/1:1:1:0,1:0,0:1:0,0:24:0:32:0:1:0:60:2:1:0:1 -11 64574200 . G A 106 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCTTCATCAGTGCTCCT;RSEQ=CCACATTTGACCTCTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:26.7:1:28.8:1:1:0:60:26:1:0:1.1 1/1:1:1:0,1:0,0:1:0,0:13:0:31:0:1:0:60:2:1:0:1 -11 64574381 . AC A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.22591;SOR=Inf;LSEQ=AGTGAGACTGGATGGGCGAT;RSEQ=CCCCCAACACACAAAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:144,9:0:2,0:22.3:1:31.9:1:1:0:60:306:1:0:0.1 0/1:140:2:2,0:125,13:0.0143:2,0:24.5:1:30.5:1:1:0:60:4:0.0144:0:0 -11 64574397 . A T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10448;SOR=0;LSEQ=CGATACCCCCCAACACACAA;RSEQ=GTTCTCTTCTCATCTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:3:1,2:175,26:0.0147:2,2:6.3:1:21.7:1:0.05007:13.1558:60:2:0.01:0:2 0/0:228:0:0,0:175,52:0:2,0:19.7:1:29.3:1:1:0:60:24.222:1:0:0.2 -11 64574773 . A G 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63474;SOR=2.35802;LSEQ=ATCGGGCAGAGGTGGGGGTC;RSEQ=GAACCAACAGGGACCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:1:1,0:60,173:0.0043:2,0:27:0:9:0:0.26068:0:60:0:0:0:7 0/1:299:3:1,2:88,208:0.01:2,2:30.7:1:31:1:1:1.18:60:6:0.0102:0:1 -11 64575295 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19765;SOR=Inf;LSEQ=AGGGGTGTGGCCCAAGAAAA;RSEQ=GGAGTCCCTTGGGTGGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:178,60:0:2,0:24.9:1:30.7:1:1:0:60:78.333:1:0:0.1 0/1:191:2:1,1:140,49:0.0105:2,2:14:1:32.5:1:0.45605:2.83851:60:4:0.0105:0:1 -11 64575346 . G T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.21915;SOR=4.6799;LSEQ=GTATGAAGGGGACAAGGCTG;RSEQ=GGGGAGGGAACAATACCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:1:0,1:302,161:0.0022:2,0:1:0:15:0:0.34914:0:60:0:0:0:1 0/1:499:5:1,4:319,175:0.01:2,2:10.6:1:26.6:1:0.0581:7.26295:60:10:0.0101:0:1 -11 64575505 . C T 197 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04041;LSEQ=ACAGGGCGAGGTGGACATCC;RSEQ=GGAGACCCAGGGCCTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:862:94:44,50:311,456:0.109:2,2:23.5:1:30.2:1:0.26743:1.29:60:30.333:0.1067:0:1.1 0/0:1017:5:1,4:474,535:0.0049:2,2:8.6:1:30.2:1:0.37875:3.53998:60:10:0.005:0:1 -11 64575740 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTCCCACGTGTTCAAA;RSEQ=ACTCTCTCCCTGTTTACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:1,30:0.0606:1,2:29:1:26.5:1:0.11932:21.57:60:4:0.0606:0:1 0/0:6:0:0,0:0,6:0:0,0:11.2:1:31.5:1:1:0:60:12:1:0:0.2 -11 64577021 . GA G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.15585;SOR=Inf;LSEQ=AGTTTCCCAACTGCAAAGAG;RSEQ=AAATAACACCTGCCGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:159,15:0:2,0:22.3:1:29.9:1:1:0:60:57:1:0:0.1 0/1:114:2:1,1:103,8:0.0175:2,2:25.5:1:27:1:0.1536:12.19759:60:4:0.0182:0:0 -11 64577541 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10717;SOR=Inf;LSEQ=GCACCACGTCGTCGATGGAG;RSEQ=GCAGCGGGAACAGCGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:70,224:0:2,0:22.3:1:30.2:1:1:0:60:97:1:0:0.2 0/1:267:3:1,2:67,196:0.0112:2,2:26:1:23:1:1:1.46:60:2:0.0078:0:1.3 -11 64577567 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19132;SOR=Inf;LSEQ=GGGAACAGCGTCTTCTGGGC;RSEQ=GCCTTCAGCCCCATGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:29,162:0:2,0:25.8:1:30.8:1:1:0:60:62.667:1:0:0.3 0/1:149:2:1,1:29,116:0.0134:2,2:35.5:1:31:1:0.36763:3.95:60:4:0.0134:0:1 -11 64577620 . G C 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.0064;SOR=Inf;LSEQ=GCGGCCTGCAAGGCAAGCCG;RSEQ=GGGAGGGAGGGTCGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:12,77:0:2,0:25.1:1:31.1:1:1:0:60:88:1:0:0.5 0/1:53:5:1,4:5,43:0.0943:2,2:31.8:1:30.2:1:0.46547:2.11:60:10:0.0962:0:1 -11 65375490 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20683;SOR=Inf;LSEQ=GCCACAGCAAGGCAGTCAAT;RSEQ=CCACGGTATGGCACCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:126,82:0:2,0:24.6:1:31.9:1:1:0:60:51:1:0:0.2 0/1:174:2:1,1:99,73:0.0115:2,2:42.5:1:29.5:1:1:1.35374:60:4:0.0117:0:1.5 -11 66625801 . TCC T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10145;SOR=Inf;LSEQ=TCGCCCAGCTCGGTCAGCTC;RSEQ=CGCCTGGACCTCACCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:0:2,0:22.8:1:31:1:1:0:60:32:1:0:0.2 0/1:8:2:1,1:3,3:0.25:2,2:36.5:1:29.5:1:1:1:60:4:0.25:0:2 -11 66626394 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGACATCGCCGCCTCCGC;RSEQ=CGCACTGCTGCCGAGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:1:28.5:1:1:0:60:4:1:0:1 -11 66676732 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGCTGCTGGTGTGGGGCC;RSEQ=GAGCTGGAGGAAGTATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 66677336 . T C 258 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTGGCCAGGACACGGGCCA;RSEQ=TGTATGGTCACAAACCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:282:282:155,127:0,0:1:0,2:26.1:1:31.8:1:1:0:60:69.5:1:0:1.9 1/0:342:202:104,98:73,67:0.5906:2,2:24.6:1:31:1:0.91285:1.02662:60:201:0.6:0:1.8 -11 66677366 . T C 246 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAAACCATGCAGTTTGGTA;RSEQ=GGCTGGAACACCGGGTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:277:277:130,147:0,0:1:0,2:26:1:30.4:1:1:0:60:33.625:1:0:1.9 1/0:314:162:72,90:74,76:0.5159:2,2:26:1:30.4:1:0.42721:1.21633:60:324:0.5192:0:2 -11 66677428 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5048;SOR=0;LSEQ=TGACCACTCACTGCGGCAGA;RSEQ=CAACACAGCATGATCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:41,107:0.0133:2,2:14:1:29:1:0.48295:2.59:60:4:0.0137:0:2 0/0:119:0:0,0:33,86:0:2,0:24.6:1:31.5:1:1:0:60:58.5:1:0:0.4 -11 66677453 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51128;SOR=0;LSEQ=ACAGCATGATCCATGCTGTC;RSEQ=TCAATTTACACAGAAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:13,82:0.0206:2,2:6:0:33:1:0.26912:6.12:60:4:0.0208:0:2 0/0:69:0:0,0:10,59:0:2,0:26.5:1:30.4:1:1:0:60:68:1:0:0.1 -11 67194847 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTGCTGGGATTACAGGTG;RSEQ=GAGCCACCGTGACCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:1:32:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 67196182 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.519;SOR=0;LSEQ=GCGGCTCCGCACGCCCAGAG;RSEQ=GGGCTCCGACTCTTTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:32,159:0.0104:2,2:10.5:1:26.5:1:0.31347:4.91:60:4:0.0107:0:1 0/0:128:0:0,0:19,109:0:2,0:24.3:1:30.3:1:1:0:60:127:1:0:0.2 -11 67196237 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=6.79897;LSEQ=AGATCCCGGTCTCTATTAAG;RSEQ=TCTGATCCCACCCTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:4,2:40,60:0.0566:2,2:30.7:1:33:1:0.23012:2.97:60:12:0.0583:0:1 0/1:65:19:10,9:25,21:0.2923:2,2:19.9:1:31.8:1:1:1.07028:60:18:0.2813:0:1.1 -11 67196456 . G A 89 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04836;SOR=3.68807;LSEQ=CCCTCGGTTTCTCACAGGAC;RSEQ=CATGTCCCCTTGCCGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:975:3:2,1:482,489:0.0031:2,2:17.3:1:27.7:1:0.62231:2.03:60:6:0.0032:0:1 0/1:888:10:7,3:426,451:0.0113:2,2:16.4:1:26.8:1:0.2142:2.47:60:4:0.0092:0:1.4 -11 67196544 . C G 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=3.41005;LSEQ=AATGGAGTGGGGAAGGGGAA;RSEQ=TGGGGAGCACTGGAGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:807:81:41,40:346,375:0.1004:2,2:22.8:1:31.5:1:0.72524:1.11:60:19.25:0.0986:0:1.4 0/1:718:198:101,97:256,261:0.2758:2,2:23.8:1:31.1:1:0.73866:1.06:60:65:0.2798:0:1.3 -11 67196740 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13831;SOR=Inf;LSEQ=GGGCGCACCCTCCTCCTGGC;RSEQ=TCACAGCCTCCATCTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:70,196:0:2,0:24.7:1:31.3:1:1:0:60:28.556:1:0:0.1 0/1:158:2:1,1:42,114:0.0127:2,2:25.5:1:28.5:1:0.4715:2.69:60:4:0.0127:0:1 -11 67196744 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13754;SOR=Inf;LSEQ=GCACCCTCCTCCTGGCCTCA;RSEQ=AGCCTCCATCTGGAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:66,191:0:2,0:24.2:1:31.9:1:1:0:60:84.667:1:0:0.1 0/1:152:2:1,1:40,110:0.0132:2,2:31:1:30:1:0.46802:2.73:60:4:0.0132:0:1 -11 67196900 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16935;SOR=Inf;LSEQ=ACTGCCCCACCCTTGGCAGG;RSEQ=CCTAGGCCTCCTGATCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:238,42:0:2,0:23.4:1:31:1:1:0:60:45.667:0.9964:0:0.1 0/1:197:2:1,1:159,36:0.0102:2,2:8.5:1:26:1:0.34114:4.37026:60:4:0.0106:0:1 -11 67199034 . G A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29255;SOR=0;LSEQ=CTGGGGGTCGCGGGGGGGCA;RSEQ=CGAGCCAGCAAAGGAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:3:2,1:37,208:0.0121:2,2:6:1:22.7:1:0.0653:11.06:60:2:0.0085:0:1 0/0:151:0:0,0:23,128:0:2,0:24:1:30.9:1:1:0:60:24.167:1:0:0.2 -11 67199035 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2922;SOR=0;LSEQ=TGGGGGTCGCGGGGGGGCAG;RSEQ=GAGCCAGCAAAGGAAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:1,2:32,206:0.0124:2,2:35.7:1:31.3:1:0.35838:3.20:60:6:0.0132:0:1 0/0:147:0:0,0:21,125:0:2,0:24.3:1:29.2:1:1:0:60:47.667:0.9931:0:0.2 -11 67199959 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16125;SOR=Inf;LSEQ=TCCCCACGGCAGCTCTGTGA;RSEQ=GCAGGTAGGGCGGGAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:250,18:0:2,0:25.9:1:32.2:1:1:0:60:43.667:1:0:0.1 0/1:181:2:2,0:168,11:0.011:2,0:27:1:30.5:1:1:0:60:4:0.011:0:1 -11 67200819 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.08405;LSEQ=CTCCTCCTCCAGCCGCCCTT;RSEQ=ACCGCAGAGAACCGGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:999:63:35,28:498,437:0.0631:2,2:26.4:1:27.8:1:0.79457:1.10:60:11.6:0.0592:0:1.2 0/1:879:284:163,121:335,260:0.3231:2,2:23.3:1:29:1:0.77144:1.05:60:141:0.3249:0:1.2 -11 67201008 . C T 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=3.28897;LSEQ=CTGTGGGGAAGCCAGGGCCA;RSEQ=CCCGGCCTGTGCAGTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:21:0,21:6,170:0.1066:1,1:24.4:1:30.3:1:1:0:60:20:0.1047:0:1 0/1:138:39:2,37:3,96:0.2826:1,2:20.7:1:28.8:1:0.62124:1.72:60:38:0.2794:0:1.1 -11 67201615 . C T 192 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0;SOR=22.89346;LSEQ=CCCAGGGCAGAGGGAGTGAC;RSEQ=GGGGGGCAAGCAGGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1264:5:0,5:653,604:0.004:2,0:2.6:1:23.8:1:0.02595:0:60:4:0.0032:0:1.4 0/1:1031:86:45,41:501,442:0.0834:2,2:20.9:1:29.9:1:0.91048:1.03271:60:42:0.0833:0:1.2 -11 67202044 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.41877;LSEQ=TGTCGCATGGCCCTGCCTCC;RSEQ=CCCCCCAGGGCTTCACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:51:26,25:304,219:0.0885:2,2:26.1:1:30.3:1:0.37381:1.33404:60:50:0.0896:0:1.1 0/1:469:141:87,54:191,133:0.3006:2,2:23.6:1:29.4:1:0.6079:1.12:60:69.5:0.3082:0:1.1 -11 67202156 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=6.37139;LSEQ=CCTCAACAGTAGCCCCCGGG;RSEQ=CCCCGTCAGGTACTGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:701:48:19,29:286,366:0.0685:2,2:21:1:28.7:1:0.65162:1.1924:60:23:0.0671:0:1.2 0/1:686:219:93,126:211,255:0.3192:2,2:26.6:1:28.9:1:0.51017:1.12088:60:108.5:0.3191:0:1.2 -11 67202826 . G A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19145;SOR=4.62855;LSEQ=CACGGAGGGCCGCCCGCCAC;RSEQ=CCCCGCGCTCAACTGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:0.0909:1,0:21.5:1:26:1:1:0:60:4:0.0952:0:1 0/1:6:2:0,2:0,4:0.3333:0,0:27.5:1:30.5:1:1:0:60:4:0.3333:0:1 -11 67203369 . G T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCGCCCTCCGTGTCACT;RSEQ=TCTCTGGCTTCCTCAGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:1:32:0:1:0:60:4:1:0:1 -11 67817154 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGTCCAGGCCACGCTGGTG;RSEQ=TCCTGGCCTTGGCCATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,3:0.1667:2,2:32.5:1:29.5:1:1:2.16028:60:4:0.1818:0:1 0/0:4:0:0,0:2,2:0:2,0:23.5:1:30.3:1:1:0:60:8:1:0:0 -11 67875171 . T C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CTTAGAAAGTGTTTCTAAAA;RSEQ=ACAAATTTCAAGCCGCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21:1:33:1:1:0:60:4:1:0:1 0/1:5:1:1,0:3,1:0.2:2,0:12:0:32:0:1:0:60:2:0.2:0:1 -11 67963527 . A G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCTACTCAGGAGGCTGA;RSEQ=GCAGGAGGATCACTTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:28.5:1:1:0:60:4:1:0:1.5 -11 68132394 . A AC 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0.04415;LSEQ=CCGTATTTTGGGGCTGCTAC;RSEQ=CCCAGCTTTCCCCTGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:82:69,13:2,1:0.9647:2,2:22.8:1:31.9:1:0.42133:2.61:60:164:0.9647:0.2235:0 1/0:50:27:21,6:19,4:0.54:2,2:23.1:1:30.2:1:0.73555:1.34894:60:54:0.54:0.14:0.1 -11 68132507 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50144;SOR=0;LSEQ=AAGCTTGGCCATCCCAGCAA;RSEQ=AGGGACAGTGTTCCTATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:56,80:0.0145:2,2:38.5:1:29:1:1:1.42:60:4:0.0148:0:1 0/0:117:0:0,0:51,66:0:2,0:25.4:1:31.2:1:1:0:60:57.5:1:0:0.2 -11 68132551 . C A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.67133;LSEQ=TGCTGGGTCCACACATAGCA;RSEQ=AAAGACAAGACAAGCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:21,58:0.0247:2,2:7:1:30.5:1:0.47191:2.72:60:4:0.0263:0:1 0/1:60:1:1,0:18,41:0.0167:2,0:1:0:26:0:0.31667:0:60:2:0.0167:0:1 -11 68132731 . A G 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=CATAGGAGCTTGGTGGGAGG;RSEQ=AGCAGATGGGGAGATGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:28.4:1:31.6:1:1:0:60:10:0.8333:0:1 0/0:2:0:0,0:0,2:0:0,0:31:1:31.5:1:1:0:60:4:1:0:0 -11 68132743 . A AG 73 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGAGGAAGCAGATGGGG;RSEQ=GATGTCACTCCATGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:27:1:31.7:1:1:0:60:10:1:0.2:0.8 1/1:2:2:0,2:0,0:1:0,0:18:1:32:0:1:0:60:4:1:0:0 -11 68758369 . C A 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTATACACAGCACATATAC;RSEQ=TATACACAGTAAACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:53,1:0,0:1:0,1:26.7:1:29.6:1:1:0:60:17:1:0:1.3 1/1:58:58:53,5:0,0:1:0,2:20.5:1:29.8:1:1:0:60:57:1:0:1.1 -11 68758426 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19467;SOR=0;LSEQ=ACACGGACACACCGAGCACA;RSEQ=ATATAACGATGACCACGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:98,44:0.0138:2,2:24.5:1:32:1:0.52885:2.21363:60:4:0.0142:0:2 0/0:183:0:0,0:119,64:0:2,0:22.7:1:28.9:1:1:0:60:182:1:0:0.9 -11 68758434 . G T 53 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18586;SOR=0.21133;LSEQ=ACACCGAGCACATATATAAC;RSEQ=ATGACCACGAACTCACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:4:1,3:112,59:0.0229:2,2:12.8:1:26.8:1:0.12798:5.63675:60:8:0.023:0:2.5 0/0:204:1:0,1:126,77:0.0049:2,0:1:0:22:0:0.38235:0:60:2:0.005:0:2 -11 68758439 . C T 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03449;SOR=Inf;LSEQ=GAGCACATATATAACGATGA;RSEQ=CACGAACTCACAGTTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:120,67:0:2,0:25.1:1:31.1:1:1:0:60:36.4:1:0:1.4 0/1:227:6:5,1:129,92:0.0264:2,2:33.7:1:29:1:0.40483:3.55:60:12:0.0267:0:2.2 -11 68758487 . T C 249 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACACAGTTAAAGGCAGTCC;RSEQ=ACCCTACAGCTCAGGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:262:262:129,133:0,0:1:0,2:26.5:1:31.1:1:1:0:60:31.75:1:0:1.9 1/0:317:204:94,110:53,59:0.6435:2,2:25.8:1:30.8:1:0.90621:1.05101:60:101:0.6495:0:1.6 -11 68758509 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0551;LSEQ=CCCTACAGCTCAGGGTGTGT;RSEQ=TAACAAGGTGAGGGACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:235:213:92,121:11,11:0.9064:2,2:26.4:1:29.4:1:0.65287:1.31365:60:25.625:0.9031:0:2.2 0/1:283:98:41,57:75,109:0.3463:2,2:23.2:1:29.7:1:0.89919:1.05:60:97:0.3489:0:2.1 -11 68758558 . TG T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49832;SOR=Inf;LSEQ=ACTCAGGTGGGAAGGGGAGC;RSEQ=GGGGGAGCCAGGTGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:39,109:0:2,0:27.1:1:31:1:1:0:60:48.333:1:0:1.7 0/1:149:2:1,1:46,101:0.0134:2,2:16.5:1:26:1:0.53283:2.18:60:4:0.0136:0.0067:1 -11 68758581 . G A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0.09222;LSEQ=GGGGAGCCAGGTGAGGGAGC;RSEQ=GGGTGCTGGCTGCAGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:102:21,81:2,8:0.9107:2,2:24:1:30.7:1:1:1.04:60:24.5:0.9074:0:1.6 0/1:79:38:12,26:7,34:0.481:2,2:27:1:30.7:1:0.18815:2.22:60:76:0.481:0:1.6 -11 68758590 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16246;SOR=Inf;LSEQ=GGTGAGGGAGCGGGGTGCTG;RSEQ=CTGCAGGAGAAGTGTGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:16,81:0:2,0:23.5:1:32.1:1:1:0:60:96:1:0:1.3 0/1:66:2:1,1:14,50:0.0303:2,2:24.5:1:29:1:0.40559:3.48:60:4:0.0303:0:2 -11 68758840 . A C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGAGACCAGGGGCCCCG;RSEQ=AGCTCTGAGAGAGGAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9.5:1:31.5:1:1:0:60:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 68759641 . T G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCAGAGGACCCCTCCCGG;RSEQ=GGGGAGATGCTCAGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69069479 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02474;SOR=Inf;LSEQ=GGGCTGGGTTCCCTGCAGAT;RSEQ=GGAGGGCTAGGTGCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:151,80:0:2,0:25.3:1:31.5:1:1:0:60:56.75:0.9956:0:0.1 0/1:154:4:2,2:94,56:0.026:2,2:19.3:1:27.5:1:0.63223:1.67262:60:8:0.026:0:1.5 -11 69069489 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06908;SOR=Inf;LSEQ=CCCTGCAGATGGGAGGGCTA;RSEQ=GTGCCTGTCTCCTTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:160,103:0:2,0:24.7:1:31.5:1:1:0:60:64.75:1:0:0.1 0/1:184:3:3,0:103,78:0.0163:2,0:28.7:1:25.3:1:0.26336:0:60:2:0.011:0:2.3 -11 69069589 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17192;SOR=Inf;LSEQ=AGGAGAGGAAAGTGACTCAC;RSEQ=TGCCCCCCTTGCCTGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:97,154:0:2,0:23.4:1:31.6:1:1:0:60:61.75:0.996:0:0.1 0/1:179:2:1,1:78,98:0.0112:2,2:26.5:1:30.5:1:1:1.25:60:4:0.0112:0:1 -11 69069591 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.17319;SOR=Inf;LSEQ=GAGAGGAAAGTGACTCACCT;RSEQ=CCCCCCTTGCCTGTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:93,148:0:2,0:23.6:1:31.7:1:1:0:60:39.167:0.9958:0:0.1 0/1:173:2:1,1:75,95:0.0116:2,2:8.5:1:31:1:1:1.26:60:4:0.0116:0:1.5 -11 69069627 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18216;SOR=Inf;LSEQ=TCCTCAGCAGCCACACCCAG;RSEQ=CTAGGCTCTCCCGCAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:33,106:0:2,0:24.7:1:31.1:1:1:0:60:45.333:1:0:0 0/1:104:2:0,2:37,65:0.0192:2,0:24:1:24.5:1:0.53715:0:60:4:0.0196:0:1.5 -11 69069783 . T C 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGTGTCCTCGTCTGTAG;RSEQ=CGGGCTGTCGGCAGGCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:23.8:1:31.6:1:1:0:60:10:0.5556:0:1 0/0:1:0:0,0:0,1:0:0,0:19:0:15:0:1:0:60:0:0:0:2 -11 69456000 . G C 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=GCAGAAGAGCGCGAGGGAGC;RSEQ=CGGGGCAGCAGAAGCGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:216,10:0:1,0:23.3:1:29.7:1:1:0:60:36.667:1:0:0.1 0/1:131:10:10,0:110,11:0.0763:2,0:29.8:1:31.4:1:1:0:60:20:0.0775:0:1.2 -11 69456326 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16156;SOR=Inf;LSEQ=AGACTTCCCTGCAACTTGTT;RSEQ=CCCAGACCCACGTTTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:29,186:0:2,0:24.4:1:31.6:1:1:0:60:29.714:1:0:0.2 0/1:145:2:1,1:40,103:0.0138:2,2:16:1:31.5:1:0.48697:2.56:60:4:0.0141:0:1 -11 69456327 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16386;SOR=Inf;LSEQ=GACTTCCCTGCAACTTGTTG;RSEQ=CCAGACCCACGTTTCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:27,184:0:2,0:24.3:1:30.7:1:1:0:60:22.444:1:0:0.2 0/1:144:2:1,1:40,102:0.0139:2,2:8:1:29:1:0.4898:2.53:60:4:0.0145:0:1 -11 69457746 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.10483;SOR=Inf;LSEQ=ATGGGGGGTGCGGGGGCGTG;RSEQ=GGGGGGGCGGCGCGACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:143,22:0:2,0:15.7:1:31.2:1:1:0:60:17.333:0.9936:0:0.2 0/1:150:3:1,2:119,26:0.02:2,2:11.3:1:26:1:0.09187:8.95221:60:6:0.0216:0:1.3 -11 69457756 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08322;SOR=Inf;LSEQ=CGGGGGCGTGCGGGGGGGCG;RSEQ=CGCGACCTGGCGGCGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:218,53:0:2,0:17.6:1:31.6:1:1:0:60:66.75:1:0:0.2 0/1:211:3:1,2:160,48:0.0142:2,2:18.7:1:27.7:1:0.14048:6.58996:60:6:0.0149:0:1 -11 69458055 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06131;SOR=Inf;LSEQ=CCCCCCGCCCCCCGCGAGCC;RSEQ=CACGCAGGACCACGGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:105,322:0:2,0:24.4:1:31.3:1:1:0:60:41.7:1:0:0.2 0/1:279:3:2,1:77,199:0.0108:2,2:14.3:1:24.3:1:0.19417:5.13:60:2:0.0074:0:1 -11 69458081 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13213;SOR=Inf;LSEQ=AGGACCACGGGGCCGGGGAA;RSEQ=GTGCAGGCGGTGGCGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:28,183:0:2,0:20.1:1:31.3:1:1:0:60:34.167:1:0:0.2 0/1:121:2:1,1:20,99:0.0165:2,2:6:1:29:1:0.31818:4.86:60:4:0.0165:0:1 -11 69458455 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06417;SOR=Inf;LSEQ=CAGCATTCGCCAGCCCTCCC;RSEQ=TCCAACATCCAGGACCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:0:1,0:22:1:31.7:1:1:0:60:50:1:0:0.2 0/1:9:2:1,1:6,1:0.2222:2,2:30.5:1:29:1:0.41667:4.58262:60:4:0.25:0:1.5 -11 69462642 . G A 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95947;LSEQ=GATGTGGAGCCTCAGATACC;RSEQ=AGTGCTTCCCTTCAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:54:52,2:72,2:0.4219:1,1:27.2:1:30.2:1:1:1.38102:60:53:0.4173:0:1.2 0/1:51:21:21,0:29,1:0.4118:1,1:18.1:1:30.4:1:1:0:60:42:0.4118:0:1 -11 69462664 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTTCCCTTCAGGCCGGG;RSEQ=CGCTTGCTCAGAGCCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:2,0:173,11:0.0107:2,0:21.5:1:29:1:1:0:60:4:0.0111:0:1.5 0/0:84:0:0,0:79,5:0:2,0:22.4:1:32.1:1:1:0:60:168:1:0:0.3 -11 69462666 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCCCTTCAGGCCGGGCC;RSEQ=CTTGCTCAGAGCCAGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:2,0:182,13:0.0102:2,0:20:1:29:1:1:0:60:4:0.0104:0:1.5 0/0:89:0:0,0:82,7:0:2,0:22.2:1:29.5:1:1:0:60:88:1:0:0.3 -11 69462856 . C T 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAGGAGCCCCAACAACTT;RSEQ=CTGTCCTACTACCGCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1550:0:0,0:751,799:0:2,0:25.1:1:31:1:1:0:60:69.455:1:0:0.3 0/1:1292:57:27,30:592,642:0.0441:2,2:28.5:1:29.1:1:1:1.02456:60:27.5:0.0432:0:1.2 -11 69462910 . G A 263 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24324;SOR=1.12461;LSEQ=AGAGTGATCAAGTGTGACCC;RSEQ=GTAAGTGAGGGTGATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1017:393:153,240:228,395:0.3864:2,2:25.6:1:30.6:1:0.46478:1.10:60:55.143:0.3879:0:1.1 0/1:779:323:114,209:172,284:0.4146:2,2:25.6:1:30.4:1:0.49813:1.11018:60:52.833:0.4128:0:1.2 -11 69463478 . AG A 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTAAAATGACAATCAAA;RSEQ=GGTTTGTGGCATTTACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:33:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69465507 . C A 54 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCTGAAAAGGCAGGGTT;RSEQ=AAAGGGCCTCCTGTCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:23:1:27.3:1:1:0:60:8:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69465681 . A G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48236;SOR=1.70316;LSEQ=ACCAGGTGGGAGGTGGAGGC;RSEQ=TTTGGTCCTGAGTGTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:11:11,0:17,2:0.3667:2,0:19.8:1:28.9:1:0.51954:0:60:10:0.3448:0:1.3 1/0:10:5:5,0:5,0:0.5:0,0:10.6:1:30.6:1:1:0:60:10:0.5:0:1.2 -11 69465799 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12062;SOR=Inf;LSEQ=TTGCTCTTATAAAGGCTTCC;RSEQ=GGTCATGGCACCTGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:263,33:0:2,0:22.8:1:29.6:1:1:0:60:41.286:1:0:0.1 0/1:158:2:1,1:134,22:0.0127:2,2:12.5:1:29:1:0.27074:5.97924:60:4:0.0127:0:1 -11 69465872 . CCT C 94 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.60583;SOR=1.3979;LSEQ=CTCTTCCCACCTCTCCCCAC;RSEQ=CTCTCTCTCAGGACTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:916:7:2,5:537,372:0.0076:2,2:36.6:1:31:1:0.13105:3.60389:60:14:0.0077:0:0 0/1:751:8:6,2:439,300:0.0107:2,2:32.3:1:31.5:1:0.48448:2.05:60:16:0.0108:0.0013:1 -11 69465987 . AGAG A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.35914;SOR=0.73229;LSEQ=AAGGCCGCCGAGGAGGAGGA;RSEQ=GAGGAGGAGGAGGTGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1153:28:12,16:545,577:0.0243:2,2:18.7:1:31.1:1:0.57225:1.25913:60:56:0.0246:0.0104:0.4 0/1:894:16:8,8:407,470:0.0179:2,2:23.4:1:31.3:1:0.80515:1.15:58.1:32:0.0182:0.0056:0.6 -11 69466115 . C A 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.01721;LSEQ=GAGCCGGCCCCAGGTGCTCC;RSEQ=CTGACAGTCCCTCCTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:105:13,92:15,141:0.4023:2,2:19.1:1:29.7:1:0.54245:1.33:60:104:0.4094:0:1.2 0/1:187:76:13,63:12,99:0.4064:2,2:19.9:1:29.1:1:0.27437:1.70:60:37:0.4066:0:1.1 -11 69511849 . A C 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29984;SOR=0;LSEQ=GCATCTTGATTGGCAGATGG;RSEQ=GACAGGGAACGCCCCAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:4:4,0:149,4:0.0255:1,0:27.8:1:33.5:1:1:0:60:8:0.0261:0:1 0/0:88:0:0,0:86,2:0:1,0:24.6:1:29.1:1:1:0:60:176:1:0:0.1 -11 69512089 . T C 331 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.39411;LSEQ=TAATCCCTGGCAAATGCTCA;RSEQ=TTGGAATCATGTTTCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1448:1334:560,774:50,63:0.9213:2,2:24.7:1:31.9:1:0.69168:1.09687:60:77.471:0.921:0:1.1 1/1:1306:1261:537,724:20,22:0.9655:2,2:24.4:1:31.3:1:0.52962:1.22546:60:113.636:0.9653:0:1.2 -11 69512114 . T C 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCATGTTTCATGCACACG;RSEQ=TGGTGTCCGGTTGCACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1077:0:0,0:372,702:0:2,0:24.3:1:30:1:1:0:60:118.333:0.9972:0:0.9 0/1:934:41:12,29:349,542:0.0439:2,2:21.6:1:30.2:1:0.25147:1.55542:60:12.667:0.0413:0:2 -11 69512199 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26878;SOR=0;LSEQ=CGCTAATTCTTGCCTTCCCA;RSEQ=CCTGCCGTGCAGCTGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:3:2,1:18,233:0.0118:2,2:5.3:1:25.7:1:0.0169:25.02:60:6:0.012:0:1.3 0/0:182:0:0,0:20,162:0:2,0:25.5:1:31.7:1:1:0:60:44.5:1:0:0.1 -11 69513939 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21441;SOR=Inf;LSEQ=CCTAAAGCTAAACAGAACGT;RSEQ=GACTCAGGACTGTTCTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:167,11:0:2,0:22.8:1:32:1:1:0:60:58.333:1:0:0.1 0/1:154:2:1,1:135,17:0.013:2,2:14.5:1:30:1:0.22078:7.74581:60:4:0.0132:0:1 -11 69514371 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06691;SOR=Inf;LSEQ=AGAAAACAGGCAGCTCTGAG;RSEQ=AATCCACAGTGGACAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:81,256:0:2,0:23.4:1:31.8:1:1:0:60:66.4:0.997:0:0.1 0/1:232:3:1,2:50,179:0.0129:2,2:12:1:28.3:1:0.52687:1.78:60:6:0.0132:0:1 -11 69514657 . C A 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAATCCAGGAGTTTGAGA;RSEQ=CAGCCTGGGCAACATGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:13.8:1:28.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69515423 . G A 76 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCCTTTATCATTCTAAG;RSEQ=CCTTCTGGTCTGCAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:32.4:1:27.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69515534 . C CCCAGG 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CAGATCTCAGCAGCCCCTCC;RSEQ=CCAGGCCAGGCCAGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:24.5:1:32.6:1:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69515695 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.1202;SOR=Inf;LSEQ=CCTTGGCGACCCAGGACAGG;RSEQ=GCAGGCGGGAGCCGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:110,3:0:1,0:26.4:1:32.1:1:1:0:60:55.5:1:0:0.1 0/1:61:2:2,0:55,2:0.0328:1,0:10:1:31:0:1:0:60:4:0.0328:0:1 -11 69515696 . G A 70 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00786;SOR=12.04941;LSEQ=CTTGGCGACCCAGGACAGGC;RSEQ=CAGGCGGGAGCCGGAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:1,0:114,4:0.0084:1,0:46:0:29:0:1:0:60:2:0.0084:0:1 0/1:64:6:6,0:54,4:0.0938:2,0:26.5:1:27.2:1:1:0:60:12:0.0952:0:1.5 -11 69515734 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18953;SOR=Inf;LSEQ=GGCTGGGCAGTAAACACACT;RSEQ=CAGGACGGCCTCAGTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:188,50:0:2,0:21.9:1:31.7:1:1:0:60:58.5:1:0:0.1 0/1:184:2:1,1:135,47:0.0109:2,2:23:1:30.5:1:0.45474:2.85277:60:4:0.0112:0:1 -11 69515786 . G T 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29347;SOR=0.37093;LSEQ=TCTGCAAAGGTCACTGAACT;RSEQ=CAGGTGGGTGACGAGGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:6:2,4:343,214:0.0107:2,2:20:1:24.5:1:0.21281:3.19882:60:2:0.0073:0:1.2 0/0:503:2:0,2:321,180:0.004:2,0:1:0:23:1:0.13046:0:60:1:0.002:0:1 -11 69516025 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02188;SOR=Inf;LSEQ=AGAAATTAGTATCACTTTCT;RSEQ=CATACAGAAAACGAAATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:1,147:0:1,0:24.9:1:31.4:1:1:0:60:73:1:0:0.2 0/1:94:4:0,4:1,89:0.0426:1,0:17.8:1:29.5:1:1:0:60:8:0.0426:0:1 -11 69517971 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02002;SOR=Inf;LSEQ=TTTCTCTCCTTCAGGCCTCC;RSEQ=CCCGGGGACAGGCGCCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:323,109:0:2,0:23.1:1:30:1:1:0:60:53:1:0:0.1 0/1:262:4:2,2:174,84:0.0153:2,2:20.5:1:28.3:1:0.59965:2.06522:60:8:0.0159:0:1.8 -11 69518455 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17126;SOR=Inf;LSEQ=GCAGTCCACGACGCCGTCGG;RSEQ=ACGGATGCGCAGGAAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:181,69:0:2,0:25.9:1:32.3:1:1:0:60:82.333:1:0:0.2 0/1:177:2:1,1:117,58:0.0113:2,2:18.5:1:28.5:1:1:2.00866:60:4:0.0116:0:1 -11 69518486 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03773;SOR=Inf;LSEQ=AGGAAGCAGCTGGAGAGCCC;RSEQ=TGGGGGCCGGAGGTGTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:0:0,0:225,135:0:2,0:26.2:1:30:1:1:0:60:35:0.9972:0:0.2 0/1:286:4:3,1:167,115:0.014:2,2:11:1:27.5:1:0.64898:2.06:60:8:0.0141:0:1.5 -11 69518534 . G T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04354;SOR=Inf;LSEQ=AGGCGGATGGGGTCGCCCCA;RSEQ=CCGTAGTGCACGTGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:178,171:0:2,0:25.3:1:32:1:1:0:60:86.25:1:0:0.2 0/1:295:4:1,3:150,140:0.0136:2,2:18.5:1:25.5:1:0.35926:3.20262:60:3:0.0106:0:1.5 -11 69518589 . G A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25013;SOR=0;LSEQ=CGAGGGGGCGCCCGGCCACG;RSEQ=CCAGCCAGAGGCCGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:2,1:107,145:0.0118:2,2:34.7:1:31.7:1:0.57755:2.70:60:6:0.0118:0:2 0/0:232:0:0,0:101,131:0:2,0:23.4:1:30.6:1:1:0:60:24.778:1:0:0.2 -11 69518636 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25552;SOR=0;LSEQ=ACGTGGACCACCACACACCC;RSEQ=CTCCGCATGGCACCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:2,1:75,125:0.0148:2,2:28:1:28.3:1:0.55858:3.31:60:6:0.0154:0:1 0/0:166:0:0,0:67,98:0:2,0:26.8:1:30.5:1:1:0:60:54:1:0:0.2 -11 69518660 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18012;SOR=Inf;LSEQ=CGCATGGCACCTCCCTGGGG;RSEQ=TCTCGGCGCAGCTCCGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:51,107:0:2,0:24.8:1:31.3:1:1:0:60:18.75:1:0:0.2 0/1:117:2:1,1:45,70:0.0171:2,2:18.5:1:25:1:1:1.55:60:4:0.0172:0:2 -11 69529910 . AGAGG A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=4.000;MSILEN=4;SSF=0.4;SOR=Inf;LSEQ=GGAAAGAAAGAAAGAAAGAG;RSEQ=GAGGGAGGGAGGAAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:38:1:33:1:1:0:60:4:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:25:1:32:1:1:0:60:4:0.6667:0:0 -11 69530825 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19886;SOR=Inf;LSEQ=ATCCACGCCCAGGCCACAGA;RSEQ=AATAGCCCCTTTAGGACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:4,14:0:2,0:21.7:1:30.9:1:1:0:60:36:1:0:0.3 0/1:15:2:1,1:3,10:0.1333:2,2:6:1:30.5:1:0.47619:3.03:60:4:0.1429:0:1 -11 69586371 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14323;SOR=Inf;LSEQ=AACAGCAGTTTAAGATGTGT;RSEQ=GTCCTGTCTTAGCGGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:97,4:0:1,0:25.1:1:32.6:1:1:0:60:49.5:1:0:0.1 0/1:62:2:2,0:58,2:0.0323:1,0:19:1:29.5:1:1:0:60:4:0.0328:0:1.5 -11 69588020 . C T 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.42158;LSEQ=AGAAAGTGCACCAAGGTGAC;RSEQ=CTCGGCACTGCCCTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:168:137,31:177,23:0.4553:2,2:26.1:1:31:1:0.07554:1.73866:60:83:0.4573:0:1.1 0/1:219:57:51,6:140,22:0.2603:2,2:24:1:30.9:1:0.64969:1.33:60:114:0.2627:0:1.1 -11 69588729 . G A 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGGGGCTGGAGAAGCCAC;RSEQ=AGCCTGCTAGCCATGTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:421:421:298,123:0,0:1:0,2:23.8:1:29.9:1:1:0:60:104.25:1:0:1.1 1/1:283:267:185,82:9,6:0.9435:2,2:22.6:1:29.6:1:0.56724:1.50:60:65.75:0.9427:0:1.1 -11 69589142 . G A 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0.2887;LSEQ=CGGCGGCCGCACCCAGTCCC;RSEQ=GACCTTCAGACGCGAGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:1,0:0.8889:0,0:16.4:1:31.6:1:0.11111:0:60:16:0.8889:0:1.4 1/0:3:2:0,2:0,1:0.6667:0,0:25:1:30.5:1:1:0:60:4:0.6667:0:1.5 -11 69589182 . C G 52 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=GACCCCAGCGGTTCCCCAGC;RSEQ=TGGGCCAGGCCGGGGCGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:1,1:0.6:2,0:36:1:33.3:1:0.4:0:60:6:0.6:0:2 1/0:2:1:0,1:0,1:0.5:0,0:28:0:28:0:1:0:60:2:0.5:0:2 -11 69589308 . A G 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCGGGAGGCGGCGCCCG;RSEQ=CCTCAGGGGTTGCGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30.5:1:1:0:60:4:1:0:1 1/1:4:4:2,2:0,0:1:0,2:32:1:30.3:1:1:0:60:8:1:0:1 -11 69589450 . C T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.58197;SOR=2.50361;LSEQ=GGTCTCAGAGTGTGACTGAG;RSEQ=GGGTTGGCCCGGCGGCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:9,9:0.0526:2,0:1:0:27:0:1:0:60:2:0.0556:0:1 0/1:16:2:1,1:7,7:0.125:2,2:18:0:30:1:1:1:60:4:0.125:0:3.5 -11 69589509 . T C 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63709;SOR=0.43558;LSEQ=TTCGCGCCTGGCCGCGCCAC;RSEQ=CACTGTCGCGGGTGTCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:2,1:181,76:0.0115:2,2:22.3:1:24.7:1:1:1.18994:60:2:0.0079:0:1 0/0:198:1:1,0:130,67:0.0051:2,0:2:0:32:0:1:0:60:2:0.0053:0:1 -11 69589556 . G A 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=50.03179;LSEQ=CCGCCGATGCGGCCGTCGGG;RSEQ=AGCGCCTGGAGGTGGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:667:1:1,0:386,280:0.0015:2,0:1:0:26:0:1:0:60:2:0.0015:0:1 0/1:571:40:23,17:304,225:0.0701:2,2:29.2:1:28.9:1:1:1.00:60:80:0.071:0:1.1 -11 69589711 . C T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43352;SOR=2.18984;LSEQ=CGAGAGCGCCACCAGGCTCT;RSEQ=CCAGCGGCGCTCCAGCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:2:0,2:157,208:0.0054:2,0:1:0:20:1:0.50909:0:60:1:0.0028:0:1 0/1:337:4:1,3:149,184:0.0119:2,2:21.3:1:28:1:0.63185:2.42353:60:8:0.012:0:1 -11 69589804 . G T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2632;SOR=0;LSEQ=CCAGGGCGCCAGCAAGGCCA;RSEQ=CAGGACCGCCGGGAGCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:141,153:0.0101:2,2:24:1:32:1:0.61024:2.16:60:6:0.0103:0:1 0/0:225:0:0,0:101,123:0:2,0:19:1:31.7:1:1:0:60:36.333:0.9954:0:0.4 -11 69589820 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17079;SOR=Inf;LSEQ=GCCAGCAGGACCGCCGGGAG;RSEQ=AGCGCTACCGCGGCCGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:121,131:0:2,0:21.8:1:32:1:1:0:60:62:1:0:0.3 0/1:178:2:1,1:82,94:0.0112:2,2:18.5:1:28.5:1:1:1.15:60:4:0.0116:0:1.5 -11 69589836 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56484;SOR=3.06959;LSEQ=GGAGCAGCGCTACCGCGGCC;RSEQ=TCCCGGGCCCCGACATCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:1:1,0:96,95:0.0052:2,0:1:0:27:0:1:0:60:2:0.0053:0:1 0/1:126:2:1,1:60,64:0.0159:2,2:40.5:1:30.5:1:1:1.07:60:4:0.0159:0:1 -11 69589842 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14432;SOR=Inf;LSEQ=GCGCTACCGCGGCCGTCCCG;RSEQ=GCCCCGACATCCCGGCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:89,91:0:2,0:24.7:1:30.3:1:1:0:60:21.5:0.9885:0:0.3 0/1:112:2:1,1:56,54:0.0179:2,2:41:1:30:1:1:1.03671:60:4:0.0183:0:1 -11 69589865 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.51095;SOR=0;LSEQ=CCCGACATCCCGGCCCGAGG;RSEQ=CCGTGCGTCGGTCAGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:63,64:0.0155:2,2:20.5:1:28.5:1:1:1.02:60:4:0.0157:0:1 0/0:93:0:0,0:46,46:0:2,0:23.6:1:31.5:1:1:0:60:184:0.9892:0:0.5 -11 69589868 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16726;SOR=Inf;LSEQ=GACATCCCGGCCCGAGGGCC;RSEQ=TGCGTCGGTCAGGCGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:62,63:0:2,0:24.4:1:30.2:1:1:0:60:124:1:0:0.3 0/1:87:2:1,1:42,43:0.023:2,2:9.5:1:28:1:1:1.02:60:4:0.0233:0:1.5 -11 69589929 . T G 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00223;SOR=Inf;LSEQ=GCAGAGCTGCGCCTGTGGCG;RSEQ=CCCGCGGGAGCGCACGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:6,14:0:2,0:20.6:1:30.2:1:1:0:60:40:1:0:0.3 0/1:14:6:3,3:2,6:0.4286:2,2:12.8:1:30.7:1:0.58042:2.76:60:12:0.4286:0:1.2 -11 69589956 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCGCACGGCCGACCTCG;RSEQ=GCAGGAGTGCGCAACCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,6:0.2:2,2:22:1:28.5:1:1:2.65:60:4:0.2:0:1.5 0/0:2:0:0,0:1,1:0:2,0:7.5:1:30:1:1:0:60:4:1:0:1.5 -11 69589959 . A G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GCGCACGGCCGACCTCGGGC;RSEQ=GGAGTGCGCAACCGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:2,2:0.4286:2,0:27:1:31.7:1:0.42857:0:60:6:0.4286:0:1.3 1/1:2:2:1,1:0,0:1:0,2:7.5:1:30.5:1:1:0:60:4:1:0:1.5 -11 69591515 . TC T 73 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.62174;LSEQ=GCTGCCTCTGGGTCCTGGGG;RSEQ=CCCCAGATGAGCCTGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:6,0:0.4545:0,2:18.8:1:31.5:1:0.45455:0:60:10:0.5:0.0909:0 0/1:3:1:1,0:2,0:0.3333:0,0:12:0:33:0:1:0:60:2:0.5:0:0 -11 69591699 . A C 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTCCCTCAGCCTGGGGCCA;RSEQ=CCGAACACACCCTCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:260:260:253,7:0,0:1:0,1:25:1:31.9:1:1:0:60:64:1:0:1.1 1/1:169:153:140,13:15,1:0.9053:1,2:22.9:1:30.9:1:1:1.39042:60:37.25:0.903:0:1.1 -11 69591784 . T TC 231 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=303.94244;LSEQ=GCAGAGGGACTCTGATGTCT;RSEQ=CCCCCGGCTTTTGATAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1106:1:1,0:644,458:9e-04:2,0:20:0:33:0:1:0:60:2:9e-04:0:0 0/1:954:205:107,98:426,323:0.2149:2,2:23.7:1:30.2:1:0.23495:1.2077:60:33.167:0.2124:0.0346:0.2 -11 69591809 . C T 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3826;LSEQ=CGGCTTTTGATAGGATGAGG;RSEQ=TCCTTTCTTCCCAGGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1448:779:426,353:347,320:0.538:2,2:25.6:1:29.7:1:0.31554:1.11:60:76.9:0.5396:0:1.1 0/1:1243:383:198,185:439,420:0.3081:2,2:25.2:1:29.1:1:0.85394:1.02:60:53.714:0.3079:0:1.2 -11 69592058 . T G 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29464;SOR=0;LSEQ=GGCTTCCACTTTGCTCCGGG;RSEQ=GCTCCCTGAGCACACTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:79:0,79:0,0:1:0,1:25.4:1:31.1:1:1:0:60:38.5:1:0:1.2 1/1:33:32:3,29:0,1:0.9697:0,2:22.2:1:30:1:1:0:60:31:0.9688:0:1.2 -11 69592140 . A T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35484;SOR=0;LSEQ=AACAAAAGCACAGGTAAGGA;RSEQ=GAATTGCGGATGAAGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:1:0,1:21.2:1:30.6:1:1:0:60:40:1:0:1.7 1/1:11:10:2,8:0,1:0.9091:0,2:20.3:1:30.2:1:1:0:60:20:0.9091:0:1.4 -11 69623641 . G T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGCTGAAGGAGGCACCGA;RSEQ=ATTTTCACTTGTGTTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:28.7:1:31:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69623866 . G A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03573;LSEQ=TCTGACCCTGGGCTCTCTGA;RSEQ=TCTGGGCTCTCTGACCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:27:27,0:86,3:0.2328:1,1:24.3:1:30.8:1:1:0:60:54:0.2348:0:1 0/1:46:11:11,0:35,0:0.2391:1,0:29.2:1:29.5:1:1:0:60:10:0.2222:0:1.5 -11 69623871 . G T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00148;SOR=Inf;LSEQ=CCCTGGGCTCTCTGAGTCTG;RSEQ=GCTCTCTGACCCCTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:123,3:0:1,0:25.5:1:30.8:1:1:0:60:14.75:1:0:0.3 0/1:49:5:5,0:43,0:0.102:1,0:20.8:1:29.6:1:1:0:60:10:0.1042:0:1.2 -11 69623935 . G T 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.04787;SOR=Inf;LSEQ=CCTCACAGTCCCAGGCTCAG;RSEQ=AGAGCCTCCTCACCTGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:347,88:0:2,0:22:1:30.8:1:1:0:60:38.545:1:0:0.1 0/1:249:3:1,2:181,65:0.012:2,2:14.7:1:26.7:1:0.17714:5.52328:60:6:0.0122:0:1 -11 69624283 . A C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01024;SOR=0.26811;LSEQ=AGAGTTTTCAAAGAAAGTAA;RSEQ=CTCTCTCTCTCTCTCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:45:0,45:0,11:0.7627:0,1:15.6:1:30.7:1:1:0:59.6:21.5:0.7679:0:1.4 0/1:24:11:0,11:1,12:0.4583:1,0:17.5:1:29.6:1:1:0:59.1:10:0.4545:0:1.6 -11 69625025 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTCAGAGTCAAGAGGCTG;RSEQ=CACGCCAAGATGTCGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:2,0:167,7:0.0114:1,0:12.5:1:31:1:1:0:60:4:0.0115:0:1 0/0:85:0:0,0:78,7:0:2,0:22.4:1:31.9:1:1:0:60:27.333:1:0:0.1 -11 69625385 . C T 131 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.88617;LSEQ=GCCCCAGGCGTACTAGACAC;RSEQ=GTCCGGTACAGCCGGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:988:1:0,1:404,582:0.001:2,0:1:0:25:0:1:0:60:2:0.001:0:1 0/1:791:21:10,11:350,419:0.0265:2,2:17.5:1:30:1:1:1.09:60:42:0.027:0:1.3 -11 69625473 . G A 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=79.87438;LSEQ=CGGCGCTGTAGTGCTCCTGC;RSEQ=GGGATGAGATATCATGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:1:1,0:231,409:0.0016:2,0:1:0:29:0:0.36193:0:60:2:0.0016:0:1 0/1:468:52:21,31:170,246:0.1111:2,2:19.5:1:29.7:1:1:1.02009:60:25:0.1082:0:1.1 -11 69625496 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16188;SOR=4.8193;LSEQ=GATGAGATATCATGGTCAGT;RSEQ=CCCCGGGGAGACTGTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:1:1,0:142,320:0.0022:2,0:1:0:25:0:0.30886:0:60:2:0.0022:0:1 0/1:290:3:2,1:108,179:0.0103:2,2:16.3:1:26.7:1:0.55949:3.30:60:6:0.0106:0:1.7 -11 69625511 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10877;LSEQ=TCAGTGCCCCGGGGAGACTG;RSEQ=GGCAGCGTCAGGGCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:355:301:62,239:14,40:0.8479:2,2:23.9:1:30.1:1:0.37225:1.34799:60:74.25:0.8462:0:1.1 0/1:202:76:25,51:35,91:0.3762:2,2:22.9:1:30.3:1:0.52518:1.27:60:75:0.375:0:1.1 -11 69625730 . G A 100 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=CCAGACAACTCCCAGCTCCT;RSEQ=CTCTCTGGGTTCCACCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:26.3:1:29.1:1:1:0:60:22:1:0:1.1 1/0:2:1:1,0:0,1:0.5:0,0:18:0:23:0:1:0:60:2:0.5:0:1 -11 69626472 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGCCTGGCATGAGGCAC;RSEQ=TGATCAATCAGTGCCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69627317 . C G 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.702;SOR=1.35502;LSEQ=ACTGAGGCCCAGGGGTGGTG;RSEQ=CAGGCCCTACATTACAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:12:12,0:48,1:0.1967:1,0:26.9:1:29.7:1:1:0:60:11:0.1897:0:1.2 0/1:12:3:3,0:9,0:0.25:0,0:29.3:1:32:0:1:0:60:6:0.25:0:1 -11 69627441 . A T 33 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0451;SOR=Inf;LSEQ=CCGACTTCCCCACCCCACAC;RSEQ=CTGGGTACACCATGTTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:358,69:0:2,0:24.6:1:30.2:1:1:0:60:141.333:1:0:0.6 0/1:237:3:0,3:187,47:0.0127:2,0:14:1:21.3:1:0.00895:0:60:2:0.0085:0:1 -11 69627451 . C A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10327;LSEQ=CACCCCACACACTGGGTACA;RSEQ=CATGTTAGTGTCTGGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:513:292:225,67:172,49:0.5692:2,2:24.2:1:30.2:1:0.91518:1.04518:60:584:0.5692:0:1.1 0/1:334:40:31,9:210,84:0.1198:2,2:23.1:1:29.3:1:0.57277:1.38:60:80:0.1205:0:1.1 -11 69627540 . G A 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTCGATCCTGCAGCAGGT;RSEQ=AGTCCTCTCAGGGCCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1361:0:0,0:644,716:0:2,0:25.4:1:31.6:1:1:0:60:70.579:0.9993:0:0.2 0/1:1070:24:10,14:523,523:0.0224:2,2:25.8:1:29.6:1:0.53667:1.39956:60:48:0.0226:0:1.2 -11 69627662 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14242;LSEQ=CAGGGGGCTCAGGCTCTCCC;RSEQ=AGGTGGGAGATTGGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:354:304:60,244:12,38:0.8588:2,2:24.8:1:31:1:0.4555:1.28325:60:100.333:0.8575:0:1.1 0/1:244:113:32,81:38,93:0.4631:2,2:25.5:1:30.5:1:1:1.03414:60:112:0.4609:0:1.2 -11 69627674 . T A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.2841;SOR=0;LSEQ=GCTCTCCCAAGGTGGGAGAT;RSEQ=GGGGGCAGTGTAGATCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:54,228:0.0105:2,2:13:1:21.3:1:0.09964:8.35:60:2:0.0071:0:2.3 0/0:183:0:0,0:52,131:0:2,0:23.9:1:29.6:1:1:0:60:90.5:1:0:0.7 -11 69627762 . A G 186 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGGTGTTGGCTCAGGGGCC;RSEQ=GGGCCATAGACTCCAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:1,64:0,0:1:0,1:22.2:1:31:1:1:0:60:31.5:1:0:1.1 0/1:17:8:0,8:0,9:0.4706:0,0:21.6:1:30:1:1:0:60:16:0.4706:0:1 -11 69628073 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGGGGGCTTCCGGAAGC;RSEQ=GGAGGAGGCTCAACCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:40.5:1:28:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69628099 . A G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTCAACCTCTGGATGAC;RSEQ=GCCCCCCTGGGAGCAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:31.3:1:30.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69629390 . G A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTCCTAGGCAAGCTGGCC;RSEQ=CACGCAGGACTGTGGTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:20:1:31.5:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:1:0,0:25:0:26:0:1:0:60:2:1:0:1 -11 69630842 . C A 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGATGGGGGAAACCTTTG;RSEQ=TAACCTGGCATTCTCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:15,1:0.2:1,0:12:1:29.3:1:1:0:60:8:0.2:0:1.3 0/0:1:0:0,0:1,0:0:0,0:35:0:29:0:1:0:60:2:1:0:0 -11 69630973 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23662;LSEQ=AGGGTCTGGTCCTAGCTTGG;RSEQ=TCCCGTGTACCCTTGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:167:84:84,0:81,2:0.503:1,1:25.5:1:30.1:1:0.24551:0:60:83:0.5123:0:2.2 0/1:78:15:15,0:62,1:0.1923:1,1:16.1:1:30.3:1:1:0:60:30:0.1923:0:2.2 -11 69630978 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=0.3029;LSEQ=CTGGTCCTAGCTTGGGTCCC;RSEQ=TGTACCCTTGGCAAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:184:155:154,1:28,1:0.8424:1,1:24.3:1:30.3:1:0.2911:5.42:60:154:0.8415:0:1.7 1/0:94:58:57,1:36,0:0.617:1,1:20.8:1:30.1:1:1:0:60:57:0.6129:0:1.3 -11 69633358 . C T 32 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=ACACCCCGGGCGCACCATGC;RSEQ=TTCTCCCGGGCCAGACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:14.6:1:32.1:1:1:0:60:20:1:0:0.1 1/1:2:2:1,1:0,0:1:0,2:10:0:32:1:1:0:60:4:1:0:1.5 -11 69633436 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.62244;SOR=1.77317;LSEQ=CCTTCTCCCGGGCCCGACCC;RSEQ=TCCCGGCGCCGCTTCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:2:0,2:195,43:0.0083:2,0:1:0:23.5:1:0.03452:0:60:4:0.0084:0:2 0/1:136:2:1,1:102,32:0.0147:2,2:16.5:1:29.5:1:0.42778:3.15418:60:4:0.0148:0:1.5 -11 69633617 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20793;SOR=Inf;LSEQ=GACGCCGCCACGGCCGCCCG;RSEQ=ATCGCGCCGCAACCGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:51,119:0:2,0:13.4:1:32.4:1:1:0:60:340:1:0:0.3 0/1:143:2:1,1:58,83:0.014:2,2:38.5:1:29.5:1:1:1.43:60:4:0.0142:0:1 -11 69633631 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50274;SOR=0;LSEQ=CGCCCGCATCGCGCCGCAAC;RSEQ=GCGCCCCAGGGCCCGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:38,74:0.0175:2,2:40.5:1:31.5:1:1:1.94:60:4:0.018:0:1 0/0:93:0:0,0:35,57:0:2,0:16.4:1:29.9:1:1:0:60:184:0.9892:0:0.4 -11 69633633 . C A 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04488;SOR=5.23992;LSEQ=CCCGCATCGCGCCGCAACCG;RSEQ=GCCCCAGGGCCCGCTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:2,0:36,67:0.019:2,0:1:0:27:1:0.12875:0:60:4:0.0192:0:1 0/1:86:8:3,5:31,47:0.093:2,2:18.1:1:29.6:1:1:1.09812:60:7:0.0843:0:1.1 -11 69633645 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23106;SOR=Inf;LSEQ=CGCAACCGCGCCCCAGGGCC;RSEQ=GCTGCGGGCCAGCCGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:38,36:0:2,0:22.6:1:30.4:1:1:0:60:73:1:0:0.5 0/1:69:2:1,1:34,33:0.029:2,2:38:0:30:1:1:1.02986:60:4:0.0299:0:1 -11 69633650 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CCGCGCCCCAGGGCCCGCTG;RSEQ=GGGCCAGCCGGGCTCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:1,2:39,36:0.0385:2,2:26.3:1:27.3:1:0.61039:2.14595:60:6:0.0395:0:1 0/0:66:0:0,0:34,32:0:2,0:25.7:1:30.9:1:1:0:60:132:1:0:0.4 -11 69633669 . C T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63145;LSEQ=GCGGGCCAGCCGGGCTCCAG;RSEQ=AGGCTGAGCAGTAGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:51,46:0.0202:2,2:15.5:1:27.5:1:1:1.10754:60:4:0.0204:0:1.5 0/1:78:1:0,1:39,38:0.0128:2,0:1:0:23:0:1:0:60:2:0.0128:0:1 -11 69633682 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51037;SOR=0;LSEQ=GCTCCAGCAGGCTGAGCAGT;RSEQ=GCAGCCAGATTAGGCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:55,51:0.0185:2,2:31:1:31:1:1:1.07765:60:4:0.0187:0:1 0/0:78:0:0,0:38,40:0:2,0:28.4:1:29.3:1:1:0:60:77:1:0:0.4 -11 69633721 . CGCG C 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0.74588;LSEQ=TCGTGGCATCGCGCCCGCCC;RSEQ=GCGGCGGCGGCTGCAGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:4:2,2:28,32:0.0615:2,2:27.3:1:32:1:1:1.14:60:8:0.0615:0:0.3 0/1:43:2:1,1:18,22:0.0465:2,2:3.9:1:32.3:1:1:1.22:60:8:0.0438:0.0556:0.5 -11 69633828 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13306;SOR=Inf;LSEQ=GCCTGGAGATGCTGACTCCG;RSEQ=CTTCGCGGGAAAGGTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:25.4:1:31.9:1:1:0:60:40:1:0:0.3 0/1:12:2:1,1:6,4:0.1667:2,2:11:0:28:0:1:1.4491:60:4:0.1818:0:1.5 -11 69634091 . C A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCGGGGTTCGGGCCGGG;RSEQ=GCCGTCTGCATACACTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:32:1:1:0:60:4:1:0:1.5 -11 69656028 . A C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26564;SOR=0.35262;LSEQ=ACAACCACCAGCACCACCAC;RSEQ=ACACAACAGCATCATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:5,6:2,1:0.7857:2,2:32:1:32.3:1:1:2.2554:60:22:0.7857:0:1.4 1/0:18:10:7,3:5,3:0.5556:2,2:30.2:1:28.5:1:1:1.37:60:9:0.5625:0:1.1 -11 69656104 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15796;SOR=0;LSEQ=AACAACCACAAAAGCAGCAA;RSEQ=AACTACCACAACGACAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:11,4:0.1176:2,2:13:0:32:1:0.51471:2.56905:60:4:0.1176:0:1 0/0:25:0:0,0:13,12:0:2,0:28.8:1:29.1:1:1:0:60:50:1:0:0 -11 69656286 . A ACAACAG 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=3.000;MSILEN=6;SSF=0.23836;SOR=2.22769;LSEQ=CAGCATCAGCAGCAACCACA;RSEQ=CAACAGCAACAGCAACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:33:14,19:5,4:0.7857:2,2:33.6:1:31.9:1:0.7075:1.67486:59.8:66:0.7857:0.0476:0.1 1/1:37:33:15,18:3,1:0.8919:2,2:35:1:30.9:1:0.33977:3.48361:60:66:0.8919:0:0.2 -11 69656312 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.49231;SOR=Inf;LSEQ=GCAACAGCAACAACCACCAC;RSEQ=ACTACCACAACAAGAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:14,18:0:2,0:16.9:1:31.7:1:1:0:60:64:1:0:0.2 0/1:33:2:1,1:13,18:0.0606:2,2:37.5:1:30:1:1:1.37:60:4:0.0606:0:1 -11 69656411 . A AGAAACG 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.606;SOR=0.30817;LSEQ=ACAGCAACAACCACCACAAC;RSEQ=GCAACAACCACCACAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:11,7:0.1429:2,0:18.7:1:31.8:1:0.09023:0:60:6:0.15:0:0.3 0/1:21:1:0,1:14,6:0.0476:2,0:20:0:32:0:0.33333:0:60:2:0.0476:0:0 -11 69656500 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24157;SOR=0;LSEQ=CCACAAAACAACAGCAACAA;RSEQ=CACAACAGCAACAGCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:23,19:0.0455:2,2:24:0:32:1:1:1.20525:60:4:0.0476:0:1.5 0/0:45:0:0,0:23,22:0:2,0:21.9:1:29.2:1:1:0:59.5:14:1:0:0.4 -11 69656515 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.2365;SOR=Inf;LSEQ=AACAACCACAACAGCAACAG;RSEQ=ATCATCAACAGCAACAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:0:2,0:22.9:1:31.8:1:1:0:60:94:1:0:0.3 0/1:45:2:1,1:21,21:0.0444:2,2:21.5:1:24.5:1:1:1:60:4:0.0465:0:2 -11 69656529 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.24118;SOR=Inf;LSEQ=CAACAGCATCATCAACAGCA;RSEQ=CAGCAACAACAACAACGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:0:2,0:26.9:1:29.8:1:1:0:60:86:1:0:0.2 0/1:42:2:1,1:21,19:0.0476:2,2:7.5:1:27.5:1:1:1.10263:60:4:0.0476:0:2 -11 69656545 . C T 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05609;SOR=Inf;LSEQ=AGCAACAGCAACAACAACAA;RSEQ=GGCAGCAACAATAATAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:21,21:0:2,0:28.5:1:30.9:1:1:0:60:84:1:0:0.1 0/1:45:5:2,3:21,19:0.1111:2,2:38:1:31.4:1:0.66515:1.63945:60:10:0.119:0:1.4 -11 69656564 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49413;SOR=0;LSEQ=ACGGCAGCAACAATAATAGC;RSEQ=ACAGCATATTCAACAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:18,22:0.0476:2,2:31.5:1:28:1:1:1.22:60:4:0.05:0:1 0/0:40:0:0,0:18,22:0:2,0:24.2:1:29.3:1:1:0:60:19:1:0:0.3 -11 69871665 . AATG A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATAGTGGTGATGGTGATGAC;RSEQ=ATGATGATGATGATGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69872433 . G A 49 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TAATGATGGCATTGATGATG;RSEQ=TGGTGGTGGTGGTGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:0.6:2,0:20:1:31.3:1:0.4:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69872459 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTGGTGGTGGTGGTGAC;RSEQ=GTGATGGTGGTGGTGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:34.5:1:31.5:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 69872725 . T C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30705;SOR=0.23787;LSEQ=AGTGGCGACTGATATCACCC;RSEQ=TGCTGCCATCATTCAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:33:17,16:1,0:0.9706:0,2:23:1:31.7:1:1:0:60:66:0.9706:0:1.1 1/1:26:23:13,10:1,2:0.8846:2,2:26.7:1:30:1:0.58:2.51:60:46:0.8846:0:1.2 -11 71952339 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5175;SOR=0;LSEQ=AGAACTTGTAGGGCACTGCG;RSEQ=GTGTGTGCAGGGGGGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:16,39:0.0351:2,2:7:1:29:1:0.51128:2.39:60:4:0.0351:0:1 0/0:37:0:0,0:11,26:0:2,0:18.6:1:29.8:1:1:0:60:74:1:0:0.9 -11 71952356 . CG C 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17035;SOR=5.18188;LSEQ=GCGGGTGTGTGCAGGGGGGC;RSEQ=GGGGGGGGGCAAAAAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:0,1:5,21:0.0345:2,0:45:0:31:0:1:0:60:2:0.0385:0:0 0/1:25:4:0,4:2,19:0.16:2,0:31.5:1:31.3:1:1:0:60:8:0.1818:0:0.5 -11 71991307 . A C 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGTGCTCTCGGTTGCACA;RSEQ=TAAACGGACGTTTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:173,271:0:2,0:24.5:1:30.7:1:1:0:60:73:1:0:0.1 0/1:433:19:10,9:176,238:0.0439:2,2:23.9:1:31.6:1:0.47854:1.50:60:38:0.0443:0:1.3 -11 71991390 . C T 68 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28653;SOR=0.3963;LSEQ=CCCTGTCTGCTGATGGTTTG;RSEQ=GCTGTGCCATGAGCGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:5:1,4:157,227:0.0129:2,2:16.4:1:29.4:1:0.65231:2.76031:60:10:0.013:0:1.2 0/0:390:2:1,1:169,219:0.0051:2,2:7:1:27.5:1:1:1.29:60:4:0.0052:0:1 -11 71991682 . G C 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00285;SOR=Inf;LSEQ=CAGGATGGTCTCGATCTCCT;RSEQ=ACCTCGTGATCCGCCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:68,4:0:2,0:23.7:1:32.4:1:1:0:53.5:71:1:0:0.1 0/1:58:7:7,0:51,0:0.1207:1,0:23.1:1:31.3:1:1:0:58:14:0.1207:0:1.4 -11 71991729 . G T 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28213;SOR=2.56631;LSEQ=CCCAAAGTGCTAGGATTACA;RSEQ=GCATGAGCCACCGTGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:146,31:0.0112:2,2:19:1:31:1:0.32641:4.65138:60:4:0.0113:0:1 0/1:177:5:1,4:140,32:0.0282:2,2:15.8:1:27:1:0.00635:17.10429:60:10:0.0289:0:1 -11 71992099 . C T 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CCATCCGAAGAAGCATAGAT;RSEQ=AAGATCCCAGTCCCGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:193,156:0:2,0:23.4:1:31.4:1:1:0:60:33.9:1:0:0.1 0/1:281:13:9,4:165,102:0.0463:2,2:21.2:1:29.3:1:0.77207:1.39:60:26:0.0469:0:1.1 -11 71992298 . A AT 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1253;SOR=0;LSEQ=CAAACCAGATCATAAGGGGA;RSEQ=TTTTTTTTTAAAACAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:4:1,3:17,118:0.0288:2,2:12.3:1:27.3:1:0.42952:2.30:60:8:0.0296:0:0 0/0:122:0:0,0:26,96:0:2,0:21.2:1:30.1:1:1:0:60:121:1:0:0.1 -11 71994119 . CT C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTGCTTAATCTGCCATA;RSEQ=TTTTTCTCTTTTTTCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:33.5:1:1:0:60:4:1:0:0.5 -11 72301370 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49648;SOR=Inf;LSEQ=CAGGCGCCGCTCAGCTCCGC;RSEQ=CCGGGCCCGCCGCCGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:16,16:0:2,0:23.3:1:31.3:1:1:0:60:64:1:0:0.2 0/1:38:2:1,1:18,18:0.0526:2,2:15:0:32:0:1:1:60:4:0.0526:0:1.5 -11 72326111 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51918;SOR=0;LSEQ=GACTCCGGCTTCAGTTGTTA;RSEQ=TCCAACAGGGCCGCGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:12,17:0.0645:2,2:37:1:29.5:1:1:1.40:60:4:0.069:0:1.5 0/0:19:0:0,0:7,12:0:2,0:24.7:1:31.5:1:1:0:60:38:1:0:0.2 -11 74401763 . C T 271 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.00226;LSEQ=GGAGTAGTACAGGCATAAAA;RSEQ=GGGGAAAGGCATTCCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:490:489:224,265:0,1:0.998:0,2:26.1:1:30.4:1:1:0:60:121.25:0.9979:0:1.1 1/0:502:263:134,129:120,119:0.5239:2,2:26.1:1:29.4:1:0.9288:1.03:60:64.75:0.5243:0:1.1 -11 74401849 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58372;SOR=2.57839;LSEQ=AGAAAGTTGTAGCAGTGGCG;RSEQ=CCTGGGAACGGGGATCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:1,0:67,163:0.0043:2,0:1:0:26:0:0.29437:0:60:2:0.0044:0:2 0/1:180:2:1,1:49,129:0.0111:2,2:5.5:1:28.5:1:0.47952:2.62:60:4:0.0112:0:1 -11 74401859 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19308;SOR=Inf;LSEQ=AGCAGTGGCGGCCTGGGAAC;RSEQ=GGGATCCCTTTGGTGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:44,148:0:2,0:23.8:1:30.7:1:1:0:60:95:1:0:0.2 0/1:151:2:1,1:35,114:0.0132:2,2:26:0:32.5:1:0.42119:3.23:60:4:0.0132:0:1.5 -11 74402547 . A C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTTGGCCCAGTTGTCAC;RSEQ=GGGCAGGAGAGGCCCGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 74790414 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21234;SOR=0;LSEQ=CCACTTTGGGAAGAGAACCA;RSEQ=CTTTTCCTATACTTGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:42,30:0.027:2,2:43:1:30:1:1:1.39351:60:4:0.0274:0:1 0/0:86:0:0,0:51,35:0:2,0:23.4:1:30.9:1:1:0:59.3:85:1:0:0.2 -11 74790567 . AT A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23248;SOR=Inf;LSEQ=TTTGAGTCTTTTCCATTCTG;RSEQ=TTGACTTTTGTGCATTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:108,88:0:2,0:25.6:1:30.2:1:1:0:51.7:97:1:0:0.3 0/1:183:2:1,1:99,82:0.0109:2,2:15.5:1:30.3:1:1:1.20606:60:4:0.011:0.0055:0 -11 74790631 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49951;SOR=0;LSEQ=TCTTCACTGGTGCTTTTTCT;RSEQ=CAGTTTCCTCATCATCGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:83,89:0.0115:2,2:39:1:30.5:1:1:1.07:60:4:0.0116:0:1 0/0:159:0:0,0:71,88:0:2,0:22.1:1:29.3:1:1:0:58.2:158:1:0:0.2 -11 74790660 . C T 111 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.00017;SOR=18.68904;LSEQ=TCATCATCGAAATCATCCTC;RSEQ=TCCTCCTCTTCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:1:0,1:65,79:0.0069:2,0:1:0:26:0:1:0:60:2:0.0072:0:1 0/1:121:14:5,9:45,61:0.1157:2,2:16.4:1:29.4:1:0.7759:1.3248:60:28:0.1186:0:1 -11 74790719 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51484;SOR=0;LSEQ=ATCATCTTCATCTGCAGCAA;RSEQ=TTTTTCTTTTTTCTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:52,81:0.0148:2,2:33:1:29.5:1:1:1.55:60:4:0.0152:0:1 0/0:93:0:0,0:37,56:0:2,0:25.5:1:31.1:1:1:0:60:92:1:0:0.2 -11 74790730 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1848;SOR=Inf;LSEQ=CTGCAGCAAGTTTTTCTTTT;RSEQ=TCTGTGGAACCTTGCTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:50,74:0:2,0:25:1:29.8:1:1:0:60:61:1:0:0.1 0/1:94:2:1,1:36,55:0.0213:2,2:5:0:32.5:1:1:1.52:60:4:0.0213:0:0 -11 74790785 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18566;SOR=Inf;LSEQ=CTGCTTTCTAGATATACTCA;RSEQ=GAGTTTCACATCCTCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:55,50:0:2,0:23:1:30.8:1:1:0:60:51.5:1:0:0.1 0/1:80:2:1,1:46,32:0.025:2,2:8.5:1:28.5:1:1:1.43083:60:4:0.025:0:1 -11 74790792 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17627;SOR=Inf;LSEQ=CTAGATATACTCAAGAGTTT;RSEQ=ACATCCTCCTCTTCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:59,55:0:2,0:22.7:1:31.1:1:1:0:60:27.5:1:0:0.1 0/1:83:2:1,1:48,33:0.0241:2,2:22.5:1:30.5:1:1:1.44782:60:4:0.0247:0:1 -11 74790806 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20998;SOR=Inf;LSEQ=GAGTTTCACATCCTCCTCTT;RSEQ=ATCTTCTGACTCTACATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:66,54:0:2,0:24.5:1:31.6:1:1:0:60:119:1:0:0.1 0/1:102:2:1,1:59,41:0.0196:2,2:36:1:29.5:1:1:1.43376:60:4:0.02:0:1 -11 74790951 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5236;SOR=0;LSEQ=GTACAGACATTTTCAAAGTT;RSEQ=CCAGTGTTACCTTAATTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:28,38:0.0294:2,2:31:1:28:1:1:1.35:60:4:0.0294:0:1 0/0:42:0:0,0:14,28:0:2,0:28.2:1:31:1:1:0:60:13:1:0:0.1 -11 74791099 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22476;SOR=Inf;LSEQ=CTTAAAGTGATCATCTTTGT;RSEQ=GGCCTTTAGTTCACAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:65,72:0:2,0:24.7:1:30.3:1:1:0:56.3:136:1:0:0.1 0/1:124:2:1,1:58,64:0.0161:2,2:24.5:1:28.5:1:1:1.10:57:4:0.0163:0:1 -11 74791304 . A C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.91231;LSEQ=TGATAGTTGGGATGAGAAAC;RSEQ=CATGGGATTTCTGTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:0.2308:0,0:32:1:32.7:1:1:0:60:6:0.2727:0:1 0/1:14:3:0,3:0,11:0.2143:0,0:17.3:1:32.3:1:1:0:60:6:0.2308:0:1 -11 76059229 . T C 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.52244;LSEQ=ACATAGAATTATTAATAAAG;RSEQ=GTTTGTTCCCACTTACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:286:177:80,97:49,60:0.6189:2,2:27.1:1:30.9:1:1:1.01:60:58:0.6148:0:1.1 0/1:327:150:73,77:77,99:0.4587:2,2:23.8:1:30.7:1:0.43524:1.22:60:300:0.4587:0:1.1 -11 76059287 . CT C 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.12958;LSEQ=ATCAGGCTTCAACTGTGTAA;RSEQ=TTTTTTTTCCAAAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:2:0,2:84,116:0.0099:2,0:22.5:1:31:1:0.51175:0:60:4:0.0101:0:0.5 0/1:179:2:1,1:65,111:0.0112:2,2:28.5:1:31:1:1:1.70:60:4:0.0112:0:0 -11 76059298 . CA C 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50528;SOR=0;LSEQ=ACTGTGTAACTTTTTTTTTC;RSEQ=AAAAAAAGAGATATGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:71,108:0.011:2,2:37:0:30:1:1:1.52:60:4:0.0112:0:0 0/0:144:0:0,0:52,91:0:2,0:23.4:1:29.5:1:1:0:60:142:1:0:0.3 -11 76302988 . G T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCCCTGAACATGATCGT;RSEQ=TTCTTGTCCATCAAGTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:18.5:1:32:0:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 77034453 . TC T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50246;SOR=0;LSEQ=ACATGACTATTTAACATTCT;RSEQ=CCCAGTAACCATTACAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:25,172:0.0101:2,2:35:1:30:1:0.24481:6.76:60:4:0.0101:0:1.5 0/0:167:0:0,0:29,138:0:2,0:22.4:1:30.9:1:1:0:60:166:1:0:0 -11 77043396 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGGAAGAGGGGGGGGAA;RSEQ=GGGAAGGGAAGGGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9:1:33.5:1:1:0:44:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 77043421 . A AG 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AGGGAAGGGAAAGGAAGGGA;RSEQ=GGGAAGGGAAGGGAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:19.8:1:30.2:1:1:0:52:8:1:0.5:0.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 77047515 . T G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2683;SOR=3.33217;LSEQ=GCCTATTTCCTATTGAACCC;RSEQ=GAAGAGAAATAGAAGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:0,2:0,21:0.087:1,0:40.5:1:23.5:1:1:0:60:1:0.0455:0:4 0/1:8:2:0,2:0,6:0.25:0,0:35.5:1:32:0:1:0:60:4:0.25:0:1 -11 77051507 . T TA 71 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.41233;SOR=0.27143;LSEQ=GGGTAGAATAAAGTTATCGT;RSEQ=AAAAAAAAAATCATGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:6,0:44,0:0.1176:1,0:40.2:1:27.8:1:1:0:60:12:0.1224:0:0 0/1:29:1:1,0:25,2:0.0345:2,0:45:0:28:0:1:0:60:2:0.0357:0:0 -11 77051605 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23218;SOR=0;LSEQ=ACCAATTCCACAGAGCCCAG;RSEQ=CTGAGATCTCACTGTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:2,0:174,16:0.0104:2,0:26.5:1:30:1:1:0:60:4:0.0105:0:1 0/0:207:0:0,0:187,20:0:2,0:24.8:1:31.1:1:1:0:60:68:1:0:0.2 -11 77051683 . G C 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=0.66386;LSEQ=CCCAAGACTGCTTGGCCCTT;RSEQ=GCCTTACCTCACGGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:732:277:172,105:278,176:0.3784:2,2:24.2:1:30.5:1:0.87548:1.04:60:137.5:0.3798:0:1.1 0/1:973:280:157,123:420,271:0.2878:2,2:25.4:1:30.1:1:0.19413:1.21393:60:69:0.2875:0:1.1 -11 77051820 . C T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.53143;LSEQ=ACGAGGTAACTGCAGGAATA;RSEQ=AGATAAAGGGTGAGAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:52:17,35:175,357:0.0889:2,2:24.5:1:28.8:1:1:1.00921:60:104:0.0903:0:1.1 0/1:691:212:68,144:162,315:0.3068:2,2:24.1:1:27.9:1:0.66215:1.08898:60:41.4:0.3062:0:1.1 -11 77051859 . C A 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36464;SOR=0.31944;LSEQ=AACAATCAGAGTACACTGAG;RSEQ=CATAGCACTGGGTTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:39,248:0.0103:2,2:14.7:1:22:1:0.0534:12.52:60:2:0.0071:0:1 0/0:301:1:1,0:54,246:0.0033:2,0:1:0:27:0:0.18272:0:60:2:0.0034:0:2 -11 77052071 . T C 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CTAAGATCTCTAGCTTGAAG;RSEQ=GATACAATAAAATTATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:21.3:1:29:1:1:0:60:6:0.4286:0:1 0/0:2:0:0,0:0,2:0:0,0:30.5:1:31.5:1:1:0:60:4:1:0:0 -11 77054749 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0843;SOR=Inf;LSEQ=ACAGAGAGCTCAGCATCACA;RSEQ=AAGACTCATAAATGGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:177,1:0:1,0:25.7:1:32.3:1:1:0:60:88:1:0:0.1 0/1:140:3:3,0:135,2:0.0214:1,0:29.3:1:29:1:1:0:60:6:0.0219:0:1.3 -11 77055059 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50022;SOR=0;LSEQ=AGTACCAGACCTTAAGTACT;RSEQ=AGGAAACAAAGATGAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:7,129:0.0145:2,2:6:1:30.5:1:0.11298:17.30:60:4:0.015:0:1.5 0/0:121:0:0,0:3,118:0:1,0:22.5:1:31.9:1:1:0:60:59.5:1:0:0 -11 77060092 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02005;SOR=Inf;LSEQ=AGGCTGGAGAACTGCTTGAA;RSEQ=CTAGTAGGCGGAGGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:23,0:0:1,0:21.7:1:32:1:1:0:59.8:46:1:0:0.2 0/1:10:3:3,0:7,0:0.3:0,0:33.7:1:29.7:1:1:0:60:6:0.3333:0:1.3 -11 77060203 . T C 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23182;SOR=Inf;LSEQ=AAAACCTAGAACTGTTCCTG;RSEQ=TGACCTAACAAGGGCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:142,33:0:2,0:18.6:1:29.1:1:1:0:59.6:20.875:1:0:0.9 0/1:163:2:1,1:112,48:0.0123:2,2:17:0:34:0:0.51476:2.31971:60:4:0.0128:0:1 -11 77060417 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24423;SOR=Inf;LSEQ=AAATGCAGTTCTACACACAA;RSEQ=CTGTGAGTGTCAAAAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:41,154:0:2,0:23.8:1:30.1:1:1:0:60:64:0.9948:0:0.1 0/1:192:2:1,1:47,143:0.0104:2,2:32:1:27.5:1:0.43848:3.02:60:4:0.0107:0:1 -11 77060418 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=AATGCAGTTCTACACACAAT;RSEQ=TGTGAGTGTCAAAAACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:36,153:0.0105:2,2:5:0:31:1:0.35073:4.21:60:4:0.0106:0:1.5 0/0:189:0:0,0:45,144:0:2,0:23.7:1:31.3:1:1:0:60:36.8:1:0:0.2 -11 77064358 . A G 49 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.37769;LSEQ=CGTTCTCTCACTGTCACTGC;RSEQ=GGGGTATTTTTAGCAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:3,0:25,0:0.1071:1,0:37:1:31.3:1:1:0:60:6:0.1071:0:1 0/1:14:2:2,0:11,1:0.1429:2,0:3.5:1:29.5:1:1:0:60:4:0.1429:0:1 -11 77064501 . CA C 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.81433;SOR=0.8702;LSEQ=AGAACAAGGTTTATGAGAGG;RSEQ=AAAAAAAAGCAAAATCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:9:6,3:268,59:0.0267:2,2:18.7:1:30.2:1:0.37536:2.2643:60:3.5:0.0211:0.0119:0 0/1:386:9:7,2:279,96:0.0233:2,2:27.9:1:32.3:1:1:1.20:60:18:0.0235:0.0026:0 -11 77064672 . AT A 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.06454;SOR=Inf;LSEQ=AGAAACAGAGACCATGAATC;RSEQ=TTTTTCCCAAATCAAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:116,324:0:2,0:25.9:1:30.2:1:1:0:60:145.667:1:0:0.1 0/1:502:5:3,2:150,345:0.01:2,2:28.8:1:29.2:1:0.17005:3.44:60:10:0.0101:0.002:0.4 -11 77069746 . A G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76897;SOR=1.31208;LSEQ=TTGGGACTATCTGCAAACCA;RSEQ=TGATAAATAAACACATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:14:14,0:29,0:0.3256:1,1:31.7:1:31.2:1:1:0:60:13:0.3333:0:1.9 0/1:18:7:7,0:9,1:0.3889:2,0:27.3:1:33.3:1:1:0:60:14:0.3889:0:1.9 -11 77069790 . G A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63074;SOR=0.8177;LSEQ=TGTCTTTAATCATACAGAAA;RSEQ=TACCTTTAGTCAAGGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:43:43,0:58,1:0.4216:1,1:18.8:1:30.7:1:1:0:60:86:0.43:0:1.3 0/1:67:25:25,0:39,2:0.3731:1,1:16.1:1:30.4:1:0.52214:0:60:50:0.3731:0:1.4 -11 77069989 . GCAT G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.39187;SOR=1.435;LSEQ=CAATCACTGGTGGTGGGGTA;RSEQ=CATCATCATCATCATCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:806:13:5,8:360,432:0.0161:2,2:32.5:1:33.4:1:0.78091:1.33286:60:26:0.0164:0:0.2 0/1:957:22:8,14:423,507:0.023:2,2:23.4:1:31.1:1:0.51684:1.45949:59.5:44:0.0234:0.0042:0.2 -11 77070163 . CT C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21329;SOR=Inf;LSEQ=GAAACCCCATCCTGATATCC;RSEQ=TCTGAAATACACATTAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:2,65:0:1,0:21.5:1:29.8:1:1:0:60:15.75:1:0:0.2 0/1:58:2:1,1:0,56:0.0345:1,2:22:1:28:1:0.03448:0:60:4:0.0345:0.0172:0 -11 77085318 . C A 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05417;SOR=0;LSEQ=CTCTGCCTCTACCACACTGT;RSEQ=TTGATCCTTACCTCCACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:4:2,2:243,132:0.0106:2,2:31.8:1:28.3:1:0.61659:1.83783:60:8:0.0107:0:1 0/0:405:0:0,0:257,147:0:2,0:22.9:1:31:1:1:0:60:79.8:0.9975:0:0.1 -11 77087565 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCAAGGTGGGTGGATCA;RSEQ=GAGGTCAATAGGTCAAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29:1:1:0:60:4:1:0:1 -11 77090037 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=AGAATCTAGACCTTCTAGCA;RSEQ=AAAACCTGTGTTCTCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:43.7:1:33:1:1:0:60:6:0.375:0:1 1/1:4:4:3,1:0,0:1:0,2:17:1:31.3:1:1:0:60:8:1:0:1 -11 77090211 . T C 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00289;SOR=1.92144;LSEQ=TTTCTTCTCTCATCCCAGAC;RSEQ=AATAGGCATGTGAGCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:207:105:91,14:91,11:0.5072:2,2:22.9:1:30.8:1:0.67132:1.27125:60:34:0.5:0:1.1 1/0:161:107:93,14:46,8:0.6646:2,2:22.2:1:30.6:1:0.80985:1.15:60:214:0.6688:0:1.1 -11 77090466 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1143;SOR=5.32739;LSEQ=CATGCAAGACTAACAGGAAG;RSEQ=CACAGTCACAGGGGAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:1,0:82,281:0.0027:2,0:1:0:28:0:0.22802:0:60:2:0.0028:0:1 0/1:345:5:4,1:62,277:0.0145:2,2:6.8:1:26.2:1:0.00537:17.66:60:10:0.0148:0:1 -11 77090518 . T C 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98084;LSEQ=GAGCTAACTTTGACACTTGC;RSEQ=AGCAGCAAAAGATGCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:63:2,61:3,104:0.3706:1,1:23.2:1:32.9:1:1:1.14:60:126:0.375:0:1 0/1:112:41:0,41:4,67:0.3661:2,1:22:1:31.8:1:0.29461:0:60:40:0.367:0:1.1 -11 77579869 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGGCGCTTAATTTGAACCC;RSEQ=GGTACCTTTCTCTCTGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:20:1:32:0:1:0:60:4:1:0:0.5 0/1:8:2:1,1:5,1:0.25:2,2:29:1:29.5:1:0.46429:3.87298:60:4:0.25:0:1 -11 77580044 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGCACGTTGGGTAATACC;RSEQ=TAGACTCTTCCAGTTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:0:2,0:34.9:1:30.4:1:1:0:60:36:1:0:0 0/1:51:2:1,1:27,22:0.0392:2,2:29:1:29.5:1:1:1.22232:60:4:0.0392:0:1 -11 77580208 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23151;SOR=Inf;LSEQ=AGGCCTAGAGGACATATATT;RSEQ=GGTGCATCTCCTCTTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:37,25:0:2,0:20.7:1:31.3:1:1:0:60:30:1:0:0.1 0/1:58:2:1,1:31,24:0.0345:2,2:15.5:1:28.5:1:1:1.28581:60:4:0.0351:0:1 -11 77580275 . CA C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49789;SOR=Inf;LSEQ=TGGAAGATGGTTGTTCCAGC;RSEQ=AAAGGTCCTGAGCCTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:38,43:0:2,0:27:1:29.7:1:1:0:60:162:1:0:0.1 0/1:88:2:1,1:36,50:0.0227:2,2:44.5:1:28:1:1:1.38:60:4:0.0227:0:1 -11 77580291 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49635;SOR=0;LSEQ=CAGCCAAAAGGTCCTGAGCC;RSEQ=TTTAAAATGCTTTTTCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:29,38:0.029:2,2:25:1:30.5:1:1:1.31:60:4:0.0308:0:1 0/0:68:0:0,0:26,42:0:2,0:27.4:1:29.5:1:1:0:59.9:67:1:0:0.3 -11 77580354 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.06494;SOR=Inf;LSEQ=GATTTCGTTTATTTATCTCT;RSEQ=TTTCTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:0,15:0:1,0:10.1:1:30.1:1:1:0:57.3:14:1:0:0.7 0/1:6:2:0,2:0,4:0.3333:0,0:20:1:31:1:1:0:57.5:4:0.3333:0:3 -11 77580548 . ACGGT A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTTTTATTTTTTGTAGAGAC;RSEQ=CGGTCTCCCTATGTTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:31.5:1:1:0:60:4:1:0:0.5 -11 78881609 . T C 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2566;SOR=2.64395;LSEQ=CTCCTAAGCAGTGGAAATAG;RSEQ=GACACAGACATGCACACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:3,3:4,2:0.5:2,2:30.2:1:30.5:1:1:1.88578:60:12:0.5:0:1 1/0:15:11:7,4:3,1:0.7333:2,2:25.4:1:31:1:1:1.65645:60:22:0.7857:0:1.1 -11 81184872 . T A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATCTAGAGGCAAAGAGAA;RSEQ=CTGTATGATTCAAGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 81185086 . T G 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63325;SOR=0.41977;LSEQ=AATTTAGAACATATCTCTAA;RSEQ=CTGTCTGATGTATAATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:6,0:0.5:0,0:35.3:1:33.2:1:1:0:60:12:0.5:0:1.2 0/1:7:2:2,0:5,0:0.2857:0,0:27.5:1:33.5:1:1:0:60:4:0.2857:0:1 -11 81185227 . C CT 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50225;SOR=Inf;LSEQ=TTTTGTTCTACCCAACTTTC;RSEQ=TTTTCTCCTTCCATGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:88,31:0:2,0:22.7:1:31.3:1:1:0:59.8:118:0.9916:0:0.2 0/1:144:2:1,1:105,37:0.0139:2,2:20.5:1:32:1:0.4595:2.81355:60:4:0.0139:0:0 -11 81185242 . G T 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=0;LSEQ=CTTTCCTTTTCTCCTTCCAT;RSEQ=TTTCCTTTACTAAAAATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:11:6,5:92,47:0.0728:2,2:27.9:1:30.1:1:0.51475:1.62566:60:22:0.0743:0:1.1 0/0:208:0:0,0:134,74:0:2,0:22.9:1:31.3:1:1:0:60:416:1:0:0.2 -11 81185331 . G T 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGACACTTTAAAAATAATT;RSEQ=TATAACAACCACGTAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:220:220:90,130:0,0:1:0,2:24.8:1:30.1:1:1:0:60:109:1:0:1.1 1/0:265:143:64,79:47,75:0.5396:2,2:24.3:1:29.7:1:0.32013:1.29:60:286:0.5396:0:1.1 -11 81185416 . T G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.25932;SOR=Inf;LSEQ=TTGGCATTTGCTTTTTAGTA;RSEQ=TTTTAGAGATGGTTACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:15,47:0:2,0:23.8:1:29.6:1:1:0:60:30:1:0:0.3 0/1:82:3:1,2:17,62:0.0366:2,2:32.3:1:32:1:0.52954:1.81:60:6:0.037:0:1 -11 81185452 . TC T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.05466;SOR=0;LSEQ=CTCAAACATCCCAAAAGTCA;RSEQ=TTTGAAAGAGATCTCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:0,5:1,30:0.1389:1,0:34.6:1:30.8:1:1:0:60:10:0.1389:0:0 0/0:33:0:0,0:1,32:0:1,0:28.3:1:32.2:1:1:0:60:66:1:0:0 -11 81187272 . G T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATACAAGGTTTGTATTTG;RSEQ=ACATAATTGAGTTTGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 83267886 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATCCAGTGGAAGGCAAG;RSEQ=TGGGATGATGCGGGGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:29:1:1:0:60:4:1:0:1 -11 83269046 . C G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00401;SOR=0.2205;LSEQ=ACCAACTCCAAGCAGGAGGA;RSEQ=AATATGGAATCTATAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:56:56,0:5,0:0.918:0,1:24.8:1:33:1:1:0:60:112:0.918:0:1.1 1/0:55:39:38,1:16,0:0.7091:1,1:21.9:1:32.4:1:1:0:60:78:0.7091:0:1.1 -11 83269191 . C T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20024;LSEQ=ACTGGCTCTAGTTGTAGTCC;RSEQ=TTACTTAGTCCAAAACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:568:500:258,242:36,32:0.8803:2,2:25.4:1:30.4:1:0.89734:1.05515:60:70.429:0.8788:0:1.1 1/0:625:372:188,184:134,119:0.5952:2,2:25.5:1:30.1:1:0.56887:1.10192:60:73.4:0.5929:0:1.1 -11 85956145 . TG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.21886;SOR=0;LSEQ=CTGGGCGCGATTTGCGACAG;RSEQ=GGGGGGGCGGTGGAGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:24,0:0.0769:1,0:9:1:31.5:1:1:0:60:4:0.08:0.0385:0 0/0:29:0:0,0:26,3:0:2,0:16.9:1:30.7:1:1:0:59.5:58:1:0:0.5 -11 85956190 . A G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50043;SOR=Inf;LSEQ=GGCAGCGGCAACTTTGCGGC;RSEQ=AGCTCGGGCCGGGCTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:83,6:0:2,0:23.4:1:30.5:1:1:0:60:88:1:0:0.1 0/1:104:2:1,1:91,11:0.0192:2,2:33:0:30.5:1:0.21845:7.96356:52.5:4:0.0194:0:2.5 -11 85956212 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50154;SOR=Inf;LSEQ=GCTCGGGCCGGGCTTGCTTG;RSEQ=CGGCGGTGTGGCGGAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:118,19:0:2,0:23.7:1:29.7:1:1:0:60:44.667:1:0:0.1 0/1:162:2:1,1:124,36:0.0123:2,2:18:1:30:1:0.40572:3.41116:60:4:0.0126:0:1 -11 85956421 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19178;SOR=0;LSEQ=GGCAGTTACGAGACTGCGGA;RSEQ=TGAAAGTTTTAAATTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:32,127:0.0124:2,2:21.5:1:31.5:1:0.36894:3.92:60:4:0.0127:0:1 0/0:206:0:0,0:61,145:0:2,0:21.8:1:31:1:1:0:60:67.667:1:0:0.2 -11 85956426 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19499;SOR=0;LSEQ=TTACGAGACTGCGGAGTGAA;RSEQ=GTTTTAAATTCTTTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:29,115:0.0137:2,2:5:0:32:1:0.36986:3.92:60:4:0.0141:0:1 0/0:184:0:0,0:52,132:0:2,0:21:1:30.3:1:1:0:60:60.333:1:0:0.2 -11 85956427 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.25509;SOR=Inf;LSEQ=TACGAGACTGCGGAGTGAAA;RSEQ=TTTTAAATTCTTTTAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:27,118:0:2,0:19.6:1:31.7:1:1:0:60:35.25:1:0:0.3 0/1:177:3:1,2:45,129:0.0169:2,2:7.7:1:25.7:1:1:1.43:60:2:0.0115:0:2 -11 85956438 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5061;SOR=Inf;LSEQ=GGAGTGAAAGTTTTAAATTC;RSEQ=TTTAAAACGGGGGGCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:16,94:0:2,0:19.3:1:30.1:1:1:0:60:54:1:0:0.3 0/1:142:2:1,1:29,111:0.0141:2,2:14.5:1:30:1:0.37908:3.78:60:4:0.0142:0:1.5 -11 85961166 . C T 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2605;SOR=0;LSEQ=AATATAAAATATCTACAAAC;RSEQ=TTCTAACCTGTAGCTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:7,1:0.3846:2,0:20.8:1:32:1:1:0:60:10:0.3846:0:1 0/0:4:0:0,0:4,0:0:0,0:38.3:1:31:1:1:0:60:8:1:0:0 -11 85961287 . TA T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.501;SOR=0;LSEQ=CCAGTAGAGTTATTTACTGC;RSEQ=AAAACAGTATTGCTGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:148,12:0.0123:2,0:24:1:33:0:1:0:60:4:0.0125:0:0 0/0:140:0:0,0:126,14:0:2,0:25:1:28.5:1:1:0:60:139:1:0:0.1 -11 85961525 . T A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11801;SOR=Inf;LSEQ=AGATCCTTTGGGCTGAATGC;RSEQ=AGGCTTCAGAAATTATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:64,231:0:2,0:24.7:1:28.7:1:1:0:60:97.333:1:0:0.1 0/1:285:3:3,0:67,215:0.0105:2,0:13:1:22.7:1:0.01434:0:60:2:0.007:0:2.3 -11 85961620 . G GT 81 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30167;SOR=0.38427;LSEQ=GTTACAATGTTTTCTGAAGG;RSEQ=TTTTTTTTTTTGTAGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:7:0,7:1,48:0.1186:1,0:17:1:29.2:1:1:0:60:14:0.125:0.0339:0 0/1:41:2:0,2:2,37:0.0488:2,0:36.5:1:27:1:1:0:60:4:0.0541:0:0.5 -11 85961646 . G A 126 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=22.16623;LSEQ=TTTTTTGTAGTTCAGACTGC;RSEQ=TATCTATTTTAGTCCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:0,3:0,32:0.0857:1,0:15:1:32.3:1:1:0:60:6:0.0882:0:1 1/0:29:20:2,18:0,9:0.6897:0,2:21.4:1:29.3:1:1:0:60:19:0.6786:0:1.3 -11 85963130 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20603;SOR=Inf;LSEQ=GAAGGGGATAGGTTAGTTTA;RSEQ=TGTCATTTTCTGGTTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:187,47:0:2,0:23.9:1:31.7:1:1:0:60:57.5:1:0:0.1 0/1:195:2:1,1:149,44:0.0103:2,2:6.5:1:29:1:0.4092:3.35969:60:4:0.0104:0:1.5 -11 85963147 . G A 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00182;SOR=Inf;LSEQ=TTACTGTCATTTTCTGGTTT;RSEQ=TAAGATACATTAATCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:229,79:0:2,0:25.1:1:31.9:1:1:0:60:76:1:0:0.1 0/1:260:8:7,1:181,70:0.0308:2,2:25.1:1:29.8:1:0.45231:2.70:60:16:0.031:0:1.1 -11 85963553 . G GT 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTGGTTGAAAGAATTGGC;RSEQ=TCCTTTTTTTTTTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:16.3:1:30.2:1:1:0:60:8:1:0.2:0.8 1/1:2:2:0,2:0,0:1:0,0:4.9:1:30.2:1:1:0:60:8:1:0.8857:0 -11 85963619 . C T 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTATTTATCATTCAAATAG;RSEQ=GTAAGAACTGGCTGTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:0.6:0,2:30.3:1:28.8:1:1:0:60:12:0.6:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 85963632 . T C 60 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAAATAGCGTAAGAACTGGC;RSEQ=GTGATTTTTTTAAAATTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:0.625:0,2:31.8:1:26:1:1:0:60:10:0.625:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 85965909 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGACCTCATGATCCGCA;RSEQ=GCCTTGGCCTCCCAAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:20.5:1:30.5:1:1:0:58:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 85965938 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCAAAATGCTGGGATTA;RSEQ=AGGCGTGAGCCACCGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:32.5:1:32.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 85966177 . G T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.63607;LSEQ=TCTGTAGTATATTTAAGATA;RSEQ=GATTGCGATTAAAATATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:210:167,43:99,28:0.6213:2,2:22.9:1:30.7:1:0.78323:1.10:60:69:0.6179:0:1.1 1/1:276:244:194,50:22,10:0.8841:2,2:23.7:1:29.7:1:0.17481:1.76:60:60:0.8824:0:1.1 -11 85966542 . A C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00823;SOR=0.10508;LSEQ=AGCTAGGCAAAAAGAAAAAG;RSEQ=AAAGAATCCATTGTGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:18:0,18:0,7:0.72:0,1:26.6:1:32:1:1:0:60:36:0.72:0:2 0/1:10:2:0,2:1,7:0.2:2,0:29.5:1:33.5:1:1:0:60:4:0.25:0:2 -11 85966560 . A G 42 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.03123;SOR=15.03322;LSEQ=AGAAAAGAATCCATTGTGGG;RSEQ=TGGATGTGCTGGTTGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:0,18:0.0526:1,0:7:0:33:0:1:0:60:2:0.0526:0:1 1/0:6:3:0,3:1,2:0.5:2,0:21.3:1:27:1:1:0:60:2:0.4:0:1 -11 85966575 . G A 110 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52322;SOR=0.24759;LSEQ=GTGGGATGGATGTGCTGGTT;RSEQ=GGTGCAGATGTCTATAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:11:0,11:0,5:0.6875:0,0:24.7:1:31.8:1:1:0:60:22:0.6875:0:2.7 0/1:3:1:0,1:0,2:0.3333:0,0:14:0:33:0:1:0:60:2:0.3333:0:3 -11 85966586 . T C 100 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57738;LSEQ=GTGCTGGTTGGGTGCAGATG;RSEQ=CTATAGAGATAGGAGCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:0,9:0,5:0.6429:0,0:20:1:31.6:1:1:0:60:18:0.6429:0:2.9 1/0:2:1:0,1:0,1:0.5:0,0:3:0:29:0:1:0:60:2:0.5:0:3 -11 85967064 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTTATAGAGGTATGGGG;RSEQ=TAGAGCAGAGGTTAAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:16.5:1:32.5:1:0.33333:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 85967298 . A G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.58396;LSEQ=CTCAAATCACCATTGTATAT;RSEQ=TTTGGTTGTATAAGGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:6:5,1:49,2:0.1053:1,2:30.5:1:31.5:1:0.28828:4.67695:60:12:0.1071:0:1.2 1/0:29:17:17,0:12,0:0.5862:0,1:14.5:1:31:1:1:0:60:34:0.5862:0:1.2 -11 85967605 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03453;SOR=Inf;LSEQ=CTTCTTTTGAATCCACAACT;RSEQ=TAAAAACTTGTAATGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:41,217:0:2,0:22.8:1:32:1:1:0:60:50.6:1:0:0.1 0/1:197:4:3,1:43,150:0.0203:2,2:5.5:1:25:1:0.04034:10.30:60:8:0.0203:0:1 -11 85967609 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0791;SOR=Inf;LSEQ=TTTTGAATCCACAACTGTAA;RSEQ=AACTTGTAATGTTAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:36,198:0:2,0:23.3:1:30.3:1:1:0:60:77:1:0:0.1 0/1:177:3:1,2:34,140:0.0169:2,2:25:1:30.7:1:0.48582:2.05:60:6:0.0171:0:1 -11 85967709 . G A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22022;SOR=0.41982;LSEQ=TTGGATGAGTCTTTTGAGAC;RSEQ=TTTGTCACATTTGGGTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:0,15:0,17:0.4688:1,1:22.1:1:31.5:1:1:0:60:30:0.4688:0:1 0/1:15:4:0,4:1,10:0.2667:2,0:27.8:1:29.8:1:1:0:60:8:0.2667:0:1 -11 85968400 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13501;SOR=Inf;LSEQ=GTCTTTTTTTTTTTTTTTTT;RSEQ=CCTTTTCACCTCAAGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:36,1:0:1,0:20.5:1:28.5:1:1:0:58.9:11.333:1:0:0.9 0/1:22:2:2,0:20,0:0.0909:1,0:15:1:29:1:1:0:60:4:0.0909:0:1.5 -11 85968623 . C T 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26906;LSEQ=CAAGAGATCCAAATCTTCTC;RSEQ=TGTCAGTAAGTAAAGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:831:454:221,233:181,194:0.5463:2,2:25.9:1:30.2:1:0.94436:1.02:60:55.75:0.5446:0:1.1 0/1:781:191:87,104:276,314:0.2446:2,2:25.4:1:30.2:1:0.80251:1.05069:60:190:0.2442:0:1.1 -11 85969117 . T A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTATCTGTTAGTTATTT;RSEQ=TCCTGATCTTCTTACTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:37.5:1:29:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 85975154 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20358;SOR=Inf;LSEQ=TAGTAGTTTTTCTTTCACAA;RSEQ=ATGTTGAAAGTTCACAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:143,6:0:1,0:24.9:1:32.3:1:1:0:60:73.5:1:0:0 0/1:123:2:1,1:115,6:0.0163:1,2:20:1:31:0:0.11102:17.81892:60:4:0.0165:0:1 -11 85975481 . A ATATT 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=5.000;MSILEN=4;SSF=0.48034;SOR=0.45795;LSEQ=GAATAAAACAAGTAAAGACT;RSEQ=TATTTATTTATTTATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:15:0,15:0,17:0.4545:1,1:25.9:1:29.5:1:1:0:59.7:30:0.4688:0.0606:0.1 0/1:11:3:0,3:0,8:0.2727:0,0:46:1:30.5:1:1:0:60:6:0.2727:0:0 -11 85977117 . G A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.47793;LSEQ=ATATAAAACTTTTTGGTTTT;RSEQ=CATACAGGATTATGATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:528:331:199,132:127,70:0.6269:2,2:26.4:1:28.8:1:0.35479:1.20302:60:330:0.6286:0:1.1 1/1:507:433:257,176:41,27:0.854:2,2:26.4:1:28.4:1:1:1.03984:60:215.5:0.8569:0:1.1 -11 85977296 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20439;SOR=Inf;LSEQ=TGAAACAATTTGCTATGTTG;RSEQ=GCTATTGAATATAAGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:43,160:0:2,0:21:1:29.8:1:1:0:60:66.667:1:0:0 0/1:168:2:1,1:43,123:0.0119:2,2:7:1:29.5:1:0.45637:2.84:60:4:0.0121:0:1 -11 85979270 . T G 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATGTTTATAAACAAAGTATC;RSEQ=ATCATAGGACAAAGATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:20.3:1:29.8:1:1:0:60:8:0.5:0:1 1/0:4:2:2,0:2,0:0.5:0,0:21.5:1:29:1:1:0:60:4:0.5:0:1 -11 85979624 . C A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29501;SOR=2.65728;LSEQ=GTATGGTAACTGCAGTTAAG;RSEQ=TGTACTTCCATCGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:2:0,2:165,273:0.0045:2,0:8:1:14.5:1:0.53018:0:60:0:0:0:3 0/1:500:6:4,2:206,288:0.012:2,2:10.3:1:25.3:1:0.24387:2.79:60:5:0.0109:0:1.3 -11 85980945 . G T 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06833;SOR=0;LSEQ=TTATGTAACTATCTATGGTA;RSEQ=GAGGTTTTGGTCATTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:5:5,0:62,1:0.0735:1,0:18.2:1:32:1:1:0:60:10:0.0746:0:2 0/0:52:0:0,0:52,0:0:1,0:23.8:1:32.6:1:1:0:60:104:1:0:1 -11 85980958 . A G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=6.06202;LSEQ=TATGGTAGGAGGTTTTGGTC;RSEQ=TTTCCAGTTCTGGGCTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:53:52,1:25,0:0.6795:1,1:26.5:1:29.7:1:1:0:60:52:0.6933:0:1.1 1/1:70:65:62,3:5,0:0.9286:0,1:24.5:1:30.3:1:1:0:60:130:0.9286:0:1 -11 85981150 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2261;SOR=0;LSEQ=CCGTGCCATTTTACATTCCC;RSEQ=CCAGCAATGTATGAGAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:10,71:0.0241:2,2:17.5:1:31.5:1:0.2489:6.82:60:4:0.0247:0:2 0/0:91:0:0,0:15,76:0:2,0:21:1:29.2:1:1:0:59.7:44.5:1:0:0 -11 85988444 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GAAATTAGGTGTTTATGTTC;RSEQ=ATAACATAAACATTATCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:2,5:0.2222:2,0:19.5:1:29:0:1:0:60:4:0.2222:0:1 0/0:5:0:0,0:0,5:0:0,0:8.8:1:31.8:1:1:0:60:10:1:0:0.2 -11 85989348 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50154;SOR=0;LSEQ=AAGTGCTTTTCGTATGACTT;RSEQ=GAACATCTGCTTATTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:167,29:0.0101:2,2:25:1:30:0:0.28073:5.67881:60:4:0.0102:0:1 0/0:170:0:0,0:146,24:0:2,0:22.5:1:31.7:1:1:0:60:169:1:0:0.1 -11 86333286 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14555;SOR=Inf;LSEQ=GCCAATAGTCACATGGATAG;RSEQ=TTGTGCCAGAGCTAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:74,3:0:1,0:20.2:1:31.1:1:1:0:60:76:1:0:0.1 0/1:48:2:1,1:42,4:0.0417:2,2:17.5:1:32:0:0.19947:9.50264:60:4:0.0444:0:1 -11 86333332 . TA T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=CTGCATGTGGGTTCTCATTT;RSEQ=CGCCTCCCTATCAATGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:110,50:0:2,0:23:1:28.6:1:1:0:60:159:0.9876:0:0.1 0/1:164:2:1,1:108,54:0.0122:2,2:28.5:1:28.5:1:1:1.99095:60:4:0.0123:0:0 -11 86333335 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49851;SOR=Inf;LSEQ=CATGTGGGTTCTCATTTTAC;RSEQ=CCTCCCTATCAATGGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:112,55:0:2,0:23:1:30.4:1:1:0:60:166:1:0:0.1 0/1:168:2:1,1:110,56:0.0119:2,2:8.5:1:28:1:1:1.95587:60:4:0.012:0:1 -11 86333379 . C T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11482;SOR=0;LSEQ=TAAAAATGCATTACATACTA;RSEQ=AGACACTGCCATATCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:160,134:0.0101:2,2:13.3:1:26.3:1:0.59474:2.38124:60:6:0.0103:0:1.7 0/0:313:0:0,0:182,130:0:2,0:24.7:1:31:1:1:0:60:38:1:0:0.5 -11 86333429 . TA T 190 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.12304;LSEQ=CAGGGATTGTGGGAGGGCAT;RSEQ=AAAAAAAAAAAGTTGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:81:31,50:106,101:0.2691:2,2:28.8:1:30:1:0.05037:1.68963:59.8:80:0.2667:0:0.3 0/1:324:14:7,7:150,156:0.0432:2,2:28.7:1:29.4:1:1:1.04:60:28:0.0438:0:0.4 -11 86333434 . A T 210 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=12.000;MSILEN=1;SSF=0.01812;SOR=1.48236;LSEQ=ATTGTGGGAGGGCATTAAAA;RSEQ=AAAAAAAGTTGTTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:126:59,67:72,84:0.4452:2,2:22.7:1:28.9:1:1:1.03:60:30.5:0.4373:0:1.2 1/0:322:175:81,94:73,74:0.5435:2,2:24.5:1:28.2:1:0.57648:1.14433:60:42.75:0.5429:0:1.1 -11 86333534 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=CTGGTAGATCTGATAGATTA;RSEQ=TGATTCAGTCAAAGGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:26,91:0.0168:2,2:21:1:29:1:0.40379:3.45:60:4:0.0174:0:1 0/0:108:0:0,0:30,77:0:2,0:21.9:1:31.2:1:1:0:60:34.667:0.9905:0:0.1 -11 86333541 . A G 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50267;SOR=0;LSEQ=ATCTGATAGATTACTGATTC;RSEQ=GTCAAAGGTGAGGCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:21,84:0.0185:2,2:24.5:1:25.5:1:0.37048:3.93:60:4:0.0192:0:1 0/0:88:0:0,0:22,66:0:2,0:21.5:1:30.7:1:1:0:60:87:1:0:0.1 -11 86335117 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGAGACCAGGATTTTAT;RSEQ=CCTCTTTGAGGTCGGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:31:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 86805562 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTCTTTCAATTCCCTCC;RSEQ=CCTAGTCTTTCCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29.7:1:31.3:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 86805605 . A G 91 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03186;SOR=0.05395;LSEQ=TAGAAATTACAGTATAGGCT;RSEQ=GGTGTGGTGGTATGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:1,0:0.875:0,0:21.7:1:32.6:1:1:0:60:14:0.875:0:1.4 0/1:5:1:1,0:4,0:0.2:0,0:31:0:31:0:1:0:60:2:0.2:0:2 -11 86805759 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=GATTCATCTTGTGTCTTTCT;RSEQ=AGCACTCAATGAATCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:42,22:0:2,0:27.7:1:31.5:1:1:0:60:31:1:0:0.1 0/1:76:2:1,1:44,30:0.0263:2,2:13.5:1:24:1:1:1.45909:60:4:0.0267:0:1 -11 86805789 . C A 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00761;SOR=Inf;LSEQ=TGAATCTGCAACCAGAACCT;RSEQ=AGGTGACTTATAGTTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:44,33:0:2,0:29:1:31.7:1:1:0:60:154:1:0:0.1 0/1:89:8:3,5:45,36:0.0899:2,2:25.5:1:30.3:1:0.46254:2.06624:60:16:0.092:0:1.1 -11 86805885 . A C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.06792;LSEQ=CATTTGTGTAGCTTCTTGTA;RSEQ=CATAGGATTTTGAAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:46:12,34:2,1:0.9388:2,2:24.9:1:30.5:1:0.19263:5.43188:60:14.333:0.9348:0:1.1 1/0:32:16:5,11:4,12:0.5:2,2:27.9:1:31.8:1:1:1.35:60:32:0.5:0:1.1 -11 86806069 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52314;SOR=0;LSEQ=GCATGTTGTTCCCGGGGGTG;RSEQ=TCAATGGGTTTCCATCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:19,11:0.0625:2,2:27.5:1:31.5:1:1:1.69662:60:4:0.0645:0:2 0/0:19:0:0,0:13,6:0:2,0:24.3:1:29.3:1:1:0:60:18:1:0:0.3 -11 86806071 . C G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=0.07357;LSEQ=ATGTTGTTCCCGGGGGTGTT;RSEQ=AATGGGTTTCCATCAGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:27:19,8:1,3:0.871:2,2:25.3:1:30:1:0.11537:6.64:60:26:0.8667:0:1.3 0/1:19:6:4,2:9,4:0.3158:2,2:21.8:1:33.3:1:1:1.11798:60:12:0.3333:0:1 -11 86806128 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49474;SOR=0;LSEQ=AAGCATTTTACTTTATCACC;RSEQ=TTACCTAAAGCATAAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:34,11:0.0426:2,2:17.5:1:30:1:0.44958:3.0025:60:4:0.0426:0:2.5 0/0:45:0:0,0:35,10:0:2,0:24:1:31.1:1:1:0:60:90:1:0:0.1 -11 86806164 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22936;SOR=0;LSEQ=AATTCAGCTCCTGCATGCTG;RSEQ=TGCTTGTTAACTGAGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:49,12:0.0317:2,2:22:1:29:1:0.37276:3.96297:60:4:0.0328:0:1 0/0:68:0:0,0:49,19:0:2,0:27.9:1:32.4:1:1:0:60:136:1:0:0 -11 86806220 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49933;SOR=0;LSEQ=AATGATCTGTGCTTCATAAT;RSEQ=CTCCATGGATGGATTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:92,42:0.0147:2,2:24.5:1:30.5:1:0.53399:2.17663:60:4:0.015:0:1 0/0:123:0:0,0:71,52:0:2,0:23.2:1:31.5:1:1:0:60:246:1:0:0 -11 86806279 . CA C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10411;LSEQ=GGGAAATTCCTATCAGAACT;RSEQ=ACAATGTCAGATTCACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:197:177:111,66:11,9:0.8985:2,2:26.6:1:31.5:1:0.62788:1.37:60:354:0.8985:0.1168:0.1 0/1:157:75:38,37:40,42:0.4777:2,2:26.7:1:31.4:1:0.87356:1.08:60:150:0.4808:0.0764:0.1 -11 86806299 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50472;SOR=0;LSEQ=CAACAATGTCAGATTCACTT;RSEQ=AAATATTAACATTCTGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:117,71:0.0105:2,2:29:1:29.5:1:1:1.64332:60:4:0.0106:0:1 0/0:152:0:0,0:84,68:0:2,0:24.4:1:31:1:1:0:59.9:37:1:0:0.1 -11 86806422 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00194;SOR=Inf;LSEQ=TCTACCACAATAAAAGCACT;RSEQ=CACTTGGTCATCAATACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:175,210:0:2,0:27.6:1:32:1:1:0:60:54:1:0:0.1 0/1:412:10:5,5:193,209:0.0243:2,2:26.3:1:28.2:1:1:1.08:60:20:0.0244:0:1.1 -11 86806471 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.23015;SOR=0;LSEQ=AGTTCAGCACTAACTCTCTC;RSEQ=CTTGGGGTTAAGTGGGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:46,136:0.0109:2,2:11:1:29:1:0.44666:2.94:60:4:0.011:0:1 0/0:199:0:0,0:63,136:0:2,0:22:1:29.2:1:1:0:60:198:1:0:0.1 -11 86806968 . A G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00287;SOR=0.04074;LSEQ=GTGGAGCTGGCAGTGAGCCG;RSEQ=GATCGCGCCACTGCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:13,2:1,0:0.9375:0,2:18.9:1:30.7:1:1:0:47.3:14:0.9333:0:1.8 0/1:9:3:3,0:6,0:0.3333:0,0:14.7:1:32.3:1:1:0:42.3:6:0.375:0:3 -11 86807017 . CA C 146 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.0745;SOR=0.46362;LSEQ=AACAGAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAAAGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:24:22,2:22,2:0.4528:2,2:22.8:1:31.9:1:1:1:56.8:48:0.4615:0.1321:2.4 0/1:58:16:15,1:34,5:0.2759:2,1:14.9:1:30.7:1:0.65953:2.18:56.8:32:0.2759:0.1207:2.1 -11 86807104 . C A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.17565;LSEQ=GAGTCTCCATATTGCCTTCT;RSEQ=TCTACTCCTGCATGACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:143:95,48:9,5:0.9108:2,2:29.1:1:28.5:1:1:1.10:59.8:22.833:0.9073:0:1.2 1/0:195:125:82,43:49,21:0.641:2,2:26.5:1:27.8:1:0.63372:1.22232:59.9:16.857:0.631:0:1.1 -11 86807151 . C CATATATATAAAGAAAT 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.0548;LSEQ=CCACATGGTGTCTCCTTCAC;RSEQ=AATATAAAGAAAACCTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:299:273:173,100:16,10:0.913:2,2:20.8:1:29.8:1:0.83486:1.08:59.6:272:0.9128:0.5753:1.4 0/1:390:142:86,56:144,104:0.3641:2,2:20.8:1:28.6:1:0.66931:1.11:59.8:284:0.3688:0.2026:0.9 -11 86807189 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.12451;LSEQ=CTTGTGCCAGTGTTGATGCT;RSEQ=AAACAGGACTACTACTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:189:111,78:141,100:0.4395:2,2:24.2:1:28.9:1:1:1.01:59.7:378:0.4437:0:2.1 0/1:552:49:30,19:273,230:0.0888:2,2:25.6:1:28.1:1:0.37096:1.33:59.8:23.5:0.0864:0:1.7 -11 86807217 . C CA 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.14967;LSEQ=ACTACTACTTGGAAAACTAG;RSEQ=AAAAGTTTTTTATCCGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:456:331:165,166:78,47:0.7259:2,2:29.3:1:29.9:1:0.02045:1.66774:59.9:109.333:0.7257:0.0417:1.4 0/1:554:157:81,76:208,189:0.2834:2,2:26.9:1:29.6:1:0.92485:1.03255:59.9:77.5:0.2818:0.0325:1.3 -11 86807218 . A AA 81 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.08726;SOR=0.23355;LSEQ=CTACTACTTGGAAAACTAGC;RSEQ=AAAGTTTTTTATCCGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:7:4,3:239,209:0.0154:2,2:18:0:29.1:1:1:1.17:60:14:0.0156:0:1.3 0/0:552:2:1,1:286,263:0.0036:2,2:18:0:32:0:1:1.08727:60:4:0.0037:0:1.5 -11 86807222 . GT AG 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACTTGGAAAACTAGCAAAA;RSEQ=TTTTTATCCGTTAAACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:38:25,13:202,202:0.0854:2,2:21.1:1:31.3:1:0.08851:1.92:59.6:76:0.0862:0:2.5 0/0:535:0:0,0:269,257:0:2,0:25:1:31.2:1:1:0:60:130.5:0.9739:0:0.5 -11 86807228 . T A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1152;LSEQ=GAAAACTAGCAAAAGTTTTT;RSEQ=ATCCGTTAAACTCTTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:459:378:182,196:35,25:0.8235:2,2:26.3:1:28.9:1:0.16503:1.50627:59.9:125:0.8542:0:1.4 0/1:530:185:96,89:166,175:0.3491:2,2:23.4:1:28.5:1:0.5229:1.14:59.9:184:0.3511:0:1.3 -11 86807229 . A AA 68 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02064;SOR=0;LSEQ=AAAACTAGCAAAAGTTTTTT;RSEQ=TCCGTTAAACTCTTCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:5:3,2:222,226:0.011:2,2:18:0:29.6:1:0.68404:1.53:60:10:0.0111:0:2.4 0/0:529:0:0,0:264,265:0:2,0:24.2:1:29:1:1:0:60:263.5:1:0:0.5 -11 86807230 . TC AT 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00087;SOR=0;LSEQ=AAACTAGCAAAAGTTTTTTA;RSEQ=CGTTAAACTCTTCTACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:9:6,3:214,223:0.0201:2,2:18.7:1:30:1:0.33292:2.08:59.4:18:0.0203:0:2.6 0/0:526:0:0,0:261,264:0:2,0:24.2:1:29.2:1:1:0:60:130.25:0.9981:0:0.5 -11 86807231 . C CC 70 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02064;SOR=0;LSEQ=AACTAGCAAAAGTTTTTTAT;RSEQ=CGTTAAACTCTTCTACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:5:3,2:212,226:0.0112:2,2:17.4:1:30.4:1:0.67734:1.60:59:10:0.0114:0:4.4 0/0:522:0:0,0:257,263:0:2,0:24.4:1:30.6:1:1:0:60:64:0.9961:0:0.5 -11 87300037 . G T 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCCTTTTGAGCTCCTTG;RSEQ=GAGAGGGGCAGCAACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:12:0:31:0:1:0:60:2:1:0:1 1/1:4:4:4,0:0,0:1:0,0:37.5:1:29.5:1:1:0:60:8:1:0:1 -11 87300291 . G C 84 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TGGGTGAGGCTTTCCTGCAG;RSEQ=ATCTCCAATAATTCCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:33.5:1:32.8:1:1:0:60:12:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:24.5:1:29:1:1:1:60:4:0.5:0:1 -11 87300400 . T C 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=TGCGGACCAGCAGTCTTAAG;RSEQ=TTTTCCTCCGAGTAGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:20.8:1:32.3:1:1:0:60:8:1:0:1 0/0:4:0:0,0:3,1:0:2,0:19:1:24.5:1:1:0:60:3:1:0:0.3 -11 87300575 . A C 95 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=TCAGACACCCTATATAGGAG;RSEQ=AATCCTACTGGCATCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:18:1:31.9:1:1:0:60:16:1:0:1.8 1/0:6:4:2,2:0,2:0.6667:0,2:15.5:1:31:1:0.46667:0:60:8:0.6667:0:1.3 -11 87300593 . G T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08081;SOR=0;LSEQ=AGAAATCCTACTGGCATCAG;RSEQ=TTGGTGCCCCTTGAGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,1:0.5714:2,2:23:1:28.8:1:1:2.44949:60:8:0.6667:0:1.8 0/0:5:0:0,0:2,3:0:2,0:27.4:1:33:0:1:0:60:10:1:0:0.8 -11 87300620 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=CCCCTTGAGATCAGAGGTTC;RSEQ=GGAAGAAAGAGCAGGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:32.1:1:31.7:1:1:0:60:14:1:0:1 0/1:10:2:2,0:6,2:0.2:2,0:45.5:1:31.5:1:1:0:60:4:0.2222:0:1.5 -11 87300621 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=CCCTTGAGATCAGAGGTTCC;RSEQ=GAAGAAAGAGCAGGCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:32.3:1:31.9:1:1:0:60:14:1:0:1 0/1:10:2:2,0:6,2:0.2:2,0:11.5:1:31.5:1:1:0:60:4:0.2:0:1 -11 87300858 . A G 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.61372;LSEQ=AACCCCATCCAAGGGTCAGC;RSEQ=GTCTCAAAGACCGAAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:2,3:0.375:2,0:27:1:30.7:1:0.46429:0:60:6:0.375:0:1 1/0:8:4:2,2:1,3:0.5:2,2:18:1:30.5:1:1:2.60:60:8:0.5:0:1 -11 88359126 . C A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTCCAGGTAGAATTCAG;RSEQ=GGCAACAGGCAGTGAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18.5:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 88359287 . AT GG 85 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGAGAGCAGCCTTTACA;RSEQ=TTACACCAAATATAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:23.8:1:32.9:1:1:0:60:12:1:0.3333:0.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 88359488 . A G 200 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TTTCACAGATGTAAAACGTG;RSEQ=CAATTAAAGCAGAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:86:86:79,7:0,0:1:0,2:22.5:1:31.2:1:1:0:60:85:1:0:1 1/0:57:45:43,2:11,1:0.7895:2,1:25.7:1:31.3:1:0.51504:1.93:60:44:0.7857:0:1.2 -11 88359567 . CA C 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=GCACTTAGTTTATAAATGCA;RSEQ=AACCTCTCCACTGTGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:170,125:0:2,0:26.6:1:30.2:1:1:0:60:590:1:0:1.9 0/1:275:12:7,5:157,106:0.0436:2,2:25.5:1:31.7:1:1:1.05772:60:24:0.044:0.0073:0.9 -11 88359606 . TG CA 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08842;LSEQ=TCATAGAGATTTCTGACTTG;RSEQ=TTTATTTGAGTTTCATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:323:318:158,160:0,0:0.9845:0,2:24.6:1:31.4:1:1:0:60:636:0.9938:0.0991:1.7 1/1:337:286:153,133:0,1:0.8487:0,2:26.1:1:30.8:1:0.4669:0:60:572:0.8563:0.0653:1.8 -11 88359607 . G A 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38956;SOR=1.83745;LSEQ=CATAGAGATTTCTGACTTGT;RSEQ=TTTATTTGAGTTTCATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:4:1,3:0,0:0.0138:0,2:25.8:1:30:1:1:0:60:8:1:0:3.3 0/1:319:8:3,5:23,22:0.0251:2,2:6.8:1:27:1:0.70398:1.72443:60:7:0.1346:0:2.5 -11 88359631 . T A 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03893;LSEQ=ATTTGAGTTTCATTTCTCCA;RSEQ=ACAATGTAATTTTTGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:290:288:133,155:0,1:0.9931:0,2:24.5:1:30:1:1:0:60:287:0.9965:0:1.9 1/1:336:285:139,146:22,27:0.8482:2,2:25.9:1:29.4:1:0.64522:1.17:60:94:0.852:0:1.9 -11 88359686 . G A 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=TTACATTCTTTTATGTGTTC;RSEQ=GAAGTGTTGTGATTCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:66,128:0:2,0:27.8:1:30.3:1:1:0:60:63.667:1:0:1.3 0/1:232:14:6,8:79,139:0.0603:2,2:29.5:1:29.1:1:0.77569:1.32:60:28:0.0606:0:2.1 -11 88359723 . G A 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCTGTGAAATTGCTAG;RSEQ=AAAAAAGTGCAGAAGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:111:111:20,91:0,0:1:0,2:23.1:1:30:1:1:0:60:36:1:0:1.3 1/1:124:124:31,93:0,0:1:0,2:23.7:1:29.4:1:1:0:60:61:1:0:1.2 -11 88359907 . G A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGTAATTAGGTTTAGAT;RSEQ=AGCTAATGAGGGTAGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:22.7:1:29.7:1:1:0:60:6:1:0:1 1/1:2:2:1,1:0,0:1:0,2:10.5:1:27:1:1:0:60:4:1:0:2 -11 88359919 . G A 24 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GTTTAGATGAGCTAATGAGG;RSEQ=TAGCCTGTTCATGATAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:25:1:29.3:1:1:0:60:6:1:0:0.7 1/1:2:2:1,1:0,0:1:0,2:10.5:1:24.5:1:1:0:60:4:1:0:2 -11 88360079 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTAGGCTGGAAAATGAG;RSEQ=CTTCACCAGAACCCAACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:8.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 90507372 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGAGACGTTGAGATCAT;RSEQ=TGGAGGAGAAGAGGCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:39:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 90507460 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53924;SOR=0.51761;LSEQ=ATGAGTTCGTCTAGTGTTGG;RSEQ=CTTTGAGGCTGCTGACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:47:0:30:0:1:0:60:2:0.2:0:1 0/1:18:2:1,1:10,6:0.1111:2,2:40.5:1:29:1:1:1.61828:60:4:0.1111:0:1 -11 90507501 . C A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGATGGGGTTTTTGTGGAGG;RSEQ=CTTTTTGATGTTGTTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:9.8:1:30:1:1:0:60:8:1:0:0.3 0/1:18:2:1,1:7,9:0.1111:2,2:39.5:1:28.5:1:1:1.27:60:4:0.1111:0:1 -11 90507561 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGCTTGTTTGTTTCTCCTGC;RSEQ=ATAGTCAGGTCCCTCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:29.7:1:30.7:1:1:1.73:60:6:0.6:0:1 1/0:5:3:1,2:0,2:0.6:0,2:25.7:1:30.7:1:1:0:60:6:0.75:0:1 -11 90507897 . G A 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08356;SOR=4.43716;LSEQ=AGCCACTTGTCTGGGATGCC;RSEQ=GGATTCCTCAGAACTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:8,5:5,7:0.52:2,2:27.8:1:30.1:1:0.43375:2.17:60:26:0.52:0:1.1 1/1:12:10:5,5:1,1:0.8333:2,2:27.9:1:29.7:1:1:1:60:20:0.8333:0:1.1 -11 90508050 . A C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19015;SOR=5.27797;LSEQ=AGACTGCAAGGAAGCCCCAC;RSEQ=CACTGAGGAAAGATGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:4,6:5,3:0.5556:2,2:30.4:1:30.7:1:0.63719:2.37182:60:20:0.5882:0:1.9 1/1:8:7:4,3:1,0:0.875:0,2:20.1:1:30.3:1:1:0:60:14:0.875:0:1.1 -11 90508316 . T G 102 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00191;SOR=30.28838;LSEQ=TCAAACAGCTTAGACAGAGG;RSEQ=CAGCTGCAGCCTGTGTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:17:1:30.5:1:1:1.58:60:4:0.2:0:1 1/1:11:10:6,4:1,0:0.9091:0,2:22.7:1:31:1:1:0:60:20:0.9091:0:1.4 -11 90508350 . G A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00333;SOR=0.0542;LSEQ=TGTTGGTCGCCCCTCCTGCC;RSEQ=GGAGTTCAGTAGGCTTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:5,4:1,1:0.8182:2,2:12.7:1:30:1:1:1.22:60:18:0.8182:0:1 0/1:12:2:1,1:6,4:0.1667:2,2:25.5:1:28.5:1:1:1.4491:60:4:0.1667:0:1 -11 90508356 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TCGCCCCTCCTGCCGGGAGT;RSEQ=CAGTAGGCTTAAGCAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:23.5:1:31:1:1:0:60:16:1:0:0.9 0/1:14:2:1,1:7,5:0.1429:2,2:38.5:1:31.5:1:1:1.36624:60:4:0.1429:0:2 -11 93267819 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGCTCAACTCTGCAGTC;RSEQ=CTTCATCTCCCAAGGGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 93269048 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51232;SOR=0;LSEQ=TGCTATTTTTTCCTTTTGGC;RSEQ=ACATAGCTAGGTTTCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:3,13:0.1111:2,2:38:1:27:1:0.40523:3.89:60:4:0.1176:0:1 0/0:11:0:0,0:2,9:0:2,0:22.2:1:29.7:1:1:0:58.2:10:1:0:0 -11 93858111 . A G 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00547;SOR=Inf;LSEQ=CCAACCTCTGGAGTTGGGCA;RSEQ=CATGGCTTCTCCCCTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:27,26:0:2,0:27.8:1:29.8:1:1:0:56.5:106:1:0:0.1 0/1:77:10:5,5:35,32:0.1299:2,2:24.9:1:30.9:1:1:1.09248:58.9:20:0.1333:0:1.2 -11 94152631 . G GGAGAGA 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=18.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGGGGAACGGGGGGGAGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:28:1:29.9:1:1:0:60:4:0.6667:0.3333:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 94153641 . C G 67 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTAAGCCAGAAAAATAATT;RSEQ=AAGTCATTTTATATTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:24.6:1:29.2:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 94155446 . C T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AACTCTTCCTCTTCCTCCTC;RSEQ=TCCTCATTCATGGTGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41.5:1:31:1:1:0:60:4:1:0:1 -11 94163159 . CAAAACA C 96 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=1;SSF=0.10931;SOR=0.26097;LSEQ=ATGTGCTGGACCACCTGAGG;RSEQ=AAAACAAAAACAAACACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:784:8:2,6:273,503:0.0102:2,2:32.4:1:32.3:1:0.71978:1.6273:60:16:0.0103:0.0013:0 0/0:746:2:1,1:290,454:0.0027:2,2:35:1:33.5:1:1:1.56:60:4:0.0027:0:0 -11 94169159 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21234;SOR=Inf;LSEQ=ATTACACGATTAAATCTTAA;RSEQ=TTATATATGAGCCACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:11,130:0:2,0:22.8:1:31.4:1:1:0:60:27.2:1:0:0.1 0/1:121:2:1,1:4,115:0.0165:1,2:19.5:1:28:1:0.08127:25.83:60:4:0.0167:0:1 -11 94170172 . G GA 61 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.71024;SOR=1.50859;LSEQ=TAAAAAAAGAGAGCAACCAA;RSEQ=AAAAAAAAAATCAAATCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:4,0:47,0:0.0784:1,0:31.5:1:30.4:1:1:0:60:8:0.0816:0.0196:0.5 0/1:35:4:4,0:31,0:0.1143:1,0:24.8:1:30.8:1:1:0:60:8:0.1143:0:0 -11 94170460 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23553;SOR=Inf;LSEQ=TAAAATAACTTAGAAAAACT;RSEQ=GCATACTTCTTTAGCTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:19,165:0:2,0:23.1:1:29.8:1:1:0:60:368:1:0:0.1 0/1:174:2:1,1:30,142:0.0115:2,2:16:1:29:1:0.32543:4.67:60:4:0.0116:0:1 -11 94170484 . TTC T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00173;SOR=Inf;LSEQ=TACTTCTTTAGCTAAAGATT;RSEQ=TGAGTCCTATCTGCAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:5,117:0:1,0:26.7:1:30.1:1:1:0:60:244:1:0:0 0/1:104:8:0,8:6,90:0.0769:2,0:28.3:1:29.8:1:1:0:60:16:0.0784:0.0192:0 -11 94179125 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=9.17272;LSEQ=AGGTTTATTTCATACAACAC;RSEQ=AAAAAATGAAAGCTAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:19:3,16:38,162:0.0856:2,2:20.6:1:31.8:1:1:1.24982:60:38:0.0864:0:1 0/1:231:107:25,82:28,94:0.4632:2,2:23.9:1:31:1:1:1.02:60:34.667:0.4602:0:1.1 -11 94180266 . T G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.81597;LSEQ=TTATATATTATAAAAATAGA;RSEQ=TTTTAAAGAACCGTGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:7:7,0:76,0:0.0833:1,0:20.7:1:33:1:1:0:60:14:0.0833:0:1.1 0/1:58:4:4,0:54,0:0.069:1,0:28:1:33.5:1:1:0:60:8:0.0741:0:1.3 -11 94189681 . T TA 50 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.07604;SOR=0;LSEQ=AAAATTGCACAATGTACTCT;RSEQ=AAAAAAAAAAACTCATATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:0,11:0.2:0,0:38:1:31.7:1:1:0:60:6:0.2:0:0 0/0:19:0:0,0:1,18:0:1,0:28.6:1:28.7:1:1:0:60:38:1:0:0.2 -11 94193020 . A G 34 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGAAATTAACCAGTGTC;RSEQ=TAGGCAAAATAAGAGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:41:1:34:0:1:0:60:4:0.2857:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 94193864 . TAAC T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0.09091;SOR=Inf;LSEQ=AGAGATACAAAGAAAGAGAA;RSEQ=AACATCAACAATAACAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:0:1,0:25.1:1:28.9:1:1:0:60:30:1:0:0 0/1:7:2:2,0:4,1:0.2857:2,0:28:1:32:0:1:0:60:4:0.2857:0:0 -11 94194303 . G T 129 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=50.25849;LSEQ=GAAGGTAAGGCCAAACTTTA;RSEQ=CAACTGCCAGCTTGCTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:0,1:3,138:0.007:1,0:30:0:14:0:1:0:60:0:0:0:4 0/1:79:21:0,21:2,56:0.2658:1,1:24.8:1:29.5:1:1:0:60:42:0.2692:0:1.3 -11 94197037 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07692;SOR=Inf;LSEQ=AGCACACCAACATGGCACAT;RSEQ=TATACATATGCAACAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:19.4:1:31.2:1:1:0:55.9:18:1:0:0 1/0:4:2:1,1:2,0:0.5:0,2:10.5:1:27.5:1:1:0:45:4:0.5:0:1.5 -11 94197260 . A G 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.71772;LSEQ=TAAGAACATTTTTTTACCTC;RSEQ=TAAAAATAACTAGCTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:568:51:34,17:326,191:0.0898:2,2:25.2:1:30.4:1:0.65068:1.17:60:50:0.0899:0:1 0/1:449:95:57,38:220,133:0.2116:2,2:29.2:1:30.1:1:0.72159:1.10251:60:190:0.2144:0:1 -11 94197568 . C T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=Inf;LSEQ=GAGCTATATCATTTATCCTA;RSEQ=TGAGAAACTAATGTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:0,40:0:1,0:22.5:1:32.2:1:1:0:60:80:1:0:0.1 0/1:19:6:1,5:0,13:0.3158:1,2:36.3:1:30.2:1:0.31579:0:60:12:0.3158:0:1 -11 94203461 . T TA 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.15455;SOR=Inf;LSEQ=ATTCCTCTCTCTCAATGACT;RSEQ=AAAAAAAAAAATCTTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:26,0:0:1,0:25.3:1:30.9:1:1:0:60:52:0.963:0:0 0/1:18:2:2,0:14,2:0.1111:2,0:26:1:30.6:1:1:0:60:4:0.1176:0.0556:0 -11 94203801 . C A 157 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04473;LSEQ=CCCTTTAATACGCAGCAAAC;RSEQ=AACATGTCTGAAGTGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:37:15,22:145,252:0.0851:2,2:27.9:1:30.3:1:0.72199:1.18:60:36:0.0845:0:1.1 0/0:484:2:2,0:197,285:0.0041:2,0:1:0:25:0:0.16855:0:60:4:0.0041:0:1 -11 94203868 . A T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=2.80321;LSEQ=TTTCCTCAGGGTGATGTGCA;RSEQ=ACGAAAGCTTTCATATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:80:14,66:16,90:0.4301:2,2:24:1:28.3:1:0.6907:1.19:60:79:0.4293:0:1.1 1/0:153:104:21,83:5,44:0.6797:2,2:22.2:1:28.4:1:0.16702:2.22:60:103:0.6821:0:1 -11 94209348 . T C 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00332;SOR=0.41887;LSEQ=ATGTTTTGTCTGATCTTGCA;RSEQ=TGACAACCTTGAAAGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:58:58,0:92,0:0.3867:1,1:25.7:1:32.4:1:1:0:60:116:0.3867:0:1 0/1:96:20:20,0:76,0:0.2083:1,1:28.1:1:31.3:1:1:0:60:40:0.2105:0:1 -11 94209741 . C CT 49 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.54138;SOR=0;LSEQ=GTTGCAGGTTCTTTTTTTAT;RSEQ=TTTTTTTTTTAACTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:0,22:0.1111:1,2:31:1:31.3:1:0.12:0:60:6:0.125:0:0 0/0:15:0:0,0:1,14:0:1,0:18.9:1:30.3:1:1:0:60:14:1:0:0.1 -11 94211833 . A T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58271;SOR=2.59969;LSEQ=TTCCAAACAGATACAAACTT;RSEQ=TCTCCAAATTTCTCAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:1,0:208,46:0.0039:2,0:26:0:13:0:1:0:60:0:0:0:7 0/1:197:2:0,2:154,41:0.0102:2,0:6.5:1:27.5:1:0.04677:0:60:4:0.0103:0:1 -11 94211916 . C T 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTACCTAAACCATATAGCG;RSEQ=AATCTTTGTGCTTCCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:779:0:0,0:457,322:0:2,0:25.6:1:32:1:1:0:60:58.923:1:0:0.1 0/1:707:34:20,14:396,277:0.0481:2,2:27.5:1:29.2:1:1:1.00072:60:68:0.0486:0:1.2 -11 94212048 . C T 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.78628;LSEQ=ACAAAGTGCATCTGCCTATG;RSEQ=AAAATAATTTCAAAGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:45:14,31:110,298:0.0991:2,2:25.8:1:28.5:1:0.59767:1.22:60:90:0.1004:0:1 0/1:396:93:28,65:101,201:0.2348:2,2:28.5:1:28.4:1:0.61365:1.16603:60:186:0.2366:0:1.2 -11 94212154 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58275;SOR=1.37542;LSEQ=TTCTACTTACAAAAACATAG;RSEQ=TGAGGATAGTGTCTTCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:9:0,9:0,55:0.1406:1,0:32.3:1:33.2:1:1:0:60:18:0.1429:0:1.1 0/1:38:7:0,7:0,31:0.1842:1,0:29:1:29.6:1:1:0:60:14:0.1892:0:2 -11 94212930 . TA T 169 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.0787;SOR=0.62616;LSEQ=TAGTTCACCCATGGAAACCT;RSEQ=AAAAAAAAAAGTTACTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:45:16,29:162,298:0.0891:2,2:28.7:1:30.8:1:1:1.01:59.2:90:0.0902:0:0.3 0/1:416:24:9,15:144,245:0.0577:2,2:25.2:1:31.1:1:1:1.02:59:48:0.0583:0:0.3 -11 94212977 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51699;SOR=0;LSEQ=CATACGGGACAAAAGCTGTT;RSEQ=TCCCTAAGATTCTCCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:0,2:18,169:0.0106:2,0:24.5:1:31:1:1:0:57.5:4:0.0106:0:1 0/0:128:0:0,0:19,109:0:2,0:21.4:1:30.3:1:1:0:59.8:256:1:0:0.2 -11 94219002 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55323;SOR=0;LSEQ=CTAAGAAAATAGCTTATATG;RSEQ=AAGGCAAAACAGTTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:120,6:0.0156:1,0:23:1:29.5:1:1:0:60:4:0.0156:0:1 0/0:64:0:0,0:57,7:0:2,0:23.8:1:31.1:1:1:0:60:128:1:0:0 -11 94219040 . CA C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17911;SOR=Inf;LSEQ=TGTTTACGTGTCTTATACAG;RSEQ=AATACCATACACAAGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:187,44:0:2,0:23.6:1:30.2:1:1:0:60:230:1:0:0.1 0/1:170:2:1,1:130,38:0.0118:2,2:14:1:29:1:0.40724:3.3898:60:4:0.012:0.0059:0.5 -11 94219325 . T TA 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.64946;SOR=0.36963;LSEQ=TAAACTACAGATGAAAGAGA;RSEQ=AAAAAAAAACTCACAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:4:0,4:4,99:0.0374:1,0:32.8:1:31.3:1:1:0:60:8:0.0381:0:0 0/1:71:1:0,1:3,67:0.0141:1,0:41:0:32:0:1:0:60:2:0.0147:0:0 -11 94223855 . A G 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACACAAAGCATACAAAATC;RSEQ=GCTTTGAGCTTTCAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:54:54,0:1,0:0.9818:0,1:24.3:1:29.2:1:1:0:60:26:1:0:1 1/1:42:42:42,0:0,0:1:0,1:22.4:1:30.1:1:1:0:60:84:1:0:1 -11 94225807 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=4.43891;LSEQ=TATTTAAAACATTCCAAATA;RSEQ=CCTTTTTGATGACTAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:14:14,0:84,1:0.1414:1,1:19.1:1:31.4:1:1:0:60:28:0.1414:0:1 0/1:99:42:39,3:53,4:0.4242:2,2:24.4:1:29.9:1:1:1.01904:60:41:0.4271:0:1 -11 94225920 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.64809;LSEQ=GCTTTAGAAACCCCAAATAA;RSEQ=AAGGGATTCCAGAAGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:58:33,25:280,234:0.1014:2,2:27.5:1:29.4:1:0.78165:1.10:60:28:0.0993:0:1.1 0/1:627:269:137,132:203,153:0.429:2,2:26.5:1:28.2:1:0.14441:1.27786:60:37.429:0.4246:0:1.2 -11 94532923 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51652;SOR=0;LSEQ=CAGAACAACGAGGAACTGCC;RSEQ=ACTTACGAGGAGGCCAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:14,7:0.087:2,2:22.5:1:30.5:1:1:1.93655:60:4:0.0909:0:1 0/0:14:0:0,0:10,4:0:2,0:24.9:1:27.4:1:1:0:60:6:1:0:0.2 -11 94532994 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49153;SOR=0;LSEQ=GCAGCAACAGCAGCAGGGGG;RSEQ=GGTGGGCCATGGTTACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:12,16:0.0667:2,2:26:1:29:1:1:1.32:60:4:0.0667:0:1 0/0:30:0:0,0:13,17:0:2,0:25.4:1:30.7:1:1:0:60:60:1:0:0.2 -11 94770943 . G T 148 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCGCCTTCGTCCGCTTTCAC;RSEQ=ACCGGAGCGACGCGCAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:39:8,31:152,361:0.0705:2,2:24.5:1:28.1:1:0.27408:1.63027:52.9:38:0.0704:0:1.1 0/0:435:0:0,0:170,265:0:2,0:25.1:1:30.2:1:1:0:59.9:86:1:0:0.2 -11 94771054 . A G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=0.23467;LSEQ=GCCGGGACCTGCCTCGCAGC;RSEQ=GCCAGGAAGAGCCACGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:48:5,43:15,69:0.3636:2,2:22.3:1:31.7:1:0.31777:1.86131:59.7:96:0.3664:0:1 0/1:119:14:4,10:27,78:0.1176:2,2:22.6:1:29.7:1:0.7567:1.15:60:28:0.1207:0:1 -11 94771066 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09145;SOR=Inf;LSEQ=CTCGCAGCAGCCAGGAAGAG;RSEQ=CACGCGGCAGGTCCTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:12,88:0:2,0:20.2:1:31.4:1:1:0:59.3:32.333:1:0:0.4 0/1:83:3:1,2:15,65:0.0361:2,2:19.7:1:28.3:1:0.47862:2.14:60:6:0.0375:0:1 -11 94771495 . T C 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01175;SOR=Inf;LSEQ=CCATCTCCAGATCTTGCTCA;RSEQ=GGTCCAGGTCTAGATCTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:290,98:0:2,0:22.7:1:30.6:1:1:0:60:387:1:0:0.1 0/1:357:6:6,0:242,109:0.0168:2,0:28:1:31.5:1:0.18336:0:59.5:12:0.0169:0:1.2 -11 94771621 . GA G 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.06846;SOR=0;LSEQ=AAGGACAAGTGCCCTCCTAG;RSEQ=AAATGATCATCAGCTAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:5:2,3:54,259:0.0157:2,2:8:1:29.2:1:0.21371:3.18:51.8:10:0.0158:0.0126:0.2 0/0:257:0:0,0:51,206:0:2,0:22.5:1:29.6:1:1:0:45.6:256:1:0:0.1 -11 94771657 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18762;SOR=Inf;LSEQ=TAACGCGTGATGGAGGACTT;RSEQ=GGGAAAAGGACTCCATACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:1,158:0:1,0:24.7:1:30.6:1:1:0:56.7:25.5:1:0:0.1 0/1:122:2:1,1:2,118:0.0164:1,2:27.5:1:30:1:0.04877:48.38:60:4:0.0165:0:1.5 -11 94771664 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5024;SOR=0;LSEQ=TGATGGAGGACTTGGGGAAA;RSEQ=GGACTCCATACTCAGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:0,2:1,138:0.0142:1,0:20.5:1:33:0:1:0:60:4:0.0144:0:1.5 0/0:117:0:0,0:2,115:0:1,0:24.4:1:31.1:1:1:0:59:116:1:0:0.1 -11 94800144 . G A 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGGCCAGGATCTTCGGG;RSEQ=CCTGGCTTCATTTGGAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:12.8:1:31.3:1:1:0:46.5:8:1:0:1 1/1:2:2:1,1:0,0:1:0,2:13:0:31.5:1:1:0:21:4:1:0:1 -11 94800652 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60762;SOR=2.20003;LSEQ=ACGGACGCGAGCTGCGGGTG;RSEQ=AGGTGGCGCGCTATGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:1:1,0:45,171:0.0046:2,0:1:0:24:0:0.21198:0:60:2:0.0048:0:1 0/1:198:2:1,1:63,133:0.0101:2,2:10.5:1:27:1:0.5431:2.10:60:4:0.0102:0:1 -11 94800663 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23009;SOR=Inf;LSEQ=CTGCGGGTGCAGGTGGCGCG;RSEQ=TATGGCCGCCGGGACCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:29,131:0:2,0:19.5:1:32.2:1:1:0:59.9:31:1:0:0.2 0/1:148:2:1,1:45,101:0.0135:2,2:20:0:30.5:1:0.52648:2.23:60:4:0.0136:0:1.5 -11 94800704 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49512;SOR=0;LSEQ=CCGCAGCCGCCAGGGAGAGC;RSEQ=ACGCGGCAGGTCCAGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,12:0.087:2,2:19:1:32.5:1:1:1.32:60:4:0.0909:0:1 0/0:18:0:0,0:8,10:0:2,0:17.7:1:31.1:1:1:0:60:36:1:0:0.1 -11 94800781 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06925;SOR=Inf;LSEQ=GGAGCCGCAGCCCCAGGCGG;RSEQ=GACACCGCAGCCGATCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:47,19:0:2,0:27.6:1:30.6:1:1:0:60:21:1:0:0.3 0/1:47:3:2,1:28,16:0.0638:2,2:17.3:1:30:1:1:1.14:60:6:0.0638:0:1.3 -11 94800810 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.19159;SOR=Inf;LSEQ=AGCCGATCCCGGGGTCCCAG;RSEQ=TGCTCCAGGTCCCGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:52,27:0:2,0:30.2:1:30.9:1:1:0:60:12.167:1:0:0.3 0/1:62:2:1,1:34,26:0.0323:2,2:37.5:1:29:0:1:1.30197:60:4:0.0323:0:2 -11 94800857 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1719;SOR=Inf;LSEQ=CTATAGGGGTTCTCGCTATA;RSEQ=CCGGTCTCCCTACAGCCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:35,25:0:2,0:19.6:1:32.1:1:1:0:60:120:1:0:0.2 0/1:43:2:1,1:20,21:0.0465:2,2:28.5:1:29:1:1:1.05:60:4:0.0526:0:1.5 -11 94800902 . G GC 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTACAGCCGGTCGCGCTACA;RSEQ=CGCTCTCCCTACAGCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:54:38,16:1,0:0.9818:0,2:27.2:1:31.4:1:1:0:60:53:0.9815:0.2364:0.1 1/1:33:33:18,15:0,0:1:0,2:24.8:1:31.2:1:1:0:59.4:66:0.9706:0.2424:0.3 -11 94801011 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.20377;SOR=Inf;LSEQ=GCCGATATCACAGCAGCCGG;RSEQ=CTCACTCGAAGTCTGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:216,7:0:1,0:25.2:1:30.1:1:1:0:60:43.6:1:0:0.1 0/1:184:2:1,1:173,9:0.0109:1,2:36.5:1:31:1:0.10602:18.28336:60:4:0.0109:0:1 -11 94801633 . A AT 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTAACGCTGTCAAGAC;RSEQ=TGCTTCAACATTGCCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:1:29:1:1:0:58.5:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 95490325 . T C 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7092;SOR=0.6645;LSEQ=GGACTGGAAGGCTGCCCGTC;RSEQ=GCCTGCCCCTCTCTGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:4,4:6,8:0.3636:2,2:21.1:1:30.3:1:1:1.32:60:16:0.3636:0:1 0/1:11:3:1,2:3,5:0.2727:2,2:27:1:28.3:1:1:1.18052:60:6:0.2727:0:1 -11 95825203 . TTGC T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.49063;SOR=1.52889;LSEQ=GCAGGCTGAGAAGATGGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:7:2,5:100,78:0.0378:2,2:30:1:29.4:1:0.24579:3.18566:60:14:0.0378:0:0 0/1:229:13:9,4:119,98:0.0568:2,2:23.4:1:31:1:0.39525:1.85:58.5:26:0.057:0.0044:0.7 -11 95825206 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.08425;SOR=0;LSEQ=GGCTGAGAAGATGGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:1,2:98,78:0.0161:2,2:20.7:1:30.7:1:0.58712:2.50014:49.3:6:0.0171:0:1.3 0/0:237:0:0,0:122,102:0:2,0:28.5:1:31.5:1:1:0:59.4:111:1:0.0253:0.5 -11 95825212 . C T 79 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.02069;SOR=Inf;LSEQ=GAAGATGGTTGTTGCTGCTG;RSEQ=TGCTGCTGCTGTTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:101,89:0:2,0:28.9:1:32.1:1:1:0:59.6:46.5:1:0:0.3 0/1:248:7:4,3:134,107:0.0282:2,2:6.9:1:28.4:1:1:1.06:42.1:14:0.0286:0.0282:6 -11 95825215 . C CTGTTGTTAA 87 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=6.000;MSILEN=3;SSF=0.0233;SOR=Inf;LSEQ=GATGGTTGTTGCTGCTGCTG;RSEQ=TGCTGCTGTTGTTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:99,90:0:2,0:29:1:32.1:1:1:0:59.6:46.25:1:0:0.3 0/1:260:8:4,4:136,116:0.0308:2,2:17.8:1:29.2:1:1:1.17169:39.4:16:0.0311:0.0308:6 -11 95825221 . C T 112 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.03807;SOR=3.13831;LSEQ=TGTTGCTGCTGCTGCTGCTG;RSEQ=TGTTGTTGCTGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:4:2,2:101,94:0.0201:2,2:18.5:1:31.5:1:1:1.07405:60:8:0.0212:0:1.3 0/1:264:16:8,8:132,116:0.0606:2,2:23.2:1:28.2:1:0.80304:1.13737:58.5:15:0.0579:0:1.8 -11 95825233 . TTG CGGCTGCTCTTA 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.07232;SOR=Inf;LSEQ=TGCTGCTGCTGTTGTTGCTG;RSEQ=TTGTTGCTGCTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:108,103:0:2,0:23.2:1:31.8:1:1:0:59.5:69.333:1:0:0.4 0/1:277:5:3,2:139,131:0.0181:2,2:10.8:1:30.7:1:1:1.41:55.2:10:0.0182:0.0144:3.4 -11 95825238 . GT AC 89 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.01143;SOR=Inf;LSEQ=CTGCTGTTGTTGCTGTTGTT;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:110,98:0:2,0:22.4:1:31.9:1:1:0:59.5:68.333:1:0:0.4 0/1:273:8:4,4:134,130:0.0293:2,2:24:0:29.8:1:1:1.03066:39.4:16:0.0296:0:5 -11 95825247 . GC AT 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.0056;SOR=Inf;LSEQ=TTGCTGTTGTTGTTGCTGCT;RSEQ=TGCTGCTGTTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:104,86:0:2,0:22.7:1:32:1:1:0:59.6:62.333:0.9947:0:0.4 0/1:244:9:5,4:118,116:0.0369:2,2:25.9:1:28.9:1:1:1.23:41.7:18:0.0381:0.0041:3.7 -11 95825251 . C T 95 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.02654;SOR=7.54817;LSEQ=TGTTGTTGTTGCTGCTGCTG;RSEQ=TGCTGTTGTTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:1,0:102,84:0.0053:2,0:44:0:30:0:1:0:45:2:0.0055:0:3 0/1:230:9:4,5:116,105:0.0391:2,2:26.4:1:30.1:1:0.74026:1.37901:39:18:0.0398:0:4.3 -11 95825254 . C T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.01705;SOR=Inf;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:100,76:0:2,0:22.3:1:31.7:1:1:0:59.9:43:1:0:0.4 0/1:215:7:5,2:108,100:0.0326:2,2:23.4:1:28:1:0.44978:2.31:57.1:6:0.029:0:1.7 -11 95825260 . TTGC T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.22742;SOR=0.4466;LSEQ=TGCTGCTGCTGCTGCTGTTG;RSEQ=TGCTGCTGCTGCTGTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:7:3,4:93,66:0.0412:2,2:29.6:1:30.6:1:0.45657:1.87147:60:14:0.0424:0:0 0/1:213:4:2,2:113,96:0.0188:2,2:36.3:1:25.5:1:1:1.17618:55:3:0.0144:0:1 -11 95825269 . C A 90 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.00987;SOR=Inf;LSEQ=TGCTGCTGTTGTTGCTGCTG;RSEQ=TGCTGCTGTTGGGCTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:99,76:0:2,0:24:1:31.4:1:1:0:59.6:28.167:1:0:0.4 0/1:218:8:4,4:111,99:0.0367:2,2:8:0:30.3:1:1:1.12062:39.4:16:0.0376:0:4 -11 95825282 . G A 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.36024;SOR=0.3135;LSEQ=GCTGCTGCTGCTGCTGTTGG;RSEQ=CTGAAATTGAGCTCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:2,1:102,93:0.015:2,2:6.3:1:26.7:1:1:1.82:60:6:0.0161:0:1 0/0:211:1:1,0:111,98:0.0047:2,0:1:0:22:0:1:0:60:2:0.0051:0:1 -11 95825332 . C A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11329;SOR=0;LSEQ=TGTTGAGCTGAAATTGAACT;RSEQ=TGCTGTTGCTGTTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:2,1:124,129:0.0117:2,2:24.7:1:30.3:1:0.61769:2.07:60:6:0.0124:0:1 0/0:272:0:0,0:138,134:0:2,0:24.9:1:31.1:1:1:0:59.7:37.857:1:0:0.3 -11 95825356 . TTGC T 85 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.03557;SOR=0.13645;LSEQ=TGTTGCTGTTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:7:2,5:118,142:0.0262:2,2:27.1:1:30.6:1:0.46394:2.07213:50.9:14:0.0266:0.0037:0.6 0/0:274:1:1,0:130,143:0.0036:2,0:19:0:32:0:0.4781:0:60:2:0.0037:0:0 -11 95825374 . TTGCTGCTGC T 190 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=13.000;MSILEN=3;SSF=0;SOR=3.51164;LSEQ=TGTTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:40:16,24:78,94:0.1786:2,2:31.1:1:29.7:1:0.59846:1.2434:59.5:80:0.1835:0.0491:0.4 0/1:226:98:40,58:56,44:0.4336:2,2:31.3:1:28.8:1:0.03433:1.83969:58.9:23.5:0.4234:0.0885:0.4 -11 95825418 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50012;SOR=Inf;LSEQ=CTGCTGCTGCTGCTGCTGTT;RSEQ=CTGCTGTTGCTGTTGGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:67,91:0:2,0:25.1:1:32.1:1:1:0:59.9:51.667:1:0:0.2 0/1:177:2:1,1:70,105:0.0113:2,2:29:1:27:1:1:1.50:60:4:0.0117:0:1.5 -11 95825428 . C A 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.87854;LSEQ=TGCTGCTGTTGCTGCTGTTG;RSEQ=TGTTGGGTGTAGTGTAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:1:0,1:61,83:0.0069:2,0:26:0:15:0:1:0:60:0:0:0:1 0/1:155:2:1,1:56,97:0.0129:2,2:15:0:31:1:1:1.73:51:4:0.0133:0:2.5 -11 95825797 . A G 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66406;SOR=0.6174;LSEQ=CCTGGTGATGGTCCAGCAGA;RSEQ=GAGGGCAAGGCTGACCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:1,4:3,2:0.5:2,2:26:1:30.8:1:0.52381:4.91839:60:10:0.5:0:1 0/1:8:3:2,1:3,2:0.375:2,2:24:1:25.3:1:1:1.29:60:2:0.2857:0:1 -11 99322049 . T C 84 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATGACCCCATGTTACATTA;RSEQ=ACAAAAGTTATGAGATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:16:1:32.7:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 99322082 . G A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=AGATGAAATTCACATTAGCC;RSEQ=ATTCTAAGAACTAGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:33.6:1:30.3:1:1:0:60:18:1:0:1 1/0:3:2:1,1:1,0:0.6667:0,2:20.5:1:28.5:1:1:0:60:4:0.6667:0:2 -11 99322134 . A T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1482;SOR=4.16771;LSEQ=TACAAATAGTACATCAAAAT;RSEQ=TTACAAATGGAATGTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:14:14,0:11,0:0.56:0,1:21.6:1:30.1:1:1:0:60:13:0.5417:0:1 1/1:13:11:10,1:2,0:0.8462:0,2:23.7:1:28.5:1:1:0:60:4.5:0.8182:0:1.2 -11 99322304 . T A 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=1.89569;LSEQ=CAGAGTTTTCTTACTGATAG;RSEQ=GGAAATTATTTTTATATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:88:44,44:87,83:0.3411:2,2:25.7:1:30.2:1:0.89591:1.04803:60:176:0.3451:0:1.9 0/1:228:113:64,49:63,52:0.4956:2,2:20.8:1:29.6:1:0.79124:1.08:60:112:0.4978:0:1.9 -11 99322321 . T C 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00081;SOR=1.85337;LSEQ=TAGTGGAAATTATTTTTATA;RSEQ=GTTAGAAAGCATCATAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:90:42,48:85,92:0.3371:2,2:24.8:1:30.8:1:0.89705:1.05572:60:89:0.3358:0:1.9 0/1:241:117:64,53:60,64:0.4855:2,2:22.1:1:30.5:1:0.36742:1.29:60:116:0.4874:0:1.8 -11 99322382 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=GTCTGAAGGATTAGGCGGTA;RSEQ=ACATAAGAAATAAAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:65,124:0.0104:2,2:37.5:1:30:1:1:1.90:60:4:0.0105:0:1 0/0:187:0:0,0:77,110:0:2,0:26.1:1:31:1:1:0:60:92.5:1:0:0.6 -11 99322415 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49761;SOR=Inf;LSEQ=AAATTATCCTTACAGTTGAT;RSEQ=TAAGATATTTATGAATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:23,81:0:2,0:24.2:1:31.6:1:1:0:60:103:1:0:0.1 0/1:105:2:1,1:32,71:0.019:2,2:13.5:1:32:0:0.53187:2.20:60:4:0.0192:0:3 -11 99322486 . A C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06899;SOR=3.63067;LSEQ=ATAAAAGCCTAACATGCTGT;RSEQ=TACACACTTTCTTTTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:0,7:0,15:0.3182:1,0:24.3:1:32.1:1:1:0:60:14:0.3182:0:1 1/0:22:14:0,14:0,8:0.6364:0,1:25:1:31.4:1:1:0:60:28:0.6364:0:1 -11 99322609 . C A 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTCTTTTAAGTCACAAGACT;RSEQ=TTCACAATTACCTTGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:41.3:1:31.3:1:1:0:60:6:0.75:0:2 0/0:1:0:0,0:0,1:0:0,0:34:0:34:0:1:0:60:2:1:0:0 -11 100240074 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGGTGCAAGACCAGCC;RSEQ=GAGCAACATAGGGAGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:29:1:1:0:60:4:1:0:1.5 -11 100353271 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=0;LSEQ=TGGTTTTCTAGCAATATTGG;RSEQ=CATTCCTTTGATTAATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:0.125:2,2:29:1:29:1:1:1.30929:60:4:0.125:0:1 0/0:10:0:0,0:6,4:0:2,0:19.2:1:30.8:1:1:0:60:20:1:0:0 -11 100850073 . G A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.77031;LSEQ=TCTTTGATGACAGTCATTTT;RSEQ=GGACCACTTTTCAAAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:9:9,0:77,6:0.0978:2,0:26.3:1:28.6:1:1:0:60:18:0.0989:0:1.6 0/1:52:24:23,1:26,2:0.4615:2,1:21.8:1:28.2:1:1:1.75:60:48:0.4615:0:1.4 -11 100850129 . G T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0148;SOR=Inf;LSEQ=AAGTTATATAACTTTTTCTG;RSEQ=AGGAATCATCATGAATATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:213,66:0:2,0:22.9:1:30.9:1:1:0:60:54.8:1:0:0.2 0/1:213:5:2,3:153,55:0.0235:2,2:30:1:27.8:1:0.12586:4.1392:60:10:0.0238:0:1 -11 100850140 . A G 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=5.52718;LSEQ=CTTTTTCTGGAGGAATCATC;RSEQ=TGAATATCCATGGAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:21:13,8:209,78:0.0682:2,2:22.6:1:30.3:1:0.31516:1.646:60:42:0.0682:0:1.9 0/1:246:71:49,22:123,52:0.2886:2,2:22.6:1:30:1:0.87858:1.06175:60:142:0.2898:0:1.8 -11 100850202 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=9.60185;LSEQ=GAGATGTTGTAGAGTTAATT;RSEQ=CCCAAAGCGACTCTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:35:17,18:275,246:0.0629:2,2:26:1:29.3:1:0.72723:1.18328:60:70:0.0635:0:1.4 0/1:438:172:94,78:133,133:0.3927:2,2:26.6:1:28.5:1:0.37844:1.20:60:171:0.3949:0:1.4 -11 100850334 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00167;SOR=3.45245;LSEQ=TGCTTGCTTCTAAAGTTCCT;RSEQ=CTTTACTCTTCTTGCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:62:1,61:1,43:0.5849:1,1:26.5:1:32.5:1:1:1.41382:60:124:0.5849:0:1 1/1:59:49:1,48:0,10:0.8305:0,1:24.3:1:33.1:1:1:0:60:98:0.8305:0:1 -11 100850432 . A AT 107 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.65134;SOR=2.12461;LSEQ=AAAGTCAGAGGCTTTTCATT;RSEQ=TTTTTTTTTTTTACTATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:0,11:1,11:0.4783:2,0:22.3:1:31.1:1:1:0:58.2:22:0.4783:0.087:1 1/0:6:4:0,4:0,2:0.6667:0,0:19:1:27.8:1:1:0:60:8:0.6667:0.1667:0.5 -11 100909580 . G GAT 59 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTATGAAATAATATGGATAA;RSEQ=ATAGTTTACTTTAACAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:10.5:1:29.5:1:1:0:60:8:0.4444:0.3333:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 100909809 . A G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.39521;LSEQ=TGACCAAAACAAAAAGACAT;RSEQ=CCACAAAATTTAATTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:251:133:128,5:116,2:0.5299:1,1:23.8:1:32.6:1:0.45249:2.25863:60:266:0.5341:0:1 0/1:169:52:50,2:109,8:0.3077:2,1:25.2:1:32.5:1:0.72547:1.83:60:104:0.3095:0:1 -11 100909991 . T C 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.4036;LSEQ=TTCAAGCAGTACAGATGAAG;RSEQ=TGTTTGACAAGCTGTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1365:707:287,420:262,393:0.5179:2,2:27.9:1:32.1:1:0.82525:1.02:60:87.375:0.5193:0:1.1 0/1:1164:352:149,203:351,460:0.3024:2,2:26.4:1:31.8:1:0.7966:1.03956:60:57.667:0.2993:0:1.1 -11 100910132 . T C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01048;SOR=0.38982;LSEQ=AAGGTGTTTTTTTCTTACCA;RSEQ=AGTGAAAATAACTCCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:126:68:0,68:0,58:0.5397:1,1:28.1:1:33:1:1:0:60:136:0.544:0:1 0/1:48:15:0,15:0,33:0.3125:1,1:24.8:1:32.6:1:1:0:60:30:0.3125:0:1 -11 100912230 . T C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGATAAATCCTAAAAAA;RSEQ=AGAAACTTGAAAAGCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:34:1:34:0:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 100912235 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAATCCTAAAAAATAGAA;RSEQ=CTTGAAAAGCATGCAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:15:1:33.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 100912252 . A T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACTTGAAAAGCATGCAA;RSEQ=TTTTAACTTTTGCTATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:39.5:1:32:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 100912510 . G GA 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03439;SOR=0.29932;LSEQ=GAGTGGTCTATATTGAAAAT;RSEQ=AAAAAAAAACACAATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:26:26,0:35,0:0.3939:1,1:30.5:1:31.2:1:1:0:59.8:52:0.3939:0:2 0/1:31:5:5,0:20,2:0.1613:2,0:20.8:1:30.4:1:1:0:60:10:0.1613:0.0323:1.6 -11 100912527 . A C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03093;SOR=0.43807;LSEQ=AATGAAAAAAAAACACAATA;RSEQ=AAAGTCTGAGCAGCATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:50:50,0:45,0:0.5263:1,1:24.9:1:29.8:1:1:0:59.7:6.143:0.4943:0:2.1 0/1:46:15:15,0:29,2:0.3261:2,1:19.8:1:30.5:1:1:0:60:14:0.3182:0:1.9 -11 100912561 . C A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00053;SOR=0.39923;LSEQ=CATGATCCAAACACTTTTAA;RSEQ=ATACAAGTATTAATCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:84:84,0:71,0:0.5419:1,1:23.9:1:30.7:1:1:0:59.9:168:0.5455:0:1.7 0/1:100:32:32,0:66,2:0.32:1,1:23.9:1:30.6:1:1:0:60:31:0.3131:0:1.5 -11 100912565 . C A 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3033;SOR=4.71652;LSEQ=ATCCAAACACTTTTAACATA;RSEQ=AAGTATTAATCTGAGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:1,0:166,0:0.006:1,0:13:0:10:0:1:0:60:0:0:0:8 0/1:108:3:3,0:103,2:0.0278:1,0:23.3:1:30.7:1:1:0:60:6:0.0288:0:1 -11 100912910 . C CTA 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=TTATAACATATATTTCTGAG;RSEQ=TATATAATGATTTCTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:16,282:0:2,0:23.9:1:32.3:1:1:0:60:58.6:1:0:0.1 0/1:185:12:0,12:9,164:0.0649:2,0:31:1:29.9:1:1:0:60:24:0.0659:0.0108:0.1 -11 100913165 . G A 75 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATGCTTCTTAAATACTT;RSEQ=GTTTGACTTAGTTTACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:17.6:1:32.4:1:1:0:60:10:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 100920568 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0531;SOR=Inf;LSEQ=TTATAATCCAAGACGTCTAC;RSEQ=TCATACATAACTATATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:260,9:0:1,0:22.7:1:31.1:1:1:0:60:133.5:1:0:0.6 0/1:163:3:2,1:154,6:0.0184:1,2:19.3:1:25.3:1:0.12411:12.25267:60:2:0.0126:0:1.7 -11 100920575 . A T 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3459;LSEQ=CCAAGACGTCTACCTCATAC;RSEQ=TAACTATATAATCATATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:301:174:164,10:121,6:0.5781:1,2:22.9:1:31.4:1:0.7983:1.22884:60:348:0.58:0:1.1 0/1:190:61:57,4:118,11:0.3211:2,2:22:1:31.5:1:0.77778:1.33:60:122:0.3245:0:1.1 -11 100920897 . A C 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02415;SOR=Inf;LSEQ=GGTTTTGGTAATTACCTTAC;RSEQ=TATTATTGAAAATGACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:4,175:0:1,0:25.2:1:31.2:1:1:0:60:43.75:1:0:0 0/1:118:4:0,4:2,112:0.0339:1,0:13.8:1:31.5:1:1:0:60:8:0.0342:0:1.3 -11 100922062 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5283;SOR=0;LSEQ=TAATGTCATCATATCAAGAA;RSEQ=ACTAAATATGTGATCATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:183,6:0.0105:1,2:36:1:29:1:0.07214:28.32449:60:4:0.0105:0:2 0/0:116:0:0,0:116,0:0:1,0:45:0:13:0:1:0:60:0:0:0:2 -11 100922112 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13638;LSEQ=AACTTTCAAAATTATCCTAC;RSEQ=TGTACACTTAAAATAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:244:184,60:207,59:0.4775:2,2:22.4:1:30.5:1:0.53123:1.14376:60:488:0.4813:0:1 0/1:434:48:33,15:274,111:0.1106:2,2:23.2:1:29.8:1:0.73759:1.12172:60:47:0.109:0:1.1 -11 100922202 . G A 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.50725;LSEQ=TACAGCATCTGCCCACTGAC;RSEQ=TGTTTGTAGGATCTCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1416:128:69,59:705,579:0.0904:2,2:21.7:1:29.9:1:0.85255:1.04114:60:41.667:0.0892:0:1.2 0/1:1253:250:138,112:520,480:0.1995:2,2:23.5:1:29.5:1:0.39557:1.14:60:61.5:0.1995:0:1.1 -11 100922387 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15508;SOR=Inf;LSEQ=ACATATAAATCTGAAAATAG;RSEQ=TATGCGTAGGGTAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:8,256:0:1,0:23:1:32:1:1:0:60:65:1:0:0.9 0/1:172:2:0,2:6,164:0.0116:1,0:27:1:29:1:1:0:60:4:0.0117:0:1.5 -11 100922404 . A T 212 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGGTATGCGTAGGGTAATA;RSEQ=AATGTTTTCAATCCCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:181:181:1,180:0,0:1:0,1:25.9:1:28.3:1:1:0:60:35.2:1:0:1.3 1/0:101:61:2,59:0,39:0.604:1,1:23.4:1:28.5:1:0.51939:0:60:122:0.604:0:1.3 -11 100922451 . T A 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00908;SOR=0.32668;LSEQ=CACTGAAAATCAGAAAACAT;RSEQ=AATAAATAATACAGCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:51:0,51:0,33:0.6071:1,1:22.5:1:30.3:1:1:0:60:102:0.6071:0:1.8 0/1:36:12:1,11:0,24:0.3333:1,2:38:1:30.8:1:0.33333:0:60:24:0.3333:0:1.8 -11 100922568 . C A 102 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATCCATCACTCATTCATG;RSEQ=AACACCCATTTAATAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:0.9091:0,0:24.4:1:30.8:1:1:0:60:20:0.9091:0:1 1/1:1:1:0,1:0,0:1:0,0:43:0:30:0:1:0:60:2:1:0:1 -11 100933092 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1587;SOR=Inf;LSEQ=TATATTGTAGTTAATTTACT;RSEQ=CATAGAGTGTTTTATTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:253,6:0:1,0:24.6:1:32.1:1:1:0:60:63.75:1:0:0.1 0/1:172:2:2,0:168,2:0.0116:1,0:31.5:1:30:0:1:0:60:4:0.0118:0:1 -11 100933412 . C A 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.20276;LSEQ=GCTTTCATTTGGAACGCCCA;RSEQ=TGGCTGTGGGAGAGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:115:49,66:518,697:0.0863:2,2:27.2:1:30.2:1:1:1.00102:60:114:0.0863:0:1.1 0/1:1236:213:101,112:449,574:0.1723:2,2:25:1:29.7:1:0.36357:1.15:60:426:0.1735:0:1.1 -11 100933494 . G GA 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.26103;SOR=2.87907;LSEQ=AATTTTCGACCTACAGAGAA;RSEQ=AAAAAAAAGAAATTCATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:2:1,1:77,360:0.0046:2,2:19:1:28.5:1:0.32412:4.65:60:4:0.0046:0:0.5 0/1:384:5:2,3:88,290:0.013:2,2:19.6:1:27.6:1:0.33538:2.19:60:10:0.0133:0.0078:0.4 -11 100933598 . G GAATGA 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.14371;LSEQ=TATGCATTTTAGCATCAATC;RSEQ=AATGAAATAGAATAAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:65:0,65:0,12:0.8442:0,1:28.6:1:30.9:1:1:0:59.9:130:0.8442:0.0909:0.2 0/1:37:16:1,15:0,21:0.4324:1,1:18.3:1:30.7:1:0.43243:0:59.7:32:0.4324:0.1081:0.1 -11 100962200 . C A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCAGCAAAGCCTAGACTCC;RSEQ=ACACATGTTACTTAATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:22.3:1:29.3:1:1:0:60:6:0.375:0:1 0/0:1:0:0,0:1,0:0:0,0:33:0:32:0:1:0:60:2:1:0:1 -11 100998019 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAAGGGAGGCAACTGCCCC;RSEQ=GTGCTGTGTCCCGCTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:24,7:0.0606:2,2:33:1:31:1:0.43182:3.27323:60:4:0.0606:0:1 0/0:15:0:0,0:14,1:0:1,0:23.5:1:32.2:1:1:0:60:30:1:0:0.3 -11 100998076 . T A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05544;SOR=2.29816;LSEQ=CGGGGAGCGCAGCGGTGCGC;RSEQ=GGGGCTGGGGCTGAGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:11:11,0:128,9:0.0743:2,0:13.3:1:31.7:1:1:0:60:22:0.0753:0:1 0/1:96:15:13,2:73,7:0.1563:2,2:26.8:1:30.7:1:0.62994:1.59535:60:30:0.1579:0:1.1 -11 100998105 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0;SOR=0.28087;LSEQ=GGCTGAGGGTTGGCGGCCGC;RSEQ=GCCGCCAACGGAACCGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:348:202:161,41:115,31:0.5805:2,2:23.4:1:30.8:1:0.89351:1.06:60:49.5:0.5773:0:1.1 0/1:272:76:59,17:146,50:0.2794:2,2:21.5:1:30.3:1:0.6406:1.19:60:37:0.2761:0:1.2 -11 100998107 . C T 56 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.00749;SOR=Inf;LSEQ=CTGAGGGTTGGCGGCCGCCG;RSEQ=CGCCAACGGAACCGCTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:0:0,0:282,78:0:2,0:24.2:1:31.8:1:1:0:60:59:1:0:0.7 0/1:288:6:1,5:210,72:0.0208:2,2:7.7:1:21.8:1:0.00586:14.42888:60:2:0.0142:0:1.8 -11 100998285 . CCGG C 73 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.28461;SOR=2.54414;LSEQ=GGTAGAGCGCGGGGGCCGCC;RSEQ=CGGCGGCGGCAGAGGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:2:1,1:140,355:0.004:2,2:14:1:30.5:1:0.48733:2.53:60:4:0.0041:0.002:0.5 0/1:491:5:1,4:159,323:0.0102:2,2:31.6:1:31.6:1:1:1.96666:60:10:0.0104:0:0.2 -11 100998330 . G A 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.60589;SOR=0.45064;LSEQ=TGGAGGGCAGGCCGTCCCGC;RSEQ=GGAGCAGGCAGCCGCTCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:36,79:0.0171:2,2:38:0:32:1:0.53434:2.18:60:4:0.0174:0:1.5 0/0:129:1:1,0:44,84:0.0078:2,0:1:0:23:0:0.34884:0:60:2:0.0078:0:1 -11 100998343 . C T 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92639;LSEQ=GTCCCGCGGGAGCAGGCAGC;RSEQ=GCTCGCGCCCGGCGCCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:36,38:0.026:2,0:1:0:25.5:1:0.49474:0:60:4:0.027:0:1 0/1:83:2:1,1:38,42:0.0241:2,2:20:0:32.5:1:1:1.10:60:4:0.0244:0:1.5 -11 100998362 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28546;SOR=0;LSEQ=CCGCTCGCGCCCGGCGCCTT;RSEQ=CAGGGCGGCGGCGCGAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:3:1,2:159,43:0.0146:2,2:9:1:27.7:1:0.12198:7.29895:60:6:0.0149:0:1 0/0:130:0:0,0:94,34:0:2,0:1:0:16:0:1:0:60:0:0:0:1 -11 100998374 . C T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.14748;SOR=0;LSEQ=GGCGCCTTGCAGGGCGGCGG;RSEQ=GCGAACGGGCCCTGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:4:2,2:235,72:0.0129:2,2:8:1:28.5:1:0.24077:3.24847:60:8:0.0129:0:1.3 0/0:217:0:0,0:150,65:0:2,0:16:1:31.3:1:1:0:60:42:1:0:0.3 -11 100998375 . G T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08527;SOR=6.0993;LSEQ=GCGCCTTGCAGGGCGGCGGC;RSEQ=CGAACGGGCCCTGCTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:1:0,1:255,83:0.0029:2,0:1:0:26:0:0.24779:0:60:2:0.003:0:1 0/1:225:4:1,3:156,64:0.0178:2,2:13.3:1:28.3:1:0.08116:7.23994:60:8:0.0179:0:1.3 -11 100998389 . C T 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78169;LSEQ=GGCGGCGCGAACGGGCCCTG;RSEQ=TGGGGCGGCGCGCCCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:5:3,2:350,128:0.0104:2,2:28.8:1:30.6:1:0.61462:1.82031:60:10:0.0106:0:1 0/0:370:3:0,3:246,121:0.0081:2,0:1:0:26.7:1:0.03703:0:60:6:0.0083:0:1 -11 100998623 . G A 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27571;LSEQ=GAGCGCGCGGAGGCCTCCGC;RSEQ=CCTTCCTCCTCCTCCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1580:892:457,435:337,346:0.5646:2,2:24.3:1:29.9:1:0.47664:1.08:60:73.333:0.5641:0:1.1 0/1:1341:353:169,184:479,508:0.2632:2,2:23.2:1:30:1:0.85245:1.02659:60:706:0.2666:0:1.2 -11 100998762 . C G 243 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CGACCGGGGTGGACGAGGCA;RSEQ=AGGGTGAACTCCGCGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1715:0:0,0:845,867:0:2,0:25.5:1:31.9:1:1:0:60:67.48:0.9982:0:0.2 0/1:1437:213:111,102:621,598:0.1482:2,2:23.8:1:31.5:1:0.7668:1.05:60:212:0.1496:0:1.2 -11 100998771 . C G 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.19218;LSEQ=TGGACGAGGCACAGGGTGAA;RSEQ=TCCGCGGCGGGGCAAAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1663:140:66,74:723,798:0.0842:2,2:25.4:1:31.9:1:1:1.01583:60:69:0.0842:0:1.2 0/1:1383:232:116,116:576,569:0.1678:2,2:23.1:1:31.3:1:0.94272:1.01229:60:115:0.1685:0:1.1 -11 100999013 . T C 185 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGGGACCAGGGCGACGCC;RSEQ=CCTGCTGCCGCCCCCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1561:0:0,0:796,763:0:2,0:23.7:1:30.5:1:1:0:60:54.679:1:0:0.2 0/1:1205:74:40,34:575,556:0.0614:2,2:25.2:1:29.9:1:0.63219:1.14:60:23.667:0.0598:0:1.2 -11 100999043 . G T 208 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01022;LSEQ=GCCCCCGGCGGGACAGCCGC;RSEQ=GCTCCTCCTCCAGCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1554:112:56,56:768,671:0.0721:2,2:23.7:1:30.6:1:0.49345:1.14446:60:55:0.0716:0:1.1 0/0:1262:1:0,1:657,603:8e-04:2,0:1:0:26:0:0.47898:0:60:2:8e-04:0:1 -11 100999190 . G A 224 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=272.50906;LSEQ=TTCACTGGGGCCCCGGACCA;RSEQ=TGAGGGCTCTCAGAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1530:1:1,0:773,756:7e-04:2,0:1:0:25:0:1:0:60:2:7e-04:0:1 0/1:1241:187:90,97:522,531:0.1507:2,2:24.9:1:29.8:1:0.75111:1.05949:60:61.333:0.15:0:1.2 -11 100999194 . G T 205 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGGCCCCGGACCAGTGA;RSEQ=GGCTCTCAGAGGCCGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1513:120:60,60:702,689:0.0793:2,2:27.6:1:29.8:1:0.92456:1.01886:60:16.143:0.0765:0:1.3 0/0:1236:0:0,0:607,628:0:2,0:23.2:1:30.6:1:1:0:60:55.136:0.9992:0:0.3 -11 100999838 . A AG 304 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.27533;LSEQ=TTTTCTCCTCCCCCGTCTCC;RSEQ=GGAGGAGGGAAAAGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:995:921:279,642:33,40:0.9256:2,2:24:1:30.9:1:0.01223:1.89713:60:69.846:0.9322:0.1508:0.1 1/0:761:589:178,411:85,82:0.774:2,2:26.2:1:30.4:1:0:2.39049:60:195.333:0.7813:0.0473:0.1 -11 101102103 . G A 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGGTCAATGGGACCGGGC;RSEQ=CCACAGAGCAGGGGGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:28:1:30.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 101102948 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52216;SOR=0;LSEQ=TGGCTGTCATGGGACCTAGA;RSEQ=AGGGGAGAAGCCGTGTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:35,23:0.0328:2,2:47:1:32.5:1:1:1.51079:60:4:0.0339:0:1 0/0:38:0:0,0:22,16:0:2,0:23.7:1:29:1:1:0:55.3:37:1:0:0.3 -11 101103015 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08368;SOR=Inf;LSEQ=TGAAAGGCATTGTCTGATTT;RSEQ=AGAAGCCTTTTCCTGTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,26:0:2,0:20:1:31.3:1:1:0:56.2:44:1:0:0.1 0/1:36:3:2,1:14,19:0.0833:2,2:13:1:28.7:1:0.57423:2.64:43:6:0.0833:0:1.3 -11 101347908 . G T 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCCAACCTTTCCTTAGACT;RSEQ=TGTAAAGATCTAGGATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:6,25:0:2,0:27.9:1:32.3:1:1:0:60:62:1:0:0 1/0:25:14:6,8:2,9:0.56:2,2:24.4:1:29.6:1:0.23368:3.22:60:28:0.56:0:1.1 -11 101981196 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTCTCAGTCGGGCGCAGCCG;RSEQ=CGCCAGGGAAAAGAAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:17:1:28:1:1:1:60:4:0.5:0:1 -11 101981277 . T C 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGGGAAAGGCAACGAGC;RSEQ=GTCCGGCCTCCGTCAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:22.3:1:30:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:26:0:32:0:1:0:60:2:1:0:1 -11 101981532 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50096;SOR=Inf;LSEQ=GCCGGGGCGTCCGGGCGTAG;RSEQ=CCTCGCTCGCCTGGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:69,35:0:2,0:23.8:1:31.7:1:1:0:60:51:1:0:0.2 0/1:122:2:1,1:76,44:0.0164:2,2:23.5:1:25.5:1:1:1.71909:60:4:0.0172:0:2 -11 101981543 . C T 125 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=18.21756;LSEQ=CGGGCGTAGCCCTCGCTCGC;RSEQ=TGGGTCAGGGGGTGCGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:0,1:85,52:0.0072:2,0:1:0:29:0:0.38406:0:60:2:0.0074:0:1 0/1:144:17:11,6:74,53:0.1181:2,2:27.7:1:30.6:1:0.7939:1.31:60:34:0.1206:0:1.3 -11 101981552 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11932;SOR=Inf;LSEQ=CCCTCGCTCGCCTGGGTCAG;RSEQ=GGGTGCGCGTCGGGGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:93,72:0:2,0:24:1:30.8:1:1:0:60:81.5:1:0:0.3 0/1:161:3:2,1:87,71:0.0186:2,2:18.3:1:23.3:1:1:1.63:60:2:0.0128:0:2 -11 101981563 . CG C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=CTGGGTCAGGGGGTGCGCGT;RSEQ=GGGGAGGCAGAAGCCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:101,83:0.0108:2,2:19.5:1:30:1:1:1.21557:60:4:0.0109:0:0 0/0:180:0:0,0:93,87:0:2,0:28:1:28.9:1:1:0:60:59:1:0:0.3 -11 101981571 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22771;SOR=0;LSEQ=GGGGGTGCGCGTCGGGGGAG;RSEQ=CAGAAGCCATGGATCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:102,90:0.0103:2,2:24.5:1:30:1:1:1.1326:60:4:0.0105:0:1.5 0/0:212:0:0,0:105,106:0:2,0:24.9:1:30.5:1:1:0:60:51.75:0.9952:0:0.3 -11 101981599 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11329;SOR=Inf;LSEQ=CATGGATCCCGGGCAGCAGC;RSEQ=GCCGCCTCAACCGGCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:100,124:0:2,0:26:1:30.1:1:1:0:60:111:1:0:0.3 0/1:211:3:2,1:91,117:0.0142:2,2:17:1:26.3:1:0.58407:2.56:60:6:0.015:0:1.3 -11 101981600 . G T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05331;SOR=Inf;LSEQ=ATGGATCCCGGGCAGCAGCC;RSEQ=CCGCCTCAACCGGCCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:97,123:0:2,0:26.5:1:30.7:1:1:0:60:35.667:1:0:0.3 0/1:205:4:2,2:87,114:0.0195:2,2:29.3:1:31.3:1:1:1.31:60:8:0.0202:0:1.5 -11 101981623 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12734;SOR=0;LSEQ=GCCTCAACCGGCCCCCCAGG;RSEQ=CCAAGGGCAGCCGCCTTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:4:1,3:71,104:0.0223:2,2:17.5:1:30.8:1:0.64951:2.04066:60:8:0.0229:0:1 0/0:153:0:0,0:61,92:0:2,0:25.5:1:31.5:1:1:0:60:37.25:1:0:0.4 -11 101981648 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.24648;SOR=Inf;LSEQ=GGGCAGCCGCCTTCGCAGCC;RSEQ=CCGCAGGGGCAGGGCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:36,68:0:2,0:21.7:1:31:1:1:0:60:33.667:1:0:0.3 0/1:106:3:2,1:41,62:0.0283:2,2:27.7:1:27.3:1:0.5647:2.99:60:6:0.0286:0:1.7 -11 101981681 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2357;SOR=Inf;LSEQ=GGCCCGCCGTCCGGACCCGG;RSEQ=CAACCGGCACCCGCGGCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:98,35:0:2,0:11.4:1:31.6:1:1:0:60:132:1:0:0.2 0/1:126:2:1,1:86,38:0.0159:2,2:13.5:1:31.5:1:0.52495:2.24694:60:4:0.016:0:1 -11 101981687 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49839;SOR=0;LSEQ=CCGTCCGGACCCGGGCAACC;RSEQ=GCACCCGCGGCGACCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:120,34:0.0128:2,2:8:1:29:1:0.3995:3.49292:60:4:0.0131:0:1 0/0:155:0:0,0:110,44:0:2,0:13.7:1:29.6:1:1:0:60:50.333:0.9934:0:0.2 -11 101981695 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61847;SOR=0.48365;LSEQ=ACCCGGGCAACCGGCACCCG;RSEQ=GGCGACCCAGGCGGCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:135,32:0.0118:2,2:27:1:29:1:0.35334:4.1697:60:4:0.0119:0:1 0/0:174:1:0,1:128,44:0.0057:2,0:1:0:24:0:0.26012:0:60:2:0.0058:0:1 -11 101981950 . CG C 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.68664;SOR=0.52169;LSEQ=CCGTCGGGCGGGCCTCAGAC;RSEQ=GGGGGGCGCTCGGGAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:4:0,4:72,271:0.0115:2,0:33.5:1:32.8:1:0.58423:0:60:8:0.0116:0:0 0/0:332:2:0,2:83,247:0.006:2,0:33.5:1:31:1:1:0:60:4:0.0061:0:0.5 -11 101981959 . G A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.08533;LSEQ=GGGCCTCAGACCGGGGGGGC;RSEQ=CTCGGGAGCCGCGGCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:47,245:0.0102:2,2:21:1:28.3:1:0.07266:10.29:60:6:0.0103:0:1 0/1:272:3:2,1:49,220:0.011:2,2:18.7:1:28.3:1:0.09123:8.88:60:6:0.0114:0:1 -11 101982041 . T TGGA 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.05027;SOR=0.40429;LSEQ=GTGGGGGTCCCGAGGCGAAG;RSEQ=GGAACTGGAGTCGTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:53:1,52:0,19:0.7361:1,1:24.3:1:30.3:1:1:0:59.9:106:0.7361:0.1806:0.3 1/0:36:19:0,19:0,17:0.5278:1,1:17.5:1:30.9:1:1:0:60:38:0.5278:0.25:0 -11 101982250 . GA G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGAAGGAAGGGGGTGGG;RSEQ=AAAGTCGGGCCTGGGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:24.3:1:32.7:1:1:0:60:6:1:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 101984718 . A G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01456;SOR=5.14418;LSEQ=ATATAATATTAAAAGTATCC;RSEQ=TTTGAAAACCTGTGTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:12:12,0:29,0:0.2927:1,0:25.3:1:30.8:1:1:0:60:24:0.2927:0:1.1 1/0:16:11:11,0:4,1:0.6875:2,0:24.7:1:30.8:1:0.3125:0:60:22:0.6875:0:1.2 -11 101985302 . C T 103 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00202;SOR=9.44239;LSEQ=GTTTGGTATGACCTAAATAC;RSEQ=TTTGTTAGTATGGGTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:0,27:0.1:1,0:11:1:31.7:1:1:0:60:6:0.1034:0:1 1/0:19:10:0,10:0,9:0.5263:0,0:19.2:1:31.2:1:1:0:60:20:0.5263:0:1 -11 102019959 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18958;SOR=Inf;LSEQ=GCACATTTAGATAGGAGATC;RSEQ=CCAGCCATTGGAGTCAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:144,33:0:2,0:25.3:1:30.3:1:1:0:60:176:1:0:0.1 0/1:137:2:2,0:110,25:0.0146:2,0:25.5:1:29.5:1:1:0:60:4:0.0146:0:1 -11 102019970 . G T 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25142;SOR=0;LSEQ=TAGGAGATCACCAGCCATTG;RSEQ=AGTCAATCTGCAACTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:165,51:0.0137:2,2:12.7:1:20.3:1:0.14605:6.40079:60:2:0.0093:0:3.3 0/0:192:0:0,0:146,46:0:2,0:21.9:1:30.8:1:1:0:60:47:1:0:0.1 -11 102020070 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=13.9338;LSEQ=ATGGTTTGTACAGGGAGATG;RSEQ=AATAAGATGGGTATGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:66:27,39:184,252:0.1312:2,2:22.8:1:29.6:1:0.89404:1.05458:60:65:0.1308:0:1.1 1/0:445:302:143,159:62,81:0.6787:2,2:25.9:1:29.2:1:0.47622:1.17:60:99.667:0.6795:0:1.1 -11 102020234 . G A 123 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=36.0863;LSEQ=GAGGGGAAAGACTAACATCA;RSEQ=TTATGTTTAAGGGAAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:0,3:0,22:0.12:1,0:15:1:32.3:1:1:0:60:6:0.12:0:1 1/1:20:17:0,17:0,3:0.85:0,1:25.2:1:30.1:1:1:0:60:34:0.85:0:1 -11 102033146 . C T 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10799;SOR=5.55301;LSEQ=ATAAGAATTGTTTTTGGAAC;RSEQ=TGGTATTTGTTTCCTAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:506:1:0,1:326,179:0.002:2,0:1:0:25:0:0.35573:0:60:2:0.002:0:1 0/1:459:5:1,4:285,169:0.0109:2,2:5:1:28.4:1:0.06939:6.71865:60:10:0.0111:0:1.8 -11 102033351 . G A 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21346;SOR=Inf;LSEQ=TGGAGTAATGCTTACGCATT;RSEQ=GTAAAAGTTGATGTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:22,194:0:2,0:23.6:1:31.1:1:1:0:60:53:1:0:0.1 0/1:186:2:1,1:32,152:0.0108:2,2:11.5:1:23:0:0.32415:4.69:60:4:0.0108:0:1 -11 102056589 . A G 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29788;SOR=0;LSEQ=TTAGTGGAGAAGAAGCAGGT;RSEQ=TATAGGTTTACCTTTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:4,0:27,1:0.125:1,0:33.3:1:33.3:1:1:0:60:8:0.1333:0:1.3 0/0:14:0:0,0:13,1:0:1,0:24.7:1:27.1:1:1:0:60:13:1:0:0 -11 102056690 . C CT 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14249;SOR=0;LSEQ=TAAATTAGTACCCCCTCCCA;RSEQ=TTTTTTTTAGGTGCACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:4:3,1:183,2:0.0211:1,2:33:1:31.5:1:0.06248:27.88466:60:8:0.0217:0:0.3 0/0:137:0:0,0:130,5:0:1,0:27.4:1:31.2:1:1:0:59.6:44:1:0:0.5 -11 102056907 . AT A 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00323;SOR=Inf;LSEQ=TTAGATGCTTTTGGTTGCTA;RSEQ=TTTTTTTGTAAATATACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:136,352:0:2,0:23.3:1:30:1:1:0:60:60:1:0:0.1 0/1:469:8:4,4:140,321:0.0171:2,2:27.1:1:30.4:1:0.25712:2.29:60:16:0.0172:0.0021:0.3 -11 102057068 . C A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00188;SOR=0.07796;LSEQ=GAATCAGATTTTTAGGGCTC;RSEQ=TCAGGTTGGGGTGGGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:0,13:0,6:0.6842:0,1:23.6:1:32.2:1:1:0:60:26:0.7222:0:1.2 0/1:15:2:0,2:1,12:0.1333:1,0:7:1:29.5:1:1:0:60:4:0.1333:0:1 -11 102076600 . A AT 122 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.02849;SOR=0.33242;LSEQ=TCACTAGTTTTTTAGGACAG;RSEQ=TTTTTTTTTTCTTTTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:17:13,4:176,36:0.0742:2,2:30.8:1:29.9:1:0.50762:1.50128:59.7:16:0.0734:0.0044:1.1 0/1:193:5:5,0:141,47:0.0259:2,0:22.8:1:30.4:1:0.33761:0:60:10:0.0265:0:0 -11 102077200 . G A 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11111;SOR=0;LSEQ=TTATTAATAACTTACGTGGC;RSEQ=GGATACACCAATATGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:19.9:1:29.6:1:1:0:60:16:1:0:1.1 0/0:1:0:0,0:0,1:0:0,0:44:0:32:0:1:0:60:2:1:0:0 -11 102080228 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTAAAGTAATTTTTATCC;RSEQ=TCTTATTTTTTACTCTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:0:0,0:362,288:0:2,0:24.3:1:30.1:1:1:0:60:37.235:0.9984:0:0.2 0/1:656:28:14,14:337,289:0.0427:2,2:25.1:1:28.5:1:0.70323:1.16581:60:27:0.0417:0:1.3 -11 102080325 . GA G 213 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.02084;SOR=0.66322;LSEQ=TATCTGATGTTTTAGCACTG;RSEQ=AAAAAAAAAAAAAAGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:111:20,91:82,110:0.3008:2,2:32.6:1:31.4:1:1e-05:3.37864:60:54.5:0.3011:0:0.7 0/1:338:75:25,50:75,143:0.2219:2,2:31.8:1:29.9:1:0.88882:1.04879:59.8:24:0.2209:0:0.6 -11 102094001 . A G 43 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=19.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GAACAAAAAAAAAAAAAAAA;RSEQ=AAGAAGAATTTTTTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:19.7:1:27.3:1:1:0:60:2:1:0:1.3 0/0:1:0:0,0:1,0:0:0,0:17:0:32:0:1:0:60:2:1:0:1 -11 102094424 . C T 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=31.47038;LSEQ=CAAAATCCAGTGTCTTCTCC;RSEQ=GGGATGTCTCAGGAATTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:872:3:1,2:442,425:0.0034:2,2:28.3:1:29.7:1:0.61778:2.0783:60:6:0.0035:0:1 0/1:744:73:37,36:309,362:0.0981:2,2:25.8:1:30:1:0.46119:1.20:60:72:0.0972:0:1.1 -11 102094548 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27388;SOR=0;LSEQ=CTTTAAAATCATTCTGCTTA;RSEQ=TGCTTGTAATAGGCTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:3:1,2:20,171:0.0155:2,2:31.3:1:25.3:1:0.2922:4.22:60:2:0.0104:0:3.3 0/0:133:0:0,0:19,114:0:2,0:21.9:1:31.1:1:1:0:60:266:1:0:0.1 -11 102094585 . CA C 34 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.24382;SOR=4.28242;LSEQ=TTTGGAACATCTGTGTGGGC;RSEQ=AAAACCATAGCTGTAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:1:0,1:4,102:0.0093:1,0:18:0:33:0:1:0:60:2:0.0096:0:0 0/1:51:2:0,2:0,49:0.0392:1,0:21:1:34:0:1:0:60:4:0.0392:0:0 -11 102098001 . G C 100 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GAGCTGCCAGCTTCAATTAG;RSEQ=ATTAACTTGTCTATTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:0.6154:0,0:25:1:33.5:1:1:0:60:16:0.6154:0:1 0/0:2:0:0,0:2,0:0:0,0:21.5:1:32.5:1:1:0:60:4:1:0:0 -11 102098113 . A C 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04571;SOR=Inf;LSEQ=ACTAATCCTCTTTGAGAATT;RSEQ=TGTTGCTGCTCAGCAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:104,2:0:1,0:23.4:1:28.2:1:1:0:60:25.5:1:0:0.1 0/1:60:3:3,0:57,0:0.05:1,0:27.3:1:32.7:1:1:0:60:6:0.0508:0:1.3 -11 102098343 . G A 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07045;SOR=0;LSEQ=TTTATTCCTCTTAGTAACCT;RSEQ=ACTTAACAGTGGGATATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:5:4,1:143,341:0.0102:2,2:11.2:1:23.4:1:0.03031:9.49:60:4:0.0083:0:1.8 0/0:387:0:0,0:127,260:0:2,0:23:1:30.8:1:1:0:60:76.4:1:0:0.3 -11 102098354 . G C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.06981;LSEQ=TAGTAACCTGACTTAACAGT;RSEQ=GGATATGTTATCACCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:403:345:85,260:10,48:0.8561:2,2:22.1:1:29.9:1:0.24585:1.57:60:171.5:0.8575:0:1.1 0/1:301:88:29,59:61,151:0.2924:2,2:24.5:1:29.7:1:0.49096:1.22:60:87:0.291:0:1.1 -11 102098365 . T A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06976;SOR=Inf;LSEQ=CTTAACAGTGGGATATGTTA;RSEQ=CACCAGGTCTCATAAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:61,262:0:2,0:22.4:1:30.1:1:1:0:60:79.75:1:0:0.9 0/1:227:3:2,1:59,165:0.0132:2,2:14.7:1:22.7:1:0.17661:5.54:60:2:0.009:0:1.3 -11 102100039 . G C 58 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TATATTTAAGGCCAAGGTAG;RSEQ=TCTATACCACTCATGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:29:1:29.3:1:1:0:60:3:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 102100367 . C A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09225;SOR=Inf;LSEQ=CCTGTGCATTTCTCTGTGCT;RSEQ=ATATGATACAGCCCTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:249,64:0:2,0:20.4:1:31.2:1:1:0:60:312:1:0:0.1 0/1:259:3:2,1:200,56:0.0116:2,2:24:1:21.7:1:0.52715:1.78111:60:2:0.0078:0:2.7 -11 102195124 . A G 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCATAGAAATAAAAATAAT;RSEQ=AAAAATTTTTCATTTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:180,1:0:1,0:23.3:1:28.5:1:1:0:60:59.333:1:0:0.1 0/1:127:17:17,0:109,1:0.1339:1,1:20.4:1:31.6:1:1:0:60:34:0.1349:0:1.1 -11 102196116 . TA T 116 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.2834;SOR=0.56789;LSEQ=AAGAAACTGAATCTGCTAAT;RSEQ=AAAAAAATATATTTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:933:14:4,10:422,497:0.015:2,2:35.9:1:30.6:1:0.28056:2.12109:60:28:0.0152:0:0 0/0:933:8:4,4:416,509:0.0086:2,2:27.3:1:31.3:1:1:1.22:60:16:0.0087:0:0 -11 102197189 . G A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03646;SOR=Inf;LSEQ=CAAGTGTGGGTTTTTATCAC;RSEQ=TGGGTAAGAAACTTAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:86,139:0:2,0:25.4:1:30.9:1:1:0:60:111.5:1:0:0.1 0/1:283:6:5,1:114,163:0.0212:2,2:10.8:1:26.7:1:0.08583:7.10:60:12:0.0214:0:1 -11 102197221 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19346;SOR=0;LSEQ=CTTAATGTACTAACTAAAAT;RSEQ=TCAGCTTCAAAAAGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:19,91:0.0179:2,2:18.5:1:28:0:0.32658:4.69:60:4:0.0179:0:1 0/0:142:0:0,0:33,109:0:2,0:21.8:1:28.8:1:1:0:60:70:1:0:0.1 -11 102197235 . GT G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.18664;SOR=0;LSEQ=TAAAATATCAGCTTCAAAAA;RSEQ=TTTTTACACTCTCCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:6,64:0.0278:2,2:21:1:29.5:1:0.18623:9.95:60:4:0.0282:0.0139:0.5 0/0:94:0:0,0:10,84:0:2,0:23:1:29.9:1:1:0:60:93:1:0:0 -11 102199589 . TTA T 184 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=11.000;MSILEN=2;SSF=0.33809;SOR=1.22847;LSEQ=GATAAGATTTCTATTTTAAT;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:71:57,14:126,17:0.3287:2,2:21.4:1:30:1:0.14954:1.81507:59.2:22.667:0.3208:0.0787:1.1 0/1:173:65:50,15:84,18:0.3757:2,2:21.8:1:29.5:1:0.42866:1.39708:59.8:64:0.3765:0.104:1.5 -11 102199609 . ATA TTTT 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.2578;SOR=0;LSEQ=TTATATATATATATATATAT;RSEQ=TTTTTTTTTTCTGCAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:194,61:0.0112:2,2:30.3:1:32.1:1:0.56318:1.58699:60:6:0.0116:0:2 0/0:215:0:0,0:152,56:0:2,0:23.7:1:27.4:1:1:0:59.2:15:0.9701:0:1.4 -11 102199610 . TA T 116 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.82317;SOR=0.85389;LSEQ=TATATATATATATATATATA;RSEQ=TTTTTTTTTTCTGCAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:13:8,5:99,34:0.048:2,2:26.5:1:31.5:1:0.33348:1.81151:60:26:0.0872:0:0 0/1:194:8:5,3:18,3:0.0412:2,2:29.6:1:29.4:1:0.30451:3.41678:58.8:16:0.0455:0:0.8 -11 102199611 . A AT 91 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.20495;SOR=0.34313;LSEQ=ATATATATATATATATATAT;RSEQ=TTTTTTTTTTCTGCAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:8:8,0:99,34:0.0295:2,0:30.6:1:30.6:1:0.19863:0:59.4:16:0.0537:0:0.3 0/1:194:2:1,1:18,3:0.0103:2,2:31:1:25:1:0.32411:5.33862:60:4:0.0114:0:1 -11 102199792 . AT A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.21978;SOR=Inf;LSEQ=TTATAATTTACGATGAATGC;RSEQ=TTTCAAATATACTGTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:3,146:0:1,0:23.1:1:30.6:1:1:0:60:48.667:1:0:0 0/1:132:2:1,1:7,123:0.0152:2,2:18:1:27:1:0.11797:16.50:60:4:0.0153:0.0076:0.5 -11 102202053 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16968;SOR=Inf;LSEQ=TGAAAAATATACTCATCTAG;RSEQ=ATATCTGAAAATATACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:12,200:0:2,0:25.1:1:32.2:1:1:0:60:211:1:0:0 0/1:149:2:0,2:12,135:0.0134:2,0:12.5:1:31:1:1:0:60:4:0.0135:0:1 -11 102206417 . T C 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=AAGACAGGGTATTGCTATGT;RSEQ=GCCCAGTCTGGTCTCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:34.8:1:31.6:1:1:0:60:10:0.625:0:1 0/0:2:0:0,0:2,0:0:0,0:29:1:31:0:1:0:60:4:1:0:0 -11 102206585 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51699;SOR=0;LSEQ=CCTAGCAATCAACATCAATG;RSEQ=CTTACTGATTACGAATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:106,4:0.0179:1,2:20.5:1:29.5:1:0.08768:23.81438:60:4:0.0183:0:1 0/0:75:0:0,0:75,0:0:1,0:23:1:31.6:1:1:0:60:36.5:1:0:0.1 -11 102206592 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17115;SOR=Inf;LSEQ=ATCAACATCAATGCCTTACT;RSEQ=ATTACGAATTAAAGATAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:119,5:0:1,0:25.5:1:32.6:1:1:0:60:123:1:0:0.1 0/1:88:2:2,0:86,0:0.0227:1,0:6:1:30:1:1:0:60:4:0.023:0:1 -11 102207024 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=7.51236;LSEQ=CTCTTATTAATAATTTATGA;RSEQ=TACTGAAAATAATTCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:56:3,53:4,66:0.4444:2,2:20.6:1:30.5:1:1:1.07015:59.2:27:0.439:0:1 1/1:106:91:3,88:2,13:0.8585:2,1:22.3:1:30.2:1:0.14551:4.41615:60:44.5:0.8641:0:1.1 -11 102207318 . C CA 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39352;SOR=0.32797;LSEQ=TTGGGTGACAGACTCTGTCT;RSEQ=AAAAAAAAATCAATCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:3,1:64,5:0.0548:2,2:20.5:1:29.8:1:0.29579:4.12759:60:8:0.0548:0:0 0/1:54:1:1,0:50,3:0.0185:2,0:13:0:32:0:1:0:60:2:0.0189:0:0 -11 102207593 . C T 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=26.65312;LSEQ=TTTATTTTCTTAGTTTTTCA;RSEQ=TGAAGAAGCAAACTGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:906:1:0,1:444,458:0.0011:2,0:1:0:25:0:1:0:60:2:0.0011:0:1 0/1:873:25:14,11:433,415:0.0286:2,2:22.4:1:30.5:1:0.68792:1.22:60:50:0.0289:0:1.1 -11 102207851 . G A 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.00196;LSEQ=TGAAGAAGAACCAAAACATC;RSEQ=TCTAAACTTTAGAATTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:916:346:107,239:184,385:0.3777:2,2:24.6:1:30.6:1:0.71443:1.06746:60:172:0.3801:0:1.1 1/0:883:693:224,469:65,122:0.7848:2,2:23.4:1:29.8:1:0.53983:1.11538:60:172.25:0.7892:0:1.1 -11 102220662 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50996;SOR=0;LSEQ=GAGTATAATGGAAGATAGCA;RSEQ=GATCTTGTCAGATTGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:158,2:0.0123:1,0:20:1:30:1:1:0:60:4:0.0124:0:1 0/0:119:0:0,0:118,1:0:1,0:23:1:31.4:1:1:0:60:238:1:0:0.1 -11 102221242 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49837;SOR=Inf;LSEQ=GGACCTGGAGATAGGGTAGC;RSEQ=TGCTTTGCCTGTGGTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:100,43:0:2,0:22:1:30.7:1:1:0:60:34.75:1:0:0.1 0/1:147:2:1,1:103,42:0.0136:2,2:38:1:29:1:0.50089:2.43545:60:4:0.0138:0:1 -11 102221559 . C CT 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.12639;LSEQ=ACGTGTTTTCAATATTTAGT;RSEQ=TTTTTTTTCCTGAAGGTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:666:7:4,3:489,168:0.0105:2,2:23.3:1:29.9:1:0.38166:2.1801:60:14:0.0106:0.003:0 0/1:592:7:5,2:421,164:0.0118:2,2:26.3:1:29.7:1:1:1.02678:60:14:0.012:0:0 -11 102221882 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05909;SOR=Inf;LSEQ=TACTTTTGTAAGTCAGTTAC;RSEQ=AGTATGACCGTACATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:0,42:0:1,0:23.1:1:30.3:1:1:0:60:41:1:0:0 0/1:14:2:1,1:0,12:0.1429:0,2:8.5:1:31:0:0.14286:0:60:4:0.1429:0:1 -11 102248406 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49245;SOR=Inf;LSEQ=TGATTGATACCATTTTGGTT;RSEQ=AAGGAAATGCTGCGGCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:28.1:1:29.4:1:1:0:60:38:1:0:0.1 0/1:23:2:1,1:10,11:0.087:2,2:9:0:33.5:1:1:1.10:60:4:0.087:0:1.5 -11 102248667 . C CT 51 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.49887;LSEQ=AACCAACATGAACTATTACC;RSEQ=TTTTTTTTTAATGAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:3,0:56,2:0.0492:1,0:21.7:1:32.7:1:1:0:60:6:0.05:0:0 0/1:40:1:1,0:38,1:0.025:1,0:31:0:32:0:1:0:60:2:0.025:0:0 -11 102248722 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22153;SOR=Inf;LSEQ=AGTTATTTTTTGTTATTAGG;RSEQ=CTGTCACTGGAAGAACAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:151,43:0:2,0:20.6:1:29.7:1:1:0:60:96:1:0:0.1 0/1:173:2:1,1:126,45:0.0116:2,2:34.5:1:30.5:1:0.46223:2.78037:60:4:0.0116:0:1 -11 102248747 . A G 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11826;SOR=Inf;LSEQ=CACTGGAAGAACAATTGAGG;RSEQ=GGTTGCAAGAAGAACGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:174,104:0:2,0:26.2:1:30:1:1:0:60:68.5:1:0:0.1 0/1:269:3:2,1:165,101:0.0112:2,2:27.7:1:25.3:1:1:1.22:60:2:0.0076:0:3.3 -11 102248753 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12065;SOR=Inf;LSEQ=AAGAACAATTGAGGAGGTTG;RSEQ=AAGAAGAACGAACTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:181,121:0:2,0:27:1:32:1:1:0:60:99.667:1:0:0.1 0/1:296:3:1,2:170,123:0.0101:2,2:21.3:1:26:1:0.57537:2.75478:60:6:0.0103:0:1.7 -11 102671697 . C T 82 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01669;SOR=11.53145;LSEQ=TCCGGACTATTTCCAGGCAG;RSEQ=CAGATTATTTCCGTGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:7,9:0.0588:2,0:19:0:31:0:1:0:60:2:0.0625:0:1 0/1:16:7:3,4:4,4:0.4375:2,2:28.1:1:29.3:1:1:1.30792:60:14:0.4375:0:1.1 -11 102916090 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2438;SOR=Inf;LSEQ=GAAAGGTGATATTGTAGACA;RSEQ=CAAGGGAATAGGTTGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:28,33:0:2,0:24.9:1:29.2:1:1:0:60:14.25:1:0:0.1 0/1:60:2:1,1:31,27:0.0333:2,2:9:0:32:0:1:1.1455:60:4:0.0339:0:1 -11 102916105 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24436;SOR=Inf;LSEQ=AGACATCAAGGGAATAGGTT;RSEQ=AAAAAGGAGTGCCCACAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:31,36:0:2,0:28.4:1:31.6:1:1:0:60:134:1:0:0.1 0/1:66:2:1,1:35,29:0.0303:2,2:8:1:31:1:1:1.20344:60:4:0.0303:0:1 -11 105610204 . GA TG 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2205;SOR=Inf;LSEQ=AACACTGAAAGTACTTAATT;RSEQ=TATATAATTAAAGTGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:84,86:0:2,0:25.5:1:31.5:1:1:0:60:84:1:0:0.7 0/1:151:2:1,1:71,77:0.0132:2,2:27:1:32.8:1:1:1.08:60:4:0.0132:0:1 -11 105610205 . A G 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00273;SOR=2.03124;LSEQ=ACACTGAAAGTACTTAATTG;RSEQ=TATATAATTAAAGTGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:172:95:45,50:39,38:0.5523:2,2:24.9:1:31.5:1:0.75925:1.13948:60:94:0.5595:0:1.1 1/0:151:108:50,58:22,19:0.7152:2,2:24.3:1:30.9:1:0.4659:1.34048:60:216:0.7347:0:1.2 -11 105610267 . T C 25 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=Inf;LSEQ=AACTTGTCATTTATGGTGAT;RSEQ=AGCTTCAGTAACTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:34,72:0:2,0:24.9:1:28.8:1:1:0:60:212:1:0:0.4 0/1:106:2:1,1:38,66:0.0189:2,2:6:0:25.5:1:1:1.73:60:4:0.0189:0:2 -11 105830380 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18803;SOR=Inf;LSEQ=TGCACCCTTTATGGAGAGAC;RSEQ=TTGTGATCATCTGGAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:29.8:1:29.2:1:1:0:60:14:1:0:0 0/1:12:2:1,1:5,5:0.1667:2,2:41:0:31:1:1:1:60:4:0.1667:0:1.5 -11 105830445 . T G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TTCAGCATTTTTTCATTGAT;RSEQ=CTTTCTCATCTTCATGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:18:1:30.9:1:1:0:60:18:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:31:0:33.5:1:1:1:56:4:0.4:0:2.5 -11 105830453 . A T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.9219;LSEQ=TTTTTCATTGATTCTTTCTC;RSEQ=TCTTCATGAGTTTGTCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:5,2:0.125:2,0:2:0:28:0:0.375:0:60:2:0.125:0:1 0/1:9:2:1,1:3,4:0.2222:2,2:23:0:32.5:1:1:1.29:56:4:0.2222:0:2.5 -11 105831145 . A G 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCACAGCCGGTGTGTTG;RSEQ=GCTGTGGGGACAAGTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:15,13:0,0:1:0,2:26.6:1:30.6:1:1:0:59.4:27:1:0:1.1 1/1:19:19:11,8:0,0:1:0,2:30.2:1:30.4:1:1:0:60:38:1:0:1.1 -11 105831347 . CA GG 67 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCCCCAAGGAGCTGAAA;RSEQ=GCTTCGACAGCAGGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:15:1:28.9:1:1:0:60:10:1:0.6:0.6 1/1:1:1:0,1:0,0:1:0,0:19:0:32:0:1:0:60:2:1:0:1 -11 105831672 . A G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGTCATGCCAGCCTTCTAG;RSEQ=CAATTTTGATGAGAGAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:33.5:1:29.5:1:1:0:60:4:1:0:0 0/1:5:2:1,1:2,1:0.4:2,2:32.5:1:33:1:1:1.7321:60:4:0.4:0:1 -11 106361902 . T C 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TGTTGGTGCTGCTGTTGTTG;RSEQ=TGCTGCTGTTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:102,99:0:2,0:28.5:1:29.8:1:1:0:60:200:1:0:0.2 0/1:252:26:13,13:120,104:0.1032:2,2:34.3:1:32.5:1:0.83623:1.15318:60:52:0.1048:0:1.2 -11 106361916 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.19183;SOR=0;LSEQ=TTGTTGTTGCTGCTGTTGTT;RSEQ=CTGCTGCTGTTGTTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:94,104:0.01:2,2:19:1:29:1:1:1.11:60:4:0.0102:0:1 0/0:256:0:0,0:119,137:0:2,0:28.8:1:31.4:1:1:0:60:41.667:1:0:0.3 -11 106361974 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5024;SOR=Inf;LSEQ=TAAAATTTTTTCAGTTATTG;RSEQ=ATTTTTTTTCAGCCGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:19,60:0:2,0:24:1:31.3:1:1:0:60:38.5:1:0:0.2 0/1:97:2:1,1:28,67:0.0206:2,2:8.5:1:25:1:0.51074:2.37:60:4:0.0211:0:1 -11 106361988 . C T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.18508;LSEQ=TTATTGCATTTTTTTTCAGC;RSEQ=GAAAAGCTTCAATTGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:8:1,7:9,46:0.127:2,2:25.4:1:30.6:1:1:1.36327:60:16:0.1311:0:1 1/0:66:34:6,28:6,25:0.5152:2,2:29:1:30.2:1:1:1.11804:60:68:0.5231:0:1 -11 107025440 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47826;SOR=Inf;LSEQ=ATGATAAGTAATGTCAGATC;RSEQ=TTCAGTCACATTCATGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:22.6:1:28.7:1:1:0:60:22:1:0:0 0/1:12:2:1,1:3,7:0.1667:2,2:11.5:1:28:1:1:2.16:60:4:0.1667:0:1 -11 108098299 . A G 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50088;SOR=0;LSEQ=ATATACATATACATATATAT;RSEQ=CCTATATGTATTTTTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:109,23:0.0148:2,2:13:0:34:0:0.32724:4.66061:60:4:0.0149:0:1 0/0:116:0:0,0:95,21:0:2,0:22.6:1:28.2:1:1:0:60:57:1:0:0.1 -11 108098301 . C T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.22113;SOR=Inf;LSEQ=ATACATATACATATATATAC;RSEQ=TATATGTATTTTTTTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:112,26:0:2,0:23.5:1:30.8:1:1:0:60:137:1:0:0.1 0/1:123:2:1,1:98,23:0.0163:2,2:16.5:1:23.5:1:0.35346:4.19239:60:4:0.0165:0:1 -11 108098309 . A AT 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.48321;SOR=1.88672;LSEQ=ACATATATATACCTATATGT;RSEQ=TTTTTTTTACAGACAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:3:2,1:132,37:0.0174:2,2:13:1:27.8:1:0.5295:1.77689:60:6:0.0176:0.0116:0.3 0/1:154:5:3,2:116,33:0.0325:2,2:21.6:1:28.9:1:0.31869:2.32793:60:10:0.0331:0.013:0.2 -11 108098459 . TAA T 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00258;LSEQ=AATTCAATTTTTCCTTGAAA;RSEQ=GTGTGATTAGTAACCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:324:172:85,87:80,72:0.5309:2,2:25.7:1:32.3:1:0.57936:1.1368:60:344:0.5325:0.071:0.1 1/0:365:194:97,97:75,96:0.5315:2,2:24.9:1:31.2:1:0.24959:1.28:59.9:388:0.5315:0.0959:0.1 -11 108098576 . C G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTAGATCGGCATTCAGATT;RSEQ=CAAACAAGGAAAATATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:149,209:0:2,0:25.1:1:31:1:1:0:60:118.333:1:0:0.1 0/1:383:27:14,13:168,188:0.0705:2,2:23.8:1:31.3:1:0.69226:1.20:60:54:0.0711:0:1.1 -11 108098647 . AT A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.20115;SOR=0;LSEQ=AAATTTATTTTACTGTCTTT;RSEQ=TTTTCTCTTTCATATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:23,117:0.0141:2,2:36.5:1:30.5:1:0.31046:5.00:60:4:0.0143:0:0 0/0:174:0:0,0:52,120:0:2,0:25.1:1:29.7:1:1:0:60:56.333:0.9883:0:0.1 -11 108099845 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21141;SOR=Inf;LSEQ=TGATGGCATGAACAGCTTTT;RSEQ=AAATTATTATAATTTAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:71,13:0:2,0:25.5:1:32.1:1:1:0:60:83:1:0:0.1 0/1:72:2:1,1:55,15:0.0278:2,2:25:1:32:0:0.3975:3.58204:60:4:0.0286:0:1 -11 108099886 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50071;SOR=Inf;LSEQ=TTCAACGAGTTTCTGAAATT;RSEQ=CATTTTGTTTTCTTGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:112,42:0:2,0:23:1:32.3:1:1:0:60:308:1:0:0.1 0/1:176:2:1,1:119,54:0.0114:2,2:14:0:27.5:1:0.53103:2.19277:60:4:0.0114:0:1 -11 108100105 . G GT 130 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.21496;SOR=0.6115;LSEQ=AACAGATTACTGTCGCGTGA;RSEQ=TTTTTTTTTTTTTTCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:25:2,23:12,20:0.3425:2,2:33.6:1:28:1:0.01322:6.68696:59.8:11.5:0.3382:0:1.9 0/1:83:20:1,19:10,39:0.241:2,1:31:1:30.4:1:0.15701:4.78873:60:40:0.2778:0:1.4 -11 108106168 . C T 32 v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTTAATTACAAAAGCAG;RSEQ=CATAAACAATAAGTAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:8,0:0.2:0,2:20:0:32:0:0.2:0:60:4:0.2222:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108106443 . T A 114 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00113;SOR=12.83217;LSEQ=CTCTTAAATTATATCATGGA;RSEQ=ACAGTGAAAGATTCATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:1:1,0:239,143:0.0026:2,0:20:0:31:0:1:0:60:2:0.0026:0:1 0/1:430:14:6,8:259,157:0.0326:2,2:30.1:1:30:1:0.16681:2.19539:60:28:0.0326:0:1.1 -11 108106635 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.02404;SOR=Inf;LSEQ=CCAAAGAAAGCACTCTGTCT;RSEQ=TATCTGTCTATATCCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:15,129:0:2,0:21.6:1:32.1:1:1:0:60:143:1:0:0.1 0/1:132:5:1,4:22,105:0.0379:2,2:25.2:1:30.4:1:1:1.19:60:10:0.0379:0:1 -11 108106782 . C T 89 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAGGTGCCTGATATCAGAGC;RSEQ=GGAATTACAGTTGAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:26.3:1:29.8:1:1:0:60:16:1:0:1 1/0:4:3:1,2:0,1:0.75:0,2:15.7:1:30:1:1:0:60:6:0.75:0:1 -11 108114506 . A G 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.6037;LSEQ=TCCTGTCTTAAAGGCATTTT;RSEQ=TATAAGATAAAATTAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:28.7:1:32.3:1:1:0:60:6:0.3:0:1 0/1:5:1:1,0:4,0:0.2:0,0:11:0:34:0:1:0:60:2:0.2:0:1 -11 108114840 . T C 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTTCCAAGGCTATTCAGTG;RSEQ=GCGAGGTAATCTAATCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:0:0,0:202,337:0:2,0:25.8:1:30:1:1:0:60:178.667:1:0:0.1 0/1:675:27:12,15:275,372:0.04:2,2:23:1:30.5:1:0.84515:1.08:60:54:0.0401:0:1.4 -11 108115360 . AT A 166 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.07181;SOR=3.01604;LSEQ=CAGTGTGAAGTAATGCTGTG;RSEQ=TTTTTTTTTTAATGAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:39:37,2:11,0:0.6964:0,2:22.6:1:31.5:1:1:0:60:78:0.6964:0.1429:0.3 1/1:32:28:28,0:4,0:0.875:0,1:28:1:30.6:1:1:0:60:56:0.875:0.0938:0.2 -11 108115419 . G GT 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.546;SOR=0.75555;LSEQ=TGTTTGAAAATTAGGGTTTT;RSEQ=TTTTTTTTTCTTTCAGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:17:14,3:133,12:0.1049:2,2:19.7:1:29.6:1:0.19622:2.35845:60:34:0.1063:0.037:0.4 0/1:123:10:8,2:97,13:0.0813:2,2:17.8:1:28:1:0.61164:1.85382:60:9:0.0744:0.0244:0 -11 108115451 . C T 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAGCATACCACTTCATAA;RSEQ=TGTTCAGTTTGTACAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:208,58:0:2,0:25:1:31.3:1:1:0:60:25.6:1:0:0.1 0/1:259:27:19,8:169,63:0.1042:2,2:22:1:30.4:1:0.82072:1.12894:60:54:0.1071:0:1.1 -11 108115456 . C T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0605;SOR=0;LSEQ=CATACCACTTCATAACTGTT;RSEQ=AGTTTGTACAGTTTGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:4:1,3:212,62:0.0144:2,2:11.5:1:28.5:1:0.04098:10.14641:60:8:0.015:0:1 0/0:281:0:0,0:198,83:0:2,0:24.9:1:30.9:1:1:0:60:55.2:1:0:0.2 -11 108115594 . C T 125 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.05224;LSEQ=AGACTTTGGCTGTCAACTTT;RSEQ=GAATTCGAGTGTGTGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:857:18:11,7:411,428:0.021:2,2:25.4:1:30.1:1:0.34787:1.64:60:17:0.02:0:1 0/0:894:1:0,1:444,448:0.0011:2,0:1:0:26:0:1:0:60:2:0.0011:0:1 -11 108115778 . T G 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06091;SOR=Inf;LSEQ=AAAGGAAATGTTTACTGTTT;RSEQ=GAATTTGCTTCTTCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:42,148:0:2,0:24.6:1:30.2:1:1:0:60:94:1:0:0.1 0/1:193:5:1,4:55,133:0.0259:2,2:16.2:1:30.2:1:1:1.65029:60:10:0.026:0:1 -11 108117335 . C T 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACACTAGTTGAAGGAACT;RSEQ=GTAATATTTTTCTCTTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29.7:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108117897 . A AT 49 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.12246;LSEQ=CATTTAGAAATTTCCTGTTA;RSEQ=TTTTTTTTTTAAACTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:0,3:15,122:0.0214:2,0:20:1:29.3:1:1:0:51.7:6:0.0217:0:1.7 0/1:125:3:0,3:15,106:0.024:2,0:21.3:1:31.3:1:1:0:60:6:0.0244:0:0 -11 108119677 . C T 45 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44845;SOR=2.03617;LSEQ=CAGGTTTTTAATGAAGATAC;RSEQ=AGATCCTTGGAGATTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:2:1,1:281,94:0.0053:2,2:8:1:20:1:0.44098:2.97886:60:1:0.0028:0:2.5 0/1:372:4:1,3:248,119:0.0108:2,2:9:1:22.5:1:0.10596:6.21933:60:3:0.0084:0:2 -11 108121410 . C CT 157 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.1958;SOR=0.64547;LSEQ=GGAATAGTTTTCAAATTATC;RSEQ=TTTTTTTTTTTTTTTAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:33:32,1:50,1:0.3267:1,1:29.5:1:31.3:1:1:1.5539:58.2:66:0.3333:0:1.1 0/1:84:20:18,2:54,2:0.2381:1,2:25.2:1:31.7:1:0.2816:2.94851:58.3:40:0.2469:0:1.9 -11 108121846 . GAC G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.50469;SOR=0;LSEQ=CTTACAGATAAACACACACA;RSEQ=ACACACACACTCACATATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:0,2:10,117:0.0155:2,0:22:1:31.5:1:1:0:60:4:0.0159:0:1.5 0/0:102:0:0,0:10,92:0:2,0:23.3:1:29.4:1:1:0:60:101:1:0:0 -11 108122592 . C G 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGCTGTTTGACTTTGGCA;RSEQ=TGACCACCAGTATAGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:715:0:0,0:395,320:0:2,0:25.9:1:31.8:1:1:0:60:78.444:1:0:0.1 0/1:729:27:14,13:395,305:0.037:2,2:30.8:1:31.8:1:0.69471:1.20226:60:54:0.0374:0:1.1 -11 108122659 . G T 139 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=6.34865;LSEQ=AAATATGTGTGAAGTAAATA;RSEQ=AAGCTTTTCTTTAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:713:4:2,2:318,389:0.0056:2,2:20.5:1:29.8:1:1:1.22:60:8:0.0057:0:1 0/1:809:28:13,15:350,431:0.0346:2,2:27.3:1:29:1:1:1.07:60:56:0.035:0:1.1 -11 108122786 . G GT 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24858;SOR=0;LSEQ=AAGTTCATTAGCATGCTGCT;RSEQ=TTTTTTTTGTTTGTTTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:3:1,2:57,158:0.0136:2,2:29.3:1:30.3:1:1:1.38:58.3:6:0.0138:0:1 0/0:211:0:0,0:62,147:0:2,0:25.4:1:31.2:1:1:0:60:208:0.9952:0:0.1 -11 108122828 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50109;SOR=0;LSEQ=GGCTCTCTCCACTTATTTGA;RSEQ=GCCAGATGGCTTTATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:8,99:0.0183:2,2:34:1:29:1:0.15902:11.73:60:4:0.0187:0:1 0/0:92:0:0,0:16,76:0:2,0:22.2:1:29.8:1:1:0:60:45:1:0:0.1 -11 108123189 . C A 58 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGATAAAGGAATGGAGTC;RSEQ=CTCGTCCACTTAACCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:11:1:29.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108123390 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20814;SOR=Inf;LSEQ=CTCCTTAAATTGTCCTTTTA;RSEQ=ATATTAAGAAATTTAGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:27,1:0:1,0:25.9:1:32:1:1:0:60:27:1:0:0.2 0/1:24:2:1,1:22,0:0.0833:1,2:29:0:27.5:1:0.08333:0:60:4:0.087:0:1 -11 108123515 . TA T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12371;SOR=Inf;LSEQ=TTACATGGCTTTTGGTCTTC;RSEQ=AGTGAAGCTTTTTGTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:180,71:0:2,0:24.9:1:28.8:1:1:0:60:502:1:0:0.1 0/1:259:4:1,3:175,80:0.0154:2,2:8.5:1:29.3:1:0.09831:6.5112:60:8:0.0156:0.0077:0.8 -11 108123719 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49846;SOR=Inf;LSEQ=TAATTTTAGCTGGGTAGTAG;RSEQ=TGCATCTTAATAATTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:2,83:0:1,0:22.6:1:32.3:1:1:0:60:84:1:0:0 0/1:94:2:1,1:3,89:0.0213:1,2:22.5:1:28.5:1:0.08373:25.83:60:4:0.022:0:1 -11 108124299 . G A 96 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAATTTGCCTTTGAGATT;RSEQ=TAACTTGTATTTTTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:23.6:1:27:1:1:0:60:11:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108127010 . C T 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCTTGGCTGCTACTGTTA;RSEQ=ATGGGTGTAATAGCTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:901:0:0,0:414,487:0:2,0:25.7:1:31.6:1:1:0:60:52:1:0:0.1 0/1:848:28:11,17:381,439:0.033:2,2:21.7:1:29:1:0.56412:1.34081:60:56:0.0334:0:1.1 -11 108127089 . A C 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00192;SOR=Inf;LSEQ=TAGGAGAATTTATACTAATA;RSEQ=AGTTTCGGATAAATTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:39,213:0:2,0:24.4:1:30.2:1:1:0:60:49.4:1:0:0.1 0/1:273:10:1,9:84,176:0.0366:2,2:29.6:1:32.4:1:0.17854:4.2785:60:20:0.0373:0:1.8 -11 108127101 . A C 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00086;SOR=Inf;LSEQ=TACTAATAAAGTTTCGGATA;RSEQ=ATTTGAATGAAATGTATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:32,177:0:2,0:23.6:1:30.2:1:1:0:60:103.5:1:0:0.1 0/1:215:11:2,9:61,143:0.0512:2,2:22.4:1:31.8:1:0.51477:1.91452:60:22:0.0514:0:2 -11 108127288 . T C 115 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTCTGGGGTACATGATG;RSEQ=AGAGCATGCAGGTTTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1:0,1:18.5:1:31.1:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108128397 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1973;SOR=Inf;LSEQ=TTCTCTGTCACCCAGGCTGG;RSEQ=GTGCAGTGGGATTGTCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:8,114:0:2,0:25.4:1:31.1:1:1:0:60:29.5:1:0:0 0/1:98:2:1,1:11,85:0.0204:2,2:25:1:28:1:0.23101:7.44:60:4:0.0204:0:1 -11 108129657 . A G 246 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00592;LSEQ=TAGAGAAAACACTGTCTGCC;RSEQ=AGAATAATTGTTTTTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:292:291:229,62:0,0:0.9966:0,2:22.8:1:30.1:1:1:0:60:144.5:0.9966:0:1.1 1/0:233:147:107,40:55,31:0.6309:2,2:23:1:29.4:1:0.1848:1.50:60:146:0.6348:0:1.1 -11 108137775 . T A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00724;SOR=0;LSEQ=TCAGGTGATCCACCTGGCTC;RSEQ=GCCTCCCAAATTGCTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:74:74,0:0,0:1:0,1:26.3:1:30.5:1:1:0:60:148:1:0:1.1 1/1:32:28:27,1:4,0:0.875:0,1:21.9:1:30.5:1:1:0:60:56:0.875:0:1 -11 108138045 . C T 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGTTAGTGATGCAAACGAA;RSEQ=CTGGAGAGAGCCAAAGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:283,443:0:2,0:26.1:1:31.6:1:1:0:60:144.2:0.9972:0:0.1 0/1:713:30:12,18:291,392:0.0421:2,2:28.4:1:28.7:1:0.85175:1.11332:60:29:0.0412:0:1.2 -11 108138214 . A AT 32 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01831;LSEQ=GTTCCTTTCTTATATACTTT;RSEQ=TTTTTTTTTTATTTTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:0,2:3,52:0.0351:2,0:36.5:1:32:0:1:0:60:4:0.0357:0:0 0/1:28:1:0,1:1,26:0.0357:1,0:44:0:26:0:1:0:60:2:0.0357:0:0 -11 108138923 . G GT 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATGATCATTTGTCTAAGG;RSEQ=TTTTTTTTTCTCATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:13,0:0.1333:1,0:30.5:1:28:1:1:0:60:4:0.1429:0:0 0/0:3:0:0,0:3,0:0:0,0:31:1:32:1:1:0:60:6:1:0:0.3 -11 108139091 . C T 53 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01073;SOR=Inf;LSEQ=GTTAATATGACTATATATGG;RSEQ=TGTTGTGCCCTTCTCTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:212,73:0:2,0:21.9:1:31.7:1:1:0:60:70.25:1:0:0.1 0/1:195:5:0,5:141,49:0.0256:2,0:7.8:1:23:1:0.00142:0:60:4:0.0207:0:1.2 -11 108139183 . A G 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATCTGTCAAAGCAAGATCT;RSEQ=CTTTTCTTAGACATGCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:0:0,0:441,329:0:2,0:24.4:1:28.7:1:1:0:60:153:0.9987:0:0.1 0/1:629:28:16,12:323,276:0.0445:2,2:26.4:1:31.6:1:0.84694:1.14:60:56:0.0448:0:1.1 -11 108141677 . T C 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.73886;LSEQ=GTGATCTGCCTGCTTCAGCC;RSEQ=CCCAAAGTGCTGGGATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:2,0:121,0:0.0163:1,0:30:1:31:1:1:0:60:4:0.0163:0:1 0/1:83:1:1,0:81,1:0.012:1,0:38:0:27:0:1:0:60:2:0.0122:0:2 -11 108141701 . G T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00333;SOR=1.97236;LSEQ=AAAGTGCTGGGATTACAGGT;RSEQ=TGAGCCACTGCACCCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:71:64,7:101,12:0.3859:2,2:21.4:1:30.1:1:1:1.09:60:70:0.3825:0:1.1 1/0:139:77:68,9:54,8:0.554:2,2:26.9:1:29.3:1:1:1.12:59.6:76:0.5588:0:1.1 -11 108141940 . G A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.25749;LSEQ=TAACTGATGTGTTCTGTTAA;RSEQ=CTTATAAAGTTGAACTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:3:0,3:174,180:0.0084:2,0:4.7:1:13.3:1:0.24837:0:51.7:0:0:0:3.3 0/1:286:3:0,3:146,136:0.0105:2,0:6.3:1:21:1:0.11473:0:60:2:0.0081:0:1.3 -11 108142186 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34444;SOR=3.4359;LSEQ=CTTTTGCTATCTGTGGATAC;RSEQ=AATGCAAGTTTTGTATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:1,0:84,235:0.0031:2,0:1:0:27:0:0.26562:0:60:2:0.0032:0:1 0/1:281:3:2,1:74,204:0.0107:2,2:18:1:28:1:0.17891:5.47:60:6:0.0108:0:1 -11 108142191 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10195;SOR=Inf;LSEQ=GCTATCTGTGGATACGAATG;RSEQ=AAGTTTTGTATCCACATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:69,223:0:2,0:24.4:1:32:1:1:0:60:96.333:1:0:0.1 0/1:257:3:1,2:63,191:0.0117:2,2:14.7:1:27.3:1:1:1.51:60:6:0.0117:0:1 -11 108143182 . C T 232 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACATATTGGAAGTAACTTA;RSEQ=AATAACCTTTCAGTGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:179:179:155,24:0,0:1:0,2:23.2:1:31.1:1:1:0:60:178:1:0:1.1 1/0:156:124:111,13:27,5:0.7949:2,2:21.8:1:29.8:1:0.53355:1.58:60:123:0.7935:0:1.1 -11 108143456 . C G 255 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTTTTCCCGTAGGCTGATC;RSEQ=TTATTCAAAATGGGCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1030:305:172,133:394,328:0.2961:2,2:25.3:1:30.9:1:0.63091:1.08:60:100.667:0.2964:0:1.1 0/0:925:0:0,0:500,423:0:2,0:8:0:15:0:1:0:60:0:0:0:1 -11 108148332 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGCCCCTCACAGCATAG;RSEQ=CCCTCACGGCTTCCCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:8:0:26:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:22.5:1:33:0:1:0:60:4:1:0:1 -11 108150207 . CT C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19283;LSEQ=TTTGTTTGTTTGTTTGCTTG;RSEQ=TGTTTTAAGATTGTTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:192:127,65:141,66:0.4812:2,2:25.2:1:32:1:0.74901:1.09317:60:384:0.4873:0.0777:0.1 0/1:383:58:33,25:220,105:0.1514:2,2:28:1:31.9:1:0.13197:1.58534:60:116:0.1522:0.0052:0.1 -11 108150405 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16275;SOR=Inf;LSEQ=ATCCCATAAATTACTTCACC;RSEQ=AGTTTGGTATAAGAGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:8,114:0:2,0:23.4:1:30.8:1:1:0:60:121:1:0:0 0/1:83:2:1,1:8,73:0.0241:2,2:10:1:32:1:0.20629:8.66:60:4:0.0241:0:1 -11 108151269 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGTGTGTGTGTGATAC;RSEQ=GGTATACAATGTGAAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:39.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108151707 . T TA 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=0;SOR=0.15041;LSEQ=TTTACATTACATTTTTTTTT;RSEQ=AATTTCTTTTTAAGTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:149:140:106,34:5,0:0.9396:0,2:24.7:1:28.3:1:0.59127:0:60:45.667:0.9448:0.2953:0.4 1/0:163:114:80,34:34,6:0.6994:2,2:23.6:1:27.7:1:0.0926:2.396:59.8:37:0.6938:0.184:0.4 -11 108151729 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10628;SOR=0;LSEQ=ATTTCTTTTTAAGTCCCATA;RSEQ=TGCTGAGAACCCTGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:2,1:179,71:0.0119:2,2:23.3:1:24.3:1:1:1.25939:60:2:0.0081:0:3.3 0/0:280:0:0,0:192,88:0:2,0:23.4:1:31.1:1:1:0:60:39:1:0:0.2 -11 108151839 . T G 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGCGAAAAACAGGCTTTG;RSEQ=TTGCCCTGTGTAAATCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:0:0,0:257,267:0:2,0:26.1:1:29.8:1:1:0:60:73.857:1:0:0.1 0/1:564:35:16,19:240,288:0.0621:2,2:20.9:1:30.5:1:1:1.01:60:34:0.0608:0:1.1 -11 108151929 . CT C 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24873;SOR=0;LSEQ=AGTATTTTATTAGAAGCTTC;RSEQ=TAGGTCACTGTGAAATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:2,1:35,140:0.0169:2,2:21.3:1:29:1:0.11002:7.87:60:6:0.0171:0.0056:0.3 0/0:166:0:0,0:41,125:0:2,0:20.9:1:29.8:1:1:0:60:82:1:0:0.1 -11 108153361 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18185;SOR=Inf;LSEQ=GTTGTTTCTAGGTCCTACTC;RSEQ=AAATAATATTAACAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:133,20:0:2,0:23:1:31.2:1:1:0:60:75.5:0.9934:0:0.1 0/1:115:2:1,1:100,13:0.0174:2,2:24:1:27.5:1:0.2296:7.44943:60:4:0.0175:0:1 -11 108153392 . A AT 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.1159;SOR=0;LSEQ=AACAAGCATTTAAATGATTT;RSEQ=TTTTTTTCATTTTTCTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:232,60:0.0102:2,2:16:1:27:1:0.11296:7.66002:60:6:0.0102:0.0068:0.7 0/0:309:0:0,0:229,79:0:2,0:20.7:1:28.5:1:1:0:60:101.667:0.9967:0:0.1 -11 108154931 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.2186;SOR=Inf;LSEQ=AAAAGTTATATATAACCTGT;RSEQ=TTTTAAATTTTTCTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:139,21:0:2,0:22.8:1:28.4:1:1:0:60:39:1:0:0.1 0/1:141:2:1,1:114,25:0.0142:2,2:5:0:31:1:0.33587:4.49103:60:4:0.0143:0:1.5 -11 108155333 . A G 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00905;SOR=Inf;LSEQ=TGTGGTAATCATTATCTAGC;RSEQ=TAGCCAACCCATGAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:0,64:0:1,0:26.5:1:31.2:1:1:0:60:128:1:0:0.3 0/1:43:5:0,5:0,38:0.1163:1,0:23.4:1:31.4:1:1:0:60:10:0.119:0:1 -11 108155397 . G A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06073;SOR=0;LSEQ=TCTGATTGGCTTTTAACTAA;RSEQ=TAGAAATGTTTTAAATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:0,29:0,0:1:0,1:25.3:1:31.4:1:1:0:60:58:1:0:1.3 1/1:10:8:1,7:0,2:0.8:0,2:22.5:1:30.1:1:1:0:60:16:0.8:0:1 -11 108158134 . T C 121 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11111;SOR=0;LSEQ=ATTTTCATACTTTTTCCTCT;RSEQ=AGTCTACAGGTTGGCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:15,1:0,0:1:0,1:25.5:1:30.4:1:1:0:60:15:1:0:1 1/0:2:1:1,0:1,0:0.5:0,0:45:0:30:0:1:0:60:2:0.5:0:1 -11 108159356 . G A 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGATTGCCATGTCTTAAA;RSEQ=TACTGCTTTTACAGTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:9.5:1:30.5:1:1:0:37.8:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108160242 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14502;SOR=Inf;LSEQ=TATAAAATGTGTAGGTATTC;RSEQ=AATATTTGAAGAAAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:99,14:0:2,0:22.5:1:30.5:1:1:0:60:112:1:0:0 0/1:70:2:1,1:60,8:0.0286:2,2:21:1:29:1:0.24224:7.12928:60:4:0.029:0:1 -11 108160632 . C T 150 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACAAAGACTCACTCTGTC;RSEQ=GCCCAGGCTGGGTGCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:30:0,30:1,25:0.5357:1,1:24.4:1:30.7:1:0.46429:0:60:60:0.5455:0:1.1 0/0:46:0:0,0:0,46:0:1,0:9:0:16:0:1:0:60:0:0:0:2 -11 108163323 . G GT 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.26011;SOR=0.61136;LSEQ=AGAACTTACTGGTTGTTGTT;RSEQ=TTTTTTTTTCTCCCTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:20:16,4:270,77:0.0545:2,2:27.6:1:29.8:1:1:1.14:59.8:40:0.0549:0.0109:0.2 0/1:294:10:9,1:221,60:0.034:2,2:28.8:1:28.6:1:0.69378:2.44:60:9:0.031:0:1.2 -11 108163733 . A G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTATCTACTGTGCTGAAGT;RSEQ=GAGAGGTAGTCAAAACTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:4,6:0,0:1:0,2:22.1:1:30:1:1:0:60:20:1:0:1 1/1:2:2:0,2:0,0:1:0,0:31:1:28.5:1:1:0:60:4:1:0:1 -11 108165219 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCACGCCTGTAATCCCAG;RSEQ=GCTTTGGAAGGCTAAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108165406 . GC AG 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=0.17439;LSEQ=GAACCGGGGAGGCGGAGGTA;RSEQ=AGTGAGCCTTGATAGCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:0,0:0.875:0,0:30.6:1:32.6:1:1:0:60:14:1:0:1.1 1/0:4:2:2,0:2,0:0.5:0,0:19:1:29.5:1:1:0:60:4:0.5:0:1.5 -11 108165542 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20915;SOR=Inf;LSEQ=CCTTGATTAGTAGTAATAGA;RSEQ=ACATGAGTCAGTGTCTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:123,1:0:1,0:22.5:1:31.8:1:1:0:60:16.714:1:0:0.1 0/1:105:2:1,1:100,3:0.019:1,2:10.5:1:29:1:0.07509:28.9907:60:4:0.0196:0:1.5 -11 108165634 . A G 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCAATACGTGTTAAAAGCA;RSEQ=GTTACATTTTCTCTTTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:640:0:0,0:416,223:0:2,0:24.9:1:30.3:1:1:0:60:105.5:0.9984:0:0.1 0/1:669:24:13,11:367,278:0.0359:2,2:25.4:1:29.4:1:0.83559:1.11686:60:11:0.0331:0:1 -11 108170042 . CT C 33 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGGTTGATTCTCTCTCT;RSEQ=TTTTTTTTTTTTCTTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:33.5:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108170271 . G A 155 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00021;SOR=0;LSEQ=TGACCTCAGGTGATCCGCCC;RSEQ=CCTCTGTCTCCCAAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:34,1:0,0:1:0,1:25.1:1:30.3:1:1:0:58.9:70:1:0:1.1 1/0:14:8:8,0:6,0:0.5714:0,0:32.5:1:29.4:1:1:0:60:7:0.5385:0:1.3 -11 108170373 . T G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00361;SOR=Inf;LSEQ=CAGCATTATAGTTTTGAAAT;RSEQ=AGAAAATTTCAGTTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:136,7:0:1,0:24.7:1:30.4:1:1:0:60:142:1:0:0.1 0/1:119:7:5,2:102,10:0.0588:2,2:18.9:1:31:1:0.14736:4.00468:60:14:0.0588:0:1 -11 108172385 . C T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.03162;SOR=Inf;LSEQ=TTTTTTTCAGTGTCAAAGTT;RSEQ=GATCAGCAGCTGTTACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:354,200:0:2,0:23.5:1:30.4:1:1:0:60:54.4:1:0:0.1 0/1:601:6:2,4:355,240:0.01:2,2:6.8:1:25.3:1:0.22961:2.95295:60:5:0.0084:0:1.3 -11 108172526 . G T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05911;SOR=Inf;LSEQ=CAAGAAAAAAGGTCTCTTAA;RSEQ=TAATAAATGTTTATTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:103,282:0:2,0:25.4:1:31.8:1:1:0:60:54:1:0:0.1 0/1:376:4:2,2:109,260:0.0106:2,2:20.3:1:30:1:0.58555:2.38:60:8:0.0108:0:1.3 -11 108173801 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19639;SOR=Inf;LSEQ=TAATTCCTTGTTTATGACCT;RSEQ=TTTATCTAAAGAGTGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:26,142:0:2,0:23:1:32.2:1:1:0:60:336:0.9941:0:0.1 0/1:135:2:1,1:22,111:0.0148:2,2:31.5:1:29.5:1:0.31277:4.96:60:4:0.015:0:1 -11 108175462 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14686;LSEQ=TTCATGATATTTTACTCCAA;RSEQ=ATACAAATGAATCATGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:271:154,117:149,123:0.4982:2,2:24.6:1:30:1:0.66597:1.09:60:53.2:0.4935:0:1.1 0/1:614:78:40,38:280,256:0.127:2,2:25.8:1:29.5:1:0.90385:1.03901:60:38:0.125:0:1.1 -11 108175681 . A G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.061;SOR=Inf;LSEQ=CACTTTACAGGATTAAATCT;RSEQ=TAACCTCTAAATTTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:1,76:0:1,0:23.8:1:31.7:1:1:0:60:76:1:0:0.1 0/1:51:3:0,3:1,47:0.0588:1,0:7.7:1:32:0:1:0:60:6:0.0588:0:1 -11 108178575 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.51228;SOR=Inf;LSEQ=TAAACAAGAAGGAAGAAGGT;RSEQ=TGTAAGCAAGAATGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:102,39:0:2,0:24.9:1:32.2:1:1:0:60:140:1:0:0.1 0/1:197:2:1,1:136,58:0.0102:2,2:28:0:28:1:0.51251:2.33343:60:4:0.0102:0:1 -11 108178730 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24019;SOR=Inf;LSEQ=AGGTAATGTAATGAGTGTTG;RSEQ=TTCTTACGTTTAGGATCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:60,133:0:2,0:25.6:1:31.9:1:1:0:60:63.333:1:0:0.2 0/1:186:2:1,1:48,136:0.0108:2,2:18:1:27.5:1:0.45853:2.81:60:4:0.0109:0:1 -11 108178767 . T C 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CTAGAGTGTAACTTGTTAAC;RSEQ=ATCGGCTGAATTTTAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:13,92:0:2,0:21:1:28.8:1:1:0:60:210:0.9906:0:0.1 0/1:75:10:1,9:8,57:0.1333:2,2:24.5:1:31.4:1:1:1.25948:60:20:0.1333:0:1 -11 108181094 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50057;SOR=Inf;LSEQ=ATTAATGTTGGCATTGTCTC;RSEQ=ATAAGGGTATATAGTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:15,102:0:2,0:23.8:1:30.3:1:1:0:60:234:1:0:0 0/1:135:2:1,1:28,105:0.0148:2,2:21.5:1:30.5:1:0.38474:3.70:60:4:0.015:0:1 -11 108181123 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49618;SOR=0;LSEQ=ATATAGTAAAGATTTATTTT;RSEQ=CCTCCTGTTCCCCATTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:2,62:0.0303:1,2:23.5:1:29:1:0.08951:25.52:60:4:0.0308:0:1 0/0:65:0:0,0:2,63:0:1,0:24.1:1:32.1:1:1:0:60:31.5:1:0:0.2 -11 108181511 . A C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTGATTTATTTCTGTGACTA;RSEQ=TTAAGTTTCATTTCTTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12.5:1:33.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:33:1:27:1:1:0:60:4:1:0:0 -11 108183167 . A G 283 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGAAGAAGGAAGCCAGA;RSEQ=TACAACTATTTCTAGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:547:547:280,267:0,0:1:0,2:26.3:1:32.1:1:1:0:60:135.75:1:0:1.1 1/1:548:548:279,269:0,0:1:0,2:26.6:1:31.2:1:1:0:60:108.6:1:0:1.1 -11 108183413 . ACT A 115 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.05;SOR=0;LSEQ=AGACTTGAGTTCTAATACTG;RSEQ=CTGCCACTTCTTGAGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:1,11:0,0:1:0,2:25.1:1:32.2:1:1:0:60:24:1:0.25:0.1 1/0:4:2:0,2:0,2:0.5:0,0:26:1:31:1:1:0:60:4:0.5:0.25:0 -11 108186258 . G A 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AACTTTTAAAAAATTTTTCA;RSEQ=TAGTTCTAAACTGTGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31:1:30.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:4:0:30:0:1:0:60:2:1:0:1 -11 108186653 . T C 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TACTAGGTAAATTGCATTTT;RSEQ=CTAAACAACGGTATAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:255,201:0:2,0:23.6:1:30.1:1:1:0:60:151:1:0:0.1 0/1:506:17:9,8:239,250:0.0336:2,2:20.5:1:31.5:1:0.8083:1.18:60:34:0.0337:0:1.4 -11 108186662 . C A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06218;SOR=Inf;LSEQ=AATTGCATTTTTCTAAACAA;RSEQ=GGTATAGTAATTCTGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:0:0,0:261,207:0:2,0:22.7:1:31:1:1:0:60:233:0.9957:0:0.1 0/1:492:5:4,1:254,233:0.0102:2,2:8.8:1:26:1:0.37544:3.66:60:10:0.0103:0:1 -11 108186956 . T C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06639;SOR=Inf;LSEQ=AGAGATAAGACTAGAACTTA;RSEQ=CTGTTTTTCAGAGGATTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:2,69:0:1,0:22.3:1:30.2:1:1:0:60:70:1:0:0.1 0/1:50:3:1,2:1,46:0.06:1,2:23.7:1:33:0:0.11755:18.99:60:6:0.0625:0:1 -11 108187830 . T AAAAA 48 LongAT STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.14286;SOR=0;LSEQ=ACTACCATACCCAGCTATTT;RSEQ=AAAAAAAAAAAAAAATTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,0:0.75:0,0:14.7:1:30.3:1:1:0:50:6:0.75:0.5:2.3 0/0:3:0:0,0:1,0:0:0,0:21:1:32:0:1:0:60:2:0.3333:0:2 -11 108188342 . TTATATA T 105 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=19.000;MSILEN=2;SSF=0.03136;SOR=0;LSEQ=TGAATATAACAGGAGTTGTT;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:13:0,13:0,36:0.2097:1,1:37.8:1:28.6:1:1:0:58.2:26:0.2167:0.0161:1.5 0/0:20:0:0,0:0,13:0:1,0:15.3:1:26.6:1:1:0:58.6:12:0.6316:0:0.7 -11 108188377 . T C 81 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=17.000;MSILEN=2;SSF=0.07641;SOR=3.64412;LSEQ=TATATATATATATATATATA;RSEQ=ATACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:4:0,4:0,26:0.1176:1,0:21:1:32.5:1:1:0:50:8:0.1333:0:3 0/1:18:6:0,6:0,12:0.3333:0,0:30.3:1:31.7:1:1:0:55.8:12:0.3333:0:3 -11 108188379 . T C 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0.37747;SOR=1.85878;LSEQ=TATATATATATATATATATA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:0,11:0,19:0.3235:1,0:28.5:1:32.6:1:1:0:54.2:22:0.3667:0:2 0/1:19:9:0,9:0,8:0.4737:0,0:29.1:1:31.2:1:1:0:57.2:18:0.4737:0:2.4 -11 108188462 . T A 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06061;SOR=0;LSEQ=TATATATATATAAAAAAATA;RSEQ=ATAGTAGATGTTGCAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:24.2:1:31.2:1:1:0:60:12:0.75:0:1.5 0/0:3:0:0,0:0,3:0:0,0:19:1:29:1:1:0:60:6:1:0:0 -11 108192159 . G T 133 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.84695;LSEQ=TTTCTCAAGGTATGTAATTC;RSEQ=TATGACTTTGTTATCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:568:1:0,1:195,372:0.0018:2,0:9:0:31:0:1:0:60:2:0.0018:0:1 0/1:646:24:10,14:234,387:0.0372:2,2:33.8:1:29.2:1:0.67478:1.18:60:23:0.0362:0:1.3 -11 108193671 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12795;SOR=0;LSEQ=AGTCTGGCAGGATGACAAAG;RSEQ=AAAGTGTTTTGGGTCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:5,13:0.1:2,2:27:1:31.5:1:0.52105:2.46:60:4:0.1:0:1 0/0:35:0:0,0:17,18:0:2,0:23.3:1:28.6:1:1:0:60:70:1:0:0.1 -11 108195976 . GT G 168 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.03798;SOR=0.4895;LSEQ=TAAGTTCCAGAACTTACATA;RSEQ=TTTTTTTTTTTTTTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:41:37,4:56,5:0.3388:2,2:22.3:1:31.5:1:1:1.2085:59.4:40:0.3361:0.0826:0.7 0/1:80:16:12,4:44,5:0.2:2,2:23.9:1:33:1:0.20684:2.87587:56.3:32:0.2078:0:1.7 -11 108196509 . G C 139 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08696;SOR=0;LSEQ=GTTATAAAATGAGAAGATAC;RSEQ=TAACTTACTATATTGATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:6,15:0,0:1:0,2:23.3:1:31.8:1:1:0:60:42:1:0:1.1 1/0:2:1:0,1:0,1:0.5:0,0:14:0:34:0:1:0:60:2:0.5:0:1 -11 108196712 . CATT C 217 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0;SOR=0.08449;LSEQ=TGAATGGTAGTTGCTGCTTT;RSEQ=ATTATTATTATTCATGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:128:123:109,14:4,0:0.9609:0,2:26.2:1:31.3:1:1:0:60:60.5:0.9758:0.1406:0.1 1/0:107:72:58,14:32,3:0.6729:2,2:22.6:1:31.2:1:0.17213:2.55482:60:144:0.6729:0.1495:0.1 -11 108196957 . G GT 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.80034;SOR=0.86039;LSEQ=TGCCAGCTGTGCAGCGGTTT;RSEQ=TTTTTTTTATTGGCTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:8:1,7:112,237:0.0224:2,2:32.6:1:27.5:1:0.4439:3.29961:60:7:0.0199:0:0.8 0/1:362:7:1,6:138,216:0.0193:2,2:33.1:1:30.6:1:0.25687:3.82221:60:14:0.0198:0:0 -11 108196973 . G A 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.31452;LSEQ=GTTTGTTTTTTTTATTGGCT;RSEQ=GATTAGTGTTTTACTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:77,212:0.0103:2,2:27.7:1:25:1:0.17904:5.47:60:2:0.007:0:1.3 0/1:297:4:3,1:97,196:0.0135:2,2:1.8:1:24.5:1:0.11261:6.02:60:8:0.0137:0:1 -11 108196975 . A G 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12046;SOR=0;LSEQ=TTGTTTTTTTTATTGGCTGG;RSEQ=TTAGTGTTTTACTGTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:1,2:73,207:0.0106:2,2:13.7:1:26.3:1:1:1.42:60:2:0.0072:0:2.7 0/0:289:0:0,0:97,192:0:2,0:22.9:1:28.9:1:1:0:60:35.125:1:0:0.2 -11 108198249 . C CT 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50705;SOR=0;LSEQ=CAAAAGCAGATGAGGAAAAA;RSEQ=TTTTTTTTTCCCACCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:2,0:48,1:0.0392:1,0:13.5:1:32.5:1:1:0:60:4:0.0392:0:0 0/0:37:0:0,0:37,0:0:1,0:19:1:31.3:1:1:0:60:74:1:0:0 -11 108198297 . T TC 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.03299;SOR=Inf;LSEQ=ACATTTTTAACCTGCTTTTT;RSEQ=CCCCGTACATGAAGGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:128,10:0:2,0:23.5:1:30.6:1:1:0:60:137:1:0:0 0/1:104:4:4,0:87,13:0.0385:2,0:23:1:32.5:1:1:0:60:8:0.0385:0.0096:0 -11 108198313 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17308;SOR=Inf;LSEQ=TTTTTCCCCGTACATGAAGG;RSEQ=CAGTTGGGTACAGTCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:169,24:0:2,0:24.5:1:31.5:1:1:0:60:47.25:1:0:0.1 0/1:138:2:1,1:116,20:0.0145:2,2:31.5:1:28:1:0.28213:5.68462:60:4:0.0146:0:1 -11 108199583 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCGTCCTGGGCCACATG;RSEQ=GGCCCATGGGCCGTGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:3,0:22,0:0.12:1,0:31.7:1:30.3:1:1:0:60:6:0.12:0:1.7 0/0:7:0:0,0:7,0:0:0,0:33.3:1:31.6:1:1:0:60:14:1:0:0.1 -11 108200142 . T G 131 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=11.000;MSILEN=1;SSF=0.13261;SOR=0.12554;LSEQ=TTTCGGTTTTTGTTTTTTGT;RSEQ=TTTTTTTTTGAGACAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:18:1,17:0,1:0.9474:0,1:20.1:1:31.6:1:1:0:60:17:0.9444:0:1 1/0:6:4:1,3:0,2:0.6667:0,2:16.5:1:32:1:1:0:60:8:0.6667:0:1 -11 108201207 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51078;SOR=0;LSEQ=AAAAACTTAGACATAAGCCC;RSEQ=TTGATGTCAGGAATCGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:9,111:0.0164:2,2:20.5:1:30:1:0.15784:11.75:60:4:0.0165:0:1 0/0:88:0:0,0:15,73:0:2,0:22.8:1:31.8:1:1:0:60:176:1:0:0.1 -11 108201215 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17084;SOR=Inf;LSEQ=AGACATAAGCCCCTTGATGT;RSEQ=AGGAATCGTGTATACCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:8,102:0:2,0:24.2:1:32:1:1:0:60:109:1:0:0.1 0/1:78:2:1,1:13,63:0.0256:2,2:30:1:27.5:1:0.32867:4.71:60:4:0.0256:0:1 -11 108202154 . C CT 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.77947;SOR=0.74614;LSEQ=CTTGTTTCTTAATTTTGTGT;RSEQ=TTTTTTTTAATGGTAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:8:6,2:193,48:0.0321:2,2:29.1:1:30.5:1:0.66315:1.33857:60:16:0.0327:0.004:0.1 0/1:207:5:2,3:149,53:0.0242:2,2:29.6:1:31.2:1:0.12371:4.18173:57:10:0.0243:0:0.6 -11 108203501 . G A 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12475;SOR=Inf;LSEQ=ATTAATAGGATCGAACAGAG;RSEQ=CTGCAAATAGAATAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:244,129:0:2,0:24.4:1:31.2:1:1:0:60:40.444:1:0:0.1 0/1:397:4:2,2:239,153:0.0101:2,2:36:1:28:1:0.64614:1.56022:60:8:0.0103:0:1 -11 108203632 . G GT 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.3768;SOR=0.27877;LSEQ=TGGAAGACTCAGAGAAGTAT;RSEQ=TTTTTTTTAAAGAAGAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:4:1,3:63,193:0.0153:2,2:32.8:1:30.5:1:1:1.02:60:8:0.0156:0.0038:0 0/0:232:1:0,1:54,177:0.0043:2,0:45:0:32:0:1:0:60:2:0.0043:0:0 -11 108203640 . T A 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCAGAGAAGTATGTTTTTTT;RSEQ=AAAGAAGAAACGTTACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:49,172:0:2,0:23.4:1:28.7:1:1:0:60:109.5:1:0:0.1 0/1:200:15:4,11:39,146:0.075:2,2:23.4:1:28.9:1:0.74332:1.36:60:30:0.075:0:1.2 -11 108203769 . G A 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTATATCTGATGGCTTCA;RSEQ=CATTCCCTGGTTACTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:0,16:0,0:1:0,1:20.6:1:30.5:1:1:0:60:32:1:0:1.2 1/1:9:9:1,8:0,0:1:0,2:16.8:1:28.4:1:1:0:60:18:1:0:1.2 -11 108204456 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGCTTTGACTCTGAGCT;RSEQ=CATAGTGGCCAAAGCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:34,1:0.0541:1,2:10:0:30.5:1:0.10661:24.39295:60:4:0.0571:0:1 0/0:17:0:0,0:17,0:0:1,0:24.2:1:30.5:1:1:0:60:16:1:0:0.2 -11 108204557 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50747;SOR=0;LSEQ=TCTGCTGACTATTCCTGCTT;RSEQ=ACCTTCAATGCTGTTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:139,59:0.01:2,2:15.5:1:25.5:1:0.51106:2.34463:60:4:0.0101:0:1.5 0/0:153:0:0,0:118,35:0:2,0:23.8:1:31.6:1:1:0:60:75.5:1:0:0.1 -11 108204717 . A AT 106 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00436;SOR=10.54262;LSEQ=TAATTTGCAATTAACTCTTG;RSEQ=TTTTTTTTAAACTAAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:0,1:64,144:0.0048:2,0:27:0:11:0:1:0:60:0:0:0:0 0/1:248:12:4,8:87,149:0.0484:2,2:25.9:1:29.8:1:1:1.16711:60:24:0.05:0.0081:0.2 -11 108204881 . C T 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AAAATACTCAAAAGCTTCTC;RSEQ=TGCTTTCTTTTCCATTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:12.4:1:30.2:1:1:0:60:4:1:0:0 1/0:5:3:0,3:0,2:0.6:0,0:28:1:29:1:1:0:60:6:0.6:0:1 -11 108204945 . GT G 28 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTATGAAGGTCTATAGACT;RSEQ=TACTTTCATTGGCCAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:28.5:1:1:0:60:4:1:0:0 1/1:1:1:0,1:0,0:1:0,0:20:0:26:0:1:0:60:2:1:0:0 -11 108205329 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGAAATGTAGCTGTATC;RSEQ=TGTGGATTAACTGCTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108205383 . G A 54 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAGGTGATTTCGCTGAAT;RSEQ=TTTCCTTAAAATGCCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:18.3:1:27:1:1:0:60:8:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 108205659 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18842;SOR=Inf;LSEQ=CTTTAAGTGCAAATAGTGTA;RSEQ=CTGACCTATTATCAATCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:162,29:0:2,0:23.1:1:30.8:1:1:0:60:62.667:1:0:0.1 0/1:147:2:1,1:114,31:0.0136:2,2:25.5:1:27:1:0.38915:3.63573:60:4:0.0137:0:1 -11 108205861 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11324;SOR=Inf;LSEQ=GCCTTCCCTTCTCTGGCTTA;RSEQ=CCCTTAGAGTTTTAGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:69,200:0:2,0:23.2:1:31.8:1:1:0:60:43.833:0.9962:0:0.1 0/1:255:3:2,1:73,179:0.0118:2,2:13.3:1:26.7:1:0.20762:4.87:60:6:0.0118:0:1 -11 108205865 . T C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11678;SOR=Inf;LSEQ=TCCCTTCTCTGGCTTAGCCC;RSEQ=TAGAGTTTTAGTGATGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:58,193:0:2,0:22.7:1:30:1:1:0:60:40.833:1:0:0.1 0/1:241:3:1,2:62,176:0.0124:2,2:24:1:25.3:1:1:1.42:60:2:0.0085:0:1.3 -11 108205919 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07542;SOR=Inf;LSEQ=TTTTCTTTCTGCTTTATTTG;RSEQ=GATTTTGTCTTTATTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:1,81:0:1,0:25:1:31.2:1:1:0:60:40:1:0:0.1 0/1:61:3:0,3:1,57:0.0492:1,0:23:1:31.3:1:1:0:60:6:0.05:0:1 -11 108206747 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1974;SOR=Inf;LSEQ=TAAAAGATGCCATTTGGTTG;RSEQ=GTGAAGTGGCTCATGCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:19,193:0:2,0:23:1:31.3:1:1:0:60:105:1:0:0 0/1:170:2:1,1:17,151:0.0118:2,2:13.5:1:27.5:1:0.20111:8.66:60:4:0.0118:0:1 -11 108206868 . TA T 74 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.27249;SOR=0;LSEQ=ACCCCATCTTGACAAAAAGT;RSEQ=AAAAAAAAAAAAAAGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:21.7:1:29:1:1:0:60:12:0.3333:0.0556:0.5 0/0:5:0:0,0:1,4:0:2,0:20.8:1:28.8:1:1:0:60:10:1:0:0.2 -11 108213851 . GA G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50517;SOR=0;LSEQ=GAGAAATATTAATACAACTT;RSEQ=AAAAAAATGCTTTGCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:2,0:79,1:0.0244:1,0:31.5:1:34:0:1:0:60:4:0.025:0:0 0/0:63:0:0,0:63,0:0:1,0:24:1:29:1:1:0:60:126:1:0:0 -11 108218196 . T C 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=AATATAAGAGACAGATAAAT;RSEQ=GAAGCAGTAAATATTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:77:0,77:0,0:1:0,1:21.5:1:30.1:1:1:0:60:76:1:0:1.1 1/1:54:44:0,44:1,9:0.8148:2,1:23.8:1:30.5:1:0.18519:0:60:88:0.8148:0:1 -11 108224677 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20376;SOR=Inf;LSEQ=CATGGGCTGGGCATGGTTCT;RSEQ=TGCACCTGTAATCCCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:10,117:0:2,0:21.3:1:30.4:1:1:0:60:126:1:0:0.7 0/1:105:2:1,1:7,96:0.019:2,2:18.5:1:30.5:1:0.14725:12.89:60:4:0.0192:0:1.5 -11 108224696 . TG CA 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03284;SOR=Inf;LSEQ=TTTGCACCTGTAATCCCAGC;RSEQ=CTCAAGAGGCTGAAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:1,86:0:1,0:22.7:1:28.5:1:1:0:60:174:1:0:1.1 0/1:66:4:0,4:1,61:0.0606:1,0:9.3:1:31.1:1:1:0:60:8:0.0606:0.0303:0.5 -11 108224697 . G A 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17384;SOR=0;LSEQ=TTGCACCTGTAATCCCAGCT;RSEQ=CTCAAGAGGCTGAAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:86:86:1,85:0,0:1:0,1:22.6:1:30.2:1:1:0:60:85:1:0:1.1 1/1:62:60:1,59:0,0:0.9677:0,1:23.8:1:30.2:1:1:0:60:120:1:0:1 -11 108224757 . A T 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00047;SOR=0;LSEQ=GTTTGAGTCCAGCCTAGGCA;RSEQ=TACAGCAAGACCCTGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:1,12:0,12:0.52:0,1:20.6:1:31.3:1:1:0:60:26:0.52:0:2 0/0:15:0:0,0:0,15:0:1,0:14.5:1:30.9:1:1:0:58.7:30:1:0:1.1 -11 108224791 . CACACAA C 92 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=21.000;MSILEN=2;SSF=0.00033;SOR=0;LSEQ=TGTATCTAAAAAAATACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:8:1,7:0,0:1:0,2:18.5:1:30.9:1:1:0:55.4:16:1:0.75:1.6 0/0:6:0:0,0:0,6:0:0,0:28:1:30.5:1:1:0:56.7:12:1:0:1.5 -11 108225473 . G A 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=0;LSEQ=ACTACACATGAGAGTATACA;RSEQ=ATAAAGATACGTTGACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:13:9,4:218,58:0.0447:2,2:18.7:1:30:1:0.48654:1.66714:60:26:0.045:0:2.1 0/0:266:0:0,0:192,73:0:2,0:22:1:31.5:1:1:0:60:87.333:1:0:0.8 -11 108225483 . C T 259 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01127;LSEQ=AGAGTATACAGATAAAGATA;RSEQ=GTTGACAACATTGGTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:356:354:270,84:1,1:0.9944:2,2:23.7:1:30.6:1:0.42103:3.20:60:353:0.9972:0:1.1 1/0:319:212:144,68:77,30:0.6646:2,2:23.5:1:29.7:1:0.52104:1.21131:60:52:0.6603:0:1.1 -11 108225628 . AT A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.03968;SOR=Inf;LSEQ=TATTTTATAAGGAAGACTTT;RSEQ=TTTTTTTCTTACCAGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:119,290:0:2,0:22.6:1:30.3:1:1:0:60:80.8:0.9975:0:0.5 0/1:332:4:1,3:98,230:0.012:2,2:16:1:29.5:1:1:1.27734:60:8:0.0121:0.006:1 -11 108225661 . A G 243 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCAGGTAGACTGTGTATCTC;RSEQ=TCAGGAAGTCACTGATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:206:206:33,173:0,0:1:0,2:22.3:1:31.7:1:1:0:60:205:1:0:1.1 1/0:149:119:23,96:5,25:0.7987:2,2:22.8:1:31:1:1:1.20:60:238:0.8041:0:1 -11 108235681 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09925;SOR=Inf;LSEQ=AGGAAACATGAAGTGTGCAT;RSEQ=ATGTTTGTTCCCCTCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:75,0:0:1,0:24.6:1:32.7:1:1:0:60:150:1:0:0.1 0/1:35:2:1,1:33,0:0.0571:1,2:37:1:29.5:1:0.05714:0:60:4:0.0571:0:1 -11 108235730 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50948;SOR=0;LSEQ=CATGTGACTGGCTTATTTGT;RSEQ=TGATACTGGTTCTACTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:136,18:0.0127:2,2:13.5:1:32:1:0.22945:7.38177:60:4:0.0131:0:1 0/0:116:0:0,0:96,20:0:2,0:22:1:28.1:1:1:0:60:115:1:0:0.1 -11 108235739 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50258;SOR=0;LSEQ=GGCTTATTTGTATGATACTG;RSEQ=TTCTACTGTTTCTAAGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:148,31:0.011:2,2:25:1:28.5:1:0.32314:4.7149:60:4:0.0114:0:1 0/0:151:0:0,0:116,34:0:2,0:21.7:1:31.1:1:1:0:60:300:1:0:0.1 -11 108235752 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20123;SOR=Inf;LSEQ=GATACTGGTTCTACTGTTTC;RSEQ=AAGTATGTGATTAAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:184,60:0:2,0:21.5:1:30:1:1:0:60:47.8:1:0:0.1 0/1:199:2:1,1:148,49:0.0101:2,2:19:1:33:1:0.44033:3.00013:60:4:0.0101:0:1 -11 108237839 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTCCTGCCTCAGCCTCC;RSEQ=GAGTAGCTGGGACTACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 110097796 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22509;SOR=Inf;LSEQ=TGCTAGACTTGAATTTCATA;RSEQ=ACTTTTCAATATATATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:123,98:0:2,0:25.4:1:31.5:1:1:0:60:109.5:1:0:1.2 0/1:200:2:1,1:108,90:0.01:2,2:10:0:31:1:1:1.1989:60:4:0.0102:0:1.5 -11 110097811 . A G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=0.1381;LSEQ=TCATAGACTTTTCAATATAT;RSEQ=TAAAAGGAAAGTGAGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:237:187:98,89:26,23:0.789:2,2:25:1:32.2:1:1:1.02651:60:374:0.789:0:1.7 0/1:218:74:36,38:75,68:0.3394:2,2:24.7:1:31.1:1:0.66781:1.1634:60:73:0.3395:0:1.8 -11 110097851 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13491;LSEQ=GAGATAGATATTCCCTTATG;RSEQ=TTCTGAAAAACACGATTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:178:70,108:15,25:0.8128:2,2:27.7:1:31.5:1:0.85981:1.08:60:88:0.8148:0:1.7 0/1:220:81:34,47:59,80:0.3682:2,2:27.5:1:31.2:1:1:1.0194:60:80:0.367:0:1.7 -11 110644532 . T C 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.65376;SOR=1.08491;LSEQ=GTGCCATATCTTCTCATAGG;RSEQ=GCAGGCAATAGCATTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:105:44,61:111,110:0.3221:2,2:24.8:1:30.8:1:0.19172:1.39751:60:104:0.325:0:1 0/1:244:83:39,44:78,83:0.3402:2,2:26.3:1:30.2:1:0.89264:1.05996:60:40.5:0.3418:0:1.3 -11 110665848 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16507;SOR=Inf;LSEQ=AAAAGTTCATAGCATTGAAA;RSEQ=AGATTGAGAAATTGTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:169,86:0:2,0:25.7:1:30.1:1:1:0:60:510:1:0:0.1 0/1:175:2:1,1:107,66:0.0114:2,2:17.5:1:30:1:1:1.61651:60:4:0.0115:0:1 -11 110665914 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.51337;LSEQ=GCACACACAGCTTAAAAGTT;RSEQ=TGAATCTGTGTAATTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:34:13,21:132,157:0.1053:2,2:27.4:1:31.7:1:0.46854:1.35689:60:33:0.1025:0:1.4 1/0:255:147:66,81:50,58:0.5765:2,2:27.1:1:30.9:1:0.89883:1.05774:60:48:0.5737:0:1.4 -11 110665974 . T C 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=12.42914;LSEQ=TAAATATAACACTTTTTTTC;RSEQ=CTTGAATGAAAAATTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:17:2,15:33,88:0.1232:2,2:23.1:1:31.5:1:0.23798:2.79565:60:34:0.1232:0:1.8 1/0:130:83:27,56:12,35:0.6385:2,2:20.5:1:30.3:1:0.43296:1.40:60:40.5:0.6378:0:1.7 -11 110697305 . C G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.28683;LSEQ=CCATGTGCTGGAATGCTGAT;RSEQ=CTTAACCATGTTGCCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:28:13,15:187,195:0.0683:2,2:21.6:1:31.4:1:0.84655:1.10623:60:27:0.0667:0:1.1 0/1:354:175:80,95:92,87:0.4944:2,2:24.7:1:31.4:1:0.28997:1.25493:60:57.333:0.4928:0:1.1 -11 110697444 . G A 121 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=13.26791;LSEQ=TTTAGCACTGTGTATCCACC;RSEQ=GTAGTCACTTCCCTCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:1,46:0.04:1,0:37:1:29.5:1:1:0:60:4:0.0426:0:1 0/1:47:17:2,15:1,29:0.3617:1,2:26.6:1:29.8:1:0.54394:3.75:60:16:0.3478:0:1.1 -11 111273583 . TTAA T 186 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=0;SOR=0.14767;LSEQ=TGTTTTCAGCCAAGACCAAA;RSEQ=TAATAATAATAATAATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:101:72:65,7:21,1:0.7129:1,2:25.4:1:30.3:1:0.67577:2.24554:60:23:0.7041:0.1287:0.1 0/1:64:17:16,1:38,7:0.2656:2,1:22.8:1:30:1:0.42666:2.91:60:34:0.2698:0.0781:0 -11 111273686 . T A 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08082;LSEQ=AAGAATTTCAATGGAACTGA;RSEQ=CACCGCTTTGCAGAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:398:364:189,175:14,19:0.9146:2,2:26.4:1:29.8:1:0.3639:1.46:60:181:0.9141:0:1.1 0/1:419:194:99,95:121,104:0.463:2,2:25.5:1:29.5:1:0.62397:1.11616:60:47.5:0.4612:0:1.1 -11 111734964 . C A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81392;LSEQ=AACCCACGAACTGGCCCGGC;RSEQ=CTCACGTGCACCATGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:30,22:0.037:2,2:12.5:1:26.5:1:1:1.35569:60:4:0.0377:0:1 0/1:66:2:1,1:41,23:0.0303:2,2:24.5:1:27.5:1:1:1.76614:60:4:0.0313:0:1 -11 111734995 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49728;SOR=Inf;LSEQ=CCATGTCTGGCTCCTCCAGC;RSEQ=TTGCCGCTATGAAGAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:39,36:0:2,0:26.4:1:30.5:1:1:0:60:74:1:0:0.2 0/1:80:2:1,1:41,37:0.025:2,2:47:1:30:1:1:1.10668:60:4:0.0253:0:1 -11 111956184 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09423;SOR=0;LSEQ=CATAACTCCATGAAGTGATG;RSEQ=ACCTAAAAGGAAAGAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:32,208:0.0123:2,2:31.3:1:28.3:1:0.35585:3.23:60:6:0.0123:0:1 0/0:291:0:0,0:58,233:0:2,0:21.8:1:31.7:1:1:0:60:144.5:1:0:0.1 -11 111956187 . C A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25287;SOR=Inf;LSEQ=AACTCCATGAAGTGATGCAC;RSEQ=TAAAAGGAAAGAAAAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:28,202:0:2,0:22.8:1:32.1:1:1:0:60:75.667:1:0:0.1 0/1:268:3:1,2:44,219:0.0112:2,2:13.3:1:24.7:1:0.42783:2.48:60:6:0.0113:0:1 -11 111956291 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19821;SOR=Inf;LSEQ=ACAAAACCATTCTTTAAATC;RSEQ=ACCACGGAGTCACTTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:2,36:0:2,0:16.8:1:31:1:1:0:60:76:1:0:0 0/1:31:2:0,2:0,29:0.0645:1,0:26.5:1:33:0:1:0:60:4:0.0645:0:1 -11 111956989 . C A 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAGTGGGGTGACGGCGA;RSEQ=ACCAAAACCCACAGTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:41.3:1:30.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 111957494 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21987;SOR=Inf;LSEQ=GACAGCTGTGTTTGCGCATG;RSEQ=GCGACGGGTGTGCACCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:157,1:0:1,0:22.2:1:32.4:1:1:0:60:51.667:1:0:0 0/1:140:2:2,0:134,4:0.0143:1,0:39:1:29.5:1:1:0:60:4:0.0146:0:1 -11 111957551 . G T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03222;SOR=Inf;LSEQ=CCCAGCATTTCCTCTTCCCT;RSEQ=TTTTCTTTCGTCGTCGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:499:0:0,0:375,124:0:2,0:22.7:1:31.9:1:1:0:60:123.75:1:0:0.1 0/1:557:6:1,5:378,173:0.0108:2,2:5.5:1:27.2:1:0.01421:10.87459:60:12:0.0109:0:1 -11 111957665 . G A 197 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=87.41396;LSEQ=GGAGGCTGAGTGCCGTTTGC;RSEQ=GTGCCCTAGGAGGCCGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1217:1:1,0:595,621:8e-04:2,0:1:0:28:0:0.48973:0:57:2:8e-04:0:1 0/1:1341:90:39,51:595,656:0.0671:2,2:26.7:1:30.4:1:0.44676:1.18594:60:89:0.0671:0:1.1 -11 111957819 . G T 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03045;SOR=0.56019;LSEQ=TCACAGCAATGACCACTGTA;RSEQ=TCTAGGGGTCCAGATGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:143:81:1,80:1,61:0.5664:1,1:25.2:1:30.6:1:1:1.30895:60:162:0.5745:0:1.1 0/1:109:46:0,46:2,61:0.422:1,1:22.9:1:29.4:1:0.50765:0:60:22:0.4112:0:1.2 -11 111959562 . A G 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATGTGTGTTTCTCACATC;RSEQ=ACTTTTATGAATCTGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:559:0:0,0:386,172:0:2,0:23.8:1:30:1:1:0:60:54.8:0.9982:0:0.1 0/1:609:32:24,8:388,187:0.0525:2,2:22.8:1:29.8:1:0.44068:1.45:60:64:0.0534:0:1.7 -11 111959625 . C T 178 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=28.36124;LSEQ=GCATCTCTCCACTGGACTAG;RSEQ=GAGAGGGTTGTCAGTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:986:2:0,2:508,476:0.002:2,0:2.5:1:29:1:0.23476:0:55:4:0.0021:0:1 0/1:1155:63:37,26:569,523:0.0545:2,2:28:1:29.8:1:0.36401:1.31:53.5:126:0.0552:0:1.4 -11 111959859 . T C 43 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.04774;SOR=Inf;LSEQ=TTGTTGAAAACTTTAAAATA;RSEQ=ATATAAAATATGTATATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:0,72:0:1,0:25.8:1:27.8:1:1:0:60:17:1:0:0 0/1:42:3:0,3:0,39:0.0714:1,0:39:1:27.3:1:1:0:60:2:0.0488:0:1 -11 111965497 . T C 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAATTTCACTGTGGTTTTT;RSEQ=ATTGATGTTATGATTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:731:0:0,0:482,249:0:2,0:24.2:1:29.1:1:1:0:60:65.455:1:0:0.1 0/1:756:35:23,12:455,265:0.0463:2,2:23.9:1:30.5:1:0.85842:1.12:60:70:0.0467:0:1.1 -11 113282222 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18398;SOR=Inf;LSEQ=CATGCCCTCTCACCCAGGGC;RSEQ=GCCACCTACCTGCTCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:138,89:0:2,0:26.8:1:30.6:1:1:0:60:226:1:0:0.4 0/1:171:2:1,1:97,72:0.0117:2,2:37:1:29.5:1:1:1.34483:60:4:0.0117:0:1 -11 113282275 . C A 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TGCACTTTTTCCAGGACCTC;RSEQ=TGCACAGGTGTGATATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:145,166:0:2,0:24.7:1:31.3:1:1:0:60:76.75:1:0:0.8 0/1:243:46:21,25:97,100:0.1893:2,2:24.6:1:27.9:1:0.74385:1.15408:60:14.333:0.1807:0:1.1 -11 113282295 . T G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10088;LSEQ=CTGCACAGGTGTGATATTTA;RSEQ=CCTGGAAGCAATGTGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:272:255:114,141:5,11:0.9375:2,2:26.3:1:32:1:0.43694:1.78:60:62.75:0.9401:0:1.2 1/0:218:131:58,73:37,50:0.6009:2,2:26.9:1:31.8:1:0.88918:1.07:60:262:0.6093:0:1.1 -11 113282319 . A G 33 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59699;SOR=2.34951;LSEQ=GGAAGCAATGTGTACATGGA;RSEQ=TGCCCTACAGGCACAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:1,0:81,145:0.0044:2,0:10:0:14:0:0.36123:0:60:0:0:0:7 0/1:194:2:1,1:80,112:0.0103:2,2:10:0:33.5:1:1:1.40:60:4:0.0105:0:2.5 -11 113282324 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20888;SOR=Inf;LSEQ=CAATGTGTACATGGAATGCC;RSEQ=TACAGGCACAGGAGGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:76,142:0:2,0:25.8:1:31.7:1:1:0:60:108:1:0:0.9 0/1:184:2:1,1:76,106:0.0109:2,2:16:0:31:0:1:1.39:60:4:0.0111:0:1.5 -11 113282396 . A G 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.023;SOR=Inf;LSEQ=GGCCACAGAGCTGAGCCCCT;RSEQ=TGGACTGCAGCAGAGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:6,77:0:2,0:25.7:1:31:1:1:0:60:82:1:0:0.1 0/1:34:3:0,3:6,25:0.0882:2,0:10:1:31.7:1:1:0:60:6:0.0882:0:1 -11 113283499 . G T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGGGACGGGTCGGGGAGA;RSEQ=TCAGCTGGTGGTGGCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:20:0:34:0:1:0:60:2:1:0:0 -11 113872373 . T A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACGTCAGCACTGCATCGC;RSEQ=GTCTGACAGCTCTCACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:18,14:0,0:1:0,2:24.3:1:29.8:1:1:0:60:31:1:0:1.3 1/1:20:20:14,6:0,0:1:0,2:20.4:1:30.1:1:1:0:60:40:1:0:1.2 -11 113872478 . C A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04862;SOR=5.88717;LSEQ=TCCCGTCTTGGCATCTGATT;RSEQ=TCAGAGGACCTGGAATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:2,5:0.3636:2,0:23.5:1:30.3:1:0.49091:0:60:8:0.4:0:1.8 1/0:14:11:1,10:0,3:0.7857:0,2:25:1:30.3:1:1:0:60:22:0.7857:0:1.1 -11 115127176 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTGCTGGCCCTGTTCT;RSEQ=AGTCACTGGAGTCAGCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:0.0556:2,2:21:0:30.5:1:1:1.26:60:4:0.0571:0:1 0/0:17:0:0,0:7,10:0:2,0:27.7:1:31.9:1:1:0:60:34:1:0:0 -11 116658823 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49491;SOR=0;LSEQ=AAAAAGCCGCAGACTCCGGG;RSEQ=ACTCGGGGAACAATGTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:0.0769:2,2:28.5:1:31:1:1:1:60:4:0.08:0:1.5 0/0:21:0:0,0:12,9:0:2,0:26.1:1:31.8:1:1:0:60:42:1:0:0.2 -11 116728931 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51163;SOR=0;LSEQ=GCGCTCTGTCATGCTCTGTC;RSEQ=CCCAAGGCTGGGAGCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:2,0:122,2:0.0159:1,0:10.5:1:31.5:1:1:0:60:4:0.016:0:1 0/0:90:0:0,0:85,5:0:2,0:26.9:1:30.4:1:1:0:60:89:1:0:0.1 -11 116729013 . TTGC T 86 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.2029;SOR=2.67337;LSEQ=TATTCTTGCTGTTGCTGCTG;RSEQ=TGCTGCTGCTGCCGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:3:2,1:223,206:0.0069:2,2:36:1:31:1:1:1.85:60:6:0.007:0:0 0/1:381:7:3,4:189,185:0.0184:2,2:30.1:1:30.9:1:0.72223:1.36106:60:14:0.0185:0:0.6 -11 117049938 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50529;SOR=0;LSEQ=GTCCTGTCTCCTGTCGCCGC;RSEQ=GCCGCCGCCACCACCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:0.0769:2,2:19.5:1:30:1:1:1:60:4:0.0833:0:1 0/0:18:0:0,0:10,8:0:2,0:28.3:1:29.2:1:1:0:60:17:1:0:0.2 -11 117226715 . G GAGCAGCAGC 87 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=10.000;MSILEN=3;SSF=0.00087;SOR=0.04884;LSEQ=TTGTCTGGGCCTGACTTGGA;RSEQ=AGCAGCAGCAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:4,3:13,5:0.28:2,2:29.4:1:31.3:1:0.63956:1.89552:60:14:0.28:0:0 0/1:56:1:1,0:23,30:0.0179:2,0:42:0:33.2:0:0.44444:0:50:2:0.0182:0:1 -11 117226726 . G GCAGCAA 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.10031;SOR=0;LSEQ=TGACTTGGAGAGCAGCAGCA;RSEQ=CAGCAGCAGCAACAGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:15,9:0.0769:2,2:37.5:1:32.6:1:1:1.63293:60:4:0.0769:0:0.5 0/0:55:0:0,0:23,32:0:2,0:29.1:1:31.9:1:1:0:59.8:26.5:1:0:0.3 -11 117226746 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAGCAGCAGCAACAGCAAC;RSEQ=TGGCCTCACACCTGGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:26.9:1:31.4:1:1:0:60:50:1:0:0 0/1:51:2:1,1:20,29:0.0392:2,2:18.5:1:28.5:1:1:1.44:60:4:0.04:0:1.5 -11 117226849 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=GGGTATGGCTCAGTCAGACT;RSEQ=GGGTCTCAGAGATCAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:40:1:32:0:1:0:60:4:0.2857:0:1 0/0:6:0:0,0:0,6:0:0,0:29.3:1:30.5:1:1:0:60:12:1:0:0.2 -11 118307175 . GC G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.51158;SOR=0;LSEQ=GCCCCCCCCTCCGCCTCCCC;RSEQ=CCCCCTGTGTTGTCGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:51,28:0.0247:2,2:23.5:1:30.5:1:1:1.80711:60:4:0.0253:0:0 0/0:57:0:0,0:37,20:0:2,0:18.7:1:30.2:1:1:0:60:56:1:0:0.8 -11 118307282 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.49474;SOR=Inf;LSEQ=GACCCGGGACCACCGGGGGC;RSEQ=GCGGCGGCGGGGGGCGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:9,36:0:2,0:16.6:1:31.1:1:1:0:60:90:1:0:0.1 0/1:47:2:1,1:16,29:0.0426:2,2:16:0:32.5:1:1:1.79:60:4:0.0435:0:1.5 -11 118307284 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.49412;SOR=Inf;LSEQ=CCCGGGACCACCGGGGGCGG;RSEQ=GGCGGCGGGGGGCGCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:9,34:0:2,0:15.3:1:30.3:1:1:0:60:86:1:0:0.1 0/1:43:2:1,1:14,27:0.0465:2,2:19:1:27.5:1:1:1.90:60:4:0.0465:0:1 -11 118307391 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.44582;LSEQ=TGGCGGCCCCGGGGCGCCCC;RSEQ=CTCCCCCCCGGCTGTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:20,4:0.04:2,0:1:0:27:0:0.2:0:60:2:0.0435:0:1 0/1:35:2:1,1:25,8:0.0571:2,2:6.5:1:28:1:0.45378:3.00458:60:4:0.0571:0:1 -11 118307409 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50904;SOR=Inf;LSEQ=CCCCTCCCCCCCGGCTGTGG;RSEQ=GGCCGCGGCGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:73,13:0:2,0:11.7:1:31.9:1:1:0:60:27.667:0.9881:0:0.2 0/1:118:2:1,1:93,23:0.0169:2,2:22:0:32:1:0.3668:3.97957:60:4:0.0174:0:1.5 -11 118307413 . CGCG C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.39166;SOR=1.50049;LSEQ=TCCCCCCCGGCTGTGGCGGC;RSEQ=GCGGCGGCGGCGGGAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:8:7,1:98,16:0.064:2,2:13.5:1:32.5:1:1:1.14:59.4:16:0.0645:0.016:0.3 0/1:161:15:10,5:119,27:0.0932:2,2:14.5:1:29.8:1:0.18098:2.19083:60:14:0.0892:0.0186:0.3 -11 118307703 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53179;SOR=0;LSEQ=GTCCGGGGTCTCGACCCTCT;RSEQ=CGGAGCCCCCTCCCCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:42,151:0.0103:2,2:10:0:31.5:1:0.39329:3.56:60:4:0.0104:0:1.5 0/0:115:0:0,0:34,80:0:2,0:23.1:1:31.6:1:1:0:60:113:0.9912:0:0.1 -11 118307774 . A T 53 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.31207;SOR=0;LSEQ=GGACCATCTCGGGGTCCCTG;RSEQ=CCCGGGGCGAATGGCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:2,42:0.0833:1,0:28:1:26.8:1:1:0:60:3:0.0667:0:1.5 0/0:20:0:0,0:0,20:0:1,0:28:1:29.8:1:1:0:60:40:1:0:0.1 -11 118308285 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCAAGCAGACCGATCCTCC;RSEQ=CCATCCCGCCCTACCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:7:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:28:1:1:0:60:4:1:0:1 -11 118339693 . TTTTA T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=5.000;MSILEN=4;SSF=0.50931;SOR=0;LSEQ=GGCTGATGAGCTAGACTTCT;RSEQ=TTTATTTATTTATTTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:0,2:0,94:0.0208:1,0:44.5:1:28.5:1:1:0:60:4:0.0208:0:0 0/0:70:0:0,0:1,69:0:1,0:22.5:1:30.3:1:1:0:60:140:1:0:0.1 -11 118341921 . A G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGATTGAAGAGCAGCGT;RSEQ=TTCAAATTTGTTCAAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:37.7:1:32.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 118342292 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47302;LSEQ=TTGAACTCAGTACAAAATGG;RSEQ=CAGTGCTAAGTTATATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:2,0:148,29:0.0112:2,0:44:1:29:1:1:0:60:4:0.0114:0:1 0/1:122:2:1,1:97,23:0.0164:2,2:17.5:1:28:1:0.35605:4.14982:60:4:0.0164:0:1 -11 118342294 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51924;SOR=0;LSEQ=GAACTCAGTACAAAATGGCC;RSEQ=GTGCTAAGTTATATTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:156,31:0.0106:2,2:17.5:1:28.5:1:0.31071:4.96899:60:4:0.0108:0:1 0/0:125:0:0,0:100,25:0:2,0:22.4:1:30:1:1:0:60:250:1:0:0.1 -11 118342310 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18934;SOR=Inf;LSEQ=GGCCAGTGCTAAGTTATATT;RSEQ=AGCTTAGTTAAAACCTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:190,56:0:2,0:23.6:1:31.3:1:1:0:60:122:1:0:0.1 0/1:190:2:1,1:145,43:0.0105:2,2:18:1:28.5:1:0.41047:3.34498:60:4:0.0106:0:1 -11 118342819 . T G 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=ACAGAAAGGATAAAGACCCC;RSEQ=TCGGGTCTCCTCATTAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:18:10,8:431,438:0.0202:2,2:25.1:1:31.3:1:0.64252:1.27:60:36:0.0206:0:1 0/0:710:0:0,0:347,361:0:2,0:23.9:1:30.1:1:1:0:60:63.364:0.9986:0:0.2 -11 118344493 . TAG T 85 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.20535;SOR=2.62903;LSEQ=AGCGTGGAGAAGGACAAGAG;RSEQ=AGAGAGAGACCGGGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:746:3:1,2:491,251:0.004:2,2:27:1:27.7:1:0.26736:3.90457:60:6:0.0041:0.0013:0.3 0/1:666:7:4,3:417,242:0.0105:2,2:25.9:1:30.4:1:0.71209:1.29182:60:14:0.0106:0:0.1 -11 118347812 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51722;SOR=0;LSEQ=GGTCCTCTGAAAAACAGATG;RSEQ=CAAGAGGGGATTAAATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:82,104:0.0106:2,2:16.5:1:28:1:1:1.27:60:4:0.0108:0:1 0/0:127:0:0,0:65,62:0:2,0:21.4:1:31.7:1:1:0:60:254:1:0:0.1 -11 118347839 . T C 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27211;SOR=0;LSEQ=GGGATTAAATACATGAGGAT;RSEQ=TTATTAGAAGAAATGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:123,115:0.0124:2,2:22.7:1:25:1:1:1.87:60:2:0.0085:0:1.7 0/0:168:0:0,0:97,71:0:2,0:21.9:1:29.6:1:1:0:60:83:1:0:0.1 -11 118347943 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50344;SOR=0;LSEQ=ACCCCCATGAAGGAGCAGGG;RSEQ=AAGGAAGGCAGAATCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:18,105:0.016:2,2:29:1:30.5:1:0.28194:5.70:60:4:0.0161:0:1 0/0:101:0:0,0:23,78:0:2,0:17.7:1:30.8:1:1:0:60:202:1:0:0 -11 118348712 . C T 81 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22096;SOR=2.38799;LSEQ=AATTGCTGGCTCAGAAGATG;RSEQ=TGAACCTCTTGCTCCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:598:3:0,3:376,219:0.005:2,0:1:0:21.7:1:0.05073:0:60:2:0.0034:0:1.3 0/1:588:7:3,4:362,219:0.0119:2,2:14.1:1:29:1:0.4354:2.20089:60:14:0.0121:0:1.1 -11 118350811 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14865;SOR=Inf;LSEQ=ATACAGATTCACTGATTGTT;RSEQ=CAGACAAAATGAACACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:201,49:0:2,0:25.7:1:32.4:1:1:0:60:82.333:1:0:0.1 0/1:158:2:1,1:118,38:0.0127:2,2:40:1:29:1:0.43393:3.07797:60:4:0.0127:0:1 -11 118351035 . CT C 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.52458;SOR=1.54548;LSEQ=ACACCCAGTAGAAGAGAATA;RSEQ=TTTTTTTTTAAAGTACAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:5:1,4:19,159:0.0273:2,2:24:1:31.4:1:0.44317:2.08:60:10:0.0282:0.0109:0.6 0/1:120:5:1,4:22,91:0.0417:2,2:18:1:31:1:1:1.03:60:10:0.0417:0.0083:0.2 -11 118351046 . A T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.6854;LSEQ=AAGAGAATACTTTTTTTTTT;RSEQ=AAGTACAACTCTTTCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:5:0,5:11,131:0.034:2,0:14.6:1:30:1:1:0:60:10:0.034:0:3 0/1:85:2:0,2:8,75:0.0235:2,0:21:1:29.5:1:1:0:60:4:0.0238:0:1.5 -11 118354750 . T A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.03254;SOR=Inf;LSEQ=AAGCAAGACCCAGTCTCTTT;RSEQ=AAAAAAAAATTCAAAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,0:0:1,0:18.1:1:30.5:1:1:0:60:47:0.9792:0:0.1 0/1:24:3:3,0:21,0:0.125:1,0:18:1:29.7:1:1:0:60:6:0.125:0:1 -11 118355063 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23437;SOR=Inf;LSEQ=GTGATCATAAAGTATATTGA;RSEQ=TGTCAAAGACTTTAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:37,165:0:2,0:22:1:32.1:1:1:0:60:66.333:1:0:0.1 0/1:191:2:1,1:43,146:0.0105:2,2:39:1:30:1:0.4086:3.37:60:4:0.0106:0:1 -11 118355642 . A C 185 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCTTGACTTCTGTTCCTAT;RSEQ=ACACCCAGGGTGGTTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1008:0:0,0:481,525:0:2,0:25.9:1:28.8:1:1:0:60:58.176:0.998:0:0.1 0/1:839:63:31,32:378,396:0.0751:2,2:25.2:1:31.1:1:1:1.01:60:62:0.075:0:1.1 -11 118355770 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51279;SOR=0;LSEQ=AATTACTATAGTCTGTTTTG;RSEQ=TGGTATTTAGCAGGTACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:0,2:5,147:0.013:1,0:17.5:1:33.5:1:1:0:60:4:0.013:0:1 0/0:109:0:0,0:8,101:0:2,0:24.6:1:30.5:1:1:0:60:108:1:0:0 -11 118359161 . G A 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07824;SOR=0;LSEQ=AGTACTCTGAATCTCCCGCA;RSEQ=TGTCCAATACTGTACTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:27,0:0,0:1:0,1:19.3:1:31.1:1:1:0:60:54:1:0:1 1/1:11:9:9,0:2,0:0.8182:0,0:22.9:1:29.8:1:1:0:60:18:0.8182:0:1.1 -11 118359261 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25531;SOR=0;LSEQ=AACCCAAAGTATATAAGAAG;RSEQ=GTATGGTTGATTATGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:2,1:135,11:0.0201:2,2:18.3:1:30:1:0.22406:5.99104:60:6:0.0203:0:1 0/0:121:0:0,0:109,12:0:2,0:24.5:1:31.2:1:1:0:60:120:1:0:0.1 -11 118360465 . G T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01842;SOR=Inf;LSEQ=GTAATAGGTGTTGGGTGAAG;RSEQ=TAATATGATGCTTATCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:357,98:0:2,0:23.2:1:31.4:1:1:0:60:64:1:0:0.1 0/1:374:5:3,2:276,93:0.0134:2,2:12.8:1:25:1:0.6046:1.97445:60:4:0.0109:0:1 -11 118360822 . A T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0342;SOR=Inf;LSEQ=AAAACAAGAAATTCCTATTG;RSEQ=ATTTCTTTTCTTCTTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:205,74:0:2,0:21.7:1:29.9:1:1:0:60:68.75:1:0:0.1 0/1:212:4:1,3:158,50:0.0189:2,2:8.5:1:23.5:1:0.04911:9.35479:60:8:0.0189:0:1.3 -11 118361882 . C T 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3732;SOR=3.91258;LSEQ=CACGGGTATGTGAGCCAAAG;RSEQ=ACTGCTGTAAACTTTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:1:0,1:229,67:0.0034:2,0:1:0:12:0:0.22896:0:60:0:0:0:1 0/1:306:4:1,3:202,100:0.0131:2,2:11.3:1:26.8:1:0.11257:6.02256:60:8:0.0133:0:1 -11 118362385 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18995;SOR=Inf;LSEQ=ATGGCTTTATAGTAAGTTCA;RSEQ=TGGAATAGTTTCCTCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:185,37:0:2,0:22.6:1:31.9:1:1:0:60:54.5:1:0:1 0/1:172:2:1,1:143,27:0.0116:2,2:8.5:1:28.5:1:0.29988:5.21913:60:4:0.0118:0:1.5 -11 118362393 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1911;SOR=Inf;LSEQ=ATAGTAAGTTCAGTGGAATA;RSEQ=TTTCCTCTTCTTCCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:207,46:0:2,0:22.6:1:32.2:1:1:0:60:125.5:1:0:1 0/1:197:2:1,1:160,35:0.0102:2,2:12.5:1:28:1:0.33285:4.52157:60:4:0.0103:0:2 -11 118362414 . T C 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TTTCCTCTTCTTCCTCTCTC;RSEQ=CATTCTTCAGAGGACCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:371:371:290,81:0,0:1:0,2:23.2:1:31.1:1:1:0:60:60.833:1:0:1.1 1/1:300:271:203,68:20,8:0.9033:2,2:24.1:1:30:1:0.65441:1.19:60:44.167:0.9075:0:1.1 -11 118362869 . T C 102 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAATGAGAAATTTGGACTT;RSEQ=ATACTCTGAAGGTGATAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:23.2:1:29.6:1:1:0:60:10:1:0:1.2 1/1:1:1:0,1:0,0:1:0,0:22:0:34:0:1:0:60:2:1:0:1 -11 118363418 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAAAAAGAAGAAGAACC;RSEQ=CATGGATCACTTTACCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:27.7:1:31:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 118363424 . A C 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAGAAGAACCGCATGG;RSEQ=TCACTTTACCTCAGAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:20:1:28:1:1:0:60:3:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 118364071 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5042;SOR=0;LSEQ=ATATTTAGAAATGTCACGTG;RSEQ=CTTTAGATACCTAAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:3,77:0.0244:1,0:7:1:32.5:1:1:0:60:4:0.0244:0:1 0/0:64:0:0,0:0,64:0:1,0:23.2:1:32.4:1:1:0:60:63:1:0:0.1 -11 118365162 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51975;SOR=0;LSEQ=AATGCTTACCTATAAGTAAT;RSEQ=ACCCTGTGAATACAATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:41,135:0.0112:2,2:33.5:1:31.5:1:0.41725:3.27:60:4:0.0114:0:1 0/0:117:0:0,0:15,102:0:2,0:21.3:1:28.8:1:1:0:60:116:1:0:0.2 -11 118365163 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51834;SOR=0;LSEQ=ATGCTTACCTATAAGTAATT;RSEQ=CCCTGTGAATACAATGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:41,131:0.0115:2,2:23.5:1:31.5:1:0.42555:3.17:60:4:0.0115:0:1 0/0:116:0:0,0:15,101:0:2,0:20.9:1:30.1:1:1:0:60:232:1:0:0.2 -11 118365168 . G A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TACCTATAAGTAATTACCCT;RSEQ=TGAATACAATGAACTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:38,125:0:2,0:24.2:1:32:1:1:0:60:162:1:0:0.1 0/1:103:11:1,10:14,78:0.1068:2,2:15.1:1:30.7:1:1:1.78626:60:22:0.1078:0:1.1 -11 118365263 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CCCTGATTCTTTGAGAGGAA;RSEQ=TTGGTGAGGTTGCCAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:83,20:0:2,0:25.7:1:31.5:1:1:0:60:19.6:1:0:0.2 0/1:55:9:6,3:39,7:0.1636:2,2:34.1:1:31.6:1:0.33983:2.72289:60:18:0.1667:0:1 -11 118365319 . C G 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27257;SOR=0;LSEQ=TGGTGGCCTGAAATTATCCT;RSEQ=GTATTAACAGAGAAGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:2,1:187,49:0.0126:2,2:6.7:1:25.7:1:0.50712:1.90201:60:2:0.0086:0:1 0/0:166:0:0,0:127,38:0:2,0:22.7:1:30.8:1:1:0:60:81.5:1:0:0.1 -11 118366327 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50933;SOR=0;LSEQ=GTGAATGGCTCCTACATGGG;RSEQ=CAACAGGTGATATCAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:146,10:0.0127:2,2:13:1:25.5:1:0.13481:13.96849:60:4:0.0131:0:1 0/0:117:0:0,0:103,14:0:2,0:20:1:30.6:1:1:0:60:38:1:0:0.1 -11 118366362 . T A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11095;SOR=Inf;LSEQ=AAGAATTTATTTTATACAGT;RSEQ=CTAGGTATACTGTAGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:239,81:0:2,0:23.6:1:30.2:1:1:0:60:105.667:1:0:0.1 0/1:297:3:2,1:215,78:0.0101:2,2:14.7:1:22.3:1:1:1.37661:60:2:0.0069:0:1.7 -11 118367110 . G A 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03488;SOR=Inf;LSEQ=CTTTGCAACACAGGGCCCTA;RSEQ=TTAATACATACTCCAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:125,350:0:2,0:24.2:1:31.7:1:1:0:60:58.375:1:0:0.1 0/1:363:4:3,1:102,257:0.011:2,2:8.3:1:26.3:1:0.07469:7.51:60:8:0.0111:0:1 -11 118368665 . A G 161 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=42.46474;LSEQ=TTATAGGATGCTGGTCGTTT;RSEQ=CTATATATTGGCCAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:1:1,0:370,230:0.0017:2,0:44:0:14:0:1:0:60:0:0:0:3 0/1:528:35:21,14:293,198:0.0663:2,2:22.1:1:31.5:1:1:1.01:60:34:0.0654:0:1.1 -11 118368822 . T G 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGTAAATTTTATGAAAGAGA;RSEQ=TCCCTCTCAGTTTCCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:26,174:0:2,0:23.4:1:30:1:1:0:60:32.333:1:0:0.1 0/1:185:16:4,12:33,135:0.0865:2,2:26.2:1:31.4:1:0.53308:1.36:60:32:0.0879:0:1 -11 118370615 . C G 125 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=ACTGTGAAGATAAGCTCTTT;RSEQ=CTATTGGATATCAGTAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:15:8,7:208,288:0.0293:2,2:28.2:1:32.1:1:0.43201:1.58:60:30:0.0299:0:1.1 0/0:530:0:0,0:229,301:0:2,0:24.9:1:30.7:1:1:0:60:52:1:0:0.1 -11 118372187 . G GA 60 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.41321;SOR=2.17144;LSEQ=GAGTGAGACTGTGTCTCAAA;RSEQ=AAAAAAAAAAAAAGATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:3,1:16,1:0.1667:1,2:24.5:1:30:1:0.35238:4.76102:60:8:0.1818:0.0417:0.3 0/1:13:4:2,2:8,1:0.3077:2,2:17.5:1:30:1:0.2028:6.5151:60:8:0.3333:0.0769:0.3 -11 118372452 . C G 220 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCATCACCAGACCGACCT;RSEQ=CTCATTCACAAACCTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1401:119:69,50:677,600:0.0849:2,2:25.4:1:32:1:0.33682:1.22:60:118:0.0856:0:1.1 0/0:1404:0:0,0:737,664:0:2,0:24.8:1:30.9:1:1:0:60:86.563:0.9978:0:0.2 -11 118373018 . AAT A 121 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.66454;SOR=1.22869;LSEQ=TAGATTTCCAGTTACCTATA;RSEQ=ATATATATATATAGTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:15:15,0:159,7:0.0829:1,1:28.1:1:31.2:1:1:0:60:30:0.0838:0.0055:0.1 0/1:100:10:10,0:87,2:0.1:1,0:26.3:1:31.5:1:1:0:60:20:0.1031:0:0 -11 118373861 . C T 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=45.48845;LSEQ=AACAGATCATCCATTATCAA;RSEQ=GAACATATGGGATCTAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:636:1:0,1:334,301:0.0016:2,0:1:0:25:0:0.47484:0:60:2:0.0016:0:1 0/1:552:37:22,15:278,237:0.067:2,2:25.4:1:30:1:0.60922:1.25:60:74:0.0674:0:1 -11 118377394 . T A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26521;SOR=0;LSEQ=AATACTAGCTAGGCTGGGTC;RSEQ=GTGGGATTTCATGTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:36,230:0.0112:2,2:12:1:31.3:1:0.05325:12.57:60:6:0.0113:0:1.3 0/0:199:0:0,0:29,170:0:2,0:21.8:1:30:1:1:0:60:198:1:0:0.1 -11 118379970 . T A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10254;SOR=Inf;LSEQ=TATCAATGCTAAAAGGATTA;RSEQ=GAGAATCACCCACTTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:80,253:0:2,0:22.4:1:30:1:1:0:60:36:1:0:0.2 0/1:294:3:2,1:77,214:0.0102:2,2:10:1:24:1:0.17687:5.52:60:2:0.0069:0:2.7 -11 118380007 . T TA 114 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11392;SOR=2.12134;LSEQ=ACCTACTTATTTTCTACATT;RSEQ=AAAAAAAAAAATCTAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:9:0,9:9,126:0.0616:2,0:31.8:1:31:1:1:0:60:18:0.0643:0:1.6 0/1:106:13:1,12:5,87:0.1226:2,1:24.5:1:31:1:0.55692:1.44:60:26:0.13:0:0.4 -11 118380850 . A G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05193;SOR=Inf;LSEQ=GAAGGTGAGTGGATTAAATC;RSEQ=GGTTGACCCATCAGCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:116,271:0:2,0:23.8:1:30.7:1:1:0:60:95.75:1:0:0.1 0/1:355:4:2,2:119,232:0.0113:2,2:16.5:1:31.3:1:0.60794:1.95:60:8:0.0115:0:1.3 -11 118382820 . GA G 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.52828;LSEQ=TAAGGCAGAGTTGATTCTGT;RSEQ=AAAAAAAATCAGTTAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:3:0,3:21,172:0.0153:2,0:23.7:1:33:0:1:0:60:6:0.0156:0:0 0/0:123:1:0,1:14,108:0.0081:2,0:38:0:32:0:1:0:60:2:0.0081:0:0 -11 118390255 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12684;SOR=Inf;LSEQ=CCTCTGGCAGAGTGACTATA;RSEQ=CATAGGCATTTCTGTAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:220,34:0:2,0:24.2:1:32:1:1:0:60:41.333:1:0:0.1 0/1:141:2:1,1:123,16:0.0142:2,2:32:1:28:1:0.22736:7.48819:60:4:0.0145:0:1 -11 118390798 . G A 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.14272;LSEQ=CGGTAAGTCTTGAGTGGGGA;RSEQ=CAGTCATTAGAAACTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:2:1,1:232,446:0.0029:2,2:16.5:1:29:1:1:1.92:60:4:0.003:0:1 0/1:642:24:10,14:238,380:0.0374:2,2:28.6:1:29.6:1:0.83166:1.14:60:48:0.0378:0:1.5 -11 118391365 . CA C 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.3055;SOR=4.20628;LSEQ=GACAGAGCGAAACTCCATCT;RSEQ=AAAAAAAAAGGGGGGCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:25,1:0.037:1,0:23:0:33:0:1:0:60:2:0.0385:0:1 0/1:21:3:3,0:17,1:0.1429:1,0:10.3:1:30.9:1:1:0:60:6:0.15:0.0476:0 -11 118391375 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=0.05454;LSEQ=AACTCCATCTCAAAAAAAAA;RSEQ=GGGGGGCGCTCATTTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:32:31,1:0,0:0.9143:0,1:18.5:1:32.1:1:1:0:59.6:31:0.9394:0:1.1 0/1:31:11:11,0:18,1:0.3548:1,0:15.5:1:31.3:1:1:0:60:22:0.3793:0:1 -11 118391456 . T A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49853;SOR=0;LSEQ=TTGTCTCTAGGAACCTTCGA;RSEQ=TCAAGACTCAAAACATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:123,46:0.0117:2,2:7:0:31.5:1:0.47534:2.65605:60:4:0.0118:0:1.5 0/0:170:0:0,0:122,48:0:2,0:24.2:1:29.5:1:1:0:60:41.5:1:0:0.1 -11 118392935 . C A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07569;SOR=Inf;LSEQ=TGCAAGGAGGCGGGGCCATC;RSEQ=AAAGCAACGCTGAAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:73,253:0:2,0:23.3:1:31.8:1:1:0:60:64.2:1:0:0.1 0/1:240:3:1,2:61,176:0.0125:2,2:28.7:1:23:1:1:1.44:60:2:0.0085:0:2.7 -11 118432275 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20964;SOR=Inf;LSEQ=CAAGCTCCCTCAGAGCTCAG;RSEQ=AGCAGGCTGCTGAGAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:8,21:0:2,0:24.6:1:31.1:1:1:0:60:58:1:0:0.1 0/1:25:2:1,1:8,15:0.08:2,2:30.5:1:30.5:1:1:1.83:60:4:0.08:0:2 -11 118432279 . A G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03845;SOR=Inf;LSEQ=CTCCCTCAGAGCTCAGGAGC;RSEQ=GGCTGCTGAGAGCTAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:6,21:0:2,0:25.4:1:31.3:1:1:0:60:54:1:0:0.1 0/1:23:4:2,2:6,13:0.1739:2,2:22.3:1:31.8:1:0.58893:2.09:60:8:0.1739:0:1.5 -11 118432350 . G GA 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGATAAACATATGGACA;RSEQ=AAAAAAAAAAGATTTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:0,9:0.1818:0,0:18.5:1:32:0:1:0:60:4:0.1818:0:0 0/0:3:0:0,0:1,2:0:2,0:19.3:1:31.7:1:1:0:60:6:1:0:0.7 -11 119077003 . C T 71 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCCTCCGCCCGGATAGCCGG;RSEQ=GGCGGCGGCGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:2,1:0.6667:2,2:29.3:1:27.8:1:1:2.24:60:5:0.625:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 119077091 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07006;SOR=Inf;LSEQ=TCGCTCGCAGTCGAGCCGAG;RSEQ=CGGCGGACCCGCCTGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:230,58:0:2,0:25.8:1:31.6:1:1:0:60:47:1:0:0.2 0/1:203:3:1,2:157,43:0.0148:2,2:13.3:1:25.3:1:0.1242:7.20733:60:6:0.0149:0:1.3 -11 119077232 . GCAC G 166 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=1;SOR=1.02757;LSEQ=ATGAAGGACGCCTTCCAGCC;RSEQ=CACCACCACCACCACCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:904:35:20,15:463,402:0.0387:2,2:27.5:1:31.7:1:0.73156:1.16:59.9:70:0.0396:0.0033:0.2 0/1:931:37:18,19:474,414:0.0397:2,2:29.2:1:31.9:1:0.61624:1.20828:59.9:74:0.0407:0.0064:0.1 -11 119140830 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTTTAGTGTAATAGTAT;RSEQ=TATATCATCTGTATCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29:1:1:0:60:4:1:0:1.5 -11 119144148 . G T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTATTTTTCTTTTCTT;RSEQ=TTTTGCAGCAAGGTTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:19.7:1:30.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 119144402 . A G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCCAAAGGCATGCACC;RSEQ=TGGCTCCTGGTCCCCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:29,1:0,0:1:0,1:22.2:1:29.4:1:1:0:60:60:1:0:1 1/1:13:13:12,1:0,0:1:0,1:25.5:1:30.2:1:1:0:60:26:1:0:1.2 -11 119144809 . A T 55 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.80112;LSEQ=AGCTTTTTTTTTTTTTTTTT;RSEQ=AATAACATTTGGGGTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:4:1,3:6,120:0.0305:1,2:15.3:1:27.8:1:0.20075:6.46:56.3:8:0.031:0:2.3 0/1:122:3:1,2:8,109:0.0246:2,2:12:1:27.7:1:0.21017:6.59:56.7:6:0.0252:0:2 -11 119144869 . CA C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50128;SOR=0;LSEQ=ATTCATTTTAGGAACTATGC;RSEQ=AAAAAAAGATTAAAACTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:0,37:0.0513:1,0:32:1:32:0:1:0:60:4:0.0513:0:0 0/0:30:0:0,0:1,29:0:1,0:27:1:30.4:1:1:0:60:60:1:0:0.5 -11 119145274 . A G 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TTTCAGTTTGTTGTTGTTCA;RSEQ=CCCCACTACTGTTAATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:11,2:6,0:0.6842:0,2:29.2:1:29.3:1:1:0:60:5.5:0.6471:0:1.8 0/0:2:0:0,0:2,0:0:0,0:15.5:1:30.5:1:1:0:60:4:1:0:0 -11 119145463 . GT G 130 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.37569;SOR=1.41126;LSEQ=ATGAACTGAGAGTTGGTGTT;RSEQ=TTTTTTTTTTTCTCATTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:16:14,2:244,49:0.0506:2,2:21:1:32:1:1:1.40:60:32:0.0506:0.0095:0.6 0/1:257:18:13,5:189,49:0.07:2,2:19.6:1:31.2:1:0.54771:1.48101:59.4:36:0.0717:0.0233:0.3 -11 119145705 . G GT 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.16317;LSEQ=GATTTATTCTTCTGAATTTC;RSEQ=TTATCTTGAGACTTCTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:260:155:29,126:21,83:0.5962:2,2:20.8:1:29.8:1:0.87256:1.09889:60:154:0.5969:0.1423:0 0/1:279:54:11,43:54,171:0.1935:2,2:25.7:1:29.6:1:0.72016:1.23359:60:108:0.1949:0.0323:0.1 -11 119146659 . G C 269 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTTGCCTTGCCTTCCACC;RSEQ=TAATACCAGCATAATCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:434:434:343,91:0,0:1:0,2:25.2:1:30.8:1:1:0:60:35.167:1:0:1.1 1/0:387:217:160,57:122,47:0.5607:2,2:24.1:1:29.7:1:0.8172:1.08:60:35.167:0.5538:0:1.1 -11 119148322 . AT A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.7544;SOR=1.35719;LSEQ=AAGTATTATTTTTTGGAAGT;RSEQ=TTTTTTTTTGAAGTAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:7:7,0:97,2:0.066:1,0:26.9:1:31.1:1:1:0:60:14:0.066:0:0 0/1:57:5:5,0:50,2:0.0877:1,0:20.2:1:31.2:1:1:0:60:10:0.0877:0:0.2 -11 119148573 . G T 269 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00163;LSEQ=AGGTGAGTTTTGTTTCACAT;RSEQ=ATAACCATATCACTGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:639:638:231,407:0,0:0.9984:0,2:25.4:1:28.9:1:1:0:60:211.667:0.9984:0:1.1 1/0:598:306:108,198:107,183:0.5117:2,2:23.4:1:28.7:1:0.73295:1.07182:60:612:0.5126:0:1.1 -11 119148851 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17414;SOR=Inf;LSEQ=AGTTATTTATTCAACTAATA;RSEQ=TCTTTTAATTTTTTTTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:208,58:0:2,0:22.8:1:32.3:1:1:0:60:87.667:1:0:0.1 0/1:191:2:1,1:144,45:0.0105:2,2:26:0:31.5:1:0.42463:3.17599:60:4:0.0106:0:1 -11 119148859 . AT A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.41054;SOR=2.64693;LSEQ=ATTCAACTAATAGTCTTTTA;RSEQ=TTTTTTTAATCAAAGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:2:2,0:220,77:0.0067:2,0:31:1:32.5:1:1:0:60:4:0.0067:0:0 0/1:228:4:3,1:167,57:0.0175:2,2:28.5:1:28.8:1:1:1.02:58.8:8:0.0175:0.0044:0.3 -11 119149126 . CT C 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.00271;LSEQ=GGGTTAGGTTTAAACTTTTA;RSEQ=TTTTTTTGATCTCTAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:4:1,3:179,66:0.016:2,2:22.8:1:33.8:1:0.06585:8.05645:60:8:0.0161:0:0 0/1:187:3:3,0:135,49:0.016:2,0:20:1:31:1:0.56809:0:60:6:0.0163:0:0 -11 119149355 . TATG T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.39051;SOR=0.64869;LSEQ=AGGGAGCTCCCTCCCCAAAT;RSEQ=ATGATGATGATGATGAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:14:5,9:161,294:0.0299:2,2:26.6:1:30.6:1:1:1.01:60:28:0.0306:0.0064:0 0/1:409:8:2,6:139,261:0.0196:2,2:22.3:1:27.1:1:0.71981:1.59601:58.1:7:0.0172:0.0049:0.6 -11 119149481 . T A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.27746;SOR=0;LSEQ=TGAGTTGTCTTCTAAAGCCG;RSEQ=AAAACACTTAACGATATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:2,1:27,141:0.0175:2,2:19.3:1:27.7:1:0.07487:10.22:60:6:0.0176:0:1.3 0/0:114:0:0,0:27,87:0:2,0:21:1:28.2:1:1:0:60:56:1:0:0.1 -11 119155618 . G T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.15376;LSEQ=TGCCATCCACAGCTTTAGGA;RSEQ=AGTTGAAAGATGCCATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:296:192:164,28:88,16:0.6486:2,2:23.3:1:30.7:1:0.86525:1.06:60:191:0.6497:0:1.1 0/1:245:54:48,6:155,36:0.2204:2,2:25.5:1:29.6:1:0.2228:1.85:60:108:0.2231:0:1 -11 119155649 . G C 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCATTTCCCCAAACGAAA;RSEQ=TAATCTGTTAAATTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:572:0:0,0:407,164:0:2,0:23:1:31.8:1:1:0:60:62.444:0.9982:0:0.4 0/1:540:45:30,15:339,155:0.0833:2,2:24.5:1:30.1:1:0.86705:1.09336:60:21.5:0.081:0:1.3 -11 119156346 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50665;SOR=0;LSEQ=CCAGGCACAGTGGCTCATGT;RSEQ=TGTAATCCCAGCAATTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:15,130:0.0136:2,2:30.5:1:30:0:0.2065:8.42:60:4:0.0139:0:1 0/0:113:0:0,0:17,96:0:2,0:22.9:1:31.8:1:1:0:60:226:1:0:0.1 -11 119157009 . C CA 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGTGAAACTTTGTCT;RSEQ=AAAAAAAAAATGTGTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:30.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 119167825 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12987;SOR=Inf;LSEQ=ACCTGCTTGGCTTGCTACCT;RSEQ=CACATACTGTTATCCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:18,187:0:2,0:23.5:1:32.1:1:1:0:60:50.25:1:0:0 0/1:116:2:1,1:8,106:0.0172:2,2:7.5:1:24.5:1:0.14978:12.55:60:4:0.0174:0:1 -11 119168007 . T A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17063;SOR=Inf;LSEQ=TTAACATTTATTAGTGATAT;RSEQ=GGCAAAACGAGAAGATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:160,24:0:2,0:22.3:1:30.5:1:1:0:60:183:1:0:0.1 0/1:130:2:1,1:109,19:0.0154:2,2:29:0:28.5:1:0.28503:5.61724:60:4:0.0154:0:1 -11 119168330 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16131;SOR=Inf;LSEQ=GGTACGTGCCACCATGCCCG;RSEQ=CTAATTTTTGTATTTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:0,35:0:1,0:23.5:1:31.2:1:1:0:59.5:16.5:1:0:0.5 0/1:24:2:0,2:1,21:0.0833:1,0:17:1:30.5:1:1:0:60:4:0.0833:0:1 -11 119168370 . G A 110 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57609;SOR=0.39061;LSEQ=TAGAGACGGGGTTTCACTAT;RSEQ=TTGGCCAGGCTGGCCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:0,12:0,8:0.5714:0,0:22.7:1:30.8:1:1:0:58.5:24:0.5714:0:1 0/1:3:1:0,1:0,1:0.3333:0,0:47:0:29:0:1:0:60:2:0.3333:0:1 -11 119169032 . C T 99 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00169;SOR=14.07352;LSEQ=ATGTATTAGAAGATGAAGTG;RSEQ=GTCAGAAGAAGATAACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:0,1:305,126:0.0023:2,0:1:0:29:0:0.29398:0:60:2:0.0023:0:1 0/1:347:11:9,2:221,115:0.0317:2,2:22.8:1:28.8:1:0.346:2.34:60:10:0.0293:0:1.1 -11 119170148 . G T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09668;SOR=Inf;LSEQ=ATTAGCACATTTTTATTGCT;RSEQ=TTGTTAAATGAGGATTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:169,9:0:2,0:21.1:1:32.4:1:1:0:60:177:1:0:0 0/1:152:3:1,2:138,11:0.0197:2,2:9:1:21.3:1:0.01939:23.76087:60:2:0.0134:0:1.7 -11 119342538 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTACCCGGCAGGACTCAGG;RSEQ=CACCCAGCCATACCCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:29.5:1:1:0:60:4:1:0:1 -11 119343746 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1705;SOR=Inf;LSEQ=CGTGCTGGTGGTGTCGGGAG;RSEQ=GAAGGCAGGGAACAAGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:23,36:0:2,0:25.6:1:30.4:1:1:0:60:58:1:0:0.2 0/1:42:2:1,1:13,27:0.0476:2,2:33.5:1:29.5:1:1:2.04:60:4:0.0476:0:1 -11 119841508 . A G 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACTGCAGTGCCGCTGGA;RSEQ=TCAGCGCGGAGCAGTTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:14,11:0,0:1:0,2:25.6:1:32.3:1:1:0:60:50:1:0:2.2 1/1:39:39:18,21:0,0:1:0,2:28.1:1:31.5:1:1:0:60:78:1:0:2.1 -11 119841515 . C T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18984;LSEQ=CAGTGCCGCTGGAATCAGCG;RSEQ=GGAGCAGTTAGTTCTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:22:12,10:2,1:0.88:2,2:26.9:1:29.5:1:1:1.63407:60:44:0.88:0:2.3 1/1:39:35:16,19:2,2:0.8974:2,2:30.9:1:29.5:1:1:1.18225:60:70:0.8974:0:2.2 -11 119841603 . G C 43 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TCCAAGGCTGTATTAGCAGG;RSEQ=GGCTGTCAATCTCCAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:17:1:27.7:1:1:0:60:6:0.5:0:1 0/0:2:0:0,0:0,2:0:0,0:29:1:32:0:1:0:60:4:1:0:0 -11 120490037 . G T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATACCCCCATTGCATCTTG;RSEQ=AAGTAACTAACTTGTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:27:1:1:0:60:4:1:0:1 -11 120490585 . CT C 113 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.1557;SOR=2.01536;LSEQ=TTACCCAGTCTCTGCTATTT;RSEQ=TTTTTTTTTTTTAATACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:12:11,1:38,4:0.2105:2,2:29.8:1:32:1:1:1.15:59.6:24:0.2105:0.0351:0.4 0/1:37:13:11,2:20,0:0.3514:1,2:21.5:1:30.8:1:0.14773:0:60:26:0.3514:0.0811:0.5 -11 120490614 . TA T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50599;SOR=0;LSEQ=TTTTTAATACTGAAAAGAGT;RSEQ=ACAGTGTATTATAATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:67,19:0.0227:2,2:19.5:1:29:1:0.40491:3.46244:60:4:0.0227:0:0.5 0/0:67:0:0,0:54,13:0:2,0:22.3:1:27.3:1:1:0:60:21.333:1:0:0.2 -11 120490713 . C T 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.3301;SOR=1.26233;LSEQ=AATTGGGAGTTTGGGAATCT;RSEQ=GGTGGAGCTGTTAGCGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:78:36,42:40,53:0.4535:2,2:23.9:1:29.7:1:0.75774:1.13:60:38:0.4497:0:1.1 1/0:170:87:37,50:39,44:0.5118:2,2:25.5:1:29.8:1:0.64374:1.19651:60:174:0.5148:0:1 -11 120490857 . G T 31 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.77618;LSEQ=ACTCAACATGGCTTTATCAT;RSEQ=CCTGATGTTAATGCATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:130,67:0.0101:2,2:8:0:31:0:1:1.93344:60:4:0.0103:0:1 0/0:128:1:0,1:90,37:0.0078:2,0:1:0:23:0:0.29688:0:60:2:0.0081:0:1 -11 120490870 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18542;SOR=Inf;LSEQ=TTATCATGCCTGATGTTAAT;RSEQ=CATGTTCTCTTTTTACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:162,78:0:2,0:23.5:1:32.3:1:1:0:59.9:239:1:0:0.1 0/1:182:2:1,1:124,56:0.011:2,2:6.5:1:27.5:1:0.52948:2.20365:60:4:0.011:0:1.5 -11 120491016 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19121;SOR=Inf;LSEQ=TCTACTTTGCTTCCTCAGGA;RSEQ=CTTTAGTAGTTTCCCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:56,184:0:2,0:23.6:1:29.6:1:1:0:60:47:1:0:0.1 0/1:187:2:1,1:54,131:0.0107:2,2:14.5:1:27.5:1:0.50285:2.41:60:4:0.0108:0:1.5 -11 120491113 . C T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04363;SOR=0.24496;LSEQ=CATGTACTGCCCCGTAGCTA;RSEQ=CATAACCCAGTCCCCATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:18:0,18:2,21:0.439:2,1:25.9:1:30.1:1:0.49512:0:60:17:0.4359:0:1.1 0/1:19:3:0,3:0,16:0.1579:1,0:17:1:30:1:1:0:60:6:0.1579:0:1 -11 121232535 . G C 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAGTTCTTGCAGTCTAGA;RSEQ=TTTCTCCTCCGATGGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:200,60:0:2,0:24.8:1:32:1:1:0:45.3:85.667:1:0:0 0/1:215:26:20,6:145,43:0.1209:2,2:25.9:1:31.3:1:1:1.01157:46.6:25:0.1179:0:1.1 -11 121232681 . G A 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=102.32015;LSEQ=TAGCTTCAAAACTGCTCGTA;RSEQ=ACATTCATCACTGTTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:719:1:1,0:362,355:0.0014:2,0:1:0:26:0:1:0:49:2:0.0014:0:1 0/1:560:70:34,36:252,238:0.125:2,2:21:1:29.5:1:0.70218:1.12088:40.4:140:0.1264:0:1.1 -11 121232811 . A G 276 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02141;LSEQ=GGCAATTGGTACTCTTCCAC;RSEQ=ATCCCTCCTGTGATACAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:515:511:165,346:2,1:0.9922:2,2:27.5:1:30.7:1:0.24764:4.18111:40.4:55.778:0.9941:0:1.3 1/0:672:492:199,293:85,91:0.7321:2,2:27.4:1:30.5:1:0.07594:1.37459:44.3:97.4:0.7368:0:1.1 -11 121232871 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06761;LSEQ=ATTAGGCCGAAGCTGTAGAT;RSEQ=TCAGCCATGATGTAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:57:11,46:30,34:0.4672:2,2:12.2:1:30.5:1:0.00194:3.64883:33:114:0.4672:0:2.1 0/1:414:23:3,20:162,229:0.0556:2,2:11.2:1:29.6:1:0.00741:4.70241:32.3:46:0.0562:0:2.2 -11 121232886 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.04336;LSEQ=TAGATGTCAGCCATGATGTA;RSEQ=GGCTGGAAGTGGTTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:17:10,7:21,28:0.2576:2,2:22.1:1:27.8:1:0.27605:1.89:29.5:4.667:0.2258:0:2.7 0/1:342:5:1,4:145,191:0.0146:2,2:21:1:31.4:1:0.39715:3.02814:25.8:10:0.0147:0:2.8 -11 121232936 . TA GG 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.09204;LSEQ=GTCCAGCACTTCTGGAGCCA;RSEQ=TAGCGTTTGGTGCCCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:18:18,0:28,23:0.2609:2,1:22.2:1:31.2:1:0.00026:0:31.1:36:0.2647:0.1014:1.1 0/1:257:8:7,1:119,130:0.0311:2,2:11.6:1:29.6:1:0.03322:7.60:32:16:0.0315:0.0195:1.1 -11 121233089 . C T 179 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=48.89878;LSEQ=TAGGTCTCGATGAGCAATTG;RSEQ=GGGCTTTCCTTGGGTGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:624:2:0,2:392,229:0.0032:2,0:1:0:26.5:1:0.13711:0:41.5:4:0.0032:0:1 0/1:500:68:43,25:246,186:0.136:2,2:23.5:1:29.5:1:0.35722:1.30:35.6:136:0.1388:0:1.1 -11 121233279 . T C 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.11338;LSEQ=CCTGTACCTTTAATGTCTGC;RSEQ=GCTATGAAACCAAGTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:452:380:252,128:38,33:0.8407:2,2:26.8:1:30.6:1:0.04342:1.71:37.3:41.222:0.8432:0:1.1 0/1:487:182:112,70:169,135:0.3737:2,2:27.5:1:30:1:0.21778:1.28:37.1:364:0.3784:0:1.1 -11 121233387 . T A 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAATACTTTCACCGCCAC;RSEQ=TTTTCGCCACGCCATTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:766:0:0,0:437,325:0:2,0:26:1:31:1:1:0:39:68.273:0.9947:0:0.1 0/1:535:58:37,21:288,189:0.1084:2,2:25.6:1:30.7:1:0.67073:1.16:39.4:57:0.1075:0:1.1 -11 121233586 . G C 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06372;LSEQ=CTTCATCCGTTCCAAATCAC;RSEQ=ATTGTAACGACGTCTGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1052:955:350,605:35,59:0.9078:2,2:24.3:1:31.5:1:0.9111:1.02541:56.5:67.214:0.9109:0:1.1 0/1:953:367:140,227:245,340:0.3851:2,2:25.1:1:30.8:1:0.27775:1.16819:56.5:60.167:0.3824:0:1.1 -11 121233618 . CAAT C 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTCTGCTTGAGATGCTCTTG;RSEQ=AATGTCTCCAAGATGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:643:0:0,0:168,475:0:2,0:24.5:1:30.2:1:1:0:59:159.75:1:0:0.8 0/1:568:19:6,13:159,390:0.0335:2,2:24.3:1:31.4:1:0.8:1.13:59.7:38:0.0335:0.0035:0.2 -11 121777266 . T TA 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCATATACTACTCAGTT;RSEQ=GACTACTTTTATTTTGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:42:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:28.5:1:1:0:60:4:1:0:1 -11 121779353 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18473;SOR=Inf;LSEQ=CCTCACTTGCCAAAGGAAGC;RSEQ=GGGGTGGGAAGATGGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:95,37:0:2,0:22.5:1:29.5:1:1:0:60:32:1:0:0.1 0/1:100:2:1,1:74,23:0.02:2,2:6.5:1:30:1:0.42795:3.17085:60:4:0.0204:0:1 -11 121779422 . A G 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATTGTGCACATGCTGCTA;RSEQ=GTGCCCAGTGGCACCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:136,131:0:2,0:26.4:1:30.4:1:1:0:60:65.75:1:0:0.7 0/1:261:17:10,7:127,116:0.0651:2,2:25.2:1:30.5:1:0.6264:1.30:60:34:0.0656:0:1.1 -11 121779467 . T C 250 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03679;LSEQ=CTTTTACATTATTAATTACC;RSEQ=TGAAATTCAGCCACATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:250:239:103,136:3,7:0.956:2,2:24:1:31.7:1:0.52387:1.76:60:238:0.9558:0:1.1 0/1:235:104:47,57:58,72:0.4426:2,2:24.2:1:30.8:1:1:1.02:60:103:0.4421:0:1.2 -11 121779484 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24825;SOR=Inf;LSEQ=ACCTTGAAATTCAGCCACAT;RSEQ=GTCCCTCTGCCTGCCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:78,125:0:2,0:25.1:1:31.5:1:1:0:60:100.5:0.995:0:1 0/1:208:3:1,2:81,124:0.0144:2,2:30:1:27.7:1:1:1.30483:60:6:0.0146:0:2.3 -11 121779497 . G A 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62311;SOR=2.90476;LSEQ=GCCACATGGTCCCTCTGCCT;RSEQ=CCTGGACCAGTGCTTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:1:1,0:60,107:0.006:2,0:1:0:26:0:0.3631:0:60:2:0.006:0:2 0/1:175:3:2,1:67,105:0.0171:2,2:5.3:1:26:1:0.56265:3.11:60:6:0.0173:0:1.3 -11 121779543 . C T 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.27689;LSEQ=GCCATTGGAAACTGACTGTG;RSEQ=TCCAAGAGCCCCCAAGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:4:1,3:22,58:0.0476:2,2:23:1:29:1:1:1.13623:60:8:0.0482:0:1 0/1:88:32:7,25:15,41:0.3636:2,2:28.5:1:29.7:1:0.7986:1.30272:60:64:0.3678:0:1 -11 121779664 . T C 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00588;SOR=0;LSEQ=GGCTTTATGCATTTATCTCT;RSEQ=GGTTCCAGGCACAGCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,1:0.9286:0,1:17:1:30.9:1:1:0:60:26:0.9286:0:1.4 0/0:3:0:0,0:0,3:0:0,0:32.3:1:26.3:1:1:0:60:2:1:0:0.7 -11 121779687 . A G 77 d7;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.375;SOR=0;LSEQ=TTCCAGGCACAGCTTTGCAT;RSEQ=TATATGTGTATACGTACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:18.6:1:33.2:1:1:0:60:10:1:0:2 1/0:3:2:0,2:0,1:0.6667:0,0:8:0:32:0:1:0:60:4:0.6667:0:1 -11 121939883 . C T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23582;SOR=Inf;LSEQ=TGTTACCGTCCACCTTTTCT;RSEQ=TGATCACTGAGACAAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:121,31:0:2,0:21.8:1:31.3:1:1:0:60:75:1:0:0.1 0/1:144:2:1,1:108,34:0.0139:2,2:14:0:27.5:1:0.42832:3.14522:60:4:0.0139:0:1.5 -11 121939976 . A G 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.48195;LSEQ=ACTGCCTCTTTTATGACCAC;RSEQ=TTCTCCATCTTAACAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:192:108,84:119,106:0.4593:2,2:28:1:30.6:1:0.55403:1.14:60:47:0.4563:0:1.1 0/1:434:126:67,59:159,149:0.2903:2,2:25.7:1:30.1:1:0.83247:1.06:60:252:0.293:0:1.1 -11 121940064 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21329;SOR=Inf;LSEQ=TTGTTTAAAATTGCCCACTG;RSEQ=ATACAGCCATTGTAAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:52,156:0:2,0:25:1:30.9:1:1:0:60:40.6:1:0:0.2 0/1:179:2:1,1:51,125:0.0112:2,2:18.5:1:26:1:0.5001:2.44:60:4:0.0114:0:1 -11 121940113 . TA T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.18608;SOR=0.31546;LSEQ=AGGTGGGAAAATATCAGACT;RSEQ=AAAAAAAAAGCCTAGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:8:0,8:1,54:0.127:1,0:32:1:31.1:1:1:0:60:16:0.1356:0:0.3 0/1:46:2:0,2:1,43:0.0435:1,0:18:1:32:0:1:0:60:4:0.0444:0:0 -11 123605723 . GA G 129 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.2291;SOR=2.35757;LSEQ=TCACACAACACTTGGCATTT;RSEQ=AAAAAAAAAAATCATTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:16,0:11,0:0.5714:0,1:19.5:1:31.9:1:1:0:60:32:0.5714:0.1429:0.1 1/0:21:16:15,1:3,0:0.7619:0,1:26.2:1:32.3:1:1:0:60:32:0.7619:0.0952:0.3 -11 123605822 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TACAATACTAATTATTTATC;RSEQ=AGACAAAGCTTTCCAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:132,40:0.0115:2,2:11.5:1:27:0:0.41678:3.27181:60:4:0.0116:0:1 0/0:137:0:0,0:106,31:0:2,0:22.6:1:30:1:1:0:60:136:1:0:0.1 -11 123605937 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.25577;LSEQ=CTTAAAAGTTTGAGAACCGA;RSEQ=GTCCAGTGAAGTAGACTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:213:106,107:118,132:0.46:2,2:26.3:1:30.7:1:0.64094:1.11:60:105.5:0.4607:0:1.1 1/0:491:385:192,193:53,53:0.7841:2,2:25.5:1:29.6:1:1:1.0052:60:76:0.7835:0:1.1 -11 123606029 . A C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08544;LSEQ=ATCCTACAACGTATGCATTG;RSEQ=CAGAAGAGTTCCTGCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:84:18,66:27,71:0.4615:2,2:24.4:1:31.9:1:0.39072:1.39182:60:168:0.4641:0:1 0/1:177:12:3,9:42,123:0.0678:2,2:19.1:1:31.7:1:1:1.02426:60:24:0.0686:0:1.2 -11 123855651 . C G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0117;SOR=Inf;LSEQ=GGTTATGACCGCCCCTCCCC;RSEQ=CAGGAACTCAGCAGGCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:12,1:0:1,0:31.2:1:31.9:1:1:0:60:26:1:0:0.2 1/0:8:4:4,0:4,0:0.5:0,0:23:1:31.5:1:1:0:60:8:0.5:0:1 -11 123855790 . GA G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50221;SOR=0;LSEQ=ATGAGTTGCACAGTTCCATG;RSEQ=AAAAGCATGGTTTCCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:26,35:0.0317:2,2:33.5:1:32:1:1:1.34:60:4:0.0317:0:0 0/0:50:0:0,0:24,26:0:2,0:28.5:1:29.8:1:1:0:60:100:1:0:0.1 -11 123856980 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAAATCTGGCTCTCATA;RSEQ=GAGCTTAGTAGCTTGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 125496956 . G T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTCCATGCCCACAAAT;RSEQ=GCTTCTCAGGGTTTAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:19.1:1:31.4:1:1:0:60:22:1:0:1.2 1/1:7:7:0,7:0,0:1:0,0:11.9:1:29.9:1:1:0:60:14:1:0:1.4 -11 125497145 . G A 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATCGCATCTACCCCATA;RSEQ=GAGCTTAGGACAGTCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:25.5:1:30.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 125497342 . A G 84 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=TGTATTTCACATTTTAGAAA;RSEQ=GAGTAGTGTGTGTTGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:6,0:23,1:0.2:1,0:23.8:1:32.7:1:1:0:60:12:0.2069:0:1 0/1:5:1:1,0:4,0:0.2:0,0:2:0:29:0:1:0:60:2:0.2:0:1 -11 125497461 . G T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.37158;SOR=3.91191;LSEQ=AATCTTTGGAAGTTTTAGAA;RSEQ=AAATGGAATTCTGTAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:1:0,1:103,57:0.0062:2,0:1:0:23:0:0.36025:0:60:2:0.0063:0:1 0/1:167:4:1,3:101,62:0.024:2,2:5.5:1:28.5:1:0.30016:4.84127:60:8:0.0241:0:1.5 -11 125497466 . G T 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGAAGTTTTAGAAGAAAT;RSEQ=GAATTCTGTAATGTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:107,62:0:2,0:25.7:1:31.7:1:1:0:60:83.5:1:0:0.1 0/1:183:70:44,26:67,46:0.3825:2,2:22.4:1:29.1:1:0.64437:1.16:60:69:0.3791:0:1.1 -11 125498872 . G C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.59564;LSEQ=TAAGAGGAAGCAGAGGCTTT;RSEQ=AAGTCATGGCTTGCATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:38.5:1:32:1:1:0:60:4:0.2857:0:1 0/1:5:2:2,0:3,0:0.4:0,0:20.5:1:29.5:1:1:0:60:4:0.4:0:1 -11 125499052 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49852;SOR=Inf;LSEQ=GCACATTTGTAAATGTCTAA;RSEQ=CTTCAAATTAAGAAGCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:143,26:0:2,0:24.7:1:32.4:1:1:0:60:168:1:0:0.3 0/1:169:2:2,0:130,37:0.0118:2,0:23.5:1:31.5:1:1:0:60:4:0.0119:0:1.5 -11 125499059 . A T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.24024;SOR=0;LSEQ=TGTAAATGTCTAAGCTTCAA;RSEQ=TTAAGAAGCTATGTGGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:154,31:0.0107:2,2:17:0:31:1:0.31373:4.90546:60:4:0.0108:0:1.5 0/0:194:0:0,0:141,53:0:2,0:23.5:1:29.5:1:1:0:60:96:1:0:0.4 -11 125499063 . A G 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00178;SOR=2.10609;LSEQ=AATGTCTAAGCTTCAAATTA;RSEQ=GAAGCTATGTGGTTGCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:36:30,6:140,30:0.1748:2,2:25.8:1:31.6:1:1:1.07:60:35:0.1707:0:1.3 0/1:204:63:44,19:102,39:0.3088:2,2:24.4:1:30.7:1:0.73865:1.12868:60:62:0.3069:0:1.1 -11 125502981 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21013;SOR=Inf;LSEQ=ACACCAGTGATTTTTTTTCA;RSEQ=TAAAACTTAATTCCTGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:144,9:0:2,0:25.9:1:32.5:1:1:0:60:152:1:0:0.1 0/1:130:2:2,0:116,12:0.0154:2,0:18:1:31.5:1:1:0:60:4:0.0156:0:1 -11 125505095 . C G 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02064;SOR=Inf;LSEQ=AACTCCTGGGCTCAAGCAGT;RSEQ=CTTCTGCCTCAGCCTCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:0:1,0:19.8:1:32.2:1:1:0:60:26:1:0:0.2 1/0:6:3:3,0:3,0:0.5:0,0:29:1:32.7:1:1:0:60:6:0.5:0:1.3 -11 125505377 . G GA 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58485;SOR=1.15117;LSEQ=AGGAGTATTCTGACTGGAAA;RSEQ=AAAAAAAAACATACCTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:39:21,18:442,400:0.0442:2,2:28.8:1:30.1:1:1:1.06:59.9:78:0.0452:0:0.2 0/1:969:49:25,24:470,440:0.0506:2,2:29.9:1:29.2:1:1:1.02543:60:48:0.0506:0.0021:0.3 -11 125505504 . C CT 93 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.99582;LSEQ=GCTATTTGAATTTTTTCTTA;RSEQ=TTTTTTTTTTGTTTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:9:0,9:29,206:0.0364:2,0:31.1:1:30.8:1:0.60441:0:60:18:0.0377:0:0.1 0/1:248:9:1,8:32,204:0.0363:2,2:29.6:1:29.6:1:1:1.25383:60:18:0.039:0:0.1 -11 125507219 . C CTT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.1161;SOR=Inf;LSEQ=GTAATTTAGTAGCTTTAATT;RSEQ=TTTCTCTTCCCCAGGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:59,0:0:1,0:22.9:1:32.1:1:1:0:60:118:1:0:0.1 0/1:31:2:2,0:29,0:0.0645:1,0:8.5:1:31.6:1:1:0:60:4:0.0645:0.0323:0 -11 125507256 . G C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17585;SOR=Inf;LSEQ=ATAATATTTAGACATAAGTA;RSEQ=GCTAACAGAAAATGTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:113,4:0:1,0:23.5:1:32.5:1:1:0:60:116:1:0:0.2 0/1:85:2:1,1:75,8:0.0235:2,2:7:1:26:1:0.20168:8.89809:60:4:0.0235:0:1 -11 125507277 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.34503;SOR=1.36275;LSEQ=GCTAACAGAAAATGTGTTTC;RSEQ=TACCTCAAGCCATAGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:26:24,2:139,26:0.1361:2,2:20.5:1:31.7:1:0.37997:2.24:60:52:0.1368:0:1 0/1:130:23:20,3:81,26:0.1769:2,2:26:1:30.3:1:0.28428:2.13:60:46:0.1783:0:1 -11 125507402 . CA C 98 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.14984;SOR=2.74184;LSEQ=AGAATTACCATTCCAGACAT;RSEQ=AAAAAGATAGATGGTACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:3:1,2:272,307:0.0052:2,2:29.7:1:31.3:1:1:1.77031:60:6:0.0052:0:0 0/1:642:9:4,5:317,316:0.014:2,2:26.6:1:31.2:1:1:1.25351:60:18:0.0142:0.0016:0 -11 125507588 . TTTTG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16173;SOR=Inf;LSEQ=AGAAAAAAATACAGAAATAA;RSEQ=TTTATTAATAATTATAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:1,25:0:1,0:18.4:1:29:1:1:0:60:12:1:0:0.2 0/1:18:2:0,2:0,16:0.1111:1,0:27:1:29:1:1:0:60:4:0.125:0.0556:1.5 -11 125513857 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.09816;SOR=Inf;LSEQ=CCCCATGAAGAATAATACAT;RSEQ=TATGTGTTTTTTCATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:95,246:0:2,0:22.7:1:32.1:1:1:0:60:84.25:1:0:0.1 0/1:293:3:2,1:68,218:0.0102:2,2:17.7:1:29.3:1:0.14659:6.36:60:6:0.0103:0:1 -11 125514274 . T A 161 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=118.09797;LSEQ=AACTTTTAAATCACATGTAT;RSEQ=CTTTTTTGGTCAAGGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:1:1,0:48,97:0.0068:2,0:45:0:28:0:0.33562:0:60:2:0.0069:0:1 0/1:102:46:25,21:23,33:0.451:2,2:22:1:29.3:1:0.23234:1.70:60:92:0.451:0:1.1 -11 125514323 . A G 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15427;SOR=0;LSEQ=GGGAGGCCTTCATGCAAAAT;RSEQ=ATTTTAAGTCAGACTAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:4:4,0:109,54:0.024:2,0:25:1:32.8:1:0.30579:0:60:8:0.0244:0:1 0/0:110:0:0,0:87,23:0:2,0:24:1:28.5:1:1:0:60:109:1:0:0.3 -11 125514573 . G A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10578;LSEQ=TTTTCATTATACCTTTTCCT;RSEQ=AAGAAGAATTTAAATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:298:244:59,185:14,40:0.8188:2,2:23.5:1:29.4:1:0.86129:1.0971:60:47.8:0.8185:0:1 0/1:307:99:28,71:66,142:0.3225:2,2:23.7:1:28.9:1:0.59716:1.17795:60:48.5:0.318:0:1.1 -11 125514591 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4998;SOR=0;LSEQ=CTGAAGAAGAATTTAAATAT;RSEQ=TGAGTAAAAGCTATCATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:30,169:0.01:2,2:18.5:1:33.5:1:0.28532:5.56:60:4:0.0102:0:2 0/0:183:0:0,0:45,138:0:2,0:25.3:1:29.8:1:1:0:60:182:1:0:0.4 -11 125516454 . CA C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTGTGAAATGATTTTTC;RSEQ=AAGCACCTGTACCATTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31.5:1:1:0:60:4:1:0:1 -11 125516476 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCACCTGTACCATTTTAC;RSEQ=TTCCCATCAGTAATGTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:1:29.5:1:1:0:60:4:1:0:1 -11 125523456 . C CTG 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=1.20624;LSEQ=CTTGGCTATTGTGAATAATG;RSEQ=TGTAGGGTTGCAAATTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:17,0:0.1905:1,0:25.5:1:30.7:1:1:0:60:8:0.1905:0.0476:0.3 0/1:9:2:2,0:7,0:0.2222:0,0:13.5:1:32.3:1:1:0:60:4:0.25:0.1111:0 -11 125525195 . A G 281 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4898;SOR=0;LSEQ=ATATTGTGAGCAGCCAGAAG;RSEQ=TTTGGCTTCCTGCCACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:500:500:223,277:0,0:1:0,2:25.1:1:31.4:1:1:0:60:70.429:1:0:1.1 1/1:480:479:208,271:1,0:0.9979:0,2:25.5:1:30.6:1:0.43542:0:60:78.833:0.9979:0:1.1 -11 125525262 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18889;SOR=Inf;LSEQ=GGTGAATATAGTGCTGCTAT;RSEQ=TTGACATTATTCTTCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:58,169:0:2,0:22.2:1:32:1:1:0:60:112.5:1:0:0.6 0/1:175:2:1,1:44,128:0.0114:2,2:24.5:1:32:0:0.45147:2.89:60:4:0.0116:0:3 -11 125525277 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51461;SOR=0;LSEQ=GCTATGTTGACATTATTCTT;RSEQ=CTAGAGAAGATTATCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:32,136:0.0118:2,2:8.5:1:27.5:1:0.35148:4.20:60:4:0.012:0:2 0/0:118:0:0,0:27,91:0:2,0:22:1:31.3:1:1:0:60:236:1:0:0.5 -11 126528035 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACCCAAATGCTGCCATGT;RSEQ=TGTAGTGGTAATGCTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 126528388 . G T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60106;SOR=2.28765;LSEQ=TGAATGTTCACCACTGCAGT;RSEQ=CCCTCATTTAGCCTAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:0,1:130,42:0.0058:2,0:1:0:25:0:0.24855:0:60:2:0.0059:0:1 0/1:152:2:1,1:111,39:0.0132:2,2:18:1:25.5:1:0.45835:2.82298:60:4:0.0133:0:1 -11 126528497 . C G 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=1.76839;LSEQ=TCTTTTATACTTTGCCAGCC;RSEQ=TACATTGCTGGATATACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:218:103,115:123,128:0.4648:2,2:24.4:1:31:1:0.71197:1.07273:60:108:0.4635:0:1.1 1/0:378:229:106,123:66,79:0.6058:2,2:25.9:1:30.4:1:0.91543:1.03:60:228:0.608:0:1.1 -11 126528579 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50871;SOR=0;LSEQ=TCGTTAAGACTTTTTCTTTG;RSEQ=CTTTAAGGTGCCATATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:48,138:0.0106:2,2:23:1:28:1:0.45437:2.86:60:4:0.0108:0:1.5 0/0:141:0:0,0:38,103:0:2,0:23.3:1:29.5:1:1:0:60:282:1:0:0.3 -11 126529001 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGAAAACTACAGAAAAT;RSEQ=ATACATTTTCCCTCTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 126595573 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12722;SOR=Inf;LSEQ=GCACTGCTGCAGGCTGGACC;RSEQ=TGAGCCCGCTCTGCCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:31,24:0:2,0:24:1:31.1:1:1:0:60:110:1:0:0.7 0/1:31:2:1,1:15,14:0.0645:2,2:25.5:1:31.5:1:1:1.06901:60:4:0.0667:0:2 -11 126595594 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17335;SOR=Inf;LSEQ=TGAGCCCGCTCTGCCCTCGC;RSEQ=GCAAGGCTGCTGCTGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:46,36:0:2,0:23.2:1:30.4:1:1:0:60:40:1:0:1 0/1:59:2:1,1:33,24:0.0339:2,2:29.5:1:27.5:1:1:1.36746:60:4:0.0351:0:2 -11 126595633 . A C 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0163;SOR=0;LSEQ=TGGATGTGCGGGGCTGGTGG;RSEQ=GCTCTGTGGCCTGGGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:92:92:43,49:0,0:1:0,2:26.6:1:30.8:1:1:0:60:45:1:0:1.2 1/1:74:69:33,36:2,3:0.9324:2,2:25.3:1:30.7:1:1:1.37:60:138:0.9324:0:1.4 -11 126595635 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03772;SOR=Inf;LSEQ=GATGTGCGGGGCTGGTGGAG;RSEQ=TCTGTGGCCTGGGTCCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:43,49:0:2,0:26:1:32:1:1:0:60:29.667:1:0:1.2 0/1:74:4:2,2:32,38:0.0541:2,2:27.3:1:31:1:1:1.18:60:8:0.0548:0:3.3 -11 126595642 . G C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04069;SOR=Inf;LSEQ=GGGGCTGGTGGAGCTCTGTG;RSEQ=CCTGGGTCCAGTCTGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:39,43:0:2,0:26.4:1:31.3:1:1:0:60:19.5:0.975:0:1.2 0/1:70:4:2,2:31,35:0.0571:2,2:23.8:1:32:1:1:1.13:60:8:0.0571:0:3.3 -11 126595646 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50622;SOR=0;LSEQ=CTGGTGGAGCTCTGTGGCCT;RSEQ=GGTCCAGTCTGCACAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:37,42:0.0244:2,2:29.5:1:29:1:1:1.13:60:4:0.0253:0:2 0/0:62:0:0,0:30,32:0:2,0:23.2:1:30.3:1:1:0:60:124:1:0:1.2 -11 126595819 . T C 51 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTAACTTTCACCCCCAG;RSEQ=TTCTCTGGTGATGTAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:23:1:32.3:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:60:2:1:0:1 -11 127528679 . T A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10992;SOR=Inf;LSEQ=CAGTCAACAATCCATATAGT;RSEQ=GTGTGCCACCGCCGCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:41,46:0:2,0:27.8:1:30:1:1:0:60:86:1:0:0.1 0/1:81:3:2,1:40,38:0.037:2,2:16.7:1:27:1:1:1.89:60:6:0.0375:0:1 -11 127528695 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.49724;SOR=0;LSEQ=TAGTTGTGTGCCACCGCCGC;RSEQ=GCCTCCTGCTCCTTCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:38,48:0.0227:2,2:9.5:1:29.5:1:1:1.26:60:4:0.023:0:1 0/0:85:0:0,0:42,43:0:2,0:29.1:1:29.6:1:1:0:60:84:1:0:0.3 -11 127528712 . GCTC G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.49693;SOR=Inf;LSEQ=CGCCGCCTCCTGCTCCTTCT;RSEQ=CTCCTCCTCCTTCTTCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:32,49:0:2,0:28.7:1:32.4:1:1:0:60:162:1:0:0.2 0/1:82:2:1,1:34,46:0.0244:2,2:28.5:1:32.5:1:1:1.35:60:4:0.0253:0:0.5 -11 127795759 . G T 24 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05983;LSEQ=ATCAGTAATAACATTCTGTA;RSEQ=ATAGCTAGACCCCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:104,55:0.0124:2,2:32.5:1:28.5:1:1:1.88301:60:4:0.0125:0:1 0/1:152:2:0,2:99,51:0.0132:2,0:1:0:24.5:1:0.12008:0:60:4:0.0133:0:1 -11 127795770 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49882;SOR=Inf;LSEQ=CATTCTGTAGATAGCTAGAC;RSEQ=CCACTCCATTGATATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:117,73:0:2,0:24.2:1:30.6:1:1:0:60:46.5:1:0:0.3 0/1:196:2:1,1:126,68:0.0102:2,2:19:0:30.5:1:1:1.84682:60:4:0.0104:0:1 -11 127795846 . T C 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67147;SOR=0.91935;LSEQ=GGCTAGTATAGTATTCCTAA;RSEQ=CTATTTTTCCCGTTATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:116:57,59:70,76:0.4427:2,2:24.7:1:31.6:1:0.90116:1.05:60:232:0.4514:0:1 0/1:308:130:61,69:86,92:0.4221:2,2:26.8:1:30.8:1:0.81838:1.05716:60:260:0.4235:0:1.1 -11 127795857 . C T 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTCCTAATCTATTTTTCC;RSEQ=GTTATAGAAAATTAGATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:116,139:0:2,0:24.1:1:30:1:1:0:60:84:1:0:0.5 0/1:283:20:12,8:119,143:0.0707:2,2:21.2:1:29.9:1:0.24816:1.80:60:40:0.0709:0:1.1 -11 127797395 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGAGTAGCTGGGACTA;RSEQ=AGGCGCCAGCCAACACGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35.5:1:28.5:1:1:0:60:4:1:0:1.5 -11 128571043 . A G 107 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47619;SOR=0.33027;LSEQ=TGTTGATTAAATATGGCATT;RSEQ=GGGGAGGGAGGAGAAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:10,0:3,0:0.7692:0,0:21.7:1:32.5:1:1:0:60:20:0.7692:0:2 1/0:2:1:1,0:1,0:0.5:0,0:4:0:30:0:1:0:60:2:0.5:0:2 -11 128571080 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19486;SOR=0.31249;LSEQ=CTCTATTTCACCAGATGACA;RSEQ=AAAACTGTGATTATCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:20,0:4,0:0.8333:0,1:23.2:1:31.9:1:1:0:60:40:0.8696:0:1.6 1/0:10:6:6,0:4,0:0.6:0,0:22:1:32.8:1:1:0:60:12:0.6:0:1.2 -11 128571179 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49786;SOR=0;LSEQ=CCTGGGCTACAATTTTAGTT;RSEQ=CTTTTGAGAATGAGTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:94,15:0.018:2,2:33:1:30:0:0.26863:6.09988:60:4:0.0183:0:1 0/0:107:0:0,0:84,23:0:2,0:23.1:1:31.1:1:1:0:59.9:214:1:0:0.3 -11 128571224 . GA G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.28877;LSEQ=GTGCTTGAGAGGAGAAAAAA;RSEQ=AAAAAAAAAGTCTCTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:298:221:154,67:48,23:0.7416:2,2:22.2:1:31.8:1:0.7686:1.10:59.9:442:0.7466:0.1611:1 0/1:285:129:89,40:100,55:0.4526:2,2:26.7:1:31.8:1:0.45055:1.22:60:258:0.4574:0:1 -11 128571257 . A G 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.29382;LSEQ=CTCTCTAAAACTCAAATCAA;RSEQ=TTTCTGTGGGCCTTCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:461:365:221,144:56,40:0.7918:2,2:25.6:1:32:1:0.72595:1.10:59.9:59.833:0.7907:0:1.1 1/0:476:251:149,102:122,103:0.5273:2,2:25.9:1:31.7:1:0.26724:1.23:60:124.5:0.5309:0:1.2 -11 128571294 . A G 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00373;SOR=Inf;LSEQ=GACAAGTCTGACATTCTTCC;RSEQ=TGAGTTGGCTGGGCCGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:239,246:0:2,0:27.7:1:30.4:1:1:0:59.9:68.286:1:0:0.7 0/1:483:8:4,4:228,246:0.0166:2,2:16.3:1:30.4:1:1:1.08:60:16:0.0168:0:1.8 -11 128680191 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGCAAGCAGAAAGGCA;RSEQ=ATCAACAATGACATAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:5:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 128680394 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18357;SOR=Inf;LSEQ=TGGCAATTCCTCCTGGAGCT;RSEQ=CTCTCCGACAGCGCCAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:24,2:0:2,0:20.9:1:32.6:1:1:0:60:52:1:0:0.2 0/1:20:2:1,1:15,3:0.1:2,2:23:1:28:1:0.36842:4.47215:60:4:0.1:0:1 -11 128680448 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51064;SOR=0;LSEQ=TGGGAGGGGACCAACGGGGA;RSEQ=TTCAAAATGACGGACCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:45,21:0.0294:2,2:42:1:33:1:0.54565:2.11677:60:4:0.0294:0:1 0/0:48:0:0,0:30,18:0:2,0:24.7:1:31.4:1:1:0:60:96:1:0:0.2 -11 128680462 . AC A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51284;SOR=0;LSEQ=CGGGGAGTTCAAAATGACGG;RSEQ=CCCGATGAGGTGGCCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:44,32:0.0256:2,2:34.5:1:30.5:1:1:1.36929:60:4:0.0263:0:0 0/0:54:0:0,0:32,22:0:2,0:27.5:1:30.4:1:1:0:60:53:1:0:0.2 -11 128682606 . G T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGCTGGTCTATCCAGACT;RSEQ=GTCTGTGAGATTTAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:50:0:29:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:21:1:28.5:1:1:0:60:4:1:0:1 -11 129529524 . G T 118 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.00351;SOR=0;LSEQ=ATCAATGAATCCAGGAGCTG;RSEQ=TTTTTTGAAAAAAATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:6,10:0,0:1:0,2:20.7:1:29.6:1:1:0:59.9:32:1:0:1.2 0/1:4:1:1,0:1,2:0.25:2,0:25:0:26:0:1:0:60:2:0.25:0:1 -11 130715999 . G T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28495;SOR=3.72976;LSEQ=ATTAACCTCATTCTTATGGA;RSEQ=CTCCCTTTAAAATATTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:1,0:94,2:0.0103:1,0:48:0:14:0:1:0:60:0:0:0:2 0/1:53:2:2,0:49,2:0.0377:1,0:41:1:31.5:1:1:0:60:4:0.0392:0:1 -11 130716055 . T C 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17872;SOR=Inf;LSEQ=AAACCAGACTCGGCAATAAA;RSEQ=GTAAAACCCAAGTCCCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:189,52:0:2,0:23:1:30.4:1:1:0:60:240:1:0:0.1 0/1:177:2:1,1:128,47:0.0113:2,2:24:1:25:1:0.46995:2.70539:60:4:0.0114:0:1 -11 130716157 . C T 213 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=78.36855;LSEQ=AAAATCCTCTGATTCTATTG;RSEQ=ATAATCTCCAAAAGCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:786:4:1,3:411,370:0.0051:2,2:30:1:28:1:0.35102:3.32774:60:8:0.0052:0:1 0/1:601:172:95,77:220,208:0.2862:2,2:25.4:1:28.8:1:0.41668:1.17:60:344:0.2905:0:1.2 -11 130716235 . C A 45 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04057;SOR=Inf;LSEQ=TCCCTGTTTAGTAGAGTCCC;RSEQ=ATTTCCAATTTAGGACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:133,311:0:2,0:25.3:1:31.5:1:1:0:60:62.429:1:0:0.1 0/1:363:4:3,1:128,231:0.011:2,2:7:1:22.8:1:0.13584:5.39:60:3:0.0084:0:1.8 -11 130716312 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17634;SOR=Inf;LSEQ=AGATAAGGTCAAGGAGAAGG;RSEQ=CTTACATTATGTCAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:2,94:0:1,0:24.2:1:31.3:1:1:0:60:31:1:0:0.5 0/1:70:2:0,2:2,66:0.0286:1,0:19:1:30.5:1:1:0:60:4:0.029:0:1.5 -11 130716344 . T C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21125;SOR=0.42476;LSEQ=TCAGCCCCATTATCTGAGCT;RSEQ=GAGAGCCTCCCTTGGCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:59:53:2,51:0,6:0.8983:0,1:22.6:1:30.2:1:1:0:60:52:0.8966:0:1.1 1/0:33:26:2,24:0,7:0.7879:0,2:20.5:1:30.2:1:1:0:60:52:0.7879:0:1.1 -11 131050894 . G C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10717;LSEQ=AATATACTACTCCGTCTGAT;RSEQ=GAAAGAATGGCCTCATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:251:235:119,116:8,7:0.9363:2,2:25.9:1:30.2:1:1:1.11356:60:46:0.935:0:1.2 1/0:213:130:69,61:38,42:0.6103:2,2:26.1:1:30.1:1:0.47842:1.25:60:129:0.6085:0:1.1 -11 131085743 . T A 86 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00976;SOR=17.54038;LSEQ=TCATTCCTCTTTCCCCAGCA;RSEQ=TGCAAGAGGCCACCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:5,3:0.2727:2,2:14.7:1:30:1:1:1.18:60:6:0.2727:0:1 1/1:9:8:5,3:1,0:0.8889:0,2:14.8:1:28.8:1:1:0:60:16:0.8889:0:1.1 -11 131085828 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCCTAGCCAATGGTTCC;RSEQ=GGAAAAACACAAGAGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:6,11:0.1053:2,2:40.5:1:30.5:1:1:1.77:60:4:0.1053:0:1.5 0/0:3:0:0,0:0,3:0:0,0:25.3:1:30.7:1:1:0:60:6:1:0:2 -11 131085891 . C T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGGCCTGTTTACCACTCTG;RSEQ=GTGGTGAGCGGGGAGGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:23.3:1:30.4:1:1:0:60:14:0.875:0:1.9 1/1:2:2:0,2:0,0:1:0,0:34.5:1:31.5:1:1:0:60:4:1:0:3 -11 131085910 . T C 76 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCGTGGTGAGCGGGGAGGAC;RSEQ=ATTCTGCCTAACTAGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:20:1:32.8:1:1:0:60:10:0.8333:0:2 1/1:2:2:0,2:0,0:1:0,0:15.5:1:30.5:1:1:0:60:4:1:0:3 -11 131086171 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGTCTGCATCCTGCAAT;RSEQ=GTTTTGAACTCATTAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 131904413 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAAGTGGGCAACTGGATA;RSEQ=TGGCAGATGGGTTTACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:36.3:1:30:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -11 131904754 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14084;SOR=Inf;LSEQ=AGTTGCTAAATCCCTGTGCT;RSEQ=ATCAAAAATGTTCCCACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:110,24:0:2,0:24.3:1:31.9:1:1:0:60:66:1:0:0.1 0/1:81:2:1,1:65,14:0.0247:2,2:31:1:28.5:1:0.33796:4.51981:60:4:0.0247:0:1 -11 131904861 . A T 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.88691;SOR=0.97395;LSEQ=CATATTTCTGGTCTCCTAGC;RSEQ=TCTTGATTATTCAGTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:182:89,93:121,122:0.4272:2,2:26.5:1:30.5:1:0.92193:1.03631:60:59.667:0.4262:0:1.1 0/1:385:162:79,83:116,107:0.4208:2,2:24.8:1:30.6:1:0.53741:1.13862:60:161:0.4226:0:1.1 -11 131904927 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10123;SOR=Inf;LSEQ=GTTTTTCTTCCCATGGTTTT;RSEQ=ATTAACAAAAAATAATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:71,165:0:2,0:23.3:1:31.6:1:1:0:60:46.2:1:0:0.4 0/1:207:3:2,1:78,126:0.0145:2,2:14.7:1:26.3:1:0.56067:3.21:60:6:0.0148:0:1.3 -11 131904958 . T A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00625;SOR=Inf;LSEQ=AATAATCTGTTTTGCTGTTG;RSEQ=TTGCTTTGAGTAACTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:25,98:0:2,0:23.6:1:30.1:1:1:0:60:246:1:0:0.3 0/1:95:6:1,5:20,69:0.0632:2,2:21.7:1:29.7:1:1:1.44411:60:12:0.0638:0:1 -11 131905008 . T C 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18061;SOR=0.38761;LSEQ=CTGAGAGAAATTTAAAATGT;RSEQ=CCTTTCTAAAAAACCGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:47:0,47:0,4:0.9216:0,1:23.7:1:30.7:1:1:0:60:46:0.92:0:1.1 1/1:33:27:0,27:0,6:0.8182:0,1:22.6:1:31.2:1:1:0:60:54:0.8182:0:1.3 -11 131905556 . G A 31 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AGTGGGAGGGGTGTGTGTGT;RSEQ=TGTATGTGTGTGTGCCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:0:32:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:31:1:1:0:60:4:1:0:1.5 -11 132534870 . A G 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00044;SOR=1.59847;LSEQ=TGCAACGGGTTGACTTTGAA;RSEQ=TCTGACATAACATGACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:486:265:124,141:96,125:0.5453:2,2:26.3:1:31.8:1:0.46577:1.14:60:87.333:0.5436:0:1.1 1/0:461:303:134,169:74,84:0.6573:2,2:26.1:1:31.5:1:0.62259:1.1108:60:606:0.6573:0:1.1 -11 132534934 . G A 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07302;SOR=0;LSEQ=ACAGTGCCACACTAACACCA;RSEQ=CTGGAGGGGAGATGTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:5:4,1:71,202:0.018:2,2:17:1:27.8:1:0.01978:11.27:60:10:0.0184:0:1.2 0/0:211:0:0,0:72,139:0:2,0:22.4:1:31.6:1:1:0:60:104.5:1:0:0.5 -11 132534972 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18487;SOR=Inf;LSEQ=CATTAATACATAGGAAGGGT;RSEQ=CATGCCCACGTGTGTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:17,99:0:2,0:25.2:1:31.6:1:1:0:60:28:1:0:0.2 0/1:88:2:1,1:17,69:0.0227:2,2:39:1:28.5:1:0.36912:3.97:60:4:0.0233:0:1 -11 133495417 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20009;SOR=Inf;LSEQ=CCATGATGAGTGACAATCAT;RSEQ=CTATTTTATACTAATATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:136,3:0:1,0:26:1:32.2:1:1:0:60:45.333:1:0:0 0/1:113:2:1,1:103,8:0.0177:2,2:10:1:28:1:0.1536:12.19759:60:4:0.0182:0:1 -11 133495458 . C T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76153;LSEQ=TGTACACCAAGCTATTTCAT;RSEQ=GGCTGCAATAAATTCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:1,2:233,57:0.0102:2,2:14.7:1:27.7:1:0.10432:8.09327:60:6:0.0103:0:1 0/0:256:2:1,1:171,83:0.0078:2,2:20.5:1:28.5:1:0.54945:2.05398:60:4:0.0079:0:1 -11 133495556 . G C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.77201;LSEQ=GAAGCCTCCCAAGGAACTTT;RSEQ=AGGGAAATTGTAGCCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:739:53:25,28:334,350:0.0717:2,2:24.6:1:31.5:1:0.88691:1.06874:60:106:0.0724:0:1.1 0/1:620:267:134,133:176,174:0.4306:2,2:24.9:1:31.3:1:1:1.00394:60:52.4:0.4295:0:1.2 -11 133495639 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.08412;SOR=Inf;LSEQ=CCACTTCACCATACTTCCTC;RSEQ=CCCAGCCCCTACATGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:109,259:0:2,0:23.7:1:30.5:1:1:0:60:35.8:1:0:0.2 0/1:288:3:2,1:96,188:0.0104:2,2:5:1:26:1:0.26941:3.90:60:6:0.0106:0:1 -11 133495676 . C T 144 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=4.76265;LSEQ=TTCCATTAAACTGTGATTCC;RSEQ=TTGGAAATAGGCTTAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:12:1,11:19,181:0.0566:2,2:21.7:1:30.4:1:1:1.15391:60:24:0.0569:0:1.4 0/1:121:27:1,26:16,78:0.2231:2,1:23.1:1:30.4:1:0.11544:5.28443:60:54:0.225:0:1.3 -11 133495735 . G C 96 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00562;SOR=5.88046;LSEQ=TATTCCCTGTCATAATGCTT;RSEQ=TCTCAATAGATACTTATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:0,4:1,71:0.0526:1,0:16.3:1:33:1:1:0:60:8:0.0541:0:2.3 0/1:32:8:0,8:0,24:0.25:1,0:20.8:1:32.3:1:1:0:60:16:0.25:0:1.9 -12 401969 . C A 152 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTTCTGTGCTGCGCACACAG;RSEQ=ATTCTCATCATCAGACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1679:41:19,22:796,839:0.0244:2,2:27:1:28.5:1:0.87459:1.09847:60:9.25:0.0222:0:1.2 0/0:1130:0:0,0:552,577:0:2,0:24.8:1:31.6:1:1:0:60:111.9:0.9991:0:0.1 -12 404988 . CA C 96 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53977;SOR=0.52848;LSEQ=AAAAATACCATAAAACAAAG;RSEQ=AAAAAAATTAAAACTATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:8:1,7:128,379:0.0155:2,2:28.1:1:32.3:1:0.6861:2.36116:60:16:0.0159:0:0.1 0/0:363:3:0,3:116,243:0.0083:2,0:30.7:1:33.3:1:0.55418:0:60:6:0.0083:0:0 -12 405043 . G A 129 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAAAGCAAATATTGAGACTA;RSEQ=CCCCCCATCCCCCAATACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:21:1,20:4,133:0.1321:1,1:25.7:1:29.4:1:0.51469:1.66:60:42:0.1419:0:1 0/1:106:14:1,13:5,87:0.1321:2,1:26.4:1:29.1:1:0.582:1.33:60:28:0.1359:0:1.3 -12 406292 . G A 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62598;SOR=1.066;LSEQ=ATGTGGGTCACCACCTCCTC;RSEQ=GATTTGATGGGAATCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1616:216:109,107:698,701:0.1337:2,2:25.8:1:30.3:1:0.88402:1.02:60:42.2:0.1322:0:1.2 0/1:885:125:58,67:384,375:0.1412:2,2:26.7:1:30.2:1:0.44008:1.18267:60:124:0.1417:0:1.1 -12 406427 . G C 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TTTAACTTATTTTATGACAA;RSEQ=GCCCAAAATGGAGGCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:29:2,27:17,232:0.1043:2,2:24:1:30.1:1:1:1.01:60:58:0.1058:0:1.1 0/0:135:0:0,0:16,119:0:2,0:25:1:30:1:1:0:60:44:1:0:0.1 -12 416059 . T A 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81006;LSEQ=TCAATAGCTTTTTTTTTTTT;RSEQ=AAACAAACCCAATGATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:7:5,2:413,144:0.0124:2,2:26.7:1:26.6:1:1:1.14691:59.3:6:0.011:0:1.7 0/1:397:4:2,2:271,122:0.0101:2,2:33.5:1:27.3:1:0.59205:2.21641:58.8:8:0.0104:0:1.8 -12 416764 . C A 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTTCATCTGTGGCTAGAGC;RSEQ=TGCCGCGCTCTATCTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1194:85:45,40:608,500:0.0712:2,2:25.2:1:30.2:1:0.7359:1.08082:60:41.5:0.0709:0:1.1 0/0:807:0:0,0:428,379:0:2,0:24.2:1:30.8:1:1:0:60:114.286:1:0:0.2 -12 416952 . CT C 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.84843;SOR=0.88725;LSEQ=TTTAGCTTGCCAGCTGGATC;RSEQ=TTTTTTTGGGAACTTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1155:17:9,8:540,597:0.0147:2,2:25.9:1:32.3:1:0.80775:1.24:60:34:0.0148:9e-04:0.2 0/1:841:11:4,7:433,397:0.0131:2,2:26.4:1:31.4:1:0.36945:1.90723:60:22:0.0132:0:0.6 -12 418777 . G T 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10627;SOR=3.81155;LSEQ=TATGGAAAAGACAATTTTGG;RSEQ=AAAAGAGCAGAATACTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:5:5,0:65,0:0.0714:1,0:17.6:1:29.6:1:1:0:60:10:0.0725:0:1 0/1:13:3:3,0:10,0:0.2308:0,0:12.3:1:30.7:1:1:0:60:6:0.2308:0:1 -12 418916 . C T 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=1.97867;LSEQ=CTGTGAGTCTGCTAATATCT;RSEQ=TACAGAGTTTTGTATTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:851:94:73,21:582,175:0.1105:2,2:22.1:1:30:1:1:1.05:60:188:0.1115:0:1.1 0/1:522:103:71,32:296,123:0.1973:2,2:22:1:30.2:1:0.71982:1.08445:60:206:0.1985:0:1 -12 419624 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCAGGCAACATGATGAAA;RSEQ=CCCATCTCCACCAAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:27:1:33.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 420274 . G A 44 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.02729;SOR=Inf;LSEQ=ACAATTTGAGTTCTCTTATG;RSEQ=GGTTTGGCAATATACTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:65,238:0:2,0:25.2:1:30.8:1:1:0:60:59.6:1:0:0.1 0/1:209:4:3,1:53,151:0.0191:2,2:6.8:1:22:1:0.06046:8.44:60:3:0.0146:0:1.5 -12 421994 . A G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTGTGAGAGAATGTCAT;RSEQ=CCACATATTGCTAGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:23,1:0.0769:1,0:21:1:34:0:1:0:60:4:0.0769:0:1 0/0:10:0:0,0:9,1:0:2,0:19.6:1:28.2:1:1:0:60:20:1:0:0 -12 427077 . G A 77 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53924;SOR=0;LSEQ=GGGAGAGAGGAGAATCTCCC;RSEQ=GTTTCCTTCAGGCCCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:6,0:14,0:0.3:1,0:19.7:1:30:1:1:0:60:12:0.3:0:2 0/0:3:0:0,0:3,0:0:0,0:19.7:1:29:1:1:0:60:6:1:0:0 -12 427165 . CA C 134 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.011;SOR=2.91762;LSEQ=ATACATTAAAATCCTAAACG;RSEQ=AAAAAAAAAAAAGTCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:17:17,0:92,2:0.1491:1,1:30.6:1:32.8:1:1:0:60:34:0.1491:0.0175:1 0/1:50:17:17,0:29,0:0.34:1,1:29.7:1:32.9:1:1:0:58.8:34:0.3542:0:0.4 -12 427575 . A G 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00018;SOR=1.80976;LSEQ=AAGAATCTGGGGTTTCATCC;RSEQ=TCATGGCCTCCTGAGCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:84:26,58:294,494:0.0962:2,2:26.5:1:30.9:1:0.28451:1.32721:60:41:0.095:0:1.1 0/1:625:101:43,58:209,312:0.1616:2,2:26.8:1:30.3:1:0.65896:1.11:60:49.5:0.1602:0:1.1 -12 427687 . T A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.28639;SOR=0;LSEQ=TTAAAACATACAAAAGAGTA;RSEQ=GAAATAGACATAGTCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:1,2:5,134:0.0211:1,2:16:1:30.3:1:0.12231:12.69:60:6:0.0219:0:1.3 0/0:89:0:0,0:2,87:0:1,0:21.8:1:30.5:1:1:0:60:88:1:0:0.1 -12 430050 . G GA 133 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.43298;SOR=1.38814;LSEQ=ATAGCAGCATATATGTGAGA;RSEQ=AAAAAAAAAATCAGAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:20:20,0:176,7:0.0971:1,1:25.6:1:30.9:1:1:0:59.8:40:0.0976:0.0194:0.5 0/1:100:13:13,0:87,0:0.13:1,1:24.6:1:28.5:1:1:0:60:12:0.1224:0.03:0.3 -12 431504 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.16142;SOR=Inf;LSEQ=TCAAAGATAATGTACGGCTT;RSEQ=ACAGGCCGGATAAAATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:192,43:0:2,0:21.7:1:30.9:1:1:0:60:38.167:0.9957:0:0.1 0/1:159:2:1,1:124,33:0.0126:2,2:17:1:24.5:1:0.38301:3.717:60:4:0.0129:0:1 -12 431510 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16269;SOR=Inf;LSEQ=ATAATGTACGGCTTCACAGG;RSEQ=CGGATAAAATTTTGGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:211,56:0:2,0:21.6:1:31.6:1:1:0:60:65.75:1:0:0.1 0/1:181:2:1,1:136,43:0.011:2,2:36:1:30:1:0.42812:3.13816:60:4:0.0112:0:2 -12 431517 . A C 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=3e-04;SOR=Inf;LSEQ=ACGGCTTCACAGGCCGGATA;RSEQ=AATTTTGGTTTTTACTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:239,77:0:2,0:21.4:1:30.1:1:1:0:60:157:1:0:0.1 0/1:220:9:8,1:148,63:0.0409:2,2:25:1:30.3:1:0.45319:3.39:60:18:0.0419:0:1 -12 431586 . T A 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTCTTCTTAGGTTTACCTG;RSEQ=GTTTCTGCTTTTTGCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:463,257:0:2,0:24.9:1:29.9:1:1:0:60:89:1:0:0.1 0/1:542:32:20,12:306,203:0.059:2,2:23.6:1:29.1:1:0.85395:1.11:60:31:0.0578:0:1.1 -12 432200 . A G 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10736;SOR=0.59321;LSEQ=ACTAAAACAAAGCCTCTTTT;RSEQ=AAGTGACAATCAATTCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:34:29,5:382,155:0.0594:2,2:18.4:1:30.5:1:0.0791:2.35:60:10.333:0.055:0:1.2 0/1:443:16:11,5:303,123:0.0361:2,2:27.1:1:31.7:1:0.78539:1.11943:60:32:0.0364:0:1.1 -12 432368 . G A 47 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2717;SOR=2.6986;LSEQ=GAGGTCTTCTAATGGGTAGC;RSEQ=ATATCTACAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:3:2,1:172,350:0.0057:2,2:18:1:17.3:1:0.25629:4.06:60:0.5:0.0021:0:3 0/1:327:5:4,1:127,195:0.0153:2,2:13.8:1:20.6:1:0.16164:6.11:60:1.5:0.0103:0:2.6 -12 432374 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06475;SOR=Inf;LSEQ=TTCTAATGGGTAGCGATATC;RSEQ=ACAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:130,248:0:2,0:10.2:1:28.6:1:1:0:59.6:10.118:0.9914:0:0.6 0/1:258:3:2,1:106,143:0.0116:2,2:11.7:1:21:1:0.57808:2.69:53.3:2:0.0093:0:2.7 -12 432406 . G A 127 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03266;SOR=1.92132;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AAAACAGAAATAAAAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:25:23,2:3,250:0.0899:1,2:7.5:1:28.4:1:0:813.01:58.4:7.333:0.0809:0:2.2 0/1:169:27:26,1:0,141:0.1598:1,1:6.3:1:26.9:1:0:0:55.8:8:0.1463:0:3.3 -12 432411 . C A 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09792;SOR=2.65705;LSEQ=AAAAAAAAAAAAAAAGAAAA;RSEQ=AGAAATAAAAACCTCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:6:6,0:4,234:0.0246:1,0:5:1:25.8:1:0:0:60:12:0.0247:0:3.2 0/1:143:9:8,1:0,134:0.0629:1,2:6.9:1:21.4:1:0:0:58:2:0.0432:0:4.8 -12 432654 . T A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06091;SOR=2.70084;LSEQ=TCAAGCCTAGAAGTAGACAG;RSEQ=GAAGTTTAGAAGTCCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:11:9,2:67,5:0.1325:2,2:27.2:1:29:1:0.23126:2.92489:60:10:0.1266:0:2.4 0/1:34:10:10,0:24,0:0.2941:1,0:27.9:1:29.7:1:1:0:60:20:0.2941:0:2.1 -12 432666 . G C 119 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00804;SOR=3.32368;LSEQ=GTAGACAGTGAAGTTTAGAA;RSEQ=TCCAGAGTAAAGGAGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:12:10,2:88,8:0.1111:2,2:23.1:1:32.1:1:0.30691:2.17968:60:24:0.1121:0:1.8 0/1:44:13:13,0:31,0:0.2955:1,1:28.5:1:32.2:1:1:0:60:26:0.2955:0:1.8 -12 433026 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13052;SOR=Inf;LSEQ=CTTAAGTTACTACATTTTTT;RSEQ=CTATAGACAAATCTCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:5,154:0:1,0:24.7:1:29.6:1:1:0:60:30.8:0.9935:0:0.1 0/1:91:2:1,1:9,80:0.022:2,2:11.5:1:28.5:1:0.20879:8.48:60:4:0.0225:0:1 -12 433151 . A G 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATTAAAGTTTGGTATCT;RSEQ=AGGATGCACATTTGAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:0,15:0.1667:1,2:27:1:33.3:1:0.16667:0:60:6:0.1765:0:1.3 0/0:5:0:0,0:0,5:0:0,0:16.8:1:31.6:1:1:0:60:10:1:0:0 -12 437579 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAAGTATTCTAAATCCCA;RSEQ=CCTTGGGGTTAGTCCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:40.5:1:32:0:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 437591 . G T 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCCCAGCCTTGGGGTTA;RSEQ=TCCATCCTTCCTATTCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:40:1:33:0:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 438242 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15481;SOR=Inf;LSEQ=AACTCGCTTATAACATATCC;RSEQ=AGCACAGAACCACTACTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:41,228:0:2,0:23.3:1:31.5:1:1:0:60:66.25:1:0:0.1 0/1:175:2:1,1:35,138:0.0114:2,2:12:1:28.5:1:0.37005:3.90:60:4:0.0117:0:1 -12 442584 . C CA 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.61169;SOR=1.37646;LSEQ=AACAGAGCAAGACCCTGTTT;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:417:8:7,1:339,67:0.0192:2,2:28.9:1:30.5:1:1:1.38:60:16:0.0197:0:0.4 0/1:305:8:5,3:241,55:0.0262:2,2:17.6:1:29:1:0.18079:2.61837:60:16:0.0266:0.0066:0.6 -12 442620 . C T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=4;SSF=0.00015;SOR=1.67237;LSEQ=AGAAAAAACAAACAAACAAA;RSEQ=AAACAACTGAAGGAAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1041:112:80,32:642,287:0.1076:2,2:25.7:1:30.2:1:0.66515:1.12:60:111:0.1087:0:1.2 0/1:858:144:101,43:440,273:0.1678:2,2:24.8:1:29:1:0.05863:1.46:60:71:0.1675:0:1.1 -12 443372 . G C 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=TAATCCACTAGACTTTAGTA;RSEQ=AGTTCATGCATGCTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:339,108:0:2,0:24.1:1:31.8:1:1:0:60:73.5:0.9955:0:0 0/1:261:9:7,2:187,65:0.0345:2,2:18.1:1:31.1:1:1:1.22:60:18:0.0349:0:1.1 -12 459805 . C A 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCTCTTCTTCTGGCAGAAT;RSEQ=TTTCTCCGCCCATCCTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1658:25:15,10:872,759:0.0151:2,2:23.6:1:29.4:1:0.551:1.31:60:50:0.0152:0:1.1 0/0:1088:0:0,0:575,512:0:2,0:25.5:1:31.3:1:1:0:60:82.615:1:0:0.2 -12 459955 . G GA 92 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.77612;SOR=0.71449;LSEQ=GTGGGAACCATCTACACAGG;RSEQ=AAAAAAAAGATGACAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:811:9:5,4:239,562:0.0111:2,2:29.8:1:29.1:1:0.13807:2.93:60:18:0.0112:0.0012:0.3 0/0:503:4:0,4:167,332:0.008:2,0:28:1:29.5:1:0.30697:0:60:8:0.008:0:0.3 -12 459976 . T A 45 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01877;SOR=Inf;LSEQ=AAAAAAAAGATGACAAATTA;RSEQ=TAAACCACTATAACTATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:0:0,0:114,426:0:2,0:22.1:1:30:1:1:0:60:53:0.9981:0:0.1 0/1:320:4:3,1:82,234:0.0125:2,2:11.8:1:22.8:1:0.05886:8.49:60:3:0.0096:0:1.5 -12 460226 . C T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTAGGAAATCAAGGAGGAA;RSEQ=AAGGAAATGTAAACAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:0,14:1,1:0.875:2,1:16:1:27.8:1:0.125:0:60:28:0.9333:0:1 1/1:2:2:1,1:0,0:1:0,2:11.5:1:28.5:1:1:0:60:4:1:0:1 -12 461598 . C A 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12024;LSEQ=TTCCCTAGGTAAAGTAAATC;RSEQ=AGTCAACCCTAGACAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:135:117:1,116:0,18:0.8667:1,1:28.1:1:31.1:1:1:0:60:234:0.8731:0:1.5 1/1:58:51:0,51:0,7:0.8793:0,1:24.5:1:30.4:1:1:0:60:50:0.8772:0:1.5 -12 461637 . C T 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4425;SOR=0.59168;LSEQ=AAACAAATATCAGCTACTTA;RSEQ=AATACCGTATCAGGAAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:68:1,67:0,5:0.9315:0,1:21.9:1:28.9:1:1:0:60:67:0.9306:0:1.9 1/1:27:24:0,24:0,3:0.8889:0,1:25:1:28.4:1:1:0:60:48:0.8889:0:2 -12 461807 . A G 75 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCTAGGGATGCCTAAC;RSEQ=TTCTTGGCATACCCAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:36.2:1:29.3:1:1:0:60:5:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 463405 . T TA 159 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.09522;SOR=0.62225;LSEQ=AAACATAGAGATCAACCTGT;RSEQ=AAAAAAAAAATAAATGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:856:44:10,34:254,551:0.0514:2,2:30.2:1:29.2:1:0.24532:1.56657:59.9:21:0.05:0.0035:0.1 0/1:644:21:8,13:214,406:0.0326:2,2:28:1:29.1:1:0.81637:1.17:59.5:42:0.0333:0:0.3 -12 463460 . G C 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATAATAAATTTTTACCA;RSEQ=GAACTCCTTAGCTGAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:16,260:0:2,0:23.8:1:31.3:1:1:0:60:68:1:0:0.1 0/1:168:16:2,14:8,144:0.0952:2,2:16.3:1:28.8:1:0.2437:2.55:60:15:0.0915:0:1.1 -12 463930 . C CA 49 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAACAGCAAGACTCCGTCT;RSEQ=AAAAAAAAAAGGAAAGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:31:1:31:1:1:0:58.3:6:0.75:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 464254 . T C 270 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27277;SOR=0.75052;LSEQ=TAAACACATACCATGATATA;RSEQ=CAGGATAGAAAGTGCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:402:356:296,60:35,11:0.8856:2,2:22:1:31.9:1:0.22487:1.55:60:117.667:0.8869:0:1.1 1/1:245:209:172,37:30,5:0.8531:2,2:22.7:1:31:1:0.80956:1.28941:60:208:0.8595:0:1.1 -12 465673 . C G 212 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATCTGAAGTTTCTTCAGTT;RSEQ=CGTGTTTCTACTCACATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1196:98:38,60:437,661:0.0819:2,2:27:1:32.2:1:0.91432:1.04384:60:196:0.0832:0:1.2 0/0:932:0:0,0:384,547:0:2,0:25.2:1:30.6:1:1:0:60:83.636:0.9989:0:0.1 -12 466176 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCGAATGGCCAGACACA;RSEQ=TGGCTCACACCTGTAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:31:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:14:0:30:1:1:0:60:4:1:0:1.5 -12 476972 . G A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGATCAAGGCTGCAGC;RSEQ=AGCCATGATCACACCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 493157 . C T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16864;SOR=5.49748;LSEQ=ATTTGATATTCCTAAATTCA;RSEQ=AAGCCTGTGCTCTAATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:1:0,1:375,122:0.002:2,0:1:0:27:0:0.24699:0:60:2:0.002:0:1 0/1:365:4:1,3:257,104:0.011:2,2:9.3:1:26.3:1:0.07749:7.36756:60:8:0.0111:0:1 -12 493443 . A G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00577;SOR=0.23242;LSEQ=GGCCTGTTAGGAACCCAGCC;RSEQ=CACAGCAGGAGGTGAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:75:0,75:0,7:0.9146:0,1:24.9:1:32:1:1:0:60:24:0.9114:0:1.1 1/0:38:27:1,26:0,11:0.7105:0,1:28:1:32.3:1:1:0:60:54:0.7105:0:1 -12 495217 . G T 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02861;SOR=0.39176;LSEQ=AATTATTCCCTTAAAGGGGG;RSEQ=TTTTGCCACAAATCATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:152:141:4,137:0,11:0.9276:0,1:23.7:1:29.7:1:1:0:60:22.5:0.9247:0:1.1 1/1:84:70:3,67:0,14:0.8333:1,1:21.6:1:30.5:1:1:0:60:140:0.8333:0:1 -12 495652 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCAATAAACAATCATTTC;RSEQ=TTACACTTATTTCCACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 497910 . T G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48392;SOR=2.0153;LSEQ=AAGAGACACCACTTTCTCGC;RSEQ=TTCAGACGTGTCTACATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:50:50,0:7,0:0.8772:0,1:26.8:1:28.8:1:1:0:60:15.667:0.8704:0:1.2 1/1:31:29:28,1:2,0:0.9355:0,1:20.5:1:30.8:1:1:0:60:58:0.9355:0:1.2 -12 497958 . T G 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00217;SOR=Inf;LSEQ=AAGAAACCGAGGCAAAAACA;RSEQ=CCAGAAACAGGCTCCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:149,1:0:1,0:22.7:1:31.3:1:1:0:60:74:1:0:0.2 0/1:110:7:6,1:101,2:0.0636:1,2:36.1:1:32:1:0.18056:8.0519:60:14:0.066:0:1.6 -12 500430 . C A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTTGAGACCAGCCTGGC;RSEQ=AACATGGTGAAATCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30.5:1:1:0:60:4:1:0:1 -12 1022352 . A G 155 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=0.05979;LSEQ=TCTGTCCAGAGCCTCTCCCT;RSEQ=CTAGAGTGATGGACAAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:25:25,0:44,0:0.3623:1,1:23.1:1:33.4:1:1:0:60:50:0.3623:0:1 0/1:31:1:1,0:30,0:0.0323:1,0:21:0:26:0:1:0:60:2:0.0323:0:1 -12 1022452 . C T 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21594;LSEQ=CAGAATGAAGCAAGATAAAT;RSEQ=GCAATGACGTTCATTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:294:205:191,14:80,9:0.6973:2,2:22.8:1:30.4:1:0.34979:1.53:60:204:0.7034:0:1.1 0/1:169:56:50,6:98,15:0.3314:2,2:23.9:1:30.4:1:0.80543:1.27:60:112:0.3353:0:1 -12 1022453 . G A 123 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=38.59166;LSEQ=AGAATGAAGCAAGATAAATC;RSEQ=CAATGACGTTCATTCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:1:1,0:271,25:0.0034:2,0:22:0:14:0:1:0:60:0:0:0:8 0/1:173:20:15,5:135,18:0.1156:2,2:21.4:1:28.6:1:0.15136:2.48306:60:19:0.1105:0:1.2 -12 1022569 . A C 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AGCCTCAGTTAAGATGGATC;RSEQ=TATTTCCTTTTCTTCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1193:0:0,0:575,616:0:2,0:25.1:1:30.3:1:1:0:60:118.1:0.9983:0:0.1 0/1:948:22:14,8:444,479:0.0232:2,2:32.4:1:29.5:1:0.19531:1.89:60:21:0.0223:0:1.4 -12 1022679 . A G 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAAAATAAACTGACAGCTA;RSEQ=TGATTTCTGGATTATATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:42,269:0:2,0:22.2:1:31:1:1:0:60:61.2:1:0:0.1 0/1:222:66:16,50:39,117:0.2973:2,2:18.2:1:31.5:1:1:1.04148:60:132:0.2973:0:1 -12 1023218 . G T 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCTGGGTCTGCTCTAGAC;RSEQ=AGGGCTTGACCACACCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:895:0:0,0:352,541:0:2,0:25.3:1:30.5:1:1:0:60:62.786:0.9977:0:0.1 0/1:603:46:20,26:234,322:0.0763:2,2:21.5:1:29.3:1:0.87742:1.06:60:92:0.0772:0:1.2 -12 1023273 . T A 50 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01283;SOR=Inf;LSEQ=CACAGCCCACTTTTCAGAGT;RSEQ=GTCTTCAAGAGTCTCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:0:0,0:152,356:0:2,0:25.1:1:29.9:1:1:0:60:55.444:0.996:0:0.1 0/1:369:5:5,0:133,230:0.0136:2,0:8.6:1:21.6:1:0.00708:0:60:4:0.0111:0:1.2 -12 1023348 . C G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11479;SOR=Inf;LSEQ=AAGTATTCTCACAGAAAGCA;RSEQ=TGGAAAAACTGGCCCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:28,133:0:2,0:25.5:1:32.1:1:1:0:60:25.833:1:0:0.2 0/1:83:2:1,1:15,66:0.0241:2,2:29:1:33:1:0.35028:4.29:60:4:0.025:0:1 -12 1023503 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11345;SOR=Inf;LSEQ=GAACCCCCTCAACAAAACCA;RSEQ=ACGAAAATGAGGATTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:220,33:0:2,0:21.6:1:31.9:1:1:0:60:49.6:1:0:0.1 0/1:129:2:1,1:106,21:0.0155:2,2:17.5:1:27.5:1:0.31311:4.9549:60:4:0.0156:0:2.5 -12 1023997 . TA T 60 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTGTCTGGCTCGCTTGT;RSEQ=ACAGCCATAACCCTTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:35.3:1:30:1:1:0:60:8:1:0:0 1/1:1:1:0,1:0,0:1:0,0:40:0:30:0:1:0:60:2:1:0:0 -12 1025332 . C T 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGAAACGGGAAAATGTA;RSEQ=AGCAGATTTAAATATCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:62,3:0,0:1:0,1:22.1:1:31:1:1:0:60:64:1:0:1.1 1/1:18:18:18,0:0,0:1:0,1:22.6:1:30.1:1:1:0:60:36:1:0:1.2 -12 1025475 . C T 69 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.336;SOR=2.10048;LSEQ=GCTACACTTCCTCCTGCAGA;RSEQ=GCCTCCCAGGGCCCTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:4:1,3:508,250:0.0052:2,2:6:1:28.8:1:0.10936:6.08073:60:8:0.0053:0:1.3 0/1:547:6:2,4:353,188:0.011:2,2:11.7:1:26.8:1:0.19088:3.74596:60:5:0.0093:0:1 -12 1026061 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15584;SOR=Inf;LSEQ=TTCTCCCTGACTCACAGATT;RSEQ=CGATTCCTGGAAAATCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:14,229:0:2,0:23.7:1:32:1:1:0:60:39.5:1:0:0.1 0/1:159:2:1,1:9,148:0.0126:2,2:7:1:27.5:1:0.1222:15.65:60:4:0.0126:0:1 -12 1026078 . G A 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56177;SOR=3.1907;LSEQ=ATTGCGATTCCTGGAAAATC;RSEQ=CATTTGACATCCTCCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:1:0,1:2,179:0.0055:1,0:15:0:31:0:1:0:60:2:0.0056:0:1 0/1:115:2:1,1:3,110:0.0174:1,2:23:0:32:0:0.06865:31.90:60:4:0.0177:0:1 -12 1034307 . A G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTATTTTTAGTAGAGAC;RSEQ=GGGTTTCACCGTGTTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:21.4:1:30.9:1:1:0:44.1:14:1:0:1.1 1/1:3:3:3,0:0,0:1:0,0:17.7:1:30:1:1:0:48:6:1:0:1 -12 1034704 . GA G 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00463;SOR=11.52286;LSEQ=CAAAACTCCTAAGGGCAAGA;RSEQ=AAAAAAGGTGAAACAGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1130:1:0,1:408,719:9e-04:2,0:18:0:33:0:1:0:60:2:9e-04:0:0 0/1:791:8:3,5:304,479:0.0101:2,2:30.4:1:31.3:1:1:1.05769:60:16:0.0102:0:0 -12 1034742 . G A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02111;SOR=Inf;LSEQ=GGTTAAGAATTGTTACACAT;RSEQ=AATATCAGAGAATAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:634:0:0,0:146,488:0:2,0:22.7:1:31.3:1:1:0:60:78.25:1:0:0.1 0/1:392:4:3,1:101,285:0.0102:2,2:10:1:26.5:1:0.05971:8.41:60:8:0.0103:0:1 -12 1034788 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10631;SOR=Inf;LSEQ=TTTGTACAGGTTGCTTCTCA;RSEQ=GAGCAGCAGAGGAAGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:5,242:0:1,0:23.6:1:31.2:1:1:0:60:122.5:1:0:0.1 0/1:120:2:1,1:4,114:0.0167:1,2:8.5:1:28.5:1:0.08193:25.60:60:4:0.0169:0:1 -12 1034943 . C T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGAGTATGAAAAGATTA;RSEQ=GGCGCCATTCACAAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:22:1:31:1:1:0:60:10:0.2632:0:1 0/0:2:0:0,0:0,2:0:0,0:23.5:1:31:1:1:0:60:4:1:0:0 -12 1035947 . C A 75 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCGTGACTGTGTAACTA;RSEQ=GTTAACTATGCTACCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:21.9:1:26.9:1:1:0:60:6:1:0:1.4 1/1:1:1:1,0:0,0:1:0,0:3:0:29:0:1:0:60:2:1:0:1 -12 1036042 . C T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51648;SOR=0;LSEQ=AGTAGGAGTGGGAAGGCCTC;RSEQ=GGCACACATGACTGAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:0.2727:0,0:30.3:1:32:1:1:0:60:6:0.2727:0:1 0/0:4:0:0,0:4,0:0:0,0:16:1:30.5:1:1:0:60:8:1:0:0.8 -12 1036239 . C CA 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.43326;SOR=2.26999;LSEQ=TGTGGATGTGTTACCTCTTC;RSEQ=AAAAAAAATCGAAATCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:3:3,0:330,57:0.0077:2,0:8.7:1:31.3:1:1:0:60:6:0.0078:0.0051:0 0/1:231:4:3,1:183,44:0.0173:2,2:34:1:29:1:0.58232:1.38421:60:8:0.0179:0:0 -12 1036481 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13205;SOR=Inf;LSEQ=ACGAGAGCGGCAGGCGTGCC;RSEQ=CAACTCCCCTGTTCCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:53,293:0:2,0:23.7:1:29.8:1:1:0:60:114.333:1:0:0.1 0/1:198:2:1,1:41,155:0.0101:2,2:28:1:29.5:1:0.3801:3.75:60:4:0.0104:0:1 -12 1036498 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11111;SOR=Inf;LSEQ=GCCACAACTCCCCTGTTCCT;RSEQ=AAGCAGCAGGGTTCAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:17,227:0:2,0:25.8:1:32:1:1:0:60:47.8:1:0:0.1 0/1:123:2:1,1:17,104:0.0163:2,2:13.5:1:27:1:0.27229:5.97:60:4:0.0164:0:1 -12 1036562 . AG A 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00068;SOR=0;LSEQ=GCTACAGGGGCACGGGCAGA;RSEQ=GCTGGGTGAGAATCCATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:22:0,22:0,52:0.2973:1,1:22.9:1:32.6:1:1:0:60:44:0.2973:0.0676:0.2 0/0:26:0:0,0:0,26:0:1,0:20.9:1:29.6:1:1:0:60:25:1:0:0.3 -12 1036626 . C T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGCCTGGACATGTGCCTG;RSEQ=GGTCAAGGTGTCAAGACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:20:0,20:0,0:0.9524:0,1:23.3:1:28:1:1:0:60:9:0.9474:0:1.5 1/1:8:8:1,7:0,0:1:0,2:30.4:1:30.4:1:1:0:60:16:1:0:1.1 -12 1038602 . AT CA 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACAACTTATTAACAAAAC;RSEQ=ATTTTTGTTTTCATCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:0,0:0.8333:0,0:20.6:1:30.7:1:1:0:60:10:1:0.1667:0.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 1038742 . A G 103 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=CCAAAAAATACATCCTTTGC;RSEQ=ACAATTTTTATATATGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:11,0:10,0:0.5238:0,0:21.7:1:30:1:1:0:60:22:0.5238:0:1.1 0/0:2:0:0,0:2,0:0:0,0:39:1:29.5:1:1:0:60:4:1:0:0 -12 1038766 . C G 115 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53613;SOR=0;LSEQ=ATTTTTATATATGGTGAAAA;RSEQ=TTTTAGGTGTCAGCTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:12,0:21,0:0.3636:1,0:19.6:1:32.1:1:1:0:60:24:0.3636:0:1.2 0/0:3:0:0,0:3,0:0:0,0:27.3:1:30.7:1:1:0:60:6:1:0:0 -12 1038854 . C T 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00168;SOR=0;LSEQ=AGAGTATTTGAATTCCACCA;RSEQ=TCTAGGGAACGCTGGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:25:25,0:140,2:0.1497:1,1:24.8:1:31.1:1:1:0:60:50:0.1515:0:1.1 0/0:51:0:0,0:48,3:0:2,0:22:1:31.6:1:1:0:60:102:1:0:0.1 -12 1038978 . C CT 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.24413;LSEQ=GGCAGCAGGTCTACTCCATC;RSEQ=CCTCACCTTCAGCTGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1021:252:140,112:395,373:0.2468:2,2:27.2:1:30.3:1:0.27575:1.18:60:35:0.2448:0.0264:0.1 0/1:770:57:27,30:391,321:0.074:2,2:26.8:1:29.7:1:0.27329:1.35286:60:56:0.0739:0.0156:0.1 -12 1039099 . G A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05441;SOR=7.45142;LSEQ=AAGAGGACACTGACCGCTGG;RSEQ=CCACAACCATTCCTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:1:1,0:218,249:0.0021:2,0:46:0:16:0:0.46795:0:60:0:0:0:1 0/1:254:4:3,1:102,148:0.0157:2,2:21.5:1:29:1:0.30958:4.33:60:8:0.0159:0:1 -12 1039105 . A G 107 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=19.79253;LSEQ=ACACTGACCGCTGGGCCACA;RSEQ=CCATTCCTCCTGCTGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:1:0,1:216,233:0.0022:2,0:22:0:13:0:1:0:60:0:0:0:1 0/1:236:10:5,5:94,132:0.0424:2,2:25:1:32.3:1:0.74586:1.40:60:20:0.0431:0:1 -12 1039335 . A G 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAACAAATGTTTTTAAGG;RSEQ=AAAGCTGTGTTAATTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:916:0:0,0:313,603:0:2,0:25:1:30:1:1:0:60:113.5:1:0:0.1 0/1:652:31:13,18:233,388:0.0475:2,2:28.5:1:30.1:1:0.70481:1.20:60:30:0.0464:0:1.2 -12 1039439 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55067;SOR=0;LSEQ=GTCCTTAAACATTCTTCTCG;RSEQ=GAGGCTGAGGTGGGAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:0,2:0,89:0.022:1,0:18.5:1:32.5:1:1:0:60:4:0.0227:0:1 0/0:46:0:0,0:1,45:0:1,0:21:1:29.8:1:1:0:60:22:1:0:0.1 -12 1040143 . TA T 90 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.52273;SOR=0;LSEQ=CAAGACCCTGTCTTTAAAAA;RSEQ=AAAAAAAAAAAAGATGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:7,0:10,0:0.3684:0,0:27:1:32.3:1:1:0:60:14:0.3684:0.0526:0 0/0:3:0:0,0:3,0:0:0,0:11.7:1:29.3:1:1:0:60:6:1:0:0 -12 1040219 . G A 78 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=37.17724;LSEQ=GACCATGCCCAGGCCCCTTC;RSEQ=GATGAGAATGAAGTCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:1:1,0:73,0:0.0135:1,0:16:0:30:0:1:0:60:2:0.0135:0:2 0/1:17:6:6,0:10,1:0.3529:2,0:38.2:1:30.5:1:1:0:60:12:0.3529:0:1.2 -12 1040307 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.268;SOR=3.90453;LSEQ=GCAGACTTCCGAATCCCTGA;RSEQ=GACCCAGAGAGGGAACTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:0,1:255,31:0.0035:2,0:1:0:28:0:0.1115:0:60:2:0.0035:0:3 0/1:148:2:1,1:125,21:0.0135:2,2:21:1:29:1:0.27606:5.83878:60:4:0.0135:0:1.5 -12 1040373 . T C 301 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGCCTGCTTTCCAGGCACA;RSEQ=GAATTCTCCTACCTTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:800:800:539,261:0,0:1:0,2:26:1:31.3:1:1:0:60:159:1:0:1.1 1/0:528:321:199,122:130,77:0.608:2,2:27.1:1:30.2:1:0.92674:1.03499:60:44.857:0.605:0:1.1 -12 1041951 . C G 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03954;SOR=Inf;LSEQ=TACTAGGTACTGCCCCCGCA;RSEQ=GCACCGCGTCAACGTACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:87,1:0:1,0:23.2:1:32.3:1:1:0:59.9:87:0.9886:0:0 0/1:47:3:3,0:40,4:0.0638:2,0:13.7:1:33.7:1:1:0:50:6:0.0638:0:2 -12 1041953 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.01382;SOR=Inf;LSEQ=CTAGGTACTGCCCCCGCACG;RSEQ=ACCGCGTCAACGTACTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:90,1:0:1,0:23.7:1:32.1:1:1:0:59.9:29.333:1:0:0 0/1:49:4:4,0:41,4:0.0816:2,0:12:1:31.8:1:1:0:51.3:8:0.0816:0:1.8 -12 1041961 . CAACGTACTAGGTACTGCTCACACACGTACTAGGTA C 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=59;MSI=3.000;MSILEN=1;SSF=0.61812;SOR=0.83185;LSEQ=TGCCCCCGCACGCACCGCGT;RSEQ=AACGTACTAGGTACTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:112:69:68,1:42,1:0.6161:1,1:16:1:31.7:1:1:1.61:59.7:138:0.6216:0.2054:0.1 1/0:56:32:31,1:21,3:0.5714:2,1:22:1:32:1:0.30318:4.32:58.9:64:0.5818:0.125:0.2 -12 1041979 . T C 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13878;SOR=Inf;LSEQ=GTCAACGTACTAGGTACTGC;RSEQ=CACACACGTACTAGGTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:33,1:0:1,0:25.5:1:29.6:1:1:0:60:33:1:0:0 0/1:48:2:2,0:18,3:0.0417:2,0:44:0:30:1:1:0:60:4:0.0909:0:8 -12 1041981 . A C 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.14098;SOR=Inf;LSEQ=CAACGTACTAGGTACTGCTC;RSEQ=CACACGTACTAGGTAAACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:32,1:0:1,0:24.2:1:28.5:1:1:0:60:66:1:0:0 0/1:48:2:2,0:18,3:0.0417:2,0:42:0:30:1:1:0:60:4:0.087:0:8 -12 1041983 . A G 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.14098;SOR=Inf;LSEQ=ACGTACTAGGTACTGCTCAC;RSEQ=CACGTACTAGGTAAACGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:32,1:0:1,0:22.2:1:28.8:1:1:0:60:66:1:0:0 0/1:48:2:2,0:18,3:0.0417:2,0:40:0:29.5:1:1:0:60:4:0.0909:0:8 -12 1041986 . C G 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14175;SOR=Inf;LSEQ=TACTAGGTACTGCTCACACA;RSEQ=GTACTAGGTAAACGTACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:30,1:0:1,0:20.5:1:30.1:1:1:0:60:30:1:0:0 0/1:47:2:2,0:17,3:0.0426:2,0:37:0:31.5:1:1:0:60:4:0.0909:0:8 -12 1041991 . TAG CGC 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13538;SOR=Inf;LSEQ=GGTACTGCTCACACACGTAC;RSEQ=GTAAACGTACTAGGTACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:26,1:0:1,0:18.2:1:28.7:1:1:0:60:12.5:1:0:0 0/1:43:2:2,0:14,2:0.0465:2,0:30:0:29.7:1:1:0:60:4:0.1111:0:6 -12 1041996 . A C 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13011;SOR=Inf;LSEQ=TGCTCACACACGTACTAGGT;RSEQ=AACGTACTAGGTACTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:23,1:0:1,0:15.1:1:26:1:1:0:60:48:1:0:0 0/1:40:2:2,0:12,1:0.05:1,0:27:0:30:1:1:0:60:4:0.1333:0:6 -12 1042103 . C T 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=18.9679;LSEQ=TGCCCTAACTTTACTCACTT;RSEQ=ACCTCATTCTTTCCCGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:759:2:0,2:509,248:0.0026:2,0:1:0:23.5:1:0.1082:0:60:4:0.0027:0:1 0/1:523:25:18,7:316,182:0.0478:2,2:21:1:29.7:1:0.52284:1.48:60:50:0.0483:0:1.3 -12 1042261 . G GA 144 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.88026;SOR=0.91038;LSEQ=CTCTATATAAATAAAAAGCG;RSEQ=AAAAAAAAAACAACCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:29:7,22:92,347:0.0611:2,2:27:1:29.8:1:0.64361:1.20:60:58:0.0647:0:0.1 0/1:340:19:3,16:80,234:0.0559:2,2:30.1:1:29.6:1:0.42447:1.82054:60:38:0.0579:0:0.1 -12 1043521 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTGTAATTCCAGCTACT;RSEQ=GGGAGGCTGAGGTAGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 1820080 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51531;SOR=0;LSEQ=TGACAAGGAGTTTAAAAATA;RSEQ=GGGCCTGAAGGCGAGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:2,0:21,7:0.0667:2,0:29.5:1:31:1:1:0:60:4:0.0667:0:1.5 0/0:19:0:0,0:12,7:0:2,0:18.4:1:29.6:1:1:0:60:38:1:0:0.3 -12 2017413 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CGGCGCGGAGAGGCGTGAGG;RSEQ=CGACGTTTGATGACAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:29.4:1:32.1:1:1:0:60:18:1:0:0.1 0/1:6:2:1,1:2,2:0.3333:2,2:5.5:1:32:1:1:1:60:4:0.3333:0:1 -12 2017754 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTCCACACGACCGGGTTCA;RSEQ=ACCTGAACACCCCCCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:28.5:1:30:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 2017892 . T A 41 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CGCCAACTCCCACGCCGGAC;RSEQ=GCGTCACGGACATCCCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:8:1:32:1:1:0:57:4:1:0:0.5 1/1:3:3:1,2:0,0:1:0,2:31:1:26:1:1:0:26.3:2:1:0:1 -12 2018088 . C A 27 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=GCCAACTCCCACGCCAGGTT;RSEQ=CTGCACCCCACACCCGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:26.6:1:31.8:1:1:0:60:10:1:0:0.4 1/1:2:2:1,1:0,0:1:0,2:27:1:27:1:1:0:60:4:1:0:2.5 -12 2018124 . T C 41 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GGCTCCTCCTCACGACACTG;RSEQ=GGCCCGCGCTGGCCTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:0.25:2,0:47:0:28:0:1:0:60:2:0.25:0:2 1/1:3:3:1,2:0,0:1:0,2:22.3:1:26.3:1:1:0:60:6:1:0:2.7 -12 2018272 . C G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTCACCTAACTGTCCAAGAC;RSEQ=ACTGCCTTCCTCACCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:22.5:1:31.5:1:1:0:60:4:1:0:0.5 1/0:3:2:1,1:1,0:0.6667:0,2:17:0:32:1:1:0:60:4:1:0:1.5 -12 2018280 . T G 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGTCCAAGACCACTGCCT;RSEQ=CCTCACCAGCCTCTGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:50:0:30:0:1:0:60:2:1:0:0 0/1:5:2:1,1:2,1:0.4:2,2:5.5:1:31.5:1:1:1.7321:60:4:0.5:0:1 -12 2018987 . A G 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCAGTGGATCGCCACCCT;RSEQ=CGCCGCCACCCTATGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:36:1:33:0:1:0:60:4:1:0:1 -12 2403450 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23368;SOR=Inf;LSEQ=CGAGAAGACATGGCAGCGGT;RSEQ=GTGGGTCCTGGCAGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:13,26:0:2,0:25.4:1:31.3:1:1:0:60:78:1:0:0.1 0/1:37:2:0,2:14,21:0.0541:2,0:6.5:1:30.5:1:0.51652:0:60:4:0.0541:0:1 -12 3001081 . C A 44 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AAAATAAAATAAAATAAAAT;RSEQ=AATCAGTCAATCAATTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:14.3:1:28.3:1:1:0:60:6:0.6:0:1 0/0:2:0:0,0:2,0:0:0,0:19:1:33:0:1:0:60:4:1:0:1.5 -12 3001202 . C A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56854;SOR=1.62419;LSEQ=TTCCAAACTCCTGTGTTGGG;RSEQ=CACTGAGCTCGCTAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:5,0:22,3:0.1613:2,0:14.8:1:30.2:1:1:0:60:10:0.1786:0:2.2 0/1:46:11:11,0:31,4:0.2391:2,0:25.5:1:29.4:1:0.55881:0:60:22:0.25:0:2.3 -12 3001213 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55116;SOR=Inf;LSEQ=TGTGTTGGGCCACTGAGCTC;RSEQ=CTAGCCTGGGCAACGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:31,3:0:2,0:23.6:1:29.6:1:1:0:59.6:33:1:0:1.3 0/1:68:2:1,1:56,10:0.0294:2,2:27:1:27.5:1:0.29939:5.38694:60:4:0.0303:0:1.5 -12 3001248 . T TA 139 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=4e-05;SOR=0.27095;LSEQ=GCAGTGACATCCTGTCACCT;RSEQ=AAAAAAAAAATGATTTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:32:25,7:25,8:0.4384:2,2:30.1:1:27.9:1:1:1.14:59.5:15:0.4225:0:2.2 0/1:167:29:20,9:83,37:0.1737:2,2:23.5:1:28.3:1:1:1.0094:59.7:28:0.1697:0:2 -12 3001268 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.197;LSEQ=TAAAAAAAAAATGATTTGAC;RSEQ=TGTAAGTATTTAGTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:112:72:52,20:27,13:0.6429:2,2:25:1:29.5:1:0.66724:1.25:59.5:17:0.6355:0:2.7 0/1:211:55:38,17:103,53:0.2607:2,2:26.3:1:28.9:1:0.7408:1.15:59.8:17.333:0.2537:0:2.6 -12 3001275 . T G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19653;LSEQ=AAAATGATTTGACGTGTAAG;RSEQ=ATTTAGTTTGATATTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:122:78:55,23:31,13:0.6393:2,2:25.2:1:31.2:1:1:1.00:59.7:77:0.6364:0:2.6 0/1:237:61:40,21:116,60:0.2574:2,2:27:1:30.3:1:1:1.01494:59.8:60:0.2575:0:2.6 -12 3001344 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20565;LSEQ=TTTTTAAAAATTGTCACAAA;RSEQ=TTGTTGGGGGTAAAGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:157:89,68:51,40:0.6331:2,2:26.1:1:30.3:1:1:1.03:60:77.5:0.6301:0:1.6 0/1:482:126:71,55:195,159:0.2614:2,2:23.4:1:29.5:1:0.83517:1.05:60:30.5:0.2552:0:1.4 -12 3001424 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28288;SOR=Inf;LSEQ=TGCACTCTGAAATTTGTTCA;RSEQ=TGTGCTTTTTTTTTTCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:48,107:0:2,0:23.6:1:31.2:1:1:0:60:21.143:1:0:0.5 0/1:243:3:1,2:76,164:0.0123:2,2:24.7:1:24:1:1:1.08:60:2:0.0087:0:2 -12 3001429 . C CT 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.69584;SOR=0.83734;LSEQ=TCTGAAATTTGTTCACTGTG;RSEQ=TTTTTTTTTTCCCAAGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:13:3,10:38,95:0.0872:2,2:22.3:1:28.9:1:1:1.33089:60:12:0.0845:0.0067:0.8 0/1:216:16:4,12:55,143:0.0741:2,2:26.7:1:27.9:1:1:1.15309:58.8:7:0.0693:0:0.8 -12 3001493 . A G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00952;SOR=0.30141;LSEQ=GTAAGTGGTAGAGGAGATAA;RSEQ=GTTAGTATTCAGCATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:22:0,22:1,16:0.5641:1,1:26.3:1:31.6:1:0.4359:0:60:44:0.5789:0:1.5 0/1:54:15:0,15:1,38:0.2778:1,1:24.9:1:27.9:1:1:0:60:6.5:0.25:0:1.7 -12 3001523 . C A 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25903;SOR=0.45705;LSEQ=CAGCATCTCTGGTTGAATTC;RSEQ=GAAAATATTTGTTCAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:0,12:1,11:0.5:2,0:26.1:1:31.5:1:1:0:60:24:0.5:0:1.8 0/1:29:9:0,9:1,19:0.3103:1,0:28.4:1:31.8:1:1:0:60:18:0.3103:0:2 -12 3001616 . AT A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGTTTGATATGACTCAG;RSEQ=TTTTTGGGGAAAAAAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:12:1:30:1:1:0:60:4:0.2857:0.125:2 0/0:3:0:0,0:0,3:0:0,0:22.3:1:28.3:1:1:0:60:6:1:0:1.7 -12 3001627 . A G 24 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGACTCAGATTTTTTGGGG;RSEQ=AAAAAAAACGGGATGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:12.5:1:24:1:1:0:60:4:0.3333:0:2 0/0:2:0:0,0:0,2:0:0,0:21:1:30.5:1:1:0:60:4:1:0:0 -12 3001716 . T G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGACGGAGTCTCTCTCTG;RSEQ=CGCCAGGCGGTAGTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:7.5:1:29.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 3361739 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24976;SOR=Inf;LSEQ=CACATGCGGGGAGCCTGCCG;RSEQ=TAGCTGGGCCTGGGCCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:54,29:0:2,0:23.1:1:31:1:1:0:60:15.6:1:0:0.2 0/1:96:3:1,2:59,34:0.0313:2,2:12.3:1:30.3:1:0.55403:3.42401:60:6:0.0316:0:1 -12 3361743 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22543;SOR=0;LSEQ=TGCGGGGAGCCTGCCGCTAG;RSEQ=TGGGCCTGGGCCGACTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:57,31:0.0222:2,2:34:1:32:1:1:1.82563:60:4:0.0227:0:1 0/0:99:0:0,0:62,37:0:2,0:24:1:31.6:1:1:0:60:98:1:0:0.1 -12 3361750 . TGG T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49841;SOR=Inf;LSEQ=AGCCTGCCGCTAGCTGGGCC;RSEQ=GCCGACTCTTGCAAGATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:67,42:0:2,0:23.6:1:30.4:1:1:0:60:17.167:1:0:0.1 0/1:117:2:1,1:69,45:0.0171:2,2:21.5:1:30:1:1:1.52748:60:4:0.0172:0:0 -12 3361755 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49937;SOR=Inf;LSEQ=GCCGCTAGCTGGGCCTGGGC;RSEQ=GACTCTTGCAAGATCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:69,46:0:2,0:24.3:1:29.4:1:1:0:60:22:1:0:0.2 0/1:128:2:1,1:75,51:0.0156:2,2:24.5:1:31.5:1:1:1.46602:60:4:0.0157:0:1 -12 3361756 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49935;SOR=Inf;LSEQ=CCGCTAGCTGGGCCTGGGCC;RSEQ=ACTCTTGCAAGATCCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:71,47:0:2,0:24.3:1:29.5:1:1:0:60:38.333:1:0:0.2 0/1:131:2:1,1:75,53:0.0153:2,2:13:0:32:0:1:1.41122:60:4:0.0153:0:1.5 -12 3361799 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21375;SOR=0;LSEQ=ATCACAGCCGGAGTCAGCTG;RSEQ=TGGTTTGGGAAGCCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:69,86:0.0127:2,2:43.5:1:33:1:1:1.24:60:4:0.013:0:1 0/0:182:0:0,0:91,91:0:2,0:26.5:1:29.6:1:1:0:60:90:1:0:0.2 -12 3361806 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50116;SOR=Inf;LSEQ=CCGGAGTCAGCTGTTGGTTT;RSEQ=GGAAGCCTTCCCTGGTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:62,90:0:2,0:27.2:1:31.1:1:1:0:60:75:1:0:0.1 0/1:176:2:1,1:84,90:0.0114:2,2:22:0:31.5:1:1:1.07:60:4:0.0117:0:1 -12 4383036 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42528;SOR=0.44157;LSEQ=CACCACCCAATCCTCGCCTC;RSEQ=CTTCTGCTCCACCTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:14,0:5,1:0.7:2,1:29.1:1:31.1:1:0.3:0:60:28:0.7:0:1 1/0:10:5:5,0:4,1:0.5:2,0:18.4:1:32.2:1:1:0:60:10:0.5:0:1 -12 4383158 . T C 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.71495;LSEQ=AAAACAAAAACAGAAAAACC;RSEQ=TTTTCCAGGCCGGGGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:217:181,36:0,0:0.9954:0,2:21.9:1:31:1:1:0:60:35.167:0.9953:0:1.1 1/1:156:155:119,36:0,0:0.9936:0,2:20.9:1:30.4:1:1:0:60:30:0.9934:0:1.2 -12 4383246 . G T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01924;SOR=Inf;LSEQ=AGGTGGACCCGGTCCGCAGG;RSEQ=CCGTGCGGGACCGCAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:334,230:0:2,0:24.9:1:31.1:1:1:0:60:55.4:0.9946:0:0.2 0/1:473:5:2,3:257,211:0.0106:2,2:27.4:1:27.6:1:0.66228:1.82466:60:10:0.0108:0:1 -12 4383433 . A G 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08573;SOR=Inf;LSEQ=GGTGGCGCTCGCCAGGAGCC;RSEQ=GGACCCCTCCGGATGCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:78,258:0:2,0:24:1:30.9:1:1:0:60:111:1:0:0.1 0/1:266:3:2,1:74,189:0.0113:2,2:6.7:1:24.7:1:0.19726:5.07:60:2:0.0076:0:2.7 -12 4383448 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18074;SOR=Inf;LSEQ=GAGCCAGGACCCCTCCGGAT;RSEQ=CTCGGGTCCCCGGCCGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:46,217:0:2,0:22.1:1:31.9:1:1:0:60:51.6:1:0:0.1 0/1:195:2:1,1:39,154:0.0103:2,2:26.5:1:28.5:1:0.36902:3.91:60:4:0.0104:0:1 -12 4384964 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13904;SOR=Inf;LSEQ=TTATAGGATCCCTGGGAATA;RSEQ=CAAAGCACTGATGGGCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:18,3:0:2,0:19.8:1:31:1:1:0:60:20:1:0:0.1 0/1:13:2:1,1:9,2:0.1538:2,2:18:1:29:1:0.42308:3.87298:60:4:0.1538:0:1 -12 4385055 . C CA 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.6505;SOR=0.36938;LSEQ=CTGGTCCCCTCCCCCTCCCA;RSEQ=AAAAAAAAATTAATTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:4:4,0:127,4:0.0296:1,0:15.8:1:27.8:1:1:0:60:3:0.0234:0.0148:0 0/1:90:1:1,0:89,0:0.0111:1,0:23:0:25:0:1:0:60:2:0.0111:0:0 -12 4385068 . A AT 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.57006;SOR=2.90165;LSEQ=CCTCCCACAAAAAAAAATTA;RSEQ=TTTTTTTTGTTTCGATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:1:1,0:206,3:0.0047:1,0:34:0:28:0:1:0:60:2:0.005:0:0 0/1:147:2:2,0:145,0:0.0136:1,0:20.5:1:30.7:1:1:0:60:4:0.014:0.0068:0.5 -12 4388084 . C G 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.94325;SOR=1.01968;LSEQ=TTCATTGCTCTGTGTGCCAC;RSEQ=GGTAAGATGAGGCTTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:440:224:71,153:66,148:0.5091:2,2:26:1:30.9:1:0.91793:1.04:60:223:0.5126:0:1.1 1/0:358:184:65,119:53,121:0.514:2,2:25.6:1:29.9:1:0.36853:1.25:60:368:0.5169:0:1.1 -12 4388271 . C T 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60784;SOR=2.28225;LSEQ=TTATCTGAGCTTTATATATT;RSEQ=GCTTTCTCTGCTAAACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:0,8:0.3846:0,0:17.4:1:30.6:1:1:0:60:10:0.3846:0:1 1/0:5:3:0,3:0,2:0.6:0,0:33.3:1:31.7:1:1:0:60:6:0.6:0:1 -12 4397766 . G C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14031;SOR=0.37274;LSEQ=TCTGTGCATTCATTGTGTGC;RSEQ=CTTAGATAAGCTGTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:24,0:22,0:0.5217:1,1:23.3:1:31.9:1:1:0:60:48:0.5217:0:1 0/1:14:4:3,1:9,1:0.2857:2,2:17.5:1:31.3:1:0.50549:2.73861:60:8:0.3077:0:1 -12 4408673 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCAGAAAGCATCTGGT;RSEQ=GGCCCCTTGATTACCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:33:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 4409270 . TA T 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.48696;SOR=0.51558;LSEQ=TTGTGTTTTAGGGTGAAACT;RSEQ=AAAAAAAAATTCTGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:6:0,6:2,92:0.06:1,0:34.7:1:31.8:1:1:0:58.5:12:0.0606:0:0.3 0/1:63:2:0,2:2,59:0.0317:1,0:29.5:1:32:0:1:0:60:4:0.0328:0:0 -12 4411343 . CT C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGTCTCACTCCCAGGGAC;RSEQ=TTTTGGTCATGGAGGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:30:1:1:0:60:4:1:0:0 -12 4554413 . C T 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGGGTTCTCCTCGTGGGT;RSEQ=CCGCTGATCCGGCCGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:559:0:0,0:335,224:0:2,0:26.4:1:30.7:1:1:0:60:49.818:1:0:0.1 0/1:502:93:57,36:239,170:0.1853:2,2:21.8:1:28.5:1:0.64195:1.13:60:22.25:0.1813:0:1.2 -12 4554548 . G C 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=GCAATCTCTCCAGCTAGCCC;RSEQ=GCGCGAGACCTGGACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:236:236:20,216:0,0:1:0,2:21.6:1:29.7:1:1:0:60:46.2:1:0:1.1 1/1:189:178:22,156:2,9:0.9418:2,2:22:1:29.7:1:0.6341:1.57137:60:177:0.9415:0:1.1 -12 4554630 . A G 34 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04966;SOR=Inf;LSEQ=GGGTGCCTGCAGGCGAGGGC;RSEQ=CCACCATGCCCACTAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:0,61:0:1,0:27.3:1:29.6:1:1:0:60:29.5:1:0:0.3 0/1:18:2:0,2:1,15:0.1111:1,0:23.5:1:34:0:1:0:60:4:0.1111:0:1 -12 4946467 . T G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTACATCTCTTCATCAC;RSEQ=ATCCTTTGTAATAAACCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 4947235 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.18244;SOR=Inf;LSEQ=GGAGGGATGGGGTGGTTATC;RSEQ=TCATCTGACTGCCTTCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:135,36:0:2,0:23.6:1:30.4:1:1:0:60:170:1:0:0.1 0/1:128:2:1,1:100,26:0.0156:2,2:16:1:30.5:1:0.37869:3.79308:60:4:0.016:0:1.5 -12 4947259 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25612;SOR=0;LSEQ=TCTGACTGCCTTCGGCTGCA;RSEQ=GGTCTCATAAGTTCCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:2,1:175,77:0.0118:2,2:19.3:1:30:1:1:1.13577:60:6:0.0121:0:2 0/0:208:0:0,0:143,65:0:2,0:24.9:1:31.2:1:1:0:60:103:1:0:0.5 -12 4947332 . A G 285 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01111;LSEQ=CCCTCTCCCAGAGCTTAAGA;RSEQ=CCCCTTCCTCAGACGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:497:496:250,246:1,0:0.998:0,2:26.6:1:31.9:1:1:0:60:61:0.998:0:1.5 1/1:422:357:173,184:35,29:0.846:2,2:26.1:1:31.7:1:0.41574:1.28287:60:70.4:0.8441:0:1.5 -12 4947385 . C T 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06748;LSEQ=GGAACACTGTCTCTTTTGTT;RSEQ=TTGGGATGTCCTCCATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:328:323:99,224:1,2:0.9848:2,2:24.5:1:29.8:1:1:1.13087:60:45.143:0.9875:0:1.7 1/1:235:191:59,132:19,24:0.8128:2,2:24.8:1:29.6:1:0.10833:1.76668:60:46.75:0.8095:0:1.8 -12 4947423 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14146;SOR=Inf;LSEQ=AAAATTTCAGAGCTGCCTGG;RSEQ=AATCAAGTTGAGTGGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:24,151:0:2,0:24:1:31.3:1:1:0:60:86.5:1:0:1.2 0/1:106:2:0,2:22,82:0.0189:2,0:34:1:29.5:1:1:0:60:4:0.019:0:2 -12 4947496 . G A 148 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=AAAGCTTTGCCTGCAGCCTC;RSEQ=TGGCTCCTGGCTTGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:0,28:0,0:1:0,1:23.1:1:30.9:1:1:0:60:27:1:0:1 1/0:19:10:0,10:0,9:0.5263:0,0:33.5:1:28.3:1:1:0:60:9:0.5294:0:1.4 -12 6775800 . TA T 28 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGAAATCTGCCATGATT;RSEQ=AAAAAAAAAAAAAAAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:28.5:1:1:0:60:4:1:0:4 -12 6777069 . TTGC T 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=41;MSI=14.000;MSILEN=3;SSF=0.14671;SOR=0.2843;LSEQ=TGGAAGTGTGGTGGTGGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:5,6:5,2:0.55:2,2:27.9:1:29.5:1:0.36652:2.8187:59.5:22:0.55:0.05:0.4 0/1:12:3:1,2:4,2:0.25:2,2:26.7:1:29.8:1:0.52381:3.38757:60:6:0.2727:0.0833:0.7 -12 6887493 . A ACCGGAG 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=23;MSI=4.000;MSILEN=6;SSF=0.12972;SOR=0;LSEQ=ATAGAGGAGCTGGAGCAAGA;RSEQ=CCGGAGCCGGAGCCGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:8,6:0.2222:2,2:32.3:1:30.8:1:1:1.31198:60:8:0.2353:0:0 0/0:12:0:0,0:7,5:0:2,0:23.6:1:29.4:1:1:0:60:24:1:0:0.1 -12 6988887 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=CCTGGGGACAGAGAACAGTG;RSEQ=CTGCCCCATGGCTAGCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:0:2,0:23.3:1:31.5:1:1:0:60:20:1:0:0 0/1:5:2:1,1:3,0:0.4:0,2:16:1:28.5:1:0.4:0:60:4:0.4:0:1 -12 7023774 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48649;SOR=0;LSEQ=CTCTCTCAGCGCCGCCGTCG;RSEQ=CACCGCCACCGCCACCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:37:0:31.5:1:1:1.11803:60:4:0.1053:0:2.5 0/0:18:0:0,0:11,7:0:2,0:21.7:1:31.6:1:1:0:60:36:1:0:0.3 -12 7023804 . T G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03293;SOR=0.175;LSEQ=CGCCACCGCCACTACCACCG;RSEQ=CTGAGTCTGCAGTCCCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:5,5:3,3:0.625:2,2:27:1:32:1:1:1:60:20:0.625:0:1.5 0/1:14:3:2,1:6,5:0.2143:2,2:26:1:31.3:1:1:1.61:60:6:0.2308:0:1.7 -12 7023866 . T C 66 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AGCCCCTGTGGCCCCCTCCC;RSEQ=TCGCCGCGGCGCCCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:19.8:1:33:1:1:0:60:8:1:0:1.5 0/1:5:2:1,1:1,2:0.4:2,2:19:1:30:1:1:1.73:60:4:0.4:0:2 -12 7024304 . G T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGGAGAGATGGAAGAAGT;RSEQ=GGGATCTGTCGAGGCGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:31.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:31.5:1:1:0:60:4:1:0:1 -12 7044647 . A AG 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATGATTTTATGCAAGAG;RSEQ=GCCCCAAATCTCAGGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12:1:32.2:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 7045844 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20814;SOR=Inf;LSEQ=CTACTGGGGCCCAGTCCACC;RSEQ=CCCACCCACCAGTCTCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:17,11:0:2,0:26:1:29.5:1:1:0:60:27:1:0:0 0/1:24:2:1,1:15,7:0.0833:2,2:22:1:27.5:1:1:2.07024:60:4:0.0833:0:1 -12 7045891 . ACAGCAGCAGCAGCAG A 145 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=15.000;MSILEN=3;SSF=0.00648;SOR=0.29351;LSEQ=CATCACCACCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:23:13,10:11,10:0.4792:2,2:31.5:1:32.1:1:1:1.18:60:46:0.4792:0.0417:0 0/1:57:12:6,6:15,14:0.2105:2,2:25.4:1:31.3:1:1:1.06961:60:24:0.2143:0.0175:0.5 -12 7061466 . A G 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCTCCCCTCCCTGCACC;RSEQ=GCTGGGGCTCTCAATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:18.3:1:32.3:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 8200060 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTCAAAAAACAAAAAAC;RSEQ=GAAGGAAGAGGAGATAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 8200557 . ACAG A 47 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.60984;SOR=3.0661;LSEQ=CAGCAGCCACCGCCACCTCA;RSEQ=CAGCAGCAGCAGCAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:14,10:0.04:2,0:41:0:34:0:0.44:0:60:2:0.0417:0:0 0/1:26:3:1,2:12,11:0.1154:2,2:23:1:30:1:1:2.11883:60:6:0.1154:0.0385:0.3 -12 8679272 . A C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22857;SOR=0;LSEQ=TTATTATCCATCTTCTATAG;RSEQ=TTACTTCTATCAATTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:6,0:0.3333:0,2:22.7:1:32:1:0.33333:0:60:6:0.3333:0:1 0/0:6:0:0,0:5,1:0:2,0:19.5:1:29.7:1:1:0:60:12:1:0:0.5 -12 8679478 . TTTG T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.26744;SOR=0;LSEQ=GGGGCTTTTGTGGGGGCCCT;RSEQ=TTGTTGTTGTTGATGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:3,0:19,29:0.0588:2,0:14.3:1:26.3:1:0.07395:0:60:6:0.0588:0.0392:0.7 0/0:35:0:0,0:15,20:0:2,0:23.1:1:30.2:1:1:0:60:70:1:0:0.1 -12 8679767 . T C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32763;SOR=2.08494;LSEQ=TGTTGAAGGGTCTCACCCAG;RSEQ=TGGGTGGCACAGGGAGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:3,2:10,3:0.2778:2,2:20:1:32.4:1:0.58275:2.11727:60:10:0.2941:0:1.6 0/1:20:9:4,5:6,5:0.45:2,2:21.7:1:30.2:1:1:1.46966:60:18:0.4737:0:1.2 -12 8679821 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23077;SOR=0;LSEQ=AGCCCTTTGTCCCTTGGTGG;RSEQ=GAGGGTGTGTTTTGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:0.1053:2,2:26.5:1:29:1:1:1.77272:60:4:0.1053:0:2.5 0/0:20:0:0,0:10,10:0:2,0:25.7:1:29.6:1:1:0:60:19:1:0:0.6 -12 8680419 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49091;SOR=0;LSEQ=GGATGCTAGGCCCCGGTGGC;RSEQ=TGCGTTTGTGAGTGGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:0.0833:2,2:27.5:1:30:1:1:1:60:4:0.0833:0:1.5 0/0:21:0:0,0:12,9:0:2,0:26:1:29.9:1:1:0:60:20:1:0:0.3 -12 8947153 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGATTGAGAGGTGACAGC;RSEQ=TGCTGGCAGTCCTCAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17.5:1:30.5:1:1:0:48:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 8947476 . A G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCTGGGCCAGCAGCTGTG;RSEQ=AGGGTGTACTGGGTCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:20.3:1:32.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 8948830 . A G 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCGCCTCCCAGGTTCAT;RSEQ=CCATTCTCCTGCCCCAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:29:1:31.8:1:1:0:56.3:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 9084931 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGAAATGACTGAGCAAGG;RSEQ=AGTTCTTTCTCTGAGATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 9085099 . G A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=3.38757;LSEQ=ATGAATTTACTTTTAATTTA;RSEQ=AATGATTATTATTCTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:15:1:32:1:1:0:60:4:0.3333:0:2 1/0:3:2:2,0:1,0:0.6667:0,0:13.5:1:32:0:1:0:60:4:0.6667:0:1.5 -12 9085143 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07143;SOR=Inf;LSEQ=TTTTCTCTCTGTTGTATTCT;RSEQ=GGATTGTTCCTATAGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:0:1,0:24.3:1:32.9:1:1:0:60:30:1:0:0.1 0/1:6:2:1,1:4,0:0.3333:0,2:45.5:1:30.5:1:0.33333:0:60:4:0.3333:0:1.5 -12 9085255 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49823;SOR=Inf;LSEQ=GATCCAGCAGCAGATTGCCA;RSEQ=CCACCACCAGCAGCAGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:124,12:0:2,0:25.6:1:30.8:1:1:0:37.3:44.333:1:0:0.2 0/1:139:2:1,1:121,16:0.0144:2,2:21.5:1:26.5:1:0.23042:7.36784:33:4:0.0144:0:1 -12 9085320 . T G 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACACAGCTACACACCTCCAG;RSEQ=TGGCGCAGCAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:25:13,12:109,106:0.1042:2,2:27.9:1:31:1:1:1.05:33.2:50:0.1055:0:1 0/0:284:0:0,0:147,137:0:2,0:31.5:1:28.2:1:1:0:35.8:39.571:1:0:0.1 -12 9085324 . CGCA C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.12187;SOR=2.1616;LSEQ=AGCTACACACCTCCAGTTGG;RSEQ=GCAGCAGCAGCAGCAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:6:3,3:105,121:0.0259:2,2:36.3:1:31.7:1:1:1.15:41:12:0.026:0:0 0/1:276:15:6,9:131,130:0.0543:2,2:36.5:1:31.9:1:0.59706:1.50929:34.9:30:0.0551:0:0.1 -12 9392975 . C G 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16574;SOR=0.33531;LSEQ=GGGGATAAAAAAGAAAGCGA;RSEQ=AGTTCAGGGACTCTGGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:7,4:4,0:0.7333:0,2:18.3:1:31.6:1:0.51648:0:54.5:22:0.7333:0:1.2 0/1:17:8:4,4:6,3:0.4706:2,2:26.9:1:29.9:1:0.63719:1.91839:56:7:0.4375:0:1 -12 9393053 . C G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.1718;LSEQ=GCGAGCAAGGAGGCTGACGA;RSEQ=GCACAATGCAAAGACGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:5,15:0.0909:2,2:34:1:27:1:0.48052:2.83:55.5:4:0.0909:0:2 0/1:19:2:1,1:8,9:0.1053:2,2:21:0:32.5:1:1:1.12:60:4:0.1053:0:2.5 -12 9393068 . C T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.48178;LSEQ=GACGACGCACAATGCAAAGA;RSEQ=GGCTTTTCAGAGCAGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:3,15:0.1:2,2:19:1:29.5:1:0.36842:4.47:55.5:4:0.1:0:2 0/1:14:2:1,1:5,7:0.1429:2,2:6:0:32:0:1:1.37:60:4:0.1429:0:2.5 -12 9847990 . C T 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGCCACCCGATGGAAGATT;RSEQ=GATGGACATGGACATGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:144,184:0:2,0:25.3:1:30.2:1:1:0:58.4:81:1:0:0.1 0/1:342:54:23,31:126,162:0.1579:2,2:18:1:29.6:1:1:1.04818:56:108:0.1602:0:1.2 -12 9848109 . TA T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0393;SOR=0;LSEQ=AAAATGAGACCAGTTATCTT;RSEQ=AGAACGGTCAGCTCAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:4:1,3:79,71:0.026:2,2:22.8:1:28:1:0.3514:3.31394:60:8:0.0263:0.013:1.8 0/0:190:0:0,0:94,96:0:2,0:23.2:1:28.5:1:1:0:58.2:62.333:1:0:0.2 -12 9848119 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2127;SOR=0;LSEQ=CAGTTATCTTTAAGAACGGT;RSEQ=AGCTCAGGGGCTGGTGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:88,68:0.0127:2,2:23:1:28:1:1:1.29197:60:4:0.0129:0:1 0/0:184:0:0,0:97,87:0:2,0:25.1:1:30.9:1:1:0:59.7:45:1:0:0.2 -12 9848179 . C T 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGCAGAGGCCATGAATGA;RSEQ=GAAGGCAGTCCAATTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:104,70:0:2,0:24.4:1:30.7:1:1:0:58.1:42.5:1:0:0.1 0/1:197:20:14,6:109,68:0.1015:2,2:13.6:1:30.7:1:0.6272:1.45:60:40:0.1031:0:1.1 -12 9848235 . C T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37685;SOR=3.60892;LSEQ=GAAAATGTCTGTACAGCCAA;RSEQ=GGTTTCTCTTGGGGGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:1:0,1:176,134:0.0032:2,0:1:0:25:0:0.43408:0:60:2:0.0033:0:1 0/1:347:4:1,3:192,151:0.0115:2,2:12.5:1:27:1:0.32637:3.80075:57.3:8:0.0116:0:1 -12 9848339 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09595;SOR=0;LSEQ=AGCACTTAGTAGCTGTGAAG;RSEQ=AAGGTGCAGAGTCAGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:2,1:82,171:0.0117:2,2:28.7:1:23.3:1:0.25145:4.15:55:2:0.0079:0:1.3 0/0:302:0:0,0:113,187:0:2,0:25.5:1:30.5:1:1:0:59.7:99:0.9933:0:0.1 -12 9848363 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60573;SOR=0.44945;LSEQ=GTGCAGAGTCAGAAGATGAA;RSEQ=AAGAGGAGGATGTGAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:58,134:0.0103:2,2:22.5:1:28.5:1:0.51685:2.30:60:4:0.0104:0:1.5 0/0:215:1:1,0:76,138:0.0047:2,0:1:0:25:0:0.35814:0:60:2:0.0047:0:1 -12 9848411 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=TATCTGGAAAGCAGTCTGCC;RSEQ=CTGGAGGTGGGCAGAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:57,58:0:2,0:20.7:1:31.1:1:1:0:60:37.333:1:0:0.7 0/1:129:2:1,1:63,64:0.0155:2,2:32.5:1:31.5:1:1:1.02:60:4:0.0163:0:1 -12 9848438 . CTT C 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02523;SOR=0.49961;LSEQ=GTGGGCAGAAAAAAGTAAAA;RSEQ=GCTGCTGCTGCTGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:35:22,13:25,19:0.2536:2,2:21.5:1:31.6:1:0.64874:1.28:60:70:0.2536:0.0435:0.2 0/1:145:21:13,8:46,31:0.1448:2,2:31.3:1:31.6:1:1:1.09:60:42:0.1469:0:0 -12 9848439 . T TTGCTGC 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=6.000;MSILEN=3;SSF=1e-04;SOR=0.23686;LSEQ=TGGGCAGAAAAAAGTAAAAC;RSEQ=TGCTGCTGCTGCTGATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:33:21,12:25,19:0.2391:2,2:24.6:1:31.8:1:0.64095:1.33:59.7:66:0.2391:0.0217:2.1 0/1:145:10:6,4:46,31:0.069:2,2:16.7:1:30.5:1:1:1.01:60:20:0.0699:0.0345:1.1 -12 9848454 . A C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0;SOR=3.48086;LSEQ=AAAACTTGCTGCTGCTGCTG;RSEQ=TGATGATGATGATGAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:58:40,18:82,47:0.3085:2,2:22.2:1:32.3:1:0.51041:1.27:59.7:116:0.3085:0:2 1/0:174:106:70,36:42,23:0.6092:2,2:24.4:1:31.9:1:0.86957:1.06:59.9:212:0.6235:0:1.7 -12 9848460 . A C 52 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.3722;SOR=0.256;LSEQ=TGCTGCTGCTGCTGATGATG;RSEQ=TGATGATGAAGATGATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:4:3,1:130,65:0.02:2,2:29.8:1:26.3:1:1:1.50:60:3:0.0153:0:4 0/0:193:1:1,0:124,67:0.0052:2,0:13:0:26:0:1:0:60:2:0.0053:0:4 -12 9848467 . T A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0;SOR=0.15639;LSEQ=GCTGCTGATGATGATGATGA;RSEQ=GAAGATGATGATGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:70:45,25:99,50:0.3196:2,2:27.7:1:30.9:1:0.76211:1.09952:57.8:140:0.3241:0:2.1 0/1:220:15:9,6:131,74:0.0682:2,2:28.3:1:30.1:1:0.78535:1.17927:55.3:30:0.0694:0:2.2 -12 9848470 . A T 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGATGATGATGATGATGA;RSEQ=GATGATGATGATGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:76:49,27:97,52:0.3378:2,2:27.8:1:30.7:1:1:1.02776:57.8:37:0.3426:0:2.2 0/0:223:0:0,0:128,75:0:2,0:23.4:1:30:1:1:0:59.9:49.75:0.99:0:0.9 -12 9848473 . T A 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.21586;SOR=0.20242;LSEQ=GATGATGATGATGATGAAGA;RSEQ=GATGATGATGATGATGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:5:3,2:141,81:0.0219:2,2:30.4:1:31.4:1:1:1.15971:56:10:0.0225:0:3.6 0/0:222:1:1,0:136,85:0.0045:2,0:10:0:31:0:1:0:55:2:0.0046:0:2 -12 9848648 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.29909;LSEQ=AAAAACAGGAAAAATCTCCT;RSEQ=AAACACCAAAAGGATCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:70:21,49:37,98:0.3415:2,2:23.8:1:31.7:1:0.7446:1.13:56.8:140:0.3415:0:1 0/1:224:30:11,19:56,138:0.1339:2,2:24.8:1:31.4:1:0.3967:1.42:56.1:60:0.1345:0:1.2 -12 10646574 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CAGACACCCTATACAGGAGT;RSEQ=ATCCTACTGGTGTCAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:23.1:1:33:1:1:0:60:14:1:0:0.4 0/1:6:2:1,1:2,2:0.3333:2,2:10:1:28.5:1:1:1:60:4:0.4:0:1 -12 10646752 . G C 74 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAACCCTACAGAAGAGGGA;RSEQ=CTGACCATTGAAAGAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:22.4:1:32.2:1:1:0:60:10:1:0:1.2 -12 10646985 . C T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAGCAAGGGCACATAAC;RSEQ=GGATAGAGGATGAAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:23.5:1:32:0:1:0:60:4:1:0:1 -12 11664166 . CT C 83 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.55635;SOR=0.64784;LSEQ=CACACAACTTTTTCTGGGGC;RSEQ=TTTTTTGGGGGAGGTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:7:3,4:289,357:0.0107:2,2:25.6:1:29.7:1:1:1.07926:60:14:0.0108:0.0031:1.4 0/0:574:4:2,2:245,321:0.007:2,2:26.5:1:31.8:1:1:1.31:60:8:0.0071:0.0017:1 -12 11664178 . G A 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=1.68137;LSEQ=TCTGGGGCCTTTTTTTGGGG;RSEQ=AGGTGGGCAGGCTACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:593:329:135,194:118,144:0.5548:2,2:25.9:1:29.6:1:0.35753:1.17724:60:22.5:0.5497:0:1.1 1/0:514:348:140,208:70,95:0.677:2,2:27.2:1:28.8:1:0.70071:1.09454:60:37.667:0.674:0:1.2 -12 11802929 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50282;SOR=Inf;LSEQ=CGCTCCAGACCCCCGGGGCG;RSEQ=CTGCCGGGAGAGATGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:51,1:0:1,0:24.2:1:31.5:1:1:0:60:51:1:0:0.1 0/1:66:2:1,1:59,4:0.0303:2,2:21:1:30:1:0.14904:13.30416:60:4:0.0313:0:1 -12 11802997 . G T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12877;SOR=Inf;LSEQ=CTGGCCGTGGAGCCTTTCTG;RSEQ=GTTGGGGAGAGGAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:221,106:0:2,0:27.5:1:31.2:1:1:0:60:53.5:1:0:0.1 0/1:384:4:1,3:246,134:0.0104:2,2:25.5:1:25:1:0.13185:5.48249:60:3:0.0079:0:1.8 -12 11803168 . C A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62337;SOR=2.93678;LSEQ=CAGGGCAGTCGTGCTGGGCT;RSEQ=CTCAGAGCAGGCTGTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:1,0:49,159:0.0048:2,0:1:0:23:0:0.23923:0:60:2:0.0049:0:1 0/1:215:3:2,1:56,156:0.014:2,2:9:1:28.3:1:0.17778:5.52:60:6:0.0144:0:1.3 -12 11803220 . A C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAGGAAATTATTTGGGGCG;RSEQ=GAGGGAAAGAGATGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:71:0,71:0,0:1:0,1:25.2:1:29.7:1:1:0:60:70:1:0:2 1/1:58:58:0,58:0,0:1:0,1:28.1:1:29.9:1:1:0:60:116:1:0:2 -12 11803228 . A G 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTATTTGGGGCGAGAGGGAA;RSEQ=GAGATGCAGCTCGCGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:67:0,67:0,0:1:0,1:24.2:1:31.1:1:1:0:60:32.5:1:0:2 1/1:54:54:0,54:0,0:1:0,1:27.3:1:30.4:1:1:0:60:53:1:0:2.1 -12 11803278 . T TC 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.56239;SOR=1.45474;LSEQ=CTTTAGCGTAACCTTGCTAC;RSEQ=CCCCCCCACCGCCGAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:15:0,15:0,10:0.5769:0,1:29.2:1:31.5:1:1:0:60:30:0.6:0.0385:1.5 1/0:21:14:1,13:0,7:0.6667:0,1:23.9:1:31.7:1:1:0:60:28:0.6667:0.0476:1.7 -12 11803303 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49275;SOR=0;LSEQ=CCCACCGCCGAGCCCCTGCC;RSEQ=GCTCCTCGGCCCCCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:0,12:0.1429:0,0:29.5:1:32:0:1:0:60:4:0.1429:0:2 0/0:10:0:0,0:1,9:0:2,0:21.4:1:28.6:1:1:0:60:9:1:0:1.1 -12 11904983 . A G 34 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATATTGCTACAGAAGAGAAA;RSEQ=CATGGCTTTAATATAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:44:0:34:0:1:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:1:0,2:23:0:34:0:1:0:60:4:1:0:1.5 -12 11905187 . T C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.54017;SOR=0;LSEQ=GATGGCAGAGTTTTGTTATA;RSEQ=AGCCCCAAGGCTAGGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:27,0:0.1:1,0:19:1:33.7:1:1:0:60:6:0.1:0:1 0/0:14:0:0,0:13,1:0:1,0:18.1:1:30.3:1:1:0:60:28:1:0:0.2 -12 11905349 . T C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01235;SOR=Inf;LSEQ=CCAAGCTTTCATTGTCTCTC;RSEQ=CCCCCTCCCCTCTTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:286,192:0:2,0:24.8:1:29.9:1:1:0:60:33.143:1:0:0.1 0/1:446:6:3,3:279,161:0.0135:2,2:25.2:1:24.8:1:0.67379:1.73059:60:2:0.0093:0:1.7 -12 11905554 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=AGGGACAGAGGATTGATGGC;RSEQ=TGGGGCGGGGGTGGCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:26,125:0.0131:2,2:30:0:32:0:0.32276:4.74:60:4:0.0134:0:2.5 0/0:120:0:0,0:20,100:0:2,0:23.4:1:30.4:1:1:0:60:39:1:0:0.2 -12 11905560 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01896;SOR=Inf;LSEQ=AGAGGATTGATGGCGTGGGG;RSEQ=GGGGGTGGCAGGCAGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:19,102:0:2,0:25.5:1:29.6:1:1:0:60:39.333:1:0:0.1 0/1:102:5:1,4:15,82:0.049:2,2:29.2:1:28.6:1:0.58188:1.36:60:10:0.05:0:1 -12 11905568 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50945;SOR=0;LSEQ=GATGGCGTGGGGCGGGGGTG;RSEQ=CAGGCAGTGGGCTCCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:17,97:0.0172:2,2:16:0:32:0:0.28741:5.57:60:4:0.0177:0:2.5 0/0:85:0:0,0:8,77:0:2,0:25:1:31.5:1:1:0:60:27.333:1:0:0.2 -12 11905668 . G A 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACACCCCCCTACCCCCA;RSEQ=ATACCTTTGAAAAATTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:0,22:0,0:1:0,1:25:1:30.3:1:1:0:60:21:1:0:1.1 1/1:8:8:0,8:0,0:1:0,0:22.3:1:30.1:1:1:0:60:16:1:0:1 -12 11905742 . TA T 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCTGACTATGACATGT;RSEQ=AAAAAAAAAGAAACCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:26:1:30.8:1:1:0:60:4:0.2222:0.1111:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 11992035 . C A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50124;SOR=0;LSEQ=AGCTGTCTAACTGACAAGAC;RSEQ=TTTCTCTCTTTCTTTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:2,0:174,16:0.0104:2,0:6.5:1:27:0:1:0:60:4:0.0106:0:4 0/0:166:0:0,0:141,24:0:2,0:21.3:1:30:1:1:0:60:40.25:0.9938:0:0.1 -12 11992168 . G A 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00045;SOR=1.8363;LSEQ=AGGCCAATTGACAGCAACAC;RSEQ=TTTGAAATGAATGGCAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:828:60:29,31:380,388:0.0725:2,2:23.1:1:30.2:1:0.89399:1.04688:60:59:0.072:0:1.2 0/1:741:93:43,50:321,327:0.1255:2,2:25.5:1:30.6:1:0.58037:1.14125:60:92:0.1255:0:1.2 -12 12006277 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19133;SOR=Inf;LSEQ=ATTGTATCTTTGGCACCGTG;RSEQ=CAGGCACTTAGCTGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:180,20:0:2,0:23.9:1:31.7:1:1:0:60:27.571:1:0:0 0/1:156:2:1,1:131,23:0.0128:2,2:31:1:27.5:1:0.28486:5.59704:60:4:0.013:0:1 -12 12006544 . G A 226 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01033;LSEQ=CTGAGGTTTAGACAAATCCA;RSEQ=GAAGTTTAATTGTTAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:170:83,87:421,407:0.17:2,2:21.5:1:30.6:1:0.67391:1.08415:60:41.5:0.169:0:1.1 0/0:949:2:2,0:477,469:0.0021:2,0:16.5:1:28:1:0.49953:0:60:4:0.0021:0:1 -12 12006736 . G T 191 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=26.43951;LSEQ=ATATAGTAGGCACCGTAAAG;RSEQ=TGTGGTGGAAGGGTCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1678:4:0,4:842,830:0.0024:2,0:1.5:1:22.8:1:0.06109:0:60:3:0.0018:0:1.8 0/1:1480:88:39,49:669,723:0.0595:2,2:28.1:1:29.6:1:0.51117:1.16245:60:87:0.0596:0:1.1 -12 12007114 . T A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11691;SOR=Inf;LSEQ=GTAAGGAGTGTGCAACTAGA;RSEQ=CCCGCGCATGCACAGTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:141,114:0:2,0:26.2:1:30.6:1:1:0:60:62.75:1:0:0.1 0/1:245:3:1,2:128,114:0.0122:2,2:19:1:24:1:0.60444:2.23844:60:2:0.0084:0:1.7 -12 12007343 . G C 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=14.3934;LSEQ=ACCTGGAGGTTGGGGACCCC;RSEQ=CCTTAGAAATCCAGCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1020:164:102,62:534,321:0.1608:2,2:24.9:1:30.9:1:1:1.01117:60:81:0.1599:0:1.1 1/0:858:630:402,228:131,94:0.7343:2,2:24.7:1:30.1:1:0.14927:1.26:60:56.273:0.736:0:1.1 -12 12007720 . G GA 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.4603;SOR=0.86708;LSEQ=TAAAAGTTGGAAGAAGGAAA;RSEQ=AAAAAAAAACCCAAATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1884:67:40,27:974,832:0.0356:2,2:29.8:1:29.4:1:0.38364:1.27:60:21.333:0.0346:0.0011:0.3 0/1:1743:54:28,26:867,809:0.031:2,2:25:1:30.1:1:1:1.00:60:108:0.0313:0.0017:0.3 -12 12007893 . C G 319 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04363;LSEQ=ATTTAATTTAGGCCCTGGAC;RSEQ=TAGTTCCAGAATAGGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1515:1234:489,745:116,161:0.8145:2,2:26.7:1:31.1:1:0.49802:1.09762:60:175.286:0.8169:0:1.1 0/1:1638:263:115,148:613,757:0.1606:2,2:23.8:1:30.4:1:0.78668:1.04213:60:64.75:0.1604:0:1.2 -12 12008004 . C T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25146;SOR=0;LSEQ=CTTTGAGAGGCCGAGGCGGG;RSEQ=GGATCACGAGGTCAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:22,211:0.0126:2,2:21:1:29.3:1:0.26582:4.74:55:6:0.0133:0:1 0/0:210:0:0,0:22,188:0:2,0:24.4:1:28.6:1:1:0:56.1:22.333:1:0:0.2 -12 12008057 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18067;SOR=Inf;LSEQ=GGCTAACATGGTGAAACCCC;RSEQ=TCTCTACTAAAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:18,98:0:2,0:21.4:1:30.1:1:1:0:48.5:7.923:1:0:0.5 0/1:87:2:0,2:8,77:0.023:2,0:6:1:30:1:1:0:43.5:4:0.0282:0:2.5 -12 12008071 . TAC T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18707;SOR=Inf;LSEQ=AACCCCGTCTCTACTAAAAA;RSEQ=AAAAAAAAAAAAAAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:26,56:0:2,0:20.6:1:28.6:1:1:0:49:40:1:0:1 0/1:63:2:0,2:16,45:0.0317:2,0:32.5:1:27:1:1:0:59.5:4:0.0351:0:3 -12 12008218 . C T 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00141;SOR=8.15262;LSEQ=CCACTGCACTCCAGCCTGGG;RSEQ=GACAGAGCGAGACTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:2:1,1:304,121:0.0047:2,2:22.5:1:28.5:1:0.49027:2.5062:60:4:0.0047:0:1 0/1:379:14:8,6:264,101:0.0369:2,2:16.3:1:28.9:1:0.23213:1.95659:60:28:0.0372:0:1 -12 12008864 . G A 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0872;LSEQ=AAGCTTGACATTAAGGCAAG;RSEQ=AATATATTACCTAGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1837:1146:594,552:325,362:0.6238:2,2:24.7:1:29.9:1:0.06669:1.20:60:51.091:0.6217:0:1.1 0/1:1727:218:111,107:778,727:0.1262:2,2:24.3:1:29:1:0.88474:1.03158:60:42.6:0.1249:0:1.2 -12 12008944 . AT A 135 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.6423;SOR=1.20631;LSEQ=CTCTTAGTCTTTCTCTCATT;RSEQ=TTTTTTTGTTAATCTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2050:19:13,6:1036,991:0.0093:2,2:23.8:1:29.9:1:0.16771:2.07:60:38:0.0093:0.0034:0.7 0/1:2061:23:14,9:1023,1015:0.0112:2,2:22.7:1:30:1:0.40243:1.54:60:46:0.0112:0.0029:0.2 -12 12009529 . A G 322 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13758;LSEQ=TCCTCCTGCCTTTCAGCTAT;RSEQ=TGGTGCCCTTGATGACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1677:1051:529,522:325,300:0.6267:2,2:25.5:1:32.1:1:0.51181:1.06894:60:74.071:0.6262:0:1.1 0/1:1413:265:138,127:551,595:0.1875:2,2:24:1:31.5:1:0.24708:1.17:60:264:0.1876:0:1.2 -12 12009741 . A G 253 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATATGTTAACATACAGAAAG;RSEQ=TCTGGTTCTGAAAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1524:267:132,135:648,604:0.1752:2,2:26.2:1:31.4:1:0.50073:1.09716:60:43.5:0.1764:0:1.1 0/0:1382:0:0,0:699,683:0:2,0:24.9:1:29.1:1:1:0:60:52.154:1:0:0.1 -12 12009751 . G GA 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.69006;SOR=0.91562;LSEQ=ATACAGAAAGATCTGGTTCT;RSEQ=AAAAAAAAATCTGTCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1566:57:26,31:780,719:0.0364:2,2:29:1:29.8:1:0.34835:1.29324:59.6:56:0.0362:0.0051:0.2 0/1:1406:47:22,25:699,658:0.0334:2,2:28.2:1:29.6:1:0.55531:1.20701:60:94:0.0338:7e-04:0.1 -12 12009874 . G A 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11233;LSEQ=CCAAGATGACACATGTTGCT;RSEQ=CCAACTTGGCATAGGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2269:1378:743,635:472,417:0.6073:2,2:26.1:1:28.8:1:0.73008:1.03:60:80.059:0.6073:0:1.1 0/1:1940:287:143,144:823,827:0.1479:2,2:25.9:1:28.5:1:1:1.00212:60:94.667:0.1481:0:1.1 -12 12010056 . G A 313 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.0802;LSEQ=CCTTGTGATTTCACCTCGTC;RSEQ=TGGCCACAAACTTAACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1886:1210:599,611:333,340:0.6416:2,2:24.4:1:30.6:1:1:1.00:60:92.077:0.6429:0:1.1 0/1:1626:204:107,97:701,721:0.1255:2,2:24.7:1:29.9:1:0.41096:1.13:60:101:0.1252:0:1.1 -12 12010544 . G T 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10315;LSEQ=GACAGTGACACAGGGCTCCA;RSEQ=CAATAAGTAAGCCAGGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1795:1160:611,549:334,296:0.6462:2,2:25.7:1:30.4:1:0.92104:1.01387:60:88.231:0.6462:0:1.1 0/1:1540:244:133,111:678,617:0.1584:2,2:24.3:1:29.2:1:0.57617:1.09:60:47.8:0.1573:0:1.1 -12 12010736 . C T 319 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.80685;LSEQ=TAAGGGCTAAGTTTCTCATT;RSEQ=CTCTGGCTCTGTCTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1886:1530:771,759:182,170:0.8112:2,2:24.3:1:30.2:1:0.67917:1.05392:60:108.286:0.8129:0:1.1 1/1:1563:1473:762,711:42,43:0.9424:2,2:24.1:1:29.4:1:0.73805:1.10:60:91.063:0.9443:0:1.1 -12 12011325 . A AAT 252 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0;SOR=6.85522;LSEQ=TTTTGGGTTTTATCCCCTTA;RSEQ=ATATATATATATATTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1210:108:59,49:536,550:0.0893:2,2:30.2:1:30.3:1:0.31398:1.24:59.9:107:0.0901:0:1 0/1:960:386:203,183:284,251:0.4021:2,2:26.4:1:29.4:1:0.89373:1.01998:59.8:772:0.4055:0.0771:0.9 -12 12011338 . AT A 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.86956;SOR=0.89506;LSEQ=CCCCTTAAATATATATATAT;RSEQ=TTTTTTTTAATTGTCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1196:22:9,13:582,581:0.0184:2,2:21.4:1:30.1:1:0.51955:1.44648:59.8:21:0.0178:0.0042:0 0/1:970:16:10,6:485,455:0.0165:2,2:16.6:1:28.8:1:0.45533:1.56:60:32:0.0166:0.0093:0.8 -12 12011340 . T A 218 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTTAAATATATATATATAT;RSEQ=TTTTTTTAATTGTCATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1197:181:90,91:502,509:0.1512:2,2:22.4:1:29.2:1:1:1.00:59.9:44.25:0.15:0:1.1 0/0:951:0:0,0:237,215:0:2,0:21.1:1:29.7:1:1:0:59.9:112:0.9978:0:0.2 -12 12011342 . T A 118 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=9.000;MSILEN=1;SSF=0.00011;SOR=6.40495;LSEQ=TTAAATATATATATATATTT;RSEQ=TTTTTAATTGTCATTTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1213:4:2,2:607,602:0.0033:2,2:24:1:28:1:1:1.0083:58.8:8:0.0033:0:2 0/1:963:20:11,9:484,459:0.0208:2,2:16.1:1:27.4:1:0.82337:1.16:60:40:0.0209:0:2.1 -12 12011520 . G A 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.41972;LSEQ=AGGGAGAAGGAGCAAGATCC;RSEQ=GATTTCTCAAACGTTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1673:269:134,135:669,735:0.1608:2,2:24:1:30.8:1:0.54894:1.09:60:133.5:0.1612:0:1.1 1/0:1410:828:404,424:299,283:0.5872:2,2:24.3:1:30.5:1:0.35789:1.10876:60:164.6:0.587:0:1.1 -12 12011764 . TGAG T 182 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=3.95718;LSEQ=AACATGGAAATCGCAAGTGA;RSEQ=GAGAACTTTCAAGCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1474:26:17,9:601,607:0.0176:2,2:11.3:1:28.5:1:0.16414:1.91:59.2:12:0.0167:0.0136:1.3 0/1:1341:89:43,46:239,237:0.0664:2,2:8:1:28.2:1:0.81748:1.07863:59.8:88:0.066:0.0559:1.2 -12 12011768 . GAGAA AG 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=7.75793;LSEQ=ACATGGAAATCGCAAGTGAT;RSEQ=CTTTCAAGCATCGAAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1474:221:113,108:601,607:0.1499:2,2:25.5:1:31.6:1:0.71509:1.06:60:72.667:0.1513:0.0312:0.3 1/0:1341:775:389,386:239,237:0.5779:2,2:27.2:1:31.3:1:1:1.00066:60:1550:0.5814:0.05:0.2 -12 12011772 . A G 244 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCGCAAGTGATGAGGAGA;RSEQ=CTTTCAAGCATCGAAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1241:0:0,0:611,594:0:2,0:24.4:1:30:1:1:0:60:91.692:0.9983:0:0.1 0/1:578:236:113,123:170,169:0.4083:2,2:15.1:1:31:1:0.61161:1.09476:59.9:38.333:0.4078:0:1.1 -12 12012053 . G C 226 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=40.000;MSILEN=1;SSF=0.51247;SOR=0.83301;LSEQ=AGATGAGGTATATGAATCTG;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:230:196:53,143:0,25:0.8522:1,2:10.8:1:29.8:1:9e-04:0:59.8:6.84:0.9771:0:1.4 1/1:203:168:73,95:9,21:0.8276:2,2:11.7:1:29.6:1:0.2273:1.79:60:14.273:0.9181:0:1.4 -12 12012106 . T C 141 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01327;SOR=0.20704;LSEQ=TTTTTTTTGAGAAGGAGTCT;RSEQ=GCTCTGTCGCCCAGGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:78:4,74:0,1:0.963:0,2:25.9:1:22.5:1:1:0:42.6:1.889:0.9808:0:1.8 1/1:76:64:0,64:0,11:0.8421:0,1:29.4:1:20.6:1:1:0:43.3:1.37:0.8222:0:1.7 -12 12012681 . T C 319 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.72481;LSEQ=TTTCATAAATATTTGTAGTG;RSEQ=AGGCGCCCTGAAAATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1418:468:263,205:524,425:0.33:2,2:25.3:1:32.3:1:0.73345:1.04:60:92.6:0.3293:0:1.1 1/0:1368:1051:554,497:165,150:0.7683:2,2:24.7:1:31.8:1:0.94873:1.01:60:104.1:0.7677:0:1.1 -12 12012801 . A G 328 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03841;LSEQ=GTGTGGCAGGTCCTGCTTAC;RSEQ=TTACTGCCAAATTTGTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1591:1587:742,845:3,0:0.9975:0,2:24.8:1:30.9:1:0.10265:0:60:104.8:0.9981:0:1.1 1/1:1493:1401:669,732:51,40:0.9384:2,2:25.1:1:30.4:1:0.13078:1.39475:60:279.2:0.9388:0:1.1 -12 12013189 . A G 319 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.29908;LSEQ=GATTCTCTAGTCTTGCTGGA;RSEQ=TCGTGTTGATGACTGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1638:303:147,156:686,647:0.185:2,2:25.6:1:31.7:1:0.37304:1.12511:60:59.6:0.1854:0:1.1 1/0:1657:1245:610,635:204,205:0.7514:2,2:24.8:1:31.1:1:0.77578:1.0359:60:68.167:0.7495:0:1.1 -12 12013292 . G A 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.47116;LSEQ=ACAGAGCCAGAGAGCATGCC;RSEQ=GCACGTATATGCGTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1505:271:133,138:623,610:0.1801:2,2:25.3:1:30.4:1:0.68754:1.0597:60:32.875:0.1794:0:1.1 1/0:1371:1025:507,518:187,157:0.7476:2,2:23.5:1:30.4:1:0.11961:1.21675:60:145.429:0.7507:0:1.1 -12 12013498 . C CA 249 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.37054;LSEQ=GACAGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAACAAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:795:300:185,115:214,184:0.3774:2,2:28.9:1:30.3:1:0.03743:1.38:52.2:600:0.4011:0:0.7 0/1:742:136:75,61:305,261:0.1833:2,2:25.8:1:29.3:1:0.84813:1.05:52.7:44.333:0.1908:0.0162:1 -12 12013572 . G A 312 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.78678;LSEQ=CTTAGAATAGCCAAGCATTC;RSEQ=GTAAATGTTATTCATTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1591:1268:688,580:173,141:0.797:2,2:26.1:1:30.6:1:0.80047:1.03433:60:73.588:0.7989:0:1.6 1/1:1481:1357:726,631:63,58:0.9163:2,2:25.3:1:30:1:0.77611:1.06:59.9:40.121:0.9175:0:1.3 -12 12013612 . G A 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05217;LSEQ=ATGATTCAATATTTCTGGCT;RSEQ=TTATTTGGTTGTTTCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1775:1437:759,678:173,164:0.8096:2,2:24.7:1:29.4:1:0.62833:1.06:60:64.318:0.8095:0:1.5 0/1:1842:334:174,160:784,722:0.1813:2,2:23.6:1:28.6:1:1:1.00:60:54.667:0.1794:0:1.6 -12 12013626 . T TC 255 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.00809;LSEQ=CTGGCTGTTATTTGGTTGTT;RSEQ=CCCCCCCTCTGTTTGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1779:296:149,147:772,707:0.1664:2,2:28.3:1:31.1:1:0.56688:1.07722:60:48.333:0.1659:0.0157:1 0/0:1862:3:3,0:925,931:0.0016:2,0:42.3:1:31.3:1:0.12419:0:60:6:0.0016:0:0.3 -12 12013985 . C A 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=16.89262;LSEQ=CACTGCTTGCATTTTATGTC;RSEQ=CCTTGCAGTATCTGGCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2012:323:161,162:837,849:0.1605:2,2:25.3:1:29.9:1:0.95165:1.01:60:79.75:0.161:0:1.1 1/0:1664:1271:652,619:188,201:0.7638:2,2:24.7:1:29.5:1:0.32465:1.13:60:114.545:0.766:0:1.1 -12 12014424 . G A 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.90024;LSEQ=TTGCATCTGTCTGGGCCCTC;RSEQ=GCCTATTACAGGAGGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1345:253:109,144:534,558:0.1881:2,2:23.6:1:30.5:1:0.10809:1.26405:60:62.25:0.1868:0:1.1 1/0:1211:889:411,478:147,169:0.7341:2,2:23.5:1:30.2:1:0.94769:1.01161:60:67.385:0.7337:0:1.1 -12 12014774 . T C 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCAGGCCTTATACATGAT;RSEQ=GAGAGGATTACCCAAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1925:0:0,0:888,1036:0:2,0:24.5:1:30.1:1:1:0:60:95.2:0.9995:0:0.1 0/1:1761:66:31,35:813,882:0.0375:2,2:24:1:30.6:1:0.90065:1.04069:60:132:0.0378:0:1.9 -12 12014808 . T C 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACAGACCTAATTGACTTA;RSEQ=TGGAAATCCAATCCTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1738:0:0,0:785,952:0:2,0:25.2:1:30.5:1:1:0:60:85.85:1:0:0.1 0/1:1730:60:29,31:793,874:0.0347:2,2:24.2:1:30.8:1:1:1.03:60:29:0.0339:0:2 -12 12015401 . G A 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=13.69562;LSEQ=TTATTATCTCACTTTTCTGG;RSEQ=GGCTAGAAGTCCAAGGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1376:253:127,126:587,535:0.1839:2,2:23.4:1:30.4:1:0.5775:1.08849:60:62.25:0.1843:0:1.1 1/0:1104:834:434,400:134,132:0.7554:2,2:25:1:29.6:1:0.6726:1.07:60:40.7:0.7544:0:1.1 -12 12015706 . G T 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08971;LSEQ=ACATCCTGAGGGTACTAGGG;RSEQ=TTAGGACTTCAACTTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1030:669:400,269:195,165:0.6495:2,2:24.1:1:29.4:1:0.08554:1.26:60:40.813:0.6485:0:1.1 0/1:815:116:65,51:398,301:0.1423:2,2:23.4:1:28.9:1:0.91944:1.03744:60:37.667:0.1402:0:1.1 -12 12015905 . A G 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11451;LSEQ=AGAGGGAGAAAGTGAAACCC;RSEQ=GTGGACTGAGGCTTGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1805:1165:592,573:344,294:0.6454:2,2:24.8:1:30.3:1:0.21796:1.13244:60:128.444:0.6465:0:1.1 0/1:1665:287:140,147:705,669:0.1724:2,2:24.8:1:29.7:1:0.43699:1.10643:60:56.4:0.1723:0:1.2 -12 12016007 . C T 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGTGGGCTTAGGGAAAGCA;RSEQ=GGTGGTGGAAATGTGATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1848:0:0,0:925,922:0:2,0:24.3:1:31.9:1:1:0:60:72.88:1:0:1.2 0/1:1811:87:49,38:901,822:0.048:2,2:22.2:1:29.8:1:0.50972:1.18:60:42.5:0.0475:0:1.2 -12 12016008 . G A 329 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02252;LSEQ=CGTGGGCTTAGGGAAAGCAC;RSEQ=GTGGTGGAAATGTGATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1843:1839:923,916:0,0:0.9978:0,2:24.5:1:30.4:1:1:0:60:53.088:0.9983:0:1.2 1/1:1814:1654:857,797:89,68:0.9118:2,2:24.3:1:30.1:1:0.27712:1.21706:60:46.257:0.9111:0:1.6 -12 12016045 . C T 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.22578;LSEQ=CCTGGTGTGTGAGATGCAAA;RSEQ=TTGATCTTAGCCTTTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1938:289:142,147:798,850:0.1491:2,2:25.4:1:30.5:1:0.84831:1.03:60:40.286:0.1474:0:1.8 1/0:2019:1377:691,686:322,317:0.682:2,2:24:1:29.7:1:0.96183:1.00842:60:85.063:0.6815:0:1.7 -12 12016089 . C T 220 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00641;LSEQ=TGGAAACTTATCGGTCAAAA;RSEQ=TTTCACTAAAGGCAGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1860:138:66,72:822,898:0.0742:2,2:25.1:1:31:1:1:1.00:60:276:0.0749:0:1.3 0/0:1949:1:0,1:934,1011:5e-04:2,0:1:0:29:0:1:0:60:2:5e-04:0:2 -12 12016183 . G T 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.01517;LSEQ=GGGTCAAATTTTTATGAATT;RSEQ=TAAGTAGAGAAACTTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1551:271:147,124:638,642:0.1747:2,2:22.9:1:30.3:1:0.20393:1.19:60:270:0.1752:0:1.1 0/1:1473:677:336,341:391,405:0.4596:2,2:24:1:29.8:1:0.87538:1.02:60:337.5:0.4601:0:1.1 -12 12016373 . G A 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=66.51219;LSEQ=ACACTTCCAACCAGAATGAC;RSEQ=GTTCCCTGCCAGTCCTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1853:1:0,1:927,922:5e-04:2,0:7:0:21:0:0.49892:0:60:2:5e-04:0:1 0/1:1758:61:26,35:801,893:0.0347:2,2:23.2:1:30.5:1:0.51537:1.20734:60:122:0.0349:0:1.1 -12 12016807 . G A 150 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=36.82532;LSEQ=AGACTGAAACAAAGCTTGCA;RSEQ=GGTCTCATTGCAGGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1258:1:1,0:707,547:8e-04:2,0:1:0:29:0:1:0:60:2:8e-04:0:1 0/1:1054:30:17,13:583,440:0.0285:2,2:22.6:1:30.6:1:1:1.01323:60:60:0.0288:0:1.3 -12 12017285 . T C 330 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17884;SOR=0.33202;LSEQ=CCGTTTTGAAATTTATAAGA;RSEQ=GGGAAATGGATTCAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1673:1671:833,838:0,2:0.9988:0,2:25.4:1:30.9:1:0.49971:0:60:91.833:0.9988:0:1.1 1/1:1670:1664:807,857:0,2:0.9964:0,2:25.2:1:30.3:1:0.50019:0:60:103:0.9964:0:1.1 -12 12017687 . TA T 244 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=1.96487;LSEQ=GCAAGGTTAATTAAGCACTT;RSEQ=AAAAAAAAAAAGCTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1406:181:81,100:615,582:0.1287:2,2:28.8:1:30.6:1:0.11052:1.30431:60:180:0.1304:0.0092:0.2 0/1:1222:275:136,139:451,442:0.225:2,2:28.3:1:30.2:1:0.78286:1.04285:59.9:550:0.2295:0.0025:0.2 -12 12017688 . A T 98 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.17759;SOR=0.49074;LSEQ=CAAGGTTAATTAAGCACTTT;RSEQ=AAAAAAAAAAAGCTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1406:14:10,4:615,582:0.01:2,2:11.3:1:25.9:1:0.18022:2.36:60:3.667:0.008:0:1.6 0/0:1222:6:0,6:451,442:0.0049:2,0:18.8:1:16.3:1:0.01506:0:60:0.5:0.0017:0:2.7 -12 12017753 . A G 183 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGTAAAGAGAATTGTGTA;RSEQ=TGAATCACCATGTACCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1900:0:0,0:1056,842:0:2,0:25.3:1:30.3:1:1:0:60:69.296:0.9989:0:0.2 0/1:1933:60:29,31:1020,852:0.031:2,2:23.8:1:31:1:0.35945:1.27958:59.9:19:0.0301:0:1.2 -12 12017875 . T C 197 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTACAGCAAATCTCAGATA;RSEQ=ATAATTTCCCTTGTAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1014:0:0,0:303,709:0:2,0:24.6:1:29.1:1:1:0:60:125.5:0.998:0:0.2 0/1:1048:78:25,53:346,624:0.0744:2,2:21.3:1:31.4:1:0.5415:1.17538:60:156:0.0751:0:1.1 -12 12018042 . A G 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACTACAAAAAATTAGCC;RSEQ=GGCATGGTGGCGGGCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:64:41,23:0,0:1:0,2:21.2:1:27.7:1:1:0:50.6:7:1:0:1.1 1/1:23:23:10,13:0,0:1:0,2:21.9:1:29:1:1:0:50.7:10.5:1:0:1 -12 12018349 . T C 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATAAATGTTTTTTACAGTT;RSEQ=GGATCAGAATCCAAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1483:0:0,0:702,781:0:2,0:25.8:1:30.2:1:1:0:60:113.077:1:0:0.2 0/1:1549:51:25,26:691,803:0.0329:2,2:23.3:1:30.5:1:0.77562:1.12:60:102:0.033:0:1.1 -12 12018392 . C T 239 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01438;LSEQ=TATACATTGCAGATGGTTAA;RSEQ=GTATCTCTTAAGTTTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1441:242:120,122:576,623:0.1679:2,2:23.4:1:30.3:1:0.67273:1.06:60:79.667:0.1683:0:1.1 0/0:1384:4:0,4:634,746:0.0029:2,0:1:0:25.3:1:0.12973:0:60:8:0.0029:0:1 -12 12018911 . T C 203 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTATTCTACTCTGTTTTTT;RSEQ=CTATATTCTCCTTCTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1760:90:45,45:888,782:0.0511:2,2:22.9:1:31.4:1:0.58862:1.13547:59.8:180:0.0516:0:1.1 0/0:1566:0:0,0:804,761:0:2,0:23.1:1:29.3:1:1:0:60:119.385:0.9994:0:0.1 -12 12019055 . G A 192 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=30.00672;LSEQ=CCCTTTCTTCTCTCATCTCC;RSEQ=TTCTGCTATTAAGTCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2351:3:2,1:1108,1238:0.0013:2,2:4:1:23.3:1:0.60541:2.23:60:2:9e-04:0:3.3 0/1:2220:82:43,39:1039,1095:0.0369:2,2:24.7:1:30.3:1:0.57382:1.16:60:164:0.0373:0:1.1 -12 12019081 . G A 217 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=84.31834;LSEQ=CTATTAAGTCCATCTAGTCC;RSEQ=GTCTTTCATTTCAGATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2114:2:1,1:985,1124:9e-04:2,2:8:1:29:1:1:1.14:60:4:0.001:0:1 0/1:1973:146:70,76:858,965:0.074:2,2:25.7:1:30.3:1:0.86343:1.04:60:72:0.0738:0:1.1 -12 12019132 . C CT 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.05437;SOR=0.65296;LSEQ=TTATAGAATCTTTATTTTGC;RSEQ=TTTTTTTTTAATTCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1676:55:21,34:814,801:0.0328:2,2:23.7:1:29.8:1:0.09907:1.64483:59.8:26.5:0.0322:0.0042:0.2 0/1:1615:35:18,17:770,810:0.0217:2,2:18.5:1:29.2:1:0.86461:1.11:60:70:0.022:0.0062:0.4 -12 12019755 . GG AT 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGGCACTTGGGCTATTC;RSEQ=TAATCAGACAAGAATTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1809:0:0,0:876,928:0:2,0:25.2:1:30.3:1:1:0:60:119.267:0.9972:0:0.1 0/1:1618:54:24,30:761,797:0.0334:2,2:25.4:1:29.6:1:0.58072:1.19341:60:108:0.0338:0.0019:1 -12 12019756 . G T 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=27.58839;LSEQ=CCTGGCACTTGGGCTATTCG;RSEQ=TAATCAGACAAGAATTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1825:5:0,5:886,931:0.0027:2,0:1:0:24.6:1:0.06263:0:60:4:0.0022:0:1.2 0/1:1603:113:58,55:700,735:0.0705:2,2:26.4:1:29.7:1:0.62596:1.11:60:112:0.0732:0:1.2 -12 12020114 . C T 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=26.26413;LSEQ=TATGGTTTCTTTCATTTCTA;RSEQ=CCGTAAGAAGGTTAGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1810:295:160,135:803,706:0.163:2,2:25.2:1:30.5:1:0.75023:1.04:60:41.143:0.1616:0:1.6 1/1:1604:1342:704,638:139,122:0.8367:2,2:24.6:1:29.1:1:0.8391:1.03252:60:45.276:0.8358:0:1.5 -12 12020170 . C T 307 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=11.14793;LSEQ=TATTGTTGAACTGAAATTGC;RSEQ=CCTTTCCTTGTTTAGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1961:331:178,153:835,792:0.1688:2,2:24.3:1:30.3:1:0.43309:1.10:60:109.333:0.1703:0:1.5 1/0:1832:1271:649,622:288,271:0.6938:2,2:25.4:1:29.8:1:0.87899:1.01851:60:104.917:0.6948:0:1.5 -12 12021354 . G GT 78 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53407;SOR=1.34089;LSEQ=TGAGTGTCATAAGGTTGGGG;RSEQ=TTTTTTTCTTTTTTCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:989:10:0,10:340,632:0.0101:2,0:15.7:1:25.5:1:0.0182:0:38.4:4:0.0086:0:3.3 0/1:962:13:0,13:353,574:0.0135:2,1:15.3:1:21.3:1:0.00274:0:39.9:1.6:0.0087:0:3.7 -12 12021412 . C T 36 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34001;SOR=3.51094;LSEQ=GACAAAGTTTTGCTCTGTCA;RSEQ=CCAGGCTGGAGTGCAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:1:0,1:60,114:0.0057:2,0:21:0:14:0:1:0:40:0:0:0:7 0/1:152:3:1,2:30,119:0.0197:2,2:25.7:1:23.3:1:0.49812:1.97:53.3:2:0.0202:0:4.7 -12 12021474 . C T 115 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=25.02595;LSEQ=CTCCACCTCCTGGGTTCAAG;RSEQ=GATTCTCATGTCTCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:0,1:116,64:0.0055:2,0:16:0:31:0:0.35912:0:60:2:0.0061:0:1 0/1:122:15:10,5:73,33:0.123:2,2:17.1:1:29.5:1:1:1.10512:59.6:30:0.1327:0:1.3 -12 12021657 . T C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=8.95664;LSEQ=ACTCCTAGAGTTAGAGAATA;RSEQ=GAAAATTTTAGTTGTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1156:180:104,76:599,377:0.1557:2,2:25:1:31:1:0.3623:1.16093:60:179:0.1569:0:1.1 1/0:1035:645:377,268:223,166:0.6232:2,2:24.8:1:30.3:1:0.74519:1.05:60:70.667:0.6217:0:1.1 -12 12021980 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54757;SOR=0;LSEQ=GGAGACCCAGACCATCCTGG;RSEQ=TAACACGGTGAAACCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:0,2:16,126:0.0139:2,0:39:1:31.5:1:1:0:60:4:0.0145:0:1 0/0:75:0:0,0:3,72:0:1,0:24.3:1:31.7:1:1:0:59.8:24:1:0:0.1 -12 12022012 . TA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCCATCTCTACTAAAAA;RSEQ=AAAAAAATTAGCCGAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:0,2:31,73:0.0189:2,0:13.5:1:31.5:1:1:0:60:4:0.0196:0:0.5 0/0:39:0:0,0:6,33:0:2,0:24:1:30.1:1:1:0:60:78:1:0:0.1 -12 12022098 . A T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=6.44735;LSEQ=GAGAATGGCATGAACCCGGG;RSEQ=GGCAGAGCTTGCAGTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:27:24,3:79,12:0.2288:2,2:23.5:1:30.6:1:1:1.21:53.5:54:0.2328:0:1 1/0:88:58:56,2:30,0:0.6591:1,1:24.2:1:30.3:1:0.54545:0:57.4:57:0.6628:0:1.1 -12 12022118 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23196;SOR=Inf;LSEQ=AGGCAGAGCTTGCAGTGAGC;RSEQ=GAGATCGTGCCACTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:122,12:0:2,0:23.9:1:30.4:1:1:0:54.9:32.5:1:0:0.3 0/1:125:2:2,0:122,1:0.016:1,0:11.5:1:32.5:1:1:0:40:4:0.0161:0:2.5 -12 12022119 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.11304;SOR=Inf;LSEQ=GGCAGAGCTTGCAGTGAGCC;RSEQ=AGATCGTGCCACTGCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:129,12:0:2,0:22.9:1:29.5:1:1:0:55.2:34.25:1:0:0.3 0/1:133:3:3,0:128,2:0.0226:1,0:16.3:1:31:1:1:0:59.3:6:0.0233:0:1.3 -12 12022128 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50018;SOR=0;LSEQ=TGCAGTGAGCCGAGATCGTG;RSEQ=CACTGCACTCCAGCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:2,0:153,16:0.0117:2,0:20.5:1:29:1:1:0:60:4:0.0121:0:1 0/0:152:0:0,0:149,3:0:1,0:24.6:1:31.6:1:1:0:57.8:24.333:1:0:0.8 -12 12022175 . G GA 203 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.00314;SOR=1.59006;LSEQ=GTGAGACTCCATCTCAAACA;RSEQ=AAAAAAAAAAAAAATATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:95:78,17:230,66:0.2204:2,2:28.4:1:30.5:1:0.3907:1.32:59.6:190:0.2448:0:1 0/1:419:130:100,30:183,47:0.3103:2,2:27.5:1:29:1:0.59338:1.16757:59.1:129:0.3325:0:0.8 -12 12022496 . T C 208 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACCCCGAGCAGCGGCCCC;RSEQ=CCGGTCCCCCCTGGACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1450:0:0,0:612,837:0:2,0:23.9:1:30:1:1:0:60:34.341:0.9993:0:0.3 0/1:1423:117:57,60:590,712:0.0822:2,2:24:1:30.3:1:0.49856:1.15:60:38:0.0822:0:1.2 -12 12022533 . C T 268 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACATGATCCGCCGCCTCTC;RSEQ=CCGGCTGAGAGAGCTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1239:474:201,273:334,430:0.3826:2,2:23.7:1:30.2:1:0.67962:1.05496:60:58.25:0.3835:0:1.2 0/0:1148:0:0,0:526,620:0:2,0:23.8:1:30.2:1:1:0:60:70.625:0.9982:0:0.2 -12 12023023 . C G 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=21.89073;LSEQ=TAGGCGCCCTCCAAGGCTCT;RSEQ=TGAGGGCAATTGGAGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:609:99:46,53:224,285:0.1626:2,2:20.7:1:32.1:1:0.65996:1.10:60:198:0.1639:0:1.1 1/1:532:431:205,226:51,50:0.8102:2,2:23.2:1:31.2:1:0.65833:1.12424:60:106.75:0.8102:0:1.1 -12 12023373 . G T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4157;SOR=2.48056;LSEQ=GGAGAGGAAAACAGGATTAT;RSEQ=GTATTGGAGGCAGGTGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:2:0,2:166,152:0.0063:2,0:10.5:1:20.5:1:0.23082:0:60:1:0.0032:0:1.5 0/1:260:4:3,1:131,125:0.0154:2,2:31.5:1:30.3:1:0.62281:2.85:60:8:0.0155:0:1 -12 12023773 . C A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.9542;LSEQ=GATATAAGGCAGAATGAAGT;RSEQ=AGCCCCATTTCCCATTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:60:33,27:172,154:0.1554:2,2:25.6:1:29.7:1:0.77979:1.09:60:120:0.1567:0:1 1/0:327:260:140,120:35,32:0.7951:2,2:22.9:1:28.6:1:0.8909:1.07:60:85.667:0.7957:0:1.2 -12 12023843 . C A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTCTGCCAGAGTAATAAAG;RSEQ=GCTGTAGAAGCAAAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:0:0,0:304,240:0:2,0:24.1:1:31.2:1:1:0:60:271:0.9982:0:0.2 0/1:483:19:10,9:252,212:0.0393:2,2:28.9:1:29.4:1:1:1.06964:60:38:0.0396:0:1.3 -12 12023844 . G A 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=28.29782;LSEQ=GTCTGCCAGAGTAATAAAGC;RSEQ=CTGTAGAAGCAAAGCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:548:1:1,0:306,241:0.0018:2,0:1:0:26:0:1:0:60:2:0.0018:0:1 0/1:487:24:11,13:251,212:0.0493:2,2:21.9:1:29.5:1:0.52974:1.39825:60:48:0.0494:0:1.5 -12 12023941 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.61834;LSEQ=TACTGAAGTGACTGTGCTTT;RSEQ=GATAGTGGGAAGGAGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:90:38,52:185,244:0.1727:2,2:23.5:1:29.8:1:0.90719:1.03747:60:29:0.1703:0:1.1 1/0:491:348:156,192:61,81:0.7088:2,2:24.5:1:29.6:1:0.76379:1.08:60:115:0.7128:0:1.1 -12 12024150 . C T 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62462;SOR=2.80693;LSEQ=CCTTTTTTTTTTTTTTTTTT;RSEQ=CACACTCTGTTGCCCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:1,0:69,200:0.0037:2,0:2:0:12:0:0.25926:0:55:0:0:0:1 0/1:290:3:2,1:93,194:0.0103:2,2:16.3:1:22.3:1:0.25084:4.15:60:2:0.008:0:1.7 -12 12024162 . GC G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49948;SOR=Inf;LSEQ=TTTTTTTTCCACACTCTGTT;RSEQ=CCAGGCTGGAGTGCAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:36,136:0:2,0:20.8:1:30.2:1:1:0:58.4:18.111:1:0:1.3 0/1:187:2:1,1:54,129:0.0107:2,2:25.5:1:30:1:0.50734:2.38:60:4:0.0112:0:0 -12 12024284 . G A 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=12.63994;LSEQ=AGGCGCCCGCCACCATGCCC;RSEQ=GCTAATTTTTTTCATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:1,4:13,14:0.1563:2,2:28.6:1:27.2:1:0.3547:3.57931:56:4:0.1481:0:1.6 1/0:21:15:8,7:1,5:0.7143:2,2:28.4:1:30:1:0.1778:5.28:60:14:0.7:0:1.1 -12 12024412 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24828;SOR=Inf;LSEQ=AGGATTACAGGCGTGAGCCA;RSEQ=CGCGCCTGGCCGGTACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:153,43:0:2,0:24.8:1:31.6:1:1:0:60:64.333:1:0:0.2 0/1:202:3:1,2:146,53:0.0149:2,2:13:1:26:1:0.18068:5.45406:60:6:0.0149:0:1 -12 12024543 . C A 49 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06194;SOR=Inf;LSEQ=TACATCAGGGATGTTGAATC;RSEQ=AGAAAATAAAATGGCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:171,248:0:2,0:25.9:1:31.6:1:1:0:59.9:82.8:1:0:0.1 0/1:433:5:4,1:177,250:0.0115:2,2:22.6:1:21.2:1:0.16623:5.63:60:1.5:0.0071:0:2.4 -12 12025110 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=7.56461;LSEQ=TGTGGAAGGGTCATTTGTAC;RSEQ=GGGGAAACCACAGAGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:94:42,52:237,248:0.1623:2,2:27.3:1:30.4:1:0.4993:1.18283:60:46:0.1603:0:1.2 1/0:447:266:127,139:86,92:0.5951:2,2:25.7:1:29.8:1:0.92303:1.02306:60:265:0.5968:0:1.1 -12 12025234 . G A 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=7.39742;LSEQ=TGGCTGCTGTCCATAGTGCT;RSEQ=CCCTCGTGGGCCTGGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:461:3:2,1:274,183:0.0065:2,2:12.7:1:28:1:1:1.33:60:6:0.0066:0:1.3 0/1:432:20:10,10:222,190:0.0463:2,2:22.7:1:28.3:1:0.82:1.168:60:40:0.0468:0:1.2 -12 12025363 . A C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.06518;LSEQ=CACATGGTTTAGACTTGAGG;RSEQ=GTTATTTTTCCCTTATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:645:522:202,320:52,69:0.8093:2,2:26.8:1:30.3:1:0.4097:1.19352:60:51.2:0.8127:0:1.1 0/1:717:155:73,82:262,293:0.2162:2,2:25.4:1:30.5:1:1:1.00444:59.9:154:0.2271:0:1.2 -12 12025428 . CTTTTTTTTTTT C 218 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=21.000;MSILEN=1;SSF=0;SOR=0.19023;LSEQ=AGTCTCTTAAAATTATATTA;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:219:113:19,94:22,64:0.516:2,2:27.7:1:32.1:1:0.15752:1.69598:59.7:112:0.5209:0.0183:0.6 0/1:244:41:11,30:45,131:0.168:2,2:30:1:30.9:1:0.84525:1.07:59.6:40:0.1778:0.0082:0.5 -12 12025712 . G T 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63313;SOR=0.42065;LSEQ=ATTGCTGGGATTACAGGCAT;RSEQ=AACCACTGCACCCAGCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:1,2:121,30:0.0195:2,2:16:1:27:1:0.10969:7.91573:60:6:0.0197:0:1 0/0:121:1:0,1:94,26:0.0083:2,0:1:0:21:0:0.22314:0:60:2:0.0085:0:1 -12 12025714 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50703;SOR=0;LSEQ=TGCTGGGATTACAGGCATGA;RSEQ=CCACTGCACCCAGCCTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:121,34:0.0127:2,2:15:0:33.5:1:0.39727:3.52187:60:4:0.0127:0:3.5 0/0:121:0:0,0:93,27:0:2,0:23:1:29.3:1:1:0:60:39:0.9915:0:0.1 -12 12025719 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50601;SOR=0;LSEQ=GGATTACAGGCATGAACCAC;RSEQ=GCACCCAGCCTATACTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:133,43:0.0112:2,2:20:0:32.5:1:0.43433:3.069:60:4:0.0115:0:3.5 0/0:139:0:0,0:102,37:0:2,0:22.3:1:30.1:1:1:0:60:45.333:1:0:0.1 -12 12025722 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50332;SOR=0;LSEQ=TTACAGGCATGAACCACTGC;RSEQ=CCCAGCCTATACTACTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:138,44:0.0108:2,2:23:0:33:1:0.43033:3.11276:60:4:0.0109:0:3.5 0/0:152:0:0,0:110,41:0:2,0:21.9:1:29.5:1:1:0:60:302:0.9934:0:0.1 -12 12025753 . A T 44 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05694;SOR=Inf;LSEQ=ACTACTATTTTTTTCATCTC;RSEQ=TTCCCCAATATCAGTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:217,105:0:2,0:24.3:1:30.3:1:1:0:59.9:39.25:1:0:0.2 0/1:309:4:1,3:190,115:0.0129:2,2:6.8:1:22.3:1:0.15745:4.93106:60:3:0.01:0:1.3 -12 12025940 . C T 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAATATTCATGTAAAATAA;RSEQ=CCTGGGGCCTAGATCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:265,235:0:2,0:25.1:1:31.3:1:1:0:60:54.556:1:0:0.1 0/1:499:37:23,14:237,225:0.0741:2,2:27.8:1:29.6:1:0.23319:1.56:60:74:0.0754:0:1.1 -12 12026415 . CAGCTGTTAGATGAGAAAACTTAGTTCCTTAAAGCTTTTCAAATGAGCACAGCACAAAAAGAAATGAAGGTGCTGCTGAATGTCAAACTGATGAGTACTATAGCTGGAGGGTATAGATGGAAATAGTACTCATGAATGTGGATCACAAAATGAAGCTAAATTCTTACTATTCAGATATGATTTGTTCAGGTGCCCTAGAATTTATGCATTTGGACACCTTCTGTGTATAAGGCACTGTTCTGCATTCTTGATGGGGTGGGGACAGCCTCAGAGAGGTATAAGACACAGTCTTTATCATGAAAGAGCTGAGCACAGTTAACTATAAAAGCGAAGCACATGACATGTATCTTAGAAGGGCTCCTGTTAAGTACCACAGGAGGTCAGAGTAGGGATGTCAGGGCAAGCTACATGGAGGGCTGGCTTTTAGCTGGGCTTGGATGAATGCTTAGAATGTGGACAAGTGGAGATTAGAGAAAAACAGGTCATTCCAGATGGAGAAAACTTACCAGGAGCAAAGCAAGATAAGGCTCGGTGTATTTTTTCTATTTCAGGTAGAAATGTAAATCTACAAGTTGAGATCTATTGAGGTCATTTAAAAATCTATCATTTTTCAGGCTGGGTACTGTGGCTCACGCCTGTAATCCCAGTACTTTGGAAGGCCAAGGCTGGCAGATCACCTGAGGTCAGGATTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTATCAAAAAA C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.0864;LSEQ=GCCTTTAAATCTCCGTAAAG;RSEQ=TACAAAAATTCGTCGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:149:113:20,93:13,23:0.7584:2,2:24:1:31.5:1:0.03602:2.60878:53.5:55.5:0.7603:0.1946:0.7 0/1:203:43:8,35:59,101:0.2118:2,2:21.2:1:31.1:1:0.02804:2.54495:50.4:86:0.2129:0.0739:0.4 -12 12026417 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52114;SOR=Inf;LSEQ=CTTTAAATCTCCGTAAAGCA;RSEQ=CTGTTAGATGAGAAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:13,23:0:2,0:22.2:1:32.1:1:1:0:60:72:1:0:0 0/1:185:2:1,1:57,98:0.0108:2,2:6.5:1:29:1:1:1.71:60:4:0.0127:0:1 -12 12026437 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51559;SOR=Inf;LSEQ=GCTGTTAGATGAGAAAACTT;RSEQ=GTTCCTTAAAGCTTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:12,20:0:2,0:26.8:1:29.3:1:1:0:60:15:1:0:0.1 0/1:169:2:1,1:60,79:0.0118:2,2:7:0:31.5:1:1:1.31:60:4:0.0143:0:1 -12 12026524 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50517;SOR=Inf;LSEQ=GATGAGTACTATAGCTGGAG;RSEQ=GTATAGATGGAAATAGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:23,21:0:2,0:21:1:31:1:1:0:60:88:1:0:0.1 0/1:162:2:1,1:61,71:0.0123:2,2:6.5:1:28.5:1:1:1.16:60:4:0.0152:0:1.5 -12 12026529 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21013;SOR=0;LSEQ=GTACTATAGCTGGAGGGTAT;RSEQ=GATGGAAATAGTACTCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:23,21:0.0154:2,2:18:1:27:0:1:1.09307:60:4:0.0444:0:1 0/0:153:0:0,0:59,66:0:2,0:27.2:1:29.4:1:1:0:60:61.5:1:0:0.1 -12 12026792 . AG A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07765;SOR=0;LSEQ=CTCCTGTTAAGTACCACAGG;RSEQ=GTCAGAGTAGGGATGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:47,34:0.012:2,2:29.5:1:32.5:1:1:1.37686:60:4:0.0244:0:0 0/0:431:0:0,0:251,152:0:2,0:25.6:1:31.1:1:1:0:60:79.6:1:0:0.1 -12 12026871 . A G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00335;SOR=Inf;LSEQ=GATGAATGCTTAGAATGTGG;RSEQ=CAAGTGGAGATTAGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:63,57:0:2,0:24.8:1:30.2:1:1:0:60:119:1:0:0.1 0/1:559:20:9,11:257,254:0.0358:2,2:22.9:1:30.9:1:0.65712:1.23616:60:40:0.0382:0:1.1 -12 12027101 . G C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=8.60001;LSEQ=TGGCAGATCACCTGAGGTCA;RSEQ=GATTTCGAGACCAGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:11:1,10:0,0:0.1158:0,2:23.4:1:30.4:1:1:0:60:22:1:0:1.5 1/0:75:40:2,38:0,7:0.5333:0,2:25.1:1:29:1:1:0:60:80:0.8511:0:1.7 -12 12027136 . C T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=10.2047;LSEQ=CCTGGCCAACATGGTGAAAC;RSEQ=CCATCTCTATCAAAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:7:0,7:0,0:0.0769:0,0:23.7:1:30.4:1:1:0:60:14:1:0:2.1 0/1:56:26:0,26:0,2:0.4643:0,1:25.5:1:28.3:1:1:0:60:12:0.9231:0:2.2 -12 12027175 . G T 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01606;SOR=0;LSEQ=ACAAAAATTCGTCGGGCATG;RSEQ=TGGTGCACACCTGTAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:77:7,70:0,0:1:0,2:23.7:1:30.3:1:1:0:53.3:76:1:0:1.2 1/1:27:24:0,24:0,3:0.8889:0,1:21.2:1:30.5:1:1:0:53.3:48:0.8889:0:1.5 -12 12027310 . CA C 66 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGTGATACTCTGTCT;RSEQ=AAAAAAAAAAAAATGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:1,3:2,5:0.3077:2,2:29.8:1:33:1:1:1.18052:60:8:0.3077:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 12027342 . A G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.17582;SOR=7.29544;LSEQ=AAATGTGTGTGTATATATAT;RSEQ=TGTGTGTATATATATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:2,7:0.1818:2,0:31.5:1:32.5:1:0.10909:0:60:4:0.2222:0:2 1/0:3:2:2,0:1,0:0.6667:0,0:23:1:33.5:1:1:0:56:4:0.6667:0:3 -12 12027372 . GTA G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATATATACACACACATATAT;RSEQ=TATATATATGCGTATGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:5,2:1,1:0.875:2,2:22.7:1:32.4:1:1:2.24:53.4:14:0.875:0.125:3.1 1/1:6:6:6,0:0,0:1:0,0:31:1:33.3:1:1:0:48.8:12:1:0:2.3 -12 12027405 . C T 83 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGTATGTATATATACACACA;RSEQ=ACGTGTATGTGCGTGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:35.3:1:29.7:1:1:0:48.5:12:1:0:4.3 1/1:7:7:7,0:0,0:1:0,0:23.4:1:29.6:1:1:0:46.4:14:1:0:2.3 -12 12027407 . C T 82 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTATATATACACACACA;RSEQ=GTGTATGTGCGTGTGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:34.7:1:29.7:1:1:0:48.5:12:1:0:4.3 1/1:7:7:7,0:0,0:1:0,0:21.4:1:29.4:1:1:0:46.4:14:1:0:2.3 -12 12027429 . C CACGTGTGTGCGCGTGTGTATGTGTATATATGTGTGT 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.00078;SOR=Inf;LSEQ=TGTATGTGCGTGTGTACACA;RSEQ=ATATGTGTATGTGCGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:14.9:1:31:1:1:0:42.4:16:1:0:3.3 1/1:5:5:5,0:0,0:1:0,0:26.6:1:28.1:1:1:0:42.6:10:1:1:2 -12 12027431 . TATGTGTA CGTGTG 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.07537;SOR=0;LSEQ=TATGTGCGTGTGTACACACA;RSEQ=TGTGCGTGTGTACACACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:3,0:0.625:0,2:23.4:1:29.6:1:1:0:46.2:10:0.625:0.125:3 0/0:5:0:0,0:5,0:0:0,0:1:0:28:1:1:0:42.6:10:1:0:2 -12 12027447 . T C 61 d7;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACATATGTGTATGTGCGTG;RSEQ=GTACACACATATATGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:2,0:0.6667:0,2:10:0:30.5:1:1:0:47:8:0.6667:0:5.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 12027586 . A ATG 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTGTGTGTGTATATACACAT;RSEQ=TGTGTGTATATGTATATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,0:0.5:0,0:32:1:30.5:1:1:0:60:4:0.5:0:1 -12 12027594 . A G 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.00561;SOR=Inf;LSEQ=GTATATACACATATGTGTGT;RSEQ=TATGTATATATGTGTGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:0:1,0:7.1:1:28.9:1:1:0:51.4:32:1:0:1.2 0/1:14:4:4,0:9,0:0.2857:0,0:17.8:1:30.8:1:1:0:60:8:0.3077:0:1.3 -12 12027596 . A G 163 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.02284;SOR=0.08345;LSEQ=ATATACACATATGTGTGTAT;RSEQ=TGTATATATGTGTGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:32:32,0:1,0:0.9697:0,1:8.5:1:32.6:1:1:0:51.2:31:0.9688:0:1.2 1/0:14:10:10,0:3,0:0.7143:0,0:7.1:1:31.7:1:1:0:53.7:20:0.8333:0:1 -12 12027618 . G GTA 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.2283;SOR=0.2865;LSEQ=GTATATATGTGTGTATATAT;RSEQ=TATATGTGTGTATATATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:71:63,8:1,0:0.9726:0,2:18.8:1:29.7:1:1:0:56:142:0.9861:0.3288:0.6 1/1:22:20:20,0:1,0:0.9091:0,1:24.7:1:30:1:1:0:56.9:40:0.9091:0:0.7 -12 12027660 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.14728;SOR=Inf;LSEQ=ATATGTATATGTGTATATAT;RSEQ=TGTGTATATATATATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:153,71:0:2,0:23.4:1:29.1:1:1:0:59.4:223:1:0:0.2 0/1:140:2:1,1:92,46:0.0143:2,2:6.5:1:28.5:1:1:1.98939:60:4:0.0144:0:2.5 -12 12027664 . GTA G 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.16133;SOR=0;LSEQ=GTATATGTGTATATATATGT;RSEQ=TATATATATGAAATTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:5:3,2:158,83:0.0203:2,2:28.6:1:32:1:1:1.26778:59:10:0.0204:0:0.2 0/0:154:0:0,0:97,57:0:2,0:24.9:1:28.9:1:1:0:59.8:76:1:0:0.2 -12 12027745 . A C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4921;SOR=0.76702;LSEQ=CATACCATTAAGATACATGC;RSEQ=GAATTGTTCTCACTCATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:21:10,11:101,146:0.0778:2,2:26.1:1:30.5:1:0.64589:1.31:60:42:0.0778:0:1 0/1:247:15:5,10:97,135:0.0607:2,2:30.8:1:29.9:1:0.59716:1.435:60:30:0.0607:0:1 -12 12027759 . T A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24824;SOR=0;LSEQ=ACATGCAGAATTGTTCTCAC;RSEQ=CATAGGTGGGAATTGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:3,0:74,135:0.0142:2,0:10.3:1:21.3:1:0.04672:0:60:2:0.01:0:1.3 0/0:210:0:0,0:81,129:0:2,0:24.9:1:29.1:1:1:0:59.6:69:1:0:0.3 -12 12027764 . G A 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24811;SOR=Inf;LSEQ=CAGAATTGTTCTCACTCATA;RSEQ=GTGGGAATTGAACAATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:65,128:0:2,0:22.5:1:30.4:1:1:0:59.3:31.167:1:0:0.3 0/1:196:3:1,2:73,120:0.0153:2,2:31.3:1:30.7:1:1:1.21544:39:6:0.0155:0:7 -12 12027771 . A G 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12271;SOR=Inf;LSEQ=GTTCTCACTCATAGGTGGGA;RSEQ=TTGAACAATGAGAACACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:53,111:0:2,0:23:1:30.3:1:1:0:59.2:163:1:0:0.3 0/1:163:3:1,2:56,104:0.0184:2,2:29:1:32:1:1:1.07645:39:6:0.0189:0:7 -12 12027779 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49853;SOR=Inf;LSEQ=TCATAGGTGGGAATTGAACA;RSEQ=TGAGAACACATGGACACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:42,95:0:2,0:23.8:1:30:1:1:0:58.6:44.667:1:0:0.4 0/1:144:2:1,1:45,97:0.0139:2,2:12:0:33.5:1:0.53836:2.14:48:4:0.014:0:6.5 -12 12027790 . T G 28 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71907;SOR=0.72354;LSEQ=AATTGAACAATGAGAACACA;RSEQ=GGACACAGGAAGGGGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:4:0,4:24,80:0.0367:2,0:24.3:1:14:1:0.57328:0:50:0:0:0:3 0/1:112:3:1,2:30,78:0.0268:2,2:7:1:26.3:1:1:1.30:45.3:2:0.0198:0:5.3 -12 12027797 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22409;SOR=Inf;LSEQ=CAATGAGAACACATGGACAC;RSEQ=GGAAGGGGAACATCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:13,81:0:2,0:24.9:1:29.6:1:1:0:57.6:7.545:1:0:0.7 0/1:85:2:1,1:13,70:0.0235:2,2:8.5:1:28.5:1:0.30392:5.23:60:4:0.026:0:1 -12 12027811 . C T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.181;SOR=Inf;LSEQ=GGACACAGGAAGGGGAACAT;RSEQ=ACACACCGGGTCCTGTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:13,66:0:2,0:23.1:1:29.8:1:1:0:56.8:6.9:1:0:0.9 0/1:59:2:0,2:3,54:0.0339:2,0:28.5:1:26:1:1:0:40.5:4:0.0364:0:6.5 -12 12027885 . C T 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00143;SOR=Inf;LSEQ=GATATACCTAATGTAAATGA;RSEQ=GAGTTAATGGGTGCAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:45,27:0:2,0:23.9:1:30.8:1:1:0:42.8:35:1:0:0.7 0/1:29:5:3,2:18,6:0.1724:2,2:27.2:1:31:1:0.59682:1.94799:43.6:10:0.1786:0:1.8 -12 12027966 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51223;SOR=0;LSEQ=TTGTGCACATGTACCCTAAA;RSEQ=CTTAAAGTATAATTAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:173,25:0.01:2,2:24.5:1:31.5:1:0.24367:6.8044:60:4:0.0102:0:1.5 0/0:144:0:0,0:125,19:0:2,0:22.6:1:30.4:1:1:0:58.1:143:1:0:0.1 -12 12027980 . TA T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=5.65432;LSEQ=CCTAAAACTTAAAGTATAAT;RSEQ=AAAAAAAAAGATACATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:57:49,8:191,46:0.1906:2,2:21.5:1:29.8:1:0.44674:1.47:59.3:56:0.1911:0.0502:0 1/0:215:123:101,22:74,16:0.5721:2,2:22.8:1:29.9:1:1:1.00739:59.4:122:0.5701:0.1209:0.1 -12 12028142 . A C 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=34.08331;LSEQ=AGCTTATTTTTAAAGGTGTC;RSEQ=CTTACTTTGCAAAGGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:1:0,1:367,387:0.0013:2,0:24:0:11:0:1:0:60:0:0:0:2 0/1:670:29:13,16:279,361:0.0433:2,2:25.7:1:28.3:1:1:1.05:60:8.667:0.0393:0:1 -12 12028157 . G T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.89309;LSEQ=GTGTCACTTACTTTGCAAAG;RSEQ=ATAAGGAGAACTGTTATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:689:101:44,57:287,301:0.1466:2,2:25:1:28.9:1:0.33467:1.23482:60:100:0.1464:0:1.1 1/0:623:338:144,194:117,168:0.5425:2,2:24.6:1:28.3:1:0.7445:1.07:60:83.5:0.5413:0:1.1 -12 12028566 . A AG 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGACTTGATTTCAAAGGT;RSEQ=GAAGGGCCTTTTACAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:206,216:0:2,0:24.6:1:29.5:1:1:0:60:139.667:0.9976:0:0.1 0/1:377:34:13,21:164,179:0.0902:2,2:28.1:1:30.4:1:0.36808:1.4785:60:68:0.0912:0.0106:0.1 -12 12028629 . T G 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00046;SOR=Inf;LSEQ=CAAGAGTCTAGCCTCGAGCT;RSEQ=CTGTTCAGTGTTTTTCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:207,199:0:2,0:24.8:1:30:1:1:0:60:57:1:0:0.1 0/1:356:10:6,4:181,165:0.0281:2,2:27.8:1:31.6:1:0.75363:1.37:60:20:0.0283:0:1.1 -12 12028735 . G GT 83 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.06929;SOR=6.93036;LSEQ=GCCAAATCCAGCCACCATGC;RSEQ=TTTTTTTTAAATCAAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:1:1,0:225,248:0.0021:2,0:33:0:32:0:0.47679:0:60:2:0.0021:0:0 0/1:484:7:3,4:236,240:0.0145:2,2:23.1:1:29.8:1:1:1.31038:60:14:0.0146:0.0041:0.3 -12 12029748 . G A 266 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGAGGCTATCGCTGGTCA;RSEQ=TTGGGTCATTAATCCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:478:477:279,198:0,0:0.9979:0,2:24.6:1:30:1:1:0:60:52:0.9979:0:1.2 1/1:358:358:190,168:0,0:1:0,2:25.8:1:29.6:1:1:0:60:70.6:1:0:1.2 -12 12029765 . A G 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGTTGGGTCATTAATCCT;RSEQ=CAGCAGGCAAGACACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:78:45,33:251,203:0.1463:2,2:21.7:1:31.8:1:0.7131:1.10:60:156:0.1477:0:1.8 0/0:431:0:0,0:232,199:0:2,0:22.8:1:28.3:1:1:0:60:70.833:1:0:0.8 -12 12030052 . A C 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49939;SOR=Inf;LSEQ=ATATATACAAAGATTCAATT;RSEQ=GGGAAGCCTCTGAAGTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:325:323:172,151:0,0:0.9938:0,2:23.3:1:30.5:1:1:0:60:79.75:0.9969:0:1.5 1/1:313:313:169,144:0,0:1:0,2:23.8:1:30.4:1:1:0:60:103.333:1:0:1.6 -12 12030117 . A G 284 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47856;SOR=0;LSEQ=GAGAAAGCAGTTTGAGGCTT;RSEQ=TCCTCAGGGGCTTCAAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:462:462:284,178:0,0:1:0,2:24.9:1:32.1:1:1:0:60:91.4:1:0:1.4 1/1:424:423:253,170:0,0:0.9976:0,2:25.2:1:31.2:1:1:0:60:69.5:0.9976:0:1.8 -12 12030123 . A G 213 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGTTTGAGGCTTATCCTC;RSEQ=GGGGCTTCAAGGACTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:0:0,0:291,202:0:2,0:24.4:1:30.5:1:1:0:60:122.25:1:0:1.2 0/1:437:159:95,64:153,125:0.3638:2,2:23.2:1:29.2:1:0.36706:1.21:60:52:0.3611:0:2.2 -12 12030306 . A G 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGCTAAAAGACCTCGTAAA;RSEQ=GAGAAGTGTGAAGGGATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:287:235:124,111:27,25:0.8188:2,2:27.2:1:31.1:1:1:1.03:59.8:28.375:0.8195:0:1.5 1/1:323:323:156,167:0,0:1:0,2:26.4:1:30.2:1:1:0:59.8:34.889:1:0:1.4 -12 12030352 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12129;SOR=Inf;LSEQ=AGTGCTGGGGGCAAGTCTCA;RSEQ=CCCTCGGCCTTTGTTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:155,148:0:2,0:24.3:1:31.3:1:1:0:60:29.3:1:0:0.6 0/1:298:3:2,1:153,141:0.0101:2,2:9.7:1:26.7:1:1:1.84:60:6:0.0103:0:1.7 -12 12030834 . TC T 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00758;SOR=0;LSEQ=TTAATTGCTACGTGTCACTG;RSEQ=CCCCCCTGCCTCACTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:8:3,5:167,210:0.0208:2,2:30.6:1:31.5:1:1:1.32445:60:16:0.0212:0:0.1 0/0:373:0:0,0:168,203:0:2,0:23.6:1:30.7:1:1:0:60:52:0.9945:0:0.2 -12 12030905 . G A 50 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26302;SOR=0;LSEQ=GTGTGGGAGCTGTGGGTACA;RSEQ=CCAGCACAACTGCCTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:1,2:87,124:0.014:2,2:22:0:32:0:1:1.40109:60:6:0.0142:0:1 0/0:161:0:0,0:64,97:0:2,0:23.6:1:31.6:1:1:0:60:39.25:1:0:0.1 -12 12030945 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17111;SOR=Inf;LSEQ=AGCCACGCAGGGCACTGACA;RSEQ=GGAAGGCCTGTGTGGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:86,133:0:2,0:26:1:31.3:1:1:0:60:72:1:0:0.1 0/1:155:2:1,1:62,91:0.0129:2,2:23.5:1:31.5:1:1:1.46:60:4:0.0129:0:1 -12 12031015 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.509;SOR=0;LSEQ=CCTTGGAGATTTACTTTTGT;RSEQ=CTCCTGCTTCCCCTCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:90,102:0.0103:2,2:32:1:31:1:1:1.13:60:4:0.0105:0:1 0/0:145:0:0,0:75,69:0:2,0:22.8:1:31.7:1:1:0:60:143:0.9931:0:0.1 -12 12031080 . C T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25502;SOR=0;LSEQ=GAGGGGATGAATAAGATGAG;RSEQ=ACTGGGGAGGGGAGGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:1,2:118,96:0.0138:2,2:19.3:1:25.7:1:0.59034:2.44837:60:6:0.0144:0:1 0/0:179:0:0,0:110,69:0:2,0:24.1:1:31.8:1:1:0:60:88.5:1:0:0.1 -12 12031265 . G A 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGAGTGGAAAATAATAGAA;RSEQ=GGGCTTGAGGAGACTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:61:35,26:187,134:0.1597:2,2:27.9:1:29.7:1:0.88862:1.0366:60:19.333:0.1538:0:1.1 0/0:396:0:0,0:214,182:0:2,0:24.6:1:30.7:1:1:0:60:78.2:1:0:0.2 -12 12031465 . A C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3411;LSEQ=TTTCGGATACCGGTGTTTCC;RSEQ=AGCCTTCTCCACACCTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:401:265:160,105:77,59:0.6608:2,2:24.8:1:31.5:1:0.51997:1.17:60:87.333:0.6583:0:1.1 0/1:371:148:81,67:125,97:0.3989:2,2:23.2:1:30.5:1:0.83092:1.06574:60:73:0.4022:0:1.1 -12 12031758 . AG A 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0.21764;LSEQ=ATCTAGAATAGAGGAGGAGG;RSEQ=GGGAAAAAAAAAAAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:440:45:20,25:210,179:0.1023:2,2:28.2:1:30.4:1:0.26982:1.46516:59.3:21.5:0.1036:0.0136:1.1 0/1:414:10:7,3:208,182:0.0242:2,2:36.4:1:30.5:1:0.35157:2.04:60:20:0.0269:0:1.5 -12 12031762 . G AA 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.14906;SOR=1.39362;LSEQ=AGAATAGAGGAGGAGGAGGG;RSEQ=AAAAAAAAAAAAAACAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:40:16,24:193,143:0.0939:2,2:29.6:1:29.1:1:0.04324:2.02066:57.8:19:0.0957:0:2.6 0/1:404:51:23,28:155,98:0.1262:2,2:28:1:29.2:1:0.0423:1.92122:59.6:102:0.1342:0:2.2 -12 12031783 . G A 145 LongAT STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=7.93212;LSEQ=AAAAAAAAAAAAAACAAGCA;RSEQ=CAGATGGCCCCCTGAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:6:5,1:181,234:0.0141:2,2:20.3:1:14.8:1:0.09185:6.44:50.8:0.2:0.0028:0:4.2 0/1:411:42:18,24:149,217:0.1022:2,2:24.2:1:26.9:1:0.86871:1.09:60:7.4:0.1042:0:2.2 -12 12031894 . G C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13551;LSEQ=TTGCTTACTATATTGTAAGA;RSEQ=ATTCAGCAGCATCCCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:252:174:65,109:35,42:0.6905:2,2:24.7:1:32:1:0.26379:1.39551:60:173:0.692:0:1.1 0/1:186:43:20,23:62,81:0.2312:2,2:22.1:1:31.5:1:0.72928:1.14:60:42:0.2283:0:1 -12 12032028 . C CT 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.12717;SOR=0.45532;LSEQ=TTTGTAAAGCTTAGTAGCAA;RSEQ=TTTTTTTTTCATATGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:16:6,10:220,186:0.0376:2,2:28.8:1:29.3:1:0.21023:1.96816:58.8:32:0.038:0.0023:0.7 0/1:344:6:3,3:173,162:0.0174:2,2:28.5:1:28.3:1:1:1.06766:60:12:0.0175:0.0029:0.3 -12 12032858 . C T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71125;SOR=1.52497;LSEQ=GCTGAAAAATTCCAGGTGAG;RSEQ=CGTGGCAACAACCTCTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:3:1,2:226,225:0.0066:2,2:31.3:1:29:1:1:2.00591:60:6:0.007:0:1 0/1:399:4:2,2:200,195:0.01:2,2:31.3:1:30.3:1:1:1.02558:60:8:0.0102:0:1 -12 12032964 . T A 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34981;SOR=3.34488;LSEQ=CATGGCTTGAATGTCAATTG;RSEQ=TTAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:1:1,0:104,113:0.0046:2,0:6:0:20:0:0.48165:0:40:2:0.0051:0:1 0/1:198:3:3,0:102,93:0.0152:2,0:6:1:21.7:1:0.24896:0:53.3:2:0.0109:0:1.3 -12 12032986 . GG AA 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52585;SOR=1.73665;LSEQ=TAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAAAAATCTATTGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:4:4,0:146,122:0.0142:2,0:9:1:31.3:1:0.1302:0:51.3:8:0.0172:0:1.8 0/1:245:6:6,0:115,115:0.0245:2,0:9:1:30.7:1:0.02958:0:51.7:12:0.0286:0:1.5 -12 12033441 . AT A 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTGCAGGTTAAGCCCTTAC;RSEQ=TGGAGAAATGGTCTGGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:212,275:0:2,0:24.4:1:30:1:1:0:60:39.583:1:0:0.1 0/1:401:40:22,18:173,188:0.0998:2,2:25.4:1:29.8:1:0.40988:1.33:59.9:39:0.1003:0.0175:0.3 -12 12033536 . C T 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGAAACATGCAGTGAAAA;RSEQ=GCCCATGCTTGTGGTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:205,222:0:2,0:24.2:1:30.8:1:1:0:60:60:1:0:0.4 0/1:380:34:15,19:151,194:0.0895:2,2:26:1:30.1:1:1:1.01:60:68:0.0902:0:1.9 -12 12033570 . C G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.32524;LSEQ=GTTAGAGAACTGTCCGCTTT;RSEQ=TTTTTGCTCTACAGTAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:175:91,84:97,91:0.4821:2,2:24.1:1:31.6:1:1:1.02:60:34:0.4802:0:1.2 0/1:293:68:36,32:107,117:0.2321:2,2:25.9:1:31.7:1:0.49031:1.23:60:136:0.2345:0:1.4 -12 12033609 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09047;SOR=Inf;LSEQ=CTTCTGAGTGGAGTGCCTTC;RSEQ=GCCTAGAGTCAAGAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:187,169:0:2,0:27:1:30.3:1:1:0:60:117.667:1:0:0.4 0/1:291:3:1,2:151,137:0.0103:2,2:19.3:1:27.7:1:0.60756:2.19859:60:6:0.0104:0:1.7 -12 12033871 . C T 274 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.48135;LSEQ=TCGTCCTGATTTACTGGCTT;RSEQ=TTTTCCCCCTAGAGATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1210:570:248,322:287,344:0.4711:2,2:26:1:30:1:0.52257:1.08317:60:80.429:0.4707:0:1.2 0/1:1190:357:161,196:367,459:0.3:2,2:26:1:29.8:1:0.84857:1.03:60:70.4:0.2986:0:1.2 -12 12033974 . C A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29137;LSEQ=CCCAAACCCCTGGGCTCAAG;RSEQ=AATTCTCCCACCTCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:97:8,89:9,93:0.485:2,2:26.5:1:30.4:1:1:1.07618:60:96:0.4898:0:1 0/1:163:35:1,34:4,124:0.2147:1,1:24.3:1:30.3:1:1:1.09617:60:70:0.2174:0:1 -12 12034171 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24898;SOR=Inf;LSEQ=TATAATTATAAGCCACCACA;RSEQ=CCAACCCTAATTTACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:175,113:0:2,0:24.5:1:31.3:1:1:0:60:47:1:0:0.1 0/1:299:3:1,2:181,114:0.01:2,2:9:1:28.3:1:0.56241:3.16287:60:6:0.0102:0:1 -12 12034259 . G T 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=22.22017;LSEQ=AGATTATGGAAAATTAAAAT;RSEQ=TGTCTGCCATTTGATAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:1:0,1:318,231:0.0018:2,0:1:0:14:0:0.42182:0:60:0:0:0:1 0/1:539:21:15,6:285,233:0.039:2,2:21.5:1:29.7:1:0.1795:2.04:60:20:0.0377:0:1.3 -12 12034818 . T C 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATTATTCTCAGTCTGCAG;RSEQ=AGGACACTGATTTCTCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:172,227:0:2,0:24.9:1:28.5:1:1:0:60:56:0.9949:0:0.1 0/1:394:19:11,8:151,223:0.0482:2,2:23.8:1:31.9:1:0.15422:2.03:60:38:0.0487:0:1.2 -12 12034979 . G C 187 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=82.76675;LSEQ=TTGTTAGAATGGGGTTCAAA;RSEQ=TCCAGGACTATGGTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:624:1:0,1:343,280:0.0016:2,0:13:0:14:0:0.45032:0:60:0:0:0:2 0/1:536:63:36,27:244,228:0.1175:2,2:25.8:1:31.4:1:0.42453:1.25:60:126:0.1189:0:1.1 -12 12035282 . C G 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15719;LSEQ=CCTAAGATTTTATAAACATA;RSEQ=ACCCATTAACGAGTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:152:74,78:95,83:0.4606:2,2:23.4:1:31.7:1:0.43967:1.20575:60:151:0.459:0:1.1 0/1:305:36:19,17:139,128:0.118:2,2:25.2:1:32.1:1:1:1.03:60:72:0.118:0:1.1 -12 12035459 . C T 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.43552;SOR=2.16769;LSEQ=CTATAAAATAGGAATAGCAA;RSEQ=AGCACCTGCCTCATAAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:2:0,2:240,182:0.0047:2,0:1:0:23.5:1:0.18774:0:60:4:0.0048:0:1 0/1:393:4:1,3:221,168:0.0102:2,2:6.8:1:25.8:1:0.32146:3.93341:60:8:0.0103:0:1 -12 12035482 . G A 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCTGCCTCATAAGGCGGC;RSEQ=TAAGGGTCAGATGTAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:0:0,0:310,228:0:2,0:23.9:1:30.7:1:1:0:60:133.5:0.9981:0:0.1 0/1:433:18:12,6:229,186:0.0416:2,2:20.8:1:30.8:1:0.46842:1.62:60:36:0.0421:0:1.1 -12 12035649 . C T 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02526;SOR=0.69;LSEQ=CCACTTCATAAGTGAGGCAA;RSEQ=AGAACCTCAGGAAGATTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:112:55,57:273,249:0.1767:2,2:24.9:1:29.4:1:0.60253:1.13602:60:55:0.1768:0:1.1 0/1:574:74:42,32:251,249:0.1289:2,2:24.9:1:28.8:1:0.32011:1.30:60:73:0.129:0:1.1 -12 12035664 . A G 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.52411;LSEQ=GGCAACAGAACCTCAGGAAG;RSEQ=TTAAGAAGCGTGTCCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:629:475:237,238:77,77:0.7552:2,2:25.6:1:31.3:1:1:1.00421:59.9:46.5:0.7536:0:1.6 1/0:599:370:187,183:116,112:0.6177:2,2:25.5:1:30.6:1:1:1.01354:60:40.111:0.6171:0:1.6 -12 12035698 . T TC 270 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1e-05;SOR=0.5755;LSEQ=CCAGGGTGGCCCAACTGAAT;RSEQ=CCCCTTGTAAATATACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:613:432:197,235:89,92:0.7047:2,2:26.2:1:30.9:1:0.42591:1.15372:59.9:85.4:0.7046:0.1077:1.6 1/0:579:335:160,175:112,130:0.5786:2,2:25.4:1:30.6:1:0.73605:1.06:60:82.75:0.5848:0.0915:1.6 -12 12035714 . C T 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=5e-05;SOR=0.58453;LSEQ=GAATTCCCCTTGTAAATATA;RSEQ=CCCCAGAGAAGGGTGTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:560:410:186,224:73,75:0.7321:2,2:24.6:1:30.2:1:0.44215:1.17185:59.9:40:0.7299:0:1.6 1/0:509:313:145,168:88,106:0.6149:2,2:25.8:1:29.1:1:0.85485:1.04:59.9:51.167:0.6128:0:1.6 -12 12036197 . A C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00108;SOR=Inf;LSEQ=AGAACAAGGGGAAGGTGTAC;RSEQ=TCATGTCTTCTTCTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:66,147:0:2,0:19.6:1:29.6:1:1:0:59.5:13.2:1:0:1.1 0/1:243:11:5,6:80,152:0.0453:2,2:23.6:1:27:1:0.52278:1.58:58.2:4.5:0.0393:0:2.7 -12 12036213 . T C 195 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=35.000;MSILEN=1;SSF=0.17107;SOR=0.67724;LSEQ=GTACATCATGTCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:122:88:29,59:3,23:0.7213:2,2:13.5:1:30.2:1:0.04544:3.73:59.1:11.571:0.8438:0:2.1 1/0:121:77:31,46:5,12:0.6364:2,2:14:1:26.8:1:0.58252:1.61:59.7:4.133:0.7949:0:2.4 -12 12036301 . T C 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.144;SOR=Inf;LSEQ=GCAGTGGTGCGATCTCGACT;RSEQ=ACTGCAACTTCCACCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:27:7,20:0,5:0.8438:0,2:26.9:1:31.7:1:0.56028:0:60:26:0.8387:0:1.3 1/1:21:21:2,19:0,0:1:0,2:16.7:1:27.3:1:1:0:58.1:3.2:1:0:2 -12 12036449 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1714;SOR=Inf;LSEQ=ACGTTGGTCAGGCTGGTCTC;RSEQ=AACTCCTGGCCTCAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:135,3:0:1,0:26.1:1:30.2:1:1:0:59:68:1:0:0.3 0/1:98:2:2,0:96,0:0.0204:1,0:12.5:1:30:1:1:0:50:4:0.0206:0:4 -12 12036458 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57955;SOR=2.65705;LSEQ=AGGCTGGTCTCAAACTCCTG;RSEQ=CCTCAAGTGATCCACCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:1:1,0:150,2:0.0065:1,0:43:0:32:0:1:0:54:2:0.0067:0:1 0/1:116:2:2,0:114,0:0.0172:1,0:18:1:29.5:1:1:0:50:4:0.0175:0:3.5 -12 12036464 . A G 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59532;SOR=2.37191;LSEQ=GTCTCAAACTCCTGGCCTCA;RSEQ=GTGATCCACCTGCCTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:1,0:155,2:0.0063:1,0:12:0:14:0:1:0:60:0:0:0:2 0/1:134:2:2,0:130,1:0.0149:1,0:18:1:31.5:1:1:0:50:4:0.015:0:4 -12 12036529 . A G 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00482;SOR=0.6947;LSEQ=GTGAGCCACCACGCCCGGCC;RSEQ=TGTCTTCTCTTTTAATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:516:359:235,124:94,57:0.6957:2,2:22.2:1:29.9:1:0.54318:1.15:59.8:38.889:0.6903:0:1.1 1/0:559:343:228,115:133,81:0.6136:2,2:23:1:29.6:1:0.31637:1.21:59.8:67.6:0.6112:0:1.2 -12 12036821 . T C 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCAGAGTCACCAAGCCACA;RSEQ=AGTTTTTCTTTTCCCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:989:0:0,0:579,409:0:2,0:25.3:1:29.7:1:1:0:60:81.333:0.999:0:0.1 0/1:936:49:26,23:494,392:0.0524:2,2:26.4:1:31.6:1:0.7684:1.11466:60:98:0.0527:0:1.2 -12 12037081 . G A 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=0.29992;LSEQ=CCGTCTTTCACATGGGTTCT;RSEQ=CCCAGGTTTAAGTTTGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:44:19,25:283,286:0.0717:2,2:25.5:1:29.1:1:0.43666:1.30143:60:88:0.0728:0:1.2 0/1:575:13:6,7:274,287:0.0226:2,2:27.8:1:28.6:1:1:1.11361:60:26:0.0229:0:1 -12 12037089 . T C 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACATGGGTTCTGCCCAGGT;RSEQ=TAAGTTTGGGTCACGACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:606:0:0,0:292,313:0:2,0:25.1:1:30.1:1:1:0:60:99.833:1:0:0.2 0/1:575:39:20,19:266,269:0.0678:2,2:24.7:1:31.1:1:0.86981:1.06:60:38:0.0675:0:1.3 -12 12037178 . G A 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36585;SOR=1.30786;LSEQ=GGATCATCTCTGAGGCCTCC;RSEQ=GTGGGTCAAAGGTCACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:27:14,13:234,229:0.0551:2,2:26.4:1:30.3:1:1:1.05:60:26:0.0538:0:1.1 0/1:522:37:16,21:252,233:0.0709:2,2:23.4:1:30.3:1:0.31284:1.41857:60:36:0.0702:0:1.2 -12 12037318 . C G 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00098;SOR=1.62629;LSEQ=TGGATTCTTTTTTGATTCTT;RSEQ=TGGTTAGTGCCTCAACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1122:80:49,31:606,435:0.0713:2,2:24.8:1:32.2:1:0.63888:1.13:60:160:0.0719:0:1 0/1:1225:136:74,62:612,476:0.111:2,2:21.8:1:31.3:1:0.71436:1.07715:60:44.333:0.1097:0:1.1 -12 12039518 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCAGGTGTGTATGTACG;RSEQ=GATGAGTCATGATGTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 12043677 . C G 66 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90182;LSEQ=CCCTAGTCTTTTTAAATAAG;RSEQ=ATTTTACCACTTTTTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:4,0:36,0:0.1:1,0:12.8:1:33:0:1:0:60:8:0.1:0:1 0/1:11:1:1,0:9,1:0.0909:2,0:39:0:32:0:1:0:60:2:0.0909:0:2 -12 12044195 . T C 61 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGAATTCTGGCGGAGGGCA;RSEQ=GAGCCTGGGACTCCATGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:15.8:1:30.8:1:1:0:60:8:0.5:0:1 1/0:2:1:0,1:0,1:0.5:0,0:36:0:31:0:1:0:60:2:0.5:0:1 -12 12268134 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23825;SOR=0;LSEQ=TTTGCAGTGTTTCCCCATTC;RSEQ=TGAGATTGCCTTTCCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:2,0:166,7:0.0114:1,0:20.5:1:31.5:1:1:0:60:4:0.0116:0:1.5 0/0:183:0:0,0:165,18:0:2,0:1:0:17:0:1:0:60:0:0:0:1 -12 12268230 . A G 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTCTGTTTTCCTTCTAGG;RSEQ=AAAAGAATGGGAGGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:0:0,0:403,351:0:2,0:25.9:1:29.7:1:1:0:60:74.4:1:0:0.1 0/1:931:38:23,15:469,421:0.0408:2,2:25.6:1:30.1:1:0.40772:1.38:60:18:0.0396:0:1.3 -12 12268329 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12425;SOR=Inf;LSEQ=ACTTGGTTTCCCTTTAATTG;RSEQ=TATTTGGGCTCAAATACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:105,278:0:2,0:24.2:1:31.4:1:1:0:60:62.833:1:0:0.1 0/1:396:4:2,2:113,279:0.0101:2,2:19.5:1:29.5:1:0.58309:2.46:60:8:0.0103:0:1 -12 12268526 . C T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=TTATAAGCTAATTTAAGATC;RSEQ=TGGAAAAGAGGGAAGTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:0,9:0,3:0.75:0,0:28:1:29.4:1:1:0:60:8:0.7273:0:1.3 1/1:6:6:0,6:0,0:1:0,0:25.7:1:31:1:1:0:60:12:1:0:1.5 -12 12308013 . T C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=CGTGATGCACGCCTGTAAAC;RSEQ=CAGCTACTCAGGAGGCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:43:1:32.3:1:1:0:60:6:0.6:0:1.7 1/0:3:2:2,0:1,0:0.6667:0,0:42.5:1:31:1:1:0:60:4:0.6667:0:1 -12 12308074 . G A 110 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00288;SOR=0.066;LSEQ=TGGGAGGCGGATGTTGCAGT;RSEQ=AGCCAAGATCACGCCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:14,0:14,0:0.5:1,1:19.1:1:28.9:1:1:0:60:28:0.5:0:2.1 0/1:17:1:1,0:16,0:0.0588:1,0:13:0:29:0:1:0:60:2:0.0588:0:2 -12 12308087 . G A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=0.08927;LSEQ=TTGCAGTGAGCCAAGATCAC;RSEQ=CCACTTTACTCCAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:17:17,0:16,0:0.5152:1,1:25.5:1:30.5:1:1:0:60:34:0.5152:0:1.8 0/1:24:2:2,0:22,0:0.0833:1,0:17:1:31.5:1:1:0:60:4:0.0833:0:2 -12 12308115 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4955;SOR=0;LSEQ=ACTCCAGCCTGGGTGACAGT;RSEQ=TGAGACTCTGTCTCAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:49,5:0.0357:2,2:17:1:29:1:0.20455:9.03696:60:4:0.0357:0:2 0/0:55:0:0,0:44,11:0:2,0:20.7:1:31.7:1:1:0:60:110:1:0:0.1 -12 12308124 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49678;SOR=Inf;LSEQ=TGGGTGACAGTGTGAGACTC;RSEQ=GTCTCAAACAAACAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:58,17:0:2,0:20.6:1:30.3:1:1:0:60:74:1:0:0.5 0/1:77:2:1,1:50,25:0.026:2,2:29.5:1:30:1:1:1.98074:60:4:0.026:0:1.5 -12 12308128 . T TCAAA 97 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=7.000;MSILEN=4;SSF=0.00169;SOR=Inf;LSEQ=TGACAGTGTGAGACTCTGTC;RSEQ=CAAACAAACAAACAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:60,20:0:2,0:20.8:1:30:1:1:0:60:25.667:1:0:0.4 0/1:89:10:6,4:52,27:0.1124:2,2:18.5:1:29.4:1:0.73421:1.28022:58.5:20:0.1124:0.0449:0.9 -12 12308149 . C T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23513;SOR=Inf;LSEQ=CAAACAAACAAACAAACAAA;RSEQ=AAAAAGTCTTTCAGCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:78,50:0:2,0:22:1:31.3:1:1:0:60:31:1:0:0.3 0/1:121:2:1,1:64,55:0.0165:2,2:13:0:26.5:1:1:1.16217:60:4:0.0165:0:2 -12 12308159 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49831;SOR=Inf;LSEQ=AACAAACAAACAAAAAGTCT;RSEQ=TCAGCCAGAACTGCCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:84,63:0:2,0:24.7:1:29.8:1:1:0:60:48:1:0:0.3 0/1:148:2:1,1:74,72:0.0135:2,2:29.5:1:27.5:1:1:1.02759:60:4:0.0135:0:1.5 -12 12308181 . C T 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCCAGAACTGCCATCTTC;RSEQ=AGTAATTTGCCAAAATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:84,79:0:2,0:31.2:1:31.4:1:1:0:59.8:39.75:1:0:0.2 0/1:172:23:11,12:71,76:0.1337:2,2:31.4:1:29.3:1:1:1.01903:59.3:46:0.1353:0:1.2 -12 12308216 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49827;SOR=Inf;LSEQ=ATGATGAACACAAAGGGAAA;RSEQ=AGGAGAGGCACCCGATACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:60,84:0:2,0:22:1:31.2:1:1:0:59.8:143:1:0:0.1 0/1:145:2:1,1:63,79:0.0138:2,2:20:0:31:1:1:1.25:60:4:0.0139:0:1.5 -12 12308391 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.24677;SOR=0;LSEQ=CAAAACTGGAAGGGTCTACA;RSEQ=TGTTACCCAGCATGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:94,96:0.0104:2,2:34.5:1:31:1:1:1.02:60:4:0.0105:0:1 0/0:194:0:0,0:92,102:0:2,0:29.2:1:29.8:1:1:0:59.9:96:1:0:0.2 -12 12308441 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22322;SOR=Inf;LSEQ=TAAACAAAAAAGTTAAGGGC;RSEQ=AGATTCTTGCCAACAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:25,66:0:2,0:22.5:1:29.5:1:1:0:60:29.333:1:0:0.1 0/1:82:2:1,1:23,57:0.0244:2,2:15.5:1:27.5:1:0.50226:2.45:60:4:0.0253:0:1.5 -12 12308503 . T C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22868;SOR=Inf;LSEQ=AAGCACGCTAAGAGCCGAGA;RSEQ=AGCTTCCTAAAGGAAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:1,29:0:1,0:22.3:1:28.2:1:1:0:60:29:1:0:0.2 0/1:28:2:0,2:2,24:0.0714:2,0:22.5:1:34:0:1:0:60:4:0.0714:0:1 -12 12308741 . TA T 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAAGACTTCTGGACTGT;RSEQ=AAAAAAAAAAAAAGGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:21.5:1:32:0:1:0:60:4:1:0:0.5 0/0:1:0:0,0:0,1:0:0,0:2:0:26:0:1:0:60:2:1:0:0 -12 12767452 . G A 39 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACTGTTGCCCAGGCTGG;RSEQ=GTGCGTTGGTGTGATCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:33.7:1:25:1:1:0:60:2:1:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 12767856 . A G 71 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GGCTGGAGTGCAGTGGCACG;RSEQ=TCTCAGCTCACTGCAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:32:1:31:1:1:0:60:10:1:0:1 0/0:1:0:0,0:0,1:0:0,0:41:0:32:0:1:0:60:2:1:0:0 -12 12864389 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGGAAAGAGAGTGGCGG;RSEQ=TTCTGAGGGGGTCACATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 12865175 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.22475;SOR=Inf;LSEQ=GAACTCTGCCCATCTCCCCA;RSEQ=ATCCCACTGGATGAACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:10,198:0:1,0:24.4:1:32.5:1:1:0:60:103:1:0:0 0/1:188:2:1,1:13,173:0.0106:2,2:19:1:25:1:0.14376:12.86:60:4:0.0109:0:1 -12 12867300 . G T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTGGGGCTGCAGAACTT;RSEQ=GGTGAGAGCGCTGCATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:29.5:1:1:0:60:4:1:0:1 -12 12869972 . G T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCGGGGCTTAGGCGCCGC;RSEQ=GCGAACCCGCCAACGCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 12870695 . T C 173 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00268;SOR=0.07977;LSEQ=CTTCCGAGAGGGGTTCGGGC;RSEQ=GCGTAGGGGCGCTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:51:41,10:0,1:0.9808:0,2:23.4:1:30.6:1:0.21154:0:60:50:1:0:1.2 1/1:60:48:37,11:8,4:0.8:2,2:25.8:1:29.8:1:0.47249:1.67:60:47:0.7966:0:1.2 -12 12870726 . G GT 27 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20535;SOR=0;LSEQ=GCTTTGTTTTGTTCGGTTTT;RSEQ=TTTTTTTGAGAGTGCGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:91,26:0.0168:2,2:20:0:27.5:1:0.40379:3.45326:60:4:0.0168:0:0 0/0:143:0:0,0:99,44:0:2,0:23.4:1:31.3:1:1:0:60:70.5:1:0:0.5 -12 12870750 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50398;SOR=Inf;LSEQ=TTTTGAGAGTGCGAGAGAGG;RSEQ=GGTCGTGCAGACCCGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:114,36:0:2,0:28.6:1:31.8:1:1:0:60:49:1:0:0.4 0/1:185:2:1,1:124,59:0.0108:2,2:39.5:1:29:1:0.54465:2.09254:60:4:0.011:0:1 -12 12870758 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50272;SOR=Inf;LSEQ=GTGCGAGAGAGGCGGTCGTG;RSEQ=AGACCCGGGAGAAAGATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:121,43:0:2,0:27.2:1:32.2:1:1:0:60:81:1:0:0.3 0/1:199:2:1,1:129,68:0.0101:2,2:26:1:28.5:1:1:1.89062:60:4:0.0102:0:1 -12 12871099 . T G 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01006;SOR=0.63717;LSEQ=GGCGCAGGAGAGCCAGGATG;RSEQ=CAGCGGGAGCCGCCCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:100:40,60:117,173:0.2564:2,2:28.3:1:32.2:1:1:1.01441:60:200:0.2584:0:1.2 0/1:411:74:31,43:133,203:0.18:2,2:22.6:1:30.6:1:0.79337:1.10:60:17.5:0.1754:0:1.2 -12 12871104 . G A 49 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19348;SOR=0.22107;LSEQ=AGGAGAGCCAGGATGTCAGC;RSEQ=GGAGCCGCCCGGCGGCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:4:3,1:142,219:0.011:2,2:27.3:1:24.8:1:0.30534:4.61:60:3:0.0083:0:2 0/0:410:1:1,0:170,238:0.0024:2,0:1:0:25:0:0.41809:0:60:2:0.0025:0:2 -12 12871147 . C A 45 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05156;SOR=0;LSEQ=AATTGGGGCTCCGGCTAACT;RSEQ=TGAGGACACGCATTTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:4:2,2:118,189:0.0129:2,2:17.8:1:22.5:1:0.64119:1.60:60:3:0.0099:0:3.3 0/0:340:0:0,0:140,199:0:2,0:25.6:1:31.4:1:1:0:60:83.75:0.997:0:0.3 -12 12871188 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24939;SOR=Inf;LSEQ=ACCCAAAGACTGATCCGTCG;RSEQ=ACAGCCAGACGGGGTTAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:72,149:0:2,0:26.5:1:31:1:1:0:60:109.5:0.991:0:0.2 0/1:240:3:2,1:93,144:0.0125:2,2:10.7:1:26.3:1:0.5641:3.08:60:6:0.0126:0:1.3 -12 12871220 . A G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21572;SOR=Inf;LSEQ=GGGTTAGCGGAGCAATGCGC;RSEQ=GGAATAAGGAAGCGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:44,118:0:2,0:24.3:1:31.2:1:1:0:60:324:1:0:0.2 0/1:141:2:1,1:39,100:0.0142:2,2:34:0:30:1:0.48835:2.54:60:4:0.0144:0:1.5 -12 12872961 . G T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63605;SOR=2.31679;LSEQ=AAAAATTTTAAAATAACAGG;RSEQ=ATTAAGGTGAGATTCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:0,1:130,41:0.0058:2,0:20:0:11:0:0.24419:0:60:0:0:0:2 0/1:224:3:1,2:153,67:0.0134:2,2:17:1:25.7:1:0.22686:4.53237:60:6:0.0136:0:1 -12 12873124 . G GCAGC 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAAGCAACCTTAACATGC;RSEQ=CAGCCCTTGTTGGTTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:104,174:0:2,0:24.1:1:31.1:1:1:0:60:68.5:1:0:0.1 0/1:319:96:36,60:96,126:0.3009:2,2:24.3:1:31.2:1:0.38608:1.26889:59.9:192:0.3048:0.0596:0.1 -12 12873211 . A T 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02984;SOR=0;LSEQ=TTTGATCTGGCCCTGTTCTG;RSEQ=CATGCAATGAGGCATTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:6:1,5:1,65:0.0833:1,2:23.2:1:30.3:1:0.1608:11.96:60:12:0.0833:0:1.7 0/0:63:0:0,0:4,59:0:2,0:23:1:29.6:1:1:0:60:62:1:0:0.4 -12 12873233 . G C 188 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGCAATGAGGCATTTGTAG;RSEQ=ATTTAGTAATATTGCTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:51:0,51:0,0:1:0,1:25.2:1:33.2:1:1:0:60:102:1:0:1.1 0/1:40:19:0,19:0,21:0.475:1,1:24.4:1:31.9:1:1:0:60:38:0.475:0:1.1 -12 12873653 . C T 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTATCCCTGGCCTCTCACA;RSEQ=TAGATGCCAGCAGTATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:44:1:33:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 12874136 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23032;SOR=Inf;LSEQ=CTAAAATTTTAGGCACTCTT;RSEQ=AATGATCTGCCTCTAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:96,40:0:2,0:20:1:28.8:1:1:0:60:272:1:0:0.1 0/1:126:2:1,1:92,32:0.0159:2,2:13.5:1:29:1:0.45676:2.84645:60:4:0.0161:0:1 -12 12874159 . TG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49904;SOR=0;LSEQ=TGATCTGCCTCTAAAAGCGT;RSEQ=GATGTAGCATTATGCAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:124,72:0.0101:2,2:26:1:31:1:1:1.71719:60:4:0.0102:0:1 0/0:188:0:0,0:119,68:0:2,0:24:1:30.8:1:1:0:60:92.5:0.9946:0:0.1 -12 12874329 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24802;SOR=Inf;LSEQ=CTTGCTTTGATTTACAGCAA;RSEQ=TAGATAAATATTTGACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:54,120:0:2,0:25:1:31.8:1:1:0:60:57:1:0:0.1 0/1:179:3:2,1:56,120:0.0168:2,2:21.7:1:22.7:1:0.24562:4.25:60:2:0.0112:0:3.3 -12 13685698 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50324;SOR=Inf;LSEQ=GAAAAATTGTGTACTTGTTG;RSEQ=TTTCATAGGGAGAATGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:123,42:0:2,0:22.1:1:29.4:1:1:0:60:22.571:1:0:0.1 0/1:200:2:1,1:146,52:0.01:2,2:23:1:30:1:0.46075:2.79059:60:4:0.0102:0:1 -12 13685700 . T C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20553;SOR=0;LSEQ=AAAATTGTGTACTTGTTGAT;RSEQ=TCATAGGGAGAATGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:129,42:0.0116:2,2:16:1:27.5:1:0.43642:3.04717:60:4:0.0117:0:1 0/0:208:0:0,0:150,58:0:2,0:22.1:1:29.5:1:1:0:60:68.333:1:0:0.1 -12 13685707 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18012;SOR=0;LSEQ=TGTACTTGTTGATTTCATAG;RSEQ=GAGAATGGGGAGGGACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:137,51:0.0105:2,2:14:0:31.5:1:0.47352:2.67001:60:4:0.0108:0:1.5 0/0:257:0:0,0:173,84:0:2,0:21.8:1:30:1:1:0:60:35.714:1:0:0.1 -12 13685730 . C T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3077;SOR=0.22215;LSEQ=GAATGGGGAGGGACACAGTG;RSEQ=AAGCAGAGTGGGGAGATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:3:1,2:160,86:0.012:2,2:15.3:1:27.3:1:0.28561:3.70019:60:6:0.0123:0:1 0/0:371:1:0,1:223,147:0.0027:2,0:1:0:27:0:0.39892:0:60:2:0.0027:0:1 -12 13685742 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0142;SOR=Inf;LSEQ=ACACAGTGCAAGCAGAGTGG;RSEQ=GAGATCAAATTGTAGAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:167,105:0:2,0:28.3:1:30.8:1:1:0:60:53.4:1:0:0.4 0/1:424:9:5,4:242,173:0.0212:2,2:24.2:1:29.4:1:1:1.11877:60:18:0.0214:0:1 -12 13685816 . T C 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATTTCCTCAGGCATGTCGG;RSEQ=GCAATAAGATGTCAGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:265:265:111,154:0,0:1:0,2:25.7:1:30.5:1:1:0:60:87.333:1:0:1.1 1/0:364:255:111,144:53,55:0.7005:2,2:22.7:1:30:1:0.35716:1.24934:60:62.75:0.6992:0:1.1 -12 13685894 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51644;SOR=Inf;LSEQ=GTTTTGTGGGTTCATGCAAT;RSEQ=CATTTCTTGCTGGTAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:35,91:0:2,0:25.4:1:31.5:1:1:0:60:252:1:0:0.4 0/1:185:2:1,1:52,130:0.0108:2,2:41:0:30.5:1:0.49424:2.49:60:4:0.011:0:1.5 -12 13720021 . A T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13355;SOR=0;LSEQ=ACCCATAAAGCAATGTCGGA;RSEQ=CTGCCAATAGAAAAGGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:42,2:0.0435:1,2:20:0:32.5:1:0.12754:17.3476:60:4:0.0435:0:1.5 0/0:79:0:0,0:66,13:0:2,0:21.8:1:29.6:1:1:0:60:38.5:1:0:0.3 -12 13720043 . G A 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TGCCAATAGAAAAGGTGTTC;RSEQ=CAGATGAAGGTGATGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:63,12:0:2,0:21.4:1:29.9:1:1:0:60:150:1:0:0.1 0/1:123:23:17,6:64,35:0.187:2,2:26.6:1:29.9:1:0.46929:1.54:60:46:0.1917:0:1.2 -12 13720074 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30245;SOR=Inf;LSEQ=TGATGAGGCTGAGAGCCATG;RSEQ=CCGCCCCCAACATGTAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:84,48:0:2,0:26.6:1:31.3:1:1:0:60:65:1:0:0.1 0/1:211:4:2,2:120,87:0.019:2,2:21.3:1:29.3:1:1:1.37715:60:8:0.019:0:1 -12 13720095 . A G 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29544;SOR=Inf;LSEQ=CCGCCCCCAACATGTAGAAG;RSEQ=CCCCTGCCATGTTGTCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:94,66:0:2,0:29.4:1:29.5:1:1:0:60:79:1:0:0.1 0/1:267:3:1,2:146,117:0.0112:2,2:17.7:1:24.3:1:0.58828:2.48732:60:2:0.0075:0:1 -12 13720163 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17805;SOR=0;LSEQ=TTCTCATTGTGACAAATGCC;RSEQ=GTGAGCCAGAGAGCTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:33,75:0.0182:2,2:21:1:28.5:1:0.5246:2.25:60:4:0.0185:0:1 0/0:150:0:0,0:54,96:0:2,0:24.6:1:30:1:1:0:60:149:1:0:0.1 -12 13720168 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50484;SOR=Inf;LSEQ=ATTGTGACAAATGCCAGTGA;RSEQ=CCAGAGAGCTTCCAGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:32,73:0:2,0:22.7:1:31.7:1:1:0:60:104:1:0:0.1 0/1:133:2:1,1:44,87:0.015:2,2:32:1:28:1:1:1.97:60:4:0.0153:0:1 -12 13720272 . A G 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AGAGAAAAGGGAGAAAGAGG;RSEQ=GTATTGAGCAAGAAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,0:0.9286:0,1:24:1:31.5:1:1:0:60:26:1:0:1.2 1/1:14:14:0,14:0,0:1:0,1:16.8:1:30.6:1:1:0:60:28:1:0:1.1 -12 13761586 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13759;SOR=0;LSEQ=CCACATATTCCTCTTGGATC;RSEQ=TGAAGGCAGCTAAGTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:66,41:0.0183:2,2:35.5:1:30:1:1:1.60242:60:4:0.0185:0:1 0/0:184:0:0,0:113,71:0:2,0:25.5:1:29.9:1:1:0:60:183:1:0:0.1 -12 13764741 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.52274;SOR=Inf;LSEQ=GCCACGGCTGAGACGATGAG;RSEQ=AGCATCACAAACATCATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:28,37:0:2,0:25.8:1:32.3:1:1:0:60:64:1:0:0.5 0/1:103:2:1,1:51,50:0.0194:2,2:40:0:30:0:1:1.01981:60:4:0.0194:0:2.5 -12 13764774 . G A 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.85579;SOR=1.10444;LSEQ=ATCATCACCCATACGTCAGC;RSEQ=CTGAATGGCTCTGAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:19:7,12:13,21:0.3519:2,2:29.5:1:29.1:1:1:1.06006:60:38:0.3654:0:1.2 0/1:80:30:12,18:22,28:0.375:2,2:17.1:1:29.1:1:0.81698:1.17616:60:29:0.3671:0:1.3 -12 13764791 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=AGCGCTGAATGGCTCTGAGG;RSEQ=AGGGAAAAAAGCAGTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:12,22:0.0556:2,2:27.5:1:27.5:1:1:1.80:60:4:0.0588:0:2 0/0:55:0:0,0:21,34:0:2,0:21.8:1:29.3:1:1:0:60:110:1:0:0.4 -12 13764855 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48538;SOR=Inf;LSEQ=ATTCGAATTAATTCACATAT;RSEQ=CATTTCATATTTTAGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:28.1:1:29.6:1:1:0:60:16:1:0:0.5 0/1:11:2:0,2:0,9:0.1818:0,0:29.5:1:30.5:1:1:0:60:4:0.1818:0:1 -12 13767996 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21739;SOR=0;LSEQ=TGCTCCTTTTTTCCTTATTT;RSEQ=ACTTCCCCATCCATACGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:0.25:0,0:31:1:30.7:1:1:0:60:6:0.25:0:1 0/0:11:0:0,0:11,0:0:0,0:21.2:1:31:1:1:0:60:22:1:0:0.2 -12 13768136 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12303;SOR=0;LSEQ=AAGGGCACAGAGAAGTCGAC;RSEQ=ACCTCCGATCGTTCCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:35,44:0.0247:2,2:44.5:1:28:1:1:1.25:60:4:0.0253:0:1 0/0:149:0:0,0:69,80:0:2,0:29:1:30.5:1:1:0:60:73.5:1:0:0.2 -12 13768146 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11692;SOR=0;LSEQ=AGAAGTCGACCACCTCCGAT;RSEQ=GTTCCTCATTGATGGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:32,46:0.025:2,2:19:1:29.5:1:1:1.43:60:4:0.0256:0:1 0/0:153:0:0,0:66,86:0:2,0:28.5:1:29.9:1:1:0:60:75:0.9934:0:0.1 -12 13768161 . G C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53761;SOR=Inf;LSEQ=CCGATCGTTCCTCATTGATG;RSEQ=TGAGTGAGCCCACTGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:29,50:0:2,0:27.2:1:31.7:1:1:0:60:78:1:0:0.2 0/1:141:2:1,1:49,90:0.0142:2,2:31:1:26:1:1:1.83:60:4:0.0146:0:1.5 -12 13768354 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATGCATAAAGTGAGCA;RSEQ=GTTTTAAACTTATATTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:31.5:1:27.5:1:1:0:60:4:1:0:1.5 -12 16089825 . C T 49 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGTCTTGTCTTGTCTTGTC;RSEQ=TGTCCTGTCCTGTCCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:0,1:0.6:0,0:22.3:1:31.3:1:0.25:0:46.3:6:0.75:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 16089830 . C T 46 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGTCTTGTCTTGTCCTGTC;RSEQ=TGTCCTGTCCTGTCCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:0,2:0.6:0,0:17.3:1:29.3:1:0.1:0:46.3:6:0.75:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 16089835 . C T 30 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGTCTTGTCCTGTCCTGTC;RSEQ=TGTCCTGTCCTGTCCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,2:0.5:0,0:19:1:30:1:0.33333:0:39.5:4:0.5:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 16089840 . C T 29 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGTCCTGTCCTGTCCTGTC;RSEQ=TGTCCTGTCCTGTCCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,2:0.5:0,0:14:1:29.5:1:0.33333:0:39.5:4:0.5:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 16089845 . C T 30 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTGTCCTGTCCTGTCCTGTC;RSEQ=TGTCCTGTCCTGTCCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,2:0.5:0,0:9:1:30:1:0.33333:0:39.5:4:0.6667:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 16089876 . T C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTCCTGTCCTGTCTTGTCC;RSEQ=GTCCCGTCCTGTCCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:28:16,12:0,0:0.9655:0,2:6:1:30.5:1:1:0:59.1:56:1:0:1.4 1/1:12:12:5,7:0,0:1:0,2:5:0:26.3:1:1:0:60:5:1:0:1.3 -12 16089886 . T C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGTCTTGTCCTGTCCCGTCC;RSEQ=GTCCTGCCCTGCCCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:34:16,18:0,0:1:0,2:15:1:29.9:1:1:0:58.3:68:1:0:1.6 1/1:12:12:5,7:0,0:1:0,2:15:0:26.6:1:1:0:60:11:1:0:1.3 -12 16394674 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CTGAAAGGCTCCCAGCACAA;RSEQ=TTGGAAGTTTCTGTTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:0:1,0:28.9:1:31.9:1:1:0:60:30:1:0:0.1 0/1:21:2:1,1:19,0:0.0952:1,2:8:1:28:1:0.09524:0:60:4:0.1053:0:1.5 -12 16394763 . GTTAAC G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08242;LSEQ=AATCACAGACACAGAAATAT;RSEQ=TTAATAATGTGGCAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:108:95:68,27:10,3:0.8796:2,2:28.5:1:32:1:1:1.32029:60:190:0.8796:0.0833:0.3 0/1:94:35:25,10:40,19:0.3723:2,2:25.6:1:31.5:1:0.81882:1.19:60:70:0.3763:0.0319:0.5 -12 16394823 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=TGAAGCAATATTAATATATT;RSEQ=CCTAATCTTAGAAAAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:93,83:0:2,0:24.9:1:32.2:1:1:0:60:352:1:0:1.3 0/1:182:2:1,1:104,76:0.011:2,2:26:0:31.5:1:1:1.36601:60:4:0.011:0:2.5 -12 16394848 . G T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05649;LSEQ=ATCTTAGAAAAGGCTGCAGT;RSEQ=TCTTGAAAGCTTGAAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:190:166:79,87:9,15:0.8737:2,2:25.9:1:30.2:1:0.38883:1.51:60:165:0.873:0:2.3 0/1:215:60:28,32:77,78:0.2791:2,2:24.6:1:29.8:1:0.7616:1.12757:60:120:0.2817:0:2.4 -12 16394883 . G C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05939;LSEQ=AATCATTTCTGCCTCTGCCT;RSEQ=AAGTTCTGAAATCATCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:153:133:52,81:6,13:0.8693:2,2:29.6:1:31.6:1:0.61932:1.39:60:43.333:0.8667:0:2.8 0/1:178:50:18,32:52,76:0.2809:2,2:28.1:1:31.8:1:0.6118:1.21505:60:100:0.2809:0:2.7 -12 16394899 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05415;LSEQ=GCCTGAAGTTCTGAAATCAT;RSEQ=GCCCTGTAAAATTTTAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:141:123:44,79:5,13:0.8723:2,2:24.1:1:30:1:0.60297:1.44:60:60.5:0.8705:0:2.8 0/1:157:42:15,27:40,75:0.2675:2,2:24.5:1:29.7:1:1:1.04:60:84:0.2675:0:2.8 -12 16753352 . C T 55 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGGCAGCGCCATAACCAA;RSEQ=TGCCTGAGTGTGCAGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:22.3:1:27.5:1:1:0:60:3:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 16753737 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50462;SOR=0;LSEQ=TAGAAGATACCGGTCCTTGA;RSEQ=CTTTCGGTTGCAGCCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:38,146:0.0108:2,2:25.5:1:27:1:0.37629:3.81:60:4:0.0111:0:1 0/0:149:0:0,0:41,107:0:2,0:22:1:28.6:1:1:0:60:48.333:1:0:0.1 -12 16753747 . G A 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGGTCCTTGATCTTTCGGTT;RSEQ=CAGCCAGCACAACCTTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:25:7,18:17,113:0.1613:2,2:22.4:1:29.2:1:0.07212:2.57:60:50:0.1678:0:1 0/0:112:0:0,0:22,89:0:2,0:23.1:1:32:1:1:0:60:222:1:0:0.1 -12 16753965 . A G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGAAACAAAAAGTCTCA;RSEQ=ACTTTATCAAGTGCTTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:15.7:1:32:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 17903151 . C A 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0247;SOR=0;LSEQ=ATTTAACAGCTTACTATGTG;RSEQ=CACATTTTCTGAGAGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:34:34,0:0,0:1:0,1:23.1:1:30.3:1:1:0:60:68:1:0:1.1 1/1:15:12:12,0:3,0:0.8:0,0:19:1:29:1:1:0:60:24:0.8:0:1.6 -12 17903230 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49793;SOR=Inf;LSEQ=CAATAGAAACGATTCGTATC;RSEQ=CACTTTGAAAATGAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:88,30:0:2,0:22.8:1:30.1:1:1:0:60:117:1:0:0.2 0/1:120:2:1,1:94,24:0.0167:2,2:35:1:31.5:1:0.37465:3.85789:60:4:0.0168:0:1 -12 17903235 . T A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49807;SOR=0;LSEQ=GAAACGATTCGTATCACACT;RSEQ=TGAAAATGAAAACAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:97,31:0.0154:2,2:29:0:31:1:0.43315:3.0953:60:4:0.0161:0:1 0/0:129:0:0,0:99,30:0:2,0:22.2:1:30.1:1:1:0:60:128:1:0:0.1 -12 17903260 . C T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09258;SOR=0;LSEQ=AATGAAAACAAACAAAGACA;RSEQ=TGAGAGGTTAAATAACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:1,2:127,61:0.0157:2,2:14.3:1:23.3:1:0.25342:4.13006:60:2:0.0107:0:3 0/0:230:0:0,0:156,74:0:2,0:24.5:1:31.1:1:1:0:60:114:1:0:0.3 -12 17903344 . G A 244 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02777;LSEQ=TAAAATGTGTGAATTAAAAG;RSEQ=AAAGATACAAGCATTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:314:311:153,158:1,1:0.9904:2,2:25.8:1:29.9:1:1:1.03258:60:76.75:0.9935:0:1.2 1/0:449:333:163,170:56,58:0.7416:2,2:24.6:1:29.2:1:1:1.00697:60:82.25:0.7393:0:1.3 -12 17903404 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25303;SOR=Inf;LSEQ=TGTCAGATGATTCTCTGCAA;RSEQ=GTTTGACCATAGGTACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:80,159:0:2,0:26.5:1:30.1:1:1:0:60:58.75:1:0:1.3 0/1:279:3:2,1:95,181:0.0108:2,2:10.7:1:28:1:0.27783:3.79:60:6:0.0108:0:1.3 -12 17903428 . T G 239 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGACCATAGGTACAAAACTA;RSEQ=TGGATAATCTTATGCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:170:170:38,132:0,0:1:0,2:24.9:1:32.3:1:1:0:60:169:1:0:1.3 1/0:176:135:41,94:12,28:0.767:2,2:22.5:1:31.2:1:1:1.02:60:134:0.7657:0:1.5 -12 17903475 . C T 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATTGAAATGAGGAAATTTT;RSEQ=GAAACCTTTCTGCTATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:3,66:0:1,0:23.1:1:29.9:1:1:0:60:138:1:0:0.8 1/0:55:30:2,28:1,24:0.5455:1,2:18.1:1:29.8:1:1:1.70:60:60:0.5455:0:1.7 -12 18192630 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52367;SOR=0;LSEQ=AGGCTTCTGAAAGCAGACAA;RSEQ=GCCTTTCAAATTCTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:17,10:0.069:2,2:8:0:32:0:1:1.66781:60:4:0.0714:0:2 0/0:17:0:0,0:13,4:0:2,0:23.8:1:31.1:1:1:0:60:34:1:0:0.1 -12 18192679 . T C 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.50588;SOR=0;LSEQ=GAGTTGGGCAACATGGCTTC;RSEQ=CCCCTTCCTAGGTCCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:17,11:0.0667:2,2:44:0:31.5:1:1:1.52251:60:4:0.0714:0:2 0/0:21:0:0,0:10,11:0:2,0:27:1:29.7:1:1:0:59.2:42:1:0:0.1 -12 18397905 . C G 52 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGTGGCTCCAAGCAAGTTCT;RSEQ=TGTTCCCTCTTAGTCTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:30:1:33.3:1:1:0:60:6:0.6:0:1 0/0:1:0:0,0:1,0:0:0,0:10:0:32:0:1:0:60:2:1:0:0 -12 18398027 . A T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74165;SOR=1.4204;LSEQ=ACTGAAAAATACTTTAAGAG;RSEQ=TTACGTGGGCATCTGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:8,0:21,0:0.2759:1,0:33.3:1:29.5:1:1:0:60:16:0.2759:0:2 0/1:17:6:6,0:11,0:0.3529:0,0:17.2:1:31:1:1:0:60:12:0.375:0:1.8 -12 18398063 . A G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTTAGAAGCCTCAATTG;RSEQ=GGAATTATTGTGAGTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:45:44,1:0,0:1:0,1:24.6:1:31.3:1:1:0:60:44:1:0:1.3 1/1:36:36:36,0:0,0:1:0,1:26.9:1:31.6:1:1:0:60:72:1:0:1.2 -12 18398236 . G A 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32249;SOR=1.17034;LSEQ=CCAATTTTAACTCAGTCAGC;RSEQ=CTGCATTTTACACATTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:114:45,69:136,189:0.2597:2,2:25.6:1:29.5:1:0.74022:1.10309:60:56:0.2593:0:1.1 0/1:426:124:57,67:132,170:0.2911:2,2:23.1:1:29.1:1:0.66949:1.10:60:61:0.2891:0:1.1 -12 18398330 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21136;SOR=Inf;LSEQ=TTTACTTACATCTCAATATT;RSEQ=TATCATAAAATTGTTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:19,85:0:2,0:24.8:1:30.5:1:1:0:60:208:1:0:0 0/1:89:2:1,1:11,75:0.0225:2,2:11:0:33.5:1:0.25549:6.57:60:4:0.0227:0:1.5 -12 18398431 . G GA 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.30025;SOR=3.60185;LSEQ=CCCAAGAGTGATTTGGGAGG;RSEQ=AAAAAAATCTACTGTATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:0.2083:1,0:34.2:1:31.8:1:1:0:60:10:0.2083:0:0 1/0:6:3:0,3:0,3:0.5:0,0:33.7:1:31.3:1:1:0:60:6:0.5:0:0 -12 18406957 . AG A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=2e-05;SOR=4.13673;LSEQ=AACCTGAGTAAGAAAAAAAA;RSEQ=ATGCATCCTAAGAGCCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:16:12,4:75,20:0.1441:2,2:22.4:1:30.6:1:0.74609:1.24739:60:32:0.1509:0.027:0.3 0/1:97:40:31,9:45,12:0.4124:2,2:25.2:1:30:1:1:1.08775:60:80:0.4124:0.1237:0.6 -12 18406979 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58226;SOR=2.60501;LSEQ=ATGCATCCTAAGAGCCTAGT;RSEQ=CTTAAAGTGGAGAAACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:144,47:0.0052:2,0:13:0:27:0:0.25:0:60:2:0.0053:0:1 0/1:149:2:1,1:116,31:0.0134:2,2:36:1:27.5:1:0.38455:3.69909:60:4:0.0135:0:1.5 -12 18407043 . G A 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.39492;LSEQ=TTGAGAATAGAAGAATATAT;RSEQ=TTTTTCTTATTTTATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:76:50,26:187,126:0.1949:2,2:25.3:1:28.7:1:0.36103:1.29:60:75:0.1938:0:1.8 0/1:354:130:79,51:144,78:0.3672:2,2:19.7:1:28.3:1:0.49192:1.19121:60:64:0.3647:0:1.9 -12 18407074 . A G 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.08612;LSEQ=TTTATTTTTAAAGAGTTAGA;RSEQ=GAATTTAAAAACCAACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:101:60,41:218,184:0.2008:2,2:25:1:31.8:1:0.37203:1.23:60:202:0.2024:0:1.6 0/1:529:182:99,83:193,154:0.344:2,2:27.3:1:31:1:0.85401:1.05057:60:181:0.3441:0:1.7 -12 18434981 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10736;SOR=0;LSEQ=TTATCAAGGAGATATTTGGA;RSEQ=CAGAGTCAACCCTCTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:1,2:168,78:0.012:2,2:10.7:1:23.3:1:0.2424:4.27986:60:2:0.0081:0:2 0/0:276:0:0,0:182,94:0:2,0:24.4:1:31.4:1:1:0:60:54.2:1:0:0.1 -12 18435398 . GCCC G 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=4e-05;SOR=1.6994;LSEQ=TAAAGAATGCTCCTGGGGAA;RSEQ=CATAGGAAAACATCATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:137:67,70:253,254:0.2114:2,2:25:1:32.1:1:0.84785:1.04061:60:274:0.2154:0.0386:0.6 0/1:626:196:83,113:213,216:0.3131:2,2:25.6:1:31.6:1:0.10096:1.34189:60:195:0.3166:0.0495:0.5 -12 18435452 . C T 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.84662;LSEQ=CAGATTCAGTATTTTAGCTC;RSEQ=ATCATTCACAAGTTTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:637:140:66,74:228,269:0.2198:2,2:27:1:29.2:1:0.84787:1.05:60:45.667:0.2182:0:1.1 0/1:558:191:87,104:171,194:0.3423:2,2:25.5:1:29.3:1:0.78875:1.05361:60:382:0.3441:0:1.1 -12 18439648 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05875;SOR=Inf;LSEQ=TTTTCTATGTGTAAATATTA;RSEQ=TTCAATTTTTAAAAAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:0:1,0:24.9:1:32.6:1:1:0:60:88:1:0:0 0/1:29:3:3,0:25,1:0.1034:1,0:30.7:1:30:1:1:0:60:6:0.1034:0:1 -12 18443729 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59244;SOR=2.41974;LSEQ=AATTACATTGTGGGCAATAT;RSEQ=TTTTAAACTGTGTCTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:163,25:0.0053:2,0:16:0:31:0:0.13757:0:60:2:0.0053:0:1 0/1:157:2:1,1:124,31:0.0127:2,2:26.5:1:28.5:1:0.36714:3.95285:60:4:0.0131:0:1 -12 18443809 . C A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=20.04176;LSEQ=AATCAGAGAAAGATATCATG;RSEQ=AGCTGATGTTAATTTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:1:1,0:371,269:0.0016:2,0:1:0:29:0:1:0:60:2:0.0016:0:1 0/1:592:18:12,6:318,254:0.0304:2,2:24.2:1:29.2:1:0.47117:1.60:60:36:0.0308:0:1.1 -12 18443955 . C A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTATGCCATGTGGTAAGCAA;RSEQ=CTTGCAAATAAGTCTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:125,281:0:2,0:26.1:1:31.2:1:1:0:60:66.667:1:0:0.1 0/1:346:15:5,10:121,209:0.0434:2,2:24.7:1:29.3:1:1:1.15744:60:30:0.0439:0:1.1 -12 18444144 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTTTCTTCAAGAAGTAT;RSEQ=TTCACATAGCTCACCCGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:0,14:0.1765:1,0:29.3:1:28.7:1:1:0:60:6:0.1765:0:1.7 0/0:2:0:0,0:0,2:0:0,0:20:1:33:0:1:0:60:4:1:0:0 -12 18444163 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCACATAGCTCACCCGA;RSEQ=AATATTTTATCTTCCTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:0.2:0,0:44.5:1:33:0:1:0:60:4:0.2:0:2 0/0:1:0:0,0:0,1:0:0,0:12:0:30:0:1:0:60:2:1:0:0 -12 18446881 . C T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCAGAAATTCTGCATTTTTG;RSEQ=ACAAATGACCAGCTACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:0:0,0:368,310:0:2,0:27.1:1:31.8:1:1:0:60:44.2:1:0:0.1 0/1:624:21:11,10:324,278:0.0337:2,2:19.5:1:27.1:1:1:1.05938:60:42:0.0341:0:1 -12 18446924 . T G 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00571;SOR=Inf;LSEQ=AAGATCATATTCTAAGTGTA;RSEQ=GTGGCTCTGAAGAATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:657:0:0,0:267,388:0:2,0:25.5:1:30.3:1:1:0:60:130:0.9985:0:0.1 0/1:605:7:3,4:254,344:0.0116:2,2:20.1:1:28.4:1:1:1.02:60:6:0.01:0:1.1 -12 18466738 . TCACA T 116 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=12.000;MSILEN=2;SSF=0.00659;SOR=3.82464;LSEQ=AATATGTAATGCATATATAT;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:13:13,0:40,0:0.2167:1,1:23.5:1:32.7:1:1:0:59.6:26:0.2203:0.0167:0.1 1/0:27:14:14,0:11,0:0.5185:0,1:20.6:1:30.6:1:1:0:60:28:0.5185:0.1852:0.6 -12 18467005 . C T 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTATCTCGAAAGGTAAGA;RSEQ=TTTCTTAGCATTGGTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:770:0:0,0:292,478:0:2,0:25.5:1:31.8:1:1:0:60:76:1:0:0.1 0/1:505:40:14,26:174,291:0.0792:2,2:25.6:1:30.2:1:0.86522:1.11025:60:80:0.0795:0:1.1 -12 18467122 . T C 198 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AATACATGTTTATTTAAATA;RSEQ=ATTCATTGAAACATGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:67:1,66:0,37:0.6442:1,1:23.4:1:32.7:1:1:0:60:134:0.6442:0:1 0/0:51:0:0,0:0,51:0:1,0:20.8:1:28.9:1:1:0:60:102:1:0:0.2 -12 18473690 . C G 34 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03968;SOR=Inf;LSEQ=TCTTTCAGGTTTATTCTCAA;RSEQ=AAAAGCCAAGCTTTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:0:1,0:27.8:1:31.9:1:1:0:60:44:1:0:0 0/1:6:2:2,0:4,0:0.3333:0,0:38.5:1:34:0:1:0:60:4:0.3333:0:1 -12 18473729 . T C 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTACTTTTGAAAAGGCTTA;RSEQ=ATAGTTAAGGAGAGCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:2,0:46,0:0.0417:1,0:26:0:34:0:1:0:60:4:0.0417:0:1 0/0:13:0:0,0:13,0:0:1,0:23.2:1:31.2:1:1:0:60:26:1:0:0.2 -12 18473881 . T G 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03952;LSEQ=ACTCAATAAATATTAATATA;RSEQ=TCTGCTGTCTACAGCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:659:444:289,155:136,79:0.6737:2,2:24.4:1:31.9:1:0.66471:1.08:60:110:0.6728:0:1.1 0/1:452:34:22,12:264,154:0.0752:2,2:25:1:31.4:1:1:1.07:60:68:0.0754:0:1.1 -12 18473928 . T C 219 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACAGTCAGTTTTATCTGAA;RSEQ=CAACTTCTAGAATTTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1011:0:0,0:512,499:0:2,0:27.1:1:30.1:1:1:0:60:37.885:1:0:0.5 0/1:705:145:69,76:279,281:0.2057:2,2:28.8:1:30.6:1:0.64242:1.09347:60:47.333:0.2023:0:1.1 -12 18477895 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10751;SOR=Inf;LSEQ=ATGGGCAAAACAATTTGTGA;RSEQ=AAATGTTTGTGCTAAAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:0:0,0:280,90:0:2,0:24.5:1:30.4:1:1:0:60:740:1:0:0.1 0/1:181:2:1,1:137,42:0.011:2,2:26:1:29:1:0.41971:3.23548:60:4:0.011:0:1 -12 18477900 . G T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11379;SOR=5.95238;LSEQ=CAAAACAATTTGTGATAAAT;RSEQ=TTTGTGCTAAAGGTAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:1:1,0:304,102:0.0025:2,0:20:0:31:0:1:0:60:2:0.0025:0:1 0/1:207:3:3,0:150,54:0.0145:2,0:12.7:1:26.7:1:0.56902:0:60:6:0.0145:0:1 -12 18478126 . A T 106 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02117;SOR=2.78025;LSEQ=GCAAATTTTGAAGATGACAA;RSEQ=AATGAATAAAACAGAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:10:0,10:9,212:0.0433:1,0:23:1:28.9:1:1:0:60:20:0.0442:0:1 0/1:116:13:0,13:8,95:0.1121:2,1:25.4:1:28.9:1:0.59456:0:60:26:0.113:0:1.1 -12 18496149 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53383;SOR=0;LSEQ=ATGATGCCAAGAAATATTTT;RSEQ=TTGTTTTACCATGACAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:132,37:0.0117:2,2:11:1:28.5:1:0.39608:3.5334:60:4:0.0118:0:1 0/0:99:0:0,0:82,17:0:2,0:23.5:1:31.8:1:1:0:60:98:1:0:0.1 -12 18496249 . A AT 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.29544;SOR=2.26968;LSEQ=AATAACAAGTATAATTTTAC;RSEQ=TTTTTTTTCAGAATTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:3:1,2:284,268:0.0054:2,2:35:1:31:1:0.61441:2.11662:60:6:0.0055:0:0 0/1:410:5:3,2:207,198:0.0122:2,2:34.4:1:29.8:1:1:1.43:60:10:0.0124:0:0.4 -12 18499636 . C T 226 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=197.32436;LSEQ=TACCAGCTAATCAATGTCTA;RSEQ=TGTAACAGCTTTTATGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1768:2:1,1:876,887:0.0011:2,2:12.5:1:27:0:1:1.01:60:4:0.0011:0:1 0/1:1132:207:110,97:454,466:0.1829:2,2:28:1:29.5:1:0.35601:1.16:60:68:0.182:0:1.1 -12 18499777 . C G 276 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40206;SOR=0;LSEQ=ACCTGGGTGCACAGGTGAGT;RSEQ=GTGGTGAGTTTTTCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:464:464:110,354:0,0:1:0,2:26.1:1:31.2:1:1:0:60:76.333:1:0:1.1 1/1:312:311:98,213:0,0:0.9968:0,2:24.3:1:30:1:1:0:60:50.833:0.9967:0:1.1 -12 18514467 . G GA 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCTGTCTGGCTTCCCACT;RSEQ=AAAAAAAAAAACCTTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:31:1:28:1:1:0:60:4:0.6667:0:0 -12 18515791 . AT A 81 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.15416;SOR=3.51397;LSEQ=AATATTCCAGACAAGAAATT;RSEQ=TTTTTTTCTTGGTCAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:2:1,1:220,378:0.0033:2,2:26.5:1:31:1:1:1.72:60:4:0.0034:0:0 0/1:516:6:4,2:200,310:0.0116:2,2:36.7:1:31.5:1:0.21942:3.09:60:12:0.0117:0:0.2 -12 18515907 . T TA 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01345;SOR=Inf;LSEQ=TAAAAGCAAGGGATGTAATT;RSEQ=AAAAAAAATATGCTGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:1,81:0:1,0:25.9:1:28.5:1:1:0:60:164:1:0:0.1 0/1:62:5:0,5:2,55:0.0806:1,0:31.8:1:26.8:1:1:0:60:4:0.0656:0:0 -12 18524061 . T G 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATTATAAGAACATTTTCAT;RSEQ=AAAATATCAGTACAATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:24:17,7:262,85:0.0647:2,2:26.5:1:31.9:1:0.62703:1.26836:60:48:0.0652:0:1 0/0:303:0:0,0:217,86:0:2,0:24.1:1:29.1:1:1:0:60:74.75:1:0:0.1 -12 18534672 . CTG C 152 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.66645;SOR=0.87276;LSEQ=CCTCATGAAGTGACTCCTGT;RSEQ=TGTGTGTGTGTGTTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:29:22,7:327,92:0.0644:2,2:19.8:1:31.3:1:0.81729:1.13063:60:58:0.0659:0.0178:0 0/1:388:22:17,5:273,90:0.0567:2,2:20.1:1:31.6:1:1:1.12:60:44:0.0587:0.0155:0 -12 18534866 . C A 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGCAAGTATTGGTTGATA;RSEQ=GTAGTTTGTTGTCAATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:29,215:0:2,0:24:1:30:1:1:0:60:47.8:0.9917:0:0.1 0/1:242:56:10,46:44,141:0.2314:2,2:21.8:1:30.4:1:0.46448:1.43341:60:55:0.2282:0:1 -12 18544512 . G A 30 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02778;SOR=Inf;LSEQ=CTCAACCTTCCTTCCAGGAG;RSEQ=TAGAAAGTTGTTTTAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:24.9:1:31.3:1:1:0:60:14:1:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:30:0:1:0:60:4:1:0:1.5 -12 18552446 . A C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08812;SOR=2.28085;LSEQ=TGATGAAATAACCTATGAAA;RSEQ=TATCCGAAGAAGGTAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:10:9,1:70,1:0.1235:1,2:17.2:1:31.7:1:0.23302:7.43114:60:20:0.1266:0:1 0/1:45:11:11,0:33,1:0.2444:1,0:21.1:1:30.8:1:1:0:60:22:0.2444:0:1 -12 18552467 . T TA 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0852;SOR=2.18879;LSEQ=TATCCGAAGAAGGTAAAAGA;RSEQ=GTTTTTGAAAGTAAACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:12:11,1:94,1:0.1121:1,2:24.2:1:28.8:1:0.21266:8.2242:60:24:0.1132:0.028:0.7 0/1:69:15:14,1:53,1:0.2174:1,1:20.5:1:28.3:1:0.39003:3.69192:60:30:0.2174:0.0435:0.7 -12 18573787 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49971;SOR=Inf;LSEQ=TTTTACCTTATGCACTGGGG;RSEQ=TAGAATTCATTCTCTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:101,5:0:1,0:25.6:1:31.1:1:1:0:60:34.333:1:0:0.1 0/1:120:2:1,1:107,11:0.0167:2,2:15.5:1:28.5:1:0.19076:9.35658:60:4:0.0174:0:1 -12 18573810 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5081;SOR=Inf;LSEQ=GAATTCATTCTCTGTTCTCC;RSEQ=TGACATGTCTTATGCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:131,19:0:2,0:23.5:1:30.8:1:1:0:60:49:1:0:0.1 0/1:198:2:1,1:155,41:0.0101:2,2:9:1:28.5:1:0.3801:3.74735:60:4:0.0102:0:1 -12 18574172 . A T 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.15636;SOR=4.47754;LSEQ=CATTAATTCCAAAAAGGAAA;RSEQ=TTTTTTAAAAATGATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:0.2143:0,0:31:1:29.3:1:1:0:60:6:0.2308:0:2 1/0:7:4:0,4:1,2:0.5714:2,0:32.8:1:31:1:0.42857:0:60:8:0.5714:0:2.8 -12 18574178 . T A 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.12193;SOR=6.4865;LSEQ=TTCCAAAAAGGAAAATTTTT;RSEQ=AAAAATGATTTCATTTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:0.2143:0,0:32.7:1:28.7:1:1:0:60:6:0.2143:0:2 1/0:6:4:0,4:1,1:0.6667:2,0:26.8:1:25.8:1:0.33333:0:60:3:0.6:0:2.8 -12 18576730 . C T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00049;SOR=6.15159;LSEQ=TTTTGTTATTAGTCATATAC;RSEQ=GACTCATAAAATCATCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:6:6,0:51,0:0.1053:1,0:32.3:1:32.3:1:1:0:60:12:0.1071:0:1 0/1:40:17:16,1:23,0:0.425:1,1:26.9:1:30.3:1:0.425:0:60:34:0.425:0:1.2 -12 18576807 . C G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00116;SOR=Inf;LSEQ=TTCTCTAGTCTTTTCTCAAG;RSEQ=CTCTGAAGTCCCTCTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:194,35:0:2,0:23.6:1:31.7:1:1:0:60:37.167:1:0:0.1 0/1:266:11:8,3:214,40:0.0414:2,2:19.8:1:31.4:1:0.39371:1.99987:60:22:0.0423:0:1.2 -12 18576994 . C T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09204;SOR=0;LSEQ=GTAAGATTAACTAAATCAGG;RSEQ=AAGGATGCCTTTTTAATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:1,2:65,215:0.0105:2,2:24:1:27:1:0.55062:1.65:60:6:0.0108:0:3.3 0/0:345:0:0,0:93,251:0:2,0:24.2:1:31.3:1:1:0:60:33.4:1:0:0.2 -12 18577002 . C G 125 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00033;SOR=14.78777;LSEQ=AACTAAATCAGGCAAGGATG;RSEQ=CTTTTTAATTGCCACCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:0,1:51,202:0.0039:2,0:46:0:29:0:1:0:60:2:0.004:0:1 0/1:290:16:4,12:71,201:0.0552:2,2:28.4:1:31.4:1:1:1.05949:60:32:0.0557:0:1.1 -12 18641326 . T C 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACTTACTGTTCCGGCTGGA;RSEQ=GTGGTTTAAAAAATTAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:55,1:0,0:1:0,1:20.7:1:31.8:1:1:0:60:17.667:1:0:1 1/1:74:74:69,5:0,0:1:0,2:21:1:31.3:1:1:0:60:148:1:0:1.1 -12 18641364 . TTC T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTACATACAAGAATTTTT;RSEQ=TCTCTCTTTCCTTCAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:118,30:0:2,0:24.7:1:29.8:1:1:0:60:28.6:1:0:0.4 0/1:185:21:16,5:124,40:0.1135:2,2:23.8:1:29:1:1:1.03:60:42:0.1148:0.0216:0.4 -12 18644191 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13904;SOR=Inf;LSEQ=CATGCCTTAGTTTCCCATTT;RSEQ=TCCAACATGCCCTATTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:19,1:0:1,0:28.2:1:30.2:1:1:0:60:9:1:0:1.1 0/1:13:2:1,1:10,1:0.1538:2,2:24.5:1:28.5:1:0.29487:7.41607:60:4:0.1538:0:2 -12 18644222 . G C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06574;SOR=0;LSEQ=CCTATTGTCTTTAGCCCACT;RSEQ=TCTTCTCATGCCTGAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:30,1:0,0:1:0,1:24.8:1:30.2:1:1:0:60:14.5:1:0:1.3 1/1:22:19:17,2:3,0:0.8636:0,2:26.8:1:31.6:1:1:0:60:38:0.8636:0:1.2 -12 18648812 . G A 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29475;SOR=0;LSEQ=AAGTAAAGGCTCCAGTTGAT;RSEQ=GACTAAATTTTTTAAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:16,0:0.2:1,0:24.3:1:27.3:1:1:0:60:8:0.2222:0:1 0/0:8:0:0,0:8,0:0:0,0:20:1:31.1:1:1:0:60:16:1:0:0.1 -12 18648909 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50068;SOR=Inf;LSEQ=ACAACAAAGTCTGCAAGGGG;RSEQ=TATGATTTTGGGGAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:117,17:0:2,0:22.1:1:31.6:1:1:0:60:43.667:1:0:0.1 0/1:154:2:1,1:131,21:0.013:2,2:11.5:1:25.5:1:0.26611:6.11791:60:4:0.0133:0:1 -12 18648919 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25318;SOR=Inf;LSEQ=CTGCAAGGGGCTATGATTTT;RSEQ=GGGAAAAGGTTTGCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:132,25:0:2,0:22.5:1:31.7:1:1:0:60:51.333:1:0:0.1 0/1:186:3:1,2:149,34:0.0161:2,2:15:1:27.7:1:0.09632:8.61851:60:6:0.0163:0:1 -12 18648928 . G T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13647;SOR=Inf;LSEQ=GCTATGATTTTGGGGAAAAG;RSEQ=TTTGCTTTTTGGGGATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:143,40:0:2,0:23:1:30.9:1:1:0:60:44.75:1:0:0.1 0/1:239:4:2,2:177,58:0.0167:2,2:8.3:1:26:1:0.2626:3.03442:60:8:0.0169:0:1 -12 18649057 . C T 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48787;SOR=1.10806;LSEQ=TACTTTCATCAATGCTAATC;RSEQ=GATGGGCAAAAACATCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:110:57,53:156,196:0.2381:2,2:26.3:1:30.7:1:0.18888:1.35:60:220:0.2397:0:1.1 0/1:692:178:92,86:230,283:0.2572:2,2:24.1:1:30.4:1:0.11749:1.32:60:177:0.258:0:1.1 -12 18649158 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50382;SOR=Inf;LSEQ=GATTTATTACTCACAAAAAG;RSEQ=AATTGTTGTGGCTATTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:12,110:0:2,0:23.6:1:30.3:1:1:0:59.8:60:1:0:0.1 0/1:151:2:1,1:13,136:0.0132:2,2:8:1:28.5:1:0.1774:10.12:60:4:0.0137:0:1 -12 18650325 . C A 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.84709;LSEQ=AACAACATTCCAAGCAGCAC;RSEQ=TCTAATTTGATGGTTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:42:1:31.5:1:1:0:60:4:0.2857:0:1 0/1:4:1:1,0:2,1:0.25:2,0:7:0:31:0:1:0:60:2:0.25:0:1 -12 18655952 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTCTCTGTTCATCATCAA;RSEQ=ATTGGCTTGCTACCATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:14:1:32:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 18656122 . AGTAGT TTTTCTGGATTACCCAGAATA 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.1222;SOR=Inf;LSEQ=GAAAAGGAAAGGGGTAATCC;RSEQ=GCTGGAAGCTATTGTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:47,1:0:1,0:25.6:1:30.8:1:1:0:60:47:1:0:0.2 0/1:56:4:3,1:50,2:0.0714:1,2:26.3:1:30.5:1:0.20274:7.69123:60:8:0.0727:0.0536:1 -12 18656174 . G C 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01835;SOR=0.49697;LSEQ=CTAAGGCTCCCTCATCTTGT;RSEQ=ATGAAGGAATTGTCTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:32:29,3:82,24:0.2319:2,2:26.5:1:31.5:1:0.12837:2.81:60:64:0.2353:0:1.8 0/1:192:25:21,4:129,37:0.1302:2,2:26.3:1:31.6:1:0.60615:1.50:60:50:0.1316:0:1.8 -12 18656225 . G A 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24062;SOR=0.80855;LSEQ=TCTCTACCAGGATTGGTGCA;RSEQ=ATGGTACCTGATGCTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:69:46,23:152,95:0.2184:2,2:21.9:1:30:1:0.48321:1.25:60:138:0.2204:0:1.4 0/1:494:91:51,40:233,168:0.1842:2,2:23.8:1:29.8:1:0.72585:1.08758:60:182:0.1869:0:1.3 -12 18658178 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15606;SOR=0;LSEQ=CCTCTGATGCTAATGCATTT;RSEQ=CTCATTTTTTGTTGTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:155,27:0.0109:2,2:24.5:1:29:0:0.2819:5.65551:60:4:0.0109:0:1 0/0:281:0:0,0:213,68:0:2,0:20:1:31.7:1:1:0:60:280:1:0:0.1 -12 18690977 . A G 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=GAAGGAAATTTATCTATTAC;RSEQ=GTAGAGAAAAAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:13:13,0:41,0:0.2407:1,1:24.9:1:28.5:1:1:0:60:12:0.2264:0:1.3 0/0:52:0:0,0:52,0:0:1,0:18.8:1:30.3:1:1:0:60:104:1:0:0.1 -12 18690983 . G GA 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.00267;LSEQ=AATTTATCTATTACAGTAGA;RSEQ=AAAAAAAAAAGAAAATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:7:7,0:61,0:0.1014:1,0:23.4:1:31.4:1:1:0:60:14:0.1045:0:0.6 0/1:59:6:6,0:53,0:0.1017:1,0:17.5:1:29.9:1:1:0:60:12:0.1017:0.0508:0 -12 18691017 . G A 100 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00748;SOR=9.77964;LSEQ=AATTCAAATGAAAATAAGTC;RSEQ=TTATAACTGCTGATTTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:1,0:131,20:0.0066:2,0:29:0:13:0:1:0:60:0:0:0:4 0/1:180:11:10,1:142,27:0.0611:2,2:19.1:1:29.1:1:1:1.90:60:10:0.0565:0:1.3 -12 18691253 . C T 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=ACCTGCTGGAAATGGTAAGT;RSEQ=CCTTGGGAAAAAAAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:38,154:0:2,0:23.4:1:30.8:1:1:0:60:31:1:0:0.1 0/1:265:19:3,16:61,185:0.0717:2,2:24.7:1:28.9:1:0.57812:1.75531:60:38:0.0717:0:1.2 -12 18691260 . G GA 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.32883;SOR=0.57021;LSEQ=GGAAATGGTAAGTCCCTTGG;RSEQ=AAAAAAAAACAAAAATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:10:2,8:30,128:0.0595:2,2:31.5:1:30.1:1:1:1.07:60:20:0.0629:0:0.1 0/1:230:8:1,7:51,171:0.0348:2,2:18.5:1:27:1:0.68674:2.08216:59.4:3:0.0268:0.013:0.1 -12 18699424 . C A 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50414;SOR=Inf;LSEQ=AATGTACGCAGACACATGTT;RSEQ=CACAGTGGAGATGATTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:26,136:0:2,0:21.9:1:30.9:1:1:0:60:39.5:1:0:0.1 0/1:200:2:1,1:39,159:0.01:2,2:8.5:1:23.5:1:0.3608:4.04:60:4:0.0103:0:1 -12 18715593 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25595;SOR=Inf;LSEQ=CATAAATGAAATGAGTAGAT;RSEQ=CAGAGGAGTGTCACTCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:157,54:0:2,0:24:1:32.2:1:1:0:60:69.333:1:0:0.1 0/1:258:3:1,2:192,63:0.0116:2,2:20.7:1:27.7:1:0.15734:6.04239:60:6:0.0117:0:1 -12 18715673 . A G 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00052;SOR=Inf;LSEQ=CTGGAGTGTTTCCCTGTTAA;RSEQ=TTGAATAACTTGATCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:275,180:0:2,0:25.4:1:30.4:1:1:0:60:226.5:1:0:0.1 0/1:777:17:10,7:440,317:0.0219:2,2:27.3:1:31.5:1:1:1.03:60:34:0.0222:0:1 -12 18715728 . T G 175 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCCATAAGCCCTGCCAAA;RSEQ=CTACTTCACAGACTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:45:21,24:238,248:0.0846:2,2:27.7:1:31.9:1:0.87635:1.09657:60:90:0.0854:0:1 0/0:946:0:0,0:469,476:0:2,0:25:1:29:1:1:0:60:71.692:0.9989:0:0.1 -12 18715842 . G A 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=22.03433;LSEQ=GTAATGTAAGTTTAAAGTCC;RSEQ=TCATCTTGACTTACGTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:0,1:77,180:0.0039:2,0:24:0:33:0:1:0:60:2:0.004:0:1 0/1:379:30:11,19:104,245:0.0792:2,2:27.5:1:29.6:1:0.41631:1.36:60:60:0.0806:0:1.1 -12 18716461 . G A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0725;SOR=0;LSEQ=CTGTCCTTTTACATTGTTTT;RSEQ=CCTTCAGTACTTGTCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:2,1:49,165:0.0138:2,2:16.3:1:24:1:0.13841:6.66:60:6:0.014:0:1 0/0:302:0:0,0:88,214:0:2,0:23.3:1:31.2:1:1:0:60:59.4:1:0:0.1 -12 18719837 . C T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06686;SOR=0;LSEQ=ACAATCTTAAGATGAAAAGG;RSEQ=CAGTTTTCAAACTAATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:0,3:190,70:0.0114:2,0:13:1:26:1:0.02075:0:60:6:0.0118:0:1 0/0:385:0:0,0:268,117:0:2,0:24:1:31.2:1:1:0:60:37.5:1:0:0.1 -12 18719891 . A G 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTTAAAACAGGTTTCCTC;RSEQ=TTGGTGGCACCTACCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:296,223:0:2,0:24.4:1:30.4:1:1:0:60:73.143:1:0:0.1 0/1:829:32:17,15:442,354:0.0386:2,2:29.6:1:30.1:1:0.85682:1.10156:60:64:0.0392:0:1.1 -12 18719938 . G T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00853;SOR=0;LSEQ=CAGATCACAGAAGATTCAGA;RSEQ=ATCTAAATCATTACATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:5:2,3:203,270:0.0104:2,2:14.8:1:27.4:1:1:1.12746:60:10:0.0106:0:1 0/0:760:0:0,0:337,420:0:2,0:26.4:1:31.1:1:1:0:60:74.7:0.9973:0:0.2 -12 18719972 . T G 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGGAACAGATATTAAATG;RSEQ=ATCACATGAAGTTACAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:119,249:0:2,0:24.2:1:28.7:1:1:0:60:736:0.9946:0:0.1 0/1:544:45:16,29:172,326:0.0827:2,2:24.9:1:31.6:1:0.87157:1.05:60:90:0.0833:0:1.2 -12 18720023 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.516;SOR=Inf;LSEQ=TTAATTTTTCTATTTTTACA;RSEQ=AAAACATCAACTATTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:14,114:0:2,0:23.8:1:28.1:1:1:0:60:20.333:1:0:0.3 0/1:187:2:1,1:33,151:0.0107:2,2:35:1:33:0:0.33298:4.52:60:4:0.0108:0:2 -12 18720057 . T C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00482;SOR=0.29863;LSEQ=TTTTATATTTTATTCGTGAG;RSEQ=GTGGTGGTTTATGTCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:23:1,22:1,33:0.4035:1,1:14.2:1:29.3:1:1:1.49:60:22:0.3929:0:1.1 0/1:72:12:1,11:2,58:0.1667:1,2:21.7:1:30.8:1:0.42622:2.59:60:24:0.1667:0:1 -12 18747387 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18415;LSEQ=AATGAATAGCAGTAACAAAT;RSEQ=TAAGAAATAAAGAAATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:47:40,7:62,9:0.395:2,2:24.3:1:32.3:1:0.7871:1.20361:60:94:0.395:0:1.2 0/1:150:16:14,2:113,21:0.1067:2,2:27.6:1:31.9:1:1:1.30:60:32:0.1074:0:1.1 -12 18747528 . C T 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.4889;LSEQ=GTAAATTTGTCATTATATTA;RSEQ=GTACAGTGATTTTCAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:84:24,60:54,112:0.336:2,2:26.9:1:29.9:1:0.56536:1.20447:60:41:0.3347:0:1 0/1:434:86:40,46:135,213:0.1982:2,2:24.2:1:29.5:1:0.21978:1.37:60:172:0.1986:0:1.1 -12 18762113 . G A 45 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=AGGTTCACTGATTTCTAAAG;RSEQ=CCACACTTTTAATCTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:34:1:28.7:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:0:0,0:25:0:18:0:1:0:60:0:0:0:0 -12 18762450 . A C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.27882;LSEQ=TTTCCAACTGAACTCACTGA;RSEQ=ATTCTATTCTTTTATCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:164:98,66:167,107:0.3744:2,2:26:1:31.9:1:0.84019:1.05097:60:81:0.375:0:1.1 0/1:602:86:52,34:303,212:0.1429:2,2:30:1:31.2:1:0.81352:1.07:60:85:0.1426:0:1.2 -12 18793300 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50231;SOR=Inf;LSEQ=TTTGGTCTGGATATTTAGTA;RSEQ=CTCTGTATTTGTTTTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:135,30:0:2,0:21.2:1:32.2:1:1:0:60:330:1:0:0.1 0/1:196:2:1,1:149,45:0.0102:2,2:5:1:27:1:0.41523:3.28587:60:4:0.0102:0:1 -12 18793583 . G A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03185;SOR=Inf;LSEQ=AAAATTTGCAGTAATTGGCA;RSEQ=CATTATTTCATAAAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:2,92:0:1,0:21.3:1:32.6:1:1:0:60:188:0.9895:0:0.1 0/1:71:4:1,3:2,65:0.0563:1,2:27.3:1:29.5:1:0.16184:9.97:60:8:0.0571:0:1 -12 18800501 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATTTATGGGGTATAAAA;RSEQ=GTGAAGTATATTTAAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:20.3:1:30:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 18800755 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50444;SOR=Inf;LSEQ=TTAAAAGCAATACTCAAAAA;RSEQ=GAGATGTATTTAAGCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:104,10:0:2,0:24.8:1:30:1:1:0:60:56:1:0:0.1 0/1:143:2:1,1:127,14:0.014:2,2:20:1:29.5:1:0.19945:8.79957:60:4:0.0143:0:1 -12 18800840 . G T 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04746;SOR=Inf;LSEQ=ATGAAGTCACAGAGCTCCAA;RSEQ=GACATGTCTTAATGCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:263,162:0:2,0:25.7:1:31.6:1:1:0:60:211.5:1:0:0.1 0/1:671:7:1,6:372,292:0.0104:2,2:5.9:1:26.4:1:0.04856:7.62404:60:14:0.0105:0:1.1 -12 18800989 . CA C 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTATGAACATATGCATTATT;RSEQ=TTAACTACTTGTATTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:55,166:0:2,0:22.7:1:30.4:1:1:0:60:43.2:1:0:0.6 0/1:259:44:12,32:63,152:0.1699:2,2:23.3:1:30.7:1:0.85685:1.10486:60:43:0.1693:0.0386:0.6 -12 18801017 . T C 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00344;SOR=0;LSEQ=ACTTGTATTTTTTTCACTTC;RSEQ=GGGCCTCTGAATCACATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:136:136:17,119:0,0:1:0,2:23.5:1:29.6:1:1:0:60:67:1:0:1.1 1/1:140:131:26,105:0,0:0.9357:0,2:20.6:1:29.4:1:1:0:60:64.5:0.9348:0:1.1 -12 18801024 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24472;SOR=0;LSEQ=TTTTTTTCACTTCTGGGCCT;RSEQ=TGAATCACATAAGTAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:11,103:0.0171:2,2:29.5:1:30.5:1:0.197:9.01:60:4:0.0174:0:2 0/0:119:0:0,0:23,96:0:2,0:20.8:1:31.3:1:1:0:60:58.5:1:0:1 -12 20290640 . G GT 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28587;SOR=Inf;LSEQ=TCAGCACATTAAAAAATTTA;RSEQ=TTTTTTTTAGGATTACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:62,51:0:2,0:22.8:1:31.6:1:1:0:60:226:1:0:0.5 0/1:179:3:1,2:99,77:0.0168:2,2:13.7:1:25.3:1:0.58396:2.55808:60:6:0.0168:0.0112:0.7 -12 20290667 . C G 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00489;SOR=1.9266;LSEQ=TTAGGATTACATTCAATGTA;RSEQ=TTTCTGATAAATTCATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:50:22,28:41,38:0.3846:2,2:24.2:1:31.7:1:0.47003:1.36981:60:24:0.378:0:1.4 1/0:203:111:55,56:51,41:0.5468:2,2:26.9:1:30.8:1:0.48054:1.26503:60:54.5:0.5423:0:1.2 -12 20290713 . GA G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5117;SOR=Inf;LSEQ=GAGTATCCTCATAAAGAGAG;RSEQ=AAATTACTGTAATCTGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:40,69:0:2,0:25.9:1:30:1:1:0:60:53.5:1:0:0.6 0/1:152:2:1,1:60,89:0.0132:2,2:29:1:32.5:1:1:1.48:60:4:0.0135:0:1 -12 20290733 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=0.24331;LSEQ=GAAAATTACTGTAATCTGAT;RSEQ=ACTGTACTTTTACATATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:24:9,15:20,37:0.2963:2,2:21.3:1:31.5:1:1:1.11:60:48:0.2963:0:1.8 0/1:130:12:4,8:45,73:0.0923:2,2:16.9:1:31.6:1:1:1.23093:60:24:0.093:0:2 -12 20290761 . T G 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00301;SOR=Inf;LSEQ=TTTTACATATCCAGCATCAC;RSEQ=TGAGGGGAGCCCAAATATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:8,35:0:2,0:22.8:1:30.3:1:1:0:60:86:1:0:0.3 0/1:66:12:4,8:12,42:0.1818:2,2:24.3:1:30.7:1:0.4646:1.73:60:24:0.1846:0:1.3 -12 21590621 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGGAGTCCAGAGTCCCG;RSEQ=TGCTCCGCCGCGATATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 21591785 . G C 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16494;SOR=0.48884;LSEQ=TGATGCAGGCACCGTATTAA;RSEQ=GGCTGAGTGTTCAACTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:20:19,1:9,0:0.6897:0,1:24.2:1:31.8:1:1:0:60:40:0.6897:0:2.3 1/0:54:28:27,1:26,0:0.5185:1,1:25.7:1:32.1:1:1:0:60:56:0.5185:0:2.5 -12 21591814 . GTA G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0.72837;SOR=1.17825;LSEQ=GTTCAACTATGAACAGCATG;RSEQ=TATACCATGCTGGGGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:27:26,1:25,1:0.5094:1,1:25.6:1:31.3:1:1:1.04:60:54:0.5094:0.0755:2.3 1/0:89:49:47,2:37,3:0.5506:2,1:24.9:1:31:1:0.65378:1.89:60:48:0.5455:0.1124:2.3 -12 21591828 . G A 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27858;SOR=1.4511;LSEQ=AGCATGGTATATACCATGCT;RSEQ=GGGACTCACAGCCTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:30:28,2:32,2:0.4688:2,2:26.9:1:27.4:1:1:1.14047:60:29:0.4603:0:2.5 1/0:121:68:60,8:44,8:0.562:2,2:21.2:1:28.5:1:0.59695:1.36:60:136:0.562:0:2.5 -12 21591837 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53431;SOR=Inf;LSEQ=TATACCATGCTGGGGACTCA;RSEQ=AGCCTGCTGGAAGAGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:70,14:0:2,0:23:1:31.1:1:1:0:60:20:1:0:1.2 0/1:146:2:1,1:118,26:0.0137:2,2:9.5:1:27:1:0.3367:4.47247:60:4:0.0138:0:1.5 -12 21591847 . G A 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01964;SOR=1.78252;LSEQ=TGGGGACTCACAGCCTGCTG;RSEQ=AAGAGACAATATTACAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:50:40,10:43,10:0.4854:2,2:22.1:1:29.8:1:1:1.07423:60:100:0.495:0:2.3 1/0:196:123:94,29:51,22:0.6276:2,2:18.9:1:29:1:0.31794:1.40:60:246:0.6308:0:2.3 -12 21591921 . T G 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00389;SOR=1.5245;LSEQ=TTAGAGGTGCCTGTGGAGTA;RSEQ=GTAGGGAGTGAATTAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:317:173:88,85:68,75:0.5457:2,2:27.8:1:31.7:1:0.57366:1.14:60:172:0.5548:0:1.3 1/0:558:361:192,169:94,103:0.647:2,2:26.9:1:30.6:1:0.24934:1.24:60:71.2:0.6508:0:1.3 -12 21591985 . T C 18 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6183;SOR=0.54993;LSEQ=AGGTATTTTTAAAATCTCAT;RSEQ=ATGAAAGAATGAGTGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:34,106:0.0141:2,0:17:1:29.5:1:0.06293:0:60:4:0.0146:0:1.5 0/0:257:2:1,1:74,180:0.0078:2,2:18.5:1:18:1:0.50092:2.42:60:1:0.0039:0:1 -12 21592011 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1252;SOR=0;LSEQ=AGAATGAGTGAAAGTTTACC;RSEQ=AGTATTCAAGAAAAGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:9,70:0.0247:2,2:6.5:1:28.5:1:0.23302:7.43:60:4:0.0247:0:2 0/0:147:0:0,0:24,123:0:2,0:22.2:1:30.1:1:1:0:60:294:1:0:0.3 -12 21592094 . G T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02751;LSEQ=CTTAAAGCATAGATCATAAG;RSEQ=AGTCTTAGCATGCTGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:0.7:0,0:18:1:29:1:1:0:60:14:0.7:0:1 1/0:17:12:0,12:0,5:0.7059:0,0:16.2:1:29:1:1:0:60:24:0.7059:0:1 -12 21599302 . T G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGAGGCGGAGCTTGCAG;RSEQ=GAGCCCAGATCGCACCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:32.5:1:1:0:60:4:1:0:1.5 -12 21600406 . G C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23412;SOR=2.86676;LSEQ=GCATTTGAATGAATCAGAGT;RSEQ=CTTCCCGTTACCATTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:42:1:28.2:1:1:0:60:4:0.4444:0:2.2 1/0:16:12:12,0:4,0:0.75:0,0:30.3:1:31.9:1:1:0:60:24:0.75:0:2 -12 21600443 . T C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.008;SOR=4.2707;LSEQ=GAAAAATATCCCACATGCAG;RSEQ=GCATGTCTGCCTTCTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:13,0:13,0:0.5:1,1:15.9:1:30.6:1:1:0:60:12:0.48:0:1.5 1/1:43:35:35,0:8,0:0.814:0,1:19.5:1:32.2:1:1:0:60:70:0.814:0:1.4 -12 21600496 . GT G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5515;SOR=Inf;LSEQ=ACATTTTTGTTTTTTTAACA;RSEQ=TTATTATAATTTCTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:70,22:0:2,0:24.2:1:28.8:1:1:0:60:17.4:1:0:0.1 0/1:181:2:2,0:135,44:0.011:2,0:10:1:31.3:1:1:0:60:4:0.0112:0.0055:0 -12 21600639 . T G 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45368;SOR=1.26997;LSEQ=TATGTAAAATACATGCATAC;RSEQ=GCCAGGCGCGGTGGCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:35:7,28:7,23:0.5385:2,2:24.2:1:30.9:1:0.77087:1.21369:60:70:0.5385:0:1.1 1/0:149:89:17,72:13,46:0.5973:2,2:23.8:1:30.2:1:0.6809:1.19545:60:178:0.5973:0:1.1 -12 21600649 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55284;SOR=Inf;LSEQ=ACATGCATACTGCCAGGCGC;RSEQ=GTGGCTCACACCTGTAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:8,42:0:2,0:21.5:1:30.9:1:1:0:60:100:1:0:0.7 0/1:111:3:2,1:18,90:0.027:2,2:11.7:1:27.3:1:0.08309:9.69:53.3:2:0.0185:0:2.7 -12 21600737 . G A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.73454;SOR=1.32136;LSEQ=GAGACCGTCCTGGCTAACAC;RSEQ=GTGAAATCCCGTCTCTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:0,9:0,8:0.5294:0,0:24.2:1:30.2:1:1:0:60:18:0.6:0:1 1/0:15:9:0,9:1,4:0.6:2,0:32.2:1:31.6:1:0.35714:0:58.3:18:0.6429:0:1 -12 21600838 . A G 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28613;SOR=4.35427;LSEQ=GAGGCTGAGGCAGGAGAATG;RSEQ=CATGAACCCGGGAGATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:2,3:0.2857:2,0:13:1:32.5:1:0.42857:0:43.5:4:0.2857:0:4.5 1/0:6:4:4,0:2,0:0.6667:0,0:28.5:1:31.5:1:1:0:42:8:0.6667:0:4.5 -12 21600840 . A G 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28613;SOR=4.35427;LSEQ=GGCTGAGGCAGGAGAATGAC;RSEQ=TGAACCCGGGAGATTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:2,3:0.2857:2,0:15:1:30:1:0.42857:0:43.5:4:0.2857:0:4.5 1/0:6:4:4,0:2,0:0.6667:0,0:30.5:1:31:1:1:0:42:8:0.6667:0:4.5 -12 21600853 . A C 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18092;SOR=4.07442;LSEQ=GAATGACATGAACCCGGGAG;RSEQ=TTGCAGTGAGCTGAGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:2,3:0.375:2,0:20.3:1:33:1:0.19643:0:42.3:6:0.375:0:5 1/0:11:8:8,0:3,0:0.7273:0,0:23.8:1:32.9:1:1:0:48.5:16:0.7273:0:3.3 -12 21600865 . T C 114 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03819;SOR=6.9247;LSEQ=CCCGGGAGATTGCAGTGAGC;RSEQ=GAGATCACGCCGCTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:2,3:0.25:2,0:40:1:32.5:1:0.42857:0:43.5:4:0.2857:0:4.5 1/0:21:15:15,0:6,0:0.7143:0,1:18.6:1:29.4:1:1:0:52.5:6.5:0.6842:0:2.7 -12 21600915 . T TA 123 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.34449;SOR=1.71444;LSEQ=CGACAGAGCGAGACTCCATC;RSEQ=AAAAAAAAAAAAAACACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:6,2:15,4:0.2759:2,2:20.6:1:29.8:1:1:1.23941:51.3:16:0.2963:0.069:3.6 0/1:58:23:16,7:20,10:0.3966:2,2:29.9:1:27.2:1:1:1.14:58.7:22:0.4231:0:2.1 -12 21600952 . CG TA 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=CATGCGTACTTTTGATAGCA;RSEQ=TGTGAAGGTATCTCTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:9:6,3:21,16:0.1837:2,2:29.4:1:27.8:1:0.71598:1.51:57.8:8:0.2051:0:1.8 0/0:93:0:0,0:48,43:0:2,0:25.9:1:29:1:1:0:59.9:7.273:1:0:1.4 -12 21600953 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATGCGTACTTTTGATAGCAC;RSEQ=TGTGAAGGTATCTCTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:38:22,16:1,0:0.7755:0,2:26.8:1:29.1:1:1:0:59.7:18:1:0:1.7 1/1:92:92:48,44:0,0:1:0,2:26.6:1:28.3:1:1:0:59.9:14.333:1:0:1.4 -12 21600970 . T A 35 v4;q23;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03929;SOR=0;LSEQ=CACGTGTGAAGGTATCTCTC;RSEQ=AAAATTGACCTCATTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:3,0:26,20:0.0577:2,0:10.3:1:22.3:1:0.2602:0:53.3:2:0.0435:0:5.3 0/0:99:0:0,0:48,51:0:2,0:27.1:1:28.5:1:1:0:60:10:1:0:1.1 -12 21601106 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09293;SOR=0;LSEQ=GATGATATCAATTTCACATA;RSEQ=CTGGCATCAGGGCCTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:97,62:0.0124:2,2:34:1:30.5:1:1:1.55998:60:4:0.0125:0:1 0/0:366:0:0,0:201,165:0:2,0:27.4:1:30.8:1:1:0:59.9:90.5:1:0:0.2 -12 21601137 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09647;SOR=0;LSEQ=GGCCTTCACAGCCACCATAG;RSEQ=TTTTCTCTTCCCCATCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:82,84:0.0118:2,2:7:1:29:1:1:1.02:60:4:0.012:0:1 0/0:374:0:0,0:164,209:0:2,0:26.2:1:30.5:1:1:0:59.9:36.3:0.9973:0:0.2 -12 21601160 . G A 43 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04001;SOR=0;LSEQ=TTCTCTTCCCCATCCATTTT;RSEQ=TTCTTATGAAATGCTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:2,1:54,88:0.0207:2,2:20.3:1:27.3:1:0.55933:3.23:60:6:0.021:0:1 0/0:277:0:0,0:105,172:0:2,0:24.9:1:30.8:1:1:0:60:68.25:1:0:0.2 -12 22968378 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20347;LSEQ=GACCTCTTCCTATGTCATGC;RSEQ=AATTCAATGCTATATTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:243:160:74,86:40,43:0.6584:2,2:26.4:1:29.9:1:0.78784:1.08073:60:79:0.6639:0:1.1 0/1:409:115:50,65:140,154:0.2812:2,2:25.3:1:29.3:1:0.50842:1.18133:60:56.5:0.279:0:1.1 -12 22968455 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51971;SOR=Inf;LSEQ=TCTAAGCCTTGGTTTTCTAA;RSEQ=CCATAAAATGGAGTGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:18,79:0:2,0:24.2:1:31.9:1:1:0:60:96:1:0:0.4 0/1:148:2:1,1:37,109:0.0135:2,2:33:1:30:0:0.44889:2.92:60:4:0.0136:0:1 -12 23617055 . G T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGTGTGACCCATGGACACAA;RSEQ=GAAGAGCAGTGTGATGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:25.5:1:28.5:1:1:1:60:4:0.5:0:1 0/0:3:0:0,0:2,1:0:2,0:27.7:1:31.7:1:1:0:60:6:1:0:0.3 -12 23617764 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16304;SOR=Inf;LSEQ=TGAGGAATCTGGGCAGCCCA;RSEQ=ATGAGTGGGTTTCCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:33.7:1:31.3:1:1:0:60:28:1:0:0.2 0/1:10:2:1,1:5,3:0.2:2,2:42:1:29:1:1:1.58108:60:4:0.2:0:1 -12 23617776 . T TC 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16923;SOR=Inf;LSEQ=GCAGCCCAGATGAGTGGGTT;RSEQ=CCCCCCAGCAAAACACACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:31.9:1:29.9:1:1:0:60:30:1:0:0.2 0/1:11:2:1,1:5,4:0.1818:2,2:38:1:30:1:1:1.22474:60:4:0.1818:0:0 -12 23618113 . G A 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02778;SOR=0;LSEQ=AAGAAAAACAAGCAGAAAGT;RSEQ=ACAACAACAGCATCAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:26.3:1:29.3:1:1:0:60:14:1:0:1 0/0:2:0:0,0:1,1:0:2,0:25:1:21:1:1:0:60:1:1:0:1.5 -12 24796145 . AAGAG A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGGGCTGTGAAAGAAAGA;RSEQ=AGGGAGGAGAGAAAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:29.5:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 25362465 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAACTGCATGCACCAAAA;RSEQ=CCCCAAGACAGAAATCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:16,1:0,0:1:0,1:29.6:1:30.4:1:1:0:54.8:34:1:0:1.1 1/1:2:2:2,0:0,0:1:0,0:23:1:27.5:1:1:0:60:4:1:0:1 -12 25362552 . A C 142 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=7e-04;SOR=0.05055;LSEQ=CTCTGGGAATACTGGCACTT;RSEQ=GAGGAAAAAAAAACTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:23:23,0:0,0:0.9583:0,1:30.3:1:31.5:1:1:0:60:46:0.9583:0:1.1 1/0:23:12:12,0:9,2:0.5217:2,0:24.8:1:32.1:1:0.21739:0:60:24:0.5455:0:1 -12 25362556 . G GA 35 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39224;SOR=2.28916;LSEQ=GGGAATACTGGCACTTAGAG;RSEQ=AAAAAAAAACTTCCACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:30,0:0.0606:1,0:22:1:30.6:1:1:0:60:4:0.0625:0.0303:0.5 0/1:23:3:2,1:19,1:0.1304:1,2:33:1:22.3:1:0.24901:7.95767:60:2:0.0909:0:1 -12 25362777 . A G 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTTTTCTTCTTTTTACC;RSEQ=TCTTTGCTCATCTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:0:0,0:309,354:0:2,0:25.1:1:30.2:1:1:0:60:59.273:1:0:0.1 0/1:532:67:33,34:235,230:0.1259:2,2:25.6:1:30.4:1:0.89634:1.05262:60:66:0.1277:0:1.1 -12 25362854 . C T 128 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=15.37897;LSEQ=ATCATCAACACCCTGAAATA;RSEQ=ATAAAAAGTATTAAAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:2:1,1:129,272:0.005:2,2:23:1:13:1:0.54165:2.10:60:0:0:0:2.5 0/1:322:23:9,14:101,198:0.0714:2,2:22.2:1:28.5:1:0.65042:1.26:60:46:0.0721:0:1 -12 25368084 . T C 93 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAACTTTTCCCTTAAAAA;RSEQ=AAAGGTAAATATCAGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:28.6:1:33.3:1:1:0:60:14:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 25368462 . C T 301 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.57104;LSEQ=AATCTGTATTGTCGGATCTC;RSEQ=CTCACCAATGTATAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:982:980:431,549:0,0:0.998:0,2:25.5:1:30.3:1:1:0:60:64.333:0.999:0:1.1 1/1:771:770:329,441:0,0:0.9987:0,2:24.8:1:29.5:1:1:0:60:76:0.9987:0:1.1 -12 25369027 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGAACCTTGAGTTTTAT;RSEQ=TTAAATTTTAACACCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 25378026 . G A 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAAAATGCATTAAATGA;RSEQ=TAACAGAATTTCTGTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:30.8:1:31.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 25378224 . ATATATATATATATATATATATATA T 78 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=22;MSI=24.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGTTGCCCTGTTCTTTAT;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:0,0:0.6667:0,0:17.7:1:30.4:1:1:0:60:12:0.6667:0.6667:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 25378456 . T C 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TATTGTTTTATTTCCTAGTA;RSEQ=AGCATAATTGAGAGAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:188,10:0:2,0:23.6:1:31.1:1:1:0:60:65:1:0:0.1 0/1:110:12:12,0:94,4:0.1091:1,0:23.3:1:32.1:1:1:0:60:24:0.1091:0:1 -12 25378716 . G GA 68 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.52632;SOR=1.55177;LSEQ=TTAATTTGTTCTCTGGGAAA;RSEQ=AAAAAAAAGTTATAGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:5:2,3:159,461:0.008:2,2:6.2:1:29.3:1:0.60753:1.93:60:10:0.0081:0.0064:0.6 0/1:405:5:1,4:131,269:0.0123:2,2:29:1:29.6:1:1:1.94516:60:10:0.0125:0.0025:0 -12 25379793 . C T 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGCTATACACACGATTG;RSEQ=TTTTAAGACTGTTAAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:31.7:1:29:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 25380071 . T G 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=TAAACATTATTTAAAAATTT;RSEQ=TATTAAATATTATATGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:131,3:0:1,0:23.7:1:30.7:1:1:0:60:66:1:0:0.1 0/1:69:8:8,0:61,0:0.1159:1,0:22.4:1:31.5:1:1:0:60:16:0.1159:0:1 -12 25398018 . T A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=GAACATCATGGACCCTGACA;RSEQ=ACTCCCAAGGAAAGTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:0:1,0:24.4:1:31:1:1:0:60:44:1:0:0.1 0/1:11:2:2,0:9,0:0.1818:0,0:15:1:31.5:1:1:0:60:4:0.1818:0:1 -12 25398285 . C A 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GGCACTCTTGCCTACGCCAC;RSEQ=AGCTCCAACTACCACAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:114:49,65:386,494:0.1146:2,2:25.4:1:29.9:1:0.92017:1.03649:60:37:0.1129:0:1.1 0/0:666:0:0,0:289,377:0:2,0:24.7:1:30.8:1:1:0:60:221:1:0:0.1 -12 25398346 . T A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05592;SOR=Inf;LSEQ=AGGCCTTATAATAAAAATAA;RSEQ=GAAAATGTGACTATATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:98,330:0:2,0:24.4:1:30.1:1:1:0:60:52.5:1:0:0.2 0/1:266:3:1,2:74,189:0.0113:2,2:12.3:1:25:1:1:1.28:60:2:0.0078:0:3 -12 26409893 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.14154;SOR=Inf;LSEQ=AGAAGGCACTCACCTTTGCT;RSEQ=CTCTCCAGCCTCCTTGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:17,12:0:2,0:24.2:1:31.6:1:1:0:60:28:1:0:0.2 0/1:18:2:1,1:10,6:0.1111:2,2:8.5:1:27:1:1:1.61828:60:4:0.1176:0:1.5 -12 26410047 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.54579;SOR=0;LSEQ=AGAAGGTGACAACAGCAGCA;RSEQ=CAACAACAACAACAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:32,26:0.0333:2,2:6:0:31.5:1:1:1.22648:49.5:4:0.0333:0:2.5 0/0:31:0:0,0:17,14:0:2,0:24.1:1:32.1:1:1:0:60:62:1:0:0.1 -12 26410050 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=5.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGGTGACAACAGCAGCAGCA;RSEQ=CAACAACAACAACAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:33,28:0.0317:2,2:27:1:31.5:1:1:1.17549:60:4:0.0317:0:1 0/0:31:0:0,0:17,14:0:2,0:25.6:1:30:1:1:0:60:62:1:0:0.1 -12 26410211 . A G 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1369;SOR=0;LSEQ=CTCCTCCAAATGATTGCAGT;RSEQ=TCTCTCCATCAAGGGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:23,17:0,0:1:0,2:32.4:1:32:1:1:0:60:39:1:0:1.1 1/1:24:22:13,9:1,1:0.9167:2,2:19:1:30.8:1:1:1.42:60:21:0.913:0:1.3 -12 26412198 . C A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATGAATCCAAAAGCTAG;RSEQ=AGAAGAGAAGAAATAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:14:1:28.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 27330424 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5414;SOR=0;LSEQ=AATACAATAATTACATGGCA;RSEQ=TGCTTGATAATTCTGTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:115,19:0.0147:2,2:39:1:30:1:0.27342:5.925:60:4:0.0148:0:1 0/0:74:0:0,0:60,14:0:2,0:21.6:1:31.1:1:1:0:60:36:1:0:0.2 -12 27330516 . T C 231 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCAGAAAAAGGAGACTTA;RSEQ=TTCTGCTAAGACGCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:211,199:0:2,0:26.6:1:30.3:1:1:0:60:81:1:0:0.1 1/0:279:159:79,80:60,60:0.5699:2,2:26.2:1:31.6:1:1:1.01261:60:158:0.5745:0:1.2 -12 27330606 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53192;SOR=0;LSEQ=ACATGTAGCTATCAACCAAA;RSEQ=TTTGAGCAGAAAACTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:27,131:0.0125:2,2:18.5:1:29:1:0.32028:4.78:60:4:0.0126:0:1 0/0:94:0:0,0:22,72:0:2,0:23.4:1:30.8:1:1:0:60:188:1:0:0.3 -12 27578740 . G A 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00256;SOR=0;LSEQ=TCTAGAGAGTCAACCATCAT;RSEQ=AATTATAAGGTTCTATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:13,0:12,0:0.52:0,1:30.8:1:28.8:1:1:0:60:26:0.52:0:1 0/0:11:0:0,0:11,0:0:0,0:17.6:1:31.3:1:1:0:60:22:1:0:0.1 -12 27578843 . C T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69302;LSEQ=TCTTTTCCCCTTCAAGGATG;RSEQ=CTTTAAAGTTTATTTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:147,50:0.01:2,2:25.5:1:27.5:1:0.44785:2.92069:60:4:0.0102:0:1 0/0:144:1:0,1:95,48:0.0069:2,0:1:0:24:0:0.34028:0:60:2:0.007:0:2 -12 27578846 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1771;SOR=Inf;LSEQ=TTTCCCCTTCAAGGATGCCT;RSEQ=TAAAGTTTATTTTAATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:156,58:0:2,0:22.2:1:29.4:1:1:0:60:29.571:1:0:0.2 0/1:156:2:1,1:103,51:0.0128:2,2:25.5:1:33.5:1:1:2.00984:60:4:0.0129:0:2 -12 27578912 . A G 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.76452;LSEQ=GGGAAGGCAAAATAAGCAGT;RSEQ=GGTTCTTTCCAGGTCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:48:21,27:192,187:0.1121:2,2:27.8:1:31.7:1:0.44401:1.31923:60:96:0.1129:0:1.1 1/1:368:295:150,145:35,38:0.8016:2,2:28:1:30.6:1:0.696:1.12:60:72.75:0.7995:0:1.1 -12 27578968 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19885;SOR=Inf;LSEQ=TTAGCCAGGCTGTGATACAT;RSEQ=CTCAACCTTGGGTTGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:73,155:0:2,0:22.9:1:31.7:1:1:0:60:56:1:0:0.2 0/1:184:2:1,1:59,123:0.0109:2,2:8.5:1:28.5:1:0.54704:2.08:60:4:0.0111:0:1 -12 27580442 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51923;SOR=Inf;LSEQ=GGCCTCAGGAGGCCTACCTA;RSEQ=TTATTTTGCCTACCCTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:19.1:1:32.3:1:1:0:58.6:30:1:0:0.5 0/1:25:2:1,1:13,10:0.08:2,2:13.5:1:28:1:1:1.28628:60:4:0.08:0:1 -12 27705987 . A G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAAGGAAGTGCACGCAG;RSEQ=GGCCTAGGAGAAGATTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:3,16:0,0:1:0,2:26.1:1:31.5:1:1:0:60:38:1:0:1.1 1/1:11:11:3,8:0,0:1:0,2:15.9:1:30.4:1:1:0:60:22:1:0:1 -12 27706244 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGTCCAGCTGGGCCGGG;RSEQ=ATGGTGCTCACCCACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 28073093 . T C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.55708;SOR=0;LSEQ=CATGCAGCTTTCTGAGTTCC;RSEQ=GTGTCCCTAGATTTATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:197,87:0.0105:2,2:45.3:1:25.7:1:1:1.13167:60:2:0.0071:0:2 0/0:165:0:0,0:110,55:0:2,0:24:1:30.5:1:1:0:60:330:1:0:0.2 -12 28073101 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13385;SOR=Inf;LSEQ=TTTCTGAGTTCCTGTGTCCC;RSEQ=AGATTTATGATGTGCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:213,112:0:2,0:27.2:1:29.9:1:1:0:60:53.167:1:0:0.4 0/1:188:2:1,1:117,69:0.0106:2,2:24.5:1:30:1:1:1.6906:60:4:0.0106:0:1.5 -12 28073172 . T A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33119;LSEQ=CATTTGAAGGAGAAATGATC;RSEQ=AGAGATTTGTGCTGGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:388:280:128,152:51,56:0.7216:2,2:26.2:1:29.8:1:0.73401:1.08125:60:45.667:0.7211:0:1.1 0/1:286:132:60,72:69,85:0.4615:2,2:26.2:1:30:1:1:1.03:60:131:0.4596:0:1.1 -12 28073457 . G C 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTCCTATGCCCTGTCCCC;RSEQ=CTATTTCAGCACTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:15:1:30.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:17:0:32:0:1:0:60:2:1:0:1 -12 29426005 . T C 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=3.76419;LSEQ=CCTGATGCCAGTAGGATTGC;RSEQ=CCTGTATAGAGTGTCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:14:1:29.5:1:0.4:0:60:4:0.4:0:1 1/0:4:3:2,1:1,0:0.75:0,2:6.3:1:29:1:1:0:60:6:0.75:0:1.3 -12 29426031 . T G 63 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.44461;LSEQ=ATAGAGTGTCTGACAACCCC;RSEQ=GTAGGAAGGTCTCACCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:3,2:0.4444:2,2:19.5:1:31.5:1:0.52381:3.76419:60:8:0.4444:0:1.3 0/1:4:1:1,0:2,1:0.25:2,0:47:0:26:0:1:0:60:2:0.25:0:2 -12 29426387 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4408;SOR=0.45138;LSEQ=CAGTGTGTGTGTGGCTGCCA;RSEQ=GGTGTGTAGGGCTGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:3,4:0.5333:2,2:29.5:1:29.8:1:1:1.23147:60:16:0.5333:0:1.1 0/1:12:4:2,2:4,4:0.3333:2,2:20:1:30.3:1:1:1:60:8:0.3333:0:1.3 -12 29426859 . C A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCTCTCAGGTGGGCCAC;RSEQ=GCACCACACTGCTCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:44:0:31.5:1:1:1:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 29811355 . A C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GTTCCAGTAGGCCAGACTCC;RSEQ=TTCCACTCGTTCACAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:7.3:1:28.7:1:1:0:60:6:1:0:0.7 1/0:4:2:1,1:2,0:0.5:0,2:18.5:1:30.5:1:1:0:60:4:0.5:0:1 -12 29811514 . A G 26 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=ACTTGTTTGTTTATAACAAC;RSEQ=CCAACAGCAGCTGGGTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:33:0:26:1:1:1:60:4:0.1111:0:1.5 0/0:11:0:0,0:7,4:0:2,0:21.8:1:27.3:1:1:0:60:10:1:0:0 -12 29811614 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19615;SOR=0;LSEQ=AACCATTCCCTTGATGTCAA;RSEQ=AATATCACCTTTCTTATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,9:0.1111:2,2:25.5:1:29.5:1:1:1.27:60:4:0.1111:0:1.5 0/0:22:0:0,0:9,13:0:2,0:24.4:1:32.1:1:1:0:60:44:1:0:0.2 -12 30533133 . A T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGGCTCTGTGTCAGGGA;RSEQ=ATCAGAGTTCTGTCCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:0:31:1:1:0:60:4:1:0:1.5 -12 30848675 . C T 98 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17222;SOR=0;LSEQ=CAGCCTCCTCTTCCGCGACC;RSEQ=CTGGATTACCTCACACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:6,3:14,13:0.25:2,2:18.8:1:31:1:0.70027:1.83:60:18:0.25:0:1.7 0/0:10:0:0,0:5,5:0:2,0:20.7:1:30.3:1:1:0:60:20:1:0:0.3 -12 30848763 . CT C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.2029;SOR=Inf;LSEQ=CTCCGCGCCCCCTGTCCTCC;RSEQ=TTTTCCCCCCCACAACTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:8,16:0:2,0:19.2:1:28.4:1:1:0:60:7:1:0:0.6 0/1:21:2:1,1:10,9:0.0952:2,2:44:1:32:1:1:1.10554:60:4:0.0952:0:0 -12 31932814 . A C 118 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01992;SOR=0.10853;LSEQ=ATCCCCTCGGAGGGTTTTAC;RSEQ=AACATTTACAATTTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:14,0:19,0:0.4242:1,1:12.4:1:31.1:1:1:0:60:28:0.4242:0:1 0/1:14:1:1,0:12,1:0.0714:1,0:6:0:31:0:1:0:60:2:0.0769:0:1 -12 31932960 . C T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06833;SOR=Inf;LSEQ=TTTTGATCTTGTGATTCATG;RSEQ=CAGGGTCATGATGTCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:250,127:0:2,0:24.9:1:31.6:1:1:0:60:61.833:1:0:0.1 0/1:463:5:1,4:288,170:0.0108:2,2:12.8:1:24.4:1:0.06867:6.74957:60:4:0.0087:0:1 -12 31933059 . A G 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTACCAATACCTGCATCCT;RSEQ=TAAGTGTTTTGCAATACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:770:0:0,0:384,386:0:2,0:25.7:1:29.1:1:1:0:60:69:1:0:0.1 0/1:890:43:20,23:406,440:0.0483:2,2:24.4:1:30.5:1:0.8769:1.06109:60:42:0.0478:0:1.2 -12 31933213 . C T 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.07299;LSEQ=CTTTACTGTGGGTTCTGGTA;RSEQ=GCCAAAGAAGGCAGTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:21:0,21:1,61:0.253:1,1:29.1:1:30.9:1:1:0:60:42:0.253:0:1 0/1:45:12:0,12:1,32:0.2667:1,0:27.3:1:30:1:1:0:60:24:0.2727:0:1.1 -12 31938381 . G A 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03577;SOR=Inf;LSEQ=ATTCAAAGTAAAAATCATGT;RSEQ=TGCATGACGAACTGTATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:62,1:0:1,0:28.8:1:32.2:1:1:0:60:30.5:1:0:0 0/1:50:4:4,0:46,0:0.08:1,0:10.5:1:25.5:1:1:0:60:3:0.0625:0:1 -12 31944567 . T G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCACTTTTCGCATTCATCC;RSEQ=GAGTGAAAGATGGAATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:163,6:0:1,0:23.1:1:30.9:1:1:0:58.9:32.8:1:0:0.1 0/1:144:21:20,1:118,5:0.1458:1,1:25.3:1:29.7:1:1:1.17854:58.3:42:0.1479:0:1 -12 31944691 . A C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28706;LSEQ=ATGCCATAAAAACTGCCTTC;RSEQ=CTTAAGCTCTCTCTCCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1299:465:280,185:478,355:0.358:2,2:24.4:1:30.9:1:0.34746:1.12:51.2:50.667:0.3585:0:1.1 0/1:1704:235:130,105:822,646:0.1379:2,2:27.3:1:30.2:1:0.8875:1.02774:50.7:57.75:0.1371:0:1.1 -12 31945622 . G T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCATTTCAATCCCACCTCC;RSEQ=TCACAAAGCATTCTTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 31950904 . AT A 41 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGTAAATCCTTTGTGGG;RSEQ=TTTTTTACATACTATAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:17.7:1:26.1:1:1:0:60:6:0.75:0.5:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 31950931 . A G 40 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATACTATAACCATTCAT;RSEQ=CATTCAACACATATTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:27.3:1:25.7:1:1:0:60:2:0.6667:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 31957141 . TA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50222;SOR=0;LSEQ=AGTGGAAGCCAGTGTCTCTA;RSEQ=ATGAAGGTTGTAGAGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:52,1:0.0357:1,2:24:1:30:1:0.07205:37.11322:60:4:0.0385:0:0 0/0:44:0:0,0:44,0:0:1,0:26.3:1:27.5:1:1:0:60:43:1:0:0.1 -12 31957306 . A G 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.30271;LSEQ=TAGTGCAAAACTTCAGAATA;RSEQ=ATAAAAGTTGACTTCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:831:550:312,238:159,120:0.6619:2,2:26.9:1:31.6:1:1:1.01073:60:274:0.6642:0:2.3 0/1:1046:389:217,172:344,309:0.3719:2,2:25.8:1:31.4:1:0.33604:1.13:60:76.8:0.371:0:2.1 -12 31957321 . C T 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2899;LSEQ=GAATAAATAAAAGTTGACTT;RSEQ=AGTAACACATGGGTATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:899:605:325,280:154,140:0.673:2,2:26.7:1:29.2:1:0.72201:1.06:60:604:0.6764:0:2.4 0/1:1170:437:235,202:368,365:0.3735:2,2:25.5:1:28.6:1:0.25078:1.15:60:144.667:0.3741:0:2.1 -12 31957372 . CT C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.26247;SOR=1.66893;LSEQ=TTCCCTCCCATTTACTGCAT;RSEQ=TTTTTTTGATCTTTGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:811:9:2,7:368,431:0.0111:2,2:19.7:1:32.1:1:0.19121:2.98468:60:18:0.0111:0.0025:1.1 0/1:1142:21:10,11:529,591:0.0184:2,2:27.5:1:31.6:1:1:1.02:60:42:0.0185:0.0026:0.4 -12 31957381 . G A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09939;LSEQ=ATTTACTGCATCTTTTTTTT;RSEQ=ATCTTTGGTGCTCTCACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:752:531:233,298:93,127:0.7061:2,2:23.8:1:29.1:1:0.74633:1.07:60:105.2:0.7079:0:1.9 0/1:1065:205:93,112:393,464:0.1925:2,2:24.9:1:28.9:1:0.93785:1.02001:60:410:0.1947:0:1.8 -12 31957584 . G A 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05883;SOR=5.19189;LSEQ=TTATTAGCTTTTAGTACTGC;RSEQ=GGAGATTTTTTTTTTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:1,8:0,21:0.3:1,2:11.8:1:29.4:1:0.3:0:60:8:0.2857:0:1 1/0:10:7:0,7:0,3:0.7:0,0:19.9:1:31.7:1:1:0:60:14:0.7778:0:1 -12 31957589 . A AT 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05645;SOR=Inf;LSEQ=AGCTTTTAGTACTGCGGGAG;RSEQ=TTTTTTTTTTCAAGAGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,23:0:1,0:21.3:1:30.9:1:1:0:60:22:1:0:0.3 0/1:8:2:0,2:0,6:0.25:0,0:32.5:1:30.5:1:1:0:60:4:0.25:0:0.5 -12 32411399 . A G 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTCTCTCCGTGTGTGGA;RSEQ=ACGAGAGATCTAAGAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.3:1:31:1:1:0:60:6:1:0:1.7 1/1:1:1:1,0:0,0:1:0,0:38:0:34:0:1:0:60:2:1:0:1 -12 32411442 . G C 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22797;SOR=0;LSEQ=ACACAAGACAAAGAGATAAA;RSEQ=AGAAGACAGCTGGGCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:4,1:0.4444:2,0:27:1:33.8:1:1:0:60:8:0.4444:0:2.3 0/0:4:0:0,0:4,0:0:0,0:8.3:1:32.8:1:1:0:60:8:1:0:0.8 -12 32411481 . C T 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0419;SOR=0;LSEQ=GGGGACCACTACCACCAAGA;RSEQ=GCAGAGACCAGTAATGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:5,1:0.5714:2,0:24.8:1:31.8:1:0.42857:0:60:16:0.5714:0:2.3 0/0:6:0:0,0:6,0:0:0,0:27.3:1:31.8:1:1:0:60:12:1:0:1.3 -12 32411515 . G A 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00328;SOR=Inf;LSEQ=ATGGCCCCGAATGGTTGGGC;RSEQ=TGCTGATATTTATCGTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:17,3:0:2,0:21:1:30.2:1:1:0:60:40:1:0:1.1 0/1:19:7:5,2:12,0:0.3684:0,2:19.6:1:29.7:1:0.12281:0:58:14:0.3684:0:3 -12 32411529 . C T 86 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0288;SOR=8.76036;LSEQ=TTGGGCGTGCTGATATTTAT;RSEQ=GTATACAAGACAACGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:19,7:0.037:2,0:1:0:26:0:0.2963:0:60:2:0.037:0:2 0/1:31:8:5,3:17,6:0.2581:2,2:22.5:1:28.8:1:0.65951:1.66957:56.9:16:0.2667:0:2.9 -12 32411544 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00041;SOR=0.18193;LSEQ=TTTATCGTATACAAGACAAC;RSEQ=GGGCAGGGTAAGGAGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:26:15,11:11,7:0.5909:2,2:22.3:1:30:1:1:1.14868:54.7:52:0.6047:0:1.3 0/1:44:9:5,4:20,15:0.2045:2,2:26.7:1:29.3:1:1:1.06509:54.9:18:0.2143:0:2.6 -12 32412038 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGGCGTAAGAGAGGGC;RSEQ=CACCTCTTGCCTTCTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 33147320 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGCTGTGGTCAGCACTCTC;RSEQ=CTGCTGGAAATGCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:9,18:0:2,0:25.4:1:30.9:1:1:0:60:54:1:0:0.1 0/1:55:2:1,1:18,33:0.0364:2,2:28.5:1:31:0:1:1.81:60:4:0.0364:0:1 -12 33147332 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACTCTCCCTGCTGGAAAT;RSEQ=CTTTCTTTGAGCTTTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:7,15:0:2,0:25.8:1:31.9:1:1:0:60:44:1:0:0 0/1:47:2:1,1:16,29:0.0426:2,2:5.5:1:28:1:1:1.79:60:4:0.0435:0:1 -12 38600022 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.198;SOR=0;LSEQ=AGTATGGTTCTGCTACATTT;RSEQ=AGTAGAACGCTTACCTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:104,34:0.0143:2,2:23:1:26.5:1:0.43885:3.02923:60:4:0.0144:0:1 0/0:174:0:0,0:131,42:0:2,0:25.3:1:31.3:1:1:0:59.9:172:0.9942:0:0.1 -12 38600037 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19544;SOR=0;LSEQ=CATTTCAGTAGAACGCTTAC;RSEQ=TGAACAGATATAACATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:127,49:0.0112:2,2:18:0:32.5:1:0.48403:2.57588:60:4:0.0114:0:1.5 0/0:224:0:0,0:158,66:0:2,0:25.6:1:30.4:1:1:0:59.9:448:1:0:0.1 -12 38600255 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19973;SOR=Inf;LSEQ=AGAGAGATGAAACCAACTGA;RSEQ=CTAAACACACAAACAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:16,96:0:2,0:25.5:1:29.8:1:1:0:60:55:1:0:0.2 0/1:91:2:1,1:9,80:0.022:2,2:6.5:1:26.5:1:0.20879:8.48:60:4:0.0222:0:1 -12 38601013 . T G 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00152;SOR=0.57066;LSEQ=GCCTAAACACAAAATTTTCA;RSEQ=GTAAAGCATGAATTAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:98:34,64:75,128:0.3256:2,2:23.8:1:31.3:1:0.79811:1.10257:60:196:0.3289:0:1.1 0/1:366:79:28,51:107,178:0.2158:2,2:23.1:1:30.6:1:0.79301:1.09467:60:78:0.2137:0:1.1 -12 38601111 . A T 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.01692;SOR=0;LSEQ=TACAAGAAATGTAAAAAAAC;RSEQ=CATTAAAATCAACCCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:0,7:0,28:0.2:1,0:33.3:1:26.7:1:1:0:60:6:0.1765:0:1.1 0/0:26:0:0,0:2,24:0:2,0:24.9:1:29.8:1:1:0:59.4:52:1:0:0 -12 40763955 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAATAACAATTCAGAATCTG;RSEQ=CTGCTTAAAGGCACCTACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:272,258:0:2,0:25.6:1:31.3:1:1:0:60:57.889:1:0:0.7 0/1:428:28:15,13:211,187:0.0654:2,2:27.5:1:27.6:1:1:1.02:60:13:0.0621:0:1.2 -12 40763973 . C G 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.04926;SOR=0.77115;LSEQ=TGGCTGCTTAAAGGCACCTA;RSEQ=GTACGTGGTTCTTTCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:540:341:153,188:102,95:0.6315:2,2:25.4:1:31.4:1:0.1284:1.3186:60:67.2:0.6304:0:1.1 1/0:441:251:124,127:98,90:0.5692:2,2:25.3:1:30.6:1:0.62968:1.11495:60:61.75:0.5704:0:1.2 -12 40764063 . G A 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21925;SOR=Inf;LSEQ=AGGGAGGCACCTGACCCAAA;RSEQ=GCCTGCTGTCTGAACACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:40,140:0:2,0:24.7:1:30.8:1:1:0:60:59:1:0:0.3 0/1:159:2:1,1:41,116:0.0126:2,2:11:1:23:1:0.45976:2.81:60:4:0.0129:0:1.5 -12 43130905 . G A 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25359;SOR=0;LSEQ=GTTTTCTGGCATGAAACATA;RSEQ=TTTTATTTGTTTTCAGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:8,0:10,0:0.4444:0,0:32.4:1:30.3:1:1:0:60:16:0.4444:0:1 0/0:4:0:0,0:4,0:0:0,0:10.3:1:33.3:1:1:0:60:8:1:0:0.3 -12 43130986 . C G 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00073;SOR=Inf;LSEQ=AATTTTTTTTCTTAGGCTTA;RSEQ=GCGTCCCCTCTAATGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:0:1,0:18.3:1:32.3:1:1:0:60:76:1:0:0.1 0/1:35:9:8,1:23,3:0.2571:2,2:26.8:1:31.9:1:1:1.04:60:18:0.2571:0:1.1 -12 43131131 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=5.49478;LSEQ=ATACAAATTGTTGAGAATAA;RSEQ=ATCTATGTGAGCAATCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:59:23,36:49,71:0.3296:2,2:26.5:1:32:1:0.8719:1.07973:60:118:0.3315:0:1.1 1/0:234:171:71,100:30,33:0.7308:2,2:28.1:1:31.2:1:0.45764:1.27903:60:342:0.7308:0:1.1 -12 43131140 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17664;SOR=0;LSEQ=GTTGAGAATAATATCTATGT;RSEQ=AGCAATCACATTGGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:60,97:0.0125:2,2:14.5:1:28:1:1:1.61:60:4:0.0126:0:2 0/0:220:0:0,0:92,128:0:2,0:28.2:1:30.8:1:1:0:60:109:1:0:0.8 -12 43131208 . T C 143 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.0116;LSEQ=TAGATCGGGTATGTATTCTT;RSEQ=TGGAGTTATCAAATATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:24:4,20:0,10:0.7059:0,2:22.1:1:31.4:1:0.29576:0:60:23:0.697:0:1.2 0/1:40:1:0,1:3,36:0.025:2,0:19:0:34:0:1:0:60:2:0.025:0:2 -12 43954690 . C T 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTGGTTCTCACAAAG;RSEQ=GTGCTTCTCTGAATGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18.3:1:28.7:1:1:0:60:6:1:0:1 1/1:4:4:3,1:0,0:1:0,2:22.5:1:30.5:1:1:0:60:8:1:0:1 -12 43954956 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.55133;LSEQ=CTTGTGGGGCACTCTTTTTT;RSEQ=AACAGTATCTATTCCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:0,1:37,71:0.0092:2,0:14:0:29:0:1:0:60:2:0.0093:0:1 0/1:141:2:1,1:53,86:0.0142:2,2:39.5:1:29.5:1:1:1.62:60:4:0.0146:0:1.5 -12 43955005 . C T 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13042;SOR=0;LSEQ=ATATCACCTTTCTTATAGAT;RSEQ=CGCATATATGTGGCCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:9,29:0,0:1:0,2:24.4:1:30.9:1:1:0:59.3:76:1:0:1.1 1/1:50:46:13,33:2,2:0.92:2,2:26.7:1:29.2:1:0.57371:2.48557:60:92:0.92:0:1 -12 43955023 . A C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18712;SOR=0;LSEQ=ATCCGCATATATGTGGCCAA;RSEQ=GGAACAACTCCATGTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:8,21:0.0645:2,2:32:0:32.5:1:0.50323:2.53:46:4:0.0645:0:2.5 0/0:40:0:0,0:10,30:0:2,0:29.4:1:30.2:1:1:0:60:39:1:0:0.9 -12 46121662 . T A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCCTGGGTTGTCAGGA;RSEQ=CTTCCTAGCCACAACCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:27:1:1:0:60:4:1:0:1.5 -12 46123143 . G A 80 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCATCGGCTCGCCTTGCCC;RSEQ=TCGCCCGCTCGCGCGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:4,3:0,0:1:0,2:32.7:1:28.7:1:1:0:60:14:1:0:1.1 -12 46123558 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12073;SOR=0;LSEQ=GGCTCTGGTAGGAAGCGCTG;RSEQ=GAGCGGGGGGCGCTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:148,38:0.0106:2,2:24.5:1:29:0:0.37274:3.85745:60:4:0.0108:0:1 0/0:354:0:0,0:262,92:0:2,0:23.9:1:30.5:1:1:0:60:87.5:1:0:0.1 -12 46123788 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1563;SOR=0;LSEQ=CCGCCCGGGCCGGGCACGGG;RSEQ=TCCCGGCTGACAAGTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:0,2:85,92:0.0112:2,0:21:1:28.5:1:0.49846:0:60:4:0.0114:0:1 0/0:273:0:0,0:147,124:0:2,0:23.2:1:30.7:1:1:0:60:66.75:1:0:0.1 -12 46123810 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05472;SOR=0;LSEQ=CCCGGCTGACAAGTGCGGGG;RSEQ=TTTTTCTCTCCCGCAGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:1,2:116,76:0.0154:2,2:12.3:1:28.7:1:0.56502:3.03496:60:6:0.0156:0:1.3 0/0:317:0:0,0:198,119:0:2,0:25:1:31.3:1:1:0:60:34.222:1:0:0.1 -12 46123959 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10079;SOR=0;LSEQ=TTGTATTTCCCTCTCGCTGG;RSEQ=CTCCTCCAAAAAGTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:48,124:0.0115:2,2:27:1:29:1:0.48508:2.57:60:4:0.0115:0:1 0/0:373:0:0,0:125,248:0:2,0:22.5:1:30.7:1:1:0:60:40.444:1:0:0.1 -12 46123990 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52432;SOR=Inf;LSEQ=AAGTCTCCTTTGACCCCGGA;RSEQ=TGGGCGCTTGGGGCTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:11,92:0:2,0:23.8:1:32:1:1:0:60:206:1:0:0.1 0/1:164:2:1,1:28,133:0.0122:2,2:7.5:1:27.5:1:0.32508:4.68:60:4:0.0125:0:1.5 -12 46124911 . A T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51217;SOR=Inf;LSEQ=GATGCCTTAGGTATCTACAG;RSEQ=TCTCTGTAGAATGGGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:131,8:0:2,0:22.6:1:29.8:1:1:0:60:22.167:1:0:0.1 0/1:194:2:1,1:174,18:0.0103:2,2:12:1:25:1:0.18674:9.43585:60:4:0.0104:0:1 -12 46204991 . CA C 74 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.67919;SOR=0.6129;LSEQ=GACAGAGCGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAGAACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:20.6:1:32:1:1:0:56:10:0.4167:0.1538:0.2 0/1:11:3:3,0:8,0:0.2727:0,0:25.3:1:32.7:1:1:0:60:6:0.2727:0:0 -12 46205132 . T C 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30156;SOR=Inf;LSEQ=TTAGAAAAGGAAAACAAATA;RSEQ=GTGGTGAGAGTTAAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:128,16:0:2,0:22.2:1:30.6:1:1:0:60:71:1:0:0.1 0/1:258:4:2,2:210,44:0.0155:2,2:19:1:29:1:0.1471:4.73123:60:8:0.0157:0:1 -12 46208438 . A G 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0063;SOR=0;LSEQ=CAAAACTCCATCTCAAAAAA;RSEQ=TAATAAACTTCCCTCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:0.8462:0,0:28.4:1:32.5:1:1:0:60:22:0.8462:0:1.1 0/0:4:0:0,0:4,0:0:0,0:10.3:1:30.8:1:1:0:60:8:1:0:0.3 -12 46208593 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12905;SOR=0;LSEQ=GAATTTTTAATTCGCCAAAT;RSEQ=ATTATAATAAATTGGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:2,0:125,63:0.0105:2,0:25.5:1:31.5:1:1:0:60:4:0.0106:0:1 0/0:338:0:0,0:216,122:0:2,0:26.5:1:31.5:1:1:0:59.9:66.6:1:0:0.1 -12 46208631 . C A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6758;SOR=0.59063;LSEQ=CTTTCACTGTTATCTGAACT;RSEQ=CCAAATGAAGCAGACTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:3:2,1:128,98:0.0131:2,2:11:1:27:1:1:1.53:60:6:0.0132:0:1 0/0:386:3:3,0:226,157:0.0078:2,0:16:1:20:1:0.27421:0:60:2:0.0053:0:3 -12 46208668 . C T 44 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0477;SOR=0;LSEQ=TTGCTGTTAATGTATGCAGT;RSEQ=TCCTGTCAAATGAAAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:109,128:0.0125:2,2:11.7:1:28:1:1:1.6995:60:6:0.0127:0:1 0/0:420:0:0,0:209,211:0:2,0:24:1:30.9:1:1:0:60:104:1:0:0.1 -12 46209382 . TTG T 29 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=11.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGCATCCTACTTAAAGAGA;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:0 -12 46211214 . T A 28 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AATGATGGCCAAATGGTATG;RSEQ=ACATTTTGGTATTTTAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:21:1:28.5:1:0.33333:0:60:4:0.3333:0:1.5 1/1:1:1:1,0:0,0:1:0,0:9:0:30:0:1:0:60:2:1:0:1 -12 46211353 . T TTA 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.23913;SOR=0;LSEQ=TATATTATATTTTATATATA;RSEQ=TATATATATATATTTAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:32,0:0.0588:1,0:7.5:1:29.3:1:1:0:60:4:0.0606:0.0294:0.5 0/0:35:0:0,0:33,2:0:2,0:24.8:1:30.3:1:1:0:60:70:1:0:0.2 -12 46211396 . T C 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03904;SOR=0.504;LSEQ=TGTTCTGTATTCAAGGGATA;RSEQ=TCACCATAAAGGTATCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:28:20,8:72,10:0.2545:2,2:20.8:1:31.1:1:0.07198:2.84761:60:27:0.2477:0:1.1 0/1:157:23:19,4:108,26:0.1465:2,2:24:1:30.9:1:1:1.14:60:46:0.1474:0:1 -12 46211435 . AT A 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.16249;SOR=Inf;LSEQ=ATCTTTGATATACTTAAGGT;RSEQ=TTTTTTTCTTTGTTAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:177,64:0:2,0:24.7:1:31:1:1:0:60:482:1:0:0.2 0/1:371:5:4,1:246,120:0.0135:2,2:15.8:1:30.2:1:1:1.95:60:10:0.0137:0.0054:0.4 -12 46211714 . G GT 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.38685;SOR=1.38363;LSEQ=TATATAATTCTTCTGTAAAA;RSEQ=TTTTTTTTTTAAGGTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:13:3,10:29,149:0.0674:2,2:26.5:1:30.2:1:0.45989:1.54:60:26:0.0688:0:0 0/1:253:23:4,19:45,178:0.0909:2,2:27.6:1:29.3:1:1:1.19998:60:22:0.0891:0.0079:0.3 -12 46215128 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50024;SOR=Inf;LSEQ=TAGTTTTGTTGTTTTTCCAA;RSEQ=CCTATTATTAAATAATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:72,0:0:1,0:23.9:1:32.7:1:1:0:60:144:1:0:0.9 0/1:85:2:2,0:77,6:0.0235:2,0:22.5:1:28.5:1:1:0:60:4:0.0235:0:1 -12 46215147 . A C 74 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.40552;SOR=3.4664;LSEQ=AGCCTATTATTAAATAATTA;RSEQ=TTGAAAGAATTTATTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:1,0:90,4:0.0105:1,0:45:0:12:0:1:0:60:0:0:0:5 0/1:140:5:4,1:118,17:0.0357:2,2:20.2:1:32.2:1:0.50287:1.72709:60:10:0.0365:0:1 -12 46215163 . G A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08642;LSEQ=ATTAATTGAAAGAATTTATT;RSEQ=CATTTTATTGAATGTACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:134:121:107,14:9,4:0.903:2,2:23.9:1:28.2:1:0.07521:3.35:60:59.5:0.9015:0:1.1 0/1:196:87:69,18:89,18:0.4439:2,2:22.2:1:27.9:1:0.57829:1.28814:60:42.5:0.4404:0:1.1 -12 46215315 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55696;SOR=Inf;LSEQ=GATTCATTGAGTTACATGCA;RSEQ=CTAAGCCAACAATAGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:31,123:0:2,0:24:1:32.1:1:1:0:60:76:1:0:0.1 0/1:268:3:1,2:67,198:0.0112:2,2:11.3:1:28.3:1:1:1.48:60:6:0.0114:0:1 -12 46215342 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54044;SOR=Inf;LSEQ=CAACAATAGATCAGTGGTTG;RSEQ=TTATTTAATATACATAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:11,73:0:2,0:23.4:1:31.9:1:1:0:60:41:1:0:0.1 0/1:153:2:0,2:21,130:0.0131:2,0:30.5:1:28:1:1:0:60:4:0.0132:0:4.5 -12 46230031 . C T 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATGGGGTCTCACTCTTC;RSEQ=GCCCAGGCTGGAGTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:14.3:1:32:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 46230789 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06847;SOR=Inf;LSEQ=GCTGAGGTAAGCATGTGACT;RSEQ=TACCTTAAACTAGTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:61,205:0:2,0:23.4:1:31.8:1:1:0:60:52.2:1:0:0.2 0/1:329:5:4,1:83,241:0.0152:2,2:8.2:1:25:1:0.01848:11.51:60:10:0.0154:0:1 -12 46231546 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16021;SOR=0;LSEQ=TGAGTAAAAGTGTTTAATAT;RSEQ=GTACTGTACAAAACCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:42,110:0.013:2,2:32.5:1:30:0:0.48179:2.60:60:4:0.0134:0:1 0/0:230:0:0,0:58,172:0:2,0:22.1:1:30.3:1:1:0:60:229:1:0:0.1 -12 46240570 . T TA 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.65104;SOR=2.5233;LSEQ=GTTAATGGGTTCAATATCCA;RSEQ=AAAAAAAAGTATGGCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:1,0:69,7:0.013:2,0:30:0:25:0:1:0:60:2:0.0135:0:1 0/1:124:4:3,1:106,14:0.0323:2,2:35.5:1:28.5:1:0.40698:2.49808:60:8:0.0323:0:0 -12 46240594 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12511;SOR=0;LSEQ=AAAAAGTATGGCAAATAGTG;RSEQ=CTAACTTTTAAGAAATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:99,21:0.0164:2,2:43.5:1:30.5:1:0.32936:4.62913:60:4:0.0167:0:1.5 0/0:222:0:0,0:169,53:0:2,0:22.6:1:29.1:1:1:0:60:444:1:0:0.1 -12 46240638 . G T 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01393;SOR=0;LSEQ=CTAATGTATTTTTTTCTTTA;RSEQ=CTTCCAGAGCAGTTGTAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:4:2,2:174,81:0.0154:2,2:28:1:26.8:1:0.59529:2.14124:60:3:0.0118:0:1 0/0:492:0:0,0:311,181:0:2,0:23.2:1:31.9:1:1:0:60:163:1:0:0.1 -12 46240657 . C T 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09891;SOR=Inf;LSEQ=AGCTTCCAGAGCAGTTGTAG;RSEQ=GCAGCATGTTGCTCCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:190,121:0:2,0:26.3:1:31.1:1:1:0:60:76.75:1:0:0.1 0/1:591:6:2,4:341,244:0.0102:2,2:17.5:1:27.5:1:0.2438:2.79024:60:12:0.0103:0:1 -12 46240661 . G T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01321;SOR=0;LSEQ=TCCAGAGCAGTTGTAGCGCA;RSEQ=CATGTTGCTCCACCTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:4:2,2:190,125:0.0125:2,2:27.8:1:31.3:1:0.65167:1.51791:60:8:0.0127:0:1.3 0/0:619:0:0,0:362,257:0:2,0:25.4:1:31.7:1:1:0:60:87.429:1:0:0.1 -12 46240772 . G GA 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.16642;SOR=Inf;LSEQ=CTTGGGAGGAGTAAAGCAAA;RSEQ=AAAAAAAGGAAATGTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:46,135:0:2,0:23.7:1:31.2:1:1:0:60:180:1:0:0.1 0/1:329:5:3,2:87,237:0.0152:2,2:23.2:1:27.8:1:0.12826:4.07:60:10:0.0153:0.003:0.2 -12 46242781 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12681;SOR=0;LSEQ=CCATAGTTCTTTAAATAAAG;RSEQ=CCATTTACGTCACTTACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:30,104:0.0147:2,2:40:1:31:1:0.40523:3.43:60:4:0.0149:0:1 0/0:245:0:0,0:67,178:0:2,0:23.1:1:28.6:1:1:0:60:48:1:0:0.1 -12 46242790 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13944;LSEQ=TTTAAATAAAGTCCATTTAC;RSEQ=TCACTTACAACATCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:1:0,1:19,91:0.009:2,0:25:0:27:0:1:0:60:2:0.009:0:1 0/1:195:2:1,1:46,147:0.0103:2,2:10:1:28:1:0.4249:3.17:60:4:0.0104:0:1 -12 46243742 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53041;SOR=Inf;LSEQ=TAATTTCTTAAAACTATTTT;RSEQ=TCTTAAGTAAAATAATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:53,15:0:2,0:22.9:1:31.2:1:1:0:60:21.667:1:0:0.1 0/1:115:2:1,1:93,20:0.0174:2,2:22.5:1:27.5:1:0.33318:4.56229:60:4:0.0177:0:1 -12 46243835 . A T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10567;SOR=0.16128;LSEQ=TCAGGAATCCCTCATGGATC;RSEQ=CAAACCATAGGAAACCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:1,2:161,74:0.0126:2,2:8.7:1:28:1:0.23979:4.32166:60:6:0.0128:0:1 0/0:488:1:0,1:307,180:0.002:2,0:1:0:23:0:0.3709:0:60:2:0.0021:0:1 -12 46246569 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.093;SOR=0;LSEQ=GCTGCAGCGCAACAATGGTT;RSEQ=CTGTGCCAGCAGGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:71,121:0.0103:2,2:31:1:28:1:1:1.70:60:4:0.0104:0:1 0/0:441:0:0,0:179,262:0:2,0:23.6:1:31.7:1:1:0:60:219.5:1:0:0.1 -12 46254499 . CAT C 155 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.00181;SOR=0.34887;LSEQ=ATGGTAGAAATGTATAACAA;RSEQ=AATCAAATTTATAAGACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:30:27,3:81,3:0.2632:1,2:19.6:1:31.6:1:0.18559:2.96569:60:60:0.2655:0.0789:0 0/1:154:17:16,1:127,10:0.1104:2,1:22.1:1:30:1:1:1.26:60:34:0.1118:0.026:0.1 -12 46254505 . C G 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=GAAATGTATAACAACATAAT;RSEQ=AAATTTATAAGACTATACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:11:11,0:98,10:0.0924:2,0:29.1:1:32.5:1:0.59561:0:60:22:0.0932:0:1.1 0/0:177:0:0,0:157,19:0:2,0:21.8:1:30.8:1:1:0:60:24.143:1:0:0.1 -12 46285536 . A T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2563;SOR=Inf;LSEQ=AATATACTTGAATACATCCA;RSEQ=GTGTCTACTACTTTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:160,55:0:2,0:25.3:1:30.4:1:1:0:60:214:1:0:0.1 0/1:264:3:0,3:183,78:0.0114:2,0:6:1:22:1:0.02814:0:60:2:0.0077:0:1 -12 46286262 . C CAT 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTCATATCTTGTCATTAT;RSEQ=ATATATATATATATACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31.3:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 46287120 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50375;SOR=Inf;LSEQ=TTAAAATAACCAGCTTAAAG;RSEQ=GGTTGGCAGGGTGGTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:75,2:0:1,0:24.2:1:31.4:1:1:0:60:154:1:0:0.1 0/1:97:2:2,0:92,2:0.0206:1,0:5.5:1:29:1:1:0:60:4:0.022:0:1 -12 46287390 . C CT 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.08914;SOR=Inf;LSEQ=GTATGATTTAGATCTTTATT;RSEQ=TTTTTTTTCCTTTCTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:152,151:0:2,0:23.7:1:31.3:1:1:0:60:59.6:1:0:0 0/1:506:6:2,4:266,233:0.0119:2,2:20.8:1:28.2:1:0.42634:2.27964:60:12:0.012:0.004:0.5 -12 46287550 . A G 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTGAATTTAGTTTATTTT;RSEQ=TTTTTACATATAAGTTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:13:3,10:25,88:0.1032:2,2:29.5:1:29.1:1:1:1.06:60:5.5:0.0894:0:1.2 0/0:210:0:0,0:61,149:0:2,0:22.5:1:29.1:1:1:0:60:104:1:0:0.1 -12 46298435 . T C 51 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAGCTAAGATTGCGCCA;RSEQ=TACACTCCAGCCTGGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:30.3:1:32.3:1:1:0:48.7:6:1:0:2 1/1:1:1:1,0:0,0:1:0,0:50:0:30:0:1:0:54:2:1:0:2 -12 46298437 . A G 50 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGCTAAGATTGCGCCATT;RSEQ=CACTCCAGCCTGGCAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:28.3:1:32:1:1:0:48.7:6:1:0:2 1/1:1:1:1,0:0,0:1:0,0:48:0:29:0:1:0:54:2:1:0:2 -12 46298916 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50179;SOR=Inf;LSEQ=GTCAGCCACATTTCACATAC;RSEQ=GTTACTGAAGAAAGCACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:38,130:0:2,0:24.1:1:30.1:1:1:0:60:32.6:1:0:0.1 0/1:197:2:1,1:36,159:0.0102:2,2:23:1:26.5:1:0.34114:4.37:60:4:0.0103:0:1 -12 46298934 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49961;SOR=Inf;LSEQ=ACTGTTACTGAAGAAAGCAC;RSEQ=AAGTCTTAATGGAACAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:16,98:0:2,0:23.1:1:32.2:1:1:0:60:113:1:0:0.1 0/1:128:2:1,1:11,115:0.0156:2,2:8.5:1:30:1:0.17938:10.05:60:4:0.0159:0:1 -12 46515942 . C CT 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.05636;SOR=3.19211;LSEQ=AGAATGAACCAATGGACTTA;RSEQ=GACTTACATTACGAACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:5:5,0:61,2:0.0735:1,0:37.4:1:31.4:1:1:0:60:10:0.0758:0:0.2 0/1:54:11:11,0:43,0:0.2037:1,0:23.9:1:31.4:1:1:0:60:22:0.2037:0.037:0 -12 46516045 . A G 226 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCTCTACATGCAAAATA;RSEQ=CATTGTTACATGTGCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:322,178:0:2,0:24:1:29.8:1:1:0:60:82.333:1:0:0.1 0/1:678:141:88,53:340,195:0.208:2,2:23.9:1:31.7:1:0.8444:1.05003:60:69.5:0.2087:0:1.4 -12 46516129 . C A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.08395;LSEQ=ATGTTAACTGGCAGGGACTA;RSEQ=GTAATTATGGGACTAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:40:18,22:296,364:0.0571:2,2:25:1:30.5:1:1:1.01:60:19:0.0553:0:1.1 1/0:943:518:240,278:182,242:0.5493:2,2:24.1:1:30.1:1:0.32331:1.15:60:171.667:0.552:0:1.2 -12 46516197 . G A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATTTTTATGAAAGACAAAAT;RSEQ=AAAAGGGACACAATGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:63,234:0:2,0:24.1:1:31.4:1:1:0:60:296:1:0:0.1 0/1:305:18:5,13:55,231:0.059:2,2:29:1:29.8:1:0.36629:1.61:60:36:0.059:0:1.5 -12 46955238 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14544;SOR=0;LSEQ=GCTCAGAAGATATCACTAAA;RSEQ=AAGCCGAACACGGTGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:72,125:0.0101:2,2:12:0:31:1:1:1.73:60:4:0.0102:0:1 0/0:322:0:0,0:129,193:0:2,0:21:1:30.9:1:1:0:60:63.4:1:0:0.2 -12 46955268 . T C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2757;SOR=Inf;LSEQ=ACGGTGGTGCATGCCTATAG;RSEQ=CCCAGCTATTCAGGAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:16,74:0:2,0:21.2:1:29.6:1:1:0:60:21.5:1:0:0.2 0/1:134:3:0,3:32,97:0.0224:2,0:8.7:1:25.3:1:1:0:60:2:0.0152:0:1 -12 46955302 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49885;SOR=Inf;LSEQ=GAGGCCAAGACGGGAGGATT;RSEQ=CTTGAGCCCAGGAATTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:0,49:0:1,0:28.4:1:31.5:1:1:0:59.5:15.333:1:0:0.3 0/1:58:2:0,2:0,56:0.0345:1,0:25:1:31:1:1:0:60:4:0.0345:0:1 -12 46955381 . CA C 82 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.2245;SOR=0.27267;LSEQ=AAAACAAAACAAAAAACAAC;RSEQ=AAAAAAAAAAAAATAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,8:0.3529:0,0:29.8:1:32:1:1:0:49.3:12:0.3529:0:1.3 0/1:16:2:0,2:0,14:0.125:1,0:14:1:31.5:1:1:0:56:4:0.125:0.0625:0 -12 46955423 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CACTGTGAAAGGAAAATAAA;RSEQ=CCCAGGAGCCCCAAATCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:11.5:1:30.5:1:1:0:46.5:4:0.5:0:1.5 0/0:4:0:0,0:0,4:0:0,0:7.5:1:30.5:1:1:0:58.5:8:1:0:0.5 -12 49027335 . C T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=2.61246;LSEQ=TTGACCCTTGCCATACCCTC;RSEQ=GTGTTACAGAAATCATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:10.2:1:30.6:1:1:0:60:10:0.7143:0:1 1/1:8:7:6,1:1,0:0.875:0,2:27:1:30.1:1:1:0:60:6:0.8571:0:1.6 -12 49027446 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTGTTGCTGTCGCTGCTG;RSEQ=TGCTGTCGCTGCTGCTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:15,17:0:2,0:25.2:1:29.6:1:1:0:60:64:1:0:0.2 0/1:72:2:1,1:35,34:0.0278:2,2:48:0:32.5:1:1:1.029:60:4:0.029:0:1 -12 49208028 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49479;SOR=Inf;LSEQ=GTCTCCATGAAGGGGGGTCC;RSEQ=TCTCTCCCCGCCCCAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:14,28:0:2,0:26:1:30.3:1:1:0:60:20:1:0:0 0/1:45:2:1,1:20,23:0.0444:2,2:16:0:31.5:1:1:1.15:60:4:0.0455:0:1.5 -12 49209368 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGCGGGCGTGGGGCGAGG;RSEQ=CAGGCGTGCAGGCGGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:21:1:29.5:1:1:1:60:4:0.5:0:1 -12 49413580 . T TA 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGTTGAGGAAGCAGCTT;RSEQ=AAAAAAAAAAAATCTCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:28:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 49413694 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCCTCCAGCAGGCCCGC;RSEQ=CGTCCACCACCACCAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:26.5:1:29.5:1:1:1:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 49415492 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.22246;SOR=Inf;LSEQ=GGCTCTGGCTGCTACCTCTC;RSEQ=TCCCCCTCATCCCTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:175,44:0:2,0:22.6:1:30.9:1:1:0:60:108.5:1:0:0.1 0/1:196:2:1,1:149,45:0.0102:2,2:40:1:31.5:1:0.41523:3.28587:60:4:0.0103:0:1 -12 49415498 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10839;SOR=Inf;LSEQ=GGCTGCTACCTCTCTTCCCC;RSEQ=TCATCCCTTTCAGGGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:194,54:0:2,0:22.7:1:31:1:1:0:60:61:1:0:0.1 0/1:227:3:2,1:164,59:0.0132:2,2:8.3:1:27:1:1:1.38766:60:6:0.0133:0:1.3 -12 49415513 . G T 62 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03102;SOR=Inf;LSEQ=TCCCCCTCATCCCTTTCAGG;RSEQ=AAGAGGTTGTGGGTAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:233,80:0:2,0:24.1:1:31.2:1:1:0:60:155.5:1:0:0.1 0/1:335:6:0,6:221,107:0.0179:2,0:5.3:1:24:1:0.00137:0:60:12:0.0182:0:1 -12 49416046 . TC T 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.41066;LSEQ=GGGACCACTAAATCCCTCCT;RSEQ=CTCGTCATCTCTCACCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1207:526:276,250:327,354:0.4358:2,2:29.3:1:31.7:1:0.13141:1.19:60:525:0.4379:0.0232:0.2 0/1:1242:299:150,149:496,447:0.2407:2,2:26.3:1:31:1:0.4659:1.10213:60:298:0.2425:0.0362:0.2 -12 49416292 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52549;SOR=0;LSEQ=CCCACCACAGCTTTCCTCCT;RSEQ=CTCTCCTGTGACCAATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:141,37:0.0111:2,2:26:1:30:1:0.37858:3.77366:60:4:0.0114:0:1 0/0:112:0:0,0:93,19:0:2,0:23.6:1:31.9:1:1:0:60:55:1:0:0.1 -12 49416696 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22005;SOR=Inf;LSEQ=CCATGACAAGACAGCTCTCC;RSEQ=TCAGACCAAGTACATACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:45,174:0:2,0:21.8:1:31.8:1:1:0:60:42.8:1:0:0.1 0/1:194:2:1,1:42,150:0.0103:2,2:21:1:29:1:0.39506:3.54:60:4:0.0105:0:1 -12 49418267 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53668;SOR=0;LSEQ=TCCCCATTTTCTCCACGGGA;RSEQ=CTCTGATCTGTATCCTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:129,9:0.0143:2,2:21.5:1:30:1:0.13823:13.65041:60:4:0.0145:0:1 0/0:79:0:0,0:69,10:0:2,0:25.5:1:29.6:1:1:0:60:78:1:0:0.1 -12 49418291 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18264;SOR=Inf;LSEQ=TGATCTGTATCCTAAATCCT;RSEQ=ATAATGGGACCAGAGGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:164,38:0:2,0:24.2:1:31.1:1:1:0:60:66.333:0.995:0:0.1 0/1:152:2:1,1:123,27:0.0132:2,2:11.5:1:27.5:1:0.33548:4.49163:60:4:0.0133:0:1 -12 49418435 . A C 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCATGAGTGGCAGCTCCAT;RSEQ=AGGGGGTGGCGCCCATAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:0:0,0:284,305:0:2,0:25.2:1:29.1:1:1:0:60:195.333:1:0:0.1 0/1:511:40:20,20:215,255:0.0783:2,2:25.4:1:31:1:0.62364:1.19:60:39:0.0778:0:1.1 -12 49418727 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08451;SOR=Inf;LSEQ=CTCAATGATGCGATTCCACA;RSEQ=GGCTAAGAAGCAGGGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:106,261:0:2,0:25.7:1:30.4:1:1:0:60:182.5:1:0:0.1 0/1:288:3:1,2:70,214:0.0104:2,2:32.7:1:28.7:1:0.57517:1.53:60:6:0.0107:0:1.3 -12 49418788 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12867;SOR=Inf;LSEQ=TCTGCTCACTGACCTCCAGT;RSEQ=CCTAACCCCAATCCAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:14,146:0:2,0:22.4:1:30.4:1:1:0:60:21.857:1:0:0.2 0/1:90:2:1,1:12,76:0.0222:2,2:21.5:1:28:1:0.26941:6.12:60:4:0.0227:0:1 -12 49419677 . G C 33 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTAGGTTGGGTGAGGCA;RSEQ=ATGATAGTCTCAGAACTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:13.5:1:33.5:1:1:0:60:4:0.25:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 49421160 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17497;SOR=Inf;LSEQ=TCCTCATCTAACTAGCTCCC;RSEQ=CCTTCCCCTCACCCATATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:25,169:0:2,0:22.5:1:29.6:1:1:0:60:37.8:1:0:0.7 0/1:140:2:1,1:20,118:0.0143:2,2:20.5:1:27.5:1:0.27842:5.78:60:4:0.0149:0:1.5 -12 49421179 . G C 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTTCCCCTCACCCATAT;RSEQ=CCACCCTCCCAAAAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:135:135:7,128:0,0:1:0,2:25.6:1:31.4:1:1:0:60:134:1:0:1.1 1/1:93:93:5,88:0,0:1:0,2:24.7:1:30.7:1:1:0:60:30:1:0:1.1 -12 49421241 . CT C 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.13819;LSEQ=CCTCTTTTTTCTTTTCTTTT;RSEQ=TTTTTTTTTGAGACACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:0,2:7,50:0.0339:2,0:42.5:1:32:0:1:0:60:4:0.0351:0:0 0/1:26:1:0,1:1,24:0.0385:1,0:49:0:34:0:1:0:60:2:0.0385:0:0 -12 49421368 . G A 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04448;SOR=0;LSEQ=TCAGCCTTTCGAGTAGCTGG;RSEQ=ATTACAGGCACGCACCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:13,3:9,3:0.5714:2,2:30.5:1:30.4:1:1:1.43:60:32:0.5714:0:1.1 0/0:5:0:0,0:4,1:0:2,0:28:1:32.8:1:1:0:60:10:1:0:0 -12 49421427 . G A 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=TTTTTGTTTTTAGTAGAGAC;RSEQ=GGGTTTCGCCATGTTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:77,1:0:1,0:23:1:30:1:1:0:60:38:1:0:0.2 0/1:45:8:8,0:37,0:0.1778:1,0:27.4:1:30.8:1:1:0:60:16:0.1905:0:1 -12 49421535 . C T 73 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18065;SOR=3.26326;LSEQ=ATGTGAGCCACCGCGCCTGG;RSEQ=CGGCAGCCCCTTTTTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:2:1,1:317,132:0.0044:2,2:19.5:1:28.5:1:0.5033:2.39626:60:4:0.0045:0:2.5 0/1:488:7:2,5:321,160:0.0143:2,2:12.1:1:26.1:1:0.04686:4.99783:60:14:0.0147:0:1.1 -12 49422007 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1956;SOR=Inf;LSEQ=TACCAGCTGGGTGGGGACAA;RSEQ=GACACCTAGAACCCACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:4,124:0:1,0:23.2:1:31.3:1:1:0:60:41.667:1:0:0.2 0/1:102:2:0,2:4,96:0.0196:1,0:11:1:32:0:1:0:60:4:0.0202:0:1 -12 49422033 . T G 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04833;SOR=Inf;LSEQ=CTAGAACCCACTCCCCAGGG;RSEQ=AGTTCTATCCTATGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:2,87:0:1,0:24.9:1:27.9:1:1:0:60:43.5:1:0:0.3 0/1:52:3:0,3:0,49:0.0577:1,0:19.3:1:32.7:1:1:0:60:6:0.0588:0:1 -12 49422094 . A G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63785;SOR=0.4721;LSEQ=CTCACAGCAGCCTTTCCCAA;RSEQ=CTGCTGTGGGCACTGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:1,22:1,14:0.5897:1,1:24:1:33:1:1:1.55221:60:46:0.6053:0:1.1 0/1:5:2:0,2:0,3:0.4:0,0:36.5:1:34:0:1:0:60:4:0.4:0:1 -12 49422519 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20613;SOR=Inf;LSEQ=TAGGTACTCAGTACATGTGC;RSEQ=TGAACGACTACATTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:169,18:0:2,0:24.7:1:31:1:1:0:60:36.4:1:0:0.1 0/1:156:2:1,1:138,16:0.0128:2,2:23.5:1:26:1:0.2067:8.3964:60:4:0.0128:0:1 -12 49422795 . G A 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGCCTCTCCCCCAGCTTC;RSEQ=GACAACCCAGGTGAACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:258,258:0:2,0:22.8:1:30.1:1:1:0:60:45.909:1:0:0.1 0/1:431:41:20,21:190,200:0.0951:2,2:25.5:1:30.6:1:1:1.00:60:82:0.0967:0:1.1 -12 49422826 . A G 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGAACTGGGCCTGGCCCAC;RSEQ=TCCAGAGTAGCACATACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:0:0,0:313,250:0:2,0:25.5:1:30.3:1:1:0:60:79.429:1:0:0.1 0/1:465:25:13,12:232,206:0.0538:2,2:20.8:1:29.6:1:1:1.03951:60:50:0.0545:0:1.9 -12 49422857 . C T 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACATACCTGGGATGCTGGC;RSEQ=CGAGGAATGAGGGGGATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:751:0:0,0:413,338:0:2,0:25.2:1:30.6:1:1:0:60:34.762:1:0:0.1 0/1:627:38:18,20:313,276:0.0606:2,2:25.9:1:29.4:1:0.50713:1.25959:60:76:0.0615:0:1.6 -12 49423300 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09823;SOR=Inf;LSEQ=AGAAAAGTCAGGTGAGGGTG;RSEQ=CCAGGGCTGATGGTACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:66,241:0:2,0:23:1:31.4:1:1:0:60:22.615:1:0:0.2 0/1:264:3:2,1:65,195:0.0114:2,2:7.3:1:28.7:1:0.16056:5.95:60:6:0.0114:0:1 -12 49423328 . AT A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50542;SOR=0;LSEQ=TGATGGTACCTTCTCCCAAT;RSEQ=TTTAGGCCTAATTAGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:19,136:0.0126:2,2:14.5:1:25.5:1:0.23926:7.00:60:4:0.013:0.0063:1.5 0/0:125:0:0,0:21,103:0:2,0:25.7:1:29.9:1:1:0:60:248:0.992:0:0.1 -12 49423925 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16084;SOR=Inf;LSEQ=AAATCAGTCCTGAAAGGGCC;RSEQ=TTCCTACCTCAGGTGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:169,2:0:1,0:23.4:1:30.9:1:1:0:60:56:1:0:0.1 0/1:115:2:1,1:113,0:0.0174:1,2:38.5:1:30.5:1:0.01739:0:60:4:0.0177:0:1 -12 49424187 . C A 67 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36787;SOR=1.94321;LSEQ=GGGGGTGGGGTGGGGGGCAG;RSEQ=GACGAGGGTGGTGTCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:725:4:3,1:280,441:0.0055:2,2:2:1:26.5:1:0.30503:4.71:60:3:0.0043:0:1.5 0/1:656:7:5,2:289,359:0.0107:2,2:14:1:24.1:1:0.25241:3.10:57.7:6:0.0093:0:2.3 -12 49424230 . G A 48 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02562;SOR=Inf;LSEQ=TACTCAGGTTATTCTGAGGG;RSEQ=TGGGGGGTGGGGTGTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:189,154:0:2,0:19.2:1:29:1:1:0:59.7:7.167:1:0:0.8 0/1:323:5:5,0:176,140:0.0155:2,0:13:1:21:1:0.07077:0:60:1.5:0.0107:0:1.6 -12 49424259 . G T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19655;SOR=4.4477;LSEQ=GGGGTGTTGTGTGCAAGATG;RSEQ=CATAGGGAGACTGATATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:1:0,1:195,176:0.0027:2,0:18:0:14:0:0.47581:0:60:0:0:0:2 0/1:337:4:2,2:171,161:0.0119:2,2:27.8:1:29:1:1:1.06195:60:8:0.0127:0:1.3 -12 49424534 . G A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGATAGCAGGCTCCGTTAG;RSEQ=GGCAGCAGGGACAGCTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:828:0:0,0:383,445:0:2,0:26.4:1:31:1:1:0:60:68:1:0:0.2 0/1:670:32:12,20:296,342:0.0478:2,2:26.7:1:30.4:1:0.36686:1.44172:60:31:0.047:0:1.1 -12 49424616 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.3349;LSEQ=ATCGCTGTCTTGCACAGCTG;RSEQ=GGGACAGGGTGCCCCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:564:282:167,115:169,112:0.5:2,2:22.4:1:30.4:1:0.86367:1.03903:60:34.25:0.4946:0:1.1 0/1:379:95:62,33:155,129:0.2507:2,2:24.3:1:29.3:1:0.07327:1.56:60:46.5:0.248:0:1 -12 49424873 . TTCTG T 179 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0.02638;SOR=0.56915;LSEQ=CTCCTCAGAGCCCTCATCTC;RSEQ=TCTGACCCAGGCTCACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:58:23,35:186,296:0.1072:2,2:27:1:30.6:1:0.88725:1.05:60:57:0.1069:0.0074:0 0/1:391:25:9,16:122,244:0.0639:2,2:21.7:1:30.2:1:0.82782:1.12:59.8:50:0.0658:0.0128:0.2 -12 49425823 . AGCT A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.3244;SOR=1.65481;LSEQ=GCTGCATGAGGAGTGCCTGT;RSEQ=GCTGCTGCTGCTGAGGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:7:7,0:379,288:0.0104:2,0:26.4:1:31.9:1:0.02223:0:60:14:0.0105:0.0015:0.3 0/1:527:9:7,2:292,223:0.0171:2,2:22.4:1:31.9:1:0.3121:2.67:60:18:0.0173:0.0019:0 -12 49425978 . T C 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.4705;LSEQ=GGTCCTGGTTTGGGAGGTTG;RSEQ=GGCCCTGTATTATTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1407:520:231,289:390,492:0.3696:2,2:25.2:1:30.8:1:0.95565:1.01:60:73.286:0.3685:0:1.2 0/1:1189:257:121,136:446,485:0.2161:2,2:24.3:1:30.4:1:0.83265:1.03357:60:41.833:0.2136:0:1.2 -12 49426156 . G A 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07335;SOR=4.24025;LSEQ=GCCCATGGCTTCCTCCACCT;RSEQ=CTGTGTGGAGCAGGCTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:2:2,0:317,252:0.0035:2,0:11:1:18.5:1:0.50602:0:60:1:0.0018:0:2 0/1:408:6:6,0:216,186:0.0147:2,0:18.3:1:25.7:1:0.03374:0:60:12:0.015:0:1.5 -12 49426176 . TTGC T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.0116;SOR=Inf;LSEQ=GCTGTGTGGAGCAGGCTAAC;RSEQ=TGCTGCTGTTGTCCTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:584:0:0,0:357,227:0:2,0:24.4:1:30:1:1:0:60:82.429:1:0:0.1 0/1:408:5:3,2:242,161:0.0123:2,2:22:1:30:1:1:1.00207:60:10:0.0123:0.0025:0.4 -12 49426460 . A G 209 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=148.25166;LSEQ=ACCCAGGGCTCCAGGGCTAG;RSEQ=AAAGTGTTGAAGAGGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1363:1:0,1:729,631:7e-04:2,0:2:0:16:0:0.46436:0:60:0:0:0:1 0/1:1150:113:60,53:538,497:0.0983:2,2:24.7:1:30.7:1:0.84332:1.05:60:55.5:0.0976:0:1.3 -12 49426669 . AGCT A 79 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.33832;SOR=2.05471;LSEQ=GTTGCTGCTGCTGTTGTTGA;RSEQ=GCTGCTGCTGTTGCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:640:4:1,3:188,446:0.0063:2,2:25.3:1:30.5:1:1:1.26411:60:8:0.0064:0.0016:0.3 0/1:470:6:2,4:123,340:0.0128:2,2:21.3:1:30.8:1:0.65953:1.38:60:12:0.013:0.0043:1 -12 49426729 . AGCT A 134 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.85218;SOR=1.0751;LSEQ=GAAGTTGCTGTTGCTGTTGT;RSEQ=GCTGCTGCTGCTGCTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:17:7,10:189,228:0.039:2,2:29.4:1:33:1:0.8076:1.18375:60:34:0.04:0.0046:0 0/1:311:13:6,7:140,155:0.0418:2,2:23.2:1:29.2:1:1:1.0536:60:12:0.0391:0.0096:0.5 -12 49426771 . AGCT A 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=1;SOR=0.93295;LSEQ=GAAGTTGCTGTTGCTGTTGC;RSEQ=GCTGCTGCTGCTGAAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:13:6,7:275,201:0.0266:2,2:24.5:1:30.5:1:0.41105:1.5946:60:12:0.0248:0.0082:0.2 0/1:322:8:5,3:181,132:0.0248:2,2:30.4:1:32.4:1:1:1.21:60:16:0.0252:0:0 -12 49426905 . TTGC T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.26034;SOR=1.47748;LSEQ=CCTTGCTGTTGGTGCTGTTG;RSEQ=TGCTGCTGCTGCTGGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:781:18:7,11:358,403:0.023:2,2:24.6:1:30.5:1:0.63433:1.39537:60:36:0.0234:0:0.1 0/1:653:22:10,12:312,315:0.0337:2,2:25:1:29.6:1:0.829:1.18825:58.2:44:0.0345:0.0077:0.5 -12 49426908 . C T 92 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.00936;SOR=0;LSEQ=TGCTGTTGGTGCTGTTGTTG;RSEQ=TGCTGCTGCTGCTGGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:761:8:5,3:345,388:0.0105:2,2:17.1:1:30.8:1:0.48618:1.87:60:16:0.011:0:1.3 0/0:638:0:0,0:303,313:0:2,0:25.3:1:31.5:1:1:0:60:50.333:0.9983:0:0.2 -12 49426945 . A G 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGACCAGCCTGTGTCCC;RSEQ=TAAGGCCCTGACCCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:722:0:0,0:324,398:0:2,0:24.6:1:30.4:1:1:0:60:89.25:1:0:0.2 0/1:578:18:7,11:248,311:0.0311:2,2:23.8:1:29.9:1:0.81048:1.25262:60:36:0.0319:0:1.2 -12 49427265 . TTGC T 93 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.79963;SOR=1.17675;LSEQ=AGAAGGTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:9:3,6:230,341:0.0155:2,2:25.4:1:29.6:1:0.74656:1.3483:60:18:0.0156:0.0034:0 0/1:385:7:5,2:170,208:0.0182:2,2:17:1:28.2:1:0.25278:3.05:60:14:0.0183:0.0078:0.1 -12 49427652 . C T 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16072;SOR=0.84795;LSEQ=AGAGCCAGCACAGCTGAGTG;RSEQ=TGTTGCTGTTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:268:148,120:195,172:0.4149:2,2:24:1:29.2:1:0.62898:1.09:60:37.286:0.4136:0:1.2 0/1:578:217:118,99:202,158:0.3754:2,2:23.2:1:28.8:1:0.72959:1.07249:60:53.25:0.3763:0:1.2 -12 49427676 . C T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=0.94985;LSEQ=TGCTGTTGTTGCTGCTGCTG;RSEQ=TGCTGTTGTTGCTGCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:11:7,4:394,352:0.0145:2,2:19.5:1:30.9:1:0.55387:1.56:34:22:0.0147:0:2.7 0/1:724:10:7,3:367,344:0.0138:2,2:20.2:1:28.9:1:0.3438:2.18:36.2:9:0.0126:0:3 -12 49427679 . C T 127 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=3;SSF=0.01393;SOR=2.49672;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGTTGTTGCTGCTGCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:10:7,3:411,358:0.0128:2,2:29.1:1:29.7:1:0.3538:2.03:60:20:0.0131:0:1.7 0/1:731:23:13,10:365,343:0.0315:2,2:25.5:1:28.1:1:0.67698:1.22:60:22:0.0305:0:1.4 -12 49427684 . G T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10048;LSEQ=TTGCTGCTGCTGCTGCTGTT;RSEQ=TTGCTGCTGCTTGTTCCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:820:10:6,4:435,375:0.0122:2,2:11:1:30:1:0.75946:1.29:31.4:20:0.0123:0:2.9 0/1:746:10:6,4:376,360:0.0134:2,2:10.2:1:28.5:1:0.75297:1.44:36.2:9:0.0122:0:2.9 -12 49427687 . G A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=1.0912;LSEQ=CTGCTGCTGCTGCTGTTGTT;RSEQ=CTGCTGCTTGTTCCGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:834:9:6,3:441,384:0.0108:2,2:9.1:1:28.6:1:0.51567:1.74:28.2:18:0.0109:0:3.1 0/1:765:9:6,3:381,374:0.0118:2,2:9.2:1:27.7:1:0.50556:1.96:35.8:8:0.0107:0:3.1 -12 49427789 . C T 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=3e-05;SOR=8.84413;LSEQ=GGTCAGGCTGGGGCATGCTC;RSEQ=CCCCATGCCAACCCTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:896:3:1,2:494,398:0.0033:2,2:15.3:1:23.7:1:0.58932:2.47995:60:2:0.0023:0:1.7 0/1:727:21:11,10:389,316:0.0289:2,2:15.9:1:29:1:0.82688:1.11893:60:42:0.0294:0:1 -12 49427919 . T C 195 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=130.80951;LSEQ=AGCTTCTCAGCATCAGCTTC;RSEQ=GGGAACTCACGGCCAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1246:1:0,1:586,657:8e-04:2,0:7:0:8:0:1:0:60:0:0:0:5 0/1:998:95:47,48:443,459:0.0952:2,2:26.2:1:29.8:1:1:1.01:60:46.5:0.0943:0:1.2 -12 49428239 . G T 79 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01626;SOR=8.91072;LSEQ=GGGTTGGGACGAGGCTGGGA;RSEQ=GGATCACCAGCACTCCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:864:1:0,1:458,403:0.0012:2,0:1:0:28:0:0.46868:0:60:2:0.0012:0:1 0/1:782:8:3,5:397,377:0.0102:2,2:21.3:1:26.5:1:0.49649:1.75383:60:7:0.0091:0:1.3 -12 49428717 . G A 172 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01971;LSEQ=TCTGCAGCAAATTTGTCCAG;RSEQ=TCTGGAGAGGGGAGAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:748:57:23,34:229,462:0.0762:2,2:28.5:1:29.5:1:0.30744:1.36:60:13.25:0.0723:0:1.3 0/0:617:1:1,0:239,377:0.0016:2,0:1:0:24:0:0.38898:0:60:2:0.0017:0:1 -12 49428748 . C A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01125;SOR=Inf;LSEQ=GGAGAACCAAGTGAGCTGGG;RSEQ=TATGGGGCCAATGCTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:143,373:0:2,0:24.3:1:32:1:1:0:60:56.333:1:0:0.2 0/1:357:5:4,1:106,246:0.014:2,2:11:1:25:1:0.03296:9.22:60:10:0.0141:0:1.2 -12 49428841 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53593;SOR=0;LSEQ=AATGGCACGGCAAGGCAGAA;RSEQ=GACCACTGAATTAGGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:0,80:0.0244:1,0:32.5:1:32:1:1:0:60:4:0.0256:0:1.5 0/0:46:0:0,0:3,43:0:2,0:22.5:1:30.9:1:1:0:60:45:1:0:0.2 -12 49430855 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07263;SOR=Inf;LSEQ=CTAGCCTCAGTGCCCATTTA;RSEQ=GGATAACAATAATCACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:155,14:0:2,0:24:1:32:1:1:0:60:41.25:1:0:0.1 0/1:122:3:1,2:99,20:0.0246:2,2:16:1:26.3:1:0.08346:9.61997:60:6:0.0248:0:1 -12 49431301 . G A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.07056;SOR=Inf;LSEQ=CAGTAGGGAATGCTGCTGCT;RSEQ=CTGTTGCTGCTGCTGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:161,194:0:2,0:22.9:1:32.1:1:1:0:60:58.167:1:0:0.1 0/1:251:3:3,0:109,139:0.012:2,0:11.7:1:20.7:1:0.08752:0:60:2:0.0081:0:1.3 -12 49431305 . TTGC T 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0.86242;LSEQ=AGGGAATGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGGGCAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:5:3,2:159,183:0.0144:2,2:19.8:1:29.7:1:0.66757:1.72:60:10:0.0146:0.0086:0.2 0/1:241:3:1,2:106,130:0.0124:2,2:31.7:1:27.7:1:1:1.62757:60:6:0.0127:0:0 -12 49431654 . C T 213 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01494;LSEQ=CCATCCGGGTATCCCGGCTG;RSEQ=CCATCATGCTCTGTCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:914:148:81,67:411,355:0.1619:2,2:24.8:1:29.6:1:0.85721:1.04:60:36:0.1609:0:1.2 0/0:696:2:0,2:370,323:0.0029:2,0:1:0:23.5:1:0.21832:0:60:4:0.0029:0:1 -12 49432840 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09706;SOR=Inf;LSEQ=GCAAGAACATGGGCTTAGGG;RSEQ=AGTGAGGAAGGATAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:59,99:0:2,0:23.8:1:32.4:1:1:0:60:51.667:1:0:0.1 0/1:72:2:1,1:16,54:0.0278:2,2:35.5:1:26:1:0.41901:3.30:60:4:0.0282:0:1 -12 49433005 . C T 80 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0865;SOR=4.44264;LSEQ=GGAACCTCCTGGAGCCTCAC;RSEQ=GGCTGTTCACATCCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:725:2:0,2:434,288:0.0028:2,0:1:0:25:0:0.16011:0:60:4:0.0028:0:1 0/1:576:7:1,6:332,237:0.0122:2,2:5.9:1:28.6:1:0.04551:8.37784:60:14:0.0123:0:1 -12 49433406 . C CA 80 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.5014;SOR=0.50913;LSEQ=TCGTAGTCGCTGGCGCTATG;RSEQ=AAAAAAAAGAGAAGAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:7:5,2:277,120:0.0173:2,2:8.7:1:28.7:1:1:1.08:59.3:14:0.018:0.0124:1 0/0:225:2:2,0:136,87:0.0089:2,0:40:1:31:1:0.52357:0:60:4:0.0091:0:0 -12 49434074 . C A 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.53737;SOR=1.09242;LSEQ=GCGGGCAGGGCTGCTGGGAA;RSEQ=CCCCCAGCCCCCAGCGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:240:139,101:187,134:0.4255:2,2:23.4:1:30:1:1:1.01399:60:79:0.424:0:1.1 0/1:351:157:80,77:105,89:0.4473:2,2:24.9:1:29.1:1:0.59149:1.13512:60:156:0.4509:0:1.1 -12 49435057 . G T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.04005;SOR=Inf;LSEQ=AGGCACTTGGGCGGGCACCT;RSEQ=GGGTGGGAGCTTGAGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:241,233:0:2,0:24.3:1:31.3:1:1:0:60:93.8:1:0:0.1 0/1:386:4:2,2:182,199:0.0104:2,2:17:1:31.8:1:1:1.09:60:8:0.0105:0:1.3 -12 49435814 . C T 152 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=15.39109;LSEQ=GTCAGAGAAGACTTGGCAGG;RSEQ=GACTCCTCCACCTGCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:857:3:1,2:412,441:0.0035:2,2:13.7:1:26.7:1:1:1.86716:60:6:0.0036:0:1 0/1:662:34:18,16:303,324:0.0514:2,2:21.5:1:30:1:0.60334:1.20:60:68:0.0525:0:1.1 -12 49436066 . G T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02247;SOR=Inf;LSEQ=TGCCACCTGAGCCCGTCCAG;RSEQ=GGCTGTCGGGCTCACCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:72,296:0:2,0:24.2:1:31.3:1:1:0:60:121.667:1:0:0.1 0/1:234:4:2,2:60,170:0.0171:2,2:25.5:1:29.3:1:0.28643:2.82:60:8:0.0173:0:1.3 -12 49436153 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28775;SOR=0;LSEQ=AGTCACAGGGCGCAGGGATG;RSEQ=CAAGTCCCACCCCAGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:3:2,1:45,62:0.0273:2,2:18:1:30.7:1:0.57469:2.73:60:6:0.0283:0:1 0/0:68:0:0,0:28,40:0:2,0:23.9:1:31.2:1:1:0:60:21.667:1:0:0.1 -12 49436229 . G T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28906;SOR=0;LSEQ=AGAGGAGGGTCACTAACAAG;RSEQ=GAATGGGGAGGAGCAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:199,33:0.0128:2,2:12.3:1:29.3:1:0.37563:2.99531:60:6:0.0133:0:1 0/0:146:0:0,0:135,11:0:2,0:22.2:1:31.1:1:1:0:60:35.5:1:0:0.1 -12 49436235 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56394;SOR=3.11734;LSEQ=GGGTCACTAACAAGGGAATG;RSEQ=GGAGGAGCAGGGGAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:1,0:225,36:0.0038:2,0:30:0:12:0:1:0:60:0:0:0:2 0/1:169:2:1,1:152,15:0.0118:2,2:12:1:29.5:1:0.1809:9.8438:60:4:0.0121:0:1 -12 49436248 . G A 163 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGAATGGGGAGGAGCAGGG;RSEQ=AAGTGCTGCAGGAGTCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:46:41,5:226,54:0.1411:2,2:23.7:1:29.6:1:0.21623:1.96:60:22:0.1406:0:1.1 0/0:240:0:0,0:198,42:0:2,0:22.3:1:31:1:1:0:60:79:1:0:0.1 -12 49436724 . A G 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.44125;LSEQ=TCAGGTGACACCACAGGTCT;RSEQ=CAAATGATCATGGCCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:160:67,93:79,109:0.4598:2,2:24.4:1:32:1:1:1.00601:60:39:0.4548:0:1.1 0/1:231:63:28,35:65,103:0.2727:2,2:24.4:1:32:1:0.45372:1.27:60:126:0.2727:0:1 -12 49437399 . T G 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=GTTGGATTCTCTCACACCAC;RSEQ=CACTCCCACATAACTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:785:0:0,0:503,282:0:2,0:24.2:1:30.3:1:1:0:60:59.385:1:0:0.1 0/1:656:46:32,14:367,241:0.0701:2,2:30.5:1:29.2:1:0.27254:1.50:60:22:0.068:0:1.1 -12 49438164 . C T 174 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=85.61668;LSEQ=CGCACCACCCCACCACCCCA;RSEQ=AACCCCATCCCAGGACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1222:1:0,1:642,579:8e-04:2,0:1:0:24:0:0.47463:0:60:2:8e-04:0:1 0/1:1067:70:40,30:556,441:0.0656:2,2:23.3:1:28.4:1:0.90108:1.06:60:69:0.0653:0:1.2 -12 49438347 . T C 113 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-04;SOR=19.23849;LSEQ=ATGGAGGCAAATCAGAACTA;RSEQ=AGGCCCTTTTAACCTTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:1:0,1:67,239:0.0033:2,0:33:0:14:0:1:0:60:0:0:0:3 0/1:202:12:0,12:28,161:0.0594:2,0:23.7:1:31.7:1:0.38025:0:60:24:0.06:0:1 -12 49438415 . G A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04415;SOR=Inf;LSEQ=TGCCTCAGAGCCACTTAGAC;RSEQ=AGACAGCAGTGCTTAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:162,63:0:2,0:24.7:1:30.5:1:1:0:60:55.25:1:0:0.2 0/1:124:3:2,1:93,28:0.0242:2,2:30.7:1:29.3:1:0.55368:1.6531:60:6:0.0248:0:1 -12 49438490 . C A 221 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACTCCCAGAGTCACGCTCC;RSEQ=CCTACTCTGCCGCTCCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:181:127,54:281,149:0.2958:2,2:25.7:1:29.5:1:0.26034:1.25:60:44.25:0.294:0:1.1 0/0:556:0:0,0:359,196:0:2,0:23.3:1:29.9:1:1:0:60:38.643:0.9982:0:0.2 -12 49438500 . C T 81 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18274;SOR=0.31256;LSEQ=GTCACGCTCCCCCTACTCTG;RSEQ=CGCTCCCTAAGATTCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:7:2,5:440,253:0.01:2,2:21:1:29.1:1:0.10728:4.33842:60:14:0.0102:0:1 0/0:636:2:0,2:385,248:0.0031:2,0:12:1:24.5:1:0.15462:0:60:4:0.0032:0:1 -12 49438794 . G A 48 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37558;SOR=0.2741;LSEQ=TCCCTGGATGGAAGCCCCAG;RSEQ=GAAACCAGAACTGCAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:4:2,2:42,202:0.0161:2,2:17.8:1:24:1:0.14578:4.77:60:3:0.0123:0:1.5 0/0:225:1:1,0:43,181:0.0044:2,0:1:0:23:0:0.19556:0:60:2:0.0046:0:1 -12 49438807 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5848;SOR=2.55536;LSEQ=GCCCCAGGGAAACCAGAACT;RSEQ=CAAGTTTCAACCTATGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:1,0:19,177:0.0051:2,0:1:0:23:0:0.10152:0:60:2:0.0052:0:1 0/1:155:2:1,1:16,137:0.0129:2,2:7.5:1:27.5:1:0.20796:8.34:60:4:0.0131:0:1 -12 49439376 . A G 71 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAAAGCTTGCAATGTGCC;RSEQ=AGCTTGTGCCACTGCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:31.2:1:30.6:1:1:0:52.2:10:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 49439521 . A G 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27492;SOR=0.58313;LSEQ=CATTGCCCGGGAAGCTGGAG;RSEQ=CCTTGGTTCTAGGCATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:29:29,0:37,0:0.4394:1,1:23.7:1:31.8:1:1:0:60:58:0.4394:0:1 0/1:32:10:10,0:22,0:0.3125:1,0:15.7:1:30.9:1:1:0:60:20:0.3125:0:1.1 -12 49439659 . C T 291 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97299;LSEQ=GAGCTAGACTAGATGATGTC;RSEQ=GACGTCTGGTCTGGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:705:703:443,260:0,1:0.9972:0,2:26.3:1:30.8:1:0.37074:0:60:350.5:1:0:1.1 1/1:686:684:391,293:0,0:0.9971:0,2:26.1:1:30.5:1:1:0:60:113:0.9971:0:1.1 -12 49440635 . AT A 77 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.13196;SOR=0.19569;LSEQ=AAGAGGTAGAACTTCTTTTT;RSEQ=TTTTTTTTGGAGATGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:6:2,4:8,151:0.0364:2,2:26.3:1:29.8:1:0.04367:9.14:60:12:0.0375:0.0061:0.3 0/0:137:1:0,1:26,110:0.0073:2,0:40:0:32:0:1:0:60:2:0.0075:0:0 -12 49441376 . AT A 99 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTCAGCTAATTTTTGTT;RSEQ=TTTTTAGAAGAGACGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:0.9:0,0:22:1:31.4:1:1:0:60:18:0.9:0.3:0.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 49441898 . T A 43 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41306;SOR=2.57337;LSEQ=TGTCCAACTAGATCTCCCCA;RSEQ=CCCACTCAGATCCAGTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:2:1,1:103,343:0.0045:2,2:13:1:14:0:0.41079:3.32:60:0:0:0:1 0/1:351:4:3,1:90,257:0.0114:2,2:6.8:1:21.5:1:0.05855:8.50:60:3:0.0089:0:1 -12 49441959 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.14216;SOR=Inf;LSEQ=TTGCGACCAGAGTCAGGAAC;RSEQ=CCATCCCACAGCGTTAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:6,127:0:1,0:24.3:1:31.2:1:1:0:60:65.5:1:0:0.2 0/1:81:2:1,1:1,78:0.0247:1,2:35.5:1:29.5:1:0.04907:55.56:60:4:0.026:0:2 -12 49442356 . C CA 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.92943;SOR=1.03023;LSEQ=TCTCATTAGCTGGGTATCCC;RSEQ=AAAGTAGGTCCAGTTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:127:119,8:171,21:0.3981:2,2:28.1:1:29.9:1:0.17054:1.82:60:62.5:0.3968:0.0094:0.1 0/1:227:92:80,12:118,17:0.4053:2,2:23.7:1:30.1:1:1:1.04102:59.8:184:0.4144:0.1057:0.1 -12 49442511 . TTCC T 103 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.19544;SOR=2.17281;LSEQ=TGCATGGTGTCATCATCTTC;RSEQ=TCCTCCTCCTTACTGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:931:5:2,3:377,545:0.0054:2,2:16:1:31.6:1:1:1.03758:60:10:0.0055:0.0021:0 0/1:862:10:4,6:346,502:0.0116:2,2:17.5:1:31.2:1:1:1.03383:58:20:0.0118:0.0046:1.5 -12 49442561 . CAG C 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AATGTCAGCAACCTGATGGG;RSEQ=AGAGTTATGGAAAGTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:137,368:0:2,0:23.2:1:30.7:1:1:0:60:62.125:1:0:0.1 0/1:383:42:11,31:96,244:0.1097:2,2:23.9:1:31.9:1:0.85711:1.10851:60:84:0.1108:0.0052:0.3 -12 49442788 . A G 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05421;SOR=Inf;LSEQ=GACATAGCCAGACAGGCCCT;RSEQ=GACGAGCAGGCAGGTAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:185,17:0:2,0:26.1:1:28.2:1:1:0:60:66.333:1:0:0.5 0/1:124:3:2,1:105,16:0.0242:2,2:21.7:1:22.7:1:0.35998:3.23613:60:2:0.0165:0:2 -12 49442813 . T C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25388;LSEQ=AGCAGGCAGGTAGGCAAGCA;RSEQ=GCAAGGGACTGGCAGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:135:107,28:137,31:0.4426:2,2:22.9:1:31:1:0.66262:1.15591:60:66.5:0.4448:0:1.1 0/1:221:37:29,8:140,44:0.1674:2,2:24.5:1:29.8:1:0.83508:1.14:60:74:0.1713:0:1.2 -12 49443136 . GA G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49462;SOR=Inf;LSEQ=GAGTCCCACTCAGGGCAAGG;RSEQ=AAAGGCCAAACTCCCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:5,42:0:2,0:23.6:1:29.9:1:1:0:60:46:1:0:0.2 0/1:47:2:1,1:1,44:0.0426:1,2:21.5:1:29.9:1:0.08418:31.47:60:4:0.0444:0.0213:0 -12 49443666 . AC A 91 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.07376;SOR=3.28765;LSEQ=AACTCCATGGACAGGGAGCC;RSEQ=CCCCCTCCGGGTCTGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:948:3:0,3:447,498:0.0032:2,0:31.3:1:33:0:0.25164:0:60:6:0.0032:0:0 0/1:774:8:3,5:376,390:0.0103:2,2:22.5:1:30.5:1:0.72561:1.60587:60:16:0.0105:0.0026:0.6 -12 49444545 . G A 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09499;SOR=0.78386;LSEQ=GGTGGGGCCGCAGCTGTGAT;RSEQ=ATGGGTGAGAGTGGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:166:63,103:97,123:0.4301:2,2:25:1:29.1:1:0.25142:1.28847:60:54.333:0.4289:0:1.2 0/1:401:149:58,91:109,143:0.3716:2,2:28.2:1:28.8:1:0.404:1.19539:60:28.8:0.3673:0:1.3 -12 49444932 . CG C 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.21748;SOR=0.20272;LSEQ=ACAGATGCGATTCCTCAGGC;RSEQ=GGGGGACAGGCATGGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:5:3,2:212,282:0.01:2,2:25.2:1:31.2:1:0.6561:1.99:60:10:0.0101:0:0.2 0/0:492:1:0,1:218,270:0.002:2,0:17:0:31:0:1:0:60:2:0.0021:0:1 -12 49445028 . G A 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=10.896;LSEQ=CAGGCACAGGAGACAGGTGC;RSEQ=GCTCCTCAGTCTGGGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:556:2:2,0:304,249:0.0036:2,0:1:0:26:0:0.50438:0:60:4:0.0037:0:1 0/1:554:21:8,13:297,236:0.0379:2,2:22.5:1:30.1:1:0.12233:2.0424:60:20:0.0372:0:1.1 -12 49445780 . G A 209 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=75.35248;LSEQ=GCTTCAGGTGGCGGGGAAGT;RSEQ=GGCAATTCCTCAGGTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1920:2:1,1:921,996:0.001:2,2:4.5:1:20.5:1:1:1.08:60:1:5e-04:0:1 0/1:1934:141:67,74:863,925:0.0729:2,2:22.8:1:29.4:1:0.93029:1.03044:60:282:0.0737:0:1.2 -12 49446040 . C T 202 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=62.44615;LSEQ=TGCCTCAGGAAGTGGGGATG;RSEQ=GGGCAATTCCTCAGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1424:2:0,2:732,690:0.0014:2,0:1:0:25:0:0.23598:0:60:4:0.0014:0:1 0/1:1460:118:56,62:672,668:0.0808:2,2:24.2:1:29.4:1:0.63134:1.11369:60:117:0.0817:0:1.3 -12 49447715 . A T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32358;SOR=3.87753;LSEQ=AGTACAAAAATCCAAGGCAC;RSEQ=TTTGGTCTCTCATTTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:0,1:174,70:0.0041:2,0:1:0:25:0:0.2898:0:60:2:0.0041:0:1 0/1:192:3:0,3:145,44:0.0156:2,0:12.7:1:21.3:1:0.01396:0:60:2:0.0108:0:2.7 -12 49447863 . G A 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01587;SOR=Inf;LSEQ=GCAGGGGAAGTGGTAAAGCC;RSEQ=TGGACATCCAGGTGAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:0:0,0:241,257:0:2,0:24.6:1:30.8:1:1:0:60:123.5:1:0:0.1 0/1:541:7:3,4:242,291:0.0129:2,2:23.1:1:30.7:1:1:1.10858:60:14:0.0131:0:1.4 -12 49448463 . C T 177 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=70.11477;LSEQ=CAAATGGCAACTCAAAGCGC;RSEQ=GTAGCTCCCGCTGCCCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:1:0,1:378,504:0.0011:2,0:2:0:28:0:1:0:60:2:0.0011:0:1 0/1:895:66:27,39:408,421:0.0737:2,2:23:1:29.4:1:0.20312:1.39931:60:32:0.0726:0:1.1 -12 49448590 . G A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0459;SOR=Inf;LSEQ=CCCAGCAACCCCATGATCTG;RSEQ=CATGCCCATGCTTCCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:158,229:0:2,0:24.9:1:31.6:1:1:0:60:47.375:1:0:0.1 0/1:335:4:3,1:129,202:0.0119:2,2:14.5:1:26.5:1:0.30426:4.68:60:8:0.0122:0:1.3 -12 50412621 . AT A 33 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAACCTGTTCTCTTGTCC;RSEQ=TTTTTTTTTTTTAATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,0:0.3333:0,0:44:1:33:0:1:0:60:4:0.3333:0:0 0/0:1:0:0,0:1,0:0:0,0:31:0:31:0:1:0:60:2:1:0:0 -12 50412911 . C A 270 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.24511;LSEQ=CCTCTGGTTCCTCCCCTTCC;RSEQ=ACAGCATAATCACTAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:612:571:301,270:21,19:0.933:2,2:27.1:1:29.9:1:1:1.01:60:46.583:0.9317:0:1.1 1/0:763:590:289,301:90,81:0.7733:2,2:27.2:1:29.4:1:0.43466:1.15702:60:52.636:0.773:0:1.2 -12 50412969 . C G 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTATCTACCATACCCACCC;RSEQ=CTTATCACTTGCAGGTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:162,269:0:2,0:24.8:1:30.9:1:1:0:60:85.2:1:0:1 0/1:525:45:22,23:177,303:0.0857:2,2:28.6:1:30.7:1:0.14729:1.64:60:90:0.0865:0:2 -12 50413015 . T G 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACTTCAATTGCACTCCCT;RSEQ=CCTCCAGTCCTTCCCCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:217:217:52,165:0,0:1:0,2:24.5:1:31.8:1:1:0:60:53.25:1:0:1.1 1/1:250:250:67,183:0,0:1:0,2:22.5:1:31.4:1:1:0:60:61.5:1:0:1.2 -12 50413034 . C A 96 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01599;SOR=0.1107;LSEQ=TTCCTCCAGTCCTTCCCCTA;RSEQ=TGCTTCAGGCAGTTGCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:8:0,8:19,129:0.0513:2,0:24:1:32:1:0.59685:0:60:16:0.0513:0:2.1 0/0:169:1:1,0:29,139:0.0059:2,0:1:0:25:0:0.17751:0:60:2:0.0059:0:2 -12 50479374 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=CGCGGGCCGGGGGCGGGGCC;RSEQ=AGCGGGGACATGGGAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:51,137:0.0105:2,2:39.5:1:30.5:1:0.47352:2.67:60:4:0.0108:0:3 0/0:177:0:0,0:48,129:0:2,0:25.1:1:29.9:1:1:0:60:34.4:1:0:0.3 -12 50479408 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50505;SOR=0;LSEQ=GAGTGACAGGGGTGGGGGGA;RSEQ=AAGTAGGAGGGACTCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:5,96:0.0192:1,2:16:1:28.5:1:0.11365:17.61:60:4:0.0211:0:3 0/0:81:0:0,0:6,75:0:2,0:21.6:1:29.8:1:1:0:60:10.571:1:0:0.5 -12 50479935 . C T 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.07888;LSEQ=GACATCTCTGGGTCCTCTCC;RSEQ=CTCTGTAGAGACCAGGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:39:24,15:477,338:0.0457:2,2:26.2:1:31.1:1:0.74247:1.13:60:78:0.046:0:1.1 0/1:825:106:58,48:402,317:0.1285:2,2:25.1:1:29.4:1:0.83462:1.04947:60:105:0.1288:0:1.1 -12 50480150 . AGAGG A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=4.000;MSILEN=4;SSF=0.53964;SOR=0.7616;LSEQ=AAGTAAGATGATCCTGGGGC;RSEQ=GAGGGAGGGAGGGAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:13:3,10:101,246:0.0358:2,2:29.8:1:32.2:1:0.76408:1.3675:60:26:0.0364:0:0.1 0/1:400:11:2,9:138,251:0.0275:2,2:28.1:1:31:1:0.34193:2.46939:60:22:0.0277:0.0025:0.1 -12 50480262 . T TTGGTGGTGGTGGTGGTGGTGG 129 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=14.000;MSILEN=3;SSF=0.00472;SOR=0.24547;LSEQ=GAACTCATCCTTGAGAATGC;RSEQ=TGGTGGTGGTGGTGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:20:6,14:13,28:0.2041:2,2:22.4:1:30:1:1:1.08195:58.3:40:0.2151:0.0918:0.5 0/1:85:5:4,1:17,21:0.0588:2,2:42.2:1:25.3:1:0.18528:4.77:52:10:0.0602:0:0.6 -12 50480308 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2032;SOR=Inf;LSEQ=TCTTTGAGAGAAGCTTTGCA;RSEQ=TCCCTTCACATTACTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:124,35:0:2,0:21.4:1:32:1:1:0:59.7:158:1:0:0.1 0/1:131:2:1,1:102,27:0.0153:2,2:31.5:1:30.5:1:0.38309:3.728:57.5:4:0.0155:0:1 -12 50480699 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20218;SOR=Inf;LSEQ=TAGGCAGAGAGCCAAAGGAG;RSEQ=GGACCCAGGAACCTTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:26,168:0:2,0:21.7:1:30.7:1:1:0:60:47.5:1:0:0.2 0/1:159:2:1,1:27,130:0.0126:2,2:13:0:31.5:1:0.32211:4.75:60:4:0.0126:0:2 -12 50482211 . T C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15497;LSEQ=AGATATTTTTTGAGTTTTTT;RSEQ=CCATTGTTGTTGGGGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:118:79:77,2:38,1:0.6695:1,1:22.3:1:30.9:1:1:1.01:60:25.333:0.6609:0:1.1 0/1:97:23:22,1:71,3:0.2371:1,1:22.3:1:31.3:1:1:1.07494:60:46:0.2396:0:1.2 -12 50482230 . CT C 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.57541;SOR=2.75615;LSEQ=TTCCATTGTTGTTGGGGTTC;RSEQ=TTTTCATAGGATTTTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:1,0:170,17:0.0053:2,0:12:0:32:0:1:0:60:2:0.0054:0:0 0/1:138:2:1,1:125,11:0.0145:2,2:23.5:1:33:1:0.16693:10.92357:60:4:0.0145:0:0 -12 50482247 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19109;SOR=Inf;LSEQ=TTCCTTTTTCATAGGATTTT;RSEQ=TCTTGGGAAGTTTCTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:206,38:0:2,0:24.1:1:32:1:1:0:60:121:1:0:0.3 0/1:190:2:1,1:142,46:0.0105:2,2:31:1:28.5:1:0.43453:3.06455:60:4:0.0107:0:1.5 -12 50482261 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09287;SOR=Inf;LSEQ=GATTTTGTCTTGGGAAGTTT;RSEQ=TTCTGGCCTTTCCTAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:248,77:0:2,0:24.7:1:31.1:1:1:0:60:45.429:1:0:0.3 0/1:270:3:1,2:173,94:0.0111:2,2:12:1:29.7:1:0.28862:3.66211:60:6:0.0114:0:1 -12 50483610 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24839;SOR=Inf;LSEQ=AGTCATTACAGAAGCTCTTC;RSEQ=CTCCCACCCCAGCTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:205,27:0:2,0:21.7:1:31.1:1:1:0:60:45.4:1:0:0.1 0/1:233:3:1,2:190,40:0.0129:2,2:20:1:26.7:1:0.08454:9.36179:60:6:0.0129:0:1 -12 50484013 . G A 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTCATCCCCTATACTTTG;RSEQ=TTCCCTGCAGCCTCCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:0:0,0:470,311:0:2,0:26:1:31.4:1:1:0:60:54.786:0.9987:0:0.1 0/1:785:59:38,21:407,318:0.0752:2,2:23.7:1:29.1:1:0.27421:1.41:60:118:0.0768:0:1.1 -12 50484405 . C T 186 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTGGGAGGCAGTGCTGTGC;RSEQ=GGAGCTGCCTTGTGCCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:72:15,57:56,206:0.2149:2,2:26.2:1:30.2:1:1:1.03291:60:35:0.2121:0:1.2 0/0:352:0:0,0:112,239:0:2,0:21.3:1:29.1:1:1:0:60:57.5:0.9971:0:0.1 -12 50484460 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=GTCAAATTTTCAGGAATTTT;RSEQ=CAAACAGGTTGTTAAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:2,113:0.0169:1,0:19:1:32:0:1:0:60:4:0.0172:0:1 0/0:107:0:0,0:5,102:0:1,0:25.1:1:32.2:1:1:0:60:106:1:0:0 -12 50484603 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TTACATTTTATTGTATTTGT;RSEQ=CTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:7:1:29.5:1:1:0:60:4:0.4:0:1.5 0/0:3:0:0,0:0,3:0:0,0:14:1:31:1:1:0:60:6:1:0:0.3 -12 50485350 . G T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACAGGCGTGAGCCACCGC;RSEQ=CCCGGCCTTTTGTTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39.5:1:31:0:1:0:60:4:1:0:1 -12 50488458 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13004;SOR=Inf;LSEQ=TCAAAATACGGTGACACCCA;RSEQ=TATATGTCAGGTACTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:1,124:0:1,0:22.9:1:32:1:1:0:60:61.5:1:0:0.1 0/1:71:2:0,2:1,68:0.0282:1,0:11:1:27.5:1:1:0:60:4:0.029:0:1.5 -12 50488547 . G A 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90182;LSEQ=TCTCAACAGCACTGAGCCTC;RSEQ=GTTTCTGATTTGTGGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:0,4:0,36:0.1:1,0:23.8:1:31.8:1:1:0:60:8:0.1053:0:1 0/1:11:1:0,1:0,10:0.0909:0,0:4:0:32:0:1:0:60:2:0.0909:0:1 -12 50490554 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19705;SOR=Inf;LSEQ=TAGGTTGGAAGTGGCATGTG;RSEQ=AGTTGTCAGGCACCACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:142,29:0:2,0:21.8:1:30.8:1:1:0:60:41.75:1:0:0.1 0/1:137:2:1,1:110,25:0.0146:2,2:30:1:27.5:1:0.34468:4.33413:60:4:0.0148:0:1 -12 50492873 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09705;SOR=Inf;LSEQ=TATCTGCCTTGGTCTTGCTT;RSEQ=GGGCGTTCCAGGGGATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:53,261:0:2,0:22.5:1:31:1:1:0:60:61.8:1:0:0.1 0/1:268:3:1,2:63,202:0.0112:2,2:14.7:1:29.7:1:0.56051:1.60:60:6:0.0115:0:1 -12 50492911 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50232;SOR=0;LSEQ=CTGTTGGTTCAAGGACAACA;RSEQ=CAGAATGAAGAGGGTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:3,145:0.0133:1,2:15.5:1:29:1:0.0528:42.03:60:4:0.0134:0:1 0/0:125:0:0,0:6,119:0:1,0:25.8:1:31:1:1:0:60:40.667:1:0:0.1 -12 51491761 . G A 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCGAGATCACACCACC;RSEQ=CACAACAGCCTGGGCGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:32:0:1:0:60:4:1:0:1 -12 51493260 . CAA C 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAGAATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:2,0:0.3333:0,0:21.5:1:32.5:1:1:0:60:4:0.3333:0:0 0/0:1:0:0,0:1,0:0:0,0:19:0:32:0:1:0:60:2:1:0:0 -12 51493439 . G T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10351;SOR=0;LSEQ=TGTGTCCAGAACAACCTACC;RSEQ=AAGAAAGTACCATTTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:1,2:90,39:0.0227:2,2:5:1:27:1:0.22762:4.5556:60:6:0.0233:0:1 0/0:148:0:0,0:103,45:0:2,0:21.9:1:29.8:1:1:0:60:147:1:0:0.1 -12 51493511 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26971;SOR=Inf;LSEQ=TGCTGTTGTTGCTGCTCCCT;RSEQ=AACTGCAGTGATTCCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:87,121:0:2,0:27.5:1:31.7:1:1:0:60:103:1:0:0.1 0/1:292:3:2,1:127,162:0.0103:2,2:25.7:1:28.3:1:0.58529:2.54:60:6:0.0104:0:1 -12 51493543 . T A 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.4628;LSEQ=TTCCTGACAAACATAAATGG;RSEQ=TAACCTTGGACGCACCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:1:1,0:40,94:0.0074:2,0:1:0:26:0:0.3037:0:60:2:0.0074:0:1 0/1:185:2:1,1:60,123:0.0108:2,2:14.5:1:24.5:1:0.55194:2.04:60:4:0.011:0:1 -12 52401452 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16844;SOR=Inf;LSEQ=AAGGTCCGAGAGCCCCCGGT;RSEQ=GGAGAAGCGGGCCGGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:22,6:0:2,0:20.4:1:31.1:1:1:0:60:27:1:0:0.1 0/1:20:2:2,0:12,6:0.1:2,0:11:1:26.5:1:1:0:60:4:0.1:0:1 -12 52401505 . G C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50695;SOR=0;LSEQ=TTCTCACTCTGAGGAAGTGC;RSEQ=TGGGGAGCCGCTGACTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:32,31:0.0308:2,2:16:0:33.5:1:1:1.03176:60:4:0.0308:0:1.5 0/0:48:0:0,0:25,23:0:2,0:27.6:1:30.5:1:1:0:60:96:1:0:0.2 -12 52906415 . C A 112 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00024;SOR=0.0165;LSEQ=TTACTCTCCAGCCTGGGCAA;RSEQ=AATAGCAAAACTCTGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:12,0:1,0:0.9231:0,0:22.6:1:31.3:1:1:0:55.4:24:0.9231:0:2.4 0/1:9:1:1,0:8,0:0.1111:0,0:18:0:32:0:1:0:60:2:0.125:0:2 -12 52906434 . G A 77 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=0.02121;SOR=0;LSEQ=ACAATAGCAAAACTCTGTAG;RSEQ=AAAAAAAAAAAAAACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:15,0:0.2857:1,2:10.5:1:30:1:0.07143:0:54.2:12:0.3529:0:3.8 0/0:19:0:0,0:15,2:0:2,0:16.5:1:28.7:1:1:0:56.5:4.667:0.875:0:1.2 -12 52906449 . C A 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTAGGAAAAAAAAAAAAAA;RSEQ=AAAAAACCAGAGTGCTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:4,0:0:0,0:15.8:1:33:1:1:0:60:8:1:0:0 0/1:40:19:15,4:14,7:0.475:2,2:10.6:1:28.2:1:0.48824:1.85:55.5:8.5:0.4857:0:2.6 -12 52906524 . CA TG 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07224;LSEQ=GCTGCTGTTGCTCCTGTTGC;RSEQ=CCGCTGCCGCTGCCTATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:142:112:46,66:15,11:0.7887:2,2:30.3:1:31.2:1:0.1324:1.94686:60:224:0.8116:0.007:2.4 0/1:100:21:12,9:36,43:0.21:2,2:30:1:31.1:1:0.46193:1.59:60:42:0.2121:0:2.3 -12 52906525 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=17.52819;LSEQ=CTGCTGTTGCTCCTGTTGCC;RSEQ=CCGCTGCCGCTGCCTATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:7:5,2:13,10:0.0493:2,2:19.9:1:27.4:1:0.66932:1.88:60:6:0.2069:0:2.6 0/1:98:47:18,29:14,14:0.4796:2,2:27.3:1:30.4:1:0.34494:1.60068:59.9:22.5:0.6164:0:1.4 -12 52906534 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15266;SOR=Inf;LSEQ=CTCCTGTTGCCACCGCTGCC;RSEQ=CTGCCTATGCCTCTGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:61,77:0:2,0:27.7:1:30.7:1:1:0:60:276:1:0:2.1 0/1:89:2:1,1:36,50:0.0225:2,2:17.5:1:28.5:1:1:1.38:60:4:0.0233:0:1 -12 52906536 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0;SOR=0.07505;LSEQ=CCTGTTGCCACCGCTGCCGC;RSEQ=GCCTATGCCTCTGTTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:136:110:46,64:13,12:0.8088:2,2:27.5:1:29.7:1:0.37929:1.50257:60:220:0.8088:0:2.5 0/1:84:20:11,9:23,41:0.2381:2,2:26.9:1:29.7:1:0.19144:2.16:60:40:0.2381:0:2.5 -12 52906545 . C T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16033;SOR=0;LSEQ=ACCGCTGCCGCTGCCTATGC;RSEQ=TCTGTTACCAGAAAAGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:5:1,4:53,70:0.0388:2,2:31:1:30.8:1:0.39615:3.00602:60:10:0.0394:0:1 0/0:75:0:0,0:30,45:0:2,0:24.3:1:31.2:1:1:0:60:150:1:0:1.2 -12 52906586 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0059;SOR=0.23455;LSEQ=TCATCCTCCGGGTTATAGGA;RSEQ=AAAACACACATGGCACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:37:2,35:0,8:0.8222:0,2:21:1:30.2:1:1:0:60:36:0.8372:0:2.5 1/0:33:17:2,15:4,12:0.5152:2,2:20.1:1:30:1:0.39832:2.4317:60:34:0.5152:0:2.2 -12 52906763 . G C 33 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=CCACAAGAAAGATAGAGAGA;RSEQ=AGAGAGAAACCTGAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:7.5:1:33:0:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:44:0:33:0:1:0:60:2:1:0:0 -12 52921215 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=27.81327;LSEQ=TCAGCAGAGGCCTCAACCTC;RSEQ=GGATAGTCTGTGAAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:53:37,16:173,100:0.1626:2,2:26:1:30.5:1:0.43432:1.34:60:52:0.161:0:1.9 1/1:213:180:111,69:19,14:0.8451:2,2:27.6:1:30.1:1:0.69995:1.18:60:59:0.8429:0:1.8 -12 52921279 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.06662;LSEQ=ACTCAGCAGTCAGTATACCA;RSEQ=AACATCTTCCAGCAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:76:33,43:171,206:0.1678:2,2:28.1:1:31.7:1:0.8012:1.08142:60:37:0.1663:0:2.4 1/1:323:264:125,139:29,30:0.8173:2,2:26.1:1:31.2:1:0.88555:1.07468:60:87:0.8156:0:2.3 -12 52921294 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=19.83049;LSEQ=TACCATAACATCTTCCAGCA;RSEQ=CCCCAAGAGAGAGGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:74:28,46:147,199:0.1762:2,2:26.5:1:30.2:1:0.51685:1.21301:60:148:0.1775:0:2.3 1/1:274:222:99,123:24,27:0.8102:2,2:27.2:1:29.2:1:0.7575:1.10397:60:110:0.8118:0:2.3 -12 52921297 . C A 152 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATAACATCTTCCAGCAGCC;RSEQ=CAAGAGAGAGGGACCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:34:12,22:156,219:0.0831:2,2:29.7:1:30:1:0.58576:1.3051:60:68:0.0848:0:1.2 0/0:272:0:0,0:121,151:0:2,0:26.6:1:30.2:1:1:0:60:67:1:0:1.8 -12 52921334 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14361;SOR=Inf;LSEQ=CTGCCCTGGAGTATAGACAG;RSEQ=GGAGGTGCCCTTGGAGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:76,167:0:2,0:23.6:1:30.8:1:1:0:60:120.5:0.9918:0:0.5 0/1:150:2:1,1:43,105:0.0133:2,2:14:1:27.5:1:0.50201:2.43:60:4:0.0133:0:2 -12 53030453 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.50212;SOR=0;LSEQ=ATCTTTTCCCAGCAGCAGCA;RSEQ=CAGCAACAGCAACAGCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:75,62:0.0144:2,2:28:1:31:1:1:1.20801:60:4:0.0144:0:1 0/0:116:0:0,0:59,57:0:2,0:27.5:1:29.9:1:1:0:60:115:1:0:0.2 -12 53030489 . C T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CACGGGTATCATGTATTGCC;RSEQ=GATTATTGTGTTTCACAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:18:7,11:35,54:0.1682:2,2:27.6:1:29.5:1:1:1.01835:60:17:0.1635:0:1 0/0:92:0:0,0:39,53:0:2,0:26.6:1:29.4:1:1:0:60:91:1:0:0.3 -12 53030543 . T C 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24578;SOR=3.87584;LSEQ=AAAGATAATCTCCTTTAATC;RSEQ=CCACAACAGTACTATGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:35:1,34:0,6:0.8537:0,1:25.1:1:31.4:1:1:0:60:34:0.85:0:1.1 1/1:24:23:2,21:0,1:0.9583:0,2:22.2:1:31.2:1:1:0:60:46:0.9583:0:1 -12 53129862 . T C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTGCCCCCTGTCACGGCA;RSEQ=AGGCCGCAGCAGCACTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28.5:1:33.5:1:1:0:60:4:1:0:1.5 1/1:1:1:0,1:0,0:1:0,0:33:0:34:0:1:0:60:2:1:0:1 -12 53130248 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28215;SOR=0;LSEQ=CTGACATTGGCCTCATTTTT;RSEQ=CTTCACCAGATCCAAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:1,2:141,40:0.0163:2,2:12:1:27.7:1:0.13094:6.95219:60:6:0.0168:0:1 0/0:119:0:0,0:87,32:0:2,0:25.4:1:30.6:1:1:0:60:58.5:1:0:0.2 -12 53130297 . G T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08243;SOR=Inf;LSEQ=TTAGGCTCCCTACAATGGAT;RSEQ=GGCTGCTTCCTACTGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:201,152:0:2,0:25:1:31.1:1:1:0:60:38.222:1:0:0.4 0/1:273:3:0,3:164,106:0.011:2,0:16:1:22:1:0.06259:0:60:2:0.0075:0:2.7 -12 53130344 . G A 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.11134;LSEQ=CAAACATCAGGGCATTTGCT;RSEQ=TAATTAGGTGATTTTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:213:97,116:117,134:0.4591:2,2:24.3:1:29.8:1:0.85196:1.04409:60:212:0.4599:0:1.1 1/0:338:217:103,114:64,56:0.642:2,2:27.9:1:28.4:1:0.30858:1.26402:60:42.4:0.6366:0:1.1 -12 53130451 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13771;SOR=Inf;LSEQ=AAATATTCACAGGAGACCTT;RSEQ=TCTCAGTTAATTGTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:20,91:0:2,0:20.5:1:31.8:1:1:0:60:110:1:0:0.1 0/1:66:2:1,1:7,57:0.0303:2,2:21.5:1:26.5:1:0.22937:7.68:60:4:0.0303:0:1 -12 53130531 . T C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21603;SOR=4.82289;LSEQ=CATCCACTGCGGTGGGGTCC;RSEQ=CGGGATGCAGGGGCCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:23:1,22:0,19:0.5476:1,1:24.7:1:32.3:1:1:0:60:46:0.5476:0:1 1/1:7:6:0,6:0,1:0.8571:0,0:22.7:1:32.5:1:1:0:60:12:0.8571:0:1 -12 53130533 . G A 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACTGCGGTGGGGTCCTC;RSEQ=GGATGCAGGGGCCATCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:0,5:1,33:0.1282:1,0:34.2:1:32.4:1:1:0:60:10:0.1282:0:1 0/0:7:0:0,0:0,7:0:0,0:19.6:1:31.7:1:1:0:60:14:1:0:0.9 -12 53607024 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGCTCCTCCAGGTCCATG;RSEQ=GGTCTATGGGGACAAGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:9.5:1:32:1:1:0:60:4:1:0:0.5 0/1:10:2:1,1:2,6:0.2:2,2:21.5:1:30:1:1:2.65:60:4:0.2222:0:1.5 -12 53609418 . C A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50121;SOR=Inf;LSEQ=CCCCCGTCTGCCCACTCCCA;RSEQ=CACGTACACACCTTGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:34,24:0:2,0:24.3:1:31.5:1:1:0:60:116:1:0:0.2 0/1:71:2:1,1:38,31:0.0282:2,2:14:0:27.5:1:1:1.22227:60:4:0.029:0:1 -12 53609436 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22289;SOR=0;LSEQ=CACCACGTACACACCTTGCA;RSEQ=CCTTCACAAGAGCTGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:34,28:0.0313:2,2:28:1:28.5:1:1:1.21058:60:4:0.0317:0:1 0/0:71:0:0,0:41,30:0:2,0:32.2:1:31.6:1:1:0:60:70:1:0:0.2 -12 53858379 . CT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.51087;SOR=0;LSEQ=TGAAATCTGCCACTAGGTAA;RSEQ=TTTTTTTTTAATTCACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:13,0:0.1333:1,0:14.5:1:33.5:1:1:0:60:4:0.1333:0:0 0/0:9:0:0,0:9,0:0:0,0:26.2:1:30.6:1:1:0:60:18:1:0:0 -12 53858460 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50153;SOR=Inf;LSEQ=GGAAAAAGGAAAAAAATAAA;RSEQ=AACTTTTTTTGTGTGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:45,10:0:2,0:16.9:1:31.2:1:1:0:60:17.333:1:0:0.1 0/1:68:2:1,1:55,11:0.0294:2,2:21.5:1:28.5:1:0.32397:4.83054:60:4:0.0303:0:1 -12 53858463 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=7.000;MSILEN=1;SSF=1;SOR=1.55053;LSEQ=AAAAGGAAAAAAATAAACAA;RSEQ=TTTTTTTGTGTGAATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:1:1,0:44,12:0.0175:2,0:17:0:20:0:1:0:60:2:0.0182:0:2 0/1:74:2:1,1:57,15:0.027:2,2:23:1:28.5:1:0.388:3.71165:60:4:0.027:0:1 -12 53858514 . TG T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51072;SOR=Inf;LSEQ=AGGTGCCGGATTGACAGCCC;RSEQ=GAGACTGAAATCCTCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:70,56:0:2,0:29.6:1:30.9:1:1:0:60:24.2:1:0:0.1 0/1:173:2:1,1:93,78:0.0116:2,2:44:1:30.5:1:1:1.19109:60:4:0.012:0:0 -12 53858548 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51465;SOR=Inf;LSEQ=CTCTATTTATCCACAGGACA;RSEQ=GTACAGCACAGGCAGCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:45,67:0:2,0:26.6:1:30.9:1:1:0:60:36.333:1:0:0.1 0/1:163:2:1,1:69,92:0.0123:2,2:26:1:29:1:1:1.33:60:4:0.0124:0:1 -12 53877562 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTTCACCTAGGGCCATAA;RSEQ=AGATCTCAGTCTCAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:29:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:19:1:29:1:1:0:60:4:1:0:1 -12 53878882 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24151;SOR=Inf;LSEQ=TGAAACCATCTGGGCAACTG;RSEQ=AGGGCACGGGCAGATGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:75,29:0:2,0:22.4:1:30.6:1:1:0:60:25:1:0:0.2 0/1:101:2:1,1:68,31:0.0198:2,2:36:0:31:1:0.53545:2.17486:60:4:0.02:0:1.5 -12 53878911 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23719;SOR=0;LSEQ=GGCAGATGGAGACTGTTGCT;RSEQ=CCCACACCCCAGATAATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:96,62:0.0125:2,2:42.5:1:32:1:1:1.54398:60:4:0.0129:0:1.5 0/0:168:0:0,0:97,71:0:2,0:24.7:1:29.1:1:1:0:60:55:1:0:0.1 -12 53878931 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49885;SOR=0;LSEQ=TCCCACACCCCAGATAATGG;RSEQ=TGAGGAATCTACGTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:102,89:0.0104:2,2:32.5:1:29:1:1:1.14525:60:4:0.0108:0:1 0/0:186:0:0,0:97,89:0:2,0:28.5:1:31.7:1:1:0:60:92:1:0:0.2 -12 53879009 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50103;SOR=0;LSEQ=GCCAAAGGACCTAGGGATGA;RSEQ=GGGACATCACTTGTGCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:11,60:0.0274:2,2:15.5:1:29:1:0.30365:5.27:60:4:0.0278:0:1.5 0/0:60:0:0,0:10,50:0:2,0:21.7:1:29.7:1:1:0:60:29:1:0:0.2 -12 54338916 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.05782;SOR=Inf;LSEQ=GTTCATCACCAAAGAGAAGC;RSEQ=CCGGCGCATCTCCGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:222,73:0:2,0:22.7:1:29.7:1:1:0:60:31.778:1:0:0.1 0/1:187:3:1,2:120,64:0.016:2,2:11:1:23.7:1:0.28468:3.72213:60:6:0.0165:0:1 -12 54339029 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.15368;SOR=Inf;LSEQ=AATCGAAAGCGCCTCATCTC;RSEQ=ACTCCACCTGACCACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:38,183:0:2,0:24.2:1:32.1:1:1:0:60:109.5:1:0:0.3 0/1:143:2:1,1:35,106:0.014:2,2:26:1:29.5:1:0.44145:3.00:60:4:0.0141:0:1 -12 54339052 . C A 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.28516;SOR=1.35622;LSEQ=TCCACCTGACCACCCACCCG;RSEQ=TGCTTGCCCCATCTATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:66:4,62:4,78:0.4459:1,2:23.4:1:31.1:1:1:1.26:60:132:0.449:0:1 1/0:90:47:6,41:2,41:0.5222:1,2:22.6:1:29.4:1:0.27046:2.97:60:46:0.5169:0:1.1 -12 54340765 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGCTCTATTGCCCCAGAG;RSEQ=GCCCCGAATACCTTCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:48.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 54943389 . CGCG C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.48988;SOR=0;LSEQ=AGGAGGCGGCTCTGGCAGCG;RSEQ=GCGGCGGCGGCGGTAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:0.0952:2,2:29:1:32.5:1:1:1.10554:60:4:0.0952:0:0.5 0/0:18:0:0,0:8,10:0:2,0:31.6:1:29.2:1:1:0:60:17:1:0:0.5 -12 55213743 . AA GG 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTCATTTAGAAACCTC;RSEQ=GCAGAGGGTTTGGAGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:28.5:1:1:0:60:4:1:0:1 -12 55215117 . T C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTACAGAGGTTTCTTC;RSEQ=ACAATATAGTGTGTCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:35,0:0,0:1:0,1:22.2:1:31.1:1:1:0:60:34:1:0:1.1 1/1:15:15:15,0:0,0:1:0,1:18.3:1:30.9:1:1:0:60:30:1:0:1.1 -12 55215314 . C A 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00149;SOR=1.5711;LSEQ=AAGAAGACGGACCATAGGAA;RSEQ=TTCCAGGATAATGTTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:121:56,65:168,202:0.2459:2,2:25.2:1:30.5:1:0.91637:1.04:60:120:0.2459:0:1.4 0/1:478:162:66,96:146,170:0.3389:2,2:23.8:1:30.2:1:0.28494:1.24861:60:324:0.3411:0:1.4 -12 55215378 . G A 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGACCGAAGTTGTGAGA;RSEQ=TTGCCATGATGGTGAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:234:69,165:0,0:1:0,2:25.7:1:30.4:1:1:0:60:57.5:1:0:1.4 1/1:235:235:74,161:0,0:1:0,2:24.8:1:29.7:1:1:0:60:57.75:1:0:1.4 -12 55215401 . T G 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08469;SOR=1.63034;LSEQ=GCCATGATGGTGAGGGCTGA;RSEQ=AGCAGGACAGTCACATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:33:6,27:33,103:0.1953:2,2:24.9:1:31.5:1:0.64524:1.43882:60:66:0.1976:0:2.3 0/1:148:42:13,29:27,79:0.2838:2,2:24:1:31.3:1:0.54059:1.31:60:84:0.2857:0:2.2 -12 55215403 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22519;SOR=Inf;LSEQ=CATGATGGTGAGGGCTGATA;RSEQ=CAGGACAGTCACATTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:38,122:0:2,0:22.9:1:32.1:1:1:0:60:52.333:1:0:1.2 0/1:145:2:1,1:37,106:0.0138:2,2:25:1:29:1:0.4568:2.84:60:4:0.014:0:2 -12 55215404 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22209;SOR=Inf;LSEQ=ATGATGGTGAGGGCTGATAG;RSEQ=AGGACAGTCACATTAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:38,123:0:2,0:22.2:1:32.3:1:1:0:60:322:1:0:1.2 0/1:144:2:1,1:37,105:0.0139:2,2:12:0:31:1:0.4595:2.81:60:4:0.014:0:3.5 -12 55215754 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTAGGCTGCATCCTGCTG;RSEQ=CACGGCATCTTCCACCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:31:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 55427158 . A C 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05131;SOR=0;LSEQ=AGTGATTGAGTAAAAGCTAA;RSEQ=AGATGAGGCAAAAATCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:7:7,0:95,3:0.0667:1,0:24.4:1:31:1:1:0:60:14:0.068:0:1 0/0:58:0:0,0:55,3:0:2,0:21.6:1:29.8:1:1:0:60:28:1:0:0.1 -12 55427311 . A T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27273;LSEQ=TAGGCAATGATCTTATTCTC;RSEQ=AGAGACAACTACTCTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:306:126,180:61,71:0.6986:2,2:26.5:1:29.3:1:0.34467:1.22678:60:60.2:0.7:0:1.1 0/1:429:166:76,90:130,133:0.3869:2,2:25.8:1:29:1:0.48819:1.1571:60:332:0.3915:0:1.1 -12 55427394 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22896;SOR=Inf;LSEQ=ATTTTACTGTAAATCAAATT;RSEQ=AGGAATTATGCTATTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:49,138:0:2,0:24.9:1:31.5:1:1:0:60:374:0.9947:0:0.3 0/1:173:2:1,1:45,126:0.0116:2,2:34:1:29:0:0.46223:2.78:60:4:0.0118:0:1 -12 55427428 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=TTCCTAGAATTGTACAATTG;RSEQ=CCCTTTTCCTTCCTCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:12,76:0.0222:2,2:14:1:29:1:0.26941:6.12:60:4:0.0225:0:1 0/0:81:0:0,0:6,75:0:2,0:22.9:1:30.6:1:1:0:60:39.5:1:0:0.1 -12 55807231 . TTGCTGC T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGTTGCTGCTGTTGCTGTTG;RSEQ=TGCTGCTGCTGCGCCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:51,27:0.025:2,2:35.5:1:29:1:1:1.87302:27:4:0.0253:0:0 0/0:13:0:0,0:11,2:0:2,0:29.5:1:29:1:1:0:37.2:12:1:0:0.5 -12 55807292 . C T 27 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00561;SOR=Inf;LSEQ=TGTGAAGGAGCTGGGACTGC;RSEQ=AGTGCTGGAACTGCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:30,50:0:2,0:21.1:1:31.3:1:1:0:38.4:160:1:0:0.2 0/1:7:2:1,1:4,1:0.2857:2,2:23.5:1:27.5:1:1:3.1622:44.5:4:0.2857:0:1 -12 55807293 . A G 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01159;SOR=8.94328;LSEQ=GTGAAGGAGCTGGGACTGCC;RSEQ=GTGCTGGAACTGCTGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:10:10,0:20,50:0.125:2,0:15.8:1:27.7:1:2e-05:0:40:20:0.1266:0:1 1/0:7:4:4,0:1,2:0.5714:2,0:19:1:28.5:1:0.14286:0:35.3:8:0.5714:0:1.5 -12 55807417 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19886;SOR=Inf;LSEQ=TGGATCTGTGTGTAGGTGGC;RSEQ=GAGCTAATAAGTGTCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:2,16:0:2,0:23.3:1:29.6:1:1:0:57.3:17:1:0:0.2 0/1:15:2:1,1:0,13:0.1333:1,2:35:1:29.5:1:0.13333:0:60:4:0.1333:0:1 -12 55807588 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=GCTGCAGGCAAGGGCTGCAC;RSEQ=ACTCCTGTACCCTTCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:49:0:27:0:1:0:48:2:0.3333:0:2 1/0:3:2:1,1:1,0:0.6667:0,2:16:1:30:0:1:0:27:4:0.6667:0:1 -12 56383796 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18367;SOR=Inf;LSEQ=AGTTTGAGATCTGGGACACA;RSEQ=CTGGGCAGGAGCGATATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:42,48:0:2,0:29.2:1:32.4:1:1:0:60:180:1:0:0.1 0/1:68:2:1,1:33,32:0.0294:2,2:25.5:1:28.5:1:1:1.03078:60:4:0.0303:0:1 -12 56421196 . AAACAACAAC A 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=8.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCTCCCATCTAATAATTAAA;RSEQ=AACAACAACAACAACAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:28.8:1:1:0:60:4:1:0.5:0 -12 56421614 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23775;SOR=Inf;LSEQ=GTGCCTCCTTCACCCAGAAG;RSEQ=GGAACCTGCTGCGCCACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:58,35:0:2,0:23.8:1:30.5:1:1:0:60:45.5:1:0:0.2 0/1:89:2:1,1:55,32:0.0225:2,2:31.5:1:28.5:1:1:1.70775:60:4:0.0233:0:1 -12 56421720 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50511;SOR=Inf;LSEQ=TGCACTCACTGGTCACCTCC;RSEQ=CACACACTCAGGTCAGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:7,31:0:2,0:22.8:1:30.6:1:1:0:60:37:1:0:0.1 0/1:51:2:1,1:12,37:0.0392:2,2:21:1:28:1:0.44863:3.00:60:4:0.04:0:1 -12 56422162 . A C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTAAAAATACAAAAAAAA;RSEQ=AAAAATTAGCCGGGCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:1:32:1:1:0:54.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 56473808 . T C 73 d7;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=GTCCGAGGCTCCGCAATCCC;RSEQ=ACTCCAGCCTCGCGCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:28.6:1:31.6:1:1:0:60:10:1:0:1.4 0/1:5:1:1,0:4,0:0.2:0,0:9:0:24:0:1:0:60:2:0.2:0:1 -12 56473874 . CCT C 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=0.72668;SOR=0.63347;LSEQ=TCCCTCTGCGTTCCTCCCTC;RSEQ=CTCTCTCTCTCTCTCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:11,0:0.4211:0,0:14.4:1:29.6:1:1:0:60:16:0.4211:0.2632:1.5 0/1:16:5:5,0:10,1:0.3125:2,0:13:1:30.4:1:1:0:56:10:0.3125:0.1875:0.8 -12 56473994 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.5663;LSEQ=GCCGCAGCAGCCACCAATTC;RSEQ=CCAGCGGTTCAGGTGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:157,16:0.0114:2,2:7.5:1:28.5:1:0.18535:9.5498:60:4:0.0116:0:1 0/0:154:1:1,0:129,24:0.0065:2,0:8:0:32:0:1:0:60:2:0.0066:0:1 -12 56473999 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.56754;LSEQ=AGCAGCCACCAATTCGCCAG;RSEQ=GGTTCAGGTGGCTCTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:162,25:0.0106:2,2:18.5:1:28.5:1:0.25684:6.37375:60:4:0.0108:0:1 0/0:166:1:1,0:130,35:0.006:2,0:46:0:28:0:1:0:60:2:0.0061:0:1 -12 56474006 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22582;SOR=Inf;LSEQ=ACCAATTCGCCAGCGGTTCA;RSEQ=GTGGCTCTTGCCTCGATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:183,34:0:2,0:24.5:1:31.8:1:1:0:60:107.5:1:0:0.2 0/1:197:2:1,1:150,45:0.0102:2,2:15:1:28:1:0.41339:3.30784:60:4:0.0104:0:1 -12 56474379 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05812;SOR=0.09823;LSEQ=GGACCCTCACGCCACCCTTC;RSEQ=CCAGAGCGTCGCCGACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:1,18:0,1:0.95:0,1:29.2:1:30.4:1:1:0:60:18:0.9474:0:1.2 1/0:8:5:0,5:0,3:0.625:0,0:15.8:1:31.6:1:1:0:60:10:0.625:0:1 -12 56474480 . A G 85 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=TGCAGGGAGGGGAGCAGGGA;RSEQ=CTTCATTCTGTAAACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:23.9:1:30.4:1:1:0:60:6:0.8571:0:1.3 0/0:1:0:0,0:1,0:0:0,0:8:0:31:0:1:0:60:2:1:0:0 -12 56477694 . A T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38044;LSEQ=CTCCTTCCTGCAGGTTAGTG;RSEQ=GCCCACCCTCCTTCCTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:562:383:122,261:57,122:0.6815:2,2:25.7:1:30:1:1:1.00:60:190.5:0.6865:0:1.1 0/1:573:257:90,167:110,203:0.4485:2,2:26.1:1:29.6:1:1:1.00546:60:127.5:0.4529:0:1.1 -12 56478002 . A C 79 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGATGAGGAAGGGGCCCT;RSEQ=CTGGTATGAGGCACTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:15.7:1:30.8:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 56478607 . G A 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53586;SOR=0.63275;LSEQ=GCACTATTGTACTCCAGCCT;RSEQ=GGCAACAAGAGCGTAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:9,0:24,0:0.2727:1,0:22.4:1:26.8:1:1:0:60:18:0.2727:0:1.7 0/1:21:4:3,1:17,0:0.1905:1,2:28.5:1:27:1:0.19048:0:60:8:0.1905:0:1 -12 56478639 . TA T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.64202;SOR=0.4654;LSEQ=CGTAACTCCGTCTCAAATTT;RSEQ=AAAAAAAGAAAAAAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:3,0:75,0:0.0385:1,0:15.3:1:29.8:1:1:0:60:6:0.0385:0.0128:1 0/1:55:1:1,0:53,1:0.0182:1,0:17:0:32:0:1:0:60:2:0.0182:0:0 -12 56478658 . A C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=8e-05;SOR=0.30682;LSEQ=TTAAAAAAAAGAAAAAAAGA;RSEQ=AGGAAAGAAAGAAGGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:119:78:78,0:40,0:0.6555:1,1:23.5:1:32:1:1:0:60:38:0.6667:0:1 0/1:79:29:28,1:48,2:0.3671:1,1:25.4:1:31.4:1:1:1.16:60:28:0.359:0:1.1 -12 56480269 . C T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.35988;SOR=3.19518;LSEQ=GTGGAGAGGTAAGGAAGAGG;RSEQ=GTTCCGCTGCGGCCCTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:1:0,1:200,70:0.0037:2,0:1:0:25:0:0.26199:0:60:2:0.0037:0:1 0/1:256:3:1,2:193,60:0.0117:2,2:6.3:1:28:1:0.14643:6.37421:60:6:0.0122:0:1 -12 56480474 . C A 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCAAGATTGCTCCCCAGTC;RSEQ=CACCAAACCAGAGTGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:123,286:0:2,0:25.3:1:30.7:1:1:0:60:44.444:1:0:0.1 0/1:346:36:13,23:106,203:0.104:2,2:28.2:1:28.9:1:0.85408:1.08:60:72:0.1059:0:1.1 -12 56480583 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0483;LSEQ=TGACTCAGCAGCCCACCAGG;RSEQ=CAGACCATTCCAGTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:53:1,52:0,3:0.9464:0,1:21.8:1:29.6:1:1:0:60:52:0.9455:0:1.2 0/1:29:13:0,13:0,16:0.4483:1,1:22.5:1:30.8:1:1:0:60:26:0.4483:0:1 -12 56480648 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05263;SOR=Inf;LSEQ=TTCAAGAAAAGGAGCAGGCC;RSEQ=AGCATGGTGGCTCATGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:1,14:0:1,0:20.7:1:31.1:1:1:0:60:30:1:0:0.8 0/1:5:2:0,2:0,3:0.4:0,0:12:1:29.5:1:1:0:60:4:0.4:0:1 -12 56480920 . C CAAA 25 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=21.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:25:1:25.8:1:0.33333:0:42.5:4:1:0.3333:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 56481264 . G T 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.38373;SOR=0.30048;LSEQ=CCCTGGCTTTTTGCTTCCCG;RSEQ=GATTGAGGTGCCTGTGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:4:2,2:195,34:0.0172:2,2:23.5:1:30.8:1:0.11389:5.66842:60:8:0.0176:0:1 0/0:192:1:0,1:153,38:0.0052:2,0:1:0:24:0:0.20312:0:60:2:0.0053:0:1 -12 56482180 . T G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13387;LSEQ=TGAAGAGACTTTTGAATCTA;RSEQ=AGGGCAGCACTTAAGGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:121:110:92,18:10,1:0.9091:2,2:25.7:1:32.2:1:1:1.94759:60:54:0.9231:0:1.1 1/0:58:33:30,3:22,3:0.569:2,2:26.1:1:31.2:1:1:1.36:60:15.5:0.5536:0:1.2 -12 56482227 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16059;SOR=Inf;LSEQ=GGCAGATGGGGACAAATCCA;RSEQ=TGCAGAGCTGGAGGGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:216,27:0:2,0:23.9:1:32.3:1:1:0:60:80:1:0:0.4 0/1:163:2:1,1:136,24:0.0123:2,2:29:1:27.5:1:0.28564:5.57262:60:4:0.0125:0:1.5 -12 56486447 . G T 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33958;SOR=3.52209;LSEQ=TTAGTGGAGAATGATATTTA;RSEQ=AAACCAAATGCTGAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:1:0,1:220,26:0.004:2,0:12:0:11:0:0.10931:0:60:0:0:0:2 0/1:212:3:2,1:170,39:0.0142:2,2:20.3:1:23:1:0.46773:2.16965:60:2:0.0095:0:2.3 -12 56486473 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05763;SOR=Inf;LSEQ=AAATGCTGAGGCTGGGTGTG;RSEQ=TCATTGCCATTGAGTTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:287,107:0:2,0:23:1:31.6:1:1:0:60:42.778:1:0:0.1 0/1:380:4:3,1:268,108:0.0105:2,2:36.8:1:29:1:1:1.21:60:8:0.0107:0:2 -12 56487077 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18151;SOR=Inf;LSEQ=CTAACATGAATCCTTTGAAT;RSEQ=GTTAATGTTCCCTTAGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:156,71:0:2,0:24.7:1:29:1:1:0:60:74.667:1:0:0.1 0/1:169:2:1,1:128,39:0.0118:2,2:22:1:28.5:1:0.41843:3.25338:60:4:0.012:0:1 -12 56487201 . T C 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59977;SOR=1.10358;LSEQ=TTCCGATCCCTGAAGGAAAT;RSEQ=AGTGCTGGGCGTATCTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:75:38,37:187,185:0.1678:2,2:24.8:1:31.7:1:1:1.02:60:150:0.1689:0:1 0/1:456:83:37,46:177,196:0.182:2,2:19.8:1:30.4:1:0.71548:1.12244:60:26.667:0.1782:0:1.1 -12 56487296 . G A 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21796;SOR=4.7822;LSEQ=TCGGGGGCCTACGGAAGAGC;RSEQ=ACTAGACATCAAGCATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:1:1,0:157,230:0.0026:2,0:21:0:14:0:0.40722:0:60:0:0:0:2 0/1:410:5:4,1:180,224:0.0122:2,2:8.8:1:26.8:1:0.179:4.96:60:10:0.0125:0:1 -12 56487359 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50114;SOR=Inf;LSEQ=GGGAAAGGGTCTGCTAGGTG;RSEQ=TGAGAATAGGGAGTCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:54,108:0:2,0:23.7:1:32:1:1:0:60:80:1:0:0.2 0/1:187:2:1,1:58,127:0.0107:2,2:34:0:30.5:1:0.53263:2.18:60:4:0.0108:0:1 -12 56487853 . AC A 109 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.13555;SOR=0.43549;LSEQ=AAGGTCAGGACTTGGAAGTG;RSEQ=CCCCCCCTCCCTTTATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:916:11:7,4:496,405:0.012:2,2:29.5:1:31.6:1:0.76267:1.43:60:22:0.0123:0.0011:0.1 0/0:950:5:3,2:519,422:0.0053:2,2:24.8:1:30.6:1:1:1.22:60:10:0.0053:0.0011:0.2 -12 56487860 . CCT C 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.00049;SOR=Inf;LSEQ=GGACTTGGAAGTGACCCCCC;RSEQ=CCCTTTATTCCCCACTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:956:0:0,0:514,441:0:2,0:24.6:1:31.5:1:1:0:60:105.111:1:0:0.2 0/1:1000:12:6,6:534,448:0.012:2,2:23.3:1:30.4:1:0.77894:1.19175:59.6:24:0.0122:0:0.6 -12 56487861 . CT C 146 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTTGGAAGTGACCCCCCC;RSEQ=CCCTTTATTCCCCACTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:960:0:0,0:514,445:0:2,0:24.5:1:30:1:1:0:60:28.969:1:0:0.2 0/1:1004:30:15,15:519,439:0.0299:2,2:25.8:1:29.8:1:0.71166:1.18203:59.3:29:0.0305:0.009:1.1 -12 56488913 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00095;SOR=3.30436;LSEQ=GGAGGTGGAGGCCATGTCTT;RSEQ=GGATCAGCTCTGGGCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:34:31,3:59,1:0.3617:1,2:26.6:1:28.1:1:0.13295:5.60123:60:68:0.3656:0:1 1/0:52:34:32,2:17,1:0.6538:1,2:24.3:1:28.2:1:1:1.06128:60:68:0.6538:0:1 -12 56488937 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18058;SOR=Inf;LSEQ=TCAGCTCTGGGCTCCAGGAT;RSEQ=GGATGCCACGGTAAGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:119,17:0:2,0:24:1:31.6:1:1:0:60:67:1:0:0.2 0/1:101:2:1,1:84,15:0.0198:2,2:20:1:29:1:0.29307:5.45444:60:4:0.02:0:1 -12 56488953 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.20991;SOR=Inf;LSEQ=GGATGGGATGCCACGGTAAG;RSEQ=TCTGAAACAAGCTTTTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:158,33:0:2,0:22.9:1:29.7:1:1:0:60:190:1:0:0.2 0/1:162:2:1,1:124,36:0.0123:2,2:21.5:1:28.5:1:0.40572:3.41116:60:4:0.0123:0:1 -12 56488985 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05701;SOR=Inf;LSEQ=CTTTTATATGTTAGGCTGTT;RSEQ=AAATTGAGCCTCTGCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:253,96:0:2,0:24.2:1:32.1:1:1:0:60:173.5:1:0:0.1 0/1:335:4:2,2:231,100:0.0119:2,2:15.8:1:23.5:1:0.58815:2.30358:60:3:0.0091:0:2 -12 56489401 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23953;SOR=Inf;LSEQ=AAGTATAGTTGACATTTGTA;RSEQ=GGAAGATGCAAACCCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:151,54:0:2,0:25.5:1:30.3:1:1:0:60:101.5:1:0:0.1 0/1:197:2:1,1:145,50:0.0102:2,2:11.5:1:32.5:1:0.45172:2.88131:60:4:0.0104:0:1 -12 56489421 . TA T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2489;SOR=Inf;LSEQ=AGGAAGATGCAAACCCAGGA;RSEQ=ATGTTGGGTTTCTATATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:181,75:0:2,0:25.7:1:28.6:1:1:0:60:84.333:1:0:0.1 0/1:267:3:1,2:182,82:0.0112:2,2:18.7:1:27.7:1:0.23375:4.41147:60:6:0.0116:0.0037:0.3 -12 56489429 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=GCAAACCCAGGATAATGTTG;RSEQ=GTTTCTATATATCCCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:203,94:0:2,0:24.1:1:31.1:1:1:0:60:73.25:1:0:0.1 0/1:300:3:1,2:203,94:0.01:2,2:20.7:1:29.3:1:0.24087:4.2959:60:6:0.0102:0:1 -12 56489613 . T C 211 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGTACTTAGCTTACTTTTG;RSEQ=TTTTTCTTTTCTTTTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:97:33,64:120,211:0.2266:2,2:24.2:1:32.1:1:0.71918:1.10276:60:96:0.2264:0:1.1 0/0:444:0:0,0:156,288:0:2,0:25.6:1:29.6:1:1:0:60:73:1:0:0.2 -12 56490760 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.05146;SOR=Inf;LSEQ=TGGGGGTGGGGGGGCCTGGG;RSEQ=TGGCTGTGCACATGCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:152,81:0:2,0:23.5:1:31.6:1:1:0:60:32.286:1:0:0.2 0/1:139:3:2,1:94,42:0.0216:2,2:27.7:1:28:1:1:1.11812:60:6:0.0221:0:1 -12 56491480 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14685;SOR=Inf;LSEQ=AAAGGTTGGGGACCACTGCT;RSEQ=AGAGGTACCTTCAAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:127,9:0:2,0:21.9:1:32.1:1:1:0:60:135:1:0:0.1 0/1:85:2:1,1:80,3:0.0235:1,2:21.5:1:25.5:1:0.09244:23.23849:60:4:0.0253:0:1 -12 56491758 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24551;SOR=Inf;LSEQ=AAGGGTAAGGAGGCGGGGGT;RSEQ=GAGTGAAGCATGGGGATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:40,156:0:2,0:24.4:1:31.1:1:1:0:60:64.333:1:0:0.2 0/1:193:2:1,1:48,143:0.0104:2,2:19.5:1:28:1:0.4443:2.96:60:4:0.0105:0:1 -12 56491880 . T G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02479;SOR=6.35728;LSEQ=TTAGTTCAGAGGGCAACAAA;RSEQ=AAAATAATGATCAAGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:1,4:2,15:0.2273:2,2:22.8:1:32.4:1:1:1.82:60:10:0.2273:0:1 1/0:12:8:1,7:0,4:0.6667:0,2:22.1:1:32.4:1:1:0:60:16:0.6667:0:1.3 -12 56492032 . CA C 67 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0.45926;LSEQ=CCCCGTCTCTACTAAATATA;RSEQ=AAAAAAAAAAAAATTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:4,0:0.3636:0,0:26.8:1:33.5:1:1:0:52:8:0.3636:0:1.3 0/1:5:1:1,0:0,0:0.2:0,0:18:0:31:0:1:0:60:2:0.2:0:0 -12 56492721 . C CT 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.60234;SOR=2.27041;LSEQ=GCTGAGCCCAACCATTTTCT;RSEQ=TTTTTTTCTTTTTTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:1:0,1:29,152:0.0052:2,0:43:0:31:0:1:0:60:2:0.0061:0:4 0/1:169:2:0,2:30,133:0.0118:2,0:16.5:1:31:1:1:0:54.5:4:0.014:0:2 -12 56492729 . C T 47 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=1.02234;LSEQ=CAACCATTTTCTCTTTTTTT;RSEQ=TTTTTTTTTCTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:12:0,12:19,124:0.0759:2,0:24.1:1:13.3:1:0.36315:0:56.3:0.2:0.0159:0:3.3 0/1:129:10:0,10:22,95:0.0775:2,0:16.7:1:22.2:1:0.20827:0:51.4:1.5:0.0577:0:2.9 -12 56493381 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26733;SOR=0;LSEQ=GTGTGAGCCACCGCGCCCGG;RSEQ=CATGGAATGTATTCTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:3:1,2:195,38:0.0127:2,2:23.3:1:29:1:0.07525:10.10548:60:6:0.0128:0:1 0/0:171:0:0,0:139,32:0:2,0:22.4:1:31.9:1:1:0:60:84.5:1:0:0.1 -12 56493822 . A C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.42881;LSEQ=CGGCCACGTGGGGTAAGACA;RSEQ=CTTCTAATTACCCAACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:534:145:60,85:173,215:0.2715:2,2:24:1:31.6:1:0.55631:1.13964:60:47.333:0.2689:0:1.1 1/0:538:302:117,185:109,126:0.5613:2,2:23.9:1:30.8:1:0.07871:1.36703:60:150:0.5618:0:1.2 -12 56494812 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39916;SOR=3.00412;LSEQ=TTCCTCATCATGTAAATTTC;RSEQ=TTGCATTATTTTCTGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:1:0,1:172,80:0.004:2,0:1:0:25:0:0.32016:0:60:2:0.004:0:1 0/1:339:4:1,3:229,106:0.0118:2,2:11.5:1:27.5:1:0.09961:6.44278:60:8:0.0119:0:1.3 -12 56494872 . C T 144 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=10.88947;LSEQ=CAGTTTCTGGGAGCAGTGAA;RSEQ=GGTGCCCCCGTCCAGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:2:0,2:261,207:0.0043:2,0:1:0:25.5:1:0.19721:0:60:4:0.0043:0:1 0/1:584:26:14,12:286,270:0.0445:2,2:25.2:1:30.7:1:0.84348:1.10:60:52:0.045:0:1.2 -12 56494991 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.87936;LSEQ=GAGAAAGTGTCAATGTGTAG;RSEQ=AGCCGGAGCAGGAGCCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:155:91,64:239,180:0.27:2,2:22.7:1:30:1:0.77559:1.07:60:154:0.273:0:1.1 1/0:593:306:159,147:158,128:0.516:2,2:23.7:1:29.2:1:0.45819:1.14096:60:75.5:0.5198:0:1.1 -12 56494998 . A T 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.02745;SOR=1.41346;LSEQ=TGTCAATGTGTAGGAGCCGG;RSEQ=GCAGGAGCCGGAGCCCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:89:52,37:310,223:0.1429:2,2:23.1:1:29.7:1:1:1.01:60:88:0.1436:0:1.2 0/1:624:119:62,57:275,229:0.1907:2,2:24.7:1:29.6:1:0.68269:1.10385:60:118:0.1934:0:1.1 -12 56495306 . C T 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13556;SOR=0.85145;LSEQ=TACCTAGCCTTTCTTCTCAA;RSEQ=CCCCAGGTACTCCCTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1052:231:126,105:470,351:0.2196:2,2:26.3:1:30:1:0.49893:1.11574:60:37.5:0.2166:0:1.1 0/1:1097:212:115,97:476,409:0.1933:2,2:27.5:1:29.2:1:0.93892:1.02:60:105:0.1928:0:1.2 -12 56495877 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21534;SOR=Inf;LSEQ=ACTCAGGGAGCATTTAATGG;RSEQ=AGCTAGTGCCTTTAGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:13,110:0:2,0:24.3:1:32.5:1:1:0:60:122:1:0:0.1 0/1:107:2:1,1:18,87:0.0187:2,2:7:1:29.5:1:0.32499:4.73:60:4:0.0192:0:1 -12 57486033 . A C 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=2.41711;LSEQ=GGACCCCACAGGAGAGGAGG;RSEQ=GGCCCCGGGCATTCCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1315:312:171,141:528,473:0.2373:2,2:24.3:1:30.8:1:0.55878:1.09:60:51:0.2378:0:1.1 0/1:1223:525:287,238:376,321:0.4293:2,2:23.4:1:30.8:1:0.8167:1.03:60:86.5:0.4314:0:1.1 -12 57486176 . G C 192 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGGGTGTGAGGAGGTCTG;RSEQ=TGAGGCAGCGGGGAAGTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1766:0:0,0:864,899:0:2,0:24.9:1:31.5:1:1:0:60:52.424:0.9988:0:0.2 0/1:1964:63:31,32:937,959:0.0321:2,2:24.4:1:32.2:1:1:1.00857:60:126:0.0325:0:1.2 -12 57486278 . G A 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=77.33787;LSEQ=TTCTGCATGAGGGACAACAC;RSEQ=CTCTTATTACGGAGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1477:1:1,0:705,769:7e-04:2,0:15:0:25:0:0.47864:0:60:2:7e-04:0:1 0/1:1485:74:39,35:690,721:0.0498:2,2:23.5:1:29.4:1:0.55234:1.16:60:73:0.0498:0:1.2 -12 57486647 . A G 296 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.58015;LSEQ=GCTGGGTTCTGTGCTCTGCC;RSEQ=GTCGAGTGGCCCTCGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1518:706:347,359:407,402:0.4651:2,2:24.5:1:30.2:1:0.68036:1.04745:60:63.182:0.4664:0:1.2 1/0:1669:966:492,474:359,343:0.5788:2,2:26.2:1:29.9:1:0.96044:1.00835:60:95.6:0.5787:0:1.1 -12 57487340 . G A 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15095;SOR=3.63398;LSEQ=CGTCTCCCACGACCGCGTGG;RSEQ=CCGCCTCAGCCCCTGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:2:1,1:245,199:0.0045:2,2:21.5:1:31.5:1:1:1.23057:60:4:0.0045:0:1 0/1:372:6:3,3:194,172:0.0161:2,2:22.7:1:29.3:1:1:1.12754:60:12:0.0164:0:1.7 -12 57487729 . T G 307 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.63394;LSEQ=AGCAGGCTAGGAGTTGTGGG;RSEQ=ATGGGGATGGGGATGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1800:782:372,410:489,526:0.4344:2,2:24.1:1:31:1:0.81189:1.02462:60:64.167:0.4355:0:1.3 1/0:1811:1008:471,537:384,413:0.5566:2,2:24.3:1:30.8:1:0.56897:1.06002:60:71:0.5566:0:1.3 -12 57487777 . G C 203 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGAGGAGCCCAAAGCAGT;RSEQ=ATGCTTTGTGTGTGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1436:0:0,0:669,765:0:2,0:25:1:31.5:1:1:0:60:109.308:0.9986:0:0.6 0/1:1326:91:39,52:573,657:0.0686:2,2:24.3:1:31.2:1:0.51492:1.16273:60:182:0.0695:0:1.1 -12 57487814 . A C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.1791;LSEQ=AGGGGGAAGAGGGAGTGGGC;RSEQ=GGCGGAGGGCCGGGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1359:574:262,312:358,422:0.4224:2,2:24.6:1:30:1:0.956:1.01023:60:40:0.4185:0:1.3 1/0:1164:814:390,424:169,178:0.6993:2,2:24.1:1:29.3:1:0.8474:1.03219:60:73:0.6983:0:1.3 -12 57488293 . A T 246 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=115.63214;LSEQ=AATTCAATAAACCTAAACTG;RSEQ=GCCCATCTTCACAGCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1951:3:0,3:1001,946:0.0015:2,0:3:1:27:1:0.11508:0:60:6:0.0016:0:1 0/1:2023:306:151,155:851,865:0.1513:2,2:23.6:1:29.9:1:0.95058:1.00987:60:152:0.1525:0:1.2 -12 57488303 . C T 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31127;SOR=0.85104;LSEQ=ACCTAAACTGAGCCCATCTT;RSEQ=ACAGCTTTCTTTGCCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1925:89:45,44:937,899:0.0462:2,2:20.6:1:28.8:1:1:1.0191:60:88:0.0461:0:1.1 0/1:2095:83:38,45:1003,1003:0.0396:2,2:21.6:1:28.6:1:0.50197:1.18411:60:166:0.04:0:1.2 -12 57496677 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50992;SOR=0;LSEQ=GTTGTCTTGGTTGCCATGGA;RSEQ=GATGACCACCAGGGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:14,22:0.0526:2,2:43:0:31.5:1:1:1.55:60:4:0.0526:0:1.5 0/0:26:0:0,0:11,15:0:2,0:25.6:1:28.4:1:1:0:60:25:1:0:0.3 -12 57674222 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.5224;SOR=Inf;LSEQ=AGTTGCTGCTGCTGCTGCTG;RSEQ=TGTTGCTGCTGGGCAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:26.4:1:32.7:1:1:0:60:46:1:0:0.2 0/1:38:2:1,1:17,19:0.0526:2,2:40.5:1:26.5:1:1:1.11:60:4:0.0526:0:1 -12 57674241 . CA C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13788;SOR=0;LSEQ=GCTGTTGCTGCTGGGCAGTA;RSEQ=AGGGAGAAGCCCCCGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:10.5:1:30.5:1:1:1:60:4:0.1:0.05:0.5 0/0:33:0:0,0:13,20:0:2,0:22.9:1:30.2:1:1:0:60:66:1:0:0.2 -12 57856933 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGAAGATCCCCAGAGTACA;RSEQ=AGACTACAAGACTGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34.5:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 57857000 . G A 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTCCCCTCACTCAGCGA;RSEQ=TGATGCTTTTTTTGTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:6:1:29.3:1:1:0:60:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 57857354 . T C 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10501;SOR=0.6624;LSEQ=TGTCTTAGAGGGGTGGGGGA;RSEQ=ACCAGGGATGTTCTGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:117:117,0:47,1:0.7091:1,1:23:1:32:1:0.29091:0:60:116:0.7073:0:1.1 1/0:128:79:79,0:48,1:0.6172:1,1:26.6:1:31.6:1:0.38281:0:60:78:0.6142:0:1.1 -12 57857647 . G T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02224;SOR=Inf;LSEQ=TGGGCCCACCCCCACCCCAT;RSEQ=CCAGTTTCCTATCTACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:167,288:0:2,0:23:1:31.7:1:1:0:60:36.917:0.9955:0:0.1 0/1:289:4:2,2:94,189:0.0138:2,2:31.3:1:25.8:1:0.60357:2.01:60:3:0.0111:0:2.5 -12 57858015 . GA TG 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01888;SOR=Inf;LSEQ=AGCACCATCAAGAAGTCACA;RSEQ=TGGGGCCGGGCGCGGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:3,98:0:1,0:22.4:1:31.5:1:1:0:60:49.5:1:0:0.1 0/1:61:4:0,4:1,56:0.0656:1,0:16.8:1:29.9:1:1:0:60:8:0.0678:0.0164:0.8 -12 57858414 . A G 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29197;LSEQ=GGTTAGGTGCATGGAGAGAC;RSEQ=TGCCCCTTTACCATATCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:750:542:409,133:152,55:0.7227:2,2:22.8:1:29.7:1:0.57276:1.11:60:59.222:0.7242:0:1.1 0/1:697:301:225,76:275,119:0.4319:2,2:22:1:29.4:1:0.17277:1.28:60:99.333:0.4319:0:1.1 -12 57858421 . T C 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCATGGAGAGACATGCCCC;RSEQ=TTACCATATCCGTCTCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:842:0:0,0:599,243:0:2,0:23.1:1:30.3:1:1:0:60:59.143:1:0:0.7 0/1:816:54:39,15:518,244:0.0662:2,2:22.8:1:29.7:1:0.65009:1.22:60:26:0.0644:0:1.1 -12 57858835 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.3988;LSEQ=TTCCAGAAATCCTCCAAATA;RSEQ=CCCAATCCTTCCTGAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:780:550:401,149:162,65:0.7051:2,2:23.1:1:29.6:1:0.65984:1.08:60:54:0.7031:0:1.1 0/1:707:345:250,95:260,102:0.488:2,2:22.9:1:29.2:1:0.86701:1.03:60:56.5:0.4864:0:1.1 -12 57859058 . T C 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGAGAGTCCCCATATTGC;RSEQ=ACCTGATTTCCCTCAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1245:0:0,0:498,747:0:2,0:26.2:1:29:1:1:0:60:68.167:1:0:0.2 0/1:1262:57:23,34:516,689:0.0452:2,2:26:1:31:1:0.78469:1.10703:60:56:0.0448:0:1.2 -12 57859431 . G A 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26116;LSEQ=CTGGTTGGCAAGTGCCGGGA;RSEQ=GAACCCTTGGAAGGTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1586:1161:581,580:210,214:0.732:2,2:24.5:1:30.6:1:0.86498:1.02:60:104.545:0.7325:0:1.2 0/1:1612:671:334,337:453,485:0.4163:2,2:24:1:30.3:1:0.5781:1.06:60:166.75:0.4177:0:1.2 -12 57859783 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03737;SOR=Inf;LSEQ=GTGGGACATGGTGGAATCCG;RSEQ=CTGAGGGCAGGAGGTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:89,322:0:2,0:23.4:1:31.7:1:1:0:60:50.375:1:0:0.1 0/1:324:4:2,2:67,253:0.0123:2,2:8:1:25:1:0.20013:3.76:60:8:0.0125:0:1.3 -12 57859932 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29067;LSEQ=TTCCTCCTTGAGGTGGAGTC;RSEQ=TGGAAGAGGAACAGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:363:268:228,40:83,12:0.7383:2,2:23.8:1:30.1:1:0.73333:1.2128:60:52.6:0.7346:0:1.1 0/1:260:117:106,11:129,14:0.45:2,2:24.6:1:29.7:1:1:1.05:60:57.5:0.4457:0:1.1 -12 57860046 . C T 209 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=21.32527;LSEQ=ATCAACAGCGAGCACATCCA;RSEQ=GGGGAGCGGAAGGAGTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1447:7:2,5:762,677:0.0048:2,2:10.6:1:28.9:1:0.26494:2.81198:60:14:0.0049:0:1 0/1:1426:134:65,69:652,638:0.094:2,2:23.5:1:29.6:1:0.71669:1.08475:60:133:0.0942:0:1.1 -12 57860293 . T C 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01506;SOR=0;LSEQ=CCATAAACAAATATTAAAAA;RSEQ=AATGTTTGTGTGACTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:10:0,10:3,144:0.0637:1,0:14.1:1:32.3:1:1:0:60:20:0.0645:0:1 0/0:97:0:0,0:4,93:0:1,0:22.1:1:28.3:1:1:0:60:47.5:1:0:0.1 -12 57860665 . C T 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTGCACTCCAGCCTGGG;RSEQ=GACAGAGCAAAACTCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:24.3:1:30:1:1:0:54:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 57860826 . T C 109 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGCCCGTTCCCCCAAGA;RSEQ=GACCCCATCTTGGGACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:13,0:3,0:0.8125:0,1:30.9:1:29.7:1:1:0:60:12:0.8:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 57860972 . T C 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00263;SOR=Inf;LSEQ=TCTTGCCTGCCCTTGTCCCC;RSEQ=AGTTTTGGGAATTCTCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:151,2:0:1,0:25.5:1:30.7:1:1:0:60:16:1:0:0.2 0/1:93:6:6,0:86,1:0.0645:1,0:30.5:1:27.5:1:1:0:60:5:0.0556:0:1 -12 57861484 . A G 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78096;SOR=0.83211;LSEQ=CTAACCTCTAACCAGCCAAA;RSEQ=GGCTAACCTAAAAGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:59:18,41:5,16:0.7375:2,2:23.1:1:30.1:1:0.77956:1.40:60:10.8:0.7297:0:1.3 1/0:20:14:0,14:1,5:0.7:2,1:22.4:1:30.8:1:0.3:0:60:28:0.7:0:1.1 -12 57861785 . T C 202 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TCCACTCAACAGAAGCCGTA;RSEQ=GTATGTAAGCTCCCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1656:0:0,0:865,790:0:2,0:26:1:30.4:1:1:0:60:77.81:1:0:0.1 0/1:1604:108:58,50:790,704:0.0673:2,2:25.2:1:30:1:0.9206:1.03:60:107:0.0676:0:1.1 -12 57863084 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54282;SOR=0;LSEQ=TGCTCCCCCATCTCTTACCT;RSEQ=CTTAGCCCTTTCTACACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:2,0:156,5:0.0123:1,0:33:1:31:1:1:0:60:4:0.0125:0:1 0/0:88:0:0,0:87,1:0:1,0:24.4:1:31.6:1:1:0:60:43:1:0:0 -12 57865284 . C T 194 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01996;LSEQ=GCAGGGAAGATGCCCCCGCC;RSEQ=AGGAACCTTCCTACCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1567:93:45,48:760,713:0.0593:2,2:24.1:1:29.8:1:0.59328:1.13689:60:92:0.0595:0:1.1 0/0:1592:2:0,2:816,773:0.0013:2,0:1:0:23:1:0.23712:0:60:4:0.0013:0:1.5 -12 57865321 . G A 312 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25787;LSEQ=GAGTCCCAAGTTTCTGGGGG;RSEQ=TTCCCAGGTTAGCCCAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1675:1262:645,617:189,217:0.7534:2,2:24.9:1:30.3:1:0.12337:1.20:60:69.111:0.7535:0:1.1 0/1:1852:816:420,396:508,526:0.4406:2,2:24.2:1:29.2:1:0.32566:1.10:60:61.769:0.4417:0:1.2 -12 57865821 . G C 329 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.59076;LSEQ=GATCCCTACCTGGGGAAACA;RSEQ=AATTCCTCAACTCTAGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1620:1221:585,636:174,222:0.7537:2,2:25.3:1:32.1:1:0.18268:1.17:60:110:0.7544:0:1.1 1/0:1721:1108:526,582:295,316:0.6438:2,2:24.2:1:31.2:1:0.76229:1.03293:60:84.231:0.6453:0:1.2 -12 57865928 . A C 279 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTGGGGGAGCTGCAGTCCC;RSEQ=TGCACAAGATGCCCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:430:430:73,357:0,0:1:0,2:23.5:1:31.9:1:1:0:60:214:1:0:1.1 1/1:367:347:67,280:5,15:0.9455:2,2:22.8:1:31:1:0.56238:1.39166:60:37.556:0.9441:0:1.1 -12 57865994 . A T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13736;SOR=Inf;LSEQ=TATAGTCTGTATACGTTTTG;RSEQ=GGAGAAATTTGATAATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:3,131:0:1,0:23.8:1:31.3:1:1:0:60:43.667:0.9924:0:0.7 0/1:80:2:1,1:2,76:0.025:1,2:23.5:1:32:0:0.07405:31.23:60:4:0.026:0:1.5 -12 57982794 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GGACCACTGCCACCAAGACG;RSEQ=GGAGACCGATAGTGGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:25.2:1:31.8:1:1:0:60:10:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:20:1:27:0:1:0:60:4:0.6667:0:1 -12 57983043 . C A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28205;SOR=0.16243;LSEQ=TTTCACTATTTCTTCTACCG;RSEQ=TATCTACTAAGAACTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:1,6:1,0:0.875:0,2:16.3:1:31.1:1:0.25:0:60:14:0.875:0:1 1/0:8:4:1,3:0,4:0.5:0,2:32.8:1:30.5:1:1:0:60:8:0.5:0:1 -12 58142216 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57182;SOR=2.85052;LSEQ=AAAGATGGAGGAGGACCCTC;RSEQ=ATAGCCTCAGAGATAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:0,1:181,22:0.0049:2,0:1:0:24:0:0.11275:0:60:2:0.0051:0:2 0/1:144:2:1,1:117,25:0.0139:2,2:15.5:1:29:1:0.32955:4.60871:60:4:0.0139:0:1 -12 58142488 . T TTTC 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.02524;SOR=Inf;LSEQ=TGGGATGAGCTTTCTTCTTT;RSEQ=TTCTTTTTTTTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:10,205:0:1,0:20.1:1:29.9:1:1:0:59.3:20.5:1:0:0.7 0/1:144:4:0,4:6,134:0.0278:1,0:19.5:1:30.9:1:1:0:60:8:0.0288:0.0069:0 -12 58142854 . C A 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00617;SOR=0.47131;LSEQ=AGCTGTAATAAAAACTACAG;RSEQ=CCATCTACCAACCAAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:72:71,1:91,3:0.4337:1,1:25.2:1:30.1:1:0.63379:2.33:60:144:0.439:0:1.1 0/1:102:27:25,2:72,3:0.2647:1,2:26.4:1:29.3:1:0.606:1.90631:60:54:0.2647:0:1 -12 58143030 . TG T 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00431;SOR=Inf;LSEQ=CTGCACTGGGCGGGGCCCTC;RSEQ=GGGGGAAAGGCTCCACGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:797:0:0,0:362,433:0:2,0:23.8:1:31.3:1:1:0:60:98.375:0.9975:0:0.1 0/1:680:7:4,3:324,349:0.0103:2,2:18.9:1:28.2:1:0.71664:1.44:60:14:0.0104:0.0044:0.3 -12 58143349 . C T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26357;SOR=0;LSEQ=ATATCTTAGTTGAATGGTTA;RSEQ=TGCTTAGTGGCTCAAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:44,235:0.0106:2,2:30.7:1:29.3:1:0.4076:2.66:60:6:0.0108:0:1 0/0:212:0:0,0:51,161:0:2,0:22.4:1:31.6:1:1:0:60:105:1:0:0.1 -12 58143486 . T TA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGACCTTGTCTCTTTTTT;RSEQ=AAAAAAAAAGAAATGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:0,22:0.0833:1,0:8.5:1:31.5:1:1:0:60:4:0.087:0.0417:0.5 0/0:10:0:0,0:0,10:0:0,0:26.5:1:27.8:1:1:0:60:20:1:0:0 -12 58143777 . TA T 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGACAGAGCAAGACTCCATC;RSEQ=AAAAAAAAAAAAGCCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:34.5:1:29:0:0.33333:0:56.5:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 58144349 . C CA 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.3646;SOR=0.49327;LSEQ=AACACAGCAAGCCCTGGTCT;RSEQ=AAAAAAAAAGAATGGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:8:7,1:165,28:0.0398:2,2:17.8:1:29.5:1:1:1.19:59.4:16:0.0408:0.01:0.6 0/1:150:3:2,1:118,28:0.02:2,2:18:1:29.3:1:0.48019:2.09441:60:6:0.0201:0.0067:0.3 -12 58144359 . G T 188 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCCTGGTCTCAAAAAAAAA;RSEQ=AATGGGCAAGGTATGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:91:74,17:135,28:0.3583:2,2:22.8:1:28.9:1:0.86409:1.10717:60:12:0.3443:0:1.1 0/0:198:0:0,0:151,46:0:2,0:20.7:1:31.3:1:1:0:60:196:1:0:0.1 -12 58144665 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36948;LSEQ=TACGGGCAATCACTCTCCTA;RSEQ=TCCCAACCAGAACCCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:216:135,81:159,93:0.4615:2,2:22.6:1:30.4:1:0.92372:1.02576:60:42.2:0.4577:0:1.1 0/1:387:93:61,32:184,110:0.2403:2,2:24.4:1:29.5:1:0.62369:1.14:60:92:0.2421:0:1.1 -12 58145156 . C T 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.05414;SOR=0.75477;LSEQ=TAAATGCTCACTTTTCAATC;RSEQ=CCTTTAACCCAACATGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:229:66,163:90,204:0.4362:2,2:23:1:29.9:1:0.70034:1.08938:60:37.167:0.4381:0:1.1 0/1:331:122:34,88:61,148:0.3686:2,2:24.4:1:29.3:1:0.89984:1.06659:60:60:0.3681:0:1.1 -12 58145598 . C CA 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.82001;LSEQ=TGCAGCAACAAAGGGACTCC;RSEQ=AAAAAAAAAGCGCAAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:0,2:2,93:0.0206:1,0:32:1:31:1:1:0:60:4:0.022:0:0 0/1:59:1:0,1:3,55:0.0169:2,0:41:0:32:0:1:0:60:2:0.0175:0:0 -12 58638231 . G A 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATGGAGTTGTTTAGAAAC;RSEQ=TGGAGTTGTTTGTTTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:11,15:0,0:1:0,2:25.3:1:30:1:1:0:60:52:1:0:1.1 1/1:17:17:9,8:0,0:1:0,2:21.7:1:30.5:1:1:0:60:34:1:0:1.3 -12 58638253 . G T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03759;SOR=Inf;LSEQ=GGAGTTGTTTGTTTGGCCAC;RSEQ=TATATGTGAATTTCTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:27.2:1:30.5:1:1:0:60:25:1:0:0.9 0/1:22:4:2,2:7,10:0.1818:2,2:28.5:1:30:1:1:1.40:60:8:0.1818:0:2 -12 58638327 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.12281;SOR=Inf;LSEQ=GTTCAAAAAGGAATGCCCCA;RSEQ=TAATGCTGCCATGGCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:23.2:1:32.2:1:1:0:60:50:1:0:0.2 0/1:14:2:2,0:5,7:0.1429:2,0:7:1:30:1:0.46154:0:60:4:0.1429:0:2 -12 58638335 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAATGCCCCACTAATGCT;RSEQ=CCATGGCAAAACCGGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:22:1:27.5:1:1:1.11:60:4:0.0952:0:1 0/0:10:0:0,0:6,4:0:2,0:22.4:1:31.8:1:1:0:60:20:1:0:0.5 -12 58638348 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11084;SOR=Inf;LSEQ=TAATGCTGCCATGGCAAAAC;RSEQ=GGAACACTCTATAGTGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:28.7:1:30.4:1:1:0:60:38:1:0:0.2 0/1:10:2:2,0:4,4:0.2:2,0:28:1:32.5:1:0.46667:0:60:4:0.2:0:2 -12 58639786 . G A 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCCCCCCACCTAGTCCT;RSEQ=AAGACATAAGGTGCTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:9:1:26:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 58814924 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1464;SOR=Inf;LSEQ=TATTGCCTTATTTAGTAGAT;RSEQ=TTTTGTACGTTGTGTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:201,108:0:2,0:25.3:1:32.3:1:1:0:60:618:1:0:0.9 0/1:192:2:1,1:123,67:0.0104:2,2:16.5:1:27:1:1:1.82974:60:4:0.0105:0:1.5 -12 58814968 . A G 279 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGACATCATCCCAAATGCT;RSEQ=TCAATGTCAAAATGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:429:429:227,202:0,0:1:0,2:25.6:1:32:1:1:0:60:84.8:1:0:1.1 1/0:259:164:88,76:53,41:0.6332:2,2:25.9:1:30.9:1:0.69823:1.11593:60:53.667:0.6289:0:1.1 -12 58814990 . A G 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01454;SOR=9.80928;LSEQ=CAATGTCAAAATGACAGAAA;RSEQ=GGATGTAGAGCGTCCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:1:0,1:212,234:0.0022:2,0:28:0:32:0:1:0:60:2:0.0023:0:3 0/1:278:6:3,3:126,145:0.0216:2,2:19.2:1:31.3:1:1:1.15:60:12:0.0219:0:1.3 -12 58815319 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TAAAAAAATGAAAGCAAACA;RSEQ=CAAATAAAACAACATATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:39:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 59868733 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTATGAGATGCCACCCAG;RSEQ=GTTTATAGGAAAAGGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:15,10:0.0741:2,2:36:1:31.5:1:1:1.47706:60:4:0.0741:0:1 0/0:9:0:0,0:6,3:0:2,0:18.8:1:28.1:1:1:0:60:8:1:0:0 -12 59868991 . T C 60 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCTACCAAGGACCCCTGGAC;RSEQ=GACCCACTGGCCCTTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:1,1:0.6667:2,2:18.3:1:30.3:1:1:2.44949:56:8:0.6667:0:1 0/0:1:0:0,0:0,1:0:0,0:6:0:32:0:1:0:52:2:1:0:0 -12 60263226 . A G 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6636;SOR=0.9173;LSEQ=ACTTCTCAGAATTCCATTCA;RSEQ=CTAAGCATTCTGGGCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:137:74,63:81,68:0.479:2,2:24.4:1:32.1:1:1:1.01406:60:274:0.479:0:1.1 0/1:247:113:66,47:73,61:0.4575:2,2:26.6:1:31.4:1:0.6068:1.17:60:112:0.4553:0:1.1 -12 60263339 . A G 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=TTTTTAATGCACAAATGGAA;RSEQ=GAACCATGATGTTAGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:10,69:0:2,0:23.1:1:31.3:1:1:0:60:158:1:0:0.1 0/1:73:11:1,10:12,50:0.1507:2,2:21.2:1:28.7:1:0.67596:2.37692:60:10:0.1389:0:1.3 -12 60263362 . CA C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.22492;SOR=Inf;LSEQ=ACCATGATGTTAGTGCCTTG;RSEQ=AAAAAAGGTAGGCCACTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:1,45:0:1,0:28.7:1:30.5:1:1:0:60:92:1:0:0.1 0/1:42:2:0,2:3,37:0.0476:2,0:19.5:1:34:0:1:0:60:4:0.0476:0:0.5 -12 61873046 . G A 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CCACAACTAATATAAGTCAC;RSEQ=TCTTCACATAGTAAATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:18:9,9:165,159:0.0525:2,2:21.3:1:30.6:1:1:1.03764:60:36:0.0529:0:2.7 0/0:332:0:0,0:183,149:0:2,0:27.3:1:29.8:1:1:0:60:109.667:1:0:1.5 -12 61873055 . T C 269 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97162;LSEQ=ATATAAGTCACGTCTTCACA;RSEQ=AGTAAATATCAGGAATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:353:352:175,177:0,0:0.9972:0,2:26.5:1:31.9:1:1:0:60:57.667:0.9971:0:1.3 1/1:343:342:190,152:0,0:0.9971:0,2:26.8:1:31.1:1:1:0:60:84.5:0.9971:0:1.6 -12 61873087 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0;SOR=4.66378;LSEQ=GGAATGGAGTATGCAAAAAC;RSEQ=TGTAAATATTCATAATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:78:32,46:116,157:0.2222:2,2:28.3:1:30.9:1:0.89672:1.06194:60:77:0.2219:0:2.1 1/0:327:187:85,102:64,76:0.5719:2,2:25.5:1:30:1:1:1.0105:60:92.5:0.5728:0:1.9 -12 61873147 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24803;SOR=0;LSEQ=ACAGTTTAGAAAGTAATTTT;RSEQ=CATTTATTTTTTACATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:2,1:44,107:0.0195:2,2:11.7:1:28.3:1:0.2127:4.81:60:6:0.0196:0:1 0/0:146:0:0,0:41,105:0:2,0:25.7:1:32:1:1:0:60:145:1:0:0.5 -12 61873411 . T C 67 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCAATACATTAAAGGTA;RSEQ=TCAAAAGTTAGACCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:15:1:33.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 62168965 . G T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGGATGTGGAGCAACAA;RSEQ=AACTCTCATTCATTGCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:27.5:1:1:0:60:4:1:0:1 -12 62169686 . C T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGCAGGAACTTCCATA;RSEQ=TTCAGTAATATGCCAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:1:0,2:30.1:1:31.4:1:1:0:60:16:1:0:1 1/1:2:2:2,0:0,0:1:0,0:10.5:1:30.5:1:1:0:60:4:1:0:1 -12 62169944 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50598;SOR=0;LSEQ=TTGTAAACAGACAATTTAAG;RSEQ=GCATGATTCTTGCCAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:26,70:0.0204:2,2:24.5:1:28.5:1:0.47717:2.66:60:4:0.0206:0:1 0/0:75:0:0,0:24,51:0:2,0:22.1:1:29.5:1:1:0:60:17.75:1:0:0.4 -12 62169948 . T C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13589;SOR=0.59283;LSEQ=AAACAGACAATTTAAGGGCA;RSEQ=GATTCTTGCCAAAAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:39:8,31:14,39:0.4239:2,2:21.7:1:29.4:1:0.62341:1.3861:60:38:0.4176:0:1 0/1:66:20:4,16:15,31:0.303:2,2:20.5:1:29.3:1:0.38276:1.91725:60:19:0.2969:0:1.2 -12 62290554 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52521;SOR=0;LSEQ=TGTCACATTGTCAACCAAAT;RSEQ=CTAAATATATATTCTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:96,31:0.0155:2,2:28.5:1:27.5:1:0.43605:3.0637:60:4:0.0155:0:1 0/0:80:0:0,0:58,22:0:2,0:24.1:1:30.7:1:1:0:60:19:1:0:0.4 -12 62290583 . C T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15731;SOR=Inf;LSEQ=ATATTCTGATTTCTAAGAGA;RSEQ=CCTGGAACCTAAATTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:122,75:0:2,0:25.4:1:31.3:1:1:0:60:64.667:1:0:0.4 0/1:130:2:0,2:74,54:0.0154:2,0:12.5:1:27:1:0.18366:0:60:4:0.0157:0:4 -12 62290629 . T C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.9145;LSEQ=GATGTAACTGCTTGCATTAT;RSEQ=TATGATGTTTCCTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:63:30,33:85,101:0.253:2,2:22.7:1:31.3:1:0.88388:1.08:60:126:0.254:0:1.9 1/0:187:117:54,63:31,39:0.6257:2,2:24.2:1:31.6:1:0.87967:1.08:60:116:0.627:0:1.8 -12 62290646 . T A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57867;SOR=2.68383;LSEQ=TATTTATGATGTTTCCTTTC;RSEQ=TTTGCCTGCCATCAAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:1,0:96,129:0.0044:2,0:1:0:27:0:0.4292:0:60:2:0.0044:0:1 0/1:170:2:1,1:72,95:0.0118:2,2:18.5:1:30:1:1:1.32:60:4:0.0118:0:3 -12 62290651 . C G 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.07004;SOR=0;LSEQ=ATGATGTTTCCTTTCTTTTG;RSEQ=CTGCCATCAAGCTATTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:5:2,3:86,122:0.0235:2,2:18.4:1:30.8:1:1:1.05711:60:10:0.0236:0:3.6 0/0:167:0:0,0:70,97:0:2,0:26.7:1:31.2:1:1:0:60:82.5:1:0:1.2 -12 62290656 . C T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=4.44311;LSEQ=GTTTCCTTTCTTTTGCCTGC;RSEQ=ATCAAGCTATTTGTGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:45:14,31:65,90:0.225:2,2:25.1:1:29.1:1:0.22687:1.59555:60:90:0.2261:0:2.2 1/0:163:92:36,56:28,42:0.5644:2,2:27.9:1:29.2:1:1:1.03683:60:184:0.5679:0:1.9 -12 62290662 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09643;SOR=Inf;LSEQ=TTTCTTTTGCCTGCCATCAA;RSEQ=CTATTTGTGATACAAATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:68,115:0:2,0:25.8:1:32.1:1:1:0:60:182:1:0:0.6 0/1:156:3:3,0:61,92:0.0192:2,0:9.3:1:28:1:0.06713:0:60:6:0.0196:0:1.3 -12 62290742 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00021;SOR=0.08292;LSEQ=TAGATAATATCTTATCTCTA;RSEQ=TGAGGGTCCAGATGATCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:20:3,17:0,20:0.5:1,2:22.3:1:32.1:1:0.23077:0:60:40:0.5:0:1.3 0/1:27:2:0,2:4,21:0.0741:2,0:16.5:1:33.5:1:1:0:60:4:0.0741:0:1 -12 62290795 . C T 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39211;SOR=0.25813;LSEQ=TTCATGCAATATTACTTTTC;RSEQ=ATATTATTTGATACATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:0,8:0,18:0.3077:1,0:28:1:28.3:1:1:0:60:16:0.32:0:1.5 0/1:10:1:0,1:0,9:0.1:0,0:19:0:30:0:1:0:60:2:0.1:0:1 -12 62755589 . T A 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCAAAATGTTTTCTAAAAG;RSEQ=TTACCATTTACTTCTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:0:0,0:350,243:0:2,0:25.7:1:29.8:1:1:0:60:117.6:0.9983:0:0.5 0/1:395:91:54,37:169,135:0.2304:2,2:23.6:1:28.9:1:0.54888:1.17:60:90:0.2314:0:1.1 -12 62755631 . G A 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49652;LSEQ=TGATTTATAAACTATTCTGG;RSEQ=CAGGGGAGAGGGTCAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:630:390:183,207:112,128:0.619:2,2:26.2:1:29.8:1:1:1.01:60:77:0.621:0:1.1 0/1:457:204:91,113:114,139:0.4464:2,2:25.8:1:29.3:1:0.92498:1.01838:60:101:0.4459:0:1.1 -12 63294744 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12237;SOR=Inf;LSEQ=TTTCCGAGTCACATCTGAGA;RSEQ=CTCACCCTCTCTAAACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:213,50:0:2,0:23.1:1:30.4:1:1:0:60:51.6:1:0:0.1 0/1:142:2:2,0:99,41:0.0141:2,0:19.5:1:30.5:1:1:0:60:4:0.0141:0:1 -12 63294746 . T C 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04193;SOR=Inf;LSEQ=TCCGAGTCACATCTGAGATC;RSEQ=CACCCTCTCTAAACTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:217,61:0:2,0:22.9:1:30.5:1:1:0:60:38.714:1:0:0.1 0/1:149:3:2,1:104,42:0.0201:2,2:45:1:31:1:1:1.2362:60:6:0.0203:0:1 -12 63294859 . G A 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00685;SOR=0.68462;LSEQ=TCCGCCTCTATTTCCATGTA;RSEQ=CCGGATACATTTTTGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:517:294:129,165:90,131:0.5687:2,2:24.8:1:29.8:1:0.52856:1.14:60:97:0.5706:0:1.1 0/1:350:166:81,85:83,101:0.4743:2,2:24.2:1:29.1:1:0.52069:1.16:60:82:0.4824:0:1.1 -12 63295001 . T C 139 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0053;SOR=0.09094;LSEQ=CTGATACCATATGTTCCCAG;RSEQ=GGGCAACAGCCAATCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:24:1,23:1,44:0.3478:1,1:26.9:1:30.5:1:1:1.89:60:48:0.3478:0:1 0/1:22:1:0,1:1,20:0.0455:1,0:3:0:26:0:1:0:60:2:0.0455:0:1 -12 65379265 . G A 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.64205;LSEQ=TCTGACAAGGCATTTCATAA;RSEQ=CTTCACCCAAGCACCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:13:9,4:140,69:0.0586:2,2:22.8:1:29.6:1:1:1.11:60:26:0.0586:0:1.4 0/1:178:40:25,15:88,49:0.2247:2,2:27.9:1:29.9:1:0.85333:1.07709:60:80:0.2286:0:1 -12 65379373 . G C 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.7449;SOR=0.94404;LSEQ=AGACATGTTCTTTATACAAA;RSEQ=CAGCCTGCTACAGCTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:305:164:77,87:58,83:0.5377:2,2:24.7:1:31.6:1:0.35516:1.27:60:328:0.5395:0:1.1 1/0:300:157:73,84:66,74:0.5233:2,2:26.7:1:30.4:1:1:1.02621:60:156:0.5324:0:1.1 -12 65379582 . CT C 34 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.07353;SOR=Inf;LSEQ=ATAATCTTGTAAGTTTTGGG;RSEQ=TTTTTTTTTTTTTGCCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,9:0:0,0:17.4:1:27.7:1:1:0:60:8:0.7273:0:1.4 0/1:5:2:0,2:0,3:0.4:0,0:41:1:34:0:1:0:60:4:0.4:0:0 -12 66431043 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21517;SOR=Inf;LSEQ=TACAAAGGGAAAGAAGACAG;RSEQ=CACCCAATATATGTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:63,52:0:2,0:25.1:1:31.4:1:1:0:59.6:56.5:1:0:0.1 0/1:100:2:1,1:46,52:0.02:2,2:19:1:29.5:1:1:1.13:60:4:0.0204:0:1 -12 66431045 . AC A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19776;SOR=Inf;LSEQ=CAAAGGGAAAGAAGACAGGC;RSEQ=CCAATATATGTTCTCTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:65,53:0:2,0:23.9:1:31.6:1:1:0:59.3:117:1:0:0.1 0/1:95:2:1,1:44,49:0.0211:2,2:13:1:29.5:1:1:1.11:60:4:0.0215:0.0105:0.5 -12 66431148 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11122;SOR=Inf;LSEQ=TATTGTAGATGTAAGAGAAT;RSEQ=GGTACTTTTCAAAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:123,81:0:2,0:22.8:1:31.3:1:1:0:60:50:1:0:0.1 0/1:190:3:1,2:113,74:0.0158:2,2:16:1:27.7:1:0.56494:3.0359:57.3:6:0.0159:0:1 -12 66431273 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.19832;SOR=Inf;LSEQ=AGGGCAAGATTCTTGTCAAG;RSEQ=GAATTAACGTGCATATTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:16,88:0:2,0:23.2:1:30.8:1:1:0:59.8:208:1:0:0.1 0/1:84:2:1,1:16,66:0.0238:2,2:12:1:30:1:0.36575:4.03:60:4:0.0241:0:1 -12 66943027 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00436;SOR=0.39207;LSEQ=AGGGAATTATAATGGGGTGG;RSEQ=GAGCATCAGCTTGTGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:42:42,0:41,5:0.4773:2,1:17.8:1:33:1:0.0567:0:60:84:0.4828:0:1.2 0/1:80:21:21,0:55,4:0.2625:2,1:28.8:1:32.6:1:0.56835:0:60:42:0.2692:0:1.2 -12 66943069 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0996;SOR=Inf;LSEQ=AGAATTATTGCTGGACGGTG;RSEQ=AGAAGCAAAATGATAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:164,42:0:2,0:25.5:1:31.6:1:1:0:60:33.333:1:0:0.6 0/1:179:3:1,2:131,45:0.0168:2,2:17.7:1:28:1:0.16906:5.75275:60:6:0.017:0:1.3 -12 66943117 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3276;LSEQ=CTGAACAGGAGCAGACAGAG;RSEQ=TATTTCCCTAAGCTTACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:189:114,75:120,85:0.4797:2,2:24.4:1:31.9:1:0.75844:1.08:60:62:0.4781:0:1.6 0/1:410:95:50,45:182,133:0.2317:2,2:25.8:1:31.3:1:0.40917:1.23094:60:46.5:0.2285:0:1.6 -12 66943175 . A G 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.47553;LSEQ=ATGCCTTAGTAAGGGGAATT;RSEQ=GGGCACGCACCAGAATACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:234:100,134:110,127:0.4968:2,2:27.2:1:31.2:1:0.45858:1.16026:60:77:0.4946:0:1.5 0/1:476:152:65,87:154,169:0.3193:2,2:24.6:1:30.4:1:0.32557:1.21915:60:304:0.322:0:1.4 -12 66943230 . T A 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06305;SOR=0;LSEQ=TACTACTATTGAAAAAAATA;RSEQ=TATTGCTCATACTACAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:5:4,1:91,200:0.0169:2,2:6:1:24.6:1:0.03813:8.72:60:4:0.0137:0:1.8 0/0:267:0:0,0:87,180:0:2,0:24.4:1:29.7:1:1:0:60:88:1:0:0.3 -12 66943257 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49961;SOR=0;LSEQ=TCATACTACAGTTTTATCTG;RSEQ=ATATTACTTTTGGTGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:40,142:0.0109:2,2:12.5:1:29:1:0.39695:3.52:60:4:0.0109:0:1 0/0:168:0:0,0:41,127:0:2,0:23.3:1:28:1:1:0:60:55:1:0:0.2 -12 66943270 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50352;SOR=0;LSEQ=TTATCTGTATATTACTTTTG;RSEQ=TGGTGCCACTAGGAAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:22,119:0.014:2,2:11.5:1:28.5:1:0.29676:5.31:60:4:0.0143:0:1.5 0/0:116:0:0,0:18,97:0:2,0:25:1:31.1:1:1:0:60:114:1:0:0.1 -12 66943275 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19018;SOR=Inf;LSEQ=TGTATATTACTTTTGGTGGT;RSEQ=CCACTAGGAAGTTTATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:18,121:0:2,0:22.6:1:31.8:1:1:0:60:33.75:1:0:0.1 0/1:108:2:1,1:15,91:0.0185:2,2:18:1:27:1:0.27553:5.91:60:4:0.0189:0:1 -12 68307522 . G A 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.31658;LSEQ=TTATATCTCTATTCAGTCTC;RSEQ=TTTCTGATGCCCCCAACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:195:173:89,84:12,10:0.8872:2,2:26.5:1:30.4:1:0.82427:1.13186:60:85.5:0.886:0:1.1 1/0:195:139:74,65:29,27:0.7128:2,2:25:1:29.7:1:0.87518:1.06:60:138:0.7113:0:1.1 -12 68307536 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24814;SOR=0;LSEQ=AGTCTCGTTTCTGATGCCCC;RSEQ=AACATACTCCATCAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:1,2:95,103:0.0149:2,2:21.3:1:29:1:1:1.83927:60:6:0.0151:0:2 0/0:199:0:0,0:103,96:0:2,0:24.5:1:30.4:1:1:0:60:98.5:1:0:0.7 -12 68307594 . T C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.91089;LSEQ=TGAGGACAGAGTTAAAGCTT;RSEQ=CCCTAGGATCATGTGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:0,1:34,80:0.0087:2,0:42:0:11:0:1:0:60:0:0:0:2 0/1:121:2:1,1:37,81:0.0165:2,2:20.5:1:29:1:0.53487:2.17:60:4:0.0167:0:2.5 -12 68316282 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAGACGTTTAATTTCCAAA;RSEQ=TGTACAAGAGGGGAATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29:1:1:0:60:4:1:0:2 -12 68316304 . C G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACAAGAGGGGAATGTTTT;RSEQ=AAATCCTGTTTCACAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:46.5:1:32:1:1:0:60:4:1:0:2 -12 68616970 . G T 91 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38577;SOR=0.29539;LSEQ=TTTACCCCAGGGCATAAACT;RSEQ=CACAGCTTGTAAGACAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:8,0:16,0:0.3333:1,0:20.4:1:30.6:1:1:0:60:16:0.3333:0:1.8 0/1:8:1:1,0:7,0:0.125:0,0:9:0:32:0:1:0:60:2:0.125:0:2 -12 68617021 . C G 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31147;SOR=1.55597;LSEQ=TGATAGGCTTGAGGTGGGAG;RSEQ=AGGGAAGAAGGAAAGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:32:32,0:40,0:0.4444:1,1:23.3:1:30.6:1:1:0:60:9.667:0.4328:0:1.3 1/0:36:20:20,0:15,1:0.5556:1,1:20:1:29.8:1:0.44444:0:60:9:0.5294:0:1.1 -12 68617104 . C T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05692;SOR=Inf;LSEQ=TATTTGGCCACAGGAGGGAG;RSEQ=CAGACCCTTTGGGAAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:236,63:0:2,0:23.7:1:31.5:1:1:0:60:73.75:1:0:0.2 0/1:287:4:1,3:218,65:0.0139:2,2:5:1:25.5:1:0.04259:9.95724:60:8:0.0144:0:1.3 -12 68617219 . C T 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=1.56308;LSEQ=CCAGAGTTCCTAGACATATC;RSEQ=AGGTTTCCTAAGCTTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:220:97,123:205,253:0.324:2,2:24.7:1:29.1:1:0.93424:1.02743:60:43:0.3214:0:1.1 0/1:775:332:147,185:215,227:0.4284:2,2:23.4:1:28.9:1:0.24448:1.1917:60:54.333:0.4261:0:1.1 -12 69201797 . C G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACACCCCCACCCCGCCTCA;RSEQ=AGCCCGCCGCGCCCGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:39.3:1:31.7:1:1:0:60:6:1:0:1.7 1/1:2:2:1,1:0,0:1:0,2:11:0:31:1:1:0:60:4:1:0:1.5 -12 69202164 . A G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10913;LSEQ=CTGGCCCGGAGAGTGGAATG;RSEQ=TCCCCGAGGCCCAGGGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:159:118:95,23:31,10:0.7421:2,2:23.6:1:31.1:1:0.50881:1.33:60:38.333:0.7372:0:1.1 0/1:97:23:19,4:58,16:0.2371:2,2:18:1:30.2:1:0.77463:1.31:60:10.5:0.2234:0:1 -12 69202171 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.53681;SOR=0;LSEQ=GGAGAGTGGAATGATCCCCG;RSEQ=GGCCCAGGGCGTCGTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:147,40:0.0106:2,2:27.5:1:30:1:0.38771:3.64261:60:4:0.0107:0:2.5 0/0:107:0:0,0:85,22:0:2,0:23.1:1:29.2:1:1:0:60:106:1:0:0.3 -12 69202255 . C A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03015;SOR=Inf;LSEQ=GACTCCAAGCGCGAAAACCC;RSEQ=GGATGGTGAGGAGCAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:541:0:0,0:281,257:0:2,0:26:1:30.1:1:1:0:60:52.8:0.9944:0:0.4 0/1:388:4:2,2:201,181:0.0103:2,2:22.3:1:31.5:1:1:1.11019:60:8:0.0105:0:1 -12 69202326 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08351;LSEQ=CTGGGCTCTGACGGTGTCCC;RSEQ=TCTATCGCTGGTTCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:404:330:122,208:31,41:0.8168:2,2:23.7:1:30.4:1:0.3505:1.28823:60:109:0.8175:0:1.1 0/1:281:76:30,46:81,122:0.2705:2,2:26.7:1:30:1:1:1.01797:60:37:0.2681:0:1.2 -12 69202580 . T G 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=CCGGGGGCTGCGGGGCCGCT;RSEQ=CGGCGCGGGAGGTCCGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,5:0:2,0:32.9:1:27.9:1:1:0:60:7:1:0:0.3 1/0:3:2:0,2:0,1:0.6667:0,0:21.5:1:33:0:1:0:60:4:0.6667:0:2.5 -12 69202810 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06494;SOR=Inf;LSEQ=TCCCAGCTGTGTTCAGTGGC;RSEQ=ATTGGAGGGTAGACCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:55,2:0:1,0:23.1:1:30.2:1:1:0:60:114:1:0:0.2 0/1:20:2:1,1:16,2:0.1:2,2:9:1:27.5:1:0.28421:6.73285:60:4:0.1:0:1 -12 69202867 . G C 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00482;SOR=0;LSEQ=CTTTTTCTCTGCTGATCCAG;RSEQ=TAAGCACCGACTTGCTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:13:13,0:119,2:0.097:1,1:27.7:1:30.6:1:1:0:60:12:0.0916:0:1 0/0:75:0:0,0:73,2:0:1,0:21.9:1:31.7:1:1:0:60:150:1:0:0.1 -12 69202888 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15714;SOR=Inf;LSEQ=TAAGCACCGACTTGCTTGTA;RSEQ=CTTTAGTTTTAACTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:178,7:0:1,0:24.7:1:32:1:1:0:60:36:1:0:0.2 0/1:122:2:1,1:110,10:0.0164:2,2:10.5:1:28.5:1:0.17288:10.53577:60:4:0.0164:0:1 -12 69202971 . C CT 76 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54146;SOR=1.67523;LSEQ=ATTTCCAGTTTTCATCGTGT;RSEQ=TTTTTTTTCCTTGTAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:822:5:2,3:530,287:0.0061:2,2:36.6:1:31:1:0.35177:2.76637:60:10:0.0062:0:0 0/1:591:6:3,3:357,228:0.0102:2,2:19:1:29.7:1:0.68311:1.56451:60:12:0.0102:0.0034:0.3 -12 69203312 . G A 117 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0797;SOR=0.07842;LSEQ=CCATTACATTGTTAAGCGTG;RSEQ=TTGAAGTTACGTTTGTTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:1,15:0,2:0.8889:0,1:21.9:1:29.3:1:1:0:60:7:0.875:0:1.3 0/1:3:1:0,1:0,2:0.3333:0,0:40:0:27:0:1:0:60:2:0.3333:0:1 -12 69203524 . T A 76 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGCGTACCCACATATA;RSEQ=TTACATTTGAATTTAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:23.3:1:29.5:1:1:0:60:5:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 69207162 . G A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.59054;SOR=0.71865;LSEQ=GCTCTTTTGGATTGGATACT;RSEQ=TCTGTGATCACAACTGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:67:67,0:14,0:0.8272:1,1:23.1:1:29.1:1:1:0:60:134:0.8272:0:1 1/0:31:24:22,2:7,0:0.7742:0,2:27.5:1:28.8:1:1:0:60:48:0.7742:0:1.1 -12 69207194 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07044;SOR=Inf;LSEQ=AACTGATACTTGATGATTCC;RSEQ=TGATACTTGCATAATGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:136,1:0:1,0:28.6:1:30.5:1:1:0:60:136:1:0:0.6 0/1:50:2:2,0:47,1:0.04:1,0:18.5:1:28:1:1:0:60:4:0.0408:0:1.5 -12 69207561 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13959;SOR=Inf;LSEQ=GTTTGGACTATATTTTAAAG;RSEQ=TGAAAATTCTAATTATACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:0,31:0:1,0:23:1:32.7:1:1:0:60:62:1:0:0.1 0/1:19:2:0,2:1,16:0.1053:1,0:22.5:1:31:1:1:0:60:4:0.1053:0:1 -12 69210757 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08338;SOR=Inf;LSEQ=GTTTAGTCCATTGTAAAAAG;RSEQ=CATCTGGGCTAACATTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:77,262:0:2,0:24.3:1:30.9:1:1:0:60:47.429:1:0:0.1 0/1:264:3:1,2:73,187:0.0114:2,2:35.3:1:29:1:1:1.28:60:6:0.0117:0:1 -12 69210789 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13024;SOR=Inf;LSEQ=ACATTTCAGTTCACCTCTAC;RSEQ=CTCATTCACTTTTGTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:16,185:0:2,0:24.5:1:31.3:1:1:0:60:200:1:0:0 0/1:114:2:1,1:12,100:0.0175:2,2:22:1:29.5:1:0.21596:8.05:60:4:0.0179:0:1 -12 69211456 . C T 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGAATCACTTGAACCAGG;RSEQ=AGGTGGAGGTTGTGGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21:0:29.5:1:1:0:58:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 69214011 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.552;SOR=0;LSEQ=TGTGCAGTAGTTCATACTAA;RSEQ=TATGTATGTAGAAGTCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:2,0:120,3:0.016:1,0:7:1:27.5:1:1:0:60:4:0.0163:0:1 0/0:63:0:0,0:62,1:0:1,0:24.5:1:32.2:1:1:0:59.9:126:1:0:0.1 -12 69214081 . AT A 172 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.38109;SOR=0.79037;LSEQ=TAAAATGTACATCTCTTGTT;RSEQ=TTTTTTTTTTTCTGTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:49:36,13:304,86:0.1096:2,2:23.9:1:30.7:1:0.47168:1.27574:60:23.5:0.1059:0.0224:0.2 0/1:282:25:17,8:182,72:0.0887:2,2:24:1:29:1:0.81691:1.18875:60:24:0.086:0.0248:0.1 -12 69214691 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACATGTATATATACATGG;RSEQ=TAAGTCAATAAGTGTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:26.5:1:30:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 69218038 . T G 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=19.744;LSEQ=TTTAATGTTTATTGAAAGGT;RSEQ=AAATTGCATAAGGGTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:7:7,0:147,10:0.0427:2,0:23.7:1:32.3:1:1:0:60:14:0.044:0:1 0/1:89:42:40,2:40,7:0.4719:2,1:25.7:1:31.4:1:0.16342:3.46:60:41:0.4713:0:1.2 -12 69218083 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07761;SOR=Inf;LSEQ=ACTGATAGCATATCTACTGA;RSEQ=TAGCGCCCCGCCGCCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:245,79:0:2,0:26.7:1:32.1:1:1:0:60:161:1:0:0.2 0/1:242:3:1,2:167,72:0.0124:2,2:12.7:1:27:1:0.2223:4.60582:60:6:0.0126:0:1 -12 69218090 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08858;SOR=Inf;LSEQ=GCATATCTACTGAGTAGCGC;RSEQ=CCGCCGCCCCCCGCCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:279,94:0:2,0:25.4:1:30.5:1:1:0:60:40.444:1:0:0.2 0/1:301:3:1,2:196,102:0.01:2,2:8.3:1:30.7:1:0.27494:3.82452:60:6:0.0101:0:1 -12 69218096 . G A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.47512;SOR=1.74516;LSEQ=CTACTGAGTAGCGCCCCGCC;RSEQ=CCCCCCGCCCACCACCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:3:1,2:293,117:0.0073:2,2:34:1:30.3:1:0.20059:4.98598:60:6:0.0074:0:1 0/1:317:4:2,2:201,112:0.0126:2,2:21.8:1:29.5:1:0.62067:1.79105:60:8:0.0132:0:1.3 -12 69218525 . CT C 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.1676;SOR=Inf;LSEQ=AGACTTAATTAAATTGTTCC;RSEQ=TTTTTTGGTTGAGATGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:2,130:0:1,0:23.5:1:30.3:1:1:0:60:131:1:0:0 0/1:92:2:0,2:4,86:0.0217:1,0:17:0:34:0:1:0:60:4:0.0217:0:0.5 -12 69222357 . C A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07327;SOR=0.16568;LSEQ=GAGCAAGACCCTTTCTCAGA;RSEQ=AATAAATAAATAAACAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:26:26,0:4,0:0.8667:0,1:17.7:1:31:1:1:0:60:52:0.8667:0:1.1 1/0:6:3:3,0:3,0:0.5:0,0:9:1:30.3:1:1:0:60:6:0.5:0:1 -12 69222464 . C G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12648;LSEQ=TTGAACTAATTTTATTGAAA;RSEQ=TAAGTTTCTGTACAAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:165:155,10:30,0:0.8418:1,2:21.8:1:32.1:1:0.36564:0:60:54:0.8438:0:1.1 0/1:80:32:30,2:45,3:0.4:2,2:25.8:1:32:1:1:1:60:64:0.4051:0:1 -12 69222528 . A AT 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.43433;SOR=2.25326;LSEQ=AAATCACAGTACAGCAATTT;RSEQ=TTTTTTTTCCTTACATATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:3:3,0:388,155:0.0055:2,0:24.3:1:30.7:1:0.56197:0:60:6:0.0056:0:0.3 0/1:325:4:3,1:215,106:0.0123:2,2:21:1:30.3:1:1:1.48:60:8:0.0124:0:0 -12 69222809 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGAATGTACATGTGTCTTA;RSEQ=GAGATTGATAGAAAACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:3,221:0:1,0:24.5:1:30.4:1:1:0:60:111:1:0:0 0/1:95:10:0,10:1,84:0.1053:1,0:21.6:1:30.3:1:1:0:60:20:0.1064:0:1.1 -12 69229553 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15115;SOR=Inf;LSEQ=CAGGGATGAGTTAGGAAACA;RSEQ=ATACAGAGGTCAAGAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:148,10:0:2,0:23.8:1:32.4:1:1:0:60:78:1:0:0.1 0/1:101:2:1,1:93,6:0.0198:2,2:19:1:24:1:0.13446:14.42391:60:4:0.0198:0:1 -12 69230189 . G T 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19706;SOR=0.19028;LSEQ=TATTTAATATCTCCATATTA;RSEQ=TTATTTATGAAGTAAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:11,1:2,0:0.8571:0,2:25.4:1:30.1:1:1:0:60:24:0.8571:0:1.3 1/0:4:2:2,0:2,0:0.5:0,0:19.5:1:28:1:1:0:60:4:0.5:0:1 -12 69230735 . C CT 48 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGGTGCTGGAATTTGAA;RSEQ=TTTTTTTTTTTTTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,3:0.3333:0,0:16.7:1:30.7:1:1:0:60:6:0.5:0.1111:4.3 0/0:2:0:0,0:0,1:0:0,0:12:1:34:1:1:0:60:2:0.5:0:0 -12 69232879 . ATAAC A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10672;SOR=0.26584;LSEQ=AATTTCCAGTATACCAATAT;RSEQ=TAACTATAGTCCTCATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:25:24,1:7,1:0.7576:2,1:20.2:1:31.4:1:0.43182:3.27:60:50:0.7813:0.1212:0 0/1:9:4:4,0:5,0:0.4444:0,0:19:1:31.4:1:1:0:60:8:0.4444:0.1111:0 -12 69233067 . G A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0078;SOR=Inf;LSEQ=ATTGAAGGACTATTGGAAAT;RSEQ=CACTTCATGCAATGAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:774:0:0,0:492,282:0:2,0:24.4:1:31.9:1:1:0:60:63.5:1:0:0.1 0/1:474:5:3,2:296,172:0.0105:2,2:27:1:27.6:1:1:1.14694:60:10:0.0106:0:1 -12 69233215 . A G 195 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=124.60604;LSEQ=GAAAACTCAACACAAGCTGA;RSEQ=GAGGGCTTTGATGTTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1397:1:0,1:652,744:7e-04:2,0:18:0:31:0:1:0:60:2:7e-04:0:1 0/1:975:80:38,42:420,475:0.0821:2,2:23.1:1:31:1:1:1.02:60:160:0.0828:0:1.2 -12 71002542 . G T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATTTAATGCAATGGAAGC;RSEQ=TAAACCACATCACTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:27.5:1:1:0:60:4:1:0:1 -12 72825422 . GT G 97 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.04952;SOR=0.1084;LSEQ=GCCAATAACAGGAAGAAGAG;RSEQ=TTTTTTTTTTTTGAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:5,4:6,5:0.45:2,2:14.9:1:30.9:1:1:1.04:60:18:0.45:0.25:0.1 0/1:13:1:0,1:7,5:0.0769:2,0:34:0:30:0:0.46154:0:60:2:0.0769:0:4 -12 72825540 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48667;SOR=0;LSEQ=TTACATGTTTTACATGGATA;RSEQ=CACACAGGTTGATGTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:32:1:30:1:1:1.36624:60:4:0.1429:0:1 0/0:11:0:0,0:3,8:0:2,0:29.8:1:32.4:1:1:0:60:22:1:0:0.1 -12 72825619 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=CCAATAGCTGCTCTCAGGAA;RSEQ=CACAGATGTTTTGAAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:27:1:32.3:1:1:0:60:20:1:0:0 0/1:10:2:1,1:6,2:0.2:2,2:18:1:27:1:1:2.64575:60:4:0.2:0:1 -12 72825701 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2139;SOR=0;LSEQ=ATCAGAAGTTCAGTGGACTT;RSEQ=TGATAACAAATTTCACGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:0.125:2,2:27.5:1:30:0:1:1.30929:60:4:0.125:0:1 0/0:18:0:0,0:10,8:0:2,0:17.4:1:31.9:1:1:0:60:36:1:0:0.1 -12 73053766 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14194;SOR=Inf;LSEQ=ACCAAGATGAGGAGACCGGT;RSEQ=GTGGCCCCAAATGGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:18,1:0:1,0:24:1:32.1:1:1:0:60:18:1:0:0.1 0/1:12:2:2,0:10,0:0.1667:0,0:16:0:30:0:1:0:60:4:0.1667:0:1 -12 73053891 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19719;SOR=Inf;LSEQ=CATGATCATGGGACAGGGGG;RSEQ=CCTTCCCTTTTAGGTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:37,45:0:2,0:25.6:1:30.7:1:1:0:57.4:15.4:1:0:0.2 0/1:66:2:1,1:30,34:0.0303:2,2:12:0:31:0:1:1.13:60:4:0.0308:0:1.5 -12 73053894 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50071;SOR=0;LSEQ=GATCATGGGACAGGGGGCCC;RSEQ=TCCCTTTTAGGTAGCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:34,41:0.026:2,2:12.5:1:30.5:1:1:1.20:60:4:0.026:0:1.5 0/0:64:0:0,0:29,34:0:2,0:21.8:1:30.2:1:1:0:57.1:126:0.9844:0:0.2 -12 73729972 . CA C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.52;SOR=Inf;LSEQ=TCTGGCACATATTTGGAGTT;RSEQ=AAAAATGGTAGTTATGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:22.6:1:29.6:1:1:0:60:18:1:0:0 0/1:16:2:1,1:6,8:0.125:2,2:18.5:1:28.5:1:1:1.31:60:4:0.125:0:0 -12 73931078 . A G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGCAACCAAGTTATCCAG;RSEQ=TTCTGTCATTAGGGCTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:25:0:32:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:14:1:29:1:1:0:60:4:1:0:1 -12 76424463 . A T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=6;SSF=0.44444;SOR=0;LSEQ=GAGTGTGGATGTGGATGTGG;RSEQ=TGCGGATACGGGTGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:19.5:1:30:1:1:1.7321:60:4:0.4:0:2 0/0:4:0:0,0:2,2:0:2,0:29.8:1:29.3:1:1:0:60:8:1:0:0.3 -12 76424896 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50387;SOR=Inf;LSEQ=TGGGTTGGGACGGCTCGGCC;RSEQ=GCCCCTGCCCGGGCTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:24,18:0:2,0:24.1:1:30:1:1:0:60:84:1:0:0.2 0/1:55:2:1,1:29,24:0.0364:2,2:38.5:1:30.5:1:1:1.20416:60:4:0.0377:0:1 -12 76424910 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23467;SOR=Inf;LSEQ=TCGGCCGGCCCCTGCCCGGG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:32,26:0:2,0:23.3:1:31.3:1:1:0:60:57:1:0:0.2 0/1:55:2:1,1:26,27:0.0364:2,2:17.5:1:29:1:1:1.04:60:4:0.0364:0:1 -12 76424916 . TTGC T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.4955;SOR=0;LSEQ=GGCCCCTGCCCGGGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:27,27:0.0357:2,2:28.5:1:30:1:1:1:60:4:0.0357:0:0.5 0/0:55:0:0,0:25,30:0:2,0:29.3:1:29.6:1:1:0:60:110:1:0:0.2 -12 76424928 . C T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.2389;SOR=Inf;LSEQ=GGCTGTTGTTGCTGCTGCTG;RSEQ=TGCTGCTGTTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:28,29:0:2,0:28.4:1:31.9:1:1:0:60:56:1:0:0.2 0/1:55:2:1,1:22,31:0.0364:2,2:7:0:27.5:1:1:1.40:60:4:0.037:0:2 -12 76424931 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.23467;SOR=Inf;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:29,29:0:2,0:28.3:1:31.6:1:1:0:60:28:1:0:0.2 0/1:55:2:1,1:22,31:0.0364:2,2:34:1:31:1:1:1.40:60:4:0.0364:0:1.5 -12 76424937 . TTGC T 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.82148;SOR=0.84409;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:46:21,25:3,5:0.7931:2,2:31:1:30.7:1:0.72012:1.39:60:92:0.7931:0.069:0.1 1/0:55:42:14,28:7,4:0.7636:2,2:33.6:1:30.1:1:0.08963:3.41178:60:84:0.7636:0.0182:0.3 -12 76424952 . C G 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.09269;SOR=Inf;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TGGTGTTGCAGCTGCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:22,29:0:2,0:31.7:1:31.9:1:1:0:60:24.5:1:0:0.1 0/1:44:3:2,1:13,28:0.0682:2,2:19.3:1:29:1:0.26427:4.15:60:6:0.0698:0:2 -12 77053902 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCACTTAAAAAAAAAAAT;RSEQ=GTGTCTCCTAAGTTAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:19:1:30.5:1:0.33333:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 77054134 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GTCAGGCTTTTAGCTTGTAA;RSEQ=AACAGTAAACCCTTTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:71,48:0:2,0:23.8:1:31.1:1:1:0:60:118:1:0:0.1 0/1:136:3:1,2:77,56:0.0221:2,2:21.7:1:27:1:0.57523:2.72969:60:6:0.0226:0:1 -12 77054179 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21012;SOR=0;LSEQ=CCGCCATCTTCCAGTAATTC;RSEQ=CCAAAATGACGAACACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:73,88:0.0123:2,2:16:1:30.5:1:1:1.20:60:4:0.0125:0:1 0/0:192:0:0,0:90,102:0:2,0:29.6:1:30.4:1:1:0:56.6:26.429:1:0:0.2 -12 77054235 . G T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02143;LSEQ=ACCCCATATATGTTCTCTAG;RSEQ=CCTTTTAGAAAACATGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:60:28,32:23,22:0.5714:2,2:26.1:1:30.5:1:0.69622:1.19277:54.7:120:0.5769:0:1.1 0/1:110:3:2,1:49,58:0.0273:2,2:28.3:1:30.3:1:0.59568:2.35:57.7:6:0.0275:0:1 -12 77054292 . AG A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=10.9244;LSEQ=TATATGCGAATCTATAAGAA;RSEQ=GTGATATTGTAGACATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:14:8,6:44,27:0.1647:2,2:29.7:1:32.9:1:0.77019:1.21929:40.1:28:0.1667:0.0118:0.1 1/0:83:57:30,27:17,9:0.6867:2,2:23.1:1:30.6:1:0.34285:1.68922:51:56:0.6747:0.1566:0.1 -12 77054502 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17553;SOR=Inf;LSEQ=AAGAGCTGAGATAGCTTCCT;RSEQ=AAACGCGTGAAGGAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:8,44:0:2,0:20.5:1:31.4:1:1:0:46.2:104:1:0:0 0/1:38:2:1,1:4,32:0.0526:2,2:44:0:30:0:0.24893:7.27:49.5:4:0.0541:0:1.5 -12 77054686 . AT A 28 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AATAGGTGTTAAAAAAAAAA;RSEQ=AAATAAAGGACCTCTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:1:28:1:1:0:36:4:1:0.5:2 -12 77781871 . G A 267 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00676;LSEQ=TCCTGTAGTGTGAAGAACAG;RSEQ=TGTTCTACGGCCTAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:475:473:228,245:1,1:0.9958:2,2:24.8:1:30.1:1:1:1.07437:60:93.6:0.9957:0:1.1 1/0:464:285:150,135:84,94:0.6142:2,2:24.6:1:28.9:1:0.29329:1.24:60:56:0.61:0:1.2 -12 77814031 . T C 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.41555;SOR=0.77069;LSEQ=AGTCAGGAAATATTTTTTAT;RSEQ=ACCAAGCATTTTGAATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:38:19,19:93,104:0.1617:2,2:29.5:1:31.8:1:0.85951:1.12:60:76:0.1624:0:1.1 0/1:201:26:11,15:88,87:0.1294:2,2:29.1:1:30.5:1:0.53039:1.37711:60:52:0.1294:0:1 -12 77814083 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51552;SOR=0;LSEQ=ACATATTAATACAATGAGTA;RSEQ=GTAAAACTATAGATGTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:72,122:0.0102:2,2:13:1:26.5:1:1:1.69:60:4:0.0105:0:1 0/0:135:0:0,0:52,83:0:2,0:24.8:1:30.3:1:1:0:60:44:1:0:0.2 -12 78288358 . G GCT 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTAACCAACCCTCACTA;RSEQ=GCCACCAGCAAAATTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31:1:33:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 78288587 . C T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.65944;SOR=0.58664;LSEQ=CTGACATGCAAGAATGTGGA;RSEQ=TCAGTGTAGACAGATCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:0.4667:0,0:27.6:1:32.4:1:1:0:60:14:0.4667:0:1 0/1:6:2:2,0:3,1:0.3333:2,0:50:0:30.5:1:1:0:60:4:0.3333:0:1 -12 78288719 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50272;SOR=0;LSEQ=AATACAGCATCTTTGGAGAG;RSEQ=TTCATCCAGTTCACTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:139,58:0.0101:2,2:33:1:30.5:1:0.50612:2.38471:60:4:0.0102:0:1 0/0:166:0:0,0:112,54:0:2,0:25.1:1:31.5:1:1:0:60:82:1:0:0.2 -12 78288720 . T C 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08975;SOR=Inf;LSEQ=ATACAGCATCTTTGGAGAGC;RSEQ=TCATCCAGTTCACTACTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:144,62:0:2,0:24.3:1:30.6:1:1:0:60:102:1:0:0.2 0/1:168:3:1,2:113,52:0.0179:2,2:22.7:1:24.3:1:0.24212:4.30428:60:2:0.0124:0:1 -12 78288811 . T C 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.68756;SOR=1.07662;LSEQ=CCATCTGCAGAGGAGTAACT;RSEQ=ATTAAAATATTAGTAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:136:52,84:92,103:0.4096:2,2:23.1:1:31.5:1:0.11557:1.44125:60:135:0.4116:0:1.1 0/1:304:130:57,73:83,91:0.4276:2,2:26.5:1:31.5:1:0.56121:1.16751:60:260:0.4333:0:1.1 -12 78288910 . GA G 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.02947;SOR=0;LSEQ=AAAGGACAGGAGTGTTTCTT;RSEQ=AAAAAAAAATTCTCACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:6:2,4:9,66:0.0741:2,2:19.2:1:32.3:1:0.18577:3.58:60:12:0.075:0.0123:0.2 0/0:73:0:0,0:15,58:0:2,0:24.2:1:30:1:1:0:60:146:1:0:0.2 -12 81101931 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49938;SOR=Inf;LSEQ=TCAGCTATATTGAGCGGCTG;RSEQ=AGGACCTGCTGCACCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:12,19:0:2,0:23.1:1:31.2:1:1:0:60:30:1:0:0.2 0/1:39:2:1,1:17,20:0.0513:2,2:24:1:27:1:1:1.17:60:4:0.0513:0:1 -12 81110990 . G A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AAGCAGAGCTGCAGGGCTCA;RSEQ=ATGAGGACGAGCACGTGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:6:1:28:1:1:0:60:4:0.5:0:1 0/0:2:0:0,0:1,1:0:2,0:4.5:1:28.5:1:1:0:60:4:1:0:0.5 -12 81111172 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50662;SOR=0;LSEQ=GAAACCCTCAAGAGGTGTAC;RSEQ=ACGACCAACCCCAACCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:38,12:0.0385:2,2:38.5:1:30:1:0.44118:3.08248:60:4:0.04:0:1 0/0:38:0:0,0:26,12:0:2,0:22:1:30.4:1:1:0:60:76:1:0:0.2 -12 81111256 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19522;SOR=Inf;LSEQ=GAGAGCCTGCAGGAGTTGCT;RSEQ=AGAGAGCAGGTGGAGAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:21,39:0:2,0:22.6:1:31.8:1:1:0:60:120:1:0:0.1 0/1:48:2:1,1:18,28:0.0417:2,2:21:1:28:1:1:1.54:60:4:0.0426:0:1 -12 81163925 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49646;SOR=Inf;LSEQ=TGCCAGTCCGAGACAGCCTT;RSEQ=CTTCTCACAGGAATTATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:57,11:0:2,0:19.5:1:30.3:1:1:0:60:136:1:0:0.2 0/1:70:2:1,1:58,10:0.0286:2,2:26:1:31:1:0.29151:5.57762:60:4:0.0286:0:1 -12 81163991 . G T 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04548;SOR=Inf;LSEQ=TCTCCATGGCTTTTCTAGAG;RSEQ=AAACCTAACAGTGTGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:142,101:0:2,0:27.5:1:31:1:1:0:60:47.6:1:0:0.8 0/1:210:4:2,2:119,87:0.019:2,2:16:1:26.8:1:1:1.36573:60:8:0.0192:0:1.3 -12 81164017 . T C 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.40462;LSEQ=TAACAGTGTGGGTTTATCAA;RSEQ=CATTTTGACAAGACTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:270:222:115,107:25,22:0.8222:2,2:28.9:1:31.5:1:0.87393:1.05712:60:221:0.8216:0:1.1 1/0:261:170:87,83:49,42:0.6513:2,2:27.6:1:30.7:1:0.69838:1.11257:60:55.667:0.6498:0:1.2 -12 81164078 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49849;SOR=Inf;LSEQ=AATAAAAATTATGAACAAAG;RSEQ=AAGTGTAGTAAATCTGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:47,113:0:2,0:25.3:1:29.8:1:1:0:60:39:1:0:0.5 0/1:163:2:1,1:59,102:0.0123:2,2:25:1:29.5:1:1:1.72:60:4:0.0123:0:1.5 -12 81164095 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=AAGAAAGTGTAGTAAATCTG;RSEQ=TAATAGAAAAACTGACTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:28,95:0.016:2,2:9:1:27:1:0.41161:3.35:60:4:0.0161:0:3 0/0:117:0:0,0:37,80:0:2,0:21.2:1:31.1:1:1:0:60:28.25:1:0:0.4 -12 81164122 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50905;SOR=0;LSEQ=AAAAACTGACTATGCCTTGT;RSEQ=GGAAAATTTTTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:6,64:0.0278:2,2:11.5:1:30.5:1:0.18623:9.95:60:4:0.0294:0:1 0/0:52:0:0,0:6,46:0:2,0:26.5:1:29.8:1:1:0:60:104:1:0:0.1 -12 81164213 . A G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61297;SOR=0.37275;LSEQ=AAATTGTTCAATTTTTAAGC;RSEQ=GGTCCATTGTTATGATTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:23:1:32:1:1:0:60:14:0.875:0:1.3 1/0:14:10:0,10:0,4:0.7143:0,0:23.7:1:30.3:1:1:0:60:20:0.7143:0:1.1 -12 81164375 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTGTTTGTTTGTTTTT;RSEQ=TCCCATCATTTTCGGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 81205188 . A ATATGTG 27 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.48571;SOR=Inf;LSEQ=GTATATTCATATATACATAT;RSEQ=TGTGTGTGTGTATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:25.2:1:27.7:1:1:0:60:12:1:0:0.2 0/1:9:2:2,0:7,0:0.2222:0,0:7.5:1:27.8:1:1:0:60:4:0.2222:0.1111:3 -12 81205196 . G A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.26316;SOR=Inf;LSEQ=ATATATACATATATGTGTGT;RSEQ=TGTATATATATATATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:24.6:1:31.9:1:1:0:60:14:1:0:0.1 0/1:12:3:3,0:9,0:0.25:0,0:12.7:1:29.3:1:1:0:60:6:0.2727:0:2.3 -12 81205319 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51304;SOR=Inf;LSEQ=ATTAGCAATTGCTGCTGCTG;RSEQ=CGACGCCTGGCTGTTCGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:0:2,0:27:1:31.5:1:1:0:60:56:1:0:0 0/1:42:2:1,1:16,24:0.0476:2,2:24:1:28:1:1:1.49:60:4:0.0488:0:1 -12 82298329 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCAAAGCACTGGAATAG;RSEQ=CAGTTTATCTACTTCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:29:1:1:0:60:4:1:0:2.5 -12 82298338 . C T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGGAATAGCCAGTTTAT;RSEQ=TACTTCATTATCCTACTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:26.5:1:1:0:60:4:1:0:2.5 -12 82298472 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCAAAACCGCTCAGGC;RSEQ=TAGACCTCCTCACTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:0.25:2,2:20.5:1:32.5:1:0.46429:3.87298:60:4:0.2857:0:1 0/0:3:0:0,0:3,0:0:0,0:16.7:1:29.3:1:1:0:60:6:1:0:1 -12 82298568 . A G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14974;SOR=0.39858;LSEQ=CAGGGATAGTATGAGACACC;RSEQ=CCCAGCGTTTACAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:10:7,3:19,3:0.3125:2,2:16.1:1:28.7:1:0.34615:2.62113:60:9:0.2903:0:1 0/1:33:5:3,2:20,8:0.1515:2,2:27.8:1:30.6:1:0.6269:1.63932:60:10:0.1515:0:1 -12 82298589 . G GC 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CCCAGCGTTTACAGGAAAAG;RSEQ=CTTGTGAAATCAGACAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:13:7,6:28,10:0.2549:2,2:24.4:1:31.9:1:0.29846:2.35547:60:26:0.2549:0.0588:0.8 0/0:62:0:0,0:37,24:0:2,0:19.6:1:31.2:1:1:0:60:122:0.9839:0:0.2 -12 82298604 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24828;SOR=Inf;LSEQ=AAAAGGCTTGTGAAATCAGA;RSEQ=AACGCCTTTCAAACTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:43,29:0:2,0:22.6:1:32.1:1:1:0:59.8:144:1:0:0.3 0/1:82:3:1,2:47,32:0.0366:2,2:27.3:1:26.3:1:0.56694:2.89884:60:6:0.037:0:1 -12 82764072 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06776;SOR=Inf;LSEQ=TGATGGCCTCGATCCTAGAG;RSEQ=AAACAGATTTGACAAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:0:2,0:23:1:30.8:1:1:0:60:26:1:0:0.4 0/1:10:3:2,1:5,2:0.3:2,2:12.7:1:28.7:1:1:1.22183:60:6:0.3:0:1.3 -12 82764174 . C A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.5046;LSEQ=GGAGAAGCCAGGTTGCCCAA;RSEQ=TCCAGAGGTTGGTATAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:17,18:0.0541:2,2:6:1:28.5:1:1:1.06:40:4:0.0541:0:7.5 0/1:36:1:1,0:18,17:0.0278:2,0:3:0:27:0:1:0:40:2:0.0278:0:7 -12 82764479 . TTCTA T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGTTTTTTCTTTACTAT;RSEQ=TCTTTTTCTCTCTTTGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:30:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 82764823 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGCATGTAGGATTAAATGA;RSEQ=CACACTTACTATCTGTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:29.5:1:1:0:60:4:1:0:2 -12 83193586 . G C 34 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACAACAGAGGTCTTGCC;RSEQ=ATGAATCCCTCAGAGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:24:1:34:0:1:0:60:4:0.4:0:1 0/0:2:0:0,0:0,2:0:0,0:9:1:32.5:1:1:0:60:4:1:0:0 -12 87754814 . G C 53 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTTTTGCATTTGCTGAG;RSEQ=AGTCTTTTACTTCCAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:34.7:1:33.7:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:1:0,0:24:0:28:0:1:0:60:2:1:0:1 -12 87756302 . G C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCATTTATATTCCTCT;RSEQ=TAAACTGGTTATTCTAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:16.7:1:32.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 87756513 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49059;SOR=Inf;LSEQ=CATTTGGAGGAGAAGAGGCA;RSEQ=TCTGACTTTTTGGGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:27.2:1:32.6:1:1:0:60:40:1:0:0.1 0/1:23:2:1,1:11,10:0.087:2,2:5.5:1:28.5:1:1:1.09544:60:4:0.087:0:1 -12 87756606 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19821;SOR=Inf;LSEQ=TTTGAAGCTGCTGACCCTTG;RSEQ=ATGGGGTTTTTGTGGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:0:2,0:26:1:30.8:1:1:0:60:37:1:0:0.4 0/1:31:2:1,1:14,15:0.0645:2,2:28:0:31.5:1:1:1.07:60:4:0.0645:0:1 -12 87756803 . GC G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5013;SOR=Inf;LSEQ=TTCAAGGAGGCTGGAGAGCA;RSEQ=AAAAATGGGCACCTGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,14:0:2,0:21.2:1:32:1:1:0:60:46:0.9583:0:0.4 0/1:32:2:1,1:14,16:0.0625:2,2:10.5:1:31.5:1:1:1.14:60:4:0.0625:0:0 -12 87756834 . G A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=0;LSEQ=CACCTGCTCCTTCTTCTGGG;RSEQ=ACTTCTGACCTCTAGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,2:0.6667:2,2:28:1:29.7:1:1:1.85:60:12:0.6667:0:1.2 0/0:18:0:0,0:7,11:0:2,0:18.2:1:30.3:1:1:0:60:36:1:0:0.2 -12 87757148 . G A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAACCTGAGCCTCTAGCC;RSEQ=AAGTTATTGGAGATCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:1:0,2:24.5:1:27.9:1:1:0:60:7:1:0:1.1 1/1:4:4:2,2:0,0:1:0,2:24.5:1:26.3:1:1:0:60:3:1:0:1.3 -12 87757324 . A G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAGGGGAAAAGCACAGACC;RSEQ=GAGCTATAGCAATGGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:4,5:0,0:1:0,2:21.8:1:29.7:1:1:0:60:18:1:0:1 1/1:15:15:6,9:0,0:1:0,2:25.1:1:30.1:1:1:0:60:30:1:0:1.1 -12 87757467 . A G 52 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGCAGCTGGTGCTGGTC;RSEQ=CCCCTCCCCAGAGGAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:13.3:1:33:1:1:0:60:6:1:0:1 -12 87757632 . G C 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAGAAAAAGCACAGTTT;RSEQ=CCCCGCTGGGTGGCACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:8:0:33:0:1:0:60:2:1:0:1 1/1:5:5:1,4:0,0:1:0,2:21.4:1:30.4:1:1:0:60:10:1:0:1 -12 87757684 . T G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTGGATGGGGGAAGGGG;RSEQ=TTCCCCTTCCCCATGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:16:1:31.3:1:1:0:60:6:1:0:1 1/1:3:3:2,1:0,0:1:0,2:32:1:30.7:1:1:0:60:6:1:0:1 -12 87815695 . C G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17849;SOR=0;LSEQ=CCAACTCCAGAGGTTGGTAT;RSEQ=AGAGTTTGAAAGGCGTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:30,37:0.0286:2,2:24:0:33.5:1:1:1.23:24:4:0.0299:0:1 0/0:95:0:0,0:44,51:0:2,0:26.7:1:30.4:1:1:0:59.4:46.5:1:0:0.5 -12 87815751 . AA GC 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11196;SOR=Inf;LSEQ=TTTCCTGTAAACACTGGGCA;RSEQ=ATCTCATACTATCCCTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:9,16:0,1:0.8621:0,2:26.4:1:32.2:1:1:0:60:50:0.8929:0.0345:1 1/1:28:28:10,18:0,0:1:0,2:17.3:1:32:1:1:0:59.6:56:1:0.25:0.9 -12 90837901 . GA G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16691;SOR=Inf;LSEQ=CTCATGGGACCTAGAAAGGG;RSEQ=AAAGCCATGTCTCCCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:39,37:0:2,0:30:1:30.1:1:1:0:60:75:1:0:0.1 0/1:53:2:1,1:26,25:0.0377:2,2:14:0:33:0:1:1.03924:60:4:0.0377:0:0.5 -12 90837982 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52688;SOR=0;LSEQ=TCAGAAGCCTTTTCCTGTAA;RSEQ=TGCCAGGCAGCATCTCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:2,16:0.1:2,2:36:0:33.5:1:0.28421:6.73:60:4:0.1:0:1.5 0/0:11:0:0,0:3,8:0:2,0:24:1:30.1:1:1:0:60:22:1:0:0.1 -12 91237913 . A T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2048;SOR=Inf;LSEQ=TAGAAACACTGATTTAAAAA;RSEQ=TCAGAATTGAGGAACTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:112,87:0:2,0:25.9:1:30.5:1:1:0:60:198:1:0:0.5 0/1:165:2:1,1:92,71:0.0121:2,2:30:0:30.5:1:1:1.29371:60:4:0.0123:0:1.5 -12 91237920 . T A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-04;SOR=0.45116;LSEQ=ACTGATTTAAAAAATCAGAA;RSEQ=TGAGGAACTAATGAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:77:41,36:70,60:0.372:2,2:25.2:1:30.3:1:1:1.02428:60:76:0.3689:0:1.1 0/1:171:36:20,16:71,64:0.2105:2,2:25.3:1:29.1:1:0.85144:1.13:60:35:0.2071:0:1 -12 91237933 . GA G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.20914;SOR=Inf;LSEQ=ATCAGAATTGAGGAACTAAT;RSEQ=AAAGGTGGAATACAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:104,109:0:2,0:25.7:1:29.8:1:1:0:60:70:1:0:0.5 0/1:180:2:1,1:91,87:0.0111:2,2:24:0:30.5:1:1:1.04573:60:4:0.0112:0:0.5 -12 91237962 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49978;SOR=0;LSEQ=GAATACAGAGGAAATATTCA;RSEQ=CATATATTAAATCATCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:74,103:0.0112:2,2:28:1:29:1:1:1.39:60:4:0.0113:0:1 0/0:162:0:0,0:70,92:0:2,0:24.7:1:28.9:1:1:0:60:53:1:0:0.2 -12 91237979 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49963;SOR=0;LSEQ=TCATCATATATTAAATCATC;RSEQ=CAAGAGCATCCTGTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:56,92:0.0133:2,2:28.5:1:30:1:1:1.64:60:4:0.0136:0:2 0/0:135:0:0,0:52,83:0:2,0:26.5:1:29.3:1:1:0:60:134:1:0:0.2 -12 91238015 . G A 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAAAAAAATACATCATAAG;RSEQ=ATATGAGCTAACTGTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:18:5,13:9,44:0.2535:2,2:20.1:1:29.6:1:0.32418:1.86:60:36:0.2535:0:1.1 0/0:88:0:0,0:26,62:0:2,0:24.4:1:31.1:1:1:0:60:176:1:0:0.1 -12 91742514 . G A 28 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ACCAAGAGGAGGCATCAGGG;RSEQ=TAAGAGGCGATTCTGGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:24.5:1:28.5:1:1:0:60:4:0.4:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:2:0:31:0:1:0:60:2:0.3333:0:3 -12 91742590 . G A 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.7086;SOR=0.69934;LSEQ=AGGTGATCAGACACTACATG;RSEQ=GGAATGGTTGGGAATGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:3,2:12,3:0.25:2,2:23.8:1:31.2:1:0.55979:2.52201:60:10:0.25:0:2 0/1:16:3:3,0:9,4:0.1875:2,0:15.3:1:27:1:0.52857:0:60:6:0.1875:0:2.3 -12 91742612 . A C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22092;SOR=0;LSEQ=GAATGGTTGGGAATGAGGAA;RSEQ=CTGCTCAGATATACAGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:20,11:0,0:1:0,2:23.5:1:31.6:1:1:0:60:62:1:0:1.2 1/1:28:26:16,10:1,1:0.9286:2,2:25:1:30.9:1:1:1.57:60:52:0.9286:0:1.4 -12 92562048 . A G 43 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59006;SOR=0.28733;LSEQ=AGGAAGACAAGAATTCATAA;RSEQ=GGAAAAGATTAAAACATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:8,1:0.25:2,0:48.3:1:27.3:1:1:0:60:2:0.1818:0:1 0/1:12:1:1,0:9,2:0.0833:2,0:20:0:34:0:1:0:60:2:0.0833:0:1 -12 92787049 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4873;SOR=Inf;LSEQ=TGAGAAAGGAGGACTTTGCA;RSEQ=CTTCTTAGGGGAAGAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:15,2:0:2,0:24.7:1:31.8:1:1:0:59:34:1:0:0.8 0/1:19:2:2,0:16,1:0.1053:1,0:37:0:33:0:1:0:60:4:0.1053:0:1 -12 92787053 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05021;SOR=0.24098;LSEQ=AAAGGAGGACTTTGCACCTT;RSEQ=TTAGGGGAAGAGTGTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:11,1:5,1:0.6667:2,2:25.5:1:28.9:1:1:2.10:58.6:11:0.6471:0:1.2 0/1:19:6:6,0:12,1:0.3158:1,0:30.5:1:29.7:1:1:0:60:12:0.3333:0:1 -12 92787130 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51075;SOR=Inf;LSEQ=CCGGCATTTACAGGAAAAGG;RSEQ=TTCTGAAATCAGACAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:43,22:0:2,0:24.3:1:32:1:1:0:56.9:130:1:0:0.1 0/1:91:2:1,1:58,31:0.022:2,2:22:1:28:1:1:1.85738:60:4:0.0227:0:1 -12 92787198 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19176;SOR=0;LSEQ=GTTGGGCGACATGGCTTCTC;RSEQ=CCTTTCTAGTTCCCATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:39,60:0.0198:2,2:22.5:1:29.5:1:1:1.53:60:4:0.0198:0:1 0/0:129:0:0,0:53,76:0:2,0:28.1:1:29.7:1:1:0:58.4:24.8:1:0:0.1 -12 92787216 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19069;SOR=0;LSEQ=TCCCCTTTCTAGTTCCCATG;RSEQ=CAGCCATCTTGTGATTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:28,55:0.0235:2,2:23.5:1:31:1:1:1.95:60:4:0.0235:0:1 0/0:109:0:0,0:39,70:0:2,0:22.6:1:28.4:1:1:0:59.9:35.333:1:0:0.2 -12 92820481 . T A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20808;SOR=0;LSEQ=TAGGAGGATTGGCTCAGTCA;RSEQ=CTTGGCTGAGGCTCATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:30.5:1:30.8:1:1:0:60:8:0.5:0:1.5 0/0:4:0:0,0:4,0:0:0,0:19.3:1:31.5:1:1:0:60:8:1:0:0 -12 92820493 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGTCATCTTGGCTGAGG;RSEQ=TCATGAAACCAGGTGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:31:1:29:1:1:0:60:4:0.1667:0:2 0/0:5:0:0,0:5,0:0:0,0:21.4:1:33.8:1:1:0:60:10:1:0:0 -12 92820605 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13437;SOR=Inf;LSEQ=TTTGATGGTAGAAGGTATTT;RSEQ=GGGACTATTCCATTTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:103,4:0:1,0:24.4:1:30.6:1:1:0:60:214:0.9907:0:0.1 0/1:63:2:1,1:59,2:0.0317:1,2:14.5:1:30:1:0.0937:24.29032:60:4:0.0317:0:2 -12 92820633 . T C 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00122;SOR=Inf;LSEQ=TTCCATTTGAAATGAGAAGG;RSEQ=ACCTGACATTCTTTGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:147,31:0:2,0:23.1:1:29.5:1:1:0:60:88:1:0:0.1 0/1:139:8:7,1:99,32:0.0576:2,2:14.3:1:33:1:0.68004:2.25:60:16:0.0584:0:1 -12 92820637 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50547;SOR=0;LSEQ=ATTTGAAATGAGAAGGTACC;RSEQ=GACATTCTTTGAATTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:151,37:0.0105:2,2:32.5:1:31:1:0.36085:4.04034:60:4:0.0106:0:1 0/0:150:0:0,0:113,37:0:2,0:20.3:1:30.1:1:1:0:60:49:1:0:0.2 -12 92820752 . T C 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02439;SOR=1.49077;LSEQ=TTATCTAACTCATTCTCACT;RSEQ=CTTATTCCATGATGAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:71:30,41:178,208:0.1554:2,2:24.9:1:30.3:1:0.6048:1.16915:60:16.75:0.1506:0:1.1 0/1:432:93:49,44:154,185:0.2153:2,2:28.5:1:30.5:1:0.24129:1.34:60:45.5:0.2131:0:1.2 -12 92820790 . ATTG A 97 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.07887;SOR=3.32926;LSEQ=TGACATAAATGAGGTTTTTT;RSEQ=TTGTTGTTGTTGTTTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:0,3:96,192:0.0103:2,0:24.7:1:29:1:0.55328:0:60:6:0.0104:0.0034:0.7 0/1:268:9:3,6:103,156:0.0336:2,2:29.9:1:30.7:1:1:1.31919:60:18:0.034:0:0.2 -12 92820822 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50666;SOR=0;LSEQ=GTTGTTTTCTGGACACAAGG;RSEQ=AAGGTAGCTACCTGGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:33,136:0.0117:2,2:27:1:30.5:1:0.35906:4.07:60:4:0.012:0:1 0/0:132:0:0,0:34,98:0:2,0:21.9:1:31.7:1:1:0:60:264:1:0:0.2 -12 92821133 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGAAGCTAAACTGAGAA;RSEQ=TCTTGCAAATCATTGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:26.5:1:31:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 92821237 . G GGA 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGGCAGGGAGAGTTGAT;RSEQ=GGGGGGGCGGGGTTCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:48:0:31:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:26.5:1:32:1:1:0:60:4:1:0:1 -12 92821245 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGAGTTGATGGGGGGGG;RSEQ=GGGGTTCACACATCTTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:39:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31.5:1:1:0:60:4:1:0:1 -12 93919097 . C T 48 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGTAATCCCAGCTACTC;RSEQ=GGAGGTTGAGGCAGGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:13:1:30.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:21:0:31:0:1:0:60:2:1:0:5 -12 93919227 . G A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.35207;SOR=1.50431;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAGAAAAATTAGGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:15:14,1:29,20:0.2:2,1:13.6:1:29.6:1:0.01369:9.40:49.1:30:0.2727:0:2.9 0/1:84:23:23,0:24,26:0.2738:2,1:14.3:1:24.3:1:0:0:46.1:2.833:0.2742:0:3.5 -12 93919243 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20095;SOR=0;LSEQ=AAAAGAAAAGAAAAATTAGG;RSEQ=GCCATAATGTTCTTCCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:68,28:0.0204:2,2:20:0:31:1:0.50642:2.40383:60:4:0.0211:0:2.5 0/0:120:0:0,0:77,43:0:2,0:19.5:1:29.4:1:1:0:58.2:12.333:1:0:2.1 -12 93919278 . C A 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25082;SOR=Inf;LSEQ=CCATCAATAAAATTTGTTTC;RSEQ=CACGTGGAAATGCACAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:103,61:0:2,0:26.6:1:30.4:1:1:0:59.8:22.429:1:0:2.5 0/1:186:3:2,1:100,83:0.0161:2,2:10:1:23.7:1:1:1.66:60:2:0.0112:0:3.3 -12 93919282 . G A 218 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.033;LSEQ=CAATAAAATTTGTTTCCCAC;RSEQ=TGGAAATGCACAACCATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:162:160:100,60:2,0:0.9877:0,2:27.9:1:29.8:1:0.53071:0:59.9:31:0.9873:0:2.6 1/0:192:139:76,63:29,23:0.724:2,2:27.7:1:28.6:1:1:1.04497:59.8:16.375:0.712:0:2.7 -12 93919285 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20569;SOR=0;LSEQ=TAAAATTTGTTTCCCACGTG;RSEQ=AAATGCACAACCATGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:103,59:0.0122:2,2:23:1:28.5:1:1:1.73945:60:4:0.0127:0:3.5 0/0:197:0:0,0:108,89:0:2,0:27.2:1:30:1:1:0:59.9:23.625:1:0:2 -12 93919297 . C G 222 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04668;LSEQ=CCCACGTGGAAATGCACAAC;RSEQ=ATGGGGCATTTTTACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:181:178:108,70:2,0:0.9834:0,2:27:1:29.8:1:0.52204:0:60:43.5:0.9831:0:2.5 1/0:214:157:86,71:32,25:0.7336:2,2:26.3:1:28.9:1:0.87776:1.0565:60:18.625:0.7268:0:2.6 -12 93919335 . T A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25093;SOR=Inf;LSEQ=TCTGAGTGGCCACATGGGGG;RSEQ=GCTGAGTCGAAAGGCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:103,91:0:2,0:24.8:1:29.9:1:1:0:60:388:1:0:2.5 0/1:219:3:3,0:113,103:0.0137:2,0:6:1:20.7:1:0.24921:0:60:2:0.0093:0:3.7 -12 93919341 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21716;SOR=0;LSEQ=TGGCCACATGGGGGTGCTGA;RSEQ=TCGAAAGGCACATTTAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:0,2:95,92:0.0106:2,0:9:1:30:1:0.24603:0:60:4:0.0106:0:4 0/0:216:0:0,0:107,109:0:2,0:10:0:14:0:1:0:60:0:0:0:5 -12 93919355 . T A 225 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03509;LSEQ=TGCTGAGTCGAAAGGCACAT;RSEQ=TAACAACGTGTTGTTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:195:193:89,104:0,2:0.9897:0,2:23.6:1:29.7:1:0.50124:0:60:192:0.9897:0:2.9 1/0:214:165:80,85:23,25:0.771:2,2:22.3:1:28.7:1:1:1.02:60:54:0.7714:0:3 -12 93919390 . G A 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0.21541;LSEQ=TACTGTGAGCAAGGCTATTC;RSEQ=GGGATGCGTTTTGCTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:178:169:67,102:4,5:0.9494:2,2:24.5:1:30.5:1:1:1.21653:60:83.5:0.9489:0:3.1 1/1:176:141:67,74:16,19:0.8011:2,2:25.7:1:29.8:1:1:1.07:59.8:46:0.7977:0:3.1 -12 93919397 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23756;SOR=0;LSEQ=AGCAAGGCTATTCGGGGATG;RSEQ=GTTTTGCTATGCATCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:66,97:0.0121:2,2:23.5:1:31.5:1:1:1.47:60:4:0.0123:0:4.5 0/0:173:0:0,0:77,96:0:2,0:26.5:1:30.1:1:1:0:59.8:56.667:1:0:2.5 -12 93919402 . T C 36 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24797;SOR=Inf;LSEQ=GGCTATTCGGGGATGCGTTT;RSEQ=GCTATGCATCCCCCCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:65,97:0:2,0:26.2:1:30:1:1:0:60:80:1:0:2.9 0/1:168:3:1,2:74,91:0.0179:2,2:14.3:1:23:1:1:1.62186:50:2:0.012:0:5 -12 93919408 . G A 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.2005;LSEQ=TCGGGGATGCGTTTTGCTAT;RSEQ=CATCCCCCCAAAATCCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:148:60,88:5,4:0.9427:2,2:26.6:1:29.1:1:0.49036:1.82603:60:147:0.9423:0:3.2 1/0:167:128:60,68:16,22:0.7665:2,2:27.6:1:28.1:1:0.71142:1.21:60:31:0.7654:0:3.2 -12 93919441 . A G 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=0.22931;LSEQ=ATCCCAATACATGCAGTAAT;RSEQ=AAGATGATTAATATAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:145:135:50,85:6,4:0.931:2,2:23.8:1:31.2:1:0.18508:2.5328:60:32.75:0.9291:0:2.9 1/0:151:114:47,67:15,22:0.755:2,2:24.1:1:31.2:1:1:1.03:60:113:0.7533:0:2.9 -12 93919495 . G A 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00299;SOR=0.2213;LSEQ=TGACTCTGTCTTTTTCATGG;RSEQ=GAATTTCCTCCCCAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:76:24,52:3,2:0.9383:2,2:26:1:30.5:1:0.32694:3.19806:60:75:0.9494:0:1.9 1/0:78:60:21,39:7,11:0.7692:2,2:29.5:1:30:1:0.78484:1.17925:60:59:0.7662:0:1.7 -12 93919724 . G T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTTAGGAAACAGCAAA;RSEQ=CCCTATAAAAGGAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:46.5:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 95539120 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53613;SOR=Inf;LSEQ=GATTCTGTACTGGTCAGGTT;RSEQ=CTGAATCTTTTCTTAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:20.7:1:28.9:1:1:0:60:11:1:0:0.2 0/1:23:2:1,1:13,8:0.087:2,2:23.5:1:28.5:1:1:1.58984:60:4:0.087:0:1 -12 95539279 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTCAGCAAGAATCCTCTTA;RSEQ=GTTGGTTTAGCCAGAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:40.5:1:32.5:1:1:0:60:4:1:0:0 0/1:5:2:1,1:0,3:0.4:0,2:20:1:32:0:0.4:0:54:4:0.4:0:4 -12 95539282 . TG CA 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGCAAGAATCCTCTTAAGT;RSEQ=GTTTAGCCAGAATCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:37.5:1:31.5:1:1:0:60:4:1:0:0 0/1:5:2:1,1:0,3:0.4:0,2:24:1:32:1:0.4:0:54:4:0.4:0:3 -12 95539285 . T C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGAATCCTCTTAAGTTGG;RSEQ=TTAGCCAGAATCTCCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:34.5:1:31:0:1:0:60:4:1:0:0 0/1:5:2:1,1:0,3:0.4:0,2:26:1:32.5:1:0.4:0:54:4:0.4:0:3 -12 95843286 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22125;SOR=Inf;LSEQ=AGGGGAGAAGCCATGTCGCC;RSEQ=AACTCCAGAGGTTGGTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:42,34:0:2,0:29.3:1:31.5:1:1:0:59.3:152:1:0:0.1 0/1:68:2:1,1:35,31:0.0294:2,2:29.5:1:30:1:1:1.12701:60:4:0.0299:0:1.5 -12 95843385 . T A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1079;SOR=Inf;LSEQ=CTCATACTATCCCTGACTGA;RSEQ=TAGTGTAAAAACAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:2,17:0:2,0:28.4:1:30.1:1:1:0:60:38:1:0:0.1 0/1:21:4:1,3:4,13:0.1905:2,2:19.8:1:26.5:1:1:1.08:60:3:0.15:0:1 -12 97487531 . C T 52 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6044;SOR=0.42404;LSEQ=TTGTCTACAGTAGACCAGTC;RSEQ=GAGATATTTGGAAAAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:15.7:1:33:1:1:0:60:6:0.3333:0:1 0/1:6:1:1,0:5,0:0.1667:0,0:33:0:33:0:1:0:60:2:0.1667:0:1 -12 97487633 . G T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02771;LSEQ=CACAGAAGTACTGCAGGACT;RSEQ=ACTTACAGGGTAAAAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:55:54,1:4,1:0.9167:2,1:30.6:1:30.5:1:0.16102:12.19:60:110:0.9167:0:1 0/1:36:8:8,0:28,0:0.2222:1,0:33.8:1:30.4:1:1:0:60:16:0.2222:0:1 -12 97487819 . GT G 141 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.15392;SOR=1.61183;LSEQ=TGGCATGTTTAGGGATACGT;RSEQ=TTTTTTTTTTGTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:16:9,7:238,305:0.0284:2,2:29.5:1:31.2:1:0.44462:1.65:60:32:0.0284:0:0.4 0/1:556:25:11,14:240,288:0.045:2,2:26.2:1:30.5:1:1:1.06051:59.2:50:0.0461:0:0.5 -12 97487825 . T TTTG 133 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTAGGGATACGTGTTTTT;RSEQ=TTTTTGTTTTTTTTTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:0:0,0:219,294:0:2,0:21.1:1:29.9:1:1:0:59:127.25:1:0:1.4 0/1:526:21:10,11:220,284:0.0399:2,2:21.7:1:30.3:1:0.82337:1.17:60:42:0.0403:0.0114:0.1 -12 97487829 . TTG GT 116 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AGGGATACGTGTTTTTTTTT;RSEQ=TTTTTTTTTTGTAACTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:17:8,9:203,282:0.0333:2,2:8.2:1:28.5:1:0.80357:1.23:60:34:0.0336:0.0294:0.2 0/0:505:0:0,0:206,287:0:2,0:21.3:1:29.3:1:1:0:59:69.429:0.9838:0:1 -12 97487831 . G GT 170 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.82593;SOR=0.93905;LSEQ=GGATACGTGTTTTTTTTTTT;RSEQ=TTTTTTTTTTGTAACTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:46:4,42:110,176:0.0966:2,2:16.7:1:30.9:1:4e-05:6.53517:57.7:92:0.1565:0:0.7 0/1:493:45:14,31:148,209:0.0913:2,2:21.8:1:28.9:1:0.20024:1.56632:55.9:44:0.1092:0.002:1.2 -12 97487833 . T G 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.32798;SOR=1.84768;LSEQ=ATACGTGTTTTTTTTTTTGT;RSEQ=TTTTTTTTGTAACTTTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:6:1,5:195,282:0.0124:2,2:13.7:1:30.2:1:0.40862:3.45021:60:5:0.0105:0:2.5 0/1:484:11:6,5:191,281:0.0227:2,2:7.5:1:24.6:1:0.36803:1.76:60:1.75:0.0146:0:2.3 -12 97487836 . T TG 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0;SOR=0.10149;LSEQ=CGTGTTTTTTTTTTTGTTTT;RSEQ=TTTTTGTAACTTTAACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:129:39,90:152,200:0.2665:2,2:22:1:28.4:1:0.0115:1.75183:58.7:3.778:0.2262:0.0455:1.3 0/1:479:17:6,11:188,274:0.0355:2,2:24.3:1:32.5:1:0.80317:1.25732:60:34:0.0358:0.0063:0.3 -12 97487948 . G A 25 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20457;SOR=Inf;LSEQ=AAAGAACAGATGGTCACAGT;RSEQ=TACAAAAAGGTCTACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:7,82:0:2,0:21.5:1:31.8:1:1:0:60:43.5:1:0:0 0/1:74:2:1,1:11,61:0.027:2,2:6:0:25.5:1:0.29989:5.35:60:4:0.0274:0:1 -12 98095696 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.57135;LSEQ=GCTTGGCCAAACTTTAATCA;RSEQ=GCTTCTGAACCATTTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:19,23:0.0455:2,2:34:1:29:1:1:1.21:60:4:0.0465:0:1.5 0/1:38:1:0,1:24,13:0.0263:2,0:1:0:27:0:0.36842:0:60:2:0.0278:0:1 -12 100534396 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGCTGAGGCAGGAGAA;RSEQ=TGATTGAAGCCAGGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:29:1:1:0:60:4:1:0:1 -12 100536318 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09677;SOR=Inf;LSEQ=GAAGCCGCAGGCTGACTCCA;RSEQ=TGCGGGCTGGGGTGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:0:2,0:21.5:1:32.1:1:1:0:60:42:1:0:0.1 0/1:10:2:1,1:5,3:0.2:2,2:36:1:28.5:1:1:1.58108:60:4:0.2:0:1 -12 100967441 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48768;SOR=Inf;LSEQ=TCGAAACAGGCGGCGGCCAG;RSEQ=GGCTACTGACCCTGAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:0:2,0:26.7:1:30.8:1:1:0:60:26:1:0:0 0/1:16:2:1,1:10,4:0.125:2,2:31:0:29.5:1:1:2.34522:60:4:0.125:0:1 -12 100967543 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49231;SOR=0;LSEQ=GAGTTGTCGCCCCGCTGGGA;RSEQ=AAGTGACCCTCCTGCGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:3,10:0.1333:2,2:18:1:28:1:0.47619:3.03:60:4:0.1333:0:1 0/0:11:0:0,0:2,9:0:2,0:25.3:1:29.9:1:1:0:60:10:1:0:0 -12 101083978 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48846;SOR=Inf;LSEQ=TTTAGCAAGATGAATTCCAG;RSEQ=TGATTCGTATGTAACCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:22.6:1:31:1:1:0:60:18:1:0:0 0/1:21:2:1,1:5,14:0.0952:2,2:5.5:1:25.5:1:0.5:2.65:60:4:0.0952:0:1.5 -12 102796005 . G GAT 29 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=0.04329;SOR=Inf;LSEQ=TCTTGAGAGGCAGGGACTAA;RSEQ=ATATATATATATATATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:0:1,0:17.5:1:32:1:1:0:60:34:1:0:0.8 0/1:5:2:2,0:3,0:0.4:0,0:8:1:29.8:1:1:0:60:4:0.4:0.2:0.5 -12 102796022 . A AT 29 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.39665;LSEQ=TAAGATATATATATATATAT;RSEQ=TTTTTTTTTTCTTTTCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:15,1:0.1053:1,0:15.5:1:29.8:1:1:0:60:4:0.1111:0.0526:1 0/1:7:1:1,0:6,0:0.1429:0,0:50:0:28:0:1:0:60:2:0.1429:0:0 -12 102796024 . TT A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.53962;SOR=0;LSEQ=AGATATATATATATATATAT;RSEQ=TTTTTTTCTTTTCTATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:3,0:14,1:0.1579:1,0:16.7:1:28.1:1:1:0:60:6:0.1667:0.0526:0.7 0/0:7:0:0,0:7,0:0:0,0:27.9:1:29.9:1:1:0:60:14:1:0:0.1 -12 102796522 . G C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70889;SOR=0.65555;LSEQ=GACAGGCCCTTAGTACTTTT;RSEQ=CCAAACCTCACTCAGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:30:1,29:0,6:0.8333:0,1:27.7:1:31.6:1:1:0:60:60:0.8571:0:1.1 1/0:17:13:0,13:0,4:0.7647:0,1:18.8:1:31.2:1:1:0:60:26:0.7647:0:1.1 -12 102811349 . AT A 49 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.12774;LSEQ=TTGCCTCTTTTATAATTTTT;RSEQ=TTTTTTTTTTCATTTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:17,0:0.15:1,0:8.3:1:31.3:1:1:0:60:6:0.15:0.1:0 0/1:6:1:1,0:5,0:0.1667:0,0:15:0:32:0:1:0:60:2:0.1667:0:0 -12 102811559 . A ATCATCCTTGCCTCTGTCTGATCTCTATTTTCCTCTTATTGCACACTTTCCTCAACCACACCCACCTCT 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=2.000;MSILEN=1;SSF=0.00056;SOR=Inf;LSEQ=TTGCTGTCTGCTCCTCTCTC;RSEQ=TCATCCTTGCCTCTGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:921:0:0,0:589,331:0:2,0:24.7:1:30:1:1:0:60:47.421:1:0:0.1 0/1:832:10:2,8:508,314:0.012:2,2:15.4:1:25.2:1:0.01665:6.45753:60:9:0.011:0.012:0.7 -12 102813524 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51299;SOR=0;LSEQ=TGCAATCTGCTTTCTTCAGT;RSEQ=TTCCACCCAGCTCCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:27,160:0.0106:2,2:8:1:29:1:0.27502:5.84:60:4:0.0108:0:1 0/0:134:0:0,0:19,115:0:2,0:21.9:1:31.3:1:1:0:60:25.8:1:0:0.2 -12 102869354 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60032;SOR=0.43475;LSEQ=AGTTATTCACACACTCCCTG;RSEQ=GGTTGTAAATCCACAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:157,40:0.0101:2,2:22.5:1:29:1:0.37044:3.88917:60:4:0.0103:0:1 0/0:228:1:0,1:154,73:0.0044:2,0:1:0:24:0:0.32456:0:60:2:0.0044:0:1 -12 102869479 . G A 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21947;SOR=4.63989;LSEQ=GCATCCACCAGCTCAGCCCC;RSEQ=CAGAGCGTCTCCGGTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:0,1:203,205:0.0024:2,0:19:0:32:0:1:0:60:2:0.0025:0:1 0/1:444:5:3,2:219,219:0.0113:2,2:23:1:29:1:1:1.50:60:10:0.0114:0:1 -12 102869600 . G T 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GCCCAAGAAACAGAGGGAGG;RSEQ=TCAGGTTTCCTCCTTGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:104,200:0:2,0:25.8:1:31.2:1:1:0:60:32.778:1:0:0.2 0/1:272:14:5,9:92,165:0.0515:2,2:20.7:1:29.6:1:1:1.00362:60:28:0.0522:0:1 -12 102869603 . A G 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6651;SOR=1.77361;LSEQ=CAAGAAACAGAGGGAGGGTC;RSEQ=GGTTTCCTCCTTGATCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:2:1,1:98,192:0.0068:2,2:33:1:29.5:1:1:1.95:60:4:0.0069:0:1 0/1:248:3:2,1:80,165:0.0121:2,2:6.3:1:23.7:1:0.25477:4.10:60:2:0.0081:0:1 -12 102869641 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28811;SOR=3.66927;LSEQ=TTGCAAGGGGAGTGGGGTGG;RSEQ=ACAGAAGTGCATTGACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:33,133:0.006:2,0:50:0:30:0:1:0:60:2:0.0061:0:1 0/1:92:2:1,1:18,72:0.0217:2,2:14.5:1:28:1:0.37219:3.92:60:4:0.0225:0:1 -12 102871775 . CT C 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAATAGATTTCTCTTTTT;RSEQ=TTTTTTTTTTTTTTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:40.5:1:31.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 102872095 . G GA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.5107;SOR=0;LSEQ=AGAAAGACATGAGAAAAAAA;RSEQ=AAAAAAAAATCAGAAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:2,0:62,0:0.0313:1,0:11.5:1:31:0:1:0:60:4:0.0323:0:0 0/0:45:0:0,0:43,2:0:1,0:25.3:1:31.8:1:1:0:59.2:21.5:1:0:0.2 -12 102872155 . C CT 226 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.0022;SOR=0.45673;LSEQ=AAACCCAAATTTTAAAAGTT;RSEQ=TTTTTTTTTTAATCTTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:191:150:139,11:27,1:0.7853:1,2:25.5:1:31.4:1:0.69421:2.12946:60:300:0.7853:0.0942:0.3 1/0:128:80:72,8:37,4:0.625:2,2:23.4:1:30.4:1:1:1.02755:60:79:0.632:0.125:0.2 -12 102873754 . G GA 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATCTGCACCTGCAAAA;RSEQ=AAAAAAAAAATCCCCAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:42.5:1:30:1:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 104974951 . T C 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03297;SOR=Inf;LSEQ=GGATGCTTCTTGCATCCTTA;RSEQ=CCTTGAGGACTTTGGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:11,0:0:0,0:24.2:1:31.5:1:1:0:60:22:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:12.5:1:30.5:1:1:0:60:4:0.6667:0:2 -12 104975016 . G T 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04779;SOR=Inf;LSEQ=TAGCTTCAGGGTGTTGACTT;RSEQ=CATTAGCTTCTGCTGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:20,1:0:1,0:25.3:1:32.1:1:1:0:60:42:1:0:0 0/1:13:3:2,1:10,0:0.2308:0,2:32:1:28:1:0.23077:0:60:6:0.2308:0:1.7 -12 104975209 . G A 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-04;SOR=2.33376;LSEQ=GAGAAAGCTTGATAATTGAG;RSEQ=AAAATTTATCCCTATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:36:15,21:92,122:0.144:2,2:23.2:1:30.2:1:1:1.05552:60:72:0.1463:0:1.1 0/1:287:81:37,44:93,113:0.2822:2,2:26.5:1:29.1:1:1:1.02:60:26:0.2746:0:1.1 -12 104975323 . C T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03869;SOR=Inf;LSEQ=ATTGTCGAGTGACTGGAAAC;RSEQ=GTTGATTTAAAGGAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:5,37:0:2,0:24.6:1:29.8:1:1:0:60:41:1:0:0.1 0/1:35:4:0,4:3,28:0.1143:2,0:14.5:1:30.5:1:1:0:60:8:0.1143:0:1 -12 105192655 . C T 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18108;SOR=0.50466;LSEQ=AGTGACTAGGCTTGTTTGTA;RSEQ=GGGAAGTATTGTCAAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:57:33,24:7,4:0.8382:2,2:28.3:1:30.1:1:1:1.26829:60:56:0.8358:0:1 1/0:54:39:23,16:8,7:0.7222:2,2:25.1:1:30:1:0.76485:1.25:60:78:0.7222:0:1.1 -12 106214220 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25614;SOR=0;LSEQ=CCTCTTGTCCTCACTCTTGG;RSEQ=AGTTTCTTCTCTGGTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:3:1,2:113,67:0.0164:2,2:17:1:28:1:0.55766:3.35:60:6:0.0166:0:1.3 0/0:148:0:0,0:99,48:0:2,0:24.6:1:31.6:1:1:0:60:72.5:0.9932:0:0.3 -12 106214293 . G A 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAAAGAGAGATCAAATCT;RSEQ=TGGAGACCCTTGCTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:112,137:0:2,0:26.5:1:31.8:1:1:0:60:48.8:1:0:0.2 0/1:218:50:27,23:83,85:0.2294:2,2:25.9:1:28.8:1:0.6301:1.20:60:100:0.2315:0:1.1 -12 106214315 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23209;SOR=Inf;LSEQ=GGAGACCCTTGCTCTTTGAG;RSEQ=ACCTTGCCTGCAGCCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:82,124:0:2,0:26.2:1:31.8:1:1:0:60:50.5:1:0:0.1 0/1:192:2:1,1:77,113:0.0104:2,2:35:1:28.5:1:1:1.46:60:4:0.0105:0:1 -12 106214318 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2282;SOR=Inf;LSEQ=GACCCTTGCTCTTTGAGCAC;RSEQ=TTGCCTGCAGCCCTTAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:82,123:0:2,0:25.3:1:31.5:1:1:0:60:204:1:0:0.1 0/1:188:2:1,1:75,111:0.0106:2,2:26:1:29:1:1:1.48:60:4:0.0109:0:1 -12 106214322 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50069;SOR=0;LSEQ=CTTGCTCTTTGAGCACCTTG;RSEQ=CTGCAGCCCTTAAGCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:79,120:0.01:2,2:25.5:1:29.5:1:1:1.52:60:4:0.0102:0:1 0/0:177:0:0,0:72,104:0:2,0:23.3:1:31:1:1:0:60:87:0.9943:0:0.3 -12 106214325 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50063;SOR=0;LSEQ=GCTCTTTGAGCACCTTGCCT;RSEQ=CAGCCCTTAAGCTGACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:73,118:0.0104:2,2:30.5:1:29:1:1:1.61:60:4:0.0105:0:1 0/0:170:0:0,0:68,102:0:2,0:23:1:31.2:1:1:0:60:41.5:1:0:0.3 -12 106589370 . C T 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTACTTGCTGCTCCTTAA;RSEQ=GGGAGGGTGTGGGCAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:22.4:1:31.4:1:1:0:60:10:0.7143:0:1 1/1:1:1:1,0:0,0:1:0,0:4:0:30:0:1:0:60:2:1:0:1 -12 106589658 . C G 221 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TGCAAACCAGCCGAGAAGCG;RSEQ=AGCATGACCAAGATCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:172,152:0:2,0:24.6:1:31.9:1:1:0:60:323:1:0:0.1 1/0:287:163:88,75:67,57:0.5679:2,2:27.2:1:30.1:1:1:1.00179:60:22.286:0.5591:0:1.2 -12 106589663 . T G 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00457;SOR=Inf;LSEQ=ACCAGCCGAGAAGCGCAGCA;RSEQ=GACCAAGATCAACAATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:166,162:0:2,0:25:1:30.3:1:1:0:60:108.333:1:0:0.1 0/1:286:7:4,3:146,132:0.0245:2,2:22.1:1:29.4:1:1:1.20:60:6:0.0214:0:1.1 -12 106589765 . G A 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20982;SOR=Inf;LSEQ=CCCAAGTCCTTGTTTGACTT;RSEQ=CTGTGCAACTTACAGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:28,98:0:2,0:20.4:1:32:1:1:0:60:62:1:0:0.1 0/1:107:2:1,1:21,84:0.0187:2,2:8:1:23:1:0.37048:3.93:60:4:0.0194:0:1.5 -12 107194087 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAGCTTTTACTCATGGC;RSEQ=GAAGGCAAAGCTGGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:32:0:1:0:60:4:1:0:1 -12 107194580 . G A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13153;SOR=0.32598;LSEQ=AAGTAAGGAAATTCCAAAGA;RSEQ=ATTGTATATAGGAAAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:15,0:23,1:0.3846:1,1:26.5:1:29.3:1:1:0:60:14:0.3684:0:1.1 0/1:18:3:3,0:14,1:0.1667:1,0:6:1:25.7:1:1:0:60:2:0.1176:0:1 -12 107194707 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24847;SOR=0;LSEQ=GTGACAGTGTTCATCTTGCA;RSEQ=CCTTGCCTAGTGTACTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:1,2:146,93:0.0124:2,2:15:1:30:1:0.56301:3.12467:60:6:0.0126:0:1.3 0/0:239:0:0,0:147,92:0:2,0:25.7:1:31.8:1:1:0:60:478:1:0:0.2 -12 107194776 . T G 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51683;SOR=0.89303;LSEQ=CCCTAAAGATTAAATGAGTA;RSEQ=TGTTCTCTCATTTGGTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:299:157:67,90:51,91:0.5251:2,2:24.5:1:31.9:1:0.23889:1.33:60:156:0.5235:0:1.1 0/1:310:154:71,83:69,87:0.4968:2,2:26.7:1:31.2:1:0.8195:1.08:60:153:0.5:0:1.1 -12 107194826 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2453;SOR=0;LSEQ=AAACAAATGAAGATACCGCT;RSEQ=TATTTGCCAACATACTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:58,124:0.0109:2,2:19.5:1:27.5:1:0.53968:2.13:60:4:0.0109:0:2 0/0:187:0:0,0:62,125:0:2,0:25.4:1:31.3:1:1:0:60:186:1:0:0.4 -12 107194832 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23711;SOR=0;LSEQ=ATGAAGATACCGCTGTATTT;RSEQ=CCAACATACTAACTTTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:44,113:0.0126:2,2:41:1:29.5:1:0.48722:2.55:60:4:0.0128:0:1 0/0:167:0:0,0:50,117:0:2,0:1:0:12:0:1:0:60:0:0:0:1 -12 107194904 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50054;SOR=0;LSEQ=ACAGGGCTTTCTGAAAAATA;RSEQ=GCTTAAGTAGTAAAAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:4,36:0.0476:2,2:14.5:1:30.5:1:0.22648:8.16:60:4:0.0488:0:1 0/0:33:0:0,0:2,31:0:2,0:24.8:1:30.7:1:1:0:60:66:1:0:0 -12 107610649 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21212;SOR=Inf;LSEQ=AGTACGAGATGCCGCCCAGC;RSEQ=TTTACAGGAAAAGTCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:13.9:1:30.5:1:1:0:58.3:48:1:0:0 0/1:21:2:1,1:12,7:0.0952:2,2:41.5:1:30.5:1:1:1.66897:60:4:0.0952:0:1.5 -12 107610748 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTTTCTAGGTCCCGTGG;RSEQ=AGCCATCTTGCTATTACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:14,16:0.0625:2,2:35.5:1:28:1:1:1.14:50:4:0.0625:0:1 0/0:14:0:0,0:5,9:0:2,0:21.3:1:32.6:1:1:0:48.9:28:1:0:0.1 -12 108602855 . C G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05095;LSEQ=AGGTTTTGTCCTTCCTACTC;RSEQ=CAGAGCCAGAGCAAGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:69:62,7:20,3:0.75:2,2:26:1:29.6:1:0.70662:1.32:60:68:0.764:0:1.1 0/1:77:10:10,0:50,17:0.1299:2,0:30.6:1:30.5:1:0.10568:0:60:20:0.1316:0:1 -12 108602871 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22258;SOR=Inf;LSEQ=ACTCCCAGAGCCAGAGCAAG;RSEQ=AATGCTCTTTTCATTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:95,22:0:2,0:22.4:1:31.6:1:1:0:60:116:1:0:0.6 0/1:105:2:1,1:73,30:0.019:2,2:13.5:1:28:1:0.50531:2.41012:60:4:0.0192:0:2.5 -12 108602874 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2194;SOR=Inf;LSEQ=CCCAGAGCCAGAGCAAGCAA;RSEQ=GCTCTTTTCATTTGTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:98,24:0:2,0:22.4:1:30.1:1:1:0:60:39.667:1:0:0.6 0/1:108:2:1,1:73,33:0.0185:2,2:16.5:1:30.5:1:0.53254:2.19426:60:4:0.0187:0:2.5 -12 108602893 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20425;SOR=Inf;LSEQ=ATGCTCTTTTCATTTGTTTA;RSEQ=AGAGTGGGGTAGCCACTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:128,63:0:2,0:20.7:1:31.8:1:1:0:60:382:1:0:0.7 0/1:158:2:1,1:100,56:0.0127:2,2:15.5:1:25:1:1:1.77872:60:4:0.0127:0:1 -12 108602970 . C A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13653;LSEQ=ATTTCAAAAAAACTTGAAAA;RSEQ=CTTGCAGTGCCTGGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:347:261:117,144:36,50:0.7522:2,2:25.5:1:29.6:1:0.70743:1.13:60:51.2:0.7485:0:1.8 0/1:308:90:42,48:103,115:0.2922:2,2:29:1:29.4:1:1:1.02353:60:89:0.2918:0:1.7 -12 108603016 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17103;LSEQ=TAGGAATAAATATTTCCTTG;RSEQ=TGAATGTGTGAGCTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:215:168:64,104:16,31:0.7814:2,2:26:1:31.4:1:0.73315:1.19:60:41:0.7773:0:2.5 0/1:193:73:29,44:48,72:0.3782:2,2:25:1:31:1:1:1.01144:60:146:0.3822:0:2 -12 108603024 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49959;SOR=0;LSEQ=AATATTTCCTTGATGAATGT;RSEQ=TGAGCTCATTTTTGTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:66,122:0.0105:2,2:28.5:1:31.5:1:1:1.84:60:4:0.0109:0:3 0/0:174:0:0,0:64,109:0:2,0:24.5:1:31:1:1:0:60:56.667:0.9942:0:0.8 -12 108603028 . G A 29 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60289;SOR=2.2622;LSEQ=TTTCCTTGATGAATGTGTGA;RSEQ=CTCATTTTTGTCTTCTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:1,0:62,116:0.0056:2,0:1:0:25:0:0.35196:0:60:2:0.0057:0:3 0/1:159:2:1,1:56,101:0.0126:2,2:18:0:29:1:1:1.80:60:4:0.0127:0:1.5 -12 108603041 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0793;LSEQ=TGTGTGAGCTCATTTTTGTC;RSEQ=TCTCTCGAAGGGGTGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:150:119:42,77:10,21:0.7933:2,2:21.9:1:31.2:1:0.83418:1.14:60:38.667:0.7891:0:2.6 0/1:134:31:12,19:30,73:0.2313:2,2:23.8:1:31.1:1:0.37796:1.53:60:62:0.2331:0:2.5 -12 109003754 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18354;SOR=0;LSEQ=CCAGGGTGAGCATTAACTGG;RSEQ=ACCGACTGTGTGCCAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:5,10:0.1176:2,2:29.5:1:30.5:1:1:1.91:60:4:0.1176:0:1.5 0/0:22:0:0,0:9,13:0:2,0:27.6:1:31:1:1:0:60:44:1:0:0.1 -12 109004229 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTGAATATCTGGGGGCA;RSEQ=GGCTGCAGAGTGGGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:29:1:1:0:60:4:1:0:1 -12 109592181 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CACAGTGGCGACCTCTGACT;RSEQ=ACATTTTAAATTTCCCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:21,25:0:2,0:24.1:1:31.3:1:1:0:60:92:1:0:0.1 0/1:101:2:1,1:47,52:0.0198:2,2:9:0:31:1:1:1.11:60:4:0.0198:0:1.5 -12 109592193 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11109;SOR=0;LSEQ=CTCTGACTCACATTTTAAAT;RSEQ=TCCCATATTTTCCACCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:15,22:0.0513:2,2:23:1:31:1:1:1.45:60:4:0.0526:0:1 0/0:77:0:0,0:37,40:0:2,0:22.8:1:30.1:1:1:0:60:76:1:0:0.3 -12 109960852 . TC T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50587;SOR=0;LSEQ=TCGCCTCTGTGTCCTTTCCC;RSEQ=CCTCACCTCTGACAGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:132,66:0.01:2,2:8.5:1:26:1:1:1.99258:60:4:0.0103:0.005:0.5 0/0:157:0:0,0:106,51:0:2,0:21.7:1:30.6:1:1:0:60:156:1:0:0.1 -12 109960962 . T C 246 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06449;SOR=0.77947;LSEQ=CCTTACGGTCCTCTGACAGG;RSEQ=GTCATCAAGTCCGAGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:496:269:129,140:113,111:0.5423:2,2:24.7:1:30.5:1:0.58857:1.1046:60:52.8:0.5443:0:1.2 0/1:427:205:99,106:108,113:0.4801:2,2:26.8:1:31:1:0.92295:1.02328:60:410:0.4812:0:1.1 -12 109961122 . C T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26167;SOR=0.4372;LSEQ=CTGTCTTCCTCTCGCCAGCC;RSEQ=ATTCCCCACATAAAAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:13:0,13:1,37:0.2549:1,1:23.6:1:28.2:1:1:0:60:26:0.2549:0:1.2 0/1:31:4:0,4:1,26:0.129:1,0:19.5:1:30:0:1:0:60:8:0.129:0:1 -12 111855461 . A T 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGAGATGGGCTTTCACC;RSEQ=TGTTGCCCAGGCTGGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:23:1:33:0:1:0:42:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 111855854 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13997;SOR=Inf;LSEQ=TCTGCTGTGGTGCCCGGTGT;RSEQ=TAATGGGGCCTACACCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:284,27:0:2,0:21.2:1:32.2:1:1:0:60:50.833:0.9967:0:0.1 0/1:187:2:1,1:166,19:0.0107:2,2:11.5:1:28:1:0.20298:8.53933:60:4:0.0108:0:1 -12 111856247 . G A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18936;SOR=4.63262;LSEQ=GCCGTGGGCCCCCAGCCAAG;RSEQ=CCGAGGCGTCCCCGGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:1:1,0:100,230:0.003:2,0:1:0:25:0:0.30514:0:60:2:0.0031:0:1 0/1:290:4:3,1:102,184:0.0138:2,2:6.5:1:27.5:1:0.13671:5.38:60:8:0.0142:0:1.3 -12 111856273 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24561;SOR=0;LSEQ=GCGTCCCCGGAGCCAGGCCC;RSEQ=GGCCCCGCCGCCCCTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:54,84:0.0142:2,2:29:0:32:1:1:1.55:60:4:0.0144:0:2.5 0/0:143:0:0,0:70,73:0:2,0:20.7:1:29.6:1:1:0:60:46.667:1:0:0.4 -12 111856274 . G C 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49818;SOR=0;LSEQ=CGTCCCCGGAGCCAGGCCCC;RSEQ=GCCCCGCCGCCCCTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:56,78:0.0145:2,2:16:1:26.5:1:1:1.39:60:4:0.0149:0:1 0/0:138:0:0,0:70,68:0:2,0:21.4:1:30:1:1:0:60:137:1:0:0.4 -12 111856282 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.10008;SOR=0;LSEQ=GAGCCAGGCCCCGGCCCCGC;RSEQ=GCCCCTGGCCTGCCCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:1,2:64,51:0.0254:2,2:13.7:1:29.7:1:0.58699:2.49063:60:6:0.0259:0:2 0/0:135:0:0,0:75,60:0:2,0:21:1:30:1:1:0:60:134:1:0:0.4 -12 111856294 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50442;SOR=Inf;LSEQ=GGCCCCGCCGCCCCTGGCCT;RSEQ=CCCAAGGCCCGCAGCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:82,56:0:2,0:20:1:32.2:1:1:0:60:45:1:0:0.3 0/1:172:2:1,1:97,71:0.0116:2,2:31.5:1:28.5:1:1:1.36363:60:4:0.0116:0:1 -12 111856296 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50191;SOR=Inf;LSEQ=CCCCGCCGCCCCTGGCCTGC;RSEQ=CAAGGCCCGCAGCTCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:85,57:0:2,0:19.8:1:31.3:1:1:0:60:46.333:1:0:0.3 0/1:168:2:1,1:97,69:0.0119:2,2:31:0:31.5:1:1:1.40287:60:4:0.0119:0:1.5 -12 111856309 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24282;SOR=Inf;LSEQ=GGCCTGCCCAAGGCCCGCAG;RSEQ=TCTGAGGAGCTGGCCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:112,81:0:2,0:17.5:1:32.2:1:1:0:60:95.5:1:0:0.3 0/1:188:2:1,1:102,84:0.0106:2,2:19.5:1:26.5:1:1:1.21302:60:4:0.0107:0:1 -12 111856329 . C T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.70631;SOR=1.63071;LSEQ=CTCTGAGGAGCTGGCCCCGC;RSEQ=GCGGCCGCCCGGGCCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:0,3:155,107:0.0113:2,0:1:0:27.7:1:0.07038:0:60:6:0.0115:0:1 0/1:218:4:2,2:114,100:0.0183:2,2:27.8:1:26.3:1:1:1.13931:60:3:0.0142:0:1.5 -12 111856596 . G A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09728;SOR=6.07335;LSEQ=CTCCATGGACAGCGGGGCAC;RSEQ=CTGGCAGCGCGGGAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:1:1,0:285,288:0.0017:2,0:1:0:31:0:0.49826:0:60:2:0.0018:0:1 0/1:476:5:4,1:224,245:0.0105:2,2:10:1:28:1:0.20026:4.36:60:10:0.0107:0:1 -12 111856604 . C T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09605;SOR=6.15241;LSEQ=ACAGCGGGGCACGCTGGCAG;RSEQ=GCGGGAGGCTGGCGCTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:1:0,1:315,279:0.0017:2,0:36:0:31:0:0.47059:0:60:2:0.0017:0:1 0/1:487:5:1,4:244,237:0.0103:2,2:9.8:1:26.6:1:0.21301:4.10736:60:10:0.0104:0:1 -12 111856738 . T A 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=4e-04;SOR=1.77296;LSEQ=TGCGCCCTTCGCCTTCACCC;RSEQ=GGGGAGAGCGCGGGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:95:35,60:133,295:0.1813:2,2:22.1:1:30.1:1:0.27702:1.29:60:46.5:0.182:0:1.1 0/1:390:110:45,65:104,175:0.2821:2,2:20.8:1:29:1:0.56279:1.16:60:35.667:0.2816:0:1.2 -12 111856750 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06212;SOR=Inf;LSEQ=CTTCACCCTGGGGAGAGCGC;RSEQ=GGCTGGGGAGGTGTGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:98,328:0:2,0:23.4:1:30.3:1:1:0:60:84.2:1:0:0.3 0/1:281:3:2,1:79,199:0.0107:2,2:6.7:1:28:1:0.20044:5.00:60:6:0.0109:0:1.3 -12 111884415 . T C 130 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00647;SOR=3.1341;LSEQ=GAAGGCACCCTGGACCTCAC;RSEQ=ACAGGCTCAGAGCCTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:15:15,0:99,1:0.1304:1,1:28.7:1:31.3:1:1:0:60:30:0.1327:0:1 0/1:56:18:17,1:37,1:0.3214:1,1:19.5:1:31.4:1:0.54351:2.14358:60:36:0.3273:0:1.1 -12 111884449 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17467;SOR=Inf;LSEQ=CTGCCCAGCAACACCATGGA;RSEQ=ACTCTCTCTAAAAGGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:170,2:0:1,0:23.4:1:31:1:1:0:60:85:1:0:0.2 0/1:124:2:2,0:117,5:0.0161:1,0:12:1:28.5:1:1:0:60:4:0.0161:0:1 -12 111884608 . T C 301 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.42155;LSEQ=CCAGCATCCAGGAGGTCCGG;RSEQ=GGTGCACACGGCTTGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1589:907:474,433:365,315:0.5708:2,2:24.8:1:30.7:1:0.57673:1.05844:60:99.778:0.5712:0:1.1 1/0:1350:883:445,438:240,225:0.6541:2,2:24.8:1:30.5:1:0.68851:1.04988:60:50.941:0.6526:0:1.2 -12 111885351 . ATGGGG A 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=5.000;MSILEN=5;SSF=0;SOR=1.78794;LSEQ=TTTCAGGGGATAGCCAAGGT;RSEQ=TGGGGTGGGGTGGGGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1288:203:119,84:646,293:0.1576:2,2:33.4:1:27.9:1:0.00651:1.55573:60:4.342:0.1599:0.014:0.7 0/1:1057:265:135,130:427,293:0.2507:2,2:35.5:1:25.2:1:0.02025:1.40284:60:2.232:0.2128:0.0161:1.1 -12 112036753 . GGCT G 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=9.000;MSILEN=3;SSF=0.45161;SOR=0;LSEQ=CATTGGCAGCCGCGGGCGGC;RSEQ=GCTGCTGCTGCTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:9,8:0,0:1:0,2:31:1:32.5:1:1:0:60:34:1:0:0.9 1/1:14:13:8,5:1,2:0.9286:2,2:28.5:1:30.2:1:0.55:2.97:58.2:12:0.9231:0.3571:1.5 -12 112036797 . C T 129 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=3;SSF=0.7365;SOR=1.48686;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:7,7:3,3:0.7:2,2:24.4:1:30.6:1:1:1:60:28:0.7368:0:1.2 1/0:27:21:12,9:3,3:0.7778:2,2:21.1:1:29.4:1:1:1.32:58.9:42:0.7778:0:1.1 -12 112037526 . A G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCCGGATCCGCCTTCCTC;RSEQ=AGGCGGGTCTGCCCTTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 112856810 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63423;SOR=2.36613;LSEQ=CGGCCGGCTGGCTCTGCCCC;RSEQ=CGTCCGGTCCCGAGCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:150,42:0.0052:2,0:1:0:25:0:0.2228:0:60:2:0.0053:0:1 0/1:246:3:1,2:191,52:0.0122:2,2:7:1:28:1:0.12222:7.26668:60:6:0.0123:0:1.3 -12 112856954 . G C 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGAGCCCCGAGGGGCCCGGC;RSEQ=CGGGCCTCGGCCCGGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:101,211:0:2,0:24.1:1:31.2:1:1:0:60:61.4:0.9935:0:0.2 0/1:385:26:10,16:132,226:0.0675:2,2:26.3:1:30.5:1:1:1.07:60:52:0.0684:0:1.8 -12 112856963 . G A 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24898;SOR=0.30686;LSEQ=AGGGGCCCGGCGCGGGCCTC;RSEQ=GCCCGGCCACCGCCGCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:5:4,1:76,169:0.02:2,2:9.2:1:27.6:1:0.03747:8.81:60:10:0.0202:0:1 0/0:322:2:2,0:110,210:0.0062:2,0:1:0:25:1:0.12028:0:60:4:0.0063:0:1 -12 112856983 . C A 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=GGCCCGGCCACCGCCGCGTT;RSEQ=GGTTAGCCCCGTCCGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:23,105:0:2,0:16.9:1:30.6:1:1:0:60:256:1:0:0.2 0/1:160:13:4,9:36,110:0.0813:2,2:18.4:1:29.1:1:0.73899:1.36:60:26:0.0813:0:2.2 -12 112884001 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61495;SOR=0.4745;LSEQ=TTTCTACTCTGCTCATAATG;RSEQ=GTCTTAGCTGTGTTGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:133,9:0.0139:2,2:17.5:1:30:1:0.13452:14.07477:60:4:0.014:0:1 0/0:151:1:1,0:139,11:0.0066:2,0:41:0:32:0:1:0:60:2:0.0067:0:1 -12 112888054 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25113;SOR=Inf;LSEQ=TAAAATCCGACGTGGAAGAT;RSEQ=AGATCTGATTTTACTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:142,31:0:2,0:21.9:1:32.1:1:1:0:60:346:1:0:0.1 0/1:197:3:1,2:158,36:0.0152:2,2:13:1:23.7:1:0.0958:8.63933:60:6:0.0152:0:1 -12 112888372 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50091;SOR=0;LSEQ=TCCCTTGTGCCCTGAGTGTC;RSEQ=GAAATGCATGACGGTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:21,143:0.012:2,2:26.5:1:30.5:1:0.24819:6.68:60:4:0.0123:0:1 0/0:144:0:0,0:27,117:0:2,0:21.9:1:31:1:1:0:60:143:1:0:0.1 -12 112891235 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12072;SOR=Inf;LSEQ=GTCTGGCAAGATGTTACCTT;RSEQ=GGGTGATTTTTCTGCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:39,180:0:2,0:26.4:1:30.1:1:1:0:60:53.75:1:0:0.1 0/1:215:3:2,1:45,167:0.014:2,2:13.3:1:21:1:0.12111:7.33:60:2:0.0093:0:1 -12 112891241 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.23211;SOR=Inf;LSEQ=CAAGATGTTACCTTTGGGTG;RSEQ=TTTTCTGCTGACAGAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:31,161:0:2,0:27.1:1:30.2:1:1:0:60:47:1:0:0.1 0/1:179:2:1,1:34,143:0.0112:2,2:10.5:1:28.5:1:0.35371:4.16:60:4:0.0112:0.0056:0.5 -12 112891260 . A G 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.25221;SOR=0;LSEQ=GATTTTTCTGCTGACAGAAG;RSEQ=CAGACACCATTACATTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:3:2,1:7,136:0.0205:1,2:17:1:24:1:0.00987:35.74:60:2:0.0141:0:1 0/0:124:0:0,0:14,110:0:2,0:22.8:1:29.8:1:1:0:60:123:1:0:0 -12 112892552 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.56825;LSEQ=AATCCTAATAGAGAATTTTG;RSEQ=AAACATACAGAGGTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:4,98:0.0192:1,0:26:1:30:0:1:0:60:4:0.0196:0:1 0/1:91:1:0,1:8,81:0.011:2,0:1:0:31:0:1:0:60:2:0.0111:0:1 -12 112915336 . G GT 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.73064;SOR=1.31581;LSEQ=CTGGGCTTTAATTTTTATGT;RSEQ=TTTTTTTTTCAATCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:4:4,0:159,3:0.0241:1,0:22.3:1:29.6:1:1:0:60:8:0.0241:0.006:0 0/1:127:4:4,0:118,5:0.0315:1,0:20.5:1:30.8:1:1:0:60:8:0.032:0.0079:0 -12 112915434 . C T 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=18.85877;LSEQ=CAGTCCAGGACTTATGTGAC;RSEQ=GTGGTCTCTTTTTCTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:802:2:0,2:460,340:0.0025:2,0:1:0:26.5:1:0.18154:0:60:4:0.0025:0:1 0/1:821:37:21,16:461,323:0.0451:2,2:26.8:1:30.1:1:0.8649:1.08731:60:17.5:0.0434:0:1.1 -12 112919869 . C A 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TAACTTTCTTTTTTTCTGAT;RSEQ=TCTTCCAGAGTAAATGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:294,108:0:2,0:24.5:1:31.3:1:1:0:59.8:79.4:0.9975:0:0.1 0/1:368:26:16,10:245,96:0.0707:2,2:25.2:1:28.4:1:0.26784:1.59286:58.9:25:0.0693:0:1.2 -12 112924509 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18058;SOR=Inf;LSEQ=AGGGCTTGCTTTTACCTACC;RSEQ=ACTCCTAGCTCTTTAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:19,116:0:2,0:23:1:32.1:1:1:0:60:66.5:0.9925:0:0.1 0/1:101:2:1,1:14,85:0.0198:2,2:26.5:1:26.5:1:0.27624:5.90:60:4:0.0202:0:1 -12 112924520 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16378;SOR=Inf;LSEQ=TTACCTACCCACTCCTAGCT;RSEQ=TTTAACTGTAGGAAGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:10,104:0:2,0:21:1:32.2:1:1:0:60:113:1:0:0.1 0/1:78:2:1,1:6,70:0.0256:2,2:16.5:1:25.5:1:0.17249:10.88:60:4:0.026:0:1 -12 112924706 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26302;SOR=Inf;LSEQ=CTGAGTCCACCAGAAGTTGT;RSEQ=CATTAAACAACTTCATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:21,16:0:2,0:23:1:32.1:1:1:0:60:74:1:0:0.1 0/1:52:3:2,1:31,18:0.0577:2,2:24:1:28.3:1:1:1.16:60:6:0.0577:0:1 -12 112924732 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50484;SOR=Inf;LSEQ=AACAACTTCATCCTGGCTCT;RSEQ=CAGTTTCTCCTTATTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:34,22:0:2,0:25.4:1:32.4:1:1:0:60:112:1:0:0.1 0/1:73:2:1,1:37,34:0.0274:2,2:36:0:28.5:1:1:1.08696:60:4:0.0274:0:1 -12 112924762 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19201;SOR=0;LSEQ=CTTATTCTTCATGATGTTTG;RSEQ=TTTGTAGCTGTTGACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:28,29:0.0339:2,2:19.5:1:29:1:1:1.04:60:4:0.0345:0:1 0/0:75:0:0,0:35,40:0:2,0:28.6:1:31.7:1:1:0:60:150:1:0:0.2 -12 112927003 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20407;SOR=Inf;LSEQ=CCAGCCTGAGGGCTGGCATG;RSEQ=GGATTCTCATTCTCTTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:39,157:0:2,0:25.1:1:29.9:1:1:0:60:64.333:1:0:0.1 0/1:162:2:1,1:34,126:0.0123:2,2:24:1:27.5:1:0.38647:3.67:60:4:0.0124:0:1 -12 112938755 . CCAGAGTG C 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGGTCTTGTTGCCCAGG;RSEQ=CAGTGGTGCGATCATAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 112939836 . A AT 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.11322;LSEQ=TATTCTCAACCCGTCTATCA;RSEQ=TTTTTTTTTCTTTCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:2,0:87,0:0.0222:1,0:28:1:32.5:1:1:0:60:4:0.023:0:0 0/1:81:2:2,0:79,0:0.0247:1,0:8.5:1:31:1:1:0:60:4:0.025:0.0123:0.5 -12 112939853 . C T 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00068;SOR=0.30219;LSEQ=TCAATTTTTTTTTCTTTCTC;RSEQ=CTCTTTTTTCTTTTTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:37:35,2:82,0:0.3083:1,2:20.8:1:31.6:1:0.09486:0:60:74:0.3162:0:1.1 0/1:110:13:13,0:96,1:0.1182:1,1:31.2:1:29.8:1:1:0:60:12:0.1143:0:1.1 -12 112939880 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24428;SOR=Inf;LSEQ=TTTCTTTTTTTGGGCAAAAT;RSEQ=CCTTTTTTGCTTTTTATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:168,30:0:2,0:23:1:27.8:1:1:0:60:32:1:0:0.3 0/1:194:2:1,1:165,26:0.0103:2,2:28:1:30:1:0.26085:6.24638:60:4:0.011:0:1 -12 112939889 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.24917;SOR=Inf;LSEQ=TTGGGCAAAATACCTTTTTT;RSEQ=CTTTTTATCCCCTTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:199,40:0:2,0:22.8:1:31.7:1:1:0:60:28.875:1:0:0.3 0/1:254:3:2,1:196,54:0.0118:2,2:6.7:1:28.7:1:0.52226:1.80985:60:6:0.0125:0:1.3 -12 113097659 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.43671;LSEQ=ATCTGTCTGCATCATTCTTC;RSEQ=GGTGCCCCTTTGCTTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:5,11:0.1111:2,0:31.5:1:23.5:1:1:0:60:1:0.0667:0:1.5 0/1:13:2:1,1:5,6:0.1538:2,2:43.5:1:29.5:1:1:1.18:60:4:0.1538:0:1 -12 115109566 . G T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24842;SOR=Inf;LSEQ=AAGGGCTAACGCCATGGCGG;RSEQ=CCCGTGGTTTATTTTATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:187,28:0:2,0:24.4:1:30.6:1:1:0:60:25.875:1:0:0.1 0/1:221:3:1,2:176,42:0.0136:2,2:5:1:20.3:1:0.10182:8.26708:60:2:0.0093:0:1 -12 115109672 . C A 141 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02338;LSEQ=GGACGCGCTGCGGGACCTGT;RSEQ=CGGCTTGGCTTCCAAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:37:21,16:400,362:0.0463:2,2:23.2:1:27.1:1:0.73647:1.19:60:17.5:0.0446:0:1.2 0/0:885:1:1,0:463,421:0.0011:2,0:1:0:21:0:1:0:60:2:0.0011:0:1 -12 115109963 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19222;SOR=4.55627;LSEQ=GATGGAGTAGGGGCTGTAGC;RSEQ=CAGCCGCGGGCGCATGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:1:0,1:252,193:0.0022:2,0:18:0:26:0:0.43498:0:60:2:0.0023:0:1 0/1:394:4:3,1:213,177:0.0102:2,2:23.5:1:28.5:1:0.6301:2.49:60:8:0.0104:0:1.8 -12 115110038 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06263;SOR=0;LSEQ=GGAGGCTGCCGCAGAGGAGG;RSEQ=GGCCGCCGCTGCGGCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:5:2,3:219,248:0.0106:2,2:15:1:26.2:1:1:1.32382:60:4:0.0087:0:1.4 0/0:439:0:0,0:218,220:0:2,0:24.3:1:29.9:1:1:0:60:61.571:0.9977:0:0.2 -12 115110078 . C T 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=0;LSEQ=TACGTGTAGGGGTAAGGGAA;RSEQ=AGGCTTCCGAAAGGGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:14:7,7:156,241:0.0341:2,2:20.3:1:30.3:1:0.42078:1.54:60:28:0.0347:0:1.2 0/0:357:0:0,0:141,216:0:2,0:26.3:1:30.9:1:1:0:60:38.667:1:0:0.2 -12 115110222 . C T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08521;SOR=Inf;LSEQ=CCATGAATCCCTGGTATGTT;RSEQ=TGTTGTTGTTGTTGTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:0,40:0:1,0:20.1:1:29.3:1:1:0:60:4:1:0:0.8 0/1:17:2:1,1:1,14:0.1176:1,2:24:1:26.5:1:0.22794:10.25:60:4:0.125:0:4 -12 115110241 . GT G 52 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.62202;SOR=1.68152;LSEQ=TCTGTTGTTGTTGTTGTTGT;RSEQ=TTTTTTTTTTGGGGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:0,14:0.1429:1,0:32.3:1:33:1:1:0:60:6:0.1667:0:0.7 0/1:9:2:1,1:0,7:0.2222:0,2:31:0:33:1:0.22222:0:60:4:0.25:0:4 -12 115112258 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=AGGCCAGGCAGGGGGCCCTG;RSEQ=GCCAGGTGCGCGGCGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:34,151:0:2,0:19.1:1:31.3:1:1:0:60:45.25:1:0:0.2 0/1:194:2:1,1:50,142:0.0103:2,2:11:1:30.5:1:0.45767:2.82:60:4:0.0105:0:1 -12 115112260 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23439;SOR=0;LSEQ=GCCAGGCAGGGGGCCCTGGG;RSEQ=CAGGTGCGCGGCGGCCGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:30,144:0.0114:2,2:22.5:1:28.5:1:0.32208:4.74:60:4:0.0118:0:1 0/0:187:0:0,0:48,138:0:2,0:21:1:30.9:1:1:0:60:25.571:0.9944:0:0.2 -12 115112273 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50449;SOR=Inf;LSEQ=CCCTGGGCCAGGTGCGCGGC;RSEQ=GCCGCGTCCGTCTGCACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:18,86:0:2,0:19.4:1:31.6:1:1:0:60:208:1:0:0.1 0/1:131:2:1,1:35,94:0.0153:2,2:29:1:31.5:1:0.47563:2.66:60:4:0.0154:0:1 -12 115112274 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50479;SOR=Inf;LSEQ=CCTGGGCCAGGTGCGCGGCG;RSEQ=CCGCGTCCGTCTGCACCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:19,82:0:2,0:19.3:1:32.6:1:1:0:60:202:1:0:0.1 0/1:128:2:1,1:34,91:0.0156:2,2:27.5:1:28:1:0.47682:2.65:60:4:0.016:0:1 -12 115112315 . G T 127 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01105;SOR=0.24201;LSEQ=AGCGGCGCGAAGGCCTCCTT;RSEQ=CCCGGGAGCGCGCGCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:18:12,6:63,29:0.1636:2,2:20.1:1:30.6:1:1:1.08538:60:36:0.1651:0:1.2 0/1:89:4:2,2:63,22:0.0449:2,2:9.3:1:26.3:1:0.29336:2.824:60:3:0.0345:0:3 -12 115112565 . G T 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00654;SOR=Inf;LSEQ=TGGTGGTGGAGATCTTGGCC;RSEQ=CGTCGCAGGCCTCGGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:0:0,0:214,318:0:2,0:24.6:1:30.6:1:1:0:60:34.467:0.9981:0:0.1 0/1:510:7:3,4:228,273:0.0137:2,2:11.3:1:29.6:1:1:1.11329:60:14:0.014:0:1 -12 115112986 . C T 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCAGATTTCACATGCAT;RSEQ=TCCCCATTCGATTGCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:28.8:1:30.8:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 115114036 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.60927;LSEQ=GCTTTTAAAGGGCAAGTGCC;RSEQ=TGGTTGGTGCCCCATCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:81:72,9:157,14:0.3202:2,2:22.3:1:31.1:1:0.4858:1.39986:60:80:0.3213:0:1.1 1/0:154:85:76,9:62,7:0.5519:2,2:26.3:1:31:1:1:1.04856:60:84:0.5563:0:1.1 -12 115117029 . G T 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAGGACAAAGCCCAAGAG;RSEQ=GGGGGAGGAGTGGGTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:42.5:1:30:0:1:0:60:4:0.4:0:1 1/1:1:1:1,0:0,0:1:0,0:38:0:32:0:1:0:60:2:1:0:1 -12 115117337 . G A 215 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTGGTATGCAGTCACAGC;RSEQ=ATGAATTCAGTTTCGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:152:89,63:407,344:0.1683:2,2:25.2:1:29.7:1:0.37148:1.19:60:304:0.1698:0:1.1 0/0:1097:0:0,0:586,510:0:2,0:26:1:30.2:1:1:0:60:77.286:0.9991:0:0.2 -12 115117564 . G A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14792;SOR=5.14195;LSEQ=TCCCCACCGCAGGGTACCAC;RSEQ=CTTGTACCGAGCCCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:1:0,1:71,74:0.0068:2,0:42:0:32:0:1:0:60:2:0.0069:0:1 0/1:87:3:3,0:42,42:0.0345:2,0:19:1:31:1:0.24218:0:60:6:0.0345:0:1.7 -12 115117604 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15477;SOR=Inf;LSEQ=CTTGGAGTACCCCCTGGGTA;RSEQ=GTTTCGCTCCACAGATGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:134,41:0:2,0:22.1:1:31.8:1:1:0:60:174:1:0:0.1 0/1:114:2:1,1:88,24:0.0175:2,2:13.5:1:26.5:1:0.39202:3.61257:60:4:0.0177:0:1.5 -12 115117664 . GC G 76 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.73094;SOR=0.69074;LSEQ=TGCTCCTCAGTTGCCAAAGG;RSEQ=CCCCCCCACCCTCACCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:5:3,2:306,152:0.0108:2,2:15:1:32.8:1:1:1.34127:59:10:0.0112:0.0022:1.4 0/0:401:3:2,1:249,146:0.0075:2,2:23.7:1:30.7:1:1:1.17:60:6:0.0077:0.0025:0.3 -12 115118579 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21412;SOR=Inf;LSEQ=ACAAGTTTGCTATGCTTAGG;RSEQ=AGAAGCAAAGGAGAAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:154,37:0:2,0:25.2:1:31.3:1:1:0:60:37.2:1:0:0.3 0/1:165:2:1,1:130,33:0.0121:2,2:16.5:1:26:0:0.37066:3.89593:60:4:0.0122:0:1 -12 115118589 . G A 157 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATGCTTAGGGAGAAGCAAA;RSEQ=GAGAAGTCTGGGCTGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:35:26,9:152,38:0.1556:2,2:25.7:1:30.7:1:0.49752:1.38248:60:70:0.157:0:1 0/0:203:0:0,0:158,45:0:2,0:24.3:1:31.8:1:1:0:60:100.5:1:0:0.1 -12 115118997 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=2.8966;LSEQ=AAAAGAAAGATAAACCACCC;RSEQ=TAATCTTGGGTTTGATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:35:6,29:7,64:0.3302:2,2:21.9:1:30.7:1:0.34801:1.88:60:70:0.3365:0:1.1 1/0:95:56:5,51:6,33:0.5895:2,2:20.6:1:30.2:1:0.35004:1.8422:60:55:0.5914:0:1 -12 115120322 . CT C 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTCTTGCAGTAGAGTGC;RSEQ=TTTTTTTTTTTCTTTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,0:0.2:0,0:26.5:1:32.5:1:1:0:60:4:0.2222:0:0 0/0:3:0:0,0:2,1:0:2,0:5.3:1:29.3:1:1:0:60:6:1:0:0.3 -12 115121027 . G A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06321;SOR=Inf;LSEQ=CACTCCAGGCGGGGCGCTGG;RSEQ=CTCCAGCCGGGGACAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:114,239:0:2,0:24.5:1:31.4:1:1:0:60:57.833:1:0:0.1 0/1:390:5:4,1:151,234:0.0128:2,2:14.6:1:26:1:0.08371:6.17:60:10:0.0131:0:1 -12 115121189 . G A 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.67683;LSEQ=GCACTTCAAAGGGAGGAGGG;RSEQ=AAGTGTCTTTTGGAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:21.5:1:29.7:1:1:0:60:12:0.3333:0:1.2 0/1:8:2:0,2:1,5:0.25:2,0:13.5:1:32:0:1:0:60:4:0.25:0:1 -12 115121203 . A G 29 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46619;LSEQ=GGAGGGGAAGTGTCTTTTGG;RSEQ=GAATGGGAGGCCGCTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:0,12:0.1429:0,0:31.5:1:29.5:1:1:0:60:4:0.1538:0:1 0/1:5:1:0,1:1,3:0.2:2,0:12:0:32:0:1:0:60:2:0.2:0:1 -12 117193175 . T A 31 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATAGCCCAGAGGTCTTTT;RSEQ=TTTTTTTTTTTTTAACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:49:0:26:0:1:0:60:2:1:0:4 1/0:4:3:2,1:0,1:0.75:0,2:33.3:1:20:1:1:0:59.3:2:0.6667:0:4 -12 117193213 . C T 47 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTATTATGCCATGAATTCA;RSEQ=AGGGAATAGGTTCCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.3:1:30:1:1:0:50.7:6:1:0:2 1/1:1:1:0,1:0,0:1:0,0:17:0:26:0:1:0:58:2:1:0:6 -12 117193323 . C G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCAGGTACCTTTCTCTTC;RSEQ=GCTTCTTTCTTTTTCTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1:0,2:17.1:1:30.6:1:1:0:55.4:20:1:0:1 1/1:11:10:9,1:1,0:0.9091:0,2:23.4:1:30.6:1:1:0:60:20:0.9091:0:1.1 -12 117193476 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49937;SOR=Inf;LSEQ=ACAATGCCAACAGCATGCTG;RSEQ=GTAACATTGTAGACTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:87,80:0:2,0:25.5:1:30.6:1:1:0:57.3:40.75:1:0:0.2 0/1:181:2:1,1:98,81:0.011:2,2:28.5:1:29:1:1:1.20859:60:4:0.0112:0:1 -12 117193507 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.50231;SOR=Inf;LSEQ=AGACTCTTCCAGTTTTGCCA;RSEQ=GGTAACACTTACGGGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:70,95:0:2,0:30.3:1:30.2:1:1:0:57.5:40.25:1:0:0.2 0/1:196:2:1,1:87,107:0.0102:2,2:25.5:1:27.5:1:1:1.23:60:4:0.0104:0:1.5 -12 117193527 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4994;SOR=Inf;LSEQ=TGGTAACACTTACGGGGCAT;RSEQ=CCTTTTTGAACAGTACCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:61,88:0:2,0:23.2:1:30:1:1:0:59.6:73.5:1:0:0.2 0/1:163:2:1,1:72,89:0.0123:2,2:8:1:29.5:1:1:1.23:60:4:0.0124:0:1.5 -12 117549739 . A C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.73172;SOR=1.48323;LSEQ=CTGACTCAGCAGAGCTCAGA;RSEQ=CCTACTCTCCGCTGACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:2,3:3,7:0.3333:2,2:26.6:1:31.6:1:1:1.51:60:10:0.3333:0:1.2 0/1:21:9:6,3:6,6:0.4286:2,2:30.8:1:31:1:0.66049:1.93:60:18:0.45:0:1.4 -12 117683444 . T C 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.76457;LSEQ=TGACTGTAGTGAACGTTGTA;RSEQ=GTGAAATGTGTGCCACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:1,3:0.5:2,2:28:1:31.5:1:1:1:60:8:0.5:0:2 0/1:7:3:0,3:1,3:0.4286:2,0:20:1:22:1:1:0:60:2:0.3333:0:2 -12 117683447 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.18452;LSEQ=CTGTAGTGAACGTTGTATGT;RSEQ=AAATGTGTGCCACACCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:1,2:0.625:2,2:20.4:1:30.8:1:1:1.8258:60:10:0.625:0:1.8 1/0:6:4:1,3:0,2:0.6667:0,2:16:1:26.5:1:1:0:60:8:0.6667:0:1.8 -12 117838703 . T A 78 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0068;SOR=17.95587;LSEQ=GAATATATTTGAAACTCCAC;RSEQ=TGCACCTAGGAGAAAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:13,1:0.0667:1,0:4:0:32:0:1:0:60:2:0.0667:0:1 1/0:10:6:6,0:4,0:0.6:0,0:42.8:1:30.2:1:1:0:60:12:0.6:0:1 -12 117838835 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23425;SOR=Inf;LSEQ=CCTATGCTGAGACTGTTTCC;RSEQ=ATGGACATGGCAATGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:111,26:0:2,0:24.4:1:30.1:1:1:0:60:136:1:0:0.1 0/1:129:2:1,1:93,34:0.0155:2,2:35.5:1:29.5:1:0.47057:2.71039:60:4:0.0156:0:1.5 -12 117838844 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23311;SOR=Inf;LSEQ=AGACTGTTTCCAATGGACAT;RSEQ=GCAATGATTTGCTCTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:121,37:0:2,0:24.3:1:31.4:1:1:0:60:51.667:1:0:0.1 0/1:148:2:1,1:105,41:0.0135:2,2:23:1:27.5:1:0.48842:2.54233:60:4:0.0136:0:1 -12 117838846 . CA T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23566;SOR=Inf;LSEQ=ACTGTTTCCAATGGACATGG;RSEQ=ATGATTTGCTCTGTGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:123,44:0:2,0:23.7:1:31.6:1:1:0:60:40.75:0.9939:0:0.2 0/1:159:2:1,1:113,44:0.0126:2,2:37.5:1:28.8:1:0.48722:2.55071:60:4:0.0129:0:0.5 -12 117838929 . T C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.30722;LSEQ=AAGGGTCATTACCAAGTTCT;RSEQ=GTCCACATAGCCTCTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:128:64,64:82,108:0.4025:2,2:25.6:1:30.3:1:0.25206:1.32:60:63:0.4013:0:1.1 1/0:317:193:87,106:58,66:0.6088:2,2:25.5:1:30:1:0.81757:1.07048:60:47.25:0.6058:0:1.1 -12 117870842 . G T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10007;SOR=0;LSEQ=TCTAAGAATCCATAAGTAAT;RSEQ=AAAATACATGGATATGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:4,6:0.2857:2,2:6:1:29.5:1:1:1.46:60:8:0.2857:0:1 0/0:12:0:0,0:4,8:0:2,0:21.2:1:30:1:1:0:60:24:1:0:0.1 -12 118034656 . G T 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89051;SOR=1.05331;LSEQ=GGAGGAAGAGCAAGCACCAT;RSEQ=CTCACTATAGCTTTGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:139:71:71,0:68,0:0.5108:1,1:23.7:1:30.2:1:1:0:60:70:0.5072:0:1.1 1/0:84:44:41,3:38,2:0.5238:2,2:24.1:1:30.3:1:1:1.38487:60:88:0.5301:0:1.1 -12 118034737 . C T 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGCAGATAAACACTTCATAT;RSEQ=TTCCCTTCAAGTTACTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:354,162:0:2,0:24.3:1:31.5:1:1:0:60:128:1:0:0.1 0/1:422:15:7,8:278,129:0.0355:2,2:28.5:1:29.7:1:0.09416:2.45712:59.6:30:0.0361:0:1 -12 118035029 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54772;SOR=0;LSEQ=TTTAGTCACTGTGGTAGACT;RSEQ=AATAATGCCCCAGCCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:7,84:0.0215:2,2:23.5:1:26.5:1:0.1655:11.29:60:4:0.0215:0:1 0/0:48:0:0,0:0,48:0:1,0:25.8:1:31.7:1:1:0:60:96:1:0:0.1 -12 118035090 . T C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31303;SOR=3.29503;LSEQ=GCTGGAATCAGTGACTGTTA;RSEQ=TAGGTTTGTGTGAAAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:7:0,7:0,24:0.2258:1,0:20.6:1:31.4:1:1:0:60:14:0.2333:0:1 1/0:6:3:0,3:0,3:0.5:0,0:25.3:1:34:0:1:0:60:6:0.5:0:1 -12 119594500 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=CTCCCGCAGCCCTAGTCCGG;RSEQ=CTCCCGCAGCCGGAGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:51,40:0:2,0:25:1:30.6:1:1:0:60:21.75:1:0:0.2 0/1:99:2:1,1:52,45:0.0202:2,2:18.5:1:31:1:1:1.15386:60:4:0.0211:0:1 -12 119594501 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49804;SOR=Inf;LSEQ=TCCCGCAGCCCTAGTCCGGG;RSEQ=TCCCGCAGCCGGAGCCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:51,40:0:2,0:25.3:1:31.8:1:1:0:60:90:0.989:0:0.2 0/1:99:2:1,1:52,45:0.0202:2,2:19:1:29.5:1:1:1.15386:60:4:0.0213:0:1 -12 119594521 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.21382;SOR=0;LSEQ=CTCCCGCAGCCGGAGCCGGA;RSEQ=CAGGAGCCGGAGCCGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:53,47:0.0196:2,2:17:1:29:1:1:1.12633:60:4:0.0204:0:1 0/0:118:0:0,0:62,56:0:2,0:25.9:1:31.3:1:1:0:60:38.333:1:0:0.3 -12 120534993 . G T 64 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02044;SOR=8.81871;LSEQ=GTCCCCCGAGGAACCTCCGT;RSEQ=GGCCTCGGGCTGGGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:765:1:0,1:599,165:0.0013:2,0:1:0:25:0:0.21699:0:60:2:0.0013:0:1 0/1:525:6:3,3:392,127:0.0114:2,2:14.3:1:25:1:0.16454:3.07833:60:5:0.0096:0:1 -12 120535169 . G A 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=89.58282;LSEQ=AGGACCAGCTCCGTGATGCA;RSEQ=TTGAACATCTGTGGAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1332:1:1,0:558,773:8e-04:2,0:1:0:26:0:0.41967:0:60:2:8e-04:0:1 0/1:1077:68:26,42:421,588:0.0631:2,2:22.7:1:30:1:0.61269:1.15642:60:136:0.0638:0:1.2 -12 120535238 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13736;SOR=5.32781;LSEQ=CAGGAGGCCCCTGCTGGCCT;RSEQ=CACGGCTGCCTCCCCGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:1:0,1:80,429:0.002:2,0:34:0:32:0:1:0:60:2:0.002:0:1 0/1:289:3:1,2:59,227:0.0104:2,2:27.3:1:27.3:1:0.50384:1.92:60:6:0.0106:0:1 -12 120535242 . G A 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=38.23069;LSEQ=AGGCCCCTGCTGGCCTGCAC;RSEQ=GCTGCCTCCCCGCCTTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:1:0,1:64,408:0.0021:2,0:17:0:33:0:1:0:60:2:0.0021:0:1 0/1:266:20:4,16:46,200:0.0752:2,2:20.2:1:30.6:1:0.77469:1.09:60:40:0.076:0:1 -12 120536571 . C T 159 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=12.71925;LSEQ=GGCCAGCAGCATGGAGAAGG;RSEQ=GGCCACGGGTGTGTGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:734:5:2,3:566,163:0.0068:2,2:7.8:1:28.2:1:0.07929:5.19327:60:10:0.0069:0:1 0/1:560:45:28,17:372,143:0.0804:2,2:21.2:1:29:1:0.16945:1.57803:60:44:0.08:0:1.2 -12 120536777 . C T 140 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=18.97215;LSEQ=GTCAGCGCAGCCCTGAGGGG;RSEQ=GCAGCCGGCTGCCTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1343:2:1,1:664,674:0.0015:2,2:15.5:1:28.5:1:1:1.02:60:4:0.0015:0:1 0/1:944:26:17,9:451,466:0.0275:2,2:24.3:1:29.8:1:0.1146:1.95:60:52:0.0278:0:1.1 -12 120536783 . C T 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGCCCTGAGGGGCGCAGC;RSEQ=GGCTGCCTCTCTCCCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1315:0:0,0:659,656:0:2,0:24:1:30.3:1:1:0:60:92.929:1:0:0.1 0/1:931:67:34,33:430,433:0.072:2,2:24.7:1:30:1:0.89977:1.04:60:134:0.0725:0:1.2 -12 120536820 . G A 184 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=119.20592;LSEQ=CCCAACCCCGACCCGGCCCT;RSEQ=AGTGCAGCCTCACCTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1398:1:1,0:724,672:7e-04:2,0:1:0:24:0:1:0:60:2:7e-04:0:1 0/1:1029:81:45,36:489,458:0.0787:2,2:22.7:1:29.1:1:0.56273:1.17:60:162:0.0798:0:1.1 -12 120537042 . C G 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCTGCCCACGTCAGGACA;RSEQ=TGACCCGGAAAAGGTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:31,307:0:2,0:22.9:1:32.1:1:1:0:60:47.286:1:0:0.1 0/1:232:38:5,33:29,165:0.1638:2,2:22:1:30.4:1:1:1.15928:60:37:0.1623:0:1.3 -12 120537079 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54376;SOR=0;LSEQ=AGGGTGGCCCTGGAGCCTGG;RSEQ=CTCTCACTCAGCCTCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:0,2:3,172:0.0113:1,0:26:1:31.5:1:1:0:60:4:0.0115:0:1 0/0:95:0:0,0:1,94:0:1,0:21.1:1:32.1:1:1:0:59.8:30.667:1:0:0.3 -12 120537094 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00289;SOR=Inf;LSEQ=CCTGGGCTCTCACTCAGCCT;RSEQ=GGCAGATGCCCCCGAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:3,139:0:1,0:25:1:29.8:1:1:0:59.9:34.5:1:0:0.2 0/1:66:5:0,5:1,60:0.0758:1,0:13:1:30:1:1:0:60:10:0.0769:0:2.6 -12 120541567 . G T 58 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00478;SOR=Inf;LSEQ=TCCACCATGACCAGGCACCG;RSEQ=TCGCTCAACTGTGTCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:792:0:0,0:573,219:0:2,0:22.3:1:30.7:1:1:0:60:30.68:1:0:0.6 0/1:554:6:3,3:389,159:0.0108:2,2:11.8:1:22.7:1:0.36498:2.44207:60:5:0.0092:0:2.8 -12 120541570 . G A 221 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01217;LSEQ=ACCATGACCAGGCACCGGTC;RSEQ=CTCAACTGTGTCCACAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:184:141,43:455,198:0.2196:2,2:22.3:1:29.5:1:0.07962:1.43:60:25.286:0.2153:0:2 0/0:587:2:1,1:402,181:0.0034:2,2:17:1:32:0:0.5258:2.21767:60:4:0.0035:0:1 -12 120541597 . G A 236 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00703;LSEQ=TGTGTCCACAGGTCAGTGGC;RSEQ=CGGGTTGGGTGGGAGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1232:276:178,98:578,374:0.224:2,2:25.4:1:29.2:1:0.26181:1.18:60:22:0.2198:0:1.7 0/0:989:2:2,0:595,389:0.002:2,0:11:1:23.5:1:0.52177:0:60:1:0.001:0:1.5 -12 120541599 . G A 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTCCACAGGTCAGTGGCGC;RSEQ=GGTTGGGTGGGAGTGGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1277:0:0,0:775,499:0:2,0:25.2:1:29.9:1:1:0:60:56.909:0.9976:0:0.5 0/1:1045:28:18,10:608,407:0.0268:2,2:20.5:1:30.8:1:0.69974:1.20:60:56:0.0272:0:1.2 -12 120546136 . G A 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGTTCCCAACATCAGGCA;RSEQ=AGGCAACTCTGTTTGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:252,38:0:2,0:23.2:1:31.7:1:1:0:60:31.222:1:0:0.1 0/1:196:18:14,4:149,29:0.0918:2,2:20:1:31.4:1:0.51281:1.4648:60:36:0.0938:0:2.1 -12 120546145 . C G 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AACATCAGGCAGAGGCAACT;RSEQ=TGTTTGGTGCCAGGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:289,70:0:2,0:22.1:1:31.2:1:1:0:60:118.667:1:0:0.1 0/1:234:34:26,8:157,43:0.1453:2,2:23.2:1:32.1:1:0.82298:1.12285:60:68:0.1485:0:1.6 -12 120546378 . C T 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03161;SOR=Inf;LSEQ=GTCCCAACTCTTAAGAAGCT;RSEQ=GGTGGGACCCAGCTCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:2,171:0:1,0:25.6:1:29.7:1:1:0:60:27.833:1:0:0.1 0/1:81:3:0,3:0,78:0.037:1,0:31:1:32:0:1:0:60:6:0.0375:0:1 -12 120554361 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49248;SOR=0;LSEQ=CGAGGCCCCCGCGGGCCGCG;RSEQ=CCGGCAGGGCCCGCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:21,7:0.0667:2,2:10.5:1:29:1:0.46897:2.87249:60:4:0.0667:0:1 0/0:27:0:0,0:21,6:0:2,0:4.3:1:30.9:1:1:0:60:54:1:0:0.4 -12 120554466 . G A 238 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00243;LSEQ=CCGGGCCATGGCGGGCGGGG;RSEQ=CGGTGCGCGCGGGCGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:291:170,121:224,169:0.423:2,2:27.1:1:29.2:1:0.75437:1.06:60:35.375:0.4268:0:1.2 0/0:560:1:1,0:299,257:0.0018:2,0:1:0:24:0:1:0:60:2:0.0018:0:1 -12 120554510 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07029;SOR=Inf;LSEQ=CGGTACTGGCCTCGCGATCC;RSEQ=CAGCTCCCTTCGGGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:159,248:0:2,0:23.4:1:30.4:1:1:0:60:36:1:0:0.5 0/1:287:3:2,1:106,178:0.0105:2,2:26.3:1:30.3:1:0.55871:3.34:60:6:0.0107:0:1 -12 120554520 . T C 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCGCGATCCGCAGCTCCCT;RSEQ=CGGGCTGCTCCGGCAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:107,236:0:2,0:22.9:1:29.3:1:1:0:60:33.3:0.9911:0:0.4 0/1:251:16:5,11:77,158:0.0637:2,2:22.1:1:30.6:1:1:1.07186:60:32:0.0645:0:1.3 -12 120554596 . CCCT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52989;SOR=0;LSEQ=GAAACACCTCCCTCCGCTCC;RSEQ=CCTCCTCCTCAGCAGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:0,2:5,63:0.0286:2,0:26:1:30.5:1:1:0:60:4:0.0294:0.0143:0 0/0:41:0:0,0:5,36:0:2,0:19.5:1:30.7:1:1:0:60:40:1:0:0.1 -12 121416596 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0309;SOR=Inf;LSEQ=TTTCTAAACTGAGCCAGCTG;RSEQ=AGACGGAGCTCCTGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:0:0,0:331,255:0:2,0:24.1:1:32.1:1:1:0:60:82.714:1:0:1 0/1:599:6:2,4:312,280:0.01:2,2:6.7:1:24.3:1:0.43049:2.22569:60:5:0.0085:0:2.3 -12 121416622 . C G 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32546;LSEQ=GAGCTCCTGGCGGCCCTGCT;RSEQ=GAGTCAGGGCTGAGCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:627:437:252,185:102,87:0.697:2,2:25.1:1:31.6:1:0.42944:1.16:60:108.25:0.6984:0:1.9 0/1:610:261:130,131:182,167:0.4279:2,2:24.2:1:30.4:1:0.62337:1.09803:60:86:0.4293:0:1.9 -12 121416650 . A C 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29184;LSEQ=GGCTGAGCAAAGAGGCACTG;RSEQ=TCCAGGCACTGGGTGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:664:458:237,221:111,95:0.6898:2,2:25.8:1:31.8:1:0.61547:1.0894:60:44.8:0.6892:0:1.9 0/1:623:245:128,117:193,181:0.3933:2,2:25.8:1:31.7:1:0.93446:1.03:60:80.667:0.3954:0:1.9 -12 121416988 . A G 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22542;SOR=0.66944;LSEQ=CCCTTCTGAGTTGAGTCCCC;RSEQ=TGACCTTCAGCCTTTAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:63:0,63:1,38:0.6058:1,1:24.7:1:32:1:0.38235:0:60:62:0.62:0:1.1 1/0:77:39:2,37:1,37:0.5065:1,2:23:1:31.1:1:1:1.98:60:38:0.5:0:1.2 -12 121417829 . C A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCCCTCCCCAGCGGCTC;RSEQ=CTGACCTCCACCCTACAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:33:0:31.5:1:1:1:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 121424400 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTGTTTGTTTGTTTTT;RSEQ=GAGACGGAGTCTCACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:28.5:1:1:0:60:4:1:0:2 -12 121424406 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGTTTGTTTTTTGAGAC;RSEQ=GAGTCTCACTCTGTTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:29:1:1:0:60:4:1:0:2 -12 121426478 . C T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99058;LSEQ=CATAAATGACCATACCTCAC;RSEQ=GTCCCTGAGTCTATGTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:19:18,1:23,0:0.4524:1,1:28.3:1:31.4:1:0.45238:0:60:38:0.4634:0:1.3 0/1:20:9:9,0:11,0:0.45:0,0:23.7:1:30.2:1:1:0:60:18:0.45:0:1.6 -12 121426545 . G A 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38983;SOR=0;LSEQ=TGCACAGTCCCCACCCTCAG;RSEQ=GTTGACAAGGTTCCAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:144:144:135,9:0,0:1:0,2:23.5:1:29.8:1:1:0:60:23:1:0:1.5 1/1:92:91:84,7:0,0:0.9891:0,2:20.6:1:29.2:1:1:0:60:29.333:1:0:1.5 -12 121426594 . G A 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.81868;SOR=0.95575;LSEQ=CAGCCCCACCTATGGGGAGA;RSEQ=ACAGCCCTTGCTGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:357:182:142,40:134,40:0.5098:2,2:24:1:30:1:0.89903:1.06:60:90:0.5158:0:1.4 0/1:329:164:117,47:114,51:0.4985:2,2:23.2:1:29.7:1:0.71789:1.11:60:40:0.4923:0:1.3 -12 121426869 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24943;SOR=0;LSEQ=CTACCCCGCATCTTCCCTGG;RSEQ=AGGGCCCAGGACTCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:2,1:77,213:0.0102:2,2:16.7:1:22:1:0.17795:5.49:60:2:0.007:0:1.3 0/0:275:0:0,0:60,215:0:2,0:22:1:30.9:1:1:0:60:54:1:0:0.1 -12 121426901 . G C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14953;SOR=0.55663;LSEQ=CTCTCCCCTAACTCATAGGT;RSEQ=GGGGCTGGAAGCTTCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:27:7,20:13,137:0.1525:2,2:18.9:1:29.6:1:0.01702:3.65:60:26:0.1512:0:1.1 0/1:110:10:1,9:7,93:0.0909:2,2:29.7:1:30.5:1:0.5458:1.47:60:20:0.0917:0:1 -12 121426907 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53715;SOR=0;LSEQ=CCTAACTCATAGGTGGGGGC;RSEQ=GGAAGCTTCACCATCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:14,149:0.0121:2,2:30:1:29.5:1:0.17406:10.32:60:4:0.0127:0:1 0/0:93:0:0,0:5,88:0:2,0:24.4:1:30.7:1:1:0:60:186:1:0:0.1 -12 121427310 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACCTCAGGTGATCCACCC;RSEQ=CCTCAGCCTCCCAAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30:1:29:0:1:0:40.5:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:30:1:31:1:1:0:50:4:1:0:1 -12 121428455 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATAGGAAAGGGAGGAAAG;RSEQ=TAGGAAAGGGAGGAAAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38.5:1:27.5:1:1:0:60:4:1:0:1.5 -12 121431225 . G A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50658;SOR=1.45281;LSEQ=GTAAGCTCCTCTGGTTCAGC;RSEQ=CCATGGCAATGAGAAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:16:16,0:45,0:0.2623:1,1:20.7:1:29.4:1:1:0:60:32:0.2623:0:1.5 0/1:41:14:14,0:25,2:0.3415:2,1:25.1:1:29.8:1:0.53902:0:60:28:0.3415:0:1.6 -12 121431272 . T A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00063;SOR=0.36749;LSEQ=CAAGGTCAGGGGAATGGACG;RSEQ=GGGAAGGTGAGAGTGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:60:60,0:84,7:0.3974:2,1:24.9:1:29.8:1:0.04227:0:60:29:0.3946:0:1.2 0/1:108:21:19,2:76,11:0.1944:2,2:23.5:1:29.7:1:1:1.37:60:42:0.1944:0:1.1 -12 121431300 . C T 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.46319;LSEQ=TGAGAGTGGCCAGTACCCCA;RSEQ=TCACGGCTTTCTGTGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:61:46,15:159,30:0.244:2,2:22.4:1:30.3:1:0.12911:1.72406:60:60:0.2439:0:1.2 0/1:212:94:73,21:92,25:0.4434:2,2:22.1:1:29.3:1:0.86851:1.05832:60:46:0.4402:0:1.1 -12 121431569 . G T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11794;SOR=Inf;LSEQ=GCTGCGGCAAGGCCAGGGAA;RSEQ=GGGAAGGTGACTCTAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:54,185:0:2,0:22.6:1:30.9:1:1:0:60:33.143:1:0:0.1 0/1:231:3:1,2:65,162:0.013:2,2:35.3:1:24.3:1:1:1.24:60:2:0.0089:0:2.7 -12 121431590 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20027;SOR=Inf;LSEQ=GGGAAGGTGACTCTAGGTCC;RSEQ=GTAAAAGGCTGTCCAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:19,131:0:2,0:23.7:1:30.4:1:1:0:60:74:1:0:0.1 0/1:122:2:1,1:20,100:0.0164:2,2:13.5:1:26:1:0.31581:4.90:60:4:0.0168:0:1 -12 121432114 . CG C 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.81091;SOR=0.8595;LSEQ=CTGGCCATGGACACGTACAG;RSEQ=GGCCCCCCCCAGGGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:738:9:5,4:328,399:0.0122:2,2:26.8:1:30.9:1:0.73853:1.52:59.4:18:0.0127:0.0027:0.2 0/1:762:8:2,6:346,407:0.0105:2,2:26.4:1:31.1:1:0.30085:2.54744:60:16:0.0106:0:0.4 -12 121432117 . G CC 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.19186;SOR=0.59158;LSEQ=GCCATGGACACGTACAGCGG;RSEQ=CCCCCCCCAGGGCCAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:737:18:5,13:323,390:0.0244:2,2:30.8:1:29.9:1:0.15722:2.15119:60:36:0.0251:0:1.2 0/1:754:11:6,5:336,403:0.0146:2,2:24.5:1:31.2:1:0.56013:1.44:60:22:0.0148:0:1.2 -12 121432154 . G A 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=19.83641;LSEQ=GCCCGGGACCTGCGCTGCCC;RSEQ=CTCACAGCTCCCCTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:2:1,1:276,368:0.0031:2,2:1.5:1:26.5:1:1:1.33:60:4:0.0032:0:1.5 0/1:655:38:18,20:277,340:0.058:2,2:19.9:1:29.3:1:0.86689:1.10:60:76:0.0605:0:1.2 -12 121432302 . T G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.87726;SOR=1.05946;LSEQ=TCACCTAAACCTCTTTGCAC;RSEQ=TCAGTTTGGTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:39:0,39:0,60:0.3939:1,1:26.3:1:32.4:1:1:0:60:78:0.3939:0:1 0/1:76:31:2,29:2,43:0.4079:1,2:24.8:1:31.3:1:1:1.47:60:62:0.4133:0:1.1 -12 121433453 . C G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCACTGTGTTCACACAA;RSEQ=TCCATCCATTCCACTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:32.5:1:1:0:60:4:1:0:1.5 -12 121433844 . A G 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15675;SOR=Inf;LSEQ=GTATAGCACTAGGCAGTGGG;RSEQ=GGAATGGAGCTAATAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:19,0:5,0:0.7917:0,1:25.4:1:29.4:1:1:0:60:8.5:0.7727:0:1.6 1/1:11:11:8,3:0,0:1:0,2:18.4:1:31:1:1:0:60:22:1:0:1.1 -12 121434630 . C CTCATTCAT 271 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=6.000;MSILEN=4;SSF=0.38087;SOR=0.90077;LSEQ=AGCTGGAAGAGCCACTGGGA;RSEQ=TCATTCATTCATTCATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:707:442:239,203:125,132:0.6252:2,2:24.5:1:30.9:1:0.18207:1.24:59.9:441:0.6246:0.1853:0.1 1/0:548:329:162,167:97,114:0.6004:2,2:23:1:30.1:1:0.48075:1.14:59.8:328:0.6063:0.2044:0.2 -12 121434833 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.41784;LSEQ=AAATTACAGCAGGGTAAGGG;RSEQ=GACTGATGTTTTCTAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:190:53,137:149,336:0.2815:2,2:22.6:1:30.5:1:0.51341:1.14603:60:62.333:0.2821:0:1.1 0/1:635:309:103,206:101,224:0.4866:2,2:22:1:29.5:1:0.55272:1.11:60:27.091:0.4838:0:1.2 -12 121435221 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15047;SOR=Inf;LSEQ=GGTGCCCTTGGGAGGTCTTG;RSEQ=GCAGGGGTGGGATATAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:132,24:0:2,0:22.3:1:30.3:1:1:0:60:30.2:1:0:0.2 0/1:100:2:1,1:76,21:0.02:2,2:15.5:1:29.5:1:0.39683:3.55875:60:4:0.0208:0:1 -12 121435342 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.69409;LSEQ=TGGGCAGCAGCCTGACCACC;RSEQ=TGCAGCCCGTCCAGTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:719:187:97,90:309,222:0.2601:2,2:25.2:1:30.6:1:0.14505:1.29097:60:61.333:0.2592:0:1.3 0/1:744:362:192,170:198,183:0.4866:2,2:26.2:1:29.8:1:0.82553:1.04:60:31.909:0.4808:0:1.4 -12 121435427 . G A 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.23123;LSEQ=GCAGAGCCATGTGACCCAGA;RSEQ=CCCCTTCATGGCCACCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:735:179:101,78:286,269:0.2435:2,2:24.5:1:30.1:1:0.26412:1.22:60:358:0.2472:0:1.8 0/1:660:276:145,131:219,165:0.4182:2,2:23.1:1:28.7:1:0.26714:1.19878:60:45:0.418:0:1.8 -12 121435475 . G A 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.99349;LSEQ=GCAGAGCCCCCACGGTGAGC;RSEQ=CCCTGTGCCCCACACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:883:229:130,99:337,316:0.2593:2,2:24.3:1:30.1:1:0.1912:1.23:60:228:0.2609:0:1.5 0/1:895:368:209,159:291,230:0.4112:2,2:25.7:1:29.5:1:0.78417:1.04:60:121.667:0.4148:0:1.5 -12 121435587 . G T 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.87982;LSEQ=TGTGTCTCTGGGACAAGTGT;RSEQ=TTTCCGTGATTGAGGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1301:378:175,203:449,473:0.2905:2,2:26.7:1:29.8:1:0.4633:1.10106:60:46.25:0.2879:0:1.1 0/1:1370:596:284,312:377,395:0.435:2,2:25.7:1:29.7:1:0.70255:1.04852:60:84.143:0.4347:0:1.2 -12 121435778 . C T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03945;SOR=0;LSEQ=ATGAATTTCTAAAATCTATT;RSEQ=AGATTTTAGAAAGGTAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:0,7:0,53:0.1167:1,0:20.1:1:27:1:1:0:60:6:0.1053:0:1.6 0/0:41:0:0,0:0,41:0:1,0:21.9:1:32.7:1:1:0:60:82:1:0:0.1 -12 121437114 . G A 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.50268;LSEQ=GTGGCCCAGTACACCCACAC;RSEQ=GGCCTGCTCCCGCAGACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:944:136:75,61:453,354:0.1441:2,2:26:1:30.5:1:0.85218:1.04077:60:135:0.1467:0:1.2 0/1:872:68:38,30:449,354:0.078:2,2:23.4:1:29.8:1:1:1.00134:60:67:0.0783:0:1.2 -12 121437221 . T C 294 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99904;LSEQ=CAGGCCTGCTGGCCCTCCCT;RSEQ=GGCCTGTGACAGAGCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1112:873:428,445:109,126:0.7851:2,2:24.2:1:30.2:1:0.50826:1.11:60:66.154:0.7854:0:1.2 1/0:1153:905:458,447:130,117:0.7849:2,2:25:1:30:1:0.61531:1.08434:60:81.273:0.7849:0:1.2 -12 121437382 . A G 283 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16006;LSEQ=TCCCCAGCCAGGACCCTGCC;RSEQ=GCATCCAGCACCTGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:674:670:241,429:1,0:0.9941:0,2:25.2:1:30.2:1:0.36066:0:60:50.538:0.997:0:1.2 1/1:586:583:226,357:1,0:0.9949:0,2:24.6:1:29.3:1:0.3887:0:60:52:0.9948:0:1.2 -12 121437474 . C T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCCTTACTGTCCCTGCCC;RSEQ=CTTCCATGTTGGTCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:16,157:0:2,0:23.8:1:30.9:1:1:0:60:33.6:1:0:0.3 0/1:147:17:4,13:24,106:0.1156:2,2:29.2:1:28.1:1:0.74203:1.36:60:7.5:0.1064:0:1.2 -12 121438382 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCTGTTGCTGGCAGCTC;RSEQ=GGGGAGTGAATTCTGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28.5:1:1:0:60:4:1:0:1.5 -12 121438709 . G GTT 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52828;SOR=1.8317;LSEQ=CTGGCTGGGAGGCTCCCTTT;RSEQ=AAGAACCGAGGGTAGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:51:39:39,0:12,0:0.7647:0,1:23.2:1:30.3:1:1:0:59.7:78:0.7647:0.2549:0.1 1/1:21:18:17,1:3,0:0.8571:0,1:25.3:1:30.4:1:1:0:60:36:0.8571:0.2381:0 -12 121438776 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1697;SOR=Inf;LSEQ=GTGATCCAGGAGGTGTGGCC;RSEQ=TGCCTCCCCATCCTGAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:166,26:0:2,0:25.6:1:30.4:1:1:0:59.9:23:1:0:0.3 0/1:135:2:1,1:115,18:0.0148:2,2:9.5:1:27:1:0.26258:6.24548:60:4:0.015:0:1.5 -12 121438844 . T C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.37208;LSEQ=GTGGGTGCCTGGTGGGTGGC;RSEQ=AGCAGCCTTGTTTGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:543:141:105,36:266,136:0.2597:2,2:23.9:1:31.2:1:0.0741:1.49:60:69.5:0.2593:0:1.2 0/1:493:224:152,72:175,93:0.4544:2,2:26.7:1:30.3:1:0.56628:1.12:60:73.667:0.4576:0:1.2 -12 121439192 . G T 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50149;SOR=0.5741;LSEQ=ACCCGTGGAGGCTGCTCGGG;RSEQ=TGCACAGGAGGGGGTCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:0.3913:1,0:24:1:30.1:1:1:0:60:18:0.3913:0:1.1 0/1:15:4:0,4:0,11:0.2667:0,0:32.3:1:31.5:1:1:0:60:8:0.2857:0:1 -12 121440878 . A G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=CTTGCTCCATTGCTTAGGCT;RSEQ=GAGTGCAGTGGCGCAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:33:1:1:0:56:4:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:45:0:22:0:1:0:60:2:1:0:0 -12 122849293 . TC T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54098;SOR=Inf;LSEQ=AAATGTTCCTGCTTCGCCTT;RSEQ=GGCCGGAACCGCCATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:48,34:0:2,0:27.1:1:29.9:1:1:0:57.5:26.333:1:0:0.2 0/1:150:2:1,1:85,63:0.0133:2,2:20:1:28.5:1:1:1.34646:53.5:4:0.0135:0.0067:0.5 -12 122849392 . A C 193 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.03404;LSEQ=TCTCTAGGCCTTTTAGAAAA;RSEQ=ATGGAGTTGCTCCTTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:67:21,46:1,0:0.9853:0,2:21.5:1:31.9:1:0.32353:0:49:134:0.9853:0:1.1 1/0:68:47:11,36:3,18:0.6912:2,2:27.3:1:31.5:1:0.52352:1.82:50.4:94:0.6912:0:1.1 -12 122849912 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17447;SOR=0;LSEQ=TCTACAATGTTACCCAGCAT;RSEQ=CTGTTGGCATTGTTGTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:73,111:0.0107:2,2:7:0:31.5:1:1:1.52:60:4:0.0108:0:1.5 0/0:260:0:0,0:104,155:0:2,0:24.6:1:31.6:1:1:0:60:128.5:0.9961:0:0.1 -12 122974253 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.15733;LSEQ=AGGCAGATAACCAGAAAGAT;RSEQ=AAAAATATATAGTTTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:170:122:61,61:27,21:0.7176:2,2:25.1:1:29:1:0.49862:1.28381:60:244:0.7262:0:1 0/1:274:78:37,41:93,99:0.2847:2,2:26.6:1:28.5:1:0.89395:1.04081:60:77:0.2862:0:1.1 -12 122974288 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28727;SOR=Inf;LSEQ=TTACATTACTGGTCAATATT;RSEQ=ATAATATAACCCTCACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:53,73:0:2,0:25.7:1:31.4:1:1:0:60:62:1:0:0.6 0/1:201:3:1,2:82,116:0.0149:2,2:22.7:1:30.3:1:1:1.41145:60:6:0.0153:0:1.3 -12 122974833 . G C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAAGTCTGAGCCACAAG;RSEQ=TAAAAGAACGCTGTGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12.5:1:28:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 124159885 . A T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=Inf;LSEQ=GCCGATGTAGAGGGCTCTGC;RSEQ=GTGATGAGTGCTACTGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:20.5:1:31.1:1:1:0:60:30:1:0:0.1 1/0:8:6:4,2:2,0:0.75:0,2:32.5:1:30.2:1:1:0:60:12:0.75:0:1 -12 124160021 . C G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GTTACCTGGAGACTCCTTTA;RSEQ=TGCCGCTTCCCTTATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:22.3:1:32.7:1:1:0:60:6:1:0:0 1/0:4:2:0,2:0,2:0.5:0,0:38.5:1:33:0:1:0:60:4:0.5:0:1 -12 124786017 . T A 29 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTTCCTGGGGGCAGGTGTGG;RSEQ=CTGTCCTGTCTGCCCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:0:29.5:1:1:0:60:4:1:0:2.5 0/0:1:0:0,0:0,1:0:0,0:27:0:31:0:1:0:60:2:1:0:0 -12 124786053 . C T 29 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCCAGTGCTCGGCCTCCCTG;RSEQ=GGGGCACGGTACATGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:29.5:1:1:0:60:4:1:0:2.5 0/0:1:0:0,0:0,1:0:0,0:38:0:32:0:1:0:60:2:1:0:0 -12 124786741 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=GACCCTCTTTCCAAATAAGG;RSEQ=GACAGTTGCAGGTACCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:0.1667:2,2:26:1:29:1:1:2.16:60:4:0.1667:0:1 0/0:7:0:0,0:2,5:0:2,0:15.7:1:30:1:1:0:60:14:1:0:0 -12 124787795 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGTGGGCTATGGCCTGTGCA;RSEQ=CAGCCAGGAAGGTGGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 124885756 . CAA C 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=14.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACAGAACAAGACCCTGTCT;RSEQ=AAAAAAAAAAAAGAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:5:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:30:1:1:0:60:4:1:0:1.5 -12 124887058 . G GGCTGCTGCTGCT 112 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=37;MSI=16.000;MSILEN=3;SSF=0.00094;SOR=0;LSEQ=CCTGGCTGCTGCGGGGCATG;RSEQ=GCTGCTGCTGCTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:6,6:11,7:0.3243:2,2:25.2:1:31.3:1:0.71062:1.54757:56.1:24:0.3243:0.1081:1 0/0:25:0:0,0:6,3:0:2,0:39.3:1:27.8:1:1:0:60:8:0.3333:0:0.2 -12 124887126 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52247;SOR=Inf;LSEQ=TGCTGTCAGACCCCGGGGGA;RSEQ=GGCAGAGGGGAGTGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,19:0:2,0:30.1:1:31.3:1:1:0:59.9:33:1:0:0.5 0/1:55:2:1,1:24,29:0.0364:2,2:34.5:1:31.5:1:1:1.20:60:4:0.0385:0:1 -12 124913905 . TG T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTGTTGTGGCATCTGGA;RSEQ=GGGGAGCGCCAGGGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:0:32.5:1:1:0:60:4:1:0:0.5 -12 124915134 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACCCCGGGCCCTGACGTCG;RSEQ=GGGCCCTGGGCTCAGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:40:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28:1:1:0:60:4:1:0:1 -12 124915344 . G A 32 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01515;SOR=Inf;LSEQ=ACTTCTGCTCCTGGGAGAGC;RSEQ=CAGGGGGCACTGCGGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:29.6:1:31.5:1:1:0:60:20:1:0:0.2 1/1:2:2:1,1:0,0:1:0,2:6:0:32:0:1:0:60:4:1:0:1 -12 124915431 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGCAGACACACAGGTGCG;RSEQ=GCGCACACACACAAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:43.5:1:31.5:1:1:0:60:4:0.6667:0:1 1/1:2:2:1,1:0,0:1:0,2:37:0:32.5:1:1:0:60:4:1:0:1.5 -12 125257551 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGCCACGCAGGGGCGA;RSEQ=GCAGGCCGAGCAGGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 125658603 . C T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.41961;SOR=2.0742;LSEQ=GACATAACAGCCATCACCAA;RSEQ=CCCATTGTATAAATGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:2,2:9,8:0.1905:2,2:16:1:30.5:1:1:1.1187:60:8:0.1905:0:1.3 0/1:12:4:2,2:6,2:0.3333:2,2:34.5:1:30:1:0.54747:2.71347:60:8:0.3636:0:1.5 -12 125658628 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15455;SOR=Inf;LSEQ=TTGTATAAATGGTGAAACTG;RSEQ=GGCTCAGAGAGGCTGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:0:2,0:28.9:1:31.4:1:1:0:60:54:1:0:0.3 0/1:18:2:1,1:10,6:0.1111:2,2:36.5:1:29.5:1:1:1.61828:60:4:0.1111:0:2 -12 127625632 . TAA T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTATCTTTATTTGTT;RSEQ=AGTCTGTTTTGTCAGAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:0:32.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 127626655 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTTCAGCTGTTGATACTTCG;RSEQ=TATGCTTCACAAAGTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:30.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:29:1:1:0:60:4:1:0:1 -12 127627037 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17787;SOR=0;LSEQ=GGTTTTTGAGGCTGCTGACC;RSEQ=TTGGATGGGGTTTTTATGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:18.5:1:31:1:1:2.64575:60:4:0.2:0:1 0/0:13:0:0,0:7,6:0:2,0:28:1:30.9:1:1:0:60:26:1:0:0.8 -12 127627056 . C G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.02374;SOR=13.52403;LSEQ=CCTTGGATGGGGTTTTTATG;RSEQ=GGGCCTTTTTGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:5,2:0.3636:2,2:22.3:1:31.3:1:0.57576:2.28835:55:8:0.3636:0:1 1/1:10:9:5,4:0,1:0.9:0,2:37.8:1:30.6:1:1:0:60:18:0.9:0:1.1 -12 127627064 . TTTG T 87 v4;MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.02997;SOR=9.28145;LSEQ=GGGGTTTTTATGCGGGCCTT;RSEQ=TTGTTGTTGTTGTTGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:24.5:1:29.5:1:1:1.58108:60:4:0.2:0:1 1/0:11:8:4,4:1,2:0.7273:2,2:33:1:29.3:1:1:1.88:60:16:0.7273:0.0909:1 -12 127627596 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11905;SOR=Inf;LSEQ=TTCTGCAGGGAAGCCCCGCC;RSEQ=ACTGAAGAAGGATGGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:25.1:1:31.3:1:1:0:59.5:36:1:0:0.1 0/1:10:2:1,1:5,3:0.2:2,2:45:1:30:1:1:1.58108:60:4:0.2:0:1 -12 127627683 . TC T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05641;SOR=Inf;LSEQ=GCGTTGAGCTGTGGGACAAG;RSEQ=TTGGGACCAAGCTGTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:25.3:1:32.3:1:1:0:60:32:1:0:0.1 0/1:11:3:1,2:3,5:0.2727:2,2:26:1:28:1:1:1.18052:60:6:0.2727:0:0 -12 127627843 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=CCCTCCCCCATGAGGCTAAA;RSEQ=GGCTTAGAGAGCAGGCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:0,6:0.25:0,2:26:1:30.5:1:0.25:0:60:4:0.25:0:1 0/0:4:0:0,0:2,2:0:2,0:24.3:1:32:1:1:0:60:8:1:0:0.3 -12 128101812 . A T 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21651;SOR=0.42049;LSEQ=ACACTAACAAGTCAGGGATA;RSEQ=CAGGAGACACCATCCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:10,3:0.4091:2,0:29.9:1:31.7:1:0.24026:0:60:18:0.4091:0:1.1 0/1:27:6:5,1:20,1:0.2222:1,2:33:1:29.5:1:0.40171:3.74166:60:12:0.2308:0:1 -12 128101865 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17774;SOR=0;LSEQ=TCTTCTGAAATCAGACAATG;RSEQ=CTTTCAAACTCTTATACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:39,20:0.0328:2,2:20:1:29.5:1:1:1.92731:60:4:0.0339:0:1.5 0/0:83:0:0,0:43,40:0:2,0:26.1:1:30.6:1:1:0:57.9:19.75:1:0:0.2 -12 128101958 . C T 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07622;SOR=0.13343;LSEQ=ATCTTGCTATTACTCACCTT;RSEQ=GGGCCCTGTATTTTTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:2,3:3,15:0.2174:2,2:24.8:1:30.6:1:0.29068:3.13:54.6:10:0.2174:0:1 0/1:29:1:0,1:6,22:0.0345:2,0:12:0:31:0:1:0:60:2:0.0345:0:1 -12 129468836 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21041;SOR=Inf;LSEQ=CAGCATTGTCCTTGCTTCAA;RSEQ=TTTTAGGATGTCTGAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:22,1:0:1,0:21.2:1:31.9:1:1:0:60:46:1:0:0.3 0/1:20:2:1,1:18,0:0.1:1,2:23.5:1:27:1:0.1:0:60:4:0.1:0:1 -12 129468880 . A AT 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05953;SOR=Inf;LSEQ=CTTTCATGTTTTCAACCATC;RSEQ=TTTTTTTAATGGCACAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:51,11:0:2,0:23.7:1:30.3:1:1:0:60:61:1:0:0.1 0/1:70:5:4,1:47,18:0.0714:2,2:33.4:1:30.6:1:1:1.52:60:10:0.0714:0:0 -12 129468945 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51919;SOR=Inf;LSEQ=CCTCAAATTAAACTCCTTAA;RSEQ=CTCTGATGCCCTGGGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:63,54:0:2,0:25.8:1:29.6:1:1:0:60:234:1:0:0.1 0/1:177:2:1,1:90,84:0.0113:2,2:10.5:1:28:1:1:1.07098:60:4:0.0116:0:1 -12 129468954 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51778;SOR=Inf;LSEQ=AAACTCCTTAAACTCTGATG;RSEQ=CCTGGGGATGAGAACAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:59,57:0:2,0:24.6:1:31.4:1:1:0:60:115:1:0:0.1 0/1:173:2:1,1:83,88:0.0116:2,2:49.5:1:30:1:1:1.06:60:4:0.0118:0:1 -12 129468990 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51098;SOR=Inf;LSEQ=AACTAGCTTGGATCTCGTGC;RSEQ=GTGTAATTCAATGTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:35,55:0:2,0:26.3:1:30.8:1:1:0:60:180:1:0:0 0/1:125:2:1,1:44,79:0.016:2,2:32.5:1:31:1:1:1.79:60:4:0.0163:0:1 -12 129468991 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51055;SOR=Inf;LSEQ=ACTAGCTTGGATCTCGTGCC;RSEQ=TGTAATTCAATGTTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:35,54:0:2,0:26.4:1:31.7:1:1:0:60:178:1:0:0 0/1:123:2:1,1:43,78:0.0163:2,2:39:1:30.5:1:1:1.80:60:4:0.0164:0:1 -12 130908927 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11109;SOR=0;LSEQ=ACGCTGCTCTGCCGGGTCAG;RSEQ=GTCCGCCGCCGGGCCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:14,16:0.0625:2,2:30:1:31.5:1:1:1.14:60:4:0.0667:0:1.5 0/0:63:0:0,0:33,30:0:2,0:26.7:1:30.8:1:1:0:60:62:1:0:0.3 -12 130908945 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11108;SOR=0;LSEQ=AGCGTCCGCCGCCGGGCCAG;RSEQ=AGCGGCCTCGGGCCCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:11,15:0.0714:2,2:22.5:1:30.5:1:1:1.35:60:4:0.0741:0:1.5 0/0:55:0:0,0:26,29:0:2,0:25.9:1:32.3:1:1:0:60:110:1:0:0.3 -12 130908949 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCGCCGCCGGGCCAGCAGC;RSEQ=GCCTCGGGCCCCTCCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:0:2,0:27.5:1:29:1:1:0:60:10.5:1:0:0.3 0/1:51:2:1,1:23,26:0.0392:2,2:25:0:28.5:1:1:1.13:60:4:0.04:0:2 -12 130962191 . C A 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.67919;SOR=1.63158;LSEQ=ATACGATCTCATGCTAAATG;RSEQ=TTAGAGAAATGGCATCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:7,1:0.2727:2,0:25:1:31.7:1:1:0:60:6:0.2727:0:1 0/1:13:5:5,0:7,1:0.3846:2,0:30.2:1:29.6:1:1:0:60:10:0.3846:0:1 -12 130962254 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19918;SOR=0;LSEQ=CTCTGCTAATAAACTCTGGA;RSEQ=GAGAAACGCTGCTCCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:20,18:0.05:2,2:8:0:32:0:1:1.10818:60:4:0.05:0:1.5 0/0:49:0:0,0:24,25:0:2,0:27.4:1:30.1:1:1:0:60:15.333:1:0:0.3 -12 131517730 . T G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGCCCGAGCTCTTTTT;RSEQ=TGTGCGGGCAGGGCCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35:1:30:1:1:0:60:4:1:0:1 -12 131518875 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.26092;LSEQ=TGAATGGAATGCTCTTCCCC;RSEQ=GGGTCCCCGCATGGTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:5,2:5,3:0.4667:2,2:37:1:31.7:1:1:1.46:60:14:0.4667:0:1 1/0:19:10:4,6:5,4:0.5263:2,2:20.7:1:29.4:1:0.65628:1.81296:60:20:0.5263:0:1.3 -12 131518981 . T A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16619;SOR=3.21651;LSEQ=TCGCCACATCAGCTGGCTCC;RSEQ=TTTCTTTCCTGGAAGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:1,3:4,8:0.25:2,2:29:1:29.8:1:1:1.46398:60:8:0.25:0:1 1/0:19:10:4,6:4,5:0.5263:2,2:15:1:29:1:1:1.18851:60:20:0.5263:0:1.1 -12 131534668 . G C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.09565;SOR=Inf;LSEQ=TGCAGGAAGCTGGGAATTCA;RSEQ=TGTGTCCTCCTGGGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:0:1,0:22.3:1:32.4:1:1:0:60:26:1:0:0.1 0/1:12:3:3,0:9,0:0.25:0,0:24.7:1:32.7:1:1:0:60:6:0.25:0:1.3 -12 131534763 . G GTCA 167 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=8.000;MSILEN=3;SSF=0.01491;SOR=0.37747;LSEQ=TTGAAATCACCATCGTCATC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:44:21,23:17,9:0.6286:2,2:33.6:1:30.6:1:0.21495:2.04726:59.9:88:0.6286:0.0286:0.1 0/1:49:19:9,10:14,16:0.3878:2,2:30.6:1:30.4:1:1:1.03:60:38:0.3878:0.0204:0.1 -12 131621997 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGGGCCTGGCACCTGCC;RSEQ=TGTACTTGGCTGGGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 131622735 . T C 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=TGGTCGCTCACGAGCAGCTC;RSEQ=GCCCGCACCTCCAACGCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:35:0:32:0:1:1:60:4:0.5:0:1 1/1:8:8:4,4:0,0:1:0,2:26.8:1:30:1:1:0:60:16:1:0:1.4 -12 131827160 . A G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTCCTGCTGGATAGGGGC;RSEQ=AAGAAGGGGCCCTGCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:35:1:32:1:1:0:60:4:1:0:1.5 -12 131827178 . T A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAAGAAGGGGCCCTGCAG;RSEQ=TGTAGTGTCCTCCAGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:21.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 -12 131827402 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49803;SOR=0;LSEQ=GACCTAGAAAGGGGAGAAGC;RSEQ=ATGTCACCCAACTCCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:38,26:0.0303:2,2:34.5:1:29.5:1:1:1.45294:60:4:0.0313:0:1 0/0:58:0:0,0:35,23:0:2,0:27.5:1:30.7:1:1:0:57.8:57:1:0:0.1 -12 131827799 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTATGGCTCTGCGCTGAC;RSEQ=GACTTGAACTTTGAGGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:32:1:1:0:51.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 131944873 . C CT 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.41421;LSEQ=CACCCACCCCTGCTCCTCCC;RSEQ=GCCCTCTCCATTAATCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:22.5:1:32.5:1:1:0:60:8:0.5714:0.1429:0 0/1:3:1:1,0:1,1:0.3333:2,0:13:0:31:0:1:0:60:2:0.3333:0:4 -12 131944995 . C A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15936;LSEQ=AAAGGGAATTAATTTATTCT;RSEQ=AAGCCAAATATAAATCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:50:47,3:13,1:0.7813:1,2:23.1:1:28.2:1:1:1.20:60:24:0.7742:0:1.7 0/1:53:19:17,2:34,0:0.3585:1,2:20.9:1:28.7:1:0.12409:0:60:38:0.3585:0:1.7 -12 131945052 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24661;SOR=0;LSEQ=TCTTAGATTACTCATCTCCT;RSEQ=GTATCTTTTCCACCAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:142,39:0.0109:2,2:20.5:1:29:1:0.39032:3.60751:60:4:0.011:0:3 0/0:185:0:0,0:134,51:0:2,0:25.8:1:31.1:1:1:0:60:91.5:1:0:0.8 -12 131945067 . A G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27088;LSEQ=CTCCTGGTATCTTTTCCACC;RSEQ=GGACGAGTGAATGAGCGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:226:171:127,44:35,18:0.7566:2,2:23.9:1:29.9:1:0.29171:1.48:60:41.75:0.7626:0:1.8 0/1:241:110:70,40:91,39:0.4564:2,2:24.3:1:29.4:1:0.33533:1.33171:60:220:0.4641:0:1.7 -12 131945098 . G A 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=ATGAGCGAACCTAAGTGTGG;RSEQ=TGCACAGAGTGTCACCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:201,144:0:2,0:23.8:1:31.2:1:1:0:60:85.25:0.9971:0:1.2 0/1:365:14:7,7:201,149:0.0384:2,2:22.8:1:29.1:1:0.59379:1.34785:60:28:0.0387:0:2.6 -12 131945101 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02628;SOR=0;LSEQ=AGCGAACCTAAGTGTGGGTG;RSEQ=ACAGAGTGTCACCATATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:5:2,3:203,149:0.014:2,2:20:1:26:1:0.6544:2.03951:60:4:0.0113:0:1.2 0/0:380:0:0,0:214,166:0:2,0:23.5:1:31.5:1:1:0:60:94:1:0:0.8 -12 131945129 . A G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26452;LSEQ=GTCACCATATTCTGGAACTC;RSEQ=AGTTGTGTTTGGGTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:426:326:164,162:45,53:0.7653:2,2:27.5:1:30.4:1:0.48995:1.19:60:325:0.7665:0:1.4 0/1:482:223:115,108:129,130:0.4627:2,2:26.5:1:30.2:1:0.71551:1.07:60:222:0.4664:0:1.5 -12 131945207 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24044;SOR=Inf;LSEQ=CTGTGCCAGGCAGAGCTAAT;RSEQ=TCCATGCATTTCACAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:53,145:0:2,0:22.4:1:32:1:1:0:60:197:1:0:0.4 0/1:191:2:1,1:53,135:0.0105:2,2:36.5:1:29:1:0.48872:2.53:60:4:0.0106:0:1 -12 131945210 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2293;SOR=Inf;LSEQ=TGCCAGGCAGAGCTAATGTC;RSEQ=ATGCATTTCACAAACACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:49,142:0:2,0:21.6:1:31.7:1:1:0:60:94.5:1:0:0.4 0/1:176:2:1,1:47,127:0.0114:2,2:17:1:28:1:0.47221:2.68:60:4:0.0115:0:2 -12 131945403 . A G 81 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAATGACAGGCAAAGAAA;RSEQ=TAAACCCTATAAATTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:22.7:1:31.5:1:1:0:60:12:0.8571:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 132001302 . AG TT 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05779;SOR=0;LSEQ=TTCTTCTGTACTTATAAGAA;RSEQ=ATCAAAGACTTTAAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:1,4:0.375:2,0:20.7:1:28.3:1:1:0:60:6:0.375:0:1 0/0:11:0:0,0:1,10:0:2,0:23.2:1:29.9:1:1:0:60:22:1:0:0.1 -12 132547073 . C T 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.23636;SOR=0;LSEQ=ATTTCCAGCTTCTCAGGCAG;RSEQ=AGCAGCAGCAGCAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:16,9:0.0741:2,2:28:1:30:1:1:1.73837:60:4:0.0741:0:1 0/0:28:0:0,0:16,12:0:2,0:27.2:1:31.6:1:1:0:59.6:56:1:0:0.6 -12 132547087 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=1.84836;LSEQ=AGGCAGCAGCAGCAGCAGCA;RSEQ=CAACAACAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:1,0:15,13:0.0345:2,0:22:0:31:0:1:0:60:2:0.04:0:2 0/1:32:2:1,1:15,15:0.0625:2,2:10.5:1:31.5:1:1:1:57.5:4:0.0645:0:2 -12 132547090 . A G 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.10584;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAACAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:2,3:13,11:0.1724:2,2:24.4:1:32.6:1:0.65134:1.738:57:10:0.1724:0:2.4 0/1:32:6:3,3:13,13:0.1875:2,2:23.3:1:30.3:1:1:1:59.2:12:0.1875:0:1.8 -12 132547093 . A ACAG 86 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=44;MSI=15.000;MSILEN=3;SSF=0.06548;SOR=0.18678;LSEQ=CAGCAGCAGCAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:1,6:12,8:0.25:2,2:28.6:1:30.7:1:0.07681:8.31296:60:14:0.2692:0.0357:0.1 0/1:35:2:1,1:14,14:0.0571:2,2:29.5:1:33.3:1:1:1:60:4:0.0571:0:0 -12 132547162 . G A 96 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00345;SOR=0.06658;LSEQ=CAGCAGCAGCAACAGACGAC;RSEQ=ACGACCTCTCAGGTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:5,4:7,9:0.36:2,2:27.6:1:30.3:1:0.68817:1.58:58.3:18:0.36:0:1.3 0/1:29:1:0,1:11,17:0.0345:2,0:9:0:31:0:1:0:55:2:0.0345:0:3 -12 132547192 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14194;SOR=Inf;LSEQ=CAGGTGCAAGTTCCACAGAT;RSEQ=CAGGGCCAGGCCCAGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:29.3:1:31.2:1:1:0:60:38:1:0:0.4 0/1:12:2:1,1:2,8:0.1667:2,2:33:1:26:0:0.45455:3.46:60:4:0.1667:0:1.5 -12 132548569 . AC A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGGTTCAACCACTGATG;RSEQ=CCCCCCCCGGCCCACAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:31.5:1:1:0:37:4:1:0:0.5 -12 132827994 . A T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATCCGCTTTCCGGGGAGGGG;RSEQ=GCGGCTGCTCTCGTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:22:1:29.5:1:1:1.7321:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 132829434 . CA C 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=CAACAACAGCGAAACTGCCT;RSEQ=AAAAAAAAAAAAGACACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:20:1:30:1:1:0:60:4:0.2857:0.1429:2.5 0/0:7:0:0,0:6,1:0:2,0:17.1:1:30.1:1:1:0:60:14:1:0:1 -12 132829699 . T A 29 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.13333;SOR=0;LSEQ=AGACTTCCACTATTTCTTCT;RSEQ=CTGCTATCTACTACGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:27:1:29.5:1:1:0:43.5:4:0.5:0:2 0/0:6:0:0,0:1,5:0:2,0:23.3:1:28:1:1:0:52.8:12:1:0:0 -12 132829701 . T C 30 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=ACTTCCACTATTTCTTCTTC;RSEQ=GCTATCTACTACGAACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:25:1:30.5:1:1:0:43.5:4:0.5:0:2 0/0:6:0:0,0:1,5:0:2,0:23.3:1:29.2:1:1:0:52.8:12:1:0:0 -12 132834097 . C A 27 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATGCCCTCATCCCCACGCC;RSEQ=TCGTCCCCACGCCCTCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:27:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:0:2,0:34.5:1:29.5:1:1:0:60:4:1:0:0 -12 132834622 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACCCACCCTGACCAAGG;RSEQ=CTCACCCCTGCTGGGGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:19,12:0.0606:2,2:33:0:31.5:1:1:1.56069:60:4:0.0667:0:1.5 0/0:16:0:0,0:7,9:0:2,0:21.2:1:30.9:1:1:0:60:32:1:0:0.1 -12 132834744 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11077;SOR=Inf;LSEQ=GGGTCCATAAGAGGTCAGCT;RSEQ=TGTCCACCACGGGGCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,12:0:2,0:25.2:1:28.5:1:1:0:60:16:1:0:0.1 0/1:9:2:0,2:3,4:0.2222:2,0:24.5:1:30:1:0.5:0:60:4:0.2222:0:1.5 -12 132836476 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGGGTGGACAGGGGTGG;RSEQ=TCCTGGCCCTGGTGCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:0:33.5:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 132836492 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGATCCTGGCCCTGGTGC;RSEQ=GGGAACACCCTGAGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:0:32:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 132836505 . A T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTGCAGGGAACACCCTG;RSEQ=GCATTGTGGGTGCGGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:30:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 132836516 . T C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACCCTGAGCATTGTGGG;RSEQ=GCGGGGCCTGCCTGGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 133132275 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51049;SOR=0;LSEQ=TGACTCCGGCATCCCTGGCT;RSEQ=GTGGTTGCATTGCTCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:38,44:0.0238:2,2:23:1:29:1:1:1.16:60:4:0.0247:0:1.5 0/0:60:0:0,0:26,34:0:2,0:25.2:1:31.2:1:1:0:60:120:1:0:0.3 -12 133132329 . G C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=0.66254;SOR=0.56365;LSEQ=GTCCTCACATGGCCCCTCCT;RSEQ=TGTGTGTGTCTTTGTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:27:4,23:2,7:0.75:2,2:21.4:1:32.7:1:0.62698:1.61846:60:54:0.75:0:1.1 1/0:8:5:2,3:1,2:0.625:2,2:28.8:1:32:1:1:1.29:60:10:0.625:0:1 -12 133133082 . ACC CT 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCAGGCCTTCGTGCTGC;RSEQ=CCAACCCCTGTCCTGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:1:29.9:1:1:0:40:4:1:0.5:2 1/1:1:1:1,0:0,0:1:0,0:20:0:33:0:1:0:43:2:1:0:3 -12 133133150 . TG CC 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCCCCTCCACCCACCCC;RSEQ=TCCTGTGGGACGCTCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:30:0:33.5:0:1:0:40:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:24:1:32.3:1:1:0:51.5:4:1:0:2.5 -12 133133283 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCTCCTCTCCAGGCCTTC;RSEQ=TGCTGCCTCCAACCCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:30:1:1:0:31.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 133200748 . T C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CGGGTTAGGGTCTGGATTCC;RSEQ=GGGGAAACCAGCCCACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41.5:1:30.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:26:0:29:0:1:0:60:2:1:0:0 -12 133201204 . G T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20284;SOR=Inf;LSEQ=TCAGGGTGGTCAGTGGTCTG;RSEQ=TCACTGGAAGCACGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:167,13:0:2,0:25.5:1:31.5:1:1:0:60:89:1:0:0.1 0/1:148:2:1,1:123,23:0.0135:2,2:13:1:27.5:1:0.29895:5.25658:60:4:0.0137:0:4 -12 133201443 . GAGGCCAAGG C 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACCCCAGTCCACTCAGAGAG;RSEQ=AGGCCAGGCTGAGCCGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:0:0,0:341,299:0:2,0:24:1:30.1:1:1:0:60:31:1:0:0.1 0/1:572:25:15,10:300,243:0.0437:2,2:28.1:1:31.6:1:0.68565:1.21:60:50:0.0446:0.0052:0.1 -12 133201947 . T C 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACCTTCCTGTGGCCGAGCTG;RSEQ=GCAACTCCCTCTTCCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:4,2:1,2:0.6667:2,2:31.3:1:30.8:1:0.52381:3.39:60:12:0.6667:0:1.7 1/1:2:2:1,1:0,0:1:0,2:23:1:28:1:1:0:60:4:1:0:1.5 -12 133202004 . C T 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11993;LSEQ=TGGGAGTGTCTGCCTCCTTC;RSEQ=GCTAGAACGAAGCACCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:10,2:8,1:0.5714:2,2:15.6:1:31.3:1:1:1.56568:60:24:0.5714:0:1.3 1/0:5:3:2,1:2,0:0.6:0,2:24.7:1:30:1:1:0:60:6:0.6:0:1.3 -12 133202131 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50035;SOR=0;LSEQ=AGGCCCCTTGGAAGACACCA;RSEQ=GGCGTGCCTCAGGACCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:125,5:0.0152:1,2:25.5:1:29:1:0.08917:22.91347:60:4:0.0154:0:1.5 0/0:115:0:0,0:105,10:0:2,0:21.6:1:31.9:1:1:0:60:114:1:0:0.2 -12 133202215 . G A 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29643;LSEQ=TCCAGGGCACACGGGCAGGC;RSEQ=GCATGCACGACTCACCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:681:447:270,177:127,105:0.6564:2,2:26.7:1:30.3:1:0.16338:1.26:60:73.5:0.6592:0:1.1 0/1:620:224:131,93:225,167:0.3613:2,2:24.8:1:30.1:1:0.79987:1.05:60:111:0.3633:0:1.1 -12 133202428 . G A 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06486;SOR=0.64272;LSEQ=TGCCATGGGCAGGATCTCAG;RSEQ=AGAGGAAGGGGCTGTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:174:93:14,79:14,66:0.5345:2,2:23.6:1:30:1:0.68398:1.19572:60:30:0.5294:0:1.1 0/1:132:56:11,45:16,60:0.4242:2,2:24.6:1:29.6:1:1:1.09016:60:112:0.4341:0:1.1 -12 133202626 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2874;SOR=0;LSEQ=TGACCCACAGAGCTGGAGCT;RSEQ=CAGAAGCCCTCAAGACACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:2,1:156,39:0.0152:2,2:21.7:1:22:1:0.49383:1.99173:60:2:0.0104:0:1.7 0/0:124:0:0,0:105,19:0:2,0:23.9:1:31.9:1:1:0:60:61:1:0:0 -12 133202907 . C A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0162;SOR=Inf;LSEQ=GTGTCCAGGGACAGCACCTG;RSEQ=AGAGACCACAGCCCACATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:109,256:0:2,0:24.5:1:32:1:1:0:60:59.833:1:0:0.1 0/1:287:5:3,2:97,185:0.0174:2,2:12.4:1:27.2:1:0.34632:2.85:60:10:0.0175:0:1.2 -12 133208511 . G C 51 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGGCCCTCTCCCTTCTC;RSEQ=GGTCGGCTGGCAGCAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:24.7:1:32.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:49:0:32:0:1:0:60:2:1:0:1 -12 133208611 . A G 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=TGGCTGCATGTGACAGGGAC;RSEQ=TGATAAATGTTGGTGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:18:1:28.5:1:1:0:60:4:0.6667:0:1 1/1:5:5:3,2:0,0:1:0,2:19.8:1:31.2:1:1:0:60:10:1:0:1 -12 133208739 . A G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.79104;SOR=0.78758;LSEQ=AGCCTCATCCTGCATTCATT;RSEQ=ACATCCTTACCATGCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:26:26,0:16,1:0.6047:1,1:19.3:1:31.2:1:0.39535:0:60:12:0.5854:0:1.3 1/0:22:12:10,2:10,0:0.5455:0,2:19.3:1:32.2:1:0.48052:0:60:24:0.5455:0:1.1 -12 133208752 . T A 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.077;SOR=0;LSEQ=ATTCATTAACATCCTTACCA;RSEQ=GCACAGGTATGTCGGTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:5:5,0:41,1:0.1064:1,0:23:1:30.2:1:1:0:60:10:0.1087:0:1 0/0:32:0:0,0:31,1:0:1,0:20:1:30.9:1:1:0:60:64:1:0:0.4 -12 133208886 . C T 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.00094;SOR=0.64532;LSEQ=GTGTCCTCTCCTCACACGCA;RSEQ=GCTGGCACTCTCACCTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:466:308:203,105:96,62:0.6609:2,2:25.7:1:30.5:1:0.30763:1.25:60:76:0.658:0:1.3 1/0:535:298:189,109:153,83:0.557:2,2:24:1:29.4:1:0.78546:1.06296:60:36.25:0.5524:0:1.3 -12 133208979 . T C 272 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2638;SOR=0.88939;LSEQ=GGGAGGACAGGAAACATCTC;RSEQ=GAGAGCTCAGTGGAGTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:809:540:265,275:137,130:0.6675:2,2:24.5:1:30.3:1:0.60053:1.09349:60:76.143:0.6696:0:1.2 1/0:908:582:286,296:153,173:0.641:2,2:25:1:29.7:1:0.53394:1.09:60:63.667:0.6395:0:1.2 -12 133209593 . T C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74487;SOR=1.32326;LSEQ=CTCGCTGACACCTGAGTTCA;RSEQ=TGTCAGAGAGAAAACTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:0,12:0,12:0.5:0,0:28.1:1:33.2:1:1:0:60:24:0.5217:0:1.3 1/0:14:8:0,8:0,6:0.5714:0,0:24.1:1:32.1:1:1:0:60:16:0.5714:0:1 -12 133209653 . C T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGCCTCTCACTGGGTAGCG;RSEQ=GTGAAAGACAGCTCCCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:17.3:1:31:1:1:0:60:8:0.5:0:2.5 0/0:1:0:0,0:0,1:0:0,0:3:0:27:0:1:0:60:2:1:0:0 -12 133209660 . G A 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACTGGGTAGCGCGTGAAA;RSEQ=ACAGCTCCCAACACAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:20.3:1:31.3:1:1:0:60:6:0.375:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 133210659 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13759;SOR=Inf;LSEQ=CCAACTGCTGGGCAGGCTCC;RSEQ=CCCGATCTGATTTTCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:143,2:0:1,0:22.8:1:29.6:1:1:0:60:71.5:1:0:0 0/1:86:2:1,1:79,5:0.0233:2,2:32.5:1:29.5:1:0.13543:14.51227:60:4:0.0233:0:2 -12 133210985 . C T 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01172;SOR=0.6766;LSEQ=CTGTAACACATGAGACAACG;RSEQ=GGCTGTGTTTGCACCATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:380:270:62,208:27,82:0.7105:2,2:25.5:1:30.1:1:0.69062:1.10434:60:89:0.712:0:1.2 1/0:391:244:80,164:44,102:0.624:2,2:25.1:1:29.4:1:0.65338:1.13:60:47.8:0.6224:0:1.2 -12 133211059 . T C 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCCTCCAACCTGGGTCCA;RSEQ=CTGCCCCGTTTGACCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:31:0,31:0,61:0.337:1,1:23.9:1:31.4:1:1:0:60:30:0.3333:0:1.5 0/0:71:0:0,0:1,70:0:1,0:22.2:1:29.5:1:1:0:60:142:1:0:0.4 -12 133212382 . G A 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=GTGCAGTGTCTGCTGCTCAC;RSEQ=GCCAGGCCCGCCGGGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:114,2:0:1,0:24.9:1:29.6:1:1:0:60:28:1:0:0.1 0/1:91:10:9,1:80,1:0.1099:1,2:17.1:1:31.1:1:0.20879:8.48355:60:20:0.1124:0:1.2 -12 133212393 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50059;SOR=0;LSEQ=GCTGCTCACGGCCAGGCCCG;RSEQ=CGGGGCCCTGAGCACTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:2,0:125,6:0.0149:1,0:26:1:28.5:1:1:0:60:4:0.0153:0:1 0/0:116:0:0,0:106,10:0:2,0:22.1:1:32.1:1:1:0:60:232:1:0:0.1 -12 133212582 . G A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=TCGAGAGAAAGAAATTGTCA;RSEQ=AGAATGGAAGGTCTCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:527:0:0,0:220,306:0:2,0:24.8:1:31.4:1:1:0:60:130.5:1:0:0.1 0/1:670:20:11,9:290,359:0.0299:2,2:22.8:1:28.7:1:0.37228:1.51:60:40:0.0302:0:1.1 -12 133212692 . T C 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40899;SOR=0.73267;LSEQ=TATTTCCCCTTGTATCTATC;RSEQ=GTACCCTCCACTTACTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:101:71:1,70:2,28:0.703:2,1:23.1:1:30.4:1:0.20969:4.90895:60:70:0.7:0:1.2 1/0:71:45:0,45:1,25:0.6338:1,1:19.3:1:30.2:1:0.3662:0:60:90:0.6338:0:1.2 -12 133212737 . C T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40198;SOR=1.78534;LSEQ=AATTTGAAAGTTCATTCAGA;RSEQ=CACATCATCCCTCAGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:22:1,21:0,17:0.5641:1,1:26:1:30.1:1:1:0:60:21:0.5526:0:1.8 1/0:20:14:0,14:0,6:0.7:0,1:31:1:28.9:1:1:0:60:13:0.6842:0:1.8 -12 133214441 . C T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.73374;SOR=1.59958;LSEQ=CTGCTACCGCGCACAGGTGG;RSEQ=GGTAACCCCCTTTTCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:17:15,2:10,0:0.6296:0,2:13.1:1:28.7:1:0.51567:0:60:16:0.64:0:2.5 1/0:15:11:10,1:4,0:0.7333:0,2:26.1:1:29.6:1:1:0:60:22:0.7333:0:1.4 -12 133214517 . G A 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.26206;SOR=0.6912;LSEQ=CGACCTCCCAGCCCACCCAG;RSEQ=AGGAGAGCTGGCACCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:68:63,5:33,1:0.6667:1,2:24.6:1:29.6:1:0.66071:2.59855:60:67:0.6634:0:2.3 1/0:69:40:35,5:23,6:0.5797:2,2:28.9:1:29.2:1:0.50728:1.81:60:80:0.5882:0:2.1 -12 133214522 . G C 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54565;SOR=0.81987;LSEQ=TCCCAGCCCACCCAGGAGGA;RSEQ=AGCTGGCACCTCAGGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:72:65,7:36,1:0.6606:1,2:24.3:1:31.3:1:0.2611:3.83989:60:35:0.6542:0:2.2 1/0:83:51:45,6:26,6:0.6145:2,2:24.5:1:30.9:1:0.52285:1.72:60:102:0.622:0:1.8 -12 133214754 . G A 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.36264;SOR=0.31672;LSEQ=CAAGTTGAGAGTCCGTGGTG;RSEQ=AGACGCCACAGTCATGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:76,218:0.0101:2,2:11.7:1:22.3:1:0.16975:5.70:60:2:0.0069:0:1.3 0/0:312:1:1,0:85,226:0.0032:2,0:1:0:23:0:0.27564:0:60:2:0.0032:0:1 -12 133214768 . A G 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55805;SOR=0.87525;LSEQ=GTGGTGGAGACGCCACAGTC;RSEQ=TGGAGAGCCAGAGGGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:154:29,125:18,59:0.6667:2,2:22.6:1:31.6:1:0.48838:1.31338:60:153:0.6711:0:1.1 1/0:231:147:29,118:17,67:0.6364:2,2:23.2:1:30.4:1:1:1.0323:60:72.5:0.6332:0:1.1 -12 133215534 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07429;SOR=Inf;LSEQ=TCTCTGCAGGATGTGCAGGC;RSEQ=ACGCTGCAGCAGCAGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:35,1:0:1,0:24.1:1:30.2:1:1:0:60:72:1:0:0.1 0/1:14:2:1,1:12,0:0.1429:0,2:26:1:29.5:1:0.14286:0:60:4:0.1429:0:1 -12 133215853 . T A 55 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0125;SOR=Inf;LSEQ=GTGGTACTGGGTGATCTCCT;RSEQ=CACCCAGCCCACGACCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:212,391:0:2,0:24:1:29.9:1:1:0:60:66:1:0:0.1 0/1:563:6:6,0:206,351:0.0107:2,0:6.7:1:21.3:1:0.00273:0:60:5:0.0091:0:2 -12 133216124 . T TCCCTCAACACAA 59 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=CTTGTTCAGGCTTCACCGCA;RSEQ=CCCAAACTCTGTGTGTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,2:0.5714:0,0:19.3:1:29.7:1:1:0:60:8:0.5714:0.2857:0 1/0:2:1:0,1:0,1:0.5:0,0:40:0:31.8:0:1:0:60:2:0.5:0:0 -12 133218493 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.17299;SOR=Inf;LSEQ=GCCAGCTCCAGCACCACCAG;RSEQ=CCCCTGGGCCTGACTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:35,128:0:2,0:22.2:1:30.5:1:1:0:60:22.286:0.9873:0:0.2 0/1:118:2:1,1:19,96:0.0169:2,2:19:1:27:1:0.31388:4.95:60:4:0.0172:0:2 -12 133218724 . C T 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=0.55697;LSEQ=TCACAGAATGGCAGAAACAC;RSEQ=AGCCAGGTCTCATGGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:242:168,74:81,37:0.6704:2,2:25.2:1:29.8:1:0.90357:1.04:60:39.333:0.6724:0:1.1 1/0:356:189:121,68:106,61:0.5309:2,2:25.2:1:29.4:1:1:1.02:60:62:0.5269:0:1.1 -12 133219582 . C A 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02763;SOR=Inf;LSEQ=GGGCATCTGGTTGCTGCGCA;RSEQ=CTAGACCAACGCAGGCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:136,327:0:2,0:24.3:1:31.3:1:1:0:60:45.3:1:0:0.2 0/1:443:5:3,2:136,302:0.0113:2,2:16:1:28.2:1:0.18059:3.32:60:10:0.0115:0:1 -12 133219602 . G A 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20224;SOR=4.31876;LSEQ=CCTAGACCAACGCAGGCCAC;RSEQ=TCAGCCTCCCCCTGCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:1:1,0:84,246:0.003:2,0:1:0:27:0:0.2568:0:60:2:0.0031:0:1 0/1:309:4:2,2:91,214:0.0129:2,2:21:1:30.5:1:0.5865:2.34:60:8:0.0132:0:1.3 -12 133219609 . T C 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.13002;LSEQ=CAACGCAGGCCACGTCAGCC;RSEQ=CCCCCTGCGCAGGAGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:1,2:69,226:0.0101:2,2:30.3:1:24.3:1:0.55352:1.63:60:2:0.007:0:1.7 0/1:264:3:0,3:74,187:0.0114:2,0:23.7:1:33:0:0.56176:0:60:6:0.0116:0:1 -12 133219800 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12019;SOR=0;LSEQ=ATGTGCTGCCATGGAGGGCC;RSEQ=AGGACTCACAGTGTCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:1,2:182,82:0.0112:2,2:23.7:1:28.3:1:0.23375:4.41147:60:6:0.0115:0:2.3 0/0:273:0:0,0:191,82:0:2,0:24.5:1:30.6:1:1:0:60:135.5:1:0:0.6 -12 133219831 . T C 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=0.6083;LSEQ=GTGTCCAGCACAAAGACGGA;RSEQ=GCCCTGCGCTGTGAGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:412:276:171,105:82,54:0.6699:2,2:25.3:1:31:1:0.74804:1.07:60:91:0.6757:0:1.2 1/0:411:227:138,89:116,67:0.5523:2,2:23.5:1:30.1:1:0.61012:1.11629:60:55.75:0.5533:0:1.2 -12 133219989 . A T 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=ATGGGCGGCTGGTGCAGGCC;RSEQ=TACCTGGTTCCAGGTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:656:0:0,0:350,306:0:2,0:23.8:1:30.5:1:1:0:60:108.333:1:0:0.1 0/1:610:12:6,6:316,282:0.0197:2,2:26.4:1:30.7:1:1:1.12036:60:24:0.0199:0:1.1 -12 133220098 . CCA C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.57225;SOR=1.27232;LSEQ=CCTCACCAGCTGTTTATTGA;RSEQ=CACACACACAGCCCAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:953:12:7,5:453,487:0.0126:2,2:30:1:32.7:1:0.5681:1.50:60:24:0.0128:0:0.1 0/1:1002:16:8,8:480,504:0.016:2,2:27.2:1:31.9:1:1:1.05:60:32:0.0162:0.003:0.3 -12 133220142 . G A 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2248;SOR=2.67614;LSEQ=CCAGGGCCCGGAACAGTAAC;RSEQ=GAACCTGGAAGAATCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:3:3,0:299,429:0.0041:2,0:1.7:1:26.7:1:0.0701:0:60:6:0.0042:0:1 0/1:734:8:7,1:327,399:0.0109:2,2:7.1:1:26.4:1:0.02646:8.52:60:16:0.011:0:1.1 -12 133220168 . G A 46 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02324;SOR=Inf;LSEQ=TGGAAGAATCGGGCAGACAG;RSEQ=CCGGCAAGGGCTGGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:168,347:0:2,0:24.1:1:31.2:1:1:0:60:56.222:1:0:0.1 0/1:461:5:5,0:164,292:0.0108:2,0:10.8:1:20.2:1:0.00637:0:60:1.5:0.0066:0:1 -12 133220206 . C T 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=Inf;LSEQ=GTGGGGGCTCTGGCTGCCCA;RSEQ=GTGACTTCTGCCCGGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:36,226:0:2,0:23.2:1:30:1:1:0:60:42.667:1:0:0.1 0/1:193:9:0,9:26,158:0.0466:2,0:21.2:1:30.6:1:0.61165:0:60:18:0.0469:0:1 -12 133220230 . T G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.00021;SOR=Inf;LSEQ=ACTTCTGCCCGGGATGTGGC;RSEQ=GTGCCCCTGCAGCTGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:18,162:0:2,0:21.9:1:30.4:1:1:0:60:59:1:0:0.1 0/1:119:9:0,9:8,102:0.0756:2,0:23.6:1:30.3:1:1:0:60:18:0.0776:0:1.2 -12 133220321 . T A 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60758;SOR=0.80394;LSEQ=ACCTGTGGGAACGAGTCCAC;RSEQ=GTCGCTGCTGTTCCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:115:79:55,24:25,11:0.687:2,2:27.1:1:31.1:1:1:1.01:60:158:0.687:0:1.1 1/0:58:37:30,7:16,5:0.6379:2,2:24.1:1:30.9:1:0.74089:1.33:60:74:0.6379:0:1.1 -12 133220380 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08474;SOR=Inf;LSEQ=CTTTCCTCCATACCACCCTG;RSEQ=TGGAGCCTCCCCCAGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:190,73:0:2,0:22.6:1:31.8:1:1:0:60:51.6:1:0:0.3 0/1:207:3:2,1:148,56:0.0145:2,2:23.7:1:28.7:1:1:1.31955:60:6:0.0147:0:1.3 -12 133220454 . G A 140 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=23.84707;LSEQ=ATACGCCCTCGATGTCTGGC;RSEQ=CTGACAGCTCAGCGTTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:1:1,0:265,238:0.002:2,0:1:0:25:0:1:0:60:2:0.002:0:2 0/1:641:29:14,15:336,275:0.0452:2,2:27:1:28.9:1:0.56786:1.30853:60:58:0.0455:0:1.2 -12 133220526 . T C 215 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACTGAATACTCATAGAGA;RSEQ=TGTAGACCATGTTGGAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:0:0,0:210,291:0:2,0:26.3:1:30.2:1:1:0:60:61.625:0.996:0:0.1 0/1:537:125:55,70:185,226:0.2328:2,2:24.1:1:31:1:0.91824:1.04177:60:61.5:0.2316:0:1.2 -12 133220600 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49986;SOR=Inf;LSEQ=GATGATCTCGTCACTGGGCG;RSEQ=AAGTGGTAATGTCTGTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:42,129:0:2,0:22.7:1:28.5:1:1:0:60:170:1:0:0.2 0/1:189:2:1,1:46,140:0.0106:2,2:43:1:32.5:1:0.4385:3.02:60:4:0.0109:0:1 -12 133220652 . A AG 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35555;SOR=0.6945;LSEQ=CACACGCTATTCGGAGTCCT;RSEQ=GACTTCTGGTGCCCCTAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:39:0,39:1,26:0.5909:1,1:22.2:1:30.9:1:0.40909:0:60:38:0.5846:0.1515:0.6 1/0:52:26:0,26:1,25:0.5:1,1:20.8:1:29.2:1:1:0:60:52:0.5:0.1923:0.7 -12 133220670 . G A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82244;SOR=1.14403;LSEQ=CTAGACTTCTGGTGCCCCTA;RSEQ=CGACGGGGTACACCCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:29:0,29:0,24:0.5472:1,1:20.9:1:28.9:1:1:0:60:58:0.5686:0:1 1/0:31:18:0,18:0,13:0.5806:1,1:24.7:1:28.7:1:1:0:60:36:0.5806:0:1.1 -12 133224393 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTCCCACCTGTTCTCTG;RSEQ=GGTCTCGATGCCTCTGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35:1:32.5:1:1:0:60:4:1:0:2 -12 133224410 . C T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGTCTCGATGCCTCTG;RSEQ=GTCCGCTTTCCTCTTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:1:32:0:1:0:60:4:1:0:2 -12 133225446 . G T 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00607;SOR=0.61894;LSEQ=GAGATGGAGGCTGGAGGCCA;RSEQ=GCTAGATCATGGGAAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:213:175,38:80,18:0.6827:2,2:23:1:30.5:1:1:1.04:60:41.6:0.6797:0:1.1 1/0:275:157:122,35:89,28:0.5709:2,2:24.8:1:29.7:1:0.77301:1.10:60:77.5:0.572:0:1.1 -12 133225670 . C A 52 v4;Bias;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.05633;SOR=Inf;LSEQ=CTCGCTGATCTGAAAGGCCA;RSEQ=ACGGACATACAGCACATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:109,241:0:2,0:24.8:1:31.7:1:1:0:60:42.75:1:0:0.1 0/1:334:4:4,0:98,232:0.012:2,0:10.3:1:26:1:0.00834:0:60:8:0.0122:0:1 -12 133225705 . C T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26364;SOR=0;LSEQ=CATCACAGGACACACTGGAA;RSEQ=CCACAGACGGGGCCACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:3:1,2:63,165:0.013:2,2:20.3:1:24:1:1:1.31:60:2:0.009:0:1 0/0:173:0:0,0:53,120:0:2,0:22.9:1:30.5:1:1:0:60:56.667:1:0:0.1 -12 133225713 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.002;SOR=Inf;LSEQ=GACACACTGGAACCCACAGA;RSEQ=GGGGCCACCTTCCAGGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:60,143:0:2,0:22.5:1:30.2:1:1:0:60:39.6:1:0:0.2 0/1:145:7:2,5:43,95:0.0483:2,2:19.7:1:30.1:1:1:1.13063:60:14:0.0493:0:1.1 -12 133225753 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51587;SOR=0;LSEQ=CTTGCAGCTCCCAGCACAGG;RSEQ=CCTTAGGCCTCCCTACGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:67,79:0.0135:2,2:41:0:31.5:1:1:1.18:60:4:0.0144:0:1 0/0:101:0:0,0:52,49:0:2,0:21.3:1:31.5:1:1:0:60:49.5:1:0:0.1 -12 133225761 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51463;SOR=0;LSEQ=TCCCAGCACAGGGCCTTAGG;RSEQ=CTCCCTACGATGGGCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:70,74:0.0137:2,2:42:0:31:1:1:1.06:60:4:0.0144:0:1 0/0:101:0:0,0:61,40:0:2,0:21.7:1:32.1:1:1:0:60:100:1:0:0.1 -12 133226159 . T C 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03425;SOR=0.70661;LSEQ=TGAGATGGGAATGCCCGCCA;RSEQ=GACTTTCTCACAAGCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:374:249:126,123:58,65:0.6658:2,2:23.4:1:30.6:1:0.58191:1.15:60:48.8:0.6649:0:1.7 1/0:284:166:74,92:54,63:0.5845:2,2:22:1:30.3:1:0.80936:1.06539:60:82:0.5836:0:1.6 -12 133226196 . G A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00662;SOR=0.64425;LSEQ=GCCTCCCTAGGGGTCAGGAC;RSEQ=CATCTCGGGCTCCCTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:383:252:138,114:81,49:0.658:2,2:24.8:1:30.2:1:0.19012:1.36445:60:83:0.6622:0:1.7 1/0:291:161:113,48:71,59:0.5533:2,2:23.4:1:30:1:0.00718:1.95:60:79.5:0.554:0:1.5 -12 133226249 . G T 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03696;SOR=0.1392;LSEQ=CAGAGACAGACAGTATCACA;RSEQ=CTGTGTGCCTTACCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:7:1,6:378,239:0.0112:2,2:11.3:1:26.7:1:0.01651:9.45822:60:14:0.0116:0:1.1 0/0:635:1:0,1:402,232:0.0016:2,0:1:0:24:0:0.36693:0:60:2:0.0016:0:1 -12 133233705 . T C 275 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13067;SOR=0;LSEQ=GATCCCGCCCAGCCCAGCCT;RSEQ=GGGGCCCCACCGTCACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:462:462:320,142:0,0:1:0,2:24.1:1:30.5:1:1:0:60:91.4:1:0:1.1 1/1:556:552:366,186:0,3:0.9928:0,2:25.2:1:30.2:1:0.03908:0:60:45:0.9926:0:1.1 -12 133234389 . CAT C 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.25263;SOR=0.76077;LSEQ=AAAACATAATCCAACTCAGA;RSEQ=ATTCTGCTCTGTCTAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:108:86,22:47,11:0.6506:2,2:22.4:1:31.6:1:1:1.09247:59.9:107:0.6485:0.1205:0.1 1/0:157:92:71,21:50,15:0.586:2,2:24.5:1:30.8:1:1:1.01:59.9:91:0.5833:0.1019:0 -12 133234741 . C CGTGT 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.62584;SOR=0.46163;LSEQ=TCCTCGGGGAGTAACACGTG;RSEQ=GTATGTGTAAACACGTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:0,12:0,4:0.75:0,0:21.8:1:31.5:1:1:0:60:24:0.75:0.125:0 1/0:7:4:1,3:0,3:0.5714:0,2:9:1:28.6:1:1:0:60:8:0.5714:0.4286:0.5 -12 133235577 . A C 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTGCTTTTTTCTCCAA;RSEQ=GTGGTTTCAAACTGTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:35.3:1:33.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 133235789 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00112;SOR=0.36766;LSEQ=GCCCTCACCTCTCTGTGATG;RSEQ=GGGGAGCCCTCACCTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:90:68,22:19,5:0.7895:2,2:25.7:1:31:1:0.79361:1.2273:60:29:0.7838:0:1.3 1/0:102:59:46,13:31,12:0.5784:2,2:25.6:1:30.3:1:0.64167:1.37:60:28.5:0.5816:0:1.3 -12 133235817 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11574;SOR=0;LSEQ=CCTCACCTCTCCGTGACGGA;RSEQ=GGAGCCCTCACCTGTCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:2,1:118,33:0.0194:2,2:21.3:1:24:1:0.52951:1.78013:60:2:0.0136:0:3 0/0:162:0:0,0:123,39:0:2,0:1:0:16:0:1:0:60:0:0:0:1 -12 133235824 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49884;SOR=Inf;LSEQ=TCTCCGTGACGGAGGGAGCC;RSEQ=TCACCTGTCCGTGATGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:136,37:0:2,0:23.5:1:30.9:1:1:0:60:42.25:1:0:0.6 0/1:181:2:1,1:134,45:0.011:2,2:27.5:1:29:1:0.44475:2.95614:60:4:0.0113:0:1 -12 133235831 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24686;SOR=0;LSEQ=GACGGAGGGAGCCCTCACCT;RSEQ=TCCGTGATGGGAGGAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:153,43:0.0101:2,2:32:0:31.5:1:0.39594:3.52874:60:4:0.0109:0:1.5 0/0:200:0:0,0:147,53:0:2,0:22.6:1:30.8:1:1:0:60:21.222:1:0:0.5 -12 133236000 . C T 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.66041;LSEQ=CGCTTTGCTGTGCTGATGGA;RSEQ=GTAGACTTCTGCTCCCCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:703:471:221,250:112,120:0.67:2,2:24.7:1:30.1:1:0.7485:1.0557:60:38.25:0.6701:0:1.2 1/0:887:508:242,266:187,191:0.5727:2,2:25.4:1:29.6:1:0.6343:1.07606:60:45.182:0.5706:0:1.2 -12 133236030 . C T 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCCCCGTAATCTTCCAG;RSEQ=TTCCGAGACATGGAACGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:0:0,0:266,349:0:2,0:24.5:1:32:1:1:0:60:67.333:1:0:0.7 0/1:800:39:16,23:340,420:0.0488:2,2:22.4:1:29.6:1:0.74197:1.16347:60:38:0.0477:0:1.7 -12 133236094 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03299;SOR=Inf;LSEQ=CAGAGTCAGGCATGTTGGCT;RSEQ=CCTAGAGAAAGACAATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:123,254:0:2,0:24.3:1:31.8:1:1:0:60:61.833:1:0:0.2 0/1:434:6:5,1:155,272:0.0138:2,2:10:1:24.7:1:0.02773:8.74:60:12:0.014:0:1.3 -12 133237555 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04636;SOR=0;LSEQ=GGTGGAGGGTAGGCCTTTAC;RSEQ=TTGCTGTACAGCACGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:4:2,2:282,112:0.0101:2,2:8.8:1:25.5:1:0.32414:2.51118:60:3:0.0078:0:1.5 0/0:458:0:0,0:310,147:0:2,0:14:0:18:0:1:0:60:0:0:0:2 -12 133237827 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20959;SOR=Inf;LSEQ=AGCTGTGCCTCATCCTCTCT;RSEQ=CCCGCCTCTTCCCTTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:13,138:0:2,0:25.5:1:32:1:1:0:59.9:29.2:1:0:0.3 0/1:128:2:1,1:2,124:0.0156:1,2:28.5:1:26:1:0.04651:50.84:60:4:0.0161:0:1.5 -12 133237831 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50274;SOR=0;LSEQ=GTGCCTCATCCTCTCTGCCC;RSEQ=CCTCTTCCCTTTCCAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:10,129:0.0141:2,2:40:1:29:1:0.15046:12.35:60:4:0.0146:0:1 0/0:117:0:0,0:3,114:0:1,0:25.5:1:32.4:1:1:0:59.6:234:1:0:0.2 -12 133238026 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23139;SOR=Inf;LSEQ=CCAGGTCTGTTTCTATCCTG;RSEQ=CTCCTGATCCAACCTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:156,15:0:2,0:24.4:1:30.9:1:1:0:60:27.5:1:0:0.5 0/1:159:2:1,1:142,15:0.0126:2,2:16:1:31.5:1:0.1917:9.19828:60:4:0.0128:0:2 -12 133238040 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11359;SOR=Inf;LSEQ=ATCCTGGCTCCTGATCCAAC;RSEQ=TCCTTTCTGGGCTAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:193,37:0:2,0:23.1:1:30.7:1:1:0:60:31.857:1:0:0.5 0/1:217:3:1,2:177,37:0.0138:2,2:13.7:1:28:1:0.08397:9.41755:60:6:0.014:0:2 -12 133238076 . T C 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08532;SOR=0.78453;LSEQ=ATTTAATCTATCTCAATCCA;RSEQ=GTCCTTTCTAAAGCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:422:259:186,73:114,49:0.6137:2,2:22.5:1:31.2:1:0.74091:1.09:60:63.75:0.6159:0:1.1 1/0:447:248:167,81:135,64:0.5548:2,2:25.9:1:30.1:1:0.91942:1.02306:60:48.6:0.5535:0:1.1 -12 133238275 . G A 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06276;SOR=Inf;LSEQ=CATTGGTGAAGCCTTCCTGA;RSEQ=AAACAAGAGTGAAGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:132,276:0:2,0:23.4:1:31.3:1:1:0:60:50:1:0:0.1 0/1:442:5:4,1:134,302:0.0113:2,2:14.8:1:27.2:1:0.03511:8.97:60:10:0.0115:0:1.4 -12 133238313 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23893;SOR=0;LSEQ=GGGCAGCTTCACTCATGATG;RSEQ=CCCAAACCTGGAAACCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:25,159:0.0108:2,2:23.5:1:29.5:1:0.26068:6.26:60:4:0.0108:0:1 0/0:194:0:0,0:39,155:0:2,0:22.7:1:31.2:1:1:0:60:37.8:1:0:0.1 -12 133240181 . A G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGAGAGAAGAGGGGCT;RSEQ=TGGTGGGAAATGGGAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29:1:33.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 133240782 . A G 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03451;SOR=0.65652;LSEQ=TGAGTTCCCCTTTCCTTTTC;RSEQ=CCCAGTGTGTGGCCTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:291:184:64,120:43,64:0.6323:2,2:23.4:1:30.8:1:0.37908:1.25874:59.6:25.286:0.6277:0:1.2 1/0:183:97:35,62:26,60:0.5301:2,2:21.4:1:30.7:1:0.43494:1.30:58.6:31.333:0.5251:0:1.2 -12 133241144 . C A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02573;SOR=Inf;LSEQ=GGAGGAGGAAAGGAGAGATG;RSEQ=GACAGGGACAAGGGAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:4,106:0:1,0:24.5:1:30.2:1:1:0:60:54:1:0:0.1 0/1:75:4:0,4:3,68:0.0533:1,0:19.8:1:30:1:1:0:60:8:0.0556:0:1 -12 133241785 . A G 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19911;SOR=Inf;LSEQ=CCTCCAACATTCCTTGAATC;RSEQ=GATGAACGGCCCTCCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:114,7:0:2,0:23.9:1:29.9:1:1:0:60:39.333:1:0:0.1 0/1:98:2:1,1:91,5:0.0204:2,2:16:0:28.5:1:0.11929:16.70476:60:4:0.0204:0:1 -12 133241792 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60443;SOR=2.23919;LSEQ=CATTCCTTGAATCAGATGAA;RSEQ=GGCCCTCCATGCACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:1,0:127,10:0.0072:2,0:38:0:33:0:1:0:60:2:0.0074:0:1 0/1:124:2:1,1:110,12:0.0161:2,2:24.5:1:29.5:1:0.19945:8.84796:60:4:0.0164:0:1 -12 133242073 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10663;SOR=Inf;LSEQ=CATGGAGCACCTCACAGATT;RSEQ=TTCCATTTCACATTCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:48,216:0:2,0:25:1:32:1:1:0:60:131:0.9962:0:0.2 0/1:240:3:1,2:46,190:0.0125:2,2:16.7:1:29.3:1:0.48315:2.06:60:6:0.0126:0:1.3 -12 133242140 . A G 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11276;SOR=0.52731;LSEQ=TTGAAAATTTTCAAATCTAT;RSEQ=GAAAACCTAAAAAACCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:53:1,52:0,22:0.7067:1,1:23.3:1:31.3:1:1:0:60:52:0.7123:0:1.2 1/0:43:24:0,24:0,19:0.5581:1,1:22.8:1:31.2:1:1:0:60:48:0.5581:0:1 -12 133243788 . T A 80 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAACAATAGGCGAAGGCAG;RSEQ=TGGGTTCGTAAAACTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:13.3:1:28.7:1:1:0:60:14:0.7778:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -12 133243817 . C T 65 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAAACTTGATGTACTCAAA;RSEQ=GGCCAGCCAGCTGTAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:36:1:32.8:1:1:0:60:8:0.8:0:1.8 1/1:1:1:1,0:0,0:1:0,0:2:0:30:0:1:0:60:2:1:0:1 -12 133244013 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11768;SOR=Inf;LSEQ=CAGAGGATCCCAGGCAAGGA;RSEQ=CCAAGAGTGCCCACTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:176,29:0:2,0:24.1:1:31.7:1:1:0:60:50.25:1:0:0.1 0/1:198:3:2,1:165,30:0.0152:2,2:21.7:1:29.7:1:0.4017:2.73094:60:6:0.0154:0:1.3 -12 133244668 . CA C 71 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=GACAGAGTGAGACCTCATTT;RSEQ=AAAAAAAAAAGAAAGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:3,0:0.5:0,0:28:1:31:1:1:0:60:10:0.5556:0:0 0/0:3:0:0,0:3,0:0:0,0:16.7:1:31.3:1:1:0:60:6:1:0:0.3 -12 133245149 . A G 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31775;SOR=0.83994;LSEQ=AGACACACCGGCTTCCCACC;RSEQ=AGTGGAGAAAGGCGGCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:333:205:124,81:67,60:0.6156:2,2:22:1:30.4:1:0.17239:1.37:60:67.333:0.6196:0:1.1 1/0:272:156:95,61:76,39:0.5735:2,2:22.6:1:30:1:0.44497:1.25024:60:77:0.5878:0:1.1 -12 133245556 . G A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62399;SOR=2.88805;LSEQ=AGCGAAACTCAGTAGAGGCT;RSEQ=GTGACCAAGCTTGCCTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:1:1,0:64,206:0.0037:2,0:1:0:23:0:0.23985:0:60:2:0.0037:0:1 0/1:283:3:2,1:75,205:0.0106:2,2:10.3:1:21:1:0.18084:5.43:60:6:0.0108:0:1 -12 133245584 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22239;SOR=Inf;LSEQ=AGCTTGCCTCGTGTGCAGTT;RSEQ=ACCAACCCCTTTTAGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:28,144:0:2,0:23.9:1:31.9:1:1:0:60:85:1:0:0.1 0/1:154:2:1,1:31,121:0.013:2,2:7.5:1:29:1:0.37348:3.86:60:4:0.0132:0:1.5 -12 133245594 . T C 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.60505;LSEQ=GTGTGCAGTTCACCAACCCC;RSEQ=TTTAGACATTCAGGAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:19,131:0.0131:2,2:23:1:30:1:0.2466:6.74:60:4:0.0132:0:1 0/0:126:1:0,1:23,102:0.0079:2,0:37:0:29:0:1:0:60:2:0.008:0:1 -12 133248977 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15811;LSEQ=TAGCCTGCCTCAGGTTTGAC;RSEQ=CTGTGGCTGCACGTGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:26,119:0.0135:2,2:8:1:28:1:0.33464:4.51:60:4:0.0137:0:1 0/1:128:2:1,1:25,101:0.0156:2,2:7.5:1:29.5:1:0.36626:3.98:60:4:0.0159:0:1 -12 133249017 . G A 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10946;SOR=0.54429;LSEQ=GTTGTGCCCGAGAAAGCTCC;RSEQ=GAAGGACTCATGTGCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:90:62:13,49:4,24:0.6889:2,2:21.1:1:31.4:1:0.56788:1.58:60:124:0.6889:0:1.1 1/0:55:30:5,25:3,22:0.5455:2,2:24:1:30.8:1:0.71527:1.46:60:29:0.5577:0:1.1 -12 133249139 . T A 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76702;SOR=0.93611;LSEQ=TGGGGAGAAGGGGCTTTATT;RSEQ=CAGCCCCTGCAGCTTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:223:139:114,25:69,15:0.6233:2,2:24.2:1:28.4:1:1:1.00873:60:278:0.6233:0:1 1/0:209:127:100,27:63,19:0.6077:2,2:21.7:1:28.7:1:0.73621:1.12:60:126:0.6058:0:1.1 -12 133250017 . C A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01971;SOR=Inf;LSEQ=CGTGTGTCCCGGAGACACAG;RSEQ=CTGCTGGGTGGAGCGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:96,40:0:2,0:25:1:32.1:1:1:0:60:272:1:0:0.1 0/1:83:4:3,1:54,24:0.0482:2,2:19.5:1:29.5:1:1:1.33:60:8:0.0482:0:1.3 -12 133250118 . C T 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00502;SOR=0.65099;LSEQ=GCTCCGTGGCCATCTGGATG;RSEQ=GTGCACACGGCAGCAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:398:262:174,88:90,46:0.6583:2,2:25.3:1:29.4:1:1:1.01:60:51.4:0.6607:0:1.1 1/0:338:188:118,70:94,55:0.5562:2,2:24.8:1:29.3:1:1:1.01383:60:36.6:0.5562:0:1.1 -12 133250359 . T C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2614;SOR=0;LSEQ=GCCCGGGAACCCCTGAGAAC;RSEQ=GGCAAAACTGGGCACCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:47,194:0.0123:2,2:32.7:1:31.7:1:0.48325:2.06:60:6:0.0127:0:1 0/0:187:0:0,0:37,150:0:2,0:22.3:1:29.8:1:1:0:60:45.75:1:0:0.2 -12 133250442 . A G 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0946;SOR=0.44004;LSEQ=CAAGGCCCCACATGGTGTAG;RSEQ=CACCTTGTGAAAACCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:48:0,48:0,16:0.75:1,1:21.9:1:30.8:1:1:0:60:15:0.7377:0:1.1 1/0:30:17:1,16:0,13:0.5667:1,1:26.2:1:32.6:1:1:0:60:34:0.5667:0:1 -12 133250550 . C T 43 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00714;SOR=Inf;LSEQ=CCTCGCCTTCCTCCCATCCT;RSEQ=AGCAGAGTTTGTGGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:1,11:0:2,0:22.7:1:31.8:1:1:0:60:11:1:0:1.3 1/0:4:3:1,2:0,1:0.75:0,2:39.7:1:27.3:1:1:0:60:6:0.75:0:2 -12 133250569 . T G 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4965;SOR=Inf;LSEQ=TCAGCAGAGTTTGTGGCCTC;RSEQ=CCGACGGGCGCCCCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:0.6667:0,0:25.7:1:29.2:1:1:0:60:5:0.625:0:2.2 1/1:4:4:1,3:0,0:1:0,2:40:1:32:1:1:0:60:8:1:0:2 -12 133252176 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1572;SOR=Inf;LSEQ=CCTTTCTCCATTCCTCCCTC;RSEQ=GACCCAGGGAGGAACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:99,158:0:2,0:23.7:1:30.1:1:1:0:60:18.769:1:0:0.1 0/1:170:2:0,2:47,121:0.0118:2,0:26:1:31:1:1:0:60:4:0.0125:0:1 -12 133252462 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07684;SOR=Inf;LSEQ=TTCTCTTCTTCAAGCTATTC;RSEQ=AAATTCCTCTCCCAAAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:41,151:0:2,0:25.5:1:31.7:1:1:0:60:47:1:0:0.1 0/1:143:3:1,2:21,119:0.021:2,2:16:1:28.3:1:0.39651:2.81:60:6:0.0211:0:1 -12 133252556 . T C 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01098;SOR=0.47533;LSEQ=TCTGGCAGAAAAGACGGTCA;RSEQ=ACCCTGAGAACAAAGCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:125:86:68,18:25,14:0.688:2,2:24.7:1:32:1:0.08225:2.10:60:42:0.6885:0:1.2 1/0:92:47:41,6:36,9:0.5109:2,2:26:1:31.2:1:0.40587:1.70:60:46:0.5055:0:1.2 -12 133252796 . C G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.18603;LSEQ=GGTGATGAGGTAGCCCTAGC;RSEQ=AAGTTCATTAGCAATCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:114:30,84:74,165:0.3211:2,2:23.3:1:30.8:1:0.38542:1.25496:60:113:0.321:0:1.1 1/0:394:237:74,163:51,103:0.6015:2,2:26:1:30.2:1:0.73952:1.09041:60:46.4:0.601:0:1.1 -12 133252947 . T C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.38856;SOR=1.64755;LSEQ=TCCTGAGAAGAGACGCTCTG;RSEQ=GTGTGGATTCCCACTCGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:13:9,4:17,20:0.26:2,2:15.5:1:31.4:1:0.2025:2.60:60:26:0.2653:0:1.2 0/1:19:7:4,3:4,8:0.3684:2,2:25.6:1:29.4:1:0.37652:2.53:60:6:0.3333:0:1.9 -12 133253286 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23798;SOR=Inf;LSEQ=CAAGCTCTAAACTCCCCATT;RSEQ=GGCCTCCCTGAACACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:24,176:0:2,0:23.5:1:30.8:1:1:0:60:99:1:0:0.3 0/1:191:2:1,1:35,154:0.0105:2,2:21.5:1:31:1:0.34224:4.35:60:4:0.0105:0:1.5 -12 133253310 . A G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59251;SOR=0.84901;LSEQ=CTCCCTGAACACCCACCCCC;RSEQ=GCCTGCTCTACCTCCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:52:4,48:2,73:0.4094:1,2:22.7:1:30:1:0.22593:3.01:60:25:0.4132:0:1.1 0/1:108:40:2,38:6,62:0.3704:2,2:26.8:1:30.3:1:0.70743:1.8292:60:39:0.375:0:1 -12 133253995 . G A 150 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=31.70224;LSEQ=GGGTGATTTCTACCGGAAAA;RSEQ=CATTTCCTCGGTATCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:1:1,0:320,362:0.0015:2,0:1:0:26:0:0.46999:0:60:2:0.0015:0:1 0/1:742:33:14,19:312,397:0.0445:2,2:26:1:29.9:1:1:1.0665:60:32:0.0438:0:1.3 -12 133254042 . C T 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06184;SOR=Inf;LSEQ=CAATGAGCCTGCAAAACACA;RSEQ=AGTGTGCTAACTAGAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:0:0,0:195,275:0:2,0:24.9:1:31.8:1:1:0:60:41.727:1:0:0.3 0/1:471:5:2,3:198,267:0.0106:2,2:16.4:1:27.8:1:1:1.11214:60:10:0.0107:0:1.8 -12 133254083 . T C 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.28229;SOR=1.18739;LSEQ=ACATCCAGGAAAGTCTATTC;RSEQ=TCTGTGGATTCACCCATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:134:68,66:118,113:0.3661:2,2:24.8:1:31.6:1:1:1.0135:60:43.667:0.3649:0:1.1 0/1:349:142:82,60:118,88:0.4069:2,2:21.2:1:30.8:1:1:1.02:60:70:0.407:0:1.2 -12 133256349 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20262;SOR=Inf;LSEQ=AAGAGTTGGCGACTTCAAGG;RSEQ=ACCTTGTCCAACTCTGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:46,56:0:2,0:26.3:1:32.2:1:1:0:60:101:1:0:0.1 0/1:84:2:2,0:23,59:0.0238:2,0:25.5:1:29:1:0.08606:0:60:4:0.0241:0:1 -12 133256904 . C T 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55591;SOR=0.83505;LSEQ=CTCCTATATCCCATGAACAG;RSEQ=CTAGGGCCAGGGTAGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:37:8,29:10,61:0.3426:2,2:32.5:1:28.6:1:0.41509:1.67:60:11.333:0.3269:0:1.4 0/1:99:30:7,23:11,58:0.303:2,2:23.6:1:29.1:1:0.40429:1.60:60:60:0.3125:0:1.1 -12 133256988 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0177;SOR=Inf;LSEQ=GGGCAAGAATCTGAAAGACA;RSEQ=GCTACTTCTCACCATTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:35,16:0:2,0:22.9:1:31.4:1:1:0:60:50:1:0:0.3 0/1:19:3:1,2:7,9:0.1579:2,2:27.7:1:29.7:1:1:1.52085:60:6:0.1667:0:1 -12 133257837 . C A 141 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02541;LSEQ=CCGTTCCAGGCGCTTGAGTG;RSEQ=CGAAACTGAGGAAGTGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:28:10,18:203,251:0.0579:2,2:22.7:1:29.5:1:0.43438:1.45467:60:56:0.0587:0:1 0/0:643:1:1,0:283,358:0.0016:2,0:1:0:22:0:0.44237:0:60:2:0.0016:0:1 -12 133257887 . C T 99 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00833;SOR=9.3869;LSEQ=TGAGTGAAAGAAGGGAACCC;RSEQ=GTGCTTAATTTGTAATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:1:0,1:87,250:0.003:2,0:42:0:32:0:1:0:60:2:0.003:0:1 0/1:405:11:3,8:132,262:0.0272:2,2:15.8:1:28.9:1:0.75825:1.34259:60:22:0.0275:0:1 -12 133257929 . C CT 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCTGCTGCTTCTTTTTTT;RSEQ=TTTTTTTTCTTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:18,148:0:2,0:20.9:1:32.4:1:1:0:60:82:0.9939:0:0.1 0/1:175:20:4,16:27,128:0.1143:2,2:23.9:1:30.5:1:0.75875:1.18:60:40:0.1163:0:0.3 -12 133257938 . C CT 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17345;SOR=3.48685;LSEQ=CTTCTTTTTTTCTTTTTTTT;RSEQ=TTTTTTTTTGAGACGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:12,129:0.014:2,2:25:1:29.5:1:0.17414:10.37:60:4:0.0144:0.007:0.5 0/1:148:7:3,4:24,117:0.0473:2,2:8.9:1:29.1:1:0.11424:3.61:60:14:0.0486:0.027:0.4 -12 133257961 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24312;SOR=Inf;LSEQ=TTTTTTTGAGACGGAGTCTT;RSEQ=CTCTGTCGCCTAGGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:1,53:0:1,0:19.7:1:32.7:1:1:0:59.4:53:1:0:0.2 0/1:54:2:0,2:4,48:0.037:2,0:25:1:32:0:1:0:60:4:0.0385:0:1 -12 133257999 . GGCTCA G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52933;SOR=0.5735;LSEQ=GAGTGCAGTGGTGTGATCTC;RSEQ=CTGCAAGCTCCGCCTCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:0,10:0,17:0.3704:1,0:23.9:1:32.5:1:1:0:56.3:20:0.3704:0.0741:0.3 0/1:20:5:0,5:0,15:0.25:1,0:10:1:29.1:1:1:0:57.4:10:0.25:0.15:0.4 -12 133258088 . C T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.60839;LSEQ=CACAGGCGACAGCCACCACG;RSEQ=CTGGCTAATTTTTTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:0,6:0,5:0.5455:0,0:17.8:1:31.5:1:1:0:53:12:0.5455:0:1.2 1/0:3:2:0,2:0,1:0.6667:0,0:9:1:31:0:1:0:53.5:4:0.6667:0:1 -12 133263743 . A C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGCGGGCGGCTGCGGGA;RSEQ=CCGGGCCTCCCTCCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:11,4:0,0:1:0,2:12.1:1:31.9:1:1:0:60:30:1:0:1.5 1/1:21:21:16,5:0,0:1:0,2:16.7:1:30.7:1:1:0:60:42:1:0:1.8 -12 133263819 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12303;SOR=Inf;LSEQ=CCGGAGGGCCGGCCCGAGAG;RSEQ=CTCAGGAGGGCGCCCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:196,90:0:2,0:22.8:1:31.5:1:1:0:60:25:1:0:0.6 0/1:284:3:1,2:186,95:0.0106:2,2:5.3:1:25.7:1:0.26952:3.89553:60:6:0.0108:0:1.3 -12 133263825 . G A 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=1.9804;LSEQ=GGCCGGCCCGAGAGCCTCAG;RSEQ=AGGGCGCCCCTCACCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:95:64,31:151,75:0.296:2,2:22.4:1:29.9:1:1:1.03:60:30.667:0.2958:0:1.4 0/1:341:155:103,52:118,68:0.4545:2,2:23.4:1:29.1:1:0.5714:1.14:60:37.75:0.4562:0:1.3 -12 133263950 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24905;SOR=Inf;LSEQ=GGGGAGAAATTTGGCGCGCT;RSEQ=CCACCCAGACTCGCGAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:94,172:0:2,0:24.1:1:30.1:1:1:0:60:19.462:1:0:0.2 0/1:279:3:1,2:95,180:0.0108:2,2:29.7:1:23:1:1:1.05536:60:2:0.0075:0:2.3 -13 20847593 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54884;SOR=Inf;LSEQ=CTCCTAGAGTACCTTCGCCC;RSEQ=TTTCTCCAGGCTGACTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:35,32:0:2,0:29.5:1:32:1:1:0:60:134:1:0:1.1 0/1:130:2:1,1:65,61:0.0154:2,2:22:1:28.5:1:1:1.06508:60:4:0.0155:0:2 -13 20847602 . G C 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34314;SOR=Inf;LSEQ=TACCTTCGCCCCTTTCTCCA;RSEQ=GCTGACTCCTCCTTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:69:34,35:0,0:0.9857:0,2:29.3:1:31:1:1:0:60:138:0.9857:0:1.1 1/1:134:134:66,68:0,0:1:0,2:25:1:29.9:1:1:0:60:133:1:0:1.3 -13 20847634 . A C 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01154;SOR=Inf;LSEQ=CTTTGCAAGCCCTATCCTGC;RSEQ=ACCCTGATTGTCGCTGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:27,35:0:2,0:26.2:1:29.6:1:1:0:60:61:1:0:0.9 0/1:93:9:3,6:35,49:0.0968:2,2:29.4:1:28.9:1:0.73303:1.42327:60:8:0.087:0:2.1 -13 21004618 . A G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=4.70489;LSEQ=CACTCAGGCTGCCATGACCC;RSEQ=TGAAGAGGGACAACCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:21:19,2:44,6:0.2958:2,2:20.8:1:29:1:1:1.29:60:20:0.2899:0:1.1 1/0:72:48:42,6:20,4:0.6667:2,2:26.9:1:29.7:1:0.72208:1.39:60:96:0.6667:0:1.1 -13 21004660 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23105;SOR=0;LSEQ=AGGGTGGACATCGTGAGTCA;RSEQ=CAGAACTACCAGAGCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:104,50:0.0128:2,2:25:0:31.5:1:0.54839:2.06944:60:4:0.0129:0:1 0/0:168:0:0,0:113,55:0:2,0:23.2:1:31.7:1:1:0:60:167:1:0:0.6 -13 21004678 . C T 44 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25001;SOR=Inf;LSEQ=CAGCAGAACTACCAGAGCAG;RSEQ=CCAACTCACCCCTCCGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:115,74:0:2,0:26:1:31.6:1:1:0:60:93.5:1:0:0.4 0/1:209:3:2,1:130,75:0.0144:2,2:27:0:28:1:1:1.15:60:6:0.0147:0:1.3 -13 21004709 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24879;SOR=Inf;LSEQ=CCTCCGCCTGCCCTCCTCCA;RSEQ=CAGCAAAAGGAAACACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:159,121:0:2,0:25.4:1:32:1:1:0:60:92.333:1:0:0.4 0/1:287:3:3,0:157,127:0.0105:2,0:17:1:26.7:1:0.25733:0:60:6:0.0107:0:1 -13 21004738 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.14755;LSEQ=GGAAACACCAGAGTCCTCCA;RSEQ=GGCTCTTGCAATGGAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:93:42,51:120,113:0.2853:2,2:26.7:1:30.2:1:0.32767:1.28849:60:45.5:0.2826:0:1.4 1/0:351:219:106,113:71,61:0.6239:2,2:26:1:30:1:0.3781:1.24003:60:72:0.6243:0:1.4 -13 21004758 . T C 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGCTCTTGCAATGGAGAGT;RSEQ=CTTTGTGTACACCTCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:18:8,10:147,156:0.0561:2,2:24.4:1:31:1:0.81122:1.17729:60:36:0.057:0:1.7 0/0:359:0:0,0:168,191:0:2,0:26.1:1:29:1:1:0:60:58.833:1:0:1.1 -13 21004816 . G A 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCCAAACCCTTCCTTGA;RSEQ=TGGGCTCACACCTTTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:183:183:60,123:0,0:1:0,2:25.5:1:30.2:1:1:0:60:35.6:1:0:1.4 1/1:175:175:61,114:0,0:1:0,2:23.1:1:29.8:1:1:0:60:174:1:0:1.7 -13 21004828 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50068;SOR=0;LSEQ=TTCCTTGAGTGGGCTCACAC;RSEQ=TTTCATATTGGAGAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:40,112:0.013:2,2:7:0:32:1:0.46286:2.78:60:4:0.0134:0:3.5 0/0:134:0:0,0:38,96:0:2,0:21.6:1:31.2:1:1:0:60:268:1:0:1.7 -13 21004834 . T G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.98654;LSEQ=GAGTGGGCTCACACCTTTCA;RSEQ=ATTGGAGAAAGCAAGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:25:8,17:28,86:0.1799:2,2:19.7:1:31.6:1:0.45606:1.44:60:50:0.1838:0:2.5 1/0:108:69:16,53:12,27:0.6389:2,2:23.4:1:31.3:1:0.4934:1.46675:60:138:0.6389:0:2.1 -13 21006781 . C T 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTTGTCTTCAAAGCTTC;RSEQ=TCCCAGCCCACCACCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:15:0:32:0:1:1:60:4:0.5:0:2.5 0/0:1:0:0,0:1,0:0:0,0:42:0:29:0:1:0:60:2:1:0:0 -13 21006784 . C A 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTCTTCAAAGCTTCCTC;RSEQ=CAGCCCACCACCCCCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:18:0:32:0:1:1:60:4:0.5:0:2.5 0/0:1:0:0,0:1,0:0:0,0:45:0:25:0:1:0:60:2:1:0:0 -13 21549384 . G A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=11.01031;LSEQ=GGGTGGGCCTTCAGGTCATC;RSEQ=GCCCCATTCCGCCCCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:2:1,1:114,274:0.0051:2,2:18.5:1:21.5:1:0.50333:2.40:60:1:0.0026:0:1 0/1:502:27:10,17:168,306:0.0538:2,2:22:1:29.7:1:0.83943:1.07:60:54:0.0549:0:1.1 -13 21549395 . G A 48 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17133;SOR=0.18786;LSEQ=CAGGTCATCGGCCCCATTCC;RSEQ=CCCCAGGCGGTGGTCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:4:2,2:89,229:0.0124:2,2:15.3:1:24:1:0.31735:2.56:60:3:0.0096:0:1.8 0/0:425:1:0,1:138,286:0.0024:2,0:8:0:30:0:1:0:60:2:0.0024:0:1 -13 21549485 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2419;SOR=Inf;LSEQ=CTGGGCTGGAATGTGGAGCG;RSEQ=GTTCTCCCAGTTGATCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:17,92:0:2,0:21.7:1:30.2:1:1:0:60:108:1:0:0.1 0/1:106:2:1,1:29,75:0.0189:2,2:31.5:1:30.5:1:0.48787:2.56:60:4:0.019:0:1 -13 21553234 . T C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTAGTGGGATTACAGGCA;RSEQ=GAGCCACTGCGCCTGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 21553971 . C T 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCACTCAATCCCTACACAGG;RSEQ=ATGAATTCTCCTCCGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:125,314:0:2,0:23.6:1:31.7:1:1:0:60:47.778:0.9977:0:0.1 0/1:507:64:19,45:147,295:0.1262:2,2:22.8:1:28:1:0.66951:1.17986:60:128:0.128:0:1.2 -13 21554217 . A T 64 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTTAGCAAATAGTTACT;RSEQ=GCCAGAATTTTATGTTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:22.6:1:27.6:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 21555544 . CT GA 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.45294;LSEQ=GAAAGCTAGAGCCAGCGAGA;RSEQ=CAGCTCACGTCTGAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:76:56,20:151,43:0.2794:2,2:24:1:30.6:1:0.52269:1.25303:60:152:0.2879:0.0147:2 0/1:289:141:101,40:108,39:0.4879:2,2:23.6:1:30.3:1:0.79195:1.09637:60:282:0.4896:0.0381:2 -13 21555545 . T A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21724;SOR=4.79068;LSEQ=AAAGCTAGAGCCAGCGAGAC;RSEQ=CAGCTCACGTCTGAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:1,0:152,43:0.0037:2,0:36:0:29:0:1:0:60:2:0.0053:0:3 0/1:283:5:2,3:107,41:0.0177:2,2:7.8:1:25.2:1:0.14347:3.87387:60:4:0.0267:0:2.2 -13 21555554 . G A 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.17322;LSEQ=GCCAGCGAGACTCAGCTCAC;RSEQ=TCTGAAGGGAAGGAGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:95:68,27:159,55:0.3074:2,2:23.3:1:30.2:1:0.67566:1.14733:60:94:0.3082:0:1.9 0/1:346:170:116,54:120,56:0.4913:2,2:24.3:1:29.5:1:1:1.00:60:33:0.4896:0:2 -13 21557131 . C CAAAA 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=24.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=ACAAGAGCGAAACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:19.7:1:32:1:1:0:49.8:12:1:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:12.5:1:30.4:1:1:0:50:4:0.6667:0.3333:3 -13 21557174 . TA T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54017;SOR=0;LSEQ=AAACCTGAAATCCACTACCT;RSEQ=AAAAAAAATGCATATCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:2,0:27,0:0.069:1,0:23:1:32:0:1:0:60:4:0.069:0:0 0/0:15:0:0,0:15,0:0:1,0:21.3:1:26.7:1:1:0:58.7:6.5:1:0:0.6 -13 21557284 . G T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64168;LSEQ=AAATGATTAGGAGCCACTAG;RSEQ=ATGGGAAATTTAGTTGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:164,17:0.0109:2,2:8.5:1:27.5:1:0.18753:9.4038:60:4:0.011:0:1 0/0:143:1:0,1:118,24:0.007:2,0:1:0:23:0:0.17483:0:60:2:0.0071:0:1 -13 21557960 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20024;SOR=Inf;LSEQ=TCCAGCCTGTGTAGAAGGAA;RSEQ=AGGAAGGAGGAAGAATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:27,165:0:2,0:24.4:1:30.4:1:1:0:60:191:1:0:0.1 0/1:156:2:1,1:22,132:0.0128:2,2:37:1:31:1:0.27395:5.89:60:4:0.0129:0:1 -13 21558264 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATTTTTAGTAGAAACAG;RSEQ=GTTTCATCATGTTGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:28:1:1:0:60:4:1:0:1 -13 21562371 . C T 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=33.29472;LSEQ=AGCAGGTGCTTCGGGTAGGG;RSEQ=GGAGGCGGGCACCTCCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:1:0,1:132,285:0.0024:2,0:1:0:25:0:1:0:60:2:0.0024:0:1 0/1:405:30:9,21:142,231:0.0741:2,2:25.5:1:29.7:1:0.43735:1.43311:60:60:0.075:0:1.1 -13 21562482 . C CGGGGCG 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=23;MSI=5.000;MSILEN=1;SSF=1;SOR=0.92453;LSEQ=GCGTCCAAGCCCTCCGCAGC;RSEQ=GGGGCGGGGGCGGGGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:0,3:12,61:0.0395:2,0:6.6:1:30.7:1:1:0:60:6:0.0409:0.0389:1.3 0/1:82:3:0,3:22,55:0.0366:2,0:16:1:31.1:1:0.55738:0:60:6:0.0375:0.0244:1.3 -13 21562608 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50384;SOR=Inf;LSEQ=ACCGGGTGCAAGATGTGCGC;RSEQ=GCCGTGACAGCCGTCACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:91,41:0:2,0:26.2:1:29.8:1:1:0:60:131:1:0:0.2 0/1:163:2:1,1:103,57:0.0123:2,2:27.5:1:27.5:1:1:1.79995:60:4:0.0126:0:1.5 -13 21562636 . G T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.58572;SOR=0.39375;LSEQ=CAGCCGTCACGGTGTTGGGG;RSEQ=CGGGCAGGGAGGGCTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:109,67:0.0112:2,2:22:1:31.5:1:1:1.62219:60:4:0.0114:0:1 0/0:225:1:0,1:125,99:0.0044:2,0:1:0:26:0:0.44444:0:60:2:0.0046:0:1 -13 21562756 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24945;SOR=0;LSEQ=CCACGTGCGCGCGCGGCGGC;RSEQ=CCTCCAGGCCCGGCTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:2,1:185,85:0.011:2,2:5.7:1:28:1:1:1.08789:60:6:0.0112:0:1.7 0/0:255:0:0,0:161,94:0:2,0:23.3:1:30.1:1:1:0:60:126.5:1:0:0.4 -13 21562789 . C T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02913;SOR=Inf;LSEQ=GCTTCTGCAGGGAGTCCCGG;RSEQ=GGGCCAGGGTGGCAGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:207,120:0:2,0:24.6:1:30.8:1:1:0:60:53.5:1:0:0.7 0/1:320:5:1,4:188,127:0.0156:2,2:8.8:1:26.4:1:0.16302:5.89078:60:10:0.0161:0:2 -13 21562832 . C T 262 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26008;SOR=1.18913;LSEQ=CTGCTGGACGGAGGTGCTGC;RSEQ=CAATTCATACAGGTCCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:541:426:252,174:68,47:0.7874:2,2:24.6:1:30.5:1:1:1.00:60:41.6:0.7909:0:1.2 1/1:573:467:262,205:58,48:0.815:2,2:26.6:1:29.6:1:0.82883:1.06:60:37.917:0.8213:0:1.2 -13 21562948 . G A 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50623;LSEQ=GCACATGCAGCTGGTGGGCC;RSEQ=CGGGACCGGCCTGCTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:549:430:214,216:57,59:0.7832:2,2:24:1:29.6:1:0.91704:1.03:60:60.429:0.7833:0:1.1 1/0:642:415:204,211:116,108:0.6464:2,2:24.4:1:29.5:1:0.56188:1.11075:60:82:0.6457:0:1.2 -13 21563506 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.34358;SOR=3.45142;LSEQ=ATCAGTGGGTTCTGGCACTT;RSEQ=CAGGCTGGTCCCCACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:1:1,0:69,271:0.0029:2,0:1:0:24:0:0.20528:0:60:2:0.003:0:1 0/1:298:3:2,1:57,238:0.0101:2,2:8.3:1:27:1:0.1011:8.27:60:6:0.0102:0:1.3 -13 21563518 . C A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25717;SOR=0;LSEQ=TGGCACTTCCAGGCTGGTCC;RSEQ=CACTCTAGCGCTGCCCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:32,249:0.0106:2,2:7:1:23:1:0.31062:3.86:60:2:0.0072:0:1 0/0:229:0:0,0:29,200:0:2,0:23:1:30.7:1:1:0:60:37.167:1:0:0.1 -13 21563642 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15239;SOR=Inf;LSEQ=AGGACCAGTTGCCCTAATGT;RSEQ=TTAGCAGAGTGGAGACAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:0,32:0:1,0:21.1:1:31.3:1:1:0:60:31:1:0:0.5 0/1:21:2:1,1:0,19:0.0952:1,2:34.5:1:30.5:1:0.09524:0:60:4:0.0952:0:1 -13 21563715 . C T 72 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGACTGCGTCCACATCC;RSEQ=GAGGTGCGTCCCTGCCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:0.5833:0,0:19.1:1:25.9:1:1:0:60:2.5:0.5:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 21565327 . C T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09659;SOR=Inf;LSEQ=CTGGCTCTGGCCAGGCCAGG;RSEQ=CAGGTTGGACCCCTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:245,31:0:2,0:24.5:1:31.8:1:1:0:60:68:1:0:0 0/1:235:3:2,1:194,38:0.0128:2,2:10.3:1:22.3:1:0.4213:2.53915:60:2:0.0087:0:2 -13 21566131 . C A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGGGGCCCATGGAGCCACAC;RSEQ=GGTCCAGGACAGGTAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28:1:31.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:19.5:1:30:1:1:0:60:4:1:0:0 -13 21619782 . A T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20549;SOR=0;LSEQ=CTGACTGCCCCAGCTGTCCC;RSEQ=TAGCTGCCTCTGCACATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:113,19:0.0149:2,2:12.5:1:26:0:0.27719:5.82241:60:4:0.0153:0:1 0/0:161:0:0,0:130,31:0:2,0:23.8:1:29.9:1:1:0:60:322:1:0:0.1 -13 21620085 . T C 307 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=5.29729;LSEQ=ACCGAAGACTTGGATGGCTG;RSEQ=TTTAACCCCTCACGAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:842:454:192,262:171,217:0.5392:2,2:25.3:1:32.1:1:0.62538:1.07522:60:150.333:0.5395:0:1.1 1/1:951:819:374,445:60,69:0.8612:2,2:25.1:1:31.8:1:0.9243:1.03462:60:135.5:0.8612:0:1.2 -13 21620222 . T TA 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.51857;SOR=1.41136;LSEQ=TCTTAAAGTGTTTTATTATT;RSEQ=AAAAAAAAAAACTGTCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:11:0,11:4,75:0.1209:2,0:28.3:1:30.1:1:1:0:59.5:22:0.1222:0:0.1 0/1:86:14:0,14:2,68:0.1628:1,1:33.4:1:29.5:1:1:0:60:28:0.1647:0.0116:0 -13 22057796 . G A 71 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGAAAAAAGAGGGGCTA;RSEQ=TTTTTCTTAGCCAGGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:19.2:1:30.6:1:1:0:60:10:1:0:1 1/1:3:3:3,0:0,0:1:0,0:16:1:30:1:1:0:60:6:1:0:1.3 -13 22057951 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50658;SOR=Inf;LSEQ=AAAGATATGTCTAAAGGCTG;RSEQ=TGTCTCCTCTTGGCAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:63,43:0:2,0:23.7:1:29.5:1:1:0:60:105:1:0:0.2 0/1:138:2:1,1:86,50:0.0145:2,2:22:1:29:1:1:1.71285:60:4:0.0146:0:1 -13 22058032 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=2.00912;LSEQ=CGACACGGCGTGCTTGGCCA;RSEQ=CTCCCCGGGCAGCAGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:1:1,0:34,58:0.0108:2,0:1:0:26:0:0.37634:0:60:2:0.0109:0:1 0/1:140:3:2,1:49,87:0.0214:2,2:22.3:1:26.7:1:0.55426:3.52:58:6:0.0221:0:1 -13 22058168 . A G 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49762;SOR=Inf;LSEQ=TTAACGAATGGCCTTGGAAG;RSEQ=GATGCGGGTGTCGGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:69:47,22:0,0:0.9718:0,2:26.4:1:31.4:1:1:0:60:138:0.9718:0:1.1 1/1:64:64:45,19:0,0:1:0,2:22.4:1:30.8:1:1:0:60:63:1:0:1.1 -13 22058175 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4966;SOR=0;LSEQ=ATGGCCTTGGAAGAGATGCG;RSEQ=GTGTCGGGGTGGACCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:49,23:0.027:2,2:20.5:1:29.5:1:0.54646:2.1068:60:4:0.0278:0:2 0/0:73:0:0,0:50,23:0:2,0:23:1:31.2:1:1:0:60:146:1:0:1 -13 22058205 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18552;SOR=0;LSEQ=TGGACCTGCTTCAGCAGAGT;RSEQ=GCTCTCCTTGCGGCTGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:57,27:0.0233:2,2:37.5:1:30.5:1:0.54774:2.09123:60:4:0.0235:0:1.5 0/0:113:0:0,0:68,44:0:2,0:26.1:1:28.6:1:1:0:60:111:0.9911:0:0.6 -13 22058257 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50285;SOR=Inf;LSEQ=CCAACCTTCTGCGCCTTGGT;RSEQ=ACCGCCTTCTTGGAGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:61,66:0:2,0:24.6:1:31.1:1:1:0:60:62.5:1:0:0.2 0/1:154:2:1,1:71,81:0.013:2,2:14.5:1:27.5:1:1:1.14:60:4:0.0132:0:1 -13 22058292 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49896;SOR=0;LSEQ=GCCCTTCTTCAGGGAGGGAG;RSEQ=AGACTTGGCTGGCTCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:48,73:0.0163:2,2:22.5:1:27.5:1:1:1.52:60:4:0.0163:0:1.5 0/0:112:0:0,0:42,70:0:2,0:27.9:1:31.7:1:1:0:60:111:1:0:0.3 -13 22058311 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17342;SOR=Inf;LSEQ=GCAGACTTGGCTGGCTCAGG;RSEQ=ATCTTCAAACACCAGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:37,73:0:2,0:24.6:1:31.5:1:1:0:60:21:1:0:0.4 0/1:79:2:1,1:24,53:0.0253:2,2:36.5:1:29.5:1:0.53554:2.18:60:4:0.0256:0:1.5 -13 22058339 . G A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27126;SOR=0;LSEQ=AACACCAGAAGTATGTCCCT;RSEQ=ATGGTCTTTTTCACAAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:3:0,3:13,42:0.0517:2,0:22.7:1:29.7:1:1:0:60:6:0.0536:0:1.7 0/0:39:0:0,0:9,30:0:2,0:17.5:1:30.7:1:1:0:60:18.5:1:0:0.8 -13 22058353 . C T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCTGATGGTCTTTTTCA;RSEQ=AAGGATAACTGAGTAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:5,31:0,0:1:0,2:22.5:1:28.3:1:1:0:60:35:1:0:1.1 1/1:20:20:1,19:0,0:1:0,1:21:1:27.2:1:1:0:60:9:1:0:1.3 -13 24942750 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTTGCTTTTCTGTTCTG;RSEQ=TCTGCTGATCTGTTTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 24942936 . C A 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35;SOR=0;LSEQ=AACAGCTGGGCCCGGGGCAC;RSEQ=ACTACCATCAAAATGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:31.4:1:30.2:1:1:0:58.8:26:1:0:2.2 1/1:7:6:5,1:1,0:0.8571:0,2:14.8:1:29.8:1:1:0:60:12:0.8571:0:2 -13 24942948 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18803;SOR=0;LSEQ=CGGGGCACCACTACCATCAA;RSEQ=ATGCGGAGACCGGTAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:15,0:0,0:1:0,1:27.9:1:30.7:1:1:0:59:14:1:0:2 1/1:12:10:8,2:1,1:0.8333:2,2:16.5:1:31.5:1:0.45455:3.46:60:20:0.8333:0:1.6 -13 24943276 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGGACAAGGAGCGTGACCA;RSEQ=TGAAGCACAGCACCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:50:0:34:0:1:0:60:2:1:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:31:1:28.5:1:1:2.45:60:4:0.3333:0:2 -13 24943283 . A G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=AGGAGCGTGACCACTGAAGC;RSEQ=CAGCACCACAGAGAGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:44:0:32:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:31:1:29:1:1:0:60:4:0.6667:0:2 -13 25693092 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATCATCCCCAGAACCACC;RSEQ=TGAGAGTGAGCCTGGTAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45:1:30:1:1:0:60:4:1:0:1 -13 25694006 . G C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACAAAGTATTGGCTGTGC;RSEQ=CCTGGCACTATCAGGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:34:0:28:0:1:0:60:2:0.5:0:1 1/1:2:2:2,0:0,0:1:0,0:47:1:29.5:1:1:0:60:4:1:0:1 -13 25694340 . A T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.77475;LSEQ=GCTCCTAATGACCTCATGAC;RSEQ=GCTGAATCTCCTGATCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:71:32,39:88,122:0.2527:2,2:26.6:1:30.9:1:0.67832:1.14:60:142:0.2563:0:1.2 0/1:322:156:64,92:77,87:0.4845:2,2:25.3:1:29.9:1:0.31157:1.2713:60:38:0.481:0:1.1 -13 25694388 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22043;SOR=Inf;LSEQ=CAACACAGAGAAAGGAGAGA;RSEQ=ACCTAGGGTGTCTAGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:62,125:0:2,0:22.7:1:29.4:1:1:0:60:25.714:1:0:0.4 0/1:166:2:1,1:57,107:0.012:2,2:40:0:31.5:1:1:1.87:60:4:0.0122:0:1 -13 25694405 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49829;SOR=0;LSEQ=AGAAACCTAGGGTGTCTAGG;RSEQ=TGCAACTCAGGGACCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:32,95:0.0155:2,2:41:1:30.5:1:0.44767:2.94:60:4:0.0161:0:1 0/0:123:0:0,0:39,84:0:2,0:24:1:31.7:1:1:0:60:122:1:0:0.5 -13 25694435 . C A 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=GGGACCTGTGGCTCCTGCAC;RSEQ=AAGCATGTGAATCACCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:18,79:0:2,0:23.5:1:31.6:1:1:0:60:47.5:1:0:0.4 0/1:73:10:2,8:17,46:0.137:2,2:28.8:1:29.7:1:1:1.47092:60:20:0.1389:0:1.1 -13 25694482 . C A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02454;SOR=0.27779;LSEQ=TGGTTTCCTAAGAAAATCTG;RSEQ=CCTGTTCATGCATTATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:19:1,18:1,25:0.413:1,1:25.6:1:29.9:1:1:1.38:60:38:0.4318:0:1.1 0/1:31:5:0,5:4,22:0.1613:2,0:21.8:1:27.6:1:1:0:60:10:0.1667:0:1 -13 26828732 . GC G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.22278;SOR=0;LSEQ=CTTCCCCGGTCCCCACCCCT;RSEQ=CCCCCGGCCCCCCGACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:119,27:0.0135:2,2:36:1:28.5:1:0.34363:4.34614:60:4:0.0153:0:3.5 0/0:165:0:0,0:131,34:0:2,0:23:1:29.4:1:1:0:60:10.786:1:0:0.9 -13 26828746 . C T 93 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=8;SSF=0.35851;SOR=2.25511;LSEQ=ACCCCTGCCCCCCGGCCCCC;RSEQ=GACCCAGCTCTCCGGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:0,3:158,36:0.0152:2,0:1:0:25.7:1:0.00728:0:60:6:0.016:0:1 0/1:237:8:7,1:175,54:0.0338:2,2:9.3:1:31:1:0.68518:2.15:60:16:0.0342:0:1.1 -13 26828808 . C T 58 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07291;SOR=0.23509;LSEQ=GACTTTAAAGTGAAGCTGAG;RSEQ=AGCGAGCGGGAGCGGGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:6:2,4:309,182:0.0121:2,2:15.8:1:22.7:1:0.20308:3.38695:60:5:0.0103:0:1.8 0/0:699:2:1,1:406,291:0.0029:2,2:28:1:28.5:1:1:1.39449:60:4:0.0029:0:1 -13 26828973 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50267;SOR=Inf;LSEQ=GCAGGCCGAGGCAGGTAGCC;RSEQ=GGAGGGAGAGCGGGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:18,136:0:2,0:24.7:1:30.1:1:1:0:60:153:1:0:0.1 0/1:186:2:1,1:28,156:0.0108:2,2:23:0:31.5:1:0.28823:5.49:60:4:0.0109:0:2.5 -13 26828980 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50075;SOR=Inf;LSEQ=GAGGCAGGTAGCCCGGAGGG;RSEQ=GAGCGGGCCGCCGGGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:14,127:0:2,0:23.6:1:31.1:1:1:0:60:46:1:0:0.1 0/1:162:2:1,1:19,141:0.0123:2,2:16:0:32.5:1:0.23234:7.26:60:4:0.0123:0:2.5 -13 26829388 . G T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTATTTTATTTGAGGAAA;RSEQ=GAAGGCAGCGAGTGAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:33:1:30:1:1:1.73:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 26911643 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20969;SOR=Inf;LSEQ=TATATTTATTTATATTTTAC;RSEQ=TTATAAAAATGCACATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:170,19:0:2,0:22.2:1:31.2:1:1:0:60:62:1:0:0.1 0/1:161:2:1,1:134,25:0.0124:2,2:12:0:32:0:0.29775:5.2756:60:4:0.0126:0:1 -13 26911849 . A G 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00357;SOR=Inf;LSEQ=CCAACTATATAAGGCTCTGT;RSEQ=TTGTATTTGTCATATTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:21,182:0:2,0:23.2:1:30.9:1:1:0:60:406:1:0:0.1 0/1:204:9:1,8:27,168:0.0441:2,2:27.7:1:31.8:1:1:1.28426:60:18:0.0443:0:1.1 -13 26922450 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAACGCAGGGGTCCCTGC;RSEQ=TCAGCACCGGTACGTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 26922759 . A C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATTTGTCTTCCTCAAAA;RSEQ=TGGTTTCTGATGCCAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:35:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:14:1:29:1:1:0:60:4:1:0:1.5 -13 26923073 . G A 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00105;SOR=0;LSEQ=TTACTGAAGTATCCGTCTCA;RSEQ=AATTGTGTGGGTGCTTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:67:66,1:0,0:1:0,1:24.3:1:29.4:1:1:0:60:12.4:1:0:1.1 1/1:53:45:45,0:8,0:0.8491:0,1:26.6:1:29.9:1:1:0:60:21.5:0.8431:0:1.2 -13 26927833 . T C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02043;SOR=Inf;LSEQ=ATTATACATCAAATTATCTT;RSEQ=TCCTTTTTTTAAGCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:152,14:0:2,0:23.1:1:30.1:1:1:0:60:40.5:1:0:0.2 0/1:143:5:5,0:121,17:0.035:2,0:19:1:32.4:1:1:0:60:10:0.0355:0:1 -13 26928092 . C A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09547;SOR=Inf;LSEQ=TTTCTAGTCGTCTGTAGATA;RSEQ=CAGTGCTATATGTAGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:9,149:0:2,0:26.4:1:31:1:1:0:60:51.667:1:0:0.1 0/1:134:3:1,2:14,117:0.0224:2,2:15:1:29.3:1:0.30163:4.11:60:6:0.0229:0:2 -13 26929683 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACTTGAACGCAGGAAGC;RSEQ=GAGGTTGCAGTGAGCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:29.5:1:1:0:60:4:1:0:1 -13 26957049 . TA T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.23953;SOR=Inf;LSEQ=GTCACAGTGTAGCACTTTTT;RSEQ=AAACTTTTGCAGGCAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:50,155:0:2,0:23.1:1:29.5:1:1:0:60:101.5:1:0:0.1 0/1:197:2:1,1:63,132:0.0102:2,2:35:1:31:1:0.54532:2.09:60:4:0.0103:0:0 -13 26959325 . A AT 138 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05211;SOR=2.15649;LSEQ=AAAATCATTTACTTAGCATG;RSEQ=TTTTTTTTTTATTATTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:10:9,1:192,30:0.0431:2,2:24.6:1:30.7:1:1:1.40:60:20:0.0452:0:0 0/1:282:25:17,8:211,45:0.0887:2,2:25.9:1:29.8:1:0.10424:2.19907:60:50:0.0906:0.0071:0.1 -13 26959593 . T G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02562;SOR=0.33454;LSEQ=TTATAAAAGTAAGAGCAGAC;RSEQ=GAGTGTGATGGCTCATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:22:0,22:0,30:0.4231:1,1:29.7:1:30.5:1:1:0:60:21:0.4118:0:1 0/1:41:8:0,8:2,31:0.1951:2,0:25.1:1:31.4:1:1:0:60:16:0.1951:0:1.3 -13 26967477 . C CT 164 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.63602;SOR=1.14122;LSEQ=TTCCTTGCCTATTTTTCTTT;RSEQ=TTTTTTTTTTTCTTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:37:28,9:270,83:0.0923:2,2:27.2:1:31.3:1:1:1.04549:58.9:74:0.0992:0:1.1 0/1:404:42:32,10:269,87:0.104:2,2:28.5:1:30.5:1:1:1.03:59.8:84:0.1144:0:0.4 -13 26967849 . C T 128 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13043;SOR=0;LSEQ=ATGGAAATATTTATGGGTTT;RSEQ=CTGAATTTCAGGACTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:1,19:0,0:1:0,1:19:1:29.8:1:1:0:60:40:1:0:1.2 1/0:3:2:0,2:0,1:0.6667:0,0:13.5:1:26:1:1:0:60:4:0.6667:0:1 -13 26971195 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15895;SOR=Inf;LSEQ=TTCAATATATATTTTATATC;RSEQ=GTTATGATCAAAATAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:126,12:0:2,0:24:1:30:1:1:0:60:68:1:0:0.1 0/1:92:2:2,0:84,6:0.0217:2,0:45:1:29.5:1:1:0:60:4:0.0217:0:1 -13 26971442 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22656;SOR=Inf;LSEQ=TGAGGCTTTTTTGGATCAAT;RSEQ=TATGTGGTTACTTAGCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:16,164:0:2,0:23.1:1:30:1:1:0:60:89:1:0:0 0/1:164:2:1,1:18,144:0.0122:2,2:28.5:1:29:1:0.21891:7.81:60:4:0.0123:0:1 -13 26974562 . G A 259 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAACTGTGAGAAGCAATACC;RSEQ=TCATGTTTGTATGATTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:405:405:305,100:0,0:1:0,2:24.7:1:30:1:1:0:60:56.857:1:0:1.1 1/0:469:356:246,110:77,36:0.7591:2,2:25.7:1:29.8:1:0.90723:1.05:60:70.2:0.7614:0:1.1 -13 26975608 . CCAG C 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=1.01154;LSEQ=GTTTAACCAATTGAGAAGAA;RSEQ=CAGCAGCAGCAGGGCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:699:19:12,7:464,216:0.0272:2,2:26.2:1:31.9:1:0.62489:1.25263:60:38:0.0275:0.0029:0.1 0/1:764:21:16,5:485,256:0.0275:2,2:20.1:1:31:1:0.35948:1.69:60:42:0.0277:0.0052:0.1 -13 27793359 . T C 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.15755;SOR=Inf;LSEQ=GACAATGCCTTTCAAACTCT;RSEQ=ATAACAACCTCTGGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:32,31:0:2,0:25.8:1:28.7:1:1:0:59.1:20:1:0:0.1 0/1:97:5:3,2:42,50:0.0515:2,2:40:1:27.2:1:0.66051:1.78:60:4:0.0421:0:1.2 -13 27793370 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53325;SOR=Inf;LSEQ=TCAAACTCTTATAACAACCT;RSEQ=TGGAGTTGAGCAACATGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:28,29:0:2,0:26.9:1:31.9:1:1:0:59.2:114:1:0:0.2 0/1:99:2:1,1:41,56:0.0202:2,2:18:1:32:0:1:1.36:60:4:0.0206:0:1.5 -13 27793387 . G C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.54772;SOR=Inf;LSEQ=CCTCTGGAGTTGAGCAACAT;RSEQ=GCTTCTCCCCTTTCTAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:22,26:0:2,0:24.3:1:30.5:1:1:0:59.3:23:1:0:0.1 0/1:93:2:1,1:37,54:0.0215:2,2:23:0:32.5:1:1:1.45:60:4:0.0222:0:1 -13 27793407 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCTTCTCCCCTTTCTAGGT;RSEQ=CCGTGGCAGCCATCTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:15,20:0:2,0:24.9:1:30.5:1:1:0:59:34:1:0:0.1 0/1:74:2:1,1:27,45:0.027:2,2:5.5:1:28:1:1:1.65:60:4:0.0274:0:1 -13 27793546 . G A 83 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATGAGCTCAATTAACA;RSEQ=CTTCTACCAAGGACCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:19.7:1:29.7:1:1:0:56.7:14:1:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 27825902 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GCAGCGTGCGCCGGGTCGGG;RSEQ=CTGGGCCGTGGGCTGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:22.7:1:31:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 27827811 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTTTGCAGTTCTCACTT;RSEQ=GCTACTGAAATGTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:25.8:1:30.9:1:1:0:60:18:1:0:1.1 1/1:8:8:8,0:0,0:1:0,0:27:1:31.4:1:1:0:60:16:1:0:1 -13 27827942 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49412;SOR=0;LSEQ=CACAAAGGGAAAGAGGAGAG;RSEQ=CACCCGATATATGTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:21,20:0.0465:2,0:6:1:29.5:1:0.49059:0:60:4:0.0488:0:1 0/0:43:0:0,0:20,23:0:2,0:25.5:1:31:1:1:0:59.6:42:1:0:0.1 -13 27828041 . A G 53 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.58204;SOR=0.31051;LSEQ=TTTGTGTTCTGTTGTGTTCA;RSEQ=CATGTGTTGTAGTTCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:24:1:33.7:1:1:0:60:6:0.3:0:1 0/1:9:1:0,1:1,7:0.1111:2,0:10:0:33:0:1:0:60:2:0.1111:0:1 -13 27829310 . G A 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAATCTTAGAATACTTT;RSEQ=CAGTTACTTAAAGTCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:52,0:0,0:1:0,1:28.7:1:28.4:1:1:0:60:51:1:0:1.1 1/1:48:48:47,1:0,0:1:0,1:22.7:1:28.5:1:1:0:60:96:1:0:1 -13 27829408 . C T 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02131;SOR=Inf;LSEQ=ACTGTTCAAAAAGGAATGCC;RSEQ=CACAAGTGTTACCATGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:155,103:0:2,0:27.5:1:30.6:1:1:0:52.3:42:1:0:0.1 0/1:341:7:3,4:196,137:0.0205:2,2:31.3:1:29.3:1:0.45482:1.90379:54.3:14:0.021:0:1.4 -13 28270502 . G A 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26573;SOR=6.78852;LSEQ=TGAAATAAGATGGAATATTC;RSEQ=TAACAAACTATTTAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:5,1:0.1429:2,0:35:0:32:0:1:0:60:2:0.1429:0:2 1/0:7:4:2,2:3,0:0.5714:0,2:18.8:1:30.5:1:0.42857:0:60:8:0.5714:0:1.8 -13 28270611 . C T 126 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55906;SOR=0;LSEQ=TTCTTCACATAATTGATGAA;RSEQ=GTGGTTTCCACTTTGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:33:1:30.8:1:1:0:60:10:1:0:1 1/0:28:21:13,8:4,3:0.75:2,2:27:1:28.9:1:1:1.21:60:42:0.75:0:1 -13 28270714 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00024;SOR=0.03884;LSEQ=CTTTTGGTGTTTCAGTTTTT;RSEQ=TCTCTTTTTGAAGGATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:8,5:0,2:0.8667:0,2:18.2:1:30.2:1:0.2:0:60:12:0.8571:0:1.2 0/1:17:3:1,2:5,9:0.1765:2,2:15.7:1:29:1:1:1.10434:60:6:0.1765:0:1.7 -13 28270899 . A C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16949;SOR=Inf;LSEQ=TCTTCTTCTTCTTCATCAGC;RSEQ=GCAACTTTTTTCTGTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:23,12:0:2,0:23:1:30.5:1:1:0:60:34:1:0:0.1 0/1:25:2:1,1:14,9:0.08:2,2:23:1:31.5:1:1:1.52748:60:4:0.08:0:1 -13 28270918 . A C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09061;SOR=Inf;LSEQ=CAGCAACTTTTTTCTGTGAA;RSEQ=TCTTGCTACCACCTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:25,13:0:2,0:26.2:1:31.2:1:1:0:60:76:1:0:0.3 0/1:32:3:1,2:19,10:0.0938:2,2:41.7:1:33:1:0.54032:3.63479:60:6:0.0938:0:1.7 -13 28270984 . T A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00575;SOR=Inf;LSEQ=AGAGTTTTACAACCTCCTCC;RSEQ=TTTCATCTTCTGACTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:78,20:0:2,0:22.2:1:31.1:1:1:0:60:196:1:0:1.1 0/1:93:7:5,2:60,26:0.0753:2,2:16.7:1:30.4:1:1:1.08:60:14:0.0761:0:1.1 -13 28270989 . A C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25696;LSEQ=TTTACAACCTCCTCCTTTTC;RSEQ=TCTTCTGACTCTGCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:60:48,12:31,7:0.6122:2,2:21.2:1:31.4:1:1:1.10597:60:120:0.6122:0:1.5 0/1:101:29:21,8:50,22:0.2871:2,2:26.6:1:31.5:1:0.81479:1.15:60:58:0.29:0:1.3 -13 28271025 . G C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29336;SOR=1.30329;LSEQ=TCTTCCTCTACAGCTACTAC;RSEQ=TGCTGTCCACTATTATGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:53:30,23:79,39:0.3099:2,2:24:1:31.1:1:0.22938:1.54882:60:106:0.3099:0:1.1 0/1:157:58:34,24:62,37:0.3694:2,2:21.1:1:30.6:1:0.73461:1.18155:60:116:0.3694:0:1.1 -13 28271052 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.224;SOR=Inf;LSEQ=CCACTATTATGCACTGGCCC;RSEQ=GAACCACACTTCAGTCGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:118,94:0:2,0:26.7:1:30.4:1:1:0:60:424:1:0:1.2 0/1:191:2:1,1:98,91:0.0105:2,2:30.5:1:28:1:1:1.07648:60:4:0.0105:0:1.5 -13 28271068 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17707;LSEQ=GCCCTGAACCACACTTCAGT;RSEQ=GTAAAAGCACAGGTGGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:227:159:91,68:32,36:0.7004:2,2:27.6:1:29.8:1:0.19085:1.50:60:52:0.6964:0:1.5 0/1:209:61:29,32:69,79:0.2919:2,2:24.5:1:29.4:1:1:1.04:60:122:0.2961:0:1.5 -13 28271142 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16602;LSEQ=GCAAACATTTTCAAAGTTGC;RSEQ=GGTGTTACTTTAATTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:134:97:32,65:15,22:0.7239:2,2:24.4:1:30.4:1:0.425:1.38145:60:47.5:0.7197:0:1.8 0/1:126:38:12,26:35,53:0.3016:2,2:23.9:1:29.4:1:0.42725:1.42681:60:37:0.3033:0:1.9 -13 28271189 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=0.23423;LSEQ=ATAATTCATTGCCTCTGCTT;RSEQ=AACAATGTGCAATTTATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:46:12,34:5,15:0.697:2,2:23.8:1:29.2:1:1:1.06:60:45:0.6923:0:1.8 0/1:49:17:3,14:6,26:0.3469:2,2:18.7:1:27.2:1:1:1.07532:60:16:0.3333:0:1.8 -13 28271317 . T C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06416;SOR=2.5369;LSEQ=CTGGGGCCTCAGGGGGCTCA;RSEQ=TTCCATGTCCACCAAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:9:3,6:15,23:0.1915:2,2:24.4:1:32.8:1:1:1.29714:60:18:0.2045:0:1 0/1:45:17:7,10:13,15:0.3778:2,2:27.1:1:31.2:1:0.76669:1.23224:60:34:0.3778:0:1.1 -13 28271536 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATATGGGCCTGCAGTTT;RSEQ=CTTTTTTGGTTGTATCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28589267 . C T 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03003;SOR=0.73764;LSEQ=CTGTACCTTTCTGATTTCAA;RSEQ=CAAATTACAGTCTGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:156:113,43:143,72:0.4194:2,2:24.5:1:30.5:1:0.25578:1.32:60:51:0.4169:0:1.1 0/1:518:180:119,61:213,125:0.3475:2,2:25.1:1:29.2:1:0.50216:1.14:60:89:0.347:0:1.1 -13 28589495 . C G 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=15.73853;LSEQ=GATCTGCCATGTGCCAGACA;RSEQ=TGTTGCAGGCACACGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:4:0,4:23,76:0.0388:2,0:26:1:33:1:0.57259:0:60:8:0.0392:0:2 0/1:97:38:1,37:4,55:0.3918:2,1:20.6:1:31.4:1:0.64538:2.6673:60:76:0.4:0:1.7 -13 28589509 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.69735;LSEQ=CAGACACTGTTGCAGGCACA;RSEQ=GGGCTGCGGCTGGGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:4:0,4:26,51:0.0494:2,0:12:1:31.3:1:0.29993:0:60:8:0.05:0:2 0/1:76:29:3,26:6,41:0.3816:2,2:22:1:31:1:1:1.26442:60:58:0.3867:0:1.9 -13 28589662 . C G 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10369;LSEQ=TGTTGGGGGGAGGGGTGGGG;RSEQ=GGCACCGAGAGAGCAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:239:236:180,56:0,0:0.9874:0,2:23.7:1:30.3:1:1:0:60:25.222:0.9956:0:1.2 1/1:393:350:249,101:27,11:0.8906:2,2:23.3:1:29.4:1:1:1.00:60:22.333:0.891:0:1.2 -13 28589905 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50078;SOR=Inf;LSEQ=GACATGACTTCTTTTCTTTT;RSEQ=TATTAAGATGAAATGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:18,132:0:2,0:24.4:1:32.4:1:1:0:60:149:1:0:0.1 0/1:172:2:1,1:14,154:0.0116:2,2:7:1:29:1:0.16916:10.66:60:4:0.0118:0:1 -13 28592165 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATAAATATTCATTAATTC;RSEQ=TATTTAAGTATTTAGCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28592546 . T C 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00166;SOR=1.66884;LSEQ=GTGAGTGCAGTTGTTTACCA;RSEQ=GATAACGACACAACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:89:72,17:180,58:0.2722:2,2:21.7:1:31.3:1:0.37584:1.36:60:178:0.2738:0:1.2 0/1:411:158:116,42:169,84:0.3844:2,2:24.7:1:30.6:1:0.18692:1.37:60:157:0.3839:0:1.1 -13 28592796 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4973;SOR=Inf;LSEQ=GGAGTGCAATCTTTCTTCTA;RSEQ=ACTCAACTTCAGTAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:4,88:0:1,0:24.2:1:31.4:1:1:0:60:45:1:0:0.1 0/1:93:2:1,1:8,83:0.0215:2,2:14:1:25.5:1:0.18513:9.84:60:4:0.0217:0:1 -13 28593787 . T C 38 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTTACCCCAGGTCTGCAACC;RSEQ=GCCTCCTCCTCCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:41.3:1:24.3:1:1:0:60:2:1:0:2.3 0/1:3:1:1,0:1,1:0.3333:2,0:18:0:30:0:1:0:60:2:0.3333:0:1 -13 28597427 . A G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49957;SOR=Inf;LSEQ=TAAAATAAACAAGAAAACAT;RSEQ=TATAAGCACATCTTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:160,23:0:2,0:22.2:1:28.7:1:1:0:60:90.5:1:0:0.1 0/1:199:2:2,0:165,32:0.0101:2,0:25.5:1:34:0:1:0:60:4:0.0103:0:1 -13 28597447 . ATC A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1031;LSEQ=ATATAAGCACATCTTTTCAA;RSEQ=TTTTTTTTGGTTTGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:257:174:134,40:60,18:0.677:2,2:24.6:1:31:1:1:1.00:59.9:348:0.677:0.1479:0.1 0/1:322:57:46,11:210,54:0.177:2,2:26.6:1:30.3:1:1:1.08:59.9:114:0.1792:0.0217:0.1 -13 28597839 . G A 61 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=0.33854;LSEQ=TTGGAACTGCTTTGATGACC;RSEQ=ATGACCTCCTGATTGATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:27.3:1:30.8:1:1:0:60:8:0.4444:0:1 0/1:5:1:0,1:1,3:0.2:2,0:30:0:32:0:1:0:60:2:0.2:0:1 -13 28598825 . T C 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90412;LSEQ=AAAATAGTCCTCAGTGTTTA;RSEQ=TAGTTGAATGTTGACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:0.4:0,0:20.3:1:31.8:1:1:0:60:12:0.4:0:1 0/1:8:3:3,0:5,0:0.375:0,0:21.3:1:32.7:1:1:0:60:6:0.375:0:1 -13 28599112 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23838;SOR=Inf;LSEQ=TTTTGTTTTTTCATTATTTA;RSEQ=ATTATTCTTCTCAGCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:44,141:0:2,0:23:1:32.1:1:1:0:60:184:1:0:0.1 0/1:177:2:1,1:46,129:0.0113:2,2:39.5:1:28.5:1:0.46167:2.79:60:4:0.0114:0:1 -13 28601389 . TAC T 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAATTGGTCCTGAAATAGT;RSEQ=AGTTTCAATTATAGGCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:93:23,70:64,148:0.3049:2,2:25.6:1:30.8:1:0.40864:1.31494:59.9:186:0.3079:0.0525:0.1 0/0:398:0:0,0:132,266:0:2,0:24.9:1:28.8:1:1:0:60:78.6:1:0:0.1 -13 28601621 . C T 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTTTTGTATGTGTGGCCTCA;RSEQ=CAATACCACTGGCCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:1,0:0.75:0,0:21:1:31.7:1:0.25:0:60:6:0.75:0:1 0/0:1:0:0,0:0,1:0:0,0:30:0:33:0:1:0:60:2:1:0:0 -13 28601651 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCTCCTGGATTCTCCAG;RSEQ=TGGCAACTGAAAGTAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:20.5:1:31:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28601994 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTAACCACTCTCACCAC;RSEQ=CCTGTGCACCAGCTTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:28.5:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28602216 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49954;SOR=Inf;LSEQ=ACTGTGACTGAGAAAAGACA;RSEQ=AGAATTAAAAAGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:142,10:0:2,0:22.6:1:30.4:1:1:0:60:49.667:1:0:0.4 0/1:167:2:1,1:147,17:0.012:2,2:24.5:1:30:1:0.2057:8.43051:60:4:0.012:0:1 -13 28602226 . AAG A 208 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=11.000;MSILEN=2;SSF=0.32849;SOR=1.21585;LSEQ=AGAAAAGACAAAGAATTAAA;RSEQ=AGAGAGAGAGAGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:96:81,15:17,1:0.4974:1,2:23.6:1:30.6:1:0.46069:3.12519:60:192:0.5:0.0933:0.1 1/0:227:124:102,22:11,1:0.5463:2,2:22.4:1:30:1:0.69028:2.36095:59.9:248:0.5511:0.1233:0.2 -13 28602256 . C T 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35605;SOR=0.85943;LSEQ=GAGAGAGAGAGAGCAAACAT;RSEQ=CTCTTTGTCATCAAGCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:120:88,32:166,66:0.3409:2,2:22.2:1:29.8:1:0.80216:1.09:59.9:39:0.3401:0:1.1 0/1:429:132:93,39:203,93:0.3077:2,2:23.3:1:29.5:1:0.73484:1.09:59.9:131:0.3141:0:1.1 -13 28602604 . T C 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.46553;LSEQ=AGCACTTTGGGAGGCCGAGG;RSEQ=GGGTGGATCACTTGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:0,9:0.3077:0,0:21:1:31.3:1:1:0:60:8:0.3077:0:1 0/1:5:2:0,2:0,3:0.4:0,0:10.5:1:30:0:1:0:60:4:0.4:0:1 -13 28607517 . T C 39 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCCTATAAAAACTAAA;RSEQ=AGGCCTGGCACAGTGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18.7:1:25:1:1:0:60:2:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28607710 . G C 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGAGGAGCCTGAGCCCAG;RSEQ=GGGTGGAGGCTGCAGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:42.5:1:32:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28607916 . T A 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35812;SOR=0.73433;LSEQ=CCATTTTTAGCCTTGAAACA;RSEQ=GGCAAACAGTAACCATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:79:46:45,1:31,2:0.5823:2,1:20:1:30:1:0.56809:2.86:60:22:0.5714:0:1.5 1/0:93:47:46,1:45,1:0.5054:1,1:21:1:30.2:1:1:1.02:60:94:0.5109:0:1.5 -13 28607989 . T G 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=0.5304;LSEQ=AACTGTGCCTCCCATTTTTG;RSEQ=GCATCTTTGTTGCTGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:393:263:184,79:87,43:0.6692:2,2:25.5:1:31:1:0.56341:1.15:59.9:86.667:0.6684:0:1.2 1/0:516:267:175,92:161,88:0.5174:2,2:25.5:1:30.3:1:0.85369:1.04:60:65.75:0.5157:0:1.2 -13 28608459 . T C 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTGTACTTGTGACAAAT;RSEQ=AGCAGGGTTAAAACGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:244,220:0:2,0:27:1:29.3:1:1:0:60:231:1:0:0.1 0/1:752:32:16,16:385,335:0.0426:2,2:26.2:1:31.4:1:0.7207:1.14904:60:64:0.0427:0:1.2 -13 28608709 . G A 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02924;SOR=0;LSEQ=CCCACAGACAATCAGGCAAT;RSEQ=TCCCTGTAAAGGATACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:0,11:0,13:0.4583:1,0:22.4:1:30.5:1:1:0:60:22:0.4583:0:1 0/0:8:0:0,0:0,8:0:0,0:20.6:1:31.8:1:1:0:60:16:1:0:0.3 -13 28608811 . T G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACAAGAATTACATCTGG;RSEQ=CCAGGCACGATGGCTCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:35:1:32:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28609396 . T C 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.63707;SOR=2.00059;LSEQ=TCCATGGAGATTCACCACAC;RSEQ=GGGAGTTTCTGCTTCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:0.5455:0,0:18.3:1:31.3:1:1:0:60:12:0.5455:0:2 1/0:7:5:5,0:2,0:0.7143:0,0:20.4:1:32:0:1:0:60:10:0.7143:0:2 -13 28609399 . G C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.52862;LSEQ=ATGGAGATTCACCACACTGG;RSEQ=AGTTTCTGCTTCTCCCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:0.6154:0,0:15.3:1:32.1:1:1:0:60:16:0.6154:0:1.9 1/0:7:5:5,0:2,0:0.7143:0,0:22.4:1:34:0:1:0:60:10:0.7143:0:2 -13 28609813 . G GA 130 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.02603;LSEQ=GTGATCTCTTCTGTGCAGCT;RSEQ=AAAAAAAAAATAGCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:17:7,10:117,216:0.0478:2,2:28:1:30.4:1:0.61145:1.29:60:34:0.0494:0:1.2 0/1:470:23:10,13:166,276:0.0489:2,2:28.7:1:28.8:1:0.66022:1.28:59.1:22:0.0492:0:0.9 -13 28609825 . A G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38789;LSEQ=GTGCAGCTGAAAAAAAAAAT;RSEQ=GCAAAGAATTTAGACAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:314:216:66,150:32,66:0.6879:2,2:23.5:1:31.3:1:0.79276:1.10158:60:107:0.6926:0:1.7 0/1:393:181:56,125:67,144:0.4606:2,2:22.1:1:29.7:1:0.9132:1.03848:59.7:21.625:0.4541:0:1.7 -13 28609846 . A T 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37791;LSEQ=GCAAAGAATTTAGACAGGTG;RSEQ=GCTGTCATCAGATTGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:221:151:34,117:19,51:0.6833:2,2:22.5:1:29.9:1:0.49938:1.2805:60:302:0.6895:0:1.9 0/1:243:109:16,93:33,101:0.4486:2,2:22.6:1:29.6:1:0.07633:1.89422:59.8:108:0.4557:0:2.1 -13 28609991 . T C 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14107;SOR=0.74608;LSEQ=AAATATTTCATCATTTCCTC;RSEQ=TAAACTGTATTCATGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:126:108,18:62,15:0.6207:2,2:23.3:1:31.1:1:0.33475:1.45:60:62:0.6231:0:2 1/0:222:122:105,17:82,18:0.5495:2,2:21.3:1:30.4:1:0.46118:1.35:60:121:0.5576:0:2.1 -13 28609997 . T C 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06392;SOR=0.69945;LSEQ=TTCATCATTTCCTCTTAAAC;RSEQ=GTATTCATGAAAGAGTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:222:140:121,19:65,17:0.6306:2,2:23.7:1:31:1:0.18804:1.66:60:45.667:0.6313:0:1.9 1/0:261:142:116,26:93,26:0.5441:2,2:21.3:1:29.8:1:0.53469:1.25:60:70:0.5469:0:1.9 -13 28610183 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.40739;LSEQ=CGAGCACTTGAGGTTTCCCT;RSEQ=TAGAAAAGAACGTGTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:349:234:64,170:34,81:0.6705:2,2:24.9:1:32:1:0.70441:1.11461:60:77:0.6676:0:1.1 0/1:521:236:80,156:96,188:0.453:2,2:24.6:1:31.1:1:1:1.00:60:472:0.4538:0:1.1 -13 28610219 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17634;SOR=0;LSEQ=GAAATAAGCTCACTGGCTGG;RSEQ=CATAGTGGTTCACTCCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:30,135:0.012:2,2:17:1:27:1:0.33771:4.44:60:4:0.0121:0:2 0/0:230:0:0,0:47,183:0:2,0:20.7:1:31.7:1:1:0:60:229:1:0:0.5 -13 28610355 . T A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26923;SOR=0;LSEQ=TAATAAAATAAAATAAGCTC;RSEQ=TGGAGTATGGTACTTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:1:0,1:22.7:1:30.8:1:1:0:60:18:1:0:1 1/1:7:6:0,6:0,1:0.8571:0,0:13.7:1:30:1:1:0:60:12:0.8571:0:1.3 -13 28611149 . A G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.45755;SOR=2.19472;LSEQ=AAAATAACATAAAAAATAAA;RSEQ=AGATATATGATCAATGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:6,0:0.5714:0,0:20.4:1:32.9:1:1:0:60:16:0.5714:0:1 1/0:20:15:15,0:5,0:0.75:0,1:23:1:33:1:1:0:60:30:0.75:0:1.1 -13 28611186 . G C 137 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02753;LSEQ=CCAGTAGATATGAGAGTAAA;RSEQ=TTTCAAAACACTTCAGCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:20:20,0:25,0:0.4444:1,1:23.9:1:31.8:1:1:0:60:19:0.4318:0:2 0/1:48:1:1,0:47,0:0.0208:1,0:19:0:32:0:1:0:60:2:0.0208:0:3 -13 28611215 . GT G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=13.67538;LSEQ=CACTTCAGCGTACAAAAACA;RSEQ=TTTGTAGTAGCCCTTCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:4:4,0:33,0:0.0556:1,0:13.8:1:31.2:1:1:0:60:8:0.0597:0.0417:1.3 0/1:80:36:36,0:41,1:0.45:1,1:25.8:1:31.1:1:1:0:60:72:0.4675:0.1125:0.1 -13 28611219 . TGT GC 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGCGTACAAAAACAGTTT;RSEQ=AGTAGCCCTTCTAAGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:31:31,0:33,0:0.4306:1,1:26.8:1:30.9:1:1:0:60:30:0.4478:0.0972:0.8 0/0:80:0:0,0:41,1:0:1,0:25.3:1:28.1:1:1:0:60:20:0.5195:0:0.2 -13 28611450 . G A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09302;SOR=0;LSEQ=TTGAAAAAGAATTAAAGACA;RSEQ=ATTTAGCCCAATTGCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:3,0:82,199:0.0105:2,0:8.7:1:24:1:0.02615:0:60:2:0.0071:0:3 0/0:344:0:0,0:107,237:0:2,0:22.5:1:31.3:1:1:0:60:343:1:0:0.1 -13 28611480 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21677;SOR=Inf;LSEQ=AATTGCTACAGGAGATGCTG;RSEQ=AACTAATGACAGTGTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:32,166:0:2,0:21.1:1:31.6:1:1:0:60:38.6:1:0:0.1 0/1:173:2:1,1:39,131:0.0116:2,2:25.5:1:27.5:1:0.41208:3.33:60:4:0.0116:0:1 -13 28611489 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.219;SOR=Inf;LSEQ=AGGAGATGCTGCAACTAATG;RSEQ=CAGTGTGCATGGGAGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:18,144:0:2,0:22:1:29.9:1:1:0:60:161:1:0:0.1 0/1:143:2:1,1:27,114:0.014:2,2:21:1:30:1:0.35438:4.16:60:4:0.0141:0:1 -13 28611669 . C T 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAGATTTCAGGTCCCTT;RSEQ=CAAATCACTGACTCAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:22.6:1:27.8:1:1:0:60:10:1:0:1.6 1/1:2:2:0,2:0,0:1:0,0:20.5:1:29.5:1:1:0:60:4:1:0:1 -13 28611710 . A G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATTTTAAGATGATCACC;RSEQ=TGTGAGTCATATGCCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:24.7:1:33.3:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28622356 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=6.98223;LSEQ=AAACTGTCCTTCTCAAGGGC;RSEQ=ACAAGCAAGGAGAATTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:47:37,10:69,19:0.3481:2,2:22.6:1:30:1:1:1.02:60:94:0.3534:0:1 1/0:176:139:105,34:30,6:0.7898:2,2:24.7:1:29.8:1:0.37971:1.61494:60:68.5:0.7874:0:1.1 -13 28623180 . A T 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACTAGTATTTATTGTCC;RSEQ=TTTTGTGTCAGGCTCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:13.3:1:32:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28623588 . G A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3706;SOR=0.40048;LSEQ=CAAGTGTAGTATCCGGTGTC;RSEQ=TTTCTTGCCACTGATGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:145,148:0.0101:2,2:19.3:1:27.7:1:0.62119:2.04:60:6:0.0101:0:1 0/0:492:2:1,1:241,248:0.0041:2,2:3:1:26.5:1:1:1.03:60:4:0.0041:0:1 -13 28623699 . G T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22131;LSEQ=GTTTTAATAAAACAGAGTTT;RSEQ=CATTTAATGTTTTCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:294:184:120,64:66,44:0.6259:2,2:22.5:1:30:1:0.38379:1.25:60:368:0.6259:0:1.5 0/1:456:123:69,54:197,135:0.2697:2,2:21.9:1:29:1:0.59243:1.14169:60:60.5:0.2677:0:1.6 -13 28623759 . C T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21602;LSEQ=CTGCATTTTCAGAATACAAA;RSEQ=TTGTCCTATTACCTCCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:527:310:180,130:122,94:0.5882:2,2:27:1:30.5:1:0.72098:1.07:60:102.333:0.587:0:1.3 0/1:798:188:96,92:324,286:0.2356:2,2:25.7:1:29.4:1:0.67627:1.08555:60:61.667:0.2363:0:1.4 -13 28623938 . G GA 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.31052;LSEQ=GATGAAAACATCCCAAGTGA;RSEQ=AAAAAAAAAGTGATTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:84:18,66:16,78:0.4516:2,2:28.2:1:30.2:1:0.56718:1.33:59.8:168:0.4492:0.0323:0.2 0/1:192:39:9,30:38,110:0.2031:2,2:27.3:1:28.8:1:0.83738:1.15069:60:78:0.2086:0.0052:0.1 -13 28624294 . G A 244 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=105.07206;LSEQ=TGGCACAGCACCTTATGTCC;RSEQ=TCCCAAATAATTCATGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:838:3:3,0:399,436:0.0036:2,0:21.3:1:28.3:1:0.10997:0:60:6:0.0036:0:1.3 0/1:1108:304:150,154:400,403:0.2744:2,2:25.4:1:29.6:1:0.89308:1.01901:60:75:0.2745:0:1.2 -13 28624374 . G T 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTACAGCTGCAATTAGAAAA;RSEQ=AAGTACCATTTGGCTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:92,260:0:2,0:23.8:1:31.3:1:1:0:60:175:1:0:0.1 0/1:490:24:7,17:153,313:0.049:2,2:20.7:1:28.3:1:0.82542:1.1867:60:48:0.0495:0:1.1 -13 28624407 . AC A 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01109;SOR=Inf;LSEQ=GCTAAACAAGTTTTAAAATT;RSEQ=AAATGAATGCTCAAGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:22,153:0:2,0:22.9:1:32:1:1:0:60:57.333:1:0:0.1 0/1:228:8:1,7:39,181:0.0351:2,2:31.6:1:30.3:1:1:1.50589:60:16:0.0356:0:0 -13 28624587 . C T 97 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11739;SOR=0.13795;LSEQ=CACTAAGGAGAATTACATAA;RSEQ=AAAACAGTTTAAAATTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:0.7333:0,0:22.7:1:28.2:1:1:0:60:22:0.7333:0:1.9 0/1:4:1:0,1:1,2:0.25:2,0:16:0:29:0:1:0:60:2:0.25:0:1 -13 28626325 . A G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCACAACCTTTGCCTCCC;RSEQ=GGTTCAAGAGATTCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:27:1:28.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28631647 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.21668;SOR=0;LSEQ=TTTTGGAAAATGTGTGAAAC;RSEQ=AAAAACAAAATTTCATAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:14,116:0.0152:2,2:28.5:1:32.5:1:0.21513:8.04:60:4:0.0153:0:1 0/0:151:0:0,0:15,135:0:2,0:19.8:1:28.7:1:1:0:60:149:0.9933:0:0 -13 28635285 . G A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGATCATCTGAGGTCAG;RSEQ=AGTTCGAAGCCAGCCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:36:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:5:0:27:1:1:0:60:4:1:0:1 -13 28635909 . C CA 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.22277;SOR=0.57179;LSEQ=CAGAGAGAGACCCTGACTCA;RSEQ=AAAAAAAAAAGGTTTACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:15:13,2:110,16:0.1056:2,2:21:1:28.5:1:1:1.05727:60:6.5:0.0977:0.0423:0.6 0/1:190:12:9,3:153,23:0.0632:2,2:16.3:1:29.4:1:0.22017:2.20552:60:24:0.0656:0.0263:0 -13 28636084 . G A 288 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69777;SOR=1.40362;LSEQ=CAGGAAATGTTCCCTGGGGC;RSEQ=TCGACCAGCACTTGCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:607:604:291,313:1,0:0.9951:0,2:24.7:1:30.4:1:0.48264:0:60:74.5:0.9967:0:1.1 1/1:851:848:399,449:0,0:0.9965:0,2:24:1:29.7:1:1:0:60:120.143:1:0:1.1 -13 28636312 . C T 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09802;LSEQ=ATGCATGCTGACACACTGCA;RSEQ=GCAACACCCACACAAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:44:1,43:0,21:0.6769:1,1:25.9:1:30.5:1:1:0:60:88:0.6769:0:1.5 0/1:36:6:0,6:2,28:0.1667:2,0:25.5:1:30.2:1:1:0:60:12:0.1714:0:1.8 -13 28636354 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04875;SOR=0.24106;LSEQ=ACCCACTGAGAACACGTTGC;RSEQ=GACTGAAGGTCCTATTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:21:0,21:0,11:0.6563:0,1:24.1:1:31.1:1:1:0:60:42:0.6563:0:2 0/1:13:4:0,4:0,9:0.3077:0,0:27.5:1:27.8:1:1:0:60:8:0.3077:0:2.3 -13 28636446 . G A 83 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTACGGACTGTCATGGCGT;RSEQ=TGTCCCCCTACCTCTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:19.4:1:29.7:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28644510 . C A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTGGTACCAGATGTGAGG;RSEQ=CATAATATACTTAAATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:58:58,0:0,0:1:0,1:23.4:1:30.1:1:1:0:60:57:1:0:1.1 1/1:44:44:44,0:0,0:1:0,1:25.3:1:29.6:1:1:0:60:88:1:0:1 -13 28644538 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20448;SOR=0;LSEQ=TACTTAAATACATAAAGAGA;RSEQ=GCCCATTTAGCCATGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:83,3:0.0227:1,2:23.5:1:30.5:1:0.08934:24.1044:60:4:0.0233:0:1.5 0/0:106:0:0,0:100,6:0:2,0:20:1:30.4:1:1:0:60:105:1:0:0.5 -13 28644563 . A G 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61354;SOR=0.47044;LSEQ=ATTTAGCCATGGTAGGCTTC;RSEQ=ATAACTTACAAATTACGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:148,37:0.0107:2,2:12:0:32:1:0.36599:3.96033:60:4:0.0107:0:1.5 0/0:198:1:1,0:160,37:0.0051:2,0:20:0:32:0:1:0:60:2:0.0051:0:1 -13 28644610 . A C 168 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAAAACAGCTAAAGGTATA;RSEQ=TTTTAATGTTACTTTACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:39:24,15:234,125:0.098:2,2:24.8:1:31.9:1:0.72449:1.16952:60:38:0.0964:0:1.1 0/0:513:0:0,0:311,201:0:2,0:25.1:1:29.6:1:1:0:60:127:0.998:0:0.1 -13 28644830 . A G 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=Inf;LSEQ=ATTTATCTTGCAACCAAACA;RSEQ=CAAAACAAAGTGTAATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:2,54:0:1,0:27.3:1:30.3:1:1:0:60:55:1:0:0 0/1:43:13:0,13:1,29:0.3023:1,1:22:1:30.8:1:1:0:60:12:0.2927:0:1.3 -13 28644885 . T C 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02158;SOR=Inf;LSEQ=ATGAAAGTATGTAGGAAATT;RSEQ=GATTTTATGCAAGTTTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:0,20:0:1,0:27.2:1:31.3:1:1:0:60:40:1:0:0 0/1:14:4:0,4:0,10:0.2857:0,0:40.3:1:29:1:1:0:60:8:0.2857:0:1.3 -13 28645341 . A T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTAGTAGAGACGGGGT;RSEQ=TCGCCACGTTAGCCAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:29:0:1:0:60:4:1:0:1 -13 28674453 . C T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12884;SOR=Inf;LSEQ=GTGGGCGAGTCCGGAGGGCG;RSEQ=GAAAGAGGGGAGGGGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:11,0:0:0,0:29.5:1:33.5:1:1:0:60:22:1:0:0 0/1:19:5:3,2:12,2:0.2632:2,2:24.2:1:28.4:1:0.27219:3.66084:60:10:0.2632:0:1 -13 28674526 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50714;SOR=Inf;LSEQ=CGAGGCGGCTGGGCCGGAGG;RSEQ=GGCGCGCGCCCGGGTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:32,37:0:2,0:27.9:1:29.4:1:1:0:60:33.5:1:0:0.1 0/1:92:2:1,1:40,50:0.0217:2,2:17:1:29:1:1:1.25:60:4:0.0222:0:1 -13 28674528 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.18135;SOR=0;LSEQ=AGGCGGCTGGGCCGGAGGAG;RSEQ=CGCGCGCCCGGGTCCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:30,36:0.0294:2,2:21:1:29.5:1:1:1.20:60:4:0.0303:0:2 0/0:91:0:0,0:41,50:0:2,0:28.3:1:30.4:1:1:0:60:44.5:1:0:0.2 -13 28674533 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.08503;SOR=0;LSEQ=GCTGGGCCGGAGGAGGCGCG;RSEQ=GCCCGGGTCCACACTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:3:1,2:31,40:0.0405:2,2:17.7:1:27.7:1:1:1.5412:60:6:0.0435:0:2 0/0:93:0:0,0:41,52:0:2,0:30.2:1:29.5:1:1:0:60:45.5:1:0:0.2 -13 28674558 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=1.28541;LSEQ=GGGTCCACACTGCGGGGTGG;RSEQ=GGCTGAGGGACCGCGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:0,1:44,57:0.0098:2,0:1:0:25:0:1:0:60:2:0.0101:0:3 0/1:159:2:1,1:73,84:0.0126:2,2:42.5:1:28.5:1:1:1.15:60:4:0.0126:0:1 -13 28674579 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51559;SOR=Inf;LSEQ=GGCTGAGGGACCGCGAGGGG;RSEQ=TGCGAGCGAGCGAGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:52,71:0:2,0:22.3:1:32:1:1:0:60:60.5:1:0:0.5 0/1:179:2:1,1:79,98:0.0112:2,2:9.5:1:28.5:1:1:1.24:60:4:0.0113:0:1 -13 28674580 . TGCGA T 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.51408;SOR=Inf;LSEQ=GCTGAGGGACCGCGAGGGGC;RSEQ=GCGAGCGAGCGGGGCCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:52,71:0:2,0:22.3:1:32.2:1:1:0:60:60.5:1:0:0.5 0/1:176:2:1,1:75,99:0.0114:2,2:36:0:33.5:1:1:1.32:60:4:0.0116:0:0 -13 28674589 . G T 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.16473;SOR=0.17552;LSEQ=CCGCGAGGGGCTGCGAGCGA;RSEQ=CGAGCGGGGCCTTACCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:4:2,2:49,69:0.0328:2,2:31:1:31.8:1:1:1.40:60:8:0.0333:0:1.5 0/0:170:1:0,1:74,94:0.0059:2,0:1:0:22:0:1:0:60:2:0.006:0:1 -13 28674591 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.51307;SOR=Inf;LSEQ=GCGAGGGGCTGCGAGCGAGC;RSEQ=AGCGGGGCCTTACCGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:50,68:0:2,0:22.4:1:30.7:1:1:0:60:236:1:0:0.5 0/1:167:2:1,1:73,92:0.012:2,2:20.5:1:26:1:1:1.26:60:4:0.012:0:2.5 -13 28674611 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51533;SOR=Inf;LSEQ=GAGCGGGGCCTTACCGAGCA;RSEQ=CGGCAGCTGGCCGCCGTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:43,53:0:2,0:23.9:1:32:1:1:0:60:47:1:0:0.6 0/1:140:2:1,1:63,74:0.0143:2,2:39.5:1:26.5:1:1:1.17:60:4:0.0145:0:2 -13 28674618 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51529;SOR=Inf;LSEQ=GCCTTACCGAGCAGCGGCAG;RSEQ=TGGCCGCCGTCGCGCGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:39,43:0:2,0:25.8:1:32.1:1:1:0:60:40:1:0:0.7 0/1:120:2:1,1:56,61:0.0167:2,2:28.5:1:29.5:1:1:1.09:60:4:0.0168:0:1 -13 28674626 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16615;SOR=0;LSEQ=GAGCAGCGGCAGCTGGCCGC;RSEQ=GTCGCGCGCCAACGCCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:32,36:0.0286:2,2:37:0:32:1:1:1.12:60:4:0.0299:0:1.5 0/0:101:0:0,0:50,51:0:2,0:23.2:1:29.7:1:1:0:60:49.5:1:0:0.5 -13 28674628 . T C 140 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00388;SOR=0.31859;LSEQ=GCAGCGGCAGCTGGCCGCCG;RSEQ=CGCGCGCCAACGCCGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:23:10,13:23,24:0.3286:2,2:26:1:31.1:1:0.79989:1.24193:60:22:0.3188:0:1.5 0/1:97:13:7,6:41,42:0.134:2,2:27.8:1:31.9:1:1:1.19:60:26:0.1383:0:1.3 -13 28674630 . G A 31 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.57039;SOR=0.34962;LSEQ=AGCGGCAGCTGGCCGCCGTC;RSEQ=CGCGCCAACGCCGGCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:31,35:0.0294:2,2:15:0:31.5:1:1:1.13:60:4:0.0308:0:1.5 0/1:96:1:1,0:47,48:0.0104:2,0:1:0:27:0:1:0:60:2:0.0109:0:1 -13 28674704 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGCCCTGCGATGCCGCCT;RSEQ=GAGCGGCGCGCCTCGCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:27.3:1:30.5:1:1:0:60:17:1:0:0.3 0/1:38:2:1,1:20,16:0.0526:2,2:8.5:1:30:1:1:1.24262:60:4:0.0541:0:1.5 -13 28674713 . C T 28 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.09512;SOR=0;LSEQ=CGATGCCGCCTGGAGCGGCG;RSEQ=GCCTCGCGCTGCAGGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:0.1538:2,2:29.5:1:28:1:1:1.18321:60:4:0.1538:0:1 0/0:28:0:0,0:15,11:0:2,0:31.5:1:30.2:1:1:0:60:52:0.9286:0:0.2 -13 28877146 . CA C 50 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.26071;SOR=0;LSEQ=GGAGTTACATTCTTGTTAGT;RSEQ=AAAAAAAAAAAGCACTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:3,0:27,2:0.0909:2,0:23.3:1:31.7:1:1:0:60:6:0.0938:0.0303:0 0/0:23:0:0,0:22,0:0:1,0:22.7:1:29.6:1:1:0:59.3:21:0.9545:0:0.8 -13 28877518 . AG A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.12162;SOR=Inf;LSEQ=CTCTCAAGCTAAAGAAAGAA;RSEQ=GAAAGAAATCAAATATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:51,171:0:2,0:22.8:1:31.1:1:1:0:60:110:1:0:0.1 0/1:219:3:2,1:66,150:0.0137:2,2:18:1:28.3:1:0.22824:4.51:60:6:0.0137:0.0046:0.3 -13 28877629 . A AC 102 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.49568;SOR=0.51786;LSEQ=CTAGAGTTCATGGTTTTGGA;RSEQ=CCCCCCCCCCCTCAATTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:0,11:1,12:0.44:1,0:27.7:1:29.6:1:1:0:59.5:10:0.4545:0.04:1.2 0/1:14:4:1,3:0,10:0.2857:0,2:27.8:1:22.4:1:0.28571:0:60:1:0.1667:0.0714:0.5 -13 28880609 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAAGATTTTCTGCATG;RSEQ=TTTCCCCAGAGCTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:2,0:27,0:0.069:1,0:23:1:32:0:1:0:60:4:0.0714:0:1 0/0:13:0:0,0:12,1:0:1,0:20.2:1:28.8:1:1:0:60:26:1:0:0.2 -13 28881158 . G A 87 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATACATTTAGGCAAAAGGG;RSEQ=AAATGGCAAGTAACAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:27.7:1:31.1:1:1:0:60:14:1:0:1.1 1/1:1:1:0,1:0,0:1:0,0:20:0:32:0:1:0:60:2:1:0:1 -13 28881375 . G A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCCCCCAGCCCTTGGTCATG;RSEQ=TCTCCAGCAATTAGACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:44:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:18:0:31:1:1:0:60:4:1:0:1.5 -13 28881464 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTAATACGGCATGTTCCA;RSEQ=TAAGTGGATCCCACGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:36:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28882948 . G A 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0.26969;LSEQ=CTGAAGAAGGGGTCTATCGG;RSEQ=GTGCACTAGGTACCTTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:630:608:373,235:12,8:0.9651:2,2:24.9:1:30:1:1:1.06:60:37:0.9673:0:1.1 1/1:625:551:332,219:43,26:0.8816:2,2:25.4:1:29.1:1:0.79476:1.09081:60:49.091:0.8795:0:1.1 -13 28883061 . G A 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21442;LSEQ=ATGAACTTGAAAGCATTTAC;RSEQ=TATCTAATGAAGAAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:501:483:154,329:6,12:0.9641:2,2:24.9:1:30.6:1:1:1.06804:60:95.6:0.9637:0:1.1 1/1:560:477:171,306:31,52:0.8518:2,2:24.3:1:29.6:1:0.80518:1.06668:59.6:78.5:0.8517:0:1.1 -13 28883337 . A G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATCAGAGAATGCCAGAC;RSEQ=TAGGAGAGACTGGAGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:30.7:1:33:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28885408 . C A 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCAACAATAGCCTTCTT;RSEQ=CAAAATGTATACTAAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:12:1:28.3:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28885452 . C T 96 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGTAAAGTGCTATTATGC;RSEQ=TTAAGCCTCCTTTTAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:7,1:1,0:0.8889:0,2:25.8:1:32.1:1:1:0:60:16:0.8889:0:1.5 1/1:1:1:1,0:0,0:1:0,0:23:0:33:0:1:0:60:2:1:0:1 -13 28885589 . ATCTT A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=4.000;MSILEN=4;SSF=0.16715;SOR=Inf;LSEQ=TATGGGTGGTGATCAACATA;RSEQ=TCTTTCTTTCTTTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:0:1,0:24.1:1:31.8:1:1:0:59.6:120:1:0:0.5 0/1:42:2:2,0:40,0:0.0476:1,0:40.5:1:32:0:1:0:60:4:0.0476:0:0.5 -13 28885593 . TTCTTTCTTTCTTTCTC T 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=2e-05;SOR=0;LSEQ=GGTGGTGATCAACATAATCT;RSEQ=TCTTTCTTTCTTTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:17:17,0:43,0:0.2833:1,1:29.5:1:31.3:1:1:0:58.5:34:0.2833:0.0167:0.8 0/0:46:0:0,0:46,0:0:1,0:23.2:1:31.1:1:1:0:60:92:1:0:0.5 -13 28885668 . TTTCC T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24872;SOR=0;LSEQ=TTCTTTCTCTTTCGTCTTTC;RSEQ=TTCTTTTTTTTGTTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:3,0:208,39:0.012:2,0:26:1:28.7:1:1:0:60:6:0.0121:0.004:0 0/0:241:0:0,0:191,50:0:2,0:22.7:1:29.7:1:1:0:60:47.2:1:0:1.1 -13 28885672 . C T 243 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.72387;SOR=1.34848;LSEQ=TTCTCTTTCGTCTTTCTTTC;RSEQ=TTCTTTTTTTTGTTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:255:251:210,41:0,0:0.9843:0,2:23.9:1:31.2:1:1:0:60:250:0.9921:0:1.1 1/1:257:254:200,54:0,0:0.9883:0,2:22.8:1:30.5:1:1:0:60:83.667:0.9882:0:1.1 -13 28885675 . C CT 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.37077;SOR=3.05174;LSEQ=TCTTTCGTCTTTCTTTCCTT;RSEQ=TTTTTTTTGTTGGAAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:1:1,0:218,45:0.0037:2,0:13:0:32:0:1:0:60:2:0.0039:0:1 0/1:264:3:1,2:203,55:0.0114:2,2:11.7:1:29.3:1:0.12114:7.30616:60:6:0.0117:0.0038:1 -13 28885997 . TAC T 63 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.81251;LSEQ=TTTGAGAAGATAATTCTGTA;RSEQ=ACACACACACACCCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:4:2,2:76,75:0.0258:2,2:36.5:1:31.5:1:1:1.01325:60:8:0.026:0:0 0/1:95:2:2,0:46,46:0.0211:2,0:30:1:30:1:0.49485:0:60:4:0.0213:0:0 -13 28886013 . CT C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.1401;SOR=Inf;LSEQ=TGTATACACACACACACACC;RSEQ=TTTTTTAAACTTCTGATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:104,64:0:2,0:23.3:1:31:1:1:0:60:83:1:0:0.4 0/1:101:2:2,0:65,34:0.0198:2,0:33:1:33:0:0.54891:0:60:4:0.0204:0:0 -13 28886032 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16132;SOR=Inf;LSEQ=CCTTTTTTTAAACTTCTGAT;RSEQ=TCAGCTATTATATTAATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:132,49:0:2,0:25.8:1:31.6:1:1:0:60:44.25:1:0:0.7 0/1:122:2:1,1:97,23:0.0164:2,2:21.5:1:29:1:0.35605:4.14982:60:4:0.0168:0:1.5 -13 28886056 . T TA 131 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.74304;SOR=0.84885;LSEQ=GCTATTATATTAATAGCTCT;RSEQ=AAAAAAAAAACAAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:24:16,8:176,60:0.0923:2,2:25:1:28.7:1:0.46461:1.46435:60:48:0.0927:0.0231:1 0/1:214:17:14,3:152,44:0.0794:2,2:22.9:1:28.1:1:0.76964:1.35:60:16:0.0755:0.0047:1.1 -13 28886113 . A G 298 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2643;SOR=2.82352;LSEQ=TTCAAAGGCATTTTGATGTA;RSEQ=ATAAATTTAGTTTTACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:681:676:414,262:0,1:0.9927:0,2:27.2:1:31.7:1:0.38848:0:60:66.6:0.9985:0:1.1 1/1:766:764:457,307:1,0:0.9974:0,2:26.3:1:31.2:1:1:0:60:46.75:0.9987:0:1.2 -13 28886388 . A G 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28955;SOR=5.18096;LSEQ=ATTTTTAGGTTTGGGTTTAT;RSEQ=GCACCAGCACTTAAAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:1:0,1:0,39:0.025:1,0:16:0:33:0:1:0:60:2:0.027:0:1 0/1:25:3:0,3:1,21:0.12:1,0:22.7:1:31.7:1:1:0:60:6:0.12:0:1 -13 28891487 . T C 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34437;SOR=0;LSEQ=CCCAGCATATCTGGGCCTGA;RSEQ=GGGCTGAGGGGAGCATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:99:99:99,0:0,0:1:0,1:22.8:1:32:1:1:0:60:32:1:0:1.1 1/1:52:51:50,1:0,0:0.9808:0,1:23:1:31.2:1:1:0:60:102:0.9808:0:1.2 -13 28891815 . C A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17795;SOR=Inf;LSEQ=GAGGGGACAATTCAGTGTTT;RSEQ=TTTCCTCCCTTTAAAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:2,170:0:1,0:24.1:1:32.4:1:1:0:60:85:1:0:0.1 0/1:126:2:1,1:7,116:0.0159:2,2:20:0:29.5:1:0.12439:15.56:60:4:0.016:0:1.5 -13 28893377 . A C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATCATATAAAGCCCTTTT;RSEQ=CAGTAGAGGGCAGACATGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:29,0:0.0645:1,0:24.5:1:32:1:1:0:60:4:0.0645:0:1 0/0:6:0:0,0:6,0:0:0,0:22.7:1:27.7:1:1:0:60:12:1:0:0 -13 28893484 . T C 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTTCTAATCTAAAGGCTGTC;RSEQ=AACCAAAGGACATTCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:188:188:146,42:0,0:1:0,2:22.6:1:31:1:1:0:60:93:1:0:1.1 1/0:189:137:106,31:44,7:0.7249:2,2:25.1:1:30.1:1:0.22209:1.83283:60:136:0.7273:0:1.1 -13 28893526 . G T 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12528;SOR=5.61816;LSEQ=AGATGCAGACATTTATTTCT;RSEQ=GGCTGTTTGATTTCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:1:0,1:247,145:0.0025:2,0:1:0:15:0:0.3715:0:60:0:0:0:3 0/1:425:6:2,4:254,165:0.0141:2,2:15:1:27.8:1:0.22097:3.07052:60:12:0.0144:0:1 -13 28893642 . A G 186 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=72.15211;LSEQ=ATTTTGTCAAAGATAGATTC;RSEQ=GGAGCCATCCATTTCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:1:0,1:208,302:0.002:2,0:18:0:27:0:1:0:60:2:0.002:0:1 0/1:604:75:34,41:233,296:0.1242:2,2:24.8:1:29.9:1:0.90126:1.05:60:74:0.124:0:1.1 -13 28893719 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49872;SOR=Inf;LSEQ=AGAAGGGCATGAAAACAAAG;RSEQ=ACATTCAACCCGAGTGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:31,158:0:2,0:23.8:1:31.9:1:1:0:60:46.25:1:0:0.1 0/1:192:2:1,1:47,143:0.0104:2,2:17.5:1:31:1:0.43848:3.02:60:4:0.0105:0:2 -13 28895524 . G C 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGGGACTACAGCTGAGGAA;RSEQ=TGTAAATATTTACCAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:191,23:0:2,0:23.4:1:32.1:1:1:0:60:70.333:0.9953:0:0.1 0/1:231:27:23,4:163,41:0.1169:2,2:21.5:1:31.2:1:0.61415:1.44:60:26:0.1145:0:1.1 -13 28901505 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08397;SOR=Inf;LSEQ=GTTTTAAGTTTAATCATTAA;RSEQ=AACACAATACAGGTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:236,22:0:2,0:23.2:1:32.2:1:1:0:60:257:1:0:0.1 0/1:202:3:1,2:181,18:0.0149:2,2:5:1:28.3:1:0.02639:19.44549:60:6:0.0149:0:1 -13 28901750 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50047;SOR=Inf;LSEQ=CCAGTCAGCCATTTGCCAGC;RSEQ=TTCAGCCTGCCTGAGAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:21,149:0:2,0:24.7:1:32:1:1:0:60:84:1:0:0.1 0/1:192:2:1,1:32,158:0.0104:2,2:45:1:30:1:0.31495:4.88:60:4:0.0106:0:2 -13 28901759 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21907;SOR=0;LSEQ=CATTTGCCAGCCTTCAGCCT;RSEQ=CCTGAGAAACCTCAAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:13,121:0.0147:2,2:14.5:1:30.5:1:0.19597:9.01:60:4:0.0147:0:1 0/0:154:0:0,0:25,129:0:2,0:24.1:1:31.9:1:1:0:60:37.5:1:0:0.1 -13 28903707 . G T 68 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45145;SOR=0.40202;LSEQ=GGCAGAGAACTGTTCTCCCA;RSEQ=CCTGTGCAGGGGGAGACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:5:2,3:328,148:0.0104:2,2:13:1:29.6:1:0.18091:3.31513:60:10:0.0105:0:1.2 0/0:476:2:0,2:311,163:0.0042:2,0:1:0:25:0:0.11968:0:60:4:0.0043:0:1 -13 28903895 . G A 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCAAGGAAGAGTCAGGGC;RSEQ=ACAGGACAATGGGGCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:96,298:0:2,0:24.2:1:30.7:1:1:0:60:196:1:0:0.1 0/1:373:22:3,19:94,257:0.059:2,2:29.5:1:30.6:1:0.21596:2.31221:60:44:0.0595:0:1.1 -13 28904316 . G T 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGGGCAGAATGGCTACT;RSEQ=TTGTAAACATCTTTGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:21:1:31.3:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28912726 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAGTGAAACTTAAATGA;RSEQ=TCCCCTAGGGCTTTCTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30.5:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28912964 . G C 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAATGCCTCTCTCTCCGCC;RSEQ=CCCTTCACTTACCACTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:12.3:1:28:1:1:0:60:6:1:0:1 1/1:2:2:1,1:0,0:1:0,2:16.5:1:32.5:1:1:0:60:4:1:0:1.5 -13 28913463 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11153;SOR=Inf;LSEQ=AAATAAAGAGATCTCAAAGT;RSEQ=ATCGAGAAGAAAACAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:65,241:0:2,0:22.7:1:31.8:1:1:0:60:101:1:0:0.1 0/1:285:3:2,1:77,205:0.0105:2,2:6:1:26:1:0.18696:5.29:60:6:0.0106:0:1 -13 28913502 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18338;SOR=4.8023;LSEQ=TTACAAATCCTAGATATTCC;RSEQ=TTAACATCCACTGTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:1:0,1:13,121:0.0074:2,0:27:0:14:0:1:0:60:0:0:0:6 0/1:115:4:0,4:8,102:0.0348:2,0:22.3:1:30.3:1:1:0:60:8:0.0351:0:1.8 -13 28919218 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCAAAGTGCTGGGATTACAG;RSEQ=CATGTACCACCGTGCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:40:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:33.5:1:1:0:60:4:1:0:4 -13 28919223 . TA AG 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTGCTGGGATTACAGTCATG;RSEQ=CCACCGTGCCCAGTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:25:1:31.5:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:22:0:33:1:1:0:60:4:1:0:3 -13 28919330 . G A 85 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31818;SOR=0.14907;LSEQ=AGACTCTATTAACATATTTT;RSEQ=TATCAAAAATACCTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:0.9:0,0:20.3:1:27:1:1:0:60:18:0.9:0:1 1/0:2:1:1,0:1,0:0.5:0,0:26:0:30:0:1:0:60:2:0.5:0:1 -13 28919462 . T C 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02173;SOR=0;LSEQ=TGTGTTCACCAGGTCAGAGA;RSEQ=AGGAATGAGAGGGAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:81:79,2:0,0:1:0,1:25.8:1:32.4:1:1:0:60:162:1:0:1 1/1:52:48:48,0:4,0:0.9231:0,1:23.2:1:31.4:1:1:0:60:96:0.9412:0:1.1 -13 28919696 . G A 58 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.03365;SOR=Inf;LSEQ=TTGTCCGAGGTTCCTGGAGA;RSEQ=AAAAAAAATCACAATAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:128,296:0:2,0:25.4:1:31.4:1:1:0:60:83.8:0.9929:0:0.1 0/1:500:6:5,1:174,318:0.012:2,2:5.2:1:22.7:1:0.02451:9.10:60:2:0.0081:0:1.8 -13 28931455 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=TTCTGGGAACGACTTCTCCC;RSEQ=CAGACACTGTGTTCGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:6:1:28.5:1:1:0:60:4:0.1818:0:1 0/0:6:0:0,0:5,1:0:2,0:14.5:1:28.2:1:1:0:60:12:1:0:0.2 -13 28931611 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49825;SOR=Inf;LSEQ=GACTGGAGCAGGCAGCAGGA;RSEQ=ACTGGGAGGTGGAAAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:121,21:0:2,0:25.3:1:31.6:1:1:0:60:46.333:1:0:0.1 0/1:143:2:1,1:116,25:0.014:2,2:7.5:1:28.5:1:0.33163:4.56949:60:4:0.0141:0:1 -13 28942716 . TATG T 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.22111;SOR=0.65998;LSEQ=ATGATGATAATGATGATAGC;RSEQ=ATGATGATGATGATGACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:25:17,8:369,105:0.05:2,2:21.5:1:30.1:1:0.32421:1.65191:60:50:0.0507:0.02:0.4 0/1:596:20:15,5:400,175:0.0336:2,2:25.3:1:30.3:1:0.80514:1.31:60:40:0.0342:0.0017:0 -13 28942736 . CGAT C 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0;SOR=3.96648;LSEQ=TATGATGATGATGATGATGA;RSEQ=GATGATGATGATGACAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:741:12:8,4:464,263:0.0162:2,2:28.3:1:30.4:1:1:1.13:60:24:0.0164:0.0027:0.2 0/1:962:59:30,29:542,358:0.0613:2,2:25.5:1:29.7:1:0.17147:1.46287:60:28.5:0.0601:0.0052:0.4 -13 28942882 . C T 37 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62337;SOR=0.33554;LSEQ=ACAGAGTTTTGCTCTTGTTG;RSEQ=CCAGGCTGGAGTGCAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:3:1,2:25,198:0.0132:2,2:24:1:23.7:1:0.30815:3.92:49.7:2:0.0101:0:2.3 0/0:225:1:0,1:25,199:0.0044:2,0:41:0:30:0:1:0:60:2:0.005:0:1 -13 28943002 . C T 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.20759;SOR=3.40536;LSEQ=CAGGTGCCCACCACCATACC;RSEQ=GGCTAATTTTTGTGTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:0,16:0.1111:1,0:12:1:32:1:1:0:60:4:0.1111:0:1.5 0/1:13:4:0,4:0,9:0.3077:0,0:24.5:1:28:1:1:0:58.3:3:0.25:0:1.5 -13 28958893 . A AT 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03213;SOR=Inf;LSEQ=TTGCTATCAGCATGAACCAG;RSEQ=TCCCAGTGTTTGGGGCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:94,2:0:1,0:25.5:1:30.2:1:1:0:60:47:1:0:0.2 0/1:72:4:4,0:66,2:0.0556:1,0:29:1:30.8:1:1:0:60:8:0.0571:0.0139:0.5 -13 28958955 . C A 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00512;SOR=1.74125;LSEQ=ACTGGAAGCAGGTGACGGGA;RSEQ=TGTTAAGGGAAAGGGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:50:38,12:206,72:0.1524:2,2:21.2:1:30.2:1:0.86149:1.11:60:49:0.1541:0:1 0/1:352:84:65,19:193,73:0.2386:2,2:20.3:1:28.9:1:0.47721:1.29:60:27:0.2382:0:1.1 -13 28959273 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51521;SOR=0;LSEQ=AGAAACAGCAAAACTCAACT;RSEQ=TTAGGTTTCATTTTCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:1,77:0.025:1,2:24:1:30:1:0.04968:54.82:60:4:0.025:0:1 0/0:54:0:0,0:2,52:0:1,0:23.5:1:30.2:1:1:0:60:53:1:0:0 -13 28963676 . G A 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92922;LSEQ=CCCCCCGGAGCAGCCCCCTC;RSEQ=GCCTGAATGGGGGGCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:23:22,1:8,0:0.7419:0,1:24.8:1:30:1:1:0:60:22:0.7333:0:1 1/0:11:8:8,0:3,0:0.7273:0,0:25.5:1:30.3:1:1:0:60:16:0.7273:0:1.1 -13 28963702 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=1.19131;LSEQ=AATGGGGGGCCCAGAGCTGG;RSEQ=GCCCGGGGGTCTCATTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:6:6,0:41,2:0.1224:1,0:32.3:1:30.5:1:1:0:60:12:0.125:0:1 0/1:21:3:3,0:17,1:0.1429:1,0:21.7:1:30:1:1:0:60:6:0.15:0:1 -13 28964198 . C T 126 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=0.14334;LSEQ=AGTTTCAGGTCCTCTCCTTC;RSEQ=GTCGGCATTTTTTCCAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:18:6,12:179,295:0.0366:2,2:28.1:1:30.4:1:0.8076:1.21306:60:36:0.0369:0:1.2 0/0:555:3:1,2:238,314:0.0054:2,2:22.7:1:26.3:1:1:1.51483:60:6:0.0055:0:1 -13 28964325 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07053;LSEQ=AAAGATCTTAAGAATTGTTC;RSEQ=TGCACAAATTATCTCAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:63:2,61:0,5:0.9265:0,1:22.7:1:30.7:1:1:0:60:30.5:0.9242:0:1.1 0/1:56:26:0,26:0,30:0.4643:1,1:22.7:1:30.3:1:1:0:60:52:0.4643:0:1 -13 28970917 . C T 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05352;SOR=0;LSEQ=AGAATACAGGGAAATAACTC;RSEQ=TTACGAGATCCGATGAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:37,1:0,0:1:0,1:22.4:1:32.2:1:1:0:60:76:1:0:1 1/1:24:21:21,0:3,0:0.875:0,1:22.1:1:31.3:1:1:0:60:42:0.875:0:1 -13 28970996 . TA T 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.75373;SOR=0.74336;LSEQ=GTTTGACAATTCTATGGAAT;RSEQ=AAAAAAAATCACTCAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:6:6,0:133,4:0.042:1,0:21.3:1:30.8:1:1:0:60:12:0.0423:0.007:0 0/1:127:4:4,0:112,11:0.0315:2,0:23:1:31:1:1:0:60:8:0.0317:0.0079:0 -13 28971220 . G A 189 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02893;LSEQ=AGCCATCTGCAAAAGAAAAG;RSEQ=AAACTTTAGCTAGCAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:76:17,59:43,162:0.2705:2,2:24:1:30.3:1:0.86998:1.09:60:152:0.2714:0:1.1 0/1:284:3:3,0:78,202:0.0106:2,0:1:0:24.3:1:0.02283:0:60:6:0.0107:0:1 -13 28973703 . C T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGACCTGTGTAGGTAAC;RSEQ=TGGGAATGGCCGTGGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:25.3:1:30.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28979545 . C T 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCAGTGATTCTCAATCCC;RSEQ=GTTAGGTACTGGAATCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24.5:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 28979837 . G T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.367;SOR=0.32264;LSEQ=TGAACATTTAAATTACTTCT;RSEQ=GTGCCAATAAACCTAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:219,37:0.0116:2,2:13.7:1:28.3:1:0.37998:2.94221:60:6:0.0118:0:1.3 0/0:266:1:1,0:191,74:0.0038:2,0:43:0:29:0:1:0:60:2:0.0038:0:1 -13 28980036 . T TA 140 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.76642;SOR=1.13966;LSEQ=GGAACAAAAGTCACACCTAT;RSEQ=AAAAAAAAAAGTTGTCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:22:6,16:69,216:0.0712:2,2:23.3:1:28.9:1:0.79732:1.17:60:21:0.0705:0.0032:0.7 0/1:336:27:8,19:83,222:0.0804:2,2:30:1:29.6:1:0.82279:1.13:60:54:0.0831:0:0 -13 28980065 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=Inf;LSEQ=AAGTTGTCACAATGTGGCTT;RSEQ=ACAGCATGGTTCAGTCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:23,155:0:2,0:22.6:1:28.5:1:1:0:60:88:1:0:0.2 0/1:193:2:1,1:26,164:0.0104:2,2:9:1:28:1:0.26211:6.21:60:4:0.0104:0:1 -13 28980150 . A AG 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54565;SOR=0.47242;LSEQ=AGTCACAAATTTTATGTGTG;RSEQ=TCTTCTTTTCCTTAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:45:0,45:0,1:0.9783:0,1:24.3:1:32.3:1:1:0:60:44:0.9778:0.1957:0.1 1/1:22:21:0,21:0,1:0.9545:0,1:19.7:1:31.6:1:1:0:60:42:0.9545:0.2273:0 -13 29001208 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50898;SOR=Inf;LSEQ=ATATACAGTACATCCCACAT;RSEQ=CAGATTCCCATCTGCGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:95,18:0:2,0:21.7:1:31.7:1:1:0:60:36.667:1:0:0.1 0/1:152:2:2,0:128,22:0.0132:2,0:24:1:31.5:1:1:0:60:4:0.0132:0:1 -13 29001476 . G A 29 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59918;SOR=0.43164;LSEQ=CTGGAAAGGAGATGAAGAAC;RSEQ=GGACAGAAGTCAAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:44,149:0.0103:2,2:6:0:29:1:0.4092:3.36:60:4:0.0104:0:1 0/0:225:1:1,0:59,165:0.0044:2,0:1:0:28:0:0.26667:0:60:2:0.0045:0:1 -13 29001586 . T A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14474;SOR=Inf;LSEQ=ACAAGAAACAAAAAAACAAA;RSEQ=AAACCCTCCTATTTGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:7,28:0:2,0:26.1:1:27.9:1:1:0:60:16.5:1:0:0.2 0/1:22:2:1,1:0,20:0.0909:1,2:5:0:29:1:0.09091:0:60:4:0.0952:0:0 -13 29001721 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCGCCTATGGAATACAA;RSEQ=AAACAAACACGAGATTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:33,8:0.0465:2,0:24.5:1:30:1:1:0:60:4:0.0465:0:2.5 0/0:19:0:0,0:19,0:0:1,0:24.5:1:31.5:1:1:0:60:38:1:0:0 -13 29001807 . G T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00509;LSEQ=ATTTTGCTATCTTTGATGTT;RSEQ=TTACGCTGATTTTTGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:181,16:0.0101:2,2:25:1:27.5:1:0.16395:11.00534:60:4:0.0102:0:1 0/1:198:2:1,1:172,23:0.0101:2,2:1.5:1:27:1:0.22936:7.34332:60:4:0.0102:0:1 -13 29002081 . TA T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.216;SOR=Inf;LSEQ=GTGGTTAAAAACATGATCAG;RSEQ=AGTCATTTCACACGGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:38,186:0:2,0:22.5:1:29.7:1:1:0:60:111:1:0:0.1 0/1:195:2:0,2:34,159:0.0103:2,0:13:1:29:1:1:0:60:4:0.0105:0.0051:3 -13 29002098 . C A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32198;SOR=3.90923;LSEQ=CAGTAAGTCATTTCACACGG;RSEQ=CTCTCAATATCACTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:1,0:16,145:0.0062:2,0:1:0:25:0:0.10494:0:60:2:0.0064:0:1 0/1:126:3:1,2:15,108:0.0238:2,2:14.7:1:21:1:0.33696:3.54:60:2:0.0161:0:1.3 -13 29004064 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.19501;SOR=Inf;LSEQ=AGAATCTACAGAGTTCTGAG;RSEQ=TCTCTGGGGCTGTCTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:54,1:0:1,0:27.2:1:32.2:1:1:0:60:110:1:0:0.1 0/1:44:2:2,0:41,1:0.0455:1,0:16:1:31.5:1:1:0:60:4:0.0476:0:1 -13 29004123 . G C 75 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06198;SOR=Inf;LSEQ=TCAGGAATTCGAGTCATTAG;RSEQ=CTCTTGCAGCTTCCCACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:152,25:0:2,0:24.1:1:31.3:1:1:0:60:58:1:0:0 0/1:193:5:4,1:150,37:0.0259:2,2:24.6:1:32.4:1:1:1.01344:60:10:0.0263:0:1 -13 29012114 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATACATAACATTTTTCA;RSEQ=GATTTCAGTTCTTTCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:11,0:0.2:0,0:20.7:1:30.3:1:1:0:60:6:0.2143:0:1 0/0:4:0:0,0:4,0:0:0,0:30:1:28.3:1:1:0:60:3:1:0:0.3 -13 29012584 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51513;SOR=0;LSEQ=GTAGGCATTGCCACAGTCAC;RSEQ=TCATTCTCCCTTAATGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:0,48:0.04:1,0:26:1:32.5:1:1:0:60:4:0.0417:0:1 0/0:33:0:0,0:1,32:0:1,0:19.2:1:30:1:1:0:60:32:1:0:0 -13 29041007 . A T 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGACTCATTTGCAAAGCAA;RSEQ=AGCAAACAGAATGTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:160,49:0:2,0:24.5:1:30:1:1:0:60:40.8:1:0:0.1 0/1:232:21:19,2:150,61:0.0905:2,2:22.1:1:30.4:1:0.07106:3.85:60:42:0.0925:0:1.1 -13 29041544 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53231;SOR=0;LSEQ=AAGCTGGATGCCTATGGTTT;RSEQ=CACTTTGCAGATCACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:2,0:92,11:0.019:2,0:18:1:30:0:1:0:60:4:0.0194:0:1 0/0:61:0:0,0:60,1:0:1,0:7:0:14:0:1:0:60:0:0:0:7 -13 29041581 . C A 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04583;SOR=Inf;LSEQ=GGAGATCACTGAGGTCCCTA;RSEQ=CTTTTTACTCTGCCAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:164,34:0:2,0:23.1:1:31.8:1:1:0:60:65:1:0:0.1 0/1:172:4:4,0:137,31:0.0233:2,0:29.3:1:31:1:1:0:60:8:0.0241:0:1 -13 29041776 . T C 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00092;SOR=Inf;LSEQ=TGAAAAACAAATTTTTAAAA;RSEQ=GTATTATTTGTAAATTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:60,215:0:2,0:22.5:1:30.4:1:1:0:60:90.667:1:0:0.1 0/1:291:11:2,9:67,213:0.0378:2,2:21:1:30.7:1:1:1.41392:60:22:0.0381:0:1.7 -13 29041794 . T C 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01572;SOR=Inf;LSEQ=AATGTATTATTTGTAAATTG;RSEQ=CTTCTTACCTTTTTTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:17,153:0:2,0:25.1:1:30.4:1:1:0:60:84:1:0:0.1 0/1:190:7:0,7:28,154:0.0368:2,0:23.9:1:31.7:1:0.59648:0:60:14:0.0372:0:2.3 -13 29041826 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10797;SOR=Inf;LSEQ=TTTTTAAGTTATCTTTCCAT;RSEQ=AAGGTGAGTTTTTCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:3,85:0:1,0:24.5:1:31.6:1:1:0:60:43:1:0:0.1 0/1:81:3:0,3:4,74:0.037:2,0:30.3:1:30.7:1:1:0:60:6:0.0375:0:2.7 -13 29068175 . A C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CACGGACTGGACCGCGCACC;RSEQ=CGCCTGCTCCCGGCAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:32.5:1:1:0:60:4:1:0:1.5 -13 29069018 . C A 52 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05108;SOR=0;LSEQ=CTGCTCGCCCGGTGCCCGCG;RSEQ=TCCCCGCGGCCAACGACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:4:3,1:41,145:0.0211:2,2:24.8:1:26:1:0.03934:10.44:60:3:0.016:0:2.8 0/0:208:0:0,0:62,146:0:2,0:24.7:1:32:1:1:0:60:103:1:0:0.2 -13 29069024 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49905;SOR=Inf;LSEQ=GCCCGGTGCCCGCGCTCCCC;RSEQ=CGGCCAACGACCCGGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:33,129:0:2,0:22.9:1:31.6:1:1:0:60:53:0.9938:0:0.3 0/1:174:2:1,1:48,124:0.0115:2,2:18.5:1:29:1:0.48508:2.57:60:4:0.0117:0:1 -13 29069039 . G A 93 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02556;SOR=0.17709;LSEQ=TCCCCGCGGCCAACGACCCG;RSEQ=CCGCCAGAGTCCGTCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:9:3,6:18,73:0.09:2,2:15.8:1:29.6:1:0.39198:2.01:60:18:0.0909:0:1.1 0/1:117:2:1,1:30,85:0.0171:2,2:7.5:1:26.5:1:0.46139:2.80:60:4:0.0175:0:1 -13 29678908 . AT A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03881;SOR=0;LSEQ=CCATAGCTTTTCAAAAAAAT;RSEQ=TTACATTGAAAGAGGGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:4:3,1:144,148:0.0135:2,2:22:1:27.5:1:0.36908:3.07:60:8:0.0137:0.0068:2.3 0/0:369:0:0,0:175,194:0:2,0:23.9:1:29.4:1:1:0:60:60.5:1:0:0.9 -13 29678920 . A G 252 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04765;LSEQ=AAAAAAATATTTACATTGAA;RSEQ=GAGGGAACGTAATTTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:290:281:133,148:3,6:0.969:2,2:24.2:1:31.1:1:0.5087:1.79:60:55.2:0.9684:0:1.7 1/0:340:203:92,111:64,72:0.5971:2,2:24.3:1:30.7:1:0.82413:1.07224:60:49.75:0.594:0:1.8 -13 29678955 . G A 236 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.034;LSEQ=TTCTAACTTAGAAATTAAGC;RSEQ=TAAACTTAACATATCGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:226:220:82,138:1,5:0.9735:2,2:26.8:1:30.4:1:0.41831:2.96:60:109:0.9732:0:1.8 1/0:271:150:56,94:50,70:0.5535:2,2:24.9:1:29.5:1:0.53088:1.19816:60:49:0.5485:0:2 -13 29678976 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25026;SOR=Inf;LSEQ=TAAACTTAACATATCGGTCT;RSEQ=ACCCAGGATGTGGCTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:56,128:0:2,0:25.3:1:31.4:1:1:0:60:368:1:0:1.6 0/1:205:3:1,2:73,129:0.0146:2,2:43:1:23.7:1:1:1.13113:60:2:0.0099:0:1.3 -13 29678997 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12446;SOR=Inf;LSEQ=ACCCAGGATGTGGCTCCTTA;RSEQ=TTCTTTTATAATGTTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:32,101:0:2,0:24.3:1:32:1:1:0:60:132:1:0:1.2 0/1:148:4:2,2:41,103:0.027:2,2:30.8:1:29.8:1:0.57996:2.49:60:8:0.0272:0:2.3 -13 29679002 . T C 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24903;SOR=Inf;LSEQ=GGATGTGGCTCCTTAGTTCT;RSEQ=TTATAATGTTCAGAGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:24,94:0:2,0:24.9:1:30.3:1:1:0:60:117:1:0:1.1 0/1:131:3:1,2:38,90:0.0229:2,2:13.3:1:24.3:1:1:1.18:60:2:0.0154:0:2 -13 29679010 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49768;SOR=Inf;LSEQ=CTCCTTAGTTCTTTTATAAT;RSEQ=TTCAGAGATGAAAAAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:22,83:0:2,0:23.6:1:31.8:1:1:0:60:51.5:1:0:1 0/1:107:2:1,1:30,75:0.0187:2,2:7.5:1:27.5:1:0.49744:2.48:60:4:0.019:0:1 -13 29679113 . A G 126 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05263;SOR=0;LSEQ=AGTGTCGGAAACATACTATT;RSEQ=CCTAATGTGTATAGGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:1:0,1:26.3:1:32.5:1:1:0:60:30:1:0:1.5 1/0:5:3:0,3:0,2:0.6:0,0:7.7:1:26.3:1:1:0:60:2:0.5:0:1.3 -13 29679161 . G A 97 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=AATCAGAAAATCTGAAATTC;RSEQ=AAATGCTCCAAAACCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:25.6:1:30.8:1:1:0:60:18:1:0:2.1 0/1:3:1:0,1:0,2:0.3333:0,0:40:0:32:0:1:0:60:2:0.3333:0:2 -13 29679209 . T C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GAACACTGACACGATGCCCA;RSEQ=GGGAAATAGTCACTGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:21.7:1:31:1:1:0:60:6:1:0:1.7 0/0:2:0:0,0:0,2:0:0,0:36.5:1:30.5:1:1:0:60:4:1:0:0 -13 30073814 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTTTTATATCCTTAGCTTG;RSEQ=CATCTCAGGCAGGAACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:0:2,0:19.7:1:30.7:1:1:0:60:20:1:0:0.1 0/1:26:2:1,1:8,16:0.0769:2,2:9:0:31.5:1:1:1.94:60:4:0.0769:0:1.5 -13 30440094 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12395;SOR=Inf;LSEQ=TCTCATCCTCCCAGGGGATG;RSEQ=CCTACTGCCCTCCTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:187,130:0:2,0:26.6:1:31.5:1:1:0:60:316:1:0:0.1 0/1:325:4:2,2:203,118:0.0123:2,2:18.8:1:29.5:1:0.62792:1.71725:60:8:0.0125:0:1 -13 30440177 . G A 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00131;SOR=Inf;LSEQ=TGAAGCGGTCCACAGAGCTA;RSEQ=AGAGGCAATTTTCAGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:119,184:0:2,0:27.3:1:31.4:1:1:0:60:100:0.9934:0:0.1 0/1:364:11:8,3:151,200:0.0302:2,2:30.3:1:29.3:1:0.06529:3.52:60:22:0.0306:0:1.2 -13 30440216 . G A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12608;SOR=Inf;LSEQ=GAGAGTCTAGGCATTTCCCT;RSEQ=GCTTCTCCACACATCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:45,141:0:2,0:23.6:1:30.8:1:1:0:60:25.571:1:0:0.1 0/1:211:4:3,1:56,149:0.019:2,2:7.5:1:25.8:1:0.06903:7.89:60:8:0.0196:0:1 -13 32183145 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCCAGTGAGAAATCGAG;RSEQ=GCAGCGCCGGTGGGCTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32183766 . A G 78 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGTAGCTTGATGGCCTC;RSEQ=ATTCTAGAGGAAACAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:22:1:30.3:1:1:0:37.5:12:1:0:1 1/1:2:2:2,0:0,0:1:0,0:26.5:1:31:0:1:0:40:4:1:0:1 -13 32183909 . G A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37622;SOR=1.84055;LSEQ=GGTATAAGAATTTGAAAGGC;RSEQ=TTGTCTGATTTCAGAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:5,4:6,8:0.3913:2,2:32.1:1:29.3:1:0.68017:1.63:58.2:18:0.4091:0:1.8 1/0:22:12:5,7:4,6:0.5455:2,2:23.5:1:29.1:1:1:1.07:58.3:11:0.5238:0:1.5 -13 32183944 . C T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCTTTCCTGTAAACGC;RSEQ=GGGCAGCATCTCATACTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:7,6:0,0:1:0,2:27.6:1:26.2:1:1:0:58.8:3.333:1:0:1.5 1/1:11:11:2,9:0,0:1:0,2:25.9:1:29.5:1:1:0:57.2:10:1:0:1.6 -13 32507296 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22823;SOR=0;LSEQ=CTGACCTCCCTAATAGGATA;RSEQ=CATTTCATCAAGGTGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:73,6:0.0247:2,2:23:1:31.5:1:0.16636:11.34129:60:4:0.0253:0:1 0/0:88:0:0,0:80,8:0:2,0:24.6:1:32.6:1:1:0:60:87:1:0:0 -13 32507426 . T C 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00064;SOR=1.73359;LSEQ=TTGTTAACTTTTGGTTGTTT;RSEQ=CTGTCTAGTTTGAGGACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:86:39,47:147,157:0.2205:2,2:27.9:1:31:1:0.62749:1.12802:60:85:0.2214:0:1.1 0/1:404:133:63,70:123,148:0.3292:2,2:25.7:1:30.7:1:0.75035:1.08:60:132:0.33:0:1.1 -13 32507524 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23579;SOR=Inf;LSEQ=TATGCCAGAAGAGTGAAAAT;RSEQ=TATTTCTTTATTTGCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:12,104:0:2,0:22.7:1:30.6:1:1:0:60:115:1:0:0.1 0/1:110:2:1,1:22,86:0.0182:2,2:25:1:30:0:0.37598:3.85:60:4:0.0183:0:1 -13 32507566 . AT A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05161;SOR=3.75602;LSEQ=AAATTGCAATTATAAAGACA;RSEQ=TCATTTAGCTTATATCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:41:0,41:1,12:0.7593:1,1:23.3:1:31:1:0.24074:0:60:82:0.7593:0.1667:0.1 1/1:39:36:0,36:0,3:0.9231:0,1:23.4:1:30.5:1:1:0:60:72:0.9231:0.1026:0 -13 32507665 . G A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCATATGCGTTGGTTAC;RSEQ=TAGCATGAAGACCTATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:34.6:1:32:1:1:0:60:14:1:0:1 1/1:2:2:0,2:0,0:1:0,0:15:1:28:1:1:0:60:4:1:0:1 -13 32747122 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.76462;LSEQ=AAAGTAAATGTTTGAAAATT;RSEQ=GATTCAATAGTATCCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:76:32,44:123,127:0.2331:2,2:26.2:1:29.9:1:0.29638:1.33052:60:75:0.2351:0:1.1 1/0:410:219:108,111:97,93:0.5341:2,2:24.6:1:29.9:1:0.76642:1.0718:60:438:0.5381:0:1.1 -13 32747212 . C G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0632;LSEQ=GTGTAATACCAAGTGGTATA;RSEQ=ATGAAAGGAGTTGTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:50:9,41:18,56:0.4032:2,2:23.9:1:31.5:1:0.50735:1.45988:60:100:0.4032:0:1 0/1:148:6:2,4:34,108:0.0405:2,2:20.3:1:31.5:1:0.63336:1.58:60:12:0.0411:0:1 -13 32890572 . G A 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.62364;LSEQ=TTTGCAGACTTATTTACCAA;RSEQ=CATTGGAGGAATATCGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:17:11,6:266,190:0.0359:2,2:24.3:1:28.8:1:0.80287:1.31:60:16:0.0342:0:1.1 0/1:513:61:39,22:253,199:0.1189:2,2:24:1:29.4:1:0.27156:1.39:60:122:0.1206:0:1.1 -13 32890587 . C T 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=ACCAAGCATTGGAGGAATAT;RSEQ=GTAGGTAAAAATGCCTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:292,245:0:2,0:25.9:1:30.5:1:1:0:60:133.25:1:0:0.1 0/1:560:16:11,5:291,253:0.0286:2,2:23.9:1:29.3:1:0.31033:1.91:60:32:0.029:0:1 -13 32890716 . TA T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.24046;SOR=0;LSEQ=TACACCGAGAAAGTGTTTTC;RSEQ=AAAAATGCTTGCTAAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:25,139:0.012:2,2:26.5:1:29.5:1:0.28952:5.47:60:4:0.0122:0:0 0/0:172:0:0,0:28,144:0:2,0:24.3:1:29.6:1:1:0:60:344:1:0:0.1 -13 32893197 . AT A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.67546;SOR=0.79885;LSEQ=CTGGTTAAAACTAAGGTGGG;RSEQ=TTTTTTTTTAAATAGATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:12:10,2:169,40:0.0541:2,2:20.5:1:30.4:1:1:1.18:60:24:0.0553:0.009:0.2 0/1:275:12:8,4:201,62:0.0436:2,2:28.1:1:28.2:1:0.49008:1.61781:60:11:0.0404:0.0036:0.4 -13 32893214 . A T 33 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66303;SOR=0.5505;LSEQ=GGGATTTTTTTTTTAAATAG;RSEQ=TTTAGGACCAATAAGTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:218,79:0.01:2,2:13:1:21.3:1:1:1.37816:60:2:0.0071:0:3.3 0/0:362:2:0,2:248,111:0.0055:2,0:1:0:28:0:0.09738:0:60:4:0.0057:0:1 -13 32893514 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49904;SOR=0;LSEQ=ACTACAAACTAGGAATTTAG;RSEQ=CAAACCTGTGTTAAAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:38,132:0.0116:2,2:10:1:28.5:1:0.4031:3.44:60:4:0.0117:0:1 0/0:161:0:0,0:43,118:0:2,0:25.1:1:31.3:1:1:0:60:52.667:1:0:0.1 -13 32893527 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.2207;SOR=Inf;LSEQ=AATTTAGGCAAACCTGTGTT;RSEQ=AAATCTTAGCTCATTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:25,111:0:2,0:24.1:1:30.2:1:1:0:60:272:1:0:0 0/1:121:2:1,1:29,90:0.0165:2,2:35.5:1:32:1:0.43595:3.07:60:4:0.0165:0:1 -13 32893584 . CT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.5082;SOR=0;LSEQ=CAAATCAGTCTCTCTGGCCT;RSEQ=TTTTCCTCACTCGAAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:0,34:0.0556:1,0:8:1:30.5:1:1:0:60:4:0.0571:0.0278:0.5 0/0:25:0:0,0:1,24:0:1,0:26.9:1:30.2:1:1:0:60:50:1:0:0.1 -13 32893791 . A G 74 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTAAACTATATTTCTGCA;RSEQ=GCTATCACAGAGGACAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:22.2:1:32.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32899115 . C G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18754;SOR=Inf;LSEQ=TCCCTATACATTCTCATTCC;RSEQ=AGTATAGAGGAGACTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:104,4:0:1,0:24.6:1:30.4:1:1:0:60:17:1:0:0.1 0/1:83:2:1,1:78,3:0.0241:1,2:7.5:1:28:1:0.09462:22.66097:60:4:0.0241:0:3 -13 32899388 . A C 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0674;LSEQ=TACATATATTTGTTCTATAA;RSEQ=GATGAATCTGATTTTTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:49:3,46:3,51:0.4757:2,2:25.1:1:29.9:1:1:1.11:60:98:0.4757:0:1.2 0/1:158:9:1,8:12,137:0.057:2,2:21.6:1:30.4:1:0.54796:1.42:60:18:0.057:0:1 -13 32899468 . G T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02155;SOR=Inf;LSEQ=TTTAAATAATCTTTTAGGTT;RSEQ=AGTCCTTTAATAGAATAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:0:1,0:22.8:1:32.3:1:1:0:60:46:1:0:0.4 0/1:22:5:0,5:0,17:0.2273:1,0:18.8:1:28.8:1:1:0:60:10:0.2273:0:1 -13 32900149 . T C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08443;LSEQ=TAGTATTCCAACAATTTATA;RSEQ=GAATGAGAATCTTCTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:64:53,11:61,11:0.4638:2,2:21.7:1:31.7:1:0.81817:1.14975:60:63:0.4667:0:1.1 0/1:163:11:10,1:122,30:0.0675:2,2:18.4:1:30.8:1:0.69192:2.45:60:22:0.0692:0:1 -13 32900933 . T A 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02754;SOR=0;LSEQ=GGAATAAATACAAATACATT;RSEQ=AGTGGTAGTCCAGTGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:1,12:0,12:0.52:0,1:28:1:30.3:1:1:0:60:26:0.52:0:1 0/0:6:0:0,0:0,6:0:0,0:31.2:1:28.3:1:1:0:60:12:1:0:0 -13 32902941 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTTATCCAGAAGTCCTAC;RSEQ=CACAGTAAAGTTTGTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29.5:1:1:0:60:4:1:0:1 -13 32903685 . C T 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08322;SOR=0.73325;LSEQ=TGCTAACAATTTTGGAATGC;RSEQ=TTGTTAAATTATTTATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:117:33,84:35,118:0.4317:2,2:22.7:1:30.8:1:0.32586:1.32:60:234:0.4317:0:1.1 0/1:288:103:29,74:64,121:0.3576:2,2:20.9:1:30.3:1:0.29412:1.34828:60:102:0.3579:0:1.1 -13 32905207 . G A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.40908;SOR=3.5011;LSEQ=GAACTACAGGTTTTTTTGTT;RSEQ=TTGTTGTTTTGATTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:1:0,1:87,175:0.0038:2,0:18:0:29:0:1:0:60:2:0.0042:0:1 0/1:380:5:3,2:138,237:0.0132:2,2:11.8:1:23.2:1:0.3645:2.57:60:4:0.0111:0:2.4 -13 32905219 . AT A 155 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.01313;SOR=2.53617;LSEQ=TTTTTGTTGTTGTTGTTTTG;RSEQ=TTTTTTTTTTTGAGGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:9:3,6:46,129:0.0486:2,2:24.4:1:31.7:1:0.7019:1.40:60:18:0.0497:0.0054:0.6 0/1:287:33:9,24:82,162:0.115:2,2:30.1:1:30.8:1:0.55617:1.34839:60:66:0.1154:0.0035:0.4 -13 32905245 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.45079;LSEQ=TTTTTTTGAGGTGGAGTCTT;RSEQ=CTCTGTCACCCGTGATCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:1,0:16,77:0.0106:2,0:1:0:12:0:0.18085:0:60:0:0:0:1 0/1:130:2:1,1:23,105:0.0154:2,2:17:1:28:1:0.33631:4.49:60:4:0.0159:0:1.5 -13 32905265 . G A 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTGTCACCCGTGATCTC;RSEQ=GTTTACCGCAACCTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:68:1,67:0,0:1:0,1:21.1:1:31.1:1:1:0:60:67:1:0:1.3 1/1:81:81:3,78:0,0:1:0,1:22.8:1:30.9:1:1:0:60:39.5:1:0:1.3 -13 32906480 . A C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08861;LSEQ=ACATTGGAAAGTCAATGCCA;RSEQ=ATGTCCTAGAAGATGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:274:134,140:202,195:0.4083:2,2:24.6:1:31.8:1:0.63787:1.08215:60:90.333:0.4081:0:1.1 0/1:730:42:18,24:334,353:0.0575:2,2:25.2:1:31.5:1:0.52625:1.26117:60:84:0.0583:0:1.1 -13 32906729 . A C 230 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTAGATTCAAATGTAGCA;RSEQ=ATCAGAAGCCCTTTGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:805:0:0,0:471,334:0:2,0:24.6:1:29.8:1:1:0:60:60.923:1:0:0.1 0/1:890:166:101,65:411,313:0.1865:2,2:24.1:1:31.2:1:0.38408:1.18:60:165:0.1864:0:1.1 -13 32906980 . A G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.10951;LSEQ=ATTTCTAGCCTACCAAAATC;RSEQ=GAGAAGCCATTAAATGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:118:59,59:109,83:0.3806:2,2:25:1:30.5:1:0.29076:1.31208:60:117:0.3824:0:1.1 0/1:350:22:12,10:172,156:0.0629:2,2:23.3:1:29:1:1:1.09:60:44:0.063:0:1.1 -13 32907420 . GA G 80 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.76656;SOR=1.31154;LSEQ=TGATGAAACATCTTATAAAG;RSEQ=AAAAAAATACCGAAAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:4:2,2:274,219:0.008:2,2:25.8:1:30.5:1:1:1.25057:60:8:0.0081:0.002:0.3 0/1:666:7:4,3:364,293:0.0105:2,2:15.9:1:28.6:1:1:1.07:60:14:0.0106:0.003:0.3 -13 32907535 . CT C 156 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.78612;SOR=1.08105;LSEQ=GCTGATTCAGGTACCTCTGT;RSEQ=TTTTTTTTTTGTAAATAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:27:8,19:97,222:0.0771:2,2:30:1:32.2:1:1:1.03762:60:54:0.0806:0:0 0/1:374:31:10,21:101,237:0.0829:2,2:31.7:1:31.5:1:0.83837:1.12:60:62:0.0864:0:0.2 -13 32907767 . C T 39 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGTTTTATTTTAAGTTC;RSEQ=GGGGTACATGTGCAGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:40:1:25:1:1:0:60:2:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32910056 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGAGACTGTCTCATTCTG;RSEQ=TACCTAGTCTGGAGTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:42.5:1:31.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32910328 . T C 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56858;SOR=0.88579;LSEQ=GTGCCCAAACACTACCTTTT;RSEQ=AACTTAGTGAAAAATATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:85:82,3:126,9:0.3864:2,1:23.1:1:32.1:1:0.37745:1.95:60:170:0.3899:0:1.1 0/1:257:92:81,11:145,20:0.358:2,2:22:1:31.1:1:1:1.02:60:184:0.358:0:1.1 -13 32910351 . G T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10368;LSEQ=CTTAGTGAAAAATATTTAGT;RSEQ=AATGTGATTGATGGTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:182:151,31:174,25:0.4777:2,2:23.3:1:29.9:1:0.24759:1.42752:60:90:0.4787:0:1.1 0/1:440:38:27,11:306,96:0.0864:2,2:22:1:28.8:1:0.55259:1.2978:60:76:0.087:0:1.1 -13 32910721 . T C 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0999;LSEQ=GCATGTCACCCAGTACAACA;RSEQ=TCAAAAGTGGAATACAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1600:676:341,335:463,460:0.4225:2,2:26.9:1:32:1:0.91942:1.01:60:83.5:0.4241:0:1.1 0/1:1866:127:65,62:843,895:0.0681:2,2:24.8:1:31.1:1:0.58195:1.11:60:41.333:0.0673:0:1.1 -13 32911463 . A G 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08802;LSEQ=AAAAAAATAATGATTACATG;RSEQ=ACAAATGGGCAGGACTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1557:692:356,336:472,391:0.4444:2,2:23.4:1:31.2:1:0.21971:1.13924:60:75.889:0.445:0:1.1 0/1:1780:117:62,55:859,801:0.0657:2,2:21.5:1:30.7:1:0.84834:1.05:60:116:0.0661:0:1.2 -13 32911888 . A G 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.2197;LSEQ=GAATTTACTCAGTTTAGAAA;RSEQ=CCAAGCTACATATTGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1580:65:35,30:738,774:0.0411:2,2:25.8:1:32.3:1:0.44919:1.22:60:64:0.041:0:1.2 0/1:1732:317:159,158:705,708:0.183:2,2:24.8:1:32:1:0.95049:1.01:60:316:0.1835:0:1.1 -13 32912299 . T C 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=1.72584;LSEQ=AGTAAATGTCATGATTCTGT;RSEQ=GTTTCAATGTTTAAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1406:129:59,70:609,666:0.0917:2,2:23.8:1:30.6:1:0.7116:1.08481:60:128:0.0918:0:1.1 0/1:1549:230:120,110:632,686:0.1485:2,2:27.1:1:30.4:1:0.25291:1.18:60:56.5:0.1468:0:1.1 -13 32912582 . A C 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TATTTACTGATCAGCACAAC;RSEQ=TATGTCTTAAATTATCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1569:0:0,0:786,782:0:2,0:24.6:1:30.6:1:1:0:60:70.273:0.9994:0:0.2 0/1:1855:54:22,32:914,883:0.0291:2,2:23.9:1:31.2:1:0.16726:1.50527:60:108:0.0294:0:1.1 -13 32912885 . G A 125 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.08569;LSEQ=ATAACTTTTCCTTAAATTCT;RSEQ=AATTACATTCTGACATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1573:21:10,11:763,788:0.0134:2,2:21:1:28.5:1:1:1.06509:60:20:0.0128:0:1.1 0/0:1728:2:1,1:855,869:0.0012:2,2:16:1:27:1:1:1.02:60:4:0.0012:0:1 -13 32913055 . A G 342 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09958;SOR=0.3381;LSEQ=AAGATCAAAGAACCTACTCT;RSEQ=TTGGGTTTTCATACAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1756:1753:864,889:0,0:0.9983:0,2:24.4:1:32.1:1:1:0:60:145.083:0.9983:0:1.1 1/1:1985:1975:929,1046:3,0:0.995:0,2:23.5:1:31.3:1:0.10443:0:60:140.071:0.9954:0:1.1 -13 32913562 . A C 188 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=54.19072;LSEQ=ACTTCATTACTTGAAGCAAA;RSEQ=AAATGGCTTAGAGAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1594:1:1,0:771,822:6e-04:2,0:27:0:13:0:0.48432:0:60:0:0:0:4 0/1:1914:63:32,31:909,939:0.0329:2,2:25.1:1:31.5:1:0.89817:1.07:60:126:0.0331:0:1.2 -13 32915005 . G C 343 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.13525;SOR=0.19919;LSEQ=TTGGTATTAGGAACCAAAGT;RSEQ=TCACTTGTTGAGAACATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1629:1628:789,839:0,0:0.9994:0,2:25.4:1:31.8:1:1:0:60:100.75:0.9994:0:1.1 1/1:1951:1945:988,957:0,0:0.9969:0,2:24.5:1:31.4:1:1:0:60:175.818:0.9969:0:1.1 -13 32915410 . CAATT C 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=3.47959;LSEQ=CAGTAGACTTGGTATGCTAA;RSEQ=AAGAGTGTTATAAACTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1097:54:21,33:368,674:0.0492:2,2:27.1:1:32.2:1:0.66198:1.17:60:108:0.0497:0.0073:0.1 0/1:1159:177:65,112:382,600:0.1527:2,2:24:1:31:1:0.61531:1.09697:60:354:0.1542:0.0233:0.1 -13 32915524 . C A 130 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00042;SOR=4.65365;LSEQ=TTCGTATACAGATTTGATAT;RSEQ=TTGGTATACAGATTCGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:7:0,7:2,140:0.047:1,0:19.6:1:31.3:1:1:0:60:14:0.0476:0:1 0/1:112:21:0,21:1,90:0.1875:1,1:17.5:1:29.8:1:1:0:60:20:0.1835:0:1.1 -13 32915806 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTCAGGAGATCGAGACC;RSEQ=TCCCGGCTAAAACGGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:24:1:33.5:1:1:0:49.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32916789 . A G 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGCTCCTAGGCTGCAAACCT;RSEQ=TACAGCATGTTACTGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:8:0:27:0:1:0:60:2:1:0:0 -13 32918941 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08578;SOR=0.37638;LSEQ=ACCTCTTTATACTCTTAAAA;RSEQ=TTACTGAGGACCTAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:22:0,22:0,30:0.4231:1,1:23.8:1:31.7:1:1:0:60:21:0.42:0:1.6 0/1:28:6:0,6:0,22:0.2143:1,0:35.5:1:33:0:1:0:60:12:0.2143:0:1.7 -13 32918967 . G A 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34993;SOR=0.45134;LSEQ=GAGGACCTAAAAGAGCATTT;RSEQ=TTTATGTGGAATATATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:15:0,15:0,20:0.4286:1,1:20:1:31.4:1:1:0:60:30:0.4286:0:1.9 0/1:16:4:0,4:0,12:0.25:0,0:27.3:1:32:0:1:0:60:8:0.25:0:2 -13 32920844 . T C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAACATTTATTGAGCATC;RSEQ=GTTACATTCACTGAAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:67:66,1:0,0:1:0,1:23.8:1:31.3:1:1:0:60:134:1:0:1 1/1:44:44:44,0:0,0:1:0,1:21:1:30.5:1:1:0:60:43:1:0:1.1 -13 32921098 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50714;SOR=0;LSEQ=AAAGTCTCGTTTTTATAAAT;RSEQ=AACATTTCTAAAAATAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:25,144:0.0117:2,2:33:1:28:1:0.28173:5.67:60:4:0.0118:0:1 0/0:131:0:0,0:19,112:0:2,0:25.4:1:31.2:1:1:0:60:262:1:0:0.1 -13 32921146 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01364;SOR=Inf;LSEQ=GTTAAGAAGTTAACACTTCC;RSEQ=GTTTTATAAAATTTATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:0,68:0:1,0:23.2:1:30:1:1:0:60:136:1:0:0 0/1:52:5:0,5:0,47:0.0962:1,0:15:1:31.4:1:1:0:60:10:0.0962:0:1 -13 32921148 . T TTTTATAAAA 124 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=4.000;MSILEN=1;SSF=0.02724;SOR=0.2755;LSEQ=TAAGAAGTTAACACTTCCCG;RSEQ=TTTATAAAATTTATAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:17:0,17:0,51:0.25:1,1:29.8:1:30.5:1:1:0:60:34:0.25:0.0294:0 0/1:48:4:0,4:0,44:0.0833:1,0:27.5:1:29.7:1:1:0:60:8:0.0851:0.0208:0 -13 32921362 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTTTTATCTCTCCTCTC;RSEQ=AAACCTTTAAAAAAGTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:38:1:32:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32928936 . A G 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=TGAGGGTCTGCAACAAAGGC;RSEQ=TATTCCTAAATATTTATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:339,45:0:2,0:21.8:1:30.4:1:1:0:60:127:1:0:0.1 0/1:361:14:11,3:275,72:0.0388:2,2:23.1:1:30.9:1:1:1.04155:60:28:0.0389:0:1.1 -13 32929232 . A G 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=5.7705;LSEQ=CCACCTTTTAAAACTAAATC;RSEQ=CATTTTCACAGAGTTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1542:72:36,36:723,747:0.0467:2,2:23.8:1:30.9:1:0.90453:1.03:60:71:0.0465:0:1.2 0/1:1892:417:207,210:739,732:0.2204:2,2:23.8:1:30.6:1:0.86783:1.02419:60:138:0.2195:0:1.1 -13 32929387 . T C 341 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31741;SOR=2.3371;LSEQ=AAACAACTCCAATCAAGCAG;RSEQ=AGCTGTAACTTTCACAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1457:1451:712,739:0,0:0.9959:0,2:25.2:1:32.1:1:1:0:60:110.615:0.9965:0:1.2 1/1:1699:1696:857,839:0,2:0.9982:0,2:26.3:1:31.8:1:0.24516:0:60:168.6:0.9982:0:1.1 -13 32929478 . C T 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06881;LSEQ=GCCTTTCAGTTAGATATTTC;RSEQ=GTTGTTAAATAATGTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1177:589:229,360:238,348:0.5004:2,2:26.8:1:30.6:1:0.55157:1.07507:60:146.25:0.5004:0:1.2 0/1:1444:93:38,55:582,766:0.0644:2,2:27.4:1:29.8:1:0.7455:1.09966:60:45.5:0.0634:0:1.2 -13 32930673 . C T 208 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00967;LSEQ=CAGTCTGTATCTTGCAAAAA;RSEQ=ATCCACTCTGCCTCGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:133:64,69:206,235:0.2317:2,2:26.3:1:29.5:1:0.84295:1.06:60:132:0.2316:0:1.1 0/0:690:2:1,1:332,356:0.0029:2,2:15:0:24:1:1:1.07:60:4:0.0029:0:1.5 -13 32930936 . G A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTAGGCCTGCCTCATCCT;RSEQ=CTAAAGTGATCTGTGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:0,18:0,0:1:0,1:27.6:1:28.6:1:1:0:60:8:1:0:1.5 1/1:3:3:0,3:0,0:1:0,0:22.3:1:32:0:1:0:60:6:1:0:1 -13 32931817 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50027;SOR=Inf;LSEQ=GGTTTGTTATAATTGTTTTT;RSEQ=TTGTGTGATACATGTTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:119,13:0:2,0:21.6:1:28.6:1:1:0:60:264:1:0:0.1 0/1:150:2:1,1:130,18:0.0133:2,2:33:1:32:1:0.23803:7.05649:60:4:0.0134:0:1 -13 32936646 . T C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.1632;LSEQ=TTTTTATGATAATATTCTAC;RSEQ=TTTATTTGTTCAGGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:314:285:195,90:19,10:0.9076:2,2:24.4:1:31.2:1:0.83462:1.14:60:70.25:0.9094:0:1.1 1/0:403:248:166,82:97,58:0.6154:2,2:25.6:1:30.4:1:0.39085:1.21:60:40.333:0.6111:0:1.1 -13 32936865 . C T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09986;SOR=0;LSEQ=TTACATTACGTAATCATATA;RSEQ=GGCAGTATGGTTAAGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:81,213:0.0101:2,2:30:1:25.7:1:1:1.31:60:2:0.0068:0:2.3 0/0:342:0:0,0:116,225:0:2,0:24:1:30:1:1:0:60:67.2:0.997:0:0.1 -13 32943782 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAGTGGCACAATCTCGG;RSEQ=TCACTGCACCCTCTGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32944098 . G A 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATTTGCTTTTTGTATTA;RSEQ=CCATAATCATTCTCAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:27.5:1:30:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32944777 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52473;SOR=0;LSEQ=TTGTTTGAGATGGAGTTTCG;RSEQ=TCTCTTGCCCAGGCTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:0,2:9,97:0.0185:2,0:28:1:30:1:1:0:60:4:0.019:0:1 0/0:67:0:0,0:1,66:0:1,0:21.8:1:31.9:1:1:0:60:134:1:0:0 -13 32945021 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49782;SOR=0;LSEQ=ATTACAGATGTGAGCCACTG;RSEQ=GCCTGGCCTGATACAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:92,21:0.0174:2,0:31.5:1:30.5:1:1:0:60:4:0.0174:0:1 0/0:114:0:0,0:98,16:0:2,0:22.9:1:29.9:1:1:0:60:56:1:0:0.1 -13 32945054 . A T 44 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0494;SOR=Inf;LSEQ=ACAATTAACTTGAATGTTAT;RSEQ=TATGTGACTTTTTTGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:177,59:0:2,0:22.7:1:28.7:1:1:0:60:46.2:1:0:0.1 0/1:212:4:1,3:152,56:0.0189:2,2:7:1:22:1:0.06637:8.04905:60:3:0.0143:0:3.3 -13 32945537 . A T 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTATGCCTGGAACTAGG;RSEQ=CCTATTGTGGTGTCAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:29.7:1:26.7:1:1:0:60:6:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32950727 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.10345;SOR=Inf;LSEQ=TTTAAATCTCCCTTCTTTGG;RSEQ=TGTTTTATGCTTGGTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:174,17:0:2,0:26.7:1:30.7:1:1:0:59.8:22.875:1:0:0.2 0/1:170:3:2,1:138,29:0.0176:2,2:26:1:25.3:1:0.44361:2.36392:60:2:0.0119:0:1.7 -13 32953182 . A G 60 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38462;SOR=Inf;LSEQ=TATTTCTCAAAATAATGAGC;RSEQ=TTCAGATATTAGCCATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:30.5:1:30.3:1:1:0:60:8:0.3333:0:1.3 1/1:1:1:1,0:0,0:1:0,0:42:0:32:0:1:0:60:2:1:0:1 -13 32953388 . T C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11814;LSEQ=TTGTCCTGTTTAAAGCCATC;RSEQ=AGTTACAATAGATGGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:311:286:258,28:22,2:0.9196:2,2:24:1:31.2:1:1:1.19316:60:94.333:0.9188:0:1.1 1/0:251:144:129,15:88,19:0.5737:2,2:23.5:1:30.3:1:0.09762:1.85:60:143:0.5743:0:1.1 -13 32953550 . G A 197 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCAGTTGGAAATTAGGAAG;RSEQ=CCATGGAATCTGCTGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1566:0:0,0:766,799:0:2,0:25:1:31.5:1:1:0:60:81.368:0.9994:0:0.1 0/1:1675:107:56,51:798,770:0.0639:2,2:22.4:1:29.3:1:0.84169:1.06:60:106:0.0641:0:1.1 -13 32954022 . C CA 106 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.093;SOR=0.40722;LSEQ=TAACATACAGTTAGCAGCGA;RSEQ=AAAAAAAACTCAGTATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:12:7,5:309,299:0.0194:2,2:14:1:29.8:1:0.77272:1.35:60:24:0.0196:0.0145:0.3 0/0:753:6:4,2:381,363:0.008:2,2:26.8:1:30.7:1:0.68692:1.90:60:12:0.008:0:1.2 -13 32954302 . A AT 78 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.75293;SOR=1.44501;LSEQ=GGTAATGCACAATATAGTTA;RSEQ=TTTTTTTTATTGATTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:4:1,3:85,313:0.0099:2,2:22:1:30:1:1:1.23:60:8:0.0101:0:0 0/1:420:6:2,4:114,299:0.0143:2,2:22.2:1:30.2:1:0.67058:1.31:60:12:0.0145:0.0024:0 -13 32954357 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50814;SOR=0;LSEQ=TTTAAAATCTCTTATGATTA;RSEQ=TTGGAGCTACCAGTTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:6,128:0.0147:1,2:28:1:31:1:0.10065:19.83:60:4:0.0147:0:1 0/0:102:0:0,0:5,97:0:1,0:22.4:1:31.3:1:1:0:60:101:1:0:0 -13 32954561 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTTTTCTTACTATTTCT;RSEQ=GTGTATGTGTTTATCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:23:1:29:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:0,1:0:0,0:23:0:31:0:1:0:60:2:1:0:0 -13 32968591 . G A 73 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAATGTGTGCGTATACCT;RSEQ=CTTCCACATGACCTCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:36:1:28.5:1:1:0:60:12:0.75:0:2 1/1:1:1:1,0:0,0:1:0,0:27:0:30:0:1:0:60:2:1:0:2 -13 32968607 . A G 78 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.37796;LSEQ=ACCTGCTTCCACATGACCTC;RSEQ=GTAAAAGAATGTGTTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:39:1:30.2:1:1:0:60:12:0.75:0:2 1/0:2:1:1,0:1,0:0.5:0,0:43:0:30:0:1:0:60:2:0.5:0:2 -13 32968790 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49937;SOR=Inf;LSEQ=TTAAAATTCATCTAACACAT;RSEQ=TATAATAACATTCTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:145,22:0:2,0:24.5:1:31.1:1:1:0:60:82.5:1:0:0.1 0/1:181:2:1,1:149,30:0.011:2,2:30:1:29:1:0.314:4.90237:60:4:0.0112:0:1.5 -13 32968793 . T C 134 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATTCATCTAACACATCTA;RSEQ=AATAACATTCTTTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:18:13,5:137,28:0.0984:2,2:22.9:1:32.3:1:0.32836:1.87439:60:36:0.0994:0:1.1 0/0:205:0:0,0:166,39:0:2,0:23:1:29.1:1:1:0:60:101.5:1:0:0.2 -13 32969137 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=TTTGACAGTCCAGTATCAAG;RSEQ=AAATAGCTTTTATACAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:5,157:0:1,0:25.3:1:31.5:1:1:0:60:324:1:0:0 0/1:164:2:1,1:14,148:0.0122:2,2:30:1:27.5:1:0.17507:10.25:60:4:0.0122:0:1 -13 32969248 . A G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83701;LSEQ=GGAATGGGGAAATGACAGCA;RSEQ=CTAGAAAGAGAAGAATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:0.1304:1,0:22:1:33:0:1:0:60:6:0.1304:0:1 0/1:18:2:0,2:0,16:0.1111:1,0:29:1:34:0:1:0:60:4:0.1111:0:1 -13 32970736 . G C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAGCCCCAATCTTCCA;RSEQ=CTTCAATCCAGATCATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:38:1:32.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 32970928 . C CT 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.51472;SOR=0;LSEQ=CACATTTAGGGTTTTTCATT;RSEQ=TTTTTTGGTCCAAACTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:2,0:60,2:0.0313:1,0:27:1:33.5:1:1:0:60:4:0.0328:0:0 0/0:43:0:0,0:43,0:0:1,0:22.6:1:31.5:1:1:0:60:86:1:0:0.3 -13 32970980 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21126;SOR=Inf;LSEQ=TAAAGGAAATACTTTTGGAA;RSEQ=CATAAATATGTGGGTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:140,24:0:2,0:24.1:1:30.4:1:1:0:60:328:1:0:0.1 0/1:140:2:1,1:109,29:0.0143:2,2:16.5:1:30.5:1:0.38386:3.71257:60:4:0.0144:0:1 -13 32971425 . T C 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTGAAAAGTGTTTTTTG;RSEQ=CATTTATTTCACTGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:18.7:1:31:1:1:0:60:12:1:0:1 1/1:4:4:0,4:0,0:1:0,0:30.5:1:32.8:1:1:0:60:8:1:0:1 -13 32972745 . C GAATTATATCT 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=Inf;LSEQ=GAAAAACAATTTATATCTGT;RSEQ=AGTGAATCCACTAGGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:0:0,0:256,254:0:2,0:23.6:1:29.7:1:1:0:60:101:1:0:0.1 0/1:622:25:14,11:305,290:0.0402:2,2:25.3:1:30:1:0.68716:1.21:59.8:50:0.0408:0.0161:0.9 -13 32972914 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16455;SOR=0;LSEQ=AAAAATATATCTAAGCATTT;RSEQ=CAAAGGCGACAATAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:53,125:0.0111:2,2:45.5:1:29.5:1:0.51117:2.35:60:4:0.0113:0:1.5 0/0:263:0:0,0:86,177:0:2,0:23.9:1:31.8:1:1:0:60:86.667:1:0:0.1 -13 32973012 . A C 100 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02681;SOR=4.74152;LSEQ=TACTTATGTTGCACAATGAG;RSEQ=AAAGAAATTAGTTTCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:0,3:0,34:0.0811:1,0:23:1:33.3:1:1:0:60:6:0.0811:0:2 0/1:30:9:0,9:0,21:0.3:1,0:33.7:1:31.7:1:1:0:60:18:0.3:0:1 -13 33833810 . C T 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.21952;LSEQ=AGGAAATCGCCAAAAAGTGA;RSEQ=AATACGCTTGCTTGAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:566:180:79,101:176,210:0.318:2,2:26:1:29.5:1:0.7176:1.07133:60:360:0.3214:0:1.1 1/0:627:319:140,179:146,162:0.5088:2,2:26.1:1:28.8:1:0.3792:1.15203:60:105.333:0.5089:0:1.1 -13 33834013 . G C 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54972;SOR=0;LSEQ=AATTCCCACATGTCATGGGA;RSEQ=GGACCTGCTACTCAGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:0,4:0,20:0.1667:1,0:24.3:1:28.8:1:1:0:60:8:0.1667:0:1.5 0/0:8:0:0,0:0,8:0:0,0:7:0:11:0:1:0:60:0:0:0:4 -13 34298817 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTGCATCTTTGCTGTGG;RSEQ=GCAAGCTAAAAATTTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 34298900 . A G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGACATATTTGCTAAACA;RSEQ=ATATGTCAAATGTCTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:22.5:1:30.5:1:1:0:60:4:0.4:0:2 0/0:1:0:0,0:1,0:0:0,0:21:0:32:0:1:0:60:2:1:0:1 -13 34298947 . A C 58 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAAAGAACATGACTAATT;RSEQ=AGGAAGATTATTTCCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:32.8:1:29:1:1:0:60:3:0.75:0:1 1/1:2:2:2,0:0,0:1:0,0:19:1:30:1:1:0:60:4:1:0:1 -13 34299233 . A G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.58782;LSEQ=AAGTTTATTTGCCATTGTTC;RSEQ=CCCAGTCTTTAGCACGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:84:37,47:151,183:0.201:2,2:27.1:1:30.4:1:0.9026:1.04804:60:27:0.198:0:1.1 1/0:470:252:115,137:104,114:0.5362:2,2:26.1:1:30.5:1:0.71083:1.08661:60:83:0.5343:0:1.1 -13 34299330 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.65991;LSEQ=TATGTCTTAGTTCCTCATGT;RSEQ=CTTTCTTGTGGAAGGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:13,95:0.0182:2,2:25.5:1:28.5:1:0.23937:7.08:60:4:0.0185:0:1 0/1:83:1:0,1:12,70:0.012:2,0:11:0:29:0:1:0:60:2:0.0122:0:1 -13 34348208 . A G 68 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACATCTAATTTGCTTCTAA;RSEQ=ATGCAAGATTGAATAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:37:1:34.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 34348415 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.49669;SOR=Inf;LSEQ=CCAGGCAAGCATGCCCCTAG;RSEQ=ATAGGAGAGGCCACATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:58,7:0:2,0:26.2:1:31.4:1:1:0:60:130:1:0:0 0/1:69:2:1,1:65,2:0.029:1,2:17.5:1:29.5:1:0.08568:26.73959:60:4:0.0299:0:1 -13 34348532 . A G 254 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCAATGGGGTAAGTTGGGAA;RSEQ=AGGACGCTCTCTACTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:261:261:124,137:0,0:1:0,2:27:1:31.7:1:1:0:60:260:1:0:1.2 0/1:408:180:89,91:113,114:0.4412:2,2:26.5:1:31.2:1:1:1.01347:60:89:0.4406:0:1.3 -13 34348548 . T A 45 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15349;SOR=Inf;LSEQ=GGAAAAGGACGCTCTCTACT;RSEQ=TCAGGATCCTATGGTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:120,140:0:2,0:24.3:1:29.9:1:1:0:60:85.667:1:0:1.2 0/1:390:4:3,1:177,209:0.0103:2,2:12.8:1:22.5:1:0.339:3.53:60:3:0.0079:0:2 -13 34348601 . T C 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAAGGCTCCCAGAGGTGC;RSEQ=GCTTGCTTGCTGATATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:45,100:0:2,0:26.4:1:30.5:1:1:0:60:290:1:0:1.2 0/1:200:49:18,31:45,106:0.245:2,2:22.6:1:29.3:1:0.38014:1.37:60:98:0.2462:0:1.8 -13 34348610 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.16742;SOR=0;LSEQ=CCCAGAGGTGCTGCTTGCTT;RSEQ=CTGATATACAACCTGCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:30,89:0.0165:2,2:14.5:1:28.5:1:0.44835:2.93:60:4:0.0167:0:3 0/0:174:0:0,0:50,124:0:2,0:22.8:1:31.8:1:1:0:60:86:1:0:1.4 -13 34348618 . A C 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGCTTGCTTGCTGATAT;RSEQ=CAACCTGCTTGTCACTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:115:115:26,89:0,0:1:0,2:23.5:1:31:1:1:0:60:114:1:0:1.3 1/1:153:153:38,115:0,0:1:0,2:21.9:1:31:1:1:0:60:75.5:1:0:1.4 -13 34348632 . A T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19633;SOR=0;LSEQ=TGATATACAACCTGCTTGTC;RSEQ=CTGGGCTTGGTTGGAAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:16,74:0.0217:2,2:5:0:29.5:1:0.33708:4.52:60:4:0.022:0:1 0/0:115:0:0,0:18,97:0:2,0:22.3:1:29.2:1:1:0:60:37.333:1:0:1.2 -13 34348725 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08098;SOR=Inf;LSEQ=AGAAACTGCCAATAAAAATA;RSEQ=TAACAGCAGGCTGGGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:0:1,0:19.8:1:31.9:1:1:0:58.8:34:1:0:1.2 0/1:14:3:0,3:0,11:0.2143:0,0:7.7:1:30.7:1:1:0:60:6:0.2308:0:1 -13 34348737 . T C 100 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02288;SOR=0;LSEQ=TAAAAATAATAACAGCAGGC;RSEQ=GGGCGCGGTGGCTCACGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:21:1:30.3:1:1:0:58:20:1:0:2 1/0:8:4:0,4:0,3:0.5:0,0:19:1:24.3:1:1:0:60:3:0.5:0:1.8 -13 34348744 . G A 97 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05495;SOR=0;LSEQ=AATAACAGCAGGCTGGGCGC;RSEQ=GTGGCTCACGCCTGTAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:20.3:1:32.4:1:1:0:57.5:16:1:0:2.3 1/0:6:3:0,3:0,3:0.5:0,0:17.3:1:31:1:1:0:60:6:0.6:0:2 -13 35153749 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53846;SOR=Inf;LSEQ=TTAGCATGATCCATCCACAA;RSEQ=CCAAGGAATGCCAAAGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:23.7:1:32.1:1:1:0:60:36:1:0:0.2 0/1:34:2:1,1:17,15:0.0588:2,2:32.5:1:28:1:1:1.12916:60:4:0.0588:0:1 -13 35153868 . G A 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTACCAATGTCTTGTTTTC;RSEQ=GATTTCCAGCCTCCAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,1:0.5:0,0:16:1:32.5:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:1:0,0:10:0:33:0:1:0:60:2:1:0:2 -13 35155046 . A G 24 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTAGAATGGTAGGGATC;RSEQ=GAGGGAGTCACTTCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:24.5:1:1:0:60:4:1:0:1.5 -13 35516626 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=Inf;LSEQ=CGCGGGGGGCGGGCCGGGCC;RSEQ=GACAGACCGGGAGAGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:0:2,0:20.2:1:30.1:1:1:0:60:20:1:0:0.1 0/1:12:2:1,1:6,4:0.1667:2,2:30:0:29.5:1:1:1.4491:60:4:0.1667:0:1 -13 41032399 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49913;SOR=Inf;LSEQ=TGTAGGGGGGAAGAAGGTTG;RSEQ=TGGTGTCCTTGCTCACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:94,49:0:2,0:21.6:1:31.2:1:1:0:60:142:1:0:0.8 0/1:155:2:1,1:96,57:0.0129:2,2:22.5:1:27:1:1:1.67823:60:4:0.0131:0:2.5 -13 41032426 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2185;SOR=0;LSEQ=CCTTGCTCACTGGGACAGTC;RSEQ=CCCAGGGGACACGAGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:91,69:0.0123:2,2:21:1:29.5:1:1:1.31655:60:4:0.0125:0:1 0/0:184:0:0,0:101,82:0:2,0:27.1:1:30.2:1:1:0:60:60:1:0:0.4 -13 41032432 . G C 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCACTGGGACAGTCGCCCAG;RSEQ=GGACACGAGACATATACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:56:31,25:61,52:0.3294:2,2:31.9:1:30.8:1:1:1.06:60:55:0.3293:0:2 0/0:191:0:0,0:101,89:0:2,0:27.3:1:29.9:1:1:0:60:46.5:0.9947:0:0.4 -13 41032438 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20508;SOR=0;LSEQ=GGACAGTCGCCCAGGGGACA;RSEQ=GAGACATATACAGCCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:93,75:0.0117:2,2:45:1:30.5:1:1:1.23841:60:4:0.0118:0:3 0/0:206:0:0,0:107,99:0:2,0:26:1:29.7:1:1:0:60:50.5:1:0:0.5 -13 41032459 . C T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.35825;LSEQ=GAGACATATACAGCCAGTCT;RSEQ=CTTGTGCCTACCAGGGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:179:117:54,63:34,27:0.6536:2,2:26.1:1:30:1:0.26945:1.46592:60:234:0.661:0:1.6 0/1:221:89:45,44:60,72:0.4027:2,2:22.4:1:28.6:1:0.49371:1.23:60:28.667:0.3963:0:1.1 -13 41032473 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20508;SOR=0;LSEQ=CAGTCTCCTTGTGCCTACCA;RSEQ=GGTCTGGCAGCCCATTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:76,93:0.0117:2,2:27:1:32:1:1:1.22:60:4:0.012:0:3 0/0:206:0:0,0:88,118:0:2,0:25.6:1:30.5:1:1:0:60:67.667:1:0:0.5 -13 41032524 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24463;SOR=Inf;LSEQ=CCCAGCAAATTAGGGGTTGG;RSEQ=TAAGCAGCTGTGGAGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:33,84:0:2,0:23.6:1:31.5:1:1:0:60:116:1:0:0.5 0/1:115:2:1,1:33,80:0.0174:2,2:39.5:1:30.5:1:0.50572:2.40:60:4:0.0174:0:1.5 -13 41032536 . G T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49724;SOR=0;LSEQ=GGGGTTGGGTAAGCAGCTGT;RSEQ=GAGCCTTTTACTTCAGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:17,71:0.0222:2,2:14:0:28:1:0.3618:4.09:60:4:0.0227:0:2 0/0:88:0:0,0:23,64:0:2,0:24:1:30.5:1:1:0:60:42.5:1:0:0.4 -13 41032542 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49761;SOR=0;LSEQ=GGGTAAGCAGCTGTGGAGCC;RSEQ=TTTACTTCAGGGATCTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:0,2:17,66:0.0235:2,0:38.5:1:32:1:1:0:60:4:0.0244:0:1 0/0:79:0:0,0:18,61:0:2,0:22.2:1:30.4:1:1:0:60:78:1:0:0.3 -13 41032620 . GCA G 87 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=1;SOR=0.87141;LSEQ=ACATGAGCACGTGCACGCAT;RSEQ=CACACACACACACACACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:1,5:0,12:0.3158:0,2:29.8:1:33.7:1:0.33333:0:60:12:0.3158:0:0 0/1:7:2:0,2:0,3:0.2857:0,0:42:1:33:0:1:0:60:4:0.3333:0:0 -13 41133502 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52068;SOR=0;LSEQ=AAAACTGTAAGCTGCAAAAA;RSEQ=GACAGAGAATGAATGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:93,0:0.0211:1,2:6:0:32.5:1:0.02105:0:60:4:0.0213:0:1 0/0:61:0:0,0:58,3:0:1,0:23.9:1:31.8:1:1:0:60:60:1:0:0.1 -13 41161770 . G A 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12884;SOR=0;LSEQ=TCCATCTATACCTAAAGCAC;RSEQ=GCTCAAGTGCTTGGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:10,1:14,0:0.44:1,2:23.6:1:29.7:1:0.44:0:60:22:0.44:0:1.6 0/0:5:0:0,0:5,0:0:0,0:25.8:1:31.4:1:1:0:60:10:1:0:0 -13 41161979 . C G 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGTGTTCACAGTAGCCTCT;RSEQ=CCCACCTTTTAAAAGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1029:68:48,20:647,313:0.0661:2,2:26.9:1:31.8:1:0.68778:1.16:60:67:0.0654:0:1.1 0/0:1138:0:0,0:712,426:0:2,0:25.4:1:30.6:1:1:0:60:102.455:1:0:0.2 -13 41162086 . G A 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTAAGGCCTTTCATGTGAAA;RSEQ=AGAGTCAATGCACTAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1623:0:0,0:747,874:0:2,0:24.2:1:31.7:1:1:0:60:123.692:0.9988:0:0.1 0/1:1802:64:31,33:813,925:0.0355:2,2:21.4:1:29.9:1:0.80015:1.07:60:128:0.0358:0:1.2 -13 41162225 . C T 147 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=80.91724;LSEQ=AGCCCAGGATAGAAAGGATT;RSEQ=AATTCAATTAACAGAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:1:0,1:3,187:0.0052:1,0:38:0:30:0:1:0:60:2:0.0053:0:1 0/1:123:37:1,36:1,85:0.3008:1,1:20.1:1:28.4:1:0.51286:2.34:60:74:0.3008:0:1 -13 41183050 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGATGGATCCTAGAGAT;RSEQ=GGTGGGAAGGGGGTACGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:32:0:1:0:60:4:1:0:1.5 -13 41185309 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.21528;LSEQ=ATATATTCTCAGAACAATGA;RSEQ=TTTTGTTCTACCCTGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:343:249:46,203:12,82:0.7259:2,2:23.1:1:30.8:1:0.25866:1.55:60:248:0.7273:0:1.1 0/1:353:128:32,96:48,177:0.3626:2,2:24.3:1:29.4:1:0.43088:1.23:60:41.667:0.3592:0:1.1 -13 41218947 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07272;SOR=0;LSEQ=TCCTTTTACTAATGTTAAGA;RSEQ=ACTTCTCCATCCAGTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:3:2,1:236,50:0.0104:2,2:15.7:1:24:1:0.44273:2.35109:60:2:0.007:0:1 0/0:402:0:0,0:320,82:0:2,0:21.4:1:31.9:1:1:0:60:401:1:0:0.1 -13 41219125 . G A 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=64.46334;LSEQ=ACTAAACCAGACTACTGCTG;RSEQ=CGACAGAGTCGAGACAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:1:1,0:268,426:0.0014:2,0:1:0:26:0:0.38705:0:60:2:0.0015:0:1 0/1:905:77:28,49:325,502:0.0851:2,2:26.7:1:29.2:1:0.71429:1.13278:60:76:0.085:0:1 -13 41239549 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16198;SOR=Inf;LSEQ=CGCGCACGCACACCTACTGC;RSEQ=GTCCCCGACCGGACCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:70,2:0:1,0:21.8:1:30.6:1:1:0:60:35:1:0:0.2 0/1:49:2:1,1:47,0:0.0408:1,2:10.5:1:31:1:0.04082:0:60:4:0.0408:0:1 -13 41239928 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19844;SOR=0;LSEQ=GCCCCGCGAGCGGCCCAGCG;RSEQ=CGGCGGGGGGCACCGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:32,136:0.0118:2,2:12.5:1:27.5:1:0.35148:4.20:60:4:0.0122:0:1 0/0:211:0:0,0:60,148:0:2,0:14.6:1:31.7:1:1:0:60:68.333:0.9856:0:0.3 -13 41239932 . CG C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1.52175;LSEQ=CGCGAGCGGCCCAGCGGCGG;RSEQ=GGGGGCACCGGCGGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:1:0,1:21,104:0.0078:2,0:10:0:32:0:1:0:60:2:0.0078:0:0 0/1:170:2:1,1:44,123:0.0118:2,2:28.5:1:32:1:0.46281:2.78:60:4:0.012:0:0.5 -13 41239943 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50693;SOR=Inf;LSEQ=CAGCGGCGGCGGGGGGCACC;RSEQ=GCGGGTGCTGCGACAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:13,56:0:2,0:11.4:1:30.9:1:1:0:60:33.5:0.9853:0:0.2 0/1:93:2:1,1:27,63:0.0215:2,2:11.5:1:29.5:1:0.51839:2.31:60:4:0.022:0:1.5 -13 41240087 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19905;SOR=0;LSEQ=CCACCGCCGCCGCCACGGAG;RSEQ=CGGGCGCCTGCGGGAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:61,39:0.0196:2,2:34.5:1:31.5:1:1:1.55699:60:4:0.0198:0:1.5 0/0:126:0:0,0:76,50:0:2,0:15.8:1:31.3:1:1:0:59.9:62:1:0:0.3 -13 41240157 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58048;SOR=0.37821;LSEQ=CATGAAGTCGGCGCTGACAG;RSEQ=GGCAGCCGAGGCCGAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:78,88:0.0119:2,2:33.5:1:31.5:1:1:1.13:60:4:0.0121:0:1.5 0/0:221:1:0,1:107,112:0.0045:2,0:1:0:30:0:1:0:60:2:0.0046:0:1 -13 41240180 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51503;SOR=Inf;LSEQ=CAGCCGAGGCCGAGGGCAGG;RSEQ=CCGCCGCGGCGTCGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:61,67:0:2,0:17.9:1:31.5:1:1:0:60:41.667:1:0:0.2 0/1:185:2:1,1:84,99:0.0108:2,2:24:0:31.5:1:1:1.18:60:4:0.0111:0:2.5 -13 41240375 . G A 83 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2377;SOR=2.32631;LSEQ=CCCCCGCCCCTCCCCCAGCC;RSEQ=CAGGAGAGCCAAGAGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:3:2,1:257,409:0.0045:2,2:3:1:20.7:1:0.56288:3.18:60:0.5:0.0015:0:1 0/1:771:8:4,4:324,439:0.0104:2,2:24.8:1:27.9:1:0.72873:1.35:60:7:0.0093:0:1.3 -13 41240379 . G A 154 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=45.39553;LSEQ=CGCCCCTCCCCCAGCCGCAG;RSEQ=AGAGCCAAGAGGGGGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:645:1:1,0:234,408:0.0016:2,0:1:0:26:0:0.36547:0:60:2:0.0016:0:1 0/1:728:48:22,26:273,407:0.0659:2,2:23.6:1:27.7:1:0.45022:1.26:60:15:0.0629:0:1.1 -13 41240855 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCGCGGCCAATGGGCATG;RSEQ=GGCACCGCCGCCCGGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:27:1:1:0:60:4:1:0:2.5 -13 41240899 . G T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCGCCGGGCTGGGTGGG;RSEQ=CCCGGTTTTCCACGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:1:27.5:1:1:0:60:4:1:0:2.5 -13 41862213 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23009;SOR=0;LSEQ=GCAAGACTCACAAGGGAGAA;RSEQ=CATATTAAAAATATGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:0,2:81,65:0.0135:2,0:19.5:1:28.5:1:0.20325:0:60:4:0.0139:0:1 0/0:160:0:0,0:87,73:0:2,0:19.3:1:31.7:1:1:0:60:39:1:0:0.1 -13 41862285 . T A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.86717;SOR=1.07899;LSEQ=AATCTTCTTGTCCAGATGTA;RSEQ=CCCATAAGCCCAGATTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:17:8,9:113,115:0.0694:2,2:28.1:1:30.4:1:1:1.10498:60:34:0.0717:0:1.1 0/1:282:21:10,11:134,126:0.0745:2,2:30:1:29.9:1:0.822:1.16919:60:42:0.0755:0:1.1 -13 41862317 . T C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00774;SOR=Inf;LSEQ=AGATTCACTGGCTTTCCATC;RSEQ=ACCTTAACATTGGCAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:74,123:0:2,0:26.6:1:28.9:1:1:0:60:31.833:1:0:0.1 0/1:216:8:4,4:90,118:0.037:2,2:26.1:1:31.5:1:0.73043:1.31:60:16:0.0374:0:1 -13 41862325 . C A 28 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.84642;LSEQ=TGGCTTTCCATCTACCTTAA;RSEQ=ATTGGCAGCAGAATAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:1:1,0:67,117:0.0054:2,0:1:0:27:0:0.36757:0:60:2:0.0055:0:1 0/1:201:2:1,1:84,115:0.01:2,2:10:0:28.5:1:1:1.37:60:4:0.0101:0:1 -13 41862553 . C G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60839;SOR=0.46982;LSEQ=AGGTGCATGGCTGCAGGTGG;RSEQ=AGGGGATGGGGTGCCAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:39:1:32.3:1:1:0:60:12:0.75:0:1 1/0:7:4:0,4:0,3:0.5714:0,0:19:1:31:1:1:0:60:8:0.5714:0:1.3 -13 42178299 . C T 45 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43766;SOR=0.46715;LSEQ=CCCTGAAGCTCAGAGCCAAC;RSEQ=TGGCAGTGTCCTGGTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:4:0,4:152,127:0.0141:2,0:10.3:1:22.8:1:0.04478:0:60:3:0.0108:0:2.5 0/0:301:2:0,2:163,136:0.0066:2,0:18:1:19.5:1:0.20937:0:60:1:0.0034:0:2 -13 42178332 . A C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=8.92624;LSEQ=GGTGCTCTCAATGTCCAGGG;RSEQ=AAGGAACACTTGTCAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:28:12,16:129,166:0.0864:2,2:27.5:1:32.3:1:1:1.03604:60:56:0.0889:0:1.1 0/1:303:139:65,74:79,84:0.4587:2,2:26.1:1:31.7:1:0.81748:1.07045:60:138:0.457:0:1.1 -13 42178403 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23395;SOR=Inf;LSEQ=TATCATGTTGTTCACATATA;RSEQ=TTTATATAAAATCTTATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:53,129:0:2,0:22.9:1:31.8:1:1:0:60:90:1:0:0.2 0/1:171:2:1,1:53,115:0.0117:2,2:20:1:28:1:0.53568:2.16:60:4:0.0118:0:1.5 -13 42178450 . A AT 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.25234;SOR=0;LSEQ=TCCTAAATAACTGCATATAG;RSEQ=TTTTTTTTAAAGTACATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:0,3:5,52:0.05:2,0:30.7:1:29.7:1:1:0:60:6:0.0508:0:0 0/0:48:0:0,0:5,43:0:2,0:21.5:1:30.4:1:1:0:60:47:1:0:0 -13 42830030 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24935;SOR=Inf;LSEQ=GAAGGTTGCTGCAAAATTGG;RSEQ=TGCACGTACAGGCTTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:217,41:0:2,0:25.1:1:32.1:1:1:0:59.9:128:1:0:0.1 0/1:275:3:1,2:201,71:0.0109:2,2:17:1:27.7:1:0.17298:5.61898:60:6:0.0109:0:1 -13 42830686 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49825;SOR=0;LSEQ=AGTGATTTAAGTAAATTTAT;RSEQ=ATGAAAATAAACGTGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:20,110:0.0152:2,2:18.5:1:31:1:0.29389:5.39:60:4:0.0153:0:1 0/0:127:0:0,0:25,102:0:2,0:24.2:1:29.8:1:1:0:60:126:1:0:0 -13 43549586 . C T 26 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGATTAGTTCTTTCATCAG;RSEQ=ACAACTCATTGCCTCTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:26:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:45:0:30:0:1:0:60:2:1:0:1 -13 43549782 . G A 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67662;SOR=0.51406;LSEQ=AAAAGTGCTGCTTCTTTCAG;RSEQ=TGGAGGTAATCCCACACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:21.3:1:30.7:1:1:0:60:12:0.4286:0:1 0/1:11:3:3,0:8,0:0.2727:0,0:19.3:1:29.7:1:1:0:60:6:0.2727:0:1 -13 43549921 . AAC A 99 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.01652;SOR=0.17541;LSEQ=ATGATGTATTTCTTCACTTA;RSEQ=ACACACACACACATAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:10:6,4:168,76:0.0394:2,2:16.3:1:30:1:0.51213:1.47132:59.5:20:0.0397:0.0157:0.2 0/0:281:2:0,2:183,90:0.0071:2,0:23:1:32:0:0.11111:0:60:4:0.0071:0:0 -13 43549923 . C A 38 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.25076;SOR=Inf;LSEQ=GATGTATTTCTTCACTTAAA;RSEQ=ACACACACACACATAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:173,77:0:2,0:23.3:1:31.6:1:1:0:59.9:82.333:1:0:0.1 0/1:286:3:2,1:185,91:0.0105:2,2:32.7:1:24:1:1:1.01643:60:2:0.0072:0:1.7 -13 43549952 . C CA 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01606;SOR=1.48897;LSEQ=ACACATAAGTAAAAGCCACA;RSEQ=AAAAAAAAGTTAGCAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:81:44,37:167,98:0.2334:2,2:30:1:29:1:0.19297:1.43141:60:26:0.2308:0.0144:0.4 0/1:439:137:81,56:170,123:0.3121:2,2:29.9:1:30.1:1:0.83464:1.05:60:136:0.3134:0:0.4 -13 43550021 . A G 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00012;SOR=1.81216;LSEQ=TATGAAGTACAATATTGTAG;RSEQ=GACTCACCATCTTTAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:343:194:87,107:64,84:0.5656:2,2:26.8:1:30.7:1:0.82619:1.07:60:47.5:0.5621:0:1.1 1/0:400:281:130,151:48,71:0.7025:2,2:25.5:1:29.8:1:0.32205:1.27:60:45.833:0.7033:0:1.1 -13 43550043 . CA C 75 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.10611;SOR=0.1776;LSEQ=ACTCACCATCTTTAAGAGGC;RSEQ=AAAACCAATGATGGGACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:5:2,3:112,191:0.0162:2,2:30:1:32.5:1:1:1.14:60:10:0.0164:0.0032:0.8 0/0:343:1:0,1:125,217:0.0029:2,0:50:0:29:0:1:0:60:2:0.0029:0:0 -13 43550089 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49855;SOR=0;LSEQ=GAGATGGAGACCAACTGGTA;RSEQ=GTATACTTACAAAATGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:41,130:0.0116:2,2:16:0:32.5:1:0.42768:3.14:60:4:0.0117:0:1.5 0/0:172:0:0,0:39,133:0:2,0:24.6:1:30.5:1:1:0:60:171:1:0:0.6 -13 43550139 . C A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11877;SOR=2.21108;LSEQ=TCCTCAGTAAAAATAACTGT;RSEQ=AGAAATTCATATTTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:36:1,35:0,19:0.6545:1,1:25.8:1:30.8:1:1:0:60:72:0.6545:0:1 1/1:47:38:1,37:0,9:0.8085:0,1:22.6:1:30.4:1:1:0:60:76:0.8085:0:1.1 -13 43550243 . A G 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26316;SOR=0;LSEQ=ACTGTTTCACAGACACTGGC;RSEQ=GAAGACATGAAATTCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:0,7:0,9:0.4375:0,0:29.3:1:31.1:1:1:0:60:14:0.4375:0:2 0/0:3:0:0,0:1,2:0:2,0:18:1:31.7:1:1:0:60:6:1:0:0 -13 43550270 . T A 102 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAAATTCCTGGATCAGAG;RSEQ=CAAAGACTTTATTACTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:26.2:1:31:1:1:0:60:20:1:0:1.9 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 43603669 . CT C 89 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.81998;LSEQ=TTTGTAAACAATTTTGGTGC;RSEQ=TTTTTTTTTTCCCCAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:6,1:20,0:0.2593:1,2:23.7:1:31.8:1:0.25926:0:60:14:0.2593:0.0741:0 0/1:18:4:4,0:14,0:0.2222:1,0:26.3:1:30.9:1:1:0:60:8:0.2222:0.0556:0 -13 43603680 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17857;SOR=Inf;LSEQ=TTTTGGTGCCTTTTTTTTTT;RSEQ=CCCCAGCTGTAGCAGCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:27,1:0:1,0:28.1:1:30.5:1:1:0:60:27:1:0:0.5 0/1:21:2:2,0:19,0:0.0952:1,0:42.5:1:31:1:1:0:60:4:0.0952:0:1 -13 43603871 . C T 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.67016;LSEQ=GACATGGCCCATTTGTTGAT;RSEQ=TGCTGGCATTATTTAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:46:16,30:103,141:0.1586:2,2:23.9:1:29.1:1:0.41486:1.36822:60:14.333:0.153:0:1.3 0/1:364:122:50,72:101,140:0.3352:2,2:24.9:1:29.8:1:0.91046:1.03876:60:121:0.338:0:1.1 -13 43603878 . C A 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07141;SOR=Inf;LSEQ=CCCATTTGTTGATCTGCTGG;RSEQ=ATTATTTAAATAATGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:103,161:0:2,0:24.2:1:31.8:1:1:0:60:43:1:0:0.3 0/1:340:5:4,1:129,206:0.0147:2,2:24.6:1:27.2:1:0.07889:6.35:60:10:0.0148:0:1.2 -13 43604158 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAGATAAATGAGACTAT;RSEQ=CCTCTTTGACTTTTGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:35:1:29.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 46174403 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07;SOR=Inf;LSEQ=CAATTGAAGAGTGGTGACAA;RSEQ=AATTCTTTGCTTGACCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:22.4:1:31.7:1:1:0:60:36:1:0:0.1 0/1:7:2:1,1:4,1:0.2857:2,2:12.5:1:28.5:1:1:3.1622:60:4:0.2857:0:1 -13 46174493 . A AT 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=GTAAAATCCAGTTTCATTTT;RSEQ=TTTTTTTTTTATTTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:4,15:0.0952:2,2:45.5:1:30:1:0.42857:3.46:60:4:0.0952:0:1 0/0:21:0:0,0:10,11:0:2,0:25.3:1:28.1:1:1:0:60:42:1:0:0 -13 46407969 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.20715;SOR=0;LSEQ=GCATGGCGATGACTCACCCT;RSEQ=GCCTTCTTGCCCACAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:45,22:0.029:2,2:33.5:1:31:1:1:2.02266:60:4:0.0294:0:1 0/0:82:0:0,0:52,30:0:2,0:24:1:30.5:1:1:0:60:19.5:1:0:0.4 -13 46408024 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19735;SOR=0;LSEQ=GAAGAGCTCAGCCAGGCTTT;RSEQ=AACAATCAATCAGGAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:64,60:0.0159:2,2:25.5:1:28:1:1:1.06615:60:4:0.0161:0:1 0/0:157:0:0,0:80,77:0:2,0:23.7:1:28.6:1:1:0:60:77.5:1:0:1.1 -13 46408037 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=18.73136;LSEQ=AGGCTTTTAACAATCAATCA;RSEQ=GAGTTTTCCTGAGGCGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:11:5,6:56,67:0.0821:2,2:24.6:1:31.1:1:1:1.00296:60:22:0.0853:0:1.7 1/0:159:100:45,55:31,27:0.6289:2,2:27.3:1:30.2:1:0.32581:1.40024:60:49:0.6242:0:1.7 -13 46408045 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22045;SOR=0;LSEQ=AACAATCAATCAGGAGTTTT;RSEQ=CTGAGGCGTCTGCACAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:57,83:0.014:2,2:20.5:1:27.5:1:1:1.45:60:4:0.0144:0:1 0/0:161:0:0,0:75,86:0:2,0:25.7:1:30.7:1:1:0:60:79.5:1:0:1.2 -13 46408057 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49854;SOR=Inf;LSEQ=GGAGTTTTCCTGAGGCGTCT;RSEQ=CACAGACTTTTGGCTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:62,77:0:2,0:27.1:1:31.7:1:1:0:60:45.333:1:0:0.3 0/1:146:2:1,1:64,80:0.0137:2,2:39:1:29:0:1:1.25:60:4:0.0137:0:3 -13 46408073 . G A 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=25.95169;LSEQ=GTCTGCACAGACTTTTGGCT;RSEQ=GTCTTCTCAGAAGCTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:9:4,5:52,70:0.0687:2,2:27:1:29.6:1:1:1.08:60:18:0.0709:0:2 1/0:115:76:31,45:16,23:0.6609:2,2:27.6:1:29:1:1:1.00973:60:37:0.6607:0:2 -13 46751970 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50244;SOR=Inf;LSEQ=CAGTCAAGTGTACAGAGGGG;RSEQ=TGACTACTGATGCTGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:24.1:1:31.4:1:1:0:60:34:1:0:0.5 0/1:24:2:1,1:14,8:0.0833:2,2:27:1:30:1:1:1.70775:60:4:0.0833:0:2 -13 46751989 . C T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.05738;SOR=0.19373;LSEQ=GCTGACTACTGATGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:3,3:5,9:0.3:2,2:21.2:1:30.3:1:0.64241:1.75:60:12:0.3158:0:1 0/1:27:2:1,1:14,11:0.0741:2,2:34.5:1:28.5:1:1:1.2613:60:4:0.0741:0:2 -13 46752000 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.16522;SOR=0;LSEQ=ATGCTGTTGCTGCTGCTGCT;RSEQ=CTGCTGATGGTGATGATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:6,11:0.1053:2,2:28.5:1:28:1:1:1.77:60:4:0.1053:0:1 0/0:27:0:0,0:15,12:0:2,0:33:1:32.1:1:1:0:60:54:1:0:0.2 -13 46752059 . T TA 81 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.59993;LSEQ=ATGACACAGAATAATTTGTT;RSEQ=ATAAAAGCACTTATCATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:1,1:0.6667:2,0:28.3:1:31.3:1:0.33333:0:60:8:0.6667:0.1667:0 1/0:13:7:2,5:3,3:0.5385:2,2:13.7:1:29.1:1:0.59207:2.32357:60:14:0.5385:0.2308:0 -13 46832942 . C CA 62 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=21.000;MSILEN=1;SSF=1;SOR=1.47558;LSEQ=GACAGAGCAAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:4,0:15,0:0.2105:1,0:6:1:31.2:1:1:0:55:8:0.2105:0.1579:2 0/1:7:2:2,0:5,0:0.2857:0,0:44.5:1:29.5:1:1:0:44.5:4:0.2857:0:5 -13 46833150 . A C 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.04945;LSEQ=TTTGAGTAAAGCACACATTT;RSEQ=CTGAGGCCTACATTTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:73:41,32:129,127:0.2219:2,2:25.6:1:31.2:1:0.42669:1.26:60:146:0.226:0:1.9 0/1:401:148:67,81:131,120:0.3691:2,2:25.3:1:30.5:1:0.21358:1.31884:60:48.333:0.3671:0:1.9 -13 46833167 . C T 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=1.88403;LSEQ=TTTACTGAGGCCTACATTTT;RSEQ=GTTCCTAAGGTTTTGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:70:37,33:114,133:0.2201:2,2:27.3:1:29.9:1:0.3447:1.31:60:69:0.2219:0:2 0/1:380:132:58,74:116,132:0.3474:2,2:26.9:1:29.8:1:0.6655:1.12087:60:264:0.3511:0:2 -13 46833227 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=TGTGAGGCAGCATGGAGGCA;RSEQ=GAAAGCTCAGCTTCTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:48,114:0:2,0:24.9:1:31:1:1:0:60:161:1:0:0.5 0/1:175:2:1,1:55,118:0.0114:2,2:24.5:1:27.5:1:0.53885:2.14:60:4:0.0115:0:1.5 -13 46833228 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.88868;LSEQ=GTGAGGCAGCATGGAGGCAG;RSEQ=AAAGCTCAGCTTCTGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:1,0:45,113:0.0063:2,0:1:0:28:0:0.28931:0:60:2:0.0063:0:1 0/1:169:2:1,1:53,114:0.0118:2,2:7.5:1:28:1:0.53825:2.14:60:4:0.012:0:1.5 -13 48095708 . G A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCATTTGGGGTTCCATTC;RSEQ=TAAGACCATCAGTAGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:6:0:32:0:1:0:60:2:1:0:1 1/0:5:3:2,1:2,0:0.6:0,2:21:1:31.3:1:1:0:60:6:0.6:0:1 -13 48095852 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16641;SOR=0;LSEQ=AAGCCATGTTGCCCAACTCC;RSEQ=GAGGTTGGTATAAGAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:10,14:0.0769:2,2:28:1:31.5:1:1:1.38:60:4:0.0769:0:1 0/0:37:0:0,0:19,18:0:2,0:34.5:1:30.1:1:1:0:59.2:74:1:0:0.3 -13 48095922 . A G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGTAAATGCTGGGTGGC;RSEQ=TCTCGTATGATCCCTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:19.9:1:32.6:1:1:0:60:14:1:0:1.1 1/1:18:18:5,13:0,0:1:0,2:18.9:1:31.6:1:1:0:60:36:1:0:1.1 -13 48877985 . G T 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.06144;SOR=6.46756;LSEQ=GACGGGGCGTGCCCCGACGT;RSEQ=CGCGCGCGTCGTCCTCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:0,1:239,151:0.0026:2,0:1:0:26:0:0.38875:0:60:2:0.0026:0:1 0/1:368:6:3,3:217,145:0.0163:2,2:15.7:1:25.7:1:0.688:1.49483:60:5:0.0139:0:1.7 -13 48878084 . CGCCGCCGCT C 185 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCGAAAAACGGCCGCCAC;RSEQ=GCCGCCGCGGAACCCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:232,314:0:2,0:21.3:1:30.8:1:1:0:60:33.125:0.987:0:0.3 0/1:699:67:39,28:287,342:0.0959:2,2:28.8:1:30.6:1:0.05395:1.66:60:134:0.0978:0.0114:0.3 -13 48878114 . ACCG A 98 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.2193;SOR=2.85222;LSEQ=GCCGCCGCGGAACCCCCGGC;RSEQ=CCGCCGCCGCCCCCTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:2:0,2:190,188:0.0052:2,0:8.5:1:32.5:1:0.49868:0:60:4:0.0054:0.0026:1 0/1:608:9:4,5:316,282:0.0148:2,2:33:1:31.1:1:0.74173:1.39992:60:18:0.015:0.0016:0.2 -13 48878251 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51361;SOR=Inf;LSEQ=GGGTGTGCGTAGGGCGGGCG;RSEQ=CAAGGCGGCTCGGCGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:14,66:0:2,0:20.3:1:31.3:1:1:0:60:39:1:0:0.7 0/1:115:2:1,1:21,92:0.0174:2,2:28:1:28:1:0.34737:4.30:60:4:0.0187:0:1.5 -13 48878271 . T C 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGCGGCTCGGCGGGGA;RSEQ=CCGTCCTCGCCAGGGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:4,34:0,0:1:0,2:18.2:1:31.1:1:1:0:60:18:1:0:1.4 1/1:57:57:4,53:0,0:1:0,2:17:1:31.8:1:1:0:60:114:1:0:1.3 -13 48878292 . G A 116 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10673;SOR=0;LSEQ=CCGTCCTCGCCAGGGGCCGG;RSEQ=TCCCGGCGGGAGGAGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:1,12:0,0:1:0,1:18.4:1:31.5:1:1:0:60:26:1:0:2.1 1/0:16:12:0,12:0,4:0.75:0,0:10.3:1:30.3:1:1:0:60:24:0.75:0:2.2 -13 48878344 . C A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCGCCACGGCGGAGCGTCTG;RSEQ=AGAATGGTGACAGGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:9:1:30.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:17:0:31.5:1:1:0:60:4:1:0:1.5 -13 48881154 . G C 92 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TTCCTTCACAGAAGTGTTTT;RSEQ=CTGCTTTGAAGTATATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:2,0:0.8:0,0:26.5:1:30.9:1:1:0:60:16:0.8:0:1 1/1:1:1:1,0:0,0:1:0,0:7:0:31:0:1:0:60:2:1:0:1 -13 48881570 . A AT 95 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.15725;SOR=2.59993;LSEQ=TTTTCTTAAAACGTTTTGAA;RSEQ=TTTTTTTTTCTCATTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:74,215:0.0103:2,2:34.7:1:31:1:1:1.45:60:6:0.0105:0:0 0/1:342:9:2,7:93,240:0.0263:2,2:30.3:1:30.1:1:1:1.35508:60:18:0.0268:0:0.1 -13 48916172 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTGTATACTATATACTA;RSEQ=GCCAAAGGCTTTATAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:35.5:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 48916672 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24781;SOR=Inf;LSEQ=AATCAGTTATAATACAGTTT;RSEQ=AACATAGTATCCAGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:147,25:0:2,0:23.7:1:29.9:1:1:0:60:56.333:1:0:0.1 0/1:171:2:1,1:132,37:0.0117:2,2:15:1:30:1:0.39608:3.5334:60:4:0.0118:0:1 -13 48916895 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00248;LSEQ=GCCTCTGCCATAAAAGGAAA;RSEQ=GAATTCTGGATTTTCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:8:2,6:28,145:0.0442:2,2:16.9:1:30.4:1:0.62115:1.72:60:16:0.0442:0:1 0/1:158:7:0,7:32,118:0.0443:2,0:29.4:1:29:1:0.34593:0:60:14:0.0446:0:1.3 -13 48916904 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20571;SOR=Inf;LSEQ=ATAAAAGGAAACGAATTCTG;RSEQ=ATTTTCCTCTCAATAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:17,133:0:2,0:22.3:1:31.8:1:1:0:60:300:1:0:0.1 0/1:125:2:1,1:15,107:0.016:2,2:13:1:28.5:1:0.24233:6.94:60:4:0.0163:0:1 -13 48919167 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23035;SOR=0;LSEQ=GATTTGAAAACGAAATAACA;RSEQ=AAATTTTTAAGGTTACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:136,36:0.0115:2,2:20:1:28.5:1:0.38104:3.74018:60:4:0.0116:0:1 0/0:188:0:0,0:142,46:0:2,0:23.5:1:30.8:1:1:0:60:61.667:1:0:0.1 -13 48919358 . T G 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTAAACATTTTATTAGG;RSEQ=TTACACTCTGATTTTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:273:273:73,200:0,0:1:0,2:24.2:1:31.4:1:1:0:60:53.6:1:0:1.1 1/1:290:289:97,192:0,0:0.9966:0,2:24.1:1:30.6:1:1:0:60:143.5:0.9965:0:1.1 -13 48919381 . A G 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01453;SOR=Inf;LSEQ=ACACTCTGATTTTTTATGTC;RSEQ=TTGTTCACAATTAGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:34,155:0:2,0:22.5:1:30.6:1:1:0:60:62:1:0:1 0/1:187:6:2,4:42,139:0.0321:2,2:23.2:1:30.8:1:0.62699:1.65:60:12:0.0323:0:2 -13 48919455 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18365;SOR=Inf;LSEQ=GTATTAATTCTTAGACTTGT;RSEQ=CCTTTTAATGTTAGCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:1,53:0:1,0:24.8:1:31.6:1:1:0:60:53:1:0:0.3 0/1:41:2:0,2:2,37:0.0488:2,0:35.5:1:29:1:1:0:60:4:0.0488:0:1 -13 48921884 . A G 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00027;SOR=0;LSEQ=TATACTTCTTAAAAGAAGAT;RSEQ=AATAAAGCATGAGAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:185:185:145,40:0,0:1:0,2:21.9:1:32:1:1:0:60:184:1:0:1.1 1/1:255:240:175,65:10,5:0.9412:2,2:23.9:1:31.4:1:0.56351:1.34:60:79:0.9405:0:1.1 -13 48921934 . A T 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.16782;SOR=0.17979;LSEQ=CTAAATTACGAAAAAATGTT;RSEQ=AAAAGTCATAATGTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:1,3:232,155:0.0102:2,2:13.3:1:27.5:1:0.30755:4.47361:60:8:0.0103:0:1.3 0/0:540:1:0,1:299,240:0.0019:2,0:1:0:24:0:0.4463:0:60:2:0.0019:0:1 -13 48922031 . TA T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.38014;SOR=0.54054;LSEQ=ACAGAATGTTATTTTTCACT;RSEQ=AAAAAAAAGATTTTTATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:7:1,6:79,175:0.0268:2,2:24.6:1:31:1:0.67946:2.70035:60:14:0.0268:0:0 0/1:341:5:0,5:122,214:0.0147:2,0:32.4:1:28.6:1:0.16458:0:60:10:0.0148:0:0 -13 48922078 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51035;SOR=Inf;LSEQ=CTCAAACATCTTGATAGTTA;RSEQ=GGTTAGTTTGATCGATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:2,82:0:1,0:24.5:1:31.5:1:1:0:60:168:1:0:0 0/1:116:2:0,2:12,102:0.0172:2,0:10:1:31.5:1:1:0:60:4:0.0174:0:1 -13 48922984 . A AT 93 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.03875;LSEQ=TTATGCATTTAACTAAGGTC;RSEQ=TTTTTTTTTTAATGCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:8:7,1:56,0:0.1231:1,2:24:1:31.1:1:0.125:0:60:16:0.1231:0:0.1 0/1:55:7:6,1:48,0:0.1273:1,2:20.3:1:29.6:1:0.12727:0:60:14:0.1273:0.0364:0.3 -13 48923061 . G GT 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.1844;LSEQ=TTCAGTGATACATTTTTCCT;RSEQ=TTTTTTTTCTGCTTTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:196,91:0.0103:2,2:14:1:28.8:1:1:1.07664:60:6:0.0106:0.0069:0.7 0/1:327:4:4,0:214,109:0.0122:2,0:28.5:1:30.8:1:0.30545:0:60:8:0.0123:0:0 -13 48923200 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19552;SOR=0;LSEQ=AAATGCTAATATTTCAAATG;RSEQ=AATAATTAAATTGGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:33,128:0.0123:2,2:20:1:29.5:1:0.37469:3.84:60:4:0.0123:0:1 0/0:205:0:0,0:48,157:0:2,0:21.8:1:28.3:1:1:0:60:204:1:0:0.1 -13 48934140 . A AT 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08349;SOR=0.5791;LSEQ=AACTTTCTTTAAAAATGTAC;RSEQ=TTTTTTTTTCAGGGGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:24:15,9:171,71:0.0899:2,2:24.1:1:31.1:1:0.4841:1.44297:60:48:0.0913:0.0075:0.5 0/1:370:20:10,10:234,116:0.0541:2,2:22.4:1:28.9:1:0.14633:2.01318:60:40:0.0548:0.0189:0.4 -13 48934316 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23219;SOR=0;LSEQ=TCATTCAGCAGTTGCTTATT;RSEQ=AATGTCTAGTGGGTACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:20,118:0.0143:2,2:15:1:27.5:1:0.27842:5.78:60:4:0.0144:0:1 0/0:150:0:0,0:34,116:0:2,0:22.1:1:30.8:1:1:0:60:49:1:0:0.1 -13 48934329 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23579;SOR=Inf;LSEQ=GCTTATTGAATGTCTAGTGG;RSEQ=TACCAAACATGGTTCTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:12,104:0:2,0:21.9:1:31.9:1:1:0:60:115:1:0:0.1 0/1:110:2:1,1:15,93:0.0182:2,2:21:1:26.5:1:0.27089:6.04:60:4:0.0185:0:1 -13 48938897 . TA T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.21831;SOR=Inf;LSEQ=TCTAAGAAAATAATAAAAAA;RSEQ=AAAAAGTTATACACAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:0:1,0:17.8:1:28.4:1:1:0:60:29.5:1:0:0.1 0/1:54:2:2,0:52,0:0.037:1,0:15:0:32:0:1:0:60:4:0.037:0:0 -13 48939018 . C T 51 q23 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01465;SOR=0;LSEQ=TAATGATCATGTTGTAACTT;RSEQ=ATCTTTTTCAGGTGAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:5:1,4:217,150:0.0134:2,2:5:1:22:1:0.16451:5.76167:60:4:0.011:0:1.8 0/0:491:0:0,0:280,211:0:2,0:24.2:1:31.3:1:1:0:60:162.667:1:0:0.1 -13 48939204 . A AT 63 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.68764;SOR=0.58741;LSEQ=ATCAATTTACTGTGTATCAC;RSEQ=TTTTTTTTTTGCCCAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:4:0,4:1,61:0.0606:1,0:34.8:1:31.5:1:1:0:60:8:0.0625:0:0 0/1:55:2:0,2:3,50:0.0364:2,0:37.5:1:30.5:1:1:0:60:4:0.0385:0:0 -13 48941548 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22999;SOR=0;LSEQ=ATGTATATTATACAAAAATT;RSEQ=TTTAATGAAATCTGTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:139,18:0.0126:2,2:9:1:28:1:0.22538:7.54319:60:4:0.0127:0:1 0/0:172:0:0,0:146,26:0:2,0:21.3:1:31.1:1:1:0:60:171:1:0:0.1 -13 48942787 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.22377;LSEQ=ATTATAATTTTGTTATTCAT;RSEQ=GCTTTATAGTGTTTCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:2:2,0:42,180:0.0089:2,0:1:0:23:0:0.03788:0:60:4:0.0093:0:1 0/1:275:3:2,1:56,216:0.0109:2,2:22:1:25.3:1:0.11363:7.64:60:6:0.011:0:1 -13 48943142 . C CA 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGCGAAACTCCGTCT;RSEQ=AAAAAAAAAATGTGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:34.5:1:31:1:1:0:58:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 48947469 . G T 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACATTTAACTTGGGAGAT;RSEQ=GAAAACATTTCATTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:144:144:117,27:0,0:1:0,2:19.5:1:30.4:1:1:0:60:288:1:0:1.1 1/1:137:137:109,28:0,0:1:0,2:20.8:1:29.6:1:1:0:60:136:1:0:1.1 -13 48950990 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50526;SOR=Inf;LSEQ=AAAAGTCATATATTATGGAG;RSEQ=AGAAAATATTAATTCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:89,12:0:2,0:23.5:1:32.2:1:1:0:60:32.667:1:0:0.1 0/1:129:2:1,1:102,25:0.0155:2,2:32.5:1:29:1:0.36374:4.02033:60:4:0.0156:0:1.5 -13 48951025 . A G 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00859;SOR=Inf;LSEQ=CTGATTACACAGTATCCTCG;RSEQ=CATTGATTTCTGTTTTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:170,58:0:2,0:23.7:1:30.1:1:1:0:60:75:1:0:0.1 0/1:265:8:5,3:175,82:0.0302:2,2:32.8:1:31.1:1:0.71405:1.2792:60:16:0.0304:0:1.1 -13 48951239 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24184;SOR=Inf;LSEQ=AAAGCAGCATCTTTCCAGTT;RSEQ=GTATAAATACTCTAACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:13,126:0:2,0:24.3:1:29.7:1:1:0:60:68.5:1:0:0.1 0/1:135:2:0,2:7,126:0.0148:2,0:42:0:30.5:1:1:0:60:4:0.015:0:2.5 -13 48953655 . C CA 142 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.54336;SOR=0.75216;LSEQ=AAAACAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:20:20,0:14,1:0.4878:1,1:30.9:1:30.8:1:0.42857:0:60:40:0.4878:0:0.2 0/1:60:25:25,0:22,1:0.4167:1,1:28:1:30.6:1:0.47917:0:60:50:0.4167:0:0.5 -13 48953730 . C T 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19667;SOR=0.28111;LSEQ=TTCTTTTTGTTTGTTTGTAG;RSEQ=GATACAAACTTGGAGTTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:4:1,3:176,117:0.0135:2,2:12:1:28:1:0.30674:4.49061:60:8:0.0141:0:1 0/0:524:2:0,2:308,213:0.0038:2,0:1:0:24.5:1:0.16853:0:60:4:0.0039:0:1.5 -13 48953826 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28384;SOR=Inf;LSEQ=AAAAAATTTCAGCCGGGCGC;RSEQ=GTGGCTCACGCCTGCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:51,131:0:2,0:23.2:1:30.1:1:1:0:60:44.5:1:0:0.1 0/1:283:3:2,1:93,187:0.0106:2,2:12.7:1:26.3:1:0.26162:4.00:48:6:0.0107:0:2 -13 48953840 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.42858;LSEQ=GGGCGCGGTGGCTCACGCCT;RSEQ=CAATCCCAGCACTTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:1,0:28,110:0.0072:2,0:1:0:23:0:0.20863:0:60:2:0.0073:0:1 0/1:195:2:1,1:42,151:0.0103:2,2:26.5:1:27:1:0.39329:3.56:60:4:0.0104:0:1 -13 48954021 . G C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36111;SOR=0;LSEQ=CAGGAGAATCCCTTGAACCA;RSEQ=GGAGGTGGAGGTTGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:17,6:0,0:1:0,2:27.3:1:27.9:1:1:0:60:4.75:1:0:1.2 1/1:13:12:11,1:0,0:0.9231:0,2:24.7:1:31.4:1:1:0:60:24:0.9231:0:1.4 -13 48954173 . A T 63 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.773;SOR=1.30814;LSEQ=CAACTTCTTTTTTTTTTTTT;RSEQ=AATTATCTGTTTCAGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:4:2,2:295,195:0.0081:2,2:5:1:18:1:0.65264:1.51148:60:1:0.0043:0:3 0/1:757:8:5,3:400,349:0.0106:2,2:16.6:1:21:1:0.7305:1.45:57.5:1.667:0.0069:0:2.6 -13 48954175 . A T 168 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.18834;LSEQ=ACTTCTTTTTTTTTTTTTAA;RSEQ=TTATCTGTTTCAGGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:5:2,3:306,207:0.0097:2,2:13.2:1:21.6:1:0.39952:2.21392:60:1.5:0.0065:0:3.4 0/1:778:64:33,31:376,338:0.0823:2,2:26.2:1:28.1:1:0.89655:1.04497:60:15:0.0855:0:1.4 -13 48954282 . CT C 162 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.37104;SOR=0.77265;LSEQ=AGAAGTAAGTATTTTATAAT;RSEQ=TTTTTTTTTTCCTTTAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:35:15,20:116,181:0.1048:2,2:24.7:1:31.7:1:0.71598:1.17:59.7:70:0.1064:0.009:0.1 0/1:398:33:14,19:137,227:0.0829:2,2:28.9:1:31.8:1:0.58034:1.22:60:66:0.0855:0:0.3 -13 48954329 . A T 50 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22958;SOR=4.16629;LSEQ=TGAATGACAACATTTTTCAT;RSEQ=TGTCTTTATTGGCGTGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:0,1:164,204:0.0027:2,0:1:0:26:0:1:0:60:2:0.0028:0:1 0/1:446:5:2,3:203,238:0.0112:2,2:11.6:1:21.8:1:1:1.27871:60:1.5:0.0072:0:2.4 -13 48954450 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49953;SOR=Inf;LSEQ=TGGTGTGTTTCTTTGGTCGG;RSEQ=GGAGAGGGATAGTGTGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:9,90:0:2,0:23.3:1:30.3:1:1:0:60:18.8:1:0:0.1 0/1:112:2:1,1:14,96:0.0179:2,2:9:1:29.5:1:0.25097:6.66:60:4:0.0182:0:1 -13 48955201 . T A 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGAAAAACACAGATTTGC;RSEQ=TACACTCAAAATTGGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:27.3:1:30.7:1:1:0:60:14:1:0:1.3 1/1:2:2:2,0:0,0:1:0,0:20.5:1:29:1:1:0:60:4:1:0:1.5 -13 48955363 . CT C 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.42612;SOR=0.63896;LSEQ=TAATATTTCATAAATAGTTA;RSEQ=TTTTTTTTTCATTTTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:8:7,1:93,15:0.069:2,2:33.1:1:32.5:1:1:1.13:60:16:0.069:0:0 0/1:133:6:6,0:112,15:0.0451:2,0:22.2:1:32.8:1:1:0:60:12:0.0458:0:0.3 -13 48955407 . C T 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67671;SOR=0.62229;LSEQ=TACATCTCAGAATCTTGATT;RSEQ=TGGAACAGATTTGTCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:1,2:188,74:0.0113:2,2:8.7:1:21.7:1:0.19858:5.04497:60:2:0.0077:0:1 0/0:284:2:0,2:215,67:0.007:2,0:3:1:27:1:0.05838:0:60:4:0.0074:0:1 -13 48955445 . C T 52 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22149;SOR=4.50549;LSEQ=TCCCATGGATTCTGAATGTG;RSEQ=TTAATTTAAAAGCCTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:1:0,1:248,168:0.0024:2,0:1:0:26:0:0.40528:0:60:2:0.0024:0:1 0/1:466:5:0,5:272,189:0.0107:2,0:7.2:1:22.6:1:0.01213:0:60:4:0.0088:0:1.6 -13 48955623 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.10678;SOR=Inf;LSEQ=AATTCATTCATGTGCATATG;RSEQ=CTAACAAATTATTGTTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:40,145:0:2,0:25.6:1:31.9:1:1:0:60:184:1:0:0.3 0/1:168:3:1,2:42,123:0.0179:2,2:23.7:1:25.3:1:1:1.46:60:6:0.0183:0:1.3 -13 48955659 . C CAA 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.74215;SOR=1.45686;LSEQ=TAGTGAGAGGTGTTTCTTAA;RSEQ=ATCTACCTCAAGAACATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:5:0,5:2,90:0.0515:1,0:29:1:30.7:1:1:0:60:10:0.0521:0.0103:0.8 0/1:68:5:0,5:3,60:0.0735:1,0:15.2:1:31.1:1:1:0:60:10:0.0758:0.0441:0.4 -13 48955676 . T A 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.40517;SOR=0;LSEQ=TAACATCTACCTCAAGAACA;RSEQ=ATAGGGAATTTAATGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:69:2,67:0,0:1:0,1:23.3:1:30.9:1:1:0:60:138:1:0:1 1/1:47:46:0,46:0,1:0.9787:0,1:21.9:1:30.6:1:1:0:60:92:0.9787:0:1 -13 49026852 . C T 72 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTCTCTCCACTTTCTT;RSEQ=GTTTTTTTTCTGTCTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:29.6:1:31.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 49027044 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22873;SOR=Inf;LSEQ=GCCTAAAATTCATAGTACTT;RSEQ=CCATGTCAAACAATATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:147,15:0:2,0:24.1:1:28.5:1:1:0:60:324:1:0:0.1 0/1:149:2:1,1:128,18:0.0134:2,2:6:1:27.5:1:0.24104:6.94841:60:4:0.0135:0:1 -13 49033747 . G A 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00685;SOR=0;LSEQ=AACAGCATTATAATTAGAGC;RSEQ=ATTTCATGATTTGAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:219:181,38:0,0:1:0,2:22.9:1:30:1:1:0:60:218:1:0:1.1 1/1:214:207:172,35:7,0:0.9673:0,2:23.2:1:30:1:0.60219:0:60:102.5:0.967:0:1.1 -13 49034022 . A AT 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.215;LSEQ=CCCTACTTACTTGTTAACTG;RSEQ=TTCTTTCTTTCTTTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:260:245:30,215:4,11:0.9423:2,2:26.7:1:30.3:1:0.11627:2.59329:58.8:48:0.9412:0.1269:0.2 1/0:207:161:26,135:12,32:0.7778:2,2:31:1:29.5:1:0.12368:1.94006:58.1:25.833:0.7828:0.0048:0.1 -13 49034073 . C CT 122 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=15.000;MSILEN=4;SSF=1e-04;SOR=0;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TTTCTTTCTTTCTTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:15:0,15:0,49:0.2344:1,1:16.7:1:31.3:1:1:0:56.3:30:0.25:0.0625:0.8 0/0:53:0:0,0:0,52:0:1,0:14.4:1:31.4:1:1:0:52.5:16.333:1:0:0.4 -13 49034081 . CTTTCT TCTTTC 131 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=16.000;MSILEN=4;SSF=0.00431;SOR=0.21593;LSEQ=TTTCTTTCTTTCTTTCTTTC;RSEQ=TTTTCTTTCTTTCTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:20:0,20:0,28:0.4167:1,1:22.1:1:30.5:1:1:0:45.8:40:0.4255:0.125:0.8 0/1:38:5:0,5:0,30:0.1316:1,0:27.6:1:28.9:1:1:0:40:10:0.1429:0:1.8 -13 49034085 . CTT TC 99 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=15.000;MSILEN=4;SSF=0.00213;SOR=0;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TTTCTTTCTTTCTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:0,9:0,10:0.2727:0,0:12.6:1:31.4:1:1:0:53.9:18:0.5:0.0606:0.6 0/0:31:0:0,0:0,23:0:1,0:8.4:1:32.5:1:1:0:50.6:46:1:0:0.3 -13 49034104 . TCTC T 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.11371;SOR=0;LSEQ=TCTTTTTCTTTCTTTCTTTC;RSEQ=TTTCTTTCTTTTTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,0:0.4667:0,0:17.1:1:30.9:1:1:0:37.7:14:0.5:0.3333:0.7 0/0:5:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 49034105 . C T 75 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1;LSEQ=CTTTTTCTTTCTTTCTTTCT;RSEQ=TCTTTCTTTCTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:0,6:0,0:0.4:0,0:29.2:1:29.3:1:1:0:36.7:12:0.4286:0:2.8 0/1:5:2:0,2:0,0:0.4:0,0:42:1:19.5:1:1:0:40:1:0.25:0:2 -13 49034154 . A G 68 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCACTCTGTTACCCAGGCT;RSEQ=GAGTGCAGTGGCGCAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:29.6:1:22.9:1:1:0:44.4:1.667:1:0:1.8 1/1:5:5:0,5:0,0:1:0,0:30.6:1:21.2:1:1:0:51.4:0.667:1:0:1.2 -13 49037825 . G T 150 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02587;LSEQ=TTTTTTAAGAACAAAACCAT;RSEQ=TAATAAAATTCTGACTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:34:25,9:199,58:0.1168:2,2:20.8:1:29.6:1:0.66496:1.23426:60:33:0.1158:0:1 0/0:294:1:1,0:216,77:0.0034:2,0:27:0:32:0:1:0:60:2:0.0034:0:1 -13 49038039 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15863;SOR=Inf;LSEQ=ACATAACATAGGTAATTCAT;RSEQ=TGATCTCATTTATTCATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:19,157:0:2,0:23.2:1:30.2:1:1:0:60:87:1:0:0.1 0/1:117:2:1,1:14,101:0.0171:2,2:32:1:31:1:0.24094:7.00:60:4:0.0171:0:1 -13 49038459 . A T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTGTGGAAAGTGAGTTG;RSEQ=GGGGTATTTTTCCCATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:20.5:1:29:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:20:1:28.5:1:1:0:60:4:1:0:1 -13 49047529 . G C 233 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTGGTGAATCATTCGGGGT;RSEQ=AGTATTTTCTTTCTATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:159:63,96:89,140:0.4077:2,2:27.4:1:31.9:1:0.91595:1.03:60:158:0.4083:0:1.1 0/0:508:0:0,0:217,290:0:2,0:25.9:1:31:1:1:0:60:100.4:0.998:0:0.1 -13 49050784 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02688;SOR=Inf;LSEQ=CTATAACTTGAGGTTGCTAA;RSEQ=TATGAAACACTGGCATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:74,13:0:2,0:23.3:1:31.8:1:1:0:60:174:1:0:0 0/1:84:5:4,1:66,13:0.0595:2,2:25.8:1:30:1:1:1.26538:60:10:0.0595:0:1 -13 49051012 . C T 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAATGTTTTCCAGTAGC;RSEQ=GAGATGGTCATCTGGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:160:160:38,122:0,0:1:0,2:25:1:30.5:1:1:0:60:320:1:0:1.1 1/1:166:166:43,123:0,0:1:0,2:23.3:1:29.9:1:1:0:60:40.5:1:0:1.1 -13 49051029 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23125;SOR=Inf;LSEQ=AGCCGAGATGGTCATCTGGG;RSEQ=AATCCAGAGTCTCAGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:22,107:0:2,0:22.2:1:31:1:1:0:60:63.5:1:0:0.9 0/1:120:2:0,2:20,98:0.0167:2,0:28:1:29.5:1:1:0:60:4:0.0169:0:2 -13 49051428 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20112;SOR=Inf;LSEQ=ATCGAAAGCATCATAGTTAC;RSEQ=GGAAATTTGAGTTTTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:145,61:0:2,0:25.7:1:30.5:1:1:0:60:67.667:1:0:0.1 0/1:168:2:1,1:130,36:0.0119:2,2:23:1:28:1:0.393:3.57536:60:4:0.0119:0:1 -13 49051481 . T A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.8477;SOR=0.88903;LSEQ=TGAAATGTTTTGCATTTTTT;RSEQ=AATCTGCAGTAAACATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:14:9,5:183,144:0.0409:2,2:19.5:1:28.9:1:0.59405:1.41:60:28:0.0414:0:1.3 0/1:383:14:9,5:211,158:0.0366:2,2:27.3:1:28.5:1:0.78454:1.35:60:28:0.037:0:1.1 -13 49051605 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49983;SOR=Inf;LSEQ=TACACTGCAAGAAGTCTTTT;RSEQ=GTTATATAAAAGAATGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:34,142:0:2,0:23.1:1:30.2:1:1:0:60:175:1:0:0.1 0/1:194:2:0,2:47,144:0.0103:2,0:19:1:31.5:1:1:0:60:4:0.0104:0:1 -13 49051632 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49752;SOR=Inf;LSEQ=TAAAAGAATGTATAATTTCT;RSEQ=CAGTTGGCAGGTTTGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:14,81:0:2,0:22:1:29.7:1:1:0:60:30.667:1:0:0 0/1:98:2:1,1:16,80:0.0204:2,2:22.5:1:26:1:0.31833:4.88:60:4:0.0206:0:1 -13 49051848 . G A 78 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCAGAACTACAAAGAGGA;RSEQ=CTATTTGGGAGTGTTAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:25.3:1:30.2:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 49054037 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49958;SOR=Inf;LSEQ=TGCTTTTGCAAGGTCCTGAG;RSEQ=GCCATCAGTTTGACATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:119,23:0:2,0:25.7:1:31.3:1:1:0:60:70:1:0:0.1 0/1:157:2:2,0:130,25:0.0127:2,0:20.5:1:30.5:1:1:0:60:4:0.013:0:1 -13 49054056 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24875;SOR=Inf;LSEQ=GCGCCATCAGTTTGACATGA;RSEQ=CATAATATATATGGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:163,68:0:2,0:22:1:31.5:1:1:0:60:45.2:1:0:0.1 0/1:241:3:2,1:175,63:0.0124:2,2:11:1:27.7:1:1:1.38686:60:6:0.0126:0:1 -13 49054299 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51237;SOR=0;LSEQ=CTTTCCCAGGTTCTGTTTAT;RSEQ=GCCACATTTAATATCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:0,2:10,100:0.0179:2,0:24.5:1:25.5:1:1:0:60:4:0.0183:0:1 0/0:79:0:0,0:4,75:0:2,0:21.6:1:30.2:1:1:0:60:38.5:1:0:0.1 -13 50950167 . C A 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01318;SOR=Inf;LSEQ=CAGAATCCAGACCAAAGTCA;RSEQ=GGTGAACTGGCATGAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:19.3:1:31.1:1:1:0:60:24:1:0:1 0/1:22:9:6,3:8,5:0.4091:2,2:26.6:1:30.3:1:1:1.24:60:18:0.4091:0:2.1 -13 50950203 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACAACAACAACAGCAGC;RSEQ=GCAGCAGCAGCAACAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:10,9:0,0:1:0,2:32.2:1:31.4:1:1:0:60:38:1:0:1.1 1/1:36:36:20,16:0,0:1:0,2:31.4:1:30.8:1:1:0:60:72:1:0:1.5 -13 50950213 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.54413;SOR=Inf;LSEQ=CAACAGCAGCGGCAGCAGCA;RSEQ=CAACAATATAGACACATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:30.4:1:33:1:1:0:60:40:1:0:1.1 0/1:39:2:1,1:19,18:0.0513:2,2:28:1:27.5:1:1:1.05412:60:4:0.0513:0:2 -13 51448137 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TTTTTGCTGAAGACAGGCCA;RSEQ=GGTGATCAGACATCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:20:1:30.5:1:1:0:60:8:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:18:0:32.5:1:1:1:60:4:0.5:0:1 -13 51448230 . C A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ATCAGATATTGAGGATGGGA;RSEQ=CACTTGCTAAACCAACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:5.5:1:29.5:1:1:2.44949:60:4:0.3333:0:1.5 0/0:4:0:0,0:3,1:0:2,0:31.3:1:31.5:1:1:0:60:8:1:0:0 -13 51449467 . G A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71669;SOR=0.72259;LSEQ=ATCTGCAGTTGCCAAGCTGG;RSEQ=AACTCAGGAGAGCCAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:5,2:4,6:0.4118:2,2:21.1:1:29.6:1:0.33484:3.46:60:14:0.4118:0:1.1 0/1:12:4:2,2:4,4:0.3333:2,2:40.8:1:29.3:1:1:1:60:8:0.3636:0:1 -13 51449485 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48308;SOR=0;LSEQ=GGGAACTCAGGAGAGCCAAG;RSEQ=GTGTAAGTTCTAATCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:4,8:0.1429:2,2:37.5:1:29.5:1:1:1.90:60:4:0.1429:0:1 0/0:12:0:0,0:5,7:0:2,0:18.5:1:30.8:1:1:0:60:24:1:0:0.6 -13 51774946 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23171;SOR=Inf;LSEQ=GACCATCTGTAGCTTGATGG;RSEQ=CTTGATCCTGGAGGAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:18,3:0:2,0:22.4:1:31.5:1:1:0:60:20:1:0:0 0/1:20:2:1,1:16,2:0.1:2,2:39:1:28.5:1:0.28421:6.73285:60:4:0.1:0:1 -13 51775024 . T A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50232;SOR=0;LSEQ=GAGTAATAGCAAGATGGCTG;RSEQ=CACGGGGCCTAGAAAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:75,58:0.0148:2,2:12:0:31.5:1:1:1.29061:60:4:0.0149:0:1 0/0:112:0:0,0:66,46:0:2,0:22.1:1:28.7:1:1:0:60:55:1:0:0.2 -13 51775043 . GA G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=GTCACGGGGCCTAGAAAGGG;RSEQ=AAAGGCATGTCGCCCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:92,79:0.0115:2,2:36:1:32:1:1:1.16353:60:4:0.0118:0:0 0/0:168:0:0,0:90,77:0:2,0:23.8:1:28.8:1:1:0:60:40.75:1:0:0.2 -13 51775049 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.245;SOR=Inf;LSEQ=GGGCCTAGAAAGGGGAAAAG;RSEQ=CATGTCGCCCAACTCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:94,82:0:2,0:28.9:1:31.6:1:1:0:59.9:175:1:0:0.2 0/1:173:2:1,1:90,81:0.0116:2,2:25:1:25.5:1:1:1.11043:60:4:0.0119:0:1 -13 51775062 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24804;SOR=Inf;LSEQ=GGAAAAGGCATGTCGCCCAA;RSEQ=TCCAGAGGTTGGTATAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:91,90:0:2,0:31.4:1:32:1:1:0:59.8:59.333:1:0:0.2 0/1:185:3:1,2:88,94:0.0162:2,2:29:1:26:1:1:1.86625:60:2:0.011:0:2.3 -13 51775082 . G GT 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.02686;SOR=Inf;LSEQ=CTCCAGAGGTTGGTATAAGA;RSEQ=TTTGAAGGGCATTGTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:76,97:0:2,0:28.4:1:32.3:1:1:0:59.8:346:1:0:0.3 0/1:165:5:2,3:69,91:0.0303:2,2:24.6:1:29.1:1:1:1.13646:60:10:0.0307:0.0121:0.2 -13 51775127 . C T 121 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01956;SOR=0.35043;LSEQ=GAAGCTTTTTTCTGTAAACG;RSEQ=CGGGTAGTGTCTCATACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:19:6,13:10,26:0.3455:2,2:23.2:1:28.6:1:0.76517:1.20:60:18:0.3333:0:1.3 0/1:71:11:3,8:17,43:0.1549:2,2:17.6:1:29.9:1:1:1.05349:60:22:0.1594:0:1 -13 51775149 . C T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.62622;SOR=1.3444;LSEQ=GGGTAGTGTCTCATACTATC;RSEQ=CTGACTGGTTAGTGTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:13:1,12:3,24:0.325:2,1:16.6:1:30.3:1:1:1.48581:60:26:0.325:0:1 0/1:33:13:1,12:2,18:0.3939:2,1:18.9:1:28.7:1:1:1.32209:60:26:0.4194:0:1 -13 54073225 . C T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTAAGGAGTGGGAAGACGAG;RSEQ=ACAAAAAATTGTGAATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:24:1:29.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 54073461 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49836;SOR=Inf;LSEQ=TCTCTGTACAGAGTGACTAT;RSEQ=TCAGACCCATTGAAGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:85,62:0:2,0:25:1:31.8:1:1:0:60:72.5:1:0:0.8 0/1:150:2:2,0:82,66:0.0133:2,0:15.5:1:26.5:1:0.50389:0:60:4:0.0135:0:1 -13 54073469 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.36615;LSEQ=CAGAGTGACTATGTCAGACC;RSEQ=ATTGAAGGGTCCACTTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:114:64,50:18,22:0.7403:2,2:23.4:1:29.6:1:0.27027:1.56:60:228:0.7403:0:1.2 1/0:153:78:39,39:44,31:0.5098:2,2:26:1:29.6:1:0.33105:1.41607:60:156:0.5098:0:1.3 -13 54073555 . A G 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14661;LSEQ=TTAAAAGATTATAAGGAAAA;RSEQ=CAATAAAAATATGTTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:60:11,49:3,13:0.7895:2,2:23.7:1:32.6:1:1:1.0276:60:120:0.7895:0:1.3 0/1:74:26:9,17:13,35:0.3514:2,2:21.3:1:31.5:1:0.59638:1.42:60:52:0.3562:0:1.3 -13 54075135 . C A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGGACTACAGGTGTGTGC;RSEQ=ACTACATCTGGCTAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:29:1:1:0:60:4:1:0:4 -13 54891366 . GCACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT G 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.66685;SOR=0.48195;LSEQ=TGTTGAGAAAGGAGGATTCT;RSEQ=CAGGGATAGTACGAGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:4,1:6,1:0.4167:2,2:28:1:32.5:1:1:1.4491:56.8:10:0.4167:0.0833:0 0/1:12:3:2,1:7,2:0.25:2,2:17:1:28.8:1:1:1.66417:60:6:0.25:0.25:0 -13 55384564 . T G 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTCCCAAATTAATGTTCT;RSEQ=TTTAGTGAGCACCTGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:194:194:135,59:0,0:1:0,2:22.9:1:31.8:1:1:0:60:63.667:1:0:1.3 1/1:234:201:126,75:20,13:0.859:2,2:24.1:1:31.1:1:0.84767:1.09:60:200:0.8621:0:1.3 -13 55384646 . A C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19448;LSEQ=TGACTCTGAAGGTTGTTCGC;RSEQ=TGCTGTTACCAAATCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:369:327:150,177:24,18:0.8862:2,2:28.1:1:31.1:1:0.19063:1.57137:60:45.714:0.8864:0:1.2 1/0:354:213:103,110:65,76:0.6017:2,2:24.6:1:30.9:1:0.74444:1.09:60:212:0.6127:0:1.3 -13 55384686 . T A 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.25212;SOR=0;LSEQ=TGTATTTCAGCTCCAGCATC;RSEQ=TCAATTTCATAAAGGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:2,1:101,195:0.01:2,2:9.3:1:26.3:1:0.27353:3.84:60:6:0.0101:0:1.7 0/0:261:0:0,0:100,161:0:2,0:27.4:1:29.6:1:1:0:60:51.2:1:0:0.5 -13 65163895 . T C 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.15211;SOR=0;LSEQ=GTTTGTTGTTATTGTTGCTG;RSEQ=TGCTGTTGCTGTTGTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:16,10:0.0714:2,2:13:0:34:0:1:1.57244:28:4:0.0714:0:1 0/0:43:0:0,0:19,24:0:2,0:29.4:1:29.4:1:1:0:60:86:1:0:0.3 -13 65163931 . A G 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0172;SOR=9.4511;LSEQ=TGCTTTTACTAAGTGCTTTC;RSEQ=AAAAATAGAATCATAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:12,14:0.037:2,0:1:0:30:0:1:0:60:2:0.037:0:1 0/1:33:9:4,5:10,14:0.2727:2,2:17.6:1:29.4:1:1:1.12:60:18:0.2727:0:1.1 -13 67591492 . T C 180 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GTTTCACTTTAAGTGAATTA;RSEQ=ACCATCACTTTTGGGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:49:48,1:0,0:1:0,1:21.6:1:32.2:1:1:0:60:48:1:0:1.6 0/1:16:7:7,0:8,1:0.4375:2,0:16.9:1:31:1:1:0:60:14:0.4375:0:1 -13 67591561 . CA TG 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGGCATTGATATTCCCTAA;RSEQ=GTTTAAAATACCCCTGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:35:35,0:69,1:0.3333:1,1:23.3:1:31.5:1:1:0:60:70:0.3333:0.0381:1.4 0/0:64:0:0,0:63,1:0:1,0:25.8:1:31.3:1:1:0:60:128:1:0:0.2 -13 67591727 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04527;LSEQ=TTTTGTCTCAAACATGAAAG;RSEQ=GAAATAGGATAAATGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:279:256:77,179:4,16:0.9176:2,2:22.5:1:31:1:0.44845:1.72:60:127:0.917:0:1.1 0/1:273:91:37,54:65,117:0.3333:2,2:21.8:1:29.8:1:0.42954:1.23:60:44.5:0.3296:0:1.1 -13 67591752 . A C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24759;SOR=0;LSEQ=TAGGATAAATGATATTTTAA;RSEQ=CATTTTTACTATTTTAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:29,124:0.0129:2,2:16.5:1:28.5:1:0.35065:4.22:60:4:0.0129:0:2 0/0:156:0:0,0:38,118:0:2,0:24.2:1:29.6:1:1:0:60:312:1:0:0.4 -13 67591966 . A G 66 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CAAAAATTTTAAACATTTTT;RSEQ=CTGTACACAGAGAAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:12.5:1:33.3:1:1:0:60:8:1:0:1 0/0:1:0:0,0:0,1:0:0,0:7:0:32:0:1:0:60:2:1:0:0 -13 68406117 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49479;SOR=Inf;LSEQ=CTTCCACTTTGGGAAGGGAA;RSEQ=CACTTTTTCTATACTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:0:2,0:22.1:1:31.8:1:1:0:60:84:1:0:0.2 0/1:45:2:1,1:24,19:0.0444:2,2:27:1:28:1:1:1.25655:60:4:0.0455:0:1 -13 68406186 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23287;SOR=Inf;LSEQ=ACTTGGTTCTTTTGGTGTTT;RSEQ=AGGAGTTCTTTCCCGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:39,13:0:2,0:24.3:1:29.5:1:1:0:60:51:1:0:0.3 0/1:49:2:2,0:33,14:0.0408:2,0:22:1:31:1:1:0:60:4:0.0408:0:1 -13 68406205 . T A 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00044;SOR=0;LSEQ=TTAGGAGTTCTTTCCCGTTT;RSEQ=TTGTAGGATTTTTGTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:10:8,2:37,16:0.1587:2,2:28.5:1:27.7:1:0.71026:1.72:60:20:0.1724:0:1 0/0:68:0:0,0:49,19:0:2,0:23:1:29.7:1:1:0:60:33:1:0:0.2 -13 68406302 . A G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21398;LSEQ=ATTTTTGGCTGGAGTATCTC;RSEQ=TATAGATTTCTTCACTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:133:74:33,41:29,30:0.5564:2,2:23.8:1:30.8:1:0.7266:1.19935:55.3:73:0.5573:0:2 0/1:133:28:13,15:49,56:0.2105:2,2:24.5:1:30.5:1:1:1.00954:55.2:56:0.2121:0:2.1 -13 68406306 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23466;LSEQ=TTGGCTGGAGTATCTCATAT;RSEQ=GATTTCTTCACTGGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:74:34,40:31,30:0.5481:2,2:23.1:1:31.2:1:0.60675:1.21392:55.3:73:0.5489:0:2 0/1:136:30:14,16:48,58:0.2206:2,2:22.8:1:30.8:1:1:1.06:55.5:29:0.2148:0:2.1 -13 68406623 . T A 46 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31476;SOR=0.23984;LSEQ=AAAGCCCCCAAGGGAAACCA;RSEQ=TGGATGTACAGGCATTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:117,176:0.0101:2,2:8:1:29.3:1:0.5668:3.00:60:6:0.0104:0:1.3 0/0:409:1:1,0:175,233:0.0024:2,0:1:0:25:0:0.43032:0:60:2:0.0025:0:1 -13 68406678 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51318;SOR=Inf;LSEQ=ACTTTAATTGGAATCCCTTC;RSEQ=TAATTCATGGCCTCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:34,84:0:2,0:21.6:1:31.2:1:1:0:60:236:0.9833:0:0.1 0/1:170:2:1,1:58,110:0.0118:2,2:32.5:1:29:1:1:1.89:60:4:0.0118:0:1 -13 68406761 . G A 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18893;LSEQ=CGTTCTTAAAGATAACTGGT;RSEQ=CTCATTTTCATCATTATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:42:23,19:32,33:0.3925:2,2:22.7:1:29.4:1:0.69247:1.25:60:84:0.3962:0:1.1 0/1:148:16:6,10:71,61:0.1081:2,2:25.8:1:28.6:1:0.29103:1.93124:60:15:0.1034:0:1.1 -13 68406770 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51175;SOR=Inf;LSEQ=AGATAACTGGTGCTCATTTT;RSEQ=ATCATTATCCACCTTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:57,49:0:2,0:26.2:1:31.8:1:1:0:60:52:1:0:0.5 0/1:148:2:1,1:76,70:0.0135:2,2:11:1:28.5:1:1:1.0851:60:4:0.0136:0:1 -13 68406783 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50736;SOR=Inf;LSEQ=TCATTTTCATCATTATCCAC;RSEQ=TTAAAGTGATCATCTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:62,49:0:2,0:25.6:1:31.7:1:1:0:60:110:1:0:0.5 0/1:146:2:1,1:81,63:0.0137:2,2:7:0:32:0:1:1.28347:60:4:0.014:0:1.5 -13 68406829 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19396;SOR=0;LSEQ=TTAGTTCACTACTGAAAAGA;RSEQ=AATTCTAGGGCCTCAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:85,41:0.0156:2,2:34.5:1:32:1:0.55032:2.06041:60:4:0.0156:0:1.5 0/0:162:0:0,0:101,61:0:2,0:21.3:1:28.7:1:1:0:60:324:1:0:0.2 -13 68406834 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50787;SOR=Inf;LSEQ=TCACTACTGAAAAGATAATT;RSEQ=TAGGGCCTCAGGGGGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:85,43:0:2,0:26.2:1:31.3:1:1:0:60:41.667:1:0:0.2 0/1:169:2:1,1:107,60:0.0118:2,2:25.5:1:24.5:1:1:1.77681:60:4:0.012:0:1.5 -13 68406850 . G C 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03931;SOR=Inf;LSEQ=AATTCTAGGGCCTCAGGGGG;RSEQ=ACATGTCCATGTCCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:102,57:0:2,0:23.8:1:31.1:1:1:0:60:318:1:0:0.1 0/1:211:6:4,2:132,73:0.0284:2,2:22.3:1:31.2:1:1:1.11:60:12:0.029:0:1 -13 68930918 . G T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10785;SOR=0;LSEQ=AATGGTAGGGACATGGGATA;RSEQ=TTCAATACCAGTGGTACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:2,1:132,104:0.0126:2,2:26.7:1:31.7:1:1:1.57:60:6:0.0127:0:1.3 0/0:262:0:0,0:139,123:0:2,0:24.1:1:30.8:1:1:0:60:86.333:1:0:0.4 -13 68930985 . G T 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49003;SOR=1.13761;LSEQ=AAATAAATACATGCTTCCCA;RSEQ=AATAAAGTTTACAGGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:260:136:64,72:61,63:0.5231:2,2:24.2:1:28.8:1:0.80387:1.08893:60:44.333:0.5236:0:1.1 1/0:281:156:75,81:56,69:0.5552:2,2:23.9:1:28.1:1:0.63093:1.14:60:25:0.5455:0:1.1 -13 68931132 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23178;SOR=Inf;LSEQ=CAAAGCTGGCTAGTAATTGA;RSEQ=GAACACAGCCTGAAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:1,34:0:1,0:24.3:1:29.8:1:1:0:60:34:1:0:0.1 0/1:33:2:1,1:1,30:0.0606:1,2:23:1:27:1:0.11932:21.57:60:4:0.0606:0:1 -13 71158022 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTTCAGGAAATGTAATG;RSEQ=TTTCTACATTGCACTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 71158178 . T TAC 69 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=50;MSI=26.000;MSILEN=2;SSF=0.0052;SOR=Inf;LSEQ=AAAGGAGCTAGAACAGAACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:33,1:0:1,0:25.3:1:30.5:1:1:0:58.8:33:0.8684:0:0.7 0/1:23:5:5,0:17,0:0.2174:1,0:8.2:1:29.9:1:1:0:56:10:0.2174:0.1739:0.8 -13 71158314 . C T 53 Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2646;SOR=0.35547;LSEQ=CCCAGGAGCCCTGCCTGCCC;RSEQ=GACACCCAGCCCAGCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:432:5:0,5:260,167:0.0116:2,0:9.4:1:23.2:1:0.00966:0:60:4:0.0094:0:1.2 0/0:483:2:0,2:286,195:0.0041:2,0:1:0:24.5:1:0.16585:0:60:4:0.0042:0:1 -13 71158340 . C T 80 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18977;SOR=3.01668;LSEQ=CCAGCCCAGCTTGCCAATGG;RSEQ=GGACTCAAACGCCGCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:2:0,2:276,233:0.0039:2,0:1:0:25.5:1:0.211:0:60:4:0.004:0:1 0/1:597:7:3,4:310,280:0.0117:2,2:22.4:1:28.6:1:0.71374:1.47522:48.9:14:0.0119:0:1.3 -13 71158400 . G A 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01614;SOR=0;LSEQ=CAGACCACCGTGTTCAGTTT;RSEQ=TATTTTCGATTGAGAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:5:3,2:119,200:0.0154:2,2:11.6:1:26.4:1:0.36892:2.51:55.4:10:0.0157:0:1 0/0:413:0:0,0:151,262:0:2,0:23.4:1:30.8:1:1:0:60:102.25:1:0:0.2 -13 72248871 . T TAATAGAGTGCTCCATTCAAGTTTGAAAACTA 82 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACGGCAGGCACAGGAAAC;RSEQ=AATAAATTGCATGATGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:41.3:1:29.4:1:1:0:60:14:1:1:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 72249107 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49914;SOR=0;LSEQ=GTGTTCGCAGCCGCCACCGC;RSEQ=CTGCCGTCGCTCTCCAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:2,0:87,2:0.022:1,0:28.5:1:29.5:1:1:0:60:4:0.0222:0:4 0/0:80:0:0,0:71,9:0:2,0:29.9:1:29.4:1:1:0:55.4:25.667:1:0:0.1 -13 72249162 . A AG 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10048;SOR=0;LSEQ=GCTCGCCGAGCTCCAGCCGA;RSEQ=GAGAAGGGGGGTAAGTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:183:183:144,39:0,0:1:0,2:21.5:1:31.5:1:1:0:44.2:366:1:0.3005:0.1 1/1:160:157:98,59:1,1:0.9813:2,2:19.2:1:30.3:1:1:1.66:43.7:156:0.9811:0.325:0.1 -13 72249269 . C T 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00091;SOR=Inf;LSEQ=GAAGTAACTGGCTACAAAAG;RSEQ=CGCTCGCAAGAGTGCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:169,213:0:2,0:21.5:1:31:1:1:0:52.7:41.444:1:0:0.1 0/1:385:11:4,7:173,200:0.0286:2,2:17.1:1:28.5:1:0.55692:1.51216:58.7:22:0.0289:0:1 -13 72249284 . C T 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37438;SOR=0.26481;LSEQ=AAAAGCCGCTCGCAAGAGTG;RSEQ=GCCCTCTACTGGAGGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:4:2,2:137,195:0.0119:2,2:11.5:1:29.3:1:1:1.42:56.5:8:0.0121:0:1 0/0:315:1:0,1:134,179:0.0032:2,0:1:0:25:0:1:0:60:2:0.0032:0:1 -13 72249375 . ACTT A 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTTATCAGAAGTCCACTGA;RSEQ=CTGATTCGCAGACTTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:143,142:0:2,0:24.9:1:32.3:1:1:0:59.2:284:1:0:0.1 0/1:221:20:10,10:95,106:0.0905:2,2:29.1:1:31.4:1:0.81951:1.12:60:40:0.0909:0.009:0.2 -13 72249466 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23066;SOR=Inf;LSEQ=GCTTCCAGAGCGCAGCTATC;RSEQ=GTGCTTTGCAGGAGGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:142,49:0:2,0:27.1:1:29.8:1:1:0:42.7:46.75:1:0:0.1 0/1:177:2:1,1:111,64:0.0113:2,2:17:1:29:1:1:1.72863:46.5:4:0.0115:0:1 -13 72249469 . G T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23172;SOR=Inf;LSEQ=TCCAGAGCGCAGCTATCGGT;RSEQ=CTTTGCAGGAGGCAAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:140,48:0:2,0:27:1:31.9:1:1:0:42:93:1:0:0.1 0/1:175:2:2,0:111,61:0.0114:2,0:20.5:1:23:1:0.54202:0:56.5:4:0.0116:0:1 -13 72249638 . C CA 51 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.12614;SOR=0;LSEQ=GATGGGAAACATTTCATTCT;RSEQ=AAAAAAAAAATTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:4:1,3:77,224:0.0131:2,2:37.3:1:25.5:1:1:1.03116:51:3:0.0102:0:0.3 0/0:273:0:0,0:81,191:0:2,0:27.9:1:30.8:1:1:0:54.7:33:1:0:0.4 -13 72249647 . AAT A 64 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.37283;SOR=0.25447;LSEQ=CATTTCATTCTCAAAAAAAA;RSEQ=TTTTTTTTTTCTCTTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:4:0,4:45,216:0.015:2,0:33.8:1:32.3:1:1:0:60:8:0.0152:0:0 0/0:259:1:1,0:63,193:0.0039:2,0:35:0:32:0:0.24903:0:60:2:0.004:0:0 -13 72249648 . AT A 227 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=7e-05;SOR=2.10703;LSEQ=ATTTCATTCTCAAAAAAAAA;RSEQ=TTTTTTTTTTCTCTTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:268:158:18,140:21,45:0.5896:2,2:28.2:1:31.5:1:0.00044:3.60489:58.8:157:0.597:0.0112:0.1 1/0:262:197:36,161:25,31:0.7519:2,2:26.6:1:29.9:1:0.00014:3.58471:57.9:48.25:0.7539:0.2023:0.3 -13 72249649 . T A 126 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCATTCTCAAAAAAAAAA;RSEQ=TTTTTTTTTTCTCTTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:19:3,16:21,45:0.0709:2,2:16.7:1:29.8:1:0.24944:2.46533:57:38:0.0722:0:1.1 0/0:262:0:0,0:25,31:0:2,0:13.1:1:28.9:1:1:0:51:55:0.2148:0:0.2 -13 72249771 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20479;SOR=0;LSEQ=ATAGGGGACAGAAATCAGGT;RSEQ=TTGGCAGTTTTTCCGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:2,18:0.0909:2,2:12.5:1:32.5:1:0.25974:7.55:54:4:0.0909:0:1 0/0:26:0:0,0:3,23:0:2,0:23.5:1:30.2:1:1:0:51:52:1:0:0.2 -13 72278395 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50096;SOR=Inf;LSEQ=ACATAGAGTTGATCCTTTGG;RSEQ=CACGAATATGCAAATCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:30,8:0:2,0:25:1:32.3:1:1:0:60:76:1:0:0.1 0/1:48:2:1,1:31,15:0.0417:2,2:32:0:31:1:1:2.03311:60:4:0.0417:0:1 -13 72278445 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24774;SOR=Inf;LSEQ=TGTAGACATCAAGAGAATGC;RSEQ=TACTGTTCAAAAAGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:58,35:0:2,0:23.5:1:30.7:1:1:0:60:186:1:0:0.1 0/1:102:3:1,2:53,46:0.0294:2,2:17:1:27.7:1:0.59995:2.28605:60:6:0.0294:0:1 -13 72278472 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49932;SOR=Inf;LSEQ=TCAAAAAGGAATGCTCCACA;RSEQ=GTGTTACCATGGCAAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:75,50:0:2,0:25.6:1:31.5:1:1:0:60:250:1:0:0.1 0/1:138:2:1,1:72,63:0.0145:2,2:17:1:29:1:1:1.14174:60:4:0.0148:0:1 -13 72278495 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23623;SOR=Inf;LSEQ=GTTACCATGGCAAAACTGGA;RSEQ=GAGTCTACCATGTTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:71,67:0:2,0:27.5:1:30.5:1:1:0:60:276:1:0:0.2 0/1:131:2:1,1:63,66:0.0153:2,2:17:1:28.5:1:1:1.05:60:4:0.0154:0:2 -13 72278579 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02016;SOR=0.3033;LSEQ=TGCAAAGAGAATTAATGTGC;RSEQ=TACTGAGTATATGAAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:51:28:3,25:3,20:0.549:2,2:21.9:1:31.8:1:1:1.2445:60:56:0.549:0:1.1 0/1:30:8:2,6:2,20:0.2667:2,2:26.1:1:29:1:0.28352:3.18:60:16:0.2667:0:1.1 -13 73277800 . C T 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATATTCTGGCCTTTCGGC;RSEQ=GGAACCGCCATCTTCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:1:0,2:21.9:1:30.9:1:1:0:60:16:1:0:1.1 1/1:7:7:6,1:0,0:1:0,2:21.1:1:31.3:1:1:0:60:14:1:0:1 -13 73277913 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15852;SOR=0;LSEQ=ACATGGAGTTGTCCCTTTGG;RSEQ=CACGTATATGCGAAATCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:13,8:0.087:2,2:11:0:31.5:1:1:1.58984:60:4:0.087:0:1.5 0/0:34:0:0,0:18,16:0:2,0:27:1:31.8:1:1:0:59.6:68:1:0:0.1 -13 73333369 . T A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTGCCTTTCTACCAA;RSEQ=TCCCAAACATTCACAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 73334081 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4995;SOR=0;LSEQ=GAATACATCTCAACCTCATC;RSEQ=TCCCCTTCCCCACTGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:7,105:0.0175:2,2:19.5:1:29.5:1:0.136:14.10:60:4:0.0177:0:1 0/0:101:0:0,0:9,92:0:2,0:23:1:31.4:1:1:0:60:49.5:1:0:0.1 -13 73334603 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25182;SOR=0;LSEQ=AAACAGAAATAACTACGTCC;RSEQ=TTCTTTGACAAAATATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:212,49:0.0114:2,2:8.3:1:24.7:1:0.09644:8.55153:60:6:0.0114:0:2 0/0:231:0:0,0:171,60:0:2,0:23.1:1:30.6:1:1:0:60:114.5:1:0:0.1 -13 73335383 . G T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13694;LSEQ=TTTTCTGGCATGTATTTGGA;RSEQ=ATCAGGATAAATTCTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:49:47,2:46,1:0.5104:1,1:25.2:1:31.2:1:1:1.94429:60:98:0.5104:0:1.1 0/1:97:12:12,0:82,2:0.1237:1,0:22.9:1:30.8:1:1:0:60:24:0.1263:0:1.1 -13 73335469 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAAAGAAAAAGTGCCCCCC;RSEQ=GAAAAGAAAACAAACATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:0:0,0:367,198:0:2,0:26.6:1:29.8:1:1:0:60:55.5:1:0:0.2 0/1:638:21:13,8:381,233:0.0329:2,2:25.2:1:30.2:1:1:1.00626:60:20:0.0319:0:1.1 -13 73335767 . C T 100 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0071;SOR=9.91728;LSEQ=TTCATTTTTTCTAGCAGTAT;RSEQ=GACAAAAGGCAAATACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:1:0,1:229,153:0.0026:2,0:1:0:26:0:0.40209:0:60:2:0.0026:0:1 0/1:436:11:6,5:249,175:0.0252:2,2:19.5:1:29.1:1:0.76734:1.18524:60:22:0.0257:0:1.2 -13 73337440 . C CA 63 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.6835;SOR=1.70177;LSEQ=GTGACAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAACCAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:2,0:30,0:0.0625:1,0:31:1:30:1:1:0:60:4:0.0645:0:0 0/1:39:4:4,0:35,0:0.1026:1,0:25.3:1:31.5:1:1:0:60:8:0.1026:0:0 -13 73337683 . AT A 86 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.37899;SOR=0.51715;LSEQ=GTTCAGAAAATTCCTCATGA;RSEQ=TTTTTTTGCAACAGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:7:4,3:228,293:0.0133:2,2:17.3:1:30.7:1:0.70479:1.71:60:14:0.0134:0.0076:0.9 0/0:725:5:0,5:332,387:0.0069:2,0:26.4:1:29.6:1:0.06593:0:60:10:0.007:0:0 -13 73338175 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCACACTCCTGTAGTCCC;RSEQ=GCTACTTGAGAGGCTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 73338276 . C A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAGGCTGGGTGACAGAG;RSEQ=AAGACTCTGTGTCAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:25.5:1:28.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 73340242 . AAAGAC A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00066;SOR=Inf;LSEQ=TATAGTCAAGCAAGCCAATA;RSEQ=AAAAGTATAGAAATTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:43,182:0:2,0:22.5:1:30.2:1:1:0:60:36.5:1:0:0.1 0/1:268:12:2,10:53,203:0.0448:2,2:17.6:1:30.6:1:1:1.30421:60:24:0.0451:0.0187:0.1 -13 73343039 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17104;LSEQ=CTCAACTGAGCTTCAGCATA;RSEQ=GTCAGAGATGCCTAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:356:324:66,258:6,26:0.9101:2,2:24.3:1:30.4:1:1:1.11:60:107:0.9093:0:1.1 1/0:401:254:67,187:34,113:0.6334:2,2:24.9:1:30.1:1:0.55073:1.19:60:253:0.6341:0:1.1 -13 73344848 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58935;SOR=0.48705;LSEQ=GTTTATATCTCAGGTACTTA;RSEQ=ATGTATATGTTTTTTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:19,0:3,0:0.8636:0,1:24.3:1:30.6:1:1:0:60:18:0.8571:0:1 1/0:8:6:5,1:2,0:0.75:0,2:23:1:28:1:1:0:60:12:0.8571:0:1 -13 73345369 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=TTCTCAAATAACATTAATTA;RSEQ=ACAAGGAAAGAAAAGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:7,154:0.0123:1,2:8.5:1:31.5:1:0.09604:20.64:60:4:0.0126:0:1 0/0:150:0:0,0:18,132:0:2,0:22.4:1:29.9:1:1:0:60:49:1:0:0.1 -13 73345443 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00349;SOR=Inf;LSEQ=GTCAAATAAAAGGTTTGTTT;RSEQ=TATAAAAGCACTTATACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:2,41:0:1,0:20.9:1:32.9:1:1:0:60:86:1:0:0.1 0/1:30:6:0,6:0,24:0.2:1,0:12.2:1:27:1:1:0:60:5:0.1786:0:1.7 -13 73345851 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.2132;SOR=Inf;LSEQ=TTAAAGCCACATTATTCCAT;RSEQ=TATTTTTCTTAGCTAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:95,7:0:2,0:23.7:1:32.3:1:1:0:60:204:1:0:0.1 0/1:88:2:1,1:83,3:0.0227:1,2:22.5:1:31.5:1:0.08934:24.1044:60:4:0.0227:0:1 -13 73345995 . G A 56 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03239;SOR=Inf;LSEQ=TTGATCCAAGGCATTTCCTG;RSEQ=CCTAATAAAATGGCTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:0:0,0:243,279:0:2,0:26.8:1:31.2:1:1:0:60:39.154:1:0:0.1 0/1:586:6:5,1:265,315:0.0102:2,2:20.2:1:21.8:1:0.09975:5.93:60:2:0.007:0:2.2 -13 73346089 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22651;SOR=Inf;LSEQ=CTTGACTGGGTAAATGTACC;RSEQ=AATGGAGTTTTAATAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:31,116:0:2,0:21.4:1:28.5:1:1:0:60:48:1:0:0.1 0/1:134:2:1,1:29,103:0.0149:2,2:23:1:28.5:1:0.39895:3.51:60:4:0.0152:0:1 -13 73346722 . GA G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50276;SOR=0;LSEQ=CTATACCCAACAAAATGCAG;RSEQ=AAAGAGGGCCCGTGGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:2,0:65,6:0.0274:2,0:29.5:1:32.5:1:1:0:60:4:0.0282:0:0 0/0:58:0:0,0:58,0:0:1,0:26.4:1:29.5:1:1:0:60:57:1:0:0.1 -13 73347990 . C CA 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.44379;SOR=2.07839;LSEQ=TTAGGAATAAAGATTTTACA;RSEQ=AAAAAAAATCTGAGGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:2:0,2:140,168:0.0064:2,0:39:1:31:0:0.50308:0:60:4:0.0066:0:0 0/1:301:4:2,2:130,166:0.0133:2,2:23.3:1:30.1:1:1:1.28:60:8:0.0134:0.0033:0 -13 73348372 . A C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27931;SOR=0;LSEQ=AAGAACATGCATGCCAAACC;RSEQ=AACCACAGACATTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:0,3:0,16:0.1579:1,0:24:1:33.7:1:1:0:60:6:0.1579:0:1 0/0:11:0:0,0:0,11:0:0,0:23:1:30.5:1:1:0:60:22:1:0:0.2 -13 73349225 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00033;SOR=0.30857;LSEQ=AAACCATGTGTATGACATGC;RSEQ=TTAAATATACAGAACTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:110:62:61,1:46,1:0.5636:1,1:25.7:1:30.8:1:1:1.32:60:61:0.5648:0:1 0/1:67:19:18,1:48,0:0.2836:1,1:22.8:1:30.1:1:0.28358:0:60:18:0.2727:0:1.3 -13 73349321 . C CA 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.85728;SOR=0.92926;LSEQ=ATAATACAAAGCTACACAGA;RSEQ=AAAAAAAAATCCTGCTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:15:9,6:345,215:0.026:2,2:24.3:1:31.2:1:1:1.06964:59:30:0.0262:0.0035:0.7 0/1:660:16:10,6:399,244:0.0242:2,2:29.3:1:30.1:1:1:1.02:60:32:0.0249:0.0015:0.4 -13 73349359 . G C 268 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.9592;SOR=1.00656;LSEQ=AGATTCATACCATTCGTTCT;RSEQ=TCTCTTCTTCTTTCTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:306:165,141:224,176:0.4334:2,2:27.1:1:31.7:1:0.59374:1.08747:60:50:0.4317:0:1.1 0/1:862:375:211,164:273,212:0.435:2,2:27.8:1:31.4:1:1:1.00089:60:124:0.4382:0:1.1 -13 73349527 . C T 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00022;SOR=Inf;LSEQ=AGATTATCTGTTTAAAACAA;RSEQ=AGAGGGCACGTGCCCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:58,196:0:2,0:23.7:1:32.3:1:1:0:60:253:0.9961:0:0.1 0/1:266:13:5,8:71,182:0.0489:2,2:22.5:1:28.9:1:0.52886:1.60:60:26:0.0498:0:1 -13 73349918 . CA C 64 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.81051;LSEQ=CTGACAAATTGTGAGCACTG;RSEQ=AAAAAAAAAAGAAAAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:3,1:26,2:0.125:2,2:35.5:1:32:1:0.33952:4.04395:60:8:0.125:0:0.8 0/1:29:3:3,0:22,3:0.1034:2,0:18.3:1:31.1:1:1:0:60:6:0.1071:0.0345:0.3 -13 73349930 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.79251;LSEQ=GAGCACTGCAAAAAAAAAAA;RSEQ=AAAAAAGTTACTATTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:2,0:46,3:0.0392:2,0:7.5:1:30.5:1:1:0:60:4:0.0435:0:1.5 0/1:32:1:1,0:28,3:0.0313:2,0:7:0:25:0:1:0:60:2:0.0345:0:1 -13 73350079 . T C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22086;LSEQ=TTGCCTCTTTATTTTCTTCA;RSEQ=TGTCGCCATGAATCCATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:550:233:155,78:190,127:0.4236:2,2:24.9:1:32.2:1:0.12933:1.33:60:232:0.4241:0:1.1 0/1:681:95:58,37:328,258:0.1395:2,2:26.4:1:30.4:1:0.37374:1.23:60:22.75:0.1348:0:1.1 -13 73350257 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00718;SOR=Inf;LSEQ=AAGAAGCAAACCAAAAGATG;RSEQ=CGCTAATAAGTCTTCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:31,135:0:2,0:26.3:1:31.1:1:1:0:60:40.5:1:0:0.1 0/1:168:8:2,6:36,123:0.0476:2,2:14.3:1:29.4:1:1:1.14:60:16:0.0482:0:1.4 -13 73351707 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.516;SOR=Inf;LSEQ=AAAATGGATAGTCTTGTTTG;RSEQ=GACAGTATACACGTCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:14,113:0:2,0:22:1:30.1:1:1:0:60:126:0.9921:0:0.1 0/1:187:2:0,2:25,160:0.0107:2,0:26:1:32:0:1:0:60:4:0.0107:0:1 -13 73352630 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24228;SOR=Inf;LSEQ=AGAAAAAGTCAATGGTATAT;RSEQ=TTTTCTCTTGAATGTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:0,46:0:1,0:25.1:1:32.5:1:1:0:60:45:1:0:0 0/1:48:3:0,3:1,44:0.0625:1,0:12.3:1:30:1:1:0:60:6:0.0625:0:1 -13 73353348 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTACTGCAACCTCTACC;RSEQ=CCGGGTTCAAGTGATCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29:1:1:0:60:4:1:0:3.5 -13 73354335 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGCCTGGCATAGTGGTGC;RSEQ=TGACTGTAATCCCAGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 73354919 . G C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23465;SOR=Inf;LSEQ=AATGTCATAAATTACTCACA;RSEQ=GAACCCTCTCCCGAATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:112,12:0:2,0:25:1:32:1:1:0:60:40.333:1:0:0.1 0/1:117:2:1,1:104,11:0.0171:2,2:15:0:32:1:0.1954:9.09546:60:4:0.0174:0:1 -13 73354930 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49833;SOR=Inf;LSEQ=TTACTCACAGGAACCCTCTC;RSEQ=CGAATTTTGCTAATCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:128,21:0:2,0:24.9:1:30.9:1:1:0:60:148:1:0:0 0/1:150:2:1,1:128,20:0.0133:2,2:29:1:30.5:1:0.26121:6.27012:60:4:0.0133:0:1 -13 73355574 . A G 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00739;SOR=Inf;LSEQ=AACTAAATTTTTTAAAGCAC;RSEQ=AGGAAAAGAACCTCGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:37,75:0:2,0:24.6:1:30.4:1:1:0:60:55:1:0:0.1 0/1:91:6:1,5:20,65:0.0659:2,2:20.3:1:29.8:1:1:1.53188:60:5:0.0562:0:1 -13 73355673 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49966;SOR=Inf;LSEQ=CAAAGACCCGCCTCCCTGGG;RSEQ=CTCAGTTTCCCTGTCATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:124,32:0:2,0:23:1:31.6:1:1:0:60:38:1:0:0.1 0/1:172:2:1,1:130,40:0.0116:2,2:15.5:1:29.5:1:0.42098:3.22243:60:4:0.0116:0:1 -13 73355679 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50139;SOR=Inf;LSEQ=CCCGCCTCCCTGGGCCTCAG;RSEQ=TTCCCTGTCATACCCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:132,35:0:2,0:23.1:1:29.5:1:1:0:60:40.75:1:0:0.1 0/1:195:2:1,1:145,48:0.0103:2,2:23:1:32.5:1:0.44039:3.00014:60:4:0.0104:0:1 -13 73356410 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAACCTTGTGCTTCCGAC;RSEQ=GGAGACGCCTTTGGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:47:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 75628825 . GACA G 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.38801;SOR=0.5376;LSEQ=ACAGCTATTTAAAGGAATCA;RSEQ=ACAACCAAGGTAGCCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:14,0:13,0:0.5185:1,1:25.1:1:33.3:1:1:0:60:28:0.5185:0.1111:0.1 0/1:22:8:8,0:13,1:0.3636:1,0:31.5:1:33:1:1:0:60:16:0.3636:0.0455:0.3 -13 75629027 . C T 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03114;SOR=0.71752;LSEQ=AAAATTTGGATTCAGAACTC;RSEQ=CAAGCCAACCAGAAATTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:129:64,65:103,84:0.4082:2,2:26.6:1:30.3:1:0.36042:1.24447:60:42:0.4078:0:1.1 0/1:426:141:68,73:134,150:0.331:2,2:26.7:1:29.3:1:0.91787:1.04:60:34.25:0.327:0:1.1 -13 75629056 . A G 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07363;SOR=0;LSEQ=CCAGAAATTGAGGAACCAAA;RSEQ=TCAAGGGGAAAACAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:130,165:0.01:2,2:26.3:1:26.3:1:1:1.57345:60:2:0.0068:0:2 0/0:413:0:0,0:176,236:0:2,0:26.1:1:29.8:1:1:0:60:81.4:1:0:0.4 -13 75629119 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49835;SOR=0;LSEQ=TTAGGAATGGGCTGAATGGA;RSEQ=CAAGAAGTAGAAAAAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:34,116:0.0132:2,2:16.5:1:29:1:0.40868:3.38:60:4:0.0136:0:1 0/0:151:0:0,0:44,107:0:2,0:22.6:1:32:1:1:0:60:150:1:0:0.2 -13 75629124 . A C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24721;SOR=Inf;LSEQ=AATGGGCTGAATGGAGCAAG;RSEQ=AGTAGAAAAAGTCAGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:27,107:0:2,0:23.5:1:29.7:1:1:0:60:32.5:1:0:0.1 0/1:134:2:1,1:36,96:0.0149:2,2:17:1:28.5:1:0.4775:2.64:60:4:0.0152:0:1.5 -13 75909122 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1467;SOR=0;LSEQ=ATATATAACCCATCTCCACA;RSEQ=TGGCCACTGCACAGACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:70,21:0.0215:2,2:18.5:1:29.5:1:0.41912:3.27985:60:4:0.022:0:1.5 0/0:149:0:0,0:104,45:0:2,0:24.9:1:29.5:1:1:0:60:73.5:1:0:0.3 -13 75909125 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5228;SOR=Inf;LSEQ=TATAACCCATCTCCACAATG;RSEQ=CCACTGCACAGACACTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:73,25:0:2,0:23.9:1:31.4:1:1:0:60:48:1:0:0.4 0/1:154:2:1,1:104,48:0.013:2,2:20.5:1:26.5:1:0.53654:2.15477:60:4:0.0133:0:1 -13 75909164 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.53238;SOR=Inf;LSEQ=CCTCATCCCACCCAGGCTGT;RSEQ=CCACTCCCTGCTGGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:78,40:0:2,0:26.8:1:31.7:1:1:0:60:38.333:1:0:0.7 0/1:201:2:1,1:112,87:0.01:2,2:18:1:27:1:1:1.28571:60:4:0.0103:0:1.5 -13 75909166 . C CA 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00097;SOR=0.40265;LSEQ=TCATCCCACCCAGGCTGTGC;RSEQ=ACTCCCTGCTGGGGCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:128:108:71,37:12,8:0.8438:2,2:25:1:29.3:1:0.61936:1.28:60:35:0.84:0.1641:0.8 1/0:225:154:85,69:38,32:0.6844:2,2:23.6:1:29.3:1:1:1.04:60:308:0.6875:0.1689:0.8 -13 75909196 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32121;LSEQ=TGGGGCTGCCACCCCAACAC;RSEQ=TGCACATCCTCAGCCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:150:123:63,60:13,14:0.82:2,2:25.2:1:29.7:1:0.8335:1.13:60:29.75:0.8151:0:1.2 1/0:241:143:70,73:49,48:0.5934:2,2:24:1:29.9:1:0.89542:1.06429:60:70.5:0.6026:0:1.1 -13 75909238 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18078;SOR=0;LSEQ=GGCACCCATCCCTGTGAATG;RSEQ=TCGCTCCCCTCCACTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:62,80:0.0139:2,2:31.5:1:29.5:1:1:1.29:60:4:0.0143:0:2 0/0:194:0:0,0:79,115:0:2,0:25.6:1:31.9:1:1:0:60:96:1:0:0.6 -13 75909241 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18703;SOR=0;LSEQ=ACCCATCCCTGTGAATGCTC;RSEQ=CTCCCCTCCACTGTGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:60,81:0.014:2,2:24:0:31:0:1:1.35:60:4:0.0142:0:1.5 0/0:187:0:0,0:74,113:0:2,0:25.8:1:30.9:1:1:0:60:92.5:1:0:0.5 -13 75909256 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51027;SOR=Inf;LSEQ=TGCTCGCTCCCCTCCACTGT;RSEQ=GCTCTGACACCCGCACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:49,79:0:2,0:24.9:1:31.4:1:1:0:60:127:0.9922:0:0.7 0/1:176:2:1,1:65,109:0.0114:2,2:19.5:1:29:1:1:1.67:60:4:0.0114:0:1 -13 75909295 . G T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.82886;LSEQ=GGCCTTCCCTCTGCCAGTAT;RSEQ=CTGCCTCCTACAACCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:24,53:0.0253:2,2:6:1:29:1:0.53554:2.18:60:4:0.026:0:1 0/1:95:2:1,1:23,70:0.0211:2,2:26:1:28:1:0.44345:3.00:60:4:0.0213:0:1 -13 76833565 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50139;SOR=Inf;LSEQ=GAAGGGTTGGTCTTGTCTTA;RSEQ=GAGTGGCAGAGGTGAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:96,14:0:2,0:21.7:1:29.9:1:1:0:60:54:1:0:0.1 0/1:130:2:1,1:103,25:0.0154:2,2:32.5:1:31.5:1:0.36124:4.05956:60:4:0.0156:0:1 -13 76833573 . A T 52 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.065;SOR=Inf;LSEQ=GGTCTTGTCTTAAGAGTGGC;RSEQ=GAGGTGAAAGAAAATCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:104,21:0:2,0:22.9:1:30.3:1:1:0:60:250:1:0:0.1 0/1:149:5:2,3:114,30:0.0336:2,2:7.2:1:22.8:1:0.07235:5.61133:60:1.5:0.0204:0:1.2 -13 76833590 . C T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25497;SOR=Inf;LSEQ=GGCAGAGGTGAAAGAAAATC;RSEQ=ACGTATAATGAATCTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:128,52:0:2,0:24.1:1:31.4:1:1:0:60:179:1:0:0.1 0/1:218:3:1,2:157,58:0.0138:2,2:17.3:1:21.3:1:0.18431:5.36417:60:2:0.0094:0:1 -13 76833621 . G T 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCTGTGGAGTTCAAACCT;RSEQ=CATTGTTCAACCTGTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:195,124:0:2,0:25.3:1:31.9:1:1:0:60:78.75:0.9968:0:0.2 0/1:374:29:19,10:210,135:0.0775:2,2:28.1:1:29.2:1:0.69474:1.22:60:58:0.0784:0:1.1 -13 76833684 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.30163;LSEQ=GCATCCTGGCAGTATACAAA;RSEQ=CTTGCTACCCTGTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:84:40,44:164,182:0.1953:2,2:24.7:1:32:1:1:1.01:60:83:0.1967:0:1.1 0/1:575:256:122,134:148,170:0.4452:2,2:24.7:1:31.6:1:0.80127:1.05:60:127:0.4464:0:1.1 -13 76833862 . G T 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4455;SOR=0.41614;LSEQ=TTATTGGACATTTATTGTTT;RSEQ=CAATGCACAGTTTCAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:0,7:0,20:0.2593:1,0:28.7:1:30.7:1:1:0:60:14:0.2593:0:1 0/1:16:2:0,2:0,14:0.125:1,0:12:1:26.5:1:1:0:60:4:0.125:0:1 -13 78503715 . T G 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATCTTAGTTCTTCTGAAG;RSEQ=TTAGATGCTGGTTCATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:1:0,2:31.9:1:32.4:1:1:0:60:18:1:0:2.2 1/1:7:7:6,1:0,0:1:0,2:8.7:1:31.1:1:1:0:60:14:1:0:1.9 -13 78503731 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GAAGTTTAGATGCTGGTTCA;RSEQ=GCCCTGAAAACCCATTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:1:0,2:28.1:1:30.4:1:1:0:60:11:1:0:1.9 1/1:8:7:6,1:1,0:0.875:0,2:17.1:1:32.3:1:1:0:60:14:0.875:0:1.9 -13 78503873 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21778;SOR=0;LSEQ=TCTGGGAAAGAGGAGAGCAT;RSEQ=GACTTCAGGAACGCTGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:78,64:0.0139:2,2:27.5:1:29.5:1:1:1.21706:60:4:0.014:0:1 0/0:164:0:0,0:89,75:0:2,0:24.7:1:30.8:1:1:0:60:53.667:1:0:0.2 -13 78503886 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50006;SOR=Inf;LSEQ=AGAGCATGGACTTCAGGAAC;RSEQ=CTGACTCCTGGCCATTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:76,71:0:2,0:28.6:1:30.8:1:1:0:60:146:1:0:0.3 0/1:165:2:1,1:81,82:0.0121:2,2:35:1:28.5:1:1:1.01:60:4:0.0123:0:1 -13 78503966 . A G 170 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00368;SOR=0.11855;LSEQ=ATCCTCTGGGTAAAAGAAAG;RSEQ=GTAAGAATAGTGTCTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:45:9,36:0,2:0.9574:0,2:21.1:1:31:1:1:0:60:90:0.9574:0:1.1 1/0:36:26:1,25:1,9:0.7222:2,1:23.4:1:30.2:1:0.48413:2.68742:60:52:0.7222:0:1.3 -13 78504047 . T C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTGCGTGGAATACAGTGA;RSEQ=TGTCTAGGAAATGTCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:23.3:1:32.7:1:1:0:60:22:1:0:1.4 1/1:8:8:0,8:0,0:1:0,0:24.1:1:32.8:1:1:0:60:16:1:0:1.4 -13 79333573 . CA C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAAGGTGAGACACCATCT;RSEQ=AAAAAAAAAAAAAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 79335274 . C T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01412;SOR=Inf;LSEQ=TTTATAAAAGCATAGCCTTT;RSEQ=GGCCAGAACCACCATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:27,20:0:2,0:25.8:1:30.1:1:1:0:60:46:1:0:0.2 0/1:37:5:3,2:17,15:0.1351:2,2:29.2:1:28.4:1:1:1.31:60:10:0.1351:0:1.6 -13 79335295 . A G 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19394;SOR=Inf;LSEQ=GGCCAGAACCACCATCTTCC;RSEQ=GTAAATCGCCAAAATGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:30,24:0:2,0:27.7:1:30.6:1:1:0:60:108:1:0:0.1 0/1:43:2:1,1:20,21:0.0465:2,2:24.5:1:24:1:1:1.05:60:4:0.0465:0:1 -13 79335305 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50011;SOR=0;LSEQ=ACCATCTTCCAGTAAATCGC;RSEQ=AAAATGATAAACAAAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:26,26:0.037:2,2:23:1:28:1:1:1:60:4:0.0377:0:1 0/0:44:0:0,0:21,23:0:2,0:29:1:30.4:1:1:0:59.5:21:1:0:0.5 -13 79335332 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49608;SOR=0;LSEQ=ATAAACAAAAGGGAAAGAGG;RSEQ=GAGGCACCCAATATATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:22,26:0.04:2,2:20.5:1:30:1:1:1.18:60:4:0.04:0:1 0/0:45:0:0,0:20,25:0:2,0:18.8:1:29.9:1:1:0:59.5:90:1:0:0.4 -13 79335334 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22649;SOR=Inf;LSEQ=AAACAAAAGGGAAAGAGGAG;RSEQ=GGCACCCAATATATGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:0:2,0:22.8:1:30.2:1:1:0:60:48:1:0:0.2 0/1:45:2:1,1:19,24:0.0444:2,2:16:0:31:1:1:1.26:60:4:0.0455:0:2.5 -13 79335579 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4918;SOR=Inf;LSEQ=TTGCCAATAGAATTAATGTG;RSEQ=GTATTGAGCACACAAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:10,21:0:2,0:27.2:1:31.3:1:1:0:60:62:1:0:0.2 0/1:31:2:1,1:15,14:0.0645:2,2:25.5:1:28:1:1:1.06901:60:4:0.0667:0:1 -13 79335796 . TA T 42 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATTCATGGCATAATAGGTGT;RSEQ=AAAAAAAAAAAAGACCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:21:1:26.8:1:1:0:60:2:0.5:0.25:0 0/0:2:0:0,0:1,1:0:2,0:3:0:28.5:1:1:0:60:4:1:0:0.5 -13 80561254 . G T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00377;SOR=5.23198;LSEQ=TTGATTTTTCAGTTTGTTCA;RSEQ=GTTTGACTTCTTAGAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:10:10,0:24,0:0.2941:1,0:25.6:1:32.2:1:1:0:60:20:0.303:0:1 1/0:26:18:18,0:8,0:0.6923:0,1:23.9:1:30.1:1:1:0:60:17:0.68:0:1 -13 80561304 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49709;SOR=0;LSEQ=TCTAAGCTCCTTACATGCCA;RSEQ=AACAAAGGCAGAAGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:65,7:0.027:2,0:17.5:1:29:1:1:0:60:4:0.0278:0:1.5 0/0:69:0:0,0:62,7:0:2,0:25.4:1:31.7:1:1:0:60:68:1:0:0.7 -13 80561354 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18697;SOR=0;LSEQ=TTAAAATATTCACATTTATC;RSEQ=GCAGTATCTGTGGAGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:130,46:0.0112:2,2:27.5:1:29:1:0.45947:2.80659:60:4:0.0114:0:1 0/0:233:0:0,0:168,65:0:2,0:20.3:1:30.6:1:1:0:60:115.5:1:0:1 -13 80561367 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.01433;LSEQ=ATTTATCTGCAGTATCTGTG;RSEQ=AGTCCCATCAATTTTGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:73:52,21:110,50:0.3133:2,2:21:1:30:1:0.76027:1.12:60:146:0.3188:0:1.7 1/0:295:191:123,68:68,36:0.6475:2,2:22.7:1:29.2:1:0.89903:1.04412:60:94.5:0.6473:0:1.6 -13 80561434 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.03023;SOR=0;LSEQ=GGATTTTCCCATTTTGCAAA;RSEQ=AAAAAAAAGATCATCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:4:2,2:191,186:0.0105:2,2:17.5:1:25.5:1:1:1.02682:60:3:0.0079:0:2.8 0/0:532:0:0,0:249,282:0:2,0:25.2:1:31:1:1:0:60:87.5:0.9981:0:1 -13 80561436 . A T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=3.94035;LSEQ=ATTTTCCCATTTTGCAAAGA;RSEQ=AAAAAAGATCATCGGGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:128:62,66:130,124:0.3351:2,2:25:1:29.4:1:0.66487:1.1157:60:256:0.336:0:1.4 1/0:529:352:164,188:81,96:0.6654:2,2:24.8:1:28.4:1:0.9264:1.03:60:351:0.6648:0:1.4 -13 85271335 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00179;SOR=0.20207;LSEQ=AAATAAAATAAATAGACTAC;RSEQ=AGCTAGACTAGTAAAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:21:5,16:4,8:0.6364:2,2:20:1:31.6:1:0.69046:1.5767:60:42:0.6563:0:1.1 0/1:39:10:4,6:10,19:0.2564:2,2:25.9:1:30.2:1:1:1.26:60:20:0.2632:0:1 -13 87971222 . G A 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTCATTAAATAGCACAGT;RSEQ=GAAATGTGGAAGCGATCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:153,38:0:2,0:23.1:1:31.9:1:1:0:60:190:1:0:0.1 0/1:160:22:16,6:112,26:0.1375:2,2:24.4:1:28.9:1:0.39126:1.61004:60:44:0.1384:0:1 -13 87971336 . C T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.39288;LSEQ=TCTTCATAATGAGATGGGCC;RSEQ=TTTCCTCTTAGAAGAGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:495:315:148,167:89,90:0.6364:2,2:26.6:1:30.4:1:0.57505:1.11559:60:104:0.6367:0:1.1 0/1:501:204:94,110:138,158:0.4072:2,2:25.3:1:30.1:1:0.92747:1.02205:60:67:0.4077:0:1.1 -13 87971354 . A T 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTTTCCTCTTAGAAGAGT;RSEQ=GTCACAAGTTGAAAGTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:202,271:0:2,0:26.7:1:29.7:1:1:0:60:93.6:1:0:0.6 0/1:444:36:13,23:184,224:0.0811:2,2:27.8:1:30:1:0.38196:1.4521:60:72:0.0818:0:1.1 -13 88542298 . AT A 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.571;LSEQ=CAGTTAAGAATACTCACCTC;RSEQ=TTTTTTTTTATCTCAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:18,0:0.1:1,0:9:1:31.3:1:1:0:60:4:0.1:0.05:0 0/1:17:1:1,0:13,3:0.0588:2,0:30:0:32:0:1:0:60:2:0.0625:0:0 -13 88542455 . A G 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.06356;LSEQ=AATGGTTATAGGGCACCGCA;RSEQ=TGTATGTGAGAGCATAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:46:26,20:166,121:0.1377:2,2:30:1:32.6:1:0.87363:1.05512:60:92:0.1407:0:1.1 0/1:304:100:55,45:115,89:0.3289:2,2:25.7:1:31.1:1:0.90221:1.05699:60:99:0.3333:0:1.1 -13 88542881 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61673;SOR=0.47958;LSEQ=GTGGGACAATTTCTTTTCAG;RSEQ=AGGTGACAGGCAGTCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:0,2:46,63:0.018:2,0:31.5:1:29.5:1:0.51024:0:60:4:0.0185:0:1.5 0/0:115:1:0,1:51,63:0.0087:2,0:42:0:28:0:1:0:60:2:0.009:0:1 -13 88542916 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49704;SOR=Inf;LSEQ=CATCAGATAGCAACTAGTTT;RSEQ=ATAGAGGCTCATTTGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:28,57:0:2,0:25.7:1:31.4:1:1:0:60:170:1:0:0.1 0/1:85:2:1,1:28,55:0.0235:2,2:10.5:1:27:1:1:1.95:60:4:0.0235:0:1 -13 88543077 . AG A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49574;SOR=Inf;LSEQ=GAAACCAAGGGCTCTGTCAC;RSEQ=GGGGAGACAGAGTGGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:0:2,0:20.7:1:31.7:1:1:0:60:78:1:0:0.1 0/1:44:2:1,1:30,12:0.0455:2,2:16:1:29.5:1:0.50846:2.44164:60:4:0.0476:0:0 -13 88543179 . C T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2369;SOR=0;LSEQ=CTGAGTCTTCCAGAAGGCAT;RSEQ=GTGCAGTGAGCAGTGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:47,34:0.0241:2,2:7:0:28.5:1:1:1.37686:60:4:0.0241:0:1 0/0:87:0:0,0:53,34:0:2,0:25.3:1:29.8:1:1:0:60:20.75:1:0:0.1 -13 88543183 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24267;SOR=Inf;LSEQ=GTCTTCCAGAAGGCATCGTG;RSEQ=AGTGAGCAGTGGGGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:52,34:0:2,0:23.8:1:31.9:1:1:0:60:42:1:0:0.1 0/1:84:2:2,0:49,33:0.0238:2,0:21:1:28:1:0.51721:0:60:4:0.0247:0:1 -13 88543265 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50393;SOR=Inf;LSEQ=TCAATAGAGCTGGGTGGCTG;RSEQ=AGCAGTCTTCGGGGACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:86,70:0:2,0:26.2:1:29.9:1:1:0:60:77:1:0:0.1 0/1:192:2:1,1:100,90:0.0104:2,2:35:0:32.5:1:1:1.1105:60:4:0.0104:0:1.5 -13 88543278 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18814;SOR=0;LSEQ=GTGGCTGAAGCAGTCTTCGG;RSEQ=GACCAGGAGAAGCCTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:79,75:0.0128:2,2:25.5:1:29:1:1:1.053:60:4:0.013:0:1 0/0:203:0:0,0:100,103:0:2,0:28.1:1:30.4:1:1:0:60:49.75:1:0:0.2 -13 88543512 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4997;SOR=0;LSEQ=ATTTGGGGAATGGGTTTTTT;RSEQ=TCCACTGCCCTTATCTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:119,74:0.0103:2,2:6.5:1:27.5:1:1:1.60399:60:4:0.0104:0:1 0/0:178:0:0,0:112,66:0:2,0:22.8:1:30.9:1:1:0:60:177:1:0:0.2 -13 88543630 . C T 46 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02784;SOR=Inf;LSEQ=TTTTTTTTTTTTCTTTGCAT;RSEQ=AAGGTGCCAGGACCTCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:162,124:0:2,0:21:1:30:1:1:0:59.8:8.226:1:0:0.5 0/1:280:5:3,2:149,123:0.0179:2,2:5.8:1:20.2:1:1:1.24:60:1.5:0.012:0:1.4 -13 88543770 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02586;SOR=Inf;LSEQ=GGAATAACACCCAAAGAGCA;RSEQ=TTATCTTCTTGAATTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:141,180:0:2,0:25.4:1:32.1:1:1:0:60:320:1:0:0.1 0/1:300:5:2,3:134,161:0.0167:2,2:8.2:1:30.2:1:1:1.24754:60:10:0.0168:0:1.2 -13 88543882 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52661;SOR=0;LSEQ=CTATGATGCCAGAGAAGGAA;RSEQ=AACTATTCTTGCTGCCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:48,87:0.0146:2,2:16:1:32.5:1:1:1.80:60:4:0.0149:0:1 0/0:84:0:0,0:28,56:0:2,0:19.6:1:29.7:1:1:0:60:83:1:0:0.1 -13 88544037 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17616;SOR=Inf;LSEQ=TTTTTTTCCATGGCCTCATG;RSEQ=TCCACACAAATTTGTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:76,27:0:2,0:26.3:1:29.8:1:1:0:60:33.333:1:0:0.2 0/1:75:2:1,1:49,24:0.0267:2,2:16.5:1:30:1:1:2.02078:60:4:0.0267:0:1 -13 88544040 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.16872;SOR=Inf;LSEQ=TTTTCCATGGCCTCATGTTC;RSEQ=ACACAAATTTGTTCCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:78,26:0:2,0:26.2:1:31.3:1:1:0:60:103:1:0:0.2 0/1:73:2:2,0:49,22:0.0274:2,0:23.5:1:27:1:1:0:60:4:0.0278:0:3 -13 88544233 . G A 50 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10957;SOR=5.49343;LSEQ=ATGAAGTGCCACATGTCTCT;RSEQ=GATCAATTCCTTAACATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:1:1,0:154,239:0.0025:2,0:1:0:24:0:0.3934:0:60:2:0.0026:0:1 0/1:362:5:4,1:139,218:0.0138:2,2:5:1:21.8:1:0.08181:6.24:60:4:0.0113:0:1 -13 88544358 . G A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCCAGTCAGCCACTGAGAA;RSEQ=CGATTGCCATCCCACACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:83,105:0:2,0:26.5:1:31.8:1:1:0:60:187:1:0:0.1 0/1:166:17:9,8:78,71:0.1024:2,2:25.5:1:30.5:1:1:1.02:60:34:0.103:0:1.1 -13 88544427 . C A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.66858;SOR=1.70228;LSEQ=CAGTGGTGGCCTGTACACTG;RSEQ=TAGACCAGAGAGCTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:53,88:0.014:2,2:1:0:28.5:1:1:1.65:60:4:0.0143:0:1 0/1:127:3:2,1:54,70:0.0236:2,2:25:1:27.3:1:0.58257:2.57:60:6:0.0244:0:1 -13 88544519 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23931;SOR=Inf;LSEQ=CTTTTCCCTTCATTACCAGT;RSEQ=TACACTACTGTTTCTATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:60,70:0:2,0:25.6:1:31.7:1:1:0:60:64:1:0:0.1 0/1:125:2:1,1:69,54:0.016:2,2:27:1:29.5:1:1:1.27524:60:4:0.0163:0:1 -13 88544588 . A G 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49873;SOR=0;LSEQ=TTCACCATGATTTCCCTGAC;RSEQ=GCAGCAACACCTGGTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:91,93:0.0108:2,2:30.5:1:26:1:1:1.02:60:4:0.0109:0:1 0/0:181:0:0,0:92,89:0:2,0:26.3:1:30:1:1:0:60:35.2:1:0:0.1 -13 88544636 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50027;SOR=Inf;LSEQ=GTATATAATATGAGCCTTTG;RSEQ=TTTTCGTGTAACTCGATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:63,69:0:2,0:23.6:1:30.3:1:1:0:60:65:1:0:0.1 0/1:150:2:1,1:64,84:0.0133:2,2:27:1:28:1:1:1.31:60:4:0.0134:0:0 -13 88544720 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50905;SOR=Inf;LSEQ=TCAGGTGTTTTGTAGGGATA;RSEQ=TAAAGAAATTCATGGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:27,44:0:2,0:25:1:31.6:1:1:0:60:34.5:1:0:0.2 0/1:97:2:2,0:38,57:0.0206:2,0:19:1:26:1:0.16753:0:60:4:0.0208:0:1 -13 88544737 . A T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12605;SOR=Inf;LSEQ=ATAGTAAAGAAATTCATGGC;RSEQ=TATTCACCAGAATTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:28,36:0:2,0:23.9:1:29.7:1:1:0:60:15:1:0:0.2 0/1:77:4:2,2:33,40:0.0519:2,2:22:1:30.3:1:1:1.21:60:8:0.0519:0:1 -13 88544795 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20858;SOR=Inf;LSEQ=AAAACTGATGTTTCAACAGT;RSEQ=GGTGAACCTACTTCCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:45,46:0:2,0:24.5:1:31.4:1:1:0:60:44.5:1:0:0.1 0/1:77:2:1,1:36,39:0.026:2,2:28:1:28.5:1:1:1.08:60:4:0.0267:0:1 -13 88544803 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21082;SOR=Inf;LSEQ=TGTTTCAACAGTGGGTGAAC;RSEQ=TACTTCCTCTTCACTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:48,48:0:2,0:25.7:1:31.6:1:1:0:60:192:1:0:0.2 0/1:82:2:1,1:42,38:0.0244:2,2:18:0:32.5:1:1:1.10391:60:4:0.0247:0:1 -13 88545032 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49862;SOR=Inf;LSEQ=TTCTGGGTTGTGTTCTTTTA;RSEQ=TTTGTTAATGATGAACTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:99,50:0:2,0:27.2:1:31.5:1:1:0:60:23.833:1:0:0.2 0/1:156:2:1,1:94,60:0.0128:2,2:30:0:30:1:1:1.56196:60:4:0.013:0:1.5 -13 88545081 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21129;SOR=0;LSEQ=GGACACTTGAAGGTGGTTTC;RSEQ=ATTGTATTACACCCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:94,84:0.0111:2,2:47:0:32:1:1:1.11835:60:4:0.0111:0:1 0/0:211:0:0,0:98,113:0:2,0:24.4:1:28.9:1:1:0:60:41.2:1:0:0.1 -13 88545085 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21762;SOR=0;LSEQ=ACTTGAAGGTGGTTTCTATT;RSEQ=TATTACACCCTTCTCCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:92,91:0.0108:2,2:8.5:1:30.5:1:1:1.01093:60:4:0.0109:0:1 0/0:211:0:0,0:99,112:0:2,0:24.9:1:31.1:1:1:0:60:69.333:1:0:0.1 -13 88545141 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6195;SOR=2.05601;LSEQ=CATTACATGCAACAAGGCTT;RSEQ=TCAGTGTACTTTCAACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:62,109:0.0058:2,0:1:0:23:0:0.36628:0:60:2:0.0058:0:1 0/1:168:2:1,1:69,97:0.0119:2,2:30.5:1:28:1:1:1.40:60:4:0.012:0:1 -13 88545143 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24334;SOR=Inf;LSEQ=TTACATGCAACAAGGCTTGT;RSEQ=AGTGTACTTTCAACATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:61,109:0:2,0:28:1:31.8:1:1:0:60:55.667:1:0:0.1 0/1:166:2:1,1:67,97:0.012:2,2:30.5:1:27:1:1:1.44:60:4:0.0123:0:1 -13 88545378 . G A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0437;SOR=Inf;LSEQ=ATTCTTGCAACAACTGTCAA;RSEQ=AGTAATTCTACCTTGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,9:0:2,0:25.1:1:32.2:1:1:0:60:42:1:0:0 0/1:13:3:2,1:8,2:0.2308:2,2:13.7:1:30.7:1:1:1.88511:60:6:0.2308:0:1 -13 88545458 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32879;SOR=3.70854;LSEQ=GCTTAAAAAGAGATAACTAG;RSEQ=TGTTCTCTGCTCTGATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:44,16:0.0164:2,0:1:0:27:0:0.27869:0:60:2:0.0172:0:1 0/1:51:3:1,2:31,17:0.0588:2,2:14.3:1:29.7:1:0.54747:3.55085:60:6:0.0588:0:1.3 -13 88545493 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24136;SOR=0;LSEQ=ATTCTTCATCATTCTCTGAC;RSEQ=TTGATGGGGAAGAATTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:47,22:0.0282:2,2:20.5:1:31:1:0.54608:2.11156:60:4:0.029:0:1.5 0/0:73:0:0,0:43,30:0:2,0:28.4:1:30.2:1:1:0:60:72:1:0:0.4 -13 88545521 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50473;SOR=Inf;LSEQ=GGAAGAATTCTCTGGTGGGG;RSEQ=TTCTGAGAGCTGAGTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:37,24:0:2,0:24.6:1:31.9:1:1:0:60:60:1:0:0.2 0/1:79:2:1,1:43,34:0.0253:2,2:18:1:27.5:1:1:1.26091:60:4:0.0256:0:2 -13 88545547 . A G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=6.34583;LSEQ=AGAGCTGAGTCAAGACCTCT;RSEQ=TGGCTGCCACTTCCTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:7:4,3:36,19:0.1129:2,2:17.4:1:32.1:1:0.69093:1.41267:60:14:0.1129:0:1 0/1:80:36:18,18:25,19:0.45:2,2:24.8:1:30.1:1:0.6532:1.31125:60:17:0.4416:0:1.1 -13 88546181 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19304;SOR=Inf;LSEQ=ATCTATTGTAGTCCATGGAT;RSEQ=CTGACTTGGGGACATTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:93,85:0:2,0:28.2:1:29.9:1:1:0:60:58.333:1:0:0.1 0/1:140:2:1,1:72,66:0.0143:2,2:37.5:1:32:1:1:1.09022:60:4:0.0147:0:1.5 -13 88546266 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20035;SOR=Inf;LSEQ=CCTCTGGGGTCTCTTGATTT;RSEQ=CTTTATAACCTCCAAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:31,56:0:2,0:23.5:1:31.1:1:1:0:60:86:1:0:0 0/1:71:2:1,1:27,42:0.0282:2,2:29.5:1:27.5:1:1:1.55:60:4:0.0286:0:1 -13 88546371 . G A 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.60322;LSEQ=TTTCTCTTCTTGCAACTAGT;RSEQ=CATTCACCAAAGTTGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:74,50:0.0159:2,2:24:1:26.5:1:1:1.47525:60:4:0.0159:0:1 0/0:104:1:1,0:62,41:0.0096:2,0:37:0:29:0:1:0:60:2:0.0098:0:1 -13 88546432 . C CT 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.23064;SOR=0.41872;LSEQ=CCTCATATTGCTTTCATTTC;RSEQ=TTTTTTTTTCAAAGTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:8:6,2:142,33:0.0435:2,2:27.4:1:29.9:1:0.64988:1.43123:57.5:16:0.0442:0.0054:0.8 0/1:161:3:3,0:125,33:0.0186:2,0:35:1:32:1:1:0:60:6:0.0191:0:0 -13 88546805 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24879;SOR=Inf;LSEQ=GGCAAAATGTATATAGCACT;RSEQ=TGGACCACAAACCCATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:127,154:0:2,0:23.9:1:31.4:1:1:0:60:69.25:1:0:0.1 0/1:288:3:2,1:119,166:0.0104:2,2:22.3:1:27:1:0.57431:2.78:60:6:0.0106:0:1 -13 88546844 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21034;SOR=Inf;LSEQ=GAGACAGTGCCATAGGGCTC;RSEQ=GGCCATTTGGGAGGAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:59,134:0:2,0:23.2:1:30.5:1:1:0:60:192:1:0:0.1 0/1:164:2:1,1:51,111:0.0122:2,2:20:1:29:1:0.53494:2.17:60:4:0.0122:0:1 -13 88546965 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17065;SOR=Inf;LSEQ=GTTGTTGGTCTAAGATAGTA;RSEQ=CAAAGAGCTCTTCTTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:48,55:0:2,0:27.5:1:31.7:1:1:0:60:102:1:0:0.2 0/1:73:2:1,1:34,37:0.0274:2,2:32.5:1:29.5:1:1:1.09:60:4:0.0278:0:1 -13 88546991 . AG A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=4.50032;LSEQ=AGCTCTTCTTGGACTGGAAT;RSEQ=CACCAGGAACCTTTGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:10:4,6:45,49:0.0952:2,2:16.8:1:30.3:1:0.74585:1.37336:60:20:0.098:0.0381:0 0/1:68:22:9,13:25,21:0.3235:2,2:26.5:1:32:1:0.43722:1.70578:60:44:0.3284:0.0441:0.2 -13 88547033 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52012;SOR=0;LSEQ=TCTGGGGTCTTACCCAGGGC;RSEQ=TTGGCATGAAGTTGCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:50,41:0.0215:2,2:25.5:1:29.5:1:1:1.21689:60:4:0.0225:0:1 0/0:60:0:0,0:35,25:0:2,0:24.3:1:30.5:1:1:0:60:59:1:0:0.1 -13 88547421 . A T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.594;SOR=2.39341;LSEQ=TGGCAGTTGTTCTTTGTGGC;RSEQ=AAGGAGCACACACAATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:1:0,1:68,100:0.0059:2,0:1:0:24:0:1:0:60:2:0.006:0:1 0/1:142:2:0,2:56,84:0.0141:2,0:13:1:25.5:1:0.51893:0:60:4:0.0142:0:1 -13 88547636 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20184;SOR=Inf;LSEQ=TCTTGGCTCTTACTTTTGAT;RSEQ=AAAGAGGGATTTTGTACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:66,67:0:2,0:29.2:1:28.8:1:1:0:60:132:1:0:0.2 0/1:109:2:1,1:57,50:0.0183:2,2:33:1:32.5:1:1:1.13863:60:4:0.0183:0:1 -13 88547685 . T TG 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=6.67761;LSEQ=CCTCTATATTAAGAAGAATG;RSEQ=GGTGTCTTGCATTGGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:15:6,9:24,47:0.1744:2,2:21.3:1:31.5:1:0.76707:1.30:60:30:0.1765:0.0349:0.1 1/0:85:50:22,28:12,22:0.5882:2,2:24:1:30.8:1:0.5001:1.43:59.9:100:0.5882:0.0941:0.1 -13 88547915 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24861;SOR=Inf;LSEQ=GGTTCTGAAAAGAAACCTCA;RSEQ=TCCTATCCAAATTCATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:187,83:0:2,0:23.5:1:31.8:1:1:0:60:53:1:0:0.1 0/1:270:3:2,1:172,95:0.0111:2,2:26.3:1:31:1:1:1.10:60:6:0.0113:0:1 -13 88548165 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52442;SOR=0;LSEQ=AAGCCTTGTGTGGCAGGACC;RSEQ=AGACATAGCTGCAGGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:1,100:0.0194:1,2:43.5:1:30.5:1:0.03864:71.17:60:4:0.0196:0:1 0/0:64:0:0,0:4,60:0:2,0:24.9:1:31.8:1:1:0:60:63:1:0:0 -13 90822777 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49646;SOR=0;LSEQ=ATGCCTAGCCCAGTAGAAAT;RSEQ=GTATGGACTAAATGGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:2,0:57,5:0.0313:2,0:14:1:32:0:1:0:60:4:0.0317:0:1 0/0:60:0:0,0:53,7:0:2,0:24.3:1:31.6:1:1:0:60:59:1:0:0.1 -13 90822829 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63114;SOR=2.44903;LSEQ=TTTCTCTTCTATCACATAGT;RSEQ=TTTGGGCTTGAGAAGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:1:0,1:120,42:0.0061:2,0:1:0:30:0:0.2638:0:60:2:0.0063:0:1 0/1:201:3:1,2:137,61:0.0149:2,2:16.3:1:28.3:1:0.23192:4.45447:60:6:0.0149:0:1.7 -13 90822835 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19233;SOR=0;LSEQ=TTCTATCACATAGTGTTTGG;RSEQ=CTTGAGAAGGGACTGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:124,44:0.0118:2,2:21:1:29:1:0.46049:2.79791:60:4:0.012:0:1 0/0:217:0:0,0:144,73:0:2,0:24.9:1:31:1:1:0:60:107.5:1:0:0.4 -13 90822837 . TTG T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25996;SOR=Inf;LSEQ=CTATCACATAGTGTTTGGGC;RSEQ=AGAAGGGACTGTCACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:129,49:0:2,0:24.2:1:30.1:1:1:0:60:177:1:0:0.7 0/1:229:3:1,2:148,78:0.0131:2,2:15:1:25.7:1:0.27995:3.7718:60:6:0.0133:0.0087:1.3 -13 90822839 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19524;SOR=0;LSEQ=ATCACATAGTGTTTGGGCTT;RSEQ=AGAAGGGACTGTCACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:130,48:0.011:2,2:11.5:1:27.5:1:0.47145:2.69085:60:4:0.0112:0:3 0/0:228:0:0,0:146,79:0:2,0:25.6:1:31.4:1:1:0:60:111.5:1:0:0.5 -13 90822845 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58385;SOR=0.38813;LSEQ=TAGTGTTTGGGCTTGAGAAG;RSEQ=GACTGTCACCCTGACTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:134,55:0.0105:2,2:8:1:29.5:1:0.50152:2.42352:60:4:0.0106:0:1 0/0:245:1:0,1:156,88:0.0041:2,0:1:0:22:0:0.36327:0:60:2:0.0041:0:5 -13 90822855 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25886;SOR=Inf;LSEQ=GCTTGAGAAGGGACTGTCAC;RSEQ=CTGACTGGGACTGCATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:149,81:0:2,0:23.9:1:30.9:1:1:0:60:56.5:1:0:1 0/1:291:3:1,2:174,114:0.0103:2,2:11.3:1:27.3:1:0.56551:3.04078:60:6:0.0104:0:2.3 -13 90822896 . G C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=0.55127;LSEQ=CATATATATTCTGCAAAAGC;RSEQ=CTGACATGACTGTGCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:350:203:107,96:83,64:0.58:2,2:26.8:1:30.9:1:0.51527:1.16305:60:100.5:0.5776:0:2.1 0/1:412:178:93,85:120,114:0.432:2,2:25.7:1:30.4:1:0.92075:1.04:60:177:0.436:0:2.1 -13 90822912 . T C 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00073;SOR=0.60912;LSEQ=AAGCGCTGACATGACTGTGC;RSEQ=AAAACTAAGTTAGTGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:353:202:100,102:79,70:0.5722:2,2:28.2:1:31:1:0.51932:1.15068:60:32.667:0.5681:0:2.1 0/1:430:193:94,99:120,117:0.4488:2,2:25:1:30.4:1:0.69927:1.08:60:47.25:0.4458:0:2 -13 90823086 . AT A 51 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.25339;SOR=0;LSEQ=GTGCAGGTAAATGCTTAAAT;RSEQ=TTTTTTTTTTTGAGACGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:2,25:0.1:2,0:21:1:32.3:1:1:0:60:6:0.1071:0:0 0/0:22:0:0,0:1,20:0:1,0:26.1:1:29.9:1:1:0:60:20:0.9524:0:0.1 -13 92901774 . A G 128 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=27.62043;LSEQ=AGCAGAAGTCAGAACTGGCT;RSEQ=AGAATTTATTTATGTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:2,0:67,3:0.0278:1,0:28.5:1:33.5:1:1:0:60:4:0.029:0:1 0/1:40:18:18,0:21,1:0.45:1,1:17.7:1:30.8:1:1:0:60:36:0.45:0:1.3 -13 92901900 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.06338;SOR=Inf;LSEQ=CTGAAAATTTTTAGTGGGGG;RSEQ=GTTGATGGCATGCTCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:196,192:0:2,0:24.8:1:30.2:1:1:0:60:28.846:1:0:0.2 0/1:430:5:1,4:216,209:0.0116:2,2:15.8:1:25.8:1:0.21226:4.12173:60:4:0.0094:0:1.4 -13 92901901 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.06337;SOR=Inf;LSEQ=TGAAAATTTTTAGTGGGGGG;RSEQ=TTGATGGCATGCTCAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:197,193:0:2,0:24.7:1:30.9:1:1:0:60:38:1:0:0.2 0/1:432:5:4,1:215,210:0.0116:2,2:16.8:1:25.2:1:0.37251:3.90:60:4:0.0094:0:2 -13 92901914 . T G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=22.32749;LSEQ=TGGGGGGGTTGATGGCATGC;RSEQ=CAATGGTTTAGTATATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:11:6,5:170,204:0.0286:2,2:23.1:1:29.5:1:0.55861:1.44:59.5:10:0.0264:0:2.7 0/1:423:168:79,89:123,132:0.3972:2,2:28.2:1:30.6:1:0.84258:1.04968:59.7:167:0.4005:0:2.4 -13 92901926 . T G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=22.64599;LSEQ=TGGCATGCTCAATGGTTTAG;RSEQ=ATATTTGAGTTAGTGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:10:5,5:156,200:0.0272:2,2:20.5:1:30.2:1:0.75412:1.28:59.5:9:0.0251:0:2.3 0/1:425:165:76,89:117,141:0.3882:2,2:27:1:30.6:1:0.92043:1.03:59.5:164:0.3905:0:2.6 -13 92901981 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=31.55862;LSEQ=GTGAGTAGAGAATGCAGAGC;RSEQ=GACCAGGCAATTCAGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:4:1,3:73,161:0.0168:2,2:27.5:1:29.8:1:1:1.35864:60:8:0.0171:0:4 0/1:216:76:19,57:52,88:0.3519:2,2:25.5:1:30.5:1:0.0948:1.76813:59.6:75:0.3488:0:3.4 -13 92901984 . C G 190 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=38.02013;LSEQ=AGTAGAGAATGCAGAGCGGA;RSEQ=CAGGCAATTCAGGAATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:0,3:66,157:0.0133:2,0:23.7:1:24.7:1:0.55777:0:60:2:0.009:0:5 0/1:203:69:16,53:50,84:0.3399:2,2:26.8:1:31.2:1:0.05716:1.96537:59.9:22:0.3402:0:3.5 -13 92901995 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49906;SOR=0;LSEQ=CAGAGCGGACCAGGCAATTC;RSEQ=GGAATCTATGTTGGTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:46,133:0.011:2,2:36.5:1:30:1:0.45298:2.87:60:4:0.0111:0:1 0/0:170:0:0,0:50,120:0:2,0:23.9:1:30.3:1:1:0:60:340:1:0:1.3 -13 92902025 . C T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=19.2763;LSEQ=GTTGGTTGTTTAATTGCTTC;RSEQ=GTTTTGTCAACATCTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:4:0,4:16,98:0.0339:2,0:17.3:1:28.3:1:1:0:60:8:0.0345:0:3.3 0/1:86:35:5,30:9,42:0.407:2,2:24.5:1:29.7:1:0.77226:1.28202:60:34:0.4048:0:2.6 -13 93770081 . C G 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=2.16028;LSEQ=AAGTAGCCCATATTCAATCT;RSEQ=TTTTGTTATATAGTACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:21:1:32.7:1:1:0:60:6:0.3:0:1 1/0:2:1:1,0:1,0:0.5:0,0:46:0:32:0:1:0:60:2:0.5:0:1 -13 93770238 . TAC T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.00687;SOR=Inf;LSEQ=TATATGCATATATATATGTA;RSEQ=ACACACACATATATATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:101,11:0:2,0:23.9:1:28.8:1:1:0:59.8:224:1:0:0.2 0/1:113:8:6,2:95,10:0.0708:2,2:22.9:1:29.8:1:0.20173:3.1202:60:16:0.0714:0.0088:0.4 -13 93770333 . A G 256 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06044;SOR=1.26957;LSEQ=AGAGTGGAGGAAAAATGGCA;RSEQ=TGGGTCACAGTAATTACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:192:99,93:137,121:0.4257:2,2:27.4:1:31.9:1:0.77507:1.06345:60:95:0.4241:0:1.2 0/1:596:289:148,141:157,150:0.4849:2,2:25.8:1:31.4:1:1:1.00:60:95.333:0.4839:0:1.2 -13 93770390 . C T 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGTACTATTCTTAAAATAA;RSEQ=CATAGGGCTTTGGTTATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:102,188:0:2,0:24.6:1:31.3:1:1:0:60:95.667:1:0:0.4 0/1:397:33:13,20:140,223:0.0831:2,2:26.1:1:28.9:1:1:1.04:60:32:0.0818:0:1.8 -13 95364018 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54257;SOR=0;LSEQ=GCCGCCCAGGCCGTAGGGCA;RSEQ=CGGGAAGGCGAACTTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:60,4:0.0303:2,0:13.5:1:32.5:1:1:0:60:4:0.0308:0:1.5 0/0:35:0:0,0:35,0:0:1,0:21.4:1:31.9:1:1:0:60:70:1:0:0.8 -13 95364046 . C G 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15965;SOR=1.52077;LSEQ=GCGAACTTGTCCTTCTTGAG;RSEQ=AGCGTCTTGGGCTTGCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:55:49,6:61,4:0.4583:2,2:24.1:1:31.7:1:0.50973:1.85758:60:110:0.4583:0:1.1 1/0:87:49:44,5:32,6:0.5632:2,2:22.5:1:30.5:1:0.52295:1.64:60:23.5:0.5529:0:1.2 -13 95364090 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10837;SOR=Inf;LSEQ=CCGGTACTTGTAGTCGGGGT;RSEQ=CTCCTTCATGTGCATGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:202,57:0:2,0:25.4:1:32.3:1:1:0:60:85.333:1:0:0.3 0/1:237:3:2,1:164,70:0.0127:2,2:29:1:28.3:1:1:1.1706:60:6:0.0128:0:1.7 -13 95364307 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.10439;SOR=Inf;LSEQ=TCCACCGGCTTGGACATGCT;RSEQ=TCGCCCTGCCGCGGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:28,198:0:2,0:23.7:1:32:1:1:0:60:112:1:0:0.4 0/1:203:3:2,1:40,160:0.0148:2,2:5.7:1:28:1:0.10927:7.89:60:6:0.0149:0:1.7 -13 95364334 . GCCT G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50446;SOR=0;LSEQ=TGCCGCGGCTGCAGCCCGCC;RSEQ=CCCGGGCCCTCGCCCTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:4,114:0.0167:1,2:13.5:1:34:0:0.08193:25.60:60:4:0.0169:0:0 0/0:95:0:0,0:6,89:0:2,0:26.1:1:31.4:1:1:0:60:190:1:0:0.8 -13 95364337 . T G 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.31577;SOR=1.36675;LSEQ=CGCGGCTGCAGCCCGCCGCC;RSEQ=CCCGGGCCCTCGCCCTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:115:66:0,66:3,44:0.5739:2,1:26.5:1:32.4:1:0.06925:0:60:65:0.5856:0:1.1 1/0:91:59:3,56:2,30:0.6484:2,2:24.7:1:31.9:1:1:1.24135:60:58:0.6591:0:1.3 -13 95413053 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19481;SOR=Inf;LSEQ=ACTTGTTTGTTTACAATGAT;RSEQ=CCAACAGCATGCTAGGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:14,17:0:2,0:27.1:1:32.3:1:1:0:60:62:1:0:0 0/1:25:2:1,1:10,13:0.08:2,2:30:1:29.5:1:1:1.29:60:4:0.0833:0:1 -13 95413146 . G C 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=TGGACAGTACCCATTCCCTT;RSEQ=GTGTCTACATTATCGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:3,7:0.2143:2,2:19.3:1:30.7:1:1:1.15:60:6:0.2143:0:1 0/0:5:0:0,0:3,2:0:2,0:25.4:1:30.8:1:1:0:60:10:1:0:0 -13 95413279 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=GTTCGTCATTTTATCAAATT;RSEQ=CTGGAAGCTGGGAGTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:12.4:1:29.4:1:1:0:60:14:1:0:0.3 0/1:5:2:1,1:1,2:0.4:2,2:12.5:1:27.5:1:1:1.73:60:4:0.4:0:1 -13 96897256 . T A 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02347;SOR=0.5384;LSEQ=ACAGCATGTACAAAATATTA;RSEQ=TTTTAATCTGTTTCAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:66:39,27:25,11:0.6471:2,2:25.6:1:30.4:1:0.39217:1.56652:60:132:0.6471:0:1.1 0/1:127:63:39,24:35,29:0.4961:2,2:23.8:1:29.5:1:0.47306:1.34:60:62:0.496:0:1.2 -13 96897357 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49607;SOR=0;LSEQ=TTGTGTGTCATTACTAAATC;RSEQ=TCCCAGATGATTGAAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:12,49:0.0317:2,2:5.5:1:29.5:1:0.37276:3.96:60:4:0.0323:0:1.5 0/0:61:0:0,0:16,45:0:2,0:26.7:1:29.4:1:1:0:60:60:1:0:0 -13 99176306 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCCCGTCCACACCCAG;RSEQ=CCCAAAGCAGGCAGGGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:27.5:1:1:0:60:4:1:0:1 -13 99177868 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAGCCGGGCTCGCCACCCC;RSEQ=GTATAGGCAGGAGGATCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:48.5:1:19.5:1:1:0:60:1:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:29.5:1:28.5:1:1:0:60:4:1:0:1.5 -13 99177963 . C T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCCTCGAGCCCCACAAGC;RSEQ=GCCTCACACTGATGAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:21:1:31.3:1:1:0:60:8:0.5714:0:1.3 0/0:1:0:0,0:1,0:0:0,0:39:0:31:0:1:0:60:2:1:0:0 -13 99178276 . G A 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41291;SOR=1.14596;LSEQ=GAAGGACAGGCTTTGGTTGG;RSEQ=TAAGTCAGGGTTGGTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:328:232:135,97:49,47:0.7073:2,2:26.1:1:30.1:1:0.27135:1.33:60:57:0.7081:0:1.1 1/0:426:313:164,149:62,51:0.7347:2,2:25.2:1:28.8:1:0.66182:1.10424:60:38.125:0.7332:0:1.1 -13 99178332 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13716;SOR=Inf;LSEQ=TGAGGGATGGTGGCTGGAGT;RSEQ=CGGTGGAGGGAGGAGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:115,172:0:2,0:26.8:1:31.6:1:1:0:60:94.667:1:0:0.5 0/1:375:4:3,1:165,206:0.0107:2,2:23:1:24.8:1:0.32928:3.73:60:8:0.0108:0:1.8 -13 99178385 . C T 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGAAAGGGGCTTTCGAAA;RSEQ=AGGTCCGTCTTTGCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:10,99:0:2,0:21.9:1:32.8:1:1:0:60:218:1:0:0.1 0/1:129:23:3,20:16,90:0.1783:2,2:21.7:1:28.4:1:1:1.18368:60:46:0.1811:0:1.1 -13 99565179 . T C 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTATGAACCCCCAAACA;RSEQ=CCAGAAACAAAAAAGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7:0:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 99566435 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42894;LSEQ=ATCATACTGCATGAGTACAC;RSEQ=TCACCTCGTAATCAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:407:262:129,133:80,65:0.6437:2,2:27.6:1:30.7:1:0.25684:1.26818:60:130:0.6484:0:1.1 0/1:385:168:89,79:101,114:0.4364:2,2:27:1:29.9:1:0.25847:1.27:60:83:0.4368:0:1.1 -13 99566465 . G T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.12454;SOR=0;LSEQ=AATCAGGTCAGAAAAAGAGA;RSEQ=AGGTAATCACAATGTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:4:2,2:157,196:0.0112:2,2:25:1:30:1:1:1.25:60:8:0.0112:0:2 0/0:337:0:0,0:142,195:0:2,0:24.1:1:31.1:1:1:0:60:111.333:1:0:0.5 -13 102276430 . G T 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGGATTCCTGGAGATAT;RSEQ=CTTAGATGTTTACTAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:18:1:30.5:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 102276717 . A G 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16293;SOR=1.29418;LSEQ=CATTTATGTTTTATGCCCCA;RSEQ=TAACTACACTTCCTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:320:223:125,98:50,47:0.6969:2,2:26.3:1:31.9:1:0.4662:1.20:60:73.333:0.7029:0:1.6 1/0:338:253:149,104:45,40:0.7485:2,2:26.2:1:31.4:1:0.37547:1.27:60:125.5:0.747:0:1.6 -13 102276769 . G A 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01033;SOR=1.47875;LSEQ=GAGCCTTGAAGTGTTCACCT;RSEQ=AAAGCATTTTAAAATAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:355:211:99,112:66,77:0.5944:2,2:26.1:1:28.9:1:0.91382:1.03:60:34.167:0.5908:0:1.6 1/0:415:284:136,148:62,67:0.6843:2,2:26.1:1:28.4:1:1:1.00701:60:46.333:0.6814:0:1.6 -13 102276854 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2225;SOR=Inf;LSEQ=AGGACTCAGGATACAGATTG;RSEQ=CCTGGGGTTGCTCATGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:45,108:0:2,0:24.3:1:29.8:1:1:0:60:152:1:0:0.2 0/1:138:2:1,1:34,102:0.0145:2,2:33.5:1:30:1:0.4443:2.97:60:4:0.0145:0:1 -13 103337240 . A G 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00969;SOR=0.46456;LSEQ=TTAGCTTGACAAATTCCACA;RSEQ=GAAAGTATATTGGGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:45:42,3:54,7:0.4245:2,2:23.4:1:32.2:1:0.5121:1.81:60:90:0.4245:0:1 0/1:110:28:25,3:69,13:0.2545:2,2:20.1:1:32:1:0.75701:1.56:60:56:0.2545:0:1 -13 103337266 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60248;SOR=0.44067;LSEQ=TATATTGGGATTTTTACAAT;RSEQ=ATTTCACGTAAGCTGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:137,53:0.0104:2,2:24:1:28:1:0.48446:2.57019:60:4:0.0104:0:1 0/0:217:1:1,0:155,61:0.0046:2,0:2:0:28:0:1:0:60:2:0.0046:0:1 -13 103337294 . G T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65928;SOR=0.52533;LSEQ=GTAAGCTGTTGATCAATTTG;RSEQ=AGAAAACTGACATATTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:191,105:0.01:2,2:30.7:1:27.7:1:0.29187:3.62156:60:6:0.0102:0:1 0/0:378:2:0,2:228,148:0.0053:2,0:1:0:24:1:0.15684:0:60:4:0.0053:0:1 -13 103337357 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34796;LSEQ=GATGTCTCCCCATTTACTTA;RSEQ=GTTAGTTTTAATTTGTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:205:101,104:90,102:0.5164:2,2:25.6:1:30.7:1:0.68783:1.10:60:67.333:0.5127:0:1.1 0/1:569:154:80,74:215,195:0.2707:2,2:26.3:1:30.1:1:0.9249:1.01984:60:50.333:0.2692:0:1.2 -13 103337590 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07368;SOR=Inf;LSEQ=CAATAATTTCACTGTGGATC;RSEQ=CCTGCAGTTCCAGGGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:0:0,0:22.9:1:32:1:1:0:60:22:1:0:0.2 0/1:9:3:0,3:2,4:0.3333:2,0:31:1:30.7:1:0.5:0:60:6:0.3333:0:1 -13 103498375 . T C 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=CAACGGCCATTCTCTGGACC;RSEQ=GTCTTTCTTCCGGGAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:8,1:0:2,0:21.7:1:31.2:1:1:0:60:18:1:0:0.1 1/0:3:2:2,0:1,0:0.6667:0,0:19:1:32:0:1:0:60:4:0.6667:0:1 -13 103498470 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50662;SOR=0;LSEQ=ATTAGTGCCGTCCCCCACTG;RSEQ=AAAACCGTGGCTTCTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:2,0:82,1:0.0235:1,0:14.5:1:31.5:1:1:0:60:4:0.0244:0:1 0/0:64:0:0,0:63,1:0:1,0:21:1:31.5:1:1:0:60:128:1:0:0 -13 103498545 . C T 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=24.35945;LSEQ=CTTCCTCCCGGGGTCCTAGG;RSEQ=GGCGGTGCAGTCCGTCGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:1:0,1:292,48:0.0029:2,0:1:0:25:0:0.1437:0:60:2:0.003:0:1 0/1:388:26:17,9:266,96:0.067:2,2:24:1:28.1:1:0.36702:1.46536:60:25:0.066:0:1.1 -13 103504270 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GATTTTAAAATGCAGTATGT;RSEQ=AATAGGGGTAACAAGAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:0:1,0:25.1:1:31.4:1:1:0:60:18:1:0:0.1 0/1:13:2:2,0:11,0:0.1538:0,0:10:1:29.5:1:1:0:60:4:0.1538:0:1 -13 103504331 . T C 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14632;SOR=0;LSEQ=TAGGTAGATCCCATGAGAGC;RSEQ=AAATGTTTTTCAATTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:4,0:47,0:0.0784:1,0:17.5:1:30.5:1:1:0:60:8:0.0816:0:1 0/0:34:0:0,0:34,0:0:1,0:22.1:1:31.1:1:1:0:60:68:1:0:0.1 -13 103504399 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18573;SOR=Inf;LSEQ=ACGTTTGGATAATATCAGTT;RSEQ=TTAGGAAATTGAAGTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:185,19:0:2,0:24.6:1:28.3:1:1:0:60:67:1:0:0.1 0/1:155:2:1,1:132,21:0.0129:2,2:18:1:30.5:1:0.26452:6.16443:60:4:0.0133:0:2 -13 103504409 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20265;SOR=Inf;LSEQ=AATATCAGTTATTAGGAAAT;RSEQ=GAAGTTGTGAGGATGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:207,33:0:2,0:24.3:1:30.3:1:1:0:60:119:1:0:0.1 0/1:197:2:1,1:161,34:0.0102:2,2:28:1:30.5:1:0.32451:4.68167:60:4:0.0103:0:2 -13 103504517 . T C 283 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGGAGTCCGGGATCGCCA;RSEQ=GGGAACTCAATAGAAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:949:0:0,0:520,429:0:2,0:25.3:1:30.4:1:1:0:60:93.9:1:0:0.1 1/0:1167:671:367,304:264,228:0.575:2,2:25.5:1:30.2:1:0.76584:1.04:60:166.75:0.5765:0:1.1 -13 103506235 . T A 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04922;SOR=0;LSEQ=AGCAAAAGGCAAGAGGAAAA;RSEQ=TATAGTCGTGTTAGAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:4:3,1:140,219:0.011:2,2:15:1:28:1:0.30447:4.67:60:8:0.0112:0:1 0/0:406:0:0,0:146,260:0:2,0:27.3:1:29.8:1:1:0:60:49.75:1:0:0.2 -13 103506362 . AT A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.64342;SOR=2.06759;LSEQ=AATGAGACAAGTAGGCTGCC;RSEQ=TTTGACCTGGTAATTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:33:3,30:0,3:0.9167:0,2:28.2:1:31.5:1:1:0:60:66:0.9167:0.1111:0 1/1:24:23:3,20:0,1:0.9583:0,2:22.4:1:30.1:1:1:0:60:46:0.9583:0.2083:0.1 -13 103506509 . A C 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGGTGAGCAGCCCCGCCA;RSEQ=GGTTCCTTCCTTTCTCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:78:78:71,7:0,0:1:0,2:27.5:1:32:1:1:0:60:156:1:0:1 1/1:58:58:58,0:0,0:1:0,1:22.8:1:31.3:1:1:0:60:57:1:0:1.1 -13 103506587 . C T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13987;SOR=Inf;LSEQ=CAGGTCAGGTCCCTGTTCAC;RSEQ=ATCCTGAGCAGGGTCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:191,81:0:2,0:24.7:1:31.3:1:1:0:60:67:1:0:0.2 0/1:365:4:1,3:252,109:0.011:2,2:16:1:27:1:0.08781:6.8953:60:8:0.0112:0:1 -13 103507049 . G A 36 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGCTGCTTTTCAATCCA;RSEQ=TATGGTCTCTCTCACCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:8.3:1:23:1:1:0:60:2:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 103507111 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATTCTTGTTGCTAAATC;RSEQ=AGCAGACGCTTTGCACGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:29:1:33.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 103508356 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25003;SOR=Inf;LSEQ=ATACAAGTATTTTTGTAAGG;RSEQ=GTCCTTAAAAATCATAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:158,68:0:2,0:24.9:1:30.9:1:1:0:59.9:36.667:1:0:0.3 0/1:248:3:1,2:166,79:0.0121:2,2:15:1:29.7:1:0.24941:4.17592:60:6:0.0122:0:1.3 -13 103508378 . C T 165 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01711;LSEQ=TCCTTAAAAATCATAGATAT;RSEQ=GTAAAAGTATGTTTGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:46:30,16:158,109:0.1465:2,2:25.8:1:30:1:0.51555:1.29:60:92:0.1494:0:1.1 0/0:343:1:1,0:206,136:0.0029:2,0:16:0:32:0:1:0:60:2:0.0029:0:1 -13 103508537 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21178;SOR=0;LSEQ=ATGAAAATGAATATTAATGA;RSEQ=GTATATCAAACTGTGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:4,61:0.0299:2,2:7.5:1:28.5:1:0.14473:13.75:60:4:0.0308:0:1.5 0/0:78:0:0,0:6,71:0:2,0:18:1:30:1:1:0:60:154:0.9872:0:0 -13 103510556 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22307;SOR=Inf;LSEQ=TTATATAAACATAATACATA;RSEQ=CCTTAATGTTGAATAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:75,5:0:2,0:26.9:1:31.1:1:1:0:60:79:1:0:0.1 0/1:73:2:1,1:62,9:0.0274:2,2:8.5:1:29:1:0.25685:6.58787:60:4:0.0274:0:1.5 -13 103510559 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22374;SOR=Inf;LSEQ=TATAAACATAATACATATCC;RSEQ=TAATGTTGAATAGAACTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:78,5:0:2,0:27.4:1:31.1:1:1:0:59.6:40.5:1:0:0.2 0/1:75:2:1,1:64,9:0.0267:2,2:21.5:1:33:1:0.25045:6.79808:60:4:0.027:0:1 -13 103510604 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25462;SOR=Inf;LSEQ=TGAAATGTAAATTTCATGGT;RSEQ=CTGTGATTTTATCTTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:150,36:0:2,0:23.1:1:31.7:1:1:0:60:45.5:1:0:0.1 0/1:224:3:1,2:154,65:0.0134:2,2:23.7:1:29.3:1:0.21713:4.70089:60:6:0.0136:0:1.7 -13 103510896 . C T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAGTAAACAGCATTTCTA;RSEQ=ATCTCAGATTCTAAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:1,47:0:1,0:22.6:1:32.5:1:1:0:60:47:1:0:0.1 1/0:24:16:0,16:0,8:0.6667:0,1:19.8:1:28.6:1:1:0:60:32:0.6667:0:1 -13 103510997 . T C 111 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCGAGACTAGGTCTTTT;RSEQ=TCCTGGTCTTTGTTCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:22.7:1:33.5:1:1:0:60:20:1:0:1.1 1/1:1:1:0,1:0,0:1:0,0:12:0:33:0:1:0:60:2:1:0:1 -13 103513578 . G A 67 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CGAACTCCTGACCTCCGGTG;RSEQ=TCCACCCATCTCGGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:22.2:1:29.2:1:1:0:42.8:10:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 103514091 . T C 257 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACCATCATTTATATATT;RSEQ=ACATTAAAAAATCAAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:279:279:74,205:0,0:1:0,2:24:1:31.7:1:1:0:60:138.5:1:0:1.1 1/1:272:272:71,201:0,0:1:0,2:23.4:1:31.5:1:1:0:60:67:1:0:1.1 -13 103518769 . T C 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTTTCCTTTACCACCTTC;RSEQ=TCAGACCCCTGGGGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:246:246:74,172:0,0:1:0,2:23.5:1:31.4:1:1:0:60:40:1:0:1.2 1/1:288:288:81,207:0,0:1:0,2:23:1:31.1:1:1:0:60:95:1:0:1.2 -13 103518782 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22219;SOR=0;LSEQ=CACCTTCTTCAGACCCCTGG;RSEQ=GGAATGCACTGCATGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:49,142:0.0103:2,2:39:0:30:1:0.45202:2.88:60:4:0.0106:0:2 0/0:217:0:0,0:52,165:0:2,0:23.5:1:29.7:1:1:0:60:35.167:1:0:1.2 -13 103518784 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22336;SOR=0;LSEQ=CCTTCTTCAGACCCCTGGGG;RSEQ=AATGCACTGCATGAAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:48,136:0.0108:2,2:34:1:30.5:1:0.45853:2.81:60:4:0.0109:0:2 0/0:207:0:0,0:48,159:0:2,0:23.7:1:30.6:1:1:0:60:68:1:0:1.2 -13 103518844 . C T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00406;SOR=0.38704;LSEQ=TGCTCAGGGCCTGGTGATGC;RSEQ=GTTCCCTGGGGGTCACTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:53:22,31:20,19:0.5761:2,2:24.6:1:31.4:1:0.40088:1.47682:60:52:0.5843:0:1.4 0/1:67:23:5,18:14,30:0.3433:2,2:20.5:1:30.1:1:0.56892:1.66747:60:22:0.3385:0:1.7 -13 103518918 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20141;SOR=Inf;LSEQ=TGAAGTGGTAGGCACTGCTC;RSEQ=CCCTGTGCTCAGGGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:104,44:0:2,0:22.8:1:30.4:1:1:0:60:36:1:0:0.2 0/1:121:2:1,1:88,31:0.0165:2,2:31:1:25.5:1:0.46061:2.80983:60:4:0.0169:0:1.5 -13 103518945 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23083;SOR=Inf;LSEQ=GCTCAGGGCCTGGCGGTGCC;RSEQ=TTCCCTGGGCGTCACTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:130,75:0:2,0:25:1:31:1:1:0:60:33.167:1:0:0.1 0/1:191:2:2,0:129,60:0.0105:2,0:31:1:27.5:1:1:0:60:4:0.0106:0:1 -13 103518970 . C A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24892;SOR=Inf;LSEQ=CTGGGCGTCACTGTGTACCC;RSEQ=TCACTCTGCAGGAACTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:163,100:0:2,0:25.3:1:31.2:1:1:0:60:86.667:1:0:0.1 0/1:275:3:1,2:176,96:0.0109:2,2:23.7:1:29.3:1:0.28975:3.64841:60:6:0.0112:0:1 -13 103518989 . T A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.109;SOR=0;LSEQ=CCTCACTCTGCAGGAACTCC;RSEQ=GCGCCTGTTCGGCATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:172,115:0.0103:2,2:10:1:22.7:1:1:1.34:60:2:0.0071:0:1 0/0:316:0:0,0:189,127:0:2,0:25:1:30.3:1:1:0:60:44.143:1:0:0.2 -13 103519251 . C T 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00756;SOR=Inf;LSEQ=ATTTACCTTCAGAGTTTGTC;RSEQ=TAGGAAGTTTTCTTTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:18,119:0:2,0:22.3:1:32:1:1:0:60:67.5:1:0:0.1 0/1:151:8:2,6:19,124:0.053:2,2:13.1:1:30.9:1:0.30781:2.16:60:16:0.0537:0:1.1 -13 103519256 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23389;SOR=0;LSEQ=CCTTCAGAGTTTGTCCTAGG;RSEQ=AGTTTTCTTTCCAAGGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:15,109:0.0159:2,2:17:1:30:1:0.23873:7.07:60:4:0.016:0:1 0/0:134:0:0,0:14,120:0:2,0:25.2:1:30.1:1:1:0:60:133:1:0:0.1 -13 103519771 . G A 52 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTTGGGAAAGGCTTTACTC;RSEQ=TGTAACTTCAAGGCAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:29.8:1:26.3:1:1:0:60:3:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 103520764 . G A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGTTTTCCATTTTCTAGA;RSEQ=ATGATGAAATCAGAGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:0,35:0,0:1:0,1:21:1:30.4:1:1:0:60:34:1:0:1.1 1/1:9:9:0,9:0,0:1:0,0:29.4:1:30.9:1:1:0:60:18:1:0:1 -13 103524611 . GA G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.70836;SOR=0.82717;LSEQ=AATCCTCATGACACCAAAGT;RSEQ=AAAAAAAATTACGGACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:15:10,5:427,328:0.0195:2,2:34.5:1:31.4:1:0.6004:1.54:60:14:0.0186:0:0.4 0/1:866:14:7,7:478,372:0.0162:2,2:31.6:1:30.6:1:0.78736:1.28456:60:28:0.0165:0.0012:0.1 -13 103524762 . C T 229 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAGAGAATATCCTTTGCTT;RSEQ=TTAAAAGAGAAGGAAACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:121,285:0:2,0:22.9:1:31.7:1:1:0:60:134.333:0.9951:0:0.1 1/0:426:217:62,155:66,143:0.5094:2,2:25:1:29.6:1:0.52685:1.15346:60:216:0.5082:0:1.1 -13 103524795 . T A 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24855;SOR=0;LSEQ=GAAACACCTTGTCAAATATG;RSEQ=GTTTGGTTTAAAACTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:3:1,2:38,195:0.0127:2,2:17.3:1:20.7:1:0.41982:2.55:60:2:0.0085:0:1.3 0/0:229:0:0,0:42,187:0:2,0:22.4:1:29.8:1:1:0:60:228:1:0:0.5 -13 103525564 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14219;SOR=Inf;LSEQ=GACCTTTTTATTTGTCACTT;RSEQ=TTTAAATATCTTTCAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:189,70:0:2,0:21.3:1:32.1:1:1:0:60:85.333:1:0:0.1 0/1:355:4:2,2:251,100:0.0113:2,2:21.5:1:24.5:1:0.32567:2.50257:60:3:0.0085:0:2.5 -13 103525883 . C A 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.03106;SOR=0;LSEQ=CTTCATTTTCTATGATCACT;RSEQ=TTAGGGCTGAACTTTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:0,7:0.3636:0,0:22.3:1:29.5:1:1:0:60:8:0.3636:0:1.3 0/0:13:0:0,0:0,13:0:1,0:21.8:1:32.2:1:1:0:60:26:1:0:0.1 -13 103527121 . C T 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTCGTGATCCACCCACCT;RSEQ=GGCCTCCCAGAGTGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24:1:29.7:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 103527149 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTGCTGGGGTTACAGG;RSEQ=GTGAGCCACCATGCCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:31:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 103527528 . A C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00603;SOR=Inf;LSEQ=GGAGAGAACTGGGTTTTGGG;RSEQ=GATAATGAATTAATATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:40,0:0:1,0:24.5:1:30.3:1:1:0:60:39:1:0:0.1 0/1:17:4:4,0:13,0:0.2353:1,0:26.8:1:32.3:1:1:0:60:8:0.2353:0:1.3 -13 103527849 . G C 288 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.66027;SOR=1.88937;LSEQ=AGCTACTTGATAAGGCAAAA;RSEQ=GAAAAACCCAGAAGAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:591:588:255,333:0,0:0.9949:0,2:26.4:1:30.9:1:1:0:60:97:0.9949:0:1.2 1/1:743:741:348,393:0,0:0.9973:0,2:26:1:30.3:1:1:0:60:246:0.9973:0:1.2 -13 103527930 . G C 275 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGCTTTCAGATTCTAAA;RSEQ=GAAAGAATACATGCGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:460:460:229,231:0,0:1:0,2:28.1:1:30.9:1:1:0:60:114:1:0:1.3 1/1:564:563:249,314:0,0:0.9982:0,2:26:1:30.2:1:1:0:60:186.667:0.9982:0:1.3 -13 103528002 . G C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19211;LSEQ=CTGATGGATCTTCAAGTGAA;RSEQ=ATGCTGAAAGTTCATCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:110:47,63:104,125:0.3245:2,2:27.5:1:31.2:1:0.72635:1.11488:60:17.333:0.3142:0:1.3 0/1:427:36:18,18:180,211:0.0843:2,2:23.5:1:31.5:1:0.72778:1.17:60:72:0.0847:0:1.4 -13 103528235 . A G 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.24818;SOR=0;LSEQ=AAACTAAGACGTGCGAGGGG;RSEQ=AGAAAAAGGAAAACCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:1,2:16,70:0.0337:2,2:35:1:26:1:0.47483:2.16:60:2:0.0227:0:1.3 0/0:79:0:0,0:16,63:0:2,0:26.3:1:29.9:1:1:0:60:158:1:0:0.1 -13 103528250 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22515;SOR=Inf;LSEQ=AGGGGAAGAAAAAGGAAAAC;RSEQ=TAATTAAAAAATATGTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:13,54:0:2,0:22.8:1:32.3:1:1:0:60:134:1:0:0.2 0/1:61:2:1,1:10,49:0.0328:2,2:18:1:31.5:1:0.3306:4.72:60:4:0.0333:0:1 -13 103528337 . G A 80 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGTAATAAAATTAACTGGT;RSEQ=GCACGGTCTTTGTATTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:0.7:0,0:18.1:1:28.7:1:1:0:59.1:6:0.6667:0:2 1/1:1:1:0,1:0,0:1:0,0:49:0:30:0:1:0:60:2:1:0:1 -13 103529284 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCAGCAGTCTTTGAACG;RSEQ=CTCCTAGATGTGTTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:33.5:1:1:0:60:4:1:0:1 -13 104189531 . GAG A 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTAGGATAGACAGAGAGACA;RSEQ=AGAGAGAGAGAGAAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23.5:1:31.8:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 104189681 . G A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15882;SOR=0.17679;LSEQ=GGGATTTTTCCATTTGCAAG;RSEQ=CTCTTGAAATATTTTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:0.8333:0,0:30.2:1:28.7:1:1:0:60:20:0.8333:0:1 0/1:9:4:4,0:5,0:0.4444:0,0:22.3:1:30.5:1:1:0:60:8:0.4444:0:1 -13 104189781 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50376;SOR=Inf;LSEQ=TGGTTTTGATGAATTTGCTG;RSEQ=GATCCAGGAGTGTTCAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:47,35:0:2,0:28.4:1:31.4:1:1:0:60:81:1:0:0 0/1:103:2:1,1:54,47:0.0194:2,2:27:0:31:1:1:1.14738:60:4:0.0194:0:1 -13 104377661 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGGCAAAAGAATAATT;RSEQ=TAAAATTAAGAGGATTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:37:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 104377856 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTAACTAATATGGATCCT;RSEQ=TAAATTGTGTGAATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:9.5:1:31:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 104378073 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20046;SOR=0;LSEQ=TTTGACACATTTGTAAAACC;RSEQ=TCGCTCTTTGGGACTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:88,24:0.0175:2,2:14:1:29.5:1:0.39202:3.61257:60:4:0.0183:0:1 0/0:140:0:0,0:102,38:0:2,0:22.3:1:29.8:1:1:0:60:139:1:0:0.1 -13 104378182 . G C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2383;LSEQ=GTTCACTGGCTCCTTACTTC;RSEQ=TCAGTCCCATTGCTTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:340:222:106,116:61,55:0.6529:2,2:27:1:31.5:1:0.42379:1.21302:60:221:0.6558:0:1.1 0/1:385:119:62,57:125,141:0.3091:2,2:26.7:1:30.7:1:0.37849:1.23:60:118:0.3089:0:1.1 -13 104378270 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49965;SOR=Inf;LSEQ=CCTACTTGGTTATCTCAAGC;RSEQ=ACAGCTGCTCCTAGTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:32,100:0:2,0:24:1:29.1:1:1:0:60:131:1:0:0.3 0/1:147:2:1,1:39,106:0.0136:2,2:13:1:30.5:1:0.47153:2.70:60:4:0.0138:0:1 -13 104378280 . C G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49897;SOR=Inf;LSEQ=TATCTCAAGCTACAGCTGCT;RSEQ=CTAGTTGGTGCCTCCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:23,85:0:2,0:22.2:1:31.4:1:1:0:60:107:1:0:0.1 0/1:119:2:1,1:26,91:0.0168:2,2:7:0:31.5:1:0.40379:3.45:60:4:0.0169:0:1.5 -13 104378348 . A C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71446;SOR=0.6111;LSEQ=GGAGACTCATGCCTGAACTC;RSEQ=ACTTCTCTATGTCTAGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:0,6:0,23:0.2069:1,0:28:1:32.2:1:1:0:60:12:0.2069:0:1.7 0/1:22:3:0,3:1,18:0.1364:1,0:26:1:34:0:1:0:60:6:0.1364:0:1.3 -13 104378382 . A G 129 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00174;SOR=0.03601;LSEQ=TAGGTAGTGTCCACATGCAG;RSEQ=TATTGATATAATGTATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:0,3:0.85:0,1:22.1:1:31.8:1:1:0:60:34:0.85:0:1.3 0/1:7:1:0,1:0,6:0.1429:0,0:33:0:33:0:1:0:60:2:0.1429:0:2 -13 104378499 . G A 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.40825;LSEQ=TTATATTGGATGTTATCTAA;RSEQ=GAAGAGGCTTTCAATTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:35:1:31.3:1:1:0:60:6:1:0:1 1/0:2:1:0,1:0,1:0.5:0,0:28:0:33:0:1:0:60:2:0.5:0:1 -13 105247235 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22414;SOR=Inf;LSEQ=GAAACTGAAGAGAGAAGCCA;RSEQ=AAATATCAAGAAGATGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:22.4:1:32:1:1:0:60:30:1:0:0 0/1:14:2:1,1:7,5:0.1429:2,2:16:0:31:1:1:1.36624:60:4:0.1429:0:1.5 -13 106236098 . G A 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGAATATCTTAGCCTACA;RSEQ=AAGTGAAGTGAACCAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:191,185:0:2,0:24.9:1:31.4:1:1:0:60:61.667:1:0:0.1 0/1:345:84:45,39:129,132:0.2435:2,2:28.5:1:30:1:0.53239:1.18:60:168:0.2463:0:1.1 -13 106236146 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24951;SOR=0;LSEQ=GAACCTGATCTGCCGGAGCA;RSEQ=AATATCCAACTGAGTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:1,2:111,184:0.0101:2,2:18.7:1:28.7:1:1:1.20574:60:6:0.0102:0:1 0/0:279:0:0,0:112,167:0:2,0:25.3:1:31:1:1:0:60:68.75:1:0:0.3 -13 106826378 . C T 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01752;SOR=0.66614;LSEQ=TTATGCTTCATCCTACGGCA;RSEQ=GTATATAAAAAAGAAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:103:55,48:106,107:0.3249:2,2:24.1:1:30.4:1:0.55114:1.16:60:50.5:0.3217:0:1.4 0/1:375:91:39,52:143,139:0.2427:2,2:22.8:1:28.9:1:0.22786:1.37053:60:29.333:0.2398:0:1.1 -13 106826430 . G T 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.09836;LSEQ=ACAATTGTGGGTTGTTTCAC;RSEQ=TTTCAGTGAAAGGAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:62:21,41:84,130:0.2246:2,2:27.6:1:30.3:1:0.4621:1.26049:60:124:0.2271:0:1.5 0/1:326:9:4,5:123,194:0.0276:2,2:32.2:1:29.9:1:0.74007:1.26:60:18:0.0278:0:1.2 -13 106826445 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.25284;SOR=Inf;LSEQ=TTCACGTTTCAGTGAAAGGA;RSEQ=AGAAGACACAAGAATGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:78,152:0:2,0:27.1:1:31.5:1:1:0:60:114:0.9956:0:0.5 0/1:269:3:1,2:94,171:0.0112:2,2:25.3:1:27.7:1:1:1.09904:60:6:0.0113:0:1 -13 108490042 . A G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43478;SOR=0;LSEQ=CACCAGCTGCGCAGACTCCC;RSEQ=GGAGTCAGCGTGACATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:14,12:0,0:1:0,2:27.4:1:29.9:1:1:0:60:52:1:0:1.1 1/1:20:19:10,9:1,0:0.95:0,2:23.8:1:27.5:1:1:0:60:18:0.9474:0:1.2 -13 109078075 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGGCTCACTGCAACCTC;RSEQ=GCCTCCCAGGTTCAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 109078371 . A C 63 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACCTCCCAAAGTCCTCAT;RSEQ=CTCCTAATACCATCATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:26.3:1:31.5:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:1:0,0:26:0:33:0:1:0:60:2:1:0:1 -13 109078699 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28815;LSEQ=ACATTAACCTAAGAAAAGTT;RSEQ=TCTTCTAATGTAAGTGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:443:269:125,144:76,97:0.6072:2,2:25.9:1:29.2:1:0.62545:1.11:60:52.8:0.6097:0:1.1 0/1:458:141:67,74:144,173:0.3079:2,2:25.2:1:28.9:1:0.68591:1.09:60:282:0.3092:0:1.1 -13 110408608 . C T 263 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.08478;LSEQ=AGCGTCTTCTTTTAATGATA;RSEQ=TCTCTGACATGTGACATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:419:400:250,150:14,4:0.9547:2,2:25.1:1:30.5:1:0.22066:2.09668:60:79:0.9587:0:1.1 1/0:431:276:164,112:87,68:0.6404:2,2:23.7:1:29.9:1:0.54193:1.14:60:137:0.6462:0:1.1 -13 110408755 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21603;SOR=Inf;LSEQ=AACCCACAGCTAGGACCTGG;RSEQ=TCATTTTCATAAACTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:30,178:0:2,0:22.7:1:32:1:1:0:60:207:0.9952:0:0.1 0/1:182:2:1,1:44,136:0.011:2,2:24.5:1:28.5:1:0.4344:3.07:60:4:0.0112:0:1 -13 110408810 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22387;SOR=Inf;LSEQ=ACATGTATTCATTCTGTTTT;RSEQ=CAGAGGTGAGTTCAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:2,52:0:1,0:21.1:1:31.1:1:1:0:60:26:1:0:0.1 0/1:49:2:0,2:1,46:0.0408:1,0:18.5:1:31:0:1:0:60:4:0.0417:0:1 -13 110414458 . C T 84 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05639;SOR=0.23025;LSEQ=TGTATAAATTTTACAGTGCA;RSEQ=GGCTACAGCAGATTGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:8:3,5:267,121:0.0202:2,2:17:1:28:1:0.11641:3.66418:60:16:0.0204:0:1 0/0:424:2:0,2:263,159:0.0047:2,0:1:0:27:1:0.14363:0:60:4:0.0047:0:1 -13 110414506 . G C 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=TGTACACGGTTCTTTTCTGA;RSEQ=TGTTATTGTTAAAAACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:0:0,0:396,325:0:2,0:26.1:1:31.9:1:1:0:60:54.462:1:0:0.1 0/1:797:17:7,10:437,342:0.0213:2,2:20.9:1:31.4:1:0.22933:1.82398:60:34:0.0216:0:1 -13 110414665 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60505;SOR=2.23411;LSEQ=CAAAAAGTTCCAAGAATTGC;RSEQ=GGTGGACCCTTTCTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:1:0,1:25,191:0.0046:2,0:18:0:14:0:1:0:60:0:0:0:7 0/1:195:2:1,1:32,161:0.0103:2,2:12.5:1:27.5:1:0.31055:4.97:60:4:0.0104:0:1 -13 110414685 . A G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12362;LSEQ=GGGTGGACCCTTTCTTTTAA;RSEQ=TTATGAAATGTTAGACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:58:3,55:3,80:0.4113:1,2:22.9:1:31.2:1:0.69:1.45:60:28:0.4058:0:1.1 0/1:114:9:2,7:10,95:0.0789:2,2:18.3:1:32.2:1:0.24065:2.68:60:18:0.0804:0:1.1 -13 110419164 . T C 75 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTCATCCACCTTGGCTC;RSEQ=GACTCCCCTGCATGTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:30.2:1:32.6:1:1:0:60:10:1:0:1.2 1/1:3:3:2,1:0,0:1:0,2:20.3:1:29.7:1:1:0:60:6:1:0:1 -13 110419354 . C A 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGATCTTGTAGACATTTTC;RSEQ=AATGCTCATGGGCTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:161,3:0:1,0:26.2:1:31.4:1:1:0:60:163:1:0:0.8 0/1:96:15:15,0:80,1:0.1563:1,1:28.9:1:30.7:1:1:0:60:30:0.1596:0:1.1 -13 110419392 . G A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGAGCCTCACACACCAGAG;RSEQ=ACCCAGATCTGCGAAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:260,14:0:2,0:24.6:1:30.9:1:1:0:60:26.4:1:0:1 0/1:208:15:13,2:180,13:0.0721:2,2:29.2:1:29.9:1:0.29526:2.11992:60:30:0.0743:0:1 -13 110419404 . C T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00966;LSEQ=CACCAGAGGACCCAGATCTG;RSEQ=GAAATGCTTTGGTCAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:324:311:279,32:12,1:0.9599:1,2:23.7:1:29.7:1:1:1.37514:60:33.556:0.9587:0:1.1 0/1:275:51:43,8:191,33:0.1855:2,2:23.4:1:28.3:1:0.82978:1.07653:60:16:0.1791:0:1.2 -13 110419621 . G A 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGCTCCTGTCCAGGCGG;RSEQ=CCACACCGGGAATGTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:534:0:0,0:134,400:0:2,0:25.7:1:31.5:1:1:0:60:34.6:1:0:0.1 0/1:436:36:9,27:110,290:0.0826:2,2:22:1:29.7:1:0.84673:1.1376:60:72:0.0843:0:1.3 -13 110419697 . G C 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=AGGAGAAGGAGGTGTGGAAG;RSEQ=AGAAAATACCCAGCAACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:4,154:0:1,0:23.7:1:31.7:1:1:0:60:78:1:0:0.2 0/1:102:12:1,11:3,87:0.1176:1,2:22.2:1:32.8:1:0.39872:2.60:60:24:0.1176:0:1.6 -13 110428702 . A G 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0119;SOR=0;LSEQ=GACAGAGTTTCCAAGGCTTC;RSEQ=CCTTTACCCATTCAAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:27:1:27:1:1:0:60:5:1:0:2.2 0/0:3:0:0,0:2,1:0:2,0:35.3:1:28.3:1:1:0:60:6:1:0:0.3 -13 110428923 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01497;LSEQ=ATAACACACAGAAGCATCTT;RSEQ=CATTATTTGCACCTACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:170:155,15:49,12:0.7359:2,2:25.6:1:28.7:1:0.03485:2.52:59.9:84:0.7336:0:1.1 0/1:177:7:7,0:151,19:0.0395:2,0:26.7:1:29.4:1:1:0:60:14:0.0407:0:1.1 -13 110428933 . C A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=28.40884;LSEQ=GAAGCATCTTGCATTATTTG;RSEQ=ACCTACAGAGCAAAATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:1,0:225,44:0.0037:2,0:20:0:14:0:1:0:60:0:0:0:4 0/1:198:19:16,3:153,26:0.096:2,2:23.6:1:28.7:1:1:1.10282:60:38:0.0969:0:1.1 -13 110429191 . G A 231 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47788;SOR=0;LSEQ=GAGTCAGAATAACCACTGCA;RSEQ=TCTTGAAGAACCCACTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:177:177:6,171:0,0:1:0,1:23.9:1:31:1:1:0:60:58:1:0:1.1 1/1:162:161:10,151:0,0:0.9938:0,2:25.4:1:30.5:1:1:0:60:160:1:0:1.1 -13 110434028 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGGACGGACCCACGCA;RSEQ=CCGGATGAAGACAGTCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 110434223 . A G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=6.93152;LSEQ=GTTCCTGGCAAGTTCTCTGA;RSEQ=GGAAGAGAACAGGGCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:15:14,1:41,0:0.2679:1,1:15.2:1:33:1:0.26786:0:60:30:0.2727:0:1.2 1/0:36:26:25,1:10,0:0.7222:0,1:23:1:31.9:1:1:0:60:52:0.7222:0:1.2 -13 110434295 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19105;SOR=Inf;LSEQ=GCTGTCGGCTTCTGGGTCAA;RSEQ=GTCCCCAAAAAGTGGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:207,10:0:1,0:23.8:1:31.7:1:1:0:60:26.125:1:0:0.2 0/1:169:2:1,1:154,13:0.0118:2,2:13:1:28:1:0.15927:11.4525:60:4:0.012:0:2 -13 110434310 . G A 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=12.28086;LSEQ=GTCAAGGTCCCCAAAAAGTG;RSEQ=GAGCAGTGAAACCCAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:7:7,0:248,22:0.0253:2,0:35.1:1:28.9:1:1:0:60:14:0.026:0:1.1 0/1:227:55:43,12:150,22:0.2423:2,2:21.3:1:29:1:0.12777:1.8968:60:54:0.2389:0:1.1 -13 110434577 . AGCG A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.47142;SOR=0.75493;LSEQ=TCTTGTCTCCCGGCTGAGGA;RSEQ=GCGGCGGCGGCGGCTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:18:10,8:314,217:0.0326:2,2:30:1:31.7:1:0.81007:1.15729:60:36:0.0334:0.0036:0.3 0/1:524:13:8,5:277,234:0.0248:2,2:34.2:1:31.7:1:0.77973:1.35:60:26:0.0254:0.0019:0.5 -13 110434592 . G T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.00533;SOR=Inf;LSEQ=GAGGAAGCGGCGGCGGCGGC;RSEQ=GCTGCGGCTGGGGTGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:0:0,0:364,211:0:2,0:24.6:1:29.6:1:1:0:60:27.75:1:0:0.2 0/1:520:7:2,5:291,220:0.0135:2,2:13.3:1:30.1:1:0.24824:3.29943:60:14:0.0139:0:1.1 -13 110434713 . C T 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01546;SOR=9.11336;LSEQ=TCCACCGCTCCCAGGACAAC;RSEQ=GACCAAGCCCCCGGGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:813:1:1,0:404,407:0.0012:2,0:40:0:31:0:0.49877:0:60:2:0.0012:0:1 0/1:720:8:3,5:365,346:0.0111:2,2:22.1:1:29.5:1:0.49608:1.75682:60:16:0.0113:0:1.3 -13 110435231 . C T 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=2.13725;LSEQ=AGGACAACGATGAGGCGGCG;RSEQ=CCGGGCCCTGGGCGGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:101:32,69:106,241:0.2244:2,2:27.5:1:29.1:1:0.90259:1.05:60:32.667:0.2222:0:1.1 0/1:442:169:64,105:97,176:0.3824:2,2:25.4:1:28.4:1:0.68424:1.11:60:32.8:0.3796:0:1.2 -13 110435264 . G T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.62992;SOR=0.39977;LSEQ=CGGTGGCAACGGCCGAGGCG;RSEQ=GGGGCAGGCGGTACAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:3:1,2:69,180:0.0119:2,2:6.7:1:23:1:1:1.30:56:2:0.008:0:3 0/0:209:1:0,1:63,145:0.0048:2,0:1:0:25:0:1:0:60:2:0.0048:0:1 -13 110435280 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19742;SOR=Inf;LSEQ=GGCGGGGGGCAGGCGGTACA;RSEQ=CTCCCCCGGGGCCGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:96,151:0:2,0:16.6:1:32.4:1:1:0:60:122.5:1:0:0.4 0/1:198:2:2,0:80,116:0.0101:2,0:25.5:1:28:1:0.17028:0:60:4:0.0102:0:1.5 -13 110435292 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10062;SOR=Inf;LSEQ=GCGGTACAGCTCCCCCGGGG;RSEQ=CGGCGGCGGTGGCGGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:131,122:0:2,0:17.7:1:31.7:1:1:0:60:49.6:1:0:0.4 0/1:221:3:1,2:126,92:0.0136:2,2:19:1:28.3:1:0.5762:2.72673:60:6:0.0138:0:1 -13 110435302 . T C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=11.90858;LSEQ=TCCCCCGGGGCCGGCGGCGG;RSEQ=GGCGGCGGCTGCAGAGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:11:7,4:171,95:0.0397:2,2:26.6:1:31.5:1:1:1.02849:60:22:0.0404:0:1.5 0/1:266:88:57,31:110,66:0.3308:2,2:18.3:1:31.6:1:0.78698:1.10:60:176:0.3346:0:1.6 -13 110435308 . C T 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=19.97933;LSEQ=GGGGCCGGCGGCGGTGGCGG;RSEQ=GGCTGCAGAGACGACGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:2:1,1:191,95:0.0069:2,2:17.5:1:18.5:1:1:2.00532:60:1:0.0035:0:1.5 0/1:301:37:24,13:169,95:0.1229:2,2:18.9:1:28:1:1:1.04:60:36:0.1208:0:2 -13 110435472 . C T 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=20.39155;LSEQ=GAAGTCGAGGTTCATGTAGT;RSEQ=GGAGAGCGGAGACCGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:487:1:1,0:199,287:0.0021:2,0:29:0:12:0:0.41068:0:60:0:0:0:1 0/1:471:19:9,10:174,276:0.0403:2,2:27.5:1:30:1:0.47738:1.43:60:38:0.0408:0:1.2 -13 110435526 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1924;SOR=Inf;LSEQ=GGTGCCCGGGGTGCCTGAGC;RSEQ=CAGCGACGAGGCCGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:55,176:0:2,0:23:1:30.7:1:1:0:60:37.5:1:0:0.1 0/1:181:2:1,1:48,131:0.011:2,2:34.5:1:29.5:1:0.46924:2.71:60:4:0.0112:0:1 -13 110435527 . C A 28 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58605;SOR=2.53362;LSEQ=GTGCCCGGGGTGCCTGAGCC;RSEQ=AGCGACGAGGCCGGGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:0,1:53,172:0.0044:2,0:1:0:27:0:1:0:60:2:0.0045:0:7 0/1:180:2:1,1:49,129:0.0111:2,2:10:0:28:1:0.47952:2.62:60:4:0.0114:0:1 -13 110435541 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17709;SOR=Inf;LSEQ=TGAGCCCAGCGACGAGGCCG;RSEQ=GCTGCTGGCGGACAAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:60,143:0:2,0:23.3:1:31.3:1:1:0:60:100.5:1:0:0.1 0/1:148:2:1,1:48,98:0.0135:2,2:8:1:29:1:1:2.03:60:4:0.0136:0:1 -13 110435560 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59452;SOR=2.3857;LSEQ=GGGCTGCTGGCGGACAAGAG;RSEQ=GAGGAGGACGAGGCCGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:1:0,1:73,103:0.0056:2,0:1:0:26:0:1:0:60:2:0.0057:0:1 0/1:150:2:1,1:61,87:0.0133:2,2:13:1:28.5:1:1:1.42:60:4:0.0135:0:1 -13 110435585 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23405;SOR=Inf;LSEQ=AGGACGAGGCCGCCGACGCC;RSEQ=GCAGGGGAGGCGCGGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:110,89:0:2,0:22.8:1:30.8:1:1:0:60:65.333:1:0:0.2 0/1:187:2:1,1:102,83:0.0107:2,2:20:1:30.5:1:1:1.22755:60:4:0.0108:0:1 -13 110435596 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05683;SOR=Inf;LSEQ=GCCGACGCCAGCAGGGGAGG;RSEQ=GCGGGCGGCGACAGGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:123,84:0:2,0:23.7:1:30.9:1:1:0:60:50.75:1:0:0.3 0/1:199:4:2,2:113,82:0.0201:2,2:16.3:1:24.3:1:1:1.37577:60:3:0.0153:0:1 -13 110435602 . C T 90 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06208;SOR=4.5948;LSEQ=GCCAGCAGGGGAGGCGCGGG;RSEQ=GGCGACAGGCGGGCCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:2:0,2:133,78:0.0094:2,0:9.5:1:30:1:0.13996:0:60:4:0.0096:0:1 0/1:215:9:4,5:124,82:0.0419:2,2:25:1:28.7:1:0.49022:1.88452:60:8:0.0377:0:2.1 -13 110435668 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12704;SOR=Inf;LSEQ=TCGCCGGGGCTCTTGGGCTC;RSEQ=GGTGGCAGTGGGTACTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:142,158:0:2,0:25.2:1:30:1:1:0:60:74:1:0:0.2 0/1:342:4:1,3:174,164:0.0117:2,2:14.5:1:29.8:1:0.36142:3.17312:60:8:0.0119:0:1 -13 110435756 . C G 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00074;SOR=Inf;LSEQ=TCACCGCCCGGCCGCGCTGG;RSEQ=CCAAGAAGCCCTCCGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:48,81:0:2,0:19.6:1:31.3:1:1:0:60:42:1:0:0.3 0/1:164:13:5,8:52,99:0.0793:2,2:24:1:32.4:1:0.76854:1.19:60:26:0.0807:0:2 -13 110435766 . C T 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=GCCGCGCTGGCCCAAGAAGC;RSEQ=CTCCGGGCGGCCGCCGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:51,73:0:2,0:20:1:31.3:1:1:0:60:123:1:0:0.2 0/1:159:13:6,7:51,95:0.0818:2,2:24.5:1:30.8:1:0.54736:1.59:60:26:0.0818:0:1.9 -13 110435789 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49833;SOR=Inf;LSEQ=CCGGGCGGCCGCCGCTAGGC;RSEQ=GCACGGGCGAAGGCACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:75,65:0:2,0:22.8:1:30.7:1:1:0:60:139:1:0:0.2 0/1:144:2:1,1:70,72:0.0139:2,2:25.5:1:31:0:1:1.03:60:4:0.0143:0:1 -13 110435790 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24737;SOR=Inf;LSEQ=CGGGCGGCCGCCGCTAGGCC;RSEQ=CACGGGCGAAGGCACTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:77,65:0:2,0:22.8:1:30.9:1:1:0:60:46.333:1:0:0.2 0/1:143:3:2,1:70,70:0.021:2,2:24:1:31.3:1:1:1.99:60:6:0.0216:0:1 -13 110435794 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49831;SOR=Inf;LSEQ=CGGCCGCCGCTAGGCCGCAC;RSEQ=GGCGAAGGCACTACAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:81,64:0:2,0:23.9:1:30.6:1:1:0:60:71.5:1:0:0.2 0/1:147:2:1,1:76,69:0.0136:2,2:39.5:1:30.5:1:1:1.10072:60:4:0.0139:0:1.5 -13 110435800 . A T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24287;SOR=0;LSEQ=CCGCTAGGCCGCACGGGCGA;RSEQ=GGCACTACAGGGTGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:91,62:0.0129:2,2:24:0:32.5:1:1:1.46399:60:4:0.013:0:1 0/0:159:0:0,0:88,71:0:2,0:22.8:1:30.3:1:1:0:60:52:1:0:0.4 -13 110435821 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23531;SOR=Inf;LSEQ=GGCACTACAGGGTGAGGGGG;RSEQ=TGCGTGGGGCCGGCCCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:105,59:0:2,0:27.8:1:32:1:1:0:60:40:1:0:0.2 0/1:155:2:1,1:88,65:0.0129:2,2:16:1:32:0:1:1.35115:60:4:0.0132:0:1.5 -13 110435831 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49864;SOR=0;LSEQ=GGTGAGGGGGCTGCGTGGGG;RSEQ=CGGCCCCGAAGGCGCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:108,49:0.0126:2,2:40:0:31:1:0.53141:2.19205:60:4:0.0129:0:1 0/0:152:0:0,0:91,61:0:2,0:24.4:1:31.5:1:1:0:60:49.667:1:0:0.3 -13 110435889 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19596;SOR=Inf;LSEQ=CGTGGCCTGAGGCTCCAGAC;RSEQ=CTCCTCCTCCAGGATGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:123,69:0:2,0:23.8:1:30:1:1:0:60:37.4:1:0:0.9 0/1:153:2:1,1:86,65:0.0131:2,2:18:1:27.5:1:1:1.32061:60:4:0.0135:0:1 -13 110435914 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.00738;LSEQ=TCCTCCAGGATGCGCCCCAC;RSEQ=GGGGAGCTCATGAGCACGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:170:104,66:33,20:0.7589:2,2:26.9:1:29.7:1:1:1.04691:60:20.25:0.7535:0:1.2 0/1:179:4:3,1:97,78:0.0223:2,2:20:1:28.5:1:0.63124:2.40:60:3:0.0172:0:1 -13 110435953 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.09417;LSEQ=TACTGGTCGCTGTCCCCGCC;RSEQ=CAGGTGTAGGGGGCCTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:76:50,26:151,71:0.255:2,2:22.9:1:30.5:1:0.77702:1.10554:60:37:0.2543:0:1.3 1/0:231:147:91,56:52,32:0.6364:2,2:25.7:1:30.5:1:1:1:60:48:0.6372:0:1.2 -13 110436031 . G T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.03126;SOR=Inf;LSEQ=CCCCTGAGCGGCTCCCCGCC;RSEQ=GGGTGCAGGGCTGCGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:0:0,0:351,201:0:2,0:24.9:1:29.8:1:1:0:60:60.333:1:0:0.2 0/1:586:6:1,5:348,232:0.0102:2,2:16.2:1:28:1:0.04224:7.4755:60:12:0.0103:0:1 -13 110436232 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.47116;LSEQ=CTGGCCTTGTAGCCGCCCCC;RSEQ=CTCGCCGGGAATGTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:133:36,97:74,234:0.3016:2,2:23.3:1:29:1:0.549:1.17:60:18:0.2958:0:1.2 1/0:490:323:108,215:59,108:0.6592:2,2:22.5:1:29.5:1:0.68844:1.08735:60:160.5:0.6605:0:1.2 -13 110436287 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=GTGCTGGCCCCGCAGGCCCC;RSEQ=CAGAAGGCACGGCGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:45,104:0:2,0:18.4:1:31.8:1:1:0:59.9:73.5:1:0:0.3 0/1:162:2:1,1:63,97:0.0123:2,2:11:1:28:1:1:1.54:60:4:0.0127:0:1.5 -13 110436312 . C T 42 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=3;SSF=0.62343;SOR=2.85182;LSEQ=AGGCACGGCGGCGGCGGCGG;RSEQ=GGCGGCGGCCCTGGGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:1:0,1:114,49:0.0061:2,0:1:0:26:0:0.30488:0:60:2:0.0064:0:1 0/1:174:3:0,3:120,51:0.0172:2,0:17.7:1:27:1:0.02874:0:60:6:0.0176:0:1.7 -13 110436315 . C T 28 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.49874;SOR=Inf;LSEQ=CACGGCGGCGGCGGCGGCGG;RSEQ=GGCGGCCCTGGGCTGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:130,53:0:2,0:17:1:31.3:1:1:0:59.9:60:1:0:0.2 0/1:188:2:1,1:128,58:0.0106:2,2:21.5:1:28.5:1:0.53032:2.19668:60:4:0.011:0:1 -13 110436667 . C T 171 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=81.50094;LSEQ=CGCTGCCGGGCTGGCGTGGT;RSEQ=AGGGAGTAGGTCCTCTTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:1:0,1:434,359:0.0013:2,0:1:0:23:0:0.4534:0:60:2:0.0013:0:1 0/1:664:62:33,29:315,287:0.0934:2,2:25.5:1:28.8:1:1:1.04:60:124:0.0944:0:1.1 -13 110436790 . ACCG A 100 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.02451;SOR=0.12788;LSEQ=GTCATGTACCCGTAGAACTC;RSEQ=CCGCCGCCGCCGTCTCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:9:4,5:367,461:0.0107:2,2:20.4:1:31.7:1:1:1.00:60:18:0.0109:0.0036:0.3 0/0:722:1:1,0:336,379:0.0014:2,0:25:0:26:0:0.47067:0:60:2:0.0014:0:0 -13 110436793 . G A 95 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.06486;SOR=2.92062;LSEQ=ATGTACCCGTAGAACTCACC;RSEQ=CCGCCGCCGCCGTCTCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:834:4:2,2:365,458:0.0048:2,2:14.5:1:28.5:1:1:1.25:60:8:0.0049:0:1 0/1:720:10:6,4:333,373:0.0139:2,2:27.4:1:28.8:1:0.52959:1.68:60:20:0.0142:0:1.3 -13 110436914 . C T 51 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37574;SOR=0.27455;LSEQ=ACTCGTCCAGGGACATGAAG;RSEQ=CGGGGTCGCTGGGGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:4:1,3:54,198:0.0156:2,2:18.3:1:25.5:1:1:1.22:60:3:0.0122:0:2 0/0:231:1:0,1:58,172:0.0043:2,0:1:0:25:0:1:0:60:2:0.0045:0:1 -13 110436922 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20641;SOR=Inf;LSEQ=AGGGACATGAAGCCGGGGTC;RSEQ=CTGGGGGAGCCCGAGGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:48,176:0:2,0:24.3:1:31.3:1:1:0:60:36.333:1:0:0.2 0/1:187:2:1,1:46,139:0.0107:2,2:24.5:1:29:1:0.44052:3.00:60:4:0.0112:0:1 -13 110436986 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22547;SOR=Inf;LSEQ=GGCCGGGGCCGTGGTGCAGC;RSEQ=GATGCGGCAGAGGCGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:9,38:0:2,0:12.8:1:31.8:1:1:0:60:94:1:0:0.3 0/1:43:2:1,1:12,29:0.0465:2,2:17:0:32.5:1:0.51827:2.36:60:4:0.0465:0:1.5 -13 110436991 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18045;SOR=Inf;LSEQ=GGGCCGTGGTGCAGCGGATG;RSEQ=GGCAGAGGCGGGTGCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:11,33:0:2,0:11.3:1:30.3:1:1:0:60:43:1:0:0.4 0/1:33:2:1,1:8,22:0.0606:2,2:12:1:28:1:0.48992:2.65:60:4:0.0606:0:1 -13 110437024 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12783;SOR=Inf;LSEQ=TGCGGGCCGGGCGGCGGCGG;RSEQ=TAGGAGCCCGAGCCGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:32,21:0:2,0:17.5:1:31.4:1:1:0:60:52:1:0:0.6 0/1:30:2:1,1:16,12:0.0667:2,2:20.5:1:30.5:1:1:1.32044:60:4:0.0667:0:1 -13 110437035 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCGGCGGGTAGGAGCCCG;RSEQ=GCCGTGGCCGCTGCTGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:41,28:0.0282:2,2:24.5:1:31:1:1:1.45623:60:4:0.0299:0:1.5 0/0:35:0:0,0:20,15:0:2,0:22.9:1:27.5:1:1:0:60:6:1:0:0.6 -13 110437072 . G T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.54398;LSEQ=GACGACAGGGAGCCGGGGCT;RSEQ=GTGGCGGCGGGCGGCGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:45,45:0.0217:2,2:43:1:30:1:1:1:60:4:0.023:0:1 0/1:84:1:0,1:42,41:0.0119:2,0:1:0:25:0:1:0:60:2:0.0123:0:1 -13 110437076 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49714;SOR=0;LSEQ=ACAGGGAGCCGGGGCTGGTG;RSEQ=CGGCGGGCGGCGAGTGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:43,42:0.023:2,2:40.5:1:30.5:1:1:1.02354:60:4:0.0247:0:1 0/0:85:0:0,0:42,43:0:2,0:24.3:1:30.7:1:1:0:60:27.333:1:0:0.4 -13 110437087 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23097;SOR=0;LSEQ=GGGCTGGTGGCGGCGGGCGG;RSEQ=GAGTGCGCCACGGGCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:40,39:0.0247:2,2:43:1:30.5:1:1:1.02533:60:4:0.025:0:1 0/0:87:0:0,0:43,44:0:2,0:25.9:1:28.8:1:1:0:60:8.667:1:0:0.4 -13 110437165 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48308;SOR=Inf;LSEQ=AGCAGCGCCACCTTGCTCCC;RSEQ=CGGCCGCCGCAGCCGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:25.6:1:31.6:1:1:0:60:24:1:0:0.3 0/1:14:2:1,1:5,7:0.1429:2,2:9:0:28:1:1:1.37:60:4:0.1538:0:1 -13 110437366 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49843;SOR=Inf;LSEQ=GGCGGGGTGGCGGCCAGGCT;RSEQ=TCGGTGCGCGAGCGGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:98,37:0:2,0:14.2:1:32.1:1:1:0:60:134:0.9926:0:0.2 0/1:142:2:1,1:93,47:0.0141:2,2:5:1:29.5:1:1:1.96856:60:4:0.0143:0:1 -13 110437374 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24084;SOR=Inf;LSEQ=GGCGGCCAGGCTGTCGGTGC;RSEQ=CGAGCGGCGCACCAGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:133,46:0:2,0:17.4:1:30.9:1:1:0:60:178:1:0:0.2 0/1:173:2:1,1:114,57:0.0116:2,2:24:1:27.5:1:1:1.99142:60:4:0.0118:0:1 -13 110437376 . G T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62302;SOR=0.33602;LSEQ=CGGCCAGGCTGTCGGTGCGC;RSEQ=AGCGGCGCACCAGGCCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:3:1,2:139,46:0.016:2,2:10.3:1:28.3:1:0.16077:5.97234:60:6:0.016:0:1.3 0/0:185:1:0,1:123,61:0.0054:2,0:1:0:23:0:0.33514:0:60:2:0.0056:0:1 -13 110437379 . C T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24829;SOR=0;LSEQ=CCAGGCTGTCGGTGCGCGAG;RSEQ=GGCGCACCAGGCCCGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:1,2:148,51:0.0148:2,2:11:1:22:1:0.16902:5.74266:60:2:0.0101:0:2.3 0/0:197:0:0,0:132,65:0:2,0:22.1:1:31.4:1:1:0:60:196:1:0:0.3 -13 110437497 . G A 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00605;SOR=Inf;LSEQ=CGATTGGCTCTTACTGCGCG;RSEQ=CCGGAACTCGAAGAGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:0:0,0:366,296:0:2,0:25.5:1:31.2:1:1:0:60:40.375:1:0:0.2 0/1:620:7:4,3:311,302:0.0113:2,2:21.4:1:29.9:1:1:1.29:60:14:0.0115:0:1 -13 110437862 . G A 54 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3864;SOR=0.30662;LSEQ=CCAGCCCGTAGCTGTCCTCG;RSEQ=CCCCGGCGGCGCCGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:4:3,1:36,221:0.0153:2,2:14.3:1:27:1:0.01117:18.07:60:8:0.0154:0:1 0/0:211:1:1,0:28,181:0.0047:2,0:1:0:22:0:0.1381:0:60:2:0.0049:0:1 -13 110437871 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2196;SOR=Inf;LSEQ=AGCTGTCCTCGGCCCCGGCG;RSEQ=CGCCGGCAGAGCCGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:19,163:0:2,0:21.9:1:32.8:1:1:0:60:364:1:0:0.1 0/1:161:2:1,1:17,142:0.0124:2,2:9:1:28:1:0.21172:8.15:60:4:0.0126:0:1 -13 110437958 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.49896;SOR=0;LSEQ=GGGGCGCGTCTCCGGCGGCC;RSEQ=CGCGGCCCTCGCTGACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:98,25:0.0159:2,2:17:0:32:0:0.37406:3.86344:60:4:0.0165:0:1.5 0/0:115:0:0,0:93,20:0:2,0:15.7:1:29.5:1:1:0:60:21.6:0.9818:0:0.1 -13 110437991 . C T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.11235;SOR=0;LSEQ=TGACCAGGTCGGTGAGCGCG;RSEQ=GGTACCAGCCCTCCTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:1,2:204,84:0.0103:2,2:15.7:1:26.3:1:0.20951:4.82702:60:6:0.0107:0:1 0/0:311:0:0,0:208,103:0:2,0:26.1:1:30.9:1:1:0:60:43.429:1:0:0.2 -13 110438203 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67449;SOR=1.6298;LSEQ=AGCCGCGGCGGTTGCGGCGC;RSEQ=GACCCCCCGCCCGCCGTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:0,2:56,142:0.01:2,0:1:0:25.5:1:1:0:60:4:0.0102:0:1 0/1:185:3:0,3:61,121:0.0162:2,0:7:1:27.7:1:0.55194:0:60:6:0.0169:0:1.7 -13 110438216 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.61086;SOR=0.46345;LSEQ=GCGGCGCCGACCCCCCGCCC;RSEQ=CCGTCGCCTCGTCGCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:54,106:0.0123:2,2:7.5:1:28:1:1:1.95:60:4:0.0127:0:1 0/0:174:1:1,0:75,98:0.0057:2,0:1:0:25:0:0.43678:0:60:2:0.006:0:1 -13 110438218 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49926;SOR=Inf;LSEQ=GGCGCCGACCCCCCGCCCGC;RSEQ=GTCGCCTCGTCGCCGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:57,105:0:2,0:13:1:30.4:1:1:0:60:80:1:0:0.2 0/1:175:2:0,2:76,97:0.0114:2,0:8:1:29:1:0.50581:0:60:4:0.0118:0:1 -13 110438226 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49988;SOR=Inf;LSEQ=CCCCCCGCCCGCCGTCGCCT;RSEQ=GTCGCCGCCCGCGCCGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:64,84:0:2,0:12.8:1:30.3:1:1:0:60:147:1:0:0.2 0/1:165:2:1,1:76,86:0.0121:2,2:11.5:1:29.5:1:1:1.13:60:4:0.0123:0:1.5 -13 110438241 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24806;SOR=Inf;LSEQ=CGCCTCGTCGCCGCCCGCGC;RSEQ=GGGTCCGCGCAGCACGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:80,52:0:2,0:20.1:1:30.2:1:1:0:60:65:1:0:0.2 0/1:141:3:1,2:79,59:0.0213:2,2:33.3:1:28.7:1:0.57849:2.65947:60:6:0.0217:0:1 -13 110438293 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24104;SOR=0;LSEQ=CCATGCTTCTGCTTGCGCAG;RSEQ=TAGCCGCACTTGCGCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:91,84:0.0113:2,2:35.5:1:31:1:1:1.08283:60:4:0.0114:0:1.5 0/0:183:0:0,0:94,88:0:2,0:27.3:1:30:1:1:0:60:21.75:1:0:0.3 -13 110438296 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24811;SOR=Inf;LSEQ=TGCTTCTGCTTGCGCAGGTA;RSEQ=CCGCACTTGCGCACGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:91,85:0:2,0:27.2:1:31.8:1:1:0:60:175:1:0:0.1 0/1:182:3:1,2:92,87:0.0165:2,2:17:1:26.3:1:0.61473:2.10653:60:6:0.0169:0:1 -13 110438338 . G A 25 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.21284;SOR=Inf;LSEQ=TTGTTGTTGTTGTTGTTGTT;RSEQ=TTGAGGTTGGGGCCGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:33,75:0:2,0:22.3:1:31.8:1:1:0:60:53:1:0:0.1 0/1:93:2:1,1:31,60:0.0215:2,2:5.5:1:25.5:1:1:1.92:60:4:0.0217:0:1.5 -13 110438392 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51613;SOR=0;LSEQ=GGCGGCCCGTGCCGCGGCGG;RSEQ=CTCGCCATCGCGGGCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:2,16:0.1:2,2:12:1:28:1:0.28421:6.73:60:4:0.1053:0:1 0/0:12:0:0,0:2,10:0:2,0:6:0:19:0:1:0:60:0:0:0:5 -13 110438877 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.23077;SOR=Inf;LSEQ=TGCTGCTGGTGTTGCTGCTG;RSEQ=TGCTGCCAACGGCGACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:27:1:31.1:1:1:0:60:19:1:0:0.4 0/1:19:2:1,1:9,8:0.1053:2,2:20.5:1:29.5:1:1:1.11803:60:4:0.1053:0:1.5 -13 110439354 . C T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGGGCTTGAGCTTCCGC;RSEQ=GGGGAGGGGGCGCCGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 111118948 . C T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03452;SOR=0.19517;LSEQ=TGGCTGATTGCTGTGGTTCA;RSEQ=TCTGAAAGTAAACAAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:12:10,2:26,5:0.2791:2,2:18.8:1:31.1:1:1:1.03904:60:24:0.2791:0:1.1 0/1:29:2:2,0:20,7:0.069:2,0:14.5:1:31:1:1:0:60:4:0.069:0:1 -13 111119004 . A G 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50173;SOR=0;LSEQ=ATAATTCATTTTGAAATCGC;RSEQ=GGCTATCTCCATTGCTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:91,38:0.0153:2,2:38:0:30.5:1:0.5084:2.37681:60:4:0.0156:0:1 0/0:110:0:0,0:72,37:0:2,0:26:1:30.6:1:1:0:60:108:0.9908:0:0.7 -13 111119009 . A T 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59134;SOR=2.43409;LSEQ=TCATTTTGAAATCGCAGGCT;RSEQ=TCTCCATTGCTGGCAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:0,1:97,41:0.0072:2,0:1:0:27:0:0.30216:0:60:2:0.0072:0:1 0/1:115:2:1,1:73,40:0.0174:2,2:22:0:32:0:1:1.81481:60:4:0.0175:0:1.5 -13 111119019 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50425;SOR=0;LSEQ=ATCGCAGGCTATCTCCATTG;RSEQ=TGGCAGATGCTTCCAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:103,52:0.0127:2,2:30.5:1:28:1:1:1.97156:60:4:0.0129:0:1 0/0:126:0:0,0:79,47:0:2,0:26.8:1:32:1:1:0:60:125:1:0:0.7 -13 111119052 . C G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.21545;LSEQ=CCAGACAAAAGAAAAGCATC;RSEQ=ACACTGACTTGCAGGGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:38:25,13:83,59:0.2111:2,2:29.7:1:30.1:1:0.45989:1.36:60:76:0.2135:0:1.9 1/0:160:85:51,34:47,28:0.5313:2,2:21.2:1:29.4:1:0.74773:1.11826:60:170:0.5313:0:1.9 -13 111119077 . A G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.05032;LSEQ=TGACTTGCAGGGTAGCAGCC;RSEQ=GATTAACTCGGTTTGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:46:25,21:77,69:0.2396:2,2:22.3:1:30.7:1:0.86717:1.07:60:92:0.2408:0:1.8 0/1:165:81:43,38:44,40:0.4909:2,2:25.8:1:29.5:1:1:1.03:60:162:0.4939:0:2.1 -13 111119136 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.204;SOR=0;LSEQ=AGGGAATCAATTGTTTGCCA;RSEQ=CACAGTGCCAGTTTTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:38,89:0.0155:2,2:37.5:1:30.5:1:0.5149:2.32:60:4:0.0157:0:1 0/0:156:0:0,0:60,96:0:2,0:25.3:1:32:1:1:0:60:155:1:0:0.8 -13 111119146 . A T 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTTTGCCAGCACAGTGCC;RSEQ=GTTTTTATTTGACTAGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:32,84:0:2,0:26.2:1:30.6:1:1:0:60:115:1:0:0.2 0/1:140:56:21,35:27,57:0.4:2,2:26.2:1:29.7:1:0.58661:1.26:60:112:0.4029:0:1.6 -13 111119152 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50044;SOR=Inf;LSEQ=GCCAGCACAGTGCCAGTTTT;RSEQ=ATTTGACTAGACTGGCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:28,83:0:2,0:26.1:1:28.4:1:1:0:60:222:1:0:0.2 0/1:128:2:1,1:41,84:0.0156:2,2:26:1:32.5:1:1:2.04:60:4:0.0159:0:1 -13 111119957 . T C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGTGAGAAAGAGTCTGGG;RSEQ=GCCCTTCACAGAGCCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:31.5:1:1:0:60:4:1:0:1.5 -13 111415092 . T C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTCTCACAAAGTGTGCTTC;RSEQ=CTGGGTGGAGCAGGCTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:19.5:1:30:1:1:1:60:4:0.3333:0:1.5 0/0:2:0:0,0:2,0:0:0,0:13.5:1:32.5:1:1:0:60:4:1:0:0 -13 111415746 . A T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTACATAAGGGACGTCA;RSEQ=ATAAGTGGGATCAGACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:48:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 111588789 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCTAACAGAGGAGGAAGAAG;RSEQ=TAAGATTAACTCCCTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:11:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 111588868 . C T 92 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTACAGACCGAATGAAAA;RSEQ=ATCCAGGAGAAAGAGTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:2,0:0.8:0,0:25.1:1:30.9:1:1:0:60:16:0.8:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -13 111588967 . T C 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01539;SOR=0;LSEQ=ACAAATTAAAGACGAACTAT;RSEQ=GAGCTGGGTACTCGGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:45:44,1:0,0:1:0,1:26.4:1:30.9:1:1:0:60:21.5:1:0:1.4 1/1:26:22:22,0:4,0:0.8462:0,1:22.3:1:31.5:1:1:0:60:44:0.8462:0:1 -13 111589079 . C T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25548;SOR=0;LSEQ=CAGGTCGTCGCGTCGGGCTC;RSEQ=TGGGATTTGGCGGCAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:243,52:0.0101:2,2:17.7:1:25.3:1:0.4455:2.32811:60:2:0.0069:0:1.7 0/0:246:0:0,0:193,53:0:2,0:21.8:1:30.4:1:1:0:60:122:1:0:0.3 -13 111589152 . G A 248 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71868;SOR=1.03943;LSEQ=CTGAGTGGAGTACACCAAGA;RSEQ=CGGGCGCACCTCTTGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:769:342:192,150:234,193:0.4447:2,2:26.4:1:29.7:1:0.71578:1.06:59.3:84.5:0.4453:0:1.6 0/1:755:343:191,152:212,198:0.4543:2,2:27:1:29.5:1:0.30445:1.17:59.8:48:0.4534:0:1.7 -13 111589204 . G C 302 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01127;LSEQ=AGCATCCCCAAGGACTCGCT;RSEQ=CGGATGGCCATCATGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:879:876:435,441:1,0:0.9966:0,2:26.3:1:30.9:1:0.49715:0:59.6:42.8:0.9965:0:1.5 1/0:792:607:291,316:91,93:0.7664:2,2:24.9:1:30.6:1:0.73676:1.06245:59.8:45.692:0.7674:0:1.7 -13 111589278 . G A 283 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00469;LSEQ=GTACCACTTCTCCTGCTTGC;RSEQ=GAAGGTGGGCCACTCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:623:622:278,344:0,0:0.9984:0,2:24.1:1:30.6:1:1:0:60:87.857:0.9984:0:1.4 1/0:618:460:223,237:80,75:0.7443:2,2:24.3:1:30.2:1:0.5166:1.1334:60:64.714:0.7438:0:1.4 -13 111589587 . G C 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00201;SOR=1.69618;LSEQ=TTGACCCCTGGTACCACCCA;RSEQ=GCTGCTTTGTCAAGAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:72:35,37:260,266:0.1202:2,2:24.2:1:30:1:0.90082:1.03325:60:35:0.1193:0:1.1 0/1:526:99:50,49:218,209:0.1882:2,2:26.2:1:30.2:1:1:1.02216:60:198:0.1904:0:1.1 -13 111589752 . G A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAGGCGATGAGGTGGATGGA;RSEQ=TGGATGAAGTGGCCAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:0:0,0:301,286:0:2,0:26.2:1:32.4:1:1:0:60:194.667:1:0:0.1 0/1:529:15:7,8:269,245:0.0284:2,2:23.6:1:30.4:1:0.79488:1.25427:60:30:0.0286:0:1 -13 111590028 . A G 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0434;SOR=0.61732;LSEQ=AGCTGGTCTTCAAGAGCGAC;RSEQ=CTTATTACTGCACCGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:54:26,28:189,187:0.1256:2,2:26.5:1:30.4:1:0.88443:1.08822:60:26:0.1224:0:1.1 0/1:430:35:17,18:198,197:0.0814:2,2:26.7:1:31.1:1:1:1.06408:60:70:0.0818:0:1.1 -13 111590169 . C T 224 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAAAGCAGGACCGTATATT;RSEQ=CCCCCAGAAACCAGTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:192:192:91,101:0,0:1:0,2:23.3:1:29.6:1:1:0:60:26.429:1:0:1.1 1/0:178:99:55,44:43,36:0.5562:2,2:23.7:1:29.6:1:1:1.05:60:48.5:0.5543:0:1.1 -13 111590176 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49948;SOR=0;LSEQ=AGGACCGTATATTCCCCCCA;RSEQ=AAACCAGTGACCCAGTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:89,93:0.0109:2,2:21.5:1:29:1:1:1.04:60:4:0.0112:0:2 0/0:169:0:0,0:96,73:0:2,0:26.8:1:31.9:1:1:0:59.9:168:1:0:0.6 -13 111590409 . AAAG A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.85038;SOR=0.92069;LSEQ=AGCACTAAAGAGGAGGTGGA;RSEQ=AAGAAGAAGAAGATGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:15:6,9:202,259:0.0315:2,2:22.9:1:29.8:1:1:1.1695:60:30:0.0321:0.0063:0.5 0/1:447:13:6,7:175,258:0.0291:2,2:22.6:1:29.4:1:0.77678:1.26:60:26:0.0291:0.0045:0.2 -13 111590550 . A G 289 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGTCCCCCTGGGGGGCAGA;RSEQ=GTGAAGGCAGAGCCTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:599:599:301,298:0,0:1:0,2:23.8:1:31.4:1:1:0:59.8:73.875:1:0:1.1 1/0:600:424:230,194:90,85:0.7067:2,2:23.9:1:30.7:1:0.53014:1.12:59.9:59.571:0.7044:0:1.1 -13 111590720 . ACT A 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.95618;SOR=0.99109;LSEQ=TCCTGACTCTGGTCTGGAAC;RSEQ=CTGCACATGTTCTGGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:939:241:122,119:372,325:0.2567:2,2:25.3:1:31.8:1:0.5007:1.11634:59.9:240:0.2589:0.0415:0.1 0/1:808:206:102,104:317,284:0.255:2,2:22.4:1:30.8:1:0.46719:1.1379:59.7:412:0.2594:0.0545:0.1 -13 111590727 . A G 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00034;SOR=0.68254;LSEQ=TCTGGTCTGGAACACTCTGC;RSEQ=CATGTTCTGGAGAAAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:920:312:172,140:311,296:0.3391:2,2:16.9:1:30.2:1:0.26548:1.17:58.6:30.2:0.3352:0:2 0/1:802:208:107,101:313,279:0.2594:2,2:17:1:30.9:1:0.74715:1.05885:58:103:0.2604:0:2 -13 111590733 . T C 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=0.65724;LSEQ=CTGGAACACTCTGCACATGT;RSEQ=CTGGAGAAAGGTGGGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:908:284:155,129:319,303:0.3128:2,2:12.3:1:30.6:1:0.38967:1.14:58.4:24.818:0.3085:0:2.1 0/1:821:189:97,92:327,305:0.2302:2,2:12.4:1:30.7:1:0.93404:1.01685:57.8:30.5:0.2296:0:2.1 -13 111590803 . T A 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02885;SOR=0;LSEQ=TCGTTAAAGGAACCAACTCC;RSEQ=ATTACAAGCTGAAGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:3,2:205,288:0.01:2,2:9:1:24.8:1:0.6538:2.10:59:4:0.0081:0:1 0/0:512:0:0,0:224,286:0:2,0:24.7:1:29:1:1:0:59.9:71.857:1:0:0.1 -13 111590930 . C T 264 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGTCCAAGGAGGACACCA;RSEQ=TGAACACTTCATGAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:410:410:227,183:0,0:1:0,2:25.4:1:30.5:1:1:0:60:101.5:1:0:1.1 1/0:366:257:144,113:60,48:0.7022:2,2:21:1:29.7:1:1:1.02:60:84.667:0.6997:0:1.1 -13 111591170 . G A 280 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00668;LSEQ=CCATGGTGGGGTGTGAGATC;RSEQ=ACCTTCAGATGCCCTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:609:607:286,321:0,0:0.9967:0,2:23.4:1:30.3:1:1:0:60:201.333:0.9983:0:1.1 1/0:571:382:187,195:93,96:0.669:2,2:22.9:1:29.6:1:1:1.01018:60:94.5:0.6714:0:1.1 -13 111591265 . G A 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.444;LSEQ=TGGTGTCCCAGGGCAGCAGC;RSEQ=ACTCTCAGATCCTGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:39:19,20:207,228:0.0823:2,2:25.9:1:29.6:1:1:1.05:59.2:78:0.0833:0:1.9 0/1:467:84:41,43:177,206:0.1799:2,2:21.6:1:29.5:1:0.71762:1.11:60:83:0.1804:0:1.7 -13 111591283 . T C 280 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01651;LSEQ=GCGACTCTCAGATCCTGGAT;RSEQ=TCTCAAATCGCTTTTACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:478:475:224,251:1,0:0.9937:0,2:24.5:1:31.6:1:0.47269:0:59.5:58.375:1:0:1.2 1/0:433:313:151,162:57,63:0.7229:2,2:26.5:1:31.5:1:0.91472:1.03:59.8:103.333:0.7243:0:1.3 -13 111592184 . C A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24857;SOR=0;LSEQ=CGGTGACTCTGGTATTAATT;RSEQ=ACCCTAAGCGCTTCTGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:1,2:42,155:0.015:2,2:15.7:1:30.3:1:0.51827:1.84:60:6:0.0152:0:1 0/0:190:0:0,0:39,151:0:2,0:20.3:1:31.4:1:1:0:60:94:1:0:0.1 -13 111592285 . A G 179 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00021;SOR=0;LSEQ=GATTTTGCAGAAATGCATTA;RSEQ=AAGCTTTTTCCCAAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:3,50:0,0:1:0,2:25.5:1:31.4:1:1:0:60:106:1:0:1.1 1/0:14:9:0,9:1,4:0.6429:2,0:28.1:1:31.9:1:0.35714:0:60:18:0.6429:0:1.2 -13 111840700 . T G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAAACTGAGATAACAGA;RSEQ=GCTTGTTGTTTGGGCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:29.5:1:32:1:1:1:60:4:0.5:0:1 -13 111842645 . C G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89376;LSEQ=GTTGCCCAACTCCAGAGGTT;RSEQ=GTATAAGAGTTTGAAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:3:2,1:26,24:0.0566:2,2:13.7:1:30.3:1:1:1.83:34.7:6:0.0566:0:1 0/1:59:3:1,2:29,27:0.0508:2,2:14.7:1:31.7:1:0.61195:2.12132:36.7:6:0.0517:0:1.7 -13 111842646 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49602;SOR=Inf;LSEQ=TTGCCCAACTCCAGAGGTTC;RSEQ=TATAAGAGTTTGAAAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:27,25:0:2,0:30.3:1:31:1:1:0:57.5:104:1:0:0.2 0/1:56:2:1,1:28,26:0.0357:2,2:10:1:29.5:1:1:1.07547:60:4:0.037:0:1 -13 111842678 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49743;SOR=Inf;LSEQ=GAAAGGCATTGTCTGACTTC;RSEQ=GAAGCCTTTTCCCGTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:19,24:0:2,0:28.1:1:30:1:1:0:60:42:1:0:0.1 0/1:50:2:1,1:20,28:0.04:2,2:23.5:1:29:1:1:1.39:60:4:0.04:0:1.5 -13 112722084 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.51746;SOR=0;LSEQ=GCGGGGGCGGAGGCGGGGGC;RSEQ=GCGGCGGCGGCGGGGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:69,5:0.0263:2,2:5:0:32.5:1:0.15263:12.68865:60:4:0.0267:0:1 0/0:50:0:0,0:45,5:0:2,0:10.9:1:29.7:1:1:0:60:24:1:0:0.1 -13 112722133 . C T 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06299;SOR=0;LSEQ=CCAGGACCGGGTCAAACGGC;RSEQ=CATGAACGCCTTCATGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:5:1,4:257,88:0.0142:2,2:12.8:1:27.8:1:0.01811:11.58614:54.8:10:0.0147:0:1.2 0/0:319:0:0,0:216,103:0:2,0:24.2:1:30.2:1:1:0:58.8:78.75:1:0:0.2 -13 112722356 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20462;SOR=Inf;LSEQ=CCGCGCCGCAAGACCAAGAC;RSEQ=CTGCTCAAGAAGGACAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:47,178:0:2,0:24.9:1:31.3:1:1:0:60:55.25:0.991:0:0.2 0/1:188:2:1,1:44,142:0.0106:2,2:5.5:1:29:1:0.4224:3.20:60:4:0.0108:0:1 -13 112722387 . G A 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11048;SOR=0.32337;LSEQ=AGGACAAGTACTCGCTGGCC;RSEQ=GCGGGCTCCTGGCGGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:14:0,14:5,82:0.1386:2,1:25.1:1:32.3:1:1:0:60:28:0.1386:0:1.1 0/1:61:3:0,3:5,52:0.0492:2,0:34.7:1:33:0:1:0:60:6:0.0508:0:1 -13 114443604 . GCA G 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.49734;SOR=0;LSEQ=ACACACAGGTGCACACATGC;RSEQ=CACACACACACCTCTACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:12,13:0.0741:2,2:29:0:34:1:1:1.08:60:4:0.0741:0:0 0/0:21:0:0,0:10,11:0:2,0:33.4:1:30.6:1:1:0:60:20:1:0:0.7 -13 114826465 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCCCCACAGCCGGCAGA;RSEQ=GGAGCCCCCCACAGCCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:28:1:1:0:60:4:1:0:1 -13 114828023 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48949;SOR=0;LSEQ=GTGCAGCAATAGACATCACA;RSEQ=CCCACGTCCGCACGCAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:0.1:2,2:23:1:29:1:1:1.23603:60:4:0.1:0:1 0/0:17:0:0,0:8,9:0:2,0:28.6:1:30.9:1:1:0:60:34:1:0:0.8 -13 114828045 . G A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00089;SOR=Inf;LSEQ=CCACGTCCGCACGCAGACTC;RSEQ=GACACGCGTGCTCACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:20.7:1:31:1:1:0:60:30:1:0:0.4 1/0:12:7:3,4:2,3:0.5833:2,2:26:1:31.4:1:1:1.11:60:14:0.5833:0:1.6 -13 114828075 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=GCTCACAGCCCACGTCCGCA;RSEQ=GCAGACTCAGACACGCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:22.8:1:30:1:1:0:60:20:1:0:0.5 1/0:6:3:0,3:0,3:0.5:0,0:8.3:1:31.3:1:1:0:60:6:0.5:0:2.3 -14 19487423 . T C 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01138;SOR=Inf;LSEQ=ACCCAGTCTGTCAGGTATTC;RSEQ=ACCATCTTATTCCTATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:166,41:0:2,0:20.8:1:30.4:1:1:0:26.9:50.75:1:0:0.1 0/1:145:5:4,1:120,20:0.0345:2,2:22:1:29.8:1:0.54806:1.49522:25:10:0.035:0:1 -14 19487493 . C CCA 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.06998;SOR=Inf;LSEQ=TTTTCTGAAGTCATACCCCC;RSEQ=CACACACACACCTTCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:112,207:0:2,0:28.4:1:30:1:1:0:27.9:23.538:0.9935:0:0.1 0/1:226:3:1,2:74,148:0.0133:2,2:32.7:1:30.8:1:1:1:29:6:0.0135:0:0.3 -14 19487496 . C A 91 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.00658;SOR=0;LSEQ=TCTGAAGTCATACCCCCCCA;RSEQ=ACACACACCTTCAGTCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:10:4,6:100,205:0.0317:2,2:25.5:1:27.6:1:0.73483:1.37:29.7:9:0.029:0:1.1 0/0:222:0:0,0:69,153:0:2,0:27.4:1:30.6:1:1:0:28.5:110:1:0:0.1 -14 19487547 . G T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02149;SOR=Inf;LSEQ=ATGGTGCAAATAATTTGGCA;RSEQ=ATAACCCAGGTGACATGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:5,107:0:1,0:21.9:1:31.4:1:1:0:26.9:27:1:0:0.1 0/1:71:4:0,4:1,66:0.0563:1,0:11.5:1:29.5:1:1:0:30.8:8:0.0563:0:1 -14 19487907 . A C 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08932;SOR=0;LSEQ=CTCTTTTGAGAACTCACCTA;RSEQ=ATTTCATCTCTCGGCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:6:6,0:68,17:0.0659:2,0:30.2:1:33.7:1:0.58916:0:24.7:12:0.0667:0:1.2 0/0:50:0:0,0:31,19:0:2,0:24.1:1:28.6:1:1:0:28:49:1:0:0 -14 19487914 . T C 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.00846;SOR=0;LSEQ=GAGAACTCACCTAAATTTCA;RSEQ=CTCTCGGCAAAATGAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:12:12,0:69,17:0.1212:2,0:22.8:1:32.6:1:0.11916:0:26.3:24:0.1212:0:1.2 0/0:52:0:0,0:32,20:0:2,0:23.4:1:29:1:1:0:27.9:104:1:0:0 -14 19488019 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31772;SOR=0.59676;LSEQ=GACCATATTCCCAAGCACAC;RSEQ=AACGTACCTATACAGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:24:24,0:102,32:0.1519:2,1:17:1:26.5:1:0.00447:0:24.5:7:0.1364:0:2.8 0/1:83:8:8,0:56,19:0.0964:2,0:18.5:1:29.1:1:0.18841:0:24.8:16:0.0964:0:2.6 -14 19488023 . G A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37336;SOR=0.58417;LSEQ=ATATTCCCAAGCACACAAAC;RSEQ=TACCTATACAGACATAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:19:19,0:96,48:0.1166:2,1:18.2:1:28.7:1:0.00103:0:24.4:18:0.1118:0:3.2 0/1:84:6:6,0:51,27:0.0714:2,0:25:1:28.8:1:0.17023:0:24.5:12:0.0723:0:3.2 -14 19488038 . T C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24852;SOR=0.58496;LSEQ=CAAACGTACCTATACAGACA;RSEQ=AGAGACAATAAAAAAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:24:13,11:67,70:0.1491:2,2:15.7:1:30.9:1:0.66425:1.23:25.3:48:0.1529:0:3.9 0/1:97:9:4,5:42,46:0.0928:2,2:18.9:1:29.7:1:1:1.13976:24.4:18:0.0947:0:3.8 -14 19488054 . G A 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14746;SOR=0.5417;LSEQ=GACATAGAGACAATAAAAAA;RSEQ=TTATCAGATACAGACACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:30:8,22:49,115:0.1546:2,2:22.1:1:29.5:1:0.82934:1.17084:27.3:60:0.1554:0:3.9 0/1:100:9:3,6:28,60:0.09:2,2:23.4:1:27.4:1:1:1.07:24.3:18:0.0909:0:4.1 -14 19488114 . A G 177 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41618;SOR=0.72542;LSEQ=TTAACCATCAAATAAAACGA;RSEQ=CTAAACGTAAGTTTGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:42:6,36:18,173:0.1795:2,2:28.3:1:33:1:0.39857:1.60:28.1:84:0.1834:0:3.7 0/1:95:13:1,12:7,75:0.1368:2,1:31.4:1:33.4:1:1:1.11871:26.2:26:0.1398:0:3.5 -14 19488121 . G A 170 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.506;SOR=0.76757;LSEQ=TCAAATAAAACGAACTAAAC;RSEQ=TAAGTTTGAAAACAGTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:42:6,36:17,149:0.2019:2,2:25:1:31.6:1:0.42131:1.46:28.1:84:0.2029:0:3.7 0/1:80:13:1,12:7,60:0.1625:2,1:28.5:1:31.5:1:1:1.39464:26.2:26:0.1625:0:3.5 -14 19488142 . C T 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47016;SOR=0.73303;LSEQ=TAAGTTTGAAAACAGTAAGA;RSEQ=ATTTATTTATAGGAGAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:51:6,45:14,74:0.3643:2,2:21.7:1:29.1:1:0.6195:1.41548:27:50:0.3623:0:2.4 0/1:44:13:1,12:5,26:0.2955:2,1:27.1:1:29.2:1:0.65232:2.27011:26.9:26:0.2955:0:2.5 -14 19488190 . CAG AC 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99002;LSEQ=TTCTGGTTACCTTGTTGTCA;RSEQ=CCTAGTTTGTGTGCAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:9:4,5:31,18:0.1552:2,2:18.9:1:31.4:1:0.46011:2.12325:26.8:18:0.1579:0.0345:1.4 0/1:26:4:3,1:14,8:0.1538:2,2:31.3:1:32.2:1:1:1.68:34.5:8:0.1538:0:1 -14 19488241 . T C 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03525;LSEQ=AATTATTTTATCAATTACTA;RSEQ=CAATATCAATGTGTGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:13:10,3:95,11:0.1092:2,2:27.5:1:31.8:1:0.18107:2.56395:26.2:26:0.1121:0:1.6 0/1:71:8:6,2:58,5:0.1127:2,2:24.9:1:30.5:1:0.17524:3.75991:31.4:16:0.1143:0:1.5 -14 19488253 . T C 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AATTACTATCAATATCAATG;RSEQ=GTGAGAGGTTTTTCTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:138,20:0:2,0:23.5:1:29.6:1:1:0:27.2:30.6:1:0:0.3 0/1:91:16:14,2:68,7:0.1758:2,2:23.8:1:31.9:1:0.65559:1.38233:27.4:32:0.1778:0:1 -14 19488256 . G A 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.7943;SOR=0.72883;LSEQ=TACTATCAATATCAATGTGT;RSEQ=AGAGGTTTTTCTTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:12:12,0:132,20:0.0732:2,0:13.1:1:29:1:0.36407:0:24:24:0.0736:0:1.3 0/1:92:5:5,0:77,10:0.0543:2,0:12.4:1:29.6:1:1:0:24:10:0.0549:0:1.2 -14 19488265 . T A 46 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.60266;LSEQ=TATCAATGTGTGAGAGGTTT;RSEQ=TCTTGTCTCTTAAATCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:3:3,0:136,21:0.0188:2,0:19.7:1:29.3:1:1:0:24:6:0.019:0:2 0/1:88:1:1,0:79,8:0.0114:2,0:20:0:30:0:1:0:24:2:0.0114:0:2 -14 19488346 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52889;SOR=0;LSEQ=CAGATTTAACATCATTGTTT;RSEQ=AATGCTAGCTTGCTCTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:24,99:0.016:2,2:26:1:27:1:0.36129:4.06:25:4:0.0161:0:1 0/0:75:0:0,0:9,66:0:2,0:31.8:1:30.7:1:1:0:25.5:36.5:1:0:0.1 -14 19488473 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32044;SOR=3.03346;LSEQ=AATAAAACCTATAGAGAGAA;RSEQ=AAATATATTAATGATTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:0,3:0,19:0.1364:1,0:15:1:27.3:1:1:0:26:6:0.1429:0:1 0/1:9:3:0,3:0,6:0.3333:0,0:9:1:28.7:1:1:0:27:6:0.3333:0:1 -14 19488792 . C G 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.93413;LSEQ=TCATTATTTCAAACAAGTCA;RSEQ=TCTATTCATAGGGAAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:3:3,0:56,0:0.0508:1,0:35:1:33:0:1:0:24.7:6:0.0508:0:2 0/1:21:1:1,0:20,0:0.0476:1,0:18:0:34:0:1:0:25:2:0.0476:0:1 -14 19488825 . G A 95 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06138;SOR=0;LSEQ=GAAAGGTGAAAAATAAAAAA;RSEQ=AGCACACTTTACCTGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:9:9,0:120,0:0.0698:1,0:22.3:1:30.2:1:1:0:24.2:18:0.0709:0:2 0/0:52:0:0,0:52,0:0:1,0:17.7:1:31.8:1:1:0:36.1:25:1:0:0.3 -14 19488836 . A G 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67899;SOR=1.71467;LSEQ=AATAAAAAAGAGCACACTTT;RSEQ=CCTGTCCTTAGGAGTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:4:4,0:149,0:0.0261:1,0:28.5:1:33.5:1:1:0:24.8:8:0.0265:0:1.5 0/1:68:3:3,0:65,0:0.0441:1,0:12.7:1:31.7:1:1:0:25:6:0.0448:0:1 -14 19488869 . G C 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.64064;SOR=0.8899;LSEQ=AGTCAAAAAACTTGCTGATG;RSEQ=GTCTTCTTCAATTTGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:71:71,0:193,0:0.2689:1,1:21.6:1:32.6:1:1:0:33.3:142:0.2741:0:1.2 0/1:146:36:36,0:110,0:0.2466:1,1:23.3:1:31.9:1:1:0:36.1:35:0.2414:0:1 -14 19488974 . C G 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.5137;LSEQ=TGAAGTCCCACTTTCTCAAG;RSEQ=TTACACACCATTAACGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1289:173:111,62:620,496:0.1342:2,2:32.9:1:31.5:1:0.03905:1.43:26.3:172:0.1349:0:1.1 0/1:773:57:36,21:365,350:0.0737:2,2:31.7:1:30.9:1:0.09778:1.64:27.5:56:0.0731:0:1 -14 19489164 . CC AT 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11579;SOR=Inf;LSEQ=CCCCAAGGGCACAAAGGAAG;RSEQ=AGTCATGTTGATCCATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:0,157:0:1,0:22.2:1:31.3:1:1:0:25.4:51.333:0.9935:0:0.6 0/1:82:2:0,2:0,80:0.0244:1,0:5:1:30.1:1:1:0:24.5:4:0.0256:0.0122:0.5 -14 19489165 . C T 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22828;SOR=0.62458;LSEQ=CCCAAGGGCACAAAGGAAGC;RSEQ=AGTCATGTTGATCCATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:35:0,35:0,120:0.2258:1,1:8.7:1:29.4:1:1:0:25.8:70:0.2303:0:1 0/1:78:12:0,12:0,65:0.1538:1,0:9.2:1:29.2:1:1:0:24.7:24:0.1558:0:1.3 -14 19489178 . C G 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58903;SOR=0.78946;LSEQ=AGGAAGCCAGTCATGTTGAT;RSEQ=CATGCCTGTAGGGAGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:37:0,37:0,70:0.3458:1,1:28.4:1:32.1:1:1:0:24.2:74:0.3524:0:1.3 0/1:51:15:0,15:0,36:0.2941:1,1:22.7:1:30.5:1:1:0:24.5:6.5:0.2766:0:1.2 -14 19489184 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55097;SOR=0;LSEQ=CCAGTCATGTTGATCCATGC;RSEQ=TGTAGGGAGTCTGTGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:3:0,3:0,95:0.0306:1,0:27.3:1:30:1:1:0:25:6:0.0313:0:1 0/0:48:0:0,0:0,48:0:1,0:20.1:1:32.3:1:1:0:24.8:47:1:0:0.6 -14 19489240 . T C 90 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.59816;LSEQ=TCCTCCACTCACATGGGACA;RSEQ=TCGCCTCTTAACAATGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:0,29:0.1944:1,0:9.4:1:32.3:1:1:0:24:14:0.2:0:2 0/1:8:1:0,1:0,7:0.125:0,0:3:0:31:0:1:0:24:2:0.1429:0:2 -14 19489254 . A G 104 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62208;SOR=1.74124;LSEQ=GGGACATTCGCCTCTTAACA;RSEQ=TGGTCTTGTGAAGCTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:0,9:0,16:0.36:1,0:20.4:1:33.1:1:1:0:24.9:18:0.36:0:1.2 1/0:4:2:0,2:0,2:0.5:0,0:23:1:25:1:1:0:25.5:1:0.3333:0:1 -14 19489268 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAACAATGGTCTTGTGAAG;RSEQ=TTTCAACAGCCTAAACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:0,18:0.1:1,0:23:1:32.5:1:1:0:26:4:0.1111:0:2 0/0:3:0:0,0:0,3:0:0,0:6.3:1:30.3:1:1:0:25:6:1:0:0.7 -14 19489669 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGTTGGAGAGGCGGGGGG;RSEQ=AGAGAGACAAGAAAGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:27.5:1:29:1:1:0:33:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 19492018 . C CGT 139 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=34;MSI=18.000;MSILEN=2;SSF=0.00013;SOR=0.057;LSEQ=CCCAACAATGCAATAAACTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:28:2,26:11,32:0.3373:2,2:35:1:29.1:1:0.06325:4.38835:24:56:0.359:0:0.5 0/1:36:1:0,1:6,19:0.0278:2,0:48:0:27.5:0:1:0:21:2:0.0323:0:0 -14 19889273 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGACCTCAAAGCCCTCTGTG;RSEQ=TTCTCCATCGATACCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:10:1:30.5:1:1:0:47:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 19889793 . C G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGCAGGCCTGCCGCTACCCC;RSEQ=ACCCGGGCCGCGCCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:44:0:33:0:1:0:26:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:28.5:1:1:0:47:4:1:0:1 -14 19890157 . GGCC G 89 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCAGCCGGGCAGCAGC;RSEQ=GCCAAGCATGGCAAGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:3,4:6,8:0.3333:2,2:30.7:1:31.9:1:1:1:54.3:14:0.35:0:0.4 0/0:1:0:0,0:1,0:0:0,0:13:0:32:0:1:0:60:2:1:0:1 -14 19890214 . T C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCACCACGTCCCGGGATGG;RSEQ=GGGCGTCGGGTGGGAGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:29:1:32.3:1:1:0:48.3:6:0.75:0:1.3 1/1:2:2:1,1:0,0:1:0,2:41:1:31.5:1:1:0:60:4:1:0:1 -14 20084203 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAAGCTTCACAAGACCA;RSEQ=TGTTAAGAGGCGAATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:2,0:32,1:0.0571:1,0:27:1:32.5:1:1:0:32:4:0.0571:0:1 0/0:6:0:0,0:6,0:0:0,0:19.8:1:31:1:1:0:30:12:1:0:0 -14 20084250 . T G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08119;SOR=Inf;LSEQ=GTGGAGGAGGACCCATAGAT;RSEQ=TGTCTGACACAGACTCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:69,0:0:1,0:20.7:1:30.1:1:1:0:32:33.5:1:0:0.3 0/1:28:2:2,0:26,0:0.0714:1,0:25:1:33.5:1:1:0:40:4:0.0714:0:1 -14 20084306 . C T 65 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04496;SOR=8.16099;LSEQ=ATGACTGGCTTCCTTTGTGC;RSEQ=CTTGGGGGAGTGTGCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:1,0:183,0:0.0054:1,0:35:0:29:0:1:0:27:2:0.0056:0:1 0/1:93:4:4,0:89,0:0.043:1,0:17.3:1:32.5:1:1:0:33.5:8:0.0435:0:1 -14 20084444 . G C 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00026;SOR=1.40895;LSEQ=AACGCAGATACACCTGTCAG;RSEQ=AAATATATGGATCAGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1235:481:280,201:320,433:0.3895:2,2:26.3:1:32.1:1:0:1.88:38.2:59.125:0.3899:0:1.1 0/1:752:356:202,154:167,229:0.4734:2,2:25.1:1:31.7:1:8e-05:1.80:40.2:177:0.4739:0:1.1 -14 20084587 . C T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.10822;LSEQ=ATTTAACAAATTGAAGAAGA;RSEQ=CCATCAGCAAGTTTTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:7:0,7:0,194:0.0348:1,0:19.3:1:29.9:1:1:0:33.4:14:0.035:0:1.4 0/1:130:5:0,5:0,125:0.0385:1,0:34.8:1:30.4:1:1:0:37:10:0.0388:0:1.8 -14 20084621 . T C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43011;SOR=1.33424;LSEQ=TTTTGACTCCTAAGGACAGG;RSEQ=AAAGTGTGCTCTTTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:39:0,39:0,83:0.3197:1,1:26.4:1:32.8:1:1:0:31.1:78:0.3197:0:1.1 0/1:70:27:0,27:0,43:0.3857:1,1:21.2:1:33.1:1:1:0:33.1:54:0.3913:0:1.3 -14 20084718 . A G 119 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53668;SOR=0;LSEQ=TCAGATTATTTAAATTAGGT;RSEQ=CTCACAGTTTTTAAAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:3,9:8,14:0.3529:2,2:20.8:1:33.2:1:0.70493:1.68798:38.8:24:0.3529:0:1 0/0:3:0:0,0:0,3:0:0,0:24:1:32:0:1:0:40:6:1:0:0 -14 20084805 . G C 104 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55575;SOR=0;LSEQ=GCTTCTAGGAACTCTGATGT;RSEQ=TATGTGTGCCTGAGGGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:10:10,0:22,3:0.2857:2,0:20.5:1:31.4:1:0.54163:0:40:20:0.303:0:1.9 0/0:4:0:0,0:4,0:0:0,0:25.8:1:32.5:1:1:0:40:8:1:0:0 -14 20084844 . A C 125 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11544;SOR=0.18924;LSEQ=TACGTGCCTTGTATATGGGT;RSEQ=TGAGTGTCTGTGTATATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:16:16,0:77,1:0.1702:1,1:32.1:1:31.4:1:1:0:39.8:32:0.1798:0:1.6 0/1:27:1:1,0:25,0:0.037:1,0:29:0:31:0:1:0:40:2:0.037:0:1 -14 20085023 . C A 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=1.55018;LSEQ=TTGACTGATACCAATACTCA;RSEQ=TTTGTAGATATAATGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1276:873:457,416:212,191:0.6842:2,2:29.9:1:30.4:1:0.95196:1.01036:56.5:71.75:0.6833:0:1.2 1/0:741:571:308,263:93,77:0.7706:2,2:28.7:1:29.8:1:0.93016:1.03129:56.4:141.75:0.7704:0:1.2 -14 20085114 . G A 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34397;SOR=0.87698;LSEQ=GCATTGAAACAATGATGTTA;RSEQ=ATCTGGTCAGGTAAGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:275:33,242:137,207:0.4443:2,2:21.3:1:30.2:1:0:4.84108:41.2:90.667:0.4437:0:1.4 0/1:347:143:17,126:85,119:0.4121:2,2:21.9:1:29.6:1:0:5.26972:40.6:70.5:0.4135:0:1.3 -14 20085180 . A T 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00342;SOR=0.31705;LSEQ=TTAAGATTTAAGAGACAAGA;RSEQ=AAACCTCTTACACATTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:43:9,34:53,186:0.1525:2,2:26.2:1:29.3:1:1:1.07619:40.5:86:0.153:0:1.4 0/1:130:7:1,6:27,96:0.0538:2,2:18.3:1:28.9:1:1:1.68156:33.4:14:0.0543:0:1.7 -14 20085189 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36581;SOR=0.57602;LSEQ=AAGAGACAAGAAAAACCTCT;RSEQ=ACACATTGATATTGATAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:20:0,20:58,179:0.0778:2,1:19.1:1:31.8:1:0.00946:0:37.7:40:0.0784:0:2.6 0/1:108:5:0,5:22,81:0.0463:2,0:42.2:1:32.8:1:0.58089:0:40:10:0.0467:0:1.8 -14 20085200 . A G 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32771;SOR=0;LSEQ=AAAACCTCTTACACATTGAT;RSEQ=TTGATAGTAATTGATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:5:1,4:45,160:0.0238:2,2:37.2:1:29:1:1:1.12439:43:4:0.0193:0:1.4 0/0:92:0:0,0:18,74:0:2,0:23.6:1:29.9:1:1:0:43.9:91:1:0:0.4 -14 20085204 . A G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.80292;SOR=0.76364;LSEQ=CCTCTTACACATTGATATTG;RSEQ=TAGTAATTGATAAAATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:16:1,15:43,145:0.0784:2,1:18.2:1:30.6:1:0.20231:4.42687:37.6:15:0.0743:0:2.8 0/1:82:5:1,4:15,62:0.061:2,2:27.4:1:32.8:1:1:1.03:37:10:0.0633:0:2 -14 20085213 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGATATTGATAGTAATT;RSEQ=ATAAAATAATTTGCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:44,134:0.0111:2,2:11:1:28.5:1:0.43855:3.02:48.5:4:0.0112:0:1 0/0:71:0:0,0:15,56:0:2,0:25.4:1:31.3:1:1:0:41.8:34.5:1:0:0.3 -14 20085241 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0814;SOR=Inf;LSEQ=AATTTGCCATTCTTTACTGC;RSEQ=CACAAACTAGGCTGTGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:54,75:0:2,0:24.1:1:30.3:1:1:0:39.7:42:1:0:0.4 0/1:52:2:1,1:17,33:0.0385:2,2:27.5:1:28.5:1:1:1.91:25:4:0.0385:0:1 -14 20085253 . CTG GT 103 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29153;SOR=0.26055;LSEQ=TTTACTGCACACAAACTAGG;RSEQ=TGACAACAAGGTAACCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:10:2,8:64,50:0.0806:2,2:23.6:1:31.2:1:0.04427:5.0582:36:20:0.0806:0.0081:3.2 0/1:45:1:1,0:18,26:0.0222:2,0:42:0:31:0:0.42222:0:25:2:0.0222:0:2 -14 20085262 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06508;SOR=Inf;LSEQ=CACAAACTAGGCTGTGACAA;RSEQ=AAGGTAACCAGAAATTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:73,54:0:2,0:22.4:1:32.4:1:1:0:39.5:126:1:0:0.4 0/1:44:2:1,1:18,23:0.0455:2,2:21:1:29:1:1:1.27:47:4:0.0476:0:1 -14 20085303 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57729;SOR=0;LSEQ=ATGCTCTCCTATAAATAAAT;RSEQ=TCTTACTGTTTTCAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:4:1,3:120,31:0.0258:2,2:27.8:1:30.8:1:0.03331:11.37114:33.8:8:0.0268:0:3.5 0/0:59:0:0,0:48,11:0:2,0:21.6:1:32.1:1:1:0:40.3:58:1:0:0.4 -14 20085324 . C T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55444;SOR=0;LSEQ=TCTTACTGTTTTCAAACTTA;RSEQ=GATTAGTTCGTTTTATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:2,1:172,26:0.0149:2,2:29.7:1:24.3:1:0.35279:3.27906:30.3:2:0.0102:0:3.7 0/0:109:0:0,0:101,8:0:2,0:21:1:31.6:1:1:0:44.9:218:1:0:0.6 -14 20085331 . T C 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55511;SOR=0;LSEQ=GTTTTCAAACTTACGATTAG;RSEQ=TCGTTTTATTTGATGGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:3:2,1:200,26:0.0131:2,2:13:1:31:1:0.31486:3.8108:29.3:6:0.0133:0:4.7 0/0:126:0:0,0:117,9:0:2,0:22.4:1:30:1:1:0:45.2:62:1:0:0.6 -14 20085357 . C T 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21324;SOR=1.25184;LSEQ=TTATTTGATGGTTAAAGTAT;RSEQ=TTGAATGCCTTATCTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:151:130,21:158,33:0.4415:2,2:24.7:1:30.1:1:0.45626:1.29:31.3:29.2:0.4358:0:1.5 0/1:201:100:86,14:85,16:0.4975:2,2:27.7:1:29.7:1:0.84348:1.16:31.2:49:0.4949:0:1.2 -14 20085407 . A G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2121;SOR=0.58953;LSEQ=ATAATTTTTTTATTGTCTCT;RSEQ=TGTCTGTATAGGTACGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:26:12,14:427,179:0.0411:2,2:36.9:1:32.2:1:0.0148:2.77796:30.1:52:0.0419:0:3.5 0/1:365:9:4,5:254,102:0.0247:2,2:39.7:1:31:1:0.13022:3.10183:36.1:18:0.025:0:3.4 -14 20085422 . C T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.1617;SOR=0.56776;LSEQ=TCTCTATGTCTGTATAGGTA;RSEQ=GTTTGTGTGCTTGGGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:27:12,15:455,225:0.0381:2,2:29.1:1:30.3:1:0.02153:2.52418:30.6:54:0.0384:0:3.4 0/1:409:9:4,5:266,134:0.022:2,2:32:1:29.8:1:0.17526:2.47537:36.1:18:0.0226:0:3.4 -14 20085423 . G A 217 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01009;LSEQ=CTCTATGTCTGTATAGGTAC;RSEQ=TTTGTGTGCTTGGGAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:724:139:94,45:378,207:0.192:2,2:25.2:1:30.6:1:0.55273:1.14:31.2:278:0.1928:0:1.2 0/0:419:1:1,0:276,142:0.0024:2,0:1:0:24:0:1:0:60:2:0.0024:0:1 -14 20085426 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.21295;SOR=0.58397;LSEQ=TATGTCTGTATAGGTACGTT;RSEQ=GTGTGCTTGGGAATATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:741:26:12,14:457,258:0.0351:2,2:27.1:1:29.8:1:0.09536:2.06444:30.1:25:0.0339:0:3.5 0/1:433:9:4,5:273,151:0.0208:2,2:28.9:1:29.9:1:0.29361:2.25543:36.1:18:0.021:0:3.4 -14 20085538 . T G 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.35542;LSEQ=ATTTTGCCGAGAGATGAAAT;RSEQ=TAGGTGAGTTCTCAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:97:16,81:101,366:0.172:2,2:22.5:1:32.7:1:0.27481:1.39628:39.5:194:0.1741:0:1.1 0/1:364:25:5,20:86,252:0.0687:2,2:18.8:1:31.2:1:0.6394:1.36395:41.6:50:0.0698:0:1 -14 20085849 . G C 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=ATCCGCCCGCCTCGGCCTCC;RSEQ=AAAGTGCTGGGTAAATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:2,0:0.7143:0,2:27.4:1:30.2:1:1:0:51.4:10:0.7143:0:1.2 0/0:2:0:0,0:1,1:0:2,0:11:1:27.5:1:1:0:60:4:1:0:0 -14 20085937 . A G 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.04858;SOR=Inf;LSEQ=AGGAAGGAAGACATAAAAAG;RSEQ=GAGCAGTTTACATGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:13,17:0:2,0:31.6:1:29.3:1:1:0:48.2:14:1:0:0.3 0/1:9:2:1,1:0,7:0.2222:0,2:23:1:29:1:0.22222:0:53.5:4:0.2222:0:1 -14 20086119 . C T 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04912;SOR=Inf;LSEQ=CAGTATCCACGTTGCTTGTT;RSEQ=CTTCTGGCTTTTACATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:70,9:0:2,0:24.9:1:31.8:1:1:0:27.7:158:1:0:0.1 0/1:23:2:1,1:17,4:0.087:2,2:37.5:1:30.5:1:0.39526:3.91152:25:4:0.087:0:1 -14 20086143 . A T 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32454;SOR=0;LSEQ=CTGGCTTTTACATCTATGAT;RSEQ=GCAGTATCTCTTTTATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:5:4,1:88,9:0.049:2,2:30:1:29.8:1:0.40958:2.41542:25:10:0.05:0:2 0/0:37:0:0,0:33,4:0:2,0:20.4:1:28.5:1:1:0:27.3:74:1:0:0.1 -14 20086203 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09627;SOR=Inf;LSEQ=ATCTGCCAAATTATTTGCAC;RSEQ=ATAAGTAATCTTACATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:288,50:0:2,0:21.7:1:31:1:1:0:33.8:66.6:0.997:0:0.9 0/1:153:2:1,1:133,18:0.0131:2,2:11.5:1:27:1:0.23366:7.21793:49:4:0.0134:0:1 -14 20086236 . GT G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=0.33946;LSEQ=ACATGACTGAAGGTGTGTGT;RSEQ=GGGGGGGTATGACTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:766:141:94,47:247,102:0.1841:2,2:23.8:1:31.7:1:0.38666:1.21028:40.3:282:0.2895:0.0339:1.9 0/1:408:29:20,9:173,94:0.0711:2,2:27.9:1:31.7:1:0.83767:1.21:40.7:58:0.0727:0.0049:2 -14 20086239 . G T 65 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.02153;SOR=9.44548;LSEQ=TGACTGAAGGTGTGTGTGTG;RSEQ=GGGGGTATGACTTCAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:790:1:0,1:549,240:0.0013:2,0:1:0:26:0:0.30506:0:60:2:0.0013:0:3 0/1:422:5:2,3:276,141:0.0118:2,2:26:1:28.2:1:0.34311:2.92805:49.6:10:0.012:0:1.2 -14 20086240 . G T 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.41693;SOR=1.12069;LSEQ=GACTGAAGGTGTGTGTGTGG;RSEQ=GGGGTATGACTTCAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:204:135,69:427,175:0.2525:2,2:24.4:1:28.9:1:0.21727:1.24673:37.3:39.8:0.2506:0:2 0/1:437:120:76,44:209,108:0.2746:2,2:24.2:1:28.2:1:0.653:1.12007:41.8:29:0.2691:0:2 -14 20086244 . G A 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37215;LSEQ=GAAGGTGTGTGTGTGGGGGG;RSEQ=TATGACTTCAGAAAAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:892:156:105,51:498,234:0.1749:2,2:24.1:1:29.9:1:0.85075:1.03363:40.1:38:0.1737:0:2 0/1:479:35:25,10:277,159:0.0731:2,2:27.4:1:28.2:1:0.46406:1.43:39.9:16.5:0.0702:0:2 -14 20086290 . T C 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.51387;LSEQ=GTTTCTCTTTTCTCCACCAT;RSEQ=CTATAGGAATAAGATGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1191:210:105,105:510,470:0.1763:2,2:29.4:1:30.9:1:0.59529:1.08503:37.9:51.5:0.1759:0:1.7 0/1:646:64:35,29:302,278:0.0991:2,2:30.2:1:30.4:1:0.7922:1.11:37.8:63:0.0995:0:1.6 -14 20086381 . G GT 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=GATGTAAAATGTCTTACAAG;RSEQ=TAAAAAAAATGACTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:43,309:0:2,0:26.1:1:31.7:1:1:0:24.9:57.667:0.9971:0:0.1 0/1:146:7:0,7:13,126:0.0479:2,0:28.1:1:29.6:1:1:0:25:14:0.0486:0.0068:0.4 -14 20086382 . T TAAAA 142 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=12.000;MSILEN=1;SSF=0.22843;SOR=0.53405;LSEQ=ATGTAAAATGTCTTACAAGG;RSEQ=AAAAAAAATGACTTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:26:0,26:42,266:0.0754:2,1:31.6:1:30.3:1:0.05748:0:24.9:52:0.0762:0.0029:0.2 0/1:144:6:0,6:13,121:0.0417:2,0:38:1:30.8:1:1:0:25:12:0.042:0:0.2 -14 20086572 . G A 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24451;SOR=0;LSEQ=GACTTTCAGGAAAAATAAAT;RSEQ=TGCGAGAGCGGTATGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:0,7:0.4167:0,0:32.4:1:29.8:1:1:0:24.8:10:0.4167:0:1 0/0:4:0:0,0:0,4:0:0,0:15.5:1:32:1:1:0:41:8:1:0:0.5 -14 20087645 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.10436;SOR=Inf;LSEQ=AGCCTCAGAGGTACTGTGTT;RSEQ=TTTTTCTTTTAGGCATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:0:0,0:279,116:0:2,0:23.4:1:31.1:1:1:0:35:97.75:1:0:0.1 0/1:189:2:1,1:126,61:0.0106:2,2:16:1:26:1:0.54965:2.05702:47:4:0.0107:0:1 -14 20087787 . G C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10392;SOR=0.28079;LSEQ=GGTAAGAAATACTATGTTTG;RSEQ=TGTCTCCTCTCAACAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:18:0,18:0,103:0.1488:1,1:19.6:1:32.6:1:1:0:27.2:36:0.1488:0:1 0/1:43:2:0,2:0,41:0.0465:1,0:24:1:33.5:1:1:0:25:4:0.0476:0:1 -14 20088816 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAAGAAAGTAAGAAAATT;RSEQ=TGTCGAACCTCCCCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:31.5:1:1:0:51:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 20347304 . A G 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28;SOR=0;LSEQ=GTAGTTGGATTGATAGTAAA;RSEQ=TTCTGTGGCTGATAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:18,0:0,0:1:0,1:25.4:1:32.3:1:1:0:60:36:1:0:1 1/1:7:6:6,0:1,0:0.8571:0,0:11.2:1:32.5:1:1:0:60:12:0.8571:0:1.2 -14 20347432 . T G 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09705;SOR=1.68841;LSEQ=TGGTACCTCTGCATGTTATA;RSEQ=AAACACTTAAAAATCTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:75:64,11:92,8:0.4286:2,2:22.1:1:30.9:1:0.21948:1.96874:60:17.75:0.4226:0:1.2 1/0:59:33:26,7:22,4:0.5593:2,2:20.1:1:32.1:1:0.73968:1.4711:60:66:0.5593:0:1.1 -14 20347539 . T C 196 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=120.41479;LSEQ=TTCACCAAGGATAACTGCAG;RSEQ=GACATGGCCATGGACTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:687:2:1,1:357,328:0.0029:2,2:27.5:1:29.5:1:1:1.08827:60:4:0.003:0:2 0/1:325:85:49,36:124,116:0.2615:2,2:25.6:1:30.6:1:0.37702:1.27:60:84:0.2609:0:1.8 -14 20347564 . A C 186 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=79.05085;LSEQ=TGGCCATGGACTCGTTAAGC;RSEQ=ATAGTAAGGATGGTGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:668:3:1,2:295,369:0.0045:2,2:25.3:1:26:1:1:1.59784:60:2:0.003:0:2 0/1:311:82:37,45:96,133:0.2637:2,2:24.4:1:29.4:1:0.69655:1.14:60:19.5:0.2566:0:1.9 -14 20347644 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09513;SOR=Inf;LSEQ=GAGAATACAAGATAAGCAGG;RSEQ=AAGTATAATTTTAAGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:58,192:0:2,0:23.3:1:31.7:1:1:0:60:40.667:1:0:0 0/1:112:2:1,1:23,87:0.0179:2,2:6:0:31.5:1:0.38417:3.72:60:4:0.0183:0:2 -14 20893115 . T A 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TAGGCACAGGAGACAAGTGA;RSEQ=ACCTAGAGTCCCACACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:28:18,10:239,117:0.0729:2,2:23.1:1:29.8:1:0.8352:1.13447:60:56:0.0737:0:1.2 0/0:213:0:0,0:143,70:0:2,0:25.1:1:28.6:1:1:0:60:41.6:1:0:0.1 -14 20893219 . T G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=8.34454;LSEQ=ATAAGAGAGATATCAGAAAT;RSEQ=TCACCCTCACCAGCAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:584:91:32,59:214,279:0.1558:2,2:25.9:1:32.1:1:0.16572:1.41338:60:182:0.1574:0:1.1 1/0:402:244:109,135:79,79:0.607:2,2:26.2:1:31.4:1:0.30767:1.23786:60:488:0.6085:0:1.1 -14 20893275 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17724;SOR=Inf;LSEQ=GTTGGGGGAGCTATTAGAGA;RSEQ=CATCTAGAACACCTTGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:61,212:0:2,0:22.7:1:31.8:1:1:0:60:44.5:1:0:0.3 0/1:199:2:1,1:66,131:0.0101:2,2:22:1:25.5:1:1:1.98:60:4:0.0102:0:1 -14 20893369 . C T 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07669;SOR=2.93554;LSEQ=GTCTTGCCAGGTCACCACCA;RSEQ=GGCTGCCCAATCTGTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:44:0,44:1,17:0.7097:1,1:23.7:1:29.9:1:0.29032:0:60:43:0.7049:0:1 1/1:33:29:0,29:1,3:0.8788:2,1:28:1:30.2:1:0.12121:0:60:28:0.875:0:1.1 -14 20969716 . C T 75 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTCCATGGTACATGTAC;RSEQ=ATGGTTTGCTTAATGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,1:0.7143:2,0:18.8:1:32.6:1:0.28571:0:60:10:0.8333:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 20969733 . A G 81 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCATGGTTTGCTTAATGC;RSEQ=TCACCCATTGAAGAACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:35.2:1:31.5:1:1:0:60:12:1:0:1.8 1/1:2:2:2,0:0,0:1:0,0:5.5:1:30.5:1:1:0:60:4:1:0:1 -14 21336860 . A AT 76 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CATGCCTGGCTTATTTTTGT;RSEQ=TTTTTAGTACAGACGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:25.8:1:32.8:1:1:0:58.6:10:1:0:0 0/0:1:0:0,0:1,0:0:0,0:2:0:25:0:1:0:60:2:1:0:0 -14 21337266 . T G 294 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00382;LSEQ=GAGCTGGTTTTAGAAACAGG;RSEQ=GGAGATCACCGAGTCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:744:742:341,401:0,0:0.9973:0,2:27.2:1:30.9:1:1:0:60:81.444:0.9973:0:1.1 1/0:480:281:137,144:97,101:0.5854:2,2:26.7:1:30.3:1:1:1.00945:60:139.5:0.5837:0:1.1 -14 21337344 . A G 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55898;SOR=3.37126;LSEQ=AATGTCTAAAATACAGCAAA;RSEQ=GAGAAGGCATTCGAATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:1:1,0:86,230:0.0032:2,0:21:0:14:0:0.27445:0:60:0:0:0:4 0/1:189:2:1,1:54,133:0.0106:2,2:23:1:32.5:1:0.49842:2.45:60:4:0.0107:0:1.5 -14 21337644 . G A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCGTGTGCCACTACGCCC;RSEQ=GCTAATTTTTGTATTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:1:31:1:1:0:49.5:4:1:0:3 1/1:1:1:0,1:0,0:1:0,0:15:0:33:0:1:0:60:2:1:0:2 -14 22394783 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTCAACATTCCTATCCA;RSEQ=GAAGTGATCATTATTTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:25.7:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 22395250 . A T 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.47212;SOR=1.15639;LSEQ=TTTCGTATGTTTTTATTCAG;RSEQ=AAAATGATATTTTTTCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:330:194:92,102:61,74:0.5879:2,2:25.1:1:28.5:1:0.73646:1.09:60:193:0.5902:0:1.1 1/0:212:132:59,73:39,41:0.6226:2,2:25.4:1:28.8:1:0.57338:1.17602:60:131:0.6238:0:1.1 -14 22395264 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.15298;SOR=Inf;LSEQ=ATTCAGAAAAATGATATTTT;RSEQ=TCTAATTGTAAAGGATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:124,171:0:2,0:26.1:1:30.1:1:1:0:60:294:1:0:0.7 0/1:190:2:1,1:76,112:0.0105:2,2:9:1:27.5:1:1:1.47:60:4:0.0106:0:1.5 -14 22395357 . G A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32811;SOR=1.50952;LSEQ=GTATATAACTGTTCCCACAC;RSEQ=TTCATCTATATATATGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:87:52:4,48:2,33:0.5977:2,2:25.6:1:31:1:1:1.37:60:51:0.593:0:2 1/0:39:27:5,22:2,10:0.6923:2,2:22.2:1:29.7:1:1:1.13:60:26:0.6842:0:2 -14 22395359 . T C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41934;SOR=1.48328;LSEQ=ATATAACTGTTCCCACACGT;RSEQ=CATCTATATATATGCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:49:4,45:2,33:0.5833:2,2:26.3:1:31.5:1:1:1.46:60:98:0.5833:0:2 1/0:37:25:4,21:2,10:0.6757:2,2:22.9:1:30.9:1:1:1.04861:60:50:0.6757:0:2 -14 22395405 . A T 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33085;SOR=0;LSEQ=AAATTATCTTTTATATATTC;RSEQ=TTTTTACTGATATTCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:7:0,7:0,36:0.1628:1,0:18:1:31:1:1:0:60:14:0.1628:0:1.6 0/0:9:0:0,0:0,9:0:0,0:26.9:1:31.4:1:1:0:60:18:1:0:1.6 -14 22395437 . C T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCCAGTACAAACAAATG;RSEQ=TATTTAAAAATCATCTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:0.2083:1,0:28.6:1:30.8:1:1:0:60:10:0.2083:0:1.8 0/0:4:0:0,0:0,4:0:0,0:17:1:32:1:1:0:60:8:1:0:1 -14 22395549 . C A 27 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AGTTTATTTTATGAACCTAG;RSEQ=CTAACCTTAACCCAACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:33:1:27.5:1:1:0:60:4:0.6667:0:2 0/0:2:0:0,0:1,1:0:2,0:34:1:32:1:1:0:60:4:1:0:0 -14 22395557 . T C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TTATGAACCTAGCCTAACCT;RSEQ=AACCCAACACCTAAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:41:1:30:1:1:0:60:4:0.5:0:2 0/0:2:0:0,0:1,1:0:2,0:26:1:29.5:1:1:0:60:4:1:0:0 -14 22592304 . G A 113 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00068;SOR=0.056;LSEQ=CTGGTGGCAAGTGAGGAGGA;RSEQ=GGTAGCATTCACCTAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:4,10:6,12:0.4375:2,2:17.9:1:29.9:1:1:1.24135:60:28:0.4375:0:1 0/1:25:1:1,0:10,14:0.04:2,0:9:0:32:0:0.44:0:60:2:0.04:0:1 -14 22592311 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21647;SOR=Inf;LSEQ=CAAGTGAGGAGGAGGGTAGC;RSEQ=TTCACCTAGAGCAAAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:6,21:0:2,0:24.1:1:30.3:1:1:0:60:26:1:0:0.4 0/1:24:2:1,1:10,12:0.0833:2,2:18.5:1:32.5:1:1:1.19:60:4:0.0833:0:1 -14 23549896 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.4902;SOR=Inf;LSEQ=TCTTCCTCCTCCTCCTCCTC;RSEQ=TCTTCTTCCTCCTCTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:26.8:1:31.4:1:1:0:60:25:1:0:0.2 0/1:26:2:1,1:12,12:0.0769:2,2:27:0:31.5:1:1:1:60:4:0.0769:0:1 -14 23574095 . GGCA G 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=11.000;MSILEN=3;SSF=1;SOR=0.82409;LSEQ=CAACCCTGAGGACTAGTGGC;RSEQ=GCAGCAGCAGCAGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:3,8:5,4:0.55:2,2:38.3:1:32.5:1:0.36185:3.12593:60:22:0.5789:0:1.1 1/0:8:4:1,3:2,0:0.5:0,2:18.3:1:29.9:1:0.4:0:60:8:0.5:0.125:1.3 -14 23574116 . A G 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=3;SSF=0.19138;SOR=5.16794;LSEQ=GCAGCAGCAGCAGCAGCAGC;RSEQ=GCAGCAGCAGCATCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:3,8:5,5:0.5238:2,2:33.6:1:29.7:1:0.387:2.54034:60:10:0.5:0:1.1 1/1:7:6:2,4:1,0:0.8571:0,2:27.5:1:29.5:1:0.42857:0:60:12:0.8571:0:1.2 -14 23586789 . C T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.30819;SOR=4.4708;LSEQ=TCTAGCTCCTGGGTGAGCTG;RSEQ=TCCACGCGGCTGCGGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:1,0:305,58:0.0027:2,0:42:0:14:0:1:0:60:0:0:0:6 0/1:246:3:1,2:196,47:0.0122:2,2:18.3:1:29.3:1:0.10204:8.23893:60:6:0.0123:0:1 -14 23586796 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39398;SOR=2.26069;LSEQ=CCTGGGTGAGCTGCTCCACG;RSEQ=GGCTGCGGAGGCGCTCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:2:0,2:333,91:0.0047:2,0:1:0:25.5:1:0.04726:0:60:4:0.0048:0:1 0/1:284:3:1,2:210,71:0.0106:2,2:7.7:1:26.7:1:0.16326:5.87016:60:6:0.0106:0:1 -14 23586802 . C T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01809;LSEQ=TGAGCTGCTCCACGCGGCTG;RSEQ=GGAGGCGCTCGTTCTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:6:2,4:364,113:0.0124:2,2:10:1:24.5:1:0.03274:6.41097:60:5:0.0105:0:1.8 0/1:317:4:1,3:225,88:0.0126:2,2:12.5:1:23.8:1:0.07298:7.61416:60:3:0.0096:0:1.3 -14 23586970 . C T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6236;SOR=1.76183;LSEQ=TCTTGCCCTTGTGTAAGGGG;RSEQ=CAGCCGGGGAGGGCGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:2:0,2:25,252:0.0072:2,0:24:1:19.5:1:1:0:60:1:0.0037:0:3.5 0/1:159:2:0,2:11,146:0.0126:2,0:16:1:24.5:1:1:0:60:4:0.0128:0:1 -14 23586985 . G A 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.65714;LSEQ=AGGGGCCAGCCGGGGAGGGC;RSEQ=CCTTCAGGAGGGGACTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:0,3:1,188:0.0156:1,0:18.7:1:23:1:1:0:60:2:0.0106:0:1.3 0/1:97:1:0,1:1,95:0.0103:1,0:22:0:32:0:1:0:60:2:0.0104:0:2 -14 23587046 . A C 131 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01173;SOR=0.10491;LSEQ=AGGGGCCTGGAGGGGAAGGC;RSEQ=CGGAGAGACGGAGAGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:19:0,19:1,58:0.2436:1,1:20.2:1:31:1:1:0:60:18:0.2368:0:1.2 0/1:31:1:0,1:3,27:0.0323:2,0:8:0:32:0:1:0:60:2:0.0323:0:1 -14 23587231 . G A 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGATGCACAGGGTCCTCT;RSEQ=CTTGAGACCAAAACTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:1,7:0.2:2,0:11.5:1:30:1:1:0:60:4:0.2:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 23652004 . G A 99 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2368;SOR=0.20049;LSEQ=CCACAGGCACTGACCAATCC;RSEQ=ATCTCTTTCTTCAGGGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:9,0:20,1:0.3:1,0:32.2:1:31.4:1:1:0:60:18:0.3103:0:1 0/1:13:1:1,0:11,1:0.0769:2,0:16:0:32:0:1:0:60:2:0.0833:0:1 -14 23652305 . A C 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.06062;LSEQ=TATTCCTACTCCGCATTCAC;RSEQ=CTTTCTGGTCACTCGCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1331:520:255,265:408,403:0.3907:2,2:26.9:1:31:1:0.6536:1.05204:60:36.143:0.3941:0:1.2 0/1:1177:44:21,23:576,557:0.0374:2,2:20.5:1:27.6:1:0.7593:1.13248:59.2:5.286:0.0329:0:2 -14 23652708 . T A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.7955;LSEQ=AGATCTGGTTTCCACCTGCT;RSEQ=TGGGTTTCTTTTCCCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:0,19:1,4:0.7917:2,1:29:1:31.5:1:0.20833:0:60:38:0.7917:0:1.1 1/0:8:6:0,6:0,2:0.75:0,0:18.7:1:29:1:1:0:60:12:0.75:0:1 -14 23764410 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51083;SOR=0;LSEQ=ACTGGAGGGCGAAGAAACCT;RSEQ=GTCATTACAGGCCTGGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:62,50:0.0175:2,2:29.5:1:30:0:1:1.23764:60:4:0.0187:0:1.5 0/0:82:0:0,0:42,40:0:2,0:27.7:1:29:1:1:0:60:10.714:1:0:0.5 -14 23764564 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGTGCAGCTTAGTGGT;RSEQ=CTTTGCAGGAGGCAAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:125,45:0.0116:2,2:25.5:1:28:1:0.4645:2.75839:60:4:0.012:0:1 0/0:81:0:0,0:57,24:0:2,0:22.3:1:31.2:1:1:0:60:80:1:0:0.1 -14 23764577 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98505;LSEQ=TAGTGGTGCTTTGCAGGAGG;RSEQ=AAGCAAAGCCTATCTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:145,52:0.0101:2,2:29:1:28:1:0.46272:2.77154:60:4:0.0103:0:1 0/0:101:1:0,1:73,27:0.0099:2,0:19:0:30:0:0.27723:0:60:2:0.0102:0:1 -14 23764654 . CA C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.064;SOR=Inf;LSEQ=CAAACGTGTAACACCTATGT;RSEQ=AAAGACATCCAGCTAGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:193,194:0:2,0:27.1:1:29.8:1:1:0:60:63.5:1:0:0.1 0/1:259:3:2,1:127,129:0.0116:2,2:10.7:1:25.5:1:0.62209:2.03:60:6:0.0118:0.0077:1 -14 23764732 . TA T 77 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.5477;SOR=1.58135;LSEQ=GATGGGGGAAACTTCATTCT;RSEQ=AAAAAAAAAAGTCTCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:6:0,6:34,124:0.0361:2,0:27.8:1:30.5:1:0.34628:0:60:12:0.0364:0:0.7 0/1:107:6:1,5:28,71:0.0561:2,2:23.8:1:30:1:1:1.96093:60:12:0.0571:0:0 -14 23764745 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15964;SOR=Inf;LSEQ=TCATTCTTAAAAAAAAAAAG;RSEQ=CTCTGCTTCCTGTCATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:19,117:0:2,0:23.6:1:29.5:1:1:0:60:135:1:0:0.4 0/1:91:2:1,1:23,66:0.022:2,2:39.5:1:31:1:0.46007:2.83:60:4:0.0233:0:1 -14 23764770 . C G 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=GCTTCCTGTCATTGGTAGTT;RSEQ=TGAATGTTAGATATTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:20:2,18:3,69:0.2174:1,2:31.3:1:33:1:0.29708:2.52:59.8:40:0.2198:0:1.2 0/0:53:0:0,0:6,47:0:2,0:24.6:1:31.4:1:1:0:59.8:16.667:1:0:0.4 -14 23764788 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGAATGTTAGATATTTT;RSEQ=TCCCCATGGGGTCAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:5,75:0.0244:2,2:18:1:32:1:0.14182:13.78:60:4:0.0253:0:1.5 0/0:33:0:0,0:4,29:0:2,0:24.7:1:30.8:1:1:0:60:66:1:0:0.3 -14 23851325 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01171;SOR=Inf;LSEQ=CTGGCAAGAGGGAGAAGTGT;RSEQ=TGGGGACAAATCCCTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:35,33:0:2,0:29.1:1:31.9:1:1:0:60:67:1:0:0.2 0/1:21:3:1,2:8,10:0.1429:2,2:25.3:1:30:1:1:1.56568:60:6:0.1429:0:1.7 -14 23851400 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCAGGGCCCCAGGGATC;RSEQ=TGTGGTCCCACGTTAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:0.125:1,0:7.5:1:32:1:1:0:60:4:0.125:0:1 0/0:3:0:0,0:0,3:0:0,0:29.3:1:32:1:1:0:60:6:1:0:0 -14 23992742 . T G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.39457;SOR=0.67093;LSEQ=GGCTGCTAAGAGGCCCTCAC;RSEQ=GCTGCCCCCAGTGCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:23:21,2:23,1:0.4894:1,2:24.5:1:29.4:1:0.60851:2.15523:60:46:0.4894:0:1.2 0/1:41:16:14,2:22,3:0.3902:2,2:20.8:1:29.7:1:1:1.0464:60:32:0.3902:0:1 -14 23992764 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21325;SOR=Inf;LSEQ=CTGCCCCCAGTGCTCCCAGC;RSEQ=GCTGTCCCCTGTAGTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:55,26:0:2,0:21.6:1:30.1:1:1:0:60:80:1:0:0.4 0/1:70:2:1,1:46,22:0.0286:2,2:19:1:28:1:1:2.06711:60:4:0.029:0:1 -14 23992778 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20171;SOR=Inf;LSEQ=CCCAGCGGCTGTCCCCTGTA;RSEQ=TTTGGCCTTCTTTTCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:69,42:0:2,0:23:1:31.6:1:1:0:60:36:1:0:0.3 0/1:91:2:1,1:52,37:0.022:2,2:21:1:28.5:1:1:1.40004:60:4:0.0222:0:1 -14 24002092 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53051;SOR=0;LSEQ=CAGCCACCTCCTTCCATTCA;RSEQ=CTTCCGGGAGGCTCCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:19,109:0.0154:2,2:10.5:1:26.5:1:0.28503:5.62:60:4:0.0155:0:1 0/0:77:0:0,0:13,63:0:2,0:21.9:1:32.2:1:1:0:60:152:1:0:0.1 -14 24002880 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11176;SOR=Inf;LSEQ=CCGCGGAGGGTGGGAGTGAT;RSEQ=CCTCTGGTGGACTTCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:215,11:0:1,0:22.4:1:32.1:1:1:0:60:74.333:1:0:0.1 0/1:114:2:1,1:99,13:0.0175:2,2:12:1:31.5:1:0.23149:7.37604:60:4:0.0177:0:1 -14 24002887 . G T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTGGGAGTGATGCCTCTG;RSEQ=TGGACTTCCCTGCCCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:223,25:0:2,0:22.6:1:30.8:1:1:0:60:30:1:0:0.1 0/1:130:19:13,6:95,16:0.1462:2,2:24.8:1:29.2:1:0.09299:2.71415:60:38:0.1496:0:1.2 -14 24002902 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11425;SOR=Inf;LSEQ=CTCTGGTGGACTTCCCTGCC;RSEQ=ACCAGGGCCCGCCTGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:243,87:0:2,0:22.8:1:30.5:1:1:0:60:32:1:0:0.1 0/1:169:2:1,1:118,49:0.0118:2,2:15:1:27.5:1:0.50542:2.39406:60:4:0.012:0:1.5 -14 24003268 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.06971;SOR=Inf;LSEQ=AGGGGCTGGGGTGTAGTCAT;RSEQ=AGCTAGGCGATAGGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:3,174:0:1,0:23.7:1:32.1:1:1:0:60:28.5:1:0:0.1 0/1:64:2:1,1:2,60:0.0313:1,2:35.5:1:29.5:1:0.09226:24.70:60:4:0.0313:0:1 -14 24153786 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1455;SOR=Inf;LSEQ=GGTAGAGAAGATATAATTTG;RSEQ=TGACGTGGGATGTGAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:0:2,0:24.6:1:32.4:1:1:0:60:34:1:0:0.2 0/1:11:2:1,1:5,4:0.1818:2,2:36.5:1:27.5:1:1:1.22474:60:4:0.2:0:1.5 -14 24324170 . C T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTATTAATTTACAGTGACC;RSEQ=ATGATCCTGTTTTGATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:21.3:1:30.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 24324349 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52193;SOR=0;LSEQ=TAGAGATATTAAATGATTAG;RSEQ=CTTATTTGGTAAATTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:24,18:0.0455:2,2:16.5:1:29.5:1:1:1.32452:60:4:0.0465:0:2.5 0/0:27:0:0,0:15,12:0:2,0:19.7:1:31.7:1:1:0:60:54:1:0:0.1 -14 24324391 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GGAACACTGTCAAATGATGA;RSEQ=TGATGCTAGATCTTCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:36,30:0.0294:2,2:29:0:32:1:1:1.19677:60:4:0.0294:0:2.5 0/0:43:0:0,0:20,23:0:2,0:29.4:1:31.4:1:1:0:60:86:1:0:0.1 -14 24851624 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=ATACATCTAGAAAGACCCTG;RSEQ=TTCCAAATAATGTCACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:0.1667:2,2:38.5:1:32.5:1:1:2.16:60:4:0.1667:0:1 0/0:9:0:0,0:4,5:0:2,0:17:1:29:1:1:0:60:18:1:0:0.1 -14 25195504 . C CAA 47 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CATCTTTTGGAGGCTCCCAT;RSEQ=AAAAAAAAAACATAATAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:23.7:1:29.7:1:1:1.73:60:6:0.6:0.2:0.3 0/0:2:0:0,0:2,0:0:0,0:36.5:1:31:1:1:0:60:4:1:0:0 -14 25195808 . G A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01494;SOR=Inf;LSEQ=GTGTCCCAGTCCCGGAATGC;RSEQ=CAGATTCTTATGGCCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:11,14:0:2,0:23:1:31.7:1:1:0:60:50:1:0:0 0/1:15:4:2,2:5,6:0.2667:2,2:24.5:1:28.5:1:1:1.19:60:8:0.2857:0:1 -14 25196787 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.49352;SOR=0;LSEQ=GATGAGAAAGAACCAATGAA;RSEQ=AAATGCTGAAAACCCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:14,22:0.0526:2,2:36:0:33:1:1:1.55:60:4:0.0541:0:2.5 0/0:36:0:0,0:16,20:0:2,0:29.1:1:30.5:1:1:0:60:35:1:0:0.2 -14 25196793 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49352;SOR=0;LSEQ=AAAGAACCAATGAAAAAATG;RSEQ=TGAAAACCCAAAAGGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:14,22:0.0526:2,2:30:0:32:0:1:1.55:60:4:0.0526:0:2.5 0/0:36:0:0,0:16,20:0:2,0:27:1:32.7:1:1:0:60:72:1:0:0.2 -14 25197223 . T C 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAAGAAATCTGGGACTT;RSEQ=GTAAAAAGACCAAACCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:50:0:29:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:36:1:28.5:1:1:0:60:4:1:0:1 -14 25438138 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14529;SOR=Inf;LSEQ=TCTTGCACAACACTTTCAAA;RSEQ=TACAGATTAGCTTCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:146,60:0:2,0:23.8:1:29.3:1:1:0:60:17.727:1:0:0.3 0/1:128:2:1,1:85,41:0.0156:2,2:5.5:1:30:1:0.55032:2.06041:60:4:0.0161:0:1 -14 25438143 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14101;SOR=Inf;LSEQ=CACAACACTTTCAAAATACA;RSEQ=ATTAGCTTCCCCACCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:161,65:0:2,0:23.7:1:31.3:1:1:0:60:44.2:1:0:0.3 0/1:137:2:1,1:90,45:0.0146:2,2:21.5:1:27.5:1:1:1.98916:60:4:0.0149:0:1 -14 25438186 . C T 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGTGCTGCATTAGAACCAGG;RSEQ=CATCTGTACTTTGAGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:263,179:0:2,0:26.4:1:31.2:1:1:0:60:25:0.9953:0:0.4 0/1:249:11:9,2:134,104:0.0442:2,2:19.9:1:29.3:1:0.12325:3.48:60:22:0.0449:0:1.8 -14 25438196 . T C 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGAACCAGGCCATCTGTAC;RSEQ=TTGAGAAATTCTAGAGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:40:24,16:253,179:0.0847:2,2:31.8:1:31.2:1:1:1.06:60:80:0.0862:0:1.6 0/0:264:0:0,0:146,118:0:2,0:25.3:1:30.1:1:1:0:60:51.8:1:0:0.5 -14 25438250 . A G 247 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.56031;SOR=1.09929;LSEQ=CTAGGGCTGCCAATCACTGA;RSEQ=ATAAAGGGCAGTATTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:243:120,123:132,150:0.4629:2,2:24:1:31.2:1:0.59932:1.11:60:47.6:0.4595:0:1.2 0/1:296:144:65,79:74,78:0.4865:2,2:27.9:1:30.4:1:0.56181:1.1525:60:19.571:0.4757:0:1.1 -14 25438321 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10907;SOR=Inf;LSEQ=TCCATGGGTATCTATTTACA;RSEQ=AAATTATTTCATCAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:88,203:0:2,0:23:1:28.7:1:1:0:60:57.2:1:0:0.3 0/1:144:2:1,1:53,89:0.0139:2,2:5:0:32:0:1:1.67:60:4:0.014:0:1 -14 27035112 . A G 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.46853;LSEQ=TTCATACAGAAAAAAATATA;RSEQ=TGATTCAGAAAAGTGATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:294:124,170:48,55:0.7406:2,2:26.5:1:32:1:0.4884:1.19593:60:97:0.7386:0:1.1 1/0:306:175:82,93:59,71:0.5719:2,2:25.4:1:31.1:1:0.81721:1.06:60:86.5:0.571:0:1.2 -14 27035196 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14793;SOR=Inf;LSEQ=ATGATGCAATTGAAAGATAG;RSEQ=CAGGAGTATGTTTCATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:45,143:0:2,0:24.6:1:31.6:1:1:0:60:61.667:1:0:0.3 0/1:118:2:1,1:36,80:0.0169:2,2:35:0:30.5:1:0.53064:2.21:60:4:0.0171:0:1.5 -14 27035215 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52205;SOR=0;LSEQ=GGCAGGAGTATGTTTCATGG;RSEQ=AAACAAAGGGATGAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:21,110:0.015:2,2:23.5:1:28.5:1:0.30451:5.14:60:4:0.0153:0:1 0/0:85:0:0,0:20,65:0:2,0:23.6:1:32.2:1:1:0:60:170:1:0:0.1 -14 27036114 . C T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGAAATCAATCCTTAGA;RSEQ=AAACATTCAATTTTTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:0:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 29235537 . C G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCCCACTCTTCCCACTACCA;RSEQ=CACCACCCCCGCTTTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 29237128 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50419;SOR=0;LSEQ=ACGAGTTCATCATGAAGAAC;RSEQ=TCCCTTACTACCGCGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:98,46:0.0137:2,2:43:0:32.5:1:0.54171:2.11842:60:4:0.0137:0:1 0/0:117:0:0,0:75,42:0:2,0:22.2:1:29.9:1:1:0:60:116:1:0:0.2 -14 29237161 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19502;SOR=Inf;LSEQ=GCGAGAACAAGCAGGGCTGG;RSEQ=AGAACTCCATCCGCCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:114,93:0:2,0:28:1:31.9:1:1:0:60:68:1:0:0.2 0/1:165:2:1,1:87,76:0.0121:2,2:14.5:1:25.5:1:1:1.1438:60:4:0.0123:0:1.5 -14 29237172 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1974;SOR=Inf;LSEQ=CAGGGCTGGCAGAACTCCAT;RSEQ=CGCCACAATCTGTCCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:106,106:0:2,0:28.7:1:31.1:1:1:0:60:69.667:1:0:0.2 0/1:170:2:1,1:85,83:0.0118:2,2:18:0:30:1:1:1.02396:60:4:0.012:0:1.5 -14 29237182 . C A 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59553;SOR=2.37113;LSEQ=AGAACTCCATCCGCCACAAT;RSEQ=TGTCCCTCAACAAGTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:1,0:93,109:0.0049:2,0:1:0:23:0:0.46305:0:60:2:0.005:0:1 0/1:172:2:1,1:79,91:0.0116:2,2:5:0:30:0:1:1.15:60:4:0.0116:0:1.5 -14 29237224 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18529;SOR=Inf;LSEQ=TGAAGGTGCCGCGCCACTAC;RSEQ=ACGACCCGGGCAAGGGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:45,84:0:2,0:21.8:1:30.4:1:1:0:60:42:1:0:0.2 0/1:98:2:1,1:33,63:0.0204:2,2:25.5:1:27.5:1:1:1.90:60:4:0.0206:0:1 -14 29237265 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53824;SOR=0;LSEQ=TACTGGATGCTGGACCCGTC;RSEQ=AGCGACGACGTGTTCATCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:10,52:0.0313:2,2:13:0:31:0:0.31647:5.01:60:4:0.0317:0:1.5 0/0:35:0:0,0:6,29:0:2,0:20.2:1:30.9:1:1:0:60:70:1:0:0.2 -14 29237270 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.11874;SOR=Inf;LSEQ=GATGCTGGACCCGTCGAGCG;RSEQ=CGACGTGTTCATCGGCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:10,48:0:2,0:23.7:1:29.5:1:1:0:60:57:1:0:0.1 0/1:31:2:1,1:4,25:0.0645:2,2:10.5:1:29.5:1:0.30108:5.70:60:4:0.0645:0:1.5 -14 31375248 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17546;SOR=Inf;LSEQ=GGCTTGGACTCTGGAATCAG;RSEQ=TGATGCAGTACTTTACCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:177,97:0:2,0:25.6:1:32.2:1:1:0:60:136:1:0:0.2 0/1:198:2:1,1:117,79:0.0101:2,2:21.5:1:28:1:1:1.47797:60:4:0.0103:0:1 -14 31375294 . CT C 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0624;SOR=Inf;LSEQ=GCCTGAGCAGCAATTTCTCT;RSEQ=TTAACATACTAAATTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:204,190:0:2,0:25.2:1:30.3:1:1:0:60:48.25:1:0:0.4 0/1:260:3:2,1:135,122:0.0115:2,2:17.3:1:29:1:1:1.80:60:6:0.0116:0.0038:1.3 -14 31375322 . A T 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01682;SOR=1.48077;LSEQ=TACTAAATTAAACTAGCCAG;RSEQ=TCAATGCACAATTAGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:167:77,90:114,126:0.4103:2,2:25.6:1:29.5:1:0.84007:1.05734:60:54.667:0.4121:0:1.1 1/0:262:133:63,70:67,62:0.5076:2,2:25.5:1:29.2:1:0.53673:1.19987:60:65.5:0.5097:0:1.1 -14 31581199 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=6;SSF=0.50686;SOR=0;LSEQ=TCTGTCTCAAAAAAACAAAA;RSEQ=CAAAAACAAAAACAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:129,38:0.0118:2,2:17:1:31.5:1:0.40934:3.36384:60:4:0.012:0:1 0/0:130:0:0,0:100,30:0:2,0:20.2:1:29.9:1:1:0:59.8:260:1:0:0.1 -14 31581306 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1869;SOR=Inf;LSEQ=GGGGCATTCCTTTTTGAACA;RSEQ=TACCCATTCCCTTAATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:77,139:0:2,0:22.8:1:31.5:1:1:0:60:53:1:0:0.1 0/1:165:2:1,1:51,112:0.0121:2,2:18:1:25.5:1:0.5323:2.18:60:4:0.0122:0:2 -14 32175558 . G T 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55808;SOR=3.3264;LSEQ=GTTAGTTGAGCTCATTTGGG;RSEQ=TTCCATTTGTAAGATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:9.5:1:28:1:0.4:0:60:4:0.4:0:1 1/0:7:5:3,2:2,0:0.7143:0,2:20.2:1:30.6:1:1:0:60:10:0.8333:0:1.2 -14 32175775 . C T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02101;SOR=4.30116;LSEQ=AAGCCTTTTCCTGTAAATGC;RSEQ=GGGTGGCATCTTCTACTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:2,5:6,14:0.2593:2,2:18:1:30.9:1:1:1.06872:48.3:14:0.2593:0:1 1/0:23:14:6,8:3,6:0.6087:2,2:25.3:1:29.3:1:1:1.47:57.7:28:0.6087:0:1.1 -14 33106799 . A T 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGTAGTGACAAGGGGT;RSEQ=GATTGGTATAATGAACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:20.3:1:32.3:1:1:0:60:6:0.75:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 33106864 . G A 47 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGAAGAGAGCTGATATA;RSEQ=AGGCAGGGATTAGAGTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:0.25:0,0:13.7:1:29.7:1:1:0:60:6:0.25:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 33106926 . G T 64 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAGTGCATTAACAATGAGAT;RSEQ=AGGGTGGAGAGTGGGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:25,0:0.1667:1,0:10.6:1:27.6:1:1:0:60:4:0.1379:0:1.6 0/1:6:1:1,0:5,0:0.1667:0,0:37:0:32:0:1:0:60:2:0.1667:0:1 -14 33107026 . A G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=3.76423;LSEQ=AAATATGATAATGGGAGTTG;RSEQ=TTGCAGAATGGTGTAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:53:51,2:93,1:0.3605:1,1:22.1:1:31.8:1:0.29491:3.61335:60:106:0.363:0:1.4 1/0:69:47:45,2:21,1:0.6812:1,1:26.3:1:31.1:1:1:1.07:60:94:0.6812:0:1.7 -14 33107053 . C T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.62504;LSEQ=AATGGTGTAGGTCATCGGAA;RSEQ=TGAGGAAGCCAAGAAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:25:23,2:186,25:0.1059:2,2:21.8:1:30.6:1:0.74807:1.54:60:50:0.1073:0:1.6 0/1:138:49:39,10:78,10:0.3551:2,2:23.5:1:29.1:1:0.20627:1.98932:60:23.5:0.3507:0:1.5 -14 33107172 . A G 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.94564;LSEQ=GATCCCAGGGCAAGTGCCAT;RSEQ=ATCTTCAACCAATGAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:874:248:119,129:271,355:0.2838:2,2:27.7:1:31.5:1:0.22732:1.21:60:496:0.2857:0:1.1 0/1:565:246:116,130:144,175:0.4354:2,2:25.9:1:31.3:1:0.67061:1.08:60:245:0.4367:0:1.1 -14 33107318 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17002;SOR=1.93619;LSEQ=ACTGTCTTGTGCATATTATG;RSEQ=TGAGTGGAGAGAGGAAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:19:0,19:0,45:0.2969:1,1:24.3:1:29.4:1:1:0:60:5.333:0.2667:0:1.7 0/1:31:14:0,14:0,17:0.4516:1,1:31:1:30.9:1:1:0:60:28:0.4516:0:1 -14 33107381 . AG A 52 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.45285;SOR=2.67506;LSEQ=AAGGGCTAGTGGGGATGTCA;RSEQ=GGGGAATATGAGCTGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:0,17:0.15:1,0:38.3:1:33:0:1:0:60:6:0.1579:0:0 0/1:3:1:0,1:0,2:0.3333:0,0:30:0:26:0:1:0:60:2:0.3333:0:0 -14 33941242 . C A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0485;SOR=Inf;LSEQ=GTCACTGTCTCCCTCTCTGC;RSEQ=CTCATGGAGCTTGTATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:32.7:1:30:1:1:0:60:21:1:0:0.2 0/1:21:4:2,2:8,9:0.1905:2,2:33.8:1:28.8:1:1:1.12:60:8:0.1905:0:1 -14 33941280 . G A 45 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60435;SOR=0.38068;LSEQ=CTAGCTGGAGGAGAGAACAA;RSEQ=CAAGTAAACTATATGTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:3,8:0.2143:2,2:9:1:28.7:1:1:1.31:60:6:0.2143:0:1 0/1:11:1:0,1:3,7:0.0909:2,0:15:0:30:0:1:0:60:2:0.0909:0:1 -14 33960172 . TGCA T 75 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.15749;SOR=0;LSEQ=GCAAAAATACAATTTTTCAC;RSEQ=GCAGCAGCAGCAGCAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:5:3,2:29,17:0.098:2,2:31.4:1:32.6:1:1:1.13435:60:10:0.098:0:0 0/0:27:0:0,0:17,10:0:2,0:28:1:31.9:1:1:0:60:54:1:0:0.1 -14 34552277 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52273;SOR=Inf;LSEQ=ATGATGTTTGTGTTCCCAGA;RSEQ=CAAATGGTTCTTTTAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:8,4:0:2,0:20.2:1:28.8:1:1:0:60:5:1:0:0.1 0/1:21:2:1,1:12,7:0.0952:2,2:39:1:28.5:1:1:1.66897:60:4:0.0952:0:1 -14 34769895 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGGATCTACGGCCACCACCA;RSEQ=GAGCCAAGAAGAGGCAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:32:0:33:0:1:0:60:2:1:0:0 -14 34770002 . G A 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTAAAGTGAGAGAATAA;RSEQ=TTTATGTGGTTTAAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:30:1:1:0:60:4:1:0:1.5 1/1:1:1:0,1:0,0:1:0,0:31:0:29:0:1:0:60:2:1:0:1 -14 34771783 . G T 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTCAGTCTGGTTTCCTG;RSEQ=GACGCTTGTCACCACTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:5,3:2,1:0.7273:2,2:26.4:1:30.4:1:1:1.18052:60:16:0.7273:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 35871093 . C T 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00536;SOR=0.44984;LSEQ=CACAATAAGACGTTTTGGGC;RSEQ=AGGCAGTGTGCAGTGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:363:292:283,9:66,4:0.8044:2,1:24.2:1:31.3:1:0.28773:1.90:60:96.333:0.805:0:1.1 1/0:74:48:47,1:26,0:0.6486:1,1:26.4:1:31.8:1:1:0:60:96:0.6486:0:1.1 -14 35871135 . TTTC T 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAGTACACCCTTTAAATTT;RSEQ=TTCTTTTTTCTTTTTTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1014:0:0,0:858,156:0:2,0:20.5:1:30.1:1:1:0:60:52.368:1:0:0.7 0/1:281:23:18,5:216,43:0.0819:2,2:14.6:1:29.7:1:0.56198:1.39355:59.1:46:0.083:0.0356:0.3 -14 35871168 . C CT 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.26577;SOR=1.50488;LSEQ=CTTTTTTTAGAAAAATAAAA;RSEQ=TTTTTTTTTGTACAAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1822:29:24,5:1340,446:0.0159:2,2:28.2:1:31.3:1:0.39496:1.60:59.5:58:0.0162:0.0022:0.7 0/1:547:13:6,7:370,164:0.0238:2,2:28.5:1:29:1:0.12476:2.62691:60:26:0.024:0.0037:0.5 -14 35871217 . G A 343 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.35168;LSEQ=TGTTCTTTCAGCCCCTTTGC;RSEQ=CTCATAACGTCAGACGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3715:3026:1771,1255:386,299:0.8145:2,2:26.3:1:29.7:1:0.30357:1.09:60:54.018:0.816:0:1.1 1/0:1127:684:375,309:247,194:0.6069:2,2:26.2:1:29.4:1:0.71276:1.04909:60:56:0.6092:0:1.1 -14 35871292 . G A 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=55.34324;LSEQ=AACAAGGGGAAAAAAGACAC;RSEQ=TTAAGCTTCCGGAGCGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3095:3:3,0:1170,1921:0.001:2,0:1:0:25.7:1:0.05441:0:60:6:0.001:0:1.7 0/1:941:48:21,27:360,533:0.051:2,2:24.5:1:29.9:1:0.65291:1.15:60:47:0.0505:0:1.4 -14 35871407 . A G 282 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12685;SOR=0.59443;LSEQ=AATGAACTTTACAGGCTGAG;RSEQ=GAGTTTGCCTTTAATGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:574:530:99,431:9,32:0.9233:2,2:23.7:1:31.2:1:0.67825:1.22397:59.8:43.167:0.925:0:1.1 1/1:106:93:11,82:2,10:0.8774:2,2:21.4:1:30.5:1:0.64195:1.48457:59.9:30:0.8824:0:1 -14 35871430 . T TTTAAAAAAGAGTAAGCTA 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60107;SOR=0;LSEQ=GTTTGCCTTTAATGCTTCTC;RSEQ=TTAAAAAAAGAGGGGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:7:6,1:113,328:0.0156:2,2:7.9:1:27.9:1:0.00175:17.30:57.6:6:0.0138:0.0134:3.1 0/0:71:0:0,0:20,51:0:2,0:18:1:30.7:1:1:0:59.7:70:1:0:0.8 -14 35871441 . A AGTAAGCTATTAAAAAAAGG 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=0.0218;SOR=1.79307;LSEQ=ATGCTTCTCTTTAAAAAAAG;RSEQ=GGGGGGGCAGGTACATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:566:301:94,207:17,34:0.5318:2,2:27:1:30.1:1:0.74734:1.10076:59.7:99.333:0.5438:0.3481:1 1/0:79:53:25,28:8,9:0.6709:2,2:18.4:1:30.7:1:1:1.00:59.8:106:0.6709:0.4304:0.6 -14 35871960 . G A 161 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=82.2902;LSEQ=AGCCTGACTCAGTGCGTCGG;RSEQ=GGCAGGAAGCACCAACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4498:2:1,1:2542,1946:4e-04:2,2:11:1:15.5:1:1:1.30618:60:0:0:0:2 0/1:1330:47:24,23:694,585:0.0353:2,2:22.6:1:29.1:1:0.766:1.13678:60:22.5:0.0343:0:1.1 -14 35872068 . G A 203 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=68.66328;LSEQ=AGTGTAGACACGTGTGGCCT;RSEQ=GAAGAACAAAAGGAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4470:6:6,0:1736,2724:0.0013:2,0:1.3:1:24.5:1:0.0035:0:60:12:0.0014:0:1 0/1:1443:122:53,69:552,768:0.0845:2,2:23.8:1:29.4:1:0.7738:1.07:60:121:0.0844:0:1.2 -14 35872094 . C T 128 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=66.09338;LSEQ=ACAAAAGGAAAAAAGTATAA;RSEQ=CACCTGTTTCAACCCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3127:1:0,1:1071,2049:3e-04:2,0:27:0:14:0:1:0:60:0:0:0:3 0/1:965:20:6,14:337,606:0.0207:2,2:20.6:1:29.7:1:0.81399:1.29725:60:40:0.0211:0:1.2 -14 35872221 . G T 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02153;SOR=Inf;LSEQ=AGGCATCCAATAGGCACTTT;RSEQ=CACACATATTTTCTCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:881:0:0,0:542,339:0:2,0:23.7:1:32.2:1:1:0:60:37.304:1:0:0.1 0/1:152:2:0,2:95,55:0.0132:2,0:21.5:1:28:1:0.13907:0:60:4:0.0133:0:1 -14 35872307 . C T 125 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.10166;LSEQ=GCCCACCTGCCCCTTCTCCA;RSEQ=GTCACCTGCCCTCCGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2482:3:0,3:1698,781:0.0012:2,0:1:0:26.3:1:0.03143:0:60:6:0.0012:0:1 0/1:644:19:14,5:431,194:0.0295:2,2:20.8:1:29.5:1:0.80366:1.26:60:38:0.0298:0:1.1 -14 35872765 . G A 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTTCACTCTCTAGGATGTG;RSEQ=GCTGATGTGAAGTAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:766:0:0,0:632,134:0:2,0:23.9:1:31.1:1:1:0:60:37.3:1:0:0.9 0/1:152:9:8,1:124,19:0.0592:2,2:27.6:1:30.3:1:1:1.22:60:18:0.0612:0:1 -14 35872792 . A G 325 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11902;LSEQ=GTGAAGTAAAAGGTGAGGGT;RSEQ=AATAGTGCTCAGTGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1078:1051:962,89:23,4:0.975:2,2:24:1:32.4:1:0.28291:1.88:60:94.545:0.9747:0:1.1 1/1:253:208:198,10:41,1:0.8221:1,1:24.4:1:32:1:0.69638:2.06589:60:68.333:0.8266:0:1.1 -14 35872835 . ACT A 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.88969;SOR=0.97622;LSEQ=TTCAGAAAGGATCTGGGGTG;RSEQ=CTGCTACATCAGCTACGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2284:264:209,55:1534,483:0.1156:2,2:25.1:1:31.8:1:0.28103:1.20:60:528:0.1169:0.0245:0.5 0/1:654:74:50,24:428,152:0.1131:2,2:23.1:1:30:1:0.26673:1.35093:59.9:36:0.1113:0.0275:0.4 -14 35872920 . G T 230 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01114;LSEQ=TGCAGGTTGTTCTGGAAGTT;RSEQ=AGGAAGGCCAGGTCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5601:257:124,133:2686,2655:0.0459:2,2:24.3:1:28.8:1:0.52397:1.08507:60:84.667:0.0457:0:1.2 0/0:1871:1:0,1:969,901:5e-04:2,0:1:0:23:0:0.4821:0:60:2:5e-04:0:1 -14 35872926 . G A 225 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=145.80107;LSEQ=TTGTTCTGGAAGTTGAGGAA;RSEQ=GCCAGGTCTCCCTTCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5798:4:4,0:2886,2897:7e-04:2,0:10.5:1:24.5:1:0.06213:0:60:3:5e-04:0:2.3 0/1:1898:174:90,84:869,854:0.0917:2,2:24:1:30.3:1:0.75108:1.05:60:348:0.0926:0:1.1 -14 35873369 . T TG 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCCGGCCTAGAGGACGGGTC;RSEQ=GGGGGGAGGGGGCGTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:32.5:1:1:0:60:4:1:0:0.5 0/0:2:0:0,0:1,1:0:2,0:2:1:27:0:1:0:60:4:1:0:0 -14 35873544 . C T 52 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84684;LSEQ=TGGTCCCCCGGCTCGGGCTC;RSEQ=AGGCCCGGCGCCTCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:4:1,3:314,28:0.0116:2,2:7.8:1:26.3:1:0.00247:32.80297:60:8:0.0117:0:1 0/0:102:1:1,0:88,13:0.0098:2,0:14:0:33:0:1:0:60:2:0.0099:0:1 -14 35873553 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14779;SOR=3.26372;LSEQ=GGCTCGGGCTCCAGGCCCGG;RSEQ=GCCTCCCACCCCCAGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:3:1,2:444,63:0.0059:2,2:19.3:1:29:1:0.0441:13.95925:60:6:0.0061:0:1 0/1:158:3:2,1:130,25:0.019:2,2:16.3:1:30.3:1:0.41909:2.57937:60:6:0.0194:0:1 -14 35873567 . A T 138 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=92.86099;LSEQ=GCCCGGCGCCTCCCACCCCC;RSEQ=GGCCGCGCGCGTCCCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:857:1:0,1:691,159:0.0012:2,0:1:0:25:0:0.18801:0:60:2:0.0012:0:1 0/1:275:27:22,5:182,64:0.0982:2,2:21.1:1:29.2:1:0.48912:1.54:60:12.5:0.0951:0:1.6 -14 35873570 . C T 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00379;SOR=Inf;LSEQ=CGGCGCCTCCCACCCCCAGG;RSEQ=CGCGCGCGTCCCGCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:917:0:0,0:733,184:0:2,0:22:1:31.8:1:1:0:60:31.75:1:0:0.3 0/1:304:4:2,2:225,75:0.0132:2,2:11.5:1:27.5:1:0.2666:2.98684:60:8:0.0136:0:1 -14 35873770 . G A 369 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.118;LSEQ=AGGCCGCTGTCGTGGCGGTC;RSEQ=TCCAGTAGCCGCTCCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5059:4461:1895,2566:255,331:0.8818:2,2:24.9:1:30.5:1:0.65687:1.0432:60:68.703:0.8835:0:1.2 0/1:1816:850:373,477:434,532:0.4681:2,2:23.8:1:29.6:1:0.6703:1.04325:60:43.737:0.4674:0:1.2 -14 35873840 . G A 80 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00488;SOR=4.68166;LSEQ=ACTCCTGGGGGCGCTCGGCC;RSEQ=CCTGGAACATGGCGCGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2016:6:6,0:539,1470:0.003:2,0:1:0:25.8:1:0.00038:0:60:12:0.003:0:2 0/1:580:8:5,3:178,394:0.0138:2,2:9.6:1:26.8:1:0.11663:3.68:60:16:0.014:0:1.5 -14 35873905 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCTGGGCCGCGGGCTGCGCG;RSEQ=TGCTTCCTCGCTGGGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:16,69:0.023:2,2:26:1:30.5:1:0.35445:4.21:60:4:0.0233:0:1 0/0:19:0:0,0:3,16:0:2,0:12.6:1:32.9:1:1:0:60:38:1:0:0.1 -14 35873907 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCCGCGGGCTGCGCGCT;RSEQ=CTTCCTCGCTGGGGCGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:18,64:0.0235:2,2:37.5:1:28.5:1:0.40333:3.49:60:4:0.0238:0:1 0/0:16:0:0,0:2,14:0:2,0:12.9:1:32.9:1:1:0:60:32:1:0:0.1 -14 35888950 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAGTGAGTGCAGAGGCCCG;RSEQ=AGAAGGATGCACCTTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:40,27:0.029:2,2:7.5:1:27.5:1:1:1.47282:60:4:0.0294:0:2.5 0/0:15:0:0,0:7,8:0:2,0:21.5:1:30:1:1:0:60:30:1:0:0.8 -14 35888987 . A G 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGACAGCAGGGAGTCAGC;RSEQ=TGGGGGAAGTCGTGTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:100:51,49:0,0:1:0,2:25.5:1:30.9:1:1:0:60:200:1:0:1.2 1/1:14:14:6,8:0,0:1:0,2:27.8:1:30.9:1:1:0:60:28:1:0:1.2 -14 36417338 . C T 57 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCACAGGCCGGAGGACA;RSEQ=GGAGGGTAATCACAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:1,2:0.5714:2,2:8:1:28.5:1:1:1.81:43:8:0.8:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36417343 . G A 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGCCGGAGGACACGGAG;RSEQ=GTAATCACAGGCCGGAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:3,2:1,2:0.5556:2,2:11.2:1:32:1:1:2.60:38.6:10:0.5556:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36417345 . T A 54 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCGGAGGACACGGAGGG;RSEQ=AATCACAGGCCGGAGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:3,2:0.4444:2,2:13.8:1:27:1:0.52381:3.76419:38.3:3:0.5:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36417392 . T C 91 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=TAATCACAGGCCGGAGGACA;RSEQ=GGAGAGAAATCACAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:4,4:9,6:0.3478:2,2:24:1:30.5:1:0.68502:1.47341:38.5:16:0.4:0:2.3 1/1:1:1:1,0:0,0:1:0,0:4:0:30:0:1:0:24:2:1:0:3 -14 36417446 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCACAGGCCGGAGGACA;RSEQ=GGAGGGTAATCACAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:0.1538:2,2:13:1:28.5:1:1:1.67325:30:4:0.1667:0:3 0/0:2:0:0,0:1,1:0:2,0:45.5:1:31:1:1:0:24:4:1:0:3 -14 36417451 . G A 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=ACAGGCCGGAGGACACGGAG;RSEQ=GTAATCACAGGCCGGAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:3,2:5,3:0.3846:2,2:15:1:29.2:1:1:1.10211:33.2:10:0.3846:0:2.6 1/1:2:2:1,1:0,0:1:0,2:43:1:30.5:1:1:0:24:4:1:0:3 -14 36417453 . T A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=AGGCCGGAGGACACGGAGGG;RSEQ=AATCACAGGCCGGAGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:4,4:0.2727:2,2:19:1:28.7:1:1:1.88:30.7:6:0.3:0:2.7 1/1:2:2:1,1:0,0:1:0,2:41:1:29.5:1:1:0:24:4:1:0:3 -14 36417707 . C T 47 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGGAGAGAAATCACAGGC;RSEQ=GGAGGATATGGAGAGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:4,3:0.3:2,2:20:1:29.7:1:1:2.41422:36:6:0.3:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36417714 . T C 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAATCACAGGCCGGAGGA;RSEQ=ATGGAGAGAAATCACAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:4,3:0.3:2,2:13:1:30.7:1:1:2.41422:36:6:0.3333:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36417741 . T C 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAATCACAGGCCGGAGGA;RSEQ=ATGGAGGGTAATCACAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:1,1:0.7143:2,2:17.6:1:32:1:1:1.41:46.8:10:0.7143:0:2.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36417743 . T C 53 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCACAGGCCGGAGGATA;RSEQ=GGAGGGTAATCACAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:1,1:0.6667:2,2:19.8:1:26.5:1:1:2.45:45:3:0.6:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36417777 . A T 41 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCGGAGGATATGGAGAG;RSEQ=AATCACAGGCCGGAGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:13.3:1:26.3:1:1:0:47.7:6:1:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36418423 . A G 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAGGCTGGAGGATATGGAG;RSEQ=GTAATCACAGGCCGGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:19:1:28.3:1:1:0:46.7:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36492295 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCTTTCCTGTTTTCAG;RSEQ=AGTATAAAGAAGATTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:26,33:0.0328:2,2:27.5:1:30.5:1:1:1.26:60:4:0.0333:0:2 0/0:15:0:0,0:7,8:0:2,0:24.8:1:32:1:1:0:60:30:1:0:0.1 -14 36558077 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.31552;LSEQ=TAGCCCCACCCTTATTTAAG;RSEQ=ACACAGTTGGAAGAAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3897:138:56,82:1724,2030:0.0354:2,2:25.3:1:32.4:1:0.22428:1.24349:60:137:0.0357:0:2.5 0/1:566:242:112,130:156,168:0.4276:2,2:26.2:1:31.5:1:0.67136:1.07766:60:241:0.4296:0:2.6 -14 36558089 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=18.72462;LSEQ=TATTTAAGTACACAGTTGGA;RSEQ=GAAGGTCTGTAATACTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3656:120:47,73:1554,1979:0.0328:2,2:27:1:31.1:1:0.30514:1.21957:60:39:0.0326:0:2.8 0/1:535:208:92,116:147,178:0.3888:2,2:27.2:1:30.6:1:0.85845:1.04122:60:207:0.392:0:2.9 -14 36558104 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=46.18797;LSEQ=TTGGAAGAAGGTCTGTAATA;RSEQ=TGCATTTAACTCGCTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3287:103:37,66:1293,1886:0.0313:2,2:27.4:1:30.4:1:0.35984:1.22284:60:102:0.0315:0:2.8 1/0:477:286:117,169:80,110:0.5996:2,2:25.7:1:29.8:1:0.84936:1.05037:60:572:0.6008:0:2.3 -14 36558246 . G C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.39439;LSEQ=TGATTAGAGTGATGCTTTTT;RSEQ=TTAGGAAAGGGTGAAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:9:0,9:1,263:0.033:1,0:24.8:1:33.1:1:1:0:60:18:0.0333:0:1.8 0/1:33:11:0,11:1,21:0.3333:1,0:29.3:1:33.3:1:1:0:60:22:0.3333:0:1.9 -14 36558266 . A T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.26553;LSEQ=GTTAGGAAAGGGTGAAAGTC;RSEQ=CTGCTATAAGCCATGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:6:0,6:1,175:0.033:1,0:21.2:1:31.3:1:1:0:60:12:0.0331:0:2.2 0/1:23:9:0,9:2,12:0.3913:2,0:19.6:1:29.8:1:0.50198:0:60:18:0.3913:0:2.1 -14 36983065 . A C 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGGCCAGGGTGGGGAGC;RSEQ=GCTTTGGGATGCTAAACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:25.6:1:30.6:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36983623 . A G 138 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCGGATGGAGCCAGCGT;RSEQ=ATTGATGGCAAGAAAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:23,1:0,0:1:0,1:25.3:1:30.3:1:1:0:60:11:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36983798 . G A 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATGATAAGGCCGAGGGT;RSEQ=CCACAGCCTACTAAAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:257:257:255,2:0,0:1:0,1:24.2:1:28.2:1:1:0:60:50.4:1:0:1.1 1/1:15:15:14,1:0,0:1:0,1:20.9:1:29.3:1:1:0:60:30:1:0:1 -14 36983940 . C A 44 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01336;SOR=9.69132;LSEQ=CTGGGGCAGGTTAAGCGAAG;RSEQ=TCCAATTCCGTGGGATCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2372:3:2,1:1893,476:0.0013:2,2:21.7:1:16.3:1:0.49026:1.98785:60:0.5:4e-04:0:3.3 0/1:247:3:2,1:180,63:0.0121:2,2:25.3:1:28:1:1:1.42634:60:6:0.0124:0:1.3 -14 36984074 . C T 165 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=26.55752;LSEQ=CACAGCTGACCATTCCAACG;RSEQ=AAGTGGTCAAATTTGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8346:16:1,15:4155,4168:0.0019:2,1:3.9:1:23.9:1:0.00051:14.9529:60:7:0.0017:0:1.5 0/1:1338:65:29,36:636,635:0.0486:2,2:24.2:1:27.4:1:0.44601:1.24313:60:20.667:0.047:0:1.2 -14 36984376 . G T 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGCTCTTGGTGGGGGAGC;RSEQ=GGAGAGAGGGATTGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:117:116:2,114:0,1:0.9915:0,1:27.8:1:30:1:1:0:60:115:1:0:2.7 1/1:3:3:0,3:0,0:1:0,0:33.3:1:27.7:1:1:0:60:6:1:0:2.3 -14 36984383 . A G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGGTGGGGGAGCGGGAGAG;RSEQ=GGGATTGGGAAGAGATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:114:113:2,111:0,0:0.9912:0,1:27.2:1:31.1:1:1:0:60:36.667:0.991:0:2.8 1/1:3:3:0,3:0,0:1:0,0:31:1:29.7:1:1:0:60:6:1:0:2.3 -14 36984399 . T C 190 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28278;SOR=0.17505;LSEQ=AGAGAGGGATTGGGAAGAGA;RSEQ=GCAGACGAATAACGAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:103:88:2,86:0,15:0.8544:1,1:24.1:1:29.5:1:1:0:60:87:0.8529:0:2.9 1/0:2:1:0,1:0,1:0.5:0,0:27:0:32:0:1:0:60:2:0.5:0:3 -14 36984603 . A AG 118 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGGCAAGGGTGACCCGGA;RSEQ=GGGCTACAGCCCATCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:1,13:0,2:0.875:0,1:24.8:1:31.1:1:1:0:60:28:0.875:0.1875:0 1/1:1:1:1,0:0,0:1:0,0:29:0:34:0:1:0:60:2:1:0:0 -14 36986190 . A AC 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.04286;SOR=0;LSEQ=TTGAATCACCAAAAAAAGAC;RSEQ=CCCCAAAGCTGTTTTATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:44:39,5:10,0:0.8148:0,2:23.2:1:32.5:1:0.57075:0:60:88:0.8148:0.1111:0.4 0/0:2:0:0,0:2,0:0:0,0:31:1:32:0:1:0:60:4:1:0:0 -14 36986218 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGTTTTATGCCCTTCTCT;RSEQ=CTTAAAGATTCCTTGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:2,0:88,5:0.0211:2,0:20:1:29:1:1:0:60:4:0.0215:0:1 0/0:5:0:0,0:5,0:0:0,0:19:1:29.6:1:1:0:60:4:1:0:0.4 -14 36986265 . C CT 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.07594;SOR=0.3303;LSEQ=GCTTGGTTGTTTTTCATTTT;RSEQ=TTTTTTTAAAAAAAAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:149:146,3:91,5:0.6032:2,1:21.4:1:31.1:1:0.2686:2.66:59.9:23.833:0.6085:0.1619:0.5 0/1:12:4:4,0:8,0:0.3333:0,0:18.5:1:30.3:1:1:0:60:8:0.3333:0.0833:0 -14 36986272 . T TTA 143 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.61856;SOR=0;LSEQ=TGTTTTTCATTTTCTTTTTT;RSEQ=AAAAAAAAAAACCCACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:29:29,0:234,7:0.1062:1,1:19.4:1:29.5:1:1:0:60:58:0.1094:0.0256:0.7 0/0:12:0:0,0:12,0:0:0,0:28.3:1:30.5:1:1:0:60:24:1:0:0.7 -14 36986273 . A T 181 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.00348;SOR=6.01193;LSEQ=GTTTTTCATTTTCTTTTTTT;RSEQ=AAAAAAAAAACCCACAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:68:66,2:198,5:0.2482:1,1:19.6:1:29.8:1:1:1.1992:59.4:33:0.251:0:1.3 1/0:12:8:8,0:4,0:0.6667:0,0:32.3:1:31.1:1:1:0:60:16:0.6667:0:1 -14 36986296 . A AG 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00396;SOR=Inf;LSEQ=AAAAAAAACCCACAAATTTT;RSEQ=GGGGGGGAAAAAAAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:333,6:0:1,0:24.6:1:25.7:1:1:0:59.8:5.054:0.9792:0:0.6 0/1:24:2:2,0:22,0:0.0833:1,0:8:1:29.5:1:1:0:60:4:0.0909:0.0417:1 -14 36986300 . GGGGAAAA TGGGGGGGGG 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00344;SOR=0.30001;LSEQ=AAAAAAACCCACAAATTTTA;RSEQ=AAAGAAAGACGTCCAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:561:417:406,11:109,3:0.7433:1,1:21.3:1:31.2:1:1:1.02:59.9:207.5:0.7685:0.3743:0.3 0/1:28:13:13,0:15,0:0.4643:1,1:15.3:1:31:1:1:0:60:26:0.4643:0.1786:0.1 -14 36986598 . G A 88 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0957;SOR=2.71251;LSEQ=GCAGCGCCGCGGGGCTGGCG;RSEQ=CGTGGTGCGCCAGGTCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2622:10:8,2:593,2017:0.0038:2,2:12:1:26.7:1:0.00021:13.59:60:20:0.0039:0:1 0/1:389:4:3,1:122,263:0.0103:2,2:9.5:1:23.5:1:0.09961:6.43:60:3:0.0078:0:1.5 -14 36986634 . C T 29 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03946;SOR=14.80267;LSEQ=CCGGAGACTGGCCTGCGCTG;RSEQ=CTGGCTGGTGGCCCGGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1212:1:0,1:191,1019:8e-04:2,0:19:0:32:0:1:0:60:2:8e-04:0:1 0/1:165:2:1,1:43,120:0.0121:2,2:14:1:29.5:1:0.46341:2.77:60:4:0.0123:0:1 -14 36986669 . G A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00071;SOR=Inf;LSEQ=GGGTGTGCGCCAAGGCCGGC;RSEQ=CCACCGCTGCCCACGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:77,196:0:2,0:17:1:31.6:1:1:0:60:90:0.9963:0:0.3 0/1:28:3:2,1:6,19:0.1071:2,2:19.7:1:29.3:1:0.18803:5.84:60:6:0.1111:0:1.3 -14 36986678 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGCCGGCGCCACCGCT;RSEQ=CCCACGGAGATGGCCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:65,107:0.0115:2,2:15.5:1:30:1:1:1.64:60:4:0.0117:0:1.5 0/0:17:0:0,0:6,11:0:2,0:22.5:1:32.6:1:1:0:60:34:1:0:0.4 -14 36986682 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCGGCGCCACCGCTGCCC;RSEQ=CGGAGATGGCCGCTGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:62,96:0.0125:2,2:5:1:30.5:1:1:1.54:60:4:0.0127:0:2.5 0/0:16:0:0,0:6,10:0:2,0:19.9:1:30.2:1:1:0:60:32:1:0:0.4 -14 36986692 . C T 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00768;SOR=Inf;LSEQ=ACCGCTGCCCACGGAGATGG;RSEQ=CGCTGCCGCCGCCTGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:52,77:0:2,0:14.9:1:31.4:1:1:0:60:63.5:0.9922:0:0.4 0/1:13:2:1,1:4,7:0.1538:2,2:23:1:31.5:1:1:1.67:60:4:0.1538:0:1 -14 36986695 . C T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCCCACGGAGATGGCCG;RSEQ=TGCCGCCGCCTGCGCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:48,66:0.0172:2,2:6.5:1:25:1:1:1.37:60:4:0.0175:0:1.5 0/0:11:0:0,0:5,6:0:2,0:12.4:1:31.6:1:1:0:60:22:1:0:0.6 -14 36986706 . T C 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGGCCGCTGCCGCCGCC;RSEQ=GCGCGGCCTGCGCCTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:35,35:0.0278:2,2:40:0:31.5:1:1:1:60:4:0.0286:0:1.5 0/0:9:0:0,0:5,4:0:2,0:7.3:1:29.7:1:1:0:60:18:1:0:0.7 -14 36986741 . C T 30 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01273;SOR=Inf;LSEQ=TGGTGCTGCGCCTGCTGCTG;RSEQ=GCGTGGCCTTGTAGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:109,60:0:2,0:20:1:31:1:1:0:60:32.8:1:0:0.3 0/1:22:2:1,1:13,7:0.0909:2,2:24:0:30.5:1:1:1.80284:60:4:0.0909:0:1.5 -14 36986818 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05176;SOR=9.16406;LSEQ=GCCGTCTTTCACCAGGACCG;RSEQ=CACCGCCACGCGTCGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:2:1,1:442,284:0.0027:2,2:26:1:28:1:1:1.55531:60:4:0.0028:0:2 0/1:81:2:1,1:52,27:0.0247:2,2:13:1:31.5:1:1:1.90939:60:4:0.025:0:1 -14 36986850 . G T 57 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13103;SOR=3.95684;LSEQ=GTCGCGGCGACTGCTGCTGA;RSEQ=CCTGTTGCTGCTGCGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1590:5:3,2:1172,411:0.0031:2,2:21.2:1:24.6:1:0.60976:1.90008:60:4:0.0026:0:2.2 0/1:162:2:1,1:116,44:0.0123:2,2:15.5:1:29:1:0.47964:2.61812:60:4:0.0125:0:1.5 -14 36986866 . G T 52 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00274;SOR=12.08664;LSEQ=CTGAGCCTGTTGCTGCTGCG;RSEQ=GCACCCGGTGCCCCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2002:3:1,2:1461,536:0.0015:2,2:15.3:1:28:1:0.17802:5.44599:60:6:0.0015:0:1.3 0/1:224:4:1,3:157,63:0.0179:2,2:21.8:1:26:1:0.07786:7.40055:60:8:0.0182:0:1.3 -14 36986888 . CCCG C 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.06591;SOR=2.00535;LSEQ=CACCCGGTGCCCCCGCCGCC;RSEQ=CCGCCGCCGCTGTCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2843:38:25,13:2004,795:0.0134:2,2:30.5:1:31:1:0.46942:1.31068:60:76:0.0136:0.0011:0.3 0/1:378:10:5,5:240,126:0.0265:2,2:26.9:1:27.9:1:0.32712:1.90135:60:9:0.0243:0.0026:0.3 -14 36987119 . C A 32 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00731;SOR=14.42934;LSEQ=AGCACCCGGCGCTTCCTGCG;RSEQ=GGCGCGCTTGGCAGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2604:2:2,0:1128,1467:8e-04:2,0:1:0:27:1:0.18923:0:60:4:8e-04:0:1 0/1:273:3:3,0:112,156:0.011:2,0:7:1:20.7:1:0.07527:0:60:2:0.0075:0:1.3 -14 36987198 . C T 36 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01787;SOR=8.61365;LSEQ=CCATGCCGCTCATGTTCATG;RSEQ=CGCTCGCCGGGCCCATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2402:3:2,1:952,1445:0.0012:2,2:14.3:1:32:0:0.56687:3.03:60:6:0.0013:0:1 0/1:281:3:1,2:128,150:0.0107:2,2:13.3:1:23.3:1:1:1.70355:60:2:0.0074:0:2.7 -14 36987253 . C T 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01142;SOR=Inf;LSEQ=CGACAAACGCACAGCGTCGG;RSEQ=CGGGGCCAGGCCGAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1383:0:0,0:411,970:0:2,0:24.7:1:31.1:1:1:0:60:52.115:0.9985:0:0.2 0/1:166:2:1,1:64,100:0.012:2,2:33:1:29:1:1:1.56:60:4:0.0122:0:1.5 -14 36987283 . T C 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01037;SOR=Inf;LSEQ=GCCGAGCCAGGCCACCCCTG;RSEQ=TTTCCGCGCCATTGGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:798:0:0,0:131,666:0:2,0:23.2:1:30.1:1:1:0:60:65.417:0.9987:0:0.2 0/1:91:2:1,1:25,63:0.022:2,2:9:1:30.5:1:0.49663:2.49:60:4:0.0225:0:1 -14 36988175 . G A 309 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCCCGCGGCCCCGCAGTGG;RSEQ=GCGGCCTCACTTACTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1727:1415:961,454:211,99:0.8193:2,2:23.8:1:29.6:1:1:1.00688:60:25.698:0.8161:0:1.3 0/0:235:0:0,0:143,92:0:2,0:24.1:1:29.6:1:1:0:60:38.167:1:0:0.3 -14 36988274 . G A 61 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04686;SOR=4.9641;LSEQ=GGTGTCCTGGTACGGCGGCA;RSEQ=CTCGCTCATGTTGCCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2233:5:5,0:1025,1201:0.0022:2,0:1:0:26.4:1:0.02086:0:60:10:0.0023:0:1.2 0/1:272:3:2,1:125,144:0.011:2,2:22.3:1:32:0:0.60028:2.30:60:6:0.0111:0:1.3 -14 36988279 . C A 42 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01135;SOR=12.13697;LSEQ=CCTGGTACGGCGGCAGCTCG;RSEQ=TCATGTTGCCCAGGTTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2183:2:2,0:987,1189:9e-04:2,0:1:0:28:0:0.20608:0:60:4:9e-04:0:1 0/1:272:3:2,1:118,150:0.011:2,2:6.7:1:26.7:1:0.58573:2.53:60:6:0.0114:0:1.3 -14 36988331 . G A 46 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00412;SOR=26.08275;LSEQ=CCCCACGGCGGAGTGCGAGA;RSEQ=CTGGGGCACCCCCGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1694:1:1,0:615,1077:6e-04:2,0:1:0:27:0:0.36385:0:60:2:6e-04:0:1 0/1:197:3:2,1:71,123:0.0152:2,2:17.3:1:29.3:1:0.55638:3.44:60:6:0.0157:0:1 -14 36988345 . G A 66 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22178;SOR=2.61472;LSEQ=GCGAGAGCTGGGGCACCCCC;RSEQ=CCGCCGTCATGTGGTAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1564:7:5,2:519,1037:0.0045:2,2:8.6:1:23.7:1:0.04601:4.99:60:2.5:0.0033:0:1.1 0/1:172:2:1,1:64,105:0.0116:2,2:6.5:1:27.5:1:1:1.64:60:4:0.0119:0:1 -14 36988369 . G C 34 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00795;SOR=Inf;LSEQ=CCGTCATGTGGTAGGCGGCG;RSEQ=TGACGGCGCCGTGGTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1435:0:0,0:586,847:0:2,0:22:1:31.5:1:1:0:60:64.136:0.9993:0:0.1 0/1:141:2:1,1:58,80:0.0142:2,2:15.5:1:34:0:1:1.38:60:4:0.0144:0:1 -14 36988419 . C T 95 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03357;SOR=3.3485;LSEQ=TGCTGCATGGCCGCTGTTGG;RSEQ=GGTGCCGCCTGGCCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2569:12:5,7:1723,832:0.0047:2,2:11.4:1:26.7:1:0.06828:2.89796:60:11:0.0044:0:1.5 0/1:323:5:2,3:213,104:0.0155:2,2:14.8:1:25.6:1:0.33744:3.06039:60:4:0.0126:0:1.2 -14 36988598 . GA G 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.47111;SOR=1.26362;LSEQ=GGAGGAGGAAGGAAGAGGAG;RSEQ=AAAAAAAGGGAGAGGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5119:56:22,34:1998,3057:0.0109:2,2:32.3:1:31.4:1:1:1.01008:60:112:0.0112:0:0.1 0/1:798:11:4,7:320,465:0.0138:2,2:22.6:1:30.8:1:1:1.20401:60:22:0.0143:0.0013:0.2 -14 36988635 . C CT 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.25965;SOR=1.43198;LSEQ=GGGAAGGCGAAGCCTCGCTG;RSEQ=TTTTTTTTTCTCCCTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2516:62:12,50:590,1854:0.0246:2,2:25.9:1:30.5:1:0.45304:1.32581:60:61:0.0249:0.002:0.2 0/1:315:11:2,9:71,232:0.0349:2,2:29.1:1:27.5:1:1:1.37584:60:10:0.0331:0:0.3 -14 36989078 . G T 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00556;SOR=Inf;LSEQ=AACCGAGAGCGGGGAGGGCA;RSEQ=GAGGTGGGGTGGGGGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:458,31:0:2,0:23.5:1:32.1:1:1:0:60:68.857:1:0:0.2 0/1:40:2:2,0:31,7:0.05:2,0:17.5:1:30.5:1:1:0:60:4:0.05:0:1 -14 36989188 . C T 76 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=6.78695;LSEQ=AGTGGAACCACTTTCCAATT;RSEQ=GGTCGGGGTTCCCCGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4006:8:0,8:2794,1204:0.002:2,0:1:0:25.6:1:7e-05:0:60:16:0.002:0:1 0/1:522:7:1,6:330,185:0.0134:2,2:5.7:1:25.4:1:0.01106:10.65627:60:6:0.0119:0:1.3 -14 36989596 . A G 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16449;SOR=9.37581;LSEQ=ACAACCCGCCCCCGCAGCTC;RSEQ=GGGGTTTTTCAGTGGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:4:0,4:2,78:0.0476:1,0:20.5:1:32.5:1:1:0:60:8:0.05:0:1.3 0/1:3:1:0,1:0,2:0.3333:0,0:1:0:29:0:1:0:60:2:0.3333:0:1 -14 36989638 . A C 159 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCTAACACGCCTCCCCC;RSEQ=AGGTCTTCCCCCCCCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:34:1,33:0,2:0.7907:0,1:19:1:31.4:1:1:0:60:33:0.8684:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36989645 . TCCCC T 132 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGCCTCCCCCAAGGTCT;RSEQ=CCCCCCCCCCACCCCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:22:0,22:2,8:0.6471:2,1:27.5:1:29.7:1:0.09073:0:60:21:0.7778:0.1471:1.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 36990890 . C A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=5e-04;SOR=Inf;LSEQ=CCTCCGCCCTCCCACCTGCG;RSEQ=CCGCGTTTTTGTGCGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:731:0:0,0:712,19:0:1,0:25:1:32.1:1:1:0:60:59.917:1:0:0.1 0/1:64:3:3,0:60,1:0.0469:1,0:21.7:1:30.3:1:1:0:60:6:0.0469:0:1 -14 36990941 . T A 27 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0115;SOR=Inf;LSEQ=CTGGGGAGGCCACCCTACGT;RSEQ=TGCGCAGGGAGACGCGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1619:0:0,0:1339,280:0:2,0:23.7:1:30:1:1:0:60:58.963:1:0:0.1 0/1:195:2:1,1:153,40:0.0103:2,2:18.5:1:27.5:1:0.37716:3.79039:60:4:0.0104:0:1 -14 36990957 . G T 44 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01159;SOR=12.03615;LSEQ=ACGTTTGCGCAGGGAGACGC;RSEQ=CTCGCCGCTGGTGTTGCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2205:2:1,1:1645,552:9e-04:2,2:3:0:31:1:0.4398:2.97826:60:4:9e-04:0:1.5 0/1:277:3:1,2:188,86:0.0108:2,2:20.3:1:28:1:0.23779:4.34632:60:6:0.0111:0:1 -14 36991229 . C T 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGTGGGTTTCCCAGTCAC;RSEQ=CAGCTTCTTTCTCTCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1319:0:0,0:26,1292:0:1,0:25.1:1:31.3:1:1:0:60:44.448:1:0:0.1 0/1:140:9:0,9:2,129:0.0643:1,0:24.4:1:29.6:1:1:0:60:18:0.0672:0:1.1 -14 37050384 . G A 28 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0115;SOR=Inf;LSEQ=CTGCCAGGTCAGGCGACTCC;RSEQ=CCGCCCCTGGAGCGCGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:770:0:0,0:545,225:0:2,0:22.1:1:30.1:1:1:0:60:84.556:1:0:0.1 0/1:93:2:1,1:55,36:0.0215:2,2:18:0:28:1:1:1.52059:60:4:0.0217:0:1 -14 37050396 . G A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.01235;SOR=Inf;LSEQ=GCGACTCCGCCGCCCCTGGA;RSEQ=CGCGAGCGCGCTTCAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:900:0:0,0:594,304:0:2,0:24.7:1:31.7:1:1:0:60:55.125:0.9989:0:0.1 0/1:113:2:1,1:64,45:0.0177:2,2:21.5:1:28:1:1:1.4176:60:4:0.0177:0:1 -14 37050436 . A G 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01298;SOR=Inf;LSEQ=GTAGCGATGATTCTGGAACC;RSEQ=GATCTTGACCTGCGTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1326:0:0,0:743,583:0:2,0:27.9:1:30.5:1:1:0:60:50:1:0:0.2 0/1:171:2:1,1:87,82:0.0117:2,2:30.5:1:28.5:1:1:1.06064:60:4:0.0121:0:1 -14 37050466 . G A 61 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14134;SOR=3.77283;LSEQ=CTGCGTGGGCGTGAGGCGAA;RSEQ=CAGGCTCGCCAGCTGCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1120:5:4,1:516,599:0.0045:2,2:3.2:1:26.6:1:0.18927:4.64:60:10:0.0045:0:1 0/1:120:2:1,1:52,66:0.0167:2,2:9.5:1:30:0:1:1.27:46.5:4:0.0168:0:1.5 -14 37051128 . C G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAGGCATGGAGAGGGGG;RSEQ=GGGGGGTGGGGTGGGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:4,0:0.2857:0,0:6:0:32.5:1:0.06667:0:50:4:0.2857:0:1.5 0/0:1:0:0,0:1,0:0:0,0:49:0:30:0:1:0:60:2:1:0:0 -14 37052721 . C G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCCCATAGCCTCAACGGCA;RSEQ=TCTCACTGCCTGGGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 37127253 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.1;SOR=Inf;LSEQ=CCAGCGGTCCAGGGCGGACC;RSEQ=TCCCTCGCCCTGGGCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:17.3:1:31:1:1:0:60:6:1:0:0.7 1/1:2:2:1,1:0,0:1:0,2:19:1:28.5:1:1:0:60:4:1:0:1 -14 37128564 . C A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTCGTCTCTCGGTCGGT;RSEQ=TCAGCGGGTCGCTGACTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 38054959 . AGT A 104 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.70689;SOR=0.39658;LSEQ=CAAATGTACTCCTTTTTAAA;RSEQ=GTGTGTGTGTTGGGGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:992:11:11,0:979,2:0.0111:1,0:19.3:1:30.2:1:1:0:56:10:0.0104:0.001:1.4 0/0:226:1:1,0:224,1:0.0044:1,0:28:0:28:0:1:0:60:2:0.0045:0:0 -14 38054972 . T TG 265 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00238;SOR=0.59327;LSEQ=TTTTAAAAGTGTGTGTGTGT;RSEQ=GGGGGGGGGGGCGGGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1033:285:285,0:638,11:0.2759:1,1:31.2:1:32.5:1:0.02236:0:59.8:70.25:0.3022:0:1.7 0/1:255:47:43,4:179,3:0.1843:1,2:28.1:1:29.7:1:0.03408:5.49311:59.1:14.667:0.193:0.0353:1.9 -14 38054994 . G T 74 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36274;SOR=1.4454;LSEQ=GGGGGGGGGGCGGGGGGATT;RSEQ=GCTAAGGAGGTTTCCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2129:22:10,12:1274,828:0.0103:2,2:17:1:16.6:1:0.18802:1.84577:59.7:0.294:0.0027:0:3.6 0/1:538:8:3,5:310,216:0.0149:2,2:19.1:1:21.3:1:0.28509:2.38803:60:1.667:0.0105:0:2.1 -14 38055101 . A G 338 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.5041;LSEQ=CTTGGTTTCAGAAATTAAAT;RSEQ=AAGAGAAAAGAAAAAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2217:1836:656,1180:132,249:0.8281:2,2:23.7:1:31.2:1:0.72428:1.05:60:58.226:0.8265:0:1.8 1/0:576:408:158,250:64,104:0.7083:2,2:25.3:1:30.7:1:0.92511:1.03:60:50:0.7042:0:1.8 -14 38055123 . G C 321 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.45117;LSEQ=AGAGAAAAGAAAAAGCCCCT;RSEQ=ATGTGTAATCTTGAAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1423:1130:268,862:86,203:0.7941:2,2:23.1:1:31.7:1:0.03956:1.36232:60:101.727:0.7959:0:2.3 1/0:378:240:69,171:39,96:0.6349:2,2:23.2:1:31.2:1:1:1.00678:60:79:0.632:0:2.2 -14 38055177 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13179;LSEQ=AAAAGTTAAACCAAGGCAAC;RSEQ=TCACACTTAAATTCTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:482:394:6,388:0,88:0.8174:1,1:23.4:1:30.1:1:0.5979:0:60:38.4:0.8153:0:2.2 0/1:100:37:0,37:1,62:0.37:1,1:24.3:1:30.1:1:1:0:60:74:0.3737:0:2.4 -14 38055445 . C T 88 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAGGGGGAGGAGTGCT;RSEQ=ACTCTCACCATGTGCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:0.9091:0,0:24.4:1:26.7:1:1:0:60:20:0.9091:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 38058065 . C T 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=88.53626;LSEQ=GTTGGGATTGGAAGCTTTTT;RSEQ=CTCTCTTTGGGACTTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3660:5:1,4:1677,1975:0.0014:2,2:16.4:1:28:1:0.38311:3.39536:60:10:0.0014:0:1 0/1:971:105:48,57:404,461:0.1081:2,2:26.8:1:28.9:1:0.91757:1.04064:60:51.5:0.1082:0:1.1 -14 38058622 . AC A 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAATGCAAAATAGCGGCT;RSEQ=CCTAAAATGTCCTGTCGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:26.3:1:31.3:1:1:0:60:8:0.8:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 38060427 . T A 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTTGCACTGGGGGAAAGGT;RSEQ=GTGCATGAAAAATGAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:822:0:0,0:802,20:0:1,0:26:1:30.6:1:1:0:60:90.333:1:0:0.1 0/1:154:7:7,0:143,4:0.0455:1,0:21.4:1:29.4:1:1:0:60:14:0.0458:0:1.1 -14 38060646 . C T 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00079;SOR=1.62726;LSEQ=GGGCTGAGGGCTCGATGGGG;RSEQ=TCCTGGTGGTCACCGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5413:188:85,103:2589,2634:0.0347:2,2:25.5:1:29.9:1:0.26546:1.19102:60:93:0.035:0:1.1 0/1:1392:77:37,40:655,658:0.0553:2,2:22.8:1:29.1:1:0.8149:1.07607:60:37.5:0.0549:0:1.2 -14 38060768 . G A 227 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05818;LSEQ=TTATGCTGCTGCTCCGAGGA;RSEQ=GACATGAGGTTGTTGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7246:172:93,79:3576,3493:0.0237:2,2:25.2:1:30.7:1:0.3961:1.15:60:85:0.0238:0:1.1 0/0:2124:3:3,0:1070,1047:0.0014:2,0:1:0:26.7:1:0.24976:0:60:6:0.0014:0:1 -14 38061106 . T A 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00868;SOR=0;LSEQ=AGAGGCGCCAGAGGGGTCCT;RSEQ=GCGGCTCTCAGGGCCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:755:28:20,8:379,347:0.0371:2,2:22:1:29.7:1:0.05361:2.29:60:56:0.0376:0:1.3 0/0:155:0:0,0:81,74:0:2,0:19.5:1:29.8:1:1:0:60:50.667:1:0:0.1 -14 38061137 . G A 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02635;SOR=Inf;LSEQ=GGGCCGCCCTTGGCGCCGCT;RSEQ=CCCCCGCTTCCGCTCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:787:0:0,0:629,157:0:2,0:23.3:1:32.2:1:1:0:60:48.125:0.9987:0:0.1 0/1:153:2:2,0:116,35:0.0131:2,0:17.5:1:30:0:1:0:60:4:0.0133:0:1 -14 38061649 . C T 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00161;SOR=Inf;LSEQ=CTGCTGCGCACCCATGGCGC;RSEQ=CATGCCGCTCGGGCTCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:960:0:0,0:600,360:0:2,0:23.6:1:30.8:1:1:0:60:49.526:1:0:0.2 0/1:242:4:0,4:134,104:0.0165:2,0:10.8:1:25.3:1:0.03845:0:60:8:0.0169:0:1 -14 38061742 . C T 317 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.63908;LSEQ=CGAGCCCCCCGGCATGCCGG;RSEQ=TACTGCGCCGGGACTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2070:1651:1237,414:307,107:0.7976:2,2:23.2:1:29.7:1:0.75191:1.04:60:102.188:0.7991:0:1.1 1/0:496:355:249,106:99,42:0.7157:2,2:20.6:1:29.1:1:1:1.00344:60:58.167:0.7166:0:1.1 -14 38062062 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACCCGGGGCAAATGGCTAA;RSEQ=CGCCCTCCCCAGACCGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:0,2:2,194:0.0101:1,0:25:1:31.5:1:1:0:60:4:0.0102:0:1 0/0:16:0:0,0:0,16:0:1,0:18.7:1:31.9:1:1:0:60:32:1:0:0.1 -14 38062506 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TAAGTTTTGGAAAAATAAAA;RSEQ=TAAAAGTAGATCCATAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:32.5:1:33.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:36:1:29:1:1:0:60:4:1:0:1 -14 38064009 . G C 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44611;SOR=2.92363;LSEQ=CGAGAAGGCGCCCCCGGCCC;RSEQ=CCTGCCTGCCTTGCCTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:61:57,4:9,1:0.8592:2,2:8:1:31.2:1:0.54307:1.57:60:60:0.8571:0:1.2 1/1:19:18:16,2:1,0:0.9474:0,2:8.5:1:31.1:1:1:0:60:36:0.9474:0:1.3 -14 38064215 . G C 357 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38599;LSEQ=CAATACAACCATCCAGCCCT;RSEQ=TGCGAAGCGACGGGCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3110:2503:785,1718:194,405:0.8048:2,2:24.7:1:31.7:1:0.62493:1.04832:60:74.848:0.8061:0:1.1 1/0:767:471:158,313:105,185:0.6141:2,2:25.6:1:31.2:1:0.48024:1.12418:60:46.1:0.6122:0:1.2 -14 38064347 . CGCG C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GAGCTGCGGGGCGCGGCGTG;RSEQ=GCGGCGGCGGCGGCGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:14:1:30.9:1:1:2.45:60:4:0.3333:0.1667:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 38064738 . G T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTAGGGAAAGAGGGAAAT;RSEQ=GGGAGGGAGGGGGTGTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:25:1:28:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 38068148 . C A 175 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=35.82493;LSEQ=CGCGGGCCCCCACCCCCCAC;RSEQ=CAGATAAGAAGCTTAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2604:8:7,1:261,2335:0.0031:2,2:1:0:25:1:0:62.31:60:7:0.0028:0:1.5 0/1:623:62:28,34:55,505:0.0995:2,2:28.1:1:29.4:1:0:7.52:60:30:0.1015:0:1.1 -14 38068225 . G T 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0316;SOR=Inf;LSEQ=AGACCTGTGGTCGTTAACGC;RSEQ=GTTCAAAGCCGACCCCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:784:0:0,0:10,773:0:1,0:23.9:1:30.8:1:1:0:60:40.211:0.9987:0:0.3 0/1:170:2:0,2:1,166:0.0118:1,0:27.5:1:31.5:1:1:0:60:4:0.0122:0:1.5 -14 38068315 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGTCACACGTGCGTGTG;RSEQ=CTGGCCTTCGCAGGTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:2,157:0.0124:1,0:9.5:1:31:0:1:0:60:4:0.0132:0:1 0/0:24:0:0,0:1,23:0:1,0:19.5:1:31.6:1:1:0:60:48:1:0:0.5 -14 38345849 . A G 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0445;LSEQ=AGTCTGAAGTTTTTCTACAG;RSEQ=GTATATTTATCACCATAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1266:1080:470,610:84,100:0.8531:2,2:25.3:1:30.8:1:0.62979:1.09014:60:66.5:0.8539:0:1.1 0/1:410:84:30,54:145,181:0.2049:2,2:23.3:1:29.8:1:0.17373:1.44072:60:20:0.2:0:1.1 -14 38882673 . T A 103 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=0;LSEQ=AAAGACCTCATCCAAAGGTC;RSEQ=GCATCCTCAAAGACTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:7,3:2,3:0.6667:2,2:27.6:1:31.3:1:0.32867:3.20:60:20:0.6667:0:1.1 0/0:2:0:0,0:1,1:0:2,0:35:0:32:0:1:0:60:4:1:0:0.5 -14 38882750 . G T 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03846;SOR=Inf;LSEQ=AAAATGCTGAAAACCCAAAA;RSEQ=GCCAGAGTGCCTCTTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,6:0:2,0:17.4:1:31.2:1:1:0:60:18:0.9:0:0.3 1/0:3:2:1,1:1,0:0.6667:0,2:10.5:1:28.5:1:1:0:60:4:0.6667:0:1.5 -14 38910644 . G C 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=TAAGAGTCTATGCCATAGGA;RSEQ=GTACCATGGGAGTTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:12.8:1:33:1:1:0:60:10:0.7143:0:1 0/0:1:0:0,0:1,0:0:0,0:3:0:30:0:1:0:60:2:1:0:0 -14 38910715 . A ACAGCAG 93 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=33;MSI=13.000;MSILEN=3;SSF=0.0446;SOR=4.17933;LSEQ=CAACAGAGGCATGAGTGGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:2,2:16,10:0.125:2,2:37.3:1:31.6:1:1:1.57434:60:8:0.125:0:0.3 0/1:21:8:3,5:8,5:0.381:2,2:33.1:1:31:1:0.387:2.54034:59.4:16:0.381:0.0952:0.3 -14 38910766 . TAG T 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00572;SOR=0;LSEQ=CAGAGCCATCTTAAGGTTTA;RSEQ=AGTCTCAGTGAGCTCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:7,9:1,5:0.7273:2,2:21.6:1:31.1:1:0.35116:3.68:60:32:0.7273:0.1364:0 0/0:5:0:0,0:2,3:0:2,0:14:1:30.8:1:1:0:60:10:1:0:0 -14 38912633 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTACACTCCTTCCAATGG;RSEQ=GTATAAGCATTCCCTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 38935684 . A AT 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTCTGGCTGCTCTTAAC;RSEQ=TTTTTTTCTTCATTTTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:0:32:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 38937149 . A C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGCTGGCTGCTGACCTTC;RSEQ=CACAAGGAGCTCAAATGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:21:1:32.7:1:1:0:60:6:1:0:1.3 1/1:2:2:2,0:0,0:1:0,0:9:1:31:0:1:0:60:4:1:0:2.5 -14 39630513 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAACCTATACACATTTA;RSEQ=TTATCAACTCTAGTTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:9,1:0.1667:2,0:42:1:33:1:1:0:60:4:0.1667:0:1 0/0:1:0:0,0:1,0:0:0,0:22:0:32:0:1:0:60:2:1:0:0 -14 39630822 . A T 311 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26223;LSEQ=GCCTTCACTTAAGCTCGCTC;RSEQ=CTCCGTGTCTGGCGAGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1273:1202:674,528:41,29:0.9442:2,2:26.9:1:30.4:1:0.71168:1.10742:60:56.238:0.944:0:1.1 1/1:549:448:239,209:53,47:0.816:2,2:26.9:1:29.5:1:1:1.01:60:39.727:0.8168:0:1.1 -14 39630971 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08111;SOR=Inf;LSEQ=CACTAGCCTCCTGCAGCACC;RSEQ=CAATGACTGTGCTCTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:241,260:0:2,0:22.3:1:30.9:1:1:0:60:44.545:1:0:0.1 0/1:200:2:1,1:102,96:0.01:2,2:23.5:1:28:1:1:1.06221:60:4:0.0103:0:1 -14 39631046 . A G 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02709;SOR=Inf;LSEQ=TCACCAACCTCTAGAAAGGC;RSEQ=GCTTCCAGATGAGAAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:608:0:0,0:249,359:0:2,0:25.9:1:30.4:1:1:0:60:75:1:0:0.1 0/1:262:3:1,2:112,147:0.0115:2,2:20.3:1:25.3:1:1:1.52146:60:2:0.0079:0:1 -14 46002586 . TC T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=TTTACTCTTGGTTCTCTAGT;RSEQ=CTTTAGTTGTGATGTTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:26.4:1:32.6:1:1:0:60:14:1:0:0 0/1:6:2:1,1:0,4:0.3333:0,2:22:1:29.5:1:0.33333:0:55.5:4:0.3333:0:2.5 -14 46730763 . T C 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07886;SOR=7.25322;LSEQ=ATTTTATAACACTATAAATG;RSEQ=ATTTTAGGGATTTGAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:1,0:27,3:0.0323:2,0:9:0:28:0:1:0:60:2:0.0333:0:1 0/1:25:5:5,0:18,1:0.2:1,0:31.6:1:31.4:1:1:0:60:10:0.2083:0:2 -14 46730797 . G T 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=25.89105;LSEQ=GAGGTTTTATTGTTTCTTTT;RSEQ=CCTTTCTTACATTTTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:1,0:57,14:0.0139:2,0:6:0:32:0:1:0:60:2:0.0139:0:1 0/1:59:16:13,3:31,12:0.2712:2,2:17.1:1:27.6:1:0.7376:1.66:60:15:0.2586:0:1.4 -14 46730800 . T C 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTTTTATTGTTTCTTTTGCC;RSEQ=TTCTTACATTTTAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:61,16:0:2,0:24.2:1:31.5:1:1:0:60:154:1:0:0.1 0/1:61:13:8,5:37,11:0.2131:2,2:19.4:1:29.9:1:0.2968:2.07417:60:26:0.2131:0:1.1 -14 46730802 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50272;SOR=0;LSEQ=TTTATTGTTTCTTTTGCCTT;RSEQ=CTTACATTTTAATATATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:63,15:0.025:2,2:23:1:28.5:1:0.36203:4.09878:60:4:0.0263:0:1 0/0:64:0:0,0:47,17:0:2,0:21.3:1:29:1:1:0:60:128:1:0:0.6 -14 46730842 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50397;SOR=0;LSEQ=TTTGGAAATCTTGACTGTAA;RSEQ=CACTATCTGAAAATAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:104,43:0.0134:2,2:25:1:29:1:0.50481:2.40245:60:4:0.0137:0:1 0/0:120:0:0,0:70,50:0:2,0:26.9:1:31.9:1:1:0:60:119:1:0:0.6 -14 46730851 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19639;SOR=Inf;LSEQ=CTTGACTGTAAGCACTATCT;RSEQ=AAAATAAAGTTGAAAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:112,57:0:2,0:25.9:1:31.7:1:1:0:60:83.5:1:0:0.2 0/1:135:2:1,1:78,55:0.0148:2,2:8.5:1:28:1:1:1.41442:60:4:0.0149:0:1 -14 46730853 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20344;SOR=Inf;LSEQ=TGACTGTAAGCACTATCTGA;RSEQ=AATAAAGTTGAAAATATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:112,59:0:2,0:26:1:29.6:1:1:0:60:33.2:1:0:0.2 0/1:141:2:1,1:81,58:0.0142:2,2:40.5:1:31.5:1:1:1.39317:60:4:0.0143:0:1 -14 46730899 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=8.88467;LSEQ=TCTTTGGTGAGTAAATAATA;RSEQ=CAATTAATACCACTTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:25:15,10:110,109:0.1025:2,2:21.1:1:31.2:1:0.40285:1.48:60:50:0.1037:0:1.1 1/0:204:103:53,50:49,52:0.5049:2,2:23.7:1:30.3:1:0.77951:1.12:60:33.333:0.5025:0:1.1 -14 46730999 . CAGTGAGT GAGG 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15196;SOR=Inf;LSEQ=CCAGAAGGGGCAAATCCAAG;RSEQ=AAGTGGTAGAAACAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:19,70:0:2,0:22.2:1:31.6:1:1:0:60:43.5:0.9886:0:0.1 0/1:58:2:1,1:14,42:0.0345:2,2:10:1:28:1:0.45372:2.93:60:4:0.0351:0.0172:0 -14 46731001 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15603;SOR=Inf;LSEQ=AGAAGGGGCAAATCCAAGCA;RSEQ=TGAGTAAGTGGTAGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:17,68:0:2,0:22.3:1:32:1:1:0:60:84:1:0:0.1 0/1:56:2:1,1:12,41:0.0357:2,2:37:1:31:1:0.4202:3.32:60:4:0.0364:0:1 -14 46732517 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGCGATTTTGGTTATC;RSEQ=TGAGTTGAACCTTCATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:30:1:1:0:60:4:1:0:1.5 -14 46853609 . C G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.27494;SOR=2.71757;LSEQ=AAGACGCAGAAACAGTATTG;RSEQ=CCCCAAAGGGCTGGGCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:8,0:10,0:0.4444:0,0:29:1:32.4:1:1:0:60:16:0.4444:0:2 1/0:13:9:8,1:4,0:0.6923:0,2:24.8:1:28.8:1:1:0:60:8:0.6667:0:2.3 -14 46853617 . G T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16619;SOR=3.21651;LSEQ=GAAACAGTATTGCCCCCAAA;RSEQ=GGCTGGGCGTGCTGATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:9:9,0:12,0:0.4286:0,0:32.2:1:31.8:1:1:0:60:18:0.4286:0:1.9 1/0:14:10:8,2:4,0:0.7143:0,2:21.8:1:28.5:1:1:0:60:9:0.6923:0:2.2 -14 46853709 . A T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14318;SOR=0;LSEQ=TTGATAAGGTCAAGCAAGTC;RSEQ=CGTGATCATGGGACAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:4:2,2:37,46:0.046:2,2:16.5:1:29.5:1:1:1.24:56:8:0.0476:0:1.3 0/0:61:0:0,0:28,33:0:2,0:26.3:1:29.3:1:1:0:58.2:60:1:0:0.2 -14 46853878 . G A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=ACTTCAAAGAGGAACCAGGA;RSEQ=TATGGGAGGAACGTGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:3,1:0.2:2,0:30:0:33:0:0.4:0:60:2:0.2:0:1 1/1:3:3:0,3:0,0:1:0,0:14.7:1:31.3:1:1:0:60:6:1:0:1 -14 47138865 . A C 30 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72707;LSEQ=CCTGGGTCTCCAGCTAGCCA;RSEQ=CTGCAGATCTTGAAACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:15,11:0.0714:2,0:16:1:30.5:1:0.50529:0:60:4:0.0741:0:1.5 0/1:19:1:1,0:10,8:0.0526:2,0:11:0:32:0:1:0:60:2:0.0526:0:1 -14 48351255 . A C 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATAAGTAGGCAGTAGT;RSEQ=AGAGATATGGAGATCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:35.7:1:30.7:1:1:0:60:6:0.3:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 48351280 . T A 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATATGGAGATCAACTATAGA;RSEQ=GAGATGAGTCATGGCCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:17:1:30.3:1:1:0:60:6:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 48351622 . G T 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43294;LSEQ=CACTTGAAAAACATCATGTC;RSEQ=TGGTAAAAGAGAAAGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:438:356:161,195:38,44:0.8128:2,2:25.7:1:30.2:1:0.90232:1.04594:60:38.556:0.8107:0:1.2 1/0:400:261:112,149:60,79:0.6525:2,2:26.8:1:29.8:1:1:1.01037:60:86:0.6565:0:1.1 -14 48351664 . A G 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18694;LSEQ=ATTTTTTCCAGTGGAAGAAA;RSEQ=TGTGGATTTTATCAAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:46:21,25:78,175:0.1538:2,2:28.5:1:32.4:1:0.06081:1.88:60:92:0.1544:0:1.8 0/1:244:8:4,4:70,166:0.0328:2,2:14.4:1:32.5:1:0.24946:2.36:60:16:0.0331:0:2.1 -14 48577206 . G A 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGAACCACTTGACTTCA;RSEQ=GAAGAATGAGATTTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:31:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:0,1:0:0,0:8:0:31:0:1:0:60:2:1:0:0 -14 49042348 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=TCTTTATTAGTCTTGCTAGC;RSEQ=GTGTATCAATTTTGTTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:22:1:30.5:1:1:0:50:4:0.2857:0:1 0/0:7:0:0,0:6,1:0:2,0:30.9:1:28.9:1:1:0:51.9:14:1:0:0 -14 49042424 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51234;SOR=0;LSEQ=TTTGAAGGGATTTTTGTGTC;RSEQ=CTATGTCCTTCAGTTCTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:17,13:0.0625:2,2:31.5:1:29.5:1:1:1.29665:60:4:0.0625:0:1 0/0:21:0:0,0:12,9:0:2,0:26.5:1:30.4:1:1:0:60:42:1:0:0.1 -14 49557446 . C T 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=1.63931;LSEQ=GATCCAATGAGTTTTTGGAC;RSEQ=CAGCTTGTAGGTCCCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:733:371:172,199:160,199:0.5061:2,2:27:1:30.2:1:0.6558:1.07:60:91.75:0.5069:0:1.5 1/0:571:358:165,193:100,113:0.627:2,2:25.3:1:29.3:1:0.86251:1.03509:60:70.6:0.6326:0:1.4 -14 49557507 . T A 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04557;SOR=0.11876;LSEQ=ATATATACCCTGGCCTGTGG;RSEQ=ATAGGGGCATTATGGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:381:380:107,273:0,0:0.9974:0,2:24.1:1:29.9:1:1:0:60:37:1:0:1.4 1/1:276:270:91,179:2,4:0.9783:2,2:23.7:1:29:1:1:1.02:60:37.571:0.9777:0:1.5 -14 49557539 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16328;SOR=Inf;LSEQ=ATGGTAGAAAGAGCTTAGTA;RSEQ=AAACCACTAAAATGACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:40,179:0:2,0:23.6:1:31.2:1:1:0:60:35.5:1:0:1 0/1:149:2:1,1:34,113:0.0134:2,2:13.5:1:28:1:0.41584:3.29:60:4:0.0135:0:1.5 -14 49557544 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15882;SOR=Inf;LSEQ=AGAAAGAGCTTAGTAGAAAC;RSEQ=ACTAAAATGACCTCCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:32,171:0:2,0:23.2:1:31.9:1:1:0:60:49.75:1:0:0.9 0/1:135:2:1,1:28,105:0.0148:2,2:23.5:1:27.5:1:0.38474:3.70:60:4:0.0149:0:2 -14 49557562 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13052;SOR=Inf;LSEQ=ACCACTAAAATGACCTCCCA;RSEQ=TAATATTATCTCTGACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:18,142:0:2,0:21.5:1:31.3:1:1:0:60:21.857:1:0:0.8 0/1:91:2:1,1:10,79:0.022:2,2:6.5:1:28.5:1:0.22833:7.58:60:4:0.0225:0:2 -14 49557672 . C A 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28871;SOR=0;LSEQ=CTCCATCAGCCAGAAATAGC;RSEQ=AGTCTCATTGGATCATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:25.8:1:30:1:1:0:60:10:0.2632:0:1.2 0/0:6:0:0,0:0,6:0:0,0:24.5:1:32.3:1:1:0:60:12:1:0:0.3 -14 49557843 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAAAGGGTAAAAATAAAA;RSEQ=TGGCCATTTAAACCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:20.5:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 50232682 . C CG 25 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGTCTCCAGGTACCCA;RSEQ=GGGGCTTGGAACTATACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:25.1:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 50234258 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=TGGTTACGGCTTCGGAAACG;RSEQ=TTTTCAAGCCAACTCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:17,13:0.0625:2,2:32.5:1:29.5:1:1:1.29665:60:4:0.0625:0:1 0/0:32:0:0,0:17,15:0:2,0:27.5:1:31.2:1:1:0:60:64:1:0:0.2 -14 50234786 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTGAGCGGCAGCCTCGC;RSEQ=TCCGGAGCTCGGCGGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 -14 50455087 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12857;LSEQ=TCACGATCCTGTGTGCAGAA;RSEQ=GCTATTGTGGAAAGCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:428:304:136,168:52,72:0.7103:2,2:25.3:1:30.3:1:0.66775:1.12:60:59.8:0.7069:0:1.1 0/1:414:99:47,52:150,165:0.2391:2,2:24.3:1:30.1:1:1:1.00579:60:198:0.2426:0:1.1 -14 50456628 . G TTT 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TTCCACATTGATTTAAATTG;RSEQ=TTTTTTTGCTTTTATGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:1:30.7:1:1:0:60:4:1:0.5:1.5 -14 50550133 . C CTCTG 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTCTATCCAGCCAATCTCT;RSEQ=TCTGTCTTTCTCTCTCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16:1:34.1:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 50550946 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21463;SOR=Inf;LSEQ=GGATCTCTGGATGGTATTTA;RSEQ=CAAACAGAAATACAGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:141,60:0:2,0:23.2:1:32:1:1:0:60:99.5:1:0:0.2 0/1:174:2:1,1:120,52:0.0115:2,2:11.5:1:27:1:0.51764:2.29535:60:4:0.0116:0:1.5 -14 50551034 . A G 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.35815;LSEQ=AAATATGTCCCACATACTGC;RSEQ=TGGGGTACATTTAAGACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:408:228:106,122:83,95:0.5588:2,2:25.1:1:30.7:1:1:1.00555:60:44.6:0.5603:0:1.1 1/0:407:305:152,153:48,51:0.7494:2,2:25.4:1:30.2:1:0.81829:1.06:60:75.25:0.7506:0:1.1 -14 51598192 . T G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATCCAGCACTTTCAGAG;RSEQ=CCGAGGTGGGCAGAGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 51598375 . C T 87 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04412;SOR=Inf;LSEQ=CAGGGACAGAATTCAGATCT;RSEQ=CCTGGGCCTGAGCCTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:12.2:1:28.6:1:1:0:60:10:1:0:0.2 1/0:12:7:4,3:1,3:0.5833:2,2:19.7:1:31.1:1:0.54545:3.52:60:14:0.5833:0:1.1 -14 51598580 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20588;SOR=Inf;LSEQ=CCCAACTGGGTGAGACCCTC;RSEQ=AACATGGGTTGTCAGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:39.4:1:31.8:1:1:0:60:18:1:0:0.2 0/1:8:2:1,1:2,4:0.25:2,2:16:1:29:1:1:1.83:60:4:0.25:0:1.5 -14 51598610 . A G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=TGTCAGACACCATATACAGG;RSEQ=GCAATCCTAGTGGCATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:25:1:30:1:1:2.24:60:4:0.2222:0:1 1/0:3:2:0,2:1,0:0.6667:0,0:40:1:31:1:0.33333:0:60:4:0.6667:0:1.5 -14 51598843 . T C 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02419;SOR=Inf;LSEQ=AACAATAGCATCATCAACAA;RSEQ=AACAAAAACAACAAAAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:22.6:1:29.6:1:1:0:60:44:1:0:0.1 0/1:10:3:1,2:4,3:0.3:2,2:21.7:1:28.3:1:1:2.41422:60:6:0.3:0:1 -14 51598867 . CA C 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.01217;SOR=Inf;LSEQ=AAAAACAACAAAAAGACCCC;RSEQ=AAAAACCCCATCCAAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:34.2:1:29.6:1:1:0:60:24:1:0:0.4 0/1:14:4:2,2:6,4:0.2857:2,2:31.8:1:30.5:1:1:1.45647:60:8:0.2857:0:0.8 -14 51598912 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=AGCCTCAAAGACTGAAACAA;RSEQ=ACCAACTCACAAAGACGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:8,13:0:2,0:18.3:1:30.1:1:1:0:60:20:1:0:0.4 0/1:14:2:1,1:6,6:0.1429:2,2:21.5:1:28.5:1:1:1:60:4:0.1429:0:1 -14 51605639 . A G 55 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCTGCATTTAGAGGCTG;RSEQ=TAAAGGTTACAGTACAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:26.5:1:27.5:1:1:0:60:3:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 51606001 . C G 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67923;SOR=0.92376;LSEQ=AGGACTTTGATTCTGTCTTG;RSEQ=TCCTCCCTTCAGCACTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:147:75,72:91,92:0.4455:2,2:28:1:31.3:1:0.82557:1.05:60:48:0.4404:0:1.1 0/1:270:115:57,58:76,79:0.4259:2,2:25.3:1:30.9:1:1:1.02:60:114:0.4318:0:1.1 -14 51606027 . G A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25226;SOR=0;LSEQ=CCTTCAGCACTTGACCACTG;RSEQ=GGTGTGACTTCTGTTGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:118,171:0.0103:2,2:5.3:1:27.3:1:0.57031:2.89:60:6:0.0105:0:1 0/0:254:0:0,0:104,150:0:2,0:26.7:1:29.9:1:1:0:60:41.333:1:0:0.4 -14 51606336 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAAGCAAAGAACTGAATG;RSEQ=TGTGCAACTACTTTCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36.5:1:31:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 52143744 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTTACTTGCTTTTTTCC;RSEQ=TAATGTTGTTTTTTGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 52145105 . T C 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGAGACTTTTGCAGAAA;RSEQ=TATTTTGTGGACAGTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:12.5:1:32.3:1:1:0:60:8:1:0:1 1/1:3:3:3,0:0,0:1:0,0:18.3:1:33:0:1:0:60:6:1:0:1 -14 52145244 . T C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03366;SOR=0.32405;LSEQ=TGACCAACGCTGACTCCCAT;RSEQ=GTGGGGGAAAAGTGTGTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:20:9,11:15,17:0.3846:2,2:24.8:1:30.8:1:1:1.07686:60:40:0.3922:0:1.2 0/1:36:6:2,4:14,16:0.1667:2,2:24.2:1:30.7:1:0.67224:1.72372:60:12:0.1667:0:1.2 -14 52640477 . C G 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00033;SOR=4.94032;LSEQ=ATAAAGTTTTGATAAACCAT;RSEQ=CAATGCCTATCTGCCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:6:5,1:107,16:0.0465:2,2:25.3:1:30.8:1:0.57941:1.33418:60:12:0.0465:0:1.2 0/1:123:24:22,2:83,16:0.1951:2,2:23.8:1:31:1:0.5214:2.11:60:23:0.1933:0:1.4 -14 52640520 . AAG A 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.28256;SOR=0.82633;LSEQ=CCCCCAAAAAAAGAAAAAGA;RSEQ=AAGGGCAGTGATATTAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:129:85,44:129,56:0.4095:2,2:23.3:1:30.3:1:0.53836:1.19176:60:258:0.4135:0.0762:1 0/1:302:110:71,39:124,68:0.3642:2,2:23.6:1:30.2:1:1:1.00165:60:220:0.3667:0.053:1.1 -14 52640564 . C A 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00422;SOR=0.68042;LSEQ=CTTTCTAAATATATTTAAGC;RSEQ=TCGTTTAAAGGAAGTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:206:113,93:148,133:0.4221:2,2:27.6:1:30.5:1:0.64663:1.09:60:205:0.4236:0:1.1 0/1:473:157:85,72:165,149:0.3319:2,2:28.8:1:29.3:1:0.76948:1.07:60:51.333:0.3341:0:1.2 -14 52640760 . ACTA T 108 MAF0.05;MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=42;MSI=15.000;MSILEN=3;SSF=0.01375;SOR=0.08954;LSEQ=CAGAGCTAGCCAAAATGCTT;RSEQ=CTACTACTACTACTACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:0,11:0,10:0.4231:0,0:22.7:1:31.4:1:1:0:60:22:0.44:0.1154:0.6 0/1:17:1:0,1:0,16:0.0588:1,0:44:0:32.8:0:1:0:60:2:0.0588:0:1 -14 52640795 . T C 68 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=3;SSF=1;SOR=0.45926;LSEQ=ACTACTACTACTACTACTAC;RSEQ=ACTACTAAAATCTTCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:0,7:0.3636:0,0:23.3:1:34:0:1:0:60:8:0.4:0:2.8 0/1:5:1:0,1:0,4:0.2:0,0:23:0:32:0:1:0:60:2:0.2:0:2 -14 52640913 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGACCACCCTGGCTAACA;RSEQ=GGTGTAACCCCGTCTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:15.5:1:29:1:1:0:59.5:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 54776972 . C A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=TGGAGGACTGAATTAAGATT;RSEQ=CACTCGGGCTGGAGGTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:43.5:1:25:1:1:1.58108:60:4:0.2:0:1 0/0:7:0:0,0:4,3:0:2,0:28.1:1:32:1:1:0:60:14:1:0:0.1 -14 54908166 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16429;SOR=Inf;LSEQ=ACCGCCACCGCTACCGCCGC;RSEQ=GCGCCAGCCCTCTCAGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:25,8:0:2,0:13.7:1:30.3:1:1:0:60:66:1:0:0.1 0/1:23:2:1,1:18,3:0.087:2,2:18:1:29:1:0.32411:5.33862:60:4:0.087:0:1 -14 55397563 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15485;SOR=Inf;LSEQ=TTCATTTCTCTGGGATAAAT;RSEQ=CCCAAGAGGGCAATTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:0:2,0:27.9:1:31.5:1:1:0:60:46:1:0:0.2 0/1:31:2:1,1:11,17:0.0645:2,2:39.5:1:29.5:1:1:1.52:60:4:0.0645:0:1 -14 55397566 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15892;SOR=Inf;LSEQ=ATTTCTCTGGGATAAATGCC;RSEQ=AAGAGGGCAATTGCTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:24,22:0:2,0:28.2:1:31:1:1:0:60:45:1:0:0.2 0/1:31:2:1,1:12,17:0.0645:2,2:31:1:29.5:1:1:1.40:60:4:0.0645:0:1 -14 55878636 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGAAGGGGGGCTGGGAT;RSEQ=CCGGCGAGCCCCCGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 55880341 . G C 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TCCATTGGTTCTAAGTGCTT;RSEQ=TCTGGGTGGAGCAGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:29:1:32:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:0:0,0:16:0:34:0:1:0:60:2:1:0:0 -14 55880714 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49803;SOR=Inf;LSEQ=GGCCAAAGGAACAACTCCAT;RSEQ=TTTTCTAAAAGGCCTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:73,30:0:2,0:22.8:1:31.4:1:1:0:60:206:1:0:0.5 0/1:109:2:1,1:71,35:0.0183:2,2:9.5:1:28.5:1:1:2.01429:60:4:0.019:0:2 -14 55880730 . A G 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.47142;SOR=0.82028;LSEQ=CCATCTTTTCTAAAAGGCCT;RSEQ=GAGAACATGTATCAGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:136:69:48,21:38,29:0.5074:2,2:24.2:1:31.6:1:0.1549:1.74:60:138:0.5111:0:1.1 0/1:142:65:38,27:52,25:0.4577:2,2:22:1:30.2:1:0.29678:1.47376:60:31.5:0.45:0:1.3 -14 55880744 . A G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22245;SOR=0;LSEQ=AGGCCTAGAGAACATGTATC;RSEQ=GGTGCCTCACCTCTTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:104,64:0.0117:2,2:8:0:31.5:1:1:1.62012:60:4:0.0117:0:1 0/0:191:0:0,0:122,69:0:2,0:22.4:1:29.9:1:1:0:60:62.667:1:0:0.6 -14 55880745 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24939;SOR=Inf;LSEQ=GGCCTAGAGAACATGTATCA;RSEQ=GTGCCTCACCTCTTTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:105,68:0:2,0:22.9:1:31.3:1:1:0:60:56.667:1:0:0.5 0/1:189:3:1,2:118,67:0.0159:2,2:5:1:29.3:1:0.55548:3.49779:60:6:0.0161:0:1 -14 55880810 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24871;SOR=Inf;LSEQ=CTGGAAGATGGCCCTTCCGG;RSEQ=TAAAAGGAAACGCATTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:104,119:0:2,0:27.1:1:32.1:1:1:0:60:222:1:0:0.2 0/1:233:3:2,1:112,118:0.0129:2,2:23.7:1:27.7:1:0.61541:2.10:60:6:0.0129:0:1.7 -14 55880918 . A G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20739;SOR=0.48296;LSEQ=TCAGTTTTTAAAATAACACA;RSEQ=AAGGAGTCATTTTGAATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:22:0,22:0,14:0.6111:1,1:24.5:1:30.5:1:1:0:60:44:0.6286:0:1 0/1:28:12:0,12:0,16:0.4286:1,0:15.8:1:30.1:1:1:0:60:24:0.4286:0:1.3 -14 57024413 . T A 25 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14106;SOR=Inf;LSEQ=GTCATGTAACGAGCGGCCCT;RSEQ=CCAAGTTCTAACAACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:44,20:0:2,0:19.3:1:29.7:1:1:0:60:63:1:0:0.1 0/1:39:2:1,1:24,13:0.0513:2,2:13:0:25:1:1:1.81575:60:4:0.0513:0:1 -14 57141318 . T G 61 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTACTGAAGGAGAACTTG;RSEQ=GGGTCAGTGTGGATGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:5,0:0.5:0,2:26.4:1:26.6:1:1:0:60:4:0.4444:0:2.4 1/1:1:1:1,0:0,0:1:0,0:39:0:32:0:1:0:60:2:1:0:1 -14 57141401 . G A 102 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31484;SOR=0;LSEQ=AGGAACAGGTGAAGGAAACA;RSEQ=CTTTCAGACACAAGTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:11,0:32,0:0.2558:1,0:23.3:1:29.5:1:1:0:60:10:0.2439:0:1.1 0/0:6:0:0,0:5,1:0:2,0:27.5:1:32.3:1:1:0:60:12:1:0:0.2 -14 57141480 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12337;SOR=Inf;LSEQ=AACAGGTAAAGCAGGGGAAG;RSEQ=CCTTTTGTGAAGCAGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:129,40:0:2,0:21.7:1:31.5:1:1:0:60:41.25:1:0:0.2 0/1:92:2:1,1:73,17:0.0217:2,2:8:0:31:0:0.35475:4.20162:60:4:0.022:0:1.5 -14 57141489 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52082;SOR=0;LSEQ=AGCAGGGGAAGCCCTTTTGT;RSEQ=AAGCAGAGATACAGAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:146,44:0.0104:2,2:15.5:1:28:1:0.41476:3.29229:60:4:0.0105:0:1 0/0:125:0:0,0:94,31:0:2,0:22.3:1:31.6:1:1:0:60:61.5:1:0:0.2 -14 57141493 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15833;SOR=Inf;LSEQ=GGGGAAGCCCTTTTGTGAAG;RSEQ=AGAGATACAGAAAGATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:152,50:0:2,0:24.7:1:31.7:1:1:0:60:39.4:1:0:0.1 0/1:134:2:1,1:96,36:0.0149:2,2:36.5:1:29.5:1:0.4775:2.64405:60:4:0.0152:0:1 -14 57141496 . A T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27374;SOR=0;LSEQ=GAAGCCCTTTTGTGAAGCAG;RSEQ=GATACAGAAAGATGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:2,1:156,52:0.0142:2,2:34.3:1:29:1:1:1.49685:60:6:0.0146:0:1 0/0:145:0:0,0:104,41:0:2,0:23.2:1:29.7:1:1:0:60:144:1:0:0.2 -14 57141603 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2916;LSEQ=CCAGGTTAGGCACAGCTGGG;RSEQ=TTGGCTTCAGGCTATTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:304:126,178:57,76:0.6941:2,2:24:1:29.7:1:0.83325:1.05937:60:100.333:0.6968:0:1.6 0/1:352:140:69,71:107,105:0.3977:2,2:24.7:1:29.3:1:0.9133:1.04847:60:69:0.3977:0:1.7 -14 57141647 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22042;LSEQ=TCTCATTTCCTGGGATTGGC;RSEQ=GAGCAGGATGTCTTTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:281:213:66,147:20,48:0.758:2,2:26.6:1:30.1:1:0.88041:1.08:60:41.6:0.7564:0:1.8 0/1:260:106:41,65:61,93:0.4077:2,2:25:1:30:1:0.89786:1.03972:60:34.333:0.4104:0:1.8 -14 57141681 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49969;SOR=0;LSEQ=TTCTCATTGCCATGACAGAA;RSEQ=CCAAGAGGGAAAACCCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:33,132:0.012:2,2:37:1:30:1:0.36671:3.96:60:4:0.0121:0:2 0/0:151:0:0,0:41,109:0:2,0:24.6:1:31.8:1:1:0:60:49:0.9932:0:0.6 -14 57141867 . G T 44 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.52381;SOR=0.26566;LSEQ=GGGCTTCGAACTTTATAAGA;RSEQ=AGTGGAAGCAACATGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:41:1:28.3:1:1:0:60:6:0.6:0:1.7 0/1:4:1:0,1:0,3:0.25:0,0:16:0:30:0:1:0:60:2:0.25:0:1 -14 57141908 . G T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGAACATATGGGTTTGG;RSEQ=GTATTCAGCGTTACCTAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:7:1:31.5:1:1:0:60:4:0.6667:0:2 0/0:1:0:0,0:0,1:0:0,0:16:0:25:0:1:0:60:2:1:0:0 -14 57255538 . C CA 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50465;SOR=0;LSEQ=TTATGGTTTCTTTGACTGTT;RSEQ=AAAAAAAGATACAGAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:86,46:0.0148:2,2:30.5:1:29:1:1:1.86036:60:4:0.0149:0:0 0/0:107:0:0,0:66,41:0:2,0:28:1:30.7:1:1:0:60:34.667:1:0:0.3 -14 57255551 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50404;SOR=0;LSEQ=GACTGTTCAAAAAAAGATAC;RSEQ=GAATAGATGTGACAAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:86,60:0.0135:2,2:16:1:29.5:1:1:1.42975:60:4:0.0137:0:1 0/0:119:0:0,0:74,45:0:2,0:28.6:1:30.2:1:1:0:60:238:1:0:0.3 -14 57255601 . A G 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAAATGAATTTAGCCATGC;RSEQ=GTTATGCTACATATGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:88,89:0:2,0:24.4:1:30.7:1:1:0:60:176:1:0:0.1 0/1:145:49:22,27:44,52:0.3379:2,2:21.5:1:29.1:1:1:1.03821:60:98:0.3427:0:1.1 -14 57255604 . T C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23785;SOR=0.40304;LSEQ=AATGAATTTAGCCATGCAGT;RSEQ=ATGCTACATATGTAGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:9:4,5:80,84:0.052:2,2:19.9:1:31:1:1:1.18928:60:18:0.052:0:1.1 0/1:139:3:1,2:62,74:0.0216:2,2:41.3:1:31.7:1:1:1.66972:60:6:0.0216:0:1.3 -14 57255651 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.50697;SOR=0;LSEQ=GTATATAATATTATATCATC;RSEQ=CTCTTCTTGAATTCTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:50,83:0.0148:2,2:32:1:30.5:1:1:1.65:60:4:0.0149:0:1 0/0:103:0:0,0:39,64:0:2,0:26.6:1:29.9:1:1:0:60:206:1:0:0.4 -14 57542776 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21212;SOR=Inf;LSEQ=ACGCTGACTCCTGACTCTAG;RSEQ=TTATTTGTTCAGTAGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:0:2,0:24.2:1:30.3:1:1:0:60:23:1:0:0.2 0/1:21:2:1,1:10,9:0.0952:2,2:27:0:30:1:1:1.10554:60:4:0.1:0:1 -14 57732994 . T G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=6.71077;LSEQ=AAAGATACTTCCCGTGACTC;RSEQ=TACTACAACCTAGATGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:28:14,14:299,229:0.0504:2,2:27.5:1:29.8:1:0.55928:1.30503:60:13:0.0474:0:2.5 0/1:468:123:69,54:193,151:0.2628:2,2:24.6:1:30.1:1:1:1.00029:60:60.5:0.2613:0:2.7 -14 57733016 . G A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.81939;LSEQ=ACTACAACCTAGATGCTATG;RSEQ=CAGTAGTTACAGGAAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:30:12,18:298,273:0.0499:2,2:24.4:1:30.3:1:0.26058:1.63601:60:60:0.0504:0:2.7 0/1:496:131:68,63:191,174:0.2641:2,2:26.4:1:28.6:1:1:1.01696:60:25.2:0.2598:0:2.8 -14 57733023 . T C 281 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29837;SOR=1.15772;LSEQ=CCTAGATGCTATGGCAGTAG;RSEQ=TACAGGAAACTGAGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:599:438:222,216:76,84:0.7312:2,2:26.7:1:32.1:1:0.51846:1.14:60:61.571:0.733:0:1.2 1/0:498:378:199,179:60,59:0.759:2,2:26.5:1:31.5:1:0.67552:1.09:60:53:0.7556:0:1.7 -14 57733423 . TTA T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATGTATGTTATATATACG;RSEQ=TATATATATATGTGTATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:34:1:31:1:1:0:60:6:0.6:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 59555994 . G A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01764;SOR=5.90054;LSEQ=TGAACACTACCTGCTCACCA;RSEQ=GTGCAAGGAACTGATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:6:5,1:31,0:0.1622:1,2:23.8:1:28.8:1:0.16216:0:60:12:0.1667:0:1 1/0:11:6:6,0:5,0:0.5455:0,0:15.7:1:27.8:1:1:0:60:5:0.5:0:1.2 -14 59556100 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51779;SOR=0;LSEQ=GCACAACATCCCCTGGCAGG;RSEQ=CCACTTGCAGTCCAGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:156,37:0.0103:2,2:34:1:29.5:1:0.35258:4.17369:60:4:0.0107:0:1 0/0:131:0:0,0:106,25:0:2,0:23.6:1:31.6:1:1:0:60:64.5:1:0:0.2 -14 59556112 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58375;SOR=2.57711;LSEQ=CTGGCAGGCCCACTTGCAGT;RSEQ=CAGTCTGGCAACATGGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:1,0:164,53:0.0046:2,0:18:0:11:0:1:0:60:0:0:0:3 0/1:170:2:1,1:123,45:0.0118:2,2:29.5:1:28:1:0.46913:2.71443:60:4:0.0121:0:1.5 -14 59556134 . C T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32051;SOR=3.97053;LSEQ=AGTCTGGCAACATGGTCATG;RSEQ=AGACAGAGTGAAAGGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:1:0,1:212,113:0.0031:2,0:1:0:25:0:0.34969:0:60:2:0.0031:0:1 0/1:248:3:1,2:156,89:0.0121:2,2:9.7:1:25.7:1:0.55629:3.48713:60:6:0.0121:0:1.7 -14 59556157 . A T 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.40892;LSEQ=ACAGAGTGAAAGGGCTTTTA;RSEQ=GATTTAAAGTCAAGAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:22:9,13:261,181:0.0474:2,2:23.1:1:30.1:1:0.12038:2.07954:60:44:0.0485:0:2 0/1:344:62:38,24:156,126:0.1802:2,2:25.8:1:29.9:1:0.40085:1.28:60:124:0.1813:0:1.7 -14 59556205 . G C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.51516;LSEQ=CAGTGCAGAAGACAGGAGAT;RSEQ=TCACCTAATCGTTTTAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:118:62,56:245,243:0.1941:2,2:27.8:1:31.8:1:0.68215:1.10:60:117:0.195:0:1.4 1/0:427:261:125,136:80,86:0.6112:2,2:26.8:1:31.3:1:1:1.01207:60:51.2:0.6095:0:1.3 -14 59556269 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30483;SOR=4.71151;LSEQ=TTTCTGTAAGTCAAGGCCTA;RSEQ=CCAACTGGCTTAGGCGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:1:1,0:102,257:0.0028:2,0:47:0:32:0:0.28611:0:60:2:0.0028:0:1 0/1:231:3:2,1:81,147:0.013:2,2:10:1:27.3:1:0.29368:3.61:60:6:0.013:0:1.7 -14 59556292 . A ATCATTCAT 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=5.000;MSILEN=4;SSF=0;SOR=3.87652;LSEQ=AACTGGCTTAGGCGTGGTTC;RSEQ=TCATTCATTCATTCACTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:23:2,21:39,164:0.0983:2,2:32:1:31.2:1:0.26702:2.48926:59.3:46:0.0987:0.0128:0.3 0/1:141:42:9,33:25,55:0.2979:2,2:23.6:1:29.1:1:0.29279:1.65993:59.9:84:0.2979:0.1064:0.4 -14 59556318 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10558;SOR=Inf;LSEQ=CATTCATTCACTTATGAATG;RSEQ=CATGCTTTTTAGCCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:6,127:0:1,0:25.2:1:30.3:1:1:0:60:266:1:0:0.1 0/1:65:2:1,1:5,58:0.0308:2,2:13.5:1:28:1:0.1774:10.68:60:4:0.0308:0:1 -14 59556354 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.01853;LSEQ=TTTCTGCAGTATATAATGAA;RSEQ=AGTAGAACCAAGTTCACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:8:0,8:0,56:0.125:1,0:14.3:1:33:1:1:0:60:16:0.127:0:1 1/0:24:19:0,19:0,5:0.7917:0,1:18.8:1:31.9:1:1:0:59.7:38:0.7917:0:1.1 -14 59556404 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02809;SOR=0.11467;LSEQ=GTGCTTGTTTTGGGATATCT;RSEQ=TATAAAAGCAAGACTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:0,16:0,5:0.7619:0,1:20.9:1:31.3:1:1:0:60:32:0.7619:0:1.1 0/1:8:2:0,2:1,5:0.25:2,0:28.5:1:33:0:1:0:60:4:0.25:0:1.5 -14 61655082 . A C 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00057;SOR=Inf;LSEQ=CTCAGCTTCTGCCCCCGCCC;RSEQ=CAGCCTGCAAACCGAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:20,8:0:2,0:22:1:29.8:1:1:0:60:56:1:0:0 0/1:14:6:3,3:8,0:0.4286:0,2:27.7:1:30:1:0.05495:0:60:12:0.4286:0:1.3 -14 61655194 . GC G 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01765;SOR=Inf;LSEQ=GGCAGCGGCTCGGGCAGGCG;RSEQ=CTTGTGGCTCCGCAACCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,17:0:2,0:25.8:1:31.2:1:1:0:60:52:1:0:0.1 0/1:23:5:2,3:5,13:0.2174:2,2:24.2:1:31.8:1:0.62139:1.69:60:10:0.2174:0.087:0.4 -14 61655422 . A AGTGTGTGT 27 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=35;MSI=21.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCACCCCCAGACGTTGCTGT;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:34:0:29:0:1:0:60:2:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:19.5:1:27.4:1:1:1:51.5:4:0.5:0.25:0 -14 61799651 . G T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50265;SOR=0;LSEQ=CTGTGGTCCTTCCGGTGTCA;RSEQ=AGTTTTGTGGTTCTGGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:136,27:0.0121:2,2:46:0:29.5:1:0.31146:4.96456:60:4:0.0121:0:1 0/0:137:0:0,0:106,31:0:2,0:20.5:1:30.8:1:1:0:60:33.25:1:0:0.1 -14 61799771 . C G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.43515;LSEQ=TCTGAAATTATTTTGGGAAG;RSEQ=GCACCCAAAAGTCATACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:111:54,57:145,188:0.25:2,2:28.3:1:31:1:0.37869:1.23:60:222:0.2528:0:1.1 1/0:366:261:122,139:47,57:0.7131:2,2:24.6:1:30:1:0.81682:1.06:60:42.5:0.7163:0:1.1 -14 61799782 . G T 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06899;SOR=0;LSEQ=TTTGGGAAGCGCACCCAAAA;RSEQ=TCATACGTGTATTAGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:5:2,3:195,252:0.011:2,2:19.4:1:29.6:1:1:1.16032:60:10:0.0111:0:1.8 0/0:365:0:0,0:161,204:0:2,0:24.6:1:31.3:1:1:0:60:730:1:0:0.7 -14 61799788 . C T 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGCGCACCCAAAAGTCATA;RSEQ=GTGTATTAGCCTAATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:58:20,38:159,224:0.1315:2,2:25.7:1:30.2:1:0.38945:1.34776:60:57:0.1323:0:1.1 0/0:353:0:0,0:155,198:0:2,0:24.7:1:30:1:1:0:60:87.25:1:0:0.7 -14 61799843 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17967;SOR=Inf;LSEQ=TATTTATTTGCAAGCTGTGG;RSEQ=CCTCTTAGATGCTTTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:74,189:0:2,0:25.4:1:31.7:1:1:0:60:86.667:1:0:0.3 0/1:194:2:1,1:59,133:0.0103:2,2:14.5:1:29:1:0.52401:2.24:60:4:0.0104:0:1.5 -14 61799920 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=5.85898;LSEQ=AGAGCAGATTCCATCTAAAT;RSEQ=AGTGCTTTTGAAACTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:18:0,18:1,41:0.3:1,1:21.7:1:29.1:1:1:0:60:36:0.3051:0:1.1 1/0:25:18:0,18:0,7:0.72:0,1:25.8:1:28.1:1:1:0:60:36:0.72:0:1 -14 61800094 . G A 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGGACACAGGACCTCAG;RSEQ=TTGAGAAACCTCAGTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:18.8:1:32.8:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 61884484 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00323;SOR=Inf;LSEQ=TTTAAAAAAAGAAAGAAAGA;RSEQ=GAGCCTGTAGTGTGATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:113,3:0:1,0:21.5:1:32.6:1:1:0:60:115:1:0:0.1 0/1:56:5:5,0:49,2:0.0893:1,0:24.6:1:30.4:1:1:0:60:10:0.0893:0:1.2 -14 61884632 . T C 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGATGAGGAAGCCACACA;RSEQ=GGGTTATTTCTCTACTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:0:0,0:297,354:0:2,0:24.9:1:30.1:1:1:0:60:53.25:1:0:0.1 0/1:479:73:34,39:200,206:0.1524:2,2:24:1:30.2:1:0.70413:1.1134:60:146:0.1537:0:1.9 -14 61884646 . A G 204 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACACATGGGTTATTTCTCT;RSEQ=CTGAAAGGGTAGAGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:253,348:0:2,0:25.5:1:28.8:1:1:0:60:74.125:1:0:0.1 0/1:441:83:40,43:160,198:0.1882:2,2:23.5:1:32.1:1:0.62486:1.15:60:82:0.1872:0:1.9 -14 61884724 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17642;SOR=Inf;LSEQ=GTGTCTTTTGCCATCTCAAA;RSEQ=GCCAGCTGTTTATTGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:54,196:0:2,0:23.6:1:31.4:1:1:0:60:124:0.992:0:0.1 0/1:183:2:1,1:49,132:0.0109:2,2:35:0:31:0:0.47289:2.68:60:4:0.011:0:1.5 -14 62805991 . A G 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAATTTAAGGGCCTTTTCT;RSEQ=TCTTGACTCTTCCTGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:19.5:1:29.3:1:1:0:60:3:0.5:0:1.3 1/1:1:1:0,1:0,0:1:0,0:1:0:29:0:1:0:60:2:1:0:2 -14 62907490 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49194;SOR=0;LSEQ=GAAAAAGGAGATATTGCATA;RSEQ=TGGTGACTGGACCCTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:6.5:1:29:1:1:1.62:60:4:0.1111:0:1 0/0:14:0:0,0:5,9:0:2,0:21.9:1:30.6:1:1:0:60:28:1:0:0.1 -14 62907565 . A G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTTGCAGCAGCAGCAAA;RSEQ=ACCCAGGAATGGTAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:19.7:1:33:0:1:0:60:6:1:0:1 1/1:2:2:0,2:0,0:1:0,0:18:1:33:0:1:0:60:4:1:0:1.5 -14 63589720 . GC G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16777;SOR=Inf;LSEQ=CAAAAGATAGAAAGGCCCAT;RSEQ=CCCGGGTCCACAACCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:179,61:0:2,0:23:1:31.5:1:1:0:60:47:1:0:0.1 0/1:167:2:1,1:118,47:0.012:2,2:27:1:31.1:1:0.49347:2.49486:60:4:0.0123:0.006:0 -14 63589724 . C T 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00161;SOR=Inf;LSEQ=AGATAGAAAGGCCCATGCCC;RSEQ=GGGTCCACAACCACCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:191,65:0:2,0:23.1:1:30.6:1:1:0:60:84.333:1:0:0.1 0/1:173:7:5,2:117,49:0.0405:2,2:18.9:1:30.9:1:1:1.05:60:14:0.0414:0:1 -14 63589734 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16113;SOR=Inf;LSEQ=GCCCATGCCCCGGGTCCACA;RSEQ=CCACCAGCTTTGCTGGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:212,84:0:2,0:24.7:1:29.8:1:1:0:60:73:1:0:0.1 0/1:199:2:1,1:134,62:0.0101:2,2:23:1:31:1:0.53623:2.1521:60:4:0.0103:0:1 -14 63589819 . G T 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGGCTACATGTTTGGTAAAG;RSEQ=GATCTATTTCGCTGACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:598:0:0,0:341,257:0:2,0:24.4:1:30.8:1:1:0:60:48.833:1:0:0.1 0/1:391:12:6,6:210,169:0.0307:2,2:30.3:1:29.6:1:0.77337:1.2419:60:24:0.0311:0:1.1 -14 63589829 . C T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGGTAAAGGGATCTATTT;RSEQ=GCTGACATGGCCTCCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:0:0,0:331,269:0:2,0:26.1:1:30.6:1:1:0:60:149:1:0:0.1 0/1:412:19:10,9:216,177:0.0461:2,2:23.8:1:29.4:1:1:1.09805:60:38:0.0465:0:1.1 -14 63590051 . G T 45 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02443;SOR=Inf;LSEQ=ATGGTGCAGAGGTTCCTCTT;RSEQ=GGACTGGGATTTCATCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:559:0:0,0:268,291:0:2,0:25:1:31.3:1:1:0:60:68.875:1:0:0.1 0/1:367:4:1,3:187,173:0.0109:2,2:15:1:22.8:1:0.35715:3.23319:60:3:0.0083:0:1 -14 64619727 . A G 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00023;SOR=Inf;LSEQ=ATCTCCATACCCCAAACCCA;RSEQ=CAGAGTATCTGGCATTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:55,6:0:2,0:24:1:30.6:1:1:0:60:122:1:0:0.2 0/1:51:10:9,1:34,7:0.1961:2,2:26.4:1:30.5:1:1:1.83:60:9:0.18:0:1.3 -14 64619788 . C T 168 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00179;SOR=0.41024;LSEQ=CAGTGATGAAGCAGTGTCTC;RSEQ=ATGTACAGGGAGATGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:47:34,13:86,39:0.2733:2,2:24.4:1:30.4:1:0.71241:1.18:60:46:0.2706:0:1.6 0/1:165:22:14,8:85,58:0.1333:2,2:21:1:30.5:1:0.81711:1.19:60:44:0.1358:0:1.7 -14 64619793 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49974;SOR=0;LSEQ=ATGAAGCAGTGTCTCCATGT;RSEQ=CAGGGAGATGCCTCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:129,55:0.0108:2,2:35.5:1:32:1:0.51264:2.33343:60:4:0.011:0:1.5 0/0:169:0:0,0:100,68:0:2,0:24.3:1:28.9:1:1:0:60:336:0.9941:0:0.5 -14 64619797 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49995;SOR=0;LSEQ=AGCAGTGTCTCCATGTACAG;RSEQ=GAGATGCCTCAGGGAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:135,60:0.0102:2,2:25.5:1:32:1:0.5245:2.23976:60:4:0.0104:0:1 0/0:178:0:0,0:104,74:0:2,0:23.9:1:30.7:1:1:0:60:356:1:0:0.5 -14 64619850 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41949;LSEQ=ATGTAGCCTCTATGAGCTAG;RSEQ=AGCATAGTCAGCTCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:274:137:70,67:69,67:0.5:2,2:26.6:1:30:1:1:1.01:60:67.5:0.4963:0:1.2 0/1:227:67:35,32:83,77:0.2952:2,2:24.3:1:29.1:1:1:1.01:60:66:0.292:0:1.2 -14 64619878 . A C 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00895;SOR=Inf;LSEQ=TCAGCTCCAGGAGGACTCTA;RSEQ=AGTTTGGAAGAAACACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:110,157:0:2,0:26:1:30:1:1:0:60:266:1:0:0.5 0/1:226:6:3,3:107,113:0.0265:2,2:22.5:1:31.5:1:1:1.06:60:12:0.0271:0:1.2 -14 64619897 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20834;SOR=Inf;LSEQ=AAAGTTTGGAAGAAACACTA;RSEQ=ATGGTGTTGAAGAGAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:80,154:0:2,0:25.7:1:32.1:1:1:0:60:468:1:0:0.5 0/1:197:2:1,1:88,107:0.0102:2,2:22.5:1:29.5:1:1:1.21:60:4:0.0103:0:1.5 -14 64619929 . A C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22039;SOR=Inf;LSEQ=GAGAGAGTATAAAGGAAGAA;RSEQ=GGGTGCAAGACATCTAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:40,112:0:2,0:22.7:1:31.2:1:1:0:60:304:1:0:0.3 0/1:135:2:1,1:47,85:0.0148:2,2:30:1:28.5:1:1:1.80:60:4:0.015:0:1 -14 64699816 . C T 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.32198;LSEQ=ACTGGAGTTCACGCTTCAGC;RSEQ=TGTGACCTCTGTGGGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:20.5:1:30.5:1:1:0:60:4:0.6667:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:14:0:33:0:1:0:60:2:0.3333:0:1 -14 64699990 . TG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53187;SOR=0;LSEQ=TCCAGCAGCAGGTCATACAC;RSEQ=GGACCACATTTTTGCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:28,26:0.0357:2,2:31.5:1:31:1:1:1.07547:60:4:0.0364:0:0 0/0:32:0:0,0:16,16:0:2,0:32.8:1:30.5:1:1:0:60:64:1:0:0.2 -14 64700009 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53026;SOR=0;LSEQ=CTGGGACCACATTTTTGCAC;RSEQ=TCATGTTGAGCAGATGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:24,26:0.0385:2,2:15.5:1:32.5:1:1:1.08:60:4:0.0385:0:1 0/0:30:0:0,0:13,16:0:2,0:26.7:1:29.1:1:1:0:60:28:0.9655:0:0.1 -14 65009431 . AGCG A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.13664;SOR=Inf;LSEQ=AAGGTGGTCCTGGCGGCGGC;RSEQ=GCGGCGGCGGTTCAGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:26:1:32.4:1:1:0:60:46:1:0:0.1 0/1:14:2:1,1:6,6:0.1429:2,2:26.5:1:32:1:1:1:60:4:0.1429:0:0.5 -14 65471386 . C CT 32 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCTTTTTCTTTCTTTTT;RSEQ=TTTTTTTTTTTGAGACAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:32.5:1:1:0:60:4:1:0:0 -14 65472857 . G T 61 q23;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53688;SOR=0.52487;LSEQ=TTATAAATAGGTCCAGCTTT;RSEQ=TTTGTTACCTTTGTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:8:0,8:229,10:0.0324:1,0:14.4:1:20.5:1:0:0:53.8:1.667:0.0215:0:4.3 0/1:174:3:0,3:166,5:0.0172:1,0:14.3:1:16.3:1:6e-05:0:53.3:0.5:0.006:0:5.3 -14 65473196 . G A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90046;LSEQ=GAGAACGAGCTCTCTTAAAT;RSEQ=TAATGGTATCCTTGGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:0,7:0,22:0.2414:1,0:16.1:1:31.6:1:1:0:60:14:0.2414:0:1 0/1:9:2:0,2:0,7:0.2222:0,0:28.5:1:32:0:1:0:60:4:0.2222:0:1 -14 65473875 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAATATAAGGCTGAAG;RSEQ=CAAACATCACCATCATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 65543062 . AT A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5355;SOR=0;LSEQ=GCTTCTACGTAAAAATAAAA;RSEQ=TTAAAAAAAAAAGGGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:2,0:152,2:0.0128:1,0:15.5:1:27.5:1:1:0:60:4:0.0134:0.0064:0.5 0/0:89:0:0,0:83,6:0:2,0:21.9:1:29.8:1:1:0:60:43.5:1:0:0.3 -14 65543065 . TA T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58909;SOR=1.47735;LSEQ=TCTACGTAAAAATAAAAATT;RSEQ=AAAAAAAAAGGGAGAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:9:9,0:153,2:0.0545:1,0:14.2:1:30.9:1:1:0:59.4:18:0.0549:0.0182:0.6 0/1:89:7:6,1:77,5:0.0787:2,2:20.6:1:29.8:1:0.39742:2.52895:60:14:0.0805:0.0225:0.3 -14 65543076 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=ATAAAAATTTAAAAAAAAAA;RSEQ=GGAGAAAGAGAAAAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:189,3:0:1,0:22.6:1:32.2:1:1:0:60:47:1:0:0.6 0/1:113:3:2,1:104,6:0.0265:2,2:16.3:1:29:1:0.17603:8.2921:60:6:0.0273:0:1.3 -14 65543102 . C T 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00067;SOR=0.46279;LSEQ=AAGAGAAAAATAAAGAGTCT;RSEQ=TTAAATGGTTCTGAGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:89:79,10:184,17:0.3058:2,2:27.5:1:29.1:1:0.51192:1.36854:60:11.714:0.2929:0:1.3 0/1:201:34:27,7:140,27:0.1692:2,2:21.2:1:29.6:1:0.61528:1.3422:60:33:0.1692:0:1.1 -14 65543920 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATAGCCCCTACATGCAG;RSEQ=CTGCCTGGCCCAGTAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:60,4:0.0303:2,0:17.5:1:31.5:1:1:0:60:4:0.0303:0:1 0/0:31:0:0,0:28,3:0:2,0:16.6:1:31.1:1:1:0:60:30:1:0:0.1 -14 65544275 . A G 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12092;SOR=Inf;LSEQ=GAACACCTGGAGTCTCTGGT;RSEQ=CTTACACAGCACATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:2,164:0:1,0:24.6:1:30.5:1:1:0:60:332:1:0:0.1 0/1:89:2:1,1:2,85:0.0225:1,2:9:0:34:0:0.06665:34.90:60:4:0.0225:0:1 -14 65544367 . C A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.36717;SOR=1.70199;LSEQ=CTGCAGGCAGAGCACCTGAG;RSEQ=CCCAAGAAGGGGAGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:14:8,6:31,17:0.2258:2,2:31.5:1:30.4:1:0.75478:1.36056:60:28:0.2295:0:1.2 0/1:18:6:3,3:8,4:0.3333:2,2:22.5:1:30.8:1:0.6267:1.92154:60:12:0.3529:0:1 -14 65544450 . C T 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TTCCACTGTCTCCTCACTGG;RSEQ=GCCTCAGGTCCTTCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:123,30:0:2,0:25:1:31.3:1:1:0:60:29.6:1:0:0.1 0/1:110:11:8,3:76,22:0.1:2,2:29.5:1:28.5:1:0.71217:1.29221:60:22:0.1028:0:1.3 -14 65544475 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17173;SOR=Inf;LSEQ=CAGGTCCTTCCTCAGGACGG;RSEQ=TCTAACACTCAGTTACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:186,62:0:2,0:24.7:1:31.8:1:1:0:60:61:1:0:0.1 0/1:176:2:1,1:116,58:0.0114:2,2:25:1:27.5:1:1:1.99157:60:4:0.0118:0:2 -14 65544558 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17783;SOR=5.01902;LSEQ=CATGACTGGCTCTGACTCTG;RSEQ=AGGCCCAGGTGCCAAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:1:0,1:312,153:0.0021:2,0:1:0:12:0:0.33047:0:60:0:0:0:3 0/1:374:4:1,3:233,137:0.0107:2,2:11:1:25.3:1:0.14967:5.07997:60:8:0.0108:0:1.3 -14 65544815 . G A 182 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCAATCCAGGCAGTGAGG;RSEQ=AACCTGGCCTGCAGCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:72:7,65:15,120:0.3462:2,2:23.4:1:29.5:1:0.81758:1.15993:60:144:0.3478:0:1.1 0/0:121:0:0,0:21,100:0:2,0:22.8:1:30.5:1:1:0:60:120:1:0:0.1 -14 65544917 . ATTTATTTT A 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=7.000;MSILEN=1;SSF=0.57728;SOR=0;LSEQ=ACTGTAGGCTTTATTTATTT;RSEQ=TTTATTTTTTTGAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:1,4:0,40:0.1111:1,2:27.8:1:32.4:1:0.11111:0:60:10:0.1111:0:0 0/0:13:0:0,0:0,13:0:1,0:22.2:1:30.7:1:1:0:60:26:1:0:0.2 -14 65545076 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=ATTATAGGTGTGCGCCACCA;RSEQ=GCCCATCTAATTTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:26.8:1:31.3:1:1:0:60:8:1:0:0 1/1:2:2:1,1:0,0:1:0,2:47:1:30.5:1:1:0:60:4:1:0:1 -14 65550816 . T A 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00051;SOR=0.44382;LSEQ=CATTTTGCTGATTACCAGGG;RSEQ=AAGGCAGAGCTATCAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:82:68,14:116,25:0.3677:2,2:24:1:30.6:1:1:1.05:60:164:0.3677:0:1.1 0/1:166:34:25,9:103,29:0.2048:2,2:20.6:1:29.1:1:0.6478:1.27668:60:68:0.2048:0:1 -14 65551042 . C A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11234;SOR=Inf;LSEQ=TAAATAAACATGTGGAAAAG;RSEQ=AATTAATTTCACAAGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:66,230:0:2,0:23.9:1:32.1:1:1:0:60:147:1:0:0.1 0/1:277:3:2,1:77,197:0.0108:2,2:12.7:1:24.7:1:0.19666:5.08:60:6:0.0109:0:1 -14 65551114 . CA C 80 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.52624;SOR=1.63389;LSEQ=CTGAATTAGTTACCCTCTTC;RSEQ=AAAAAAAAAATTCCAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:5:0,5:0,51:0.0877:1,0:22.6:1:32:1:1:0:60:10:0.0943:0:0 0/1:44:6:0,6:1,37:0.1364:1,0:21.2:1:31:1:1:0:60:12:0.1364:0.0227:0 -14 65560024 . TA T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAGTGCTCATTTACAA;RSEQ=AAGTATTAACTTTGAACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:30.3:1:30.3:1:1:0:60:6:0.6:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 65568176 . G T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24879;SOR=Inf;LSEQ=AGTTTACTACAATATTAAAA;RSEQ=TAATAGTACGATCTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:173,51:0:2,0:23:1:31.9:1:1:0:60:43.8:1:0:0.4 0/1:235:3:0,3:172,60:0.0128:2,0:10.7:1:20.7:1:0.0186:0:60:2:0.0086:0:3.7 -14 65568208 . CA C 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.01581;SOR=Inf;LSEQ=TCTCTTTTTCTCTCTGACCC;RSEQ=AAAAGGAATAGAACTGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:0:0,0:261,192:0:2,0:23.6:1:29.6:1:1:0:60:49.333:1:0:0.5 0/1:491:7:4,3:280,203:0.0143:2,2:29.3:1:31.7:1:1:1.03443:60:14:0.0145:0.002:0.3 -14 65568215 . G A 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.52714;LSEQ=TTCTCTCTGACCCCAAAAAG;RSEQ=AATAGAACTGAACGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:182:102,80:166,126:0.3832:2,2:24.2:1:29.8:1:0.92413:1.03325:60:59.667:0.3825:0:1.1 0/1:507:125:73,52:214,168:0.2465:2,2:25:1:28.7:1:0.6782:1.10:60:61.5:0.244:0:1.1 -14 65568285 . C A 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GCAGATTGAAACCTCGGTTG;RSEQ=TCTTCCTGGAATAAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:29:12,17:145,250:0.0684:2,2:21:1:29.6:1:0.69118:1.22:60:28:0.068:0:1.2 0/0:433:0:0,0:161,270:0:2,0:23:1:31:1:1:0:59.9:22.944:1:0:0.3 -14 65568304 . GA G 138 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.24689;SOR=0.66107;LSEQ=GCTCTTCCTGGAATAAGAGA;RSEQ=AAAAAAAAAATAGAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:24:7,17:79,179:0.0845:2,2:27:1:30.2:1:1:1.07157:59.6:48:0.0863:0.0035:0.1 0/1:261:15:6,9:69,174:0.0575:2,2:26.5:1:30.5:1:0.38193:1.68:60:30:0.0593:0.0038:0.1 -14 65568563 . C T 69 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCTCCCTGCAGACCCAG;RSEQ=TCGGGCATCTAGGCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:0.625:2,2:13.6:1:29.8:1:1:2.60168:60:10:0.625:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 65569147 . A G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27342;SOR=0;LSEQ=TCACCGACAACAACAAGCCG;RSEQ=GTCCCCCCCACACACACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:23,265:0.0103:2,2:20:1:31:1:0.2283:5.69:60:6:0.0105:0:1 0/0:202:0:0,0:20,182:0:2,0:23.1:1:30.6:1:1:0:60:32.667:1:0:0.1 -14 65569163 . ACACT A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=5.000;MSILEN=4;SSF=0.0014;SOR=Inf;LSEQ=GCCGAGTCCCCCCCACACAC;RSEQ=CACTCACTCACTCACTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:6,212:0:1,0:24.1:1:32.5:1:1:0:60:53.5:1:0:0.2 0/1:143:7:0,7:6,131:0.049:1,0:31.9:1:30.6:1:1:0:60:14:0.05:0.007:0 -14 65569195 . TCA T 31 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.69635;LSEQ=TCACTCACTCGCTCTCTCAC;RSEQ=CACACACACACAACACGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:0,2:5,109:0.0172:1,0:31.5:1:31.5:1:1:0:60:4:0.0177:0:0 0/1:83:1:0,1:5,77:0.012:2,0:49:0:31:0:1:0:60:2:0.0122:0:0 -14 65733333 . CT C 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTTTATAGTCTAGAGGT;RSEQ=TTTTTTTTTTTTTAACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:32.5:1:31:1:1:0:60:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 65733748 . C T 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67756;SOR=1.9605;LSEQ=TACGATATCACCTTTCTTTC;RSEQ=TTCTTTCTTTCTTTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:0.1667:2,2:18:1:29:1:1:1.45:60:4:0.1667:0:1 0/1:21:6:2,4:7,8:0.2857:2,2:24.7:1:30.5:1:0.65944:1.70461:51.7:12:0.2857:0:1 -14 65733761 . TTCTTTC T 26 v4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=20.000;MSILEN=4;SSF=0.10145;SOR=0;LSEQ=TTCTTTCCTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:13.5:1:26.9:1:0.46429:3.87:50:4:0.25:0.125:0 0/0:16:0:0,0:7,9:0:2,0:28.4:1:27.9:1:1:0:56.9:32:1:0:0.3 -14 65733798 . T TC 33 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=20.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=TCTTTCTTTCTTTCTTTCTT;RSEQ=CTTTCTTTCTTTCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:48:0:29:0:1:0:40:2:1:0:0 1/0:4:2:0,2:0,2:0.5:0,0:26.5:1:33:0:1:0:35:4:0.5:0:1 -14 65734343 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49981;SOR=0;LSEQ=GTGGCCAAAGGAACAACTCC;RSEQ=TGTTTTCTAAAGGGCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:132,18:0.0132:2,2:5:1:30.5:1:0.2351:7.16421:52.5:4:0.0136:0:1.5 0/0:136:0:0,0:116,20:0:2,0:24.3:1:29.9:1:1:0:56.2:135:1:0:0.1 -14 65734376 . G T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12561;SOR=Inf;LSEQ=GGCCTAGAGAACATATATCG;RSEQ=GTGCCTCTCCTCTTTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:215,117:0:2,0:20:1:30.4:1:1:0:57.8:46.429:1:0:0.1 0/1:365:4:1,3:233,128:0.011:2,2:10.5:1:28.3:1:0.13389:5.43509:58:8:0.0111:0:1 -14 65734491 . T A 140 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0134;SOR=0.41902;LSEQ=TAGGCAGAGGCAGAAATGGA;RSEQ=ATCAGGGCCTGCTCAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:29:5,24:32,120:0.1602:2,2:22.9:1:28.9:1:0.80338:1.27831:60:13.5:0.1543:0:1 0/1:176:13:2,11:26,137:0.0739:2,2:22.5:1:29.2:1:1:1.04356:60:26:0.0751:0:1.1 -14 65734498 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23299;SOR=Inf;LSEQ=AGGCAGAAATGGATATCAGG;RSEQ=CCTGCTCAAGGGCACATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:19,123:0:2,0:24.6:1:31.4:1:1:0:60:34.5:1:0:0.3 0/1:133:2:0,2:10,121:0.015:2,0:16:1:31.5:1:1:0:60:4:0.0154:0:1 -14 65734529 . GGT G 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.52071;SOR=0;LSEQ=GGCACATGGATGTGTTGGCG;RSEQ=GTGTGTGTGTCGTGGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:0,2:2,88:0.0217:1,0:28.5:1:33.5:1:1:0:60:4:0.0217:0:0.5 0/0:59:0:0,0:2,57:0:1,0:17:0:14:0:1:0:60:0:0:0:5 -14 65734600 . G A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03339;SOR=5.24205;LSEQ=GCGAAGTGGAGAGAGAAGAG;RSEQ=ATATGGGAGTGAACAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:4:0,4:0,35:0.1026:1,0:15.3:1:30.3:1:1:0:60:8:0.1081:0:1 0/1:13:5:1,4:0,8:0.3846:0,2:17:1:30.4:1:0.38462:0:60:10:0.3846:0:1.2 -14 65934921 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15652;SOR=Inf;LSEQ=GCGGAGCATTCCTTTTTGAA;RSEQ=AGTACCCATTCCCTTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:31,11:0:2,0:24.2:1:29.8:1:1:0:60:20:1:0:0.1 0/1:28:2:1,1:20,6:0.0714:2,2:28.5:1:33.5:1:0.44444:3.16227:50:4:0.0714:0:1 -14 65935016 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11551;SOR=Inf;LSEQ=CATGTTTACTAAAAGGCCTA;RSEQ=AGAACATATATCGGGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:111,47:0:2,0:21:1:31.5:1:1:0:60:157:1:0:0.1 0/1:151:3:1,2:86,61:0.0199:2,2:16.7:1:28:1:0.5725:2.80024:60:6:0.0204:0:1 -14 65935096 . C A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09689;SOR=Inf;LSEQ=TGGAAGATGGTGGTTCCGGC;RSEQ=GAAAGGTTGGATTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:134,145:0:2,0:22.8:1:27.4:1:1:0:59.4:7.455:1:0:0.7 0/1:238:3:2,1:118,117:0.0126:2,2:5.7:1:31:1:1:1.98:60:6:0.0143:0:1.3 -14 65935102 . G GT 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00941;SOR=Inf;LSEQ=ATGGTGGTTCCGGCCGAAAG;RSEQ=TTGGATTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:120,136:0:2,0:21.4:1:29.1:1:1:0:59.3:8.481:1:0:0.8 0/1:221:6:0,6:107,107:0.0271:2,0:15.7:1:25.1:1:0.02948:0:55:12:0.0302:0.0045:3.3 -14 65935103 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0927;SOR=Inf;LSEQ=TGGTGGTTCCGGCCGAAAGG;RSEQ=TGGATTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:118,134:0:2,0:21:1:25.9:1:1:0:59.4:4.143:1:0:0.8 0/1:211:3:3,0:101,107:0.0142:2,0:5.3:1:21.3:1:0.11798:0:60:2:0.0112:0:1.3 -14 65935106 . GA TT 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.587;SOR=2.51628;LSEQ=TGGTTCCGGCCGAAAGGTTG;RSEQ=TTTTTTTTTTTTTTTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:109,118:0.0043:2,0:9:0:27:0:1:0:60:2:0.0049:0:1 0/1:186:2:0,2:93,87:0.0108:2,0:25:1:29:0:0.23775:0:60:4:0.0121:0:2 -14 65995797 . C T 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01705;SOR=Inf;LSEQ=TCTTTTTTCTCAATTTTCCT;RSEQ=TCATATGACATAACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:122,87:0:2,0:27.8:1:31.5:1:1:0:60:68.667:0.9952:0:0.1 0/1:169:5:2,3:88,76:0.0296:2,2:23.6:1:29:1:0.66555:1.73118:60:10:0.0299:0:1.2 -14 65995849 . T A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06742;SOR=Inf;LSEQ=GCACATTGATTCTAATCATC;RSEQ=GTTTTCCTTCATTTTGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:68,101:0:2,0:24.5:1:30.2:1:1:0:60:168:1:0:0.1 0/1:117:3:2,1:43,71:0.0256:2,2:15.7:1:25.7:1:0.55784:3.27:60:6:0.0259:0:1 -14 68181468 . G A 72 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGATATAAGTTGAAAAGA;RSEQ=ACTAAGGGATTTTTGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:26.2:1:31.2:1:1:0:60:10:1:0:1 1/1:1:1:0,1:0,0:1:0,0:46:0:32:0:1:0:60:2:1:0:1 -14 68290372 . T G 213 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATTTAACATTTTTATTGA;RSEQ=AAGTTTTATGCACAAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:119,343:0:2,0:23:1:28.7:1:1:0:60:56.75:0.9978:0:0.1 0/1:392:125:37,88:79,187:0.3189:2,2:24.2:1:30.6:1:1:1.00476:60:40.667:0.3169:0:1.3 -14 68290426 . T C 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCTCTTAAACTTGAAATA;RSEQ=GAAAATGTAGGCTTACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:6,166:0:1,0:23.4:1:30.5:1:1:0:60:171:1:0:0.1 0/1:110:29:0,29:6,75:0.2636:2,1:18.4:1:30.5:1:0.33772:0:60:28:0.2569:0:2.1 -14 68290442 . CA C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53639;SOR=0;LSEQ=AATATGAAAATGTAGGCTTA;RSEQ=AAAAAAAGATAAATGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:0,2:3,125:0.0153:1,0:31:1:34:0:1:0:60:4:0.0159:0:0 0/0:74:0:0,0:1,73:0:1,0:22.6:1:29.7:1:1:0:60:36:1:0:0.5 -14 68290464 . G A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AAAAAAAGATAAATGATGGT;RSEQ=CTTTTCCATAGGCTAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:1,95:0:1,0:27.2:1:32:1:1:0:60:31:1:0:0.1 0/1:40:7:0,7:1,32:0.175:1,0:28.4:1:31.4:1:1:0:60:14:0.175:0:2.4 -14 68290520 . T G 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01056;SOR=Inf;LSEQ=TTGGGTGCATTTCCAACTGC;RSEQ=ATTTCATTTACCCAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:0:1,0:22.6:1:27.1:1:1:0:60:12:1:0:0.4 0/1:12:3:0,3:1,8:0.25:2,0:15:1:30:1:1:0:60:6:0.25:0:1.7 -14 68291907 . G A 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=CACAAGTGTAGCGCTCATAC;RSEQ=CACCTGGATTGGATGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:34.3:1:29.8:1:1:0:60:18:1:0:0.1 1/0:3:2:2,0:1,0:0.6667:0,0:25.5:1:30:1:1:0:60:4:0.6667:0:2 -14 68292097 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16381;SOR=Inf;LSEQ=TTATACTTTTGTCTACATAA;RSEQ=CAGTATCAATTGAAGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:234,29:0:2,0:22.7:1:32.5:1:1:0:60:262:1:0:0 0/1:180:2:1,1:154,24:0.0111:2,2:13.5:1:25:1:0.25916:6.30741:60:4:0.0112:0:1 -14 68301767 . G GA 212 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=55.40266;LSEQ=TTTGAATATATATAGAGGTT;RSEQ=AAAAAAAACTTAATCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:5:3,2:394,183:0.0086:2,2:29:1:28.8:1:0.65518:1.43442:60:10:0.0087:0.0017:0 0/1:517:168:95,73:215,128:0.325:2,2:24:1:28.7:1:0.21015:1.29003:59.9:41:0.3222:0.0542:0.1 -14 68301990 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17073;SOR=Inf;LSEQ=GAAAAAGTTTAGTTAAAAAA;RSEQ=ATAAATTATTTCTGGAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:3,117:0:1,0:21.9:1:32.4:1:1:0:60:59:1:0:0.1 0/1:85:2:1,1:2,81:0.0235:1,2:33.5:1:29:1:0.06975:33.24:60:4:0.0235:0:1 -14 68331675 . A T 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.25354;SOR=0.63227;LSEQ=GCTTGTGATGTTTATCTAAA;RSEQ=AACTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:221:209:209,0:0,6:0.9457:0,1:21.9:1:30.6:1:0:0:53.2:103.5:0.9764:0:1.2 1/1:204:187:184,3:0,1:0.9167:0,1:24:1:29.3:1:0.02128:0:54.4:36.4:0.9286:0:1.1 -14 68331956 . GCCTT TCC 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24881;SOR=0;LSEQ=ATTTACCACCCCTCCCCCTT;RSEQ=TTTTTTTTTTTTGAGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:3:0,3:0,80:0.0345:1,0:20:1:21.7:1:1:0:60:2:0.0328:0.023:3 0/0:76:0:0,0:2,66:0:1,0:18.8:1:26.4:1:1:0:58.7:2.091:0.9583:0:1 -14 68352497 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17578;SOR=Inf;LSEQ=TCTATTGATAAGGCTTAGGA;RSEQ=TTTCTCAAGTAAAATTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:180,16:0:2,0:24.4:1:32.1:1:1:0:60:64.333:1:0:0.1 0/1:142:2:1,1:123,17:0.0141:2,2:21:1:28.5:1:0.23824:7.05987:60:4:0.0141:0:1 -14 68352528 . C T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08487;SOR=Inf;LSEQ=AAAATTAATTAGAGATTCAG;RSEQ=AATGTGGCTTTAAGTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:278,97:0:2,0:21.7:1:31.4:1:1:0:60:33.091:1:0:0.1 0/1:295:3:1,2:213,78:0.0102:2,2:20.7:1:21:1:0.18091:5.42404:60:2:0.0068:0:1.7 -14 68352905 . G A 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03695;SOR=Inf;LSEQ=TTAAATGAATAAAATGTTCT;RSEQ=TATTTAATTAATTAAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:1,22:0:1,0:22.9:1:32.3:1:1:0:60:46:1:0:0 0/1:6:2:1,1:0,4:0.3333:0,2:12.5:1:29.5:1:0.33333:0:60:4:0.3333:0:1.5 -14 68353893 . A G 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAGAGGCATCCTCCTTGA;RSEQ=GTATTTGGCTGAGGAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:827:0:0,0:361,465:0:2,0:26.9:1:30.6:1:1:0:60:90.778:0.9988:0:0.1 0/1:707:33:15,18:297,376:0.0467:2,2:22.7:1:31.1:1:1:1.05:60:66:0.0473:0:1.1 -14 68354012 . TAG T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.17631;SOR=Inf;LSEQ=ATGGTATCAAATAATAAAAT;RSEQ=AGGAAAATGTAAAACAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:30,142:0:2,0:24.3:1:30.9:1:1:0:60:85:1:0:0 0/1:125:2:1,1:32,91:0.016:2,2:28.5:1:32.5:1:0.45987:2.82:60:4:0.0161:0:0 -14 68354015 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51059;SOR=0;LSEQ=GTATCAAATAATAAAATTAG;RSEQ=GGAAAATGTAAAACAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:28,136:0.012:2,2:20.5:1:30:1:0.31975:4.79:60:4:0.0123:0:1 0/0:121:0:0,0:30,91:0:2,0:24.1:1:30.4:1:1:0:60:59.5:1:0:0.1 -14 68679132 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51284;SOR=0;LSEQ=ACTCAGAGCCTTACATAGAG;RSEQ=TGTTAGCAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:54,40:0.0208:2,2:46.5:1:30.5:1:1:1.34571:60:4:0.0211:0:1 0/0:67:0:0,0:38,29:0:2,0:24.4:1:31.6:1:1:0:60:66:1:0:0.1 -14 68679150 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15566;SOR=Inf;LSEQ=AGCTGTTAGCAGCAGCAACA;RSEQ=CAGCAGCACCAGCAGCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:64,58:0:2,0:27:1:30.3:1:1:0:60:244:1:0:0.1 0/1:80:2:1,1:41,37:0.025:2,2:6:1:27.5:1:1:1.10668:60:4:0.0253:0:1 -14 68757735 . G T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGTTTCTCCACATTGGCAA;RSEQ=GCTGGTCTCAAACTCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:48:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:18.5:1:28.5:1:1:0:60:4:1:0:1 -14 68818292 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43071;LSEQ=GGTACATTGACTAAGAGAGC;RSEQ=CATTACAGGAGAGTGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:0.8462:0,0:24.4:1:30.6:1:1:0:60:22:0.8462:0:1.1 1/1:9:8:8,0:1,0:0.8889:0,0:24.4:1:30.9:1:1:0:60:16:0.8889:0:1.1 -14 68818383 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49875;SOR=0;LSEQ=AGGCATTGATTAGAGGAGAG;RSEQ=GCTCTATGGAGAGGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:61,36:0.0202:2,2:19:1:29.5:1:1:1.68496:60:4:0.0204:0:1.5 0/0:89:0:0,0:51,38:0:2,0:23.6:1:30.5:1:1:0:60:21.25:1:0:0.3 -14 68818394 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49758;SOR=Inf;LSEQ=AGAGGAGAGCGCTCTATGGA;RSEQ=AGGAGTCAGCGTGGACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:61,43:0:2,0:31.2:1:32.1:1:1:0:60:208:1:0:0.1 0/1:104:2:1,1:56,46:0.0192:2,2:21.5:1:29.5:1:1:1.21507:60:4:0.0194:0:1 -14 68818442 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=AAGAGTGAGGGAATGTGCGG;RSEQ=ATTAGACCACAGTCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:33,44:0:2,0:20.6:1:30.8:1:1:0:60:76:1:0:0.1 0/1:86:2:1,1:39,45:0.0233:2,2:38:0:28.5:1:1:1.15:60:4:0.0233:0:1 -14 68818450 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49849;SOR=Inf;LSEQ=GGGAATGTGCGGGATTAGAC;RSEQ=ACAGTCAGGGAGCAGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:26,39:0:2,0:20.2:1:31.2:1:1:0:60:130:1:0:0.1 0/1:74:2:1,1:33,39:0.027:2,2:30.5:1:31:1:1:1.18:60:4:0.027:0:1 -14 68878038 . A G 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38862;SOR=1.38457;LSEQ=TGGTAATGAACTGAGCCTCC;RSEQ=AGTACTCTCTGGACTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:21:20,1:100,4:0.168:1,1:21.8:1:29.7:1:1:1.24762:60:42:0.168:0:1 0/1:96:21:21,0:72,3:0.2188:1,1:23.1:1:28.7:1:1:0:60:20:0.2128:0:1.1 -14 68878369 . C A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00096;SOR=4.93741;LSEQ=CCAGCAGCAGCTATTAGGGC;RSEQ=TAAAGAAACCAGCATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:7:0,7:1,65:0.0959:1,0:31.7:1:29.7:1:1:0:60:14:0.0972:0:1 0/1:49:17:0,17:1,31:0.3469:1,1:26.7:1:30:1:1:0:60:34:0.3542:0:1.1 -14 68878582 . A G 41 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=TTTGTTGAGGACTAATTTGT;RSEQ=TATGAATTAAATAATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:26.3:1:26.3:1:1:0:60:2:0.6667:0:2 0/0:1:0:0,0:1,0:0:0,0:9:0:29:0:1:0:60:2:1:0:0 -14 68934690 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00998;SOR=4.08535;LSEQ=ACAGAATAGTTGGAATAAGC;RSEQ=TACAGCCTTTTAAGGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:23:23,0:40,1:0.3594:1,1:29:1:30.3:1:1:0:60:46:0.3594:0:1.2 1/0:20:14:14,0:6,0:0.7:0,1:20.7:1:29.4:1:1:0:60:28:0.7:0:1 -14 68934769 . A T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.67524;SOR=1.68352;LSEQ=AAAATGGTTTTTTTTTTTTT;RSEQ=AATAAGCCTTGTGACTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:3,0:194,5:0.0149:1,0:21.3:1:32.3:1:1:0:60:6:0.015:0:1.3 0/1:121:3:3,0:114,4:0.0248:1,0:35.7:1:30.3:1:1:0:60:6:0.0268:0:2.3 -14 68935112 . G A 93 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00587;SOR=5.36938;LSEQ=GGCCAGTGATATTTACCCTA;RSEQ=TGAGAGCAAGAGAGCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:5:0,5:2,80:0.0575:1,0:15.4:1:30.6:1:1:0:60:10:0.0588:0:1 0/1:32:8:0,8:0,24:0.25:1,0:31.8:1:31:1:1:0:60:16:0.25:0:1 -14 68944245 . T C 126 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00061;SOR=5.49177;LSEQ=GCCAGTGGCTCTGTGGGCAA;RSEQ=ACGTATGAAAGAGGACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:6:6,0:101,1:0.0556:1,0:19.7:1:30.8:1:1:0:60:12:0.0566:0:1 0/1:65:16:15,1:48,1:0.2462:1,1:20.6:1:31.6:1:0.43462:3.13049:60:32:0.2462:0:1.1 -14 68944321 . AT A 195 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.44279;SOR=1.14252;LSEQ=AGTTAGTGCATTTCATAACA;RSEQ=TTTTTTTTTTCAAACTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:89:74,15:427,61:0.1537:2,2:22.3:1:30.2:1:0.30519:1.41798:60:21.25:0.1507:0.0397:0.9 0/1:448:77:64,13:304,65:0.1719:2,2:22.8:1:29.1:1:1:1.05:60:10:0.1606:0.0469:1.2 -14 68944693 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACCAGGCACCTCAAAG;RSEQ=GGTTTAACCACATTAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:0,18:0.1:1,0:24:1:32:0:1:0:60:4:0.1053:0:1 0/0:2:0:0,0:0,2:0:0,0:13.5:1:30:1:1:0:60:4:1:0:0.5 -14 68963082 . T C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTCCTCTCTGCAGCAG;RSEQ=GTTCCCCAGATATGCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:39:1:33:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:0:0,0:26:0:31:0:1:0:60:2:1:0:0 -14 68963737 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19544;SOR=Inf;LSEQ=GGGGGCATGAACTTTTTTCC;RSEQ=CATAACTTCAATAAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:192,32:0:2,0:22.4:1:30.6:1:1:0:59.9:23.889:1:0:1 0/1:178:2:1,1:150,26:0.0112:2,2:25:1:28.5:1:0.28109:5.68028:60:4:0.0114:0:2 -14 68963746 . C T 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14673;LSEQ=AACTTTTTTCCCCATAACTT;RSEQ=AATAAACAACAGTTTTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:269:229:191,38:31,9:0.8513:2,2:22:1:29.8:1:0.36999:1.46:60:75.333:0.8561:0:1.1 0/1:213:97:81,16:91,25:0.4554:2,2:23.4:1:29.1:1:0.38664:1.39:60:47.5:0.4545:0:1.1 -14 68963946 . G A 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30393;SOR=4.76378;LSEQ=TATTGGGAAAGAGTCTTGTG;RSEQ=TGAAACACCCATCGTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:1:1,0:47,235:0.0035:2,0:1:0:25:0:0.16961:0:60:2:0.0036:0:1 0/1:180:3:1,2:22,155:0.0167:2,2:14.3:1:23:1:0.33807:3.49:60:2:0.0113:0:1.3 -14 69059620 . G GATCT 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTCATTCTTATGGTCTGA;RSEQ=ATCAGGAAGGTCCATGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:29.4:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 69060959 . GGA G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGTGAGTGAGGCGGTGGG;RSEQ=GAGAGAGAGGAAAAGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:2,1:58,2:0.0476:1,2:29.3:1:32:1:0.13827:12.89309:60:6:0.0508:0:0 0/0:15:0:0,0:14,1:0:1,0:21.1:1:29.5:1:1:0:60:14:1:0:0.1 -14 69061064 . G A 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTTTGCACATGTCTACC;RSEQ=TTATGTACATTCCTATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:344,45:0:2,0:23.3:1:29.8:1:1:0:60:54.571:1:0:0 0/1:246:26:22,4:203,17:0.1057:2,2:22.6:1:29.8:1:0.25319:2.16241:60:52:0.1061:0:1.1 -14 69061259 . C G 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGCTCCAGAAATCCTCC;RSEQ=ACCTCAGCCTCCTGAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:76:0,76:1,151:0.3333:1,1:26:1:31.9:1:1:0:60:152:0.3393:0:1.1 0/0:143:0:0,0:2,141:0:1,0:24.7:1:31.5:1:1:0:60:70.5:1:0:0.1 -14 69117298 . G A 84 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08954;SOR=0;LSEQ=TAAAATCAGACCAGAACCTG;RSEQ=GGATGAGCCAAGAAATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:7:7,0:48,1:0.125:1,0:31.7:1:30.1:1:1:0:60:14:0.1273:0:1 0/0:28:0:0,0:28,0:0:1,0:24.5:1:31:1:1:0:60:27:1:0:0.4 -14 69117377 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13024;SOR=Inf;LSEQ=GTTTAAAGTAGCATCTAATT;RSEQ=AAAACAACTAGTTTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:198,3:0:1,0:26.3:1:31.3:1:1:0:60:66:1:0:1 0/1:114:2:2,0:110,2:0.0175:1,0:18:1:29.5:1:1:0:60:4:0.0175:0:1 -14 69117387 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07619;LSEQ=GCATCTAATTCAAAACAACT;RSEQ=GTTTCTCAGAGGGCTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:242:218:210,8:24,0:0.9008:1,1:25.6:1:32.5:1:1:0:60:217:0.9004:0:1.1 0/1:145:59:54,5:81,4:0.4069:1,2:23.5:1:32:1:0.4873:1.86654:60:118:0.4097:0:1 -14 69117450 . T C 205 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGATGAATCCTCTCAAAA;RSEQ=AGGAAAAGCTAGGTTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:734:89:60,29:412,233:0.1213:2,2:23.6:1:31.8:1:0.55645:1.17:60:88:0.1214:0:1.8 0/0:526:0:0,0:332,194:0:2,0:23.6:1:29:1:1:0:60:525:1:0:0.4 -14 69117512 . T C 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14215;LSEQ=ACACAGAATTTTGGCACATT;RSEQ=GCATATCTGGTTTCTCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1196:1007:510,497:89,98:0.842:2,2:26.6:1:30.6:1:0.47385:1.13:60:124.875:0.8416:0:1.2 0/1:938:404:204,200:269,264:0.4307:2,2:27:1:30.2:1:1:1.00:60:201:0.4309:0:1.1 -14 69117751 . C T 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04113;SOR=0;LSEQ=CTGGGTTAACAGTACAGTAA;RSEQ=TGAAGTTTCTAAATATGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:0,36:0,0:1:0,1:23.3:1:30.4:1:1:0:60:72:1:0:1.1 1/1:20:17:0,17:0,3:0.85:0,1:25.7:1:30.5:1:1:0:60:34:0.85:0:1 -14 69118621 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTGAATCATCCCGGAAC;RSEQ=GTCTTGGTGCTGTGGTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 69798284 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGGTGAGTTCTGCTCCC;RSEQ=GGGGTGGGGCTGTAGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:29:1:1:0:60:4:1:0:1 -14 70439711 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27899;SOR=0;LSEQ=CTTGGCCATGGGAGTCAAGG;RSEQ=CCCTGGGAGTGAGTCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:2,1:11,8:0.1364:2,2:32.7:1:31.3:1:1:1.43:60:6:0.1429:0:1.3 0/0:13:0:0,0:8,5:0:2,0:22.4:1:31.5:1:1:0:60:26:1:0:0.1 -14 70439776 . A G 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06213;SOR=0;LSEQ=TTCCCCAGAGGTGATTATTG;RSEQ=CCAAGGAGGAGAGAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:2,5:6,6:0.3684:2,2:22.4:1:31:1:0.63325:2.38223:60:14:0.3889:0:1.3 0/0:9:0:0,0:4,5:0:2,0:27.8:1:29.2:1:1:0:60:18:1:0:0 -14 71133586 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49677;SOR=0;LSEQ=GATGGTGATGATGATGATGA;RSEQ=GATGATGATGAAGAGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:0.1111:2,2:28.5:1:31.5:1:1:1.61828:60:4:0.1111:0:1.5 0/0:13:0:0,0:8,5:0:2,0:25.2:1:28.5:1:1:0:60:26:1:0:0.1 -14 71133607 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50758;SOR=0;LSEQ=GATGATGATGAAGAGATGAT;RSEQ=ATTGCCTCTGGTAGCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:0.1:2,2:18:1:27:1:1:1.54:60:4:0.1:0:1 0/0:13:0:0,0:7,6:0:2,0:29.6:1:30.2:1:1:0:60:26:1:0:0.1 -14 71133638 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GTAGCTTATTCCTAAGGCTG;RSEQ=CTACAACAAAGTCCCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:0.1538:2,2:24:1:30:1:1:2.45:60:4:0.1538:0:1 0/0:7:0:0,0:3,4:0:2,0:22.9:1:32.6:1:1:0:60:14:1:0:0.1 -14 73128902 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51278;SOR=0;LSEQ=CACTTACCACATCCAACTCG;RSEQ=AGAAATAAAAATACCTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:138,43:0.0109:2,2:28:1:30:1:0.42407:3.18409:60:4:0.0109:0:1 0/0:130:0:0,0:98,31:0:2,0:24.9:1:32.1:1:1:0:60:128:0.9922:0:0.3 -14 73128962 . G T 43 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04438;SOR=Inf;LSEQ=TTAAAAAGCCTGAGAGAGCA;RSEQ=AGTTGATCTTTATTTTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:217,182:0:2,0:25.7:1:31.6:1:1:0:60:198.5:1:0:0.5 0/1:340:4:1,3:179,157:0.0118:2,2:11:1:21.8:1:0.34582:3.40895:60:3:0.0089:0:1.5 -14 73128983 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.41225;LSEQ=AGTTGATCTTTATTTTCTTA;RSEQ=TTAAAATGTGGGGCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:177:85,92:117,121:0.4255:2,2:27.5:1:32:1:0.843:1.04649:60:354:0.4255:0:1.1 1/0:343:220:104,116:59,64:0.6414:2,2:27.9:1:30.8:1:0.91073:1.02817:60:54:0.6372:0:1.2 -14 73129086 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12959;SOR=Inf;LSEQ=CAAAATTGCGCTTAACTTTT;RSEQ=AAGTAGGAGGTACTTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:17,103:0:2,0:24.5:1:31.2:1:1:0:60:240:1:0:0.1 0/1:68:2:1,1:10,56:0.0294:2,2:25.5:1:27.5:1:0.29939:5.39:60:4:0.0294:0:1 -14 73129120 . C A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00126;SOR=4.86973;LSEQ=TTTAAACAAAAATACTGTGC;RSEQ=ATGTCAGCACTTTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:16:1,15:2,51:0.2319:1,1:32.6:1:30.8:1:0.55289:1.69:60:32:0.2319:0:1 1/0:25:15:0,15:0,10:0.6:0,1:30.4:1:30.6:1:1:0:60:30:0.625:0:1 -14 73208742 . C T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCACACAGACTTCGTCCC;RSEQ=CAGTCCCTGCTCCTTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:1:31.5:1:1:0:60:4:1:0:2 -14 74204636 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGATTACAGGCGTGCAG;RSEQ=ACCACACCTGGCTAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:16.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 74205878 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23153;SOR=0;LSEQ=GGTTGCTGCGAGGGTTGCTG;RSEQ=GGCATGGAATAGAAGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:9,4:0.1875:2,2:25.3:1:30.7:1:1:1.11662:60:6:0.1875:0:1.3 0/0:13:0:0,0:8,5:0:2,0:19.7:1:30.8:1:1:0:60:26:1:0:0.2 -14 74207345 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGGCAGCAAAAGCCACA;RSEQ=TGGCTCCCCTCTCCTCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 75181614 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAACCTAAAAAGAAAGAAAA;RSEQ=AAGGATCCCAGCGCATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:25.5:1:30:1:1:0:60:4:1:0:0 -14 75182937 . G A 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAGTGGTCACCATAGCA;RSEQ=TGACCATGTTTAATGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9.5:1:32:0:1:0:60:4:1:0:1 1/0:2:1:0,1:0,1:0.5:0,0:34:0:31:0:1:0:60:2:0.5:0:1 -14 75189967 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09344;SOR=Inf;LSEQ=TCTTAATGTGAATTTTTTTC;RSEQ=CTGGCAGGTATCCCATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:28,14:0:2,0:21:1:30.6:1:1:0:60:41:1:0:0.1 0/1:19:2:2,0:13,4:0.1053:2,0:44.5:1:32:1:1:0:60:4:0.1053:0:1 -14 75189968 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAATGTGAATTTTTTTCC;RSEQ=TGGCAGGTATCCCATGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:27,13:0.0476:2,2:10:1:29:1:1:2.03815:60:4:0.0476:0:1 0/0:19:0:0,0:15,4:0:2,0:26.3:1:30.8:1:1:0:60:38:1:0:0.3 -14 75190034 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21201;SOR=Inf;LSEQ=AGAAATTGGGGCAGAAGTAT;RSEQ=GAGTGGCTCTAAGGTAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:26,32:0:2,0:27.6:1:30.6:1:1:0:60:116:1:0:0.1 0/1:50:2:1,1:22,26:0.04:2,2:42.5:1:29:1:1:1.18:60:4:0.04:0:1.5 -14 75322327 . A G 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.8737;LSEQ=GAAAGTAAATCTGTGGCTCA;RSEQ=AGAGACTTCGGTATTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:134:62,72:165,171:0.2851:2,2:25.8:1:31.4:1:0.60995:1.12027:60:43.667:0.2829:0:1.1 1/0:456:277:138,139:83,96:0.6075:2,2:25.1:1:31:1:0.50238:1.15:60:33.625:0.6031:0:1.2 -14 76119531 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5312;SOR=0;LSEQ=GTTAGGGAGGGAATAGGATC;RSEQ=GAATGCACATCAGAAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:22,10:0.0588:2,2:12:1:28.5:1:1:2.1448:60:4:0.0606:0:1 0/0:19:0:0,0:14,5:0:2,0:24:1:29.5:1:1:0:60:38:1:0:0 -14 76119728 . C T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.59564;LSEQ=AGGCCAAGGTGGGTGGATCA;RSEQ=GAGGTCAGGAGTTCGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:25.5:1:31.5:1:1:0:60:4:0.2857:0:1.5 0/1:5:2:0,2:0,3:0.4:0,0:13:0:32:0:1:0:60:4:0.4:0:1 -14 76996321 . T C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAGTGCTGGGATTACAGG;RSEQ=GTGAGCCACCACACACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:0:31.5:1:1:0:60:4:1:0:1.5 -14 76998511 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTCCCGGCATGACTTCTG;RSEQ=GTAAACCTGCCAGTTCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:29.5:1:1:0:60:4:1:0:1 -14 77427469 . G C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2106;LSEQ=GGGTGGGGGTCTCTGTCCTA;RSEQ=CATTTGGTTGCAGCACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:267:156,111:37,33:0.7899:2,2:25:1:31.1:1:0.418:1.25:59.9:32.375:0.792:0:1.4 0/1:358:158:85,73:112,87:0.4413:2,2:25.2:1:30.5:1:0.669:1.1053:59.8:30.6:0.4397:0:1.6 -14 77427556 . T A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12005;SOR=Inf;LSEQ=CACACCTTCACACCGAAATG;RSEQ=GCTCCATTCCCTTTGCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:86,179:0:2,0:24.6:1:28.7:1:1:0:60:11.619:1:0:0.7 0/1:259:3:2,1:84,171:0.0116:2,2:16.7:1:22:1:0.25839:4.05:59.3:2:0.0083:0:3 -14 77427558 . C A 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12409;SOR=0;LSEQ=CACCTTCACACCGAAATGTG;RSEQ=TCCATTCCCTTTGCTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:4:2,2:80,178:0.0153:2,2:26.3:1:31.5:1:0.59149:2.22:60:8:0.0167:0:2 0/0:248:0:0,0:78,170:0:2,0:24:1:30.4:1:1:0:59.9:14.5:1:0:0.6 -14 77427574 . A AT 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.00612;LSEQ=TGTGCTCCATTCCCTTTGCT;RSEQ=TTTTTTTTTCTTTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:7:4,3:39,117:0.0409:2,2:27.3:1:29.9:1:0.07945:3.96:60:14:0.0522:0:0.6 0/1:170:7:2,5:43,110:0.0412:2,2:21.9:1:29.9:1:1:1.02:58.1:14:0.0507:0:1.1 -14 77427579 . T TTTTTC 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=0.01396;SOR=Inf;LSEQ=TCCATTCCCTTTGCTATTTT;RSEQ=TTTTCTTTTCTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:32,119:0:2,0:20.7:1:30.1:1:1:0:59.4:74.5:1:0:0.9 0/1:148:6:0,6:38,102:0.0405:2,0:16.8:1:29.2:1:0.3398:0:60:12:0.0411:0.0203:1.2 -14 77427662 . A G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05419;SOR=Inf;LSEQ=TGGCACGATCTCGGCTCACT;RSEQ=CAACCTCTGCCTCCTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:0,17:0:1,0:25.6:1:27.9:1:1:0:60:16:1:0:0.4 0/1:12:3:1,2:0,9:0.25:0,2:36.7:1:32.3:1:0.25:0:60:6:0.25:0:2 -14 77427671 . G C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07174;SOR=Inf;LSEQ=CTCGGCTCACTACAACCTCT;RSEQ=CCTCCTGGGTTCGAGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:0:1,0:33:1:31:1:1:0:60:13:1:0:0.1 0/1:11:3:1,2:0,8:0.2727:0,2:30.3:1:30.7:1:0.27273:0:60:6:0.2727:0:2 -14 77493590 . G C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=AGTCGCGCGGTGTGGCTGCT;RSEQ=CTTCCCAGGCTCACCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:20:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:29.5:1:1:0:60:4:1:0:1.5 -14 77493760 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.1578;SOR=0;LSEQ=ATCAACGTGGTTGAGCTGTT;RSEQ=TTGCTGCTGCTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:21,21:0.0455:2,2:37:0:31:0:1:1:60:4:0.0455:0:2.5 0/0:66:0:0,0:28,23:0:2,0:29.7:1:30.4:1:1:0:59.8:50:0.7692:0:0.9 -14 77493761 . TTGCTGC T 151 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=10.000;MSILEN=3;SSF=0.00116;SOR=3.4964;LSEQ=TCAACGTGGTTGAGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:14:5,9:25,16:0.2545:2,2:25.8:1:30.6:1:0.1277:2.7583:59.6:28:0.2545:0.0364:0.4 1/0:75:41:21,20:21,11:0.5467:2,2:23.3:1:28.3:1:0.24182:1.80327:60:82:0.5467:0.3067:1 -14 77493769 . G A 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=3;SSF=0.83506;SOR=0.85813;LSEQ=GTTGAGCTGTTGTTGCTGCT;RSEQ=CTGCTGCTGCTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:14:12,2:22,23:0.2373:2,2:7.7:1:28.6:1:0.02786:6.10:30.5:13:0.2281:0:8 0/1:76:16:14,2:29,28:0.2105:2,2:8.8:1:28.1:1:0.00971:6.61:32.9:32:0.2192:0:8 -14 77493784 . GC AT 118 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=10.000;MSILEN=3;SSF=0.84393;SOR=0.87012;LSEQ=CTGCTGCTGCTGCTGCTGCT;RSEQ=TGCTGCTGTTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:16:12,4:22,31:0.2286:2,2:22.3:1:31.1:1:0.02401:4.14:29.6:32:0.2319:0:6.8 0/1:83:17:14,3:31,35:0.2048:2,2:24.2:1:29.1:1:0.01294:5.17:32.4:34:0.2048:0:6.9 -14 77493787 . G A 122 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=3;SSF=0.44166;SOR=0.71334;LSEQ=CTGCTGCTGCTGCTGCTGCT;RSEQ=CTGCTGTTGCTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:18:14,4:20,31:0.2571:2,2:23.6:1:29.4:1:0.00628:5.29:28.6:36:0.2609:0:6.7 0/1:86:17:14,3:31,38:0.1977:2,2:26.2:1:27.6:1:0.00667:5.61:32.4:34:0.2:0:6.9 -14 77493788 . CTGCTGT TTGC 147 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=10.000;MSILEN=3;SSF=0.00071;SOR=0.25815;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:27:13,14:22,17:0.3553:2,2:36.1:1:31.1:1:0.61774:1.38661:59.3:54:0.3553:0.0395:1.5 0/1:89:11:3,8:28,26:0.1236:2,2:28.8:1:31.3:1:0.19045:2.82719:60:22:0.1507:0.0112:1 -14 77493793 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.85248;SOR=0.92916;LSEQ=CTGCTGCTGCTGCTGCTGCT;RSEQ=TTGCTGCTGCTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:17:13,4:11,24:0.2237:2,2:30.1:1:29.9:1:0.00315:6.80:29.1:34:0.3269:0:6.9 0/1:90:19:14,5:27,34:0.2111:2,2:29.5:1:27.3:1:0.03526:3.47:31.6:38:0.2405:0.0111:6.4 -14 77493796 . G T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.84913;SOR=0.88302;LSEQ=CTGCTGCTGCTGCTGCTGTT;RSEQ=CTGCTGCTGCTGCTGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:17:13,4:23,37:0.2208:2,2:30.8:1:31.5:1:0.00659:5.11:29.1:34:0.2237:0:6.9 0/1:90:18:14,4:29,42:0.2:2,2:30.3:1:28.6:1:0.00748:4.98:32.1:17:0.191:0:6.8 -14 77493797 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=1.70265;LSEQ=TGCTGCTGCTGCTGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:1,0:35,41:0.013:2,0:24:0:32:0:0.46753:0:20:2:0.0133:0:4 0/1:91:2:0,2:43,46:0.022:2,0:24.5:1:27.5:1:0.49597:0:55:4:0.0225:0:1.5 -14 77493800 . C T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.8529;SOR=0.93177;LSEQ=TGCTGCTGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:17:13,4:23,27:0.2208:2,2:28:0:31.2:1:0.04747:3.74:29.1:34:0.2237:0:6.9 0/1:91:19:14,5:27,34:0.2088:2,2:25.7:1:28.3:1:0.03526:3.47:33.5:38:0.2088:0:6.5 -14 77493805 . G A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0.96843;LSEQ=CTGCTGCTGTTGCTGCTGCT;RSEQ=CTGCTGCTGTTGCTGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:18:13,5:23,38:0.2278:2,2:22:1:29.7:1:0.01465:4.21:28.6:36:0.2278:0:6.5 0/1:90:20:14,6:26,44:0.2222:2,2:20.9:1:27.2:1:0.01144:3.89:31.3:40:0.2247:0:6.1 -14 77493809 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.63162;SOR=0.76788;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGTTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:10:0,10:36,33:0.1266:2,0:21:0:29.5:1:0.00151:0:29.8:20:0.1299:0:3 0/1:90:9:2,7:37,44:0.1:2,2:20.4:1:30.3:1:0.28966:2.9113:41.3:18:0.1023:0:2.9 -14 77493814 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.46216;SOR=0.67322;LSEQ=TTGCTGCTGCTGCTGCTGCT;RSEQ=TTGCTGTTGCTGTTGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:10:0,10:35,33:0.1282:2,0:17:0:30.8:1:0.00167:0:29.8:20:0.1282:0:3 0/1:89:8:1,7:37,44:0.0899:2,2:17:0:30.1:1:0.13095:5.79433:39:16:0.0909:0:3 -14 77493815 . T C 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.02072;SOR=0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGTTGCGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:5:3,2:32,41:0.0641:2,2:19.2:1:32.8:1:0.65218:1.91:60:10:0.0641:0:2 0/0:89:0:0,0:38,51:0:2,0:20:1:29.5:1:1:0:51.2:88:1:0:2.2 -14 77493860 . C T 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.10145;SOR=0;LSEQ=GCGGCGGCCGCCGCTGCTGC;RSEQ=GCCGCCGCCGCCGCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,3:0.25:2,2:39:1:31.5:1:1:1.41:60:4:0.2857:0:2 0/0:16:0:0,0:5,10:0:2,0:9.7:1:28.7:1:1:0:60:30:1:0:0.8 -14 77493875 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=GCTGCCGCCGCCGCCGCCGC;RSEQ=TCCTTAGCCGACAGGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:24:1:33.5:1:1:0:60:4:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:18.5:1:29:1:1:1.73:60:4:0.5:0:2 -14 78149694 . C G 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13116;SOR=Inf;LSEQ=TTCTTTTTCTGATCATTTTA;RSEQ=TACACGTTTCAGGAAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:23.3:1:31.9:1:1:0:60:16:1:0:0.6 0/1:13:4:2,2:5,4:0.3077:2,2:25.5:1:30.8:1:1:1.22862:60:8:0.3077:0:1 -14 78149834 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23279;SOR=Inf;LSEQ=GCTGGGGAACACTGTAGACT;RSEQ=TTCCAGTTTTGCCATGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:0:2,0:29.3:1:31.1:1:1:0:60:36:1:0:0.1 0/1:35:2:1,1:16,17:0.0571:2,2:28.5:1:29.5:1:1:1.06:60:4:0.0571:0:1 -14 78150099 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAATTTTTGTATTTTTAGTA;RSEQ=AGACAGGGTTTCCCCATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:28.5:1:1:0:60:4:1:0:1 -14 78150227 . C T 64 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19394;SOR=0;LSEQ=GTCCAGCTGACAATATCATC;RSEQ=CTCTTACAGATGCGCATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:16.8:1:32:0:1:0:60:8:1:0:1.3 0/1:7:3:2,1:3,1:0.4286:2,2:29:1:30:1:1:1.41418:60:6:0.4286:0:1 -14 78150336 . C T 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01238;SOR=0;LSEQ=CCCTTTGTCTTCGTCATTTT;RSEQ=GCAAATTACTGGAAGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:11:7,4:3,2:0.6875:2,2:24.7:1:30.2:1:1:1.16:60:22:0.6875:0:1.2 0/0:6:0:0,0:3,3:0:2,0:31.3:1:30.2:1:1:0:60:12:1:0:0 -14 78514879 . CT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53715;SOR=0;LSEQ=TGGTGGTTTTCTGTCTCTTT;RSEQ=TGGTGAGTTTCTCTAAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:28,36:0.0299:2,2:28.5:1:33:0:1:1.28:60:4:0.0308:0:0 0/0:37:0:0,0:16,21:0:2,0:19.3:1:29.6:1:1:0:60:36:1:0:0.2 -14 78514913 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.53623;SOR=0;LSEQ=CTAAAGCGGCAGTTCTCAAA;RSEQ=TGTGGTGTGCATCAGGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:5,23:0.0667:2,2:10:1:27:0:0.36552:4.29:60:4:0.0667:0:1 0/0:16:0:0,0:5,11:0:2,0:18.3:1:30.1:1:1:0:60:32:1:0:0.1 -14 78628632 . T C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GAGGGTGCAGATGGCAGTGG;RSEQ=GGTGAGGAGGCAGCGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:10,17:0.069:2,2:21:1:27.5:1:1:1.67:60:4:0.0714:0:1 0/0:6:0:0,0:2,4:0:2,0:34:1:27.3:1:1:0:60:5:1:0:0.3 -14 78958326 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1908;SOR=Inf;LSEQ=GGTGCTGAGATTCGGATTCC;RSEQ=CCTCTGCTGCTTACCATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:17,12:0:2,0:27.3:1:30.9:1:1:0:60:58:1:0:0.1 0/1:23:2:1,1:13,8:0.087:2,2:32:1:30.5:1:1:1.58984:60:4:0.087:0:1 -14 78958489 . G A 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGATATGACATACATTAT;RSEQ=GGTCTATCACATGATAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:34.3:1:32.7:1:1:0:60:6:1:0:1 1/1:2:2:0,2:0,0:1:0,0:14:1:30:1:1:0:60:4:1:0:1 -14 80471794 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17502;SOR=Inf;LSEQ=CCTATGTGCTGTCTATATCT;RSEQ=ACATATGATAGTGTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:158,85:0:2,0:24.2:1:31.2:1:1:0:60:33.714:0.9958:0:0.3 0/1:176:2:1,1:112,62:0.0114:2,2:18:0:31:1:1:1.79994:60:4:0.0114:0:1 -14 80471852 . A G 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTTTCTACTCAAACATTCC;RSEQ=TGAACTCACTCCCCAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:55:27,28:184,164:0.1365:2,2:28.9:1:30.7:1:0.66375:1.16306:60:110:0.1389:0:1.5 0/0:333:0:0,0:168,165:0:2,0:25.9:1:29.5:1:1:0:60:46.571:1:0:0.7 -14 80471876 . G A 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.07193;LSEQ=ACTCACTCCCCAGTGAGGAA;RSEQ=ATGGAGGCAAAAGCGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:160:74,86:131,130:0.38:2,2:25.8:1:30:1:0.48214:1.17066:60:159:0.3831:0:1.1 1/0:318:178:85,93:67,73:0.5597:2,2:25.5:1:29.7:1:1:1.00418:60:356:0.5615:0:1.1 -14 80471918 . T C 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.42223;LSEQ=CCTTCATTTGTCCATAAGAA;RSEQ=ATTGATTTGTTTATGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:121:47,74:53,100:0.4416:2,2:25.3:1:32.1:1:0.52793:1.20:60:242:0.4449:0:1.2 0/1:220:55:24,31:63,102:0.25:2,2:22.1:1:31.2:1:0.52529:1.25:60:110:0.2523:0:1.2 -14 80472006 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=6.56947;LSEQ=TTTCATGGAAACTAGAGTGT;RSEQ=ACAGCCAAGGCTGGAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:15:1,14:2,56:0.2055:1,1:20.6:1:30.9:1:0.50389:1.98:60:30:0.2055:0:1 1/0:41:26:2,24:1,14:0.6341:1,2:23.8:1:30.7:1:1:1.16:60:52:0.6341:0:1 -14 80952019 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCAATTAAATAAGATTTGG;RSEQ=ACATAATAGGTCCACAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:2,0:167,7:0.0113:1,0:15:1:30.5:1:1:0:60:4:0.0116:0:1 0/0:70:0:0,0:67,3:0:1,0:26.9:1:31.9:1:1:0:60:34:1:0:0.7 -14 80952038 . A G 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACATAATAGGTCCACAAG;RSEQ=ATTTAGCAATGAATGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:224,35:0:2,0:23.9:1:30.1:1:1:0:60:128.5:1:0:0.4 0/1:109:10:9,1:87,12:0.0917:2,2:20.2:1:30.6:1:1:1.24:60:20:0.0943:0:2.8 -14 80952091 . T C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=6.70708;LSEQ=TTGAATTAAGGGAAATAATG;RSEQ=TTTCTCGAGTGGAAGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:105:66,39:322,198:0.1677:2,2:27.2:1:32.1:1:0.9124:1.04:60:104:0.168:0:3 1/0:365:210:133,77:85,70:0.5753:2,2:24.5:1:31.8:1:0.10666:1.42:60:104:0.5762:0:3 -14 80952097 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.05337;LSEQ=TAAGGGAAATAATGTTTTCT;RSEQ=GAGTGGAAGGCCACTAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:114:69,45:338,221:0.1691:2,2:27:1:30:1:1:1.00:60:113:0.1694:0:3 1/0:400:236:144,92:88,76:0.59:2,2:25.2:1:29.9:1:0.15046:1.35:60:117:0.5879:0:2.8 -14 80952108 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.45719;LSEQ=ATGTTTTCTCGAGTGGAAGG;RSEQ=CACTAGTGCTGAGGAAACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:756:126:71,55:347,283:0.1667:2,2:26.7:1:29.8:1:0.84458:1.05:60:62:0.168:0:2.8 0/1:441:208:123,85:123,109:0.4717:2,2:27.5:1:29.3:1:0.21193:1.28:60:207:0.4737:0:2.8 -14 80952410 . A G 45 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26667;SOR=Inf;LSEQ=TTTAACTGTTGCAATTAGCT;RSEQ=GAAGGGTGGGGAATCCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:0.2143:0,0:23.3:1:28.7:1:1:0:60:6:0.2143:0:1 1/1:1:1:0,1:0,0:1:0,0:17:0:32:0:1:0:60:2:1:0:1 -14 81376407 . G T 16 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.39215;LSEQ=TACCTCACCAGATACCAAAT;RSEQ=ATGATCCTATTTTCCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:108,69:0.0112:2,2:21:0:31:1:1:1.56112:60:4:0.0112:0:1.5 0/1:129:2:0,2:79,48:0.0155:2,0:19:1:16:1:0.14838:0:60:1:0.0079:0:1.5 -14 81376490 . T C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=2.74611;LSEQ=TAATATAATGTATATTAATA;RSEQ=CTCACTTGATATAAATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:70:32,38:108,108:0.2448:2,2:27.1:1:31.5:1:0.58315:1.18678:60:69:0.2447:0:1.1 0/1:210:99:46,53:60,51:0.4714:2,2:22.9:1:31:1:0.33322:1.35351:60:48.5:0.4686:0:1.2 -14 81376511 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17096;SOR=Inf;LSEQ=CTCACTTGATATAAATGCAT;RSEQ=ATTTAAAGATTAGGTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:132,151:0:2,0:24.9:1:31.5:1:1:0:60:93.333:1:0:0.3 0/1:200:2:1,1:92,106:0.01:2,2:25.5:1:28:1:1:1.15:60:4:0.0102:0:1 -14 81422178 . C A 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACGCATCCCCAGCTTACCG;RSEQ=CCAGTACGCAGACTCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:846:0:0,0:365,481:0:2,0:25.3:1:31.5:1:1:0:60:83.6:1:0:0.2 0/1:760:70:29,41:305,385:0.0921:2,2:24.6:1:28.6:1:0.70556:1.11983:60:22.333:0.0897:0:1.2 -14 81422220 . A C 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCCGGGAGAGATCAGGGT;RSEQ=GGACCCAGAGATCAAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:161,324:0:2,0:24.2:1:30:1:1:0:60:160.667:1:0:0.2 0/1:419:28:12,16:145,246:0.0668:2,2:25.6:1:30.4:1:0.54983:1.27:60:56:0.0676:0:1.1 -14 81422257 . G C 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23665;SOR=0.74528;LSEQ=GGCATCTGCAGAGGTGGCCC;RSEQ=AAGTGCACAAAAGCAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:60:8,52:32,152:0.2459:2,2:24.2:1:32.6:1:0.55003:1.36676:60:120:0.2459:0:1.1 0/1:174:34:8,26:26,114:0.1954:2,2:21.2:1:31.2:1:0.48095:1.35:60:33:0.1953:0:1.1 -14 81422286 . C G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=AAAAGCAGCTCAATAACAGC;RSEQ=CGAAGTAGTGTGTGAGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:8,139:0:2,0:21.9:1:31:1:1:0:60:35.75:1:0:0.2 0/1:89:7:1,6:4,78:0.0787:1,2:23.6:1:31.1:1:0.34264:3.18:60:14:0.0805:0:1.1 -14 81528412 . T A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACTGTCATGCTTTTTAAT;RSEQ=ATGTGTTTTTATAATTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:278,36:0:2,0:24.3:1:30:1:1:0:60:77.5:1:0:0.1 0/1:229:36:27,9:154,39:0.1572:2,2:21.8:1:28.3:1:0.50873:1.31457:60:72:0.1586:0:1 -14 81534271 . C CTA 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=14.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAACATTCCACAGGGTGACA;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:28:1:30:1:1:0:60:4:0.5:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 81534440 . T C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=0.10165;LSEQ=ACAAGATCTGAAAAAAAAAG;RSEQ=AGTAAGTAATTTTAACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:61:61,0:12,0:0.8356:0,1:24.9:1:32:1:1:0:60:29.5:0.831:0:1 0/1:24:8:8,0:16,0:0.3333:1,0:23.1:1:33:1:1:0:60:16:0.3333:0:1.3 -14 81534709 . A T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00776;SOR=Inf;LSEQ=GTGCAGCATAGACCTAAGCC;RSEQ=CAACCACTCTTGACTGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:145,328:0:2,0:24.9:1:29.9:1:1:0:60:235.5:1:0:0.1 0/1:290:5:2,3:90,194:0.0172:2,2:11.4:1:28.6:1:0.65491:1.44:60:10:0.0174:0:1.4 -14 81536844 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCGGGCATGGTGGTGTGT;RSEQ=CCTGTAATCCCAGCTACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:31.5:1:1:0:60:4:1:0:1 -14 81554209 . G T 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30224;SOR=0;LSEQ=TGCATATTTTTCTCATGAAC;RSEQ=TTTGTTAAAACTGATTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:4:2,2:322,37:0.011:2,2:14.8:1:29.3:1:0.05877:8.59999:60:8:0.011:0:1 0/0:215:0:0,0:193,21:0:2,0:21.7:1:30.3:1:1:0:60:213:0.9953:0:0.1 -14 81554592 . C T 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00033;SOR=Inf;LSEQ=CAGAGACCTGCTCCAAGAAA;RSEQ=AGGAGGGAGAAAATGCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:1,26:0:1,0:23.3:1:31.5:1:1:0:60:26:1:0:0.3 1/0:9:5:0,5:0,4:0.5556:0,0:20.2:1:29.2:1:1:0:60:10:0.5556:0:1.2 -14 81557084 . G A 77 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATAATTTTTTCCAATTAAAC;RSEQ=AGAAAATCACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:24.7:1:30:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 81558806 . C T 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTTATTTAAGTGCATATG;RSEQ=GCAGCAAGACCCCTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:280,69:0:2,0:24.9:1:31.6:1:1:0:60:68.8:1:0:0.1 0/1:232:23:19,4:159,49:0.0991:2,2:23.7:1:29.8:1:0.60945:1.46:60:46:0.1004:0:1.1 -14 81558965 . A G 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGACACTGTGAGTATTACC;RSEQ=GTTCTACTCCCTCCATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:0:0,0:242,441:0:2,0:25.4:1:30.6:1:1:0:60:84.375:1:0:0.1 0/1:583:87:33,54:194,302:0.1492:2,2:23.8:1:29.4:1:0.90529:1.05109:60:42.5:0.1473:0:1.2 -14 81559160 . C T 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03226;SOR=Inf;LSEQ=GGTAACAAGACAAGAGGATT;RSEQ=CATTACGGCAGTGGTTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:0,25:0:1,0:22.6:1:31.8:1:1:0:60:50:1:0:0.1 0/1:6:2:1,1:0,4:0.3333:0,2:32.5:1:28:1:0.33333:0:60:4:0.3333:0:1 -14 81562582 . A T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAAAAACATACGCATTC;RSEQ=GATGAATGTCTTTCAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:34:1:30.5:1:0.33333:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 81562808 . A G 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00283;SOR=Inf;LSEQ=GGGCATTCAAACTGAGAAAT;RSEQ=TTATCTTGTTTCCAACAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:95,1:0:1,0:23.5:1:28.7:1:1:0:60:192:1:0:0.1 0/1:45:5:5,0:40,0:0.1111:1,0:23.4:1:33.6:1:1:0:60:10:0.1111:0:1.2 -14 81562876 . C A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00443;SOR=Inf;LSEQ=CATATGTGGGACCTGAAAAA;RSEQ=CTTTATGTACATTTATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:298,49:0:2,0:23:1:31.8:1:1:0:60:85.75:1:0:0 0/1:239:6:4,2:198,34:0.0251:2,2:14.2:1:28:1:0.22524:2.89388:60:12:0.0255:0:1 -14 81562998 . T C 215 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTAGGAAGCTGTACAACAA;RSEQ=GGCTTTACTTCAGTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1221:0:0,0:583,637:0:2,0:24.3:1:30.3:1:1:0:60:109.909:0.9992:0:0.1 0/1:954:147:67,80:378,429:0.1541:2,2:24.4:1:30:1:0.7882:1.05205:60:146:0.154:0:1.1 -14 81563195 . G A 134 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01278;SOR=0;LSEQ=AACATGGAAATGAGGTCAAG;RSEQ=AACTTGGCAGGGGCCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:0,20:1,82:0.1942:1,1:19.8:1:31.2:1:1:0:60:40:0.198:0:1.1 0/0:25:0:0,0:0,25:0:1,0:26.2:1:31.7:1:1:0:60:50:1:0:0 -14 81563267 . G GGTGT 77 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=17.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTCCAAAGCTTTTCTCCCT;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:0,6:0,14:0.24:1,0:37.7:1:29.9:1:1:0:57:12:0.2609:0.04:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 81573148 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATACAAAAATTAGTCAG;RSEQ=CATGATGGCGATCGCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29.5:1:1:0:60:4:1:0:1 -14 81574283 . T A 47 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.25;SOR=0;LSEQ=CTCTGACAGTCCTCAGCATC;RSEQ=CTCACCACCCTCACCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.3:1:29.7:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:0:0,0:39:0:28:0:1:0:60:2:1:0:0 -14 81574429 . G A 81 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAAAAATACAGTTGCCACTG;RSEQ=CCTGAAAAATAGGGAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:0.7273:0,0:18.6:1:27.1:1:1:0:60:3:0.6667:0:1.4 0/0:1:0:0,0:0,1:0:0,0:22:0:34:0:1:0:60:2:1:0:0 -14 81574686 . AT TC 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.38172;SOR=1.81577;LSEQ=TTCTTAAAATCACCTAATTC;RSEQ=TCTCTCTCTCTCTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:5:5,0:249,23:0.0179:2,0:6:0:32.8:1:1:0:60:10:0.0182:0:1 0/1:218:7:5,2:185,26:0.0321:2,2:6:0:30.4:1:0.22242:2.8271:60:14:0.0324:0:1 -14 81574687 . T TTCTC 245 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=8.000;MSILEN=2;SSF=0;SOR=0.43282;LSEQ=TCTTAAAATCACCTAATTCA;RSEQ=TCTCTCTCTCTCTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:329:237:210,27:64,4:0.7204:2,2:21.7:1:31.1:1:0.25517:2.05306:59.9:236:0.7307:0.231:0.2 1/0:224:118:105,13:77,13:0.5268:2,2:25.9:1:30.8:1:0.52775:1.36:60:236:0.5463:0.0759:0.3 -14 81574816 . G C 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGAGTAAGACATACAAAA;RSEQ=AATATTTTAGTCTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:909:0:0,0:459,440:0:2,0:22.2:1:30.2:1:1:0:59.9:9.576:0.9988:0:0.3 0/1:801:21:14,7:389,376:0.0262:2,2:20.5:1:30:1:0.18633:1.93:60:20:0.028:0:1.1 -14 81574828 . C CT 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.63394;SOR=0.8481;LSEQ=ATACAAAAGAATATTTTAGT;RSEQ=TTTTTTTTTCTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:833:23:11,12:434,349:0.0276:2,2:20.7:1:30.3:1:0.5267:1.35607:58.1:22:0.0301:0.0024:0.3 0/1:723:17:10,7:376,303:0.0235:2,2:23.5:1:31:1:0.81085:1.15:60:34:0.0267:0:0.5 -14 81574844 . TT AC 248 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0.34195;SOR=0.89907;LSEQ=TAGTCTTTTTTTTTCTTTTT;RSEQ=TTTTTTGGAATAAATGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1010:294:158,136:365,309:0.2911:2,2:13.4:1:30.3:1:0.94412:1.01674:59.6:72.5:0.3005:0:1.1 0/1:790:213:106,107:299,257:0.2696:2,2:16.1:1:30:1:0.33349:1.17415:59.8:70:0.2749:0.0013:1.1 -14 81574959 . A G 321 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33598;LSEQ=TTTTCCTGGCTGTATAGGCT;RSEQ=CCTCTTGGAAGAAAGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1349:1152:485,667:83,113:0.854:2,2:25.1:1:31.6:1:1:1.01014:60:38.724:0.8514:0:1.5 1/0:1064:705:284,421:159,199:0.6626:2,2:23.5:1:31.5:1:0.21121:1.18423:60:87.125:0.6619:0:1.5 -14 81575005 . C A 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29348;LSEQ=TTGAGACTCAGAAGGCCCCA;RSEQ=GCTCCAGTATGCCATCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:824:707:214,493:42,75:0.858:2,2:24.1:1:30.6:1:0.2361:1.28963:60:46.133:0.8564:0:1.8 1/0:607:388:139,249:83,135:0.6392:2,2:24.9:1:30.4:1:0.59882:1.10118:60:63.667:0.6388:0:1.8 -14 81575078 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5565;SOR=0;LSEQ=CTCACAGAGGCTCTGTTCAT;RSEQ=GAGCAGCTGCTGTTTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:19,218:0.0125:2,2:13:1:24:1:0.23063:5.66:60:2:0.0086:0:1.7 0/0:137:0:0,0:18,119:0:2,0:22.4:1:30.4:1:1:0:60:136:1:0:0.5 -14 81575419 . T C 73 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTTGGTTTTGCCTCAG;RSEQ=TTAGAATCTCATCATTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:24:1:31.8:1:1:0:60:10:0.8333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 81606214 . A G 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGAAGAAAATCAGAGGGT;RSEQ=AGTGGCAGGGACCCGGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:0:0,0:206,452:0:2,0:24.2:1:29.4:1:1:0:60:130.6:0.9985:0:0.1 0/1:568:41:13,28:191,336:0.0722:2,2:23.2:1:31.2:1:0.61549:1.2239:60:82:0.0737:0:1 -14 81609779 . G A 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=21.40184;LSEQ=ATGTGCAACCTGGCCTTTGC;RSEQ=GATTTCTGCATGGGGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:986:3:3,0:403,580:0.003:2,0:1:0:27:1:0.06951:0:60:6:0.0031:0:1 0/1:782:48:18,30:343,391:0.0614:2,2:26:1:30.3:1:0.23432:1.46136:60:23:0.0601:0:1.1 -14 81610105 . T A 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=22.54796;LSEQ=TAGCTATGCCAAAGTCAGTA;RSEQ=CTGCCTGCCCATGGACACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1003:2:2,0:475,526:0.002:2,0:1:0:29:0:0.22592:0:60:4:0.002:0:1 0/1:811:35:14,21:391,384:0.0432:2,2:21.8:1:29.9:1:0.29978:1.52654:60:70:0.0441:0:1.3 -14 81610583 . G C 327 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01127;LSEQ=GTTCAAAAGGTTACCCACGA;RSEQ=ATGAGGCAGGGTCTCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1219:1216:614,602:0,0:0.9975:0,2:24.6:1:32:1:1:0:60:120.6:0.9983:0:1.1 1/1:967:793:433,360:83,90:0.8201:2,2:24.2:1:31.2:1:0.12991:1.30:60:98.125:0.8211:0:1.2 -14 81610634 . C G 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTATGAACTGATTGAAAA;RSEQ=TCCCATCTAACCCCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1236:0:0,0:561,675:0:2,0:25.2:1:31.9:1:1:0:60:87.286:1:0:0.6 0/1:1057:48:23,25:488,518:0.0454:2,2:25.5:1:31.7:1:1:1.02399:60:96:0.0456:0:1.6 -14 81610715 . C A 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=28.01933;LSEQ=TAAGTTAACACTACACTACT;RSEQ=ACAATGGTAGGGGAACTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:644:1:1,0:172,471:0.0016:2,0:1:0:24:0:0.26863:0:60:2:0.0016:0:1 0/1:502:21:8,13:152,329:0.0418:2,2:25:1:28:1:0.63276:1.33:60:9.5:0.0382:0:1.6 -14 81610869 . C A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01552;SOR=Inf;LSEQ=TGGAGAGTGATTAGTATTAA;RSEQ=CTAATCATTGCCCCCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:0:1,0:27.5:1:30.2:1:1:0:60:11:1:0:0.4 0/1:13:3:0,3:1,9:0.2308:2,0:18.3:1:31:1:1:0:60:6:0.2308:0:1.3 -14 81610942 . C T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGAAATCAAAATAATCTA;RSEQ=ACTATCTAGAAGACTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:28.5:1:28.2:1:1:0:60:20:1:0:1 1/1:4:4:0,4:0,0:1:0,0:12.3:1:29.8:1:1:0:60:8:1:0:1.3 -14 82491812 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05495;SOR=0;LSEQ=CACTCACCATCTCACTTGGC;RSEQ=AGGGGGAGGGGGTTCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:2,1:0.5:2,0:25.7:1:29:1:0.4:0:60:6:0.5:0:1 0/0:8:0:0,0:3,5:0:2,0:31.4:1:30.9:1:1:0:60:16:1:0:0 -14 83401758 . A G 261 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.93827;SOR=0.98667;LSEQ=GAGAAAAGTAAGACAGAAAG;RSEQ=AATTTTGTGCCTTTAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:482:363:149,214:54,65:0.7531:2,2:26.2:1:30.8:1:0.45413:1.19274:60:50.857:0.7511:0:1.1 1/0:413:310:140,170:44,59:0.7506:2,2:27.2:1:30.8:1:0.73166:1.10:60:102.333:0.7506:0:1.2 -14 83401847 . A T 127 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01357;SOR=2.60306;LSEQ=TTTTAAACTATATTTTCCAA;RSEQ=CACAAGCTATTTAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:14:2,12:5,75:0.1489:2,2:16.1:1:30.3:1:0.27864:2.47:60:28:0.1489:0:1.7 0/1:70:22:2,20:5,43:0.3143:2,2:19.3:1:28.6:1:1:1.16037:60:44:0.3188:0:1.7 -14 83401883 . T A 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26679;SOR=1.70344;LSEQ=AGAATTACCTTCAACAATAG;RSEQ=TGATTAAAAACAAAGTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:28:0,28:0,22:0.56:1,1:26.3:1:31.4:1:1:0:60:56:0.56:0:1.2 1/0:35:24:0,24:0,11:0.6857:0,1:29.1:1:30.4:1:1:0:60:48:0.6857:0:1.4 -14 83401953 . TGAGAG CT 98 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=2;SSF=0.60647;SOR=2.96045;LSEQ=TAGTGTGTATAATATGGATA;RSEQ=AGAGAGAGAGAGAGAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:0,9:0,3:0.6923:0,0:24.2:1:31:1:1:0:60:18:0.75:0.1538:0.6 1/1:8:7:0,7:0,1:0.875:0,0:26.6:1:31.8:1:1:0:60:14:0.875:0.25:0.6 -14 84027719 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GGGAATCTGCTGAAGCCTAC;RSEQ=GAACCCCTTGCGGGAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:28:1:29.2:1:1:0:60:12:1:0:0 0/1:6:2:0,2:2,2:0.3333:2,0:27:1:31.5:1:0.46667:0:60:4:0.3333:0:1 -14 84028114 . A G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCCTGAGCCCCTAGGA;RSEQ=GGAGGGGTGGCCACAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:7.5:1:33:1:1:1:60:4:0.5:0:1 0/0:1:0:0,0:0,1:0:0,0:22:0:33:0:1:0:60:2:1:0:0 -14 84782145 . C G 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05359;SOR=0;LSEQ=AGAGGGGTGGACATGACAAA;RSEQ=GGCTGCCTCACCTGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:6,3:0.375:2,2:24.5:1:29.8:1:1:1:60:5:0.3333:0:1.2 0/0:11:0:0,0:6,5:0:2,0:19:1:30.1:1:1:0:60:22:1:0:0.1 -14 85172722 . G A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTTTCTGGTTTTAAT;RSEQ=CACATCACTAATGCTAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15.5:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 85173181 . G C 220 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGGTAGACAACAGTTATT;RSEQ=TTTTGTTAGTAGGAACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:258,182:0:2,0:25.4:1:32:1:1:0:60:219:1:0:0.2 0/1:379:129:77,52:153,97:0.3404:2,2:25.3:1:31.4:1:0.82456:1.06502:59.8:63.5:0.3378:0:1.2 -14 85173227 . T C 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0;SOR=2.35087;LSEQ=GCTAGCTAGATGATCAAACA;RSEQ=ACACATGCCCAGATTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:91:41,50:215,240:0.1667:2,2:26.2:1:31.9:1:0.73097:1.09229:60:90:0.1664:0:1.2 0/1:450:144:71,73:150,156:0.32:2,2:26.1:1:30.9:1:1:1.01:60:47:0.3176:0:1.2 -14 85173316 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15156;SOR=Inf;LSEQ=AATTTCCTTTAAAATTTCCC;RSEQ=TTCTTTCCCTGTATTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:47,153:0:2,0:23:1:30:1:1:0:60:39:1:0:1.1 0/1:128:2:1,1:22,104:0.0156:2,2:16.5:1:30.5:1:0.32825:4.65:60:4:0.016:0:1.5 -14 85173319 . C A 228 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00771;LSEQ=TTCCTTTAAAATTTCCCTTT;RSEQ=TTTCCCTGTATTTTTAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:192:191:41,150:0,1:0.9948:0,2:22.4:1:30.1:1:1:0:60:30.833:1:0:1.1 1/0:118:70:11,59:7,41:0.5932:2,2:20.6:1:29.5:1:1:1.09:60:34:0.5913:0:1.2 -14 85173327 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.13497;SOR=Inf;LSEQ=AAATTTCCCTTTCTTTCCCT;RSEQ=TATTTTTAATTGGCATTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:29,132:0:2,0:22.4:1:32:1:1:0:60:79.5:1:0:1.1 0/1:94:2:1,1:12,80:0.0213:2,2:16:1:27.5:1:0.25875:6.44:60:4:0.0213:0:2 -14 85955817 . G T 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.51228;LSEQ=AGATGACTCCAGTCTCAGCT;RSEQ=CCATCTGACCACATTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:0.2222:1,0:42.3:1:31.3:1:1:0:60:8:0.2222:0:1 0/1:8:1:1,0:7,0:0.125:0,0:1:0:29:0:1:0:60:2:0.125:0:1 -14 87812897 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55079;SOR=0;LSEQ=TTAATAAAAAGAAACGGTTT;RSEQ=CTGGCCCTTAGCTTTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:157,25:0.0109:2,2:22:1:28:0:0.2633:6.17764:60:4:0.0109:0:1 0/0:94:0:0,0:81,13:0:2,0:23.5:1:30.7:1:1:0:60:30.333:1:0:0 -14 87812927 . G T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55969;SOR=3.32461;LSEQ=AGCTTTGTGGAACAAAACAT;RSEQ=CTAGAGAGAAACAAAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:1,0:202,93:0.0034:2,0:31:0:14:0:1:0:60:0:0:0:8 0/1:179:2:1,1:125,52:0.0112:2,2:25.5:1:26.5:1:0.50568:2.39058:60:4:0.0112:0:1 -14 87813007 . A T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.42527;LSEQ=GAAACCTCAGGTACTCCTGA;RSEQ=GACTCAGTTAAAAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:260:122,138:144,142:0.4762:2,2:27:1:30.4:1:0.44121:1.14679:60:129:0.4743:0:1.9 1/1:337:270:133,137:40,25:0.8012:2,2:26:1:29.7:1:0.09672:1.64566:60:66.5:0.8036:0:1.9 -14 87813031 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=5.688;LSEQ=TCAGTTAAAAATAGAATATG;RSEQ=GAGGATGTAAGTGTGCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:254:113,141:128,147:0.4792:2,2:24:1:30.5:1:0.66265:1.08634:60:83.667:0.4772:0:1.9 1/1:331:278:132,146:27,25:0.8399:2,2:24:1:29.6:1:0.65048:1.1939:60:45.333:0.8369:0:1.8 -14 87813148 . T A 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04453;SOR=0;LSEQ=TACAGAAAGCCCTAGGTCTC;RSEQ=GGTTTGGGGCTTTCCTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:7:1,6:13,106:0.0556:2,2:21.9:1:32.1:1:0.57092:1.36:60:14:0.0588:0:1.1 0/0:80:0:0,0:14,66:0:2,0:21.2:1:30.3:1:1:0:60:160:1:0:0.2 -14 87813214 . G A 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08817;SOR=0;LSEQ=CTGCATAACCTACCAATTCA;RSEQ=GAATGCCTCTTTGGCATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:7:0,7:0,37:0.1591:1,0:18.7:1:31:1:1:0:60:14:0.1591:0:1.6 0/0:20:0:0,0:0,20:0:1,0:20.7:1:29.8:1:1:0:60:19:1:0:0.1 -14 87813312 . A C 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=CTTGTAGTATCATCCATCCA;RSEQ=GTTCTTGCCATGGGCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:15:1:29.4:1:1:0:60:10:0.7143:0:1 0/0:1:0:0,0:0,1:0:0,0:12:0:32:0:1:0:60:2:1:0:0 -14 87813714 . G A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTTCTACAGCCTCCCTGAG;RSEQ=CATTTCAGAGCCTAGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:9:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:31:1:1:0:60:4:1:0:1.5 -14 88360375 . C T 108 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=GCTGACTCCCCCAAGTCTAC;RSEQ=GTGTTTTGTTCCTGGGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:3,9:10,12:0.3529:2,2:27.8:1:30.2:1:0.29195:2.43465:60:24:0.3529:0:2 0/0:30:0:0,0:13,17:0:2,0:30.3:1:29.6:1:1:0:60:60:1:0:0.1 -14 88360384 . T A 100 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=CCCAAGTCTACCGTGTTTTG;RSEQ=TCCTGGGTTATCTTTGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:2,9:6,7:0.4583:2,2:24.2:1:29.1:1:0.2108:3.64266:60:22:0.4583:0:2.1 0/0:26:0:0,0:12,14:0:2,0:28.6:1:29.1:1:1:0:60:52:1:0:0 -14 90358295 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.49206;SOR=Inf;LSEQ=CGCCGAGTGCTACCGCCGCG;RSEQ=GCTGCAGCTGCGGGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:10,2:0:2,0:29.4:1:31.9:1:1:0:60:24:1:0:0.1 0/1:16:2:1,1:12,2:0.125:2,2:13:0:32:0:0.35:5.09912:60:4:0.125:0:1.5 -14 90833201 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06396;SOR=Inf;LSEQ=TCTGATCATTTTCCTTCACG;RSEQ=GTTTCAGGAAGCTATCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:51,6:0:2,0:25.1:1:32.4:1:1:0:56.1:114:1:0:0.2 0/1:39:3:1,2:29,7:0.0769:2,2:7.7:1:27.3:1:0.12737:7.69244:60:6:0.0811:0:1 -14 90833430 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49784;SOR=Inf;LSEQ=ATCAACTTTCTTATAGATTC;RSEQ=CATATATGTGGCCAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:27,89:0:2,0:22.7:1:31.3:1:1:0:55:57:1:0:0 0/1:116:2:1,1:28,86:0.0172:2,2:25.5:1:28:1:0.43913:3.04:54.5:4:0.0175:0:1 -14 90833540 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21178;SOR=Inf;LSEQ=TCATTTTGGCGAATTACTGG;RSEQ=ACATGGCGGTTCCGGCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:26,52:0:2,0:28.2:1:29.4:1:1:0:54.2:18.5:1:0:0.1 0/1:67:2:1,1:32,33:0.0299:2,2:23.5:1:27.5:1:1:1.03:48.5:4:0.0299:0:1 -14 92132168 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCGCAGTGAGCCTGGGC;RSEQ=ACAGAACAAGACTCCGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 92134102 . A G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21476;SOR=0.26233;LSEQ=CAGGGATAGTAAGAGATGCT;RSEQ=CCTGGCGTTTACAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:4,2:6,3:0.4:2,2:30.7:1:33.5:1:1:1:39.5:12:0.4:0:2.8 0/1:14:2:1,1:9,3:0.1429:2,2:27.5:1:31:1:0.50549:2.73861:47:4:0.1429:0:2.5 -14 92134105 . T C 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10577;SOR=0.21075;LSEQ=GGATAGTAAGAGATGCTACC;RSEQ=GGCGTTTACAGGAAAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:4,2:6,3:0.4:2,2:30.7:1:31.8:1:1:1:39.5:12:0.4:0:2.8 0/1:17:2:1,1:10,5:0.1176:2,2:24.5:1:28.5:1:1:1.91491:47:4:0.1176:0:2.5 -14 92134141 . T C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=0.07133;LSEQ=AGGCTTCTGAAATCAGACAA;RSEQ=GCCTTTCAAACTCTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:16:10,6:6,7:0.5517:2,2:22.2:1:31.4:1:0.46666:1.90:41.1:32:0.5517:0:1.7 0/1:26:2:1,1:16,8:0.0769:2,2:8:0:32:0:1:1.94371:33:4:0.0833:0:1.5 -14 92134321 . C T 62 d7;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=AGATGGTCTTACAAATGGAA;RSEQ=CCCAAATGAGCTCAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:13.5:1:31:1:1:0:55.5:8:1:0:1 0/1:6:1:0,1:2,3:0.1667:2,0:24:0:29:0:1:0:60:2:0.1667:0:1 -14 92391945 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCTGGGAGCCAGTCTC;RSEQ=CCCATGGCAGGAAAACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:29.5:1:1:0:60:4:1:0:1.5 -14 92392303 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AGGGTGTGCTGGAGGTGAGT;RSEQ=CTGGGAGACTGAGTGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:0:2,0:30.6:1:32:1:1:0:60:42:1:0:0.2 0/1:28:2:1,1:12,14:0.0714:2,2:22.5:1:29:1:1:1.16:60:4:0.0714:0:1 -14 95556508 . CA C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAAAGCTGACATAAACT;RSEQ=AAAAAAAAAAAACAAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:14.5:1:32:0:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 95556644 . A C 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15781;SOR=0;LSEQ=GCGCAAAAAACTAAAACTAC;RSEQ=ATTAGTTCCAAAATTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:6,0:22,0:0.2143:1,0:31.3:1:32:1:1:0:60:12:0.2222:0:1 0/0:11:0:0,0:11,0:0:0,0:14.9:1:30.2:1:1:0:60:22:1:0:0 -14 95556747 . A T 223 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=0.01584;LSEQ=TCAATTCATTCCACTCACTA;RSEQ=CAACTTTAAGTCTTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:156:155:154,1:1,0:0.9936:0,1:25:1:30.7:1:1:0:60:37.75:1:0:1.1 1/0:120:85:82,3:31,4:0.7083:2,1:23.5:1:30.2:1:0.19182:3.48:60:170:0.7143:0:1.1 -14 95556765 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21129;SOR=Inf;LSEQ=TAACAACTTTAAGTCTTCCT;RSEQ=TCCGATTTAAATAATTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:200,11:0:2,0:23:1:30.2:1:1:0:60:51.75:1:0:0.8 0/1:180:2:1,1:159,19:0.0111:2,2:12.5:1:31:1:0.21043:8.18141:60:4:0.0114:0:2 -14 95556791 . AT A 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.74194;SOR=1.40152;LSEQ=TTTAAATAATTTTCCCCTTA;RSEQ=TTTTTTTGTTTTGTTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:3,1:331,56:0.0102:2,2:17.8:1:32.3:1:0.46895:1.96606:60:8:0.0103:0.0026:0.5 0/1:350:5:4,1:268,77:0.0143:2,2:22.2:1:30.2:1:1:1.15:60:10:0.0144:0.0029:0.2 -14 95557284 . A G 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACAGTGTAAATATTTTTC;RSEQ=GAATCATTAGTTTACAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:216,56:0:2,0:22:1:30.3:1:1:0:60:271:1:0:0 0/1:207:21:16,5:153,33:0.1014:2,2:24.6:1:28.9:1:0.55132:1.44602:60:42:0.1029:0:1 -14 95559858 . A G 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATTTCTGATCCATTTAAAAA;RSEQ=GGAAGGATAAGCTACACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:25.7:1:30.3:1:1:0:60:6:0.75:0:1.3 0/0:2:0:0,0:2,0:0:0,0:17:1:24.5:1:1:0:60:4:1:0:0 -14 95560444 . G A 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCATAAAGGTGCTTGGTTAT;RSEQ=AGGTAGTCCAAAATCGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:26:9,17:168,268:0.0563:2,2:18:1:29.3:1:0.83618:1.18362:60:52:0.057:0:1 0/0:385:0:0,0:157,226:0:2,0:24.5:1:31.1:1:1:0:60:382:0.9948:0:0.1 -14 95560556 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14216;SOR=Inf;LSEQ=TTTACACTATCCCCACATAG;RSEQ=AACTGATCCCCAAATCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:11,122:0:2,0:24:1:32.4:1:1:0:60:132:1:0:0.1 0/1:81:2:1,1:12,67:0.0247:2,2:18:1:29.5:1:0.29691:5.40:60:4:0.0253:0:1 -14 95562347 . G A 124 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=8.03444;LSEQ=TCTTCAAACAACCATATTCC;RSEQ=AGTCTTTCAATACAGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:925:3:3,0:436,486:0.0032:2,0:1:0:26.7:1:0.10651:0:60:6:0.0033:0:1 0/1:745:19:11,8:331,394:0.0255:2,2:20.7:1:29.3:1:0.35354:1.64:60:38:0.0257:0:1.2 -14 95562735 . C T 87 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03776;SOR=3.95636;LSEQ=AGGATCCAGATAGCACATTG;RSEQ=ATCCCAAGAGCTGTAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:977:3:0,3:501,473:0.0031:2,0:1:0:25.7:1:0.11527:0:60:6:0.0031:0:1 0/1:747:9:4,5:386,352:0.012:2,2:24.7:1:27.6:1:0.74356:1.37015:60:18:0.0123:0:1 -14 95562999 . C A 181 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GCTCTCCTCCTCCTCATCCT;RSEQ=CTCCTCGTAATCCTCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1043:82:36,46:417,543:0.0786:2,2:25.2:1:28.5:1:1:1.02:60:164:0.0795:0:1.1 0/0:796:0:0,0:352,442:0:2,0:25.1:1:30.6:1:1:0:60:55.714:0.9987:0:0.2 -14 95566068 . TACACACACACAC T 203 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=20.000;MSILEN=2;SSF=0;SOR=0.08266;LSEQ=GAAAAGTAAATCCCTCCAGT;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:109:88,21:51,0:0.3244:1,2:25.7:1:30.1:1:0.00024:0:59.1:108:0.3263:0.0595:1.3 0/1:184:7:6,1:41,0:0.038:1,2:26.9:1:30.6:1:0.14583:0:60:14:0.0391:0:1 -14 95566108 . C A 266 MSI6 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0;SOR=0.03433;LSEQ=CACACACACACACACACACA;RSEQ=AAACTTACCATTTCATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:514:508:369,139:4,1:0.9883:2,2:25.5:1:29.7:1:1:1.50562:59.5:49.8:0.996:0:1.3 1/0:382:284:202,82:60,34:0.7435:2,2:25:1:29.2:1:0.19809:1.39:59.6:46.333:0.7534:0:1.4 -14 95569500 . C T 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57302;SOR=0;LSEQ=TGTAAAGCAATACTCATCAA;RSEQ=TGCCAGGTAGTTCTGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:5,0:35,0:0.125:1,0:28:1:32.2:1:1:0:60:10:0.125:0:1 0/0:8:0:0,0:8,0:0:0,0:22.6:1:31:1:1:0:60:16:1:0:0.1 -14 95571390 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17683;SOR=Inf;LSEQ=ATGATCTGTGTTCTTTCTGG;RSEQ=TGACTGCACAGGCATACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:203,54:0:2,0:27.5:1:32:1:1:0:60:84.667:1:0:0.1 0/1:187:2:1,1:135,50:0.0107:2,2:5.5:1:29.5:1:0.47214:2.68328:60:4:0.011:0:1 -14 95571416 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09676;SOR=Inf;LSEQ=GCACAGGCATACCTAAAATC;RSEQ=GCAGGAAGTGATCTGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:242,82:0:2,0:25.5:1:30.5:1:1:0:60:63.8:1:0:0.1 0/1:276:3:1,2:195,78:0.0109:2,2:9:1:26.7:1:0.20239:4.96639:60:6:0.0109:0:1 -14 95571635 . G GA 165 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.31253;SOR=0.75402;LSEQ=TACAAAGCGCACACACAAAA;RSEQ=AAAAAAAAAAAGACCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:50:4,46:73,285:0.1163:2,2:26.5:1:29.4:1:0.03446:2.93949:58.9:24:0.1368:0.0116:0.7 0/1:266:24:3,21:45,184:0.0902:2,2:30:1:29.8:1:0.58476:1.70873:59.6:48:0.1048:0:0.3 -14 95572298 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15559;SOR=Inf;LSEQ=TCCACGGGTGGGCAGGGGGA;RSEQ=AGTGAACCTCTGCATGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:208,43:0:2,0:23.5:1:32.3:1:1:0:60:82.667:1:0:0.1 0/1:164:2:1,1:131,30:0.0122:2,2:40:1:31:1:0.34515:4.31203:60:4:0.0123:0:1 -14 95572302 . G C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1537;SOR=Inf;LSEQ=CGGGTGGGCAGGGGGACAGT;RSEQ=AACCTCTGCATGTCTAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:233,50:0:2,0:22.6:1:32.1:1:1:0:60:69.75:1:0:0.1 0/1:183:2:1,1:146,35:0.0109:2,2:10:0:29.5:1:0.35561:4.12715:60:4:0.011:0:1 -14 95572575 . C CA 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25473;SOR=0;LSEQ=CGATATCTAAAAAAGAAAAA;RSEQ=AAAAAAACAATCAGTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:49,244:0.0101:2,2:8.3:1:26.8:1:0.07787:9.84:60:6:0.0102:0.0068:0.3 0/0:247:0:0,0:59,188:0:2,0:22.8:1:31.2:1:1:0:60:122.5:1:0:0.1 -14 95573590 . A ATT 29 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=ATTCCCATGTGAATAAGTGA;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:5,0:0.1429:0,0:44:0:32.5:0:1:0:60:2:0.1429:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:60:4:1:0:0 -14 95573883 . G A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGCGTGAGCCACCGTGCCC;RSEQ=ACCTAGTGCATCTTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:0:0,0:316,128:0:2,0:22.3:1:29.8:1:1:0:60:62.429:0.9977:0:0.1 0/1:327:16:11,5:224,87:0.0489:2,2:26.5:1:28.9:1:0.77893:1.16972:60:32:0.0494:0:1 -14 95574226 . G T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07733;SOR=4.11548;LSEQ=TTTTTTCTTACCAACATTAA;RSEQ=AGGTAGAACACAGTATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:2:1,1:451,318:0.0026:2,2:26:1:27.5:1:1:1.41756:60:4:0.0026:0:1 0/1:566:6:1,5:320,240:0.0106:2,2:12.2:1:24.5:1:0.08992:6.64636:60:12:0.0108:0:1 -14 95577966 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAGGCAAAGTCTATTTT;RSEQ=GCATCCATATATTCCAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:0,2:2,67:0.0282:1,0:22.5:1:27.5:1:1:0:60:4:0.0294:0:1 0/0:26:0:0,0:0,26:0:1,0:16.1:1:31.2:1:1:0:60:52:1:0:0.1 -14 95578448 . CT C 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02599;SOR=0;LSEQ=TCTATAAAGTCCTCTATATG;RSEQ=TTTTTTTTACAATGGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:8:8,0:243,76:0.0244:2,0:21.5:1:31.6:1:0.20568:0:59.4:16:0.0246:0.0091:0.1 0/0:206:0:0,0:151,55:0:2,0:21.2:1:30.5:1:1:0:60:412:1:0:0.2 -14 95578673 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08661;SOR=Inf;LSEQ=TATGAAACCACTGCCCCAAC;RSEQ=TTTTTAAAGTTCAATTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:23,206:0:2,0:21.6:1:30.9:1:1:0:60:113.5:1:0:0.5 0/1:96:2:1,1:20,74:0.0208:2,2:21.5:1:29.5:1:0.39145:3.64:60:4:0.0211:0:1 -14 95578675 . T C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.09036;LSEQ=TGAAACCACTGCCCCAACAT;RSEQ=TTTAAAGTTCAATTTACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:96:8,88:12,113:0.4344:2,2:21.2:1:32:1:0.8163:1.16733:60:47:0.4332:0:1.1 0/1:93:6:1,5:18,69:0.0645:2,2:27.3:1:31.7:1:1:1.30087:60:12:0.0645:0:1 -14 95579370 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.17969;SOR=Inf;LSEQ=TGCAAGTCTTAGAAAAGCTG;RSEQ=AAAAATCCACTAATGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:189,39:0:2,0:23.5:1:30.1:1:1:0:60:113:1:0:0.1 0/1:169:2:1,1:134,33:0.0118:2,2:13.5:1:29:1:0.36285:4.01535:60:4:0.0119:0:1 -14 95579653 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGTCATGTGCCTCTTC;RSEQ=CCTCTACTGAATTTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:0,2:0,81:0.0241:1,0:37.5:1:30.5:1:1:0:60:4:0.025:0:1 0/0:37:0:0,0:1,36:0:1,0:20.4:1:31.6:1:1:0:60:74:1:0:0 -14 95581506 . C G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAAAGAAAATCTTATACTTG;RSEQ=TCTTTTGTCTCTGAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:24.5:1:29.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 95581843 . T TA 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTTTTTGCCTTTTGATT;RSEQ=AAAAAAAAATGAAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:39,0:0.0488:1,0:21.5:1:29.5:1:1:0:60:4:0.0513:0:0 0/0:10:0:0,0:9,1:0:2,0:22.2:1:30.3:1:1:0:60:20:1:0:0.2 -14 95581961 . G A 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGGTTTAGACTTAAACTGT;RSEQ=CAACATTCCCAGGTTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:306,66:0:2,0:22.8:1:32:1:1:0:60:123:1:0:0.1 0/1:249:13:11,2:182,53:0.0522:2,2:26.6:1:28:1:0.73873:1.60:60:26:0.0528:0:1.1 -14 95582395 . GAC G 78 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=16.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACTGTACCGTGCCTACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:1,5:4,11:0.2857:2,2:18.2:1:30.3:1:1:1.77078:60:12:0.2857:0.1429:1.2 0/0:2:0:0,0:0,1:0:0,0:9:0:32:0:1:0:60:2:0.5:0:0 -14 95582544 . A C 97 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATTTCCCAGACGTTCATCCC;RSEQ=AATAACATATGTGATGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:7,2:0.5:2,2:24:1:30.8:1:1:1.69618:60:8:0.4706:0:1.3 1/0:2:1:1,0:1,0:0.5:0,0:37:0:30:0:1:0:60:2:0.5:0:1 -14 95582735 . G T 50 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65392;SOR=0.40009;LSEQ=ATACAAAGAATAACAAAGAA;RSEQ=CCACATTAATTTTTTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:4:1,3:293,65:0.011:2,2:11.5:1:25:1:0.02209:13.38552:60:3:0.0084:0:1 0/0:225:1:0,1:179,44:0.0044:2,0:1:0:23:0:0.20089:0:60:2:0.0045:0:1 -14 95582744 . A AT 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.22297;SOR=3.04116;LSEQ=ATAACAAAGAAGCCACATTA;RSEQ=TTTTTTTTCCCAATCTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:2:2,0:334,97:0.0046:2,0:18:1:32:1:1:0:60:4:0.0046:0.0023:0.5 0/1:287:4:2,2:211,71:0.0139:2,2:23.8:1:29:1:0.26989:2.9582:60:8:0.0141:0.007:0 -14 95583035 . G GA 124 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.41529;SOR=0.64656;LSEQ=TCGAAATTTCCTAAGTACCT;RSEQ=AAAAAAAAAATCCACCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:18:7,11:83,286:0.0455:2,2:33:1:29.8:1:0.14815:2.19:60:36:0.0489:0:0.3 0/1:268:8:1,7:79,179:0.0299:2,2:33.4:1:29.3:1:0.44201:3.07934:60:16:0.031:0:0.1 -14 95583060 . C A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27453;SOR=0;LSEQ=AAAAAATCCACCAAGAAAAG;RSEQ=ACTTCTAAGAAAATTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:2,1:37,239:0.0107:2,2:12.7:1:22:1:0.05222:12.71:60:2:0.0076:0:2.7 0/0:192:0:0,0:37,155:0:2,0:23:1:31.1:1:1:0:60:47:1:0:0.1 -14 95583087 . CA C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.16216;SOR=Inf;LSEQ=AAGAAAATTTCTAAAATGAA;RSEQ=AAAAAAATTAGTAAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:10,145:0:2,0:24.4:1:29.4:1:1:0:60:24.833:1:0:0.3 0/1:105:2:0,2:6,97:0.019:2,0:18:1:29:1:1:0:60:4:0.0194:0:1.5 -14 95583900 . C T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0804;SOR=0;LSEQ=AAAAAGGGAGACCCTATGGG;RSEQ=ACTTTGTCTGTATATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:5:2,3:230,48:0.0177:2,2:12:1:27:1:0.04236:7.11288:60:10:0.0179:0:1 0/0:199:0:0,0:150,49:0:2,0:23.5:1:31.8:1:1:0:60:65.333:1:0:0.1 -14 95590985 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGTCCCAGAACTACCAATAC;RSEQ=GCACGACAGTCTGATAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:126,363:0:2,0:25.6:1:30.7:1:1:0:60:80.5:1:0:0.1 0/1:332:13:5,8:102,217:0.0392:2,2:27.7:1:30.9:1:0.76285:1.33:60:26:0.0393:0:1.1 -14 95591009 . C CA 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.95374;LSEQ=CGACAGTCTGATAGTATCTA;RSEQ=AAAAAAAAGAAAAGAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:6:0,6:67,251:0.0185:2,0:10.7:1:28.9:1:0.35151:0:60:12:0.0189:0.0062:0.2 0/1:227:4:1,3:58,165:0.0176:2,2:25.5:1:23.5:1:1:1.05429:60:3:0.0134:0.0044:0.3 -14 95591070 . G A 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGTAGCATTTTCATGTGGG;RSEQ=TTTAACTGGGATTTCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:33:1,32:1,46:0.4125:1,1:26.8:1:31:1:1:1.43:60:66:0.4177:0:1.3 0/0:48:0:0,0:3,45:0:2,0:22.4:1:31.1:1:1:0:60:96:1:0:0.1 -14 95595654 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72973;SOR=0.64391;LSEQ=ATTCTTGAACTCACAGGTAA;RSEQ=GGTACTTATAGAGAATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:24:24,0:23,0:0.5106:1,1:21.9:1:32.5:1:1:0:60:48:0.5106:0:1.1 0/1:10:4:4,0:5,1:0.4:2,0:17.8:1:32:1:1:0:60:8:0.4:0:1 -14 95595739 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.29635;SOR=3.57154;LSEQ=GTACTCTCTGCAAGGTACTA;RSEQ=AAAAACACCAAAGACTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:1,0:172,11:0.0054:2,0:11:0:32:0:1:0:60:2:0.0056:0:2 0/1:104:2:1,1:94,8:0.0192:2,2:6:1:28.5:1:0.16636:11.13707:60:4:0.0196:0:1 -14 95596279 . G A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12722;LSEQ=TATTCATTCATTCATACACT;RSEQ=CAGCCAAACTCCCAATATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:53:52,1:64,4:0.4344:2,1:23.4:1:28.7:1:0.38416:3.22:60:106:0.4344:0:1 0/1:68:6:6,0:60,2:0.0882:1,0:27:1:28:1:1:0:60:12:0.0882:0:1.2 -14 95596304 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10636;SOR=Inf;LSEQ=CAAACTCCCAATATTGATAA;RSEQ=TAATATTATTGCTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:176,11:0:2,0:24.1:1:32.3:1:1:0:60:374:1:0:0.3 0/1:91:2:1,1:84,5:0.022:2,2:23.5:1:28.5:1:0.12821:15.42515:60:4:0.0222:0:1 -14 95596542 . C A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02772;SOR=Inf;LSEQ=ATGAGAACCTAAAATAAAAT;RSEQ=AACATCAGTAAACAAACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:127,322:0:2,0:23.9:1:31.6:1:1:0:60:63.143:1:0:0.1 0/1:311:4:3,1:103,204:0.0129:2,2:10.8:1:26.8:1:0.11644:5.91:60:8:0.0129:0:1 -14 95598045 . T C 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TTGGCTCTCTGGACTACTAA;RSEQ=GATTAACAGTCTACAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:9,178:0:1,0:25.1:1:30.2:1:1:0:60:61.333:1:0:0.1 0/1:104:10:0,10:2,92:0.0962:1,0:19.4:1:30.4:1:1:0:60:20:0.098:0:1 -14 95598665 . G C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27947;SOR=Inf;LSEQ=CATTCAAAAGAAATACAGAA;RSEQ=CAGAACATTTAAGAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:23,0:16,0:0.5897:1,1:28.3:1:31.7:1:1:0:60:22:0.5789:0:1.1 1/1:4:4:4,0:0,0:1:0,0:25.8:1:30.5:1:1:0:60:8:1:0:1 -14 95599049 . T G 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28405;SOR=0;LSEQ=AAAAAAAAGTTATGCACTTC;RSEQ=TACCTAAGTACAAAATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:61,223:0.0104:2,2:17.3:1:24:1:0.51956:1.82:60:2:0.007:0:3.3 0/0:185:0:0,0:48,136:0:2,0:20.5:1:29.9:1:1:0:60:91:0.9945:0:0.1 -14 95600006 . G C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25359;SOR=Inf;LSEQ=AGGATCATTTTAGGAGTCAA;RSEQ=CATTCTGTACCTTACCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:0,10:0,8:0.5556:0,0:28:1:32.1:1:1:0:60:20:0.5882:0:1 1/1:4:4:0,4:0,0:1:0,0:21.3:1:32.3:1:1:0:60:8:1:0:1 -14 95600072 . T G 52 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAATGAATCAAGCAACT;RSEQ=CACAAAGAGATGTACATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:46:1:33.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 96640647 . TG T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.08867;SOR=Inf;LSEQ=GGCAGATGGCATTTGAGCGG;RSEQ=GGGCTGCGTGAGCTCCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:22.5:1:31.4:1:1:0:60:40:1:0:0.1 0/1:9:2:1,1:3,4:0.2222:2,2:22:1:30:1:1:1.29:60:4:0.2222:0:0 -14 98238063 . TA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=GCACTATTGCTTGATTGTAG;RSEQ=ACAGACCTGATTTGTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:10,5:0.1176:2,2:29:1:31:1:1:1.91491:60:4:0.1176:0:0 0/0:17:0:0,0:10,6:0:2,0:23.8:1:28.3:1:1:0:60:32:0.9412:0:0.4 -14 98238140 . G T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.13004;LSEQ=CTGACTCAGGACTGTGGCTT;RSEQ=TTTGGTGAATGAAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:17:8,9:8,13:0.4474:2,2:20.3:1:29.6:1:0.74297:1.43:60:34:0.4474:0:1.2 0/1:23:11:4,7:5,7:0.4783:2,2:21.8:1:29.6:1:1:1.23792:60:22:0.5:0:1.3 -14 98830005 . A C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.6171;LSEQ=GCATGATTAGAAGTAAAGGA;RSEQ=TCCAAGATGGTACAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:34:18,16:217,231:0.0705:2,2:24.1:1:31.7:1:0.72252:1.20:60:33:0.0688:0:1 0/1:311:146:65,81:82,83:0.4695:2,2:23.9:1:31.2:1:0.36567:1.23031:60:292:0.474:0:1.3 -14 98830038 . C T 143 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=56.16962;LSEQ=CAAGGTCAAAATGGAGTGAG;RSEQ=CAGATTTCTGTGGCCTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:1:0,1:165,235:0.0025:2,0:45:0:26:0:1:0:60:2:0.0025:0:8 0/1:251:31:15,16:90,130:0.1235:2,2:28.1:1:29:1:0.44299:1.35:60:62:0.1255:0:1.8 -14 98830090 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10598;SOR=Inf;LSEQ=TGTCCAGGAGGACAAGCCGA;RSEQ=CCACATTGAATTGTAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:43,159:0:2,0:24.5:1:30.8:1:1:0:60:39.4:1:0:0.2 0/1:98:2:1,1:22,73:0.0204:2,2:35.5:1:29:1:0.41989:3.27:60:4:0.0208:0:1 -14 98830132 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08859;SOR=Inf;LSEQ=GAATTGTGTAAGTCAAAGAG;RSEQ=AATAAGGAGTGTTACAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:4,101:0:1,0:22.2:1:30.9:1:1:0:60:34:1:0:0.1 0/1:45:2:1,1:3,40:0.0444:2,2:31:1:27.5:1:0.17172:11.69:60:4:0.0455:0:1 -14 99364299 . A G 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=GTAAATATTTTAGCTTTGCA;RSEQ=GCCCAGTGGTCCCTGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:28.7:1:31:1:1:0:60:46:1:0:0.2 0/1:26:10:5,5:8,8:0.3846:2,2:25.5:1:30.3:1:1:1:60:20:0.3846:0:1.2 -14 100615989 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.51919;SOR=0;LSEQ=TGCACCAGCACCAGCACCAG;RSEQ=ACCGCCCACTTGAGGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:12,20:0.0588:2,2:27.5:1:30.5:1:1:1.64:60:4:0.0606:0:1.5 0/0:21:0:0,0:9,12:0:2,0:26.7:1:30.7:1:1:0:60:20:1:0:0.3 -14 101529758 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=5;SSF=0.50307;SOR=0;LSEQ=AGTTCTACGGTCAGTGGGGT;RSEQ=TGGTCTTTCAGGACAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:60,68:0.0154:2,2:35.5:1:30:0:1:1.13:60:4:0.0155:0:1 0/0:106:0:0,0:45,61:0:2,0:26.4:1:31.2:1:1:0:60:52:1:0:0.1 -14 101529781 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51564;SOR=0;LSEQ=GTCTTTCAGGACAGTTGCTT;RSEQ=TGTGAACTCAGAAAATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:46,61:0.0183:2,2:30:1:29.5:1:1:1.32:60:4:0.0185:0:1 0/0:74:0:0,0:30,44:0:2,0:20.5:1:31.1:1:1:0:60:148:1:0:0.1 -14 101875648 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGAGGCCCCTCCTGGCGT;RSEQ=GCCATAAAAGCCACAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:29.5:1:30:1:1:1:60:4:0.125:0:1 0/0:1:0:0,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 -14 102309693 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATCAACTGTTAGAGATA;RSEQ=GAAATAAGATGGAACATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:32:0:1:0:60:4:1:0:1 -14 102901263 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07143;SOR=Inf;LSEQ=CTCTGGCATGCTGTCACTGA;RSEQ=GATGACACAGGTCAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:12,3:0:2,0:22.6:1:29.9:1:1:0:60:14:1:0:0.1 0/1:6:2:1,1:3,1:0.3333:2,2:28.5:1:28:1:1:2.44949:60:4:0.3333:0:1 -14 103269755 . C A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50004;SOR=1.96266;LSEQ=CCCTGGGTCTTGGGCAGTTA;RSEQ=CTTCCGTGTGTCTCAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:1,10:1,10:0.5:2,2:23.1:1:30.6:1:1:1:60:22:0.5:0:1 1/0:15:10:2,8:0,5:0.6667:0,2:25.8:1:29:1:0.52381:0:60:20:0.6667:0:1 -14 103613192 . A C 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGGGCTGGGCGGCACAG;RSEQ=GGCTTGTACGCATAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:29.5:1:1:0:60:4:1:0:1 -14 103614902 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50056;SOR=0;LSEQ=AGATAACAAAGCCCTTTCAG;RSEQ=CGGAACCGCCGTTTTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:19,13:0.0588:2,2:14.5:1:31.5:1:1:1.44493:60:4:0.0588:0:2 0/0:26:0:0,0:14,12:0:2,0:29.7:1:30.5:1:1:0:60:25:1:0:0.6 -14 103614968 . G A 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29612;SOR=2.58973;LSEQ=GGGAAAGAGGAGAGGCACCC;RSEQ=ATGTATGTTCTCCAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:32:16,16:5,2:0.8205:2,2:25.4:1:30.6:1:0.41788:2.444:59.2:64:0.8205:0:1.1 1/1:26:24:12,12:0,2:0.9231:0,2:24:1:29.7:1:0.48308:0:60:23:0.92:0:1.2 -14 103615117 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17718;SOR=Inf;LSEQ=GTGTCACCATGGCAAAGCTG;RSEQ=AAGAGTCTACGATGTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:68,62:0:2,0:30.1:1:30.9:1:1:0:59.8:42.333:1:0:0.1 0/1:95:2:1,1:48,45:0.0211:2,2:35.5:1:28:1:1:1.06598:60:4:0.0211:0:1 -14 103615319 . T G 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41667;SOR=0;LSEQ=GGTACCTGGGCCGGGCACTG;RSEQ=GGCTCACGCCTGTAATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:31.4:1:29.3:1:1:0:60:6:1:0:1 1/1:5:4:1,3:0,1:0.8:0,2:30.8:1:29.3:1:1:0:55:8:0.8:0:1.3 -14 103615399 . A G 28 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGAGTTCGAGACCAGCCTG;RSEQ=CCAACATGGTGAAAACTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:20:1:28:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:1:0,0:13:0:34:0:1:0:40:2:1:0:2 -14 103615566 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCATTGCACTCCAGCCTG;RSEQ=GCAACAAGAGTGAAACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30.5:1:1:0:56:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 103615590 . CAA C 33 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=22.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGTGAAACTCCATCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:33:0:1:0:56:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 103615604 . A C 33 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=22.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATCTCAAAAAAAAAAAAA;RSEQ=AAAAAAAACAAAAAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:33:0:1:0:56:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 103707780 . G A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01372;SOR=0.14574;LSEQ=TACATTGGTTCTTTAAAATG;RSEQ=CATCAGTGCCTTTTGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:11:8,3:22,11:0.25:2,2:28.4:1:31:1:1:1.32:60:22:0.25:0:1.1 0/1:44:2:1,1:25,17:0.0455:2,2:22.5:1:28:1:1:1.45743:60:4:0.0455:0:1 -14 103707824 . C G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24453;SOR=0;LSEQ=CGCCATCTTCCAGGAATTCG;RSEQ=CAAAATGATGAATGCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:36,30:0.0294:2,2:22:0:31:1:1:1.19677:60:4:0.0299:0:1.5 0/0:69:0:0,0:33,36:0:2,0:29.3:1:30.7:1:1:0:60:68:1:0:0.2 -14 103707879 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15146;SOR=Inf;LSEQ=ACCCGGTACATGTTCTCCAG;RSEQ=CGTTTTGGAAAACATGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:0:2,0:25.4:1:31.9:1:1:0:60:102:1:0:0.5 0/1:33:2:1,1:10,21:0.0606:2,2:41.5:1:29:1:1:2.05:60:4:0.0606:0:2 -14 103707881 . G A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02936;SOR=0.22477;LSEQ=CCGGTACATGTTCTCCAGGC;RSEQ=TTTTGGAAAACATGGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:16:9,7:16,16:0.3265:2,2:22.4:1:30.7:1:0.76481:1.28:60:32:0.3333:0:1.1 0/1:31:3:2,1:8,20:0.0968:2,2:37.3:1:30:1:0.23693:4.71:60:6:0.0968:0:1.7 -14 103707954 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51518;SOR=0;LSEQ=AAAGGTGACACTGTAGACAT;RSEQ=AAGAGAATGGGAACTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:45,23:0.0286:2,2:26:0:31:1:1:1.93656:60:4:0.0286:0:1.5 0/0:47:0:0,0:32,14:0:2,0:24:1:32.2:1:1:0:60:92:0.9787:0:0.1 -14 103708015 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50025;SOR=0;LSEQ=TCACCATGGCAAAGCTGGAA;RSEQ=AGTCTACAGTGTTCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:56,65:0.0163:2,2:39.5:1:30.5:1:1:1.16:60:4:0.0164:0:1 0/0:107:0:0,0:57,50:0:2,0:28.9:1:31.3:1:1:0:59.9:214:1:0:0.1 -14 103708044 . G C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18912;SOR=Inf;LSEQ=GTGTTCCCCAGCATGCTGTT;RSEQ=GCATTGCTGTAGACAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:54,74:0:2,0:23:1:30.8:1:1:0:59.8:31:1:0:0.1 0/1:99:2:1,1:40,57:0.0202:2,2:46:0:30:1:1:1.42:60:4:0.0202:0:1.5 -14 103708045 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1925;SOR=Inf;LSEQ=TGTTCCCCAGCATGCTGTTG;RSEQ=CATTGCTGTAGACAAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:54,72:0:2,0:22.8:1:31.5:1:1:0:59.8:125:1:0:0.1 0/1:99:2:1,1:40,57:0.0202:2,2:37.5:1:28.5:1:1:1.42:60:4:0.0204:0:1 -14 103708279 . G A 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20808;SOR=0;LSEQ=GGGAAGGAGCCTGAACTGCT;RSEQ=GAACCTATTCCCTATGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:0,4:0.5:0,2:38:1:30:1:1:0:60:8:0.5:0:1 0/0:4:0:0,0:2,2:0:2,0:34.5:1:32:1:1:0:60:8:1:0:0 -14 104146361 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31005;LSEQ=GGTCAGAAACAAGAGCTTAC;RSEQ=TGGCTGCTCTCTTGATGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:318:275:128,147:22,20:0.8648:2,2:24.6:1:30.7:1:0.51025:1.26234:60:136.5:0.8667:0:1.4 1/0:283:188:82,106:43,52:0.6643:2,2:24.7:1:30.1:1:0.8012:1.0687:60:61.667:0.6631:0:1.3 -14 104146367 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10786;SOR=Inf;LSEQ=AAACAAGAGCTTACATGGCT;RSEQ=CTCTCTTGATGTCCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:134,161:0:2,0:26.3:1:31.8:1:1:0:60:58:1:0:1.2 0/1:269:3:2,1:118,148:0.0112:2,2:25:1:27.7:1:0.58757:2.50:60:6:0.0113:0:2.7 -14 104146409 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22512;SOR=Inf;LSEQ=GTCCTGAGCGTCCTGCATTT;RSEQ=CCCTGAGAGGGCGTCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:76,135:0:2,0:25.1:1:31:1:1:0:60:51.75:1:0:1.2 0/1:191:2:1,1:67,122:0.0105:2,2:19.5:1:28:1:1:1.81:60:4:0.0105:0:3 -14 104146421 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3451;LSEQ=CTGCATTTCCCCTGAGAGGG;RSEQ=GTCCAGATCTTTGGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:178:113:37,76:21,44:0.6348:2,2:22.7:1:29.8:1:1:1.02:60:112:0.6328:0:1.7 0/1:155:58:15,43:33,64:0.3742:2,2:23.3:1:30.1:1:0.3697:1.47445:60:116:0.3742:0:1.5 -14 104146611 . AT A 66 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAATTTTTTAGCACATGG;RSEQ=TTTTTTTTTTTTTTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,8:0.3125:0,0:22.2:1:28.8:1:1:0:60:4:0.2857:0.0625:0 0/0:2:0:0,0:0,1:0:0,0:6:0:31:0:1:0:60:2:0.5:0:0 -14 104540660 . G A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00501;SOR=0.15989;LSEQ=GTTCCTGTTTAAAACAGTAT;RSEQ=TACTAAAAAACCCAAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:25:25,0:6,1:0.7813:2,1:29.8:1:28.5:1:0.21875:0:60:24:0.8:0:1 0/1:17:6:6,0:11,0:0.3529:0,0:19.2:1:29.5:1:1:0:60:12:0.3529:0:1.2 -14 104540796 . G T 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08474;SOR=0;LSEQ=GCATGTGGTCGTGTATATTT;RSEQ=CTTCCAGGCTATTTATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:5:2,3:277,155:0.0114:2,2:24.8:1:28.6:1:0.35706:2.67423:60:10:0.0116:0:1.2 0/0:297:0:0,0:179,118:0:2,0:25.8:1:31.6:1:1:0:60:73.25:1:0:0.3 -14 104540855 . T C 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00018;SOR=0.58612;LSEQ=TAACTTAACCAAAACCTACT;RSEQ=TCTACTCTGAAAAGTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:489:297:139,158:88,104:0.6074:2,2:25:1:31.4:1:0.85308:1.04:60:296:0.6091:0:1.1 0/1:345:164:72,92:83,98:0.4754:2,2:25.2:1:31.1:1:0.74576:1.08195:60:81:0.4751:0:1.1 -14 104540915 . C T 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11561;SOR=3.98546;LSEQ=ACAGGCAGTATCTCAATAAT;RSEQ=GGAATTCAGGTAACAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:2:1,1:51,181:0.0085:2,2:23:1:28.5:1:0.3958:3.52:60:4:0.0086:0:1 0/1:150:5:1,4:38,106:0.0333:2,2:16.2:1:30.2:1:1:1.43073:60:10:0.034:0:2.2 -14 104541169 . G T 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTACATTCATTTGAAAAG;RSEQ=CTTTTTAAGCAAGAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:17.5:1:30.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 104575466 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTGGGCCGGCCGGTCCC;RSEQ=GTCCCTGTGCACAGGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7.5:1:28:1:1:0:60:4:1:0:2 -14 104576448 . G A 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGAGGCCAGGACGACTCC;RSEQ=AGGGACCCAAAAAGGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15.5:1:31.5:1:1:0:60:4:1:0:1 1/1:4:4:2,2:0,0:1:0,2:28:1:30.3:1:1:0:60:8:1:0:1 -14 104579210 . C G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGGTGGGGTGCATGGA;RSEQ=GTGACTTGGCCAAGTGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:9:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:14:1:30:1:1:0:60:4:1:0:1 -14 105236277 . GA TT 47 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGAGGCCCAGGGCCCCAGA;RSEQ=GATGACAGATAGCTGGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:30:1:30.2:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 105236532 . CA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.09773;SOR=Inf;LSEQ=GGAGGGTGCTGCCCACAGCA;RSEQ=AAAACGTCTTTCCATCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:165,1:0:1,0:24.9:1:30.8:1:1:0:60:332:1:0:0.1 0/1:76:2:1,1:74,0:0.0263:1,2:31:1:30.5:1:0.02632:0:60:4:0.0263:0:0 -14 105236553 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09487;SOR=Inf;LSEQ=AAAAACGTCTTTCCATCTGG;RSEQ=CTCGAGAGGACAGCGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:238,8:0:1,0:24.1:1:31.3:1:1:0:60:40:1:0:0.1 0/1:110:2:2,0:103,5:0.0182:1,0:10.5:1:32:0:1:0:60:4:0.0183:0:1 -14 105236847 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.29083;SOR=3.62184;LSEQ=TAGGAAGCCAACCTCTTAAA;RSEQ=CACGGCCAGCACGCTGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:1:1,0:62,292:0.0028:2,0:13:0:15:0:0.17746:0:60:0:0:0:1 0/1:197:2:1,1:41,153:0.0102:2,2:30:1:30:1:0.38352:3.70:60:4:0.0106:0:1 -14 105236856 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55489;SOR=0;LSEQ=AACCTCTTAAAGCACGGCCA;RSEQ=CACGCTGCCATACTGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:51,237:0.0103:2,2:14.3:1:31:0:0.44724:2.32:60:6:0.0105:0:1.3 0/0:157:0:0,0:29,126:0:2,0:23.6:1:31.7:1:1:0:60:154:1:0:0.1 -14 105237004 . CA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.09267;SOR=Inf;LSEQ=GATTTTAAAACATCTGAAGC;RSEQ=AAAAAGCTGAACACTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:349,36:0:2,0:24.7:1:30.3:1:1:0:60:54:1:0:0.1 0/1:169:2:1,1:155,12:0.0118:2,2:11.5:1:30.5:1:0.14835:12.45001:60:4:0.012:0.0059:0.5 -14 105237401 . A G 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09636;SOR=9.46398;LSEQ=GAGACAACCCTCAACAGCTG;RSEQ=GACGCAAAGCTGCCCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:0,31:0.0313:1,0:36:0:8:0:1:0:60:0:0:0:2 0/1:8:2:0,2:0,6:0.25:0,0:23.5:1:29:1:1:0:60:4:0.25:0:1 -14 105238591 . CCTGAG C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.99199;LSEQ=TACCAGGACTGCAGCAGGCT;RSEQ=GTGAGGGCGAGTGTGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:97:84,13:173,16:0.338:2,2:24.2:1:30.9:1:0.21625:1.67023:59.9:194:0.3415:0.0836:1 1/0:119:72:56,16:41,6:0.605:2,2:19.4:1:30.2:1:0.23301:1.94196:60:144:0.605:0.1849:1.3 -14 105238604 . C T 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.55886;LSEQ=GCAGGCTCCTGAGGTGAGGG;RSEQ=GAGTGTGTGGGAAATCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:122:100,22:209,37:0.3315:2,2:21.8:1:28.8:1:0.45503:1.24192:59.9:29.5:0.3287:0:1.1 1/0:159:89:67,22:55,15:0.5597:2,2:18.7:1:27.8:1:0.70688:1.20258:60:28.667:0.5513:0:1.4 -14 105238624 . C T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11797;SOR=5.82453;LSEQ=CGAGTGTGTGGGAAATCTGG;RSEQ=GAGCGTGCCACGTGCATGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:507:1:0,1:381,125:0.002:2,0:1:0:25:0:0.24852:0:60:2:0.002:0:1 0/1:263:3:1,2:178,82:0.0114:2,2:11:1:25.3:1:0.23997:4.3147:60:6:0.0118:0:2 -14 105238636 . G C 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATCTGGCGAGCGTGCCAC;RSEQ=TGCATGCGTGAGTGTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:712:0:0,0:491,219:0:2,0:23.2:1:30:1:1:0:60:63.545:0.9986:0:0.3 0/1:348:59:40,19:189,99:0.1695:2,2:23.2:1:30.5:1:0.88021:1.10:60:118:0.173:0:1.7 -14 105238643 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09539;SOR=4.10535;LSEQ=GCGAGCGTGCCACGTGCATG;RSEQ=GTGAGTGTGGATATGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:2:0,2:524,255:0.0026:2,0:1:0:25:0:0.108:0:60:4:0.0026:0:1 0/1:383:4:2,2:244,135:0.0104:2,2:23:1:29.3:1:0.61955:1.80436:60:8:0.0106:0:1.5 -14 105238820 . G C 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAACAAGGCCACAGTGTCG;RSEQ=TACCGCCACCTGCCCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:48:13,35:170,403:0.0772:2,2:23.4:1:32.1:1:0.86918:1.13548:60:96:0.0782:0:1.1 0/0:343:0:0,0:111,231:0:2,0:25.9:1:30.7:1:1:0:60:170:0.9971:0:0.2 -14 105239144 . C T 107 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=27.81468;LSEQ=GAGGTGCCAGGACCGCCTGG;RSEQ=GCAGGGGCAGGTGCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:0,1:273,35:0.0032:2,0:1:0:25:0:0.1165:0:60:2:0.0033:0:1 0/1:144:12:10,2:109,23:0.0833:2,2:22.2:1:30:1:1:1.05:60:24:0.0857:0:1.1 -14 105239146 . C G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.51027;LSEQ=GGTGCCAGGACCGCCTGGCG;RSEQ=AGGGGCAGGTGCAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:109:94,15:191,23:0.3375:2,2:23:1:31.1:1:0.46662:1.32392:60:35.333:0.3376:0:1.9 1/0:146:82:69,13:52,12:0.5616:2,2:25.4:1:30.6:1:0.66398:1.22:60:40:0.5556:0:1.9 -14 105239192 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.12018;LSEQ=GGGGATGGAGGTGTAGCCTG;RSEQ=AGCTGGGATGGGCGGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:229:157,72:332,127:0.3328:2,2:25.3:1:31.6:1:0.32665:1.19852:59.9:31.714:0.3274:0:1.5 1/0:394:240:164,76:102,52:0.6091:2,2:22.9:1:31.7:1:0.66125:1.10:60:79:0.6108:0:1.5 -14 105239465 . AG A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.03436;SOR=Inf;LSEQ=ATGGGCAGGACTCGGCATCA;RSEQ=GGGTGTCCGGGACACTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:176,423:0:2,0:23.1:1:31.2:1:1:0:60:53.455:0.9983:0:0.1 0/1:291:3:2,1:76,212:0.0103:2,2:22:1:28:1:0.17608:5.54:60:6:0.0105:0.0034:0.3 -14 105239531 . C T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33836;SOR=3.06919;LSEQ=ACAGAGAGGACACAGCATTG;RSEQ=GTGTGCTCAGGACGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:2:0,2:338,201:0.0037:2,0:26:1:30:1:0.14036:0:60:4:0.0038:0:1.5 0/1:267:3:1,2:183,81:0.0112:2,2:22.7:1:28:1:0.22891:4.49004:60:6:0.0114:0:1 -14 105239894 . C T 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68036;SOR=0.95151;LSEQ=CGGTCCTCGGAGAACACACG;RSEQ=TCCCGGGACAGGTGGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:985:277:115,162:327,381:0.2812:2,2:25.5:1:29.8:1:0.19985:1.2088:60:54.4:0.2813:0:1.1 0/1:564:153:76,77:182,228:0.2713:2,2:27.9:1:29.6:1:0.29575:1.24:60:152:0.2724:0:1.2 -14 105240530 . T C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCACACTGCCCCACACCA;RSEQ=ACACCCCCACATCACACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:31:3,28:0,0:0.9688:0,2:24.3:1:31.4:1:1:0:60:30:1:0:1.7 1/1:10:10:1,9:0,0:1:0,2:25.7:1:31.1:1:1:0:60:20:1:0:1.7 -14 105241021 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGCCTCCTGGAGCCTCG;RSEQ=CAGAGTGCAAGGAAGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:19,1:0.0909:1,2:36.5:1:29.5:1:0.17749:13.78761:60:4:0.0909:0:1 0/0:5:0:0,0:4,1:0:2,0:15.2:1:32.2:1:1:0:60:10:1:0:0 -14 105241103 . C G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACAGCCCCTAGCCCACA;RSEQ=TGGGCACCTCCACAGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:4,0:66,3:0.0548:1,0:35.3:1:31.8:1:1:0:60:8:0.0556:0:1.3 0/0:17:0:0,0:15,2:0:2,0:24.5:1:31.1:1:1:0:60:16:1:0:0.2 -14 105241155 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1013;SOR=Inf;LSEQ=AGGCCTGTCTCACCAGCGGC;RSEQ=GAGTCCACGGTGTGTAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:141,10:0:2,0:20:1:28.9:1:1:0:60:24.167:1:0:0.2 0/1:71:2:1,1:61,8:0.0282:2,2:23.5:1:32.5:1:0.23903:7.24626:60:4:0.0282:0:1 -14 105241182 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11002;SOR=Inf;LSEQ=ACGGTGTGTAAAGCCCTCAC;RSEQ=TGCCCAAGAAGACAGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:224,47:0:2,0:22.5:1:29.7:1:1:0:60:44.167:1:0:0.2 0/1:135:2:1,1:102,31:0.0148:2,2:28.5:1:31.5:1:0.41924:3.25432:60:4:0.015:0:1 -14 105241378 . C T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07732;LSEQ=GTGAGCTGCCACCCCGCACC;RSEQ=TCATCTCCACCCTGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1569:400:193,207:605,562:0.2549:2,2:23.3:1:30.4:1:0.22388:1.15449:60:49:0.2539:0:1.1 0/1:815:21:9,12:398,392:0.0258:2,2:22.4:1:28.8:1:0.51665:1.35323:60:42:0.0262:0:1 -14 105241607 . G A 214 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCCCAGCTGGTCGGCATGC;RSEQ=TGGGGTGGCATGAGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:128:26,102:64,273:0.2753:2,2:22.6:1:30.6:1:0.7929:1.09:60:41.667:0.2717:0:1.1 0/0:225:0:0,0:45,179:0:2,0:21:1:30.2:1:1:0:60:31:0.9954:0:0.2 -14 105242072 . TCTC T 130 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.20376;SOR=1.61762;LSEQ=TGAGCCCGACCGGAAGTCCA;RSEQ=CTCCTCCTCCTGCTTCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2128:17:8,9:1061,1048:0.008:2,2:26.2:1:31.9:1:0.81282:1.13888:60:34:0.0081:0.0019:0.1 0/1:1244:16:8,8:594,634:0.0129:2,2:26.4:1:30.8:1:1:1.07:60:32:0.013:0.0016:0.2 -14 105242228 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.71359;LSEQ=GCCAGCCTCACAAGCGTGGT;RSEQ=CCACAGCTGTCGGGGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:75:2,73:6,176:0.2918:1,1:22.2:1:31.5:1:1:1.24329:60:74:0.296:0:1.1 1/0:104:63:1,62:0,41:0.6058:1,1:21.8:1:31.9:1:1:0:60:126:0.63:0:1.1 -14 105242374 . G A 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53924;SOR=0;LSEQ=AGGACTCTGTCCCCACAACC;RSEQ=GACTCCAACCCCCAGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:26.8:1:30.6:1:1:0:60:10:0.2632:0:1.2 0/0:4:0:0,0:1,3:0:2,0:26:1:30.8:1:1:0:60:8:1:0:0.5 -14 105242826 . C T 108 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05819;SOR=0;LSEQ=CCTCAGTTTCCCCACCCAAA;RSEQ=CCCACAGGCAGGACTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:11:10,1:47,1:0.1864:1,2:30.3:1:31.3:1:0.34074:4.52871:60:22:0.1864:0:1 0/0:18:0:0,0:16,2:0:2,0:24.1:1:32:1:1:0:60:36:1:0:0.5 -14 105242831 . C T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20778;SOR=1.88835;LSEQ=GTTTCCCCACCCAAACCCCA;RSEQ=AGGCAGGACTGGGCCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:19:18,1:46,1:0.2879:1,1:19.6:1:29.8:1:0.49604:2.5143:60:38:0.2879:0:1.2 0/1:23:10:9,1:12,1:0.4348:1,2:19.6:1:29.9:1:1:1.31655:60:20:0.4348:0:1 -14 105242966 . T C 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01171;SOR=1.42057;LSEQ=AAGCGCTGGGGCTGCCCAAG;RSEQ=GCCTGGCCTGGCCGCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:662:235:171,64:303,123:0.355:2,2:24.9:1:31.3:1:0.71832:1.08:60:77.333:0.3575:0:1.1 0/1:319:140:98,42:119,60:0.4389:2,2:26:1:30.3:1:0.54619:1.18:60:45.667:0.4363:0:1.1 -14 105243148 . C T 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04324;SOR=Inf;LSEQ=TGTCTGCGTGCATCCCCCTG;RSEQ=CCCTCCCAGGGCCCTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:159,392:0:2,0:23.4:1:31.1:1:1:0:60:77.714:1:0:0.2 0/1:299:3:1,2:91,204:0.01:2,2:10:1:23.3:1:1:1.12:60:2:0.0069:0:2.3 -14 105243151 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35297;SOR=2.74551;LSEQ=CTGCGTGCATCCCCCTGCCC;RSEQ=TCCCAGGGCCCTCACCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:2:1,1:147,379:0.0038:2,2:7:1:29.5:1:0.48242:2.57:60:4:0.0038:0:1 0/1:290:3:2,1:86,200:0.0103:2,2:14.7:1:27:1:0.22083:4.62:60:6:0.0108:0:1 -14 105243199 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10664;SOR=Inf;LSEQ=TGCACCAGCCAGCTCCCCTT;RSEQ=CATACCACCCACCAGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:14,218:0:2,0:23.2:1:32.1:1:1:0:60:37.667:1:0:0.3 0/1:113:2:1,1:14,97:0.0177:2,2:10.5:1:29:1:0.24889:6.73:60:4:0.0182:0:1 -14 105243220 . G A 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13585;SOR=1.59791;LSEQ=CATACCACCCACCAGGTCCT;RSEQ=GGAAGCCCCATCTCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:54:2,52:1,105:0.3375:1,1:20.1:1:30.9:1:0.26345:4.00:60:26:0.3399:0:1 0/1:69:31:1,30:3,35:0.4493:2,1:26.9:1:30.9:1:0.62187:2.53941:60:30:0.4478:0:1.2 -14 105244329 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGCCCACTGCCCCGGAAC;RSEQ=GTTCCCCGGAGAAAAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:6.5:1:30.5:1:1:1:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 105244349 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTCCCCGGAGAAAAGCCC;RSEQ=GGACAGAGGCCCAGCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:31.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 105245969 . C T 30 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=TCGGCCCAGAGACCCCCGCC;RSEQ=AGCCAGCCTCGGCCTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:21.4:1:30.2:1:1:0:60:10:1:0:0.4 1/1:2:2:1,1:0,0:1:0,2:36.5:1:30.5:1:1:0:43:4:1:0:7.5 -14 105245986 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=GCCCAGCCAGCCTCGGCCTC;RSEQ=GGACTCTGCCCAGAAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:18.1:1:28.1:1:1:0:60:6:1:0:0.4 0/1:5:2:1,1:2,1:0.4:2,2:47:1:30:1:1:1.7321:43:4:0.4:0:7.5 -14 105245993 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=CAGCCTCGGCCTCAGGACTC;RSEQ=GCCCAGAAACCCCTGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:18.5:1:28.9:1:1:0:60:7:1:0:0.4 0/1:5:2:1,1:2,1:0.4:2,2:40.5:1:30:1:1:1.7321:43:4:0.4:0:7.5 -14 105246001 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=GCCTCAGGACTCTGCCCAGA;RSEQ=ACCCCTGCCCAGCCGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:24:1:25.9:1:1:0:60:2.5:1:0:0.3 0/1:5:2:1,1:2,1:0.4:2,2:32.5:1:30.5:1:1:1.7321:43:4:0.4:0:7.5 -14 105246007 . T C 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=GGACTCTGCCCAGAAACCCC;RSEQ=GCCCAGCCGGCCTCGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:26.6:1:27.3:1:1:0:60:2.5:1:0:0.3 0/1:5:2:1,1:2,1:0.4:2,2:26.5:1:28.5:1:1:1.7321:43:4:0.4:0:7.5 -14 105246016 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=CCAGAAACCCCTGCCCAGCC;RSEQ=GCCTCGGCCTCGGGACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:31:1:29.3:1:1:0:60:14:1:0:0.7 0/1:5:2:1,1:2,1:0.4:2,2:17.5:1:29:1:1:1.7321:43:4:0.4:0:7.5 -14 105246024 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCCTGCCCAGCCGGCCTCGG;RSEQ=CTCGGGACTCAGCCCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:34.9:1:29:1:1:0:60:6:1:0:0.7 0/1:8:2:1,1:4,2:0.25:2,2:6:0:31.5:1:1:1.8258:60:4:0.25:0:2 -14 105246028 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GCCCAGCCGGCCTCGGCCTC;RSEQ=GGACTCAGCCCAGAGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:32:1:28.9:1:1:0:60:16:1:0:0.8 0/1:8:2:1,1:4,2:0.25:2,2:5.5:1:29.5:1:1:1.8258:43:4:0.25:0:7.5 -14 105246056 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GCCCAGAGACCCCGGCCCAG;RSEQ=CAGCCTCGGCCTCGGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:24.4:1:32.3:1:1:0:60:16:1:0:0.8 0/1:9:2:1,1:4,3:0.2222:2,2:38:0:31:0:1:1.29098:60:4:0.2222:0:2 -14 105246325 . T A 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.91668;SOR=1.02847;LSEQ=GTTGCTTGCCAGCCCAGGAC;RSEQ=TGGAGGCTCCAGGGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:100:92,8:182,14:0.3378:2,2:24.8:1:30.1:1:0.81684:1.12995:60:200:0.3413:0:1.3 0/1:154:53:49,4:95,6:0.3442:2,2:22.3:1:29.9:1:0.73735:1.29026:60:106:0.3442:0:1.3 -14 105246407 . G A 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.5374;LSEQ=CCCAAATCTGAATCCCGAGA;RSEQ=GCCAAGGGGATACTTACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1313:420:251,169:515,378:0.3199:2,2:26.7:1:30.5:1:0.50923:1.09:60:59:0.3189:0:1.2 0/1:818:165:96,69:368,285:0.2017:2,2:24.9:1:30:1:0.72519:1.08:60:164:0.2037:0:1.3 -14 105246681 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12731;SOR=Inf;LSEQ=GAGTCCCAGGGGGCAGGCGC;RSEQ=GTACGGGAGCTGTTTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:0,73:0:1,0:19.8:1:31:1:1:0:60:35.5:1:0:0 0/1:41:2:0,2:2,37:0.0488:2,0:21.5:1:32.5:1:1:0:60:4:0.0488:0:1 -14 105246692 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15309;SOR=Inf;LSEQ=GGCAGGCGCGGTACGGGAGC;RSEQ=GTTTCTTAGGGCCAGCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:0,49:0:1,0:22.6:1:30.5:1:1:0:60:98:1:0:0 0/1:32:2:0,2:2,28:0.0625:2,0:11:1:31.5:1:1:0:60:4:0.0625:0:1 -14 105247366 . A G 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCAGGTACACGGGAAC;RSEQ=TTCTCCCTCAAGTTTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:0:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -14 105258801 . C T 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0402;SOR=Inf;LSEQ=AAGACATGGGGCCCAGGACA;RSEQ=TCACCCTAGGCCAGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:253,8:0:1,0:24:1:32.3:1:1:0:60:86:1:0:0.3 0/1:137:3:2,1:131,3:0.0219:1,2:13:1:28.7:1:0.08567:20.00289:60:6:0.0221:0:1.3 -14 105258892 . CA TG 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03712;SOR=1.23313;LSEQ=GACCCTGGGGCTACTACCCC;RSEQ=TCTCTCCCTCCCCAGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1177:357:214,143:478,338:0.3033:2,2:27.4:1:31.4:1:0.6988:1.06:60:714:0.3064:0.0093:1.1 0/1:770:269:155,114:271,225:0.3494:2,2:25.3:1:30.8:1:0.44651:1.13:60:538:0.3539:0.0429:1 -14 105258893 . A G 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.56565;LSEQ=ACCCTGGGGCTACTACCCCC;RSEQ=TCTCTCCCTCCCCAGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1184:632:371,261:120,84:0.5338:2,2:25.2:1:30.3:1:1:1.005:60:62.2:0.7549:0:1.1 0/1:743:292:164,128:112,101:0.393:2,2:25.2:1:29.9:1:0.46915:1.16:60:47.667:0.5755:0:1.2 -14 105259002 . G A 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06093;SOR=4.82688;LSEQ=GTGCCCGAGGCTCCCGCGAC;RSEQ=CTCACGCGCTCCTCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:2:1,1:262,537:0.0025:2,2:8:1:26.5:1:0.54915:2.05:60:4:0.0025:0:1 0/1:502:6:4,2:168,328:0.012:2,2:5:1:28:1:0.18767:3.89:60:12:0.0122:0:1.7 -14 105259042 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10205;SOR=Inf;LSEQ=CTGGCGCTCCCCGAGCCCAG;RSEQ=TGGCCTGGCCACAGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:52,373:0:2,0:25:1:31.8:1:1:0:60:29.357:1:0:0.1 0/1:200:2:1,1:26,171:0.01:2,2:33:1:29.5:1:0.25354:6.47:60:4:0.0101:0:1 -14 105615026 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGTCCATCTCAGGGTGAT;RSEQ=AGGGGCCCACAGGGGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:15:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:12.5:1:31:0:1:0:60:4:1:0:1.5 -14 105617042 . C T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0985;SOR=0.42687;LSEQ=GCAGGGGCTGCTGGCACACT;RSEQ=GTCTCGTTCCAGCTCGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:15:7,8:11,15:0.3659:2,2:21.9:1:30.5:1:1:1.19:60:30:0.3846:0:1.1 0/1:51:10:4,6:18,23:0.1961:2,2:29.8:1:29.4:1:1:1.17025:60:20:0.1961:0:1.1 -14 105800258 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACACGCACCTGCCTGTG;RSEQ=CTCACCCGGGCTAAAATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:28:1:1:0:60:4:1:0:1.5 -14 105801668 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCCTGGAGTGGCTGTGAC;RSEQ=CTGTGGCCGGCGCCTGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:31.5:1:1:0:60:4:1:0:1.5 -14 105801780 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16875;SOR=Inf;LSEQ=TGTGGCCGGCGCCTGGCGTG;RSEQ=CTCTGACGCTGTGGCCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:24,14:0:2,0:20.5:1:31:1:1:0:59.2:76:1:0:0.1 0/1:27:2:1,1:16,9:0.0741:2,2:13.5:1:27.5:1:1:1.73837:60:4:0.0769:0:1.5 -14 105801859 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5023;SOR=0;LSEQ=GTTCCTTCCCCTATTCTGGG;RSEQ=CAGGTGGGGACCACCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:18,16:0.0556:2,2:11:1:27.5:1:1:1.12132:60:4:0.0571:0:1 0/0:27:0:0,0:14,13:0:2,0:19.7:1:30.6:1:1:0:60:26:1:0:0.1 -14 105905512 . A G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACCCCTGAGGTGTCTGC;RSEQ=TGGCTGGAAGCACCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:0,1:0.6667:0,0:11:1:29.5:1:0.33333:0:52:4:0.6667:0:5 -14 105905524 . A T 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GTGTCTGCATGGCTGGAAGC;RSEQ=CCCTCCCTGGTCACTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:12:0:31:0:1:0:60:2:1:0:0 1/0:4:3:2,1:0,1:0.75:0,2:17.7:1:31.3:1:1:0:47.7:6:0.75:0:5 -14 105905552 . C A 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TGGTCACTCAGGCAGCCCTG;RSEQ=AGGGCTGTGAGCTCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:32:1:34.3:1:1:0:60:6:1:0:0.3 1/0:4:3:2,1:0,1:0.75:0,2:38.7:1:28.7:1:1:0:47.7:6:0.75:0:5 -14 105905572 . CCAA TCCAC 44 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.1;SOR=Inf;LSEQ=CAGGGCTGTGAGCTCTGCCC;RSEQ=CCCTGAGGTGTCTGCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:41:1:32.7:1:1:0:60:6:1:0:0.3 1/1:3:3:2,1:0,0:1:0,2:35.3:1:27.9:1:1:0:47.7:6:1:0:5 -14 105905591 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCCAACCCTGAGGTGTCTGC;RSEQ=TGGCTGGAAGCGCCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:21:1:30.3:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:23:1:28.5:1:1:0:48:4:1:0:5.5 -14 105905603 . G A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GTGTCTGCGTGGCTGGAAGC;RSEQ=CCCTCCCTGGTCACTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:9:1:30.7:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:11:1:27:1:1:0:48:4:1:0:5.5 -14 105905995 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05472;SOR=Inf;LSEQ=GTCCCCACCAGTGGACACAT;RSEQ=GTTCCAGCAGAGAGTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:113,70:0:2,0:24.6:1:31.4:1:1:0:60:90.5:1:0:0.5 0/1:113:3:1,2:66,44:0.0265:2,2:14.7:1:28.3:1:0.56561:2.97064:60:6:0.0268:0:1 -14 105906059 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14361;SOR=Inf;LSEQ=CTCTCTGTGCCTGCCTGCAG;RSEQ=GCTCCTGAGCCCCCGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:84,102:0:2,0:27.9:1:30.4:1:1:0:60:22.25:1:0:1 0/1:114:2:1,1:46,66:0.0175:2,2:16.5:1:29.5:1:1:1.43:60:4:0.0179:0:1 -14 105906063 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52855;SOR=0;LSEQ=CTGTGCCTGCCTGCAGGGCT;RSEQ=CTGAGCCCCCGATCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:76,102:0.0111:2,2:43:1:30:1:1:1.34:60:4:0.0114:0:2 0/0:109:0:0,0:43,66:0:2,0:26.4:1:30.7:1:1:0:60:218:1:0:0.7 -14 105906073 . C T 222 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01908;LSEQ=CTGCAGGGCTCCTGAGCCCC;RSEQ=GATCCCCTGGAGCCAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:163:161:62,99:0,0:0.9877:0,2:25.5:1:30.4:1:1:0:60:52.667:0.9875:0:1.2 1/0:98:59:23,36:12,26:0.602:2,2:27.5:1:30.2:1:0.52009:1.38:60:118:0.6082:0:1.2 -15 20487945 . T C 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCTCTCTGCGCCTGCGC;RSEQ=GGCGCTGTGCGCCTTTGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:26.5:1:1:0:60:4:1:0:2 -15 20487948 . C T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTCTGCGCCTGCGCTGG;RSEQ=GCTGTGCGCCTTTGCGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:26.5:1:1:0:60:4:1:0:2 -15 20488202 . G A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAGCACAGACCTTGGGA;RSEQ=CACTGCATCGCTTTGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:31:0:31:0:1:0:60:2:1:0:1 1/1:3:3:1,2:0,0:1:0,2:24.3:1:29.7:1:1:0:60:6:1:0:1.3 -15 20488509 . G A 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77661;LSEQ=CTTTTTGTAAGATTACAGAG;RSEQ=ACATAGATTAAGTTGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:7,0:17,1:0.28:1,0:24.1:1:30.9:1:1:0:48.4:14:0.28:0:1 0/1:13:3:2,1:9,1:0.2308:2,2:30:1:30:1:0.42308:3.87298:41.7:6:0.2308:0:1.3 -15 20488870 . G A 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19376;LSEQ=TGGGACTGCTGGGTATAACC;RSEQ=TGCTGTGGACTGCTGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1873:354:150,204:638,878:0.189:2,2:25.8:1:30.7:1:0.95235:1.01:52.2:353:0.1906:0:1.1 0/1:2408:104:46,58:1047,1254:0.0432:2,2:24.5:1:29.8:1:0.84079:1.05273:52.8:51:0.0427:0:1.1 -15 20489033 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21383;SOR=Inf;LSEQ=ATCTTGGCTAACTGTAGCCT;RSEQ=TGCCTTCTGGGTCAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:7,204:0:1,0:21.9:1:32:1:1:0:50.2:104.5:1:0:0.1 0/1:182:2:0,2:3,177:0.011:1,0:12.5:1:26:1:1:0:53.5:4:0.0111:0:1 -15 20489155 . T C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05126;SOR=Inf;LSEQ=ATGGGGTTTTGCCATGTTGC;RSEQ=CACGCTGGTCTTGAACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:32:16,16:6,4:0.7442:2,2:27.6:1:30.4:1:0.72253:1.48564:48.1:15:0.7317:0:1.1 1/1:13:13:7,6:0,0:1:0,2:23.5:1:29.8:1:1:0:50.7:12:1:0:1.2 -15 20489199 . C T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48345;SOR=1.84705;LSEQ=CTCAAGTGATCCTCCTGCCT;RSEQ=GGCCTCCCAAAGTGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:3,2:28,12:0.1087:2,2:27.4:1:31.6:1:0.63945:1.53943:57.8:10:0.1163:0:1.6 0/1:27:5:5,0:18,4:0.1852:2,0:18:1:31.2:1:0.56125:0:55.4:10:0.1852:0:1 -15 20489217 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13258;SOR=Inf;LSEQ=CTCGGCCTCCCAAAGTGCTG;RSEQ=GATTACAAGCATGAGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:45,10:0:2,0:21.3:1:30.4:1:1:0:56:17.333:1:0:0.6 0/1:32:2:2,0:26,4:0.0625:2,0:19:1:31:0:1:0:55.5:4:0.0645:0:2 -15 20489310 . A G 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00606;SOR=1.61627;LSEQ=TTCATTATGCTGAAAAAGAA;RSEQ=TCTTTATATCTGAATGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:104:102,2:195,8:0.3388:1,1:24.6:1:32.9:1:0.50367:2.09:38.8:208:0.341:0:1 0/1:267:121:116,5:142,4:0.4532:1,1:22.6:1:32:1:0.73572:1.5277:38.7:120:0.4528:0:1.1 -15 20489490 . A T 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AGTCTGGGCAGAAGTCTCAG;RSEQ=GAAAGGTATGAATATGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2246:0:0,0:1061,1184:0:2,0:26:1:30.5:1:1:0:58.8:65.029:0.9995:0:0.1 0/1:2811:41:19,22:1371,1398:0.0146:2,2:20.7:1:29.1:1:0.75404:1.13548:58.7:40:0.0145:0:1.2 -15 20489500 . G A 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=12.93289;LSEQ=GAAGTCTCAGAGAAAGGTAT;RSEQ=AATATGAAAGGGTTAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2176:2:2,0:988,1185:9e-04:2,0:1:0:25:1:0.20707:0:60:4:9e-04:0:1 0/1:2721:32:16,16:1268,1420:0.0118:2,2:18.9:1:29.8:1:0.85905:1.12:47.4:64:0.0118:0:2.9 -15 20489511 . G A 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGGTATGAATATGAAAG;RSEQ=GTTAAGAATTTGTGGTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2034:0:0,0:876,1157:0:2,0:26.4:1:30.8:1:1:0:58.7:52.5:1:0:0.1 0/1:2492:27:15,12:1107,1356:0.0108:2,2:13.8:1:29.5:1:0.33164:1.53:46.5:26:0.0106:0:3.1 -15 20489700 . C A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTACTACTTAGCTGTGTGG;RSEQ=CTTAGGCAAGTTATTTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:0,2:4,86:0.0217:1,0:23.5:1:25.5:1:1:0:48.5:4:0.0222:0:2.5 0/0:44:0:0,0:3,41:0:2,0:19.3:1:31.8:1:1:0:42.3:88:1:0:0 -15 20489800 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGAGGGTTAGGTATAAT;RSEQ=TAAACAAGTGCCTTGTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:1,2:2,26:0.0968:2,2:43.3:1:29:1:0.27119:5.85:60:6:0.0968:0:1 0/0:6:0:0,0:1,5:0:2,0:18.3:1:30.8:1:1:0:60:12:1:0:0.2 -15 20489987 . A G 73 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AAAATTAAATGTCAAATAAC;RSEQ=TAACATAGGTAATTGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:3,2:0.5:2,0:24.8:1:31.8:1:0.16667:0:49.6:10:0.5:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 20490242 . G A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68063;SOR=1.74603;LSEQ=TTAGTTTGACCTTGAGTCTA;RSEQ=CAACAAGAGAGGGAACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:7,2:16,0:0.36:1,2:21:1:30.2:1:0.12:0:50.9:18:0.375:0:1.2 1/0:8:4:4,0:4,0:0.5:0,0:11:1:28:1:1:0:48.5:8:0.5:0:1.3 -15 20490280 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11104;SOR=Inf;LSEQ=GGCAGCGAAGAGGTCGTGAC;RSEQ=GATGTCCCAGCAACAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:33,4:0:2,0:24.3:1:31.4:1:1:0:54:74:1:0:0.3 0/1:19:2:2,0:15,2:0.1053:2,0:13.5:1:31.5:1:1:0:54:4:0.1176:0:2 -15 20490358 . G A 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00902;SOR=Inf;LSEQ=ACTCTGAATACAGAGAGTGA;RSEQ=GAAGATTAGGGGGCCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:106,9:0:2,0:23.3:1:32:1:1:0:49.4:230:1:0:0.1 0/1:99:6:6,0:82,11:0.0606:2,0:15.3:1:30.5:1:1:0:49.2:12:0.0606:0:1.3 -15 20490398 . T C 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05187;SOR=Inf;LSEQ=CTGCTGACTCCCTGACGATC;RSEQ=CAGACCCTCTCTGCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:208,16:0:2,0:24.8:1:31.1:1:1:0:54:55:1:0:0 0/1:206:4:4,0:174,28:0.0194:2,0:21:1:29.5:1:1:0:56.8:8:0.0195:0:1 -15 20490445 . T A 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGCCTGTTAATTCTGGCA;RSEQ=ACTGTTACTGATAATATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:348,116:0:2,0:24.2:1:29.8:1:1:0:47.7:57:1:0:0.5 0/1:431:31:22,9:280,119:0.0719:2,2:24.4:1:29:1:1:1.04:42.7:30:0.0708:0:1.8 -15 20490501 . C T 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.91966;LSEQ=GATTTGCCCAATTGTTGCTT;RSEQ=AGCTCTGGACCTTGTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:951:759:501,258:116,76:0.7981:2,2:25.4:1:29.5:1:0.15108:1.27:44.1:125.5:0.7977:0:1 1/1:839:798:517,281:21,18:0.9511:2,2:25.6:1:29.2:1:0.17358:1.58:44.4:398:0.9522:0:1.1 -15 20490520 . G T 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGCTCTGGACCTTGTCAA;RSEQ=AAGTTGTTGGTAGTGGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1096:0:0,0:639,457:0:2,0:26.4:1:31.4:1:1:0:50.5:67.5:1:0:0.7 0/1:1062:62:33,29:591,408:0.0584:2,2:22.4:1:28.7:1:0.3559:1.27264:50:124:0.0588:0:1.7 -15 20490549 . GT G 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=3.3196;LSEQ=GGTAGTGGATCCAAAGGCAT;RSEQ=TTTACAACAGAAGAAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1255:73:42,31:621,560:0.0582:2,2:30.5:1:31.8:1:0.46896:1.22:56.4:146:0.0588:0.0072:0.5 0/1:1369:233:137,96:609,526:0.1702:2,2:29.4:1:31.5:1:0.16993:1.23:55.5:466:0.1718:0.0066:0.5 -15 20490611 . T C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16369;LSEQ=GGGTGTGGGACAGTGCCTGC;RSEQ=AGCATAAAATACATGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:999:173:61,112:321,505:0.1732:2,2:27.5:1:31.8:1:0.39081:1.1669:53.3:172:0.1734:0:1.1 0/1:1268:42:13,29:497,729:0.0331:2,2:25.6:1:31.1:1:0.26294:1.52036:52.8:41:0.0327:0:1.3 -15 20490624 . A T 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00157;SOR=Inf;LSEQ=TGCCTGCTAGCATAAAATAC;RSEQ=TGGGAAGCCCTGCTGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:876:0:0,0:318,558:0:2,0:25.8:1:30.4:1:1:0:53.3:108.5:1:0:0.3 0/1:1082:11:1,10:403,667:0.0102:2,2:22.4:1:29.5:1:0.06158:6.03619:53.5:22:0.0103:0:1.8 -15 20490770 . A G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16955;SOR=0.3032;LSEQ=TTTTTTTTTTGAGACAGGTT;RSEQ=TCATTCTGTCACCCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:7:0,7:0,43:0.14:1,0:16.6:1:32.1:1:1:0:45:14:0.1522:0:1.1 0/1:43:2:1,1:2,38:0.0465:2,2:8.5:1:33:1:0.13937:15.71:41:4:0.0513:0:1 -15 20491106 . T C 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=CCCAGCCATGTCCACTGCTC;RSEQ=TCATAGGTGGGGTGCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:16.5:1:29:1:1:1.73:60:4:0.4:0:1.5 0/0:3:0:0,0:1,2:0:2,0:30.7:1:29:1:1:0:60:6:1:0:0 -15 20494786 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCCCTGCTCATCTCCCG;RSEQ=TCCTGCAGCATGAAACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:32.5:1:1:0:49.5:4:1:0:1.5 -15 20495041 . G GC 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGTGAGACCCAGCCCCTG;RSEQ=CCCCTGATTGTCACCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:24.3:1:32.2:1:1:0:43.5:8:1:0.25:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:33.5:1:1:0:47:4:1:0:0 -15 20495201 . GA G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.40345;SOR=1.42482;LSEQ=TGGACTCCTGTGGGAAGGTA;RSEQ=GGGGGGCAACACATAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:17:16,1:43,4:0.2237:2,1:25.9:1:32.4:1:1:1.48:57:34:0.2297:0.0132:0.1 0/1:48:14:12,2:32,0:0.2917:1,2:19.1:1:31.3:1:0.08792:0:58.6:28:0.3182:0.0625:0.1 -15 20495268 . C T 153 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=7e-05;SOR=3.89392;LSEQ=GATGATTCTTGGACGGACAT;RSEQ=TTTTCCTCCCTCTTTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:11:11,0:248,21:0.0393:2,0:24.1:1:30.9:1:1:0:50.9:22:0.0397:0:1.1 0/1:247:34:30,4:192,21:0.1377:2,2:23.4:1:30.1:1:0.75904:1.21801:46.4:33:0.1347:0:1.1 -15 20495408 . G A 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.44064;SOR=0.93889;LSEQ=TTCAAGATCTTCTGTGTGAG;RSEQ=AAAATGAATCCACAGCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1695:350:203,147:721,624:0.2065:2,2:26.3:1:29.8:1:0.14837:1.20:57.2:57.333:0.2057:0:1.1 0/1:2134:419:229,190:908,801:0.1963:2,2:27.5:1:29.2:1:0.58515:1.06:57.3:103.75:0.1967:0:1.1 -15 20495453 . G A 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.01539;LSEQ=AGGTTCTAGCCCAGGTATTC;RSEQ=TATTCCTGATGATCACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1493:26:15,11:626,841:0.0174:2,2:18.6:1:29.8:1:0.16111:1.83:57.6:25:0.0168:0:1 0/1:1777:268:122,146:655,852:0.1508:2,2:24.7:1:29.6:1:0.54795:1.09:58.1:133:0.1506:0:1.1 -15 20495643 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16327;SOR=Inf;LSEQ=GGATATGTTTAATATCTAAC;RSEQ=CATAATAGACAGATAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:12,61:0:2,0:22.4:1:29.9:1:1:0:55.8:72:1:0:0.3 0/1:50:2:1,1:6,42:0.04:2,2:9.5:1:29.5:1:0.26286:6.56:60:4:0.04:0:1 -15 20495645 . A C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25021;SOR=0.54502;LSEQ=ATATGTTTAATATCTAACAC;RSEQ=TAATAGACAGATAAGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:17:1,16:11,43:0.2394:2,1:24.9:1:31.6:1:0.26992:4.03265:57.9:16:0.2353:0:1.2 0/1:48:7:0,7:6,35:0.1458:2,0:31.6:1:32.9:1:0.57252:0:58.1:14:0.1489:0:1 -15 20495660 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12147;SOR=Inf;LSEQ=AACACATAATAGACAGATAA;RSEQ=CACAGCTAGGGATTGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:6,51:0:2,0:21.3:1:32:1:1:0:53.4:27.5:1:0:0.3 0/1:31:2:1,1:2,27:0.0645:2,2:24.5:1:27:1:0.1871:11.22:24:4:0.0667:0:1 -15 20496402 . T C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00245;SOR=8.41354;LSEQ=AAGCCATAGGGAGAGAAATA;RSEQ=CTATTAGATAAGCATGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:7,0:22,3:0.2188:2,0:25.9:1:33.9:1:1:0:52.7:14:0.2188:0:1 1/0:14:10:8,2:4,0:0.7143:0,2:26.7:1:30.7:1:1:0:52.4:20:0.7143:0:1 -15 20496514 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2447;SOR=Inf;LSEQ=TCAAATGCCCCCACTTTACT;RSEQ=GAAGTATATTGAGGAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:137,29:0:2,0:22.8:1:32.1:1:1:0:49.7:332:1:0:0.1 0/1:163:2:1,1:142,19:0.0123:2,2:21.5:1:27.5:1:0.23101:7.31161:37:4:0.0125:0:1 -15 20496622 . A T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3018;LSEQ=TACTAGTCGAAAGTGGCCTC;RSEQ=TGAAGGGGAAGCCGAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:798:117:60,57:401,279:0.1466:2,2:25.7:1:30.4:1:0.12896:1.36485:40.5:234:0.1492:0:1.4 0/1:1157:57:28,29:627,473:0.0493:2,2:26:1:28.9:1:0.27344:1.37252:39.6:27.5:0.0484:0:1.6 -15 20496657 . C T 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=0.58529;LSEQ=AGGGTGCCGAGACCACAAAG;RSEQ=GCCCGGCTGTGTGTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:132:59,73:361,328:0.1606:2,2:27.2:1:30:1:0.10733:1.36125:42.8:43:0.1608:0:1.8 0/1:1202:121:62,59:550,530:0.1007:2,2:24.1:1:29.6:1:1:1.01:47.9:242:0.1019:0:1.8 -15 20496692 . A G 276 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.6642;LSEQ=GCTGCTGTGTTGTGAACTCC;RSEQ=TGGTTTGAACATGAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:707:445:177,268:114,148:0.6294:2,2:23.6:1:31:1:0.34304:1.16602:37.7:110.25:0.6309:0:1.4 1/0:1032:547:210,337:214,270:0.53:2,2:23.7:1:30.4:1:0.06587:1.27161:40.7:135.75:0.5344:0:1.3 -15 20496770 . T C 145 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0258;SOR=2.57405;LSEQ=AGTCTGTTTTTTATAGTGTG;RSEQ=ATTTTAATTATGGAAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:8:0,8:50,279:0.0237:2,0:20.5:1:32.5:1:0.61048:0:50.4:16:0.024:0:1.4 0/1:390:23:3,20:61,306:0.059:2,2:26.7:1:32.1:1:1:1.32808:51.8:46:0.0593:0:1.4 -15 20496886 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22649;SOR=Inf;LSEQ=TTCTTTAGTTGAATGGCTTT;RSEQ=TTATTTATTTATTTGAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:3,46:0:2,0:20.5:1:31.5:1:1:0:49.1:23.5:1:0:0.1 0/1:45:2:1,1:7,36:0.0444:2,2:31:1:29.5:1:0.32727:4.88:40:4:0.0444:0:1.5 -15 20496906 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20964;SOR=Inf;LSEQ=GTTATTTATTTATTTGAGAC;RSEQ=GAGTCTCACTCTGTTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:2,27:0:2,0:23.2:1:31.1:1:1:0:51.8:58:1:0:0 0/1:25:2:1,1:3,20:0.08:2,2:5:1:30:1:0.3:5.92:47.5:4:0.08:0:1.5 -15 20498452 . C T 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCTGGAGTGCAATGGTG;RSEQ=GATCTCGGCTCACTGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:0:29.5:1:1:0:60:4:1:0:1 -15 21126936 . T C 38 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.50549;SOR=2.73861;LSEQ=TTTAACATGACTTAACCTTT;RSEQ=GTTTGTATTTTTTTGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:0.25:0,0:23.3:1:24.3:1:1:0:40.3:2:0.2857:0:3.3 1/0:2:1:1,0:1,0:0.5:0,0:40:0:31:0:1:0:60:2:0.5:0:1 -15 21126976 . G A 30 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.46553;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=GACTTTCTCTTTCTAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:3,1:3,0:0.3077:0,2:12.5:1:15.3:1:1:0:30.8:0.333:0.1667:0:2.5 0/1:5:2:1,1:1,0:0.4:0,2:25.5:1:30.5:1:1:0:37.5:4:0.6667:0:3.5 -15 21129077 . A T 27 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGTTGGAAGGGGAATTT;RSEQ=AGATAGCTAGATTATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:83,32:0.0171:2,2:5:0:27:1:0.4863:2.56949:50:4:0.0172:0:0 0/0:47:0:0,0:35,12:0:2,0:22.2:1:28:1:1:0:31.8:94:1:0:0.1 -15 21129163 . C A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58204;SOR=0;LSEQ=GGTGGCTTTCTATCTAAAAT;RSEQ=CCTGCTTCATACAGTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:4:2,2:170,150:0.0123:2,2:38.3:1:29.8:1:1:1.13289:49.5:8:0.0125:0:1.3 0/0:130:0:0,0:66,63:0:2,0:25:1:30.8:1:1:0:39.7:128:1:0:0.1 -15 21129206 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07015;SOR=Inf;LSEQ=TGTCAGGATTCATAAATCTG;RSEQ=GGAACATGGCACTTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:81,123:0:2,0:22.6:1:30.2:1:1:0:35.3:101:1:0:0.1 0/1:74:2:1,1:28,44:0.027:2,2:20:1:30.5:1:1:1.56:27:4:0.0274:0:1 -15 21129228 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07644;SOR=Inf;LSEQ=GAACATGGCACTTCCTGCTG;RSEQ=ACTGATACTGTTCTGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:48,92:0:2,0:24.8:1:31.5:1:1:0:32.3:27:1:0:0.1 0/1:54:2:1,1:15,37:0.037:2,2:14:1:27.5:1:0.50874:2.42:27:4:0.037:0:1 -15 21131904 . GCA G 42 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCATTACTTGACATACCTCA;RSEQ=CACACACACACAAAATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:3,0:47,23:0.0411:2,0:21.7:1:27:1:0.547:0:34.3:2:0.0278:0:0 0/0:21:0:0,0:14,6:0:2,0:19.4:1:31.4:1:1:0:33.2:40:0.9524:0:0.2 -15 21134146 . G T 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07156;SOR=0;LSEQ=TTGAACAAATATGTTCTGAA;RSEQ=GATTTGCTATGTGCCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:5:1,4:220,38:0.019:2,2:5.2:1:27.4:1:0.00254:22.70253:54.2:10:0.0193:0:1.4 0/0:203:0:0,0:156,47:0:2,0:23:1:31.4:1:1:0:43.1:202:1:0:0.3 -15 21134222 . G A 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05169;SOR=1.31236;LSEQ=TGAGAACAAGGAACCACACT;RSEQ=GCCAGAGCCATCGCTATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:146:94,52:284,154:0.2491:2,2:28.1:1:29.2:1:0.92066:1.02015:42.5:145:0.2522:0:1.1 0/1:468:142:83,59:182,143:0.3034:2,2:25.4:1:28.6:1:0.68482:1.11:44.7:34.5:0.302:0:1.1 -15 21134223 . GC TT 123 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00066;SOR=4.85422;LSEQ=GAGAACAAGGAACCACACTG;RSEQ=CAGAGCCATCGCTATAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:5:2,3:373,208:0.0085:2,2:17.2:1:28.6:1:0.35653:2.68509:29.4:10:0.0088:0:1.6 0/1:474:19:9,10:257,196:0.0401:2,2:13.2:1:29.1:1:0.48248:1.45572:33.1:38:0.0409:0.0042:1.4 -15 21134235 . G A 121 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2602;SOR=1.59289;LSEQ=CCACACTGGCCAGAGCCATC;RSEQ=CTATAGGGAGCTCTCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:615:14:3,11:381,220:0.0228:2,2:8.1:1:30.2:1:0.0032:6.33124:28.7:28:0.0232:0:1.2 0/1:447:16:1,15:249,182:0.0358:2,1:11.6:1:30.4:1:3e-05:20.4228:26.6:32:0.036:0:1.4 -15 21134359 . A T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00964;SOR=Inf;LSEQ=TGTTGAGGGATTTTCATCAG;RSEQ=ACTTCCATAAATGTAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:9,208:0:1,0:25.6:1:30.4:1:1:0:28.6:53.25:1:0:0.1 0/1:101:4:0,4:2,95:0.0396:1,0:15.5:1:28.3:1:1:0:25.5:8:0.0408:0:1 -15 21134375 . G A 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69214;SOR=1.51901;LSEQ=TCAGAACTTCCATAAATGTA;RSEQ=CTGTCTGGAGATCCTTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:5:0,5:8,167:0.0278:1,0:13.8:1:29.6:1:1:0:29.6:10:0.0282:0:1.2 0/1:72:3:0,3:2,67:0.0417:1,0:23.3:1:29.3:1:1:0:31.3:6:0.0417:0:1 -15 21134388 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGTAGCTGTCTGGAGAT;RSEQ=CTTGTAGTACCCTAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:0,2:8,144:0.013:2,0:9.5:1:31:0:1:0:27:4:0.0132:0:1 0/0:58:0:0,0:2,56:0:1,0:25:1:31.3:1:1:0:28.6:116:1:0:0.2 -15 21134398 . C T 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69619;SOR=1.47327;LSEQ=GTCTGGAGATCCTTGTAGTA;RSEQ=CCTAAACCTGATGTGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:6:0,6:10,117:0.0451:2,0:31.5:1:30.7:1:1:0:29.2:12:0.0462:0:1 0/1:46:3:0,3:4,39:0.0652:2,0:23:1:31:0:1:0:31.3:6:0.0652:0:1 -15 21134491 . G C 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03558;SOR=Inf;LSEQ=ACAAGCCAGTTCTCTAGGCT;RSEQ=TGTATTTCTATATGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:69,33:0:2,0:18.2:1:32.6:1:1:0:33.7:204:1:0:0 0/1:51:3:3,0:39,9:0.0588:2,0:18.3:1:28.7:1:1:0:34.7:6:0.0588:0:1 -15 21134524 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16549;SOR=Inf;LSEQ=TGAAACTTTCATTTGATCTC;RSEQ=CCTATGGAGTGCATGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:141,41:0:2,0:24.9:1:30.4:1:1:0:34.3:90:1:0:0.1 0/1:126:2:1,1:95,29:0.0159:2,2:12:1:29.5:1:0.42095:3.23769:49.5:4:0.016:0:1 -15 21134536 . C T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15568;SOR=Inf;LSEQ=TTGATCTCACCTATGGAGTG;RSEQ=ATGAGACCACCGTCTATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:178,56:0:2,0:25.2:1:32.1:1:1:0:34.8:77:1:0:0.1 0/1:153:2:0,2:112,39:0.0131:2,0:18.5:1:23.5:1:0.07052:0:38.5:4:0.0132:0:1 -15 21134628 . G A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16378;SOR=5.87794;LSEQ=CAACCTCCGAGACATGCCAC;RSEQ=TTTCCTGCCACCTGTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:1,0:102,162:0.0038:2,0:1:0:26:0:0.38868:0:51:2:0.0038:0:1 0/1:183:4:1,3:58,121:0.0219:2,2:9.5:1:29.5:1:1:1.43536:49.3:8:0.0221:0:1.3 -15 21135195 . A AGT 82 MSI6 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=35;MSI=18.000;MSILEN=2;SSF=0.00014;SOR=10.01261;LSEQ=TGTTTTGTTTTGTCTTTGAG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:5:5,0:110,3:0.042:1,0:16.6:1:31.2:1:1:0:31.8:10:0.0459:0.0168:1.2 0/1:29:9:6,3:20,0:0.3103:1,2:20.8:1:26.1:1:0.02299:0:35.7:18:0.3214:0.1379:0.4 -15 21135235 . CG C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGTGTGTGTGTGGCGG;RSEQ=GGGGGCTTTATTTGCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:99,24:0.016:2,2:37.5:1:31.5:1:0.36129:4.06202:27:4:0.0167:0:0 0/0:30:0:0,0:22,8:0:2,0:33.7:1:28:1:1:0:37.1:60:1:0:0.4 -15 21135409 . G GA 29 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.33028;SOR=4.19592;LSEQ=CTTGCCTGGTCCAAATCTCT;RSEQ=AAAAAAAAAAATTAGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:0,2:4,23:0.069:2,0:15.5:1:29.5:1:1:0:27:4:0.069:0.0345:2.5 0/1:4:1:0,1:1,2:0.25:2,0:39:0:32:0:1:0:27:2:0.25:0:0 -15 21136600 . A T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29402;SOR=3.59065;LSEQ=ATCATCTGCTGCTTGGTTTG;RSEQ=TGTTCCCATAACCCAGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:1,0:142,112:0.0039:2,0:28:0:12:0:1:0:27:0:0:0:3 0/1:143:2:1,1:80,61:0.014:2,2:13.5:1:24.5:1:1:1.30895:38.5:4:0.0141:0:1 -15 21136674 . C A 104 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03893;SOR=2.65683;LSEQ=GCGGAGAAAAGAGAAACAGC;RSEQ=AACAATTTTTTTGAAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:7:7,0:126,185:0.022:2,0:32.7:1:30.4:1:0.00204:0:28.6:14:0.0221:0:1.1 0/1:230:13:13,0:93,124:0.0565:2,1:35.9:1:28.2:1:3e-05:0:29:12:0.0526:0:1 -15 21136691 . CCA C 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=1.03832;LSEQ=AGCCAACAATTTTTTTGAAG;RSEQ=CACACACACACACCTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:10:2,8:91,166:0.0375:2,2:25:1:30.9:1:0.50173:2.18718:48.6:9:0.0342:0.0037:0.1 0/1:206:8:4,4:78,120:0.0388:2,2:25.8:1:32.3:1:0.71552:1.54:42.4:16:0.039:0:0.1 -15 21136727 . T A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTAATTGTGTAAGATTTC;RSEQ=TACAGTGCAAATAATTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:27,130:0:2,0:24.1:1:29.8:1:1:0:50:30.4:1:0:0.1 0/1:93:12:1,11:18,63:0.129:2,2:27.3:1:30.3:1:0.44802:3.11364:52.7:24:0.1304:0:1 -15 21136755 . C T 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.34024;LSEQ=CAAATAATTTGGCAGATAAC;RSEQ=CAGGTGACATGACGACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:14:1,13:7,91:0.125:2,1:31.4:1:29.1:1:1:1:38.8:13:0.1171:0:1 0/1:69:33:9,24:3,33:0.4783:2,2:28.4:1:27.9:1:0.0563:4.04:41.3:10:0.4615:0:1.2 -15 21136800 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07869;SOR=Inf;LSEQ=AGAGATACTGATGTCACAGA;RSEQ=GTAAAAGCCAGAAGGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:5,55:0:2,0:26.7:1:30.1:1:1:0:56:59:1:0:0.2 0/1:46:3:1,2:5,38:0.0652:2,2:42.7:1:26.3:1:0.34914:3.64:27:2:0.0465:0:2 -15 21136951 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GCCACAGGCACAAAGCTTAC;RSEQ=GAAATTTGAGGAGAGACGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:24,3:0:2,0:20.6:1:31.2:1:1:0:43.7:54:1:0:0.1 0/1:13:2:2,0:9,2:0.1538:2,0:16.5:1:27.5:1:1:0:43.5:4:0.1538:0:2 -15 21136968 . C T 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0247;SOR=Inf;LSEQ=TACGGAAATTTGAGGAGAGA;RSEQ=GTAGAGAAACACAAACGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:31,3:0:2,0:23.6:1:32.4:1:1:0:47.5:68:1:0:0.1 0/1:15:3:3,0:10,2:0.2:2,0:11.3:1:28.3:1:1:0:49:6:0.2:0:1.7 -15 21136985 . G A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00079;SOR=7.71643;LSEQ=AGACGTAGAGAAACACAAAC;RSEQ=TGTAAATTGCTCTCTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:4:4,0:49,3:0.0714:2,0:14.8:1:30.5:1:1:0:27.3:8:0.0714:0:3.3 0/1:29:11:11,0:16,2:0.3793:2,0:19.9:1:30.1:1:0.51232:0:30.5:22:0.3793:0:1 -15 21136992 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54639;SOR=0;LSEQ=GAGAAACACAAACGTGTAAA;RSEQ=TGCTCTCTTTTTATGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:2,0:59,2:0.0313:1,0:12:1:30:1:1:0:30.5:4:0.0313:0:5.5 0/0:33:0:0,0:31,2:0:2,0:20.2:1:29.5:1:1:0:44.3:32:1:0:0.4 -15 21137016 . C T 80 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26079;SOR=0.27201;LSEQ=TCTCTTTTTATGTCTTCCTT;RSEQ=CTACCAATAACCAGATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:6:6,0:104,7:0.0508:2,0:17:1:31.2:1:1:0:36.8:12:0.0522:0:4 0/1:70:1:1,0:62,7:0.0143:2,0:21:0:32:0:1:0:40:2:0.0143:0:3 -15 21137023 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09174;SOR=0.25633;LSEQ=TTATGTCTTCCTTCCTACCA;RSEQ=TAACCAGATATCTACTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:13:13,0:124,7:0.0903:2,1:12.5:1:32.4:1:1:0:37.8:26:0.0909:0:3.5 0/1:81:2:2,0:69,10:0.0247:2,0:15.5:1:32:1:1:0:37:4:0.025:0:3 -15 21137038 . C G 144 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02139;SOR=0.24162;LSEQ=TACCAATAACCAGATATCTA;RSEQ=TCTATTTCTGTACTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:20:20,0:144,10:0.1149:2,1:19.7:1:33.5:1:0.60718:0:37.7:40:0.1156:0:3.5 0/1:99:3:3,0:86,10:0.0303:2,0:21.7:1:33.7:1:1:0:31.7:6:0.0306:0:3.3 -15 21137110 . A C 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18393;SOR=0.6397;LSEQ=CTCTTTTGAGAACTCACCTA;RSEQ=ATTTCATCTCTTGGCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:42:27,15:283,113:0.0957:2,2:19.3:1:31.4:1:0.37259:1.39026:38.1:84:0.0966:0:3.1 0/1:221:14:10,4:147,60:0.0633:2,2:23:1:30.9:1:1:1.02:31.6:28:0.0645:0:3.1 -15 21137122 . T C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62872;SOR=0.80254;LSEQ=CTCACCTAAATTTCATCTCT;RSEQ=GGCAAAATAAGAGGTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:34:19,15:317,174:0.0648:2,2:23:1:29.9:1:0.35625:1.4372:38.3:68:0.0655:0:3.1 0/1:247:13:9,4:157,77:0.0526:2,2:25.5:1:30:1:1:1.10:31.4:26:0.0531:0:3.1 -15 21137131 . A G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.769;SOR=0.89322;LSEQ=ATTTCATCTCTTGGCAAAAT;RSEQ=AGAGGTCATCTCTCCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:589:38:21,17:346,205:0.0645:2,2:22:1:31.5:1:0.38857:1.36554:39.3:76:0.0652:0:2.6 0/1:293:17:13,4:171,105:0.058:2,2:20.2:1:31:1:0.30461:1.99:33.4:34:0.0592:0:2.6 -15 21137248 . G A 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04533;SOR=0.64838;LSEQ=ACCTATACAGACACAGAGAC;RSEQ=ATAAAAAAATTATCAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:93:25,68:166,310:0.1632:2,2:17.2:1:30.4:1:0.15048:1.45559:41.2:186:0.1661:0:1.6 0/1:312:35:12,23:93,184:0.1122:2,2:14.5:1:30.2:1:1:1.03:39.6:70:0.1136:0:1.3 -15 21137268 . T C 142 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.67292;SOR=0.75681;LSEQ=GATAAAAAAATTATCAGATA;RSEQ=AGACAAAAGAGAAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:20:0,20:121,294:0.046:2,1:10.8:1:32.9:1:0.00166:0:41.7:40:0.0466:0:3.4 0/1:199:7:1,6:54,138:0.0352:2,2:5.1:1:31.7:1:0.6759:2.33966:43.1:14:0.0355:0:2.4 -15 21137279 . G T 94 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06332;SOR=0;LSEQ=TATCAGATATAGACAAAAGA;RSEQ=AAAGCATTCAAAGTACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:9:0,9:86,255:0.0257:2,0:6.6:1:29.8:1:0.11988:0:33.7:18:0.026:0:4.7 0/0:150:0:0,0:35,115:0:2,0:22.8:1:30.9:1:1:0:54.2:149:1:0:0.2 -15 21137282 . A G 63 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32097;SOR=0;LSEQ=CAGATATAGACAAAAGAGAA;RSEQ=GCATTCAAAGTACTTTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:4:0,4:82,246:0.012:2,0:9.8:1:31.8:1:0.57559:0:28.5:8:0.0123:0:5.5 0/0:143:0:0,0:33,110:0:2,0:22.3:1:30.6:1:1:0:54:70.5:1:0:0.2 -15 21137292 . G A 40 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55655;SOR=0;LSEQ=CAAAAGAGAAAGCATTCAAA;RSEQ=TACTTTAGTCATCAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:0,3:51,206:0.0115:2,0:11.3:1:25.3:1:1:0:28.7:2:0.0078:0:5.3 0/0:113:0:0,0:19,94:0:2,0:21.9:1:31.3:1:1:0:52.8:112:1:0:0.2 -15 21137321 . C A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.71627;LSEQ=TCATCAAATAAAATGAACTA;RSEQ=ATGTAAGTCTGAAAACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:6:1,5:25,139:0.0353:2,2:19.7:1:31.5:1:1:1.11:37.7:12:0.0357:0:1 0/1:52:25:0,25:2,25:0.4808:2,1:23:1:31.2:1:0.49095:0:38.4:50:0.4902:0:1.2 -15 21137353 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAACAATATTTATTTTTAT;RSEQ=AGAACATACACACCTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:24,72:0.0204:2,2:39.5:1:29.5:1:0.44709:2.96:49:4:0.0206:0:1 0/0:22:0:0,0:2,20:0:2,0:20.2:1:31.9:1:1:0:41.7:44:1:0:0.5 -15 21137586 . T C 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCCTTCAGTATGATTATC;RSEQ=AGCAAGTTCTTCATTATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:536:0:0,0:313,223:0:2,0:22.8:1:29.6:1:1:0:49.2:267:1:0:0.1 0/1:344:27:18,9:190,127:0.0785:2,2:25.6:1:30.5:1:0.54453:1.34:47.1:54:0.0789:0:1 -15 21138387 . G A 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31232;SOR=0.75159;LSEQ=TGTGTCAGACAAATCTGCGC;RSEQ=TCCTCCTCCACTCAGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:92:30,62:77,117:0.3217:2,2:25.1:1:30.1:1:0.29553:1.35866:32.6:45:0.3237:0:1.1 0/1:99:26:10,16:38,35:0.2626:2,2:27.3:1:28.7:1:0.26088:1.72745:35.2:25:0.2577:0:1.1 -15 21138405 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08154;SOR=Inf;LSEQ=GCGTCCTCCTCCACTCAGAT;RSEQ=GGACATTCGACTCCTAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:112,216:0:2,0:24.3:1:31:1:1:0:38.1:40:0.9969:0:0.4 0/1:132:2:1,1:56,74:0.0152:2,2:22.5:1:32.5:1:1:1.32:49:4:0.0153:0:1 -15 21138413 . C T 87 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=21.86721;LSEQ=CTCCACTCAGATGGGACATT;RSEQ=GACTCCTAACAATGGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:1:0,1:109,224:0.003:2,0:18:0:31:0:1:0:27:2:0.003:0:1 0/1:129:8:4,4:50,71:0.062:2,2:30.9:1:29:1:0.71914:1.42:47.9:16:0.062:0:1.1 -15 21138417 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08245;SOR=Inf;LSEQ=ACTCAGATGGGACATTCGAC;RSEQ=CCTAACAATGGTCATGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:110,209:0:2,0:25.9:1:29.8:1:1:0:39.5:34.444:1:0:0.4 0/1:129:2:1,1:55,72:0.0155:2,2:36.5:1:27:1:1:1.31:49:4:0.0156:0:1 -15 21138442 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08259;SOR=Inf;LSEQ=ACAATGGTCATGTGAAACTT;RSEQ=CAGCAGCCTAAACACAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:92,182:0:2,0:28.6:1:30.2:1:1:0:41.8:90.333:1:0:0.3 0/1:111:2:1,1:43,66:0.018:2,2:35.5:1:27.5:1:1:1.53:54.5:4:0.0185:0:1 -15 21138486 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAAAGCATGAATTAAA;RSEQ=CTACATTAGTTGAGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:40,108:0.0133:2,2:15:1:28.5:1:0.47329:2.68:39:4:0.0135:0:1 0/0:49:0:0,0:14,34:0:2,0:18.9:1:30.5:1:1:0:45.9:23:0.9787:0:0.3 -15 21138490 . C A 108 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04297;SOR=2.83877;LSEQ=CAAAGCATGAATTAAACCTA;RSEQ=ATTAGTTGAGACTTGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:11:0,11:28,90:0.0853:2,0:10:1:31.4:1:0.11981:0:28.6:22:0.0866:0:1.4 0/1:38:8:1,7:10,20:0.2105:2,2:8.6:1:28.5:1:0.39471:3.40527:31.6:7:0.1944:0:1.3 -15 21139928 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06481;SOR=Inf;LSEQ=GTATCTTCCCAAGCCTAAAA;RSEQ=GAAGGCAATTATCACTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:0:1,0:25.2:1:30.6:1:1:0:26.8:59:1:0:0.1 0/1:21:2:2,0:19,0:0.0952:1,0:33.5:1:32:1:1:0:27:4:0.0952:0:1 -15 21140121 . G T 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00193;SOR=1.7672;LSEQ=TTCCAAAATTGAGGGTGGGC;RSEQ=CCTAGGAGGGGTGTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:82:55,27:273,160:0.1592:2,2:26.9:1:30:1:0.53258:1.19:31.8:40:0.1581:0:1.1 0/1:283:71:47,24:132,79:0.2509:2,2:29.8:1:29.7:1:0.66946:1.17:33.5:70:0.2545:0:1.1 -15 21140222 . G C 103 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00173;SOR=13.95735;LSEQ=ATCACTCTTTCTGAAGTGCT;RSEQ=CTGTTCCTAAGCAAATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:1:1,0:320,294:0.0016:2,0:1:0:16:0:1:0:21:0:0:0:1 0/1:494:11:6,5:264,219:0.0223:2,2:21.2:1:30:1:1:1.00456:35.2:22:0.0225:0:1.3 -15 21140271 . C T 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.31974;LSEQ=CAAGTCACTGCACTTAGAGC;RSEQ=CTGCCTGCCCATGGAGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:680:14:5,9:261,405:0.0206:2,2:31.1:1:29.5:1:1:1.15971:38.1:28:0.0211:0:1.1 0/1:540:45:17,28:201,294:0.0833:2,2:25.4:1:29.4:1:0.75331:1.12577:41.4:90:0.0841:0:1.1 -15 21140344 . A G 146 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=3.85084;LSEQ=GAGCAGAGCAAATGCCTCAA;RSEQ=TGATAAAGCCAAAAACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:11:2,9:24,200:0.0468:2,2:16.5:1:32.1:1:0.34883:1.85:36.1:22:0.048:0:1 0/1:163:26:3,23:16,119:0.1595:2,2:22.9:1:31.2:1:1:1.03063:35.9:52:0.1615:0:1 -15 21140427 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07636;SOR=Inf;LSEQ=AATGTCCACAGCACAAAATA;RSEQ=CTATTCCCACCTATAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:8,64:0:2,0:23.7:1:32.3:1:1:0:43:35:1:0:0.4 0/1:28:2:0,2:3,23:0.0714:2,0:10:1:30:1:1:0:49:4:0.0741:0:1 -15 21140470 . A G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45252;SOR=2.42652;LSEQ=CAAAACATATGCCAATGTGC;RSEQ=TAAAACTTCACTATCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:20:3,17:2,7:0.6897:2,2:21.7:1:31.3:1:0.63282:1.5908:48.7:40:0.6897:0:1.1 1/1:13:11:3,8:0,2:0.8462:0,2:26.5:1:30.7:1:1:0:46.9:22:0.9167:0:1 -15 21140577 . C G 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06897;SOR=9.08993;LSEQ=TATAGCATATTAAAAACTCA;RSEQ=TGGGAGACTATTTCAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:0,1:10,10:0.0476:2,0:5:0:31:0:1:0:60:2:0.05:0:1 0/1:9:3:1,2:4,2:0.3333:2,2:33.3:1:32:1:0.52381:3.38757:40:6:0.3333:0:1 -15 21140708 . A G 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0182;SOR=1.81045;LSEQ=ACCTTAAATACATTCTCACA;RSEQ=TTAGATGCCACGTGCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:36:33,3:149,26:0.1706:2,2:24:1:32.4:1:0.4273:1.91:37.1:72:0.1706:0:1.1 0/1:173:47:38,9:98,28:0.2717:2,2:23.2:1:31.7:1:0.83515:1.21:40.9:94:0.2749:0:1.1 -15 21140800 . T C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27695;SOR=0;LSEQ=GCTGACAGAGGCAAACTCCA;RSEQ=GAATGTGCTACAGTTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:90,142:0.0128:2,2:27.3:1:25.3:1:0.56258:3.14:27:2:0.0086:0:3 0/0:158:0:0,0:46,111:0:2,0:21.8:1:28.8:1:1:0:32.3:30.4:0.9935:0:0.1 -15 21140945 . C T 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0304;SOR=1.41723;LSEQ=TTCCACAGAAACATGTACAG;RSEQ=GCCACACTTCTAGTTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:115:86,29:290,113:0.2207:2,2:26.9:1:27.3:1:0.63564:1.16:33.7:4.227:0.2009:0:1.5 0/1:349:100:83,17:172,76:0.2865:2,2:24.2:1:27.9:1:0.0107:2.15:36.5:5.667:0.2824:0:1.6 -15 21140946 . G A 128 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=24.10709;LSEQ=TCCACAGAAACATGTACAGC;RSEQ=CCACACTTCTAGTTTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:2:1,1:381,143:0.0037:2,2:12:1:11.5:1:0.47296:2.65855:37:0:0:0:5.5 0/1:362:30:23,7:237,88:0.0829:2,2:24.6:1:26.2:1:0.82986:1.22:34.4:4:0.0811:0:1.7 -15 21141162 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0868;SOR=2.12198;LSEQ=AGCATACAATAACTCACAAG;RSEQ=GTTTTCTCCTTTAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:13:1,12:2,57:0.1806:1,1:22.8:1:31.3:1:0.45491:2.34:42.8:26:0.1831:0:1.3 0/1:50:16:2,14:1,33:0.32:1,2:27.3:1:28:1:0.23673:4.55:47.4:7:0.2979:0:1.4 -15 21936715 . G A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.78769;LSEQ=ACATCGATTTAAGAAATCCC;RSEQ=AAATATTGGGGAAAGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:9,0:7,0:0.5625:0,0:22.4:1:31:1:1:0:59.3:18:0.5625:0:1.7 1/0:4:2:2,0:2,0:0.5:0,0:17:1:32:0:1:0:60:4:0.5:0:2 -15 21936770 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47288;SOR=0.68559;LSEQ=TCTGGGATTCCATTAGTTGC;RSEQ=ATTAGGCACAAGGCCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:22:17,5:15,5:0.5238:2,2:22.9:1:31.6:1:1:1.13:60:44:0.5238:0:1.5 0/1:28:12:10,2:12,4:0.4286:2,2:30.8:1:29.3:1:0.67298:1.64:60:11:0.4074:0:1.3 -15 21936782 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13894;SOR=Inf;LSEQ=TTAGTTGCTATTAGGCACAA;RSEQ=GCCCTCAAGGGATTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:40,13:0:2,0:25.1:1:31.6:1:1:0:59.8:52:1:0:0.7 0/1:32:2:1,1:23,6:0.0625:2,2:13:1:27.5:1:0.40645:3.62563:60:4:0.0625:0:2 -15 21936839 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50557;SOR=0;LSEQ=CCTTCTACCATCTCAGTAGC;RSEQ=ATGATACCCAGAGACCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:61,17:0.025:2,2:24:1:29.5:1:0.40158:3.5154:60:4:0.0253:0:1.5 0/0:61:0:0,0:46,15:0:2,0:24.8:1:30.5:1:1:0:60:122:1:0:0.5 -15 21936861 . T C 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65007;SOR=0.75988;LSEQ=TGATACCCAGAGACCATACA;RSEQ=TGACTTTAGGGCCATAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:13:7,6:68,12:0.1398:2,2:32.2:1:32.8:1:0.01698:4.7457:60:26:0.1429:0:1.6 0/1:82:9:7,2:55,18:0.1098:2,2:24.8:1:30.9:1:1:1.14:60:18:0.1111:0:1.8 -15 21936913 . A G 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11412;SOR=0.67161;LSEQ=CACTTCTGGTGCCATCCAGT;RSEQ=TGGCGTTCTGACCACGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:49:29,20:104,72:0.2178:2,2:23.8:1:32.5:1:1:1.00:60:98:0.2197:0:1.5 0/1:216:34:19,15:106,76:0.1574:2,2:23.8:1:31.9:1:0.85095:1.10061:60:68:0.1589:0:1.6 -15 21936925 . C T 146 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.65559;LSEQ=CATCCAGTATGGCGTTCTGA;RSEQ=CACGGTACTGCGTTTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:4:2,2:128,108:0.0167:2,2:24:1:29.5:1:1:1.18434:60:8:0.0169:0:1.3 0/1:228:35:17,18:109,84:0.1535:2,2:30.2:1:28.5:1:0.46078:1.372:60:70:0.1563:0:1.4 -15 21936929 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04901;SOR=Inf;LSEQ=CAGTATGGCGTTCTGACCAC;RSEQ=GTACTGCGTTTGCTCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:137,118:0:2,0:28.1:1:30:1:1:0:59.6:84:0.996:0:0.4 0/1:229:4:2,2:121,103:0.0175:2,2:29:1:28.3:1:1:1.17392:60:8:0.0179:0:1.5 -15 21936992 . C T 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01121;SOR=1.8863;LSEQ=CCAAAGTCAGTGAGCTTAAC;RSEQ=GATCCTTCCATTCCCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:51:16,35:32,91:0.2931:2,2:24.7:1:30.2:1:0.46372:1.30:59.9:102:0.2982:0:1.4 0/1:132:58:15,43:20,54:0.4394:2,2:21.3:1:29.9:1:1:1.06127:59.7:116:0.4427:0:1.6 -15 21937097 . G A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.20709;SOR=0.37701;LSEQ=AAACTCTCTCTGCATACAGC;RSEQ=GCAATCTGTGCTTCATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:4,5:8,21:0.2368:2,2:24.2:1:32.1:1:0.42295:2.06:60:18:0.2368:0:1 0/1:29:3:1,2:9,17:0.1034:2,2:19.7:1:30:1:1:1.05676:60:6:0.1111:0:1 -15 21937168 . C T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69665;LSEQ=CCCCCTAGCAAGGTATTCCA;RSEQ=GACCACAAACAATTCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:2,6:4,7:0.4211:2,2:16:1:30.3:1:1:1.66686:58.6:16:0.4211:0:1.1 0/1:9:3:1,2:1,5:0.3333:2,2:34.7:1:27.7:1:1:2.24:60:6:0.375:0:1 -15 21937819 . G C 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34156;SOR=0.27909;LSEQ=TTGAGGTCTGTAGTAATCGA;RSEQ=CCCAGTGTTCTGGCATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:25.6:1:33.6:1:1:0:60:10:0.625:0:1 0/1:10:3:2,1:5,2:0.3:2,2:23.3:1:31:1:1:1.22183:60:6:0.3:0:1.3 -15 21938163 . T G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCCCCAGGTGAGGCAAG;RSEQ=TCCCCACCCCAGTGAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:28:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 21938221 . G T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAGGTTGCGGAGGCGCCTG;RSEQ=TACCAAAACAGAGATATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:40:0:34:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:45:1:30:1:1:0:60:4:1:0:5.5 -15 21938234 . G T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GCGCCTGGTACCAAAACAGA;RSEQ=ATATAGACCAATGGAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:27:0:32:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:38.5:1:30:1:1:0:60:4:1:0:5.5 -15 21938238 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CTGGTACCAAAACAGAGATA;RSEQ=AGACCAATGGAACAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:23:0:29:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:34.5:1:32.5:1:1:0:60:4:1:0:5.5 -15 21938247 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAACAGAGATATAGACCAAT;RSEQ=GAACAGAACAGAGCCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:14:0:32:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:25.5:1:31:1:1:0:60:4:1:0:5.5 -15 21938261 . C G 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAATGGAACAGAACAGAG;RSEQ=CCTCAGAAATAATACCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:33:1:1:0:60:4:1:0:5.5 -15 22132861 . C G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGTTATCATGTTGTTGAGTA;RSEQ=TACTTAATCAGAATATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:31:1:1:0:27:4:1:0:1 -15 22133134 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50082;SOR=0;LSEQ=TCTCTCTATATTTACTATCA;RSEQ=TTAAAAAATTCTGTTAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:72,21:0.0211:2,2:21.5:1:30.5:1:0.41142:3.37286:56:4:0.0213:0:1 0/0:80:0:0,0:51,28:0:2,0:26.9:1:28.8:1:1:0:44.6:38.5:1:0:0.1 -15 22133202 . C T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.35313;LSEQ=CTTGCAACATAAAAAATTGG;RSEQ=TTCCCAGCTTTGGAATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:0,3:0,57:0.05:1,0:20:1:28.7:1:1:0:35.7:6:0.05:0:1 0/1:45:3:0,3:0,42:0.0667:1,0:5.7:1:29.3:1:1:0:33.3:6:0.0682:0:1 -15 22133339 . T G 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54067;SOR=0;LSEQ=TTTGTGTTGTCTACTGAGTA;RSEQ=GTAAAACAGTCCATAATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:0,4:0,12:0.25:0,0:29:1:32.3:1:1:0:33.5:8:0.25:0:1 0/0:6:0:0,0:0,6:0:0,0:25.2:1:30.8:1:1:0:35.7:12:1:0:0.2 -15 22133456 . T C 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAAATCTCAAGATATTA;RSEQ=TCTTTGAACCACAAAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:34.3:1:33:1:1:0:27:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 22136741 . TATATATATATAA T 27 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=15.000;MSILEN=2;SSF=1;SOR=1.8258;LSEQ=TATATATATATATATATATA;RSEQ=ATAAATAATATATAGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:44:1:27.5:1:1:0:45:4:0.3333:0:0 1/0:2:1:1,0:1,0:0.5:0,0:38:0:27:0:1:0:45:2:0.5:0:1 -15 22136743 . TATATATATAA T 48 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0.46429;SOR=0;LSEQ=TATATATATATATATATATA;RSEQ=ATAAATAATATATAGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:1,0:0.5:0,0:34.7:1:30.3:1:1:0:57:6:0.75:0:0.3 0/0:2:0:0,0:1,0:0:0,0:44:0:26:0:1:0:60:2:1:0:0 -15 22136889 . G C 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53924;SOR=0;LSEQ=CTCTGCTTCTCAACCAAAAA;RSEQ=AAAGCAATCTACATTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:12,2:0.2222:2,2:26:1:31.5:1:0.19706:5.25538:33.5:8:0.2222:0:1.5 0/0:5:0:0,0:4,1:0:2,0:17.6:1:33.6:1:1:0:29.6:10:1:0:0.8 -15 22136896 . A G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37826;SOR=2.98519;LSEQ=TCTCAACCAAAAAGAAAGCA;RSEQ=TCTACATTTCAAGGTTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:6,2:8,2:0.4444:2,2:20.6:1:33.5:1:1:1.31198:30.3:16:0.4444:0:1.1 1/0:7:5:4,1:2,0:0.7143:0,2:19:1:33.2:1:1:0:29.6:10:0.7143:0:1 -15 22136976 . G A 56 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43471;SOR=2.06616;LSEQ=GGTTAAGGCTGGACCGGTAT;RSEQ=TATCTGCCACAGGTTTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:4:4,0:44,4:0.0769:2,0:16.8:1:27.8:1:1:0:27:8:0.0784:0:1.3 0/1:27:4:4,0:22,1:0.1481:1,0:24.8:1:28.3:1:1:0:27:8:0.1481:0:1 -15 22137283 . A G 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GTTTAAACTCCCATCTCCCA;RSEQ=TTGCTTACCCTTAGCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:12.5:1:32:1:1:0:27:4:0.6667:0:1.5 0/0:4:0:0,0:0,4:0:0,0:11:1:30:1:1:0:25.5:8:1:0:0 -15 22138292 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGAAATCTTACCTGTTG;RSEQ=TAGAAAGACACTGGCCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:0,9:0.1818:0,0:28:1:30:1:1:0:24:4:0.1818:0:1 0/0:4:0:0,0:0,4:0:0,0:25.8:1:29.8:1:1:0:27:8:1:0:0 -15 22140008 . TT CC 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AAAAAATCCTACAGCCTTCA;RSEQ=GTAGTCTGTTTCAGAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,0:0.6:0,0:27:1:32:1:1:0:27:6:0.6:0:1 0/0:2:0:0,0:2,0:0:0,0:24.5:1:29:1:1:0:27:4:1:0:0 -15 22140237 . G A 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15959;LSEQ=AAAAGCTGAAAATTTAGTTG;RSEQ=AAGGGGAATTTAAGATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:67:54,13:165,50:0.2376:2,2:18.3:1:30:1:0.61497:1.26:32.1:66:0.2383:0:1.1 0/1:254:12:11,1:198,44:0.0472:2,2:27:1:29.3:1:0.69849:2.44:27.7:24:0.0478:0:1.1 -15 22140359 . G A 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01011;SOR=1.38723;LSEQ=GCTTCATACAGTGAGACAAT;RSEQ=TCAGGATTCATAAATCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:848:145:66,79:313,390:0.171:2,2:23.7:1:29:1:0.85467:1.04:40:35.25:0.1683:0:1.1 0/1:773:172:73,99:255,346:0.2225:2,2:24.6:1:27.9:1:1:1.00:38.9:27.667:0.2178:0:1.1 -15 22140512 . A C 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19007;SOR=1.44991;LSEQ=ACAAAGAGTTCAAAGGTCAA;RSEQ=ATTTGCACAACAACTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:64:2,62:8,83:0.4129:2,1:25.5:1:32.8:1:0.19768:2.96957:54.2:128:0.4183:0:1.2 1/0:95:48:1,47:9,38:0.5053:2,1:29.2:1:32.1:1:0.00763:10.905:54.4:47:0.5109:0:1.1 -15 22143081 . GCA G 94 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.90546;LSEQ=TCATTACTTGACATACCTCA;RSEQ=CACACACACACAAAATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:8:7,1:209,60:0.0289:2,2:22.1:1:31.6:1:1:2.01:32.6:16:0.0295:0.0072:0 0/1:267:7:5,2:190,69:0.0262:2,2:21:1:32.1:1:1:1.10103:40:14:0.0266:0.0075:0.1 -15 22143096 . A C 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00091;SOR=Inf;LSEQ=CCTCAGCACACACACACACA;RSEQ=AATGAATGATACAAACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:253,108:0:2,0:22.9:1:29.8:1:1:0:34.2:35.1:0.9943:0:0.1 0/1:367:11:8,3:243,111:0.03:2,2:25.4:1:30.6:1:1:1.22:28.5:22:0.0306:0:1.1 -15 22145336 . A G 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGAAGGATTTGCTATGT;RSEQ=CCAGGCACTTTTCTTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:26,2:0,0:1:0,2:9.2:1:32.3:1:1:0:28.7:27:1:0:1.7 1/1:25:25:24,1:0,0:1:0,1:10:1:32.4:1:1:0:29.1:50:1:0:1.8 -15 22145400 . GC TT 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03978;SOR=1.45223;LSEQ=GAGAACAAGGAACCACACTG;RSEQ=CAGAGCCATCACTATAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:85:61,24:122,53:0.3257:2,2:27.1:1:30.3:1:0.77371:1.10:36.8:84:0.3268:0.023:1.1 0/1:274:113:81,32:109,51:0.4124:2,2:26.3:1:29.7:1:0.59371:1.18:36.9:112:0.4179:0.0365:1.1 -15 22145430 . T A 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3696;SOR=3.06632;LSEQ=TCACTATAGGGAGCTCTCCT;RSEQ=GATCACCCATCACTGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:1,0:188,113:0.0033:2,0:1:0:24:0:1:0:49:2:0.0034:0:2 0/1:297:3:3,0:183,108:0.0101:2,0:15:1:20.3:1:0.30041:0:50:2:0.007:0:1.7 -15 22145575 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58623;SOR=2.50037;LSEQ=GTCTGGAGATCCTTGTAGTA;RSEQ=CCTAAACCTGATGTGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:1,0:21,37:0.0169:2,0:8:0:32:0:0.37288:0:27:2:0.0172:0:1 0/1:48:2:2,0:11,35:0.0417:2,0:35:1:28.5:1:0.06915:0:27:4:0.0426:0:1 -15 22145664 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.60941;LSEQ=TCTTACAAGCCAGTTCTCTA;RSEQ=GCTGTGTATTTCTATATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:116,30:0.0135:2,2:21.5:1:28.5:1:0.37617:3.82015:38.5:4:0.0139:0:1 0/0:121:1:0,1:99,21:0.0083:2,0:1:0:24:0:0.18182:0:50:2:0.0083:0:1 -15 22146284 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18947;SOR=Inf;LSEQ=CTTTAAAAATCATAAAACAC;RSEQ=GTTATTTTCCTAATCCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:11,0:0:0,0:13.2:1:29.5:1:1:0:33.1:10:1:0:0.5 0/1:9:2:1,1:7,0:0.2222:0,2:17.5:1:27:0:0.22222:0:21:4:0.2222:0:1 -15 22146341 . T G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=2e-05;SOR=0.09686;LSEQ=TTCTTTGTTTTCTTTTTTGT;RSEQ=TTTTTGTTTTTGTTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:24:23,1:43,2:0.3478:1,1:27.3:1:33.3:1:1:1.07:49.5:48:0.3478:0:1.1 0/1:62:3:3,0:54,5:0.0484:2,0:20.3:1:34:0:1:0:37:6:0.0492:0:1 -15 22146376 . GGT G 164 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=15.000;MSILEN=2;SSF=0.65371;SOR=0.8571;LSEQ=TTGTTTTGTCTTTGAGTGTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:34:32,2:81,5:0.2394:2,2:32.1:1:32.3:1:1:1.0124:27.5:68:0.2519:0.007:0.4 0/1:113:24:22,2:68,3:0.2124:1,2:31.8:1:31.7:1:0.59753:2.04274:31.2:48:0.2243:0.0088:0.4 -15 22146586 . G GA 47 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.17466;LSEQ=CTTGCCTGGTCCAAATCTCT;RSEQ=AAAAAAAAAAATTAGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:0,3:2,21:0.1154:2,0:26.7:1:30:1:1:0:27:6:0.1364:0:2.7 0/1:15:2:0,2:0,11:0.1333:0,0:3:1:28.8:1:1:0:39.5:6:0.1527:0.122:1 -15 22147532 . C T 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66719;SOR=0.48387;LSEQ=CACTAACTTCCCAAACATAC;RSEQ=GCTCTCGCACATTTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:13,0:0.2778:1,0:18.4:1:27.8:1:1:0:27:4:0.2353:0:1 0/1:13:2:2,0:11,0:0.1538:0,0:27:1:32.5:1:1:0:27:4:0.1538:0:1 -15 22147570 . C CA 28 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.96936;LSEQ=TTTACAGAAAGTCTATCAGT;RSEQ=AAAAAAAAGTAGTAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:31,0:0.0606:1,0:17:1:28.5:1:1:0:27:4:0.0625:0.0303:0.5 0/1:17:1:1,0:16,0:0.0588:1,0:17:0:25:0:1:0:27:2:0.0588:0:0 -15 22147643 . A TGTGTATTT 153 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=3e-04;SOR=0.24579;LSEQ=TTTGACATCTAAAAAATTTA;RSEQ=ATACACATAAAATACAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:32:27,5:129,13:0.1839:2,2:22.8:1:30.6:1:0.33223:1.8301:32.9:64:0.1882:0.0805:1 0/1:153:8:7,1:131,14:0.0523:2,2:28:1:30.8:1:0.57091:1.33392:40.8:16:0.0537:0.0196:0.6 -15 22147856 . AT A 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00199;SOR=0;LSEQ=GAAAAGAGAAACAGCAAACA;RSEQ=TTTTTTGAAGCCACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:8:3,5:187,364:0.0143:2,2:30.1:1:30.4:1:1:1.17:47.6:16:0.0144:0:0.1 0/0:653:0:0,0:244,408:0:2,0:26.6:1:29.8:1:1:0:45.2:129.4:0.9985:0:0.2 -15 22147868 . CCA C 133 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.8634;SOR=0.90227;LSEQ=AGCAAACAATTTTTTTGAAG;RSEQ=CACACACACACACCTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:17:4,13:136,318:0.036:2,2:27.1:1:31.4:1:0.78783:1.38907:42.9:16:0.0344:0.0085:0.4 0/1:552:18:5,13:192,339:0.0326:2,2:27.9:1:32.1:1:0.61928:1.47159:42:36:0.033:0:0.4 -15 22147906 . A G 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAATTGTGTAAGATTTCTT;RSEQ=CAGTGCAAATAATTTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:26,196:0:2,0:23.9:1:30:1:1:0:46.8:73:1:0:0.4 0/1:217:21:4,17:35,161:0.0968:2,2:25.4:1:32.7:1:1:1.08:50.6:42:0.0972:0:1.2 -15 22147948 . T C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00745;SOR=2.98148;LSEQ=TAACTCAGGTGACATGACGA;RSEQ=TTTATAGAAGAGATACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:17:1,16:5,65:0.1954:2,1:30.8:1:32.2:1:1:1.22799:28.2:34:0.1954:0:1.9 0/1:45:19:0,19:3,23:0.4222:2,1:20.1:1:31.5:1:0.25152:0:32.5:38:0.4222:0:1.6 -15 22147955 . G A 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTGACATGACGATTTTATA;RSEQ=AAGAGATACTGATGTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:75:6,69:0,0:0.9868:0,2:25.9:1:30.5:1:1:0:45:74:0.9867:0:1.3 1/1:35:35:2,33:0,0:1:0,2:27.5:1:29.5:1:1:0:43.9:34:1:0:1.4 -15 22148122 . G T 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15039;SOR=0;LSEQ=AGGCTTGCCACAGGCACAAA;RSEQ=CTTACGGAAATTTGAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:3,2:22,7:0.1471:2,2:25.8:1:31.6:1:0.59084:2.04473:38:10:0.1515:0:1 0/0:18:0:0,0:16,2:0:2,0:25.1:1:28.4:1:1:0:40.2:3.5:1:0:0.3 -15 22148127 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12338;SOR=Inf;LSEQ=TGCCACAGGCACAAAGCTTA;RSEQ=GGAAATTTGAGGAGAGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:27,9:0:2,0:28.7:1:31.3:1:1:0:40.6:35:1:0:0.2 0/1:20:2:2,0:14,4:0.1:2,0:15:1:30:1:1:0:43.5:4:0.1053:0:1 -15 22148210 . T A 84 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16224;SOR=0.22051;LSEQ=CTTCCTACCAATAACCAGAT;RSEQ=TCTACTCTATTTCTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:8:8,0:76,8:0.087:2,0:23.1:1:28:1:1:0:33.9:16:0.087:0:1 0/1:49:1:0,1:45,3:0.0204:2,0:36:0:31:0:0.08163:0:27:2:0.0204:0:1 -15 22148395 . T C 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.28444;LSEQ=ATGGACCATATTCCCAAGCA;RSEQ=ACGAACATACCTATACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:868:541:250,291:121,205:0.6233:2,2:26.2:1:32:1:0.00885:1.45:39:179.333:0.6234:0:1.1 1/1:858:752:341,411:44,62:0.8765:2,2:27.9:1:31.4:1:0.46757:1.17:40:149.4:0.8757:0:1.1 -15 22148440 . G T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAATAAAAAAATTATCA;RSEQ=ATATAGACAAAAGAGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:108,370:0:2,0:23.2:1:31.1:1:1:0:49.7:67.286:0.9979:0:0.5 0/1:473:23:8,15:115,334:0.0486:2,2:24.1:1:27.5:1:0.33471:1.55:48.7:22:0.0474:0:1.6 -15 22148845 . A G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.34101;LSEQ=AAACTATAGAAAGAACAAAT;RSEQ=TATTAATCATTTGCCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:267:205:60,145:17,43:0.7678:2,2:24.8:1:31.6:1:1:1.05:56.2:33.167:0.7713:0:1.1 1/0:238:126:33,93:36,76:0.5294:2,2:24.1:1:30.9:1:0.32068:1.33328:54.6:125:0.5365:0:1 -15 22149585 . T C 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77329;SOR=0.73535;LSEQ=CCTCCTCCACTCAGATGGGA;RSEQ=ATTCGACTCCTAACAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:7:7,0:163,296:0.015:2,0:7.4:1:32.7:1:0.00079:0:28.7:14:0.0151:0:1 0/1:451:5:5,0:195,251:0.0111:2,0:7.2:1:31.4:1:0.01667:0:31.8:10:0.0112:0:1 -15 22149704 . T C 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15827;SOR=0.69239;LSEQ=AAATTACTCTTTATCCAACA;RSEQ=TTCTTCCATGACAAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:43:7,36:11,103:0.2739:2,2:23.5:1:32.4:1:0.26684:1.81:41.8:86:0.2792:0:1 0/1:174:36:3,33:32,105:0.2069:2,2:22.3:1:31.7:1:0.0606:3.33398:43.3:72:0.2093:0:1.2 -15 22149715 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49814;SOR=Inf;LSEQ=TATCCAACATTTCTTCCATG;RSEQ=CAAAAGTACAAAAAATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:8,126:0:2,0:23.6:1:30.2:1:1:0:37:268:1:0:0.3 0/1:135:2:1,1:19,114:0.0148:2,2:37.5:1:30:1:0.27529:5.87:27:4:0.0152:0:1 -15 22149809 . A G 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.4878;SOR=Inf;LSEQ=CTGATTTATTTTTGTCATAC;RSEQ=CTAATATAATCGCCCAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:0,21:0:1,0:18.1:1:30.1:1:1:0:30.4:42:1:0:0 0/1:21:2:0,2:0,19:0.0952:1,0:14:0:34:0:1:0:27:4:0.1:0:1 -15 22150216 . A T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AATTGTATGGTATATTAAAC;RSEQ=GTTATCCCCCCAAAAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:30.5:1:1:0:49:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:27:1:31.5:1:1:0:50:4:1:0:0 -15 22151261 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21135;SOR=Inf;LSEQ=CAAAAGCTATTCCTGATTAC;RSEQ=CATATGTGACAATAGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:162,56:0:2,0:25.6:1:30:1:1:0:34.6:53.5:1:0:0.1 0/1:186:2:1,1:131,52:0.0108:2,2:5:1:30:0:0.49201:2.50487:49.5:4:0.0109:0:1 -15 22151308 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24874;SOR=Inf;LSEQ=TGAGGGTGGGCGCCTAGGAG;RSEQ=GGTGTTTCTCTTGCTAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:157,101:0:2,0:28.6:1:30.3:1:1:0:33.5:35.857:1:0:0.1 0/1:266:3:2,1:155,107:0.0113:2,2:35:1:24.3:1:1:1.38:27:2:0.0077:0:2 -15 22151505 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.21942;SOR=Inf;LSEQ=AAAAGGCAGAGTAGGAGGAG;RSEQ=AGAGCAAATGCCTCAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:28,153:0:2,0:23.4:1:32.2:1:1:0:40.8:180:1:0:0.1 0/1:160:2:0,2:32,126:0.0125:2,0:15:1:29:1:1:0:27:4:0.0126:0:1 -15 22151947 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21705;SOR=Inf;LSEQ=ACTATTCACATTTACCTGTT;RSEQ=ACATCACATTGCTGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:73,64:0:2,0:26.9:1:31.1:1:1:0:34.5:67.5:1:0:0.1 0/1:120:2:1,1:61,57:0.0167:2,2:11.5:1:27.5:1:1:1.06954:27:4:0.0171:0:1 -15 22152077 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.503;SOR=0;LSEQ=GTGGCGGAAACAGGACATGG;RSEQ=AACCAGAACAGCTTCACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:2,0:109,20:0.0153:2,0:23:1:31:0:1:0:27:4:0.0159:0:1 0/0:107:0:0,0:96,11:0:2,0:24.3:1:31.9:1:1:0:27.5:52.5:1:0:0.1 -15 22152167 . AG A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.05266;SOR=0;LSEQ=CCTTGTTGGCAAATCGGGGA;RSEQ=GGGGGGCGGGGGCGGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:4:2,2:162,181:0.0114:2,2:15.3:1:29.5:1:1:1.12:48.8:8:0.0116:0.0029:0.3 0/0:379:0:0,0:184,194:0:2,0:27.1:1:29.7:1:1:0:38:46.25:0.9973:0:1 -15 22152188 . A G 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0307;SOR=Inf;LSEQ=GGGGGGGCGGGGGCGGTTGC;RSEQ=CTTCATCCTGCTGCACTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:153,233:0:2,0:23.4:1:29.5:1:1:0:40.9:95.5:1:0:0.9 0/1:394:6:0,6:159,229:0.0152:2,0:29.7:1:29.8:1:0.08529:0:22:12:0.0155:0:3.2 -15 22152276 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22367;SOR=0;LSEQ=ATGTATAAAACCCAACAATG;RSEQ=AATAAACTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:18,81:0.0198:2,2:23.5:1:28.5:1:0.34238:4.41:33.5:4:0.0211:0:1 0/0:112:0:0,0:22,90:0:2,0:46:0:11:0:1:0:21:0:0:0:4 -15 23699447 . A T 79 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTGTGTGGCTCCTCTTA;RSEQ=GTAATACTCTGCTTCGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29:1:32:1:1:0:60:6:1:0:2 1/1:6:6:5,1:0,0:1:0,2:15.3:1:30.7:1:1:0:60:12:1:0:1.8 -15 23699462 . C G 84 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTAAGTAATACTCTGCTT;RSEQ=GTCCATATAAGCAGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:21:1:32.3:1:1:0:60:12:1:0:1.5 1/1:6:6:6,0:0,0:1:0,0:23.2:1:32.8:1:1:0:60:12:1:0:1.8 -15 23699616 . G T 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.59083;SOR=2.43877;LSEQ=GATTGAAACATTTTAGCGGC;RSEQ=GGGTGCGGGGGTTGATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:1:0,1:75,34:0.0091:2,0:1:0:25:0:0.31818:0:60:2:0.0093:0:1 0/1:91:2:1,1:59,30:0.022:2,2:19.5:1:32.5:1:1:1.95108:60:4:0.022:0:1 -15 23699713 . A G 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02935;SOR=0;LSEQ=AGAGAGTGCGTAGCAGAGCA;RSEQ=GCAATTCAGGAATCTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:27,79:0,0:1:0,2:20.7:1:30.9:1:1:0:59.8:105:1:0:1.2 1/1:111:105:34,71:3,3:0.9459:2,2:21.7:1:30.9:1:0.39832:2.07331:60:210:0.9459:0:1.1 -15 23699735 . G GTTGT 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.82932;LSEQ=CAATTCAGGAATCTATGTTG;RSEQ=TTAATTACTTTTGTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:57:9,48:1,3:0.9344:2,2:22.5:1:30.8:1:0.52113:1.75818:59.7:114:0.9344:0.2951:1 1/1:64:59:15,44:2,3:0.9219:2,2:16.2:1:30.1:1:0.60231:1.93273:60:118:0.9219:0.4219:1 -15 25903846 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ACACACAGGTGGAGATGCAG;RSEQ=GGGCAGCCAGCGGGCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:33.5:1:29.5:1:1:1:60:4:0.5:0:1 0/0:2:0:0,0:1,1:0:2,0:42.5:1:31:1:1:0:60:4:1:0:0 -15 25904406 . AC A 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAACAAAAACAAAAAA;RSEQ=AAAAGAAAAGAAATTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:32:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 25904539 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTCTACTCCTGCAGCCT;RSEQ=GTGTGTAGCGCCCACTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:25:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:34:0:31:1:1:0:60:4:1:0:1.5 -15 25905150 . A G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56923;SOR=0.38278;LSEQ=GCCCGGGAAGCCTGGGCGCC;RSEQ=GGAACCCCAGAACACCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:4,3:0,1:0.875:0,2:22.1:1:26.6:1:1:0:60:6:0.8571:0:1.1 1/0:7:5:2,3:1,1:0.7143:2,2:10.8:1:29.2:1:1:1.41418:60:10:0.7143:0:1 -15 26216159 . G T 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53877;SOR=0;LSEQ=GCAAGGGTTGACTGGCCAGC;RSEQ=GGGAGATGAGGCTGGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:21,0:0.125:1,0:40.7:1:32.7:1:1:0:60:6:0.1304:0:1.3 0/0:10:0:0,0:10,0:0:0,0:22.2:1:31:1:1:0:60:20:1:0:0.6 -15 26216249 . T G 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.36929;LSEQ=ACTTTTTGGATGAAGGCCAG;RSEQ=AACATAGAAGAGATTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:19:17,2:83,12:0.1667:2,2:23.2:1:30.6:1:1:1.23:60:18:0.1622:0:1.2 1/0:63:44:38,6:17,2:0.6984:2,2:21.9:1:29.6:1:1:1.33614:60:43:0.6935:0:1.1 -15 26216271 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55889;SOR=3.33131;LSEQ=ACATAGAAGAGATTTTCTGG;RSEQ=AGAAGCCATAGACTGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:1,0:139,35:0.0057:2,0:12:0:14:0:1:0:60:0:0:0:2 0/1:106:2:1,1:76,28:0.0189:2,2:26.5:1:28:1:0.47421:2.68457:60:4:0.019:0:1 -15 26216370 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=11.10564;LSEQ=AAAAATTGTTGAGATTTACG;RSEQ=GTGGCTATTCATAGCATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:86:43,43:216,199:0.1713:2,2:28:1:29.6:1:0.81271:1.08525:60:42:0.1711:0:1.7 1/0:304:212:104,108:45,47:0.6974:2,2:25.9:1:29.4:1:1:1.01:60:52:0.6933:0:1.7 -15 26216374 . G C 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTGTTGAGATTTACGCGTG;RSEQ=CTATTCATAGCATGACCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:0:0,0:253,239:0:2,0:27:1:31.1:1:1:0:60:27.941:0.9979:0:0.4 0/1:296:35:16,19:124,133:0.1182:2,2:26.2:1:30.7:1:0.85766:1.10676:60:34:0.1172:0:1 -15 26216409 . C T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.67476;LSEQ=ACCGTCATCCATCTCTTACT;RSEQ=GGAATGTTCAGAAGGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:68:26,42:131,195:0.1726:2,2:24.1:1:30.1:1:0.78723:1.08501:60:136:0.1757:0:1.9 1/0:224:150:57,93:25,49:0.6696:2,2:24.7:1:29.8:1:0.55897:1.20:60:149:0.6712:0:1.8 -15 26216422 . A AG 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=TCTTACTCGGAATGTTCAGA;RSEQ=GGCATAGCCTCTCAGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:130,212:0:2,0:24.5:1:30.4:1:1:0:60:84.5:1:0:0.4 0/1:203:7:3,4:67,129:0.0345:2,2:31.4:1:28.6:1:0.69427:1.44:60:14:0.0345:0:1.6 -15 26216430 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.14193;SOR=Inf;LSEQ=GGAATGTTCAGAAGGCATAG;RSEQ=CTCTCAGACATTCTTCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:97,195:0:2,0:25.2:1:31.1:1:1:0:60:145:1:0:0.4 0/1:177:2:1,1:57,118:0.0113:2,2:36.5:1:30:1:0.54924:2.06:60:4:0.0114:0:2 -15 26216553 . A G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00463;SOR=21.83515;LSEQ=ATGAGGGGGCTCACTCATCC;RSEQ=CGGAAAGTGGCCATAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:7:0,7:0,42:0.1429:1,0:24.4:1:33.7:1:1:0:60:14:0.1458:0:2.7 1/1:5:4:1,3:1,0:0.8:0,2:7:1:32.8:1:0.4:0:60:8:0.8:0:2.3 -15 26216557 . A G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02773;SOR=13.535;LSEQ=GGGGGCTCACTCATCCACGG;RSEQ=AAGTGGCCATAAAAGGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:8:0,8:0,39:0.1702:1,0:19.4:1:32.3:1:1:0:60:16:0.1702:0:2.6 1/0:4:3:1,2:1,0:0.75:0,2:7:1:31:1:1:0:60:6:0.75:0:2.7 -15 26216566 . A G 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30894;SOR=5.323;LSEQ=CTCATCCACGGAAAGTGGCC;RSEQ=TAAAAGGGATATTTTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:6:0,6:0,34:0.15:1,0:18.7:1:32.8:1:1:0:60:12:0.15:0:2.8 1/0:2:1:0,1:1,0:0.5:0,0:24:0:33:0:1:0:60:2:0.5:0:3 -15 26933094 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15954;SOR=Inf;LSEQ=GAATCTTAGTAACTTTCATC;RSEQ=TTTCCAGAGCACGCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:92,14:0:2,0:24.6:1:31.3:1:1:0:60:212:1:0:0 0/1:71:2:1,1:61,8:0.0282:2,2:34.5:1:32.5:1:0.23903:7.24626:60:4:0.0282:0:2 -15 26933113 . T C 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05293;SOR=Inf;LSEQ=CTTTTCCAGAGCACGCTTTT;RSEQ=GAGTCCAGTGGACAACCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:128,35:0:2,0:23.7:1:30.3:1:1:0:60:326:1:0:0.1 0/1:99:3:2,1:73,23:0.0303:2,2:22:1:29.3:1:0.56949:1.57878:60:6:0.0306:0:1 -15 26933228 . G C 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=1.76387;LSEQ=TTTCTTCATTTCATAATGAC;RSEQ=ACAAGACTGGTCATTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:114:52,62:138,149:0.2843:2,2:25.5:1:31:1:0.65948:1.10401:60:113:0.2839:0:1.7 0/1:279:115:50,65:76,87:0.4122:2,2:23.7:1:30.7:1:0.62628:1.13511:60:37.333:0.4103:0:1.6 -15 26933242 . T C 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69965;SOR=0.91255;LSEQ=AATGACGACAAGACTGGTCA;RSEQ=TTGAGTGGAAAGCTCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:87:34,53:131,159:0.2296:2,2:25.7:1:31.5:1:0.32724:1.28346:60:86:0.2293:0:2 0/1:262:56:24,32:87,117:0.2137:2,2:24:1:30.6:1:1:1.01:60:27:0.2093:0:2.1 -15 26933734 . C T 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAGGTGTGTCACCGATG;RSEQ=TATTTGTGGAGTTTCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:30:1:30:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 31862323 . C T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=ACCCCGCCCTTCATTGAACA;RSEQ=ATGTGGCAGATTGGCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:28:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:1 -15 31863093 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22868;SOR=Inf;LSEQ=GGCACTCTGATTCCCGACTC;RSEQ=GAGAGTCAGTGGGCTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:0:2,0:25.6:1:30.6:1:1:0:60:60:1:0:0.4 0/1:28:2:1,1:14,12:0.0714:2,2:34.5:1:28.5:1:1:1.16024:60:4:0.0714:0:1 -15 31863103 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.20814;SOR=0;LSEQ=TTCCCGACTCTGAGAGTCAG;RSEQ=GGGCTTGTAACGGCAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:10,12:0.0833:2,2:19.5:1:33:1:1:1.19:60:4:0.087:0:1 0/0:28:0:0,0:15,13:0:2,0:22.6:1:28.9:1:1:0:60:27:1:0:0.1 -15 32220788 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49951;SOR=Inf;LSEQ=TCACTTAGGAACGAATATGA;RSEQ=TGGAACTCATTCATGTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:56,44:0:2,0:27.6:1:30.7:1:1:0:60:200:1:0:0.1 0/1:113:2:1,1:65,46:0.0177:2,2:37.5:1:32.5:1:1:1.40862:60:4:0.0177:0:1.5 -15 32220789 . TG T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21979;SOR=0;LSEQ=CACTTAGGAACGAATATGAT;RSEQ=GAACTCATTCATGTTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:56,44:0.0196:2,2:15.5:1:32:1:1:1.26969:60:4:0.0196:0:0.5 0/0:115:0:0,0:67,48:0:2,0:26.4:1:30.8:1:1:0:60:230:1:0:0.1 -15 32220854 . A G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00348;SOR=Inf;LSEQ=CAGATCCACCTACACTAAAA;RSEQ=TGACCCTAAAGTAAATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:34,49:0:2,0:26.1:1:30.5:1:1:0:60:82:1:0:0.1 0/1:92:9:4,5:29,54:0.0978:2,2:22.9:1:31.1:1:0.71703:1.48:60:18:0.1:0:1.1 -15 33009478 . A T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07211;SOR=9.12257;LSEQ=AGCCTTGACTTTTGACGGTC;RSEQ=TTTAGTTTTATTCTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:17,0:0.0556:1,0:29:0:28:0:1:0:60:2:0.0588:0:1 0/1:8:3:2,1:5,0:0.375:0,2:25.7:1:31.3:1:0.375:0:60:6:0.375:0:2 -15 33009574 . C G 205 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCTTGGCGGGCGAGGAGAG;RSEQ=AGGGTGTCATGTTGGCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:92:92:91,1:0,0:1:0,1:22.4:1:31.5:1:1:0:60:91:1:0:1.1 0/1:45:20:19,1:24,1:0.4444:1,1:24:1:31.1:1:1:1.25655:60:40:0.4444:0:1.1 -15 33009607 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53456;SOR=0;LSEQ=TGGCGACAGGCTCCTGCTGG;RSEQ=GGCCAGCGAGCCCGCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:2,0:151,7:0.0125:1,0:20.5:1:32:0:1:0:60:4:0.0127:0:1.5 0/0:92:0:0,0:88,4:0:1,0:22.9:1:32.4:1:1:0:60:91:1:0:0.4 -15 33009934 . GA G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16145;SOR=Inf;LSEQ=TTCCCTCTCCAACGGGAGCG;RSEQ=AAATGTGATTTGCTGTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:3,96:0:1,0:22.3:1:30.4:1:1:0:60:48.5:1:0:0.2 0/1:67:2:1,1:4,61:0.0299:2,2:11:0:33:0:0.14473:13.75:60:4:0.0299:0:0.5 -15 33010736 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCCGCCAGAGCGCAGGA;RSEQ=CATCCGGACCTGCTAGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:27.5:1:1:0:60:4:1:0:1 -15 33015206 . G A 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07281;LSEQ=ATGCAGCTTAATTTAATTTA;RSEQ=TGATATGAGTAGGCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:102:4,98:1,25:0.7969:1,1:22.4:1:31.1:1:1:1.02:60:50:0.8:0:1 0/1:73:16:2,14:2,55:0.2192:1,2:16.9:1:29.7:1:0.20696:3.83:60:32:0.2192:0:1.2 -15 33022582 . A T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=Inf;LSEQ=TAAGTGAACGTAATACAAAG;RSEQ=CAAATGTGGTTGGTGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:10:1:28:1:1:0:60:4:0.1818:0:1 1/1:1:1:1,0:0,0:1:0,0:1:0:29:0:1:0:60:2:1:0:1 -15 33023486 . C A 284 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=1693.49347;LSEQ=AGCATGTCCTAGGAATGCAG;RSEQ=CCCAGGAAGTCCCAGACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2038:1:1,0:925,1109:5e-04:2,0:1:0:26:0:0.45504:0:60:2:5e-04:0:1 0/1:1855:846:396,450:458,546:0.4561:2,2:25:1:29.3:1:0.63974:1.05:60:140:0.4583:0:1.2 -15 33023670 . C T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=16.01121;LSEQ=AGTCTCTGCTAGAGAGCACT;RSEQ=CCTATTTTGTAAACATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:16:0,16:0,104:0.1322:1,1:18.3:1:30.2:1:1:0:60:32:0.1368:0:1.6 1/0:49:35:0,35:0,14:0.7143:1,1:18.5:1:29.5:1:1:0:60:34:0.7083:0:1.5 -15 33023685 . A C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=13.47794;LSEQ=GCACTCCCTATTTTGTAAAC;RSEQ=TATCTGCTTTAATGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:10:0,10:0,74:0.119:1,0:23.8:1:30.7:1:1:0:60:9:0.1139:0:2.1 1/0:26:17:0,17:0,9:0.6538:0,1:25.2:1:32.7:1:1:0:60:34:0.6538:0:2 -15 33023951 . T C 34 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCTCTTCTTAAGTTGA;RSEQ=AGTGACTATGTCAGTCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:18:1:34:0:1:0:60:4:0.25:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 33026667 . A T 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATTATGTATTATGTCTGCTT;RSEQ=AATCATTTAAAAACGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:366,135:0:2,0:22:1:28.7:1:1:0:60:166:1:0:0.1 0/1:505:18:10,8:325,162:0.0356:2,2:26.4:1:28.8:1:0.32143:1.60339:60:36:0.036:0:1.3 -15 33026886 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1639;SOR=Inf;LSEQ=CTGTGTGTGTGAGCGTGCGT;RSEQ=TGTGTTTGGTAGTGTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:23,210:0:2,0:24.5:1:30.3:1:1:0:60:115.5:1:0:0.1 0/1:159:2:1,1:14,143:0.0126:2,2:5.5:1:29.5:1:0.18032:9.90:60:4:0.0128:0:1 -15 33027179 . T A 77 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACACAGAAATGATAATA;RSEQ=CTTCATTTCAGGGTGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:30.2:1:29.8:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 33033059 . A T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33352;SOR=3.64513;LSEQ=CTTAAGGAAAATTCTTATGG;RSEQ=CTTAGCTTGAGTTTCAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:0,1:244,75:0.0031:2,0:1:0:26:0:0.2375:0:60:2:0.0032:0:1 0/1:265:3:1,2:186,76:0.0113:2,2:7:1:21.7:1:0.20793:4.86117:60:2:0.0077:0:1 -15 33033107 . A G 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAATCAATCATGGTGGCCA;RSEQ=ACGGAATGAGCATTCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:0:0,0:377,233:0:2,0:24.6:1:30.1:1:1:0:60:151.5:1:0:0.1 0/1:520:49:32,17:290,181:0.0942:2,2:30.9:1:31.8:1:0.64609:1.17:60:98:0.0955:0:1.1 -15 33033236 . GA G 108 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19057;SOR=0.41732;LSEQ=GGGATAGGGGGAAAGTAGTT;RSEQ=AAAAAAATAGTTGTAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:11:3,8:140,345:0.0222:2,2:33.4:1:31.4:1:1:1.08196:60:22:0.0224:0:0.1 0/0:427:4:2,2:145,278:0.0094:2,2:39.3:1:31:1:0.61042:1.91:60:8:0.0095:0:0 -15 33035271 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22807;SOR=Inf;LSEQ=ACGACCAACTGAATGAAAAG;RSEQ=CAATCTATGGAACAGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:77,22:0:2,0:22.4:1:31.5:1:1:0:60:198:1:0:0.7 0/1:91:2:1,1:65,24:0.022:2,2:42.5:1:30:1:0.47619:2.67395:60:4:0.0233:0:2 -15 33035284 . C G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.34683;LSEQ=TGAAAAGGCAATCTATGGAA;RSEQ=AGAAGACACGGGGTGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:133:88:66,22:27,18:0.6617:2,2:22.9:1:31.9:1:0.10907:1.99:60:176:0.6617:0:1.1 1/1:108:100:67,33:4,3:0.9259:2,2:24.1:1:31.2:1:0.68544:1.52:60:49:0.9245:0:1.1 -15 33035342 . G A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00898;SOR=Inf;LSEQ=CAGAATGCTCATTCCATTTG;RSEQ=CCACCATGATTGGTTTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:82,100:0:2,0:27.2:1:31.4:1:1:0:60:90:1:0:0.4 0/1:155:6:4,2:63,86:0.0387:2,2:22.2:1:26.2:1:0.40373:2.71:60:5:0.0329:0:1.2 -15 33035503 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATATCTGCTGGCAGCCAC;RSEQ=TTTCCCAGGTATATGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:0.2:0,0:32.5:1:32.5:1:1:0:60:4:0.2:0:1 0/0:2:0:0,0:0,2:0:0,0:8.5:1:33:0:1:0:60:4:1:0:0 -15 34638342 . G T 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTGCTACACCCCGTCAAA;RSEQ=GTATCACACTTGGGGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:818:0:0,0:465,353:0:2,0:25.6:1:31.4:1:1:0:60:73.364:1:0:0.1 0/1:740:19:9,10:374,345:0.0257:2,2:15.8:1:29.7:1:0.81712:1.2042:60:38:0.026:0:1.1 -15 34638544 . G A 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.24525;LSEQ=GTGGTGGGAGAGAGGATCAG;RSEQ=GGTATGTGTCTTAGGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:704:498:251,247:114,91:0.7074:2,2:25:1:30.2:1:0.21406:1.23241:60:40.5:0.7043:0:1.1 0/1:656:244:119,125:204,207:0.372:2,2:25.6:1:29.4:1:0.87165:1.03516:60:29.5:0.3682:0:1.2 -15 34638784 . T G 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32733;SOR=3.78048;LSEQ=AACTAGGCTGGAATGTATTA;RSEQ=AAACTGCCTCTGCTTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:1:0,1:40,185:0.0044:2,0:11:0:15:0:1:0:40:0:0:0:7 0/1:181:3:1,2:39,137:0.0166:2,2:27:1:31:1:0.53402:1.75:60:6:0.0169:0:1.3 -15 34638841 . A G 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTGTAATCCCAGCACTTT;RSEQ=GGAGGTCGAGGCGGGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:20:0,20:1,0:0.9524:0,1:20.3:1:32.2:1:0.04762:0:49.3:40:0.9524:0:4.3 1/1:18:18:0,18:0,0:1:0,1:19.7:1:30.3:1:1:0:54.8:17:1:0:4.2 -15 34638843 . G A 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTAATCCCAGCACTTTAG;RSEQ=AGGTCGAGGCGGGTGGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:20:0,20:1,0:0.9524:0,1:18.3:1:29.4:1:0.04762:0:49.3:9:0.9474:0:4.3 1/1:18:18:0,18:0,0:1:0,1:17.7:1:31.2:1:1:0:54.8:36:1:0:4.2 -15 34638847 . TC CT 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23423;SOR=Inf;LSEQ=AATCCCAGCACTTTAGGAGG;RSEQ=GAGGCGGGTGGATTACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:1,0:0.85:0,1:13.4:1:32.3:1:0.05556:0:49.6:34:0.8947:0:3.1 1/1:17:17:0,17:0,0:1:0,1:13.6:1:32:1:1:0:54.8:34:1:0:3.2 -15 34638862 . T C 47 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGGTCGAGGCGGGTGGAT;RSEQ=ACCTGAGGTCAGGTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:1,0:0.75:0,0:5.3:1:31.7:1:0.25:0:53.7:6:0.75:0:4.7 1/1:3:3:0,3:0,0:1:0,0:2.7:1:30:1:1:0:60:6:1:0:4 -15 34639015 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.35496;SOR=1.91254;LSEQ=AATCACTTGAACCCAGGAGG;RSEQ=GGAGGTTGCAGTGAGCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:8,0:14,0:0.3636:1,0:20:1:29.1:1:1:0:60:16:0.4:0:1.4 1/0:19:10:10,0:7,0:0.5263:0,0:28.2:1:27.5:1:1:0:60:9:0.6:0:1.8 -15 34639360 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.212;SOR=Inf;LSEQ=GGGGTGTGGTGGCTCACACC;RSEQ=GTTATCTCTGCACTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:35,173:0:2,0:20.7:1:30.2:1:1:0:60:28.714:1:0:0.1 0/1:178:2:1,1:38,138:0.0112:2,2:28:1:29:1:0.39116:3.60:60:4:0.0115:0:1.5 -15 34639365 . T A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20736;SOR=Inf;LSEQ=GTGGTGGCTCACACCAGTTA;RSEQ=CTCTGCACTTTGGAAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:27,153:0:2,0:22.1:1:29.7:1:1:0:60:29:1:0:0 0/1:151:2:1,1:27,122:0.0132:2,2:9:1:24.5:1:0.33748:4.46:60:4:0.0134:0:1.5 -15 34640054 . AAAAAAT A 264 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=6.000;MSILEN=6;SSF=0.87772;SOR=0.97104;LSEQ=ACAGAGCGAGACTCCATCTC;RSEQ=AAAAATAAAAATAAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:349:221,128:83,0:0.7968:1,2:26.3:1:30.6:1:0:0:59.9:698:0.8041:0.0023:0.1 1/0:625:495:292,203:113,15:0.792:2,2:19.8:1:29.6:1:0:5.22528:59.8:246.5:0.7952:0.232:0.1 -15 34640218 . C T 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03516;LSEQ=CATGAAACCTAGTGCCGCCC;RSEQ=GTCTCCATCCCCTGCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:404:403:31,372:0,1:0.9975:0,2:24.5:1:30.2:1:1:0:60:56.571:0.9975:0:1.1 1/1:348:325:31,294:4,18:0.9339:2,2:20.9:1:30.3:1:0.25896:2.10172:60:324:0.9337:0:1.1 -15 34640378 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCACTGTTGGTGACAGGGGA;RSEQ=GGGGGCCCTTGCCTCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:22:1,21:0,0:0.9565:0,1:18:1:29.1:1:1:0:60:21:0.9545:0:1.2 1/1:12:12:1,11:0,0:1:0,2:25.1:1:29.5:1:1:0:60:24:1:0:1.3 -15 35384455 . TAA T 80 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=14.000;MSILEN=1;SSF=0.13579;SOR=0;LSEQ=TTAACTTAGTTGCATGTCTG;RSEQ=AAAAAAAAAAAATATTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:2,0:0.3158:0,0:30.7:1:31.2:1:1:0:60:12:0.3158:0:0 0/0:8:0:0,0:2,0:0:0,0:19:1:22:1:1:0:60:1:0.1429:0:1.5 -15 35384456 . A T 96 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0.40483;SOR=0.38384;LSEQ=TAACTTAGTTGCATGTCTGT;RSEQ=AAAAAAAAAAAAATATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:9,0:2,0:0.4737:0,0:21.1:1:30.4:1:1:0:60:18:0.4737:0:1.1 0/1:8:2:2,0:2,0:0.25:0,0:10:1:31:0:1:0:60:4:0.2857:0:1 -15 35384578 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=ACACGTCCATTACTTCGGGG;RSEQ=CTTTGGTGGATTTTTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:2,0:131,1:0.0149:1,0:30:0:31.5:1:1:0:60:4:0.0154:0:1 0/0:105:0:0,0:102,3:0:1,0:24.3:1:31.4:1:1:0:60:16.5:1:0:0.2 -15 35384660 . C T 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00433;SOR=Inf;LSEQ=AGGTCTCCCGCGGGCGTCAG;RSEQ=AGGGGCGGCGGCGGGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:0:0,0:359,233:0:2,0:24.2:1:31.7:1:1:0:60:52.818:0.9983:0:0.2 0/1:673:9:2,7:392,272:0.0134:2,2:10.7:1:24.1:1:0.03782:5.03268:60:8:0.012:0:1 -15 35384908 . C A 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28173;SOR=0.83293;LSEQ=TGTTGAGGTGCAGGAACACT;RSEQ=TGATGAATTTTTTGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:339:233:147,86:68,37:0.6873:2,2:24:1:29.1:1:0.80773:1.075:60:45.6:0.6847:0:1.1 1/0:317:205:132,73:68,43:0.6467:2,2:23.9:1:28.6:1:0.62543:1.14:60:67.333:0.6495:0:1.1 -15 35385071 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07035;LSEQ=GCTGTGATTGACTTGAACAA;RSEQ=CGTTGGTTTAACGGACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:287:147,140:199,218:0.4054:2,2:26.2:1:30.5:1:0.39882:1.15:59.7:94.667:0.4063:0:1.1 0/1:810:37:17,20:363,409:0.0457:2,2:26.7:1:28.9:1:1:1.04411:60:36:0.0448:0:1.1 -15 35385244 . G A 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12611;SOR=5.53582;LSEQ=GGAGCTGTGTGGGCAGCGTC;RSEQ=CAAGAAGCATAGATCAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:1:1,0:190,212:0.0025:2,0:1:0:27:0:0.47395:0:60:2:0.0025:0:1 0/1:441:6:3,3:196,238:0.0136:2,2:20.7:1:27.7:1:1:1.21:60:5:0.0115:0:1.2 -15 35385293 . T C 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGAGCGTCATTCTCGGTC;RSEQ=GGAGACCGTGGTCATGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:211,146:0:2,0:26.3:1:30.3:1:1:0:60:31.455:1:0:0.5 0/1:363:26:9,17:176,161:0.0716:2,2:24.6:1:29.7:1:0.10361:2.06085:60:25:0.0708:0:1.2 -15 35385338 . T C 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=6;SSF=0.00652;SOR=0.69913;LSEQ=GGTGGCGGTGGCGGTGGCGG;RSEQ=GGCCCAGGCGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:493:313:177,136:95,85:0.6349:2,2:22.3:1:30.3:1:0.45212:1.16:59.9:33.778:0.6373:0:1.2 1/0:494:271:157,114:122,87:0.5486:2,2:22.5:1:30:1:0.92599:1.0182:60:23.636:0.5417:0:1.2 -15 35385342 . CCAGGC GGTGGCGGCGGCCCA 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=3;SSF=0.00093;SOR=Inf;LSEQ=GCGGTGGCGGTGGCGGTGGC;RSEQ=GGCGGCGGCGGACGGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:0:0,0:277,226:0:2,0:21.8:1:30:1:1:0:59.9:32.533:1:0:0.8 0/1:512:11:8,3:294,207:0.0215:2,2:15:1:29.7:1:0.53765:1.88:60:22:0.0219:0.0195:0.7 -15 35385344 . AGGC A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.25129;SOR=1.35665;LSEQ=GGTGGCGGTGGCGGTGGCCC;RSEQ=GGCGGCGGCGGACGGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:27:14,13:254,230:0.0527:2,2:26.6:1:31.2:1:1:1.02542:58.9:26:0.052:0.0117:0.7 0/1:541:38:20,18:294,208:0.0702:2,2:30:1:31.2:1:0.49848:1.27153:60:76:0.0717:0:0.6 -15 35385430 . C A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03161;SOR=Inf;LSEQ=CTGAGCCATGCCATTTTTAC;RSEQ=TTACGTCTGCTAGAAAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:0:0,0:200,276:0:2,0:25.7:1:31.4:1:1:0:54.7:58.5:1:0:0.5 0/1:519:6:5,1:223,290:0.0116:2,2:11.7:1:26.5:1:0.09151:6.48:57.2:12:0.0117:0:1.2 -15 35385434 . C T 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08066;SOR=1.26762;LSEQ=GCCATGCCATTTTTACCTTA;RSEQ=GTCTGCTAGAAAGTGTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:169:67,102:123,161:0.3722:2,2:24.9:1:30:1:0.49099:1.16268:47.4:55.333:0.3739:0:1.2 0/1:466:200:86,114:113,152:0.4292:2,2:25.7:1:29.6:1:1:1.01:46.6:49:0.4279:0:1.2 -15 35385567 . TA T 101 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00602;SOR=5.4523;LSEQ=AAATTTGTAGTGATAACAGT;RSEQ=AAAAAAAAAAGATTCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:4:0,4:0,59:0.0625:1,0:34.5:1:29.3:1:1:0:60:8:0.0625:0:0.3 0/1:37:10:2,8:0,27:0.2703:1,2:27:1:30.5:1:0.06757:0:60:20:0.2778:0:0 -15 35385596 . T C 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01875;SOR=0;LSEQ=AAAGATTCTCCATAAATAGG;RSEQ=CGGGCGCGGTGCCTCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:10:0,10:0,21:0.3226:1,0:15.2:1:30.5:1:1:0:60:9:0.3103:0:1 0/0:15:0:0,0:0,15:0:1,0:20.2:1:28.1:1:1:0:60:14:1:0:0.4 -15 36871957 . C T 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCAAGCAGGCGAGGACC;RSEQ=GGGCCTGTGCCGCTTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:19.3:1:32:1:1:0:60:8:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 36872369 . T C 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=0;LSEQ=CGGTGAGTTCATGGCAGCCT;RSEQ=CCAAGGCCTTGCAATTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:127:116,11:0,0:1:0,2:27.2:1:31.5:1:1:0:60:126:1:0:1.1 1/1:158:145:121,24:9,4:0.9177:2,2:23.4:1:30.5:1:0.24874:2.23:60:35.25:0.9276:0:1.1 -15 36872487 . G C 295 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01709;LSEQ=CAGAGGTTAATTGACAGATA;RSEQ=TAGGAATGAATGATGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:664:663:368,295:0,1:0.9985:0,2:26.4:1:31.8:1:0.44578:0:60:65.3:0.9985:0:1.6 1/1:813:747:393,354:33,29:0.9188:2,2:26.1:1:31:1:1:1.02498:60:45.688:0.9183:0:1.5 -15 36872498 . T A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.39702;LSEQ=TGACAGATAGTAGGAATGAA;RSEQ=GATGGGTGGGAATATGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:674:371:198,173:156,147:0.5504:2,2:27.3:1:30.3:1:0.64234:1.08:60:73.2:0.5487:0:2 0/1:838:274:139,135:286,276:0.327:2,2:25.9:1:29.8:1:1:1.00641:60:53.8:0.3276:0:2.1 -15 36872595 . C T 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39137;SOR=0.31721;LSEQ=AAGGGAGCATAGAGGTAAAG;RSEQ=GGCTTCATACTGTTTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:4:1,3:81,242:0.0122:2,2:23.8:1:30.5:1:1:1.00412:60:8:0.0125:0:1 0/0:256:1:0,1:59,195:0.0039:2,0:23:0:32:0:1:0:60:2:0.0039:0:1 -15 36872619 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51538;SOR=0;LSEQ=TTCATACTGTTTGACTGTGG;RSEQ=TTGTACTGTTAACTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:27,161:0.0105:2,2:20:1:28.5:1:0.27368:5.87:60:4:0.0106:0:1 0/0:131:0:0,0:18,113:0:2,0:20.2:1:32.2:1:1:0:60:130:1:0:0.1 -15 36872642 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15587;SOR=Inf;LSEQ=GTACTGTTAACTGTGGAATT;RSEQ=AGTGACCTCAAGGGTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:3,102:0:1,0:21.5:1:30.4:1:1:0:60:51.5:1:0:0.1 0/1:69:2:1,1:4,63:0.029:2,2:9.5:1:30:1:0.14066:14.19:60:4:0.029:0:1 -15 38456417 . C T 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTGGGTTTAATTATGAG;RSEQ=CTTTCTTTAACAGTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:26.3:1:32:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 38456861 . C T 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.23503;LSEQ=AGCAGTAACACCTAGTCAAA;RSEQ=AGGTTGCAGCCAGAAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:257:120,137:133,158:0.4681:2,2:26.9:1:28.9:1:0.86373:1.04:60:41.833:0.4665:0:1.2 1/0:567:376:182,194:90,100:0.6631:2,2:26.3:1:28.4:1:0.85872:1.04:60:74.2:0.6637:0:1.2 -15 38457016 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02107;SOR=Inf;LSEQ=GGATCAGGGATCGGAACCAT;RSEQ=CTTGAATTCCAGCATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:1,42:0:1,0:26.3:1:32.8:1:1:0:60:42:1:0:1 0/1:28:4:0,4:0,24:0.1429:1,0:26.5:1:27.8:1:1:0:60:8:0.1429:0:2.5 -15 38457024 . T C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58467;SOR=1.40643;LSEQ=GATCGGAACCATGCTTGAAT;RSEQ=CCAGCATAAAAAAAGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:21:0,21:1,15:0.5676:1,1:28.9:1:32.7:1:0.43243:0:60:42:0.5833:0:1.6 1/0:20:13:0,13:0,7:0.65:0,1:15.1:1:31.5:1:1:0:60:26:0.65:0:1.1 -15 38457041 . G A 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01832;SOR=0;LSEQ=AATTCCAGCATAAAAAAAGA;RSEQ=CACAAATCAGAAACACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:0,12:1,18:0.3871:1,0:24.3:1:29.6:1:1:0:60:11:0.3667:0:2 0/0:11:0:0,0:0,11:0:0,0:21.7:1:31.4:1:1:0:60:22:1:0:1.5 -15 39564293 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29498;LSEQ=ATTTCATGGAAATTTTTTCA;RSEQ=CAGGCTATAAATTCCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:132:70,62:102,114:0.3782:2,2:27.5:1:30:1:0.32073:1.26:60:264:0.3815:0:1.1 0/1:316:48:22,26:134,129:0.1519:2,2:28.1:1:29.7:1:0.53401:1.22681:60:47:0.1506:0:1.1 -15 39564351 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08961;SOR=Inf;LSEQ=GACATTATGTTCTATACCTT;RSEQ=TCCACTCCCCTGATTATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:99,143:0:2,0:24.6:1:32:1:1:0:60:120:1:0:0.3 0/1:197:3:2,1:65,129:0.0152:2,2:21.3:1:25.7:1:0.26722:3.94:60:6:0.0153:0:1 -15 40243559 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03948;SOR=3.80123;LSEQ=GAGCCACCACGCCCGACCCA;RSEQ=AGTGGATTCTTAAGCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:3,4:9,3:0.35:2,2:24.1:1:28.6:1:0.32609:3.68811:60:14:0.3684:0:1.3 1/0:28:19:12,7:7,2:0.6786:2,2:25.8:1:28.9:1:0.67003:1.99246:60:38:0.6786:0:1.1 -15 40243698 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15819;SOR=0;LSEQ=AACCAGATAGGCCTCACTTG;RSEQ=CTTCTGCAAAGCACCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:34:1:29:1:1:1.12:60:4:0.1053:0:1 0/0:28:0:0,0:14,14:0:2,0:23:1:31.9:1:1:0:59.9:56:1:0:0.1 -15 40328575 . G C 283 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTTGTTGCTGCTGTTGTTG;RSEQ=TGCTGTTGCTGCTGCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:498:494:218,276:1,1:0.992:2,2:25.4:1:31.7:1:1:1.26544:59.9:40.167:0.9938:0:1.2 0/0:624:0:0,0:10,14:0:2,0:24:1:30.6:1:1:0:60:23:0.8846:0:0.1 -15 40328665 . G A 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18183;SOR=0.61467;LSEQ=CTTTTTGTCTCTCTTCTTCA;RSEQ=CCCATCCATGTTAGCTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:89:66:0,66:0,23:0.7416:1,1:21.7:1:29.1:1:1:0:59.7:21:0.75:0:1.3 1/0:80:51:2,49:0,29:0.6375:1,1:23.8:1:29.7:1:0.53196:0:60:102:0.6375:0:1.2 -15 40329033 . A G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAGGAAGACGGTATTAGC;RSEQ=TTGAAATTCACACCCTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:8.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 40626252 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1707;SOR=Inf;LSEQ=CCAGAACAGCTCCCGCCCAG;RSEQ=ACAGCCCAGATCTGCCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,7:0:2,0:24.8:1:30.2:1:1:0:60:44:1:0:0 0/1:16:2:1,1:9,5:0.125:2,2:12:1:33:0:1:1.73197:60:4:0.125:0:1 -15 40626319 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51373;SOR=0;LSEQ=TGGCAGTCTCCGTCGCCTAC;RSEQ=GGCTGGATTACTGGTAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:12,17:0.0645:2,2:17.5:1:30:1:1:1.40:60:4:0.0645:0:1.5 0/0:20:0:0,0:7,13:0:2,0:26.8:1:29.1:1:1:0:60:40:1:0:0.3 -15 40627784 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TGACTCCCCCTTCGGCCCCT;RSEQ=TGGGGATGCCAGGGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:33:0:30:0:1:0:60:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29:1:1:0:60:4:1:0:1 -15 40949823 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23636;SOR=Inf;LSEQ=TGTCCATGCCTTCTCCCAGT;RSEQ=TCTGGTGGTTTGCTGGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:13,15:0:2,0:29.9:1:30.1:1:1:0:60:13:1:0:0.1 0/1:27:2:1,1:15,10:0.0741:2,2:36:1:28.5:1:1:1.47706:60:4:0.0741:0:1 -15 40949857 . T G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49667;SOR=Inf;LSEQ=TGGCAATCTTTGGCATTCCT;RSEQ=GGCTTGTAAATGCATAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,17:0:2,0:26:1:29.5:1:1:0:60:25:1:0:0 0/1:32:2:1,1:13,17:0.0625:2,2:9:0:33:1:1:1.30:52.5:4:0.0625:0:1.5 -15 40990288 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAACTTTGTGCCTGTTGA;RSEQ=CAACCTCTCTCCTTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:0:30.5:1:1:0:60:4:1:0:1 -15 40991153 . A G 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00125;SOR=Inf;LSEQ=ACTACCAAGGTCAAGACCCA;RSEQ=ATTAGACTTTTCAGAAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:1,106:0:1,0:24.4:1:30.6:1:1:0:60:52.5:1:0:0.1 0/1:70:7:0,7:1,62:0.1:1,0:15.4:1:31.6:1:1:0:60:14:0.1014:0:1 -15 40991430 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCTCACCGCAACCTCTGC;RSEQ=TCCCAGGTTCAAGCGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:10.5:1:33.5:1:1:0:41:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 40993120 . T TC 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.51662;SOR=0;LSEQ=CCTGGAACCAACTTCCCATC;RSEQ=CCCCCCGCCCCCCCAAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:39,0:0.0476:1,0:14:1:25.5:1:1:0:60:4:0.05:0.0238:2.5 0/0:27:0:0,0:26,1:0:1,0:27.9:1:31.7:1:1:0:60:54:1:0:0.2 -15 40993435 . T A 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13527;SOR=Inf;LSEQ=TTAACCTAGGGAGGCATTAG;RSEQ=GGGAATAGTACAAAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:87,190:0:2,0:24.2:1:29.4:1:1:0:60:26.7:1:0:0.1 0/1:355:4:3,1:122,229:0.0113:2,2:13.8:1:26.3:1:0.12722:5.60:60:8:0.0114:0:1.3 -15 40993451 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25735;SOR=Inf;LSEQ=TTAGTGGGAATAGTACAAAA;RSEQ=GGAATGTAGTGAAAGACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:45,163:0:2,0:23.6:1:31.2:1:1:0:60:416:1:0:0.1 0/1:259:3:2,1:72,184:0.0116:2,2:19.3:1:29:1:0.19723:5.07:60:6:0.0117:0:1 -15 40993554 . C T 32 v4;q23;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.25527;SOR=0;LSEQ=TTCTTTTCTTCTTTTCTTTT;RSEQ=TTTTCTTTTTTTTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:0,3:3,33:0.0769:2,0:17.3:1:20.7:1:1:0:60:2:0.0625:0:5.3 0/0:29:0:0,0:0,29:0:1,0:22:0:13:0:1:0:60:0:0:0:4 -15 40993559 . C CT 45 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.07798;LSEQ=TTCTTCTTTTCTTTTCTTTT;RSEQ=TTTTTTTTTTCTTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:1,2:2,29:0.0811:2,2:23.7:1:28.7:1:0.24883:6.51:60:6:0.1034:0.027:0.3 0/1:23:2:0,2:0,20:0.087:1,0:29:1:31:0:1:0:60:4:0.1:0:0.5 -15 40993710 . C T 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63287;SOR=1.91506;LSEQ=AGCCTCCCAAGTAGCTGGGA;RSEQ=TACACTACAGGCACATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:29.5:1:30:1:1:0:60:4:0.2857:0:1 0/1:9:4:4,0:5,0:0.4444:0,0:38.8:1:29.8:1:1:0:60:8:0.4444:0:1 -15 40993966 . T A 44 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40454;SOR=2.91573;LSEQ=CCTTGAAGTTTTATGTAGTA;RSEQ=AAAGCAGATTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:0,1:112,118:0.0043:2,0:26:0:13:0:1:0:40:0:0:0:7 0/1:319:4:3,1:170,144:0.0125:2,2:9:1:22.3:1:0.62849:2.53:60:3:0.0107:0:2.5 -15 40993970 . G A 49 q23;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50377;SOR=0.58224;LSEQ=GAAGTTTTATGTAGTATAAA;RSEQ=CAGATTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:5:0,5:98,98:0.0248:2,0:24.6:1:21.2:1:0.05978:0:41:1.5:0.0181:0:6.2 0/1:275:4:1,3:151,120:0.0145:2,2:24:1:21.3:1:0.32793:3.7579:47.5:1:0.0086:0:4.5 -15 40994067 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24262;SOR=Inf;LSEQ=TCTTGGTCTACTGCACCCTC;RSEQ=GCCTCTCAGGTTCAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:0:1,0:19.2:1:23:1:1:0:60:3:1:0:0.6 0/1:33:3:0,3:0,30:0.0909:1,0:14.7:1:29.3:1:1:0:60:6:0.1071:0:1 -15 40998302 . TA T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTCTTTTTTCTTTATATA;RSEQ=TTTTTTTGCCATCAAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:200,44:0:2,0:23.2:1:28.6:1:1:0:60:80.333:1:0:0.2 0/1:213:26:22,4:151,34:0.1221:2,2:25.1:1:30.3:1:1:1.24:60:52:0.125:0.0235:0 -15 40998305 . T A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=4.85644;LSEQ=TCTTTTTTCTTTATATATAT;RSEQ=TTTTTGCCATCAAGATCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:45:41,4:165,42:0.1779:2,2:25.7:1:28.8:1:0.08854:2.60:60:44:0.1753:0:1 1/0:226:116:94,22:87,23:0.5133:2,2:23:1:27.6:1:0.74136:1.13:59.8:22.2:0.5023:0:1.1 -15 40998342 . T G 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTGTGGTAAGGAATATTA;RSEQ=TTTGTTGATTTAATATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:311,152:0:2,0:25.4:1:30.6:1:1:0:60:91.6:1:0:0.2 0/1:497:42:32,10:303,152:0.0845:2,2:21.9:1:32:1:0.23182:1.60:60:84:0.0857:0:1 -15 40998563 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20572;SOR=Inf;LSEQ=AGGTTATAAAACAAAACTGA;RSEQ=ATATTTGTGTAGCATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:18,184:0:2,0:24.9:1:30.6:1:1:0:60:201:1:0:0 0/1:169:2:1,1:18,149:0.0118:2,2:9.5:1:30.5:1:0.21281:8.08:60:4:0.012:0:1 -15 41001187 . T G 204 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTACAGTTTCTACATGTTTG;RSEQ=ATTATGCTAAGAGTTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:665:0:0,0:418,247:0:2,0:25.7:1:28.9:1:1:0:60:82.125:1:0:0.1 0/1:718:97:61,36:373,248:0.1351:2,2:24.1:1:31:1:0.65567:1.13:60:96:0.1343:0:1.2 -15 41001354 . T C 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08488;SOR=Inf;LSEQ=GCTAATCAAATAAGCAAGCA;RSEQ=TACTTCATTCCTGCTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:55,245:0:2,0:23.1:1:30.2:1:1:0:60:74:0.9966:0:0.1 0/1:237:3:1,2:46,188:0.0127:2,2:26:1:29.3:1:0.48638:2.04:60:6:0.0128:0:1.3 -15 41001367 . G A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07774;SOR=Inf;LSEQ=GCAAGCATTACTTCATTCCT;RSEQ=CTATTTGCAAGCATCTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:28,203:0:2,0:23.2:1:31.9:1:1:0:60:76:1:0:0.1 0/1:173:3:1,2:25,145:0.0173:2,2:16.7:1:20.3:1:0.3884:2.88:60:2:0.0118:0:1 -15 41003463 . G A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACAAACAAACAAAAACA;RSEQ=ACAATTAAAAATATTAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 41011311 . G A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16188;SOR=5.92436;LSEQ=TGTCACCCAGGCTAGAGTGC;RSEQ=GTGGCGTGATCTCAGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:1,6:0,9:0.4375:0,2:25.9:1:31.7:1:0.4375:0:60:14:0.4375:0:1.1 1/1:6:5:0,5:0,1:0.8333:0,0:29.8:1:29:1:1:0:60:10:0.8333:0:2 -15 41020653 . GA G 67 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAAGACTCCGTCTCAAA;RSEQ=AAAAAAAAAAAGAATGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:22.5:1:33.8:1:1:0:60:8:0.4:0:0.3 0/0:1:0:0,0:1,0:0:0,0:2:0:32:0:1:0:60:2:1:0:1 -15 41021123 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51403;SOR=0;LSEQ=TAGTAGTTTGAATTAGAAAT;RSEQ=AGGAGGTTTAAGTATAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:0,2:0,136:0.0145:1,0:27:1:33.5:1:1:0:60:4:0.0145:0:1 0/0:96:0:0,0:2,94:0:1,0:23.2:1:31.4:1:1:0:60:95:1:0:0.1 -15 41021635 . TG T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50584;SOR=0;LSEQ=ATGAATATGAGATTTTAGGG;RSEQ=GTAAGGAAGGGACCAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:141,36:0.0111:2,2:23.5:1:29.5:1:0.3716:3.87705:60:4:0.0117:0.0056:0.5 0/0:141:0:0,0:120,21:0:2,0:23.5:1:30.7:1:1:0:60:34.25:1:0:0.3 -15 41021973 . TG T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21012;SOR=Inf;LSEQ=ATTAGTTATTCGTTATTTTG;RSEQ=GGGGAAAGTGGTGGCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:160,58:0:2,0:22.7:1:32.1:1:1:0:60:71.667:1:0:0.1 0/1:185:2:1,1:129,54:0.0108:2,2:37:1:30:1:0.50734:2.37625:60:4:0.011:0:0 -15 41022006 . G T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18792;SOR=4.67394;LSEQ=TGGCAGCATTAAGGCTTTTG;RSEQ=AGTGTCTATGGCCACAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:1:0,1:251,103:0.0028:2,0:1:0:23:0:0.29296:0:60:2:0.0029:0:1 0/1:308:4:1,3:205,97:0.013:2,2:12.3:1:25.3:1:0.10394:6.29946:60:8:0.0132:0:1 -15 41023027 . T G 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCATGCCCGGCCTAAATTT;RSEQ=TCTTTTTTTAATGTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:13,0:0.1875:1,0:20:1:33:1:1:0:60:6:0.1875:0:1 0/0:4:0:0,0:4,0:0:0,0:6.5:1:29.5:1:1:0:55:8:1:0:0.3 -15 41023425 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09705;SOR=Inf;LSEQ=CTTAAGTGCTGCAGCCTAAT;RSEQ=AGAGTGCACTGCTCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:65,229:0:2,0:23.1:1:30.9:1:1:0:60:57.8:1:0:0.1 0/1:251:3:1,2:60,188:0.012:2,2:35.3:1:22.7:1:0.56792:1.56:60:2:0.0081:0:1.3 -15 41794852 . C T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCTTCCCTTCTGGGCCA;RSEQ=GCTGGGCGGGGCCCTGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:31.5:1:1:0:60:4:1:0:1 -15 41796991 . G T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CAGGAATCTGTCTTGGATGT;RSEQ=AAGATGCCCTCCAGGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:40.7:1:31.7:1:1:0:60:12:1:0:0 0/1:10:2:1,1:4,4:0.2:2,2:39:1:27.5:1:1:1:60:4:0.2:0:1 -15 41798217 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0769;SOR=0;LSEQ=CAGGGCTCTGCAGGAAGACA;RSEQ=GTTGGAAGGGAGTGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:7,11:0.1429:2,0:31.7:1:31.3:1:0.52105:0:60:6:0.15:0:1 0/0:27:0:0,0:11,15:0:2,0:24:1:29:1:1:0:60:52:0.963:0:0.2 -15 41804302 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22158;SOR=0;LSEQ=GCGCCGCCCCATCCCCACTG;RSEQ=CTGCGCTCACTCCGGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:68,31:0.0198:2,2:6.5:1:27:1:0.53545:2.17486:60:4:0.0202:0:1 0/0:113:0:0,0:67,46:0:2,0:24.7:1:30.3:1:1:0:60:36.667:1:0:0.2 -15 41804336 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49805;SOR=Inf;LSEQ=GGGACAGGCGTCCTCTCCCT;RSEQ=CTGCCCCACCAGGATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:57,69:0:2,0:28.6:1:31.8:1:1:0:60:62:1:0:0.2 0/1:128:2:1,1:56,70:0.0156:2,2:26:1:29:1:1:1.25:60:4:0.0159:0:1 -15 41804342 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23922;SOR=Inf;LSEQ=GGCGTCCTCTCCCTGCTGCC;RSEQ=CACCAGGATGTACAGCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:56,73:0:2,0:28.2:1:30.5:1:1:0:60:24.8:1:0:0.2 0/1:124:2:1,1:52,70:0.0161:2,2:21.5:1:28:1:1:1.34:60:4:0.0164:0:1 -15 41849048 . G GGAAGAA 147 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=7.000;MSILEN=3;SSF=0.34685;SOR=0.21972;LSEQ=GGAAGGGGAAGAGAGGGAGA;RSEQ=GAAGAAGAAGAAGAAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:29:29,0:0,0:0.9667:0,1:26.5:1:30.3:1:1:0:59.7:28:0.9655:0.1667:0.1 1/1:7:6:6,0:1,0:0.8571:0,0:24.3:1:30.5:1:1:0:60:12:0.8571:0.1429:0 -15 41849438 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50539;SOR=0;LSEQ=TTAATTTTTGTTTATGCTGT;RSEQ=AGGTCAGTTTGCTGAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:132,57:0.0105:2,2:14:0:30.5:1:0.51623:2.30445:60:4:0.0105:0:1.5 0/0:151:0:0,0:103,48:0:2,0:21.9:1:31.5:1:1:0:59.4:74.5:1:0:0.1 -15 41849457 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0834;SOR=Inf;LSEQ=TGAGGTCAGTTTGCTGAGAA;RSEQ=GAAACCAATGAGGTCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:161,80:0:2,0:24.4:1:31.2:1:1:0:56.8:119.5:1:0:0.1 0/1:188:3:1,2:126,59:0.016:2,2:19:1:29.7:1:0.24628:4.235:56.3:6:0.0163:0:1 -15 41849686 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20126;SOR=Inf;LSEQ=CAGTATGTAATACCTGTAGA;RSEQ=CAGTTAGTAACTTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:5,105:0:1,0:21.2:1:30.4:1:1:0:59.6:220:1:0:0.1 0/1:90:2:0,2:7,81:0.0222:2,0:16.5:1:31:1:1:0:60:4:0.0227:0:1.5 -15 41863181 . G A 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=GAGGGTCACTTGGGAGGAAG;RSEQ=TTGGCAGGGAGCAGAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:36:1:30.5:1:1:0:60:4:0.6667:0:1 0/1:4:1:1,0:3,0:0.25:0,0:3:0:28:0:1:0:60:2:0.25:0:1 -15 41865488 . C T 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGCAGAAGGCTGACTCTCTC;RSEQ=CTCAATGCCCCTTGTAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:22,5:0:2,0:28:1:31:1:1:0:60:54:1:0:0.1 1/0:18:10:7,3:5,3:0.5556:2,2:23.5:1:29.4:1:1:1.37:60:20:0.5556:0:1 -15 41865510 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22817;SOR=Inf;LSEQ=TCAATGCCCCTTGTAGGCTG;RSEQ=CAGAGGACATGACAGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:29,12:0:2,0:26.5:1:30.4:1:1:0:60:40:1:0:0.1 0/1:38:2:1,1:22,14:0.0526:2,2:15:1:31.5:1:1:1.55221:60:4:0.0526:0:1 -15 41865525 . G T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.02666;SOR=Inf;LSEQ=GGCTGGCAGAGGACATGACA;RSEQ=TGTGTGTGGCTGACTTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:31,18:0:2,0:25.4:1:31.9:1:1:0:60:98:1:0:0.1 0/1:50:6:5,1:27,17:0.12:2,2:11.2:1:31:1:0.39907:3.09:60:12:0.12:0:1 -15 41867443 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAGGGAAATCTTGAGTA;RSEQ=ACAAGCCAGGCCCTGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 41961003 . G GT 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.57834;SOR=1.44287;LSEQ=AAGGGTGTTTTTTGTTTTTG;RSEQ=TTTTTTTTTGCTTGTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:6:5,1:220,9:0.0255:1,2:27:1:30.2:1:0.23187:4.82321:60:12:0.0259:0.0043:0 0/1:192:7:5,2:179,6:0.0365:1,2:23.4:1:25.4:1:0.02882:11.51991:60:2.5:0.0267:0:0.7 -15 41961017 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25231;SOR=0;LSEQ=TTTTTGGTTTTTTTTTGCTT;RSEQ=TTTCTTAGGATGGGAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:2,1:273,23:0.01:2,2:22.7:1:23.3:1:0.22268:5.86556:60:2:0.0069:0:2.7 0/0:260:0:0,0:236,24:0:2,0:23.8:1:31.1:1:1:0:60:25:1:0:0.1 -15 41962213 . G A 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=AAGATTGAGATGGGCCAGGT;RSEQ=TTGGATTTAACATCTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:0:0,0:68,327:0:2,0:26:1:31.9:1:1:0:60:97.75:1:0:0.1 0/1:356:11:2,9:64,281:0.0309:2,2:22.1:1:29.5:1:1:1.02485:60:22:0.0313:0:1.1 -15 41986740 . T C 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTTTTTTTCTTTTTTTTT;RSEQ=TTGAGACGGAGTCTTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:31:1:1:0:50:4:1:0:1.5 -15 41989730 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCAAGCCATTCTCGTGCC;RSEQ=CAGCCTCACGAGTAGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 41991315 . A T 302 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00941;LSEQ=AATTGATAGAAGATTTGAAG;RSEQ=CTTTGCGGCACAAGCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1230:1227:599,628:1,1:0.9976:2,2:26.2:1:29.5:1:1:1.04839:60:57.429:0.9983:0:1.1 1/0:1434:1138:568,570:145,147:0.7936:2,2:26:1:28.8:1:0.94778:1.01:60:58.895:0.7936:0:1.1 -15 41991376 . CT C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.03995;LSEQ=AGGTAATAGACTAGCGACTT;RSEQ=TTTTTTTTGTTTTCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:21:7,14:226,489:0.0285:2,2:30.4:1:32.1:1:0.81673:1.08:59.8:42:0.0287:0.0014:0.9 0/1:776:23:7,16:258,492:0.0296:2,2:26.1:1:31.3:1:0.82507:1.1983:60:46:0.03:0.0026:0.4 -15 41991391 . CT C 222 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTTCTTTTTTTTTGTTTT;RSEQ=TTTTTTCTTTCTTCCCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:577:0:0,0:146,430:0:2,0:22.1:1:30.3:1:1:0:60:95:0.9982:0:0.5 0/1:601:131:27,104:151,318:0.218:2,2:27:1:31.6:1:0.0096:1.82731:60:130:0.2174:0.01:0.4 -15 41991800 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCCGCCTCCTGGGTTCA;RSEQ=GCCATTCTCCTGCCTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25:1:31:0:1:0:32:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 41999771 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16715;SOR=Inf;LSEQ=ACCTTAAATTGAATCTGCTA;RSEQ=AGTTTGTTTTTTTCATTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:58,2:0:1,0:23.6:1:31.8:1:1:0:60:59:1:0:0.1 0/1:42:2:1,1:37,2:0.0476:2,2:23:1:24.5:1:0.14268:15.3059:60:4:0.0476:0:1 -15 41999827 . A AC 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.51296;SOR=0;LSEQ=CTCCTTTCTCTCTCGACCTT;RSEQ=CCCCCCCGCCATCTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:2,0:177,3:0.011:1,0:25:1:33.5:1:1:0:60:4:0.0114:0:1.5 0/0:129:0:0,0:121,8:0:2,0:23.5:1:28.4:1:1:0:60:128:1:0:0.1 -15 42003382 . ACAG A 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03402;SOR=0.5651;LSEQ=CAGATTAGTTTGCGGCAGGC;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1304:35:18,17:688,579:0.0268:2,2:23.7:1:31.9:1:0.7349:1.12214:59.9:70:0.0272:0.0038:0.1 0/1:1499:23:12,11:781,691:0.0153:2,2:21.3:1:31.5:1:1:1.03605:60:46:0.0156:0.0033:0.3 -15 42004962 . G C 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AGACCATACACTCTCTATAG;RSEQ=AGTTACTGAACTCTGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:21.8:1:32.1:1:1:0:60:18:1:0:1 0/0:1:0:0,0:0,1:0:0,0:41:0:31:0:1:0:60:2:1:0:0 -15 42005039 . T C 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCGTTCCAGTGAAACTT;RSEQ=ATGACACAGGCTGGATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:24:1:32.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 42005145 . G A 23 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCATCCTTGATAGTTTT;RSEQ=CCCATAATTGTCTGTACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:2,0:49,0:0.0392:1,0:13:1:23.5:1:1:0:60:4:0.0444:0:1 0/0:14:0:0,0:12,2:0:2,0:32.4:1:30.9:1:1:0:60:13:1:0:0.4 -15 42005772 . A G 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTAGAATAATACAACCT;RSEQ=CCTTAATCCCGATCAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:0,119:0:1,0:22:1:30:1:1:0:60:58.5:1:0:0.1 0/1:80:18:0,18:1,61:0.225:1,1:19.9:1:31.8:1:1:0:60:36:0.225:0:1.1 -15 42006104 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCAAAAAGACCCTCTG;RSEQ=TCATGGTTGGAGATTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:13:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 42021512 . T C 221 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTTCAGCAGCAAACTTCA;RSEQ=GTCATTCTAGCCCTGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1642:0:0,0:759,882:0:2,0:25.4:1:30.4:1:1:0:60:77.143:0.9994:0:0.2 0/1:1681:166:72,94:728,784:0.0988:2,2:27.1:1:30.1:1:0.25262:1.21216:60:82:0.0983:0:1.2 -15 42026363 . C T 70 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATCTTCCCACCTCGGCCT;RSEQ=TCGGAATGCTGGGATTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:28.6:1:30.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 42026764 . C T 311 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00959;LSEQ=TTAAAACAACTCACCTGTGA;RSEQ=TTGGAGGATGATTCTGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1290:1287:606,681:1,0:0.9977:0,2:25.7:1:30.2:1:0.47127:0:60:60.286:1:0:1.1 1/1:1323:1064:517,547:121,136:0.8042:2,2:26.2:1:29.5:1:0.67698:1.06:60:58.111:0.8028:0:1.1 -15 42026894 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2053;SOR=Inf;LSEQ=CATCAATTCAGAATATGTCT;RSEQ=CCTACCCTGTTTCAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:2,170:0:1,0:25.1:1:32.6:1:1:0:60:171:1:0:0 0/1:143:2:0,2:4,137:0.014:1,0:17.5:1:31:0:1:0:60:4:0.0144:0:1 -15 42028295 . G GT 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.63657;SOR=0.43859;LSEQ=AAGAACGTGAGAATGTGACA;RSEQ=TTTTTTTTCAGAGTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:3:3,0:118,0:0.0248:1,0:36:1:30.7:1:1:0:60:6:0.0248:0:0.3 0/1:91:1:1,0:89,1:0.011:1,0:18:0:30:0:1:0:60:2:0.011:0:0 -15 42028354 . C A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=10.01698;LSEQ=AAATAATCTTTCAACTTTTT;RSEQ=TTTTTTATTATTATTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:102:82,20:258,71:0.2367:2,2:20.7:1:28.8:1:0.78141:1.13:60:204:0.2389:0:1.1 1/0:387:293:207,86:64,30:0.7571:2,2:21.5:1:28.2:1:0.6981:1.13:60:145.5:0.7558:0:1.1 -15 42030102 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGAGAATCATTTGAACC;RSEQ=GGGAGGTGGAGGTTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7.5:1:28.5:1:1:0:60:4:1:0:1 -15 42032383 . C G 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11534;LSEQ=AGAATCTGAAGGCGTTTGTC;RSEQ=CAGCAAAACGGCCAATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1537:1145:548,597:174,212:0.745:2,2:23.7:1:30.7:1:0.34634:1.12:60:51.045:0.7437:0:1.1 0/1:1775:447:220,227:622,701:0.2518:2,2:24.9:1:30.4:1:0.44325:1.09:60:48.667:0.2514:0:1.2 -15 42032503 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08257;SOR=Inf;LSEQ=ATTAGAGAAATATGTACTTT;RSEQ=GCATTATTCTTATTCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:2,255:0:1,0:22.8:1:31:1:1:0:60:50.4:1:0:0.1 0/1:200:3:1,2:3,194:0.015:1,2:9.3:1:22.7:1:0.0591:29.58:60:2:0.0101:0:1 -15 42032655 . T C 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04348;SOR=0;LSEQ=TATTTTTTAATAACACTGAC;RSEQ=TGAAGGCAAGTTTTATAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:3,19:0,0:1:0,2:25.3:1:31.7:1:1:0:60:44:1:0:1 0/0:1:0:0,0:0,1:0:0,0:29:0:26:0:1:0:60:2:1:0:0 -15 42034002 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACTGCAGCATCCACCTCC;RSEQ=GGGTTCAAACCATTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 42034594 . G GA 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.50578;SOR=0;LSEQ=AGAAACTCCATCTTAAAAAA;RSEQ=AAAAAAAAGAAATTGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:72,0:0.027:1,0:10:1:28.4:1:1:0:60:4:0.0278:0.0135:0 0/0:56:0:0,0:56,0:0:1,0:23.4:1:32.8:1:1:0:60:112:1:0:0.1 -15 42035713 . C A 70 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAATACTAAAAAACATTA;RSEQ=AATGGAAGTGGTGGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:30.8:1:30.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 42041712 . G A 315 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.01217;LSEQ=GTTGCTTCCCTTCAGATGAA;RSEQ=AGAGAATCTCAGAATCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1420:1414:653,761:1,0:0.9958:0,2:24:1:30.1:1:0.46219:0:60:87.375:0.9964:0:1.1 1/0:1398:1036:520,516:174,187:0.7411:2,2:24.7:1:30:1:0.54119:1.08:60:128.5:0.7422:0:1.1 -15 42043067 . G A 128 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17957;SOR=0.1619;LSEQ=TGGGGGATAGGTGCTTGAGA;RSEQ=TCCCTACCGAGTTAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:17:2,15:0,5:0.7727:0,2:25.8:1:31.5:1:1:0:60:34:0.7727:0:1 0/1:3:1:0,1:0,2:0.3333:0,0:22:0:28:0:1:0:60:2:0.3333:0:1 -15 42046568 . A G 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0175;LSEQ=TGGTTTTATAAGGGGAACAA;RSEQ=CATTTGAAAAGTTTAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:233:222,11:0,0:0.9957:0,1:24.6:1:32:1:1:0:60:57.25:0.9957:0:1.2 1/1:182:146:136,10:35,1:0.8022:1,2:24.8:1:32.1:1:0.69539:2.56348:60:72:0.8045:0:1 -15 42046575 . A T 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00081;SOR=0;LSEQ=ATAAGGGGAACAAACATTTG;RSEQ=AAAGTTTAGGTGTGCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:13:11,2:235,17:0.0491:2,2:18.3:1:30:1:0.23672:2.50094:60:26:0.0504:0:2.2 0/0:214:0:0,0:194,20:0:2,0:23:1:29.2:1:1:0:60:213:1:0:0.7 -15 42049890 . A AC 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCACACCTTGGGAAAAAGAA;RSEQ=CTGGTTGTAATTTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:46:43,3:175,17:0.1925:2,2:26.4:1:32.2:1:0.77249:1.39:59.9:45:0.1915:0.0335:0.2 0/0:217:0:0,0:184,33:0:2,0:23.2:1:30.1:1:1:0:60:434:1:0:0.1 -15 42050095 . T A 47 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37347;SOR=0.25167;LSEQ=TAAAATTGTTAACATTTATC;RSEQ=TAGGGTTGAAACAACATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:4:2,2:105,291:0.01:2,2:11.8:1:23.5:1:0.29114:2.76:60:3:0.0076:0:1.3 0/0:395:1:1,0:110,284:0.0025:2,0:1:0:23:0:0.28101:0:60:2:0.0026:0:1 -15 42052933 . AT A 137 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.05582;SOR=0.31126;LSEQ=AGGTTTTCATTGAAAGTCAG;RSEQ=TTTTTTTTTTTTCTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:21:0,21:0,13:0.5676:1,1:28.6:1:31.2:1:1:0:60:42:0.5676:0:0.1 0/1:21:6:0,6:0,12:0.2857:0,0:27.8:1:30.7:1:1:0:60:12:0.3:0:0.2 -15 42053846 . G GT 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.74867;LSEQ=CTCTTAAGATGTCAGATTAA;RSEQ=TTTTTTTTCATTAGAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:182,5:0.0106:1,0:36.5:1:31.5:1:1:0:60:4:0.0107:0:0 0/0:126:1:1,0:122,3:0.0079:1,0:10:0:29:0:1:0:60:2:0.0079:0:0 -15 42055810 . T G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAGCCAGGTGTGGTGGC;RSEQ=CATGCCTGTAATCTCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:0:32.5:1:1:0:50:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 42057318 . G A 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12411;SOR=0;LSEQ=AGTTATCCCTAACATCTCAC;RSEQ=GTGACCAAGGAAGGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:4:3,1:73,322:0.01:2,2:10.3:1:27.8:1:0.02306:13.11:60:8:0.0101:0:1 0/0:392:0:0,0:96,296:0:2,0:23.2:1:29.5:1:1:0:60:48:1:0:0.1 -15 42057362 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16741;SOR=Inf;LSEQ=TGTTCTGTAATGATAAAGAG;RSEQ=TATTCTGTTGGCATTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:2,198:0:1,0:26.1:1:32.3:1:1:0:60:49:1:0:0.1 0/1:139:2:0,2:5,132:0.0144:1,0:42.5:1:31:1:1:0:60:4:0.0147:0:1 -15 42057369 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51975;SOR=0;LSEQ=TAATGATAAAGAGCTATTCT;RSEQ=TTGGCATTTGCCTTGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:0,2:1,172:0.0114:1,0:8:1:31.5:1:1:0:60:4:0.0115:0:1 0/0:115:0:0,0:4,111:0:1,0:21.7:1:31.4:1:1:0:60:114:1:0:0.1 -15 42057370 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1536;SOR=Inf;LSEQ=AATGATAAAGAGCTATTCTG;RSEQ=TGGCATTTGCCTTGGTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:1,172:0:1,0:26.6:1:30.6:1:1:0:60:172:1:0:0.1 0/1:112:2:1,1:3,107:0.0179:1,2:33:0:30.5:1:0.07046:31.02:60:4:0.0179:0:1.5 -15 42057373 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14664;SOR=Inf;LSEQ=GATAAAGAGCTATTCTGTTG;RSEQ=CATTTGCCTTGGTAAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:1,169:0:1,0:25.8:1:32.3:1:1:0:60:41.5:1:0:0.1 0/1:106:2:0,2:5,99:0.0189:1,0:26.5:1:31:1:1:0:60:4:0.0189:0:1 -15 42058105 . C T 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AGAGTGCTGAATTTAGACTA;RSEQ=AAATCCCTAAGATGGTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:168,1:0:1,0:26.2:1:32.6:1:1:0:60:168:1:0:0.1 0/1:101:11:11,0:85,5:0.1089:2,0:26.9:1:31.2:1:1:0:60:22:0.11:0:1 -15 42059521 . A T 283 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01495;LSEQ=GCCAGGCTGTGAGGGGAAAT;RSEQ=GATCTCACCTCCTTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:696:693:172,521:0,2:0.9957:0,2:23.8:1:30:1:1:0:60:68.3:1:0:1.1 1/0:604:468:116,352:34,102:0.7748:2,2:21.7:1:29.8:1:1:1.01148:60:92.6:0.7768:0:1.1 -15 42059612 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15721;SOR=Inf;LSEQ=TGCAGTGGATAATGATGGGA;RSEQ=AAAGGGGGTAGGGTGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:1,120:0:1,0:25.1:1:31.2:1:1:0:60:39.333:1:0:0.2 0/1:80:2:1,1:3,75:0.025:1,2:23:1:29.5:1:0.0981:21.80:60:4:0.0256:0:1 -15 42607721 . G A 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAGGATGCAGAGAAATTG;RSEQ=AACATTGCTGGTGGAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:30:1:1:0:60:4:1:0:1 -15 42608498 . A G 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGAAAACAGCTGGGCCC;RSEQ=GGGGACCACTACCACCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:19,1:0,0:1:0,1:23.2:1:29.3:1:1:0:56:40:1:0:1.1 1/1:12:12:12,0:0,0:1:0,0:27.3:1:29.8:1:1:0:58.1:24:1:0:1.2 -15 42608658 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51415;SOR=Inf;LSEQ=CGTGATCATGGGACGGGGGC;RSEQ=CTTCCCTTTTAGGCAGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:24,42:0:2,0:25.2:1:30.8:1:1:0:58.8:65:1:0:1.1 0/1:96:2:1,1:44,50:0.0208:2,2:45:1:30.5:1:1:1.13:60:4:0.0213:0:3.5 -15 42608672 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50153;SOR=Inf;LSEQ=GGGGGCCCTTCCCTTTTAGG;RSEQ=AGCCAAAGCAGAGAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:21,34:0:2,0:23.1:1:31.1:1:1:0:58.6:26.5:1:0:1.6 0/1:68:2:1,1:31,35:0.0294:2,2:42:1:28.5:1:1:1.13:60:4:0.0294:0:3.5 -15 42608677 . A G 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTCCCTTTTAGGCAGCC;RSEQ=AAGCAGAGAGGGAAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:19,29:0,0:1:0,2:24:1:30.1:1:1:0:58.4:47:1:0:1.8 1/1:59:59:27,32:0,0:1:0,2:21.7:1:30.5:1:1:0:59.6:118:1:0:1.5 -15 42608712 . G A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCATTTTCTTCTATGC;RSEQ=TTTTCTTCTATGCACTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:5,25:0,0:1:0,2:24.4:1:30.5:1:1:0:60:60:1:0:2.3 1/1:26:26:5,21:0,0:1:0,2:19.4:1:30:1:1:0:60:52:1:0:2.3 -15 42608758 . T C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCAAGGACTTTAAGACTT;RSEQ=CACTATTTATTCTACCGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:1,17:0,0:1:0,1:25:1:30.5:1:1:0:60:17:1:0:2.6 1/1:15:15:2,13:0,0:1:0,2:30.5:1:31.8:1:1:0:60:30:1:0:2.3 -15 42608793 . A C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCGCTATCTACTATGAACTT;RSEQ=AAAGAGAAACATGAAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:23.1:1:32.6:1:1:0:60:14:0.875:0:2.6 1/1:10:10:1,9:0,0:1:0,2:21.5:1:33.3:1:1:0:60:20:1:0:2.3 -15 45003317 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGATCTTAATCTTCTGGG;RSEQ=TTCCGTTTTCTCGAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:21.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 45003364 . T G 57 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCGAGCAGTTAACTGGC;RSEQ=GGGGCACCATTAGCAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:29.3:1:28.8:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 45003619 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49981;SOR=Inf;LSEQ=CTCTCTCTAACCTGGCACTG;RSEQ=GTCGCTGGCTTGGAGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:116,1:0:1,0:26.2:1:32.6:1:1:0:60:234:1:0:0.1 0/1:132:2:1,1:126,4:0.0152:1,2:11:1:29:1:0.0746:28.29628:60:4:0.0153:0:1 -15 45005933 . T G 183 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTTAATATGTTCTTATTA;RSEQ=TAGAAGCTCAGATGCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:241,61:0:2,0:22:1:30.7:1:1:0:60:150:1:0:0.1 0/1:315:54:39,15:199,62:0.1714:2,2:20.9:1:31.8:1:0.60183:1.23368:60:108:0.172:0:1.2 -15 45007543 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50088;SOR=Inf;LSEQ=AAATGTAAACACTTGGTGCC;RSEQ=GATATAGCTTGACACCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:86,11:0:2,0:24.1:1:31:1:1:0:60:47.5:1:0:0.1 0/1:114:2:1,1:99,13:0.0175:2,2:25.5:1:31.5:1:0.23149:7.37604:60:4:0.0175:0:1 -15 45007947 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22934;SOR=0;LSEQ=CTGAAAGTTGTGTATGAGTA;RSEQ=TCATATCATAAAGCTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:21,142:0.0121:2,2:6.5:1:30.5:1:0.24959:6.63:60:4:0.0123:0:1 0/0:179:0:0,0:38,141:0:2,0:24.3:1:31.4:1:1:0:60:178:1:0:0.1 -15 45008414 . G A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=4e-05;SOR=19.11658;LSEQ=TGTATTCATGGGTAGGAACA;RSEQ=CAGCCTATTCTGCCAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:1,0:144,20:0.0061:2,0:23:0:32:0:1:0:60:2:0.0062:0:1 0/1:162:17:15,2:126,19:0.1049:2,2:31.3:1:29.8:1:1:1.13:60:34:0.1063:0:1 -15 45008498 . C CT 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.6357;SOR=0.76432;LSEQ=AAGTAAAACTTAATGTCTTC;RSEQ=TTTTTTTTCTCCACTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:589:9:3,6:323,257:0.0153:2,2:30.2:1:31.2:1:0.19779:2.50976:60:18:0.0155:0:0.2 0/1:768:9:6,3:421,337:0.0117:2,2:20.6:1:27.7:1:0.73828:1.60:60:8:0.0106:0.0039:1.1 -15 45008608 . T A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.13524;SOR=Inf;LSEQ=TCACTGTCCTGAGGACTATT;RSEQ=ATAGACAGCTCTAACATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:62,223:0:2,0:23.9:1:28.5:1:1:0:60:94:1:0:0.1 0/1:365:4:3,1:105,256:0.011:2,2:16.3:1:27:1:0.07949:7.27:60:8:0.011:0:1.8 -15 45010012 . G C 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCCACAGGTAGCTCTAG;RSEQ=AGGGCTGGCAACTTAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:508:0:0,0:311,196:0:2,0:24.6:1:30.9:1:1:0:60:125.75:0.998:0:0.1 0/1:623:26:16,10:364,232:0.0417:2,2:28.5:1:31.8:1:1:1.02:60:52:0.0423:0:1 -15 45010022 . A G 223 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGCTCTAGGAGGGCTGGC;RSEQ=ACTTAGAGGTGGGGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:0:0,0:334,229:0:2,0:24.9:1:29.7:1:1:0:60:50.182:1:0:0.1 0/1:710:188:106,82:305,216:0.2648:2,2:25.6:1:29.6:1:0.60641:1.09219:60:36.6:0.2629:0:1.1 -15 45154900 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19803;SOR=0;LSEQ=AATAGCAAGATGGCTGTCAC;RSEQ=GGACCTAGAAAGGGGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:25,16:0.0465:2,2:15:1:28.5:1:1:1.54582:60:4:0.0465:0:1 0/0:53:0:0,0:32,21:0:2,0:23.2:1:29.5:1:1:0:59.2:52:1:0:0.3 -15 45466409 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGTCAGGATTACTCAGAC;RSEQ=TGAGGGCAGATGTTTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 45466432 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCAGATGTTTTATTGAA;RSEQ=TTTAATCCCCACCCCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:32:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 45467512 . CG C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTGGCAGGCGGGACTCC;RSEQ=GGGCCAGGGGGCCCCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:32:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 45467540 . C G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGCCCCCTCACCTTCCG;RSEQ=GGTGGCCCCATCCTCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:26.7:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 45468594 . A T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04186;SOR=Inf;LSEQ=GTGGCCTCCTGTACCACTTC;RSEQ=GGTCACACAAGTCACATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:243,162:0:2,0:26.1:1:30:1:1:0:60:39.5:1:0:0.6 0/1:336:4:1,3:190,142:0.0119:2,2:6.3:1:23.8:1:0.31908:3.99835:60:3:0.0091:0:1.5 -15 45468626 . T C 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.27645;LSEQ=TCACATCTGCTTCTCCAAAA;RSEQ=GACTATTGGAAAGGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:418:275:147,128:73,70:0.6579:2,2:25.3:1:30.4:1:0.68004:1.10:60:67.75:0.661:0:1.2 1/1:366:298:137,161:30,38:0.8142:2,2:26.9:1:29.9:1:0.78932:1.08:60:148:0.8177:0:1.1 -15 45470189 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61708;SOR=0.48044;LSEQ=TTCAGGTCTCACAGGTCACA;RSEQ=CTGCTTCTCCAAAATGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:58,56:0.0172:2,2:40:1:29.5:1:1:1.03541:60:4:0.0179:0:1 0/0:120:1:1,0:57,61:0.0083:2,0:1:0:25:0:0.48739:0:60:2:0.0085:0:1 -15 45470200 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24205;SOR=0;LSEQ=CAGGTCACAGCTGCTTCTCC;RSEQ=AAATGACTCTGAAAGGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:47,59:0.0185:2,2:32:1:31.5:1:1:1.25:60:4:0.0187:0:1 0/0:111:0:0,0:47,64:0:2,0:28.1:1:29.9:1:1:0:60:110:1:0:0.1 -15 45507632 . CCGT C 141 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04316;SOR=0.08502;LSEQ=TCGAGTTGTGTTTGCAGCCG;RSEQ=CGCTGCCGCGCCGCCGTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:22:19,3:1,0:0.9565:0,2:25.5:1:31.8:1:1:0:60:44:1:0.1739:0 1/0:8:5:5,0:2,1:0.625:2,0:30:1:33.4:1:0.375:0:60:10:0.625:0:0.2 -15 45507789 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49814;SOR=0;LSEQ=CAAACTGGACGGTGGTAAAG;RSEQ=ACCAGGAAGCAACTGGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:44,41:0.023:2,2:9.5:1:27.5:1:1:1.07227:60:4:0.0233:0:1.5 0/0:79:0:0,0:43,36:0:2,0:26.3:1:31.4:1:1:0:60:38.5:1:0:0.1 -15 45507792 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=0;LSEQ=ACTGGACGGTGGTAAAGCAC;RSEQ=AGGAAGCAACTGGCTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:42,42:0.0233:2,2:22.5:1:28:1:1:1:60:4:0.0241:0:1.5 0/0:80:0:0,0:45,35:0:2,0:25.3:1:30.5:1:1:0:60:79:1:0:0.1 -15 45507889 . C A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24524;SOR=0;LSEQ=GGCCTGGTACTGTGGCACTC;RSEQ=GTGAAATTAGGCGTTATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:61,67:0.0154:2,2:16:0:30:1:1:1.10:60:4:0.0156:0:1.5 0/0:132:0:0,0:64,68:0:2,0:29.3:1:30.2:1:1:0:60:131:1:0:0.1 -15 45507947 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.5022;SOR=0;LSEQ=TCGCAAACTCCCCTTCCGGC;RSEQ=TCTGGTGAGAGAAATTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:40,50:0.0217:2,2:5.5:1:29.5:1:1:1.25:60:4:0.022:0:1.5 0/0:75:0:0,0:39,34:0:2,0:22.8:1:29.9:1:1:0:60:35.5:0.9726:0:0.2 -15 45508034 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50915;SOR=0;LSEQ=AGGAGTCAAGTAAGGCCTAT;RSEQ=TTGTTGGCCTTTTTGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:60,18:0.025:2,2:35:1:28.5:1:0.42089:3.27133:60:4:0.025:0:1 0/0:58:0:0,0:47,11:0:2,0:25.5:1:31.3:1:1:0:60:28:1:0:0.1 -15 45508100 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.23527;SOR=0;LSEQ=AGCATGTAACAGTTATGCCA;RSEQ=AAGATATCCAGCTAGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:105,80:0.0107:2,2:37.5:1:32.5:1:1:1.31056:60:4:0.0111:0:1.5 0/0:198:0:0,0:106,92:0:2,0:27.6:1:29.7:1:1:0:59.9:197:1:0:0.2 -15 45508137 . G A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35884;SOR=0.31158;LSEQ=ACTCCGCACACGTGGAGAAC;RSEQ=TGCTTAAGAATCCACTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:2,1:95,112:0.0143:2,2:23.7:1:28:1:0.59658:2.35:60:6:0.0148:0:1.3 0/0:223:1:1,0:97,125:0.0045:2,0:50:0:29:0:0.43946:0:60:2:0.0046:0:1 -15 45508175 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50127;SOR=0;LSEQ=TGATGGGAAACATTTCATTC;RSEQ=CAAAAAAAAAAATTATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:52,98:0.0132:2,2:17.5:1:27.5:1:1:1.88:60:4:0.014:0:2.5 0/0:130:0:0,0:43,87:0:2,0:23.2:1:28.4:1:1:0:59.6:17.571:1:0:0.2 -15 45508176 . CA C 114 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.83129;SOR=1.09321;LSEQ=GATGGGAAACATTTCATTCT;RSEQ=AAAAAAAAAATTATCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:12:2,10:51,85:0.0811:2,2:29.5:1:31.9:1:0.21303:2.98141:60:24:0.0816:0:0.1 0/1:125:11:4,7:36,78:0.088:2,2:27:1:31.5:1:0.74358:1.24:59.1:22:0.0902:0:0.4 -15 45508183 . A G 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.50178;SOR=0;LSEQ=AACATTTCATTCTCAAAAAA;RSEQ=AAAATTATCTTATTCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:39,89:0.0154:2,2:9.5:1:30:1:0.52236:2.27:60:4:0.0154:0:2.5 0/0:109:0:0,0:29,80:0:2,0:24:1:30.4:1:1:0:59.5:218:1:0:0.2 -15 45508196 . T A 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.66399;LSEQ=CAAAAAAAAAAATTATCTTA;RSEQ=TCCTGTTATTGGTAGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:29,81:0.0179:2,2:25:1:27.5:1:0.46573:2.76:60:4:0.018:0:1 0/1:84:1:1,0:18,65:0.0119:2,0:1:0:24:0:0.22619:0:60:2:0.0123:0:1 -15 45508233 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14849;SOR=Inf;LSEQ=TCTGAACATTAGATTTTTTT;RSEQ=CCCCCATGGGGTCAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:8,55:0:2,0:23.6:1:29.7:1:1:0:60:20:1:0:0.1 0/1:40:2:0,2:6,32:0.05:2,0:22:1:32.5:1:1:0:60:4:0.05:0:1 -15 45929970 . T C 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=GTTGCCTGTGTCTAGCTTTG;RSEQ=TAATCCGATGTGTTGTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:27.3:1:27.3:1:1:0:60:2:0.5:0:1 0/0:7:0:0,0:1,6:0:2,0:26.1:1:28.6:1:1:0:60:14:1:0:0.1 -15 47969373 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4955;SOR=0;LSEQ=CTACAGACTGGTACCAGTCT;RSEQ=CGACCTGGAGGTTGGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:0.0952:2,2:23:0:32:0:1:1.66897:60:4:0.0952:0:1.5 0/0:16:0:0,0:9,7:0:2,0:23.1:1:31.6:1:1:0:60:32:1:0:0.1 -15 47969386 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18018;SOR=Inf;LSEQ=CCAGTCTGCGACCTGGAGGT;RSEQ=GGGACCCCTGTTGTAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:27.2:1:31.6:1:1:0:60:42:1:0:0.1 0/1:16:2:1,1:7,7:0.125:2,2:21.5:1:29.5:1:1:1:60:4:0.125:0:0 -15 48073099 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACCCTGGGAACACTGAAAA;RSEQ=ACATTGATTACATTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:29:1:1:0:60:4:1:0:1.5 -15 48073424 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGTCTAACAACTATTTG;RSEQ=TTTTGTTCACATCTGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:12.5:1:30.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 48073651 . T C 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54961;SOR=0;LSEQ=GTGGCAAAAGGCATGGGGAA;RSEQ=GTGGCATGTTTGGAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:107,14:0.0163:2,2:15.5:1:24.5:1:0.22991:7.41827:60:4:0.0165:0:1.5 0/0:63:0:0,0:55,8:0:2,0:23.3:1:29.6:1:1:0:60:30.5:1:0:0.6 -15 48073702 . T C 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01097;SOR=1.67407;LSEQ=CTGAGGTCTTATATTTCCCT;RSEQ=AGGAGAGAAGGTAGCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:148:99,49:82,39:0.5502:2,2:23.8:1:31.2:1:0.89679:1.04052:60:73:0.553:0:1.5 1/0:183:123:79,44:42,17:0.6721:2,2:26.3:1:30.9:1:0.40364:1.37365:60:40:0.6667:0:1.5 -15 48073768 . G C 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00258;SOR=1.57493;LSEQ=ACAGGCTTTCATTGGGAAAG;RSEQ=AGAAAGAGAATGAAGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:411:215:99,116:96,97:0.5231:2,2:25.9:1:32.1:1:0.48774:1.15921:60:70.667:0.5261:0:1.3 1/0:352:223:109,114:64,65:0.6335:2,2:25.5:1:31.7:1:0.91227:1.02971:60:110.5:0.6332:0:1.5 -15 48073801 . G A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AAGGATCTTAGAAACTAAAC;RSEQ=GGAGTGTCAGAATACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:157,223:0:2,0:27.5:1:30.3:1:1:0:60:75:0.9947:0:0.5 0/1:328:14:5,9:137,177:0.0427:2,2:25.7:1:30.5:1:0.59633:1.39185:60:28:0.0429:0:1.8 -15 48073820 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.31846;SOR=4.03493;LSEQ=CGGGAGTGTCAGAATACCCT;RSEQ=AAAACTTCTCTAAGAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:1:1,0:125,212:0.003:2,0:1:0:26:0:0.37278:0:60:2:0.003:0:2 0/1:253:3:2,1:98,152:0.0119:2,2:5.3:1:25.3:1:0.56403:3.09:60:6:0.012:0:2 -15 48073862 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5118;SOR=0;LSEQ=AACTAGTTGAAAGACAGAAG;RSEQ=GCATGTAGAGAACATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:33,123:0.0126:2,2:20.5:1:30:1:0.38515:3.69:60:4:0.0126:0:1.5 0/0:114:0:0,0:33,81:0:2,0:21.5:1:30:1:1:0:60:27.5:1:0:0.2 -15 48073867 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56814;SOR=2.94494;LSEQ=GTTGAAAGACAGAAGGGCAT;RSEQ=TAGAGAACATTCTGCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:1:1,0:28,114:0.007:2,0:1:0:27:0:0.2028:0:60:2:0.007:0:2 0/1:98:2:1,1:24,72:0.0204:2,2:5:1:29.5:1:0.44709:2.96:60:4:0.0206:0:1 -15 48073968 . T A 89 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20623;SOR=0.19007;LSEQ=TCATGCTTAGCTGGACTCTT;RSEQ=GATAAAAGTTGAAGGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:0,14:0.3333:1,0:28.6:1:31.9:1:1:0:60:14:0.3333:0:1 0/1:12:1:0,1:1,10:0.0833:2,0:5:0:31:0:1:0:60:2:0.0909:0:2 -15 48074071 . A C 53 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GACTAGTAAGCTAGGTACCT;RSEQ=AGTGTTTCTACATACTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:29.7:1:33.7:1:1:0:60:6:0.5:0:1 0/0:3:0:0,0:0,3:0:0,0:11.3:1:31:1:1:0:60:6:1:0:0 -15 48633020 . T C 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24894;SOR=0;LSEQ=AATATTTGCAAGACTGCTGC;RSEQ=TAACAATGTCAGCGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:190,106:0.01:2,2:14:1:30.3:1:0.29651:3.56885:60:6:0.0101:0:1.7 0/0:290:0:0,0:185,105:0:2,0:25.8:1:30.3:1:1:0:60:71.5:1:0:0.3 -15 48633092 . C T 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06649;SOR=0.74732;LSEQ=ATTTTTATTTATGACTCAAT;RSEQ=GTATTTCAATCTGGGTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:375:222:106,116:70,83:0.592:2,2:27.1:1:29.9:1:0.75241:1.08:60:221:0.5957:0:1.4 1/0:323:168:69,99:74,80:0.5201:2,2:24.4:1:29.6:1:0.21856:1.32598:60:83:0.522:0:1.4 -15 48633153 . C T 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=0.47417;LSEQ=AAAACCTTTAAAACCCAAAT;RSEQ=GTAATTTTCTCCTAGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:124:48,76:38,62:0.5536:2,2:25.6:1:30.2:1:1:1.03:60:248:0.5561:0:1.6 0/1:219:81:31,50:44,94:0.3699:2,2:26.1:1:29.7:1:0.37717:1.32:60:162:0.3733:0:1.6 -15 48633174 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=GTAATTTTCTCCTAGTCTTT;RSEQ=TGGCAAGTGTGCCGTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:62,106:0.0118:2,2:14.5:1:27.5:1:1:1.70:60:4:0.012:0:1.5 0/0:157:0:0,0:52,105:0:2,0:25.7:1:29.7:1:1:0:60:314:1:0:0.6 -15 48633243 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1591;SOR=Inf;LSEQ=CTGCCAGCTTAAAATAGGAA;RSEQ=TGGTCGCCATTTGATAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:0,55:0:1,0:26.1:1:31.3:1:1:0:60:110:1:0:0.1 0/1:37:2:0,2:0,35:0.0541:1,0:5:1:32:1:1:0:60:4:0.0556:0:1 -15 50243260 . G GT 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGTGGTCTGAGAGACT;RSEQ=TTTTTTTGTGATTTCAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30.3:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 50244547 . T C 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10264;SOR=0.25169;LSEQ=CCAATCAATCATAGGTTTGG;RSEQ=GTTTTTATGAAGTCCCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:3,3:0.4545:2,2:26.6:1:29.8:1:1:1.44544:60:10:0.4545:0:1 0/1:24:4:1,3:10,10:0.1667:2,2:27:1:31.5:1:0.59627:2.87331:60:8:0.1818:0:1.3 -15 50244675 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATATCCTTTCTTCTGTTT;RSEQ=GTCAATTCGGCTGTTGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:18.5:1:32.5:1:0.33333:0:60:4:0.6667:0:1 0/0:1:0:0,0:0,1:0:0,0:35:0:32:0:1:0:60:2:1:0:0 -15 50245053 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09994;SOR=Inf;LSEQ=TTGTCTCATTTTGGTCTTTG;RSEQ=GGCTGCTGACCCTTGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:22,17:0:2,0:21.8:1:29.9:1:1:0:60:38:1:0:0.2 0/1:19:2:1,1:10,7:0.1053:2,2:41.5:1:27:1:1:1.40151:60:4:0.1053:0:1 -15 50245089 . C CTTTTGT 100 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=5.000;MSILEN=1;SSF=0.07616;SOR=0.15721;LSEQ=GATGGGGTTTTTGTGGGGGC;RSEQ=TTTTGTTGTTGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:3,6:14,15:0.2368:2,2:27.7:1:31.6:1:0.47571:1.83674:60:18:0.2368:0.0526:0.2 0/1:22:1:1,0:10,11:0.0455:2,0:34:0:31.2:0:1:0:60:2:0.0476:0:0 -15 50245683 . G T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50226;SOR=Inf;LSEQ=AGACCTGAAGAGGCCCTCTG;RSEQ=CCGCAGACTACCACAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:26.3:1:31.9:1:1:0:60:44:1:0:0.5 0/1:30:2:1,1:13,15:0.0667:2,2:27.5:1:26.5:1:1:1.15:60:4:0.0667:0:5 -15 50245685 . C T 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00521;SOR=0;LSEQ=ACCTGAAGAGGCCCTCTGGC;RSEQ=GCAGACTACCACAGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:2,4:10,8:0.25:2,2:22.8:1:30.3:1:0.64041:2.40592:60:12:0.25:0:1.2 0/0:30:0:0,0:14,16:0:2,0:31:1:29.7:1:1:0:60:60:1:0:0.6 -15 50245701 . C A 25 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51711;SOR=Inf;LSEQ=TGGCCGCAGACTACCACAGC;RSEQ=AGTGTGTTGAGCTGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:0:2,0:19.9:1:32.4:1:1:0:60:36:1:0:0.5 0/1:29:2:1,1:11,16:0.069:2,2:9.5:1:25.5:1:1:1.44:60:4:0.069:0:5 -15 50245712 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49245;SOR=Inf;LSEQ=TACCACAGCCAGTGTGTTGA;RSEQ=CTGTGGGGACAAGTCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,10:0:2,0:14.7:1:32.5:1:1:0:60:36:0.9474:0:0.4 0/1:23:2:1,1:9,12:0.087:2,2:30:1:29.5:1:1:1.32:60:4:0.087:0:1 -15 50245985 . C T 46 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22222;SOR=0.13854;LSEQ=AGCTGAGAATGTGCACATTC;RSEQ=GGAGTTGGGATGCTAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:2,0:0.6:0,2:16.3:1:29.3:1:0.4:0:60:6:0.6:0:1 0/1:7:1:0,1:3,3:0.1429:2,0:50:0:31:0:1:0:60:2:0.1429:0:1 -15 52311700 . C T 58 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCCTCCATTGTGTGTGA;RSEQ=CCTCCGGCGGCTGCCGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:33.8:1:29.3:1:1:0:60:8:1:0:1 -15 52312068 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=CTCGCCTTACTGGCACGCTG;RSEQ=CTTTCGAAATGCTCCCGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:10:1:28.5:1:1:1.58108:60:4:0.2:0:1 0/0:17:0:0,0:10,7:0:2,0:22.5:1:31.8:1:1:0:60:34:1:0:0.1 -15 52312203 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAGAGCCCTGAAGTCCGCC;RSEQ=AAGTTTTGAGTCTTGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:18:1:30.5:1:1:0:60:4:1:0:0 0/1:15:2:1,1:4,9:0.1333:2,2:11.5:1:29.5:1:1:2.12:60:4:0.1429:0:1 -15 53253417 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2139;SOR=Inf;LSEQ=TGTTGGGGCTGTCTTAATGG;RSEQ=CCATTGTCAAAGGGCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:20.4:1:29.5:1:1:0:60:17:1:0:0.8 0/1:16:2:1,1:9,5:0.125:2,2:18:1:26.5:1:1:1.73197:60:4:0.125:0:2 -15 53253466 . A G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.57522;SOR=2.67662;LSEQ=GAACAACAGCAGCAGCAGCA;RSEQ=CAACAACAACCACAACGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:25:11,14:1,1:0.9259:2,2:29.5:1:32.8:1:1:1.2613:60:50:0.9259:0:1.2 1/1:35:34:15,19:1,0:0.9714:0,2:28.8:1:32:1:0.45714:0:60:68:0.9714:0:1.2 -15 53613642 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49898;SOR=Inf;LSEQ=GTGACAAAGATTCTTTGCTT;RSEQ=ATCAAACTTTAGTCAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:82,52:0:2,0:27.3:1:31.7:1:1:0:60:268:1:0:0.1 0/1:145:2:1,1:82,61:0.0138:2,2:18.5:1:27.5:1:1:1.34147:60:4:0.0139:0:1 -15 53613659 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50271;SOR=Inf;LSEQ=CTTGATCAAACTTTAGTCAG;RSEQ=CTCCTGAACCTTCTCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:84,70:0:2,0:28.7:1:31.6:1:1:0:60:308:1:0:0.1 0/1:185:2:0,2:93,90:0.0108:2,0:5.5:1:25:1:0.24595:0:60:4:0.011:0:1 -15 53613677 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25269;SOR=Inf;LSEQ=AGGCTCCTGAACCTTCTCCT;RSEQ=GGCCCATCTGTGCATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:86,82:0:2,0:27.2:1:31.4:1:1:0:60:167:1:0:0.1 0/1:197:3:2,1:92,101:0.0152:2,2:10.3:1:26.7:1:0.60819:2.19:60:6:0.0155:0:1 -15 53613961 . T C 58 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCATGCTATATTCAGAG;RSEQ=TGTGGCTTATATCTCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:34:1:29.3:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 53613980 . C G 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGTGGCTTATATCTCTCT;RSEQ=ACACTGCAAAATTCTATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:40.3:1:28.3:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 54532000 . A G 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00357;SOR=Inf;LSEQ=TGCCATGTAATATTTTGAGT;RSEQ=TAGTTTGGGCACAAGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:58,5:0:2,0:23.6:1:29:1:1:0:60:126:1:0:0 0/1:43:6:5,1:34,3:0.1395:2,2:24.5:1:31.7:1:0.46483:2.21301:60:12:0.1429:0:1.5 -15 54532057 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.25187;SOR=0;LSEQ=GTAGGAGAAAGCTGCATATT;RSEQ=CTTGCTGAATCTCAAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:3:1,2:103,47:0.0196:2,2:14:1:27.7:1:0.24045:4.33626:60:6:0.0197:0:1.3 0/0:131:0:0,0:92,39:0:2,0:22:1:31.7:1:1:0:60:130:1:0:0.3 -15 54532082 . T C 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAATCTCAAAGCATCTAG;RSEQ=CTTCTTTTGAGTAAATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:116,83:0:2,0:24.1:1:29.9:1:1:0:60:198:1:0:0.3 0/1:191:23:14,9:101,67:0.1204:2,2:22.4:1:30.3:1:1:1.03:60:22:0.1164:0:1.8 -15 54532120 . T C 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03058;SOR=Inf;LSEQ=ATAAAGTCTGAAGAATTTTA;RSEQ=TGATAAACTCCTACACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:114,130:0:2,0:26.3:1:30.4:1:1:0:60:80.333:1:0:0.5 0/1:256:6:4,2:125,125:0.0234:2,2:21.7:1:27.8:1:0.68384:1.99:60:5:0.0196:0:2.3 -15 54532140 . A T 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.92776;SOR=1.01709;LSEQ=TTGATAAACTCCTACACTGT;RSEQ=CCTTTCTTATGTTTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:96:41,55:66,80:0.3967:2,2:28.1:1:29.8:1:0.79145:1.10624:60:47:0.3966:0:1.1 0/1:262:105:51,54:66,91:0.4008:2,2:26.3:1:29.2:1:0.31268:1.30:60:104:0.4:0:1.3 -15 54532164 . G T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10412;SOR=0;LSEQ=TTCTTATGTTTTAAAACATG;RSEQ=TATTTGATTTGAACTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:1,2:73,124:0.015:2,2:22.3:1:29.3:1:1:1.17651:60:6:0.0151:0:1 0/0:224:0:0,0:87,135:0:2,0:26.5:1:31.1:1:1:0:60:221:0.991:0:0.5 -15 54609467 . C T 187 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=113.21845;LSEQ=ATGTTAGCACTAATGATAAA;RSEQ=GTGTGGTGAAGATTGTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:1:1,0:219,257:0.0021:2,0:44:0:33:0:0.46122:0:60:2:0.0021:0:1 0/1:410:79:36,43:155,175:0.1927:2,2:27.5:1:29.7:1:0.90023:1.05782:60:158:0.1955:0:1.3 -15 54609538 . T A 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.259;SOR=0.77695;LSEQ=CATGACGTTTCCTGAATTAT;RSEQ=CAAATTTTCACATATAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:222:117:29,88:25,80:0.527:2,2:24.4:1:29.5:1:0.87697:1.05:60:234:0.527:0:1 0/1:166:77:22,55:27,62:0.4639:2,2:25.4:1:28.9:1:0.86529:1.08815:60:76:0.4606:0:1.2 -15 55966241 . T G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGGGTGGGGAAGCCTAG;RSEQ=ATTCTACAGTTATAACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:32.3:1:33:0:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 55966445 . G C 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02268;SOR=Inf;LSEQ=AAGAGTTCAGATGGGTTCTA;RSEQ=AGTTAGCTTCTCTGTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:37,0:0:1,0:27.5:1:31.8:1:1:0:60:36:1:0:0.1 0/1:25:4:4,0:20,1:0.16:1,0:27.8:1:31.8:1:1:0:60:8:0.16:0:1 -15 55966487 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59162;SOR=2.4132;LSEQ=AACCTTGTTCTACCATGTAC;RSEQ=ACTCTGTGATCTTGACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:1:1,0:59,3:0.0159:1,0:4:0:28:0:1:0:60:2:0.0164:0:2 0/1:53:2:1,1:49,2:0.0377:1,2:42.5:1:30.5:1:0.11103:20.20728:60:4:0.0377:0:1 -15 55966523 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24233;SOR=Inf;LSEQ=CCAAATTAACCTCTCTTACC;RSEQ=AGGTTTCTTCAGACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:90,25:0:2,0:22.4:1:29.8:1:1:0:60:56.5:1:0:0 0/1:112:2:1,1:88,22:0.0179:2,2:11.5:1:29:1:0.37001:3.93424:60:4:0.0179:0:1 -15 55966642 . C A 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.38392;SOR=0.83694;LSEQ=GAACAGACCTCACACACACA;RSEQ=AAAATCTATCTTTATTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:68:31,37:155,169:0.173:2,2:21.5:1:29.8:1:0.79:1.09441:60:33:0.1732:0:1.1 0/1:396:59:32,27:175,159:0.149:2,2:23.1:1:29.6:1:0.88769:1.08:60:58:0.1491:0:1.3 -15 55966688 . C A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10274;SOR=0;LSEQ=TTCACCTTAGACATGCATAA;RSEQ=AGAGGTTGTTAATAGCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:107,187:0.0101:2,2:24.3:1:29.3:1:0.55672:3.48:60:6:0.0103:0:1.7 0/0:336:0:0,0:147,189:0:2,0:25.7:1:31.3:1:1:0:60:83:1:0:0.3 -15 56872926 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.19206;LSEQ=CACATCTTTGATGAGCTTCC;RSEQ=TTGTAACAAAATTCTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:15:15,0:2,0:0.8824:0,1:30.2:1:31.7:1:1:0:60:30:0.8824:0:1 1/1:10:9:9,0:1,0:0.9:0,0:23.9:1:29.4:1:1:0:60:8:0.8889:0:1.1 -15 56873003 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49692;SOR=Inf;LSEQ=GTGAGCCTCAATAGACAGAT;RSEQ=TGTCCTCTTATAATAATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:50,14:0:2,0:21.1:1:31.8:1:1:0:60:128:1:0:0.1 0/1:69:2:1,1:48,19:0.029:2,2:17.5:1:29:1:0.49872:2.48788:60:4:0.029:0:1.5 -15 56873061 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=TATGGGAAGCATTGTCAATT;RSEQ=ATAAGTGATGCTAGATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:51,60:0:2,0:30.6:1:31.7:1:1:0:60:222:1:0:0.1 0/1:122:2:1,1:61,59:0.0164:2,2:41.5:1:28.5:1:1:1.03362:60:4:0.0164:0:1 -15 59161834 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17149;SOR=0;LSEQ=TAAACCTTTCGGCCGGAACC;RSEQ=CCATCTTCCAGTAATTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:81,72:0.0128:2,2:34:1:30:1:1:1.12414:60:4:0.013:0:1 0/0:220:0:0,0:110,110:0:2,0:11:0:16:0:1:0:60:0:0:0:1 -15 59161897 . A T 19 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.79925;LSEQ=AGGGGAGAGGCACCCAATAT;RSEQ=TGTTCTCTAGGTCTTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:34,73:0.0183:2,2:12.5:1:28.5:1:0.54111:2.13:60:4:0.0194:0:1 0/1:136:2:0,2:46,88:0.0147:2,0:10:1:19:1:0.54902:0:60:1:0.0078:0:4.5 -15 59162013 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51039;SOR=Inf;LSEQ=GGTACTGTTCAAAAAGGAAT;RSEQ=CCCCACAAGTGTTACCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:40,35:0:2,0:23.1:1:28.4:1:1:0:58.8:74:1:0:0.1 0/1:104:2:1,1:59,43:0.0192:2,2:9.5:1:29:1:1:1.36784:60:4:0.0192:0:1 -15 59162117 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49648;SOR=0;LSEQ=AAGGGCAAGATTCTTGCCAA;RSEQ=AGAATTAATGTGTGTATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:10,28:0.05:2,2:20.5:1:31:1:0.47949:2.72:60:4:0.05:0:1 0/0:34:0:0,0:9,25:0:2,0:20.4:1:31.6:1:1:0:60:68:1:0:0 -15 59341646 . A G 46 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGCAGTTCAGGCTCCTGTCC;RSEQ=TTGGTTCTCACAAAGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:5:0:33:0:1:0:60:2:1:0:0 1/0:4:3:2,1:0,1:0.75:0,2:31.3:1:29.3:1:1:0:60:6:0.75:0:1 -15 59342553 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48663;SOR=Inf;LSEQ=GCCCTAGAGAACAAATTGGA;RSEQ=GTGCCTCTTCTTTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:0:2,0:24:1:31.6:1:1:0:60:32:1:0:0.3 0/1:18:2:1,1:7,9:0.1111:2,2:20:0:31.5:1:1:1.27:60:4:0.1111:0:1 -15 59502492 . TTGTACATTGAC T 200 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATTCAATAACAACTTCCAT;RSEQ=ATTTTACTCATATCCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:96:45,51:105,113:0.3057:2,2:27.2:1:30.4:1:0.90252:1.05295:59.8:192:0.3097:0.051:0.2 0/0:484:0:0,0:242,242:0:2,0:24.8:1:29.5:1:1:0:60:95.8:1:0:0.3 -15 59502497 . C A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23657;LSEQ=AATAACAACTTCCATTTGTA;RSEQ=ATTGACATTTTACTCATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:293:149:73,76:30,34:0.5085:2,2:25.2:1:30:1:0.88123:1.09:60:73.5:0.7033:0:1.1 0/1:489:96:48,48:195,198:0.1963:2,2:26.9:1:30.1:1:1:1.02:60:192:0.1983:0:1.2 -15 59502520 . CAT C 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACATTTTACTCATATCCA;RSEQ=GTTCATATTTACTGCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:148,167:0:2,0:25.3:1:30.4:1:1:0:60:44:1:0:0.5 0/1:471:40:19,21:199,231:0.0849:2,2:24.3:1:31:1:1:1.05:60:80:0.0862:0.0106:0.9 -15 59502553 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15539;SOR=Inf;LSEQ=ACTGCCAGAATAAAGCCGTA;RSEQ=TGTTCTCTTTTCACACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:86,148:0:2,0:25.8:1:32.3:1:1:0:59.9:468:0.9957:0:0.4 0/1:356:4:2,2:138,214:0.0112:2,2:26.5:1:29.3:1:0.6476:1.55:60:8:0.0113:0:2 -15 59817922 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49254;SOR=Inf;LSEQ=TTGCCATGGTAACATTTGTG;RSEQ=GGTATTCCTTTTTGAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:0:2,0:20.7:1:30.7:1:1:0:60:66:1:0:0.1 0/1:34:2:1,1:15,17:0.0588:2,2:7.5:1:27:1:1:1.13:60:4:0.0606:0:1 -15 59845063 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19046;SOR=0;LSEQ=ATCTTGCCCTTAACTGTTTG;RSEQ=TTACAACAATGCCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:39,23:0.0313:2,2:33.5:1:30.5:1:1:1.68102:60:4:0.0317:0:1.5 0/0:82:0:0,0:47,34:0:2,0:23.2:1:29.3:1:1:0:59.7:162:1:0:0.3 -15 59845138 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1653;LSEQ=CGTGGTAACACTTGTGGGGC;RSEQ=TTCCTTTTTGAACAGTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:61:22,39:3,10:0.8243:2,2:21.1:1:30.8:1:0.52273:1.87:56.9:122:0.8243:0:1 0/1:83:36:11,25:16,31:0.4337:2,2:23:1:29.8:1:0.8154:1.17077:57.6:35:0.4268:0:1.1 -15 59845326 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0188;SOR=0;LSEQ=TGGAAGATGGCGGTTCCCGC;RSEQ=GAAAGGCGCCTTAGTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:3,4:0.3636:2,0:24.8:1:29.3:1:0.23636:0:60:8:0.3636:0:2 0/0:16:0:0,0:5,11:0:2,0:22.8:1:28.6:1:1:0:60:32:1:0:0.3 -15 60297406 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50046;SOR=Inf;LSEQ=CGCGGCGGCCGGACCAGCCA;RSEQ=GCAAGGGCAGCTTCTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:21.9:1:30.6:1:1:0:60:19:1:0:0.1 0/1:27:2:1,1:14,11:0.0741:2,2:8:1:29:1:1:1.2613:60:4:0.0741:0:1 -15 60297427 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50588;SOR=Inf;LSEQ=GCAAGGGCAGCTTCTGGGCG;RSEQ=TGCACCCAAGCTGCGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:25.8:1:30.6:1:1:0:60:13:1:0:0.1 0/1:21:2:1,1:9,10:0.0952:2,2:27:1:28.5:1:1:1.11:60:4:0.0952:0:1 -15 60297536 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GCCCAGCAAGCCAGCCGACG;RSEQ=GGCGCAGTACCTGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:32.7:1:30.2:1:1:0:60:12:1:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:29:1:28:1:1:2.45:60:4:0.3333:0:1 -15 60297613 . CCCG C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=GCACGCACCTGCCACAGATG;RSEQ=CCGCCGCCTACAACTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:35.5:1:32.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:30:1:1:0:60:4:1:0:0.5 -15 61656824 . A G 52 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=GAATAGGGCCTGTTTAACAA;RSEQ=GTACTTTGTCCTTTGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:0.5:2,2:10.3:1:33.3:1:1:3.11:60:6:0.5:0:1 0/0:6:0:0,0:3,3:0:2,0:22.3:1:29.7:1:1:0:60:12:1:0:0.2 -15 61657223 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05455;SOR=Inf;LSEQ=ATGGGTGCCGCCCTTCCCCC;RSEQ=CCCATGAAGCTTAGTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:13.9:1:31.4:1:1:0:60:16:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:38.5:1:28.5:1:1:0:60:4:0.6667:0:1 -15 62266250 . C T 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01314;SOR=0.58734;LSEQ=AGTGATCTAGAACTTATAAG;RSEQ=CTAACATATAAGAAAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:104:49,55:35,26:0.6303:2,2:26.2:1:30:1:0.25886:1.50717:60:51:0.6335:0:1.1 1/0:224:112:60,52:54,58:0.5:2,2:27.5:1:29.3:1:0.50406:1.24:60:111:0.5023:0:1.1 -15 62374593 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=GGACAGCCAGATATCAACTG;RSEQ=TACACAAATGAAATAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:20.5:1:29.5:1:1:0:60:4:0.4:0:1 1/0:4:2:2,0:2,0:0.5:0,0:31:1:31.5:1:1:0:60:4:0.5:0:1 -15 62374729 . A G 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCACAAAATTGATGAAC;RSEQ=TGGCCTCCACTTTGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:16,11:0,0:1:0,2:28.9:1:31.1:1:1:0:60:54:1:0:1.1 1/1:35:35:17,18:0,0:1:0,2:25.9:1:29.9:1:1:0:60:70:1:0:1.3 -15 62374857 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16304;SOR=Inf;LSEQ=CGTGCTTTGAAGGATTCTTG;RSEQ=CCTTTTAATCTTGTGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:24.3:1:29.9:1:1:0:60:28:1:0:0.4 0/1:10:2:1,1:3,5:0.2:2,2:42:1:29:1:1:1.58:57.5:4:0.2:0:2.5 -15 62374864 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.15584;SOR=Inf;LSEQ=TGAAGGATTCTTGACCTTTT;RSEQ=ATCTTGTGTTGATGGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:26.2:1:28.8:1:1:0:60:26:1:0:0.4 0/1:9:2:1,1:3,4:0.2222:2,2:35:1:31.5:1:1:1.29:57.5:4:0.2222:0:2.5 -15 62374869 . T TG 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17143;SOR=Inf;LSEQ=GATTCTTGACCTTTTAATCT;RSEQ=GTGTTGATGGTTTTGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:28.6:1:29.3:1:1:0:60:24:1:0:0.5 0/1:9:2:1,1:2,5:0.2222:2,2:29:1:29.5:1:1:2.24:57.5:4:0.2222:0:2.5 -15 62374877 . T C 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21739;SOR=0;LSEQ=ACCTTTTAATCTTGTGTTGA;RSEQ=GGTTTTGAGTCTTTTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:4,5:0.25:2,2:37:1:30.3:1:1:1.53983:60:6:0.25:0:1 0/0:11:0:0,0:4,7:0:2,0:24.4:1:28.9:1:1:0:59.5:22:1:0:0.9 -15 62374915 . T C 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30245;SOR=4.19343;LSEQ=ACTCTGATTTTGTTGTTTTG;RSEQ=ATTTTGGGTTGAAATACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:23:1:31.5:1:1:2.24:60:4:0.2222:0:1.5 1/0:7:4:1,3:2,1:0.5714:2,2:24:1:32.8:1:0.48571:4.4496:60:8:0.5714:0:1.3 -15 62374942 . T A 28 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.62174;LSEQ=GGTTGAAATACCTCCTGTAG;RSEQ=TTTCTTCCCTGAAGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:1,5:0.25:2,0:17:1:28:1:0.10714:0:60:4:0.25:0:1.5 0/1:6:1:0,1:3,2:0.1667:2,0:29:0:32:0:1:0:60:2:0.1667:0:2 -15 62375036 . T G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.70357;SOR=1.76214;LSEQ=CCATCCTTTGTCAGCAGCAC;RSEQ=TTTTACTTTTTTCTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:4,3:5,4:0.4375:2,2:20.4:1:30.7:1:1:1.06:60:14:0.4375:0:1.9 1/0:12:7:4,3:2,3:0.5833:2,2:20.9:1:31:1:1:1.89:60:14:0.5833:0:1.3 -15 62375068 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=TCTGTGGAAGCTTGCTACCA;RSEQ=CTGCAGGGGCAGATCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:0:2,0:40.2:1:31.1:1:1:0:60:12:1:0:1 0/1:13:2:1,1:5,6:0.1538:2,2:35:1:28.5:1:1:1.18:60:4:0.1538:0:2 -15 62375236 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51446;SOR=0;LSEQ=TGGGTGGTGTTATTTCAAAG;RSEQ=CCCAAAGGGAAACTGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:22,20:0.0455:2,2:17:1:30.5:1:1:1.09762:60:4:0.0455:0:1 0/0:29:0:0,0:15,14:0:2,0:26.7:1:31.5:1:1:0:60:58:1:0:0.1 -15 62375334 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51111;SOR=0;LSEQ=ATTATCTCTGCTTCAACAAC;RSEQ=TGCAATTCATCCTTTGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:11,20:0.0606:2,2:33.5:1:31.5:1:1:1.78:60:4:0.0606:0:1 0/0:22:0:0,0:8,13:0:2,0:27.1:1:30.4:1:1:0:60:42:0.9545:0:0.3 -15 62375389 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04885;SOR=4.21228;LSEQ=TGGTTCTTAAAGATAACTGG;RSEQ=GCTCATTTGTATCATTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:4,3:3,8:0.3889:2,2:23.7:1:30:1:0.3322:3.29:60:14:0.3889:0:1 1/0:19:14:8,6:1,4:0.7368:2,2:25.3:1:30.7:1:0.30341:4.89:60:28:0.7368:0:1.1 -15 62375453 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23153;SOR=0;LSEQ=ACCCTTTAGCTCGCAACTGA;RSEQ=AAGATAGTTCTGGGCCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:11,2:0.1875:2,2:12.7:1:28:1:0.48929:2.54679:60:6:0.1875:0:1.3 0/0:13:0:0,0:7,6:0:2,0:18.7:1:30.5:1:1:0:60:26:1:0:0.5 -15 62375494 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15385;SOR=Inf;LSEQ=GAGGCTTAAGTACATGTCCA;RSEQ=CAAATCTTCCATAGGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:27.7:1:30:1:1:0:60:48:1:0:0.1 0/1:16:2:1,1:7,7:0.125:2,2:11:1:32:1:1:1:60:4:0.125:0:1 -15 63054439 . C G 262 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00358;LSEQ=ATTCACTCATGTCTTCGACC;RSEQ=TGACTTTGATTTCTCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:394:393:188,205:1,0:0.9975:0,2:25.2:1:30.5:1:0.4797:0:60:77.6:1:0:1.1 1/0:420:245:109,136:78,94:0.5833:2,2:25.8:1:30.2:1:0.92038:1.03526:60:121.5:0.5855:0:1.1 -15 63766676 . C T 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CACCTGGGATCCTTGCTGCT;RSEQ=TGGGAAAGATAAACTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:165,173:0:2,0:26.6:1:31.4:1:1:0:60:41.25:1:0:0.1 0/1:419:56:26,30:193,170:0.1337:2,2:24.1:1:28.9:1:0.3896:1.3091:60:17.667:0.1286:0:1.2 -15 63766778 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23287;SOR=0;LSEQ=GGACTTTTAGACTTGGAAGA;RSEQ=ATCTTGGTGGAAAAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:24,106:0.0152:2,2:15:1:28:1:0.34409:4.35:60:4:0.0154:0:2 0/0:141:0:0,0:29,112:0:2,0:21.3:1:31:1:1:0:60:69.5:1:0:0.1 -15 63766788 . GA G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=ACTTGGAAGAGATCTTGGTG;RSEQ=AAAAAAGGAAGGGAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:18,97:0.0171:2,0:23:1:33.5:1:1:0:60:4:0.0174:0:0 0/0:104:0:0,0:17,87:0:2,0:21.9:1:29.3:1:1:0:60:33.667:1:0:0.1 -15 63995032 . T C 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATTTAGCTGGCCGGGCA;RSEQ=GGTGGCTCACGCCTGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:21.8:1:31.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 63995340 . C T 53 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23669;SOR=3.96003;LSEQ=AAAAAAAAGAGTAAATTTAG;RSEQ=TTTGATGCCTCTGAAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:1,0:148,58:0.0048:2,0:31:0:12:0:1:0:60:0:0:0:6 0/1:267:5:4,1:182,77:0.0187:2,2:21.8:1:23.2:1:1:1.69:50.8:4:0.0175:0:5.4 -15 63995423 . C T 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCCTACATATTCACTTTCT;RSEQ=AGACCAAGGGCTTAGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:477:477:231,246:0,0:1:0,2:24.7:1:28.7:1:1:0:60:118.25:1:0:1.1 1/1:616:531:279,252:37,47:0.862:2,2:23.2:1:28.5:1:0.15965:1.41:60:105.2:0.8623:0:1.1 -15 64923588 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52241;SOR=Inf;LSEQ=AATGCCAACAGCGTGCTGGG;RSEQ=GACACTGTAGACTCTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:39,34:0:2,0:29.3:1:31:1:1:0:60:146:1:0:0.1 0/1:115:2:1,1:60,53:0.0174:2,2:36.5:1:30.5:1:1:1.13085:60:4:0.018:0:1.5 -15 64923740 . CT C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49291;SOR=0;LSEQ=CTTCATATTTTCTTTTCTTT;RSEQ=TTTTTTTTAGACGGAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:6,18:0.0769:2,2:38:1:31:1:0.47385:2.85:60:4:0.0769:0:0 0/0:22:0:0,0:5,15:0:2,0:17.2:1:30.2:1:1:0:59.5:40:0.9091:0:0.3 -15 66679601 . G C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.27696;LSEQ=CGGCCCGGACTTGGTCCTGC;RSEQ=CAGCGGGCGCGGGGCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:119:98,21:137,25:0.422:2,2:23.3:1:30.8:1:0.62826:1.1736:60:38.667:0.4173:0:1.1 0/1:280:47:35,12:189,43:0.1679:2,2:18.3:1:30.6:1:0.31425:1.50458:60:94:0.1691:0:1.3 -15 66679602 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24872;SOR=0;LSEQ=GGCCCGGACTTGGTCCTGCG;RSEQ=AGCGGGCGCGGGGCAGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:1,2:239,48:0.0103:2,2:17.3:1:27.3:1:0.07795:9.83407:60:6:0.0105:0:1 0/0:287:0:0,0:228,59:0:2,0:20:0:13:0:1:0:60:0:0:0:4 -15 66679649 . T TC 210 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAGCGAGAGGTGCTGCCC;RSEQ=CCCCCCGGAGTTGGAAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:756:0:0,0:510,242:0:2,0:24.4:1:30.3:1:1:0:60:31.696:0.9959:0:0.4 0/1:832:115:71,44:438,274:0.1382:2,2:28.1:1:30.7:1:1:1.01:60:230:0.1415:0.0048:0.2 -15 66679684 . A G 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGCGCGTTACCCGGGTCCA;RSEQ=AATGCCCAAGAAGAAGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1041:76:46,30:552,412:0.073:2,2:27.6:1:31.9:1:0.63068:1.14:60:75:0.0733:0:1.1 0/0:1240:0:0,0:664,575:0:2,0:24.4:1:29.6:1:1:0:60:60.95:0.9992:0:0.3 -15 66679819 . G C 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGCTGGGGAGGCCCGAGCC;RSEQ=GGGAGCAGGAGCGCGCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:121,303:0:2,0:24.1:1:30.5:1:1:0:60:105:0.9976:0:0.1 0/1:400:33:10,23:126,241:0.0825:2,2:28.8:1:30:1:0.70499:1.20199:60:66:0.0831:0:1.1 -15 66679850 . TG T 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCGCGCCAGGCTCCGATC;RSEQ=GTTTGTCACGTACGTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:32,217:0:2,0:23.7:1:31:1:1:0:60:34.571:1:0:0.1 0/1:207:24:4,20:26,157:0.1159:2,2:18.1:1:30.9:1:0.75848:1.21:60:48:0.1176:0.0386:1 -15 66694155 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50335;SOR=Inf;LSEQ=GATTCCATGGGAATGGAGGG;RSEQ=CGTGGCAGGAAGAGAGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:109,15:0:2,0:24.5:1:31.6:1:1:0:60:248:1:0:0.1 0/1:152:2:1,1:131,19:0.0132:2,2:7:1:27:1:0.2466:6.74443:60:4:0.0133:0:1 -15 66694161 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49938;SOR=Inf;LSEQ=ATGGGAATGGAGGGGCGTGG;RSEQ=AGGAAGAGAGCACGGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:135,26:0:2,0:21.5:1:32:1:1:0:60:52.667:1:0:0 0/1:175:2:1,1:146,27:0.0114:2,2:13:1:26.5:1:0.29517:5.32823:60:4:0.0116:0:1 -15 66694351 . C A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30534;SOR=0.21361;LSEQ=ATCACATGCAAATTTTTCTT;RSEQ=CTTTCTGATCATTTTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:80,186:0.0112:2,2:13:1:28:1:0.22119:4.62:60:6:0.0112:0:1 0/0:417:1:1,0:150,266:0.0024:2,0:1:0:24:0:0.36211:0:60:2:0.0024:0:1 -15 66694420 . A T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00394;SOR=Inf;LSEQ=ATTTTGAAGTTTTATAAATG;RSEQ=TGTGGTTACTACATTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:2,69:0:1,0:31.2:1:31.2:1:1:0:60:70:1:0:0.3 0/1:84:9:1,8:1,74:0.1071:1,2:18.9:1:28.4:1:0.20396:8.78:60:18:0.1084:0:1.7 -15 66694431 . A G 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02656;SOR=2.36522;LSEQ=TTATAAATGATGTGGTTACT;RSEQ=CATTGTTCCATTGTGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:18:0,18:0,49:0.2687:1,1:26.7:1:32.7:1:1:0:60:36:0.2687:0:1 0/1:60:28:0,28:0,32:0.4667:1,1:21.4:1:31.4:1:1:0:60:56:0.4667:0:1.2 -15 66694558 . A C 83 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTAACATCTGTCATCTCT;RSEQ=CACAACTAGCAGGAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:23.7:1:32.2:1:1:0:60:12:1:0:1 1/1:2:2:0,2:0,0:1:0,0:33:1:32.5:1:1:0:60:4:1:0:1 -15 66727325 . C G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00818;SOR=Inf;LSEQ=ACTTCTTTGGGTTGACTTCT;RSEQ=TGGTGACAGTATTGACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:159,49:0:2,0:24.5:1:31.1:1:1:0:60:40.6:1:0:0.1 0/1:236:8:7,1:165,62:0.0339:2,2:13.6:1:32.8:1:0.68556:2.62:60:16:0.0345:0:1.1 -15 66727597 . G C 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=2.00941;LSEQ=TGAGTTTGCCTTGATTAACA;RSEQ=GTAATTGGATTATTTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:74:16,58:33,160:0.2761:2,2:21:1:29.1:1:0.3836:1.34:60:36:0.2738:0:1.1 0/1:357:155:38,117:50,152:0.4342:2,2:22.7:1:30:1:1:1.01278:60:76.5:0.4334:0:1.1 -15 66727632 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23751;SOR=Inf;LSEQ=TCTCAGGGTACTTAGAAGCC;RSEQ=GGGGACCAGGGTAGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:7,145:0:1,0:28.7:1:29.5:1:1:0:59.8:18:1:0:0.4 0/1:145:2:1,1:18,125:0.0138:2,2:27.5:1:32:0:0.24569:6.79:60:4:0.0146:0:1 -15 66727689 . A ATTT 118 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=18.000;MSILEN=1;SSF=0.00718;SOR=5.21326;LSEQ=TACCTTTTTGTGCTGTTTGA;RSEQ=TTTTTTTTTTTTTTTAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:1,21:0.0833:1,0:34.8:1:30.5:1:1:0:60:8:0.0909:0:2 0/1:43:14:0,14:2,17:0.3256:2,1:23.6:1:31:1:0.49621:0:55.4:28:0.3256:0.0233:1.5 -15 66728951 . A C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00238;SOR=0.2217;LSEQ=CATTTCTTGGTTGAGCAGAA;RSEQ=CTTGTTTGTAACAACTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:26:25,1:33,3:0.4194:2,1:21.9:1:32.2:1:0.63296:2.25:60:25:0.4098:0:1.1 0/1:44:6:6,0:36,2:0.1364:2,0:14:1:31.2:1:1:0:60:12:0.1364:0:1 -15 66729173 . G A 65 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00853;SOR=Inf;LSEQ=TGCAACTCTCCGTACATCGT;RSEQ=GGCTTCTATGGTGCGTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:0:0,0:263,356:0:2,0:25.3:1:31.3:1:1:0:59.9:55.273:0.9984:0:0.1 0/1:705:8:7,1:286,411:0.0113:2,2:9.9:1:21.9:1:0.01054:10.03:58.4:3:0.0086:0:1.3 -15 66729250 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23947;SOR=0;LSEQ=GGTATGTGACACCCTCTCAG;RSEQ=CTCTGGAGCAATGGCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:30,164:0.0102:2,2:5:1:28.5:1:0.29199:5.39:60:4:0.0106:0:1 0/0:204:0:0,0:46,158:0:2,0:23.1:1:31.1:1:1:0:60:67:1:0:0.1 -15 66735551 . C T 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCCTGCCTCAGCCACAGC;RSEQ=GAAAGTTATCACTTGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:149:149:119,30:0,0:1:0,2:20.8:1:31.1:1:1:0:59.9:298:1:0:1.1 1/1:155:136:105,31:16,3:0.8774:2,2:23.4:1:30.7:1:0.76725:1.57047:60:135:0.8766:0:1.1 -15 66735925 . C CAG 93 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGTGTGTCTTGAAAAA;RSEQ=GGGCCAGGCACAGTGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:27.4:1:31.3:1:1:0:60:16:1:0.25:0.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 66736741 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAGCCGGGGGTGGTAGCG;RSEQ=ATGCCCGTAATCCCAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:8:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 66773935 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCAGAACAAAGGGCCTT;RSEQ=GTGTACAGTGTTTGCAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:34,0:0.0556:1,2:10:0:32:0:0.05556:0:60:4:0.0606:0:1.5 0/0:11:0:0,0:10,1:0:2,0:22.4:1:32.5:1:1:0:60:22:1:0:0.2 -15 66773975 . G A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03229;SOR=0.36723;LSEQ=CAAGGGCTGCCTCTGATGGC;RSEQ=GACGGGGGTGTGGTCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:24:24,0:35,1:0.4:1,1:26.6:1:29.4:1:1:0:60:11:0.386:0:1.2 0/1:41:8:8,0:30,3:0.1951:2,0:20.6:1:30.8:1:1:0:60:16:0.1951:0:1 -15 66774285 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23005;SOR=Inf;LSEQ=GAGGAGCCCAGTGGGTGCCT;RSEQ=TCCTGTGGAGCCAGAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:22,176:0:2,0:23.3:1:30.4:1:1:0:60:65:1:0:0.1 0/1:183:2:1,1:30,151:0.0109:2,2:32:1:30.5:1:0.31087:4.97:60:4:0.0111:0:1 -15 66774559 . A G 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCAGGATGCTCAGATAT;RSEQ=ATCCACCCCAAACTACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18.5:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 66779698 . C T 170 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAGAAAACACCCAGGTGGC;RSEQ=GGGTGCAGTGGTTCACGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:52:12,40:33,150:0.2203:2,2:21.4:1:29.9:1:0.42772:1.36:60:51:0.2237:0:1.2 0/0:248:0:0,0:57,190:0:2,0:21.6:1:29.5:1:1:0:60:122.5:0.9959:0:0.1 -15 66779707 . T A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24838;SOR=0;LSEQ=ACCCAGGTGGCCGGGTGCAG;RSEQ=GGTTCACGCCTGTAATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:2,1:29,166:0.0152:2,2:10:1:28:1:0.06447:11.22:60:6:0.0155:0:1.7 0/0:190:0:0,0:29,160:0:2,0:22.7:1:29.7:1:1:0:60:62:1:0:0.1 -15 66781452 . T TA 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.65171;LSEQ=TTGGACTGCAGAGAAGACTT;RSEQ=AAAAAAAAGTAGCACTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:148,16:0.012:2,2:38:1:29.5:1:0.19489:9.00409:60:4:0.0121:0:0 0/0:127:1:1,0:108,18:0.0079:2,0:11:0:27:0:1:0:60:2:0.0079:0:0 -15 66781718 . C T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57426;SOR=2.78641;LSEQ=TTCTGCAGGCAGAGTTTTGC;RSEQ=CTTTACCCTCCCGTCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:1:0,1:16,187:0.0049:2,0:26:0:14:0:1:0:60:0:0:0:2 0/1:148:2:1,1:10,136:0.0135:2,2:7:1:26.5:1:0.14359:13.01:60:4:0.0139:0:1 -15 66781887 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1733;SOR=Inf;LSEQ=ACCTTAGTTTAACTCAGCAA;RSEQ=AATGTATTAACTTACTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:53,15:0:2,0:21.6:1:32.2:1:1:0:60:136:1:0:0.1 0/1:49:2:1,1:45,2:0.0408:1,2:6:0:32:0:0.1199:18.56672:60:4:0.0426:0:1 -15 66781953 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49959;SOR=Inf;LSEQ=GGATGAATCAAGCCCAGGCA;RSEQ=TCCTCGGCCTCTAGTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:152,21:0:2,0:25.7:1:30:1:1:0:60:33.6:1:0:0.1 0/1:189:2:1,1:156,31:0.0106:2,2:25:1:30.5:1:0.31071:4.96899:60:4:0.0108:0:1.5 -15 66782048 . C T 200 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCTTACCTTGTCTTTCTT;RSEQ=CTTTAAGCTTAATAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:110:60,50:288,246:0.1708:2,2:23.7:1:29.6:1:0.91678:1.02:60:35.667:0.1709:0:1.2 0/0:819:0:0,0:431,388:0:2,0:25.1:1:30.7:1:1:0:60:57.5:1:0:0.2 -15 66782192 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21673;SOR=0;LSEQ=CAGTACTTCCAGAGCCCATT;RSEQ=ATTCCCTGCCCACTGTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:18,146:0.012:2,2:14.5:1:27.5:1:0.21643:7.92:60:4:0.012:0:1 0/0:190:0:0,0:27,163:0:2,0:21.5:1:31.5:1:1:0:60:189:1:0:0.1 -15 66782260 . C G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05784;SOR=Inf;LSEQ=AAACACCAGTCTCCTTTGCT;RSEQ=TCCCATCAGTTTAAGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,65:0:1,0:25.9:1:32.2:1:1:0:60:31.5:1:0:0.3 0/1:42:3:0,3:2,37:0.0714:2,0:19:1:32.3:1:1:0:60:6:0.0714:0:1 -15 66783025 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2026;SOR=Inf;LSEQ=CGCTTTTGGGCCTCCTTCCC;RSEQ=TGCCTGTCTCTGTTCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:1,112:0:1,0:23.4:1:31.2:1:1:0:59.1:55.5:1:0:0.1 0/1:93:2:1,1:3,88:0.0215:1,2:32.5:1:28.5:1:0.08462:25.55:60:4:0.0217:0:1.5 -15 67358478 . G A 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGCGCTCCTCGCCGCCCGC;RSEQ=CGCCCTCCCCAGCCATGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:224,40:0:2,0:25:1:30.4:1:1:0:60:65:1:0:0.1 0/1:251:44:34,10:163,44:0.1753:2,2:23.6:1:29:1:0.84095:1.08919:60:13.667:0.1673:0:1.1 -15 67358480 . G T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12393;SOR=0;LSEQ=GCGCTCCTCGCCGCCCGCGC;RSEQ=CCCTCCCCAGCCATGTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:4:2,2:231,43:0.0144:2,2:17.5:1:29.8:1:0.12406:5.32294:60:8:0.0146:0:1 0/0:267:0:0,0:208,59:0:2,0:23.8:1:30:1:1:0:60:88:1:0:0.4 -15 67430223 . T C 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGTCCTCCCTTTGGATTTCT;RSEQ=CTGTCTGGGTGTTGCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:92:92:90,2:0,0:1:0,1:24.8:1:31.4:1:1:0:60:91:1:0:1.1 1/1:56:56:56,0:0,0:1:0,1:23.1:1:30.2:1:1:0:60:13:1:0:1.1 -15 67430489 . C T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.10447;SOR=0;LSEQ=CTCTTTCTTGAACTCGTCTC;RSEQ=CCACCCGTCCACAGGGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:2,1:44,165:0.0142:2,2:28.3:1:26.3:1:0.11944:7.40:60:2:0.0098:0:2 0/0:237:0:0,0:66,170:0:2,0:23.5:1:30.2:1:1:0:60:235:0.9958:0:0.2 -15 67430538 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23161;SOR=Inf;LSEQ=GATCTGTCAGAGTTTCTCCG;RSEQ=GCTTCTCTTTCTCTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:1,89:0:1,0:23.6:1:30.7:1:1:0:60:44:1:0:0.1 0/1:84:2:1,1:4,78:0.0238:1,2:25:1:25.5:1:0.11618:17.55:60:4:0.0241:0:1 -15 67430552 . T C 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0217;SOR=9.71314;LSEQ=TCTCCGGGCTTCTCTTTCTC;RSEQ=GGGTGGGGATGTGGACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:0,1:0,76:0.013:1,0:35:0:10:0:1:0:60:0:0:0:1 0/1:61:7:0,7:3,51:0.1148:2,0:20.6:1:28.6:1:1:0:60:14:0.1148:0:1 -15 67430733 . T C 90 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTGCCATCGCAGTGGAT;RSEQ=TGCGGAAGAGGGTTCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:17.3:1:32.3:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 67432161 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGAAGCTGTGCTTGGAA;RSEQ=GTGAATGTGTTTAGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 67455276 . A G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCATTGTGTGTAATTGT;RSEQ=GGTTTCTGTGATGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:28.5:1:32:0:1:0:60:4:0.5:0:1 -15 67456266 . C G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTGAGTGACAGAGCAA;RSEQ=ACCCTGTATCAAAAGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29.5:1:1:0:53.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 67457335 . A G 315 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01429;LSEQ=CTGCACAGCCACCACGAGCT;RSEQ=CGGGCCATGGAGCTGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:931:926:468,458:0,0:0.9946:0,2:25.9:1:32:1:1:0:60:91.6:0.9967:0:1.2 1/0:884:641:323,318:120,123:0.7251:2,2:25.7:1:31.6:1:0.82133:1.04:60:63.1:0.7278:0:1.2 -15 67457480 . T TC 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGCCAGGGGTCATCACCTC;RSEQ=CCCCGGCTCCCCATCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:39:25,14:42,89:0.0975:2,2:10.6:1:29.1:1:0.00064:3.75:59.6:12:0.0916:0.07:1.3 0/0:217:0:0,0:82,135:0:2,0:21:1:29.3:1:1:0:60:30:1:0:0.7 -15 67457485 . G CC 245 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=AGGGGTCATCACCTCTCCCC;RSEQ=GCTCCCCATCCCCCCGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:400:230:74,156:42,89:0.575:2,2:28.3:1:31.3:1:1:1.01:60:229:0.5827:0.0375:1.1 0/0:217:0:0,0:82,135:0:2,0:21:1:29.3:1:1:0:60:30:1:0:0.7 -15 67457698 . A G 151 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=31.91396;LSEQ=ACACTAACTTCCCCGCAGGC;RSEQ=TCGAGCCCCAGAGCAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1017:1:0,1:443,573:0.001:2,0:16:0:32:0:1:0:60:2:0.001:0:1 0/1:1017:31:12,19:448,537:0.0305:2,2:29.5:1:30.6:1:0.58321:1.32056:60:62:0.031:0:1.1 -15 67457805 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.52317;SOR=0;LSEQ=GTCCTGTGGCCCCAATCTCT;RSEQ=CCCCCTGGCCGTCCCCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:0,2:4,194:0.01:1,0:31.5:1:31.5:1:1:0:60:4:0.0102:0:1 0/0:128:0:0,0:0,128:0:1,0:20.6:1:32.2:1:1:0:60:24.6:1:0:0.2 -15 67458805 . G A 80 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGGACGCCTCCCTGGAGG;RSEQ=GGTGGGGCTTAACCCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:0,0:0.875:0,0:29.6:1:28.7:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 67458930 . C T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05585;LSEQ=AAAGGCAGTTATGATCCAAG;RSEQ=GGGAGTCAGAGGTGGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:65:63,2:4,1:0.9155:2,1:25.9:1:30.2:1:0.20205:7.40:60:130:0.9286:0:1 0/1:30:11:10,1:19,0:0.3667:1,2:25.9:1:30:1:0.36667:0:60:22:0.3667:0:1.2 -15 67458957 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGGTGGACAGGGGCGAG;RSEQ=ACAACAGAACCAAGAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:121,4:0.0157:1,0:14:1:28:1:1:0:60:4:0.0161:0:1.5 0/0:63:0:0,0:62,1:0:1,0:21.3:1:30.8:1:1:0:60:30.5:1:0:0.3 -15 67459245 . TCATCCCTTC T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=2.000;MSILEN=1;SSF=0.00255;SOR=Inf;LSEQ=CTGATTAGCAGCTGGTGGGT;RSEQ=CATCCCTTCCTCTTCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:50,288:0:2,0:24.8:1:32.2:1:1:0:60:111.667:1:0:0.1 0/1:254:7:2,5:70,177:0.0276:2,2:26:1:32:1:1:1.01:60:14:0.0277:0:0 -15 67459280 . TC T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53466;SOR=0;LSEQ=CTTCCTCTTCGCCCTCTCCC;RSEQ=CCTCCCTTCTATCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:16,173:0.0105:2,0:7:1:32:1:1:0:60:4:0.0105:0.0052:1 0/0:110:0:0,0:18,92:0:2,0:23.7:1:31:1:1:0:60:109:1:0:0 -15 67462798 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20534;SOR=Inf;LSEQ=GGGTTTTCTTTCTGCTGTGT;RSEQ=GGCTACCCCTCCTTGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:183,30:0:2,0:23:1:32:1:1:0:60:52.25:1:0:0.1 0/1:177:2:1,1:149,26:0.0113:2,2:18:1:29.5:1:0.28255:5.64254:60:4:0.0115:0:0 -15 67463026 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50478;SOR=0;LSEQ=TGTGGGGAGGGGGCCCTGAA;RSEQ=GTAAGGCTCTCCCCCGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:20,156:0.0112:2,2:16.5:1:29:1:0.22262:7.64:60:4:0.0116:0:1 0/0:142:0:0,0:14,128:0:2,0:24.3:1:30.2:1:1:0:60:46.333:1:0:0.1 -15 67473310 . C CTAAA 73 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=10.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=CGGGGCAGGGCCTTTATGAG;RSEQ=TAAATAAATAAATAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:33.2:1:31.5:1:1:0:60:10:0.7143:0:0 1/1:2:2:1,1:0,0:1:0,2:36:1:28:1:1:0:60:4:1:0:0 -15 67473790 . C T 241 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGCTGACACGGAGACACAT;RSEQ=GGTATGGGGTGGCTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:259:95,164:137,236:0.4098:2,2:24.1:1:30.1:1:1:1.00214:59.9:63.75:0.414:0:1.3 0/0:589:0:0,0:239,347:0:2,0:24:1:29.9:1:1:0:59.9:64.111:0.9948:0:0.4 -15 67473814 . GC G 77 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.31846;SOR=2.28199;LSEQ=ATGGGGTGGCTCCATTCCCC;RSEQ=CCCCCCACCCTGCCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:3:1,2:128,304:0.0069:2,2:20:1:31.3:1:1:1.19:60:6:0.0079:0:1 0/1:386:6:3,3:133,245:0.0155:2,2:22.3:1:29.8:1:0.67018:1.84:60:12:0.0187:0:0.3 -15 67473822 . A C 81 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26253;SOR=1.44333;LSEQ=GCTCCATTCCCCGCCCCCCC;RSEQ=CCCTGCCCCTGCCACTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:18:17,1:7,288:0.0575:1,1:8.3:1:22.6:1:0:625.00:60:3.5:0.0465:0:2.7 0/1:284:23:23,0:24,235:0.081:2,1:9.4:1:18.1:1:0:0:59.6:1.3:0.0492:0:2.7 -15 67473823 . C A 49 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02305;SOR=Inf;LSEQ=CTCCATTCCCCGCCCCCCCA;RSEQ=CCTGCCCCTGCCACTCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:19,286:0:2,0:23.2:1:30.9:1:1:0:60:42.571:1:0:0.5 0/1:273:5:4,1:38,230:0.0183:2,2:10.2:1:21.2:1:0.00219:23.73:60:1.5:0.0119:0:1.2 -15 67473827 . G C 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.32857;SOR=3.75429;LSEQ=ATTCCCCGCCCCCCCACCCT;RSEQ=CCCCTGCCACTCTATCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:1:1,0:6,270:0.0036:1,0:35:0:15:0:0.02527:0:60:0:0:0:6 0/1:223:3:1,2:18,198:0.0135:2,2:11.7:1:24.7:1:0.23934:5.42:60:2:0.0097:0:2 -15 67476756 . C T 46 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CGCCTGGCCCCCATCCCTAT;RSEQ=GTAGAGACAAACGAAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:8.3:1:29.3:1:1:0:60:6:1:0:2 0/0:1:0:0,0:1,0:0:0,0:25:0:33:0:1:0:60:2:1:0:0 -15 67476768 . C T 50 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATCCCTATCGTAGAGACAAA;RSEQ=GAAGACTCAGAGGGTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.3:1:32:1:1:0:60:6:1:0:2 1/0:2:1:1,0:1,0:0.5:0,0:2:0:28:0:1:0:60:2:0.5:0:1 -15 67476952 . G T 210 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01447;LSEQ=CCGTTTGCCTGGGGAAGCTG;RSEQ=CAGTCACTGGGAGCAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:133:132,1:6,0:0.9568:0,1:24:1:29.8:1:1:0:60:132:0.9565:0:1.9 0/1:72:17:17,0:55,0:0.2361:1,1:20.7:1:29.6:1:1:0:60:34:0.2429:0:2 -15 67476970 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02003;LSEQ=TGGCAGTCACTGGGAGCAGC;RSEQ=CTGCTGTTCTGCCTCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:156:147:141,6:8,1:0.9423:2,1:26.1:1:30.9:1:0.34587:2.91:60:35.75:0.9408:0:1.9 0/1:132:32:29,3:93,7:0.2424:2,2:19.9:1:30.8:1:0.70422:1.37085:60:64:0.2443:0:1.6 -15 67479505 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAGTGAGGAGATGGGTT;RSEQ=AAGGGGAGGGACTGGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:37,2:0.0488:2,0:7:1:28:1:1:0:60:4:0.0526:0:1.5 0/0:8:0:0,0:8,0:0:0,0:29.9:1:30.9:1:1:0:60:16:1:0:0.4 -15 67479678 . A AG 210 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGCCACTTCCATCCCCAC;RSEQ=GCCCTGTTTCTGTGTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:787:99:66,33:418,265:0.1258:2,2:29.6:1:31.8:1:0.32028:1.27:60:98:0.1284:0.0038:0.1 0/0:708:0:0,0:419,288:0:2,0:25.1:1:30.1:1:1:0:60:77.556:0.9986:0:0.2 -15 67479911 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1644;SOR=Inf;LSEQ=TGACTCTGGACAGCAGAGCA;RSEQ=GCAGGGCTCCTCAGAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:54,238:0:2,0:24.1:1:31.2:1:1:0:60:145:0.9966:0:0.1 0/1:201:2:1,1:37,162:0.01:2,2:7:1:29:1:0.34313:4.33:60:4:0.0102:0:1 -15 67482591 . C T 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08584;SOR=Inf;LSEQ=CCTGGGTAGAGGAGTTTGGC;RSEQ=GGGTAGTTTCAGCAAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:75,1:0:1,0:26.7:1:30.8:1:1:0:60:37:1:0:0.1 0/1:32:2:2,0:28,2:0.0625:2,0:26:1:33:0:1:0:60:4:0.0625:0:1 -15 67482696 . AC GT 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGCTTTCTGACTTGTGTA;RSEQ=CCCCTGGAGATTTTTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:0:0,0:360,135:0:2,0:22.9:1:29.7:1:1:0:60:48.5:1:0:0.2 0/1:405:21:17,4:269,109:0.0519:2,2:17.8:1:30.3:1:0.4574:1.72:60:42:0.0528:0.0123:0.8 -15 67483276 . C T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGTTCACCTTGGAAGGG;RSEQ=GTTCTAGGTAGGAAGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:34.7:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 69264924 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89676;LSEQ=GGGTTGCTGGCAAGCTTTGG;RSEQ=ATTCCTTGGTTTATAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:32,37:0.0282:2,2:31.5:1:28:1:1:1.15:60:4:0.0282:0:1 0/1:79:2:1,1:34,43:0.0253:2,2:24.5:1:31:1:1:1.26:60:4:0.0253:0:1 -15 69264941 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21212;SOR=0;LSEQ=TGGCATTCCTTGGTTTATAG;RSEQ=AACATCACCCTGATCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:22,32:0.0357:2,2:25:0:32:1:1:1.44:60:4:0.0385:0:1.5 0/0:65:0:0,0:26,39:0:2,0:23.7:1:27.9:1:1:0:60:12:1:0:0.2 -15 69265832 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAATGGTGCAATCTCGG;RSEQ=TCACTGCAAGCTCCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:0:31:1:1:0:60:4:1:0:1.5 -15 70348128 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGCATCTAGATTCTCGT;RSEQ=GACAATTAGAGGACTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:29:1:1:0:60:4:1:0:1.5 -15 70349888 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52923;SOR=0;LSEQ=GGTGGGATGTTGTGGAGGCC;RSEQ=GCGTAGGCGCCAGGACTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:16:0:32.5:1:1:1.46:60:4:0.1176:0:1.5 0/0:9:0:0,0:5,4:0:2,0:30.1:1:30.3:1:1:0:60:18:1:0:0 -15 70351649 . C A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTCCCTGCTCAGGCTG;RSEQ=CAGTAATACTAGAACAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:1:31.5:1:1:0:60:4:1:0:1 -15 71891715 . G A 26 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACACAGAGCCCACTTCCT;RSEQ=TCTAACTATTTTTTCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:26.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:4:0:30:0:1:0:60:2:1:0:1 -15 71892037 . T G 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09508;SOR=4.92176;LSEQ=GATGAGGAGCATTTTATAAA;RSEQ=TAAGAGCTGTTCCCTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:2,0:67,1:0.0286:1,0:14.5:1:30.5:1:1:0:60:4:0.0299:0:1.5 0/1:39:5:5,0:34,0:0.1282:1,0:17.6:1:31.2:1:1:0:60:10:0.1282:0:1.6 -15 71892101 . C T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30495;SOR=1.60082;LSEQ=TGGCAGTGGGCCAGGAGGAA;RSEQ=GTGTGTGCATTCAAGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:10:6,4:158,45:0.0469:2,2:23.5:1:29.7:1:0.24327:2.32962:60:20:0.0481:0:1.6 0/1:205:15:11,4:142,48:0.0732:2,2:24.3:1:29.9:1:1:1.07538:60:30:0.0739:0:1.5 -15 71892119 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21708;SOR=4.84336;LSEQ=AACGTGTGTGCATTCAAGGG;RSEQ=AAATGTCATCTCTCTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:1:0,1:200,99:0.0033:2,0:1:0:23:0:0.33333:0:60:2:0.0034:0:1 0/1:313:5:1,4:203,105:0.016:2,2:9.4:1:24.8:1:0.05163:7.68286:60:10:0.0162:0:1 -15 71892168 . C G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14999;SOR=1.67882;LSEQ=AGGCCCACTTTGAGCCGAAA;RSEQ=ACTGGGAGCCGCATAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:493:14:6,8:249,229:0.0284:2,2:18.4:1:31.9:1:0.59179:1.44868:60:28:0.0292:0:1.9 0/1:577:27:14,13:298,249:0.0468:2,2:29.9:1:30.9:1:0.84451:1.1111:60:26:0.0455:0:1.8 -15 71892215 . A G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13493;LSEQ=TCTTCCCCACAATGCCCCCC;RSEQ=GTATGGGAAGCTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:456:350:146,204:49,57:0.7675:2,2:25.9:1:30:1:0.43396:1.20066:60:30.818:0.7652:0:1.2 0/1:507:156:69,87:163,188:0.3077:2,2:25:1:29:1:0.69944:1.09301:60:25:0.3049:0:1.3 -15 71892532 . T A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCTGTGCAAGACTTACTCAC;RSEQ=CAGAAAGCTCTGTATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 71950355 . C T 111 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00144;SOR=6.46031;LSEQ=GACGTCTGTCCCATCTTTGG;RSEQ=GACTCTCATTCATTCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:2,1:142,20:0.0182:2,2:24.3:1:29.7:1:0.33706:3.50896:60:6:0.0183:0:1.3 0/1:121:13:10,3:85,23:0.1074:2,2:16.8:1:30:1:1:1.10774:60:26:0.1074:0:1 -15 71950447 . C A 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=16.27164;LSEQ=TCTCCACTCTAGGTAAGGCC;RSEQ=GCTCCACACTGCAGTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:1:1,0:229,261:0.002:2,0:1:0:26:0:0.46843:0:60:2:0.0021:0:2 0/1:499:16:9,7:243,237:0.0321:2,2:22.1:1:30.5:1:0.8008:1.25:60:32:0.0324:0:2.6 -15 71950471 . C T 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACACTGCAGTCATTGTTA;RSEQ=CACCGAAAAGCAAGTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:0:0,0:189,256:0:2,0:26.4:1:31.3:1:1:0:60:62.571:1:0:0.1 0/1:448:60:26,34:182,206:0.1339:2,2:26.1:1:28.5:1:0.67711:1.15497:60:19:0.1298:0:1.7 -15 71950475 . C T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=ACTGCAGTCATTGTTACCAC;RSEQ=GAAAAGCAAGTCTGAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:178,248:0:2,0:26.8:1:30.1:1:1:0:60:70:0.9976:0:0.1 0/1:430:16:7,9:191,223:0.0372:2,2:27.7:1:29.9:1:1:1.10094:60:32:0.0376:0:3 -15 71950538 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50416;SOR=0;LSEQ=TGGGGGTTGCTGATGCCATA;RSEQ=GATGAAAATCTAATTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:43,131:0.0114:2,2:38:1:31.5:1:0.43857:3.02:60:4:0.0114:0:1 0/0:142:0:0,0:25,116:0:2,0:24.1:1:30.2:1:1:0:60:282:1:0:0.2 -15 71950542 . GA G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5061;SOR=0;LSEQ=GGTTGCTGATGCCATAGGAT;RSEQ=AAATCTAATTCTTCAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:34,116:0.0132:2,2:26:1:32.5:1:0.40868:3.38:60:4:0.0132:0:0 0/0:118:0:0,0:18,100:0:2,0:26:1:29.6:1:1:0:60:117:1:0:0.2 -15 72427055 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49895;SOR=0;LSEQ=TTGGAAAAAACATGGAGTTG;RSEQ=TCCTTTGGCCATGTATATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:27,13:0.0476:2,2:21.5:1:31:1:1:2.03815:60:4:0.0476:0:1 0/0:34:0:0,0:18,16:0:2,0:26.5:1:29.6:1:1:0:60:68:1:0:0.1 -15 72427143 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20031;SOR=Inf;LSEQ=GTTCAAAAAGGAATGTCCCA;RSEQ=AAGTGTTACCATGGCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:68,40:0:2,0:24.1:1:31:1:1:0:60:35:1:0:0.1 0/1:88:2:1,1:53,33:0.0227:2,2:23.5:1:30.5:1:1:1.59707:60:4:0.023:0:1.5 -15 72427149 . T C 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1929;SOR=Inf;LSEQ=AAAGGAATGTCCCAGAAGTG;RSEQ=TACCATGGCAAAACTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:69,44:0:2,0:26.1:1:29.7:1:1:0:60:112:1:0:0.1 0/1:89:2:1,1:55,32:0.0225:2,2:23:0:34:0:1:1.70775:60:4:0.0227:0:1.5 -15 72427153 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50199;SOR=0;LSEQ=GAATGTCCCAGAAGTGTTAC;RSEQ=ATGGCAAAACTGGAAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:64,44:0.0182:2,2:42:1:28.5:1:1:1.44946:60:4:0.0183:0:1 0/0:91:0:0,0:56,35:0:2,0:30.4:1:30.6:1:1:0:60:90:1:0:0.1 -15 72427442 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGAGTCTGGCTCTGTC;RSEQ=CCCAGGCTGGAATGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 73191863 . T C 127 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06267;SOR=0;LSEQ=ACCAGCTTTTTCTATACTTG;RSEQ=TTGCATTTTTGCTTTAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:10,5:0,0:1:0,2:28.2:1:32.7:1:1:0:60:30:1:0:1.1 1/0:22:16:7,9:6,0:0.7273:0,2:29.1:1:31.8:1:0.04608:0:60:32:0.7273:0:1.2 -15 73191920 . G GT 122 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.14046;SOR=0.45548;LSEQ=CCCTTTTGGTGTTTTAGGAG;RSEQ=TTTTTTTTTTTCCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:13,3:3,3:0.5714:2,2:30.8:1:30.7:1:0.28286:4.00:60:32:0.5714:0:0.8 0/1:40:15:9,6:14,9:0.375:2,2:31.3:1:30.6:1:1:1.03607:60:30:0.3947:0:0.6 -15 73192251 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26991;SOR=0;LSEQ=TGATTCTGCAGCTTCCTCCA;RSEQ=AGCTACTAAGTGCTGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:3:1,2:130,90:0.0135:2,2:11:1:28:1:0.57039:2.87512:60:6:0.0136:0:1 0/0:158:0:0,0:92,66:0:2,0:26.2:1:31.1:1:1:0:59.7:78:1:0:0.1 -15 73192349 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09391;SOR=Inf;LSEQ=CAAAGTCCCCAAGGGAAACC;RSEQ=TTGACTGTACAGACATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:100,128:0:2,0:25.1:1:31.3:1:1:0:60:227:1:0:0.1 0/1:191:3:2,1:87,101:0.0157:2,2:16.3:1:30.3:1:0.59896:2.31:60:6:0.0159:0:1.3 -15 73192415 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21907;SOR=Inf;LSEQ=GACTGTCTTCATAATTCATT;RSEQ=TTTCTGCTTCAACAATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:82,97:0:2,0:24.3:1:32:1:1:0:60:178:1:0:0.1 0/1:158:2:1,1:67,89:0.0127:2,2:8.5:1:26.5:1:1:1.33:60:4:0.0129:0:1 -15 73192458 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49878;SOR=0;LSEQ=TTCATCCTTTGCACCAGCTC;RSEQ=TAAACTGACTGTTCCTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:73,114:0.0106:2,2:35:1:29:1:1:1.56:60:4:0.0106:0:1 0/0:183:0:0,0:77,106:0:2,0:28.6:1:31.3:1:1:0:60:90.5:1:0:0.2 -15 73192681 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50337;SOR=0;LSEQ=GCTCCAGAGAACAGCCATGC;RSEQ=GGATGGAATCACACCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:5,16:0.087:2,2:36.5:1:30:1:0.46245:3.01:60:4:0.087:0:1 0/0:16:0:0,0:4,12:0:2,0:23.5:1:30.8:1:1:0:60:32:1:0:0.1 -15 73454308 . T G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=TGTTTTAGGAAGTTTGTTTG;RSEQ=TTTTTTTTCTCCTGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:8,7:0,0:1:0,2:22.8:1:30.7:1:1:0:60:14:1:0:1.1 1/1:16:14:8,6:1,1:0.875:2,2:25.8:1:31.1:1:1:1.31:60:28:0.875:0:1.1 -15 73454432 . A T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23734;SOR=Inf;LSEQ=CATACAGATTTCTTCAGTGG;RSEQ=GCTTATTCTTGTCTCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:0:2,0:23.2:1:29.4:1:1:0:60:12.5:1:0:0.2 0/1:29:3:0,3:12,14:0.1034:2,0:5.7:1:22.3:1:0.24631:0:60:2:0.0769:0:1 -15 73455034 . T C 93 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=CAGATGTGAGTCATCATGCC;RSEQ=GGCCAGTTGCCAGTATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:22.4:1:31.4:1:1:0:60:10:1:0:1.4 1/0:12:9:7,2:1,2:0.75:2,2:18.6:1:29.6:1:0.23636:5.73:60:18:0.75:0:1.2 -15 73991904 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08956;SOR=Inf;LSEQ=GAGAACCTTTGGAGACAAAG;RSEQ=CCTTGCGTCCTCTTTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:277,75:0:2,0:22.2:1:30.8:1:1:0:60:26.077:1:0:0.1 0/1:286:3:1,2:218,65:0.0105:2,2:8.7:1:28:1:0.13792:6.65026:60:6:0.0106:0:1.3 -15 73992124 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08565;SOR=Inf;LSEQ=TGGCAGTTGGGGAGGGGGTG;RSEQ=CCACGCCTGTTAGGGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:43,316:0:2,0:23.9:1:31.1:1:1:0:60:38.889:1:0:0.1 0/1:284:3:1,2:46,233:0.0106:2,2:31:1:27:1:0.42253:2.52:60:6:0.0111:0:1 -15 73993242 . T C 28 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCCCCTCCTCCCCTCCTCC;RSEQ=CCTCCTCTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:28:1:1:0:28:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 73994122 . G GA 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATTCTCTCTCCTCCAGA;RSEQ=AAACCACTATTGACATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:25.3:1:29.5:1:1:0:60:8:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 73994523 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.53933;SOR=0;LSEQ=AGGGCCTGGGGTTAGCAGGG;RSEQ=CAGGGAGCGGGACTAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:160,20:0.011:2,2:9:1:26:1:0.21802:7.83134:60:4:0.0114:0:1 0/0:101:0:0,0:83,17:0:2,0:24.1:1:30.8:1:1:0:60:49:0.9899:0:0.2 -15 73994543 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15686;SOR=Inf;LSEQ=GCAGGGAGCGGGACTAGGGA;RSEQ=GCCCACCCCTCCTCAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:212,48:0:2,0:23.5:1:31.5:1:1:0:60:27.889:1:0:0.1 0/1:171:2:1,1:117,52:0.0117:2,2:7:1:29.5:1:0.52508:2.23821:60:4:0.0118:0:1 -15 73994806 . C T 175 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=35.13027;LSEQ=CAACCGCACGGCCCTCTTCC;RSEQ=GGACCTGCTGGCACAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:931:2:1,1:459,468:0.0021:2,2:21:1:25:1:1:1.02:60:1:0.0011:0:1 0/1:810:57:27,30:351,399:0.0704:2,2:24:1:30.1:1:1:1.02:59.8:56:0.07:0:1.7 -15 73994847 . C A 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACGCATCCCTGAGGCTGCAG;RSEQ=GCGTGCGTGTGGCGGACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:916:0:0,0:445,471:0:2,0:25.7:1:30.6:1:1:0:54.5:44.8:1:0:0.1 0/1:726:49:22,27:342,333:0.0675:2,2:27.9:1:29:1:0.46232:1.26004:54.6:23.5:0.0656:0:1.7 -15 73995165 . A C 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAACAAGGACCTGCGGCC;RSEQ=GGGGACACGGTGACCATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:905:0:0,0:462,443:0:2,0:25.1:1:30.3:1:1:0:42.4:36.708:1:0:0.2 0/1:719:44:19,25:335,334:0.0612:2,2:24.4:1:29.6:1:0.43733:1.31921:43.9:43:0.0608:0:2 -15 73995173 . C T 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGACCTGCGGCCAGGGGACA;RSEQ=GGTGACCATCACGTGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:942:0:0,0:472,469:0:2,0:25.2:1:30.5:1:1:0:43.3:46.05:0.9989:0:0.2 0/1:760:46:20,26:366,347:0.0605:2,2:27.1:1:29.5:1:0.36168:1.37061:45.3:22:0.0586:0:2 -15 73995327 . G A 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00086;SOR=Inf;LSEQ=CACAGCATCCTGCGGGTGGT;RSEQ=CTGGGTGCAAATGGCACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:681:0:0,0:271,410:0:2,0:25.6:1:31.8:1:1:0:57.7:34.842:1:0:0.2 0/1:576:9:6,3:230,337:0.0156:2,2:12.2:1:25.9:1:0.17038:2.92:55.2:18:0.0159:0:1.1 -15 73995386 . C T 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=CCCCGTGCTGCAGCAGGATG;RSEQ=GCACAGCTCTGTCACCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:135,282:0:2,0:26:1:30:1:1:0:60:33.75:1:0:0.1 0/1:325:10:5,5:108,207:0.0308:2,2:26.8:1:30.7:1:0.3254:1.91:60:20:0.0313:0:1 -15 73995431 . G T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00395;SOR=Inf;LSEQ=CCAGAGAAGCCCCACAGGTT;RSEQ=CTTTGCTTAAATGTCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:67,185:0:2,0:24.6:1:32:1:1:0:60:62:0.996:0:0.1 0/1:213:7:2,5:72,134:0.0329:2,2:27.1:1:28.7:1:1:1.34151:60:14:0.0333:0:1.1 -15 73995930 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.50948;SOR=0;LSEQ=ATTGATGGGGGAAGAGTTTG;RSEQ=GGGACTCGGGTGGTAGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:153,35:0.0105:2,2:16:1:30:1:0.34386:4.32436:60:4:0.0108:0:1 0/0:141:0:0,0:108,32:0:2,0:24.8:1:30.7:1:1:0:60:45.667:0.9928:0:0.1 -15 73995991 . C T 125 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=22.63084;LSEQ=CCACCCTGCCCCTCTGACCC;RSEQ=GCCCCCAGGAGCCGTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:1:0,1:328,165:0.002:2,0:1:0:25:0:0.33603:0:60:2:0.002:0:1 0/1:432:19:11,8:254,159:0.044:2,2:19.7:1:29.6:1:0.81145:1.16139:60:18:0.0423:0:1.2 -15 73996066 . G A 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGCACCGATGCCACCCTGC;RSEQ=CTGCTCCTTCTCCCCCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:743:0:0,0:422,320:0:2,0:24.2:1:30.6:1:1:0:60:81.444:0.9986:0:0.1 0/1:718:43:29,14:368,306:0.0599:2,2:23.7:1:29.5:1:0.11451:1.72:60:86:0.0603:0:1.7 -15 73996101 . G A 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGAGCCTGGCTTCAGCCTG;RSEQ=CACAGCTCAACCTCATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:919:0:0,0:492,426:0:2,0:24.5:1:31.2:1:1:0:59.9:47.316:0.9989:0:0.1 0/1:908:61:34,27:448,398:0.0672:2,2:23.9:1:28.9:1:0.69256:1.12:60:60:0.067:0:1.5 -15 73996359 . G A 140 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=36.09391;LSEQ=GTGAGCACCAGGAGGGCGAC;RSEQ=CCTTCCCCTTGGTTCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:1:1,0:194,368:0.0018:2,0:1:0:25:0:0.34636:0:45:2:0.0018:0:1 0/1:514:31:17,14:179,302:0.0603:2,2:15.4:1:28.3:1:0.05758:2.05:53.6:62:0.0611:0:1.1 -15 73996364 . C T 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCAGGAGGGCGACGCCTT;RSEQ=CCCTTGGTTCACCCTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:0:0,0:190,362:0:2,0:22.7:1:31:1:1:0:57.5:60.333:1:0:0.1 0/1:466:22:7,15:164,280:0.0472:2,2:19.6:1:28.9:1:0.82124:1.25448:55.1:21:0.0456:0:1.2 -15 73996391 . G T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06068;SOR=Inf;LSEQ=GTTCACCCTCCATTCCCTCT;RSEQ=CAGCCCACCCTCTGCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:141,256:0:2,0:24:1:32:1:1:0:59.5:78.4:1:0:0.1 0/1:258:3:1,2:92,162:0.0116:2,2:31.7:1:24:1:1:1.13527:60:2:0.0079:0:2.7 -15 73996590 . G A 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.12114;LSEQ=GGGGACACGGTGACCATCAC;RSEQ=TGCTCCAGCTACCGGGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1029:3:2,1:526,499:0.0029:2,2:25.7:1:30:1:1:1.90:34.3:6:0.003:0:1 0/1:949:65:37,28:482,402:0.0685:2,2:19.4:1:30.1:1:0.79654:1.10:42:130:0.0694:0:1.1 -15 73996790 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04181;SOR=Inf;LSEQ=CCCCGTGCTGCAGCAGGATG;RSEQ=GCACGGCTCTGTCACCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:78,240:0:2,0:25.6:1:29.8:1:1:0:59.5:38.75:1:0:0.2 0/1:264:4:0,4:78,182:0.0152:2,0:8:1:29.8:1:0.32277:0:60:8:0.0154:0:1 -15 73996842 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1936;SOR=Inf;LSEQ=AGATGAACAGCTGGGGAAGG;RSEQ=CGGAGCGAGTAACTCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:21,139:0:2,0:22.7:1:29.7:1:1:0:60:52.333:1:0:0.1 0/1:127:2:1,1:26,99:0.0157:2,2:41:0:32.5:1:0.38133:3.76:60:4:0.0159:0:1 -15 74000503 . G A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01676;SOR=Inf;LSEQ=TGTCCACATCAGCCAGGGTT;RSEQ=TATCAGGGTTTGGGGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:55,1:0:1,0:28:1:32:1:1:0:60:55:1:0:0.9 0/1:33:4:4,0:27,2:0.1212:2,0:21:1:29.5:1:1:0:60:8:0.1212:0:1 -15 74000506 . T G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00285;SOR=0.26671;LSEQ=CCACATCAGCCAGGGTTGTA;RSEQ=CAGGGTTTGGGGAGTGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:46:45,1:13,0:0.7667:1,1:26.3:1:32.5:1:1:0:60:92:0.7667:0:1.1 0/1:41:19:18,1:21,1:0.4634:1,1:15.6:1:31.6:1:1:1.16227:60:38:0.4872:0:1.2 -15 74000729 . G C 198 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=CTGTGGGTGACCGTGGGGCT;RSEQ=TCTGTCTGTCTCATTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1339:0:0,0:694,643:0:2,0:25.8:1:32.1:1:1:0:60:101.846:0.9992:0:0.2 0/1:1293:89:46,43:644,553:0.0688:2,2:27.6:1:30.7:1:0.74149:1.08854:60:43.5:0.0686:0:1.3 -15 74000839 . G A 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33402;LSEQ=GTGTGTGTGTATGTGTGTGC;RSEQ=TGCGCATGCACACTTATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:578:437:102,335:31,110:0.7561:2,2:23.8:1:30.6:1:0.81822:1.08:60:144.667:0.7574:0:1.1 1/0:478:243:60,183:62,173:0.5084:2,2:22.6:1:29.6:1:0.67633:1.09286:60:120.5:0.5074:0:1.1 -15 74001902 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25132;SOR=0;LSEQ=CACTCAGGCCCTGTTCACCA;RSEQ=CTTCCTGCACTCTCAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:183,71:0.0116:2,2:12.3:1:30:1:0.19518:5.11663:60:6:0.0118:0:1 0/0:228:0:0,0:166,62:0:2,0:22.8:1:32:1:1:0:60:113:1:0:0.1 -15 74001993 . T C 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCTTGCCTTTGCAGGAGC;RSEQ=GAGGACCAGGATGGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:759:0:0,0:412,346:0:2,0:26.5:1:30.5:1:1:0:60:83.222:0.9987:0:0.1 0/1:763:48:26,22:366,347:0.0629:2,2:27.1:1:29.6:1:0.76631:1.12:60:47:0.0626:0:2.1 -15 74002006 . G A 167 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=57.51741;LSEQ=CAGGAGCTGAGGACCAGGAT;RSEQ=GGGAGGGAGAAGGCTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:761:1:1,0:392,367:0.0013:2,0:1:0:24:0:1:0:60:2:0.0013:0:1 0/1:752:53:28,25:343,356:0.0705:2,2:22.5:1:29.2:1:0.66966:1.16:60:106:0.071:0:2 -15 74002854 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGAGAGGCAGGTTTCC;RSEQ=CTGAGCCATTTGGGATGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:36.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 74003518 . A C 171 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=51.25247;LSEQ=TGACAGCAAAGAAGGTAAAG;RSEQ=CACCTGGGCTTGAGGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1039:1:1,0:446,592:0.001:2,0:9:0:13:0:0.43022:0:60:0:0:0:6 0/1:891:42:18,24:372,477:0.0471:2,2:27:1:31.8:1:1:1.03979:60:84:0.0477:0:1.2 -15 74003533 . G A 157 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=58.34454;LSEQ=TAAAGACACCTGGGCTTGAG;RSEQ=TTGTGTCTGTGTATGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:965:1:1,0:399,565:0.001:2,0:24:0:12:0:0.41451:0:60:0:0:0:2 0/1:787:45:20,25:310,432:0.0572:2,2:22.3:1:28.6:1:0.75704:1.11:60:21.5:0.0555:0:1.2 -15 74003625 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15312;SOR=Inf;LSEQ=GACCTGAGGCCCCCTCTGCA;RSEQ=AAGAGCAGCCTCAACTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:34,196:0:2,0:21.4:1:31.6:1:1:0:60:75.667:0.9956:0:0.1 0/1:149:2:1,1:35,111:0.0134:2,2:22:1:31:1:0.42857:3.14:60:4:0.0135:0:1 -15 74005132 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11208;SOR=Inf;LSEQ=GCCGTGGTCAGCACGGGGGC;RSEQ=GTCCGTTGGGCTGCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:146,6:0:1,0:24.9:1:30.8:1:1:0:60:49.667:1:0:0.1 0/1:77:2:2,0:69,6:0.026:2,0:23:1:32:0:1:0:60:4:0.0267:0:1 -15 74005246 . CT C 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.9777;LSEQ=ATCTAATGCTTTTCCCTTCC;RSEQ=TTTTTTTCTTCCCATCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:798:9:6,3:418,370:0.0113:2,2:18.9:1:31.6:1:0.51344:1.77:60:18:0.0115:0.0025:0.2 0/1:816:9:4,5:444,362:0.011:2,2:26:1:28.6:1:0.73854:1.53232:60:8:0.01:0.0025:0.2 -15 74005600 . C T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTTCTTAGGGACACAGTA;RSEQ=ACTGACCACATCACCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:0,11:0,1:0.9167:0,0:23.9:1:28.6:1:1:0:60:22:0.9167:0:1.1 1/1:4:4:1,3:0,0:1:0,2:26:1:29.8:1:1:0:60:8:1:0:1.3 -15 74567019 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12217;SOR=Inf;LSEQ=AGAAAATTAAGAACCAATCA;RSEQ=CAGGCTGTCCCAAGGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:122,143:0:2,0:27.4:1:32:1:1:0:60:65.25:1:0:0.7 0/1:262:3:2,1:120,139:0.0115:2,2:12.3:1:27:1:0.5994:2.31:60:6:0.0116:0:2.3 -15 74567025 . T C 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78969;SOR=0.94733;LSEQ=TTAAGAACCAATCAGCAGGC;RSEQ=GTCCCAAGGGGCAAGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:268:162:74,88:49,57:0.6045:2,2:24.8:1:30.4:1:1:1.02221:60:161:0.603:0:1.1 1/0:257:152:66,86:49,56:0.5914:2,2:26.6:1:29.4:1:0.61249:1.13957:60:75:0.5906:0:1.2 -15 74567036 . G A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2485;SOR=0;LSEQ=TCAGCAGGCTGTCCCAAGGG;RSEQ=CAAGAGGCACTGCCTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:2,1:105,142:0.012:2,2:13.7:1:31.7:1:0.57778:2.69:60:6:0.0121:0:2.3 0/0:250:0:0,0:106,144:0:2,0:25.2:1:30.7:1:1:0:60:30.25:1:0:0.7 -15 74567042 . G A 103 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00524;SOR=10.66054;LSEQ=GGCTGTCCCAAGGGGCAAGA;RSEQ=GCACTGCCTGCTTTAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:1,0:97,147:0.0041:2,0:12:0:19:0:0.4:0:60:0:0:0:1 0/1:239:10:4,6:96,133:0.0418:2,2:33.9:1:31.3:1:1:1.08237:60:20:0.0424:0:1.1 -15 74567043 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11811;SOR=Inf;LSEQ=GCTGTCCCAAGGGGCAAGAG;RSEQ=CACTGCCTGCTTTAATGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:98,147:0:2,0:24.2:1:31.5:1:1:0:60:48:1:0:0.7 0/1:237:3:2,1:98,136:0.0127:2,2:35.7:1:22.7:1:0.57474:2.76:60:2:0.0087:0:2 -15 74567061 . A G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12227;SOR=Inf;LSEQ=AGGCACTGCCTGCTTTAATG;RSEQ=GTGTGCCCCCTCCCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:70,136:0:2,0:23.5:1:30.3:1:1:0:60:40.2:1:0:0.6 0/1:204:3:1,2:75,126:0.0147:2,2:14:1:29.7:1:1:1.18952:60:6:0.0155:0:2 -15 74567064 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49873;SOR=Inf;LSEQ=CACTGCCTGCTTTAATGAGT;RSEQ=TGCCCCCTCCCACCCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:61,136:0:2,0:23.7:1:31.8:1:1:0:60:196:1:0:0.6 0/1:197:2:1,1:72,123:0.0102:2,2:15.5:1:28:1:1:1.70:60:4:0.0105:0:2 -15 74567129 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22658;SOR=Inf;LSEQ=TAACTAGTCTGGGTAGGAGA;RSEQ=GTGCCACTCACTACAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:6,65:0:2,0:24.1:1:31.3:1:1:0:60:142:1:0:0.1 0/1:65:2:1,1:12,51:0.0308:2,2:26:1:30.5:1:0.3625:4.12:60:4:0.0313:0:1 -15 75094100 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=Inf;LSEQ=TGCATCGAGACCTGGCTGCC;RSEQ=GCAATGTGCTGGTGTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:68,63:0:2,0:26.7:1:30.4:1:1:0:60:130:1:0:0.1 0/1:145:2:1,1:75,68:0.0138:2,2:30.5:1:31.5:1:1:1.10219:60:4:0.0139:0:1.5 -15 75094101 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22437;SOR=0;LSEQ=GCATCGAGACCTGGCTGCCC;RSEQ=CAATGTGCTGGTGTCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:67,62:0.0153:2,2:11:1:30:1:1:1.07998:60:4:0.0154:0:1 0/0:145:0:0,0:76,69:0:2,0:28:1:30.8:1:1:0:60:144:1:0:0.1 -15 75095483 . T C 41 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCCTTGTGAGATGGAAT;RSEQ=GTAATAAACCACGCCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:21:1:26:1:1:0:60:2:1:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 76023634 . TAC T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.18363;SOR=Inf;LSEQ=CACAGACCCACACCTTACTC;RSEQ=ACACACACACCTGGTACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:17,20:0:2,0:28.1:1:28.6:1:1:0:60:36:1:0:0.6 0/1:29:2:1,1:16,11:0.069:2,2:11.5:1:30.5:1:1:1.43545:54.5:4:0.0741:0:0.5 -15 76023637 . A G 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=2;SSF=0.57941;SOR=0.70365;LSEQ=AGACCCACACCTTACTCTAC;RSEQ=CACACACACCTGGTACCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:10:4,6:14,14:0.2632:2,2:32.6:1:32.2:1:0.719:1.48412:60:20:0.2632:0:1.2 0/1:30:6:3,3:14,9:0.2:2,2:17.7:1:29.2:1:0.66932:1.53146:60:12:0.2:0:1.3 -15 76023673 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49254;SOR=0;LSEQ=CCACCACTGCCTTCAAACAC;RSEQ=CTGCCCCATCCCTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:14,18:0.0588:2,2:16:0:32:0:1:1.28:60:4:0.0588:0:1.5 0/0:33:0:0,0:16,17:0:2,0:26.6:1:29.3:1:1:0:59.7:32:1:0:0.5 -15 76023721 . T C 116 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.04564;SOR=0;LSEQ=TCATCTCATGCACAGATACG;RSEQ=GCCCACCCAGGCTCACTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:1:0,2:23.5:1:29.8:1:1:0:60:14:1:0:1.1 1/0:17:12:5,7:0,5:0.7059:0,2:15.3:1:30.5:1:0.24451:0:60:24:0.7059:0:1.4 -15 77033879 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19656;SOR=0;LSEQ=TCAACTGTAAATATTTAGGA;RSEQ=GGAGATAAAAATAAACTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:2,0:89,68:0.0126:2,0:30.5:1:32:1:0.50736:0:60:4:0.0127:0:1 0/0:199:0:0,0:113,86:0:2,0:26.1:1:30.7:1:1:0:60:198:1:0:0.3 -15 77033880 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19848;SOR=0;LSEQ=CAACTGTAAATATTTAGGAG;RSEQ=GAGATAAAAATAAACTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:92,68:0.0123:2,2:38:0:31:0:1:1.35037:60:4:0.0124:0:1 0/0:201:0:0,0:111,88:0:2,0:25.8:1:29.8:1:1:0:60:27.429:0.9897:0:0.3 -15 77033898 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25743;SOR=Inf;LSEQ=AGGGAGATAAAAATAAACTG;RSEQ=TGGCAGCTGCAATGGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:82,71:0:2,0:25.2:1:31.6:1:1:0:60:75.5:1:0:0.1 0/1:192:3:3,0:102,87:0.0156:2,0:14:1:26.7:1:0.2527:0:60:6:0.0159:0:1 -15 77033900 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2023;SOR=0;LSEQ=GGAGATAAAAATAAACTGGT;RSEQ=GCAGCTGCAATGGAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:0,2:83,70:0.0129:2,0:23:1:29.5:1:0.21416:0:60:4:0.0132:0:1 0/0:189:0:0,0:102,87:0:2,0:26.6:1:30.8:1:1:0:60:93.5:1:0:0.3 -15 77033934 . G A 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=4.38387;LSEQ=AAAATGTAGCTGCCTACAGA;RSEQ=TTAGAGAACTGCAGGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:10:4,6:81,74:0.0606:2,2:25.3:1:31.8:1:0.52571:1.63698:60:20:0.061:0:1 0/1:199:44:20,24:79,76:0.2211:2,2:22.4:1:29.5:1:0.60892:1.24598:60:88:0.2211:0:1.2 -15 77033958 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24239;SOR=0;LSEQ=GAGAACTGCAGGTGTATGTA;RSEQ=ACATAGGACTCCAAAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:79,96:0.0113:2,2:35.5:1:31:1:1:1.21:60:4:0.0114:0:1 0/0:182:0:0,0:85,97:0:2,0:27.1:1:28.7:1:1:0:60:181:1:0:0.4 -15 77034023 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49744;SOR=Inf;LSEQ=TCTGGCTGATACACAAAAAG;RSEQ=TGTCAAGAAGAGATTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:21,74:0:2,0:22.6:1:29.4:1:1:0:60:18:1:0:0 0/1:97:2:1,1:30,65:0.0206:2,2:24.5:1:30:1:0.5393:2.15:60:4:0.0211:0:1.5 -15 77034175 . G A 60 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GATAAAGGAGATGGTGAGCT;RSEQ=ATGAGTTCCACTCAATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:22:1:30.3:1:1:0:60:8:0.5714:0:1.3 1/1:1:1:0,1:0,0:1:0,0:49:0:29:0:1:0:60:2:1:0:1 -15 78163623 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTTGAGGGGGGCTCCTG;RSEQ=TCACCTCCCCACCCCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:35.5:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 78164029 . CAGAGAGAGAGAGAG C 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=31;MSI=22.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCACAGGGACACAGGGAGC;RSEQ=AGAGAGAGAGAGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:28.1:1:1:0:60:4:1:1:0 -15 78164594 . T C 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.0261;SOR=Inf;LSEQ=CGCCAGTGAGCCTGGGTGGG;RSEQ=GCATATCTGTGCAGGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:86,4:0:1,0:24.1:1:29.5:1:1:0:60:44:1:0:0.4 0/1:62:4:4,0:53,5:0.0645:2,0:17:1:33.5:1:1:0:60:8:0.0656:0:2 -15 78164597 . A G 71 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.037;SOR=8.03947;LSEQ=CAGTGAGCCTGGGTGGGTGC;RSEQ=TATCTGTGCAGGAGATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:1,0:92,4:0.0103:1,0:46:0:30:0:1:0:60:2:0.011:0:1 0/1:64:5:4,1:54,5:0.0781:2,2:16.6:1:30.6:1:0.39903:2.64245:60:10:0.082:0:1.8 -15 78164645 . TG T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.26361;SOR=0;LSEQ=GAGAGAGGGACGGGGTGGGG;RSEQ=GGGGGAGTAAGAGGTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:178,88:0.0112:2,2:17:1:31.7:1:1:1.01133:60:6:0.0115:0.0037:1.3 0/0:202:0:0,0:132,69:0:2,0:22.8:1:30.5:1:1:0:60:200:1:0:0.5 -15 78164649 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.31946;SOR=3.99886;LSEQ=GAGGGACGGGGTGGGGTGGG;RSEQ=GGAGTAAGAGGTGTGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:1:0,1:184,98:0.0035:2,0:1:0:25:0:0.34982:0:60:2:0.0036:0:1 0/1:214:3:1,2:136,75:0.014:2,2:15.7:1:28:1:0.29431:3.60373:60:6:0.0143:0:1.3 -15 78164706 . T C 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.37615;LSEQ=GTGCGCATGTGTGGTATAAG;RSEQ=GTGGGTCGCGTCTGCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:83:47,36:230,181:0.167:2,2:21:1:30.6:1:1:1.03:60:40.5:0.167:0:1.3 0/1:446:144:77,67:161,140:0.3229:2,2:24.6:1:30.1:1:1:1.00065:60:71:0.3264:0:1.2 -15 78164773 . GGT G 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0;SOR=7.20699;LSEQ=TGAAGGCAGTGGTGGTACCA;RSEQ=GTGTGTGTGTGGAGTAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:5:1,4:135,221:0.0138:2,2:27.4:1:27.6:1:0.65394:2.43826:60:4:0.0113:0.0028:1.2 0/1:381:35:12,23:144,202:0.0919:2,2:31.3:1:31.2:1:0.47253:1.36525:59.3:34:0.0909:0:0.2 -15 78164805 . T C 235 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02465;LSEQ=TGGAGTAAGGTGTGGGTCTG;RSEQ=GCATTTGTGTGTGTGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:233:231:50,181:0,0:0.9914:0,2:23.3:1:30:1:1:0:59.9:45.2:0.9912:0:1.1 1/0:203:150:48,102:16,37:0.7389:2,2:22.1:1:29.5:1:0.86471:1.09:59.6:29:0.736:0:1.2 -15 78164810 . T TTG 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.21998;SOR=Inf;LSEQ=TAAGGTGTGGGTCTGTGCAT;RSEQ=TGTGTGTGTGTCTTGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:45,165:0:2,0:22.8:1:29.8:1:1:0:59.9:51.5:1:0:1.1 0/1:186:2:1,1:56,128:0.0108:2,2:34:1:30.5:1:0.52014:2.27:60:4:0.0111:0:1.5 -15 78164840 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03569;SOR=Inf;LSEQ=GTCTTGCTCCACGTGTGTGC;RSEQ=GTAAGGGACATGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:7,99:0:2,0:22.5:1:31.2:1:1:0:59.7:105:1:0:1 0/1:83:4:0,4:15,64:0.0482:2,0:30.3:1:31.5:1:1:0:60:8:0.05:0:1.8 -15 78165100 . A T 60 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCCCTGGCTGAGGTAACCCA;RSEQ=CATGGAGCCAGGCCTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:27.5:1:30.3:1:1:0:43.8:8:0.8:0:1.8 0/0:1:0:0,0:0,1:0:0,0:13:0:31:0:1:0:41:2:1:0:0 -15 79155088 . C T 46 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGAAAGCCATGTGCAGA;RSEQ=GAAGGCAGAAACTGGGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:13:1:29.3:1:1:0:60:6:1:0:1 -15 79155920 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19514;SOR=0;LSEQ=GGTAACACTTGTGGGGCATT;RSEQ=CTTTTTGAACAGTACCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:78,112:0.0104:2,2:32.5:1:29:1:1:1.43:45:4:0.0105:0:1 0/0:242:0:0,0:103,138:0:2,0:22.4:1:30.7:1:1:0:54.2:119.5:0.9958:0:0.2 -15 79155946 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25348;SOR=Inf;LSEQ=TGAACAGTACCCATTCCCTT;RSEQ=ATGTCTACAATATCACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:49,76:0:2,0:21.4:1:31.8:1:1:0:49.6:250:1:0:0.1 0/1:150:3:1,2:61,86:0.02:2,2:12:1:22.3:1:1:1.41542:53.3:2:0.0137:0:3.3 -15 79155960 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50785;SOR=Inf;LSEQ=TCCCTTGATGTCTACAATAT;RSEQ=ACCTTTCTTATAGATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:35,62:0:2,0:22.3:1:31.9:1:1:0:46.6:96:1:0:0.1 0/1:129:2:1,1:48,78:0.0155:2,2:7.5:1:26:1:1:1.62:49:4:0.016:0:1.5 -15 79156044 . C A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.53324;LSEQ=AGAGAACATATATTGGGTGC;RSEQ=TCTCCTCTTTCCCTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:70,63:0.0148:2,2:42.5:1:31:1:1:1.11024:22:4:0.015:0:1 0/0:126:1:0,1:69,56:0.0079:2,0:11:0:32:0:0.45238:0:49:2:0.008:0:1 -15 80448068 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.54425;LSEQ=CACACAAGACAAGGGGGGCA;RSEQ=GGTAGGGAGGGTGAGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:0,1:34,21:0.0179:2,0:1:0:28:0:0.39286:0:56:2:0.0185:0:1 0/1:73:2:1,1:42,29:0.0274:2,2:15:1:29:1:1:1.44076:60:4:0.0274:0:1 -15 81411834 . C T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57576;SOR=2.74155;LSEQ=AAATTAACAGATTTTAATAA;RSEQ=GTTATATAATTTTTGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:2,1:0.5714:2,0:17:1:31.8:1:0.42857:0:60:8:0.5714:0:1.5 1/1:5:4:4,0:0,1:0.8:0,0:16.3:1:30:1:0.2:0:60:8:0.8:0:1.5 -15 81411917 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49306;SOR=Inf;LSEQ=CAGCACCACTTACCATTTGG;RSEQ=AATGGCTCCCATACAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:27.1:1:31.4:1:1:0:60:46:1:0:0.7 0/1:27:2:1,1:13,12:0.0741:2,2:28:1:27:1:1:1.0801:60:4:0.0741:0:2 -15 81411922 . G C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03058;SOR=6.00757;LSEQ=CCACTTACCATTTGGCAATG;RSEQ=CTCCCATACAATTTACCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:6,8:3,4:0.6667:2,2:30.7:1:30.7:1:1:1:60:28:0.7:0:1.1 1/1:27:25:13,12:1,1:0.9259:2,2:34.9:1:31.3:1:1:1.08:60:50:0.9259:0:1.3 -15 86582918 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49153;SOR=Inf;LSEQ=TCTTCACTTCACCAAACTTT;RSEQ=GTCAGGATCCTGAACCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:0:2,0:26:1:28.5:1:1:0:60:28:1:0:0.2 0/1:30:2:1,1:17,11:0.0667:2,2:8.5:1:29:1:1:1.52251:60:4:0.0667:0:1.5 -15 86582925 . A C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25622;SOR=Inf;LSEQ=TTCACCAAACTTTAGTCAGG;RSEQ=TCCTGAACCTTCTCCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:20,12:0:2,0:26:1:30.1:1:1:0:60:64:1:0:0.2 0/1:43:3:2,1:22,17:0.0698:2,2:28:1:31.3:1:1:1.53:60:6:0.0714:0:1 -15 86583133 . A G 90 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02564;SOR=0;LSEQ=AGCCAGAATCCCCCTTACCC;RSEQ=TGAGGATGTTCCCTCTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:2,6:0,0:1:0,2:28.1:1:30:1:1:0:60:16:1:0:1.8 0/1:7:3:1,2:1,3:0.4286:2,2:41.7:1:30.3:1:1:1.41:60:6:0.4286:0:2 -15 87255595 . C CT 130 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.83136;SOR=1.13677;LSEQ=GATTACAGAGACGATGTGTA;RSEQ=TTTTTTTTTTTTTAATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:18:17,1:48,0:0.2571:1,1:21.6:1:31.4:1:0.27273:0:60:36:0.2609:0.0857:1.2 0/1:46:13:12,1:33,0:0.2826:1,1:21.5:1:31.2:1:0.28261:0:59.2:26:0.2826:0.0217:0.8 -15 87255699 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0143;SOR=Inf;LSEQ=GAGATTAGGCAATTGGGCTT;RSEQ=AAAGTGGAATATGAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:240,158:0:2,0:25:1:31.3:1:1:0:60:65.333:1:0:0.8 0/1:389:6:2,4:219,163:0.0154:2,2:5.8:1:28.2:1:0.40908:2.68033:60:12:0.0157:0:1.7 -15 87255720 . A C 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00091;SOR=0.64038;LSEQ=AAAGTGGAATATGAAACTTA;RSEQ=TGTGGCTAAGTGATGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:453:250:140,110:100,102:0.5519:2,2:24.4:1:31.8:1:0.18489:1.30:60:61.5:0.5553:0:1.1 0/1:456:201:108,93:142,113:0.4408:2,2:27.2:1:30.9:1:0.70514:1.08192:60:66:0.442:0:1.2 -15 87255748 . A C 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.10189;SOR=0.80538;LSEQ=AAGTGATGCACTTGGGTAGA;RSEQ=ATAATGCCCAGGCTAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:200:92,108:129,132:0.4329:2,2:27.4:1:32:1:0.51045:1.14689:60:199:0.4364:0:1.1 0/1:507:193:91,102:157,156:0.3807:2,2:27.7:1:31.3:1:0.52288:1.12779:60:192:0.3802:0:1.1 -15 87255833 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2429;SOR=Inf;LSEQ=TCCGCCTGTACTCTGAGAAT;RSEQ=AACATTTACATTTTGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:45,150:0:2,0:24.9:1:31.3:1:1:0:60:64:1:0:0.2 0/1:190:2:1,1:51,137:0.0105:2,2:18:1:27.5:1:0.47352:2.67:60:4:0.0107:0:2 -15 87255983 . C T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23575;SOR=0.31353;LSEQ=CAAGGCATCTGGTCCAATTC;RSEQ=GGACTCATTAAGTAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:0,10:0,9:0.5263:0,0:16.1:1:28.5:1:1:0:60:9:0.5:0:1.1 0/1:8:2:0,2:1,5:0.25:2,0:17:1:28.5:1:1:0:60:4:0.25:0:1.5 -15 88125886 . GT G 51 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCCCTAAAATTGGAGGG;RSEQ=TTTTTTTTTTTTTTGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:21.7:1:32.2:1:1:0:60:6:0.375:0.125:0.3 0/0:2:0:0,0:2,0:0:0,0:24:1:32:0:1:0:60:4:1:0:3 -15 88125977 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49643;SOR=Inf;LSEQ=GCAATGCACCTGTTTGGTGT;RSEQ=TGGCACTCAGGAGATACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:49,2:0:1,0:25.1:1:31.2:1:1:0:60:50:0.9804:0:0 0/1:57:2:2,0:52,3:0.0351:2,0:31.5:1:32.5:1:1:0:60:4:0.0351:0:1 -15 88126035 . G T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1233;SOR=Inf;LSEQ=AACTAGATCTAGACAGCCAT;RSEQ=GGAAAAGAACAACAGGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:140,49:0:2,0:24.6:1:32:1:1:0:60:188:1:0:0.2 0/1:196:4:1,3:143,49:0.0204:2,2:6.3:1:25:1:0.05791:8.63885:60:3:0.0156:0:1 -15 88126117 . G T 201 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00403;LSEQ=AATGCTACCTCTGGGAATCG;RSEQ=ATCATTCAGGAAAAGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:130:66,64:94,100:0.3976:2,2:25.9:1:28.7:1:0.73413:1.10:60:64:0.4:0:1.2 0/0:379:1:0,1:173,204:0.0026:2,0:44:0:30:0:1:0:60:2:0.0027:0:1 -15 88126129 . A C 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=1.99372;LSEQ=GGGAATCGGATCATTCAGGA;RSEQ=AAGACACCGGCTGCTCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:74:34,40:119,130:0.2284:2,2:25.4:1:31.5:1:0.79253:1.07665:60:36:0.2271:0:1.2 0/1:377:140:65,75:99,138:0.3714:2,2:24.5:1:31:1:0.39146:1.21:60:69:0.373:0:1.2 -15 88126191 . C T 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGACAAAAAGAATCCTGC;RSEQ=GGAAGCTGATTAGGCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:53,115:0:2,0:22.9:1:29.9:1:1:0:60:55:1:0:0.4 0/1:170:35:12,23:45,90:0.2059:2,2:22.6:1:30.1:1:1:1.04:60:70:0.2108:0:1.1 -15 88126196 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24278;SOR=Inf;LSEQ=CAAAAAGAATCCTGCCGGAA;RSEQ=CTGATTAGGCCAGACAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:40,117:0:2,0:22:1:31.8:1:1:0:60:77.5:1:0:0.4 0/1:153:2:1,1:50,100:0.0131:2,2:21.5:1:29:1:1:1.99:60:4:0.0132:0:1 -15 88126197 . C A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=AAAAAGAATCCTGCCGGAAG;RSEQ=TGATTAGGCCAGACAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:40,117:0:2,0:21.6:1:31.5:1:1:0:60:30.4:1:0:0.4 0/1:150:12:3,9:46,92:0.08:2,2:26:1:29.7:1:0.75166:1.49621:60:24:0.0805:0:1.1 -15 88126291 . A C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0336;SOR=3.46417;LSEQ=TTCAGAGAAAAGGAGGCACC;RSEQ=TTGATATAAATAACACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:16:0,16:0,20:0.4444:1,1:13.4:1:32.8:1:1:0:60:32:0.4444:0:1.1 1/0:23:17:1,16:0,6:0.7391:0,1:20.5:1:32.7:1:1:0:60:34:0.7391:0:1.1 -15 88311418 . C A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.47868;LSEQ=TTTCCCCCCAGCAAAGCACA;RSEQ=CCCCTCCACCAAGGACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:9,6:0.1176:2,0:39.5:1:30.5:1:0.51471:0:60:4:0.1176:0:1.5 0/1:12:2:1,1:6,4:0.1667:2,2:39:1:29.5:1:1:1.4491:60:4:0.1667:0:1.5 -15 88311747 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AATAAACAAACAGAAAGCAA;RSEQ=AATAGCATCAACAACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:37.5:1:32.5:1:1:1.83:60:4:0.25:0:2 0/1:12:3:1,2:2,7:0.25:2,2:26:1:31.3:1:1:1.66:60:6:0.25:0:1.7 -15 88311755 . T TCAA 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=0.57471;LSEQ=AACAGAAAGCAATAATAGCA;RSEQ=CAACAACAACAAAAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:40:1:31.5:1:1:1.41:60:4:0.2857:0:2 0/1:11:2:1,1:2,7:0.1818:2,2:36.5:1:29.7:1:0.49091:3.06:60:4:0.1818:0:2 -15 88311773 . A G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.61991;SOR=2.00863;LSEQ=CATCAACAACAACAAAAAAA;RSEQ=ACCCCACAAAAACCCTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:1,2:0.625:2,2:24.2:1:31.2:1:1:1.29:60:10:0.625:0:1.4 1/0:9:7:2,5:1,1:0.7778:2,2:28:1:29.6:1:1:2.23609:60:14:0.7778:0:1.4 -15 88419947 . AAT A 63 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=11.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAGATAGTTAGATATATA;RSEQ=ATATATATATATATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:3,1:13,0:0.2353:1,2:14:1:31.5:1:0.23529:0:60:8:0.25:0:0.3 0/0:3:0:0,0:3,0:0:0,0:21.3:1:30.7:1:1:0:60:6:1:0:0.7 -15 88420004 . C CT 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.77654;LSEQ=TACAGGGTTTTTTTTTCTTT;RSEQ=TTTTTTTTTCCTTTTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:2,0:46,1:0.04:1,0:40:1:33:0:1:0:60:4:0.0426:0:0.5 0/1:32:1:1,0:30,1:0.0313:1,0:34:0:32:0:1:0:60:2:0.0323:0:1 -15 88420286 . G A 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06953;SOR=7.02268;LSEQ=CAGCACCCCAGCATGACATC;RSEQ=TACACCTCTTTGGGGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:1:1,0:288,406:0.0014:2,0:1:0:25:0:0.41583:0:60:2:0.0015:0:1 0/1:698:7:6,1:291,400:0.01:2,2:9.7:1:25.6:1:0.046:8.23:60:6:0.0087:0:1.3 -15 88423051 . C T 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGTTCACACATGACTCTA;RSEQ=CAGTTATAAAACTGGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:32.8:1:30.5:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 88423336 . A AT 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.79138;SOR=1.14349;LSEQ=ACCACATTTCCTACAGTTCC;RSEQ=TTTTTTTTTTCCTACTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:12:12,0:101,1:0.1043:1,0:26.6:1:31.5:1:1:0:60:24:0.1071:0.0261:0.3 0/1:51:6:6,0:44,1:0.1176:1,0:24.5:1:29.2:1:1:0:60:12:0.1176:0:0.2 -15 88423463 . C T 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.22554;LSEQ=CTGAGATAGCTCTTATGAGC;RSEQ=CTCCCCCAATCAAGATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:837:665:422,243:102,69:0.7945:2,2:24.9:1:30.3:1:0.37593:1.17:60:46.5:0.7949:0:1.1 0/1:668:311:187,124:217,139:0.4656:2,2:25.9:1:29.6:1:0.87385:1.03517:60:37.875:0.4647:0:1.1 -15 88423710 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21162;SOR=Inf;LSEQ=GTGACCAGATGGCCAGAATG;RSEQ=GTGTTATCTGTCTGCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:13,193:0:2,0:23.8:1:31.3:1:1:0:60:102:1:0:0.1 0/1:176:2:1,1:26,148:0.0114:2,2:27:1:29:1:0.28403:5.60:60:4:0.0116:0:1 -15 88428702 . C A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.18957;LSEQ=ATACTTGAAATAGAACAATA;RSEQ=GGGAGAGTTACTCTATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:91:91,0:21,0:0.7982:1,1:22.2:1:30.5:1:1:0:60:90:0.7965:0:1 0/1:47:20:20,0:27,0:0.4255:1,1:25.5:1:29.2:1:1:0:60:9:0.4:0:1.1 -15 88428899 . T TA 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01079;SOR=1.92186;LSEQ=TGGGACAATGAACTATTCAT;RSEQ=AAAAAAAATACGCTTAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1755:24:11,13:907,824:0.0137:2,2:29.9:1:29.3:1:0.54407:1.30066:60:48:0.0138:0.0023:0 0/1:1772:46:22,24:874,849:0.026:2,2:27.4:1:29.1:1:0.76583:1.12296:60:92:0.0262:0.0028:0.2 -15 88429076 . A G 220 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACACATGTTCAAGAAGCC;RSEQ=TCAAGAATAAGATTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:118:118:0,118:0,0:1:0,1:23.8:1:32.1:1:1:0:60:28.5:1:0:1.1 1/0:55:31:1,30:0,24:0.5636:1,1:21.7:1:30.9:1:1:0:60:62:0.5741:0:1 -15 88429142 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06633;SOR=Inf;LSEQ=TTGCATGGCAAAAGACAACA;RSEQ=AAGCATAGCTAAAAGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,35:0:1,0:27.3:1:28.4:1:1:0:60:70:0.9722:0:0.5 0/1:13:2:0,2:0,11:0.1538:0,0:29.5:1:33.5:1:1:0:60:4:0.1538:0:1 -15 88459632 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14299;SOR=Inf;LSEQ=CTCCACAGGAGTAGAGAGAC;RSEQ=TGAATGACTCAACACCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:107,4:0:1,0:21.4:1:29.6:1:1:0:60:54.5:1:0:0.1 0/1:68:2:2,0:66,0:0.0294:1,0:17.5:1:28.5:1:1:0:60:4:0.0294:0:1 -15 88459695 . A T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1862;SOR=4.72528;LSEQ=TCCTCTCCTTTCCCGAGGAC;RSEQ=GAATCCAATATAAGCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:1:0,1:280,100:0.0026:2,0:1:0:26:0:0.26509:0:60:2:0.0027:0:1 0/1:325:4:1,3:234,87:0.0123:2,2:5:1:28.3:1:0.0661:8.00848:60:8:0.0124:0:1 -15 88459998 . CT C 64 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.38411;SOR=2.18617;LSEQ=TACCTATGAAAAGCACAAGG;RSEQ=TTTTTTTTTTTTAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:0,4:0,18:0.1818:1,0:32:1:32.3:1:1:0:60:8:0.1818:0:0.3 0/1:9:3:0,3:0,6:0.3333:0,0:34:1:33:1:1:0:60:6:0.375:0:0 -15 88472228 . G T 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16588;SOR=0;LSEQ=TGTCCAAGAAGAAAGAAGGA;RSEQ=TGGGCAATTGAGAACATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:6:6,0:35,0:0.1463:1,0:27.7:1:31.8:1:1:0:60:12:0.15:0:1 0/0:17:0:0,0:17,0:0:1,0:16.6:1:32.2:1:1:0:60:34:1:0:0.1 -15 88472341 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08201;SOR=Inf;LSEQ=ATGTGTGTGCCAGAGTGACA;RSEQ=GGTTAATGGACAATGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:195,38:0:2,0:24.7:1:32:1:1:0:60:76.667:1:0:0.1 0/1:180:3:2,1:143,34:0.0167:2,2:18:1:28.3:1:0.47938:2.09245:60:6:0.0167:0:1 -15 88472655 . G T 225 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACAAGGATCATTGCATCTG;RSEQ=CCCATGGGCCCTGCAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:195:52,143:91,208:0.3947:2,2:23.7:1:29.6:1:0.41699:1.20268:60:47.75:0.3979:0:1.1 0/0:375:0:0,0:112,262:0:2,0:24.1:1:31.4:1:1:0:60:40.556:0.9973:0:0.2 -15 88472697 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12327;SOR=Inf;LSEQ=TGGGGAGAAGAGAGGGGGCA;RSEQ=AGAGAAATCAGGAGATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:53,226:0:2,0:24.3:1:31.1:1:1:0:60:54.8:0.9964:0:0.4 0/1:152:2:1,1:28,122:0.0132:2,2:29.5:1:27.5:1:0.3462:4.30:60:4:0.0132:0:1 -15 88472729 . T A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATCAAGGAGAAAGGCCT;RSEQ=CCTGGGTCCCTGCCCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:9,142:0.0131:2,2:9:1:26:1:0.12685:15.02:60:4:0.0132:0:1 0/0:73:0:0,0:7,66:0:2,0:24.6:1:29.4:1:1:0:60:146:1:0:0.1 -15 88476518 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=ACACACCACTGGGTTACCAA;RSEQ=AAATATGAATCTAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:1,74:0.026:1,2:17.5:1:32.5:1:0.05161:52.69:60:4:0.0263:0:1.5 0/0:44:0:0,0:0,44:0:1,0:20.3:1:27.5:1:1:0:60:43:1:0:0.1 -15 88483456 . T C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCCTCCTTAATCAGCC;RSEQ=GCTCTACAACAGCTCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:44.7:1:31.3:1:1:0:60:6:1:0:1 1/1:2:2:1,1:0,0:1:0,2:23:1:28:1:1:0:60:4:1:0:1 -15 88485503 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCTGACGACCGCTCCTC;RSEQ=CAAGCCACAGGCTGCAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 88522524 . A G 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07325;SOR=Inf;LSEQ=TAGAGCTTCCAACCTCTCAG;RSEQ=GGGCCCAGCCTACCAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:300,117:0:2,0:24.3:1:30:1:1:0:60:103.25:1:0:0.1 0/1:301:3:2,1:214,84:0.01:2,2:31:1:26:1:1:1.27277:60:2:0.0068:0:1 -15 88522711 . G GA 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.8888;SOR=1.04229;LSEQ=AAACCTATAAAAAACAAAAA;RSEQ=AAAAAAAAACAGAAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:28:8,20:98,293:0.0664:2,2:26:1:29.7:1:0.65711:1.20:60:56:0.0697:0:0.1 0/1:377:26:10,16:99,248:0.069:2,2:23.5:1:28.2:1:0.27355:1.56:57.9:25:0.0696:0.008:0.6 -15 88522723 . G A 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.03702;SOR=Inf;LSEQ=AACAAAAAGAAAAAAAAACA;RSEQ=AAAAAAGCAAAATAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:64,286:0:2,0:22.9:1:31:1:1:0:60:28.167:1:0:0.2 0/1:275:4:3,1:63,207:0.0145:2,2:8:1:27.3:1:0.04457:9.75:60:8:0.0147:0:1 -15 88523033 . G T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGAAAGGAGGAGACCCT;RSEQ=ACGATGAGCTGAGGGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:33:1:29.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 88523035 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAAGGAGGAGACCCTGA;RSEQ=GATGAGCTGAGGGGTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:31:1:31.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 88524624 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10214;SOR=Inf;LSEQ=GCAGACATGGGGGAATTAAT;RSEQ=GTCAGTATTAAACCCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:57,262:0:2,0:25.5:1:31.4:1:1:0:59.9:158.5:1:0:0.1 0/1:281:3:2,1:69,209:0.0107:2,2:15.3:1:26.7:1:0.15826:6.01:60:6:0.0108:0:1 -15 88524788 . A G 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03324;SOR=0;LSEQ=ATCTAGATCCTAAGAATCTC;RSEQ=CCCTGGCATTATAGAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:0.4:0,0:23.1:1:33.5:1:1:0:60:16:0.4:0:1 0/0:9:0:0,0:0,9:0:0,0:29.6:1:30.6:1:1:0:60:18:1:0:0 -15 88576090 . G A 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=26.02466;LSEQ=TTCCATCCCAGTACTTACAC;RSEQ=TGTCCGGCTTGTGGCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:875:2:1,1:476,396:0.0023:2,2:21:1:14.5:1:1:1.20176:60:0:0:0:1 0/1:870:49:23,26:450,370:0.0563:2,2:27.9:1:29.6:1:0.30324:1.37433:60:48:0.0558:0:1.2 -15 88576185 . G C 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01024;SOR=0.75861;LSEQ=ATGACCACAGTGTCGGGCCC;RSEQ=GCATCCAGTGACGAGGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:674:386:160,226:117,169:0.5727:2,2:25.6:1:30.1:1:0.93685:1.02:60:63.333:0.5723:0:1.2 1/0:732:369:164,205:164,195:0.5041:2,2:24.4:1:29.2:1:0.76589:1.05118:60:40:0.5028:0:1.1 -15 88576215 . G A 194 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=99.96749;LSEQ=GACGAGGGCGTGGTGATGCC;RSEQ=TGGTTGATGTGGTGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:1:1,0:245,358:0.0017:2,0:1:0:29:0:0.40728:0:60:2:0.0017:0:2 0/1:681:97:48,49:251,333:0.1424:2,2:25.2:1:29.4:1:0.26927:1.30:60:23.25:0.1386:0:1.3 -15 88576339 . T A 23 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50114;SOR=0;LSEQ=CCGGCCAGTTTCCAGCCCTG;RSEQ=CCACAGACAACCCCCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:12,94:0.0185:2,2:21.5:1:23.5:1:0.22724:7.57:60:4:0.0189:0:1 0/0:91:0:0,0:12,79:0:2,0:26.8:1:29:1:1:0:60:90:1:0:0.1 -15 88576408 . TATATATATATATATAT C 107 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=24;MSI=20.000;MSILEN=2;SSF=0.01605;SOR=0;LSEQ=TTTACTTTTGGGGGGTGTGT;RSEQ=ATATATATATATATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:0,11:0,8:0.4231:0,0:14.2:1:31.1:1:1:0:60:10:0.4348:0.3077:0.8 0/0:10:0:0,0:0,6:0:0,0:7:1:29:1:1:0:60:12:0.6:0:0 -15 88610388 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5016;SOR=0;LSEQ=CCTTCCCTTGGATCAGTTCC;RSEQ=TGCAACACGTGGTGCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:109,49:0.0125:2,2:10:1:28.5:1:0.52869:2.21225:60:4:0.0127:0:2 0/0:136:0:0,0:89,47:0:2,0:26.4:1:29.8:1:1:0:60:135:1:0:0.4 -15 88610457 . C T 240 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02229;LSEQ=GAGTTGTACAGACTCCCACA;RSEQ=GCCATTTTTTTTCACTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:248:245:115,130:0,0:0.9879:0,2:26.6:1:30.3:1:1:0:59.9:48:0.9877:0:1.2 1/0:267:172:83,89:39,50:0.6442:2,2:28.7:1:29.6:1:0.51544:1.19:60:56.333:0.645:0:1.1 -15 88610461 . A AT 73 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.27117;SOR=0.36992;LSEQ=TGTACAGACTCCCACACGCC;RSEQ=TTTTTTTTCACTTCCTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:5:3,2:109,129:0.0204:2,2:27:1:31.8:1:0.66403:1.77:60:10:0.0208:0:1.2 0/0:262:2:1,1:117,140:0.0076:2,2:30:1:30:1:1:1.20:60:4:0.0078:0:1 -15 88612019 . A G 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGCAAGAAGGGCAAGGAGGG;RSEQ=GCAGATTTTGGGGCTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:27:1:1:0:60:4:1:0:1.5 -15 88669128 . G A 53 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAACTTCAAAAACAAGA;RSEQ=GAAAACCGTGTCCTCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:29:1:26.5:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 88669163 . T C 72 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACTAGGAGTCCCTTTAC;RSEQ=CACCCGTAATGAAAATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:23.4:1:31.2:1:1:0:60:10:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 88669382 . G C 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGAGTTTCCATCAGTACCA;RSEQ=TTAGACCCCATGACCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:144:144:143,1:0,0:1:0,1:23.3:1:32.2:1:1:0:60:47:1:0:1.1 1/1:99:80:78,2:19,0:0.8081:1,1:24.5:1:31.7:1:1:0:60:160:0.8081:0:1.1 -15 88669644 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16724;SOR=Inf;LSEQ=GAGAGTCAGCAACAATCACA;RSEQ=AAAACCCAATTTCCTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:42,241:0:2,0:22.8:1:31.2:1:1:0:60:39.429:0.9964:0:0.1 0/1:197:2:1,1:39,156:0.0102:2,2:11.5:1:28:1:0.36569:3.96:60:4:0.0102:0:1 -15 88670278 . C CT 116 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.18709;SOR=1.87042;LSEQ=GAACGTAGTTCAATTCATTA;RSEQ=TTTTTTTTTTCAAAGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:8:8,0:112,8:0.0625:2,0:22.1:1:31.3:1:1:0:60:16:0.0625:0.0078:0 0/1:126:14:13,1:107,4:0.1111:1,1:20.7:1:30.7:1:0.45353:2.04251:60:28:0.1111:0.0317:0.3 -15 88670293 . G C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49939;SOR=Inf;LSEQ=CATTACTTTTTTTTTTCAAA;RSEQ=TTTCAAGTAAGATAATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:137,17:0:2,0:24.1:1:31.9:1:1:0:60:37.5:1:0:0.1 0/1:168:2:1,1:148,18:0.0119:2,2:15:0:30:1:0.214:8.02946:60:4:0.012:0:1 -15 88671809 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.74783;LSEQ=TACCCTTCATTTCCCTTTCA;RSEQ=AGTTCACTCAGATGCCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:106,9:0.0171:2,2:20.5:1:31:1:0.16431:11.22625:60:4:0.0174:0:1 0/1:78:1:0,1:72,5:0.0128:2,0:1:0:22:0:0.07692:0:60:2:0.013:0:1 -15 88677817 . G A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGATCAGGTCATTCATCC;RSEQ=TTAAATGGAGGGTTAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:15.5:1:27:0:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 88678680 . T C 203 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACACAGAGTCTACCACCTCC;RSEQ=GCAGTAGCCTTCCAGCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:110:110:11,99:0,0:1:0,2:21.1:1:30:1:1:0:60:109:1:0:1.1 1/0:75:57:10,47:4,14:0.76:2,2:22.1:1:29.7:1:0.73146:1.33734:60:114:0.76:0:1.1 -15 88679065 . C T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04248;SOR=Inf;LSEQ=CCCTGACAACACCTTGGCCC;RSEQ=TCTCCAGCCTCCTATGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:208,68:0:2,0:25.2:1:31:1:1:0:60:91:1:0:0.1 0/1:231:4:1,3:158,69:0.0173:2,2:13.3:1:25.8:1:0.09094:6.80696:60:8:0.0173:0:1 -15 88679324 . C A 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30594;SOR=4.60159;LSEQ=TAGCTTCTACAAGGATGGCT;RSEQ=TGCTACCTAATCCCCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:1:1,0:38,262:0.0033:2,0:1:0:23:0:0.12957:0:60:2:0.0034:0:1 0/1:198:3:2,1:38,157:0.0152:2,2:11.3:1:23.3:1:0.10447:8.14:60:6:0.0153:0:1.7 -15 88679785 . G A 302 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01792;LSEQ=CCATTGCAAGTGATAACAGC;RSEQ=TTGTCACCCTCTCGTACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:962:961:414,547:1,0:0.999:0,2:24.8:1:30.5:1:0.43139:0:60:63.067:1:0:1.1 1/1:709:670:306,364:20,17:0.945:2,2:25.3:1:29.9:1:0.39734:1.39878:60:82.75:0.9457:0:1.2 -15 88680100 . G A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGGTGGGGGCAGTGCTTA;RSEQ=GGAATGCATTTCTGGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:1:0,2:24.8:1:31.8:1:1:0:60:16:1:0:1 1/1:3:3:1,2:0,0:1:0,2:29.3:1:28.3:1:1:0:60:6:1:0:1 -15 88680645 . G T 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.00109;SOR=Inf;LSEQ=ACTCACTCACCACACTGACT;RSEQ=ATGTTCATGCGGAAGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:953:0:0,0:522,431:0:2,0:25.9:1:31.6:1:1:0:60:62.533:1:0:0.4 0/1:844:9:5,4:461,373:0.0107:2,2:18.4:1:30.4:1:1:1.01:60:18:0.0108:0:1.7 -15 88680684 . G A 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.84786;LSEQ=GGAAGCTGGGAGCCATCAGC;RSEQ=TTGATGCAGTAGAGGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1106:367:190,177:373,365:0.3318:2,2:24.6:1:30.4:1:0.70207:1.05:60:121.333:0.3315:0:1.2 0/1:1005:481:252,229:262,260:0.4786:2,2:25.7:1:29.8:1:0.48764:1.09:60:159.333:0.4794:0:1.2 -15 88680943 . G T 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGAAGTGGAAAAATCCTT;RSEQ=TAAGTCCATAAATTGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:2,50:0:1,0:25.9:1:32.4:1:1:0:60:104:1:0:0.3 1/0:15:9:0,9:0,6:0.6:0,0:20.4:1:31.4:1:1:0:60:18:0.6:0:1.1 -15 88680987 . T A 119 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAATAAACTCATTTTTT;RSEQ=AAAAAAAGAAATCCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:1:0,1:25.6:1:31.5:1:1:0:60:28:1:0:1.1 1/1:2:2:0,2:0,0:1:0,0:3.5:1:29:1:1:0:60:4:1:0:1.5 -15 88690725 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15501;SOR=Inf;LSEQ=TAATCATTTCACTGGAGCCT;RSEQ=GCTTTGTTTTCCTTCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:10,154:0:2,0:24.7:1:31:1:1:0:60:40:1:0:0.1 0/1:107:2:1,1:14,91:0.0187:2,2:26.5:1:29:1:0.26186:6.31:60:4:0.0189:0:1 -15 88726253 . G C 29 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCTTCTTGCAACCCCCCCCC;RSEQ=CCCCCCGCCAGTCCTAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:7:0:29.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:47:0:30:0:1:0:60:2:1:0:0 -15 88726405 . G A 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12797;SOR=0;LSEQ=GAAAGTGAACACACTTGGGT;RSEQ=TCAGGAGACTGACTCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:23.2:1:26.5:1:1:0:60:12:0.4286:0:1 0/0:5:0:0,0:5,0:0:0,0:27.8:1:31:1:1:0:60:10:1:0:0 -15 88726569 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16665;SOR=Inf;LSEQ=CTGGAGGCAAAAAGCCAGGT;RSEQ=TAGACCTCAGGTCTCCGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:222,44:0:2,0:25.7:1:31.2:1:1:0:60:65.5:1:0:0.6 0/1:184:2:1,1:146,35:0.0109:2,2:19.5:1:27.5:1:0.35561:4.12715:60:4:0.011:0:1.5 -15 88726586 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17552;LSEQ=GGTCTAGACCTCAGGTCTCC;RSEQ=GTTTCACTGCCCCAAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:341:190:150,40:112,39:0.5572:2,2:25.9:1:30.1:1:0.30473:1.30:60:94:0.5579:0:1.1 0/1:266:48:37,11:158,60:0.1805:2,2:22.5:1:30.3:1:0.59132:1.28:60:96:0.1825:0:1 -15 88726814 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28232;SOR=0;LSEQ=GGGGGTGAGGCTAAGGCTGG;RSEQ=CCTGCAGCCGCCCTGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:1,2:7,130:0.0214:2,2:33:1:29:1:0.16292:8.93:60:6:0.0221:0:1 0/0:90:0:0,0:6,84:0:2,0:22.9:1:31:1:1:0:60:29:1:0:0.1 -15 88727336 . C G 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01628;SOR=0.45213;LSEQ=CCAACTCTACCAAAAGAAGA;RSEQ=CTGGGGGAGAAAGCACGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:97:57:55,2:39,1:0.5876:1,1:25.6:1:32.6:1:1:1.41327:60:114:0.5876:0:1 0/1:64:25:23,2:38,1:0.3906:1,2:26.1:1:30.3:1:0.55537:3.24132:60:11.5:0.371:0:1.4 -15 88727443 . C T 147 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=15.87254;LSEQ=GGGAAAGGCCTCTCTGTGGC;RSEQ=GGGTGTACTCACAGCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:578:2:1,1:330,245:0.0035:2,2:13.5:1:30.5:1:1:1.34622:60:4:0.0035:0:1 0/1:631:33:18,15:343,255:0.0523:2,2:24.7:1:29.2:1:0.85693:1.12071:60:15.5:0.0501:0:1 -15 88727612 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24849;SOR=Inf;LSEQ=AGCCACAGAGACCTGGCTTT;RSEQ=ATCCCCGATGAGCTAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:14,125:0:2,0:24:1:31.6:1:1:0:60:138:1:0:0.1 0/1:150:3:1,2:19,128:0.02:2,2:15:1:28.3:1:0.35106:3.33:60:6:0.02:0:1 -15 88727751 . A T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20156;SOR=0.22573;LSEQ=GAATTAACTGGATTCATTGG;RSEQ=TCCAAGTTCCTGGCCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:0.6111:0,0:34:1:29.5:1:1:0:60:22:0.6471:0:1.1 0/1:8:2:0,2:0,6:0.25:0,0:23:1:29:1:1:0:60:4:0.2857:0:1 -15 88799100 . C T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01653;SOR=Inf;LSEQ=CAGGAGGGAGACGCAGAGCG;RSEQ=GGGGGAGGCAGGCTGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:590:0:0,0:426,164:0:2,0:25.6:1:31.5:1:1:0:60:97.333:1:0:0.1 0/1:466:5:2,3:294,167:0.0107:2,2:17.2:1:28:1:0.35978:2.63491:60:10:0.0108:0:1 -15 88799443 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20546;SOR=Inf;LSEQ=AGAGGGGGGTGGGGTGGGGG;RSEQ=AGTGGGGAGAGCAGGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:11,68:0:2,0:13.4:1:28.3:1:1:0:56.6:6.182:1:0:1.9 0/1:66:2:1,1:12,50:0.0303:2,2:9:0:30.5:1:0.36756:4.04:60:4:0.0364:0:1.5 -15 88799494 . A G 36 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGGCGAGGGAGGGGGGA;RSEQ=GGGGGAGGGGGGGCCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:2,0:0.5:0,0:7.7:1:23.3:1:0.1:0:60:2:0.6667:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 90627426 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17192;SOR=Inf;LSEQ=GAGGGGCTGTGAGGCTCACC;RSEQ=TCTGCCGCGCTCAGGAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:181,23:0:2,0:27.9:1:31.4:1:1:0:60:203:1:0:0.1 0/1:145:2:1,1:123,20:0.0138:2,2:29.5:1:29:1:0.26954:6.02616:60:4:0.0142:0:1 -15 90627616 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32607;LSEQ=AGCACCACTCACATCAGGGG;RSEQ=GGCTCCAGGCCTTGCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:399:263:83,180:38,98:0.6591:2,2:23:1:30.1:1:0.4918:1.19:60:51.6:0.6565:0:1.1 0/1:396:153:53,100:73,170:0.3864:2,2:24.3:1:30.1:1:0.37574:1.23:60:50:0.3836:0:1.1 -15 90628537 . G A 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=43.90226;LSEQ=TCCCGATAGTGGCGGGTGAC;RSEQ=GTCCCATGAGCGGCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1345:3:3,0:671,662:0.0022:2,0:26.7:1:19.3:1:0.2495:0:60:0.5:9e-04:0:4 0/1:1307:117:58,59:615,562:0.0895:2,2:24.1:1:27.8:1:0.6279:1.11308:60:8.75:0.0935:0:1.4 -15 90628591 . G A 215 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=57.00896;LSEQ=CCATCAGGGCAGACCAGGAC;RSEQ=GACGTCATCAGGCCAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1408:3:3,0:660,743:0.0021:2,0:4.3:1:22.3:1:0.1046:0:60:2:0.0015:0:2 0/1:1362:148:66,82:577,633:0.1087:2,2:27.7:1:29.9:1:0.48679:1.13241:60:20.143:0.112:0:1.9 -15 90628594 . C T 193 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=36.10505;LSEQ=TCAGGGCAGACCAGGACGGA;RSEQ=GTCATCAGGCCAAGGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1412:3:1,2:661,746:0.0021:2,2:30.7:1:25:1:1:1.77142:60:2:0.0015:0:1 0/1:1359:97:44,53:596,664:0.0714:2,2:29.4:1:29.3:1:0.7521:1.08109:60:18.4:0.0738:0:2.1 -15 90628777 . T C 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0097;SOR=Inf;LSEQ=AGGACAGGGACTGTTCCAGG;RSEQ=CTCTTCACCCTCCTGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:1,104:0:1,0:25.6:1:30:1:1:0:60:104:0.9905:0:0.1 0/1:50:4:0,4:1,45:0.08:1,0:21.5:1:31.3:1:1:0:60:8:0.0816:0:1 -15 90630560 . G A 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04085;SOR=Inf;LSEQ=CAGGTTGGGGATCCCTCCCT;RSEQ=AGCCTCGGAGCTGAGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:0:0,0:207,205:0:2,0:22.8:1:31.5:1:1:0:60:67.667:1:0:0.1 0/1:338:4:1,3:160,174:0.0118:2,2:11.3:1:26.3:1:0.62446:2.75094:60:3:0.0091:0:1.3 -15 90630832 . G A 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35536;SOR=3.25958;LSEQ=AGGGGGAGAGACAGGGCCCT;RSEQ=GCGTGGTGCCCTAGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:1:1,0:35,172:0.0048:2,0:1:0:23:0:0.17308:0:60:2:0.0049:0:1 0/1:193:3:2,1:33,157:0.0155:2,2:10.7:1:25:1:0.08524:9.35:60:6:0.0158:0:1 -15 90630859 . C T 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00284;SOR=Inf;LSEQ=TGCCCTAGCCTGGCGATTGC;RSEQ=GGCAACCTCCCACCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:8,106:0:2,0:23:1:30.1:1:1:0:60:228:1:0:0.3 0/1:90:7:1,6:7,76:0.0778:2,2:27.4:1:29:1:0.49116:1.79:60:14:0.0787:0:1.6 -15 90630892 . C A 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0325;SOR=0.40163;LSEQ=CCTCCCAGGGCAAGGCCCAG;RSEQ=TCTCCAGGAACGGTACCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:35:0,35:1,26:0.5645:1,1:23.9:1:31.6:1:0.43548:0:60:70:0.5645:0:1 0/1:47:16:1,15:0,31:0.3404:1,1:29.9:1:29.3:1:0.34043:0:60:32:0.3404:0:1.3 -15 90631247 . G A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01818;SOR=Inf;LSEQ=GCATTGGAGCTGGAACTGGG;RSEQ=ATAAAGAGGCATTCTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:20.8:1:26.9:1:1:0:60:3.5:1:0:1.4 1/1:2:2:1,1:0,0:1:0,2:26.5:1:28.5:1:1:0:60:4:1:0:1 -15 90631255 . G A 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=GCTGGAACTGGGGATAAAGA;RSEQ=GCATTCTCTTCTGATAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:0,2:0.75:0,2:22.8:1:27.3:1:0.42857:0:60:5:0.7143:0:2.2 0/0:2:0:0,0:1,1:0:2,0:26.5:1:30:1:1:0:60:4:1:0:1 -15 90631491 . C A 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04088;SOR=Inf;LSEQ=CCATTTCTGCCTCTTTGTGG;RSEQ=CTAAGAATGAGGCCATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:116,7:0:2,0:26.8:1:32.3:1:1:0:60:40:1:0:0 0/1:102:4:4,0:93,5:0.0392:2,0:27.3:1:31:0:1:0:60:8:0.0412:0:1 -15 90631540 . G T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12427;SOR=0;LSEQ=GAAAGCCACGAGACAGAGAT;RSEQ=AAGAGACAAGCTGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:4:2,2:249,104:0.0112:2,2:21.8:1:29.5:1:0.58521:2.38765:60:8:0.0114:0:1 0/0:343:0:0,0:245,96:0:2,0:22.8:1:31.3:1:1:0:60:67.2:1:0:0.2 -15 90631774 . C T 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTAGGCGAGGAGCTCCAGT;RSEQ=GGGGGGTGCCCAGGTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:0:0,0:263,213:0:2,0:23.7:1:30.5:1:1:0:60:94.2:0.9979:0:0.1 0/1:390:31:18,13:175,183:0.0795:2,2:22.8:1:29.8:1:0.35418:1.45:60:62:0.0801:0:1 -15 90632057 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49835;SOR=0;LSEQ=TGAACCCCAAGCAACAACAC;RSEQ=GCCAGACGGGGGTCCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:8,142:0.0132:2,2:24:1:29:1:0.11528:16.79:60:4:0.0132:0:1 0/0:151:0:0,0:17,134:0:2,0:19.3:1:30.5:1:1:0:60:49.333:1:0:0.1 -15 90633317 . TTCC T 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTGACCACATCAGCATTACC;RSEQ=TCCTCCTCCTCCTCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:46:1:31.3:1:1:0:60:8:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 90633416 . A G 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=TGGCCTGGGAGATGGAAGAC;RSEQ=TGGATTCTGTTCTCAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:0.7:0,0:16.3:1:27:1:1:0:60:14:0.7:0:1.4 0/0:1:0:0,0:1,0:0:0,0:6:0:31:0:1:0:60:2:1:0:0 -15 90633685 . G T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12408;SOR=Inf;LSEQ=GAAGCCTGTGACCCTCCCTG;RSEQ=CCCGCCCACCTCCACACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:275,121:0:2,0:25.2:1:31:1:1:0:60:23.75:1:0:0.1 0/1:400:4:3,1:250,144:0.01:2,2:31.5:1:26.3:1:1:1.73:60:3:0.0077:0:2 -15 90633954 . G A 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26003;SOR=0;LSEQ=AAGGGCAGGATAAGAAGTCT;RSEQ=CAGGCCATGGCAGGGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:2,1:5,110:0.0254:1,2:8.7:1:26:1:0.00886:39.29:60:6:0.0261:0:1 0/0:90:0:0,0:4,85:0:1,0:20.4:1:32.1:1:1:0:60:178:0.9889:0:0.1 -15 90634287 . GCA G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAACCTTTGTCCCATGAAC;RSEQ=CACACAGTGTGGGGCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:16:1:33.5:1:0.33333:0:60:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 90634599 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02041;SOR=0.1581;LSEQ=GGGGACAGGCCCCCGCCTGA;RSEQ=GACTTCTGAACAATTAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:23:23,0:4,0:0.8519:0,1:24.8:1:30.2:1:1:0:60:22:0.8462:0:1.1 0/1:13:6:6,0:7,0:0.4615:0,0:17:1:28.2:1:1:0:60:5:0.4167:0:2.2 -15 90634678 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1852;SOR=Inf;LSEQ=AGAGCTGCTGCTGCCTACCA;RSEQ=GACAACGGGGGGGTCCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:132,5:0:1,0:25.1:1:32.4:1:1:0:60:136:1:0:0.2 0/1:104:2:1,1:99,3:0.0192:1,2:17:1:32:0:0.0758:28.74616:60:4:0.0192:0:1 -15 90634684 . CG C 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.20014;SOR=0.71201;LSEQ=GCTGCTGCCTACCAGGACAA;RSEQ=GGGGGGTCCTAGGGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:159:111:106,5:42,3:0.6981:2,1:24.9:1:32.1:1:0.69075:1.51:59.9:222:0.707:0.1132:0.1 1/0:119:74:68,6:44,1:0.6218:1,2:26.4:1:31.1:1:0.25142:3.84738:59.9:148:0.6325:0.0924:0.2 -15 90634941 . A G 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.02615;LSEQ=GAGGGGGGCCCTCTCCTCCC;RSEQ=GCCAGGCCCGCCCTTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:203:201:32,169:0,0:0.9901:0,2:24.3:1:30.7:1:1:0:60:39.2:0.9949:0:1.1 1/0:195:141:31,110:11,43:0.7231:2,2:22.6:1:29.7:1:0.84858:1.10:60:140:0.7292:0:1.1 -15 90634994 . GC G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00019;SOR=0.17334;LSEQ=AGAAAGCCAGGGCTCCAGCT;RSEQ=CCGGTGTCCACTCCCCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:27:0,27:0,40:0.403:1,1:24.3:1:31.5:1:1:0:60:54:0.4091:0.0299:0.6 0/1:58:6:0,6:0,52:0.1034:1,0:21.8:1:32.3:1:1:0:60:12:0.1034:0.0345:0.8 -15 90635649 . C CTCTT 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCTTCCTCCCTTTCTCTCT;RSEQ=TCTTTCTTGGCAGGGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:11:0:25.5:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:31.5:1:1:0:50:4:1:0:0 -15 90645546 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49968;SOR=Inf;LSEQ=CTTGCGAGGTGGGGGCTGTC;RSEQ=GGGCCGCCGGCGCCCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:121,61:0:2,0:21.2:1:30.6:1:1:0:60:59.667:1:0:0.2 0/1:199:2:1,1:125,72:0.0101:2,2:23:1:32:0:1:1.73098:60:4:0.0102:0:1 -15 90645566 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25235;SOR=Inf;LSEQ=AGGGCCGCCGGCGCCCAGGC;RSEQ=GGCCGCGAGCCTGAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:142,100:0:2,0:24.8:1:30.4:1:1:0:60:241:1:0:0.2 0/1:279:3:1,2:161,115:0.0108:2,2:5.3:1:29:1:0.57389:2.7897:60:6:0.0108:0:1.3 -15 90645573 . G T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37902;SOR=3.50149;LSEQ=CCGGCGCCCAGGCCGGCCGC;RSEQ=AGCCTGAGGCTCTGCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:1:0,1:157,114:0.0037:2,0:1:0:23:0:0.42279:0:60:2:0.0038:0:1 0/1:313:4:1,3:171,138:0.0128:2,2:21.8:1:26:1:0.33048:3.70281:60:8:0.0128:0:1 -15 90645593 . C T 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.41763;SOR=0.40947;LSEQ=GAGCCTGAGGCTCTGCAGAG;RSEQ=GAGCGCACGACCCGCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:4:1,3:171,148:0.0124:2,2:19.8:1:28.5:1:0.34318:3.45387:60:8:0.0127:0:1 0/0:392:2:0,2:203,187:0.0051:2,0:1:0:26:1:0.23182:0:60:4:0.0052:0:1 -15 90645601 . C T 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06853;SOR=Inf;LSEQ=GGCTCTGCAGAGCGAGCGCA;RSEQ=GACCCGCAGGTAGCCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:169,160:0:2,0:27.1:1:30.4:1:1:0:60:40.125:1:0:0.2 0/1:406:5:2,3:199,202:0.0123:2,2:32:1:29.2:1:1:1.47631:60:10:0.0126:0:1.6 -15 90645618 . G T 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17162;SOR=0.18846;LSEQ=GCACGACCCGCAGGTAGCCG;RSEQ=CCATCCCAAGCTGGAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:4:1,3:148,168:0.0125:2,2:5.5:1:28.5:1:0.62622:2.63548:60:8:0.0128:0:1.3 0/0:421:1:0,1:195,222:0.0024:2,0:1:0:23:0:1:0:60:2:0.0024:0:1 -15 91290552 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18887;SOR=0;LSEQ=TGAATCAAGTCCTTCCTCCC;RSEQ=TCAAAAAACATTGTGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:130,22:0.0129:2,2:36.5:1:29.5:1:0.27723:5.80143:60:4:0.0129:0:1 0/0:201:0:0,0:160,41:0:2,0:26.8:1:30.1:1:1:0:60:66:1:0:0.1 -15 91290600 . T C 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.13479;SOR=0.2831;LSEQ=TACCTAACTCCACTGATTTC;RSEQ=TTTTCCCTCACTTTTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:5:3,2:237,156:0.0126:2,2:23.4:1:31.2:1:1:1.01279:60:10:0.0126:0:1 0/0:558:2:1,1:338,217:0.0036:2,2:7.5:1:31:1:1:1.55627:60:4:0.0036:0:1 -15 91292193 . T G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAGGTGGGGTTTCACCATGT;RSEQ=GGCCAGGCTGGTCTCGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:28.5:1:1:0:60:4:1:0:1 -15 91292543 . T C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.11371;SOR=0;LSEQ=AAAAATTAGTTTTGTAGAGT;RSEQ=GGGGGGTTTCTTAAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:124,29:0.0191:2,2:20:1:25.3:1:0.47552:2.12527:60:2:0.0132:0:2 0/0:166:0:0,0:119,47:0:2,0:22.9:1:29.1:1:1:0:60:22.714:1:0:0.1 -15 91292544 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.62371;SOR=2.81205;LSEQ=AAAATTAGTTTTGTAGAGTT;RSEQ=GGGGGTTTCTTAAAATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:0,1:127,30:0.0063:2,0:22:0:14:0:0.1962:0:60:0:0:0:1 0/1:170:3:1,2:119,48:0.0176:2,2:30.3:1:28.3:1:0.2071:4.90482:60:6:0.0182:0:1 -15 91292908 . A G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCCGGGATACTGCTCTCA;RSEQ=GAAATTAGAATTTAGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:0:0,0:235,276:0:2,0:23.6:1:30.7:1:1:0:60:55.778:1:0:0.1 0/1:546:25:11,14:251,269:0.0458:2,2:25.3:1:31.4:1:0.68882:1.18719:60:50:0.046:0:1.1 -15 91292969 . G A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCAATGATTGGGATGATAT;RSEQ=GATGACTTTGATACTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:26:15,11:238,254:0.0502:2,2:21.3:1:30.2:1:0.42263:1.45:60:52:0.051:0:1.2 0/0:541:0:0,0:275,264:0:2,0:25:1:30.8:1:1:0:60:133.75:0.9963:0:0.1 -15 91293298 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22902;SOR=0;LSEQ=TCATTTGGAAGATGAAAGAG;RSEQ=TAACAATTATTTTATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:33,105:0.0143:2,2:20.5:1:27:1:0.42806:3.15:60:4:0.0145:0:1.5 0/0:152:0:0,0:41,109:0:2,0:22.4:1:30.6:1:1:0:60:49:0.9866:0:0.2 -15 91294897 . T C 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTAAAGGGAGAGGATCCA;RSEQ=ACAAAGTGGTGTGATTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:67,0:0:1,0:23.1:1:31.6:1:1:0:60:66:1:0:0 0/1:60:25:25,0:35,0:0.4167:1,1:28.7:1:31.4:1:1:0:60:50:0.4167:0:1 -15 91295363 . C T 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28547;SOR=0;LSEQ=TTGCATTCTAAAGATGAAGT;RSEQ=CCATTATGATTAATTACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:0,8:1,14:0.3478:1,0:26.8:1:30.3:1:1:0:59.4:16:0.3478:0:1.8 0/0:4:0:0,0:0,4:0:0,0:16.5:1:32:1:1:0:60:8:1:0:0 -15 91295410 . A ATT 49 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACAATTTTAGGTAGCTG;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:24.3:1:31.3:1:1:0:58.3:6:0.4286:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 91297987 . A T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05445;SOR=Inf;LSEQ=TAAGGGTTTCAAAATTATAC;RSEQ=TTTATTGAGTCTAGCCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:200,67:0:2,0:24.2:1:29.9:1:1:0:60:88:1:0:0.1 0/1:251:4:2,2:170,77:0.0159:2,2:9.3:1:23.5:1:0.59225:2.20015:60:3:0.0122:0:1.8 -15 91298024 . AT A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.63628;SOR=1.35875;LSEQ=TATAGTATGATTGGCTTAAC;RSEQ=TTTTTTTATTTGCAGTACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:7:3,4:288,173:0.015:2,2:30.9:1:31.1:1:0.43432:2.21572:60:14:0.0151:0.0021:0 0/1:544:11:5,6:306,226:0.0202:2,2:31.6:1:29.6:1:0.54136:1.62327:60:22:0.0204:0.0018:0.2 -15 91303269 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07395;SOR=Inf;LSEQ=GACTTAAGCAATCCTCCTGC;RSEQ=TTGGCCTCCCCAAAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:0:1,0:24:1:29.6:1:1:0:60:8.667:1:0:0.4 0/1:22:3:3,0:19,0:0.1364:1,0:11.3:1:30.3:1:1:0:60:6:0.1429:0:1.3 -15 91303325 . CT C 146 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.0961;SOR=1.80786;LSEQ=GCCACCATGCCTAGCCAAGA;RSEQ=TTTTTTTTTTTCCCTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:15:12,3:72,12:0.1471:2,2:17.2:1:30.7:1:0.69485:1.49325:59.3:14:0.1429:0.0588:0.6 0/1:126:30:24,6:75,14:0.2381:2,2:17.7:1:29.8:1:0.58148:1.33585:59.8:14:0.2258:0.0714:0.2 -15 91303355 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16843;SOR=0;LSEQ=TTTCCCTCAAAGAAAAATAT;RSEQ=AACAACATAATTATTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:134,41:0.0112:2,2:9:1:29.5:1:0.4193:3.24116:60:4:0.012:0:1 0/0:255:0:0,0:181,74:0:2,0:22.5:1:28:1:1:0:60:14.938:1:0:0.3 -15 91303814 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.49853;SOR=Inf;LSEQ=TTAATACGTTGTTCTCTTTT;RSEQ=TCTCTTCAGAAGGAAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:130,24:0:2,0:21.9:1:31.2:1:1:0:60:29.8:1:0:0.1 0/1:159:2:1,1:126,31:0.0126:2,2:26.5:1:28:1:0.36303:4.01635:60:4:0.0127:0:1 -15 91303818 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.49896;SOR=Inf;LSEQ=TACGTTGTTCTCTTTTCTCT;RSEQ=TTCAGAAGGAAACTTCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:135,29:0:2,0:22.5:1:31.3:1:1:0:60:53.667:0.9938:0:0.1 0/1:175:2:1,1:138,35:0.0114:2,2:26:1:27.5:1:0.37005:3.90177:60:4:0.0116:0:1 -15 91304138 . G GA 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00892;SOR=2.29546;LSEQ=GGCTGAAACACCAAGACTAG;RSEQ=AAAAAAAAATGAAAGCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:14:6,8:314,376:0.0198:2,2:28.4:1:30.3:1:1:1.11328:60:28:0.02:0:0.1 0/1:813:36:17,19:362,409:0.0443:2,2:30.6:1:29.8:1:1:1.01:59.4:72:0.0453:0.0025:0.4 -15 91306067 . A C 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02618;SOR=Inf;LSEQ=ACTTGTAGGGAAGGAAAGCC;RSEQ=GTAAAGAGTTTAAGAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:0:1,0:22.4:1:30.4:1:1:0:60:66:1:0:0.1 0/1:37:6:6,0:30,1:0.1622:1,0:22.3:1:31.5:1:1:0:60:12:0.1714:0:1 -15 91308699 . C G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22437;SOR=0;LSEQ=AGAAACAATTAAATTTCAGT;RSEQ=CTCTGGATAACCTTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:15,132:0.0134:2,2:31:1:29:0:0.20388:8.55:60:4:0.0136:0:1.5 0/0:165:0:0,0:21,143:0:2,0:23.6:1:31.3:1:1:0:60:81:0.9939:0:0.1 -15 91308705 . G C 75 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06419;SOR=Inf;LSEQ=AATTAAATTTCAGTCCTCTG;RSEQ=ATAACCTTTTTATTAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:13,114:0:2,0:22.1:1:31.1:1:1:0:60:62.5:1:0:0.1 0/1:149:5:0,5:17,127:0.0336:2,0:22:1:32.6:1:1:0:60:10:0.0342:0:1.4 -15 91308728 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.80625;LSEQ=AACCTTTTTATTAAATAGTT;RSEQ=GTGATTTGTAAAAAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:1:0,1:3,65:0.0145:1,0:23:0:28:0:1:0:60:2:0.0147:0:1 0/1:77:2:0,2:3,72:0.026:1,0:21:1:31:1:1:0:60:4:0.0263:0:2 -15 91310275 . T A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12419;SOR=Inf;LSEQ=TTTGTATTTATATCATTATT;RSEQ=TAAAATATATTAAAGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:119,247:0:2,0:23.6:1:30.1:1:1:0:60:365:1:0:0.1 0/1:378:4:3,1:109,265:0.0106:2,2:7:1:25.8:1:0.07983:7.25:60:8:0.0107:0:1 -15 91310290 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24865;SOR=Inf;LSEQ=TTATTTTAAAATATATTAAA;RSEQ=ACCACTAGAATACATATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:61,202:0:2,0:21.9:1:31.5:1:1:0:60:262:1:0:0 0/1:268:3:1,2:53,212:0.0112:2,2:20.7:1:29.7:1:0.49231:1.99:60:6:0.0112:0:1 -15 91312313 . G A 205 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=204.56313;LSEQ=TTTGAAGACCACAGAATCAT;RSEQ=AGGTGATGTGTTTCAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:1,0:245,64:0.0032:2,0:40:0:13:0:1:0:60:0:0:0:1 0/1:373:149:113,36:160,63:0.3995:2,2:24.2:1:28.5:1:0.40406:1.24:60:148:0.4011:0:1.1 -15 91312650 . A AT 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17399;SOR=1.54992;LSEQ=CAAGTAGTCTGAAAAGCAGT;RSEQ=TTTTTTTTTCCAACTAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:16:10,6:355,272:0.0249:2,2:28.1:1:30.2:1:0.7998:1.28:60:15:0.0237:0.0047:0.2 0/1:762:29:14,15:424,307:0.0381:2,2:29.1:1:29.7:1:0.34009:1.47895:59.8:28:0.0371:0:0.2 -15 91312823 . T C 218 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CTCAGACCTCAGGTGTAAGT;RSEQ=GTTGCACGTCACGTATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:132,304:0:2,0:24.1:1:30.1:1:1:0:60:61.286:0.9977:0:0.1 0/1:409:171:57,114:82,153:0.4181:2,2:23.5:1:29.5:1:0.75198:1.07168:60:41.75:0.4154:0:1.2 -15 91312859 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21343;SOR=Inf;LSEQ=TTTGAGAACCCTGGGGCAGT;RSEQ=ACTGCCAGAGCTGCTACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:38,192:0:2,0:22.2:1:31.3:1:1:0:60:114:1:0:0.1 0/1:198:2:1,1:39,156:0.0101:2,2:31:0:30.5:1:0.36569:3.96:60:4:0.0102:0:1 -15 91325622 . A C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAGACTCTGTCTCAAAA;RSEQ=AAAACAAAACAAAACAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:21.7:1:31.7:1:1:0:52.7:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 91325922 . C T 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCATGACCTAATTATCTC;RSEQ=CGGAGGCTCCAACTCCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:38,2:0:2,0:27.1:1:30.9:1:1:0:60:80:1:0:0.1 0/1:31:14:13,1:17,0:0.4516:1,1:20.4:1:31:1:0.45161:0:60:28:0.4667:0:1.1 -15 91326099 . C T 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGAAATACTATGTATTAC;RSEQ=GAAAAAGCCTAAAAAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:0:0,0:324,276:0:2,0:24.4:1:30.3:1:1:0:60:65.667:1:0:0.1 0/1:670:21:13,8:338,309:0.0313:2,2:25.9:1:30:1:0.50648:1.48:60:20:0.0305:0:1.1 -15 91328376 . C G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01434;SOR=Inf;LSEQ=AGCATATAACCAAACATGCA;RSEQ=ATGTAGAATGCAAACTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:8,111:0:2,0:24:1:32.8:1:1:0:60:58.5:1:0:0 0/1:122:7:2,5:14,101:0.0574:2,2:12.3:1:31.1:1:0.2287:2.85:60:14:0.0579:0:1 -15 91333714 . CATATT C 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00151;SOR=Inf;LSEQ=AAGTTATCAGTATAAAAACT;RSEQ=AGTTATACTAAATAGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:0:1,0:20.9:1:29.3:1:1:0:60:28:1:0:0.1 0/1:13:5:5,0:8,0:0.3846:0,0:12.8:1:32.1:1:1:0:60:10:0.3846:0.0769:0 -15 91334179 . G A 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGTTTTCCTTAAATAATC;RSEQ=TAGAAAAATAGAGGAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:0,46:0:1,0:25.8:1:32:1:1:0:60:45:1:0:0 0/1:38:18:0,18:0,20:0.4737:1,1:27.3:1:30:1:1:0:60:36:0.4737:0:1.2 -15 91334258 . T A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00312;SOR=Inf;LSEQ=AAAAGTGGTAAGTGCTTATT;RSEQ=TGTAAAACTCAAATGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:0:1,0:20.9:1:30:1:1:0:60:34:1:0:0 1/0:10:5:0,5:1,4:0.5:2,0:15.8:1:30.4:1:1:0:60:10:0.5:0:1.6 -15 91337479 . G A 249 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=476.91975;LSEQ=CATTACTGTGAAAATATAAC;RSEQ=GAATGCAGGAGAATACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:623:1:0,1:333,289:0.0016:2,0:7:0:17:0:0.46549:0:60:0:0:0:3 0/1:702:303:154,149:206,192:0.4316:2,2:24.8:1:30.3:1:0.81935:1.03805:60:100:0.4317:0:1.1 -15 91337623 . AT A 171 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=76.69193;LSEQ=TTAAAATTCTTTATAATTAA;RSEQ=TTTTTTTCTCTTACTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:0,1:14,113:0.0078:2,0:33:0:33:0:1:0:60:2:0.0079:0:0 0/1:132:50:8,42:10,72:0.3788:2,2:25.9:1:30.4:1:0.6046:1.37:60:100:0.3906:0.0303:0.1 -15 91341599 . T G 213 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTTGAATGTTTGAGTTAC;RSEQ=TCAATTGAAATTGAACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:65,197:0:2,0:22.9:1:30:1:1:0:60:51.4:1:0:0.1 0/1:277:125:39,86:46,106:0.4513:2,2:23.7:1:30.6:1:0.89631:1.04:60:250:0.4562:0:1.1 -15 91346630 . C CA 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14547;SOR=2.91678;LSEQ=ACAGAAATGAGTGTCTGTGC;RSEQ=GGGGTTTGTGATCTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:23:21,2:13,0:0.6389:1,2:23:1:31.2:1:0.5254:0:60:46:0.6389:0.1667:0 1/1:25:21:21,0:4,0:0.84:0,1:26.4:1:28.5:1:1:0:60:20:0.8333:0.28:0.1 -15 91346700 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1416;SOR=Inf;LSEQ=TTAGCCTCTTCTATTTGAGG;RSEQ=TGATGATATACGTACATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:140,10:0:2,0:23.5:1:31.4:1:1:0:60:74:1:0:0.1 0/1:91:2:1,1:82,7:0.022:2,2:6.5:1:26.5:1:0.16899:11.02463:60:4:0.023:0:1 -15 91346923 . C A 227 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGATGCTCGGAAATAAAGC;RSEQ=CAAACTGTACTAAATGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:0:0,0:207,339:0:2,0:26.6:1:30.9:1:1:0:60:67.25:1:0:0.1 0/1:547:199:81,118:140,206:0.3638:2,2:26.8:1:29.8:1:1:1.01:60:98.5:0.3662:0:1.1 -15 91347135 . C A 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00102;SOR=Inf;LSEQ=TCAACCCAAGTAATATGACA;RSEQ=CTGTCAAAAGTAATTTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:6,14:0:2,0:21:1:30.2:1:1:0:60:9:1:0:0.5 1/0:12:6:2,4:2,4:0.5:2,2:15.2:1:30.7:1:1:1:60:12:0.5:0:1 -15 91347297 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51889;SOR=0;LSEQ=ACTATCTGCATGACAGAATA;RSEQ=AATTGCCCCCCAAAAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:72,9:0.0241:2,2:10:1:29.5:1:0.22774:7.64189:60:4:0.0244:0:2 0/0:54:0:0,0:52,2:0:1,0:25.2:1:32.6:1:1:0:60:108:1:0:0.8 -15 91347302 . G A 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.83733;SOR=1.11127;LSEQ=CTGCATGACAGAATAGAATT;RSEQ=CCCCCCAAAAATGCAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:73:63,10:17,2:0.7935:2,2:21:1:28.6:1:1:1.34507:60:72:0.8:0:1.1 1/1:58:47:46,1:10,1:0.8103:2,1:26.3:1:28.9:1:0.34604:4.43:60:94:0.8103:0:1 -15 91347755 . A G 87 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGCTGGAGTGCTGTGGC;RSEQ=TGATCATGACTCACTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:31:1:32.6:1:1:0:60:10:1:0:2 1/1:8:7:1,6:0,1:0.875:0,2:16.4:1:31.3:1:1:0:60:14:0.875:0:1.1 -15 91347784 . C T 63 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ACTCACTGCAGCCTCAACCT;RSEQ=CTGGGCTCAAGTGATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:34:1:31.5:1:1:0:60:8:1:0:2 0/1:3:1:0,1:1,1:0.3333:2,0:25:0:31:0:1:0:60:2:0.3333:0:2 -15 91351930 . G A 44 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AGTAACAATTTGGTTATGCC;RSEQ=TCTAGGGTGGGGTGTACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:29:1:28.3:1:1:0:60:6:0.75:0:1.7 0/0:1:0:0,0:1,0:0:0,0:47:0:29:0:1:0:60:2:1:0:0 -15 91352248 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13816;SOR=Inf;LSEQ=TACAAAATTGGCCTGTGTTC;RSEQ=CAGTACCCTGCAGTTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:0:1,0:29:1:31.8:1:1:0:60:120:1:0:0 0/1:36:2:2,0:34,0:0.0556:1,0:29.5:1:32.5:1:1:0:60:4:0.0556:0:1 -15 91352501 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11059;SOR=0;LSEQ=CATCGCCAGGTTAGTACACA;RSEQ=CCATGTGTGTTCTCTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:1,2:81,217:0.01:2,2:27:1:25.3:1:1:1.34:60:2:0.0068:0:2 0/0:325:0:0,0:87,237:0:2,0:23.2:1:31.8:1:1:0:60:80:0.9969:0:0.1 -15 91352774 . A G 73 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGATCAGAGCCCTGGGT;RSEQ=CCAGTTCCAGATCTGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:0.7143:0,2:38.2:1:31.8:1:1:0:60:10:0.7143:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 91354377 . TA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.24482;SOR=0;LSEQ=GCGTGTCTCTTCATATACAC;RSEQ=AAAACACGTGGACCAGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:132,33:0.012:2,2:48:1:31:1:0.36671:3.95564:60:4:0.0123:0:0 0/0:170:0:0,0:127,43:0:2,0:23.6:1:28:1:1:0:60:84:1:0:0.1 -15 91354494 . G A 117 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=14.38961;LSEQ=GAGGCCCCGGAAGAAGTGCC;RSEQ=CTGAGGAGCTCGACGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:1:1,0:239,211:0.0022:2,0:1:0:29:0:1:0:60:2:0.0022:0:1 0/1:549:17:9,8:289,243:0.031:2,2:24.3:1:28.7:1:1:1.05702:60:16:0.0294:0:1.6 -15 91354505 . C T 236 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=375.1691;LSEQ=AGAAGTGCCGCTGAGGAGCT;RSEQ=GACGAGGAAATACCCGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:1:0,1:242,210:0.0022:2,0:1:0:27:0:0.46578:0:60:2:0.0022:0:1 0/1:576:261:144,117:168,144:0.4531:2,2:23.7:1:29.5:1:0.8006:1.05:60:260:0.4577:0:1.1 -15 91354520 . C T 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCTCGACGAGGAAATACC;RSEQ=GTATCTTCCCACTACTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:271,192:0:2,0:23.2:1:30.3:1:1:0:60:65.143:1:0:0.1 0/1:602:36:21,15:311,251:0.0598:2,2:22.9:1:31.1:1:0.86295:1.13:60:72:0.0609:0:1.2 -15 91354521 . G A 154 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.12306;LSEQ=AGCTCGACGAGGAAATACCC;RSEQ=TATCTTCCCACTACTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:465:1:1,0:273,191:0.0022:2,0:1:0:25:0:1:0:60:2:0.0022:0:1 0/1:606:37:18,19:319,249:0.0611:2,2:23.1:1:29.7:1:0.39677:1.3516:60:74:0.0619:0:1.4 -15 91357029 . G C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCCTTTCCACCGACCCAGT;RSEQ=TGCTCCCCGGATTGAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:32:1:1:0:60:4:1:0:1.5 -15 91358271 . G GGAA 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=3.0731;LSEQ=TAGCTCTGTGCAGGTTGAGA;RSEQ=GAAGGTCATTCATTTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:69:64,5:54,7:0.5308:2,2:30:1:30.9:1:0.54633:1.65:60:68:0.5271:0:0.2 1/0:202:157:128,29:39,5:0.7772:2,2:21.4:1:29.9:1:0.36372:1.76272:59.8:156:0.78:0.2129:0.1 -15 91359755 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGTGACGTTACTCAGGAG;RSEQ=GTGTAGCTGGGGAGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 91792303 . C T 83 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATACATCTACGTTTTCACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:3,4:5,4:0.35:2,2:23.3:1:29.9:1:1:1.61372:60:14:0.4375:0:1.1 0/0:2:0:0,0:1,0:0:0,0:28:0:33:0:1:0:60:2:1:0:0 -15 91792337 . CAT C 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=19.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACACACACACACACACACA;RSEQ=GTTTATGATCTGGCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,5:0.3333:0,0:27.5:1:32.5:1:1:0:60:4:0.3333:0.1667:1.5 0/0:1:0:0,0:0,1:0:0,0:14:0:32:0:1:0:60:2:1:0:0 -15 92757222 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50187;SOR=0;LSEQ=ACAACGCCTTTCAAACTCTT;RSEQ=TACCAACTTCTGGAGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:29,27:0.0345:2,2:26:1:30.5:1:1:1.07272:60:4:0.0364:0:1 0/0:46:0:0,0:25,21:0:2,0:30.5:1:29.3:1:1:0:60:45:1:0:0.2 -15 92829095 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2014;SOR=0;LSEQ=CATGTATGTGGACATGAGCC;RSEQ=CCTGAGGCCCCAGAACTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:78,76:0.0128:2,2:37.5:1:28.5:1:1:1.02615:60:4:0.0132:0:1 0/0:191:0:0,0:108,83:0:2,0:25.7:1:29.9:1:1:0:59.8:30.833:1:0:0.2 -15 92829116 . T C 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25679;SOR=Inf;LSEQ=CCTGAGGCCCCAGAACTATC;RSEQ=TTTCGGTTGTGAACTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:88,86:0:2,0:27.8:1:30.1:1:1:0:59.9:23.857:1:0:0.2 0/1:216:3:1,2:114,99:0.0139:2,2:40.3:1:27:1:0.6003:2.2944:60:2:0.0095:0:1.3 -15 92829136 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50025;SOR=Inf;LSEQ=TTTTCGGTTGTGAACTAAAG;RSEQ=CCGACAAAGATTACCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:93,83:0:2,0:26.7:1:31.1:1:1:0:59.9:18.556:1:0:0.2 0/1:197:2:1,1:103,91:0.0102:2,2:32:1:28:1:1:1.13115:60:4:0.0105:0:1 -15 92829186 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24803;SOR=0;LSEQ=AATGATGAAAATGGACACCA;RSEQ=TTATTTTTAAGAACAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:3:1,2:97,90:0.0158:2,2:26:1:24:1:0.61137:2.14715:60:2:0.0107:0:2 0/0:188:0:0,0:88,100:0:2,0:24.3:1:31.2:1:1:0:60:187:1:0:0.1 -15 92829220 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24271;SOR=Inf;LSEQ=CAGTCAGTTTAGGGGCGGGT;RSEQ=CAAAGGATGAATTGGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:89,101:0:2,0:27:1:32.1:1:1:0:60:380:1:0:0.2 0/1:185:2:1,1:81,102:0.0108:2,2:30.5:1:28:1:1:1.26:60:4:0.011:0:1 -15 92829291 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49875;SOR=0;LSEQ=GTCCAATTAAAGTAACACTG;RSEQ=CAACTTTGAAAATGTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:60,47:0.0183:2,2:19:1:28:1:1:1.2737:60:4:0.0187:0:1 0/0:99:0:0,0:53,46:0:2,0:24.4:1:31.4:1:1:0:59.3:198:1:0:0.1 -15 92829320 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23298;SOR=Inf;LSEQ=AAAATGTCTGTACAGCCAAC;RSEQ=GTTTCCCTTGGGGACTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:84,43:0:2,0:20.3:1:30:1:1:0:59.5:62.5:1:0:0.1 0/1:119:2:1,1:72,45:0.0168:2,2:13:1:31:0:1:1.59341:60:4:0.0168:0:1 -15 92829336 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49823;SOR=Inf;LSEQ=CAACGGTTTCCCTTGGGGAC;RSEQ=CTGAAATAACACCACCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:90,52:0:2,0:22.6:1:30.5:1:1:0:60:46.333:1:0:0.1 0/1:142:2:1,1:86,54:0.0141:2,2:23:1:28.5:1:1:1.58714:60:4:0.0144:0:1 -15 92829360 . T A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24918;SOR=Inf;LSEQ=AAATAACACCACCAGTGATC;RSEQ=TACGGTTGAAGTGTGGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:115,78:0:2,0:25.4:1:30.1:1:1:0:59.5:26.571:1:0:0.2 0/1:208:3:1,2:118,86:0.0144:2,2:18.7:1:24:1:0.57593:2.73089:60:2:0.0098:0:3.3 -15 92829452 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0.08101;LSEQ=GAGTCAGAAGACGAAGAGGA;RSEQ=GAGGATGTGAGACTCTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:94:42,52:58,70:0.4234:2,2:21.6:1:30.2:1:1:1.02574:59.3:30.333:0.4155:0:1.1 0/1:179:10:6,4:74,95:0.0559:2,2:15.6:1:30.2:1:0.34558:1.92:60:20:0.0565:0:1 -15 92829486 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25183;SOR=0;LSEQ=TCTTAAGTATATCTGGAAAG;RSEQ=GGTCTGCCACTGGAGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:3:1,2:91,119:0.0141:2,2:22.7:1:24.7:1:1:1.52648:60:2:0.0094:0:1.3 0/0:185:0:0,0:88,96:0:2,0:25:1:30.5:1:1:0:59.9:91:0.9945:0:0.2 -15 92829541 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49864;SOR=Inf;LSEQ=GAAACAAGTAAAACTTGCTG;RSEQ=TGATGAAGATGATGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:69,92:0:2,0:24.9:1:31.6:1:1:0:59.9:79.5:1:0:0.2 0/1:167:2:1,1:77,88:0.012:2,2:32:1:31:0:1:1.14:60:4:0.0121:0:1 -15 92829554 . T C 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99215;LSEQ=CTTGCTGCTGATGAAGATGA;RSEQ=GGTGATGATGATTTTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:19:8,11:45,69:0.1429:2,2:28.2:1:30.8:1:1:1.11:60:38:0.1439:0:1.2 0/1:148:21:10,11:57,70:0.1419:2,2:21.2:1:29.2:1:0.81792:1.12:60:42:0.1458:0:1 -15 92829629 . CA C 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.60285;SOR=0.44298;LSEQ=TCTATACAAGATACTCCAGC;RSEQ=AAAAATGCACAAAAGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:31,59:0.0217:2,2:18.5:1:31.8:1:1:1.89:60:4:0.022:0.0109:0 0/0:103:1:0,1:45,57:0.0097:2,0:24:0:31:0:1:0:60:2:0.01:0:0 -15 92829642 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49948;SOR=Inf;LSEQ=CTCCAGCCAAAAAATGCACA;RSEQ=AAGTCAAATCAGAATAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:28,54:0:2,0:28.4:1:30.2:1:1:0:60:40:1:0:0.1 0/1:94:2:2,0:40,52:0.0213:2,0:21.5:1:30.5:1:0.19698:0:60:4:0.0215:0:1 -15 92830133 . TA T 49 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTTAAAGTATAATAATAA;RSEQ=AAAAAAAAAAGAAAAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0.75:0,2:24:1:31:1:1:0:60:6:0.75:0:0.3 1/1:1:1:0,1:0,0:1:0,0:41:0:28:0:1:0:60:2:1:0:0 -15 93545831 . G T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.49452;LSEQ=TAGGACAGGTGAGAGAAATC;RSEQ=GCATTTACATGTAAATACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:97:73,24:49,8:0.6299:2,2:24.6:1:31.1:1:0.15014:2.00507:60:194:0.6299:0:1.1 1/1:140:131:101,30:5,4:0.9357:2,2:22:1:30.7:1:0.22053:2.67:60:130:0.9353:0:1.1 -15 93545934 . T C 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00055;SOR=1.72427;LSEQ=GTTTGAGTCAAAAACAAATA;RSEQ=TAGCAAGAGTTATTGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:171:78,93:60,84:0.5429:2,2:23.1:1:31.8:1:0.49608:1.17:60:84.5:0.5452:0:1.1 1/0:372:250:110,140:61,60:0.672:2,2:25.9:1:31.2:1:0.26741:1.29302:60:61.5:0.6758:0:1.1 -15 94590208 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGTTTCTTTGCTCCGAA;RSEQ=GCTGACTTCATTTTAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:32.5:1:1:0:60:4:1:0:1 -15 94590782 . G GTATTTATT 55 d7;v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=8.000;MSILEN=4;SSF=0.04762;SOR=Inf;LSEQ=AACACAGTCCAAATTGAGAG;RSEQ=TATTTATTTATTTATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:29.3:1:32.3:1:1:0:60:8:1:0:0 1/1:5:4:4,0:1,0:0.8:0,0:26.8:1:27.8:1:1:0:60:8:0.8:0.4:0 -15 94590949 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21922;SOR=Inf;LSEQ=GAGCAGCATGTTTGTATATC;RSEQ=GGGACTTCTCTTCCAAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:102,36:0:2,0:24.4:1:30.2:1:1:0:60:33.5:1:0:0.3 0/1:122:2:1,1:86,34:0.0164:2,2:30.5:1:28.5:1:0.49316:2.50748:60:4:0.0172:0:1 -15 94590966 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61943;SOR=2.05669;LSEQ=ATCAGGGACTTCTCTTCCAA;RSEQ=CTGTGGAAGCAATTGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:121,48:0.0059:2,0:1:0:26:0:0.28824:0:60:2:0.0061:0:2 0/1:166:2:1,1:103,61:0.012:2,2:10.5:1:29:1:1:1.68289:60:4:0.0123:0:2 -15 94590975 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22331;SOR=Inf;LSEQ=TTCTCTTCCAAGCTGTGGAA;RSEQ=CAATTGGTGTGCCCATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:136,61:0:2,0:25.8:1:31.8:1:1:0:60:38.4:1:0:0.4 0/1:177:2:1,1:102,73:0.0113:2,2:27:1:27.5:1:1:1.39455:60:4:0.0118:0:2 -15 94590981 . G T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36368;SOR=3.14281;LSEQ=TCCAAGCTGTGGAAGCAATT;RSEQ=GTGTGCCCATAATTGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:0,1:139,70:0.0048:2,0:9:0:15:0:0.3381:0:60:0:0:0:4 0/1:202:3:1,2:116,83:0.0149:2,2:12:1:28.7:1:0.57381:2.78101:60:6:0.0153:0:1.7 -15 94591032 . T G 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.37684;SOR=1.17718;LSEQ=TGTCCAAGAAGCCTGGTTCT;RSEQ=ATTTTGAGAGATAAAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:155:79,76:66,51:0.5699:2,2:25.2:1:31.4:1:0.3923:1.24396:60:76.5:0.5667:0:1.1 1/0:256:156:78,78:46,54:0.6094:2,2:24.7:1:31:1:0.60835:1.17:60:77:0.6063:0:1.2 -15 94591097 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50329;SOR=0;LSEQ=TGGAGATGGGATAAAATTGG;RSEQ=GGCTCCCTGGAGGCCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:53,124:0.0112:2,2:43.5:1:30:1:0.51353:2.33:60:4:0.0116:0:1 0/0:147:0:0,0:51,96:0:2,0:24.6:1:29.8:1:1:0:60:48:1:0:0.7 -15 94591107 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20751;SOR=Inf;LSEQ=ATAAAATTGGAGGCTCCCTG;RSEQ=AGGCCTGGTGGGAAGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:37,113:0:2,0:21.6:1:30.8:1:1:0:60:49:1:0:0.6 0/1:126:2:1,1:36,88:0.0159:2,2:18:1:25.5:1:0.50273:2.42:60:4:0.0163:0:2 -15 94591144 . A G 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.065;SOR=2.05533;LSEQ=TGATCTGAAAATTGTGATCA;RSEQ=ATTTTTTGCCCCATTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:37:4,33:2,34:0.5068:2,2:21.8:1:29.7:1:0.6741:2.04:60:8.25:0.4783:0:1.2 1/0:50:34:6,28:2,14:0.68:2,2:21.3:1:30.6:1:1:1.49:60:68:0.68:0:1.1 -15 94711926 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52801;SOR=Inf;LSEQ=TTGTGCACTATCCATGCCAA;RSEQ=TGTGTAACAATTATGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:31,31:0:2,0:23.3:1:30.7:1:1:0:60:124:1:0:0.1 0/1:103:2:1,1:55,46:0.0194:2,2:8:0:33:0:1:1.19357:60:4:0.0194:0:2 -15 94711951 . G A 192 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAACAATTATGCCAAAAGTC;RSEQ=TCCAGCTAGCACATCTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:30,34:0:2,0:28.1:1:30.8:1:1:0:60:63:1:0:0.1 1/1:106:88:44,44:10,8:0.8302:2,2:31.2:1:29.8:1:0.79731:1.24737:60:87:0.8286:0:1.1 -15 94711966 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53714;SOR=Inf;LSEQ=AAGTCGTCCAGCTAGCACAT;RSEQ=TCATACGTAGAGAAGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:27,34:0:2,0:28.3:1:31.5:1:1:0:60:60:1:0:0.1 0/1:109:2:1,1:50,57:0.0183:2,2:13.5:1:27.5:1:1:1.14:60:4:0.0187:0:1 -15 94711987 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13838;SOR=0;LSEQ=TCATACGTAGAGAAGGTCCT;RSEQ=AAGAATCCTCTATGATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:17,36:0.0364:2,2:27.5:1:28:1:1:2.09:60:4:0.0364:0:1 0/0:92:0:0,0:39,53:0:2,0:24.7:1:28.2:1:1:0:60:45:1:0:0.9 -15 95084911 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02108;SOR=Inf;LSEQ=TGTCCTGACTTACTAAGATA;RSEQ=TGAGATGTCTACAGGGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:56,0:0:1,0:25:1:32.3:1:1:0:60:55:1:0:0.2 0/1:36:4:4,0:32,0:0.1111:1,0:28.8:1:31:1:1:0:60:8:0.1212:0:1 -15 95084941 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49725;SOR=0;LSEQ=TACAGGGCTAGGTAGGATTT;RSEQ=GAATACATATGGCTAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:73,3:0.0253:1,2:22:1:29.5:1:0.10057:21.21721:60:4:0.0256:0:1 0/0:74:0:0,0:71,3:0:1,0:20.4:1:31.6:1:1:0:60:73:1:0:0.3 -15 95084954 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23895;SOR=Inf;LSEQ=AGGATTTGGAATACATATGG;RSEQ=TAGAAATTTTAATTGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:96,7:0:2,0:21.8:1:32:1:1:0:60:102:1:0:0.1 0/1:99:2:1,1:87,10:0.0202:2,2:23.5:1:28.5:1:0.21088:8.34147:60:4:0.0206:0:1.5 -15 95085045 . TC T 94 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06294;SOR=0.24478;LSEQ=TAATCAAGCGGATTTTGGCA;RSEQ=CCCCCCTTTTTTAAAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:493:8:3,5:265,220:0.0162:2,2:19.3:1:31.5:1:0.47843:2.00473:60:16:0.0167:0.0061:0.9 0/0:498:2:2,0:261,235:0.004:2,0:47:1:29:0:0.50058:0:60:4:0.0041:0:1 -15 95085074 . T C 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.28862;LSEQ=TTTTTAAAAGTTTTATCTTA;RSEQ=ATCCTCTGCCCCATTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:503:317:164,153:89,95:0.6302:2,2:26.6:1:31.9:1:0.51658:1.14:60:78.25:0.631:0:1.1 0/1:510:168:85,83:167,172:0.3294:2,2:25.2:1:30.9:1:0.85036:1.05:60:167:0.33:0:1.1 -15 95085088 . T C 204 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=57.66146;LSEQ=ATCTTATATCCTCTGCCCCA;RSEQ=TTTCAAGACCATTCATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:2:1,1:229,243:0.0042:2,2:35.5:1:31:1:1:1.06:60:4:0.0043:0:1 0/1:462:91:45,46:170,200:0.197:2,2:24.6:1:31.5:1:0.5597:1.15:60:182:0.1978:0:1.2 -15 95085160 . G A 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05477;SOR=6.93728;LSEQ=GTGCTTAAACAGACACCATC;RSEQ=CATGGTTTCAGGCACATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:43,144:0.0053:2,0:27:0:32:0:1:0:60:2:0.0054:0:1 0/1:167:6:2,4:42,117:0.0359:2,2:23.8:1:27.8:1:0.65786:1.39:60:5:0.0305:0:1.2 -15 95085372 . T C 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCAGAAATGCAAACTAAA;RSEQ=TGACCAATTATCAATGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:32:1:32.5:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 95792165 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58106;SOR=2.6314;LSEQ=CAACCCCACTTCTAGGGAGG;RSEQ=AAGGGGGCGCACTTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:1,0:175,40:0.0046:2,0:5:0:31:0:1:0:60:2:0.0048:0:1 0/1:165:2:1,1:124,39:0.0121:2,2:47:1:28:1:0.4272:3.15212:60:4:0.0123:0:1 -15 95792273 . C G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0975;LSEQ=GATTCCAGCTACTTCTGGTT;RSEQ=TCGGTCCTGGTTTTACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:560:529:249,280:17,14:0.9446:2,2:25.4:1:31.6:1:0.46106:1.36469:60:87.167:0.944:0:1.1 1/0:588:367:190,177:107,114:0.6241:2,2:25:1:31.1:1:0.44442:1.14:60:90.75:0.6291:0:1.1 -15 97474261 . T C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAGTTTCCTTCAAGAGTC;RSEQ=TCCTGTCTGGAGTCCTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:17.9:1:30.4:1:1:0:60:14:1:0:2 1/1:5:5:3,2:0,0:1:0,2:18:1:31.4:1:1:0:60:10:1:0:2.2 -15 97474303 . G GC 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.73799;SOR=0.64449;LSEQ=GTCTATGTTTCTTACCAGCA;RSEQ=CCCCCCACTGCACCCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:4,5:6,3:0.5:2,2:26.3:1:32:1:0.63719:2.37182:60:18:0.5:0.1111:2 0/1:18:7:4,3:7,4:0.3889:2,2:32.1:1:30.6:1:1:1.29262:60:14:0.3889:0:2.1 -15 97474330 . G C 136 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00204;SOR=0;LSEQ=ACTGCACCCTGACTCCTGCT;RSEQ=TTTTCTTATGCCTGTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:11,8:0,0:1:0,2:25.6:1:32.2:1:1:0:60:38:1:0:2.2 1/0:23:14:8,6:4,5:0.6087:2,2:30.3:1:30.4:1:0.68017:1.63:60:13:0.5909:0:2.2 -15 97474355 . T C 114 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01047;SOR=0;LSEQ=CTTATGCCTGTCCATGTGCC;RSEQ=TCCTTTAAAGATTCTGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:7,7:0,0:1:0,2:20.9:1:30.2:1:1:0:60:13:1:0:2.2 1/0:18:11:5,6:3,4:0.6111:2,2:17.5:1:30.2:1:1:1.10:60:22:0.6111:0:2.2 -15 97475636 . TA T 50 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAGGCAATCATCTGATCT;RSEQ=AAAAAAAAAAGTCTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:29.7:1:32:0:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 97475981 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24385;SOR=0;LSEQ=TACAACCAAGAAAAATAAGT;RSEQ=GTGAGGACAAGGGCCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:143,35:0.0111:2,2:25:1:29:1:0.36089:4.04263:60:4:0.0112:0:1 0/0:184:0:0,0:127,57:0:2,0:24.2:1:29.8:1:1:0:60:35.8:1:0:0.1 -15 97476082 . T C 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34694;SOR=1.14727;LSEQ=CAGTGGATTATCCTTGGAAT;RSEQ=GACTTACCTCTGGGCTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:154:66,88:114,146:0.372:2,2:28.5:1:30.5:1:0.91834:1.04101:60:153:0.3714:0:1.1 0/1:388:157:72,85:109,119:0.4046:2,2:27.5:1:30:1:0.75553:1.08113:60:77.5:0.4036:0:1.2 -15 97476200 . C CA 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05926;SOR=0.46243;LSEQ=TTTAACAAATGTCTTCATTA;RSEQ=AAAAAAAACCCTGAAATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:58:2,56:3,10:0.7838:2,1:29.9:1:30.3:1:0.03959:8.02043:59.6:28:0.7778:0:0.4 1/0:64:40:2,38:1,21:0.625:1,2:28.3:1:31.1:1:1:1.10:59.9:80:0.6349:0.0156:0.1 -15 97476271 . T C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.59931;LSEQ=TTAAAGATGCGTTGATTTGA;RSEQ=TCTACTAGGAAAGCAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:0,7:0.5333:0,0:24.9:1:33.5:1:1:0:60:16:0.5333:0:1.3 0/1:5:2:0,2:0,3:0.4:0,0:13:1:31.5:1:1:0:60:4:0.4:0:1 -15 98674720 . C T 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TACTTTGTGCTTCCTGAGAT;RSEQ=TCCTCCTAAATGAACAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:80,4:0:1,0:23:1:30.9:1:1:0:60:41:1:0:0.6 0/1:70:12:10,2:55,3:0.1714:2,2:22.3:1:29.9:1:0.20075:3.5742:60:24:0.1739:0:1.1 -15 98674754 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=ACAACTTGCATCCAAACCTT;RSEQ=CTTTCAATGTCATCTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:127,32:0:2,0:22.5:1:31.2:1:1:0:60:78.5:1:0:0.7 0/1:161:2:1,1:118,41:0.0124:2,2:21.5:1:27:1:0.45489:2.8556:60:4:0.0126:0:2 -15 98674766 . A G 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02531;SOR=0.61689;LSEQ=CAAACCTTCCTTTCAATGTC;RSEQ=TCTTCTGGGGAAGCCCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:76:61,15:94,30:0.38:2,2:24.3:1:30.3:1:0.49102:1.30:60:152:0.3838:0:2.2 0/1:197:54:36,18:105,38:0.2741:2,2:22.3:1:29.8:1:0.37825:1.37928:60:53:0.2718:0:2.1 -15 98674786 . A G 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00326;SOR=0.58432;LSEQ=ATCTTCTGGGGAAGCCCAAC;RSEQ=ACTAGAGCTATGAAGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:112:77,35:111,60:0.3958:2,2:24.5:1:29.8:1:0.52256:1.19:60:36.333:0.3893:0:2.1 0/1:282:78:46,32:130,73:0.2766:2,2:23.9:1:29.8:1:0.49147:1.23786:60:38:0.2734:0:2.2 -15 98674828 . C T 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=56.26436;LSEQ=TCATTGACTTCAGATCCATT;RSEQ=CTGCTCTACAATTTTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:1:0,1:217,183:0.0025:2,0:38:0:28:0:0.45885:0:60:2:0.0025:0:1 0/1:397:49:30,19:188,160:0.1234:2,2:29.1:1:28.9:1:0.36192:1.34:60:98:0.1247:0:1.1 -15 98674857 . T C 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.50785;LSEQ=CAATTTTGCTTCCTAAATAT;RSEQ=GCACAAATGTGTCTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:178:90,88:103,124:0.4395:2,2:25.1:1:30.4:1:0.31723:1.23:60:177:0.4392:0:1.5 0/1:397:113:56,57:138,146:0.2846:2,2:24.7:1:29.7:1:0.91155:1.04:60:226:0.2861:0:1.4 -15 98674903 . A T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11875;SOR=0;LSEQ=AGCCCACTGTTTCTGAGTTC;RSEQ=GAACCTCATCCTTTCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:109,179:0.0103:2,2:14.7:1:27:1:0.56007:3.27:60:2:0.007:0:2.3 0/0:300:0:0,0:109,191:0:2,0:24.8:1:30.5:1:1:0:60:149:1:0:0.4 -15 99192745 . TTTTC T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.06231;SOR=Inf;LSEQ=CCTTTCATTTCCTTTTTTTC;RSEQ=TTTTCTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:234,46:0:2,0:21.2:1:29:1:1:0:57.5:17.667:1:0:1.4 0/1:304:5:5,0:239,55:0.0164:2,0:25.8:1:28.2:1:0.58847:0:54.2:4:0.0138:0.0033:1.4 -15 99192747 . TTC T 47 v4;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.10825;SOR=0;LSEQ=TTTCATTTCCTTTTTTTCTT;RSEQ=TTTTCTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:0,3:235,44:0.0105:2,0:11.3:1:29.8:1:0.00438:0:56:6:0.0112:0.0035:0.3 0/0:313:0:0,0:239,57:0:2,0:24.1:1:28.1:1:1:0:58.7:11.333:0.9819:0:1.4 -15 99226021 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18145;SOR=Inf;LSEQ=TCCTGATTAGGTGATCCACC;RSEQ=GCCTCTGCCTCCCAAAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:93,2:0:1,0:26:1:30.3:1:1:0:60:30.667:1:0:0.1 0/1:71:2:1,1:63,6:0.0282:2,2:11.5:1:26.5:1:0.18873:9.79798:60:4:0.0286:0:1 -15 99226148 . C G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.92147;LSEQ=CAGTGGTTATACTTTTCTTG;RSEQ=TATGCATTTAAGTTGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:491:291:161,130:104,95:0.5927:2,2:26.2:1:31.5:1:0.51927:1.13:60:71.75:0.5942:0:1.1 1/1:473:383:206,177:52,36:0.8097:2,2:25.7:1:30.8:1:0.40657:1.24053:60:75.6:0.8094:0:1.1 -15 99226256 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49958;SOR=0;LSEQ=CAGTGTATCTCGTGTGCACT;RSEQ=CTAGATATTCTGATCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:37,154:0.0104:2,2:17.5:1:29:1:0.35584:4.12:60:4:0.0104:0:1 0/0:177:0:0,0:38,139:0:2,0:20.7:1:31.7:1:1:0:60:87.5:1:0:0.1 -15 99227648 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGGGGAGGTGGGGGGTG;RSEQ=GGGCGGATGAATATAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:28:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:31.5:1:32:1:1:0:60:4:1:0:1 -15 99250709 . A G 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26091;SOR=0;LSEQ=AATAATACAGGATTCCTGAA;RSEQ=ACCAACTGTATTATTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:2,1:156,20:0.0168:2,2:22.3:1:28:1:0.31382:3.85324:60:2:0.0115:0:1.3 0/0:137:0:0,0:120,17:0:2,0:21.1:1:29.8:1:1:0:60:26.4:1:0:0.1 -15 99250711 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19116;SOR=Inf;LSEQ=TAATACAGGATTCCTGAAAA;RSEQ=CAACTGTATTATTGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:162,24:0:2,0:22:1:31.7:1:1:0:60:45.5:1:0:0.1 0/1:145:2:1,1:125,18:0.0138:2,2:17.5:1:28:1:0.24569:6.7853:60:4:0.014:0:1 -15 99250753 . C T 120 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=19.40321;LSEQ=AATAGTTTAAAAATTATTTC;RSEQ=TTCTAACTGAGACGTTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:1:1,0:290,116:0.0025:2,0:47:0:16:0:1:0:60:0:0:0:4 0/1:350:16:11,5:232,101:0.0457:2,2:18.6:1:30:1:1:1.04397:60:32:0.0461:0:1.2 -15 99251356 . C T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=10.10012;LSEQ=AGTAAGAATGATGCTGACTG;RSEQ=TGCTTTCTCTCTGCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:353:17:2,15:106,230:0.0482:2,2:27.5:1:31.1:1:0.10696:3.44734:60:34:0.0487:0:1.1 0/1:363:123:42,81:88,152:0.3388:2,2:23.7:1:29.7:1:0.64591:1.1162:60:122:0.3398:0:1.1 -15 99251389 . C T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00165;SOR=Inf;LSEQ=GCCTCTCTCTCTCCTCTCCT;RSEQ=CTCCTTGACCTCCCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:37,176:0:2,0:23:1:31:1:1:0:60:34.5:1:0:0.2 0/1:177:8:3,5:37,131:0.0452:2,2:22.1:1:30.3:1:0.38409:2.11:60:16:0.0462:0:1 -15 99251417 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51349;SOR=0;LSEQ=ACCTCCCTTCTCTTCTGAGT;RSEQ=CACGAGTTCCGCTGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:6,118:0.0159:1,2:25.5:1:30:1:0.10844:18.28:60:4:0.0163:0:1 0/0:88:0:0,0:8,80:0:2,0:22.7:1:32.3:1:1:0:60:176:1:0:0.3 -15 99434357 . G A 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27776;SOR=0;LSEQ=GACTGAACTTTAAAGATATC;RSEQ=ACTCTCTGCAGGTCTAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:13,0:0.3158:1,0:15.8:1:28.3:1:1:0:60:5:0.2778:0:1.5 0/0:6:0:0,0:6,0:0:0,0:19.2:1:30.2:1:1:0:60:12:1:0:0 -15 99434457 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12659;SOR=Inf;LSEQ=ATGAGTGATCTGGTGCTGGT;RSEQ=GTAGCAGTGAATGACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:84,2:0:1,0:25.4:1:32.1:1:1:0:60:42:1:0:0.2 0/1:48:2:1,1:42,4:0.0417:2,2:21:1:27.5:1:0.19947:9.50264:60:4:0.0417:0:1 -15 99434514 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50038;SOR=0;LSEQ=CCAGAGAAGGCGGTGCCTCC;RSEQ=CTGCCCGGTCTCATCTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:144,39:0.0108:2,2:5.5:1:28.5:1:0.3866:3.65885:60:4:0.0112:0:1 0/0:164:0:0,0:128,36:0:2,0:23.9:1:30.4:1:1:0:60:328:1:0:0.1 -15 99434816 . C A 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTTTGTGATCCACGACGG;RSEQ=GAGTGCATGCAGGAGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:0:0,0:220,353:0:2,0:25.4:1:30.5:1:1:0:60:70.625:0.9982:0:0.1 0/1:626:21:8,13:254,351:0.0335:2,2:24.6:1:29.7:1:0.82401:1.17561:60:42:0.0338:0:1.1 -15 99434906 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23035;SOR=Inf;LSEQ=GTGGTCACTACCCGCCCCAC;RSEQ=TCACCCGCCACCCTAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:40,161:0:2,0:22.7:1:31.6:1:1:0:60:39.2:1:0:0.1 0/1:186:2:1,1:43,140:0.0108:2,2:35:1:29.5:1:0.42009:3.23:60:4:0.0109:0:1 -15 99435582 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGAGGTCAGAGTTTGAGA;RSEQ=CAGCCTGGCCAACGTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:44.5:1:30:1:1:0:60:4:1:0:1 -15 99439963 . A AT 140 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.362;SOR=0.72834;LSEQ=CTCAATTATGTGTGTTTTTG;RSEQ=TTTTTTTTTTCTTCTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:30:22,8:296,82:0.0733:2,2:21.6:1:28.7:1:0.49904:1.31171:59.5:14:0.0702:0.022:0.4 0/1:312:17:10,7:215,79:0.0545:2,2:18.7:1:29.1:1:0.26231:1.90076:60:34:0.0557:0.0192:0.3 -15 99451887 . C T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12434;SOR=Inf;LSEQ=ACTGTGGCCAAGGGCAGGTG;RSEQ=GCTAACATCGATTTCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:267,98:0:2,0:23.3:1:31.4:1:1:0:60:90.25:1:0:0.1 0/1:381:4:1,3:253,124:0.0105:2,2:20.8:1:26.3:1:0.10994:6.0903:60:3:0.008:0:1 -15 99452153 . G A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08241;SOR=Inf;LSEQ=GTGACAGCATCCAAAACACC;RSEQ=TGGGCCCAACCATCATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:107,272:0:2,0:24.9:1:31.2:1:1:0:60:125.333:1:0:0.1 0/1:293:3:2,1:97,193:0.0102:2,2:12.3:1:21.7:1:0.2646:3.96:60:2:0.0069:0:2 -15 99454245 . A G 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGAAGAAAGATAAGTTC;RSEQ=CCTCGTTCACTGAAGTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:13.7:1:27:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99454363 . A G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30567;SOR=Inf;LSEQ=ACAAAGGATGGAGCCCTTGG;RSEQ=GCTCTGCATAGTGAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:27:26,1:5,0:0.8438:0,1:27:1:31.8:1:1:0:60:54:0.8438:0:1 1/1:11:11:10,1:0,0:1:0,2:19.3:1:29.8:1:1:0:60:10:1:0:1.1 -15 99454620 . GC G 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00095;SOR=Inf;LSEQ=ATAACCTGGCACCGGTACCG;RSEQ=CCCCTGACTACAGGGATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1053:0:0,0:519,533:0:2,0:24.7:1:31.2:1:1:0:60:41.08:0.999:0:0.2 0/1:1067:11:4,7:524,531:0.0103:2,2:25.9:1:30.6:1:0.5469:1.72606:60:22:0.0105:0.0028:0.5 -15 99454795 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54967;SOR=0;LSEQ=GAGTCCCCAGGGAGAGCCAC;RSEQ=CCAAACATCCCTACTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:0,2:2,96:0.02:1,0:17.5:1:28.5:1:1:0:60:4:0.0206:0:1 0/0:51:0:0,0:1,50:0:1,0:24.7:1:31.9:1:1:0:60:50:1:0:0.2 -15 99454924 . G A 114 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTTTAGTGAGTGATTAGAG;RSEQ=TGTTTGAATAAAATAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:1:0,0:23.7:1:31.9:1:1:0:60:24:1:0:1.3 1/1:1:1:0,1:0,0:1:0,0:40:0:30:0:1:0:60:2:1:0:1 -15 99454962 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAAAATGGGGAAAGCTTG;RSEQ=TTTTTCCAGAATTAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:25.5:1:29:1:1:0:60:4:0.5:0:3 0/0:1:0:0,0:0,1:0:0,0:2:0:33:0:1:0:60:2:1:0:1 -15 99456175 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14916;SOR=Inf;LSEQ=TATTTGTTTATTTAGACCTC;RSEQ=CATTATAGAAAGTGTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:138,9:0:2,0:23.3:1:31.6:1:1:0:60:146:1:0:0.4 0/1:93:2:1,1:83,8:0.0215:2,2:15:1:28.5:1:0.18513:9.84041:60:4:0.022:0:1 -15 99456198 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50154;SOR=0;LSEQ=TTATAGAAAGTGTGACATGC;RSEQ=GGGCCTCTGGGGAAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:2,0:172,24:0.0101:2,0:24:1:30:1:1:0:60:4:0.0102:0:2 0/0:170:0:0,0:135,35:0:2,0:23.1:1:30.3:1:1:0:60:340:1:0:0.4 -15 99456253 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21637;LSEQ=TCAGAGCCCCGAACTTTCTC;RSEQ=GAACTTAATTGTCTTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:434:333:230,103:69,32:0.7673:2,2:24.2:1:30.7:1:0.90268:1.04:60:332:0.7685:0:1.1 0/1:452:188:112,76:160,103:0.4159:2,2:25.9:1:29.8:1:0.84529:1.05395:60:61.667:0.4129:0:1.1 -15 99456553 . G A 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09916;SOR=1.39592;LSEQ=CCCAGCATCCACACTTCTTC;RSEQ=CAAGCTCACTGGCCTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:245:155:36,119:16,74:0.6327:2,2:22.3:1:29.4:1:0.33597:1.40:60:37.75:0.6266:0:1.1 1/0:235:166:48,118:21,48:0.7064:2,2:23.1:1:29.1:1:0.87531:1.07518:60:82:0.71:0:1.2 -15 99456562 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1044;SOR=Inf;LSEQ=CACACTTCTTCGCAAGCTCA;RSEQ=TGGCCTTGCTTGTACCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:38,180:0:2,0:21.9:1:31.8:1:1:0:60:53.5:1:0:0.7 0/1:195:3:1,2:47,145:0.0154:2,2:9:1:25.3:1:0.57377:1.54:60:2:0.0105:0:3.7 -15 99458718 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACACACAGACTCTCCAG;RSEQ=CCCCTTTCCACTTCCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:19:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99459642 . C T 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.37755;LSEQ=CTGGGATTACAGGCATGCAC;RSEQ=ACCATGCCCAGCTAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:3,2:8,6:0.2632:2,2:29.6:1:31:1:1:1.12:60:10:0.2632:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:26:0:33:0:1:0:54:2:0.3333:0:1 -15 99459832 . AT A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.20326;SOR=Inf;LSEQ=TAAAGGTACTGAGAGCTATT;RSEQ=TTTTCCTTACAAGCATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:195,48:0:2,0:21.3:1:30.7:1:1:0:60:120.5:1:0:0.1 0/1:200:2:1,1:146,52:0.01:2,2:37.5:1:30.5:1:0.46075:2.79059:60:4:0.0101:0:0.5 -15 99460184 . G T 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GCCTTTCTCCCCACCAGGTA;RSEQ=TGTGTAAGTCAGCAGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:35:2,33:8,111:0.2273:2,2:25:1:30.2:1:1:1.1879:60:34:0.2267:0:1.1 0/0:121:0:0,0:4,117:0:1,0:23.7:1:31.1:1:1:0:60:59.5:1:0:0.2 -15 99465274 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=0.14963;LSEQ=CTAAGGGGGCTCAATAGCTC;RSEQ=TTCTATTCCACGGTTAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:36:33,3:46,4:0.4186:2,2:24:1:31.3:1:1:1.04494:60:72:0.4186:0:1.1 0/1:52:5:3,2:45,2:0.0962:1,2:34.8:1:31.2:1:0.04168:13.36202:60:10:0.1:0:1.2 -15 99465285 . C T 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70931;SOR=1.21943;LSEQ=CAATAGCTCCTTCTATTCCA;RSEQ=GGTTAAGATTCTTCTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:22:20,2:71,8:0.2178:2,2:21.8:1:31.4:1:1:1.13:60:44:0.22:0:1.3 0/1:67:17:17,0:44,6:0.2537:2,1:23.9:1:30.1:1:0.32522:0:60:16:0.2424:0:1 -15 99465306 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.17428;SOR=Inf;LSEQ=GGTTAAGATTCTTCTGTTAC;RSEQ=CTTACTCAAGTCATAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:131,19:0:2,0:23.8:1:31.3:1:1:0:60:149:1:0:0.5 0/1:108:2:1,1:92,14:0.0185:2,2:5.5:1:28:1:0.25961:6.38302:60:4:0.0187:0:1.5 -15 99465473 . C T 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGACACCTACAACATCAC;RSEQ=GACCCGGAAGAGCTGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1047:0:0,0:502,544:0:2,0:25:1:30.2:1:1:0:60:68.733:0.999:0:0.1 0/1:1136:53:24,29:515,568:0.0467:2,2:23.3:1:29.9:1:0.77963:1.09547:60:106:0.0474:0:1.1 -15 99465709 . T A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60441;SOR=2.24043;LSEQ=CCACCTTCCTCACAACCTAG;RSEQ=GGAGAAGATGTGTTTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:1:1,0:35,119:0.0064:2,0:1:0:27:0:0.23226:0:60:2:0.0066:0:2 0/1:140:2:1,1:34,104:0.0143:2,2:16:1:27.5:1:0.43885:3.03:60:4:0.0145:0:2 -15 99465886 . C T 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AGCTTGGTCTCTCCATAGAA;RSEQ=GTGCTGGGAGCAGGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:28:1:30.5:1:1:0:60:8:0.5:0:1 0/0:2:0:0,0:0,2:0:0,0:15:1:30:1:1:0:60:4:1:0:0 -15 99466085 . C T 34 d7;v4;q23;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAAGATCAACTCCTGGAG;RSEQ=AGCCTCTGGTCTTGCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:34.7:1:21.7:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99466969 . C G 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0089;SOR=0.08391;LSEQ=CCTGCCCGCGTGGATGGGGG;RSEQ=GTTATTCTCAGTGTACGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:73:73,0:0,0:0.9865:0,1:21.6:1:31.6:1:1:0:60:72:0.9863:0:1.4 1/1:42:36:33,3:6,0:0.8571:0,2:24.9:1:30.1:1:1:0:60:17:0.85:0:1.3 -15 99467239 . G T 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00913;SOR=Inf;LSEQ=TAAAATACGGATCACAAGTT;RSEQ=AGGTAGGACTGGGGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:217,382:0:2,0:25:1:31.2:1:1:0:60:73.875:1:0:0.1 0/1:507:6:3,3:193,307:0.0118:2,2:23.5:1:28.3:1:0.68128:1.59:60:12:0.0119:0:1 -15 99467303 . C A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51039;SOR=0;LSEQ=CCATTGACAGCATATGCTAC;RSEQ=TGACTGCACAGGTTACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:19,170:0.0105:2,2:14:1:27.5:1:0.19895:8.75:60:4:0.0108:0:4.5 0/0:140:0:0,0:21,119:0:2,0:24.8:1:32:1:1:0:60:280:1:0:0.1 -15 99467708 . T C 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00024;SOR=Inf;LSEQ=TAGTTGGCAGGCCCCAGATT;RSEQ=CTCCTGCATTCATGGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:198,48:0:2,0:22.7:1:30:1:1:0:60:81:1:0:0.1 0/1:222:11:8,3:151,60:0.0495:2,2:18:1:30:1:1:1.06:60:22:0.0509:0:1.3 -15 99467930 . G A 198 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00966;LSEQ=AAAAGTAAGGCTTGTGGAGG;RSEQ=AGAAGAAACGTGGTAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:99:29,70:116,293:0.1945:2,2:25.2:1:29.9:1:0.90139:1.05:60:32:0.1924:0:1.1 0/0:431:1:1,0:144,286:0.0023:2,0:1:0:23:0:0.33643:0:60:2:0.0024:0:1 -15 99467934 . A C 219 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=293.31009;LSEQ=GTAAGGCTTGTGGAGGGAGA;RSEQ=GAAACGTGGTAAAACTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:1:1,0:130,348:0.0021:2,0:43:0:28:0:0.27349:0:60:2:0.0021:0:2 0/1:396:151:58,93:69,176:0.3813:2,2:24.8:1:30.3:1:0.03587:1.59:60:74.5:0.3791:0:1.2 -15 99467942 . GGT G 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.4598;LSEQ=TGTGGAGGGAGAAGAAACGT;RSEQ=AAAACTGAAAGCAGGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:137:33,104:59,188:0.3558:2,2:26.2:1:31.1:1:1:1.01:60:136:0.357:0.0545:0.1 0/1:336:68:19,49:84,184:0.2024:2,2:22.2:1:30.6:1:0.65975:1.17675:60:136:0.2054:0.0327:0.1 -15 99468159 . GA G 27 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATCCGAGCCTCTCCTTT;RSEQ=GGTTGTGTAACCACTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:8.5:1:27.5:1:1:0:60:4:0.2222:0.1111:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99472170 . G A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTATTTTAAATTGTCT;RSEQ=TGGAACTATCTCAAAGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15.5:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99472734 . T C 259 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0;SOR=0.00651;LSEQ=CTGAATGTGAAGAAATGAAA;RSEQ=GAGCAAATTGTTCACCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:301:297:233,64:2,1:0.9867:2,2:25.3:1:31.6:1:0.52067:1.82:60:98:0.9899:0:1.1 0/1:226:73:54,19:124,29:0.323:2,2:28.5:1:30.2:1:0.22868:1.50168:60:23.333:0.3153:0:1.1 -15 99473361 . C T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60668;SOR=2.21236;LSEQ=TCCCCATTCTGTTCTGATAC;RSEQ=GTGTGAGAGAGGATAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:0,1:179,36:0.0046:2,0:1:0:25:0:0.1713:0:60:2:0.0047:0:1 0/1:196:2:1,1:165,29:0.0102:2,2:19:1:26:1:0.28336:5.61102:60:4:0.0104:0:1 -15 99473512 . G A 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72543;SOR=1.65142;LSEQ=CTGTATGCCTCTGTGAACCC;RSEQ=GAGTACTTCAGCGCTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:3:3,0:154,306:0.0065:2,0:1:0:27:1:0.0385:0:60:6:0.0065:0:1.3 0/1:469:5:4,1:164,299:0.0107:2,2:17.6:1:26.6:1:0.05819:7.26:60:10:0.0107:0:1.4 -15 99473592 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16728;SOR=Inf;LSEQ=GCAGGTAGATCGGGAGCTTT;RSEQ=AGGAGGGTTGCTAATTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:10,141:0:2,0:20.9:1:31.5:1:1:0:60:24.167:1:0:0.1 0/1:105:2:0,2:10,93:0.019:2,0:30.5:1:30:1:1:0:60:4:0.019:0:4 -15 99473606 . A G 104 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0447;SOR=2.91063;LSEQ=AGCTTTCAGGAGGGTTGCTA;RSEQ=TTTGGGAAAGGAAGGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:6:0,6:5,96:0.0561:1,0:28:1:31.5:1:1:0:60:12:0.0571:0:1 0/1:81:12:0,12:5,64:0.1481:2,0:34.4:1:29.2:1:1:0:60:11:0.1375:0:1.4 -15 99473685 . C CT 62 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.35514;SOR=0.27405;LSEQ=TCATTAATATTTCTTTCTTT;RSEQ=TTTTTTTTTTTAATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:1,3:0,17:0.1905:1,2:21.8:1:31.3:1:0.19048:0:60:8:0.2105:0:0 0/1:17:1:0,1:0,16:0.0588:1,0:42:0:28:0:1:0:60:2:0.0714:0:0 -15 99473878 . ATGC A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTAACATCTAGTCAGAGGAT;RSEQ=TGCAGCTGACAAAACAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:32:0:1:0:60:4:1:0:0 -15 99477045 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTAATTGCCTGTCCAC;RSEQ=CTGGGCACCACCGGGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99477058 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCCACGCTGGGCACCACC;RSEQ=GGTCTCTCCCTCAGTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:30.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99477722 . G A 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTTTTTTTCAAAAATGT;RSEQ=TTTTTATGTGATGAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:19.7:1:26.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99477911 . T G 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCATGTGGAAAGTTGACA;RSEQ=CAAGCCATGCCATCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:69:69,0:0,0:1:0,1:22.8:1:32.3:1:1:0:60:138:1:0:1.1 1/1:31:31:30,1:0,0:1:0,1:26:1:32.6:1:1:0:60:62:1:0:1 -15 99478225 . G A 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GAGGCCGCAAGCATGCGTGA;RSEQ=AGGATTGAGTTTCTCAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:467:467:154,313:0,0:1:0,2:24.4:1:30:1:1:0:60:115.75:1:0:1.1 0/1:515:155:60,95:131,229:0.301:2,2:24.7:1:29.4:1:0.62044:1.10:60:50.667:0.298:0:1.2 -15 99478451 . C G 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGACCCCTGTGCTCAGAC;RSEQ=AGGCCGCAGCACCACAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:135,17:0:2,0:23.2:1:30.8:1:1:0:60:37:1:0:0.8 0/1:127:18:16,2:98,11:0.1417:2,2:26.8:1:29.5:1:1:1.11269:60:36:0.1429:0:1.8 -15 99478493 . T C 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AGTTCCAGACAACACAGGCA;RSEQ=CAGCAAGGGCCACCTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:269:269:201,68:0,0:1:0,2:24.5:1:31.4:1:1:0:60:66.25:1:0:1.1 1/1:282:264:194,70:13,5:0.9362:2,2:23.9:1:30.6:1:1:1.07:60:65:0.9386:0:1.2 -15 99478505 . A AC 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=0.19468;LSEQ=CACAGGCATCAGCAAGGGCC;RSEQ=CCTGACCCTCTGAGTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:293:287:207,80:6,0:0.9795:0,2:27.5:1:31.6:1:0.19402:0:59.9:56.4:0.9792:0.0478:1 1/1:319:288:209,79:20,9:0.9028:2,2:27.2:1:30.6:1:0.66775:1.19:60:40.143:0.9035:0.0408:1 -15 99478713 . T C 262 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00415;LSEQ=GCCTGCTCTCTTTTCCTTTA;RSEQ=AATCTCCCTGCAAGGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:306:63,243:1,2:0.9871:2,2:24.3:1:31.8:1:0.50282:1.92363:60:60.2:0.9901:0:1 0/1:252:60:12,48:48,142:0.2381:2,2:25.9:1:31.1:1:0.4892:1.35055:60:120:0.2429:0:1.2 -15 99478966 . C T 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCTGCCAAGCCAGGCCAG;RSEQ=GCCACTCCCTCCCCGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:21.4:1:31:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99479013 . T C 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCCACTCCAGTAGCTATCT;RSEQ=CTCTGCTAACTTCTCGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:23:1:27:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99481953 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAATTTATAACGATGCT;RSEQ=TTATGGGAAATAAAATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 99482380 . G GA 85 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.97486;LSEQ=CCTCGAAAGAAATTGGCATG;RSEQ=AAAAAAAAAATCCAAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:7:6,1:155,19:0.0387:2,2:20.7:1:30.4:1:0.56588:1.35707:60:14:0.0393:0.011:0.9 0/1:159:6:5,1:133,19:0.0377:2,2:23.2:1:27.8:1:0.56227:1.39666:60:5:0.0321:0:1.7 -15 99482702 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12879;SOR=Inf;LSEQ=AGTGTGTCCCTTGAGTGCAC;RSEQ=GACTCCTTCTTGGGAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:0,92:0:1,0:26.6:1:30.8:1:1:0:60:22:1:0:0.1 0/1:52:2:0,2:3,47:0.0385:2,0:36.5:1:31.5:1:1:0:60:4:0.0385:0:1 -15 99485931 . T A 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09023;SOR=0;LSEQ=GAATCAAATTGTAAATATAT;RSEQ=AAAAGTGGAGATTGCTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:10,0:7,0:0.5882:0,0:24.5:1:28.4:1:1:0:60:20:0.5882:0:1.1 0/0:4:0:0,0:3,1:0:2,0:30:1:30.8:1:1:0:60:8:1:0:0.3 -15 99491644 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14672;SOR=Inf;LSEQ=CAACAGAGGGAGGATGATAT;RSEQ=CCGCACTTAGCCCAGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:90,1:0:1,0:23.8:1:31.9:1:1:0:60:182:1:0:0.1 0/1:57:2:2,0:55,0:0.0351:1,0:31:1:31:1:1:0:60:4:0.0351:0:1 -15 99491660 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51642;SOR=0;LSEQ=ATATCCCGCACTTAGCCCAG;RSEQ=GCCTGGCTCGCTGTCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:2,0:117,1:0.0167:1,0:21.5:1:31:1:1:0:60:4:0.0169:0:1 0/0:81:0:0,0:80,1:0:1,0:23.2:1:31.4:1:1:0:60:80:1:0:0.1 -15 99492045 . G A 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72939;SOR=0.88125;LSEQ=GCCATTCTCTCTGGTCCTGC;RSEQ=CCTCCCTTGCCAGGCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:46:1,45:0,26:0.6301:1,1:20.6:1:29.4:1:1:0:60:22:0.6197:0:1.1 1/0:65:39:3,36:0,26:0.6:1,2:24.4:1:30:1:0.26875:0:60:38:0.5938:0:1.6 -15 99492061 . G A 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCGCCTCCCTTGCCAGGC;RSEQ=TGGCTAAGAGGTTTGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:1,59:0:1,0:22:1:31.9:1:1:0:60:59:1:0:0.6 0/1:46:18:0,18:2,26:0.3913:2,1:20.7:1:31.1:1:0.51304:0:60:36:0.4:0:1.9 -15 99500055 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTTTGGGTTTTGTACC;RSEQ=TGGTGGTTCTGGGTTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:17,1:0.1:1,0:34:1:29.5:1:1:0:60:4:0.1111:0:3 0/0:1:0:0,0:1,0:0:0,0:1:0:29:0:1:0:60:2:1:0:0 -15 99500064 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTTTGTACCGTGGTGGTT;RSEQ=TGGGTTCTGGGGGAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:18,1:0.0952:1,0:34:1:29:1:1:0:60:4:0.0952:0:3 0/0:4:0:0,0:4,0:0:0,0:5.8:1:30:1:1:0:60:8:1:0:0.5 -15 99500074 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGGTGGTTCTGGGTTCTG;RSEQ=GGGAAGAGAATGGAACCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:22,1:0.08:1,0:29.5:1:28.5:1:1:0:60:4:0.0833:0:3 0/0:5:0:0,0:5,0:0:0,0:13:1:32.2:1:1:0:60:10:1:0:0.4 -15 99500197 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1612;SOR=Inf;LSEQ=CAGTGCTCCCGCCGTACGCT;RSEQ=GTATGCGGGAAACCACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:192,7:0:1,0:21.9:1:29.7:1:1:0:60:17.091:1:0:0.4 0/1:134:2:1,1:125,7:0.0149:2,2:21.5:1:29:1:0.11626:16.76993:60:4:0.015:0:2 -15 99500256 . G A 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00916;SOR=0.7003;LSEQ=CTGGCCATGTGCGCCCTCCC;RSEQ=GTTTGGACCCCCTCCCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:197:141,56:223,102:0.3774:2,2:28.4:1:30:1:0.493:1.15:60:48.25:0.377:0:1.1 0/1:480:143:98,45:213,123:0.2979:2,2:23.9:1:29.7:1:0.297:1.26:60:46.667:0.2941:0:1.2 -15 99500636 . C T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01576;SOR=Inf;LSEQ=ACGGGGGCCGCAAGAACGAG;RSEQ=GGGCCTTGCCGCTGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:0:0,0:200,329:0:2,0:24.7:1:30:1:1:0:60:43.083:1:0:0.2 0/1:411:5:2,3:172,234:0.0122:2,2:12.6:1:29.4:1:1:1.10233:60:10:0.0123:0:1.6 -15 99500673 . C A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09168;SOR=Inf;LSEQ=CCAGTCTTCGACCTGCTGAT;RSEQ=CTTGGATCCTGAATCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:88,242:0:2,0:27.5:1:30.9:1:1:0:60:26.5:1:0:0.1 0/1:272:3:2,1:90,179:0.011:2,2:19.3:1:21:1:0.26501:3.96:60:2:0.0076:0:3.3 -15 99500676 . TG T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08802;SOR=Inf;LSEQ=GTCTTCGACCTGCTGATCCT;RSEQ=GATCCTGAATCTGTGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:79,233:0:2,0:27.1:1:31:1:1:0:60:33.667:1:0:0.1 0/1:251:3:2,1:78,170:0.012:2,2:21.7:1:29.3:1:0.23905:4.33:60:6:0.0121:0.004:0.3 -15 99500693 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20297;SOR=Inf;LSEQ=CCTTGGATCCTGAATCTGTG;RSEQ=AAACAGTAACGTGTGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:44,192:0:2,0:23.8:1:32.3:1:1:0:60:58:1:0:0.1 0/1:194:2:1,1:53,139:0.0103:2,2:19:1:28:1:0.48026:2.61:60:4:0.0105:0:2 -15 99500720 . C G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50037;SOR=0;LSEQ=TAACGTGTGCGCACGCGCAG;RSEQ=GGGGTGGGGGGGGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:14,102:0.0169:2,0:13:1:27.5:1:1:0:60:4:0.0174:0:3 0/0:102:0:0,0:16,84:0:2,0:42:0:8:0:1:0:60:0:0:0:3 -15 99500725 . T G 46 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.12934;SOR=0;LSEQ=TGTGCGCACGCGCAGCGGGG;RSEQ=GGGGGGGGAGAGAGAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:4:0,4:12,95:0.0357:2,0:11.5:1:23.3:1:1:0:60:3:0.028:0:2.3 0/0:91:0:0,0:14,76:0:2,0:47:0:9:0:1:0:60:0:0:0:3 -15 99500734 . A G 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.62075;SOR=0.34965;LSEQ=GCGCAGCGGGGTGGGGGGGG;RSEQ=GAGAGAGTTTTAACAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:0,3:3,70:0.039:1,0:20.3:1:30.7:1:1:0:60:6:0.04:0:2.3 0/1:72:1:0,1:7,64:0.0139:2,0:45:0:32:0:1:0:60:2:0.0141:0:3 -15 99835432 . TTGC T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.4929;SOR=Inf;LSEQ=TGTATGTGTTTTTGTTGCTG;RSEQ=TGCTGCTGCTGCTGTTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:0:2,0:27:1:30.8:1:1:0:60:58:1:0:0.2 0/1:32:2:1,1:14,16:0.0625:2,2:17:0:32:0:1:1.14:60:4:0.0625:0:0.5 -15 99835492 . A G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11095;SOR=Inf;LSEQ=TTTACGTATTGCTTTTCCCT;RSEQ=CACCTGGCATCAAAACTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:8,17:0:2,0:21.8:1:28:1:1:0:60:24:1:0:0.1 0/1:13:2:1,1:1,10:0.1538:2,2:16.5:1:34:0:0.29487:7.42:60:4:0.1538:0:1 -15 99835541 . C G 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03846;SOR=Inf;LSEQ=TGTCATAGAACATATTTAAA;RSEQ=TAATTTTCTCCCAATGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:0:0,0:25.8:1:33.2:1:1:0:60:20:1:0:0 1/0:3:2:0,2:0,1:0.6667:0,0:47:1:33:0:1:0:60:4:0.6667:0:1 -15 99856834 . A G 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=GAAGGCCTGTTTTTGCTTAT;RSEQ=GGGAAGAAAGTAGAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:116,114:0:2,0:26:1:28.9:1:1:0:60:37.333:1:0:0.4 0/1:311:15:6,9:153,143:0.0482:2,2:27.7:1:30.9:1:0.43474:1.60246:60:30:0.0485:0:1.1 -15 99856849 . G A 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42563;SOR=1.15979;LSEQ=CTTATAGGGAAGAAAGTAGA;RSEQ=AATTAATGGATGATAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:83:36,47:73,82:0.3487:2,2:29.4:1:30.3:1:0.58867:1.16153:59.9:166:0.364:0:1.2 0/1:321:123:59,64:99,99:0.3832:2,2:28:1:29.6:1:0.73201:1.08447:60:60.5:0.3929:0:1.1 -15 99856920 . TAAA T 165 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=18.000;MSILEN=1;SSF=0.16266;SOR=0.69486;LSEQ=GGATTTAAATAGAAAACTCT;RSEQ=AAAAAAAAAAAAAAACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:50:12,38:21,19:0.4237:2,2:30.6:1:29.8:1:0.00799:3.4481:59.3:100:0.4274:0:0.5 0/1:148:50:10,40:24,22:0.3378:2,2:31.6:1:29.4:1:0.00131:4.29201:59.7:100:0.3425:0.0068:0.7 -15 99857022 . G A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46819;SOR=0.5095;LSEQ=CCCTGGCGGATACAAGCTTG;RSEQ=ACACCAGGGAAGGTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:0,14:0.3333:1,0:35.4:1:29.9:1:1:0:60:14:0.3333:0:1 0/1:15:3:1,2:0,12:0.2:0,2:12:1:29:1:0.2:0:60:6:0.2:0:1.3 -15 99861491 . G A 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0728;SOR=2.11802;LSEQ=GGCAATATTTATTTGCTTAC;RSEQ=TGACTTCTGACATGCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:17:15,2:39,2:0.2931:1,2:26.1:1:30.9:1:0.57287:2.55162:60:34:0.2982:0:1.1 0/1:49:23:21,2:25,1:0.4694:1,2:20.2:1:30.7:1:0.59428:2.34:60:46:0.4792:0:1 -15 99861539 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22191;SOR=Inf;LSEQ=TAGTTATGTTATTGTATAGT;RSEQ=TAAGTTATGCATGTTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:131,29:0:2,0:23.7:1:31.3:1:1:0:60:52.333:1:0:0.2 0/1:143:2:1,1:108,33:0.014:2,2:26.5:1:28:1:0.42027:3.23912:60:4:0.0143:0:1.5 -15 99861618 . G A 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.26612;LSEQ=ACACACAAATTTGAAAATGC;RSEQ=TAAGAGACTGGGGCTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:134:74,60:147,130:0.3252:2,2:26.7:1:30.3:1:0.75165:1.09:60:66:0.3243:0:1.1 1/0:471:246:129,117:119,106:0.5223:2,2:27.2:1:29.8:1:0.92669:1.01818:60:492:0.5223:0:1.1 -15 99861641 . T G 192 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAGACTGGGGCTATTTAGC;RSEQ=TGTGGGCAGCTGGCGTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:77:35,42:155,203:0.177:2,2:25.4:1:30.7:1:0.80025:1.09:60:154:0.182:0:1.1 0/0:493:0:0,0:233,260:0:2,0:26.3:1:30.1:1:1:0:60:81.167:1:0:0.6 -15 99861714 . TA T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20481;SOR=Inf;LSEQ=TGCATTCACAGAGATAATTA;RSEQ=AGACATTAAGGAAAACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:33,143:0:2,0:22.2:1:29.9:1:1:0:60:87:1:0:0.2 0/1:146:2:1,1:31,113:0.0137:2,2:22.5:1:29.4:1:0.3915:3.60:60:4:0.0139:0.0068:0 -15 99945673 . C G 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00041;SOR=0;LSEQ=GAGAAGGCCCAGGAATCTGA;RSEQ=TAAAGTTTGGTCAAGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:4,5:1,0:0.9:0,2:17.1:1:30.7:1:1:0:60:18:0.9:0:1.2 0/0:8:0:0,0:3,5:0:2,0:26.3:1:30.8:1:1:0:60:16:1:0:0.1 -15 101020987 . G A 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1448;SOR=0.16952;LSEQ=TAAAGAGTTCTTATCTTTTC;RSEQ=AGATACATGCTAAAATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:2,0:0.8:0,0:24.6:1:31:1:1:0:60:16:0.8:0:1.6 0/1:8:3:3,0:5,0:0.375:0,0:31.7:1:31:1:1:0:60:6:0.375:0:1.3 -15 101021060 . C G 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAACCTATCTGTGGTAGG;RSEQ=GAGAGGTGTAGTGGGGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:21,10:0,0:1:0,2:21.8:1:30.7:1:1:0:60:62:1:0:1.2 1/1:36:36:25,11:0,0:1:0,2:21.7:1:30.7:1:1:0:60:72:1:0:1.1 -15 101021087 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51263;SOR=Inf;LSEQ=TGTAGTGGGGATAGAGAGGA;RSEQ=ATAGGATTGGCCTTGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:26,18:0:2,0:26.1:1:32.1:1:1:0:60:88:1:0:0.9 0/1:64:2:1,1:36,26:0.0313:2,2:29:1:28.5:1:1:1.37745:60:4:0.0317:0:1.5 -15 101022693 . A C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGGAGAGCCCTTTCTCC;RSEQ=ACACTGAGGAGTTCTCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 101094127 . T C 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=2.09375;LSEQ=ACACACACAAATGGAGGAAA;RSEQ=CCCGAGAGCATCTCGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:24.5:1:33.8:1:1:0:60:8:0.6667:0:3 1/0:4:3:2,1:1,0:0.75:0,2:27.3:1:32.7:1:1:0:60:6:0.75:0:2.3 -15 101094130 . C T 88 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=CACACAAATGGAGGAAATCC;RSEQ=GAGAGCATCTCGAATATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:30.6:1:31.4:1:1:0:60:14:1:0:2.1 1/0:4:3:2,1:1,0:0.75:0,2:28.3:1:31:1:1:0:60:6:0.75:0:2.3 -15 101094174 . C T 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.40739;LSEQ=GCTGAGGGCCCACCAGTCCA;RSEQ=AGCCCTTCCGTGACCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:7,0:5,0:0.5833:0,0:27:1:30.9:1:1:0:60:14:0.5833:0:2.1 1/0:12:8:8,0:4,0:0.6667:0,0:18.9:1:31.8:1:1:0:60:16:0.6667:0:1.3 -15 101094335 . C G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27061;LSEQ=TGTTCTCCGGCTTCAAGTCC;RSEQ=TGTAGATGATCTCCTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:53:29,24:28,27:0.4907:2,2:27.5:1:31.2:1:0.7047:1.16:60:106:0.4907:0:2 0/1:136:28:12,16:56,52:0.2059:2,2:30.3:1:30.5:1:0.52517:1.43207:60:56:0.2105:0:2 -15 101094336 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50455;SOR=Inf;LSEQ=GTTCTCCGGCTTCAAGTCCC;RSEQ=GTAGATGATCTCCTTAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:56,52:0:2,0:26:1:30:1:1:0:60:216:1:0:1.5 0/1:136:2:1,1:67,67:0.0147:2,2:42:1:30.5:1:1:1:60:4:0.0152:0:2 -15 101094342 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50224;SOR=Inf;LSEQ=CGGCTTCAAGTCCCTGTAGA;RSEQ=GATCTCCTTAGAGTGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:53,54:0:2,0:26.7:1:30.4:1:1:0:60:214:1:0:1.5 0/1:129:2:1,1:62,65:0.0155:2,2:45.5:1:28:1:1:1.05:60:4:0.0157:0:2 -15 101094352 . A G 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCCTGTAGATGATCTCCTT;RSEQ=GAGTGCAGGATGGCACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:49,57:0,0:1:0,2:27.1:1:31.2:1:1:0:60:105:1:0:1.6 1/1:129:129:59,70:0,0:1:0,2:27.2:1:30.6:1:1:0:60:128:1:0:1.4 -15 101094354 . A G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50328;SOR=Inf;LSEQ=CCTGTAGATGATCTCCTTAG;RSEQ=GTGCAGGATGGCACAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:47,56:0:2,0:27.8:1:30.2:1:1:0:60:102:1:0:1.6 0/1:127:2:1,1:58,67:0.0157:2,2:8:0:30:1:1:1.15:60:4:0.0159:0:2.5 -15 101094364 . G A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61997;SOR=0.75493;LSEQ=ATCTCCTTAGAGTGCAGGAT;RSEQ=GCACAGATGATCTCTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:9:3,6:43,52:0.0865:2,2:18.6:1:30.1:1:0.72785:1.64614:60:18:0.0865:0:1.9 0/1:120:8:4,4:49,63:0.0667:2,2:22:1:29.8:1:0.73075:1.28:60:16:0.069:0:1.9 -15 101094365 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50108;SOR=Inf;LSEQ=TCTCCTTAGAGTGCAGGATG;RSEQ=CACAGATGATCTCTGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:45,56:0:2,0:27:1:31.1:1:1:0:60:49.5:1:0:1.5 0/1:119:2:1,1:52,65:0.0168:2,2:26.5:1:27.5:1:1:1.25:60:4:0.0171:0:2 -15 101094376 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.2251;SOR=0;LSEQ=TGCAGGATGGCACAGATGAT;RSEQ=TCTGCAGAGTAGAAGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:39,57:0.0204:2,2:23.5:1:30:1:1:1.46:60:4:0.0204:0:3.5 0/0:108:0:0,0:44,64:0:2,0:27:1:31:1:1:0:60:35:1:0:1.3 -15 101094448 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51153;SOR=0;LSEQ=CCCGGAACATACTCCATGAG;RSEQ=CTGCAGAGGAAGCGCTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:9,29:0.05:2,2:36.5:1:29.5:1:0.44231:3.11:60:4:0.0526:0:1 0/0:27:0:0,0:4,23:0:2,0:25.6:1:31:1:1:0:60:26:1:0:0.2 -15 101094476 . G A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14272;SOR=0.24552;LSEQ=GGAAGCGCTAGTCATGCCCC;RSEQ=TCCAGCACAGCCTGATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:1,10:1,12:0.4583:1,2:20.5:1:29.2:1:1:1.19:60:10:0.4348:0:1 0/1:12:2:0,2:0,10:0.1667:0,0:42:1:32:0:1:0:60:4:0.1667:0:1 -15 101095940 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGGGCGGATGACTTCCTTC;RSEQ=GGACGCAGATGAGGGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:1:28.5:1:1:1:46:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 101592369 . C G 66 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGCTTTCCATTTTGGAGG;RSEQ=CTTGATAGGCCCAACTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:33.5:1:33.3:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:1:0,0:14:0:33:0:1:0:60:2:1:0:1 -15 101592629 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49862;SOR=0;LSEQ=GCTGACTCCTGTCTGTAGCC;RSEQ=TAGCGCTGAGCTCCCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:86,77:0.0121:2,2:38.5:1:31.5:1:1:1.11613:60:4:0.0123:0:1 0/0:159:0:0,0:90,69:0:2,0:29.1:1:29.9:1:1:0:60:52:1:0:0.3 -15 101592692 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22769;LSEQ=CAAACGCTGACTCCTGTCTG;RSEQ=AGCCCTAGCGCTGAGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:116:72:11,61:10,34:0.6207:2,2:23.9:1:31.9:1:0.33014:1.62383:59.3:35:0.614:0:1.2 0/1:100:27:6,21:21,52:0.27:2,2:21.4:1:31.3:1:0.61662:1.40876:60:54:0.2755:0:1.3 -15 101592701 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08896;SOR=Inf;LSEQ=ACTCCTGTCTGTAGCCCTAG;RSEQ=GCTGAGCCTTGGACCCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:14,79:0:2,0:23.4:1:30.2:1:1:0:59.4:92:1:0:0.8 0/1:76:3:1,2:12,61:0.0395:2,2:31.7:1:26.3:1:0.43512:2.50:60:6:0.0395:0:1 -15 101592773 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.02437;SOR=0.25011;LSEQ=TAACCCAAGATCATAACTAG;RSEQ=GAGAGAATCGGGGAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:17:0,17:0,11:0.6071:0,1:31.1:1:31.9:1:1:0:60:34:0.6071:0:2.5 0/1:22:6:0,6:1,15:0.2727:1,0:21:1:30.5:1:1:0:60:12:0.2727:0:2.7 -15 101592783 . G A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0177;SOR=0.20412;LSEQ=TCATAACTAGAGAGAGAATC;RSEQ=GGGAGGAAATAGGAAACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:16:1,15:0,10:0.5926:0,1:27.6:1:32.1:1:1:0:60:32:0.5926:0:2.6 0/1:18:4:0,4:1,13:0.2222:1,0:30.3:1:31.8:1:1:0:60:8:0.2222:0:3 -15 101592831 . G A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53007;SOR=0.31868;LSEQ=AGAAGAAAACTTCCAAAGGG;RSEQ=TCCTTTCTCTACGGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:1,6:0,2:0.7778:0,2:19:1:31.1:1:1:0:60:14:0.7778:0:2.9 1/0:4:2:0,2:0,2:0.5:0,0:5:1:30.5:1:1:0:60:4:0.5:0:3 -15 101592856 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTCTACGGCCACCACTTC;RSEQ=GTGGGGTTCACCCTGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:33:1:31:1:1:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -15 101593086 . A T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCCCAGGACCCACCCGCATC;RSEQ=GGGCGGGGGGGATGTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:30:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 -16 114974 . G A 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.51609;SOR=0;LSEQ=TAGCCAGGGTGGCTTCTTGC;RSEQ=CTGCAGGCTGCTCGTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:46,14:0.0323:2,2:10:0:29.5:1:0.42834:3.20861:60:4:0.0323:0:1 0/0:41:0:0,0:33,8:0:2,0:20.1:1:30.1:1:1:0:60:82:1:0:0.2 -16 115021 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50159;SOR=0;LSEQ=GGGCCTCACTCATGGTTCCT;RSEQ=GCAGAGCAAGGCAGGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:67,48:0.0171:2,2:39.5:1:29:1:1:1.39177:60:4:0.0171:0:1 0/0:98:0:0,0:61,37:0:2,0:25.4:1:30.2:1:1:0:60:31.667:1:0:0.5 -16 115041 . C T 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAGAGCAAGGCAGGCCTG;RSEQ=GGGGCATGGTGTGTTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:71,63:0:2,0:27:1:30.7:1:1:0:60:43.667:1:0:0.2 0/1:128:26:13,13:58,44:0.2031:2,2:21.2:1:29.5:1:0.6591:1.3153:60:52:0.2031:0:2 -16 115072 . A C 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGTTATTCAATAATGACAA;RSEQ=GCTGACATCTGAAGATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:83,80:0:2,0:24.7:1:30.6:1:1:0:60:80.5:0.9938:0:0.2 0/1:153:47:22,25:55,51:0.3072:2,2:27.6:1:30.4:1:0.60198:1.22385:60:94:0.3092:0:1.6 -16 337750 . C G 40 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATCCGGGCCTGGGCCCCA;RSEQ=CCAGACCTGGGTACGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:18:1:25.3:1:1:0:60:2:0.3333:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 337827 . TG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGGAGGTGCCGGGGGA;RSEQ=GGGGGGGGTCACCTGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:23.5:1:31.5:1:1:0:60:4:0.2222:0:0 0/0:1:0:0,0:1,0:0:0,0:40:0:29:0:1:0:60:2:1:0:0 -16 337871 . T C 81 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAGGGACCTCGGCTGCC;RSEQ=CACTTGGGCTGGGCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:0.3333:0,0:31:1:31.5:1:1:0:60:12:0.3333:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 338322 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17858;SOR=Inf;LSEQ=GAGGCCTGTGGCAGGGGACG;RSEQ=CGTGTCCACACCCCATCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:7,199:0:1,0:24.2:1:31.9:1:1:0:60:67.667:0.9951:0:0.2 0/1:152:2:1,1:9,141:0.0132:2,2:27.5:1:30:1:0.12766:14.91:60:4:0.0135:0:1 -16 338332 . A AC 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21436;SOR=0.68;LSEQ=GCAGGGGACGGCGTGTCCAC;RSEQ=CCCCATCCCGAGGAGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:47:1,46:1,132:0.2611:1,1:22.7:1:30.2:1:0.45512:2.85:59.9:22.5:0.2586:0.0556:0.1 0/1:124:24:1,23:3,97:0.1935:1,1:23.6:1:31.2:1:0.58201:1.40:60:48:0.2034:0.0242:0 -16 338366 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52999;SOR=0;LSEQ=AGCCTCCTGTCCATGCCCCA;RSEQ=GGCCCCCACTGCATGTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:0,2:1,105:0.0185:1,0:28.5:1:31.5:1:1:0:60:4:0.019:0:1 0/0:64:0:0,0:1,63:0:1,0:22.4:1:29.6:1:1:0:60:63:1:0:0.1 -16 339082 . CT C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCGGAAGCCCTTTTTCTT;RSEQ=TTTTTTTTTTTTGGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:39.5:1:32:1:1:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 339291 . G C 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.82922;SOR=1.10276;LSEQ=GCCCAGGCTGGTCTCGAACT;RSEQ=CTGAGCTGAGGCAATCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:26:26,0:60,0:0.3023:1,1:25.8:1:29.7:1:1:0:59.3:7.667:0.2805:0:1.5 0/1:34:11:11,0:23,0:0.3235:1,0:29.5:1:30.3:1:1:0:60:22:0.3235:0:1.1 -16 339415 . G T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.12714;LSEQ=CCACATACTCGTGCGGGGAG;RSEQ=GGGCACCCCAGCCCTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:667:214:148,66:312,138:0.3208:2,2:25.1:1:29.4:1:1:1.00821:60:34.667:0.318:0:1.1 0/1:495:28:14,14:294,173:0.0566:2,2:22.4:1:28.9:1:0.22776:1.69745:60:27:0.0556:0:1.1 -16 339665 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.18019;SOR=Inf;LSEQ=ACTGAGGTCCCACAGGGTCC;RSEQ=TCCTGCTGGCCTCAGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:13,229:0:2,0:23.9:1:32.4:1:1:0:60:79.667:1:0:0.4 0/1:179:2:1,1:19,158:0.0112:2,2:18.5:1:28:1:0.21154:8.13:60:4:0.0113:0:1 -16 339670 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17446;SOR=Inf;LSEQ=GGTCCCACAGGGTCCCTCCT;RSEQ=CTGGCCTCAGGCTGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:7,207:0:1,0:25.2:1:32.5:1:1:0:60:106:1:0:0.4 0/1:154:2:1,1:9,143:0.013:2,2:12:1:28.5:1:0.12605:15.13:60:4:0.013:0:1 -16 339672 . T C 179 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00302;SOR=0.44163;LSEQ=TCCCACAGGGTCCCTCCTGC;RSEQ=GGCCTCAGGCTGCCAGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:59:1,58:6,150:0.2744:1,1:27.3:1:30.5:1:0.67656:2.31263:60:118:0.2757:0:1.3 0/1:147:21:0,21:7,119:0.1429:2,1:21.6:1:30.2:1:0.59372:0:60:42:0.1438:0:1.2 -16 339727 . C T 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCAGGGGTGAGCAGCACCC;RSEQ=ATTCAAACACCTGGGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:30:1,29:0,63:0.3226:1,1:21.8:1:27.9:1:0.32258:0:60:14:0.3146:0:1.7 0/0:43:0:0,0:0,43:0:1,0:20.1:1:31.9:1:1:0:60:42:1:0:0.3 -16 341078 . T C 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28594;SOR=0;LSEQ=TCTCCTGCCACAGCTGCTTC;RSEQ=GAGCGTGGTACCCGAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:3:2,1:245,6:0.0118:1,2:31.3:1:29.3:1:0.08073:19.4642:60:6:0.0119:0:1 0/0:161:0:0,0:153,7:0:1,0:23.7:1:30.8:1:1:0:60:52.333:0.9937:0:0.3 -16 341109 . C T 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.41014;SOR=0.29394;LSEQ=CCCGAGCTCAAGCCCCGGGA;RSEQ=GGCGGCTCTACGATGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:5:1,4:366,114:0.0103:2,2:8:1:25.2:1:0.01366:12.75967:60:4:0.0084:0:1.2 0/0:328:1:1,0:229,98:0.003:2,0:42:0:28:0:1:0:60:2:0.0032:0:2 -16 341120 . C T 142 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.20157;LSEQ=GCCCCGGGACGGCGGCTCTA;RSEQ=GATGGGACCTGGCTTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:624:2:1,1:435,187:0.0032:2,2:39.5:1:30:1:0.51213:2.3227:60:4:0.0032:0:1 0/1:426:32:20,12:255,139:0.0751:2,2:22.4:1:28.4:1:0.8484:1.10047:60:64:0.0758:0:1.1 -16 341362 . G A 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14234;SOR=0;LSEQ=AGCCCTGGGGAGGGAGCCTC;RSEQ=ACCAATGCTGCTGCGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:4:3,1:73,216:0.0137:2,2:19.3:1:28.5:1:0.05497:8.80:60:8:0.0139:0:1 0/0:213:0:0,0:67,146:0:2,0:21.3:1:30.1:1:1:0:60:52.25:1:0:0.1 -16 341476 . T C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49008;SOR=1.70759;LSEQ=GTCCCCTCCTAGGCCTGCCT;RSEQ=GGTGGTACCCGATACTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:12:0,12:1,28:0.2927:1,0:24.3:1:29.8:1:1:0:60:24:0.3:0:1.2 0/1:12:5:0,5:0,7:0.4167:0,0:18.8:1:30.8:1:1:0:60:10:0.4167:0:1.4 -16 341500 . G A 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.03226;SOR=Inf;LSEQ=GGTACCCGATACTGCAGCGC;RSEQ=CCCCACATTCATGATCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:0,25:0:1,0:21.5:1:32.9:1:1:0:60:50:1:0:0.2 0/1:6:2:0,2:0,4:0.3333:0,0:30.5:1:32:0:1:0:60:4:0.3333:0:2 -16 343369 . TG T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAAGGGCCCAGTATGGC;RSEQ=GGGGACACCCAGAGGGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:2,0:120,3:0.016:1,0:10:1:32.5:1:1:0:60:4:0.0161:0.008:3 0/0:48:0:0,0:46,2:0:1,0:24:1:32.4:1:1:0:60:96:1:0:0.1 -16 343905 . T C 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7376;SOR=0.67566;LSEQ=AAAAACATCCCGGCCAGGCA;RSEQ=GGTGGCTCACACCTGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:0,11:0,32:0.2558:1,0:23.5:1:29.6:1:1:0:60:22:0.2619:0:1.1 0/1:16:3:0,3:1,12:0.1875:1,0:17.3:1:29.3:1:1:0:60:6:0.1875:0:1 -16 346986 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.14378;SOR=Inf;LSEQ=CACACACTGAAGCTGCACAC;RSEQ=CTGAGACTGTGCGGAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:289,36:0:2,0:25.9:1:30:1:1:0:60:53.167:1:0:0.1 0/1:199:2:1,1:170,27:0.0101:2,2:32.5:1:27:1:0.26222:6.20101:60:4:0.0101:0:1 -16 347063 . C T 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05995;SOR=0.62426;LSEQ=GCGGGGTGCTCACCCGTGGC;RSEQ=GGTCCTGCGGTGCCTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1117:50:30,20:599,468:0.0448:2,2:23.7:1:30.6:1:0.66265:1.17:60:100:0.0454:0:1.1 0/1:915:26:13,13:510,377:0.0284:2,2:21.3:1:29.8:1:0.54708:1.35231:60:52:0.0288:0:1.1 -16 347184 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07861;LSEQ=CTGGCGCTCTTCCCCGACTC;RSEQ=GCCTTCTTGGCATTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:244:96,148:265,407:0.2661:2,2:25.7:1:30.3:1:1:1.00378:60:243:0.2703:0:1.1 0/1:831:23:9,14:347,459:0.0277:2,2:24.5:1:29.2:1:0.83193:1.17575:60:46:0.0281:0:1.2 -16 347257 . G T 105 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00168;SOR=13.95619;LSEQ=AAGAGCTGCGAGTCGCCCTG;RSEQ=CCTCCGGTGGCCGAGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:1:0,1:74,275:0.0028:2,0:26:0:17:0:1:0:60:0:0:0:1 0/1:286:11:3,8:77,196:0.0385:2,2:26.5:1:30.4:1:1:1.04744:60:22:0.0394:0:1.5 -16 347326 . G A 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGCATCTGTAAGGCTCCC;RSEQ=TGGTGCAGCCGCCGCCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:36:0,36:2,72:0.3273:1,1:21.3:1:30.3:1:1:0:60:17:0.3178:0:1.2 0/0:43:0:0,0:1,42:0:1,0:17.8:1:31:1:1:0:60:42:1:0:0.2 -16 347668 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16921;SOR=Inf;LSEQ=TGAGGAGGTTCTGGCCTTCT;RSEQ=CAGGGACACAGCCTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:212,41:0:2,0:23.5:1:32.1:1:1:0:60:49.6:1:0:0.1 0/1:178:2:1,1:140,36:0.0112:2,2:27.5:1:30.5:1:0.37345:3.84965:60:4:0.0113:0:1 -16 348222 . C T 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30006;LSEQ=CACGGCCCTGGGGGCCCTGA;RSEQ=GATGGATCGCCGTCCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:615:169:80,89:185,261:0.2748:2,2:28.1:1:30.3:1:0.20227:1.27:60:55.333:0.2753:0:1.2 0/1:451:46:20,26:171,234:0.102:2,2:26.9:1:30:1:0.87613:1.05:60:45:0.1009:0:1.4 -16 348417 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.07977;SOR=Inf;LSEQ=CTGAGGATGGAGAGGCAGGA;RSEQ=GGGGCATAGACAGAAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:0,19:0:1,0:25.5:1:28.7:1:1:0:60:18:1:0:0.4 0/1:8:2:0,2:0,6:0.25:0,0:37:1:28:1:1:0:60:4:0.25:0:2.5 -16 354143 . G A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04876;SOR=Inf;LSEQ=CCCATCTTGAGCTGGGGCTC;RSEQ=GCTGCAGAGAAAGGGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:37,0:0:1,0:22.2:1:29.7:1:1:0:60:74:1:0:0 0/1:11:2:2,0:9,0:0.1818:0,0:42:1:31.5:1:1:0:60:4:0.1818:0:1 -16 354244 . C T 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.40726;SOR=0.34872;LSEQ=TGAAGAACATCAGGACATCC;RSEQ=GGCGGCAAGAAAACAGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:4:1,3:135,50:0.0212:2,2:8.5:1:27.8:1:0.06756:7.99598:60:8:0.0213:0:1.3 0/0:134:1:0,1:101,32:0.0075:2,0:1:0:26:0:0.24627:0:60:2:0.0075:0:1 -16 354287 . C T 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGACGCGGAGCGCGACAC;RSEQ=GACGCGGCCCACTCACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:255,108:0:2,0:26.1:1:30.9:1:1:0:60:362:1:0:0.1 0/1:286:40:29,11:165,81:0.1399:2,2:24.5:1:30.5:1:0.58582:1.29:60:80:0.1444:0:1.2 -16 354312 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02209;SOR=Inf;LSEQ=CGGCCCACTCACCATGCGCA;RSEQ=GCGCTTCAGCCGCTCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:308,146:0:2,0:25.6:1:31.1:1:1:0:60:112.5:1:0:0.1 0/1:399:5:3,2:253,141:0.0125:2,2:31.6:1:29.8:1:1:1.19566:60:10:0.0128:0:1.2 -16 354493 . C T 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=63.25937;LSEQ=TTGAAAGGTCACAGGCTAAA;RSEQ=ATTTCTTTGTGAAGGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:1:0,1:78,276:0.0028:2,0:41:0:11:0:1:0:60:0:0:0:5 0/1:355:54:13,41:78,223:0.1521:2,2:25.4:1:27.8:1:0.86646:1.10285:60:108:0.1538:0:1.3 -16 358161 . C A 41 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=CCTGTCTGTGCCTGCCGCCT;RSEQ=TGTTGGCTTTCATCTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:17.5:1:29:1:1:0:60:4:1:0:0 1/1:3:3:1,2:0,0:1:0,2:13.3:1:26.3:1:1:0:60:6:1:0:1 -16 359953 . A G 287 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.68725;LSEQ=GGGAGGACGATGGGCTGAGG;RSEQ=CCGCAAAGCCGGTACTTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1129:500:270,230:345,282:0.4429:2,2:26.2:1:31.4:1:0.76343:1.04215:60:82.333:0.4427:0:1.1 1/0:1049:601:332,269:241,204:0.5729:2,2:25.6:1:31.1:1:0.75353:1.04:60:53.636:0.5712:0:1.2 -16 360144 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14956;SOR=Inf;LSEQ=CCGTGCCAATAGAGCTCCTG;RSEQ=CCCCGACCGCCGGTCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:32,213:0:2,0:21.5:1:31.8:1:1:0:60:48:1:0:0.1 0/1:155:2:1,1:24,128:0.0129:2,2:21:1:28:1:0.29921:5.25:60:4:0.0131:0:1 -16 360149 . G A 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01556;SOR=0;LSEQ=CCAATAGAGCTCCTGGCCCC;RSEQ=ACCGCCGGTCAGCAGGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:10:1,9:23,187:0.0455:2,2:18.4:1:30.1:1:1:1.10648:60:20:0.0457:0:1 0/0:129:0:0,0:17,112:0:2,0:23.2:1:30.6:1:1:0:60:42:1:0:0.1 -16 360303 . T C 29 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40351;SOR=3.42835;LSEQ=CCCAGGTGCCCAGCCACGCG;RSEQ=CTTCCTAGCTGGTATTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:0,15:0.1176:1,0:41.5:1:29.5:1:1:0:60:4:0.1176:0:2 0/1:3:1:0,1:0,2:0.3333:0,0:40:0:31:0:1:0:60:2:0.3333:0:2 -16 360317 . A G 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42208;SOR=3.20798;LSEQ=CACGCGTCTTCCTAGCTGGT;RSEQ=TTTACTGGGCACCTCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:0.125:1,0:44:1:31.5:1:1:0:60:4:0.1333:0:2 0/1:3:1:0,1:0,2:0.3333:0,0:26:0:33:0:1:0:60:2:0.3333:0:2 -16 364762 . G C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5159;SOR=0;LSEQ=TTCACATTTTCATGTTATCT;RSEQ=AATATCTCAATGTATTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:9,127:0.0145:2,2:18:1:28.5:1:0.14017:13.44:60:4:0.0146:0:1 0/0:94:0:0,0:11,83:0:2,0:21.2:1:31.3:1:1:0:60:93:1:0:0.1 -16 396070 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50385;SOR=0;LSEQ=GGTGTGGGTTAACGCCCGCC;RSEQ=CATCAGCACCTTTCCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:145,22:0.0118:2,2:12.5:1:29:1:0.25437:6.46823:60:4:0.012:0:1 0/0:137:0:0,0:108,29:0:2,0:20.2:1:30.1:1:1:0:60:67.5:1:0:0.1 -16 396077 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50052;SOR=0;LSEQ=GTTAACGCCCGCCTCATCAG;RSEQ=ACCTTTCCCTGGCTTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:155,31:0.0106:2,2:16.5:1:29:1:0.31221:4.93722:60:4:0.0108:0:1 0/0:166:0:0,0:124,41:0:2,0:20.2:1:31.4:1:1:0:60:40.25:0.9938:0:0.2 -16 396106 . C T 40 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07042;LSEQ=CTGGCTTGTTCTCCAGCTCT;RSEQ=GGAGGTGAGTACAGAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:1,2:192,81:0.0109:2,2:22.7:1:29.3:1:0.21599:4.71046:60:6:0.0109:0:1 0/1:258:3:0,3:162,93:0.0116:2,0:1:0:25.7:1:0.0505:0:60:6:0.0118:0:1 -16 396234 . G A 148 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCTTCTGAGGGAGTCTTCC;RSEQ=GGGGGAGCAGCGTCTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:795:32:17,15:451,310:0.0403:2,2:26.1:1:29.7:1:0.58265:1.28326:60:31:0.0393:0:1.9 0/0:707:0:0,0:391,316:0:2,0:23.6:1:29.6:1:1:0:60:234.667:1:0:0.6 -16 396264 . A G 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=0.69347;LSEQ=GCGTCTCTGCCATCGTCCTC;RSEQ=TCCATGTCCTGGTCACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1011:662:370,292:203,144:0.6548:2,2:24.2:1:30.6:1:0.46187:1.11242:60:81.75:0.656:0:1.2 1/0:933:530:298,232:216,185:0.5681:2,2:24.7:1:30.2:1:0.50581:1.10:60:131.5:0.568:0:1.1 -16 397044 . G T 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTGGGACTCTGCGTCAA;RSEQ=GAACAATGAGCGCTGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:0:0,0:98,270:0:2,0:23.4:1:30.9:1:1:0:60:45:1:0:0.1 0/1:320:65:21,44:81,174:0.2031:2,2:24.4:1:29.8:1:1:1.03:60:64:0.2025:0:1.1 -16 397060 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10239;SOR=Inf;LSEQ=TCAAGGAACAATGAGCGCTG;RSEQ=ACCCTAATACATCAGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:60,213:0:2,0:23.4:1:31.8:1:1:0:60:90:1:0:0.1 0/1:241:3:2,1:59,179:0.0124:2,2:14.7:1:26:1:0.15859:6.01:60:6:0.0125:0:1 -16 397764 . CT C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGATAATCATGGGTCAC;RSEQ=TCAGCCCCATCGACCGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:1:32.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 445053 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCGAGATCGCGCCACT;RSEQ=CACTCCAACCTGGGTGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:27:1:1:0:60:4:1:0:2 -16 447416 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCTGGGGTCCGACTCCCCC;RSEQ=GAGGCCTCGGGGCGCGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:30.5:1:1:0:60:4:1:0:1 -16 737793 . G A 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.45385;LSEQ=GGGGCTGGCCCATGAGGTGC;RSEQ=CCCTCAGAACAGCTGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:28.5:1:31.5:1:1:0:60:4:0.4:0:1 0/1:7:3:3,0:4,0:0.4286:0,0:17.3:1:32:0:1:0:60:6:0.4286:0:1 -16 737939 . C A 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.64518;LSEQ=CTGGGCCCGGGAGCAGGACA;RSEQ=CACGTGATTTGTAACACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:1,0:13,16:0.0333:2,0:1:0:31:0:0.46667:0:60:2:0.0357:0:1 0/1:37:2:1,1:16,19:0.0541:2,2:27.5:1:32:0:1:1.18:60:4:0.0541:0:1 -16 1032133 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17315;SOR=Inf;LSEQ=TCCCGGCCTGCATCCGCGAC;RSEQ=CCGTGTCGCAGGTGCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:33,14:0:2,0:25.7:1:30.5:1:1:0:60:94:1:0:0.1 0/1:34:2:1,1:20,12:0.0588:2,2:15:0:32:0:1:1.64076:60:4:0.0606:0:1.5 -16 1032162 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16691;SOR=Inf;LSEQ=CAGGTGCTCAAGGGCTACGA;RSEQ=TGGAGTCTGGTGCCCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:49,27:0:2,0:27:1:31.6:1:1:0:60:75:1:0:0.2 0/1:53:2:1,1:30,21:0.0377:2,2:42:1:27.5:1:1:1.41877:60:4:0.0392:0:1 -16 1032176 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51628;SOR=0;LSEQ=CTACGACTGGAGTCTGGTGC;RSEQ=CATGCCGGTGCGCGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:49,27:0.0256:2,2:31.5:1:30:1:1:1.80011:60:4:0.0263:0:1 0/0:52:0:0,0:31,21:0:2,0:28.8:1:30.1:1:1:0:60:25:1:0:0.4 -16 1032187 . CGCG C 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.73414;SOR=1.28437;LSEQ=GTCTGGTGCCCATGCCGGTG;RSEQ=GCGGCGGCGGCGGCGCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:5:3,2:44,30:0.0633:2,2:12.6:1:31:1:1:1.02:60:10:0.0641:0.038:0.6 0/1:50:4:3,1:27,19:0.08:2,2:32.8:1:33.3:1:0.64112:2.08:60:8:0.08:0:0.3 -16 1032294 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50489;SOR=0;LSEQ=CGCAAGCTGGCCGACCAGTA;RSEQ=CCGCACCTGCACAACGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:90,79:0.0117:2,2:32.5:1:31:1:1:1.13837:60:4:0.0122:0:1.5 0/0:136:0:0,0:68,68:0:2,0:28.7:1:30.6:1:1:0:59.9:33:1:0:0.3 -16 1032336 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50994;SOR=0;LSEQ=CTCAGCAAGACGCTGGGCAA;RSEQ=CTGTGGCGGTGAGTGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:59,80:0.0141:2,2:32:1:30.5:1:1:1.35:60:4:0.0143:0:1 0/0:104:0:0,0:42,61:0:2,0:24.9:1:31.8:1:1:0:60:102:1:0:0.3 -16 1032339 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16371;SOR=Inf;LSEQ=AGCAAGACGCTGGGCAAGCT;RSEQ=TGGCGGTGAGTGCCGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:60,82:0:2,0:25.9:1:32.2:1:1:0:60:284:1:0:0.2 0/1:97:2:1,1:36,59:0.0206:2,2:9.5:1:28.5:1:1:1.63:60:4:0.0213:0:1 -16 1032343 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15752;SOR=Inf;LSEQ=AGACGCTGGGCAAGCTGTGG;RSEQ=GGTGAGTGCCGGCGCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:56,80:0:2,0:24.7:1:30.4:1:1:0:60:67:1:0:0.2 0/1:90:2:1,1:32,56:0.0222:2,2:8.5:1:28.5:1:1:1.74:60:4:0.023:0:1.5 -16 1032357 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11654;SOR=Inf;LSEQ=CTGTGGCGGTGAGTGCCGGC;RSEQ=CCCCGGGGGCGGGGTTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:41,68:0:2,0:20.8:1:30.8:1:1:0:60:53.5:1:0:0.1 0/1:57:2:1,1:18,37:0.0351:2,2:12:1:30.5:1:1:2.03:60:4:0.0364:0:1 -16 1033669 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12995;SOR=Inf;LSEQ=CGGTTCCCCCTGTGGTGTGT;RSEQ=CCTGCGCCGAGGGCACAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:98,4:0:1,0:25.5:1:31.8:1:1:0:60:33:1:0:0 0/1:58:2:2,0:54,2:0.0345:1,0:15:0:30:0:1:0:60:4:0.0351:0:1 -16 1033698 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14609;SOR=Inf;LSEQ=GAGGGCACAGTGGGCGCCCT;RSEQ=GCCATCCCTGCCTCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:156,42:0:2,0:22.7:1:31.7:1:1:0:60:38.6:1:0:0.1 0/1:123:2:1,1:100,21:0.0163:2,2:14:0:32:0:0.32694:4.67566:60:4:0.0163:0:1.5 -16 1033701 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15155;SOR=Inf;LSEQ=GGCACAGTGGGCGCCCTGGC;RSEQ=ATCCCTGCCTCTGCCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:163,48:0:2,0:22.7:1:31.1:1:1:0:60:51.75:1:0:0.1 0/1:135:2:1,1:106,27:0.0148:2,2:17:1:27.5:1:0.37302:3.87333:60:4:0.0149:0:1.5 -16 1033737 . C T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08701;SOR=Inf;LSEQ=CTGTGCTGCAGCTTGCTGAG;RSEQ=GAGAGCGAGAAGCGGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:226,151:0:2,0:24.7:1:30.9:1:1:0:60:74.4:1:0:0.1 0/1:301:3:1,2:181,117:0.01:2,2:10.3:1:24.3:1:0.56443:3.08223:60:2:0.0068:0:3.3 -16 1033841 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16089;SOR=Inf;LSEQ=GCCACGGCGCAGGAAGAGCG;RSEQ=CAAAGCCGGCCACAGCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:81,187:0:2,0:22.3:1:30.8:1:1:0:60:32.5:1:0:0.1 0/1:180:2:1,1:53,125:0.0111:2,2:9:1:26:0:0.51117:2.35:60:4:0.0116:0:2.5 -16 1034954 . T C 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGAGCCGGGCCAGGCCTA;RSEQ=GGGGGCGCCTACTTCCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:0.6:2,2:26.3:1:30.3:1:1:1.73:60:6:0.6:0:1 -16 1034977 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGCCTACTTCCACGCCG;RSEQ=GGCGTCCCCCGTGTGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:6:1:29.5:1:1:1:60:4:0.5:0:1 -16 1035069 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCCGCACATCAAGACGGAG;RSEQ=AGCCGAGCCCCGGCCACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:28.7:1:31.4:1:1:0:60:14:1:0:0.4 0/1:16:2:1,1:8,6:0.125:2,2:37:0:30:1:1:1.30929:60:4:0.125:0:1.5 -16 1035074 . G T 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07609;SOR=0;LSEQ=CACATCAAGACGGAGCAGCC;RSEQ=AGCCCCGGCCACTACGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:25.5:1:28.5:1:1:3.1622:60:4:0.2857:0:1 0/0:17:0:0,0:9,8:0:2,0:31.4:1:29.6:1:1:0:60:34:1:0:0.5 -16 1035077 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAAGACGGAGCAGCCGAG;RSEQ=CCCGGCCACTACGGCGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:29.9:1:30.3:1:1:0:60:14:1:0:0.4 0/1:17:2:1,1:8,7:0.1176:2,2:35:0:31:0:1:1.13389:60:4:0.1176:0:1.5 -16 1035107 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACGGCGACCAGCCCCGAGG;RSEQ=TCGCCCGACTACGGTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:26.1:1:29.4:1:1:0:60:6:1:0:0.4 0/1:15:2:1,1:5,8:0.1333:2,2:28:1:29.5:1:1:1.55:60:4:0.1333:0:1 -16 1601287 . A G 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04565;SOR=1.70117;LSEQ=ACACAATGACCACGGCTGGC;RSEQ=GGGGTGGGCAGGTGCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:41:20,21:49,51:0.2908:2,2:27.6:1:30.2:1:1:1.00876:60:82:0.295:0:1.8 0/1:141:58:29,29:44,38:0.4113:2,2:27.3:1:29.9:1:0.73239:1.15668:60:57:0.4161:0:1.6 -16 1601299 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24397;SOR=0;LSEQ=CGGCTGGCAGGGGTGGGCAG;RSEQ=TGCAACTCTAAGCCGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:66,75:0.014:2,2:24:1:28:1:1:1.14:60:4:0.0143:0:2 0/0:146:0:0,0:74,72:0:2,0:26.4:1:30.4:1:1:0:60:35.5:1:0:0.7 -16 1601321 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24327;SOR=Inf;LSEQ=GCAACTCTAAGCCGAGGCCC;RSEQ=AAGGATCAGCAGCAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:62,69:0:2,0:27.1:1:29.7:1:1:0:60:20.833:1:0:0.7 0/1:128:2:1,1:57,67:0.0156:2,2:40.5:1:29.5:1:1:1.17:60:4:0.016:0:1 -16 1601331 . C A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.88889;SOR=1.07467;LSEQ=GCCGAGGCCCGAAGGATCAG;RSEQ=AGCAGGAGGGGCCCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:37:17,20:37,49:0.3008:2,2:26.4:1:29.7:1:0.84375:1.12:60:36:0.2975:0:1.8 0/1:117:37:16,21:34,46:0.3162:2,2:22.3:1:27.9:1:1:1.03:60:11.333:0.3036:0:1.8 -16 1601458 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCCCCAGGGTGGCAGA;RSEQ=GGGCGGCCGCAGGTAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:1:0,0:28.4:1:31.5:1:1:0:60:24:1:0:1.2 1/1:6:6:0,6:0,0:1:0,0:13.8:1:31.7:1:1:0:60:12:1:0:2.2 -16 1968638 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50714;SOR=0;LSEQ=AGGCCCTGGCTCGCTTGACT;RSEQ=CGGCATCTTCACCTCTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:17,14:0.0606:2,2:24.5:1:27.5:1:1:1.20712:60:4:0.0625:0:1 0/0:23:0:0,0:11,12:0:2,0:23.3:1:30.6:1:1:0:60:22:1:0:0.3 -16 1970124 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGTCCCCACGGTCTCAGCCG;RSEQ=CCCCATGGTCTCAGCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:30.5:1:30.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:31.5:1:1:0:48:4:1:0:4.5 -16 1970176 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAGTCCCCACGGTCTCAGC;RSEQ=GTCCCCACGGTCTCAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13.5:1:31:1:1:0:53:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:30.5:1:1:0:48:4:1:0:4.5 -16 1970194 . AG CA 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=GCCGTCCCCACGGTCTCAGC;RSEQ=TCCCCACGGTCTCAGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:43:0:30:0:1:0:46:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29:1:1:0:48:4:1:0:3.5 -16 1986839 . G A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGCTAAAACACTGAAA;RSEQ=AAACTGGCCCAGCCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:10,1:0.1538:2,0:34:1:27.5:1:1:0:60:4:0.1538:0:7 0/0:6:0:0,0:6,0:0:0,0:22.3:1:33.3:1:1:0:60:12:1:0:0 -16 1986945 . T C 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51937;SOR=0;LSEQ=GGCACCTCTTCTCTCTCGCT;RSEQ=TTGTTGCAAGGATACGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:113,34:0.0134:2,2:13:0:30:1:0.41584:3.29014:60:4:0.0137:0:1 0/0:98:0:0,0:72,26:0:2,0:20:1:29.4:1:1:0:60:48:1:0:0.3 -16 1986949 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16508;SOR=Inf;LSEQ=CCTCTTCTCTCTCGCTTTTG;RSEQ=TGCAAGGATACGCTGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:118,42:0:2,0:22:1:30:1:1:0:60:159:1:0:0.3 0/1:110:2:1,1:78,30:0.0182:2,2:17:1:32.5:1:0.48607:2.57407:60:4:0.0183:0:1 -16 1986980 . C G 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00176;SOR=0.46684;LSEQ=CGCTGCGGCCTTCTGTAAGT;RSEQ=CCCCTAATAAATGCTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:66:44,22:114,78:0.2558:2,2:22.6:1:31.8:1:0.30955:1.37:60:65:0.2549:0:1.5 0/1:210:29:18,11:109,71:0.1381:2,2:26:1:31.7:1:1:1.07:60:28:0.1359:0:1.4 -16 1987049 . C A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=AGTTCAGATCCCAACTGGCC;RSEQ=CATCTTGCAATGCTTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:94,136:0:2,0:24.8:1:30.7:1:1:0:60:31.857:1:0:0.5 0/1:261:15:7,8:111,135:0.0575:2,2:37.5:1:29.7:1:1:1.06:60:30:0.0591:0:2.4 -16 1987058 . A G 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37054;SOR=0.80996;LSEQ=CCCAACTGGCCCCATCTTGC;RSEQ=ATGCTTTGGGGCCATCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:53:20,33:58,93:0.2598:2,2:22.8:1:30.2:1:1:1.02889:60:52:0.2562:0:1.5 0/1:235:52:24,28:84,99:0.2213:2,2:25.8:1:29.7:1:1:1.01:60:104:0.2261:0:1.7 -16 1987179 . C T 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00675;SOR=0;LSEQ=ATCCACTCCCACATGCTCCC;RSEQ=GGATTTCTGTGGGTATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:8:1,7:1,31:0.2:1,2:24.9:1:28.8:1:0.3641:4.21:60:7:0.1795:0:1.3 0/0:33:0:0,0:3,30:0:2,0:20.4:1:29.8:1:1:0:60:66:1:0:0.1 -16 1987238 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTGGAGCCTTGTTCCGT;RSEQ=CCCTCCAGGGCCTGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:0,13:0.1333:1,2:9.5:1:27:1:0.13333:0:60:4:0.1429:0:1 0/0:6:0:0,0:0,6:0:0,0:25.2:1:33.5:1:1:0:60:12:1:0:0 -16 2098815 . G A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25142;SOR=0;LSEQ=TGCAGAGAAGGCTGGGTTTG;RSEQ=TCTTGCACCAGGTTCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:29,187:0.0137:2,2:12.7:1:24:1:0.35864:3.20:60:2:0.0094:0:2.3 0/0:192:0:0,0:44,148:0:2,0:21:1:30.7:1:1:0:60:95:1:0:0.1 -16 2100311 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57954;SOR=2.66396;LSEQ=AGTCTCTAGTCTGGAAAATG;RSEQ=AGTGGGAGTCTTTAGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:1,0:182,33:0.0046:2,0:10:0:30:0:1:0:60:2:0.0047:0:1 0/1:163:2:1,1:136,25:0.0123:2,2:20.5:1:27.5:1:0.2944:5.35403:60:4:0.0126:0:2 -16 2100342 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65717;SOR=1.96411;LSEQ=TTTAGGTGGTTTGTGACTTG;RSEQ=AGTTAAGGAGACCGTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:2:1,1:246,104:0.0057:2,2:21:1:21:1:0.50821:2.3589:60:1:0.0029:0:2.5 0/1:270:3:2,1:193,74:0.0111:2,2:9.7:1:27.3:1:1:1.30272:60:6:0.0113:0:1 -16 2100548 . G A 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26115;SOR=0;LSEQ=ACTATTCAGAGCCTGAGTTT;RSEQ=CTTTTTTTAGGAACATGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:2,1:43,210:0.0115:2,2:21.3:1:26.3:1:0.08072:9.63:60:6:0.0123:0:1 0/0:200:0:0,0:35,163:0:2,0:25.5:1:30.8:1:1:0:60:11.375:1:0:0.3 -16 2102486 . T A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCTGGCTAAGTTTTGTA;RSEQ=TTTTTGTCGTGACAGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:6:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:37.5:1:29:1:1:0:60:4:1:0:1.5 -16 2103242 . C T 136 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=43.79641;LSEQ=GGCTCTCAGTCACAAGCCCC;RSEQ=GTTGTTCCTCCCTGTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:1:0,1:160,21:0.0055:2,0:1:0:26:0:0.12088:0:60:2:0.0056:0:1 0/1:112:22:20,2:75,15:0.1964:2,2:19.9:1:30.5:1:0.51728:1.99:60:21:0.1909:0:1 -16 2103261 . C T 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGTTGTTCCTCCCTGTCCT;RSEQ=CGCTCACGGCACTGCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:193,42:0:2,0:23.6:1:30.9:1:1:0:60:77.333:1:0:0.1 0/1:159:14:11,3:118,27:0.0881:2,2:21.1:1:28.2:1:0.72906:1.19056:60:13:0.0839:0:1.1 -16 2103266 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16363;SOR=Inf;LSEQ=GTTCCTCCCTGTCCTCCGCT;RSEQ=ACGGCACTGCTCCAGTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:204,47:0:2,0:24.1:1:30.8:1:1:0:60:34.857:1:0:0.1 0/1:171:2:1,1:134,35:0.0117:2,2:18.5:1:28:1:0.37771:3.78908:60:4:0.012:0:1 -16 2103485 . C T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=GGCGACGCTGGGATGGGTGA;RSEQ=GTCAGGCTGCCCACTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:64,190:0:2,0:24.3:1:29.6:1:1:0:60:30.75:1:0:0.2 0/1:159:8:1,7:39,111:0.0503:2,2:18.9:1:30:1:0.68052:2.44826:60:16:0.0516:0:1.3 -16 2104217 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1704;SOR=Inf;LSEQ=CCAGGGCTGGAGTCCGGGTG;RSEQ=CCCTGCACTTCAGGGACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:208,26:0:2,0:22.3:1:31.8:1:1:0:60:77:1:0:0.1 0/1:165:2:1,1:138,25:0.0121:2,2:15:1:27.5:1:0.29113:5.43247:60:4:0.0123:0:1 -16 2105055 . A G 71 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACGTCTCCTCCGAGCC;RSEQ=CTCTCTGCTGGGGGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:3,0:0.625:0,2:33.8:1:31:1:1:0:60:10:0.7143:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 2105280 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCTGTCTGTTGCTGCCG;RSEQ=GGGACTGATGATGGGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:2,0:91,2:0.0211:1,0:25.5:1:31:1:1:0:60:4:0.0215:0:1 0/0:32:0:0,0:31,1:0:1,0:19.2:1:31.1:1:1:0:60:64:1:0:0.3 -16 2105335 . C G 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.82036;SOR=0.929;LSEQ=TTGGACACACTGTCCTGCGG;RSEQ=GGGAGGGGGAGGTGAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:68:59,9:146,14:0.2982:2,2:20.7:1:30.7:1:0.33879:1.58734:60:67:0.3032:0:1.2 0/1:159:45:35,10:99,15:0.283:2,2:24:1:30.8:1:0.22509:1.87758:60:90:0.2866:0:1.6 -16 2105400 . C T 204 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=198.87799;LSEQ=AACTGCCGCCGCTTCTCCCC;RSEQ=AGCTGACTTTGTCCTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:790:1:0,1:499,289:0.0013:2,0:1:0:26:0:0.36755:0:60:2:0.0013:0:1 0/1:590:119:78,41:289,181:0.2017:2,2:25.8:1:29.7:1:0.4591:1.19:60:238:0.2038:0:1.3 -16 2105555 . G A 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93149;LSEQ=GAGATCCTGTTCTGATAATG;RSEQ=TCCTAAGTTCAGCTCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:39,245:0.0104:2,2:10.7:1:22.3:1:0.05447:12.37:60:2:0.0072:0:3 0/0:206:2:1,1:40,163:0.0097:2,2:37:1:30.5:1:0.36078:4.04:60:4:0.0099:0:1 -16 2106113 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.072;SOR=Inf;LSEQ=TGAGCCATGCGTGTTATTGA;RSEQ=GTCATAGAGTGACTAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:321,58:0:2,0:23.5:1:31.7:1:1:0:60:125.333:1:0:0.1 0/1:271:3:2,1:222,46:0.0111:2,2:24.3:1:29.7:1:0.4366:2.40299:60:6:0.0112:0:1.3 -16 2106362 . C G 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00196;SOR=Inf;LSEQ=GTAGCCCTGGGCAAGCTGCT;RSEQ=GGTCTCTCTGAGCCTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:11,189:0:2,0:24.6:1:30:1:1:0:60:65.667:1:0:0.1 0/1:112:6:0,6:2,104:0.0536:1,0:30.3:1:29.3:1:1:0:60:12:0.0545:0:1.2 -16 2106547 . C A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10307;SOR=Inf;LSEQ=ATGGCAGCGGGGAGAGGTGG;RSEQ=AGCGCAGGCTGAAGGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:193,28:0:2,0:24.5:1:31.9:1:1:0:60:43.2:1:0:0.1 0/1:105:2:1,1:90,13:0.019:2,2:9:0:27:1:0.25:6.70931:60:4:0.0194:0:1 -16 2106864 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55382;SOR=0;LSEQ=GAATGGTTGTCTGATTCTTG;RSEQ=GGTGGCCAGACAATGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:3:0,3:26,170:0.0151:2,0:34:1:29.7:1:1:0:60:6:0.0152:0:2.3 0/0:105:0:0,0:4,100:0:1,0:27.1:1:30.1:1:1:0:60:33.667:0.9902:0:0.1 -16 2107033 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14732;SOR=Inf;LSEQ=TATAGGGCAGCAGCCAGGCG;RSEQ=GGCCAGCAGCGGGACTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:223,78:0:2,0:22.2:1:30.6:1:1:0:60:42:1:0:0.1 0/1:188:2:1,1:145,41:0.0106:2,2:17:1:28.5:1:0.39783:3.50607:60:4:0.0108:0:1 -16 2107200 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30496;SOR=4.71977;LSEQ=GTGAGTGTGGTGGGTGGGGC;RSEQ=CAGGGCAGTGGAGGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:1:1,0:137,294:0.0023:2,0:1:0:26:0:0.31944:0:60:2:0.0024:0:2 0/1:277:3:2,1:101,173:0.0108:2,2:9.3:1:27:1:0.55758:3.41:60:6:0.0113:0:1 -16 2107322 . G T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01255;SOR=Inf;LSEQ=GAGGCTGCCACTAGAGCGAG;RSEQ=CCCATGACTTCTAGGATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:3,63:0:1,0:23.7:1:32.1:1:1:0:60:32:1:0:0 0/1:21:3:0,3:1,17:0.1429:1,0:25.3:1:31:0:1:0:60:6:0.1579:0:1 -16 2108627 . G GC 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.66881;SOR=0.44141;LSEQ=CCTTCCCCAGCGGTGCTCCT;RSEQ=CCCCCCCCAAGCACAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:5:5,0:142,1:0.0338:1,0:20.8:1:31.1:1:1:0:60:10:0.0342:0.0068:0.2 0/1:66:1:1,0:64,1:0.0152:1,0:45:0:32:0:1:0:60:2:0.0152:0:0 -16 2108678 . C T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00342;SOR=Inf;LSEQ=GCTGCAGGAGCCTCGGCAAC;RSEQ=TCACACATCCATGGCGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:297,90:0:2,0:21.6:1:31:1:1:0:60:128:1:0:0.1 0/1:248:6:2,4:181,61:0.0242:2,2:13.2:1:27.3:1:0.04233:5.88235:60:12:0.0246:0:1.2 -16 2108920 . T C 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03438;SOR=Inf;LSEQ=GCTGGCAGGAACGGGAGAGC;RSEQ=CCCCTCACGCCTGCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:124,275:0:2,0:22.8:1:29.9:1:1:0:60:27.5:0.9974:0:0.1 0/1:304:4:2,2:107,193:0.0132:2,2:22.5:1:28.3:1:0.61982:1.80:60:8:0.0138:0:1.8 -16 2109252 . G C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCTCGAATTCCTGACCT;RSEQ=AAGTGATCCACCCATCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:41.5:1:33.5:1:1:0:40.5:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:19.5:1:31:1:1:0:49:4:1:0:1 -16 2110571 . C G 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66402;SOR=0.85849;LSEQ=AACGTGTGGTGGGCACTGCG;RSEQ=GCTCAGGCGTGCTACTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:99:93,6:47,2:0.6689:1,2:22.9:1:30.8:1:1:1.51216:60:32:0.6621:0:1.1 1/0:82:52:48,4:24,5:0.6341:2,2:21.8:1:29.7:1:0.27005:2.47:60:16.333:0.6282:0:1.1 -16 2110573 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11965;SOR=Inf;LSEQ=CGTGTGGTGGGCACTGCGCG;RSEQ=TCAGGCGTGCTACTCTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:146,10:0:2,0:22.5:1:32.1:1:1:0:60:77:1:0:0.7 0/1:83:2:1,1:73,8:0.0241:2,2:37:0:30:1:0.20629:8.66381:60:4:0.0247:0:1.5 -16 2110575 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11382;SOR=Inf;LSEQ=TGTGGTGGGCACTGCGCGCT;RSEQ=AGGCGTGCTACTCTCGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:154,10:0:2,0:22.3:1:31.3:1:1:0:60:53.667:1:0:0.7 0/1:84:2:1,1:72,10:0.0238:2,2:13.5:1:26.5:1:0.24613:6.91238:60:4:0.0238:0:2 -16 2110577 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54145;SOR=0;LSEQ=TGGTGGGCACTGCGCGCTCA;RSEQ=GCGTGCTACTCTCGGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:154,9:0.0121:2,2:7.5:1:32:0:0.11789:16.28546:60:4:0.0122:0:2 0/0:90:0:0,0:78,12:0:2,0:23:1:31.5:1:1:0:60:44:1:0:0.8 -16 2110583 . C A 29 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90752;LSEQ=GCACTGCGCGCTCAGGCGTG;RSEQ=TACTCTCGGTCCCAAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:166,10:0.0112:2,2:29:0:29:1:0.1201:15.86783:60:4:0.0113:0:2 0/1:98:1:1,0:81,16:0.0102:2,0:28:0:31:0:1:0:60:2:0.0105:0:2 -16 2110608 . G A 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCGGTCCCAAGGGTGACTG;RSEQ=GAGGGCGTCCCACAGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:228,38:0:2,0:24.8:1:31.2:1:1:0:60:132:1:0:0.4 0/1:179:19:15,4:125,35:0.1061:2,2:23:1:28.3:1:1:1.05:60:18:0.1017:0:1.1 -16 2110795 . G A 227 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00592;LSEQ=TCTGCTGAACATCATCGAAC;RSEQ=GCTCCTTCAGCAGCTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:905:173:71,102:331,401:0.1912:2,2:26.3:1:30.6:1:0.34964:1.18561:60:85.5:0.1924:0:1.1 0/0:717:1:1,0:319,397:0.0014:2,0:37:0:25:0:0.4463:0:60:2:0.0014:0:1 -16 2111735 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25453;SOR=4.13201;LSEQ=CGGCCTCAGAGGGCTGGGGG;RSEQ=GTCTGTCCCCATGCGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:1,0:91,3:0.0105:1,0:7:0:31:0:1:0:60:2:0.0108:0:1 0/1:47:2:2,0:44,1:0.0426:1,0:29.5:1:29:1:1:0:60:4:0.0435:0:1 -16 2111779 . T C 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90489;SOR=0.96549;LSEQ=CGGCCTGAGAGGGCTGAGGG;RSEQ=GTCTCCATGCGGTGGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:193:120:111,9:66,7:0.6218:2,2:23.2:1:31.4:1:0.60215:1.31:60:39:0.6223:0:1 1/0:119:73:67,6:44,2:0.6134:1,2:24.8:1:31.6:1:0.48278:1.9599:60:35.5:0.6121:0:1.2 -16 2112382 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15649;SOR=Inf;LSEQ=TTGTGTCTGGGCTGTGGGCT;RSEQ=CAGGCTGTGAGGCGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:170,8:0:1,0:25.2:1:32:1:1:0:60:34.6:1:0:0.1 0/1:117:2:2,0:111,4:0.0171:1,0:26:1:28.5:1:1:0:60:4:0.0171:0:1 -16 2112384 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1613;SOR=Inf;LSEQ=GTGTCTGGGCTGTGGGCTGC;RSEQ=GGCTGTGAGGCGGCTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:175,9:0:1,0:25.1:1:29.9:1:1:0:60:29.667:1:0:0.1 0/1:124:2:1,1:119,3:0.0161:1,2:19:1:30.5:1:0.06373:34.50252:60:4:0.0163:0:1 -16 2112668 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15283;SOR=Inf;LSEQ=GTCTCTGTCTGGGGCCCACC;RSEQ=GGGCTGGGTCTCAGGATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:50,239:0:2,0:22.1:1:29.9:1:1:0:60:71.25:1:0:0.1 0/1:186:2:1,1:29,153:0.0108:2,2:40.5:1:31.5:1:0.30025:5.20:60:4:0.011:0:1 -16 2113135 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65507;SOR=2.05457;LSEQ=TCTGTTGTGCACGTGCTCCC;RSEQ=CAGAGCCGGGCTCTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:2:0,2:70,329:0.005:2,0:41:1:30:1:1:0:60:4:0.0052:0:1 0/1:294:3:2,1:63,228:0.0102:2,2:5:1:26.7:1:0.12404:7.17:60:6:0.0103:0:1.7 -16 2114407 . C T 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACACACACCACTTCAACAG;RSEQ=CTGCTGGACATCATCGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:767:0:0,0:305,462:0:2,0:26:1:31.3:1:1:0:60:41.611:1:0:0.1 0/1:630:84:35,49:235,311:0.1333:2,2:25.4:1:28:1:0.90581:1.0578:60:15.8:0.1274:0:1.2 -16 2115413 . CAAAAAAAAAAAAAAA C 187 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=24.000;MSILEN=1;SSF=0;SOR=0.20264;LSEQ=GACAGAGCAAGACTCGATCT;RSEQ=AAAAAAAAAGGTGTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:66:64,2:88,1:0.3529:1,1:28.3:1:31.1:1:0.57539:2.73218:59.8:32:0.3575:0:0.2 0/1:111:11:10,1:60,6:0.0991:2,2:23:1:30.4:1:1:1:60:22:0.1048:0.0541:0 -16 2115447 . G T 45 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1604;SOR=0;LSEQ=AAAAAAAAAAAGGTGTTTGT;RSEQ=GTAGAAAGTGTTCTCACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:4:1,3:295,78:0.0106:2,2:6.3:1:22.5:1:0.0325:11.24515:55:3:0.0082:0:1.8 0/0:241:0:0,0:171,70:0:2,0:17.7:1:28.9:1:1:0:59:12.389:1:0:1.3 -16 2115481 . C T 191 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=204.33908;LSEQ=TCACGGCTGCTGACTCAGAA;RSEQ=CATGAGCCTGTGTGTAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:787:1:0,1:506,279:0.0013:2,0:1:0:27:0:0.35623:0:60:2:0.0013:0:1 0/1:532:110:68,42:258,164:0.2068:2,2:26.3:1:28.3:1:0.913:1.03:60:11.222:0.1977:0:1.3 -16 2115506 . C T 176 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=48.16833;LSEQ=AGCCTGTGTGTAAGTCCTGG;RSEQ=CTTCTCTTCAAAGGTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1013:2:1,1:589,419:0.002:2,2:6:1:29.5:1:1:1.40522:60:4:0.002:0:1 0/1:747:65:42,23:376,304:0.087:2,2:28.5:1:29.3:1:0.15299:1.48:60:130:0.0894:0:1.3 -16 2115712 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13948;SOR=Inf;LSEQ=AGCTGCATCTGCGTTGTGTT;RSEQ=GAGTCTGTTCCCCAGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:33,248:0:2,0:23.2:1:31:1:1:0:60:55.2:1:0:0.1 0/1:168:2:1,1:33,133:0.0119:2,2:9.5:1:28:1:0.36477:3.99:60:4:0.0123:0:1 -16 2115819 . A G 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75613;SOR=0.73727;LSEQ=TCTTGTGGAGGGATGGATGC;RSEQ=AGAGGCCCCGTTGTACGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:30:1,29:0,10:0.7317:0,1:23.2:1:31:1:1:0:60:29:0.7632:0:1.2 1/0:18:12:0,12:0,6:0.6667:0,0:31.9:1:30.8:1:1:0:60:11:0.6471:0:1.5 -16 2120402 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.35943;LSEQ=TCCGGGACAAGGGTGCTGTC;RSEQ=TAGGACTGCGTTTTCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:435:227:159,68:141,66:0.5218:2,2:22.8:1:31.1:1:0.67852:1.09:60:112.5:0.5245:0:1.1 0/1:302:85:61,24:146,71:0.2815:2,2:23.2:1:30.1:1:0.49276:1.24:60:84:0.2791:0:1.2 -16 2120643 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17767;SOR=Inf;LSEQ=CAGGTATCCCCGTCTCGGCA;RSEQ=GTGTGGTTCCTGGAAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:17,146:0:2,0:22.6:1:31.2:1:1:0:60:162:1:0:0.1 0/1:120:2:1,1:19,99:0.0167:2,2:29.5:1:32:0:0.30672:5.10:60:4:0.0168:0:1.5 -16 2120663 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16879;SOR=Inf;LSEQ=GGTGTGGTTCCTGGAAGCTG;RSEQ=AGAGACGGCCCCAGGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:6,108:0:2,0:22.7:1:32.2:1:1:0:60:113:1:0:0.1 0/1:80:2:1,1:7,71:0.025:2,2:19.5:1:26.5:1:0.19114:9.55:60:4:0.025:0:1 -16 2121725 . C T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06901;SOR=Inf;LSEQ=GTCCCAGGGTTGGGAAGAGC;RSEQ=AAGTCTGTTCCGTTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:242,175:0:2,0:23.1:1:31:1:1:0:60:45.333:1:0:0.1 0/1:291:3:1,2:180,108:0.0103:2,2:25.7:1:22.7:1:0.55916:3.31911:60:2:0.007:0:1 -16 2121888 . G A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03734;SOR=Inf;LSEQ=CCGCCGTGCGGCTGGGGTCC;RSEQ=TGCCCTACTCCCTGCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:0:0,0:211,283:0:2,0:23.5:1:30.9:1:1:0:60:246:1:0:1 0/1:389:4:2,2:178,207:0.0103:2,2:5.3:1:28.5:1:1:1.16:60:8:0.0105:0:2 -16 2121961 . C A 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0437;SOR=Inf;LSEQ=TGGGGCCGGGCAGGGACCAT;RSEQ=CGTCCCACGTTGGGCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:128,204:0:2,0:26.1:1:31:1:1:0:60:35.889:1:0:0.2 0/1:282:4:3,1:114,164:0.0142:2,2:7.5:1:25.8:1:0.31058:4.29:60:8:0.0146:0:1 -16 2121994 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08641;SOR=Inf;LSEQ=GGCCAGGAGGACAGGGAGCT;RSEQ=CCACCTGCCTGCTGGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:75,137:0:2,0:23.3:1:31.3:1:1:0:60:29.286:1:0:0.1 0/1:169:3:2,1:61,105:0.0178:2,2:15.7:1:28.3:1:0.55635:3.42:60:6:0.0182:0:1 -16 2122005 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.16025;SOR=Inf;LSEQ=CAGGGAGCTGCCACCTGCCT;RSEQ=CTGGGCCTCCCTCCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:68,126:0:2,0:21.9:1:31.6:1:1:0:60:47.5:1:0:0.1 0/1:130:2:1,1:42,86:0.0154:2,2:27.5:1:27:1:1:2.04:60:4:0.0159:0:1 -16 2122139 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13298;SOR=Inf;LSEQ=GCTGAGAACAGGGCTCCATA;RSEQ=CCCTTGACGCTGTGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:168,28:0:2,0:24.4:1:32:1:1:0:60:31.667:1:0:0.1 0/1:113:2:2,0:97,14:0.0177:2,0:26.5:1:28:1:1:0:60:4:0.0179:0:1 -16 2122476 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGGCTCGGGCTCCATTTC;RSEQ=CTCAAACTCAGCTGCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:2,86:0.0222:1,2:28.5:1:31:1:0.06592:35.31:60:4:0.0227:0:1 0/0:43:0:0,0:0,43:0:1,0:24:1:31.6:1:1:0:60:42:1:0:0.1 -16 2122708 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACTCCGAAAGGGAGGCC;RSEQ=TTCCTGGGAGGGAGGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:2,0:80,8:0.0222:2,0:20.5:1:29.5:1:1:0:60:4:0.0222:0:1 0/0:34:0:0,0:34,0:0:1,0:20.9:1:30.5:1:1:0:60:68:1:0:0.1 -16 2123009 . G A 72 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02475;SOR=9.04358;LSEQ=GAGGTCAGAGCAGGACAGGC;RSEQ=AGCTTGATGGGGCCTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:1:1,0:160,341:0.002:2,0:1:0:27:0:0.32072:0:60:2:0.002:0:1 0/1:394:7:5,2:132,255:0.0178:2,2:9.6:1:26:1:0.05251:4.81:60:6:0.0156:0:1.1 -16 2123028 . A G 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07035;SOR=Inf;LSEQ=CGAGCTTGATGGGGCCTGGG;RSEQ=TTCGAGGGCCTGGCCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:98,295:0:2,0:23.8:1:30.4:1:1:0:60:48.125:1:0:0.1 0/1:278:3:1,2:75,200:0.0108:2,2:18.7:1:24.3:1:1:1.33:60:2:0.0075:0:2.7 -16 2124115 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18693;SOR=Inf;LSEQ=CTAAGCCTCGGCTGTTCTCC;RSEQ=GGTGGAGCACTCGAGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:103,4:0:1,0:24.3:1:30.8:1:1:0:60:34.667:1:0:0.1 0/1:82:2:1,1:73,7:0.0244:2,2:6:1:28.5:1:0.18669:9.82164:60:4:0.0247:0:1 -16 2124148 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07833;SOR=Inf;LSEQ=GAGGTTGGCGAGGGGTAGGC;RSEQ=AGGCTGCCTCTGCTGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:201,33:0:2,0:21.7:1:30.4:1:1:0:60:233:1:0:0.1 0/1:176:3:2,1:130,42:0.017:2,2:20.7:1:25:1:0.57327:1.54337:60:2:0.0118:0:2 -16 2124170 . G T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06174;SOR=Inf;LSEQ=GGCTGCCTCTGCTGCAAGCG;RSEQ=GTGGGGCCTGAGGTGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:298,83:0:2,0:23.2:1:30.9:1:1:0:60:37.1:1:0:0.1 0/1:250:3:2,1:173,74:0.012:2,2:16:1:20.7:1:1:1.16815:60:2:0.0083:0:2.7 -16 2124176 . G T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30771;SOR=4.50692;LSEQ=CTCTGCTGCAAGCGGGTGGG;RSEQ=CCTGAGGTGTCCTGTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:1,0:316,92:0.0024:2,0:24:0:32:0:1:0:60:2:0.0025:0:1 0/1:274:3:1,2:186,84:0.0109:2,2:16.3:1:27:1:0.2343:4.40175:60:6:0.0112:0:1 -16 2124431 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15704;SOR=4.91235;LSEQ=CGCATGCACCCGAGAGGTTC;RSEQ=GGCTGTGTAACCTGTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:1:1,0:104,344:0.0022:2,0:1:0:29:0:0.23385:0:60:2:0.0023:0:1 0/1:276:3:2,1:73,200:0.0109:2,2:5.7:1:28.7:1:0.1804:5.44:60:6:0.0111:0:1.3 -16 2125687 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54798;SOR=0;LSEQ=GCCACGTCCGTGTGGCCGTG;RSEQ=CCTTCTCTCCTCTGCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:145,5:0.0132:1,2:9:1:28.5:1:0.07764:26.56453:60:4:0.0134:0:1 0/0:79:0:0,0:77,2:0:1,0:22.3:1:31.4:1:1:0:60:158:1:0:0.1 -16 2125769 . G A 134 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=42.59099;LSEQ=AGGCGCTGCACGGGACCCCG;RSEQ=CTCCCCTGACCACCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:748:1:1,0:517,228:0.0013:2,0:12:0:19:0:1:0:60:0:0:0:1 0/1:444:24:16,8:278,140:0.0541:2,2:22.3:1:29.3:1:1:1.01:60:48:0.0549:0:1.1 -16 2125788 . C T 196 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTCCCCTGACCACCCTCT;RSEQ=CATTACCGCAGCTCTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:947:0:0,0:589,358:0:2,0:25.6:1:31:1:1:0:60:71.846:1:0:0.1 0/1:650:108:67,41:337,205:0.1662:2,2:21.9:1:29.1:1:1:1.00596:60:53:0.1661:0:1.5 -16 2125834 . T C 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=45.36562;LSEQ=CCGCACCTCTACAGGAACTT;RSEQ=GCCGCGGAGCAGTATGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1416:2:0,2:742,672:0.0014:2,0:17.5:1:19:1:0.22639:0:60:1:7e-04:0:1.5 0/1:1095:66:36,30:545,483:0.0603:2,2:25.8:1:30.2:1:0.89889:1.06:60:65:0.0604:0:1.7 -16 2125937 . C G 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCTCCCAGCCGTGGCCCC;RSEQ=GCTAGGCCTTGCGGCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:779:0:0,0:313,464:0:2,0:24:1:30:1:1:0:60:50.8:0.9974:0:0.1 0/1:540:84:30,54:168,286:0.1556:2,2:23.7:1:29.2:1:0.90214:1.05724:60:41:0.1536:0:1.3 -16 2126322 . C T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0916;SOR=Inf;LSEQ=GCGCTGGGGGCTCTGCTGGG;RSEQ=AGCCTGCAGGGCTTTGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:78,66:0:2,0:25.3:1:32:1:1:0:60:35:1:0:0.1 0/1:63:2:1,1:24,37:0.0317:2,2:34:0:27:1:1:1.53:60:4:0.0328:0:1 -16 2126452 . A G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGAGGGCCTCCAGCCCCC;RSEQ=TTGCCACCCCTCACTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:649:0:0,0:430,219:0:2,0:23.9:1:30.3:1:1:0:60:107.167:1:0:0.1 0/1:489:31:20,11:294,163:0.0634:2,2:23.7:1:30:1:1:1.01:60:62:0.064:0:1.1 -16 2127762 . G A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGGTGGGGGGCACGGACCCT;RSEQ=GAGCTTGGCCCCGTGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:81,284:0:2,0:23.6:1:31.2:1:1:0:60:72:1:0:0.1 0/1:225:12:3,9:54,159:0.0533:2,2:31.2:1:30.6:1:1:1.01879:60:24:0.0541:0:1 -16 2127944 . G T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=CGCATCCCCAGGCCCCCTCG;RSEQ=GGTGCCGCTCCGAGAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:1,4:0,6:0.4545:0,2:22.6:1:27:1:0.45455:0:60:4:0.4:0:1 0/0:2:0:0,0:0,2:0:0,0:28.5:1:32:0:1:0:60:4:1:0:0 -16 2128670 . C T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGCTTGCCGGAGGCAGCCTG;RSEQ=GGGCAGAATGCAATCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:43.5:1:34:0:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:50:0:30.5:1:1:0:60:4:0.6667:0:1 -16 2128935 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12909;SOR=Inf;LSEQ=TGGGGTCTTTCCGAGCGAGG;RSEQ=CCTCAGCCGTGCATGCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:73,1:0:1,0:23.6:1:29.8:1:1:0:60:148:1:0:0.1 0/1:42:2:1,1:37,3:0.0476:2,2:31.5:1:31.5:1:0.18351:10.82458:60:4:0.0476:0:1 -16 2129003 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17767;SOR=Inf;LSEQ=CGGCCCGCCCTACCTGGCAC;RSEQ=CTGACCCTGGTCACGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:177,56:0:2,0:23.1:1:30.6:1:1:0:60:45.6:0.9956:0:0.2 0/1:171:2:1,1:121,48:0.0117:2,2:8.5:1:27.5:1:0.49219:2.50528:60:4:0.012:0:1 -16 2129455 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06058;SOR=Inf;LSEQ=TGCACCTTCCTTTCCTCCGC;RSEQ=CCTGCCAGCCTCGACACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:197,221:0:2,0:23.8:1:30.7:1:1:0:60:37:1:0:0.2 0/1:272:3:2,1:124,144:0.011:2,2:9.3:1:24.3:1:0.59901:2.32:60:6:0.0112:0:1.7 -16 2129482 . C T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38495;SOR=2.34358;LSEQ=AGCCTCGACACCGGCTGTCC;RSEQ=GAGCCCAGGCCCACGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:2:0,2:216,197:0.0048:2,0:21.5:1:20:1:0.22933:0:60:1:0.0025:0:1.5 0/1:267:3:1,2:142,121:0.0112:2,2:22.7:1:29.3:1:0.59736:2.33979:60:6:0.0115:0:1 -16 2129489 . A G 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.0629;SOR=Inf;LSEQ=ACACCGGCTGTCCCGAGCCC;RSEQ=GGCCCACGTGGCACCCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:227,191:0:2,0:23.9:1:30.5:1:1:0:60:45.444:1:0:0.1 0/1:277:3:2,1:153,121:0.0108:2,2:30.7:1:21:1:1:1.58:60:2:0.0073:0:1.3 -16 2129494 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0678;SOR=Inf;LSEQ=GGCTGTCCCGAGCCCAGGCC;RSEQ=ACGTGGCACCCTCGTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:236,188:0:2,0:24.1:1:31.3:1:1:0:60:52:0.9928:0:0.1 0/1:295:3:2,1:165,125:0.0102:2,2:7.7:1:24:1:1:1.51:60:2:0.0068:0:2.7 -16 2129518 . G T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01479;SOR=Inf;LSEQ=TGGCACCCTCGTACCAGCCT;RSEQ=GGGACTAAGTCCACCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:541:0:0,0:323,218:0:2,0:24.2:1:31.5:1:1:0:60:66.625:1:0:0.1 0/1:411:5:2,3:238,168:0.0122:2,2:5.4:1:28:1:0.65324:2.12106:60:10:0.0123:0:1.2 -16 2130395 . G A 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1666;SOR=5.6643;LSEQ=ACAGGTACTGGGCGGGGCTG;RSEQ=CCTGAGCGCCATCTTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:1:1,0:171,368:0.0019:2,0:1:0:25:0:0.31852:0:60:2:0.0019:0:1 0/1:384:4:3,1:147,231:0.0104:2,2:7.3:1:24:1:0.30431:4.70:60:3:0.008:0:1.3 -16 2130492 . G GT 101 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.40809;SOR=1.65222;LSEQ=GATATTTGGGGGTAACTTTT;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:10:0,10:0,115:0.0794:1,0:23.3:1:30.7:1:1:0:60:20:0.082:0:0 0/1:56:7:0,7:2,44:0.125:1,0:17.7:1:29.8:1:1:0:60:14:0.1296:0.0179:0.6 -16 2130577 . C G 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01032;SOR=Inf;LSEQ=TCACTGCAAGCTCCACCTCC;RSEQ=GGGTTCACGCCATTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:0:1,0:26.3:1:30:1:1:0:58.4:28:1:0:0.1 1/0:5:3:0,3:0,2:0.6:0,0:32:1:29.7:1:1:0:53.3:6:0.6:0:1 -16 2131766 . G A 86 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10639;SOR=2.50165;LSEQ=CGGTGCCGGCAGCCAGCACG;RSEQ=CCAAACCCCCTCCTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1141:5:3,2:489,645:0.0044:2,2:14.4:1:30.4:1:0.65728:1.98:60:10:0.0044:0:1 0/1:826:9:6,3:364,451:0.0109:2,2:23.3:1:27.2:1:0.3125:2.48:60:18:0.0111:0:1.6 -16 2132552 . C T 77 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24944;SOR=0.23486;LSEQ=GGCTGCAGAGCGCCACTCTG;RSEQ=CTCATAGGTGCTGTGCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:6:2,4:105,334:0.0135:2,2:25:1:30:1:0.63377:1.59:60:12:0.0138:0:1.3 0/0:313:1:0,1:92,220:0.0032:2,0:16:0:31:0:1:0:60:2:0.0032:0:1 -16 2132583 . G A 197 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGTGCTCGTCGCCTCATCC;RSEQ=CCCACCCCCATGGTCCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:94:16,78:20,137:0.373:2,2:25.6:1:30.1:1:0.35798:1.40:60:188:0.3775:0:1.1 0/0:152:0:0,0:29,122:0:2,0:20.7:1:30.8:1:1:0:60:24.167:1:0:0.1 -16 2133637 . C T 44 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72822;SOR=1.35756;LSEQ=AGGCTGGTTCTCGGAGGCCA;RSEQ=GTCAGGGCCAGGGCCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:4:1,3:283,62:0.0115:2,2:2:1:28.5:1:0.02153:13.54713:60:8:0.0116:0:1.3 0/1:258:4:1,3:204,50:0.0155:2,2:9.8:1:22:1:0.02825:12.08016:60:3:0.0118:0:1 -16 2133640 . C G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGTTCTCGGAGGCCACGT;RSEQ=AGGGCCAGGGCCTGGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:304,75:0:2,0:21.3:1:31:1:1:0:60:62.167:1:0:0.1 0/1:284:19:15,4:205,59:0.0669:2,2:17.7:1:31.4:1:1:1.08:60:38:0.0676:0:1.4 -16 2134075 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCACAGCTGGTGGCAGTGCT;RSEQ=CTGCGTCAACGGGCGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:2,0:66,11:0.0253:2,0:49:0:31:1:1:0:60:4:0.0253:0:1 0/0:33:0:0,0:30,3:0:2,0:24.6:1:31.1:1:1:0:60:15.5:1:0:0.5 -16 2134095 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08979;SOR=Inf;LSEQ=GCTGCGTCAACGGGCGGGGG;RSEQ=CGTAGCCTGGTGCTCGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:95,9:0:2,0:23.5:1:32.1:1:1:0:60:103:1:0:0.1 0/1:45:2:1,1:41,1:0.0444:1,2:33:1:30:1:0.08985:29.33286:60:4:0.0488:0:1 -16 2134721 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28054;SOR=0;LSEQ=CAGGCATCAACCCCAGGTGG;RSEQ=CCTCTTGCTTCCGGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:3:2,1:91,195:0.0104:2,2:13.3:1:28.7:1:0.2432:4.26:60:6:0.0108:0:1.3 0/0:190:0:0,0:67,123:0:2,0:22.5:1:31.3:1:1:0:60:62.333:1:0:0.2 -16 2134797 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07884;SOR=Inf;LSEQ=ACTTGCCCCAGGCCGAGCGG;RSEQ=CTGGGGTGGGGTCCTCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:152,67:0:2,0:24.1:1:31.2:1:1:0:60:26.375:1:0:0.3 0/1:86:2:1,1:45,39:0.0233:2,2:10:1:29:1:1:1.15192:60:4:0.0233:0:1 -16 2134850 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25595;SOR=4.06469;LSEQ=TGGCTGGAACCCCTGGGAGG;RSEQ=CGGTGGAGTGGGAGATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:1:1,0:267,46:0.0032:2,0:1:0:25:0:1:0:60:2:0.0033:0:1 0/1:156:2:1,1:129,25:0.0128:2,2:28.5:1:27:1:0.30645:5.07951:60:4:0.0132:0:2.5 -16 2134851 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10789;SOR=Inf;LSEQ=GGCTGGAACCCCTGGGAGGG;RSEQ=GGTGGAGTGGGAGATGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:275,47:0:2,0:25.4:1:31.5:1:1:0:60:34.778:1:0:0.5 0/1:158:2:2,0:129,27:0.0127:2,0:33:1:31:1:1:0:60:4:0.0132:0:1 -16 2134852 . G A 205 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGGAACCCCTGGGAGGGC;RSEQ=GTGGAGTGGGAGATGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:113:100,13:194,35:0.3304:2,2:23.6:1:30.2:1:0.40937:1.39:60:36.667:0.3323:0:1.1 0/0:170:0:0,0:140,29:0:2,0:22.1:1:30.2:1:1:0:60:338:1:0:0.2 -16 2134868 . G T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05542;SOR=7.39247;LSEQ=GGGCGGTGGAGTGGGAGATG;RSEQ=CCAGGCTCTGTGTTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:1:0,1:367,99:0.0021:2,0:17:0:27:0:0.21413:0:60:2:0.0022:0:1 0/1:256:4:1,3:198,54:0.0156:2,2:12:1:23.3:1:0.03557:10.86168:60:3:0.0119:0:2.5 -16 2135048 . CT C 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGGCGTGGCCTCCCTCTC;RSEQ=GCATCCGCTGGAGCTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:825:0:0,0:335,488:0:2,0:24.8:1:30.4:1:1:0:60:101.875:0.9988:0:0.1 0/1:658:20:10,10:269,365:0.0304:2,2:19.4:1:29.7:1:0.50172:1.36:60:19:0.0293:0.0106:0.2 -16 2135056 . G A 68 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04878;SOR=7.61955;LSEQ=GGCCTCCCTCTCCTGCATCC;RSEQ=CTGGAGCTGTGTGGCTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:736:1:1,0:301,433:0.0014:2,0:1:0:25:0:0.41088:0:60:2:0.0014:0:1 0/1:584:6:5,1:244,334:0.0103:2,2:9.2:1:26.5:1:0.08854:6.82:60:12:0.0104:0:1.2 -16 2135059 . G A 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14878;SOR=3.82227;LSEQ=CTCCCTCTCCTGCATCCGCT;RSEQ=GAGCTGTGTGGCTCGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:706:2:2,0:280,424:0.0028:2,0:2:1:24:0:0.15921:0:60:4:0.0029:0:1 0/1:558:6:4,2:227,324:0.0108:2,2:5.2:1:27.7:1:0.23837:2.85:60:12:0.0108:0:1.3 -16 2135073 . C T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCGCTGGAGCTGTGTGGCT;RSEQ=GGGTGAATGGTGGGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:596:0:0,0:215,380:0:2,0:24.6:1:30.1:1:1:0:60:73.375:0.9983:0:0.1 0/1:409:21:6,15:154,234:0.0513:2,2:20.9:1:27.2:1:0.36495:1.64341:60:9.5:0.0476:0:1.1 -16 2135157 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02033;SOR=Inf;LSEQ=AAGCTCCCTGTGGCAGCCTG;RSEQ=CGTGACCGGCCTGGGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:231,143:0:2,0:23.8:1:31.7:1:1:0:60:92.5:1:0:0.1 0/1:229:4:2,2:129,96:0.0175:2,2:21.8:1:30:1:1:1.34198:60:8:0.0177:0:1 -16 2135390 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13541;SOR=Inf;LSEQ=CCTCAGCCTGCAGTGGGTAG;RSEQ=GAGTCTGGGCCCCCAACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:28,203:0:2,0:23.5:1:30.6:1:1:0:60:45.2:1:0:0.2 0/1:135:2:1,1:29,104:0.0148:2,2:29:1:28:1:0.39635:3.54:60:4:0.0148:0:1 -16 2135429 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCACAGAGCTCAACACTG;RSEQ=CGGGTCCCCTACAGCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:0,2:0,118:0.0167:1,0:36:1:30.5:1:1:0:60:4:0.0169:0:1 0/0:41:0:0,0:1,40:0:1,0:25.1:1:31:1:1:0:60:82:1:0:0.1 -16 2136155 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11986;SOR=Inf;LSEQ=CTGCGGGGCAGGGCCCGGCC;RSEQ=GGGAGTGATGCCACCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:199,55:0:2,0:23.7:1:30.6:1:1:0:60:62.5:1:0:0.1 0/1:135:2:1,1:89,44:0.0148:2,2:27:0:32:0:1:2.01139:60:4:0.015:0:1.5 -16 2136455 . C T 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATCCAGTCCTGCTACCCCA;RSEQ=GCCCTGGGGCATGGCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:38:4,34:28,158:0.1696:2,2:25.6:1:29.7:1:0.61401:1.50378:60:76:0.1704:0:1.1 0/0:118:0:0,0:14,104:0:2,0:23.3:1:29.4:1:1:0:60:58:1:0:0.1 -16 2136558 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGATGGGGCTGGTGGC;RSEQ=TTGCGTCCCAAAGCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:45,39:0.0233:2,2:23.5:1:32.5:1:1:1.15192:60:4:0.0241:0:1 0/0:25:0:0,0:11,14:0:2,0:17.8:1:31.4:1:1:0:60:50:1:0:0.4 -16 2136624 . T C 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=104.1546;LSEQ=CCAGGCACCAGAGGACGTGG;RSEQ=CCCCGCAGGCCCCCAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:1,0:144,14:0.0063:2,0:25:0:28:0:1:0:60:2:0.0065:0:2 0/1:62:25:21,4:36,1:0.4032:1,2:21:1:31.3:1:0.1479:6.65145:60:50:0.4032:0:1 -16 2136663 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11556;SOR=Inf;LSEQ=CCCCTGGAGTAATCAGGAGG;RSEQ=GCCCCAGTGCAAGGCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:270,63:0:2,0:23:1:30:1:1:0:60:165.5:1:0:0.2 0/1:172:2:1,1:138,32:0.0116:2,2:13.5:1:29.5:1:0.34782:4.26202:60:4:0.0118:0:1.5 -16 2138197 . TAGTG T 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGCCCAGGTGCCACCTGA;RSEQ=AGCTCACCCCCTGCCTACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:993:0:0,0:501,488:0:2,0:24.3:1:29.3:1:1:0:60:69.643:0.9969:0:0.1 0/1:710:23:9,14:367,318:0.0324:2,2:25:1:29.8:1:0.20461:1.79375:60:46:0.033:0.007:0.3 -16 2138218 . A C 245 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTGAGCTCACCCCCTGCCT;RSEQ=CGTCCCCAGATGGCCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1094:0:0,0:537,557:0:2,0:25.3:1:28.9:1:1:0:60:120.556:1:0:0.1 0/1:852:277:158,119:306,267:0.3251:2,2:24.8:1:30.3:1:0.33965:1.16:60:20.308:0.3162:0:1.6 -16 2138269 . T C 248 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCCGCTCCAACCCCACCGA;RSEQ=ATCTACCCCTCCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1161:0:0,0:548,613:0:2,0:26.5:1:29.2:1:1:0:60:49.478:1:0:0.2 0/1:942:261:123,138:324,357:0.2771:2,2:27.2:1:30.9:1:0.94192:1.01823:60:86:0.2783:0:1.6 -16 2138398 . C T 210 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.30197;LSEQ=GGGCGGGTGTGTGGGCAGAG;RSEQ=GGTTGCCACGCCTCCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:758:6:2,4:467,285:0.0079:2,2:9.3:1:28.3:1:0.20882:3.27191:60:12:0.0081:0:1.5 0/1:467:152:92,60:187,128:0.3255:2,2:25.1:1:29:1:0.84082:1.05:60:75:0.324:0:2 -16 2138422 . C G 241 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCACGCCTCCCAGACTTA;RSEQ=TGCCCAAGCCGCCTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1005:0:0,0:591,413:0:2,0:24.8:1:31.9:1:1:0:60:82.667:0.999:0:0.1 0/1:720:223:127,96:300,194:0.3097:2,2:23:1:31:1:0.36614:1.16866:60:73.333:0.3077:0:1.7 -16 2138584 . G C 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGAAGCGCCTCATCTCCTC;RSEQ=GTGGAGGACTTCACCGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:851:0:0,0:297,550:0:2,0:24.2:1:30.1:1:1:0:60:55.467:0.9976:0:0.1 0/1:639:32:14,18:230,377:0.0501:2,2:24.7:1:29.8:1:0.57634:1.27:60:64:0.0506:0:1.2 -16 2138670 . TAA T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00142;SOR=Inf;LSEQ=TTGCCTGTCAGTGAAATAAA;RSEQ=AGTCCTGACCCCAGTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:24,204:0:2,0:23:1:30.1:1:1:0:60:75:1:0:0.1 0/1:150:7:1,6:24,119:0.0467:2,2:23.1:1:31.9:1:1:1.20863:60:14:0.0467:0:0.1 -16 2138738 . T C 34 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03798;SOR=Inf;LSEQ=GACAGCTCTTTTATTGACTT;RSEQ=GTCTGCTTGGTGCGGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:0,77:0:1,0:19.4:1:30.4:1:1:0:60:37.5:1:0:0.2 0/1:40:3:1,2:1,36:0.075:1,2:16.7:1:22:1:0.14615:14.90:60:2:0.0526:0:2 -16 2199788 . T G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCAGCCTTTCAGAGGCA;RSEQ=ACGCTGGGTGTCCAGCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:30:1:1:0:60:4:1:0:1 -16 2200882 . A G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGCAGGAGCTCAGGCTGA;RSEQ=GGAGGTGGCACAGGTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 2213760 . G GT 117 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.04436;SOR=2.62391;LSEQ=TGCCTGAGCCGGGGCTGGTG;RSEQ=TGGAAGGCTGCTGCGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:15:15,0:81,2:0.1531:1,1:27.9:1:30:1:1:0:60:14:0.1489:0.0102:0 0/1:34:11:11,0:23,0:0.3235:1,0:18.4:1:27.7:1:1:0:60:10:0.303:0.1471:0.4 -16 2213800 . G C 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.71901;LSEQ=CCCCACGGTGCCCCACAGCA;RSEQ=GTCTGCACACTTGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:1:1,0:175,6:0.0055:1,0:13:0:30:0:1:0:60:2:0.0056:0:1 0/1:93:14:14,0:77,2:0.1505:1,1:21.4:1:32.1:1:1:0:60:28:0.1538:0:1.3 -16 2213819 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11336;SOR=Inf;LSEQ=AGGTCTGCACACTTGCAGCA;RSEQ=CCCGTCTGACTCACAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:237,26:0:2,0:22.9:1:32.1:1:1:0:60:64.75:1:0:0.1 0/1:134:2:1,1:121,11:0.0149:2,2:27:1:30.5:1:0.1717:10.57526:60:4:0.0155:0:1.5 -16 2214127 . T TG 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.98699;LSEQ=GGGGTCTCAGGGGAGCTCGG;RSEQ=GGGGGGGGGTGTGGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:12:1,11:8,209:0.0502:1,2:31.8:1:31.8:1:0.38942:2.36:56.7:24:0.0583:0:1.3 0/1:121:6:0,6:3,108:0.0496:1,0:27.8:1:29.3:1:1:0:60:12:0.0594:0:0.7 -16 2214137 . T A 22 v4;pSTD;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10019;SOR=Inf;LSEQ=GGGAGCTCGGTGGGGGGGGG;RSEQ=GTGGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:8,206:0:1,0:27.6:1:29.1:1:1:0:59.7:13.267:0.995:0:0.8 0/1:101:2:1,1:2,96:0.0198:1,2:30:0:22.5:1:0.05939:39.37:60:4:0.0215:0:1.5 -16 2214324 . A T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0841;SOR=8.19409;LSEQ=ACCTGGCCTGGTCGCATGGT;RSEQ=AAGCGTGTTAGTGCTGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:7,11:0.0526:2,0:1:0:23:0:1:0:60:2:0.0556:0:1 0/1:9:3:1,2:3,3:0.3333:2,2:23.3:1:30:1:1:1.8525:39:6:0.375:0:1.3 -16 2214452 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2663;SOR=0;LSEQ=GCCTGGTCGCATGGTTAAGC;RSEQ=TGTTAGTGCTGCGTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:5,7:0.2:2,0:22:1:31:1:0.50549:0:48.3:6:0.2143:0:1.3 0/0:9:0:0,0:5,4:0:2,0:22.4:1:26.8:1:1:0:48.6:3.5:1:0:1.8 -16 2214625 . C T 27 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02;SOR=Inf;LSEQ=CATGGTTAAGCGTGTTAGTG;RSEQ=TGCGTGGCGCGGCCTGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:0:2,0:21:1:32.8:1:1:0:50.1:42:1:0:0.5 1/0:4:2:1,1:1,1:0.5:2,2:24.5:1:27.5:1:1:1:60:4:0.5:0:1 -16 2215038 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17235;SOR=0;LSEQ=GGTTAAGCGTGTGAGTGCTG;RSEQ=ATGGCCTGGCCTGGTCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:0.1429:2,2:14.5:1:28.5:1:1:1.37:57:4:0.1538:0:1.5 0/0:19:0:0,0:8,11:0:2,0:18.8:1:31.2:1:1:0:48.2:18:1:0:0.2 -16 2215248 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.13043;SOR=Inf;LSEQ=AGCGTGTTAGTGCTACGTGG;RSEQ=GCGGCCTGGTCGCATGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:20.4:1:28.9:1:1:0:51:14:1:0:0.3 0/1:9:2:1,1:3,4:0.2222:2,2:23.5:1:30.5:1:1:1.29:51:4:0.2222:0:1 -16 2215608 . G A 26 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01647;SOR=Inf;LSEQ=GCATGGTTAAGCGTGTGAGT;RSEQ=CTGTGTGGCGCAGCCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:34,10:0:2,0:21.8:1:32:1:1:0:44.3:43:1:0:1.5 0/1:7:2:1,1:4,1:0.2857:2,2:23.5:1:26.5:1:1:3.1622:52:4:0.2857:0:1.5 -16 2215612 . T C 90 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.62375;LSEQ=GGTTAAGCGTGTGAGTGCTG;RSEQ=GTGGCGCAGCCTGGTCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:9:7,2:31,8:0.1875:2,2:17.3:1:28.7:1:1:1.10474:56.1:8:0.1905:0:6.9 0/1:8:1:1,0:5,2:0.125:2,0:3:0:14:0:1:0:51:0:0:0:1 -16 2215618 . GCA CTG 94 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57669;SOR=0;LSEQ=GCGTGTGAGTGCTGTGTGGC;RSEQ=GCCTGGTCGCATGGTTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:8:6,2:32,8:0.1667:2,2:25.5:1:31.6:1:0.66555:1.32491:59.4:16:0.1818:0:6 0/0:7:0:0,0:5,2:0:2,0:19.9:1:25.1:1:1:0:45:6:1:0:0.4 -16 2215645 . G T 117 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0599;SOR=0;LSEQ=GGTCGCATGGTTAAGCGTGT;RSEQ=AGTGCTGCGTGGCCTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:14:12,2:45,5:0.2188:2,2:28.4:1:30.8:1:0.64188:1.48968:55.5:28:0.2222:0:5.2 0/0:15:0:0,0:12,3:0:2,0:21.8:1:31.6:1:1:0:53.9:30:1:0:0.5 -16 2215648 . T C 125 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06324;SOR=0;LSEQ=CGCATGGTTAAGCGTGTGAG;RSEQ=GCTGCGTGGCCTGGCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:16:14,2:48,5:0.2319:2,2:25.8:1:31.3:1:0.65954:1.36474:56.1:15:0.2239:0:4.9 0/0:15:0:0,0:12,3:0:2,0:23.6:1:30.1:1:1:0:53.9:30:1:0:0.5 -16 2215659 . CT GC 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.02062;SOR=0;LSEQ=GCGTGTGAGTGCTGCGTGGC;RSEQ=GGCCTGGTCGCATGGTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:20:18,2:56,6:0.2381:2,2:20.5:1:31:1:1:1.03658:57.6:40:0.2532:0.0119:3 0/0:19:0:0,0:16,3:0:2,0:25.8:1:31.3:1:1:0:58:38:1:0:0.3 -16 2215686 . T G 107 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0641;SOR=0;LSEQ=GGTCGCATGGTTAAGCGTGT;RSEQ=AGCGCTGCGTGGCGCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:10:10,0:114,7:0.0763:2,0:24.8:1:32.3:1:1:0:56.4:20:0.082:0:2.1 0/0:51:0:0,0:47,4:0:2,0:22.1:1:28.7:1:1:0:60:7.5:1:0:0.2 -16 2215689 . C T 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.03541;SOR=0;LSEQ=CGCATGGTTAAGCGTGTTAG;RSEQ=GCTGCGTGGCGCGGCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:11:11,0:114,7:0.0827:2,0:25.6:1:29.7:1:1:0:54.9:22:0.0948:0:2.6 0/0:54:0:0,0:50,4:0:2,0:22.5:1:30.1:1:1:0:60:6.714:1:0:0.2 -16 2215780 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01151;SOR=Inf;LSEQ=AAGTGTGTGAGTGCTGCGTG;RSEQ=CCTGGCCTGGTCGCGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:623:0:0,0:495,127:0:2,0:23.1:1:30.9:1:1:0:60:55.545:0.9984:0:0.1 0/1:434:5:3,2:313,116:0.0115:2,2:21.2:1:24:1:0.61637:1.79608:60:4:0.0095:0:1.4 -16 2216073 . G C 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96151;LSEQ=GGCGCGGGCAGCCTCACACC;RSEQ=CAGCCTGTGTCCTCACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:157:79:2,77:1,77:0.5032:1,1:24.4:1:30.4:1:1:1.99:60:25.333:0.5067:0:1.1 0/1:75:37:1,36:3,34:0.4933:2,1:21.7:1:30.9:1:0.61451:3.13091:60:74:0.5:0:1.1 -16 2217903 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGGCACTGGTTTGACCTT;RSEQ=AGAGGGAACCCAAGCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:2,0:107,2:0.018:1,0:23:1:32:0:1:0:60:4:0.0183:0:1 0/0:45:0:0,0:43,2:0:1,0:23.5:1:31.7:1:1:0:60:44:1:0:0 -16 2217925 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55333;SOR=0;LSEQ=GAGGGAACCCAAGCTTCCCC;RSEQ=GTGCCATCCCTGCATGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:2,1:149,3:0.0194:1,2:19.3:1:29:1:0.07592:22.73218:60:6:0.0195:0:1 0/0:72:0:0,0:70,2:0:1,0:24.4:1:30.6:1:1:0:60:144:1:0:0 -16 2218260 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11676;SOR=Inf;LSEQ=TCCCAGGAGGAGTTGACAGT;RSEQ=AGCTGGTGAGGCACAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:12,355:0:1,0:25.2:1:31.3:1:1:0:60:44.875:1:0:0.1 0/1:191:2:1,1:15,174:0.0105:2,2:18:1:27:1:0.16093:11.26:60:4:0.0105:0:1 -16 2218359 . G A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCTCCTGTGGCTGGACT;RSEQ=TGGGTGGCAGGGGGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:0,3:1,53:0.0526:1,0:34:1:32:0:1:0:60:6:0.0526:0:1 0/0:12:0:0,0:0,12:0:0,0:11.3:1:31.7:1:1:0:60:24:1:0:0.1 -16 2220401 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08942;SOR=Inf;LSEQ=GAGCGGGCAGCCCAGCACCC;RSEQ=GGCCCAGGCCGCCCAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:40,1:0:1,0:21.3:1:31.2:1:1:0:60:82:1:0:0.1 0/1:18:2:2,0:16,0:0.1111:1,0:15:1:29:1:1:0:60:4:0.1111:0:1 -16 2220713 . CGAG C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.64335;SOR=0.71581;LSEQ=CGCTCCACATTCTCACTGCC;RSEQ=GAGGAGGAGGAGCCGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:726:12:3,9:255,458:0.0165:2,2:20.2:1:30.9:1:0.55337:1.66922:60:24:0.0169:0.0041:0.8 0/1:589:7:2,5:214,367:0.0119:2,2:22.3:1:31.2:1:1:1.45688:60:14:0.012:0.0017:0.3 -16 2220787 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5209;SOR=0;LSEQ=GGGCTGTCACCGCAGCCGTG;RSEQ=CACGGAGGCACCTTCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:0,2:6,169:0.0113:1,0:22.5:1:32:0:1:0:60:4:0.0115:0:1 0/0:115:0:0,0:5,109:0:1,0:22.3:1:32.3:1:1:0:60:113:0.9912:0:0.1 -16 2221157 . T C 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00391;SOR=13.06197;LSEQ=CCTCTCTCAGGACGTGACCC;RSEQ=GTCCTCAGAGGACAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:1,0:198,5:0.0049:1,0:8:0:32:0:1:0:60:2:0.005:0:1 0/1:115:7:6,1:102,6:0.0609:2,2:14.4:1:30.3:1:0.3636:2.79566:60:14:0.0609:0:1 -16 2221642 . C T 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=GGCCCAGGCCTGACGCCGAC;RSEQ=GTGCCCATGGCTGCCGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:749:0:0,0:271,478:0:2,0:25.5:1:29.7:1:1:0:60:61.417:1:0:0.2 0/1:576:12:4,8:207,354:0.0208:2,2:19.5:1:29.8:1:1:1.16921:60:24:0.0211:0:1 -16 2222286 . C T 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTTCATCCACTGCCGGCA;RSEQ=GGCTGCCGGGTAGCGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1095:0:0,0:477,618:0:2,0:24.5:1:30.5:1:1:0:60:63.412:1:0:0.2 0/1:854:84:41,43:352,416:0.0984:2,2:22.9:1:29.7:1:0.64537:1.13:60:83:0.0983:0:1.1 -16 2222668 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12287;SOR=Inf;LSEQ=CACAGGCTCCGCTGAGAGCT;RSEQ=CCCGCTTGCTGGTCCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:11,203:0:2,0:23.1:1:32.1:1:1:0:60:52.5:1:0:0.4 0/1:116:2:1,1:7,106:0.0172:2,2:20.5:1:27.5:1:0.13486:14.24:60:4:0.0177:0:1 -16 2223000 . T C 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00713;SOR=Inf;LSEQ=GCGGGGGTGACGTGATGGGA;RSEQ=CTCACTTGTGAAGCAGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:44,2:0:1,0:21.3:1:31.1:1:1:0:60:45:1:0:0.2 0/1:12:3:3,0:9,0:0.25:0,0:24.7:1:33:0:1:0:60:6:0.25:0:1 -16 2223578 . G A 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00179;SOR=Inf;LSEQ=GAGCGGGCGGGGCTGGAGGG;RSEQ=CTGGGTTGTGAGACCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:223,326:0:2,0:25.3:1:31.3:1:1:0:60:35.6:1:0:0.2 0/1:377:7:4,3:145,225:0.0186:2,2:21.9:1:28.7:1:0.44149:2.06:60:14:0.0189:0:1 -16 2223629 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1195;SOR=Inf;LSEQ=CCCCGGCAGGGAGGCCTCCC;RSEQ=TGGCCTTGCCTACACTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:130,169:0:2,0:23.1:1:31.5:1:1:0:60:41.714:1:0:0.1 0/1:159:2:1,1:47,110:0.0126:2,2:22:1:31.5:1:0.51397:2.33:60:4:0.0129:0:1 -16 2223872 . T C 173 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGTGGCTCCCGCCCACCC;RSEQ=CCCCCCCGGGCCCCAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1226:0:0,0:93,659:0:2,0:23.1:1:28.3:1:1:0:60:9.899:0.9942:0:0.3 0/1:836:282:280,2:68,460:0.3373:2,1:14.9:1:21.3:1:0:925.93:56.7:1.938:0.276:0:3.4 -16 2224467 . C T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00285;SOR=Inf;LSEQ=CCTATAGGGCACCCTCCACC;RSEQ=GGAGCAGCACTGTTTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:1,97:0:1,0:21.5:1:29.8:1:1:0:60:48:1:0:0.1 0/1:46:5:0,5:1,40:0.1087:1,0:12.4:1:30.4:1:1:0:60:10:0.1087:0:1 -16 2225040 . C T 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23924;SOR=2.83784;LSEQ=CTGATGGCTGGCATGGACCT;RSEQ=GGGCCCTGCCAGGGCGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:512:2:0,2:353,155:0.0039:2,0:1:0:21:1:0.09435:0:60:1:0.002:0:1 0/1:363:4:1,3:245,114:0.011:2,2:17.8:1:29.8:1:0.10035:6.41189:60:8:0.0111:0:1.8 -16 2225064 . C T 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08655;SOR=4.43601;LSEQ=CCCTGCCAGGGCGGTGTCAG;RSEQ=ATGGACACAGCTTCTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:748:2:0,2:455,291:0.0027:2,0:23.5:1:19:1:0.15312:0:60:1:0.0013:0:1.5 0/1:595:7:3,4:360,228:0.0118:2,2:21.6:1:28.4:1:0.4401:2.10256:60:14:0.012:0:1.1 -16 2225666 . A G 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09736;SOR=Inf;LSEQ=GCCACAGGGCCTTGCCTCCT;RSEQ=CCAGCACTTCCCAGGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:119,204:0:2,0:23.4:1:29.4:1:1:0:60:322:1:0:0.1 0/1:147:2:1,1:47,98:0.0136:2,2:8:0:29:1:0.54795:2.07:60:4:0.0139:0:1 -16 2225823 . G A 221 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGGACCAACTGGCCCAC;RSEQ=ATTACTCATAGATCTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1192:0:0,0:644,547:0:2,0:26.9:1:30.5:1:1:0:60:147.875:0.9992:0:0.1 0/1:876:170:95,75:387,317:0.1941:2,2:27:1:29.9:1:0.86378:1.04:60:169:0.1945:0:1.2 -16 2225987 . CTG C 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CATCTGGGTGCAAGGCCAGA;RSEQ=TGGCCCCGTCTCCCCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:685:0:0,0:336,348:0:2,0:23.2:1:30.7:1:1:0:60:113:0.9985:0:0.1 0/1:443:18:9,9:198,226:0.0406:2,2:20.6:1:31:1:0.81359:1.14:60:36:0.0409:0.009:0.2 -16 2226435 . G A 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGGGCTGCACAGGATGGAGC;RSEQ=GGGGTGGGGACGAGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:299,252:0:2,0:23:1:30.2:1:1:0:60:60.222:1:0:0.1 0/1:304:11:8,3:156,137:0.0362:2,2:24.7:1:29.3:1:0.23431:2.34:60:22:0.037:0:1.2 -16 2226437 . G A 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04227;SOR=Inf;LSEQ=GGCTGCACAGGATGGAGCGG;RSEQ=GGTGGGGACGAGGAGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:0:0,0:306,244:0:2,0:23:1:30.9:1:1:0:60:44.833:1:0:0.2 0/1:295:3:2,1:161,131:0.0102:2,2:12.7:1:23:1:1:1.62:60:2:0.0069:0:1 -16 2226763 . C G 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18678;SOR=0;LSEQ=TCTACTCGGCACTGTCCTTG;RSEQ=TGCCCAGCCCCTCTCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:7:0,7:0,58:0.1077:1,0:29.7:1:32.4:1:1:0:60:14:0.1077:0:1 0/0:21:0:0,0:0,21:0:1,0:19.1:1:32.2:1:1:0:60:42:1:0:0.1 -16 2227368 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GCACGCCGGGACGCCACCTC;RSEQ=GCCAGCCGCCTCCACCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:40.3:1:30.8:1:1:0:60:8:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:42:1:28.5:1:1:0:60:4:1:0:2.5 -16 2587734 . G A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GACAGCTCGCCCCCTGCCCC;RSEQ=CCCAGCCCCGCCCAGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:28.5:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:0:2,0:28:1:25.5:1:1:0:60:4:1:0:1.5 -16 2588026 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.51919;SOR=Inf;LSEQ=CAGGATGAGGGCGGCCATTG;RSEQ=TGGGGCTCCGCTTCGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:0:2,0:27.9:1:32.5:1:1:0:60:34:1:0:0.3 0/1:28:2:1,1:14,12:0.0714:2,2:16:1:27:1:1:1.16024:60:4:0.0741:0:1 -16 2588050 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.49438;SOR=0;LSEQ=GGCTCCGCTTCGGGGAGGAG;RSEQ=ACGCTGAGGAGGCGCCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:22,21:0.0444:2,2:34.5:1:28.5:1:1:1.04655:60:4:0.0455:0:1 0/0:45:0:0,0:22,22:0:2,0:21.5:1:30.5:1:1:0:60:43:0.9773:0:0.3 -16 2588078 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64824;LSEQ=GGAGGCGCCGAGCCGCGCAG;RSEQ=GCTGCGGGGGAGGCGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:30,32:0.0313:2,2:20:1:28:1:1:1.07:60:4:0.0313:0:2 0/1:49:1:0,1:24,24:0.0204:2,0:1:0:24:0:1:0:60:2:0.0208:0:1 -16 2588090 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1894;SOR=Inf;LSEQ=CCGCGCAGCGCTGCGGGGGA;RSEQ=GCGCCCGCGCCGACGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:41,44:0:2,0:21.7:1:31:1:1:0:60:27.333:1:0:0.4 0/1:66:2:1,1:35,29:0.0303:2,2:7:0:32:0:1:1.20344:60:4:0.0308:0:1.5 -16 2588092 . C T 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.2482;LSEQ=GCGCAGCGCTGCGGGGGAGG;RSEQ=GCCCGCGCCGACGCGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:41,44:0.023:2,2:41:1:30.5:1:1:1.07:60:4:0.0244:0:1 0/1:70:2:0,2:35,32:0.0286:2,0:1:0:26.5:1:0.23913:0:60:4:0.0299:0:1 -16 2588101 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50368;SOR=0;LSEQ=TGCGGGGGAGGCGCCCGCGC;RSEQ=GACGCGGGGCCCATGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:57,54:0.0172:2,2:7.5:1:30:1:1:1.05507:60:4:0.0182:0:1.5 0/0:93:0:0,0:46,45:0:2,0:17.7:1:29.2:1:1:0:60:44.5:0.978:0:0.4 -16 2588131 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21961;SOR=0;LSEQ=CCCATGGCCAGGACCACCAG;RSEQ=CAGCTGGTGAGCGCGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:85,88:0.0114:2,2:16.5:1:30:1:1:1.04:60:4:0.0117:0:1 0/0:199:0:0,0:99,100:0:2,0:21.7:1:31.3:1:1:0:60:38.8:1:0:0.4 -16 2588135 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09019;SOR=0;LSEQ=TGGCCAGGACCACCAGCCAG;RSEQ=TGGTGAGCGCGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:1,2:84,88:0.0171:2,2:7.7:1:30.7:1:1:1.90232:60:6:0.0174:0:1.3 0/0:214:0:0,0:107,107:0:2,0:22.3:1:31.6:1:1:0:60:29.571:1:0:0.5 -16 2588146 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.50409;SOR=Inf;LSEQ=ACCAGCCAGCTGGTGAGCGC;RSEQ=CGGCGGCGGACTGGACGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:80,83:0:2,0:29.7:1:30.7:1:1:0:60:31.6:1:0:0.4 0/1:201:2:1,1:100,98:0.01:2,2:24:0:27:1:1:1.02031:60:4:0.0103:0:1.5 -16 2588178 . C A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13546;SOR=Inf;LSEQ=TGGACGCGCCGGTTTGTTAC;RSEQ=CTGCCGGGTCCGGCGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:69,71:0:2,0:21.3:1:31.1:1:1:0:60:34:1:0:0.3 0/1:182:4:3,1:88,90:0.022:2,2:11.8:1:28.5:1:0.62082:3.05:60:8:0.0226:0:1.5 -16 2588189 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50008;SOR=Inf;LSEQ=GTTTGTTACCCTGCCGGGTC;RSEQ=GGCGGCCGCCCGGGTCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:57,58:0:2,0:18:1:30.2:1:1:0:60:56.5:1:0:0.3 0/1:131:2:1,1:61,67:0.0153:2,2:31.5:1:27.5:1:1:1.10:60:4:0.0156:0:1 -16 2588206 . C A 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12624;SOR=Inf;LSEQ=GTCCGGCGGCCGCCCGGGTC;RSEQ=GGCGAGGCGGGGCGGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:24,30:0:2,0:18.1:1:29.4:1:1:0:60:26:1:0:0.3 0/1:66:4:3,1:29,33:0.0606:2,2:19.5:1:28.3:1:0.34823:3.36:60:8:0.0606:0:1.3 -16 2607730 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00228;SOR=Inf;LSEQ=GCCGTGCCCATCCAGTCCAG;RSEQ=GTGGTGTTATGTTCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:109,0:0:1,0:24.5:1:32:1:1:0:27.1:35.333:1:0:0 0/1:32:4:4,0:28,0:0.125:1,0:16.3:1:29.5:1:1:0:27:8:0.129:0:1 -16 2607734 . GTGT G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05899;SOR=Inf;LSEQ=TGCCCATCCAGTCCAGCGTG;RSEQ=TATGTTCCTGCCCATCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:120,0:0:1,0:24.5:1:29.6:1:1:0:27.2:59:1:0:0 0/1:39:2:2,0:37,0:0.0513:1,0:28:1:27.5:1:1:0:27:4:0.0526:0:0 -16 2608001 . G A 230 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGTGTGTCAAACGTACGT;RSEQ=ATTTCCTTGGGGAGGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1486:0:0,0:604,882:0:2,0:25.3:1:31.4:1:1:0:46:81.556:1:0:0.1 0/1:1775:252:111,141:664,859:0.142:2,2:25.3:1:28.9:1:0.8912:1.02:46:251:0.1428:0:1.1 -16 2627343 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12124;SOR=Inf;LSEQ=CTGGCTCCTGGGGGTGCATG;RSEQ=TCCGCCATGTGCGACACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:159,31:0:2,0:20.5:1:31:1:1:0:27.5:189:1:0:0.1 0/1:102:2:1,1:90,10:0.0196:2,2:10.5:1:29.5:1:0.20501:8.63084:27:4:0.0198:0:1 -16 2627803 . C G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTGGAGTGCAGTGGCAC;RSEQ=ATCTCTGCTCGCTGCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:1,10:0.2667:2,0:13.3:1:31.5:1:1:0:30:8:0.2667:0:1 0/0:2:0:0,0:0,2:0:0,0:22:1:34:0:1:0:44:4:1:0:0 -16 2635850 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGCAGCAGCCAGGGCCTG;RSEQ=GTCTGGAGGCACGGAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:28:0:27:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:29:1:1:0:60:4:1:0:1 -16 2636625 . G T 48 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13805;SOR=0;LSEQ=GGGAGGGGCTGGGGTTTTAG;RSEQ=ACCTTAGAGGCAAGTGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:4:2,2:176,51:0.0173:2,2:22.5:1:24:1:0.22642:3.42751:60:3:0.0135:0:2.5 0/0:174:0:0,0:124,50:0:2,0:22.9:1:30.7:1:1:0:60:42.5:1:0:0.2 -16 2645703 . A G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0843;SOR=Inf;LSEQ=GCTCTGTGAGGGGCAGGCCG;RSEQ=GGCTATGGGGAGTTCGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:257,67:0:2,0:23.4:1:29.3:1:1:0:60:28.455:1:0:0.1 0/1:254:3:2,1:191,59:0.0118:2,2:33.7:1:32:1:0.55772:1.6152:60:6:0.0122:0:1 -16 2645879 . G A 78 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12962;SOR=2.95534;LSEQ=GTCAGTGGTCCCGCTGCTCC;RSEQ=CACGGACACCTGCATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:3:3,0:184,323:0.0059:2,0:1:0:27.7:1:0.04879:0:60:6:0.006:0:1 0/1:465:8:6,2:176,281:0.0172:2,2:13.5:1:26.3:1:0.06139:4.77:60:16:0.0174:0:1 -16 2645965 . G A 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.87509;SOR=1.08645;LSEQ=CCATCTCTTGATTTTCATCA;RSEQ=ACATCATCTCTAGATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:59:1,58:1,70:0.4538:1,1:24:1:30.6:1:1:1.21:60:118:0.4574:0:1.1 0/1:59:28:1,27:2,29:0.4746:2,1:23.4:1:31:1:1:1.84327:60:56:0.4746:0:1.1 -16 2647348 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50404;SOR=0;LSEQ=ACCACGTGGGAAGCAGCCAC;RSEQ=GGCCTTGGCCAGAGGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:26,120:0.0135:2,2:37:1:31:1:0.3326:4.55:60:4:0.0138:0:1 0/0:119:0:0,0:24,95:0:2,0:23.9:1:30.3:1:1:0:60:38.667:1:0:0.1 -16 2647826 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57264;SOR=2.82679;LSEQ=ACCTGCCCCAGCGCGGCTTG;RSEQ=CCGCCATCCGGGACGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:1:0,1:19,171:0.0052:2,0:1:0:27:0:1:0:60:2:0.0053:0:1 0/1:136:2:0,2:11,123:0.0147:2,0:32:1:31.5:1:1:0:60:4:0.0148:0:1 -16 2647876 . C T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.01146;SOR=Inf;LSEQ=GCCAGCCATCACAAGGGGAA;RSEQ=GCAGAGGCGGAAACCTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:3,107:0:1,0:24.3:1:30.1:1:1:0:60:109:1:0:0.1 0/1:55:4:0,4:0,51:0.0727:1,0:23.5:1:32:0:1:0:60:8:0.0727:0:1 -16 2672547 . G A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04068;SOR=Inf;LSEQ=AACGCATCACGTGTGTGTAC;RSEQ=CCACGGAAAATACGCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:98,5:0:1,0:23.6:1:29.7:1:1:0:26.9:33.333:1:0:0 0/1:55:3:3,0:50,2:0.0545:1,0:28.3:1:31.3:1:1:0:27:6:0.0545:0:1 -16 2672750 . G A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0321;SOR=Inf;LSEQ=ACGTACTGCGCTGTTCCCAC;RSEQ=AATGAGTTGGCCCTGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:127,341:0:2,0:22.6:1:30.7:1:1:0:30.5:233:1:0:0.1 0/1:345:4:2,2:97,244:0.0116:2,2:9:1:24:1:0.32502:2.51:44.3:3:0.0089:0:1.3 -16 2692108 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11224;SOR=Inf;LSEQ=CAGGTGACACCCCTCAAGGG;RSEQ=CCTGAGACCTCCTGCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:257,3:0:1,0:23.2:1:30.4:1:1:0:39.4:17.571:1:0:0.1 0/1:132:2:2,0:126,4:0.0152:1,0:35.5:1:30:1:1:0:38:4:0.0153:0:1 -16 2723242 . A G 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00054;SOR=Inf;LSEQ=CGCAGGTAAGGCGGCACCCG;RSEQ=CCCTCGGGACCCCGGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:26,9:0:2,0:11.4:1:29.9:1:1:0:60:34:1:0:0.1 0/1:31:9:6,3:13,8:0.2903:2,2:15.8:1:30.1:1:1:1.22:60:8:0.2963:0:1.8 -16 2723255 . C T 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02956;SOR=8.16065;LSEQ=GCACCCGACCCTCGGGACCC;RSEQ=GGGCCGCCCCGCCTCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:0,1:35,16:0.0192:2,0:1:0:26:0:0.32692:0:60:2:0.0192:0:1 0/1:50:7:4,3:29,14:0.14:2,2:18.9:1:30.3:1:0.67685:1.53933:60:14:0.1489:0:1.9 -16 2723276 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.23573;SOR=Inf;LSEQ=GGGCCGCCCCGCCTCGCCGC;RSEQ=CGCTCACCAGCTAGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:50,30:0:2,0:28.6:1:30.7:1:1:0:60:39:1:0:0.6 0/1:76:2:2,0:47,27:0.0263:2,0:37:1:30.5:1:0.53579:0:60:4:0.0267:0:2 -16 2723303 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24108;SOR=Inf;LSEQ=CCAGCTAGGTGGTGGTCCTG;RSEQ=CTATGGGCCTCGCGTCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:55,44:0:2,0:28.5:1:31:1:1:0:60:32:1:0:0.7 0/1:96:2:1,1:55,39:0.0208:2,2:45.5:1:27.5:1:1:1.4051:60:4:0.0213:0:1.5 -16 2723305 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24126;SOR=Inf;LSEQ=AGCTAGGTGGTGGTCCTGGC;RSEQ=ATGGGCCTCGCGTCTGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:55,46:0:2,0:27.7:1:29.1:1:1:0:60:32.667:1:0:0.7 0/1:98:2:1,1:56,40:0.0204:2,2:13.5:1:28.5:1:1:1.39509:60:4:0.0208:0:1 -16 2723329 . G A 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23074;SOR=Inf;LSEQ=GGCCTCGCGTCTGCGCGGGC;RSEQ=CCTCCCCCGAAGCGCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:39,47:0:2,0:22.6:1:30:1:1:0:60:42:1:0:0.8 0/1:80:2:1,1:40,38:0.025:2,2:13:0:32:0:1:1.05198:60:4:0.025:0:4.5 -16 2723332 . T C 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23027;SOR=Inf;LSEQ=CTCGCGTCTGCGCGGGCGCC;RSEQ=CCCCCGAAGCGCTCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:36,46:0:2,0:22.4:1:29.3:1:1:0:60:19.5:0.975:0:0.9 0/1:78:2:1,1:36,39:0.0256:2,2:46.5:1:27.5:1:1:1.08:60:4:0.0256:0:4 -16 2723350 . C G 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCTCCCCCGAAGCGCTCCGC;RSEQ=GCTCGGGGCCTCCTCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:20,36:0,0:1:0,2:24.1:1:30.4:1:1:0:60:112:1:0:1.1 1/1:66:66:28,38:0,0:1:0,2:23.3:1:28.7:1:1:0:60:65:1:0:2 -16 2723368 . A C 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCCGCTCGGGGCCTCCTCAG;RSEQ=GTCCTCCTTCCCTAAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:5,29:0:2,0:26.8:1:31.5:1:1:0:60:68:1:0:1 1/0:52:29:10,19:4,17:0.5577:2,2:22.9:1:29.8:1:0.34084:2.20:60:58:0.58:0:3.1 -16 2723374 . C G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CGGGGCCTCCTCAGAGTCCT;RSEQ=CTTCCCTAAGCTGAACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:5,26:0:2,0:26:1:32:1:1:0:60:62:1:0:1 0/1:44:17:5,12:7,20:0.3864:2,2:21.2:1:31.9:1:1:1.19:60:34:0.3953:0:3.2 -16 2723442 . T C 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=CGACGCCCCGCCCCCCGCGA;RSEQ=GCCCCCGCCCCCCGCGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:12.6:1:31.4:1:1:0:60:10:1:0:0.6 0/1:9:2:1,1:1,6:0.2222:2,2:8:1:28.5:1:0.41667:4.58:60:4:0.2222:0:3 -16 2781843 . C T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28336;LSEQ=AATGCACAGTCTTGCAGTGA;RSEQ=AGCAATGTCAGGGCAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:448:368:184,184:43,37:0.8214:2,2:26.8:1:29.5:1:0.62188:1.16177:60:51.571:0.8186:0:1.1 1/0:359:203:101,102:78,77:0.5655:2,2:26.8:1:28.8:1:1:1.02296:60:202:0.5642:0:1.1 -16 2781929 . G A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03866;SOR=Inf;LSEQ=ATCAGCGTTTGTCAGCTTAC;RSEQ=TCTGCATGTTTGAGCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:60,154:0:2,0:24.3:1:31.1:1:1:0:60:52.5:1:0:0.7 0/1:172:4:2,2:48,120:0.0233:2,2:15.5:1:24.3:1:0.58073:2.48:60:3:0.018:0:2 -16 2781959 . G C 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00328;SOR=0.41441;LSEQ=TTGAGCATCTTTCTGTGAGT;RSEQ=TATGTAGGTTTATATGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:127:95:8,87:7,25:0.748:2,2:21.3:1:32.5:1:0.05693:3.0131:60:190:0.748:0:1 1/0:89:49:6,43:8,32:0.5506:2,2:21:1:32.2:1:0.38627:1.77975:60:98:0.5506:0:1.1 -16 2783453 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAACACTTTGGGAGGCC;RSEQ=AGGCGGGTGGATCACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29.5:1:1:0:60:4:1:0:1 -16 3233415 . G C 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66992;SOR=0.61559;LSEQ=GACGTGGGGAAGCAGAGGCC;RSEQ=CTTGGGGCAGCAGAGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:0.4545:2,2:15.4:1:29.8:1:1:1.30:60:10:0.4545:0:1.2 0/1:9:3:1,2:1,5:0.3333:2,2:20:1:32.3:1:1:2.24:60:6:0.3333:0:1 -16 3233737 . C A 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCGCCACATACATTACT;RSEQ=CCCGCAATACCATGCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43:0:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 3498884 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49976;SOR=Inf;LSEQ=TGTTAGTGGAGAACGAGACT;RSEQ=TCCCAGTGTGCTGCCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:99,42:0:2,0:25:1:31.5:1:1:0:60:282:1:0:0.3 0/1:157:2:1,1:91,64:0.0127:2,2:21.5:1:29:1:1:1.4186:60:4:0.0132:0:1.5 -16 3498895 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=Inf;LSEQ=AACGAGACTCTCCCAGTGTG;RSEQ=TGCCCTGACCCTCTGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:105,54:0:2,0:24.9:1:31.9:1:1:0:60:318:1:0:0.3 0/1:171:2:1,1:93,76:0.0117:2,2:14.5:1:28.5:1:1:1.22223:60:4:0.0118:0:1.5 -16 3498907 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49936;SOR=Inf;LSEQ=CCAGTGTGCTGCCCTGACCC;RSEQ=CTGAGATTGGTCTGTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:109,73:0:2,0:24.6:1:30.4:1:1:0:60:44.5:1:0:0.4 0/1:196:2:1,1:106,88:0.0102:2,2:34.5:1:29:1:1:1.20339:60:4:0.0103:0:1 -16 3498924 . T A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24832;SOR=Inf;LSEQ=CCCTCTGAGATTGGTCTGTG;RSEQ=AGCCACGTGGTGGTCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:119,98:0:2,0:23.9:1:28.8:1:1:0:60:107.5:1:0:0.4 0/1:220:3:2,1:115,102:0.0136:2,2:25.7:1:28.7:1:1:1.77:60:6:0.0137:0:2 -16 3498951 . C T 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7176;SOR=1.0835;LSEQ=GTGGTGGTCATCCTGTGCCA;RSEQ=CTCTGGTTTGGTTCTAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:98:54,44:64,71:0.4206:2,2:24.4:1:29.9:1:0.28862:1.36:60:48:0.4192:0:1.1 0/1:268:118:58,60:75,75:0.4403:2,2:22.9:1:28.9:1:0.90267:1.03437:60:58:0.4377:0:1.1 -16 3499000 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27012;SOR=Inf;LSEQ=AGTATCATCTGTGGTGATCC;RSEQ=TCTTACACACTTGCATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:66,114:0:2,0:25.9:1:30.8:1:1:0:60:59:1:0:0.4 0/1:254:3:1,2:108,143:0.0118:2,2:38.7:1:28.7:1:1:1.50814:60:6:0.0119:0:1.3 -16 3499158 . A C 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56488;SOR=3.5981;LSEQ=TGAGGCGGGTAGATCTCTGG;RSEQ=GGTCAGGAGTTCGAGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:19.3:1:30.5:1:1:0:60:8:0.5:0:1 1/1:5:4:0,4:0,1:0.8:0,0:14.5:1:31:1:1:0:60:8:0.8:0:1.5 -16 3776413 . CCGCCCACCTCAGT C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGGGGCCAACGCTGAG;RSEQ=CGCCCACCTCAGTCTCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:33:1:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 3777496 . C A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2605;SOR=0;LSEQ=GGAAAAAAAAGAACCCCCCC;RSEQ=ACCCCCCCGCCAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:20.4:1:26.8:1:1:0:60:4:0.4444:0:2.6 0/0:4:0:0,0:4,0:0:0,0:10.8:1:30.5:1:1:0:55:8:1:0:0.8 -16 3777497 . A C 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0.9371;LSEQ=GAAAAAAAAGAACCCCCCCC;RSEQ=CCCCCCCGCCAAAAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:8.2:1:28.2:1:1:0:51.6:10:0.5:0:2 0/1:5:2:2,0:3,0:0.4:0,0:14:1:30:1:1:0:50:4:0.6667:0:1.5 -16 3777693 . A AG 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAGGTCCAAGAACATGAA;RSEQ=GGGAAAAGGTGATGCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1075:0:0,0:626,446:0:2,0:25.6:1:30.4:1:1:0:60:75.571:0.9972:0:0.1 0/1:1072:38:21,17:575,458:0.0354:2,2:29.4:1:30.8:1:1:1.01631:60:37:0.0352:0.0019:0.2 -16 3778400 . TTGC T 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.35059;SOR=1.61888;LSEQ=CCAGCCATGCCGGCACTCCC;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:7:7,0:361,210:0.0121:2,0:26.6:1:31.7:1:0.0522:0:60:14:0.0122:0.0017:0 0/1:566:11:8,3:371,183:0.0194:2,2:20.7:1:31.2:1:1:1.31:57.7:22:0.0197:0.0053:0.5 -16 3778427 . T C 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGCTGTTGCTGCTGTTG;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:737:0:0,0:466,271:0:2,0:24.7:1:30.1:1:1:0:59.8:244.667:1:0.0014:0.1 0/1:738:41:24,17:423,274:0.0556:2,2:24.3:1:31.8:1:0.86964:1.09339:59.4:82:0.0559:0:1.2 -16 3778990 . G A 47 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12538;SOR=0;LSEQ=AAGGGGCGCCTGCTGCCACT;RSEQ=CCCGGGAGGCATGCTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:4:2,2:171,175:0.0114:2,2:13.5:1:23.8:1:1:1.02:60:3:0.0087:0:1 0/0:321:0:0,0:163,157:0:2,0:26.6:1:31.3:1:1:0:60:52.333:0.9968:0:0.2 -16 3778998 . G T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0244;SOR=Inf;LSEQ=CCTGCTGCCACTGCCCGGGA;RSEQ=GCATGCTGGGCATGACGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:0:0,0:180,189:0:2,0:22.4:1:31.3:1:1:0:60:51.714:1:0:0.2 0/1:337:5:3,2:163,169:0.0148:2,2:13.2:1:28:1:0.68105:1.55:60:10:0.015:0:1.2 -16 3779060 . G A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCACATTCAGGCTCACGGG;RSEQ=GCCATCTGGCTCCCCGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:237,203:0:2,0:23.7:1:30.8:1:1:0:60:39:1:0:0.1 0/1:426:31:15,16:208,187:0.0728:2,2:24.6:1:30.7:1:0.71061:1.18597:60:62:0.074:0:1.3 -16 3779115 . T C 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCTGGGGGCATGCTGTTG;RSEQ=TGATGTTCACCCGGTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:596:0:0,0:304,292:0:2,0:25.7:1:29.7:1:1:0:60:65.222:1:0:0.2 0/1:595:38:19,19:284,272:0.0639:2,2:28.8:1:31.3:1:1:1.04406:60:37:0.0631:0:1.1 -16 3779135 . GTGC G 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=1.05167;LSEQ=TTGATGTTCACCCGGTACAG;RSEQ=TGCTGCTGCTGGGCCTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:600:10:5,5:293,296:0.0167:2,2:26.3:1:31.9:1:1:1.01:60:20:0.0175:0.005:0.1 0/1:571:10:6,4:280,281:0.0175:2,2:30.9:1:29.1:1:0.75173:1.50:60:9:0.0164:0.0035:0.5 -16 3779205 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.32122;SOR=3.95145;LSEQ=CTGCAGGAGGGGGCTGGGCC;RSEQ=GGGGTGGGGGGGCCGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:1:1,0:180,177:0.0028:2,0:1:0:25:0:1:0:60:2:0.0029:0:2 0/1:275:3:3,0:120,151:0.0109:2,0:7.7:1:27.3:1:0.08924:0:60:6:0.0117:0:1.7 -16 3779222 . C T 49 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09447;SOR=6.25532;LSEQ=GCCGGGGGTGGGGGGGCCGG;RSEQ=ACCTGGCTGGTAGGCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:1:0,1:223,174:0.0025:2,0:1:0:26:0:0.4397:0:60:2:0.0026:0:1 0/1:324:5:4,1:159,160:0.0154:2,2:17:1:21.2:1:0.37116:4.01:60:1.5:0.0098:0:2.8 -16 3779237 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09627;SOR=6.13476;LSEQ=GCCGGCACCTGGCTGGTAGG;RSEQ=TTCCCTGTGGACACCGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:1:0,1:273,188:0.0022:2,0:1:0:25:0:0.40909:0:60:2:0.0023:0:1 0/1:380:5:2,3:199,176:0.0132:2,2:19.4:1:24.6:1:0.6697:1.69366:60:4:0.011:0:2 -16 3779293 . C T 65 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01408;SOR=9.56312;LSEQ=GGCCACGCTGGGGAAGCCAG;RSEQ=TGGTGACATGCTCACGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:822:1:0,1:486,333:0.0012:2,0:1:0:25:0:0.40732:0:60:2:0.0013:0:1 0/1:694:8:4,4:403,281:0.0115:2,2:18.5:1:21.8:1:0.72319:1.43337:60:1.667:0.0075:0:1.9 -16 3780053 . G A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03266;SOR=Inf;LSEQ=CCCGGACAGGGCGGGAGCAC;RSEQ=GACAAGATGGGATCATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:3,40:0:2,0:24.2:1:31.2:1:1:0:60:86:1:0:0.2 0/1:10:2:1,1:0,8:0.2:0,2:25:1:31:1:0.2:0:60:4:0.2:0:1 -16 3781441 . C T 47 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12525;SOR=0;LSEQ=GGGGGGCAGGGTGTTGATGA;RSEQ=AGGCCCAGCGTGCAGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:4:1,3:105,227:0.0119:2,2:21.8:1:23.8:1:1:1.38643:60:3:0.009:0:1.8 0/0:308:0:0,0:99,209:0:2,0:26.2:1:31.3:1:1:0:60:50.333:1:0:0.2 -16 3781450 . C G 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11117;SOR=Inf;LSEQ=GGTGTTGATGACAGGCCCAG;RSEQ=GTGCAGGTGGATCACGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:89,209:0:2,0:24.1:1:30.2:1:1:0:60:36.25:1:0:0.2 0/1:277:3:1,2:86,187:0.0108:2,2:6.7:1:24.3:1:1:1.09:60:2:0.0074:0:1.7 -16 3781492 . C A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.5544;LSEQ=GACCTGCAGGAGAGGAGGGG;RSEQ=TTTAGTCCCACACAAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:25,100:0.0157:2,2:21:1:28:1:0.36883:3.94:60:4:0.016:0:1 0/0:114:1:1,0:27,85:0.0088:2,0:1:0:22:0:0.24779:0:60:2:0.009:0:1 -16 3781508 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50988;SOR=0;LSEQ=GGGGCTTTAGTCCCACACAA;RSEQ=GGACATGGCACCTCCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:20,84:0.0189:2,2:38:1:31:1:0.35849:4.12:60:4:0.0189:0:1 0/0:77:0:0,0:14,62:0:2,0:20.9:1:29.9:1:1:0:60:18:0.9863:0:0.2 -16 3781516 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14549;SOR=Inf;LSEQ=AGTCCCACACAAGGGACATG;RSEQ=CACCTCCAGTGGTGAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:17,73:0:2,0:22.5:1:32.2:1:1:0:60:180:1:0:0.1 0/1:56:2:1,1:7,47:0.0357:2,2:30.5:1:30:0:0.26753:6.35:60:4:0.0364:0:2 -16 3781952 . C G 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GACTGCCCTGCAACAACACG;RSEQ=AAGGCTGTGAGACCAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:0:0,0:151,344:0:2,0:25.2:1:31.5:1:1:0:60:26.5:0.9979:0:0.1 0/1:388:11:2,9:109,268:0.0284:2,2:26.3:1:30.3:1:0.73567:1.82774:60:22:0.0286:0:1.1 -16 3782011 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16085;SOR=Inf;LSEQ=CACGGACGCCCAGCTCCCAG;RSEQ=CCGTGGGCATCAGGAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:4,164:0:1,0:24.1:1:31.9:1:1:0:60:32.6:1:0:0.1 0/1:113:2:0,2:6,105:0.0177:2,0:21:1:30:1:1:0:60:4:0.0182:0:1 -16 3785911 . G A 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00108;SOR=Inf;LSEQ=CCTGTGCTGCAGGTGGTGTC;RSEQ=ACGTGCATGTGTGAACGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:122,0:0:1,0:24.4:1:30.2:1:1:0:60:121:1:0:0 0/1:94:8:7,1:84,2:0.0851:1,2:24:1:30.3:1:0.23652:5.7867:60:16:0.0851:0:1 -16 3786520 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15111;SOR=Inf;LSEQ=TTCTAAGTTCTCACTTTAGG;RSEQ=TTTTATTTTTCTGCTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:110,4:0:1,0:25.9:1:32.5:1:1:0:60:56:1:0:0.1 0/1:73:2:1,1:66,5:0.0274:2,2:38.5:1:26.5:1:0.15868:12.14098:60:4:0.0286:0:1 -16 3786557 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16942;SOR=Inf;LSEQ=TCTAATCCTCATAAGTGAAG;RSEQ=TAATTAACAAGTATGCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:218,10:0:1,0:23.9:1:31.5:1:1:0:60:113:1:0:0.2 0/1:160:2:1,1:151,7:0.0125:1,2:37.5:1:29:1:0.0978:20.24495:60:4:0.0127:0:1 -16 3786594 . C G 175 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAATGCAAGAAAAAGGCACA;RSEQ=AAATATCCTCCCCTCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:51:40,11:331,70:0.1123:2,2:26.9:1:30.9:1:0.44353:1.29955:60:50:0.1124:0:1.1 0/0:367:0:0,0:286,81:0:2,0:23.6:1:31:1:1:0:60:72.4:1:0:0.1 -16 3786862 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19012;SOR=Inf;LSEQ=GATGAACGTGCCAGTGAAAT;RSEQ=GGCCCTGCCTTTAAGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:23,204:0:2,0:24.3:1:30:1:1:0:60:74.667:1:0:0.1 0/1:176:2:1,1:23,150:0.0114:2,2:22.5:1:28.5:1:0.25616:6.41:60:4:0.0116:0:1 -16 3789523 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16716;SOR=Inf;LSEQ=TGGGACACTTAAGAGCCCTG;RSEQ=TCTATCCTAACACGGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:225,62:0:2,0:25.8:1:30.9:1:1:0:59.9:46.833:1:0:0.1 0/1:199:2:1,1:168,29:0.0101:2,2:23:1:31.5:1:0.27943:5.71271:60:4:0.0102:0:1 -16 3789537 . G A 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCTGGTCTATCCTAACAC;RSEQ=GCTCACTGAATGACACGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:256,101:0:2,0:25.8:1:29.4:1:1:0:60:28.75:1:0:0.1 0/1:267:43:35,8:172,52:0.161:2,2:26.1:1:30.5:1:0.68995:1.32:60:86:0.1629:0:1.1 -16 3790186 . G T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19771;SOR=0.2593;LSEQ=AAACAGTATACTATAATATG;RSEQ=TATGTGGTCTCTCTCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:13:12,1:8,0:0.619:0,1:20.8:1:30.9:1:1:0:60:26:0.619:0:1.1 0/1:7:2:2,0:5,0:0.2857:0,0:39:1:30.5:1:1:0:60:4:0.2857:0:1 -16 3790307 . T C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03348;SOR=Inf;LSEQ=GCTGCAAAGTCTTGGAAGGA;RSEQ=GACCTCAAACTCAAGAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:101,4:0:1,0:20.2:1:31.1:1:1:0:60:210:1:0:0.1 0/1:80:4:4,0:74,2:0.05:1,0:15.8:1:32.3:1:1:0:60:8:0.05:0:1 -16 3790610 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19649;SOR=Inf;LSEQ=GCACTGCTGAGACAGTGACT;RSEQ=AGACTAGAGAATCCACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:19,219:0:2,0:25.5:1:31.6:1:1:0:60:118:1:0:0.1 0/1:190:2:1,1:23,165:0.0105:2,2:12.5:1:27:1:0.23726:7.04:60:4:0.0105:0:1.5 -16 3794705 . T G 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00073;SOR=0;LSEQ=ACATTCTTGCATTCTTACCC;RSEQ=CATGACTGGCCTGGCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:14:13,1:53,0:0.209:1,1:19.6:1:30.1:1:0.20896:0:60:28:0.209:0:1 0/0:43:0:0,0:41,2:0:1,0:17.5:1:31.8:1:1:0:60:86:1:0:0.1 -16 3795292 . G T 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.8318;LSEQ=ACTCACCCTGAAGGCCAAAT;RSEQ=ATGTCATAGTGCAGAACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:1:1,0:315,294:0.0016:2,0:4:0:31:0:1:0:60:2:0.0017:0:1 0/1:610:33:13,20:294,283:0.0541:2,2:22.7:1:28.9:1:0.21413:1.59703:60:66:0.0545:0:1.3 -16 3795363 . G A 163 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=58.08551;LSEQ=GCAATCAACGAAACTAGGAG;RSEQ=CAAAGAAGGCGCACTGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:1:1,0:177,288:0.0021:2,0:1:0:27:0:0.38197:0:60:2:0.0022:0:1 0/1:431:48:18,30:161,222:0.1114:2,2:28.6:1:29.2:1:0.64175:1.20818:60:47:0.1108:0:1.4 -16 3795409 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23235;SOR=Inf;LSEQ=ACGGAACCACAAGACCAGAG;RSEQ=CACTTGTAGAAGTCTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:42,167:0:2,0:22.1:1:29.7:1:1:0:60:68.667:1:0:0.1 0/1:195:2:1,1:48,144:0.0103:2,2:45:1:31.5:1:0.44234:2.98:60:4:0.0107:0:1 -16 3796147 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAATGCATACCTCCGAGGA;RSEQ=AGGCTGAAGGGACTGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 3801649 . T C 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=AATGGCACCGGTACCTTCCT;RSEQ=ATAGTCATTGGTAAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:242,71:0:2,0:24.6:1:29.4:1:1:0:60:51.167:1:0:0.1 0/1:303:14:11,3:208,81:0.0462:2,2:24.1:1:30.9:1:0.76439:1.43:60:28:0.0468:0:1 -16 3807171 . G A 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCGTGAGCCACCACACCC;RSEQ=GCCTGAAATTGGGCCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:17:17,0:28,0:0.3778:1,1:29.3:1:30.1:1:1:0:58.8:34:0.3778:0:1.1 0/0:63:0:0,0:58,4:0:2,0:24:1:29.2:1:1:0:60:61:1:0:0 -16 3807946 . C T 156 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0197;LSEQ=AGGCATTGTTGAACATGAGC;RSEQ=AGACGTCGTCCACGTACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:40:16,24:247,285:0.0699:2,2:25.2:1:29.5:1:0.51146:1.29941:60:80:0.0708:0:1.2 0/0:678:1:0,1:329,348:0.0015:2,0:2:0:22:0:1:0:60:2:0.0015:0:1 -16 3819388 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21851;SOR=Inf;LSEQ=GAAAGCACTGACTTCAGTAA;RSEQ=CAAGGTAACATAAATGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:32,193:0:2,0:24.8:1:32.1:1:1:0:60:55.25:1:0:0.1 0/1:198:2:1,1:32,163:0.0101:2,2:25.5:1:28:1:0.30768:5.03:60:4:0.0102:0:1 -16 3820552 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37347;SOR=3.85596;LSEQ=GAGTCTTGGCCCAAAAACAG;RSEQ=AGAGACAGAGAGGCTTACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:1:0,1:208,76:0.0035:2,0:1:0:22:0:0.27018:0:60:2:0.0036:0:1 0/1:298:4:2,2:199,94:0.0134:2,2:25.5:1:28.5:1:0.5971:2.11123:60:8:0.014:0:1 -16 3820667 . C T 164 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=48.18394;LSEQ=TGAACTGGGGTTTGAGGCTG;RSEQ=GGGGTCACCTGGGCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:1:0,1:372,319:0.0014:2,0:1:0:25:0:0.46243:0:60:2:0.0015:0:1 0/1:723:47:23,24:355,321:0.065:2,2:27.6:1:29.7:1:0.6534:1.15377:60:46:0.0652:0:1.1 -16 3820929 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25075;SOR=Inf;LSEQ=CTGGAGGGCAAGGTAGCTGG;RSEQ=TGGCCTGAGGCCCCAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:88,183:0:2,0:24.3:1:32:1:1:0:60:53.2:1:0:0.1 0/1:301:3:1,2:115,183:0.01:2,2:23:1:28:1:1:1.25588:60:6:0.01:0:1 -16 3820966 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24975;SOR=Inf;LSEQ=CATGTTGAGAGGGTTAGGAA;RSEQ=AGCAGCACCAGGCACCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:64,137:0:2,0:24.3:1:30.8:1:1:0:60:32.5:1:0:0.2 0/1:220:3:2,1:75,141:0.0136:2,2:16.3:1:27.3:1:0.283:3.74:60:6:0.0138:0:1 -16 3820999 . G C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49824;SOR=Inf;LSEQ=CACCTGTCCCTACCAGAAAT;RSEQ=GACAGAGTATGGTAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:26,100:0:2,0:22.2:1:30.6:1:1:0:60:41:1:0:0.2 0/1:131:2:1,1:39,89:0.0153:2,2:16.5:1:27.5:1:0.52236:2.27:60:4:0.0153:0:1 -16 3821077 . A AT 32 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.05714;SOR=Inf;LSEQ=ATTAAATGTATGAAAAAAAA;RSEQ=TTTTTTTTTTTGAGACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:0,27:0:1,0:21.4:1:31:1:1:0:60:26:1:0:0.1 0/1:9:2:0,2:0,7:0.2222:0,0:47.5:1:32:0:1:0:60:4:0.2222:0:0 -16 3823680 . G GA 110 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.65576;SOR=1.23083;LSEQ=AATTTCCACGAAGGAAGACA;RSEQ=AAAAAAAAAACCAAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:12:12,0:125,10:0.0811:2,0:21.6:1:30.7:1:1:0:60:24:0.0822:0.027:0.2 0/1:102:10:9,1:79,9:0.098:2,2:24.5:1:29.4:1:1:1.03:60:20:0.101:0.0294:0.4 -16 3827492 . CA C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.60416;SOR=2.24458;LSEQ=AACTGAATTCTGCTTATCAG;RSEQ=AAAAGGAATGGAAAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:157,14:0.0058:2,0:14:0:33:0:1:0:60:2:0.0059:0:0 0/1:154:2:1,1:137,15:0.013:2,2:20:1:29.7:1:0.19761:8.87634:60:4:0.0132:0.0065:0 -16 3827553 . G A 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGGGGGAGAGGAAAAAACA;RSEQ=TGAAAGTTATGGCTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:368,183:0:2,0:26.6:1:32.1:1:1:0:60:274.5:1:0:0.1 0/1:528:16:9,7:342,170:0.0303:2,2:19.3:1:30.7:1:0.42336:1.56334:60:32:0.0307:0:1.3 -16 3827931 . T C 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CATCAGATATTCTAATTCTC;RSEQ=GTTCTTAGAAATACACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:170,44:0:2,0:23:1:30.4:1:1:0:60:34.667:1:0:0.1 0/1:198:15:10,5:149,34:0.0758:2,2:21.3:1:27.8:1:0.18061:2.18078:60:14:0.0725:0:1.1 -16 3828172 . A G 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTCTCTGCTAATAAGTG;RSEQ=TAATATTCATCCTAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:158,330:0:2,0:24.9:1:30.5:1:1:0:60:53.222:1:0:0.1 0/1:488:35:12,23:152,301:0.0717:2,2:26:1:30.7:1:1:1.03:60:70:0.0728:0:1.2 -16 3828585 . G T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01496;SOR=Inf;LSEQ=CTTGGTCAGTGGCCTCAAGG;RSEQ=GAGGAGTCTGTCCCAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:92,0:0:1,0:21.1:1:31.1:1:1:0:60:91:1:0:0.1 0/1:51:4:4,0:47,0:0.0784:1,0:17.5:1:25.8:1:1:0:60:3:0.0612:0:1.3 -16 3828847 . CT C 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54089;SOR=0.81178;LSEQ=ATAACACATCTATCAAACTA;RSEQ=TTTTTTTTTCTTCTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:24:7,17:166,392:0.041:2,2:28.5:1:32.1:1:1:1.0284:60:48:0.0423:0.0017:0.1 0/1:596:20:8,12:200,375:0.0336:2,2:31:1:31.7:1:0.63877:1.25:60:40:0.0341:0:0.1 -16 3828861 . CT C 68 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.20425;LSEQ=AAACTACTTTTTTTTTTCTT;RSEQ=TTTTTTTAAAGACATGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:4:2,2:113,335:0.0088:2,2:23.8:1:30:1:0.26876:2.96:60:8:0.0089:0.0022:0.3 0/1:472:5:3,2:135,332:0.0106:2,2:20.4:1:29.4:1:0.152:3.68:60:10:0.0107:0.0021:0.4 -16 3829178 . G GA 28 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACTCCATACCAAAAAAAGAA;RSEQ=AAAAAAAAAAAAAAGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12.5:1:28.5:1:1:0:50:4:1:0:0 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 3830936 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24128;SOR=Inf;LSEQ=AAGTGACTCAAACACACTTT;RSEQ=TCTAGTAAGGTTCTTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:21,167:0:2,0:24.5:1:32:1:1:0:60:93:1:0:0.1 0/1:182:2:1,1:22,158:0.011:2,2:11:1:27.5:1:0.23739:7.05:60:4:0.011:0:1 -16 3831187 . T A 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTTGGACTGTCACTCAGA;RSEQ=CTGAAACAGGGTCTTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:0:0,0:301,158:0:2,0:26:1:30.5:1:1:0:60:75.5:1:0:0.1 0/1:543:39:25,14:319,184:0.0718:2,2:27:1:29.4:1:1:1.03:60:78:0.0726:0:1.9 -16 3831230 . G T 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=51.17085;LSEQ=GGCCCCCAGGGAAGTCGGAA;RSEQ=AGCTGATTCTGAAATCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:659:1:0,1:342,316:0.0015:2,0:1:0:23:0:0.48103:0:60:2:0.0015:0:1 0/1:789:57:29,28:367,365:0.0722:2,2:25.6:1:28.5:1:1:1.03:60:114:0.0737:0:1.7 -16 3832471 . A G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.98026;LSEQ=GAAGTGGCACAGCAAGCAAC;RSEQ=AAAACATTGCTTCATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:7,0:12,0:0.3684:0,0:15.4:1:29.9:1:1:0:60:14:0.3684:0:2 0/1:11:4:4,0:6,1:0.3636:2,0:6.3:1:29.8:1:1:0:60:8:0.3636:0:1 -16 3832939 . AACAG A 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.0566;SOR=0;LSEQ=CCAGGATGGCTATAACGACA;RSEQ=ACAGACAGACAAAAACGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:4:2,2:100,245:0.0114:2,2:13.3:1:28.3:1:0.58347:2.44:60:8:0.0115:0.0086:0.8 0/0:366:0:0,0:110,256:0:2,0:25:1:29.5:1:1:0:60:60:1:0:0.2 -16 3832959 . C A 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAGACAGACAGACAAAAA;RSEQ=GAGAGGTAAGTAAAAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:61,232:0:2,0:25.2:1:30.4:1:1:0:60:145.5:1:0:0.1 0/1:256:45:11,34:48,163:0.1758:2,2:24.7:1:30.6:1:0.84592:1.10:60:90:0.1765:0:1.2 -16 3833026 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1285;SOR=Inf;LSEQ=TGAGAAGCAAATACATTTCA;RSEQ=CAAAATACTACACATGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:0,85:0:1,0:24:1:30.4:1:1:0:60:84:1:0:0.1 0/1:48:2:0,2:2,44:0.0417:1,0:23.5:1:33:0:1:0:60:4:0.0435:0:2 -16 3833306 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCTGGGGACCAGCAGAC;RSEQ=CCTCTGAGATGAACAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:29:1:29:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 3843454 . C T 106 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00482;SOR=10.90821;LSEQ=TTTTTCATGGTTCGACAATG;RSEQ=GGGAGCGAGCAGGCCCGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:1:0,1:336,309:0.0015:2,0:35:0:28:0:0.47988:0:60:2:0.0016:0:1 0/1:781:13:8,5:394,374:0.0166:2,2:24.4:1:28.9:1:0.58002:1.52:60:26:0.0168:0:1 -16 3860539 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00055;SOR=Inf;LSEQ=AGACTTTCACTGTGAGAATG;RSEQ=TAAAAATCCACAGACCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:237,59:0:2,0:21.9:1:30.8:1:1:0:60:31.889:0.9965:0:0.4 0/1:232:9:7,2:167,55:0.0388:2,2:27.8:1:29.6:1:1:1.15:60:18:0.0395:0:1 -16 3860550 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.0188;SOR=Inf;LSEQ=GTGAGAATGGTAAAAATCCA;RSEQ=AGACCACAGCACCCACCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:268,95:0:2,0:22.3:1:31.7:1:1:0:60:71.6:1:0:0.4 0/1:301:5:1,4:213,83:0.0166:2,2:8:1:25.6:1:0.02578:10.17732:60:10:0.0168:0:1 -16 3860554 . C T 216 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAATGGTAAAAATCCACAGA;RSEQ=CACAGCACCCACCGGAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:130:93,37:181,67:0.3439:2,2:23:1:30.8:1:0.80872:1.07458:60:260:0.3476:0:1.1 0/0:322:0:0,0:222,100:0:2,0:1:0:15:0:1:0:60:0:0:0:1 -16 3860640 . A G 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTGACTGAAGTATTCTTGAT;RSEQ=TCTGTAGGGAAGGTGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:990:0:0,0:544,446:0:2,0:25.7:1:29.3:1:1:0:60:51.105:1:0:0.2 0/1:943:105:59,46:463,372:0.1113:2,2:23.6:1:31.7:1:0.91729:1.03:60:210:0.1128:0:1.2 -16 3900184 . TG T 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51639;SOR=0;LSEQ=TTCCAAGCATGAGTGGCACG;RSEQ=GAGAGCCCAAGAGGAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:188,5:0.0103:1,2:22:0:34:1:0.06075:34.42571:60:4:0.0105:0:0.5 0/0:133:0:0,0:129,4:0:1,0:23.9:1:32.1:1:1:0:60:132:1:0:0 -16 3900218 . C T 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04628;SOR=Inf;LSEQ=GGAAAAACAGGAGTGGGCCA;RSEQ=GTGGTCCCATTTTACGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:269,83:0:2,0:23.2:1:31:1:1:0:60:57.667:1:0:0.2 0/1:306:4:2,2:228,74:0.0131:2,2:14.3:1:27.5:1:0.25825:3.06714:60:8:0.0133:0:1 -16 3901285 . G A 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAACAAGACCGAAACACC;RSEQ=TCTCAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:17:1:31.3:1:1:0:60:6:0.6:0:2.7 0/0:1:0:0,0:0,1:0:0,0:5:0:32:0:1:0:60:2:1:0:0 -16 3901593 . A C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCGGGCATGGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:29:1:1:0:55:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 3929235 . GCACACACACA G 75 d7;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=14.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GACTAAAAACACACACGCGC;RSEQ=CACACACACACACACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:29.6:1:32.4:1:1:0:54.6:10:1:0.2:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 3929738 . C T 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34269;SOR=3.46623;LSEQ=CCTGCTCCGAGCTCCCGGCT;RSEQ=GATCGGTATCCGCGACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:0,1:247,39:0.0035:2,0:1:0:25:0:0.13937:0:60:2:0.0036:0:1 0/1:250:3:2,1:225,22:0.012:2,2:16.3:1:23.3:1:0.2523:5.05357:60:2:0.0082:0:2.3 -16 3929991 . C A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25828;SOR=Inf;LSEQ=CCCGGACGGGGGTCGGGGGC;RSEQ=CTGCCGGCTGCGAGGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:21,124:0:2,0:13.5:1:31:1:1:0:60:28:1:0:0.2 0/1:184:3:1,2:46,135:0.0163:2,2:16.7:1:23.3:1:1:1.46:60:2:0.0111:0:3 -16 3929992 . C A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07971;SOR=0;LSEQ=CCGGACGGGGGTCGGGGGCC;RSEQ=TGCCGGCTGCGAGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:3:2,1:16,118:0.0219:2,2:8:1:22.3:1:0.04538:14.22:60:2:0.0147:0:1.3 0/0:180:0:0,0:46,134:0:2,0:12.4:1:31.8:1:1:0:60:360:1:0:0.3 -16 4013467 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCGTGGCCCAGAGAGAA;RSEQ=GTCTGCACTGGCTGTTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 4343926 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCTTTCCTGCTGTGCAG;RSEQ=TGCGGCCGCCAGCGCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:10,4:0.125:2,2:10:1:28.5:1:1:2.34522:60:4:0.125:0:1 0/0:6:0:0,0:6,0:0:0,0:32.7:1:32.8:1:1:0:60:12:1:0:0 -16 4344012 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49383;SOR=0;LSEQ=CAGCAGCAACAGACAGTGGT;RSEQ=CCAGTAACTCAGAGGCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:18,21:0.0488:2,2:22:1:28.5:1:1:1.16:60:4:0.05:0:1 0/0:40:0:0,0:18,22:0:2,0:35.1:1:32.1:1:1:0:60:80:1:0:0.3 -16 4344056 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=TGAGAAGCAAGACGAGAGGG;RSEQ=CAGGGCTGGGAAAGGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:23.5:1:31.3:1:1:0:60:27:1:0:0.1 0/1:28:2:1,1:10,16:0.0714:2,2:28.5:1:28:1:1:1.57:60:4:0.0714:0:1 -16 5415619 . G A 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00903;SOR=Inf;LSEQ=GGTGGAGGTTGCAGTGAGCC;RSEQ=ATATCGTGCACTGTACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:19.9:1:30.8:1:1:0:60:24:1:0:0 1/0:7:4:4,0:3,0:0.5714:0,0:19.5:1:27:1:1:0:60:3:0.5:0:1 -16 5415716 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51873;SOR=Inf;LSEQ=GCTTTCCCTGGTGTGATTCC;RSEQ=TCCTGCATGGCTGTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:79,21:0:2,0:22.1:1:29.7:1:1:0:60:49:1:0:0.1 0/1:151:2:1,1:96,53:0.0132:2,2:40.5:1:29:1:1:1.8037:60:4:0.0135:0:1 -16 5415787 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26445;SOR=Inf;LSEQ=CTCTCCCACCTAAGTGCATG;RSEQ=TGCCACCCAATGGAAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:69,80:0:2,0:26.3:1:32.1:1:1:0:60:148:1:0:0.1 0/1:201:3:1,2:84,114:0.0149:2,2:22.7:1:29.7:1:1:1.47095:60:6:0.0151:0:1.3 -16 5415791 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51143;SOR=Inf;LSEQ=CCCACCTAAGTGCATGCTGC;RSEQ=ACCCAATGGAAGATTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:64,80:0:2,0:25.8:1:31.3:1:1:0:60:47:1:0:0.1 0/1:199:2:1,1:83,114:0.0101:2,2:28.5:1:29:1:1:1.37:60:4:0.0103:0:1 -16 5415812 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50367;SOR=Inf;LSEQ=ACCCAATGGAAGATTCAGTG;RSEQ=ACATGGACATGAGCCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:46,73:0:2,0:22.3:1:31:1:1:0:60:58.5:1:0:0.1 0/1:147:2:1,1:52,92:0.0136:2,2:6:0:29.5:1:1:1.76:60:4:0.0138:0:1.5 -16 5415915 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06421;LSEQ=GGATAATGATGAAAAGGAGC;RSEQ=CCAGTTATCTTTAAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:56:24,32:1,5:0.9032:2,2:22.8:1:31.3:1:0.38699:3.68:60:112:0.9032:0:1.1 0/1:49:18:7,11:12,19:0.3673:2,2:27.3:1:31.8:1:1:1.01:60:36:0.375:0:1.2 -16 5415928 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14386;SOR=Inf;LSEQ=AAGGAGCACCAGTTATCTTT;RSEQ=AGAATGGTCAGTTTAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:25,38:0:2,0:24.6:1:29.6:1:1:0:60:126:1:0:0.9 0/1:39:2:1,1:16,21:0.0513:2,2:20:1:29.5:1:1:1.30:60:4:0.0513:0:2 -16 5415971 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=9.2767;LSEQ=GTGTGAAGGATGAATCGTAC;RSEQ=TTGTGGAAGCAGAGGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:5:1,4:26,31:0.0806:2,2:21.6:1:30.8:1:0.37604:3.29782:60:10:0.0806:0:1.4 0/1:44:20:11,9:12,12:0.4545:2,2:23.5:1:30.8:1:0.77086:1.22:60:40:0.4545:0:1.3 -16 5416051 . T C 139 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00118;SOR=7.49252;LSEQ=TGAAAATGTCTGTACAGCAA;RSEQ=GGTTTCCCTTGGGGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:1,2:14,14:0.0968:2,2:27.7:1:30.7:1:1:1.9571:60:6:0.1:0:1.3 0/1:51:23:11,12:15,13:0.451:2,2:29.2:1:30.8:1:0.78125:1.25305:60:46:0.451:0:1.3 -16 5416085 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24195;SOR=Inf;LSEQ=GCTTTGAAATCATACCACCA;RSEQ=TGCTCTTACGGTTGAAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:0:2,0:21.1:1:31.9:1:1:0:60:70:1:0:0.1 0/1:39:3:1,2:18,18:0.0769:2,2:8.3:1:27.7:1:1:1.96588:60:6:0.0769:0:1 -16 5416245 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49697;SOR=Inf;LSEQ=TGGAGGTGGTAGCATGGTTC;RSEQ=ACAGAAAAAAGTAAAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:39,43:0:2,0:26.2:1:30.9:1:1:0:60:40:1:0:0.3 0/1:83:2:1,1:50,31:0.0241:2,2:5.5:1:28.5:1:1:1.60324:60:4:0.0241:0:2.5 -16 5416256 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20184;SOR=0;LSEQ=GCATGGTTCCACAGAAAAAA;RSEQ=TAAAACTTGCTGCCGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:36,40:0.0256:2,2:31.5:1:29.5:1:1:1.11:60:4:0.0256:0:1 0/0:95:0:0,0:56,39:0:2,0:22.1:1:31.1:1:1:0:60:190:1:0:0.6 -16 5416308 . A G 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00235;SOR=4.06325;LSEQ=TCATGACGATTTTGATGATG;RSEQ=TGAAGATGATGATGATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:6:3,3:33,27:0.0909:2,2:41.2:1:32.2:1:1:1.21849:60:12:0.0909:0:1 0/1:86:25:11,14:30,31:0.2907:2,2:24:1:29.4:1:0.8126:1.22869:60:11.5:0.2805:0:1.5 -16 5416313 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16087;LSEQ=ACGATTTTGATGATGATGAA;RSEQ=ATGATGATGATGATGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:56:34,22:7,4:0.8358:2,2:22.4:1:30.6:1:1:1.13025:60:112:0.8485:0:1 0/1:85:38:20,18:20,26:0.4471:2,2:27.2:1:29.8:1:0.51093:1.44:60:76:0.4578:0:1.1 -16 5416316 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.50579;SOR=Inf;LSEQ=ATTTTGATGATGATGAAGAT;RSEQ=ATGATGATGATGATTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:41,23:0:2,0:25.3:1:32.1:1:1:0:60:128:1:0:1 0/1:84:2:1,1:38,44:0.0238:2,2:27:0:31:1:1:1.16:60:4:0.0238:0:2.5 -16 5416332 . TTGA T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.25068;SOR=Inf;LSEQ=AGATGATGATGATGATGATT;RSEQ=TGATGATGATGATTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:50,18:0:2,0:25.1:1:30.6:1:1:0:60:136:1:0:0.8 0/1:81:3:0,3:41,37:0.037:2,0:6.7:1:27.3:1:0.1158:0:60:6:0.038:0.0247:1 -16 5416410 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.1753;SOR=Inf;LSEQ=TATATATGAGATACTCCAGC;RSEQ=AAAAATGCACACAAGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:197,52:0:2,0:21.8:1:31.2:1:1:0:60:123.5:0.988:0:0.1 0/1:182:2:1,1:133,47:0.011:2,2:10:0:31.5:1:0.45899:2.81066:60:4:0.0111:0:1.5 -16 5416451 . A G 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=TCAAAATGAAAAGACTCAGA;RSEQ=CCATCATCAACACCAAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:0:0,0:283,183:0:2,0:26.5:1:29.9:1:1:0:60:232:1:0:0.2 0/1:402:12:8,4:229,160:0.0299:2,2:27.2:1:30.6:1:0.76823:1.40:60:11:0.028:0:2 -16 5416455 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=4.48254;LSEQ=AATGAAAAGACTCAGAACCA;RSEQ=CATCAACACCAAGATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:41:27,14:267,185:0.0828:2,2:26.5:1:31.5:1:0.50648:1.34:60:82:0.0847:0:1 0/1:409:118:76,42:163,128:0.2885:2,2:27.8:1:30.4:1:0.12283:1.42:60:58:0.2886:0:1.3 -16 5416679 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13367;SOR=Inf;LSEQ=CCCGATCTCTGGCAGTGGAG;RSEQ=AAGTCTCTTTAAGAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:14,58:0:2,0:24:1:30.8:1:1:0:60:35:1:0:0.1 0/1:42:2:1,1:12,28:0.0476:2,2:19:1:24.5:1:0.52846:2.28:60:4:0.0488:0:1 -16 7032232 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2028;SOR=6.5151;LSEQ=TGGTTGGCTATCAGGTACCC;RSEQ=GGGAGAAATGTAGCTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:7,1:0.1111:2,0:20:0:32:0:1:0:60:2:0.125:0:2 1/0:4:2:2,0:2,0:0.5:0,0:24.5:1:31:0:1:0:60:4:0.5:0:2 -16 7032247 . T C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCCGGGGAGAAATGTAGC;RSEQ=GCTTTCAATTTGAAAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1:0,2:27.7:1:30.2:1:1:0:60:20:1:0:1.2 1/1:6:6:6,0:0,0:1:0,0:17.8:1:30:1:1:0:60:12:1:0:1.3 -16 7032415 . T C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21705;SOR=Inf;LSEQ=CAGAGTCAGGGCTCTGATCC;RSEQ=GGAGCATCAGTCATGTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:114,70:0:2,0:26.1:1:30.5:1:1:0:60:60.333:1:0:1.2 0/1:161:2:1,1:97,62:0.0124:2,2:27:0:29:1:1:1.55998:60:4:0.0124:0:2 -16 7032430 . G C 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43939;SOR=0;LSEQ=GATCCTGGAGCATCAGTCAT;RSEQ=TCTACTTAAGTCCTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:222:222:124,98:0,0:1:0,2:25.4:1:31.4:1:1:0:60:110:1:0:1.3 1/1:174:173:98,75:0,0:0.9943:0,2:25.7:1:31:1:1:0:60:85.5:0.9942:0:2 -16 7032453 . AG CC 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=14.05132;LSEQ=TACTTAAGTCCTTTCATTGC;RSEQ=CGAGCTCCTTCTCATTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:18:9,9:103,111:0.0769:2,2:27.7:1:30.1:1:1:1.08:60:36:0.0796:0.0043:1.8 1/0:194:105:59,46:42,43:0.5412:2,2:25.5:1:29.7:1:0.38244:1.31:60:210:0.5556:0.0052:1.9 -16 7032454 . G C 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66263;SOR=1.81487;LSEQ=ACTTAAGTCCTTTCATTGCA;RSEQ=CGAGCTCCTTCTCATTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:2:2,0:99,112:0.0087:2,0:32.5:1:31:0:0.22367:0:60:4:0.0096:0:3 0/1:192:3:0,3:42,43:0.0156:2,0:15:1:21.7:1:0.24295:0:60:2:0.0233:0:2 -16 7032513 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49884;SOR=0;LSEQ=GGTGGATCCTGGAGTAGTCT;RSEQ=AGACGGCCTCGCCCTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:39,101:0.0141:2,2:5:1:29:1:0.48547:2.57:60:4:0.0141:0:2 0/0:132:0:0,0:44,88:0:2,0:25.3:1:31.2:1:1:0:60:131:1:0:0.7 -16 7032523 . C T 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05977;SOR=Inf;LSEQ=GGAGTAGTCTCAGACGGCCT;RSEQ=GCCCTCTGTTCATCATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:25,88:0:2,0:24.9:1:30.1:1:1:0:60:36.667:1:0:0.3 0/1:114:5:1,4:36,73:0.0439:2,2:28.8:1:30.4:1:1:1.96233:60:10:0.0442:0:1.6 -16 8382667 . T A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.02375;SOR=0;LSEQ=AGTTTTATGTGCCTGCTCCA;RSEQ=AAAAAAAAGAAATGCGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:0.4:0,0:11.5:1:31.5:1:1:0:60:12:0.4:0:2 0/0:11:0:0,0:11,0:0:0,0:22.9:1:30.9:1:1:0:60:22:1:0:0.2 -16 8382737 . G A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.17234;LSEQ=GCCCCGTTGTGACAGCTAGA;RSEQ=CCCCTGCGTTCTTCTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:61:58,3:16,0:0.7922:1,1:30.1:1:29.4:1:1:0:60:19.333:0.7838:0:1.2 0/1:56:22:21,1:33,1:0.3929:1,1:27.5:1:28.8:1:1:1.55834:60:21:0.3818:0:1.2 -16 8382825 . G T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24894;SOR=0;LSEQ=CCTCATCTCCCTCCATTTCA;RSEQ=AGAAGACCAAATAGCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:159,120:0.0106:2,2:23.7:1:23.7:1:0.58035:2.64095:60:2:0.0072:0:1.7 0/0:271:0:0,0:153,118:0:2,0:25.9:1:31.4:1:1:0:60:89.333:1:0:0.6 -16 8382863 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10191;SOR=Inf;LSEQ=ATTCCCAGGTTTGCCATCCT;RSEQ=GTAATTTGGCTTAGCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:159,172:0:2,0:26.7:1:31.3:1:1:0:60:109.333:1:0:1.5 0/1:292:3:1,2:142,147:0.0103:2,2:26:1:29.3:1:1:1.92778:60:6:0.0103:0:1 -16 8382864 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25019;LSEQ=TTCCCAGGTTTGCCATCCTG;RSEQ=TAATTTGGCTTAGCACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:146:68,78:91,95:0.4398:2,2:27.2:1:30.5:1:0.73999:1.09845:60:145:0.4421:0:2.3 0/1:293:48:23,25:122,123:0.1638:2,2:27:1:29.3:1:0.87511:1.07782:60:47:0.1626:0:2.4 -16 8382873 . C T 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=55.56721;LSEQ=TTGCCATCCTGGTAATTTGG;RSEQ=TTAGCACTTCCTCAGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:0,1:154,173:0.003:2,0:1:0:28:0:1:0:60:2:0.0031:0:3 0/1:281:41:23,18:113,127:0.1459:2,2:24.9:1:29.3:1:0.31348:1.43:60:82:0.1459:0:1.9 -16 8382880 . C G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.34472;LSEQ=CCTGGTAATTTGGCTTAGCA;RSEQ=TTCCTCAGAGTGCTCAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:238:106,132:44,43:0.7301:2,2:26.2:1:32.2:1:0.37944:1.27328:60:476:0.7301:0:2.1 0/1:278:134:63,71:67,77:0.482:2,2:26.1:1:31.3:1:1:1.02:60:268:0.4838:0:2.1 -16 8382914 . C A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2544;SOR=0;LSEQ=TCAGAACATCCATTGCAGAC;RSEQ=CTGCTGAACCCAAAGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:2,1:94,165:0.0114:2,2:16.7:1:29:1:0.55632:3.49:60:6:0.0116:0:1.3 0/0:220:0:0,0:87,133:0:2,0:24.9:1:30.4:1:1:0:60:440:1:0:1 -16 8382920 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.24779;LSEQ=CATCCATTGCAGACCCTGCT;RSEQ=AACCCAAAGATGAGACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:239:166:59,107:25,48:0.6946:2,2:25.7:1:29.4:1:0.88394:1.06:60:332:0.6946:0:2.1 0/1:203:73:25,48:46,84:0.3596:2,2:22.3:1:28.7:1:1:1.05119:60:146:0.3596:0:2.1 -16 8383921 . G GCT 32 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCTCTCTCACTCTCTCTT;RSEQ=CTCTCTCTCTCTCTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:32:1:1:0:60:4:1:0:0.5 -16 9250704 . CG C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49519;SOR=Inf;LSEQ=AAGGCCTAGAGAACATATAT;RSEQ=GGTGCCTCTCCTTTTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:11,19:0:2,0:25.8:1:30.2:1:1:0:45.8:60:1:0:0.1 0/1:35:2:1,1:14,19:0.0571:2,2:22.5:1:31.5:1:1:1.35:41.5:4:0.0588:0:2 -16 9855916 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAACCATGCTAGCCTTCG;RSEQ=CAGACAGATGGCATTGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 9856192 . C G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTCACAGACAGAAGATC;RSEQ=ACACTTAGATCTCGGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:31.5:1:1:0:60:4:1:0:1 -16 9858404 . G A 175 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.28061;LSEQ=GCTTTGGATTCTGTGCTCAC;RSEQ=GCCACCTCCACCGTGTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:816:3:1,2:437,375:0.0037:2,2:15:1:30.7:1:0.59863:2.32832:60:6:0.0038:0:1 0/1:789:60:32,28:396,333:0.076:2,2:24.9:1:29.7:1:0.89356:1.04051:60:29:0.0743:0:1.3 -16 9862556 . G T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00516;SOR=0.15421;LSEQ=ATCTAAGTTTGCAACACCTG;RSEQ=CTTATGAATGCACAAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:38:38,0:4,1:0.8837:2,1:21.6:1:29.7:1:0.11628:0:60:18:0.9:0:1.1 1/0:17:9:9,0:8,0:0.5294:0,0:16.6:1:30.3:1:1:0:60:18:0.5294:0:1 -16 9862646 . G T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25192;SOR=0;LSEQ=AGACCCCACTGAGACATCAA;RSEQ=AACCCAAGCGCTTTTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:2,1:134,34:0.0175:2,2:13:1:31.3:1:0.49922:1.96142:60:6:0.0179:0:1 0/0:147:0:0,0:126,21:0:2,0:21.6:1:31.6:1:1:0:60:72.5:1:0:0.2 -16 9863193 . G T 23 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAATATAATATATATATA;RSEQ=AGAGAGAGTATAGCAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:22:1:23.5:1:1:0:60:4:0.25:0:1 0/0:1:0:0,0:0,1:0:0,0:36:0:28:0:1:0:60:2:1:0:0 -16 9892300 . G A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.64287;LSEQ=TAATTCAAGACTGCGGCATC;RSEQ=TAGATGAAAGCGTCCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:496:1:1,0:159,336:0.002:2,0:1:0:26:0:0.32258:0:60:2:0.002:0:1 0/1:527:26:7,19:181,319:0.0493:2,2:26.3:1:30:1:0.4051:1.5389:60:52:0.0499:0:1 -16 9893684 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTAATAAAATGCTTGAT;RSEQ=AATTTTTACATATGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:28.5:1:1:0:60:4:1:0:1 -16 9916049 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56494;SOR=3.07027;LSEQ=GGAGCAGATAGGAACTGAGG;RSEQ=ATGCCGAGAGTCAATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:1:0,1:182,29:0.0047:2,0:18:0:11:0:0.14151:0:60:0:0:0:5 0/1:139:2:1,1:120,17:0.0144:2,2:6.5:1:27:1:0.24304:6.88827:60:4:0.0145:0:1 -16 9916204 . C G 295 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.62045;LSEQ=TGCATGTAGGGATAGTTATT;RSEQ=CGAATGTTTCTCTCCGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:894:586:300,286:162,145:0.6555:2,2:24.9:1:32.1:1:0.67268:1.065:60:96.667:0.6546:0:1.1 1/0:811:439:228,211:195,172:0.5413:2,2:25:1:31.5:1:0.77702:1.04916:60:47.778:0.5402:0:1.2 -16 9916303 . A AAG 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=3e-04;SOR=Inf;LSEQ=TGGAGAGAGAACGAGAAAGG;RSEQ=AGAGAGAGAGTAGGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:141,351:0:2,0:25.6:1:29.8:1:1:0:60:53.667:1:0:0.1 0/1:397:10:4,6:115,270:0.0252:2,2:22.8:1:30.4:1:0.49675:1.56:60:20:0.0256:0.005:0.1 -16 9916317 . G A 150 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=25.54339;LSEQ=GAAAGGAAGAGAGAGAGTAG;RSEQ=AAAAGAAAGAGAAGGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:2:1,1:78,307:0.0052:2,2:11.5:1:29.5:1:0.36702:3.92:60:4:0.0052:0:1 0/1:290:34:7,27:61,195:0.1172:2,2:23.2:1:29.5:1:0.83025:1.20583:60:33:0.115:0:1 -16 9916342 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.56212;SOR=3.19604;LSEQ=GAAAGAGAAGGGAGGAGGGG;RSEQ=AGGAGAGAACAAATAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:1:0,1:23,243:0.0037:2,0:5:0:31:0:1:0:60:2:0.0038:0:1 0/1:168:2:1,1:25,141:0.0119:2,2:23:1:27.5:1:0.28636:5.55:60:4:0.012:0:1 -16 9923179 . G A 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1212;SOR=0.63652;LSEQ=CTTCTGGCTTTTGTGCATTC;RSEQ=AGTTGATGGATCTCAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:129:93:92,1:36,0:0.7209:1,1:24.1:1:30.1:1:1:0:60:30:0.72:0:1.1 1/0:103:64:64,0:39,0:0.6214:1,1:25.6:1:30.1:1:1:0:60:31:0.6139:0:1 -16 9923301 . C T 152 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=43.3348;LSEQ=TTTTTGTCACTGAGGCCGGT;RSEQ=ACTTGGTCCACAAATTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:752:1:0,1:442,309:0.0013:2,0:1:0:26:0:0.41223:0:60:2:0.0014:0:1 0/1:695:38:22,16:360,297:0.0547:2,2:24.7:1:29:1:0.74037:1.13:60:76:0.0552:0:1.2 -16 9927866 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20389;SOR=Inf;LSEQ=TTACAGGCGTGAGCCACCAT;RSEQ=CCTGGTCTAGAGTAATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:118,15:0:2,0:22.1:1:32.1:1:1:0:60:65.5:1:0:0 0/1:110:2:1,1:94,14:0.0182:2,2:8:1:28:1:0.25521:6.52103:60:4:0.0189:0:1 -16 9934691 . G A 204 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AGAGAGAGAGAACAACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:76,83:0:2,0:14.9:1:28.2:1:1:0:57.6:3.818:0.913:0:1.2 0/1:391:117:54,63:97,87:0.2992:2,2:15.1:1:29.7:1:0.28847:1.29961:59:38:0.427:0:1.8 -16 9935066 . T G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00177;SOR=0.17142;LSEQ=CAGATGAGTAAACTGAAGTT;RSEQ=AAAAGGGGAAGTGGCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:75:1,74:0,6:0.9259:0,1:26:1:31.4:1:1:0:60:150:0.9259:0:1.1 1/0:31:21:0,21:0,9:0.6774:0,1:21:1:30.3:1:1:0:60:20:0.6897:0:1 -16 9943432 . G T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35323;SOR=0.50187;LSEQ=GGAATTAAATGAATGCAAGT;RSEQ=TGGCACATCTCTAGGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:18:18,0:7,1:0.6923:2,1:24.4:1:30.3:1:0.30769:0:60:36:0.6923:0:1.4 1/0:19:10:9,1:9,0:0.5263:0,2:27:1:29.5:1:1:0:60:20:0.5556:0:1.1 -16 9943471 . T A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08336;SOR=Inf;LSEQ=TTATCTAAGTCTTTTTTAAA;RSEQ=TGATTATTGTATTATACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:57,1:0:1,0:24.1:1:30.7:1:1:0:60:18.333:1:0:0.4 0/1:46:3:3,0:41,2:0.0652:1,0:13.3:1:24.3:1:1:0:60:2:0.0444:0:2.3 -16 9943666 . C T 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.51524;LSEQ=TTCCTCACACACGTCTCGGT;RSEQ=AGGGGGTCTATGTCTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:726:507:275,232:114,105:0.6983:2,2:24.9:1:28.8:1:0.62682:1.09:60:35.214:0.6944:0:1.1 1/0:798:434:217,217:172,192:0.5439:2,2:24.3:1:28.5:1:0.47715:1.12:60:71.333:0.5473:0:1.2 -16 9943843 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10939;SOR=Inf;LSEQ=AGCACAAACACAAAGACACA;RSEQ=CTGTGCTTTCTTCCGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:76,222:0:2,0:25.4:1:31.7:1:1:0:60:36.25:0.9932:0:0.1 0/1:276:3:2,1:78,195:0.0109:2,2:26:1:30:1:0.20239:4.97:60:6:0.011:0:1 -16 9943995 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.71588;LSEQ=ATAAAGAGAAAACAGAATAT;RSEQ=GGGCAGTTCTCCATCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:23:0,23:0,8:0.7419:0,1:18:1:31.2:1:1:0:60:46:0.7419:0:1.2 1/1:6:5:0,5:0,1:0.8333:0,0:22:1:30.4:1:1:0:60:10:0.8333:0:1 -16 9944017 . G A 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54887;SOR=0;LSEQ=GGCAGTTCTCCATCCCAGCC;RSEQ=CCCTCATCCCCAGAGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:0,5:0,13:0.2778:1,0:17.2:1:29.4:1:1:0:60:10:0.2778:0:1 0/0:3:0:0,0:0,3:0:0,0:27.3:1:32:1:1:0:60:6:1:0:1 -16 9984523 . C T 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTCTATGATCATTGCTA;RSEQ=ATAGTCAACACTTATTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:32.3:1:32.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 9985492 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTAAACACAGATTTATG;RSEQ=CAAATGATACAAGGGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:27.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 10033874 . TGA T 29 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=12.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATAACTTATGGGGATTCCAC;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:29.5:1:1:0:60:4:1:0:0 -16 10273656 . C T 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25824;SOR=0;LSEQ=GTGTACACCATTTTCAGAAA;RSEQ=AAGGCAAAAGGCATTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:0.4545:0,0:10.8:1:28.2:1:1:0:60:4:0.4:0:1.8 0/0:3:0:0,0:2,1:0:2,0:11.3:1:32.7:1:1:0:60:6:1:0:0.3 -16 10273800 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19598;SOR=Inf;LSEQ=TCCGAAGACCTGCAGCAGCT;RSEQ=CCATGCAGCTGGTGGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:205,26:0:2,0:24.2:1:31.7:1:1:0:60:20:1:0:0.2 0/1:184:2:1,1:144,37:0.0109:2,2:21:1:26:1:0.37309:3.85365:60:4:0.0117:0:1 -16 10273821 . C T 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CCATGCAGCTGGTGGCTTCC;RSEQ=AGGTCCTGGCAGGGCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:20:16,4:254,63:0.0593:2,2:23.5:1:30.6:1:1:1.00791:60:19:0.0571:0:1.2 0/0:269:0:0,0:191,78:0:2,0:23.9:1:30.5:1:1:0:60:88.667:1:0:0.2 -16 10274208 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07533;SOR=Inf;LSEQ=CGCCGCCGCGCTCGGCGCCG;RSEQ=ACCGCGCCAGACCAGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:112,219:0:2,0:22.7:1:31:1:1:0:60:46.286:1:0:0.1 0/1:243:3:1,2:89,149:0.0123:2,2:27.7:1:22.7:1:1:1.19381:60:2:0.0084:0:1.3 -16 10274263 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15035;SOR=Inf;LSEQ=AGGGTCCAATAGCCCACTCT;RSEQ=CCCATAGTCGCCACTGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:60,135:0:2,0:24.8:1:32:1:1:0:60:64:1:0:0.1 0/1:124:2:1,1:38,84:0.0161:2,2:32.5:1:28:1:0.53186:2.20:60:4:0.0164:0:1 -16 10353107 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGAAGTTCTTAGAAGATAGC;RSEQ=GTAGAAGAAACAGTGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:1:0,2:16.4:1:29.3:1:1:0:59.5:24:1:0:1.1 1/1:6:5:4,1:1,0:0.8333:0,2:22.2:1:30.2:1:1:0:56.8:10:0.8333:0:1 -16 10353347 . T C 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69057;SOR=0.65808;LSEQ=CAGCCATTTGGAGCCACTAC;RSEQ=GGTCTCTGCGTCTTGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:0,4:0,13:0.2353:1,0:29.8:1:29.3:1:1:0:60:8:0.2353:0:2.5 0/1:18:3:1,2:1,14:0.1667:1,2:14:1:28.3:1:0.31373:5.92:60:6:0.1667:0:1 -16 10353357 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08462;SOR=0;LSEQ=GAGCCACTACTGGTCTCTGC;RSEQ=TCTTGGTGGTAGTGGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:0.25:0,0:35.3:1:31.7:1:1:0:60:6:0.25:0:3 0/0:14:0:0,0:1,13:0:1,0:24.6:1:31.5:1:1:0:60:28:1:0:0.5 -16 10353379 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37652;SOR=0.39596;LSEQ=CTTGGTGGTAGTGGTCCCCC;RSEQ=GGCCCAGCTGTTTTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:0.7273:0,0:18.6:1:30.8:1:1:0:60:16:0.7273:0:1.8 1/0:8:4:1,3:0,4:0.5:0,2:34.8:1:31.3:1:1:0:60:8:0.5:0:1 -16 11295290 . G T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGCCTGTGCTGGACCCA;RSEQ=GTGGTGAGCTGAGGTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:29.5:1:1:0:60:4:1:0:1 -16 11343726 . T C 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCTGCGGCGTGGGATGC;RSEQ=GGACTCGCCCTGGGTGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:19.3:1:30.3:1:1:0:60:6:1:0:1.3 -16 11345651 . T TA 80 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.69458;SOR=1.65488;LSEQ=GACAGAGCAAGACTCTGTCT;RSEQ=AAAAAAAAAAAGAAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:8,0:8,0:0.4706:0,0:28.9:1:26.8:1:1:0:60:7:0.4375:0:0.6 1/0:10:6:5,1:1,0:0.6:0,2:19.7:1:27.9:1:1:0:60:12:0.6:0.2:0.5 -16 11345660 . AAAG A 72 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.29976;SOR=0;LSEQ=AGACTCTGTCTTAAAAAAAA;RSEQ=AAGAAGAAACCTGTCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:25,0:0.1667:1,0:15.2:1:31.1:1:1:0:59:10:0.1667:0.1:0.2 0/0:11:0:0,0:10,1:0:2,0:25.4:1:29.4:1:1:0:60:22:1:0:0.5 -16 11345699 . G C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78148;SOR=0.74129;LSEQ=TTGTTGTTTAGAGTGGGATG;RSEQ=ATTTGGTCCAAGTCCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:14:14,0:31,0:0.3111:1,1:29.4:1:27.7:1:1:0:60:2.5:0.2703:0:1.5 0/1:24:6:5,1:18,0:0.25:1,2:32.8:1:29.8:1:0.25:0:60:5:0.2174:0:1.8 -16 11345753 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17419;SOR=Inf;LSEQ=TGTGTGACCTTGAGTAGGTG;RSEQ=CTGCACTTGTCTGAGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:102,2:0:1,0:21.5:1:31.4:1:1:0:60:103:1:0:0.2 0/1:75:2:1,1:70,3:0.0267:1,2:27.5:1:31:1:0.1045:20.35111:60:4:0.027:0:1 -16 11345754 . C T 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=GTGTGACCTTGAGTAGGTGG;RSEQ=TGCACTTGTCTGAGCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:105,2:0:1,0:21.3:1:32.1:1:1:0:60:106:1:0:0.2 0/1:75:9:9,0:62,4:0.12:2,0:19.6:1:29.9:1:1:0:60:18:0.1233:0:1.1 -16 11346008 . A C 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38021;LSEQ=AAACCCTCCTCTCACTTTTC;RSEQ=TTCTTGTAAATTGACGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:861:303:109,194:200,357:0.3519:2,2:24.6:1:31.6:1:1:1.00:60:150.5:0.3575:0:1.1 0/1:1064:182:75,107:354,527:0.1711:2,2:26.4:1:30.8:1:0.80386:1.04:60:90:0.1727:0:1.2 -16 11346074 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36383;SOR=3.14109;LSEQ=TTGAGAGAGAGACAGAATCT;RSEQ=CACCACCCGGGAAGCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:1,0:39,217:0.0039:2,0:1:0:24:0:0.15564:0:60:2:0.004:0:2 0/1:247:3:2,1:49,194:0.0121:2,2:8.7:1:25.7:1:0.10994:7.83:60:6:0.0125:0:1 -16 11346107 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.18118;SOR=Inf;LSEQ=AGCCACATGGCGCTGGTGCG;RSEQ=GCGCACACACACAAACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:8,133:0:2,0:21.7:1:29.3:1:1:0:59.1:27.2:1:0:0.5 0/1:105:2:1,1:6,97:0.019:2,2:5.5:1:26.5:1:0.12949:15.04:60:4:0.0192:0:1 -16 11346110 . G GCACA 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=7.000;MSILEN=2;SSF=0.50701;SOR=0;LSEQ=CACATGGCGCTGGTGCGCGC;RSEQ=CACACACACAAACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:0,2:6,120:0.0154:1,0:17.5:1:30.5:1:1:0:60:4:0.0157:0.0077:1.5 0/0:99:0:0,0:4,93:0:1,0:23.4:1:31.2:1:1:0:59.6:18.4:0.9787:0:0.6 -16 11346111 . C CAG 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=1.11194;LSEQ=ACATGGCGCTGGTGCGCGCG;RSEQ=ACACACACAAACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:7:0,7:5,116:0.0543:1,0:35.3:1:28.1:1:1:0:60:14:0.0565:0:1.3 0/1:100:6:0,6:4,90:0.06:1,0:34.5:1:28.4:1:1:0:60:12:0.0612:0.01:1 -16 11346113 . C G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.28388;SOR=1.51741;LSEQ=ATGGCGCTGGTGCGCGCGCA;RSEQ=ACACACAAACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:19:0,19:3,100:0.1545:1,1:21:1:29:1:1:0:59.5:5.333:0.1368:0:1.7 0/1:92:20:1,19:1,71:0.2174:1,1:15.8:1:30.9:1:0.38939:3.67:59.5:19:0.2159:0:1.6 -16 11346121 . AACACACAC A 133 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=14.000;MSILEN=2;SSF=0.11447;SOR=0.48385;LSEQ=GGTGCGCGCGCACACACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:23:0,23:0,80:0.213:1,1:32.6:1:29.6:1:1:0:60:22:0.2136:0.0093:0.1 0/1:78:9:0,9:0,44:0.1154:1,0:35.4:1:30.6:1:1:0:60:18:0.1216:0:0.1 -16 11346412 . GA G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCATACTTTTTTCAAAGGAG;RSEQ=AAAAAAACTGTAACATATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:11:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:28.4:1:1:0:60:4:1:0.5:1 -16 11346462 . T C 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTAGCTGACCCCTCTTT;RSEQ=GAGGAGGACCTGTTTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:29.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:34:1:28.5:1:1:0:60:4:1:0:1 -16 11346732 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGTCCTGCTTTGCCTCT;RSEQ=GGAGCCCGTTTTCCCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 11346782 . G T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCCAGCACAGCCACTGAGTG;RSEQ=TCACTAAGGGTCTGTGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:1:28.5:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:0:2,0:18.5:1:31.5:1:1:0:60:4:1:0:0.5 -16 11346954 . AAAAAAG A 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGGGTGTGGCAAAAAAA;RSEQ=AAAAGAAAAGAAAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:0.2222:2,0:31.5:1:29.5:1:1:0:60:4:0.2222:0:0 0/0:1:0:0,0:1,0:0:0,0:23:0:32:0:1:0:60:2:1:0:1 -16 11346955 . AAAAAG A 32 v4;MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0.03846;SOR=Inf;LSEQ=CAGGGGTGTGGCAAAAAAAA;RSEQ=AAAAGAAAAGAAAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:4,1:0.0909:2,0:20:0:32:0:1:0:60:2:0.125:0:0 1/1:2:2:2,0:0,0:1:0,0:14:1:32:1:1:0:60:4:1:0.5:1 -16 11346956 . AAAAG A 72 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=AGGGGTGTGGCAAAAAAAAA;RSEQ=AAAAGAAAAGAAAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:2,0:0.4545:0,2:9.4:1:31.1:1:1:0:60:10:0.7143:0.1818:0 0/0:2:0:0,0:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:1 -16 11346970 . G A 51 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AAAAAAAAAAGAAAAGAAAA;RSEQ=AAAAGAAAAGAAAAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:4,0:11,1:0.25:2,0:5:1:25.8:1:1:0:60:3:0.2308:0:2.8 0/0:2:0:0,0:2,0:0:0,0:23.5:1:25.5:1:1:0:60:1:1:0:1 -16 11347048 . T C 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93062;LSEQ=TTCCCTCCCACTTCACCTTA;RSEQ=TAAGGGATGAAATTGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:13:13,0:28,1:0.3095:1,1:29:1:31.2:1:1:0:60:26:0.3171:0:1.4 0/1:17:5:5,0:11,1:0.2941:2,0:23.8:1:33:0:1:0:60:10:0.2941:0:1 -16 11347138 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49843;SOR=0;LSEQ=CTACTTAATCCCCAAGACAG;RSEQ=CCTGGGCTGCTCTGACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:128,30:0.0125:2,2:17:0:31.5:1:0.35094:4.21365:60:4:0.0126:0:1.5 0/0:159:0:0,0:126,33:0:2,0:22:1:31:1:1:0:60:52:1:0:0.2 -16 11347168 . A G 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTCTGACTCTCTGACCATCA;RSEQ=GTTAATTTTATGTTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:183,76:0:2,0:25.3:1:30.4:1:1:0:60:85.333:1:0:0.4 0/1:276:18:12,6:175,83:0.0652:2,2:23.7:1:31.8:1:1:1.05401:60:36:0.0669:0:1.2 -16 11347199 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.20885;LSEQ=TGTTGTACTTTCAAGTCTGA;RSEQ=AAGTATTATTAAGCATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:143:89,54:158,96:0.3602:2,2:26.1:1:31.6:1:1:1.00:60:70.5:0.3597:0:1.1 0/1:457:48:31,17:252,156:0.105:2,2:21.4:1:31.5:1:0.75511:1.13:60:96:0.1064:0:1.1 -16 11347311 . T C 283 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59314;LSEQ=CCAGGCTGCTTAACCCTAAA;RSEQ=CTGAAAATGACTCAGTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:491:490:192,298:0,0:0.998:0,2:26:1:31.4:1:1:0:60:97:1:0:1.1 1/1:583:581:257,324:0,1:0.9966:0,2:26.4:1:30.9:1:1:0:60:289.5:1:0:1.1 -16 11348264 . AT A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACTCGCTAGAAAACTT;RSEQ=TTTTTTTTAAAAAAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9.5:1:31:1:1:0:60:4:1:0.5:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 11348516 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14329;SOR=Inf;LSEQ=AGCACCAGGAGGGGGAGGAC;RSEQ=CCCTCAAGAGGTGAGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:31,1:0:1,0:20.7:1:30.8:1:1:0:60:31:1:0:0.3 0/1:20:2:2,0:18,0:0.1:1,0:19.5:1:32.5:1:1:0:60:4:0.1053:0:1 -16 11348658 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00994;SOR=Inf;LSEQ=CAAGTAATAACAAAATAACA;RSEQ=GGCATCCCAGTTAATGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:318,167:0:2,0:23.2:1:30.8:1:1:0:60:68.286:1:0:0.1 0/1:597:8:3,5:373,214:0.0134:2,2:9.9:1:28.3:1:0.1514:2.89951:60:16:0.0136:0:1.1 -16 11348825 . C A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62121;SOR=0.49107;LSEQ=CAGCTCCTGCAGCGGCCGCA;RSEQ=GCGGCGCTGGCGCAGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:32,114:0.0135:2,2:21:1:28.5:1:0.39741:3.52:60:4:0.0139:0:1 0/0:150:1:1,0:40,109:0.0067:2,0:1:0:29:0:0.27333:0:60:2:0.0068:0:1 -16 11348826 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49822;SOR=Inf;LSEQ=AGCTCCTGCAGCGGCCGCAC;RSEQ=CGGCGCTGGCGCAGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:34,104:0:2,0:15.1:1:31.7:1:1:0:60:45:1:0:0.2 0/1:140:2:1,1:38,100:0.0143:2,2:6.5:1:28:1:0.48099:2.61:60:4:0.0143:0:1 -16 11348844 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24922;SOR=0;LSEQ=ACGCGGCGCTGGCGCAGCGG;RSEQ=GCCCCCAGCATGCGGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:1,2:47,44:0.0319:2,2:7.7:1:24:1:0.6129:2.11971:60:2:0.0222:0:2.3 0/0:82:0:0,0:42,39:0:2,0:12.7:1:30.8:1:1:0:60:26:0.9873:0:0.2 -16 11348857 . C T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24815;SOR=0;LSEQ=GCAGCGGGGCCCCCAGCATG;RSEQ=GGCGCGGCGCCGCCACGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:1,2:63,27:0.0323:2,2:9:1:29.3:1:0.2284:4.5803:60:6:0.0333:0:1 0/0:83:0:0,0:67,16:0:2,0:18.6:1:32.2:1:1:0:60:166:1:0:0.1 -16 11348914 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09176;SOR=0;LSEQ=AGAGGCAGTCGAAGCTCTCG;RSEQ=GGCTGCCATCCAGGTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:191,88:0.0106:2,2:24:1:29.7:1:0.23971:4.31594:60:6:0.0108:0:1 0/0:342:0:0,0:214,128:0:2,0:24.6:1:30.6:1:1:0:60:67.4:1:0:0.2 -16 11348920 . C T 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18505;SOR=0.21002;LSEQ=AGTCGAAGCTCTCGCGGCTG;RSEQ=CATCCAGGTGAAAGCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:4:2,2:200,101:0.0131:2,2:21:1:29.5:1:0.60568:1.97548:60:8:0.0133:0:1 0/0:360:1:0,1:225,133:0.0028:2,0:7:0:31:0:0.37326:0:60:2:0.0028:0:1 -16 11349077 . G A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10896;SOR=0;LSEQ=CAGCCGCTCGTGCGCCCCGT;RSEQ=CACGCTCAGGGGCCCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:128,168:0.01:2,2:27:1:27:1:1:1.52175:60:6:0.0103:0:2 0/0:327:0:0,0:144,183:0:2,0:23.9:1:31.3:1:1:0:60:53.5:1:0:0.2 -16 11349185 . CG C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21494;SOR=0;LSEQ=TGTGCGGAAGTGCGTGTCGC;RSEQ=GGGGCCGGGGCCGGGACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:32,78:0.0179:2,2:23:1:30:1:0.50434:2.42:60:4:0.0179:0:0 0/0:129:0:0,0:42,86:0:2,0:15.7:1:30.3:1:1:0:60:127:0.9922:0:0.3 -16 11349191 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21808;SOR=0;LSEQ=GAAGTGCGTGTCGCCGGGGG;RSEQ=CGGGGCCGGGACCGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:28,66:0.0208:2,2:19:0:31:0:0.51513:2.33:60:4:0.0211:0:1.5 0/0:109:0:0,0:34,75:0:2,0:13:1:31.4:1:1:0:60:108:1:0:0.3 -16 11349213 . CGGCCGCGGGCGCGCGGG C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=5.000;MSILEN=1;SSF=0.50268;SOR=0;LSEQ=GGGGCCGGGACCGCGGGGCA;RSEQ=GGCCGCGGGCGAGGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:67,25:0.0213:2,2:8:1:29.1:1:0.47884:2.6475:60:4:0.0213:0.0213:0 0/0:76:0:0,0:53,23:0:2,0:9.1:1:30:1:1:0:60:152:1:0:0.2 -16 11349252 . A G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25119;SOR=Inf;LSEQ=GCCGCGGGCGAGGAGGAGGA;RSEQ=GAGGAGGAAGGTTCTGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:153,72:0:2,0:22.4:1:30.4:1:1:0:60:74:1:0:0.2 0/1:254:3:1,2:165,85:0.0118:2,2:21:1:31:1:0.27258:3.85994:60:6:0.0122:0:1.3 -16 11349261 . A T 45 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1329;SOR=Inf;LSEQ=GAGGAGGAGGAAGAGGAGGA;RSEQ=GGTTCTGGCCGCCGTCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:178,88:0:2,0:24.9:1:30.4:1:1:0:60:52.2:1:0:0.2 0/1:332:4:1,3:211,117:0.012:2,2:6:1:22.8:1:0.13629:5.38233:55:3:0.0093:0:2 -16 11349302 . C T 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09061;SOR=0.15141;LSEQ=CTCTGCTGCTGTGGAGACTG;RSEQ=ATTGTCGGCTGCCACCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:5:2,3:232,169:0.0123:2,2:21:1:27.4:1:0.65431:2.05549:60:10:0.0126:0:1 0/0:533:1:0,1:299,233:0.0019:2,0:1:0:24:0:0.43902:0:60:2:0.0019:0:2 -16 11349403 . A C 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4899;SOR=0;LSEQ=GCGCTGCGGGAGAGACAAAG;RSEQ=GGTGAGCTGGGGCGCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:101:101:14,87:0,0:1:0,2:24.3:1:30:1:1:0:60:49.5:1:0:1.1 1/1:97:96:8,88:0,0:0.9897:0,2:23.9:1:30.2:1:1:0:60:192:0.9897:0:1.1 -16 11349847 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCGCGGCCGCGACCCCAT;RSEQ=CTGCAGCCCCCGAGGCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 11350714 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17137;SOR=Inf;LSEQ=GGCGGCGCGGGCGCCTCCAC;RSEQ=CCGGCCCAGTTCCTCGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:153,19:0:2,0:21.8:1:30.8:1:1:0:59.9:85:1:0:0.2 0/1:122:2:2,0:105,15:0.0164:2,0:15:1:29:1:1:0:60:4:0.0168:0:1 -16 11350735 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20544;SOR=Inf;LSEQ=CCGGCCCAGTTCCTCGGAAA;RSEQ=TGGGCGGGGCCGGGCAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:192,39:0:2,0:25.1:1:31.7:1:1:0:60:37.5:1:0:0.2 0/1:192:2:1,1:154,36:0.0104:2,2:7:1:26:1:0.34909:4.23325:60:4:0.0106:0:1 -16 11350811 . CTG C 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00516;SOR=1.34488;LSEQ=CTACCCGGCTGCGGAAGAAA;RSEQ=AGGCTGGGGAGGGGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:759:229:141,88:326,203:0.3017:2,2:25.4:1:31.8:1:1:1.00227:59.9:228:0.3069:0.0553:0.2 0/1:925:340:198,142:345,240:0.3676:2,2:23.2:1:31:1:0.83567:1.03092:59.9:339:0.3725:0.0822:0.2 -16 11350965 . G A 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0014;SOR=0.57542;LSEQ=GGTGCATTCTCAGACGTGAT;RSEQ=AATCCCCAAACCTGGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:123:17,106:36,167:0.3773:2,2:24.6:1:29.5:1:0.43905:1.34295:60:29.75:0.3719:0:1.1 0/1:329:85:14,71:49,194:0.2584:2,2:23.6:1:29.9:1:0.52424:1.27996:60:170:0.2623:0:1.1 -16 11350991 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=2.65552;LSEQ=CCAAACCTGGTTTCCTAGCC;RSEQ=TCCTCTCCCCCGACCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:54:1,53:7,132:0.2798:2,1:24.9:1:30.5:1:0.4463:2.79888:60:108:0.2813:0:1.2 1/0:177:90:6,84:4,83:0.5085:1,2:21.7:1:30.6:1:0.74705:1.48:60:89:0.5057:0:1 -16 11350995 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50079;SOR=0;LSEQ=ACCTGGTTTCCTAGCCCTCC;RSEQ=CTCCCCCGACCCCTTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:0,2:7,174:0.0109:1,0:11:1:30:1:1:0:60:4:0.0113:0:2 0/0:160:0:0,0:9,151:0:2,0:21.3:1:29.3:1:1:0:60:31:1:0:0.8 -16 11352604 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20858;SOR=Inf;LSEQ=GGGACCACAGGCCAGGGAAG;RSEQ=CACAGCAAGGGAGCAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:88,3:0:1,0:23.5:1:31.6:1:1:0:60:182:1:0:0 0/1:77:2:1,1:68,7:0.026:2,2:18.5:1:31.5:1:0.19822:9.15346:60:4:0.0274:0:1 -16 11352652 . G T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12372;SOR=Inf;LSEQ=AAGGTACACTCAGCACACGT;RSEQ=GGTTCTCCTCACTGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:180,45:0:2,0:24.3:1:31.4:1:1:0:60:44:1:0:0.1 0/1:235:4:1,3:172,58:0.017:2,2:6.8:1:27.8:1:0.05543:8.79585:60:8:0.0172:0:1 -16 11352793 . G C 282 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.062;LSEQ=TCCACCTTGTGGGCTGTTCT;RSEQ=CTGGAGGGCTGGGCACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:593:590:265,325:0,0:0.9949:0,2:23.5:1:30.7:1:1:0:60:64.556:0.9949:0:1.1 1/1:593:548:245,303:20,22:0.9241:2,2:25.3:1:30.6:1:0.7492:1.12408:60:90.333:0.9233:0:1.1 -16 11352843 . T A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12414;SOR=0;LSEQ=AGCCAGGCAGTGCGAAACCC;RSEQ=GAGGGGCTCAGAGTGCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:4:2,2:68,222:0.0136:2,2:5.3:1:29.5:1:0.24098:3.25:60:8:0.0137:0:2.3 0/0:280:0:0,0:77,203:0:2,0:24.5:1:30.1:1:1:0:60:279:1:0:0.8 -16 11352930 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-04;SOR=0.12796;LSEQ=GCAAGTGACCTGTCCTCTTG;RSEQ=GACCTGATTTGCCCCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:21:0,21:0,45:0.3182:1,1:28.6:1:31.9:1:1:0:60:42:0.3387:0:2 0/1:54:3:0,3:5,46:0.0556:2,0:18.7:1:33:0:1:0:60:6:0.0556:0:2 -16 11352936 . G C 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTGTCCTCTTGGGACCT;RSEQ=ATTTGCCCCAACTGCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:64:0,64:0,0:1:0,1:24.9:1:33:1:1:0:60:128:1:0:1.3 1/1:47:47:4,43:0,0:1:0,2:21.8:1:32:1:1:0:60:94:1:0:1.1 -16 11507019 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11053;SOR=Inf;LSEQ=AGGTTGGCAGTGCCCACCGA;RSEQ=GGACCTCAAAGGACAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:30.3:1:31.2:1:1:0:60:26:1:0:0.9 0/1:7:2:1,1:3,2:0.2857:2,2:16:1:29:1:1:1.41418:60:4:0.2857:0:2 -16 11507025 . T C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52322;SOR=0.24759;LSEQ=GCAGTGCCCACCGAGGGACC;RSEQ=CAAAGGACAGCTGCAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:4,7:0,1:0.9167:0,2:30.5:1:30.7:1:1:0:60:22:0.9167:0:1.1 1/0:7:5:3,2:1,1:0.7143:2,2:21.2:1:29.6:1:1:1.41:60:10:0.7143:0:1.4 -16 11508311 . T C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACCAGGGCTGCCAGGTCCA;RSEQ=GCTGACTCCACTGTCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:46:26,20:0,0:0.9787:0,2:27.7:1:31.5:1:1:0:60:92:1:0:1.2 1/1:22:22:12,10:0,0:1:0,2:22.1:1:31.1:1:1:0:60:44:1:0:1.3 -16 13872875 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52284;SOR=Inf;LSEQ=CCTGGTTTCTGGTGGTTTGC;RSEQ=GGCCACCTTTGGCATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:21,20:0:2,0:27.4:1:29.9:1:1:0:60:40:1:0:0.2 0/1:66:2:1,1:35,29:0.0303:2,2:26.5:1:28.5:1:1:1.20344:60:4:0.0303:0:1 -16 13872919 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14655;SOR=0;LSEQ=TTAATGAAGCATCTCTGCCT;RSEQ=CACCTTCACATAGAGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:8,24:0.0588:2,2:25.5:1:31:1:0.46524:2.89:60:4:0.0606:0:1 0/0:54:0:0,0:21,33:0:2,0:21.6:1:28.9:1:1:0:60:108:1:0:0 -16 14013631 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCCCCTTCCCTTGCTTTTT;RSEQ=GCAGCTTGAGGCTAGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:24:1:32:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:31:1:29.5:1:1:0:60:4:1:0:1 -16 14013666 . A C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGGTGCCAGGGGATGTGGAA;RSEQ=CTCAAAAGAGACGTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18.5:1:33:0:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:23:0:32:0:1:0:60:2:1:0:1 -16 14013993 . T A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25119;LSEQ=AGGAGTCGGCTTCCTTCGGC;RSEQ=GCGTTCGGCTGCGACCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:367:219:154,65:97,51:0.5967:2,2:24.2:1:30.3:1:0.36078:1.24:60:108.5:0.5994:0:1.2 0/1:377:102:72,30:177,98:0.2706:2,2:24.7:1:30:1:0.27293:1.33:60:101:0.2708:0:1.1 -16 14014222 . C T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56521;SOR=3.07015;LSEQ=GGTGCTCAACACGCAGCCGG;RSEQ=CGAGGAGGTGCGGCCGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:1:0,1:58,219:0.0036:2,0:43:0:30:0:1:0:60:2:0.0037:0:3 0/1:182:2:1,1:31,147:0.011:2,2:9.5:1:26.5:1:0.32477:4.68:60:4:0.0112:0:2 -16 14014240 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.23694;LSEQ=GGCCGAGGAGGTGCGGCCGC;RSEQ=CTGGCGCGGGAGTGAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:122:15,107:11,65:0.6131:2,2:26.4:1:30.3:1:0.67036:1.206:60:121:0.6142:0:1.1 0/1:125:34:4,30:9,82:0.272:2,2:24.3:1:30.1:1:0.74884:1.21:60:68:0.2764:0:1.1 -16 14020382 . C G 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=AATGAATGGCAATTACCTAC;RSEQ=TGTTCTGTAGTTTAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:238,72:0:2,0:24.9:1:31.3:1:1:0:60:76.5:0.9967:0:0.1 0/1:283:30:24,6:188,64:0.106:2,2:27.9:1:29.9:1:0.65656:1.36:60:60:0.1064:0:1 -16 14020660 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18157;SOR=Inf;LSEQ=GATGACATTATTTGTCATCT;RSEQ=TGTTTGTGAGATCTACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:22,178:0:2,0:24.3:1:30.5:1:1:0:60:199:1:0:0 0/1:149:2:1,1:16,130:0.0134:2,2:33.5:1:33:0:0.21723:7.91:60:4:0.0137:0:2 -16 14021276 . C T 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAATACAAAAATTAGCCAGG;RSEQ=GTGTTGGCACATGCCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:5:0:19:0:1:0:24:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:32:0:1:0:60:4:1:0:1.5 -16 14021754 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11355;SOR=Inf;LSEQ=TTGAAAATGTTGTTGCTTTG;RSEQ=TTTTCATTTGTTTGTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:58,2:0:1,0:22.4:1:32.1:1:1:0:60:29:1:0:0.2 0/1:31:2:1,1:29,0:0.0645:1,2:7.5:1:28:1:0.06452:0:60:4:0.0645:0:1 -16 14024407 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72447;SOR=0.72805;LSEQ=AGCCACTTCCTTGAATAATG;RSEQ=TTGCAGTTTTTTTATTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:18:18,0:13,0:0.5806:1,1:21.4:1:28.4:1:1:0:60:17:0.5667:0:1.2 1/0:10:5:5,0:5,0:0.5:0,0:12.8:1:30.6:1:1:0:60:10:0.5:0:1 -16 14025892 . C A 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14255;SOR=5.30883;LSEQ=CAGATCACAGTAGTGGGAGG;RSEQ=GGTGTGGTTGGTAGGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:1:1,0:84,2:0.0115:1,0:2:0:15:0:1:0:60:0:0:0:3 0/1:51:3:3,0:48,0:0.0588:1,0:29:1:30.3:1:1:0:60:6:0.0588:0:1 -16 14026007 . G A 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02624;LSEQ=ACTTTTTCTTTTAACTTTTC;RSEQ=TATTAGGTTGGCTGTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:487:486:279,207:0,0:0.9979:0,2:26.4:1:30.1:1:1:0:60:39.5:0.9979:0:1.1 1/1:508:471:283,188:18,16:0.9272:2,2:26.4:1:29.6:1:0.47033:1.34:60:57.875:0.9279:0:1.1 -16 14026361 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05172;SOR=Inf;LSEQ=TATACAGCATGGCAAGTCTT;RSEQ=CAGTCTATTGCCCAGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:0,22:0:1,0:28.3:1:30.3:1:1:0:60:10:1:0:0.1 0/1:7:2:0,2:0,5:0.2857:0,0:35:1:29:1:1:0:60:4:0.2857:0:1 -16 14027947 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19918;SOR=Inf;LSEQ=AGAAAGCTTAAATAAATGGG;RSEQ=ATATGTACTGATGCTCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:0:1,0:22.7:1:31.6:1:1:0:60:15.333:1:0:0.1 0/1:40:2:1,1:38,0:0.05:1,2:13:0:30:0:0.05:0:60:4:0.0513:0:1.5 -16 14028026 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09918;SOR=0;LSEQ=TAAATATTATCACATAGAAT;RSEQ=AGATATTTTTATTTCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:3:2,1:151,59:0.0141:2,2:18:1:29:1:1:1.27813:60:6:0.0142:0:1 0/0:246:0:0,0:167,78:0:2,0:24.1:1:31:1:1:0:60:60.25:0.9959:0:0.1 -16 14028199 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49992;SOR=0;LSEQ=AAACATTTGCTTCCAAAATC;RSEQ=ATCAAATGAGTCCTGATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:34,124:0.0125:2,2:24.5:1:30.5:1:0.39072:3.61:60:4:0.0127:0:1.5 0/0:143:0:0,0:35,107:0:2,0:23.5:1:28.5:1:1:0:60:70:0.9929:0:0.1 -16 14028861 . C T 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03594;SOR=0;LSEQ=ATTTGATCAATACCTAAGAC;RSEQ=CTTTTTAAATAGTTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:7:7,0:32,0:0.1795:1,0:30.4:1:31.9:1:1:0:60:14:0.1795:0:1.6 0/0:28:0:0,0:28,0:0:1,0:22.3:1:30.8:1:1:0:60:56:1:0:0 -16 14029536 . G A 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12409;SOR=0;LSEQ=GATACGTGGTTCTTTATGAC;RSEQ=CAGAGCTAACCTTTGTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:4:3,1:108,187:0.0134:2,2:22:1:28.8:1:0.14612:5.17:60:8:0.0137:0:1.3 0/0:286:0:0,0:113,173:0:2,0:26:1:30.8:1:1:0:60:70.5:1:0:0.2 -16 14031520 . G A 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCTTAGTCAAATATTT;RSEQ=TTATTTGAGCGCTCTAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:205:204:190,14:0,0:0.9951:0,2:23.2:1:28.3:1:1:0:60:39.8:0.995:0:1.2 1/1:128:128:121,7:0,0:1:0,2:23.5:1:28.2:1:1:0:60:41.667:1:0:1.1 -16 14031530 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07128;SOR=Inf;LSEQ=TCAAATATTTGTTATTTGAG;RSEQ=GCTCTAGGTTGCTGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:237,26:0:2,0:22.7:1:31.9:1:1:0:60:42.833:1:0:0.9 0/1:188:3:1,2:156,28:0.016:2,2:9.7:1:25.7:1:0.06747:10.90966:60:6:0.0161:0:1.3 -16 14031598 . C A 173 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=62.14163;LSEQ=AAAAATGCTGTTTTTCCAAC;RSEQ=TAAAAGTTCTGTCTTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:757:1:1,0:432,321:0.0013:2,0:5:0:14:0:1:0:60:0:0:0:2 0/1:736:56:31,25:381,299:0.0761:2,2:25.5:1:29.8:1:1:1.02759:60:112:0.0764:0:1.2 -16 14038545 . T C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27639;LSEQ=AAATCTAGAATTTTGAAATT;RSEQ=GTTTCAGAAGTGTTGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:359:186:136,50:121,52:0.5181:2,2:23.1:1:30.6:1:0.55855:1.17:60:92:0.5169:0:2 0/1:424:97:65,32:221,106:0.2288:2,2:22:1:30.2:1:0.90252:1.02637:60:96:0.228:0:1.9 -16 14038552 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22894;LSEQ=GAATTTTGAAATTTGTTTCA;RSEQ=AAGTGTTGACAATGTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:424:224:154,70:134,66:0.5283:2,2:22:1:29.8:1:0.75473:1.08:60:111:0.5298:0:1.9 0/1:476:97:62,35:246,130:0.2038:2,2:22.7:1:29.8:1:0.81156:1.06809:60:96:0.2038:0:1.9 -16 14038659 . T C 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTAGTAAGAGGCACAGCA;RSEQ=CTGCAGATGTTTCCACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:225,328:0:2,0:25.2:1:30.3:1:1:0:60:91.167:0.9982:0:0.1 0/1:607:29:13,16:237,340:0.0478:2,2:26.8:1:31.3:1:0.70279:1.17:60:58:0.0484:0:1.2 -16 14038727 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24197;SOR=Inf;LSEQ=TTGTCAGGCACCTCCATTGC;RSEQ=TGCAAAGGGGGCTGTGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:35,169:0:2,0:23.8:1:31.6:1:1:0:60:50:1:0:0.1 0/1:198:2:1,1:41,154:0.0101:2,2:10.5:1:28:1:0.3818:3.72:60:4:0.0103:0:1 -16 14038762 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17636;SOR=Inf;LSEQ=TGAAGTTCCAGAGTTACTCT;RSEQ=CCAAGGCTTGGTCTGTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:8,117:0:2,0:26.3:1:32.5:1:1:0:60:250:1:0:0.1 0/1:91:2:1,1:5,83:0.022:2,2:7.5:1:27.5:1:0.12959:15.24:60:4:0.022:0:1 -16 14041760 . C A 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTAGCAAGCCTTTCTCTCT;RSEQ=ACTTCCCGAGGTGCCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:19:9,10:290,350:0.0288:2,2:28.8:1:28.9:1:1:1.09:60:38:0.0288:0:1.1 0/0:751:0:0,0:357,392:0:2,0:24.6:1:31:1:1:0:60:123.833:0.9973:0:0.1 -16 14041958 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25635;LSEQ=CTGGCCATTACAGCAGATTC;RSEQ=GAAACCCTTCCCGAGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:581:311:158,153:141,128:0.5353:2,2:25.3:1:30:1:0.73911:1.06657:60:43.429:0.5371:0:1.1 0/1:584:133:70,63:228,221:0.2277:2,2:25.3:1:29.4:1:0.76717:1.08:60:32.25:0.2247:0:1.2 -16 14042077 . A G 186 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCACGTTAAGAACATCGCAG;RSEQ=ATTAGCAGCCCTGTCACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:61:26,35:269,323:0.0934:2,2:26.2:1:31.4:1:0.688:1.12089:60:122:0.0953:0:1.2 0/0:727:0:0,0:358,369:0:2,0:24.8:1:29.2:1:1:0:60:102.857:1:0:0.2 -16 16100560 . A G 30 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=CCAGCTGTGTGATACTGGAC;RSEQ=CAGTATTTAACCCTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30.5:1:31:1:1:0:60:4:1:0:1 1/0:4:2:2,0:1,0:0.5:0,0:32.5:1:30:1:1:0:60:4:0.6667:0:1.5 -16 16100673 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.30239;SOR=2.40636;LSEQ=ACTTAGAATAAAGCCTGGCA;RSEQ=ACAGAACTGCAGTTTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:4,5:5,2:0.5625:2,2:31.3:1:31.2:1:0.35752:2.90271:59.4:18:0.5625:0:1.1 1/0:25:19:9,10:3,3:0.76:2,2:27.2:1:30.4:1:1:1.10643:60:38:0.76:0:1.7 -16 16100728 . C CGGTGGCGGTGGCGGTGGCGGTGGT 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=6;SSF=2e-05;SOR=0;LSEQ=GGCGGTGGCGGTGGCGGTGG;RSEQ=GGTGGCGGTGATGGTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:5,7:6,4:0.5455:2,2:17.5:1:31:1:0.66992:2.02883:58.8:24:0.5455:0.3636:0.7 0/0:24:0:0,0:5,16:0:2,0:16.4:1:29.2:1:1:0:60:42:0.875:0:1.4 -16 16100739 . A G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0068;SOR=Inf;LSEQ=TGGCGGTGGCGGTGGCGGTG;RSEQ=TGGTGGTGGTGATGGTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:22.1:1:28.7:1:1:0:59.3:14:1:0:0.4 0/1:16:7:1,6:2,7:0.4375:2,2:8.9:1:29.9:1:1:1.659:60:6:0.4:0:2.7 -16 16100746 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.08152;SOR=Inf;LSEQ=GGCGGTGGCGGTGATGGTGG;RSEQ=GGTGATGGTGGCGATGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:24.7:1:28.6:1:1:0:59.2:26:1:0:0.2 0/1:11:3:1,2:2,6:0.2727:2,2:8.7:1:30.7:1:1:1.44:60:6:0.2727:0:3.3 -16 16100769 . ATGATGGTGG A 24 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0.88119;LSEQ=TGATGGTGGCGATGGTGATG;RSEQ=TGATGGTGGTGATGGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:38.5:1:28:0:1:2.24:60:4:0.2222:0:0 0/1:10:2:1,1:2,6:0.2:2,2:24.5:1:24:1:1:2.65:60:4:0.2:0.1:0.5 -16 17380507 . T TATCATCATCATCCTC 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=39;MSI=2.600;MSILEN=1;SSF=0.00453;SOR=0;LSEQ=CAACAATCCCCATGGATAGG;RSEQ=ATCATCATCATCCTCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:6,5:7,3:0.5238:2,2:21.9:1:30:1:0.65944:1.88324:60:22:0.5238:0.2381:0.1 0/0:11:0:0,0:7,4:0:2,0:30.5:1:29.5:1:1:0:60:22:1:0:0.1 -16 17449069 . A G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03352;SOR=0.23135;LSEQ=GAAGCCTCAGGTGCTGGCCA;RSEQ=AGCCACTGGTCTGCAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:5,11:3,7:0.6154:2,2:26.9:1:31.9:1:1:1.06:60:32:0.6154:0:1.1 0/1:19:5:2,3:7,7:0.2632:2,2:21.4:1:31.8:1:1:1.46843:60:10:0.2632:0:1.4 -16 18820808 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1951;SOR=0;LSEQ=TTGCATCACCACCGACTGTG;RSEQ=TGTGGCTTTGGATGCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:92,41:0.0148:2,2:31.5:1:29.5:1:0.52703:2.22908:60:4:0.0154:0:1 0/0:170:0:0,0:113,57:0:2,0:25.6:1:30.6:1:1:0:60:55.667:1:0:0.2 -16 18820818 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50659;SOR=Inf;LSEQ=ACCGACTGTGGTGTGGCTTT;RSEQ=GATGCCTGAGGCTGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:100,48:0:2,0:24.3:1:31.9:1:1:0:60:296:1:0:0.1 0/1:191:2:1,1:120,69:0.0105:2,2:11.5:1:28.5:1:1:1.73376:60:4:0.0106:0:1 -16 18821328 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAAAAATTCTTGCCCAAGA;RSEQ=GAGTTCAAGTCTAGGTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 20634775 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGGCCAGGGATTTGCCT;RSEQ=AGGTGTGCAGTGCGTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 20636814 . G A 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05845;SOR=Inf;LSEQ=GCTGGGTGCTCCACCAAAGC;RSEQ=CTTTCAACCTCTGCAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:17,29:0:2,0:23.3:1:31.6:1:1:0:60:92:1:0:0.2 0/1:52:5:2,3:19,28:0.0962:2,2:20.8:1:29:1:1:1.01751:60:10:0.098:0:1 -16 23614688 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.506;SOR=0;LSEQ=AACAAGCAATCATTTTAAGT;RSEQ=TCATTCAGATATTCTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:2,0:75,6:0.0241:2,0:12.5:1:32:0:1:0:60:4:0.0247:0:1 0/0:63:0:0,0:62,1:0:1,0:25.9:1:32:1:1:0:60:126:1:0:0 -16 23614719 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19958;SOR=Inf;LSEQ=ATTCTCCTTTATATTTAAAA;RSEQ=TCCAAAAAATACTAAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:139,35:0:2,0:21:1:32.1:1:1:0:60:348:1:0:0.1 0/1:141:2:1,1:118,21:0.0142:2,2:5.5:1:28:1:0.28865:5.51315:60:4:0.0144:0:1 -16 23615041 . T A 60 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75921;SOR=1.40168;LSEQ=ATTACATATCCAAAAAACAA;RSEQ=TAAAAAAAAAAAAAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:5:0,5:13,117:0.0368:2,0:28:1:17.6:1:1:0:59:0.25:0.01:0:2.2 0/1:118:6:1,5:12,98:0.0508:2,2:19.5:1:23.3:1:0.51812:1.63:60:2:0.0444:0:3.2 -16 23615042 . TA T 137 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.00188;SOR=2.84381;LSEQ=TTACATATCCAAAAAACAAT;RSEQ=AAAAAAAAAAAAAGGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:16:1,15:11,92:0.1221:2,1:29.3:1:30.5:1:1:1.78609:58.9:32:0.129:0:0.5 0/1:109:31:2,29:10,57:0.2844:2,2:27.8:1:27.8:1:0.32886:2.52321:59.4:9.333:0.2745:0.0183:1 -16 23619235 . A C 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=53.31868;LSEQ=AGCATCACACCCACGCTGAG;RSEQ=GTCGTCTTAGGGTTAATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:1:1,0:372,343:0.0014:2,0:10:0:14:0:1:0:60:0:0:0:4 0/1:806:56:33,23:381,367:0.0695:2,2:25.8:1:31.5:1:0.26954:1.38:60:112:0.0704:0:1.1 -16 23619547 . C CT 28 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.51471;SOR=4.49144;LSEQ=TCTGGCTTCTTGTTCTTCTT;RSEQ=TTTTTTTTTTTAGAGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:0,10:0.0909:0,0:22:0:31:0:1:0:60:2:0.1:0:0 0/1:6:2:1,1:0,4:0.3333:0,2:19:1:28.9:1:0.33333:0:60:4:0.3333:0.1667:0 -16 23624740 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTTGGGAGGCTGAGGCGGGT;RSEQ=GATCACCTGAGGTCAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:47:0:35:0:1:0:37:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:26.5:1:28:1:1:0:60:4:1:0:1 -16 23625138 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53361;SOR=0;LSEQ=CAGGTCCTACAGCCAGAAAA;RSEQ=TTACCAAGCAATCACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:36,0:0.0526:1,2:39:1:28.5:1:0.05263:0:60:4:0.0526:0:1 0/0:21:0:0,0:21,0:0:1,0:20.8:1:30.2:1:1:0:60:42:1:0:0.4 -16 23625224 . T C 170 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=3.1121;LSEQ=TATCCAATTTTGAAAAAAGA;RSEQ=GCCACGGGGAAGGTTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:25:23,2:162,18:0.122:2,2:17.2:1:31.9:1:1:1.28:60:50:0.1238:0:1.1 0/1:162:49:41,8:100,13:0.3025:2,2:20.1:1:30.4:1:0.4479:1.49698:60:98:0.3043:0:1.6 -16 23625230 . G A 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTGAAAAAAGATGCCAC;RSEQ=GGGAAGGTTTGTTCATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:212,33:0:2,0:21.7:1:30.1:1:1:0:60:121.5:1:0:0.2 0/1:192:30:23,7:136,26:0.1563:2,2:22.4:1:29.2:1:0.42778:1.58771:60:29:0.1526:0:2 -16 23625463 . A T 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCTTCCAACAAACCAGT;RSEQ=TTCAGAAAATATTTTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:209:209:25,184:0,0:1:0,2:23.3:1:30.3:1:1:0:60:51.25:1:0:1.1 1/1:223:222:47,175:1,0:0.9955:0,2:22.1:1:29.5:1:0.21525:0:60:110:0.9955:0:1.1 -16 23632479 . C T 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71197;LSEQ=AGGCAGAGGTTGCAGTGAGC;RSEQ=GAGATCATACCACTGTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:26.6:1:31.8:1:1:0:60:10:0.4167:0:1 0/1:9:3:3,0:6,0:0.3333:0,0:23:1:32.7:1:1:0:60:6:0.3333:0:1 -16 23632614 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19909;SOR=Inf;LSEQ=TTATTTAATCTTCACAACAA;RSEQ=CCTGTAAAATTAGAGGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:167,26:0:2,0:21:1:32.1:1:1:0:60:95.5:1:0:0.1 0/1:156:2:1,1:131,23:0.0128:2,2:24:1:29:1:0.28486:5.59704:60:4:0.013:0:1 -16 23632906 . G GA 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.46688;SOR=2.12281;LSEQ=ATAAACTAACCTAATATCAG;RSEQ=AAAAAAAAATCTAACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:0,3:2,71:0.0395:1,0:36:1:32:0:1:0:60:6:0.0417:0:0 0/1:62:5:0,5:1,55:0.0806:1,0:33.4:1:30.8:1:1:0:60:10:0.0847:0:0 -16 23634026 . A G 30 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=CCAGCAGAGGTATTTCTAAC;RSEQ=TTTAAGGGACACACAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:41.5:1:30.5:1:1:0:60:4:0.2857:0:1 1/1:1:1:1,0:0,0:1:0,0:47:0:28:0:1:0:60:2:1:0:1 -16 23634496 . T A 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24855;SOR=Inf;LSEQ=GGGTGATGTGAGGAGTAACC;RSEQ=TTTAATATTAAAGGACTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:55,202:0:2,0:20.6:1:29.9:1:1:0:59.5:20.417:1:0:0.5 0/1:259:3:1,2:63,191:0.0116:2,2:12:1:23.7:1:1:1.51:60:2:0.0083:0:1.7 -16 23635189 . AT A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.30598;LSEQ=TCAGGGATGTCATTCTATTG;RSEQ=TTTTTTTTAAACAAATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:2,0:55,0:0.0351:1,0:27.5:1:32.5:1:1:0:60:4:0.0351:0:0 0/1:44:2:2,0:41,1:0.0455:1,0:33:1:29.5:1:1:0:60:4:0.0455:0:0 -16 23636063 . C T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGTCTTGAACTCCTGAC;RSEQ=TCAGGTGATCCACCCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:32.5:1:1:0:60:4:1:0:1 -16 23637473 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50619;SOR=0;LSEQ=GTTCTGCCTTGCATGGTCAT;RSEQ=GCTCCCAATTTTGGTAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:150,19:0.0117:2,2:20.5:1:33:0:0.22085:7.72031:60:4:0.012:0:1 0/0:133:0:0,0:119,14:0:2,0:22.9:1:28.1:1:1:0:60:43.333:1:0:0.1 -16 23637824 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23964;SOR=Inf;LSEQ=TTCAATGAAACAGTAGGTAT;RSEQ=TAAAATTTAAGTCTTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:3,58:0:1,0:24.1:1:32:1:1:0:60:60:1:0:0 0/1:59:2:0,2:0,57:0.0339:1,0:32.5:1:32:0:1:0:60:4:0.0351:0:1 -16 23637843 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51163;SOR=0;LSEQ=TGTAAAATTTAAGTCTTATG;RSEQ=AGGTGAAAAGAAAGAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:0,2:2,47:0.0392:1,0:33:1:29.5:1:1:0:60:4:0.04:0:1 0/0:35:0:0,0:0,35:0:1,0:24.4:1:32.1:1:1:0:60:70:1:0:0.1 -16 23640442 . A T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22627;SOR=Inf;LSEQ=TAATAGTATTAAAGAACAAG;RSEQ=AGCTATATGACTGAATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:191,30:0:2,0:22.9:1:30:1:1:0:60:72.667:1:0:0.3 0/1:201:2:1,1:161,37:0.01:2,2:10:1:24.5:1:0.34467:4.30703:60:4:0.0101:0:1.5 -16 23640467 . G A 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29153;SOR=0.83878;LSEQ=ATATGACTGAATTCTTTTCA;RSEQ=TTCATTAAAGTTTTCATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:118:87,31:160,68:0.3401:2,2:21.4:1:30.3:1:0.5317:1.19:60:58:0.3382:0:1.1 0/1:348:105:74,31:166,76:0.3017:2,2:24.8:1:29.4:1:0.80056:1.09:60:34:0.2974:0:1.1 -16 23640630 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=AGTCACATCATTAGTCTACA;RSEQ=TTTATGTATAATGTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:64,234:0:2,0:24.6:1:31.9:1:1:0:60:98.333:1:0:0.1 0/1:301:3:2,1:80,218:0.01:2,2:14.7:1:27.3:1:0.1813:5.41:60:6:0.0101:0:1 -16 23641461 . C G 204 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=87.86603;LSEQ=TAGAACAATAAGGTCCTCTT;RSEQ=TAAGTCCTCCATTTCTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:830:1:0,1:408,419:0.0012:2,0:30:0:13:0:1:0:60:0:0:0:2 0/1:938:90:47,43:408,439:0.0959:2,2:22.2:1:31.5:1:0.50631:1.18:60:180:0.0966:0:1.1 -16 23641859 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.17644;SOR=Inf;LSEQ=AGACAATCTGTTTCACTGAT;RSEQ=ACAAAGAGAATAGGATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:2,105:0:1,0:23.4:1:31.3:1:1:0:60:34.667:1:0:0.1 0/1:78:2:1,1:2,74:0.0256:1,2:23.5:1:27.5:1:0.07592:30.41:60:4:0.0263:0:2.5 -16 23646191 . T C 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.21407;LSEQ=ATCTTGATTTACCTTTCACT;RSEQ=GAATAAATAATTTTTCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:731:65:41,24:416,248:0.0889:2,2:26.1:1:31.1:1:1:1.02:60:130:0.0904:0:1.1 0/1:946:226:139,87:421,298:0.2389:2,2:26.2:1:30.4:1:0.43896:1.13:60:225:0.2427:0:1.1 -16 23647664 . G GA 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25147;SOR=Inf;LSEQ=TATTTTTAGGTTCTGAGGAG;RSEQ=AAAAAAATGTATATAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:61,198:0:2,0:23.4:1:31:1:1:0:60:50.8:0.9961:0:0 0/1:294:3:2,1:82,207:0.0102:2,2:12:1:27:1:0.19975:5.02:60:6:0.0102:0.0034:0.7 -16 23647706 . CA C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.50096;SOR=0;LSEQ=ATTTTTCTTATAAAATAAAA;RSEQ=AAAAATACTCATTTTTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:11,99:0.0179:2,2:14:1:30.5:1:0.20367:8.66:60:4:0.018:0:0 0/0:95:0:0,0:11,84:0:2,0:20.5:1:30.4:1:1:0:60:190:1:0:0.1 -16 23647713 . T G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00052;SOR=Inf;LSEQ=TTATAAAATAAAACAAAAAA;RSEQ=ACTCATTTTTAACCTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:9,95:0:2,0:24.6:1:28.5:1:1:0:60:51:1:0:0 0/1:83:9:1,8:6,68:0.1084:2,2:22.7:1:31.1:1:0.56657:1.41:60:18:0.1084:0:1 -16 23647838 . A C 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04549;SOR=Inf;LSEQ=TTTTTTAGGCTGTGAGTAGT;RSEQ=AGGTCACTGTTACCTTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:24,29:0:2,0:27.3:1:29.6:1:1:0:60:52:1:0:0.2 0/1:47:4:2,2:19,24:0.0851:2,2:12.8:1:31:1:1:1.26:60:8:0.087:0:1 -16 23649504 . G A 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36215;SOR=3.1638;LSEQ=AGTGGAAAGGTGGAGTCAGA;RSEQ=GGAAGGGATGCAGTGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:1,0:74,205:0.0036:2,0:1:0:28:0:0.26786:0:60:2:0.0036:0:1 0/1:268:3:2,1:77,188:0.0112:2,2:13.7:1:24:1:0.20849:4.85:60:2:0.0075:0:3 -16 23652268 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19069;SOR=Inf;LSEQ=ACGCCACCACGTGAGCACCA;RSEQ=GCTATTTCCACATTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:106,3:0:1,0:22.4:1:31.9:1:1:0:60:35.333:1:0:0 0/1:85:2:2,0:82,1:0.0235:1,0:22.5:1:31:1:1:0:60:4:0.0238:0:1 -16 23652330 . G T 52 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37319;SOR=0.24972;LSEQ=AGAGGAGGGGGTGGTCAGAT;RSEQ=ATACTGCTGCCCTCGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:4:1,3:269,72:0.0116:2,2:5:1:26:1:0.03353:11.1009:60:8:0.0118:0:1 0/0:343:1:0,1:270,72:0.0029:2,0:1:0:22:0:0.21283:0:60:2:0.003:0:1 -16 24788389 . A AACAGCAGCAGCCGCAGCAGCAGCAGCC 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.15714;SOR=0;LSEQ=GCAGCCACAGCAGCAGCAGC;RSEQ=ACAGCAGCAGCCGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:13,19:0.0588:2,2:37.5:1:30.3:1:1:1.44:60:4:0.0588:0:0 0/0:51:0:0,0:21,30:0:2,0:25.8:1:29.5:1:1:0:60:102:1:0:0.2 -16 24788422 . AGCAGCCACAGCC A 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.09842;SOR=0.23716;LSEQ=GCAGCAGCAGCAGCCACAGC;RSEQ=GCAGCCGCAGCAGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:2,3:7,8:0.25:2,2:28.4:1:28.8:1:1:1.29489:60:10:0.25:0.1:1.2 0/1:42:3:2,1:14,26:0.0714:2,2:27.3:1:32:1:0.54493:3.60:60:6:0.0732:0.0238:0.7 -16 26319906 . A G 54 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GGTGCTTTATGCAACAGTGA;RSEQ=TTTGGTTGCCAGTTTAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:36:1:34.3:1:1:0:60:6:0.5:0:2 0/0:3:0:0,0:3,0:0:0,0:4:1:31:1:1:0:60:6:1:0:0.7 -16 26319948 . C A 64 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6169;SOR=0.34632;LSEQ=AGGTGTTGTTCTTCCATGAA;RSEQ=CCTTTCTGAGTCTTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:4,0:12,0:0.25:0,0:17.3:1:32:0:1:0:60:8:0.25:0:1.8 0/1:10:1:1,0:9,0:0.1:0,0:27:0:32:0:1:0:60:2:0.1:0:1 -16 26319949 . C A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.32615;SOR=3.06658;LSEQ=GGTGTTGTTCTTCCATGAAC;RSEQ=CTTTCTGAGTCTTTTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:0.1176:1,0:6:1:29:1:1:0:60:4:0.1176:0:1.5 0/1:10:3:3,0:7,0:0.3:0,0:34.7:1:29.7:1:1:0:60:6:0.3:0:1 -16 26320124 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24841;SOR=Inf;LSEQ=CTCCACCGAGTTCCCTCGGG;RSEQ=CATCAGAGCAAACTGTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:122,104:0:2,0:26.2:1:31.3:1:1:0:60:74.333:1:0:0.4 0/1:230:3:2,1:118,109:0.013:2,2:25.7:1:27.3:1:1:1.84:60:6:0.0135:0:1 -16 26320139 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24965;LSEQ=TCGGGGCATCAGAGCAAACT;RSEQ=TATTCCACAATCTAACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:91:45,46:79,80:0.3625:2,2:26:1:29.3:1:1:1.00941:60:182:0.364:0:1.1 0/1:258:32:18,14:112,114:0.124:2,2:25.3:1:28.4:1:0.57195:1.31:60:64:0.125:0:1.1 -16 26320217 . G T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10615;SOR=0;LSEQ=AAAACAAAATGTTGGATGAA;RSEQ=CTTGTATATGCAGAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:2,1:41,91:0.0222:2,2:33:1:29.3:1:0.23795:4.38:60:6:0.0227:0:1 0/0:149:0:0,0:56,93:0:2,0:23:1:31.6:1:1:0:60:48.667:1:0:0.2 -16 26320274 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15652;SOR=Inf;LSEQ=AAGTGTGTTTGCACAATATC;RSEQ=ACCCCTTGCCTGAAACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:3,39:0:2,0:20.4:1:28.3:1:1:0:60:84:1:0:0.1 0/1:28:2:1,1:2,24:0.0714:2,2:17:1:29.5:1:0.20635:10.00:60:4:0.0741:0:1 -16 27356203 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCAGAGCCCACACGTGT;RSEQ=TCCCTGAGAACAACGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 27356359 . C T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ATGGTGAGCAGGGCGGAGTG;RSEQ=GGCAGGGGTGGCTGGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:7:1:28.5:1:1:0:60:4:0.3333:0:1.5 0/0:4:0:0,0:2,1:0:2,0:25.3:1:32.7:1:1:0:60:6:1:0:0.3 -16 27356398 . C T 53 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=TGTTCCCACAGCTGCCTGGG;RSEQ=TGAGGGTGGGGTGGGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:3,0:0.5714:0,2:30.5:1:26.8:1:1:0:60:3:0.5:0:1.8 1/0:2:1:1,0:1,0:0.5:0,0:35:0:24:0:1:0:60:2:0.5:0:6 -16 27356584 . T G 183 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGTTTCCACCCCTGAACT;RSEQ=AAGTGCCCAGGAAGGCGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:56:43,13:70,40:0.3373:2,2:24.1:1:31.6:1:0.11282:1.88:60:27:0.3293:0:1.3 0/0:150:0:0,0:100,50:0:2,0:23.6:1:28.7:1:1:0:60:49:1:0:0.3 -16 27356585 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49953;SOR=0;LSEQ=CTGTTTCCACCCCTGAACTT;RSEQ=AGTGCCCAGGAAGGCGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:113,52:0.0119:2,2:16.5:1:33.5:1:0.53531:2.16202:60:4:0.012:0:2 0/0:153:0:0,0:102,50:0:2,0:23.9:1:28.1:1:1:0:60:29.4:0.9932:0:0.3 -16 27356590 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23655;SOR=Inf;LSEQ=TCCACCCCTGAACTTAAGTG;RSEQ=CCAGGAAGGCGTATTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:117,61:0:2,0:26.4:1:31.6:1:1:0:60:34.6:0.9943:0:0.6 0/1:170:2:1,1:109,59:0.0118:2,2:39.5:1:30.5:1:1:1.84045:60:4:0.0119:0:1.5 -16 27356606 . G T 48 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19009;SOR=0.21686;LSEQ=AGTGCCCAGGAAGGCGTATT;RSEQ=AGATGAGGTGTGCTTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:4:2,2:132,79:0.0186:2,2:7:1:24:1:0.63313:1.66666:60:3:0.0142:0:1 0/0:245:1:0,1:155,89:0.0041:2,0:1:0:25:0:0.36735:0:60:2:0.0041:0:2 -16 27356607 . A G 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12625;SOR=Inf;LSEQ=GTGCCCAGGAAGGCGTATTG;RSEQ=GATGAGGTGTGCTTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:139,82:0:2,0:26.2:1:29.8:1:1:0:60:26.625:1:0:0.7 0/1:250:4:3,1:156,89:0.016:2,2:10.8:1:29.8:1:1:1.71:60:8:0.0166:0:3.8 -16 27356623 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.67238;SOR=0.60167;LSEQ=ATTGAGATGAGGTGTGCTTG;RSEQ=TGGAAGGCATGCCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:1,2:155,111:0.0112:2,2:11.7:1:28:1:0.57415:2.78217:60:6:0.0114:0:2 0/0:297:2:1,1:174,121:0.0067:2,2:5:1:19:1:1:1.43619:60:1:0.0034:0:1.5 -16 27356635 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10274;SOR=0;LSEQ=TGTGCTTGCTGGAAGGCATG;RSEQ=CTGCTGCTGATTGAAAACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:160,134:0.0101:2,2:17.7:1:22.3:1:1:1.67:60:2:0.0069:0:1 0/0:336:0:0,0:191,144:0:2,0:25.4:1:31.1:1:1:0:60:54.833:1:0:0.6 -16 27356667 . T G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38789;LSEQ=TGAAAACCGAACTGGGAACA;RSEQ=TCCTTCCATTCTGTGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:321:226:107,119:40,55:0.704:2,2:25.6:1:31.7:1:0.46168:1.24:60:44.2:0.6994:0:1.2 0/1:367:176:92,84:101,90:0.4796:2,2:25.5:1:30.7:1:0.91705:1.02458:60:57.667:0.4779:0:1.4 -16 27356680 . G A 116 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.001;SOR=7.73725;LSEQ=GGGAACATTCCTTCCATTCT;RSEQ=TGTCCACTGGTCAGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:2:2,0:136,169:0.0065:2,0:21:1:27.5:1:0.20125:0:60:4:0.0066:0:2.5 0/1:372:18:10,8:176,178:0.0484:2,2:22.7:1:27.9:1:0.80988:1.26:60:36:0.0493:0:3.1 -16 27356689 . G C 112 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00133;SOR=13.24824;LSEQ=CCTTCCATTCTGTGTCCACT;RSEQ=GTCAGCTGCTGCGGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:1,0:129,170:0.0033:2,0:50:0:31:0:0.43333:0:60:2:0.0034:0:3 0/1:355:15:8,7:164,174:0.0423:2,2:26.8:1:28.8:1:0.79526:1.21:60:14:0.0403:0:3.2 -16 27356771 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50874;SOR=Inf;LSEQ=GAGTCCCTGCAGGAATCCCC;RSEQ=TTGAGCTTGCTGGGCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:10,72:0:2,0:26.4:1:31.8:1:1:0:60:40:1:0:0.1 0/1:111:2:1,1:25,84:0.018:2,2:10:1:29.5:1:0.41523:3.31:60:4:0.0185:0:1 -16 27358190 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTCCTCTGTAAAGGTAG;RSEQ=GCTGTGGGCCACATCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 28883841 . C T 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36652;SOR=0.35477;LSEQ=GCCTCCTACCTCACCTCCCC;RSEQ=ATCCCGCCCTCAGCACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:2,3:2,3:0.5:2,2:17.6:1:28.2:1:1:1:60:10:0.5:0:1 0/1:8:2:1,1:4,2:0.25:2,2:32:1:28.5:1:1:1.8258:60:4:0.25:0:1 -16 30125840 . G C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAACTGGGGCCACCTGAG;RSEQ=TCCCGAGGCCCCGTGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:11:1:30:1:1:1:60:4:0.3333:0:1.5 -16 30128808 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1087;SOR=Inf;LSEQ=TCCTAGGTCTGGTGCCTCCT;RSEQ=AGGTGTGGGACTTAGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:35,27:0:2,0:23.8:1:32.2:1:1:0:60:124:1:0:0.2 0/1:31:2:1,1:18,11:0.0645:2,2:27:1:29:1:1:1.60957:60:4:0.0645:0:1 -16 30128929 . T C 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGTATCCCTGACTTGGACTC;RSEQ=CGAGAAATCTCACCTCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:0:0,0:380,91:0:2,0:24.8:1:30.8:1:1:0:60:93.2:1:0:0.1 0/1:438:25:21,4:313,100:0.0571:2,2:24.4:1:30.2:1:0.47014:1.68:60:24:0.055:0:1.2 -16 30129191 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13306;SOR=Inf;LSEQ=GGCCACCACCTCCAAGTTAG;RSEQ=TCCAACACCAGGCAGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:68,260:0:2,0:24.2:1:30.6:1:1:0:60:24.231:1:0:0.1 0/1:190:2:1,1:23,165:0.0105:2,2:9:1:30:1:0.23726:7.04:60:4:0.0108:0:1 -16 30129206 . G T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55439;SOR=0;LSEQ=GTTAGATCCAACACCAGGCA;RSEQ=AAGGCAGAGGCCTGGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:0,3:76,209:0.0104:2,0:26.7:1:23.7:1:0.56857:0:60:2:0.0072:0:1.3 0/0:151:0:0,0:33,118:0:2,0:24.2:1:31.6:1:1:0:60:302:1:0:0.1 -16 30129542 . CA GT 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=GCCTCTGCAGCCTAAGCAGT;RSEQ=CGCCCCCTTGTCTTTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:590:0:0,0:221,369:0:2,0:24.1:1:31.8:1:1:0:60:72.75:1:0:0.1 0/1:595:15:6,9:213,364:0.0252:2,2:28.5:1:31.2:1:0.79256:1.14:60:30:0.0255:0.0017:1.1 -16 30129559 . G A 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45244;SOR=0.41829;LSEQ=AGTCACGCCCCCTTGTCTTT;RSEQ=CCTCCACTGTTCCCTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:5:3,2:196,293:0.0101:2,2:15.6:1:27.8:1:0.39656:2.24:60:10:0.0104:0:1 0/0:471:2:1,1:193,276:0.0042:2,2:27.5:1:27.5:1:1:1.43:60:4:0.0043:0:1 -16 30129936 . C T 195 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00817;LSEQ=AGGAAAACAGGCTCTGAAGG;RSEQ=GAGGCTGCACACCTCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:91:7,84:14,150:0.3569:2,2:22.5:1:30.1:1:1:1.11953:60:90:0.3571:0:1.1 0/0:223:1:0,1:30,192:0.0045:2,0:21:0:32:0:1:0:60:2:0.0045:0:1 -16 30134265 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27355;SOR=0;LSEQ=TGCCTCCTCGGGACGCTCCG;RSEQ=GTCTCCACGTCCCGGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:282,13:0.0101:1,2:29.7:1:28.3:1:0.13485:10.60833:60:6:0.0104:0:1 0/0:206:0:0,0:195,10:0:1,0:25.4:1:31.7:1:1:0:60:40:1:0:0.3 -16 30134293 . GCCT G 90 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.0435;SOR=4.70784;LSEQ=CGTCCCGGAAAGCGCTCGGC;RSEQ=CCTCCTCCTCTCCCGCGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:557:2:1,1:431,123:0.0036:2,2:32:1:30.5:1:0.39662:3.49379:60:4:0.0037:0:0 0/1:419:7:4,3:296,115:0.0167:2,2:22.9:1:32.4:1:0.40848:1.92714:60:14:0.0173:0.0024:0.1 -16 30134312 . C G 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CGCCTCCTCCTCCTCTCCCG;RSEQ=GAAGCCCCCTCCCCTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:739:0:0,0:495,240:0:2,0:24.4:1:30.7:1:1:0:60:44.938:0.9958:0:0.5 0/1:614:63:38,25:355,194:0.1026:2,2:22.5:1:30.2:1:0.4913:1.20349:60:62:0.103:0:1.4 -16 30134513 . AGCC A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=1.12325;LSEQ=TCCCCGCCCCCGCCCCCCTG;RSEQ=GCCGCCGCCGCCATCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:8:3,5:163,511:0.0116:2,2:26.8:1:29.9:1:0.41051:1.88:60:16:0.0133:0.0029:0.6 0/1:689:9:1,8:198,479:0.0131:2,2:30.4:1:32.4:1:0.45928:3.30232:60:18:0.015:0:0.1 -16 30134541 . C A 43 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05192;SOR=Inf;LSEQ=CCGCCGCCATCTCCACTCCT;RSEQ=CCCTCCCACCGCCCTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:52,346:0:2,0:23.4:1:30.6:1:1:0:59.9:15.583:1:0:0.7 0/1:365:4:3,1:52,309:0.011:2,2:6.3:1:21.8:1:0.01165:17.59:60:3:0.0085:0:1 -16 30134583 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.23431;SOR=Inf;LSEQ=CACGGCGGCCCCGCCCGAGG;RSEQ=CCCGCCCCTTCCCGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:1,88:0:1,0:18:1:31.8:1:1:0:60:43.5:1:0:0.3 0/1:84:2:0,2:2,80:0.0238:1,0:6:1:28.5:1:1:0:60:4:0.025:0:1 -16 30134811 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCACCCTCCCCTCGATGG;RSEQ=GAAGCGGCCAGGGCGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:31.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 30134816 . C G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCCCCTCGATGGCGAAG;RSEQ=GGCCAGGGCGTGACCTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:0:32:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 31009588 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATTGTGGCAAAATCTAC;RSEQ=TCGGTGAGATCAGAAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 31010999 . A G 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1888;LSEQ=AGCCAAGGATACCGATTCAG;RSEQ=GGCATTTGCTGGGCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:0.1429:0,0:18:1:32:1:1:0:60:4:0.1429:0:1 0/1:6:1:1,0:5,0:0.1667:0,0:2:0:30:0:1:0:60:2:0.1667:0:1 -16 31011122 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10939;SOR=Inf;LSEQ=TTTTCTGGTGAACCTTCATG;RSEQ=TGGTGGAACCAGCAGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:85,47:0:2,0:25.8:1:31.7:1:1:0:60:65:1:0:0.3 0/1:122:3:1,2:84,35:0.0246:2,2:13.7:1:27.3:1:0.21806:4.73022:60:6:0.0246:0:1.7 -16 31011137 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24584;SOR=Inf;LSEQ=TCATGCTGGTGGAACCAGCA;RSEQ=GGCTCAGATGCAATTTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:92,59:0:2,0:25.5:1:31.2:1:1:0:60:29.2:1:0:0.4 0/1:149:2:1,1:91,56:0.0134:2,2:31.5:1:30.5:1:1:1.61945:60:4:0.0136:0:1 -16 31011183 . A G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=2e-05;SOR=2.37401;LSEQ=CCTTTCCCTCATTTCCTATC;RSEQ=TATATCTTTCTCCAAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:70:37,33:69,67:0.3398:2,2:27.3:1:30.3:1:0.88308:1.09:60:22.333:0.3333:0:1.1 1/0:218:120:69,51:47,51:0.5505:2,2:25.5:1:29.9:1:0.1743:1.47:60:59:0.5463:0:1.1 -16 31404827 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18659;SOR=0;LSEQ=CACTCTTATGAGGAGCTGAG;RSEQ=CAGGGGAGTGCTTCATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:13,3:0.1111:2,2:20:1:29:1:0.40523:3.89444:60:4:0.1111:0:1 0/0:23:0:0,0:16,7:0:2,0:13.5:1:31:1:1:0:60:46:1:0:0 -16 31406638 . CA C 29 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACAGAGTGAGACTCCGT;RSEQ=AAAAAAAAAAGTCATGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29.5:1:1:0:60:4:1:0:1 -16 31691894 . A G 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTTTGGAAACCACTCAACT;RSEQ=TACGCTGTGAGTAGTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:204,215:0:2,0:25.7:1:29.3:1:1:0:60:58.857:1:0:0.9 0/1:476:40:21,19:207,229:0.084:2,2:27.4:1:31.1:1:0.62072:1.22:60:80:0.086:0:1.1 -16 31691912 . C T 247 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTATACGCTGTGAGTAGTTT;RSEQ=AAAGGGCATTCGCATTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:383:383:170,213:0,0:1:0,2:25.3:1:28.9:1:1:0:60:53.714:1:0:1.1 0/1:428:209:88,121:99,120:0.4883:2,2:25.4:1:28.5:1:0.55895:1.13404:60:51.25:0.4869:0:1.2 -16 31692468 . T C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCATGATACAGAATTGTCTT;RSEQ=AAAAGATGACTTGGCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28.5:1:33.5:1:1:0:53.5:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:60:2:1:0:0 -16 32368251 . T A 126 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0058;LSEQ=AGACTCAAAGAAAAGAAAGA;RSEQ=GACAGAGTGAAAGAAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:6:6,0:169,55:0.0261:2,0:14.7:1:31.3:1:0.33994:0:36:12:0.0267:0:2.7 0/1:648:17:17,0:435,196:0.0262:2,1:11.6:1:30.9:1:0.0026:0:34.4:34:0.0264:0:2.9 -16 32368273 . T C 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.77879;SOR=0.91956;LSEQ=ACAGAGTGAAAGAAGGTACA;RSEQ=TTCTTTCATGTTCAAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:19:15,4:203,94:0.0601:2,2:18.8:1:32.3:1:0.44617:1.73:34.3:38:0.0607:0:2.4 0/1:936:52:36,16:548,336:0.0556:2,2:18.4:1:31.4:1:0.37683:1.38:39:104:0.0559:0:2.4 -16 32368327 . C T 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45786;SOR=0.86142;LSEQ=CAGCAGCACACACAGCCAGG;RSEQ=GCTTTGTGGTCTCGGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:35:18,17:208,222:0.0753:2,2:33.5:1:29.8:1:0.72954:1.13:34.3:70:0.0764:0:2.4 0/1:1389:91:46,45:621,675:0.0655:2,2:29:1:29.2:1:0.66487:1.11:36.9:182:0.0661:0:2.4 -16 32368375 . TG CC 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14759;SOR=0.60926;LSEQ=CCCCTTCACGAGGCCGCTTT;RSEQ=ACTAGTAGAAGGCTGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:15:3,12:114,216:0.0435:2,2:14:1:32.1:1:0.40279:2.10713:32.3:30:0.0444:0.0087:1.8 0/1:891:24:4,20:315,548:0.0269:2,2:23.5:1:32:1:0.05218:2.87127:24.8:48:0.0271:0.0022:2 -16 32368462 . A G 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02664;SOR=Inf;LSEQ=AAGATTATCAAAGTTCCTCA;RSEQ=TGTACTTCCAGTAAAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:10,73:0:2,0:24.2:1:30.9:1:1:0:46.8:26.667:1:0:0 0/1:139:8:1,7:19,112:0.0576:2,2:21.3:1:32.5:1:1:1.18611:48.9:16:0.058:0:1 -16 32369286 . C T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00361;SOR=0;LSEQ=AATAGAGTCTTTTGAAATTG;RSEQ=CTTGCAGGTGACCTTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:15.4:1:30.8:1:1:0:50:10:0.625:0:1 0/0:12:0:0,0:11,1:0:2,0:24.3:1:31.7:1:1:0:45.5:11:1:0:0.1 -16 32369619 . T C 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.06454;LSEQ=CTTTCTCTTCATGTCTTCAT;RSEQ=CTGTGAGGGAATTAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:55:6,49:114,207:0.1463:2,2:25.3:1:31.4:1:0.00015:4.48353:33.4:110:0.1478:0:1 0/1:612:160:23,137:175,277:0.2614:2,2:20.3:1:31.1:1:0:3.75594:35.2:79:0.2638:0:1.1 -16 32369723 . CT TG 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18447;SOR=0;LSEQ=AAGAGGGAGGAAAAGATGTC;RSEQ=TCCAAGAATCATCCCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:5,59:0.0303:2,2:5:1:31:1:0.17483:10.86:37.5:4:0.0308:0.0152:1.5 0/0:87:0:0,0:10,76:0:2,0:21.7:1:32:1:1:0:48.4:85:0.9884:0:0.2 -16 32369738 . CC AA 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02267;SOR=0;LSEQ=ATGTCCTTCCAAGAATCATC;RSEQ=CTTGATGAAGCTCCCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:0,5:5,45:0.0909:2,0:17.8:1:30.3:1:1:0:51.4:10:0.0943:0.0182:0.8 0/0:60:0:0,0:8,52:0:2,0:23.7:1:31.4:1:1:0:49.6:120:1:0:0.3 -16 32369770 . T G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46672;SOR=0.52275;LSEQ=CTCCCACAGCGAAGGCATTA;RSEQ=GTGTTGCCCCCCTCTACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:2,3:0,25:0.1667:1,2:36:1:32:1:0.02299:0:32.6:10:0.1724:0:1.2 0/1:32:3:1,2:2,27:0.0938:2,2:22.3:1:29:1:0.26331:6.07:29.3:6:0.0938:0:1 -16 32369773 . G A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00496;SOR=Inf;LSEQ=CCACAGCGAAGGCATTATGT;RSEQ=TTGCCCCCCTCTACCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:2,26:0:2,0:23.7:1:31.6:1:1:0:44.4:27:1:0:0.3 0/1:31:8:0,8:2,21:0.2581:2,0:24.9:1:31.8:1:1:0:46.6:16:0.2667:0:1 -16 32369983 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=TCCGTGCAGCTCCTCAAATC;RSEQ=TTCCGGGACCACTCTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:13.5:1:31.5:1:1:0:49.8:8:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:24:1:29.5:1:1:0:22:4:1:0:4 -16 32370012 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCACTCTCCACCTGCTGCCC;RSEQ=TGCCATGAATGAGGCCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:5:0:31:0:1:0:40:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:29.5:1:1:0:22:4:1:0:4 -16 32374584 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TGTAGCCTAGCCAACACGGC;RSEQ=AAACCCCATCTCTACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:32:1:29.5:1:1:0:54.5:4:0.5:0:1 0/0:2:0:0,0:2,0:0:0,0:22:1:31:1:1:0:60:4:1:0:0 -16 32374762 . G C 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.48875;SOR=0.50341;LSEQ=GACAGAATGAGAACCTGTCT;RSEQ=AAAAAAGAAAAAAAAAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:5,1:42,3:0.1176:2,2:13.3:1:31.8:1:0.40378:2.72356:34.3:12:0.1176:0:3.7 0/1:48:3:2,1:36,9:0.0625:2,2:8.3:1:28.7:1:0.51226:1.96638:28:6:0.0638:0:3 -16 32374769 . G GA 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.49755;SOR=0;LSEQ=TGAGAACCTGTCTGAAAAAA;RSEQ=AAAAAAAAAAGACAGGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:59,5:0.0303:2,0:22.5:1:32:0:1:0:52:4:0.0308:0:0 0/0:59:0:0,0:46,12:0:2,0:21.6:1:31.2:1:1:0:52.6:13.5:0.9818:0:0.4 -16 32374780 . G T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13199;SOR=0.33071;LSEQ=CTGAAAAAAGAAAAAAAAAA;RSEQ=ACAGGTTGTAACCCATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:9:6,3:60,6:0.12:2,2:21.3:1:31.1:1:0.07049:4.83944:35.6:18:0.125:0:3.1 0/1:70:3:2,1:55,12:0.0429:2,2:26.3:1:29:1:0.46547:2.25824:28:6:0.0476:0:3 -16 32374789 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23674;SOR=Inf;LSEQ=GAAAAAAAAAAGACAGGTTG;RSEQ=AACCCATCCTCCAAGATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:75,11:0:2,0:24.3:1:29.7:1:1:0:44.8:42:1:0:0.4 0/1:82:2:1,1:64,16:0.0244:2,2:26:0:32.5:1:0.37368:3.91077:21:4:0.025:0:1.5 -16 32374808 . C A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.05817;SOR=0.30625;LSEQ=GTAACCCATCCTCCAAGATA;RSEQ=CCCCCATACATCTAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:11:6,5:84,9:0.1058:2,2:29.1:1:29.6:1:0.00622:7.52356:35.1:22:0.1068:0:2.8 0/1:115:4:2,2:91,20:0.0348:2,2:39.3:1:27.3:1:0.16472:4.46711:27:8:0.0354:0:2.5 -16 32374841 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18569;SOR=0;LSEQ=TAAAACAATTAGATTAAACA;RSEQ=ACTAAACATGTTTCTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:132,24:0.0127:2,2:33.5:1:32:1:0.29227:5.40934:36:4:0.0129:0:3 0/0:208:0:0,0:178,30:0:2,0:21.8:1:31.6:1:1:0:36.4:68.333:1:0:0.1 -16 32374884 . C T 42 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04005;SOR=0;LSEQ=GTCTCATGTCTCTCAGGCAG;RSEQ=AGGGCTTCCCATGTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:1,2:194,76:0.011:2,2:9.7:1:27:1:0.19728:5.06987:47.3:6:0.0112:0:1 0/0:523:0:0,0:347,176:0:2,0:23.7:1:31.8:1:1:0:41.3:260.5:1:0:0.1 -16 32374889 . C T 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGTCTCTCAGGCAGCAGGG;RSEQ=TTCCCATGTATTTTATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:13:9,4:195,85:0.0444:2,2:20.3:1:30.2:1:1:1.01954:41.4:26:0.0453:0:1.1 0/0:569:0:0,0:377,192:0:2,0:24.4:1:31.7:1:1:0:42:141.25:1:0:0.1 -16 32374963 . TC T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GTGTCTTAAGGCTTCTTCTG;RSEQ=ATAAAACGTGCCTTTGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:556:0:0,0:268,287:0:2,0:25:1:31.4:1:1:0:47.8:41.692:0.9982:0:0.1 0/1:1029:25:14,11:500,498:0.0243:2,2:29.8:1:30.6:1:0.68643:1.27:46.6:50:0.0246:0.0019:0.2 -16 32375126 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50311;SOR=Inf;LSEQ=GAGCAGAGAGGGTCTGAGAT;RSEQ=ATCAGGGAGTCAGCAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:12,71:0:2,0:25.4:1:32.3:1:1:0:48.1:82:1:0:0.2 0/1:103:2:1,1:7,94:0.0194:2,2:22.5:1:30.5:1:0.15001:12.63:43.5:4:0.0196:0:1.5 -16 32375166 . T C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.92566;LSEQ=GGGCCCCCTAATCTTCCTCA;RSEQ=TCTCTGTATTCAGAGTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:0,1:2,32:0.0286:2,0:12:0:34:0:1:0:23:2:0.0294:0:1 0/1:37:2:0,2:2,33:0.0541:2,0:7.5:1:32:1:1:0:24:4:0.0571:0:1 -16 33365203 . T C 56 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCACGAGAATCGCTTGAA;RSEQ=CTGGGAAGCAGAGGTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:8.8:1:33.3:1:1:0:35.5:8:1:0:1.3 1/1:4:4:3,1:0,0:1:0,2:16.8:1:28:1:1:0:30.3:3:1:0:1.3 -16 33365276 . A G 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09317;SOR=Inf;LSEQ=GGGCAACAGAGTGAGACTCC;RSEQ=TCTCAAATAAATAAATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:11,1:0:2,0:21.8:1:29.7:1:1:0:38.8:11:1:0:0.4 0/1:12:4:4,0:5,3:0.3333:2,0:21:1:28:1:0.49091:0:31.3:3:0.2727:0:1.3 -16 33365295 . T A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11275;SOR=0;LSEQ=CATCTCAAATAAATAAATAA;RSEQ=AAAGCCATTCAACTAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:4,0:21,2:0.1481:2,0:8:1:31.3:1:1:0:27.5:8:0.1481:0:1 0/0:24:0:0,0:21,3:0:2,0:18.5:1:30.2:1:1:0:32.5:48:1:0:0.3 -16 33365397 . T C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40426;SOR=0.45944;LSEQ=ACTGTGAAAAAGCAATTATT;RSEQ=CCATAATTAATATACAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:3,0:119,13:0.0222:2,0:6.7:1:29.7:1:1:0:35:6:0.0224:0:1.3 0/1:194:2:2,0:163,29:0.0103:2,0:10:1:25:0:1:0:32.5:4:0.0105:0:1 -16 33365470 . T C 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01538;LSEQ=ACAGAGTGAAAGAAGGTACA;RSEQ=TTCTTTCATGTTCAAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:58:55,3:355,216:0.0922:2,2:20.6:1:32.6:1:0:11.13:38.8:116:0.0931:0:2.4 0/1:984:92:76,16:534,358:0.0935:2,2:15.2:1:31.2:1:1e-05:3.18:37.4:45:0.0929:0:2.3 -16 33365524 . C T 239 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09322;SOR=0.84286;LSEQ=CAGCAGCACACACAGCCGGG;RSEQ=GCTTTGTGGTCTCGGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:915:220:135,85:317,353:0.2404:2,2:27.9:1:29.4:1:0.00034:1.77:42.2:54:0.24:0:2.2 0/1:1434:302:178,124:554,578:0.2106:2,2:30.3:1:29.1:1:0.0023:1.50:42.8:150:0.2117:0:2.1 -16 33365525 . G A 147 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03091;SOR=0.54117;LSEQ=AGCAGCACACACAGCCGGGC;RSEQ=CTTTGTGGTCTCGGCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:923:28:14,14:447,447:0.0303:2,2:21.7:1:30.7:1:1:1:45.2:56:0.0309:0:1.4 0/1:1442:24:12,12:723,695:0.0166:2,2:21:1:30.1:1:1:1.04027:46.7:48:0.0169:0:1.4 -16 33365547 . G A 120 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00087;SOR=12.36359;LSEQ=TTTGTGGTCTCGGCACCCTC;RSEQ=GCTTCCCCTTCACGAGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:839:1:1,0:366,472:0.0012:2,0:1:0:25:0:0.43743:0:48:2:0.0012:0:1 0/1:1306:19:11,8:590,695:0.0145:2,2:12.3:1:28.4:1:0.35683:1.62:43.3:18:0.014:0:1.6 -16 33365560 . C A 138 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00107;SOR=0.28019;LSEQ=CACCCTCGGCTTCCCCTTCA;RSEQ=GAGGCCGCTTTCGACTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:722:21:3,18:272,418:0.0291:2,2:14.1:1:31.5:1:0.02177:3.89842:34.1:42:0.0297:0:1.7 0/0:1082:9:4,5:456,612:0.0083:2,2:7.7:1:29.2:1:1:1.07:39.6:18:0.0084:0:1.7 -16 33365573 . G C 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.63092;LSEQ=CCCTTCACGAGGCCGCTTTC;RSEQ=ACTAGTAGAAGGCTGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:255:104,151:108,243:0.4208:2,2:28.2:1:31.3:1:0.01233:1.55:41.1:62.75:0.419:0:1.9 0/1:907:285:111,174:220,400:0.3142:2,2:26.1:1:30.6:1:0.33435:1.16:42.9:94:0.3151:0:2 -16 33365633 . T C 120 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01978;SOR=0.33384;LSEQ=TTCAAAAGAAAATCACTGGC;RSEQ=TCTTTAAGATTATCAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:13:2,11:30,150:0.0674:2,2:21.1:1:32.5:1:1:1.09947:32.1:26:0.0681:0:3.2 0/1:298:7:1,6:42,248:0.0235:2,2:17.7:1:33.4:1:1:1.01608:31.3:14:0.0238:0:3.1 -16 33365663 . A G 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01093;SOR=0;LSEQ=TTATCAAAGTTCCTCAATGT;RSEQ=CTTCCAGTAAAGTGGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:5:0,5:11,78:0.0532:2,0:11.8:1:33.4:1:1:0:24.8:10:0.0532:0:3.8 0/0:135:0:0,0:17,118:0:2,0:22.5:1:29.3:1:1:0:36.7:66.5:1:0:0.4 -16 33365675 . G C 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32524;SOR=0.26253;LSEQ=CTCAATGTACTTCCAGTAAA;RSEQ=TGGGGGCATTTGATGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:3:0,3:8,71:0.0366:2,0:16.3:1:32:1:1:0:30.7:6:0.0366:0:4.7 0/0:102:1:0,1:11,90:0.0098:2,0:1:0:29:0:1:0:25:2:0.01:0:4 -16 33365682 . C T 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47247;SOR=0.49975;LSEQ=TACTTCCAGTAAAGTGGGGG;RSEQ=ATTTGATGTGAAATTCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:5:0,5:4,64:0.0685:2,0:16.6:1:26.8:1:1:0:23:10:0.0694:0:5 0/1:85:3:0,3:9,73:0.0353:2,0:16.7:1:26.3:1:1:0:23.3:6:0.0353:0:4.7 -16 33365720 . T G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16958;SOR=0.30363;LSEQ=AGTACCAAAAATTACTGGTT;RSEQ=TCATCATTGACAACTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:7:0,7:3,39:0.1429:2,0:38.1:1:31.1:1:1:0:22.4:14:0.1429:0:4.7 0/1:42:2:0,2:4,36:0.0476:2,0:44.5:1:30:1:1:0:22.5:4:0.0476:0:5.5 -16 33365731 . C G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28875;SOR=0.36461;LSEQ=TTACTGGTTTTCATCATTGA;RSEQ=AACTGAGTCCTCATCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:7:0,7:3,31:0.1707:2,0:41.4:1:30.9:1:1:0:22.4:14:0.1707:0:4.7 0/1:29:2:0,2:2,25:0.069:2,0:45.5:1:31:1:1:0:22.5:4:0.069:0:5.5 -16 33365745 . T C 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29298;SOR=0.38227;LSEQ=CATTGACAACTGAGTCCTCA;RSEQ=CACAGCCCGCAACTCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:2,27:0.1944:2,0:35.7:1:32:1:1:0:22.4:14:0.1944:0:4.7 0/1:24:2:0,2:2,20:0.0833:2,0:31.5:1:32.5:1:1:0:22.5:4:0.087:0:5.5 -16 33365753 . C T 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28194;SOR=0.35978;LSEQ=ACTGAGTCCTCATCACAGCC;RSEQ=GCAACTCAGACATGCTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:7:0,7:2,24:0.2121:2,0:27.7:1:29.3:1:1:0:22.4:6:0.1875:0:4.7 0/1:23:2:0,2:2,19:0.087:2,0:23.5:1:29.5:1:1:0:22.5:4:0.087:0:5.5 -16 33365765 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50786;SOR=0;LSEQ=TCACAGCCCGCAACTCAGAC;RSEQ=TGCTTATCTAATAGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:2,24:0.0714:2,0:24:1:31.5:1:1:0:23:4:0.0714:0:5 0/0:19:0:0,0:1,18:0:1,0:20.4:1:29.5:1:1:0:49.8:38:1:0:0.6 -16 33366511 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTGGATGACAATCCCTA;RSEQ=CTGTGCTTATCTGTCTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:25,0:0.0741:1,2:12:1:28.5:1:0.07407:0:50:4:0.0741:0:1.5 0/0:9:0:0,0:8,1:0:2,0:22.4:1:32.8:1:1:0:55.9:18:1:0:0.1 -16 33366647 . CAG TA 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00206;SOR=Inf;LSEQ=AATGTTAAGCAATTATTACT;RSEQ=GAAAATCTTGAATTTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:191,23:0:2,0:22.8:1:31.2:1:1:0:60:70.333:1:0:0.1 0/1:241:10:9,1:194,35:0.0415:2,2:23.5:1:29.6:1:1:1.62:60:20:0.042:0.0041:1 -16 33366928 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.0904;LSEQ=GATGTCCGTCCAAGAATCAT;RSEQ=CCCTTGATGAAGCTCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:0,2:11,85:0.0204:2,0:34:1:30.5:1:1:0:31.5:4:0.0211:0:1.5 0/1:90:2:0,2:5,83:0.0222:2,0:11.5:1:29.5:1:1:0:22:4:0.0222:0:1 -16 33366950 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52601;SOR=0;LSEQ=CCTTGATGAAGCTCCCACAG;RSEQ=GAAGGCATTATGTGTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:0,2:7,62:0.0282:2,0:24:1:31.5:1:1:0:23.5:4:0.0294:0:1.5 0/0:43:0:0,0:5,38:0:2,0:20.3:1:30.3:1:1:0:48.2:86:1:0:0.1 -16 33368198 . CAA C 30 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=24;MSI=26.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGACTACGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:48:0:30.5:1:1:1:59.5:4:0.5:0:2.5 -16 33371341 . CG C 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=GCAGGAGGATCACTTGAACC;RSEQ=GGGGGCAGAGGTTGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:0.4:0,0:29.5:1:31.8:1:1:0:57.2:12:0.4:0:0 0/0:3:0:0,0:1,1:0:2,0:7.5:1:28.5:1:1:0:54:4:0.6667:0:0.5 -16 33371424 . G GA 99 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.06555;SOR=0.26973;LSEQ=GAGAACCTGTCTCAAAAAAG;RSEQ=AAAAAAAAAACAGGTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:9:9,0:42,2:0.1698:1,0:17.7:1:31.3:1:1:0:60:18:0.1698:0.0755:0.4 0/1:58:3:3,0:43,2:0.0517:1,0:32:1:30.3:1:1:0:60:6:0.0652:0:1 -16 33371430 . AA T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.12596;SOR=Inf;LSEQ=CTGTCTCAAAAAAGGAAAAA;RSEQ=AAACAGGTTGTAACCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:53,2:0:1,0:16:1:30.6:1:1:0:60:110:0.9821:0:0.1 0/1:68:4:4,0:58,2:0.0588:1,0:21.8:1:31:1:1:0:60:8:0.0615:0.0294:0.5 -16 33371451 . T C 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAACAGGTTGTAACCCATC;RSEQ=GCCAAGATACTCCCCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:91,9:0:2,0:22.5:1:31.3:1:1:0:60:49:1:0:0.3 0/1:137:32:29,3:97,8:0.2336:2,2:19.1:1:29.6:1:0.71846:1.25214:58.9:31:0.2331:0:3.1 -16 33371484 . T G 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCAATACATTAAAACAAT;RSEQ=AAACAGATTCAACAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:150,18:0:2,0:26:1:30.2:1:1:0:59:83:1:0:0.4 0/1:259:65:52,13:169,23:0.251:2,2:22.5:1:29.4:1:0.14599:1.83224:56:8.286:0.232:0:2.5 -16 33371537 . T G 267 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05626;SOR=1.2751;LSEQ=CCTCTGTCTCATGTCTCTCA;RSEQ=GCAGCAGGGCTTCCCATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:400:220:162,58:130,50:0.55:2,2:23.4:1:31.6:1:0.82101:1.07:51.4:72.333:0.5508:0:1.1 1/0:696:424:285,139:180,91:0.6092:2,2:23.7:1:30.7:1:0.86879:1.04:50.7:37.545:0.6065:0:1.3 -16 33371626 . A T 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=TTAAGGCTTCTTCTGTCGTA;RSEQ=AACATGCCTTTGGATCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:765:0:0,0:369,395:0:2,0:25.4:1:29.9:1:1:0:57.8:83.889:1:0:0.2 0/1:1459:22:11,11:685,751:0.0151:2,2:22.4:1:28.4:1:0.83378:1.10:54.6:44:0.0152:0:1.2 -16 33371658 . C T 245 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=217.30038;LSEQ=GGATCCACTACCAACAACTT;RSEQ=TTGACAAGGTCCAGAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:1:0,1:262,406:0.0015:2,0:6:0:31:0:1:0:49:2:0.0015:0:1 0/1:1285:317:136,181:434,530:0.2467:2,2:26.1:1:29.6:1:0.51561:1.08973:54.3:316:0.2475:0:1.2 -16 33371750 . T C 192 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTATGCCAGAATTAACAGG;RSEQ=CACCATCCAGAAAGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:38,159:0:2,0:22.4:1:29.7:1:1:0:50.8:31.833:1:0:0.1 0/1:313:71:13,58:65,177:0.2268:2,2:24.7:1:31.3:1:0.16209:1.63601:43.1:142:0.2283:0:1.5 -16 33371767 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14876;SOR=0;LSEQ=AGGTCACCATCCAGAAAGAG;RSEQ=AGAGAGGGTCTGAGATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:0,2:20,116:0.0145:2,0:26:1:27.5:1:1:0:54.5:4:0.0146:0:1.5 0/0:219:0:0,0:37,182:0:2,0:21.9:1:31.8:1:1:0:48.6:108.5:1:0:0.4 -16 33371807 . C T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGAGTCAGCAGACAGGG;RSEQ=CCCTTAATCTTCCTCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:10,68:0:2,0:22.8:1:31.4:1:1:0:54.9:77:1:0:0.1 0/1:90:20:2,18:11,59:0.2222:2,2:25:1:29.6:1:0.72481:1.66934:40.4:40:0.2247:0:2.7 -16 33371811 . T C 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGTCAGCAGACAGGGCCCC;RSEQ=TAATCTTCCTCATTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:9,65:0:2,0:22.2:1:29.8:1:1:0:55.3:36:1:0:0.1 0/1:85:19:2,17:9,56:0.2235:2,2:25.4:1:32.4:1:1:1.36128:40.4:38:0.2289:0:2.7 -16 33371874 . C G 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04712;SOR=Inf;LSEQ=CAGGAATGACAATGACACTC;RSEQ=CTGTCTCCTGCTGCTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:2,18:0:2,0:24.1:1:31.7:1:1:0:57.7:40:1:0:0.2 0/1:19:4:1,3:2,13:0.2105:2,2:24.3:1:32:1:0.53044:2.07:48.3:8:0.2222:0:3 -16 33371898 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17787;SOR=Inf;LSEQ=TCTCCTGCTGCTGGGACATC;RSEQ=GTCACTACCTCTTCGTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:1,12:0:1,0:17.4:1:30.8:1:1:0:58:12:1:0:0 0/1:10:2:1,1:2,6:0.2:2,2:18:1:29:1:1:2.65:52:4:0.2:0:3 -16 33371944 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CCTCTCTTGTTGCTAGACTC;RSEQ=AGGTCAAACTAATTAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:29:1:31.4:1:1:0:50.3:14:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:39.5:1:29:1:1:1:48.5:4:0.5:0:1.5 -16 33372475 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18586;SOR=Inf;LSEQ=GAGGTTAAATAACTTGCCTA;RSEQ=GGCCACACAGCTAAGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:30,1:0:1,0:21:1:30.3:1:1:0:42.9:30:1:0:0.1 0/1:24:2:1,1:19,3:0.0833:2,2:38:0:31.5:1:0.31159:5.62736:49.5:4:0.087:0:1.5 -16 33372477 . G A 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00131;SOR=Inf;LSEQ=GGTTAAATAACTTGCCTAAG;RSEQ=CCACACAGCTAAGTAGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:0:1,0:20.6:1:31.3:1:1:0:42.7:32:1:0:0.1 0/1:24:7:5,2:15,2:0.2917:2,2:24.6:1:27:1:0.55204:2.84592:45:6:0.2609:0:1.7 -16 33372520 . C T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=ACCCAGGACCTGAGTGCATG;RSEQ=TCTTAATAATTTCCAGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:59,3:0:1,0:26:1:31.9:1:1:0:39.8:30:1:0:0.1 0/1:60:15:12,3:42,3:0.25:2,2:17.5:1:29.3:1:0.15876:3.41114:37.1:30:0.2542:0:1.2 -16 33372666 . C T 214 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=110.61043;LSEQ=GAATACCACAAATTCTTAAC;RSEQ=CTTTCATATTCATACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:785:1:0,1:460,324:0.0013:2,0:36:0:14:0:0.41401:0:60:0:0:0:1 0/1:1285:159:103,56:646,479:0.1237:2,2:23.4:1:29.4:1:0.08572:1.36:41.6:38.75:0.1225:0:3.5 -16 33372673 . T C 225 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=6;SSF=0;SOR=103.67804;LSEQ=ACAAATTCTTAACCCTTTCA;RSEQ=ATTCATACCTTTCTCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:847:1:0,1:485,361:0.0012:2,0:8:0:14:0:0.42739:0:60:0:0:0:3 0/1:1373:150:94,56:675,548:0.1092:2,2:25.7:1:31.2:1:0.09751:1.36:39.4:300:0.1101:0:3.8 -16 33372677 . C T 212 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=114.69959;LSEQ=ATTCTTAACCCTTTCATATT;RSEQ=ATACCTTTCTCTGAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:1:0,1:502,380:0.0011:2,0:1:0:23:0:0.43148:0:60:2:0.0011:0:1 0/1:1416:163:99,64:680,573:0.1151:2,2:24.5:1:28.9:1:0.13195:1.30:39.4:326:0.1154:0:3.6 -16 33372694 . T C 244 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCATACCTTTCTCTGAGA;RSEQ=TTCTGCCCAGACTTTAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:959:0:0,0:509,450:0:2,0:25.5:1:30.4:1:1:0:59.5:52.278:1:0:0.1 0/1:1584:223:131,92:706,655:0.1408:2,2:22:1:31.3:1:0.06004:1.32:39.3:446:0.1416:0:2.7 -16 33373169 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16034;SOR=0;LSEQ=TACAGTTAGCCAAGATCAAG;RSEQ=CACTGCATGCCAGCCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:86,6:0.0213:2,2:18.5:1:27.5:1:0.14413:13.34704:43.5:4:0.0213:0:1 0/0:140:0:0,0:133,7:0:2,0:23.2:1:32.2:1:1:0:39.3:280:1:0:0.1 -16 33373185 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52358;SOR=Inf;LSEQ=CAAGCCACTGCATGCCAGCC;RSEQ=GGACAACAGAGCAAGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:110,13:0:2,0:23.6:1:31.2:1:1:0:36.8:246:1:0:0.1 0/1:194:2:2,0:174,17:0.0103:2,0:43:1:31.5:1:1:0:40:4:0.0104:0:1 -16 33373245 . G T 80 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05637;SOR=Inf;LSEQ=ACCTCCTACCAGTCTGTGAA;RSEQ=CAATGAAAATATTTCTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:258,140:0:2,0:26:1:32.1:1:1:0:53.1:198:1:0:0.1 0/1:743:8:2,6:466,269:0.0108:2,2:14.1:1:26.8:1:0.05718:5.18542:60:16:0.0109:0:1.4 -16 33373312 . G T 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCAGTCCAACACAAACAA;RSEQ=AACTTCAGGAGCCAAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:28:15,13:370,243:0.0437:2,2:22.2:1:29.2:1:0.55483:1.31901:59.6:56:0.0444:0:1.2 0/0:1267:0:0,0:708,559:0:2,0:24.6:1:31.2:1:1:0:59.3:65.684:1:0:0.3 -16 33373357 . C T 232 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTCCACATAAGGTTCTCA;RSEQ=GAGAGAGGTCTCTCCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:739:0:0,0:356,383:0:2,0:26:1:30.6:1:1:0:56.8:122.167:1:0:0.2 0/1:1315:224:102,122:528,563:0.1703:2,2:24.4:1:29.8:1:0.46307:1.12162:49.8:448:0.1714:0:2.2 -16 33373381 . TG CA 223 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGGTCTCTCCCAAAATCT;RSEQ=GAGTGCCCAAAATCAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:673:0:0,0:260,413:0:2,0:27.5:1:29.8:1:1:0:53.8:83.125:1:0:0.1 0/1:1160:158:60,98:432,562:0.1362:2,2:25.1:1:30.6:1:0.22543:1.25527:43.7:316:0.1378:0.0129:1.8 -16 33373622 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=TAGGAATCTCAACACTCAGG;RSEQ=TTTCCAACTTAACCTATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:0:0,0:20.3:1:30.3:1:1:0:52.2:8:1:0:0.1 0/1:11:2:0,2:0,9:0.1818:0,0:37:0:31.5:1:1:0:35:4:0.1818:0:4.5 -16 33373637 . T C 34 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=TCAGGCTTTCCAACTTAACC;RSEQ=ATGTCCTCTGTAATCTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:22.2:1:25.4:1:1:0:47.6:4:1:0:0 0/1:6:2:0,2:0,4:0.3333:0,0:49:0:34:0:1:0:35:4:0.4:0:4.5 -16 33375471 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTAAGGCCTTCATTGACC;RSEQ=AAAGGATAGTGGGTCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 33887632 . ATTCCG A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AGTCCATTCCATTTCATTCC;RSEQ=TTCCATTCCATTCCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:10.5:1:30:1:1:0:49.5:4:0.5:0.25:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 33887653 . C T 28 v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0.89256;LSEQ=TTCCGTTCCATTCCATTCCA;RSEQ=TCCACTCCATTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,8:0.1111:2,2:12:1:28.5:1:1:1.13:45:4:0.1111:0:5.5 0/1:10:1:0,1:4,5:0.1:2,0:16:0:26:0:1:0:44:2:0.1111:0:2 -16 33887654 . T G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11905;SOR=Inf;LSEQ=TCCGTTCCATTCCATTCCAC;RSEQ=CCACTCCATTCCACTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:14:1:30.6:1:1:0:37.6:36:1:0.1111:4.8 0/1:10:2:1,1:3,5:0.2:2,2:11.5:1:32.5:1:1:1.58:29:4:0.2222:0:5.5 -16 33887658 . C T 70 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.63282;SOR=0.34419;LSEQ=TTCCATTCCATTCCACTCCA;RSEQ=TCCATTCCACTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:2,3:7,7:0.25:2,2:11:1:30.4:1:1:1.46843:45:10:0.2632:0:5.2 0/1:10:1:1,0:3,6:0.1:2,0:15:0:31:0:0.4:0:60:2:0.1:0:6 -16 33887663 . T C 74 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63675;SOR=0.34979;LSEQ=TTCCATTCCACTCCACTCCA;RSEQ=TCCACTCCACTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:2,3:8,8:0.2273:2,2:20.6:1:32:1:1:1.47144:42:10:0.2273:0:5.8 0/1:11:1:1,0:3,5:0.0909:2,0:20:0:33:0:0.44444:0:60:2:0.1:0:6 -16 33887668 . C T 81 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.00833;SOR=14.45577;LSEQ=TTCCACTCCACTCCATTCCA;RSEQ=TCCACTCCACTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:8,9:0.0455:2,0:13:0:25:0:1:0:58:2:0.05:0:5 0/1:14:6:4,2:2,5:0.4286:2,2:17.7:1:31.5:1:0.28613:4.35:32.5:12:0.4286:0:6.7 -16 33887671 . C T 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=1;SOR=0.81227;LSEQ=CACTCCACTCCATTCCACTC;RSEQ=ACTCCACTCCACTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,10:0.087:2,2:21:1:28.5:1:1:1.11:50:4:0.0952:0:5.5 0/1:14:1:0,1:5,6:0.0714:2,0:20:0:29:0:1:0:40:2:0.0714:0:8 -16 33887673 . C T 74 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.02838;SOR=11.76131;LSEQ=CTCCACTCCATTCCACTCCA;RSEQ=TCCACTCCACTCCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:11,8:0.0455:2,0:13:0:31:0:0.45:0:32:2:0.05:0:5 0/1:16:6:3,3:4,6:0.375:2,2:28.2:1:28.8:1:1:1.46:41.8:12:0.4:0:5.5 -16 33887675 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.50244;SOR=0;LSEQ=CCACTCCATTCCACTCCACT;RSEQ=CACTCCACTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:2,0:10,11:0.0833:2,0:16:1:31.5:1:0.47826:0:50:4:0.0833:0:4.5 0/0:17:0:0,0:8,9:0:2,0:20.9:1:31.8:1:1:0:38.9:34:1:0:5.9 -16 33887678 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.63269;SOR=2.30676;LSEQ=CTCCATTCCACTCCACTCCA;RSEQ=TCCACTCCACTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:2,0:10,11:0.0833:2,0:24.5:1:33:0:0.47826:0:50:4:0.0833:0:6.5 0/1:17:3:2,1:6,8:0.1765:2,2:24.3:1:29.7:1:0.57647:2.52:42.3:6:0.1765:0:6.7 -16 33887680 . C G 51 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.63549;SOR=0.46621;LSEQ=CCATTCCACTCCACTCCACT;RSEQ=CACTCCACTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:2,1:10,12:0.12:2,2:13.3:1:32.3:1:0.59304:2.32:49.3:6:0.125:0:5.3 0/1:17:1:1,0:7,9:0.0588:2,0:17:0:34:0:0.47059:0:40:2:0.0588:0:8 -16 33887681 . C A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.15796;SOR=Inf;LSEQ=CATTCCACTCCACTCCACTC;RSEQ=ACTCCACTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:23.7:1:32.3:1:1:0:41.3:50:1:0.04:5.2 0/1:17:2:1,1:7,8:0.1176:2,2:35:0:30.5:1:1:1.13:27:4:0.1176:0:8 -16 33887682 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.15796;SOR=Inf;LSEQ=ATTCCACTCCACTCCACTCC;RSEQ=CTCCACTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,11:0:2,0:25.2:1:30.2:1:1:0:42.8:46:0.92:0:5.5 0/1:17:2:1,1:7,8:0.1176:2,2:21:1:28:1:1:1.13:37:4:0.1176:0:6.5 -16 33887687 . AC CT 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.50244;SOR=0;LSEQ=ACTCCACTCCACTCCACTCC;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:10,11:0.0833:2,2:28:0:31.3:1:1:1.10:51:4:0.0833:0:5.5 0/0:17:0:0,0:7,7:0:2,0:29.6:1:29.3:1:1:0:36.9:28:0.875:0:5.7 -16 33887688 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=1;SOR=1.38806;LSEQ=CTCCACTCCACTCCACTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,9:0.087:2,2:35.5:1:30:1:1:1:49:4:0.0952:0:6 0/1:17:2:1,1:7,8:0.1176:2,2:42:0:29:0:1:1.13:27:4:0.1176:0:8 -16 33887693 . T C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=1.38806;LSEQ=CTCCACTCCACTCCACTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,10:0.087:2,2:17.5:1:31.5:1:1:1.11:21.5:4:0.087:0:4 0/1:17:2:1,1:6,6:0.1176:2,2:38.5:1:30:1:1:1:52.5:4:0.1176:0:6.5 -16 33887695 . CC AT 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.18354;SOR=Inf;LSEQ=CCACTCCACTCCACTCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:27.7:1:31.5:1:1:0:42:44:1:0:5.2 0/1:17:2:1,1:7,8:0.1176:2,2:34:0:28.3:1:1:1.13:27:4:0.1176:0:7 -16 33887697 . A G 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.24291;SOR=0;LSEQ=ACTCCACTCCACTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:2,1:6,10:0.1364:2,2:31.7:1:30:1:0.54592:3.12:41.3:6:0.1364:0:5.3 0/0:17:0:0,0:8,9:0:2,0:31.2:1:29.3:1:1:0:38.9:34:1:0:5.7 -16 33887698 . T C 33 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=1;SOR=0.6323;LSEQ=CTCCACTCCACTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:2,0:7,12:0.0909:2,0:27.5:1:33.5:1:0.17143:0:36.5:4:0.0952:0:5 0/1:17:1:0,1:8,8:0.0588:2,0:42:0:30:0:1:0:36:2:0.0588:0:7 -16 33887701 . C CTCTCA 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.49528;SOR=0;LSEQ=CACTCCACTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:0.0909:2,2:34.5:1:30.2:1:1:1.21:58:4:0.0909:0:6.5 0/0:17:0:0,0:8,9:0:2,0:30:1:31:1:1:0:38.9:34:1:0:5.7 -16 33887703 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.31532;SOR=3.92468;LSEQ=CTCCACTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:1,0:9,10:0.05:2,0:35:0:33:0:1:0:40:2:0.0526:0:6 0/1:17:3:1,2:7,6:0.1765:2,2:35.7:1:32.3:1:1:2.21433:38.7:6:0.1765:0:7 -16 33887708 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.49206;SOR=0;LSEQ=CTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCACTCCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:35.5:1:29:1:1:1:52:4:0.1:0:5.5 0/0:16:0:0,0:7,8:0:2,0:28.7:1:28.5:1:1:0:39.2:14:0.9333:0:5.6 -16 33887710 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=1.34582;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:8,10:0.0952:2,2:4.5:1:25.5:1:1:1.24:33:4:0.0952:0:5.5 0/1:16:2:1,1:6,8:0.125:2,2:28.5:1:29.5:1:1:1.31:44:4:0.1333:0:3.5 -16 33887712 . A T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.49929;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCCACTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,9:0.0909:2,2:39:1:30:1:1:1:58:4:0.0952:0:6.5 0/0:16:0:0,0:7,9:0:2,0:24.4:1:29.6:1:1:0:38.6:32:1:0:5.6 -16 33887713 . T C 63 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.14094;SOR=6.65101;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCACTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:1,0:10,10:0.0455:2,0:10:0:34:0:1:0:33:2:0.0476:0:4 0/1:16:4:2,2:4,6:0.25:2,2:28:1:31.5:1:1:1.46:41.8:8:0.25:0:4.8 -16 33887714 . TCCACTC CCCTTTCCATTT 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.49929;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CACTCCATTCCACTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,9:0.0909:2,2:20.5:1:29.7:1:1:1:40:4:0.0952:0.0455:6.5 0/0:16:0:0,0:7,9:0:2,0:24.4:1:29.6:1:1:0:38.6:32:1:0:5.6 -16 33887718 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.63435;SOR=2.07757;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCATTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,8:0.1053:2,2:28:1:32:1:1:1:51:4:0.1111:0:5.5 0/1:15:3:2,1:5,7:0.2:2,2:23:1:29.7:1:0.56923:2.61:33.7:6:0.2:0:5.3 -16 33887721 . C T 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0.6158;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=ACTCCATTCCACTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:25:1:32:1:1:1.12:51:4:0.1053:0:5.5 0/1:15:1:0,1:8,6:0.0667:2,0:12:0:29:0:0.46667:0:40:2:0.0667:0:6 -16 33887723 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=1.06916;LSEQ=TTCCATTCCATTCCACTCCA;RSEQ=TCCATTCCACTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:20.5:1:30:1:1:1.13:52:4:0.1176:0:5.5 0/1:16:2:1,1:6,6:0.125:2,2:15:0:28.5:1:1:1:29:4:0.1333:0:5.5 -16 33887725 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=CCATTCCATTCCACTCCACT;RSEQ=CATTCCACTCCACTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,8:0.125:2,2:21:1:30.5:1:1:1.31:51:4:0.125:0:5.5 0/0:16:0:0,0:7,8:0:2,0:13.9:1:30.7:1:1:0:38.4:30:0.9375:0.0625:5.9 -16 33887726 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.22581;SOR=0;LSEQ=CATTCCATTCCACTCCACTC;RSEQ=ATTCCACTCCACTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:17.5:1:29:1:1:1.55:52:4:0.1333:0:5.5 0/0:16:0:0,0:8,8:0:2,0:13.4:1:30.4:1:1:0:38.5:32:1:0.0625:5.9 -16 33887728 . T A 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58621;SOR=0.41226;LSEQ=TTCCATTCCACTCCACTCCA;RSEQ=TCCACTCCACTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:0.1429:2,2:18.5:1:29.5:1:1:1.37:44:4:0.1429:0:5.5 0/1:16:1:1,0:6,6:0.0625:2,0:16:0:25:0:1:0:40:2:0.0667:0:7 -16 33887736 . C G 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.59304;SOR=0.43129;LSEQ=CACTCCACTCCATTCCACTC;RSEQ=ACTCCACTCCACTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:0.1667:2,2:7.5:1:29:1:1:1.45:52:4:0.1818:0:5.5 0/1:13:1:0,1:7,5:0.0769:2,0:1:1:29:1:0.46154:0:30:2:0.0769:0.0769:6 -16 33887742 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.48529;SOR=0;LSEQ=ACTCCATTCCACTCCACTCC;RSEQ=CTCCACTCCTTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:32.5:1:31.5:1:1:1:44:4:0.2:0:5.5 0/0:7:0:0,0:5,2:0:2,0:11:1:24.6:1:1:0:44.3:6:1:0:6 -16 33887747 . ACTCCT TCTAAACTCCA 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.49091;SOR=0;LSEQ=ATTCCACTCCACTCCACTCC;RSEQ=TTCCATTCCAATCCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:37.5:1:31.4:1:1:1.41418:44:4:0.2857:0:5.5 0/0:4:0:0,0:1,1:0:2,0:11:1:30:1:1:0:44:4:0.6667:0:6 -16 33887752 . T A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=ACTCCACTCCACTCCACTCC;RSEQ=TTCCATTCCAATCCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,0:0.25:0,0:17:0:33:0:1:0:40:2:0.5:0:7 1/1:3:3:1,2:0,0:1:0,2:25.7:1:29.7:1:1:0:42.3:6:1:0:6.3 -16 33887763 . A C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CTCCACTCCTTTCCATTCCA;RSEQ=TCCACTCCACTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,1:0.25:2,0:6:0:34:0:1:0:40:2:0.25:0:7 1/1:3:3:1,2:0,0:1:0,2:21.3:1:31:1:1:0:42.3:6:1:0:6.3 -16 33887765 . C A 25 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CCACTCCTTTCCATTCCAAT;RSEQ=CACTCCACTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:16:1:32.3:1:1:0:46:8:1:0:5.8 1/0:3:2:1,1:0,1:0.6667:0,2:28:0:25.5:1:1:0:41:4:0.6667:0:6 -16 33887775 . G C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CCATTCCAATCCACTCCACT;RSEQ=CATTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:15:0:32.5:1:1:0:44:4:0.6667:0:5.5 0/0:2:0:0,0:1,1:0:2,0:18:0:30.5:1:1:0:41:4:1:0:6 -16 33887777 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATTCCAATCCACTCCACTGC;RSEQ=TTCCATTCCATTCCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:13:0:33.5:1:1:0:44:4:0.6667:0:5.5 0/0:2:0:0,0:1,1:0:2,0:16:0:24:1:1:0:41:1:1:0:6 -16 33887783 . T G 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATCCACTCCACTGCATTCCA;RSEQ=TCCATTCCACTCCACTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:9.7:1:31.7:1:1:0:39.7:6:1:0:5.3 1/1:2:2:1,1:0,0:1:0,2:10:0:29.5:1:1:0:41:4:1:0:6 -16 33887793 . CTCCAC T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=CTGCATTCCATTCCATTCCA;RSEQ=TGCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:25:0:34:0:1:0:31:2:1:0:5 1/1:2:2:1,1:0,0:1:0,2:13:1:27.8:1:1:0:41:4:1:1:6 -16 33888553 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACTCCACTCCACTCAA;RSEQ=TCCATTCCAATCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:11:0:32:0:1:1:21:4:0.5:0:4 -16 33947334 . T A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTTCTCCTTATTATCAC;RSEQ=CTGCTCTCCTACTACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:1:27:1:1:0:60:4:1:0:2 -16 33947339 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCCTTATTATCACTCTGC;RSEQ=CTCCTACTACATTCCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:29:1:1:0:60:4:1:0:2 -16 33948534 . C T 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=CTTTGATTGGATTTTTCCTG;RSEQ=CTACAGACAGGAATGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:24.7:1:30.7:1:1:0:33.3:6:0.4286:0:5 0/0:4:0:0,0:4,0:0:0,0:21.5:1:28.8:1:1:0:51.8:8:1:0:2.3 -16 33948557 . A T 52 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=ACAGACAGGAATGAGTCTGC;RSEQ=GTTTTCTTTTTTAAACCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:38:1:33.3:1:1:0:33.3:6:0.375:0:5 0/0:3:0:0,0:3,0:0:0,0:24:1:26:1:1:0:60:2:1:0:2 -16 33948586 . T A 61 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.51948;LSEQ=TTTTAAACCCGAGGGGACTG;RSEQ=GCCTGAGGGTCTCGAGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:7,1:0.3333:2,0:25:1:30.8:1:1:0:33.3:8:0.3636:0:5.8 0/1:5:1:1,0:4,0:0.2:0,0:17:0:31:0:1:0:27:2:0.2:0:8 -16 33948596 . T C 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=GAGGGGACTGTGCCTGAGGG;RSEQ=CTCGAGCGCGGCCACCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:7,1:0.3333:2,0:22:1:33.8:1:1:0:34.3:8:0.3333:0:6 0/1:6:2:2,0:4,0:0.3333:0,0:14:1:29.5:1:1:0:33.5:4:0.3333:0:7.5 -16 33948611 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.22735;LSEQ=GAGGGTCTCGAGCGCGGCCA;RSEQ=CCTCCCCCAACCCCCGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:12,1:0.1875:1,0:21:1:29.7:1:1:0:35.3:6:0.1875:0:6.3 0/1:9:2:2,0:7,0:0.2222:0,0:29:1:31:1:1:0:33.5:4:0.2222:0:7.5 -16 33948617 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.63544;LSEQ=CTCGAGCGCGGCCACCCTCC;RSEQ=CCAACCCCCGACTGGCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:14,1:0.1176:1,0:24:1:31.5:1:1:0:36.5:4:0.125:0:7 0/1:11:2:2,0:9,0:0.1818:0,0:31.5:1:31.5:1:1:0:33.5:4:0.1818:0:7.5 -16 33948625 . C A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.55751;SOR=2.97834;LSEQ=CGGCCACCCTCCCCCAACCC;RSEQ=CGACTGGCGACTGTGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:14,3:0.0556:2,0:33:0:28:0:1:0:33:2:0.0556:0:8 0/1:13:2:2,0:10,1:0.1538:2,0:31.5:1:29:1:1:0:33.5:4:0.1538:0:7.5 -16 33948627 . G A 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.67409;SOR=1.78499;LSEQ=GCCACCCTCCCCCAACCCCC;RSEQ=ACTGGCGACTGTGGTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:3,0:12,3:0.1667:2,0:29.7:1:30:1:1:0:40.3:6:0.1667:0:6 0/1:15:4:3,1:10,1:0.2667:2,2:21.8:1:29.8:1:0.47619:3.02781:28.3:8:0.2667:0:6.3 -16 33948633 . C T 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32244;LSEQ=CTCCCCCAACCCCCGACTGG;RSEQ=GACTGTGGTGGTGGTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:3,0:10,4:0.1765:2,0:31.7:1:28.7:1:0.54118:0:40.3:6:0.1875:0:6 0/1:18:4:3,1:12,2:0.2222:2,2:24.8:1:29.3:1:1:1.9145:28.3:8:0.2222:0:6.3 -16 33948636 . C T 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.69476;SOR=1.49516;LSEQ=CCCCAACCCCCGACTGGCGA;RSEQ=TGTGGTGGTGGTGGTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:11,6:0.15:2,0:32.7:1:30:1:0.52105:0:40.3:6:0.1579:0:6 0/1:19:4:3,1:13,2:0.2105:2,2:26.3:1:31.5:1:0.53044:2.06666:28.3:8:0.2222:0:6.3 -16 33948637 . TGTG T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.16553;SOR=Inf;LSEQ=CCCAACCCCCGACTGGCGAC;RSEQ=GTGGTGGTGGTGGTGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:26,17:0:2,0:11.9:1:31.7:1:1:0:50.8:86:1:0:1.1 0/1:30:2:2,0:21,7:0.0667:2,0:22.5:1:32:0:1:0:60:4:0.0667:0:0 -16 33948656 . GT G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.49619;SOR=0;LSEQ=CTGTGGTGGTGGTGGTGGTG;RSEQ=TTTGTGTTCCAGCTTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:35,28:0.0308:2,2:30:1:30.5:1:1:1.24568:60:4:0.0313:0:0 0/0:63:0:0,0:38,25:0:2,0:17.4:1:28.4:1:1:0:53.1:30.5:1:0:2.3 -16 33948678 . CTGT C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.02893;SOR=Inf;LSEQ=TTTGTGTTCCAGCTTCTGTT;RSEQ=TGTTGTTGTTGTTGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:50,44:0:2,0:24.4:1:30.5:1:1:0:53.3:46:1:0:1.6 0/1:97:6:4,2:50,41:0.0619:2,2:16.2:1:29.2:1:0.69023:1.63:59:12:0.0632:0.0309:0 -16 33948681 . T C 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=1.01213;LSEQ=GTGTTCCAGCTTCTGTTCTG;RSEQ=TGTTGTTGTTGTTGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:15:10,5:42,41:0.1531:2,2:23.7:1:32.4:1:0.27712:1.94:35.8:30:0.1563:0:3.3 0/1:97:15:7,8:43,36:0.1546:2,2:31.8:1:32.9:1:0.77866:1.36053:38.4:30:0.1613:0:3.5 -16 33948693 . TTGG T 133 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.00103;SOR=0.19532;LSEQ=CTGTTCTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:10,10:36,36:0.1942:2,2:24.8:1:30.8:1:1:1:47.9:40:0.198:0.0583:1.6 0/1:112:5:3,2:47,44:0.0446:2,2:30.2:1:30.3:1:1:1.40:59:10:0.0455:0.0089:0.8 -16 33948696 . G C 142 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTGTTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:23:11,12:21,22:0.2421:2,2:33.7:1:31.5:1:1:1.0407:53.6:10.5:0.3333:0:3.6 0/0:111:0:0,0:25,28:0:2,0:25.5:1:31.1:1:1:0:59.7:106:1:0:0.2 -16 33948708 . C T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.44273;SOR=1.31599;LSEQ=TGTTGTTGGTGCTGCTGCTG;RSEQ=TGTTGCTGCTGCTGCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:25:12,13:26,30:0.2778:2,2:37:1:30.7:1:1:1.06:54.4:50:0.3205:0:4 0/1:110:37:20,17:31,36:0.3364:2,2:32.6:1:29.6:1:0.53982:1.36:55.5:36:0.3495:0:4 -16 33948711 . T C 147 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTTGGTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:24:12,12:32,35:0.2581:2,2:35.3:1:32.1:1:1:1.09:54.2:23:0.2584:0:4 0/0:111:0:0,0:34,37:0:2,0:28.5:1:30:1:1:0:55.9:142:1:0:0.7 -16 33948720 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50109;SOR=Inf;LSEQ=TGCTGCTGCTGTTGCTGCTG;RSEQ=TGCTGGTGCTGTCGTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:41,51:0:2,0:25.4:1:32.3:1:1:0:54.4:91:1:0:2.1 0/1:109:2:1,1:52,55:0.0183:2,2:13:1:32:0:1:1.06:60:4:0.0185:0:4.5 -16 33948723 . C G 69 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.06396;SOR=Inf;LSEQ=TGCTGCTGTTGCTGCTGCTG;RSEQ=TGGTGCTGTCGTCGTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:40,50:0:2,0:25.1:1:31.7:1:1:0:54.5:29:1:0:2.2 0/1:107:5:3,2:48,54:0.0467:2,2:23.2:1:30:1:0.66754:1.68:30.2:10:0.0467:0:5.4 -16 33948733 . C T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.07531;SOR=0.48624;LSEQ=GCTGCTGCTGCTGGTGCTGT;RSEQ=GTCGTTGTTTTGGTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:18:9,9:25,34:0.2338:2,2:27.9:1:28.2:1:0.59786:1.35:42.4:8:0.2162:0:4.6 0/1:101:13:7,6:40,48:0.1287:2,2:22.8:1:30.1:1:0.76698:1.40:37.1:26:0.1287:0:4.1 -16 33948736 . C T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.10791;SOR=0.49867;LSEQ=GCTGCTGCTGGTGCTGTCGT;RSEQ=GTTGTTTTGGTATTTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:18:9,9:23,32:0.2466:2,2:29.1:1:29.3:1:0.59219:1.38:42.4:17:0.2394:0:4.6 0/1:93:13:7,6:35,45:0.1398:2,2:23.5:1:30.2:1:0.55733:1.49:37.1:26:0.1413:0:4.1 -16 33948737 . G A 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05547;LSEQ=CTGCTGCTGGTGCTGTCGTC;RSEQ=TTGTTTTGGTATTTTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:23:10,13:21,26:0.3286:2,2:21.3:1:30.1:1:1:1.04929:53.7:22:0.3235:0:4 0/1:91:31:16,15:25,35:0.3407:2,2:18.9:1:29.2:1:0.38379:1.49:55.3:30:0.3333:0:3.9 -16 33948760 . CAG C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.07913;LSEQ=GTTTTGGTATTTTACAGACT;RSEQ=GGGGTGTATGTGCTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:10:3,7:14,22:0.2174:2,2:17.5:1:29.8:1:0.72266:1.47252:41.8:20:0.2222:0.0435:4.1 0/1:52:12:4,8:14,26:0.2308:2,2:16.3:1:30.6:1:1:1.07542:43.9:24:0.24:0.0577:4.2 -16 33948789 . CA TG 85 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05408;SOR=0.13256;LSEQ=TATGTGCTTGTTTGTTAGAT;RSEQ=GCATACTACTGCTTCCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:3,4:3,13:0.3043:2,2:13.6:1:30.5:1:0.31849:3.07:54.1:14:0.3043:0:5 0/1:19:1:0,1:4,14:0.0526:2,0:15:0:32:0:1:0:50:2:0.0526:0:5 -16 33948790 . A G 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89308;LSEQ=ATGTGCTTGTTTGTTAGATC;RSEQ=GCATACTACTGCTTCCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:1,3:1,10:0.1739:2,2:26.3:1:30:1:0.47619:3.03:35.5:8:0.25:0:5.3 0/1:19:3:1,2:3,12:0.1579:2,2:28.3:1:28.3:1:1:1.91:33.7:6:0.1667:0:6.3 -16 33948793 . A G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47273;SOR=1.92839;LSEQ=TGCTTGTTTGTTAGATCAGC;RSEQ=TACTACTGCTTCCGGATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:0,4:4,13:0.1905:2,0:24.3:1:31.8:1:0.54553:0:37.5:8:0.1905:0:4.3 0/1:19:6:0,6:4,9:0.3158:2,0:25.5:1:28.7:1:0.25542:0:38.8:12:0.3158:0:5 -16 33948796 . C T 62 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33977;SOR=0.21643;LSEQ=TTGTTTGTTAGATCAGCATA;RSEQ=TACTGCTTCCGGATGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:0,4:2,13:0.2105:2,0:14.5:1:31:1:1:0:49.8:8:0.2105:0:5.8 0/1:19:1:0,1:4,14:0.0526:2,0:9:0:31:0:1:0:50:2:0.0526:0:5 -16 33948803 . T C 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70895;SOR=0.67574;LSEQ=TTAGATCAGCATACTACTGC;RSEQ=TCCGGATGCAGAAGTGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:0.375:0,0:16.2:1:30.2:1:1:0:40.7:5:0.3571:0:6.2 0/1:14:4:1,3:2,8:0.2857:2,2:14.8:1:31.5:1:1:1.31:37.8:8:0.2857:0:6 -16 33948805 . C T 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69565;SOR=0.67669;LSEQ=AGATCAGCATACTACTGCTT;RSEQ=CGGATGCAGAAGTGGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:0.3333:0,0:17:1:30.6:1:1:0:36.8:10:0.3571:0:6.4 0/1:12:3:1,2:1,8:0.25:2,2:17:1:27.7:1:0.45455:3.46:33.7:6:0.25:0:6.3 -16 33948812 . C T 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.39451;SOR=2.87808;LSEQ=CATACTACTGCTTCCGGATG;RSEQ=AGAAGTGGACCTCCAGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:0,9:0,6:0.6:0,0:17.6:1:29.1:1:1:0:37.9:18:0.6:0:5.7 1/1:11:9:1,8:0,2:0.8182:0,2:26.3:1:26:1:1:0:37.9:8:0.8:0:5.7 -16 33948834 . G C 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61451;SOR=2.50099;LSEQ=GAAGTGGACCTCCAGTGTAT;RSEQ=CCTTACCCACGTGGCGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:26.3:1:32.7:1:1:0:39.3:6:0.4286:0:5.3 1/0:9:6:0,6:0,3:0.6667:0,0:28.7:1:31.2:1:1:0:41.2:12:0.6667:0:5.8 -16 33948836 . C G 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61451;SOR=2.50099;LSEQ=AGTGGACCTCCAGTGTATGC;RSEQ=TTACCCACGTGGCGAACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:25.7:1:33.7:1:1:0:39.3:6:0.4286:0:5.3 1/0:9:6:0,6:0,3:0.6667:0,0:28:1:31.5:1:1:0:41.2:12:0.6667:0:5.8 -16 33948845 . G A 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18716;LSEQ=CCAGTGTATGCCTTACCCAC;RSEQ=TGGCGAACGTTGTCTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:22.7:1:32.3:1:1:0:39.3:6:0.5:0:5.3 1/0:11:6:0,6:1,4:0.5455:2,0:25:1:30.2:1:0.45455:0:41.2:12:0.5455:0:5.8 -16 33948854 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTTACCCACGTGGCGAAC;RSEQ=TTGTCTCTGACGGGCGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:25.4:1:32.6:1:1:0:47.6:10:1:0:3.2 0/1:11:2:1,1:0,9:0.1818:0,2:17:0:32:0:0.18182:0:60:4:0.1818:0:3.5 -16 33948862 . T C 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACGTGGCGAACGTTGTCTC;RSEQ=GACGGGCGATTTATTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:34.7:1:31.3:1:1:0:55.7:6:1:0:2 0/1:8:2:1,1:0,6:0.25:0,2:25:0:29.5:1:0.25:0:60:4:0.25:0:3.5 -16 33948865 . C CG 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGCGAACGTTGTCTCTGA;RSEQ=GGGCGATTTATTCATTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:31.7:1:31.7:1:1:0:55.7:6:1:0:2 0/1:7:2:1,1:0,5:0.2857:0,2:29:0:31:1:0.28571:0:60:4:0.2857:0:3.5 -16 33948866 . G T 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=TGGCGAACGTTGTCTCTGAC;RSEQ=GGCGATTTATTCATTCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:36:0:31:0:1:0:47:2:0.3333:0:6 1/0:7:4:0,4:1,2:0.5714:2,0:24:1:30:1:0.42857:0:41.8:8:0.5714:0:6 -16 33948870 . G A 39 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=GAACGTTGTCTCTGACGGGC;RSEQ=ATTTATTCATTCCTCGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:32:0:32:0:1:0:47:2:0.3333:0:6 1/0:6:3:0,3:1,2:0.5:2,0:29:1:24.7:1:1:0:42.3:2:0.4:0:6 -16 33948881 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGACGGGCGATTTATTCAT;RSEQ=CCTCGTCCCCCTCTTACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:24:1:32:0:1:0:53.5:4:1:0:3 0/1:5:2:1,1:0,3:0.4:0,2:28.5:1:31:1:0.4:0:60:4:0.4:0:3.5 -16 33949231 . A C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCTGGTCTCAAACTCCTGG;RSEQ=CTTGACACTTCTTCCGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:30:1:1:0:50:4:1:0:4.5 0/0:1:0:0,0:0,1:0:0,0:23:0:32:0:1:0:60:2:1:0:0 -16 33949975 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAACACGTGGTGTTTGTT;RSEQ=TTTTGTCCTTGTGATAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:1:30.5:1:1:0:60:4:1:0:1 -16 33950141 . C T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGCCGGATGGATGGGA;RSEQ=GAGACTGGACCACCCCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:36.5:1:30.5:1:1:0:48.5:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 33950163 . A G 27 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTGGACCACCCCGGACC;RSEQ=TGCTGTTCTTGGGGGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30:1:27.5:1:1:0:48.5:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 33950347 . T C 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTCTCCACCACACAGA;RSEQ=GAGACGCATGAGAGGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:27:1:1:0:21:4:1:0:3 -16 33950578 . C A 62 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CACAAACCACACTAATTTAC;RSEQ=CTTTTCACAGTATGCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:24:1:31:1:1:0:57:8:1:0:3.8 1/0:4:2:1,1:1,1:0.5:2,2:12.5:1:32:0:1:1:60:4:0.5:0:6 -16 33950591 . T C 63 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AATTTACCCTTTTCACAGTA;RSEQ=GCAGTCTGAGTAAAACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:30.5:1:31.5:1:1:0:57:8:1:0:3.8 1/0:4:2:1,1:1,1:0.5:2,2:25.5:1:32.5:1:1:1:60:4:0.5:0:6 -16 33950613 . C A 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CAGTCTGAGTAAAACCCACC;RSEQ=CACCCTCCACCCGGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23.3:1:30.5:1:1:0:57:8:1:0:3.8 1/0:4:2:1,1:1,1:0.5:2,2:27:1:26:1:1:1:46.5:4:0.5:0:2 -16 33950618 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGAGTAAAACCCACCCCACC;RSEQ=TCCACCCGGCGGCTGACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.3:1:30.5:1:1:0:57:8:1:0:3.8 1/0:4:2:1,1:1,1:0.5:2,2:48:1:30:1:1:1:60:4:0.5:0:6 -16 33950626 . G A 49 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCACCCCACCCTCCACCC;RSEQ=GCGGCTGACGAAACCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:14:1:31:1:1:0:56:6:1:0:4.3 1/0:3:2:1,1:0,1:0.6667:0,2:40.5:1:30:1:1:0:60:4:0.6667:0:6 -16 33950629 . G T 48 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCCACCCTCCACCCGGC;RSEQ=GCTGACGAAACCCCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:11:1:30.3:1:1:0:56:6:1:0:4.3 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:30:1:1:0:60:4:0.6667:0:6 -16 33950648 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGGCTGACGAAACCCCTTCT;RSEQ=TACAATTTATTAAAAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:3:0:30:0:1:0:60:2:1:0:5 1/0:3:2:1,1:0,1:0.6667:0,2:18.5:1:28.5:1:1:0:60:4:0.6667:0:6 -16 33955468 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTCTTCAGTCTTACTCTC;RSEQ=TTCTCTGCCTGTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:44:0:31:0:1:0:31:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:35.5:1:30:1:1:1:39:4:0.5:0:7 -16 33955490 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCTCTGCCTGTCTGTCTCTC;RSEQ=CTCCCCATCTCTTTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:29:0:1:0:31:2:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:40:0:31:1:1:1:39:4:0.3333:0:7 -16 33955492 . TCC T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGCCTGTCTGTCTCTCTC;RSEQ=CCATCTCTTTCTGTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:32:0:29:0:1:0:31:2:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:13.5:1:31.5:1:1:1:33:4:0.3333:0:0 -16 33955497 . A C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTCTGTCTCTCTCTCCCC;RSEQ=TCTCTTTCTGTTTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:28:0:26:0:1:0:31:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:33:0:32:0:1:1:39:4:0.5:0:7 -16 33955518 . T C 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=7.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCTCTTTCTGTTTCTCTCTC;RSEQ=CTCTCTATCTCTCACTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:7:0:26:0:1:0:31:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:12:0:32.5:1:1:1:39:4:0.5:0:7 -16 33955519 . CTCTCTA C 65 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=CTCTTTCTGTTTCTCTCTCT;RSEQ=TCTCTCACTCTCTCCGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:5:0:27:0:1:0:31:2:1:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:13:1:32.8:1:1:1:36:8:0.6667:0.3333:3.5 -16 33955647 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=TTGTTTCTCTCTGTCTGTCT;RSEQ=TGTCTGTCTCTCTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:10:1:33:0:1:0:50:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:12.5:1:31.5:1:1:1:42:4:0.5:0:5.5 -16 33955653 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.46667;SOR=Inf;LSEQ=CTCTCTGTCTGTCTCTGTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:16:1:33.5:1:1:0:50:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:18.5:1:32:1:1:1:42:4:0.5:0:5.5 -16 33955683 . GT TC 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.33333;SOR=Inf;LSEQ=CTCTGTCTCTCTCCCTCCCT;RSEQ=CTGTTTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:38.5:1:33.5:1:1:0:50:4:1:0:3.5 1/1:2:2:1,1:0,0:1:0,2:16:0:32.3:1:1:0:42:4:1:0:4.5 -16 33955687 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTCTCTCTCCCTCCCTGTCT;RSEQ=TTTCTCTCTCTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:38.5:1:33.5:1:1:0:50:4:1:0:3.5 1/1:2:2:1,1:0,0:1:0,2:13:0:33.5:1:1:0:42:4:1:0:4.5 -16 33957483 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TACTACTCTTCAGAACATCT;RSEQ=ATGTTCTAGAAATCCGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:8:0:33:1:1:0:41:4:0.6667:0:5 0/0:2:0:0,0:1,1:0:2,0:22.5:1:28:1:1:0:60:4:1:0:0 -16 33957504 . TG CA 95 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.51811;LSEQ=ATGTTCTAGAAATCCGTAAG;RSEQ=AATGCTGCTGCTGCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:5,3:4,3:0.5:2,2:16.5:1:31.8:1:1:1.23:47:16:0.5:0:3.5 0/1:3:1:1,0:1,1:0.3333:2,0:13:0:31:0:1:0:47:2:0.3333:0:3 -16 33957539 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33761;SOR=0.44366;LSEQ=CTCTTGCTGCTGCTGCTGCT;RSEQ=TTGTTGCTGTTGTTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:6,6:12,5:0.4138:2,2:38:1:30.3:1:0.43844:2.32548:44.4:24:0.4138:0:3.2 0/1:17:4:3,1:8,5:0.2353:2,2:25.8:1:30:1:1:1.81:37.3:8:0.2353:0:2 -16 33957543 . T C 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00449;SOR=Inf;LSEQ=TGCTGCTGCTGCTGCTCTTG;RSEQ=TGCTGTTGTTGTTGTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:0:2,0:31.7:1:30.8:1:1:0:46.9:62:1:0:2.4 0/1:18:5:3,2:8,5:0.2778:2,2:36:1:32.8:1:1:1.06284:36.6:10:0.2778:0:2.6 -16 33957546 . CTGT C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.19724;SOR=0.34794;LSEQ=TGCTGCTGCTGCTCTTGTTG;RSEQ=TGTTGTTGTTGTTTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:6,5:12,7:0.3548:2,2:35.7:1:32.5:1:0.71163:1.41142:46.5:22:0.3667:0:3.9 0/1:19:3:2,1:9,7:0.1579:2,2:28.7:1:29.3:1:1:1.52:49:6:0.1579:0.0526:3 -16 33957549 . T C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.54098;SOR=0.61508;LSEQ=TGCTGCTGCTCTTGTTGCTG;RSEQ=TGTTGTTGTTGTTTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:8,4:4,3:0.3871:2,2:29.3:1:32.5:1:1:1.47:41.8:24:0.6316:0:2.9 0/1:18:5:3,2:6,5:0.2778:2,2:30.8:1:31:1:1:1.23:49.6:10:0.3125:0:2 -16 33957556 . T A 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.15554;SOR=0;LSEQ=GCTCTTGTTGCTGTTGTTGT;RSEQ=GTTGTTTTCAAAGCACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:3,2:15,14:0.1471:2,2:32:1:29.8:1:1:1.39:45:10:0.1471:0:3.4 0/0:17:0:0,0:10,7:0:2,0:31.4:1:30.1:1:1:0:48:34:1:0:2.1 -16 33957576 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.2868;LSEQ=TGTTGTTTTCAAAGCACACC;RSEQ=CGGCCACCGTTTATGGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:29:14,15:2,3:0.8529:2,2:24.4:1:30.5:1:1:1.39:44.8:28:0.8485:0:3.3 1/1:17:15:8,7:0,0:0.8824:0,2:26.3:1:30.6:1:1:0:46.5:30:0.8824:0:2.5 -16 33957584 . C A 74 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14179;SOR=0;LSEQ=TCAAAGCACACCTCGGCCAC;RSEQ=GTTTATGGGATCAAAAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:1,4:12,12:0.1724:2,2:19:1:32.2:1:0.34319:3.82896:43.6:10:0.1852:0:4 0/0:19:0:0,0:9,10:0:2,0:22.1:1:29.7:1:1:0:45.8:38:1:0:2.3 -16 33957603 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12281;SOR=Inf;LSEQ=CCGTTTATGGGATCAAAAGC;RSEQ=TTATAAAATATGTGTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:0:2,0:23:1:30:1:1:0:46.4:24:1:0:2.3 0/1:14:2:1,1:5,7:0.1429:2,2:15.5:1:29.5:1:1:1.37:27:4:0.1429:0:2.5 -16 33957634 . AC GT 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61262;SOR=1.77508;LSEQ=TGTGTAATTATTTCCTGAGC;RSEQ=GCCCTTCCTCCTCCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:2,9:0.2143:2,2:31.3:1:31.7:1:1:2.11:58:6:0.2143:0:2.3 0/1:6:2:0,2:0,4:0.3333:0,0:16:1:30.3:1:1:0:50:4:0.3333:0:2.5 -16 33957635 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11808;LSEQ=GTGTAATTATTTCCTGAGCA;RSEQ=GCCCTTCCTCCTCCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:1,7:1,2:0.5714:2,2:20.6:1:30.4:1:0.49091:3.05504:43.9:16:0.7273:0:2.1 1/0:5:3:0,3:0,0:0.6:0,0:26.7:1:31.3:1:1:0:38:6:1:0:1.7 -16 33957665 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTCTCTCTGTCTCTCT;RSEQ=TCTCCGTCTTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:5:0:33:0:1:0:43.5:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 33957905 . TTC T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTGTCTCTCTCTCTTTCT;RSEQ=TCTCTGTCTCCCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:21:4:1:0:2.5 -16 33957918 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTTTCTCTCTGTCTC;RSEQ=CTGTCTCTGTGTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:32:1:1:0:21:4:1:0:2.5 -16 33957977 . ACT A 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0.04762;SOR=0;LSEQ=CTGTGTCTGTCTTCTGTCTT;RSEQ=CTCTTTCTCTGCCGGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:1,0:0.8333:0,2:28.2:1:33.4:1:1:0:58.8:10:0.8333:0:2.8 0/0:3:0:0,0:2,1:0:2,0:15:1:27.7:1:1:0:34:6:1:0:1.7 -16 33957986 . C T 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTTCTGTCTTACTCTCTTT;RSEQ=TCTGCCGGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:40:0:31.5:1:1:2.44949:60:4:0.3333:0:3.5 0/0:1:0:0,0:1,0:0:0,0:34:0:27:0:1:0:60:2:1:0:0 -16 33957993 . G GGTCT 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCTTACTCTCTTTCTCTGCC;RSEQ=GTCTCTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:48:0:31.5:1:1:2.44949:60:4:0.3333:0:3.5 0/0:2:0:0,0:1,1:0:2,0:16:1:26.5:1:1:0:60:4:1:0:0 -16 33957994 . G GTCTGTCTC 42 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=13.000;MSILEN=2;SSF=0.2;SOR=0;LSEQ=CTTACTCTCTTTCTCTGCCG;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:0.5:2,2:31.7:1:27.1:1:1:1:58:2:0.4:0:2.3 0/0:4:0:0,0:2,2:0:2,0:8.5:1:29.3:1:1:0:60:8:1:0:1.3 -16 33958004 . C T 58 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=11.000;MSILEN=2;SSF=0.07619;SOR=0;LSEQ=TTCTCTGCCGGTCTCTCTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,0:0.6667:0,2:33.5:1:29.3:1:1:0:60:8:0.8:0:2.8 0/0:4:0:0,0:2,2:0:2,0:13.5:1:30.3:1:1:0:60:8:1:0:1.3 -16 33958006 . C T 29 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=2;SSF=0.13333;SOR=Inf;LSEQ=CTCTGCCGGTCTCTCTCTCT;RSEQ=TCTCTCTCTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:33.3:1:30.2:1:1:0:59:12:1:0:2.3 1/0:4:2:1,1:1,1:0.5:2,2:13:0:29.5:1:1:1:60:4:0.5:0:2.5 -16 33958028 . C A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.14286;SOR=0;LSEQ=CTCTCTCTCTGTCTCTCTCT;RSEQ=TTTGTTTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:21.3:1:24.5:1:1:0:58.5:3:0.75:0:3.3 0/0:3:0:0,0:1,2:0:2,0:36:1:33:1:1:0:60:6:1:0:1.7 -16 33958056 . A G 36 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CTCTCTGTCTCTCTCTGTCC;RSEQ=TCTCTGTCTTTCTCTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:5.3:1:23:1:1:0:51.3:2:0.6667:0:4 0/0:3:0:0,0:1,2:0:2,0:18.3:1:31.7:1:1:0:60:6:1:0:1.7 -16 33958061 . TG CA 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGTCTCTCTCTGTCCATCTC;RSEQ=TCTTTCTCTGTGTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:20:1:29.3:1:1:0:53.3:6:1:0:3 1/0:3:2:1,1:0,1:0.6667:0,2:10:1:31:1:1:0:60:4:0.6667:0.3333:2 -16 33958154 . G GTCTC 59 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTGCCTGTCTGTCTGTAG;RSEQ=TCTCTCTCTCCCTGTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:4:3,1:1,2:0.5714:2,2:17.5:1:29.5:1:0.48571:4.45:52.8:8:0.5714:0.4286:1.8 -16 33958170 . G C 49 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTAGGTCTCTCTCTCCCTGT;RSEQ=TGTCTGTTTTTTTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9:1:26:1:1:0:60:4:1:0:3 1/0:5:3:1,2:0,0:0.6:0,2:29:1:31:1:1:0:53.3:6:0.6:0:3 -16 33958176 . GT G 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTCTCTCTCCCTGTGTGTCT;RSEQ=TTTTTTTCTCTCTTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:16:1:30.5:1:1:0:60:4:1:0:3 1/0:4:2:0,2:1,0:0.5:0,0:35.5:1:31:1:0.33333:0:50:4:0.6667:0:3 -16 33958191 . T C 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGTTTTTTTTCTCTCT;RSEQ=TCTCTTTGCCTGTCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27:1:25.5:1:1:0:60:1:1:0:3 1/1:5:5:3,2:0,0:1:0,2:20.8:1:32.4:1:1:0:47.8:10:1:0:2.4 -16 33958242 . T C 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=TCTCTCTGTCTGTCTCTCTC;RSEQ=GCCTGTCTCTCTCTGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:18.5:1:22.5:1:1:1:60:1:0.3333:0:3.5 1/0:6:4:3,1:2,0:0.6667:0,2:32.3:1:30:1:1:0:58:8:0.6667:0:2.8 -16 33958255 . C G 49 d7;v4;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.03333;SOR=0;LSEQ=CTCTCTCTGCCTGTCTCTCT;RSEQ=TGTGTCTGTCTTCTGTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:30.3:1:31.3:1:1:0:60:6:1:0:3.3 0/1:7:1:0,1:4,2:0.1429:2,0:8:0:25:0:0.42857:0:40:2:0.1429:0:3 -16 33958257 . GTGTC G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=CTCTCTGCCTGTCTCTCTCT;RSEQ=TGTCTTCTGTCTTACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:31.3:1:25.3:1:1:0:60:2:1:0:3.3 0/1:7:2:1,1:3,2:0.2857:2,2:13:1:30:1:1:1.41418:47.5:4:0.2857:0:0.5 -16 33958270 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TCTCTCTGTGTCTGTCTTCT;RSEQ=TCTTACTGTCTTTCTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:31.7:1:20.7:1:1:0:60:0.5:1:0:3.3 0/1:6:2:1,1:2,2:0.3333:2,2:9.5:1:27:1:1:1:60:4:0.3333:0:2.5 -16 33958289 . CCTGT C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.4;SOR=0;LSEQ=TGTCTTACTGTCTTTCTCTG;RSEQ=CTGTCTCTCTCTCTCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:29:1:33.5:1:1:0:60:4:1:0:3.5 0/1:4:1:0,1:1,2:0.25:2,0:43:0:30:0:1:0:40:2:0.25:0:3 -16 33958313 . T C 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TCTGTCTCTCTCTCTCCTTG;RSEQ=CTGTTTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:10:1:32.5:1:1:0:60:4:1:0:3.5 0/1:4:1:0,1:1,2:0.25:2,0:39:0:32:0:1:0:40:2:0.25:0:3 -16 33958318 . TTC T 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTCTCTCTCTCCTTGTCTGT;RSEQ=TCTCTCTCTCTCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:8:0:28:0:1:0:60:2:1:0:3 1/0:4:2:0,2:1,1:0.5:2,0:29:1:31.5:1:1:0:40:4:0.5:0:1.5 -16 33958346 . G C 49 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTCTCTCTGTCTCTGTTTCT;RSEQ=TCTGTCTATCTCTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:8:0:31.3:1:1:0:53.3:6:1:0:1.7 -16 33958560 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=0.1;SOR=Inf;LSEQ=TGTCCATCTCTGTCTTTCTC;RSEQ=GTCTGTGTCTTTATCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:16.7:1:29.7:1:1:0:51.3:6:1:0:1 1/1:2:2:1,1:0,0:1:0,2:44.5:1:30:1:1:0:21:4:1:0:2.5 -16 33958567 . G C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=CTCTGTCTTTCTCTGTCTGT;RSEQ=TCTTTATCTGTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:19:1:31.7:1:1:0:51.3:6:1:0:1 1/1:2:2:1,1:0,0:1:0,2:48:1:31.5:1:1:0:21:4:1:0:2.5 -16 33958570 . T C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TGTCTTTCTCTGTCTGTGTC;RSEQ=TTATCTGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21.5:1:31:1:1:0:47:4:0.6667:0:1.5 0/0:2:0:0,0:1,1:0:2,0:46.5:1:30:1:1:0:21:4:1:0:2.5 -16 33958573 . ATCTG A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0.4;SOR=Inf;LSEQ=CTTTCTCTGTCTGTGTCTTT;RSEQ=TCTGTCTCTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:21.3:1:30.7:1:1:0:51.3:6:1:0:1 1/0:3:2:1,1:1,0:0.6667:0,2:42.5:1:29.5:1:1:0:21:4:0.6667:0:2.5 -16 33958581 . GTCTC G 53 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=6.000;MSILEN=2;SSF=0.46429;SOR=0;LSEQ=GTCTGTGTCTTTATCTGTCT;RSEQ=TCTCTCTCTTTCTGTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:3,2:0.5:2,2:14:1:34:1:1:1.29:60:6:0.5:0.3333:1.7 0/0:3:0:0,0:2,1:0:2,0:29:1:29.3:1:1:0:34:6:1:0:1.7 -16 33958659 . GTC G 33 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=16.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTGTCTCTGTCTTT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:33:0:33.5:1:1:1.73:60:4:0.4:0:0.5 0/0:2:0:0,0:1,1:0:2,0:18:1:31.5:1:1:0:60:4:1:0:0.5 -16 33958864 . T A 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGATTTCTGGACTTGGAT;RSEQ=CCTCATAGATACTACATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:1:30:1:1:0:50:4:1:0:2 1/1:3:3:2,1:0,0:1:0,2:31.3:1:27.7:1:1:0:52:6:1:0:3 -16 33959000 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATGTGCATCTGCTCGTGT;RSEQ=CTACATGAACTGTGACCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:28.5:1:30:1:1:0:50:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 33959025 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAACTGTGACCGAGCCCT;RSEQ=TCCGTTCTGTCTCAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:31:1:31.5:1:1:1.73:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 33959052 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTCAAATATGTATCTG;RSEQ=AAACACGTCTCTCCATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:36.5:1:29:1:1:1:60:4:0.5:0:3.5 0/0:1:0:0,0:1,0:0:0,0:24:0:34:0:1:0:40:2:1:0:2 -16 33959629 . T C 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACCGCCGCTTTATCCCCT;RSEQ=CTCTGTCCACAGCCGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:23:0:30.5:1:1:0:47:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 33959651 . C A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCTGTCCACAGCCGCCCCCA;RSEQ=CCCACCCCGCAACCCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:42:0:33:1:1:0:47:4:1:0:2 1/1:2:2:1,1:0,0:1:0,2:28.5:1:27:1:1:0:27:4:1:0:6.5 -16 34422819 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23279;SOR=Inf;LSEQ=AAGGAGTTCCATTGACAGCA;RSEQ=CACATCAGGGAATCAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:20,17:0:2,0:18.3:1:28.8:1:1:0:60:17.5:1:0:0.3 0/1:35:2:1,1:14,19:0.0571:2,2:31.5:1:29.5:1:1:1.35:60:4:0.0571:0:1 -16 34467290 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49619;SOR=Inf;LSEQ=ATGTGATGCTCTGCTTAGAA;RSEQ=CCTTGTGGTTCTTCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:0:2,0:27:1:31.7:1:1:0:60:94:1:0:0.1 0/1:52:2:1,1:30,20:0.0385:2,2:23.5:1:30:1:1:1.48801:60:4:0.0385:0:2.5 -16 34467307 . C T 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.5826;LSEQ=GAACCCTTGTGGTTCTTCAG;RSEQ=CAGGAGATGGAGAGAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:1:0,1:28,26:0.0182:2,0:48:0:30:0:0.49091:0:60:2:0.0185:0:1 0/1:70:2:1,1:40,28:0.0286:2,2:30:0:31.5:1:1:1.42114:60:4:0.029:0:2.5 -16 34467540 . A T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCAGTTTTTCCTCCTGT;RSEQ=TAGGGAGAGTGTTGGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 34469185 . T TG 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGGGACCCCAAGAGGCC;RSEQ=TGCCTTAATCTCCCCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:40:1:32.5:1:1:0:60:4:1:0:0.5 -16 34765942 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCACAGCTCCAGGTAGAA;RSEQ=GGCAGGTGAGCCAAAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:1:0,2:29.7:1:30.8:1:1:0:60:18:1:0:1.3 1/1:4:4:3,1:0,0:1:0,2:22.5:1:27.3:1:1:0:60:3:1:0:1 -16 46389300 . T G 50 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50893;SOR=Inf;LSEQ=ATTCGATGTTTCCATTCGAG;RSEQ=TCATTCTATTATTCCATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:24.2:1:30:1:1:0:49:10:1:0:1.4 0/1:11:3:2,1:4,4:0.2727:2,2:21.3:1:31.7:1:1:1.88:41.7:6:0.3:0:1 -16 46389303 . A T 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=CGATGTTTCCATTCGAGTTC;RSEQ=TTCTATTATTCCATTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:23.6:1:30.8:1:1:0:49:10:1:0:1.4 0/1:10:2:1,1:4,4:0.2:2,2:10.5:1:32.5:1:1:1:60:4:0.2:0:2 -16 46389408 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=TCCATTCGAGTCCATTCGAT;RSEQ=ATTCCATTCGAGTCCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:38.1:1:31.6:1:1:0:46.4:14:1:0:0.1 0/1:10:2:1,1:3,5:0.2:2,2:7.5:1:29:1:1:1.58:47:4:0.2:0:2.5 -16 46389412 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=TTCGAGTCCATTCGATGATT;RSEQ=CATTCGAGTCCATTTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:34.9:1:31:1:1:0:46.4:14:1:0:0.1 0/1:9:2:1,1:3,4:0.2222:2,2:7.5:1:27:1:1:1.29:46:4:0.2222:0:1 -16 46389578 . G A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GATTCCATTTGATTTGATTC;RSEQ=ACAGTGAGCCATTCGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:3,5:0.1111:2,0:21:0:31:0:0.44444:0:22:2:0.1111:0:3 0/1:18:2:1,1:9,7:0.1111:2,2:24.5:1:28.5:1:1:1.26772:44.5:4:0.1111:0:2 -16 46389624 . A C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53022;SOR=Inf;LSEQ=ATGATGATTCTATTTGATTC;RSEQ=ATTGGTTGACATTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:29:1:30:1:1:0:27.4:18:1:0:1.1 0/1:19:3:2,1:9,7:0.1579:2,2:40:1:30.7:1:1:1.52:22:6:0.1579:0:1.7 -16 46389625 . A C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57407;SOR=0.42643;LSEQ=TGATGATTCTATTTGATTCA;RSEQ=TTGGTTGACATTTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:15.5:1:30:1:1:1.29098:34.5:4:0.2222:0:2.5 0/1:19:2:0,2:11,6:0.1053:2,0:21:1:33:0:0.16374:0:43.5:4:0.1111:0:2 -16 46389628 . G A 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07977;SOR=0;LSEQ=TGATTCTATTTGATTCAATT;RSEQ=GTTGACATTTCCATTCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:36.5:1:30.5:1:1:1.8258:23:4:0.25:0:1 0/0:19:0:0,0:11,8:0:2,0:25.8:1:31.2:1:1:0:26.5:38:1:0:0.8 -16 46389677 . A G 75 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0608;SOR=0.11069;LSEQ=TGATGATTCCCTTTGATTCC;RSEQ=TTCAAAGATGATTCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:0.8333:0,2:24.4:1:29.4:1:1:0:22:10:0.8333:0:1.4 0/1:18:6:3,3:7,5:0.3333:2,2:21.8:1:29.3:1:1:1.3738:22.7:12:0.3333:0:1.5 -16 46389698 . A G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAAAGATGATTCCATTCT;RSEQ=GCCCATTCAATCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:36.5:1:28.3:1:1:0:22.3:8:1:0:1.5 0/1:13:2:0,2:6,5:0.1538:2,0:41.5:1:29.5:1:0.46154:0:23:4:0.1538:0:1.5 -16 46389728 . T G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATTCCATTCGATTCTAT;RSEQ=CAATGATGATTCCATTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:15.2:1:28.5:1:1:0:22.2:12:1:0:1.2 0/1:16:2:1,1:4,9:0.125:2,2:11.5:1:30.5:1:1:2.12:22:4:0.125:0:2 -16 46389974 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81844;LSEQ=TGATTCCATTTGATTCCATT;RSEQ=GATGATGATTACATTCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:7:0:25:0:1:0:41:2:0.3333:0:3 0/1:7:2:1,1:4,1:0.2857:2,2:41:1:30.5:1:1:3.1622:60:4:0.2857:0:2 -16 46389987 . A C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69289;LSEQ=TTCCATTCGATGATGATTAC;RSEQ=TTCGAGTCCATACGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:20:0:28:0:1:0:41:2:0.3333:0:3 0/1:8:2:1,1:4,2:0.25:2,2:44.5:1:31:1:1:1.8258:60:4:0.25:0:2 -16 46390009 . C A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGAGTCCATACGATGATTC;RSEQ=ACTCAATTCCATATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:31.3:1:30.7:1:1:0:53.7:6:1:0:1 0/1:8:2:1,1:3,3:0.25:2,2:17.5:1:28.5:1:1:1:50:4:0.25:0:1 -16 46390792 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=3;SSF=0.4;SOR=Inf;LSEQ=ACCATTCAATTACATTTGAT;RSEQ=ATGATCCCATTCAATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:13.3:1:31.3:1:1:0:37.3:6:1:0:0.3 1/0:3:2:1,1:0,1:0.6667:0,2:33:1:27.5:1:1:0:24:4:0.6667:0:2 -16 46390977 . T C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGATTGTTCCATTCGATTC;RSEQ=ATTCGATTCCTTTCGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:29.3:1:29.7:1:1:0:40:6:1:0:0.7 0/1:10:2:2,0:4,4:0.2:2,0:33.5:1:29.5:1:0.46667:0:24:4:0.2:0:2 -16 46391044 . G C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=ATGATTCCGTTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:20.7:1:30.3:1:1:0:31.8:12:1:0:0.7 0/1:18:2:1,1:10,6:0.1111:2,2:34.5:1:32:1:1:1.61828:25:4:0.1111:0:1 -16 46391051 . CC AA 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCGATGATT;RSEQ=GTTTGATTCCATTCGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:25.3:1:29.3:1:1:0:31.8:5:1:0:0.7 0/1:17:2:1,1:9,6:0.1176:2,2:17.5:1:28.8:1:1:1.46382:46:4:0.1176:0:3.5 -16 46391076 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=TGATTCCATTCGATGATTCC;RSEQ=TTCGATTCCTTTCTTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:28.9:1:31.6:1:1:0:27.9:20:1:0:0.7 0/1:18:2:1,1:10,6:0.1111:2,2:41.5:1:31.5:1:1:1.61828:46:4:0.1111:0:3.5 -16 46391093 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52381;SOR=Inf;LSEQ=TCCCTTCGATTCCTTTCTTT;RSEQ=ATGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:30:1:30.3:1:1:0:27.9:9:1:0:0.7 0/1:18:2:1,1:10,6:0.1111:2,2:29:0:31:1:1:1.61828:46:4:0.1176:0:3.5 -16 46391125 . G A 70 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCAATGATTCC;RSEQ=TTCGAATCTATTCCATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:25.4:1:30.4:1:1:0:24:10:1:0:1 1/1:3:3:3,0:0,0:1:0,0:17:1:27:1:1:0:30.7:6:1:0:1 -16 46391206 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16374;SOR=0;LSEQ=CATTCGATGATGATTCCATT;RSEQ=GATTCCATTCATTGAGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:4,2:0.25:2,0:18.5:1:32:0:1:0:27:4:0.25:0:3 0/0:11:0:0,0:7,4:0:2,0:26.9:1:31.6:1:1:0:27.2:22:1:0:0.6 -16 46391242 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10345;SOR=0;LSEQ=GGATTCCATTTGATTCCATT;RSEQ=AATGATGATTCCATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:4,3:0.2:2,0:46:1:29.5:1:0.5:0:27:4:0.2:0:3 0/0:20:0:0,0:10,10:0:2,0:22.3:1:30.4:1:1:0:34.7:19:1:0:1 -16 46391255 . A G 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01103;SOR=0.0826;LSEQ=TTCCATTCAATGATGATTCC;RSEQ=TTCTATTCCATTCAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:7,3:0,1:0.9091:0,2:23.2:1:29.3:1:0.36364:0:28.8:20:0.9091:0:1.8 0/1:23:10:4,6:8,5:0.4348:2,2:19.5:1:30.8:1:0.41365:2.30744:41.8:20:0.4348:0:1.7 -16 46391293 . A G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62653;SOR=0.60707;LSEQ=ATTGCATTCAATTCCATTCA;RSEQ=TGATTATCCCCTTAGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:6,6:0.1429:2,0:33.5:1:31:1:0.47253:0:27:4:0.1429:0:2 0/1:33:3:1,2:14,16:0.0909:2,2:31.3:1:31:1:1:1.7216:50:6:0.0909:0:1.7 -16 46391298 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53634;SOR=Inf;LSEQ=ATTCAATTCCATTCAATGAT;RSEQ=ATCCCCTTAGAGTAAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:9,11:0:2,0:18.7:1:27.7:1:1:0:43.1:19:1:0:1 0/1:37:2:1,1:16,19:0.0541:2,2:21.5:1:31:1:1:1.18:50:4:0.0541:0:1.5 -16 46391304 . C A 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.71807;SOR=0.72372;LSEQ=TTCCATTCAATGATTATCCC;RSEQ=TTAGAGTAAACTCAACGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:3,1:9,10:0.1739:2,2:6.8:1:30.3:1:0.59006:3.17:38:8:0.1739:0:1.3 0/1:38:5:4,1:14,19:0.1316:2,2:11.4:1:31.8:1:0.16988:5.21:33:10:0.1316:0:1.4 -16 46391309 . A C 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14692;SOR=Inf;LSEQ=TTCAATGATTATCCCCTTAG;RSEQ=GTAAACTCAACGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:21.8:1:30.1:1:1:0:43.9:48:1:0:0.9 0/1:37:4:2,2:15,16:0.1081:2,2:16.5:1:30.5:1:1:1.06:43:8:0.1143:0:1.8 -16 46391320 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06875;SOR=0;LSEQ=TCCCCTTAGAGTAAACTCAA;RSEQ=GATTCCATTCAATACCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:1,2:12,11:0.1154:2,2:31.7:1:31.3:1:1:2.11883:44.7:6:0.1154:0:1.3 0/0:36:0:0,0:19,17:0:2,0:24.9:1:30.5:1:1:0:44.8:72:1:0:0.8 -16 46391352 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20139;SOR=0;LSEQ=ATACCATTCGATGATGATTC;RSEQ=TTTTGAGTCCATTCAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:23.5:1:30:1:1:1.07415:54.5:4:0.0714:0:1 0/0:35:0:0,0:20,15:0:2,0:26:1:30.2:1:1:0:39.5:16.5:1:0:0.7 -16 46391396 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49321;SOR=Inf;LSEQ=ATTCAAGTCCATTTGATGAT;RSEQ=CCTTTCAATTCCATTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:23.2:1:29.8:1:1:0:37.2:23:1:0:0.3 0/1:28:2:1,1:19,7:0.0714:2,2:15:1:27.5:1:0.49735:2.60494:30:4:0.0714:0:1.5 -16 46391442 . GA AG 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCGAGTCCATTCGAT;RSEQ=TTCCATTCGATTGCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:22.8:1:31.9:1:1:0:30:30:1:0:0.7 0/1:45:2:1,1:23,20:0.0444:2,2:8:0:32.3:1:1:1.14642:44:4:0.0455:0:6.5 -16 46391452 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCGATGATTCCATTC;RSEQ=ATTGCATTCGATGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:22.1:1:29:1:1:0:32.8:14:1:0:0.9 0/1:49:2:1,1:24,23:0.0408:2,2:34:1:29:1:1:1.04259:36:4:0.0408:0:2 -16 46391456 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGATGATTCCATTCGATT;RSEQ=CATTCGATGATTCCATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:0:2,0:23.5:1:32.4:1:1:0:33.4:28:1:0:0.9 0/1:51:2:1,1:24,25:0.0392:2,2:32.5:1:28.5:1:1:1.04:47:4:0.0392:0:2.5 -16 46391462 . G C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCGATTGCATTC;RSEQ=ATGATTCCATTATATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:23.1:1:30.6:1:1:0:32.5:28:1:0:1.1 0/1:50:3:2,1:21,26:0.06:2,2:22.3:1:31.7:1:0.58811:2.43:39:6:0.06:0:1.7 -16 46391464 . T C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62995;LSEQ=TTCCATTCGATTGCATTCGA;RSEQ=GATTCCATTATATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:7,8:0.0625:2,0:1:0:29:0:1:0:24:2:0.0667:0:3 0/1:50:2:1,1:22,26:0.04:2,2:40.5:1:30.5:1:1:1.18:47:4:0.04:0:2.5 -16 46391465 . G T 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59461;SOR=0.48478;LSEQ=TCCATTCGATTGCATTCGAT;RSEQ=ATTCCATTATATTCCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:5.5:1:27.5:1:1:1.13:26:4:0.1176:0:1.5 0/1:50:3:2,1:20,25:0.06:2,2:33.7:1:27.3:1:0.58661:2.45:36:6:0.06:0:2.7 -16 46391474 . AT CG 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTGCATTCGATGATTCCATT;RSEQ=ATTCCATTCAACGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:22.4:1:29.6:1:1:0:34.8:36:1:0:1.2 0/1:46:2:1,1:19,25:0.0435:2,2:40:0:31.8:1:1:1.31:44:4:0.0435:0:5.5 -16 46391482 . T G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10582;SOR=0.40183;LSEQ=GATGATTCCATTATATTCCA;RSEQ=TCAACGATGATTCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:5,6:4,5:0.55:2,2:24.1:1:30.2:1:1:1.04:33.1:10:0.5263:0:1.2 0/1:46:15:7,8:11,20:0.3261:2,2:29.5:1:30.5:1:0.52972:1.57:38.1:30:0.3261:0:2.3 -16 46391487 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTATATTCCATTCAA;RSEQ=GATGATTCCATTCGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:21.7:1:30.6:1:1:0:36:46:1:0:1.1 0/1:47:2:1,1:17,28:0.0426:2,2:7.5:1:28.5:1:1:1.63:42:4:0.0435:0:2.5 -16 46391488 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTATATTCCATTCAAC;RSEQ=ATGATTCCATTCGAGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,12:0:2,0:21.1:1:30.3:1:1:0:36.5:44:0.9565:0:1 0/1:48:2:1,1:18,28:0.0417:2,2:34.5:1:32:0:1:1.54:36:4:0.0417:0:1 -16 46391489 . A G 113 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1255;SOR=3.44769;LSEQ=CCATTATATTCCATTCAACG;RSEQ=TGATTCCATTCGAGTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,11:0.087:2,2:15.5:1:30:1:1:1.21:24.5:4:0.1:0:2 0/1:48:12:2,10:17,19:0.25:2,2:25.7:1:31.6:1:0.09053:4.34775:31.5:24:0.25:0:1.7 -16 46391501 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53224;SOR=Inf;LSEQ=ATTCAACGATGATTCCATTC;RSEQ=AGTCCATTCGATGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:0:2,0:27.3:1:30.1:1:1:0:36:46:1:0:1 0/1:41:2:1,1:14,25:0.0488:2,2:21.5:1:30.5:1:1:1.76:42:4:0.0488:0:2.5 -16 46391510 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14132;SOR=0;LSEQ=TGATTCCATTCGAGTCCATT;RSEQ=GATGATTCCATTAGAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:8,14:0.0833:2,2:25.5:1:29:1:1:1.71:42:4:0.0833:0:1 0/0:39:0:0,0:12,25:0:2,0:23.2:1:29.7:1:1:0:38.9:36:0.9474:0:1.2 -16 46391511 . G C 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69621;SOR=1.65371;LSEQ=GATTCCATTCGAGTCCATTC;RSEQ=ATGATTCCATTAGAGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:9,13:0.0833:2,0:13.5:1:31.5:1:0.51087:0:25:4:0.0833:0:2 0/1:38:5:0,5:12,21:0.1316:2,0:20.6:1:32.4:1:0.15827:0:28.6:10:0.1316:0:2 -16 46391556 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23404;SOR=0;LSEQ=TGATTGCTTTGTTTTCAATT;RSEQ=GAAGATGATTACATTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:10,11:0.087:2,2:12.5:1:29:1:1:1.10:44:4:0.087:0:3.5 0/0:24:0:0,0:12,12:0:2,0:23.8:1:31:1:1:0:35.9:48:1:0:0.8 -16 46391572 . G C 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29884;SOR=2.4475;LSEQ=AATTCGAAGATGATTACATT;RSEQ=GATTCCATTCTATGATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:2,1:8,7:0.1667:2,2:18.7:1:23:1:1:1.70:38.3:2:0.1176:0:2.7 0/1:24:8:6,2:8,8:0.3333:2,2:27:1:30.5:1:0.38754:2.87:32.5:16:0.3333:0:1.8 -16 46391584 . A T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.21153;LSEQ=ATTACATTGGATTCCATTCT;RSEQ=TGATACCATTCGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:7,7:0.0667:2,0:12:0:31:0:1:0:25:2:0.0667:0:1 0/1:25:2:1,1:14,9:0.08:2,2:20.5:1:30:1:1:1.52748:43:4:0.08:0:1.5 -16 46391607 . A G 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07216;SOR=0;LSEQ=ATACCATTCGATTCCATTCA;RSEQ=TGATGATTCCACTCAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:0.1538:2,2:39:1:32.5:1:1:1.18:39:4:0.1667:0:1.5 0/0:34:0:0,0:18,16:0:2,0:21.9:1:28.8:1:1:0:37.2:33:1:0:1 -16 46391614 . T C 101 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70271;SOR=1.97321;LSEQ=TCGATTCCATTCAATGATGA;RSEQ=TCCACTCAAATCCATTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:5,5:0.1667:2,0:36.5:1:24.5:1:0.4697:0:35:1:0.0909:0:3.5 0/1:35:10:4,6:15,10:0.2857:2,2:25.5:1:30.5:1:0.45434:2.1971:36.6:20:0.2857:0:1.8 -16 46391616 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCAATGATGATT;RSEQ=CACTCAAATCCATTGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:30.3:1:29.9:1:1:0:31.4:11:1:0:1.1 0/1:37:2:1,1:19,16:0.0541:2,2:12.5:1:27:1:1:1.18197:27:4:0.0571:0:1.5 -16 46391651 . A G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58608;SOR=0.44684;LSEQ=GGATGATTCCATTCGTGTCC;RSEQ=TTCGGTGATTTCATTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:2,6:0.1818:2,2:26.5:1:31:1:1:2.65:40:4:0.1818:0:1.5 0/1:45:4:1,3:21,20:0.0889:2,2:30.5:1:24:1:0.60775:3.07613:39:3:0.0682:0:1.5 -16 46391655 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCGTGTCCATTC;RSEQ=GTGATTTCATTAGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:27.6:1:31.3:1:1:0:30.8:20:1:0:0.8 0/1:43:2:1,1:19,21:0.0465:2,2:45:0:29.5:1:1:1.10:45:4:0.0465:0:1 -16 46391686 . T C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGATTCCATTCGAGGATGA;RSEQ=TCCATTCGATTCCATTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:17.6:1:31:1:1:0:30.7:14:1:0:0.6 0/1:36:3:1,2:15,18:0.0833:2,2:27.3:1:31:1:1:1.64403:38.3:6:0.0833:0:1.3 -16 46391784 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGATTCATTTGATGATGAT;RSEQ=CCATTCGATTCCATTCGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:10:0:30:0:1:0:27:2:1:0:2 1/0:4:2:1,1:1,1:0.5:2,2:5:0:32.5:1:1:1:48:4:0.5:0:5.5 -16 46391841 . A C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGATGATGATTCCACTCG;RSEQ=GTCCATTCGATGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:22.8:1:31:1:1:0:35:8:1:0:2.3 0/1:12:2:1,1:7,2:0.1667:2,2:28:1:30.5:1:0.49091:3.05504:48:4:0.1818:0:5.5 -16 46391850 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCACTCGAGTCCATTC;RSEQ=ATGATTCCATTCGAGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:19.8:1:30.8:1:1:0:37.4:10:1:0:2 0/1:17:2:1,1:12,3:0.1176:2,2:19:1:29:1:0.42647:3.6058:48:4:0.1176:0:5.5 -16 46391853 . G C 51 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04249;SOR=0.09264;LSEQ=TCCACTCGAGTCCATTCGAT;RSEQ=ATTCCATTCGAGTCCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:0.6:2,0:13.3:1:32.3:1:0.4:0:44.3:6:0.6:0:2.3 0/1:19:2:2,0:13,4:0.1053:2,0:20:1:32.5:1:1:0:44:4:0.1053:0:3 -16 46391857 . C G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGAGTCCATTCGATGATT;RSEQ=CATTCGAGTCCATTTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:21.2:1:32.6:1:1:0:37.4:10:1:0:2 0/1:20:2:1,1:14,4:0.1:2,2:9.5:1:30.5:1:0.44737:3.24034:47:4:0.1053:0:3 -16 46391862 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCCATTCGATGATTCCATT;RSEQ=GAGTCCATTTAATGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:16.7:1:31.7:1:1:0:37.4:14:1:0:1.4 0/1:24:2:1,1:16,6:0.0833:2,2:7:1:28:1:0.50725:2.54484:48:4:0.087:0:5.5 -16 46391880 . C A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGAGTCCATTTAATGATT;RSEQ=CATTGGGTTCAATTCAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:0:2,0:21.8:1:32.1:1:1:0:41.1:22:1:0:0.8 0/1:28:2:1,1:18,8:0.0714:2,2:44:0:29:1:1:2.17949:43:4:0.0741:0:2.5 -16 46391887 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTTAATGATTCCATTGG;RSEQ=TTCAATTCAATGATGATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:25.3:1:32:1:1:0:41.6:24:1:0:0.9 0/1:29:2:1,1:19,8:0.069:2,2:39.5:1:28:1:0.53202:2.29737:47:4:0.069:0:3 -16 46391905 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGTTCAATTCAATGATGAT;RSEQ=ACATTGGATTCCGTTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,4:0:2,0:31.3:1:30.1:1:1:0:44:28:1:0:1.1 0/1:36:2:1,1:22,12:0.0556:2,2:9:1:27:1:1:1.8009:48:4:0.0571:0:1.5 -16 46391918 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATGATTACATTGGATTCC;RSEQ=TTCTATGATTCCATTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:12,4:0:2,0:31.3:1:29.3:1:1:0:44.8:15:1:0:0.9 0/1:38:2:1,1:22,14:0.0526:2,2:32.5:1:29:1:1:1.55221:47.5:4:0.0541:0:2.5 -16 46391939 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53112;SOR=Inf;LSEQ=TTCTATGATTCCATTCAATT;RSEQ=CGTTCATTGACAATTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:17,8:0:2,0:23.5:1:31.2:1:1:0:44.6:50:1:0:0.4 0/1:44:2:1,1:21,20:0.0455:2,2:9.5:1:28.5:1:1:1.04883:47:4:0.0476:0:3 -16 46391941 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12788;SOR=0;LSEQ=CTATGATTCCATTCAATTCC;RSEQ=TTCATTGACAATTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,7:0.08:2,2:30.5:1:32:1:1:2.07024:48:4:0.0833:0:2.5 0/0:44:0:0,0:22,21:0:2,0:22.6:1:29.3:1:1:0:45.5:42:1:0:0.8 -16 46391948 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15652;SOR=0;LSEQ=TCCATTCAATTCCGTTCATT;RSEQ=ACAATTTGATTCCATTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:18,8:0.0714:2,2:23.5:1:29.5:1:1:2.17949:48:4:0.0714:0:2.5 0/0:42:0:0,0:20,21:0:2,0:24.1:1:31.1:1:1:0:45.4:82:1:0:0.8 -16 46391969 . G C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53017;SOR=Inf;LSEQ=ACAATTTGATTCCATTCGAT;RSEQ=ATGATTCCATTTGAGTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:0:2,0:27.4:1:32:1:1:0:47.8:54:1:0:0.5 0/1:47:2:0,2:24,21:0.0426:2,0:36.5:1:34:0:0.23404:0:38:4:0.0426:0:1.5 -16 46391992 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50467;SOR=Inf;LSEQ=GATTCCATTTGAGTTCATTC;RSEQ=ATGATTCTATTCGATTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:22.3:1:30.1:1:1:0:51.9:70:1:0:0.3 0/1:47:2:1,1:26,19:0.0426:2,2:36.5:1:30.5:1:1:1.35916:49.5:4:0.0435:0:1.5 -16 46391995 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51163;SOR=Inf;LSEQ=TCCATTTGAGTTCATTCGAT;RSEQ=ATTCTATTCGATTCTCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:22.7:1:31.5:1:1:0:51.9:70:1:0:0.3 0/1:51:2:1,1:28,21:0.0392:2,2:11:1:27:1:1:1.32572:47:4:0.0392:0:2.5 -16 46391999 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51097;SOR=Inf;LSEQ=TTTGAGTTCATTCGATGATT;RSEQ=TATTCGATTCTCTTCGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:20,16:0:2,0:22.4:1:31.5:1:1:0:52.1:72:1:0:0.3 0/1:52:2:1,1:28,22:0.0385:2,2:11:0:31:1:1:1.26678:48:4:0.04:0:1.5 -16 46392000 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50922;SOR=Inf;LSEQ=TTGAGTTCATTCGATGATTC;RSEQ=ATTCGATTCTCTTCGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:20,16:0:2,0:22.4:1:29.7:1:1:0:52.1:72:1:0:0.3 0/1:51:2:1,1:27,22:0.0392:2,2:6:1:30.5:1:1:1.22232:47:4:0.04:0:2.5 -16 46392004 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51209;SOR=Inf;LSEQ=GTTCATTCGATGATTCTATT;RSEQ=GATTCTCTTCGATGGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:19,18:0:2,0:21.8:1:30.2:1:1:0:53.9:74:1:0:0.2 0/1:54:2:2,0:28,24:0.037:2,0:38:1:29.5:1:0.49686:0:57.5:4:0.0385:0:1 -16 46392005 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52341;SOR=Inf;LSEQ=TTCATTCGATGATTCTATTC;RSEQ=ATTCTCTTCGATGGTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:18,17:0:2,0:23.2:1:30.2:1:1:0:54.5:70:1:0:0.3 0/1:57:2:1,1:31,24:0.0351:2,2:32.5:1:29.5:1:1:1.28581:52.5:4:0.0357:0:2 -16 46392009 . C T 78 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07968;SOR=Inf;LSEQ=TTCGATGATTCTATTCGATT;RSEQ=TCTTCGATGGTGATTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:0:2,0:23.2:1:31.3:1:1:0:54.9:72:1:0:0.3 0/1:59:6:2,4:31,22:0.1017:2,2:25.7:1:30.5:1:0.39001:2.76881:52.7:12:0.1053:0:1.2 -16 46392010 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.52034;SOR=Inf;LSEQ=TCGATGATTCTATTCGATTC;RSEQ=CTTCGATGGTGATTCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:0:2,0:23.4:1:30.1:1:1:0:54.9:72:1:0:0.3 0/1:57:2:1,1:31,24:0.0351:2,2:27.5:1:29.5:1:1:1.28581:52.5:4:0.0357:0:2 -16 46392028 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53393;SOR=Inf;LSEQ=TCTCTTCGATGGTGATTCAA;RSEQ=TCTATTATATTGGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:15,20:0:2,0:27:1:30.1:1:1:0:57:70:1:0:0.3 0/1:62:2:1,1:35,25:0.0323:2,2:35:1:31:1:1:1.39226:60:4:0.0323:0:1.5 -16 46392030 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12049;SOR=0;LSEQ=TCTTCGATGGTGATTCAATT;RSEQ=TATTATATTGGATGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:13,19:0.0588:2,2:37.5:1:30.5:1:1:1.44:47.5:4:0.0588:0:2 0/0:63:0:0,0:36,26:0:2,0:24.4:1:30.8:1:1:0:56.9:61:0.9839:0:0.7 -16 46392046 . T A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.88348;LSEQ=AATTCTATTATATTGGATGA;RSEQ=TCCATTCGATTCCATTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:1,0:11,19:0.0323:2,0:5:0:26:0:0.3871:0:25:2:0.0323:0:1 0/1:70:2:2,0:39,29:0.0286:2,0:17:1:28:1:0.50766:0:57.5:4:0.0294:0:1 -16 46392047 . T G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09629;SOR=0;LSEQ=ATTCTATTATATTGGATGAT;RSEQ=CCATTCGATTCCATTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:11,19:0.0625:2,2:20.5:1:34:0:1:1.70:47.5:4:0.0625:0:2 0/0:70:0:0,0:40,30:0:2,0:25.9:1:29.1:1:1:0:52.6:34:1:0:0.7 -16 46392074 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTTGATGTTGATT;RSEQ=AATTCGATTCTATTCGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:24:1:31.7:1:1:0:52.3:27:1:0:0.3 0/1:61:2:1,1:31,28:0.0328:2,2:29.5:1:29:1:1:1.10529:48:4:0.0339:0:1.5 -16 46392082 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGATGTTGATTCAATTCGA;RSEQ=TCTATTCGATGATGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:10,16:0:2,0:22.5:1:30.9:1:1:0:51.7:52:1:0:0.3 0/1:61:2:1,1:29,30:0.0328:2,2:20:1:30:1:1:1.03:47.5:4:0.0328:0:2.5 -16 46392087 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTGATTCAATTCGATTCTA;RSEQ=TCGATGATGATTCCATTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:9,16:0:2,0:21.1:1:29.9:1:1:0:51.4:24:1:0:0.4 0/1:63:2:1,1:27,34:0.0317:2,2:42.5:1:29:1:1:1.25:60:4:0.0317:0:2.5 -16 46392094 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CAATTCGATTCTATTCGATG;RSEQ=TGATTCCATTGGATTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:0:2,0:26.3:1:31.2:1:1:0:48.3:36:1:0:0.4 0/1:59:2:1,1:24,33:0.0339:2,2:26.5:1:29.5:1:1:1.37:25:4:0.0339:0:3 -16 46392095 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AATTCGATTCTATTCGATGA;RSEQ=GATTCCATTGGATTTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:0:2,0:25.9:1:30.8:1:1:0:48.3:36:1:0:0.4 0/1:59:2:1,1:24,33:0.0339:2,2:8.5:1:28.5:1:1:1.37:60:4:0.0339:0:1.5 -16 46392099 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGATTCTATTCGATGATGAT;RSEQ=CCATTGGATTTCACTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,12:0:2,0:25.5:1:29.8:1:1:0:47.6:16:1:0:0.5 0/1:60:2:1,1:23,35:0.0333:2,2:20:1:27:0:1:1.51:47.5:4:0.0339:0:2.5 -16 46392116 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GATTCCATTGGATTTCACTT;RSEQ=ATGATTCTATTCGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,6:0:2,0:24.4:1:31.4:1:1:0:42.5:20:1:0:0.6 0/1:41:2:1,1:13,26:0.0488:2,2:26.5:1:31.5:1:1:1.96:25:4:0.0488:0:3 -16 46392123 . C T 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05088;SOR=0;LSEQ=TTGGATTTCACTTGATGATT;RSEQ=TATTCGATTCCATTCAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:0.1818:2,2:28.5:1:31.5:1:1:1.22:31:4:0.1818:0:2 0/0:36:0:0,0:11,23:0:2,0:24.3:1:31.7:1:1:0:36.2:68:0.9444:0:0.7 -16 46392125 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGATTTCACTTGATGATTCT;RSEQ=TTCGATTCCATTCAATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:20.5:1:27.3:1:1:0:35.9:10:1:0:0.5 0/1:37:2:1,1:11,24:0.0541:2,2:26.5:1:29.5:1:1:2.13:25:4:0.0541:0:3 -16 46392133 . C T 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05121;SOR=0;LSEQ=CTTGATGATTCTATTCGATT;RSEQ=CATTCAATGATGATTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:18.5:1:32:0:1:1.29:31:4:0.2222:0:2 0/0:29:0:0,0:7,22:0:2,0:24.2:1:30.7:1:1:0:36.1:28:1:0:0.4 -16 46392187 . C T 31 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09333;SOR=0;LSEQ=TGATTCCATTTCATTCCATT;RSEQ=GATGATGATTCCATTCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:42:0:31:1:1:1:31:4:0.2857:0:2.5 0/0:17:0:0,0:4,13:0:2,0:26.8:1:29.5:1:1:0:38.2:34:1:0:0.6 -16 46392204 . G T 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09333;SOR=0;LSEQ=ATTCGATGATGATTCCATTC;RSEQ=ATTCCATTCGATGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:34.5:1:30:0:1:1:31:4:0.2857:0:2.5 0/0:17:0:0,0:6,11:0:2,0:28.1:1:30.4:1:1:0:39.7:34:1:0:0.6 -16 46392238 . T A 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31545;LSEQ=ATTCCATTTGATTCCATGCG;RSEQ=CGGTGAGCAATTCGATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:1.5:1:26.5:1:1:1:35.5:4:0.3333:0:2 0/1:15:6:1,5:5,4:0.4:2,2:14.7:1:29.3:1:0.28671:5.514:35:12:0.4:0:1.5 -16 46392418 . AA GG 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCCATTTGATTTCATTC;RSEQ=TGCTTCTATTCTATTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:33:1:30.8:1:1:0:24.5:4:1:0:2.5 -16 46392431 . T A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCATTCAATGCTTCTATTC;RSEQ=ATTCCAGTCGATGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:1,0:0.6667:0,0:23.5:1:31:1:0.33333:0:24.5:4:0.6667:0:2.5 -16 46392643 . C T 84 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGATGGTGATTCAATTCTC;RSEQ=TATATTGGATGAATCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:29:1:1:0:44:4:1:0:1.5 1/1:7:7:3,4:0,0:1:0,2:21.7:1:30.1:1:1:0:45:14:1:0:1.6 -16 46392953 . G C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57576;SOR=2.28835;LSEQ=GATTCCATTCGATTCTATTC;RSEQ=AAAATGATTCCATTTGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:14.5:1:30:1:1:1.41:23:4:0.2857:0:3 1/0:4:2:1,1:1,1:0.5:2,2:12.5:1:32.5:1:1:1:43:4:0.5:0:2.5 -16 46392957 . A G 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=CCATTCGATTCTATTCGAAA;RSEQ=TGATTCCATTTGAATCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:11:0:30:1:1:1.41:43:4:0.2857:0:3 0/0:5:0:0,0:3,2:0:2,0:19.6:1:31:1:1:0:36.8:10:1:0:1.4 -16 46393026 . GC TT 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68017;SOR=0.61365;LSEQ=ATGATTCCATTCGATTCCAT;RSEQ=GACGATGATTCCATTCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:3,2:2,1:0.5556:2,2:22.8:1:31.4:1:1:1.28664:31.4:10:0.5556:0:2.2 0/1:14:6:4,2:4,2:0.4286:2,2:21.3:1:29.4:1:1:1:33.2:12:0.4286:0.0714:2.2 -16 46393043 . C T 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08867;SOR=0;LSEQ=CATGCGACGATGATTCCATT;RSEQ=GATTCCATGTGATGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:26:1:30:1:1:1.29:25:4:0.2222:0:2.5 0/0:20:0:0,0:14,6:0:2,0:19.2:1:30.4:1:1:0:45.7:40:1:0:1.8 -16 46393049 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGATGATTCCATTCGATTC;RSEQ=ATGTGATGATTCCATTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:19.7:1:30.7:1:1:0:38.6:14:1:0:2 0/1:22:2:1,1:14,6:0.0909:2,2:9.5:1:29:1:1:2.2361:56:4:0.0909:0:2.5 -16 46393052 . G T 107 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66284;SOR=0.55673;LSEQ=ATGATTCCATTCGATTCCAT;RSEQ=TGATGATTCCATTCTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:22.3:1:29.5:1:1:1:30:8:0.6667:0:2.5 1/0:23:12:9,3:5,4:0.5217:2,2:23.6:1:29.9:1:0.39721:2.30:35.9:24:0.5217:0:2.3 -16 46393053 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCGATTCCATG;RSEQ=GATGATTCCATTCTATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:23.8:1:29.2:1:1:0:40:12:1:0:1.8 0/1:23:2:1,1:13,6:0.087:2,2:13.5:1:31:1:1:2.08171:56:4:0.0952:0:2.5 -16 46393064 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATGTGATGATTCCA;RSEQ=TCTATTCTATTCGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:0:2,0:18.8:1:30.8:1:1:0:37.5:22:1:0:1.3 0/1:27:2:1,1:16,9:0.0741:2,2:33.5:1:29.5:1:1:1.73837:44.5:4:0.0741:0:2 -16 46393084 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.08792;SOR=0;LSEQ=TTCTATTCTATTCGATGATG;RSEQ=TTCCATTCGATTCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:15:1:30:1:1:1.36624:48:4:0.1429:0:1 0/0:32:0:0,0:18,14:0:2,0:27.9:1:29.2:1:1:0:43.5:64:1:0:1.3 -16 46393106 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53412;SOR=Inf;LSEQ=TCCATTCGATTCCATTCGAT;RSEQ=ATGATTGGATTCGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:29.9:1:32.2:1:1:0:39.1:36:1:0:1.1 0/1:33:2:1,1:17,14:0.0606:2,2:33.5:1:27.5:1:1:1.20712:54:4:0.0625:0:2 -16 46393118 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06128;LSEQ=CATTCGATGATGATTGGATT;RSEQ=GATTCCATTTGATGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:9,8:0.0556:2,0:37:0:28:0:1:0:24:2:0.0556:0:1 0/1:34:2:1,1:16,16:0.0588:2,2:23:1:28.5:1:1:1:46.5:4:0.0588:0:2 -16 46393128 . T G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96083;LSEQ=TGATTGGATTCGATTCCATT;RSEQ=GATGATTTCATTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:27.5:1:32.5:1:1:1.26772:24:4:0.1111:0:2.5 0/1:28:3:2,1:10,15:0.1071:2,2:21.7:1:30.7:1:0.56044:2.88:27:6:0.1071:0:2.7 -16 46393132 . G T 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.93888;LSEQ=TGGATTCGATTCCATTTGAT;RSEQ=ATTTCATTTGATTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:9,6:0.1176:2,2:30.5:1:25.5:1:1:1.46382:24:4:0.1176:0:3 0/1:27:3:1,2:10,14:0.1111:2,2:34.7:1:27.3:1:1:1.4104:41.7:6:0.1111:0:2.7 -16 46393135 . T A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2722;SOR=Inf;LSEQ=ATTCGATTCCATTTGATGAT;RSEQ=TCATTTGATTCCATTCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:0:2,0:31.7:1:29.4:1:1:0:36.5:34:1:0:1.1 0/1:27:3:1,2:10,14:0.1111:2,2:20.7:1:30:1:1:1.4104:49.7:6:0.1111:0:1.3 -16 46393142 . G C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13925;LSEQ=TCCATTTGATGATTTCATTT;RSEQ=ATTCCATTCGTTAATGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:0.1111:2,2:22:1:31:1:1:1.61828:24:4:0.1111:0:3 0/1:24:3:1,2:9,12:0.125:2,2:27:1:31.3:1:1:1.47566:41.7:6:0.1304:0:2.7 -16 46393148 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19346;SOR=0;LSEQ=TGATGATTTCATTTGATTCC;RSEQ=TTCGTTAATGATTTCGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:9,6:0.1176:2,2:28.5:1:30:1:1:1.46382:24:4:0.1176:0:2.5 0/0:21:0:0,0:8,13:0:2,0:26.1:1:29.3:1:1:0:36.2:20:1:0:0.7 -16 46393163 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15172;SOR=0;LSEQ=ATTCCATTCGTTAATGATTT;RSEQ=GATCAATTCCATTCGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:0.1667:2,2:25:1:29:1:1:1.45:46:4:0.1667:0:2 0/0:18:0:0,0:6,12:0:2,0:23.3:1:30.5:1:1:0:38.1:36:1:0:0.8 -16 46393170 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19212;SOR=0;LSEQ=TCGTTAATGATTTCGATCAA;RSEQ=TCCATTCGATGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:4,7:0.1538:2,2:18:1:31:1:1:1.67:46:4:0.1538:0:2 0/0:16:0:0,0:5,11:0:2,0:22.1:1:30.4:1:1:0:36.6:32:1:0:0.9 -16 46393218 . A T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TTCGATAATGATTACATCCG;RSEQ=GTCCATTCAGTGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:1,2:0.625:2,2:31:1:29.8:1:1:1.29:35.2:10:0.625:0:2.6 1/1:7:7:4,3:0,0:1:0,2:27.4:1:30.4:1:1:0:58.3:14:1:0:1.7 -16 46393228 . G A 79 d7 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00966;SOR=0;LSEQ=ATTACATCCGAGTCCATTCA;RSEQ=TGATTCCATTTGAGCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:31.3:1:30.7:1:1:0:37.8:12:1:0:2.3 0/1:8:2:2,0:3,3:0.25:2,0:8.5:1:30.5:1:0.46429:0:34.5:4:0.25:0:2.5 -16 46393239 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=GTCCATTCAGTGATTCCATT;RSEQ=GAGCCTGTTCGATAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:25.7:1:31.3:1:1:0:42.4:14:1:0:1.9 0/1:12:2:2,0:7,3:0.1667:2,0:5:1:32.5:1:1:0:44.5:4:0.1667:0:1.5 -16 46393243 . C A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92648;LSEQ=ATTCAGTGATTCCATTTGAG;RSEQ=CTGTTCGATAATTCCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:3,3:0.1429:2,0:35:0:31:0:1:0:27:2:0.1429:0:4 0/1:15:2:2,0:8,5:0.1333:2,0:23.5:1:30:1:0.52381:0:34.5:4:0.1333:0:2.5 -16 46393259 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGCCTGTTCGATAATTCC;RSEQ=TTTGAGTCCAACCAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:21.9:1:30.9:1:1:0:43:16:1:0:1.8 0/1:20:2:1,1:13,5:0.1:2,2:22.5:1:29:1:0.52105:2.46307:48:4:0.1:0:2 -16 46393270 . A G 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06818;SOR=0;LSEQ=GATAATTCCATTTGAGTCCA;RSEQ=CCAATGATTCCATTCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:29.5:1:31:1:1:1.29:48:4:0.2222:0:1.5 0/0:24:0:0,0:15,9:0:2,0:22.3:1:29.3:1:1:0:44.5:23:1:0:1 -16 46393280 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGAGTCCAACCAATGATT;RSEQ=CATTCATTTCCATTCAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:27.4:1:31.1:1:1:0:42.1:14:1:0:1.1 0/1:24:2:1,1:13,9:0.0833:2,2:18:1:27:1:1:1.42202:50:4:0.0833:0:1.5 -16 46393291 . C A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAATGATTCCATTCATTTC;RSEQ=ATTCAATGATTCCATTCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:30.6:1:31.9:1:1:0:38.7:14:1:0:1 0/1:24:2:1,1:13,9:0.0833:2,2:37:0:29.5:1:1:1.42202:47:4:0.087:0:1 -16 46393328 . G A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGAGTCCATTTGATCATTCC;RSEQ=GTAGGGTCCATTCGATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:24.5:1:30.3:1:1:0:40.7:12:1:0:0.5 0/1:21:2:1,1:9,10:0.0952:2,2:9.5:1:32:1:1:1.11:48:4:0.1:0:2 -16 46393575 . A T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TTCTGTGATGATTCCATGTG;RSEQ=TTGCATTCAATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21.3:1:29.8:1:1:0:53.3:8:1:0:1 0/1:5:2:1,1:1,2:0.4:2,2:29:1:30.5:1:1:1.73:59.5:4:0.4:0:2 -16 46393610 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GATTCCTTTAGATTGCATTC;RSEQ=ATTGTGATTCACTTCGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:30.3:1:32.3:1:1:0:57.7:6:1:0:1.3 0/1:6:2:1,1:1,3:0.3333:2,2:5.5:1:28.5:1:1:2.45:40:4:0.3333:0:2.5 -16 46393622 . C T 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCATTCGATTGTGATTCA;RSEQ=TTCGTCTTCATTCTATGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:18.3:1:32.3:1:1:0:57.7:6:1:0:1.3 1/1:5:5:2,3:0,0:1:0,2:16.8:1:29.2:1:1:0:48:10:1:0:2 -16 46393981 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTAGATGATGATGGCATTC;RSEQ=ATTCCTTTCAATCATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:13:1:30:1:1:0:37.6:10:1:0:0.6 0/1:11:2:1,1:7,2:0.1818:2,2:13.5:1:28:1:0.49091:3.05504:47:4:0.2:0:1.5 -16 46394021 . A G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGATTCCATTCAAAGGTG;RSEQ=TTTCATTCAAGTCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:42.2:1:31.3:1:1:0:38:12:1:0:0.7 0/1:17:2:1,1:10,5:0.1176:2,2:23.5:1:28.5:1:1:1.91491:23:4:0.1176:0:1.5 -16 46394039 . C G 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07;SOR=0;LSEQ=TGATTTCATTCAAGTCCATT;RSEQ=GATAATTGCATTCGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:22.5:1:30:1:1:1.41418:40:4:0.2857:0:1 0/0:18:0:0,0:11,7:0:2,0:27.4:1:29.9:1:1:0:31.2:36:1:0:0.4 -16 46394220 . AA CC 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCCATTCGATGATGATT;RSEQ=AATCGAATCCATTCAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:0,2:1,3:0.3333:2,0:41.5:1:31.3:1:1:0:25.5:4:0.3333:0:1 -16 46394299 . T C 50 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGATGATTCCACTTGATT;RSEQ=CATTTACGAAGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:3:3,0:3,4:0.3:2,0:18.7:1:32:1:0.2:0:35:6:0.3:0:3 -16 46394309 . A T 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTTGATTTCATTTACGA;RSEQ=GATTCCATTCGATTCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:2:0:31:0:1:0:42:2:1:0:3 1/1:9:9:6,3:0,0:1:0,2:28.7:1:30.6:1:1:0:39.1:18:1:0:2.2 -16 46394319 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATTTACGAAGATTCCATT;RSEQ=GATTCCATGTGATGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:28:1:1:0:45.5:4:1:0:2.5 0/1:11:2:1,1:6,3:0.1818:2,2:25.5:1:28:1:1:1.87089:40:4:0.1818:0:2.5 -16 46394344 . A G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATGTGATGATTCCATTCA;RSEQ=TTCTATTCAATGCTGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:26:1:30.3:1:1:0:48.3:6:1:0:2 0/1:11:2:2,0:4,5:0.1818:2,0:38:1:33.5:1:0.45455:0:50:4:0.1818:0:2.5 -16 46394369 . GA CT 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6044;SOR=0.52327;LSEQ=ATTCAATGCTGTTTCCATTT;RSEQ=TTCCATTCGACCATGATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:39.5:1:32:1:1:1:45.5:4:0.4:0:1.5 0/1:10:2:1,1:4,4:0.2:2,2:24.5:1:29.5:1:1:1:44.5:4:0.2:0:1.5 -16 46394410 . C T 79 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65566;SOR=1.82076;LSEQ=CCTTTGATTCCATTCAATGA;RSEQ=TCCATTCGGTTCCTTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:2,3:0.2857:2,0:6.5:1:31:0:0.42857:0:53:4:0.2857:0:3 0/1:14:6:4,2:2,6:0.4286:2,2:5.5:1:30.8:1:0.27739:5.18:45.5:12:0.4286:0:2.5 -16 46394412 . C T 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TTTGATTCCATTCAATGACT;RSEQ=CATTCGGTTCCTTTTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:37:1:29:1:1:1.41418:43:4:0.2857:0:3 0/0:14:0:0,0:6,8:0:2,0:16.7:1:31.4:1:1:0:49.8:28:1:0:1.4 -16 46394424 . T A 93 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.89439;LSEQ=CAATGACTCCATTCGGTTCC;RSEQ=TTTGATGATGATTCCGTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:18:1:31.7:1:1:1.73:55.3:6:0.6:0:2.3 1/0:14:8:5,3:1,5:0.5714:2,2:16.4:1:31.3:1:0.13753:7.05:44:16:0.5714:0:2.1 -16 46394485 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGATTCCATTGGATGAGTC;RSEQ=ATTCGATTACATTCGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,4:0:2,0:24.8:1:32.2:1:1:0:43.7:18:0.9:0:0.6 0/1:23:2:1,1:13,8:0.087:2,2:33:0:31:1:1:1.58984:60:4:0.087:0:2 -16 46394490 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTGGATGAGTCCATTC;RSEQ=ATTACATTCGATGATTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:27.6:1:31.2:1:1:0:43.7:18:1:0:0.6 0/1:24:2:1,1:13,9:0.0833:2,2:28:0:32:0:1:1.42202:60:4:0.0833:0:2 -16 46394491 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTGGATGAGTCCATTCG;RSEQ=TTACATTCGATGATTATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:28.1:1:31.2:1:1:0:43.7:18:1:0:0.6 0/1:24:2:1,1:13,9:0.0833:2,2:23:1:32.5:1:1:1.42202:53:4:0.0833:0:2 -16 46394499 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19488;SOR=0.17873;LSEQ=TGAGTCCATTCGATTACATT;RSEQ=GATGATTATTCCATTCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:37.5:1:30.5:1:1:1.29098:47:4:0.2222:0:1 0/1:22:1:1,0:12,9:0.0455:2,0:31:0:31:0:1:0:23:2:0.0455:0:1 -16 46394524 . T A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTATTCCATTCGAGTGCAT;RSEQ=AGATGATTCCATTCGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:35:1:29.4:1:1:0:39.1:14:1:0:0.3 0/1:17:2:1,1:8,7:0.1176:2,2:10:1:25:1:1:1.13389:47.5:4:0.1176:0:1.5 -16 46394533 . C G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00535;SOR=Inf;LSEQ=TTCGAGTGCATTAGATGATT;RSEQ=CATTCGAGTCCATTCGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:27.9:1:31.1:1:1:0:39.1:14:1:0:0.3 1/0:15:10:4,6:4,1:0.6667:2,2:24.5:1:32.8:1:0.28205:5.30481:39:20:0.6667:0:1.1 -16 46394622 . A T 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ATTCCACTCGATTCCATTCG;RSEQ=TGACTCCATTTGATCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:33.5:1:29.5:1:1:0:24:4:0.6667:0:1 0/0:4:0:0,0:0,4:0:0,0:41.3:1:32:0:1:0:31.5:8:1:0:0.8 -16 46394631 . T G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GATTCCATTCGATGACTCCA;RSEQ=TTGATCCCATTCGATGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:45:1:30.3:1:1:0:23.7:6:1:0:1 1/0:4:2:0,2:0,2:0.5:0,0:38.5:1:33:0:1:0:31.5:4:0.5:0:1 -16 46394984 . C A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAATGCTTCCACTCGATT;RSEQ=CATATGATGATGACTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:31:1:30:1:1:0:55:4:1:0:1 0/1:8:2:1,1:1,5:0.25:2,2:12:1:27.5:1:0.46429:3.87:39:4:0.25:0:2.5 -16 46395013 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATGACTCCATTCGATGAAA;RSEQ=TCGATGATGATTCCATTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35.5:1:31:1:1:0:55:4:1:0:1 0/1:9:2:1,1:1,5:0.2222:2,2:40.5:1:30.5:1:0.46429:3.87:39:4:0.25:0:2.5 -16 46395033 . C T 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02222;SOR=0;LSEQ=TTCGATGATGATTCCATTCG;RSEQ=TTGCATTCGATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:31:0:1:0:55:4:1:0:1 0/0:8:0:0,0:2,5:0:2,0:34.7:1:32:1:1:0:45.9:14:1:0:1.3 -16 46395199 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCTCATTCGATGATGATT;RSEQ=CATTCAACTCCATTCGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:26.8:1:31.6:1:1:0:30:18:1:0:0.4 0/1:22:2:1,1:13,7:0.0909:2,2:21.5:1:30.5:1:1:1.80284:25:4:0.1053:0:2 -16 46395225 . T C 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07563;SOR=0;LSEQ=AACTCCATTCGATGTTTCCA;RSEQ=TCGAGTTCATTCTATTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:38.5:1:32:1:1:1:24:4:0.2:0:1 0/0:25:0:0,0:13,12:0:2,0:33.5:1:28.6:1:1:0:29.4:24:1:0:0.4 -16 46395236 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTTTCCATTCGAGTTCAT;RSEQ=CTATTATTCCATTAGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:21.7:1:29.7:1:1:0:31.6:22:1:0:0.4 0/1:27:2:1,1:14,11:0.0741:2,2:39.5:1:28:1:1:1.2613:24:4:0.0741:0:1 -16 46395245 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGAGTTCATTCTATTATT;RSEQ=CATTAGATTCCATTCGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:28.8:1:30.2:1:1:0:31.4:18:1:0:0.3 0/1:29:2:1,1:15,12:0.069:2,2:8.5:1:31.5:1:1:1.24034:25:4:0.069:0:2 -16 46395264 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TCCATTAGATTCCATTCGAT;RSEQ=ATGATTCCATTCGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:23.3:1:30.8:1:1:0:31.8:24:1:0:0.5 0/1:30:2:1,1:12,16:0.0667:2,2:16.5:1:27:1:1:1.32:24:4:0.0667:0:1 -16 46395301 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTTGATGATTGCATTCT;RSEQ=TTTCATTTGATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:33.6:1:29.9:1:1:0:36:18:1:0:0.3 0/1:19:2:1,1:9,8:0.1053:2,2:36.5:1:30.5:1:1:1.11803:25:4:0.1053:0:2 -16 46395394 . A T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0029;SOR=0;LSEQ=TTCAATTCTATGATGATTAC;RSEQ=TTGGATTCCATTCGTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:3,3:6,7:0.3158:2,2:21:1:31.7:1:1:1.16:55.7:12:0.3158:0:1.3 0/0:27:0:0,0:13,14:0:2,0:29:1:30:1:1:0:42.8:54:1:0:0.4 -16 46395395 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16522;SOR=0;LSEQ=TCAATTCTATGATGATTACA;RSEQ=TGGATTCCATTCGTTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:24:1:31.5:1:1:1.12:47.5:4:0.1053:0:1 0/0:27:0:0,0:13,14:0:2,0:28.9:1:30:1:1:0:42.8:54:1:0:0.4 -16 46395402 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51111;SOR=Inf;LSEQ=TATGATGATTACATTGGATT;RSEQ=CATTCGTTGATGATTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:26:1:31.1:1:1:0:51.2:44:1:0:0.8 0/1:33:2:1,1:15,15:0.0606:2,2:33:0:33.5:1:1:1:42:4:0.0606:0:2.5 -16 46395424 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17293;SOR=0;LSEQ=ATTCGTTGATGATTTCATTC;RSEQ=GTTCCATTCAATGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:9,13:0.0833:2,2:19:1:29:1:1:1.42:45:4:0.0833:0:2 0/0:33:0:0,0:16,17:0:2,0:24.4:1:29.9:1:1:0:45.8:66:1:0:0.6 -16 46395425 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50376;SOR=Inf;LSEQ=TTCGTTGATGATTTCATTCG;RSEQ=TTCCATTCAATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:27.3:1:31.9:1:1:0:53.4:48:1:0:0.8 0/1:33:2:1,1:15,16:0.0606:2,2:25:1:28.5:1:1:1.06:24:4:0.0606:0:4 -16 46395428 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49875;SOR=Inf;LSEQ=GTTGATGATTTCATTCGGTT;RSEQ=CATTCAATGATGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:0:2,0:26.5:1:31.6:1:1:0:54:50:1:0:0.7 0/1:32:2:1,1:14,16:0.0625:2,2:7:0:31:1:1:1.14:42:4:0.0625:0:2.5 -16 46395442 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48986;SOR=Inf;LSEQ=TCGGTTCCATTCAATGATGA;RSEQ=TCCATTCAATTCCTTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:7,15:0:2,0:25.8:1:30.2:1:1:0:55.4:21:1:0:0.7 0/1:24:2:1,1:11,11:0.0833:2,2:42:1:31.5:1:1:1:24:4:0.0833:0:4 -16 46395495 . T A 68 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATACGATGATGATTCC;RSEQ=TTTGATTTGATTCCACAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:10:1:31.7:1:1:0:50:6:1:0:1 1/0:7:5:2,3:1,1:0.7143:2,2:5.6:1:29.4:1:1:1.41418:32:10:0.7143:0:2.2 -16 46396083 . A T 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGATTCCAGTCTCTGATG;RSEQ=TTACATTCGAGTCCATACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:33.3:1:30.3:1:1:0:24.7:6:1:0:1 -16 46396681 . A C 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAATGATTCCATTCGAGT;RSEQ=CATTTGATGATTCCATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:33:0:1:0:24:2:1:0:4 1/1:8:8:5,3:0,0:1:0,2:18.3:1:29:1:1:0:35:16:1:0:2.4 -16 46396710 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTTGATTCCATTT;RSEQ=ATAATGATTCTACTAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28:1:33.5:1:1:0:42:4:1:0:3 0/1:12:2:1,1:6,4:0.1667:2,2:36:1:30.5:1:1:1.4491:24:4:0.1667:0:2 -16 46396712 . T A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06593;SOR=0;LSEQ=TTCCATTTGATTCCATTTGA;RSEQ=AATGATTCTACTAGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:32:0:1:0:42:4:1:0:3 0/1:12:2:1,1:6,4:0.1667:2,2:22.5:1:28:1:1:1.4491:32:4:0.1667:0:4 -16 46396722 . A T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTTGATAATGATTCT;RSEQ=CTAGAGTCCATTCAATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28:1:31:1:1:0:42:4:1:0:3 0/1:13:2:1,1:6,5:0.1538:2,2:32:0:31:1:1:1.18321:47:4:0.1667:0:3.5 -16 46396732 . A G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAATGATTCTACTAGAGTCC;RSEQ=TTCAATGACTCCATTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28:1:29.5:1:1:0:42:4:1:0:3 0/1:13:2:1,1:6,5:0.1538:2,2:22:0:32.5:1:1:1.18321:47:4:0.1538:0:3.5 -16 46396737 . A G 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCTACTAGAGTCCATTCA;RSEQ=TGACTCCATTGGAGTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28:1:31:1:1:0:42:4:1:0:3 0/1:16:2:1,1:7,7:0.125:2,2:30:0:31.5:1:1:1:60:4:0.125:0:3.5 -16 46396774 . C G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCAACAATTCCATTCGA;RSEQ=TCCATTCGATGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:28:1:30.5:1:1:0:42:4:1:0:1.5 0/1:15:2:1,1:4,7:0.1333:2,2:37:1:33:1:1:1.67:33:4:0.1333:0:3 -16 46396781 . C T 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46382;LSEQ=CAATTCCATTCGACTCCATT;RSEQ=GATGATTCCATTCGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:23:0:32:0:1:0:60:2:0.5:0:2 1/0:15:9:4,5:2,4:0.6:2,2:23.8:1:29.2:1:1:1.55:50.8:18:0.6:0:2.3 -16 46396794 . C G 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCCATTCGATGATTCCATT;RSEQ=GATTCCATTTGATGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:28:1:30:1:1:0:42:4:1:0:1.5 0/1:14:3:1,2:5,6:0.2143:2,2:26.3:1:30:1:1:1.60839:45.3:6:0.2143:0:3 -16 46396799 . C G 34 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGATGATTCCATTCGATT;RSEQ=CATTTGATGATTCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:27.5:1:31:0:1:0:42:4:1:0:1.5 0/1:12:2:1,1:3,7:0.1667:2,2:12:1:34:0:1:2.16:33:4:0.1667:0:3 -16 46396804 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCGATTCCATT;RSEQ=GATGATTCCATTCGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:45:0:30:0:1:0:24:2:1:0:1 0/1:11:2:1,1:3,6:0.1818:2,2:7:1:31:1:1:1.87:33:4:0.2:0:3 -16 46396851 . T G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATTACAGTCGAGTCCATTT;RSEQ=GTGATTCCACTGGATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:15:1:30.5:1:1:0:43.5:4:1:0:3.5 -16 46401760 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGATTCTATTCGAATCCA;RSEQ=TTGATGATTTCTTTTGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:2,0:5,0:0.2857:0,0:31.5:1:30.5:1:1:0:25.5:4:0.2857:0:2.5 -16 46401783 . G C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATGATTTCTTTTGATTATA;RSEQ=TTGGTGATGATTCCATTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:12:0:33:0:1:0:25:2:1:0:1 0/1:8:2:1,1:6,0:0.25:0,2:10.5:1:31:1:0.25:0:24:4:0.2857:0:1 -16 46401829 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAATGATTCCATTCGATT;RSEQ=CAATCGATGGTGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:30.5:1:32:1:1:0:24.3:8:1:0:0.3 0/1:17:2:1,1:9,6:0.1176:2,2:25:1:29:1:1:1.46382:24:4:0.125:0:3 -16 46401848 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCAATCGATGGTGATTCCA;RSEQ=TAGAGTCCATTTAATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:22.4:1:30.9:1:1:0:25.4:16:1:0:0.4 0/1:20:2:1,1:8,10:0.1:2,2:32:1:30.5:1:1:1.24:47:4:0.1:0:1 -16 46401863 . T C 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53602;SOR=Inf;LSEQ=TTCCATTAGAGTCCATTTAA;RSEQ=GATTCCATTTGATTCCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:26.5:1:30.9:1:1:0:25.4:16:1:0:0.4 0/1:20:3:2,1:6,11:0.15:2,2:32.3:1:22.7:1:0.53684:3.42:39.3:2:0.1111:0:1.7 -16 46401894 . A C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51567;SOR=Inf;LSEQ=GATTCCAGTCTCTGATGATT;RSEQ=CATTCGAGTCCATACGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:18.7:1:27.9:1:1:0:25.1:20:1:0:0.5 0/1:17:2:1,1:5,10:0.1176:2,2:17:1:31:1:1:1.91:46.5:4:0.1176:0:1 -16 46401910 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.25853;LSEQ=GATTACATTCGAGTCCATAC;RSEQ=ATGATTCCACTCAATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:3,4:0.125:2,0:39:0:28:0:1:0:25:2:0.125:0:1 0/1:13:2:1,1:3,8:0.1538:2,2:34.5:1:31:1:1:2.45:24:4:0.1538:0:1 -16 46401929 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2;SOR=0;LSEQ=CGATGATTCCACTCAATTCC;RSEQ=TATGATGATGATTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:25.5:1:29:1:1:3.16:24:4:0.2857:0:1 0/0:8:0:0,0:1,7:0:2,0:18:1:28.9:1:1:0:24.6:7:1:0:1.4 -16 46402061 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTATTTGTGTCCCTTAGATG;RSEQ=TTCCACATGATTCCATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:27.9:1:30.3:1:1:0:24.4:14:1:0:0.6 0/1:23:2:1,1:10,11:0.087:2,2:31:1:29.5:1:1:1.10:28:4:0.087:0:1 -16 46402062 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTGTGTCCCTTAGATGA;RSEQ=TCCACATGATTCCATTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:28:1:30.1:1:1:0:24.4:14:1:0:0.6 0/1:23:2:1,1:10,11:0.087:2,2:37.5:1:30:1:1:1.10:23:4:0.087:0:1 -16 46402075 . C T 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04828;SOR=0;LSEQ=TAGATGATTCCACATGATTC;RSEQ=ATTAGATGATGATACTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:39:1:28:0:1:1.41:29:4:0.2857:0:1 0/0:23:0:0,0:10,13:0:2,0:30.9:1:30.2:1:1:0:25.3:46:1:0:0.4 -16 46402080 . G C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20427;SOR=0.22715;LSEQ=GATTCCACATGATTCCATTA;RSEQ=ATGATGATACTATTTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:21.5:1:31:1:1:2.45:22:4:0.3333:0:1 0/1:21:2:1,1:8,11:0.0952:2,2:39:1:31:1:1:1.35:22:4:0.0952:0:1 -16 46402822 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATTGGATGATGACTCCATTC;RSEQ=AGTCCATTCGATGATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:33.7:1:33.3:1:1:0:29.3:6:1:0:1.3 1/1:2:2:1,1:0,0:1:0,2:26:1:28.5:1:1:0:24:4:1:0:1 -16 46402985 . T C 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCCGTTTGATTCCATT;RSEQ=GATGATTCCCTTCGATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17:1:33:0:1:0:24:4:1:0:1.5 1/1:8:7:6,1:0,1:0.875:0,2:22.4:1:32.6:1:0.25:0:23.4:14:0.875:0:1.3 -16 46403006 . T A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATGATTCCCTTCGATTCCT;RSEQ=TCTTTGATGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:24:1:31.8:1:1:0:24:8:1:0:0.8 0/1:20:2:1,1:11,7:0.1:2,2:22.5:1:30.5:1:1:1.53525:23:4:0.1:0:2.5 -16 46403034 . C G 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=AATGATTCCATTCGAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:31.8:1:31.4:1:1:0:23.8:10:1:0:1 0/1:24:2:1,1:11,11:0.0833:2,2:38:0:31:1:1:1:23:4:0.0833:0:2.5 -16 46403050 . A G 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCAATGATTCCATTCGA;RSEQ=TCTATTCCATGATGATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:29.5:1:29.7:1:1:0:23.7:12:1:0:0.8 0/1:22:2:1,1:10,10:0.0909:2,2:30.5:1:31:1:1:1:48:4:0.0909:0:1 -16 46403056 . T G 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04274;SOR=0;LSEQ=ATGATTCCATTCGAATCTAT;RSEQ=CCATGATGATTCCTTTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:18:1:30.5:1:1:1:23:4:0.3333:0:2 0/0:21:0:0,0:10,11:0:2,0:23.9:1:28.5:1:1:0:35:42:1:0:0.6 -16 46403354 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGATTCCGTTCGAGTCC;RSEQ=TTCGATGATTCCATTCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:5:1:31:0:1:0:35.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 46403430 . G C 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59615;SOR=0.40576;LSEQ=GATTCCATTCGAGTCCATTC;RSEQ=ATGATTCCATTAGAGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:27.7:1:31:1:1:1.73:27:6:0.6:0:1.7 0/1:11:4:2,2:4,3:0.3636:2,2:36.3:1:31.3:1:1:1.29868:49:8:0.3636:0:1 -16 46403462 . T C 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10989;SOR=0;LSEQ=AGAGTACATTTAATGATTGC;RSEQ=TTGTTTTCAATTCGAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:25:1:32:1:1:1.73:27:4:0.4:0:1.5 0/0:9:0:0,0:4,5:0:2,0:25.7:1:29.7:1:1:0:40.7:18:1:0:0.6 -16 46403589 . TTCCATTCGAGGATGATTCCATTCGATTCCATTC T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.5;SOR=Inf;LSEQ=CATTCGGTGATTTCATTAGA;RSEQ=GATGATTCCATTCAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:18.3:1:31.7:1:1:0:33.7:6:1:0:1.7 0/1:6:2:1,1:4,0:0.3333:0,2:13.5:1:29.5:1:0.33333:0:47:4:0.3333:0.3333:1 -16 46403607 . C G 30 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07;SOR=0;LSEQ=GATTCCATTCGAGGATGATT;RSEQ=CATTCGATTCCATTCGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:23.5:1:30.5:1:1:1.41418:21:4:0.3333:0:3 0/0:18:0:0,0:10,6:0:2,0:15.5:1:31.3:1:1:0:45.9:32:1:0:1.1 -16 46403608 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCGAGGATGATTC;RSEQ=ATTCGATTCCATTCGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:23.4:1:32:1:1:0:34.3:14:1:0:1.3 0/1:20:2:1,1:10,6:0.1:2,2:20:1:30.5:1:1:1.61828:50:4:0.1111:0:3 -16 46403609 . A T 29 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05983;SOR=0;LSEQ=TTCCATTCGAGGATGATTCC;RSEQ=TTCGATTCCATTCGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:25.5:1:29.5:1:1:1.41418:21:4:0.3333:0:3 0/0:20:0:0,0:11,7:0:2,0:15.8:1:30.2:1:1:0:47.4:36:1:0:1.1 -16 46403626 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54117;SOR=Inf;LSEQ=TCCATTCGATTCCATTCGAT;RSEQ=ATTCCATTCAATTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:23.2:1:31.4:1:1:0:44.7:32:1:0:0.9 0/1:31:2:1,1:18,11:0.0645:2,2:35:1:29.5:1:1:1.60957:50:4:0.0645:0:3 -16 46403630 . C G 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28163;SOR=0.25741;LSEQ=TTCGATTCCATTCGATGATT;RSEQ=CATTCAATTCCATTCGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:25:1:31:1:1:1:50:4:0.1176:0:1.5 0/1:33:1:1,0:18,12:0.0303:2,0:33:0:31:0:1:0:51:2:0.0303:0:3 -16 46403636 . A G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52425;SOR=Inf;LSEQ=TCCATTCGATGATTCCATTC;RSEQ=ATTCCATTCGATGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:23:1:30.2:1:1:0:47:44:1:0:1.1 0/1:37:2:1,1:22,13:0.0541:2,2:14:0:30.5:1:1:1.66733:47:4:0.0541:0:1 -16 46403648 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13458;SOR=0;LSEQ=TTCCATTCAATTCCATTCGA;RSEQ=GATGATTCCATTCCAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:0.0769:2,2:16.5:1:30.5:1:1:1:60:4:0.0769:0:2.5 0/0:44:0:0,0:24,16:0:2,0:30.2:1:30.6:1:1:0:49.6:80:0.9302:0:0.8 -16 46403662 . C G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.00182;SOR=0.12139;LSEQ=ATTCGATGATGATTCCATTC;RSEQ=AGTCCATATGATCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:9,9:0.3333:2,2:25.4:1:31.3:1:1:1.23971:46.9:18:0.3333:0:2.2 0/1:54:3:2,1:31,19:0.0556:2,2:35:1:31.7:1:1:1.22:46.7:6:0.0566:0:1.7 -16 46403685 . G A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10072;SOR=0.27485;LSEQ=TCCATATGATCATTCCATTT;RSEQ=ATTTCATTCGATGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:2,2:11,14:0.1333:2,2:46.5:1:29.8:1:1:1.26:60:8:0.1379:0:2 0/1:75:3:2,1:43,29:0.04:2,2:10.3:1:29:1:1:1.34:47:6:0.0405:0:1.7 -16 46403697 . T TG 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TTCCATTTGATTTCATTCGA;RSEQ=GATGATTCCATTCGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:13,15:0:2,0:24.6:1:29.9:1:1:0:55.7:13:1:0:1.5 0/1:68:2:1,1:36,30:0.0294:2,2:39.5:1:30:1:1:1.19677:58:4:0.0294:0:1.5 -16 46403709 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09586;SOR=0;LSEQ=TCATTCGATGATGATTCCAT;RSEQ=CGATTCCATTCGACGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:13,16:0.0645:2,2:32.5:1:31:1:1:1.22:60:4:0.0645:0:1 0/0:68:0:0,0:37,30:0:2,0:25:1:28.8:1:1:0:52.2:134:1:0:1.2 -16 46403713 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGATGATGATTCCATTCGA;RSEQ=TCCATTCGACGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,15:0:2,0:21.6:1:30.2:1:1:0:55.7:26:1:0:1.8 0/1:65:2:1,1:34,29:0.0308:2,2:30:1:30:1:1:1.16953:50:4:0.0313:0:2 -16 46403716 . C G 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5751;SOR=0.66886;LSEQ=ATGATGATTCCATTCGATTC;RSEQ=ATTCGACGATTCCATTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:3,4:9,10:0.2692:2,2:30.7:1:30:1:1:1.19164:60:14:0.2692:0:2.3 0/1:66:13:6,7:28,25:0.197:2,2:28.6:1:29.9:1:0.7616:1.30136:57.2:26:0.197:0:1.9 -16 46403717 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07764;SOR=0;LSEQ=TGATGATTCCATTCGATTCC;RSEQ=TTCGACGATTCCATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:11,13:0.0769:2,2:16.5:1:32.5:1:1:1.17:60:4:0.08:0:1 0/0:66:0:0,0:33,31:0:2,0:27.5:1:29.2:1:1:0:51.5:63:0.9692:0:1.3 -16 46403720 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCGATTCCATT;RSEQ=GACGATTCCATTCTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:21:1:31:1:1:0:55.7:52:1:0:1.8 0/1:66:2:1,1:32,32:0.0303:2,2:33.5:1:28.5:1:1:1:60:4:0.0308:0:3 -16 46403723 . C T 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09291;SOR=2.55363;LSEQ=TTCCATTCGATTCCATTCGA;RSEQ=GATTCCATTCTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:3,4:8,9:0.2917:2,2:22:1:31:1:1:1.17684:49:14:0.2917:0:2 1/0:66:34:16,18:16,16:0.5152:2,2:29.6:1:29.3:1:1:1.12299:46.1:68:0.5152:0:1.6 -16 46403726 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06175;SOR=0;LSEQ=CATTCGATTCCATTCGACGA;RSEQ=TCCATTCTATTCCATTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:8,12:0.0909:2,2:23.5:1:33:1:1:1.47:57.5:4:0.0909:0:3 0/0:65:0:0,0:31,34:0:2,0:27.3:1:29.3:1:1:0:51.7:64:1:0:1.5 -16 46403734 . T G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCGACGATTCCATTC;RSEQ=ATTCCATTCGATGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:26.1:1:28.6:1:1:0:59.1:17:1:0:2.2 0/1:66:3:1,2:29,34:0.0455:2,2:15.3:1:32.3:1:1:1.69267:46:6:0.0462:0:3 -16 46403735 . A G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1917;SOR=0.24781;LSEQ=CCATTCGACGATTCCATTCT;RSEQ=TTCCATTCGATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:32.5:1:33.5:1:1:1.62:57.5:4:0.1111:0:3 0/1:68:2:1,1:29,37:0.0294:2,2:8:0:33:0:1:1.27:60:4:0.0303:0:1 -16 46403740 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGACGATTCCATTCTATTCC;RSEQ=TTCGATGATGATTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:5,10:0:2,0:28.8:1:29.4:1:1:0:58.9:14:1:0:2.2 0/1:68:2:1,1:28,38:0.0294:2,2:13:0:32.5:1:1:1.35:51.5:4:0.0299:0:2.5 -16 46403744 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCTATTCCATTC;RSEQ=ATGATGATTCCATTCGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:31.2:1:29.5:1:1:0:58.7:12:1:0:2.3 0/1:64:3:1,2:25,36:0.0469:2,2:20.3:1:30:1:1:1.38202:48.7:6:0.0476:0:3 -16 46403746 . TGATGATTCCATTCGAGTCCATTC T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TTCCATTCTATTCCATTCGA;RSEQ=GATGATTCCATTCGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:29.9:1:31.8:1:1:0:58.7:26:1:0:2.3 0/1:66:2:1,1:25,39:0.0303:2,2:9:1:29.6:1:1:1.55:43.5:4:0.0303:0.0303:2 -16 46403755 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCGATGATGATTC;RSEQ=ATTCGAGTCCATTCGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:25.2:1:30.1:1:1:0:58.7:12:1:0:2.3 0/1:60:2:1,1:22,34:0.0333:2,2:25:1:30.5:1:1:1.53:50:4:0.0357:0:2.5 -16 46403764 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATGATGATTCCATTCGAGT;RSEQ=CATTCGATGATTCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,6:0:2,0:22.3:1:31.3:1:1:0:58.3:20:0.9091:0:2.4 0/1:54:2:1,1:18,31:0.037:2,2:38:0:31:0:1:1.70:43:4:0.0385:0:3.5 -16 46403769 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCGAGTCCATT;RSEQ=GATGATTCCATTCGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:17.1:1:30.3:1:1:0:58.5:22:1:0:2.5 0/1:50:2:1,1:14,31:0.04:2,2:36.5:1:30:1:0.54117:2.17:60:4:0.0417:0:4.5 -16 46403773 . G C 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=0.03257;LSEQ=TCCATTCGAGTCCATTCGAT;RSEQ=ATTCCATTCGAGTCCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:1,1:0.7143:2,2:20:1:32.6:1:1:3.1622:57.6:10:0.7143:0:3 0/1:46:3:0,3:13,30:0.0652:2,0:27.3:1:32:1:0.54783:0:53.3:6:0.0667:0:2.7 -16 46403777 . C G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGAGTCCATTCGATGATT;RSEQ=CATTCGAGTCCATTTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:19.6:1:31.1:1:1:0:58.3:14:1:0:2.4 0/1:45:2:0,2:12,31:0.0444:2,0:44:1:33.5:1:1:0:36:4:0.0444:0:2 -16 46403778 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGAGTCCATTCGATGATTC;RSEQ=ATTCGAGTCCATTTAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:18.9:1:30.6:1:1:0:58.3:14:1:0:2.4 0/1:43:3:2,1:9,31:0.0698:2,2:25:1:28.3:1:0.15598:6.50:52.3:6:0.0698:0:1.7 -16 46403785 . G T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCGATGATTCCATTCGA;RSEQ=TCCATTTAATGATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:24.8:1:31.5:1:1:0:57:8:1:0:1.8 0/1:37:2:1,1:7,28:0.0541:2,2:20.5:1:29.5:1:0.39039:3.81:60:4:0.0541:0:4.5 -16 46403791 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGATTCCATTCGAGTCCAT;RSEQ=TAATGATTCCATTGGGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:18.8:1:29.5:1:1:0:57:8:1:0:1.8 0/1:36:2:1,1:6,27:0.0556:2,2:14.5:1:30.5:1:0.36471:4.24:60:4:0.0571:0:4.5 -16 46403793 . A G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCGAGTCCATTT;RSEQ=ATGATTCCATTGGGTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:16.8:1:29.3:1:1:0:57:8:1:0:1.8 0/1:34:2:1,1:6,25:0.0588:2,2:12.5:1:30:1:0.38447:3.93:60:4:0.0606:0:4.5 -16 46403837 . T C 82 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=ATGATGATTACATTGGATTC;RSEQ=GTTCTATGATTCCATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:16.5:1:32:0:1:0:39:4:1:0:1.5 1/0:10:6:0,6:1,3:0.6:2,0:17.2:1:31.8:1:0.4:0:36.8:12:0.6:0:2 -16 46403838 . G C 61 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=TGATGATTACATTGGATTCT;RSEQ=TTCTATGATTCCATTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:33.5:1:1:0:39:4:1:0:1.5 0/1:9:4:1,3:0,5:0.4444:0,2:25.3:1:30.8:1:0.44444:0:43.8:8:0.4444:0:2.3 -16 46403848 . T A 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGGATTCTGTTCTATGAT;RSEQ=CCATTCAATTCCGTTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27.5:1:31.5:1:1:0:39:4:1:0:1.5 0/1:8:3:1,2:0,5:0.375:0,2:17:1:29:1:0.375:0:42:6:0.375:0:2.3 -16 46404498 . T C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.44444;SOR=Inf;LSEQ=GATGATTCGATTCCATTCAA;RSEQ=GATGATTCCATTTGAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:25.4:1:31.2:1:1:0:39:10:1:0:1 0/1:5:2:1,1:3,0:0.4:0,2:10.5:1:29:1:0.4:0:30:4:0.4:0:5.5 -16 46404509 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.175;SOR=Inf;LSEQ=TCCATTCAATGATGATTCCA;RSEQ=TTGAGTTCATTCGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:17.1:1:30.3:1:1:0:38:18:1:0:1.2 0/1:7:2:1,1:5,0:0.2857:0,2:21.5:1:30:1:0.28571:0:30:4:0.2857:0:5.5 -16 46404531 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TGAGTTCATTCGATGATTCT;RSEQ=TTCGATTCCGTTCGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:0:2,0:26.1:1:29.6:1:1:0:39.4:20:1:0:1.1 0/1:15:2:1,1:9,4:0.1333:2,2:43.5:1:31:1:1:2.12136:30:4:0.1333:0:5.5 -16 46404536 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=TCATTCGATGATTCTATTCG;RSEQ=TTCCGTTCGATGGTGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:0:2,0:29.1:1:31.1:1:1:0:39.4:20:1:0:1.1 0/1:16:2:1,1:10,4:0.125:2,2:38:1:30:1:1:2.34522:48:4:0.125:0:1 -16 46404541 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12644;SOR=0;LSEQ=CGATGATTCTATTCGATTCC;RSEQ=TTCGATGGTGATTCAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:5,4:0.1818:2,0:44.5:1:30.5:1:0.49091:0:36:4:0.1818:0:4.5 0/0:19:0:0,0:13,6:0:2,0:24.7:1:29.3:1:1:0:42.1:18:1:0:1.5 -16 46404545 . G T 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09804;SOR=0;LSEQ=GATTCTATTCGATTCCGTTC;RSEQ=ATGGTGATTCAATTCTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:6,3:0.1818:2,0:45:1:30.5:1:1:0:36:4:0.1818:0:4.5 0/0:23:0:0,0:15,8:0:2,0:22.8:1:30.1:1:1:0:41.2:46:1:0:1.3 -16 46404551 . G T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCGATTCCGTTCGATGGT;RSEQ=ATTCAATTCTATTATATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:30.6:1:32.1:1:1:0:37.6:24:1:0:1 0/1:26:2:1,1:16,8:0.0769:2,2:37.5:1:30:1:1:1.94371:30:4:0.08:0:5.5 -16 46404562 . A C 105 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30392;SOR=2.39086;LSEQ=TTCGATGGTGATTCAATTCT;RSEQ=TTATATTGGATGATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:7,4:0.2143:2,2:25.3:1:29.3:1:1:1.13:33:6:0.2143:0:4 0/1:25:10:6,4:10,5:0.4:2,2:32.4:1:31.8:1:1:1.31789:36.8:20:0.4348:0:2.5 -16 46404569 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11098;SOR=0;LSEQ=GTGATTCAATTCTATTATAT;RSEQ=GGATGATTCCACTCGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:8,4:0.1429:2,2:24.5:1:28:1:1:1.89743:27:4:0.1429:0:1 0/0:27:0:0,0:18,9:0:2,0:30.4:1:30:1:1:0:39.9:54:1:0:1.4 -16 46404579 . C G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10569;SOR=0;LSEQ=TCTATTATATTGGATGATTC;RSEQ=ACTCGATTCCATTTGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:8,4:0.1429:2,2:17.5:1:29:1:1:1.89743:27:4:0.1429:0:3.5 0/0:28:0:0,0:18,10:0:2,0:29.5:1:30.8:1:1:0:39.4:56:1:0:1.4 -16 46404581 . C G 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2802;SOR=Inf;LSEQ=TATTATATTGGATGATTCCA;RSEQ=TCGATTCCATTTGATGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:25.3:1:31.2:1:1:0:37.5:30:1:0:1.1 0/1:28:4:2,2:16,8:0.1429:2,2:29.3:1:30.5:1:0.60147:1.94808:36.3:8:0.1481:0:2 -16 46404645 . A C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67307;SOR=1.56399;LSEQ=ATCCTTTAGATTCTACTCGA;RSEQ=GATGATTCCATTCGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:0,4:0.5556:0,2:25:1:30.4:1:0.44444:0:35.2:10:0.5556:0:1 1/0:12:8:3,5:1,3:0.6667:2,2:19.5:1:29.6:1:1:1.72:30.6:16:0.6667:0:1.5 -16 46404686 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=TTCGATGATACCATTCAATT;RSEQ=CATTCGTTGATGCTTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:27.4:1:32.4:1:1:0:34.8:10:1:0:0.6 0/1:7:2:0,2:0,5:0.2857:0,0:28.5:1:31:0:1:0:32.5:4:0.2857:0:2 -16 46404870 . C T 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGATTCCATTCGATTCTA;RSEQ=TCGAAAATGATTCCATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:29.5:1:31:1:1:0:31.5:4:0.6667:0:1.5 1/1:1:1:1,0:0,0:1:0,0:17:0:32:0:1:0:23:2:1:0:2 -16 46404902 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.10145;SOR=Inf;LSEQ=TCCATTTGAATCCATTTGAT;RSEQ=ATGATTCCATTAGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:0:2,0:13.8:1:31.3:1:1:0:48.1:32:1:0:1.5 0/1:8:2:1,1:6,0:0.25:0,2:11.5:1:26.5:1:0.25:0:60:4:0.25:0:2.5 -16 46404938 . A G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.32452;LSEQ=TCCATTTGATGATTCCATTC;RSEQ=ATTCCATTCGACGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:18:9,9:0,1:0.9474:0,2:35.8:1:30.8:1:1:0:47.6:36:0.9474:0:1.8 1/1:25:24:15,9:1,0:0.96:0,2:25:1:30.3:1:1:0:47:48:0.96:0:1.8 -16 46404943 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17143;SOR=0;LSEQ=TTGATGATTCCATTCAATTC;RSEQ=ATTCGACGATGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:32:1:29.5:1:1:1.11:60:4:0.0952:0:2 0/0:29:0:0,0:19,10:0:2,0:24.1:1:31:1:1:0:47.7:58:1:0:1.7 -16 46404947 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16471;SOR=0;LSEQ=TGATTCCATTCAATTCCATT;RSEQ=GACGATGATTCCATTCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:8,11:0.0952:2,0:46.5:1:32:0:0.21429:0:26:4:0.0952:0:3.5 0/0:30:0:0,0:19,11:0:2,0:25.3:1:30.5:1:1:0:47.9:60:1:0:1.6 -16 46404970 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11494;SOR=0;LSEQ=CGATGATTCCATTCGATTCC;RSEQ=TTTGATGATTCCATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:7,11:0.1:2,0:25:1:32:0:0.18947:0:26:4:0.1:0:3.5 0/0:38:0:0,0:21,17:0:2,0:26.5:1:30.1:1:1:0:48.4:76:1:0:1.4 -16 46404987 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.07137;SOR=0;LSEQ=TCCGTTTGATGATTCCATTC;RSEQ=ATTCTATTCGATGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:4,8:0.1429:2,2:28.5:1:31.5:1:1:1.90:55:4:0.1429:0:2.5 0/0:37:0:0,0:19,18:0:2,0:27.9:1:29.4:1:1:0:47:74:1:0:1.3 -16 46404996 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCTATTCTATT;RSEQ=GATGATGATTCCATTCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:3,9:0:2,0:13.8:1:30.4:1:1:0:44.3:24:1:0:1.5 0/1:39:2:1,1:17,18:0.0513:2,2:24:0:32:0:1:1.06:46.5:4:0.0526:0:1.5 -16 46405022 . T C 116 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83805;LSEQ=TGATTCCATTCGATTCCATT;RSEQ=GATGATGATTGGATTCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:9:1:31.3:1:1:1.7321:42.3:6:0.6:0:2 1/0:27:15:5,10:4,7:0.5556:2,2:23.1:1:29.9:1:1:1.13698:42.1:30:0.5556:0:1.3 -16 46405034 . G A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTTGATGATGATTG;RSEQ=ATTCGATTCCATTTGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:25.5:1:31.5:1:1:0:33:8:1:0:1.5 0/1:26:2:1,1:10,13:0.0769:2,2:31:0:29.5:1:1:1.29:45:4:0.0769:0:6 -16 46405048 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTGGATTCGATTCCATT;RSEQ=GATGATTTCATTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:24:1:30.8:1:1:0:33.7:12:1:0:1.3 0/1:23:2:1,1:7,12:0.087:2,2:44:0:31.5:1:1:1.67:45:4:0.087:0:6 -16 46405057 . C T 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54163;SOR=Inf;LSEQ=TCGATTCCATTTGATGATTT;RSEQ=ATTTGATTCCATTCGTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:0:2,0:18.3:1:31.5:1:1:0:33.8:20:1:0:1.5 0/1:25:3:1,2:8,14:0.12:2,2:23.7:1:28:1:1:1.13689:44.3:6:0.12:0:5 -16 46405065 . T C 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.58287;LSEQ=ATTTGATGATTTCATTTGAT;RSEQ=CCATTCGTTAATGATTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:6,4:0.0909:2,0:17:0:33:0:1:0:24:2:0.0909:0:3 0/1:29:4:2,2:9,16:0.1379:2,2:8.5:1:30.5:1:0.62208:1.74:44:8:0.1379:0:1.3 -16 46405068 . A T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80493;LSEQ=TGATGATTTCATTTGATTCC;RSEQ=TTCGTTAATGATTTCGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:6,4:0.0909:2,0:34:0:33:0:1:0:40:2:0.0909:0:1 0/1:27:2:1,1:10,15:0.0741:2,2:11.5:1:28.5:1:1:1.48:44:4:0.0741:0:2.5 -16 46405071 . C T 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTTCATTTGATTCCATT;RSEQ=GTTAATGATTTCGATCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:25.1:1:30.9:1:1:0:34.9:22:1:0:1.5 0/1:27:2:1,1:9,15:0.0741:2,2:21:0:32:0:1:1.63:45:4:0.0769:0:6 -16 46405073 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTCATTTGATTCCATTCG;RSEQ=TAATGATTTCGATCAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:26:1:30.3:1:1:0:34.9:22:1:0:1.5 0/1:26:2:1,1:9,15:0.0769:2,2:19:0:31.5:1:1:1.63:45:4:0.0769:0:6 -16 46405075 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54386;SOR=Inf;LSEQ=TTCATTTGATTCCATTCGTT;RSEQ=ATGATTTCGATCAATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:0:2,0:23:1:29.1:1:1:0:35.1:26:1:0:1.5 0/1:26:2:1,1:9,15:0.0769:2,2:17:0:33.5:1:1:1.63:45:4:0.0769:0:6 -16 46405077 . T G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12945;SOR=0;LSEQ=CATTTGATTCCATTCGTTAA;RSEQ=GATTTCGATCAATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:30:1:33:0:1:1.36624:41:4:0.1429:0:2 0/0:24:0:0,0:9,15:0:2,0:23.9:1:30.3:1:1:0:43.5:48:1:0:1.5 -16 46405090 . T C 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54196;SOR=0.27091;LSEQ=TCGTTAATGATTTCGATCAA;RSEQ=TCCATTCGATGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:10.5:1:31:1:1:1.36624:25:4:0.1429:0:2.5 0/1:24:1:0,1:10,13:0.0417:2,0:11:0:34:0:1:0:49:2:0.0435:0:2 -16 46405097 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28876;SOR=0.25972;LSEQ=TGATTTCGATCAATTCCATT;RSEQ=GATGATTCCATTCGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:43.5:1:30.5:1:1:1.36624:41:4:0.1429:0:2 0/1:25:1:1,0:11,13:0.04:2,0:4:0:28:0:0.48:0:42:2:0.04:0:2 -16 46405098 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53333;SOR=Inf;LSEQ=GATTTCGATCAATTCCATTC;RSEQ=ATGATTCCATTCGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:32.5:1:30.6:1:1:0:36.1:28:1:0:1.7 0/1:26:2:1,1:12,12:0.0769:2,2:44:1:30.5:1:1:1:43:4:0.0769:0:1 -16 46405110 . C T 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64481;SOR=2.22138;LSEQ=TTCCATTCGATGATTCCATT;RSEQ=GATTCCATTCGATAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:8,5:0.0714:2,0:35:0:32:0:0.42857:0:25:2:0.0714:0:3 0/1:27:4:2,2:12,11:0.1481:2,2:45.3:1:30.8:1:1:1.08739:45:8:0.1481:0:2.3 -16 46405116 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=TCGATGATTCCATTCGATTC;RSEQ=ATTCGATAATGATTACATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:29.9:1:31.4:1:1:0:36.8:30:1:0:1.7 0/1:28:2:1,1:13,13:0.0714:2,2:28.5:1:30.5:1:1:1:52:4:0.0714:0:2.5 -16 46405117 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11628;SOR=0;LSEQ=CGATGATTCCATTCGATTCC;RSEQ=TTCGATAATGATTACATCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:0.1333:2,2:27:1:30:1:1:1.54914:43:4:0.1333:0:2 0/0:28:0:0,0:14,14:0:2,0:26.8:1:30:1:1:0:41.6:56:1:0:1.2 -16 46405146 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11099;SOR=0;LSEQ=TGATTACATCCGAGTCCATT;RSEQ=GATGATTCCATTTGAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:11:1:31.5:1:1:1.55:43:4:0.1333:0:1.5 0/0:29:0:0,0:15,14:0:2,0:24.2:1:30.3:1:1:0:42.7:28:1:0:1.6 -16 46405156 . A C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.83745;LSEQ=CGAGTCCATTCGATGATTCC;RSEQ=TTTGAGCCTGTTCGATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:3,3:1,4:0.5455:2,2:36.7:1:32.5:1:0.54545:3.52:36.3:12:0.5455:0:2 1/0:26:13:5,8:7,6:0.5:2,2:24.8:1:30.5:1:0.6951:1.82171:44:26:0.5:0:1.9 -16 46405159 . T G 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15675;SOR=Inf;LSEQ=GTCCATTCGATGATTCCATT;RSEQ=GAGCCTGTTCGATAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:28.2:1:30.1:1:1:0:35.1:22:1:0:1.8 0/1:24:5:3,2:7,12:0.2083:2,2:32:1:31.4:1:0.61462:2.47:42.2:10:0.2083:0:2.2 -16 46405165 . T C 29 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09677;SOR=0;LSEQ=TCGATGATTCCATTTGAGCC;RSEQ=GTTCGATAATTCCATTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:4,4:0.2:2,0:25:1:29.5:1:0.46667:0:25:4:0.2:0:2 0/0:21:0:0,0:10,11:0:2,0:29:1:30.5:1:1:0:41.4:42:1:0:1.8 -16 46405191 . T C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23798;LSEQ=ATAATTCCATTTGAGTCCAA;RSEQ=CAATGATTCCATTCATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:0,1:0.8571:0,2:24:1:31.3:1:1:0:32.7:12:0.8571:0:1.8 1/1:17:15:7,8:1,1:0.8824:2,2:22.9:1:30.5:1:1:1.13389:40.4:30:0.8824:0:2 -16 46405810 . G C 95 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCCATTCGATTCCATAC;RSEQ=ATGATGATTCCATTCGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:33.8:1:33:0:1:0:23.3:8:1:0:1.3 1/1:10:8:7,1:1,1:0.8:2,2:16.3:1:31.9:1:0.37778:5.29:23:16:0.8:0:1.5 -16 46405838 . T C 29 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08276;SOR=0;LSEQ=TTCCATTCGAGTCCATTCAA;RSEQ=GGTGATTCCATTCAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:15.5:1:29.5:1:1:1.29098:23:4:0.2222:0:2 0/0:21:0:0,0:13,8:0:2,0:20.9:1:30:1:1:0:28.4:42:1:0:0.9 -16 46405869 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08571;SOR=0;LSEQ=TTCAATTCCATTCGATGATT;RSEQ=CTTTCGATTCCATTCGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:33.5:1:29.5:1:1:1.55:45.5:4:0.1333:0:2 0/0:35:0:0,0:19,16:0:2,0:24.9:1:29.3:1:1:0:33.9:16.5:1:0:1 -16 46405873 . T C 84 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16887;SOR=Inf;LSEQ=ATTCCATTCGATGATTCCTT;RSEQ=CGATTCCATTCGATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:27.5:1:29.2:1:1:0:36.6:28:1:0:1.2 0/1:36:7:4,3:15,14:0.1944:2,2:28.3:1:30:1:1:1.24:22:14:0.1944:0:1.9 -16 46405874 . C T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02469;SOR=0.22127;LSEQ=TTCCATTCGATGATTCCTTT;RSEQ=GATTCCATTCGATGATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:3,6:2,3:0.6429:2,2:33.2:1:29:1:1:1.30579:38.7:18:0.6429:0:1.6 0/1:36:10:5,5:14,12:0.2778:2,2:25.4:1:28.8:1:1:1.16167:37.3:20:0.2857:0:1.3 -16 46405885 . G A 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07216;SOR=0;LSEQ=GATTCCTTTCGATTCCATTC;RSEQ=ATGATGATGGCATTCGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:0.1538:2,2:23:1:32:0:1:2.45:47:4:0.1538:0:1 0/0:34:0:0,0:17,17:0:2,0:31.8:1:29.2:1:1:0:35.6:33:1:0:1 -16 46405934 . A C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCCTTTGATTCCATTC;RSEQ=AAGGTGATTTCATTCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:22.7:1:31:1:1:0:40:14:1:0:1 0/1:21:2:1,1:7,12:0.0952:2,2:8:0:32:0:1:1.67:50.5:4:0.0952:0:1.5 -16 46406105 . A T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGATTCCATTCAAATCCAT;RSEQ=CGATAATTCAATTCAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:7:0:31:0:1:0:25:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:21:1:31.5:1:1:0:33.5:4:1:0:3.5 -16 46406130 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AATTCAATTCAAGTCCATTC;RSEQ=ATGATGATTCCAATCGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:31.5:1:1:0:25:4:1:0:2.5 0/0:2:0:0,0:1,1:0:2,0:42.5:1:30.5:1:1:0:33.5:4:1:0:3.5 -16 46406159 . T G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAATCGAATCCATTCAAA;RSEQ=ATTCCATTCAGTTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31.5:1:1:0:25:4:1:0:2.5 1/1:2:2:1,1:0,0:1:0,2:26:1:30:1:1:0:33.5:4:1:0:3.5 -16 46406255 . T A 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52273;SOR=0.28305;LSEQ=CATTCGATTCCATGTGATGA;RSEQ=TCCATTCAATTCTATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:38.5:1:30.5:1:1:1.7321:23:4:0.4:0:2 0/1:7:1:1,0:3,3:0.1429:2,0:47:0:31:0:1:0:25:2:0.1429:0:2 -16 46406281 . T G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=TCAATTCTATTCAATGATGT;RSEQ=TCCATTTGATTCCATTCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:25.2:1:29.6:1:1:0:25:10:1:0:1.4 0/1:8:2:1,1:2,3:0.25:2,2:28.5:1:30.5:1:1:1.41:47:4:0.25:0:2 -16 46406298 . C G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGTTTCCATTTGATTCCATT;RSEQ=GACCATGATTGCCTTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:15:0:32:0:1:0:23:2:0.25:0:2 0/1:8:2:1,1:2,4:0.25:2,2:14.5:1:29.5:1:1:1.83:25:4:0.25:0:3 -16 46406304 . T C 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=CATTTGATTCCATTCGACCA;RSEQ=GATTGCCTTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:16.8:1:30.8:1:1:0:25.5:8:1:0:1.3 0/1:8:2:1,1:2,4:0.25:2,2:5.5:1:28.5:1:1:1.83:47:4:0.25:0:2 -16 46406344 . T G 59 d7;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24242;SOR=0.1553;LSEQ=CAATGATTCCATTCGGTTCC;RSEQ=TTTGATGATGATTCCGTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:0.8:0,2:11.5:1:29.8:1:1:0:24.8:8:0.8:0:1 0/1:6:2:2,0:2,1:0.3333:2,0:4:1:30.5:1:1:0:23:4:0.3333:0:1 -16 46406499 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=TTCGATTCCATTCGATGTTG;RSEQ=TTCTGTTCAAATCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:19.1:1:28.8:1:1:0:36.8:9:1:0:0.8 0/1:11:2:1,1:4,5:0.1818:2,2:16.5:1:29:1:1:1.22:24:4:0.1818:0:1 -16 46406542 . A T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19481;SOR=0;LSEQ=ATTCCACTCGATTCCATTCG;RSEQ=TGACTCCATTTGATCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:4,4:0.2:2,0:35:1:32:0:0.46667:0:23.5:4:0.2222:0:2 0/0:12:0:0,0:4,8:0:2,0:31.3:1:29.3:1:1:0:29.7:24:1:0:0.7 -16 46406544 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48052;SOR=Inf;LSEQ=TCCACTCGATTCCATTCGAT;RSEQ=ACTCCATTTGATCCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:36.9:1:32.2:1:1:0:39.3:20:1:0:0.8 0/1:12:2:1,1:3,7:0.1667:2,2:29.5:1:29:1:1:2.16:24:4:0.1667:0:1 -16 46406598 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=ATTCCCTTTGATGATCATTC;RSEQ=ATTTGATTCAATTCGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:17.3:1:31.7:1:1:0:45:6:1:0:1.3 0/1:6:2:0,2:1,3:0.3333:2,0:13.5:1:30:0:1:0:35.5:4:0.3333:0:1 -16 46406612 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=TCATTCCATTTGATTCAATT;RSEQ=GGTGATTTCATTGGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:22:1:28.7:1:1:0:45:6:1:0:1.3 0/1:5:2:1,1:1,2:0.4:2,2:30:1:27:0:1:1.73:43:4:0.4:0:3 -16 46406656 . CC TT 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=AGTGATGTTTCCATTCGACT;RSEQ=ATTCGATGATGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:25.3:1:31.3:1:1:0:38:8:1:0:1.8 0/1:5:2:1,1:1,2:0.4:2,2:32:0:31:0:1:1.73:40:4:0.4:0:3.5 -16 46406662 . G C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GTTTCCATTCGACTCCATTC;RSEQ=ATGATGATTCCATTCGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:25.3:1:31:1:1:0:38:8:1:0:1.8 1/0:4:2:1,1:1,1:0.5:2,2:37:0:32.5:1:1:1:40:4:0.5:0:3.5 -16 46406682 . C A 27 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GATGATGATTCCATTCGACT;RSEQ=CATTCGATTATGATTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:26.5:1:27.5:1:1:1:43.5:4:0.5:0:2 0/0:4:0:0,0:2,2:0:2,0:28.5:1:30:1:1:0:47.5:8:1:0:1.8 -16 46406845 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGAGTCCATTTGATGATT;RSEQ=CATTCAATTCCATTCTCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:36.4:1:32:1:1:0:29.4:20:1:0:1.4 0/1:23:2:1,1:13,8:0.087:2,2:29:1:29.5:1:1:1.58984:27:4:0.087:0:1.5 -16 46406855 . CC AA 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09697;LSEQ=TTTGATGATTCCATTCAATT;RSEQ=ATTCTCCGATGATTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:6,5:0.0833:2,0:35:0:30:0:1:0:25:2:0.0833:0:2 0/1:22:2:1,1:12,8:0.0909:2,2:30.5:1:28:1:1:1.47192:27:4:0.0909:0:2 -16 46406859 . T A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.44957;SOR=0.46684;LSEQ=ATGATTCCATTCAATTCCAT;RSEQ=CTCCGATGATTTCTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:6,4:1,1:0.8333:2,2:29.8:1:28.4:1:1:1.45:29.4:20:0.8333:0:1.2 1/0:23:16:10,6:4,3:0.6957:2,2:25.9:1:27.6:1:1:1.24:27:32:0.6957:0:1.3 -16 46406866 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5254;SOR=Inf;LSEQ=CATTCAATTCCATTCTCCGA;RSEQ=GATTTCTTTTGAGCCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:25.8:1:29.9:1:1:0:28.7:26:1:0:1.1 0/1:23:2:1,1:13,8:0.087:2,2:38:1:27.5:1:1:1.58984:25:4:0.0909:0:1 -16 46406942 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49429;SOR=Inf;LSEQ=ATTCGATGAAATTCGATGAT;RSEQ=ATTCCATTCGCTTGCTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:0:2,0:29.5:1:31.9:1:1:0:39.6:64:1:0:0.3 0/1:36:2:1,1:19,15:0.0556:2,2:40:1:28.5:1:1:1.2583:49:4:0.0556:0:1 -16 46406951 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2323;SOR=0;LSEQ=AATTCGATGATGATTCCATT;RSEQ=GCTTGCTTTCGATGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:16,16:0.0588:2,2:18:1:31.5:1:1:1:49:4:0.0588:0:1 0/0:36:0:0,0:20,16:0:2,0:31.5:1:30.4:1:1:0:40.4:72:1:0:0.6 -16 46406958 . T G 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.61558;SOR=2.96148;LSEQ=TGATGATTCCATTCGCTTGC;RSEQ=TTCGATGATGATTCCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:0,1:18,18:0.0263:2,0:36:0:30:0:1:0:49:2:0.0263:0:1 0/1:40:3:2,1:20,15:0.075:2,2:34.3:1:31:1:1:1.48:29.7:6:0.0769:0:1.7 -16 46407013 . T G 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20442;SOR=4.6263;LSEQ=TTCTATTCAATTACATTCCA;RSEQ=GACGATTCCGTTCGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:7,13:0.0476:2,0:13:0:27:0:0.38095:0:24:2:0.0476:0:1 0/1:26:5:2,3:6,15:0.1923:2,2:37:1:30.4:1:0.62785:1.63:35.4:10:0.1923:0:1 -16 46407100 . T A 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTCGATGATTCCATTCG;RSEQ=TCTCATTCGATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:25:1:32.7:1:1:0:23.7:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 46407336 . A T 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATTCCATTCGTTGATGA;RSEQ=TTCATTCGGTTCCATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:13.5:1:30:1:1:0:30.5:4:1:0:2.5 1/1:1:1:1,0:0,0:1:0,0:22:0:32:0:1:0:22:2:1:0:1 -16 46407361 . T A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGGTTCCATTCAATGATG;RSEQ=TTCCATTCAATTCCTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1:0,2:23.6:1:30.3:1:1:0:42.9:14:1:0:1.4 1/1:4:4:3,1:0,0:1:0,2:9:1:28.8:1:1:0:40.8:8:1:0:1 -16 46407397 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21169;SOR=0;LSEQ=TTCAATGTTTCCATTCAATT;RSEQ=CATACGATGATGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:0.1333:2,2:28:1:31:1:1:1.1547:48.5:4:0.1333:0:2.5 0/0:17:0:0,0:10,7:0:2,0:28.4:1:30.9:1:1:0:45.4:34:1:0:0.5 -16 46407410 . A C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.20168;SOR=0;LSEQ=TTCAATTCCATACGATGATG;RSEQ=TTCCATTTGATTTGATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:0.125:2,2:41:1:32:1:1:1.30929:48.5:4:0.1667:0:2.5 0/0:19:0:0,0:11,8:0:2,0:32.4:1:29.5:1:1:0:43:38:1:0:0.5 -16 46407431 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18018;SOR=0;LSEQ=TTCCATTTGATTTGATTCGA;RSEQ=AGTGAGCCATTCGATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:22:1:26:1:1:1:37:4:0.125:0:2 0/0:21:0:0,0:11,10:0:2,0:27.1:1:31.1:1:1:0:42:42:1:0:0.5 -16 46407438 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50925;SOR=Inf;LSEQ=TGATTTGATTCGACAGTGAG;RSEQ=CATTCGATTCAATTCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:25.4:1:30.5:1:1:0:43.1:14:1:0:1.1 0/1:23:2:1,1:10,11:0.087:2,2:6.5:1:28:1:1:1.10:50.5:4:0.087:0:1.5 -16 46407475 . A C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.659;LSEQ=ATGATGATTCTATTTGATTC;RSEQ=ATTGGTTGACATTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:1,5:0.1429:2,0:11:0:33:0:1:0:40:2:0.1429:0:2 0/1:9:2:0,2:2,5:0.2222:2,0:30.5:1:33.5:1:1:0:40:4:0.2222:0:1 -16 46407476 . A C 32 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55;SOR=0.33678;LSEQ=TGATGATTCTATTTGATTCA;RSEQ=TTGGTTGACATTTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:0,5:0.2857:0,2:34:1:32:1:0.28571:0:24:4:0.2857:0:2 0/1:9:1:0,1:2,6:0.1111:2,0:44:0:34:0:1:0:40:2:0.1111:0:1 -16 46407479 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TGATTCTATTTGATTCAATT;RSEQ=GTTGACATTTCCATTCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:20.6:1:32:1:1:0:32.7:14:1:0:1.1 0/1:8:2:1,1:0,6:0.25:0,2:38:1:29.5:1:0.25:0:24:4:0.25:0:1 -16 46407482 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=TTCTATTTGATTCAATTGGT;RSEQ=GACATTTCCATTCGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:5:1:32:0:1:0:32:4:0.2857:0:1.5 0/0:8:0:0,0:1,7:0:2,0:30.3:1:31.4:1:1:0:30.3:16:1:0:0.6 -16 46407497 . A G 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=TTGGTTGACATTTCCATTCG;RSEQ=TTCCATTCGATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:28.5:1:32.5:1:1:0:24:4:0.6667:0:2 0/0:6:0:0,0:1,5:0:2,0:22.2:1:31.5:1:1:0:29.2:12:1:0:0.7 -16 46407698 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATGATGATCCCATTCGAG;RSEQ=CCATTCAGTGATTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:27.7:1:28.3:1:1:0:36.7:18:1:0:0.9 0/1:43:2:1,1:23,18:0.0465:2,2:31.5:1:32.5:1:1:1.27044:46:4:0.0465:0:1 -16 46407719 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCAGTGATTCCATTCG;RSEQ=TTCCATTCCATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:32.8:1:28.9:1:1:0:39.5:16:1:0:1.1 0/1:50:2:1,1:24,24:0.04:2,2:26.5:1:28:1:1:1:41:4:0.04:0:5.5 -16 46407723 . C T 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.31095;SOR=Inf;LSEQ=TCAGTGATTCCATTCGTTTC;RSEQ=ATTCCATGATGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:0:2,0:29.9:1:31.2:1:1:0:38.6:36:1:0:1.1 0/1:47:5:3,2:19,21:0.1064:2,2:23.2:1:30.6:1:0.66515:1.64:41.2:10:0.1064:0:1.6 -16 46407728 . C G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GATTCCATTCGTTTCCATTC;RSEQ=ATGATGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:0:2,0:27.7:1:29.6:1:1:0:38.6:8:1:0:1.1 0/1:44:2:1,1:18,22:0.0455:2,2:26.5:1:29:1:1:1.22:41:4:0.0455:0:5.5 -16 46407732 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CCATTCGTTTCCATTCCATG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:25.7:1:29.8:1:1:0:37.2:17:1:0:1.2 0/1:45:2:1,1:19,24:0.0444:2,2:32.5:1:32:1:1:1.26:47.5:4:0.0444:0:1.5 -16 46407735 . A ATTCCT 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGTTTCCATTCCATGATG;RSEQ=TTCCATTCCATTCCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:24.4:1:29.4:1:1:0:37.2:17:1:0:1.2 0/1:40:2:1,1:16,22:0.05:2,2:24.5:1:28.7:1:1:1.36:41:4:0.0513:0.025:5.5 -16 46407744 . C G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATGATGATTCCATTC;RSEQ=ATTCCATTCAATGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:0:2,0:20.4:1:29.2:1:1:0:38.1:7.5:1:0:1.2 0/1:38:2:1,1:14,22:0.0526:2,2:10.5:1:27.5:1:1:1.55:44:4:0.0526:0:2 -16 46407745 . A T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.0391;SOR=0.23688;LSEQ=TTCCATGATGATTCCATTCC;RSEQ=TTCCATTCAATGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:5,8:1,2:0.8125:2,2:21.9:1:30.5:1:1:1.23:36.9:26:0.8667:0:1.6 1/0:38:19:7,12:8,11:0.5:2,2:25.5:1:31.1:1:1:1.23952:37.5:38:0.5135:0:1.3 -16 46407755 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCA;RSEQ=TGATTCCATTCGATTCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:25.2:1:30.4:1:1:0:32.5:20:1:0:1.1 0/1:29:2:0,2:10,16:0.069:2,0:17:1:33:0:0.52381:0:24:4:0.069:0:2 -16 46407937 . G T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=0.23036;LSEQ=TCCATTCAATGATTCCATTC;RSEQ=ATTCCAATCGATGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:26.7:1:31.3:1:1:0:25.7:6:0.75:0:1.3 0/1:8:3:3,0:3,1:0.375:2,0:29.3:1:30.7:1:1:0:23.7:6:0.375:0:1.3 -16 46407964 . A T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATCGATGATGATTCCATTAG;RSEQ=GTCCATTTAATGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:26.3:1:30.8:1:1:0:26.8:8:1:0:1.3 0/1:11:2:1,1:7,2:0.1818:2,2:33.5:1:29:1:0.49091:3.05504:24:4:0.1818:0:1.5 -16 46407977 . A T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTAGAGTCCATTTAATG;RSEQ=TTCCATTTGATTCCAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:28.8:1:29.5:1:1:0:25.3:8:1:0:1.3 0/1:12:2:1,1:6,4:0.1667:2,2:28:1:28:1:1:1.4491:24:4:0.1667:0:1.5 -16 46408060 . C T 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22183;LSEQ=CATATGATGATGATTCCATT;RSEQ=GATTCCATTCGATGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:30.5:1:30:1:1:0:23.5:4:0.6667:0:2 1/0:7:5:0,5:1,1:0.7143:2,0:18:1:31.4:1:0.28571:0:23.4:10:0.8333:0:1.6 -16 46408072 . A G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.41418;LSEQ=ATTCCATTCGATTCCATTCG;RSEQ=TGATTCCATTCTATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:39:0:33:0:1:0:23:2:0.5:0:3 1/0:5:3:0,3:1,1:0.6:2,0:13.3:1:32.7:1:0.4:0:23.3:6:0.6:0:2 -16 46408345 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCACTCGATTCCACTTGAC;RSEQ=TTGATTCCATTCGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:0:2,0:14.7:1:30.3:1:1:0:31.8:20:1:0:0.4 0/1:24:2:1,1:17,5:0.0833:2,2:22:1:31:1:0.44565:3.19373:40:4:0.0833:0:1 -16 46408354 . A C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTCCACTTGACATTGATTCC;RSEQ=TTCGATTCCATTCAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:8,4:0.0769:2,0:17:0:33:0:1:0:22:2:0.0769:0:2 0/1:26:2:2,0:17,7:0.0769:2,0:14:1:31:1:1:0:23.5:4:0.0769:0:1 -16 46408395 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.10606;SOR=0;LSEQ=CCATTTGATTCCAGTGGATG;RSEQ=TGATTGCCATCGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:31:1:30:0:1:1.55:25:4:0.1333:0:2 0/0:30:0:0,0:17,13:0:2,0:27.9:1:28.4:1:1:0:29.9:60:1:0:0.5 -16 46408404 . A G 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54017;SOR=Inf;LSEQ=TCCAGTGGATGATGATTGCC;RSEQ=TCGATTCCATTCGATCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,9:0:2,0:36.3:1:31.1:1:1:0:32.6:30:1:0:0.5 0/1:29:3:2,1:12,14:0.1034:2,2:41.7:1:29:1:0.5977:2.27:26.7:6:0.1034:0:2.7 -16 46408416 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13289;SOR=0;LSEQ=TGATTGCCATCGATTCCATT;RSEQ=GATCACTCCATTCTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:5,9:0.125:2,2:42.5:1:30:1:1:1.73:25:4:0.125:0:2 0/0:27:0:0,0:10,17:0:2,0:25.4:1:29.4:1:1:0:27.8:54:1:0:0.6 -16 46408431 . A G 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28435;SOR=Inf;LSEQ=CCATTCGATCACTCCATTCT;RSEQ=TTCCATTTGATGATGATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:23.8:1:29.7:1:1:0:30.3:26:1:0:0.5 0/1:27:4:2,2:7,16:0.1481:2,2:15.3:1:30:1:0.58154:2.21:25.5:8:0.1538:0:2.3 -16 46408603 . C A 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGATTCCATTTGATTCC;RSEQ=TTTGATTATGATTCTACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:32.7:1:31.3:1:1:0:28.7:6:1:0:2.7 1/1:5:5:5,0:0,0:1:0,0:42.8:1:29.8:1:1:0:25.2:10:1:0:2.6 -16 46408609 . TT AA 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTCCATTTGATTCCCTTTGA;RSEQ=ATGATTCTACTAGAGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:2,0:0.3333:0,0:45:0:32:0:0.33333:0:22:2:0.3333:0:3 0/1:6:2:2,0:4,0:0.3333:0,0:24.5:1:30:1:1:0:23:4:0.3333:0.1667:2 -16 46408634 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCTACTAGAGTCCATTCA;RSEQ=TGACTCCATTCGAGTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:17.6:1:30.2:1:1:0:31:10:1:0:1.8 0/1:14:2:1,1:7,5:0.1429:2,2:23.5:1:31:1:1:1.36624:27:4:0.1538:0:4 -16 46408642 . A T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52964;SOR=Inf;LSEQ=AGAGTCCATTCAATGACTCC;RSEQ=TTCGAGTCCATTCAACAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:13.7:1:30.6:1:1:0:33:14:1:0:1.9 0/1:17:3:1,2:8,6:0.1765:2,2:16:1:28:1:0.57647:2.51691:29:6:0.1765:0:3.3 -16 46408646 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCAATGACTCCATTC;RSEQ=AGTCCATTCAACAATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:13.6:1:31.3:1:1:0:34.1:16:1:0:1.8 0/1:18:2:1,1:9,7:0.1111:2,2:23.5:1:28:1:1:1.26772:27:4:0.125:0:4 -16 46408650 . C G 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08615;SOR=0;LSEQ=TTCAATGACTCCATTCGAGT;RSEQ=CATTCAACAATTCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:21.5:1:31:1:1:1.83:44.5:4:0.25:0:2.5 0/0:18:0:0,0:10,8:0:2,0:20.2:1:30:1:1:0:31.3:36:1:0:1.7 -16 46408706 . A G 93 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60003;SOR=2.5068;LSEQ=CCATTCGATTCCATTTGATG;RSEQ=TTCCATTCGAGTCCATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:1,2:0.5:2,2:22.3:1:32.3:1:1:1:31:6:0.5:0:1.3 1/0:11:8:3,5:0,3:0.7273:0,2:27.6:1:31.3:1:0.49091:0:26:16:0.7273:0:1.9 -16 46408715 . GAGTCCATTTAATCATTACAGTCT G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=0.18301;SOR=0;LSEQ=TCCATTTGATGATTCCATTC;RSEQ=AGTCCATTTGGTGATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:33.5:1:28.9:1:1:1.83:33:4:0.25:0.25:1 0/0:10:0:0,0:2,8:0:2,0:19.7:1:31.2:1:1:0:26.3:20:1:0:2.1 -16 46430990 . TCATT CC 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATGTGGTCGAATGGAATCA;RSEQ=GAATAGAATCTAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:1:28.3:1:1:0:45:4:1:0:1 -16 46431356 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGAATCATCATTGAATG;RSEQ=AATCGAATGGAATCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:9:1:28.5:1:1:0:21:4:0.5:0:3 -16 46431374 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCGAATGGAATCATC;RSEQ=AATGGACTCGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:27:1:31:1:1:0:21:4:0.5:0:3 -16 46431410 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCATCTTCGAATGGAATC;RSEQ=AATGAAATCACAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:11:2:1,1:5,4:0.1818:2,2:25:1:29:1:1:1.22474:49.5:4:0.1818:0:1.5 -16 46431441 . G A 49 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CAATCGAATGGAATGGAATG;RSEQ=AGTCATCATCTAATGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:9:0:33:0:1:0:25:2:1:0:3 0/1:10:3:1,2:3,4:0.3:2,2:18:1:31.3:1:1:1.44135:40.3:6:0.3:0:2 -16 46432638 . AA GC 88 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.60784;SOR=2.28225;LSEQ=AATCATCATAGAAAGGAATC;RSEQ=AGGGAATCATCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,2:0.4:0,2:45.5:1:30.3:1:1:0:24:4:0.4:0:1 1/0:13:8:4,4:3,2:0.6154:2,2:24.3:1:29.6:1:1:1.45385:35.5:16:0.6154:0:1.4 -16 46432713 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11905;SOR=0;LSEQ=CATCATCGAATGGACTCAAA;RSEQ=GGAATAATCTTCGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,7:0.1:2,2:38.5:1:31:1:1:1.53525:24:4:0.1:0:1 0/0:37:0:0,0:17,20:0:2,0:26.7:1:29.5:1:1:0:37.9:74:1:0:1 -16 46432731 . G A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28732;SOR=Inf;LSEQ=AATGGAATAATCTTCGAAAG;RSEQ=AATCGAATGGAATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:26.2:1:31:1:1:0:35.9:42:1:0:0.6 0/1:39:4:3,1:17,18:0.1026:2,2:35:1:28.8:1:0.60499:3.09:27.3:8:0.1026:0:1.8 -16 46432735 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53815;SOR=Inf;LSEQ=GAATAATCTTCGAAAGGAAT;RSEQ=GAATGGAATCGAATGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:26.7:1:30.4:1:1:0:36.4:44:1:0:0.6 0/1:41:2:1,1:20,18:0.0488:2,2:26.5:1:29:1:1:1.10818:40.5:4:0.0488:0:1.5 -16 46432746 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54167;SOR=Inf;LSEQ=GAAAGGAATCGAATGGAATC;RSEQ=AATGGAACAATCAAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:31.3:1:30.5:1:1:0:36.4:44:1:0:0.7 0/1:42:2:1,1:19,21:0.0476:2,2:18.5:1:28:1:1:1.10:45:4:0.0488:0:2.5 -16 46432752 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53464;SOR=Inf;LSEQ=AATCGAATGGAATCGAATGG;RSEQ=ACAATCAAATGGACTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:31.7:1:30.4:1:1:0:36.4:44:1:0:0.7 0/1:40:2:1,1:17,20:0.05:2,2:12.5:1:29:1:1:1.17:45:4:0.0526:0:2.5 -16 46432776 . A G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23372;SOR=0.46166;LSEQ=ATCAAATGGACTCCAATGGA;RSEQ=TCATCTAATGGAATCGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:4,5:6,9:0.375:2,2:16.2:1:31.8:1:1:1.19:28.9:18:0.375:0:1.3 0/1:28:6:3,3:7,15:0.2143:2,2:19.7:1:30.7:1:0.6345:2.08:38.8:12:0.2143:0:1.2 -16 46432800 . TCATCGAAT AAG 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21169;SOR=Inf;LSEQ=TCTAATGGAATCGAGTGGAA;RSEQ=GGACTCGAATGGAGTCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:6,10:0:2,0:20.1:1:30.4:1:1:0:32.5:32:0.9412:0:0.8 0/1:15:2:1,1:4,9:0.1333:2,2:40:1:28.9:1:1:2.12:23:4:0.1429:0:0 -16 46432814 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=GTGGAATCATCGAATGGACT;RSEQ=GAATGGAGTCATCATCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:2,8:0:2,0:30.5:1:30.5:1:1:0:28.5:20:1:0:1.2 0/1:10:2:1,1:3,5:0.2:2,2:11:1:29.5:1:1:1.58:46:4:0.2:0:1 -16 46432830 . CC GA 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2125;SOR=0;LSEQ=GACTCGAATGGAGTCATCAT;RSEQ=AATGAAATCGGATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:1,5:0.3333:2,2:25.7:1:30.3:1:1:2.24:24:6:0.3333:0:1 0/0:7:0:0,0:1,6:0:2,0:19:1:31.1:1:1:0:27:14:1:0:0.6 -16 46434370 . A C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATCATTGAATGGAATTG;RSEQ=ATGGAATCATCATTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:34:0:27:0:1:0:49:2:1:0:1 0/1:5:2:1,1:2,1:0.4:2,2:8.5:1:30:1:1:1.7321:45.5:4:0.4:0:3 -16 46434384 . TG AA 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GAATTGAATGGAATCATCAT;RSEQ=AATGGAATCGAATGAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:17.7:1:29.7:1:1:0:50.3:6:1:0:0.7 0/1:6:2:1,1:2,2:0.3333:2,2:23.5:1:28:1:1:1:45.5:4:0.3333:0:2 -16 46434425 . G A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81844;LSEQ=ATCAACGAATGGAATCCAAT;RSEQ=TAATCATCATAGAATTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:12:0:32:0:1:0:49:2:0.3333:0:1 0/1:7:2:1,1:2,3:0.2857:2,2:18:1:27.5:1:1:1.41:43:4:0.2857:0:1 -16 46434754 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGAATAGAATCTTCTAA;RSEQ=GGACTCAAGTGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:21.5:1:31.5:1:1:0:32:4:1:0:3.5 -16 46434780 . A C 58 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGTGGAATCATCATCGAA;RSEQ=GCAAGCGAATGGAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:25.5:1:29:1:1:0:33.8:8:1:0:2.5 -16 46434790 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCATCGAAAGCAAGCGAA;RSEQ=GGAATCATCATCGAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:36:1:29.5:1:1:1:43.5:4:0.5:0:2.5 -16 46660683 . G C 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10628;SOR=0;LSEQ=AGGCAAGGATGGCCCCATTG;RSEQ=CACTGCGGTAGTAGCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:3:1,2:137,50:0.0158:2,2:17.3:1:24:1:0.18227:5.42177:53.3:2:0.0109:0:1 0/0:210:0:0,0:150,60:0:2,0:20.9:1:30.5:1:1:0:50.8:41:1:0:0.1 -16 46660689 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62627;SOR=2.66267;LSEQ=GGATGGCCCCATTGGCACTG;RSEQ=GGTAGTAGCTCTGGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:0,1:143,66:0.0048:2,0:1:0:25:0:0.31905:0:60:2:0.0048:0:1 0/1:238:3:1,2:162,73:0.0126:2,2:12:1:30.3:1:0.23431:4.40753:55:6:0.0129:0:1 -16 49346687 . TCGGTGC T 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=2.000;MSILEN=1;SSF=0.08038;SOR=3.82508;LSEQ=TTGCAAACGCAGCGTGGCAC;RSEQ=CGGTGCCGGCATAAAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:3,3:9,6:0.2857:2,2:28.7:1:30.2:1:1:1.47083:60:12:0.2857:0:0.2 1/0:13:8:6,2:3,2:0.6154:2,2:32.5:1:31.8:1:1:1.89:60:16:0.6154:0:0 -16 52085593 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.04722;LSEQ=CTCCTTTTTCTATGGGGAGA;RSEQ=AATTAATATCCAGGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:213:99,114:25,34:0.7831:2,2:25.3:1:31.6:1:0.65816:1.18:60:105.5:0.7815:0:1.1 0/1:311:45:23,22:125,141:0.1447:2,2:27.5:1:31.6:1:0.63148:1.18:60:90:0.1456:0:1 -16 52085683 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20617;SOR=0;LSEQ=GAAACACAGAAGGCTAAGGG;RSEQ=AGACAGGTCTGGTCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:17,68:0.023:2,2:10.5:1:27.5:1:0.37289:3.92:60:4:0.023:0:1.5 0/0:104:0:0,0:25,79:0:2,0:19.6:1:30.6:1:1:0:60:103:1:0:0.3 -16 52473512 . TTGC T 26 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.48986;SOR=0;LSEQ=ATCTGTTGCATCTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:13,9:0.0833:2,2:23:1:26.5:1:1:1.42202:60:4:0.087:0.0417:2 0/0:22:0:0,0:12,10:0:2,0:29.5:1:28.4:1:1:0:60:21:1:0:0.3 -16 55216576 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49057;SOR=Inf;LSEQ=AGGGGAAAGTTGGATATAGA;RSEQ=AGGCATGCACACAGGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:0:2,0:25.4:1:32.4:1:1:0:60:54:1:0:0 0/1:27:2:1,1:18,7:0.0741:2,2:19.5:1:28:1:0.51282:2.47127:60:4:0.0769:0:1 -16 55329102 . T A 54 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTCTTGCCCACACCCCAGG;RSEQ=CTCAGGAACTACCAAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:17.5:1:27:1:1:0:60:3:1:0:1 1/1:1:1:0,1:0,0:1:0,0:8:0:31:0:1:0:60:2:1:0:1 -16 55329374 . C CCTCTCTGTCTCTCTGT 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=3.000;MSILEN=8;SSF=0.00769;SOR=0;LSEQ=AATTAATACCACAATCTCAA;RSEQ=CTCTCTGTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:6,0:14,0:0.2857:1,0:21.8:1:32.3:1:1:0:59:12:0.2857:0.1429:0.2 0/0:23:0:0,0:22,1:0:1,0:23.9:1:31.8:1:1:0:56.6:46:1:0:0.5 -16 55329381 . G GTCTCTCTGTCTCTCTGTC 110 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=16.000;MSILEN=2;SSF=0.00287;SOR=0.07002;LSEQ=ACCACAATCTCAACCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:11,0:17,0:0.3548:1,0:16:1:32:1:1:0:55.5:22:0.3548:0.2581:0.8 0/1:28:1:1,0:11,0:0.0357:0,0:39:0:32.9:0:1:0:40:2:0.0385:0:0 -16 55329465 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51082;SOR=0;LSEQ=TAGTTTTGTGTATTCTGTTT;RSEQ=TGCACCAGGACATTGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:135,12:0.0134:2,2:23:1:31:1:0.16742:10.84885:60:4:0.0137:0:1 0/0:108:0:0,0:92,16:0:2,0:21.2:1:31.9:1:1:0:60:107:1:0:0.2 -16 55329601 . A G 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18496;SOR=1.20082;LSEQ=CATTTACCAGTGAGTTAGGC;RSEQ=TCCGCACTCTTGGGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:516:227:98,129:124,165:0.4399:2,2:26.1:1:31.2:1:1:1.01:60:226:0.4414:0:1.1 0/1:412:200:96,104:91,121:0.4854:2,2:25.1:1:30:1:0.32291:1.23:60:65.667:0.484:0:1.1 -16 55329605 . G A 90 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00654;SOR=11.55364;LSEQ=TACCAGTGAGTTAGGCATCC;RSEQ=CACTCTTGGGAAACAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:1:1,0:211,292:0.002:2,0:13:0:31:0:0.42063:0:60:2:0.002:0:2 0/1:400:9:4,5:174,217:0.0225:2,2:23:1:28.7:1:1:1.0023:60:18:0.0226:0:2 -16 55329657 . G A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26823;SOR=0;LSEQ=TTTAAATGAGCATTAATTAT;RSEQ=TCATTATTAGAAATGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:66,176:0.0122:2,2:27.7:1:27.7:1:0.18724:5.29:60:6:0.0123:0:1.3 0/0:177:0:0,0:55,122:0:2,0:23.2:1:31:1:1:0:60:176:1:0:0.4 -16 56226526 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50175;SOR=Inf;LSEQ=AGCACCATTGTGAAGCAGAT;RSEQ=AAGTAAGTCCCTGTGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:5,18:0:2,0:21.9:1:31.5:1:1:0:60:46:1:0:0.1 0/1:31:2:1,1:15,14:0.0645:2,2:19.5:1:27.5:1:1:1.06901:60:4:0.0667:0:1 -16 56226542 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=AGATGAAGTAAGTCCCTGTG;RSEQ=CATTGGGATTCGTACTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:3,12:0:2,0:28.3:1:32.5:1:1:0:60:30:1:0:0 0/1:28:2:1,1:12,14:0.0714:2,2:22.5:1:28:1:1:1.16:60:4:0.0714:0:1 -16 56781830 . C T 71 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGGTTTCCATTTCCTTA;RSEQ=CTGCTTTGAGTCTGTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:20.4:1:30.8:1:1:0:60:10:1:0:1.2 1/1:1:1:1,0:0,0:1:0,0:3:0:27:0:1:0:60:2:1:0:1 -16 56781965 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08245;SOR=Inf;LSEQ=GTTTTTTCACAGCCTGACTC;RSEQ=TTTTCTCTGTCAGGCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:0:1,0:23.1:1:30.4:1:1:0:60:30:1:0:0.1 0/1:13:2:2,0:11,0:0.1538:0,0:20.5:1:29:1:1:0:60:4:0.1667:0:1.5 -16 56791999 . T G 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAGAAAAAAAAAAAAGT;RSEQ=GGGGGGAGCTTGTGCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:25.3:1:30.3:1:1:0:60:8:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 56832302 . C T 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00088;SOR=0.36714;LSEQ=TGTAGGTAGCATAGTAGATA;RSEQ=CATTATGGTTATTGTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:46:41,5:197,30:0.1685:2,2:21.7:1:30.6:1:0.8112:1.25:60:22:0.1667:0:1 0/1:217:15:13,2:175,27:0.0691:2,2:23.3:1:30.1:1:1:1.00:60:30:0.0701:0:1 -16 56832506 . G A 49 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7223;SOR=0.73057;LSEQ=TGAGGGCAAGAGGGCTGGGC;RSEQ=TGGTGGCTCACATCTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:4:3,1:103,267:0.0107:2,2:11.8:1:24.8:1:0.07064:7.73:60:3:0.0082:0:1.8 0/0:383:3:2,1:121,259:0.0078:2,2:17:1:26.3:1:0.24255:4.26:60:6:0.0079:0:1 -16 56839364 . G GT 88 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.12716;SOR=0.32812;LSEQ=TCTGTTGGGTCTTAAACCAT;RSEQ=TTTTTTTTGTTTTTTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:8:5,3:461,143:0.0131:2,2:20.5:1:29.4:1:0.40391:1.93197:60:16:0.0131:0.0049:0.6 0/0:695:3:2,1:487,205:0.0043:2,2:23.7:1:26.7:1:1:1.18748:60:6:0.0044:0:0 -16 56839439 . C T 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20683;LSEQ=TTCGGCATGGCTGAGGAGTA;RSEQ=CATCGGGAGTCAATGTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1507:296:164,132:654,555:0.1964:2,2:25.9:1:30.5:1:0.69656:1.05:60:97.667:0.1977:0:1.1 0/1:1684:81:45,36:837,762:0.0481:2,2:24.8:1:29.8:1:0.64856:1.14:60:162:0.0487:0:1.1 -16 56852311 . A C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATGTACATTTCCAGAAA;RSEQ=AGTCATTGAGGTATTGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:8,2:0,0:1:0,2:22:1:31.7:1:1:0:60:20:1:0:1.2 1/1:2:2:2,0:0,0:1:0,0:38.5:1:32.5:1:1:0:60:4:1:0:1 -16 56852389 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.29167;SOR=0.53284;LSEQ=ATCTCATGCCTGCTCTCTTC;RSEQ=CATGTGTTCATAGTAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:31:31,0:18,0:0.6327:1,1:24:1:30.6:1:1:0:60:30:0.6383:0:1.1 0/1:21:10:10,0:11,0:0.4762:0,0:31:1:30.2:1:1:0:60:20:0.4762:0:1 -16 56852494 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24927;SOR=0;LSEQ=CACAGCTCTGTTAAAGACAA;RSEQ=AATATGTTTATGATGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:234,30:0.0112:2,2:33.3:1:25:1:0.31046:3.86829:60:2:0.0075:0:1.3 0/0:253:0:0,0:212,41:0:2,0:22.4:1:31.6:1:1:0:60:62.25:1:0:0.1 -16 56852644 . G A 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AACATCGAGATGGCCTATGC;RSEQ=CGGCAAGTGAGTGTGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1134:0:0,0:525,608:0:2,0:24.5:1:30.7:1:1:0:60:58.632:0.9991:0:0.1 0/1:1325:50:23,27:616,656:0.0377:2,2:27.4:1:28.7:1:0.77437:1.10224:60:24:0.0369:0:1.2 -16 56852822 . G T 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00469;SOR=4.30841;LSEQ=GGAGAATTCTATCAAATAGG;RSEQ=TAATAGAATTACTCACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:9:1,8:0,48:0.1579:1,2:28.6:1:31.3:1:0.15789:0:60:18:0.1579:0:1 0/1:31:14:0,14:0,17:0.4516:1,1:16.6:1:30.4:1:1:0:60:28:0.4667:0:1 -16 56855192 . C T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTTCTCCCCCTGGACCC;RSEQ=GCTGCTCCCGTTCCTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:28:1:31.7:1:1:0:60:6:0.3333:0:1 0/0:1:0:0,0:1,0:0:0,0:42:0:30:0:1:0:60:2:1:0:0 -16 56855496 . C G 304 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05875;LSEQ=TGTGCTTCCGTCGCAGAGCT;RSEQ=GATGATAAGGTAGCACCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:808:803:371,432:0,0:0.9938:0,2:25.7:1:31.4:1:1:0:60:99.375:0.9938:0:1.2 1/1:1074:971:444,527:48,53:0.9041:2,2:26:1:30.7:1:0.75367:1.07488:60:137.714:0.9043:0:1.2 -16 56855549 . TC T 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18513;LSEQ=TAGAAACCGGGGTCCAGTGT;RSEQ=CGATGGGCCTAGCAACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:100:30,70:94,259:0.2203:2,2:26.1:1:30.3:1:0.52627:1.18:60:200:0.2242:0.0242:0.7 0/1:524:26:10,16:168,328:0.0496:2,2:22.8:1:29.4:1:0.67311:1.22:60:52:0.0504:0.0057:0.7 -16 56855616 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49883;SOR=0;LSEQ=GACACGCCATTCTGTGGAAT;RSEQ=AAATGTTAACTGTTCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:0,2:2,137:0.0142:1,0:39.5:1:28.5:1:1:0:60:4:0.0143:0:1 0/0:131:0:0,0:3,128:0:1,0:22.8:1:31.4:1:1:0:60:64.5:1:0:0 -16 56862766 . G T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15402;SOR=5.01119;LSEQ=CATGTACTATTTCCTCTTCT;RSEQ=CATTGAGCTTGAAGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:1,0:150,3:0.0065:1,0:34:0:13:0:1:0:60:0:0:0:3 0/1:94:3:3,0:88,3:0.0319:1,0:28.3:1:30.7:1:1:0:60:6:0.0319:0:1 -16 56863072 . C T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACACCCCCAGAGCAGTTGCC;RSEQ=TCAGATGGGCATTTTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:121,409:0:2,0:22.2:1:31.4:1:1:0:60:47.182:1:0:0.1 0/1:543:27:8,19:142,373:0.0497:2,2:26:1:30:1:0.82663:1.11:60:54:0.05:0:1.1 -16 56863215 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00526;SOR=Inf;LSEQ=GGTGATGGTGGACTCAGCTC;RSEQ=GGGTGGAGAAGAGTGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:3,34:0:2,0:23:1:30.3:1:1:0:60:74:1:0:0.2 0/1:22:5:0,5:0,17:0.2273:1,0:27:1:31.2:1:1:0:60:10:0.2273:0:1 -16 56863229 . T C 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07975;SOR=0;LSEQ=CAGCTCCGGGTGGAGAAGAG;RSEQ=GCATGGAGAAGATGTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:0,7:0,25:0.2188:1,0:22.7:1:31.3:1:1:0:60:14:0.2188:0:1 0/0:17:0:0,0:0,17:0:1,0:17.7:1:30.1:1:1:0:60:34:1:0:0.3 -16 56864398 . C T 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=1.7766;LSEQ=CACATATGAAAGCAGTCAGC;RSEQ=TTTCCTTGTTTATTTTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:702:260:192,68:312,129:0.3704:2,2:23.5:1:30.7:1:0.38608:1.17:60:85.667:0.3693:0:1 1/0:765:391:264,127:253,121:0.5111:2,2:23.9:1:30.1:1:1:1.00585:60:47.875:0.5066:0:1.1 -16 56864618 . C T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.02373;LSEQ=GTATGGTGAATGAGGTGGCA;RSEQ=GCCCAGGGGCAGCCATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:122:41,81:281,478:0.1383:2,2:27.8:1:30.2:1:0.4806:1.16117:60:244:0.1402:0:1.1 0/1:871:342:124,218:205,324:0.3927:2,2:25.6:1:29.9:1:0.4748:1.11222:60:170:0.394:0:1.1 -16 56865608 . A G 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55829;SOR=3.33894;LSEQ=AAAGCGATGGTACCGAGGGG;RSEQ=GGGGATGGGGCAGAGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:1,0:135,1:0.0073:1,0:26:0:12:0:1:0:60:0:0:0:2 0/1:83:2:2,0:81,0:0.0241:1,0:16:1:33:0:1:0:60:4:0.0244:0:1 -16 56865686 . C T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06195;SOR=Inf;LSEQ=TATGTGTTTGGGACCTGGGA;RSEQ=GCTTTCAGATGCCCTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:0:0,0:410,71:0:2,0:23.2:1:31.4:1:1:0:60:52.444:1:0:0.1 0/1:493:5:1,4:383,105:0.0101:2,2:10:1:27:1:0.00947:14.48762:60:10:0.0102:0:1 -16 56866054 . A AT 172 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=0.02565;LSEQ=GTTCCTCGTCTCCTGTCCCC;RSEQ=TTTTTTGTTGTGTAATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:49:20,29:88,87:0.2188:2,2:28.3:1:30.7:1:0.26107:1.46415:60:48:0.2192:0.0268:0.1 0/0:141:1:0,1:71,69:0.0071:2,0:12:0:31:0:0.49645:0:60:2:0.0072:0:0 -16 56866196 . T C 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.11893;LSEQ=ACCAATGCATGTGTTTCTCT;RSEQ=GGGGATTTAGTTGAACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1123:221:130,91:526,376:0.1968:2,2:24.8:1:30.5:1:0.93934:1.02:60:220:0.1984:0:1.2 0/1:1202:34:24,10:675,493:0.0283:2,2:23.6:1:29.7:1:0.15959:1.75:60:33:0.0277:0:1.1 -16 56866502 . T C 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05251;SOR=0.32841;LSEQ=TAAGAAATACATAAAACTTA;RSEQ=ATGGTCATACACAATAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:33:2,31:0,13:0.7174:1,2:22.4:1:32.2:1:1:0:60:66:0.7174:0:1.1 0/1:20:9:1,8:0,11:0.45:0,2:22.8:1:32.9:1:0.45:0:60:18:0.45:0:1.1 -16 56866801 . G T 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTGAGTGACTTAACAGG;RSEQ=TAAAGGAGATAAACACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:8,1:1,0:0.9:0,2:19.4:1:28.9:1:1:0:60:18:0.9:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 56867101 . ATCTCC A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=3.000;MSILEN=5;SSF=0.16571;SOR=1.87315;LSEQ=CTTCTTTCTAAGTTGGTTTT;RSEQ=TCTCCTCTCCTCTCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:795:8:4,4:519,268:0.0101:2,2:18.1:1:29:1:0.45579:1.93491:60:16:0.0102:0.005:0.3 0/1:963:18:9,9:585,358:0.0187:2,2:14.5:1:28.8:1:0.33192:1.63315:60:36:0.0191:0.0073:0.4 -16 56867804 . C T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTTGGATTATGTTTTCA;RSEQ=TCAAAGACCAGCATATTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:25,0:0,0:1:0,1:21.1:1:31.2:1:1:0:60:50:1:0:1.4 1/1:5:5:5,0:0,0:1:0,0:24:1:30:1:1:0:60:10:1:0:1 -16 56868700 . A G 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.98747;LSEQ=GAAGTAGAAAGGTGAGTTAA;RSEQ=TGCATCCTTAGAGAAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1318:197:90,107:507,614:0.1495:2,2:25.2:1:31.9:1:0.9382:1.02:60:64.667:0.1489:0:1.1 0/1:1565:645:293,352:421,498:0.4121:2,2:26:1:31.3:1:0.91787:1.0156:60:106.5:0.4117:0:1.2 -16 56869430 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACAGGCATTGTGCTGAG;RSEQ=GCTTTGCATAGTTTCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0.75:0,2:27.3:1:31:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 56871469 . TTTTATTGATTAC T 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01255;SOR=0.5846;LSEQ=GGGCATTATATAGTTGTTCC;RSEQ=TTTATTGATTGCTTCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:64:47,17:257,54:0.1707:2,2:26.7:1:30.8:1:0.11333:1.7186:59.7:128:0.173:0.0213:0.1 0/1:410:44:29,15:285,80:0.1073:2,2:23.6:1:30.1:1:0.08789:1.83967:59.9:88:0.1081:0.0244:0.1 -16 56871762 . T C 125 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00044;SOR=0;LSEQ=ACAGCTTTCCAAAGTGGTTC;RSEQ=ACTAACTCACCATGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:15:0,15:2,70:0.1724:1,1:26.3:1:32:1:1:0:60:30:0.1744:0:1 0/0:56:0:0,0:0,56:0:1,0:23.1:1:28.8:1:1:0:60:112:1:0:0 -16 56871781 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53663;SOR=0;LSEQ=CTACTAACTCACCATGCCAC;RSEQ=AGCACTGTGTGAGTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:1,62:0.0308:1,2:12:1:28.5:1:0.06106:44.19:60:4:0.0308:0:1 0/0:36:0:0,0:0,36:0:1,0:21.5:1:32.4:1:1:0:60:72:1:0:0 -16 56872722 . C T 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02784;SOR=0.29111;LSEQ=CCTGGCCTCAAGCAATCCTT;RSEQ=CGCCCCAGCCTCCCATGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:24:24,0:99,0:0.1951:1,1:31.5:1:30:1:1:0:60:23:0.1901:0:1.1 0/1:61:4:4,0:57,0:0.0656:1,0:21.8:1:29.8:1:1:0:60:8:0.0667:0:1 -16 56872730 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.54022;SOR=0;LSEQ=CAAGCAATCCTTCCGCCCCA;RSEQ=CCTCCCATGTAGCTGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:140,0:0.0141:1,0:20:1:31:0:1:0:60:4:0.0143:0:1 0/0:78:0:0,0:78,0:0:1,0:22.4:1:32.3:1:1:0:60:77:1:0:0.1 -16 56872804 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03085;SOR=Inf;LSEQ=TAAATGCTATTCCACTGTTA;RSEQ=GGATTACACAGAAATTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:517:0:0,0:399,117:0:2,0:23:1:31.5:1:1:0:60:171:0.9981:0:0.3 0/1:528:6:1,5:384,138:0.0114:2,2:8.7:1:26.7:1:0.00648:13.83361:60:12:0.0115:0:1 -16 56872824 . G A 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15683;LSEQ=CGGATTACACAGAAATTCCT;RSEQ=ATACACTCTTACTACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:169:106,63:383,184:0.2296:2,2:25.3:1:29:1:0.26558:1.23674:60:338:0.2312:0:1.1 0/1:807:36:24,12:485,285:0.0446:2,2:19.6:1:28.7:1:0.72609:1.18:60:72:0.0454:0:1.1 -16 56873495 . C T 234 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=74.89165;LSEQ=GTGGAAGAGAGAGTGGCTGC;RSEQ=TTCAGAAATTTCAGTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1410:3:1,2:643,764:0.0021:2,2:24.3:1:30.3:1:1:1.68265:60:6:0.0021:0:1.3 0/1:1589:219:100,119:629,736:0.1378:2,2:24.4:1:30.1:1:0.94184:1.01699:60:72:0.1376:0:1.1 -16 56873613 . T TA 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.103;LSEQ=ACAGCTTTAAGAATTCTAGT;RSEQ=ACAGTAACTATCCAGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:49:1,48:8,183:0.2042:1,1:23:1:30.7:1:0.69047:2.09308:60:98:0.2059:0.0458:0 0/1:195:5:1,4:10,180:0.0256:2,2:13.4:1:28.3:1:0.2543:4.44:59:10:0.0259:0.0051:0.2 -16 56873789 . T C 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAGGTTTCTGGTTGATCTG;RSEQ=GAAGTCTGGTTTAATTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:0.4667:0,0:23.6:1:29.4:1:1:0:60:14:0.4667:0:1 0/0:1:0:0,0:0,1:0:0,0:33:0:31:0:1:0:60:2:1:0:0 -16 56875548 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.23266;SOR=0;LSEQ=CCTGCCTGGAGCAGCCCACC;RSEQ=TCCCTCCATCTGTGGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:2,0:168,15:0.0108:2,0:29:1:32:1:1:0:60:4:0.0109:0:1 0/0:198:0:0,0:177,21:0:2,0:21.4:1:30.3:1:1:0:60:48.5:1:0:0.1 -16 56878714 . T TC 133 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.78473;SOR=0.80293;LSEQ=TTTTATTTTCTTTTTTTTTT;RSEQ=CTTTGAAATTTTGTTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:20:0,20:0,2:0.7143:0,1:26.2:1:29.5:1:1:0:60:9:0.72:0.1429:0.7 1/0:33:22:2,20:0,6:0.6667:0,2:21.3:1:29.9:1:1:0:60:21:0.6563:0.1818:0.7 -16 57429701 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20448;SOR=Inf;LSEQ=GCTGTCACGGGACCTAGAAA;RSEQ=GGGAGAAGCATGTCGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:0:2,0:27.7:1:30.7:1:1:0:60:86:1:0:0.1 0/1:36:2:1,1:17,17:0.0556:2,2:32.5:1:30:1:1:1:60:4:0.0556:0:1 -16 57429734 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20556;SOR=Inf;LSEQ=TCGCCCAACTCCAGAAGTGG;RSEQ=TATAAGAGTTTGAAAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:22,22:0:2,0:30.1:1:31.6:1:1:0:60:43:1:0:0.1 0/1:37:2:1,1:16,19:0.0541:2,2:29:0:29:1:1:1.18:60:4:0.0541:0:1 -16 57429740 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20556;SOR=Inf;LSEQ=AACTCCAGAAGTGGGTATAA;RSEQ=AGTTTGAAAGGCATTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:21,23:0:2,0:26.5:1:32:1:1:0:60:88:1:0:0.1 0/1:37:2:1,1:16,19:0.0541:2,2:17.5:1:29.5:1:1:1.18:60:4:0.0541:0:1.5 -16 57429779 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16774;SOR=Inf;LSEQ=TGATTTCAGAAGCCTTTTCC;RSEQ=GTAAACACCGGGTGGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:0:2,0:19.6:1:29.6:1:1:0:60:36:1:0:0 0/1:13:2:1,1:4,7:0.1538:2,2:11.5:1:28:1:1:1.67:60:4:0.1538:0:1.5 -16 57698702 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18301;SOR=Inf;LSEQ=GTGAGGCGTGCGTGAAGCAA;RSEQ=AACTCCTGGAGCTACAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:0:2,0:24.6:1:33.6:1:1:0:60:20:1:0:0.4 0/1:8:2:1,1:4,2:0.25:2,2:16.5:1:28:1:1:1.8258:60:4:0.25:0:1 -16 58030634 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAGTTGGGGCACTTGTAGGG;RSEQ=TTCTCGCCTGTGTGTACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27.5:1:32:0:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:30.5:1:29.5:1:1:0:60:4:1:0:1.5 -16 58032026 . G A 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01686;SOR=0;LSEQ=TGCAGGAGGATGCCATAGAC;RSEQ=GCACAGCCCAGGGGGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:5,1:7,2:0.4:2,2:32.3:1:29:1:1:1.40:60:5:0.3571:0:1.2 0/0:14:0:0,0:10,4:0:2,0:22.9:1:30.1:1:1:0:60:28:1:0:0.1 -16 58032054 . C T 20 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.8876;LSEQ=CCAGGGGGTTCTCCGCCGTG;RSEQ=CCGGAGGCAGCGTGTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:27,12:0.0488:2,2:27.5:1:31:1:0.53902:2.20143:60:4:0.05:0:1.5 0/1:46:2:0,2:29,15:0.0435:2,0:1:0:20:1:0.1314:0:60:1:0.0222:0:1.5 -16 58032133 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20877;SOR=Inf;LSEQ=CGGTGGCTGTGGCTGCTGCG;RSEQ=CTGCGTCTGTGGCGGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:16,25:0:2,0:17.9:1:31.7:1:1:0:60:82:1:0:0.1 0/1:35:2:1,1:11,22:0.0571:2,2:21.5:1:28:1:1:1.96:60:4:0.0571:0:2 -16 58529615 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=16.54653;LSEQ=TCGTCCCCCAGTGGGAGCAA;RSEQ=GCGAGGATCAGTGTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:11:6,5:104,106:0.0498:2,2:25.1:1:31.5:1:0.76807:1.22:60:22:0.0507:0:1.2 0/1:206:96:50,46:60,49:0.466:2,2:26.8:1:29.2:1:0.67668:1.12587:60:47:0.47:0:1.3 -16 58960831 . G A 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATACAGTAATTGACCAAGG;RSEQ=TACCAACTATTGTGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:24:24,0:39,1:0.375:1,1:21.5:1:30:1:1:0:60:48:0.375:0:1.2 0/0:45:0:0,0:44,1:0:1,0:22.5:1:31.4:1:1:0:60:90:1:0:0 -16 58960901 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46966;LSEQ=TGTTTCCCACCAGCTGCTCC;RSEQ=AGCCCATGAATGAGTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:2:1,1:152,51:0.0098:2,2:20:1:28.5:1:0.4439:2.96124:60:4:0.0098:0:1 0/1:210:3:2,1:139,68:0.0143:2,2:18.7:1:30.3:1:1:1.02197:60:6:0.0146:0:1 -16 58960987 . G A 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12477;SOR=Inf;LSEQ=GATGATGACTTTGGCTTGAG;RSEQ=ACTCCCCAGTAGCCTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:127,193:0:2,0:24.1:1:31.1:1:1:0:60:159:1:0:0.1 0/1:343:4:3,1:127,212:0.0117:2,2:11.5:1:27.8:1:0.15452:4.98:60:8:0.0119:0:1 -16 59584343 . G A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10373;LSEQ=TTACAAGGAAATGCACAGAT;RSEQ=AGCCTAGGTGAAGATTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:31:15,16:18,18:0.4627:2,2:26:1:29.4:1:1:1.06563:60:62:0.4627:0:1.9 0/1:99:8:4,4:42,49:0.0808:2,2:24.4:1:29.8:1:1:1.16:60:16:0.0808:0:1.8 -16 59584360 . C T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0833;LSEQ=GATGAGCCTAGGTGAAGATT;RSEQ=GATCTAAGGTTTTGACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:25:10,15:13,18:0.4464:2,2:22.3:1:29.8:1:1:1.08178:60:24:0.4364:0:2 0/1:81:5:2,3:30,46:0.0617:2,2:32.4:1:30:1:1:1.02:60:10:0.0625:0:2 -16 59584685 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGTTGACCAGCGACATTC;RSEQ=GCTGCAGTTTGTTTGGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 61579246 . A G 50 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTAAAAAGCTTCTATACA;RSEQ=CAAAGGAAACAATCAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:22:1:32:1:1:0:60:6:0.4286:0:1.3 1/1:1:1:1,0:0,0:1:0,0:8:0:32:0:1:0:60:2:1:0:1 -16 61579445 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=TTTAAAATGTTACATTAAAA;RSEQ=CGGAAGAAAAATATGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:122,10:0.0149:2,2:29.5:1:32.5:1:0.15801:11.68004:60:4:0.015:0:1.5 0/0:105:0:0,0:99,6:0:2,0:22.2:1:29.5:1:1:0:60:51.5:1:0:0.1 -16 61579446 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32201;SOR=3.90234;LSEQ=TTAAAATGTTACATTAAAAA;RSEQ=GGAAGAAAAATATGTAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:1,0:124,11:0.0073:2,0:16:0:32:0:1:0:60:2:0.0074:0:1 0/1:107:3:3,0:97,7:0.028:2,0:26.7:1:30.7:1:1:0:60:6:0.0286:0:1 -16 61579583 . C A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.78154;LSEQ=TTAGTCTTTGTTTTAATTAG;RSEQ=ATTACAAAAGAGAAACATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:121:49,72:116,180:0.2874:2,2:25.7:1:29.7:1:0.82589:1.06:60:39.333:0.2843:0:1.4 1/0:448:237:96,141:88,123:0.529:2,2:24.6:1:28.8:1:0.84753:1.05067:60:38.5:0.525:0:1.3 -16 61579609 . A G 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AAAAGAGAAACATCGCATAT;RSEQ=TTAGACATAATTTCTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:99,204:0:2,0:24.4:1:30:1:1:0:60:74.75:1:0:0.5 0/1:335:29:10,19:105,201:0.0866:2,2:23.3:1:31:1:1:1.01:60:58:0.0871:0:1.9 -16 61579618 . A G 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29469;SOR=0.77531;LSEQ=ACATCGCATATATTAGACAT;RSEQ=ATTTCTAACCTCAGAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:47:13,34:67,157:0.1734:2,2:26.1:1:31.9:1:0.86107:1.11569:60:94:0.1754:0:2 0/1:286:40:12,28:78,168:0.1399:2,2:24.9:1:31.3:1:1:1.08304:60:39:0.1368:0:1.9 -16 61579666 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22357;SOR=0;LSEQ=CCTTAAGTTCCACAGTGAGC;RSEQ=CATGCTGAATTACTGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:22,94:0.0169:2,2:19.5:1:31.5:1:0.35318:4.20:60:4:0.0169:0:2 0/0:131:0:0,0:27,104:0:2,0:21.7:1:31.7:1:1:0:60:262:1:0:0.4 -16 63438484 . A T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26113;SOR=Inf;LSEQ=TATATCTTCAGGTTACTTAA;RSEQ=AGTTTGCAAGTTCTCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:201,27:0:2,0:21.8:1:30.1:1:1:0:60:75:1:0:0.1 0/1:297:3:1,2:252,40:0.0101:2,2:5:1:22:1:0.05414:12.41225:60:6:0.0103:0:1.3 -16 63438539 . A ACTGTTGTTGCTGTTGCTG 230 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=2.000;MSILEN=3;SSF=0.39497;SOR=0.89679;LSEQ=GAGAAATCTGGTGTTGTGCC;RSEQ=CTGTTGTTGCTGTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:732:157:88,69:325,246:0.2145:2,2:23.1:1:30.8:1:0.85608:1.03586:59.2:314:0.2169:0.0915:0.3 0/1:966:190:105,85:459,316:0.1967:2,2:22.1:1:30.4:1:0.32546:1.17565:59.4:380:0.1983:0.1025:0.4 -16 63438555 . C CTGCTGTTGCTGCTGTTGT 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=23;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01382;LSEQ=TGCCACTGTTGTTGCTGTTG;RSEQ=TGCTGTTGCTGCTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:853:14:7,7:434,404:0.0164:2,2:14.6:1:30:1:1:1.07414:55.5:28:0.0166:0.0164:2.2 0/1:1082:18:9,9:580,483:0.0166:2,2:16.7:1:29.2:1:0.81264:1.20062:57.4:36:0.0168:0.0166:2.5 -16 63438619 . AT A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.24108;LSEQ=GCATGCATCTTATTTAGATT;RSEQ=TTTTACTTGTCTGAATTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:170:46,124:78,182:0.3944:2,2:22.5:1:30.6:1:0.58631:1.15489:59.9:169:0.3967:0.0626:0.1 0/1:546:74:17,57:148,323:0.1355:2,2:21.6:1:29.8:1:0.1733:1.5352:60:148:0.1375:0.0275:0 -16 63438640 . C A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09265;SOR=0;LSEQ=TTTTTACTTGTCTGAATTCA;RSEQ=CCTATTTCAAAATTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:38,241:0.0106:2,2:13:1:22.7:1:0.05372:12.49:60:2:0.0072:0:2 0/0:340:0:0,0:50,290:0:2,0:24:0:11:0:1:0:60:0:0:0:7 -16 63438757 . A T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65008;SOR=1.96752;LSEQ=TGCTTTATAAATTATTGTTA;RSEQ=ATCTTATTCTTCTGGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:0,3:0,26:0.1034:1,0:6.3:1:28.7:1:1:0:60:6:0.1034:0:1.3 0/1:16:3:0,3:1,12:0.1875:1,0:29:1:28.3:1:1:0:60:6:0.2:0:1 -16 64648860 . C T 63 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.40518;SOR=0.41704;LSEQ=TTTTGTTTATTCTTTCTCAT;RSEQ=TTCATGAGTTCGTCTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:3,1:14,4:0.1818:2,2:8.5:1:31.5:1:1:1.15827:60:8:0.1905:0:1.3 0/1:24:2:1,1:12,10:0.0833:2,2:3:0:30:1:1:1.19087:60:4:0.0909:0:1.5 -16 64649225 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=AGAGTCTCACCCAGTTGGGT;RSEQ=GCACAGGGAGCACTTCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:19:1:32.5:1:1:0:60:4:0.2857:0:1 0/0:4:0:0,0:2,2:0:2,0:28.8:1:27.3:1:1:0:60:3:1:0:0.3 -16 64649649 . C T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GCTATCGAAATGAGTTGCCA;RSEQ=CCTTCCCCCACCCAGGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:23.8:1:31.5:1:1:0:60:8:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:20:0:30:1:1:1:60:4:0.5:0:1 -16 66648874 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=Inf;LSEQ=TGCTGTCGGGGACAAATCAA;RSEQ=AGCAGCAAAGCTTTGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:6,17:0:2,0:28.2:1:28.8:1:1:0:60:46:1:0:0.1 0/1:26:2:1,1:6,18:0.0769:2,2:24.5:1:32.5:1:0.47385:2.85:60:4:0.08:0:1 -16 66648879 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22429;SOR=0;LSEQ=TCGGGGACAAATCAATAGCA;RSEQ=CAAAGCTTTGGGGCCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:5,16:0.087:2,2:25.5:1:30.5:1:0.46245:3.01:60:4:0.087:0:1 0/0:25:0:0,0:7,18:0:2,0:27.6:1:31.6:1:1:0:60:24:1:0:0.1 -16 67063200 . C A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCTGAAACAAAGGGAAG;RSEQ=GGGCGTCCGGGCGCCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:19.5:1:28.5:1:1:1:60:4:0.5:0:1.5 -16 67063247 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37078;SOR=0.25846;LSEQ=GTCAGTCGGTCAGCGCGGAG;RSEQ=CAGCCAGCGGGTGCCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:2,0:0.3333:0,0:1:0:25:0:0.33333:0:60:2:0.3333:0:1 0/1:19:2:1,1:12,5:0.1053:2,2:27.5:1:28.5:1:1:2.28037:60:4:0.1053:0:1.5 -16 67063287 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14807;SOR=0;LSEQ=CAAGCCCCGAGCGCGGCCGG;RSEQ=CGGCGCGGCCTCAGGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:116,42:0.0125:2,2:27.5:1:30.5:1:0.46651:2.74134:60:4:0.0127:0:1 0/0:255:0:0,0:183,72:0:2,0:19.5:1:31.6:1:1:0:60:62.75:1:0:0.2 -16 67063326 . C T 83 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.37872;SOR=2.08942;LSEQ=GGAAGATGCCGCGCGTCGTG;RSEQ=CCGACCAGAGAAGCAAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:3:1,2:304,165:0.0064:2,2:26:1:24.7:1:0.28654:3.67409:60:2:0.0043:0:1.3 0/1:682:9:3,6:414,259:0.0132:2,2:16.2:1:26.3:1:0.09727:3.19133:60:8:0.0119:0:1.3 -16 67063499 . G A 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0011;SOR=Inf;LSEQ=TCCCGGTCGGTGCGCCCGCG;RSEQ=AGGGGCAATCTCGCCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:46,58:0:2,0:17.5:1:32:1:1:0:60:103:1:0:0.1 0/1:96:9:4,5:32,55:0.0938:2,2:21.8:1:31:1:0.7243:1.37:60:18:0.0957:0:1.1 -16 67063546 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25457;SOR=Inf;LSEQ=CGCCCGCAGCCTCTGCTTGC;RSEQ=CTTATCGGCGCTGCGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:178,43:0:2,0:23:1:31.5:1:1:0:60:72.667:0.9954:0:0.1 0/1:266:3:1,2:200,61:0.0113:2,2:11:1:28.7:1:0.14257:6.49787:60:6:0.0115:0:1 -16 67063559 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0752;SOR=0;LSEQ=TGCTTGCCCTTATCGGCGCT;RSEQ=CGCTGGGAGGGCGGGCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:1,2:213,64:0.0107:2,2:20.7:1:28.3:1:0.13946:6.59846:60:6:0.011:0:1 0/0:382:0:0,0:262,118:0:2,0:23.2:1:31.4:1:1:0:60:62.333:0.9947:0:0.2 -16 67063560 . C T 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70473;SOR=1.87174;LSEQ=GCTTGCCCTTATCGGCGCTG;RSEQ=GCTGGGAGGGCGGGCGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:2:1,1:218,69:0.0069:2,2:25:1:20:1:0.4264:3.14398:60:1:0.0036:0:1 0/1:388:5:3,2:262,121:0.0129:2,2:33.4:1:29.8:1:0.65401:1.44211:60:10:0.0131:0:1 -16 67063612 . G T 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATTTGGCTCCTGATTTCG;RSEQ=GCCGTCTTGCCTTGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:0:0,0:373,281:0:2,0:24.4:1:30.5:1:1:0:60:31.7:1:0:0.2 0/1:869:81:42,39:434,354:0.0932:2,2:23.2:1:30:1:0.63946:1.13825:60:162:0.0945:0:1.2 -16 67070410 . G GT 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.47202;LSEQ=AAGAAAAATGATGAGTGCAT;RSEQ=TTTTTTTTTACTTTTAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:2,0:64,1:0.0299:1,0:9:1:28:1:1:0:60:4:0.0303:0.0149:0 0/1:46:2:2,0:44,0:0.0435:1,0:16:1:30.6:1:1:0:60:4:0.0435:0.0217:0 -16 67070442 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21914;SOR=Inf;LSEQ=TTTTAAGTATTCTCTGTGCT;RSEQ=CCTGGCTTAAGACATAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:113,8:0:2,0:25.4:1:32.2:1:1:0:60:39.333:1:0:0.1 0/1:107:2:1,1:101,4:0.0187:1,2:24:1:28:1:0.09169:22.69627:60:4:0.0194:0:1 -16 67070692 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.28152;SOR=Inf;LSEQ=CTTTGCAATTTAAAATACTG;RSEQ=GGGTTGTTTTGTTAGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:42,154:0:2,0:24.4:1:29.8:1:1:0:60:48:1:0:0.1 0/1:300:3:3,0:74,223:0.01:2,0:13:1:21.3:1:0.01642:0:60:2:0.0067:0:1 -16 67070698 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15764;SOR=0;LSEQ=AATTTAAAATACTGTGGGTT;RSEQ=TTTTGTTAGAGATTATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:29,144:0.0114:2,2:6:1:29:1:0.31429:4.90:60:4:0.0116:0:1 0/0:265:0:0,0:57,208:0:2,0:22.7:1:30.7:1:1:0:60:264:1:0:0.1 -16 67070721 . AT A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5077;SOR=Inf;LSEQ=TTGTTAGAGATTATCTGGTA;RSEQ=TTACATTTTAATAAAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:14,111:0:2,0:21.3:1:29.9:1:1:0:60:124:1:0:0 0/1:166:2:1,1:21,143:0.012:2,2:17:1:26.5:1:0.24819:6.68:60:4:0.0122:0.006:1.5 -16 67070808 . AT A 51 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11044;SOR=0;LSEQ=TGTTATAAGGATGTAATATA;RSEQ=TTTTTTTTTTTAATGGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:0,3:0,22:0.12:1,0:14.7:1:32.7:1:1:0:60:6:0.12:0:0 0/0:26:0:0,0:0,26:0:1,0:19.2:1:30.3:1:1:0:60:52:1:0:0.2 -16 67070862 . C T 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CCCAGGCTGGAGTGCAGTGG;RSEQ=GTGATGTTGGTTCACTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:25.3:1:30.3:1:1:0:60:6:0.5:0:1 0/0:4:0:0,0:0,4:0:0,0:25:1:28.8:1:1:0:60:8:1:0:0 -16 67100460 . CTCAA C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.23523;SOR=Inf;LSEQ=GGAGCACAGCGAAACTCCAT;RSEQ=TCAATCAGTCAATCATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:43,0:0:1,0:23.6:1:31.1:1:1:0:60:42:1:0:0 0/1:41:2:2,0:38,1:0.0488:1,0:24.5:1:33:0:1:0:60:4:0.0488:0:0 -16 67100529 . T C 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.2491;SOR=Inf;LSEQ=ATATAAGTAAGTTTAATCTT;RSEQ=TTATTTTCATGTGTCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:203,49:0:2,0:21.9:1:30.6:1:1:0:60:504:1:0:0.1 0/1:266:3:2,1:206,57:0.0113:2,2:28.3:1:26.3:1:0.52338:1.80236:60:2:0.0076:0:1 -16 67101184 . C T 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACTTTGGGAGGCTGAGG;RSEQ=AGACGGATCACCTGAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:22.5:1:26.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 67115910 . T C 41 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=TTCTGTATTTTTAGTAGAGA;RSEQ=GCGGTTTCACCATGTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:25.7:1:26:1:1:0:60:2:0.5:0:2.3 0/0:3:0:0,0:3,0:0:0,0:25.3:1:25.3:1:1:0:60:2:1:0:4 -16 67116066 . AT A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.1577;SOR=0;LSEQ=AAACAAAACCCAAATATTGT;RSEQ=TTTTTTTATAAATCAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:2,0:127,23:0.0132:2,0:30.5:1:30:1:1:0:60:4:0.0137:0:0.5 0/0:230:0:0,0:190,40:0:2,0:21.8:1:29.1:1:1:0:59.6:27.75:1:0:0.9 -16 67116355 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25772;SOR=Inf;LSEQ=GTTGTACTCTCTGGCTTTGT;RSEQ=TTTATTAAATGTAATTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:1,75:0:1,0:25.4:1:32:1:1:0:60:37:1:0:0 0/1:98:3:0,3:0,95:0.0306:1,0:35.7:1:31:1:1:0:60:6:0.0309:0:1.3 -16 67132463 . G GT 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08684;SOR=Inf;LSEQ=GTCAGACATAATTTTAATTG;RSEQ=TTTTTTTTTGCCTGTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:78,0:0:1,0:26.1:1:31.6:1:1:0:60:77:1:0:0.2 0/1:63:3:3,0:58,2:0.0476:1,0:21.3:1:30:1:1:0:60:6:0.0484:0:0 -16 67431239 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53623;SOR=Inf;LSEQ=CCCTCTCCCCAGCACAGCTG;RSEQ=CACCATCAGAGCCCAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:0:2,0:22:1:31.7:1:1:0:60:32:1:0:0.1 0/1:30:2:1,1:18,10:0.0667:2,2:22.5:1:26.5:1:1:1.76317:60:4:0.0667:0:1 -16 67450281 . T TGGCTCC 121 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=42;MSI=8.000;MSILEN=6;SSF=0.00041;SOR=0.13929;LSEQ=GAGTCCTCGAGCTCTGGCTC;RSEQ=GGCTCCGGCTCCGGCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:9,8:13,16:0.3696:2,2:21.5:1:29.7:1:0.76104:1.37:60:16:0.3556:0.1957:0.1 0/1:54:4:2,2:27,23:0.0741:2,2:28:1:29.5:1:1:1.17042:60:8:0.0741:0:0 -16 67644775 . G A 81 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09335;SOR=5.43351;LSEQ=AAGCCATTGTGGAGGAGTCC;RSEQ=AAACTTTTATTAAAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:1:1,0:240,240:0.0021:2,0:1:0:16:0:1:0:60:0:0:0:1 0/1:714:8:7,1:339,367:0.0112:2,2:12.8:1:27:1:0.03303:7.56:60:16:0.0113:0:1.1 -16 67645883 . TGCAGTTACA T 209 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACATTCCAGTGTGAGCTT;RSEQ=CGTGTCCACGGCGTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:111:66,45:227,170:0.2185:2,2:27.9:1:30.9:1:0.74457:1.10:60:110:0.2187:0.0197:0.1 0/0:723:0:0,0:406,317:0:2,0:25:1:31.8:1:1:0:60:102.286:1:0:0.1 -16 67650568 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50009;SOR=Inf;LSEQ=ATAGGGTTCCAGTCTCATAG;RSEQ=AGTTCTGTGCCACACATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:161,16:0:2,0:23.3:1:32.4:1:1:0:60:354:1:0:0.1 0/1:197:2:1,1:155,40:0.0102:2,2:10.5:1:28:1:0.37377:3.83978:60:4:0.0102:0:1 -16 67650676 . C T 101 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05524;SOR=4.10117;LSEQ=CCTCACAAGTGCCCAGACTG;RSEQ=GACATGGCCTTTGTGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:2:0,2:352,305:0.003:2,0:1:0:27:1:0.21664:0:60:4:0.0031:0:1 0/1:974:12:3,9:535,426:0.0123:2,2:11.5:1:28.4:1:0.04156:3.76278:60:24:0.0125:0:1.1 -16 67655537 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21961;SOR=Inf;LSEQ=AGTGAAAAAAATATTTTGAA;RSEQ=GATTTATATTTCGAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:35,164:0:2,0:22.1:1:30.8:1:1:0:60:23.875:1:0:0.1 0/1:176:2:1,1:35,138:0.0114:2,2:39:1:29.5:1:0.37005:3.90:60:4:0.0116:0:1 -16 67655557 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.6139;SOR=2.11838;LSEQ=GGATTTATATTTCGAAATAT;RSEQ=GGGATCAAAAATAACTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:1:0,1:13,106:0.0083:2,0:26:0:32:0:1:0:60:2:0.0084:0:1 0/1:114:2:1,1:16,96:0.0175:2,2:38.5:1:28:1:0.27713:5.85:60:4:0.0179:0:1 -16 67662204 . A T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2201;SOR=Inf;LSEQ=AATACCTGTTGGCCACATGC;RSEQ=TGCAGGTGGCAGCTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:163,22:0:2,0:24:1:30.1:1:1:0:60:91.5:1:0:0.1 0/1:164:2:1,1:132,30:0.0122:2,2:5.5:1:26.5:1:0.34326:4.34482:60:4:0.0123:0:1.5 -16 67670472 . G GTA 107 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=11.000;MSILEN=2;SSF=1;SOR=1.10658;LSEQ=AAAAAAAAAAGAAAGAAAGT;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:15:15,0:47,2:0.2174:1,1:25.6:1:27.5:1:1:0:58.3:6.5:0.25:0.0145:1.9 0/1:34:8:7,1:24,0:0.2353:1,2:14.6:1:29.2:1:0.25:0:58.1:16:0.2581:0.1176:0.4 -16 67670521 . TA T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.22524;SOR=Inf;LSEQ=ACAAGACTTCAAATAATATA;RSEQ=ATTGTTTTCTTTCATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:153,28:0:2,0:21.1:1:27.8:1:1:0:60:24.857:1:0:0.3 0/1:164:2:1,1:130,32:0.0122:2,2:13.5:1:28:1:0.36294:4.01583:60:4:0.0126:0:0 -16 67671804 . T G 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01015;SOR=Inf;LSEQ=CCTTGTGCGTCGCCAGGACT;RSEQ=CTCTGGGCTGTGTTTAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:58,181:0:2,0:24.4:1:30.1:1:1:0:60:118.5:1:0:0.1 0/1:299:8:2,6:86,205:0.0268:2,2:30.8:1:30.8:1:1:1.25759:60:16:0.027:0:1.1 -16 67876762 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50613;SOR=Inf;LSEQ=TGGGGCCGCGGCCGCCCGCC;RSEQ=CAGGCAGCAGCAGCAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:44,42:0:2,0:32.3:1:30.2:1:1:0:60:20.5:1:0:0.2 0/1:112:2:1,1:51,56:0.0179:2,2:16:1:25.5:1:1:1.10:60:4:0.0185:0:1 -16 67876778 . ACAG A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.45388;SOR=0.52539;LSEQ=CGCCGCAGGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:4:2,2:43,45:0.0435:2,2:32.8:1:32.5:1:1:1.05:60:8:0.0435:0:0 0/1:129:3:1,2:56,70:0.0233:2,2:22.3:1:33.7:1:1:1.59441:60:6:0.0234:0:0 -16 67876820 . GCAA A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.55369;SOR=Inf;LSEQ=CAGCAACAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:19,38:0:2,0:26.7:1:31.8:1:1:0:59.7:56:1:0:0.2 0/1:101:3:2,1:41,57:0.0297:2,2:12.3:1:31.3:1:0.57348:2.75:53.7:6:0.03:0.0198:1.7 -16 67876823 . ACAG A 119 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=10.000;MSILEN=3;SSF=0.04369;SOR=0.40479;LSEQ=CAACAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:14:5,9:13,30:0.2456:2,2:30.3:1:31.4:1:0.74718:1.28:60:28:0.25:0.0351:0.4 0/1:95:11:6,5:33,48:0.1158:2,2:28.9:1:31.4:1:0.51823:1.73:60:22:0.117:0.0105:0 -16 67876875 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52893;SOR=Inf;LSEQ=CCTCACCCTCTGCCTCCACT;RSEQ=CCCAGACTGCCCAGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:2,21:0:2,0:25.4:1:32.8:1:1:0:60:46:1:0:0.1 0/1:40:2:1,1:15,23:0.05:2,2:14.5:1:26.5:1:1:1.52:60:4:0.05:0:1.5 -16 68731047 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTATCCTGGCCAACATGGT;RSEQ=AAACCCTGTCTCTACTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 -16 68732300 . C G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19808;SOR=Inf;LSEQ=TACGGTGGCGGGGAGGACGA;RSEQ=TAGGCGGCCTGCCTGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:20,28:0:2,0:28.3:1:32.7:1:1:0:60:96:1:0:0.1 0/1:39:2:1,1:18,19:0.0513:2,2:17:0:30.5:1:1:1.05:60:4:0.0513:0:1.5 -16 68732304 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.18513;SOR=Inf;LSEQ=GTGGCGGGGAGGACGACTAG;RSEQ=CGGCCTGCCTGCAGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:19,28:0:2,0:27:1:32.3:1:1:0:60:94:1:0:0.1 0/1:36:2:1,1:16,18:0.0556:2,2:35:1:28.5:1:1:1.12:60:4:0.0556:0:1 -16 68732457 . G T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTCTGACGTTAGAGTGGT;RSEQ=GCTTCCTTAGCCTTTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17:1:31.5:1:1:0:60:4:1:0:1 1/1:2:2:0,2:0,0:1:0,0:20:1:30:1:1:0:60:4:1:0:1 -16 68771238 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49875;SOR=Inf;LSEQ=CCTGTGAGCTTGCGGAAGTC;RSEQ=GTTCAGACTCCAGCCCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:113,87:0:2,0:21.8:1:29.8:1:1:0:60:65.667:1:0:0.1 0/1:201:2:1,1:121,78:0.01:2,2:13:1:29.5:1:1:1.54774:60:4:0.0101:0:1 -16 68771347 . CGCT C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.86364;SOR=1.10421;LSEQ=TTGGAGCCGCAGCCTCTCGG;RSEQ=GCTGCTGCTGCTGCAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:16:9,7:254,170:0.0363:2,2:25.3:1:31.8:1:0.79903:1.16169:59.7:32:0.037:0.0091:0.8 0/1:476:19:11,8:250,205:0.0399:2,2:23.7:1:31.4:1:1:1.13:60:38:0.0409:0.0084:0.9 -16 68771372 . C T 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24393;SOR=0.83719;LSEQ=CTGCTGCTGCTGCAGGTACC;RSEQ=CGGATCCCCTGACTTGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:476:359:201,158:64,53:0.7542:2,2:25.6:1:30.1:1:0.83082:1.05:59.8:43.875:0.7548:0:1.1 1/0:496:357:204,153:73,65:0.7198:2,2:24.4:1:29.5:1:0.41996:1.19:59.9:24.5:0.7146:0:1.2 -16 68771418 . C CGCCCCAGCCCCGT 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04635;SOR=0.75685;LSEQ=CATTCGGGCCGCAAGCTCCG;RSEQ=GCCCCAGCCCTGCGCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:292:111,181:66,71:0.6667:2,2:26.3:1:30.5:1:0.05812:1.51425:59.7:145:0.6776:0.2078:0.7 1/0:475:286:127,159:90,94:0.6021:2,2:31.4:1:29.7:1:0.34496:1.19822:59.7:94.333:0.6034:0.0842:0.5 -16 68771431 . C T 81 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21632;SOR=0.41036;LSEQ=AGCTCCGCGCCCCAGCCCTG;RSEQ=GCCCCTTCCTCTCCCGTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:7:2,5:106,199:0.0224:2,2:16:1:28.9:1:1:1.3305:59.3:6:0.0196:0:2.6 0/0:323:3:1,2:128,192:0.0093:2,2:11.7:1:31:1:1:1.33219:60:6:0.0094:0:3 -16 68771447 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.10041;SOR=0;LSEQ=CCTGCGCCCCTTCCTCTCCC;RSEQ=TCGTCACCGCTTCCCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:2,1:67,162:0.0129:2,2:28.7:1:29:1:0.21164:4.80:58.3:6:0.0133:0:1 0/0:266:0:0,0:86,180:0:2,0:20.4:1:29.7:1:1:0:59.7:65.5:1:0:0.3 -16 68771547 . G C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.21989;SOR=0.46321;LSEQ=CCCCAGTGATGGGAGTGGGG;RSEQ=GTGGGTGGTGAGGGGCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:35:0,35:0,8:0.814:0,1:24.2:1:30.4:1:1:0:60:70:0.814:0:1.1 1/0:21:14:0,14:1,6:0.6667:2,1:26.1:1:29.8:1:0.33333:0:60:28:0.6667:0:1.1 -16 68771905 . A C 75 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGTCTAAGGAAAGTGGGGT;RSEQ=CTGGAGAATAAAGACATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:22.5:1:29.3:1:1:0:60:5:0.7143:0:1.3 1/1:1:1:1,0:0,0:1:0,0:32:0:32:0:1:0:60:2:1:0:1 -16 68772371 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2323;SOR=Inf;LSEQ=GGAGGGGTTGGAAAGGGGCC;RSEQ=AGAAATTGCACTCCCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:25,169:0:2,0:24.4:1:30.8:1:1:0:60:47.5:1:0:0.1 0/1:181:2:1,1:44,135:0.011:2,2:11.5:1:27.5:1:0.43646:3.05:60:4:0.0114:0:1.5 -16 68835867 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24079;SOR=0;LSEQ=AATCCAGGTTTCTCAGCCTT;RSEQ=GTACCGTTGACATTTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:14,156:0.0116:2,2:11:1:28:1:0.16728:10.80:60:4:0.0117:0:1 0/0:178:0:0,0:24,154:0:2,0:21.3:1:30:1:1:0:60:34.6:1:0:0.1 -16 68835912 . T C 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05231;SOR=Inf;LSEQ=TGATTTTGTGTTGTAGGGGT;RSEQ=GTCCTGTGCACTGTGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:0,82:0:1,0:24.3:1:30.3:1:1:0:60:81:1:0:0.1 0/1:50:3:0,3:0,47:0.06:1,0:28.7:1:29.3:1:1:0:60:6:0.0612:0:1 -16 68842244 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21327;SOR=Inf;LSEQ=GCCCACAGAAGGCTGGGGAC;RSEQ=CTGTCTGGCTAGGTTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:198,23:0:2,0:24.2:1:30.4:1:1:0:60:109.5:1:0:0.1 0/1:191:2:1,1:166,23:0.0105:2,2:17.5:1:32:1:0.2361:7.08652:60:4:0.0107:0:1 -16 68842797 . C A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37295;SOR=3.91705;LSEQ=ACACCGGGGTAACATCCACC;RSEQ=AGGATTTTTTGGTCAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:1,0:68,197:0.0038:2,0:1:0:26:0:0.2594:0:60:2:0.0038:0:1 0/1:274:4:2,2:66,204:0.0146:2,2:23.8:1:25.3:1:0.25785:3.08:60:3:0.0112:0:1.8 -16 68842895 . G A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01212;SOR=0.15287;LSEQ=TGACCTGTTGCTAAGGAGAA;RSEQ=TGATGGGAGAACGTGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:16:0,16:0,36:0.3077:1,1:25.3:1:31.6:1:1:0:60:32:0.3077:0:1 0/1:32:2:0,2:2,28:0.0625:2,0:22.5:1:28:1:1:0:60:4:0.0625:0:1 -16 68844267 . G T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10814;SOR=0;LSEQ=ATATCCACTAATGAGAATCT;RSEQ=AATACTCAGAAAGACTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:78,203:0.0106:2,2:10.7:1:26.7:1:0.1924:5.17:60:6:0.0107:0:1 0/0:311:0:0,0:94,217:0:2,0:21.1:1:31:1:1:0:60:50.833:1:0:0.1 -16 68845894 . G AGA 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.31236;SOR=0.67476;LSEQ=TAAGCTTTGCATCTAAGCTT;RSEQ=TGCCCAGAGGTTCCGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:30:21,9:55,27:0.2679:2,2:19.6:1:30.1:1:0.82307:1.14:60:60:0.2679:0.0982:0.9 0/1:86:17:11,6:49,20:0.1977:2,2:21.4:1:29.4:1:0.76874:1.33176:60:16:0.1905:0.0581:1 -16 68846222 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21824;SOR=0;LSEQ=AGGTCTTTTGTTGTTCATGA;RSEQ=CTAAGTGTCACCACTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:36,151:0.0106:2,2:40:1:30:1:0.35405:4.15:60:4:0.0107:0:1 0/0:215:0:0,0:52,163:0:2,0:22.5:1:29:1:1:0:60:70.667:1:0:0.1 -16 68847433 . C T 50 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12399;SOR=0;LSEQ=TGGCAAGATGCAGAAACTGG;RSEQ=ATCCTCACAGCTGTTCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:4:1,3:90,248:0.0117:2,2:20.8:1:25:1:1:1.08844:60:3:0.0089:0:2.8 0/0:334:0:0,0:94,240:0:2,0:23:1:31.8:1:1:0:60:110.333:1:0:0.2 -16 68847443 . G C 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CAGAAACTGGCATCCTCACA;RSEQ=CTGTTCATACCCTTGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:67,227:0:2,0:23.2:1:31.9:1:1:0:60:41:0.9965:0:0.2 0/1:266:14:2,12:64,186:0.0526:2,2:25.9:1:30.9:1:0.52822:2.05979:60:28:0.0528:0:1.1 -16 68847463 . C CA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50058;SOR=0;LSEQ=GCTGTTCATACCCTTGTCCC;RSEQ=TGGTATCTTCTTAGAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:19,163:0.0109:2,2:12:1:31:1:0.20611:8.39:60:4:0.0109:0.0054:0.5 0/0:162:0:0,0:24,138:0:2,0:20.3:1:31.4:1:1:0:60:53:1:0:0.2 -16 68847584 . T G 113 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.3547;SOR=0.27938;LSEQ=TGTAAGAAATCAAGAAACTG;RSEQ=GCTGTGTGTGGTGGCTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:0,13:0,14:0.4815:1,1:21.2:1:30.6:1:1:0:60:12:0.4615:0:1 0/1:5:1:0,1:0,4:0.2:0,0:12:0:31:0:1:0:60:2:0.2:0:1 -16 68853113 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49891;SOR=Inf;LSEQ=AACCATATAACTGAAGAAGC;RSEQ=CTTAAGCCGTTTTCAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:162,12:0:2,0:26.7:1:29.8:1:1:0:60:57:1:0:0.1 0/1:183:2:1,1:155,25:0.0109:2,2:14:0:29.5:1:0.26598:6.0992:60:4:0.0109:0:1.5 -16 68853671 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTACACATTATCGAACTC;RSEQ=GACTTCTAAGTGAGAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30.5:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 68854361 . G C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCCAGGTTCAAGCAATT;RSEQ=TCCTACCTCAGCCTCCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:30:1:1:0:60:4:1:0:1.5 -16 68855876 . G C 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12412;SOR=Inf;LSEQ=TTCATTACTGTTGCCAAGCT;RSEQ=CCACATTTTCTGTGTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:210,58:0:2,0:24.7:1:32:1:1:0:60:66:1:0:0.1 0/1:282:4:2,2:201,76:0.0142:2,2:25.8:1:32:1:0.30849:2.63413:60:8:0.0144:0:1.3 -16 68856168 . T A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11206;SOR=0;LSEQ=TTTGGCAACTTTGCTCCAAC;RSEQ=GCCATGCTTCCCTTCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:3,0:72,209:0.0106:2,0:5.7:1:25.7:1:0.01788:0:60:6:0.0108:0:1.7 0/0:304:0:0,0:78,226:0:2,0:23.3:1:30.1:1:1:0:60:75:1:0:0.1 -16 68856782 . T A 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCTGGGTGCGATGGAAG;RSEQ=CACTCTGGCCCTGGAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:26:1:1:0:60:4:1:0:1 -16 68857191 . C A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1e-04;SOR=Inf;LSEQ=ATAAAACCCAAGCAGCTCTG;RSEQ=TCTCTTCACTCGGCTTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:59,2:0:1,0:26.2:1:31.4:1:1:0:60:11.2:1:0:0.4 0/1:45:10:10,0:35,0:0.2222:1,0:23.2:1:28.6:1:1:0:60:9:0.2368:0:1.1 -16 68857273 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1663;SOR=0;LSEQ=TTTATTTTCCTCCCCTGGTC;RSEQ=CATCATTTCTTTTTATTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:145,47:0.0103:2,2:21.5:1:28.5:1:0.43459:3.06319:60:4:0.0106:0:1 0/0:281:0:0,0:207,74:0:2,0:21.9:1:30.2:1:1:0:60:92.667:1:0:0.1 -16 68857289 . T C 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1729;LSEQ=GGTCTCATCATTTCTTTTTA;RSEQ=TGCTTTCTCCAGCCCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:49:34,15:140,65:0.1929:2,2:23.3:1:32.4:1:1:1.05:60:98:0.1952:0:1 0/1:379:15:10,5:256,108:0.0396:2,2:26.3:1:33:1:0.77657:1.18461:60:30:0.0402:0:1 -16 68857441 . T C 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.39786;LSEQ=TGTGACTGTGAAGGGGCCGC;RSEQ=GGCGTCTGTAGGAAGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:483:409:182,227:34,38:0.8468:2,2:23.9:1:30.1:1:0.70097:1.11571:60:67.167:0.8466:0:1.1 1/0:729:501:231,270:103,122:0.6872:2,2:26.7:1:29.5:1:1:1.01:60:166:0.6888:0:1.1 -16 68857549 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18774;SOR=0;LSEQ=AGTAAGTCCAGCTGGCAAGT;RSEQ=ACTCAGCCTTTGACTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:29,140:0.0117:2,2:16.5:1:28:1:0.32095:4.76:60:4:0.0119:0:1.5 0/0:223:0:0,0:55,168:0:2,0:22.9:1:31:1:1:0:60:110.5:1:0:0.1 -16 68861656 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGCCCTGCTTGCCCCTC;RSEQ=GAGCTCTTCTCCATGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:28:1:1:0:60:4:1:0:1 -16 68862021 . C T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12122;SOR=0;LSEQ=CTCTGTGATAGCTGCTGCTT;RSEQ=TGGCCTTCTTTATCTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:1,2:214,75:0.0102:2,2:13.3:1:21:1:0.17099:5.66554:60:2:0.007:0:1.3 0/0:298:0:0,0:220,78:0:2,0:22.7:1:31.2:1:1:0:60:297:1:0:0.1 -16 68862182 . A G 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAACGTTTATTACTATGATG;RSEQ=AGAAGGAGGCGGAGAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:18:8,10:177,284:0.0375:2,2:31.1:1:31.2:1:0.62772:1.28:60:36:0.0384:0:1 0/0:623:0:0,0:281,342:0:2,0:24.6:1:29.1:1:1:0:60:50.917:1:0:0.2 -16 68863752 . G A 135 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00027;SOR=0.17784;LSEQ=GCTCATCTCTAAGCTCAGGA;RSEQ=GAGTTGTGTCAAAAATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:21:0,21:1,91:0.1858:1,1:24.5:1:30.8:1:1:0:60:20:0.1802:0:1 0/1:129:5:0,5:2,122:0.0388:1,0:31.6:1:30.8:1:1:0:60:10:0.0397:0:1.2 -16 68863846 . C CT 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.20635;SOR=Inf;LSEQ=GGAGCCCTGTTTTCCTTTTT;RSEQ=TTTTTTTTTCTTTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:0,15:0:1,0:17.1:1:28.9:1:1:0:58.7:4:1:0:0.1 0/1:13:2:1,1:0,10:0.1538:0,2:18.5:1:30.5:1:0.16667:0:60:4:0.1818:0:0.5 -16 68863862 . C CT 42 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.58204;SOR=0.31051;LSEQ=TTTTCTTTTTTTTTCTTTTT;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,5:0.3:0,0:19:1:26.5:1:1:0:60:2:0.3333:0.1:1.7 0/1:9:1:0,1:1,7:0.1111:2,0:27:0:29:0:1:0:60:2:0.125:0:5 -16 68867145 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51026;SOR=Inf;LSEQ=CTTCTTGCCCCAGATGACAG;RSEQ=TGTGCCCTTCCTTTCACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:110,25:0:2,0:23.9:1:31.4:1:1:0:60:66.5:1:0:0.1 0/1:184:2:1,1:143,39:0.0109:2,2:31:1:28.5:1:0.38845:3.63358:60:4:0.0111:0:1 -16 68867397 . G A 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49912;SOR=0.55428;LSEQ=TGTACGGAGGCGGCGAGGAC;RSEQ=ACTAGGGGACTCGAGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:5:4,1:125,199:0.0152:2,2:13.4:1:27.4:1:0.07951:6.33:60:10:0.0154:0:1.4 0/0:472:4:3,1:187,281:0.0085:2,2:20.3:1:26:1:0.30748:4.49:60:3:0.0065:0:2.8 -16 68867427 . G A 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63578;SOR=2.32974;LSEQ=CTCGAGAGAGGCGGGCCCCA;RSEQ=ACCCATGTGCTGGGAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:1,0:67,150:0.0046:2,0:12:0:12:0:0.31193:0:60:0:0:0:2 0/1:282:3:3,0:82,197:0.0106:2,0:5:1:20.3:1:0.02671:0:60:2:0.0073:0:1.7 -16 68867456 . C T 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.15792;LSEQ=GCTGGGAAATGCAGAAATCA;RSEQ=GTTGCTGGTGGTTTTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:23:4,19:16,76:0.2:2,2:20:1:30.5:1:1:1:60:46:0.2018:0:1.1 0/1:159:6:1,5:29,124:0.0377:2,2:22.2:1:31.3:1:1:1.16826:60:12:0.0387:0:1.2 -16 69726407 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17143;SOR=0;LSEQ=CATCCACAGTCTGAAAACAC;RSEQ=TTATCTAATCAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:0.0952:2,2:35:0:32:0:1:1.66897:60:4:0.1:0:1 0/0:29:0:0,0:18,11:0:2,0:30:1:30.1:1:1:0:60:58:1:0:0.2 -16 69726419 . ACAG A 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=1.29449;LSEQ=GAAAACACGTTATCTAATCA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:15,11:0.0714:2,0:22.5:1:31:1:0.50529:0:60:4:0.0714:0:0 0/1:33:3:2,1:17,13:0.0909:2,2:34:1:32.7:1:1:1.51:60:6:0.0909:0:0.3 -16 69727529 . ACAG A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.42688;SOR=1.84794;LSEQ=AGTAACTCTCCATCCCAGGA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:4:1,3:57,51:0.0357:2,2:30.8:1:32:1:0.35086:3.31952:60:8:0.0364:0:0 0/1:187:12:7,5:97,77:0.0642:2,2:25.9:1:31.7:1:1:1.11:60:24:0.0642:0.0107:0.1 -16 69727536 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.13433;SOR=0;LSEQ=CTCCATCCCAGGAACAGCAG;RSEQ=AGCAGCAGCAACAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:62,58:0.0164:2,2:18.5:1:29:1:1:1.06835:60:4:0.0172:0:1.5 0/0:210:0:0,0:112,98:0:2,0:24.6:1:31.8:1:1:0:60:69:1:0:0.2 -16 69727565 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.12427;SOR=0;LSEQ=CAACAGCAGCAGCAACAGCA;RSEQ=CAGCAACAACAACAGAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:49,72:0.0163:2,2:41.5:1:31:1:1:1.46:60:4:0.0167:0:1 0/0:225:0:0,0:101,124:0:2,0:27:1:31.8:1:1:0:60:74:1:0:0.2 -16 69787697 . T A 27 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09259;SOR=0;LSEQ=CTCCTAAGCCAAGAGACAAT;RSEQ=CTTTAATTTTCTTTATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:10,13:0.08:2,2:48:0:27.5:1:1:1.29:60:4:0.087:0:1 0/0:56:0:0,0:24,32:0:2,0:26.8:1:28.8:1:1:0:60:55:1:0:0.2 -16 72821597 . G A 45 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=1;SOR=0.82187;LSEQ=GCCAGGCAGTGGTACGAGCC;RSEQ=CCGCCGCCGCCGCCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:56,241:0.01:2,2:8.3:1:28.7:1:0.09672:8.52:60:6:0.0103:0:1.3 0/0:243:2:1,1:55,182:0.0082:2,2:2:1:26.5:1:0.41447:3.29:60:4:0.0085:0:1 -16 72821603 . G GCCA 48 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.70532;SOR=1.66117;LSEQ=CAGTGGTACGAGCCGCCGCC;RSEQ=CCGCCGCCGCCGCCACCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:2,1:38,199:0.0125:2,2:7.7:1:28:1:0.07291:10.31:60:6:0.0129:0.0083:0.7 0/1:194:4:4,0:42,148:0.0206:2,0:1:1:24.3:1:0.00285:0:60:6:0.0192:0.0179:1 -16 72821612 . G A 25 v4;pSTD;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=1;SOR=1.29181;LSEQ=GAGCCGCCGCCGCCGCCGCC;RSEQ=CCGCCACCGCCGCCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:47,134:0.0109:2,2:18:0:32:0:0.45685:2.83:60:4:0.0112:0:1.5 0/1:142:2:2,0:37,103:0.0141:2,0:1:0:25:1:0.07402:0:60:4:0.0145:0:1 -16 72821621 . G A 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=3;SSF=0.01149;SOR=Inf;LSEQ=CCGCCGCCGCCGCCGCCACC;RSEQ=CCGCCGCCGCCGCCACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:97,83:0:2,0:7.7:1:30.8:1:1:0:60:44:0.9888:0:0.2 0/1:142:5:3,2:70,66:0.0352:2,2:5:1:28.2:1:1:1.41:60:10:0.0365:0:1.4 -16 72821622 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.57557;SOR=2.754;LSEQ=CGCCGCCGCCGCCGCCACCG;RSEQ=CGCCGCCGCCGCCACTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:0,1:103,100:0.0049:2,0:1:0:25:0:0.4951:0:60:2:0.005:0:1 0/1:149:2:1,1:79,68:0.0134:2,2:6.5:1:29:1:1:1.16059:60:4:0.0137:0:1 -16 72821625 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.25295;SOR=0;LSEQ=CGCCGCCGCCGCCACCGCCG;RSEQ=CGCCGCCGCCACTGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:1,2:108,80:0.0157:2,2:7.7:1:28.7:1:0.57778:2.68609:60:6:0.0162:0:1 0/0:162:0:0,0:94,67:0:2,0:8.3:1:31.6:1:1:0:60:79.5:1:0:0.3 -16 72821642 . ACCG A 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.61397;SOR=1.43858;LSEQ=CCGCCGCCGCCGCCACTGCC;RSEQ=CCGCCGCCGCCGGTGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:6:5,1:210,73:0.0206:2,2:22.3:1:32.5:1:1:1.74:60:12:0.0206:0:1.3 0/1:340:10:6,4:231,97:0.0294:2,2:13.3:1:31.2:1:0.49317:1.58529:60:20:0.0295:0.0088:0.3 -16 72821645 . G A 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.76237;SOR=0.716;LSEQ=CCGCCGCCGCCACTGCCACC;RSEQ=CCGCCGCCGCCGGTGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:6:4,2:222,75:0.0194:2,2:20.7:1:29.5:1:0.64615:1.47792:60:12:0.0201:0:1 0/1:359:5:4,1:240,106:0.0139:2,2:19.6:1:29.6:1:1:1.76:60:10:0.0145:0:1 -16 72821959 . CG C 117 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.09196;SOR=0.45985;LSEQ=TTTGTCTGGGGAAGGAGCCC;RSEQ=GGGGGGACTGGGGTTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1408:15:7,8:688,702:0.0107:2,2:25.6:1:30.1:1:1:1.11997:60:30:0.0109:7e-04:0.3 0/0:1624:8:4,4:796,813:0.0049:2,2:38.3:1:30.6:1:1:1.02:60:16:0.005:0:0.5 -16 72822008 . TTGC T 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.39039;SOR=1.29254;LSEQ=GGCTGCTGCTGCTGCACTTT;RSEQ=TGCTGCTGCTGCTGTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1080:20:14,6:492,565:0.0185:2,2:25.7:1:30.2:1:0.04274:2.68:60:40:0.0187:0.0037:0.2 0/1:1218:29:14,15:563,625:0.0238:2,2:26.4:1:29.3:1:1:1.04:60:58:0.0239:0.0041:0.2 -16 72822033 . CGCT C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.70917;SOR=0.86428;LSEQ=GCTGCTGCTGCTGTAGTTGC;RSEQ=GCTGCTGCTGCTGAATTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1074:15:6,9:545,511:0.014:2,2:20.1:1:29.8:1:0.44079:1.5991:60:30:0.0142:0.0047:0.3 0/1:1075:13:5,8:511,547:0.0121:2,2:30.1:1:31.8:1:0.58206:1.49414:60:26:0.0122:0:0.1 -16 72822296 . G A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15831;LSEQ=GTGGGGTCCGAAGTCAACGC;RSEQ=GCCTGCAGGGCCTGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1801:337:185,152:776,685:0.1871:2,2:24.5:1:30.2:1:0.58573:1.07:60:36.444:0.1848:0:1.1 0/1:2134:75:39,36:1078,978:0.0351:2,2:25.5:1:30.3:1:1:1.01746:60:150:0.0355:0:1.2 -16 72822563 . TTGC T 171 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.9183;SOR=0.97041;LSEQ=GGAGGCTGCTGCACCTGTGG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1442:51:27,24:662,722:0.0354:2,2:27.9:1:30.2:1:0.47984:1.23:60:102:0.0362:0.0014:0.2 0/1:1368:47:23,24:627,653:0.0344:2,2:24.4:1:30:1:1:1.00193:60:94:0.0353:0.0073:0.3 -16 72822585 . T G 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=16.19433;LSEQ=GCTGCTGCTGCTGCTGCTGC;RSEQ=GGGGGGGTTGCTGAGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1401:4:4,0:675,716:0.0029:2,0:31:1:9.8:1:0.05587:0:60:0:0:0:2.3 0/1:1376:61:32,29:634,674:0.0443:2,2:25.1:1:29.3:1:0.60085:1.17:60:60:0.0454:0:1.1 -16 72827758 . T C 320 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0088;LSEQ=CGTTTCTGCCCAGGCCGATC;RSEQ=CCGCTGTCACCAGATTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1320:1315:699,616:1,0:0.9962:0,2:24.5:1:30.9:1:1:0:60:45.964:0.9984:0:1.1 1/0:1460:1019:529,490:225,212:0.6979:2,2:24.7:1:30:1:0.90892:1.02:60:49.95:0.6947:0:1.2 -16 72828383 . C T 243 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01438;LSEQ=TCTTGGCTTCATGCCAGTGA;RSEQ=GGGACCGGATATGAGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1364:270:134,136:530,562:0.1979:2,2:23.7:1:30.1:1:0.78573:1.04:60:37.571:0.1954:0:1.1 0/0:1416:5:2,3:720,690:0.0035:2,2:19.2:1:29:1:0.68089:1.56472:60:10:0.0036:0:1 -16 72829426 . C T 199 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=16.44928;LSEQ=CTGTAAGCCTGTGAGGGCAT;RSEQ=GGGGTACTGCAGGATGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1676:7:1,6:851,818:0.0042:2,2:1.6:1:28.3:1:0.06549:6.23641:60:14:0.0042:0:1 0/1:1673:108:49,59:777,783:0.0646:2,2:23.1:1:29.6:1:0.42613:1.19473:60:107:0.0646:0:1.1 -16 72830248 . C T 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=75.37416;LSEQ=AGCTGCGGGGGTAGCTGAGC;RSEQ=GGCAAGGTCTGCAGCGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:852:1:0,1:392,458:0.0012:2,0:19:0:15:0:1:0:60:0:0:0:1 0/1:896:73:37,36:391,430:0.0815:2,2:23.8:1:30.7:1:0.62703:1.13:60:146:0.0823:0:1.1 -16 72830539 . C G 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16928;LSEQ=TGTTTGGCAAACCTCTCGAG;RSEQ=TGTTTGAAAGGAAAGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1825:283:140,143:747,791:0.1551:2,2:24.2:1:31.5:1:0.79601:1.04:60:55.6:0.1544:0:1.2 0/1:1992:60:28,32:939,989:0.0301:2,2:30.2:1:31.1:1:0.79409:1.085:60:120:0.0307:0:1.2 -16 72831026 . T G 195 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0;SOR=39.92064;LSEQ=AGAGTTGGTTCTGCTGCTGC;RSEQ=GCGGCAAGATCTGCTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1295:2:1,1:629,664:0.0015:2,2:9.5:1:9:0:1:1.06:60:0:0:0:5 0/1:1495:87:42,45:696,711:0.0582:2,2:24.2:1:30.3:1:0.9121:1.04881:60:86:0.058:0:1.2 -16 72831196 . GTGC G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0.99443;LSEQ=ATGTAGAAAGGGAAGAGGAG;RSEQ=TGCTGCTGCTGTAGTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1623:17:10,7:837,768:0.0105:2,2:18.1:1:30.8:1:0.6331:1.31:60:34:0.0106:0.0025:0.2 0/1:1728:18:9,9:869,839:0.0104:2,2:33.8:1:31.5:1:1:1.03575:60:36:0.0105:0:0.3 -16 72832135 . T A 323 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01136;LSEQ=ACAATTATGGTATGGTCCTC;RSEQ=GCCAGAGTGGGGTCTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1530:1522:748,774:2,0:0.9948:0,2:24.9:1:30.6:1:0.24202:0:60:100.467:0.9967:0:1.1 1/0:1540:1052:520,532:250,238:0.6831:2,2:23.7:1:30.6:1:0.54688:1.0746:60:149.286:0.6839:0:1.2 -16 72832377 . G A 185 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04335;LSEQ=CAGGCTACACTGATTACAGC;RSEQ=GTACTTGTACACATGGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1542:64:29,35:726,752:0.0415:2,2:27.5:1:30.9:1:0.61015:1.16505:60:128:0.042:0:1.1 0/0:1602:3:3,0:804,792:0.0019:2,0:1:0:28.3:1:0.2496:0:60:6:0.0019:0:1 -16 72863486 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTACAGTATAATGTAGT;RSEQ=TAATAAAGAAGAATAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:75,1:0.0256:1,2:36.5:1:31:1:0.05095:53.38568:60:4:0.0267:0:1 0/0:33:0:0,0:33,0:0:1,0:19.8:1:27.6:1:1:0:60:66:1:0:0.1 -16 72863548 . C A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26719;SOR=0;LSEQ=AAATCTCCCTCCCACTCATC;RSEQ=TTTTTCTGGGCAGACTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:2,1:190,2:0.0154:1,2:32.7:1:30.3:1:0.04568:41.95002:60:6:0.0155:0:1 0/0:141:0:0,0:137,4:0:1,0:23.4:1:30.5:1:1:0:60:69.5:1:0:0.1 -16 72923189 . A T 34 d7;v4;q23;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTTGAGGCCACAAATTG;RSEQ=CTACTCTTAATACTGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:27.3:1:22:1:1:0:60:2:0.6667:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 72923450 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01983;SOR=0.2923;LSEQ=AGAAAAAAAGACAGAAAGGC;RSEQ=GGCAGGCAACAATCCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:34:34,0:27,1:0.5484:1,1:21.3:1:30:1:0.45161:0:60:16:0.5517:0:1.3 0/1:27:7:7,0:18,2:0.2593:2,0:24.7:1:30.1:1:1:0:60:14:0.2593:0:1 -16 72923905 . C T 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGCCTTGGGTAAGCCACT;RSEQ=GAAGCGGCCACTGGCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:0:0,0:226,443:0:2,0:23.4:1:30.1:1:1:0:60:132.8:0.9985:0:0.1 0/1:699:80:30,50:230,388:0.1144:2,2:23.4:1:29.5:1:1:1.01:60:160:0.1158:0:1.2 -16 72923990 . G A 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00065;SOR=Inf;LSEQ=ACATCTCCACAGCCAAACAG;RSEQ=ACAGTCTTTGATATGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:1,159:0:1,0:25.7:1:32:1:1:0:60:159:1:0:0.1 0/1:110:8:0,8:0,102:0.0727:1,0:11.5:1:29.3:1:1:0:60:16:0.0734:0:1.6 -16 72924122 . T C 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGGGGGTGGTTCCCCCA;RSEQ=GCTGTTCTTGTGATACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:0.3333:0,0:24.8:1:31:1:1:0:60:10:0.3571:0:1 0/0:2:0:0,0:0,2:0:0,0:9.5:1:32:0:1:0:60:4:1:0:0 -16 72924395 . GT G 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTGTGAGATTCCTTAGAGG;RSEQ=TTTTTTTTTTTTTTCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:28:0:28:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:22.5:1:31.5:1:1:0:60:4:1:0:0.5 -16 72983981 . GA G 30 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCCGGGAAAGGAGAAATA;RSEQ=AAAAAAAAAAAAGGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:38.5:1:30:1:1:0:60:4:0.6667:0:0 0/0:1:0:0,0:1,0:0:0,0:2:0:31:0:1:0:60:2:1:0:0 -16 72984280 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=Inf;LSEQ=AGGCCATGCCAGAGACTGTC;RSEQ=GACTCCTCCCCAGTGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:180,15:0:2,0:23.5:1:30.9:1:1:0:60:96.5:1:0:0.1 0/1:197:3:1,2:176,18:0.0152:2,2:18:1:27:1:0.02771:18.90933:60:6:0.0154:0:1 -16 72984336 . GA G 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CAACCCCCTCCTTTCAGAAA;RSEQ=GCGCCTGAGCCATAAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:0:0,0:411,192:0:2,0:26:1:30:1:1:0:60:39.2:1:0:0.1 0/1:721:18:12,6:470,229:0.025:2,2:24.2:1:31:1:1:1.02619:60:36:0.0255:0.0055:0.1 -16 72984340 . G A 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCTCCTTTCAGAAAGAGC;RSEQ=CCTGAGCCATAAGGAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:637:0:0,0:430,207:0:2,0:25.9:1:30.2:1:1:0:60:44.5:1:0:0.2 0/1:759:46:32,14:473,240:0.0606:2,2:20.4:1:28.9:1:0.74813:1.16:60:22:0.0589:0:1.3 -16 72984595 . C A 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33424;LSEQ=GCAGTGCAGCTGGAAGTTGG;RSEQ=CTTGAGCTGGGTGTTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1485:234:121,113:607,640:0.1576:2,2:24.2:1:29.5:1:0.43322:1.13:60:32.429:0.1568:0:1.2 0/1:1870:110:54,56:849,906:0.0588:2,2:22.7:1:29.5:1:0.92181:1.03:60:109:0.0593:0:1.2 -16 72984791 . G A 177 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=24.78585;LSEQ=TTGGTCTGGATGAAGCTCTC;RSEQ=CCCAGGTTCATCAGCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1194:2:2,0:579,613:0.0017:2,0:1:0:28:1:0.23657:0:60:4:0.0017:0:1 0/1:1577:63:28,35:708,804:0.0399:2,2:22.6:1:29.7:1:0.7969:1.10065:60:126:0.0406:0:1.1 -16 72984941 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20299;SOR=Inf;LSEQ=GCTGAGGCACCCCCCAGCCC;RSEQ=CCGCCACCCTCAACTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:16,209:0:2,0:23.1:1:29.6:1:1:0:60:31.143:1:0:0.1 0/1:185:2:1,1:22,161:0.0108:2,2:6:0:32:0:0.23378:7.18:60:4:0.011:0:3 -16 72985163 . C CT 47 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTTAATATTTCCTTTT;RSEQ=TTTTTTTTTTTCCCGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:0.25:0,0:20:1:29.7:1:1:0:60:6:0.3:0.0833:0.7 0/0:2:0:0,0:0,2:0:0,0:8:1:32.5:1:1:0:60:4:1:0:0 -16 72990932 . A G 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCCCTAGTCCTCTTATTGA;RSEQ=ATGATTGCCTCAGCTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:19:1:32:1:1:0:60:4:0.4:0:1.5 1/1:1:1:1,0:0,0:1:0,0:15:0:27:0:1:0:60:2:1:0:1 -16 72991286 . C T 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.71846;LSEQ=CACCATTCTCCCTGGTTAAA;RSEQ=TCCTATCATGAAAACAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:241:168,73:260,125:0.385:2,2:24.5:1:30.3:1:0.5968:1.11:60:79.333:0.3857:0:1.2 1/0:653:488:329,159:113,52:0.7473:2,2:22:1:29.8:1:0.84755:1.05014:60:161.667:0.7473:0:1.2 -16 72991660 . C G 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.62867;LSEQ=GGTTTGGTTTTTGGTTTGGT;RSEQ=GGCGAGGGGGCCCCGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1094:416:166,250:302,370:0.3803:2,2:26:1:31.5:1:0.11519:1.229:60:58.429:0.3794:0:1.4 1/1:1288:1034:447,587:120,128:0.8028:2,2:24.7:1:30.8:1:0.15458:1.23091:60:85.167:0.8041:0:1.5 -16 72991696 . TGCC T 117 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.38084;SOR=0.62341;LSEQ=CAGGAGCTACTGATATTGGC;RSEQ=GCCGCCGCCGCAGCCACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:886:13:8,5:394,477:0.0147:2,2:20.7:1:31.7:1:0.2721:1.94:60:26:0.0149:0.0045:1.3 0/0:870:8:2,6:406,447:0.0092:2,2:28.6:1:30.8:1:0.29217:2.72179:60:16:0.0093:0.0023:1.3 -16 72991712 . GCCA G 149 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00098;SOR=3.86244;LSEQ=TGGCTGCCGCCGCCGCCGCA;RSEQ=CCGCCGCCGCCGCCGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:863:7:5,2:424,429:0.0081:2,2:20.6:1:32.8:1:0.2862:2.53:60:14:0.0083:0.0012:0.1 0/1:816:25:13,12:393,387:0.0306:2,2:27.6:1:32.2:1:1:1.07:60:50:0.0314:0:0.6 -16 72991715 . A G 252 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGCCGCCGCCGCCGCAGCC;RSEQ=CCGCCGCCGCCGCCGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:851:291:152,139:268,283:0.342:2,2:22.3:1:30.8:1:0.34629:1.15:60:96:0.3466:0:1.6 0/0:813:0:0,0:83,79:0:2,0:22.9:1:29:1:1:0:60:39.5:0.9814:0:0.2 -16 72992197 . G A 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=85.20159;LSEQ=GCGTGCTGGTGATGGGGAAC;RSEQ=AAGCCCCCATCGTCACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1463:1:1,0:726,735:7e-04:2,0:1:0:27:0:0.49726:0:60:2:7e-04:0:1 0/1:1706:94:48,46:829,779:0.0551:2,2:25.6:1:29:1:1:1.01984:60:22.5:0.0535:0:1.2 -16 72992221 . G A 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.62006;LSEQ=CCCCCATCGTCACCCTCTGT;RSEQ=CTTTCATTTGGTTCTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1471:220:117,103:635,613:0.1496:2,2:24.7:1:29:1:0.5587:1.10:60:219:0.1504:0:1.2 0/1:1831:180:91,89:860,789:0.0983:2,2:22:1:28.8:1:0.69511:1.06597:60:179:0.0988:0:1.2 -16 72992269 . G A 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTCTTTATTGGCACTTTC;RSEQ=TCAGCGAAGTCCAGCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1590:0:0,0:821,765:0:2,0:23.7:1:30.8:1:1:0:60:65.083:0.9981:0:0.2 0/1:1917:73:45,28:961,882:0.0381:2,2:22.3:1:29.8:1:0.12097:1.47:60:146:0.0386:0:1.2 -16 72992443 . G A 256 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2963;SOR=1.10112;LSEQ=TGGAGCACGTTAGGCATTAA;RSEQ=GGGGAGTTAGAAATGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1668:249:127,122:712,705:0.1493:2,2:24:1:30.3:1:0.83695:1.03:60:48.8:0.1475:0:1.2 0/1:2044:331:170,161:860,839:0.1619:2,2:22.5:1:30.6:1:0.81036:1.03:60:330:0.1627:0:1.2 -16 72992614 . TTCC T 111 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.68694;SOR=1.19698;LSEQ=TCTTCTTCCTCCTCCTCTTC;RSEQ=TCCTCCTCCTCCGCCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1109:11:5,6:517,580:0.0099:2,2:28.5:1:30.6:1:1:1.06961:58.2:22:0.0103:0.0027:0.9 0/1:1097:13:6,7:503,581:0.0119:2,2:29.2:1:30.2:1:1:1.01003:60:12:0.0112:0.0018:0.2 -16 72992667 . C G 155 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=29.26803;LSEQ=TTCCTCCTCCGCCTCCTCTT;RSEQ=GGCTGGCTCTACCTTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1216:1:0,1:665,550:8e-04:2,0:30:0:33:0:0.45312:0:60:2:8e-04:0:1 0/1:1317:31:18,13:685,597:0.0235:2,2:26.7:1:31.4:1:0.71645:1.21:60:62:0.0237:0:1.1 -16 72992763 . T G 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGCCCTCTGAGGATTTGG;RSEQ=AGGACTGGAAGCCAGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1386:0:0,0:676,708:0:2,0:25.7:1:28.9:1:1:0:60:80.412:0.9985:0:0.2 0/1:1552:118:57,61:656,774:0.076:2,2:24:1:30.9:1:0.63174:1.10:60:117:0.0763:0:1.3 -16 72993586 . G C 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACTCCCACAGGCGCCCCC;RSEQ=CCCTGGGTCAGCTGGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1286:0:0,0:621,660:0:2,0:24.9:1:30.7:1:1:0:60:57.227:0.996:0:0.2 0/1:1350:94:45,49:598,647:0.0696:2,2:18.9:1:29.9:1:1:1.00642:60:30.333:0.0694:0:1.3 -16 72993622 . C T 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14549;LSEQ=CTCAGGCTCTCCACAATGTA;RSEQ=GCGGAGCCGTCCGGCTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1276:196:88,108:492,587:0.1536:2,2:24.4:1:30.4:1:0.87633:1.02863:60:97:0.1545:0:1.3 0/1:1439:37:16,21:684,713:0.0257:2,2:19.5:1:29.3:1:0.51035:1.25891:60:36:0.0254:0:1.3 -16 72993706 . G A 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1476;LSEQ=CCCTCCTCACCGGTGTCGCT;RSEQ=GCGCTCTCCTCTCTCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:193:92,101:586,551:0.1449:2,2:22.8:1:29.7:1:0.35019:1.16742:60:63.333:0.1454:0:1.3 0/1:1517:37:17,20:716,764:0.0244:2,2:22.1:1:29:1:0.86815:1.10247:60:74:0.0248:0:1.3 -16 72993708 . C T 196 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=48.62557;LSEQ=CTCCTCACCGGTGTCGCTGG;RSEQ=GCTCTCCTCTCTCAGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1332:2:1,1:680,648:0.0015:2,2:17.5:1:29:1:1:1.04936:60:4:0.0015:0:1 0/1:1496:102:53,49:664,725:0.0682:2,2:24.2:1:29.5:1:0.47254:1.18:60:50:0.0684:0:1.2 -16 72993831 . A C 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.87454;LSEQ=CTCCTTGCTGGCGGGCTCGG;RSEQ=GGGGGGCCCGGCCGACGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1053:155:80,75:465,430:0.1472:2,2:24.8:1:30.7:1:1:1.0138:60:37.75:0.1483:0:1.3 0/1:1096:501:263,238:297,292:0.4571:2,2:24.8:1:30.4:1:0.50414:1.09:60:49.1:0.4615:0:1.2 -16 72993860 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14908;LSEQ=CGGCCGACGCGGTGCTCTCC;RSEQ=CGAGGCGCTCATTGAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:994:425:232,193:321,246:0.4276:2,2:25.1:1:30:1:0.56108:1.08543:60:105.25:0.4318:0:1.1 0/1:1029:103:53,50:481,441:0.1001:2,2:24.3:1:29.2:1:0.91742:1.02894:60:19.6:0.0976:0:1.1 -16 72993925 . C T 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.64313;LSEQ=TGGCTCTCGCCTGTGGACTG;RSEQ=TCCATGCTACTGGGTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1425:229:118,111:600,595:0.1607:2,2:25.9:1:29.6:1:0.719:1.05:60:56.25:0.1604:0:1.3 0/1:1569:172:82,90:717,680:0.1096:2,2:23.9:1:29.7:1:0.37505:1.15717:60:171:0.1104:0:1.1 -16 72994134 . AAG A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.38554;SOR=0.30408;LSEQ=GGGAGGAGGGAGAGAGGGGA;RSEQ=AGAGAGAGAAAGGAAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:4:0,4:10,285:0.0134:1,0:26.8:1:31.1:1:1:0:60:8:0.0136:0.0033:0.5 0/0:244:1:0,1:16,227:0.0041:2,0:27:0:33:0:1:0:60:2:0.0042:0:0 -16 72994159 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53014;SOR=0;LSEQ=AGAGAGAAAGGAAAGAGGTT;RSEQ=GGAGGGCCGAGGCTGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:2,190:0.0103:1,2:26.5:1:30:1:0.03077:77.76:60:4:0.0107:0:1 0/0:116:0:0,0:0,116:0:1,0:22.3:1:31.2:1:1:0:60:57:1:0:0.3 -16 72994164 . G A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.86026;SOR=0.92298;LSEQ=GAAAGGAAAGAGGTTAGGAG;RSEQ=GCCGAGGCTGAGGTCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:25:0,25:3,142:0.1471:1,1:24:1:30.8:1:1:0:60:11.5:0.1429:0:1.3 0/1:102:14:0,14:0,88:0.1373:1,1:16.6:1:32.4:1:1:0:60:28:0.1429:0:1 -16 72994419 . T C 38 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGCCAGCATAGCTTCGA;RSEQ=GGGCCACAGTGGAGAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:36.7:1:24.3:1:1:0:60:2:1:0:2.3 1/1:2:2:1,1:0,0:1:0,2:24:1:29.5:1:1:0:60:4:1:0:1 -16 72994891 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCCTGTCTCCTCCACCCA;RSEQ=ACCAGTCAAGCTCCCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:36:0:27:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31.5:1:1:0:60:4:1:0:2 -16 73350538 . A G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGTCTTATACTTGTTGGG;RSEQ=ATCCCCCACTCCACTAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:11.7:1:32.3:1:1:0:60:6:1:0:1.3 1/1:2:2:2,0:0,0:1:0,0:33.5:1:31.5:1:1:0:60:4:1:0:1 -16 73350590 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACCTCAGCAAATTCTTGC;RSEQ=ATAAAATGCTTGATTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:7,1:0.2:2,2:19.5:1:31:1:0.37778:5.29155:60:4:0.2222:0:1 0/0:3:0:0,0:1,2:0:2,0:12.3:1:27.7:1:1:0:60:6:1:0:0.3 -16 73367952 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGATGCAATCAGACAGA;RSEQ=AAGAGGATGGGGTCAAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:28:1:33.5:1:1:0:60:4:0.2857:0:1 0/0:3:0:0,0:3,0:0:0,0:36.3:1:31.3:1:1:0:60:6:1:0:0.3 -16 73367985 . C T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=TCAAGGACATGGCTTATGTG;RSEQ=TGAAAGAGGAAGGAGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:11,2:0:2,0:22.5:1:32.5:1:1:0:60:26:1:0:0.2 0/1:13:2:1,1:7,4:0.1538:2,2:13:0:27:1:1:1.67325:60:4:0.1538:0:1 -16 74639138 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGACGCCTTTCCTCCTCTG;RSEQ=AGCATAAAACTGCCTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:29:1:1:0:60:4:1:0:1 -16 74640735 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17495;SOR=0;LSEQ=GGGAAAGGCGGCTGCGGCGG;RSEQ=TGAGGCTGCTGTTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:46,28:0.0263:2,2:42.5:1:28.5:1:1:1.63167:60:4:0.0274:0:1 0/0:105:0:0,0:59,46:0:2,0:24.3:1:31.2:1:1:0:60:104:1:0:0.2 -16 74640753 . TTGC T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.27717;SOR=Inf;LSEQ=GGCTGAGGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:48,37:0:2,0:26.7:1:29.6:1:1:0:60:41.5:1:0:0.2 0/1:128:3:2,1:66,59:0.0234:2,2:21.7:1:30.3:1:1:1.78:60:6:0.0236:0:0.7 -16 74640758 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51509;SOR=Inf;LSEQ=AGGCTGCTGTTGCTGTTGCT;RSEQ=CTGCTGCTGTTGCTGCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:48,37:0:2,0:26.4:1:31.4:1:1:0:60:27.333:1:0:0.2 0/1:124:2:1,1:63,59:0.0161:2,2:22:0:31:1:1:1.0672:60:4:0.0163:0:1.5 -16 74640810 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15034;SOR=0;LSEQ=TGAGGCAGCTGGGGCAGCTG;RSEQ=TGACCCGCCGGGCCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:12,34:0.0417:2,2:21.5:1:31.5:1:0.47252:2.76:60:4:0.0426:0:1 0/0:75:0:0,0:28,47:0:2,0:20.8:1:31.4:1:1:0:60:74:1:0:0.3 -16 74640828 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08062;SOR=0;LSEQ=TGCTGACCCGCCGGGCCGCC;RSEQ=CCTCCGGCCTGCCCTACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:2,1:7,26:0.0833:2,2:12:1:28:1:0.1479:6.91:60:6:0.0833:0:1 0/0:46:0:0,0:14,32:0:2,0:18.3:1:30.8:1:1:0:60:92:1:0:0.3 -16 74640849 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18659;SOR=Inf;LSEQ=CCTCCGGCCTGCCCTACGAA;RSEQ=GACACAAAGTTGGCCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:1,22:0:1,0:19.7:1:31.9:1:1:0:60:46:1:0:0 0/1:18:2:1,1:0,16:0.1111:1,2:5.5:1:28:1:0.11111:0:60:4:0.1111:0:1.5 -16 75226838 . T A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGCAACACAGCCCTTGGG;RSEQ=CACAGACCAGGCAGAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:22.5:1:29.5:1:1:0:60:4:1:0:0 0/1:7:2:0,2:0,5:0.2857:0,0:23.5:1:28.5:1:1:0:60:4:0.2857:0:1.5 -16 78785550 . C T 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AAATAGAGTTTGATATTAAA;RSEQ=AATACTCCAAGAAAGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:125,83:0:2,0:25.1:1:31.9:1:1:0:60:103:1:0:0.6 0/1:342:19:11,8:182,139:0.0556:2,2:28.4:1:28.5:1:1:1.05:60:38:0.0567:0:2.1 -16 78785563 . A C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41881;LSEQ=TATTAAACAATACTCCAAGA;RSEQ=AGCCATTTCTGCAGAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:230:139:77,62:54,37:0.6043:2,2:24.2:1:31.9:1:0.58773:1.17432:60:68.5:0.6062:0:1.2 0/1:372:145:79,66:117,110:0.3898:2,2:24.7:1:30.7:1:0.59593:1.12:60:47.333:0.388:0:1.2 -16 78785618 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16648;SOR=0;LSEQ=CAGTTCCTTACCAACACGTA;RSEQ=ACATGTTGTGATGAAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:80,117:0.0101:2,2:24:1:28:1:1:1.46:60:4:0.0102:0:2.5 0/0:288:0:0,0:114,174:0:2,0:24.6:1:30.8:1:1:0:60:31:1:0:0.4 -16 78785640 . AAAGG A 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=4.000;MSILEN=4;SSF=0.06824;SOR=Inf;LSEQ=CATGTTGTGATGAAAGAAGG;RSEQ=AAGGAAGGAAGGAGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:53,101:0:2,0:24.2:1:29.8:1:1:0:60:153:1:0:0.4 0/1:192:5:1,4:60,127:0.026:2,2:26:1:30.8:1:1:1.88428:60:10:0.0265:0.0052:0.6 -16 78785685 . AAG A 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.51611;LSEQ=AAGAAGGAGGGAGGGAGGGA;RSEQ=AGAGAGAGAGAAAAGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:0,2:8,66:0.0263:2,0:31.5:1:32:1:1:0:60:4:0.027:0:0 0/1:73:1:0,1:9,63:0.0137:2,0:21:0:33:0:1:0:60:2:0.0137:0:0 -16 78785905 . T TAAG 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATTGGCATTTTTCTTTAAA;RSEQ=AAGGAGGAGGATGAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:32.5:1:28.8:1:1:0:60:4:0.5:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 79008267 . T C 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=TAAACATCTTAATTGAACAG;RSEQ=ACGTGGGTTCTTCCCTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:33.8:1:29.3:1:1:0:60:8:1:0:0 1/1:2:2:2,0:0,0:1:0,0:31.5:1:33.5:1:1:0:60:4:1:0:1.5 -16 79008469 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16857;SOR=Inf;LSEQ=CCTTAAATATTGTGCAATGT;RSEQ=CAGGGAATTATTTCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:95,22:0:2,0:22.2:1:32.2:1:1:0:60:116:1:0:0.1 0/1:82:2:1,1:58,22:0.0244:2,2:21:1:31:0:0.48479:2.60055:60:4:0.0244:0:2 -16 79008482 . T G 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAATGTGCAGGGAATTATT;RSEQ=CAGTTTTGTTTTTTATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:106,38:0:2,0:23.3:1:30.3:1:1:0:60:143:1:0:0.3 1/0:106:54:36,18:37,15:0.5094:2,2:25.5:1:32.1:1:0.67777:1.23089:60:108:0.5192:0:1.1 -16 79008499 . T G 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00039;SOR=Inf;LSEQ=ATTTCAGTTTTGTTTTTTAT;RSEQ=TAGCACAAACCTAAATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:131,68:0:2,0:24.2:1:30.1:1:1:0:59.9:98.5:1:0:0.5 0/1:147:9:7,2:85,53:0.0612:2,2:19.6:1:32.2:1:0.48435:2.17:60:18:0.0616:0:1.7 -16 79008502 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18367;SOR=Inf;LSEQ=TCAGTTTTGTTTTTTATTTA;RSEQ=CACAAACCTAAATATTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:136,74:0:2,0:24.4:1:32.2:1:1:0:59.9:209:1:0:0.6 0/1:158:2:1,1:96,60:0.0127:2,2:16.5:1:26:1:1:1.59502:60:4:0.0127:0:1.5 -16 79008568 . C T 237 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCTGTCCTGAAGAGGAGGA;RSEQ=AGATTATTCTGTGGCTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:295:295:141,154:0,0:1:0,2:26.8:1:28.9:1:1:0:60:58:1:0:1.1 0/1:256:107:54,53:77,72:0.418:2,2:28.2:1:28.5:1:0.89937:1.04947:60:34.667:0.4143:0:1.2 -16 79008612 . T C 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GGTGTTTACAGAGTTGCCAC;RSEQ=TTGCCAAACCCCAAGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:91,138:0:2,0:25.9:1:30.3:1:1:0:60:75.333:1:0:0.9 0/1:226:15:6,9:89,121:0.0664:2,2:31.7:1:30.7:1:1:1.10286:60:30:0.0664:0:1.8 -16 79008629 . C G 215 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTTTGCCAAACCCCAAGA;RSEQ=CCACACTTGGTCTCTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:62,122:0:2,0:23.9:1:31.5:1:1:0:60:183:1:0:0.7 1/0:181:107:39,68:25,48:0.5912:2,2:26.9:1:32:1:0.87413:1.10:60:106:0.5955:0:1.2 -16 79008692 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51043;SOR=0;LSEQ=TTCAGAATGGGATGTTTAGG;RSEQ=CGTAATCTTCTGAGACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:2,45:0.0408:1,2:25.5:1:30:1:0.1199:18.57:60:4:0.0408:0:1 0/0:34:0:0,0:1,33:0:1,0:22.9:1:32.8:1:1:0:60:68:1:0:0.6 -16 79109753 . A C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00622;SOR=3.38249;LSEQ=CTTATAACTATCTCAAAAAA;RSEQ=CATATTAAGTTATTTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:13:13,0:39,0:0.25:1,1:22.4:1:31.8:1:1:0:60:12:0.2353:0:1.3 1/0:45:24:23,1:21,0:0.5333:1,1:26.5:1:32.3:1:1:0:60:48:0.5333:0:1.2 -16 79109842 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.80029;LSEQ=TTAGTTAACATCTGCTCTAA;RSEQ=GTTGGATCATGTGTGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:71:46,25:152,69:0.2432:2,2:24:1:30:1:0.56064:1.19646:60:70:0.2414:0:1.2 0/1:308:146:99,47:95,67:0.474:2,2:23.4:1:29.4:1:0.09985:1.48:60:72:0.4737:0:1.2 -16 79109859 . A G 53 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06037;SOR=0;LSEQ=TAACGTTGGATCATGTGTGG;RSEQ=GTCCCCAGTTTTCAACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:4:2,2:217,153:0.0107:2,2:17.8:1:26.8:1:1:1.41692:60:3:0.0082:0:1.5 0/0:380:0:0,0:212,167:0:2,0:25.3:1:29:1:1:0:60:33.455:0.9973:0:0.7 -16 79109935 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.44385;LSEQ=TCTTACAGTATATGTAGAAC;RSEQ=ATTTTCTTGAAAATGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:71:27,44:98,160:0.2158:2,2:25.3:1:29.3:1:1:1.00:60:142:0.2185:0:1.1 1/0:325:179:67,112:58,88:0.5508:2,2:24.8:1:28.7:1:0.73119:1.10143:60:178:0.5511:0:1.2 -16 79167309 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGATGTCAATATAAACTA;RSEQ=GACACACATTCATATTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:28.5:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 79167548 . G A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16111;LSEQ=AAGTGCTACTTTATATTTCT;RSEQ=CTGTCCTTGCCGGTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:70:67,3:23,1:0.7447:1,1:24.4:1:27.8:1:1:1.02955:60:69:0.7419:0:2 0/1:82:26:24,2:52,4:0.3171:2,2:22.2:1:28.2:1:1:1.08226:60:52:0.3171:0:2 -16 79167560 . G C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16553;LSEQ=ATATTTCTGCTGTCCTTGCC;RSEQ=GTGGCCTGCACTGGGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:97:86,11:26,5:0.7578:2,2:21.1:1:31:1:0.53525:1.50:60:96:0.7559:0:1.8 0/1:112:38:33,5:63,10:0.3393:2,2:19.9:1:29.7:1:1:1.05:60:37:0.3333:0:1.7 -16 79167688 . A G 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.17936;LSEQ=TAACTAGGCGTATAGAATTG;RSEQ=GGGGAAATGCAGGATGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:496:392:193,199:47,56:0.7903:2,2:27.6:1:30.9:1:0.57985:1.16:60:48:0.7918:0:1.1 0/1:546:220:107,113:153,171:0.4029:2,2:26.8:1:30.3:1:0.79316:1.06:60:109:0.4067:0:1.1 -16 79167824 . T G 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00603;SOR=Inf;LSEQ=TGTCAGGGAAGAGATTAATA;RSEQ=AATACTCAGTGAATTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:2,56:0:1,0:24:1:28.8:1:1:0:60:57:1:0:0.1 0/1:57:7:0,7:2,48:0.1228:1,0:30.1:1:32.1:1:1:0:60:14:0.125:0:1.1 -16 79167945 . A G 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01786;SOR=0;LSEQ=AGAGTTTGTTTCTTCCTGCT;RSEQ=TGGCCATAGAGGTTTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:20.2:1:33.2:1:1:0:60:10:1:0:1.2 0/0:3:0:0,0:0,3:0:0,0:19:1:30.7:1:1:0:60:6:1:0:0 -16 79168070 . AT A 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATTGGGATTATCTTATG;RSEQ=TTTTTTTTCTCTTTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:37:1:32.7:1:1:0:60:6:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 79890072 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49826;SOR=Inf;LSEQ=TTGAAGAGTGTTTTCCAGCT;RSEQ=GTTTCCATTCTCCTCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:19.6:1:30.6:1:1:0:60:36:1:0:0.1 0/1:24:2:1,1:14,8:0.0833:2,2:10:0:32.5:1:1:1.70775:60:4:0.087:0:1 -16 79979756 . A T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTATAAAACACTGCTCT;RSEQ=GCTAAGGGACCTAGTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:28.5:1:1:0:60:4:1:0:1 -16 79979968 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGCCTTAGGGCTGTCTC;RSEQ=CAGGTCTCCAGAGAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 79980350 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25404;SOR=0;LSEQ=CCTGTGACATTTCCAACAAT;RSEQ=CAACACTATTTGGTAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:3:2,1:133,71:0.0145:2,2:24:1:23.3:1:1:1.07:60:2:0.0099:0:1.3 0/0:173:0:0,0:111,62:0:2,0:22.7:1:31.7:1:1:0:60:172:1:0:0.6 -16 79980354 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21311;SOR=Inf;LSEQ=TGACATTTCCAACAATGCAA;RSEQ=ACTATTTGGTAAATATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:137,77:0:2,0:26.2:1:31.9:1:1:0:60:70.333:1:0:1 0/1:184:2:1,1:114,68:0.0109:2,2:6.5:1:28:1:1:1.67149:60:4:0.011:0:2.5 -16 79980355 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.21453;SOR=Inf;LSEQ=GACATTTCCAACAATGCAAC;RSEQ=CTATTTGGTAAATATTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:138,77:0:2,0:26.5:1:29.7:1:1:0:60:42:1:0:1 0/1:186:2:1,1:114,70:0.0108:2,2:26.5:1:28.5:1:1:1.62408:60:4:0.0109:0:1 -16 79980410 . A C 256 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00454;LSEQ=GGGATAAGAAATGACCTTTC;RSEQ=ATCTATATGGAGCAAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:288:287:153,134:1,0:0.9965:0,2:25.5:1:31.4:1:1:0:60:56.4:1:0:2.1 1/0:342:193:106,87:78,71:0.5643:2,2:26.2:1:30.2:1:0.66266:1.11:60:47.25:0.5608:0:2.3 -16 79980425 . A T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24745;LSEQ=CTTTCAATCTATATGGAGCA;RSEQ=GTTAATTACTAAAAAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:299:239:123,116:30,30:0.7993:2,2:24.4:1:30.3:1:0.88566:1.06:60:78.667:0.8:0:2.5 0/1:361:179:93,86:94,88:0.4958:2,2:26.6:1:29.8:1:1:1.01:60:178:0.4972:0:2.6 -16 79980463 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28731;LSEQ=CAGCAATTGGTTGTAAAGGA;RSEQ=TGTTCTGCTGTCGTCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:256:203:83,120:19,34:0.793:2,2:27.4:1:30.3:1:0.53266:1.24:60:202:0.7922:0:2.3 1/0:321:168:73,95:67,86:0.5234:2,2:24.9:1:29.9:1:1:1.01382:60:167:0.5235:0:2.3 -16 79980525 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=0;LSEQ=GGTTATGAATTATCCTTGGA;RSEQ=GAAATATGGACACATGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:12,92:0.0189:2,2:13.5:1:30.5:1:0.23127:7.41:60:4:0.0189:0:1.5 0/0:106:0:0,0:25,81:0:2,0:22.6:1:30.8:1:1:0:60:212:1:0:0.5 -16 80160491 . A C 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54629;SOR=0;LSEQ=GGGGCACTTACTCCTAACAA;RSEQ=TTCACTCTAAAGACTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:4,0:15,0:0.2105:1,0:11.5:1:27.3:1:1:0:60:3:0.1667:0:1.8 0/0:7:0:0,0:7,0:0:0,0:11.4:1:30.3:1:1:0:60:14:1:0:0.3 -16 80160551 . G A 162 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCCCTGTAACCTGCAAAG;RSEQ=GGAAGTAGCACCAGAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:42,0:0,0:1:0,1:22.5:1:30.1:1:1:0:60:41:1:0:1.3 0/1:26:6:6,0:20,0:0.2308:1,0:26.2:1:29:1:1:0:60:12:0.2308:0:1 -16 80160659 . G T 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0208;SOR=Inf;LSEQ=TTGTTGGCAGTTTATTTGAA;RSEQ=GCTCTTGTTTGTGAAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:169,107:0:2,0:23.6:1:31.4:1:1:0:60:275:1:0:0.3 0/1:359:7:3,4:222,129:0.0195:2,2:8.3:1:29.3:1:0.43118:2.28899:60:14:0.0198:0:1.1 -16 80160745 . G C 259 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00177;LSEQ=TCTCTCATCTCTTTTCATCT;RSEQ=AAACACGATTATTATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:296:295:110,185:0,0:0.9966:0,2:24.6:1:31.6:1:1:0:60:97.333:0.9966:0:1.1 0/1:364:124:51,73:90,147:0.3407:2,2:23.9:1:31:1:0.57177:1.14:60:123:0.3417:0:1.1 -16 80160786 . TA T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.08968;SOR=0;LSEQ=TGCTTTTTGGTTCCAATTAT;RSEQ=AAAAAAAGATGAGCAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:0,3:31,108:0.0211:2,0:34.7:1:30.7:1:1:0:60:6:0.0213:0:1 0/0:174:0:0,0:49,125:0:2,0:22.6:1:29.1:1:1:0:60:86:1:0:0.4 -16 80160920 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTAGGTGAGTGGAGTTGT;RSEQ=AGGGGATTGAGCCTCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:0.2:0,0:42.5:1:32:0:1:0:60:4:0.2:0:1.5 0/0:3:0:0,0:0,3:0:0,0:17:1:32:1:1:0:60:6:1:0:0 -16 80770070 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGTTCATCAGCTCCTGAA;RSEQ=CTAACTGCAAATGGTGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:28:1:1:0:60:4:1:0:1 -16 80771405 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08245;SOR=Inf;LSEQ=GCCACTGTATTAAACTGTAC;RSEQ=TTGCTCTAGGTACCGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:21,10:0:2,0:17.6:1:31.2:1:1:0:60:62:1:0:0.2 0/1:13:2:1,1:6,5:0.1538:2,2:11.5:1:28:1:1:1.18321:60:4:0.1538:0:1 -16 80771438 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49521;SOR=0;LSEQ=CCGTGAGCATGGCTCTTCAT;RSEQ=CCAGCTGTTGCCTGGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:23,20:0.0444:2,2:31:1:29:1:1:1.14642:60:4:0.0444:0:1.5 0/0:41:0:0,0:23,18:0:2,0:23.9:1:27.8:1:1:0:60:40:1:0:0.2 -16 80771447 . TG T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21026;SOR=Inf;LSEQ=TGGCTCTTCATACCAGCTGT;RSEQ=CCTGGACTGTTGTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,23:0:2,0:31:1:31.1:1:1:0:60:11.25:1:0:0.2 0/1:42:2:1,1:22,18:0.0476:2,2:11.5:1:28.5:1:1:1.21636:60:4:0.0476:0:0 -16 81818459 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCCAGGGCCTGGGGAGC;RSEQ=CCTTCACTCTAAGTCCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:60:4:1:0:1 -16 81819486 . C G 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGGTTCCTGAAGTTCATG;RSEQ=CCTGTTAACTAAACCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:187,8:0:1,0:23.9:1:32.3:1:1:0:60:47.75:1:0:0.1 0/1:193:33:32,1:158,2:0.171:1,1:23.3:1:31:1:0.43209:2.45404:60:66:0.1737:0:1.1 -16 81819768 . T C 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.78411;LSEQ=GTGGCCTGGAGCAAGACCGC;RSEQ=GACAAGATCGAGGGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1113:310:135,175:384,418:0.2785:2,2:23.7:1:29.9:1:0.20322:1.19067:60:61:0.2788:0:1.5 1/0:1517:786:374,412:354,375:0.5181:2,2:25:1:29.6:1:0.71883:1.03991:60:195.5:0.5196:0:1.5 -16 81819812 . T C 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTACTCGCTGGGTGGGGCAG;RSEQ=GTGGCCCGTCCTCTGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:777:0:0,0:296,481:0:2,0:24.3:1:29.8:1:1:0:60:96.125:1:0:0.6 0/1:1026:25:8,17:402,597:0.0244:2,2:23.2:1:30.6:1:0.53619:1.43042:60:24:0.0236:0:2.8 -16 81819820 . G A 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00293;SOR=1.38594;LSEQ=TGGGTGGGGCAGTGTGGCCC;RSEQ=TCCTCTGGGGCCCTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:698:196:70,126:176,326:0.2808:2,2:24.4:1:30.4:1:0.92977:1.03:60:97:0.2812:0:1.7 0/1:897:315:116,199:214,368:0.3512:2,2:25:1:29.4:1:1:1.00:60:51.5:0.3503:0:1.9 -16 81819853 . C T 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTGGCCTGAGCACCTGTCCA;RSEQ=CTTCCTGTCTTGTCATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:80,329:0:2,0:24.9:1:31.2:1:1:0:60:50.125:1:0:0.4 0/1:494:19:4,15:97,378:0.0385:2,2:21.4:1:28.3:1:1:1.04:60:18:0.0376:0:1.8 -16 81887628 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGGGAAAAGGTCATCAA;RSEQ=GTCAAGGTCAACCGGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:34:1:32:0:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81887820 . C T 84 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.28327;SOR=0;LSEQ=GGGTGAGCGGAAACCCCAAA;RSEQ=TCTTCAGACTCCAGGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:12,1:0.35:1,0:30.1:1:30.1:1:1:0:60:14:0.35:0:1.1 0/0:4:0:0,0:4,0:0:0,0:29:1:30.8:1:1:0:60:8:1:0:0.3 -16 81887903 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00101;SOR=0.11808;LSEQ=TCCATTTCCAGAAGGAGGGG;RSEQ=CACTGAGTCCAGACGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:24:24,0:61,2:0.2759:1,1:29.5:1:29.9:1:1:0:60:11:0.2619:0:3.1 0/1:47:2:2,0:43,2:0.0426:1,0:16.5:1:32.5:1:1:0:60:4:0.0444:0:2 -16 81887938 . T C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=0.33563;LSEQ=GCAGAGATAGCTTTGCGGGA;RSEQ=CCTGTTGGGGAAGGAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:56:55,1:98,0:0.3636:1,1:20.6:1:31.5:1:0.36364:0:60:27:0.3649:0:3.2 0/1:106:17:17,0:87,2:0.1604:1,1:16.8:1:32.1:1:1:0:60:34:0.165:0:2.4 -16 81887948 . G T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57048;SOR=2.88416;LSEQ=CTTTGCGGGATCCTGTTGGG;RSEQ=AAGGAAGGAGCCAGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:1,0:177,1:0.0056:1,0:22:0:26:0:1:0:60:2:0.0056:0:4 0/1:125:2:2,0:121,2:0.016:1,0:30.5:1:31.5:1:1:0:60:4:0.0164:0:2.5 -16 81887957 . A C 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=0.39784;LSEQ=ATCCTGTTGGGGAAGGAAGG;RSEQ=GCCAGGCTGTGCCTGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:70:69,1:122,2:0.3608:1,1:24.3:1:32.3:1:1:1.13:60:69:0.3613:0:3 0/1:153:28:28,0:119,6:0.183:1,1:23.8:1:32.4:1:0.59296:0:60:56:0.1854:0:1.9 -16 81887977 . G C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05397;LSEQ=AGCCAGGCTGTGCCTGGGCT;RSEQ=CAGTTGTGTGGCTGCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:107:96,11:141,17:0.4038:2,2:24.3:1:31.4:1:1:1.05:60:106:0.403:0:2.2 0/1:228:8:7,1:195,25:0.0351:2,2:24.1:1:31.4:1:1:1.1137:60:16:0.0356:0:2 -16 81888152 . A G 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.62233;LSEQ=GACTGCTGCTTCACCATCCT;RSEQ=TATGGCACTCAGTTCGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1217:388:188,200:404,424:0.3188:2,2:24.3:1:31.8:1:0.95094:1.01364:60:76.6:0.321:0:1.2 0/1:1410:318:149,169:511,580:0.2255:2,2:22.8:1:31:1:1:1.00:60:52:0.2251:0:1.3 -16 81888237 . G C 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.52386;LSEQ=CTCCTTCCCTGTGCCTTAGT;RSEQ=TCTTCCTGAAGAAGTTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:185:48,137:91,249:0.3517:2,2:24.1:1:31.6:1:0.91758:1.04301:60:36:0.3495:0:1.8 0/1:547:121:41,80:140,285:0.2212:2,2:24:1:31.3:1:0.91288:1.04:60:242:0.222:0:1.5 -16 81888274 . C A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.07242;LSEQ=CGCTAATAGCAGAATGCTCA;RSEQ=CCCTGCCTGCTCACTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:105:10,95:21,138:0.3977:2,2:26.4:1:29.7:1:0.43685:1.4437:60:34:0.3969:0:2 0/1:264:12:1,11:39,213:0.0455:2,2:21.2:1:29.9:1:0.69968:2.00983:60:24:0.0462:0:1.9 -16 81888279 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11785;SOR=Inf;LSEQ=ATAGCAGAATGCTCACCCCT;RSEQ=CCTGCTCACTGATGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:26,210:0:2,0:25.2:1:32:1:1:0:60:46.2:1:0:0.8 0/1:228:3:1,2:32,193:0.0132:2,2:19.7:1:22.3:1:0.3758:3.00:60:2:0.0088:0:2 -16 81888344 . G A 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.43216;SOR=0.68028;LSEQ=CCCTGCCCCTTTCTAGCTGT;RSEQ=TGTCTTTAGGTGAGTGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:27:1,26:1,57:0.3176:1,1:22.6:1:31:1:0.53697:2.17:60:26:0.3095:0:1.7 0/1:50:12:1,11:1,37:0.24:1,2:23.6:1:30:1:0.42612:3.26:60:24:0.24:0:1.3 -16 81891432 . C G 89 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTGGACACATGACTGAA;RSEQ=CTGTCTTAGGTTCAGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:0.6364:0,0:33:1:32:1:1:0:60:14:0.7:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81891475 . A G 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCATGTGTTAAATGGGAAT;RSEQ=TAATAGTACTTCCCTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:9:1:30.5:1:1:0:60:4:0.2:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81891694 . AAAGCAGG A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58523;SOR=1.51893;LSEQ=TGTGGCCCCATCTCAGACAA;RSEQ=TCCTAGGGCCATGACGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:17:17,0:26,0:0.3953:1,1:22.9:1:31.6:1:1:0:60:34:0.3953:0.093:0 1/0:20:10:10,0:9,1:0.5:2,0:28.1:1:31:1:1:0:60:20:0.5:0.05:0 -16 81891722 . GA G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02173;SOR=0.37748;LSEQ=TCCTAGGGCCATGACGGTGT;RSEQ=AAGGGGATGCTTTCTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:34:34,0:44,0:0.4359:1,1:18:1:31.9:1:1:0:60:68:0.4359:0.141:0.9 0/1:49:11:11,0:34,3:0.2245:2,0:16.7:1:32.6:1:1:0:60:22:0.2292:0.0612:0.1 -16 81891790 . C G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06427;LSEQ=GCTTCTCCCATCTTCGTGAT;RSEQ=TGTATGGGGCAGGGCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:86:80,6:183,12:0.306:2,2:24.7:1:32.1:1:0.79503:1.14318:60:85:0.3069:0:1.2 0/1:255:7:7,0:225,23:0.0275:2,0:28.1:1:31:1:1:0:60:14:0.028:0:1 -16 81891998 . G C 296 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.95244;LSEQ=TGTTGATTTGCGTAGTTGCT;RSEQ=ATTCCTTTATTCTGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:788:557:181,376:74,156:0.7069:2,2:24:1:31.6:1:1:1.01:60:78.571:0.7134:0:1.2 1/1:822:744:264,480:27,50:0.9051:2,2:25:1:31.1:1:1:1.02:60:92:0.9064:0:1.3 -16 81892037 . AGG A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.47402;SOR=1.45171;LSEQ=CTTTAGCCAACATGGGCTAC;RSEQ=GGGGAAAAAAAAAAAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:7:4,3:44,316:0.0188:2,2:14.1:1:31.7:1:0.00675:9.47:60:14:0.0196:0:2 0/1:369:10:2,8:59,299:0.0271:2,2:22.7:1:31.8:1:0.67397:1.27:60:20:0.0279:0:2 -16 81892042 . GGAAAAA AAAC 229 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0;SOR=2.18159;LSEQ=GCCAACATGGGCTACAGGGG;RSEQ=AAAAAAAAGGGACATTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:130:15,115:19,184:0.3824:2,2:23.6:1:30.9:1:0.57927:1.26:60:260:0.3927:0.0853:0.8 1/0:334:192:27,165:22,108:0.5749:2,2:22.1:1:30.3:1:0.5284:1.24398:60:191:0.5805:0.1467:0.9 -16 81892472 . TA T 106 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTAGCTTTTTGGGGAT;RSEQ=AATGACTATCATCAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:10,1:0,0:1:0,2:29.2:1:30.9:1:1:0:60:22:1:0.0909:0.5 1/1:1:1:1,0:0,0:1:0,0:23:0:32:0:1:0:60:2:1:0:0 -16 81892498 . A T 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTATCATCAGAAGGAATTG;RSEQ=CAATGTAAAGAAACCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:10,1:0.3125:2,0:27.8:1:29.8:1:1:0:60:10:0.3125:0:1 0/0:1:0:0,0:1,0:0:0,0:47:0:30:0:1:0:60:2:1:0:0 -16 81892708 . T A 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00411;SOR=0.69984;LSEQ=TCTCTCTTTCTTTTGTCTCA;RSEQ=ATTTCTTTCCAGTTGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:603:430:312,118:124,49:0.7131:2,2:23.4:1:30.2:1:0.84091:1.04:60:142.333:0.7152:0:1.2 1/0:619:393:275,118:149,77:0.6349:2,2:23.9:1:29.7:1:0.32313:1.20:60:77.6:0.6371:0:1.1 -16 81892895 . C T 138 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=32.92637;LSEQ=ACTGCGTCCATTGTGATCTG;RSEQ=GGATGCCATGTTGGGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:1:0,1:0,162:0.0061:1,0:10:0:31:0:1:0:60:2:0.0062:0:1 0/1:153:26:2,24:2,124:0.1699:1,2:16.7:1:29.5:1:0.13577:5.08:60:25:0.1656:0:1.2 -16 81892901 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22174;SOR=Inf;LSEQ=TCCATTGTGATCTGCGGATG;RSEQ=CATGTTGGGTCCTGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:0,150:0:1,0:24.5:1:31.8:1:1:0:60:149:1:0:0.3 0/1:134:2:0,2:3,129:0.0149:1,0:29:1:28.5:1:1:0:60:4:0.0152:0:1 -16 81892913 . C T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10021;LSEQ=TGCGGATGCCATGTTGGGTC;RSEQ=TGGGGTTGAGGATGACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:37:0,37:0,91:0.2891:1,1:23.5:1:31.4:1:1:0:60:74:0.296:0:1.1 0/1:103:4:0,4:2,97:0.0388:1,0:26.8:1:29.8:1:1:0:60:8:0.0392:0:1.3 -16 81902583 . C G 116 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10375;SOR=0.16168;LSEQ=CCCTCCTTATTGGGGCATCA;RSEQ=CCTACCCTGTGAGTCTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:12,0:11,0:0.5217:0,0:35.1:1:32.5:1:1:0:60:24:0.5217:0:1.1 0/1:7:1:1,0:5,1:0.1429:2,0:39:0:33:0:1:0:60:2:0.1429:0:1 -16 81902600 . G C 83 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00805;SOR=8.69723;LSEQ=TCACCCTACCCTGTGAGTCT;RSEQ=CTATGTGACCCATGTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:3,0:28,0:0.0968:1,0:8.3:1:32.7:1:1:0:60:6:0.1:0:1 1/0:12:6:6,0:5,1:0.5:2,0:17.7:1:32.3:1:1:0:60:12:0.5455:0:1.3 -16 81902729 . GC G 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24031;SOR=0.80655;LSEQ=ACCAGGCTCTCTCATAGAGG;RSEQ=TGCCTGAGGTGGGAACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:129:123,6:145,11:0.4526:2,1:23.7:1:31.4:1:0.45842:1.55:59.9:128:0.4555:0.0842:0.2 0/1:220:88:80,8:123,9:0.4:2,2:23.6:1:31:1:0.60957:1.36466:60:176:0.4037:0.0955:0 -16 81902746 . C G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGCTGCCTGAGGTGGGAA;RSEQ=TGATGGGAGCAGCTAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:327,50:0:2,0:24.1:1:32:1:1:0:60:74.4:1:0:0.2 0/1:337:24:22,2:261,51:0.0712:2,2:23.9:1:31.8:1:0.39457:2.15:60:48:0.0719:0:2.5 -16 81902751 . G T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05403;SOR=Inf;LSEQ=TGCCTGAGGTGGGAACTGAT;RSEQ=GGAGCAGCTAAATCCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:344,68:0:2,0:24.1:1:31.9:1:1:0:60:81.4:1:0:0.2 0/1:386:4:1,3:316,66:0.0104:2,2:14.3:1:26.5:1:0.01919:14.21821:60:8:0.0104:0:1 -16 81902763 . A G 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACTGATGGGAGCAGCTAA;RSEQ=TCCTGTGCTGTTGAAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:0:0,0:399,119:0:2,0:24.2:1:29.9:1:1:0:60:46.091:1:0:0.3 0/1:524:38:29,9:363,122:0.0725:2,2:19.7:1:31.2:1:1:1.08:60:37:0.0721:0:2.6 -16 81902797 . A G 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.1592;LSEQ=AAAACCCTCAAGGTGACAGA;RSEQ=CTGGGTCTCCCTCTTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:912:169:101,68:470,271:0.1853:2,2:25.1:1:31.9:1:0.37918:1.16745:60:55.333:0.1849:0:1.1 0/1:985:412:254,158:349,221:0.4183:2,2:24.6:1:31.7:1:0.94705:1.02:60:136.333:0.4191:0:1.2 -16 81902879 . C G 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTTTAAAGTGAGCAGTGC;RSEQ=AAGTTCCTTAAAGATAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1421:0:0,0:688,731:0:2,0:24.4:1:31.6:1:1:0:60:108.154:0.9986:0:0.1 0/1:1611:77:33,44:753,778:0.0478:2,2:21.7:1:30.2:1:0.29482:1.29028:60:76:0.0475:0:1.1 -16 81902990 . G A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=0.47094;LSEQ=GTGGCTTGCCTTTGAGTTCC;RSEQ=TGGAATAGTGCACAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:74:11,63:41,232:0.2133:2,2:22.2:1:30.5:1:1:1.01212:60:73:0.2135:0:1.3 0/1:336:38:6,32:50,248:0.1131:2,2:22.8:1:30.3:1:1:1.07504:60:76:0.1145:0:1.2 -16 81903055 . G A 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=3.30928;LSEQ=AGTTCAGACAGAGGGATCAT;RSEQ=GACATATCTGAGGACCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:23:0,23:1,98:0.187:1,1:23.7:1:32.1:1:1:0:60:46:0.1885:0:1.6 0/1:83:36:0,36:0,47:0.4337:1,1:22.9:1:31.1:1:1:0:60:35:0.4268:0:1.3 -16 81904375 . C TA 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=2e-05;SOR=2.51422;LSEQ=ATAGCATGCCATTTCTGAAA;RSEQ=AAAAATTATTCTATAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:49:47,2:154,16:0.2237:2,1:21.5:1:30:1:0.37523:2.43:59.8:98:0.2237:0.0822:1.1 0/1:183:77:71,6:96,10:0.4208:2,2:19.7:1:29.4:1:0.79486:1.23:59.9:154:0.4231:0.1475:1.1 -16 81904433 . TG T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.77001;LSEQ=GGTGGACATCAAAAATCATG;RSEQ=GTCACTTTTTTCATATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:678:138:81,57:348,192:0.2035:2,2:25.7:1:31.7:1:0.23519:1.27497:59.9:276:0.2057:0.0354:0.3 0/1:668:277:178,99:238,153:0.4147:2,2:26.6:1:31.1:1:0.41789:1.16:60:554:0.4184:0.0539:0.3 -16 81904674 . T C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=9e-04;SOR=3.26354;LSEQ=GGAAACATAAATGAGAATGA;RSEQ=GAAAGCATACCATTTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:18:0,18:0,75:0.1935:1,1:23.9:1:30.3:1:1:0:60:36:0.1978:0:1.4 0/1:68:30:0,30:2,35:0.4412:2,1:19.6:1:30.1:1:0.49796:0:60:60:0.4412:0:1.4 -16 81904711 . T A 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12159;SOR=2.34741;LSEQ=CATCCATTAGATTGGCAAAA;RSEQ=TCTTTAACCATGACAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:9:0,9:0,28:0.2432:1,0:26.6:1:31:1:1:0:60:18:0.2432:0:2.1 0/1:30:13:0,13:1,16:0.4333:1,1:24.8:1:30.5:1:1:0:60:26:0.4333:0:2 -16 81914000 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTTCTAGGACTCTACTC;RSEQ=GTAGAAAAACTGGCACAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:12.5:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81914303 . C A 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00642;SOR=0;LSEQ=GTGACTGCTTCTTGGGAATA;RSEQ=GACTGTGGAGGGAATGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:53,1:0,0:1:0,1:26.8:1:29.5:1:1:0:60:17:1:0:1.1 1/1:33:28:27,1:5,0:0.8485:0,1:19.4:1:30.9:1:1:0:60:56:0.8485:0:1.1 -16 81914486 . C CT 124 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.1694;SOR=1.82838;LSEQ=TAAGTGACTTGTCTAAGGTT;RSEQ=TTTTTTTTGTGTGTGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1241:8:4,4:703,529:0.0064:2,2:23.5:1:28.6:1:0.73127:1.3286:60:7:0.0057:0.0016:0.4 0/1:1535:18:10,8:832,685:0.0117:2,2:22.7:1:29.8:1:1:1.03:60:36:0.0118:0.0026:0.4 -16 81914583 . C T 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.22211;LSEQ=GGCAGCTCTTGTGTGTCGTT;RSEQ=GGGGCGGCTGTGCCGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1001:754:299,455:82,162:0.7532:2,2:25.5:1:30:1:0.09572:1.30:60:61.833:0.7533:0:1.2 0/1:1191:481:200,281:277,433:0.4039:2,2:27.2:1:29.7:1:0.39894:1.11:60:79.167:0.4015:0:1.1 -16 81914619 . A C 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACCTCGGTGCCTGGTGCCC;RSEQ=GCCGGCCTCCAGGAGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:0:0,0:169,414:0:2,0:22.9:1:30.7:1:1:0:60:71.875:1:0:0.8 0/1:669:85:21,64:186,398:0.1271:2,2:23.4:1:29.6:1:0.2098:1.42355:60:170:0.1286:0:1.1 -16 81914851 . G GT 87 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TGAGATGTGACAGGTTAATA;RSEQ=TTTTTTTTTTTAATTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:0,8:0,5:0.5714:0,0:22.3:1:29:1:1:0:60:16:0.5714:0:0.1 0/0:2:0:0,0:0,2:0:0,0:18:1:31.5:1:1:0:60:4:1:0:0 -16 81916638 . G A 117 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12532;SOR=0.18447;LSEQ=CTATTTTGGAGCAGCTAAAT;RSEQ=TAGACACCAGGGCCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:16:16,0:20,0:0.4444:1,1:15.3:1:29.3:1:1:0:60:32:0.4444:0:1.1 0/1:8:1:1,0:7,0:0.125:0,0:44:0:29:0:1:0:60:2:0.125:0:1 -16 81917099 . G T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.11666;LSEQ=GTCTTCATGGAACGATTGCA;RSEQ=TCTGCCAGATGCCAGAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:26:0,26:2,65:0.2796:1,1:20.9:1:30.2:1:1:0:60:52:0.2889:0:1.2 0/1:70:3:0,3:2,65:0.0429:1,0:13.7:1:31.7:1:1:0:60:6:0.0441:0:1 -16 81917183 . G C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.43315;SOR=2.33278;LSEQ=CCTCATGTCGGGCCTCTTTT;RSEQ=AAGGCACACATTGAGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:0,10:0,12:0.4545:0,0:23.6:1:33.4:1:1:0:60:20:0.4762:0:1.3 1/0:9:6:0,6:0,3:0.6667:0,0:16.2:1:32.3:1:1:0:60:12:0.6667:0:1 -16 81922813 . C T 173 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.8609;LSEQ=ATCTGAACAAAGTCCGTGAG;RSEQ=GGATGACAAAGTTCATTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1352:2:0,2:736,614:0.0015:2,0:1:0:25:0:0.20741:0:60:4:0.0015:0:1 0/1:1419:64:32,32:720,633:0.0451:2,2:26.6:1:28.9:1:0.70091:1.13734:60:20.333:0.0436:0:1.1 -16 81923018 . GTTTCT G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=4.000;MSILEN=1;SSF=0.55509;SOR=0;LSEQ=CTGACTGGTTAGCTGGGATT;RSEQ=TTTCTTTTCTTTTCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:3:0,3:3,152:0.019:1,0:20.3:1:31:1:1:0:60:6:0.0194:0.0063:0.3 0/0:89:0:0,0:3,86:0:1,0:19.5:1:30.5:1:1:0:60:88:1:0:0.1 -16 81924905 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12564;SOR=Inf;LSEQ=AAATATGTCGCTGCAGCCCA;RSEQ=TGCAGCCTGAGCCTTCGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:0:1,0:26.4:1:30.4:1:1:0:60:19.333:1:0:0.2 0/1:34:2:2,0:31,1:0.0588:1,0:35.5:1:30.5:1:1:0:60:4:0.0588:0:1 -16 81924989 . TC T 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.5919;SOR=2.42972;LSEQ=TCCCGCATCAGAGCTGTTCT;RSEQ=CCCCCTGGTGGGCGCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:1:1,0:190,17:0.0048:2,0:16:0:33:0:1:0:60:2:0.0049:0:0 0/1:172:2:2,0:153,17:0.0116:2,0:37:1:33:0:1:0:60:4:0.0117:0:0 -16 81924994 . C T 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.00086;SOR=Inf;LSEQ=CATCAGAGCTGTTCTTCCCC;RSEQ=CTGGTGGGCGCAGACCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:202,22:0:2,0:24:1:31.2:1:1:0:60:223:1:0:0.1 0/1:192:9:8,1:161,22:0.0469:2,2:23.8:1:30.8:1:1:1.09:60:18:0.0469:0:1.1 -16 81925026 . C T 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACCAGAAACAAGCAGACA;RSEQ=CATCCTGCCCGTCAACGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:309,110:0:2,0:23.9:1:31.6:1:1:0:60:51.375:1:0:0.1 0/1:391:25:19,6:272,93:0.0639:2,2:23.6:1:29.3:1:1:1.08:60:11.5:0.0594:0:1.4 -16 81925053 . G A 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCGTCAACGTGATGATTC;RSEQ=GTCTTCGTGTTTGACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:0:0,0:434,236:0:2,0:24.8:1:30:1:1:0:60:50.538:1:0:0.1 0/1:669:26:19,7:407,234:0.0389:2,2:21.7:1:30:1:0.40666:1.56:60:52:0.0392:0:1.1 -16 81925437 . A G 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00393;SOR=18.76572;LSEQ=AAAAAGCTAGTAAAAACAAA;RSEQ=GTAACTTAGTTTATGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:0,6:0,21:0.2222:1,0:29.2:1:27.8:1:1:0:60:5:0.2083:0:1 1/1:7:6:0,6:0,1:0.8571:0,0:18:1:30.2:1:1:0:60:12:0.8571:0:1.2 -16 81926894 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCACCAACAGTTGTTGAAT;RSEQ=TCTGTTCTGTGCCTGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:28:1:30.5:1:1:0:60:4:0.4:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81927036 . TCTC T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACGTGCTTTGACCAACT;RSEQ=CTCAAAAGAACACGTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:39.5:1:33.5:1:1:0:60:4:0.1818:0:0 0/0:1:0:0,0:1,0:0:0,0:8:0:32:0:1:0:60:2:1:0:0 -16 81927217 . G C 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0.22164;LSEQ=CTCAGAGCTTTGGCGGCTCG;RSEQ=GCGGAGAAGTTCCCCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:42:40,2:139,4:0.227:1,1:26.3:1:31.8:1:0.61988:1.73161:60:20:0.2235:0:1.2 0/1:115:7:7,0:107,1:0.0609:1,0:19.9:1:32.3:1:1:0:60:14:0.0625:0:1 -16 81927555 . C T 70 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=1.1023;LSEQ=GTGTGATGTTTCTTTGTTTT;RSEQ=TTTTTTCTTTCTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:9:0,9:1,75:0.1034:1,0:24.8:1:22.2:1:1:0:57.8:2:0.0769:0:3.8 0/1:62:7:0,7:2,53:0.1129:1,0:26:1:21.9:1:1:0:51.4:1.333:0.0784:0:4.4 -16 81927562 . C T 62 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31324;SOR=1.7196;LSEQ=GTTTCTTTGTTTTCTTTTTT;RSEQ=TTTCTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:9:0,9:1,54:0.1385:1,0:25.1:1:26.6:1:1:0:57.8:3.5:0.125:0:4.2 0/1:46:10:0,10:2,34:0.2174:2,0:30.2:1:18.9:1:1:0:54:0.667:0.1176:0:3.7 -16 81929158 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGGGCAACAGAGCGAGACT;RSEQ=TGTCTTAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:18,0:0,0:1:0,1:26.2:1:28.3:1:1:0:57.8:5:1:0:1.8 1/1:5:5:5,0:0,0:1:0,0:21.6:1:30.2:1:1:0:60:10:1:0:1.4 -16 81929164 . T TA 78 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.3287;SOR=2.87764;LSEQ=AACAGAGCGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAATGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:6,0:18,0:0.25:1,0:23.2:1:30.4:1:1:0:56.7:12:0.2609:0.0833:2.5 1/0:6:3:3,0:3,0:0.5:0,0:18.7:1:29.7:1:1:0:60:6:0.5:0:1.3 -16 81929185 . A G 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAAAAAAAAAAATGAAAA;RSEQ=AAAAGCAGCATTGAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:49,0:0:1,0:17.2:1:29.8:1:1:0:59.2:15.333:1:0:0.8 1/0:17:9:9,0:7,1:0.5294:2,0:14.4:1:28:1:0.47059:0:60:3.5:0.4667:0:1.3 -16 81929379 . G A 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCTGTCAGTGAACACAC;RSEQ=TGGTATTGAGGCTGCCGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1042:0:0,0:655,386:0:2,0:24.9:1:30.3:1:1:0:60:79.077:1:0:0.2 0/1:1092:46:28,18:644,402:0.0421:2,2:25.4:1:28.9:1:1:1.02984:60:10.5:0.0391:0:1.2 -16 81929488 . C T 305 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=331.73469;LSEQ=ACTACCAAGATCAAGTTTGA;RSEQ=GACGTCGTGCAGGCCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1736:9:1,8:842,884:0.0052:2,2:15.6:1:26:1:0.03925:7.61322:60:8:0.0047:0:1.1 1/0:1863:1182:593,589:331,348:0.6345:2,2:24:1:29.9:1:0.56363:1.06:60:130.333:0.6361:0:1.2 -16 81929527 . C G 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGACCACGCCTTTGTTAC;RSEQ=TCGAGGTCAGTTGGCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1570:0:0,0:731,839:0:2,0:25.5:1:31.3:1:1:0:60:67.261:1:0:0.2 0/1:1765:60:31,29:818,882:0.034:2,2:29.5:1:30.6:1:0.6017:1.15:60:59:0.0339:0:1.1 -16 81929641 . G A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=AGACACCTCCCTCCAAATGC;RSEQ=GGAAGGCCTGGGCCCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:6,231:0:1,0:23.4:1:30.8:1:1:0:60:46.4:1:0:0.1 0/1:214:11:0,11:2,201:0.0514:1,0:23.5:1:31.3:1:1:0:60:10:0.0481:0:1 -16 81930650 . G T 46 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=GTCTCTGTTGCAACTATTCA;RSEQ=CCCTGTTGCTGAAGTGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:13.8:1:29.8:1:1:0:60:8:1:0:0 1/0:6:3:2,1:2,1:0.5:2,2:42.7:1:29.3:1:1:1:60:6:0.5:0:1 -16 81933716 . C CAT 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATAAATGTATGCATGCACA;RSEQ=ATGCAAATTACATATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18:1:31.7:1:1:0:60:6:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81934047 . T C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.30593;LSEQ=TGAGTCCCAAGACTTGTGCC;RSEQ=TCACACCCAGGATGAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:7:7,0:39,1:0.1489:1,0:20.1:1:30.1:1:1:0:60:14:0.1556:0:1 1/1:14:12:12,0:2,0:0.8571:0,0:24.1:1:31.6:1:1:0:60:24:0.8571:0:1.1 -16 81934130 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05139;SOR=Inf;LSEQ=CAGCGCCCGGTTTCTGTCGT;RSEQ=CCAGGGAGCTGCCCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:186,10:0:2,0:24.9:1:31.5:1:1:0:60:195:1:0:0.1 0/1:117:3:2,1:112,2:0.0256:1,2:33.7:1:26.7:1:0.0756:24.79682:60:6:0.0259:0:1 -16 81934609 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGAGATAATACTGGAAC;RSEQ=CATCTGGCTAGCTTGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:0,28:0,0:1:0,1:26.8:1:31.5:1:1:0:60:56:1:0:1.2 1/1:7:7:0,7:0,0:1:0,0:20:1:30.9:1:1:0:60:14:1:0:1 -16 81937556 . T G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACTTTGTACCATGCACT;RSEQ=GGCTAGGCGTGGTCATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:24:1:33:0:1:0:60:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81937565 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCATGCACTTGGCTAGGC;RSEQ=TGGTCATATGTATCTTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:33:1:31.5:1:1:0:60:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81937574 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGCTAGGCGTGGTCATA;RSEQ=GTATCTTCTTATTCAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:38.5:1:31.5:1:1:0:60:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81938677 . A T 40 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTTTTTTATTTTTGTAG;RSEQ=TACAGGGTTTTGCCATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:14.7:1:25.3:1:1:0:60:2:0.5:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81938720 . G T 72 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGCTGGTCTAGAACTCCT;RSEQ=AGCTCAAGTGATCTGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:36:1:31.2:1:1:0:60:10:0.7143:0:2 1/1:1:1:1,0:0,0:1:0,0:14:0:32:0:1:0:60:2:1:0:3 -16 81938787 . T C 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53924;SOR=Inf;LSEQ=TAGGTGTGAGCCACTGCGCC;RSEQ=GACCAGTATGGGCAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:14,0:6,0:0.7:0,1:25.3:1:31:1:1:0:60:28:0.7:0:2.1 1/1:4:4:4,0:0,0:1:0,0:22.8:1:29.3:1:1:0:60:8:1:0:2.3 -16 81938789 . A G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27982;SOR=Inf;LSEQ=GGTGTGAGCCACTGCGCCTG;RSEQ=CCAGTATGGGCAATTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:14:14,0:8,0:0.6364:0,1:26.3:1:31.2:1:1:0:60:28:0.6667:0:2 1/1:5:5:5,0:0,0:1:0,0:19.2:1:26.8:1:1:0:60:4:1:0:2 -16 81939150 . G C 284 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.92749;LSEQ=CCCGTAGCCACTGCGGCCAC;RSEQ=CCCCTTGCAGCTGCTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:762:577:173,404:62,120:0.7572:2,2:25.4:1:30.5:1:0.31245:1.20623:60:40.214:0.7557:0:1.1 1/1:740:667:232,435:27,44:0.9014:2,2:23.4:1:30.3:1:0.6022:1.15034:60:221.333:0.9071:0:1.1 -16 81939157 . G T 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06704;SOR=0.56671;LSEQ=CCACTGCGGCCACGCCCCTT;RSEQ=CAGCTGCTTCTTGGAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:35:11,24:180,493:0.0494:2,2:20.5:1:30.7:1:0.55958:1.25:60:70:0.05:0:1.1 0/1:629:18:9,9:197,413:0.0286:2,2:21.4:1:29.3:1:0.12962:2.09:60:36:0.0292:0:1.1 -16 81939237 . C T 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09636;SOR=1.75701;LSEQ=TTAGTCAAGTGAGTTTTTGC;RSEQ=ATGTGAATTTACCTTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:204:160:2,158:0,44:0.7843:1,1:25:1:28.6:1:1:0:60:52.333:0.7811:0:1.3 1/1:111:96:1,95:0,15:0.8649:1,1:26.5:1:28.3:1:1:0:60:47:0.8624:0:1.4 -16 81939319 . A G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33444;SOR=2.80432;LSEQ=TGTCGCCCAGGCTGGAGTGT;RSEQ=GTGGTGTGATTGCGGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:0,3:0,26:0.1034:1,0:33:1:32.7:1:1:0:60:6:0.1071:0:1 0/1:12:3:0,3:0,9:0.25:0,0:23.3:1:30.3:1:1:0:60:6:0.25:0:1 -16 81939404 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTCCCTGAGTCTCTGGGACC;RSEQ=CACGTGCGCACCACCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,1:0.9:0,0:24.8:1:33.2:1:1:0:60:18:0.9:0:2.1 1/1:2:2:0,2:0,0:1:0,0:27:1:32:1:1:0:60:4:1:0:1 -16 81939407 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGAGTCTCTGGGACCACA;RSEQ=GTGCGCACCACCATGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:24.7:1:31:1:1:0:60:6:0.3:0:2 0/0:2:0:0,0:0,2:0:0,0:27:1:29:0:1:0:60:4:1:0:1 -16 81939464 . C G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAGAGATGGGATTTAGT;RSEQ=GTGTTGCCCAGGGTGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:26.5:1:32.5:1:1:0:60:4:0.6667:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81939466 . T C 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGATGGGATTTAGTCG;RSEQ=GTTGCCCAGGGTGATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:17.3:1:30:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81939473 . C T 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGATTTAGTCGTGTTGCC;RSEQ=AGGGTGATTTCAAACTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:17.5:1:29.5:1:1:0:60:4:0.6667:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81940712 . A G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATGTAAGAAACCTGCAC;RSEQ=GTGTACACATGTACCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:37.3:1:31:1:1:0:47:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81940867 . C A 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAAAGCTAAGAACTTAAC;RSEQ=CTGGTACTTTACAATAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:28.8:1:31.5:1:1:0:57.3:8:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81940910 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACTAAATTTCATCGGGG;RSEQ=AAAAAAAAAAGAAGTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:28.5:1:28.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81941160 . A G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10935;SOR=2.60977;LSEQ=TTGAATTCAGAGAATTCGCC;RSEQ=TAAATGTCTATGAAACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:6:6,0:117,1:0.0484:1,0:28.7:1:31.2:1:1:0:60:12:0.0488:0:1 0/1:85:10:10,0:74,1:0.1176:1,0:25.7:1:30.1:1:1:0:60:20:0.1176:0:1.4 -16 81941319 . C T 295 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.75817;LSEQ=CGGCACTACTGCGCCATTGC;RSEQ=GATGCCAAGCTGTCCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1103:802:398,404:151,145:0.7271:2,2:26.6:1:30.7:1:0.73386:1.05699:60:132.667:0.7303:0:1.1 1/1:1019:897:435,462:57,64:0.8803:2,2:26.5:1:30.1:1:0.84641:1.06:60:55.063:0.8801:0:1.2 -16 81941444 . C T 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.8022;SOR=0.92501;LSEQ=CCCGAGGACCAGCCAGTCCC;RSEQ=GGGACCTCCTTCCCATGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:47:6,41:14,175:0.1975:2,2:23.9:1:30.2:1:0.24619:1.82:60:46:0.1983:0:1.1 0/1:178:33:5,28:13,131:0.1854:2,2:21.5:1:29.9:1:0.33668:1.79:60:66:0.1864:0:1.1 -16 81941493 . T C 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03319;SOR=Inf;LSEQ=GCCGGCTGGCAAGGGGATGC;RSEQ=CCGCTGAAGAAGCTGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:3,92:0:1,0:23.9:1:30:1:1:0:60:22.75:1:0:0.3 0/1:46:3:0,3:1,42:0.0652:1,0:26.3:1:31.7:1:1:0:60:6:0.0652:0:1.7 -16 81941530 . CCTGGCTGGCTTGTCTCTGATTGG C 81 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.32451;SOR=0;LSEQ=TGATACTCTGGGTACCATGT;RSEQ=CTGGCTGCCCCAGGTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:0,6:3,43:0.1154:2,0:26.5:1:31.7:1:1:0:60:12:0.1176:0.0192:0.2 0/0:15:0:0,0:3,12:0:2,0:23.1:1:30.5:1:1:0:60:14:1:0:0.3 -16 81941623 . C T 25 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00833;SOR=Inf;LSEQ=TCTCTAAAGTGCCTGATTGG;RSEQ=CTTAGATGGAGGCCGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:2,12:0:2,0:22.1:1:32.5:1:1:0:60:28:1:0:0 1/1:2:2:1,1:0,0:1:0,2:8:1:25.5:1:1:0:60:4:1:0:1 -16 81942028 . C G 202 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTGCGGCCCAGGATATAC;RSEQ=CCCTACAGAACTACATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1476:0:0,0:772,702:0:2,0:24.8:1:30.8:1:1:0:60:48.133:0.9993:0:0.1 0/1:1422:104:55,49:709,606:0.0731:2,2:23.4:1:30.2:1:0.83894:1.04232:60:33.667:0.0723:0:1.2 -16 81942175 . A G 201 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=43.33769;LSEQ=GGAGAGCGAGACCTTCCCCA;RSEQ=TGACTACACCCTGTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1506:2:1,1:699,802:0.0013:2,2:34:1:14.5:1:1:1.15:60:0:0:0:1 0/1:1559:85:34,51:681,790:0.0545:2,2:24.3:1:31.5:1:0.26549:1.29282:60:170:0.0555:0:1.1 -16 81942401 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGATTAATGAGATTTCA;RSEQ=GGCAATCTTTTAAAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:3:0,3:0,44:0.0638:1,0:27.3:1:24.7:1:1:0:60:2:0.0444:0:2.3 0/0:14:0:0,0:0,14:0:1,0:21.1:1:28.3:1:1:0:60:6:1:0:0.4 -16 81942936 . G C 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGATTTGTGAAAGTCTGTGA;RSEQ=GAAGGCTCTGATGCCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:49:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:28:1:1:0:60:4:1:0:1 -16 81944404 . C T 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGAAGCTGGCCTGGTGGTT;RSEQ=AGCCGGGCCAGTCCCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:23,283:0:2,0:23.9:1:31.8:1:1:0:60:75.5:0.9967:0:0.1 0/1:269:28:2,26:24,217:0.1041:2,2:24.5:1:27.4:1:1:1.43606:60:56:0.1065:0:1.3 -16 81944804 . C A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAAAGCTGCAAAAATGT;RSEQ=CATTTCCGAGGAGGCCGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:44.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81945966 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTGTGAACCACTGTGCT;RSEQ=GGCCCAATGTATTATTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:3,0:15,0:0.1667:1,0:25.7:1:31:1:1:0:60:6:0.1667:0:1 0/0:5:0:0,0:5,0:0:0,0:25.6:1:32.8:1:1:0:60:10:1:0:0 -16 81946006 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTTGAAACAGACCCCTGG;RSEQ=GTCTTCCACTATTCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:2,0:50,0:0.0385:1,0:28:1:30:1:1:0:60:4:0.0392:0:1 0/0:20:0:0,0:18,2:0:2,0:23.5:1:30.6:1:1:0:60:19:1:0:0.1 -16 81946328 . G A 253 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00465;LSEQ=GCCATCACCTTCAGGTGGGT;RSEQ=CGAGGGTGGGAGGCACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1286:441:182,259:367,476:0.3429:2,2:25:1:28.9:1:0.44073:1.09712:60:72.5:0.3444:0:1.2 0/0:1240:3:3,0:556,681:0.0024:2,0:1:0:24:1:0.09135:0:60:6:0.0025:0:1 -16 81946368 . A C 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTACAGAGGGGCTTGGCA;RSEQ=GGACAGATGCGGAGAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:718:0:0,0:219,499:0:2,0:23.6:1:30.7:1:1:0:60:178.5:1:0:0.5 0/1:660:29:7,22:214,417:0.0439:2,2:23.4:1:30.3:1:0.31975:1.61181:60:58:0.0445:0:1.1 -16 81946423 . C T 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=2.31051;LSEQ=TGGAGGCTCACCTGCAGTGC;RSEQ=CTGCCCCCCCAGCATCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:76:1,75:12,168:0.2969:2,1:23.5:1:30.6:1:0.11621:5.33422:60:152:0.304:0:1.4 0/1:176:87:5,82:6,83:0.4943:2,2:24.6:1:29.3:1:1:1.1844:60:86:0.5181:0:1.5 -16 81946471 . G T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05101;SOR=1.9166;LSEQ=CAACCACCACAGCAAAAGCC;RSEQ=CTGCGAGAATGTGCGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:37:0,37:1,80:0.3136:1,1:26:1:29.9:1:1:0:60:36:0.3103:0:1.6 0/1:62:29:4,25:3,30:0.4677:2,2:22:1:30:1:0.69597:1.59:60:58:0.4754:0:2 -16 81946478 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54442;SOR=0;LSEQ=CACAGCAAAAGCCGCTGCGA;RSEQ=AATGTGCGCTCCTGCGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:0,2:1,99:0.0196:1,0:46.5:1:28.5:1:1:0:60:4:0.0202:0:2 0/0:54:0:0,0:7,47:0:2,0:21.8:1:31.1:1:1:0:60:26:1:0:1 -16 81946486 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01314;SOR=Inf;LSEQ=AAGCCGCTGCGAGAATGTGC;RSEQ=CTCCTGCGTGCCAGGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:0,83:0:1,0:26.8:1:32.8:1:1:0:60:166:1:0:0.6 0/1:44:4:1,3:5,35:0.0909:2,2:33:1:30:1:0.45625:2.28:60:8:0.093:0:2.3 -16 81946714 . T C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCCAGGCCTGTGATGATA;RSEQ=AGATCTGGTTTCCTCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:43.7:1:32.7:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81946744 . T A 54 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCCTCCCAACTGCAGCTGC;RSEQ=GCCCAACCACCTCTAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:11:1:27.3:1:1:0:60:8:1:0:2.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81952767 . C G 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TAAAAGCAGGTGGTGGGACA;RSEQ=ATTTGGCCTACTCTTGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:0.2727:0,0:31.7:1:32.7:1:1:0:60:6:0.2727:0:1.3 1/1:1:1:1,0:0,0:1:0,0:49:0:31:0:1:0:60:2:1:0:1 -16 81952775 . C G 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGTGGGACACATTTGGC;RSEQ=TACTCTTGACCTAGTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:18.8:1:28.8:1:1:0:60:8:0.3333:0:1 0/0:1:0:0,0:1,0:0:0,0:41:0:28:0:1:0:60:2:1:0:1 -16 81952824 . T C 67 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00169;SOR=Inf;LSEQ=CCTAAAGTCAAGTCCTGTAG;RSEQ=TGGGGAGGAGAGGAAGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:16,1:0.1053:1,0:5.5:1:28.5:1:1:0:60:4:0.1053:0:1.5 1/1:4:4:4,0:0,0:1:0,0:16.5:1:33.8:1:1:0:60:8:1:0:1 -16 81952885 . C G 110 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26915;SOR=0.23101;LSEQ=CGGCCATATTTCTTCTGAGA;RSEQ=ACAGATTCTTCTAGATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:11:10,1:39,1:0.2157:1,2:26.1:1:32:1:0.38824:3.76588:60:22:0.22:0:1.2 0/1:17:1:1,0:16,0:0.0588:1,0:8:0:33:0:1:0:60:2:0.0588:0:1 -16 81952904 . G C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.21109;SOR=4.87824;LSEQ=ACACAGATTCTTCTAGATCT;RSEQ=TTTTGAAAATACCCACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:1:1,0:71,1:0.0137:1,0:25:0:33:0:1:0:60:2:0.0139:0:1 0/1:31:2:2,0:29,0:0.0645:1,0:17.5:1:32:1:1:0:60:4:0.0645:0:1 -16 81952979 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17354;SOR=Inf;LSEQ=CTATACCCTGTTTATTTACC;RSEQ=ACTTCTCTAAGGCTGGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:268,3:0:1,0:24.6:1:30.9:1:1:0:60:29.111:1:0:0.2 0/1:194:2:2,0:190,2:0.0103:1,0:6.5:1:30.5:1:1:0:60:4:0.0105:0:1 -16 81953023 . G T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01266;SOR=Inf;LSEQ=GGTTGTATCTAATCAGTAGG;RSEQ=TTTGTGTAAAAATTGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:592:0:0,0:492,100:0:2,0:21.7:1:31.2:1:1:0:60:52.818:1:0:0.8 0/1:555:6:3,3:434,114:0.0108:2,2:12.5:1:28.2:1:0.11198:3.79493:60:12:0.0111:0:2.3 -16 81953081 . T C 309 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03549;SOR=0.30621;LSEQ=TGTCAACCCTGTGTTCTTCC;RSEQ=GCTCCAGGGCTAGGGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1249:1245:711,534:0,3:0.9968:0,2:27.6:1:30.4:1:0.07941:0:60:112.182:0.9968:0:1.1 1/1:1444:1429:810,619:2,6:0.9896:2,2:25.8:1:29.5:1:0.08478:3.92:60:63.955:0.9908:0:1.2 -16 81953368 . A G 259 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCTGAGTATTCACCATGT;RSEQ=TCTGATACTGCTGTAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:256:255:0,255:0,0:0.9961:0,1:23.2:1:32.4:1:1:0:60:254:1:0:1.1 1/1:186:186:5,181:0,0:1:0,1:24.1:1:31.5:1:1:0:60:185:1:0:1 -16 81954359 . AG A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACAGCTCTCAGCGGGGT;RSEQ=GGGGAAGGCACTGGTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:10.5:1:31.3:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81954789 . C G 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00028;SOR=1.48792;LSEQ=ATTATTCCATTTCTTTCTTT;RSEQ=TTTTTTTTTCCAGGAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:697:404:286,118:191,76:0.5796:2,2:23.3:1:31.9:1:0.86217:1.03685:60:66.333:0.5994:0:1.1 1/0:760:511:347,164:144,77:0.6724:2,2:22.8:1:31.3:1:0.49347:1.13:60:72:0.6942:0:1.1 -16 81955177 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10901;SOR=4.69654;LSEQ=AAATGTTTTTGGCTCGCTGA;RSEQ=AGAGCCTGTGGTGTTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:11:0,11:0,18:0.3793:1,0:27.9:1:26:1:1:0:60:10:0.3571:0:1.5 1/0:8:6:0,6:0,2:0.75:0,0:12.2:1:29.5:1:1:0:60:12:0.75:0:1 -16 81955238 . A G 98 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTTGCAGTGCAAATGCT;RSEQ=TCTCATATTCCCACCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:0.5:0,0:24.3:1:32.9:1:1:0:60:16:0.5:0:1 0/0:1:0:0,0:0,1:0:0,0:10:0:31:0:1:0:60:2:1:0:1 -16 81955367 . A G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCCGGCAGAGGAAGAACC;RSEQ=CAGCGAATTTTCTGTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:29:1:32.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81956680 . G T 27 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGCTTGCTGAGCACCG;RSEQ=CACTGTGATGACAGTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:23:1:27.5:1:0.4:0:60:4:0.4:0:1 0/0:1:0:0,0:0,1:0:0,0:45:0:29:0:1:0:60:2:1:0:0 -16 81956810 . G C 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53044;SOR=0;LSEQ=AGCCTAACCCTAACCCCAGC;RSEQ=CTAAACCCTAGCCCCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:11,0:0.3125:0,0:20.6:1:29.4:1:1:0:60:10:0.3333:0:1.4 0/0:3:0:0,0:3,0:0:0,0:26:1:28.7:1:1:0:60:6:1:0:0.3 -16 81956829 . C CCCTCACT 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTAAACCCTAGCCCCAAA;RSEQ=CCTAACTCCTAACCCCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:18,0:0.0952:1,0:18.5:1:29.9:1:1:0:60:4:0.1:0.0476:1.5 0/0:4:0:0,0:4,0:0:0,0:28:1:30:1:1:0:60:8:1:0:0.5 -16 81956927 . C G 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGGCTTTTTGGGGCCTT;RSEQ=GATCCTTTGCAATGCCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:77:76,1:0,0:1:0,1:25.1:1:32.6:1:1:0:60:154:1:0:1.2 1/1:45:45:44,1:0,0:1:0,1:23.1:1:31.7:1:1:0:60:90:1:0:1.3 -16 81956953 . C A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02858;SOR=Inf;LSEQ=TTTGCAATGCCAGTCCCTCT;RSEQ=CAGCAGATGACTTTGTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:117,4:0:1,0:24.2:1:31.6:1:1:0:60:242:1:0:0.7 0/1:86:4:3,1:80,2:0.0465:1,2:24.3:1:27.5:1:0.13465:12.25114:60:8:0.0482:0:1.8 -16 81956954 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02882;SOR=Inf;LSEQ=TTGCAATGCCAGTCCCTCTC;RSEQ=AGCAGATGACTTTGTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:118,4:0:1,0:24.4:1:31:1:1:0:60:39.667:1:0:0.6 0/1:87:4:4,0:80,3:0.046:1,0:11.3:1:31:1:1:0:60:8:0.0465:0:1 -16 81956999 . A G 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00057;SOR=Inf;LSEQ=CTGAAGCCTCCTGCTCCCCA;RSEQ=TGAGAAGAACCAAATGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:241,19:0:2,0:24.3:1:30.3:1:1:0:60:64:1:0:0.2 0/1:239:10:7,3:205,24:0.0418:2,2:11.1:1:28.5:1:0.09004:3.63049:60:9:0.0388:0:1.7 -16 81957227 . C T 209 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGAGTGGAGGCTGGGCTGCT;RSEQ=GGCAGGTGGGCTTGACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:133:44,89:224,392:0.1776:2,2:27.2:1:29.7:1:0.48721:1.1556:60:266:0.1807:0:1.1 0/0:775:0:0,0:284,491:0:2,0:24.8:1:29.7:1:1:0:60:63.583:1:0:0.2 -16 81957301 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50999;SOR=0;LSEQ=AGTCTGACCCCCTTTGTCAT;RSEQ=CTGGGCTGGCTTTGACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:10,174:0.0108:2,2:14:1:27:1:0.11508:16.64:60:4:0.0109:0:1.5 0/0:137:0:0,0:5,132:0:1,0:23.9:1:31.5:1:1:0:60:274:1:0:0.7 -16 81957303 . T G 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.7202;SOR=1.09267;LSEQ=TCTGACCCCCTTTGTCATCC;RSEQ=GGGCTGGCTTTGACCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:177:114:6,108:1,62:0.6441:1,2:25:1:30.8:1:0.42392:3.43:60:113:0.6457:0:1.1 1/0:134:89:3,86:2,43:0.6642:1,1:23.9:1:30.6:1:1:1.33031:60:178:0.6642:0:1.1 -16 81957349 . G T 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00993;SOR=0;LSEQ=AGTCCCTTCTTAGGAAGGTG;RSEQ=CTTGGTGCATGCTCTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:13:0,13:1,85:0.1313:1,1:21.6:1:29.7:1:1:0:60:12:0.1224:0:1.5 0/0:43:0:0,0:1,42:0:1,0:25.5:1:32.4:1:1:0:60:86:1:0:0.9 -16 81957386 . A T 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.39091;SOR=1.96974;LSEQ=TTTGAGAAAATGGATAAACA;RSEQ=CAATATTAACAGGTATCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:37:0,37:0,21:0.6379:1,1:24.1:1:30.4:1:1:0:60:74:0.6379:0:1.3 1/0:18:14:0,14:0,4:0.7778:0,1:17.5:1:30.6:1:1:0:60:28:0.7778:0:1.4 -16 81957509 . T C 65 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTAATTGCTTTCCATGCAT;RSEQ=GTCTAACCAAATCTTCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:1,4:0,4:0.5556:0,2:23.8:1:28.2:1:1:0:60:10:0.5556:0:1 1/1:1:1:0,1:0,0:1:0,0:17:0:30:0:1:0:60:2:1:0:1 -16 81959952 . A G 63 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCCTGGCTGCGGAAAAT;RSEQ=GCTCAAGAGATGGGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:24.3:1:31.8:1:1:0:60:8:1:0:1.5 1/1:1:1:0,1:0,0:1:0,0:10:0:31:0:1:0:60:2:1:0:1 -16 81960200 . A G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCACTCAGCTTATGTTA;RSEQ=TTTAGAGTCCTAATAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:31.7:1:31.3:1:1:0:60:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81960365 . C T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAAATTCACAACCTCCC;RSEQ=GAAATAGGGGTGAACTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:38.3:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81960480 . GC G 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.06964;SOR=Inf;LSEQ=ATGTGATGGGGGTAAAATCA;RSEQ=CCCCAGTAACTCATTAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:44,2:0:1,0:25.9:1:31.7:1:1:0:60:92:1:0:0.9 0/1:17:2:1,1:14,1:0.1176:1,2:26:0:34:0:0.22794:10.24702:60:4:0.1176:0:1 -16 81960497 . A C 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7855;SOR=0.8679;LSEQ=TCAGCCCCCAGTAACTCATT;RSEQ=GTAATTAAAAAATAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:60:59,1:13,0:0.8219:1,1:20.1:1:31.1:1:1:0:60:120:0.8219:0:1.1 1/1:30:24:22,2:5,1:0.8:2,2:16.9:1:31:1:0.50148:2.13:60:48:0.8:0:1.1 -16 81960958 . G C 117 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.14594;SOR=0.20046;LSEQ=ATTGAGATTGAGTTGTTGTG;RSEQ=GTGAGTTGCTGTGACAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:17:0,17:0,30:0.3617:1,1:20.6:1:28.7:1:1:0:60:16:0.3478:0:2 0/1:10:1:0,1:1,8:0.1:2,0:31:0:32:0:1:0:60:2:0.1111:0:1 -16 81961002 . T C 135 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24;SOR=0;LSEQ=CGTGTTTTAATCAGGTTGTG;RSEQ=TGGGCTTGGAAGGATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:1,18:0,5:0.7917:0,1:28.6:1:31.9:1:1:0:60:18:0.7826:0:2.9 0/0:1:0:0,0:0,1:0:0,0:14:0:32:0:1:0:60:2:1:0:0 -16 81961020 . C G 129 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTGGGCTTGGAAGGATTT;RSEQ=ATTATGCAGGAGAATTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:1,16:0,3:0.85:0,1:29.6:1:31.6:1:1:0:60:34:0.85:0:3.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81961022 . T A 125 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGGCTTGGAAGGATTTCA;RSEQ=TATGCAGGAGAATTCCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:1,17:0,2:0.9:0,1:27.4:1:30.2:1:1:0:60:17:0.8947:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81961260 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCCACTTTCAGCGTGCT;RSEQ=GCACTCCACCAAGGATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:33:0:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81961265 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTTCAGCGTGCTAGCAC;RSEQ=CCACCAAGGATGATATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:33:0:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81961639 . CTAAG C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGTTCTGCCACCTCTC;RSEQ=CCCAGGATATTCTTCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:19.3:1:32.7:1:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81961873 . G T 123 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAGTCTAGGATGTGTTT;RSEQ=GAAACCAGATCTGAGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:18:18,0:4,0:0.8182:0,1:28.3:1:29.7:1:1:0:60:17:0.8095:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81962071 . A C 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00203;SOR=0.52467;LSEQ=TTTTAAACAGTTCCACAGGC;RSEQ=GTATCTCTGCTAAACGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:246:230,16:48,2:0.8283:1,2:23.9:1:31.1:1:0.74719:1.66707:60:81:0.8265:0:1.1 1/0:254:182:168,14:62,9:0.7165:2,2:22.6:1:30.2:1:0.22859:1.74:60:59.667:0.716:0:1.1 -16 81962531 . T C 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55202;SOR=0;LSEQ=GGATCCATCTGTGTTTCCCA;RSEQ=GCGTTGCGAAGGAAAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:8:0,8:0,17:0.32:1,0:18.8:1:31.3:1:1:0:60:16:0.32:0:1.5 0/0:4:0:0,0:0,4:0:0,0:37.5:1:30.3:1:1:0:60:8:1:0:0 -16 81962574 . A C 79 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCAGCCTGGCTGAAATGC;RSEQ=GCGTGGAGTTGGGAGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:45.3:1:30.8:1:1:0:60:12:0.6:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81962621 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCCAGCTCTGCCTCTCT;RSEQ=TCGCTGTGAGACTACAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:16.5:1:31:1:1:0:60:4:0.3333:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81962627 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCTGCCTCTCTGTCGCT;RSEQ=TGAGACTACAGGCCTGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:18:1:29.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81964728 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTTTTTTTTTCCTGCAT;RSEQ=TTAAGTGTCCCTCTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:29.5:1:33:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81964977 . A G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAGTAGACGTCCCCATC;RSEQ=GTGCTAACCGTGGTCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:177,1:0:1,0:22.7:1:30.5:1:1:0:60:88:1:0:0.1 0/1:131:31:31,0:98,2:0.2366:1,1:21.2:1:30:1:1:0:60:62:0.2403:0:1 -16 81965344 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16966;SOR=Inf;LSEQ=GACTGTGGGTGGGTCCAGGC;RSEQ=GCAGGATGAGCAGGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:17,235:0:2,0:24.8:1:31.2:1:1:0:60:83:1:0:0.1 0/1:177:2:1,1:6,169:0.0113:1,2:25.5:1:28.5:1:0.07775:26.16:60:4:0.0114:0:1 -16 81965387 . A G 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54132;SOR=0;LSEQ=CTACTCAGAATTCAGGAAGG;RSEQ=GACCAGGTGGATTCAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:0,2:3,102:0.0187:1,0:33:1:26:1:1:0:60:4:0.019:0:3 0/0:58:0:0,0:2,56:0:1,0:25.9:1:30.9:1:1:0:60:28:1:0:0 -16 81968204 . T A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08272;SOR=Inf;LSEQ=ACTTCCTTTAGAGTCTGATA;RSEQ=TTTCAGAGGGGGCAGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:27,289:0:2,0:21.8:1:30.5:1:1:0:60:157:1:0:0.1 0/1:245:3:2,1:30,212:0.0122:2,2:12.3:1:27.3:1:0.04569:13.85:60:6:0.0123:0:1 -16 81968409 . G GGCT 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGACTCACAGTTCCACGT;RSEQ=GAGGAGGCCTCACAATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:0.2308:0,0:27.3:1:31.3:1:1:0:60:6:0.2308:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81968848 . T C 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGGCTGCTGGCATTCCT;RSEQ=GGCCTTCTCCTCTTCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:26.5:1:1:0:60:4:1:0:1 -16 81969436 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCTCCCAAGATCTTCTC;RSEQ=TACCCAAAACCATTCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:22:1:31:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81969515 . TA T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.35584;LSEQ=GTTCAAGGATGGTGATAGTT;RSEQ=AAAAAAAAAGTAAATTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:11,0:0.1538:0,0:34:1:32:0:1:0:60:4:0.1538:0:0 0/1:10:2:2,0:8,0:0.2:0,0:32:1:31.5:1:1:0:60:4:0.2222:0:0 -16 81970188 . C G 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1941;SOR=0.23834;LSEQ=ACCGAAGGCTGCTTGGCTTA;RSEQ=GCAGGCTTCGTGATTGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:35:0,35:0,2:0.9459:0,1:25.8:1:29.8:1:1:0:60:16.5:0.9429:0:1.2 1/1:10:8:0,8:0,2:0.8:0,0:21.5:1:31:1:1:0:60:16:0.8:0:1 -16 81970495 . A G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACATTCTTTTTATAGCC;RSEQ=CATCGGATTCCACAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:45.5:1:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81970766 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGCCAAACTGCCCTCCA;RSEQ=AGAGATCGTGGGCGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:20.5:1:29:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81971264 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16866;SOR=Inf;LSEQ=CAGCTGCCTCACATTAATTT;RSEQ=GGGAAAAGGTGAAATTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:159,1:0:1,0:24.7:1:32.7:1:1:0:60:320:1:0:0 0/1:112:2:1,1:107,3:0.0179:1,2:8:0:30.5:1:0.07046:31.01699:60:4:0.0182:0:1.5 -16 81971282 . A G 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58192;SOR=2.61454;LSEQ=TTGGGGAAAAGGTGAAATTC;RSEQ=TTCCCCACCTAGAAACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:215,13:0.0044:2,0:12:0:25:0:1:0:60:2:0.0044:0:1 0/1:176:2:1,1:160,14:0.0114:2,2:22:1:28.5:1:0.16364:11.07581:60:4:0.0114:0:1 -16 81971403 . T C 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.37674;LSEQ=CACGCATTGTTTTCTCTCAA;RSEQ=GGGCGCACGGGCTACGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1131:668:358,310:250,212:0.5906:2,2:24.4:1:31:1:0.90341:1.02112:60:132.6:0.593:0:1.1 0/1:1247:439:239,200:439,366:0.352:2,2:25.9:1:30.1:1:1:1.00372:60:72.167:0.352:0:1.1 -16 81971560 . G A 57 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.73546;SOR=1.28251;LSEQ=GCCAGCCGCCCTCCCTGGGG;RSEQ=CTGGGCCGATGCTGTCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:4:3,1:115,342:0.0087:2,2:14.8:1:28.5:1:0.05342:8.87:60:8:0.0088:0:1 0/1:361:4:1,3:87,269:0.0111:2,2:12.5:1:28.8:1:1:1.03:60:8:0.0113:0:2.3 -16 81971567 . C T 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=15.42988;LSEQ=GCCCTCCCTGGGGGCTGGGC;RSEQ=GATGCTGTCTTGAGAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:2:1,1:89,316:0.0049:2,2:6:1:27:1:0.39379:3.54:60:4:0.0051:0:1 0/1:324:23:3,20:67,233:0.071:2,2:24:1:30.4:1:0.43189:1.91385:60:46:0.0726:0:1.2 -16 81971582 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=3.38021;LSEQ=TGGGCCGATGCTGTCTTGAG;RSEQ=GCAGGGAACCCATGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:62:10,52:27,214:0.2046:2,2:22.4:1:31.4:1:0.28336:1.52:60:61:0.204:0:1.2 0/1:219:102:12,90:10,107:0.4658:2,2:25:1:30.4:1:0.50198:1.42:60:204:0.4679:0:1.2 -16 81971625 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16531;SOR=Inf;LSEQ=GGCTGGTTGTCTTGTTTAAA;RSEQ=GATCCCCATTCAGGCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:3,132:0:1,0:25:1:29.9:1:1:0:60:44:1:0:0.5 0/1:93:2:1,1:2,89:0.0215:1,2:30.5:1:30:1:0.06381:36.54:60:4:0.0215:0:1 -16 81971657 . T C 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.85253;SOR=1.12145;LSEQ=AGGCAGTGTTTGAGGATCTT;RSEQ=CTTTCTTACAGTACACTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:42:0,42:2,43:0.4828:1,1:24.8:1:30.6:1:0.49479:0:60:20:0.4706:0:1.4 1/0:43:22:1,21:1,20:0.5116:1,1:18.1:1:31.5:1:1:1.04883:60:44:0.5116:0:2.1 -16 81971677 . G A 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.45018;SOR=1.60524;LSEQ=TCTTTCTTACAGTACACTCC;RSEQ=GGGTCGTTCTGGGAGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:21:2,19:0,36:0.3621:1,2:26.4:1:31.3:1:0.13158:0:60:42:0.375:0:1.6 0/1:23:11:0,11:1,11:0.4783:2,0:23.5:1:30.1:1:1:0:60:10:0.4545:0:2.4 -16 81972268 . G A 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACTGCAGAAGGTTGCTCC;RSEQ=GCTTTTCCAGTGAATCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:134,4:0:1,0:23:1:29.9:1:1:0:60:137:1:0:0.9 0/1:90:13:13,0:76,1:0.1444:1,1:25.3:1:30.1:1:1:0:60:26:0.1461:0:1.8 -16 81972283 . T G 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05423;SOR=0.62439;LSEQ=GCTCCGGCTTTTCCAGTGAA;RSEQ=CTAGGAAAATTAGGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:187:119:118,1:65,3:0.6364:1,1:22.5:1:32.8:1:0.1374:5.40:60:238:0.6398:0:1.1 1/0:115:60:60,0:53,1:0.5217:1,1:26.1:1:32.7:1:0.47368:0:60:120:0.5217:0:1 -16 81972289 . A C 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02163;SOR=1.79634;LSEQ=GCTTTTCCAGTGAATCTAGG;RSEQ=AAATTAGGGCTGGCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:41:38,3:162,1:0.201:1,2:24.7:1:32.5:1:0.02625:12.56876:60:82:0.2103:0:1 0/1:138:43:41,2:95,0:0.3116:1,1:23.5:1:32.6:1:0.09553:0:60:86:0.3139:0:1.3 -16 81972496 . A G 218 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTGGAGCCGAGTATGACAAC;RSEQ=ACAAGTTCAAGACGACGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1731:0:0,0:806,924:0:2,0:25.3:1:30:1:1:0:60:54.806:1:0:0.2 0/1:2031:147:67,80:929,951:0.0724:2,2:23.7:1:30.4:1:0.39228:1.16632:60:146:0.0728:0:1.2 -16 81972902 . A G 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGATCAGCCTAACCTGGG;RSEQ=GATCTTAGCCCCTAGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:25.3:1:29.8:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 81973442 . T C 142 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.511;LSEQ=GAAGGATGCGGAGATTGTCT;RSEQ=ACCAGAAGGGGGCAGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:1:1,0:324,41:0.0027:2,0:28:0:15:0:1:0:60:0:0:0:7 0/1:263:24:20,4:205,34:0.0913:2,2:25.1:1:31.1:1:0.7606:1.20498:60:48:0.0916:0:1 -16 81973474 . C A 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02711;LSEQ=GCAGCTCCAATGTGGCCTCT;RSEQ=ATGAGCTTTGATCTCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:590:587:443,144:0,0:0.9949:0,2:23.8:1:28.3:1:1:0:60:44.154:0.9965:0:1.1 1/1:535:450:315,135:61,22:0.8411:2,2:24.1:1:28:1:0.60066:1.18797:60:39.909:0.8442:0:1.1 -16 81973773 . C G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07334;SOR=Inf;LSEQ=TTTCCTGGTTTGGATGGAAT;RSEQ=ACTGTAAAACCGATTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:2,121:0:1,0:24:1:32.3:1:1:0:60:246:0.9919:0:0.3 0/1:91:3:0,3:3,85:0.033:1,0:34.3:1:32:1:1:0:60:6:0.033:0:1.3 -16 81973788 . T C 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAATCACTGTAAAACCGAT;RSEQ=GGGTGGCTTGGAGAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:0,99:0:1,0:24.3:1:30:1:1:0:60:32:1:0:0.4 0/1:62:19:0,19:2,41:0.3065:1,1:29.7:1:30.7:1:1:0:60:38:0.3065:0:1.3 -16 81973805 . A T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08403;SOR=0.3446;LSEQ=GATTGGGTGGCTTGGAGAGC;RSEQ=GGTGTACAGCCTGTCGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:18:0,18:0,60:0.2308:1,1:20.3:1:30.4:1:1:0:60:17:0.2237:0:1.1 0/1:43:4:0,4:2,37:0.093:2,0:22:1:30.3:1:1:0:60:8:0.0952:0:1 -16 81973807 . G GTGCA 126 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03002;SOR=0.20284;LSEQ=TTGGGTGGCTTGGAGAGCAG;RSEQ=TGTACAGCCTGTCGTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:16:0,16:0,61:0.2078:1,1:21.8:1:31.5:1:1:0:60:32:0.2133:0.0779:1.1 0/1:40:2:0,2:2,36:0.05:2,0:39:1:31.3:1:1:0:60:4:0.0513:0:1 -16 81973837 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07356;SOR=Inf;LSEQ=TGTCGTGTAGCACACAGGTG;RSEQ=GAGGAAGTGGGTGACAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:0:1,0:24.9:1:30:1:1:0:60:10.75:1:0:0.7 0/1:18:2:0,2:1,15:0.1111:1,0:19.5:1:32.5:1:1:0:60:4:0.1111:0:2 -16 81973841 . G C 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00118;SOR=0;LSEQ=GTGTAGCACACAGGTGGGAG;RSEQ=AAGTGGGTGACAGGGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:18:0,18:0,26:0.4091:1,1:22.1:1:31.4:1:1:0:60:17:0.3953:0:1.2 0/0:17:0:0,0:1,16:0:1,0:19.7:1:31.5:1:1:0:60:34:1:0:0.6 -16 81979657 . G C 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00692;SOR=Inf;LSEQ=TTCCACAAAGTCAGCCCCCA;RSEQ=CATGGGGCACTGACTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:138,2:0:1,0:23.7:1:32:1:1:0:60:27:1:0:0 0/1:111:6:6,0:103,2:0.0541:1,0:31:1:31.8:1:1:0:60:12:0.0545:0:1 -16 81979715 . C CA 70 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.27989;SOR=0.38505;LSEQ=TATGATCCCGAGGTAGCCTC;RSEQ=AAAAAAAATCTAAGGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:5:4,1:357,121:0.0104:2,2:15.4:1:30.2:1:1:1.35:60:10:0.0105:0.0021:0.6 0/0:499:2:2,0:342,154:0.004:2,0:24:1:32:0:1:0:60:4:0.0041:0:0 -16 81980019 . T C 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0691;SOR=0.5322;LSEQ=ATACAAGAATTCCTTTTTGC;RSEQ=AATTCCCCAGAGTGTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:59:0,59:0,43:0.5784:1,1:23.5:1:31.9:1:1:0:60:58:0.58:0:1.1 0/1:57:24:0,24:3,30:0.4211:2,1:23.9:1:31.7:1:0.25564:0:60:48:0.4211:0:1.2 -16 81990505 . G T 245 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTAGGTCAGCCCCTCCACCT;RSEQ=CAAAAACTTTTGGGGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:960:316:114,202:238,404:0.3292:2,2:25.2:1:29.6:1:0.77604:1.04383:60:34.111:0.3269:0:1.1 0/0:1028:0:0,0:407,618:0:2,0:25.4:1:31.7:1:1:0:60:77.846:0.997:0:0.2 -16 81990605 . GGGCATGGTGGCTCACAGGCCA G 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTCAGAAATCCTTGGCC;RSEQ=GGCATGGTGGCTCATGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:0,135:0:1,0:23.6:1:31.4:1:1:0:60:270:1:0:0.1 0/1:102:20:0,20:2,79:0.1961:1,1:26:1:30.4:1:1:0:59.5:40:0.202:0.0098:0.1 -16 81991325 . G T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTACTCACATTATTCTCATT;RSEQ=AATCTTCATGTCAGCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:19:19,0:4,0:0.8261:0,1:23:1:30.9:1:1:0:60:38:0.8636:0:1.2 1/1:4:4:4,0:0,0:1:0,0:17.8:1:29.3:1:1:0:60:8:1:0:1 -16 81991638 . T C 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTGTAAGGGTATTGTGTGTG;RSEQ=GCGCATGTGTGTTTGCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1644:0:0,0:724,914:0:2,0:25.6:1:30.1:1:1:0:60:147.909:0.9975:0:0.2 0/1:1687:120:54,66:743,818:0.0711:2,2:23.2:1:30.8:1:0.63555:1.11008:60:119:0.0712:0:1.2 -16 81991864 . C G 104 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24632;SOR=0.23616;LSEQ=CATTTTTGGCCTCTCATGTT;RSEQ=CAAACCTCATTGAATAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:0,9:0,27:0.25:1,0:31.8:1:32.9:1:1:0:60:18:0.25:0:1.1 0/1:14:1:0,1:0,13:0.0714:1,0:17:0:33:0:1:0:60:2:0.0714:0:1 -16 82113356 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24287;SOR=0;LSEQ=GGAAAAGAAAAAGCTAGAAT;RSEQ=TAACACAAGGATTAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:121,32:0.0129:2,2:13:1:30.5:1:0.38157:3.739:60:4:0.0132:0:1 0/0:159:0:0,0:122,37:0:2,0:22.7:1:31.3:1:1:0:60:78.5:1:0:0.2 -16 82113471 . C T 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45919;SOR=1.12155;LSEQ=TGATATATCTTTGGCAAAAT;RSEQ=AATGTAATAGTAACTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:127:60,67:115,161:0.3144:2,2:25.1:1:28.9:1:0.33052:1.25:60:62.5:0.3125:0:1.1 0/1:424:144:66,78:130,149:0.3396:2,2:23.8:1:28.6:1:0.91822:1.03105:60:288:0.342:0:1.1 -16 82113555 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50162;SOR=0;LSEQ=AGCAAGGTGCATGGAGGGAG;RSEQ=GAAGCAGTCAGTCACTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:51,133:0.0108:2,2:35.5:1:30:1:0.48207:2.59:60:4:0.0109:0:1 0/0:159:0:0,0:40,119:0:2,0:24.8:1:30.2:1:1:0:60:78.5:1:0:0.2 -16 82468581 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22231;SOR=Inf;LSEQ=GGAATGGGTACTCTTCAAAA;RSEQ=GGAATGCCCCACAAGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:108,44:0:2,0:21.5:1:32:1:1:0:60:304:0.9935:0:0.1 0/1:137:2:1,1:93,42:0.0146:2,2:12:1:30.5:1:0.53081:2.20016:60:4:0.0146:0:2.5 -16 82468589 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2185;SOR=Inf;LSEQ=TACTCTTCAAAAGGGAATGC;RSEQ=CCACAAGTGTTACCATGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:129,55:0:2,0:22.8:1:31.2:1:1:0:60:183:1:0:0.1 0/1:162:2:1,1:106,54:0.0123:2,2:17:1:30:1:1:1.95425:60:4:0.0124:0:1 -16 82468594 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22094;SOR=Inf;LSEQ=TTCAAAAGGGAATGCCCCAC;RSEQ=AGTGTTACCATGGCTAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:135,64:0:2,0:24.1:1:30.1:1:1:0:60:48.75:1:0:0.1 0/1:177:2:1,1:112,63:0.0113:2,2:25:1:32.5:1:1:1.7716:60:4:0.0115:0:2.5 -16 82468627 . G A 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=GCTAGACTGGGAGAGTCTAC;RSEQ=GTGTTCCCCAGCATGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:138,114:0:2,0:29.2:1:29.9:1:1:0:60:62:1:0:0.1 0/1:215:11:6,5:113,91:0.0512:2,2:29.5:1:31.2:1:1:1.03465:60:22:0.0526:0:1.7 -16 82468649 . G A 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00227;SOR=Inf;LSEQ=TGTTCCCCAGCATGCTGTTG;RSEQ=CATTGCTGTAAACAACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:118,138:0:2,0:25.4:1:31:1:1:0:60:35.571:1:0:0.1 0/1:228:8:4,4:108,112:0.0351:2,2:20.5:1:29.3:1:1:1.04:60:16:0.036:0:2 -16 82468709 . T TC 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.05941;SOR=Inf;LSEQ=ACTGGGAGAGTCTACAGTGT;RSEQ=CCCCCGCACGCTGTTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:17,81:0:2,0:21.5:1:30.2:1:1:0:60:97:1:0:0.2 0/1:100:5:1,4:22,73:0.05:2,2:23.4:1:30.8:1:1:1.20333:60:10:0.0515:0:0 -16 82468718 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=GTCTACAGTGTTCCCCCGCA;RSEQ=GCTGTTGACATTGTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:10,72:0:2,0:21.1:1:29.8:1:1:0:60:40:1:0:0.1 0/1:92:2:1,1:19,71:0.0217:2,2:16.5:1:30.5:1:0.38939:3.67:60:4:0.0217:0:3 -16 82468726 . A G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24574;SOR=Inf;LSEQ=TGTTCCCCCGCACGCTGTTG;RSEQ=CATTGTTGTAAACAAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:11,60:0:2,0:21:1:29.8:1:1:0:60:34.5:1:0:0.2 0/1:76:3:1,2:15,58:0.0395:2,2:11.7:1:31.7:1:0.51323:1.91:60:6:0.0395:0:2.7 -16 82468755 . A T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13266;SOR=Inf;LSEQ=TAAACAAACAAGGGCAAGAT;RSEQ=CTTGCCAAGATAATTAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:5,37:0:2,0:25.7:1:29.7:1:1:0:60:84:1:0:0.1 0/1:56:4:1,3:9,43:0.0714:2,2:23.5:1:28.3:1:0.55571:1.58:60:8:0.0714:0:1.8 -16 82469001 . TAA T 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CATATTACGTGTTAAAAAAA;RSEQ=AAGACCTCTGGACTATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:26:1:31:1:1:0:60:6:1:0:0.3 1/0:4:2:1,1:1,1:0.5:2,2:14:0:28.5:1:1:1:39:4:0.5:0:2 -16 82469019 . T C 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AATAAAAGACCTCTGGACTA;RSEQ=AAAAATGTTTCTCTTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:9:1:28.7:1:1:0:60:6:1:0:0.3 1/0:3:2:1,1:0,1:0.6667:0,2:29:0:30.5:1:1:0:39:4:0.6667:0:2 -16 82469022 . A G 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AAAAGACCTCTGGACTATAA;RSEQ=AATGTTTCTCTTCATTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:6:1:28.3:1:1:0:60:6:1:0:0.3 1/0:3:2:1,1:0,1:0.6667:0,2:32:0:29:0:1:0:39:4:0.6667:0:2 -16 82728685 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00078;SOR=0.12416;LSEQ=GTGGGCAAAGTCCTGTCGGC;RSEQ=GGAGGAAGGGCATGTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:20:8,12:1,4:0.8:2,2:20.3:1:29.9:1:0.62055:2.57:60:40:0.8:0:1.1 0/1:28:9:5,4:7,12:0.3214:2,2:32.3:1:29:1:0.43188:2.08:60:18:0.3333:0:1.1 -16 83236502 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACACTGAAGACTCCAGA;RSEQ=GTGGGGAGGGATGGGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36.5:1:33:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 83238012 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49812;SOR=Inf;LSEQ=ATAGCATGTGCCGGAGTCAG;RSEQ=GTTCAGTAAATGGTAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:40,37:0:2,0:29:1:30.1:1:1:0:60:154:1:0:0.2 0/1:85:2:1,1:38,45:0.0235:2,2:40.5:1:31:1:1:1.18:60:4:0.0238:0:1 -16 84245120 . A G 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGACCTCAGGGGATCCGCCC;RSEQ=CCGCAGCCTCCCAAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:18:1:30.7:1:1:0:60:6:0.75:0:1 1/1:1:1:1,0:0,0:1:0,0:48:0:32:0:1:0:60:2:1:0:1 -16 84245226 . G A 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=TGGGATTCAACCTGTTTCCT;RSEQ=CTCCAGGGTGAACGCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:0:2,0:26.5:1:32:1:1:0:60:64:1:0:0 0/1:27:9:6,3:11,7:0.3333:2,2:27.6:1:28.3:1:1:1.26:60:18:0.3333:0:1.3 -16 84245230 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22186;SOR=Inf;LSEQ=ATTCAACCTGTTTCCTGCTC;RSEQ=AGGGTGAACGCTGACTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:0:2,0:27.9:1:31.3:1:1:0:60:64:1:0:0 0/1:29:2:1,1:17,10:0.069:2,2:14:1:29.5:1:1:1.66781:60:4:0.069:0:1 -16 84245323 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09023;SOR=Inf;LSEQ=ACTGCAGAACCAATAAGGCC;RSEQ=AAATCACATGCTTGGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:2,8:0:2,0:19.3:1:31.4:1:1:0:60:20:1:0:0 0/1:11:4:1,3:1,6:0.3636:2,2:12.8:1:29:1:1:1.87:60:8:0.3636:0:1.5 -16 84636456 . C CAA 28 pSTD;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.06462;SOR=0;LSEQ=GGGCGACAGAGACTTCATCT;RSEQ=AAAAAAAAAAAAAAGTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,2:0.2857:2,2:14:0:28:1:1:1:60:4:0.3333:0:0 0/0:19:0:0,0:11,4:0:2,0:23.5:1:27.9:1:1:0:59.1:6.5:0.7647:0:1.3 -16 84636489 . C A 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.01805;SOR=Inf;LSEQ=AAGTGCATGGAAAGGGAAGG;RSEQ=CAAAAAGGCAGTGTTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:19.7:1:30.3:1:1:0:60:21:1:0:0.2 0/1:35:8:4,4:12,14:0.2286:2,2:25.9:1:27.8:1:1:1.16:60:16:0.2581:0:1.3 -16 84636781 . A G 47 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GTGGGGGCAGACTCGCAGCC;RSEQ=GTTTTCCTTCCCCGTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:12.7:1:30:1:1:0:60:6:1:0:2 0/0:1:0:0,0:1,0:0:0,0:12:0:32:0:1:0:60:2:1:0:0 -16 84636803 . T C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TTTTCCTTCCCCGTGGACTT;RSEQ=AACAACACTCCAGCCCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:25.3:1:33.3:1:1:0:60:6:0.75:0:1.7 0/0:3:0:0,0:2,1:0:2,0:21.7:1:29.3:1:1:0:60:6:1:0:0.3 -16 84637352 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAGGGCCTGTGGGGTTGGC;RSEQ=CATCATGCCTGGGGACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:29:1:1:0:60:4:1:0:1 -16 85214736 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24571;SOR=0;LSEQ=TCCGCAGCTGCCCACAGGGT;RSEQ=CGCTGGCCCCGGGATCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:50,35:0.023:2,2:22.5:1:28:1:1:1.42258:60:4:0.0233:0:1 0/0:88:0:0,0:53,35:0:2,0:22.9:1:30.6:1:1:0:60:176:1:0:0.2 -16 85214747 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4978;SOR=Inf;LSEQ=CCACAGGGTCCGCTGGCCCC;RSEQ=GGATCCTTCTGGGTCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:65,48:0:2,0:23:1:29.7:1:1:0:60:36.667:1:0:0.2 0/1:114:2:1,1:69,43:0.0175:2,2:29.5:1:29.5:1:1:1.59771:60:4:0.0175:0:1 -16 85214767 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50035;SOR=Inf;LSEQ=GGGATCCTTCTGGGTCTCAT;RSEQ=TGGGCTCCACGCTGACACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:90,63:0:2,0:27:1:31.6:1:1:0:60:50:1:0:0.2 0/1:173:2:1,1:99,72:0.0116:2,2:26:1:30.5:1:1:1.37241:60:4:0.0116:0:1 -16 85214786 . C A 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2013;SOR=0;LSEQ=TCTGGGCTCCACGCTGACAC;RSEQ=GGCTAACTTGGTGACCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:81,77:0.0125:2,2:45:0:29.5:1:1:1.05164:60:4:0.0126:0:1.5 0/0:196:0:0,0:101,95:0:2,0:26.2:1:29.9:1:1:0:60:195:1:0:0.2 -16 85338201 . C T 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.4949;SOR=Inf;LSEQ=CTGCATGGCAGCTGCCAAGC;RSEQ=GGGGGCGGGGGGGTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:0:1,0:20.3:1:32:1:1:0:60:44:1:0:2 0/1:27:2:2,0:25,0:0.0741:1,0:15:1:33:0:1:0:60:4:0.0769:0:1 -16 85338207 . C CG 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01836;SOR=0.17312;LSEQ=GGCAGCTGCCAAGCCGGGGG;RSEQ=GGGGGGGTGGGGCATCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:11,0:0.4091:0,0:29.3:1:30.7:1:1:0:60:18:0.4091:0:3.2 0/1:29:3:3,0:24,0:0.1034:1,0:45.3:1:30:1:1:0:60:6:0.1071:0:1.7 -16 85338214 . GT G 32 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.56278;SOR=0.33462;LSEQ=GCCAAGCCGGGGGCGGGGGG;RSEQ=GGGGCATCCCTTTTGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:0,0:0.0741:0,0:22.5:1:32:0:1:0:60:4:0.0741:0:0 0/1:39:1:1,0:12,1:0.0256:1,0:29:0:33:0:1:0:60:2:0.0294:0:0 -16 85338215 . T G 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00189;SOR=0.10682;LSEQ=CCAAGCCGGGGGCGGGGGGG;RSEQ=GGGGCATCCCTTTTGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:25:25,0:0,0:0.9259:0,1:24.4:1:31.7:1:1:0:60:50:0.9259:0:2.7 1/0:39:22:18,4:12,1:0.5641:1,2:17:1:29.2:1:0.62998:2.60115:60:21:0.6176:0:2 -16 85338232 . C T 36 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0828;SOR=0;LSEQ=GGGTGGGGCATCCCTTTTGC;RSEQ=TTGAGTCCACCACCAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:2,1:35,14:0.0577:2,2:18.3:1:23.3:1:1:1.24447:60:2:0.0455:0:4 0/0:66:0:0,0:40,26:0:2,0:18.5:1:28.4:1:1:0:60:10:1:0:0.8 -16 85338253 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50409;SOR=Inf;LSEQ=TTGAGTCCACCACCAAACCT;RSEQ=GTGTCAGCTGAGAACGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:52,32:0:2,0:22.9:1:30.4:1:1:0:60:20:1:0:0.8 0/1:106:2:1,1:58,46:0.0189:2,2:18:0:31.5:1:1:1.25808:60:4:0.0192:0:1.5 -16 85338293 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19884;SOR=0;LSEQ=AAAGCCACCTGTTGGCAGCT;RSEQ=GGCCGTGATGTTCCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:58,58:0.0169:2,2:15.5:1:26.5:1:1:1:60:4:0.0171:0:1 0/0:146:0:0,0:74,72:0:2,0:27.3:1:30.9:1:1:0:60:145:1:0:0.4 -16 85338316 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19198;SOR=0;LSEQ=CCGTGATGTTCCTGCCTGAA;RSEQ=ATAAATAACACCTGCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:43,60:0.019:2,2:35:1:30.5:1:1:1.39:60:4:0.0194:0:1 0/0:134:0:0,0:60,73:0:2,0:23.2:1:31:1:1:0:60:132:0.9925:0:0.3 -16 85338340 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50537;SOR=Inf;LSEQ=AATAACACCTGCAGAAGATG;RSEQ=CAGAGACAGGCCAGGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:24,38:0:2,0:25.8:1:31.8:1:1:0:60:61:1:0:0.3 0/1:81:2:1,1:32,47:0.0247:2,2:25.5:1:28.5:1:1:1.46:60:4:0.0253:0:1 -16 85338371 . C A 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38515;SOR=1.52288;LSEQ=CCAGGGCCCTCTCGACTTCA;RSEQ=TGGGGATAAGACAGCGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:18:4,14:4,15:0.4865:2,2:23.3:1:30.6:1:1:1.07:60:36:0.4865:0:1 1/0:49:29:6,23:3,16:0.5918:2,2:23.6:1:29.2:1:1:1.38:60:28:0.5957:0:1 -16 85338398 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13564;SOR=0;LSEQ=TAAGACAGCGACCAGGCCGC;RSEQ=CTGCAGCCACAGAATGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:0,16:0.1111:1,2:19:0:32.5:1:0.11111:0:60:4:0.1111:0:1.5 0/0:30:0:0,0:1,29:0:1,0:21.8:1:29.4:1:1:0:60:60:1:0:0.6 -16 85490399 . T C 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01947;SOR=0;LSEQ=GCTGTGGCGACTCAGGGTCC;RSEQ=GGCGGGGAGAACCTGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:8,10:0.3333:2,2:20:1:27.2:1:1:1:60:8:0.32:0:1.1 0/0:13:0:0,0:4,9:0:2,0:28.2:1:29.8:1:1:0:60:26:1:0:0.1 -16 85741257 . C G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GTTCTTGTTGGTGCTTATGG;RSEQ=AGGGGCATGTGTTTGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:33:1:31.6:1:1:0:60:10:1:0:0.2 0/1:6:2:2,0:4,0:0.3333:0,0:25.5:1:30:1:1:0:60:4:0.3333:0:1 -16 85741351 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52288;SOR=Inf;LSEQ=CCAACAGCCAGGACCATGGC;RSEQ=CTCCCTTTCACCAGGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:26.2:1:30.4:1:1:0:60:29:1:0:0.1 0/1:49:2:1,1:26,21:0.0408:2,2:33.5:1:28.5:1:1:1.23267:60:4:0.0417:0:1 -16 85879417 . G A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAAAATTAGCCGGGC;RSEQ=TGGTGGCGCGCGCCTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:31.5:1:1:0:45:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 85880256 . C G 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0364;SOR=Inf;LSEQ=TCACTCAGGCTGCCTGGACT;RSEQ=CTGGGTCTCCCCCTGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:0:1,0:27.5:1:31.1:1:1:0:60:37:1:0:0.4 0/1:31:4:4,0:27,0:0.129:1,0:25:1:33:1:1:0:60:8:0.1333:0:1.8 -16 85880315 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49826;SOR=0;LSEQ=TGCATGAAAAACAGATTTCA;RSEQ=GATTTCACTAAAATTGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:2,0:104,37:0.014:2,0:17.5:1:32.5:1:1:0:60:4:0.014:0:2.5 0/0:141:0:0,0:108,33:0:2,0:23.6:1:30.5:1:1:0:60:69.5:1:0:0.9 -16 85880339 . G A 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01269;SOR=0.59566;LSEQ=TTCACTAAAATTGGTTCGAG;RSEQ=CATCCTGTGTGTCCGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:218:160:111,49:36,22:0.7339:2,2:25.7:1:30.2:1:0.32928:1.38:60:320:0.7339:0:1.9 1/0:243:151:97,54:56,35:0.6214:2,2:25.7:1:28.3:1:0.68203:1.12:60:36.75:0.6151:0:2 -16 85880399 . G C 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00053;SOR=0.57885;LSEQ=GGGCGCAGGAGAAGGTGTGT;RSEQ=GGTCAGCAGGGTTCTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:353:259:132,127:45,48:0.7337:2,2:25.6:1:30.5:1:0.71741:1.11:60:258:0.735:0:2.2 1/0:415:255:122,133:82,78:0.6145:2,2:25.7:1:30.2:1:0.54528:1.14569:60:126.5:0.6126:0:2.2 -16 85880425 . A T 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=3e-04;SOR=0.55105;LSEQ=GCAGGGTTCTCTGGGAAAGA;RSEQ=GACGGGAAGATGGCCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:327:242:118,124:37,48:0.7401:2,2:22.9:1:30:1:0.44955:1.23:60:47.4:0.7383:0:2.1 1/0:380:232:106,126:67,81:0.6105:2,2:25.8:1:29.8:1:1:1.02:60:115:0.615:0:2.1 -16 85880469 . A G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24895;SOR=Inf;LSEQ=TGGCAGCCATGGGCCACCTG;RSEQ=CTCTTCACATTGAGCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:78,138:0:2,0:25.7:1:29.6:1:1:0:60:53:1:0:1 0/1:229:3:1,2:83,143:0.0131:2,2:12:1:32.3:1:1:1.16013:60:6:0.0135:0:2 -16 85880496 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49831;SOR=0;LSEQ=ACATTGAGCCTTGGAGCTGG;RSEQ=CAGCTAGAGGGCAGTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:41,102:0.0138:2,2:16:1:26:1:0.49684:2.47:60:4:0.0141:0:2.5 0/0:142:0:0,0:43,99:0:2,0:26.3:1:30.3:1:1:0:60:22.667:1:0:0.7 -16 85880505 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49813;SOR=Inf;LSEQ=CTTGGAGCTGGCCAGCTAGA;RSEQ=GGCAGTTGGGGAGAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:33,91:0:2,0:23:1:30.6:1:1:0:60:23.8:1:0:0.8 0/1:128:2:1,1:34,92:0.0156:2,2:46.5:1:31:1:0.47367:2.68:60:4:0.016:0:3 -16 85880551 . G C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01237;SOR=0.293;LSEQ=CACAAGAGAAGGCCGAGCTG;RSEQ=GAGGGAGGGTCTCTAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:47:3,44:1,6:0.8704:2,2:23.6:1:29.8:1:0.436:2.39206:60:22.5:0.8824:0:2 1/0:53:35:5,30:2,16:0.6604:2,2:23.3:1:29.7:1:1:1.33:60:34:0.6538:0:1.9 -16 85880560 . G A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00712;SOR=0.2411;LSEQ=AGGCCGAGCTGGGAGGGAGG;RSEQ=TCTCTAAGGTGCGGTTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:38:2,36:0,6:0.8636:0,2:26.5:1:31.4:1:1:0:60:37:0.881:0:2.2 1/0:40:24:3,21:2,14:0.6:2,2:26.3:1:30:1:1:1:60:48:0.6154:0:2.1 -16 85880671 . C T 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=CTGATGTTCCAGAAGAGTGT;RSEQ=GTGAAGGAGCAAAGAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:18:1:31.8:1:1:0:60:8:0.4444:0:1 0/0:2:0:0,0:0,2:0:0,0:25:1:31.5:1:1:0:60:4:1:0:0 -16 85880822 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGGGAGGAGGCGGAGGAAG;RSEQ=GCACCTATGCTGCAGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:33:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 85880907 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGGCTCTGTGCGCTGCGC;RSEQ=GGGTGCCGGCCTGCTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:31.5:1:31:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:36:0:32:1:1:0:60:4:1:0:1 -16 85936700 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1551;SOR=0;LSEQ=GTAGCATGTATCCAGGACTG;RSEQ=TTTGGGAGAATGAGGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:0.1:2,2:27:1:30.5:1:1:1.23603:60:4:0.1053:0:1 0/0:30:0:0,0:18,12:0:2,0:30.5:1:28.9:1:1:0:60:60:1:0:0 -16 85938125 . C A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCACGTCTCTGCCTGAC;RSEQ=GATGTTTGCAGTGGGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:28.5:1:1:0:60:4:1:0:1 -16 86248076 . C A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01928;SOR=Inf;LSEQ=CACACCAGCAGCATAGGTGT;RSEQ=CCCTGGGAGCCTGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:19,11:0:2,0:28.7:1:31:1:1:0:60:29:1:0:0.2 0/1:27:5:4,1:11,11:0.1852:2,2:20.6:1:27.8:1:0.34188:3.82:60:10:0.1923:0:1.4 -16 86248135 . C G 86 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13239;SOR=4.28645;LSEQ=ACCCCAGACCTGCTGAGTCA;RSEQ=AATCTGCACTTTGACAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:7,12:0.0952:2,2:44.5:1:33:1:1:1.67:60:4:0.0952:0:1 0/1:22:7:3,4:4,11:0.3182:2,2:27.3:1:30.7:1:0.63022:1.99:60:14:0.3333:0:1.3 -16 86437690 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20789;SOR=Inf;LSEQ=AAGCTGTGCCTGGAACCCCA;RSEQ=CGGAGTCTGCAGTGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:0:2,0:26.7:1:31.9:1:1:0:60:68:1:0:0.1 0/1:29:2:1,1:14,13:0.069:2,2:12:0:32:0:1:1.07415:60:4:0.069:0:1 -16 86437767 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.22735;LSEQ=CATTATTTTTTCCTGGGTTT;RSEQ=TGTGGTTCGTCTACCTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:3,10:0.1875:2,2:26.3:1:32:1:1:1.61:60:6:0.2:0:1 0/1:9:2:1,1:1,6:0.2222:2,2:12.5:1:30:1:0.41667:4.58:60:4:0.25:0:1 -16 86437984 . G T 44 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCCGAGAAGCTGGGAT;RSEQ=ACAGGCGCACGCCACCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:33.3:1:28.3:1:1:0:60:6:1:0:1 -16 86544047 . C A 71 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CAGAGGTGCAGCCAGCCCCG;RSEQ=GCGCGCAGCCCCCTCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:0.8333:0,2:25.2:1:30.6:1:1:0:60:10:0.8333:0:1 1/1:1:1:1,0:0,0:1:0,0:5:0:31:0:1:0:60:2:1:0:1 -16 86544473 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21392;SOR=Inf;LSEQ=AGAACTCCGTGCGCCACAAC;RSEQ=TCTCGCTCAACGAGTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:111,79:0:2,0:28:1:31.4:1:1:0:60:94:1:0:0.2 0/1:164:2:1,1:92,70:0.0122:2,2:26.5:1:30.5:1:1:1.31206:60:4:0.0125:0:1 -16 86544478 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21655;SOR=Inf;LSEQ=TCCGTGCGCCACAACCTCTC;RSEQ=CTCAACGAGTGCTTCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:108,81:0:2,0:28.6:1:30.6:1:1:0:60:62:1:0:0.2 0/1:165:2:1,1:92,71:0.0121:2,2:36.5:1:25:0:1:1.29371:60:4:0.0125:0:1 -16 86544479 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21655;SOR=Inf;LSEQ=CCGTGCGCCACAACCTCTCG;RSEQ=TCAACGAGTGCTTCATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:108,81:0:2,0:28.7:1:32:1:1:0:60:62:1:0:0.2 0/1:165:2:1,1:92,71:0.0121:2,2:41.5:1:28.5:1:1:1.29371:60:4:0.0122:0:1.5 -16 86544504 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20487;SOR=Inf;LSEQ=CGAGTGCTTCATCAAGCTAC;RSEQ=CAAGGGCCTTGGGCGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:85,97:0:2,0:25.3:1:30.4:1:1:0:60:35.4:1:0:0.2 0/1:151:2:1,1:76,73:0.0132:2,2:23:1:27.5:1:1:1.04083:60:4:0.0134:0:1 -16 86544520 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08429;SOR=Inf;LSEQ=CTACCCAAGGGCCTTGGGCG;RSEQ=CCCGGCAAGGGCCACTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:61,85:0:2,0:23.5:1:31:1:1:0:60:72:1:0:0.1 0/1:115:3:2,1:53,59:0.0261:2,2:17.3:1:27.3:1:0.60572:2.21:60:6:0.0275:0:1.3 -16 86544525 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59264;SOR=2.41286;LSEQ=CAAGGGCCTTGGGCGGCCCG;RSEQ=CAAGGGCCACTACTGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:1,0:57,81:0.0072:2,0:1:0:28:0:0.41727:0:60:2:0.0074:0:1 0/1:116:2:1,1:52,62:0.0172:2,2:20.5:1:28:1:1:1.19:60:4:0.0175:0:1 -16 86546145 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCTTCAACCCCGCCGGCAGT;RSEQ=GTAGCCTCTGAGGTTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39.5:1:30:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:0:2,0:26:1:30:1:1:0:60:4:1:0:0.5 -16 86546173 . G A 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.1;SOR=0;LSEQ=CTGAGGTTGGGGGTGGTGGT;RSEQ=GCTGCCCTGGCGGTGACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:28:1:1:0:60:4:1:0:2 0/0:3:0:0,0:2,1:0:2,0:20.3:1:30:1:1:0:60:6:1:0:0.3 -16 86601049 . C T 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=AGCTACGGCGGCATGGCCAG;RSEQ=CCCATGGGCGTCTATTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:0.4545:0,0:22.6:1:28:1:1:0:60:4:0.4:0:1 0/0:4:0:0,0:4,0:0:0,0:20.8:1:31.5:1:1:0:60:8:1:0:0 -16 86601116 . TACC T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.05488;SOR=Inf;LSEQ=TGGGCCGCTCCTACGCGCCC;RSEQ=ACCACCACCAGCCCGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:27,4:0:2,0:21.6:1:26.8:1:1:0:60:9.333:1:0:0.1 0/1:10:2:1,1:8,0:0.2:0,2:17.5:1:27.4:1:0.2:0:60:4:0.2:0.1:0.5 -16 86601175 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50456;SOR=0;LSEQ=AAGCCGCCCTACAGCTACAT;RSEQ=GCGCTCATCACCATGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:44,12:0.0345:2,2:28:1:31.5:1:0.40109:3.56233:60:4:0.0345:0:1 0/0:44:0:0,0:36,8:0:2,0:22.9:1:30.7:1:1:0:60:88:1:0:0.1 -16 86601346 . C T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12401;SOR=Inf;LSEQ=TGCTTCGTCAAGGTGCCCCG;RSEQ=GACGACAAGAAGCCCGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:157,220:0:2,0:24:1:30.1:1:1:0:59.6:61.833:0.9973:0:0.1 0/1:379:4:2,2:163,212:0.0106:2,2:36.3:1:30.3:1:1:1.30:60:8:0.0108:0:1.3 -16 86601431 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2044;SOR=Inf;LSEQ=AGAACGGCAGCTTCCTGCGG;RSEQ=GCCGGCGGCGCTTCAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:18,105:0:2,0:23.8:1:29.9:1:1:0:60:40:1:0:0.1 0/1:102:2:1,1:18,82:0.0196:2,2:12.5:1:30.5:1:0.33935:4.46:60:4:0.02:0:1 -16 86612584 . C A 37 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62319;SOR=0.33753;LSEQ=ATCATGGACCGCTTCCCCTT;RSEQ=TACCACGACAACCGGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:2,1:128,71:0.0149:2,2:37:1:23.7:1:1:1.11:60:2:0.01:0:2.3 0/0:198:1:1,0:122,75:0.0051:2,0:4:0:23:0:1:0:60:2:0.0051:0:1 -16 86612596 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24963;SOR=Inf;LSEQ=TTCCCCTTCTACCACGACAA;RSEQ=CGGCAGGGCTGGCAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:141,85:0:2,0:26.4:1:31.4:1:1:0:60:74.333:1:0:0.1 0/1:245:3:2,1:141,101:0.0122:2,2:26:1:30.7:1:1:1.43:60:6:0.0123:0:1 -16 86612631 . T C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09604;SOR=0;LSEQ=GAACAGCATCCGCCACAACC;RSEQ=CTCGCTCAACGACTGCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:148,144:0.0102:2,2:27.7:1:25.3:1:0.61991:2.05071:60:2:0.0071:0:1 0/0:348:0:0,0:178,170:0:2,0:27.8:1:29.2:1:1:0:59.6:42.5:1:0:0.2 -16 86612680 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60477;SOR=0.44687;LSEQ=CCCCGCGAGAAAGGGCGGCC;RSEQ=GGCAAGGGCAGCTACTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:73,117:0.0104:2,2:26:1:30:1:1:1.60:60:4:0.0106:0:1 0/0:214:1:1,0:83,130:0.0047:2,0:1:0:23:0:0.39252:0:60:2:0.0047:0:1 -16 86612718 . T G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4977;SOR=Inf;LSEQ=GACGCTGGACCCCCGCTGCC;RSEQ=GGACATGTTTGAGAACGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:25,77:0:2,0:26.3:1:30.4:1:1:0:60:50:0.9901:0:0.1 0/1:106:2:1,1:23,80:0.0189:2,2:12.5:1:27.5:1:0.40659:3.43:60:4:0.0194:0:1 -16 86852074 . C A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55181;SOR=3.1502;LSEQ=CCACCCCAGACACAGAGAAC;RSEQ=GGAATTTGCAGTTTAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:6,12:0.0526:2,0:1:0:25:0:0.36842:0:60:2:0.0526:0:1 0/1:13:2:1,1:0,11:0.1538:0,2:19:1:28.5:1:0.15385:0:60:4:0.1538:0:1.5 -16 86858299 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11765;SOR=0;LSEQ=TCCTGCCTTCCTGCAAGGGG;RSEQ=ATTGGGAAACTTACCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:6,16:0.0833:2,0:5.5:1:31:0:1:0:60:4:0.0833:0:1 0/0:45:0:0,0:17,28:0:2,0:19.1:1:30.9:1:1:0:60:21.5:1:0:0.1 -16 87032111 . T TTGC 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.33333;SOR=0;LSEQ=GAGGAGCTGGCTTGGGGTGG;RSEQ=TGCTGCTGCTGCAGCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:32.4:1:1:0:60:4:1:0.5:2 0/0:2:0:0,0:1,1:0:2,0:22:1:31.5:1:1:0:60:4:1:0:1 -16 87032133 . G A 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06667;SOR=0;LSEQ=GCTGCTGCTGCAGCCATGTT;RSEQ=TCATCACTGCTGCTGTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31.5:1:28.5:1:1:0:60:4:1:0:2 0/0:4:0:0,0:2,2:0:2,0:28.8:1:32.8:1:1:0:60:8:1:0:1 -16 87032181 . G T 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTGTTGTGTGCGTGTTG;RSEQ=CATTGTTGTGGCCACTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:24:0:26:0:1:0:60:2:1:0:2 1/1:5:5:3,2:0,0:1:0,2:22.2:1:30.4:1:1:0:60:10:1:0:1 -16 87032404 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20093;SOR=0;LSEQ=TGCTGTCCTTGTCACGCTGT;RSEQ=GTGGTGTTGTGGCTGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:17,27:0.0435:2,2:10:1:29.5:1:1:1.57:60:4:0.0435:0:1 0/0:56:0:0,0:25,31:0:2,0:25.4:1:28.9:1:1:0:60:27:1:0:0.2 -16 87727766 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.48864;SOR=0;LSEQ=GGGCAGAACTGGACCAGGAG;RSEQ=AGGAGGGGCAGCAGCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,9:0.1111:2,2:40:1:28:1:1:1.27:60:4:0.1176:0:1 0/0:15:0:0,0:6,9:0:2,0:23:1:31.1:1:1:0:60:30:1:0:0.1 -16 88086369 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCACCACCTTTACCATTA;RSEQ=CATCTCCATCATCATCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:1:27.5:1:1:0:60:4:1:0:1.5 -16 88086471 . C A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACCAACACAACCACCCTAA;RSEQ=AATCACTACCACCACCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:46:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:47.5:1:30.5:1:1:0:60:4:1:0:1 -16 88087269 . TCAC T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CATCACCAACACAGTCACCT;RSEQ=CACCACCACCACCACCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:1:30:1:1:0:28:4:1:0:0 -16 88087947 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGTCATCTCCATCATCA;RSEQ=CACCAACACAGCCACCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15.5:1:31.5:1:1:0:53.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89250710 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12316;SOR=Inf;LSEQ=ACAGCACGTCCTAGCTCCAG;RSEQ=TGTCCCGGGGGGAAGTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:0:1,0:24:1:32.3:1:1:0:60:48:1:0:0.1 0/1:27:2:1,1:25,0:0.0741:1,2:18.5:1:27.5:1:0.07407:0:60:4:0.0741:0:1.5 -16 89250778 . AC A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50663;SOR=0;LSEQ=GCCCAAAGCCCGTCCTTCCC;RSEQ=CCCACCTCGGTGGCTAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:92,34:0.0156:2,2:22.5:1:30:1:0.47367:2.6814:60:4:0.0159:0:0 0/0:98:0:0,0:75,23:0:2,0:24.6:1:30.2:1:1:0:60:31.667:1:0:0.1 -16 89250780 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50715;SOR=0;LSEQ=CCAAAGCCCGTCCTTCCCAC;RSEQ=CCACCTCGGTGGCTAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:91,36:0.0155:2,2:12:1:28.5:1:0.49297:2.50706:60:4:0.0161:0:1 0/0:98:0:0,0:75,23:0:2,0:25:1:29.6:1:1:0:60:31.667:1:0:0.1 -16 89250882 . T C 209 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGTCCTGCCATATGTGG;RSEQ=CCCTCTAGCGGCACCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:143,174:0:2,0:25.2:1:29.5:1:1:0:60:34.222:1:0:0.1 0/1:265:109:50,59:73,83:0.4113:2,2:27.8:1:31:1:0.90096:1.0377:60:35.333:0.4173:0:1.4 -16 89250885 . C T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08826;SOR=Inf;LSEQ=GGTCCTGCCATATGTGGTCC;RSEQ=TCTAGCGGCACCTTCGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:138,176:0:2,0:24.7:1:31.2:1:1:0:60:43.857:1:0:0.1 0/1:253:3:1,2:114,134:0.0119:2,2:14.7:1:22.7:1:1:1.69804:60:2:0.0082:0:2.7 -16 89250905 . G A 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22901;LSEQ=CTCTAGCGGCACCTTCGTGA;RSEQ=TACCGCTTCCCACAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:2:2,0:98,143:0.0082:2,0:1:0:26.5:1:0.16835:0:60:4:0.0083:0:1 0/1:198:2:1,1:90,106:0.0101:2,2:14:0:31:1:1:1.18:60:4:0.0103:0:2.5 -16 89250922 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21352;SOR=Inf;LSEQ=TGAGTACCGCTTCCCACAGC;RSEQ=GGTGGGGCGGGGGCTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:69,119:0:2,0:24.7:1:30.6:1:1:0:60:93:1:0:0.1 0/1:162:2:1,1:71,89:0.0123:2,2:26:1:27.5:1:1:1.25:60:4:0.0127:0:1.5 -16 89250951 . T A 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGGCTCTGGCCTACACAG;RSEQ=CACAGTGCGCGTCCTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:28,84:0:2,0:23.9:1:30.1:1:1:0:60:224:1:0:0.1 0/1:93:37:12,25:22,34:0.3978:2,2:26.5:1:28.8:1:0.51961:1.34373:60:74:0.4022:0:1.5 -16 89335122 . C A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.41722;SOR=2.45387;LSEQ=GGAGGAGTGAAGGGAGAGCC;RSEQ=CAGACTCTGCCGACCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:2:1,1:117,308:0.0047:2,2:13:1:19:1:0.4768:2.63:60:1:0.0024:0:2.5 0/1:350:4:3,1:101,245:0.0114:2,2:8.3:1:26.8:1:0.08037:7.23:60:8:0.0116:0:1 -16 89337135 . C A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0258;SOR=Inf;LSEQ=AACTGGGCAGCGGCCTCCCC;RSEQ=CAGGCAGCGCAAAGGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:220,11:0:1,0:24:1:31.2:1:1:0:60:114.5:1:0:0.1 0/1:156:4:4,0:139,13:0.0256:2,0:32:1:30.8:1:1:0:60:8:0.0261:0:1 -16 89337143 . C A 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCGGCCTCCCCCCAGGCAG;RSEQ=GCAAAGGGGGTTGTCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:234,17:0:2,0:24.8:1:31.6:1:1:0:60:30.375:0.9959:0:0.1 0/1:192:33:27,6:138,21:0.1719:2,2:24.7:1:28.8:1:0.4212:1.45718:60:66:0.1746:0:1.1 -16 89337526 . G A 131 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00619;SOR=0;LSEQ=CTCCCTAAAATGCGCGTGGA;RSEQ=GCAGCTGGGCCTTTGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:19:0,19:1,17:0.5135:1,1:26.6:1:31:1:0.48649:0:60:18:0.5:0:1.2 0/0:9:0:0,0:0,9:0:0,0:20.3:1:28.6:1:1:0:60:8:1:0:0.8 -16 89341168 . C G 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTATCAAGGGGAGGGGAGG;RSEQ=GGGCAGGGTGCAGGCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:337,84:0:2,0:24.6:1:31.4:1:1:0:60:83.2:0.9952:0:0.1 0/1:350:43:35,8:236,68:0.1229:2,2:24.8:1:30.4:1:0.69528:1.26:60:42:0.1207:0:1.1 -16 89341429 . C T 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0;SOR=22.5634;LSEQ=TCCAGGCCCCACTGTCAACA;RSEQ=GACAGCCCCTGGGGCCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:1:0,1:296,302:0.0017:2,0:1:0:25:0:1:0:60:2:0.0017:0:1 0/1:551:20:11,9:264,267:0.0363:2,2:22.1:1:30.6:1:0.65737:1.24:60:40:0.0364:0:1.4 -16 89341682 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21206;SOR=Inf;LSEQ=TCTGGAGTTCACGGGGGTCC;RSEQ=GACTCAGCCTCCCCACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:36,143:0:2,0:20.2:1:30:1:1:0:60:358:0.9944:0:0.1 0/1:155:2:1,1:31,122:0.0129:2,2:9:1:26.5:1:0.37134:3.89:60:4:0.0132:0:1 -16 89341696 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50975;SOR=0;LSEQ=GGGTCCCGACTCAGCCTCCC;RSEQ=ACTCCTAGGAGCCTGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:16,121:0.0144:2,2:12:1:29.5:1:0.23042:7.37:60:4:0.0148:0:1 0/0:102:0:0,0:11,91:0:2,0:19.7:1:31.2:1:1:0:60:101:1:0:0.1 -16 89345122 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCAGGGGCAGGAGACACAG;RSEQ=GGGTGGCTCTCGTGAGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:29.5:1:28:1:1:0:60:4:1:0:4 0/0:2:0:0,0:1,1:0:2,0:38.5:1:29.5:1:1:0:60:4:1:0:0 -16 89345408 . G A 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00798;SOR=2.05193;LSEQ=TGGGACAAGACGGGCTGGAG;RSEQ=AAGCCGTGACTAGGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:263:212:184,28:43,8:0.8061:2,2:23:1:29.8:1:0.65199:1.22:60:34.333:0.8047:0:1.1 1/1:229:205:163,42:24,0:0.8952:1,2:22:1:29.5:1:0.00998:0:60:204:0.8987:0:1.1 -16 89345414 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25002;SOR=0;LSEQ=AAGACGGGCTGGAGGAAGCC;RSEQ=TGACTAGGGGCCCCAGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:243,49:0.0102:2,2:8.3:1:27.3:1:0.07837:9.79991:60:6:0.0103:0:1.3 0/0:271:0:0,0:216,55:0:2,0:21.9:1:30.1:1:1:0:60:270:1:0:0.8 -16 89346073 . C T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08036;SOR=Inf;LSEQ=GGCACGGGAGGCCTCAGTGT;RSEQ=GTCCTCGGGGCCGGCACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:239,118:0:2,0:21.5:1:29.5:1:1:0:49.8:26.462:1:0:0.2 0/1:272:3:1,2:174,95:0.011:2,2:11:1:24.3:1:0.29009:3.64473:60:2:0.0074:0:1 -16 89346157 . C T 73 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.0523;SOR=7.1634;LSEQ=AGGGGCACAGAGGGACGCGG;RSEQ=GGGGGGGCCTTCAGCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:649:1:0,1:337,309:0.0015:2,0:14:0:15:0:0.47913:0:60:0:0:0:1 0/1:548:6:2,4:280,259:0.0109:2,2:18.7:1:28.3:1:0.43592:2.15921:60:12:0.0113:0:1 -16 89346756 . A G 200 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGACTTGCAGTTGCTGAAG;RSEQ=AGGACTCCAGCCCGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:995:0:0,0:467,527:0:2,0:25.2:1:29.9:1:1:0:60:44.182:0.999:0:0.2 0/1:1011:86:46,40:428,497:0.0851:2,2:26.9:1:31.2:1:0.21496:1.34:60:85:0.0858:0:1.2 -16 89349023 . C T 203 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.81435;LSEQ=CCCGGCTCCTGCCCTCGGTC;RSEQ=GTGAAGCTGTCAGAGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1591:4:0,4:843,744:0.0025:2,0:1.3:1:27.5:1:0.04865:0:60:8:0.0025:0:1 0/1:1456:105:60,45:706,644:0.0721:2,2:24.1:1:30.3:1:0.3621:1.22:60:210:0.073:0:1.2 -16 89349640 . C CT 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.89808;SOR=0.94395;LSEQ=CTCTTTGCCTTTCTTGTCAT;RSEQ=TTTTTTTTCAGAGAAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1784:30:14,16:888,866:0.0168:2,2:23.7:1:29.9:1:0.71527:1.17179:60:29:0.0164:0.0022:0.2 0/1:2014:32:14,18:1023,954:0.0159:2,2:23.8:1:29.8:1:0.37961:1.37848:60:64:0.016:0.002:0.1 -16 89350038 . G A 309 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=1.45092;LSEQ=CCTTCAGCTCCTCCCGGTGC;RSEQ=CCTCCTCGGGCTTGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1615:1296:666,630:155,159:0.8025:2,2:25.3:1:29.8:1:0.52977:1.08:60:71:0.8033:0:1.1 1/1:1648:1409:711,698:117,118:0.855:2,2:23.9:1:29.6:1:0.88798:1.03:60:69.45:0.8553:0:1.2 -16 89350178 . G A 331 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.47217;LSEQ=GGGACACTTTTATGCTTTTC;RSEQ=GTCTGCTCTTTCCTCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1879:1500:754,746:194,181:0.7983:2,2:25.4:1:30.6:1:0.64421:1.06045:60:82.333:0.8002:0:1.1 1/1:2039:1930:965,965:53,51:0.9465:2,2:23.9:1:30.4:1:0.91988:1.03921:60:127.667:0.9471:0:1.2 -16 89350577 . C T 199 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=17.66645;LSEQ=TCTTCTTTAAAAATCTTCTC;RSEQ=TTCTCTTTTGAAATTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2004:5:1,4:1073,925:0.0025:2,2:10.4:1:27.8:1:0.18935:4.63627:60:10:0.0025:0:1 0/1:2197:93:55,38:1101,1002:0.0423:2,2:25.1:1:30.5:1:0.20489:1.32:59.8:186:0.0427:0:1.2 -16 89350597 . C G 252 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTCTCTTTTGAAATTTTGT;RSEQ=CTCTTTTAAATCATTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2079:231:128,103:956,889:0.1111:2,2:25.6:1:32.1:1:0.32813:1.16:59.7:114.5:0.1118:0:1.1 0/0:2294:0:0,0:1193,1099:0:2,0:24.7:1:30.9:1:1:0:59.9:133.824:0.9991:0:0.2 -16 89352149 . G A 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00058;SOR=Inf;LSEQ=GGCTCTGCAGATGTGTCTGC;RSEQ=GGAAGGTTCCCACCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:29,289:0:2,0:22.9:1:31.2:1:1:0:60:105:1:0:0.1 0/1:210:8:0,8:28,174:0.0381:2,0:21.4:1:30.3:1:0.60108:0:60:16:0.0388:0:1.3 -16 89352678 . G A 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.03253;LSEQ=ATAACACGGCAGCCCCTTCC;RSEQ=AGAACCCTGGGGTTCGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:198:155:8,147:3,40:0.7828:2,2:22.9:1:30.3:1:0.70704:1.37571:60:76.5:0.7806:0:1.1 1/0:170:134:10,124:1,35:0.7882:1,2:20.9:1:30.4:1:0.46102:2.81:60:66:0.7904:0:1 -16 89352699 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50585;SOR=0;LSEQ=AGAACCCTGGGGTTCGACCC;RSEQ=AGAGCAGCCCCTCACGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:0,2:1,121:0.0161:1,0:24:1:29.5:1:1:0:60:4:0.0164:0:2 0/0:96:0:0,0:0,96:0:1,0:23.6:1:31.4:1:1:0:60:95:1:0:0.8 -16 89352777 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05702;SOR=Inf;LSEQ=GAGGCTCTGGGTGTGGTGGG;RSEQ=GAGGCTGTGGCTCCTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:1,42:0:1,0:26.1:1:29.8:1:1:0:60:42:1:0:0.2 0/1:14:2:0,2:0,12:0.1429:0,0:17:1:31.5:1:1:0:60:4:0.1429:0:1 -16 89352786 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGGTGGGCGAGGCTGT;RSEQ=GCTCCTCTGTGGGAAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:0,35:0.0541:1,2:11.5:1:29:1:0.05405:0:60:4:0.0556:0:1 0/0:10:0:0,0:0,10:0:0,0:25.8:1:31.6:1:1:0:60:20:1:0:0.1 -16 89355278 . A G 187 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00153;SOR=0;LSEQ=TACTGTGGCACCTCGTTAGC;RSEQ=CGATCCATATCTAGCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:0,53:0,0:1:0,1:22.6:1:32.8:1:1:0:60:106:1:0:1.1 1/0:22:17:1,16:0,5:0.7727:0,1:18.6:1:32.1:1:1:0:60:34:0.7727:0:1.1 -16 89356582 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=CCTGCAGAGCAGACGCGCAC;RSEQ=CCACGAGGCCACAGCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:28.8:1:31.6:1:1:0:60:16:1:0:1.3 1/0:4:2:1,1:1,1:0.5:2,2:22:0:32:1:1:1:60:4:0.5:0:1 -16 89356652 . GCG AT 56 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGGGAGGCTCAGGGCTCCA;RSEQ=GGGGGTAGGCTCAGGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,0:0.75:0,0:30.7:1:30.6:1:1:0:54.7:6:0.75:0.25:0 1/1:4:4:3,1:0,0:1:0,2:13.3:1:28.3:1:1:0:56.5:8:1:0.5:0 -16 89356658 . GGT G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GGCTCAGGGCTCCAGCGGGG;RSEQ=AGGCTCAGGGCTCCAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:3,0:0.5:0,2:15.5:1:30:1:0.4:0:33.5:4:0.5:0.25:4.5 0/0:2:0:0,0:2,0:0:0,0:17:0:19:1:1:0:53:1:1:0:2 -16 89356701 . C G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GGTAGGCTCAGGGCTCCAGC;RSEQ=GGGGGAGGCTCAGGGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:32.1:1:30.6:1:1:0:42.4:16:1:0:3 1/1:7:6:3,3:0,0:0.8571:0,2:29.7:1:25.5:1:1:0:31.2:5:0.8333:0:3.2 -16 89356724 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.20588;SOR=0;LSEQ=GGGAGGCTCAGGGCTCCAAT;RSEQ=GGGGGAGGCTCAGGGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:37.5:1:31:1:1:1:43:4:0.25:0:2.5 0/0:9:0:0,0:4,5:0:2,0:26.9:1:30:1:1:0:29.3:18:1:0:2.2 -16 89356864 . T G 143 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00522;SOR=0;LSEQ=GGCTCAGGGCTCCAATGGGG;RSEQ=GAGGCTCAGGGCTCCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:24,0:0,0:1:0,1:34.2:1:31.3:1:1:0:54:48:1:0:2 1/0:15:10:9,1:4,0:0.6667:0,2:29:1:28.4:1:1:0:39.9:9:0.75:0:3.4 -16 89356882 . CGGGGGAGGCTCAGGGCTCCAATG C 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=60;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGAGGCTCAGGGCTCCAG;RSEQ=GGGGGAGGCTCAGGGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:48:48,0:5,0:0.8889:0,1:21.7:1:30.4:1:1:0:57.4:47:0.9038:0.2222:1 0/0:24:0:0,0:19,4:0:2,0:22:1:27.4:1:1:0:47.8:22:1:0:2.2 -16 89356903 . ATG GC 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00585;SOR=Inf;LSEQ=GGGGGAGGCTCAGGGCTCCA;RSEQ=GGGGGAGGCTCAGGGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:5,0:0:0,0:19.2:1:26.6:1:1:0:39.4:4:1:0:3 0/1:26:5:5,0:16,3:0.1923:2,0:7.2:1:31.3:1:1:0:57:10:0.25:0.1538:0.6 -16 89356928 . G T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.68625;LSEQ=GGGAGGCTCAGGGCTCCAAT;RSEQ=GGGGGAGGCTCAGGGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:3:3,0:106,5:0.0259:1,0:39:1:23.3:1:1:0:40:2:0.0187:0:3.7 0/1:56:1:1,0:50,4:0.0179:2,0:31:0:27:0:1:0:21:2:0.0185:0:3 -16 89356933 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54735;SOR=0;LSEQ=GCTCAGGGCTCCAATGGGGG;RSEQ=AGGCTCAGGGCTCCAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:2,0:113,7:0.0163:2,0:12:1:30:1:1:0:41:4:0.0171:0:5.5 0/0:64:0:0,0:59,5:0:2,0:18.5:1:30.2:1:1:0:56.8:15:1:0:0.5 -16 89356957 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16122;SOR=Inf;LSEQ=CTCAGGGCTCCAATGGGGGG;RSEQ=GGCTCAGGACTCCACTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:183,13:0:2,0:26.4:1:29.2:1:1:0:59.3:10.529:1:0:0.3 0/1:132:2:2,0:114,16:0.0152:2,0:36.5:1:32:1:1:0:60:4:0.0161:0:1 -16 89357823 . C G 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCTCGTTACCAGCCCCT;RSEQ=AAGTCTGCTAAGCCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:0,3:26,14:0.0698:2,0:28.7:1:30.7:1:0.0551:0:60:6:0.0714:0:1 0/0:9:0:0,0:7,2:0:2,0:18.7:1:31.8:1:1:0:60:18:1:0:0.2 -16 89360061 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGCGGAGGGGAGGAGGCG;RSEQ=GGTGGTATTGGGGCTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:3:0:11:0:1:0:60:0:0:0:3 0/1:7:2:1,1:3,2:0.2857:2,2:15.5:1:30:1:1:1.41418:60:4:0.2857:0:1 -16 89371407 . G A 160 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00576;SOR=0;LSEQ=AAGAGTGAAGCTCTCCAATC;RSEQ=GCCCCATGGGCCTGAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:38,3:0,0:1:0,2:25.2:1:30:1:1:0:60:40:1:0:1.1 1/0:10:7:7,0:3,0:0.7:0,0:21.6:1:31:1:1:0:60:14:0.7:0:1 -16 89371827 . G A 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCAAGATTTTGTTTCATAT;RSEQ=CCAGGAGAAGCGCATCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:198:198:5,193:0,0:1:0,1:24.3:1:30.1:1:1:0:60:98:1:0:1.8 1/1:149:124:6,118:3,22:0.8322:2,1:19.9:1:29.7:1:0.1754:2.65882:60:40.333:0.8288:0:1.8 -16 89371839 . G A 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TTTCATATGCCAGGAGAAGC;RSEQ=CATCTCTTATTTGGGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:164:164:3,161:0,0:1:0,1:22.9:1:30.3:1:1:0:60:163:1:0:2 1/1:103:86:3,83:2,14:0.835:2,1:20.3:1:30.4:1:0.17395:3.87639:60:172:0.8431:0:2 -16 89371953 . G T 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.21053;SOR=0;LSEQ=CGGGGTCGGGCTGTGGCTCA;RSEQ=CCCTGACTCTGGCCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:0,30:0,0:1:0,1:22.4:1:30.2:1:1:0:60:60:1:0:1.1 1/1:8:7:0,7:0,1:0.875:0,0:28.1:1:30.3:1:1:0:60:14:0.875:0:1 -16 89372039 . C G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGAGAAAGCAGAGGAGACA;RSEQ=ACACGCGCTACCTCTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:19:1:32.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89372046 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCAGAGGAGACACACACGC;RSEQ=CTACCTCTCACTCCGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19:1:33:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89372563 . A G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCCCACTCCGCAGACACGC;RSEQ=CCACCTCCCACTCCGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:35.5:1:32:0:1:0:42:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:8.5:1:28.5:1:1:0:32:4:1:0:3 -16 89373230 . T C 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACACGCGCCACCTCCCA;RSEQ=TCCACAGACACGCGCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:29:1:1:0:53:4:1:0:2 -16 89373234 . A G 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGCGCCACCTCCCATTCC;RSEQ=CAGACACGCGCCACTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:28.5:1:1:0:53:4:1:0:2 -16 89382073 . G A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGAGGAGCTTGGGACAGA;RSEQ=CAAGTGGGAGCAGACACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:32:0:1:0:60:4:1:0:1.5 -16 89383725 . T C 71 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22619;SOR=0.14055;LSEQ=CAGAGAAGGGTCAAGCACTT;RSEQ=GTAGTGGCAGAAAGGGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:17.6:1:30.8:1:1:0:60:10:0.8333:0:1.2 0/1:3:1:0,1:0,2:0.3333:0,0:1:0:30:0:1:0:60:2:0.3333:0:1 -16 89384555 . G T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCTCTGCGACACACGGT;RSEQ=CGAGCGCACTTCTTCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89653419 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12369;SOR=Inf;LSEQ=ACTGGCCTCAGTGTCCCTGG;RSEQ=GGGGGTGGACGCTGACTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:71,71:0:2,0:27.7:1:30.5:1:1:0:60:34.5:1:0:0.2 0/1:154:4:1,3:77,73:0.026:2,2:19.5:1:26.5:1:0.36359:3.14271:60:8:0.0263:0:1 -16 89653442 . G A 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36395;SOR=0.3186;LSEQ=GGGTGGACGCTGACTCCGCC;RSEQ=GCCGGAAGTTCCACAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:1,2:61,79:0.021:2,2:10.7:1:29.7:1:1:1.5398:60:6:0.0214:0:1 0/0:148:1:1,0:64,83:0.0068:2,0:1:0:28:0:0.43919:0:60:2:0.0068:0:1 -16 89653445 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24756;SOR=Inf;LSEQ=TGGACGCTGACTCCGCCGGC;RSEQ=GGAAGTTCCACAGGGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:60,77:0:2,0:25.7:1:30.2:1:1:0:60:67.5:1:0:0.2 0/1:143:3:1,2:58,80:0.021:2,2:19:1:26.7:1:1:1.44633:60:2:0.0144:0:1 -16 89653446 . G A 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.96612;LSEQ=GGACGCTGACTCCGCCGGCC;RSEQ=GAAGTTCCACAGGGTGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:1,0:59,76:0.0074:2,0:1:0:25:0:0.44118:0:60:2:0.0074:0:1 0/1:139:2:1,1:57,80:0.0144:2,2:26:0:32.5:1:1:1.40:60:4:0.0145:0:1.5 -16 89653456 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49839;SOR=Inf;LSEQ=TCCGCCGGCCGGAAGTTCCA;RSEQ=AGGGTGTACTCCTTCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:50,72:0:2,0:24.7:1:32:1:1:0:60:60:1:0:0.2 0/1:129:2:1,1:49,78:0.0155:2,2:42:0:30.5:1:1:1.59:60:4:0.0159:0:1.5 -16 89653457 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49839;SOR=Inf;LSEQ=CCGCCGGCCGGAAGTTCCAC;RSEQ=GGGTGTACTCCTTCCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:50,72:0:2,0:24.3:1:30.7:1:1:0:60:121:1:0:0.2 0/1:129:2:1,1:49,78:0.0155:2,2:21.5:1:31:0:1:1.59:60:4:0.0156:0:2 -16 89653458 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23714;SOR=0;LSEQ=CGCCGGCCGGAAGTTCCACA;RSEQ=GGTGTACTCCTTCCTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:49,71:0.0164:2,2:25.5:1:30:1:1:1.44:60:4:0.0167:0:1 0/0:128:0:0,0:49,79:0:2,0:24:1:30.7:1:1:0:60:127:1:0:0.4 -16 89653459 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49865;SOR=Inf;LSEQ=GCCGGCCGGAAGTTCCACAG;RSEQ=GTGTACTCCTTCCTGGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:49,72:0:2,0:23.8:1:30.8:1:1:0:60:120:1:0:0.2 0/1:130:2:1,1:48,80:0.0154:2,2:5:0:31:1:1:1.66:60:4:0.0155:0:1.5 -16 89653520 . T C 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01755;SOR=Inf;LSEQ=TCCACTTCACCGTGAGTCCA;RSEQ=GGCCCCGCCCCATGCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:2,32:0:2,0:24.2:1:29.9:1:1:0:59.4:33:1:0:0.6 0/1:21:4:0,4:0,17:0.1905:1,0:28.3:1:29.5:1:1:0:60:8:0.1905:0:1.5 -16 89653524 . C CCCGCCCCATG 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.78961;LSEQ=CTTCACCGTGAGTCCATGGC;RSEQ=CCGCCCCATGCCGCCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:8:0,8:1,21:0.2667:1,0:29.6:1:31.4:1:1:0:57.5:16:0.2667:0:1.1 0/1:18:4:0,4:0,14:0.2222:1,0:21.5:1:31.7:1:1:0:60:8:0.2353:0.1667:0.3 -16 89653563 . G T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTCCGTGGCCCCGCCCC;RSEQ=CCCCGCCCCCTCAGTCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:1,15:0,0:1:0,1:19.9:1:28.7:1:1:0:58.8:7:1:0:1.7 1/1:4:4:0,4:0,0:1:0,0:23.5:1:26.8:1:1:0:60:3:1:0:1.5 -16 89653580 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCCCCGCCCCCTCAGTC;RSEQ=GTGGCCCCGCCCCTCCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:22:0:32:0:1:0:50:4:0.2857:0:3 0/0:2:0:0,0:0,2:0:0,0:20.5:1:31.5:1:1:0:60:4:1:0:2 -16 89653593 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGTCCGTGGCCCCGCCC;RSEQ=TCCCCGCCCCCTCAGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:9:0:32:0:1:0:50:4:0.25:0:3 0/0:1:0:0,0:0,1:0:0,0:22:0:34:0:1:0:60:2:1:0:3 -16 89653624 . A C 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGTCTGTGGCCCCGCCC;RSEQ=TCCCCGCCCCCTCAGTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:21.5:1:32.8:1:1:0:60:8:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89804855 . C T 104 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00103;SOR=11.03216;LSEQ=CCCGCAAACGCTGAGTGACT;RSEQ=GGGGCCGGACAGTTCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:39,0:0.0488:1,0:28.5:1:32:0:1:0:60:4:0.0488:0:1 0/1:27:10:8,2:17,0:0.3704:1,2:25.5:1:31.4:1:0.12821:0:60:20:0.4:0:1.2 -16 89805218 . C T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.25027;SOR=0;LSEQ=GAGTTGTATTGCCAGCCAGG;RSEQ=AGGCACATGGCCCAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:1,2:153,101:0.0117:2,2:18.7:1:26.7:1:0.56603:3.01649:60:6:0.0119:0:1 0/0:233:0:0,0:135,98:0:2,0:23.4:1:32:1:1:0:60:232:1:0:0.3 -16 89805261 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.40544;LSEQ=TCAATTCTCATGTCCCCCAC;RSEQ=TGGCCCAAGGTGGGCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:111:62,49:172,123:0.2734:2,2:27.6:1:30.5:1:0.65431:1.10489:60:54.5:0.2732:0:1.1 0/1:406:193:114,79:124,87:0.4754:2,2:22.8:1:29.8:1:1:1.01:60:95.5:0.4775:0:1.1 -16 89805301 . G C 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=Inf;LSEQ=TGACGTTACCTCTGCCACGT;RSEQ=TGAGAAGCTCTTTTTCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:268,260:0:2,0:25.3:1:31.9:1:1:0:60:51.8:1:0:0.3 0/1:631:16:10,6:324,291:0.0254:2,2:23.8:1:30.7:1:0.46144:1.50:60:32:0.0255:0:1.6 -16 89805465 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17592;SOR=Inf;LSEQ=CCCATAGTCTGCATGCTGTG;RSEQ=CGGAACATTCTTTGGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:118,118:0:2,0:23.3:1:31.8:1:1:0:60:46.2:1:0:0.1 0/1:171:2:1,1:93,76:0.0117:2,2:5.5:1:27.5:1:1:1.22223:60:4:0.0119:0:1 -16 89805977 . G A 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1385;SOR=1.27007;LSEQ=GAGGTCTGCAACACCAAGAA;RSEQ=TGGCTCAGGCAACTCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:101:35,66:93,181:0.2693:2,2:25.8:1:30.5:1:0.90282:1.03:60:202:0.2708:0:1.1 0/1:417:133:45,88:109,175:0.3189:2,2:24.4:1:29.7:1:0.38583:1.21746:60:65.5:0.3172:0:1.2 -16 89806018 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=ATCTCTGCCTATTATCAGTG;RSEQ=TGGGGACACCCCTGGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:41,151:0:2,0:22.8:1:31.9:1:1:0:60:47:1:0:0.3 0/1:192:2:1,1:52,138:0.0104:2,2:22:1:27:1:0.47693:2.64:60:4:0.0106:0:1.5 -16 89806347 . A T 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.92509;SOR=1.03337;LSEQ=CGTTCTTAACCATTTGCAAG;RSEQ=TGCCTCTGAAAAGAGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:76:58,18:140,46:0.289:2,2:22.1:1:30.1:1:1:1.06:60:152:0.2912:0:1 0/1:284:84:65,19:149,51:0.2958:2,2:22.9:1:29.3:1:0.65329:1.17:60:168:0.2989:0:1.1 -16 89806445 . C T 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAGCCAGGATATCTTCCT;RSEQ=TTCTCTAAACACTCGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:668:0:0,0:344,323:0:2,0:25:1:31.3:1:1:0:60:59.636:0.9985:0:0.1 0/1:846:54:25,29:408,383:0.0638:2,2:26.3:1:29.9:1:0.48384:1.2354:60:108:0.0647:0:1.4 -16 89807081 . T C 23 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.68623;SOR=1.48439;LSEQ=AACCCACGGCCTGGGAGTTC;RSEQ=CACTCACACTTCCGCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:3,0:70,0:0.0411:1,0:32.3:1:25.3:1:1:0:60:2:0.0328:0:6.7 0/1:50:3:3,0:47,0:0.06:1,0:43:1:14.7:1:1:0:60:0:0:0:6 -16 89807142 . G T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35675;SOR=3.2395;LSEQ=CTGGAAACCCTGACTTGGAA;RSEQ=CTGGCTGCCTGGTGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:1:0,1:180,42:0.0045:2,0:1:0:25:0:0.19283:0:60:2:0.0046:0:1 0/1:209:3:1,2:160,46:0.0144:2,2:28.7:1:27.3:1:0.13262:6.87246:60:6:0.0146:0:1.7 -16 89807147 . C T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2489;SOR=0;LSEQ=AACCCTGACTTGGAAGCTGG;RSEQ=TGCCTGGTGCCCCTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:188,53:0.0123:2,2:6:1:24.3:1:0.12833:7.01943:60:2:0.0083:0:2.3 0/0:232:0:0,0:172,60:0:2,0:23.1:1:31.5:1:1:0:60:115:1:0:0.1 -16 89807457 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19426;SOR=Inf;LSEQ=TAATTGAGAATTAATTACTA;RSEQ=TGGCTGGGTCATTTCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:0:1,0:22.3:1:32.2:1:1:0:60:52:1:0:0.2 0/1:21:2:1,1:1,18:0.0952:1,2:19.5:1:30.5:1:0.18571:13.08:60:4:0.0952:0:1.5 -16 89809404 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49801;SOR=Inf;LSEQ=AACCATACAACCACGCCATA;RSEQ=AAACCAAGTCCTTATTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:7,113:0:2,0:23.8:1:31.5:1:1:0:60:119:1:0:0.1 0/1:123:2:1,1:12,109:0.0163:2,2:16.5:1:31:1:0.20099:8.77:60:4:0.0165:0:1 -16 89811196 . T C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=5.5622;LSEQ=TGCCTCGGCCTCCCCAGTAG;RSEQ=TGGGATTACAGGCGCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:6:6,0:49,1:0.1034:1,0:26.3:1:28.8:1:1:0:60:5:0.0909:0:1.3 0/1:43:17:15,2:25,1:0.3953:1,2:27.2:1:32.6:1:0.55231:3.23828:58.8:34:0.3953:0:1.2 -16 89811516 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.20028;SOR=Inf;LSEQ=AGCACACAGATGAGGGTGGC;RSEQ=GAGATGGACACACCTCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:37,192:0:2,0:21.2:1:30.1:1:1:0:60:56.25:1:0:0.2 0/1:186:2:1,1:24,160:0.0108:2,2:25:1:31:1:0.25138:6.55:60:4:0.011:0:1 -16 89811530 . C A 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.17627;LSEQ=GGTGGCTGAGATGGACACAC;RSEQ=TCCGCTGCCCCAGCCATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:13,160:0.0114:2,2:23.5:1:20.5:1:0.15402:11.90:60:1:0.0058:0:1 0/1:149:2:1,1:13,134:0.0134:2,2:22.5:1:26:1:0.17967:9.97:60:4:0.0138:0:1 -16 89812582 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCTCTGCTCCGAAGTCC;RSEQ=AAGAAAGCATAGTCAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:33:1:29:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89812778 . G A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02419;SOR=Inf;LSEQ=CCTGCGGGTGCCATGGTGAC;RSEQ=GCGGTGGGGGCAGGGACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:0:1,0:28.5:1:30.5:1:1:0:60:44:1:0:0.1 0/1:10:3:3,0:7,0:0.3:0,0:33.7:1:31.3:1:1:0:60:6:0.3:0:1 -16 89812930 . G A 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=61.56097;LSEQ=CGTGCTGCAGAGATGCCAGA;RSEQ=GCAGCTGTGGAGTCTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:1:1,0:240,104:0.0029:2,0:40:0:15:0:1:0:60:0:0:0:2 0/1:315:48:36,12:181,86:0.1524:2,2:22.8:1:29.9:1:0.39785:1.42:60:23:0.1479:0:1.2 -16 89813156 . G T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21182;SOR=4.12852;LSEQ=GGACCCACAACTAGTAGAGT;RSEQ=AAGGAACTCACAGGAAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:143,126:0.0037:2,0:1:0:24:0:0.47037:0:60:2:0.0037:0:1 0/1:264:4:2,2:148,112:0.0152:2,2:13:1:27.8:1:1:1.32:60:8:0.0155:0:1 -16 89813387 . A G 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09774;SOR=Inf;LSEQ=CTGCTGTGGATTCAGTTTTG;RSEQ=GAAAAACACTCGCTAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:32,153:0:2,0:19.7:1:31.1:1:1:0:60:184:1:0:0.1 0/1:159:3:1,2:31,125:0.0189:2,2:28.7:1:27.7:1:0.49286:2.01:60:6:0.019:0:1 -16 89814818 . T G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62671;LSEQ=GTGTCAAAATCATTAAAACT;RSEQ=GAGGGAAACTAAAGGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:27.4:1:32:1:1:0:60:10:0.625:0:1 1/0:4:2:2,0:2,0:0.5:0,0:22.5:1:31:1:1:0:60:4:0.5:0:1 -16 89815049 . T C 176 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=23.32989;LSEQ=TGACAGATCGGACGGACACG;RSEQ=GCACACGGGGCACCTACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:2:1,1:312,205:0.0038:2,2:28:0:32.5:1:1:1.52064:60:4:0.0039:0:1 0/1:678:56:31,25:346,275:0.0826:2,2:26.4:1:30.4:1:1:1.01464:60:55:0.0821:0:1.1 -16 89815203 . G A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1365;SOR=Inf;LSEQ=GAAGGGGCTGTATTGGTGGC;RSEQ=ACAGCACAGCGTACACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:72,185:0:2,0:26.1:1:30.9:1:1:0:60:84.667:1:0:0.1 0/1:334:4:3,1:116,213:0.012:2,2:7.3:1:27:1:0.13224:5.48:60:8:0.0123:0:1 -16 89815217 . C T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.12359;LSEQ=GGTGGCGACAGCACAGCGTA;RSEQ=ACTCTGCTCCTTCCCAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:11:2,9:58,149:0.0505:2,2:25.6:1:29:1:0.73127:1.74771:60:22:0.0516:0:1.2 0/1:228:80:24,56:51,97:0.3509:2,2:22.9:1:28.6:1:0.55577:1.22571:60:160:0.3556:0:1.2 -16 89816108 . C T 70 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2527;SOR=0.32085;LSEQ=GCTGCCCTGCCCAGGTGGTG;RSEQ=TGCCCTGCCCAGGTGGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:5:2,3:293,191:0.0102:2,2:10:1:30.2:1:0.3899:2.29703:60:10:0.0104:0:1.4 0/0:606:2:2,0:354,249:0.0033:2,0:25.5:1:31:1:0.51484:0:60:4:0.0034:0:1.5 -16 89818340 . G C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51049;SOR=4.09114;LSEQ=AGGTGCCCGCCACCACGCCC;RSEQ=GCTAAATTTTTGTATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:12.3:1:30:1:1:0:60:6:0.3:0:1 1/0:3:2:2,0:1,0:0.6667:0,0:29.5:1:28:1:1:0:60:4:0.6667:0:3 -16 89818422 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15938;SOR=Inf;LSEQ=TCTCCTGACTGTGTGATCCG;RSEQ=CTGCCTCGGCCTCCCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:78,1:0:1,0:24.5:1:32.5:1:1:0:60:158:1:0:0.3 0/1:53:2:1,1:51,0:0.0377:1,2:9.5:1:30:1:0.03774:0:60:4:0.0385:0:1 -16 89818491 . T C 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-04;SOR=1.85946;LSEQ=CCTGGCAATAAATATCTTAA;RSEQ=AGCACGCGGCTTAAATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:73:49,24:131,38:0.3017:2,2:24.1:1:32.3:1:0.10858:1.68473:60:146:0.3017:0:1.1 0/1:258:115:85,30:100,43:0.4457:2,2:22:1:31.4:1:0.49095:1.22:60:114:0.4436:0:1.2 -16 89818732 . C G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08126;SOR=0.42564;LSEQ=TGAGTGATGGCTGTGCTTCT;RSEQ=TGACAGTGTGACCCTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:16:0,16:1,63:0.2:1,1:20.5:1:33.1:1:1:0:60:32:0.2025:0:1 0/1:94:9:0,9:3,82:0.0957:1,0:25.7:1:32.7:1:1:0:60:18:0.0957:0:1 -16 89819092 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCATACAGAGATAGGAG;RSEQ=TGAGGGGATATACTGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:27.5:1:1:0:23:4:1:0:1 -16 89825171 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22121;SOR=0;LSEQ=CTTCGTGGCCAGCGGTTCCC;RSEQ=ATAACCAGGGAATAGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:17,144:0.0123:2,2:22:1:29:1:0.20927:8.26:60:4:0.0126:0:1 0/0:183:0:0,0:29,154:0:2,0:21.8:1:31.7:1:1:0:60:366:1:0:0.1 -16 89828669 . C G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01144;SOR=Inf;LSEQ=CCTTCTTTCTAAGTATAAAA;RSEQ=GGCTATTTTAGTCTGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:0:0,0:31.6:1:30.9:1:1:0:60:22:1:0:0.1 1/0:7:4:0,4:1,2:0.5714:2,0:16:1:31.5:1:0.42857:0:60:8:0.5714:0:1 -16 89831149 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23015;SOR=0;LSEQ=CTAGACTCGAGACGAGGAGA;RSEQ=AGTCGGCACACACACACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:98,13:0.0177:2,2:7.5:1:28.5:1:0.23341:7.30276:60:4:0.0182:0:1 0/0:122:0:0,0:95,27:0:2,0:24.2:1:30.5:1:1:0:60:23.4:1:0:0.2 -16 89831155 . GCA G 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.35023;SOR=0.2998;LSEQ=TCGAGACGAGGAGACAGTCG;RSEQ=CACACACACCCTAGACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:3:3,0:102,18:0.0244:2,0:27.3:1:30.3:1:1:0:60:6:0.0252:0:0 0/0:135:1:1,0:101,33:0.0074:2,0:42:0:29:0:1:0:60:2:0.0076:0:1 -16 89831510 . C A 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCCGGCCGTTTCTTCATTG;RSEQ=GCAAGTTTCACTGTGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:101,208:0:2,0:25.2:1:30.5:1:1:0:60:153.5:1:0:0.1 0/1:323:66:24,42:92,164:0.2043:2,2:27.6:1:30.1:1:1:1.02:60:65:0.2038:0:1.1 -16 89831549 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50144;SOR=0;LSEQ=GGCTGAGCAAATGCTCAGGT;RSEQ=GAAACAGACCATCAACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:16,138:0.0128:2,2:26.5:1:29:1:0.2067:8.40:60:4:0.013:0:1 0/0:133:0:0,0:27,106:0:2,0:19.6:1:30.5:1:1:0:60:65.5:1:0:0.3 -16 89833477 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66848;SOR=0.58269;LSEQ=AAAGCGGCAGCAGACCTCGG;RSEQ=CTTCCGGTCCGAAAGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:1,2:178,49:0.013:2,2:11.3:1:28:1:0.12443:7.18216:60:6:0.0132:0:1 0/0:262:2:0,2:194,66:0.0076:2,0:1:0:23:1:0.06663:0:60:4:0.0077:0:1 -16 89833576 . G C 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ATAAGGCCTGGAGATAAGCA;RSEQ=CTGCACAAAGTATCTCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:685:0:0,0:353,332:0:2,0:25.8:1:31.9:1:1:0:60:47.929:1:0:0.1 0/1:974:52:24,28:488,432:0.0534:2,2:26.2:1:30.6:1:0.39209:1.31752:60:104:0.0543:0:1.1 -16 89833715 . G C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1201;SOR=Inf;LSEQ=ATGAAGGAAAAAGTTACTTT;RSEQ=AATTTCATAAAACTGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:4,111:0:1,0:23.3:1:31:1:1:0:60:37.333:1:0:0.1 0/1:113:3:0,3:4,106:0.0265:1,0:12:1:31.7:1:1:0:60:6:0.0275:0:1 -16 89833740 . C T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21275;SOR=Inf;LSEQ=TCATAAAACTGAATTTAGTG;RSEQ=ATTCCGAACTGGATGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:0,73:0:1,0:23.7:1:32.5:1:1:0:60:72:1:0:0.1 0/1:63:2:1,1:1,60:0.0317:1,2:17:0:27:1:0.06298:42.79:60:4:0.0323:0:1 -16 89833774 . C G 102 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00264;SOR=9.62543;LSEQ=TGGCCTGAGCATTGGTCCTT;RSEQ=GTTTTTTGGTTCGTTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:0,34:0.0556:1,0:38.5:1:23.5:1:1:0:60:1:0.0286:0:1 0/1:27:10:1,9:1,16:0.3704:1,2:25:1:31:1:1:1.74:60:20:0.3704:0:1.1 -16 89833881 . G T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=5.78427;LSEQ=TGCCTCCCGGGTTCAAGCGA;RSEQ=TCTCCTGCCTCAGCCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:0.2:0,0:33:0:32:0:1:0:60:2:0.2:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:33:1:31:1:1:0:60:4:0.6667:0:1 -16 89836323 . C T 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.18896;LSEQ=CAGGGACAGGAAGGCCAGCA;RSEQ=CAGGTGCAGGAGGACCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:54:22,32:333,370:0.0712:2,2:22.4:1:30.2:1:0.39684:1.30863:60:53:0.0712:0:1.2 0/1:834:164:78,86:299,368:0.1966:2,2:26.1:1:28.8:1:0.541:1.12:60:22.429:0.1915:0:1.2 -16 89836436 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25432;SOR=0;LSEQ=GCACTCAGGCTCGGGCCCTG;RSEQ=AACGAGAATGAGGGTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:1,2:83,178:0.0113:2,2:32:1:28:1:1:1.07:60:6:0.0117:0:1.3 0/0:222:0:0,0:82,138:0:2,0:24.4:1:31.2:1:1:0:60:30.429:0.9907:0:0.3 -16 89836507 . T C 249 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.81705;LSEQ=TCCAGGGCACTGAAGACGAA;RSEQ=TGAGAAGTAGCAGCCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:241:240:139,101:0,0:0.9959:0,2:21.2:1:31.6:1:1:0:60:29:1:0:1.1 1/1:197:196:126,70:0,1:0.9949:0,2:22.3:1:30.9:1:0.36041:0:60:31.667:0.9948:0:1.1 -16 89836718 . T A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13379;SOR=Inf;LSEQ=TAGCCATTCAGTCCTGCACA;RSEQ=CCCTCCAACAGCTAATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:74,156:0:2,0:24.5:1:29.5:1:1:0:60:27.75:1:0:0.1 0/1:292:4:3,1:107,181:0.0137:2,2:13.3:1:26.8:1:0.15183:5.05:60:8:0.0142:0:1.5 -16 89836722 . T A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.25762;SOR=Inf;LSEQ=CATTCAGTCCTGCACATCCC;RSEQ=CCAACAGCTAATCCAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:69,153:0:2,0:23.7:1:29.2:1:1:0:60:17.5:1:0:0.2 0/1:277:3:2,1:98,174:0.0108:2,2:5:1:27.7:1:0.29983:3.53:60:6:0.0112:0:1 -16 89836737 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50052;SOR=Inf;LSEQ=ATCCCTCCAACAGCTAATCC;RSEQ=ACCACCAGCGGCCGAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:41,137:0:2,0:22.2:1:29.6:1:1:0:60:21.25:1:0:0.2 0/1:201:2:1,1:62,136:0.01:2,2:21.5:1:27:1:0.53186:2.18:60:4:0.0105:0:1 -16 89836781 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=10.92106;LSEQ=CCAAGCTGTTCCCCAAAACA;RSEQ=TGGTCTTTCTGGAAGACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:5:1,4:25,68:0.051:2,2:14.2:1:31:1:1:1.46536:60:10:0.0515:0:1.4 0/1:102:38:6,32:15,49:0.3725:2,2:21:1:29.7:1:0.45112:1.62512:60:18:0.36:0:1.4 -16 89836863 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23325;SOR=Inf;LSEQ=TGATGAAACTCAGCATCGCC;RSEQ=CATGCTCCTGCGGAGACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:112,17:0:2,0:20.2:1:29.8:1:1:0:60:63.5:1:0:0.3 0/1:121:2:1,1:104,15:0.0165:2,2:13:1:29.5:1:0.24793:6.7441:60:4:0.0168:0:1 -16 89836865 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=6.4714;LSEQ=ATGAAACTCAGCATCGCCGC;RSEQ=TGCTCCTGCGGAGACGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:8:8,0:108,18:0.0597:2,0:17.1:1:29.5:1:0.5972:0:60:16:0.0606:0:2.1 0/1:123:36:32,4:74,13:0.2927:2,2:21.7:1:31.1:1:0.77555:1.40:60:72:0.2927:0:2.1 -16 89836872 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.42041;LSEQ=TCAGCATCGCCGCATGCTCC;RSEQ=GCGGAGACGAGCTCATGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:8:8,0:116,19:0.0559:2,0:20.6:1:30.6:1:0.59747:0:60:16:0.0559:0:2.1 0/1:130:36:32,4:79,15:0.2769:2,2:25:1:30.8:1:0.58756:1.51:60:72:0.2813:0:2 -16 89836899 . T C 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGAGCTCATGAGTCCCTGG;RSEQ=CTGCAGACTTGGCCCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:165,38:0:2,0:26.1:1:29.8:1:1:0:60:100.5:1:0:0.2 0/1:210:45:35,10:126,39:0.2143:2,2:25.4:1:31.6:1:1:1.08:60:44:0.2126:0:1.1 -16 89836964 . G A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03607;SOR=Inf;LSEQ=CCACTCAGGGAGCTGCCCGC;RSEQ=CCTTCACCTCTCCGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:0:0,0:281,201:0:2,0:24.5:1:30.5:1:1:0:60:79.333:0.9979:0:0.1 0/1:597:6:2,4:332,259:0.0101:2,2:29.7:1:26:1:0.41299:2.55973:60:5:0.0085:0:1 -16 89838002 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.10659;SOR=0;LSEQ=GAGCAAGTCAAACAGAAATT;RSEQ=AGAGAAGGCTCCATGCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:179,39:0.0136:2,2:13.7:1:28.7:1:0.4523:2.28405:60:6:0.0136:0:1.3 0/0:244:0:0,0:188,56:0:2,0:20.6:1:31:1:1:0:60:39.667:1:0:0.3 -16 89838078 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=14.50172;LSEQ=CTGCTTTGTTCTGAGCCCCT;RSEQ=CACCTACCATGTGTTCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:737:25:13,12:404,307:0.0339:2,2:24.2:1:32.8:1:0.684:1.2144:60:50:0.034:0:1.1 0/1:921:311:171,140:345,264:0.3377:2,2:26.7:1:31.6:1:0.67357:1.06983:60:76.75:0.3381:0:1.1 -16 89838113 . C T 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCCGTGGCTCCAGTCTCGG;RSEQ=GTGTTGATGCTGAGCTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:0:0,0:420,381:0:2,0:25.1:1:30.9:1:1:0:60:199.25:1:0:0.2 0/1:980:34:18,16:487,458:0.0347:2,2:24.8:1:27.5:1:1:1.06:60:33:0.034:0:1.3 -16 89838275 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15385;LSEQ=GAACCCCGAAAGGAGGGATA;RSEQ=AGCTGCGGCCTAGAGAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:2:0,2:45,172:0.0091:2,0:31:1:28.5:1:1:0:60:4:0.0092:0:1.5 0/1:190:2:1,1:36,152:0.0105:2,2:25:1:27:1:0.35238:4.18:60:4:0.0107:0:1 -16 89839572 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17013;SOR=Inf;LSEQ=TTTAAACTACTGGACTACTA;RSEQ=GAAGACACACCAGCCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:141,5:0:1,0:25.2:1:32.9:1:1:0:60:145:1:0:0.1 0/1:103:2:1,1:94,7:0.0194:2,2:21:1:25.5:1:0.15001:12.628:60:4:0.0194:0:1 -16 89839581 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.18244;SOR=Inf;LSEQ=CTGGACTACTAGGAAGACAC;RSEQ=CCAGCCTGATGTCACTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:163,8:0:1,0:25.3:1:30.8:1:1:0:60:170:1:0:0.1 0/1:128:2:1,1:112,14:0.0156:2,2:14:1:28:1:0.22146:7.76299:60:4:0.0157:0:1 -16 89839915 . G A 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03173;SOR=0;LSEQ=AGCTGCTGTGTGTGGCAGAC;RSEQ=GAGGGACTGGGAGTCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:6:0,6:2,70:0.0759:1,0:33:1:31.8:1:1:0:60:12:0.0759:0:1 0/0:66:0:0,0:2,64:0:1,0:23.5:1:30.3:1:1:0:60:65:1:0:0.2 -16 89842029 . C G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=6.38224;LSEQ=CGGACCCTGTACCCAAAGCA;RSEQ=CGGCTTGAGCTGGCACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:7:7,0:84,2:0.0753:1,0:23.9:1:31.3:1:1:0:60:14:0.0753:0:1.1 0/1:93:32:32,0:57,4:0.3441:2,1:22.3:1:31.9:1:0.29468:0:60:31:0.337:0:1.1 -16 89842050 . A T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.49823;SOR=Inf;LSEQ=CGGCTTGAGCTGGCACAGCC;RSEQ=CCCCCGAGCTCACTCGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:128,13:0:2,0:24.1:1:30:1:1:0:60:34.25:1:0:0.1 0/1:142:2:1,1:122,18:0.0141:2,2:19:0:28.5:1:0.25052:6.62399:60:4:0.0142:0:1.5 -16 89842374 . T G 91 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00877;SOR=11.37732;LSEQ=AGCCTGTTTTTACAAAAAAA;RSEQ=ATTAAAAAATATATATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:0,1:1,49:0.0196:1,0:15:0:32:0:1:0:60:2:0.02:0:1 0/1:37:7:0,7:0,30:0.1892:1,0:21.3:1:32.6:1:1:0:60:14:0.1944:0:1 -16 89845110 . A T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=23.37468;LSEQ=TATTTTACCAATAAAACACA;RSEQ=TAGTGGTCTAACAAATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:5:4,1:174,42:0.0226:2,2:30.2:1:30.8:1:1:1.03555:60:10:0.0231:0:1.2 0/1:227:80:56,24:109,38:0.3524:2,2:25.7:1:28.6:1:0.53472:1.22817:60:19:0.347:0:1.7 -16 89845194 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.88549;LSEQ=GAAGTAGTCATCCCCTTCTA;RSEQ=CCGTTGCTGCATACCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:764:33:18,15:399,332:0.0432:2,2:31.8:1:31.3:1:1:1.0015:60:15.5:0.0413:0:1.1 0/1:832:257:137,120:319,256:0.3089:2,2:24.1:1:31.5:1:0.59783:1.09135:60:50.4:0.3088:0:1.3 -16 89845455 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49972;SOR=0;LSEQ=TGCATCAGTCAGAGCAGCGA;RSEQ=AAGGCAATTCCCACAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:34,153:0.0105:2,2:11.5:1:29:1:0.33688:4.45:60:4:0.0105:0:1 0/0:173:0:0,0:26,147:0:2,0:24.4:1:31.1:1:1:0:60:56.667:1:0:0.1 -16 89845456 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23404;SOR=Inf;LSEQ=GCATCAGTCAGAGCAGCGAG;RSEQ=AGGCAATTCCCACAGACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:30,153:0:2,0:25.8:1:30.3:1:1:0:60:182:1:0:0.1 0/1:172:2:1,1:24,146:0.0116:2,2:29:1:33:0:0.2703:5.98:60:4:0.0118:0:1 -16 89846050 . C T 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02299;SOR=Inf;LSEQ=TAACGGCAGGATCCTCGATT;RSEQ=ACAGCCCTGACTCCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:24,1:0:1,0:24:1:31.2:1:1:0:60:50:1:0:0.2 0/1:5:2:2,0:3,0:0.4:0,0:17.5:1:31.5:1:1:0:60:4:0.4:0:1 -16 89846195 . A G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.53521;LSEQ=CACCCTGCAGGCATCAGAGC;RSEQ=GAGTCTGCACATACTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:10:8,2:144,16:0.0588:2,2:20.9:1:30.7:1:0.2861:2.23596:60:20:0.0602:0:1 0/1:158:46:40,6:98,14:0.2911:2,2:25.3:1:29.9:1:1:1.04967:60:92:0.293:0:1.1 -16 89846203 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.12092;SOR=Inf;LSEQ=AGGCATCAGAGCAGAGTCTG;RSEQ=ACATACTGCAGGCATCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:161,22:0:2,0:23.8:1:31.3:1:1:0:60:25.143:0.9944:0:0.1 0/1:181:3:2,1:153,24:0.0166:2,2:19:1:28.3:1:0.36321:3.15816:60:6:0.0168:0:1 -16 89849480 . C T 251 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=117.42069;LSEQ=GAGGAGGGAGCGGTACTTGC;RSEQ=GGGAACCAGGGGTGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1111:3:0,3:495,612:0.0027:2,0:8.7:1:29.7:1:0.2581:0:60:6:0.0027:0:1.7 0/1:1375:332:166,166:497,544:0.2415:2,2:23.9:1:30:1:0.48822:1.09:60:54.333:0.2406:0:1.2 -16 89849539 . G A 76 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11516;SOR=3.54836;LSEQ=AGATAGCAGAGCGCAGCACC;RSEQ=TTAGTCTGGGAACTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:651:2:2,0:215,434:0.0031:2,0:1:0:26.5:1:0.11077:0:60:4:0.0031:0:1 0/1:739:8:7,1:277,454:0.0108:2,2:5.5:1:25.6:1:0.00633:11.44:60:16:0.0109:0:1.4 -16 89849583 . C T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=6.99135;LSEQ=TCCAGGGAGGCCACAATTCA;RSEQ=TTCCAACATCCACAGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:13:3,10:32,212:0.0506:2,2:23.5:1:30.2:1:0.39539:1.98:60:26:0.051:0:1.5 0/1:272:74:14,60:36,162:0.2721:2,2:21.3:1:29.4:1:0.86225:1.05:60:73:0.2704:0:1.4 -16 89849629 . T A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=5.97856;LSEQ=AGAAACACAGCCCTTTACAG;RSEQ=CAGACTTATGAGTATGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:8:0,8:1,111:0.0667:1,0:24.8:1:31:1:1:0:60:16:0.0678:0:1.9 0/1:93:28:0,28:0,65:0.3011:1,1:26.7:1:30.9:1:1:0:60:56:0.3011:0:1.9 -16 89849735 . G A 49 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04096;SOR=18.0326;LSEQ=TTGGGAGGCTGAGGCGGGCA;RSEQ=ATCACGAGGTCAGGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,9:0.1:0,0:15:0:31:0:1:0:60:2:0.1:0:2 1/0:4:3:0,3:0,1:0.75:0,0:16:1:31:0:1:0:60:6:0.75:0:2 -16 89849740 . C T 48 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02424;SOR=Inf;LSEQ=AGGCTGAGGCGGGCAGATCA;RSEQ=GAGGTCAGGAGATGGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:0,7:0.125:0,0:10:0:31:0:1:0:60:2:0.125:0:2 1/1:3:3:0,3:0,0:1:0,0:11:1:30.7:1:1:0:60:6:1:0:2 -16 89851156 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50418;SOR=0;LSEQ=GGGAAGGGCCTGGCTGAGAG;RSEQ=CTCAGAGCAGATCTGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:2,0:151,5:0.0127:1,0:27:1:31.5:1:1:0:60:4:0.013:0:1 0/0:127:0:0,0:118,9:0:2,0:24.2:1:30.8:1:1:0:60:41.333:1:0:0.1 -16 89851445 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.50139;SOR=0;LSEQ=CCTAGGCAGTGTCCTGTGTG;RSEQ=AGAGAAGAGCGTGAAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:0,2:6,122:0.0154:1,0:24:1:28:1:1:0:60:4:0.0155:0:1 0/0:110:0:0,0:5,105:0:1,0:24.1:1:31.7:1:1:0:60:220:1:0:0.1 -16 89851575 . G A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGTCGGCCTCCTAAACA;RSEQ=AAAGGAAAAAAGAGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:0,23:0,0:1:0,1:19.6:1:28.9:1:1:0:60:10.5:1:0:1.1 1/1:7:7:1,6:0,0:1:0,2:14.4:1:30.1:1:1:0:60:14:1:0:1 -16 89857622 . T C 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07258;SOR=8.68014;LSEQ=ACATGCAGAGGAAGATCCGC;RSEQ=GAGGCCCCGACAGGGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:22,0:0.0435:1,0:41:0:32:0:1:0:60:2:0.0476:0:1 0/1:10:3:3,0:6,1:0.3:2,0:36:1:29.7:1:1:0:60:6:0.3:0:1.3 -16 89857700 . A G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00077;SOR=5.64596;LSEQ=GGCCACTCGGCAAAGCTGAC;RSEQ=GCAAGGTTGCTCACTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:5:5,0:73,1:0.0633:1,0:31.6:1:29.6:1:1:0:60:10:0.0649:0:1 0/1:61:17:16,1:44,0:0.2787:1,1:28.5:1:28.9:1:0.27869:0:60:16:0.2667:0:1.1 -16 89857755 . C T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12357;SOR=Inf;LSEQ=TGGGGACAGCATGGTCCCCA;RSEQ=TCCCAGGCCTTCTGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:186,71:0:2,0:22.7:1:31.5:1:1:0:60:50.4:1:0:0.1 0/1:260:4:1,3:174,82:0.0154:2,2:12.5:1:26.3:1:0.10379:6.31758:60:8:0.0156:0:1 -16 89857964 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.55191;LSEQ=TCTAGTTAAGAACCATGACA;RSEQ=AGTCACAGCAAGGCAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:24:9,15:92,197:0.0767:2,2:23.3:1:31.6:1:0.65025:1.28:60:48:0.0777:0:1.4 0/1:391:138:46,92:94,158:0.3529:2,2:27.1:1:30.5:1:0.44249:1.18934:60:26.6:0.3491:0:1.3 -16 89858024 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.38151;LSEQ=TGAGTTATGCTGGGTGATCA;RSEQ=GTATTCCAGAAGGAGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:10:1,9:15,95:0.0833:2,2:26.5:1:31.7:1:1:1.41733:60:20:0.0833:0:1.8 0/1:106:35:1,34:12,59:0.3302:2,1:18.3:1:30.6:1:0.05611:6.82704:60:70:0.3333:0:1.9 -16 89858184 . A G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38;SOR=0;LSEQ=TGCTTATGGAAGCGTCTGAC;RSEQ=AAGAATGTTCCATCGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:23,8:0,0:1:0,2:23:1:30.4:1:1:0:60:62:1:0:1 1/1:19:18:16,2:0,0:0.9474:0,2:27.3:1:30.8:1:1:0:60:36:1:0:1.1 -16 89858277 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49839;SOR=Inf;LSEQ=CACAGTCAGCTGGGACTCTG;RSEQ=TGACACCCCCCTACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:137,13:0:2,0:25.1:1:31.8:1:1:0:60:29:1:0:0.2 0/1:153:2:1,1:135,16:0.0131:2,2:17:1:28:1:0.21053:8.21502:60:4:0.0132:0:1 -16 89858288 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.21153;SOR=0;LSEQ=GGGACTCTGCTGACACCCCC;RSEQ=TACACACACTCTTGACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:170,15:0.0107:2,2:23.5:1:29.5:1:0.16422:11.00601:60:4:0.0109:0:1 0/0:219:0:0,0:178,41:0:2,0:21.2:1:30.2:1:1:0:60:72:1:0:0.2 -16 89858505 . T C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.36847;LSEQ=AAAGCATCCGCTCCCTTCAA;RSEQ=ATCCAAGCAAACCAATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:22:6,16:79,245:0.0636:2,2:31.5:1:30.7:1:0.79875:1.16:60:10:0.0588:0:2.1 0/1:377:114:30,84:70,193:0.3024:2,2:23.5:1:30.8:1:1:1.0155:60:56:0.3019:0:1.6 -16 89858525 . C G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.42373;LSEQ=TATCCAAGCAAACCAATGTG;RSEQ=GACAGATGACCCCTCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:21:4,17:27,190:0.0882:2,2:23.4:1:30.4:1:0.49228:1.65:60:20:0.0858:0:2.1 0/1:233:70:10,60:25,138:0.3004:2,2:21.5:1:30.2:1:1:1.08658:60:69:0.304:0:2 -16 89858657 . C G 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20997;SOR=3.33229;LSEQ=CTCACAGTGGCCAGCACCTG;RSEQ=TTGGAGAGAATTCTCCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:6,13:0.0952:2,2:33:1:32.5:1:1:2.08:60:4:0.1:0:1 0/1:15:4:2,2:4,7:0.2667:2,2:28.3:1:30.8:1:1:1.68:60:8:0.2857:0:1 -16 89858759 . C T 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=TGATGAGGACAGCCACATCT;RSEQ=ACCAGACATCCCTGAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:52,8:0:2,0:24.4:1:32:1:1:0:60:120:1:0:0.1 0/1:54:11:10,1:40,3:0.2037:2,2:27.7:1:30.5:1:1:1.32573:60:22:0.2037:0:1.1 -16 89858960 . A AG 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.1661;SOR=0;LSEQ=TGAACAGCATCAGATGCTGC;RSEQ=GGGGGAGAAACAGACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:60,138:0.01:2,2:30.5:1:32:1:0.51804:2.29:60:4:0.0101:0:0 0/0:290:0:0,0:95,195:0:2,0:24.9:1:30.5:1:1:0:60:57:1:0:0.2 -16 89858963 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17517;SOR=0;LSEQ=ACAGCATCAGATGCTGCAGG;RSEQ=GGAGAAACAGACAAAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:56,139:0.0102:2,2:12.5:1:29:1:0.49601:2.47:60:4:0.0104:0:1 0/0:273:0:0,0:85,188:0:2,0:25:1:30.5:1:1:0:60:135.5:1:0:0.2 -16 89859008 . G A 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00044;SOR=5.78811;LSEQ=TCAGAGATCAAAAAGTTGTG;RSEQ=GTTTTTGTTAAGGACCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:4:0,4:5,66:0.0533:2,0:32.5:1:31.5:1:1:0:60:8:0.0541:0:1 0/1:101:25:4,21:9,67:0.2475:2,2:19.4:1:29.7:1:0.73099:1.41:60:24:0.2424:0:1.1 -16 89859015 . GT G 125 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00917;SOR=4.21183;LSEQ=TCAAAAAGTTGTGGGTTTTT;RSEQ=TAAGGACCAGCCCCACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:4:0,4:3,59:0.0606:1,0:36.5:1:32.5:1:1:0:60:8:0.0615:0:1 0/1:79:17:2,15:6,56:0.2152:2,2:21.9:1:30.8:1:1:1.24:60:34:0.2208:0.0253:1.1 -16 89860182 . TG GA 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTATTTTTTTGATGC;RSEQ=AGTCTCACTCTGTCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:28.5:1:1:0:60:4:1:0:1 -16 89861243 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50049;SOR=Inf;LSEQ=AGGACACCCACTGGGCAGAC;RSEQ=ATGCCTGGGCCATCAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:39,19:0:2,0:24.7:1:30:1:1:0:60:116:1:0:0 0/1:70:2:1,1:39,29:0.0286:2,2:31:1:31:1:1:1.33905:60:4:0.029:0:1 -16 89862132 . G C 94 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00291;SOR=9.85376;LSEQ=TTTTCTTATAAAAATCTGTT;RSEQ=CTTTCAGGTAAAAGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:41,0:0.0465:1,0:31:1:33:0:1:0:60:4:0.0476:0:1 0/1:24:8:7,1:16,0:0.3333:1,2:27.4:1:31.4:1:0.33333:0:60:16:0.3333:0:1 -16 89862155 . G C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06701;SOR=Inf;LSEQ=TTCAGGTAAAAGGATATTTA;RSEQ=TAACAATCTCAGGCATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:57,0:0:1,0:24.6:1:32.8:1:1:0:60:114:1:0:0.2 0/1:40:3:3,0:36,1:0.075:1,0:27.3:1:33:0:1:0:60:6:0.0769:0:2 -16 89862202 . C T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTCTCTGGTTCAAGACAGA;RSEQ=GTAAAAGAGGTCCTAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:131,2:0:1,0:25.7:1:31.9:1:1:0:60:65.5:1:0:0.2 0/1:106:21:19,2:80,4:0.1981:1,2:23.1:1:29:1:0.34458:2.08751:60:20:0.1942:0:1.1 -16 89862212 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50657;SOR=0;LSEQ=TCAAGACAGACGTAAAAGAG;RSEQ=TCCTAGAATTCCTGGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:156,9:0.012:2,0:25:1:31.5:1:1:0:60:4:0.0121:0:1 0/0:129:0:0,0:120,9:0:2,0:23.6:1:31:1:1:0:60:63.5:1:0:0.3 -16 89862493 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=Inf;LSEQ=CACGCCACCCACCAATCCCA;RSEQ=CACAAACTGTGGCTCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:15,140:0:2,0:24.8:1:32.1:1:1:0:60:154:1:0:0.1 0/1:167:2:1,1:18,147:0.012:2,2:9.5:1:27:1:0.21521:7.98:60:4:0.012:0:1 -16 89862571 . T G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=0;LSEQ=AGGCCACTATAACCACAGAC;RSEQ=TGAAACTGAATCCAAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:1,37:0.05:1,0:19.5:1:34:0:1:0:60:4:0.0526:0:1 0/0:24:0:0,0:0,24:0:1,0:18.9:1:30.4:1:1:0:60:48:1:0:0 -16 89865242 . T C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17157;SOR=6.87863;LSEQ=GGCCAGCTCTAGAGCCTGAA;RSEQ=CACACCCAGGGAAGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:12,0:0.0769:0,0:12:0:33:0:1:0:60:2:0.0833:0:1 0/1:5:2:2,0:3,0:0.4:0,0:31:1:31:1:1:0:60:4:0.4:0:1 -16 89865380 . GA G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49833;SOR=Inf;LSEQ=TTCCGACCTCATCCTCACAG;RSEQ=AAAGGCTGACCAGAGCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:126,18:0:2,0:25.3:1:29.7:1:1:0:60:47:1:0:0.1 0/1:147:2:1,1:126,19:0.0136:2,2:8.5:1:30.5:1:0.2544:6.48926:60:4:0.0139:0.0068:0.5 -16 89865385 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49849;SOR=Inf;LSEQ=ACCTCATCCTCACAGGAAAA;RSEQ=GCTGACCAGAGCGTTCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:135,25:0:2,0:24.5:1:31.6:1:1:0:60:39:1:0:0.1 0/1:163:2:2,0:135,25:0.0123:2,0:34:1:32:0:1:0:60:4:0.0125:0:1 -16 89865404 . C A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24961;SOR=Inf;LSEQ=AGGCTGACCAGAGCGTTCCC;RSEQ=GGGCTTTCCCATGGTCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:174,56:0:2,0:23.8:1:30.2:1:1:0:60:37.333:0.9956:0:0.2 0/1:250:3:2,1:177,69:0.012:2,2:36.7:1:25:1:1:1.28129:60:2:0.008:0:1.7 -16 89865408 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25077;SOR=Inf;LSEQ=TGACCAGAGCGTTCCCCGGG;RSEQ=TTTCCCATGGTCGCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:182,61:0:2,0:24.1:1:31.3:1:1:0:60:26:1:0:0.2 0/1:271:3:1,2:189,79:0.0111:2,2:6.3:1:26.7:1:0.21367:4.75341:60:6:0.0112:0:1 -16 89865690 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.59955;SOR=0.43306;LSEQ=ATGTCAGCACACGGCGGCAG;RSEQ=CCACCAGAAACAATCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:0,2:32,114:0.0135:2,0:28:1:29:1:1:0:60:4:0.0138:0:1 0/0:170:1:0,1:40,129:0.0059:2,0:22:0:31:0:1:0:60:2:0.0061:0:1 -16 89866043 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.13603;LSEQ=TCTCTGCAGTACATCAACCG;RSEQ=GACCTGTCAAAATAGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:617:35:14,21:275,307:0.0567:2,2:28.8:1:31.3:1:0.4864:1.34301:60:70:0.0575:0:1.1 0/1:722:217:102,115:236,269:0.3006:2,2:26.3:1:30.1:1:1:1.01:60:42.4:0.2994:0:1.1 -16 89866160 . A G 166 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=58.469;LSEQ=AAGTAAAGAAACGGCACTTC;RSEQ=GGAGGCCGAGGCGGGCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:1,73:0.026:1,0:16:1:32:0:1:0:60:4:0.0263:0:1 1/0:73:45:0,45:0,28:0.6164:1,1:23.2:1:30.3:1:1:0:59.6:44:0.6111:0:1.2 -16 89869466 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATGTTGCCAACACACA;RSEQ=AAATGATACATACTGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:26,0:0.0714:1,0:10:1:29:1:1:0:60:4:0.0714:0:1 0/0:6:0:0,0:6,0:0:0,0:26.7:1:32.3:1:1:0:60:12:1:0:0 -16 89869704 . T C 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.95061;LSEQ=GCTCCACAGTTCTTCTCAGA;RSEQ=CTGAGTTTTTCTGAAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:1:0,1:335,434:0.0013:2,0:1:0:14:0:1:0:60:0:0:0:1 0/1:910:46:24,22:420,443:0.0505:2,2:24.4:1:30.6:1:0.65331:1.15:60:45:0.0504:0:1.5 -16 89869761 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=2.50415;LSEQ=GAACAAAATCTGAAAAACCA;RSEQ=AAAACCAAAGTTATTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:144:45,99:116,223:0.2981:2,2:22.9:1:32.1:1:0.59794:1.14408:60:143:0.2979:0:1.1 1/0:607:313:105,208:107,186:0.5157:2,2:24.4:1:31.3:1:0.44475:1.13933:60:43.714:0.5134:0:1.2 -16 89869803 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.1791;SOR=0;LSEQ=CATCATGGTCTCCAAGCAAC;RSEQ=GTGAATGGCACAGACCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:38,152:0.0104:2,2:32.5:1:29.5:1:0.36584:3.96:60:4:0.0106:0:1 0/0:261:0:0,0:56,205:0:2,0:23.3:1:29.9:1:1:0:60:51.2:1:0:0.6 -16 89871800 . G A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01885;SOR=Inf;LSEQ=ACAGCATGCATGTCGGGATG;RSEQ=CTGGAGACACACACAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:0:0,0:208,306:0:2,0:24.7:1:31.5:1:1:0:60:63.25:1:0:0.2 0/1:632:7:5,2:265,359:0.0111:2,2:23:1:26.4:1:0.14405:3.38:60:6:0.0096:0:1.1 -16 89871879 . A AT 87 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.02891;LSEQ=GAGTTGAGCCATATGTCCCA;RSEQ=TTTTTTTTTTGAGACAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:8:0,8:18,128:0.0516:2,0:33.8:1:29.3:1:0.5972:0:60:16:0.0523:0:0.1 0/1:132:7:0,7:15,107:0.053:2,0:32.1:1:30.1:1:1:0:60:14:0.0547:0:0.4 -16 89872187 . G GTTGT 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTTCTTTGACTCATTAT;RSEQ=TTAACTTTCAAATATTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:29.5:1:30.4:1:1:0:60:4:0.4:0.2:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89874477 . AG A 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CTCCGTCTCAAAAAAAAAAC;RSEQ=ACAAAAAGCAAACAAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:21.1:1:31:1:1:0:59.6:24:1:0.3333:4.8 1/1:8:7:7,0:0,0:0.875:0,0:22:1:31.6:1:1:0:60:14:1:0.25:5.1 -16 89874486 . G A 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAACAGACAAAAA;RSEQ=CAAACAAAACCAAAACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:25.1:1:31.2:1:1:0:59.5:22:1:0:5.3 1/1:8:8:8,0:0,0:1:0,0:28.1:1:31.8:1:1:0:60:16:1:0:5.3 -16 89874491 . C A 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACAGACAAAAAGCAAA;RSEQ=AAAACCAAAACACCATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:26.5:1:31.2:1:1:0:59.5:22:1:0:5.3 1/1:8:8:8,0:0,0:1:0,0:31.4:1:31.6:1:1:0:60:16:1:0:5.3 -16 89874494 . A C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGACAAAAAGCAAACAA;RSEQ=ACCAAAACACCATAAACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:27.4:1:32.8:1:1:0:59.5:22:1:0:5.3 1/1:9:9:9,0:0,0:1:0,0:28.8:1:32.2:1:1:0:60:18:1:0:5.1 -16 89874496 . CC AA 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACAAAAAGCAAACAAAA;RSEQ=AAAACACCATAAACGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:28.2:1:31.1:1:1:0:59.5:22:1:0:4.3 1/1:9:9:9,0:0,0:1:0,0:29.8:1:31.4:1:1:0:60:18:1:0:4.1 -16 89874559 . A C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.82136;SOR=0.80811;LSEQ=TCCTCCAGGTCTAGTCTAGT;RSEQ=TAAATATGCAATGCAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:18:18,0:44,1:0.2857:1,1:27.7:1:31.3:1:1:0:59.7:17:0.2742:0:2.1 0/1:41:10:10,0:31,0:0.2439:1,0:23.4:1:30.7:1:1:0:60:20:0.2439:0:2.2 -16 89874624 . G T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46837;LSEQ=GCCAGAAATCAAACCCGTCT;RSEQ=ATTCTGGGCTTTGAAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:2:1,1:197,44:0.0082:2,2:1:0:27:1:0.3367:4.43848:60:4:0.0082:0:1 0/1:249:3:1,2:190,56:0.012:2,2:9.7:1:26.3:1:0.13633:6.71834:60:6:0.0121:0:1 -16 89874628 . C T 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70243;SOR=0.9286;LSEQ=GAAATCAAACCCGTCTGATT;RSEQ=TGGGCTTTGAAATATAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:75:61,14:147,39:0.2874:2,2:24.3:1:30.1:1:0.73624:1.16:60:36.5:0.2852:0:1.1 0/1:279:76:55,21:152,49:0.2724:2,2:20.6:1:29.3:1:0.64237:1.18366:60:75:0.2778:0:1.2 -16 89874756 . G A 148 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.19178;LSEQ=GTACGTGAAGATGCCACACC;RSEQ=CTTCAAGCAACAAAGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:2:2,0:193,330:0.0038:2,0:1:0:28.5:1:0.13751:0:60:4:0.0038:0:1 0/1:728:35:18,17:292,399:0.0481:2,2:26.6:1:28.9:1:0.29793:1.45:59.6:70:0.0496:0:1.3 -16 89874817 . AC A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.19995;SOR=0;LSEQ=ACAAAAACAAAAACAAAAAA;RSEQ=CCCCAGCATTCTGAGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:0,2:19,172:0.0104:2,0:25.5:1:29.5:1:1:0:60:4:0.0105:0.0052:3.5 0/0:238:0:0,0:39,199:0:2,0:22.1:1:31.1:1:1:0:60:237:1:0:0.1 -16 89874822 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19791;SOR=0;LSEQ=AACAAAAACAAAAAAACCCC;RSEQ=AGCATTCTGAGTCCTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:15,159:0.0114:2,2:29.5:1:26.5:1:0.17403:10.30:60:4:0.0115:0:1.5 0/0:219:0:0,0:33,186:0:2,0:21.9:1:31.1:1:1:0:60:108.5:1:0:0.1 -16 89875033 . G T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCTTCTCTCTTCCTAC;RSEQ=CACTGTAGCCTACTTCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:10.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89875316 . CTA C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCCCCCTAACTCACACT;RSEQ=TTTTTTTTTTTTTGAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:0:33:0:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89876261 . CAA C 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGCAAAACTCCATCT;RSEQ=AAAAAAAAAAAGATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:1:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -16 89876801 . AT A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAAAAAAATTACATAC;RSEQ=TTTTTTTTAATAGTTTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31:1:1:0:60:4:1:0:0 -16 89877066 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58146;SOR=0.38124;LSEQ=TGCCTCCATCCAGATCAACA;RSEQ=AACATTGCCTGGAACACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:124,38:0.0122:2,2:30:1:29.5:1:0.42017:3.234:60:4:0.0122:0:1 0/0:214:1:0,1:151,62:0.0047:2,0:1:0:24:0:0.29439:0:60:2:0.0048:0:1 -16 89877076 . T A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19628;SOR=0;LSEQ=CAGATCAACAGAACATTGCC;RSEQ=GGAACACTGGAGAGTCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:139,52:0.0104:2,2:13:0:32:1:0.47485:2.65725:60:4:0.0105:0:1.5 0/0:242:0:0,0:166,76:0:2,0:24.9:1:30.4:1:1:0:60:79.667:1:0:0.2 -16 89877235 . A T 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAAGAGAGATTACATTTTTT;RSEQ=AAAAACAAATTACCTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:131,168:0:2,0:24.1:1:29.3:1:1:0:60:148.5:1:0:0.1 0/1:342:18:6,12:109,215:0.0526:2,2:26.8:1:28.4:1:1:1.01391:60:36:0.0528:0:1.1 -16 89877285 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2006;SOR=Inf;LSEQ=GCTATGTCCTATTTTCCCAA;RSEQ=CAGCTTAAAAGTAACAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:139,102:0:2,0:24.7:1:31.7:1:1:0:60:119.5:1:0:0.1 0/1:196:2:1,1:91,103:0.0102:2,2:13:1:29.5:1:1:1.13:60:4:0.0104:0:1 -16 89877546 . G C 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATCTAAAACCAAAGACTT;RSEQ=CTGTTTAAAATGCCTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:33,184:0:2,0:24:1:31.9:1:1:0:60:53.25:1:0:0 0/1:245:20:6,14:36,189:0.0816:2,2:18.3:1:30.9:1:0.12365:2.24:60:19:0.0788:0:1.2 -16 89877579 . CA C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.24651;SOR=Inf;LSEQ=CCTTATTTTAAGATGCAGCA;RSEQ=AAAAAAATTGCCTTTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:3,104:0:1,0:23.7:1:30.6:1:1:0:60:214:1:0:0.1 0/1:108:3:0,3:3,102:0.0278:1,0:31.3:1:33.3:1:1:0:60:6:0.0283:0:0 -16 89877720 . C T 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TTATACATTGGTATTTGTTA;RSEQ=GTTTCCCATGACACAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:0,7:0.4167:0,2:19.4:1:31.2:1:0.41667:0:60:10:0.4167:0:1 0/0:2:0:0,0:0,2:0:0,0:10:1:31.5:1:1:0:60:4:1:0:0 -16 89877929 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50266;SOR=Inf;LSEQ=AGGGATTTCCCAACATTCTG;RSEQ=CATGCACCTGGTGGGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:35,18:0:2,0:26.9:1:31.6:1:1:0:60:52:1:0:0.2 0/1:67:2:1,1:42,23:0.0299:2,2:36.5:1:26.5:1:1:1.8087:60:4:0.0308:0:1.5 -16 89877964 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49765;SOR=Inf;LSEQ=GCAGGTGCAGTCACAGCTGT;RSEQ=CTCAGTCCGCAGGCCACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:37,29:0:2,0:23.5:1:31.9:1:1:0:60:132:1:0:0.3 0/1:73:2:1,1:39,32:0.0274:2,2:29:1:28.5:1:1:1.21543:60:4:0.0278:0:1 -16 89877975 . A G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06148;SOR=0.4865;LSEQ=CACAGCTGTGCTCAGTCCGC;RSEQ=GGCCACCAAGTGGAACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:22:11,11:27,22:0.3099:2,2:26.5:1:28.6:1:0.79853:1.22372:60:21:0.3:0:1 0/1:84:15:8,7:36,33:0.1786:2,2:27.8:1:29.8:1:1:1.05:60:30:0.1786:0:1.3 -16 89878077 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49468;SOR=Inf;LSEQ=AAGTGAGAAACGGTGGGCAA;RSEQ=CTGGAAGCAGGCAATGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:5,35:0:2,0:25.8:1:30.9:1:1:0:60:80:0.9756:0:0 0/1:44:2:1,1:15,27:0.0455:2,2:15.5:1:27.5:1:1:1.77:60:4:0.0465:0:1 -16 89878134 . ATTTTT A 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=9.000;MSILEN=1;SSF=0.7241;SOR=0.73485;LSEQ=TTATTTGTCTTCCAAAATTA;RSEQ=TTTTGTTTTATTTTTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:0,6:0,8:0.4286:0,0:20.2:1:31.8:1:1:0:60:12:0.4286:0.0714:0 0/1:17:6:0,6:1,10:0.3529:2,0:23.5:1:30:1:1:0:60:12:0.3529:0.1176:0 -16 89880822 . C G 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1553;SOR=Inf;LSEQ=ACTACACACACCAGTGGAAA;RSEQ=CCATCGCCTGAGAAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:49,1:0:1,0:23:1:31.9:1:1:0:60:100:1:0:0.1 0/1:78:4:4,0:71,3:0.0513:1,0:23.8:1:29:1:1:0:60:3:0.039:0:1 -16 89880844 . A G 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01918;SOR=Inf;LSEQ=CATCGCCTGAGAAAATTTAC;RSEQ=TTTCTACTTAATTTAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:99,4:0:1,0:19.7:1:30.7:1:1:0:60:102:1:0:0.1 0/1:132:7:7,0:112,11:0.053:2,0:21.7:1:30:1:1:0:60:14:0.0534:0:1 -16 89881076 . C A 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AATTCAAGCTCCAGGCCAGG;RSEQ=GTAGTGGCTCACGCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:54,176:0:2,0:23:1:30:1:1:0:60:56.5:0.9956:0:0.1 0/1:307:20:6,14:86,201:0.0651:2,2:25.1:1:30.8:1:1:1.00:60:40:0.0662:0:1.2 -16 89882191 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50042;SOR=Inf;LSEQ=GCCAGGCCACCGCGCCCGCC;RSEQ=CCTCGGGTGTTTTCTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:134,14:0:2,0:24.1:1:30:1:1:0:60:296:1:0:0.1 0/1:168:2:2,0:153,12:0.0119:2,0:20:1:31:0:1:0:60:4:0.0123:0:1 -16 89882928 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09031;SOR=0;LSEQ=ACGCCGCCCACTCCCGCGGC;RSEQ=TGCCGCGCCCACCTACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:1,2:124,75:0.0149:2,2:30.3:1:29.7:1:0.55907:3.28653:60:6:0.0151:0:1 0/0:247:0:0,0:140,107:0:2,0:22.9:1:30.4:1:1:0:60:34.286:1:0:0.4 -16 89882934 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.25392;SOR=Inf;LSEQ=CCCACTCCCGCGGCCTGCCG;RSEQ=GCCCACCTACCCAGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:137,95:0:2,0:22:1:30.8:1:1:0:60:57:1:0:0.2 0/1:275:3:1,2:152,120:0.0109:2,2:11.7:1:27:1:0.58622:2.52493:60:6:0.0112:0:1 -16 89883000 . G C 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTCCTGGCCCGAGGCGGA;RSEQ=TTCGGGACCCACGAGTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:218,201:0:2,0:26.7:1:32:1:1:0:60:82.8:0.9976:0:0.2 0/1:496:59:31,28:227,210:0.119:2,2:22.5:1:31.1:1:1:1.02:60:118:0.1207:0:1.2 -16 89883007 . A T 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCCGAGGCGGAGTTCGGG;RSEQ=CCCACGAGTCGGACATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:206,200:0:2,0:27.4:1:29.8:1:1:0:60:57:1:0:0.2 0/1:482:75:39,36:209,198:0.1556:2,2:27.2:1:28.6:1:1:1.03:60:24:0.1542:0:1.3 -16 89883047 . C A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10307;SOR=0;LSEQ=CTTGGCGCCTACAGCCCCGG;RSEQ=GGCGGCTCCCTGCGCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:2,1:108,146:0.0117:2,2:5.3:1:27.3:1:0.57785:2.69:60:6:0.0118:0:1 0/0:290:0:0,0:125,164:0:2,0:25.6:1:30.1:1:1:0:60:47.167:1:0:0.4 -16 90001819 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GCCACCGTGTTCCGGGGCCG;RSEQ=ATGTCCATGAAGGAGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:7,1:0.2:2,2:22.5:1:31.5:1:0.37778:5.29155:60:4:0.2:0:1 0/0:6:0:0,0:5,1:0:2,0:20.7:1:31.3:1:1:0:60:12:1:0:0 -16 90240595 . A G 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09408;SOR=3.24243;LSEQ=GCCCCCATCCCCAGGGATTG;RSEQ=GGCCGTAGGGGGCCCGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:7:2,5:21,22:0.14:2,2:26.1:1:31.7:1:0.42952:2.34707:26.6:14:0.14:0:1 0/1:20:7:4,3:6,7:0.35:2,2:27.4:1:30:1:1:1.52:32.6:14:0.35:0:1.3 -16 90241383 . C T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24988;SOR=2.89085;LSEQ=CCCAGGGGCAGTGGCAGTGC;RSEQ=CGTCTCTGATATGCTCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:5,0:15,0:0.25:1,0:37.2:1:31:1:1:0:20:10:0.25:0:1 1/0:12:6:6,0:6,0:0.5:0,0:27:1:31:1:1:0:20.2:12:0.5:0:1 -16 90241518 . G A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TTCACCTGGAAGGCCAGGTC;RSEQ=TATTTCTGCATCTCATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:93,68:0:2,0:27.4:1:30.5:1:1:0:30.9:160:1:0:0.1 0/1:118:12:5,7:56,50:0.1017:2,2:24.4:1:29.3:1:0.54972:1.56203:31.5:24:0.1017:0:1.3 -16 90241590 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50005;SOR=0;LSEQ=TGGCTGACGGTCCGGTTATC;RSEQ=TGGTTGGGGTGACCCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:53,48:0.0194:2,2:29.5:1:31.5:1:1:1.1031:20:4:0.0196:0:1.5 0/0:89:0:0,0:50,39:0:2,0:24:1:30.5:1:1:0:27:43.5:1:0:0.3 -16 90241603 . C T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=GGTTATCCTGGTTGGGGTGA;RSEQ=CCTGGTGCGCCCCGCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:58,49:0:2,0:23:1:31.5:1:1:0:26.9:106:1:0:0.4 0/1:95:12:7,5:45,38:0.1263:2,2:19:1:29.2:1:1:1.18:25.6:24:0.129:0:1.3 -16 90241617 . G A 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07963;SOR=0.55756;LSEQ=GGGTGACCCTGGTGCGCCCC;RSEQ=CCAGGGCCTGGTGCCGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:32:9,23:57,30:0.2689:2,2:27.2:1:29.7:1:0.00036:4.78649:23.6:31:0.265:0:1.5 0/1:106:18:7,11:56,32:0.1698:2,2:24.2:1:29.9:1:0.0665:2.72253:26.4:36:0.1698:0:1.7 -16 90241631 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4995;SOR=0;LSEQ=CGCCCCGCCAGGGCCTGGTG;RSEQ=CGCCTGCTGAAGATCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:69,69:0.0143:2,2:13:1:27.5:1:1:1:21:4:0.0143:0:1 0/0:126:0:0,0:74,52:0:2,0:23.2:1:31.3:1:1:0:30.4:252:1:0:0.4 -16 90241653 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22566;SOR=Inf;LSEQ=GCCTGCTGAAGATCATGAGC;RSEQ=CCACTCATGGGCCACCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:78,85:0:2,0:26.6:1:30.6:1:1:0:34:53.333:1:0:0.4 0/1:148:2:1,1:74,72:0.0135:2,2:31.5:1:28.5:1:1:1.02759:21:4:0.0137:0:2.5 -16 90241654 . C T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05099;SOR=Inf;LSEQ=CCTGCTGAAGATCATGAGCG;RSEQ=CACTCATGGGCCACCGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:80,84:0:2,0:26.7:1:31.3:1:1:0:34.1:81:1:0:0.4 0/1:150:4:2,2:74,72:0.0267:2,2:16.8:1:27.5:1:1:1.0276:40:8:0.0272:0:2 -16 90241686 . C T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11521;SOR=0.28447;LSEQ=CACCGGATGTGGTCCTTGTC;RSEQ=GATTTGTTGGGGCTGCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:8:8,0:87,107:0.0396:2,0:23.4:1:31.6:1:0.00203:0:20.6:16:0.0406:0:1.5 0/1:173:2:2,0:79,92:0.0116:2,0:23:1:31.5:1:0.21777:0:21:4:0.012:0:1 -16 90241687 . G C 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.86839;SOR=0.89396;LSEQ=ACCGGATGTGGTCCTTGTCC;RSEQ=ATTTGTTGGGGCTGCGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:23:4,19:89,88:0.115:2,2:26.7:1:32.6:1:0.00332:4.77139:28.5:46:0.115:0:1.7 0/1:173:18:7,11:74,81:0.104:2,2:24.3:1:31.6:1:0.61924:1.43266:33.1:36:0.1047:0:1.8 -16 90241730 . G T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63655;SOR=0.43724;LSEQ=CTTCTCAGAAGATGAGTCCT;RSEQ=TTCCTTGCTCAGGGCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:0,3:52,84:0.0216:2,0:8:1:31:0:0.29246:0:20.3:6:0.0222:0:2 0/0:105:1:0,1:37,66:0.0095:2,0:7:0:31:0:1:0:20:2:0.0095:0:3 -16 90241739 . T G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05979;SOR=2.85191;LSEQ=AGATGAGTCCTGTTCCTTGC;RSEQ=CAGGGCACTGAGGGACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:6:0,6:47,70:0.0488:2,0:24.8:1:33.3:1:0.08141:0:25:12:0.05:0:1 0/1:78:10:1,9:22,46:0.1282:2,2:15.4:1:32.7:1:0.26558:4.24409:25.6:20:0.1299:0:1 -16 90242276 . C A 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GTTCCTGGCAGGGGCTCACA;RSEQ=CTCCTCGCCCCCTCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:17.5:1:31.5:1:1:0:31:4:1:0:1 0/0:4:0:0,0:1,3:0:2,0:26:1:32.3:1:1:0:27.3:8:1:0:0 -17 114669 . C A 231 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAATTCACAGTGGTCAATG;RSEQ=AAGACAAAACTCAGTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:129,164:0:2,0:27.7:1:32.2:1:1:0:60:586:1:0:0.1 1/0:376:250:112,138:61,65:0.6649:2,2:25.7:1:29.1:1:0.51302:1.15587:60:61.5:0.6613:0:1.1 -17 114710 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25593;SOR=Inf;LSEQ=TTACTAATGTACACATAACT;RSEQ=CAAAACATGAAAATGTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:66,130:0:2,0:23.1:1:32:1:1:0:60:195:1:0:0.1 0/1:240:3:2,1:80,157:0.0125:2,2:10.3:1:28.3:1:0.26954:3.90:60:6:0.0127:0:2 -17 953191 . C CA 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCCAACCAGCTTGGAAC;RSEQ=AAAATCACGAAAGAGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:25.5:1:32:0:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 953435 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50017;SOR=Inf;LSEQ=CAAACTCCTGGGGAAAGATG;RSEQ=GACAAAGGGCCCTGAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:76,77:0:2,0:25.9:1:30.8:1:1:0:60:75.5:1:0:0.4 0/1:172:2:1,1:84,84:0.0116:2,2:30.5:1:28.5:1:1:1:60:4:0.0119:0:2.5 -17 953456 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=2.37948;LSEQ=GACAAAGGGCCCTGAACCTC;RSEQ=GAAGCTGGGAGGCCTGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:58:24,34:51,61:0.3412:2,2:29.1:1:29.9:1:0.6286:1.18325:60:28:0.3373:0:1.2 1/0:190:105:50,55:40,45:0.5526:2,2:26.2:1:30.1:1:1:1.02:60:51.5:0.5538:0:1.2 -17 953482 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50113;SOR=Inf;LSEQ=TGGGAGGCCTGGCTTTCCGG;RSEQ=AGGTGCGTGCCTCAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:60,93:0:2,0:27.4:1:32.2:1:1:0:60:152:1:0:0.5 0/1:177:2:1,1:77,98:0.0113:2,2:27.5:1:28:1:1:1.27:60:4:0.0115:0:2 -17 953491 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24992;SOR=Inf;LSEQ=TGGCTTTCCGGCAGGTGCGT;RSEQ=CCTCAGCTTTGCAAGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:55,86:0:2,0:25.3:1:31.8:1:1:0:60:27.2:1:0:0.4 0/1:158:3:2,1:60,95:0.019:2,2:32.3:1:29.3:1:0.56164:3.14:60:6:0.0192:0:1.3 -17 953660 . G A 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=AGAAGCCAGAGGAGCAGGGA;RSEQ=CAGAAAGGGGGGTGCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:19.7:1:31:0:1:0:60:6:0.5:0:1 0/0:6:0:0,0:0,6:0:0,0:16.8:1:31:1:1:0:60:12:1:0:0 -17 986739 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25567;SOR=Inf;LSEQ=GCTCCTTGTCCCTCAGGGTG;RSEQ=CTATGTGGGGAGCGGCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:121,121:0:2,0:25:1:31.2:1:1:0:60:59.5:1:0:0.8 0/1:294:3:1,2:146,145:0.0102:2,2:24:1:29:1:1:2.00917:60:6:0.0103:0:2 -17 986742 . A G 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.4736;LSEQ=CCTTGTCCCTCAGGGTGGCT;RSEQ=TGTGGGGAGCGGCCTACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:157:74,83:47,43:0.6356:2,2:25.2:1:31.8:1:0.5087:1.22494:60:156:0.6393:0:1.2 0/1:292:132:61,71:82,78:0.4521:2,2:24.3:1:31:1:0.41206:1.22277:60:264:0.4583:0:1.2 -17 986746 . G T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25428;SOR=Inf;LSEQ=GTCCCTCAGGGTGGCTATGT;RSEQ=GGGAGCGGCCTACCTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:116,130:0:2,0:24.7:1:31.2:1:1:0:60:122:0.9959:0:0.7 0/1:294:3:1,2:142,149:0.0102:2,2:19.7:1:31.7:1:1:1.90202:60:6:0.0103:0:1.3 -17 986754 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13424;SOR=Inf;LSEQ=GGGTGGCTATGTGGGGAGCG;RSEQ=CCTACCTCTGAGATCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:113,132:0:2,0:25:1:31.4:1:1:0:60:80.667:1:0:0.7 0/1:311:4:3,1:146,161:0.0129:2,2:14:1:23.5:1:0.35283:3.30:60:3:0.0098:0:1.3 -17 1359199 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50978;SOR=Inf;LSEQ=GGCTGGGCGGGCGACGGTGG;RSEQ=ACCGGCGGGCGCGGGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:77,34:0:2,0:23.6:1:32:1:1:0:60:54.5:1:0:0.2 0/1:151:2:1,1:106,43:0.0132:2,2:6:1:27:1:0.49925:2.44842:60:4:0.0132:0:1 -17 1359204 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76758;LSEQ=GGCGGGCGACGGTGGCACCG;RSEQ=CGGGCGCGGGCCGCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:0,2:83,42:0.0157:2,0:1:0:27:1:0.11824:0:60:4:0.0163:0:1 0/1:165:2:1,1:112,51:0.0121:2,2:15.5:1:29.5:1:0.5323:2.18459:60:4:0.0123:0:1 -17 1359205 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5061;SOR=Inf;LSEQ=GCGGGCGACGGTGGCACCGG;RSEQ=GGGCGCGGGCCGCTGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:85,45:0:2,0:24.3:1:30.5:1:1:0:60:20.667:1:0:0.2 0/1:167:2:1,1:113,52:0.012:2,2:5:1:28.5:1:0.53531:2.16202:60:4:0.0122:0:1.5 -17 1359206 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5047;SOR=Inf;LSEQ=CGGGCGACGGTGGCACCGGC;RSEQ=GGCGCGGGCCGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:88,46:0:2,0:24.3:1:29.7:1:1:0:60:43.667:1:0:0.2 0/1:168:2:1,1:113,51:0.0119:2,2:24:1:30:0:0.52968:2.204:60:4:0.0121:0:2 -17 1359227 . A T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.19159;SOR=0;LSEQ=GGCGCGGGCCGCTGCTGTTG;RSEQ=TGATGTAGTGGGAGACGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:119,71:0.0104:2,2:11:0:31.5:1:1:1.67128:60:4:0.0112:0:1.5 0/0:246:0:0,0:150,95:0:2,0:25.2:1:28.4:1:1:0:60:39.833:1:0:0.2 -17 1359363 . T G 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.78849;SOR=1.18102;LSEQ=CGCCTCCTGCCGACTCAACC;RSEQ=CCCCCAGTACCAGCTACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:19:1,18:0,9:0.6786:0,1:22.2:1:31.2:1:1:0:60:38:0.6786:0:1 1/0:35:25:2,23:0,9:0.7143:0,2:26.1:1:32.8:1:1:0:60:50:0.7143:0:1.1 -17 1384066 . A G 28 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCGAAGAGTCTCCTCCTC;RSEQ=CCCCCCTCCAGCAGCTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:20:1:28:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:2:0:26:0:1:0:60:2:1:0:1 -17 1454299 . GTTGCGGGGCGGAGTCAGCGGGACCTGATGGGACACGAAGGGCGAGTGAGAGTA G 90 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=52;MSI=1.000;MSILEN=1;SSF=0.18613;SOR=3.08006;LSEQ=CACGAAGGGCAAGTGAGAGT;RSEQ=TTGCGGGGCGGAGTCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:2:2,0:206,62:0.0074:2,0:34.5:1:34:0:1:0:60:4:0.0075:0:0 0/1:311:7:6,1:221,83:0.0225:2,2:30.7:1:32.4:1:0.67889:2.25:55.7:14:0.0227:0:0.9 -17 1454506 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17066;SOR=Inf;LSEQ=GGGCAGCCAGATGGCTGACA;RSEQ=AGTAAAGCTTCTCTTGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:0,76:0:1,0:23.2:1:32.1:1:1:0:60:37:1:0:0.1 0/1:54:2:1,1:4,48:0.037:2,2:20:1:28:1:0.1782:10.84:60:4:0.0377:0:1 -17 1760942 . C G 76 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCCAAAGCCTCACCAAC;RSEQ=CACCCCCCACCCGGCCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:25.8:1:29.5:1:1:0:55.2:12:0.8571:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 1761160 . G C 154 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACAAGGGGAAAACTAGACC;RSEQ=TTTTCCACTATTAAGGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:26,3:0,0:1:0,2:18.6:1:31.8:1:1:0:32:58:1:0:1.1 0/1:72:24:22,2:42,5:0.3333:2,2:16.4:1:30.4:1:1:1.30:31.7:48:0.3333:0:1 -17 1761209 . T C 41 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04836;SOR=0;LSEQ=TCTACTGCTCCAAGGAGATC;RSEQ=GAAAATACAAAAGGATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:2,1:95,44:0.0211:2,2:40.7:1:26.3:1:1:1.07895:34.3:2:0.0145:0:1 0/0:246:0:0,0:155,91:0:2,0:34.7:1:30.1:1:1:0:35.5:60.5:1:0:0.2 -17 1761431 . T C 290 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTCAGGCCTTTTCCTAGGT;RSEQ=CCACATCAAGTGTCGGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:684:684:362,322:0,0:1:0,2:25.9:1:30.9:1:1:0:46.8:67.4:1:0:1.1 1/1:928:744:374,370:88,96:0.8017:2,2:25.1:1:30.5:1:0.56529:1.10:45:73.4:0.8022:0:1.3 -17 1761445 . C T 135 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01944;SOR=0.44192;LSEQ=CTAGGTTCCACATCAAGTGT;RSEQ=GGATCCCATTCCAGGTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:782:24:8,16:366,392:0.0307:2,2:8.7:1:29.6:1:0.21234:1.8659:33.3:48:0.031:0:5.4 0/1:1015:14:7,7:479,521:0.0138:2,2:7.9:1:29.6:1:1:1.09:30.5:28:0.0139:0:5.9 -17 1761446 . G A 232 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGTTCCACATCAAGTGTC;RSEQ=GATCCCATTCCAGGTATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:797:0:0,0:384,413:0:2,0:23.4:1:30.3:1:1:0:48:98.625:1:0:1 0/1:1023:188:83,105:405,429:0.1838:2,2:24:1:30.8:1:0.29378:1.19408:36.6:376:0.1863:0:1.8 -17 1761447 . G A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08246;SOR=0.53978;LSEQ=AGGTTCCACATCAAGTGTCG;RSEQ=ATCCCATTCCAGGTATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:797:20:7,13:375,402:0.0251:2,2:10.9:1:30:1:0.26545:1.73124:29.9:40:0.0255:0:6.5 0/1:1022:14:8,6:476,532:0.0137:2,2:9.8:1:29.6:1:0.59221:1.49:30.1:28:0.0139:0:6.3 -17 1761457 . C T 133 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04456;SOR=0.53085;LSEQ=TCAAGTGTCGGATCCCATTC;RSEQ=AGGTATGATACATGAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:810:26:8,18:389,394:0.0321:2,2:17.6:1:28.5:1:0.07216:2.21937:28.8:52:0.0323:0:6.2 0/1:983:17:8,9:448,518:0.0173:2,2:17.1:1:29.2:1:1:1.03:30.9:34:0.0174:0:6.1 -17 1761482 . C T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74114;SOR=1.09845;LSEQ=ATGATACATGAGAGGGAAGA;RSEQ=GAGTGCAAACTTAGCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:893:37:12,25:420,434:0.0414:2,2:33.3:1:30.6:1:0.0633:2.01459:32.7:74:0.0418:0:6.3 0/1:1103:50:25,25:526,526:0.0453:2,2:22.3:1:30.2:1:1:1:35.3:100:0.0457:0:6.1 -17 1761502 . T A 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.01536;LSEQ=CGAGTGCAAACTTAGCTGTG;RSEQ=GGATCAGTGCTGGCCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:932:39:12,27:429,464:0.0418:2,2:32.4:1:31.4:1:0.04803:2.07872:32.3:78:0.0421:0:6.4 0/1:1154:49:25,24:552,553:0.0425:2,2:31.1:1:30.2:1:1:1.04:34.6:98:0.0428:0:6.3 -17 1761504 . G A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.91352;SOR=1.03513;LSEQ=AGTGCAAACTTAGCTGTGTG;RSEQ=ATCAGTGCTGGCCCCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:932:39:12,27:425,468:0.0418:2,2:31.8:1:30.7:1:0.04841:2.04177:32.3:78:0.0425:0:6.4 0/1:1156:50:25,25:551,555:0.0433:2,2:31.2:1:29.5:1:1:1.01:34.7:49:0.0429:0:6.4 -17 1761536 . CA GG 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13583;SOR=1.57693;LSEQ=CCCCAGACACAGGGACTTCA;RSEQ=AGTTCCAAATAAGACTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:907:19:5,14:399,487:0.0209:2,2:22.9:1:31.6:1:0.16007:2.29206:35.3:38:0.0211:0.0022:5.7 0/1:1164:38:18,20:560,564:0.0326:2,2:23.4:1:30.5:1:0.86933:1.10313:36.6:76:0.0329:0:5.4 -17 1761548 . A T 144 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03058;SOR=1.96816;LSEQ=GGACTTCACAAGTTCCAAAT;RSEQ=AGACTCAAAGTTCCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:883:14:4,10:385,484:0.0159:2,2:17.6:1:28.9:1:0.28692:1.98717:38.6:28:0.016:0:5.6 0/1:1171:36:16,20:558,575:0.0307:2,2:14.4:1:28:1:0.61429:1.21284:37.8:72:0.0312:0:5.4 -17 1761764 . C CT 189 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.22155;LSEQ=GGGTTCTGGTCTCTCTTTTT;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:100:23,77:33,78:0.4292:2,2:26.1:1:28.5:1:0.27947:1.41404:59.5:11.5:0.424:0.0129:0.4 0/1:330:47:18,29:83,191:0.1424:2,2:26.9:1:29.8:1:0.30849:1.43:59.5:94:0.1478:0.0061:0.5 -17 1761776 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.18224;SOR=0;LSEQ=CTCTTTTTCTTTTTTTTTTT;RSEQ=AGACAGAGTCTTGCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:38,142:0.0109:2,2:6.5:1:28:1:0.38358:3.70:55:4:0.0117:0:1.5 0/0:245:0:0,0:62,180:0:2,0:21.7:1:29.7:1:1:0:59.8:14.125:0.9956:0:0.3 -17 1762323 . G A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCTATCTCAGCCTCCCA;RSEQ=GTAGCTAGGACTACAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:28:0:27:0:1:0:54:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:29:0:32.5:1:1:0:60:4:1:0:1 -17 3568401 . G A 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00404;SOR=0;LSEQ=TGCTGTGGCTTCTGTAGGTG;RSEQ=GAAGCCCGTCTCACAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:8,0:16,0:0.3333:1,0:29.3:1:30:1:1:0:60:16:0.3478:0:1.1 0/0:22:0:0,0:22,0:0:1,0:24.4:1:31.1:1:1:0:60:44:1:0:0.1 -17 3568479 . C A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.53552;LSEQ=GAGAGGAAGGGGTTTCCTTT;RSEQ=GGCCGGAACCGCCATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:1:1,0:75,58:0.0075:2,0:25:0:11:0:1:0:60:0:0:0:5 0/1:175:2:1,1:94,79:0.0114:2,2:41.5:1:29:0:1:1.18868:60:4:0.0114:0:1 -17 3568499 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18573;SOR=0;LSEQ=CGGCCGGAACCGCCATCTTC;RSEQ=AGTAATTCGCCAAAATGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:82,71:0.0129:2,2:22:1:29.5:1:1:1.15385:60:4:0.0131:0:1.5 0/0:204:0:0,0:108,96:0:2,0:29.6:1:30.9:1:1:0:55.5:203:1:0:0.2 -17 3568536 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5135;SOR=Inf;LSEQ=GACGAACACAAAGGGAAAGA;RSEQ=GAGAGGCACCGGATATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:56,70:0:2,0:24.4:1:31.4:1:1:0:57.4:125:1:0:0.1 0/1:179:2:1,1:79,98:0.0112:2,2:28:1:28.5:1:1:1.24:60:4:0.0114:0:1 -17 3568547 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.48808;LSEQ=AGGGAAAGAGGAGAGGCACC;RSEQ=GATATATGTTCTCTAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:1,0:57,56:0.0087:2,0:1:0:25:0:1:0:60:2:0.0091:0:1 0/1:155:2:1,1:71,82:0.0129:2,2:17:1:29:1:1:1.15:53:4:0.0129:0:1 -17 3568607 . C T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03316;SOR=Inf;LSEQ=TTCCTTTGGCCACATATATG;RSEQ=GAATCTATAAGAAAGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:43,33:0:2,0:23.5:1:31:1:1:0:59:152:1:0:0.1 0/1:93:6:4,2:50,37:0.0645:2,2:29.8:1:31:1:1:1.47:59:12:0.0652:0:1 -17 3568739 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.506;SOR=Inf;LSEQ=AGCATGCTGTTGGCATTGTT;RSEQ=TAAACAAACAAGTTAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:47,84:0:2,0:23.6:1:31.5:1:1:0:53.3:130:1:0:0.1 0/1:168:2:1,1:66,100:0.0119:2,2:12:1:27.5:1:1:1.51:52:4:0.012:0:1 -17 3568758 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.499;SOR=Inf;LSEQ=TGTAAACAAACAAGTTAAGG;RSEQ=CAAGATTCTTGCCAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:22,74:0:2,0:22.8:1:31.6:1:1:0:51.2:47:1:0:0.1 0/1:107:2:1,1:30,75:0.0187:2,2:32:1:30.5:1:0.49744:2.48:21:4:0.0187:0:1 -17 3958105 . T G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00859;SOR=0.10197;LSEQ=AGGGGCAAGCCTGGACTCAG;RSEQ=GAGACTGACCATGACCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:13:13,0:4,0:0.7647:0,1:20.9:1:32.2:1:1:0:60:26:0.7647:0:1.5 0/1:13:3:3,0:10,0:0.2308:0,0:18.7:1:30.3:1:1:0:60:6:0.2308:0:1.3 -17 3958194 . G A 196 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18238;LSEQ=GGCGGGATGGTGAAAGGTGC;RSEQ=TAGATTTGAGGTGTTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:139:89:85,4:47,3:0.6403:2,1:22:1:30.4:1:0.70198:1.35:60:43.5:0.635:0:1.1 0/1:164:40:39,1:113,11:0.2439:2,1:26.2:1:30:1:0.29666:3.77:60:39:0.2422:0:1.3 -17 3958212 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1895;SOR=0;LSEQ=GCGTAGATTTGAGGTGTTGA;RSEQ=GCAGAAGTGGGAAACCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:161,31:0.0103:2,2:18:1:29:1:0.3034:5.12774:60:4:0.0105:0:1.5 0/0:251:0:0,0:194,57:0:2,0:23.6:1:31.2:1:1:0:60:40.833:1:0:0.4 -17 3958282 . G T 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAAGAAAGTTTCTGGCTT;RSEQ=GGTACGTGGTTGGACGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:0:0,0:283,219:0:2,0:25.8:1:31.3:1:1:0:60:49.2:1:0:0.5 0/1:711:99:57,42:324,287:0.1392:2,2:23.6:1:28.7:1:0.44735:1.20:60:32:0.1366:0:1.7 -17 3958341 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26187;LSEQ=GAAACACTGCAAAAGGAGTA;RSEQ=TGTCCCTGGCACTTACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:473:300:127,173:76,96:0.6342:2,2:24.2:1:30.3:1:0.7004:1.07824:60:299:0.6375:0:1.1 0/1:673:210:96,114:209,252:0.312:2,2:24.2:1:29.7:1:0.93357:1.02:60:104:0.3123:0:1.3 -17 4540268 . G C 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=0;LSEQ=CACTGCAAGGCCTTCGAATA;RSEQ=AGACTTGGCGCATTTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:13:7,6:87,83:0.0707:2,2:27.8:1:32.5:1:1:1.11:60:26:0.0718:0:2 0/0:218:0:0,0:105,113:0:2,0:26.1:1:31:1:1:0:59.6:35.333:1:0:0.5 -17 4540277 . C T 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51914;SOR=1.1615;LSEQ=GCCTTCGAATAGAGACTTGG;RSEQ=GCATTTCCTCCTTTCGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:55:26,29:72,66:0.285:2,2:28.1:1:30:1:0.63265:1.21554:59.8:54:0.2888:0:1.3 0/1:218:69:34,35:71,78:0.3165:2,2:28.2:1:29.5:1:0.88447:1.07:59.9:68:0.3208:0:1.2 -17 4540313 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49897;SOR=Inf;LSEQ=GCGTCTCCCAGGTGCCTTAG;RSEQ=CCAGTGCCTTTGCAGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:80,108:0:2,0:27.2:1:32:1:1:0:60:376:1:0:0.5 0/1:197:2:1,1:84,111:0.0102:2,2:28:1:31:1:1:1.32:60:4:0.0105:0:3 -17 4540315 . C A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2482;SOR=Inf;LSEQ=GTCTCCCAGGTGCCTTAGCC;RSEQ=AGTGCCTTTGCAGATGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:79,107:0:2,0:27.1:1:31.4:1:1:0:60:25.571:1:0:0.5 0/1:192:3:3,0:80,109:0.0156:2,0:5.3:1:25.3:1:0.07912:0:55.7:6:0.0161:0:3.3 -17 4540322 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23953;SOR=Inf;LSEQ=AGGTGCCTTAGCCCAGTGCC;RSEQ=TTGCAGATGGTGCTCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:73,107:0:2,0:26.3:1:30.3:1:1:0:60:59:0.9944:0:0.4 0/1:174:2:1,1:71,101:0.0115:2,2:30:1:29.5:1:1:1.42:60:4:0.0118:0:2 -17 4540328 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22188;SOR=Inf;LSEQ=CTTAGCCCAGTGCCTTTGCA;RSEQ=ATGGTGCTCAGTAAATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:67,102:0:2,0:26.3:1:31.6:1:1:0:60:83.5:1:0:0.4 0/1:151:2:1,1:59,90:0.0132:2,2:6.5:1:28:1:1:1.52:60:4:0.0135:0:1 -17 4540355 . G A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00197;SOR=Inf;LSEQ=CTCAGTAAATTTTGATAAGG;RSEQ=GCTGAGCTTTCTCAAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:38,78:0:2,0:24.2:1:30.4:1:1:0:60:37.667:1:0:0.3 0/1:102:8:2,6:33,61:0.0784:2,2:23.8:1:28.5:1:0.71176:1.61581:60:16:0.0825:0:1.3 -17 5828753 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22435;SOR=Inf;LSEQ=TCCCTTCTCCCTAAGCCCAC;RSEQ=TCATGACCACAGAGTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:32,13:0:2,0:22:1:31.6:1:1:0:60:90:1:0:0.1 0/1:41:2:1,1:25,14:0.0488:2,2:21:1:27.5:1:1:1.75924:60:4:0.0488:0:1 -17 5828945 . G T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12727;SOR=11.0937;LSEQ=AAATAGTACTGAGTCCCTTT;RSEQ=TACCTTTACCCAGCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:0,8:0.1111:0,0:38:0:28:0:1:0:60:2:0.1111:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:8:1:29.5:1:1:0:60:4:0.6667:0:1 -17 6563456 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50161;SOR=0;LSEQ=AGCCCCTTATCGAAATGCAC;RSEQ=AAGCACCATCTTCAAAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:77,46:0.016:2,2:9.5:1:29:1:1:1.66666:60:4:0.0161:0:1.5 0/0:105:0:0,0:72,33:0:2,0:23:1:29.6:1:1:0:60:51.5:1:0:0.1 -17 6563475 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49846;SOR=0;LSEQ=CTAAGCACCATCTTCAAAGG;RSEQ=GCTGGGCTAAGGCACCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:88,64:0.0128:2,2:48:1:31:1:1:1.37209:60:4:0.0128:0:1 0/0:152:0:0,0:97,55:0:2,0:25:1:30.9:1:1:0:60:75:1:0:0.2 -17 6563487 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23857;SOR=0;LSEQ=TTCAAAGGCGCTGGGCTAAG;RSEQ=CACCAGGGAGACGCGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:101,77:0.0111:2,2:11:1:29:1:1:1.30968:60:4:0.0112:0:1 0/0:188:0:0,0:114,74:0:2,0:25.4:1:31.1:1:1:0:60:61.667:1:0:0.2 -17 6563489 . A C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24904;SOR=Inf;LSEQ=CAAAGGCGCTGGGCTAAGGC;RSEQ=CCAGGGAGACGCGAAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:102,81:0:2,0:28.9:1:30.3:1:1:0:59.9:366:1:0:0.1 0/1:197:3:1,2:115,79:0.0152:2,2:26:1:25.7:1:0.56947:2.89555:60:2:0.0103:0:1 -17 6563538 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22079;SOR=0;LSEQ=CCAAGTCTCTATTCGAAGGC;RSEQ=TTGCAATGTAGCTGGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:2,0:79,95:0.0114:2,0:23:1:30.5:1:0.21039:0:57:4:0.0117:0:1 0/0:198:0:0,0:95,103:0:2,0:28.9:1:30.3:1:1:0:59.1:48.5:1:0:0.2 -17 6563566 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50489;SOR=Inf;LSEQ=GTAGCTGGAGAGACACATAG;RSEQ=GCTAGTCTGCAGAAGCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:42,76:0:2,0:23.9:1:30.5:1:1:0:60:117:1:0:0.1 0/1:149:2:1,1:51,96:0.0134:2,2:9:0:32:0:1:1.87:60:4:0.0137:0:1.5 -17 6846966 . GA G 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.06479;SOR=0.39134;LSEQ=AAACTGAGTGAGTGTGGGAA;RSEQ=AAAAAAAAAAGATTCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:14:11,3:99,32:0.0959:2,2:25.2:1:31.3:1:1:1.18:59.6:13:0.0909:0.0205:0.4 0/1:151:6:5,1:109,35:0.0397:2,2:30.2:1:31.3:1:1:1.60:60:12:0.0403:0:0 -17 6846975 . A G 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=GAGTGTGGGAAGAAAAAAAA;RSEQ=AAGATTCCTTTGAGAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:122,46:0:2,0:24.5:1:30.1:1:1:0:60:83:1:0:0.2 0/1:176:2:1,1:130,44:0.0114:2,2:42.5:1:31:1:0.44708:2.93259:60:4:0.0115:0:1 -17 6846995 . C T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34195;SOR=0.28742;LSEQ=AAAGATTCCTTTGAGAGATG;RSEQ=GCCTTTTGAGCATAATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:2,1:147,86:0.0127:2,2:6.7:1:29:1:1:1.17:60:6:0.0133:0:1.7 0/0:273:1:0,1:180,92:0.0037:2,0:1:0:25:0:0.34066:0:60:2:0.0038:0:2 -17 6847073 . A G 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00011;SOR=1.79712;LSEQ=TAATTCATTAATGGAGCAGC;RSEQ=GCATTACTCTAAACAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:106:47,59:94,129:0.3212:2,2:25.8:1:29.8:1:0.72198:1.09:60:25.5:0.3148:0:1.1 0/1:435:200:90,110:102,133:0.4598:2,2:27:1:29.1:1:0.77169:1.07:60:49:0.4548:0:1.1 -17 6847226 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16471;SOR=Inf;LSEQ=ACAGAGCCCTCAGAAATAAC;RSEQ=CCGCATATCTACAACTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:0:1,0:25.4:1:31.4:1:1:0:39:14:1:0:0.2 0/1:21:2:0,2:0,19:0.0952:1,0:31:1:30.5:1:1:0:40:4:0.0952:0:1 -17 7216540 . G A 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCATACTCACTGAGTCGGA;RSEQ=AAGCCAGTCTGCTGGTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1021:0:0,0:529,491:0:2,0:24.3:1:31.5:1:1:0:60:52.684:1:0:0.2 0/1:1499:65:36,29:752,680:0.0434:2,2:27:1:29.1:1:0.70401:1.12:60:64:0.0432:0:1.1 -17 7217342 . G T 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCTTCATGATGCTGAAAT;RSEQ=GGAGGCTGTGACCTCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:960:0:0,0:461,498:0:2,0:24.9:1:31.6:1:1:0:60:136:1:0:0.1 0/1:1119:66:30,36:510,542:0.059:2,2:22.5:1:29.8:1:0.70372:1.12903:60:132:0.0597:0:1.1 -17 7217463 . T C 289 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.91477;LSEQ=TGCTGGTATGCAGCTGATGT;RSEQ=AGGGTGGTCAGGTCACTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1005:355:164,191:299,350:0.3532:2,2:26.3:1:31.5:1:1:1.01:60:43.375:0.3526:0:1.2 1/0:1244:636:293,343:306,301:0.5113:2,2:26.9:1:31.1:1:0.13984:1.18992:59.8:69.667:0.5114:0:1.1 -17 7217497 . AG A 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTGGAGTGAAAGGAAGAC;RSEQ=GTCAAAGTCAAGGACAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:813:0:0,0:338,475:0:2,0:25:1:31.2:1:1:0:60:44.167:1:0:0.4 0/1:1035:34:16,18:465,532:0.0329:2,2:25.7:1:31.3:1:1:1.02:60:68:0.0332:0.0029:0.9 -17 7217944 . G A 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=0.52936;LSEQ=ATCAGGCAGAATGAAGAAGA;RSEQ=GCAGGGTAGTGAAAACAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:102:32,70:76,266:0.2297:2,2:23.9:1:30.5:1:0.06599:1.60:60:101:0.2301:0:1.1 0/1:521:71:21,50:114,336:0.1363:2,2:22.1:1:30.7:1:0.46724:1.24:60:142:0.1381:0:1.1 -17 7218443 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24906;SOR=Inf;LSEQ=AGACCTCAGACGGGGCCTGC;RSEQ=GGGAGGCGGGCGCTCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:15,149:0:2,0:21.9:1:31.6:1:1:0:60:81:0.9939:0:0.1 0/1:179:3:1,2:26,150:0.0168:2,2:10:1:24:1:0.38953:2.86:60:2:0.0112:0:1 -17 7218670 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCTTCTCTGCGCTTTCT;RSEQ=AGCGGCTCCGACGCGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:28:1:1:0:60:4:1:0:1.5 -17 7481682 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49851;SOR=Inf;LSEQ=TCGGTCGAGGTGGACGGTTT;RSEQ=GCCGTAAAGGTGTGGCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:39,24:0:2,0:21.3:1:30.9:1:1:0:58.1:62:1:0:0.1 0/1:72:2:1,1:39,31:0.0278:2,2:36:1:29.5:1:1:1.25402:60:4:0.0278:0:1 -17 7492708 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23554;SOR=0;LSEQ=TGGCCTCCTCCACGAAGGGC;RSEQ=GCTTCTCGTCCTCGTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:62,44:0.0185:2,2:22:1:32:1:1:1.40451:60:4:0.0185:0:1 0/0:114:0:0,0:66,48:0:2,0:27.3:1:30:1:1:0:60:56:1:0:0.3 -17 7492728 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25015;SOR=Inf;LSEQ=CGCTTCTCGTCCTCGTCCAG;RSEQ=AGCTTCCACTGCGCGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:66,48:0:2,0:26.2:1:32:1:1:0:60:228:1:0:0.1 0/1:130:3:1,2:70,57:0.0231:2,2:25.3:1:26.7:1:0.59019:2.43955:60:6:0.0231:0:1 -17 7492804 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49898;SOR=Inf;LSEQ=TCTGCTGCGCCATCTGGCGG;RSEQ=GCTGAGCGGAGCTCCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:40,62:0:2,0:29.8:1:30.5:1:1:0:60:101:1:0:0.1 0/1:113:2:1,1:48,62:0.0177:2,2:7.5:1:28.5:1:1:1.29:60:4:0.0179:0:1.5 -17 7569510 . C A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05827;SOR=0;LSEQ=GATTCTCCTGCCTCAGCCTC;RSEQ=CGAGTAGCTGGGATTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:3:1,2:153,58:0.014:2,2:11.7:1:21.7:1:0.19049:5.2278:60:2:0.0094:0:2.3 0/0:338:0:0,0:240,97:0:2,0:22.8:1:29.8:1:1:0:59.8:55.167:0.997:0:0.2 -17 7569527 . C T 38 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30436;SOR=0.20866;LSEQ=CTCCCGAGTAGCTGGGATTA;RSEQ=AGGTGTGATCCACCGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:1,2:179,119:0.01:2,2:8.7:1:24.3:1:0.56682:2.99729:60:6:0.0102:0:1 0/0:478:1:0,1:293,184:0.0021:2,0:1:0:26:0:0.38703:0:60:2:0.0021:0:1 -17 7569534 . G T 44 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06444;SOR=0.14459;LSEQ=GTAGCTGGGATTACAGGTGT;RSEQ=ATCCACCGTGCCTGGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:4:0,4:179,128:0.0129:2,0:17:1:22:1:0.0316:0:60:3:0.0099:0:2 0/0:533:1:0,1:319,213:0.0019:2,0:1:0:23:0:0.4015:0:60:2:0.0019:0:2 -17 7569698 . A C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.31172;LSEQ=TTTGAGTGGGAGGGTAGGGA;RSEQ=CATGTCTGCCATAGGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:76:0,76:0,38:0.6667:1,1:23.7:1:31.2:1:1:0:60:75:0.6637:0:1.1 0/1:128:49:1,48:1,77:0.3828:1,1:22.4:1:31.3:1:1:1.60:60:48:0.381:0:1.1 -17 7572869 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70518;SOR=1.78828;LSEQ=AGACCCAAAACCCAAAATGG;RSEQ=AGGGGAGGGAGAGATGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:2:0,2:191,51:0.0082:2,0:1:0:25:1:0.04648:0:60:4:0.0085:0:1 0/1:343:5:1,4:242,96:0.0146:2,2:8.8:1:23.8:1:0.02676:10.00876:60:10:0.0149:0:1.2 -17 7572873 . G T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14306;SOR=Inf;LSEQ=CCAAAACCCAAAATGGCAGG;RSEQ=GAGGGAGAGATGGGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:216,63:0:2,0:22.8:1:30.7:1:1:0:60:38.857:1:0:0.2 0/1:385:4:1,3:269,112:0.0104:2,2:16.3:1:25.5:1:0.08164:7.1641:60:8:0.0106:0:1 -17 7573085 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52495;SOR=Inf;LSEQ=GCCCCTTTTCCCTGACCAAT;RSEQ=CTTTGAAGGGCCTAAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:4,113:0:1,0:23.5:1:31.6:1:1:0:60:22.4:1:0:0.1 0/1:187:2:1,1:20,165:0.0107:2,2:25:1:28:1:0.21252:8.07:60:4:0.0108:0:1 -17 7573086 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14396;SOR=0;LSEQ=CCCCTTTTCCCTGACCAATG;RSEQ=TTTGAAGGGCCTAAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:3,108:0.0177:1,2:5:1:30:1:0.06985:31.32:60:4:0.0182:0:1 0/0:184:0:0,0:21,163:0:2,0:21.2:1:31.9:1:1:0:60:91:1:0:0.1 -17 7573135 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49756;SOR=Inf;LSEQ=GAATTCAAATCAAGATGGTG;RSEQ=CCACACCCCATGCAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:1,59:0:1,0:24.9:1:30.9:1:1:0:60:19:1:0:0.1 0/1:67:2:0,2:2,63:0.0299:1,0:23:1:28.5:1:1:0:60:4:0.0299:0:1 -17 7573889 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17414;SOR=0;LSEQ=GGCTTTCCAACCTAGGAAGG;RSEQ=AGGGGAGTAGGGCCAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:158,31:0.0105:2,2:32:1:27:1:0.30774:5.0325:60:4:0.0106:0:1 0/0:266:0:0,0:206,60:0:2,0:23.2:1:31.5:1:1:0:60:43.333:1:0:0.2 -17 7573894 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26938;SOR=Inf;LSEQ=TCCAACCTAGGAAGGCAGGG;RSEQ=AGTAGGGCCAGGAAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:171,39:0:2,0:23.1:1:31:1:1:0:60:69:1:0:0.1 0/1:294:3:1,2:227,64:0.0102:2,2:9:1:27.3:1:0.12757:7.03148:60:6:0.0105:0:1.3 -17 7573897 . T A 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=AACCTAGGAAGGCAGGGGAG;RSEQ=AGGGCCAGGAAGGGGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:182,47:0:2,0:22.4:1:29.4:1:1:0:60:113.5:1:0:0.1 0/1:317:13:11,2:233,71:0.041:2,2:22.6:1:28.2:1:0.73966:1.67:60:12:0.0382:0:1.1 -17 7574074 . G A 73 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08762;SOR=Inf;LSEQ=GAGAAGTAAGTATATACACA;RSEQ=TACCTGAGTTAAAAGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:100,213:0:2,0:24.7:1:31.6:1:1:0:60:51.167:1:0:0.2 0/1:503:6:4,2:155,342:0.0119:2,2:21.7:1:28.3:1:0.08274:4.40:60:12:0.012:0:1 -17 7576276 . T A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATCTCTACTAAAAAAAAAAA;RSEQ=AAATAAATAACAAAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:36:1:30.5:1:1:0:60:4:1:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:12:0:31:1:1:0:60:4:0.6667:0:3.5 -17 7576348 . C T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01923;SOR=Inf;LSEQ=AGCTACTCAGTGGGCTGAGG;RSEQ=AGGAGAATCGCTTGAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:22.3:1:32.6:1:1:0:60:18:1:0:0.2 1/0:7:4:4,0:3,0:0.5714:0,0:12.5:1:27.3:1:1:0:60:8:0.5714:0:2.3 -17 7576474 . T C 29 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.2155;LSEQ=AAAAAAAAAGCAGGCTAGGC;RSEQ=AAGCTATGATGTTCCTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:1:1,0:86,18:0.0095:2,0:14:0:15:0:1:0:60:0:0:0:1 0/1:173:2:1,1:143,27:0.0116:2,2:5:0:29.5:1:0.29988:5.21913:60:4:0.012:0:2 -17 7576477 . G A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29246;SOR=Inf;LSEQ=AAAAAAGCAGGCTAGGCTAA;RSEQ=CTATGATGTTCCTTAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:96,20:0:2,0:15.5:1:30.8:1:1:0:59.8:9.545:1:0:0.4 0/1:191:3:2,1:158,30:0.0157:2,2:10.7:1:23:1:0.41396:2.61568:60:2:0.0112:0:2.3 -17 7576478 . C T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19728;LSEQ=AAAAAGCAGGCTAGGCTAAG;RSEQ=TATGATGTTCCTTAGATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:1:1,0:95,20:0.0086:2,0:20:0:25:0:1:0:40:2:0.0094:0:4 0/1:194:2:1,1:160,32:0.0103:2,2:16:1:25.5:1:0.312:4.93914:60:4:0.0111:0:1.5 -17 7576501 . G A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00106;SOR=Inf;LSEQ=TGATGTTCCTTAGATTAGGT;RSEQ=TATTAAATCCATTTTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:142,43:0:2,0:26.3:1:31:1:1:0:60:11.333:1:0:0.2 0/1:344:17:13,4:234,89:0.0494:2,2:20.8:1:26.7:1:1:1.24:60:34:0.0518:0:1.2 -17 7576841 . A G 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TCCACTTGATAAGAGGTCCC;RSEQ=AGACTTAGTACCTGAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:213,153:0:2,0:25.3:1:30.2:1:1:0:60:365:1:0:0.1 0/1:598:22:11,11:322,252:0.0368:2,2:23.1:1:29.1:1:0.66337:1.27724:60:21:0.0354:0:1.2 -17 7577407 . A C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03271;LSEQ=GTGGATGGGTAGTAGTATGG;RSEQ=AGAAATCGGTAAGAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:122:71:57,14:47,4:0.582:2,2:22.3:1:32.4:1:0.07628:2.86327:60:70:0.5983:0:2 0/1:163:7:6,1:137,18:0.0429:2,2:22.7:1:31.3:1:0.58975:1.2665:60:14:0.0449:0:2 -17 7577427 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02986;LSEQ=AAGAAATCGGTAAGAGGTGG;RSEQ=CCCAGGGGTCAGAGGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:94:78,16:54,7:0.6065:2,2:24.2:1:30:1:0.48837:1.57791:60:93:0.6078:0:1.8 0/1:230:10:8,2:179,38:0.0435:2,2:25.2:1:28.7:1:0.69041:1.1767:60:20:0.0452:0:1.7 -17 7577709 . C T 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00015;SOR=0;LSEQ=TTTTTTGAGATGGAATCTCG;RSEQ=TCTGTCGCCCAGGCTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:11:1,10:0,31:0.2619:1,2:21.5:1:30.7:1:0.2619:0:48.8:22:0.2683:0:2.1 0/0:45:0:0,0:0,44:0:1,0:23:1:31.2:1:1:0:51.6:21:1:0:1.3 -17 7578115 . T C 253 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0262;LSEQ=AAGCCCCCCTACTGCTCACC;RSEQ=GGAGGGCCACTGACAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:361:358:254,104:0,3:0.9917:0,2:24.2:1:30.2:1:0.02553:0:60:118.333:0.9916:0:1.1 1/0:511:387:277,110:84,40:0.7573:2,2:23.8:1:29.5:1:0.42888:1.20:60:54.286:0.757:0:1.1 -17 7578117 . G T 53 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16592;SOR=0.17455;LSEQ=GCCCCCCTACTGCTCACCTG;RSEQ=AGGGCCACTGACAACCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:4:1,3:263,112:0.0106:2,2:19.8:1:26.8:1:0.0852:7.00449:60:8:0.0108:0:1.5 0/0:539:1:0,1:377,161:0.0019:2,0:1:0:22:0:0.30056:0:60:2:0.0019:0:1 -17 7578210 . T C 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGGCACCACCACACTATG;RSEQ=CGAAAAGTGTTTCTGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:724:0:0,0:358,365:0:2,0:25.1:1:29.9:1:1:0:60:79.333:0.9986:0:0.2 0/1:1197:84:38,46:537,573:0.0702:2,2:24.6:1:31.2:1:0.65084:1.13435:60:41:0.069:0:1.3 -17 7578449 . C T 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04498;SOR=Inf;LSEQ=CTGTGACTGCTTGTAGATGG;RSEQ=CATGGCGCGGACGCGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:200,196:0:2,0:23.8:1:31.5:1:1:0:60:55.571:1:0:0.4 0/1:562:6:3,3:307,249:0.0107:2,2:16.2:1:28.8:1:1:1.23246:60:5:0.0091:0:1.2 -17 7578461 . C A 218 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GTAGATGGCCATGGCGCGGA;RSEQ=GCGGGTGCCGGGCGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:145:79,66:142,132:0.3461:2,2:20.9:1:30.4:1:0.60895:1.11:60:35.25:0.3431:0:1.2 0/0:625:0:0,0:342,281:0:2,0:23.5:1:29.9:1:1:0:60:61.3:0.9967:0:0.2 -17 7578640 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.50089;SOR=Inf;LSEQ=AGACGGCAGCAAAGAAACAA;RSEQ=CATGCGTAAGCACCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:3,67:0:1,0:28.3:1:29.5:1:1:0:60:69:1:0:1.2 0/1:84:2:0,2:1,81:0.0238:1,0:9:1:32.5:1:1:0:60:4:0.0247:0:1 -17 7578645 . C T 176 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=GCAGCAAAGAAACAAACATG;RSEQ=GTAAGCACCTCCTGCAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:66:3,63:0,0:1:0,1:28.6:1:29.2:1:1:0:60:15.5:1:0:1.3 1/0:70:55:1,54:0,15:0.7857:1,1:23.1:1:29.9:1:1:0:60:26.5:0.7794:0:1.3 -17 7578679 . A G 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.31476;SOR=4.02412;LSEQ=GCAACCCACTAGCGAGCTAG;RSEQ=GAGAGTTGGCGTCTACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:0,1:1,44:0.0217:1,0:18:0:15:0:1:0:60:0:0:0:6 0/1:36:3:0,3:0,33:0.0833:1,0:18:1:29.7:1:1:0:60:6:0.0968:0:3.3 -17 7578711 . CTTT C 63 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=18.000;MSILEN=1;SSF=0.70339;SOR=1.64348;LSEQ=TCTACACCTCAGGAGCTTTT;RSEQ=TTTTTTTTTTTTTTTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:0,4:0,9:0.2:0,0:33:1:30:1:1:0:56.3:8:0.2105:0:2.5 0/1:17:5:0,5:0,10:0.2941:0,0:24.4:1:27.4:1:1:0:60:4:0.25:0.0588:1.8 -17 7578837 . A G 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCCACCTCAGCCTCCT;RSEQ=AGTGGCTGGGACTATAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:10.5:1:31:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 7579219 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=TGACAGGAAGCCAAAGGGTG;RSEQ=AGAGGAATCCCAAAGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:70,4:0.0263:2,2:21:1:30.5:1:0.12807:15.75751:60:4:0.0263:0:1 0/0:67:0:0,0:63,4:0:2,0:26.8:1:29.4:1:1:0:60:66:1:0:0 -17 7579258 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50327;SOR=Inf;LSEQ=CAAACAAAAGAAATGCAGGG;RSEQ=GATACGGCCAGGCATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:130,23:0:2,0:23.6:1:31.3:1:1:0:60:152:1:0:0.1 0/1:186:2:1,1:148,35:0.0108:2,2:27:1:31:1:0.35217:4.18349:60:4:0.0109:0:1 -17 7579259 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50414;SOR=Inf;LSEQ=AAACAAAAGAAATGCAGGGG;RSEQ=ATACGGCCAGGCATTGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:132,25:0:2,0:23.5:1:31.3:1:1:0:60:156:1:0:0.1 0/1:194:2:1,1:151,41:0.0103:2,2:5.5:1:28.5:1:0.387:3.65121:60:4:0.0107:0:1.5 -17 7579472 . G C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=2.28637;LSEQ=CTGCTGGTGCAGGGGCCACG;RSEQ=GGGGAGCAGCCTCTGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:156:83,73:123,133:0.3786:2,2:26.3:1:30.5:1:0.36067:1.23:60:51:0.3787:0:1.1 1/0:601:350:172,178:135,115:0.5824:2,2:24.5:1:30:1:0.24731:1.21446:60:37.889:0.577:0:1.2 -17 7579579 . C T 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=8.6037;LSEQ=AAATCATCCATTGCTTGGGA;RSEQ=GGCAAGGGGGACTGTAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:2:0,2:221,183:0.0049:2,0:1:0:26:0:0.20702:0:60:4:0.005:0:1 0/1:565:23:10,13:282,260:0.0407:2,2:20:1:30:1:0.52407:1.40914:60:46:0.0413:0:1.1 -17 7579619 . G T 198 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=29.81311;LSEQ=GGGTGAAAAGAGCAGTCAGA;RSEQ=GACCAGGTCCTCAGCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:3:0,3:299,213:0.0058:2,0:1:0:25.7:1:0.07318:0:60:6:0.006:0:1 0/1:685:102:55,47:343,240:0.1489:2,2:21.4:1:29.7:1:0.3847:1.22092:60:101:0.1494:0:1.1 -17 7579643 . CCCCCAGCCCTCCAGGT C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.30524;LSEQ=CAGGTCCTCAGCCCCCCAGC;RSEQ=CCCCAGCCCTCCAGGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:583:487:256,231:64,31:0.8353:2,2:28.6:1:31:1:0.00933:1.86095:59.6:120.75:0.84:0.1304:0.2 1/0:810:492:268,224:177,136:0.6074:2,2:27.6:1:30.3:1:0.61083:1.08768:59.7:245:0.6171:0.0975:0.3 -17 7579801 . G C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.51984;LSEQ=TAGGGGGCTGGGGTTGGGGT;RSEQ=GGGGTGGTGGGCCTGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:232:114,118:184,203:0.373:2,2:23.5:1:29.6:1:0.73978:1.07:60:32.143:0.3682:0:1.2 1/0:785:471:235,236:150,162:0.6:2,2:23.2:1:29.7:1:0.66143:1.08:60:66.286:0.5995:0:1.2 -17 7579960 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27692;SOR=Inf;LSEQ=GCTGCAAGAGGAAAAGTGGG;RSEQ=ATCCAGCATGAGACACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:58,145:0:2,0:23.6:1:30.9:1:1:0:60:39.6:1:0:0.1 0/1:301:3:1,2:88,209:0.01:2,2:21:1:27.3:1:1:1.19:60:6:0.0102:0:1 -17 7580002 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2291;SOR=Inf;LSEQ=ACCCTGGGTCACCTGGGCCT;RSEQ=CAGAGAAGGAACCCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:18,98:0:2,0:24.2:1:31.5:1:1:0:60:37.667:1:0:0.1 0/1:107:2:1,1:7,97:0.0187:2,2:15.5:1:28:1:0.14591:13.03:60:4:0.019:0:1 -17 7580052 . C T 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TGCCAGTGTCTGAGACAGCT;RSEQ=GGCTTCCTGTGGAGCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:2,48:0:1,0:26.8:1:29.9:1:1:0:60:49:1:0:0.1 0/1:46:12:0,12:1,33:0.2609:1,0:24.9:1:30.8:1:1:0:60:24:0.2609:0:1.1 -17 7580500 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01571;LSEQ=CTTACTTCAGGTGATCGGCC;RSEQ=GCCTCAGCCTCCTAAAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:64:64,0:30,0:0.6737:1,1:27.1:1:31.9:1:1:0:60:128:0.6809:0:1 0/1:98:3:3,0:94,1:0.0306:1,0:18.7:1:31:1:1:0:60:6:0.0319:0:1.3 -17 7612635 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11102;SOR=0;LSEQ=CATGTGTTGGCGGAGACGGC;RSEQ=GGCCAAGCCTTCGGAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:27:0:32.5:1:1:1.13389:60:4:0.1176:0:1.5 0/0:33:0:0,0:17,16:0:2,0:30.1:1:29.4:1:1:0:60:66:1:0:0.2 -17 7858597 . G GA 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.10756;LSEQ=TCTCAAGAAAAAAAAAAAAA;RSEQ=AAAAAAAAAGACAATATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:2,0:40,6:0.0377:2,0:13.5:1:29.4:1:1:0:60:4:0.05:0.0189:2.5 0/1:48:2:2,0:42,4:0.0417:2,0:14.5:1:30:1:1:0:60:4:0.0556:0:0.5 -17 7858638 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16033;SOR=0;LSEQ=AGACATCAAGGGAATGGGTA;RSEQ=TGTTCAAAAAGGAATGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:0,2:66,29:0.0204:2,0:12:1:29:1:0.09987:0:60:4:0.0217:0:1 0/0:146:0:0,0:98,48:0:2,0:24.3:1:31.1:1:1:0:59.4:47.667:1:0:0.2 -17 7858729 . CAAGTT C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00183;SOR=0.41925;LSEQ=GCTGTTGGCATTGTTGTAAA;RSEQ=AAGGGCAAGATTCTTGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:52:16,36:17,37:0.4906:2,2:23.3:1:31.5:1:1:1.03347:59.7:51:0.4857:0.066:0.4 0/1:129:37:7,30:29,63:0.2868:2,2:24.8:1:31:1:0.19405:1.96308:60:74:0.2868:0.0465:0.3 -17 7858774 . G A 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03958;SOR=0.40817;LSEQ=AGAGAATTAATGTGCGTATT;RSEQ=GGCACGTTAAGCACCTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:22:1,21:4,30:0.3929:2,1:25.9:1:32:1:0.63812:2.75541:59.2:44:0.3929:0:1 0/1:53:11:2,9:2,39:0.2075:1,2:23.5:1:29.1:1:0.1928:4.17:60:10:0.2041:0:1.4 -17 7858901 . A G 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54545;SOR=3.51553;LSEQ=AATGCCAGACTGCTCCACCC;RSEQ=GAGGGGTAAACACTGGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:18:1:32.3:1:1:0:60:6:0.5:0:2 1/1:5:4:0,4:0,1:0.8:0,0:19.5:1:30:1:1:0:60:8:0.8:0:1.5 -17 7858924 . C T 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGGTAAACACTGGTAAAGA;RSEQ=GCTCAGCCTCATTAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:18.5:1:32:0:1:0:60:4:0.6667:0:2.5 1/1:1:1:0,1:0,0:1:0,0:46:0:28:0:1:0:60:2:1:0:3 -17 7948175 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=TTTGAGCACTGGCAGGAGGA;RSEQ=GCCTTCTTCGCCTCCCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:20.3:1:30:1:1:1.81007:60:6:0.4286:0:1.3 1/0:3:2:1,1:1,0:0.6667:0,2:7.5:1:29.5:1:1:0:60:4:0.6667:0:1.5 -17 7948942 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=ACCTGCTGCACTCACATCTG;RSEQ=TGCCTGAGGTCTTCACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:23.6:1:32.6:1:1:0:60:14:1:0:0.7 0/1:11:2:1,1:0,9:0.1818:0,2:22:1:29:1:0.18182:0:60:4:0.1818:0:1 -17 7975986 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49996;SOR=0;LSEQ=TTTTGTTTTTTTGTTTGTTT;RSEQ=GTGTTTTGGTCTCTGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:184,9:0.0103:1,2:25:1:28.5:1:0.10019:19.45504:60:4:0.0103:0:1 0/0:176:0:0,0:162,14:0:2,0:24.3:1:31.3:1:1:0:60:43:1:0:0.1 -17 7976291 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18308;SOR=Inf;LSEQ=GCGGGCAGAGAGCTCGACAG;RSEQ=TGGGACCAGGGCCGGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:66,170:0:2,0:22.8:1:31.7:1:1:0:60:38.333:1:0:0.1 0/1:177:2:1,1:51,123:0.0113:2,2:12.5:1:27.5:1:0.50481:2.40:60:4:0.0115:0:1 -17 7976310 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16871;SOR=Inf;LSEQ=GCTGGGACCAGGGCCGGCCA;RSEQ=CACCCCCTCCTCCTGCCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:43,126:0:2,0:25.6:1:32.1:1:1:0:60:168:0.9941:0:0.2 0/1:119:2:1,1:34,83:0.0168:2,2:42.5:1:27.5:1:0.50349:2.42:60:4:0.0171:0:1 -17 7976329 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51831;SOR=0;LSEQ=AGCACCCCCTCCTCCTGCCG;RSEQ=TGGCCCTGGCCCCTCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:40,100:0.014:2,2:34.5:1:31.5:1:0.49555:2.48:60:4:0.0144:0:1 0/0:95:0:0,0:30,65:0:2,0:24:1:31.3:1:1:0:60:46.5:1:0:0.2 -17 7976694 . C T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09484;SOR=Inf;LSEQ=GTACCTCAGGAGTTTCCTTC;RSEQ=ACCAGGTGCTGACCACCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:26,172:0:2,0:23.2:1:31.8:1:1:0:60:32:1:0:0.2 0/1:167:3:1,2:23,139:0.018:2,2:19:1:22.7:1:0.37792:2.99:60:2:0.0123:0:1.7 -17 7976707 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50726;SOR=0;LSEQ=TTCCTTCCACCAGGTGCTGA;RSEQ=CACCCGCCCTCCAGTCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:18,136:0.0128:2,2:20:1:26.5:1:0.22945:7.38:60:4:0.0133:0:3 0/0:119:0:0,0:8,111:0:2,0:23.8:1:30.6:1:1:0:60:38.667:1:0:0.1 -17 7976917 . A T 184 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTTTGAGGTTGGGGCATGG;RSEQ=CGAAATTTAGAAGGTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:87:58,29:145,44:0.3152:2,2:24:1:28.6:1:0.10561:1.64468:60:28:0.3111:0:1.2 0/0:261:0:0,0:193,67:0:2,0:23.2:1:28.1:1:1:0:60:22.636:1:0:0.1 -17 7977105 . A G 256 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0157;LSEQ=GGGGGAAAAGCCCAGGCGAC;RSEQ=TCAGTCGTGCCCTGGTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:307:96,211:0,1:0.9903:0,2:25.2:1:31:1:1:0:60:152.5:0.9935:0:1.1 1/0:278:171:51,120:39,68:0.6151:2,2:21.1:1:30.5:1:0.29217:1.34797:60:170:0.6137:0:1.2 -17 7977139 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06991;SOR=Inf;LSEQ=GGTACTGGCTGCCCGGCAGA;RSEQ=GGCGCCACCATGCCCCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:17,160:0:2,0:23.7:1:31.3:1:1:0:60:354:1:0:0.9 0/1:125:3:2,1:20,102:0.024:2,2:19.7:1:25.7:1:0.07973:9.91:60:2:0.0163:0:1.7 -17 7977368 . C T 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCCTGGGGATGCCGCTC;RSEQ=GGTCCCAGACCTGGGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:30.5:1:30.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 7978751 . G A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.79772;SOR=1.17593;LSEQ=TGAGATGCCACTGCTCCAGG;RSEQ=GCCAGAGAAGAGCCTGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:18:17,1:32,1:0.3529:1,1:27.8:1:30.1:1:1:1.85775:60:36:0.36:0:1.3 0/1:23:9:9,0:13,1:0.3913:1,0:19.1:1:27:1:1:0:60:8:0.3636:0:1.4 -17 7978819 . T A 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03563;SOR=0.53175;LSEQ=TCAGTCTACAATAAAATATG;RSEQ=TCTGATCCAGCCCAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:45:43,2:104,4:0.2922:1,1:26.4:1:30:1:1:1.20772:60:21.5:0.2848:0:1.2 0/1:128:23:21,2:94,11:0.1797:2,2:18.3:1:29.3:1:1:1.23:60:22:0.1746:0:1.4 -17 7978829 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19949;SOR=Inf;LSEQ=ATAAAATATGTTCTGATCCA;RSEQ=CCCAGGAGGGCCCTAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:192,18:0:2,0:22:1:32.3:1:1:0:60:69:1:0:0.3 0/1:170:2:1,1:147,21:0.0118:2,2:30:1:28.5:1:0.24274:6.86192:60:4:0.0121:0:1 -17 7978832 . C T 41 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62795;SOR=0.38882;LSEQ=AAATATGTTCTGATCCAGCC;RSEQ=AGGAGGGCCCTAGCAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:1,2:194,19:0.0139:2,2:5.7:1:26:1:0.02553:19.77822:60:6:0.0141:0:1.7 0/0:184:1:0,1:155,28:0.0054:2,0:1:0:24:0:0.15761:0:60:2:0.0055:0:1 -17 7979075 . TC T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12885;SOR=0;LSEQ=CAGTTTGGATCCTCCTCCCC;RSEQ=CCACTCCTCAGCCAGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:4:3,1:90,255:0.0114:2,2:8.5:1:30:1:0.05948:8.44:60:8:0.0115:0.0057:0.5 0/0:298:0:0,0:79,219:0:2,0:22.9:1:30.5:1:1:0:60:48.667:1:0:0.2 -17 7979463 . A G 284 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATCCCAGGTTGTCCACCCT;RSEQ=AGAGCCACCCACTGCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:534:534:341,193:0,0:1:0,2:25.2:1:31.4:1:1:0:60:88:1:0:1.1 1/0:549:342:220,122:133,74:0.623:2,2:24.5:1:30.9:1:1:1.00:60:30.091:0.6222:0:1.1 -17 7979468 . C T 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01276;SOR=0;LSEQ=CAGGTTGTCCACCCTAAGAG;RSEQ=CACCCACTGCTGTCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:6:3,3:348,209:0.0107:2,2:20.3:1:29:1:0.67712:1.66343:60:12:0.0108:0:1.7 0/0:599:0:0,0:381,218:0:2,0:25.1:1:31.2:1:1:0:60:58.9:1:0:0.7 -17 7980013 . G T 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00385;SOR=Inf;LSEQ=CTCATTGAGGAGAACGGCCC;RSEQ=GCCAATGCTGTTGATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:326,273:0:2,0:25.5:1:29.7:1:1:0:60:48.917:0.9932:0:0.2 0/1:627:9:4,5:315,303:0.0144:2,2:27.8:1:29:1:0.74823:1.29896:60:18:0.0145:0:1.2 -17 7980112 . A G 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04876;SOR=Inf;LSEQ=AGGGCTGAAGTGGCCCCCAA;RSEQ=GGAGCTCAGCTCCCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:91,213:0:2,0:22.8:1:30.3:1:1:0:60:29.4:1:0:0.1 0/1:271:4:2,2:87,180:0.0148:2,2:12:1:31.3:1:0.59982:2.06:60:8:0.0149:0:1 -17 7980189 . TCCCCAGATGCC T 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCAAGCCCTCTCTTGTGG;RSEQ=CCCCAGGCTGACTGGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:45,55:0:2,0:23.1:1:31.5:1:1:0:60:49:1:0:0 0/1:58:15:8,7:20,23:0.2586:2,2:26.9:1:30:1:0.76708:1.31:60:30:0.2632:0.0345:0.1 -17 7980530 . A C 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00109;SOR=Inf;LSEQ=AGCTAGGTGTGGTGAAAGAG;RSEQ=AAGGGTTGGGTGAGGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:100,253:0:2,0:25.3:1:30:1:1:0:60:69.6:1:0:0.2 0/1:398:11:5,6:118,267:0.0276:2,2:23.1:1:31:1:0.32792:1.88:60:22:0.0285:0:1.1 -17 7980902 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACTGAAATCAGCCTACG;RSEQ=TATTCCATTAAGGAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:32.5:1:27.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 7982693 . C T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13726;SOR=0;LSEQ=ACACAGAGGCTCAGCGGCAG;RSEQ=GCCGCCTGCAGCCCAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:4:2,2:261,69:0.012:2,2:17.3:1:28.3:1:0.19954:3.7629:60:8:0.0121:0:1 0/0:255:0:0,0:178,77:0:2,0:23.4:1:30.8:1:1:0:60:126.5:1:0:0.1 -17 7982927 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06801;SOR=Inf;LSEQ=CGTGACCCGCGCCGCAGGTG;RSEQ=ACAGGGCGCTGGCGACTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:78,311:0:2,0:23.7:1:31.7:1:1:0:60:31.417:1:0:0.1 0/1:270:3:2,1:56,211:0.0111:2,2:17.3:1:26:1:0.11753:7.46:60:6:0.0113:0:1 -17 7982976 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.16144;SOR=Inf;LSEQ=TGGGACGGGGACAGGGACGC;RSEQ=GGGTGCGGGCTTGCCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:66,167:0:2,0:23.4:1:30.6:1:1:0:60:45.6:1:0:0.2 0/1:157:2:1,1:66,89:0.0127:2,2:33.5:1:29:1:1:1.35:60:4:0.013:0:1 -17 7983012 . G A 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61306;SOR=0.80179;LSEQ=TGGGACTGGCGCGGGCGCCG;RSEQ=AGGTGGGGAGAGACGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:25:12,13:119,80:0.1116:2,2:22.6:1:30.4:1:0.28645:1.6079:60:24:0.1076:0:1 0/1:164:15:13,2:103,46:0.0915:2,2:27.8:1:26.9:1:0.2346:2.89:60:6.5:0.0807:0:1.1 -17 7983034 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09058;SOR=Inf;LSEQ=GGTGGGGAGAGACGGGGATG;RSEQ=CCGCGAGGGAGGCCGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:195,81:0:2,0:23.1:1:31.6:1:1:0:60:24.091:1:0:0.2 0/1:226:3:2,1:171,52:0.0133:2,2:23.3:1:23.3:1:0.55328:1.64017:60:2:0.0091:0:1.7 -17 7983379 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14914;SOR=Inf;LSEQ=GGAGGAAAACGAGGCCCCCA;RSEQ=CCTGGCGCTGAGCGGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:45,75:0:2,0:26.4:1:32:1:1:0:60:29:1:0:0.1 0/1:76:2:2,0:11,63:0.0263:2,0:27.5:1:30.5:1:0.02737:0:60:4:0.0267:0:1 -17 7983462 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50706;SOR=0;LSEQ=GCGCGCGCCTCGCTGCCTCT;RSEQ=CCGTCCCACTGCCCCGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:126,25:0.0131:2,2:7:1:28:1:0.31192:4.96183:60:4:0.0132:0:1 0/0:117:0:0,0:110,7:0:2,0:23.4:1:31.2:1:1:0:60:234:1:0:0.1 -17 7983507 . G T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03927;SOR=Inf;LSEQ=GGCCTGCCTAGCACGCCGGA;RSEQ=ACCGCCTGGCTCCCCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:257,124:0:2,0:23:1:31.5:1:1:0:60:41.333:1:0:0.1 0/1:308:4:1,3:211,93:0.013:2,2:10.5:1:27:1:0.09141:6.76021:60:8:0.013:0:1 -17 7983681 . G A 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGATGGGATTCCAGGAAGA;RSEQ=GCCTTCAGAGGGGCTGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:40:16,24:105,248:0.1018:2,2:21.6:1:29.9:1:0.20657:1.57:60:39:0.1008:0:1.1 0/0:360:0:0,0:117,243:0:2,0:23.6:1:30.5:1:1:0:60:89:1:0:0.2 -17 7983799 . A G 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53911;SOR=0.72878;LSEQ=TCTGGGTCCCATGTCTCAAG;RSEQ=TCTTTGCATCTCTAGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:27:7,20:8,26:0.4426:2,2:21.9:1:32.4:1:1:1.14:60:26:0.4483:0:1 0/1:41:15:6,9:4,22:0.3659:2,2:15.1:1:31.3:1:0.13019:3.54:60:30:0.3659:0:1.1 -17 7983927 . GA G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23807;SOR=Inf;LSEQ=CGCCAAGGTTGGGGGAGAGG;RSEQ=AAGTTCTTGCAGGAGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:125,33:0:2,0:23.4:1:30.1:1:1:0:60:51.667:1:0:0.5 0/1:152:2:1,1:110,39:0.0132:2,2:38:1:29.5:1:0.46093:2.79766:60:4:0.0133:0:1 -17 7983969 . G C 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01654;SOR=0.66843;LSEQ=GTTCTCCCGTCACTCACACG;RSEQ=ACTCACATGGGCCCCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:141:105,36:97,49:0.4879:2,2:24.3:1:32.2:1:0.15551:1.47:60:69.5:0.4843:0:1.1 0/1:306:119:72,47:121,64:0.3889:2,2:22.3:1:31.1:1:0.3956:1.23328:60:28.75:0.3846:0:1.2 -17 7984157 . A C 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.10576;LSEQ=CGGGGAGGAGGCAGGCGCCC;RSEQ=GGGGAAAACCATGGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:157:91,66:301,224:0.2302:2,2:25.7:1:30.5:1:0.92682:1.03:60:156:0.2332:0:1.1 0/1:588:18:10,8:304,263:0.0306:2,2:21:1:27.7:1:1:1.08:60:8:0.0278:0:1.2 -17 7984479 . G A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGTGCTCCAGGAGGACGG;RSEQ=GAGCGAGTCATCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:836:0:0,0:384,451:0:2,0:24.3:1:30.5:1:1:0:60:35.304:0.9988:0:0.2 0/1:871:30:13,17:388,452:0.0344:2,2:27.1:1:29.9:1:0.85296:1.12237:60:60:0.035:0:1.2 -17 7984529 . C T 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGGAGACCAAGGAGAGGA;RSEQ=TCAAGGGCTGACCCTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:188,348:0:2,0:24.9:1:32.1:1:1:0:60:52.6:0.9981:0:0.1 0/1:513:42:17,25:184,285:0.0819:2,2:26:1:29.6:1:0.87053:1.05:60:41:0.0812:0:1.2 -17 7984552 . G A 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07294;SOR=0.1595;LSEQ=AAGGGCTGACCCTTGCCCCT;RSEQ=CCCACTTCAGGAAGCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:7:5,2:116,245:0.019:2,2:12.3:1:25.9:1:0.04118:5.25:60:14:0.0194:0:1 0/0:325:1:1,0:116,207:0.0031:2,0:1:0:23:0:0.36111:0:60:2:0.0032:0:1 -17 7984585 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19529;SOR=Inf;LSEQ=AGCAGGAGTTCAGCTTCTGT;RSEQ=CCCCAGGTCGTCTCTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:34,175:0:2,0:22.2:1:31.4:1:1:0:60:28.857:1:0:0.1 0/1:166:2:1,1:37,127:0.012:2,2:9:0:30.5:1:0.4065:3.40:60:4:0.0124:0:1 -17 7984600 . TG T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.14008;SOR=Inf;LSEQ=TCTGTGCCCCAGGTCGTCTC;RSEQ=GGGGGGCCCATGACCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:16,145:0:2,0:21.6:1:30.9:1:1:0:60:52.667:0.9937:0:0.1 0/1:98:2:0,2:9,87:0.0204:2,0:18.5:1:31:1:1:0:60:4:0.0206:0:1 -17 7989047 . G T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54545;SOR=4.34109;LSEQ=GAGTCAGGGAGGACTGGAGA;RSEQ=GTAGCGGGGAGCGCACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:3,1:0.375:2,0:31.3:1:30.7:1:1:0:60:6:0.4286:0:1.3 1/0:4:3:3,0:1,0:0.75:0,0:21:1:30.7:1:1:0:60:6:0.75:0:1.3 -17 7989604 . T TC 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04238;SOR=Inf;LSEQ=GCTCCCAGGCCGCCCACCCC;RSEQ=CTGGCCCCTCACCTAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:4,95:0:1,0:26.1:1:29.7:1:1:0:60:32:1:0:0.1 0/1:54:3:0,3:5,46:0.0556:2,0:31.7:1:33:0:1:0:60:6:0.0577:0:0 -17 7989668 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18937;SOR=Inf;LSEQ=CTCCCTGGACTGACGGAGGG;RSEQ=CAGGATATTGACCTGATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,24:0:1,0:19.5:1:30.8:1:1:0:60:48:1:0:0 0/1:19:2:0,2:0,17:0.1053:1,0:38.5:1:32:1:1:0:60:4:0.1053:0:1 -17 7990437 . G A 72 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03113;SOR=6.25546;LSEQ=CTGGGGAGCCCACTGCCTTC;RSEQ=GAGCTGTGCCTCAGCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:3,0:23,1:0.1111:1,0:34.7:1:30.3:1:1:0:60:6:0.12:0:1 0/1:11:5:5,0:6,0:0.4545:0,0:28:1:31.4:1:1:0:60:10:0.5:0:1.2 -17 7990527 . GACACACAGAC G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=4.000;MSILEN=2;SSF=0.4096;SOR=1.65468;LSEQ=ACCCCTCCCGGGGCCACAAA;RSEQ=ACACACAGACACACACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:5:5,0:112,2:0.042:1,0:13.8:1:30.9:1:1:0:56.6:10:0.0431:0.0084:2.2 0/1:118:8:8,0:107,3:0.0678:1,0:13.5:1:31.9:1:1:0:58.1:16:0.0721:0.0254:2.4 -17 7990545 . G C 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.72331;SOR=1.6319;LSEQ=AAGACACACAGACACACACA;RSEQ=ACACACACAGACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:3,0:149,3:0.0194:1,0:18:0:32.3:1:1:0:40:6:0.0208:0:3 0/1:160:5:3,2:149,5:0.0313:1,2:9:1:28:1:0.01567:18.68658:51:6:0.0256:0:2.2 -17 7990555 . G C 163 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACACACACAGACACACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:39:32,7:121,5:0.1931:1,2:18.5:1:31:1:0.00788:5.22407:58.1:38:0.2436:0:3.4 0/0:187:0:0,0:101,4:0:1,0:20.9:1:31.1:1:1:0:56.8:20:0.9901:0:1.4 -17 7990575 . CAG GACACAC 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.21142;SOR=0.24182;LSEQ=ACAGACACACACACACACAC;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:4:4,0:245,51:0.0129:2,0:36.3:1:31.3:1:1:0:60:8:0.0136:0:1 0/0:318:1:1,0:250,56:0.0031:2,0:19:0:32.5:0:1:0:60:2:0.0033:0:1 -17 7990719 . G A 179 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=55.34713;LSEQ=GAGTCCCGTGTTCCCGACAA;RSEQ=AGGTCGGTGCCTGTGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:791:1:0,1:341,449:0.0013:2,0:27:0:13:0:1:0:60:0:0:0:7 0/1:946:62:27,35:358,526:0.0655:2,2:24.1:1:30.1:1:0.68883:1.13:60:124:0.0665:0:1.2 -17 7990787 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11007;SOR=0;LSEQ=TCTTCAGGAGGCAAGAGGGG;RSEQ=ACTCAGTCCCAGACACCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:1,2:35,240:0.0108:2,2:24.7:1:24.7:1:0.34142:3.41:60:2:0.0074:0:1.3 0/0:301:0:0,0:66,235:0:2,0:22.6:1:31.6:1:1:0:60:59.2:1:0:0.1 -17 7990915 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51706;SOR=0.53848;LSEQ=GGTGGCGAGGTGGGGTGACT;RSEQ=GGCCTGCCAGCCAAATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:0,13:0,19:0.4063:1,1:21.8:1:32.2:1:1:0:60:26:0.4194:0:1.2 0/1:15:4:0,4:2,9:0.2667:2,0:19:1:27:1:1:0:60:3:0.2143:0:1.3 -17 7990958 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=AAAGCTGCTGCCCTTGGTGG;RSEQ=CGGGGTGGGTGCCGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:0:1,0:18.3:1:29.9:1:1:0:60:13:1:0:0.4 0/1:6:2:1,1:1,3:0.3333:2,2:18:1:26.5:1:1:2.45:60:4:0.3333:0:1 -17 7991330 . T G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGGTGGGCGGGGGAGGG;RSEQ=AGGGGGAGGGGCACTAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:31:1:30.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 8107979 . G T 63 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00119;SOR=Inf;LSEQ=ATGCTCATCCCGGCTCCTCA;RSEQ=GGTGAGCCAGCTCTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:19,0:0.0952:1,0:28:1:27.5:1:1:0:60:4:0.0952:0:1 1/1:4:4:3,1:0,0:1:0,2:29:1:31.8:1:1:0:60:8:1:0:1.3 -17 8108331 . A G 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06414;LSEQ=AGATGAGGTCCTGGGCTCCC;RSEQ=TGGGCACGGAAGCGGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:689:682:288,394:3,3:0.9898:2,2:25.8:1:30.7:1:0.70151:1.3674:60:51.462:0.9896:0:1.2 1/1:804:693:285,408:40,70:0.8619:2,2:25.6:1:30.4:1:0.40299:1.22:60:172.25:0.8634:0:2 -17 8108339 . G A 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=28.43536;LSEQ=TCCTGGGCTCCCATGGGCAC;RSEQ=GAAGCGGGGAACTTTAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:72:31,41:234,346:0.1099:2,2:24.9:1:30.4:1:0.7033:1.12:60:144:0.1115:0:2 1/0:760:592:243,349:60,105:0.7789:2,2:26.1:1:30.4:1:0.28283:1.22:60:97.667:0.7782:0:2.1 -17 8108765 . C T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACATAGGAACTCTCCTTTC;RSEQ=CTGCTGCCTGACGGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:44,214:0:2,0:22.8:1:31.1:1:1:0:60:128:0.9961:0:0.1 0/1:204:17:2,15:33,154:0.0833:2,2:22.3:1:29.2:1:0.74261:1.60385:60:34:0.0837:0:1.2 -17 8109598 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07692;SOR=10.6592;LSEQ=AGCTGGGATTACTGGCGTCC;RSEQ=CCACCATGGCCGGCTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:22:1:21:1:1:0:58:1:0.1:0:2.5 1/0:4:3:3,0:1,0:0.75:0,0:17.3:1:30.7:1:1:0:60:6:0.75:0:1 -17 8110256 . GA G 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=1.33321;LSEQ=CCAAAGGCATAAAAGAGCTG;RSEQ=AAAGATGATAGGAGCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:2:1,1:77,164:0.0082:2,2:26:1:28:1:0.53984:2.12:60:4:0.0084:0:0 0/1:274:3:2,1:88,183:0.0109:2,2:42.7:1:31.7:1:0.25196:4.14:60:6:0.011:0:0 -17 8110260 . A T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09692;SOR=0;LSEQ=AGGCATAAAAGAGCTGGAAA;RSEQ=GATGATAGGAGCAAACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:3:1,2:70,154:0.0132:2,2:32.3:1:25:1:1:1.10:60:2:0.009:0:3 0/0:266:0:0,0:88,178:0:2,0:22.9:1:30.5:1:1:0:60:132:1:0:0.1 -17 8110286 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49835;SOR=0;LSEQ=TAGGAGCAAACTGGGGTCAG;RSEQ=CGTGGCCCAGGCCGGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:42,105:0.0134:2,2:32.5:1:30:1:0.49528:2.48:60:4:0.0136:0:1 0/0:146:0:0,0:37,109:0:2,0:21:1:29.4:1:1:0:60:47.667:1:0:0.2 -17 8110298 . C T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09391;SOR=Inf;LSEQ=GGGGTCAGACGTGGCCCAGG;RSEQ=CGGGGACACCAGGGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:33,93:0:2,0:24.2:1:31.2:1:1:0:60:41:1:0:0.1 0/1:106:3:1,2:24,79:0.0283:2,2:11.7:1:22:1:0.55774:1.64:60:2:0.0196:0:3 -17 8110437 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21458;SOR=Inf;LSEQ=TGGATGAAGTGGGGCTGAAT;RSEQ=AGGAGCTGGGGGTGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:156,52:0:2,0:22.1:1:31.3:1:1:0:60:25:1:0:0.1 0/1:180:2:0,2:131,47:0.0111:2,0:5:1:26:1:0.073:0:60:4:0.0113:0:1 -17 8110764 . C A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=10.96566;LSEQ=TTTCTCTCTGCTTCCTCATC;RSEQ=CATCCTGTCCTCCGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:39:21,18:141,122:0.1291:2,2:26.1:1:29.4:1:1:1.01:60:18.5:0.1267:0:1.2 1/0:295:183:96,87:65,47:0.6203:2,2:25.5:1:29.6:1:0.39934:1.25236:60:182:0.619:0:1.1 -17 8110765 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24874;SOR=Inf;LSEQ=TTCTCTCTGCTTCCTCATCC;RSEQ=ATCCTGTCCTCCGCCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:161,138:0:2,0:25:1:31.7:1:1:0:60:98.667:1:0:0.3 0/1:299:3:1,2:163,133:0.01:2,2:25:1:28:1:0.59089:2.44394:60:6:0.0101:0:1 -17 8113163 . G GT 31 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTATTTCTATTTGCTGTCTA;RSEQ=TTTTTTTTTTTTCAGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:34:1:31.5:1:1:0:60:4:0.4:0:1 1/1:1:1:0,1:0,0:1:0,0:21:0:24:0:1:0:60:2:1:0:1 -17 8113186 . A G 96 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTTTTCAGGATATGG;RSEQ=TTGGGAATCATGGCCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:1:0,2:28.6:1:32.1:1:1:0:60:16:1:0:1 1/1:1:1:0,1:0,0:1:0,0:44:0:28:0:1:0:60:2:1:0:1 -17 8113380 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49857;SOR=Inf;LSEQ=ACTTGGGACCCGTACTTTGG;RSEQ=GCATAACGGGGAAGAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:150,9:0:2,0:23.4:1:30:1:1:0:60:38.75:1:0:0.1 0/1:164:2:2,0:143,16:0.0122:2,0:27:1:28:1:1:0:60:4:0.0127:0:1 -17 8113607 . AAG A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.32348;SOR=1.8875;LSEQ=AGCCGTGAGAAGCAGAGAAA;RSEQ=AGAGAGAGAGGGAGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:5:2,3:78,250:0.015:2,2:18.8:1:31.2:1:0.59721:2.13:60:10:0.0151:0.006:0.4 0/1:430:12:5,7:130,288:0.0279:2,2:26.8:1:29.6:1:0.52928:1.58:58.3:24:0.0282:0.0023:0.3 -17 8113620 . G C 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07644;SOR=0;LSEQ=AGAGAAAAAGAGAGAGAGAG;RSEQ=GAGGGGTTGGACCGATCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:3:1,2:48,196:0.0121:2,2:36:1:23.3:1:0.48644:2.03:60:2:0.0086:0:1.7 0/0:335:0:0,0:94,239:0:2,0:21.6:1:28.9:1:1:0:60:13.478:0.9968:0:0.2 -17 8383060 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAAGCAATCCCTTCTATGGG;RSEQ=AGAAGAAAGGCTCTGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:71,4:0.026:2,2:11:1:28:1:0.12645:15.99265:60:4:0.0267:0:2 0/0:37:0:0,0:36,1:0:1,0:21.1:1:30.9:1:1:0:60:36:1:0:0.9 -17 8383105 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.22622;SOR=Inf;LSEQ=ATACTGCATTTGTTCTCTGG;RSEQ=AGCAAATTAGCATTTCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:122,34:0:2,0:25.7:1:32.1:1:1:0:60:51:1:0:1.2 0/1:142:2:1,1:110,30:0.0141:2,2:5.5:1:27:1:0.39017:3.62301:60:4:0.0145:0:2.5 -17 8383112 . T C 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGTTCTCTGGCAGCAAA;RSEQ=TAGCATTTCATGGGCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:174:173:126,47:0,1:0.9943:0,2:25.4:1:31.9:1:0.27586:0:60:85.5:0.9942:0:1.2 1/1:169:169:132,37:0,0:1:0,2:23.9:1:31.2:1:1:0:60:168:1:0:1.2 -17 8383199 . C T 245 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1473;SOR=0.79184;LSEQ=CCTAGGAAATCACGGGGCGC;RSEQ=GTCCTAAAGCCCAGCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:241:114,127:43,60:0.6986:2,2:27.4:1:30.5:1:0.40819:1.25:60:79.333:0.7021:0:1.6 1/0:445:288:150,138:79,78:0.6472:2,2:26.6:1:30:1:0.76614:1.07:60:56.6:0.6476:0:1.7 -17 8383253 . G C 256 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57189;SOR=2.85803;LSEQ=GATGCCGTCTGTCCTCCCAG;RSEQ=CTCTGAATGCTCACAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:222:220:72,148:0,0:0.991:0,2:24.9:1:31.1:1:1:0:60:43:1:0:1.6 1/1:316:315:123,192:0,0:0.9968:0,2:24.4:1:30.9:1:1:0:60:104:0.9968:0:1.6 -17 8383262 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64124;SOR=2.20646;LSEQ=TGTCCTCCCAGGCTCTGAAT;RSEQ=CTCACAGCTCTTCTCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:1,0:58,135:0.0052:2,0:1:0:24:0:0.30412:0:60:2:0.0052:0:2 0/1:265:3:2,1:95,167:0.0113:2,2:29.3:1:27.7:1:0.55628:3.50:60:6:0.0115:0:2.3 -17 8383311 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23573;SOR=0;LSEQ=CAACTTCTGTGTCCCACTCT;RSEQ=GTTATATGTGTTCTCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:5,69:0.0263:2,2:22.5:1:28:1:0.15263:12.69:60:4:0.0267:0:2 0/0:80:0:0,0:4,76:0:2,0:21.3:1:30.7:1:1:0:60:79:1:0:1 -17 8383344 . G GC 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.41795;SOR=1.68855;LSEQ=CTCTGCCCACGTGGTGGGGA;RSEQ=CCCCCCCGAAAGGGGCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:8:0,8:1,25:0.2353:1,0:17.6:1:31.5:1:1:0:59.4:16:0.2353:0.0882:0.3 0/1:32:11:0,11:0,20:0.3438:1,0:26.9:1:31.5:1:1:0:60:22:0.3438:0.0313:0 -17 8384077 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATCTCTCACCTGGACTG;RSEQ=TGGGTGGCCTCCCGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:28:1:1:0:60:4:1:0:1 -17 8693552 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50387;SOR=Inf;LSEQ=TCTGTTTAATTAACCTGAGG;RSEQ=CAGTGACTGTTTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:68,13:0:2,0:23:1:31.6:1:1:0:60:19.25:1:0:0.2 0/1:102:2:1,1:75,25:0.0196:2,2:11.5:1:28.5:1:0.44671:2.96126:60:4:0.0196:0:1 -17 8693563 . TTTG T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.12484;SOR=Inf;LSEQ=AACCTGAGGCCAGTGACTGT;RSEQ=TTGTTGTTGTTGTTTTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:83,27:0:2,0:21.6:1:30.2:1:1:0:60:109:1:0:0.3 0/1:126:4:3,1:88,34:0.0317:2,2:22.5:1:30.1:1:1:1.16:60:8:0.0323:0.0079:1 -17 8693585 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50118;SOR=Inf;LSEQ=TGTTGTTGTTGTTGTTTTAT;RSEQ=CATGAAATGTGACCAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:97,45:0:2,0:25.8:1:31.2:1:1:0:60:141:1:0:0.4 0/1:165:2:2,0:106,55:0.0121:2,0:16:1:29.5:1:0.5501:0:60:4:0.0122:0:1 -17 8693643 . T C 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2909;SOR=1.21927;LSEQ=ATTTCAGAGGACAGCCCCTG;RSEQ=GACATTCGTCAGCTTATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:251:136:69,67:56,59:0.5418:2,2:26.4:1:30.6:1:0.80038:1.08:60:44.333:0.5407:0:1.1 1/0:276:163:82,81:60,52:0.5906:2,2:24.6:1:30.9:1:0.62456:1.13923:60:326:0.5927:0:1.1 -17 8693981 . T A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATCCCCACGCGTACATT;RSEQ=GAATTCTCAAAAGCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:40:1:32.5:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 8694016 . T C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTCCAAAAGCATTGC;RSEQ=AATAAAAAATGTAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:14.3:1:31.7:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 9756002 . G T 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20629;SOR=4.5193;LSEQ=ATTTAATCTTGGTGTTGATG;RSEQ=TTTTGAGTCTTTTCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:10,5:0.0625:2,0:29:0:32:0:0.375:0:60:2:0.0625:0:2 0/1:21:5:3,2:11,5:0.2381:2,2:31:1:26.4:1:1:1.43927:60:4:0.2:0:1.4 -17 9756083 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4878;SOR=Inf;LSEQ=ATTTCTCCACTGCTGCTTTT;RSEQ=CTTCAGTTTCCTCATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:19.7:1:29.7:1:1:0:60:19:1:0:0.4 0/1:21:2:1,1:9,9:0.0952:2,2:15:0:33:0:1:1:60:4:0.0952:0:1 -17 9756171 . A T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.7353;LSEQ=TCCATCAGCAGGAAGTTTTA;RSEQ=TTTTTTCTGTGGAAACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:9,12:0.0455:2,0:1:0:25:0:1:0:60:2:0.0476:0:2 0/1:39:3:3,0:18,18:0.0769:2,0:17.3:1:31.3:1:0.23482:0:60:6:0.0811:0:2 -17 9756198 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77659;SOR=1.24188;LSEQ=CTGTGGAAACTTGCTACCAC;RSEQ=TCCAGGGGCAGATTACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:4,7:5,3:0.5789:2,2:28.9:1:31.1:1:0.36985:2.74899:60:22:0.5789:0:1.2 1/0:38:24:12,12:6,8:0.6316:2,2:26.9:1:30:1:0.74487:1.32:58.7:11:0.6111:0:1.3 -17 9756374 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52425;SOR=Inf;LSEQ=AGCCCCCATGGAAACCATTG;RSEQ=CTGTACAGACATTTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:23.1:1:31.4:1:1:0:60:21:1:0:0.1 0/1:37:2:1,1:18,17:0.0541:2,2:32.5:1:31:0:1:1.05721:60:4:0.0571:0:1 -17 10379676 . C A 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0357;SOR=0.7615;LSEQ=CTTGAACCTGTTTTTCAAAA;RSEQ=TTCTATCTTGGTGACATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:449:233:114,119:106,110:0.5189:2,2:26.8:1:30.6:1:1:1.00589:60:232:0.5225:0:1.1 0/1:550:248:117,131:153,148:0.4509:2,2:26.6:1:29.8:1:0.44019:1.15717:60:40.333:0.4465:0:1.2 -17 10379755 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23202;SOR=Inf;LSEQ=TCACCACTTACCCCTCCTGG;RSEQ=TGTCTACACCTTTCCTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:36,155:0:2,0:24.6:1:32.3:1:1:0:60:190:1:0:0.3 0/1:178:2:1,1:46,129:0.0112:2,2:27.5:1:28:1:0.46167:2.79:60:4:0.0113:0:1 -17 10552404 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17967;SOR=0;LSEQ=TGACTTTCCAATCCTAGGAC;RSEQ=AACCAAATCAGCAGCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:136,56:0.0103:2,2:14.5:1:28:1:0.50238:2.41602:60:4:0.0105:0:1.5 0/0:263:0:0,0:171,92:0:2,0:23.2:1:30.6:1:1:0:60:130.5:1:0:0.3 -17 10552409 . A T 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6433;SOR=2.16826;LSEQ=TTCCAATCCTAGGACCAACC;RSEQ=AATCAGCAGCATGTCTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:1:0,1:143,64:0.0048:2,0:1:0:23:0:0.3125:0:60:2:0.0048:0:2 0/1:289:3:0,3:180,106:0.0104:2,0:13.3:1:20.7:1:0.05273:0:60:2:0.007:0:1.3 -17 10552488 . G A 246 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0774;SOR=0.7842;LSEQ=GTTGGGGATCTCTTGACTGA;RSEQ=CATTCCTTTAACACTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:262:131,131:74,68:0.6485:2,2:27.2:1:29.7:1:0.75462:1.08801:60:64.5:0.645:0:1.2 1/0:526:311:163,148:101,114:0.5913:2,2:25.4:1:29.8:1:0.24893:1.24:60:622:0.5924:0:1.1 -17 10552622 . C T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.71251;SOR=1.22482;LSEQ=TGGTATATGTGATTCTTCCA;RSEQ=AAAAGAACAAGCTCTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:45:3,42:4,19:0.6618:2,2:20.7:1:28.3:1:0.21572:2.89607:60:21.5:0.6515:0:1 1/0:68:48:2,46:1,19:0.7059:1,1:21.1:1:28.6:1:1:1.20698:60:96:0.7059:0:1.1 -17 10841682 . A G 52 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.87089;LSEQ=GGGAACTAGTGTTTGTGAGA;RSEQ=GAGAATGAACGTTGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:11.7:1:33.3:1:1:0:60:6:0.3333:0:2.7 1/0:2:1:1,0:1,0:0.5:0,0:5:0:33:0:1:0:60:2:0.5:0:3 -17 10841701 . G T 47 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=2.73861;LSEQ=AAGAGAATGAACGTTGTTTG;RSEQ=AATATGTTGGTGTGAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:0.25:0,0:18:1:30:1:1:0:60:6:0.25:0:2.7 1/0:2:1:1,0:1,0:0.5:0,0:24:0:32:0:1:0:60:2:0.5:0:3 -17 10841749 . A G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02654;SOR=5.98999;LSEQ=GCACCTCTTCTTGAAGACCC;RSEQ=GTTGGAGAGAAGGTAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:2,3:12,4:0.2381:2,2:24.4:1:29.2:1:0.28001:4.14056:60:10:0.2381:0:1.8 1/0:12:8:6,2:3,1:0.6667:2,2:24.8:1:28.6:1:1:1:60:16:0.6667:0:1.6 -17 10841831 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50166;SOR=Inf;LSEQ=TAAACTCTCTTAGAAAGTGG;RSEQ=GACAGCGGGGAAGTTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:3,15:0:2,0:26.4:1:31.5:1:1:0:60:36:1:0:0.1 0/1:25:2:1,1:9,14:0.08:2,2:7:0:32:0:1:1.53:60:4:0.0833:0:2.5 -17 10841838 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4958;SOR=Inf;LSEQ=TCTTAGAAAGTGGGGACAGC;RSEQ=GGGAAGTTGGGTAATCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:2,13:0:2,0:28.3:1:31.5:1:1:0:60:30:1:0:0.1 0/1:20:2:1,1:7,11:0.1:2,2:30:1:29.5:1:1:1.54:60:4:0.1:0:1 -17 11396226 . C T 200 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=0;LSEQ=GCTTCTGCTCCTCTCTTCCC;RSEQ=TCCCCTGTCCCACAGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:77,5:0,0:1:0,2:23.3:1:31.6:1:1:0:60:164:1:0:1.3 1/0:82:50:47,3:30,2:0.6098:2,2:22.1:1:31.1:1:1:1.04:60:49:0.6049:0:1.4 -17 11396312 . T C 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGAACTTGGAGATTGGCCAT;RSEQ=TGTCACTAGGTGTCTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:286:286:158,128:0,0:1:0,2:25.2:1:31.6:1:1:0:60:285:1:0:1.6 1/0:361:249:143,106:54,58:0.6898:2,2:23.5:1:31:1:0.11081:1.45:60:61.25:0.6863:0:1.7 -17 11396377 . C T 250 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01718;LSEQ=GCCTCAACACTAACATTTAT;RSEQ=CAACTTTTCCATGGAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:329:327:167,160:0,0:0.9939:0,2:25.8:1:30:1:1:0:60:80.75:0.9969:0:1.5 1/0:391:288:131,157:46,57:0.7366:2,2:25.3:1:29.1:1:0.90861:1.03:60:71:0.7358:0:1.5 -17 11396420 . G A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25032;SOR=Inf;LSEQ=AATGTTCTGGCTAATGTTTT;RSEQ=GCTAATGATTGCTGTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:81,130:0:2,0:26:1:31.1:1:1:0:60:41.2:1:0:0.8 0/1:234:3:2,1:89,142:0.0128:2,2:21:1:23.3:1:0.56174:3.17:60:6:0.013:0:2 -17 11396441 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60314;SOR=2.25891;LSEQ=GCTAATGATTGCTGTGAGTC;RSEQ=AGAGGACCTCCCTCATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:0,1:55,125:0.0055:2,0:6:0:14:0:1:0:60:0:0:0:2 0/1:161:2:1,1:52,106:0.0124:2,2:6:1:28:1:1:2.03:60:4:0.0126:0:1.5 -17 11396483 . A C 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00269;SOR=Inf;LSEQ=TAGCAGGACCACCTCCTGAC;RSEQ=ACTGTGACCACTTAGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:11,94:0:2,0:27.1:1:30.2:1:1:0:60:104:1:0:0.2 0/1:65:6:0,6:9,50:0.0923:2,0:25.3:1:29.7:1:0.58379:0:60:5:0.0794:0:1.2 -17 11396881 . G A 40 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTTTTGGTACCATGTG;RSEQ=ATACACGCGTGCGCGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:32:1:25.7:1:1:0:60:2:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 11396889 . CGT C 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTACCATGTGGATACACG;RSEQ=GCGCGCGCACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:22.3:1:29:1:1:0:60:6:1:0.6667:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 11396900 . A G 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGATACACGCGTGCGCGCGC;RSEQ=CACACACACACACATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 11914107 . T C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCACCTCAGGCTTCTTCC;RSEQ=ACTGGTTCTCACGAAGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:38.7:1:32:1:1:0:60:6:1:0:1 1/1:2:2:2,0:0,0:1:0,0:19.5:1:32:0:1:0:60:4:1:0:1 -17 11914348 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50891;SOR=Inf;LSEQ=CAGCATGCTGGGGAACATTG;RSEQ=AGACTCTTCCAGTTTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:37,41:0:2,0:30:1:28.6:1:1:0:59.7:77:1:0:0.2 0/1:106:2:1,1:56,48:0.0189:2,2:42.5:1:32.5:1:1:1.16496:60:4:0.0192:0:1 -17 11914382 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21565;SOR=0;LSEQ=TTAGCCATGGTGACACCTGT;RSEQ=GGGCATTCCTTTTTGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:34,46:0.0244:2,2:23.5:1:29:1:1:1.35:60:4:0.025:0:1 0/0:94:0:0,0:43,51:0:2,0:23.2:1:30.4:1:1:0:59.5:46:1:0:0.1 -17 11914391 . CT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.23625;SOR=0;LSEQ=GTGACACCTGTGGGGCATTC;RSEQ=TTTTGAACAGTACTCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:32,45:0.0253:2,2:13.5:1:30:1:1:1.40:60:4:0.0256:0:0 0/0:83:0:0,0:34,49:0:2,0:20.9:1:30.3:1:1:0:59.6:166:1:0:0.1 -17 11924199 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26377;SOR=Inf;LSEQ=GCCGCTCGGCTCTTCACTCC;RSEQ=AACAATGGCGGCTCCGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:0:2,0:20.9:1:31.3:1:1:0:60:32:1:0:0.3 0/1:47:3:1,2:21,23:0.0638:2,2:11.3:1:27:1:1:1.80368:60:6:0.0638:0:1.3 -17 11924222 . AGCG A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.09343;SOR=0;LSEQ=CAATGGCGGCTCCGAGCCCG;RSEQ=GCGGCGGCGGCTCCGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:0,2:13,15:0.0667:2,0:13:1:30:1:0.49195:0:60:4:0.0667:0.0333:0.5 0/0:67:0:0,0:32,35:0:2,0:21.7:1:31.9:1:1:0:60:21.333:1:0:0.5 -17 11924225 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.09987;SOR=0;LSEQ=TGGCGGCTCCGAGCCCGAGC;RSEQ=GCGGCGGCGGCTCCGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:13,15:0.0645:2,2:27.5:1:29.5:1:1:1.15:60:4:0.0667:0:1 0/0:66:0:0,0:32,34:0:2,0:22.1:1:30.5:1:1:0:60:132:1:0:0.5 -17 11924239 . CG C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14932;SOR=0;LSEQ=CCGAGCGGCGGCGGCGGCTC;RSEQ=GGGGCGGCAGCGGCAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:35,29:0.0303:2,2:12.5:1:32.5:1:1:1.20344:60:4:0.0323:0:1 0/0:104:0:0,0:54,49:0:2,0:14.9:1:29:1:1:0:60:24.75:0.99:0:0.5 -17 11924248 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=1;SOR=1.38246;LSEQ=GGCGGCGGCTCCGGGGGCGG;RSEQ=AGCGGCAGCGGCACCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:1:0,1:44,37:0.0122:2,0:1:0:24:0:0.46341:0:60:2:0.013:0:2 0/1:119:2:1,1:64,53:0.0168:2,2:9.5:1:27:1:1:1.20562:60:4:0.0172:0:1.5 -17 11924257 . C T 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16187;SOR=0.16776;LSEQ=TCCGGGGGCGGCAGCGGCAG;RSEQ=GGCACCCCCGGCCCCGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:4:1,3:56,44:0.0385:2,2:7.8:1:29:1:0.3257:3.77197:60:8:0.0392:0:1 0/0:151:1:0,1:85,65:0.0066:2,0:1:0:23:0:0.43709:0:60:2:0.0068:0:1 -17 11924279 . TC T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14744;SOR=0;LSEQ=GCACCCCCGGCCCCGTAGGG;RSEQ=CCCGGCGCCAGGCCACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:106,77:0.0108:2,2:49.5:1:31.5:1:1:1.37419:60:4:0.0109:0:1 0/0:296:0:0,0:161,131:0:2,0:19.4:1:30.9:1:1:0:60:57.4:0.9897:0:0.4 -17 11924285 . G T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65302;SOR=2.57481;LSEQ=CCGGCCCCGTAGGGTCCCCG;RSEQ=CGCCAGGCCACCCGGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:0,1:112,84:0.0051:2,0:1:0:28:0:0.43147:0:60:2:0.0052:0:1 0/1:308:4:1,3:167,137:0.013:2,2:8.8:1:27.3:1:0.33326:3.64257:60:8:0.0137:0:1.3 -17 11924302 . C T 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70934;SOR=1.64224;LSEQ=CCGGCGCCAGGCCACCCGGC;RSEQ=GTCAGCAGCATGCAGGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:2:1,1:142,117:0.0077:2,2:42:0:22:1:1:1.21277:60:1:0.0039:0:1.5 0/1:399:5:2,3:211,183:0.0125:2,2:30:1:28.6:1:0.66754:1.72713:60:10:0.0129:0:1 -17 11924308 . C A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.06012;SOR=0;LSEQ=CCAGGCCACCCGGCCGTCAG;RSEQ=AGCATGCAGGGTAAGGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:2,1:146,118:0.0112:2,2:16.3:1:22.3:1:1:1.61:60:2:0.0076:0:1 0/0:413:0:0,0:221,192:0:2,0:25.5:1:31.8:1:1:0:60:30.769:1:0:0.4 -17 11924335 . C T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.05912;SOR=0;LSEQ=CAGGGTAAGGAACGCGGCCG;RSEQ=GCCGAGATCCCAGCCCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:3:2,1:113,109:0.0133:2,2:18.3:1:23.7:1:1:1.92:60:2:0.0092:0:1.7 0/0:351:0:0,0:178,173:0:2,0:27.2:1:30.2:1:1:0:60:24.071:1:0:0.3 -17 11924367 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.18116;SOR=0;LSEQ=AGCCCCCTAGCGCGGCAACC;RSEQ=GCGTCGTCGCGGCCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:61,82:0.0138:2,2:12.5:1:29:1:1:1.34:60:4:0.014:0:1.5 0/0:195:0:0,0:82,110:0:2,0:21.7:1:28.8:1:1:0:60:37.4:0.9842:0:0.2 -17 11924373 . G A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.39102;SOR=3.13736;LSEQ=CTAGCGCGGCAACCCGCGTC;RSEQ=TCGCGGCCTGCCCCAGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:1,0:47,75:0.0081:2,0:1:0:25:0:0.39024:0:60:2:0.0084:0:1 0/1:159:4:3,1:60,95:0.0252:2,2:13.3:1:26.5:1:0.30151:4.70:60:8:0.0258:0:1 -17 11935504 . TA T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.106;SOR=Inf;LSEQ=GTTTTATTCAAAATTTAATA;RSEQ=AAAATGCAATGTCATGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:228,96:0:2,0:22.8:1:28.6:1:1:0:60:80:0.9969:0:0.1 0/1:293:3:1,2:193,97:0.0102:2,2:7.7:1:27:1:0.2646:3.95918:60:6:0.0103:0.0068:0.7 -17 11958053 . A G 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTATTTTTTCTTAGTTT;RSEQ=AGAAATTCCTCATTGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:40,0:0,0:1:0,1:21.5:1:31.9:1:1:0:60:19:1:0:1.2 1/1:21:21:21,0:0,0:1:0,1:17.1:1:31.5:1:1:0:60:42:1:0:1 -17 11958145 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49867;SOR=0;LSEQ=TGGTGTGACTTTCTTATGCC;RSEQ=TCAGAATAGTACCTGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:135,41:0.0112:2,2:25:1:30:1:0.41725:3.26525:60:4:0.0115:0:1 0/0:173:0:0,0:135,36:0:2,0:24:1:29.9:1:1:0:60:41.75:0.994:0:0.1 -17 11973193 . T A 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21963;SOR=0.21564;LSEQ=CTTACCTTTATTTTCCTGTC;RSEQ=AAGGAAGATTAGTCATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:5:4,1:204,287:0.0101:2,2:16:1:25.6:1:0.16665:5.61:60:4:0.0084:0:1 0/0:457:1:1,0:190,266:0.0022:2,0:1:0:28:0:0.41794:0:60:2:0.0022:0:1 -17 11973293 . A AGC 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.05334;SOR=2.37442;LSEQ=TGCTGAGGAGACAGTAAAAC;RSEQ=GCTTGGGGCGTTTTAGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:12:0,12:0,124:0.0882:1,0:26.6:1:31.1:1:1:0:60:24:0.0889:0.0221:0.7 0/1:80:15:0,15:0,65:0.1875:1,1:24.7:1:30.9:1:1:0:59.3:30:0.1899:0.05:0.8 -17 11999052 . A T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20144;SOR=Inf;LSEQ=AGCTGACTAATGAATATCTA;RSEQ=TTGGGACAAATGAAGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:44,201:0:2,0:24.3:1:30.8:1:1:0:60:80.667:1:0:0.1 0/1:200:2:1,1:32,166:0.01:2,2:18:1:25:1:0.30347:5.12:60:4:0.0101:0:1 -17 11999147 . G A 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.36709;SOR=0;LSEQ=TATCTTAGTGTTTAACCATG;RSEQ=TAATTTACATATTAACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:50:1,49:0,0:1:0,1:24.8:1:31.8:1:1:0:60:100:1:0:1 1/1:29:28:1,27:0,1:0.9655:0,1:25:1:30.7:1:1:0:60:56:0.9655:0:1.1 -17 11999212 . TTG T 60 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=31;MSI=16.000;MSILEN=2;SSF=1;SOR=1.11662;LSEQ=GGGGTGAATCACACGTGTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:1,3:1,6:0.3077:2,2:29.8:1:30:1:1:1.87:60:8:0.3077:0:0.3 0/1:3:1:0,1:0,2:0.3333:0,0:41:0:30:0:1:0:60:2:0.3333:0:0 -17 12013376 . GA G 31 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCTCAAAATAAAAAGG;RSEQ=AAAAAAAAAAGGAAATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:6.5:1:31:1:1:0:60:4:0.25:0.125:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 12016528 . G T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22088;SOR=4.54185;LSEQ=GAAGAAGCTAATTGTATACT;RSEQ=AATGATATCTATGTCTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:1:1,0:272,141:0.0024:2,0:40:0:13:0:1:0:60:0:0:0:3 0/1:459:5:3,2:288,166:0.0109:2,2:11.4:1:26.4:1:1:1.15625:60:4:0.0088:0:2.4 -17 12016736 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51184;SOR=0;LSEQ=TGCACAGAGAGCCTGTGCTC;RSEQ=TTTGTGCTGGCCATTAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:14,154:0.0118:2,2:10.5:1:29:1:0.16916:10.66:60:4:0.012:0:1 0/0:122:0:0,0:16,106:0:2,0:25:1:29.9:1:1:0:60:60:1:0:0.1 -17 12028818 . G GA 101 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.23103;SOR=1.85512;LSEQ=CACTATGGTTTTAAGTTGCT;RSEQ=AAAAAAAAAAAGTATGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:9:0,9:1,95:0.0833:1,0:24.8:1:31.6:1:1:0:60:18:0.09:0:1.6 0/1:76:11:1,10:0,65:0.1447:1,2:31.9:1:29.3:1:0.14474:0:60:10:0.1449:0:0.3 -17 12032395 . C A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24809;SOR=Inf;LSEQ=TAGATTTTTTTGTGGCCCTT;RSEQ=CAGTGGGGAGTAGTAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:143,38:0:2,0:20.8:1:31.2:1:1:0:60:89.5:1:0:0.2 0/1:186:3:2,1:147,35:0.0161:2,2:25:1:20.3:1:0.47962:2.08983:60:2:0.011:0:3 -17 12042934 . T A 73 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11415;SOR=Inf;LSEQ=TTAATATTTTTTCTAATTTT;RSEQ=AACTAATCATCCTACACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:22.4:1:26:1:1:0:60:4:1:0:0.4 0/1:13:6:6,0:6,1:0.4615:2,0:25.3:1:28.5:1:1:0:60:12:0.4615:0:1 -17 12043099 . A T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.24935;SOR=Inf;LSEQ=ATATTTCATCTGTGAAAAGA;RSEQ=AAATACTTAGGCAAATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:202,62:0:2,0:24.7:1:30.1:1:1:0:60:131:1:0:0.1 0/1:281:3:1,2:205,73:0.0107:2,2:6:1:25.7:1:0.1747:5.57502:60:6:0.0107:0:1 -17 12043531 . A AG 74 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGAAAAAAATTAGTGAAA;RSEQ=TTTGTGTTTATTCTGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:20.6:1:31.9:1:1:0:60:10:1:0.2:0.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 12043573 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATTCATGCAAATTTAC;RSEQ=TCATATAGCCTATTCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 12044417 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49899;SOR=Inf;LSEQ=ATTGGAAAATGTTCAGTTTG;RSEQ=GCTGTCATACAAACTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:128,10:0:2,0:23.5:1:31.3:1:1:0:60:137:1:0:0.1 0/1:149:2:1,1:133,14:0.0134:2,2:9:1:27.5:1:0.19182:9.21231:60:4:0.0137:0:2 -17 13964644 . A T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=16.71238;LSEQ=TATCCTTTTTTGGATAGCTG;RSEQ=CATGATTCTAGTTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:6:5,1:64,20:0.0667:2,2:27.2:1:30:1:1:1.56:60:12:0.0667:0:1.2 1/0:82:45:31,14:26,11:0.5488:2,2:20.6:1:28.6:1:1:1.06657:60:44:0.5432:0:1 -17 13964744 . A C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=14.71047;LSEQ=TGAATGCATCAACCAGGATG;RSEQ=AATGAACAGACAACTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:15:8,7:83,85:0.082:2,2:26.8:1:32.3:1:0.79451:1.17:60:30:0.0829:0:1.1 1/0:223:127:63,64:47,49:0.5695:2,2:25.9:1:31.1:1:1:1.03:60:30.75:0.5616:0:1.1 -17 15935500 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49565;SOR=0;LSEQ=TGGGCTGGCTCTCCTGAAAA;RSEQ=TCTCAGGGAATAAGTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:54,2:0.0345:1,2:15:1:28:0:0.10163:22.24886:60:4:0.0351:0:1 0/0:58:0:0,0:57,1:0:1,0:23.6:1:31:1:1:0:60:28:1:0:0.1 -17 15935574 . C T 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00423;SOR=10.60923;LSEQ=AACCACAAAAACTAGAGATC;RSEQ=CTCTCCTGCACCCTGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:0,1:185,79:0.0038:2,0:1:0:24:0:0.30189:0:60:2:0.0038:0:1 0/1:311:12:8,4:199,100:0.0386:2,2:24.7:1:30.8:1:1:1.01:60:24:0.0392:0:1.1 -17 15935837 . A C 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=GTTTTCATTGTCATGAACAT;RSEQ=ACTGGTATTTCATCCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:44,158:0:2,0:23.4:1:29.8:1:1:0:60:100:1:0:0.1 0/1:229:13:3,10:54,162:0.0568:2,2:28:1:30.3:1:1:1.11061:60:12:0.0529:0:1.2 -17 15935842 . G T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.36459;LSEQ=CATTGTCATGAACATAACTG;RSEQ=TATTTCATCCAATCCAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:34,149:0.0108:2,2:18.5:1:32:0:0.34342:4.33:60:4:0.011:0:2 0/1:204:3:1,2:47,153:0.0147:2,2:26.3:1:29.7:1:0.5569:1.62:60:6:0.0149:0:3 -17 15938342 . GA G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49789;SOR=Inf;LSEQ=ATGATTATATATTGCTAAAT;RSEQ=AAAAAAAGCAGAATGGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:1,115:0:1,0:23.2:1:30.2:1:1:0:60:57:1:0:0 0/1:118:2:0,2:2,114:0.0169:1,0:35:1:33:0:1:0:60:4:0.0172:0:0 -17 15942602 . CT C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.19195;SOR=Inf;LSEQ=CTGGGTAGGTTTTCAAAAAC;RSEQ=TTTTTAAGTAACGGAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:84,0:0:1,0:24.6:1:31.4:1:1:0:60:168:1:0:0 0/1:66:2:2,0:61,3:0.0303:1,0:11:1:31.3:1:1:0:60:4:0.0308:0.0152:0 -17 15943110 . C CT 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.91424;LSEQ=AGGACCCACCACACAGAGAC;RSEQ=TTTTTTTTTGGAGACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:0,2:2,40:0.0455:1,0:33:1:29.5:1:1:0:60:4:0.0455:0:0 0/1:24:1:0,1:1,22:0.0417:1,0:42:0:29:0:1:0:60:2:0.0435:0:1 -17 15943144 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66685;SOR=2.0749;LSEQ=ACAGAGTCTCTCTCTGTCGC;RSEQ=CCCAGGCTGGAGTGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:1,6:0,9:0.4375:0,2:25.4:1:32.7:1:0.4375:0:60:14:0.4375:0:1 1/0:8:5:0,5:0,3:0.625:0,0:19.4:1:32.2:1:1:0:60:10:0.625:0:1 -17 15943331 . G C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCTGATCTCGAATTCC;RSEQ=AACCTCAGGTGATCCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:19.7:1:30.3:1:1:1.73:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 15943672 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34271;SOR=3.46697;LSEQ=GCAGTCACTCCCCTGGTATA;RSEQ=AGTTGGTACTCAGTACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:1:1,0:263,82:0.0029:2,0:31:0:33:0:1:0:60:2:0.0029:0:1 0/1:301:3:1,2:223,75:0.01:2,2:6.7:1:27:1:0.16191:5.90344:60:6:0.01:0:1 -17 15943910 . T C 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05763;SOR=1.98762;LSEQ=AAAATTAATCTTTTTATTTT;RSEQ=CATGATCTCAACCTTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:40:0,40:0,34:0.5405:1,1:24.5:1:31.2:1:1:0:60:39:0.5342:0:1.4 1/0:67:47:2,45:1,19:0.7015:1,1:23.4:1:30.1:1:1:1.18111:60:22.5:0.6923:0:1.2 -17 15943962 . AT A 63 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11315;SOR=0;LSEQ=AGTGAAGATAAAATGGAAGT;RSEQ=TTTTTTTTTTTGAGACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:0,4:0,16:0.2:1,0:35.5:1:31.8:1:1:0:60:8:0.2:0:0.5 0/0:16:0:0,0:0,16:0:1,0:24.8:1:29.1:1:1:0:60:15:1:0:0.9 -17 15950172 . C T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12724;SOR=Inf;LSEQ=GACAGATGTCCTGTAAAGAG;RSEQ=CTTCAAACTCAAGCATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:216,81:0:2,0:24.7:1:31.4:1:1:0:60:36.125:1:0:0.6 0/1:340:4:1,3:243,93:0.0118:2,2:8.3:1:26.3:1:0.0698:7.78397:60:8:0.0119:0:2.3 -17 15950198 . G A 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=0.61765;LSEQ=AACTCAAGCATTACAGGAGA;RSEQ=GCAACACTGGAGATATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:444:278:182,96:107,59:0.6261:2,2:24.3:1:30.2:1:0.83759:1.05:60:68.5:0.627:0:1.1 1/0:541:275:185,90:164,100:0.5083:2,2:24.6:1:30:1:0.24107:1.25:60:90.667:0.5094:0:1.1 -17 15952093 . G C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00145;SOR=Inf;LSEQ=TGAGAAAAACGGCAACAACT;RSEQ=AAGGAAATGTTAAAGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:146,23:0:2,0:22.5:1:32.5:1:1:0:60:168:0.9941:0:0.1 0/1:138:8:6,2:108,22:0.058:2,2:20.8:1:31.3:1:0.62778:1.62968:60:16:0.058:0:1.3 -17 15952100 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20181;SOR=Inf;LSEQ=AACGGCAACAACTGAAGGAA;RSEQ=TGTTAAAGCATGAGCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:163,34:0:2,0:22.5:1:30.8:1:1:0:60:394:1:0:0.1 0/1:162:2:1,1:125,35:0.0123:2,2:18.5:1:29:1:0.39614:3.53531:60:4:0.0124:0:2 -17 15952588 . C A 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGCAGTGGCAGAAGCTG;RSEQ=GTCCTTGAGGCTCCGCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:30.3:1:31.5:1:1:0:60:8:0.8:0:1 1/1:2:2:1,1:0,0:1:0,2:10.5:1:27:1:1:0:60:4:1:0:1.5 -17 15960762 . C T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11513;SOR=Inf;LSEQ=TGAGAAACAAATTCCTTATC;RSEQ=TGTAGATATATTCCATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:100,14:0:2,0:22.7:1:31:1:1:0:60:37:1:0:0 0/1:109:3:1,2:92,14:0.0275:2,2:9:1:22.3:1:0.05583:12.60896:60:2:0.0185:0:2 -17 15961098 . CA C 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.77398;SOR=1.2718;LSEQ=TAAAATTCATTGAGTACTTG;RSEQ=AAAAAAAAATAGTATTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:5:1,4:40,108:0.0323:2,2:16.8:1:33.3:1:1:1.47808:60:10:0.0323:0.0065:0 0/1:172:7:0,7:39,126:0.0407:2,0:20.9:1:32:1:0.35254:0:60:14:0.0412:0:0 -17 15961518 . G GA 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.12216;SOR=Inf;LSEQ=GAACTTATCTTAATTTTGGA;RSEQ=AAAAAAAAAATTATTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:8,32:0:2,0:25.4:1:32.1:1:1:0:60:80:1:0:0.1 0/1:22:2:0,2:6,13:0.0909:2,0:30:1:31:1:1:0:60:4:0.0909:0:0 -17 15961641 . T C 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00604;SOR=Inf;LSEQ=AAAAAATAAAAAAGAATCGA;RSEQ=TGCTGTTTCTAAAGAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:87,9:0:2,0:25.4:1:31.1:1:1:0:60:192:1:0:0.1 0/1:56:5:5,0:51,0:0.0893:1,0:21.8:1:31.6:1:1:0:60:10:0.0893:0:1.2 -17 15961803 . TAAC T 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ACTTTCCGCTTGATTTGCCT;RSEQ=AACCTCTGGCTGATAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:962:0:0,0:523,438:0:2,0:25.7:1:28.9:1:1:0:60:72.923:1:0:0.1 0/1:1171:57:31,26:598,515:0.0487:2,2:24.6:1:30:1:1:1.03:60:114:0.0492:0.0077:0.2 -17 15961951 . A G 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.90901;SOR=1.04412;LSEQ=CTTATTTCAAAACTAATCCC;RSEQ=GGAAAAGTTTCTGAAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:83:8,75:6,51:0.5929:2,2:25:1:30.8:1:1:1.10216:60:82:0.5985:0:1.4 1/0:184:111:22,89:14,59:0.6033:2,2:22.4:1:29.6:1:1:1.04:60:36:0.6:0:1.5 -17 15961993 . T A 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.62688;SOR=1.21507;LSEQ=GTTCTTCACACCTGTAGCAT;RSEQ=TTTTCAATTCTGATCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:43:1,42:0,31:0.5811:1,1:25.3:1:31.5:1:1:0:60:86:0.5811:0:1.8 1/0:86:54:2,52:0,32:0.6279:1,1:25.5:1:30.3:1:0.52722:0:60:108:0.6353:0:1.8 -17 15962121 . A G 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTAATCCCAGCACTTTGG;RSEQ=AGGCCGAGGCAGGTGGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,2:0.6667:0,0:17.5:1:32.5:1:1:0:53:12:0.75:0:1.5 1/1:1:1:0,1:0,0:1:0,0:33:0:32:0:1:0:60:2:1:0:2 -17 15962151 . A G 64 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGTGGATCACCTGAGGTC;RSEQ=GGGGTTTGAGACCAGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:30.8:1:32.3:1:1:0:49.5:8:0.8:0:1.8 1/1:1:1:0,1:0,0:1:0,0:3:0:30:0:1:0:60:2:1:0:2 -17 15965113 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12639;SOR=Inf;LSEQ=CCATCTGGGGTGCAGAAGCT;RSEQ=CAGCATCCACAAGAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:106,201:0:2,0:24.8:1:32.3:1:1:0:60:152.5:0.9967:0:0.1 0/1:346:4:3,1:118,224:0.0116:2,2:14.5:1:24.5:1:0.12489:5.67:60:8:0.0117:0:1 -17 15965152 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4987;SOR=Inf;LSEQ=CCAGGGCATCCGCAGCAGTG;RSEQ=TGTAACGGGAGGCTGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:60,126:0:2,0:23.3:1:29.8:1:1:0:60:185:1:0:0.2 0/1:189:2:1,1:53,134:0.0106:2,2:47.5:1:31:1:0.49088:2.51:60:4:0.0109:0:1 -17 15965185 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21578;SOR=Inf;LSEQ=CTGGCAGGCCTTGGCTTATT;RSEQ=AAGGGCCCCCAGCAGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:29,88:0:2,0:26.2:1:31.5:1:1:0:60:38:1:0:0.2 0/1:102:2:1,1:25,75:0.0196:2,2:26:1:25.5:1:0.44671:2.96:60:4:0.02:0:1 -17 15965268 . G A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00123;SOR=Inf;LSEQ=CCATTTGCTGGGAATGTGGT;RSEQ=GGGAGATGGAAGGACAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:48,32:0:2,0:24.3:1:31.8:1:1:0:60:39:0.9873:0:0.1 0/1:42:6:4,2:25,11:0.1429:2,2:24:1:29.5:1:1:1.13284:60:12:0.1463:0:1.2 -17 15965366 . TA T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.07031;SOR=Inf;LSEQ=ACTATTGCAGTCACAAATTT;RSEQ=AAATGTATATGCAAGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:243,64:0:2,0:25.7:1:28.4:1:1:0:60:60.4:1:0:0.1 0/1:389:5:2,3:287,97:0.0129:2,2:12.2:1:27:1:0.10973:4.41705:60:10:0.0129:0.0077:0.6 -17 15965696 . AAAAC A 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.2355;SOR=0.51062;LSEQ=ATACCTAAATAGAAAAAAGA;RSEQ=AAGATAAGAAACTTGATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:23:0,23:0,17:0.575:1,1:21.3:1:30.6:1:1:0:60:46:0.5897:0.125:0 0/1:32:13:0,13:1,18:0.4063:1,1:29.5:1:30.8:1:1:0:60:26:0.4194:0.0938:0.3 -17 15965863 . T G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTTCAATCTTGATTCCA;RSEQ=AAATAAAACAGCACCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:33.5:1:33:0:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 15967338 . C A 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCACAGTGTACAAGATTA;RSEQ=TAAGATGTGTCCAGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:320,82:0:2,0:24.1:1:31.8:1:1:0:60:79.4:0.9975:0:0.1 0/1:488:57:47,10:335,95:0.1168:2,2:23.3:1:30.2:1:0.49648:1.33:60:114:0.1173:0:1.1 -17 15968143 . T C 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.39502;SOR=0.88016;LSEQ=ATGTTGTAAAAATGTAAACA;RSEQ=GATGGTTCTATTAGAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:389:239:177,62:108,42:0.6144:2,2:23.8:1:31.3:1:0.72418:1.11:60:118.5:0.6124:0:1.1 1/0:442:258:184,74:132,52:0.5837:2,2:24.4:1:30:1:1:1.02086:60:50.6:0.5803:0:1.1 -17 15968400 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=ACAGAACCATACATGACTTT;RSEQ=GATTTTGTCTATCTCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:16,134:0:2,0:23.7:1:30.7:1:1:0:60:29:1:0:0.1 0/1:163:2:1,1:16,145:0.0123:2,2:17:1:26:1:0.19829:8.82:60:4:0.0125:0:1 -17 15968549 . A C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.43333;LSEQ=CTCAAAGTATGGGCAGATTA;RSEQ=AGAGAGCAAATTTGTAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:6,5:4,4:0.5789:2,2:27.6:1:32.1:1:1:1.19:60:22:0.5789:0:1 1/0:6:4:1,3:1,1:0.6667:2,2:9.8:1:32.3:1:1:2.44949:60:8:0.6667:0:1 -17 15968673 . G A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.194;SOR=0.53973;LSEQ=GGGCTAAAAAGTCTACGGGA;RSEQ=GAAGGATATAGTATTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:37:33,4:15,2:0.6852:2,2:25:1:30:1:1:1.10:60:36:0.6792:0:1.1 1/0:39:21:21,0:17,1:0.5385:1,1:20:1:30.1:1:0.46154:0:60:20:0.5263:0:1 -17 15970682 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAAGTTGAATCAGGTG;RSEQ=GGACTAGACAACTTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:26.5:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 15973439 . G T 49 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21143;SOR=0.24181;LSEQ=TTTTTTTTTTTTTTTTAAAT;RSEQ=CAATAAAAAGTATCAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:4:2,2:196,79:0.0143:2,2:11.5:1:24.5:1:0.58227:2.47183:52.3:3:0.0119:0:2.5 0/0:287:1:0,1:197,87:0.0035:2,0:1:0:24:0:0.30877:0:60:2:0.0038:0:1 -17 15973844 . A T 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00156;SOR=0.63785;LSEQ=ACTTTATTGGTGTGCCCTAA;RSEQ=GGGAAAGAAACAAACATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:372:226:67,159:47,98:0.6075:2,2:26.5:1:30.5:1:0.64473:1.13773:60:112:0.6104:0:1.1 0/1:451:224:68,156:70,157:0.4967:2,2:26.2:1:29.9:1:0.91899:1.02281:60:223:0.4978:0:1.1 -17 15974579 . GA G 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.45972;SOR=1.49988;LSEQ=CTCCAGCCTGGTCCACAGAG;RSEQ=AAAAAAAAAAAGGTACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:9:9,0:65,0:0.1216:1,0:22.4:1:31.8:1:1:0:60:18:0.1216:0.0135:0.3 0/1:58:10:10,0:46,1:0.1724:1,0:24.3:1:31:1:1:0:60:20:0.1754:0.0517:0.5 -17 15975029 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22042;SOR=Inf;LSEQ=TAATGCTGATGGTTGCACAA;RSEQ=AATGCCACGGAACTGTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:31,182:0:2,0:22.9:1:32:1:1:0:60:52.25:1:0:0 0/1:189:2:1,1:27,160:0.0106:2,2:12:1:29.5:1:0.27502:5.84:60:4:0.0108:0:1 -17 15975034 . C T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.14493;LSEQ=CTGATGGTTGCACAACAATG;RSEQ=CACGGAACTGTGCACTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:0,2:24,173:0.0101:2,0:26.5:1:31.5:1:1:0:60:4:0.0102:0:1 0/1:174:2:0,2:21,150:0.0115:2,0:26:1:30.5:1:1:0:60:4:0.0118:0:1 -17 15976558 . T G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.47484;SOR=0.57408;LSEQ=CATTGTTATGTGCCACTTTA;RSEQ=ATACAGATATAAACTTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:17:17,0:6,0:0.7391:0,1:21.8:1:32.6:1:1:0:60:34:0.7391:0:1 1/0:13:8:8,0:4,1:0.6154:2,0:25.5:1:30:1:0.38462:0:60:7:0.5833:0:1 -17 15976663 . C T 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64871;LSEQ=GGTGGAAATGACAGAAATTG;RSEQ=ATACAACTTAATTCAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:2,0:172,12:0.0108:2,0:21:1:32:0:1:0:60:4:0.0109:0:1 0/0:143:1:0,1:131,11:0.007:2,0:1:0:24:0:0.08392:0:60:2:0.007:0:1 -17 15976696 . T C 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCAACAATGCAAAATTACTA;RSEQ=ATAAAATAACATGTATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:282,86:0:2,0:22.8:1:30.4:1:1:0:60:121.667:1:0:0.1 0/1:325:24:18,6:220,81:0.0738:2,2:22.5:1:31.3:1:1:1.10:60:48:0.0743:0:1.1 -17 15976916 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10571;SOR=Inf;LSEQ=CAAACAAGACTTGCTCAGAC;RSEQ=GAGCACATGGTATACAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:42,220:0:2,0:23.6:1:30.5:1:1:0:60:64.5:1:0:0.1 0/1:236:3:2,1:40,193:0.0127:2,2:15.7:1:26:1:0.08253:9.51:60:6:0.0129:0:1 -17 15976952 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2183;SOR=Inf;LSEQ=AATGTACAGTAAATAGGTTA;RSEQ=TTTCATAGTCTATCTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:8,118:0:2,0:24.2:1:32.2:1:1:0:59.8:62:1:0:0.3 0/1:111:2:1,1:12,97:0.018:2,2:7:0:31:1:0.22146:7.81:60:4:0.018:0:1.5 -17 15977005 . A T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11722;SOR=0.38666;LSEQ=TAAAACTTGTCTTAACCTAC;RSEQ=ATAAAATATGTGTAGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:27:0,27:0,18:0.6:1,1:22.1:1:28:1:1:0:60:26:0.619:0:1.3 0/1:22:8:0,8:1,13:0.3636:1,0:21.4:1:27.8:1:1:0:60:16:0.3636:0:1.5 -17 15977043 . C T 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77542;LSEQ=GATTCATGAAAATATTTTCA;RSEQ=TCATTCAAATGTGTTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:0,13:0,10:0.5652:0,1:22.8:1:30.2:1:1:0:60:26:0.5652:0:1.8 1/0:10:5:0,5:0,5:0.5:0,0:28:1:30.6:1:1:0:60:10:0.5:0:1.8 -17 15977132 . T C 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTAAGTCCCTTTCTGCA;RSEQ=GAAACTTACACAATAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:16.4:1:30.2:1:1:0:60:10:0.5556:0:1.4 0/0:1:0:0,0:0,1:0:0,0:13:0:32:0:1:0:60:2:1:0:0 -17 15978663 . T C 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01449;SOR=Inf;LSEQ=CTGCGTTGTTAATTACTTTT;RSEQ=ATCGACTAAGCTGTTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:34,0:0:1,0:18:1:31.4:1:1:0:60:68:1:0:0 0/1:12:3:2,1:9,0:0.25:0,2:20.7:1:31:1:0.25:0:60:6:0.25:0:1 -17 15983343 . G T 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCTGGTTGGAGTTCCCC;RSEQ=AGTTATACTTCCTTCTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:923:0:0,0:437,485:0:2,0:26.2:1:30.3:1:1:0:60:60.467:0.9989:0:0.2 0/1:1071:59:31,28:488,523:0.0551:2,2:26.5:1:28.3:1:0.59247:1.19:60:18.667:0.0529:0:1.1 -17 15983458 . G A 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAAACAGCCCCTACTTGGGA;RSEQ=AGTACTCAACTAAGAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:82:10,72:6,113:0.408:2,2:24.8:1:30.1:1:0.10896:2.60:60:81:0.4091:0:1.1 0/0:190:0:0,0:17,173:0:2,0:24.7:1:31.4:1:1:0:60:380:1:0:0 -17 15984054 . CA C 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.97385;LSEQ=GGTGTTCCCTAAGAAAAAAA;RSEQ=AAAAAAAATTTAAAGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:4:0,4:45,177:0.0176:2,0:20.3:1:32.4:1:0.58673:0:60:8:0.0179:0.0044:0.3 0/1:233:4:1,3:71,158:0.0172:2,2:29.3:1:32.5:1:1:1.34653:60:8:0.0174:0:0 -17 15984098 . G A 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06244;SOR=Inf;LSEQ=AAACATTGTTTTTTTCACAA;RSEQ=GTCAATTTCACAAAGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:4,75:0:2,0:24.7:1:30.4:1:1:0:60:18.75:1:0:0.2 0/1:92:5:0,5:10,77:0.0543:2,0:12.8:1:28:1:1:0:60:4:0.0449:0:1.2 -17 15989531 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22714;SOR=0;LSEQ=CTGACAAATCAGTGCGAGGA;RSEQ=GGAGGACAAGTTTTAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:156,40:0.0101:2,2:37:1:31.5:1:0.3721:3.86447:60:4:0.0102:0:1 0/0:218:0:0,0:176,42:0:2,0:21.5:1:31.3:1:1:0:60:53.5:1:0:0.1 -17 15994864 . T TCTCA 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTCAAGGACAGGACAACAAT;RSEQ=CTCACTCTGAAAATTCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:23:1:30.9:1:1:0:60:6:0.5:0.1667:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 15994888 . C T 78 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.37796;LSEQ=ACTCTGAAAATTCAGATGAA;RSEQ=GGAACATAAAGCATAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:9.8:1:30.5:1:1:0:60:12:0.75:0:1.2 1/0:2:1:1,0:1,0:0.5:0,0:16:0:21:0:1:0:60:2:0.5:0:1 -17 15995423 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10464;SOR=0;LSEQ=AACAACCAATGTAATAATTG;RSEQ=CATCTCTTAACAAGTAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:1,2:30,181:0.014:2,2:11.3:1:27.3:1:0.37616:2.99:60:2:0.0095:0:1 0/0:239:0:0,0:43,196:0:2,0:21.7:1:30.7:1:1:0:60:28.875:1:0:0.1 -17 16001624 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09568;SOR=Inf;LSEQ=TTAAAGAACAGAAGAAATAT;RSEQ=TCTATAAAGGTCTCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:160,31:0:2,0:24.9:1:32.2:1:1:0:60:190:1:0:0.1 0/1:162:3:3,0:130,29:0.0185:2,0:21:1:28.3:1:1:0:60:6:0.0186:0:1 -17 16004259 . A G 70 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCACTGCTGCCCTCCTC;RSEQ=GGCACAACAGTTATCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:22.4:1:30.2:1:1:0:60:10:1:0:1 1/1:1:1:1,0:0,0:1:0,0:30:0:31:0:1:0:60:2:1:0:1 -17 16004368 . C T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18292;SOR=0.28209;LSEQ=ATATAGGAGAAATGTATAAT;RSEQ=TGTTTCATTAAAATGATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:15,0:4,0:0.7895:0,1:17.3:1:31.2:1:1:0:60:30:0.7895:0:1 1/0:8:4:4,0:4,0:0.5:0,0:17.5:1:28.8:1:1:0:60:8:0.5:0:1 -17 16004487 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51265;SOR=0;LSEQ=ATTTACATAGGAGACATGTC;RSEQ=GCAGCCAGCACCACCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:2,0:141,8:0.0132:2,0:9:1:32:0:1:0:60:4:0.0135:0:1 0/0:107:0:0,0:99,8:0:2,0:23.7:1:30.9:1:1:0:60:52.5:1:0:0.2 -17 16004537 . G A 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.98646;LSEQ=CCAACCAGCAGAGTAAGCAC;RSEQ=GGGAGGACTTATGGAACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:23:20,3:236,57:0.0726:2,2:19.4:1:29.8:1:0.58735:1.61:60:46:0.0737:0:1.3 0/1:335:24:16,8:230,80:0.0716:2,2:26.5:1:30.2:1:0.47106:1.43583:60:48:0.0723:0:1 -17 16005187 . T C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36917;SOR=1.65164;LSEQ=AGGTGGTGATAGAAACCATG;RSEQ=TTGAAAGTAGTTGTTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:25:0,25:0,17:0.5814:1,1:21.3:1:32.6:1:1:0:60:24:0.5854:0:1 1/0:43:30:4,26:1,12:0.6977:1,2:16.1:1:32.5:1:1:1.82:60:60:0.6977:0:1 -17 16012022 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61803;SOR=2.073;LSEQ=CTGTTTCCTCAATGAAGCAA;RSEQ=TCCTACACAGTCAAATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:169,20:0.0053:2,0:1:0:26:0:0.11053:0:60:2:0.0053:0:1 0/1:184:2:1,1:153,29:0.0109:2,2:11:1:28.5:1:0.30025:5.20423:60:4:0.0109:0:1 -17 16012296 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50028;SOR=0;LSEQ=AAATTCATTTCTGAAATAAT;RSEQ=TAGAACATTGATAAGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:0,2:2,69:0.0274:1,0:40:1:31:1:1:0:60:4:0.029:0:1 0/0:61:0:0,0:3,58:0:1,0:22.4:1:31:1:1:0:60:122:1:0:0 -17 16012311 . GCA G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.50204;SOR=0;LSEQ=ATAATGTAGAACATTGATAA;RSEQ=CACACACACACCAGACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:0,48:0.04:1,0:34.5:1:32.5:1:1:0:60:4:0.0408:0:0 0/0:39:0:0,0:2,37:0:2,0:25.4:1:32.3:1:1:0:60:78:1:0:0 -17 16012494 . A T 57 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACCACTATACATGTATAAA;RSEQ=AGCCAAAAATCACATACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:40:1:28.8:1:1:0:60:8:0.5:0:1 1/1:1:1:0,1:0,0:1:0,0:10:0:29:0:1:0:60:2:1:0:1 -17 16021136 . AAAC A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.12361;SOR=Inf;LSEQ=ATAGAGTGAGACTCCATCTC;RSEQ=AACAACAACAACACTCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:196,50:0:2,0:23.2:1:30.2:1:1:0:60:122:0.9959:0:0.1 0/1:253:4:3,1:191,58:0.0158:2,2:27.3:1:30:1:1:1.0973:60:8:0.016:0.004:0 -17 16021611 . A G 50 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTATCTCTCACAGGGCT;RSEQ=GGACAACATTAGACACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:28:1:32:0:1:0:60:6:0.4286:0:1 1/1:1:1:0,1:0,0:1:0,0:39:0:32:0:1:0:60:2:1:0:1 -17 16022637 . A AT 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49913;SOR=0;LSEQ=CTCTTTGCCTTTTTGAAAGA;RSEQ=TTTTTTTTCCAATTAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:128,9:0.0143:2,2:16.5:1:30.4:1:0.13919:13.545:60:4:0.0144:0.0071:0 0/0:128:0:0,0:124,3:0:1,0:24.3:1:30.1:1:1:0:59.9:126:0.9921:0:0.1 -17 16024094 . T C 50 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GCCTCAATATTACACAGCCA;RSEQ=TAAAAAATAAAAATGGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:21:1:31.7:1:1:0:60:6:0.375:0:1 1/1:1:1:1,0:0,0:1:0,0:38:0:33:0:1:0:60:2:1:0:1 -17 16024701 . C CA 130 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.31505;SOR=0.62138;LSEQ=AAACTACCTAATCTCTCACT;RSEQ=AAAAAAAAAAAATTATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:20:0,20:0,27:0.4167:1,1:29.1:1:30.1:1:1:0:60:19:0.4043:0:0.5 0/1:62:19:0,19:0,37:0.3065:1,1:34.5:1:28.6:1:1:0:60:8.5:0.3036:0:0.3 -17 16029445 . C CT 109 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.20151;SOR=0.57855;LSEQ=TTCATCTTTCTTTTCTTCTT;RSEQ=TTTTTTTTCTGTTTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:884:12:3,9:415,455:0.0136:2,2:21.3:1:30.5:1:0.14984:2.73325:60:24:0.0137:0.0057:0.3 0/0:1393:11:5,6:662,717:0.0079:2,2:25.6:1:31:1:1:1.10785:60:22:0.008:0.0014:0.1 -17 16029600 . TA T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49818;SOR=Inf;LSEQ=TGTGATAAATTATGTCTATC;RSEQ=AAAAAATTTTAAATGATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:7,120:0:2,0:23:1:30.1:1:1:0:60:41.333:1:0:0.1 0/1:131:2:1,1:12,117:0.0153:2,2:19.5:1:29.5:1:0.18931:9.41:60:4:0.0155:0.0076:1 -17 16041149 . G A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATGCTAATCTCTGCATC;RSEQ=TTCCAATTTTAGTATTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:5,1:0.3333:2,0:31.3:1:29.7:1:1:0:60:6:0.3333:0:1 0/0:2:0:0,0:2,0:0:0,0:19:1:25.5:1:1:0:60:4:1:0:0 -17 16041306 . C A 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00946;LSEQ=TAGTTCTGTGTTCTGTGTTA;RSEQ=GATTTCTCTAATAATTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:69:45:43,2:23,1:0.6522:1,1:28.6:1:30:1:1:1.06874:60:44:0.6567:0:1.1 1/0:81:53:52,1:27,1:0.6543:1,1:24.5:1:30.1:1:1:1.91:60:106:0.6625:0:1.1 -17 16041592 . C A 34 v4;q23;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08113;SOR=0;LSEQ=AACAACTAAAAAAAAAAAAA;RSEQ=TTGGGAAAAGAAAGACTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:3,0:33,165:0.0149:2,0:5.7:1:22:1:0.00536:0:60:2:0.0104:0:1.7 0/0:262:0:0,0:53,209:0:2,0:21.5:1:30.9:1:1:0:59.8:20.833:1:0:0.6 -17 16041636 . T C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07747;SOR=0.55362;LSEQ=AGGCTGGGCGTGGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:44:3,41:1,24:0.6286:1,2:22.4:1:30:1:1:1.74:59.7:43:0.6232:0:1.2 0/1:87:42:0,42:1,43:0.4828:1,1:20.6:1:29.7:1:1:0:59.5:20:0.4762:0:1.3 -17 16041719 . CAG TGA 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04858;SOR=Inf;LSEQ=GACCAGCCTGACCAATATGG;RSEQ=AACCCCATCTCTACTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:0:1,0:24.4:1:32.5:1:1:0:59.2:60:1:0:0.5 0/1:9:2:0,2:0,7:0.2222:0,0:14.5:1:30.6:1:1:0:44.5:4:0.25:0.1111:1.5 -17 16041777 . C T 80 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.4629;LSEQ=GGGATGGTGGCACATGCCTG;RSEQ=AGTCCCACCTACTCAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:0.7:0,0:32.7:1:28.7:1:1:0:55.1:14:0.7:0:2.1 1/0:2:1:1,0:0,1:0.5:0,0:44:0:30:0:1:0:60:2:0.5:0:2 -17 16041792 . A G 87 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTGCAGTCCCACCTACTC;RSEQ=GGAAGCTGAGGCAGGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:0.7:0,0:22.9:1:31.3:1:1:0:55.1:14:0.7:0:2.1 1/1:1:1:1,0:0,0:1:0,0:42:0:28:0:1:0:60:2:1:0:2 -17 16042504 . G GA 88 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.23131;SOR=2.4083;LSEQ=ATTTGTTTCTCATTATTCTG;RSEQ=AAAAAAAATACAATTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:3:0,3:85,264:0.0085:2,0:14:1:31.7:1:1:0:60:6:0.0087:0.0028:0.7 0/1:394:8:4,4:116,270:0.0203:2,2:24.9:1:29.6:1:0.25341:2.32:60:16:0.0206:0.0025:0.3 -17 16046845 . A T 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.26966;SOR=0.73294;LSEQ=TTCCCACATTTACATACAAA;RSEQ=AAACCCTTAGCTCCTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:64:56,8:44,1:0.5872:1,2:19.6:1:30.5:1:0.07808:6.20555:60:128:0.5872:0:1.1 1/0:100:51:48,3:43,6:0.51:2,2:19.9:1:29.8:1:0.31341:2.22:60:102:0.51:0:1.1 -17 16047062 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50094;SOR=Inf;LSEQ=TAAAGACCTTATATAAAGAC;RSEQ=TATCAATTAAATTAACTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:23,149:0:2,0:23.3:1:30.9:1:1:0:60:85:1:0:0.1 0/1:197:2:0,2:31,163:0.0102:2,0:23.5:1:33:0:1:0:60:4:0.0103:0:1 -17 16047067 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23592;SOR=0;LSEQ=ACCTTATATAAAGACATATC;RSEQ=ATTAAATTAACTATAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:19,141:0.0123:2,2:22:1:29:1:0.23234:7.26:60:4:0.0126:0:1 0/0:171:0:0,0:21,150:0:2,0:22.6:1:30:1:1:0:60:84.5:1:0:0.1 -17 16047112 . CAAGTT C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=TCTGAATGGAACTTTTTAAC;RSEQ=AAGAGAAGAAACATAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:0,74:0:1,0:25.6:1:30.6:1:1:0:59.8:73:1:0:0.2 0/1:65:2:0,2:1,62:0.0308:1,0:18.5:1:33:1:1:0:60:4:0.0323:0:0 -17 16047179 . TTAA T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.7369;SOR=1.47111;LSEQ=GTAATATGCTGTGTCACCTA;RSEQ=TAACAATTTAAATGTTACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:0,14:0,13:0.5185:1,1:20.1:1:30:1:1:0:60:28:0.5185:0.0741:0 1/0:13:8:1,7:0,5:0.6154:0,2:34.5:1:30.1:1:1:0:60:16:0.6154:0:0.1 -17 16049563 . C A 106 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00578;SOR=0.09281;LSEQ=CTCCACTATTGTCCTATGAC;RSEQ=CTGCCAAATCCCCCTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:11:11,0:88,0:0.1111:1,0:17.9:1:30.8:1:1:0:55.5:22:0.1122:0:1.7 0/1:88:1:1,0:87,0:0.0114:1,0:39:0:31:0:1:0:49:2:0.0115:0:1 -17 16049626 . A T 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00193;SOR=0.64112;LSEQ=TACATACTAAAAAAATTTTT;RSEQ=AAAAAAAGAAACAATAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:373:232:177,55:110,31:0.622:2,2:20.5:1:29.7:1:0.79999:1.10229:60:464:0.6253:0:1.1 1/0:454:233:174,59:167,54:0.5132:2,2:21.8:1:29.3:1:0.82914:1.04855:59.9:115.5:0.5133:0:1.1 -17 16049641 . TA T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01291;SOR=0;LSEQ=TTTTTAAAAAAAAGAAACAA;RSEQ=AATATTTGAAGAAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:5:2,3:348,135:0.0102:2,2:20.2:1:28.8:1:0.13996:3.8541:60:10:0.0103:0.0041:0.6 0/0:674:0:0,0:469,205:0:2,0:23.4:1:28.2:1:1:0:60:167.5:1:0:0.5 -17 16052381 . C T 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AGCTGAACCCTAGCTGACCC;RSEQ=GTTTCTAATAAAAGAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:19.3:1:31.3:1:1:0:60:6:0.75:0:1 0/0:1:0:0,0:0,1:0:0,0:6:0:31:0:1:0:60:2:1:0:0 -17 16052854 . C G 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24879;SOR=Inf;LSEQ=AGAAGAGAAAAATATGGTTG;RSEQ=ATGACATTAAGAAAAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:64,194:0:2,0:25:1:32.2:1:1:0:60:50.6:1:0:0.1 0/1:267:3:2,1:64,200:0.0112:2,2:27.3:1:23.7:1:0.15204:6.20:58.3:2:0.0076:0:2 -17 16054524 . T AA 53 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TTAAAGTATAATTTTTTTTT;RSEQ=AAAAAAAAGATATCTATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:2,0:0.5714:0,0:15.3:1:26.5:1:1:0:60:8:0.5714:0.2857:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 16056442 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.4564;SOR=1.95612;LSEQ=GGATTAAATAGCTGCTCAAG;RSEQ=AAAAACAAGCTCAGGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:11,0:6,0:0.6471:0,0:26.1:1:30.4:1:1:0:60:22:0.6471:0:1 1/0:14:11:11,0:3,0:0.7857:0,0:11.4:1:29.8:1:1:0:60:22:0.7857:0:1 -17 16056614 . TA T 149 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.50374;SOR=0.81985;LSEQ=GAAAAACTACCACCAAAAAT;RSEQ=AAAAAAAAAATCACTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:30:19,11:274,122:0.0698:2,2:26.8:1:30.1:1:0.54162:1.29947:60:60:0.0711:0.0023:0.6 0/1:518:30:17,13:333,153:0.0579:2,2:26.5:1:30.5:1:0.22586:1.66263:60:60:0.0587:0.0154:0 -17 16056741 . T C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08584;SOR=0;LSEQ=GACATTGTTGTATCATATAA;RSEQ=TAAAAATTACATTATCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:70,223:0.0101:2,2:32:1:32.7:1:0.14775:6.32:60:6:0.0103:0:1 0/0:375:0:0,0:104,269:0:2,0:23.2:1:29.5:1:1:0:60:92.25:0.9946:0:0.1 -17 16062400 . TA T 80 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.684;LSEQ=AATTTTCATTAGATAGAGTT;RSEQ=AAAAAAAAAACTAAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:27.2:1:31:1:1:0:60:12:0.6:0:0.3 1/0:6:3:0,3:0,3:0.5:0,0:19.3:1:31:1:1:0:60:6:0.5:0:0 -17 16066762 . AAACTAC A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTAAGGATATGCAAATGA;RSEQ=AACTAGATACCACTTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:28:1:1:0:59.5:4:1:0:3.5 -17 16066791 . C A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGATACCACTTCACATCT;RSEQ=CAAGGATGGCTATATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35.5:1:27.5:1:1:0:59.5:4:1:0:3.5 -17 16066813 . A T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGATGGCTATATTTTTTT;RSEQ=AAAAAGGAAAATAACAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33:0:30:1:1:0:59.5:4:1:0:3.5 -17 16066828 . C G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTAAAAAAGGAAAATAA;RSEQ=AGATGTTGGCAAGGAGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:33.5:1:1:0:59.5:4:1:0:3.5 -17 16068067 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=AGAAAAAAAAAAATCAAAAA;RSEQ=AGAATGGACAAACAAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,1:0:2,0:18.8:1:28.9:1:1:0:48.3:8:1:0:0.8 0/1:10:2:1,1:5,3:0.2:2,2:20.5:1:29.5:1:1:1.58108:33:4:0.2222:0:1.5 -17 16068076 . C A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22283;SOR=0;LSEQ=AAAATCAAAAATAGAATGGA;RSEQ=AAACAAATTTCACTCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:9,1:0.2308:2,0:15:1:30.7:1:1:0:37:6:0.25:0:2.7 0/0:11:0:0,0:7,4:0:2,0:16.3:1:28.8:1:1:0:51.6:10:1:0:0.5 -17 16068095 . A G 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.22619;SOR=0;LSEQ=ACAAACAAATTTCACTCTCT;RSEQ=CAATCATATAATCAGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:11,1:0.2:2,0:34:1:33.3:1:1:0:37:6:0.2143:0:2.7 0/0:13:0:0,0:9,4:0:2,0:21.9:1:28.5:1:1:0:57.1:26:1:0:0.2 -17 16068153 . C T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50192;SOR=0;LSEQ=TGAATGTAAGAAAACCACAA;RSEQ=AGTAGCAAAAAAACAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:2,0:30,5:0.0541:2,0:14.5:1:33:0:1:0:35.5:4:0.0571:0:3 0/0:28:0:0,0:24,4:0:2,0:18:1:32.1:1:1:0:58.9:56:1:0:0.1 -17 16068159 . CA C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=TAAGAAAACCACAACAGTAG;RSEQ=AAAAAACAGCAAGTCCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:2,0:34,4:0.05:2,0:30:1:33:1:1:0:37.5:4:0.0513:0:1.5 0/0:28:0:0,0:24,4:0:2,0:20.6:1:31.1:1:1:0:60:56:1:0:0.1 -17 16068215 . A G 92 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00588;SOR=0;LSEQ=TCCTTTTATGTAAAGTTTCA;RSEQ=AATATGGAAAACTCAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:7:7,0:72,9:0.0795:2,0:21.9:1:33:1:1:0:33.3:14:0.0814:0:5.6 0/0:92:0:0,0:77,15:0:2,0:25.2:1:30.3:1:1:0:58.2:184:1:0:0.3 -17 16068234 . A T 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00092;SOR=0.20794;LSEQ=AAAATATGGAAAACTCAAAA;RSEQ=TATCTACTGTAGGGAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:22:22,0:94,28:0.1528:2,1:27.8:1:31.9:1:0.00775:0:30.5:44:0.1528:0:5.1 0/1:139:5:5,0:107,27:0.036:2,0:37.2:1:30:1:0.58293:0:23.2:10:0.036:0:5 -17 16068240 . A T 145 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00208;SOR=0.2993;LSEQ=TGGAAAACTCAAAAATATCT;RSEQ=CTGTAGGGAGACAAACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:26:26,0:103,34:0.1595:2,1:25.9:1:31:1:0.0026:0:31.4:52:0.1605:0:5 0/1:168:9:6,3:121,38:0.0536:2,2:21.2:1:28.1:1:0.68984:1.58725:36.9:18:0.0539:0:3.7 -17 16068241 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12333;SOR=Inf;LSEQ=GGAAAACTCAAAAATATCTA;RSEQ=TGTAGGGAGACAAACATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:132,35:0:2,0:21.7:1:32.1:1:1:0:55.2:334:1:0:0.9 0/1:176:4:1,3:130,42:0.0227:2,2:15.5:1:26.8:1:0.05198:9.14121:60:8:0.023:0:1 -17 16068262 . T C 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72139;SOR=0.72746;LSEQ=TGTAGGGAGACAAACATACA;RSEQ=TCTTAGAATATATTAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:4:4,0:192,61:0.0156:2,0:25:1:30.8:1:0.57544:0:36:8:0.0157:0:5.3 0/1:264:3:3,0:181,80:0.0114:2,0:23.3:1:31:1:0.55576:0:31:6:0.0114:0:5 -17 16068278 . A G 204 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31732;LSEQ=TACATTCTTAGAATATATTA;RSEQ=GCAAAGACATTTACTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:79:75,4:162,82:0.2446:2,2:24.7:1:32.4:1:0:9.44:35.6:158:0.2469:0:4.6 0/1:344:32:32,0:196,116:0.093:2,1:19.2:1:32.2:1:0:0:29.2:31:0.0909:0:4.7 -17 16068287 . A T 206 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.37194;LSEQ=AGAATATATTAAGCAAAGAC;RSEQ=TTTACTTGTTTCTTTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:94:89,5:181,99:0.2507:2,2:25.9:1:31.5:1:0:9.69:36.2:93:0.2514:0:4.7 0/1:380:42:42,0:205,132:0.1105:2,1:20.4:1:31.6:1:0:0:29.6:84:0.1111:0:4.8 -17 16068340 . C T 226 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00256;SOR=0.66475;LSEQ=CTGTTCTACTTTTGCAATTT;RSEQ=TCGATCTACACGATCCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:173:168,5:216,149:0.321:2,1:24.9:1:30.4:1:0:23.08:37.7:346:0.3234:0:5.4 0/1:569:136:133,3:231,202:0.239:2,1:27.8:1:30.2:1:0:38.61:33.6:67:0.2372:0:5.6 -17 16068343 . G A 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00989;SOR=0.70878;LSEQ=TTCTACTTTTGCAATTTCTC;RSEQ=ATCTACACGATCCATACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:174:166,8:222,153:0.3169:2,1:25.2:1:29.9:1:0:14.25:37.5:57:0.3161:0:5.4 0/1:582:144:136,8:237,201:0.2474:2,2:27.3:1:29.9:1:0:14.37:33.4:288:0.2491:0:5.5 -17 16068362 . C T 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1214;SOR=0.82112;LSEQ=CGATCTACACGATCCATACT;RSEQ=TGTATTAACTCTTCCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:590:187:180,7:231,172:0.3169:2,1:27.7:1:30.2:1:0:19.08:35.4:61.333:0.3151:0:5.3 0/1:667:184:172,12:262,221:0.2759:2,2:26.6:1:29.4:1:0:12.05:33:29.667:0.2709:0:5.2 -17 16068377 . C G 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00975;SOR=0.7472;LSEQ=ATACTCTGTATTAACTCTTC;RSEQ=TTTGAGAGTTTTGAAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:247:216,31:232,196:0.3648:2,2:23.5:1:29.6:1:0:5.87:35.8:60.75:0.366:0:4.8 0/1:756:227:193,34:277,247:0.3003:2,2:23.9:1:29.5:1:0:5.05:34.6:226:0.3029:0:4.8 -17 16068383 . G A 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00142;SOR=0.71294;LSEQ=TGTATTAACTCTTCCTTTGA;RSEQ=AGTTTTGAAGGTGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:307:236,71:222,201:0.4205:2,2:20.4:1:29.6:1:0:3.00:38.2:306:0.4232:0:4.4 0/1:833:284:215,69:277,272:0.3409:2,2:21:1:29.3:1:0:3.06:36.8:283:0.3418:0:4.3 -17 16068396 . G A 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=0.69471;LSEQ=CCTTTGAGAGTTTTGAAGGT;RSEQ=AAGCATTTTGATCATCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:918:460:291,169:221,234:0.5011:2,2:18.7:1:28.5:1:1e-05:1.82:43.6:114:0.5033:0:3.3 0/1:988:406:254,152:288,293:0.4109:2,2:19.6:1:28:1:6e-05:1.70:41.8:202:0.4118:0:3.3 -17 16068420 . G T 138 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12101;LSEQ=CATTTTGATCATCTCCACAT;RSEQ=GTTGCCCCGAAATTGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1135:31:14,17:531,572:0.0273:2,2:22.4:1:28:1:0.85589:1.12713:49.8:9.333:0.0251:0:2.5 0/0:1182:4:0,4:590,587:0.0034:2,0:1:0:24.8:1:0.12437:0:60:8:0.0034:0:1.8 -17 16068463 . C T 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33317;LSEQ=TGGAGCTTCATGTTTGCCTC;RSEQ=GAATGCTGGATCCTTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1081:430:166,264:224,427:0.3978:2,2:28.4:1:30.7:1:0.17424:1.20:47.6:429:0.4021:0:2.2 0/1:1076:194:86,108:336,546:0.1803:2,2:28.9:1:29.8:1:0.12268:1.29:50.8:63.667:0.1798:0:2.1 -17 16068464 . G A 138 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00235;SOR=4.24911;LSEQ=GGAGCTTCATGTTTGCCTCC;RSEQ=AATGCTGGATCCTTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1070:5:1,4:384,681:0.0047:2,2:27.4:1:31.6:1:0.65951:2.25403:24.8:10:0.0047:0:1.6 0/1:1073:21:2,19:415,637:0.0196:2,2:32.4:1:31.6:1:0.00533:6.18111:25.5:42:0.0198:0:1.8 -17 16068506 . T C 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00658;SOR=0.69179;LSEQ=TAAAACCAAGAAAAACAATT;RSEQ=ATTTCTCACTAATAGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:468:285:59,226:43,140:0.609:2,2:19.2:1:31.8:1:0.4926:1.17609:43.7:70.25:0.6069:0:2 1/0:459:238:43,195:71,150:0.5185:2,2:20:1:31.7:1:0.00054:2.14291:44.1:237:0.5186:0:1.7 -17 16068545 . A C 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.10685;SOR=0.673;LSEQ=CCAGATTGCCTTAAATGAAA;RSEQ=AGTCAGTTTTAAACCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:80:0,80:6,62:0.5405:2,1:22.1:1:32.6:1:0.00831:0:34.7:160:0.5405:0:3.1 0/1:154:68:0,68:9,77:0.4416:2,1:23.3:1:32.9:1:0.00481:0:36.2:136:0.4444:0:2.7 -17 16068579 . C A 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44246;SOR=0.72948;LSEQ=CCACAGCAGAGCCATGTGTA;RSEQ=TATTTGTCTAATGAAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:24:0,24:3,35:0.3871:2,1:23.7:1:32.3:1:0.27657:0:30.6:48:0.3871:0:4.8 0/1:54:17:0,17:1,36:0.3148:1,1:17.9:1:31.1:1:1:0:33.5:34:0.3148:0:4.5 -17 16068583 . T G 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31654;SOR=0.64663;LSEQ=AGCAGAGCCATGTGTACTAT;RSEQ=TGTCTAATGAAACTTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:24:0,24:3,31:0.4138:2,1:19.7:1:33.2:1:0.25953:0:29.8:48:0.4138:0:4.9 0/1:48:15:0,15:1,32:0.3125:1,1:15.9:1:32.3:1:1:0:32.7:30:0.3191:0:4.6 -17 16068597 . T C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.30811;SOR=0.53992;LSEQ=TACTATTTGTCTAATGAAAC;RSEQ=TTTAGTAGTAACTTTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:14:0,14:3,26:0.3182:2,1:14.3:1:33.6:1:0.53942:0:28.3:28:0.3333:0:5.5 0/1:35:7:0,7:1,27:0.2:1,0:11.4:1:32.6:1:1:0:30.4:14:0.2:0:5.3 -17 16068603 . T C 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25699;SOR=0.45833;LSEQ=TTGTCTAATGAAACTTTTAG;RSEQ=AGTAACTTTCATATTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:0,12:2,23:0.3243:2,0:11.3:1:32.9:1:1:0:28.5:24:0.3243:0:5.5 0/1:28:5:0,5:1,21:0.1786:1,0:6.6:1:32.6:1:1:0:30.6:10:0.1852:0:5.2 -17 16068619 . C T 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2881;SOR=0;LSEQ=TTAGTAGTAACTTTCATATT;RSEQ=ACATACATGCAAATTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:1,19:0.1304:1,0:13.3:1:30.3:1:1:0:23:6:0.1304:0:6.3 0/0:13:0:0,0:1,12:0:1,0:33.2:1:32.5:1:1:0:60:26:1:0:0.1 -17 16068682 . C G 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=ACCATGTACTATTTTGAAGA;RSEQ=CCTAAAAGCTATACAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:0.25:0,0:32.3:1:30.7:1:1:0:25:6:0.25:0:4.3 0/0:5:0:0,0:1,4:0:2,0:32.6:1:30.4:1:1:0:60:10:1:0:0 -17 16068702 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=CCCTAAAAGCTATACAAAGT;RSEQ=AGGTGAGTTAGTGTTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:28:1:33.5:1:1:0:27:4:0.2857:0:3 0/0:4:0:0,0:1,3:0:2,0:33.8:1:32.5:1:1:0:60:8:1:0:0 -17 16068716 . T C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=CAAAGTGAGGTGAGTTAGTG;RSEQ=TGATCAGCCTCTAGTATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:14:1:33.5:1:1:0:27:4:0.4:0:3 0/0:4:0:0,0:1,3:0:2,0:19.8:1:31.3:1:1:0:60:8:1:0:0 -17 16068929 . A G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCCAAGTGTTCCTATCA;RSEQ=AAGTTTTTAGGCTTTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:28.3:1:31.7:1:1:0:31:6:0.75:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 16068937 . T C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTCCTATCAAAAGTTTT;RSEQ=AGGCTTTCCAAACCAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:22:1:32.7:1:1:0:31:6:0.75:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 16097430 . C T 91 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=GTCTTTATCTTGGCCCTCAC;RSEQ=CAAGACATGCCAAGTTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:1,0:0.875:0,0:18.1:1:32.6:1:1:0:44.9:14:0.875:0:1.1 0/0:1:0:0,0:0,1:0:0,0:49:0:33:0:1:0:60:2:1:0:0 -17 16097602 . T TAAG 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0.07538;SOR=0.32754;LSEQ=AAATCAGCATAAAGCCACAG;RSEQ=AAGACAGAAATAATTAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:25:23,2:8,0:0.7576:0,2:17:1:31:1:1:0:57.5:50:0.7576:0.2121:0.2 1/0:20:10:9,1:9,1:0.5:2,2:13.8:1:30.6:1:1:1:59.3:20:0.5:0.2:0.2 -17 16097665 . TA T 134 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.87;SOR=1.07742;LSEQ=TGTAAATAGCTCTTGCAACT;RSEQ=AAAAAAAAAAAGATAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:23:23,0:88,2:0.1917:1,1:24.7:1:31.1:1:1:0:60:46:0.1917:0.0333:0.1 0/1:113:23:22,1:87,2:0.2035:1,1:20.1:1:29.8:1:0.50174:1.96314:60:46:0.2035:0.0619:0.3 -17 16097808 . GG TT 140 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20052;SOR=1.62403;LSEQ=GGTGTTGGGAAATGTATACT;RSEQ=ACAGAGTGAGGAGGATAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:13:8,5:370,345:0.0179:2,2:4.5:1:29.6:1:0.58135:1.49:42.9:26:0.0181:0.0069:3.4 0/1:976:28:19,9:474,473:0.0287:2,2:5.1:1:29.2:1:0.0832:2.11:41.4:56:0.0289:0.0102:3.5 -17 16097825 . T G 249 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41972;SOR=1.10476;LSEQ=ACTGGACAGAGTGAGGAGGA;RSEQ=AACGACTTTGTTCTGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:898:153:99,54:363,382:0.1704:2,2:10.5:1:32.1:1:0.00036:1.93:52.8:75.5:0.1693:0:3 0/1:1195:221:144,77:478,494:0.1849:2,2:11.8:1:32:1:2e-05:1.93:52.3:109.5:0.1859:0:3 -17 16097866 . A G 108 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0194;SOR=4.93635;LSEQ=AATGCTCCTTGGTTGGGAGG;RSEQ=TAACCTGAACTTGACATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:825:2:1,1:356,467:0.0024:2,2:1:0:32:1:1:1.31:43:4:0.0024:0:1.5 0/1:1096:13:7,6:485,598:0.0119:2,2:22.7:1:29.3:1:0.58142:1.44:34.3:26:0.012:0:2.3 -17 16097870 . C A 248 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.91941;SOR=1.01512;LSEQ=CTCCTTGGTTGGGAGGATAA;RSEQ=CTGAACTTGACATTATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:797:248:129,119:203,346:0.3112:2,2:28.9:1:30.1:1:8e-05:1.85:47.9:81.667:0.3113:0:3.4 0/1:1056:332:169,163:300,422:0.3144:2,2:30.3:1:29.7:1:0.00506:1.46:48.4:165:0.3155:0:3.3 -17 16097899 . C T 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38839;SOR=1.11424;LSEQ=GACATTATCAGTAAAGAAGT;RSEQ=CTCACCAGACTGTGAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:535:163:86,77:100,270:0.3047:2,2:23.3:1:29.8:1:0:3.01:44.5:162:0.3074:0:4 0/1:698:229:113,116:163,306:0.3281:2,2:22.4:1:29.2:1:0.00028:1.83:45.5:458:0.3319:0:3.8 -17 16097909 . CTG C 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00167;SOR=Inf;LSEQ=GTAAAGAAGTCCTCACCAGA;RSEQ=TGAGATCAATGCCAATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:143,313:0:2,0:22.7:1:30.2:1:1:0:51.9:113:1:0:1.3 0/1:575:11:5,6:192,370:0.0191:2,2:29.3:1:29.6:1:0.52412:1.60:34.9:22:0.0192:0.0017:2.6 -17 16097912 . T C 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.82538;SOR=1.03516;LSEQ=AAGAAGTCCTCACCAGACTG;RSEQ=GAGATCAATGCCAATAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:109:54,55:66,248:0.2571:2,2:22.1:1:30.7:1:0:3.68:41.8:218:0.2589:0:4.5 0/1:546:144:59,85:116,285:0.2637:2,2:19.6:1:30.6:1:0.00929:1.70:42.2:288:0.2662:0:4.2 -17 16097921 . T C 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32029;SOR=1.191;LSEQ=TCACCAGACTGTGAGATCAA;RSEQ=GCCAATAAACAATCATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:83:32,51:50,223:0.2331:2,2:19.7:1:30.4:1:0.00029:2.79:39.9:166:0.2345:0:4.6 0/1:425:113:26,87:75,237:0.2659:2,2:20.1:1:30.3:1:0.89766:1.05877:40.1:112:0.266:0:4.2 -17 16097956 . A G 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03005;SOR=Inf;LSEQ=ATGTTTCTAGGAAACCACCT;RSEQ=AACAGGATGAGAAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:11,160:0:2,0:22.4:1:30.5:1:1:0:54.8:56:1:0:0.7 0/1:177:6:0,6:13,158:0.0339:2,0:10.7:1:32:1:1:0:35:12:0.0345:0:3.5 -17 16098030 . C A 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28902;SOR=0.34676;LSEQ=CTAATAAATTATAACTATAG;RSEQ=TACATAAATAAAACCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:7:0,7:2,40:0.1429:1,0:40.3:1:27.1:1:1:0:31:6:0.1277:0:3.6 0/1:37:2:0,2:6,29:0.0541:2,0:26.5:1:26:1:1:0:35.5:4:0.0541:0:3 -17 16098057 . T G 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18302;SOR=0.29071;LSEQ=AATAAAACCACAATTACCAG;RSEQ=AAAAGCTTCCTCTCATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:0,10:2,28:0.25:2,0:29:1:30.8:1:1:0:29.5:20:0.2564:0:3.2 0/1:23:2:0,2:3,18:0.087:2,0:34:1:29.5:1:1:0:35.5:4:0.087:0:3 -17 16098073 . T G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18097;SOR=0.28361;LSEQ=CCAGTAAAAGCTTCCTCTCA;RSEQ=GTATTTACTTAATAAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:0,12:1,24:0.3243:1,0:20:1:28.4:1:1:0:31.3:5:0.303:0:3 0/1:17:2:0,2:2,13:0.1176:2,0:31.5:1:30.5:1:1:0:35.5:4:0.1176:0:3 -17 16098134 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=ATGCATCATTTCTTTTTATA;RSEQ=TTAAAATAGGTTAATATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:0.2143:0,0:26.7:1:30.7:1:1:0:37.7:6:0.2143:0:2.3 0/0:6:0:0,0:1,5:0:2,0:15.5:1:31.2:1:1:0:60:12:1:0:0 -17 16120448 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50761;SOR=Inf;LSEQ=CGGCGGGAGGGACTTAACAG;RSEQ=GGAACCCAACATTCCCCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:31,22:0:2,0:25.3:1:30.5:1:1:0:60:52:1:0:0.2 0/1:72:2:1,1:44,26:0.0278:2,2:17:0:32:0:1:1.67936:60:4:0.0282:0:1.5 -17 16120471 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14454;SOR=0;LSEQ=AACCCAACATTCCCCGGTGA;RSEQ=GTTTTCCAGCCGGAGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:33,25:0.0333:2,2:43:1:31:1:1:1.31382:60:4:0.0345:0:1 0/0:97:0:0,0:56,41:0:2,0:25.4:1:29.6:1:1:0:60:31.333:1:0:0.1 -17 17069105 . G A 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=GAGGAAAAGCTCAAAGACGT;RSEQ=ACCGTGAGGCTGGAGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:20.5:1:30:1:1:0:60:8:0.8:0:1 1/0:4:2:1,1:0,2:0.5:0,2:11:0:26.5:1:1:0:60:4:0.5:0:1.5 -17 17116952 . C A 163 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=53.67699;LSEQ=CAGCCATCCCTGTCTTTAGG;RSEQ=AGGTGTGTGTGACGGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:1:0,1:320,151:0.0021:2,0:48:0:15:0:0.32203:0:60:0:0:0:1 0/1:509:52:34,18:287,165:0.1022:2,2:25.3:1:28.6:1:0.87939:1.09:60:104:0.1042:0:1.2 -17 17118168 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16072;SOR=Inf;LSEQ=TTGCAGTGGCGGACGTGGAG;RSEQ=TGGAACCCCGCCCCCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:64,1:0:1,0:26.9:1:29.2:1:1:0:60:9.833:1:0:0.2 0/1:44:2:2,0:38,4:0.0455:2,0:8:1:29:1:1:0:60:4:0.0465:0:1 -17 17118199 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21659;SOR=Inf;LSEQ=CCCCCAACCTCTTCTCTCGG;RSEQ=TCCTCCCTCAGTGGCCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:107,5:0:1,0:22.6:1:31.9:1:1:0:60:55:1:0:0.1 0/1:98:2:1,1:87,9:0.0204:2,2:22:1:26:1:0.19461:9.22316:60:4:0.0206:0:1 -17 17118442 . T C 228 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=199.46232;LSEQ=GGCAGAGCAAGGGCAGGCGT;RSEQ=AGCGCGGGGCGGGGGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:2:2,0:199,240:0.0045:2,0:15:1:31.5:1:0.20717:0:60:4:0.0046:0:1.5 0/1:365:174:77,97:85,106:0.4767:2,2:22.3:1:30.7:1:1:1.01014:60:33.8:0.4801:0:1.2 -17 17118689 . G A 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=0.30619;LSEQ=ATGCTCCTCACCTCCCCTGC;RSEQ=CTAGCCCACCGTGGGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:55:17,38:49,155:0.2115:2,2:24.9:1:29.6:1:0.30033:1.41:60:54:0.2151:0:1.1 0/1:264:20:7,13:74,170:0.0758:2,2:21.8:1:28.7:1:0.62447:1.24:60:9:0.0703:0:1.2 -17 17118704 . G A 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12196;SOR=Inf;LSEQ=CCTGCGCTAGCCCACCGTGG;RSEQ=CCCCACTCCGCTCATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:31,154:0:2,0:23.5:1:31.4:1:1:0:60:29.833:1:0:0.3 0/1:183:3:2,1:41,139:0.0164:2,2:6.7:1:20:1:0.13811:6.69:60:2:0.0112:0:1.7 -17 17118786 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06701;SOR=Inf;LSEQ=AATGCTTTGGTATTTAAAAC;RSEQ=TTTCAGGTTATTCGTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:0,57:0:1,0:26.9:1:32.8:1:1:0:60:114:1:0:0 0/1:40:3:0,3:2,35:0.075:2,0:24.7:1:27:1:1:0:60:2:0.0513:0:1.3 -17 17119708 . TG T 85 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.33191;SOR=0.47577;LSEQ=ACGCACCTGAGGAGAGCACG;RSEQ=GGGGGGGATCTGCACGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:529:6:3,3:305,218:0.0113:2,2:27.3:1:33:1:0.69784:1.39816:60:12:0.0115:0:0.2 0/0:553:3:1,2:317,232:0.0054:2,2:22:1:30.7:1:0.57697:2.72782:60:6:0.0055:0:0.3 -17 17119871 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21289;SOR=Inf;LSEQ=CGAGGAAGCCCTCAGCCCCG;RSEQ=CCATCCATGCTCTACTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:16,141:0:2,0:26.3:1:31.9:1:1:0:60:38.25:1:0:0.1 0/1:135:2:1,1:23,110:0.0148:2,2:26.5:1:29:1:0.32504:4.70:60:4:0.0152:0:1.5 -17 17119875 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19915;SOR=Inf;LSEQ=GAAGCCCTCAGCCCCGGCCA;RSEQ=CCATGCTCTACTACCCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:14,137:0:2,0:26:1:30.2:1:1:0:60:150:1:0:0.1 0/1:123:2:1,1:19,102:0.0163:2,2:21:1:27.5:1:0.29988:5.26:60:4:0.0171:0:1 -17 17119903 . G A 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00439;SOR=Inf;LSEQ=CTACTACCCAAACCCCACAC;RSEQ=CCTCCTGCAGCCCGGTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:4,96:0:1,0:25.1:1:32.1:1:1:0:60:32.333:1:0:0.2 0/1:53:5:0,5:1,47:0.0943:1,0:12.6:1:28.6:1:1:0:60:10:0.1:0:1.2 -17 17120204 . T C 162 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCACACGCATCCTTCTGA;RSEQ=GATTTAAACATCATCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:33,0:0,0:1:0,1:24.1:1:32.3:1:1:0:60:66:1:0:1 0/1:23:9:9,0:13,0:0.3913:1,0:25:1:30.9:1:1:0:60:18:0.4091:0:1 -17 17120300 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20729;SOR=Inf;LSEQ=GGTTCTGTGCTGGGCAGTCG;RSEQ=TGCACCTTGGCATCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:166,31:0:2,0:20.3:1:31.1:1:1:0:60:48.25:0.9948:0:0.1 0/1:166:2:1,1:134,30:0.012:2,2:11:1:28.5:1:0.33954:4.41041:60:4:0.0121:0:1.5 -17 17120344 . C T 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCCAGGCACCAGGCCAATA;RSEQ=TGCCCTGCGCCGCACACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:241,167:0:2,0:26.2:1:31.8:1:1:0:60:67:1:0:0.2 0/1:434:122:77,45:182,130:0.2811:2,2:23.4:1:29.6:1:0.38524:1.22:60:121:0.2814:0:1.4 -17 17120352 . C T 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.85526;LSEQ=ACCAGGCCAATACTGCCCTG;RSEQ=GCCGCACACCTAAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:4:2,2:262,185:0.0089:2,2:28.8:1:30.8:1:1:1.41508:60:8:0.009:0:1 0/1:507:56:34,22:261,190:0.1105:2,2:22.6:1:29.8:1:0.77434:1.12:60:112:0.1113:0:1.9 -17 17120353 . G A 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGGCCAATACTGCCCTGC;RSEQ=CCGCACACCTAAGGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:267,190:0:2,0:26.9:1:30.4:1:1:0:60:37.083:1:0:0.2 0/1:510:34:20,14:274,202:0.0667:2,2:21.4:1:30.1:1:1:1.05:60:68:0.0673:0:1.3 -17 17120467 . C T 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31292;SOR=2.7804;LSEQ=CCCATGAGAACGTGCCAGGC;RSEQ=AGCATGCGGAAAGAAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:2:0,2:219,292:0.0039:2,0:10:1:27.5:1:0.50973:0:60:4:0.0039:0:1 0/1:651:7:3,4:286,357:0.0108:2,2:27:1:25.6:1:1:1.06807:60:6:0.0094:0:1.1 -17 17120550 . T C 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08196;SOR=0;LSEQ=TAGTAGAAATGGTTTTTCTC;RSEQ=CCCTTCCCATGAAGTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:1,2:18,119:0.0214:2,2:28.7:1:23.3:1:0.35658:3.26:60:2:0.0146:0:1.3 0/0:181:0:0,0:30,151:0:2,0:22.4:1:29.3:1:1:0:60:59.333:1:0:0.1 -17 17120668 . G C 139 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.00226;SOR=0;LSEQ=GGCCCAGGGTTAAAGGGGCA;RSEQ=AGAGAGAAGTTCCAGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:1:0,1:26.2:1:32.8:1:1:0:60:38:1:0:1.5 0/1:4:1:0,1:0,2:0.25:0,0:39:0:29:0:1:0:60:2:0.3333:0:1 -17 17122223 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20119;SOR=Inf;LSEQ=CGAGGAGGCTGTCAGTCACT;RSEQ=CCTGCAGGGTTTTGAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:65,1:0:1,0:21.7:1:30.4:1:1:0:60:65:1:0:0.9 0/1:55:2:1,1:48,5:0.0364:2,2:24.5:1:29.5:1:0.20808:8.85505:60:4:0.0364:0:1.5 -17 17122261 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49963;SOR=0;LSEQ=GTGGAGGGTCCAGAGGCAAG;RSEQ=CGTGTGGGCAGGGACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:2,0:129,19:0.0133:2,0:33:1:28.5:1:1:0:60:4:0.0139:0:4.5 0/0:135:0:0,0:102,33:0:2,0:21.2:1:30.6:1:1:0:60:26:1:0:1.1 -17 17122262 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50041;SOR=0;LSEQ=TGGAGGGTCCAGAGGCAAGG;RSEQ=GTGTGGGCAGGGACAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:134,19:0.0129:2,2:25.5:1:30:1:0.24214:6.8995:60:4:0.0132:0:1.5 0/0:136:0:0,0:100,36:0:2,0:21.5:1:30.8:1:1:0:60:33:1:0:1.1 -17 17122274 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21012;SOR=Inf;LSEQ=AGGCAAGGCGTGTGGGCAGG;RSEQ=ACAGCCCATGACTGGCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:167,37:0:2,0:22.7:1:30.9:1:1:0:60:33:1:0:1.4 0/1:174:2:1,1:121,49:0.0115:2,2:19.5:1:28.5:1:0.4981:2.45466:60:4:0.0117:0:2 -17 17122279 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.216;SOR=Inf;LSEQ=AGGCGTGTGGGCAGGGACAG;RSEQ=CCATGACTGGCTCTCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:176,48:0:2,0:23.1:1:31.7:1:1:0:60:43.8:1:0:1.5 0/1:195:2:0,2:136,57:0.0103:2,0:19:1:28:1:0.09046:0:60:4:0.0104:0:2.5 -17 17122286 . C T 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAGGGACAGCCCATGA;RSEQ=TGGCTCTCCTCCTGAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:248:248:187,61:0,0:1:0,2:24:1:30.7:1:1:0:60:81.667:1:0:1.5 1/1:233:233:165,68:0,0:1:0,2:22.9:1:29.8:1:1:0:60:232:1:0:1.3 -17 17122327 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18405;LSEQ=TGATGCGCTGTGCCCCTGCC;RSEQ=CCTACCTGCCTCATGTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:428:237:170,67:127,64:0.5537:2,2:25:1:29.8:1:0.24793:1.28:60:58.25:0.5534:0:1.5 0/1:431:80:52,28:233,117:0.1856:2,2:24.1:1:29.3:1:0.7943:1.07214:60:79:0.1863:0:1.7 -17 17122536 . T C 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=37.4004;LSEQ=TTCTAAATCTGCAAGACAGA;RSEQ=GACAAGGACAGTTACAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:584:1:0,1:184,398:0.0017:2,0:43:0:7:0:1:0:60:0:0:0:1 0/1:646:39:13,26:220,385:0.0604:2,2:22.9:1:29.7:1:0.8637:1.14265:60:38:0.0596:0:1.3 -17 17124556 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17056;SOR=Inf;LSEQ=GCACTTGGCTATCACAAAAT;RSEQ=GGGACGAGAAGCCTTTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:138,2:0:1,0:28:1:31.1:1:1:0:60:45.667:1:0:0.1 0/1:99:2:1,1:95,2:0.0202:1,2:38.5:1:29:1:0.05999:38.96618:60:4:0.0213:0:1 -17 17124625 . C T 207 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=230.09648;LSEQ=TGTGAATTTTCCCCACCTAG;RSEQ=TGGGGAACAGATTCTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:1:0,1:296,133:0.0023:2,0:1:0:26:0:0.31163:0:60:2:0.0024:0:1 0/1:420:147:103,44:182,91:0.35:2,2:23.5:1:28.8:1:0.51205:1.17:60:72.5:0.3502:0:1.1 -17 17124815 . C T 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=89.24769;LSEQ=GGTACCGCCCCACGGCCATC;RSEQ=GGGCCAAGGCCCCGGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:1:0,1:310,368:0.0015:2,0:1:0:26:0:1:0:60:2:0.0015:0:1 0/1:721:84:40,44:310,326:0.1165:2,2:24.4:1:29.8:1:0.90769:1.04596:60:41:0.115:0:1.1 -17 17125000 . G A 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59936;SOR=0.43279;LSEQ=AAGGAAAAAGCAAACCTGAC;RSEQ=CTCACCCAGCCCCTGATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:13,113:0.0156:2,2:22.5:1:26.5:1:0.20755:8.41:60:4:0.0161:0:1 0/0:147:1:0,1:8,138:0.0068:2,0:40:0:32:0:1:0:60:2:0.0068:0:1 -17 17125595 . A G 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00179;SOR=0;LSEQ=CAGGAAGAAGTGAGTTCCAC;RSEQ=TCAATATGTTTTCAGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:23.3:1:29.9:1:1:0:59.5:26:1:0:1.1 0/0:3:0:0,0:3,0:0:0,0:19.3:1:31.7:1:1:0:60:6:1:0:0 -17 17125702 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08306;SOR=Inf;LSEQ=AGGCCAGTGCTCCTCACAGA;RSEQ=GCAGCAAGCAAACACGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:61,1:0:1,0:25.6:1:32.2:1:1:0:60:124:1:0:0.1 0/1:49:3:3,0:45,1:0.0612:1,0:38.7:1:29:1:1:0:60:6:0.0638:0:1 -17 17125752 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18898;SOR=0;LSEQ=CTCCCAAATCCATGGACAAG;RSEQ=CAACCAATGTATCGTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:120,30:0.0132:2,2:34.5:1:30:1:0.36738:3.95132:60:4:0.0134:0:1 0/0:197:0:0,0:159,38:0:2,0:21.9:1:31.6:1:1:0:60:64.667:1:0:0.1 -17 17125760 . T C 73 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07673;SOR=Inf;LSEQ=TCCATGGACAAGCCAACCAA;RSEQ=GTATCGTGACTGCTCTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:138,35:0:2,0:23.7:1:30.8:1:1:0:59.9:56.667:1:0:0.1 0/1:238:5:4,1:177,55:0.021:2,2:27.4:1:31.8:1:1:1.24:60:10:0.0214:0:1 -17 17125998 . G A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24882;SOR=0;LSEQ=GAAATGCAAAGGGAAGGGAT;RSEQ=GCCTCTTTAAGCCAAAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:75,196:0.0109:2,2:20:1:22.7:1:0.19156:5.19:60:2:0.0074:0:1 0/0:265:0:0,0:81,183:0:2,0:24.6:1:30.1:1:1:0:60:51.8:0.9962:0:0.2 -17 17126002 . T A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62352;SOR=3.00612;LSEQ=TGCAAAGGGAAGGGATGGCC;RSEQ=CTTTAAGCCAAAGCTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:66,187:0.0039:2,0:1:0:30:0:0.26378:0:60:2:0.004:0:1 0/1:255:3:2,1:76,176:0.0118:2,2:17:1:27.7:1:0.22247:4.60:60:6:0.012:0:1.3 -17 17126041 . G A 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00533;SOR=Inf;LSEQ=AGCAGCTCGGACCCCTACTC;RSEQ=TTCACAGCCAACTCCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:23,96:0:2,0:23.8:1:31.5:1:1:0:60:58.5:1:0:0 0/1:110:7:1,6:12,91:0.0636:2,2:18.4:1:30:1:1:1.26:60:14:0.0648:0:1 -17 17126736 . T TCTGC 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CATTTTCATATGGCTGCCGC;RSEQ=CTGCCTGCCAGGACGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:32.3:1:29.7:1:1:0:55.8:8:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 17126792 . C T 52 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTCCTGCAATGCACACA;RSEQ=CATGAGTAAGAAACAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:28.8:1:26.3:1:1:0:60:3:1:0:2.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 17127077 . G A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53902;SOR=0;LSEQ=TGGCCTGGGAGGCTCCTCAC;RSEQ=ACCTCCAGCTCTGAAGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:3,0:24,1:0.1071:1,0:37.7:1:30.7:1:1:0:60:6:0.1071:0:1 0/0:13:0:0,0:12,1:0:1,0:22.4:1:29.6:1:1:0:60:26:1:0:0.4 -17 17127100 . G C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13788;SOR=Inf;LSEQ=CTCCAGCTCTGAAGCCAAGA;RSEQ=ACTACAATTCACACAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:0:1,0:28.5:1:32.1:1:1:0:60:66:1:0:0.2 0/1:20:2:2,0:17,1:0.1:1,0:49:0:29.5:1:1:0:60:4:0.1:0:2.5 -17 17127155 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21488;SOR=Inf;LSEQ=AGGGGAAGACGCCACGCGGT;RSEQ=TCCAGGCCTCAACCTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:84,8:0:2,0:22.1:1:31.3:1:1:0:60:29.667:1:0:0.1 0/1:80:2:1,1:68,10:0.025:2,2:6.5:1:28.5:1:0.25759:6.53105:60:4:0.0253:0:1 -17 17127173 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.20154;SOR=Inf;LSEQ=GTCTCCAGGCCTCAACCTCA;RSEQ=CACAGAGCGGCTCATGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:118,25:0:2,0:23.2:1:32:1:1:0:60:34.75:1:0:0.1 0/1:117:2:1,1:91,24:0.0171:2,2:12.5:1:28.5:1:0.38314:3.73555:60:4:0.0171:0:1 -17 17127190 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1943;SOR=Inf;LSEQ=TCAGCACAGAGCGGCTCATG;RSEQ=AGTGCAGGGCCCCCTGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:144,52:0:2,0:24.9:1:32.2:1:1:0:60:195:1:0:0.1 0/1:155:2:0,2:107,46:0.0129:2,0:14:1:24.5:1:0.09451:0:60:4:0.013:0:1 -17 17127199 . GC G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.85336;LSEQ=AGCGGCTCATGCAGTGCAGG;RSEQ=CCCCTGCCGCCCCGGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:162,76:0.0124:2,2:16.7:1:31.9:1:1:1.0655:60:6:0.0126:0.0083:0.3 0/1:188:2:1,1:118,67:0.0106:2,2:24:1:29.5:1:1:1.7555:60:4:0.0109:0.0053:0.5 -17 17127471 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29775;LSEQ=GGCAGACCTGGAGGGACACC;RSEQ=GCGACTCAGACAGCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:309:174:51,123:39,96:0.5631:2,2:26.2:1:30.6:1:1:1.02:60:57:0.5644:0:1.1 0/1:325:90:37,53:81,154:0.2769:2,2:24.4:1:29.8:1:0.30273:1.33:60:44:0.2759:0:1.2 -17 17127863 . A C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTCTTTCTTTCTTTCTTT;RSEQ=TTTGAGATGGAGTCTCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:33.5:1:1:0:60:4:1:0:1.5 -17 17129431 . A G 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCTGGCTCCGAGCCCACCC;RSEQ=GAGCACCTGGGAGCATGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:192,212:0:2,0:23.3:1:30.3:1:1:0:60:43.889:1:0:0.1 0/1:392:67:27,40:152,173:0.1709:2,2:20.5:1:29.2:1:0.34901:1.30078:60:66:0.171:0:1.2 -17 17131018 . T G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGGCAATAAGAGCAAAAC;RSEQ=CTGTCTCAAAAAAAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:0:1,0:20.8:1:30.9:1:1:0:60:18.667:1:0:0.2 0/1:32:12:12,0:20,0:0.375:1,0:18.7:1:27:1:1:0:60:11:0.3548:0:1.1 -17 17131025 . CA C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.54878;SOR=0;LSEQ=ATAAGAGCAAAACTCTGTCT;RSEQ=AAAAAAACAAAACAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:3:3,0:60,1:0.0469:1,0:33:1:31.7:1:1:0:60:6:0.0484:0:0.7 0/0:33:0:0,0:33,0:0:1,0:21:1:30.3:1:1:0:60:66:1:0:0.5 -17 17131095 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18173;SOR=Inf;LSEQ=AAGAACTGAAGGGCCCCTGA;RSEQ=AAGCAGTCTGTGTCACCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:207,9:0:1,0:25.5:1:31.7:1:1:0:60:29.857:1:0:0.2 0/1:161:2:1,1:150,9:0.0124:2,2:7.5:1:30:1:0.12073:15.85687:60:4:0.0125:0:1.5 -17 17131402 . C T 78 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.28784;SOR=2.92609;LSEQ=CCTCCGTGCAGAAGAGAGTG;RSEQ=GGGGGCCGTGGAGCTCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:2:2,0:210,362:0.0035:2,0:27:1:32:0:0.136:0:60:4:0.0035:0:1 0/1:592:6:3,3:227,359:0.0101:2,2:27.3:1:30.2:1:0.68204:1.58:60:12:0.0103:0:1 -17 17131869 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCTCCACCCAATACATA;RSEQ=CTGCTTGGCACCTGCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:20.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 18215858 . G A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=CTGGTGGGACAAATTACAAC;RSEQ=ACATATGAGATCTGCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:4,0:0.2:0,0:40:0:31:0:1:0:60:2:0.2:0:1 0/1:5:2:2,0:3,0:0.4:0,0:15:0:32:0:1:0:60:4:0.4:0:1 -17 18216013 . C A 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00932;SOR=2.03243;LSEQ=TGTACATAAAAATAAAAATT;RSEQ=TCTTTCCAAGAAAAGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:33:21,12:59,27:0.2773:2,2:18.3:1:28.3:1:0.66477:1.24628:60:66:0.2797:0:1 0/1:139:61:43,18:55,23:0.4388:2,2:23.2:1:28.3:1:1:1.001:60:122:0.4552:0:1.1 -17 18216100 . G A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19489;SOR=1.50627;LSEQ=AACACAAAGGAAAAGAGGAC;RSEQ=AGGCATCTGATGTATGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:22:7,15:53,88:0.135:2,2:27.4:1:30.2:1:0.64416:1.28862:60:21:0.1296:0:1 0/1:189:36:13,23:58,95:0.1905:2,2:23.1:1:29.5:1:1:1.07975:60:72:0.1925:0:1.1 -17 18216155 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50548;SOR=Inf;LSEQ=AAACATGGAGTTCGAGCTGG;RSEQ=CACGGTGGCTCACGCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:4,37:0:2,0:21.1:1:32.2:1:1:0:60:82:1:0:0.1 0/1:55:2:1,1:4,49:0.0364:2,2:5:0:27:1:0.17508:11.07:60:4:0.037:0:1 -17 18216574 . A G 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20322;SOR=0;LSEQ=TTACATGGCAGAACTGGAAA;RSEQ=GTCTATGTTACCCAGCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:45,52:0.0202:2,2:26:0:30:1:1:1.15:60:4:0.0206:0:1 0/0:120:0:0,0:62,58:0:2,0:32.6:1:30.1:1:1:0:60:240:1:0:0.2 -17 18216745 . C A 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13193;SOR=0.15632;LSEQ=AGTCAAAGAGAAAGGGTTCA;RSEQ=CTGAAGTGCCAGCCTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:0.7143:0,2:15.4:1:30:1:1:0:60:10:0.7143:0:1 0/1:8:2:0,2:0,6:0.25:0,0:35:1:31.5:1:1:0:60:4:0.25:0:1 -17 18575675 . T G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25789;LSEQ=CTTGAAGTAGGGCACGCAAC;RSEQ=CACCATCCACTCGTAGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:143:80,63:77,52:0.5257:2,2:26.8:1:30.6:1:0.54158:1.16544:43.8:70.5:0.5281:0:1.1 0/1:347:77:42,35:144,126:0.2219:2,2:26.9:1:30.3:1:0.8973:1.05:46.9:154:0.2292:0:1.2 -17 18575700 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08248;SOR=0;LSEQ=ATCCACTCGTAGATCTGGGA;RSEQ=AGAGTGAGCCGTCTGTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:135,158:0.0101:2,2:8.7:1:25:0:1:1.7059:53.7:6:0.0104:0:1 0/0:384:0:0,0:179,205:0:2,0:27.9:1:31.1:1:1:0:54.1:63:1:0:0.3 -17 18575752 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6037;SOR=0.444;LSEQ=TGGCGCGGGTGATCAGGTCC;RSEQ=CGTAGGACAGGTTTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:48,139:0.0106:2,2:18.5:1:28.5:1:0.45232:2.88:54.5:4:0.0108:0:1 0/0:212:1:1,0:64,147:0.0047:2,0:1:0:28:0:0.3066:0:53:2:0.0047:0:1 -17 18575767 . C A 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00772;SOR=Inf;LSEQ=GGTCCGCGTAGGACAGGTTT;RSEQ=CCCAGGCGTTCCGCCGCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:26,110:0:2,0:23.1:1:31.5:1:1:0:40.7:135:1:0:0.2 0/1:152:8:2,6:33,111:0.0526:2,2:14.8:1:30.6:1:1:1.12:48.1:16:0.0541:0:1.4 -17 18575782 . C A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04512;SOR=Inf;LSEQ=GGTTTCCCCAGGCGTTCCGC;RSEQ=GCGACGAACATTTCCTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:8,92:0:2,0:21.5:1:29.9:1:1:0:40:200:1:0:0.2 0/1:87:4:1,3:7,76:0.046:2,2:20.5:1:32.3:1:0.32499:3.54:41.3:8:0.046:0:1 -17 18575804 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4989;SOR=0;LSEQ=CGACGAACATTTCCTCGGCT;RSEQ=CCCGGAGCCCCCAGCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:1,54:0.0351:1,2:21:1:30:1:0.06955:38.52:21:4:0.0351:0:1 0/0:48:0:0,0:1,47:0:1,0:26.1:1:32.1:1:1:0:38.3:96:1:0:0.1 -17 18575988 . CCCG C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.33333;SOR=0;LSEQ=CCGGAGACCAGCGTGCGGCT;RSEQ=CCGCCGCCGCCGATCGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:1:31.5:1:1:0:60:4:1:0:0 0/0:1:0:0,0:0,1:0:0,0:27:0:33:0:1:0:60:2:1:0:0 -17 19284152 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50444;SOR=0;LSEQ=GCTCGTGGCCTGTGCACCTC;RSEQ=CCCGCTGAACATCAGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:45,28:0.0267:2,2:29.5:1:31:1:1:1.59658:60:4:0.027:0:1 0/0:58:0:0,0:40,17:0:2,0:24.7:1:30.6:1:1:0:60:114:1:0:0.1 -17 19284156 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19509;SOR=Inf;LSEQ=GTGGCCTGTGCACCTCGCCC;RSEQ=CTGAACATCAGTACTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:48,31:0:2,0:25:1:30.9:1:1:0:60:158:1:0:0.1 0/1:63:2:1,1:41,20:0.0317:2,2:42:1:30.5:1:1:2.0249:60:4:0.0323:0:1 -17 19284257 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49697;SOR=Inf;LSEQ=TATACACAGGCTATTGACCT;RSEQ=TGGTCTGTGGGCTGCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:14,40:0:2,0:23.9:1:31.4:1:1:0:60:53:1:0:0.1 0/1:60:2:1,1:19,39:0.0333:2,2:33.5:1:27.5:1:1:2.03:60:4:0.0333:0:1 -17 19301452 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21256;SOR=Inf;LSEQ=AGCCTAGGAGAGTCGCCACT;RSEQ=TCCTCAGTCCTGATGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:25,20:0:2,0:24.5:1:31.2:1:1:0:60:21.5:1:0:0.2 0/1:39:2:1,1:20,17:0.0513:2,2:27.5:1:32:1:1:1.17156:60:4:0.0513:0:1 -17 19301475 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.49568;SOR=0;LSEQ=CTCAGTCCTGATGTCCCTGG;RSEQ=CCGCCTGCCTTCTTTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:20,21:0.0465:2,2:39:1:29:1:1:1.05:60:4:0.0465:0:1 0/0:38:0:0,0:18,20:0:2,0:30.8:1:30.6:1:1:0:60:37:1:0:0.2 -17 21407795 . G T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69057;SOR=0.52952;LSEQ=AAATCTCAATCCTCAGGCAG;RSEQ=GTCTGAAATAATCACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:13,0:0.2778:1,0:26.6:1:31.4:1:1:0:60:10:0.2778:0:2.2 0/1:18:3:3,0:15,0:0.1667:1,0:31.3:1:31.7:1:1:0:60:6:0.1765:0:2.3 -17 21407854 . G A 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.83341;SOR=1.16679;LSEQ=AGAAAACCCACCTTTCGGCC;RSEQ=GAACCGCCATCTTCCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:13:7,6:18,11:0.3095:2,2:26.5:1:29.8:1:0.73773:1.39114:58.8:26:0.325:0:2.3 0/1:64:22:15,7:22,20:0.3438:2,2:25.4:1:30.6:1:0.2902:1.93:55.9:44:0.3438:0:2.1 -17 21407858 . C T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68063;SOR=1.24405;LSEQ=AACCCACCTTTCGGCCGGAA;RSEQ=CGCCATCTTCCAGTAATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:13:7,6:18,13:0.2955:2,2:27.9:1:29.9:1:1:1.18217:58.8:26:0.2955:0:2.3 0/1:67:23:15,8:23,21:0.3433:2,2:25.6:1:29.7:1:0.43665:1.70:55.4:46:0.3485:0:2.1 -17 21407860 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51194;SOR=Inf;LSEQ=CCCACCTTTCGGCCGGAACC;RSEQ=CCATCTTCCAGTAATTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:28,20:0:2,0:28.1:1:29.9:1:1:0:57.8:47:1:0:0.6 0/1:69:2:1,1:38,29:0.029:2,2:28:1:26.5:1:1:1.30515:60:4:0.0303:0:1 -17 21408107 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22943;SOR=Inf;LSEQ=CCAGCATGCTGTTGGCATTG;RSEQ=TGTAAACAAACAAGTTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:54,101:0:2,0:22.3:1:29.4:1:1:0:38.8:76.5:1:0:0.1 0/1:143:2:0,2:45,95:0.014:2,0:28:1:33.5:1:1:0:41:4:0.0141:0:1 -17 21490090 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=5.16229;LSEQ=TTAAGAGCTTTGGAATGTAA;RSEQ=GAACCAATGTGGCATGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:16:14,2:33,18:0.2388:2,2:23.6:1:30.6:1:0.11914:3.75:60:32:0.2388:0:1.5 1/0:45:28:22,6:13,4:0.6222:2,2:25:1:30.1:1:1:1.13:60:56:0.6222:0:1.6 -17 21490163 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21263;SOR=Inf;LSEQ=GATGATAAACTTAATAAATG;RSEQ=TTGAATTTCGGAAGATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:87,62:0:2,0:25.7:1:32:1:1:0:58:148:1:0:0.7 0/1:128:2:1,1:73,53:0.0156:2,2:25.5:1:29.5:1:1:1.37384:60:4:0.0159:0:1 -17 21490164 . T A 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=3.74889;LSEQ=ATGATAAACTTAATAAATGC;RSEQ=TGAATTTCGGAAGATAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:46:27,19:61,43:0.3067:2,2:30:1:30.6:1:1:1.00:53.5:92:0.3108:0:2.1 1/0:128:80:42,38:31,17:0.625:2,2:29.3:1:29.6:1:0.20097:1.6434:53.9:160:0.6299:0:2.1 -17 21490183 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4996;SOR=0;LSEQ=CTTGAATTTCGGAAGATAAT;RSEQ=TACATGTCTCAGGATCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:84,69:0.0129:2,2:25.5:1:31:1:1:1.21583:54.5:4:0.0132:0:1 0/0:140:0:0,0:75,65:0:2,0:27.4:1:29.5:1:1:0:54.6:69:1:0:1.3 -17 21490189 . G C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.17849;LSEQ=TTTCGGAAGATAATTTACAT;RSEQ=TCTCAGGATCAGTTACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:48:26,22:56,54:0.3038:2,2:25.5:1:31.6:1:0.73209:1.14:50.4:96:0.3097:0:1.9 1/0:134:78:38,40:32,24:0.5821:2,2:26.2:1:31.2:1:0.3827:1.39993:51.5:156:0.5865:0:2 -17 21490213 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21705;SOR=Inf;LSEQ=CAGGATCAGTTACTTCATAC;RSEQ=AAGGTTTATACGTGGGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:61,76:0:2,0:26.4:1:31.6:1:1:0:54:136:1:0:0.5 0/1:120:2:1,1:49,69:0.0167:2,2:5:1:24:1:1:1.40:54.5:4:0.0168:0:2 -17 21535580 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACTCTTGAATTATTTTCA;RSEQ=GATTGACTTATCAACTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16:1:33:1:1:0:24:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 21535775 . C T 59 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.582;LSEQ=TTAAATATAAAAAGAAATGA;RSEQ=GCATTAATGTTTTCAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:3,1:15,1:0.2:1,2:37:1:29.8:1:0.36842:4.47215:38.5:8:0.2:0:2.5 0/1:8:1:0,1:7,0:0.125:0,0:50:0:31:0:0.125:0:40:2:0.125:0:3 -17 21535820 . T C 50 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62393;SOR=0.44597;LSEQ=AACTTTTATTAAGTAAATAC;RSEQ=TGAGAGGAAGCTTTTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:11,2:0.1875:2,2:20.7:1:32:1:0.48929:2.54679:35.7:6:0.1875:0:3 0/1:11:1:0,1:10,0:0.0909:0,0:6:0:33:0:0.09091:0:40:2:0.1:0:3 -17 21535836 . A C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACTTGAGAGGAAGCTTTT;RSEQ=CTGGTAATTGTGGTTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:18,2:0.0909:2,2:12.5:1:33:0:0.25974:7.54971:40:4:0.0909:0:3 0/0:10:0:0,0:10,0:0:0,0:22.5:1:27.4:1:1:0:46.6:20:1:0:0.5 -17 21535856 . A T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50916;SOR=0.54221;LSEQ=ACTGGTAATTGTGGTTTTAT;RSEQ=TATGTAGCTATAGTTATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:15:13,2:8,0:0.6522:0,2:18.4:1:29.8:1:0.52569:0:38.3:14:0.6364:0:1.7 1/0:16:8:8,0:8,0:0.5:0,0:13.1:1:27:1:1:0:37.4:7:0.4667:0:1.6 -17 21535937 . T C 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04403;SOR=0.63604;LSEQ=TATTTTTTTCCCATCCTGTT;RSEQ=AGGTGGTTTCCTAGAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:249:185:172,13:58,5:0.743:2,2:25.7:1:31.3:1:0.7829:1.14:47.6:45.25:0.7418:0:1.5 1/0:156:101:93,8:49,6:0.6474:2,2:28.7:1:31.4:1:0.56542:1.42:43.7:100:0.6494:0:1.6 -17 21535940 . G A 91 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09309;SOR=0.18467;LSEQ=TTTTTTCCCATCCTGTTTAG;RSEQ=TGGTTTCCTAGAAACATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:8:5,3:230,16:0.0315:2,2:30.3:1:30.6:1:0.01574:8.46617:36.9:16:0.0323:0:3.6 0/0:168:1:1,0:151,16:0.006:2,0:12:0:28:0:1:0:37:2:0.0061:0:5 -17 21535972 . A G 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.76039;SOR=0.91932;LSEQ=AAACATGATTGTTTATTGGC;RSEQ=TTGATCTCACAGTCTGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:74:64,10:252,51:0.1958:2,2:30.3:1:29:1:0.5982:1.29:32.7:23.667:0.1924:0:2.4 0/1:268:49:46,3:161,57:0.1828:2,2:27.6:1:28.6:1:0.00201:5.40:30.6:48:0.1805:0:2.3 -17 21535979 . TCA T 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.7479;SOR=1.07489;LSEQ=ATTGTTTATTGGCATTGATC;RSEQ=CAGTCTGGTGAGGACTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:417:59:51,8:282,76:0.1415:2,2:28.9:1:30.9:1:0.22016:1.72:31.8:118:0.1436:0.0096:2.3 0/1:299:45:37,8:174,81:0.1505:2,2:24:1:29.5:1:0.07576:2.15:30.1:90:0.151:0.0334:2.4 -17 21535981 . A G 85 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08815;SOR=0.17297;LSEQ=TGTTTATTGGCATTGATCTC;RSEQ=CAGTCTGGTGAGGACTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:8:6,2:281,77:0.019:2,2:25.3:1:28.5:1:0.68415:1.21577:38:7:0.0193:0:3.5 0/0:300:1:1,0:180,81:0.0033:2,0:41:0:26:0:1:0:37:2:0.0038:0:5 -17 21536022 . T G 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42908;SOR=1.18881;LSEQ=TACTGATAATGTCAAGTTCA;RSEQ=GTTACCCTCCCAACCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:698:59:26,33:394,239:0.0845:2,2:21.8:1:30:1:0.00785:2.09008:29.9:28.5:0.0823:0:2.5 0/1:556:55:26,29:270,227:0.0989:2,2:21.8:1:29.7:1:0.32324:1.32598:32.2:17.333:0.0945:0:2.6 -17 21536065 . A G 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28911;SOR=1.15439;LSEQ=ATTCAGCACAGAACAAAGTC;RSEQ=TTATCCTCCTCACTCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:834:148:90,58:329,357:0.1775:2,2:23.4:1:30.5:1:0.00493:1.68:33.6:48.333:0.1755:0:2.5 0/1:677:135:82,53:258,282:0.1994:2,2:24:1:30.2:1:0.00717:1.69:33.7:134:0.1988:0:2.5 -17 21536104 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00132;SOR=Inf;LSEQ=AAAGTATACGTTTCCCAGCA;RSEQ=CTGCCACCAGCAGGTAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:689:0:0,0:279,410:0:2,0:25.7:1:31.1:1:1:0:53.3:75.556:1:0:0.7 0/1:537:8:4,4:256,273:0.0149:2,2:27.4:1:28.1:1:1:1.07:40.5:16:0.0151:0:3.1 -17 21536106 . T C 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00053;SOR=1.59294;LSEQ=AGTATACGTTTCCCAGCACC;RSEQ=GCCACCAGCAGGTAAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:681:147:80,67:171,340:0.2159:2,2:32.5:1:30.1:1:1e-05:2.37:36.7:35.75:0.2138:0:2.1 0/1:528:161:100,61:140,214:0.3049:2,2:28.4:1:29.5:1:0:2.50:36.1:79.5:0.3046:0:2.1 -17 21536131 . A G 67 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04692;SOR=7.97912;LSEQ=CCAGCAGGTAAGGAACAAAT;RSEQ=CTATGCAAATTGCACGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:1:1,0:164,357:0.0019:2,0:33:0:14:0:0.31609:0:25:0:0:0:7 0/1:397:6:5,1:161,230:0.0151:2,2:15:1:26.3:1:0.08644:7.11:29:5:0.0127:0:4.3 -17 21536149 . GTTTTTTG TTTTT 90 v4;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.02703;SOR=5.09374;LSEQ=AATACTATGCAAATTGCACG;RSEQ=TGTTTTTCTTTGCTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:2:1,1:112,308:0.0047:2,2:16:1:29.1:1:0.46431:2.74:31:4:0.0048:0:3 0/1:338:8:8,0:115,215:0.0237:2,0:17.3:1:30:1:0.00026:0:38.5:16:0.0242:0.0089:3 -17 21536156 . GTGTTTTTCTTTGCTTTTCCTATTTAATACACA TTTTTTCTTTTCCCATTTTATTCACC 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.08958;SOR=Inf;LSEQ=GCAAATTGCACGTGTTTTTT;RSEQ=TGTTGGTAGAAACCACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:89,278:0:2,0:24.1:1:31.7:1:1:0:53.1:51.429:1:0:0.6 0/1:299:3:1,2:96,197:0.01:2,2:16.3:1:26.5:1:1:1.03:48.3:2:0.0068:0.01:2 -17 21536158 . G T 46 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.69762;SOR=0.62285;LSEQ=AAATTGCACGTGTTTTTTGT;RSEQ=TTTTTCTTTGCTTTTCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:4:3,1:85,275:0.011:2,2:10.3:1:23.3:1:0.04534:9.63:37.8:3:0.0084:0:4.3 0/0:292:2:2,0:98,191:0.0068:2,0:1.5:1:27.5:1:0.11731:0:35.5:4:0.0069:0:5.5 -17 21536168 . G A 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.14033;LSEQ=TGTTTTTTGTGTTTTTCTTT;RSEQ=CTTTTCCTATTTAATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:91:23,68:37,182:0.2935:2,2:22.1:1:27.9:1:0.11373:1.66:39.5:17.2:0.2896:0:1.7 0/1:242:114:39,75:28,99:0.4711:2,2:22:1:27.6:1:0.04371:1.83:40.1:27.5:0.4641:0:1.8 -17 21536212 . A G 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31277;SOR=1.30459;LSEQ=TGGTAGAAACCACCAAATTT;RSEQ=CCTTTTTTTTTAAGTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:43:4,39:16,144:0.2118:2,2:32:1:31.3:1:1:1.08291:36.9:42:0.2111:0:2.7 0/1:154:40:9,31:7,106:0.2597:2,2:34.6:1:29.7:1:0.00683:4.34:41.2:12.333:0.25:0:3 -17 21536214 . CT C 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.26267;SOR=0;LSEQ=GTAGAAACCACCAAATTTAC;RSEQ=TTTTTTTTAAGTGGCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:3:0,3:17,179:0.0151:2,0:29.7:1:33:1:1:0:49:6:0.0155:0:0 0/0:150:0:0,0:15,134:0:2,0:29:1:29.7:1:1:0:50.6:48.667:1:0:1.3 -17 21536250 . G A 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47972;SOR=1.22669;LSEQ=CAAGAGCTATTTACAAAGAC;RSEQ=AGGAACCAAAGGTTGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:42:4,38:4,72:0.3559:2,2:29.3:1:31.1:1:0.45275:1.88:37.1:84:0.3621:0:2.7 0/1:94:38:7,31:3,53:0.4043:2,2:21.7:1:29.3:1:0.08386:3.93:41.4:11.667:0.3933:0:3 -17 21536277 . C T 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22545;SOR=1.70626;LSEQ=CAAAGGTTGGGAATTAATTA;RSEQ=TTCTGTCTTCTTACTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:42:4,38:1,23:0.6364:1,2:17.1:1:30.2:1:0.64546:2.39:39.8:41:0.6308:0:2.2 1/0:48:36:2,34:1,11:0.75:2,2:16.5:1:31:1:1:1.5302:44.2:72:0.75:0:1.9 -17 21536306 . A G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05391;LSEQ=TCTTACTGTGGCTTTATGCC;RSEQ=ATTTCAGGAGTTGAACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:7:2,5:1,31:0.1795:1,2:17.7:1:30.9:1:0.07736:11.16:36.9:14:0.1842:0:2.1 0/1:16:3:0,3:1,12:0.1875:1,0:29:1:32:1:1:0:34.7:6:0.1875:0:2.7 -17 21536331 . GC G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67329;LSEQ=CAGGAGTTGAACTTGTCTTT;RSEQ=TTTTGATGACAGGAGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:2,5:1,20:0.25:1,2:28.7:1:32.3:1:0.1453:7.24:34.9:14:0.25:0.0357:1.4 0/1:11:2:0,2:1,8:0.1818:2,0:33:1:33:0:1:0:36.5:4:0.2:0:2 -17 21536371 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52964;SOR=0;LSEQ=ATGATAAATAGAAAACTTAT;RSEQ=AATTCTCTAGAATTTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:1,13:0.1765:1,0:13.7:1:27.3:1:1:0:49.7:6:0.1765:0:1.7 0/0:7:0:0,0:1,6:0:2,0:16.9:1:31.3:1:1:0:41:14:1:0:0.9 -17 21536413 . T C 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=TAAGACCTATATTTATACTC;RSEQ=CAAGTTGTGGTTGAGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:10.8:1:31.8:1:1:0:32.3:8:0.5714:0:1.5 1/1:2:2:0,2:0,0:1:0,0:16:1:32.5:1:1:0:29:4:1:0:1 -17 21543246 . C T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAATGACCTCACGGATTTA;RSEQ=ATCTTAAGAGAGGAATCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:26.5:1:1:0:39:4:1:0:1.5 -17 21544157 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=ATTCTTTATAATTTCAGTAT;RSEQ=GTTACACTAGAGGCTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:9.7:1:31:0:1:0:40:6:0.4286:0:3.3 0/0:4:0:0,0:3,1:0:2,0:36.8:1:30.8:1:1:0:57.3:8:1:0:0 -17 21544178 . A G 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2605;SOR=0;LSEQ=GTTACACTAGAGGCTGATCA;RSEQ=CACTAACTCACCTGACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:22.3:1:33.3:1:1:0:36.3:8:0.3333:0:3.8 0/0:5:0:0,0:4,1:0:2,0:24.2:1:30.4:1:1:0:53.6:10:1:0:0.2 -17 21544200 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14737;SOR=Inf;LSEQ=ACTAACTCACCTGACTTTGT;RSEQ=TAGCTTTTAGGCTCTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:33.8:1:28.7:1:1:0:47.1:24:1:0:1.7 0/1:8:2:1,1:5,1:0.25:2,2:19.5:1:33.5:1:0.46429:3.87298:49:4:0.25:0:1 -17 21544219 . A G 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.55454;LSEQ=TATAGCTTTTAGGCTCTTCA;RSEQ=AATAGTACATGGTATATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:13,0:0.2353:1,0:37.8:1:31.8:1:1:0:36.3:8:0.2353:0:3.8 0/1:7:1:1,0:5,1:0.1429:2,0:23:0:34:0:1:0:30:2:0.1429:0:4 -17 21544241 . A T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTACATGGTATATCTAA;RSEQ=CTACAAAAGTGAGGTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:24,0:0.0769:1,0:12:1:30.5:1:1:0:40:4:0.0769:0:4 0/0:8:0:0,0:7,1:0:2,0:33.1:1:29.9:1:1:0:49.8:16:1:0:0.8 -17 21544245 . C T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.87847;LSEQ=TACATGGTATATCTAAACTA;RSEQ=AAAAGTGAGGTGAGAATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:21,0:0.125:1,0:16.3:1:31:1:1:0:35:6:0.125:0:3.7 0/1:9:1:1,0:7,1:0.1111:2,0:49:0:32:0:1:0:30:2:0.1111:0:4 -17 21544383 . A G 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00458;SOR=Inf;LSEQ=GGACTCTATTAGTGAGAAAT;RSEQ=AATTGTTTTTCTTGGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:253,54:0:2,0:19.8:1:28.3:1:1:0:59.1:75.75:1:0:1 0/1:268:7:7,0:198,62:0.0261:2,0:13.3:1:32.6:1:0.35883:0:30.1:14:0.0265:0:2.1 -17 21544395 . T C 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13005;SOR=1.27088;LSEQ=TGAGAAATAAATTGTTTTTC;RSEQ=TGGTTTTATTCTCTAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:148:117,31:169,58:0.3947:2,2:20.7:1:30.7:1:0.32306:1.29:58.8:23.667:0.3923:0:2.2 0/1:342:155:111,44:141,46:0.4532:2,2:21.7:1:30.5:1:0.46039:1.21434:59.6:154:0.4516:0:2.1 -17 21544404 . T C 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=AATTGTTTTTCTTGGTTTTA;RSEQ=TCTCTAAAGGATCCAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:321,136:0:2,0:22.7:1:30.5:1:1:0:59.4:64.286:1:0:1.3 0/1:427:14:8,6:287,125:0.0328:2,2:18.3:1:30:1:0.37808:1.71962:60:28:0.0329:0:1.1 -17 21544414 . G T 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00321;SOR=0.67443;LSEQ=CTTGGTTTTATTCTCTAAAG;RSEQ=ATCCAACATTTGGAGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:204:139,65:236,116:0.3669:2,2:23.7:1:29.4:1:0.85113:1.05:59.7:203:0.3718:0:1.1 0/1:509:143:95,48:247,119:0.2809:2,2:23.6:1:29:1:0.83411:1.04863:59.9:142:0.2857:0:1.2 -17 21544420 . A G 155 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=31.40818;LSEQ=TTTATTCTCTAAAGGATCCA;RSEQ=CATTTGGAGGCAAACATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:1:1,0:406,212:0.0016:2,0:1:0:31:0:1:0:21:2:0.0016:0:4 0/1:580:28:26,2:352,198:0.0483:2,2:20.3:1:32.3:1:0.00091:7.30:35:56:0.0486:0:2.3 -17 21544462 . G A 247 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.31593;SOR=0.9077;LSEQ=CTCCATCCTCTCCAATTTCG;RSEQ=GGCAACCATGTGGAGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:922:339:193,146:318,265:0.3677:2,2:27.6:1:30.1:1:0.49271:1.10:56:36.667:0.3646:0:2.3 0/1:990:342:194,148:350,298:0.3455:2,2:26.5:1:29.4:1:0.42107:1.12:55:56:0.345:0:2.3 -17 21544470 . A G 252 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34251;SOR=0.91162;LSEQ=TCTCCAATTTCGGGGCAACC;RSEQ=TGTGGAGATGATCAAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:935:346:186,160:314,273:0.3701:2,2:25.8:1:30.5:1:0.94592:1.01:55.3:56.667:0.3704:0:2.2 0/1:995:347:192,155:339,308:0.3487:2,2:26.3:1:29.9:1:0.38654:1.13:54.4:346:0.352:0:2.2 -17 21544493 . C T 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.15552;LSEQ=TGGAGATGATCAAAATGCTT;RSEQ=ACCTTCAAAACTTTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:915:82:39,43:420,412:0.0896:2,2:33.9:1:29.5:1:0.6445:1.12383:41.2:164:0.0905:0:2.6 0/1:988:173:84,89:407,408:0.1751:2,2:33:1:29:1:0.80177:1.0569:41.3:172:0.1757:0:2.7 -17 21544512 . G C 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.07023;LSEQ=TCACCTTCAAAACTTTCAAA;RSEQ=GAAGAGTTAATACAGAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:837:73:33,40:352,410:0.0872:2,2:17.7:1:30.7:1:0.90269:1.04061:40.5:72:0.0871:0:2.8 0/1:908:150:68,82:353,399:0.1652:2,2:16.8:1:30.3:1:0.78811:1.06681:41.3:74:0.1644:0:2.8 -17 21544527 . G A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00062;SOR=1.95842;LSEQ=TCAAAGGAAGAGTTAATACA;RSEQ=AGTATGGATCGTATAAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:773:41:13,28:321,411:0.053:2,2:8:1:30:1:0.14593:1.68112:38.3:82:0.0535:0:3.2 0/1:809:80:26,54:323,406:0.0989:2,2:9.6:1:29.9:1:0.04398:1.65134:38:79:0.0986:0:3.3 -17 21544570 . C T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00289;SOR=Inf;LSEQ=AAATTGCAAAAGTAGAACAG;RSEQ=AGATCCTTAAACTGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:0:0,0:249,392:0:2,0:24.8:1:32:1:1:0:59.8:127.2:1:0:0.7 0/1:599:8:4,4:244,343:0.0134:2,2:29.8:1:29.3:1:0.72474:1.40:58.5:16:0.0135:0:2.1 -17 21544587 . A G 247 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.95042;SOR=0.9859;LSEQ=CAGCAGATCCTTAAACTGAA;RSEQ=AAGAAACAAGTAAAAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:228:73,155:108,203:0.423:2,2:27:1:31.6:1:0.51974:1.12938:59.4:227:0.4227:0:1.5 0/1:522:219:77,142:122,181:0.4195:2,2:25.4:1:31.2:1:0.2732:1.2425:59.9:218:0.4208:0:1.4 -17 21544599 . A G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.09411;LSEQ=AAACTGAAAAAGAAACAAGT;RSEQ=AAAGTCTTTGCTTATAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:150:47,103:113,219:0.3112:2,2:27.5:1:31.1:1:0.60211:1.13048:59.9:36.5:0.3067:0:1 0/1:467:19:6,13:169,279:0.0407:2,2:27.1:1:31.2:1:0.6385:1.31168:60:38:0.0411:0:1.1 -17 21544646 . T C 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37169;SOR=0.822;LSEQ=AATGTGTGTTTTTCTCCCTA;RSEQ=AGAAGATATTTTTGAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:101:16,85:22,111:0.4316:2,2:22.1:1:32:1:1:1.05271:58.5:49.5:0.4286:0:2.3 0/1:190:73:16,57:28,89:0.3842:2,2:25.1:1:31.6:1:0.86004:1.1201:59:72:0.383:0:2.2 -17 21544647 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20223;SOR=Inf;LSEQ=ATGTGTGTTTTTCTCCCTAT;RSEQ=GAAGATATTTTTGAGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:35,192:0:2,0:21.6:1:30.6:1:1:0:59.2:55.75:1:0:1.3 0/1:186:2:1,1:39,145:0.0108:2,2:25:0:32.5:1:0.38477:3.68:53:4:0.011:0:1.5 -17 21544674 . T A 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.89072;SOR=0.95016;LSEQ=ATTTTTGAGTTTTCCATATT;RSEQ=TGAAACTGTACATAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:49:5,44:2,76:0.3858:1,2:21.8:1:30.9:1:0.10682:4.27:57.5:98:0.392:0:2.1 0/1:99:37:2,35:3,59:0.3737:1,2:20.9:1:30.9:1:1:1.12:57.8:74:0.3737:0:2.3 -17 21544804 . ATTTG A 85 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63948;SOR=0.34368;LSEQ=ATATGATTGTAGAGAGTGAA;RSEQ=TTTGTCCATTCTGTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:0,6:3,13:0.2727:2,0:20.5:1:33:0:0.53247:0:59.3:12:0.2727:0:1 0/1:9:1:0,1:2,6:0.1111:2,0:30:0:31:0:1:0:48:2:0.125:0:2 -17 21544812 . G T 26 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTAGAGAGTGAAATTTGTTT;RSEQ=TCCATTCTGTTTTTGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:2,16:0.1:2,0:32.5:1:26.5:1:1:0:38.5:4:0.1:0:4 0/0:6:0:0,0:1,5:0:2,0:24.8:1:28.8:1:1:0:58:5:1:0:0.5 -17 21544821 . G A 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.35116;SOR=0.27199;LSEQ=GAAATTTGTTTGTCCATTCT;RSEQ=TTTTTGATTTTTTTTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:0,7:1,8:0.4375:2,0:13:1:30.1:1:1:0:54.4:14:0.4667:0:1.9 0/1:6:1:0,1:1,4:0.1667:2,0:18:0:28:0:1:0:48:2:0.1667:0:2 -17 21809102 . C G 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGGCAGAGGTTGCAGTGAG;RSEQ=CGAGATCGTGCCACTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:32.5:1:32:1:1:0:48:4:0.4:0:4 1/1:1:1:1,0:0,0:1:0,0:3:0:30:0:1:0:40:2:1:0:4 -17 21809110 . G A 66 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGCAGTGAGCCGAGATC;RSEQ=TGCCACTGCACTCCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:24:1:28.6:1:1:0:43.2:4:1:0:3.4 1/1:1:1:1,0:0,0:1:0,0:11:0:32:0:1:0:40:2:1:0:4 -17 21809116 . C T 81 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAGCCGAGATCGTGCCA;RSEQ=TGCACTCCAGCCTGGTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:21.3:1:31.7:1:1:0:42.7:12:1:0:3.2 1/1:1:1:1,0:0,0:1:0,0:17:0:32:0:1:0:40:2:1:0:4 -17 21809154 . G A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAAGAATGAAACTCCTTT;RSEQ=TAAAAGTATTTTCTTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:20,0:0,0:1:0,1:21.2:1:28.6:1:1:0:43.9:40:1:0:1.6 1/1:3:3:3,0:0,0:1:0,0:27:1:28.3:1:1:0:40.7:6:1:0:2 -17 21809366 . C G 114 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03338;SOR=2.90999;LSEQ=AGAGATGTAAATTATCTTCC;RSEQ=AAATTCATGCATTTATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:6:2,4:221,203:0.0139:2,2:17:1:32.3:1:0.43438:2.17354:38.3:12:0.0141:0:1.7 0/1:329:13:5,8:166,150:0.0395:2,2:11.3:1:31:1:0.40045:1.76761:38.5:26:0.04:0:1.1 -17 21809394 . A T 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01385;LSEQ=TGCATTTATGAAGTTTATCA;RSEQ=CTGAGTTTTCTGACACTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:372:371:173,198:0,1:0.9973:0,2:27.2:1:30.2:1:1:0:60:60.833:0.9973:0:1.2 1/1:318:266:127,139:27,25:0.8365:2,2:25:1:29:1:0.64979:1.18142:60:52.2:0.8365:0:1.2 -17 21809479 . A G 215 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07531;LSEQ=AAGCTCTTGAAGAACATTGA;RSEQ=AGAAACCAATGGCCTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:125:20,105:1,5:0.9542:2,2:25.8:1:30.9:1:1:1.04961:59.8:19.833:0.952:0:1.3 1/0:138:84:21,63:15,39:0.6087:2,2:21.6:1:31:1:0.84279:1.15264:60:83:0.6103:0:1.4 -17 22245142 . T A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTGGAATCTGCAAGTGG;RSEQ=TGTGTGGTCCTCTTTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:28:1:1:0:25:4:1:0:1.5 -17 22246526 . T A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGACCACTCTGTGGACTTCG;RSEQ=TCGAAACGGGTATATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:39:0:28:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:31.5:1:1:0:46.5:4:1:0:1.5 -17 22247067 . T A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGGAGCTTCACATAAAA;RSEQ=CTAGACAGAAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:4.6:1:31.6:1:1:0:31:14:1:0:3.4 1/1:7:7:7,0:0,0:1:0,0:6.3:1:31:1:1:0:33.9:14:1:0:2.4 -17 22247112 . T G 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71261;SOR=0.7324;LSEQ=TACTTTGTGATGATTGAGTT;RSEQ=AACACACAGAGCTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:3,1:11,5:0.2:2,2:44:1:31.3:1:1:1.34:34.5:8:0.2:0:4.8 0/1:26:4:3,1:15,7:0.1538:2,2:33.3:1:31:1:1:1.38:35.5:8:0.1538:0:5 -17 22247115 . CA AT 80 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.03331;SOR=Inf;LSEQ=TTTGTGATGATTGAGTTTAA;RSEQ=CACAGAGCTGAACATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:15,6:0:2,0:35.7:1:32.1:1:1:0:30.8:42:1:0:3.7 0/1:29:6:4,2:16,7:0.2069:2,2:30.8:1:31.1:1:1:1.13752:40.2:12:0.2069:0:4.7 -17 22247116 . A T 133 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01495;SOR=0;LSEQ=TTGTGATGATTGAGTTTAAC;RSEQ=CACAGAGCTGAACATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:15,7:0,0:1:0,2:34.5:1:30.8:1:1:0:31.2:44:1:0:3.9 1/0:29:22:15,7:1,0:0.7586:0,2:27.2:1:30:1:1:0:32.6:44:0.9565:0:4.3 -17 22247128 . A C 80 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02969;SOR=Inf;LSEQ=AGTTTAACACACAGAGCTGA;RSEQ=CATTCCTTTGGATGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:30.5:1:29.8:1:1:0:32:52:1:0:3.9 0/1:33:6:3,3:18,9:0.1818:2,2:29.8:1:31.2:1:0.64335:1.95607:37.2:12:0.1818:0:4.7 -17 22247144 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50992;SOR=Inf;LSEQ=CTGAACATTCCTTTGGATGG;RSEQ=GCAGGTTTGAAACACACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:25.8:1:30.1:1:1:0:31.8:52:1:0:4 0/1:38:2:1,1:20,16:0.0526:2,2:34:1:29.5:1:1:1.24262:41.5:4:0.0541:0:6 -17 22247149 . GT AC 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51084;SOR=Inf;LSEQ=CATTCCTTTGGATGGAGCAG;RSEQ=TTGAAACACACTTTCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:24.9:1:31.5:1:1:0:31.7:50:1:0:4.1 0/1:37:2:1,1:19,16:0.0541:2,2:12:1:27.2:1:1:1.18197:34:4:0.0541:0.027:5 -17 22247150 . T C 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56531;SOR=0.34446;LSEQ=ATTCCTTTGGATGGAGCAGG;RSEQ=TTGAAACACACTTTCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:13,10:0.08:2,2:23:1:30.5:1:1:1.28628:39:4:0.08:0:6.5 0/1:35:1:1,0:17,16:0.0286:2,0:36:0:33:0:1:0:22:2:0.0294:0:7 -17 22247155 . A G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12898;SOR=0;LSEQ=TTTGGATGGAGCAGGTTTGA;RSEQ=ACACACTTTCTGTAGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:14,12:0,0:1:0,2:22:1:31.7:1:1:0:31.3:52:1:0:4.2 1/1:35:31:16,15:2,2:0.8857:2,2:28.3:1:30.3:1:1:1.06:33:30:0.8824:0:4.9 -17 22247162 . T C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.71405;LSEQ=GGAGCAGGTTTGAAACACAC;RSEQ=TTCTGTAGAATCTGCGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:11,11:0.0833:2,0:22:1:33.5:1:0.48188:0:26:4:0.0833:0:5 0/1:33:2:1,1:15,16:0.0606:2,2:38:1:31.5:1:1:1.06:28:4:0.0606:0:6 -17 22247165 . C T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88082;LSEQ=GCAGGTTTGAAACACACTTT;RSEQ=TGTAGAATCTGCGAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:10,12:1,1:0.9167:2,2:21.5:1:30.1:1:1:1.19087:29.3:44:0.9167:0:4.3 1/1:32:29:14,15:1,1:0.9063:2,2:28.6:1:29.9:1:1:1.06901:33.3:58:0.9355:0:4.9 -17 22247171 . A T 24 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5102;SOR=Inf;LSEQ=TTGAAACACACTTTCTGTAG;RSEQ=ATCTGCGAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:5,15:0:2,0:23:1:30.1:1:1:0:30.3:40:1:0:4.5 0/1:30:2:1,1:12,16:0.0667:2,2:18:1:24:1:1:1.32:31:4:0.0667:0:5.5 -17 22247173 . T A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.39796;LSEQ=GAAACACACTTTCTGTAGAA;RSEQ=CTGCGAGTGGATATTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:5,14:0.05:2,0:2:0:25:0:1:0:25:2:0.05:0:4 0/1:29:2:1,1:11,16:0.069:2,2:37.5:1:30:1:1:1.44:29:4:0.069:0:6 -17 22247175 . TG CA 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52643;SOR=Inf;LSEQ=AACACACTTTCTGTAGAATC;RSEQ=CGAGTGGATATTTGGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:4,12:0:2,0:26.8:1:27.6:1:1:0:31:15:1:0:4.7 0/1:28:2:1,1:10,16:0.0714:2,2:42:1:28:1:1:1.57:28:4:0.0714:0:5.5 -17 22247176 . G A 128 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06968;SOR=0;LSEQ=ACACACTTTCTGTAGAATCT;RSEQ=CGAGTGGATATTTGGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:3,12:0,0:1:0,2:28.3:1:29.7:1:1:0:29.8:30:1:0:4.9 1/0:26:20:7,13:2,2:0.7692:2,2:30.8:1:29.7:1:0.61462:1.80766:32.5:40:0.8333:0:5.3 -17 22247178 . G A 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=ACACTTTCTGTAGAATCTGC;RSEQ=AGTGGATATTTGGACCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:3,11:0,0:1:0,2:29.6:1:30.2:1:1:0:29.8:28:1:0:4.9 1/1:26:24:9,15:1,1:0.9231:2,2:28.9:1:30.3:1:1:1.63293:33.2:48:0.9231:0:5.1 -17 22247239 . T A 70 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATAACTGCACCTAACTAA;RSEQ=CGGAAGCATTCTCACAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:24.8:1:30.4:1:1:0:23.2:10:1:0:4.8 1/1:4:4:0,4:0,0:1:0,0:44:1:29:1:1:0:22:8:1:0:3.5 -17 22247254 . C G 65 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAATCGGAAGCATTCTCA;RSEQ=AAACTTCTTCGTGATGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:13:1:32.5:1:1:0:23.5:8:1:0:4.8 1/1:4:4:0,4:0,0:1:0,0:29:1:32.8:1:1:0:22:8:1:0:3.5 -17 22247264 . C G 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATTCTCACAAACTTCTT;RSEQ=GTGATGTTTGCATTCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:5:1:31.3:1:1:0:22:6:1:0:4.3 1/1:4:4:0,4:0,0:1:0,0:19:1:31.8:1:1:0:22:8:1:0:3.5 -17 22249119 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAAAAATTACACAGAAGCAT;RSEQ=CTCAGGAACTCCTTGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29:1:1:0:24:4:1:0:1.5 -17 22250152 . G C 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64472;SOR=2.36181;LSEQ=AGAAGCATTGTCAGAAACTT;RSEQ=TTTGTGATGACTGCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:3,6:2,2:0.6923:2,2:28.1:1:30.6:1:1:1.8918:24:18:0.75:0:5.8 1/1:13:11:5,6:1,1:0.8462:2,2:26.3:1:31.1:1:1:1.18321:30:22:0.8462:0:5.4 -17 22250162 . AC GT 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47826;SOR=Inf;LSEQ=TCAGAAACTTGTTTGTGATG;RSEQ=TGCATTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:29.8:1:29.4:1:1:0:27.3:22:1:0:4.4 0/1:12:2:1,1:4,6:0.1667:2,2:19:1:30.1:1:1:1.45:24:4:0.1667:0.0833:6 -17 22250163 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31078;SOR=4.00097;LSEQ=CAGAAACTTGTTTGTGATGA;RSEQ=TGCATTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:1,6:1,2:0.7:2,2:34.7:1:29.7:1:1:2.64575:24:14:0.7:0:5.7 1/1:11:10:4,6:0,0:0.9091:0,2:23.7:1:29.5:1:1:0:30.6:20:1:0:5.3 -17 22250201 . C G 52 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GTTGAAGGTTCCTTTTCAAA;RSEQ=AGCAGTTTCCAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:20.3:1:33:0:1:0:24:6:0.6:0:5.3 0/0:4:0:0,0:0,4:0:0,0:29.3:1:33.8:1:1:0:22.5:8:1:0:5 -17 22250214 . A T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.38437;LSEQ=TTTCAAACAGCAGTTTCCAA;RSEQ=CACTCTTTCTGTGGCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:7.3:1:30.3:1:1:0:24:6:0.75:0:5.3 1/0:4:2:0,2:0,1:0.5:0,0:12:1:30:1:1:0:22.5:4:0.5:0:5 -17 22250229 . C A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAACACTCTTTCTGTGG;RSEQ=ATCTGCAAGTGGATGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:8.5:1:31.5:1:1:0:21.5:4:1:0:5 -17 22251409 . C G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTTTTGAAACTCTCTTTCT;RSEQ=TGGAATCTGCAAGGGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29.5:1:1:0:48.5:4:1:0:3 -17 22251431 . C T 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCTGCAAGGGGACATG;RSEQ=AGACCTCTTTGAAGGTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:26.3:1:28.7:1:1:0:47.3:6:1:0:4 -17 22251475 . T A 50 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GAAACAGAATCATCTTCACA;RSEQ=AAAAATTACACAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:33.7:1:31.7:1:1:0:45:6:1:0:4.3 1/0:2:1:1,0:0,1:0.5:0,0:46:0:28:0:1:0:45:2:0.5:0:6 -17 22251487 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCACATAAAAATTACAC;RSEQ=GAAGCATTCTCAGGAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:33.3:1:31.7:1:1:0:45:6:1:0:4.3 1/1:2:2:1,1:0,0:1:0,2:27.5:1:28.5:1:1:0:47:4:1:0:4.5 -17 22251505 . T C 49 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACAGAAGCATTCTCAGGAAC;RSEQ=CCTTGGTGATGTTTGTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:24.3:1:31.3:1:1:0:45:6:1:0:4.3 1/0:2:1:1,0:0,1:0.5:0,0:16:0:25:0:1:0:45:2:0.5:0:6 -17 22251514 . A C 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCAGGAACTCCTTGGTG;RSEQ=TGTTTGTATTCAACTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:33.5:1:1:0:44.5:4:1:0:5 1/1:1:1:1,0:0,0:1:0,0:7:0:26:0:1:0:45:2:1:0:6 -17 22251517 . T A 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGAACTCCTTGGTGATG;RSEQ=TTGTATTCAACTTCCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:32.5:1:1:0:44.5:4:1:0:5 1/1:1:1:1,0:0,0:1:0,0:4:0:24:0:1:0:45:2:1:0:6 -17 22251644 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18182;SOR=Inf;LSEQ=TGGAAAAGGAAATATCTCCA;RSEQ=ATAAATACTAGATAGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:27.2:1:32.3:1:1:0:27.5:12:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:32:1:30:0:1:1.73:23:4:0.4:0:3 -17 22251663 . G C 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATAAATACTAGATAGAAG;RSEQ=CTTCTCAGAAACTACTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:40.3:1:31.5:1:1:0:25.8:8:1:0:2 1/1:2:2:1,1:0,0:1:0,2:39.5:1:31:1:1:0:23:4:1:0:3 -17 22251677 . A C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TAGAAGGCTTCTCAGAAACT;RSEQ=CTTTGTGATGATTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:42:1:31.5:1:1:1:29:4:0.5:0:2.5 0/0:2:0:0,0:1,1:0:2,0:36:1:27:1:1:0:23:4:1:0:3 -17 22251689 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CAGAAACTACTTTGTGATGA;RSEQ=TGCATTCACCTCACGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22.5:1:30.5:1:1:0:25.8:8:1:0:2 1/1:2:2:1,1:0,0:1:0,2:24:1:30:1:1:0:23:4:1:0:3 -17 22252070 . C G 66 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=ACCTTCCTTTGATAGTTCAG;RSEQ=TTTGAAACACTCTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:17:1:33:0:1:0:35:8:1:0:4.8 0/0:4:0:0,0:2,2:0:2,0:28:1:32:1:1:0:38:8:1:0:1.8 -17 22252093 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=Inf;LSEQ=TGAAACACTCTTTTTGTAGG;RSEQ=TCTGCAAGTGCATATTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:23:1:31.1:1:1:0:35.3:18:1:0:4.7 0/1:5:2:1,1:2,1:0.4:2,2:10:1:29.5:1:1:1.7321:23:4:0.4:0:2.5 -17 22252104 . C G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0.32733;LSEQ=TTTTGTAGGATCTGCAAGTG;RSEQ=ATATTTAGACCACTCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:1,0:0.875:0,0:36.7:1:32.6:1:1:0:31.1:14:1:0:5.4 1/0:3:2:1,1:0,1:0.6667:0,2:16.5:1:32:1:1:0:31.5:4:0.6667:0:4.5 -17 22252111 . A G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.40825;LSEQ=GGATCTGCAAGTGCATATTT;RSEQ=GACCACTCTTTGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:0.8889:0,0:35.6:1:33.4:1:1:0:30:16:0.8889:0:5.3 1/0:4:3:3,0:0,1:0.75:0,0:15.3:1:32.7:1:0.25:0:32.7:6:0.75:0:5.7 -17 22252121 . T G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.64552;LSEQ=GTGCATATTTAGACCACTCT;RSEQ=TGGCCTTCGTTCGAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:0.8889:0,0:38.5:1:33.3:1:1:0:30:16:0.8889:0:5.3 1/1:6:5:5,0:0,1:0.8333:0,0:18.8:1:33.6:1:0.16667:0:33.2:10:0.8333:0:5.2 -17 22252144 . C T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09579;LSEQ=GCCTTCGTTCGAAACGGGTA;RSEQ=ATCTTCAAATAAAATCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:6,0:7,4:0.3529:2,0:18.3:1:30.3:1:0.23739:0:30.7:12:0.375:0:5.3 0/1:8:3:3,0:4,1:0.375:2,0:36.7:1:31.7:1:1:0:28.7:6:0.375:0:5.3 -17 22252151 . AA GC 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36252;SOR=3.59095;LSEQ=TTCGAAACGGGTACATCTTC;RSEQ=ATAAAATCTAGACAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:9,3:2,1:0.7059:2,2:17.5:1:30.4:1:1:1.46:33:24:0.7059:0.1176:4.3 1/1:10:9:9,0:0,0:0.9:0,0:31:1:32.4:1:1:0:37.3:18:0.9:0:3.9 -17 22252154 . T A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.5939;LSEQ=GAAACGGGTACATCTTCAAA;RSEQ=AAAATCTAGACAGAAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:10,4:0.125:2,2:14.5:1:28:1:1:2.34522:42:4:0.125:0:5 0/1:13:1:1,0:11,1:0.0769:2,0:25:0:32:0:1:0:40:2:0.0769:0:5 -17 22252186 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52643;SOR=Inf;LSEQ=AGAAGCCTTCTCAGAAACTT;RSEQ=TCTGTGATGATTGCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:32.9:1:31.2:1:1:0:39.6:32:1:0:3.3 0/1:28:2:1,1:19,7:0.0714:2,2:24:0:33.5:1:0.49735:2.60494:43.5:4:0.0714:0:5.5 -17 22252194 . T C 69 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.35665;LSEQ=TCTCAGAAACTTCTCTGTGA;RSEQ=GATTGCATTCAACTCAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:0.1:2,2:34:1:31:1:1:1.54:49:4:0.1:0:1 0/1:38:5:3,2:19,14:0.1316:2,2:10.2:1:29.8:1:1:1.10:34.8:10:0.1316:0:2 -17 22252211 . A C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72867;SOR=1.2884;LSEQ=TGATGATTGCATTCAACTCA;RSEQ=AGCGTTGAACCCTCCTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:6,11:2,2:0.8095:2,2:30.3:1:31.9:1:0.61771:1.77896:36.6:34:0.8095:0:4.4 1/1:39:33:18,15:3,3:0.8462:2,2:27.5:1:31:1:1:1.19:43.1:66:0.8462:0:4.5 -17 22252214 . C A 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.72867;SOR=1.2884;LSEQ=TGATTGCATTCAACTCAAAG;RSEQ=GTTGAACCCTCCTATGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:6,11:2,2:0.8095:2,2:30.5:1:30.6:1:0.61771:1.77896:36.6:34:0.8095:0:4.4 1/1:39:33:15,18:2,1:0.8462:2,2:28.4:1:29.3:1:0.59286:2.34335:43.9:66:0.8462:0:4.3 -17 22252221 . C A 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55357;SOR=0.30067;LSEQ=ATTCAACTCAAAGCGTTGAA;RSEQ=CCTCCTATGGATAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:8,15:0.08:2,2:19.5:1:31.5:1:1:1.83:42:4:0.08:0:5 0/1:40:1:0,1:19,20:0.025:2,0:35:0:27:0:1:0:40:2:0.025:0:6 -17 22252229 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53007;SOR=Inf;LSEQ=CAAAGCGTTGAACCCTCCTA;RSEQ=GGATAGAGCAGTTTTGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,16:0:2,0:24.7:1:30.6:1:1:0:37.5:48:1:0:4.1 0/1:42:2:1,1:17,23:0.0476:2,2:33:0:32:0:1:1.34:30:4:0.0476:0:2.5 -17 22252240 . G T 67 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.65487;SOR=2.53296;LSEQ=ACCCTCCTATGGATAGAGCA;RSEQ=TTTTGAATCTCTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:0,1:6,14:0.0476:2,0:1:0:31:0:1:0:34:2:0.0476:0:4 0/1:44:5:2,3:17,22:0.1136:2,2:31:1:29:1:1:1.15524:43.2:10:0.1136:0:5.8 -17 22252242 . T G 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.30971;SOR=0.36894;LSEQ=CCTCCTATGGATAGAGCAGT;RSEQ=TTGAATCTCTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:4,12:1,1:0.8889:2,2:29.8:1:32.2:1:0.4902:2.79285:35.8:32:0.8889:0:4.8 1/0:43:32:13,19:5,6:0.7442:2,2:28.4:1:30.9:1:1:1.21232:41.8:64:0.7442:0:5.3 -17 22252248 . T A 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.70679;SOR=0.5767;LSEQ=ATGGATAGAGCAGTTTTGAA;RSEQ=CTCTCTTTTTGTGGAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:4,10:1,1:0.875:2,2:31:1:29.9:1:1:2.34522:37:28:0.875:0:4.9 1/1:40:32:12,20:4,4:0.8:2,2:26.3:1:28.5:1:0.6905:1.64481:41.8:64:0.8:0:5.2 -17 22252273 . T C 48 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10078;SOR=0.14488;LSEQ=CTTTTTGTGGAATCTGCAAG;RSEQ=GGATATGTGGTCCTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:1,2:3,9:0.2:2,2:13:1:30.3:1:1:1.46:35.3:6:0.2143:0:6.7 0/1:30:1:0,1:10,19:0.0333:2,0:17:0:32:0:1:0:41:2:0.0333:0:6 -17 22252284 . T A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.48587;LSEQ=ATCTGCAAGTGGATATGTGG;RSEQ=CCTCTTTGAAGATGTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:2,9:1,0:0.9167:0,2:18:1:29.4:1:0.25:0:34.8:22:0.9167:0:5.5 1/1:25:21:4,17:1,3:0.84:2,2:17.4:1:28.7:1:1:1.39562:37.8:20:0.8333:0:5.6 -17 22252290 . TT CC 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.56652;LSEQ=AAGTGGATATGTGGTCCTCT;RSEQ=GAAGATGTCTTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:2,7:1,0:0.9:0,2:19.3:1:29.9:1:0.3:0:35.1:8:0.8889:0.2:4.7 1/1:18:15:3,12:1,2:0.8333:2,2:17.8:1:30.5:1:1:1.9145:36.3:30:0.8333:0.2222:4.9 -17 22252318 . G C 73 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTGGAAACGGGAATAT;RSEQ=TTCACATAAAAACTAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:36.5:1:32.8:1:1:0:37.8:8:1:0:4.3 1/1:5:5:0,5:0,0:1:0,0:22.6:1:31.8:1:1:0:31.4:10:1:0:4.8 -17 22252999 . C T 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTATGGTAGTAAAGGAAA;RSEQ=AGCTTCATATAAAAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,1:0.75:0,0:29.3:1:31.7:1:0.25:0:29.7:6:0.75:0:5.7 1/1:4:4:4,0:0,0:1:0,0:20.3:1:30.8:1:1:0:27.5:8:1:0:5.8 -17 22253014 . A G 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.87089;LSEQ=GGAAACAGCTTCATATAAAA;RSEQ=CTAGACAGCAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,1:0.75:0,0:37.3:1:32:1:0.25:0:29.7:6:0.75:0:5.7 1/1:7:6:6,0:1,0:0.8571:0,0:18.8:1:33.2:1:1:0:23.8:12:0.8571:0:5.8 -17 22253023 . C T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.26154;SOR=5.3196;LSEQ=TTCATATAAAAACTAGACAG;RSEQ=AGCATTCTCAGAAAACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:2,1:0.5714:2,0:32.3:1:31.3:1:0.42857:0:28:8:0.5714:0:6 1/1:9:8:8,0:0,0:0.8889:0,0:20.4:1:31.5:1:1:0:23.9:16:0.8889:0:6 -17 22253031 . T A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.60784;SOR=2.28225;LSEQ=AAAACTAGACAGCAGCATTC;RSEQ=CAGAAAACTCTTTGTGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:2,1:0.625:2,0:27.2:1:31.4:1:0.375:0:27.2:10:0.625:0:6.2 1/1:10:8:8,0:2,0:0.8:0,0:25.3:1:32:0:1:0:23.9:16:0.8:0:6 -17 22253044 . T G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.13484;LSEQ=AGCATTCTCAGAAAACTCTT;RSEQ=GTGACGACTGAGTTTAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:21:1:30:1:1:0:30.1:6:0.75:0:6.6 1/1:10:8:8,0:2,0:0.8:0,0:31.8:1:33.6:1:1:0:23.9:16:0.8:0:6 -17 22253069 . G A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.15611;LSEQ=CGACTGAGTTTAACTCACAG;RSEQ=GCTGAACATTCCTTTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:30:1:29:1:1:0:31.2:12:0.75:0:6.8 1/0:9:7:7,0:2,0:0.7778:0,0:36.1:1:29.9:1:1:0:24.1:14:0.7778:0:6.1 -17 22253099 . G C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06056;SOR=7.30382;LSEQ=TCCTTTGGATGGAGCAGTTT;RSEQ=GAAACACACTATCTGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:2,2:0.4444:2,0:23.3:1:29.8:1:0.42857:0:30:8:0.4444:0:7 1/1:15:13:7,6:1,0:0.8667:0,2:11.9:1:28.5:1:1:0:23.8:26:0.8667:0:6.5 -17 22253112 . C T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12523;SOR=7.87177;LSEQ=GCAGTTTGGAAACACACTAT;RSEQ=TGTAGGATCTGCAAGCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:6,1:2,2:0.6364:2,2:12.7:1:29.4:1:0.49091:4.95:27.3:14:0.6364:0:6.6 1/1:16:15:7,8:1,0:0.9375:0,2:16.7:1:28.3:1:1:0:23.4:30:0.9375:0:6.7 -17 22253118 . G A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2668;SOR=5.56056;LSEQ=TGGAAACACACTATCTGTAG;RSEQ=ATCTGCAAGCGGATACTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:5,2:1,2:0.7:2,2:12.7:1:29.1:1:0.5:4.17:27.3:14:0.7:0:6.4 1/1:15:14:6,8:1,0:0.9333:0,2:22.8:1:28.9:1:0.46667:0:23.4:28:0.9333:0:6.8 -17 22253120 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GAAACACACTATCTGTAGGA;RSEQ=CTGCAAGCGGATACTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:17.7:1:29.9:1:1:0:26.2:20:1:0:4.7 0/1:15:2:1,1:6,7:0.1333:2,2:11.5:1:31:1:1:1.15:28.5:4:0.1333:0:6 -17 22253121 . C G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88648;LSEQ=AAACACACTATCTGTAGGAT;RSEQ=TGCAAGCGGATACTTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:5,2:5,4:0.4375:2,2:13.1:1:30:1:0.63287:1.92:27.3:6:0.4:0:6.4 0/1:27:11:5,6:8,8:0.4074:2,2:27:1:31.1:1:1:1.19191:23.4:22:0.4074:0:6.6 -17 22253128 . C T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27219;SOR=2.38145;LSEQ=CTATCTGTAGGATCTGCAAG;RSEQ=GGATACTTGGGCCTCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:10,6:0,2:0.7619:0,2:10.1:1:27.6:1:0.18301:0:29.5:7:0.7368:0:4.9 1/1:35:31:14,17:1,0:0.8857:0,2:18:1:28.6:1:0.46875:0:27.6:62:0.8857:0:5.5 -17 22253134 . C T 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6306;SOR=1.67973;LSEQ=GTAGGATCTGCAAGCGGATA;RSEQ=TTGGGCCTCTCTGAGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:26:17,9:0,2:0.9286:0,2:12:1:30.5:1:0.1455:0:33.5:52:0.9286:0:4.3 1/1:46:44:23,21:0,0:0.9565:0,2:17.3:1:29.8:1:1:0:31.5:88:0.9565:0:4.9 -17 22253137 . G A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.77854;SOR=0.76321;LSEQ=GGATCTGCAAGCGGATACTT;RSEQ=GGCCTCTCTGAGGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:3,4:18,11:0.1944:2,2:13.9:1:29:1:0.41782:2.13334:32.9:14:0.1944:0:3.6 0/1:58:9:6,3:25,24:0.1552:2,2:28.2:1:29.3:1:0.48144:1.90:28.4:18:0.1579:0:5.3 -17 22253139 . G T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20493;SOR=1.82746;LSEQ=ATCTGCAAGCGGATACTTGG;RSEQ=CCTCTCTGAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:6,5:9,8:0.2973:2,2:13.9:1:29.2:1:1:1.06:35.5:22:0.2973:0:4.9 0/1:64:28:12,16:11,11:0.4375:2,2:13.7:1:28.3:1:0.77591:1.32563:32.3:56:0.4444:0:4.5 -17 22253150 . G C 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13981;LSEQ=GATACTTGGGCCTCTCTGAG;RSEQ=ATTTCGTTGGAAACGGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:8:4,4:30,23:0.129:2,2:21.5:1:32.1:1:1:1.29861:35.5:16:0.1356:0:5.3 0/1:83:12:5,7:36,35:0.1446:2,2:24.7:1:32.1:1:0.75646:1.43371:30:24:0.1446:0:5.2 -17 22253152 . T A 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.73097;LSEQ=TACTTGGGCCTCTCTGAGGA;RSEQ=TTCGTTGGAAACGGGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:34,28:0.0313:2,2:12:1:19.5:1:1:1.21058:24:1:0.0159:0:3.5 0/1:87:2:1,1:43,42:0.023:2,2:10:1:29.5:1:1:1.02354:44.5:4:0.023:0:5 -17 22253156 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18145;SOR=0;LSEQ=TGGGCCTCTCTGAGGATTTC;RSEQ=TTGGAAACGGGATAAACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:35,33:0.0282:2,2:12:1:29:1:1:1.05974:44.5:4:0.0286:0:5 0/0:95:0:0,0:46,48:0:2,0:22.9:1:30.5:1:1:0:34.7:188:0.9895:0:3.7 -17 22253157 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50826;SOR=Inf;LSEQ=GGGCCTCTCTGAGGATTTCG;RSEQ=TGGAAACGGGATAAACCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:37,34:0:2,0:20.9:1:29.6:1:1:0:35.9:70:1:0:3.2 0/1:96:2:1,1:46,48:0.0208:2,2:27:0:31.5:1:1:1.04:45:4:0.0208:0:3.5 -17 22253163 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16928;SOR=0;LSEQ=CTCTGAGGATTTCGTTGGAA;RSEQ=CGGGATAAACCGCACAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:37,37:0.0263:2,2:19:1:31:1:1:1:44.5:4:0.027:0:5 0/0:108:0:0,0:54,54:0:2,0:24.4:1:29.6:1:1:0:35.3:107:1:0:3.6 -17 22253164 . C A 89 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04268;SOR=Inf;LSEQ=TCTGAGGATTTCGTTGGAAA;RSEQ=GGGATAAACCGCACAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:39,38:0:2,0:24.8:1:30.7:1:1:0:36:76:1:0:3.1 0/1:112:7:3,4:53,52:0.0625:2,2:19.7:1:32:1:1:1.35527:40.1:14:0.0625:0:4.6 -17 22253167 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15798;SOR=0;LSEQ=GAGGATTTCGTTGGAAACGG;RSEQ=ATAAACCGCACAGAACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:2,0:39,37:0.0253:2,0:25:1:33:0:0.49484:0:44:4:0.0256:0:6 0/0:119:0:0,0:61,58:0:2,0:24.5:1:31.3:1:1:0:36.2:238:1:0:3.5 -17 22253172 . A C 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1262;SOR=0.48154;LSEQ=TTTCGTTGGAAACGGGATAA;RSEQ=CCGCACAGAACTAAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:14:9,5:34,33:0.1687:2,2:29.4:1:32.1:1:0.39388:1.74:36.9:28:0.1728:0:3.7 0/1:124:11:6,5:57,54:0.0887:2,2:30.2:1:31.5:1:1:1.14:35.6:22:0.0894:0:3.5 -17 22253173 . C A 99 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00647;SOR=Inf;LSEQ=TTCGTTGGAAACGGGATAAA;RSEQ=CGCACAGAACTAAACAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:44,39:0:2,0:28.9:1:31.2:1:1:0:36.5:26.667:1:0:3 0/1:124:10:5,5:59,55:0.0806:2,2:23.1:1:30.1:1:1:1.07209:36.6:20:0.0806:0:5.5 -17 22253174 . C T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12512;SOR=0.53665;LSEQ=TCGTTGGAAACGGGATAAAC;RSEQ=GCACAGAACTAAACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:18:9,9:35,30:0.2169:2,2:31.6:1:29.3:1:0.79569:1.16449:31.1:8:0.2:0:4.6 0/1:124:16:7,9:57,51:0.129:2,2:33.8:1:30.6:1:0.59588:1.43276:33.6:32:0.1301:0:5.1 -17 22253175 . G A 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.34241;LSEQ=CGTTGGAAACGGGATAAACC;RSEQ=CACAGAACTAAACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:1:0,1:44,38:0.012:2,0:49:0:29:0:0.46988:0:45:2:0.012:0:4 0/1:124:2:1,1:63,59:0.0161:2,2:30.5:1:28.5:1:1:1.0672:23:4:0.0161:0:4.5 -17 22253178 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51334;SOR=Inf;LSEQ=TGGAAACGGGATAAACCGCA;RSEQ=AGAACTAAACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:46,40:0:2,0:30.7:1:32.1:1:1:0:36.3:85:1:0:3.1 0/1:123:2:1,1:62,59:0.0163:2,2:45.5:1:29.5:1:1:1.05044:45:4:0.0163:0:3.5 -17 22253182 . A C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16865;SOR=0;LSEQ=AACGGGATAAACCGCACAGA;RSEQ=CTAAACAGAAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:46,41:0.0225:2,2:32.5:1:32:1:1:1.1205:46:4:0.0225:0:4.5 0/0:127:0:0,0:63,63:0:2,0:29.3:1:30:1:1:0:36.2:252:0.9921:0:3.4 -17 22253184 . T TA 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.0977;SOR=1.6218;LSEQ=CGGGATAAACCGCACAGAAC;RSEQ=AAACAGAAGCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:27:17,10:36,35:0.2755:2,2:27.7:1:28.9:1:0.36504:1.64:37.3:26:0.2737:0.051:3.6 0/1:144:55:32,23:42,45:0.3819:2,2:26.1:1:29.3:1:0.30166:1.49:37.2:110:0.3819:0.0903:3.8 -17 22253191 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52298;SOR=Inf;LSEQ=AACCGCACAGAACTAAACAG;RSEQ=AGCATTCTCAGAACCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:56,47:0:2,0:29.3:1:30.1:1:1:0:36.2:50.5:1:0:3.2 0/1:162:2:1,1:86,73:0.0123:2,2:41.5:1:32:1:1:1.17688:45:4:0.0125:0:4.5 -17 22253194 . C A 93 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01399;SOR=Inf;LSEQ=CGCACAGAACTAAACAGAAG;RSEQ=ATTCTCAGAACCTTCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:57,49:0:2,0:28.7:1:32.3:1:1:0:36.2:212:1:0:3.2 0/1:169:9:7,2:83,77:0.0533:2,2:20.2:1:29.4:1:0.17639:3.23:37.9:18:0.0539:0:6.9 -17 22253203 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.15972;SOR=0;LSEQ=CTAAACAGAAGCATTCTCAG;RSEQ=ACCTTCTTCGTGATGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:60,53:0.0174:2,2:35.5:1:29.5:1:1:1.13085:43:4:0.0175:0:5.5 0/0:172:0:0,0:92,80:0:2,0:25.5:1:29.4:1:1:0:38.5:171:1:0:3.6 -17 22253204 . A G 105 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00699;SOR=Inf;LSEQ=TAAACAGAAGCATTCTCAGA;RSEQ=CCTTCTTCGTGATGTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:61,53:0:2,0:26:1:29.9:1:1:0:36.7:113:1:0:3.3 0/1:174:10:7,3:86,78:0.0575:2,2:24:1:31.8:1:0.34144:2.11:38.5:20:0.0585:0:6.8 -17 22253207 . T C 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01724;SOR=1.89514;LSEQ=ACAGAAGCATTCTCAGAACC;RSEQ=TCTTCGTGATGTTTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:30:16,14:49,44:0.2439:2,2:25.6:1:30.7:1:1:1.03:38.5:14:0.2353:0:3.9 0/1:179:68:40,28:55,56:0.3799:2,2:24.7:1:30.6:1:0.2803:1.45:39.5:67:0.3785:0:4.4 -17 22253213 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51463;SOR=Inf;LSEQ=GCATTCTCAGAACCTTCTTC;RSEQ=TGATGTTTGCATTCAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:66,64:0:2,0:22.8:1:30.8:1:1:0:37:64:1:0:3.4 0/1:187:2:1,1:96,89:0.0107:2,2:12.5:1:28:1:1:1.07819:41.5:4:0.0108:0:7 -17 22253219 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51483;SOR=Inf;LSEQ=TCAGAACCTTCTTCGTGATG;RSEQ=TTGCATTCAACCCACAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:63,66:0:2,0:22.8:1:29.9:1:1:0:37.3:128:1:0:3.4 0/1:186:2:1,1:94,89:0.0108:2,2:20.5:1:33.5:1:1:1.05589:44:4:0.0108:0:6.5 -17 22253220 . T C 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.71795;SOR=0.90958;LSEQ=CAGAACCTTCTTCGTGATGT;RSEQ=TGCATTCAACCCACAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:46:23,23:38,43:0.3622:2,2:24.4:1:31.6:1:0.85362:1.13:36.8:92:0.3651:0:4.2 0/1:185:63:31,32:64,58:0.3405:2,2:25.3:1:32:1:0.75664:1.13824:37.9:126:0.3424:0:4.1 -17 22253224 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1645;SOR=0;LSEQ=ACCTTCTTCGTGATGTTTGC;RSEQ=TTCAACCCACAGTGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:57,65:0.0161:2,2:20.5:1:29:1:1:1.14:41.5:4:0.0163:0:7.5 0/0:181:0:0,0:90,91:0:2,0:25.6:1:29.9:1:1:0:38.8:362:1:0:3.7 -17 22253226 . T G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15973;SOR=0;LSEQ=CTTCTTCGTGATGTTTGCAT;RSEQ=CAACCCACAGTGTTGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:55,62:0.0168:2,2:35.5:1:31:1:1:1.13:43:4:0.0171:0:5.5 0/0:178:0:0,0:88,90:0:2,0:26:1:29.4:1:1:0:38.6:356:1:0:3.7 -17 22253231 . C T 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.47814;SOR=0.63346;LSEQ=TCGTGATGTTTGCATTCAAC;RSEQ=CACAGTGTTGAACCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:109:103:47,56:3,1:0.945:2,2:26.5:1:30.7:1:0.33766:3.53488:37.1:206:0.945:0:3.6 1/1:166:152:72,80:4,3:0.9157:2,2:27.3:1:29.4:1:0.71025:1.47782:38.4:75:0.9259:0:3.9 -17 22253234 . C A 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27959;SOR=Inf;LSEQ=TGATGTTTGCATTCAACCCA;RSEQ=AGTGTTGAACCTTTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:49,56:0:2,0:27:1:32:1:1:0:36.6:104:1:0:3.5 0/1:160:3:1,2:77,79:0.0188:2,2:36.3:1:30.7:1:1:1.9415:35.3:6:0.0188:0:6.7 -17 22253235 . A G 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48356;SOR=2.01473;LSEQ=GATGTTTGCATTCAACCCAC;RSEQ=GTGTTGAACCTTTCTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:48,55:0.019:2,2:37.5:1:27:1:1:1.14:42:4:0.019:0:5 0/1:159:6:3,3:74,79:0.0377:2,2:27.8:1:28.5:1:1:1.07:32.7:12:0.038:0:5.3 -17 22253239 . T C 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00107;SOR=2.56695;LSEQ=TTTGCATTCAACCCACAGTG;RSEQ=TGAACCTTTCTTTGATAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:22:11,11:34,41:0.2268:2,2:26:1:31.7:1:0.80914:1.20:39:21:0.2188:0:4 0/1:151:65:36,29:38,48:0.4305:2,2:28.9:1:30.7:1:0.19128:1.56:39.8:20.667:0.4189:0:4.6 -17 22253240 . T G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41233;SOR=0.79003;LSEQ=TTGCATTCAACCCACAGTGT;RSEQ=GAACCTTTCTTTGATAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:37:17,20:27,32:0.3854:2,2:31.7:1:31.8:1:1:1.01:34.9:74:0.3854:0:4.1 0/1:148:49:22,27:51,48:0.3311:2,2:29.6:1:31.1:1:0.48786:1.30163:35.2:98:0.3356:0:4 -17 22253244 . C A 80 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08389;SOR=Inf;LSEQ=ATTCAACCCACAGTGTTGAA;RSEQ=CTTTCTTTGATAGTTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:43,48:0:2,0:29.4:1:31.9:1:1:0:36.2:182:1:0:3.6 0/1:141:6:2,4:67,68:0.0426:2,2:25:1:31:1:0.6811:1.96145:44.5:12:0.0429:0:4 -17 22253248 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14714;SOR=0;LSEQ=AACCCACAGTGTTGAACCTT;RSEQ=CTTTGATAGTTCAGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:40,45:0.023:2,2:13:1:29.5:1:1:1.12:43:4:0.0233:0:2 0/0:139:0:0,0:68,71:0:2,0:26.8:1:29.1:1:1:0:38.1:138:1:0:3.8 -17 22253249 . C G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.6368;SOR=0.61173;LSEQ=ACCCACAGTGTTGAACCTTT;RSEQ=TTTGATAGTTCAGGTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:37,45:0.0235:2,2:44:1:32:1:1:1.21:41.5:4:0.0235:0:7.5 0/1:138:2:1,1:65,69:0.0145:2,2:27:1:30:1:1:1.06:41.5:4:0.0146:0:4.5 -17 22253259 . T G 103 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00312;SOR=Inf;LSEQ=TTGAACCTTTCTTTGATAGT;RSEQ=CAGGTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:35,42:0:2,0:27.2:1:30.2:1:1:0:34.6:154:1:0:3.7 0/1:111:11:6,5:46,51:0.0991:2,2:24.1:1:29.8:1:0.7554:1.33:38.6:10:0.0909:0:6.2 -17 22253260 . C G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16483;SOR=0;LSEQ=TGAACCTTTCTTTGATAGTT;RSEQ=AGGTTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:33,40:0.0267:2,2:44:1:32.5:1:1:1.21:41.5:4:0.0267:0:7.5 0/0:109:0:0,0:52,56:0:2,0:25.2:1:30.8:1:1:0:37:35:0.9906:0:4.1 -17 22253263 . G C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00208;SOR=2.89841;LSEQ=ACCTTTCTTTGATAGTTCAG;RSEQ=TTTGAAACACTCTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:16:9,7:25,31:0.2222:2,2:24.4:1:32.4:1:0.57126:1.58:37.8:32:0.2254:0:4.1 0/1:99:45:25,20:23,31:0.4545:2,2:23.6:1:31.6:1:0.22931:1.68:40.2:44:0.4536:0:5 -17 22253267 . G T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50488;SOR=Inf;LSEQ=TTCTTTGATAGTTCAGGTTT;RSEQ=AAACACTCTTTTTGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:31,38:0:2,0:23.7:1:31.6:1:1:0:34.1:138:1:0:3.8 0/1:89:2:1,1:39,48:0.0225:2,2:30:1:27.5:1:1:1.23:42:4:0.0227:0:7 -17 22253271 . C A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50227;SOR=Inf;LSEQ=TTGATAGTTCAGGTTTGAAA;RSEQ=ACTCTTTTTGTAGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:29,39:0:2,0:21:1:31.5:1:1:0:33.6:136:1:0:4 0/1:84:2:1,1:36,46:0.0238:2,2:26:1:28.5:1:1:1.27:42:4:0.0238:0:7 -17 22253272 . AC GG 138 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01803;SOR=0.38078;LSEQ=TGATAGTTCAGGTTTGAAAC;RSEQ=TCTTTTTGTAGAAACTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:21:9,12:20,27:0.3088:2,2:21.5:1:31.5:1:1:1.01:33.9:42:0.3088:0.0147:3.3 0/1:83:12:2,10:34,37:0.1446:2,2:19.8:1:31.3:1:0.0596:4.522:37.6:24:0.1446:0.0241:3.2 -17 22253278 . T C 87 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.01527;SOR=Inf;LSEQ=TTCAGGTTTGAAACACTCTT;RSEQ=TTGTAGAAACTGCAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:26,38:0:2,0:16.8:1:29.8:1:1:0:33.3:128:1:0:3.8 0/1:75:7:2,5:30,38:0.0933:2,2:17:1:31.1:1:0.6916:1.95691:42.7:14:0.0933:0:6 -17 22253279 . T C 139 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01659;SOR=0.37149;LSEQ=TCAGGTTTGAAACACTCTTT;RSEQ=TGTAGAAACTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:21:9,12:15,24:0.3443:2,2:16.2:1:31.8:1:0.78715:1.20:33.1:42:0.3443:0:3.6 0/1:74:12:3,9:29,33:0.1622:2,2:19.5:1:32.3:1:0.2119:2.60418:35.7:24:0.1622:0:4.4 -17 22253282 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=Inf;LSEQ=GGTTTGAAACACTCTTTTTG;RSEQ=AGAAACTGCAAGTGGATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:23,36:0:2,0:15.2:1:28.5:1:1:0:32.6:118:1:0:3.8 0/1:69:2:1,1:27,40:0.029:2,2:19.5:1:33.5:1:1:1.47:31:4:0.029:0:5 -17 22253286 . A T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=TGAAACACTCTTTTTGTAGA;RSEQ=ACTGCAAGTGGATAACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:19,32:0:2,0:14.8:1:29.8:1:1:0:32.2:102:1:0:3.9 0/1:60:2:1,1:20,38:0.0333:2,2:20.5:1:27:1:1:1.88:23:4:0.0333:0:4.5 -17 22253291 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20126;SOR=0;LSEQ=CACTCTTTTTGTAGAAACTG;RSEQ=AAGTGGATAACTGCACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:12,28:0.0476:2,2:6.5:1:28.5:1:0.52846:2.28:40:4:0.0476:0:5 0/0:51:0:0,0:14,37:0:2,0:13.2:1:32:1:1:0:34.8:102:1:0:4.3 -17 22253295 . T G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50804;SOR=0.73608;LSEQ=CTTTTTGTAGAAACTGCAAG;RSEQ=GGATAACTGCACTTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:16:2,14:8,13:0.4211:2,2:22.1:1:30.5:1:0.13677:4.1472:27.6:32:0.4211:0:5.6 0/1:46:16:4,12:10,20:0.3478:2,2:19.7:1:29.8:1:0.73948:1.48713:28.9:32:0.3478:0:5.4 -17 22253299 . T TATTTGGACCTCTCTGAGGATTTCGTTGGAAACGGGATA 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TTGTAGAAACTGCAAGTGGA;RSEQ=AACTGCACTTCTTTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:12:4,8:2,16:0.4:2,2:12.2:1:29.6:1:0.18438:3.81:30.8:24:0.4:0.4:3.6 0/0:35:0:0,0:9,25:0:2,0:11.8:1:28.4:1:1:0:32.3:68:0.9714:0:4.4 -17 22253300 . A C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22186;SOR=0;LSEQ=TGTAGAAACTGCAAGTGGAT;RSEQ=ACTGCACTTCTTTGAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:0,2:6,21:0.069:2,0:32.5:1:33:1:1:0:22.5:4:0.069:0:6 0/0:32:0:0,0:8,24:0:2,0:11.8:1:29:1:1:0:31.6:64:1:0:4.4 -17 22253302 . C T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65618;SOR=0.444;LSEQ=TAGAAACTGCAAGTGGATAA;RSEQ=TGCACTTCTTTGAGGCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:15:2,13:1,1:0.8824:2,2:23.4:1:30:1:0.33088:5.50762:25.4:30:0.8824:0:5.3 1/0:17:13:2,11:1,3:0.7647:2,2:20.4:1:29.9:1:1:1.76214:30.4:26:0.7647:0:5.7 -17 22253307 . CT C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12011;SOR=0.23875;LSEQ=ACTGCAAGTGGATAACTGCA;RSEQ=TCTTTGAGGCCTATCGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:0,8:0,5:0.5714:0,0:29.3:1:31.8:1:1:0:25.4:16:0.5714:0.1429:5.9 0/1:13:3:0,3:2,8:0.2308:2,0:38.7:1:30.3:1:1:0:23:6:0.2308:0:6.3 -17 22253318 . CC AG 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.387;SOR=0.33035;LSEQ=ATAACTGCACTTCTTTGAGG;RSEQ=TATCGTAGTAAAGGAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:0,6:0,5:0.5455:0,0:40.8:1:32:1:1:0:22.8:12:0.5455:0:5.2 0/1:11:3:0,3:0,8:0.2727:0,0:36.7:1:31:1:1:0:23:6:0.2727:0:5.3 -17 22253322 . T C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63512;SOR=0.53515;LSEQ=CTGCACTTCTTTGAGGCCTA;RSEQ=CGTAGTAAAGGAAATAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:0,2:0.8182:0,0:34.9:1:32:1:1:0:22.9:18:0.8182:0:4.9 1/0:10:7:0,7:0,3:0.7:0,0:26.3:1:30.6:1:1:0:23:14:0.7:0:5 -17 22253349 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.175;SOR=Inf;LSEQ=AAAGGAAATAACTTCCTATA;RSEQ=AAACAAGACAGAAGCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:0:0,0:19.6:1:30.9:1:1:0:23:18:1:0:4.4 0/1:7:2:0,2:0,5:0.2857:0,0:10:1:32.5:1:1:0:23:4:0.2857:0:5 -17 22253353 . C G 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68659;LSEQ=GAAATAACTTCCTATAAAAA;RSEQ=AAGACAGAAGCTTTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:17:1:32.7:1:1:0:22.7:12:0.75:0:5.3 1/0:6:4:0,4:0,2:0.6667:0,0:19.3:1:31.5:1:1:0:23:8:0.6667:0:5 -17 22254132 . A G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=TTTGGAAACACTCTTGTTGT;RSEQ=GAATCTGCTAGTGGAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:21.5:1:32:0:1:0:22.5:4:0.6667:0:6 1/0:4:3:3,0:1,0:0.75:0,0:14:1:33:1:1:0:22.7:6:0.75:0:6.3 -17 22254137 . C G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=AAACACTCTTGTTGTAGAAT;RSEQ=TGCTAGTGGAGATTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:26.5:1:32:1:1:0:22.5:4:0.6667:0:6 1/0:4:3:3,0:1,0:0.75:0,0:19:1:32.7:1:1:0:22.7:6:0.75:0:6.3 -17 22254141 . T A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=ACTCTTGTTGTAGAATCTGC;RSEQ=AGTGGAGATTTGGAGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:28.5:1:30:1:1:0:22.5:4:0.6667:0:6 1/0:4:3:3,0:1,0:0.75:0,0:23:1:31:1:1:0:22.7:6:0.75:0:6.3 -17 22254170 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGGAGCGCTTTGAGGCCT;RSEQ=TGGTAGTAAAGGGAAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:27:1:28.8:1:1:0:22.8:10:1:0:3.6 0/1:13:2:1,1:7,4:0.1538:2,2:10:1:31.5:1:1:1.67325:41:4:0.1538:0:6.5 -17 22254186 . G T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1819;SOR=3.73633;LSEQ=GCCTATGGTAGTAAAGGGAA;RSEQ=AGCTTCACATAAAATCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:0.5:2,2:20.5:1:28.3:1:1:1:22.5:8:0.5714:0:5.5 1/1:15:12:6,6:1,2:0.8:2,2:26.8:1:28.2:1:1:1.91:26.5:24:0.8:0:5.6 -17 22254194 . C T 103 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02511;SOR=14.39433;LSEQ=TAGTAAAGGGAAGAGCTTCA;RSEQ=ATAAAATCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:29.7:1:29:1:1:1.81007:22.3:6:0.4286:0:5.7 1/1:14:13:6,7:0,1:0.9286:0,2:31.3:1:28.1:1:1:0:28.7:26:0.9286:0:5.8 -17 22254196 . T G 104 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15636;SOR=4.47754;LSEQ=GTAAAGGGAAGAGCTTCACA;RSEQ=AAAATCTAGACAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:30.3:1:31.3:1:1:1.81007:22.3:6:0.4286:0:5.7 1/0:14:11:5,6:0,1:0.7857:0,2:34.1:1:30.3:1:1:0:26.8:22:0.7857:0:5.6 -17 22254201 . T A 105 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02511;SOR=14.39433;LSEQ=GGGAAGAGCTTCACATAAAA;RSEQ=CTAGACAGAAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,1:0.4286:2,2:32:1:30.3:1:1:3.10575:22.3:6:0.5:0:5.7 1/1:14:13:6,7:0,1:0.9286:0,2:33.8:1:28.6:1:1:0:28.7:26:0.9286:0:5.7 -17 22254249 . CA AT 58 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.25075;SOR=Inf;LSEQ=TTTGTGATGATTGAGTTTAA;RSEQ=CACAGAGCTGAACATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:25.5:1:33.5:1:1:0:22.8:8:1:0:2.8 0/1:10:4:2,2:0,6:0.4:0,2:18:1:29:1:0.13333:0:40:8:0.4444:0.1:5.5 -17 22254250 . A T 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=1.22862;LSEQ=TTGTGATGATTGAGTTTAAC;RSEQ=CACAGAGCTGAACATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:19:1:31.5:1:1:0:22.5:4:0.5:0:5 1/0:9:5:0,5:0,1:0.5556:0,0:14.8:1:27.4:1:1:0:23.6:4:0.8:0:5.4 -17 22254262 . A C 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=AGTTTAACACACAGAGCTGA;RSEQ=CATTCCTTTGGATGGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:12.5:1:29:1:1:0:22.8:8:1:0:2.8 0/1:7:3:1,2:0,4:0.4286:0,2:11:1:30:1:0.42857:0:39.3:6:0.4286:0:5.7 -17 22254590 . A C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATGCTTGCATTCAACTCA;RSEQ=AGCGTTGAACCCTCCTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:11.5:1:32:0:1:0:32.5:4:1:0:6.5 -17 22254593 . C A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTGCATTCAACTCAAAG;RSEQ=GTTGAACCCTCCTATGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:3:0:29:0:1:0:24:2:1:0:8 1/1:2:2:2,0:0,0:1:0,0:14.5:1:31:0:1:0:32.5:4:1:0:6.5 -17 22254621 . T G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTATGGATAGAGCAGT;RSEQ=TTGAATCTCTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:26.5:1:33.5:1:1:0:24:4:1:0:7 1/1:2:2:2,0:0,0:1:0,0:42.5:1:33:1:1:0:32.5:4:1:0:6.5 -17 22254627 . T A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGGATAGAGCAGTTTTGAA;RSEQ=CTCTCTTTTTGTGGAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32.5:1:31:0:1:0:24:4:1:0:7 1/1:2:2:2,0:0,0:1:0,0:45:1:32:0:1:0:32.5:4:1:0:6.5 -17 22254663 . T A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCAAGTGGATATGTGG;RSEQ=CCTCTTAGAAGTTGTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32.5:1:27.5:1:1:0:24:4:1:0:7 1/1:2:2:2,0:0,0:1:0,0:11.5:1:31:0:1:0:32.5:4:1:0:6.5 -17 22254669 . TA CC 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGGATATGTGGTCCTCT;RSEQ=GAAGTTGTCTTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25.5:1:27.5:1:1:0:24:4:1:0:6 1/1:2:2:2,0:0,0:1:0,0:10:1:30.9:1:1:0:32.5:4:1:0.5:6 -17 22254675 . T A 45 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGTGGTCCTCTTAGAAG;RSEQ=TGTCTTTGGAAACGGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.3:1:28:1:1:0:24:6:1:0:4.7 1/1:3:3:3,0:0,0:1:0,0:4:1:29:1:1:0:29:6:1:0:3.7 -17 22254760 . A C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09646;SOR=3.56574;LSEQ=GTGATGTTTGTGTTCAACTC;RSEQ=CAGAGTTTCACGTTGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:19:13,6:4,2:0.7037:2,2:25.8:1:30.3:1:1:1.08:30.1:18:0.6923:0:6.4 1/1:29:26:19,7:2,1:0.8966:2,2:27.2:1:29.8:1:1:1.34:30.5:25:0.8929:0:5.2 -17 22254772 . G A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08923;SOR=0.34411;LSEQ=TTCAACTCACAGAGTTTCAC;RSEQ=TTGCTTTTCATAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:21:14,7:3,2:0.8077:2,2:33:1:30.1:1:1:1.32:31.1:42:0.8077:0:6.7 1/0:29:17:10,7:9,3:0.5862:2,2:28.2:1:29.9:1:0.44948:2.04742:32.6:34:0.6071:0:6.1 -17 22254779 . T C 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47507;SOR=1.97547;LSEQ=CACAGAGTTTCACGTTGCTT;RSEQ=TCATAGAGCAGATGAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:2,1:15,8:0.1154:2,2:41.7:1:31:1:1:1.06:36.7:6:0.1154:0:8 0/1:29:6:5,1:14,9:0.2069:2,2:25.8:1:30.3:1:0.63282:3.10:33.5:12:0.2069:0:5.7 -17 22254788 . C T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49077;SOR=2.04528;LSEQ=TCACGTTGCTTTTCATAGAG;RSEQ=AGATGAGAAACATGCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:16:10,6:4,3:0.6957:2,2:37.9:1:28.9:1:1:1.24:33.4:32:0.6957:0:7.7 1/1:23:19:11,8:3,1:0.8261:2,2:32.3:1:28.7:1:1:2.11388:33.7:38:0.8261:0:6.8 -17 22254791 . A T 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72404;SOR=1.48629;LSEQ=CGTTGCTTTTCATAGAGCAG;RSEQ=TGAGAAACATGCTTTTCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:17:11,6:3,3:0.7391:2,2:35.2:1:29.7:1:0.64302:1.78:32.8:34:0.7391:0:7.7 1/1:21:17:9,8:3,1:0.8095:2,2:33.9:1:30.1:1:0.60301:2.55208:34.9:34:0.8095:0:7.4 -17 22254793 . GA CT 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.94247;LSEQ=TTGCTTTTCATAGAGCAGAT;RSEQ=GAAACATGCTTTTCGTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:17:11,6:3,3:0.7391:2,2:32.5:1:30.6:1:0.64302:1.78:32.8:34:0.7391:0:6.7 1/0:22:16:8,8:4,2:0.7273:2,2:31.4:1:31.2:1:0.64617:1.93862:34.4:32:0.7273:0:6.3 -17 22254794 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=TGCTTTTCATAGAGCAGATG;RSEQ=GAAACATGCTTTTCGTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:3,3:0:2,0:22.3:1:29.2:1:1:0:45.8:12:1:0:0.7 0/1:23:2:1,1:3,2:0.087:2,2:21:1:28:1:1:1.41418:44:4:0.2857:0:7.5 -17 22254813 . G T 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1394;SOR=3.50199;LSEQ=GAGAAACATGCTTTTCGTAG;RSEQ=GTCTGCAAGTGGACATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:19:9,10:3,3:0.76:2,2:17.2:1:29.2:1:1:1.10643:34:38:0.76:0:6.9 1/1:37:34:12,22:1,2:0.9189:2,2:18:1:29.3:1:1:1.09:32.2:68:0.9189:0:6.2 -17 22254818 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05093;SOR=0.31228;LSEQ=ACATGCTTTTCGTAGGGTCT;RSEQ=CAAGTGGACATTTGGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:6,6:5,6:0.5217:2,2:12:1:28.5:1:1:1.19:33.6:24:0.5217:0:6.9 0/1:36:9:3,6:9,18:0.25:2,2:14.7:1:29:1:1:1:25.8:18:0.25:0:6.8 -17 22254836 . A C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15064;SOR=3.81363;LSEQ=CTGCAAGTGGACATTTGGAG;RSEQ=GATTTCAGGCCTGTGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,2:0.6667:2,2:33.5:1:32:1:1:1.85:30.3:12:0.6667:0:6.7 1/1:27:24:5,19:1,2:0.8889:2,2:33.4:1:30.3:1:0.5453:1.84904:28.4:48:0.8889:0:6.3 -17 22254838 . A C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.69439;LSEQ=GCAAGTGGACATTTGGAGAG;RSEQ=TTTCAGGCCTGTGGTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:0,1:0.8889:0,2:31.5:1:32.1:1:1:0:33:16:0.8889:0:6.6 1/1:26:22:5,17:1,2:0.8462:2,2:35.6:1:32.2:1:1:1.66053:27.8:44:0.8462:0:6.3 -17 22254848 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATTTGGAGAGATTTCAGGCC;RSEQ=GTGGTGGAAAACGAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:35.4:1:31.4:1:1:0:31.7:18:1:0:5.9 0/1:26:2:1,1:5,19:0.0769:2,2:39.5:1:31.5:1:0.41538:3.56:25:4:0.0769:0:1 -17 22254868 . C G 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83796;LSEQ=TGTGGTGGAAAACGAATTAT;RSEQ=GTCACGTAAAAACTAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:0,1:0.8889:0,2:28:1:30.1:1:1:0:30.6:7:0.875:0:6.5 1/1:23:20:4,16:1,2:0.8696:2,2:25.4:1:31.2:1:0.53924:1.93196:27.9:40:0.8696:0:6.3 -17 22254872 . A C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55676;SOR=0.34695;LSEQ=GTGGAAAACGAATTATCGTC;RSEQ=CGTAAAAACTAGAGAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:17:1:32.5:1:1:1.29:25:4:0.2222:0:6.5 0/1:23:2:0,2:5,16:0.087:2,0:21:1:31:1:1:0:36:4:0.087:0:7.5 -17 22254874 . G A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83796;LSEQ=GGAAAACGAATTATCGTCAC;RSEQ=TAAAAACTAGAGAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:0,1:0.8889:0,2:24.9:1:31.5:1:1:0:30.6:16:0.8889:0:6.5 1/1:23:20:4,16:1,2:0.8696:2,2:19.5:1:30.3:1:0.53924:1.93196:27.9:40:0.8696:0:6.3 -17 22254883 . A G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.23798;LSEQ=ATTATCGTCACGTAAAAACT;RSEQ=GAGAGAAGCATTGTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:0,1:0.8571:0,2:25.2:1:32:1:1:0:30:12:0.8571:0:6.3 1/1:17:15:3,12:0,2:0.8824:0,2:14.8:1:30.3:1:1:0:28:30:0.8824:0:6.5 -17 22254918 . C T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAACTTGTTTGTGATGA;RSEQ=TGCATTCAATTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:12.5:1:30:1:1:0:23:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22254984 . C A 26 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAACACTCTTTCTGTGG;RSEQ=ATCTGCAAGTGGATGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25.5:1:26.5:1:1:0:32:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22254999 . G A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGCATCTGCAAGTGGAT;RSEQ=TTTGGGCCTCTTTGAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:39:1:29.5:1:1:0:32:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22255005 . G A 44 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCAAGTGGATGTTTGG;RSEQ=CCTCTTTGAAGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:27:1:28:1:1:0:28.7:6:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22255009 . C AT 29 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=GCAAGTGGATGTTTGGGCCT;RSEQ=TTTGAAGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:39:0:29.8:1:1:0:32:4:0.6667:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22255035 . T G 63 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTTCGTTGGAAACGGGA;RSEQ=AATCTTCACAGAAAAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:26:1:31.8:1:1:0:27.3:8:1:0:5.5 1/1:1:1:0,1:0,0:1:0,0:26:0:33:0:1:0:23:2:1:0:4 -17 22255047 . A G 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACGGGATAATCTTCACAG;RSEQ=AAAGCTAAACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:29.5:1:33.5:1:1:0:31.5:4:0.6667:0:5 1/1:1:1:0,1:0,0:1:0,0:38:0:33:0:1:0:23:2:1:0:4 -17 22255088 . T C 34 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGAAACTTCTTTGTGATG;RSEQ=TTGCTTTCAACTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:34:0:1:0:22.5:4:1:0:4 1/1:1:1:0,1:0,0:1:0,0:12:0:33:0:1:0:23:2:1:0:4 -17 22255093 . T A 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTCTTTGTGATGTTTGC;RSEQ=TTCAACTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:32.5:1:1:0:22.5:4:1:0:4 1/1:1:1:0,1:0,0:1:0,0:7:0:31:0:1:0:23:2:1:0:4 -17 22255674 . T G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTGTAGAGACTGCAAG;RSEQ=GGATAACTGCACTTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:1:30:1:1:0:23:4:1:0:4 -17 22255681 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGACTGCAAGTGGATAA;RSEQ=TGCACTTCTTTGAGGCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:29.5:1:1:0:23:4:1:0:4 -17 22255701 . T C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCACTTCTTTGAGGCCTA;RSEQ=CGTAGTAAAGGAAATAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:32:1:1:0:23:4:1:0:4 -17 22257247 . C G 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGTGGAAAACGAATTAT;RSEQ=GTCACGTAAAAACTAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:12.5:1:33.5:1:1:0:22:4:1:0:5 -17 22257253 . G A 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAACGAATTATCGTCAC;RSEQ=TAAAAACTAGAGAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:18.5:1:32:0:1:0:22:4:1:0:5 -17 22257262 . A G 34 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTATCGTCACGTAAAAACT;RSEQ=GAGAGAAGCATTGTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:27.5:1:34:0:1:0:22:4:1:0:5 -17 22257286 . G C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGCATTGTCAGAAACTT;RSEQ=TTTGTGATGACTGCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:49.5:1:31.5:1:1:0:22:4:1:0:5 -17 22257297 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAACTTGTTTGTGATGA;RSEQ=TGCATTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:38.5:1:29.5:1:1:0:22:4:1:0:5 -17 22257348 . A T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTCAAACAGCAGTTTCCAA;RSEQ=CACTCTTTCTGTGGCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:26:1:28:1:1:0:22:4:1:0:6.5 -17 22257363 . C A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAACACTCTTTCTGTGG;RSEQ=ATCTGCAAGTGGATGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:41:1:29.5:1:1:0:22:4:1:0:6.5 -17 22257378 . G A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGCATCTGCAAGTGGAT;RSEQ=TTTGGGCCTCTTTGAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:42:1:30.5:1:1:0:22:4:1:0:6.5 -17 22258032 . CT C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTCAGGTTTGAAACACT;RSEQ=TTTAGTAGAAACTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:1:32.5:1:1:0:35:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22258225 . G C 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTAGAATCTGCAAGTG;RSEQ=ATATTTGGACCTGTCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:6:0:34:0:1:0:22:2:1:0:5 1/1:3:3:3,0:0,0:1:0,0:15.7:1:30:1:1:0:22.7:6:1:0:5.7 -17 22258238 . G C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGTGGATATTTGGACCT;RSEQ=TCTGAGGAATTCGTTGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:19:0:33:0:1:0:22:2:1:0:5 1/1:3:3:3,0:0,0:1:0,0:24.3:1:31.3:1:1:0:22.7:6:1:0:5.7 -17 22258240 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGTGGATATTTGGACCTGT;RSEQ=TGAGGAATTCGTTGCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:21:0:33:0:1:0:22:2:1:0:5 1/0:3:2:2,0:1,0:0.6667:0,0:25.5:1:30.5:1:1:0:22.5:4:0.6667:0:6 -17 22258255 . C G 66 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTCTGAGGAATTCGTTG;RSEQ=AAACGGGATAATTTCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:12.8:1:28.6:1:1:0:22.6:4:1:0:5.6 1/1:4:4:4,0:0,0:1:0,0:25:1:31:1:1:0:22.8:8:1:0:5.5 -17 22258275 . A G 92 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=CAAACGGGATAATTTCAGCT;RSEQ=AGTAAACAGAAGCAGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:25.6:1:33:1:1:0:22.7:14:1:0:6 1/0:4:3:3,0:1,0:0.75:0,0:37.3:1:33:1:1:0:22.7:6:0.75:0:5.7 -17 22258277 . G C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGGGATAATTTCAGCTAA;RSEQ=TAAACAGAAGCAGTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:27:1:30.6:1:1:0:22.7:6:1:0:6 1/1:5:5:5,0:0,0:1:0,0:28.6:1:31.8:1:1:0:24:10:1:0:5.6 -17 22258303 . C CT 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGCAGTCTCAGAATCTT;RSEQ=TTGTGATGTTTGCATTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:9,6:0,0:1:0,2:23.6:1:28.8:1:1:0:22.7:14:1:0.3333:5.3 1/1:17:17:10,7:0,0:1:0,2:21.7:1:30.9:1:1:0:27.3:34:1:0:4.9 -17 22258314 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49059;SOR=Inf;LSEQ=CAGAATCTTCTTGTGATGTT;RSEQ=GCATTCAAATCCCAGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:0:2,0:20.2:1:29.5:1:1:0:23.6:40:1:0:5.4 0/1:23:2:1,1:12,9:0.087:2,2:35:1:30.5:1:1:1.31655:23:4:0.0909:0:5 -17 22258328 . A C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.38602;SOR=0.52014;LSEQ=GATGTTTGCATTCAAATCCC;RSEQ=GAATTGAACCTTCCTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:8,7:5,5:0.6:2,2:18.9:1:29.9:1:1:1.14:30.3:30:0.6:0:6.3 0/1:23:10:6,4:6,7:0.4348:2,2:35:1:28:1:0.68017:1.71:30.4:9:0.4091:0:5.6 -17 22258331 . A G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCATTCAAATCCCAGA;RSEQ=TTGAACCTTCCTTTGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:13,12:0,0:1:0,2:23.5:1:31.5:1:1:0:27.3:50:1:0:5.8 1/1:25:25:12,13:0,0:1:0,2:31.6:1:31:1:1:0:30.6:50:1:0:5.4 -17 22258338 . C T 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23529;SOR=0;LSEQ=TTCAAATCCCAGAATTGAAC;RSEQ=TTCCTTTGAAAGTTCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:13,13:0,0:1:0,2:26.3:1:29.5:1:1:0:27.1:25:1:0:5.9 1/1:25:23:11,12:1,1:0.92:2,2:34.7:1:30.3:1:1:1.0871:31.3:46:0.92:0:5.5 -17 22258346 . G C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10327;SOR=0;LSEQ=CCAGAATTGAACCTTCCTTT;RSEQ=AAAGTTCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:13,13:0,0:1:0,2:29.8:1:31.2:1:1:0:27.1:52:1:0:5.9 1/1:24:21:10,11:0,1:0.875:0,2:35.7:1:31.2:1:1:0:32:42:0.875:0:5.5 -17 22258355 . G C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCTTCCTTTGAAAGTTCA;RSEQ=GTTTGAAACACTCTTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:10,13:0,0:1:0,2:35.9:1:31:1:1:0:27.6:46:1:0:5.8 1/1:26:25:11,14:0,1:0.9615:0,2:31:1:27.9:1:1:0:33.2:11.5:0.9583:0:5.2 -17 22258396 . C T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=AGGATCTACAAGTGGATATT;RSEQ=GGACCACTCTGTGGACTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:6,9:0,0:1:0,2:13.9:1:30.7:1:1:0:30.2:30:1:0:6.3 1/1:13:12:4,8:0,1:0.9231:0,2:20.2:1:29.3:1:1:0:35.3:24:1:0:5.6 -17 22258410 . GA TC 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATTCGGACCACTCTGTG;RSEQ=CTTCGATCGAAACGGGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:15.3:1:32.2:1:1:0:29.3:6:1:0:6.7 1/1:5:4:1,3:0,0:0.8:0,2:21.8:1:30.1:1:1:0:29.5:8:1:0:6 -17 22258417 . A T 31 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GGACCACTCTGTGGACTTCG;RSEQ=TCGAAACGGGTATATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14:1:31.5:1:1:0:22.5:4:1:0:6.5 1/0:4:2:0,2:0,2:0.5:0,0:12.5:1:31:0:1:0:22.5:4:0.5:0:7 -17 22258439 . G A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAAACGGGTATATCTTCAC;RSEQ=TAACATCTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:16:1:31.5:1:1:0:35:4:1:0:5 -17 22258441 . A G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACGGGTATATCTTCACGT;RSEQ=ACATCTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:1:0:31:0:1:0:23:2:1:0:5 1/1:2:2:0,2:0,0:1:0,0:14:1:32.5:1:1:0:35:4:1:0:5 -17 22258460 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.81007;LSEQ=TAACATCTAGACAGAAGCAT;RSEQ=CTCAGAAACTTTTCTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:11.5:1:31.5:1:1:0:22.5:4:0.5:0:5.5 1/0:3:2:2,0:1,0:0.6667:0,0:10:1:31:1:1:0:22:4:0.6667:0:5.5 -17 22258468 . A G 77 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGAAGCATTCTCAGAA;RSEQ=CTTTTCTGTGATGACTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:17.8:1:33.2:1:1:0:22.2:10:1:0:4.6 1/1:3:3:3,0:0,0:1:0,0:17:1:33.7:1:1:0:22:6:1:0:5.3 -17 22258472 . T C 84 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGCATTCTCAGAAACTT;RSEQ=TCTGTGATGACTGCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:18.5:1:32.5:1:1:0:22.3:12:1:0:4.7 1/1:3:3:3,0:0,0:1:0,0:21:1:32.7:1:1:0:22:6:1:0:5.3 -17 22258498 . A G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATGACTGCATTCAACTCAC;RSEQ=GAGTTGAACACTCCTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:8,2:0,0:1:0,2:32.5:1:31.6:1:1:0:22.4:20:1:0:4.5 1/1:4:4:3,1:0,0:1:0,2:32.8:1:30.5:1:1:0:22:8:1:0:5.3 -17 22258539 . C G 34 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4955;SOR=0;LSEQ=GAGCGCAGTTTTGAAACTCT;RSEQ=TTTCTCTGGAATCTGCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:13,6:0.0952:2,2:17:0:34:0:1:2.08171:44:4:0.0952:0:5 0/0:16:0:0,0:9,7:0:2,0:18:1:30.6:1:1:0:32:32:1:0:5.6 -17 22258545 . C G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTTTTGAAACTCTCTTTCT;RSEQ=TGGAATCTGCAAGGGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:12,7:0,0:1:0,2:25.5:1:32.4:1:1:0:24.8:38:1:0:5 1/1:20:20:11,9:0,0:1:0,2:18.7:1:30.4:1:1:0:35.6:40:1:0:6.1 -17 22258549 . A C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAACTCTCTTTCTCTGG;RSEQ=ATCTGCAAGGGGACATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:12,8:0,0:1:0,2:25.3:1:32.2:1:1:0:27.1:40:1:0:4.9 1/1:21:21:12,9:0,0:1:0,2:20.9:1:31.4:1:1:0:35:42:1:0:6.1 -17 22258553 . T C 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.97283;LSEQ=AACTCTCTTTCTCTGGAATC;RSEQ=GCAAGGGGACATGCAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:14,9:0.0417:2,0:31:0:27:0:0.41667:0:22:2:0.0417:0:8 0/1:25:2:1,1:13,10:0.08:2,2:32.5:1:29:1:1:1.28628:41.5:4:0.0833:0:7.5 -17 22258554 . G A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23469;SOR=Inf;LSEQ=ACTCTCTTTCTCTGGAATCT;RSEQ=CAAGGGGACATGCAGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:15,10:0:2,0:21.6:1:32:1:1:0:28.1:50:1:0:4.8 0/1:24:2:1,1:12,10:0.0833:2,2:14:1:26:1:1:1.19087:22:4:0.087:0:7.5 -17 22258565 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49336;SOR=Inf;LSEQ=CTGGAATCTGCAAGGGGACA;RSEQ=GCAGACCTCTTTGAAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:25.6:1:30.4:1:1:0:28.2:50:1:0:5 0/1:29:2:1,1:13,14:0.069:2,2:30.5:1:29.5:1:1:1.07:43.5:4:0.0714:0:7 -17 22258567 . C T 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46296;SOR=Inf;LSEQ=GGAATCTGCAAGGGGACATG;RSEQ=AGACCTCTTTGAAGGTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:24:14,10:0,0:0.96:0,2:25.3:1:28.8:1:1:0:28.5:48:0.96:0:4.8 1/1:29:29:14,15:0,0:1:0,2:27.9:1:28.9:1:1:0:35.7:58:1:0:6.2 -17 22258577 . T G 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24941;SOR=Inf;LSEQ=AGGGGACATGCAGACCTCTT;RSEQ=GAAGGTTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:30:1:30.3:1:1:0:29:44:1:0:5 0/1:29:3:2,1:12,14:0.1034:2,2:22.7:1:33.3:1:0.5977:2.27:39:6:0.1034:0:6.7 -17 22258582 . G A 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATGCAGACCTCTTTGAAG;RSEQ=TTTCGTTGGAAACGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:10,10:0,0:1:0,2:32.5:1:30.8:1:1:0:29.6:40:1:0:5.1 1/1:29:29:14,15:0,0:1:0,2:33.6:1:29.7:1:1:0:35.7:58:1:0:6.2 -17 22258587 . G A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49961;SOR=Inf;LSEQ=CAGACCTCTTTGAAGGTTTC;RSEQ=TTGGAAACGGAATCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:27.9:1:31:1:1:0:29:44:1:0:5.1 0/1:29:2:1,1:13,14:0.069:2,2:38:0:30:1:1:1.07:34:4:0.069:0:6 -17 22258595 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49698;SOR=Inf;LSEQ=TTTGAAGGTTTCGTTGGAAA;RSEQ=GGAATCATCTTCACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:24.3:1:30.1:1:1:0:28.8:46:1:0:5.2 0/1:29:2:1,1:13,14:0.069:2,2:26.5:1:33:1:1:1.07:41.5:4:0.069:0:7.5 -17 22258612 . A C 62 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.36226;SOR=3.54922;LSEQ=AAACGGAATCATCTTCACAT;RSEQ=AAAATTACACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:8,12:0.0476:2,0:4:0:27:0:0.42857:0:24:2:0.0476:0:6 0/1:26:4:2,2:10,12:0.1538:2,2:23.8:1:31:1:1:1.19:33.8:8:0.1538:0:6.5 -17 22258617 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCTTCACATAAAAA;RSEQ=TACACAGAAGCATTCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:3,11:0,0:1:0,2:23.7:1:31.7:1:1:0:24.6:28:1:0:6.1 1/1:23:22:10,12:0,0:0.9565:0,2:19.3:1:31.5:1:1:0:38.2:44:0.9565:0:6.7 -17 22258620 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02272;SOR=Inf;LSEQ=TCATCTTCACATAAAAATTA;RSEQ=ACAGAAGCATTCTCAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:2,7:1,3:0.6923:2,2:26:1:28.7:1:1:1.15267:23:18:0.6923:0:6.6 1/1:18:18:8,10:0,0:1:0,2:21.3:1:29.4:1:1:0:36.2:36:1:0:6.8 -17 22258626 . A T 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACATAAAAATTACACAGA;RSEQ=GCATTCTCAGGAACTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:2,9:0,0:1:0,2:26.8:1:29.7:1:1:0:23.1:22:1:0:6.3 1/1:18:17:8,9:0,0:0.9444:0,2:15.8:1:30.2:1:1:0:34.7:34:0.9444:0:6.6 -17 22258642 . CC TT 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGCATTCTCAGGAACT;RSEQ=TTGGTGATGTTTGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:2,8:0,0:1:0,2:24.8:1:29.8:1:1:0:23.1:20:1:0.1:5.4 1/1:9:9:4,5:0,0:1:0,2:10.4:1:29.6:1:1:0:30.9:18:1:0.4444:6.2 -17 22258666 . T C 82 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGATGTTTGTATTCAACT;RSEQ=CCAGAGTTGAACTTTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:24.7:1:32:1:1:0:23.2:12:1:0:5.3 1/1:1:1:0,1:0,0:1:0,0:46:0:33:0:1:0:23:2:1:0:5 -17 22258686 . C T 71 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGAGTTGAACTTTCCTT;RSEQ=GGAAAGAGCAGCTATGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:16.8:1:30.6:1:1:0:23:10:1:0:5.8 1/1:1:1:0,1:0,0:1:0,0:28:0:32:0:1:0:23:2:1:0:5 -17 22258735 . A G 34 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGAATCTGCAAGTGGAC;RSEQ=TTGGGAGGGCTGTGAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:39:1:34:0:1:0:22:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22258738 . G T 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATCTGCAAGTGGACATT;RSEQ=GGAGGGCTGTGAGGTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:36.5:1:32:0:1:0:22:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22258747 . G T 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGGACATTGGGAGGGCT;RSEQ=TGAGGTTTGTGGTGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27.5:1:32:0:1:0:22:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22258750 . A T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACATTGGGAGGGCTGTG;RSEQ=GGTTTGTGGTGGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:31.5:1:1:0:22:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22259137 . C G 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACCTAACTAAACGGAAG;RSEQ=ATTCTCACAAAATTCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:30.5:1:1:0:28:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22259145 . C G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAAACGGAAGCATTCTCA;RSEQ=AAAATTCTTCGTGATGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:31.5:1:1:0:28:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22259149 . A C 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGGAAGCATTCTCACAAA;RSEQ=TTCTTCGTGATGTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:32:1:1:0:28:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22259372 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAACCCTCCTATGGATAG;RSEQ=GCAGTTTTGAATCTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:8:0:30:0:1:0:24:4:1:0:6.5 -17 22259378 . T G 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTATGGATAGGGCAGT;RSEQ=TTGAATCTCTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:6:0:34:0:1:0:27:2:1:0:5 1/0:7:5:3,2:1,1:0.7143:2,2:7:1:31.2:1:1:1.41:28.2:10:0.7143:0:5.8 -17 22259384 . T A 93 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGGATAGGGCAGTTTTGAA;RSEQ=CTCTCTTTTTGTGGAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:6.7:1:31.3:1:1:0:39.3:6:1:0:4.7 1/1:9:9:5,4:0,0:1:0,2:9.8:1:29.6:1:1:0:35.4:18:1:0:5.7 -17 22259408 . G T 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTTTTGTGGAATCTGCAA;RSEQ=TGGATATGTGGTCCTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:30.7:1:33.7:1:1:0:39.3:6:1:0:4.7 0/1:15:4:2,2:6,5:0.2667:2,2:28.8:1:30.3:1:1:1.18545:44:8:0.2667:0:5.8 -17 22259409 . T C 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTTGTGGAATCTGCAAG;RSEQ=GGATATGTGGTCCTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:31.7:1:31.7:1:1:0:39.3:6:1:0:4.7 0/1:15:3:2,1:6,6:0.2:2,2:26.7:1:31.3:1:1:1.91:25.3:6:0.2:0:5.7 -17 22259420 . T A 118 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCAAGTGGATATGTGG;RSEQ=CCTCTTTGAAGATGTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:42.7:1:31.7:1:1:0:39.3:6:1:0:4.7 1/1:16:16:8,8:0,0:1:0,2:34.6:1:29.6:1:1:0:35.2:32:1:0:4.9 -17 22259425 . TTT GCC 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGTGGATATGTGGTCCTC;RSEQ=GAAGATGTCTTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:40.3:1:32:1:1:0:39.3:6:1:0:4.7 0/1:16:2:1,1:7,7:0.125:2,2:23:0:32.8:1:1:1:27:4:0.125:0:2 -17 22259426 . TT CC 117 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGGATATGTGGTCCTCT;RSEQ=GAAGATGTCTTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:38.3:1:32.3:1:1:0:39.3:6:1:0:3.7 1/1:16:14:7,7:0,0:0.875:0,2:40.6:1:30.8:1:1:0:36.4:28:1:0:4 -17 22259466 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGAATATCTTCACATAAAA;RSEQ=CTAAACAGAAGCATTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:7:0:32:0:1:0:27:2:1:0:4 0/1:14:2:1,1:5,7:0.1429:2,2:6.5:1:31.5:1:1:1.37:44:4:0.1429:0:5.5 -17 22259989 . T A 68 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGTAAGAACTAGATAGA;RSEQ=GCATTCTCAGAAACTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:11.4:1:29.4:1:1:0:40.4:10:1:0:6.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22260014 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAGAAACTACTTTGTGA;RSEQ=GATTGCATTCAAGTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:1:0,2:21.8:1:31:1:1:0:45.6:18:1:0:5.9 1/1:10:10:5,5:0,0:1:0,2:20.2:1:29.5:1:1:0:47.1:20:1:0:5.4 -17 22260036 . G T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGCATTCAAGTCACAGAG;RSEQ=TGAACATTCCCTTTCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:9,5:0,0:0.9333:0,2:26.4:1:31.1:1:1:0:45.6:28:0.9333:0:5.1 1/1:13:13:8,5:0,0:1:0,2:34.8:1:29.7:1:1:0:41.3:26:1:0:5.2 -17 22260051 . C G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGGTGAACATTCCCTTT;RSEQ=AGAGAGCACTTTGGAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:10,7:0,0:1:0,2:30.1:1:32.4:1:1:0:46.9:34:1:0:5.4 1/1:14:14:9,5:0,0:1:0,2:34.2:1:31.9:1:1:0:41.2:28:1:0:5.1 -17 22260053 . G C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGGTGAACATTCCCTTTCA;RSEQ=AGAGCACTTTGGAAACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:10,7:0,0:1:0,2:30.2:1:32.8:1:1:0:46.9:34:1:0:5.4 1/1:15:15:10,5:0,0:1:0,2:31.4:1:31.7:1:1:0:41.2:30:1:0:5.1 -17 22260060 . C G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCCCTTTCAGAGAGCA;RSEQ=TTTGGAAACTCTCTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:12,9:0,0:1:0,2:23.8:1:32.7:1:1:0:45.5:42:1:0:5 1/1:20:20:13,7:0,0:1:0,2:22.9:1:32.1:1:1:0:40.4:40:1:0:4.7 -17 22260077 . G C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21771;SOR=0;LSEQ=GCACTTTGGAAACTCTCTTT;RSEQ=TGTAGAATCTGCAAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:11,12:0.08:2,2:6:1:31.5:1:1:1.09:50:4:0.08:0:7 0/0:28:0:0,0:15,13:0:2,0:19.5:1:31.4:1:1:0:39.6:56:1:0:4.1 -17 22260089 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50166;SOR=Inf;LSEQ=CTCTCTTTGTGTAGAATCTG;RSEQ=AAGTGGAGATATGGACCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:0:2,0:21.9:1:32.1:1:1:0:43.1:36:1:0:4.4 0/1:25:2:1,1:12,11:0.08:2,2:31:1:30.5:1:1:1.0871:60:4:0.08:0:5.5 -17 22260101 . T C 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01204;SOR=0;LSEQ=AGAATCTGCAAGTGGAGATA;RSEQ=GGACCGCTTTGAGGCCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:1,3:2,5:0.3636:2,2:35.8:1:30.8:1:1:1.18052:52:8:0.4:0:3.3 0/0:19:0:0,0:10,9:0:2,0:37.5:1:29.9:1:1:0:34.7:38:1:0:3.5 -17 22260105 . CC AT 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32683;SOR=0.32722;LSEQ=TCTGCAAGTGGAGATATGGA;RSEQ=GCTTTGAGGCCTATGGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:2,6:0.2727:2,2:40.3:1:31.8:1:1:1.44:48:6:0.2727:0:5.7 0/1:19:2:1,1:9,8:0.1053:2,2:44:0:31:1:1:1.11803:60:4:0.1053:0:4.5 -17 22260116 . C A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31732;SOR=0.30941;LSEQ=AGATATGGACCGCTTTGAGG;RSEQ=CTATGGTAGTAAAGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:2,6:0.2727:2,2:38.7:1:31:1:1:1.44:48:6:0.3:0:5.7 0/1:20:2:1,1:9,9:0.1:2,2:34:0:31:0:1:1:60:4:0.1:0:4.5 -17 22260135 . C T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTATGGTAGTAAAGGAAA;RSEQ=AGCTTCATATAAAAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:3,8:0,0:1:0,2:16.2:1:29.3:1:1:0:41.1:22:1:0:3.8 1/1:17:17:7,10:0,0:1:0,2:21.3:1:29.4:1:1:0:36.2:34:1:0:3.2 -17 22260142 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51087;SOR=Inf;LSEQ=GTAGTAAAGGAAACAGCTTC;RSEQ=TATAAAAACTAGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:12:1:30.3:1:1:0:36.9:18:1:0:3.4 0/1:15:2:1,1:5,8:0.1333:2,2:8.5:1:29:1:1:1.55:40:4:0.1333:0:4.5 -17 22260150 . A G 113 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=2.56905;LSEQ=GGAAACAGCTTCATATAAAA;RSEQ=CTAGACAGCAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,0:0.8:0,2:12.5:1:32:1:1:0:41.5:8:1:0:4.5 1/1:12:11:4,7:0,1:0.9167:0,2:12.3:1:32.8:1:1:0:29.5:22:0.9167:0:3 -17 22260159 . C T 77 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08333;SOR=Inf;LSEQ=TTCATATAAAAACTAGACAG;RSEQ=AGCATTCTCAGAAAACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:9:0:29:0:1:0:42:2:0.3333:0:6 1/1:6:6:1,5:0,0:1:0,2:8.8:1:29.8:1:1:0:25.5:12:1:0:3.2 -17 22260167 . T A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAACTAGACAGCAGCATTC;RSEQ=CAGAAAACTCTTTCTGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:42:2:1:0:6 1/1:2:2:0,2:0,0:1:0,0:8.5:1:32:0:1:0:22:4:1:0:3.5 -17 22260654 . A G 34 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAACGGGATAATTTCAGCT;RSEQ=AGTAAACAGAAGCAGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:19.5:1:34:0:1:0:22:4:0.5:0:6.5 1/1:1:1:1,0:0,0:1:0,0:23:0:34:0:1:0:22:2:1:0:7 -17 22260656 . G C 34 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACGGGATAATTTCAGCTAA;RSEQ=TAAACAGAAGCAGTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:19.5:1:34:0:1:0:22:4:0.5:0:6.5 1/1:1:1:1,0:0,0:1:0,0:25:0:33:0:1:0:22:2:1:0:7 -17 22260820 . A G 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=AAACGGGTATATCTTCACAT;RSEQ=ACATCTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:35:1:31:0:1:0:22:4:0.2857:0:5 1/1:1:1:0,1:0,0:1:0,0:46:0:33:0:1:0:22:2:1:0:6 -17 22260847 . A G 53 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACAGAAGCATTCTCAGAA;RSEQ=CTTTTCTGTGATGACTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:30.7:1:34:0:1:0:28:6:0.5:0:5.3 1/1:1:1:0,1:0,0:1:0,0:19:0:34:0:1:0:22:2:1:0:6 -17 22260851 . T C 53 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAAGCATTCTCAGAAACTT;RSEQ=TCTGTGATGACTGCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:31:1:33.7:1:1:0:28:6:0.5:0:5.3 1/1:1:1:0,1:0,0:1:0,0:15:0:34:0:1:0:22:2:1:0:6 -17 22260877 . A G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATGACTGCATTCAACTCAC;RSEQ=GAGTTGAACACTCCTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:36:1:32.5:1:1:0:31:4:0.5:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22260996 . T C 52 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GAATCATCTTCACATAAAAA;RSEQ=TACACAGAAGCATTCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:50:0:29:0:1:0:25:2:1:0:2 1/1:3:3:3,0:0,0:1:0,0:20:1:33:0:1:0:40:6:1:0:7.3 -17 22260999 . C T 50 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25;SOR=Inf;LSEQ=TCATCTTCACATAAAAATTA;RSEQ=ACAGAAGCATTCTCAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:48:0:32:0:1:0:25:2:1:0:2 1/1:3:3:3,0:0,0:1:0,0:23:1:31.7:1:1:0:40:6:1:0:7.3 -17 22261002 . A G 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TCTTCACATAAAAATTACAC;RSEQ=GAAGCATTCTCAGGAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30:1:1:0:25:4:1:0:4.5 0/0:3:0:0,0:3,0:0:0,0:26:1:31.7:1:1:0:40:6:1:0:7.3 -17 22261005 . A T 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TCACATAAAAATTACACAGA;RSEQ=GCATTCTCAGGAACTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:32:1:1:0:25:4:1:0:4.5 1/1:3:3:3,0:0,0:1:0,0:29:1:31:1:1:0:40:6:1:0:7.3 -17 22261021 . CC TT 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CAGAAGCATTCTCAGGAACT;RSEQ=TTGGTGATGTTTGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:32.5:1:1:0:25:4:1:0:4.5 1/0:5:3:3,0:2,0:0.6:0,0:42.3:1:30:1:1:0:40:6:0.6:0:6.3 -17 22261045 . T C 58 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GGTGATGTTTGTATTCAACT;RSEQ=CCAGAGTTGAACTTTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:30.5:1:1:0:25:4:1:0:4.5 1/0:7:4:4,0:3,0:0.5714:0,0:24.5:1:29.3:1:1:0:40:8:0.5714:0:6.3 -17 22261065 . C T 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCCAGAGTTGAACTTTCCTT;RSEQ=GGAAAGAGCAGCTATGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:10:1:31:0:1:0:28.5:4:0.5:0:6 1/0:8:4:4,0:4,0:0.5:0,0:14.5:1:29.3:1:1:0:40:8:0.5:0:6.3 -17 22261106 . A C 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11029;SOR=0;LSEQ=ACTCTTTTTCTAGAATCTGC;RSEQ=AGTGGACATTGGGAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:22:1:29:0:0.33333:0:22:4:0.3333:0:1.5 0/0:11:0:0,0:10,1:0:2,0:20.2:1:29.1:1:1:0:27.4:22:1:0:4 -17 22261114 . A G 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63325;SOR=0.41977;LSEQ=TCTAGAATCTGCAAGTGGAC;RSEQ=TTGGGAGGGCTGTGAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,1:0.7143:2,0:31:1:29.6:1:0.28571:0:27:10:0.7143:0:7 1/0:12:6:6,0:3,3:0.5:2,0:27.3:1:30:1:0.18182:0:33.3:12:0.5:0:7 -17 22261117 . G T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65702;SOR=0.52901;LSEQ=AGAATCTGCAAGTGGACATT;RSEQ=GGAGGGCTGTGAGGTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:6,1:1,1:0.7778:2,2:23.1:1:29.4:1:0.41667:4.58:28.4:14:0.7778:0:7 1/0:14:9:8,1:2,2:0.6429:2,2:23.7:1:28:1:0.2028:6.52:32.4:8:0.6154:0:6.8 -17 22261126 . G T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68547;SOR=0.57547;LSEQ=AAGTGGACATTGGGAGGGCT;RSEQ=TGAGGTTTGTGGTGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:8,2:1,1:0.8333:2,2:19:1:30.3:1:0.45455:3.46:26.6:20:0.8333:0:7.1 1/0:23:17:12,5:3,3:0.7391:2,2:14.7:1:29.2:1:0.62139:2.30:32.2:34:0.7727:0:6.4 -17 22261129 . A T 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43401;SOR=0.38496;LSEQ=TGGACATTGGGAGGGCTGTG;RSEQ=GGTTTGTGGTGGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:8,2:1,1:0.8333:2,2:20.2:1:30:1:0.45455:3.46:26.6:20:0.8333:0:7.1 1/0:23:15:11,4:4,4:0.6522:2,2:19.5:1:29.5:1:0.3712:2.62:33.9:30:0.6522:0:6.7 -17 22261156 . C T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39833;SOR=0.26886;LSEQ=TGGTGGAAAAGGAAATATCT;RSEQ=CACGTAAATACTAGATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:8,4:0,1:0.9231:0,2:29.2:1:29.8:1:0.38462:0:27.6:24:0.9231:0:7.2 1/0:29:22:13,9:1,5:0.7586:2,2:29.4:1:28.8:1:0.16473:6.75:33:21:0.75:0:6.4 -17 22261160 . G C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23479;SOR=0.21112;LSEQ=GGAAAAGGAAATATCTCCAC;RSEQ=TAAATACTAGATAGAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:9,5:0,0:0.9333:0,2:26.7:1:30.8:1:1:0:29.4:28:0.9333:0:7 1/0:31:23:14,9:0,0:0.7419:0,2:28.3:1:29.8:1:1:0:33.9:22:0.7333:0:6.4 -17 22261166 . A C 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26343;SOR=0.24245;LSEQ=GGAAATATCTCCACGTAAAT;RSEQ=CTAGATAGAAGCCTTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:11,5:0.1111:2,2:46:0:32:1:1:2.09766:20:4:0.1111:0:8 0/1:35:1:0,1:19,15:0.0286:2,0:45:0:33:0:0.45714:0:55:2:0.0294:0:8 -17 22261172 . T G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25519;SOR=0.23633;LSEQ=ATCTCCACGTAAATACTAGA;RSEQ=AGAAGCCTTCTCAGAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:0.1053:2,2:40.5:1:32:1:1:1.77272:20:4:0.1053:0:8 0/1:38:1:0,1:20,17:0.0263:2,0:50:0:33:0:0.47368:0:55:2:0.027:0:8 -17 22261173 . A G 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54351;SOR=Inf;LSEQ=TCTCCACGTAAATACTAGAT;RSEQ=GAAGCCTTCTCAGAAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:0:2,0:25.6:1:29.2:1:1:0:31.3:38:1:0:6.3 0/1:38:3:2,1:18,17:0.0789:2,2:36.3:1:32.3:1:1:1.86:30:6:0.0811:0:5 -17 22261179 . C A 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40448;SOR=0.29448;LSEQ=CGTAAATACTAGATAGAAGC;RSEQ=TTCTCAGAAACTACTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:12,7:0,1:0.95:0,2:25.3:1:30.4:1:0.4:0:32:38:0.95:0:6.6 1/1:39:33:19,14:2,4:0.8462:2,2:28.9:1:30:1:0.38669:2.65:32.7:32:0.8421:0:6.2 -17 22261192 . A G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34813;SOR=0.48314;LSEQ=TAGAAGCCTTCTCAGAAACT;RSEQ=CTTTGTGATGATTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:23:14,9:1,2:0.8846:2,2:23.5:1:31.9:1:0.55577:2.98:32.8:46:0.8846:0:6.6 1/0:42:33:19,14:3,4:0.7857:2,2:26.1:1:31.8:1:0.67983:1.78:33.5:66:0.7857:0:6.3 -17 22261194 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52629;SOR=Inf;LSEQ=GAAGCCTTCTCAGAAACTAC;RSEQ=TTGTGATGATTGCATTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:22.3:1:30.8:1:1:0:31.7:52:1:0:6.3 0/1:44:2:1,1:22,20:0.0455:2,2:23.5:1:29:1:1:1.09762:22:4:0.0465:0:2.5 -17 22261224 . G T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCATTCACCTCACAGAGT;RSEQ=GAGCATTCCTATTGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:15,12:0,0:1:0,2:30.1:1:31:1:1:0:33:54:1:0:6.1 1/1:37:37:17,20:0,0:1:0,2:28.8:1:29.6:1:1:0:34.2:36:1:0:6.1 -17 22261227 . G A 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57308;SOR=2.72623;LSEQ=CATTCACCTCACAGAGTGGA;RSEQ=CATTCCTATTGACAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:26:13,13:0,0:0.9286:0,2:29.5:1:30.4:1:1:0:32.7:52:0.9286:0:6.1 1/1:37:36:17,19:0,1:0.973:0,2:28.7:1:29.8:1:1:0:33.9:72:0.973:0:6.3 -17 22261237 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50101;SOR=Inf;LSEQ=ACAGAGTGGAGCATTCCTAT;RSEQ=GACAGAGCAGTTTGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:27.8:1:30.6:1:1:0:32.1:62:1:0:6 0/1:40:2:1,1:15,23:0.05:2,2:33.5:1:30:1:1:1.52:41.5:4:0.0513:0:7.5 -17 22261240 . C T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22977;LSEQ=GAGTGGAGCATTCCTATTGA;RSEQ=AGAGCAGTTTGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:30:14,16:0,0:0.9091:0,2:25.3:1:29.6:1:1:0:32.3:60:0.9091:0:6 1/1:40:37:15,22:0,1:0.925:0,2:27.8:1:28:1:1:0:33.2:74:0.925:0:6.2 -17 22261267 . T G 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33305;SOR=0.278;LSEQ=GTTTGGAAACACTCTTGTTG;RSEQ=AGAATCTGCTAGTGGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:1,2:8,14:0.12:2,2:27.7:1:32:1:1:1.13689:23.7:6:0.12:0:5.3 0/1:28:1:0,1:9,18:0.0357:2,0:38:0:33:0:1:0:40:2:0.0357:0:5 -17 22261268 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34094;SOR=3.46514;LSEQ=TTTGGAAACACTCTTGTTGT;RSEQ=GAATCTGCTAGTGGAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:22:8,14:1,2:0.88:2,2:29:1:30.9:1:1:1.14:31.9:21:0.875:0:6.1 1/1:27:26:9,17:0,1:0.963:0,2:29.8:1:30.1:1:1:0:33.4:52:0.963:0:6.3 -17 22261273 . C G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32968;SOR=3.65513;LSEQ=AAACACTCTTGTTGTAGAAT;RSEQ=TGCTAGTGGAGATTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:20:7,13:1,2:0.8696:2,2:30.8:1:32.1:1:1:1.07:31.8:40:0.8696:0:6.2 1/1:26:25:8,17:0,1:0.9615:0,2:28.2:1:30.9:1:1:0:33.2:50:0.9615:0:6.4 -17 22261277 . T A 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTTGTTGTAGAATCTGC;RSEQ=AGTGGAGATTTGGAGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:8,15:0,0:1:0,2:28.5:1:30.3:1:1:0:30.7:46:1:0:6 1/1:24:24:6,18:0,0:1:0,2:29.3:1:30:1:1:0:33.7:48:1:0:6.3 -17 22261322 . G T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTATGGTAGTAAAGGGAA;RSEQ=AGCTTCACATAAAATCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:1,7:0,1:0.8889:0,2:12:1:26.8:1:1:0:25.9:7:0.875:0:5.6 1/1:7:7:0,7:0,0:1:0,0:13.4:1:29:1:1:0:27.7:14:1:0:5.7 -17 22261330 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAGTAAAGGGAAGAGCTTCA;RSEQ=ATAAAATCAAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:30:1:1:0:22:4:1:0:5 1/1:2:2:0,2:0,0:1:0,0:20.5:1:29.5:1:1:0:22.5:4:1:0:7 -17 22261332 . T G 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAAGGGAAGAGCTTCACA;RSEQ=AAAATCAAGACAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:33:1:1:0:22:4:1:0:5 1/1:1:1:0,1:0,0:1:0,0:37:0:32:0:1:0:22:2:1:0:8 -17 22261337 . T A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAAGAGCTTCACATAAAA;RSEQ=CAAGACAGAAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:31:0:1:0:22:4:1:0:5 1/1:2:2:1,1:0,0:1:0,2:18:1:30.5:1:1:0:24.5:4:1:0:6 -17 22261339 . A T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGAGCTTCACATAAAATC;RSEQ=AGACAGAAGCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:31:1:1:0:22:4:1:0:5 1/1:2:2:1,1:0,0:1:0,2:18:1:31:1:1:0:24.5:4:1:0:6 -17 22261386 . A T 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.14286;SOR=0;LSEQ=TTGTGATGATTGAGTTTAAC;RSEQ=CACAGAGCTGAACATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:36.8:1:30.5:1:1:0:35.8:12:1:0:3.8 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22261425 . A G 92 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGATGGAGCAGGTTTGA;RSEQ=ACACACTTTCTATAGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:22.4:1:33:1:1:0:33.7:14:1:0:4.3 1/1:1:1:1,0:0,0:1:0,0:9:0:34:0:1:0:27:2:1:0:4 -17 22261432 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCAGGTTTGAAACACAC;RSEQ=TTCTATAGAATCTGCGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:0,3:0.4:0,0:41:1:32:1:0.1:0:21.5:4:0.4:0:6 0/0:1:0:0,0:1,0:0:0,0:2:0:27:0:1:0:27:2:1:0:4 -17 22261435 . C T 62 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGTTTGAAACACACTTT;RSEQ=TATAGAATCTGCGAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:35:1:31.3:1:1:0:30.3:8:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22261437 . A G 66 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTTGAAACACACTTTCT;RSEQ=TAGAATCTGCGAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:35:1:33:1:1:0:30.3:8:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 22261446 . G A 60 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACACTTTCTATAGAATCT;RSEQ=CGAGTGGATATTTGGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:30.5:1:30:1:1:0:30.3:8:1:0:6 1/1:1:1:0,1:0,0:1:0,0:2:0:26:0:1:0:40:2:1:0:6 -17 22261448 . G A 62 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTTTCTATAGAATCTGC;RSEQ=AGTGGATATTTGGACCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:28.5:1:31:1:1:0:30.3:8:1:0:6 1/1:1:1:0,1:0,0:1:0,0:4:0:24:0:1:0:40:2:1:0:6 -17 22261513 . T A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGCACCTAACTAAACGG;RSEQ=AGCATTCTCACAAAATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:6,3:0,0:1:0,2:18.1:1:29.3:1:1:0:29.1:18:1:0:4.4 1/1:11:11:9,2:0,0:1:0,2:21.6:1:30.3:1:1:0:32.5:22:1:0:4.4 -17 22261524 . C G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAAACGGTAGCATTCTCA;RSEQ=AAAATTCTTCGTGATGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:7,3:0,0:1:0,2:25:1:31.6:1:1:0:28.4:20:1:0:4.3 1/1:16:16:11,5:0,0:1:0,2:21.6:1:31.4:1:1:0:35.5:32:1:0:4.3 -17 22261528 . A C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGGTAGCATTCTCACAAA;RSEQ=TTCTTCGTGATGTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:10,3:0,0:1:0,2:22:1:31.8:1:1:0:35.7:26:1:0:3.9 1/1:22:22:14,8:0,0:1:0,2:18:1:30.9:1:1:0:40.2:44:1:0:3.8 -17 22261534 . C G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATTCTCACAAAATTCTT;RSEQ=GTGATGTTTGCATTCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:11,6:0,0:1:0,2:20.9:1:31.5:1:1:0:39.3:34:1:0:3.4 1/1:28:28:17,11:0,0:1:0,2:17.9:1:31.3:1:1:0:42.3:56:1:0:3.3 -17 22261546 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53529;SOR=Inf;LSEQ=AAATTCTTCGTGATGTTTGC;RSEQ=TTCAAATCCCAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:0:2,0:25.8:1:30.4:1:1:0:41.1:38:1:0:3.1 0/1:35:2:1,1:21,12:0.0571:2,2:26:1:29:1:1:1.72083:50.5:4:0.0571:0:3.5 -17 22261553 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12788;SOR=0;LSEQ=TCGTGATGTTTGCATTCAAA;RSEQ=CCCAGAGTTGAACCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:14,9:0.08:2,2:38:1:31.5:1:1:1.52748:34:4:0.08:0:5 0/0:44:0:0,0:27,17:0:2,0:21.7:1:29.7:1:1:0:44.5:88:1:0:2.5 -17 22261562 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53795;SOR=Inf;LSEQ=TTGCATTCAAATCCCAGAGT;RSEQ=GAACCTTCCTTTGATAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,12:0:2,0:26.1:1:30.3:1:1:0:44.2:50:0.9615:0:2.4 0/1:48:2:1,1:27,19:0.0417:2,2:12.5:1:31:1:1:1.41046:60:4:0.0417:0:1.5 -17 22261573 . T G 34 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26183;SOR=0.24546;LSEQ=TCCCAGAGTTGAACCTTCCT;RSEQ=TGATAGTTCAGGTTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:23:0:34:0:1:1.07415:60:4:0.069:0:1.5 0/1:57:1:1,0:30,26:0.0175:2,0:30:0:34:0:1:0:23:2:0.0175:0:3 -17 22261577 . T G 101 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74799;SOR=1.59735;LSEQ=AGAGTTGAACCTTCCTTTGA;RSEQ=AGTTCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:1,2:13,13:0.1034:2,2:46.7:1:31.3:1:1:1.95415:48:6:0.1034:0:2.3 0/1:64:10:6,4:29,25:0.1563:2,2:25.2:1:30.6:1:1:1.29:44:20:0.1563:0:2.9 -17 22261592 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTGATAGTTCAGGTTTGAA;RSEQ=CACTCTTTTTGTAGGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:13,16:0:2,0:27.8:1:30.2:1:1:0:43.9:58:1:0:2.8 0/1:75:2:1,1:36,37:0.0267:2,2:24.5:1:30.5:1:1:1.03:48:4:0.0267:0:4.5 -17 22261609 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACACTCTTTTTGTAGGA;RSEQ=CTGCAAGTGGATATTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:11,14:0:2,0:25.7:1:30.3:1:1:0:44.3:50:1:0:2.9 0/1:70:2:1,1:32,36:0.0286:2,2:7.5:1:27:1:1:1.12:46.5:4:0.0286:0:3 -17 22261620 . A C 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03038;SOR=Inf;LSEQ=TTTGTAGGATCTGCAAGTGG;RSEQ=TATTTGGACCACTCTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:0:2,0:24:1:30.8:1:1:0:45.8:44:1:0:2.8 0/1:61:12:4,8:23,26:0.1967:2,2:28:1:32:1:0.52217:1.75312:46.4:24:0.2034:0:3.5 -17 22261634 . C T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGTGGATATTTGGACCACT;RSEQ=TTTGGCCTTCCTTCGAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:0:2,0:25.9:1:32.3:1:1:0:40.8:28:1:0:3.4 0/1:47:2:1,1:20,25:0.0426:2,2:14:0:26.5:1:1:1.24:26:4:0.0426:0:2.5 -17 22261636 . T G 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.54012;SOR=1.7712;LSEQ=GTGGATATTTGGACCACTCT;RSEQ=TGGCCTTCCTTCGAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:3,9:0,0:0.9231:0,2:28.7:1:33:1:1:0:37.6:24:0.9231:0:3.7 1/1:45:43:18,25:1,1:0.9556:2,2:26.3:1:31.3:1:1:1.3786:40.2:42:0.9545:0:3.4 -17 22261645 . C G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.25333;LSEQ=TGGACCACTCTTTGGCCTTC;RSEQ=TTCGAAACGGGTACATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:2,7:0,0:0.8182:0,2:23.8:1:32.6:1:1:0:36.3:18:0.8182:0:3.9 1/1:40:34:13,21:2,2:0.85:2,2:22.1:1:30.7:1:1:1.59441:39.8:68:0.85:0:3.8 -17 22261658 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCCTTCCTTCGAAACGGGT;RSEQ=CATCTTCAAATAAAATCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:0:2,0:18.1:1:31.8:1:1:0:38.1:18:1:0:4.3 0/1:28:2:1,1:8,18:0.0714:2,2:27:1:28:1:1:2.18:21:4:0.0714:0:6 -17 22261659 . C T 99 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00504;SOR=0;LSEQ=GCCTTCCTTCGAAACGGGTA;RSEQ=ATCTTCAAATAAAATCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:1,8:0,0:1:0,2:17.3:1:29.8:1:1:0:38.1:18:1:0:4.3 0/1:24:11:2,9:5,8:0.4583:2,2:13:1:28.8:1:0.38644:2.69447:41.5:22:0.4583:0:4.5 -17 22261666 . AA GC 116 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53924;SOR=0;LSEQ=TTCGAAACGGGTACATCTTC;RSEQ=ATAAAATCTAGACAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:16.7:1:32.8:1:1:0:37.3:12:1:0.1667:4.2 1/0:17:13:4,9:1,1:0.7647:2,2:14.3:1:31.4:1:1:2.12136:36.8:26:0.7647:0.1765:3.9 -17 22261667 . A C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAAACGGGTACATCTTCA;RSEQ=ATAAAATCTAGACAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:13:2:1,1:0,1:0.1538:0,2:26:1:30:1:1:0:30.5:4:0.6667:0:6 -17 22262118 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCCAAACACTCTTTCTGTGG;RSEQ=ATCTGCAAGTGGATGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:28.5:1:1:0:22:4:1:0:4.5 0/0:1:0:0,0:1,0:0:0,0:7:0:32:0:1:0:50:2:1:0:1 -17 22262133 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGTGGCATCTGCAAGTGGAT;RSEQ=TTTGGGCCTCTTTGAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:28:1:1:0:22:4:1:0:4.5 0/0:1:0:0,0:1,0:0:0,0:22:0:33:0:1:0:50:2:1:0:1 -17 22262139 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATCTGCAAGTGGATGTTTGG;RSEQ=CCTCTTTGAAGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29:1:1:0:22:4:1:0:4.5 0/0:2:0:0,0:1,1:0:2,0:17:1:32.5:1:1:0:55:4:1:0:1.5 -17 22262161 . A G 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTTGAAGATTTCGTTGG;RSEQ=AAAGGGATAATCTTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45.5:1:31.5:1:1:0:22:4:1:0:4.5 1/0:2:1:1,0:0,1:0.5:0,0:50:0:13:0:1:0:50:0:0:0:1 -17 22262808 . A T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTTTGTAGAAAGTGCAAG;RSEQ=GTATAACTGCACTTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:1:30.5:1:1:0:46:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 26046862 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CTACTTTATTATCCTACTAC;RSEQ=ACACACTCAAAGGATTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:21:1:32:0:1:0:53:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:27.5:1:1:0:60:4:1:0:1 -17 26047125 . C A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.06584;LSEQ=ACAACACCTTTCAAACTCTT;RSEQ=TACTAACCTCCGGAGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:26:15,11:3,4:0.7879:2,2:31.1:1:29:1:0.67409:1.78:59.4:52:0.7879:0:1.2 0/1:32:6:3,3:14,12:0.1875:2,2:35.2:1:29.8:1:1:1.16104:60:12:0.1935:0:1.2 -17 26368753 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGGGCGGGGCCTCGGCGG;RSEQ=TGGTTGCGCGTGTCCGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:33:0:1:0:60:2:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:41:1:29.5:1:1:0:60:4:0.6667:0:1 -17 26370249 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24362;SOR=0;LSEQ=AGCTCAGGTACAGGCTGCCG;RSEQ=AGCTGCTACAGTTAAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:91,42:0.0148:2,2:40:1:29:1:0.5372:2.1531:60:4:0.0153:0:1 0/0:138:0:0,0:87,51:0:2,0:23.4:1:31.5:1:1:0:59.9:68:1:0:0.2 -17 26370268 . G A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=GCAGCTGCTACAGTTAAGGC;RSEQ=CACCATCATCAGCACTCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:126,65:0:2,0:22.5:1:30.4:1:1:0:60:62.667:1:0:0.1 0/1:178:14:7,7:98,66:0.0787:2,2:24.1:1:28.4:1:0.5744:1.48144:60:28:0.0809:0:1.2 -17 26370299 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11364;SOR=Inf;LSEQ=AGCACTCGCATCATCCACAG;RSEQ=AGCAGCTGGATATTGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:148,115:0:2,0:26.7:1:32:1:1:0:60:51.6:1:0:0.1 0/1:249:3:2,1:138,108:0.012:2,2:27:1:30.3:1:1:1.56:60:6:0.0121:0:1.7 -17 26370323 . A G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12419;SOR=0;LSEQ=AGCTGGATATTGAGCCGGAT;RSEQ=GACCTATTGGATATGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:4:2,2:177,152:0.012:2,2:23.5:1:31.5:1:1:1.16394:60:8:0.0121:0:1 0/0:319:0:0,0:173,146:0:2,0:25.4:1:29.1:1:1:0:60:78.75:1:0:0.2 -17 26744227 . AG A 53 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGCACATGCACCATTAC;RSEQ=GTGGCTGGTGCCTGTAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:14:0:33:0:1:0:60:2:1:0:0 1/0:4:3:2,1:0,1:0.75:0,2:26:1:33.7:1:1:0:60:6:0.75:0:0 -17 26744523 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20568;SOR=0;LSEQ=GTGCTTAAGAATTAACTATG;RSEQ=TGGGAAACACTTCATTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:30,49:0.0247:2,2:22.5:1:29:1:1:1.62:60:4:0.0247:0:1 0/0:97:0:0,0:31,66:0:2,0:22.3:1:28.9:1:1:0:60:96:1:0:0.1 -17 26744679 . G A 98 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01099;SOR=0;LSEQ=GTTTTCCCATTTTCATCTGT;RSEQ=TATGAGTTTTTAGTATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:22.8:1:31.2:1:1:0:60:18:1:0:1 0/1:6:2:1,1:0,4:0.3333:0,2:29.5:1:28.5:1:0.33333:0:60:4:0.3333:0:1 -17 27403067 . C T 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12216;SOR=Inf;LSEQ=TAGGAGGAGTCAGCGTTCTG;RSEQ=GGCAAGAACCACCTTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:63,63:0:2,0:28.1:1:31:1:1:0:60:125:1:0:0.2 0/1:129:4:2,2:60,65:0.031:2,2:38:1:30.5:1:1:1.08:60:8:0.031:0:1 -17 27403076 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.49718;LSEQ=TCAGCGTTCTGCGGCAAGAA;RSEQ=CACCTTCTTAGCTTTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:56,61:0.0168:2,2:28.5:1:29.5:1:1:1.09:60:4:0.0172:0:1 0/0:119:1:1,0:52,66:0.0084:2,0:1:0:24:0:0.44538:0:60:2:0.0084:0:1 -17 27403092 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49874;SOR=0;LSEQ=AGAACCACCTTCTTAGCTTT;RSEQ=CCCAAGGTGGCAGTGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:43,58:0.0194:2,2:23.5:1:30:1:1:1.34:60:4:0.0196:0:1 0/0:93:0:0,0:37,55:0:2,0:26.7:1:29.1:1:1:0:60:91:0.9891:0:0.2 -17 28043426 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTAATTAGAGTGCTTAAT;RSEQ=TGCTCAATACACACATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:0:1,0:19.8:1:30.8:1:1:0:60:12:1:0:0 0/1:33:2:1,1:28,3:0.0606:2,2:32.5:1:28:1:0.23106:8.22492:60:4:0.0606:0:1 -17 28043488 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCAACTTGTGTACAACAAT;RSEQ=CCAGCAGCATGCTGGTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:33,20:0:2,0:19.8:1:30.5:1:1:0:60:25.5:1:0:0.2 0/1:117:2:1,1:68,46:0.0171:2,2:36.5:1:28:1:1:1.47313:60:4:0.0171:0:1 -17 28043492 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ACTTGTGTACAACAATGCCA;RSEQ=CAGCATGCTGGTTAACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:33,21:0:2,0:21.6:1:31.3:1:1:0:60:53:1:0:0.2 0/1:123:2:1,1:70,51:0.0163:2,2:22:0:31:1:1:1.36894:60:4:0.0163:0:1 -17 28043556 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.55446;SOR=Inf;LSEQ=GTAACACTTGTGGGGCATTC;RSEQ=TTTTTGAACAGTACCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:29,41:0:2,0:27.2:1:31.8:1:1:0:59.7:69:1:0:0.1 0/1:124:3:1,2:49,72:0.0242:2,2:19.3:1:29.3:1:1:1.35785:60:6:0.0246:0:1 -17 28043667 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51052;SOR=Inf;LSEQ=TCTAAAAGACCTAGAGAACA;RSEQ=ATATCGGGTGCCTCTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:4,13:0:2,0:24:1:28.1:1:1:0:60:16:1:0:0.1 0/1:26:2:1,1:5,19:0.0769:2,2:29.5:1:33.5:1:0.41538:3.56:60:4:0.08:0:2 -17 29058863 . G A 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GGCGCTTACTCTCCGGGGCC;RSEQ=CCCGGCGAGTAGCTGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:68,49:0:2,0:24.2:1:30.5:1:1:0:60:116:1:0:0.1 0/1:96:11:7,4:45,40:0.1146:2,2:24.2:1:29.3:1:0.54126:1.55:60:22:0.117:0:1.2 -17 29058866 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20773;SOR=Inf;LSEQ=GCTTACTCTCCGGGGCCGCC;RSEQ=GGCGAGTAGCTGGCCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:71,49:0:2,0:25.2:1:30.2:1:1:0:60:119:1:0:0.1 0/1:101:2:1,1:53,46:0.0198:2,2:8.5:1:29:1:1:1.15055:60:4:0.02:0:1 -17 29058972 . C T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.11159;LSEQ=AGCGCGGGGTCCGGGGGAGG;RSEQ=GGCTTCGGGGGTTCGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:4:1,3:241,113:0.0111:2,2:12.8:1:26.3:1:0.10178:6.36277:60:8:0.0117:0:1.3 0/1:485:6:2,4:300,179:0.0124:2,2:6.3:1:27.2:1:0.2051:3.34331:60:12:0.0129:0:1 -17 29059051 . GCCT G 110 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.62525;SOR=1.4205;LSEQ=GAGGCGGTGGCAGTTACTCG;RSEQ=CCTCCTCCTCCGCGGCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:743:6:3,3:412,324:0.0081:2,2:19.5:1:32.5:1:1:1.27118:60:12:0.0083:0.0013:0.3 0/1:962:11:7,4:522,424:0.0114:2,2:25.9:1:32:1:0.76282:1.42:60:22:0.0116:0:0.3 -17 29059343 . C T 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36917;SOR=0.3617;LSEQ=GAGAGCTGGAAAAGAGGGTC;RSEQ=GGGCGGGTTCTTGACTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:0,13:0,6:0.6842:0,1:21.5:1:31.2:1:1:0:37:26:0.6842:0:2.1 0/1:7:3:0,3:0,4:0.4286:0,0:20.7:1:30.7:1:1:0:35.7:6:0.4286:0:2.3 -17 29059347 . C T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64427;SOR=0.55197;LSEQ=GCTGGAAAAGAGGGTCCGGG;RSEQ=GGGTTCTTGACTCCCCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:13:0,13:0,7:0.65:0,1:20:1:31:1:1:0:37:26:0.65:0:2.1 1/0:6:3:0,3:0,3:0.5:0,0:22:1:30.3:1:1:0:35.7:6:0.5:0:2.3 -17 29061824 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25205;SOR=Inf;LSEQ=GTGATTTCCATAGCAGATGA;RSEQ=AAGTTTATATTGATTATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:144,25:0:2,0:23.5:1:31.8:1:1:0:51.4:83.5:1:0:0.1 0/1:196:3:2,1:153,40:0.0153:2,2:34.7:1:29:1:0.50745:1.90497:21.7:6:0.0153:0:1 -17 29061914 . G C 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTGTTTCCTATTACCTA;RSEQ=AGCCAACACAGATCTATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:248,187:0:2,0:25.3:1:31.5:1:1:0:40.8:61.143:1:0:0.1 0/1:602:46:22,24:309,246:0.0764:2,2:25.4:1:31.3:1:0.35529:1.36955:43.5:92:0.0771:0:1.1 -17 29062041 . CTT C 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTAACATTTTTAAAACT;RSEQ=TTTGTAGCCAATATTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:44,129:0:2,0:23.7:1:30.8:1:1:0:31.2:346:1:0:0 0/1:188:36:8,28:38,114:0.1915:2,2:27.1:1:31.8:1:0.83129:1.16576:33.5:72:0.1925:0.0213:0 -17 29062162 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2001;SOR=0;LSEQ=CTGATCAAACCATGTTAGTT;RSEQ=TATTTTAAAGTACTATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:39,89:0.0154:2,2:23.5:1:30.5:1:0.52236:2.27:48.5:4:0.0157:0:1 0/0:160:0:0,0:56,104:0:2,0:31.5:1:29.2:1:1:0:50.3:320:1:0:0.1 -17 29062189 . TA T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25692;SOR=Inf;LSEQ=AAAGTACTATTTCTCAAAAT;RSEQ=AAAAAAAGAACAAAAATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:20,92:0:2,0:26.9:1:29.9:1:1:0:53.4:111:1:0:0.1 0/1:141:3:1,2:26,112:0.0213:2,2:14.7:1:27.3:1:0.47418:2.14:50:6:0.0213:0.0071:0.3 -17 29062197 . A C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08565;SOR=0;LSEQ=ATTTCTCAAAATTAAAAAAA;RSEQ=GAACAAAAATAAGTACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:0,3:15,91:0.0275:2,0:22:1:31.3:1:1:0:27:6:0.0278:0:1 0/0:137:0:0,0:22,115:0:2,0:22.6:1:31:1:1:0:55.3:274:1:0:0.1 -17 29062213 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49846;SOR=Inf;LSEQ=AAAAAGAACAAAAATAAGTA;RSEQ=TATTTCTAACTAAAGATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:6,78:0:2,0:23.7:1:32.3:1:1:0:57.5:83:1:0:0.1 0/1:93:2:0,2:9,82:0.0215:2,0:9:1:29.5:1:1:0:57:4:0.022:0:1 -17 29086332 . A C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05217;SOR=Inf;LSEQ=TTTTGTTAGGTGTATAGACA;RSEQ=ACTTTTGGATGTCATATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:14,1:0:1,0:28.7:1:30.5:1:1:0:58.8:30:1:0:0.1 0/1:10:3:3,0:7,0:0.3:0,0:38:1:33:0:1:0:42:6:0.375:0:1 -17 29086494 . CT C 182 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.03001;SOR=1.67104;LSEQ=TTAAAATGATAAAATATTTC;RSEQ=TTTTTTTTTTTAGCTTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:40:29,11:106,64:0.1869:2,2:25.9:1:31.3:1:0.27321:1.59:59.4:80:0.1942:0.028:0.2 0/1:216:60:37,23:88,48:0.2778:2,2:24.9:1:30.9:1:0.74771:1.13887:58.5:59:0.2783:0.0463:0.4 -17 29086615 . TA T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05946;SOR=0.33928;LSEQ=GCAAGATACCTTTGTGAATG;RSEQ=AAAAAAAAGTGGGGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:10:3,7:45,112:0.0599:2,2:27.6:1:29.8:1:1:1.07:53.5:20:0.0602:0.006:0 0/1:237:5:2,3:78,153:0.0211:2,2:23.4:1:29.2:1:1:1.31:56.4:10:0.0213:0:0.2 -17 29086657 . A G 122 v4;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=10.35767;LSEQ=AGTGTAAATTTATAAAATTA;RSEQ=GTTTAATGGAAAAGATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:0,2:12,84:0.0204:2,0:20.5:1:31.5:1:1:0:60:4:0.0206:0:1 0/1:95:17:1,16:10,68:0.1789:2,1:25.8:1:30:1:0.68237:2.33625:60:34:0.1789:0:1 -17 29095749 . TG T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16279;SOR=Inf;LSEQ=AACATTCCATTTGGTGATCA;RSEQ=GCCTATCTCCTGTGTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:50,0:0:1,0:25.4:1:32.8:1:1:0:58.2:100:0.9804:0:0 0/1:35:2:1,1:32,1:0.0571:1,2:15:1:30.5:1:0.11261:22.97875:60:4:0.0571:0.0286:0.5 -17 29095920 . TCAAA T 228 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTTTGAATCCTGACCTCAA;RSEQ=CAAAACCTGGAAATTTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:0:0,0:406,321:0:2,0:24.3:1:31.4:1:1:0:56.1:59.583:0.9972:0:0.1 0/1:907:163:82,81:407,338:0.1797:2,2:27.8:1:31.1:1:0.34038:1.18922:54:326:0.1807:0.0154:0.1 -17 29096004 . C G 118 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00108;SOR=0.12164;LSEQ=AGCCACATGGTGAAGTCTTA;RSEQ=TCGTTGCTATTTAGAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:13:4,9:230,328:0.0227:2,2:29:1:32:1:0.57377:1.57655:59.8:26:0.023:0:1.1 0/0:710:2:2,0:312,395:0.0028:2,0:12:1:21.5:1:0.19579:0:51.5:1:0.0014:0:4 -17 29096006 . C T 173 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00058;SOR=0.45949;LSEQ=CCACATGGTGAAGTCTTACT;RSEQ=GTTGCTATTTAGAGTGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:56:22,34:206,300:0.0996:2,2:28.3:1:29.9:1:0.88668:1.06111:59.4:112:0.1009:0:1.1 0/1:703:34:17,17:291,376:0.0484:2,2:24.6:1:30.2:1:0.4833:1.29:58.6:68:0.0491:0:1.1 -17 29096086 . A AT 138 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.87093;SOR=1.06773;LSEQ=AAACCATGAAAATATTGGTA;RSEQ=TTTTTTTTTTTACTAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:16:2,14:38,144:0.08:2,2:26.4:1:29.3:1:0.53441:1.84247:57.3:32:0.0833:0.015:0 0/1:306:26:6,20:85,195:0.085:2,2:33.5:1:29.5:1:0.50824:1.45133:59.1:52:0.0855:0:0 -17 29096748 . C CAT 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02969;SOR=Inf;LSEQ=TAAAAATGCAAAATTGGAAA;RSEQ=GTGGTCTGTATATTATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:26,0:0:1,0:20.8:1:32:1:1:0:58.2:52:1:0:0 0/1:20:4:4,0:16,0:0.2:1,0:24.5:1:30.3:1:1:0:31.8:8:0.2:0:0.3 -17 29096821 . A G 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=22.77429;LSEQ=AATGTAGCATGTTTTATGTT;RSEQ=AGGGACCATATATCGTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:1:1,0:91,12:0.0096:2,0:48:0:34:0:1:0:60:2:0.0096:0:1 0/1:93:17:15,2:64,12:0.1828:2,2:20.2:1:31.2:1:1:1.40:56.1:34:0.1828:0:1 -17 29097009 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18477;SOR=0;LSEQ=GTTGATGAACAAGCGAGGCT;RSEQ=CCACAATGTTCTGGAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:50,139:0.0104:2,2:24.5:1:31:1:0.46376:2.76:49:4:0.0107:0:1 0/0:254:0:0,0:70,184:0:2,0:23.1:1:30.5:1:1:0:51.1:41.333:1:0:0.1 -17 29097076 . G A 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0011;SOR=Inf;LSEQ=TTTATATTGATTATTTCATT;RSEQ=CCTTTGTTTCTTTTTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:1,43:0:1,0:24:1:31.5:1:1:0:44:21:1:0:0.3 0/1:43:9:0,9:0,34:0.2093:1,0:20.2:1:30.3:1:1:0:47.2:18:0.2195:0:1 -17 29103166 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18264;SOR=Inf;LSEQ=AATTGCTTTCATCAGGACTG;RSEQ=AGTGTAGCTGTATTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:67,2:0:1,0:24.1:1:31.7:1:1:0:52.5:22:1:0:0.1 0/1:52:2:2,0:45,5:0.0385:2,0:25.5:1:32:0:1:0:27:4:0.0392:0:1 -17 29103215 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16815;SOR=Inf;LSEQ=GAGTATGTAAGCTAGTTTAT;RSEQ=AATTTAATAAATGGTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:118,5:0:1,0:29.3:1:28.3:1:1:0:43:60.5:1:0:0.1 0/1:86:2:1,1:79,5:0.0233:2,2:15.5:1:30:1:0.13543:14.51227:27:4:0.0233:0:1 -17 29103295 . T G 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TAACACAGGTTACTTTAAAG;RSEQ=ATATGTGTTTGTCTAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:198,62:0:2,0:26.8:1:29.1:1:1:0:35.3:42.333:1:0:0.1 0/1:203:34:27,7:122,47:0.1675:2,2:28.1:1:31.7:1:0.52372:1.48:33.1:68:0.1683:0:1 -17 29422537 . T G 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.33107;SOR=3.11347;LSEQ=AGAAGGGAAGGGGGGATAAG;RSEQ=GGGGGTGGCCAAGGCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:0,2:1,60:0.0317:1,0:18.5:1:9:0:1:0:60:0:0:0:3.5 0/1:32:3:0,3:0,29:0.0938:1,0:19.3:1:21.7:1:1:0:60:2:0.0769:0:2.3 -17 29422861 . A T 27 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTGTCTTATATACCCTC;RSEQ=ATAGGAGAACGATAACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:27:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29423119 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACCGTGGTTCTGAAATA;RSEQ=CTTCCCCTTCCTTGATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:0:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29482701 . C T 77 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTGCTGGATAAAGAATT;RSEQ=TATTTTGTAGATAGAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:23:1:30:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29482878 . G A 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08616;SOR=0.42172;LSEQ=AATCGGAGTTTGAGATGCAA;RSEQ=TATAGGTATCTGTGGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:36:34,2:12,1:0.7347:1,2:23.1:1:29.7:1:1:1.41:60:17:0.7234:0:1.1 1/0:28:15:15,0:13,0:0.5357:1,1:16.7:1:29.1:1:1:0:60:14:0.5185:0:1.2 -17 29482977 . G GT 157 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00742;SOR=2.15528;LSEQ=TAAGGATAAGCTGTTAACGT;RSEQ=TTTTTTTTTTCTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:21:18,3:230,47:0.0682:2,2:28.5:1:29.9:1:1:1.23:60:42:0.0712:0:0.2 0/1:308:42:33,9:206,54:0.1364:2,2:20.9:1:29.3:1:1:1.04027:59.8:84:0.1409:0.0357:0.1 -17 29482988 . C CT 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17857;SOR=0.51673;LSEQ=TGTTAACGTGTTTTTTTTTT;RSEQ=TTTTTTTTTCAGCTTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:13:8,5:267,71:0.0359:2,2:22.8:1:30.6:1:0.16525:2.34343:60:26:0.0406:0.0055:0.2 0/1:371:7:5,2:256,100:0.0189:2,2:19:1:30:1:1:1.02393:60:14:0.0209:0.0081:0 -17 29483108 . C T 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=56.84566;LSEQ=AAGTTTTCTTTGGTTATAAG;RSEQ=GGCCTCACTACTATTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:722:1:0,1:300,421:0.0014:2,0:48:0:14:0:1:0:60:0:0:0:1 0/1:779:57:24,33:327,393:0.0732:2,2:24.7:1:29.1:1:0.67962:1.14389:60:56:0.0735:0:1.1 -17 29485963 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50133;SOR=0;LSEQ=TTTTAGTCTTTCACTTTTCA;RSEQ=ATGTGTGTTGATTGGTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:147,39:0.0106:2,2:5.5:1:32.5:1:0.38116:3.73461:60:4:0.0106:0:1 0/0:162:0:0,0:122,40:0:2,0:24.4:1:31.6:1:1:0:60:80:1:0:0.1 -17 29486152 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.166;LSEQ=TAGGCAGGCTTTGTGAATTT;RSEQ=ATCTTGAGAATGATCTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:257:226:68,158:5,26:0.8794:2,2:23.7:1:29.1:1:0.13723:2.23:60:44.2:0.877:0:1.1 1/0:289:158:52,106:48,82:0.5467:2,2:22:1:29.1:1:0.53438:1.19251:60:78:0.5474:0:1.1 -17 29486194 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50122;SOR=0;LSEQ=CCCAAAGTACAGATGTGGAC;RSEQ=AAGAGGACAGTCCTATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:7,116:0.016:2,2:5.5:1:28:1:0.12439:15.56:60:4:0.0163:0:2 0/0:106:0:0,0:15,91:0:2,0:24:1:31.4:1:1:0:60:105:1:0:0.5 -17 29490132 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50137;SOR=0;LSEQ=TTTGTTCTGTGTGTGTGTTT;RSEQ=AAAATTTTCATAATAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:140,7:0.0134:1,2:26:1:28.5:1:0.10484:18.76643:60:4:0.0134:0:1.5 0/0:127:0:0,0:119,8:0:2,0:23.6:1:31.7:1:1:0:60:126:1:0:0 -17 29490382 . G A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03312;SOR=Inf;LSEQ=CTTCAATGCAGTCTTTAGTC;RSEQ=CATTTCTACCAGGTTAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:0:0,0:180,322:0:2,0:26.6:1:30.9:1:1:0:60:49.2:1:0:0.1 0/1:580:6:5,1:220,354:0.0103:2,2:17.2:1:25:1:0.03493:8.02:60:5:0.0087:0:1.3 -17 29490992 . A G 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCTCCAGAAAGTGGACT;RSEQ=CATTTTAAATGTATGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:23:1:28.3:1:1:0:60:2:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29496756 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09591;SOR=Inf;LSEQ=GTATTTTTTTTAGAGATGAT;RSEQ=TCTTGCTATGTTGCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:45,0:0:1,0:24.7:1:33:1:1:0:60:90:1:0:0.5 0/1:39:3:3,0:36,0:0.0769:1,0:22:1:30:0:1:0:60:6:0.0769:0:1 -17 29496819 . C T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0.00054;SOR=0.353;LSEQ=AGTGGTCCTCCTGCCTTGGC;RSEQ=TCCTGAAGTGCTGGGATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:69:68,1:23,0:0.75:1,1:23.3:1:30.6:1:1:0:60:68:0.7473:0:1.1 1/0:115:59:56,3:52,4:0.513:2,2:25.3:1:30.9:1:0.71205:1.43:60:118:0.5175:0:1.1 -17 29496840 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50367;SOR=Inf;LSEQ=TCCTGAAGTGCTGGGATTAC;RSEQ=GGTGTGAGATACCACACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:119,21:0:2,0:21.7:1:30.3:1:1:0:60:69:1:0:0.5 0/1:172:2:1,1:139,31:0.0116:2,2:8:1:30:1:0.33837:4.42911:60:4:0.0118:0:1 -17 29496848 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57934;SOR=0.3748;LSEQ=TGCTGGGATTACAGGTGTGA;RSEQ=ATACCACACCTGTCCCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:131,29:0.0123:2,2:16:1:28.5:1:0.33701:4.45825:60:4:0.0123:0:1.5 0/0:215:1:0,1:157,56:0.0047:2,0:1:0:24:0:0.26636:0:60:2:0.0047:0:1 -17 29508775 . G A 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1964;LSEQ=CCAGATGAATTTACAAAACT;RSEQ=TACCAGATCCCACAGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:903:736:331,405:71,91:0.8151:2,2:27.7:1:28.1:1:0.8615:1.05:59.9:9.824:0.8176:0:1.3 0/1:772:358:169,189:191,212:0.4637:2,2:27:1:27.6:1:1:1.00755:60:10.933:0.4659:0:1.4 -17 29508876 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.52704;SOR=0;LSEQ=TGACATAAAAACCTATCATC;RSEQ=TTTTCCAAGTTATTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:10,148:0.0125:2,2:12:1:29:1:0.13318:14.16:60:4:0.0132:0:1 0/0:98:0:0,0:1,97:0:1,0:23.1:1:31.1:1:1:0:60:48:1:0:0.5 -17 29509503 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08454;SOR=Inf;LSEQ=TTGTTCCTATCTAATAATGT;RSEQ=ATTTAATATATTTTTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:235,68:0:2,0:25.6:1:31.3:1:1:0:60:100:1:0:0.1 0/1:238:3:0,3:176,59:0.0126:2,0:13.3:1:25.3:1:0.01705:0:60:6:0.0127:0:1 -17 29509791 . C T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00512;SOR=0.26618;LSEQ=AAGCAAAGTATTTCAGGGAA;RSEQ=CATTTAAATGATCATTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:68:0,68:0,11:0.8608:0,1:22:1:30.6:1:1:0:60:67:0.859:0:1.8 1/0:42:26:0,26:0,16:0.619:1,1:17.5:1:29.5:1:1:0:60:25:0.6098:0:1.7 -17 29509801 . G T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00946;SOR=0.25653;LSEQ=TTTCAGGGAACCATTTAAAT;RSEQ=ATCATTTTAGGTTTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:57:0,57:0,11:0.8382:0,1:20.3:1:28.9:1:1:0:60:114:0.8507:0:1.9 1/0:30:17:0,17:0,13:0.5667:1,1:20.2:1:29.2:1:1:0:60:34:0.5667:0:2 -17 29509911 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACAAAGATTTAAAATAAT;RSEQ=CCTTAGTTTCATTCTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:0,9:0.1818:0,0:13:1:31.5:1:1:0:60:4:0.1818:0:1 0/0:1:0:0,0:0,1:0:0,0:4:0:32:0:1:0:60:2:1:0:0 -17 29527117 . G A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGCCAAGATCGTGCCTTT;RSEQ=TACTCCAGCCTGGGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:40:0:26:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:1:0,2:24:1:28:1:1:0:60:4:1:0:1 -17 29527156 . GA G 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGAAGACACCATCTTGG;RSEQ=AAAAAAAAAAAAAGAAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:30:1:32.5:1:1:0:60:4:0.3333:0:0 0/0:1:0:0,0:0,1:0:0,0:23:0:32:0:1:0:60:2:1:0:1 -17 29527250 . A AT 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.68277;SOR=0.59395;LSEQ=ATAAAGAAAATAGAAAAAGG;RSEQ=TTTTTTTTAAATTTGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:15:15,0:5,0:0.75:0,1:26.1:1:30.2:1:1:0:59.3:14:0.7778:0.05:0.1 1/0:11:7:7,0:2,1:0.6364:2,0:29:1:30.1:1:0.3:0:59.6:14:0.6364:0.0909:0 -17 29528325 . G GT 124 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.64556;SOR=0.75577;LSEQ=CAAGACCTTAAAAACTTAGT;RSEQ=TTTTTTTTTTAAACTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:17:12,5:105,63:0.0914:2,2:29.8:1:30.4:1:0.60456:1.44:60:34:0.0934:0.0054:0.2 0/1:85:6:6,0:56,23:0.0706:2,0:22.2:1:31:1:0.18385:0:60:12:0.0732:0.0235:0 -17 29528406 . C CT 155 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.29015;SOR=1.35493;LSEQ=TTTCTCATAGAAATAATCTG;RSEQ=TTTTTTTTTTCTTTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:29:22,7:327,101:0.0632:2,2:29.8:1:30.1:1:1:1.03009:60:28:0.0621:0:0.2 0/1:394:33:26,7:270,87:0.0838:2,2:27:1:30.8:1:0.83253:1.20:60:66:0.0871:0:0.3 -17 29528744 . A T 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02597;SOR=Inf;LSEQ=GTTAATAAGATGCTTTGGAA;RSEQ=GATTAAATCTAAAACGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:0,18:0:1,0:25.6:1:32.9:1:1:0:59.8:36:1:0:0 1/0:4:2:1,1:0,2:0.5:0,2:21.5:1:28.5:1:1:0:60:4:0.5:0:1 -17 29532920 . T TA 28 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTGTAAAACATTAAACT;RSEQ=AAAAAAAAAAAAAGAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:10.5:1:28.7:1:1:0:60:4:0.3333:0.1667:1 0/0:1:0:0,0:1,0:0:0,0:5:0:29:0:1:0:60:2:1:0:0 -17 29533434 . A AT 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.54107;LSEQ=TCTCACCTCCTTTCTATTGC;RSEQ=TTTTTTTTAGTGTCTTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:28,147:0.0113:2,2:30.5:1:30.5:1:0.30162:5.18:60:4:0.0116:0:1 0/0:163:1:0,1:27,135:0.0061:2,0:40:0:31:0:1:0:60:2:0.0062:0:0 -17 29533685 . CTTTTGAACAAAAATA C 97 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTTTTTTCTCCTTAAAA;RSEQ=TTTTGATTAGCCTCTCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:1,8:0,0:1:0,2:20.1:1:30.8:1:1:0:57.9:18:1:0.5556:0.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29541061 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGAGTCTATGAAATACT;RSEQ=GTATGTATGTCTGGGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29541339 . A T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00261;SOR=0.14969;LSEQ=TACTATTGAGTGTTTCTACT;RSEQ=ATACCACACATTTGGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:29:29,0:5,0:0.8529:0,1:20.1:1:30.4:1:1:0:58.6:58:0.8788:0:1.1 0/1:22:10:9,1:11,1:0.4545:2,2:20.5:1:30:1:1:1.21106:59.7:20:0.4545:0:1.1 -17 29541437 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17909;LSEQ=AGCTATTATCCTGAGTCTTA;RSEQ=GTCTGATACCATGTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:206:180:156,24:21,5:0.8738:2,2:24.5:1:31.7:1:0.37926:1.54:53.2:89:0.8725:0:1.1 1/0:172:95:77,18:64,13:0.5523:2,2:25.4:1:30.8:1:0.84248:1.14991:51.3:94:0.5529:0:1.1 -17 29544957 . CA C 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGCCATTGCACTCCGTTT;RSEQ=AAAAAAAAAAAAAAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:30.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29545987 . A AT 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00386;SOR=0.60595;LSEQ=TAATCTCTCTCGATTTATTT;RSEQ=TTTTTTTAATTGAAGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:260:179:143,36:64,14:0.6885:2,2:27.3:1:30.2:1:0.73487:1.15027:60:43.75:0.6917:0.0346:0.2 1/0:339:194:139,55:107,38:0.5723:2,2:22.6:1:29.1:1:0.71273:1.11381:60:63.667:0.5719:0.1327:0.1 -17 29546175 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13152;LSEQ=CCATGTTCTTGAAGGAAAGA;RSEQ=TGTAACTATGTACATTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:255:221:49,172:4,29:0.8667:2,2:24.2:1:32.3:1:0.25158:2.06:60:220:0.8661:0:1.1 0/1:274:126:33,93:44,103:0.4599:2,2:24.7:1:31.3:1:0.50366:1.20306:60:62:0.4627:0:1.2 -17 29546285 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06633;SOR=Inf;LSEQ=CTATACATTGTTTTATAAAA;RSEQ=TCCATGGAGAAAGAAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:2,34:0:2,0:22.8:1:32.4:1:1:0:60:35:1:0:0.2 0/1:13:2:1,1:0,11:0.1538:0,2:13.5:1:30.5:1:0.15385:0:60:4:0.1538:0:1 -17 29553332 . CGGAGAC TGGAG 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTGTGAGTTATTGTATG;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:2,0:148,3:0.0131:1,0:40:1:30.5:1:1:0:57.5:4:0.0139:0.0065:1 0/0:74:0:0,0:68,4:0:2,0:24.4:1:31.4:1:1:0:58.6:23:1:0:0.5 -17 29553336 . GAC G 178 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=39;MSI=20.000;MSILEN=2;SSF=0.00192;SOR=0.34073;LSEQ=TGTGAGTTATTGTATGCGGA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:45:45,0:89,3:0.2647:1,1:30:1:32.5:1:0.55067:0:59.3:21.5:0.2638:0:0.4 0/1:101:11:10,1:78,5:0.1089:2,2:18.4:1:32.2:1:0.53643:1.55147:60:22:0.1122:0.0297:0.1 -17 29553377 . A T 52 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35435;SOR=0.49577;LSEQ=ACACACACACACACACACAC;RSEQ=GTTTATTGCATTGTTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:7:7,0:251,39:0.0236:2,0:29.7:1:18.6:1:0.59997:0:47.1:0.167:0.0039:0:3.4 0/1:254:3:1,2:206,44:0.0118:2,2:9.3:1:22:1:0.08602:9.23919:56.7:2:0.0089:0:1.3 -17 29553485 . G A 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.0506;LSEQ=GGATGCAGCGGAACCCCCCC;RSEQ=ATTTGCCGACAAGCCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1503:175:98,77:704,621:0.1164:2,2:25.8:1:29.6:1:0.51907:1.12:59.9:28.167:0.1149:0:1.2 0/1:1538:741:381,360:417,375:0.4818:2,2:26.4:1:29.6:1:0.64539:1.05064:59.9:51.929:0.4818:0:1.2 -17 29553719 . GT G 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02189;SOR=0;LSEQ=ACAGGTAAATGTGAATAGTG;RSEQ=TTTTTTTACTCAGTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:5:2,3:69,232:0.0163:2,2:31.2:1:31.4:1:0.32906:2.23:60:10:0.0165:0:1 0/0:350:0:0,0:120,230:0:2,0:25.3:1:29.1:1:1:0:59.9:57.333:1:0:0.2 -17 29554158 . G T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12423;SOR=0;LSEQ=CTGCTCTTCCTACTCCTTTT;RSEQ=GGTGGAGCTTATCAGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:4:2,2:260,92:0.0112:2,2:18:1:29.8:1:0.28512:2.81632:60:8:0.0114:0:1 0/0:342:0:0,0:230,112:0:2,0:29:0:12:0:1:0:60:0:0:0:6 -17 29554732 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.07187;SOR=Inf;LSEQ=AAAGTAAACATATAGCTGTG;RSEQ=GAAGACTGATATTTAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:5,105:0:1,0:24.3:1:30.4:1:1:0:60:220:0.991:0:0.1 0/1:80:3:1,2:1,76:0.0375:1,2:18.7:1:30.7:1:0.07405:31.23:60:6:0.0375:0:1.7 -17 29555960 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21058;SOR=Inf;LSEQ=TTTTGTACTTTTGTCATGGA;RSEQ=GAAATGTTGGATAAAGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:169,12:0:2,0:24.6:1:30.1:1:1:0:59.8:44.25:1:0:0.1 0/1:154:2:1,1:134,18:0.013:2,2:18.5:1:28.5:1:0.23224:7.27154:60:4:0.0132:0:1 -17 29555970 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21976;SOR=Inf;LSEQ=TTGTCATGGAAGAAATGTTG;RSEQ=ATAAAGCATAATTTGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:180,20:0:2,0:26.3:1:31:1:1:0:59.9:32.333:1:0:0.1 0/1:177:2:1,1:145,30:0.0113:2,2:13.5:1:25.5:1:0.32043:4.77116:60:4:0.0114:0:1 -17 29555976 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24929;SOR=0;LSEQ=TGGAAGAAATGTTGGATAAA;RSEQ=CATAATTTGTCAAGTCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:3:1,2:188,31:0.0134:2,2:12.7:1:29:1:0.05851:11.89851:60:6:0.0136:0:1 0/0:208:0:0,0:165,43:0:2,0:22.5:1:31.8:1:1:0:60:416:1:0:0.1 -17 29556462 . GT G 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.68633;SOR=0.51239;LSEQ=TTGAAGAATACCATCAGCAA;RSEQ=TTTTTGACTCCCAAGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:4:2,2:78,266:0.0115:2,2:13.5:1:30.1:1:0.22753:3.40:60:8:0.0116:0.0029:0.3 0/0:338:2:1,1:101,235:0.0059:2,2:25:1:31:1:0.51311:2.32:60:4:0.006:0:0 -17 29556703 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55088;SOR=0;LSEQ=ACGTGCCCTGTGTATGGGTA;RSEQ=GAGTGTCTGCGTATATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:2,0:109,15:0.0159:2,0:29.5:1:31:1:1:0:60:4:0.0164:0:1 0/0:64:0:0,0:61,3:0:1,0:24:1:31.2:1:1:0:60:63:1:0:0.1 -17 29556743 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13824;SOR=Inf;LSEQ=TATGCTTATTTGGCTCTATG;RSEQ=CTGTGGGTGCACTTACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:213,21:0:2,0:25.4:1:31.9:1:1:0:60:38:1:0:0.1 0/1:139:2:1,1:123,14:0.0144:2,2:23:1:27.5:1:0.20488:8.5204:60:4:0.0149:0:1 -17 29556837 . T C 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGGCAAATCATTAATGTA;RSEQ=TTGTTCTTTCTTTAGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:837:0:0,0:452,385:0:2,0:24.6:1:30.5:1:1:0:59.9:103.625:1:0:0.1 0/1:785:30:17,13:420,334:0.0382:2,2:26:1:32:1:1:1.04:60:60:0.0385:0:1.1 -17 29557205 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.0981;SOR=Inf;LSEQ=TTTAATTCGTTTTACTTGAT;RSEQ=ACTAAAGTATTTAGAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:206,37:0:2,0:24.5:1:32.3:1:1:0:60:120.5:1:0:0.1 0/1:209:3:2,1:173,33:0.0144:2,2:17:1:22.7:1:0.4146:2.60524:60:2:0.0097:0:1 -17 29557466 . A G 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=GTCCAATGAAGTACAGAAAA;RSEQ=GAGTAGATATGCGGTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:7,170:0:1,0:25.7:1:31.6:1:1:0:59.8:87.5:1:0:0.1 0/1:124:11:0,11:4,109:0.0887:1,0:25.2:1:30.9:1:1:0:60:22:0.0887:0:1.3 -17 29558082 . T C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=4.05999;LSEQ=GTGTTTGAAATATGTAAAGA;RSEQ=GCTAATCTTTATTACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:15:0,15:2,70:0.1724:1,1:25.3:1:31.3:1:1:0:60:30:0.1744:0:1 0/1:76:35:1,34:1,40:0.4605:1,1:25.4:1:30:1:1:1.17:60:70:0.4605:0:1.2 -17 29558293 . T G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCATTGTGTTGAATCTTT;RSEQ=TAAGAAATAATTGATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:24.1:1:32.4:1:1:0:60:14:1:0:1 1/1:3:3:1,2:0,0:1:0,2:34.3:1:31.3:1:1:0:60:6:1:0:1 -17 29559089 . A T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.71145;SOR=1.52054;LSEQ=TTTTTTTTTTTTTTTTTTTC;RSEQ=GAGATTTGGACCAGGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:3:1,2:297,137:0.0068:2,2:11.7:1:20:1:0.23861:4.31966:60:2:0.0052:0:2.3 0/1:387:4:1,3:240,136:0.0103:2,2:9.5:1:23.3:1:0.14085:5.27069:48:3:0.0091:0:1.8 -17 29559092 . G T 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.29967;SOR=0.38913;LSEQ=TTTTTTTTTTTTTTTTCAGA;RSEQ=ATTTGGACCAGGCAAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:6:1,5:328,152:0.0121:2,2:17.7:1:24.2:1:0.01489:10.73356:60:5:0.0132:0:1.5 0/0:423:2:0,2:262,151:0.0047:2,0:1:0:23.5:1:0.13536:0:60:4:0.0064:0:1 -17 29559588 . G C 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=4.49785;LSEQ=AGCCACCCTGGCTGATTATC;RSEQ=CGAGAGAGGAGAGAAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:18:18,0:70,7:0.1895:2,1:27.3:1:30.5:1:0.34022:0:60:17:0.1828:0:1.1 1/0:66:34:32,2:30,2:0.5152:2,2:25.6:1:30.6:1:1:1.07:60:33:0.5077:0:1 -17 29559932 . C A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.83983;LSEQ=GAAAGTTTCATATAGAAATA;RSEQ=AAAACCTAGAGAACTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:69:31,38:152,159:0.1816:2,2:20.2:1:30.3:1:0.59553:1.17135:60:68:0.1804:0:1.1 0/1:367:169:80,89:85,113:0.4605:2,2:21.6:1:30.2:1:0.40214:1.19:60:338:0.463:0:1.1 -17 29560292 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50042;SOR=0;LSEQ=CATAGCAAATCCTTCAGAAT;RSEQ=TATTTGTTCAATAAATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:27,153:0.011:2,2:20.5:1:28.5:1:0.28474:5.58:60:4:0.011:0:1 0/0:161:0:0,0:30,131:0:2,0:22.4:1:29.6:1:1:0:59.9:322:1:0:0.1 -17 29560296 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20768;SOR=Inf;LSEQ=GCAAATCCTTCAGAATATAT;RSEQ=TGTTCAATAAATGTTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:25,144:0:2,0:23.4:1:29.6:1:1:0:59.4:23.143:1:0:0.1 0/1:142:2:1,1:22,118:0.0141:2,2:12:1:26.5:1:0.29867:5.27:60:4:0.0142:0:1 -17 29563073 . T TTG 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=8.07801;LSEQ=TCACATAGAACCGCTGTTTT;RSEQ=TGTTTTTTTTTTTTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:36:7,29:126,355:0.0687:2,2:32.9:1:30.9:1:0.43441:1.46946:60:72:0.0705:0:1.1 0/1:460:172:50,122:98,190:0.3739:2,2:25.6:1:30.4:1:0.30269:1.2579:60:171:0.375:0.1196:1.2 -17 29563085 . T G 226 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0;SOR=5.94189;LSEQ=GCTGTTTTTTGTTTTTTTTT;RSEQ=TTTGTTTGTTTGTTTTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:52:9,43:80,319:0.1153:2,2:26.5:1:31.6:1:0.71478:1.19772:60:104:0.1169:0:1.1 0/1:373:163:40,123:64,146:0.437:2,2:27.7:1:30.8:1:0.24442:1.34687:60:53.333:0.4336:0:1.1 -17 29575849 . CT C 62 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.21956;SOR=2.73279;LSEQ=TCCAGCCCTGTCAAAGTTGT;RSEQ=TTTTTTTTTTTATAGTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:4:4,0:36,2:0.093:2,0:10.5:1:31.6:1:1:0:58.8:8:0.0952:0.0698:0.5 0/1:18:4:4,0:13,1:0.2222:1,0:28.8:1:31:1:1:0:60:8:0.2222:0:0.3 -17 29585644 . T C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52458;SOR=0;LSEQ=GGTTTTCAGTTATGTGCTTT;RSEQ=GTTTTATTTGTTTATATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:0,2:2,63:0.0299:1,0:47:1:27.5:1:1:0:60:4:0.0299:0:1 0/0:41:0:0,0:3,38:0:2,0:20:1:30.9:1:1:0:60:82:1:0:0 -17 29585907 . T C 92 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17994;SOR=0;LSEQ=AGAAACACTACCTAAAATAA;RSEQ=TTATAGAATGAGGAATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:8,0:33,5:0.1739:2,0:25.1:1:30.9:1:0.5692:0:60:16:0.1739:0:1 0/0:13:0:0,0:13,0:0:1,0:31.1:1:29:1:1:0:60:12:1:0:0 -17 29586217 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50503;SOR=0;LSEQ=CGGTTTCACATAAATCCATG;RSEQ=ACCTGTTTTACATGAAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:12,128:0.0141:2,2:24:1:31:1:0.17531:10.29:60:4:0.0141:0:1 0/0:112:0:0,0:12,100:0:2,0:22.4:1:28.1:1:1:0:60:224:1:0:0.1 -17 29587277 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1843;SOR=Inf;LSEQ=CATTGTGTGAACAAGCCCTC;RSEQ=ATATTTGTAATCTTAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:109,2:0:1,0:25.7:1:31.3:1:1:0:60:110:1:0:0.1 0/1:84:2:1,1:79,3:0.0238:1,2:28:1:26.5:1:0.09352:22.9498:60:4:0.0241:0:1 -17 29587341 . G C 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTAATTCAAACATAAGTCT;RSEQ=GGTGTATCTGGTGTTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:69:44,25:235,100:0.1708:2,2:23.2:1:29.2:1:0.31797:1.33429:60:22:0.1654:0:1.2 0/0:442:0:0,0:278,164:0:2,0:24.6:1:30.5:1:1:0:60:43.2:1:0:0.1 -17 29587561 . G T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07826;SOR=Inf;LSEQ=TTCCCAGTCATGGGGATAGT;RSEQ=AACACTCTCCGTTTAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:106,290:0:2,0:23.4:1:31.3:1:1:0:60:65:1:0:0.1 0/1:297:3:1,2:79,215:0.0101:2,2:8.7:1:22:1:1:1.36:60:2:0.0068:0:2 -17 29592095 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.0999;SOR=Inf;LSEQ=GAGTAATACCTTGAAATTTT;RSEQ=GGTGCATGTTGCCAAATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:51,2:0:1,0:26.7:1:30.6:1:1:0:59.9:106:1:0:0 0/1:25:2:1,1:23,0:0.08:1,2:16.5:1:27.5:1:0.08:0:60:4:0.08:0:1 -17 29652531 . A G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTACCAGACTATTCGCCT;RSEQ=AGGAGTTTGGTGGGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:27.7:1:31.7:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29652884 . T C 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTGCTGATATACCATGTC;RSEQ=TACTGACTTTAAAGCCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:807:0:0,0:481,324:0:2,0:24.9:1:30.6:1:1:0:60:133.167:0.9975:0:0.1 0/1:712:29:17,12:378,303:0.0407:2,2:24.8:1:30.9:1:0.84941:1.14:60:58:0.041:0:1.1 -17 29653293 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.34604;LSEQ=AAGTTCCAGTCTGTGTTTTG;RSEQ=AAACGATTCATTGCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:270:195:59,136:19,55:0.7222:2,2:23.9:1:31.9:1:0.54772:1.25:60:194:0.7239:0:1 0/1:260:123:39,84:45,92:0.4731:2,2:23.6:1:31.6:1:0.89467:1.05333:60:60.5:0.469:0:1.2 -17 29653993 . GGAGTGCAGTGGCGTGATCTCA G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTCTGTTGCCTAGGCT;RSEQ=GAGTGCAGTGGCGTGATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17.5:1:33:1:1:0:36.5:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29654096 . G C 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCCCAGGTTCAAGCGATTCT;RSEQ=CTGCCTCAGCCTCCCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27.5:1:29.5:1:1:0:32.5:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:22:0:26:0:1:0:60:2:1:0:1 -17 29654876 . T A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18663;LSEQ=CGGTAGGTTTTTTAAAATTC;RSEQ=CTTCAGTTTGATTTGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:328:248:72,176:20,60:0.7561:2,2:25.7:1:29.8:1:0.56754:1.23:60:247:0.7554:0:1.1 0/1:257:94:31,63:48,115:0.3658:2,2:22.6:1:29.1:1:0.57652:1.18:60:93:0.3676:0:1.1 -17 29654913 . A T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27878;SOR=0;LSEQ=GGTTTGTTGCTTTTAAAATG;RSEQ=GACCATTTAATGAATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:1,2:21,153:0.0169:2,2:6.3:1:29.3:1:0.33008:3.60:60:6:0.0174:0:2 0/0:117:0:0,0:11,106:0:2,0:23.1:1:30.5:1:1:0:60:116:1:0:0.5 -17 29654918 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52202;SOR=0;LSEQ=GTTGCTTTTAAAATGAGACC;RSEQ=TTTAATGAATTTTAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:16,141:0.0126:2,2:24.5:1:29:1:0.20301:8.58:60:4:0.0128:0:2 0/0:102:0:0,0:7,95:0:2,0:24.5:1:29.7:1:1:0:60:101:1:0:0.5 -17 29654974 . G A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00022;SOR=0.16714;LSEQ=TGTAAATTGGAAGGTATGCA;RSEQ=TGTTGGTTAACCACTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:38:0,38:0,10:0.7917:0,1:28.2:1:31.4:1:1:0:60:76:0.7917:0:1 0/1:34:13:0,13:0,21:0.3824:1,1:22.2:1:30.8:1:1:0:60:26:0.3824:0:1 -17 29655218 . C T 59 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAAGTCAAGTCAGATTATTG;RSEQ=TTTACAAAAGAAGGCCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:34.5:1:29.8:1:1:0:60:8:0.8:0:1 0/0:1:0:0,0:0,1:0:0,0:7:0:34:0:1:0:60:2:1:0:0 -17 29661923 . C T 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01678;SOR=8.79666;LSEQ=TCAAATCTAGTTCGTTTTTG;RSEQ=AAGCATAATGATGATGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:1:0,1:349,370:0.0014:2,0:1:0:26:0:1:0:60:2:0.0014:0:1 0/1:662:8:3,5:321,333:0.0121:2,2:14.3:1:26.8:1:0.72539:1.60547:60:16:0.0123:0:1.8 -17 29663172 . A C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82573;LSEQ=AATGAATATACTCATCCTTT;RSEQ=CTGGATATTTTATAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:11,0:1,0:0.9167:0,0:20.5:1:31.5:1:1:0:60:22:0.9167:0:1 1/1:10:9:9,0:1,0:0.9:0,0:33.8:1:29.4:1:1:0:60:8:0.8889:0:1.1 -17 29663322 . A T 41 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05259;SOR=Inf;LSEQ=TTAAATTGGTAGAGTGATTA;RSEQ=AAACATGTTATTTTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:248,79:0:2,0:22.9:1:30.2:1:1:0:60:108:1:0:0.1 0/1:302:4:1,3:205,93:0.0132:2,2:9.8:1:20.5:1:0.09641:6.56823:60:3:0.0101:0:1.8 -17 29663614 . GT G 194 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.20963;LSEQ=GCTAAAACTTTGAGTCCCAT;RSEQ=TTTTTTTTTTAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:432:70:48,22:242,102:0.162:2,2:24.6:1:31.7:1:0.77578:1.08719:59.6:140:0.1632:0.0324:1.3 0/1:360:14:9,5:229,112:0.0389:2,2:31.6:1:32:1:0.77981:1.13549:60:28:0.0393:0:1.4 -17 29663623 . TTT AAA 61 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=0.06466;SOR=0;LSEQ=TTGAGTCCCATGTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:5:3,2:295,130:0.011:2,2:26.4:1:26.7:1:0.64484:1.51126:57:10:0.0111:0:2 0/0:397:0:0,0:251,137:0:2,0:23.2:1:29.1:1:1:0:59.6:76.6:0.977:0:1.1 -17 29663624 . TT AA 221 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=0.46131;LSEQ=TGAGTCCCATGTTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:187:135,52:148,75:0.4083:2,2:27.7:1:29.4:1:0.23824:1.31:59.9:92.5:0.4501:0:1.3 0/1:402:97:67,30:181,109:0.2413:2,2:25.2:1:28.5:1:0.27174:1.34:59.7:96:0.2507:0:1.3 -17 29663625 . T A 198 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGTCCCATGTTTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:125:74,51:44,19:0.2671:2,2:19.5:1:28.5:1:0.20094:1.5921:60:40.667:0.5259:0:1.4 0/0:425:0:0,0:62,36:0:2,0:22.5:1:27.4:1:1:0:59.4:15.333:0.3046:0:0.5 -17 29664354 . C A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATTAAAAAGTAATATTTT;RSEQ=TGTCTTTACTTGTTCCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:239,45:0:2,0:22.2:1:31.2:1:1:0:60:55.8:0.9964:0:0.1 0/1:257:18:15,3:179,60:0.07:2,2:28.2:1:28.3:1:0.57438:1.67:60:36:0.0709:0:1 -17 29664645 . T A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03635;SOR=Inf;LSEQ=ACTAAGTTAAAATCTTTTTT;RSEQ=AAAAATATGTTAATACTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:69,200:0:2,0:23.4:1:28.9:1:1:0:60:268:1:0:0.1 0/1:210:4:1,3:51,155:0.019:2,2:18.5:1:27.8:1:1:1.01:60:8:0.0193:0:1.8 -17 29664671 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52838;SOR=0;LSEQ=TATGTTAATACTATATAGAA;RSEQ=AAATATTGGTTTATTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:54,140:0.0102:2,2:5.5:1:29:1:0.48352:2.58:60:4:0.0104:0:1 0/0:119:0:0,0:24,94:0:2,0:23.8:1:31.2:1:1:0:60:38.333:0.9914:0:0.1 -17 29665081 . C T 54 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12177;SOR=0.1962;LSEQ=TCCATCCCTGCAACCAAGAG;RSEQ=TCTTGTTGTCTTTGGGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:5:0,5:274,206:0.0103:2,0:9.2:1:23.6:1:0.01517:0:60:4:0.0084:0:2 0/0:491:1:0,1:260,229:0.002:2,0:1:0:24:0:0.46939:0:60:2:0.0021:0:1 -17 29670190 . C G 267 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6399;SOR=0.89402;LSEQ=TAGAATATTTTTATGAAGTA;RSEQ=TATTAAGAAACCAGAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:385:343:53,290:10,30:0.8909:2,2:24.1:1:31.8:1:0.17276:1.82048:60:48:0.8889:0:1.1 1/1:332:292:63,229:10,29:0.8795:2,2:22.4:1:30.9:1:0.5426:1.25253:60:145:0.8815:0:1.1 -17 29675744 . T TAA 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAAAGGGACATCTTTTCT;RSEQ=AAAAAAAAAAATGTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:17:1:28.2:1:1:0:54.5:4:0.6667:0.3333:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 29675862 . A G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGGGAATAGAAGATCTGA;RSEQ=AGACTATCATGTTTTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:19.5:1:31.5:1:1:0:60:4:0.5:0:2 0/0:1:0:0,0:1,0:0:0,0:18:0:32:0:1:0:60:2:1:0:1 -17 29675878 . T G 74 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGAAAGACTATCATGTTTT;RSEQ=TAATTTTCCTCTTCCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:0.8333:0,2:25:1:32.2:1:1:0:60:10:0.8333:0:1.6 1/1:1:1:1,0:0,0:1:0,0:34:0:33:0:1:0:60:2:1:0:1 -17 29675971 . T A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01594;SOR=0.12774;LSEQ=TTATACATAATTAATTATTC;RSEQ=CATTCACATATGCATGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:27:27,0:4,0:0.871:0,1:23.5:1:29.8:1:1:0:60:54:0.871:0:1 0/1:9:4:3,1:5,0:0.4444:0,2:32.3:1:30.5:1:0.44444:0:60:8:0.5:0:1 -17 29676104 . CTTGT C 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=6.000;MSILEN=4;SSF=0.75329;SOR=1.39323;LSEQ=GTTCAAAAAATTAATTCTTA;RSEQ=TTGTTTGTTTGTTTGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:4:3,1:180,44:0.0175:2,2:30:1:32.9:1:1:1.36161:60:8:0.0181:0.0044:0 0/1:247:6:5,1:180,61:0.0243:2,2:23.7:1:31.7:1:1:1.69:60:12:0.0249:0:0.2 -17 29679236 . C T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17404;SOR=5.17693;LSEQ=ACGATGGTTGTATTTGTCAC;RSEQ=ATATTAATTGATTTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:1:0,1:266,70:0.003:2,0:1:0:24:0:0.21068:0:60:2:0.003:0:2 0/1:263:4:1,3:199,60:0.0152:2,2:5.8:1:26.3:1:0.04382:9.83882:60:8:0.0155:0:1.3 -17 29679246 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19385;LSEQ=TATTTGTCACCATATTAATT;RSEQ=ATTTTTCTCTATTGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:398:308:232,76:69,20:0.7739:2,2:23.2:1:28.6:1:0.77885:1.12985:60:50.333:0.7744:0:1.1 0/1:339:135:100,35:149,55:0.3982:2,2:22.9:1:28:1:0.90022:1.05:60:66.5:0.397:0:1.1 -17 29679470 . T A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12008;SOR=Inf;LSEQ=ATGTAGATTTTTTTTATTAT;RSEQ=TAAAAAAATAGATATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:75,230:0:2,0:24:1:30:1:1:0:60:100.667:1:0:0.1 0/1:298:3:2,1:75,220:0.0101:2,2:9:1:20.3:1:0.16485:5.82:60:2:0.0068:0:1.7 -17 29679587 . A C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13051;SOR=Inf;LSEQ=AAAAGAGAGTTTGATAGATC;RSEQ=GTTAAGCATTATAAGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:1,37:0:1,0:26.9:1:31.4:1:1:0:60:37:1:0:0.4 0/1:22:2:0,2:2,18:0.0909:2,0:30.5:1:27:1:1:0:60:4:0.0909:0:1 -17 29683898 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.15082;SOR=Inf;LSEQ=CTACTAAAGAAAGCTGTTGA;RSEQ=TTTTAGAAGTAACATTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:252,37:0:2,0:23.2:1:30:1:1:0:60:35.125:1:0:0.1 0/1:184:2:1,1:159,23:0.0109:2,2:15.5:1:27.5:1:0.24448:6.7878:60:4:0.0109:0:3 -17 29683915 . G T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14933;SOR=0;LSEQ=TGAATTTTAGAAGTAACATT;RSEQ=AAATAGTTAGGTGAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:4:2,2:309,80:0.0102:2,2:26.8:1:28:1:0.19348:3.84493:60:8:0.0102:0:1 0/0:271:0:0,0:212,59:0:2,0:23.7:1:31.2:1:1:0:60:53.2:1:0:0.1 -17 29684520 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15518;SOR=Inf;LSEQ=ATTTTAGCTTTGAGACAGTA;RSEQ=GTTTAATGAGGGTTAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:2,108:0:1,0:25:1:31.5:1:1:0:60:109:1:0:0.5 0/1:72:2:0,2:1,69:0.0278:1,0:19:0:32:0:1:0:60:4:0.0278:0:1 -17 29684553 . C T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=0.20152;LSEQ=TTAAGATTAGTTTTGACCTA;RSEQ=TAGATCTATTAGAAAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:75:62:2,60:0,13:0.8267:1,1:25.8:1:30.4:1:1:0:60:30:0.8219:0:1 0/1:35:17:0,17:0,18:0.4857:1,1:21.8:1:30.6:1:1:0:60:34:0.4857:0:1.1 -17 29685481 . C CT 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.31032;SOR=0.51721;LSEQ=CTAAAATGTTCCTCTGTTGA;RSEQ=TTTTTTTTTCTTTTAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:11:7,4:254,62:0.0336:2,2:19.7:1:29.8:1:0.24196:2.33354:60:22:0.0341:0.0061:0.3 0/1:283:5:3,2:217,59:0.0177:2,2:16:1:28.6:1:0.29753:2.4424:60:10:0.0178:0.0071:0.4 -17 29687463 . T TA 69 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.46142;SOR=0.46864;LSEQ=GCTTCAGATGGGGATTTACT;RSEQ=AAAAAAAAGGAACTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:5:3,2:247,42:0.017:2,2:18.8:1:30:1:0.16289:3.8939:60:10:0.0171:0:0.8 0/0:249:2:2,0:193,54:0.008:2,0:21:1:29:1:1:0:60:4:0.0081:0.004:2.5 -17 29687870 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51301;SOR=0;LSEQ=TTACCTTGTAACTGACTTGA;RSEQ=TTTTGTTATTCTATGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:0,2:0,33:0.0571:1,0:9.5:1:28.5:1:1:0:60:4:0.0571:0:1 0/0:23:0:0,0:1,22:0:1,0:26.3:1:32.2:1:1:0:60:46:1:0:0 -17 29694054 . G C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00748;SOR=0.26585;LSEQ=AAAAATACATCTACAAAGTT;RSEQ=TAAGTTCTCTCATTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:55:54,1:18,0:0.7534:1,1:21.1:1:31.4:1:1:0:60:110:0.7534:0:2 0/1:27:12:12,0:15,0:0.4444:1,0:28.9:1:30.7:1:1:0:60:11:0.4231:0:2.1 -17 29694063 . C A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01786;SOR=0.34837;LSEQ=TCTACAAAGTTGTAAGTTCT;RSEQ=TCATTTATTTACCAACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:58:57,1:20,0:0.7436:1,1:24.5:1:28.5:1:1:0:60:116:0.7436:0:1.9 1/0:36:18:18,0:18,0:0.5:1,1:23.8:1:28.2:1:1:0:60:17:0.4857:0:1.7 -17 29700960 . A T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49982;SOR=Inf;LSEQ=TGTGTCCCCGTTGTTAAGCG;RSEQ=CACATGACTGCAATGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:98,18:0:2,0:22.8:1:29.8:1:1:0:60:57:1:0:0 0/1:131:2:1,1:104,25:0.0153:2,2:9.5:1:24.5:1:0.35878:4.09878:60:4:0.0157:0:1 -17 29700989 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25849;SOR=Inf;LSEQ=TGCAATGAAATTCAGTCCTG;RSEQ=AAGGAAAAGAAGAAGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:135,50:0:2,0:24.7:1:30.9:1:1:0:60:60.667:1:0:0.1 0/1:234:3:1,2:160,71:0.0128:2,2:16.3:1:25.7:1:0.2302:4.47473:60:6:0.0131:0:1 -17 29763096 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50639;SOR=Inf;LSEQ=TGCTGGGGGGGCCCTTCCTG;RSEQ=ATTGCTGAGCAGGAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:12,5:0:2,0:28.2:1:30.4:1:1:0:60:16:1:0:0.2 0/1:25:2:1,1:11,12:0.08:2,2:41.5:1:25:1:1:1.09:60:4:0.08:0:1 -17 30263893 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCGATCGGCAGCGCGCACG;RSEQ=GCCAACCAAGCCGCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:31.5:1:1:0:50:4:1:0:1 -17 30264207 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49946;SOR=Inf;LSEQ=CGAGCGGTTGGTATTGCAGG;RSEQ=GCTTGCTCTCCGGGGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:32,34:0:2,0:27.5:1:30.2:1:1:0:60:32:1:0:0.1 0/1:77:2:0,2:40,35:0.026:2,0:24.5:1:29.5:1:0.22761:0:60:4:0.0267:0:1.5 -17 30264245 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.51078;SOR=Inf;LSEQ=GCCCGGCGGGTAGCTGGCGG;RSEQ=GGGAGGAGGCAGGAACCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:40,48:0:2,0:25.8:1:31.2:1:1:0:58.7:176:1:0:0.3 0/1:122:2:1,1:55,63:0.0164:2,2:15:1:28:1:1:1.14:52:4:0.0164:0:2 -17 30264257 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5095;SOR=Inf;LSEQ=GCTGGCGGGGGGAGGAGGCA;RSEQ=GAACCGCGATGGCGCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:36,55:0:2,0:22.8:1:31.1:1:1:0:56.6:44.5:1:0:0.3 0/1:124:2:1,1:56,66:0.0161:2,2:20:1:26.5:1:1:1.18:60:4:0.0163:0:1 -17 30264280 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20309;SOR=0;LSEQ=ACCGCGATGGCGCCTCAGAA;RSEQ=CACGGCGGTGGGGGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:32,51:0.0235:2,2:41:0:30.5:1:1:1.58:60:4:0.0247:0:1 0/0:103:0:0,0:44,59:0:2,0:22.9:1:31.5:1:1:0:56.3:33.333:1:0:0.3 -17 30264291 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49927;SOR=Inf;LSEQ=GCCTCAGAAGCACGGCGGTG;RSEQ=GGGAGGGGGCGGCTCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:28,44:0:2,0:26.6:1:31:1:1:0:54.2:144:0.9863:0:0.5 0/1:84:2:1,1:36,46:0.0238:2,2:39.5:1:30:0:1:1.27:52:4:0.0241:0:2 -17 30264306 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50854;SOR=Inf;LSEQ=CGGTGGGGGAGGGGGCGGCT;RSEQ=GGGGCCCAGCGCGGGGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:41,41:0:2,0:23.6:1:28.8:1:1:0:54.7:10.714:1:0:0.5 0/1:112:2:1,1:56,54:0.0179:2,2:5.5:1:28.5:1:1:1.03671:60:4:0.0187:0:1.5 -17 30264340 . C T 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.69102;SOR=0.68104;LSEQ=GGGTCCGGGGGAGGCGGCTT;RSEQ=GGGGGTTCGGCGGCGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:190,102:0.0102:2,2:21.3:1:29.7:1:0.28454:3.70796:60:6:0.0103:0:1 0/0:432:3:0,3:248,180:0.0069:2,0:1:0:27:1:0.07582:0:60:6:0.007:0:1 -17 30264348 . C T 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16374;SOR=0.16634;LSEQ=GGGAGGCGGCTTCGGGGGTT;RSEQ=GGCGGCGGTGGCGGCGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:4:1,3:220,120:0.0116:2,2:16:1:28.3:1:0.13248:5.47221:60:8:0.0119:0:1.3 0/0:513:1:0,1:296,216:0.0019:2,0:1:0:28:0:0.423:0:60:2:0.002:0:1 -17 30264425 . GCCT G 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.87964;SOR=0.929;LSEQ=GAGGGGGTGGCAGTTACTCG;RSEQ=CCTCCTCCTCCTCCGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:781:21:12,9:468,292:0.0269:2,2:29.4:1:31.5:1:0.65808:1.20176:60:42:0.0277:0.0013:0.4 0/1:959:24:15,9:529,405:0.025:2,2:26.3:1:32.3:1:0.67821:1.28:60:48:0.0257:0.0031:0.5 -17 30264547 . T C 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGGCCTTTGAGAGTGAGTG;RSEQ=GTGCGAGGCTTTGAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:791:0:0,0:358,432:0:2,0:25.5:1:29.9:1:1:0:51.7:64.833:0.9987:0:0.1 0/1:913:39:12,27:387,486:0.0427:2,2:21.2:1:29.9:1:0.10148:1.79058:41.7:38:0.0424:0:1.1 -17 30267579 . T TA 86 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.79221;SOR=0.81743;LSEQ=AAAGTACTATTTCTCAAAAT;RSEQ=AAAAAAAAAAACGAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:8:0,8:14,84:0.0755:2,0:35.6:1:28.9:1:0.59332:0:46.9:7:0.068:0:0 0/1:112:7:0,7:22,83:0.0625:2,0:30.1:1:29.4:1:0.34167:0:53.6:14:0.0631:0:0 -17 30274747 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=ATTAAGTGATATACTTTAGG;RSEQ=AAGAGGAAAAATTACAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:41,119:0.0123:2,2:14:1:30:1:0.4525:2.88:27:4:0.0124:0:1 0/0:162:0:0,0:52,110:0:2,0:22.6:1:29:1:1:0:42.4:53:1:0:0.1 -17 30293310 . T A 22 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22085;SOR=Inf;LSEQ=CTGAGTGTAAATTTATAAAA;RSEQ=TAAGTTTAATGGAAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:23,149:0:2,0:23.9:1:30.3:1:1:0:59.2:85:1:0:0.1 0/1:153:2:1,1:25,126:0.0131:2,2:10.5:1:22.5:1:0.31192:4.96:60:4:0.0131:0:1 -17 30293317 . TA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50011;SOR=0;LSEQ=TAAATTTATAAAATTAAGTT;RSEQ=ATGGAAAATATGTTGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:14,129:0.0138:2,2:25.5:1:30.3:1:0.19684:8.94:59.5:4:0.014:0.0069:0 0/0:128:0:0,0:17,111:0:2,0:24.1:1:29.9:1:1:0:60:256:1:0:0.1 -17 30293398 . G T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.01939;SOR=Inf;LSEQ=ATTTGTTTTTGGTGGATGGG;RSEQ=GTGCAGAGTGAAGGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:0,31:0:1,0:25.7:1:31.4:1:1:0:60:30:1:0:0 0/1:20:4:0,4:1,15:0.2:1,0:18:1:31.3:1:1:0:60:8:0.2:0:1 -17 30300060 . T C 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04566;SOR=Inf;LSEQ=GAGTGAACTTTTGAGAAGTC;RSEQ=TACTGTGGGAAATCTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:137,2:0:1,0:27.4:1:31.3:1:1:0:58.5:33.75:1:0:0.1 0/1:121:4:4,0:112,5:0.0331:1,0:14.5:1:29.8:1:1:0:58:8:0.0331:0:1 -17 30300286 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09536;SOR=Inf;LSEQ=TGATATTGGTAGATTAAATG;RSEQ=AATAATTTGCTTAATTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:109,231:0:2,0:24.9:1:30.8:1:1:0:32.3:339:1:0:0 0/1:287:3:1,2:100,184:0.0105:2,2:22.3:1:26.3:1:1:1.08665:35:6:0.0106:0:1 -17 30302411 . G A 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05871;SOR=Inf;LSEQ=GTGATCATGGCCTATCTCCC;RSEQ=TGTTTCCTATAGCTGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:73,3:0:1,0:23.3:1:29.5:1:1:0:59.2:75:1:0:0.1 0/1:79:5:5,0:71,3:0.0633:1,0:35:1:30.8:1:1:0:60:10:0.0641:0:1 -17 30302736 . AT A 141 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.31173;SOR=0.68913;LSEQ=AACCAATGAAAATATTGGTA;RSEQ=TTTTTTTTTTACTAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:22:3,19:84,214:0.0685:2,2:26.9:1:31.8:1:0.21261:2.48024:60:44:0.0705:0:0 0/1:311:15:3,12:91,202:0.0482:2,2:23.9:1:30.5:1:0.56609:1.79892:57.8:30:0.0493:0.0032:0.1 -17 30303480 . TATATC T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0587;SOR=Inf;LSEQ=TGTTTTATGTTAAGGGACCA;RSEQ=ATAACACATTTTTGTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:129,18:0:2,0:24.2:1:28.4:1:1:0:57.6:72.5:1:0:0.1 0/1:144:4:4,0:116,24:0.0278:2,0:17.5:1:30:1:1:0:46.5:8:0.028:0.0069:0 -17 30310222 . T G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00662;SOR=Inf;LSEQ=AATTCATGTTGGAAGTAGAG;RSEQ=CCTTTGTTTTTTATACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:3,172:0:1,0:23.6:1:29.7:1:1:0:55.6:34:1:0:0.2 0/1:170:7:1,6:5,158:0.0412:1,2:17.1:1:31:1:0.22599:5.16:44.1:14:0.0422:0:1.6 -17 30315287 . A G 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00051;SOR=Inf;LSEQ=TTTTTTAATTTCTACAATTT;RSEQ=TTTGAATTCATTATCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:162,6:0:1,0:22.7:1:28.1:1:1:0:60:55:1:0:0.1 0/1:132:9:8,1:115,8:0.0682:2,2:18.3:1:30.2:1:0.48131:1.78695:60:8:0.0625:0:1.1 -17 30315470 . C T 226 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTAGAAATTCAGAGAGTCT;RSEQ=CATCAGGAAAACAAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:947:179:85,94:367,400:0.189:2,2:26.4:1:30.2:1:0.93402:1.01463:60:358:0.1912:0:1.1 0/0:1114:0:0,0:541,572:0:2,0:26.1:1:30.8:1:1:0:60:84.615:1:0:0.1 -17 30320386 . G A 42 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13044;SOR=Inf;LSEQ=ACCCTTCTTAAAGTAATTAT;RSEQ=AAATGTATTTGTTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:82,229:0:2,0:23.4:1:31.3:1:1:0:60:50.833:1:0:0.1 0/1:375:4:3,1:109,259:0.0107:2,2:14:1:21:1:0.08339:7.09:60:3:0.0082:0:2 -17 30320860 . CT C 170 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.01993;SOR=0.5141;LSEQ=ATGCGTAAATTGGAGATTTG;RSEQ=TTTTTTTTTTAATTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:38:29,9:208,66:0.121:2,2:27.6:1:32.4:1:1:1.02:60:76:0.1222:0.0096:0.2 0/1:318:21:16,5:213,81:0.066:2,2:29.5:1:30.9:1:0.80517:1.22:60:42:0.0669:0.0031:0.2 -17 30321113 . T G 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.04336;SOR=Inf;LSEQ=ATCTATGTACCCACAAAAAT;RSEQ=TTTTAAATTAAAAAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:3,93:0:1,0:24:1:30.3:1:1:0:60:47:1:0:0.1 0/1:53:3:0,3:1,49:0.0566:1,0:23.7:1:32:1:1:0:60:6:0.0566:0:1 -17 30321131 . GA G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.09858;SOR=Inf;LSEQ=ATTTTTTAAATTAAAAAAGG;RSEQ=AAAAATATGCATTAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:2,69:0:1,0:23.9:1:30.9:1:1:0:60:142:1:0:0.1 0/1:33:2:0,2:1,30:0.0606:1,0:26.5:1:29:1:1:0:60:4:0.0606:0:0 -17 30321556 . AT A 149 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.34703;SOR=1.33108;LSEQ=TAGGATAGGATACTTAATAT;RSEQ=TTTTTTTTTTACATTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:27:21,6:212,51:0.0931:2,2:23.4:1:30.9:1:0.799:1.18697:60:26:0.0906:0.0172:0.1 0/1:291:35:27,8:195,60:0.1203:2,2:20.7:1:29.2:1:1:1.04:60:70:0.1215:0.0206:0.2 -17 30321567 . T G 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACTTAATATATTTTTTTTTT;RSEQ=ACATTTTTGTTGCAGTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:265,77:0:2,0:22.7:1:29.4:1:1:0:60:37:0.997:0:0.2 0/1:329:16:14,2:223,90:0.0486:2,2:21.3:1:31.6:1:0.25202:2.82:60:32:0.05:0:1.6 -17 30321762 . G C 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TAGGTAAAAAGGGCATATAA;RSEQ=AAAAGTTTAAGCTCTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:87,234:0:2,0:23.8:1:31.1:1:1:0:60:63.2:1:0:0.1 0/1:302:15:4,11:73,213:0.0497:2,2:18.9:1:32.3:1:1:1.06:60:30:0.0503:0:1.1 -17 30323737 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23779;SOR=Inf;LSEQ=ATATGTTGTATTTTTAGTTC;RSEQ=AAAACATTCTGTTTTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:114,0:0:1,0:26.1:1:31:1:1:0:60:56:1:0:0.1 0/1:109:2:2,0:102,5:0.0183:1,0:25.5:1:32:0:1:0:60:4:0.0183:0:1 -17 30323950 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11375;SOR=0;LSEQ=TTATTCTTTATGGTCTTTTG;RSEQ=TGTTTCACATTCTAGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:25,161:0.0159:2,2:9.7:1:30.3:1:0.36017:3.19:60:6:0.016:0:1.3 0/0:200:0:0,0:39,160:0:2,0:21.1:1:31.9:1:1:0:60:198:0.995:0:0.1 -17 30695964 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCGGGAGGCGGAGGTTG;RSEQ=GGTGAGCTGAGACCAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19:1:30.5:1:1:0:51:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 30696193 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.12426;SOR=0;LSEQ=TCTGGCAAAAGTAAATAGTT;RSEQ=GGATGTAAGGGTAAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:117,47:0.012:2,2:17:1:28.5:1:0.49595:2.47381:60:4:0.0123:0:1 0/0:304:0:0,0:189,114:0:2,0:24.8:1:30.4:1:1:0:60:49.5:0.9966:0:0.1 -17 30696292 . C T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14397;LSEQ=CTGCATTCGAGTATTTAGCC;RSEQ=TGCGCTTATTTTTATTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:339:316:144,172:11,12:0.9322:2,2:24.7:1:30.3:1:0.83244:1.09461:60:157:0.9318:0:1.1 1/0:452:300:131,169:71,81:0.6637:2,2:25.3:1:29.7:1:0.54944:1.1305:60:49:0.6607:0:1.2 -17 30696296 . G A 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=30.15547;LSEQ=ATTCGAGTATTTAGCCCTGC;RSEQ=CTTATTTTTATTCCCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:1:1,0:154,180:0.003:2,0:13:0:31:0:0.46269:0:60:2:0.003:0:2 0/1:435:36:15,21:177,222:0.0828:2,2:24.5:1:29.6:1:0.86137:1.11591:60:72:0.0837:0:2 -17 30696372 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5107;SOR=Inf;LSEQ=TCTTCCTCGGCCAGGACAGG;RSEQ=CCCCATCGGTAATCCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:35,94:0:2,0:22:1:31.6:1:1:0:60:128:1:0:0.4 0/1:177:2:1,1:52,123:0.0113:2,2:27.5:1:28:1:0.5104:2.35:60:4:0.0114:0:1 -17 31030528 . T G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGGTGGTATTGAACTCCTG;RSEQ=GCTAAAGTGATCCTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:21,1:0,0:1:0,1:24.4:1:30.5:1:1:0:60:21:1:0:1.1 1/1:14:14:14,0:0,0:1:0,1:22.1:1:31.9:1:1:0:60:28:1:0:1 -17 31030618 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50093;SOR=Inf;LSEQ=TATTGACGATTTTGATCTTG;RSEQ=CCTATGATTCCCTAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:79,26:0:2,0:23.7:1:31.4:1:1:0:60:34:1:0:0.2 0/1:123:2:1,1:83,38:0.0163:2,2:11:1:27:1:0.53539:2.16902:60:4:0.0167:0:1 -17 31030620 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50111;SOR=Inf;LSEQ=TTGACGATTTTGATCTTGCC;RSEQ=TATGATTCCCTAGAATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:81,28:0:2,0:23.9:1:30.9:1:1:0:60:53.5:1:0:0.2 0/1:128:2:1,1:85,40:0.0156:2,2:24.5:1:27.5:1:0.54318:2.11128:60:4:0.0156:0:1 -17 31030716 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05001;LSEQ=TCATATCCCATTCCTCTTCC;RSEQ=AGACAACAAAATATTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:238:224:110,114:5,9:0.9412:2,2:26.9:1:30.2:1:0.41357:1.73:60:223:0.9409:0:1.1 0/1:298:132:65,67:78,87:0.443:2,2:26.2:1:29.3:1:0.81528:1.08:60:65:0.4498:0:1.1 -17 31030771 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50776;SOR=Inf;LSEQ=AATATTAGAGGATTATAAAT;RSEQ=TTTGTTATGCATTTGGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:35,94:0:2,0:23.3:1:31.5:1:1:0:60:63.5:1:0:0.7 0/1:170:2:1,1:54,114:0.0118:2,2:40.5:1:28.5:1:0.54368:2.10:60:4:0.0118:0:3 -17 31030783 . T G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50474;SOR=Inf;LSEQ=TTATAAATCTTTGTTATGCA;RSEQ=TTGGTACATTGTTTTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:23,83:0:2,0:23.2:1:29.9:1:1:0:60:52:1:0:0.6 0/1:134:2:1,1:41,91:0.0149:2,2:45:0:32.5:1:0.53024:2.20:60:4:0.0152:0:1.5 -17 31030811 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=ATTGTTTTCATTAAAATTTG;RSEQ=CTAATTGTTAATTATTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:7,64:0:2,0:24.6:1:31.5:1:1:0:60:22.667:0.9855:0:0.2 0/1:81:2:1,1:18,60:0.0247:2,2:9:0:31.5:1:0.42089:3.27:60:4:0.0247:0:1 -17 31819598 . G A 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.82176;LSEQ=GGGTCACACCACCTTGTTGA;RSEQ=TGAACATACCTTTCCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:89:37,52:281,301:0.1319:2,2:27.2:1:30.8:1:0.25567:1.31149:60:178:0.1334:0:1.1 0/1:583:175:83,92:203,204:0.3002:2,2:25.6:1:29.8:1:0.6513:1.10281:60:174:0.301:0:1.1 -17 31819774 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16812;SOR=Inf;LSEQ=ACCATCTGTGATCCATGTAC;RSEQ=CATGTGACAGTGAACTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:0:1,0:24.4:1:29.5:1:1:0:60:40:1:0:0.1 0/1:29:2:1,1:1,26:0.069:1,2:7.5:1:31.5:1:0.13547:18.73:60:4:0.069:0:1 -17 31887973 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACCTTCCAAAATACCAC;RSEQ=TCGCCTCCCTGGTGTGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 31889916 . C T 98 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00057;SOR=15.25988;LSEQ=TAAACTGGGCCTGAGTGTCA;RSEQ=CCTCTTGATTCATTTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:1,0:224,166:0.0026:2,0:43:0:31:0:1:0:60:2:0.0026:0:2 0/1:292:11:5,6:159,122:0.0377:2,2:30:1:28.4:1:0.54302:1.56148:60:10:0.0348:0:1.6 -17 31889935 . G A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41012;SOR=2.71248;LSEQ=ACCCTCTTGATTCATTTTCT;RSEQ=CACTCCCTTAGTATTTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:2:1,1:216,204:0.0047:2,2:40.5:1:28.5:1:1:1.05871:60:4:0.0048:0:1 0/1:314:4:2,2:160,150:0.0127:2,2:9.8:1:28:1:1:1.06641:60:8:0.0129:0:1.3 -17 31889954 . G A 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.64873;SOR=1.07667;LSEQ=TGCACTCCCTTAGTATTTAG;RSEQ=CAACTTCCCTGCATACCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:419:231:104,127:86,100:0.5513:2,2:24.7:1:29.7:1:0.8434:1.05004:60:76:0.5534:0:1.1 1/0:302:172:83,89:61,68:0.5695:2,2:24:1:29:1:0.90743:1.04:60:56.333:0.5748:0:1.2 -17 31889971 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07259;SOR=Inf;LSEQ=TAGGCAACTTCCCTGCATAC;RSEQ=ACAGCCAGTTGCAGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:171,223:0:2,0:24.7:1:31.3:1:1:0:60:55.286:1:0:0.6 0/1:283:3:2,1:129,151:0.0106:2,2:13:1:27.7:1:0.59777:2.33:60:6:0.0107:0:1.7 -17 31890240 . G T 42 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATACTTCAGTTAGCACAG;RSEQ=ACAAGAAGGGAAATGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:13.3:1:27:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 31891106 . C A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGCACCGCGGCAGCCCC;RSEQ=CTGAGGAGGTGAGGCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:32:0:1:0:60:4:1:0:2.5 -17 31891149 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCCTGCACGGTCTTGCA;RSEQ=GGCTGAGATGAACCGGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29.5:1:1:0:60:4:1:0:2.5 -17 32421391 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50273;SOR=0;LSEQ=TTCTAACTGAATCAGAACAT;RSEQ=AACTCAGGGTGCTCAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:30,3:0.0571:2,2:21.5:1:30.5:1:0.21849:8.80417:60:4:0.0571:0:1 0/0:26:0:0,0:24,2:0:2,0:22.5:1:31.3:1:1:0:60:52:1:0:0.1 -17 32421433 . T C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51158;SOR=0;LSEQ=GACCTCACAGCCAGACAGGC;RSEQ=GCATCTCAAGCAGGCACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:50,29:0.0247:2,2:15.5:1:27.5:1:1:1.71195:60:4:0.025:0:1 0/0:57:0:0,0:35,22:0:2,0:26.5:1:30.3:1:1:0:60:56:1:0:0.2 -17 32421459 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17202;SOR=Inf;LSEQ=TCAAGCAGGCACATCTAACT;RSEQ=CTGCAGGACGCTGACTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:68,47:0:2,0:25.6:1:32.1:1:1:0:60:230:1:0:0.2 0/1:82:2:1,1:43,37:0.0244:2,2:26:1:30:0:1:1.16002:60:4:0.0247:0:1 -17 32421466 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17211;SOR=Inf;LSEQ=GGCACATCTAACTGCTGCAG;RSEQ=ACGCTGACTCCTCAATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:64,58:0:2,0:26:1:30.9:1:1:0:60:121:1:0:0.2 0/1:87:2:1,1:43,42:0.023:2,2:39:0:30.5:1:1:1.02354:60:4:0.0233:0:1.5 -17 32421557 . A G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.53115;SOR=0;LSEQ=TACATGGGAAACCAAGGCAC;RSEQ=CAGTTACACAGTTAGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:1,36:0.0513:1,2:22:1:27.5:1:0.10121:25.81:60:4:0.0526:0:1 0/0:22:0:0,0:2,20:0:2,0:20.6:1:30.5:1:1:0:60:44:1:0:0 -17 32421636 . G A 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=2.31595;LSEQ=ACAGCACAAGTCACTTTGGA;RSEQ=ATCATGAAGCAATTGCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:34.3:1:30.3:1:1:0:60:8:0.4444:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:20.5:1:28:1:1:0:60:4:0.6667:0:1 -17 33428167 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGAAGACATCTGTGGGTATG;RSEQ=AAACCACCCTCCAGGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:277,214:0:2,0:23.3:1:31.3:1:1:0:60:97.2:1:0:0.1 0/1:446:16:9,7:256,173:0.0359:2,2:24.1:1:28.6:1:0.79995:1.15056:60:32:0.0364:0:1.1 -17 33428445 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35375;SOR=3.28333;LSEQ=AGAGGACATCGATTACTACC;RSEQ=CTTCATTTTACGGAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:1:1,0:27,164:0.0052:2,0:1:0:26:0:0.14583:0:60:2:0.0052:0:1 0/1:177:3:2,1:37,137:0.0169:2,2:8:1:26.7:1:0.1226:7.29:60:6:0.0171:0:1 -17 33428487 . A G 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.79125;LSEQ=ACAGAGGCCTAGCACAGAGA;RSEQ=ATAACTTCCCCAAGGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:5:1,4:1,78:0.0595:1,2:18.2:1:32.4:1:0.11618:17.55:60:10:0.0602:0:1.2 0/1:63:3:0,3:0,60:0.0476:1,0:12:1:32:1:1:0:60:6:0.05:0:1 -17 33430203 . G T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01589;SOR=Inf;LSEQ=CACTTTGGGGTTCAGAAGCT;RSEQ=ACATTTAAGGGAAATAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:0:0,0:405,226:0:2,0:24.1:1:31.6:1:1:0:60:77.875:1:0:0.1 0/1:683:7:2,5:440,236:0.0102:2,2:7.3:1:24.4:1:0.10333:4.64997:60:6:0.0089:0:1 -17 33430316 . C T 186 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=29.26892;LSEQ=GGGCCAGGGTCTTCAGCTCT;RSEQ=GGGCCAGCTGCATCATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1065:3:0,3:500,561:0.0028:2,0:1:0:26.3:1:0.25201:0:60:6:0.0028:0:1 0/1:1086:83:34,49:449,554:0.0764:2,2:24.1:1:29.3:1:0.56595:1.16786:60:166:0.0771:0:1.2 -17 33430327 . C A 191 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02964;LSEQ=TTCAGCTCTCGGGCCAGCTG;RSEQ=ATCATCAAGGCCAAGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:981:89:41,48:423,468:0.0907:2,2:26.6:1:29.6:1:0.82456:1.05812:60:21.25:0.0889:0:1.2 0/0:1018:3:3,0:442,572:0.0029:2,0:1:0:23.3:1:0.08346:0:60:6:0.003:0:1.3 -17 33430714 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATCACAGAATGTCATCAGCA;RSEQ=CAATGTCTCCCTCGTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:0,2:1,54:0.0351:1,0:22.5:1:30.5:1:1:0:60:4:0.0392:0:1 0/0:17:0:0,0:2,15:0:2,0:15.8:1:32.2:1:1:0:60:34:1:0:0 -17 33433487 . C T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.002;SOR=1.93146;LSEQ=CATGCACCACCTGGATCCTC;RSEQ=GGAGAGCTTCTGCCTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:36:15,21:200,282:0.0692:2,2:24.3:1:30.4:1:1:1.01:60:35:0.0689:0:1.2 0/1:549:69:29,40:216,262:0.1257:2,2:22.8:1:30:1:0.69807:1.13688:60:68:0.1252:0:1.1 -17 33433554 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=Inf;LSEQ=GATAAGAGGGAGTAGGGGGG;RSEQ=CAAGGTAAGGCTGAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:41,133:0:2,0:22.9:1:29.5:1:1:0:60:28:1:0:0.1 0/1:189:2:1,1:52,135:0.0106:2,2:33:1:31.5:1:0.48328:2.58:60:4:0.0108:0:1 -17 33433555 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49937;SOR=Inf;LSEQ=ATAAGAGGGAGTAGGGGGGT;RSEQ=AAGGTAAGGCTGAGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:40,133:0:2,0:22.5:1:31.6:1:1:0:60:27.833:1:0:0.1 0/1:187:2:1,1:51,134:0.0107:2,2:11.5:1:28.5:1:0.4799:2.61:60:4:0.0109:0:1 -17 33433820 . A G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43038;SOR=0.49091;LSEQ=GAGGGTTTCCTGGAAGAATC;RSEQ=GTGTGAGTAGCATCCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:29:25,4:5,2:0.8056:2,2:24.5:1:28.9:1:0.57322:2.43:60:13.5:0.7941:0:1.4 1/0:12:8:8,0:4,0:0.6667:0,0:23.3:1:29.4:1:1:0:60:16:0.7273:0:1 -17 33434190 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16373;SOR=Inf;LSEQ=ACACTTCAGAGAGGGTCCAG;RSEQ=TGGGAGCTCCCCACCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:96,199:0:2,0:23.6:1:30.2:1:1:0:60:35.875:1:0:0.1 0/1:201:2:1,1:55,144:0.01:2,2:7.5:1:30:1:0.4806:2.60:60:4:0.01:0:1 -17 33434276 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.15614;SOR=Inf;LSEQ=TCCTTATTACCCATCTTCTC;RSEQ=CTGTTGGGCTCTGAACCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:219,68:0:2,0:23.5:1:30.9:1:1:0:60:40:1:0:0.1 0/1:188:2:1,1:150,35:0.0106:2,2:32.5:1:29.5:1:0.3488:4.23984:60:4:0.0108:0:1 -17 33434519 . GA G 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0.98308;LSEQ=AGGTTAGGAGGAAGACAGGG;RSEQ=AAAGGTACCAAGAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:1,2:37,195:0.0128:2,2:17.3:1:29.9:1:0.41235:2.62:60:6:0.0128:0.0043:0 0/1:239:3:0,3:56,179:0.0126:2,0:11.7:1:28.7:1:1:0:60:6:0.0128:0.0042:0.3 -17 33444110 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17623;SOR=Inf;LSEQ=CAATCGGCTTCCTGTTCACC;RSEQ=CTCCCTCCTTACCGTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:40,213:0:2,0:22.9:1:29.3:1:1:0:60:35.143:1:0:0.1 0/1:185:2:1,1:31,152:0.0108:2,2:29:1:28:1:0.3168:4.84:60:4:0.0109:0:1 -17 33445416 . TA T 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00228;SOR=0.24564;LSEQ=CCTTCCCATCCATTATTGGT;RSEQ=AAAAAAAAACCCCTCCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:26:26,0:267,7:0.0867:1,1:29:1:30.6:1:1:0:60:52:0.0875:0.0133:0.2 0/1:220:5:4,1:205,8:0.0227:1,2:18.2:1:30.1:1:0.19169:6.28317:60:10:0.023:0.0091:0 -17 33445549 . G A 192 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=58.9373;LSEQ=CCAGTGGACAGGATGGCAGT;RSEQ=GAGGTCTTCAGTTCCTCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1346:2:2,0:613,728:0.0015:2,0:11.5:1:26.5:1:0.20951:0:60:4:0.0015:0:1 0/1:1313:106:59,47:585,622:0.0807:2,2:20.9:1:28.6:1:0.15779:1.33:60:20.2:0.0783:0:1.3 -17 33817200 . C T 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCCGGGCTGCTGCAGCCA;RSEQ=CAGCGCTGGGACGAGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:154,268:0:2,0:24.2:1:31.4:1:1:0:60:37.364:1:0:0.1 0/1:374:19:7,12:155,198:0.0508:2,2:19.7:1:26.8:1:0.63878:1.34095:60:5.333:0.0438:0:1.1 -17 33817422 . A G 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=0.49209;LSEQ=GAAGTTCATTCAGCTCCTGA;RSEQ=CCAGTCACCCGATGGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:459:391:202,189:33,34:0.8519:2,2:26.9:1:31.6:1:0.79163:1.10:59.7:34.545:0.8501:0:1.2 1/0:421:311:162,149:61,48:0.7387:2,2:25.6:1:31.7:1:0.50509:1.16842:59.7:154.5:0.741:0:1.2 -17 33817496 . G T 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TGCAAAATAGAAGGATTTAT;RSEQ=ATATCACCAAAGCTCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:0:0,0:244,285:0:2,0:25.6:1:31.7:1:1:0:59.9:175.333:1:0:1 0/1:479:13:5,8:225,240:0.0271:2,2:32.1:1:29:1:0.57937:1.49875:60:26:0.0273:0:2.2 -17 33817525 . T C 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00288;SOR=0.13783;LSEQ=AAAGCTCTGAAAGGCATCCA;RSEQ=CTCATTAAGAAGAAGTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:475:473:231,242:0,1:0.9958:0,2:27.1:1:31.7:1:1:0:60:77.833:1:0:1.1 1/1:436:423:205,218:9,4:0.9702:2,2:24.4:1:31.1:1:0.16629:2.38811:59.8:83.6:0.9698:0:1.2 -17 33817688 . C T 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17636;SOR=1.42481;LSEQ=TCCCAAGCTGCACGCTGGAC;RSEQ=TCAAACTATTAACCGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:31:16,15:278,250:0.0555:2,2:28:1:30.8:1:1:1.04244:60:62:0.0561:0:1.1 0/1:518:40:26,14:240,238:0.0772:2,2:24.4:1:30.4:1:0.09865:1.84:60:80:0.0781:0:1.1 -17 33817706 . G GATTC 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.00013;SOR=Inf;LSEQ=ACCTCAAACTATTAACCGAG;RSEQ=ATTCAGATCGTCAAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:578:0:0,0:304,272:0:2,0:24.4:1:31.1:1:1:0:60:51.364:0.9982:0:0.2 0/1:526:12:8,4:279,235:0.0228:2,2:18.9:1:30.3:1:0.56:1.68:60:24:0.0232:0.0057:0 -17 33817716 . G A 144 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.97769;LSEQ=ATTAACCGAGGATTCAGATC;RSEQ=TCAAAGGTTAGCTTACGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:2:1,1:326,269:0.0033:2,2:30:1:29.5:1:1:1.2115:60:4:0.0034:0:1 0/1:545:31:15,16:283,231:0.0569:2,2:23.3:1:29.2:1:0.57799:1.30613:60:62:0.0572:0:1 -17 33818130 . G A 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33297;LSEQ=TGCCTCCCCTGCTGCAAGAT;RSEQ=ACCATTTGTGAACTTACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:562:433:193,240:56,73:0.7705:2,2:26:1:29.1:1:0.84049:1.05:60:53.125:0.7727:0:1.1 1/0:527:278:119,159:111,138:0.5275:2,2:25.4:1:28.8:1:0.72509:1.07457:60:91.667:0.5258:0:1.2 -17 33818293 . AT A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.25473;SOR=0;LSEQ=TGAACTCTCCTTAAAAACCA;RSEQ=TTTTTTAAATCATGGAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:2,1:43,156:0.0149:2,2:24:1:28.7:1:0.12533:7.16:60:6:0.015:0.005:0.3 0/0:167:0:0,0:46,121:0:2,0:24.4:1:29.3:1:1:0:60:54.667:1:0:0.1 -17 33818305 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18958;SOR=Inf;LSEQ=AAAAACCAATTTTTTTAAAT;RSEQ=ATGGAACCAGAACATATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:33,144:0:2,0:21.1:1:31.8:1:1:0:60:354:1:0:0.2 0/1:137:2:1,1:35,99:0.0146:2,2:25:1:27:1:0.46078:2.80:60:4:0.0146:0:2 -17 33818312 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18413;SOR=Inf;LSEQ=AATTTTTTTAAATCATGGAA;RSEQ=CAGAACATATGTCATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:22,127:0:2,0:20.9:1:31.1:1:1:0:60:148:0.9933:0:0.1 0/1:114:2:1,1:23,89:0.0175:2,2:18:1:29:1:0.3782:3.81:60:4:0.0175:0:2 -17 34100256 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50062;SOR=Inf;LSEQ=AGGTGAGCCGGATGTCAGCG;RSEQ=GGCCTGTGGCTGGGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:25,23:0:2,0:28.9:1:31:1:1:0:60:47:1:0:0.3 0/1:59:2:1,1:29,28:0.0339:2,2:32.5:1:28:1:1:1.03511:60:4:0.0351:0:1 -17 34100284 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49438;SOR=Inf;LSEQ=GGCTGGGGCCTCCCAGAACT;RSEQ=CAGCGCTGAGACGTTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:17,28:0:2,0:25:1:31.3:1:1:0:60:90:1:0:0.3 0/1:45:2:1,1:18,25:0.0444:2,2:7.5:1:28.5:1:1:1.38:60:4:0.0444:0:1 -17 34100350 . G GC 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCGAACTGCCGGCTCCG;RSEQ=AGATGCTCAGGCCAGTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:1:0,1:24.1:1:33.2:1:1:0:60:28:1:0.1429:0.1 1/1:7:7:0,7:0,0:1:0,0:27.6:1:32.6:1:1:0:60:14:1:0:0.1 -17 36059034 . A AG 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCACATCCATGGCCTT;RSEQ=TCACACCCTGCCCACACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:0:34:0:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 36061130 . G A 47 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14014;SOR=0;LSEQ=GGCTGCAGGGCTGCCAGGCT;RSEQ=CCGGCCACACTGTTGATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:4:3,1:129,185:0.0126:2,2:16.3:1:23.5:1:0.31105:4.28:60:3:0.0096:0:1 0/0:236:0:0,0:107,129:0:2,0:26.9:1:31.2:1:1:0:60:58:1:0:0.2 -17 36061152 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16483;SOR=Inf;LSEQ=CGGCCACACTGTTGATGACA;RSEQ=GGACACTCTGTGCTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:83,165:0:2,0:23.5:1:30.9:1:1:0:60:81.667:1:0:0.1 0/1:170:2:1,1:60,108:0.0118:2,2:10:0:32:0:1:1.79:60:4:0.012:0:1 -17 36061184 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12945;SOR=Inf;LSEQ=GCTTGGGAGGTGTTGAGGCC;RSEQ=GTGGGAGCAAGAGGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:12,117:0:2,0:21.7:1:30.3:1:1:0:60:128:1:0:0.1 0/1:73:2:1,1:9,62:0.0274:2,2:20:1:28.5:1:0.25685:6.59:60:4:0.0274:0:1.5 -17 36061282 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.13382;SOR=5.95526;LSEQ=CTCAATGTCCCAGTCACCGG;RSEQ=CTGAGCCTGTTACACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:0,21:0.0455:1,0:17:0:32:0:1:0:60:2:0.0455:0:2 0/1:13:3:0,3:0,10:0.2308:0,0:24.7:1:27.3:1:1:0:60:6:0.2308:0:2 -17 36061297 . C T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00165;SOR=Inf;LSEQ=ACCGGGCTGAGCCTGTTACA;RSEQ=AGGAGATTCCATGGGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:0,9:0,13:0.4091:1,0:17.3:1:29.2:1:1:0:60:18:0.4091:0:1.1 1/1:10:10:0,10:0,0:1:0,0:26.4:1:28.8:1:1:0:60:20:1:0:1.3 -17 36091780 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52119;SOR=0;LSEQ=CCAAGTTGGAGCCCAGGCCG;RSEQ=GGGCTTTGGAGGGGGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:17,43:0.0323:2,2:20.5:1:32.5:1:0.49974:2.49:60:4:0.0339:0:2 0/0:39:0:0,0:10,28:0:2,0:24.8:1:29.6:1:1:0:60:76:1:0:0.1 -17 36093022 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTCAGCGGGGGCAGAGT;RSEQ=GACTGAACAGATCTGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:29:1:1:0:60:4:1:0:1.5 -17 36097661 . CA C 27 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGTCTCTACTAAAAATAC;RSEQ=AAAAAAAAAAAAAATTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:7.5:1:27.3:1:1:0:60:4:0.6667:0.3333:0 -17 36099471 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14387;SOR=Inf;LSEQ=TTTCTGACGTACCAGGTGTA;RSEQ=AGAGCGGCACGCTTCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:119,70:0:2,0:25:1:31.7:1:1:0:60:46.25:1:0:0.1 0/1:116:2:0,2:71,43:0.0172:2,0:21.5:1:25:1:0.14843:0:60:4:0.0182:0:1 -17 36099480 . A T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06704;SOR=Inf;LSEQ=TACCAGGTGTACAGAGCGGC;RSEQ=CGCTTCTGGGTCTTCATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:115,75:0:2,0:29:1:29.8:1:1:0:60:94:1:0:0.1 0/1:131:3:1,2:75,52:0.0229:2,2:13.3:1:26:1:0.56982:2.8611:60:6:0.0234:0:1.7 -17 36099518 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50659;SOR=0;LSEQ=AGGGGTGCCCTTGTTGAGAT;RSEQ=CTGGGAGAGGTGCGACTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:97,92:0.0105:2,2:30:1:30.5:1:1:1.05408:60:4:0.0106:0:1 0/0:148:0:0,0:75,73:0:2,0:23.1:1:31.1:1:1:0:60:36:1:0:0.2 -17 36099547 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50697;SOR=0;LSEQ=GGTGCGACTGGTTCAGGCCG;RSEQ=TGACATCGACCACCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:51,82:0.0148:2,2:19:1:29.5:1:1:1.60:60:4:0.015:0:1 0/0:103:0:0,0:43,60:0:2,0:24.5:1:30.5:1:1:0:60:102:1:0:0.1 -17 36099858 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGAGGTTAGTGGGCAAAA;RSEQ=AGGACTTCCCATCTTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:19.5:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 36827523 . G A 47 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0119;SOR=Inf;LSEQ=AGGAGGAAAGTCCAAGAAGA;RSEQ=TATTTCATGCCCACCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:24.5:1:33.3:1:1:0:60:12:1:0:0 1/1:3:3:3,0:0,0:1:0,0:28:1:30:1:1:0:60:6:1:0:1 -17 37152094 . T C 50 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGCATGAGCCACTCAGC;RSEQ=GGCCATATATATATTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:28:1:32:1:1:0:60:6:1:0:2 1/1:1:1:1,0:0,0:1:0,0:48:0:29:0:1:0:60:2:1:0:1 -17 37152369 . A G 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.35136;LSEQ=CTATTTCTCATCTTTTAGTG;RSEQ=CTGACCTAAAAATTTATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:817:681:341,340:72,63:0.8335:2,2:27.4:1:31.6:1:0.51048:1.13932:60:74.667:0.8358:0:1.1 1/0:833:531:246,285:142,157:0.6375:2,2:27.5:1:31.3:1:0.77214:1.04782:60:131.75:0.6388:0:1.1 -17 37152798 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAACCTGGTGTGCTTGGC;RSEQ=CCATGCCTGCCAGGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 37618220 . C T 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00227;SOR=0;LSEQ=TGCCCTCCCCACCCCCTTCC;RSEQ=GGGGCGCTTTGGTGGGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:14:14,0:85,4:0.1359:1,1:21.7:1:31.9:1:1:0:60:28:0.1414:0:1 0/0:60:0:0,0:57,3:0:2,0:24.2:1:29.6:1:1:0:60:29:1:0:0.3 -17 37618266 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.22087;SOR=Inf;LSEQ=GGGGTTGGGGGGGTGGGTGG;RSEQ=GGTTGCTTTTTGGAGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:179,46:0:2,0:21.6:1:30.6:1:1:0:60:31.143:1:0:0.3 0/1:200:2:1,1:154,44:0.01:2,2:14.5:1:27:1:0.40025:3.47197:60:4:0.0104:0:1 -17 37618292 . C T 46 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.12438;SOR=0;LSEQ=CTTTTTGGAGTGCTGGGGAA;RSEQ=TTTTTTCCCTTCTTCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:4:1,3:253,116:0.0107:2,2:9.3:1:23.3:1:0.09764:6.5076:60:3:0.0083:0:1 0/0:356:0:0,0:246,110:0:2,0:23.2:1:30.6:1:1:0:60:43.5:1:0:0.3 -17 37619038 . G A 142 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=30.50111;LSEQ=AAACAAGATGATAGCCCCTC;RSEQ=GGAGCTTCTTATGGCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:659:1:1,0:376,281:0.0015:2,0:1:0:25:0:1:0:60:2:0.0016:0:1 0/1:586:26:16,10:317,242:0.0444:2,2:21.8:1:30.4:1:0.68918:1.22:60:52:0.0452:0:1.2 -17 37619365 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10707;SOR=0;LSEQ=TCTCTGAGTCGGAGTCCACT;RSEQ=CCCAGGTGAGCTATTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:80,154:0.0127:2,2:28:1:22.7:1:1:1.0388:60:2:0.0087:0:3.3 0/0:261:0:0,0:99,162:0:2,0:25.1:1:30.3:1:1:0:60:51.2:1:0:0.1 -17 37619376 . C A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11977;SOR=0;LSEQ=GAGTCCACTCCCCAGGTGAG;RSEQ=TATTTGTCTAACAGTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:1,2:67,140:0.0143:2,2:37:1:25.7:1:1:1.04:60:2:0.0097:0:1.3 0/0:215:0:0,0:77,138:0:2,0:25:1:31.4:1:1:0:60:70.667:1:0:0.1 -17 37626963 . G A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.65066;LSEQ=ACATTTAGTCCTGTCTCCTT;RSEQ=GGGTGCCTCTTGATTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:28:28,0:2,0:0.9333:0,1:26.9:1:27.4:1:1:0:60:27:0.931:0:1.2 1/1:10:9:8,1:1,0:0.9:0,2:20.7:1:29.3:1:1:0:60:18:0.9:0:1.2 -17 37627072 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19188;SOR=Inf;LSEQ=CATAGTTTGTTTTATTGATC;RSEQ=GTTTTCCTCCATATACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:186,43:0:2,0:23.8:1:31.1:1:1:0:60:458:1:0:0.1 0/1:179:2:1,1:133,44:0.0112:2,2:33.5:1:31:1:0.44065:3.00017:60:4:0.0113:0:1 -17 37627115 . G T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05646;SOR=Inf;LSEQ=AGTCCATTCATTTAAAACTG;RSEQ=CTTTTTATTTTTCCAGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:264,155:0:2,0:26.3:1:31.2:1:1:0:60:45.556:1:0:0.1 0/1:400:4:1,3:251,145:0.01:2,2:22:1:27.5:1:0.14523:5.17163:60:8:0.0102:0:1 -17 37627387 . A G 163 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=22.96201;LSEQ=CCTAGAAAAGAGAACAGTTC;RSEQ=GTAGAGGCTAAGGATTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:855:2:1,1:433,420:0.0023:2,2:37.5:1:10:1:1:1.03092:60:0:0:0:1.5 0/1:880:45:24,21:411,423:0.0511:2,2:26.4:1:29.7:1:0.64766:1.18:60:90:0.0513:0:1.1 -17 37646589 . T C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGATCACGCCACTGCATTC;RSEQ=AGCCTGGGCGACAGAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:0.8889:0,0:30:1:29.4:1:1:0:55.6:7:0.875:0:1.4 1/1:2:2:2,0:0,0:1:0,0:15.5:1:31:1:1:0:60:4:1:0:1 -17 37646619 . C CA 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.10417;SOR=Inf;LSEQ=GACAGAGTGATACTCTGTCT;RSEQ=AAAAAAAAAAGAAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:0:1,0:16.9:1:30.3:1:1:0:58.4:10:1:0:0.5 0/1:11:2:2,0:9,0:0.1818:0,0:34.5:1:30:1:1:0:60:4:0.1818:0:0.5 -17 37646664 . AT A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.12013;SOR=Inf;LSEQ=ATCTTTAGTTGTGATTAATT;RSEQ=TTTTTTTTATGTTATAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:80,2:0:1,0:23.9:1:31.2:1:1:0:59.9:40:1:0:0.2 0/1:44:2:2,0:42,0:0.0455:1,0:17.5:1:31.1:1:1:0:60:4:0.0455:0.0227:0 -17 37646947 . C T 144 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03021;LSEQ=AGACTCTCCAGAACCAAAGG;RSEQ=AATCACACCACCTCAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:878:32:17,15:363,483:0.0364:2,2:27.3:1:28.9:1:0.27831:1.51:60:64:0.0368:0:1.1 0/0:877:1:0,1:395,481:0.0011:2,0:1:0:27:0:1:0:60:2:0.0012:0:1 -17 37648951 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50368;SOR=0;LSEQ=GGATTACAGGCATGAGCCAC;RSEQ=GCGCCCGGCCTTCATTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:104,10:0.0172:2,2:23:1:30:1:0.18141:9.9636:60:4:0.0175:0:1 0/0:93:0:0,0:78,14:0:2,0:22.8:1:29.2:1:1:0:59.7:22:0.9888:0:0.1 -17 37648954 . G A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01858;SOR=Inf;LSEQ=TTACAGGCATGAGCCACCGC;RSEQ=CCCGGCCTTCATTTTCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:116,12:0:2,0:21.8:1:29.9:1:1:0:60:127:1:0:0.1 0/1:107:5:4,1:84,18:0.0467:2,2:14.6:1:29.8:1:1:1.16495:60:10:0.0476:0:1 -17 37649178 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19504;SOR=Inf;LSEQ=AAAATTTTAGATGTCAGAAT;RSEQ=TTAACAATTTAGCAATACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:36,196:0:2,0:23.5:1:32:1:1:0:60:57:1:0:0.1 0/1:184:2:1,1:37,145:0.0109:2,2:14:1:26:1:0.37129:3.88:60:4:0.0109:0:1 -17 37649238 . TTTTG T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=6.000;MSILEN=4;SSF=1;SOR=1.3957;LSEQ=CAAAAGTAAATTCTGAGGTG;RSEQ=TTTGTTTGTTTGTTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:0,2:1,62:0.0308:1,0:23.5:1:31.3:1:1:0:60:4:0.0313:0.0154:0 0/1:47:2:0,2:0,45:0.0426:1,0:40:1:27.5:1:1:0:60:4:0.0435:0:0 -17 37650304 . A G 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCAGGAAAGGGAATATA;RSEQ=AATTTCCTTTTTTGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:23.5:1:33:1:1:0:60:8:0.8:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 37650332 . A G 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTGTTTTTTTATTGAG;RSEQ=AGGAGTCTCACTCTGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:31.8:1:31.3:1:1:0:60:8:0.8:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 37650569 . G A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11652;SOR=0.15521;LSEQ=TTCCTAACCTCAGGTGATCC;RSEQ=CAGGCCTTGGCCTCCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:1,0:0.8333:0,0:26.5:1:31.5:1:1:0:60:20:0.9091:0:1.1 0/1:5:2:2,0:3,0:0.4:0,0:30:1:23.5:1:1:0:60:4:0.4:0:1 -17 37650988 . C A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33445;SOR=3.62464;LSEQ=TTTTACAGGGTAGACTGGTC;RSEQ=AATCTTTGCCTTTCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:1:0,1:45,240:0.0035:2,0:15:0:13:0:1:0:40:0:0:0:3 0/1:240:3:2,1:48,189:0.0125:2,2:8.3:1:21:1:0.11091:7.78:60:2:0.0092:0:1.7 -17 37651002 . C CT 108 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.82863;SOR=0.84842;LSEQ=CTGGTCCAATCTTTGCCTTT;RSEQ=TTTTTTTTTTTCTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:14:1,13:17,156:0.07:2,1:22.3:1:28.5:1:1:1.41433:57.1:6:0.08:0:1.1 0/1:150:9:1,8:17,106:0.06:2,2:23.2:1:30.2:1:1:1.28078:58.3:18:0.0826:0:0.8 -17 37651014 . C CT 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.19111;SOR=Inf;LSEQ=TTGCCTTTCTTTTTTTTTTT;RSEQ=TTTCTTTCTTTCTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:6,146:0:1,0:19.3:1:29.2:1:1:0:58.8:4.241:0.984:0:1 0/1:124:2:0,2:11,107:0.0161:2,0:41:1:29.5:1:1:0:50:4:0.02:0:6 -17 37655459 . TC T 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=18.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCTTTCTTTCTTTCTTTCTT;RSEQ=CTTTTTTTTTTTTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:48:1:28:1:1:0:50:4:1:0:3 -17 37657460 . C CT 199 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1e-05;SOR=2.31608;LSEQ=GGCATTGTTATTTCAGCATT;RSEQ=TTTTTTTTTTCTTGCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:59:45,14:217,66:0.1676:2,2:18.3:1:30.9:1:1:1.02283:59.7:118:0.1725:0.071:0.4 0/1:267:85:62,23:123,51:0.3184:2,2:27.6:1:31.1:1:0.77049:1.12:60:170:0.322:0:0.4 -17 37657481 . AT A 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06438;SOR=0;LSEQ=TTTTTTTTTTCTTGCTTTTA;RSEQ=TTTTTTTCGTCTTTATGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:5:3,2:330,155:0.0102:2,2:35.2:1:31.1:1:0.65747:1.41832:60:10:0.0104:0.002:0 0/0:432:0:0,0:270,160:0:2,0:25.8:1:29.4:1:1:0:59.8:85:0.9953:0:0.3 -17 37657755 . A C 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=CTCTGACCTTTTTAGTTTCA;RSEQ=ATGGTTAATTGGTATTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:35,196:0:2,0:21.4:1:29.9:1:1:0:60:76:0.9956:0:0 0/1:195:11:0,11:32,152:0.0564:2,0:20:1:32.5:1:0.21667:0:60:22:0.0573:0:1 -17 37665861 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22303;SOR=Inf;LSEQ=CAGAAGTTAAAATTTATTTT;RSEQ=GTAATTCCTTTACCCCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:150,26:0:2,0:23.3:1:30.2:1:1:0:60:87:1:0:0.1 0/1:158:2:1,1:123,33:0.0127:2,2:9.5:1:30.5:1:0.38515:3.68723:60:4:0.0127:0:1 -17 37666087 . T C 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00083;SOR=Inf;LSEQ=TTTTTTGAGGCAGGATCTTA;RSEQ=TCTGTTGCTCAGGCTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:17,124:0:2,0:24.3:1:30.7:1:1:0:60:282:1:0:0.1 0/1:148:11:4,7:22,115:0.0743:2,2:20.3:1:31.9:1:0.10342:2.96:60:22:0.0753:0:1.1 -17 37667944 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20414;SOR=Inf;LSEQ=TACTGTTGACTTGTACTTTG;RSEQ=TTTCTCTGTACACTGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:36,183:0:2,0:21.6:1:30.3:1:1:0:60:438:1:0:0 0/1:181:2:1,1:34,145:0.011:2,2:23.5:1:28.5:1:0.35021:4.22:60:4:0.011:0:1 -17 37669884 . G C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACCTCAGAGCAGTAGCAAA;RSEQ=TGTTGATTACATAATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:33:1:1:0:60:4:1:0:1 -17 37671714 . G T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55084;LSEQ=GTTATTTCCTTAATTACAAT;RSEQ=GCATGATAGAAAAAGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:15:15,0:2,0:0.8824:0,1:22.6:1:31.1:1:1:0:60:30:0.8824:0:1 1/1:5:4:4,0:1,0:0.8:0,0:23.5:1:27.8:1:1:0:60:8:0.8:0:1 -17 37671910 . G A 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAATCCGACATATCAATAAT;RSEQ=TAAAAATTTTTTGAGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:328:328:261,67:0,0:1:0,2:20.8:1:28.7:1:1:0:60:81:1:0:1.1 1/1:254:236:184,52:13,5:0.9291:2,2:22.5:1:28.5:1:0.56336:1.36:60:235:0.9289:0:1.1 -17 37673920 . T A 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.022;SOR=Inf;LSEQ=AGTTTATCATGGCAACACAG;RSEQ=GTAGGAAAACATTTTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:0,79:0:1,0:24.2:1:29.9:1:1:0:60:38.5:1:0:0.2 0/1:51:4:0,4:0,47:0.0784:1,0:14.8:1:32.5:1:1:0:60:8:0.0784:0:1 -17 37675838 . CTT C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAGCCACCATTGCACATC;RSEQ=TTTTTTTTTTTTTTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14.5:1:32.3:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 37676016 . A AAT 45 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTGCACCCAGCTAATTAAA;RSEQ=ATATATATATATTTGTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:2,1:33,0:0.0833:1,2:29:1:28.8:1:0.08333:0:53.3:6:0.0833:0.0278:1.7 0/0:11:0:0,0:11,0:0:0,0:24.4:1:30.4:1:1:0:60:22:1:0:0 -17 37680096 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTATTTTTAGCAGAGAC;RSEQ=AGGTTTCACCATGTTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:20:0:1:0:60:2:1:0:1 1/0:3:2:1,1:1,0:0.6667:0,2:20:1:28:1:1:0:60:4:0.6667:0:1 -17 37680863 . G T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0569;SOR=Inf;LSEQ=CCTTCCCATTTTAATCCTTT;RSEQ=CTCCTCCATTCATTCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:297,88:0:2,0:26.4:1:31.9:1:1:0:60:76:1:0:0.1 0/1:370:4:1,3:270,96:0.0108:2,2:18.8:1:28:1:0.06022:8.37951:60:8:0.0111:0:1 -17 37681332 . C T 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.73194;LSEQ=CATATGGTCCAGAAAGTCTA;RSEQ=AATAGATCATTTTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:2,5:0,5:0.5833:0,2:23.6:1:26.4:1:0.4697:0:60:6:0.5455:0:1.3 1/0:2:1:0,1:0,1:0.5:0,0:27:0:12:0:1:0:60:0:0:0:4 -17 37682001 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00372;SOR=Inf;LSEQ=TGAGGCATGAAAAAATGAGA;RSEQ=ATTTAAAATGAAATTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:70,0:0:1,0:25.6:1:31.9:1:1:0:60:34:1:0:0.1 0/1:36:5:5,0:31,0:0.1389:1,0:16.4:1:28.6:1:1:0:60:4:0.1143:0:1.8 -17 37682075 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08428;SOR=Inf;LSEQ=AGAAGGCAAAGGGCCCTTGG;RSEQ=CTATCTCATCGTCTTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:238,63:0:2,0:25.3:1:31.8:1:1:0:60:74.25:1:0:0.1 0/1:236:3:1,2:172,61:0.0127:2,2:8:1:23.3:1:0.17457:5.58969:60:2:0.0087:0:1 -17 37682200 . A G 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGCCAAACCGACCTGAGC;RSEQ=TCCCTCAAATGGCACAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:880:0:0,0:480,400:0:2,0:24.6:1:30.5:1:1:0:60:72.333:1:0:0.1 0/1:820:42:20,22:408,370:0.0512:2,2:22.9:1:31.3:1:0.63483:1.21268:60:84:0.052:0:1.3 -17 37682292 . G A 150 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=9.18223;LSEQ=CAATCCATCAGTGCCCTGAC;RSEQ=GAAGCTACTTCCCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:999:4:3,1:503,489:0.004:2,2:10.8:1:27:1:0.62444:2.91:60:8:0.0041:0:1 0/1:870:31:16,15:411,427:0.0356:2,2:24.6:1:30.3:1:0.85569:1.11:60:62:0.0361:0:1.2 -17 37682657 . A G 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CATTTTTTTTCCCCCACATC;RSEQ=ATGGCCTTGGTTTCAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:4,121:0:1,0:22.3:1:30.1:1:1:0:60:19.833:1:0:0.1 0/1:79:10:1,9:3,66:0.1266:1,2:17.9:1:32.1:1:0.42463:2.41:60:20:0.1266:0:1.1 -17 37684407 . T A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCTTGAACTGCCGACCTC;RSEQ=GGTGATCCACCCGCCTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:29.5:1:1:0:60:4:1:0:1 -17 37686731 . G A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.28457;SOR=0;LSEQ=TTGCAATTTTCTGATCCCAA;RSEQ=ATTTTATTCTTTATATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:3,0:89,2:0.0319:1,0:27.3:1:30.7:1:1:0:60:6:0.0326:0:1 0/0:59:0:0,0:57,2:0:1,0:21.5:1:32.6:1:1:0:60:58:1:0:0.1 -17 37686782 . C T 46 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12527;SOR=0;LSEQ=ATTGATATTTGTTTATGTTG;RSEQ=ACAGTGTGTGTGTTTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:4:2,2:221,32:0.0156:2,2:10.5:1:23.3:1:0.08599:6.81719:60:3:0.0118:0:1 0/0:233:0:0,0:194,38:0:2,0:23.7:1:31.8:1:1:0:60:115:1:0:0.1 -17 37687968 . A G 76 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAGTTTTGGGGTGGGGG;RSEQ=TTGTGTGTGGTTTCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:38.2:1:32.8:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 37688375 . C T 30 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=10;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:15.5:1:30.5:1:1:1:60:4:0.5:0:3 -17 37688383 . C T 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTCTGTCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:31:1:1:0:60:4:1:0:3 -17 37688393 . C G 33 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=17.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTGTCTCGCTTGCTCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:0:33.5:1:1:0:60:4:1:0:3 -17 37855686 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18794;SOR=Inf;LSEQ=ATCGCGCCATTGCTCTCCAG;RSEQ=CTGGGCAACAAGAGCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:140,7:0:1,0:23.7:1:32.1:1:1:0:59.9:35.75:1:0:0.7 0/1:113:2:1,1:109,2:0.0177:1,2:19:1:26.5:1:0.05262:44.70303:60:4:0.0185:0:1 -17 37855834 . C A 183 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=97.37283;LSEQ=TGCCCCGGGGGTCCTGGAAG;RSEQ=CACAAGGTAAACACAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1321:1:1,0:621,699:8e-04:2,0:1:0:27:0:0.47086:0:60:2:8e-04:0:1 0/1:1105:76:34,42:469,560:0.0688:2,2:26.8:1:29.4:1:0.90561:1.03453:60:152:0.0698:0:1.1 -17 37856472 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00668;SOR=Inf;LSEQ=GTCCAGCCGGAGCCATGGGG;RSEQ=CGGAGCCGCAGTGAGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:382,156:0:2,0:26.1:1:31.8:1:1:0:60:52.8:1:0:0.2 0/1:415:6:2,4:265,144:0.0145:2,2:22.8:1:24.3:1:0.19259:3.66835:60:5:0.0122:0:1.3 -17 37856502 . C T 75 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01158;SOR=6.14111;LSEQ=AGTGAGCACCATGGAGCTGG;RSEQ=GGCCTTGTGCCGCTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:841:2:1,1:533,305:0.0024:2,2:17.5:1:29.5:1:1:1.74623:60:4:0.0024:0:1 0/1:623:9:3,6:367,246:0.0144:2,2:25.7:1:23.9:1:0.16866:2.97845:60:3.5:0.0115:0:1.3 -17 37856512 . C T 84 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00667;SOR=11.4194;LSEQ=ATGGAGCTGGCGGCCTTGTG;RSEQ=CGCTGGGGGCTCCTCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:875:1:0,1:529,345:0.0011:2,0:1:0:15:0:0.39543:0:60:0:0:0:1 0/1:697:9:3,6:398,289:0.0129:2,2:13:1:26.6:1:0.17903:2.75034:60:18:0.0132:0:1.1 -17 37856623 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.37888;SOR=2.40434;LSEQ=ACCCTGCCCTGTGGATGCCC;RSEQ=GCCGAGGTCCCGCGGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:2:2,0:94,264:0.0056:2,0:12:1:26:0:0.07057:0:60:4:0.0056:0:1 0/1:226:3:2,1:63,160:0.0133:2,2:17.3:1:27:1:0.19941:5.04:60:6:0.0136:0:1 -17 37856716 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGCTCAGGGCAGCCGGG;RSEQ=CCTGGGGCCCTCGGGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:2,77:0.0247:1,2:29.5:1:28:1:0.07315:31.64:60:4:0.0256:0:1.5 0/0:26:0:0,0:0,26:0:1,0:21.5:1:31:1:1:0:60:52:1:0:0.1 -17 37861718 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GAGTCTGTTGGGGGAGGAAG;RSEQ=GTGGGGAAGAGGAGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:35:0:34:0:1:0:60:2:0.5:0:1 1/1:2:2:1,1:0,0:1:0,2:26.5:1:32:0:1:0:60:4:1:0:2 -17 37861736 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AGTGTGGGGAAGAGGAGGGG;RSEQ=TGCAAGTGGGTGAGGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:31.7:1:31.3:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:32:1:29:1:1:0:60:4:1:0:2 -17 37863268 . G A 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGGCACAGACATGAAGCT;RSEQ=CGGCTCCCTGCCAGTCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:934:0:0,0:533,400:0:2,0:25.9:1:31.8:1:1:0:60:57.313:0.9989:0:0.1 0/1:713:50:27,23:363,299:0.0701:2,2:26.3:1:28:1:1:1.03415:60:49:0.0697:0:1.2 -17 37863426 . G A 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15961;SOR=0.22179;LSEQ=GGGCAACCCAGCCAGGCCCT;RSEQ=CCTCCAGCTGGGCTGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:7:5,2:227,443:0.0103:2,2:10.9:1:23:1:0.04999:4.87:60:6:0.009:0:1.1 0/0:433:1:1,0:151,280:0.0023:2,0:1:0:23:0:0.35185:0:60:2:0.0023:0:1 -17 37864853 . AG A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.03959;SOR=Inf;LSEQ=GACCAGGGCCACTGCTAACC;RSEQ=GGGGAGGCTTTGTGTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:16,159:0:2,0:22.6:1:31.4:1:1:0:60:174:0.9943:0:0.1 0/1:92:3:2,1:11,78:0.0326:2,2:10:1:28:1:0.05135:13.46:60:6:0.0326:0.0109:0.3 -17 37864895 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAATGGTGTCCCTTCTGG;RSEQ=CAGACGCAGGCAGAGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:1,79:0.0244:1,2:10.5:1:29.5:1:0.04848:56.31:60:4:0.025:0:2.5 0/0:30:0:0,0:0,30:0:1,0:21.2:1:32.8:1:1:0:60:60:1:0:0.1 -17 37865725 . G A 53 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04945;SOR=7.5135;LSEQ=TGTAAGCCATGCCCCTCCCT;RSEQ=CTGCCTCTTCTCTCAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:1:1,0:268,447:0.0014:2,0:4:0:24:0:0.3757:0:60:2:0.0014:0:1 0/1:577:6:5,1:230,341:0.0104:2,2:7:1:20.8:1:0.04358:7.39:60:5:0.0088:0:1.7 -17 37865759 . G A 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70494;SOR=0.52312;LSEQ=CAGACAGCCTGACCCCAGCC;RSEQ=CAAACTCCCAACTTACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:5:2,3:103,322:0.0116:2,2:21.6:1:28:1:0.59965:2.08:60:10:0.0121:0:1.6 0/0:328:2:2,0:88,237:0.0061:2,0:1:0:26.5:1:0.07514:0:60:4:0.0062:0:1 -17 37865961 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05273;SOR=Inf;LSEQ=GGTCCCTCCCTTGCTGTGCA;RSEQ=TTGGCCTCGTGGCCTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:220,60:0:2,0:24.1:1:31.9:1:1:0:60:69:1:0:0.3 0/1:169:3:2,1:133,33:0.0178:2,2:21.3:1:23.7:1:0.49257:2.00525:60:2:0.0119:0:2.7 -17 37866005 . C T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.74537;LSEQ=GTTTGTGCCTCTCTCTGTTA;RSEQ=TAACCCGTCCTCTCGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:660:216:132,84:288,156:0.3273:2,2:23.3:1:30.4:1:0.38856:1.17453:60:53:0.3247:0:1.1 1/0:446:342:204,138:68,36:0.7668:2,2:23.1:1:29.9:1:0.30427:1.27708:60:341:0.7663:0:1.2 -17 37866232 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11212;SOR=Inf;LSEQ=TGGGAGGGGTGGGATAACAG;RSEQ=CTTGGGATGTCTCCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:119,174:0:2,0:24.7:1:31.6:1:1:0:60:31.556:1:0:0.1 0/1:148:2:2,0:44,102:0.0135:2,0:25:1:32:0:0.09515:0:60:4:0.0137:0:1 -17 37866257 . G T 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08991;SOR=6.79734;LSEQ=GGATGTCTCCCCTGGGCCAG;RSEQ=TAGTCTCCCTAGAAGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:1:0,1:168,128:0.0034:2,0:19:0:13:0:0.43434:0:60:0:0:0:7 0/1:133:3:2,1:64,66:0.0226:2,2:6:1:22.7:1:0.6193:2.05:60:2:0.0152:0:1.7 -17 37866797 . G T 139 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGTTTGTTTCTGTAAATGG;RSEQ=AGCATATGGGGAGCACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:34:5,29:35,155:0.1504:2,2:24.6:1:27.4:1:0.80826:1.30817:60:33:0.15:0:1 0/0:149:0:0,0:27,122:0:2,0:20.8:1:30.9:1:1:0:60:148:1:0:0.2 -17 37868366 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0602;SOR=Inf;LSEQ=TGCGCATGCAGCCTGGCCCA;RSEQ=CCCACCCTGTCCTATCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:65,281:0:2,0:24.1:1:32:1:1:0:60:56.667:1:0:0.1 0/1:224:3:2,1:49,172:0.0134:2,2:20.3:1:27.3:1:0.13061:6.94:60:6:0.0136:0:1 -17 37868715 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.11067;LSEQ=TTGATGGGTAAGAGTGGGCA;RSEQ=GATGACCTGAGACAGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:157:44,113:113,268:0.2913:2,2:23.2:1:30.5:1:0.75477:1.08272:60:51.333:0.2884:0:1.1 1/0:416:282:99,183:43,90:0.6779:2,2:21.6:1:29.5:1:0.65756:1.13:60:281:0.6787:0:1.2 -17 37868786 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51659;SOR=0;LSEQ=GGCAGCATCTCTTGGGGATG;RSEQ=CAGGAGACAGAAGTGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:9,115:0.0159:2,2:23.5:1:28.5:1:0.15302:12.17:60:4:0.0164:0:1 0/0:85:0:0,0:9,76:0:2,0:24.8:1:31.5:1:1:0:60:41.5:1:0:0.4 -17 37871440 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15853;SOR=Inf;LSEQ=TCGATGGGCAAAGGGTTTGA;RSEQ=TGAAGGCATTCATGGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:263,31:0:2,0:20.4:1:31.8:1:1:0:60:35.75:1:0:0.1 0/1:195:2:1,1:159,34:0.0103:2,2:20.5:1:29.5:1:0.32752:4.62368:60:4:0.0105:0:1 -17 37871848 . G A 170 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCAGGGAGGAGTCCCTGTG;RSEQ=GAAGCTTTGGGCCTGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:49:19,30:134,223:0.1207:2,2:26.1:1:30.3:1:0.87607:1.05:60:48:0.1206:0:1 0/0:229:0:0,0:64,165:0:2,0:24.1:1:30.1:1:1:0:60:31.714:1:0:0.2 -17 37871902 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12982;SOR=Inf;LSEQ=AGTAACCTTTCCATGAAAGT;RSEQ=TGCAGAGTGTGCTGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:208,131:0:2,0:22.6:1:31.9:1:1:0:60:338:0.9971:0:0.1 0/1:192:2:1,1:118,72:0.0104:2,2:17:1:27.5:1:1:1.63444:60:4:0.0105:0:1 -17 37871921 . TG T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06386;SOR=Inf;LSEQ=TCTGCAGAGTGTGCTGGGGA;RSEQ=GAGGAAGATGAGAATAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:265,141:0:2,0:23.7:1:31.6:1:1:0:60:57:0.9975:0:0.1 0/1:272:3:1,2:182,87:0.011:2,2:17:1:27.9:1:0.25028:4.15985:60:6:0.0112:0.0074:0.3 -17 37871951 . C T 106 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00022;SOR=17.03588;LSEQ=TGAGAATAGCCTTTGCTGAC;RSEQ=GGGAAGGGGTCCGTGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:607:1:1,0:404,202:0.0016:2,0:36:0:32:0:1:0:60:2:0.0017:0:3 0/1:438:12:9,3:291,135:0.0274:2,2:31.3:1:29.8:1:0.76039:1.39:60:11:0.0255:0:1.2 -17 37872035 . G T 167 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=84.73514;LSEQ=CAAGGGCTGGGCATCAGCTG;RSEQ=CTGGGGCTGCGCTCACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1404:1:0,1:776,625:7e-04:2,0:1:0:24:0:0.4465:0:60:2:7e-04:0:1 0/1:929:53:29,24:455,420:0.0571:2,2:27.3:1:29.2:1:0.77755:1.12:60:52:0.057:0:1.2 -17 37872206 . C T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24897;SOR=2.73576;LSEQ=GAGTGTGGTAAGACAGGGAG;RSEQ=CCAGTGTGCGCACTCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:2:1,1:130,387:0.0038:2,2:32:1:30.5:1:0.44147:2.97:60:4:0.004:0:1 0/1:383:4:1,3:86,292:0.0104:2,2:26.3:1:24.8:1:1:1.13:60:3:0.008:0:1.5 -17 37872241 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15478;SOR=Inf;LSEQ=CCCCATCTGCCAGCACACAG;RSEQ=AGTGCCCAGGGGGCCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:26,260:0:2,0:24.1:1:32.4:1:1:0:60:285:1:0:0.2 0/1:186:2:0,2:20,164:0.0108:2,0:30:1:29.5:1:1:0:60:4:0.0109:0:1 -17 37872391 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCCTTGGCATCCTTCCC;RSEQ=CCCCCTCTGTTTCTGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:48,25:0.0267:2,2:35:1:31.5:1:1:1.90229:60:4:0.0278:0:1 0/0:9:0:0,0:6,3:0:2,0:20.6:1:31.2:1:1:0:60:18:1:0:0 -17 37872475 . C T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55391;SOR=0;LSEQ=CCCTCCAGCCCACAGCCATG;RSEQ=CCACAGCCAGTTCCCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:3:2,1:150,27:0.0167:2,2:28:1:24:1:0.3997:2.75629:60:2:0.0116:0:2.7 0/0:83:0:0,0:66,17:0:2,0:21.9:1:31.8:1:1:0:60:166:1:0:0.2 -17 37872492 . G T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55592;SOR=0;LSEQ=ATGCCCACAGCCAGTTCCCT;RSEQ=GTTCACTTGGACCTGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:3:2,1:174,49:0.0132:2,2:27:1:23.7:1:0.5295:1.77033:60:2:0.0093:0:1 0/0:128:0:0,0:99,29:0:2,0:23.1:1:30.9:1:1:0:60:31:1:0:0.2 -17 37872512 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13684;SOR=Inf;LSEQ=GGTTCACTTGGACCTGGGGC;RSEQ=TCCCCTAAAAGTCCCCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:212,75:0:2,0:25.2:1:30.9:1:1:0:60:70.75:1:0:0.2 0/1:169:2:1,1:126,41:0.0118:2,2:28:0:31:0:0.43639:3.04831:60:4:0.0121:0:1.5 -17 37872907 . G T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30427;SOR=4.7663;LSEQ=TGGAGGGGGGCAGCGAGGGG;RSEQ=ATTGCCAGGGACTTGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:1:0,1:83,277:0.0028:2,0:24:0:30:0:1:0:60:2:0.0029:0:1 0/1:229:3:1,2:65,159:0.0131:2,2:26.7:1:21.7:1:1:1.22:60:2:0.0091:0:1 -17 37872933 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12203;SOR=Inf;LSEQ=CAGGGACTTGGCAGGATGGC;RSEQ=AGATGCAGTAGGGTGTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:19,198:0:2,0:24.7:1:31.1:1:1:0:60:53.25:1:0:0.2 0/1:117:2:1,1:15,99:0.0171:2,2:25.5:1:28:1:0.25787:6.42:60:4:0.0174:0:2 -17 37873523 . C T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01298;SOR=Inf;LSEQ=TAAGGGCCTGATCCTACTGC;RSEQ=CTGGGGGTGTCAGTGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:0:0,0:451,211:0:2,0:24.9:1:30.8:1:1:0:60:81.75:1:0:0.2 0/1:481:5:1,4:316,160:0.0104:2,2:5.8:1:24.4:1:0.04825:7.86585:60:4:0.0084:0:1 -17 37873562 . G GC 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.85894;SOR=0.92035;LSEQ=GCCCCCCACAAATCTTTTCT;RSEQ=CCCCCCCCAGGAGGCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1048:19:9,10:585,436:0.0181:2,2:31.3:1:31.3:1:0.48412:1.49022:60:18:0.018:0.001:0.5 0/1:778:13:10,3:432,328:0.0167:2,2:28.3:1:28.8:1:0.1691:2.53:60:5.5:0.0147:0.0039:0.5 -17 37873581 . C T 147 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=44.67604;LSEQ=TGCCCCCCCCAGGAGGCTGA;RSEQ=CAGTGTGTGGCCTGTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1174:1:0,1:636,536:9e-04:2,0:1:0:26:0:0.4578:0:60:2:9e-04:0:1 0/1:952:35:21,14:510,406:0.0368:2,2:24.8:1:28.8:1:0.72936:1.19:60:34:0.0367:0:1.2 -17 37876179 . C G 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGGGAGGGGACCCCCTGA;RSEQ=ATATGTCCCTTCCCACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:76,304:0:2,0:23.9:1:31.7:1:1:0:60:53.286:1:0:0.1 0/1:240:15:4,11:54,171:0.0625:2,2:19:1:31.5:1:0.76219:1.15:60:30:0.0628:0:1.1 -17 37876208 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11909;SOR=Inf;LSEQ=CTTCCCACCCACTCTTCCAC;RSEQ=GTGGAACCTCCTGTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:8,196:0:1,0:24:1:30:1:1:0:60:33:1:0:0.1 0/1:108:2:1,1:8,98:0.0185:2,2:37:1:28.5:1:0.16044:11.61:60:4:0.0185:0:1.5 -17 37879504 . CG C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.1806;SOR=Inf;LSEQ=CCAAACACCTTCATGTCCCC;RSEQ=TGGGCCCCCTTTGTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:207,43:0:2,0:21.6:1:29.5:1:1:0:60:24:0.9959:0:0.3 0/1:186:2:1,1:152,32:0.0108:2,2:19:1:28:1:0.32415:4.69288:60:4:0.011:0.0054:2.5 -17 37879585 . A G 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CCCCCAGCCCTCTGACGTCC;RSEQ=TCATCTCTGCGGTGGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:0:0,0:353,275:0:2,0:23.7:1:30.1:1:1:0:60:47.308:1:0:0.5 0/1:551:33:17,16:261,256:0.0599:2,2:27.1:1:31.5:1:1:1.04:60:66:0.0607:0:2.1 -17 37879588 . A G 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.76382;SOR=1.03887;LSEQ=CCAGCCCTCTGACGTCCATC;RSEQ=TCTCTGCGGTGGTTGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:637:229:123,106:231,177:0.3595:2,2:22.1:1:30.2:1:0.50658:1.1245:60:75.333:0.3622:0:1.2 0/1:562:207:109,98:170,185:0.3683:2,2:26.1:1:29.9:1:0.29447:1.21:60:50.75:0.3725:0:1.3 -17 37879762 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.6814;LSEQ=TGGGGTCTGCACCGGCCCCC;RSEQ=GCACTGACCCACCACCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:167:112,55:179,96:0.377:2,2:23.9:1:30.2:1:0.68067:1.09:60:54.667:0.3788:0:1.1 1/0:210:130:80,50:48,32:0.619:2,2:21.6:1:29.8:1:0.88449:1.07:60:260:0.6311:0:1.1 -17 37880106 . G T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16561;SOR=5.72033;LSEQ=GGACAAGTAATGATCTCCTG;RSEQ=AAGGCAGGTAGGATCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:1:0,1:286,61:0.0029:2,0:1:0:24:0:0.17816:0:60:2:0.0029:0:1 0/1:246:4:2,2:191,51:0.0163:2,2:18.8:1:28:1:0.2038:3.71909:60:8:0.0165:0:1 -17 37880725 . T C 104 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16219;SOR=0;LSEQ=ATTTCACCATGTTGGCCAGG;RSEQ=TGGTGTCAAACTCCTGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:9,0:16,3:0.3214:2,0:23.1:1:32.9:1:0.53022:0:53.9:18:0.36:0:1.3 0/0:6:0:0,0:6,0:0:0,0:30:1:30.3:1:1:0:55.7:12:1:0:0.5 -17 37880997 . G GTGT 284 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGGAAGCATACGTGATGGCT;RSEQ=GTGTGGGCTCCCCATATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1441:624:314,310:419,390:0.433:2,2:25.4:1:30.6:1:0.5943:1.06061:59.9:623:0.4357:0.0777:0.2 0/0:1127:0:0,0:581,544:0:2,0:26.2:1:30.8:1:1:0:60:79.357:0.9991:0:0.2 -17 37882611 . G GA 60 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.56698;SOR=0;LSEQ=AATAAAAAAGCAAACAAAAA;RSEQ=AAAAAAAAAATTAAAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:4:4,0:43,2:0.0816:1,0:24.5:1:30.3:1:1:0:60:8:0.0851:0:0 0/0:14:0:0,0:14,0:0:1,0:24.4:1:31.9:1:1:0:60:13:1:0:0.1 -17 37882982 . G T 41 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03744;SOR=Inf;LSEQ=TGCAGAGGGTGGGAAGGAGA;RSEQ=ATGAGTCCAGTATGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:0:0,0:233,322:0:2,0:23.3:1:31.7:1:1:0:60:78.286:1:0:0.1 0/1:280:3:1,2:113,164:0.0107:2,2:16:1:26:1:1:1.37653:60:6:0.0108:0:1 -17 37883441 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.13011;SOR=Inf;LSEQ=TCCACGGTGACTGTGTCATA;RSEQ=CCCAAAGGTGACCTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:276,51:0:2,0:23.1:1:31.7:1:1:0:60:53.5:1:0:0.1 0/1:185:2:1,1:155,28:0.0108:2,2:6:1:29:1:0.28966:5.45704:60:4:0.0109:0:1 -17 37884037 . C G 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.21015;LSEQ=CTGGTGCCACTCTGGAAAGG;RSEQ=CCAAGACTCTCTCCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1444:436:255,181:536,467:0.3019:2,2:25.4:1:31.5:1:0.08372:1.23:60:61.286:0.3034:0:1.1 1/0:1016:656:363,293:183,170:0.6457:2,2:25.2:1:31:1:0.2902:1.15:60:49.462:0.6462:0:1.2 -17 37886420 . A T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATTCAGAGCACAGACTG;RSEQ=CCCAGCAGGTGTTCTGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 37922229 . C A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCACACCGATACACATCCAT;RSEQ=ACCTCCCCTTCCTTGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:31:1:31:1:1:0:60:4:1:0:0.5 0/1:9:2:1,1:3,4:0.2222:2,2:28:1:28:1:1:1.29:60:4:0.2222:0:1.5 -17 37922259 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCTTGTTGATCACTTTGAC;RSEQ=GAGTCTCTTGGGCAGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:22:0:32:0:1:0:60:2:1:0:1 1/1:2:2:0,2:0,0:1:0,0:36.5:1:31:1:1:0:60:4:1:0:2 -17 38487414 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12977;SOR=Inf;LSEQ=CCGAGGAGGGGTGGTCTGAA;RSEQ=CCCACCAGAGCCCCCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:269,48:0:2,0:23.6:1:32.2:1:1:0:60:62.4:1:0:0.1 0/1:179:2:1,1:147,30:0.0112:2,2:15.5:1:31:1:0.31718:4.83676:60:4:0.0114:0:1 -17 38487501 . C T 175 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=97.30289;LSEQ=ACAGCAGCTCCTGCCCGACA;RSEQ=CTGGGGGCGGGCACCTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1018:1:0,1:626,390:0.001:2,0:1:0:28:0:0.38446:0:60:2:0.001:0:1 0/1:766:67:39,28:413,286:0.0875:2,2:23:1:28.9:1:0.89717:1.03673:60:66:0.0873:0:1.2 -17 38497390 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACCCAAGCTAGGCCTTTC;RSEQ=TCCAGTGAAACGTGCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:30,0:0.0625:1,2:44:0:32:1:0.0625:0:60:4:0.0625:0:1 0/0:4:0:0,0:4,0:0:0,0:12.5:1:30.3:1:1:0:60:8:1:0:0 -17 38497450 . G A 95 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20164;SOR=0;LSEQ=TAGTCCACTGGAAGGCACCA;RSEQ=CTCTTCCTTTTATCTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:9,0:78,1:0.1023:1,0:27.6:1:30.1:1:1:0:60:18:0.1023:0:1.1 0/0:21:0:0,0:20,1:0:1,0:24.5:1:32:1:1:0:60:42:1:0:0.1 -17 38497484 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCAGAGCTGGACAGTG;RSEQ=ACCAGGGGCCGGTACTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:157,3:0.0123:1,0:25:1:32:0:1:0:60:4:0.0126:0:1 0/0:52:0:0,0:49,3:0:2,0:23.9:1:32.3:1:1:0:60:104:1:0:0.1 -17 38497753 . G A 87 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08436;SOR=2.51621;LSEQ=CCCGCGCGACCCGGCCCTAC;RSEQ=CCTCCTGCCGCCGCTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1076:5:4,1:370,701:0.0046:2,2:8.2:1:22.8:1:0.05228:7.56:60:4:0.0038:0:1 0/1:947:11:10,1:356,579:0.0116:2,2:6.3:1:25.4:1:5e-04:16.23:60:10:0.0107:0:1.2 -17 38497822 . C T 71 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.56264;SOR=1.63733;LSEQ=CCGGGCAGGGGGCTGGCGGG;RSEQ=GAGCCCCGCGGGCGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:645:5:1,4:374,266:0.0078:2,2:5:1:27.2:1:0.16692:5.61066:60:10:0.0079:0:1 0/1:554:7:2,5:312,235:0.0126:2,2:16.3:1:25.6:1:0.2483:3.31219:60:6:0.0111:0:1.3 -17 38497833 . G A 153 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02798;LSEQ=GCTGGCGGGCGAGCCCCGCG;RSEQ=GCGGGCTGGCGAGCGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:693:38:21,17:427,227:0.0548:2,2:28.3:1:29.3:1:0.22381:1.52185:60:11.667:0.0515:0:1.2 0/0:618:1:1,0:377,239:0.0016:2,0:1:0:26:0:1:0:60:2:0.0016:0:1 -17 38497884 . G A 197 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00818;LSEQ=AGCGGTGGGTGGGTCACTCG;RSEQ=AGGTGAGGCGCCGCCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:109:55,54:356,275:0.1467:2,2:24.7:1:29.2:1:0.25284:1.27058:60:26.25:0.1446:0:1.1 0/0:713:1:1,0:371,341:0.0014:2,0:1:0:23:0:1:0:60:2:0.0014:0:1 -17 38498810 . A AG 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGCGGGGACTTCAGGGC;RSEQ=GGGGGCGCCCCCTGCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:2,0:55,0:0.0351:1,0:22.5:1:33:0:1:0:60:4:0.0357:0:0 0/0:20:0:0,0:20,0:0:1,0:23.8:1:30.9:1:1:0:60:40:1:0:0.5 -17 38498899 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07515;SOR=Inf;LSEQ=CGGATGGCGCCGCCGGCTGA;RSEQ=TGACGGGGGCGGCGCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:255,33:0:2,0:25.8:1:32.2:1:1:0:60:56.6:1:0:0.1 0/1:212:3:1,2:173,36:0.0142:2,2:8:1:26.3:1:0.08352:9.45639:60:6:0.0144:0:1.3 -17 38504241 . A G 75 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCCAGGCCGCCCAGGGGCA;RSEQ=GAGCTTTAGAATCAGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:24.4:1:32.4:1:1:0:60:10:1:0:1 1/1:1:1:1,0:0,0:1:0,0:26:0:34:0:1:0:60:2:1:0:1 -17 38504470 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.56122;SOR=3.23323;LSEQ=CTGCCAGCAGTGGTGAGGCT;RSEQ=GGAGAGGCTCTTAGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:1:0,1:225,15:0.0041:2,0:1:0:25:0:0.06639:0:60:2:0.0042:0:1 0/1:150:2:2,0:140,8:0.0133:2,0:17:1:29.5:1:1:0:60:4:0.0135:0:1 -17 38505824 . C G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76096;LSEQ=GGGGAAGACTCCTGCCCATC;RSEQ=TGCAGTGTTGAGGCAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:6,2:6,0:0.5714:0,2:15.1:1:30.3:1:0.47253:0:60:16:0.5714:0:1.3 1/0:6:3:2,1:3,0:0.5:0,2:13.7:1:30.7:1:1:0:60:6:0.5:0:1.3 -17 38505991 . C T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.39173;SOR=2.28058;LSEQ=ACCGTAGCCAGGCACTGCTC;RSEQ=CACTGTGGGTGTGGACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:2:0,2:296,77:0.0053:2,0:1:0:26:0:0.04394:0:60:4:0.0054:0:1 0/1:248:3:1,2:181,64:0.0121:2,2:15:1:26.3:1:0.17366:5.60871:60:6:0.0124:0:1 -17 38506208 . G A 67 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04746;SOR=7.83023;LSEQ=TAGGGCAGGGGCCGAGTCCC;RSEQ=CCTCAGTTGGGGTCTCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:1:1,0:102,313:0.0024:2,0:1:0:25:0:0.2476:0:60:2:0.0025:0:1 0/1:324:6:4,2:87,231:0.0185:2,2:8.5:1:26.2:1:0.0546:5.28:60:12:0.0188:0:1 -17 38507948 . G A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04148;SOR=Inf;LSEQ=GGGCCACAGCTGTGCTCATG;RSEQ=GGCTTCTGGGGCAGAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:41,0:0:1,0:21.1:1:31.5:1:1:0:60:82:1:0:0.1 0/1:11:2:1,1:7,2:0.1818:2,2:25.5:1:28.5:1:0.49091:3.05504:60:4:0.1818:0:1 -17 38508058 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10984;SOR=Inf;LSEQ=TGTGTGCGCGTGCTTACAAG;RSEQ=CTGGGTGACCTCCTCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:226,7:0:1,0:24.3:1:32.4:1:1:0:60:115.5:1:0:0.1 0/1:116:2:2,0:107,7:0.0172:2,0:7.5:1:29:1:1:0:60:4:0.0175:0:1 -17 38508104 . G T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=AGCTCTCTGTCAGGCTGGGG;RSEQ=TGGACGAGGCCCTGAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:357,105:0:2,0:24.1:1:31.2:1:1:0:60:91.4:0.9978:0:0.1 0/1:306:11:9,2:210,85:0.0359:2,2:18.5:1:30.1:1:0.73433:1.82:60:22:0.0365:0:1.1 -17 38508416 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55505;SOR=0;LSEQ=CCCCTTCTTGTGCCAGGCAA;RSEQ=ATCTCTGCGTCCTTCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:0,3:118,159:0.0107:2,0:28.3:1:29.7:1:0.2659:0:60:6:0.0109:0:1.3 0/0:128:0:0,0:54,74:0:2,0:22.7:1:31.5:1:1:0:60:31:1:0:0.2 -17 38508756 . C T 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCTGCCTGCCTGGACAT;RSEQ=CTGGTGAGGGTCTGCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:685:0:0,0:228,457:0:2,0:23.5:1:31.1:1:1:0:60:75.111:1:0:0.1 0/1:504:21:6,15:156,326:0.0417:2,2:26.9:1:29.4:1:0.81505:1.19588:60:42:0.0422:0:1.2 -17 38510804 . C A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13198;SOR=5.48799;LSEQ=GCTGGGCTGGGACGGGGGTG;RSEQ=AGCCCTGGAGTCTCTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:1,0:22,184:0.0048:2,0:1:0:15:0:0.11111:0:60:0:0:0:1 0/1:115:3:2,1:14,98:0.0261:2,2:17:1:28:1:0.05038:13.43:60:6:0.027:0:1 -17 38511444 . GC G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.53322;SOR=0;LSEQ=TCCATGGCCTGGGCAGGCAC;RSEQ=CCCCCGGTGGCCGAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:148,10:0.0125:2,2:23.5:1:33.5:1:0.13318:14.16324:60:4:0.0127:0:0 0/0:93:0:0,0:80,13:0:2,0:25.2:1:32.3:1:1:0:60:186:1:0:0.2 -17 38511455 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15244;SOR=Inf;LSEQ=GGCAGGCACGCCCCCCGGTG;RSEQ=CCGAGGCTGGGGGTGCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:168,17:0:2,0:24.5:1:31.1:1:1:0:60:29.833:1:0:0.1 0/1:119:2:1,1:95,22:0.0168:2,2:39.5:1:29:1:0.35052:4.24544:60:4:0.0172:0:1 -17 38511483 . C T 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30776;SOR=4.48782;LSEQ=TGGGGGTGCAGCTGTGTTCC;RSEQ=AGCTGCTCAGGGGGTGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:1:1,0:256,65:0.0031:2,0:23:0:15:0:1:0:60:0:0:0:8 0/1:217:3:1,2:165,49:0.0138:2,2:5:1:22.3:1:0.13841:6.65861:60:6:0.014:0:1 -17 38511722 . G A 45 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02791;SOR=Inf;LSEQ=GGCCCCCGACACCTGGCCCA;RSEQ=GCCCCCACATCCAAGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:70,288:0:2,0:25.6:1:31:1:1:0:60:88.5:1:0:0.1 0/1:249:4:2,2:58,185:0.0161:2,2:18:1:22.5:1:0.24889:3.17:60:8:0.0165:0:3 -17 38511741 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15541;SOR=Inf;LSEQ=AGGCCCCCACATCCAAGCCA;RSEQ=CACCCCATGTCTTTGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:31,231:0:2,0:24.7:1:31.9:1:1:0:60:42.667:1:0:0.1 0/1:171:2:1,1:27,142:0.0117:2,2:18.5:1:29.5:1:0.30148:5.18:60:4:0.0118:0:1 -17 38512197 . T C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08567;LSEQ=TTCCCACCTCGAGCCAGGCT;RSEQ=GCTGGGGCTGGGGGTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:145:119,26:163,34:0.424:2,2:24.4:1:30.9:1:0.88643:1.04728:60:71.5:0.4218:0:1.1 0/1:220:13:11,2:165,42:0.0591:2,2:28.1:1:29.1:1:1:1.40:60:12:0.0553:0:1.5 -17 38512457 . C G 165 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCAGCTCCAACAGAAGCAG;RSEQ=CCGGCCACCCACTCCCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1140:41:15,26:488,608:0.036:2,2:24.3:1:30.9:1:0.34063:1.39083:60:19.5:0.0348:0:2.2 0/0:861:0:0,0:397,461:0:2,0:25.3:1:30.9:1:1:0:60:36.304:0.9964:0:0.3 -17 38512461 . G T 158 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03159;LSEQ=GCTCCAACAGAAGCAGCCCG;RSEQ=CCACCCACTCCCCGTGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1136:40:14,26:495,599:0.0352:2,2:25.8:1:29.7:1:0.25716:1.53414:60:39:0.0356:0:2.2 0/0:869:1:0,1:405,460:0.0012:2,0:6:0:29:0:1:0:60:2:0.0012:0:1 -17 38514723 . CAGAAA C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGGAAGGAAAGAAAGGA;RSEQ=GGAAAGAAAGAAAGAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:12:0:31.5:1:1:1:60:4:0.5:0:0 -17 39611498 . T C 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TGAACTCCAGGACTGGACGC;RSEQ=GAGCCTCAGACACCAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:23.5:1:32.5:1:1:0:60:8:0.8:0:1.3 0/0:2:0:0,0:2,0:0:0,0:16:1:33:0:1:0:60:4:1:0:0 -17 39611584 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.10145;SOR=Inf;LSEQ=TGCTCTTAGAGCAAAGCAAA;RSEQ=CTACCCATATGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:18,6:0:2,0:24:1:32.3:1:1:0:59.8:48:1:0:0.2 0/1:22:3:2,1:11,7:0.1364:2,2:29.3:1:29.7:1:1:1.26:60:6:0.1364:0:1 -17 39611602 . TTGC T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.00174;SOR=0.12779;LSEQ=AAGCTACCCATATGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:20:12,8:8,4:0.6452:2,2:26.5:1:29.9:1:1:1.32148:59.8:40:0.6452:0.0968:0.2 0/1:22:4:4,0:9,9:0.1818:2,0:25.5:1:31:1:0.11497:0:60:8:0.1818:0:0.3 -17 39611655 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51373;SOR=0;LSEQ=AAACTTGGGCTTCAGAATGG;RSEQ=TCCAAAATATGACTCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:12,17:0.0645:2,2:13.5:1:29:1:1:1.40:60:4:0.0645:0:1 0/0:20:0:0,0:9,11:0:2,0:21.9:1:31.4:1:1:0:60:40:1:0:0.2 -17 39874267 . T A 56 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=TCTCTACCCATCTTAGGTCC;RSEQ=CGGCTGGGGCTCTGTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:15.8:1:28:1:1:0:60:3:1:0:1.8 0/0:1:0:0,0:1,0:0:0,0:43:0:33:0:1:0:60:2:1:0:0 -17 39874283 . T A 67 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16667;SOR=0;LSEQ=GTCCTCGGCTGGGGCTCTGT;RSEQ=ATAAAAGACAGATTACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:24.8:1:29:1:1:0:60:10:1:0:1.6 0/0:1:0:0,0:1,0:0:0,0:27:0:32:0:1:0:60:2:1:0:0 -17 40353542 . GCA G 111 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=28;MSI=15.000;MSILEN=2;SSF=0.00941;SOR=4.41734;LSEQ=ACACCATAACGTGCAAACAC;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:8:8,0:44,0:0.1481:1,0:19.6:1:32.8:1:1:0:59.4:16:0.1509:0.037:0.1 0/1:25:11:11,0:13,0:0.44:1,0:25:1:32.1:1:1:0:60:22:0.44:0.08:0.1 -17 40353722 . A G 195 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=47.73766;LSEQ=AAGAGTGATTCCTCTGGTGA;RSEQ=GATGAAGAAGCTGAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1218:2:1,1:784,432:0.0016:2,2:8.5:1:28.5:1:1:1.81377:60:4:0.0017:0:1 0/1:1097:80:50,30:616,398:0.0729:2,2:21.4:1:31:1:0.81249:1.08:60:160:0.0743:0:1.1 -17 40354031 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07771;SOR=Inf;LSEQ=AACAACCATTCAAACAGCTG;RSEQ=CTGTACAGCAACTCAGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:10,131:0:2,0:25.6:1:31.6:1:1:0:60:22.5:1:0:0.2 0/1:55:2:1,1:1,52:0.0364:1,2:18.5:1:28.5:1:0.07205:37.12:60:4:0.037:0:1 -17 40354226 . G A 72 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02177;SOR=9.54442;LSEQ=TCTCCCTCCCAAAGGCCAGA;RSEQ=CCCGGGCCAGGGCTGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:1:1,0:191,7:0.005:1,0:14:0:31:0:1:0:60:2:0.0051:0:1 0/1:108:5:5,0:101,2:0.0463:1,0:31.2:1:31.2:1:1:0:60:10:0.0481:0:1 -17 40354343 . A G 193 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=114.88209;LSEQ=CCTCCCCTGTGGACCCCCAC;RSEQ=AGAATGCCACCTACTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1534:1:0,1:921,607:7e-04:2,0:41:0:15:0:0.39765:0:60:0:0:0:7 0/1:1218:85:49,36:641,490:0.0698:2,2:24.6:1:30.2:1:0.9099:1.04:60:84:0.07:0:1.2 -17 40354558 . G T 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGTATCTTTGTCTTTCTCAG;RSEQ=GTGTAGAAGGACAAAGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:102,227:0:2,0:24.2:1:31.1:1:1:0:60:40.125:1:0:0.1 0/1:154:10:3,7:24,120:0.0649:2,2:19.1:1:29.9:1:0.38141:2.13:60:20:0.0654:0:1.1 -17 40359479 . A G 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=GTAATTGTGTGGGTTTTCAC;RSEQ=CAAGAGAGATAACACACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:264,5:0:1,0:22.5:1:30.1:1:1:0:59.7:32.625:1:0:0.3 0/1:173:12:11,1:155,6:0.0694:1,2:26.6:1:31:1:0.401:2.33234:59.6:24:0.0702:0:3.2 -17 40359505 . GCA G 248 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=36;MSI=19.000;MSILEN=2;SSF=7e-05;SOR=0.54301;LSEQ=GAGATAACACACGCAGGTAT;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:183:167,16:107,6:0.441:2,2:28.9:1:33.1:1:0.36319:1.70569:59.8:182:0.4505:0.0024:0.4 0/1:347:104:88,16:86,12:0.2997:2,2:27.5:1:32:1:0.54768:1.30133:59.8:33.667:0.2971:0:0.6 -17 40363524 . CA C 51 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGCGAAACTCTGTCT;RSEQ=AAAAAAAAAAATGAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:3,0:0.5:0,2:37:1:32.7:1:1:0:33:6:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 40367850 . G C 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00312;SOR=Inf;LSEQ=GGATTTTGCTATGTTGGCCA;RSEQ=GCTGGTCTCGAACTCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:67,0:0:1,0:22.4:1:31.9:1:1:0:59.3:21.333:1:0:0.1 0/1:44:6:6,0:37,0:0.1364:1,0:26.8:1:32:1:1:0:58:12:0.1429:0:2 -17 40367917 . A G 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=CCCAAAGTGCTGGGATTACA;RSEQ=GTGTGAGTCACTGCACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:165,0:0:1,0:21.6:1:30:1:1:0:59.8:54:1:0:0 0/1:143:12:12,0:128,3:0.0839:1,0:20.8:1:31.8:1:1:0:59:24:0.0851:0:1.9 -17 40367990 . G A 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATGAGATTCATGACACC;RSEQ=GCATTGATTTTGGGACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:777:0:0,0:569,207:0:2,0:24.9:1:29.9:1:1:0:60:47.5:0.9987:0:0.1 0/1:829:57:32,25:510,260:0.0688:2,2:24.9:1:29.9:1:0.14801:1.53167:60:56:0.0685:0:1.3 -17 40368183 . CT C 189 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.83288;SOR=0.94392;LSEQ=TCAAGTTCTTCTCCTTCTCT;RSEQ=TTTTTTTTTTTCTTATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:413:57:4,53:51,290:0.138:2,2:30.2:1:32.5:1:0.14513:2.32639:60:56:0.1489:0.0024:0.4 0/1:358:47:6,41:51,248:0.1313:2,2:28.2:1:30.5:1:0.53293:1.40394:59.9:22.5:0.1343:0.0056:0.6 -17 40368209 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.19123;SOR=Inf;LSEQ=TTTTTTTCTTATTATAACAA;RSEQ=ACTTTTATTTTCCAAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:9,248:0:1,0:20.7:1:32:1:1:0:59.8:41.833:0.996:0:0.8 0/1:201:2:1,1:16,182:0.01:2,2:25.5:1:28.5:1:0.16317:11.07:60:4:0.0101:0:1 -17 40369097 . T TA 140 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.04553;SOR=1.78472;LSEQ=AAGAAGAAGATGCTATGTGA;RSEQ=AAAAAAAAAATATTTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:23:21,2:301,32:0.0644:2,2:21.3:1:28.7:1:1:1.12:60:46:0.0652:0.0084:0.1 0/1:283:31:27,4:228,24:0.1095:2,2:20.3:1:28.3:1:0.52586:1.40552:59.8:62:0.1107:0.0389:0.1 -17 40369129 . CCA C 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.61942;SOR=1.15687;LSEQ=ATTTTGTAACATAAAGTACA;RSEQ=CACACACACACGCACACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:830:34:26,8:585,211:0.041:2,2:20.9:1:31.6:1:0.84325:1.17:60:68:0.0417:0.0096:0.1 0/1:722:34:26,8:490,197:0.0471:2,2:25.2:1:31.7:1:0.69698:1.31:59.7:33:0.0467:0:0.3 -17 40369149 . G A 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=6;SSF=0;SOR=51.73719;LSEQ=CCACACACACACACGCACAC;RSEQ=CACACGCAGAGCTGAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1032:1:0,1:701,330:0.001:2,0:20:0:32:0:0.32074:0:60:2:0.001:0:1 0/1:1024:49:31,18:622,348:0.0479:2,2:29:1:29:1:0.88007:1.03775:60:98:0.0492:0:1 -17 40369707 . C CT 45 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.18583;SOR=4.24589;LSEQ=GAAAACAGTTCCTAAGAGAA;RSEQ=TTTTTTTTTTTTTTTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:4,21:0.1:2,0:14.3:1:28.5:1:1:0:60:6:0.12:0.0333:1.3 0/1:6:2:0,2:0,4:0.3333:0,0:29:1:30:1:1:0:60:4:0.4:0:0 -17 40370235 . TG T 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.70911;SOR=1.07735;LSEQ=TGATGATGGTGGCCTTCACC;RSEQ=GGGGGGGTTCATGTGCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2450:61:29,32:1221,1165:0.0249:2,2:28:1:31.5:1:0.60558:1.15642:58.6:60:0.0248:0.002:0.1 0/1:2129:57:25,32:1024,1047:0.0268:2,2:27.8:1:30.2:1:0.42343:1.25175:60:114:0.027:0.0019:0.2 -17 40370237 . G T 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=16.72728;LSEQ=ATGATGGTGGCCTTCACCTG;RSEQ=GGGGGGTTCATGTGCACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2449:9:0,9:1245,1189:0.0037:2,0:1.9:1:26.2:1:0.00161:0:60:8:0.0033:0:1.1 0/1:2151:125:64,61:997,1025:0.0581:2,2:24.6:1:29.1:1:0.71283:1.08:59.4:250:0.0588:0:1.1 -17 40370345 . C T 209 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=85.88361;LSEQ=GGCTGCTTCTCAATGATGAA;RSEQ=GTGCTGCAGGGGACACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1989:2:0,2:847,1138:0.001:2,0:4.5:1:26:1:0.51063:0:60:4:0.001:0:1 0/1:1758:140:56,84:721,892:0.0796:2,2:24.8:1:29.4:1:0.28893:1.21231:58.1:45.667:0.079:0:1.2 -17 40370565 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATGGGCTGCAGCCCAAGG;RSEQ=CATCTCTTGCAGTGTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:145,51:0.0101:2,2:23:1:31:1:0.45726:2.82536:60:4:0.0104:0:2 0/0:73:0:0,0:56,17:0:2,0:27:1:30.8:1:1:0:60:23.333:1:0:0.1 -17 40371865 . A G 204 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=140.39309;LSEQ=AGCGGGCCAAACTGAGCTAG;RSEQ=GGAGGGGAGAGGAAACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1834:1:1,0:759,1074:5e-04:2,0:12:0:13:0:0.41439:0:60:0:0:0:2 0/1:1545:110:44,66:600,833:0.0712:2,2:26.7:1:30.2:1:0.76369:1.0804:60:109:0.072:0:1.2 -17 40372009 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCTGACAGCCAGGGGGG;RSEQ=CAAGATGAATGGGTGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:7,147:0.0128:1,2:17.5:1:28.5:1:0.10025:19.71:60:4:0.0131:0:1 0/0:76:0:0,0:4,72:0:2,0:22:1:31.1:1:1:0:60:37:1:0:0.1 -17 40375268 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14449;SOR=Inf;LSEQ=GCACTGTCTTCAATGCAAAT;RSEQ=AGTCCCTGCTACTCAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:157,2:0:1,0:24.9:1:28.5:1:1:0:60:52:1:0:0.1 0/1:98:2:1,1:94,2:0.0204:1,2:23.5:1:30:1:0.06059:38.56166:60:4:0.0206:0:1 -17 40375335 . A G 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCTTTCTCCCAACCCCACC;RSEQ=GAGCTGCTTTCCAGTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:617:0:0,0:525,91:0:2,0:24.9:1:30.2:1:1:0:60:50.333:1:0:0.1 0/1:445:27:21,6:345,73:0.0607:2,2:26.1:1:29.9:1:0.6016:1.3493:60:54:0.0614:0:1.1 -17 40375716 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.08366;SOR=Inf;LSEQ=GGAGGAAAAGCAAACGTCAT;RSEQ=ATGAGACACAGGGTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:1,128:0:1,0:23:1:32.1:1:1:0:60:31.25:1:0:0.1 0/1:53:2:0,2:3,48:0.0377:2,0:26.5:1:31.5:1:1:0:60:4:0.0385:0:1 -17 40383886 . A G 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=AAAGAAAAAAAATTTTAAAT;RSEQ=CCTTTTTATGGATCACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:130,2:0:1,0:24.4:1:28.5:1:1:0:60:65:1:0:0.1 0/1:78:3:3,0:75,0:0.0385:1,0:31.7:1:34:0:1:0:60:6:0.039:0:1 -17 40384279 . A G 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TATTATTTATTTTTATTTTT;RSEQ=TTTTTTTGAGACAGTCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:0,111:0:1,0:17.2:1:31.2:1:1:0:60:110:1:0:0.1 0/1:76:10:0,10:1,65:0.1316:1,0:23.6:1:30.3:1:1:0:60:9:0.12:0:1 -17 40441357 . AG A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14408;SOR=Inf;LSEQ=TAGGTAGGCATGGCAAGGCC;RSEQ=GGGCAGGCCCGGTTCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:292,21:0:2,0:23.4:1:32.2:1:1:0:60:61.6:1:0:0.1 0/1:192:2:1,1:171,19:0.0104:2,2:8.5:1:30.3:1:0.19797:8.79907:60:4:0.0104:0.0052:0 -17 40441819 . A G 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGTTTCCACTTTATTCC;RSEQ=GCTCCCTGACCTCCTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:702:0:0,0:535,167:0:2,0:21.8:1:30:1:1:0:60:34.1:1:0:0.1 0/1:473:26:19,7:319,128:0.055:2,2:18.2:1:30:1:1:1.09:60:52:0.0557:0:1.2 -17 40444332 . G GT 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.32019;SOR=4.01259;LSEQ=CTCTCTGAGCCTCTGTTCCT;RSEQ=TTTTTTTTTCTTTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:0,2:0,50:0.0385:1,0:35:1:31.5:1:1:0:60:4:0.04:0:0 0/1:7:1:0,1:1,5:0.1429:2,0:23:0:31:0:1:0:60:2:0.1667:0:0 -17 40447401 . T C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTGGACTTTGAAGGTGT;RSEQ=ACTATCTGCCGTTATCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:23:23,0:1,0:0.9583:0,1:21.6:1:31.9:1:1:0:60:46:0.9583:0:1.3 1/1:3:3:3,0:0,0:1:0,0:29:1:31.7:1:1:0:60:6:1:0:1.7 -17 40447500 . T C 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02655;SOR=Inf;LSEQ=CTTCTGATGCAAATGATCCT;RSEQ=CCTTCTTGCCCTAGTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:124,3:0:1,0:24.7:1:30.8:1:1:0:60:254:1:0:0.8 0/1:55:3:3,0:51,1:0.0545:1,0:24:1:32.7:1:1:0:60:6:0.0545:0:1 -17 40447558 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.08817;LSEQ=GGTTTGGGGTTTGGGGTCTG;RSEQ=AGTATTGGTGTTTCCTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:271:242:214,28:27,0:0.893:1,2:21.9:1:31.9:1:0.08958:0:60:79.667:0.8951:0:1.1 0/1:154:65:57,8:73,15:0.4221:2,2:21.5:1:31.4:1:0.49641:1.46:60:64:0.4211:0:1.1 -17 40451643 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1827;LSEQ=CCCCTGGCTGTCAGGAACCC;RSEQ=GACTTGCTCTTGATGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:119:113,6:175,6:0.3967:1,2:22.7:1:31.6:1:0.55059:1.5463:59.9:38.667:0.3919:0:1.2 0/1:159:17:15,2:135,7:0.1069:1,2:9.2:1:31.3:1:0.2474:2.5506:60:34:0.1083:0:1.1 -17 40452031 . C T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68972;SOR=0.5742;LSEQ=CTTTTTTCCTGGGGGCCTTG;RSEQ=GAGGCAGAGCAGCTTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:19:1,18:9,18:0.413:2,1:22.3:1:30.9:1:0.03106:8.64699:39.3:38:0.4222:0:1 0/1:7:2:0,2:1,4:0.2857:2,0:14:1:32:0:1:0:40:4:0.2857:0:1 -17 40452429 . C A 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01156;SOR=0;LSEQ=GCTCTTGTTTCTCCAGGGAG;RSEQ=CTGGTTCCTCAATCAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:13:2,11:17,203:0.0558:2,2:22.8:1:29.2:1:0.28676:2.16:37.2:12:0.0538:0:1.2 0/0:106:0:0,0:8,98:0:2,0:21.1:1:31.2:1:1:0:39.7:34.333:1:0:0.1 -17 40452453 . T C 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0169;SOR=0.25253;LSEQ=GTTCCTCAATCAGACTTTGG;RSEQ=CCCCATCCTGTGCACCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:28:4,24:18,111:0.1783:2,2:23.1:1:29.7:1:1:1.03:47.6:56:0.1842:0:1.9 0/1:58:3:1,2:5,50:0.0517:2,2:11.7:1:28.7:1:0.28377:4.77:38:6:0.0517:0:1.7 -17 40452506 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00683;SOR=0.24105;LSEQ=CTGCTGTCCTGGGGGTGGGA;RSEQ=GGGGCTCGGGTGTGTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:39:12,27:37,47:0.3171:2,2:27:1:30.1:1:0.17304:1.76317:51.7:38:0.314:0:1.7 0/1:40:4:1,3:20,16:0.1:2,2:29.5:1:30.3:1:0.33056:3.63371:51.8:8:0.1:0:1.8 -17 40452578 . C T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00353;SOR=Inf;LSEQ=CGCCCCTCCTGTGTACGTCT;RSEQ=TAATTCTGGGAGGCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:113,23:0:2,0:21.4:1:31.7:1:1:0:42.5:44.333:1:0:0.2 0/1:67:5:5,0:59,3:0.0746:1,0:27:1:27.6:1:1:0:44:4:0.0625:0:1.4 -17 40452675 . C A 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.56117;LSEQ=ACGGGAGCTGTGTCTTGGGG;RSEQ=CTGGCGTCTGTGAGGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1008:588:428,160:292,125:0.5833:2,2:23:1:29.6:1:0.35614:1.14:56.7:48:0.5824:0:1.1 0/1:782:344:236,108:294,139:0.4399:2,2:23.3:1:28.6:1:0.8768:1.03:57.7:56.333:0.4413:0:1.1 -17 40453240 . C T 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05835;SOR=3.56709;LSEQ=ACCACAGAGGGACTGAGAGC;RSEQ=CTTTCCCCTGCGCCAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:973:3:0,3:741,229:0.0031:2,0:1.3:1:26.3:1:0.01342:0:60:6:0.0031:0:1 0/1:641:7:2,5:464,170:0.0109:2,2:12:1:23.9:1:0.01849:6.79817:60:6:0.0095:0:1 -17 40454281 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAACAGAACTGGGCTGTCT;RSEQ=CTCGCCCAGCCCCTTGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:37.5:1:28:1:1:1:60:4:0.5:0:1 -17 40456499 . T G 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGCCCAGAGCTGAGTCCT;RSEQ=GTAAGCAGCCGCCATCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1284:0:0,0:611,673:0:2,0:23.4:1:30.1:1:1:0:60:115.727:1:0:0.1 0/1:977:59:31,28:455,461:0.0604:2,2:23.5:1:31.3:1:0.68906:1.12:60:118:0.061:0:1.3 -17 40457074 . T C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAAAAAGAAAAAAGT;RSEQ=GGGCATGGTGGCCTGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:4,6:0.1667:2,0:17:1:27:0:0.51515:0:60:4:0.1818:0:1.5 0/0:1:0:0,0:0,1:0:0,0:48:0:29:0:1:0:60:2:1:0:0 -17 40457140 . C A 29 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAGGAGGATCACTTGAG;RSEQ=CCAGGAGGTCAAGGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:0.1667:2,2:24.5:1:29:1:1:1.45:60:4:0.1667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 40457246 . G C 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAGCAGATTGCGGCCATG;RSEQ=GTGGTGGGTCTTGCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:16:1:33.7:1:1:0:59.7:6:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 40457510 . A G 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56076;SOR=3.24165;LSEQ=AGCCTGGGCAACAAGAGTGA;RSEQ=ACTCCATATCAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:1,0:192,0:0.0052:1,0:42:0:28:0:1:0:60:2:0.0053:0:2 0/1:120:2:2,0:117,1:0.0167:1,0:20:1:31.5:1:1:0:60:4:0.0167:0:3.5 -17 40457520 . CA C 153 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.07963;SOR=1.69904;LSEQ=ACAAGAGTGAAACTCCATAT;RSEQ=AAAAAAAAAATACATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:27:27,0:229,2:0.1027:1,1:18:1:32:1:1:0:58.7:54:0.1034:0.0228:0.4 0/1:178:29:27,2:147,2:0.1629:1,2:20.6:1:31.5:1:0.12477:5.36624:60:58:0.1638:0.0393:0.2 -17 40457536 . T TA 114 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.68978;SOR=1.18195;LSEQ=ATATCAAAAAAAAAAATACA;RSEQ=AAAAAAAAATAAAGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:14:13,1:326,29:0.0374:2,1:21.2:1:30:1:1:1.16:60:28:0.0403:0.008:0.6 0/1:273:12:12,0:238,21:0.044:2,0:20.1:1:29.3:1:0.60781:0:60:24:0.0474:0.011:0.1 -17 40458193 . TTG T 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.01309;SOR=0;LSEQ=TCTCTAGGTGTCTGTGTATC;RSEQ=TGTGTGTGTGAATATTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:760:9:4,5:624,126:0.0118:2,2:19.7:1:28.6:1:0.00997:6.16815:60:8:0.0108:0.0026:0.2 0/0:522:0:0,0:430,92:0:2,0:21.7:1:29.6:1:1:0:60:64.25:1:0:0.1 -17 40458684 . G GC 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12177;SOR=3.64978;LSEQ=CAAGAGCGAGATGACGGAGG;RSEQ=CCCAGGGCTGGGAGTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:0,5:0,50:0.0909:1,0:41.6:1:30.2:1:1:0:60:10:0.0943:0:0.2 0/1:11:3:0,3:0,8:0.2727:0,0:32.3:1:31.7:1:1:0:60:6:0.2727:0:0 -17 40458742 . CT C 88 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGATGTGTTTGCTAATTTT;RSEQ=TTTTTTTTTTTAGAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:0,29:0.1944:1,0:31.7:1:31.6:1:1:0:58.6:14:0.1944:0:0.4 0/0:3:0:0,0:0,3:0:0,0:11.3:1:31:1:1:0:60:6:1:0:0 -17 40459297 . T C 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=Inf;LSEQ=CACTTTATGGTCTGCTGGAG;RSEQ=GTGGTGGCAAGCAGGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:262,8:0:1,0:24.8:1:29.3:1:1:0:60:32.75:1:0:0.1 0/1:137:9:7,2:120,8:0.0657:2,2:27.6:1:32.1:1:0.13113:4.21058:60:18:0.0662:0:1.1 -17 40459562 . A G 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=2.69988;LSEQ=GGCCAGCTGTGGGCGCAGAG;RSEQ=GACTGTGGCTGTGGCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1493:244:121,123:608,637:0.1634:2,2:24.7:1:30.7:1:0.83397:1.03:60:26.111:0.1603:0:1.1 0/1:1216:420:211,209:395,397:0.3454:2,2:23.4:1:29.9:1:0.95187:1.01:60:37.182:0.3431:0:1.2 -17 40459737 . C T 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.04429;LSEQ=ACCATCGCCTGGAAGTTTGA;RSEQ=TCCCGTGAGTGCCCGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1779:278:124,154:731,768:0.1563:2,2:26.2:1:30.4:1:0.21457:1.18199:60:54.6:0.1559:0:1.2 0/1:1631:448:211,237:544,637:0.2747:2,2:25.5:1:29.5:1:0.73856:1.04:60:55:0.2735:0:1.2 -17 40460427 . C T 136 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.18283;LSEQ=ATAGACAAAGCCTTGGGCTG;RSEQ=GCCGTGGGGACTTCCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:1:0,1:61,356:0.0024:2,0:11:0:31:0:1:0:60:2:0.0024:0:1 0/1:304:23:3,20:42,238:0.0757:2,2:25.2:1:30.1:1:1:1.17587:60:46:0.0772:0:1.1 -17 40460428 . G A 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25905;LSEQ=TAGACAAAGCCTTGGGCTGC;RSEQ=CCGTGGGGACTTCCCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:77:11,66:45,282:0.1901:2,2:22.1:1:30:1:0.85642:1.04:60:154:0.1969:0:1.1 0/1:297:17:3,14:41,239:0.0572:2,2:24.2:1:27.4:1:0.72503:1.25:60:16:0.055:0:1.4 -17 40460783 . GT G 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GCCCCAAATCCATTGGTTGG;RSEQ=TTGCTTGTTGATTCTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:11,4:0.1176:2,0:34.5:1:31.5:1:1:0:60:4:0.1176:0:0 1/1:1:1:1,0:0,0:1:0,0:32:0:33:0:1:0:60:2:1:0:0 -17 40460989 . A G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.63002;LSEQ=ATGTGAGCAGGAGGGAGACT;RSEQ=CATGGGGCGTGGGCTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:630:92:71,21:428,109:0.146:2,2:22.1:1:32.2:1:0.57869:1.16107:60:184:0.1467:0:2 0/1:480:149:117,32:248,82:0.3104:2,2:21.9:1:31.4:1:0.48709:1.21:60:48.667:0.3106:0:2 -17 40461003 . C T 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=1.75221;LSEQ=GAGACTACATGGGGCGTGGG;RSEQ=TTCCACCCCACTTGGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:825:136:93,43:516,173:0.1648:2,2:21.3:1:29.8:1:0.13473:1.37852:60:135:0.1654:0:1.7 0/1:638:164:121,43:337,137:0.2571:2,2:23.3:1:29.1:1:0.5468:1.14:60:81:0.2571:0:1.8 -17 40461061 . A G 215 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=151.34178;LSEQ=TCACCACTGTTCTTCCCTTG;RSEQ=CAGCTAAAGCTGTTGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1756:1:1,0:1020,731:6e-04:2,0:4:0:32:0:1:0:52:2:6e-04:0:1 0/1:1523:121:66,55:772,626:0.0794:2,2:26:1:31.1:1:0.9242:1.02768:59:59.5:0.0795:0:1.4 -17 40461250 . T A 90 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=20.98675;LSEQ=GCCCTGGGGAGGGAGTCCCC;RSEQ=CTCCTGTAGCTGGAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:1:0,1:114,359:0.0021:2,0:4:0:13:0:1:0:60:0:0:0:6 0/1:211:9:3,6:30,172:0.0427:2,2:19.1:1:28.6:1:0.15072:2.85:60:18:0.0443:0:1 -17 40461293 . C T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGAGTGGGGCACTTTGTC;RSEQ=GTCTACACCCCGAGAAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:199,195:0:2,0:24:1:30.5:1:1:0:60:55.286:1:0:0.2 0/1:188:16:10,6:86,86:0.0851:2,2:19.8:1:31.2:1:0.43579:1.66:60:32:0.0856:0:1.1 -17 40461674 . A G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00182;SOR=3.49697;LSEQ=AAGCTAGACATAGCAGGGTC;RSEQ=AGTCCTCACTCTAGTACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:15:0,15:5,98:0.1271:1,1:16.5:1:31.8:1:1:0:60:30:0.1316:0:1.1 0/1:56:19:1,18:1,36:0.3393:1,1:20.5:1:31.7:1:1:1.97:60:38:0.3393:0:1.3 -17 40462796 . TTGTG T 175 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=11.000;MSILEN=2;SSF=0.07086;SOR=0.60732;LSEQ=CTTTGCAGGCATGCATGTGC;RSEQ=TGTGTGTGTGTGTGTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:52:1,51:2,127:0.2626:1,1:34.6:1:30.8:1:1:1.24:59.8:104:0.2653:0:0.1 0/1:152:27:0,27:0,107:0.1776:1,1:34.1:1:30.6:1:1:0:59.8:54:0.1812:0.0066:0.1 -17 40462994 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGACCTATTCCTCCTG;RSEQ=GCCCCTCATCTGCTCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:0.2:0,0:22.5:1:32:1:1:0:60:4:0.2222:0:1 0/0:1:0:0,0:0,1:0:0,0:7:0:31:0:1:0:60:2:1:0:0 -17 40467625 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1645;SOR=Inf;LSEQ=CCCAGATTGCTCAAAGATAG;RSEQ=AGAAGTAGGAGATTAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:181,0:0:1,0:25.7:1:32.1:1:1:0:60:59.333:1:0:0.1 0/1:124:2:1,1:117,4:0.0161:1,2:21:1:24.5:1:0.07997:26.27373:60:4:0.0161:0:1 -17 40467639 . T TA 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.57202;SOR=2.85013;LSEQ=AGATAGCAGAAGTAGGAGAT;RSEQ=AAAAAAAATCTGGAACCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:1,0:250,0:0.004:1,0:17:0:24:0:1:0:60:2:0.004:0:0 0/1:177:2:2,0:170,5:0.0113:1,0:19:1:28.5:1:1:0:60:4:0.0115:0:0 -17 40467934 . C T 110 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03784;SOR=0.1384;LSEQ=CACTGCTATCCAATCTCCTG;RSEQ=CCCTTAAGGCCCAGGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:12:0,12:15,343:0.0324:1,0:30.5:1:30.8:1:1:0:60:24:0.0335:0:1 0/0:217:1:0,1:12,204:0.0046:2,0:1:0:26:0:1:0:60:2:0.0047:0:1 -17 40467943 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.11567;SOR=Inf;LSEQ=CCAATCTCCTGCCCCTTAAG;RSEQ=CCCAGGGATGGTCAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:6,319:0:1,0:25.4:1:32.3:1:1:0:60:64:1:0:0.1 0/1:168:2:0,2:7,159:0.0119:1,0:45.5:1:29.5:1:1:0:60:4:0.012:0:1.5 -17 40467999 . G T 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00214;SOR=Inf;LSEQ=TCCCTGGAGGACCCTGCCTC;RSEQ=GGAAGGGTCCTTTCTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:1,115:0:1,0:22.7:1:31.3:1:1:0:60:57:1:0:0.1 0/1:50:5:0,5:2,43:0.1:1,0:17:1:29.2:1:1:0:60:10:0.1:0:1 -17 40468009 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10228;SOR=Inf;LSEQ=ACCCTGCCTCGGGAAGGGTC;RSEQ=TTTCTCATTCCCACCTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:1,83:0:1,0:26.8:1:32.7:1:1:0:60:83:1:0:0.1 0/1:40:2:1,1:1,37:0.05:1,2:8.5:1:32:0:0.09872:26.51:60:4:0.05:0:1 -17 40468489 . G A 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGTGATCCACCCACCTC;RSEQ=GCCTCCCAAAGTGCTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:3,2:0.375:2,0:30.3:1:31.3:1:0.46429:0:58:6:0.375:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 40468747 . C T 58 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00957;SOR=Inf;LSEQ=TCGGTGTGTACATGTGAGAG;RSEQ=ATCACACAAAGGGGACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:0:0,0:427,147:0:2,0:24.4:1:32.1:1:1:0:60:142.5:1:0:0.1 0/1:493:6:1,5:364,122:0.0122:2,2:6.2:1:22.8:1:0.00513:14.82251:60:5:0.0103:0:1 -17 40468975 . GA G 166 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.23858;SOR=0.71694;LSEQ=GGGGTTGACAAGACACAATG;RSEQ=AAAAAAAAAAAGAACAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:43:17,26:113,167:0.1311:2,2:27.2:1:30.6:1:1:1.03477:60:42:0.1321:0.0122:0.4 0/1:246:24:8,16:78,137:0.0976:2,2:30:1:30.9:1:0.8268:1.13811:60:48:0.0996:0:0.4 -17 40468994 . AAC A 98 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.12368;SOR=0.28117;LSEQ=GGAAAAAAAAAAAAGAACAA;RSEQ=ACACACACACAAGCCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:9:4,5:114,139:0.0341:2,2:19.9:1:31:1:1:1.02509:60:18:0.0353:0.0076:0 0/0:204:2:1,1:69,131:0.0098:2,2:29.5:1:30.5:1:1:1.89:60:4:0.0099:0:0 -17 40474864 . A G 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32913;SOR=1.65717;LSEQ=AAACCAATCCTTCAGCTGGA;RSEQ=GGATTTAGAAGTCACGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:24:22,2:96,6:0.1905:2,2:26.8:1:32.4:1:0.6471:1.44978:60:48:0.1951:0:1.8 0/1:32:9:9,0:22,1:0.2813:1,0:16.9:1:32.6:1:1:0:60:18:0.2813:0:1.9 -17 40474880 . G C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31305;SOR=1.49599;LSEQ=TGGAAGGATTTAGAAGTCAC;RSEQ=CAAATGTGTTTTGCGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:27:25,2:104,5:0.1985:1,2:27.4:1:31.3:1:0.62537:1.65692:60:54:0.203:0:1.8 0/1:48:13:13,0:33,2:0.2708:2,1:22:1:31.6:1:1:0:60:26:0.2708:0:1.6 -17 40475650 . G GA 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=3.24647;LSEQ=ATTCACACCAGGTCCTGAAG;RSEQ=AAAGAAAAAGAGTCAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1503:244:109,135:588,667:0.1623:2,2:24.2:1:29.9:1:0.57481:1.09176:60:121:0.1633:0.0299:0.1 0/1:1517:586:270,316:452,477:0.3863:2,2:27.7:1:29.2:1:0.34196:1.10895:60:44.077:0.3843:0.0257:0.2 -17 40476363 . G A 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TAAATAAATAAATAAAATAA;RSEQ=ACAAAAAAAACCAACTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:16.7:1:31.3:1:1:0:60:6:0.375:0:2.3 1/1:1:1:1,0:0,0:1:0,0:4:0:30:0:1:0:60:2:1:0:1 -17 40476667 . C G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACATGGCCCAAATGAACAGC;RSEQ=CTATGGGCCGGATCCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:443,11:0:1,0:26:1:31:1:1:0:60:44.4:1:0:0.2 0/1:325:14:14,0:300,11:0.0431:1,1:23.9:1:28.4:1:1:0:60:13:0.0413:0:1.3 -17 40476701 . C G 116 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55698;SOR=0.85956;LSEQ=CCCTTTTCTGGGCGGGTGGG;RSEQ=GGGAGGGAGAAGGGGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:746:45:1,44:667,29:0.0603:1,1:17.3:1:21.2:1:0:992.82625:60:1.5:0.0386:0:3.2 0/1:612:32:0,32:546,29:0.0523:2,1:20.3:1:23.4:1:0:0:60:2.556:0.0395:0:3.5 -17 40477739 . T C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATTATAGGCGTCCGCCACCA;RSEQ=ACCCAGCTAATTTTTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:38.3:1:29.3:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:41.5:1:32.5:1:1:0:60:4:1:0:1 -17 40481394 . AC A 241 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=144.53906;LSEQ=CTCTCTCCCTCAAGGAAAAC;RSEQ=CCCAGTTGTCTTTCATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1762:2:1,1:1002,756:0.0011:2,2:34.5:1:31:1:1:1.32517:60:4:0.0012:0:0 0/1:1622:229:128,101:793,600:0.1412:2,2:24.8:1:30.8:1:0.77389:1.04288:60:458:0.1426:0.0185:0.2 -17 40481529 . G C 300 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=0.73827;LSEQ=GGCTCTCCCTAGCCCTCTCC;RSEQ=GCAGCCAGAGGCCCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1413:927:457,470:250,233:0.6561:2,2:24.4:1:30.5:1:0.40004:1.10341:60:462.5:0.6565:0:1.1 1/0:1086:635:304,331:214,235:0.5847:2,2:24.6:1:29.8:1:0.95086:1.01:60:56.727:0.5837:0:1.1 -17 40481902 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55736;SOR=3.48544;LSEQ=AAAAACCTCTGTGCTCCTGG;RSEQ=CATTTCTTTAAACTATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:1:1,0:49,269:0.0031:2,0:1:0:25:0:0.15674:0:60:2:0.0032:0:1 0/1:184:2:1,1:25,157:0.0109:2,2:39:1:30.5:1:0.2633:6.18:60:4:0.011:0:1 -17 40483403 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10688;SOR=Inf;LSEQ=TGAAGATCTCTGAATAAAGA;RSEQ=AGAGTCTCTAGTTCAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:223,25:0:2,0:24.4:1:32.2:1:1:0:60:496:1:0:0.1 0/1:225:3:2,1:193,29:0.0133:2,2:25:1:27:1:0.35038:3.30162:60:6:0.0134:0:1.3 -17 40483466 . C A 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTATTCCTCATTTGAAAAA;RSEQ=AGAGCTAAGATAGGAGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:774:0:0,0:453,318:0:2,0:25.3:1:31.9:1:1:0:60:109.143:0.9961:0:0.1 0/1:766:27:17,10:424,313:0.0352:2,2:25.3:1:29.6:1:0.69285:1.25:60:54:0.0353:0:1.2 -17 40485635 . C T 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCACCAACTCTACCCTCA;RSEQ=CCTAACAGTGTCCCTCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:0:0,0:436,174:0:2,0:23.1:1:31.2:1:1:0:60:45.923:1:0:0.1 0/1:559:44:34,10:356,159:0.0787:2,2:24.3:1:29.3:1:0.30696:1.52:60:43:0.078:0:1 -17 40489539 . G A 203 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=31.18003;LSEQ=TTCCAGTCAGCCAGCTCCTC;RSEQ=TCCGTGAGAGTTTTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1786:4:4,0:887,894:0.0022:2,0:1:0:24.3:1:0.06187:0:60:3:0.0017:0:1 0/1:1681:110:52,58:783,788:0.0654:2,2:22.7:1:30:1:0.62297:1.10824:60:109:0.0657:0:1.2 -17 40489660 . C T 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CCTCAGACTGTCTCTAACCA;RSEQ=ATTCTTTAGTCAACTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:775:37:13,24:300,436:0.0477:2,2:24.6:1:29.5:1:0.60734:1.2699:60:74:0.0484:0:1.1 0/0:697:0:0,0:266,429:0:2,0:21.8:1:31.3:1:1:0:60:172.75:0.9971:0:0.1 -17 40489741 . G C 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCTGAAATCCCGCAAGTGA;RSEQ=CGAGACACATGGGGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:0:0,0:381,299:0:2,0:24.6:1:31.7:1:1:0:60:51.308:1:0:0.1 0/1:535:26:15,11:300,208:0.0486:2,2:22.1:1:31.3:1:1:1.05757:60:52:0.0491:0:1.1 -17 40489939 . T G 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14138;SOR=1.41649;LSEQ=TGACCTGAGGGAATACTCCT;RSEQ=GACCTGAGGGAATACTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:51:18,33:70,236:0.1421:2,2:18.7:1:31.3:1:0.07781:1.84:57.2:50:0.1458:0:1.2 0/1:242:46:15,31:45,149:0.1901:2,2:18:1:30.1:1:0.18975:1.60:57.6:45:0.1899:0:1.2 -17 40489949 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5642;SOR=3.1095;LSEQ=GAATACTCCTTGACCTGAGG;RSEQ=AATACTCCTGGACCTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:1:0,1:59,218:0.0036:2,0:35:0:26:0:1:0:60:2:0.0037:0:2 0/1:181:2:1,1:35,143:0.011:2,2:20.5:1:28:1:0.36089:4.04:60:4:0.0113:0:1 -17 40489999 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACCTGAGGGAATACTCCT;RSEQ=GACCTGAGGGAATACTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:0,83:0.0235:1,2:34:1:28.5:1:0.02353:0:60:4:0.026:0:1.5 0/0:32:0:0,0:0,32:0:1,0:26.9:1:29.2:1:1:0:38.2:15:1:0:0.3 -17 40490539 . T G 94 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43488;SOR=0.43506;LSEQ=TGACCTGAGGGAATACTCCT;RSEQ=GACCTGAGGGAATACTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:6,2:7,2:0.4706:2,2:12.8:1:31.5:1:1:1.15611:51.9:16:0.5:0:2.1 0/1:11:3:2,1:6,2:0.2727:2,2:3:1:29.3:1:1:1.44322:60:6:0.2727:0:2 -17 40490559 . G T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3966;SOR=0.58234;LSEQ=TGACCTGAGGGAATACTCCT;RSEQ=GACCTGAGGGAATACTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:21:17,4:9,2:0.6563:2,2:19.6:1:30.1:1:1:1.05695:56:20:0.6452:0:1.4 1/0:21:11:10,1:6,4:0.5238:2,2:16.4:1:31.1:1:0.14861:6.08:60:22:0.5238:0:1.3 -17 40490643 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15586;SOR=Inf;LSEQ=AGGACCCGTACCTCCCTTGC;RSEQ=CCCCGCCCGCCTTAAGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:143,8:0:2,0:25.1:1:30.2:1:1:0:60:74.5:1:0:0.2 0/1:99:2:2,0:92,5:0.0202:2,0:29:1:31.5:1:1:0:60:4:0.0204:0:1 -17 40491110 . AT A 61 v4;MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.02776;SOR=9.9182;LSEQ=GGAGACCCCCATCTCTACAA;RSEQ=TTTTTTTTTTTAATTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:13,4:0.15:2,0:29.3:1:32.7:1:1:0:60:6:0.15:0:0 1/0:6:4:3,1:2,0:0.6667:0,2:21.3:1:30.5:1:1:0:60:8:0.6667:0.1667:0.5 -17 40491135 . G A 39 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02245;SOR=Inf;LSEQ=TTTTTTTTAATTAGCTGGGC;RSEQ=TGGTGGTGCATGCCTGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:31,2:0:2,0:16.2:1:27.9:1:1:0:59.4:15.5:1:0:0.3 0/1:14:3:2,1:11,0:0.2143:0,2:20.7:1:25:1:0.21429:0:60:2:0.1538:0:1 -17 40491301 . C T 62 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35096;SOR=0.48205;LSEQ=AAAAAAAAAATTAATGAAAG;RSEQ=TCCCTGCCCGAGGCTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:7:2,5:473,159:0.0109:2,2:12.1:1:22.3:1:0.014:7.40976:60:2.5:0.0084:0:2.3 0/0:567:3:1,2:398,166:0.0053:2,2:6.3:1:21:1:0.2109:4.78008:53.3:2:0.0037:0:1.3 -17 40497421 . C CT 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.55694;SOR=3.31355;LSEQ=ATTTTGGGGGGTGGAACTTT;RSEQ=TTTTTTTTTAGAGTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:1:1,0:66,6:0.0137:2,0:36:0:32:0:1:0:60:2:0.0137:0:0 0/1:45:2:2,0:40,3:0.0444:2,0:19.5:1:32.5:1:1:0:60:4:0.0444:0:0 -17 40497828 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00632;SOR=3.64473;LSEQ=AGAGCCTGGGTGAAGGCTCT;RSEQ=TGTCGGCGGGGGGCGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:8:0,8:0,59:0.1194:1,0:26.6:1:30.8:1:1:0:60:16:0.1231:0:2.5 0/1:51:17:1,16:0,34:0.3333:1,1:32.8:1:29.3:1:0.33333:0:60:16:0.3265:0:2.8 -17 40497835 . C G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00786;SOR=3.8565;LSEQ=GGGTGAAGGCTCTCTGTCGG;RSEQ=GGGGGGCGAAGGGGAGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:8:0,8:0,47:0.1455:1,0:27.1:1:26:1:1:0:60:3:0.12:0:2.8 0/1:40:16:1,15:0,24:0.4:1,1:32.3:1:30.3:1:0.4:0:60:15:0.3947:0:3.1 -17 40497839 . G C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00915;SOR=4.29815;LSEQ=GAAGGCTCTCTGTCGGCGGG;RSEQ=GGCGAAGGGGAGGTCGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:0,6:0,45:0.1176:1,0:28.3:1:30.8:1:1:0:60:12:0.1176:0:3 0/1:38:14:1,13:0,24:0.3684:1,1:31.8:1:29.9:1:0.36842:0:60:28:0.3684:0:3.2 -17 40497840 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.17952;SOR=Inf;LSEQ=AAGGCTCTCTGTCGGCGGGG;RSEQ=GCGAAGGGGAGGTCGTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:0,51:0:1,0:27.1:1:31.2:1:1:0:60:50:1:0:0.5 0/1:38:2:0,2:1,35:0.0526:1,0:8:1:31.5:1:1:0:60:4:0.0526:0:2.5 -17 40498944 . T C 46 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03269;SOR=9.64439;LSEQ=AGGCCAGGCATGGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:0,2:0,35:0.0541:1,0:32:1:32:0:1:0:60:4:0.0541:0:1 0/1:8:3:0,3:0,5:0.375:0,0:32.7:1:29.3:1:1:0:56.3:6:0.375:0:1 -17 40500265 . C A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00087;SOR=3.56449;LSEQ=TTACAAGACCAAAGGGTGCC;RSEQ=CTTTATCTCCTGATCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:19:19,0:84,2:0.1792:1,1:26.3:1:30.7:1:1:0:60:38:0.1827:0:1.3 0/1:50:22:20,2:28,0:0.44:1,2:19.3:1:29.6:1:0.18857:0:60:21:0.4375:0:1.1 -17 40500283 . AT A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTTTATCTCCTGATCTC;RSEQ=TTTCCCCATCACCTGTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:2,0:142,3:0.0136:1,0:15:1:32:0:1:0:60:4:0.014:0:0 0/0:66:0:0,0:63,3:0:1,0:23.3:1:30.4:1:1:0:60:132:1:0:0.3 -17 40500343 . A G 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00027;SOR=Inf;LSEQ=CAGCAAGGCATGACATTAAG;RSEQ=GTTCATGTCTCTTGACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:311,76:0:2,0:21.2:1:30:1:1:0:60:192.5:0.9948:0:0.1 0/1:264:9:6,3:203,50:0.0341:2,2:23.4:1:30.2:1:0.39208:2.02353:60:18:0.0347:0:1.1 -17 40501482 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAATGTAGAAATTGGATG;RSEQ=TTGGGGTTGGGGGACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 41091622 . C T 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=AATCTCTTGACCTCGTGATC;RSEQ=GCCTGCCTTGGCGTCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:9.5:1:32.5:1:1:0:60:4:0.5:0:1.5 1/0:3:2:2,0:1,0:0.6667:0,0:21:1:33:0:1:0:60:4:0.6667:0:1 -17 41091721 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.52273;SOR=Inf;LSEQ=CAATTTACTTTAAGGTCATT;RSEQ=TTAGTGTAGGTGGATCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:14,7:0:2,0:32.4:1:30.2:1:1:0:60:42:1:0:0 0/1:35:2:1,1:20,13:0.0571:2,2:20:0:31.5:1:1:1.51907:60:4:0.0571:0:2.5 -17 41091772 . T C 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06537;SOR=0;LSEQ=TTTGACACCCTCTCTAAACA;RSEQ=GAATTTAGTTCAAATCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:1,2:11,14:0.1071:2,2:13:1:20.7:1:1:1.54711:60:2:0.0769:0:1 0/0:40:0:0,0:18,22:0:2,0:27.8:1:28.5:1:1:0:60:12.333:1:0:0.2 -17 41092106 . G C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGCAATCTCGGCTCACAG;RSEQ=AAGCTCCACCTCCCGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45:1:31:1:1:0:60:4:1:0:1 -17 41197274 . C A 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGGGTCTGACTCTCTGC;RSEQ=TTTGTGAACACAGGGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:40:1:29:1:1:0:60:6:0.5:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 41199788 . AT A 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.18023;SOR=4.92098;LSEQ=ACTGGAACTGTCACTTCATC;RSEQ=TTTTTTTGTTTGTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:1:0,1:42,253:0.0034:2,0:35:0:32:0:1:0:60:2:0.0034:0:0 0/1:244:4:1,3:43,197:0.0164:2,2:15.3:1:31:1:0.55106:1.52:60:8:0.0166:0.0082:0.8 -17 41199913 . T C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11251;SOR=3.46023;LSEQ=ATCCTTCCATCTCAGCCTCC;RSEQ=AAGTAGCTGGAACTACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:0,6:0,30:0.1667:1,0:35:1:33.3:1:1:0:60:12:0.1818:0:1 0/1:12:5:0,5:0,7:0.4167:0,0:24.4:1:30.2:1:1:0:60:10:0.4167:0:1 -17 41201364 . T C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64858;SOR=1.4312;LSEQ=GGACAATGGTCTTAAAATAG;RSEQ=AGGGGTATGGATTTTAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:8:0,8:1,68:0.1039:1,0:23.3:1:32.9:1:1:0:60:16:0.1039:0:1 0/1:14:2:0,2:1,11:0.1429:2,0:8.5:1:30.5:1:1:0:60:4:0.1429:0:1 -17 41202897 . GT G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.53846;SOR=0;LSEQ=GAGAAGGGGGACAAGGTATA;RSEQ=TTTTTTTTGCCATAGGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:32,0:0.0588:1,0:19:1:32.3:1:1:0:60:4:0.0588:0.0294:0 0/0:18:0:0,0:18,0:0:1,0:13.8:1:28.6:1:1:0:60:17:1:0:0.2 -17 41203325 . T A 75 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04977;SOR=13.25393;LSEQ=TCCAATGTCCAGAACACTAC;RSEQ=GGATTTCAGAAGATCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:0.2727:0,0:34:1:31.7:1:1:0:60:6:0.2727:0:1 1/1:7:6:0,6:0,1:0.8571:0,0:28.3:1:29.2:1:1:0:60:5:0.8333:0:1 -17 41215825 . C T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.98913;LSEQ=CAAAAACCTTAGGTGTTAAA;RSEQ=GTTAGGTGTAAAAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:104:72,32:285,132:0.1996:2,2:24.6:1:30:1:0.90647:1.04:60:25:0.1961:0:1 0/1:422:140:88,52:185,97:0.3318:2,2:25.5:1:29.3:1:0.59002:1.12667:60:45.667:0.3285:0:1.2 -17 41216021 . G A 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00134;SOR=Inf;LSEQ=GTTGAAAACAAAATCAGGAA;RSEQ=TGCTGTCCTAAGAAGCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:45,241:0:2,0:22.5:1:31.9:1:1:0:60:70.5:1:0:0.1 0/1:185:7:1,6:40,138:0.0378:2,2:20.4:1:29.6:1:1:1.73461:60:14:0.0385:0:1 -17 41219549 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.84564;LSEQ=CCAAAGTGCTGCGATTACAG;RSEQ=CATGCGCCACCGTGCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:1,0:145,38:0.0054:2,0:13:0:25:0:1:0:60:2:0.0055:0:1 0/1:200:2:1,1:153,45:0.01:2,2:38.5:1:28.5:1:0.40799:3.37375:60:4:0.0102:0:2 -17 41219560 . C T 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=41.1943;LSEQ=CGATTACAGGCATGCGCCAC;RSEQ=GTGCCTCGCCTCATGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:169,63:0.0043:2,0:1:0:26:0:0.27468:0:60:2:0.0043:0:1 0/1:238:36:27,9:148,54:0.1513:2,2:20.8:1:30.8:1:1:1.09:60:35:0.1496:0:1.2 -17 41219780 . T C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.96555;LSEQ=CAGCTCAGAATACTAGTTAT;RSEQ=CCACCATGGCATATGTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:18:1,17:26,130:0.1034:2,1:21.9:1:30.6:1:0.31414:3.38345:60:36:0.104:0:1.6 0/1:162:51:9,42:23,88:0.3148:2,2:24.8:1:30.8:1:0.832:1.21822:60:50:0.3145:0:1.7 -17 41219790 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22949;SOR=Inf;LSEQ=TACTAGTTATTCCACCATGG;RSEQ=ATATGTTTACCTATGTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:19,124:0:2,0:24:1:31.5:1:1:0:60:27.6:1:0:0.4 0/1:132:2:1,1:23,107:0.0152:2,2:5:1:27:1:0.33171:4.58:60:4:0.0155:0:1 -17 41219804 . T C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00041;SOR=4.00086;LSEQ=CCATGGCATATGTTTACCTA;RSEQ=GTAGCAATCCTGCACGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:11:0,11:5,87:0.1068:2,0:30.5:1:28.7:1:1:0:60:22:0.1078:0:2.5 0/1:83:27:3,24:3,53:0.3253:2,2:28.4:1:30.1:1:0.3852:2.19:60:54:0.3293:0:2.1 -17 41222723 . T C 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33209;SOR=2.78418;LSEQ=ATAGCTTTTCCACTAATATT;RSEQ=AATAATTATTTTCTCAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:4,1:24,0:0.1724:1,2:21.4:1:33:1:0.17241:0:60:10:0.1786:0:1 0/1:8:3:3,0:5,0:0.375:0,0:27:1:31.7:1:1:0:60:6:0.375:0:1.3 -17 41222975 . C T 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GGGGTCAGGCCAGACACCAC;RSEQ=ATGGACATTCTTTTGTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1423:0:0,0:711,711:0:2,0:24.6:1:31.6:1:1:0:60:128.273:1:0:0.1 0/1:1336:79:38,41:640,615:0.0591:2,2:26.8:1:29.6:1:0.6439:1.12271:60:158:0.0597:0:1.2 -17 41223094 . T C 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.70082;LSEQ=AGTATGAGCAGCAGCTGGAC;RSEQ=CTGGGCAGATTCTGCAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:991:184:89,95:375,431:0.1857:2,2:25.1:1:31:1:0.68257:1.08:60:45:0.1846:0:1.1 0/1:873:244:122,122:289,340:0.2795:2,2:25.4:1:30.1:1:0.29092:1.18:60:33.857:0.2778:0:1.1 -17 41226488 . C A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGAAGACTCCCAGAGCAA;RSEQ=TGTGCATGTACCACCTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:909:0:0,0:347,562:0:2,0:26:1:32:1:1:0:60:81.636:1:0:0.1 0/1:716:35:15,20:275,406:0.0489:2,2:28.3:1:29.7:1:0.86021:1.11:60:70:0.049:0:1.1 -17 41226601 . G C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=2.99294;LSEQ=TGAAAGGACAAATCATACTT;RSEQ=CTGGGCAGCCAAAGCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:29:5,24:13,133:0.1657:2,2:20.3:1:29.7:1:0.18589:2.12:60:13.5:0.1579:0:1.3 0/1:107:40:7,33:10,57:0.3738:2,2:23.8:1:30.5:1:0.78748:1.21:60:19:0.3619:0:1.4 -17 41226675 . A T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00447;SOR=5.13627;LSEQ=CTGGCAAAAAAGAGCCCGCA;RSEQ=GACAGCCTAGAAGTCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:7:0,7:1,36:0.1591:1,0:14.3:1:32:1:1:0:60:14:0.1591:0:1.9 1/0:24:12:1,11:0,12:0.5:0,2:13.1:1:28.1:1:1:0:60:11:0.5:0:1.9 -17 41226736 . GGGGTT G 33 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.47189;LSEQ=TCAGGGTTGACATATAACAT;RSEQ=GGGTTGGTCTGAGGCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:1,14:0.1176:1,0:20.5:1:33:0:1:0:60:4:0.1176:0:0 0/1:6:1:0,1:0,5:0.1667:0,0:42:0:30:0:1:0:60:2:0.2:0:0 -17 41228388 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATCCTAGAGCAATAAAAGT;RSEQ=TATAAATGCCTGTATGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:138,4:0.0139:1,2:9.5:1:30.5:1:0.06847:30.98926:60:4:0.014:0:1 0/0:65:0:0,0:64,1:0:1,0:25.7:1:31.9:1:1:0:60:31.5:1:0:0 -17 41231216 . C CA 78 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0659;SOR=0.16069;LSEQ=AAAAACAAAACAAAACAAAA;RSEQ=AAAAAAAATGAAAGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:6:4,2:366,70:0.0135:2,2:21.2:1:30.3:1:0.25364:2.60676:60:12:0.0137:0.0068:0 0/0:455:1:1,0:349,103:0.0022:2,0:30:0:32:0:1:0:60:2:0.0022:0:0 -17 41231221 . A C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=3.43885;LSEQ=CAAAACAAAACAAAACAAAA;RSEQ=AAATGAAAGGCAGAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:72:59,13:341,79:0.1463:2,2:21.6:1:32:1:1:1.05:60:144:0.1472:0:1.1 0/1:493:183:131,52:235,73:0.3712:2,2:20:1:31:1:0.28402:1.27717:60:90.5:0.3724:0:1.1 -17 41231516 . C T 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.46268;LSEQ=AAAACTGGAAAAGTCTACAA;RSEQ=GTGACCCAGCATGCTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:100:49,51:264,307:0.149:2,2:27:1:30.4:1:0.66413:1.12:57.3:24:0.1457:0:1.2 0/1:680:205:90,115:228,245:0.3015:2,2:28.4:1:29.6:1:0.31559:1.18881:57.8:50.25:0.2973:0:1.2 -17 41231536 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12387;SOR=6.03423;LSEQ=CGTGACCCAGCATGCTGTTG;RSEQ=CATCGCTGTAAACAAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:578:1:0,1:252,325:0.0017:2,0:6:0:12:0:1:0:40:0:0:0:4 0/1:579:6:4,2:249,324:0.0104:2,2:15.5:1:27:1:0.41186:2.60:55.3:12:0.0105:0:1.3 -17 41234343 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23093;SOR=Inf;LSEQ=CATAAAATGTTGGAGCTAGG;RSEQ=CCTTACTCTTCAGAAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:173,34:0:2,0:24.1:1:29.9:1:1:0:60:68:1:0:0.1 0/1:192:2:1,1:152,38:0.0104:2,2:9.5:1:26:1:0.36584:3.96135:60:4:0.0106:0:2 -17 41234470 . A G 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.40028;LSEQ=CGCAGGTCCTCAAGGGCAGA;RSEQ=GAGTCACTTATGATGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:896:147:79,68:405,342:0.1641:2,2:25.3:1:31:1:0.92806:1.0193:60:28.4:0.1617:0:1.1 0/1:821:263:132,131:289,268:0.3203:2,2:26.2:1:30.7:1:0.65422:1.07009:60:130.5:0.3258:0:1.1 -17 41234653 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.90877;LSEQ=TGAGAAGCTTTCCATTAAAT;RSEQ=AAAATATATCATACAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:1,0:22,152:0.0057:2,0:1:0:25:0:0.13143:0:60:2:0.0058:0:1 0/1:184:2:1,1:32,150:0.0109:2,2:10:1:27:1:0.32733:4.63:60:4:0.011:0:1 -17 41242804 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14789;SOR=Inf;LSEQ=GGTAGTATGAGTTCCATCAA;RSEQ=GTGCTTACAGTCTAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:0:1,0:22.8:1:32.2:1:1:0:60:43:1:0:0.1 0/1:28:2:2,0:25,1:0.0714:1,0:5:1:28:1:1:0:60:4:0.0714:0:1 -17 41242913 . C T 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6806;SOR=1.5633;LSEQ=GGGATACATACTACTGAATG;RSEQ=AAAGGACACCACACACACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:2:0,2:246,45:0.0068:2,0:1:0:23.5:1:0.02527:0:60:4:0.0069:0:1 0/1:282:3:1,2:217,62:0.0106:2,2:5:1:24.7:1:0.13011:6.93675:60:6:0.0107:0:1.7 -17 41242938 . GCA G 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.0022;SOR=7.47176;LSEQ=GACACCACACACACGCATGT;RSEQ=CACACACACACGCTTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:2:2,0:339,127:0.0043:2,0:37.5:1:32:1:1:0:60:4:0.0043:0:0 0/1:483:15:11,4:318,150:0.0311:2,2:26.3:1:31.1:1:0.78382:1.30:59.3:30:0.0314:0.0021:0.6 -17 41243108 . C A 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.35594;SOR=3.25208;LSEQ=ACTATAAACGCTGCAACTTG;RSEQ=TGTGTCTTTTTCTTCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:1:1,0:69,234:0.0033:2,0:1:0:25:0:0.23026:0:60:2:0.0033:0:1 0/1:282:3:2,1:67,212:0.0106:2,2:8.3:1:20.7:1:0.1493:6.28:60:2:0.0072:0:2.3 -17 41243190 . T G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00175;SOR=2.94509;LSEQ=ATTCCTTGCTTTGGGACACC;RSEQ=GGATTTGCTTTTATAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:22:15,7:51,48:0.1818:2,2:29:1:30.2:1:0.23623:2.01:60:44:0.1849:0:1.1 0/1:68:27:7,20:15,26:0.3971:2,2:23.7:1:30:1:0.43276:1.63643:60:54:0.3971:0:1 -17 41244000 . T C 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.39097;LSEQ=GACTCCTGCTAAGCTCTCCT;RSEQ=TCTGGACGCTTTTGCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:119:55,64:265,289:0.1766:2,2:24.9:1:31.6:1:0.76251:1.06693:60:118:0.1766:0:1.1 0/1:640:217:115,102:221,202:0.3391:2,2:25.2:1:31:1:0.86757:1.03:60:42.4:0.3354:0:1.1 -17 41244435 . T C 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.58536;LSEQ=TAATATTGCTTGAGCTGGCT;RSEQ=CTTTAAAAACATTTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:773:120:57,63:307,346:0.1552:2,2:24.2:1:30.7:1:0.92116:1.02:60:23:0.1515:0:1.1 0/1:720:232:111,121:218,269:0.3222:2,2:26.5:1:31.1:1:0.47134:1.13:60:115:0.3253:0:1.1 -17 41244880 . C G 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTTTGTTTCTTTAAGGACC;RSEQ=AGAGTGGGCAGAGAATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:56:33,23:278,270:0.0924:2,2:24.8:1:30.9:1:0.26355:1.39:60:112:0.0951:0:1.1 0/0:502:0:0,0:259,241:0:2,0:23.9:1:30.7:1:1:0:60:82.333:0.996:0:0.2 -17 41244936 . G A 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.14945;LSEQ=CATTTCCTGGATTTGAAAAC;RSEQ=GAGCAAATGACTGGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:630:110:54,56:263,254:0.1746:2,2:24.3:1:30.7:1:0.75363:1.07364:60:54:0.1731:0:1.1 0/1:630:197:99,98:237,196:0.3127:2,2:23.5:1:30.6:1:0.30262:1.19662:60:394:0.3137:0:1.1 -17 41245237 . A G 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.46316;LSEQ=ATAATCAGTACCAGGTACCA;RSEQ=TGAAATACTGCTACTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:891:159:77,82:341,389:0.1785:2,2:22.9:1:31.8:1:0.72614:1.07:60:158:0.1793:0:1.1 0/1:826:288:144,144:255,283:0.3487:2,2:25.2:1:31.5:1:0.51095:1.11:60:143:0.3501:0:1.1 -17 41245466 . G A 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.54321;LSEQ=TTCAGCTCTGGGAAAGTATC;RSEQ=CTGTCATGTCTTTTACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1131:172:98,74:514,443:0.1521:2,2:25.1:1:29.7:1:0.45494:1.14:60:85:0.1526:0:2.1 0/1:1117:350:202,148:431,334:0.3133:2,2:23.5:1:29.7:1:0.69611:1.06:60:174:0.3141:0:1.6 -17 41245471 . C T 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33676;SOR=1.11584;LSEQ=CTCTGGGAAAGTATCGCTGT;RSEQ=ATGTCTTTTACTTGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1165:178:100,78:527,460:0.1528:2,2:24.6:1:28.9:1:0.51418:1.12:60:43.5:0.1516:0:2.1 0/1:1158:194:112,82:543,421:0.1675:2,2:23.5:1:28.8:1:0.75115:1.06:60:193:0.1681:0:2 -17 41245586 . C CT 115 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00106;SOR=0.07649;LSEQ=CTGACTGGCATTTGGTTGTA;RSEQ=TTTTTTTTCTTTATCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1021:14:4,10:427,577:0.0137:2,2:23.3:1:30.3:1:0.41605:1.84904:60:28:0.0139:0.0029:0 0/0:942:1:1,0:394,543:0.0011:2,0:28:0:33:0:0.42111:0:60:2:0.0011:0:1 -17 41246481 . T C 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCTGAGCATGGCAGTTTC;RSEQ=GCTTATTCCATTCTTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:844:0:0,0:434,410:0:2,0:25.2:1:30.7:1:1:0:60:83.4:1:0:0.1 0/1:829:42:23,19:403,384:0.0507:2,2:25.1:1:29.3:1:0.75186:1.15:60:84:0.051:0:1 -17 41246902 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10659;SOR=0;LSEQ=AAATATACAAAAATAACAAG;RSEQ=TACTCAAAAACTGAATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:2,1:65,208:0.0109:2,2:21.7:1:25:1:0.14714:6.35:60:2:0.0074:0:1.3 0/0:305:0:0,0:78,227:0:2,0:25.1:1:30.8:1:1:0:60:75.25:1:0:0.1 -17 41246925 . TA T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.10001;SOR=0;LSEQ=CTCAAAAACTGAATTGTCAT;RSEQ=AAAAAATACATACTTCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:3:1,2:21,139:0.0184:2,2:26:1:29:1:0.35459:3.27:60:6:0.0185:0:0.3 0/0:187:0:0,0:29,158:0:2,0:22.8:1:30.1:1:1:0:60:374:1:0:0.1 -17 41247604 . A C 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=1.19167;LSEQ=GTGAGACCCCATCTCAAAAA;RSEQ=AAACAAACAAACAAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:17,1:0.1429:1,0:25.3:1:31.3:1:1:0:60:6:0.15:0:1.7 0/1:6:1:1,0:5,0:0.1667:0,0:11:0:32:0:1:0:60:2:0.1667:0:2 -17 41247620 . C CA 61 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.55614;SOR=0;LSEQ=AAAAAAAACAAACAAACAAA;RSEQ=AAAAAAAAAAACGAAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:4,0:25,1:0.129:1,0:33.5:1:30.8:1:1:0:60:8:0.1379:0:0.5 0/0:10:0:0,0:9,0:0:0,0:18.3:1:30.8:1:1:0:57.8:18:1:0:1.6 -17 41248164 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11491;SOR=7.79145;LSEQ=AGCACTTTGGGAGGCTGAGG;RSEQ=GGGTGGACCACTTGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:0,18:0.1:1,0:8.5:1:32:1:1:0:60:4:0.1053:0:1 1/0:4:2:0,2:0,2:0.5:0,0:35:1:31.5:1:1:0:60:4:0.6667:0:1 -17 41249094 . A G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95446;LSEQ=CCGGATGATGAAAAAAATCT;RSEQ=TACACCAAATCCCAAGTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:13:13,0:31,0:0.2955:1,1:25.9:1:31.8:1:1:0:60:26:0.3023:0:1 0/1:28:8:8,0:20,0:0.2857:1,0:31.3:1:31.9:1:1:0:60:16:0.2963:0:1 -17 41249363 . TA T 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16208;SOR=1.39536;LSEQ=GTTTTCTTAATTAAAAGGGT;RSEQ=AAAAAATGTACTTGTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:42:5,37:31,135:0.2019:2,2:25.1:1:30.6:1:0.36705:1.69538:60:84:0.2019:0.0096:0.1 0/1:203:53:8,45:35,115:0.2611:2,2:26:1:30.5:1:0.24429:1.70777:60:106:0.2637:0.0049:0.1 -17 41250836 . CT C 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCAGCCAAGATTCAGCT;RSEQ=TTTTTTTTTTTTTTGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:29.2:1:1:0:59:4:1:0.5:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 41250905 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCAATGGTGCGATCTTG;RSEQ=CTCACTGCAACCTCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:28.5:1:1:0:59:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 41251646 . T A 114 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0227;SOR=2.62708;LSEQ=GGAACTGCGTCTTTTACATT;RSEQ=TTTATAACTCACCATAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:17:17,0:74,1:0.1848:1,1:23.3:1:29.5:1:1:0:60:34:0.1848:0:1 0/1:48:18:16,2:30,0:0.375:1,2:19.2:1:27.4:1:0.13564:0:60:17:0.3617:0:1.3 -17 41251931 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21484;LSEQ=TAAAGAACAGTCAAGCAATT;RSEQ=TTGGCCAGTTCTGTGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:109:15,94:48,192:0.3123:2,2:26.7:1:31.2:1:0.17867:1.56476:60:218:0.3141:0:1 0/1:248:22:5,17:47,179:0.0887:2,2:24.3:1:29.5:1:0.78778:1.12:60:44:0.0902:0:1.2 -17 41256059 . A G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.90258;LSEQ=GCTTCTAGCCTGGGCCACAG;RSEQ=GCAAGACTCCATCTCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:0,2:148,9:0.0126:2,0:18:1:24:1:0.00438:0:60:1:0.0065:0:2 0/1:176:2:1,1:147,27:0.0114:2,2:16:1:30.5:1:0.29364:5.36459:60:4:0.0116:0:1 -17 41256065 . A G 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67354;SOR=0.60889;LSEQ=AGCCTGGGCCACAGAGCAAG;RSEQ=CTCCATCTCAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:3:2,1:168,19:0.0158:2,2:6.7:1:26.7:1:0.28506:4.3638:56.7:2:0.0109:0:1 0/0:207:2:1,1:167,37:0.0097:2,2:21:1:23.5:1:0.33564:4.46706:60:1:0.005:0:1.5 -17 41256074 . CA C 126 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.39261;SOR=0.73593;LSEQ=CACAGAGCAAGACTCCATCT;RSEQ=AAAAAAAAAAAGAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:20:16,4:180,36:0.0806:2,2:20.9:1:29.3:1:0.75485:1.24875:59.8:9:0.0738:0.0323:0.5 0/1:264:16:14,2:176,54:0.0606:2,2:28.3:1:29.9:1:0.53651:2.14:60:32:0.0611:0:0.4 -17 41256075 . AAAAAAAAAAAAG A 191 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=3.80436;LSEQ=ACAGAGCAAGACTCCATCTC;RSEQ=AAAAAAAAAAGAAAAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:25:20,5:178,36:0.1004:2,2:28.6:1:30.5:1:0.77859:1.23495:58.8:50:0.1055:0:0.6 0/1:278:83:59,24:141,39:0.2986:2,2:27.2:1:30:1:0.21577:1.46847:59.7:82:0.313:0.0144:0.3 -17 41256086 . AGAAAAAAAAAAGAAAAGAAG GAA 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.12429;SOR=Inf;LSEQ=CTCCATCTCAAAAAAAAAAA;RSEQ=AAGAAGAAGAAGAAGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:220,51:0:2,0:18.5:1:30.2:1:1:0:59.6:66.75:1:0:0.8 0/1:320:4:2,2:175,53:0.0125:2,2:26.8:1:29.2:1:0.23905:3.28073:60:8:0.0172:0:0 -17 41256087 . G GA 120 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.17202;SOR=0.56244;LSEQ=TCCATCTCAAAAAAAAAAAA;RSEQ=AAAAAAAAAAGAAAAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:17:14,3:213,59:0.0503:2,2:20.7:1:29.4:1:1:1.29:59.4:34:0.0749:0:1.2 0/1:346:10:8,2:168,58:0.0289:2,2:24.9:1:27.9:1:1:1.38:59.5:20:0.0532:0:1.3 -17 41256089 . AAAAAAAAAGAAAAG A 120 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=3;SSF=0.14851;SOR=1.93816;LSEQ=CATCTCAAAAAAAAAAAAGA;RSEQ=AAGAAGAAGAAGAAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:8:5,3:294,92:0.0203:2,2:35.4:1:30.8:1:0.40598:1.91364:60:16:0.0206:0:0.1 0/1:414:16:12,4:275,119:0.0386:2,2:30.9:1:30.2:1:0.78586:1.30:60:32:0.0392:0:0.4 -17 41256100 . AAAG A 216 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0;SOR=2.32377;LSEQ=AAAAAAAGAAAAAAAAAAGA;RSEQ=AAGAAGAAGAAGAAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:78:52,26:309,111:0.1538:2,2:21.8:1:30.2:1:0.21605:1.39093:58.9:77:0.1571:0.0316:0.4 0/1:498:148:94,54:222,107:0.2972:2,2:25.8:1:30:1:0.40418:1.19143:59.5:296:0.3142:0.012:0.3 -17 41256318 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.17281;SOR=Inf;LSEQ=ACATTATGTTTGCAGTTAGA;RSEQ=AAAAATGTATGAATTATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:60,218:0:2,0:23.3:1:31.4:1:1:0:60:277:1:0:0.1 0/1:199:2:1,1:51,146:0.0101:2,2:38.5:1:28:1:0.45531:2.84:60:4:0.0101:0:1 -17 41256860 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11793;SOR=5.2101;LSEQ=CATGGACAGCACTTGAGTGT;RSEQ=ATTCTTGGGATATTCAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:1:0,1:289,165:0.0022:2,0:1:0:25:0:0.36484:0:60:2:0.0022:0:1 0/1:440:5:1,4:270,164:0.0114:2,2:9.4:1:24.6:1:0.07325:6.55841:60:10:0.0115:0:1 -17 41257134 . T C 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2089;SOR=2.91551;LSEQ=CATCTGTATAAACCGTGTGA;RSEQ=GGCAGTGATTTAGTAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:0,4:0,27:0.129:1,0:32.5:1:28:1:1:0:60:8:0.129:0:1 0/1:13:4:0,4:1,8:0.3077:2,0:20.3:1:30.3:1:1:0:60:8:0.3077:0:1 -17 41267608 . G C 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03751;SOR=0;LSEQ=ACTATATACTCTCTGAGAAA;RSEQ=AATGAAATGGAGTTGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:6:6,0:152,2:0.0373:1,0:18.5:1:32:1:1:0:60:12:0.0387:0:1 0/0:124:0:0,0:121,3:0:1,0:25.1:1:31.8:1:1:0:60:30:1:0:0.1 -17 41267807 . AG A 96 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06564;SOR=3.06727;LSEQ=CAACTCCAGACTAGCAGGGT;RSEQ=GGGGGGAGAAAAAGAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:560:4:1,3:164,392:0.0071:2,2:18.3:1:30.9:1:1:1.2546:60:8:0.0073:0.0036:0.3 0/1:509:11:6,5:171,326:0.0216:2,2:7.4:1:27.9:1:0.20338:2.28:60:22:0.0217:0.0157:0.5 -17 41268206 . A C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCTTTTGAATTCCTTCCTAG;RSEQ=ACTTTTTTTTGTTTACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:47:0:31:0:1:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:1:0,2:25:0:33:1:1:0:60:4:1:0:1 -17 41268208 . C CTT 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TTTTGAATTCCTTCCTAGAA;RSEQ=TTTTTTTTGTTTACTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,2:0:0,0:30:1:33.5:1:1:0:60:4:0.6667:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:32.3:1:1:0:60:4:1:0:1 -17 41276152 . C CAT 47 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.62365;SOR=0.33515;LSEQ=ACTTTAACACATTAGAAAAA;RSEQ=ATATATATATATCTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:0,3:62,209:0.0109:2,0:42.3:1:30.2:1:1:0:60:6:0.011:0:0 0/0:272:1:0,1:72,196:0.0037:2,0:29:0:31:0:1:0:60:2:0.0037:0:0 -17 41276247 . A G 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17908;SOR=2.28067;LSEQ=GATTTGGAAGGTTTTAGAAT;RSEQ=ATACAAACCAAAGAACTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:9:0,9:0,34:0.2093:1,0:19.2:1:31.8:1:1:0:60:18:0.2143:0:1 0/1:29:11:1,10:0,18:0.3793:1,2:23.3:1:29.5:1:0.37931:0:60:10:0.3571:0:1.2 -17 41276348 . T C 48 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01786;SOR=Inf;LSEQ=TTCTGAATTTTTTCACATAT;RSEQ=GCTGCCAACCCCTTGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:17.2:1:29.2:1:1:0:60:10:1:0:0.2 1/1:3:3:0,3:0,0:1:0,0:32.3:1:30.3:1:1:0:60:6:1:0:1 -17 41412250 . A C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=4.91975;LSEQ=TACATACAAGACAAAGGGGG;RSEQ=AGAGTAAGGAGGGTGAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:12:6,6:63,34:0.1091:2,2:17.6:1:31.9:1:0.35091:1.84199:60:24:0.1154:0:1.2 0/1:82:31:18,13:29,21:0.378:2,2:16:1:31.5:1:1:1.00:60:62:0.3924:0:1.2 -17 41412258 . G T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26372;SOR=0;LSEQ=AGACAAAGGGGGAAGAGTAA;RSEQ=GAGGGTGAGACGTCCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:3:1,2:78,49:0.0231:2,2:17.3:1:21.7:1:0.56079:3.15478:60:2:0.0156:0:1.3 0/0:96:0:0,0:59,37:0:2,0:21.8:1:30.6:1:1:0:60:95:1:0:0.5 -17 41412300 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18663;SOR=Inf;LSEQ=TTGATAAGCTCAAGCAAGTC;RSEQ=CATGATCATGGGACAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:79,86:0:2,0:28.4:1:29.8:1:1:0:60:81.5:1:0:0.3 0/1:126:2:1,1:62,62:0.0159:2,2:35:1:29:1:1:1:60:4:0.0163:0:1.5 -17 41412303 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.506;SOR=0;LSEQ=ATAAGCTCAAGCAAGTCACA;RSEQ=GATCATGGGACAGGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:75,85:0.0123:2,2:13:0:32.5:1:1:1.13:60:4:0.0125:0:1 0/0:127:0:0,0:62,65:0:2,0:27.7:1:29.4:1:1:0:60:30.75:1:0:0.4 -17 41412324 . T G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5103;SOR=0;LSEQ=GATCATGGGACAGGGGGCCC;RSEQ=TCCCTTTTAGGTAGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:53,84:0.0143:2,2:19:1:29:1:1:1.58:60:4:0.0148:0:1 0/0:102:0:0,0:44,58:0:2,0:24.8:1:29.9:1:1:0:59.9:101:1:0:0.2 -17 42083831 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1682;SOR=Inf;LSEQ=GGGTCAGAGAAAAGAGAGGT;RSEQ=CGTGGGGGTAGGGGGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:34,30:0:2,0:24.5:1:30.4:1:1:0:60:20.333:1:0:1.1 0/1:45:2:1,1:21,22:0.0444:2,2:22:0:31:1:1:1.05:60:4:0.0444:0:2.5 -17 42083840 . T C 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.50553;SOR=Inf;LSEQ=AAAAGAGAGGTCCGTGGGGG;RSEQ=AGGGGGGCAGTCCGTGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:68:36,32:0,0:0.9714:0,2:28.1:1:32:1:1:0:60:136:0.9714:0:1.2 1/1:53:53:26,27:0,0:1:0,2:27.3:1:32.1:1:1:0:60:106:1:0:1.3 -17 42083878 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49902;SOR=0;LSEQ=CGGCTGTGGGCCAGGCTCAC;RSEQ=CGCTGACTCCGGACACAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:33,38:0.0274:2,2:46.5:1:30.5:1:1:1.15:60:4:0.0278:0:2.5 0/0:63:0:0,0:28,35:0:2,0:24.8:1:30.6:1:1:0:60:126:1:0:1 -17 42084097 . C G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGAGGGCGGTGGGCGGGC;RSEQ=GGGGACTGGGTCCCGGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:29:1:31.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:0,2:0:0,0:11:1:31.5:1:1:0:60:4:1:0:0.5 -17 42084276 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCAGTGTACTGGAAGGG;RSEQ=ACTCCGAAGGAATTAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21:1:30:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 42084377 . G A 42 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAGGGAGGTGTTCGACC;RSEQ=GGAGAGATGGGCGGGGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:4:0:32:0:1:0:60:2:1:0:1 1/1:3:3:2,1:0,0:1:0,2:19.7:1:26.7:1:1:0:60:6:1:0:1.3 -17 43341917 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13505;SOR=Inf;LSEQ=GGCTGGCAGATCCCTGGGAA;RSEQ=GGCTGAGCCTGTGTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:295,26:0:2,0:23.8:1:31.6:1:1:0:60:52.5:1:0:0.1 0/1:187:2:1,1:162,23:0.0107:2,2:9.5:1:27.5:1:0.24081:6.91631:60:4:0.0109:0:1 -17 43342141 . G C 338 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGGCTGCCCGTCTTTGGT;RSEQ=ACCAAGCTGAAGGCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1655:1655:794,861:0,0:1:0,2:25.5:1:31.7:1:1:0:60:90.944:1:0:1.2 1/0:1397:866:420,446:253,274:0.6199:2,2:25.4:1:31.3:1:0.86842:1.02:60:77.727:0.6191:0:1.2 -17 43342306 . C A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=4.0501;LSEQ=TTCCACGGGACTCAGAGAAT;RSEQ=CCACCCGGCTCAAGTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:20:3,17:24,130:0.1149:2,2:26.2:1:29.6:1:1:1.04591:60:40:0.1176:0:1 0/1:78:27:0,27:7,44:0.3462:2,1:20.9:1:30.6:1:0.08883:0:60:54:0.3462:0:1.1 -17 43342400 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07042;SOR=Inf;LSEQ=TGCTTTGAGGTCCTGGGGGA;RSEQ=GTTGAAGGCCAATTCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:165,44:0:2,0:24.9:1:31.7:1:1:0:60:40.8:1:0:0.1 0/1:76:2:2,0:66,8:0.0263:2,0:20:0:32:0:1:0:60:4:0.0263:0:1 -17 43342993 . C CG 79 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49091;SOR=0.32733;LSEQ=TTTTGTATTTTTAGTAGAGA;RSEQ=GGGGTTTCACCATGTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:2,5:0,2:0.7778:0,2:22.3:1:28.3:1:1:0:47.1:6:0.75:0.1111:0.1 1/0:2:1:0,1:0,1:0.5:0,0:17:0:32:0:1:0:53:2:0.5:0:0 -17 43343847 . G A 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCCCTCAATGGCTGTCTA;RSEQ=CTCCAGGCAGATCAGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:845:0:0,0:575,268:0:2,0:22.8:1:31.9:1:1:0:60:59.214:0.9976:0:0.1 0/1:681:36:23,13:425,217:0.0529:2,2:18.6:1:30:1:0.85668:1.10682:60:72:0.0539:0:1.4 -17 43343939 . C T 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=36.85726;LSEQ=GGGTGTCGGTGGGCCGCCCC;RSEQ=GGGCCAGCACCATGTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1820:4:1,3:947,863:0.0022:2,2:17:1:30.3:1:0.35353:3.29006:60:8:0.0022:0:1 0/1:1491:112:60,52:707,666:0.0751:2,2:23.9:1:30.1:1:0.69499:1.09:60:55:0.0747:0:1.3 -17 43344073 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=8.46695;LSEQ=AACAACAGGATTGGGTACGG;RSEQ=CTCAGGGCCCTGGGCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1358:118:46,72:532,708:0.0869:2,2:28.5:1:30:1:0.43677:1.17598:60:58:0.0872:0:1.1 0/1:1084:484:197,287:261,339:0.4465:2,2:27:1:29.1:1:0.3866:1.12153:60:95.8:0.4502:0:1.2 -17 43344420 . A C 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.31007;SOR=4.3608;LSEQ=GCCAGGGCCGGGAAAACCAC;RSEQ=CCCCTGGAGCCATGGCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:0,1:260,47:0.0032:2,0:46:0:11:0:0.15584:0:60:0:0:0:1 0/1:215:3:1,2:165,46:0.014:2,2:22.3:1:23.3:1:0.127:7.08677:60:2:0.0097:0:1 -17 43344458 . C A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCGGGGCCACAACCGACTCA;RSEQ=CTTCTCACTGTCATCCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:578:28:19,9:368,182:0.0484:2,2:24.8:1:29.4:1:1:1.04:60:56:0.0492:0:1.2 0/0:498:0:0,0:324,173:0:2,0:22.7:1:31:1:1:0:60:123.25:0.998:0:0.1 -17 43344637 . G A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36575;SOR=2.55667;LSEQ=TGTTTTCAGGGGTTCTTCCT;RSEQ=CACAGTCGGTAGAAGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:2:2,0:194,257:0.0044:2,0:14.5:1:25.5:1:0.18666:0:60:4:0.0045:0:1 0/1:269:3:1,2:74,192:0.0112:2,2:14.3:1:31.3:1:1:1.30:60:6:0.0114:0:1.3 -17 43344809 . T C 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGTTCCTGCTCCGGGACGG;RSEQ=TGCTTTCCGCTCTGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1789:0:0,0:975,813:0:2,0:24.3:1:30:1:1:0:60:161.545:1:0:0.1 0/1:1391:68:32,36:712,610:0.0489:2,2:20.4:1:31.1:1:0.31874:1.31285:60:67:0.0484:0:1.1 -17 43347336 . C G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCCTGAGACTGGCATGG;RSEQ=TAGGGGGTGCAGTCTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29:1:32:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 43347610 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01996;LSEQ=GCGCTGCCTCTGGGTCCAGG;RSEQ=GTGGCACTGTCGCAATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:109:109,0:17,0:0.8583:1,1:26.5:1:30:1:1:0:60:108:0.864:0:1.1 0/1:48:5:5,0:42,1:0.1042:1,0:27.6:1:29.6:1:1:0:60:10:0.1042:0:1.2 -17 43347965 . T A 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=30.71704;LSEQ=ACAACAGGTGAGGCCTGCCT;RSEQ=CCCTCATTTCCTGATACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:951:2:2,0:321,628:0.0021:2,0:1:0:26:1:0.11512:0:60:4:0.0022:0:1 0/1:805:49:19,30:287,469:0.0609:2,2:19.1:1:28.6:1:1:1.03:60:98:0.0623:0:1.3 -17 43348034 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14184;SOR=Inf;LSEQ=CCGGCCCCTGTTCCCGCTGT;RSEQ=CTGGGGTCTACCACAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:19,245:0:2,0:27.2:1:32:1:1:0:60:43:1:0:0.1 0/1:160:2:1,1:6,152:0.0125:1,2:8:1:26.5:1:0.08585:23.53:60:4:0.0129:0:1 -17 43348887 . G A 101 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCCAGCTAATTTTTAT;RSEQ=TTTTTGTAGAGATGGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:25.4:1:32.1:1:1:0:58.3:18:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 43350514 . G A 78 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGTGCTTCCAGCCAACC;RSEQ=TGCTCAGAGGCGCAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:17.8:1:30.2:1:1:0:60:12:0.8571:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 43350666 . A G 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=11.57319;LSEQ=CCCTTCTCTTCCCTGTGTAC;RSEQ=GGAGCATCGACAATGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:7:7,0:39,0:0.1522:1,0:23.6:1:27.9:1:1:0:60:6:0.1364:0:1.3 1/0:16:11:9,2:5,0:0.6875:0,2:18.2:1:28.5:1:1:0:60:22:0.6875:0:1.1 -17 43350765 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.15682;SOR=Inf;LSEQ=GGTTGCGGGGCTTAAACACA;RSEQ=AGGTGGACCTAAGTGTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:250,7:0:1,0:25.5:1:32.1:1:1:0:60:84.667:1:0:0.1 0/1:169:2:1,1:163,4:0.0118:1,2:18:1:27:1:0.05847:36.55401:60:4:0.012:0:1 -17 43350767 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06249;SOR=Inf;LSEQ=TTGCGGGGCTTAAACACACA;RSEQ=GTGGACCTAAGTGTTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:259,7:0:1,0:25.4:1:32.2:1:1:0:60:43.333:1:0:0.1 0/1:176:3:3,0:168,5:0.017:1,0:19.7:1:31.3:1:1:0:60:6:0.0179:0:1 -17 43351127 . G C 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.62156;LSEQ=TTAGTTTCATTAATCGTGGA;RSEQ=GAAGGGAGGAGGGTATCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1618:165:70,95:629,822:0.102:2,2:26.8:1:30.5:1:0.8684:1.03848:60:54:0.1015:0:1.1 0/1:1355:395:170,225:439,519:0.2915:2,2:27.4:1:30.3:1:0.36754:1.11942:60:78:0.2921:0:1.2 -17 43351324 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTACAGTGCTTGGCTAA;RSEQ=GGGTTGGAGAACATCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:2,0:138,57:0.0101:2,0:11.5:1:30:1:1:0:60:4:0.0104:0:1 0/0:63:0:0,0:40,23:0:2,0:22.2:1:31.2:1:1:0:60:62:1:0:0.1 -17 43352041 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10011;SOR=Inf;LSEQ=CATCCTGTCAGCACCCTAGT;RSEQ=CTCCACACACAGAGGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:24,299:0:2,0:25:1:32.1:1:1:0:60:79.75:1:0:0.9 0/1:150:2:1,1:13,135:0.0133:2,2:19:1:27:1:0.17852:10.04:60:4:0.0133:0:1.5 -17 43352049 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=0.00891;LSEQ=CAGCACCCTAGTGCTCCACA;RSEQ=ACAGAGGCTGCTGCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:267:14,253:1,28:0.899:1,2:24.4:1:28.2:1:1:1.55:60:52.4:0.8973:0:1.1 0/1:125:9:0,9:7,109:0.072:2,0:15.3:1:26.7:1:1:0:60:8:0.0656:0:1.1 -17 43352642 . T C 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCGGGAGATCAAGACCATC;RSEQ=TGGCCAACATGGCGAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:30:1:34:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 43353884 . CT C 31 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACTTAGACTGACTTAGAC;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:0:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 43362033 . G A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCCTTCCAGTTCCAGCC;RSEQ=ACCTCAGGTGGCTAGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:104,3:0.0183:1,0:14:1:25.5:1:1:0:60:4:0.0187:0:1 0/0:42:0:0,0:40,2:0:1,0:23.1:1:28.8:1:1:0:60:41:1:0:0.1 -17 43362093 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55558;SOR=0;LSEQ=TCAGACCCACGGCCACCCTG;RSEQ=GACTGTCCTGGACAGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:1,2:245,21:0.0112:2,2:6.3:1:25:1:0.01995:22.64625:60:2:0.0075:0:3 0/0:149:0:0,0:140,9:0:2,0:24.4:1:31.8:1:1:0:60:48.667:1:0:0.2 -17 43362475 . C T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=GCGAAGGCAGGGATCTGAGC;RSEQ=GGGCAGCACCAGAGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:4,111:0:1,0:21.3:1:29.8:1:1:0:60:27.75:1:0:0.1 0/1:41:6:2,4:3,32:0.1463:2,2:26.8:1:30:1:0.14759:5.02:60:12:0.1538:0:1.2 -17 43362479 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGGCAGGGATCTGAGCCGGG;RSEQ=AGCACCAGAGAGGGGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:0,2:4,99:0.019:1,0:6:1:28.5:1:1:0:60:4:0.0194:0:1 0/0:39:0:0,0:5,34:0:2,0:25.8:1:31.5:1:1:0:60:18.5:1:0:0.4 -17 43364293 . C CG 335 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.85061;SOR=1.05321;LSEQ=AGTTCTGATCGAGGCAGAGC;RSEQ=GCCGTAGGCCCTCGCCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2218:2150:1030,1120:24,33:0.9693:2,2:23.1:1:30.3:1:0.42193:1.26:59.9:62.235:0.9715:0.1898:0.2 1/1:1715:1665:812,853:19,24:0.9708:2,2:23.6:1:29.8:1:0.64361:1.20:60:103.063:0.9752:0.1866:0.2 -17 43364737 . C A 194 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=134.50457;LSEQ=GACTCTCGGACTGGCTGTCA;RSEQ=AAAAGGGACAGATTTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1466:1:1,0:602,863:7e-04:2,0:1:0:26:0:0.41132:0:60:2:7e-04:0:1 0/1:1188:100:45,55:477,611:0.0842:2,2:24.8:1:29.3:1:0.8339:1.05:60:49:0.0838:0:1.1 -17 43364865 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TCCTTGTGTGAATGCGGCAA;RSEQ=GTTTCTAAATCCCAAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:0,183:0:1,0:23.6:1:31.1:1:1:0:60:90.5:1:0:0.1 0/1:85:8:0,8:1,76:0.0941:1,0:31.9:1:31:1:1:0:60:16:0.0964:0:1.6 -17 43364882 . G GA 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00977;SOR=Inf;LSEQ=CAAGGTTTCTAAATCCCAAG;RSEQ=AACCTGTTTTCTCACTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:0,145:0:1,0:23.2:1:30.8:1:1:0:60:28:1:0:0.1 0/1:68:4:0,4:1,63:0.0588:1,0:35.5:1:30.3:1:1:0:60:8:0.0588:0:0 -17 43364914 . A G 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCACTTATCTCACTTATAAA;RSEQ=TGGGTTTGGTATTTTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:0,88:0:1,0:26.5:1:31.1:1:1:0:60:87:1:0:0.1 0/1:35:9:1,8:1,25:0.2571:1,2:19:1:32.3:1:0.45378:3.00:60:18:0.2571:0:1.4 -17 43365089 . C T 62 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAGAGTCAGGGGAGCAGACA;RSEQ=GGTTCGCTCACTGCTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:33:1:31.3:1:1:0:60:8:0.8:0:2.8 0/0:1:0:0,0:0,1:0:0,0:40:0:27:0:1:0:60:2:1:0:0 -17 43365441 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAGCAGATCATGGCCTC;RSEQ=GCCACCCTCCCTTGGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 43366493 . G T 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01684;LSEQ=CCAGGAGCTGAACCACAGGT;RSEQ=CTGAGGGAGGGAGCCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:3,0:238,3:0.0123:1,0:22.7:1:32.3:1:1:0:60:6:0.0127:0:1.3 0/1:160:2:1,1:156,2:0.0125:1,2:23:1:29:1:0.03726:63.88812:60:4:0.0127:0:1 -17 43367653 . T C 184 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00015;SOR=0;LSEQ=TCCAGTCACGATGGGCACAG;RSEQ=CTCCCCTTGCCACATCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:57:57,0:0,0:1:0,1:26.7:1:31.6:1:1:0:60:18:1:0:1 1/0:14:9:9,0:4,1:0.6429:2,0:18.1:1:29.3:1:0.35714:0:60:8:0.6154:0:1.1 -17 43368662 . CTG C 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=12.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCTAGTAGGAGGTAGATAT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:38.5:1:30.5:1:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 43369893 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGAGATTGCACCATTGCA;RSEQ=TCTCCAGCCTGAGTGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:1:32:1:1:0:60:4:1:0:1 -17 43369934 . G GA 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGACCCTGTCTCTAAAA;RSEQ=AAAAAAAAAGTCTAAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:28:1:1:0:60:4:1:0:1 -17 45356536 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24824;SOR=Inf;LSEQ=CACCCTCCCAGGAGAGGGAG;RSEQ=TAATTCAGCCAGCTCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:119,84:0:2,0:22.9:1:31.3:1:1:0:60:66.667:1:0:0.4 0/1:207:3:1,2:125,79:0.0145:2,2:23.7:1:28.3:1:0.56218:3.14661:60:6:0.0147:0:1 -17 45356545 . C T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35912;SOR=0.31196;LSEQ=AGGAGAGGGAGGTAATTCAG;RSEQ=CAGCTCGCAGGGCGCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:1,2:122,89:0.014:2,2:19.7:1:29:1:0.57607:2.72874:60:6:0.0144:0:2 0/0:227:1:0,1:134,92:0.0044:2,0:1:0:25:0:0.40969:0:60:2:0.0044:0:2 -17 45356559 . G T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10041;SOR=0;LSEQ=ATTCAGCCAGCTCGCAGGGC;RSEQ=CTGGCTGGAACCTCCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:1,2:124,105:0.0129:2,2:16.3:1:27:1:0.59635:2.35339:60:6:0.0132:0:1 0/0:266:0:0,0:148,117:0:2,0:25.6:1:30.3:1:1:0:60:131.5:0.9962:0:0.6 -17 45356561 . T C 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00466;SOR=1.68925;LSEQ=TCAGCCAGCTCGCAGGGCGC;RSEQ=GGCTGGAACCTCCCACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:76:40,36:90,72:0.3193:2,2:26.3:1:29.6:1:0.67807:1.12444:60:37:0.3162:0:1.2 0/1:269:119:70,49:83,67:0.4424:2,2:27:1:28.9:1:0.62056:1.15:60:38.667:0.4377:0:1.2 -17 45356654 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49959;SOR=Inf;LSEQ=ATCCGGTTTCCCTGGGAACT;RSEQ=AAACTTTAATATCCACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:49,127:0:2,0:25.8:1:31.3:1:1:0:60:175:1:0:0.1 0/1:192:2:1,1:66,124:0.0104:2,2:18:1:26:1:1:1.87:60:4:0.0106:0:1.5 -17 45356782 . T C 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63325;SOR=0.41977;LSEQ=GTATGTTGAGGTCACTGCCT;RSEQ=GGTGCTCTTCTGGAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:0.5:0,0:23.8:1:30.7:1:1:0:60:12:0.5:0:1 0/1:7:2:1,1:0,5:0.2857:0,2:9:1:32.5:1:0.28571:0:60:4:0.2857:0:1 -17 46005528 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57291;SOR=2.80016;LSEQ=TCGAGGAGCAAAGTGAGCCC;RSEQ=TACCCCCCACCCCGATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:1:1,0:68,39:0.0093:2,0:41:0:17:0:1:0:60:0:0:0:8 0/1:78:2:1,1:45,31:0.0256:2,2:20.5:1:28:1:1:1.44451:60:4:0.026:0:1 -17 46005574 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4995;SOR=0;LSEQ=CAACACTGCCGGAGTCGCGT;RSEQ=ATGCCATGCCCCCTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:61,77:0.0143:2,2:37.5:1:30:0:1:1.26:60:4:0.0147:0:1.5 0/0:126:0:0,0:61,65:0:2,0:28.9:1:30.6:1:1:0:60:24.2:1:0:0.4 -17 46005606 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50027;SOR=0;LSEQ=CCTCTCCTGCACCTCCCTGG;RSEQ=CCTGCCGGCCACTGTGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:33,74:0.0183:2,2:19:1:28.5:1:0.52854:2.22:60:4:0.0189:0:1 0/0:94:0:0,0:41,52:0:2,0:22.5:1:29.8:1:1:0:60:10.625:1:0:0.3 -17 46005613 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50464;SOR=0;LSEQ=TGCACCTCCCTGGCCCTGCC;RSEQ=GCCACTGTGGACGCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:26,68:0.0208:2,2:34.5:1:32:0:0.48553:2.59:60:4:0.0211:0:1 0/0:75:0:0,0:31,44:0:2,0:1:0:16:0:1:0:60:0:0:0:1 -17 46801231 . G C 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01686;SOR=0;LSEQ=GAAATTATTTCGGGCCTGGA;RSEQ=CCCGCGTAGACGCGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:10:0,10:3,191:0.049:1,0:28.6:1:29.7:1:1:0:60:9:0.0446:0:1 0/0:109:0:0,0:3,106:0:1,0:26.1:1:32.2:1:1:0:60:35.333:1:0:0 -17 46802314 . G T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29605;SOR=0;LSEQ=CCTTTTTCCTCTCTCCAAGG;RSEQ=GTCACCCCGCACCATGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:4:4,0:52,0:0.0714:1,0:12.8:1:30:1:1:0:60:8:0.0727:0:1 0/0:28:0:0,0:27,1:0:1,0:23:1:30.2:1:1:0:60:27:1:0:0.4 -17 46802329 . T C 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CAAGGGGTCACCCCGCACCA;RSEQ=GCCGCTCCCCCTCATCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:77,0:0:1,0:22.1:1:31.2:1:1:0:60:76:1:0:0.2 0/1:38:9:9,0:28,1:0.2368:1,0:22.6:1:30.8:1:1:0:60:18:0.2432:0:1 -17 46802412 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05124;SOR=Inf;LSEQ=GTTCCGAAGTCGGCGAGGGA;RSEQ=GGGGTTTACTTGCCCGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:310,19:0:2,0:20.6:1:32:1:1:0:60:46:0.9969:0:0.1 0/1:196:3:2,1:171,19:0.0153:2,2:6.7:1:27.7:1:0.28108:4.44137:60:6:0.0155:0:1 -17 46804582 . G C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACCCTGGCTTCCGGCTT;RSEQ=TTCTCTCACCACCGCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:1,47:0.04:1,2:44:0:32:1:0.07918:33.61:60:4:0.0417:0:1 0/0:11:0:0,0:3,8:0:2,0:15.2:1:30.9:1:1:0:60:22:1:0:0.2 -17 46804808 . T TAC 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCACTCCCAATACATGCGCA;RSEQ=ACACACACACACACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:43:1:30.8:1:1:1.41418:60:4:0.3333:0:0 0/0:1:0:0,0:1,0:0:0,0:13:0:16:0:1:0:60:0:0:0:1 -17 46805221 . C T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCAGACCTCCTTCAGAGT;RSEQ=CTAATAACCAAGGGAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:240,4:0:1,0:24:1:31.6:1:1:0:60:80.333:1:0:0.1 0/1:124:17:17,0:103,4:0.1371:1,1:29.4:1:30.4:1:1:0:60:34:0.1393:0:1.2 -17 46805272 . CCCT C 71 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.19815;SOR=2.39472;LSEQ=TCCTCACCAGCTCCAAGTCT;RSEQ=CCTCCTCCTCCCAGGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:616:4:4,0:511,100:0.0065:2,0:21.5:1:31.8:1:1:0:60:8:0.0066:0.0032:0 0/1:389:6:3,3:308,75:0.0154:2,2:20.8:1:27.6:1:0.09792:4.08651:60:5:0.0132:0.0051:0 -17 46805443 . A G 216 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=151.08792;LSEQ=CAGCCACCAGCGAGAGCCCA;RSEQ=GACTGGTAACTGTCCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2083:1:1,0:1055,1024:5e-04:2,0:9:0:15:0:1:0:60:0:0:0:2 0/1:1802:122:61,61:837,841:0.0677:2,2:21.7:1:31.2:1:1:1.00:60:244:0.0683:0:1.1 -17 46805590 . G A 237 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=61.43131;LSEQ=AAGGCAAACTCAGTGGGGCG;RSEQ=CTGGGGTACTCTTCCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1945:6:4,2:984,954:0.0031:2,2:18.3:1:27.8:1:0.68727:1.94:60:12:0.0031:0:1.2 0/1:1788:286:149,137:791,709:0.16:2,2:23.8:1:29.1:1:0.8466:1.0258:60:56.2:0.1597:0:1.2 -17 46806115 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGTCTTGACGCAAGAGAC;RSEQ=CAGGGGCCCGGGCACGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:0,2:4,62:0.0294:2,0:6:1:31:0:1:0:60:4:0.0299:0:1 0/0:8:0:0,0:0,8:0:0,0:25.9:1:30.5:1:1:0:60:16:1:0:0.1 -17 46806237 . T C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:44.5:1:34:0:1:0:55:4:0.2857:0:1 0/0:1:0:0,0:0,1:0:0,0:12:0:31:0:1:0:60:2:1:0:0 -17 46812059 . G A 195 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=37.25647;LSEQ=AGGGAGGGAGGAGAAAGGGA;RSEQ=GAAGGGGGTCAAATATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1969:3:3,0:987,979:0.0015:2,0:1:0:27.3:1:0.24964:0:60:6:0.0015:0:1 0/1:1692:91:41,50:775,825:0.0538:2,2:23.1:1:30.1:1:0.59008:1.14551:60:90:0.0537:0:1.1 -17 47308105 . A G 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02324;SOR=Inf;LSEQ=GTCCCCTTTAAATGCCCGGG;RSEQ=GCCGGAGCCGGAGCCGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:22,18:0:2,0:25.6:1:28.5:1:1:0:60:7:1:0:0.2 0/1:17:3:1,2:7,7:0.1765:2,2:22.7:1:23:1:1:1.9219:60:2:0.1333:0:1.3 -17 47501674 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53084;SOR=0;LSEQ=TGGTGGAGCCGCTCTTAGTA;RSEQ=CTGTGTCTGCGTGGGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:2,0:114,21:0.0146:2,0:6.5:1:31.5:1:1:0:60:4:0.0152:0:1.5 0/0:81:0:0,0:68,13:0:2,0:23.3:1:32.6:1:1:0:47.7:162:1:0:0 -17 47501831 . C T 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.41783;LSEQ=AGCTCTAACATTAACAACAG;RSEQ=GCCACATACATCATCACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:837:3:1,2:545,289:0.0036:2,2:19.3:1:28:1:0.27833:3.76557:58:6:0.0036:0:1 0/1:629:29:16,13:365,235:0.0461:2,2:19.6:1:29.1:1:0.56356:1.26148:52.1:58:0.0463:0:1.1 -17 47501902 . C T 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTGTCTCTAGCCAAAAG;RSEQ=GATCGAGGTCACTTCGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1274:0:0,0:652,619:0:2,0:27.1:1:30.9:1:1:0:56.1:114.545:0.9976:0:0.1 0/1:1085:53:27,26:513,517:0.0488:2,2:26.2:1:30:1:0.88893:1.05:56.7:106:0.0494:0:1.3 -17 47501985 . A C 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTCTCATCTTCCCACAT;RSEQ=GGCTCAATACCATCCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:910:0:0,0:413,496:0:2,0:25.3:1:29.6:1:1:0:53:63.929:1:0:0.1 0/1:636:31:14,17:265,339:0.0487:2,2:25.7:1:29.4:1:1:1.05:53.5:30:0.048:0:1.2 -17 47502352 . T C 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.00589;SOR=Inf;LSEQ=TCCTTGGCCTCCCACAGTGC;RSEQ=GGGATTATAGGTATGACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:2,115:0:1,0:25.9:1:30.5:1:1:0:60:116:1:0:0.1 0/1:89:6:2,4:7,76:0.0674:2,2:24.3:1:27.7:1:0.11056:5.26:60:12:0.069:0:1 -17 47677367 . CT C 48 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAAAACTCAATGTCCTTT;RSEQ=TTTTTTTTTTTCCTTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:10,0:0.2308:0,0:31.7:1:30.3:1:1:0:60:6:0.2308:0:1 0/0:1:0:0,0:0,1:0:0,0:32:0:25:0:1:0:60:2:1:0:0 -17 47678020 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11108;SOR=Inf;LSEQ=ACAGAAGAACCCTTAATATG;RSEQ=ATAAGAATTTGCTTGTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:1,52:0:1,0:22.6:1:32.3:1:1:0:60:106:1:0:0.1 0/1:27:2:1,1:3,22:0.0741:2,2:25:1:28.5:1:0.2792:6.49:60:4:0.0769:0:1 -17 47679378 . C A 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08899;SOR=6.8002;LSEQ=CTCCAGGGCATACTGTAAAA;RSEQ=ACAAGCACTGCTGTCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:1:1,0:157,335:0.002:2,0:1:0:25:0:0.32049:0:60:2:0.002:0:1 0/1:366:5:4,1:113,248:0.0137:2,2:12.8:1:27.2:1:0.03781:8.72:60:10:0.0138:0:1 -17 47679483 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGATACTTGAATAGAACT;RSEQ=CACAGACCATGAAAAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:0,2:0,84:0.0233:1,0:33.5:1:31.5:1:1:0:60:4:0.0235:0:1 0/0:24:0:0,0:0,24:0:1,0:25.9:1:33.1:1:1:0:60:48:1:0:0 -17 47685050 . T G 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10171;SOR=4.04942;LSEQ=GGATGATCAGCCTCATTTAA;RSEQ=AAGTCAATCTGCTTTACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:3,0:32,3:0.0789:2,0:34.7:1:33:1:1:0:60:6:0.0789:0:1 0/1:19:5:5,0:14,0:0.2632:1,0:22.8:1:32.6:1:1:0:60:10:0.2632:0:1 -17 47685200 . C G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCATCTGACTCTAGATAC;RSEQ=TGGCTAAACAGACATGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:0:0,0:375,235:0:2,0:26:1:31.2:1:1:0:60:100.667:1:0:0.1 0/1:505:36:24,12:280,188:0.0713:2,2:28.5:1:28.8:1:0.48214:1.34:60:35:0.0697:0:1.1 -17 47685477 . AATAC A 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02254;SOR=0;LSEQ=AACAATAAGTAACTAATTAT;RSEQ=ATAAAGGAAAATAAGAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:0,12:0,22:0.3529:1,0:26.4:1:31.4:1:1:0:60:24:0.375:0.0294:0 0/0:11:0:0,0:0,11:0:0,0:21.8:1:31:1:1:0:60:22:1:0:0 -17 47688526 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12467;SOR=Inf;LSEQ=TACAAAGATATATTTAGCTG;RSEQ=AGTTTGTTTTGTAGTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:119,1:0:1,0:24.4:1:32.2:1:1:0:60:29:1:0:0.1 0/1:66:2:2,0:62,2:0.0303:1,0:12:1:29.5:1:1:0:60:4:0.0308:0:1 -17 47688864 . AT A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.08912;SOR=Inf;LSEQ=CCAAGCTTTTGTTACCAGGA;RSEQ=TTTTTTGCCAGCAGATAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:53,222:0:2,0:24.3:1:30.2:1:1:0:60:67.75:1:0:0.1 0/1:223:3:1,2:52,168:0.0135:2,2:30:1:31:1:0.55884:1.61:60:6:0.0138:0:0 -17 47688881 . T TAGAG 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0;SOR=5.85517;LSEQ=GGAATTTTTTTGCCAGCAGA;RSEQ=AGACGACTTTTACCTAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:40:5,35:18,160:0.1835:2,2:27.6:1:31.1:1:0.58216:1.27:60:80:0.1887:0.0367:0.1 1/0:151:86:12,74:12,53:0.5695:2,2:23.9:1:30.8:1:0.50431:1.39307:60:172:0.5733:0.1325:0.1 -17 47688929 . A G 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00234;SOR=Inf;LSEQ=ACATTCAGATACTAATATTA;RSEQ=TCATATTATCTTGAAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:1,80:0:1,0:23.1:1:30.2:1:1:0:60:19.25:1:0:0.1 0/1:49:6:0,6:1,42:0.1224:1,0:29.3:1:31.7:1:1:0:60:12:0.1224:0:1.2 -17 47696481 . G GA 128 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00525;SOR=0.26463;LSEQ=CGTTGACTCTCTGGGGTGGG;RSEQ=AAAAAAAAAGTCATATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:22:9,13:310,309:0.0343:2,2:23:1:28.9:1:0.5162:1.44828:60:21:0.0335:0.0078:1.1 0/0:538:5:1,4:249,277:0.0093:2,2:27.8:1:31.2:1:0.37692:3.58805:60:10:0.0095:0:0 -17 47696586 . GA G 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAGAGTTGAACAAAGAGGA;RSEQ=ACATTTACCCATAGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:971:0:0,0:541,429:0:2,0:24.5:1:30:1:1:0:60:63.667:1:0:0.1 0/1:803:66:41,25:415,318:0.0822:2,2:28:1:32.1:1:0.43691:1.26:60:132:0.0834:0.0025:0 -17 47696740 . G A 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05649;SOR=6.79324;LSEQ=TAACCCTTTGGGGTTTACTC;RSEQ=CAAACACCTGTCCAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:1:1,0:215,436:0.0015:2,0:1:0:26:0:0.33129:0:60:2:0.0016:0:1 0/1:582:6:4,2:197,378:0.0103:2,2:10.7:1:28:1:0.18912:3.83:60:12:0.0107:0:1.2 -17 47696764 . G GA 159 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01092;LSEQ=ACACCTGTCCAAAACAGATA;RSEQ=AAAAAAAAAATGTCAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:34:5,29:87,273:0.0848:2,2:28.2:1:31.3:1:0.28909:1.84586:60:68:0.0883:0:0.1 0/1:362:31:10,21:83,242:0.0856:2,2:31.7:1:29.2:1:0.39976:1.39:59.4:62:0.0899:0.0055:0.2 -17 47696820 . G A 132 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00012;SOR=6.2868;LSEQ=ACTGGAAATCAGACTCAAGA;RSEQ=AGGGAGATGTTTAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:5:0,5:1,139:0.0345:1,0:22:1:28.8:1:1:0:60:10:0.0345:0:1 0/1:103:19:1,18:3,81:0.1845:1,1:29.9:1:31.1:1:0.56359:1.49:60:38:0.1863:0:1.1 -17 47696903 . CT C 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16184;SOR=6.24309;LSEQ=GTTGGGAACAACTTTTTTCT;RSEQ=TTTTTTTTGAGACATGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:1:0,1:0,36:0.027:1,0:38:0:33:0:1:0:60:2:0.0278:0:0 0/1:13:2:0,2:1,10:0.1538:2,0:30.5:1:33.5:1:1:0:60:4:0.1538:0:0.5 -17 47696933 . C T 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02463;SOR=Inf;LSEQ=GAGACATGGTCTTACTCTAT;RSEQ=GTCCAGGCTGGAGTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,24:0:1,0:21.4:1:30.2:1:1:0:60:48:1:0:0.5 0/1:5:2:0,2:0,3:0.4:0,0:28.5:1:31:1:1:0:60:4:0.4:0:1 -17 47700315 . G A 92 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02083;SOR=4.97896;LSEQ=CTATTGTTTGACCTGATAGA;RSEQ=GCTGGAAATTTTGTCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:0,3:2,55:0.05:1,0:31.3:1:25:1:1:0:60:2:0.0351:0:1.3 0/1:38:8:1,7:1,29:0.2105:1,2:15.1:1:30.8:1:0.38122:3.94:60:16:0.2105:0:1 -17 47700372 . A TT 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.06401;SOR=Inf;LSEQ=CTTACCACTGAGGTCCTAAA;RSEQ=TTTTTTTTTTTTTTCCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:0:1,0:20:1:31.3:1:1:0:60:56:1:0:0.5 0/1:10:2:1,1:0,8:0.2:0,2:11.5:1:27:1:0.2:0:60:4:0.2:0.1:1 -17 48978368 . C T 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60839;SOR=0.35798;LSEQ=ACTGAGCCCGGGGCCCCCCA;RSEQ=GACACCCTCCCTGGAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:24.3:1:30:1:1:0:60:12:0.75:0:1 1/0:8:4:4,0:4,0:0.5:0,0:21.8:1:31.8:1:1:0:60:8:0.5:0:1 -17 50657476 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTACTTCATTATCCTACTAC;RSEQ=ACACACTCTCAAAGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 50657594 . T A 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAAACCACCGAGGCCTAG;RSEQ=CCTCCTCACTGCTGAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:23:1:26:1:1:0:54.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 50802094 . A G 35 d7;v4;q23;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAGAGTCTTTAATGACC;RSEQ=GCTGATTTTTGTATTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:30.7:1:22.3:1:1:0:60:2:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 50802416 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50213;SOR=0;LSEQ=AATTTTAAGAGGAAATTCTG;RSEQ=AAACAATGATCTGGAGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:94,35:0.0153:2,2:18:1:27:1:0.47563:2.6622:60:4:0.0155:0:1 0/0:109:0:0,0:72,37:0:2,0:23:1:30.6:1:1:0:60:53.5:1:0:0.2 -17 50802507 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1641;LSEQ=GACATCTCCTCATACCAGGA;RSEQ=ATTTTACAGATGGAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:245:186:78,108:26,32:0.7592:2,2:27.1:1:31.4:1:0.76158:1.12445:60:36.2:0.7542:0:1.1 0/1:203:69:32,37:63,71:0.3399:2,2:24.6:1:31.3:1:1:1.02585:60:138:0.3399:0:1.1 -17 50802634 . T C 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.06086;LSEQ=GAAAGATACTAAAAACTCCA;RSEQ=GTACACAATCACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:29:0,29:0,7:0.8056:0,1:28.2:1:30.2:1:1:0:60:58:0.8056:0:1.1 0/1:21:4:1,3:0,17:0.1905:1,2:16.8:1:31.3:1:0.19048:0:60:8:0.1905:0:1 -17 51930401 . G C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00341;SOR=6.56081;LSEQ=CAGCTGAGGCTGGCTTTTCC;RSEQ=CAGTGGGAGCCAGGGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:4,2:11,6:0.2609:2,2:18.5:1:30.7:1:1:1.09:60:12:0.2609:0:2.2 1/0:24:17:12,5:5,2:0.7083:2,2:26.4:1:30.6:1:1:1.03991:60:34:0.7083:0:2.1 -17 51930403 . A T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00474;SOR=5.77065;LSEQ=GCTGAGGCTGGCTTTTCCGC;RSEQ=GTGGGAGCCAGGGAGGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:4,2:11,6:0.2609:2,2:20.5:1:30.7:1:1:1.09:60:12:0.2609:0:2.2 1/0:25:17:12,5:6,2:0.68:2,2:27.4:1:31.1:1:1:1.23909:60:34:0.68:0:2.1 -17 51930483 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49753;SOR=Inf;LSEQ=CCAGCTGTGGTAGTCTGTGG;RSEQ=CAGAGTGCCTCTTCAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:16,21:0:2,0:27.4:1:31.5:1:1:0:60:74:1:0:0.4 0/1:44:2:1,1:15,27:0.0455:2,2:26.5:1:30:1:1:1.77:60:4:0.0455:0:1 -17 51931019 . T C 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20808;SOR=0;LSEQ=ACAGAAGACAGACCTGATTA;RSEQ=TGAAAGAAAAACAAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:2,2:0.5:2,2:10:1:31.8:1:1:2.60168:60:8:0.5:0:1.3 0/0:4:0:0,0:0,4:0:0,0:34.5:1:31.3:1:1:0:60:8:1:0:0.3 -17 51931064 . A G 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.57651;LSEQ=ACAAGAACAGCATCATCAGC;RSEQ=TCATCAACAACGACAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:4,2:3,2:0.5455:2,2:27.3:1:29.8:1:1:1.30:60:12:0.5455:0:1 0/1:5:2:1,1:2,1:0.4:2,2:5:1:29.5:1:1:1.7321:60:4:0.4:0:1 -17 51931075 . C T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01373;SOR=0;LSEQ=ATCATCAGCATCATCAACAA;RSEQ=GACAACAACAACAACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:3,2:4,2:0.4545:2,2:35.4:1:30:1:1:1.29868:60:10:0.4545:0:1.6 0/0:12:0:0,0:6,6:0:2,0:10.6:1:29.8:1:1:0:60:24:1:0:0.6 -17 51931129 . A G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26847;SOR=Inf;LSEQ=AGCCCACGCAAGGGTCAGCA;RSEQ=CCTCAAAGACCAAAACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:23.2:1:29.5:1:1:0:60:22:1:0:0.8 0/1:18:3:2,1:7,8:0.1667:2,2:22:1:32:1:1:2.18:60:6:0.1667:0:1.3 -17 52409319 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=AGAGTGTTGTTTTTACACTA;RSEQ=CCCATCAGGGATAGCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:28.1:1:32.8:1:1:0:60:18:1:0:0.6 0/1:6:2:1,1:3,1:0.3333:2,2:27:1:28.5:1:1:2.44949:55.5:4:0.3333:0:2 -17 52409334 . C T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37285;SOR=0.35231;LSEQ=CACTAGCCCATCAGGGATAG;RSEQ=ATGAGATGCCACCTGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:4,2:5,1:0.5:2,2:18:1:29.5:1:1:2.31595:60:12:0.5:0:1.2 0/1:8:2:1,1:5,1:0.25:2,2:41.5:1:28.5:1:0.46429:3.87298:55.5:4:0.25:0:2 -17 52409443 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGCTTCTCCCCTTTCTA;RSEQ=GTCCCATGACAGCCATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:13,14:0.069:2,2:30.5:1:29.5:1:1:1.07:60:4:0.0714:0:1 0/0:12:0:0,0:5,7:0:2,0:21.6:1:29.5:1:1:0:60:11:1:0:0.3 -17 52595602 . CT C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=AGGAGAAGAGGCGCTCTGGC;RSEQ=TTTGGGTTTTCAGCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:17:1:30:1:1:1.7321:60:4:0.4:0:0 0/0:3:0:0,0:2,1:0:2,0:19.3:1:27.3:1:1:0:60:6:1:0:0 -17 52596499 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23171;SOR=Inf;LSEQ=GCTCAAACAGGCTTACACAG;RSEQ=AGGAAATCACAGCTGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:5,16:0:2,0:25.3:1:32.7:1:1:0:60:42:1:0:0.2 0/1:20:2:1,1:6,12:0.1:2,2:25:1:28.5:1:1:1.93:60:4:0.1053:0:2 -17 52596616 . T C 86 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=CCAGGGTTGGGACGCTAGGC;RSEQ=CCAGTGGTGTGGGTTCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:25.1:1:30.7:1:1:0:60:14:1:0:1 1/0:6:3:2,1:0,3:0.5:0,2:20.3:1:30:1:0.4:0:58.7:6:0.6:0:1 -17 53367223 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.9395;LSEQ=TCAGCTCTTAATCCTTCCTA;RSEQ=CACTTTGCATTCATTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:7:5,2:178,70:0.0273:2,2:29.9:1:28.4:1:1:1.01708:60:14:0.0285:0:1.1 0/1:211:71:51,20:100,40:0.3365:2,2:25.5:1:28.8:1:1:1.02:60:34.5:0.3382:0:1 -17 53367273 . G GA 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.95975;LSEQ=GCCTGTTTTCAGCCTAGTTA;RSEQ=AAAAAAAAAGGCCAGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:19:9,10:239,207:0.0404:2,2:26.7:1:30.4:1:0.64388:1.28218:59.7:38:0.0419:0.0085:0.7 0/1:386:15:10,5:199,170:0.0389:2,2:36.3:1:29.2:1:0.43112:1.71:60:30:0.04:0.0026:0.6 -17 53367300 . A G 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18324;LSEQ=AAAGGCCAGCCTCATTCATT;RSEQ=GAATTCTGCGTTCCCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:537:343:165,178:104,90:0.6387:2,2:26.1:1:31.3:1:0.24309:1.24608:60:37.111:0.6386:0:1.1 0/1:442:108:53,55:168,165:0.2443:2,2:26.5:1:30.8:1:0.8254:1.0565:60:107:0.2449:0:1.2 -17 53367453 . GAAAATGAAAAC AAAAAGAAAAT 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06553;SOR=0.43999;LSEQ=GATCTTTCTTCCTCAGTGCT;RSEQ=CAGACAAATAAGCACAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:32:0,32:0,20:0.5246:1,1:25.2:1:31.2:1:1:0:60:64:0.5246:0.1148:0.1 0/1:40:13:0,13:1,16:0.325:1,1:29.4:1:31:1:1:0:60:26:0.3421:0:0 -17 53367458 . T A 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32258;SOR=3.77405;LSEQ=TCTTCCTCAGTGCTGGAAAA;RSEQ=GAAAACCAGACAAATAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:0,17:0.0556:1,0:35:0:32:0:1:0:60:2:0.0556:0:8 0/1:16:3:0,3:0,13:0.1875:1,0:17.3:1:32.7:1:1:0:60:6:0.1875:0:1.3 -17 53367464 . C T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66403;SOR=1.64705;LSEQ=TCAGTGCTGGAAAATGAAAA;RSEQ=CAGACAAATAAGCACAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:0.0909:1,0:22.5:1:28.5:1:1:0:60:4:0.0909:0:4.5 0/1:21:3:0,3:0,18:0.1429:1,0:20.7:1:28:1:1:0:60:6:0.1429:0:2 -17 54123450 . A G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGCCCAGCCGGTGGAA;RSEQ=CTAACAGCCCCAAAGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:36.5:1:34:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 54123623 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.18857;SOR=Inf;LSEQ=AAGCAGCAGCAACAGCAGCA;RSEQ=CAGCAGCGACTGGAGCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:0:2,0:29.3:1:31.8:1:1:0:60:27:1:0:0.4 0/1:22:2:1,1:10,10:0.0909:2,2:34.5:1:29:1:1:1:60:4:0.0952:0:1 -17 54123670 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGAAGAGGTAAAGGGA;RSEQ=GCTGAGGCTGCCGCATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:4,12:0.1111:2,2:26.5:1:30:1:0.4902:2.79:60:4:0.1111:0:1 0/0:7:0:0,0:3,4:0:2,0:13:1:30.4:1:1:0:60:14:1:0:0.3 -17 54445635 . AACTT GAC 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22328;SOR=Inf;LSEQ=ACTTGAATAAACTGAAAATG;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:21,99:0:2,0:8.8:1:29.9:1:1:0:59.5:23:1:0:0.6 0/1:108:2:0,2:19,87:0.0185:2,0:19:1:30.7:1:1:0:60:4:0.0198:0.0093:1.5 -17 54445951 . C CT 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCCGGCTGAAAATGGAC;RSEQ=TTTTTTTTTAATGGCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:29:0:32:0:1:1:60:4:0.2857:0:0 0/0:2:0:0,0:1,1:0:2,0:11.5:1:28:1:1:0:51:4:1:0:0 -17 55082412 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=TTTCGGTCTCTACCTACAAT;RSEQ=CTGTGTTTTGATTAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:0:2,0:29.2:1:31.6:1:1:0:60:23:1:0:0.1 0/1:20:2:1,1:8,10:0.1:2,2:24:1:27:1:1:1.24:60:4:0.1053:0:1 -17 55816722 . A G 239 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.90908;SOR=1.05102;LSEQ=AGACTTCTCTCTGAAAATCT;RSEQ=AGCCTGCCAGGTTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:176:136,40:59,15:0.704:2,2:24.4:1:32.1:1:0.73972:1.15616:60:352:0.704:0:1.1 1/0:147:105:76,29:33,9:0.7143:2,2:24.8:1:31.2:1:0.53379:1.39604:60:51.5:0.7103:0:1.1 -17 55816832 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.65496;LSEQ=CCCTTTCTGAAACAAGACCC;RSEQ=TAGCTTCCCCTCTTTAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:640:93:41,52:257,290:0.1453:2,2:27.3:1:31.1:1:0.65348:1.12376:60:30:0.144:0:1.1 1/0:495:263:124,139:110,121:0.5313:2,2:24.6:1:30.9:1:0.92827:1.01903:60:130.5:0.5305:0:1.1 -17 55816867 . CTA TT 147 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=3.12576;LSEQ=TAGTTCTGCATCAAAAAAGT;RSEQ=AAACTTGGGCTGGCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:14:8,6:159,295:0.0298:2,2:22:1:29.8:1:0.09734:2.47:60:28:0.0302:0.0021:0.2 0/1:365:32:15,17:124,206:0.0877:2,2:24.7:1:29.5:1:0.34281:1.46:60:64:0.0882:0.011:0.3 -17 55816928 . T A 39 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0428;SOR=Inf;LSEQ=GATTGCAATCTCTTATAATT;RSEQ=AATATATTTCCTTTCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:20,151:0:2,0:23.8:1:28.2:1:1:0:60:33.2:1:0:0.1 0/1:93:3:2,1:9,81:0.0323:2,2:6:1:25:1:0.03603:16.88:60:6:0.0326:0:1 -17 56344972 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=GTGCGTCCTCAGCCAGGGAG;RSEQ=GAAGGGCAGGGCCCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:9,4:0.1333:2,2:8:1:27.5:1:1:2.12136:60:4:0.1333:0:1 0/0:12:0:0,0:7,5:0:2,0:17.7:1:29.8:1:1:0:60:24:1:0:0.1 -17 56432219 . T C 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTGTTTGCTGTGGTCCTT;RSEQ=CCTTTCCCAGGAGCAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:304,94:0:2,0:23.8:1:30.1:1:1:0:60:98.5:1:0:0.1 0/1:287:22:15,7:185,80:0.0767:2,2:15.8:1:30.6:1:1:1.07887:60:44:0.0772:0:1.2 -17 56432362 . C G 201 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAGCCTGTATTTAGAGAG;RSEQ=GGGGAGGAAAGAGGTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:172,331:0:2,0:24.5:1:30.3:1:1:0:60:54.889:0.998:0:0.2 0/1:411:98:39,59:129,183:0.2384:2,2:26.1:1:30.5:1:0.8147:1.06627:60:97:0.2413:0:1.1 -17 56434481 . C G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21028;LSEQ=GCCAGGTTGGTCTTGAACTC;RSEQ=TGGCCTCAAGGGATCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:113:111,2:139,2:0.4431:1,1:26.8:1:30.1:1:1:1.25113:60:226:0.4449:0:1.1 0/1:98:14:14,0:82,2:0.1429:1,1:26.6:1:28.6:1:1:0:60:13:0.134:0:1.1 -17 56434554 . C T 71 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00878;SOR=10.47146;LSEQ=CATGAGCCATCACACCCGGC;RSEQ=TTCCAAGTGCCTTTCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:819:1:0,1:563,255:0.0012:2,0:1:0:26:0:0.31258:0:60:2:0.0012:0:1 0/1:553:7:1,6:364,182:0.0127:2,2:9.1:1:25.6:1:0.00732:11.95076:57.1:6:0.0111:0:2 -17 56435080 . G C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.2364;LSEQ=ACCAAGGATATGCCACACTG;RSEQ=GGGTGTAATGGGGAAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:353:162,191:229,286:0.4044:2,2:26.1:1:30.9:1:0.72847:1.06:60:87.25:0.4035:0:1.1 0/1:579:80:37,43:229,269:0.1382:2,2:23.7:1:30.9:1:1:1.01:60:160:0.1396:0:1.2 -17 56435170 . CT C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00776;SOR=Inf;LSEQ=GCTCGGAGGGACCCCCCCGC;RSEQ=TTTCCTCTGTGGGTGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:616:0:0,0:264,352:0:2,0:24.7:1:30.2:1:1:0:60:33.222:1:0:0.2 0/1:377:5:1,4:162,210:0.0133:2,2:24.8:1:32.5:1:0.39457:3.07777:60:10:0.0134:0.0027:0 -17 56435257 . A G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00181;SOR=Inf;LSEQ=GGCAGATGCTGGAGGCGTCA;RSEQ=CTGGGCCAGGGGCTGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:242,184:0:2,0:24.7:1:30:1:1:0:60:59.857:1:0:0.1 0/1:294:7:3,4:167,120:0.0238:2,2:19.3:1:31.3:1:0.46031:1.85154:60:14:0.0243:0:2 -17 56435830 . C T 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07326;SOR=6.52313;LSEQ=TGTCAGGGGGCCTGGCCCGG;RSEQ=GTAGGGGCACTGGGCAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:643:1:0,1:341,301:0.0016:2,0:1:0:28:0:0.46967:0:60:2:0.0016:0:1 0/1:397:4:1,3:212,181:0.0101:2,2:11.8:1:25.8:1:0.34052:3.5035:60:3:0.0077:0:1.5 -17 56435885 . G T 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.01681;LSEQ=GGTGGATTGGAGGTGGCTCA;RSEQ=TCCCCAGCCTTGTGCATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:810:121:57,64:351,338:0.1494:2,2:23.8:1:30.2:1:0.49033:1.16577:60:59.5:0.1499:0:1.1 0/1:558:146:76,70:206,205:0.2616:2,2:26:1:29.4:1:0.70095:1.08:60:145:0.2627:0:1.2 -17 56436109 . C T 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.53244;LSEQ=GGGCATGGCCGGGATGCTGG;RSEQ=GAATGAGGTGGAGTCTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1544:193:96,97:675,674:0.125:2,2:26.1:1:29.7:1:1:1.01191:60:95.5:0.1258:0:1.2 0/1:1132:80:38,42:531,521:0.0707:2,2:25.7:1:29.3:1:0.64368:1.12636:60:160:0.0712:0:1.2 -17 56438301 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23394;LSEQ=AGGCTGTTCTCTGCTGAAGC;RSEQ=GATCCTGGGAAGAGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:922:347:145,202:246,326:0.3764:2,2:27.3:1:30.7:1:0.73118:1.05121:60:68.4:0.3762:0:1.1 0/1:631:78:33,45:241,312:0.1236:2,2:28.5:1:30.1:1:0.90306:1.05325:60:77:0.1242:0:1.2 -17 56438409 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24496;SOR=4.23501;LSEQ=TCACTCAGGTAGATCACATG;RSEQ=CCAGTTGAACATCCTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:1:0,1:9,189:0.005:1,0:46:0:12:0:1:0:60:0:0:0:5 0/1:95:2:0,2:6,86:0.0211:2,0:39.5:1:31:0:1:0:60:4:0.0217:0:1 -17 56438433 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01185;SOR=Inf;LSEQ=GTTGAACATCCTTAGGAGTT;RSEQ=GTCTCCTCGGAGCTCATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:3,130:0:1,0:21.1:1:29.8:1:1:0:60:43.333:1:0:0.1 0/1:67:4:0,4:2,61:0.0597:1,0:15.8:1:30.3:1:1:0:60:8:0.0625:0:1 -17 56440474 . G A 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00013;SOR=0;LSEQ=GTAGGTGAGGCCCAAAGACG;RSEQ=GGGAAAACTTGCCCAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:27:27,0:132,4:0.1656:1,1:19.3:1:30.4:1:1:0:60:26:0.1625:0:2.7 0/0:61:0:0,0:60,1:0:1,0:26.8:1:31.6:1:1:0:60:122:1:0:0.3 -17 56440526 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19964;LSEQ=GGATGAAGTTGGACTAGAGG;RSEQ=TTTCCAGGATCTCTCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:146:142,4:179,8:0.4384:1,1:23.3:1:29.9:1:0.56096:1.58:60:47.667:0.4373:0:2.1 0/1:171:23:21,2:140,8:0.1345:2,2:26.1:1:28.9:1:0.62601:1.66083:60:46:0.1353:0:2 -17 56440542 . G T 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.62113;SOR=1.08544;LSEQ=GAGGGTTTCCAGGATCTCTC;RSEQ=CAGCTCCAGGAGTCTAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:182:160,22:213,33:0.4252:2,2:22.4:1:31:1:0.77065:1.13:60:90:0.4296:0:1.9 0/1:229:102:86,16:106,20:0.4454:2,2:22.1:1:30.4:1:1:1.01:60:101:0.4489:0:1.3 -17 56440642 . C T 185 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=0.03396;LSEQ=TCTAGTGTGCTTACCCAGGC;RSEQ=GGGGGCTCCTTCAGCTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1697:78:43,35:857,762:0.046:2,2:24:1:29.5:1:0.72884:1.09:60:12:0.0434:0:1.1 0/0:1225:2:0,2:649,572:0.0016:2,0:1:0:29.5:1:0.22007:0:60:4:0.0017:0:1 -17 56448220 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09211;SOR=Inf;LSEQ=GAGCACAGGGTCTTCTCACA;RSEQ=CCCAGAGCTGGGTGAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:218,71:0:2,0:23.3:1:32:1:1:0:60:47.167:1:0:0.1 0/1:239:3:2,1:181,55:0.0126:2,2:36.3:1:30:1:0.55282:1.64161:60:6:0.0126:0:1 -17 56448241 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.7104;SOR=1.54045;LSEQ=CCCAGAGCTGGGTGAAGCTC;RSEQ=GGGTGTGTGTAGGGCGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:3:0,3:291,122:0.0072:2,0:1:0:22.3:1:0.02667:0:60:2:0.005:0:1.3 0/1:363:4:1,3:245,114:0.011:2,2:17.8:1:27.5:1:0.10035:6.41189:60:8:0.0113:0:1 -17 56448297 . C T 168 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=16.41739;LSEQ=TAGCCAGTGACAGGCAGGGG;RSEQ=GGGGGGCCCGTCGAGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:4:0,4:455,342:0.005:2,0:1:0:25.5:1:0.03447:0:60:8:0.0051:0:1 0/1:682:52:33,19:336,293:0.0762:2,2:28.2:1:29.5:1:0.19276:1.51:60:51:0.0767:0:1.2 -17 56492800 . T C 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=2.84755;LSEQ=CAAGGGGATCACTCTGATAA;RSEQ=AGCTTTCTGTTCTGCTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1057:138:62,76:400,517:0.1306:2,2:25.5:1:31.8:1:0.78313:1.05:60:137:0.1315:0:1.1 0/1:1068:320:139,181:331,412:0.2996:2,2:24.3:1:31.2:1:0.78775:1.04612:60:319:0.3007:0:1.1 -17 56744028 . A G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGAAAAACCACCTCCAT;RSEQ=ATCACAGTATTTCTCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:28:1:1:0:60:4:1:0:1 -17 56745294 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.16949;SOR=0;LSEQ=TTCTTTTCTTGTTTGCTTGG;RSEQ=CAAACCTTATTCAGGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,8:0.08:2,2:27:1:28:1:1:1.82581:60:4:0.08:0:2 0/0:35:0:0,0:22,13:0:2,0:19.3:1:30.1:1:1:0:60:16.5:1:0:0.8 -17 56769887 . G A 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAAAGCTGCAAGGCCCGGA;RSEQ=CCCCGTGCGGCCAGGCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:52,0:0:1,0:22.6:1:31.9:1:1:0:60:51:1:0:0 0/1:54:22:21,1:31,1:0.4074:1,1:23.1:1:29.6:1:1:1.46529:60:44:0.4151:0:1.3 -17 56769929 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21423;SOR=Inf;LSEQ=AGCCGGCCCCTTCCGCTTTA;RSEQ=GTCTGACGTCACGCCGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:124,17:0:2,0:22.6:1:32:1:1:0:60:140:1:0:0.1 0/1:122:2:1,1:102,18:0.0164:2,2:22.5:1:28:1:0.28831:5.54257:60:4:0.0165:0:1 -17 56769948 . C T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24891;SOR=0;LSEQ=ACGTCTGACGTCACGCCGCA;RSEQ=GCCCCAGCGAGGGCGTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:3:1,2:162,40:0.0146:2,2:23.7:1:29.3:1:0.1073:7.98516:60:6:0.0148:0:1 0/0:192:0:0,0:147,45:0:2,0:21.8:1:30.5:1:1:0:59.9:191:1:0:0.5 -17 56769979 . C T 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GGGCGTGCGGAGTTTGGCTG;RSEQ=TCCGGGGTTAGCAGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:261,102:0:2,0:24.9:1:31.7:1:1:0:60:35.3:1:0:0.2 0/1:355:100:63,37:170,85:0.2817:2,2:22.9:1:29.3:1:0.53582:1.17406:60:99:0.2829:0:1.2 -17 56772255 . TA T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12677;SOR=0;LSEQ=ATGTTACACTTTTAAATCTC;RSEQ=AAATTAGGGTTCTTTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:4:2,2:191,92:0.0139:2,2:13.3:1:28:1:0.59944:2.07039:60:8:0.014:0.007:0.8 0/0:252:0:0,0:177,75:0:2,0:23.5:1:28.3:1:1:0:60:83:1:0:0.1 -17 56772522 . G A 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACAACAGAAATTTGTGGT;RSEQ=CACCAGGTGTTGGAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:526:0:0,0:171,354:0:2,0:24.5:1:31.5:1:1:0:60:34:0.998:0:0.1 0/1:455:39:12,27:171,245:0.0857:2,2:22:1:28.6:1:0.23495:1.56892:60:78:0.0878:0:1.3 -17 56773769 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTCACTGCACTCCAGCCT;RSEQ=GGCGACAGAGCGAGACTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:7,0:0.2222:0,2:9.5:1:30.5:1:0.22222:0:60:4:0.2222:0:1 0/0:1:0:0,0:1,0:0:0,0:23:0:32:0:1:0:60:2:1:0:0 -17 56773819 . T C 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.00923;SOR=Inf;LSEQ=ATAAATAAAATAAAATAAAA;RSEQ=ATCCTTAATCTTGGTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:23,0:0:1,0:18.8:1:30.7:1:1:0:60:22:1:0:0.4 1/0:3:2:2,0:1,0:0.6667:0,0:37:1:33:0:1:0:60:4:0.6667:0:1 -17 56774577 . G T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GTATAAGGACTTCCATATTG;RSEQ=TTTTCCAAAAACCAAAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:24:1:33.3:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:7.5:1:31:0:1:0:60:4:1:0:1 -17 56774920 . C CA 44 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAAAAAAAAAAAAAAAC;RSEQ=AAAAAAAAAAACCACGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,0:0.75:0,2:19.3:1:28.3:1:1:0:60:6:0.75:0:0.3 -17 56780459 . C G 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGTTAAAGAATTTTGTTAT;RSEQ=CAAAGGAGAACATTTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:193,8:0:1,0:24.9:1:31.4:1:1:0:60:66:1:0:0.1 0/1:163:23:19,4:128,12:0.1411:2,2:24.6:1:31.9:1:0.24718:2.23177:60:46:0.1429:0:1 -17 56780540 . G T 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACAGGTAAAACTAATTAAGA;RSEQ=TGTTTTGTTGTTTCAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:868:0:0,0:491,377:0:2,0:26.4:1:32.1:1:1:0:60:107.5:1:0:0.1 0/1:769:57:33,24:403,308:0.0741:2,2:28.1:1:29.6:1:0.89035:1.05:60:114:0.0746:0:1.2 -17 56782275 . AT A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTTTAATTAATTAATTA;RSEQ=TTTTTTTTTGAGTCGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 56782297 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTTTGAGTCGCCCAG;RSEQ=CTGACTAACATGGCAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 56785725 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACTAAAACATAACCTC;RSEQ=AAGAGAGCAGGGACCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:29:1:1:0:55:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 56797788 . T A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCTGTCTCAAAAAAAAAAA;RSEQ=AAAATAAAAAATAAAATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:20.5:1:31:0:1:0:60:4:0.5:0:2 1/1:1:1:1,0:0,0:1:0,0:8:0:31:0:1:0:60:2:1:0:1 -17 56797975 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51962;SOR=0;LSEQ=TCCGGAGTAGCTGGGATTAC;RSEQ=GGTGCATGCCACCATGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:107,0:0.0183:1,2:18.5:1:28.5:1:0.01835:0:60:4:0.0185:0:1 0/0:71:0:0,0:71,0:0:1,0:24:1:29.9:1:1:0:60:22.667:1:0:0.2 -17 56797984 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.178;SOR=Inf;LSEQ=GCTGGGATTACAGGTGCATG;RSEQ=CACCATGTCTGGTTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:119,5:0:1,0:24.6:1:32.8:1:1:0:60:248:1:0:0.1 0/1:91:2:2,0:86,3:0.022:1,0:12.5:1:29:1:1:0:60:4:0.022:0:1 -17 56798207 . T C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1295;LSEQ=CAGATAAACATTTTAGTTTA;RSEQ=CACAGTTTTTCTTATCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:503:393:133,260:34,72:0.7813:2,2:24.8:1:31.5:1:0.81673:1.08:60:392:0.7809:0:1.1 0/1:475:150:51,99:111,212:0.3158:2,2:23.4:1:30.7:1:1:1.01634:60:300:0.3185:0:1.1 -17 56811731 . A T 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29094;SOR=0;LSEQ=AATGGGAAAAATACCTAAAT;RSEQ=TGATTCTGTGAAAGTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:0,44:0.0833:1,0:18.8:1:31.5:1:1:0:60:8:0.087:0:1 0/0:29:0:0,0:0,29:0:1,0:27:1:30.1:1:1:0:60:28:1:0:0.1 -17 58206139 . T C 283 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGCTGTTCAGGGATTCC;RSEQ=AGGGGGTCAACAGAGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:530:530:218,312:0,0:1:0,2:24.1:1:31.3:1:1:0:60:74.714:1:0:1.1 1/0:348:256:114,142:43,49:0.7356:2,2:24.9:1:30.7:1:0.71607:1.09281:60:63:0.7326:0:1.2 -17 58206188 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56083;SOR=3.26577;LSEQ=GGAGGCGGTCACTGGGGTAT;RSEQ=ACGGGGCCTCCTTGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:1:0,1:77,234:0.0032:2,0:27:0:11:0:1:0:60:0:0:0:5 0/1:192:2:0,2:60,130:0.0104:2,0:30:1:30:0:1:0:60:4:0.0105:0:2 -17 58206251 . C A 196 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAATATTTTGAAATAGCAA;RSEQ=AGACAGAAGAAAGCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:90:90:10,80:0,0:1:0,2:24:1:30.2:1:1:0:60:44:1:0:1.3 1/0:62:42:5,37:4,15:0.6774:2,2:24.4:1:30:1:0.44086:1.94964:60:84:0.6885:0:1.2 -17 58206314 . C T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22581;SOR=0;LSEQ=CCTCCAGCCCGGTGTCCCCC;RSEQ=ACCTCCCAGGGTCCCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:0,24:0,0:1:0,1:25.9:1:28.7:1:1:0:60:48:1:0:1.6 1/1:7:6:0,6:0,1:0.8571:0,0:11.8:1:29.3:1:1:0:60:12:0.8571:0:1.8 -17 58393400 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=CAAACCTCCCTTCCAGCATC;RSEQ=GATATGGGACTTCAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:23.7:1:31.1:1:1:0:60:14:1:0:0 0/1:10:2:1,1:6,2:0.2:2,2:18:0:32:0:1:2.64575:60:4:0.2:0:1 -17 58393611 . C CA 69 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.24722;SOR=0.3636;LSEQ=GATGAGTAACATTTCATTCT;RSEQ=AAAAAAAAAAAAAAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:4,8:0.2778:2,2:36.2:1:29.8:1:1:1.31:58:10:0.2941:0:0.8 0/1:25:3:2,1:7,14:0.12:2,2:31:1:28.3:1:0.5331:3.76:60:6:0.1429:0:0.7 -17 58677402 . C G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCAGCGGCGGGAGGAGG;RSEQ=AGCGCGGCCGTCGCAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:10,3:0,0:1:0,2:30.3:1:31.2:1:1:0:60:26:1:0:1.2 1/1:2:2:2,0:0,0:1:0,0:27:1:33:0:1:0:60:4:1:0:1 -17 58677659 . TC T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1143;SOR=Inf;LSEQ=CCTTCTCCGGGTCCGCCCCC;RSEQ=CCCCTTCTCGGCGTCGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:223,9:0:1,0:22.7:1:31.4:1:1:0:60:37.667:1:0:0.2 0/1:119:2:1,1:114,3:0.0168:1,2:15:1:31.5:1:0.06637:33.03137:60:4:0.0169:0:0 -17 58678009 . T A 216 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00606;LSEQ=GCCCGAGAGGCTCGCGACCC;RSEQ=CTCCCGGACGCCGGGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:853:145:79,66:375,329:0.17:2,2:23.2:1:30.2:1:0.85499:1.05:60:144:0.1735:0:1.1 0/0:808:1:1,0:440,366:0.0012:2,0:1:0:24:0:1:0:60:2:0.0013:0:1 -17 58678443 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53051;SOR=0;LSEQ=CCTTGGGGAAGATAGGATTG;RSEQ=CGTCTCCCTGCAGCCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:1,69:0.0278:1,0:27:1:29.5:1:1:0:60:4:0.0286:0:1 0/0:42:0:0,0:1,41:0:1,0:24.6:1:31:1:1:0:60:41:1:0:0.2 -17 58679806 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTTTTTTTTTAAGAGA;RSEQ=GGGCAGGGGCGGGGGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:31.5:1:1:0:60:4:1:0:2 -17 58679831 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGCGGGGGACGGGTGTG;RSEQ=GCCGCCTTACTTTGTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:31:1:1:0:60:4:1:0:2 -17 58711077 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14357;SOR=Inf;LSEQ=AACAGGAATTTTGGCTTATG;RSEQ=ATCTTTGTATTTGAAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:109,0:0:1,0:23.9:1:32.5:1:1:0:60:53.5:1:0:0.1 0/1:67:2:2,0:62,3:0.0299:1,0:24:1:28.5:1:1:0:60:4:0.0303:0:3 -17 58725145 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.181;SOR=Inf;LSEQ=TTGAATGTTATCAAATGCTT;RSEQ=TCTGCGTCTATTGAGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:209,1:0:1,0:23.7:1:30.8:1:1:0:60:104:1:0:0.1 0/1:156:2:2,0:147,6:0.0128:1,0:8:1:32.5:1:1:0:60:4:0.0132:0:1 -17 58725241 . C A 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTTCTTGCTTTTTCTGCT;RSEQ=CCTTCCCCCAGGTGATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1220:0:0,0:737,480:0:2,0:24.1:1:30.9:1:1:0:60:109.636:1:0:0.1 0/1:1025:53:33,20:573,396:0.0517:2,2:23.3:1:28.5:1:0.77426:1.14:60:52:0.0511:0:1.2 -17 58726474 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTCCCCCCAAGAGATG;RSEQ=GGTGTCACTATGTTGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29.5:1:1:0:60:4:1:0:1 -17 58733834 . GA G 124 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.49591;SOR=0.67838;LSEQ=AAAAAAAAAAAAAGAGAAAA;RSEQ=AAAAAAAAAATTGGGAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:15:15,0:119,0:0.1119:1,1:24.5:1:31.8:1:1:0:59.3:30:0.1172:0.0224:0.7 0/1:89:7:7,0:81,1:0.0787:1,0:19:1:31.7:1:1:0:60:14:0.0814:0.0225:0.6 -17 58733845 . AT A 28 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=11.000;MSILEN=1;SSF=0.51693;SOR=0;LSEQ=AAGAGAAAAGAAAAAAAAAA;RSEQ=TGGGAGCTTTGTTTGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:2,0:167,0:0.0118:1,0:21.5:1:28:0:1:0:50:4:0.013:0:2.5 0/0:115:0:0,0:111,2:0:1,0:22.6:1:28.8:1:1:0:59.5:8.417:1:0:0.5 -17 58740077 . G C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAAAATGCTTGTGACCAC;RSEQ=TGAATTTTCACCCACTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:0.2727:0,0:32.3:1:31.7:1:1:0:60:6:0.2727:0:1 0/0:1:0:0,0:1,0:0:0,0:37:0:27:0:1:0:60:2:1:0:0 -17 59477796 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.52459;SOR=0;LSEQ=TGGGCCCGCACCCGCCCGCC;RSEQ=CGCATCTGCGCTCCCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:97,34:0.015:2,2:37.5:1:30.5:1:0.45853:2.82635:60:4:0.0154:0:1.5 0/0:83:0:0,0:58,25:0:2,0:21.1:1:30:1:1:0:60:82:1:0:0.2 -17 59477818 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1438;SOR=Inf;LSEQ=GCATCTGCGCTCCCTCAAGA;RSEQ=CCTGGAGCCCGAGGACGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:154,76:0:2,0:26.1:1:31.9:1:1:0:60:31.857:1:0:0.2 0/1:141:2:1,1:92,47:0.0142:2,2:22.5:1:30:1:1:1.94751:60:4:0.0142:0:2.5 -17 59477832 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57123;SOR=2.87439;LSEQ=TCAAGAGCCTGGAGCCCGAG;RSEQ=ACGAGGTGGAGGACGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:0,1:176,102:0.0036:2,0:1:0:25:0:0.36918:0:60:2:0.0036:0:1 0/1:195:2:1,1:115,78:0.0103:2,2:45:1:29.5:1:1:1.47132:60:4:0.0104:0:1 -17 59477856 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06476;SOR=Inf;LSEQ=AGGTGGAGGACGACCCCAAG;RSEQ=TGACGCTGGAGGCCAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:167,137:0:2,0:28.4:1:31.4:1:1:0:60:75:1:0:0.2 0/1:205:3:2,1:108,94:0.0146:2,2:25.7:1:26.7:1:1:1.74:60:6:0.015:0:2 -17 59477877 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14975;SOR=Inf;LSEQ=TGACGCTGGAGGCCAAGGAG;RSEQ=TGTGGGACCAGTTCCACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:119,140:0:2,0:26.4:1:32:1:1:0:60:518:1:0:0.1 0/1:164:2:1,1:76,85:0.0122:2,2:28:0:31.5:1:1:1.12:60:4:0.0123:0:1 -17 59477903 . C A 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00131;SOR=Inf;LSEQ=GACCAGTTCCACAAGCTAGG;RSEQ=ACGGAGATGGTCATCACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:63,106:0:2,0:23:1:31.3:1:1:0:60:32.8:1:0:0.1 0/1:110:7:2,5:37,66:0.0636:2,2:20.3:1:29.1:1:1:1.39742:60:14:0.0642:0:2.1 -17 59479113 . T C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGCCAAGTATATCCTGCTGA;RSEQ=GGACATTGTAGCCGCTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:25:1:33:0:1:0:60:4:0.6667:0:1 0/0:3:0:0,0:3,0:0:0,0:24:1:30.7:1:1:0:60:6:1:0:3 -17 59480288 . CGATAGAGAGAGAGAGAGAGA C 63 d7;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATGGGGAAGAGGAAGAAC;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:13.5:1:31.5:1:1:0:60:8:0.6667:0.6667:0.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 59480291 . T G 35 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGAAGAGGAAGAACCGA;RSEQ=AGAGAGAGAGAGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:0,0:0.4:0,0:39.5:1:35.8:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 59480309 . GAGAGAGAGAGAGAGAGAGAGAGA G 33 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAGAGAGAGAGAGAGAGA;RSEQ=AAGTGGAGAGGAAGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:4,0:0.25:0,0:38:1:33:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 59480331 . GA G 68 d7;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAGAGAGAGAGAGAGAGA;RSEQ=AAGTGGAGAGGAAGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:0,0:0.6667:0,0:24.3:1:34:0:1:0:60:8:1:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 59481523 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGTTCCGACACTGTGGCACT;RSEQ=CTTTAGGCCTGTGTGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:32.5:1:33.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:27.5:1:1:0:60:4:1:0:1 -17 59760499 . A G 177 MSI6 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGACTCTGTCTCAAAAAAA;RSEQ=AAACCCAAAAACTCAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:45:44,1:0,0:1:0,1:20.1:1:32.3:1:1:0:60:90:1:0:1 0/1:15:7:7,0:6,2:0.4667:2,0:14.3:1:29.9:1:0.46667:0:60:6:0.4286:0:1 -17 59760996 . A G 305 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00234;LSEQ=TCATCTGTATCTTCAGGATC;RSEQ=TAAAGTTCAGGTGTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:974:973:507,466:1,0:0.999:0,2:24.4:1:30.8:1:1:0:60:193.6:0.999:0:1.1 1/0:842:587:291,296:126,127:0.6971:2,2:23.5:1:30.2:1:1:1.00916:60:96.833:0.6966:0:1.1 -17 59761706 . A G 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAATGTTTCCTAGCCCA;RSEQ=GTTATAATGCTGTCTGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:25.8:1:31.6:1:1:0:60:10:0.5556:0:1 0/0:1:0:0,0:0,1:0:0,0:32:0:33:0:1:0:60:2:1:0:1 -17 59763114 . A T 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=0.50127;LSEQ=ACCACCATATTTAAGGAATT;RSEQ=ATCTATACCCAAATAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:339:170:124,46:116,52:0.5015:2,2:25.4:1:29.5:1:0.47263:1.21:60:55.667:0.4985:0:1.1 0/1:209:70:50,20:81,58:0.3349:2,2:22.9:1:29.4:1:0.07034:1.79:60:140:0.3382:0:1.1 -17 59763180 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02036;SOR=Inf;LSEQ=TTCTCTATCAAAGGTAAATG;RSEQ=GAAGAACTTTTCATACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:640:0:0,0:406,234:0:2,0:23.9:1:31:1:1:0:60:41.667:1:0:0.2 0/1:390:4:3,1:225,160:0.0103:2,2:13.8:1:28:1:0.6452:2.13:60:8:0.0104:0:1.3 -17 59763347 . A G 316 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01425;LSEQ=TGCTTCCAGTAAATAAGGTG;RSEQ=GGTACTGTACTTTAAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1251:1245:607,638:1,1:0.9952:2,2:23.9:1:30.8:1:1:1.05105:60:55.591:0.9959:0:1.1 1/0:958:716:352,364:110,131:0.7474:2,2:25.9:1:30.2:1:0.37138:1.15:60:78.556:0.7489:0:1.1 -17 59763465 . T C 285 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGGAAAATTCAGCCAAGGA;RSEQ=TCCAGTGCACTTTCAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:484:484:177,307:0,0:1:0,2:24.3:1:32:1:1:0:60:120:1:0:1.1 1/0:429:338:137,201:38,53:0.7879:2,2:26.1:1:31.4:1:0.90443:1.05178:60:83.5:0.7859:0:1.1 -17 59763504 . C T 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12722;SOR=0;LSEQ=GTTGAATGGTGCTGAATCTG;RSEQ=TGCCGTACCCATTTAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:4:2,2:116,259:0.0106:2,2:16:1:30.8:1:0.5915:2.23:60:8:0.0106:0:2 0/0:332:0:0,0:127,205:0:2,0:24.4:1:31.8:1:1:0:60:82:1:0:0.7 -17 59770936 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19478;SOR=Inf;LSEQ=AATAAATCCAGTTTTCCAGT;RSEQ=GGACAGACAGAAAATTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:28,222:0:2,0:22:1:31.3:1:1:0:60:82.333:1:0:0.1 0/1:198:2:1,1:28,167:0.0101:2,2:5.5:1:29:1:0.27339:5.88:60:4:0.0103:0:1 -17 59820068 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGGTACAGTATGAGAT;RSEQ=CCCCAAAACAATTACAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:21.7:1:28.3:1:1:0:60:6:0.375:0:1 0/0:1:0:0,0:1,0:0:0,0:21:0:30:0:1:0:60:2:1:0:0 -17 59820170 . C A 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.24125;SOR=2.83771;LSEQ=AAATATCGTGAGAATTAACC;RSEQ=AAATGTGAAACAGAAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:12,0:21,0:0.3636:1,0:19.8:1:31:1:1:0:60:24:0.3636:0:1 1/0:8:5:5,0:3,0:0.625:0,0:34.6:1:30.2:1:1:0:60:10:0.625:0:1 -17 59820230 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATGGTGCTGAAAGACTTG;RSEQ=ACAATGCAGGGTTACCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:78,1:0.0247:1,2:35.5:1:30:1:0.04907:55.56665:60:4:0.0247:0:1 0/0:27:0:0,0:27,0:0:1,0:27.9:1:32.4:1:1:0:60:54:1:0:0.1 -17 59821173 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTCCCACCTCGGCCTCC;RSEQ=AAGTAGTTGGAACTATAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:2:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:37.5:1:31.5:1:1:0:60:4:1:0:1 -17 59856810 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAAAATGGCAAAACCCC;RSEQ=TCTCTACTAAAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:28.5:1:1:0:60:4:1:0:1 -17 59857393 . TAGA T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.13846;SOR=Inf;LSEQ=TTACAAAACTAAAACTTACT;RSEQ=AGAAGAAGCTGAAATACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:0:1,0:20.6:1:28.5:1:1:0:60:32:1:0:0 0/1:10:2:1,1:6,2:0.2:2,2:19:1:29:1:1:2.64575:60:4:0.2:0:0 -17 59857599 . CA C 198 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.2559;LSEQ=TAGAAACACTGAAGGCCTTC;RSEQ=AAAAAAAAAACAACAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:77:57,20:258,77:0.1842:2,2:26:1:31.6:1:0.55534:1.17517:60:154:0.1864:0.0311:0.2 0/1:330:18:11,7:229,82:0.0545:2,2:20.8:1:31.1:1:0.27645:1.77366:60:36:0.0547:0.0061:0.2 -17 59857809 . C G 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00091;SOR=2.18162;LSEQ=AAAATTATCTTTAGAAGAGG;RSEQ=TGGGCAAAGTGGCTCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:86:9,77:18,85:0.455:2,2:21.9:1:31.7:1:0.212:1.80622:60:85:0.4521:0:1.1 1/0:130:84:10,74:7,38:0.6462:2,2:23.4:1:31:1:0.59151:1.35973:60:41:0.6406:0:1 -17 59858089 . AAAC A 96 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.7578;SOR=0.72001;LSEQ=AAGAGCAAGACCCTGCCTCA;RSEQ=AACAACAACAACAACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:9:9,0:144,7:0.0563:1,0:20.6:1:30.6:1:1:0:60:18:0.0566:0.0125:0 0/1:73:3:2,1:69,0:0.0411:1,2:17.7:1:31.7:1:0.04167:0:60:6:0.0417:0:0 -17 59858343 . G A 66 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50862;SOR=1.67937;LSEQ=AGGAGTAAGTCTGTTGAATC;RSEQ=CAATTTTATAATCATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:668:4:3,1:211,453:0.006:2,2:9:1:26.8:1:0.09926:6.42:60:8:0.0061:0:1 0/1:499:5:3,2:173,321:0.01:2,2:17.6:1:28.8:1:0.35085:2.78:60:10:0.0102:0:1.2 -17 59861820 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17839;SOR=Inf;LSEQ=CATATTAAGTATAGAGGGGT;RSEQ=GGGAGGGAATTGGAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:36,229:0:2,0:22.6:1:30.1:1:1:0:60:52:0.9962:0:0.1 0/1:195:2:1,1:26,166:0.0103:2,2:38.5:1:29.5:1:0.2596:6.28:60:4:0.0104:0:1.5 -17 59870617 . A G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTAAATTAAGATGAAC;RSEQ=AAATAGGAATTTCTCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:8.3:1:30.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 59876352 . C T 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAAGGAACAATTCATTTC;RSEQ=CAAGAAGCCTAGTTAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:98,0:0:1,0:24:1:31.1:1:1:0:60:97:1:0:0.1 0/1:60:16:16,0:44,0:0.2667:1,1:22.4:1:32.1:1:1:0:60:32:0.2712:0:1 -17 59876667 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09997;SOR=Inf;LSEQ=AGATTTAAATCCATCTATAA;RSEQ=ATAAAAGAATTTTCTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:84,252:0:2,0:25.1:1:31.2:1:1:0:60:41:1:0:0.1 0/1:292:3:1,2:94,195:0.0103:2,2:21.3:1:22.7:1:1:1.04:60:2:0.0069:0:1.3 -17 59876784 . CAG C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.51765;SOR=0.52055;LSEQ=AAATGCAATTACATAAGCAA;RSEQ=AGATTCTAGGTCTTAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:39:0,39:0,2:0.9512:0,1:23.5:1:31.9:1:1:0:60:78:0.9512:0.1951:0 1/1:11:10:0,10:0,1:0.9091:0,0:15.1:1:32:1:1:0:60:20:0.9091:0.3636:0 -17 59878416 . G C 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02273;SOR=Inf;LSEQ=TCACTATGTTCCTTAAAACT;RSEQ=CTTGTTATTTTGGAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:0:1,0:26.9:1:33.1:1:1:0:60:30:1:0:0 0/1:7:3:3,0:4,0:0.4286:0,0:15.7:1:32.7:1:1:0:60:6:0.4286:0:1 -17 59878522 . C CA 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.88458;SOR=0.94207;LSEQ=TTTATTTACATAAATTAAAG;RSEQ=AAAAAAAATTAAAACATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:73:70,3:71,3:0.4932:1,1:19.5:1:30.4:1:1:1.01419:60:72:0.4898:0.1554:0.1 0/1:69:33:32,1:30,4:0.4783:2,1:22.5:1:30.7:1:0.35591:4.19:60:66:0.4783:0.1594:0.1 -17 59886113 . AG A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.0195;SOR=Inf;LSEQ=CAGCACCTAGAACAGTGGCC;RSEQ=GGGGCTGTAAGAAAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:0:0,0:135,295:0:2,0:24.9:1:31.1:1:1:0:60:52.75:1:0:0.1 0/1:361:5:3,2:128,228:0.0139:2,2:11:1:30.2:1:0.35759:2.66:60:10:0.014:0.0055:0.6 -17 59886992 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGGTTCTTAATAACTAC;RSEQ=TCCTTCTAAGTCTCAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:1:28.5:1:1:0:60:4:1:0:1 -17 59924512 . C T 167 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02021;LSEQ=CAGTGGAGAGTTGAGTTTTA;RSEQ=AGTCTTTCCTGAATCAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1268:56:26,30:617,593:0.0442:2,2:21.6:1:28.9:1:0.58491:1.20037:60:112:0.0446:0:1.1 0/0:1073:1:0,1:521,551:9e-04:2,0:1:0:24:0:1:0:60:2:9e-04:0:1 -17 59924612 . G C 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.45111;LSEQ=AGAACCAAAATGAAGTTTAA;RSEQ=GTGAACTAGAAGTTTAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:135:27,108:86,273:0.2733:2,2:22.3:1:30.4:1:0.40075:1.25949:60:134:0.274:0:1.1 0/1:414:60:14,46:114,239:0.1449:2,2:24.2:1:30.2:1:0.17762:1.56565:60:120:0.146:0:1.1 -17 59924643 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17714;SOR=Inf;LSEQ=AGTTTAACTGGCTAGTTGTT;RSEQ=TCAAAGGCCAAAACAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:30,239:0:2,0:23.1:1:32:1:1:0:60:66.25:1:0:0.3 0/1:196:2:1,1:29,165:0.0102:2,2:11.5:1:27:0:0.28336:5.61:60:4:0.0104:0:1.5 -17 59924684 . CA C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.54708;SOR=0;LSEQ=ATGTATTTTTTTCCTGCATC;RSEQ=AAAAAAGACTATTTCTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:1,116:0.0168:1,2:33:1:32.5:1:0.03347:82.30:60:4:0.0171:0:0 0/0:62:0:0,0:2,60:0:1,0:21.8:1:30.2:1:1:0:60:61:1:0:0.2 -17 59924862 . T C 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52315;LSEQ=AAAATGAACTTCTCATAAAA;RSEQ=AGTCCCATCATATGGACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:0.5:0,0:23.7:1:32.7:1:1:0:60:12:0.5:0:1 0/1:3:1:0,1:0,2:0.3333:0,0:40:0:34:0:1:0:60:2:0.3333:0:1 -17 59926633 . T TA 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.7428;LSEQ=GGAGTCTTATATAAGTAATT;RSEQ=AAAAAAAACAGCATAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:4:1,3:114,279:0.01:2,2:25:1:29.5:1:1:1.22519:60:8:0.0103:0:0.8 0/0:268:2:0,2:79,187:0.0075:2,0:35.5:1:32:0:1:0:60:4:0.0076:0:0 -17 59926645 . C T 203 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTAATTTAAAAAAAACAG;RSEQ=ATAAATAACTTACAGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:138:32,106:47,147:0.4157:2,2:20.4:1:28.6:1:0.89618:1.05894:60:276:0.4169:0:1.1 0/0:210:0:0,0:54,156:0:2,0:23:1:31.5:1:1:0:60:104:1:0:0.1 -17 59926837 . A AT 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=AATAGGAAAAGTCCAATTTG;RSEQ=TTTTTTAAATCGCCTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:0,6:0,8:0.4286:0,0:34.3:1:30.3:1:1:0:60:12:0.4286:0:0.2 0/0:2:0:0,0:0,2:0:0,0:26:1:30.5:1:1:0:60:4:1:0:0 -17 59934879 . G C 66 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCAATTGAAGTCAGGA;RSEQ=TTTGAGACCAGCCTGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:34:1:33:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 59938736 . A C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06905;SOR=Inf;LSEQ=TGAGAATATGAATGCAGTCA;RSEQ=ATACTCAATGTACTTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:150,11:0:2,0:21.8:1:30.5:1:1:0:60:79.5:1:0:0 0/1:113:3:3,0:102,8:0.0265:2,0:31.7:1:32:1:1:0:60:6:0.0265:0:1 -17 59939001 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08168;SOR=Inf;LSEQ=ACCAGAGAACCAAAACTAAG;RSEQ=GAGAAATCTGGAAACAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:2,135:0:1,0:27.5:1:30.8:1:1:0:60:21.833:1:0:0.1 0/1:106:3:0,3:4,99:0.0283:1,0:17.3:1:28:1:1:0:60:2:0.0192:0:2.3 -17 59939018 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.15639;SOR=Inf;LSEQ=AAGGGAGAAATCTGGAAACA;RSEQ=AAACTGGAATTAATAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:1,119:0:1,0:24.5:1:31.5:1:1:0:60:119:1:0:0.1 0/1:79:2:0,2:2,75:0.0253:1,0:6:1:30:1:1:0:60:4:0.0256:0:2 -17 60322868 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGCTCGCCACAACCTCC;RSEQ=CCTCCCAGGTTCAAGCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29.5:1:1:0:50:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 60324448 . C T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09227;SOR=0.24579;LSEQ=CACAATGAAGGGATGCCTTA;RSEQ=TTCCTCCAGAATATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:8:3,5:10,16:0.2353:2,2:19.5:1:31.3:1:1:1.04043:60:16:0.2353:0:1.4 0/1:29:2:0,2:13,14:0.069:2,0:28.5:1:31:0:0.48768:0:60:4:0.069:0:1 -17 61306444 . C T 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCATAAATGGTTCTTA;RSEQ=TATTTTGAGATATGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:28.5:1:1:0:54:4:1:0:1 -17 61307574 . AT A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.25361;SOR=0;LSEQ=GCAGTCCATCCATTTTATTA;RSEQ=TTTTTTCAAAAAAACAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:2,1:24,15:0.0714:2,2:7.3:1:25:1:1:1.24:60:2:0.0476:0.0238:0.3 0/0:32:0:0,0:21,11:0:2,0:23.6:1:29.5:1:1:0:60:64:1:0:0.4 -17 61307589 . A C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51489;SOR=0;LSEQ=TATTAATTTTTTTCAAAAAA;RSEQ=CAGCTCCTGGATTTGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:34,21:0.0351:2,2:13.5:1:32.5:1:1:1.60486:31:4:0.0351:0:2 0/0:38:0:0,0:23,15:0:2,0:26.3:1:29.6:1:1:0:60:76:1:0:0.3 -17 61307604 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13851;SOR=Inf;LSEQ=AAAAAACAGCTCCTGGATTT;RSEQ=TTGATTTTTTTTGAAGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:42,28:0:2,0:28.1:1:32.8:1:1:0:59.2:140:1:0:0.2 0/1:42:2:1,1:24,16:0.0476:2,2:12:0:29.5:1:1:1.48518:60:4:0.0476:0:2 -17 61307608 . A AT 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.14387;LSEQ=AACAGCTCCTGGATTTGTTG;RSEQ=TTTTTTTTGAAGGGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:2,1:40,27:0.0429:2,2:39:1:31.3:1:1:1.34:60:6:0.0429:0:0 0/1:41:2:1,1:22,17:0.0488:2,2:36:0:31.5:1:1:1.28591:60:4:0.05:0:0 -17 61307646 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTGTCTCTGTCTCCCTC;RSEQ=GTTCTGCTGTAATCTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:33,29:0.0313:2,2:24.5:1:29.5:1:1:1.13563:60:4:0.0317:0:1.5 0/0:31:0:0,0:12,19:0:2,0:26.3:1:29.7:1:1:0:60:30:1:0:0.2 -17 61307713 . C G 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24786;SOR=0;LSEQ=GTTTCTTTGCTCTTGGTTCT;RSEQ=TAGTTCTTTTAGTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:1,12:0.1875:1,0:20:1:33:0:1:0:60:6:0.1875:0:1 0/0:11:0:0,0:1,10:0:2,0:27.6:1:32.1:1:1:0:60:22:1:0:0.3 -17 61851435 . C T 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TATCTGAGGAGCCTGTGAGG;RSEQ=GTTCTGGAGCTTTAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:15.5:1:30.5:1:1:0:60:4:0.5:0:2.5 1/0:2:1:0,1:0,1:0.5:0,0:41:0:30:0:1:0:60:2:0.5:0:1 -17 61851485 . C A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGAGCCGTAGCCCCGGCC;RSEQ=CGCCCTTCTGCCCGCGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:26.7:1:28.7:1:1:0:60:6:0.4286:0:2 0/0:1:0:0,0:0,1:0:0,0:47:0:33:0:1:0:60:2:1:0:0 -17 61851573 . T C 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12195;SOR=Inf;LSEQ=GGGCCGTGAGGCGGTGGCGG;RSEQ=GGTGGCGGTGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:20:1:27.7:1:1:0:60:12.5:1:0:0.7 0/1:15:2:1,1:8,5:0.1333:2,2:12:0:28.5:1:1:1.54914:45:4:0.1429:0:2 -17 61851588 . C T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1;SOR=1.13931;LSEQ=GGCGGTGGTGGCGGTGGCGG;RSEQ=GGCGGTGGTGGTGGTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:9,5:5,9:0.5:2,2:29.4:1:27.7:1:0.2568:3.10:60:6:0.48:0:1.3 1/0:15:8:5,3:3,2:0.5333:2,2:20.6:1:27.9:1:1:1.10:60:7:0.5:0:1.1 -17 61851603 . TGGC T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.28311;SOR=0.42778;LSEQ=GGCGGCGGCGGTGGTGGTGG;RSEQ=GGCGGCGGCGGCGAAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:10,6:4,6:0.6667:2,2:27.3:1:31.9:1:0.42164:2.41:60:32:0.6667:0.125:1.2 0/1:11:5:2,3:4,2:0.4545:2,2:20.6:1:30.5:1:0.5671:2.69977:60:10:0.5:0.0909:1 -17 61851612 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.10417;SOR=Inf;LSEQ=GGTGGTGGTGGTGGCGGCGG;RSEQ=GGCGGCGAAGGGGGCGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:31.6:1:31.4:1:1:0:60:44:1:0:0.9 0/1:11:2:1,1:5,4:0.1818:2,2:8:0:30:1:1:1.22474:45:4:0.1818:0:2 -17 61851751 . T G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAGGTTTGTGCGTGGGG;RSEQ=TTCTGGACGCAAGGCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:40:1:32:1:1:0:60:4:1:0:1 1/1:2:2:0,2:0,0:1:0,0:29:1:30.5:1:1:0:60:4:1:0:1 -17 61878355 . C CCTTT 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTCTTTCTCCCTTTCTCTTT;RSEQ=CTTTTTTTCCTCTCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19:1:31.8:1:1:0:60:4:1:0.5:0.5 0/0:1:0:0,0:1,0:0:0,0:48:0:30:0:1:0:60:2:1:0:0 -17 61878535 . G A 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00699;SOR=0;LSEQ=TCTGCCTGCCTCAGCCTCCT;RSEQ=GGTAACTGGGATTACAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:3,5:0,1:0.8889:0,2:38.1:1:29:1:1:0:60:7:0.875:0:1.4 0/0:4:0:0,0:1,3:0:2,0:25.5:1:30:1:1:0:60:8:1:0:0 -17 61878584 . T A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATGCCTGGCTAATTTTTTT;RSEQ=AAATATTTTTGGTAGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:0,1:0:0,0:23:0:30:0:1:0:60:2:1:0:0 -17 62006432 . GG AC 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00215;SOR=Inf;LSEQ=GGCCCTTTGGCAAGAGCTGG;RSEQ=ACCAGGGGCTGGAGACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:0:1,0:24.5:1:30.5:1:1:0:60:19:1:0:0.1 0/1:18:4:4,0:13,1:0.2222:1,0:25.3:1:30.4:1:1:0:60:8:0.2222:0.0556:1.5 -17 62006497 . A G 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=376.68786;LSEQ=AGAGGCCAGCTGGGGGGTCC;RSEQ=GGAAAGGGGTTGGGCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:1,0:193,2:0.0051:1,0:34:0:32:0:1:0:60:2:0.0051:0:1 1/0:69:46:45,1:21,2:0.6667:2,1:23.2:1:29.5:1:0.25593:4.19:60:92:0.6765:0:1.1 -17 62006931 . G A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05566;SOR=Inf;LSEQ=GGCCAGGGAGAGGGGTGAGG;RSEQ=GTCAGGAGTGAGGTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:87,287:0:2,0:23.7:1:30.8:1:1:0:60:61.333:1:0:0.1 0/1:232:3:2,1:53,176:0.0129:2,2:12.3:1:22:1:0.14072:6.57:60:6:0.0132:0:1 -17 62006968 . TGAAG T 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=4.000;MSILEN=4;SSF=0.2466;SOR=4.20404;LSEQ=ATTCTGCAAGAACAGCTGAA;RSEQ=GAAGGAAGGAAGGAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:0,1:82,165:0.004:2,0:22:0:27:0:1:0:60:2:0.0041:0:0 0/1:119:2:1,1:25,92:0.0168:2,2:28.5:1:32.5:1:0.39069:3.63:60:4:0.0171:0:1 -17 62006984 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.09644;SOR=Inf;LSEQ=TGAATGAAGGAAGGAAGGAA;RSEQ=GAATGATTGAATTGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:104,125:0:2,0:24.4:1:30.9:1:1:0:60:18.083:0.9954:0:0.1 0/1:105:2:0,2:39,63:0.019:2,0:13:1:24.5:1:0.5267:0:60:4:0.0194:0:2.5 -17 62006997 . T C 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGGAAGGAATGATTGAAT;RSEQ=GGTGAGCCAGTGGGGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:135,105:0:2,0:24.3:1:30.4:1:1:0:60:39:1:0:0.2 0/1:99:43:22,21:30,26:0.4343:2,2:24.1:1:31:1:0.84144:1.10032:60:86:0.4343:0:1.2 -17 62007081 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16662;SOR=5.65865;LSEQ=CTGCATATGCCTGGCCTATG;RSEQ=GGTGGCCTCCTCTGCGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:1:1,0:348,165:0.0019:2,0:11:0:30:0:1:0:60:2:0.002:0:1 0/1:366:4:1,3:244,118:0.0109:2,2:14.5:1:29:1:0.10748:6.17066:60:8:0.011:0:1.3 -17 62007498 . A G 298 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1087.66011;LSEQ=GTGTTGTTGCACTTCTGCTG;RSEQ=CAGAAGTAGATGCCATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1493:3:2,1:794,692:0.002:2,2:23.7:1:31.7:1:1:1.74:60:6:0.0021:0:4 1/0:1161:798:421,377:193,169:0.6873:2,2:24.8:1:31:1:0.899:1.02264:60:45.941:0.6869:0:1.2 -17 62007552 . G A 186 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=34.21397;LSEQ=CCTTGGATGGTGAGGGTGGC;RSEQ=AGAGATTCGTTCTGGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1745:3:3,0:858,884:0.0017:2,0:1:0:26.3:1:0.11991:0:60:6:0.0017:0:1 0/1:1311:73:39,34:611,626:0.0557:2,2:26:1:30.1:1:0.54783:1.18:60:146:0.0562:0:1.5 -17 62007775 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15771;SOR=Inf;LSEQ=CCAAGGCCAGGCTCAGCATT;RSEQ=CGCTTGGCATCTTCCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:42,147:0:2,0:24.3:1:31:1:1:0:60:46.25:1:0:0.1 0/1:125:2:1,1:38,85:0.016:2,2:16:1:26.5:1:0.52839:2.22:60:4:0.0161:0:1 -17 62007805 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.53071;SOR=0;LSEQ=TCTTCCTGAGTGCCAGCCCC;RSEQ=GCAGCAGGCCCCTGCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:13,87:0.0196:2,2:27.5:1:29.5:1:0.25684:6.49:60:4:0.0198:0:1 0/0:60:0:0,0:9,51:0:2,0:23.2:1:30.6:1:1:0:60:59:1:0:0.1 -17 62007829 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.13648;SOR=Inf;LSEQ=GCAGGCCCCTGCCCTGGCTG;RSEQ=CACAGACTCCCTGGGCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:1,63:0:1,0:25.3:1:32.5:1:1:0:60:128:1:0:0.1 0/1:38:2:1,1:0,36:0.0526:1,2:16.5:1:29:1:0.05263:0:60:4:0.0526:0:1 -17 62008437 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05983;SOR=Inf;LSEQ=CTGAGTCCTAGAGGAACCCC;RSEQ=AGGCTCCCTTGCTATGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:0:1,0:27.1:1:29.8:1:1:0:60:19:1:0:0.1 0/1:7:2:2,0:4,1:0.2857:2,0:33.5:1:31.5:1:1:0:60:4:0.2857:0:1 -17 62008535 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGTGGGCTGGGGGTGGG;RSEQ=CTCAGAGGAGATCCTAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:135,2:0.0144:1,2:11.5:1:30.5:1:0.04285:55.36251:60:4:0.0153:0:1.5 0/0:65:0:0,0:62,3:0:1,0:23.7:1:31.5:1:1:0:60:64:1:0:0.2 -17 62008606 . C T 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.75112;SOR=1.35204;LSEQ=ATCAGGCAAGGGTGGGAAGG;RSEQ=GGACCGCCCCCAGGACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:5:2,3:333,112:0.0111:2,2:10.4:1:27.4:1:0.10827:4.44134:60:10:0.0114:0:1.2 0/1:334:5:2,3:235,94:0.015:2,2:11.4:1:27:1:0.14902:3.73293:60:10:0.0153:0:1 -17 62008611 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16662;SOR=5.65865;LSEQ=GCAAGGGTGGGAAGGCGGAC;RSEQ=GCCCCCAGGACAGGGACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:1:0,1:366,147:0.0019:2,0:1:0:28:0:0.28794:0:60:2:0.002:0:1 0/1:366:4:1,3:250,112:0.0109:2,2:13:1:28.5:1:0.09366:6.65864:60:8:0.0111:0:1.3 -17 62008760 . G A 242 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCAGCTGCTGGGTGGGAG;RSEQ=AAGTGGGCGGGGCCAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:290:113,177:282,396:0.299:2,2:26.7:1:29.7:1:0.47553:1.11532:60:47.333:0.298:0:1.2 0/0:713:0:0,0:294,419:0:2,0:25.1:1:30.5:1:1:0:60:46.533:1:0:0.2 -17 62008857 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57329;SOR=0;LSEQ=ACTTCCTCCTTCCATGACAG;RSEQ=AGCTTCAAGACCCCTCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:3:0,3:2,189:0.0155:1,0:29:1:29.7:1:1:0:60:6:0.016:0:1 0/0:66:0:0,0:3,63:0:1,0:23.8:1:31.7:1:1:0:60:32:1:0:0.2 -17 62008885 . C T 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACCCCTCGGTCCTCCCTG;RSEQ=CCCCAGTACTTGGGAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:3,121:0:1,0:24.7:1:31.1:1:1:0:60:30:1:0:0.1 0/1:37:11:1,10:1,25:0.2973:1,2:23.5:1:29.6:1:0.51201:2.43:60:22:0.3056:0:1.2 -17 62008965 . T G 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00342;SOR=Inf;LSEQ=CTTTCTGCCTTTGACCCTCA;RSEQ=GGTGGCTTTGAGCAGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:1,21:0:1,0:20.4:1:29.4:1:1:0:60:21:1:0:0 1/0:5:3:0,3:0,2:0.6:0,0:15.7:1:31.7:1:1:0:60:6:0.6:0:1.7 -17 62009443 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16171;SOR=Inf;LSEQ=CCATGAGAGGGAGACAGGCG;RSEQ=TAAAGAGTGAGAGACAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:224,28:0:2,0:20.3:1:31.2:1:1:0:60:41:1:0:0.1 0/1:170:2:1,1:140,28:0.0118:2,2:20.5:1:26:1:0.31291:4.93067:60:4:0.0118:0:1 -17 62009460 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06517;SOR=Inf;LSEQ=GCGGTAAAGAGTGAGAGACA;RSEQ=AGGAGGAGGGTGGAGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:291,55:0:2,0:23.3:1:32.3:1:1:0:60:68.2:1:0:0.1 0/1:234:3:1,2:174,57:0.0128:2,2:11.3:1:28.3:1:0.15745:6.04685:60:6:0.013:0:1 -17 62009719 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14612;SOR=5.14236;LSEQ=CTGCAGCCTGTCCCCTCCCC;RSEQ=CCTCTTCCTCACCAGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:1:1,0:59,278:0.003:2,0:1:0:25:0:0.17751:0:60:2:0.0031:0:1 0/1:199:3:2,1:34,162:0.0151:2,2:25.3:1:26.7:1:0.0849:9.37:60:6:0.0155:0:1 -17 63313715 . A T 71 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCATTACATCAGCTCTG;RSEQ=GTGGCAGGTTCTTTGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,0:0.7143:0,0:32.4:1:30.8:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 63314191 . G T 226 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTTATGCCAAACCACTC;RSEQ=TTCGTGCTTGGATACCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:0:0,0:347,357:0:2,0:24.3:1:30.8:1:1:0:60:87:0.9986:0:0.1 0/1:557:193:100,93:176,188:0.3465:2,2:25.6:1:29.8:1:0.47641:1.15:60:63.333:0.3473:0:1.1 -17 63314330 . A C 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TAGAAGTTATTATATATATC;RSEQ=CAAAGACTCCCATTGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:0,89:0:1,0:24:1:29.6:1:1:0:60:28.667:1:0:0 0/1:47:10:0,10:0,37:0.2128:1,0:20.9:1:30.1:1:1:0:60:9:0.1957:0:1 -17 63529650 . T A 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCAGTGTGCCTGTCCCTC;RSEQ=TTTTGCTCCCTGCTCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:30.5:1:31:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 63529821 . C T 142 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01283;SOR=0;LSEQ=GTCCCCCAGAGAACCCTCCA;RSEQ=GCAGCCTCCCTCTTGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:25,1:0,0:1:0,1:18.4:1:30.3:1:1:0:60:52:1:0:1 1/0:9:6:6,0:3,0:0.6667:0,0:30.5:1:29.8:1:1:0:60:12:0.6667:0:1 -17 63529905 . C A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16688;SOR=5.79334;LSEQ=GAGAAGGGAGCCTCCCCCAG;RSEQ=GCCTGCTGAGCCCCCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:1,0:156,2:0.0063:1,0:49:0:15:0:1:0:60:0:0:0:6 0/1:56:2:2,0:54,0:0.0357:1,0:33:1:30.5:1:1:0:60:4:0.037:0:1 -17 63531884 . C T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02051;SOR=Inf;LSEQ=ATTTAGAGGTACACTGTTGT;RSEQ=CCCAGAGCAATTGAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:109,442:0:2,0:23.6:1:31:1:1:0:60:44.917:1:0:0.1 0/1:337:4:2,2:85,247:0.0119:2,2:27.5:1:29.3:1:0.2763:2.90:60:8:0.0121:0:1 -17 63531958 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGAACCCGACTTCCATCC;RSEQ=TACGGAGACCCAACCAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:5,122:0.0155:1,2:10.5:1:31:1:0.09121:22.37:60:4:0.0163:0:1 0/0:59:0:0,0:2,57:0:1,0:22.5:1:29.8:1:1:0:60:28.5:1:0:0.2 -17 63532175 . A G 140 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAGGAATGGGATTTGTA;RSEQ=GCAATTGCTGAAATTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:16,5:0,0:1:0,2:21.2:1:32.1:1:1:0:60:42:1:0:1.1 1/1:1:1:1,0:0,0:1:0,0:4:0:31:0:1:0:60:2:1:0:1 -17 63532365 . C T 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAGAAAGAGAGGCCCTCC;RSEQ=CATTAGCCACAGACCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:351,138:0:2,0:22.3:1:30.7:1:1:0:60:96.8:1:0:0.1 0/1:314:15:12,3:217,82:0.0478:2,2:21.3:1:31.2:1:0.7669:1.51:60:30:0.0482:0:1.2 -17 63532517 . G A 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCGTGTTGGGTGGGGTCA;RSEQ=GGGAGGCATCGCAGGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1023:0:0,0:490,533:0:2,0:23.9:1:31.6:1:1:0:60:126.875:1:0:0.2 0/1:821:104:53,51:324,390:0.1267:2,2:22.6:1:30.7:1:0.29422:1.25:60:208:0.1287:0:1.3 -17 63532527 . C T 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGGGTCAGGGGAGGCAT;RSEQ=GCAGGGTCCTGGGTGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:991:0:0,0:474,515:0:2,0:24.1:1:30.3:1:1:0:60:48.45:0.9979:0:0.2 0/1:805:28:12,16:357,417:0.0348:2,2:19.9:1:29.9:1:0.84765:1.1413:60:56:0.0353:0:1.2 -17 63532746 . T C 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=ACTGGAAAATGTGACTTCAA;RSEQ=AGAAACTTGTCTATTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:28,88:0:2,0:25.9:1:27.9:1:1:0:60:13.5:1:0:0.8 0/1:55:7:0,7:2,46:0.1273:1,0:32:1:32.7:1:1:0:60:14:0.1321:0:1.9 -17 63532767 . C G 205 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAAACTTGTCTATTCTGCT;RSEQ=AGAGAGAGAGTTAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:102:102:36,66:0,0:1:0,2:26.2:1:30.8:1:1:0:60:19.4:1:0:1.1 1/0:41:27:3,24:1,13:0.6585:1,2:26:1:31.2:1:1:1.61:60:26:0.65:0:1.3 -17 63532779 . T TA 86 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.06011;SOR=0;LSEQ=ATTCTGCTCAGAGAGAGAGT;RSEQ=AAAAAAAAAACTACCATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:9:2,7:40,47:0.0938:2,2:34.1:1:27.2:1:0.29081:2.94815:60:8:0.087:0:1 0/0:38:0:0,0:7,31:0:2,0:25:1:27.7:1:1:0:60:18:1:0:0.9 -17 63532854 . G A 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=TGTGGTCTGCTCAGTCCAAC;RSEQ=TTTAATATTAAGATGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:122,20:0:2,0:24.9:1:30:1:1:0:60:46.333:1:0:0.7 0/1:60:7:4,3:50,3:0.1167:2,2:13.6:1:30.1:1:0.01736:11.513:60:14:0.1167:0:1 -17 63532914 . A G 249 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTCCGCGGACTGCAAAAAC;RSEQ=GCCATTCCCACAATACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:341:341:308,33:0,0:1:0,2:25:1:29.6:1:1:0:60:47.714:1:0:1.1 1/0:215:150:131,19:55,9:0.6977:2,2:23.7:1:29.4:1:0.82585:1.13:60:49:0.6967:0:1.1 -17 63532948 . A T 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCTCCGTACTGAGTGCCC;RSEQ=TGACCCTCGCGGCCGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:624:0:0,0:442,182:0:2,0:23:1:29.9:1:1:0:60:68.333:1:0:0.6 0/1:487:52:33,19:298,137:0.1068:2,2:20.1:1:30.1:1:0.5295:1.25175:60:104:0.1074:0:1.2 -17 63533264 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.12269;SOR=Inf;LSEQ=ATCAGACAATTCAGCAAGTC;RSEQ=GGGGGCTGGTGACACGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:62,231:0:2,0:25.3:1:30.7:1:1:0:60:96.667:0.9966:0:0.1 0/1:159:2:0,2:30,127:0.0126:2,0:12.5:1:32:0:1:0:60:4:0.0127:0:1 -17 63533423 . C A 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCCCCACACGGGACACTG;RSEQ=GGTCCGCCCGGCACTTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:0:0,0:453,306:0:2,0:24.8:1:30.7:1:1:0:60:62.25:0.996:0:0.1 0/1:539:76:48,28:271,191:0.141:2,2:25.4:1:29.6:1:0.52913:1.21:60:75:0.1412:0:1.2 -17 63533732 . ATGG A 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.7442;SOR=1.11185;LSEQ=AGCAGGGAGTGGTACTGCGA;RSEQ=TGGTGGTGGTGGTGGTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:812:22:11,11:363,422:0.0271:2,2:24.7:1:30.8:1:0.82941:1.16:60:44:0.0278:0.0037:1.8 0/1:566:17:8,9:254,294:0.03:2,2:28.9:1:30.2:1:1:1.03:60:34:0.0306:0.0035:0.8 -17 63533768 . G A 295 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.00257;LSEQ=TGGTCCGGGGAGCGGGAGCG;RSEQ=GGGCTATAGCGGCCTACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:854:853:417,436:0,0:0.9988:0,2:24.7:1:30.3:1:1:0:60:55.867:1:0:1.9 1/0:662:455:230,225:108,99:0.6873:2,2:24.2:1:29.7:1:0.73748:1.06707:60:150.667:0.688:0:2 -17 63533789 . T C 294 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11267;LSEQ=GGGCTATAGCGGCCTACGCC;RSEQ=GGAGACTGGCAGCCAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:852:848:407,441:0,1:0.9953:0,2:25.7:1:30.3:1:1:0:60:76.091:0.9952:0:1.9 1/1:696:668:336,332:14,14:0.9598:2,2:25.1:1:29.3:1:1:1.01:60:46.714:0.9589:0:1.7 -17 63534036 . AC A 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=GTTGCAACATTCGGCTCCCT;RSEQ=GCAGGAGCACGCACACCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:28,47:0:2,0:26.3:1:30.6:1:1:0:60:150:1:0:0.1 0/1:34:7:3,4:5,22:0.2059:2,2:26.9:1:32.3:1:0.31525:3.16:60:14:0.2059:0.0588:0 -17 63534154 . C T 241 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01364;LSEQ=ACCCACACGCAACCCATGCA;RSEQ=ATGCGCACACAGCCCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:244:242:218,24:1,0:0.9918:0,2:24.1:1:30.5:1:1:0:60:39.333:0.9958:0:1.2 1/0:121:75:69,6:37,9:0.6198:2,2:25.8:1:30.2:1:0.08712:2.77:60:150:0.6303:0:1.3 -17 63534221 . C T 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCATGCGCATGCAACCCA;RSEQ=GCACATGCGCACACCCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:608:0:0,0:375,233:0:2,0:24.4:1:30.7:1:1:0:60:75:1:0:1.1 0/1:434:67:39,28:237,130:0.1544:2,2:23.9:1:29.6:1:0.33572:1.30801:60:66:0.1531:0:2 -17 63534250 . T C 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12385;LSEQ=GCACACCCTAACGCACCCCA;RSEQ=GCACATGCGCATACACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:777:772:432,340:1,1:0.9936:2,2:25.8:1:31:1:1:1.27:60:95.5:0.9948:0:1.2 1/1:623:592:342,250:15,14:0.9502:2,2:25.3:1:30.4:1:0.56655:1.28:60:147:0.9545:0:1.3 -17 63534478 . G A 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=63.79762;LSEQ=TTCTCTACAGGACGTGGAAA;RSEQ=GAAAGGGAGGAGGCACGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:1:1,0:114,299:0.0024:2,0:1:0:25:0:0.27778:0:60:2:0.0024:0:1 0/1:350:47:18,29:98,205:0.1343:2,2:25.3:1:30.6:1:0.41099:1.30:60:94:0.1362:0:1.2 -17 63534504 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32852;SOR=3.75454;LSEQ=GGAGGAGGCACGTTCAGCAG;RSEQ=CTAGGTGGGCGGTGGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:1,0:56,205:0.0038:2,0:40:0:28:0:0.21756:0:60:2:0.0038:0:1 0/1:211:3:2,1:47,161:0.0142:2,2:25.7:1:27.3:1:0.13537:6.77:60:6:0.0145:0:2.3 -17 63534514 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17939;SOR=Inf;LSEQ=CGTTCAGCAGGCTAGGTGGG;RSEQ=GGTGGCTTGGCCGGAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:31,182:0:2,0:21.8:1:29.6:1:1:0:60:41.6:1:0:0.5 0/1:157:2:0,2:30,125:0.0127:2,0:27:1:30.5:1:1:0:60:4:0.0131:0:1.5 -17 63534538 . C A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10287;LSEQ=GGCTTGGCCGGAGCTTCCCG;RSEQ=ACCAGGCGCTGTGCACCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:118:100:4,96:1,17:0.8475:1,1:25.7:1:29.8:1:0.5697:1.40718:60:32.333:0.8435:0:1.2 0/1:86:31:1,30:4,51:0.3605:2,1:23.1:1:29.7:1:0.64971:2.33271:60:30:0.3571:0:1.1 -17 63534715 . T C 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGAGGCCCTGCTTGTTCT;RSEQ=TCTGTAGTACAACCAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:19:1:32.7:1:1:0:60:14:1:0:1.1 1/1:2:2:0,2:0,0:1:0,0:11:1:33:0:1:0:60:4:1:0:3 -17 63537142 . A G 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCTGGGACTACAGGCGC;RSEQ=CGTCACCACGCTAGGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15:1:30:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 63537751 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15478;SOR=Inf;LSEQ=CACATGGGCTACTGTCATAT;RSEQ=CCATCTTGAGATCCCGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:26,223:0:2,0:22.3:1:32.1:1:1:0:60:40.5:1:0:0.1 0/1:162:2:1,1:21,139:0.0123:2,2:22:1:26:1:0.25389:6.49:60:4:0.0124:0:1 -17 63537898 . T C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=TCTATGGAAACTTGGCTTCC;RSEQ=TGGATGCAGAAGCATCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:1:0,1:20.3:1:33.2:1:1:0:60:40:1:0:1 1/1:6:5:1,4:0,1:0.8333:0,2:30:1:31:1:1:0:60:10:0.8333:0:1.4 -17 63545622 . T C 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGCAAGCCCACGGAAGGG;RSEQ=GGCCAGGATACTCACACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:802:0:0,0:508,290:0:2,0:24.6:1:29.7:1:1:0:60:56:1:0:0.2 0/1:624:48:30,18:373,203:0.0769:2,2:23.9:1:31.5:1:0.75532:1.10229:60:96:0.0783:0:1.1 -17 63554307 . A G 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTTCAGCTGCTTGGAGAC;RSEQ=ATGCTGTTGTTCTCAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1310:0:0,0:642,667:0:2,0:26.7:1:30.1:1:1:0:60:86.267:0.9992:0:0.1 0/1:993:62:32,30:462,466:0.0624:2,2:26:1:30.5:1:0.79459:1.08:60:124:0.0635:0:1.2 -17 63554591 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27153;LSEQ=CCTGGTGTTGGAAGAGACAG;RSEQ=CATGGGTTTGGTGACCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:684:490:223,267:92,102:0.7164:2,2:24.4:1:29.7:1:0.67104:1.0798:60:53.444:0.7147:0:1.1 0/1:460:187:90,97:118,154:0.4065:2,2:22.8:1:28.9:1:0.3405:1.21:60:92.5:0.4139:0:1.1 -17 63554802 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14792;SOR=Inf;LSEQ=CCAGTTCCTCTCAGCAATCG;RSEQ=CGTGGTCTCTCTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:9,83:0:2,0:24.4:1:32.1:1:1:0:60:91:1:0:0 0/1:58:2:1,1:6,50:0.0345:2,2:32.5:1:28.5:1:0.22868:7.79:60:4:0.0345:0:1 -17 64938182 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCCAGGCTGGAAGCAG;RSEQ=CGGCCCGCATCCAGGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:58,3:0.0317:1,2:15.5:1:30.5:1:0.12391:16.88608:60:4:0.0328:0:1 0/0:26:0:0,0:26,0:0:1,0:26.2:1:32.2:1:1:0:60:52:1:0:0.1 -17 64938281 . C G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29753;SOR=0.71422;LSEQ=TCCCTGTCAACCTCAGGAAG;RSEQ=CAAGAAGCAGTCTTCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:33:20,13:141,104:0.1183:2,2:27:1:31.9:1:0.85161:1.13:60:66:0.1204:0:1.5 0/1:206:18:12,6:108,80:0.0874:2,2:29.2:1:31.2:1:0.61798:1.48:60:36:0.0887:0:1.6 -17 64938342 . A C 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04869;SOR=1.63652;LSEQ=CGGCTTCTCTGATCCAGCAC;RSEQ=GGCCTGCTGCCCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:36:14,22:125,153:0.1146:2,2:28.6:1:30.4:1:0.59345:1.28284:60:72:0.1161:0:1.5 0/1:240:42:22,20:88,110:0.175:2,2:24.5:1:29.6:1:0.39563:1.37:60:84:0.1772:0:1.2 -17 64938402 . GG TT 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0033;SOR=0;LSEQ=CTCCTGTGACCATTATTTCA;RSEQ=AAACAAACTCCTTTAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:11:1,10:58,124:0.057:2,2:18.7:1:29.9:1:0.17751:4.65062:60:22:0.0576:0.0052:0.9 0/0:137:0:0,0:43,94:0:2,0:24.2:1:30.4:1:1:0:60:44.667:1:0:0.3 -17 66511448 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24359;SOR=Inf;LSEQ=AAAAAAATCCCTGTGAATCA;RSEQ=TTGTCTAATGAATTTAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:56,3:0:2,0:23.2:1:32.3:1:1:0:60:58:1:0:0.2 0/1:58:2:1,1:53,3:0.0345:2,2:22:1:30:1:0.1343:15.44073:60:4:0.0351:0:1 -17 66511500 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.499;SOR=0;LSEQ=GATTGACATTTTGCTTTATA;RSEQ=TTTATACAAGCATGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:118,36:0.0128:2,2:14:1:30:1:0.41927:3.24683:60:4:0.013:0:1 0/0:145:0:0,0:104,41:0:2,0:26.9:1:31.5:1:1:0:60:290:1:0:0.1 -17 66511803 . G GA 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16573;SOR=Inf;LSEQ=TTACTAATTTGTATTTTTTG;RSEQ=AAGAAAAGGAATCTGACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:4,138:0:1,0:24.7:1:31.3:1:1:0:60:70:1:0:0.1 0/1:98:2:1,1:4,92:0.0204:1,2:23:1:26:1:0.09994:20.68:60:4:0.0204:0.0102:0.5 -17 66518663 . A G 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAATGGCTTGTACTAATG;RSEQ=CTTTTGCCCATTAATAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:0.2222:1,0:28.3:1:32:1:1:0:60:8:0.2353:0:1.3 0/0:1:0:0,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 -17 66518780 . TA T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.80298;SOR=1.19485;LSEQ=TTGGTGTTTTCCTCTTAACT;RSEQ=CATTGTTAATGGAAGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:13:13,0:70,0:0.1566:1,1:23.3:1:32.2:1:1:0:60:26:0.1566:0.012:0 0/1:44:8:8,0:36,0:0.1818:1,0:20.1:1:32:1:1:0:60:16:0.1818:0.0227:0 -17 66518875 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04617;SOR=Inf;LSEQ=ATGCCGAAGGATCTCATTTT;RSEQ=CAAACTCGTAATTTCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:291,131:0:2,0:25.1:1:32:1:1:0:60:59.286:0.9976:0:0.1 0/1:367:4:2,2:241,121:0.0109:2,2:33.8:1:27.8:1:0.60498:1.98775:60:8:0.0109:0:1 -17 66519787 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.185;SOR=Inf;LSEQ=ATACCATAATGTGGCTTGAC;RSEQ=TTTAATTGAAGCGCAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:214,49:0:2,0:22.5:1:30.1:1:1:0:60:64.75:1:0:0.1 0/1:199:2:1,1:155,42:0.0101:2,2:24:1:29.5:1:0.38633:3.65941:60:4:0.0102:0:1 -17 66519857 . C CT 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.20587;SOR=1.20717;LSEQ=TTGTCATTTGACCTTCAGTT;RSEQ=TTTTCTAGGTTATACCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:116:62,54:357,226:0.1657:2,2:29.3:1:30.6:1:0.12102:1.37515:59.9:232:0.1671:0.0229:0.1 0/1:548:106:54,52:239,203:0.1934:2,2:27.2:1:30.5:1:0.58874:1.13347:60:212:0.1959:0.0237:0.1 -17 66520274 . A AT 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.18855;SOR=Inf;LSEQ=AGAGGAGGCGAGACTAGAGG;RSEQ=TTTTTTTGGTTTTGTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:32,211:0:2,0:24.7:1:30.9:1:1:0:60:120.5:1:0:0.1 0/1:187:2:1,1:31,154:0.0107:2,2:35:1:29.5:1:0.31373:4.91:60:4:0.0109:0:0 -17 66520325 . C CT 71 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.29182;SOR=2.25334;LSEQ=TTTCCTCTTTGATCCTACCA;RSEQ=TTTTTTTTTTCTGTTATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:5:0,5:6,103:0.0431:2,0:37.4:1:31.6:1:1:0:60:10:0.0435:0:0 0/1:54:5:0,5:1,47:0.0926:1,0:16.8:1:30.9:1:1:0:60:10:0.1:0.0185:0 -17 66520427 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36842;SOR=4.47215;LSEQ=GGGAACTAATATTTTTGATA;RSEQ=AGTTTTGTTTATAATTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:0,3:1,14:0.1667:1,0:22.3:1:28.3:1:1:0:60:6:0.1765:0:1 1/0:2:1:0,1:0,1:0.5:0,0:2:0:30:0:1:0:60:2:0.5:0:1 -17 66520970 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49862;SOR=0;LSEQ=CTCTCACAGTACCACTGTAA;RSEQ=ATAAGTTTATTGTTTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:108,15:0.016:2,2:17:1:27.5:1:0.24052:7.00356:60:4:0.0164:0:1 0/0:116:0:0,0:95,21:0:2,0:20.3:1:30:1:1:0:60:232:1:0:0.1 -17 66520989 . A G 33 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.61915;SOR=2.0604;LSEQ=AAATAAGTTTATTGTTTTGT;RSEQ=ATAATTTTGATAATTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:1,0:153,40:0.0052:2,0:5:0:31:0:1:0:60:2:0.0053:0:1 0/1:189:2:1,1:135,51:0.0106:2,2:16:0:33.5:1:0.47776:2.63118:60:4:0.0106:0:1.5 -17 66521160 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08412;SOR=Inf;LSEQ=CCAATGTATTGATCGCTTCC;RSEQ=AGCAATAAGAATAGTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:21,138:0:2,0:22.6:1:30.9:1:1:0:60:78.5:1:0:0.1 0/1:125:3:2,1:22,100:0.024:2,2:10.3:1:27.7:1:0.0941:8.86:60:6:0.0242:0:1 -17 66522047 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06743;SOR=Inf;LSEQ=CGAGACAGCTATAGAAGAAT;RSEQ=CTCATGGTAAGAGACCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:113,292:0:2,0:24.5:1:31:1:1:0:60:56.857:1:0:0.1 0/1:279:3:2,1:74,202:0.0108:2,2:20:1:27.3:1:0.1812:5.42:60:6:0.0109:0:1 -17 66522186 . T TTC 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.03492;LSEQ=TTCTTTTAATAAGCGAATAT;RSEQ=TTTCTTTTAATGAGCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:0,29:0.2162:1,0:28.4:1:31.8:1:1:0:60:16:0.2162:0.0541:0.3 0/1:9:2:0,2:0,7:0.2222:0,0:18:1:31.5:1:1:0:60:4:0.2222:0.1111:0 -17 66522195 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCGAATATTTTTCTTTT;RSEQ=ATGAGCAAATACTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:0,2:0,28:0.0667:1,0:11.5:1:32:0:1:0:60:4:0.0667:0:1 0/0:7:0:0,0:0,7:0:0,0:22.4:1:30.6:1:1:0:60:14:1:0:0 -17 66523772 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14229;SOR=Inf;LSEQ=GAATTGGGCATAATATTGGC;RSEQ=GAAAATAAAAATCACAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:0:1,0:25.4:1:30.5:1:1:0:60:28:1:0:0.1 0/1:9:2:1,1:6,1:0.2222:2,2:15:1:31.5:1:0.41667:4.58262:60:4:0.2222:0:1 -17 66523900 . CTT C 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00654;SOR=Inf;LSEQ=GTTTTAAAATTTATTTGAAA;RSEQ=AATATTTATTATTCCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:121,3:0:1,0:23.8:1:31.4:1:1:0:60:61:1:0:0.1 0/1:97:6:6,0:91,0:0.0619:1,0:25.5:1:31.5:1:1:0:60:12:0.0625:0:0 -17 66524121 . C A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26774;SOR=0;LSEQ=ATGGACTTGGGAAAAGCCTT;RSEQ=TGAAAGTATAATTGCTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:2,1:34,208:0.0122:2,2:10.3:1:24.7:1:0.05733:12.02:60:6:0.0124:0:1 0/0:177:0:0,0:35,142:0:2,0:19.6:1:31.5:1:1:0:60:87.5:1:0:0.1 -17 66524987 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=16.60635;LSEQ=GCACCAAATAATACAGAGCA;RSEQ=TTATTTTGATTCTTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:50:38,12:184,93:0.1529:2,2:28.6:1:29.7:1:0.19327:1.60:60:15.667:0.1455:0:1.1 1/0:229:172:122,50:40,16:0.7511:2,2:25:1:29.9:1:1:1.02448:60:42:0.7467:0:1.1 -17 66525001 . T C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03121;SOR=Inf;LSEQ=AGAGCAGTTATTTTGATTCT;RSEQ=GTCTTTCAGAGTCTCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:391:0:0,0:252,139:0:2,0:26.4:1:30.2:1:1:0:60:129.333:1:0:0.2 0/1:285:4:2,2:186,95:0.014:2,2:23.8:1:32.3:1:0.60722:1.953:60:8:0.0141:0:1.5 -17 66525115 . T A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16767;SOR=5.56571;LSEQ=AGGGAGAACCAGGGGATGAG;RSEQ=TCTTCATTATTTTAGAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:1:1,0:179,288:0.0021:2,0:1:0:25:0:0.38462:0:60:2:0.0022:0:1 0/1:339:4:3,1:128,207:0.0118:2,2:9.3:1:26.8:1:0.30269:4.83:60:8:0.0119:0:1.3 -17 66525176 . A G 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27129;SOR=0;LSEQ=TTGAATTTTAGAGGTAAAGA;RSEQ=CTCAGAATTTAATACTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:3:1,2:23,146:0.0174:2,2:18:1:24.3:1:0.36473:3.14:60:2:0.0118:0:3.7 0/0:120:0:0,0:20,100:0:2,0:20.2:1:29.3:1:1:0:60:119:1:0:0.1 -17 66525943 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGTGACTAACTTTAAA;RSEQ=TCATTTTTTATCATATGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:133,5:0.0143:1,2:25.5:1:28:1:0.08417:24.37392:60:4:0.0145:0:2 0/0:59:0:0,0:57,2:0:1,0:25.3:1:32:1:1:0:60:58:1:0:0.3 -17 66525970 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55571;SOR=0;LSEQ=TTTATCATATGCACACATTT;RSEQ=CAAGGTAGTTAAAATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:2,1:192,24:0.0137:2,2:16.3:1:29.7:1:0.3061:3.95927:60:6:0.0139:0:1 0/0:123:0:0,0:112,11:0:2,0:21.3:1:31.8:1:1:0:60:60.5:1:0:0.6 -17 66526027 . G T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=11.15261;LSEQ=CACCCTGGGTTTGAGAGTGT;RSEQ=TGTTTGTTTAGCTTTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:88:60,28:336,158:0.1512:2,2:26.6:1:30.4:1:1:1.01:60:176:0.1522:0:1.1 1/0:419:279:193,86:90,50:0.6659:2,2:23.8:1:29.4:1:0.32142:1.25:60:54.8:0.6667:0:1.1 -17 66526233 . T C 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00047;SOR=Inf;LSEQ=TCCATAATTTTGTCTTCTCC;RSEQ=GAATTTTATTTTCTAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:40,135:0:2,0:24.5:1:30.8:1:1:0:60:350:1:0:0 0/1:91:7:2,5:13,71:0.0769:2,2:18.6:1:29.4:1:0.32475:2.16:60:14:0.0769:0:1 -17 66526316 . A T 137 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03778;LSEQ=TTTACTCATTTAATGAAATT;RSEQ=CTGATTGTCTCATATCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:23:14,9:101,32:0.1474:2,2:26.1:1:30.5:1:0.1974:2.01881:60:46:0.1484:0:1.3 0/1:92:14:13,1:63,15:0.1522:2,1:16.3:1:30.2:1:0.44998:3.07:60:28:0.1538:0:1.1 -17 66526675 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15527;SOR=Inf;LSEQ=TTATTTTCCCTACTTGCAGC;RSEQ=CCAAGTGGCCACTGGCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:10,163:0:2,0:25.6:1:32.1:1:1:0:60:85.5:1:0:0 0/1:113:2:1,1:13,97:0.0177:2,2:15:1:29:1:0.23536:7.23:60:4:0.0177:0:1 -17 66545635 . CA C 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAATGCAAAACTCCATCT;RSEQ=AAAAAAAAAAAAAAGTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:25.5:1:31:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 66547249 . G A 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.60328;LSEQ=CCTCATCATCTCAAGGAGGA;RSEQ=CATTCCCCTGGGCTAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2067:298:152,146:920,846:0.1442:2,2:26.1:1:30.1:1:0.75413:1.04454:60:148:0.1457:0:1.2 0/1:1467:312:162,150:604,550:0.2127:2,2:24:1:29.9:1:0.89854:1.01683:60:155:0.2138:0:1.2 -17 66547409 . G C 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15048;SOR=0.66622;LSEQ=TGTTTCACAAAATTTTCAAG;RSEQ=CATGTAGTTGCTGTTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:57:0,57:4,273:0.1707:1,1:26.1:1:30.9:1:1:0:60:18:0.1651:0:1.1 0/1:166:20:0,20:4,142:0.1205:1,1:24.5:1:31.8:1:1:0:60:40:0.1212:0:1 -17 68920798 . T C 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11798;LSEQ=GAATTCCTATTTTTAAGCAA;RSEQ=ATCTTCGAGGAAGCAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:0.3077:0,0:27.8:1:29.3:1:1:0:60:3:0.25:0:1.3 0/1:6:2:1,1:4,0:0.3333:0,2:29.5:1:33:0:0.33333:0:60:4:0.3333:0:1 -17 68920884 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96025;LSEQ=GCCTAGTGTGTATGCAGTAA;RSEQ=GGTGAATTCTTCTGTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:19:19,0:29,2:0.38:2,1:21.9:1:32.3:1:0.51918:0:60:38:0.38:0:1.1 0/1:27:10:10,0:17,0:0.3704:1,0:17.8:1:32.3:1:1:0:60:20:0.3704:0:1.1 -17 68920943 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0299;SOR=Inf;LSEQ=TAATTATTCTACCAGTCTTT;RSEQ=GCAATAATTTTCTCGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:117,34:0:2,0:21.8:1:31.2:1:1:0:60:302:1:0:0.2 0/1:109:4:4,0:80,25:0.0367:2,0:35.8:1:29.5:1:0.57182:0:60:8:0.0367:0:1 -17 68920957 . C T 128 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=34.98228;LSEQ=GTCTTTCGCAATAATTTTCT;RSEQ=GTATCTACTGTAATTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:1:1,0:146,48:0.0051:2,0:3:0:29:0:1:0:60:2:0.0052:0:1 0/1:130:20:15,5:85,25:0.1538:2,2:19.6:1:29.7:1:0.77962:1.1322:60:40:0.155:0:1.5 -17 68921040 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.31455;LSEQ=CAGCCATGTCTTCTGTACCC;RSEQ=TTCATTTTCTGTCTGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:444:341:165,176:50,53:0.768:2,2:27.4:1:30.4:1:1:1.00628:60:67.2:0.7742:0:1.1 1/0:410:209:103,106:99,101:0.5098:2,2:27.6:1:30.1:1:1:1.00873:60:208:0.5136:0:1.2 -17 68921097 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.86781;SOR=0.91314;LSEQ=TGCAAAGTGTACCACAGTGA;RSEQ=TTCCATGCCTCCTGGCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:21:8,13:66,161:0.084:2,2:23.2:1:29.4:1:0.45519:1.50:60:20:0.082:0:1.2 0/1:233:18:7,11:75,140:0.0773:2,2:26:1:29.4:1:0.79893:1.19:60:36:0.0779:0:1.1 -17 68921135 . A G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00069;SOR=0.34536;LSEQ=ACGGTATGCAAGAGTCACCA;RSEQ=CCTAGCATGCCCATCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:48:4,44:15,62:0.384:2,2:26:1:31.8:1:0.12491:2.64241:60:23:0.374:0:1.2 0/1:102:18:4,14:17,67:0.1765:2,2:25.1:1:31.6:1:1:1.12:60:36:0.1765:0:1.3 -17 69889050 . G A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.86332;SOR=0.92109;LSEQ=ATGGGTGTTCTCTTGTCCCC;RSEQ=TCCAATATAAACCTAGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:33:28,5:79,5:0.2821:2,2:22.1:1:30.2:1:0.1422:2.79255:60:32:0.2807:0:1 0/1:64:17:16,1:45,2:0.2656:1,1:22.2:1:30.1:1:1:1.39825:60:34:0.2656:0:1.1 -17 69889186 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.62864;LSEQ=AATAAACAGTGAAACAAAGT;RSEQ=GTTTCATCACAGGGTATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:130:63,67:154,201:0.268:2,2:29.5:1:29.7:1:0.35377:1.23:60:129:0.2727:0:1.1 0/1:326:160:74,86:74,91:0.4908:2,2:25.4:1:29.2:1:0.8243:1.06:60:159:0.4923:0:1.2 -17 69889220 . G A 47 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68029;LSEQ=GTATCAGAGTAACCCACGGA;RSEQ=CACATCACTGTATTAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:4:4,0:141,169:0.0127:2,0:10.5:1:23.5:1:0.04446:0:60:3:0.0099:0:2.5 0/0:230:2:1,1:103,125:0.0087:2,2:20:1:18.5:1:1:1.21:60:1:0.0045:0:2.5 -17 69889230 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57909;SOR=2.67536;LSEQ=AACCCACGGAGCACATCACT;RSEQ=TATTAAAATTCCATTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:1:0,1:109,130:0.0041:2,0:44:0:16:0:1:0:60:0:0:0:3 0/1:181:2:1,1:81,97:0.011:2,2:35:1:29:1:1:1.20:60:4:0.011:0:1.5 -17 69889259 . T G 130 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.03954;SOR=0.52182;LSEQ=TTCCATTGGCTGGTGGGGGG;RSEQ=GGGGGGTGGGGGGTGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:46:1,45:41,26:0.4071:2,1:7.6:1:23.7:1:0:68.55782:52.6:2.833:0.3736:0:3 0/1:95:25:0,25:40,30:0.2632:2,1:7.5:1:27.4:1:0:0:48.6:7.333:0.25:0:2.9 -17 69889266 . T G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1975;SOR=0.64227;LSEQ=GGCTGGTGGGGGGTGGGGGG;RSEQ=GGGGGGTGGGGTGCAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:49:1,48:33,14:0.49:2,1:12.9:1:25.4:1:0:106.38135:53:5.125:0.519:0:2.9 0/1:63:24:1,23:26,8:0.381:2,1:13.8:1:26.5:1:0:67.72066:49.7:7:0.3818:0:2.9 -17 69889290 . C T 49 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03166;SOR=9.63579;LSEQ=GGGTGGGGTGCAGTGGCTCA;RSEQ=GCCTGCAATCCTAGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:1:0,1:8,78:0.0115:2,0:38:0:32:0:1:0:60:2:0.0118:0:4 0/1:39:4:1,3:7,28:0.1026:2,2:26.8:1:24.8:1:1:1.32:60:3:0.0811:0:2.5 -17 70114569 . G T 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGCAGAAATGCAGGACC;RSEQ=ATCCACTCGCGAGCTGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:653:0:0,0:180,471:0:2,0:22.8:1:30.7:1:1:0:60:107.5:0.9969:0:0.1 0/1:254:13:3,10:65,175:0.0512:2,2:27.9:1:29.2:1:1:1.23708:60:26:0.0512:0:1.3 -17 70114592 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1949;SOR=5.09337;LSEQ=CCACTCGCGAGCTGACAATG;RSEQ=CACGCGCTAGACTTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:0,1:42,348:0.0026:2,0:43:0:29:0:1:0:60:2:0.0026:0:1 0/1:155:2:1,1:26,127:0.0129:2,2:10:1:31.5:1:0.31898:4.81:60:4:0.013:0:2 -17 70117442 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGCTCCGCATCCGGGCA;RSEQ=CCGAGGGGAGAGGAGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:157,8:0.012:1,0:5.5:1:31.5:1:1:0:60:4:0.0124:0:1.5 0/0:74:0:0,0:66,8:0:2,0:1:0:16:0:1:0:60:0:0:0:1 -17 70117487 . G T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13362;SOR=3.17804;LSEQ=CGAGTCCCCGAGCCGCCGCG;RSEQ=CTTCTCGCCTTTCCCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:3:0,3:384,142:0.0056:2,0:1:0:26:1:0.02028:0:60:6:0.0058:0:1 0/1:282:5:1,4:184,93:0.0177:2,2:11.6:1:25.4:1:0.04919:7.85558:60:10:0.0181:0:1.2 -17 70117975 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.10223;SOR=Inf;LSEQ=GCTCTGGAGGTAGGACCCGG;RSEQ=GGGGGCGGCGCGGCAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:102,265:0:2,0:24.2:1:30:1:1:0:60:44.875:1:0:0.2 0/1:173:2:1,1:57,114:0.0116:2,2:23:1:26.5:1:1:1.99:60:4:0.0119:0:1 -17 70118061 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGCCTCCCATCGCCCGG;RSEQ=AGTTGCCGTTCCGGGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:0,2:0,52:0.037:1,0:29.5:1:25.5:1:1:0:60:4:0.037:0:1 0/0:24:0:0,0:1,23:0:1,0:19.7:1:31.6:1:1:0:60:48:1:0:0.3 -17 70118699 . G A 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20416;SOR=0.57458;LSEQ=TTTATTTATTTTTAAGAAAA;RSEQ=TTATGAGCTGTGGTTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:100:62:60,2:38,0:0.62:1,1:21.3:1:29.5:1:0.52404:0:60:14.5:0.6105:0:1.3 0/1:29:14:13,1:15,0:0.4828:1,1:15.2:1:30.1:1:0.48276:0:60:28:0.4828:0:1.1 -17 70118935 . C T 212 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=101.65748;LSEQ=GTGCAGCACAAGAAGGACCA;RSEQ=CCGGATTACAAGTACCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1606:3:1,2:818,781:0.0019:2,2:25:1:24.3:1:0.61652:2.0938:60:2:0.0013:0:1.3 0/1:1068:171:82,89:435,461:0.1601:2,2:24.4:1:28.7:1:0.93351:1.02413:60:23.429:0.1568:0:1.1 -17 70119107 . C T 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0454;SOR=Inf;LSEQ=AGGTGCACTCCCCCGGCGAG;RSEQ=ACTCGGGTGAGTCGCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:81,267:0:2,0:25.2:1:31.9:1:1:0:60:57:1:0:0.2 0/1:194:3:1,2:51,140:0.0155:2,2:28:1:28.3:1:1:1.37:60:6:0.0155:0:1 -17 70119245 . C G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.44886;SOR=0.40015;LSEQ=ACACTGCCCTTTGCGCCCGT;RSEQ=CCGCTCCCCTCTCTACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:16:2,14:2,19:0.4211:2,2:17.5:1:32.1:1:1:1.35:60:32:0.4324:0:1.1 0/1:9:2:0,2:0,7:0.2222:0,0:22:1:30.5:1:1:0:60:4:0.2222:0:1 -17 70119631 . C T 64 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06049;SOR=3.22245;LSEQ=GAGGGTGCCTAAGACTAGGG;RSEQ=GTCTGCACAGCCCTTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1001:4:0,4:689,308:0.004:2,0:1:0:26.5:1:0.00931:0:60:8:0.0041:0:1.5 0/1:548:7:2,5:371,170:0.0128:2,2:14.1:1:23:1:0.03674:5.43717:60:2.5:0.0093:0:1 -17 70119964 . C T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.11358;SOR=5.95145;LSEQ=ACGGGCAGCTACGGCATCAG;RSEQ=AGCACCGCGGCCACCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:1:0,1:107,414:0.0019:2,0:40:0:29:0:1:0:60:2:0.0019:0:1 0/1:265:3:1,2:71,191:0.0113:2,2:15.7:1:22:1:1:1.34:60:2:0.0077:0:1 -17 70119998 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14099;SOR=Inf;LSEQ=CCCCGGCGAGCGCGGGCCAC;RSEQ=TGTGGATGTCCAAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:42,200:0:2,0:25.7:1:32.3:1:1:0:60:241:1:0:0.1 0/1:146:2:1,1:34,110:0.0137:2,2:17.5:1:29.5:1:0.42324:3.20:60:4:0.0138:0:1.5 -17 70120067 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=CACAGGCCCCGCCGGCCCCG;RSEQ=AGGCGCCCCCGCAGCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:23:0:31:1:1:2.23609:60:4:0.2222:0:1.5 0/0:7:0:0,0:4,3:0:2,0:6.7:1:29.1:1:1:0:60:14:1:0:0.3 -17 70120084 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09323;SOR=Inf;LSEQ=CCGCAGGCGCCCCCGCAGCC;RSEQ=CAGGCGGCGCCCCCACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:55,3:0:2,0:9.3:1:30.8:1:1:0:60:116:1:0:0.4 0/1:26:2:1,1:22,2:0.0769:2,2:13:0:31:1:0.22154:9.18332:60:4:0.0769:0:1.5 -17 70120097 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCAGCCGCAGGCGGCGCCC;RSEQ=CACAGCAGCCGGCGGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:103,3:0.0185:1,2:29.5:1:31.5:1:0.07304:29.87118:60:4:0.0185:0:1.5 0/0:47:0:0,0:43,4:0:2,0:15.6:1:30.8:1:1:0:60:46:1:0:0.1 -17 70120111 . G A 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00271;SOR=0;LSEQ=GCGCCCCCACAGCAGCCGGC;RSEQ=GCACCCCCGCAGCAGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:20:18,2:173,13:0.0971:2,2:22.1:1:31:1:0.64418:1.47542:60:40:0.0995:0:1.1 0/0:74:0:0,0:66,8:0:2,0:20.4:1:30.5:1:1:0:60:148:1:0:0.1 -17 70120178 . C T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05607;SOR=4.64815;LSEQ=GCGAGCCGGGCCAGTCCCAG;RSEQ=GAACGCACATCAAGACGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:836:2:0,2:684,150:0.0024:2,0:1:0:28:1:0.03288:0:60:4:0.0024:0:1 0/1:453:5:2,3:351,97:0.011:2,2:13.2:1:26.8:1:0.074:5.40095:60:10:0.0111:0:1 -17 70120551 . A C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34549;LSEQ=AGGCCTCCCACGAAGGGCGA;RSEQ=GATGGCCGAGATGATCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:531:348:53,295:34,149:0.6554:2,2:22.3:1:29.6:1:0.32612:1.26949:60:48.714:0.6545:0:1.1 0/1:313:124:32,92:37,152:0.3962:2,2:24.9:1:29.8:1:0.21109:1.43:60:248:0.3987:0:1.2 -17 70120652 . TTTC T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.56489;SOR=0;LSEQ=TTTTTTATTTTGTTTTGTTT;RSEQ=TTCTTCTTCTTCTTCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:0,3:1,72:0.0395:1,0:36:1:28:1:1:0:60:6:0.04:0:0 0/0:27:0:0,0:1,26:0:1,0:24.1:1:30:1:1:0:60:12.5:1:0:0.1 -17 70122108 . G A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGTCATCCATATTTCTCT;RSEQ=CATCTTCTCTTGGAGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:11,0:4,0:0.7333:0,0:24.9:1:28.7:1:1:0:60:22:0.7333:0:1 1/1:2:2:2,0:0,0:1:0,0:5.5:1:29.5:1:1:0:60:4:1:0:1 -17 70122227 . C CT 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05081;SOR=3.20051;LSEQ=TTTTTAAAAAAGACAGCAAA;RSEQ=TTTTTTTTTTATTTAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:7:7,0:112,1:0.0583:1,0:14.1:1:32.3:1:1:0:60:14:0.0583:0.025:0.6 0/1:42:7:7,0:35,0:0.1667:1,0:21.7:1:31.6:1:1:0:60:14:0.1707:0.0476:0 -17 70122505 . CT C 275 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.52181;LSEQ=ACCTTTCCCTTTTTCTTTCT;RSEQ=TTTTTTTTTTTGTATATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1174:433:89,344:254,411:0.3688:2,2:29.3:1:31.4:1:0:2.38685:60:38.364:0.3738:0.0068:0.4 0/1:839:196:41,155:211,388:0.2336:2,2:28.1:1:30.9:1:0.00019:2.05414:60:38.2:0.2373:0.0072:0.4 -17 70122660 . G GT 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00434;SOR=0.17848;LSEQ=CTGATTGCTGTGATGTTTTT;RSEQ=TTTTTTATCAGCACCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:40:0,40:0,28:0.5882:1,1:26.4:1:30.7:1:1:0:60:80:0.5882:0.0588:0.2 0/1:20:4:0,4:0,16:0.2:1,0:24.8:1:31.5:1:1:0:60:8:0.2105:0:0 -17 72768970 . G A 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87769;LSEQ=TGCCCACCCTTTGCAGCCTC;RSEQ=GCAGGCTCAGTCAGCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:22:10,12:6,5:0.6667:2,2:30.4:1:30.5:1:0.72068:1.42407:60:44:0.6667:0:1.1 1/0:11:7:4,3:3,1:0.6364:2,2:18.1:1:31.4:1:1:2.09375:60:14:0.6364:0:1 -17 72770751 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTGCAGTGGC;RSEQ=CGATCTCGGCTCACTGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:32:0:1:0:53:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 72839130 . A AGCTCCGGGG 64 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGCAGCGGCAGGTCCTCC;RSEQ=GCTCCGGGAAGAGCGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:27.5:1:32.4:1:1:0:60:8:1:0:0.3 -17 72840514 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52638;SOR=0;LSEQ=CAGGCGAAGACCAGCAGGGC;RSEQ=AGCCCCATGGCCACCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:137,60:0.0101:2,2:7.5:1:28:1:0.52018:2.27282:60:4:0.0104:0:1 0/0:123:0:0,0:82,41:0:2,0:23.6:1:30.4:1:1:0:60:60.5:1:0:0.2 -17 72840588 . C A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31275;SOR=4.24641;LSEQ=CAGCTTGCTGCTCATCACCT;RSEQ=GTTCTTCTCATTCTGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:1:1,0:170,196:0.0027:2,0:1:0:24:0:0.46594:0:60:2:0.0028:0:1 0/1:261:3:2,1:121,136:0.0115:2,2:22:1:28:1:0.60428:2.24:59:6:0.0117:0:1 -17 72840630 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17966;SOR=Inf;LSEQ=CCCTGAGAGCCACACTGTCT;RSEQ=CAGTTTCTGTGTCTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:61,147:0:2,0:24:1:30.8:1:1:0:60:51:0.9903:0:0.1 0/1:155:2:1,1:52,99:0.0129:2,2:42:1:29:1:1:1.90:60:4:0.0132:0:1 -17 72842873 . C A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGACACACGGATGAAGA;RSEQ=AGCGGGTGCAGGGCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 72843378 . C T 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CCAGACTCGACTGTCCAGGG;RSEQ=CTGCCCACTCACGGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:6,0:0.4167:0,0:17.6:1:31.2:1:1:0:60:10:0.4545:0:2 0/0:2:0:0,0:1,1:0:2,0:38.5:1:31:1:1:0:60:4:1:0:1 -17 72843411 . GC G 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28327;SOR=0;LSEQ=GGCCTGTCCCCACCCTCAGT;RSEQ=CCCCCCCCACCCCCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:13,0:0.35:1,0:36.4:1:33.4:1:1:0:60:14:0.3684:0:1.4 0/0:4:0:0,0:3,1:0:2,0:19:1:32.8:1:1:0:60:8:1:0:0.8 -17 72843527 . C T 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53659;SOR=0;LSEQ=CAGGTTGGCCGTGTAGCTGG;RSEQ=GAGGAAGATGACAGCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:94,77:0.0116:2,2:30:1:24.5:1:1:1.21936:60:4:0.0118:0:1 0/0:98:0:0,0:58,40:0:2,0:24.8:1:30.5:1:1:0:60:196:1:0:0.1 -17 72843551 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53487;SOR=0;LSEQ=GAAGATGACAGCAAAGAAGG;RSEQ=CCAGACCAGAACCATGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:84,95:0.011:2,2:20.5:1:29.5:1:1:1.13:60:4:0.0112:0:1 0/0:104:0:0,0:57,47:0:2,0:28.8:1:31.1:1:1:0:60:51:1:0:0.1 -17 72843567 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53456;SOR=0;LSEQ=AAGGCCCAGACCAGAACCAT;RSEQ=ATCTTGCTGGTGGTGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:62,96:0.0125:2,2:47:0:30:0:1:1.54:60:4:0.013:0:2 0/0:92:0:0,0:44,48:0:2,0:29.4:1:31.5:1:1:0:60:184:1:0:0.1 -17 72843588 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15495;SOR=Inf;LSEQ=ATCTTGCTGGTGGTGCCCCG;RSEQ=GGGTTCTCGATGGGCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:33,91:0:2,0:23.6:1:30.1:1:1:0:60:30:1:0:0.2 0/1:81:2:1,1:31,47:0.0247:2,2:26.5:1:29:1:1:1.51:60:4:0.0247:0:1.5 -17 72843609 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51765;SOR=0;LSEQ=GGGTTCTCGATGGGCACTGA;RSEQ=TTGTTGAAGACCAGCGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:14,66:0.0244:2,2:7.5:1:28.5:1:0.33424:4.59:60:4:0.0247:0:2 0/0:54:0:0,0:20,34:0:2,0:22.8:1:31:1:1:0:60:108:1:0:0.1 -17 72846043 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10938;SOR=Inf;LSEQ=TCATTGATGGTGAGGGAGCC;RSEQ=ATGGCCATGTCTGCCCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:34,52:0:2,0:25.1:1:30.4:1:1:0:60:172:1:0:0.1 0/1:43:2:1,1:14,27:0.0465:2,2:31:1:30:1:1:1.90:60:4:0.0476:0:1 -17 72846086 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53729;SOR=0;LSEQ=AGTACACCTGGGGGCCGGAC;RSEQ=CCACGGAGGTTTGAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:7,30:0.0513:2,2:22.5:1:29:1:0.37247:4.08:60:4:0.0513:0:1 0/0:21:0:0,0:5,16:0:2,0:24.3:1:32.3:1:1:0:60:42:1:0:0.1 -17 72904115 . G A 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05818;SOR=0;LSEQ=AGCCTTTTCCTGTAAACGCC;RSEQ=GGTGGCATCTCTTACTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:3,5:5,4:0.4706:2,2:30.4:1:31.4:1:0.63719:1.99353:60:16:0.4706:0:1 0/0:6:0:0,0:2,4:0:2,0:23:1:26.5:1:1:0:60:5:1:0:0.2 -17 72939446 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=4.0876;LSEQ=ACCAACTTCACTAGGTAAGA;RSEQ=TTCTCTCCCTCCCAAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:709:85:43,42:301,323:0.1199:2,2:25.9:1:30.1:1:0.72913:1.10:60:41.5:0.1179:0:1.1 0/1:542:194:95,99:163,185:0.3579:2,2:23.8:1:30.1:1:0.65444:1.09:60:193:0.3594:0:1.2 -17 72939663 . G A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00051;SOR=Inf;LSEQ=GGTTTGGCACCTGGGGAGCC;RSEQ=GCCAGGGTGTGTGAGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:0:1,0:21:1:31.7:1:1:0:60:66:1:0:0 1/0:4:3:0,3:0,1:0.75:0,0:29:1:31:1:1:0:60:6:0.75:0:1 -17 73401705 . AGCC A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.48889;SOR=Inf;LSEQ=ACAGGCACAGACTCTGCCAC;RSEQ=GCCGCCGCCGCTGCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,7:0:2,0:24:1:32.7:1:1:0:60:44:1:0:0.1 0/1:23:2:1,1:13,8:0.087:2,2:33.5:1:32:1:1:1.58984:60:4:0.087:0:0.5 -17 73584696 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49804;SOR=0;LSEQ=CTGCGGCCCACGCCGGAGCC;RSEQ=ACGGACATGGGCTCGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:33,28:0.0317:2,2:10.5:1:31:1:1:1.17549:60:4:0.0323:0:1 0/0:55:0:0,0:29,26:0:2,0:23.6:1:28.1:1:1:0:60:26.5:1:0:0.2 -17 73584728 . G T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2467;SOR=0;LSEQ=CTCGGAAGGGACAAAAACCG;RSEQ=GCCGGAGTCAGCGCTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:3:1,2:47,45:0.0316:2,2:14.3:1:31.3:1:0.61698:2.07327:60:6:0.033:0:1.3 0/0:89:0:0,0:43,46:0:2,0:24.7:1:30.1:1:1:0:60:43.5:1:0:0.2 -17 73584793 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20126;SOR=Inf;LSEQ=ACTGGCCCCACGCAGATACC;RSEQ=GGGGCCGGGAAGGGTCGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:0:2,0:22.1:1:29.4:1:1:0:60:24.5:1:0:0.1 0/1:42:2:1,1:18,22:0.0476:2,2:27:1:29:1:1:1.22:60:4:0.0476:0:1 -17 73584858 . CGA TTT 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCATTCCGGCGGGGACTC;RSEQ=CTCGAGTCCGCTGGGGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:1,11:0.1429:2,0:29.5:1:30:0:1:0:60:4:0.1429:0:1 0/0:5:0:0,0:0,5:0:0,0:31:1:26.4:1:1:0:60:4:1:0:0 -17 73586184 . C G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGGGAGCTGTGGGAACC;RSEQ=GAGGATGAGGACGAGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:1:32:0:1:0:60:4:1:0:2 -17 73586235 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTGGAGCTGAGCCTCCG;RSEQ=CCGGGCCTGGAGGCGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:28.5:1:1:0:60:4:1:0:2 -17 73774841 . G A 176 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=62.65846;LSEQ=CCGCACTATTAATCCCACTC;RSEQ=GGGAGCGGAAACCGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1218:1:1,0:612,604:8e-04:2,0:1:0:30:0:1:0:60:2:8e-04:0:1 0/1:1224:60:33,27:576,585:0.049:2,2:23.2:1:29.8:1:0.43012:1.24:60:59:0.049:0:1.1 -17 73774877 . G A 242 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGCCCTCCCCCGGCTCCA;RSEQ=GCCTTTGTCTTACCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1321:0:0,0:690,629:0:2,0:24.7:1:31.3:1:1:0:60:46.107:1:0:0.1 0/1:1391:274:147,127:595,518:0.197:2,2:23.4:1:29.9:1:1:1.01:60:67.5:0.1961:0:1.1 -17 73775270 . G C 210 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCATTTTCTTTCACCTAA;RSEQ=AAAGACGCCCCGAAGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1036:0:0,0:374,661:0:2,0:25:1:31.3:1:1:0:59.9:46.045:1:0:0.2 0/1:1258:108:44,64:460,686:0.0859:2,2:25.1:1:31.2:1:0.91847:1.03:60:35:0.085:0:1.2 -17 73775397 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15252;SOR=Inf;LSEQ=GCCCCACCTCGCGGCAGCAG;RSEQ=TGGCCGAGGGCCGCCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:0,71:0:1,0:21.5:1:31.4:1:1:0:59.8:142:1:0:0.1 0/1:46:2:0,2:5,39:0.0435:2,0:13.5:1:32:0:1:0:60:4:0.0465:0:1.5 -17 73775739 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=Inf;LSEQ=TAAACCTACGAACGCCTACC;RSEQ=AACGCCGAAGTTTTAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:31.3:1:30.2:1:1:0:60:12:1:0:0.2 0/1:8:2:1,1:3,3:0.25:2,2:8.5:1:29:1:1:1:60:4:0.2857:0:2.5 -17 73775763 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=GCCGAAGTTTTAGGCCACTT;RSEQ=TCCGACCGCCGCGCCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:30.3:1:30.6:1:1:0:60:14:1:0:0.1 0/1:7:2:1,1:2,3:0.2857:2,2:32:0:30.5:1:1:1.41:60:4:0.2857:0:2.5 -17 74017823 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51301;SOR=0;LSEQ=GTCGTCCTCCAGCTGGTTCA;RSEQ=GCTCTGCTCCTGGCTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:19,14:0.0571:2,2:31.5:1:29:1:1:1.34517:60:4:0.0571:0:1 0/0:23:0:0,0:11,12:0:2,0:30.8:1:30.4:1:1:0:60:46:1:0:0.2 -17 74681305 . C A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08939;SOR=Inf;LSEQ=TAGAGGCTGGCCCCACAAAC;RSEQ=CCGGCCCCCTTTCCCTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:195,56:0:2,0:22.2:1:30.7:1:1:0:60:82.667:1:0:0.1 0/1:204:3:2,1:158,43:0.0147:2,2:22:1:23:1:0.5195:1.83082:60:2:0.0099:0:1.7 -17 74681435 . A G 284 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06829;LSEQ=CCCTTAAATCCTACAACGAG;RSEQ=CAGCCAGAGAGAAAGCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:516:511:195,316:2,0:0.9903:0,2:24.6:1:31.6:1:0.14701:0:60:72:0.9921:0:1.1 1/1:438:383:158,225:19,36:0.8744:2,2:25.3:1:30.9:1:0.38029:1.33:60:33.818:0.8753:0:1.1 -17 74681539 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00048;SOR=3.16015;LSEQ=TTGCCCTGGCCCTGCCCAGC;RSEQ=GGTCCTCTCGGCTACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:34:3,31:5,62:0.3366:2,2:24.4:1:31:1:1:1.20:60:68:0.3366:0:1.3 1/0:68:42:3,39:3,23:0.6176:2,2:19.4:1:30.9:1:0.66765:1.68193:60:84:0.6269:0:1.1 -17 74681613 . A G 135 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07742;SOR=0;LSEQ=CTCATCTTGGGACACACACC;RSEQ=CGCCTGCCTGGGCTTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:0,22:0,0:1:0,1:18.5:1:30.4:1:1:0:60:10:1:0:1.1 1/0:9:7:0,7:0,2:0.7778:0,0:21.6:1:32:1:1:0:60:14:0.7778:0:1.4 -17 74717369 . A T 21 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22727;SOR=Inf;LSEQ=AGAGCTGGTCCCTCCAGGTC;RSEQ=GGGTTGGGACACAGTGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:0:1,0:28.5:1:30.6:1:1:0:60:34:1:0:0.2 0/1:16:2:1,1:14,0:0.125:1,2:14:1:21.5:1:0.125:0:60:4:0.125:0:1 -17 74717604 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.29868;LSEQ=GCTAGCTTTGAAAAACAAAA;RSEQ=ACAAAACAAAACGAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:14:1:30.5:1:1:0:60:4:0.3333:0:1 0/1:5:2:0,2:0,3:0.4:0,0:29.5:1:30:0:1:0:60:4:0.4:0:1 -17 74732507 . A G 325 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92119;LSEQ=CGGCTGCGAGACCTGGAACG;RSEQ=CTCCGACTCCGGGATCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1167:1161:456,705:4,1:0.9949:2,2:24.6:1:31.3:1:0.08244:6.1752:60:49.478:0.9956:0:1.1 1/1:1434:1426:583,843:6,2:0.9944:2,2:25:1:31.1:1:0.07063:4.33363:60:61:0.9943:0:1.2 -17 74732811 . C T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.99181;LSEQ=ACCACGTGCTTCGCCGCGGA;RSEQ=CTTTGTGAGGTCGCCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:0,1:61,19:0.0123:2,0:1:0:25:0:0.24691:0:60:2:0.0127:0:1 0/1:82:2:1,1:57,23:0.0244:2,2:17:1:26:1:0.50226:2.44728:60:4:0.0244:0:1 -17 74732824 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5003;SOR=Inf;LSEQ=CCGCGGACCTTTGTGAGGTC;RSEQ=CCCGGGCCTCCCGCGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:87,42:0:2,0:22:1:30.4:1:1:0:60:42:0.9921:0:0.2 0/1:148:2:1,1:90,54:0.0135:2,2:23.5:1:31.5:1:1:1.66052:60:4:0.0138:0:1 -17 74732830 . G T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62643;SOR=2.63257;LSEQ=ACCTTTGTGAGGTCGCCCGG;RSEQ=CCTCCCGCGCGCCCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:0,1:102,59:0.0062:2,0:1:0:25:0:0.37037:0:60:2:0.0064:0:1 0/1:186:3:1,2:114,69:0.0161:2,2:12.7:1:29:1:0.55896:3.28252:60:6:0.0164:0:1.3 -17 74732842 . C T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10117;SOR=0;LSEQ=TCGCCCGGGCCTCCCGCGCG;RSEQ=CCCGCCCCGCCTCCCGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:3:0,3:132,85:0.0136:2,0:15.7:1:21.7:1:0.06269:0:60:2:0.0093:0:2.3 0/0:251:0:0,0:154,97:0:2,0:23.3:1:31.2:1:1:0:60:40.833:1:0:0.3 -17 74732844 . C T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.6264;SOR=2.66306;LSEQ=GCCCGGGCCTCCCGCGCGCC;RSEQ=CGCCCCGCCTCCCGCGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:1:0,1:139,94:0.0043:2,0:1:0:29:0:0.40598:0:60:2:0.0043:0:1 0/1:265:3:0,3:161,101:0.0113:2,0:12:1:21.7:1:0.05938:0:60:2:0.0077:0:1.3 -17 74733099 . G A 310 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01039;LSEQ=CGGGACTCCTTGGTGTAGCG;RSEQ=TCCCGCGGGATGTACACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1258:1256:661,595:1,1:0.9984:2,2:24.6:1:30.2:1:1:1.11:60:49.24:0.9992:0:1.1 1/1:1421:1232:675,557:95,93:0.867:2,2:23.4:1:29:1:0.30699:1.19:60:50.333:0.8666:0:1.2 -17 74733365 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01445;SOR=Inf;LSEQ=CACTGGGAAAGGCCTTGCCG;RSEQ=AGAACAGCACGGACGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:3,141:0:1,0:24.1:1:32:1:1:0:60:27.8:1:0:0.3 0/1:110:5:0,5:1,103:0.0455:1,0:14.6:1:25.6:1:1:0:60:10:0.0476:0:1.2 -17 74733403 . G A 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71081;SOR=0.83553;LSEQ=CTCCGCAGGCTAGCGCACCT;RSEQ=AGTAACAACTGGGCGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:48:3,45:0,29:0.6234:1,2:24.6:1:30:1:0.2864:0:60:47:0.6184:0:1.2 1/0:50:29:0,29:0,21:0.58:1,1:19:1:30.4:1:1:0:60:58:0.58:0:1 -17 76356096 . T G 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGGGCCGGGCGGGCGGC;RSEQ=GGCGGCTGGCTGCGTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:28:1:1:0:60:4:1:0:1 -17 77278686 . T A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGTCACTGCACGGGGATG;RSEQ=GGCTGCAGGGCCGGCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 77280222 . T A 46 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.71649;SOR=1.47949;LSEQ=CCTTCTCCAGGACCATCGTA;RSEQ=CATTTGCCTGTTTCAGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:4:4,0:77,12:0.043:2,0:18:1:27.5:1:1:0:28:8:0.0435:0:1 0/1:64:4:4,0:50,10:0.0625:2,0:28:1:23:1:1:0:36:3:0.0484:0:1.3 -17 77280257 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09024;SOR=Inf;LSEQ=AGTACTTATAAATGGAGATG;RSEQ=CTTCTACAGGACAGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:150,59:0:2,0:25:1:32:1:1:0:59.4:208:1:0:0.2 0/1:171:3:1,2:118,50:0.0175:2,2:22:1:27:1:0.2197:4.67168:60:6:0.0179:0:1.7 -17 77280267 . G A 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00045;SOR=Inf;LSEQ=AATGGAGATGCCTTCTACAG;RSEQ=ACAGTTGATTCTCATCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:167,73:0:2,0:25.1:1:30.9:1:1:0:59.7:39:1:0:0.2 0/1:211:10:6,4:128,72:0.0474:2,2:22.2:1:27.2:1:0.75046:1.1842:60:20:0.0483:0:1.7 -17 77280338 . G C 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19514;SOR=0.81728;LSEQ=ACAGTCCGTTTCCAATGCAG;RSEQ=GTTGCTGAAGAGAATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:171:72,99:78,106:0.4803:2,2:26.8:1:30.8:1:1:1.01176:60:170:0.483:0:1.1 0/1:337:145:65,80:80,110:0.4303:2,2:25.5:1:30.4:1:0.65682:1.12:60:144:0.4324:0:1.2 -17 77280442 . A G 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATTTAATAACTTTCTTCA;RSEQ=TGTTTTGTTATTCCAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:6,84:0:2,0:20.6:1:31.2:1:1:0:60:89:1:0:0.4 0/1:34:10:1,9:3,21:0.2941:2,2:24.2:1:32.1:1:1:1.27668:60:20:0.2941:0:1.1 -17 77280452 . A G 170 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTTTCTTCAATGTTTTGTT;RSEQ=TTCCAAATCCACAACCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:37:1,36:1,24:0.5968:1,1:28.1:1:32.7:1:1:1.48993:60:74:0.5968:0:1 0/0:27:0:0,0:1,26:0:1,0:24:1:30.8:1:1:0:60:54:1:0:0.4 -17 77386058 . GGGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA G 97 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18268;SOR=0;LSEQ=TCCAGGTCTCTGTAGCCTCC;RSEQ=GGTCTCCGCAGCCTCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:10:4,6:33,5:0.2083:2,2:14:1:29.2:1:0.00507:9.23383:52.1:20:0.2174:0.125:1.2 0/0:11:0:0,0:10,1:0:2,0:33.5:1:30:1:1:0:60:22:1:0:0.9 -17 77386075 . A G 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCGGGTCTCCGCAGCCTCC;RSEQ=GGTCTCCGCAGCCTCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:36,18:0:2,0:22.8:1:28.8:1:1:0:58.9:12.5:1:0:0.3 1/0:24:16:8,8:8,0:0.6667:0,2:7.6:1:28.6:1:0.02224:0:57.6:32:0.6957:0:1.5 -17 77386084 . CAGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT C 188 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCGCAGCCTCCAGGTCTCCG;RSEQ=AGCCTCCAGGTCTCCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:62:35,27:7,2:0.8158:2,2:24.9:1:31.6:1:0.29285:2.66588:57.4:61:0.8592:0.1711:0.5 0/0:30:0:0,0:20,10:0:2,0:17.8:1:28.8:1:1:0:58.7:29:1:0:1.3 -17 77386092 . A G 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TCCAGGTCTCCGCAGCCTCC;RSEQ=GGTCTCCGCAGCCTCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:4,0:0:0,0:6.8:1:26.3:1:1:0:60:8:1:0:0.8 0/1:34:9:7,2:16,9:0.2647:2,2:11.3:1:30.8:1:0.68244:1.93:57.7:18:0.2727:0:2 -17 77386101 . C T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00546;SOR=Inf;LSEQ=CCGCAGCCTCCAGGTCTCCG;RSEQ=AGCCTCCAGGTCTCCGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:8,8:0:2,0:15.8:1:31.1:1:1:0:54.9:32:1:0:0.8 0/1:38:5:5,0:21,12:0.1316:2,0:17.8:1:25.2:1:0.15827:0:60:10:0.1429:0:2 -17 77386118 . T C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=Inf;LSEQ=CCGCAGCCTCCAGGTCTCCG;RSEQ=AGCCTCCAGGTCTCCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:13,7:0:2,0:21.5:1:28.4:1:1:0:59.2:19:1:0:0.3 0/1:48:8:6,2:25,15:0.1667:2,2:11.9:1:31.4:1:0.69381:1.78:58:16:0.1778:0:2 -17 77452609 . G T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCTCTCACCCAGGCTTTGC;RSEQ=CTGGGTTCCCAAAGGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 77453148 . A G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18618;LSEQ=ACAGATGACACACACGTGGC;RSEQ=CAGGTGTAGACAGGCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:14:14,0:24,1:0.359:1,1:27.9:1:30.4:1:1:0:60:28:0.359:0:2.5 0/1:10:4:4,0:6,0:0.4:0,0:32.5:1:29.8:1:1:0:60:8:0.4:0:1.8 -17 77453159 . C G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4938;SOR=0.50628;LSEQ=ACACGTGGCACAGGTGTAGA;RSEQ=AGGCAGGGTGAGGTCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:18,0:23,1:0.4286:1,1:26.1:1:32.4:1:1:0:60:36:0.439:0:2.2 0/1:11:3:3,0:8,0:0.2727:0,0:42.3:1:30.7:1:1:0:60:6:0.2727:0:2 -17 77453256 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51265;SOR=0;LSEQ=CCCCTGAGCAGAAGGCCTGG;RSEQ=CCCATGTCCAGCATGGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:144,45:0.0105:2,2:34.5:1:29.5:1:0.42463:3.17599:60:4:0.0108:0:1 0/0:136:0:0,0:102,34:0:2,0:23.4:1:30.6:1:1:0:60:33:1:0:0.3 -17 77453332 . A C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=0.58463;LSEQ=ACGGATGAGGGCCTCATGGC;RSEQ=TGGCCTCGGGTAGCAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:193:107,86:167,144:0.3807:2,2:26.9:1:31.1:1:0.71384:1.07:60:47.25:0.378:0:2.2 0/1:439:116:59,57:176,146:0.2642:2,2:27.3:1:30.2:1:0.51545:1.16421:60:28:0.2623:0:2.5 -17 77453340 . G A 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=95.59479;LSEQ=GGGCCTCATGGCATGGCCTC;RSEQ=GGTAGCAGTGGAAAAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:1:1,0:277,239:0.0019:2,0:1:0:31:0:1:0:60:2:0.002:0:1 0/1:441:69:36,33:189,183:0.1565:2,2:28.4:1:29.7:1:0.89594:1.06:60:68:0.156:0:3 -17 77453363 . T C 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=0.59093;LSEQ=TAGCAGTGGAAAAGGAGCTG;RSEQ=TGTGGAGACACAGGACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:510:203:105,98:144,161:0.398:2,2:24.6:1:31.8:1:0.36496:1.20:60:49.75:0.3948:0:2.4 0/1:381:107:47,60:131,143:0.2808:2,2:26.1:1:31.3:1:0.56797:1.16899:60:106:0.2797:0:2.8 -17 77453406 . A G 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.49694;LSEQ=TGGAATCAATAGCTCTCACC;RSEQ=TGTGGTGTGTGCCATCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:158:55,103:75,137:0.427:2,2:27.2:1:31.1:1:1:1.02515:60:78:0.4321:0:2.1 0/1:237:64:19,45:66,107:0.27:2,2:27.7:1:30.3:1:0.28571:1.45861:60:128:0.2712:0:2.2 -17 77453639 . A G 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCAGCAGCCCCGTGTAG;RSEQ=TGCCCCGGGACCTCCGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:33:1:27:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 77454426 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCCTTCACTCAGCTCCC;RSEQ=GCAATGTTGACGTCTCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:32.5:1:1:0:60:4:1:0:1 -17 78114602 . AT A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATAAAATGGGTACAATTT;RSEQ=TTTTTTTTTGAGACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:30:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78431533 . A G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACCTGCCACTGCCCTTCTT;RSEQ=TCCACACTCTTCCTGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:50:0:27:0:1:0:60:2:1:0:0 1/1:2:2:2,0:0,0:1:0,0:26:1:32.5:1:1:0:60:4:1:0:2.5 -17 78519169 . G A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGCAGCCAGTGGCTTG;RSEQ=GACCTGGGGTGGTGTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:39:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:0:0,0:41:0:31:0:1:0:60:2:1:0:0 -17 78519325 . C A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50499;SOR=0;LSEQ=ATCCATTTGGTTTTCGATTT;RSEQ=CCGTTTTTGTTTCTTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:79,2:0.0241:1,2:8.5:1:25:0:0.07141:32.44332:60:4:0.0244:0:1 0/0:64:0:0,0:62,2:0:1,0:24.9:1:30.7:1:1:0:60:63:1:0:0.1 -17 78519382 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49903;SOR=0;LSEQ=GCTAGTTTTTAAGGCTGGAG;RSEQ=TTCTCGAGCGCTTGCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:151,44:0.0102:2,2:28.5:1:28.5:1:0.40557:3.40461:60:4:0.0102:0:3 0/0:187:0:0,0:134,53:0:2,0:40:0:15:0:1:0:60:0:0:0:3 -17 78519392 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11607;SOR=0;LSEQ=AAGGCTGGAGGTTCTCGAGC;RSEQ=CTTGCTGCCAAGGACTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:164,54:0.0136:2,2:21.7:1:29.3:1:1:1.51537:60:6:0.0137:0:2.3 0/0:231:0:0,0:150,81:0:2,0:23.3:1:29.6:1:1:0:60:45.2:1:0:0.3 -17 78519404 . G T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36183;SOR=0.31563;LSEQ=TCTCGAGCGCTTGCTGCCAA;RSEQ=GACTCCCCCACCCCCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:183,75:0.0115:2,2:6:1:28:1:0.20877:4.84612:60:6:0.0118:0:1.3 0/0:274:1:1,0:169,104:0.0036:2,0:25:0:32:0:1:0:60:2:0.0037:0:1 -17 78519519 . T C 202 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGAACCTACCTTTGGCTTT;RSEQ=ATGAAAAAGAGGCACTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:0:0,0:274,275:0:2,0:25.5:1:29:1:1:0:60:77.429:1:0:0.1 0/1:530:87:42,45:219,224:0.1642:2,2:27.9:1:31.4:1:0.90677:1.04744:60:174:0.1657:0:1.1 -17 78599313 . G A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25909;SOR=0.32813;LSEQ=TGTGAAACCCTGCCTTCAAA;RSEQ=AAGGGCGTTACTCCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:11,0:14,0:0.44:1,0:22:1:30.5:1:1:0:60:22:0.44:0:1.1 0/1:10:2:2,0:7,1:0.2:2,0:31:1:32:0:1:0:60:4:0.2:0:1 -17 78599401 . A G 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02768;SOR=Inf;LSEQ=GTGGGTAGGGAAGGGGCTCA;RSEQ=TGTTCTGGGGGACATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:80,2:0:1,0:23:1:30.7:1:1:0:60:164:1:0:0.1 0/1:58:4:4,0:54,0:0.069:1,0:22.5:1:33.5:1:1:0:60:8:0.0714:0:1 -17 78599562 . C G 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCCCGATGTGGTGAAGAC;RSEQ=ACGCCCTGTGCACGCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:842:0:0,0:383,458:0:2,0:24.9:1:31.2:1:1:0:60:63.692:0.9988:0:0.1 0/1:893:30:14,16:394,469:0.0336:2,2:25.6:1:29.5:1:1:1.04:60:60:0.0341:0:1.4 -17 78599655 . G T 184 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=159.4796;LSEQ=GCCGGCTCTGGCCTGGGCGG;RSEQ=GCTCGCCAAGCCTGTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:0,1:18,179:0.0051:2,0:13:0:31:0:1:0:60:2:0.0051:0:1 0/1:162:73:9,64:12,77:0.4506:2,2:23.2:1:29.8:1:1:1.10751:60:146:0.4506:0:1.1 -17 78617338 . C T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30502;SOR=0.38121;LSEQ=TAAAACACTGGCCTTCACGG;RSEQ=GTGTCAGCTTGTTTGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:12:10,2:26,0:0.3077:1,2:28.3:1:29.3:1:0.09388:0:60:24:0.3158:0:1.4 0/1:14:2:2,0:12,0:0.1429:0,0:20:1:29:1:1:0:60:4:0.1538:0:1.5 -17 78617403 . G A 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00095;SOR=0.27953;LSEQ=AACACTGATCAACCTTAGGC;RSEQ=TTGTGTTACTTTTAGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:42:41,1:53,1:0.4375:1,1:19.4:1:31.1:1:1:1.28918:60:41:0.4316:0:2.1 0/1:62:11:11,0:51,0:0.1774:1,0:22.6:1:30.7:1:1:0:60:22:0.1774:0:2.1 -17 78617439 . T C 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.01789;SOR=2.26504;LSEQ=TCAAAGGTGACTTTGAAGTG;RSEQ=GTTATATAAGGAGAAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:131:108,23:30,5:0.7892:2,2:26.8:1:31.3:1:0.80152:1.27594:60:42.667:0.7901:0:1.4 1/1:133:119:99,20:12,2:0.8947:2,2:25.9:1:31.5:1:1:1.21045:60:38.667:0.8923:0:1.2 -17 78617651 . G A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2631;SOR=0;LSEQ=CTTCCCTTTCCTTCTTACAG;RSEQ=GAAACTCCAGTTCCTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:69,197:0.0112:2,2:18.7:1:30:1:0.17119:5.67:60:6:0.0113:0:1 0/0:203:0:0,0:58,145:0:2,0:23.9:1:30.1:1:1:0:60:66.667:1:0:0.1 -17 78617681 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51525;SOR=0;LSEQ=GTTCCTTGGTTTCCAACACT;RSEQ=TTTGGATCCAAGTGAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:16,128:0.0136:2,2:9.5:1:30:1:0.22003:7.79:60:4:0.0138:0:1 0/0:101:0:0,0:13,87:0:2,0:20.1:1:31.7:1:1:0:60:200:0.9901:0:0.1 -17 78681520 . A G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17256;SOR=1.53027;LSEQ=TTTTATAGATGGAGAAACTC;RSEQ=GAGCCATGTGTCCAGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:53:53,0:71,1:0.424:1,1:22.6:1:30:1:1:0:60:52:0.4194:0:1.6 1/0:66:35:34,1:30,1:0.5303:1,1:19.2:1:30.1:1:1:1.13:60:34:0.5231:0:1.7 -17 78681543 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.54219;SOR=0;LSEQ=GCCATGTGTCCAGGACCACA;RSEQ=AGCTATTAACTGCAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:182,11:0.0103:2,2:15.5:1:29:0:0.11959:15.87718:60:4:0.0104:0:1 0/0:106:0:0,0:97,9:0:2,0:24.1:1:31.2:1:1:0:60:34.333:1:0:1.2 -17 78681579 . G C 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCCAGAGGAAAGGGTAGGG;RSEQ=ATGAGTTCCAAGCATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:283,96:0:2,0:23.8:1:30.6:1:1:0:60:62.167:1:0:0.9 0/1:278:18:13,5:187,73:0.0647:2,2:24.1:1:32:1:1:1.01:60:36:0.0657:0:1.9 -17 78681590 . A G 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.2959;LSEQ=AGGGTAGGGGATGAGTTCCA;RSEQ=GCATTCCCTGGAGTCCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:457:345:247,98:75,36:0.7549:2,2:24:1:31.4:1:0.4724:1.21:60:85.25:0.7528:0:1.2 1/1:335:305:203,102:17,12:0.9104:2,2:24:1:31:1:0.41571:1.40:60:610:0.9132:0:1.3 -17 78681833 . G A 59 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34754;SOR=1.94089;LSEQ=CCAGCTTCCTTCCCGTTTCT;RSEQ=CCAAAAGCCATGCCAATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:4:3,1:190,425:0.0065:2,2:13.5:1:25.5:1:0.0922:6.69:60:8:0.0066:0:1 0/1:481:6:4,2:168,307:0.0125:2,2:11.5:1:23:1:0.19347:3.64:60:5:0.0105:0:1.2 -17 78681860 . C A 43 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14431;SOR=0;LSEQ=GCCATGCCAATTGCGGTGGT;RSEQ=GGAGCAGGTCCTGCCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:4:3,1:73,311:0.0103:2,2:10.8:1:21.8:1:0.02497:12.67:60:3:0.0079:0:1.3 0/0:279:0:0,0:75,204:0:2,0:23.4:1:29.4:1:1:0:60:54.8:1:0:0.1 -17 78681943 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09311;SOR=Inf;LSEQ=ACCCAAATGCCATAACTGAA;RSEQ=GGACCAGGTAGTCAGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:3,71:0:1,0:23.4:1:29.3:1:1:0:60:23.667:1:0:0.1 0/1:33:2:0,2:0,31:0.0606:1,0:24:1:32:0:1:0:60:4:0.0606:0:1.5 -17 78703899 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGAGGAGATGTGGAGAA;RSEQ=TTCAGTTTGATGGTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78704240 . A C 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61306;SOR=0.79275;LSEQ=ATAGTTTTGTATAAAGGCTA;RSEQ=CTCAGCGTCTCTCCAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:36:36,0:68,1:0.3429:1,1:27.8:1:31.4:1:1:0:60:35:0.3365:0:1 0/1:65:19:19,0:46,0:0.2923:1,1:20.5:1:31.1:1:1:0:60:18:0.2857:0:1.1 -17 78704264 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20303;SOR=Inf;LSEQ=AGCGTCTCTCCAGCCACCAG;RSEQ=CTCAATGTGTGTGCCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:146,18:0:2,0:23.7:1:31.2:1:1:0:60:40:1:0:0.3 0/1:135:2:1,1:116,17:0.0148:2,2:17.5:1:30.5:1:0.24975:6.66013:60:4:0.0153:0:1.5 -17 78704278 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23337;SOR=Inf;LSEQ=CACCAGGCTCAATGTGTGTG;RSEQ=CTTTTGTAACGGTGCAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:158,33:0:2,0:26.7:1:31.8:1:1:0:60:94.5:1:0:0.2 0/1:179:2:2,0:144,33:0.0112:2,0:27.5:1:31:1:1:0:60:4:0.0112:0:1 -17 78704479 . C A 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28859;SOR=2.85361;LSEQ=GTCAAGTCCTTCAAGCAGTT;RSEQ=GCACTACAGCGGGAGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:2:1,1:169,288:0.0044:2,2:2:1:25.5:1:1:1.70:60:4:0.0045:0:1 0/1:486:6:4,2:205,275:0.0123:2,2:21:1:27.5:1:0.40977:2.68:60:12:0.0125:0:1.2 -17 78704513 . G A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00182;SOR=Inf;LSEQ=AGCAGGAGCTGGAGGTGAGC;RSEQ=CTCTGGTGCTTGGAGAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:89,216:0:2,0:24:1:31.2:1:1:0:60:42.571:1:0:0.1 0/1:311:10:3,7:100,201:0.0322:2,2:20.8:1:28.6:1:1:1.16031:60:9:0.0293:0:1.1 -17 78704550 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49914;SOR=Inf;LSEQ=GCGGTGCTGGGTTTGGTTTT;RSEQ=TTTTCCCTGGGGGTGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:28,132:0:2,0:24.5:1:31.9:1:1:0:60:39:1:0:0.1 0/1:172:2:1,1:35,135:0.0116:2,2:26.5:1:30.5:1:0.37576:3.82:60:4:0.0118:0:1 -17 78704563 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.49805;SOR=Inf;LSEQ=TGGTTTTGTTTTCCCTGGGG;RSEQ=TGGGGTTTGGGTGGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:17,112:0:2,0:23.8:1:32:1:1:0:60:258:1:0:0.1 0/1:129:2:1,1:20,107:0.0155:2,2:20:0:30.5:1:0.30015:5.25:60:4:0.0156:0:1.5 -17 78704618 . G T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65947;SOR=1.89513;LSEQ=CATCCTCTGAATGGAGCAGG;RSEQ=CTCAGAATGCCAAGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:3:0,3:0,44:0.0638:1,0:20.3:1:30.3:1:1:0:60:6:0.0638:0:1 0/1:26:3:0,3:0,23:0.1154:1,0:28.3:1:29.7:1:1:0:60:6:0.12:0:1 -17 78705418 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGTTTCGATTAAGAGGC;RSEQ=TCCATCTTGTGGCCTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78727548 . C T 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GGTCCTGCAAAGAGGAAAAC;RSEQ=GGGAAGAAAACAGAGTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:21.5:1:27.5:1:1:0:60:3:0.3333:0:1.5 0/0:3:0:0,0:2,1:0:2,0:28.3:1:29.7:1:1:0:60:6:1:0:0.3 -17 78727734 . T C 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01991;SOR=0.63511;LSEQ=TTTATTCTTTCCTTCTGTGT;RSEQ=ACAGCTGCAGCTTACTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:112:95,17:205,26:0.3265:2,2:22.9:1:31.4:1:0.30249:1.4095:60:111:0.3255:0:1.1 0/1:238:56:45,11:165,17:0.2353:2,2:23.6:1:31.3:1:0.05502:2.36249:60:55:0.234:0:1.1 -17 78727756 . G T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCTGCAGCTTACTATTTG;RSEQ=TTGTGACCAGCAGCTAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:0:0,0:392,127:0:2,0:23.2:1:31:1:1:0:60:63.875:1:0:0.3 0/1:439:20:13,7:303,115:0.0456:2,2:23.5:1:29.4:1:0.45234:1.41752:60:40:0.0463:0:1.1 -17 78728057 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14201;SOR=Inf;LSEQ=AGGGACCCCAACCCATGTGG;RSEQ=CCCCAGGCATTCACCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:11,137:0:2,0:27.1:1:32.3:1:1:0:60:147:1:0:0 0/1:90:2:1,1:6,82:0.0222:2,2:30.5:1:28:1:0.15031:12.73:60:4:0.0222:0:1 -17 78728314 . G A 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTGGACTTTCTTTCAGG;RSEQ=GAAGAAAAGGCTGTTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:38.5:1:32:0:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78765080 . A C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=0.0996;LSEQ=GCCTTGACAGAATGGCAATG;RSEQ=GATTTTCTTTACAAATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:19:19,0:22,0:0.4634:1,1:21.6:1:32.4:1:1:0:60:38:0.4872:0:1.1 0/1:26:2:2,0:22,2:0.0769:2,0:9.5:1:33:1:1:0:60:4:0.0769:0:1 -17 78765219 . A G 269 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTGGGTGACTGTTCCATTC;RSEQ=TGCCGTTCACATTCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:443:443:285,158:0,0:1:0,2:25.6:1:30.6:1:1:0:60:87.6:1:0:1.1 1/0:452:301:196,105:99,51:0.6659:2,2:24.3:1:29.6:1:0.91641:1.03984:60:74.25:0.6659:0:1.1 -17 78765477 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15915;SOR=Inf;LSEQ=TGTGTTTGTGATTGTCACAC;RSEQ=GGGGCTTAGTGCAGGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:0,58:0:1,0:25.1:1:30.7:1:1:0:60:116:1:0:0.1 0/1:39:2:1,1:4,33:0.0513:2,2:21.5:1:30:0:0.24291:7.49:60:4:0.0526:0:1 -17 78795868 . A G 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04298;SOR=2.07684;LSEQ=GATTCTCCCTGCCGTGCGCC;RSEQ=AGCTTCTGCTCAGAGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:40:39,1:60,0:0.4:1,1:21.1:1:30:1:0.4:0:60:80:0.4082:0:1.3 1/0:55:32:30,2:23,0:0.5818:1,2:20.6:1:30.8:1:0.50438:0:60:64:0.5818:0:1 -17 78795895 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14151;SOR=Inf;LSEQ=TGCTCAGAGCCTTCCTCCCT;RSEQ=GCTCAGAGCCTTTCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:162,3:0:1,0:23.3:1:31.1:1:1:0:60:54:1:0:0.4 0/1:100:2:2,0:94,4:0.02:1,0:31.5:1:32:0:1:0:60:4:0.0202:0:1 -17 78796361 . T A 69 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCGGTGCACAGCCCTTAC;RSEQ=GCGCACCGGCGGCTTATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:30:1:30:1:1:0:60:10:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78796595 . C CGTGT 28 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTACACCTGTATGTGTGTG;RSEQ=GTGTATTTGTGTATGCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:0.2222:2,0:24:1:28.8:1:1:0:60:4:0.2222:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78796666 . T C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.35307;SOR=2.70428;LSEQ=CCTGTGCACACACATGTATG;RSEQ=ATGCATGTGTGCATGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:7,1:15,0:0.3478:1,2:21.4:1:31.9:1:0.34783:0:60:16:0.3478:0:1.3 1/0:5:3:3,0:1,1:0.6:2,0:22:1:34:0:0.4:0:60:6:0.6:0:1.3 -17 78796738 . CGT C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1.50725;LSEQ=TGTGTACGTGTGTGTTTAAG;RSEQ=GTGTGTGTGTTGCTGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:2,0:50,3:0.0364:2,0:30:1:34:0:1:0:60:4:0.0364:0:0 0/1:37:2:1,1:30,5:0.0541:2,2:24.5:1:29.8:1:0.3018:5.56782:60:4:0.0541:0.027:0 -17 78796907 . C G 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAAAGCTCTTCAGACAGGA;RSEQ=TTGCTGGTGGCTAGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:37:22,15:386,304:0.0507:2,2:25.6:1:31.8:1:0.73574:1.15:60:74:0.0513:0:1.1 0/0:620:0:0,0:336,283:0:2,0:25.3:1:31.1:1:1:0:60:87.429:1:0:0.2 -17 78797066 . T A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGCCGTGCTCCCCCGCCC;RSEQ=CCGTGGCACTGTGATGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:13,172:0:2,0:23.6:1:29.3:1:1:0:60:22.125:1:0:0.1 0/1:133:15:4,11:17,101:0.1128:2,2:25.9:1:29.5:1:0.25635:2.15:60:30:0.1181:0:1.1 -17 78797072 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15969;SOR=Inf;LSEQ=GTGCTCCCCCGCCCTCCGTG;RSEQ=CACTGTGATGTCATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:6,148:0:1,0:26.2:1:32:1:1:0:60:50.333:1:0:0.1 0/1:103:2:1,1:15,85:0.0194:2,2:20.5:1:25:1:0.29043:5.52:60:4:0.0196:0:1 -17 78797412 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAATTAAACTGTTGGGCT;RSEQ=ATGATCAATTAGTTTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78809957 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTCAGGCCCTCATCCTCCGG;RSEQ=CGAGGCAGCGAGGCAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:31.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:3:0:30:0:1:0:60:2:1:0:0 -17 78811244 . T C 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCCTTTCCCTGACTGCA;RSEQ=GCCGACCCCTCCTGATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:22.3:1:34:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78811497 . G A 97 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25744;SOR=0.24744;LSEQ=ATGGTGAGGATGCTGGCAGC;RSEQ=CCAGCGTTCCCGGCCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:9:9,0:35,0:0.2045:1,0:21.7:1:30.7:1:1:0:60:18:0.2045:0:1.1 0/1:17:1:1,0:16,0:0.0588:1,0:26:0:32:0:1:0:60:2:0.0588:0:1 -17 78811530 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10319;SOR=Inf;LSEQ=GCCTGCACTCTCTCCTGGCC;RSEQ=CCCCTCGGACGTCTTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:75,0:0:1,0:25.3:1:31:1:1:0:60:74:1:0:0.2 0/1:36:2:1,1:34,0:0.0556:1,2:6:1:28.5:1:0.05556:0:60:4:0.0556:0:1 -17 78820023 . T C 104 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCCCCAGCTCGGTGCCC;RSEQ=GGCCAAAAGCCTTGGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:1:0,0:23.6:1:31.6:1:1:0:60:20:1:0:1.1 1/1:1:1:1,0:0,0:1:0,0:34:0:32:0:1:0:60:2:1:0:1 -17 78820167 . C T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07214;SOR=0.36218;LSEQ=ATCCTCGCGGCCCTGCAGGG;RSEQ=GGGCCCTTCGTGAAGGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:22:22,0:120,3:0.1517:1,1:23.6:1:29.3:1:1:0:60:21:0.1489:0:2 0/1:66:4:4,0:60,2:0.0606:1,0:27.8:1:30:1:1:0:60:8:0.0625:0:2 -17 78820212 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.38377;LSEQ=CCCGGCAGGTGGCAGGGGTG;RSEQ=GCAAGACCAGGCCATCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:232:180,52:90,23:0.6725:2,2:22.8:1:30:1:0.78104:1.13:60:28:0.6667:0:1.2 0/1:184:81:68,13:82,20:0.4402:2,2:26:1:29.1:1:0.56717:1.27:60:80:0.442:0:1.2 -17 78820329 . C T 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.47101;LSEQ=CAGGTGTGGCTCACCATGGG;RSEQ=GTGGAGAACCGAAACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1118:729:369,360:188,198:0.6521:2,2:26.8:1:29.6:1:0.57115:1.08:60:59.75:0.6524:0:1.2 0/1:896:420:216,204:238,238:0.4688:2,2:24.9:1:29:1:0.68818:1.06:60:83:0.4721:0:1.1 -17 78820374 . G A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23037;LSEQ=CAGCTGCCCATCGTCCTGCA;RSEQ=GTGAGTTTCTTCAGACCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:951:342:140,202:258,351:0.3596:2,2:24.8:1:30.7:1:0.68159:1.06053:60:67.4:0.36:0:1.2 0/1:795:91:41,50:305,398:0.1145:2,2:27.4:1:30.1:1:0.8224:1.07:60:90:0.1144:0:1.2 -17 78821382 . G A 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGCCGTGGGGAGGGGCT;RSEQ=CCCAGCAGCAGGCAGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23:0:30.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78828266 . T G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTGAGTGGGTTCAGCC;RSEQ=CAGGGTCATTTGGTAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:0:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78829114 . G C 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15855;SOR=0;LSEQ=CTAAAAGCATGAACTTGTAA;RSEQ=GAAAGGAGCACCAGCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:5:5,0:86,1:0.0543:1,0:29:1:33:1:1:0:60:10:0.0556:0:1 0/0:53:0:0,0:52,1:0:1,0:24.5:1:32:1:1:0:60:52:1:0:0.1 -17 78829361 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31288;SOR=2.11341;LSEQ=GAGCCTGGTGCGTGCCTTCC;RSEQ=CATTAACCTGGGGGCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:607:3:3,0:195,409:0.0049:2,0:1:0:27.7:1:0.03435:0:60:6:0.005:0:1 0/1:481:5:4,1:178,298:0.0104:2,2:10.4:1:26:1:0.07042:6.67:60:10:0.0105:0:1 -17 78829375 . G A 192 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=185.17729;LSEQ=CCTTCCGCATTAACCTGGGG;RSEQ=CTGAGGGAGGTGGGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:1:1,0:134,366:0.002:2,0:1:0:16:0:0.26946:0:60:0:0:0:1 0/1:380:103:40,63:88,189:0.2711:2,2:22.9:1:28.8:1:0.22228:1.36:60:50.5:0.2708:0:1.2 -17 78829484 . T G 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCGAGTGTGTCCACCGTG;RSEQ=TGGTGTCCTGTCACTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:1,64:0:1,0:25.4:1:30.8:1:1:0:60:130:1:0:0.2 0/1:26:9:0,9:2,15:0.3462:2,0:22:1:29.8:1:0.52923:0:60:8:0.32:0:1.8 -17 78829531 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14212;SOR=7.02909;LSEQ=CAAGGAGCCCACTCTGTACC;RSEQ=GTGCAGCCTGCAGTGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:0,30:0.0323:1,0:8:0:32:0:1:0:60:2:0.0323:0:1 0/1:10:2:0,2:0,8:0.2:0,0:8.5:1:27:1:1:0:60:4:0.25:0:1.5 -17 78831135 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTGTTGAGCAAGCTGGC;RSEQ=GTGCCGTCACGGAGAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78831782 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2778;SOR=0;LSEQ=GAGCCCTGCGTTTCCAGCCT;RSEQ=CCCTTTCTCCAGCCTCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:1,2:29,261:0.0102:2,2:7.3:1:28.7:1:0.27764:4.46:60:6:0.0103:0:1 0/0:197:0:0,0:33,164:0:2,0:22.2:1:31.6:1:1:0:60:196:1:0:0.1 -17 78831881 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07071;SOR=Inf;LSEQ=CTCGGCAGCCACCTCTGGGT;RSEQ=GTGGGGGCTGTCACCTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:2,38:0:2,0:18.6:1:29.7:1:1:0:60:39:1:0:0.3 0/1:15:2:0,2:0,13:0.1333:1,0:30:1:32:0:1:0:60:4:0.1333:0:1 -17 78853252 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCTCCCACTCCCACATCCC;RSEQ=GGCCTGGACCTGCCATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:45:0:28:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:10.5:1:29.5:1:1:0:60:4:0.6667:0:1.5 -17 78854056 . A G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.34115;LSEQ=AGGAAAGCATGTCTGCAGGC;RSEQ=CCGGCTGCAGCTGTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:12:12,0:63,2:0.1558:1,0:27.8:1:29.8:1:1:0:60:24:0.1622:0:1 1/0:47:30:30,0:16,1:0.6383:1,1:23.8:1:30.3:1:0.3617:0:60:60:0.6383:0:1.1 -17 78854223 . A G 242 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17516;SOR=1.16322;LSEQ=CTTTCTGTCCAGTCGTGCCA;RSEQ=GCGGACCTCGTGAAGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1173:216:116,100:498,456:0.1841:2,2:26.2:1:31.3:1:0.7065:1.06:60:42.2:0.1844:0:1.2 0/1:1005:209:104,105:393,402:0.208:2,2:24.2:1:30.5:1:0.93821:1.01:60:68.667:0.2077:0:1.2 -17 78854316 . C T 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25889;SOR=1.17683;LSEQ=ACGGGGCAGCACGCTCTCCA;RSEQ=GGGCTTGGGACTCAGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:680:129:45,84:202,348:0.1897:2,2:26.4:1:30.4:1:0.76054:1.08342:60:128:0.1913:0:1.2 0/1:574:124:54,70:179,269:0.216:2,2:26:1:29.4:1:0.47192:1.16:60:123:0.2158:0:1.2 -17 78854370 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17466;SOR=Inf;LSEQ=CGCTGCACTGCGGTGGGGCC;RSEQ=TTTGACGGGGGCTACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:23,226:0:2,0:24.2:1:30:1:1:0:60:48.8:0.9959:0:0.2 0/1:180:2:1,1:33,145:0.0111:2,2:26:1:29.5:1:0.34295:4.34:60:4:0.0112:0:1 -17 78854487 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05441;SOR=5.2952;LSEQ=CTACCATGAGCGCAGCTGTT;RSEQ=TTTCGTGTCTGTCTCTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:0,4:0,28:0.125:1,0:28.5:1:32.3:1:1:0:60:8:0.125:0:2.3 0/1:9:4:0,4:0,5:0.4444:0,0:10.3:1:32:1:1:0:60:8:0.4444:0:1 -17 78854496 . C T 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GCGCAGCTGTTATTTCGTGT;RSEQ=TGTCTCTAAACAAGAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:0,4:0,27:0.129:1,0:24:1:27.8:1:1:0:60:3:0.1:0:2.3 0/0:5:0:0,0:0,5:0:0,0:5.4:1:31.4:1:1:0:60:10:1:0:0.4 -17 78857523 . A T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05965;SOR=Inf;LSEQ=GTTGTCCCGTGCAGGTACCC;RSEQ=CCACGTGCCTGCCATTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:286,82:0:2,0:24:1:29.8:1:1:0:60:39.889:1:0:0.1 0/1:237:3:1,2:169,65:0.0127:2,2:11:1:26.3:1:0.19345:5.15778:60:6:0.0129:0:1 -17 78857631 . C T 160 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03127;LSEQ=ATCTGCCTGGAGCAGCTCAA;RSEQ=GACCCGCACCCCTTGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:862:40:17,23:397,425:0.0464:2,2:27.5:1:30.2:1:0.51938:1.26346:60:39:0.046:0:1.1 0/0:659:1:0,1:342,316:0.0015:2,0:1:0:23:0:0.48103:0:60:2:0.0015:0:1 -17 78857700 . G A 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCTGGCAGAACTTCGACTC;RSEQ=GCGAGGTGGTGCGGCGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:864:0:0,0:409,455:0:2,0:25.2:1:30.2:1:1:0:60:60.714:1:0:0.2 0/1:689:76:36,40:296,317:0.1103:2,2:22:1:29.9:1:0.90366:1.03746:60:75:0.1106:0:1.2 -17 78857809 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07114;SOR=6.6261;LSEQ=CTCAGAGTCCAGTCCTCCTG;RSEQ=CTGCCGACTGCGGGGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:1:1,0:115,287:0.0025:2,0:1:0:25:0:0.28784:0:60:2:0.0026:0:1 0/1:246:4:2,2:78,164:0.0163:2,2:21:1:28.5:1:0.59776:2.10:60:8:0.0167:0:1.3 -17 78857812 . G A 39 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04874;SOR=Inf;LSEQ=AGAGTCCAGTCCTCCTGGCT;RSEQ=CCGACTGCGGGGGTAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:108,276:0:2,0:23.8:1:31.4:1:1:0:60:41.667:1:0:0.2 0/1:222:3:2,1:68,151:0.0135:2,2:12.3:1:24.7:1:0.23448:4.41:60:6:0.014:0:1 -17 78857840 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55361;SOR=0;LSEQ=CGGGGGTAAGGCAGAGGTCT;RSEQ=CTCGCGTGCGGGTGTGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:3:0,3:34,192:0.0131:2,0:32.7:1:31.3:1:1:0:60:6:0.0137:0:1 0/0:115:0:0,0:18,97:0:2,0:22.4:1:31.6:1:1:0:60:37.333:1:0:0.2 -17 78857885 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.32846;SOR=1.61884;LSEQ=CGTGTCCAGGAACTTCAGGG;RSEQ=CTGCACGCTAATAAGAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:17:1,16:3,86:0.1604:1,1:28.6:1:30.5:1:0.5085:1.78:60:34:0.1635:0:1.1 0/1:38:9:0,9:0,29:0.2368:1,0:26.3:1:28.8:1:1:0:60:18:0.2432:0:1.1 -17 78858122 . T A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCCACTTTACGGGCAAGGAG;RSEQ=CAGGCCAGTGGCTCGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:4:0:30:0:1:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:1:0,2:8:1:29.5:1:1:0:60:4:1:0:2.5 -17 78858180 . G A 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGCGGGGCACTGCCCACAGA;RSEQ=TGGCCGCGGGCTGGAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:31:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:26.5:1:1:0:60:4:1:0:3.5 -17 78858662 . A G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00285;SOR=3.5441;LSEQ=CCTTCCCCGTTGCCACTCTG;RSEQ=TAGTGCGAGGAGAGCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:19:19,0:61,0:0.2375:1,1:28.9:1:31.7:1:1:0:60:38:0.2405:0:1.3 1/0:36:19:17,2:15,2:0.5278:2,2:21.4:1:30.5:1:1:1.13:60:38:0.5429:0:1.1 -17 78858769 . C T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=AGGCAGGCTGCAGCATGGCC;RSEQ=GGTGTGGGACATGCCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:0:0,0:322,143:0:2,0:25.3:1:30.5:1:1:0:60:92:0.9978:0:0.2 0/1:348:10:7,3:233,105:0.0287:2,2:23.5:1:31.6:1:1:1.05:60:20:0.0297:0:1 -17 78859004 . C T 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02501;SOR=1.65682;LSEQ=CCAGGCTGGACCCCGTGACA;RSEQ=CTGGGGCCAAGCCCGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:51:12,39:41,200:0.1747:2,2:22.5:1:29.4:1:0.31669:1.50:60:24.5:0.1713:0:1.1 0/1:204:53:15,38:36,114:0.2598:2,2:21.7:1:28.3:1:0.58176:1.25:60:25.5:0.255:0:1.1 -17 78859110 . G A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50562;SOR=1.689;LSEQ=TTTCATTCTCTTCAAGTTGC;RSEQ=TTTCTTTACCAGACACCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:9:0,9:0,49:0.1552:1,0:18.9:1:31.7:1:1:0:60:18:0.1698:0:1 0/1:21:5:0,5:0,16:0.2381:1,0:28:1:30:1:1:0:60:10:0.2381:0:1 -17 78859284 . TC T 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAAGGTTTGTGTGCTGGG;RSEQ=CCCCCCAACACCCCATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:21.5:1:33:0:1:0:60:4:0.3333:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78860487 . G T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGAGGCACTGAGACGAA;RSEQ=CTCCCCCTCCACCGGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12:0:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78863393 . C G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGAGAGAGAGGGGAGCT;RSEQ=CCACACCCCTGGCTGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45:0:33:1:1:0:60:4:1:0:1.5 -17 78865491 . C G 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3737;LSEQ=TCATTTTCCAGCCCCAGTGA;RSEQ=TGTTATTGTCCCTTCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:506:149:112,37:268,89:0.2945:2,2:26.3:1:31.7:1:1:1.01:60:48.667:0.2949:0:1.7 0/1:319:43:32,11:204,70:0.1348:2,2:26.5:1:30.8:1:1:1.00178:60:86:0.1374:0:1.5 -17 78865546 . T C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.96605;LSEQ=GTGGTGGCTCTGAGTCATCT;RSEQ=GTGGTTCAGTATGAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:928:298:150,148:329,301:0.3211:2,2:25.7:1:30.5:1:0.62258:1.07836:60:98.333:0.3231:0:1.6 1/0:726:424:221,203:160,141:0.584:2,2:25.8:1:30.3:1:0.82098:1.04229:60:211:0.5861:0:1.3 -17 78865630 . A G 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21071;SOR=0.84934;LSEQ=TACGCCTTGCCTTCTCCAGC;RSEQ=ACCACAGGTATGGCGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:668:225:85,140:157,285:0.3368:2,2:24.3:1:30.5:1:0.60946:1.10:60:111.5:0.3384:0:1.3 0/1:521:157:57,100:140,224:0.3013:2,2:23.4:1:30.1:1:0.69398:1.09628:60:30.4:0.2957:0:1.4 -17 78865662 . C A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14315;SOR=0;LSEQ=GGCGTCTTCTCCTGTGAACC;RSEQ=GCAGAGCACCTCGCCTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:4:2,2:104,279:0.0103:2,2:30.3:1:30.5:1:0.30222:2.67:60:8:0.0104:0:1 0/0:281:0:0,0:80,201:0:2,0:24.8:1:29.1:1:1:0:60:55.2:1:0:0.4 -17 78865824 . A G 105 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.38035;SOR=0.24736;LSEQ=AAAGGGCAGGAAAGAGGGCC;RSEQ=CACTGACCCTCTTACATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:0,9:1,14:0.375:1,0:24.4:1:33.2:1:1:0:60:18:0.375:0:1.1 0/1:8:1:0,1:0,7:0.125:0,0:33:0:32:0:1:0:60:2:0.125:0:1 -17 78866410 . A G 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05162;SOR=1.9569;LSEQ=TGTGCAGCCCCTGCTCTGAC;RSEQ=TTTGTTGCAGCACAGGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:38:35,3:69,1:0.3519:1,2:24.6:1:29.3:1:0.12396:5.81345:60:76:0.3619:0:1 1/0:62:32:31,1:30,0:0.5161:1,1:25.1:1:29:1:1:0:60:31:0.5082:0:1 -17 78866732 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52661;SOR=0;LSEQ=GGTTGTTTTTTCTGAAACAC;RSEQ=GTATCTGAGTAAGCACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:22,153:0.0113:2,2:14:1:28.5:1:0.24364:6.82:60:4:0.0116:0:1 0/0:109:0:0,0:12,97:0:2,0:22.7:1:30.1:1:1:0:60:108:1:0:0.1 -17 78867041 . C T 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGTGTGTGCGCCGGGG;RSEQ=GTGTGTGCCAGGGTGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:24:1:26.5:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78867061 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGTGTGCCAGGGTGTGTG;RSEQ=GCCAGGGTGCGTGTGTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:33.5:1:28.5:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78867123 . C T 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTGTGCGCCAGGTGTGTG;RSEQ=GCGCGCCAGGTGTGTGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:2,0:0.6667:0,2:29.3:1:28.3:1:1:0:60:8:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78867242 . A G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GTGTGTGCCAGGGTGTGTGT;RSEQ=CTGGGTGTGTATACGCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:3,1:7,0:0.3636:0,2:35:1:31.8:1:0.36364:0:57.5:8:0.4:0:2.5 0/0:3:0:0,0:2,1:0:2,0:25.3:1:21.3:1:1:0:60:2:1:0:1.3 -17 78867271 . CTGTACGCGCCAGGG C 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.63336;SOR=2.17754;LSEQ=GTATACGCGCCAGGTTGTGT;RSEQ=TGTGTGCGCCAGGGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:14,1:0.25:1,2:26.4:1:32:1:0.44737:3.24034:58:10:0.25:0:1.2 0/1:7:3:3,0:3,1:0.4286:2,0:10.3:1:30.7:1:1:0:60:6:0.4286:0.2857:0.3 -17 78867363 . GGT G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.13195;SOR=Inf;LSEQ=CCAGGGTGTGTGCGCACCAG;RSEQ=GTGTGTGTACCAGGGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:75,2:0:1,0:22.4:1:30.8:1:1:0:60:24.667:1:0:0.4 0/1:45:2:1,1:41,2:0.0444:1,2:33:1:31:1:0.1303:16.94013:60:4:0.0455:0:0.5 -17 78867377 . A G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=3.000;MSILEN=1;SSF=0.715;SOR=1.14897;LSEQ=CACCAGGGTGTGTGTGTACC;RSEQ=GGGTGTGTTTGTGCCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:29:28,1:62,1:0.3152:1,1:21.4:1:30.9:1:0.53344:2.19329:60:58:0.3258:0:1 0/1:52:18:18,0:31,3:0.3462:2,1:22.2:1:28.7:1:0.54308:0:60:17:0.3469:0:1.2 -17 78867453 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06797;SOR=Inf;LSEQ=AGTCATGCCATTAACTGTAA;RSEQ=ACCAAAAGGAGGGTCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:304,76:0:2,0:24.3:1:31.6:1:1:0:60:33.545:1:0:0.2 0/1:263:3:1,2:182,77:0.0114:2,2:5.7:1:26:1:0.21696:4.69556:60:6:0.0115:0:1 -17 78867691 . T A 61 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0386;SOR=4.97406;LSEQ=TCCGCCTGCCCCTTTCTGCT;RSEQ=CCGAGGGGCCCCGAGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:884:2:2,0:309,573:0.0023:2,0:1:0:23.5:1:0.12351:0:60:4:0.0023:0:1 0/1:627:7:6,1:233,387:0.0112:2,2:5.7:1:21.9:1:0.01401:9.93:60:6:0.0097:0:1.1 -17 78867733 . A G 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.59157;LSEQ=CTCCCCACACAGAGCAGCAC;RSEQ=GACCTGTGTCTGCATCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:115:20,95:28,247:0.2949:2,2:22.6:1:30.6:1:0.0621:1.85:60:114:0.3016:0:1.1 1/0:248:149:28,121:16,83:0.6008:2,2:21:1:29.5:1:0.61595:1.20:60:28.8:0.5926:0:1.2 -17 78867822 . C T 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17167;SOR=1.98457;LSEQ=GGACTGCGAGGCAGGGAGAA;RSEQ=GTTTTGCTGGGGCAAGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:21:0,21:0,42:0.3333:1,1:20.4:1:30.9:1:1:0:60:42:0.3333:0:1.5 1/0:30:15:0,15:0,15:0.5:1,1:19.8:1:30.1:1:1:0:60:30:0.5:0:1.7 -17 78867885 . T C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19675;SOR=3.28376;LSEQ=TGGGGTAGTATTTTACAGGC;RSEQ=GCTCCGGAGCCATCGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:0,7:0,18:0.28:1,0:35:1:30.7:1:1:0:60:14:0.2917:0:2.3 1/0:7:4:0,4:0,3:0.5714:0,0:16:1:31.3:1:1:0:60:8:0.5714:0:2.5 -17 78867906 . G A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58893;SOR=2.08985;LSEQ=GCTCCGGAGCCATCGGAGCT;RSEQ=GCCAGTTTGGCTGGGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:0,6:0,13:0.3158:1,0:24:1:32.2:1:1:0:60:12:0.3158:0:2.3 1/0:4:2:0,2:0,2:0.5:0,0:26.5:1:33:0:1:0:60:4:0.5:0:3 -17 78868185 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGTCGGGCTGGGGGCTGTC;RSEQ=TCCCCGCCCTGCTCACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78869374 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGCTCAATACACATAAAC;RSEQ=GGCACGTGTGTGGTGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:31.5:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:0:2,0:16.5:1:29.5:1:1:0:60:4:1:0:0 -17 78869413 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTTCTTCAGCGTGGATACAC;RSEQ=TGAGTGCCTCTCGCCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29.5:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:0:2,0:37:1:30.5:1:1:0:60:4:1:0:0 -17 78881443 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGCCCGTGCCTGCCCCC;RSEQ=CTTCTGGTTTCCAAGTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:32:1:1:0:60:4:1:0:1.5 -17 78882329 . G A 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=GTGGTCATGCCCTCCGATCC;RSEQ=CTGAGGCATTTCAAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:31.4:1:30.3:1:1:0:60:14:1:0:1.1 0/0:1:0:0,0:1,0:0:0,0:49:0:31:0:1:0:60:2:1:0:0 -17 78882806 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.30447;LSEQ=GCATGCCAGGAACTCCAGGT;RSEQ=TGCCCGGGTCCACACCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:216:127:3,124:6,83:0.588:2,1:24.8:1:31.3:1:0.16602:2.97266:60:254:0.5907:0:2.2 0/1:139:42:2,40:5,92:0.3022:2,1:22.3:1:29.8:1:1:1.08631:60:84:0.3022:0:2 -17 78882824 . CA TG 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12367;SOR=Inf;LSEQ=GTGTGCCCGGGTCCACACCA;RSEQ=GTTTAGAAAGTAACAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:3,161:0:1,0:24:1:29.7:1:1:0:60:31.8:1:0:2.3 0/1:90:2:0,2:0,88:0.0222:1,0:29.5:1:32:0:1:0:60:4:0.0227:0:1 -17 78882825 . A G 225 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01121;LSEQ=TGTGCCCGGGTCCACACCAC;RSEQ=GTTTAGAAAGTAACAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:156:3,153:0,1:0.9936:0,1:24.9:1:31:1:1:0:60:30.2:0.9934:0:2.4 1/0:87:55:0,55:0,30:0.6322:1,1:26.9:1:29.7:1:1:0:60:17.333:0.642:0:1.8 -17 78882840 . A G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.02793;LSEQ=ACCACAGTTTAGAAAGTAAC;RSEQ=AAACGAGCTTCAGCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:117:110:2,108:0,7:0.9402:0,1:23.7:1:31.5:1:1:0:60:54:0.9474:0:2.6 0/1:67:20:0,20:0,47:0.2985:1,1:25.2:1:30.8:1:1:0:60:40:0.2985:0:2.9 -17 78882953 . G A 101 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.46629;LSEQ=GATTTACTGATGCCTGTCAA;RSEQ=GCAATTAGGGGAGGACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:0,10:0,9:0.5263:0,0:24.6:1:30.7:1:1:0:60:20:0.5263:0:1.8 0/1:3:1:0,1:0,2:0.3333:0,0:30:0:33:0:1:0:60:2:0.3333:0:2 -17 78882972 . A C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51703;SOR=Inf;LSEQ=AGGCAATTAGGGGAGGACTG;RSEQ=CATTATCTTTCAGGATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:0,10:0,6:0.625:0,0:25:1:30.2:1:1:0:60:20:0.625:0:1.9 1/1:3:3:0,3:0,0:1:0,0:19:1:31.7:1:1:0:60:6:1:0:1.3 -17 78883030 . A AT 59 d7;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTGCTGGCCCTTCTTCC;RSEQ=TTTTTTTTTTCTTTCTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:21.5:1:29.5:1:1:0:60:8:0.6667:0.1667:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78895788 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAAGGGCGGTCTTGAGTT;RSEQ=CAGGCCCCGTCACAGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78896428 . A T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0558;SOR=Inf;LSEQ=GGCCAAAGGCCTTTTCTGTG;RSEQ=TTCTGAAGCGGCTCCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:385,37:0:2,0:23:1:29.8:1:1:0:60:51.75:1:0:0.7 0/1:262:3:1,2:226,32:0.0115:2,2:13:1:27.7:1:0.04552:13.86123:60:6:0.0119:0:1 -17 78896488 . C T 317 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00097;LSEQ=GGCCTCCGCGGAGCACGTCC;RSEQ=GTCTGACCTTCACACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1397:1393:808,585:3,1:0.9971:2,2:25.8:1:30.4:1:0.64372:2.17093:60:91.867:0.9971:0:1.1 0/1:954:239:144,95:414,301:0.2505:2,2:23.9:1:30.4:1:0.5447:1.10:60:118.5:0.2511:0:1.2 -17 78896529 . C T 196 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=22.4111;LSEQ=TTCCTTTGCCCCTAGGCCAC;RSEQ=GTGAACGCCCGGCCGCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1826:6:0,6:913,907:0.0033:2,0:7.3:1:27:1:0.03099:0:60:12:0.0033:0:1.3 0/1:1409:97:48,49:667,645:0.0688:2,2:22.5:1:29.7:1:0.83369:1.05564:60:23.25:0.0671:0:1.2 -17 78896762 . C T 196 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCTCCTCCCCCCTCTCCAG;RSEQ=GGGCGTTCTTTCCCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:90:90:0,90:0,0:1:0,1:22.3:1:30.3:1:1:0:60:44:1:0:2 0/1:32:9:0,9:1,22:0.2813:1,0:20.9:1:31.3:1:1:0:60:18:0.2813:0:2 -17 78896768 . T C 203 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=TCCCCCCTCTCCAGCGGGCG;RSEQ=TCTTTCCCTCTCCCTCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:76:0,76:0,0:1:0,1:23.3:1:32.6:1:1:0:60:152:1:0:2.2 1/0:32:24:1,23:0,8:0.75:0,1:24.6:1:32.7:1:1:0:60:48:0.75:0:1.4 -17 78897056 . C G 140 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=CCGCGCCACCTCCCAGGGTG;RSEQ=TGGAGTTCAATGAGGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:19,3:0,0:1:0,2:16.8:1:31.6:1:1:0:60:44:1:0:1 1/0:4:3:3,0:1,0:0.75:0,0:25:1:32.3:1:1:0:60:6:0.75:0:1 -17 78897146 . T C 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CAGCTGGGGTTCGGGAGCCA;RSEQ=GATGGCATGCTGGGTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:89,4:0:1,0:24.3:1:31.2:1:1:0:60:92:1:0:0.2 0/1:32:10:10,0:22,0:0.3125:1,0:21.2:1:32.1:1:1:0:60:20:0.3333:0:1 -17 78897209 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04407;SOR=Inf;LSEQ=CACCTGGGAGGGTGCAGGTG;RSEQ=CCCAGGAAGTTGTTCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:231,29:0:2,0:23.8:1:31.4:1:1:0:60:42.333:1:0:0.1 0/1:143:3:2,1:116,23:0.021:2,2:14.7:1:28.7:1:0.42867:2.50048:60:6:0.0221:0:1 -17 78897547 . C T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGGGGCTCATGGCCTCAG;RSEQ=CTCAGGCTGCTCACATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:21,232:0:2,0:26.5:1:30.8:1:1:0:60:18.462:1:0:1.3 0/1:167:20:5,15:13,134:0.1198:2,2:22.2:1:29.5:1:0.04512:3.40:60:40:0.1227:0:2 -17 78897561 . C T 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02119;LSEQ=CCTCAGCCTCAGGCTGCTCA;RSEQ=ATCACCATGGGATGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:206:205:7,198:0,1:0.9951:0,1:26.2:1:28.4:1:1:0:60:67.333:0.9951:0:1.7 1/1:122:99:6,93:0,23:0.8115:1,2:21.7:1:28.3:1:0.59303:0:60:48.5:0.8083:0:1.7 -17 78897587 . A G 231 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02169;LSEQ=CATGGGATGGGGCAGGACCC;RSEQ=CCCTGCCGTCCTGGGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:138:0,138:0,1:0.9928:0,1:22.9:1:32.5:1:1:0:60:68:0.9927:0:2 1/0:63:47:0,47:0,16:0.746:1,1:22.7:1:32.3:1:1:0:60:22.5:0.7377:0:2.3 -17 78897674 . C T 149 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00106;SOR=0;LSEQ=GCACCCCTCTGCCTGCACTC;RSEQ=TTAGGAGCACTGCTGGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:1,28:0,0:1:0,1:22.7:1:30.7:1:1:0:60:58:1:0:1.7 1/0:8:4:1,3:1,3:0.5:2,2:11.3:1:31.8:1:1:1:60:8:0.5:0:1.5 -17 78897732 . CT TA 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00735;SOR=0;LSEQ=TGCACTCTTTAGGAGCACTG;RSEQ=GGGTGTGTCCCGGTTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:1:0,1:26:1:29.3:1:1:0:60:30:1:0:1.4 0/0:2:0:0,0:1,1:0:2,0:9:0:34:0:1:0:60:4:1:0:0.5 -17 78898600 . C G 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGTGCCCAGCCTCACT;RSEQ=CACAAGCACACACAGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:1:32:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:36:0:34:0:1:0:60:2:1:0:1 -17 78898778 . T C 34 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGGAGTCCCCGCTCTCAG;RSEQ=CTGGTGTCACGGGGCCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:34:0:1:0:60:4:1:0:2 1/1:1:1:0,1:0,0:1:0,0:23:0:33:0:1:0:60:2:1:0:2 -17 78898788 . C T 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCTCTCAGTCTGGTGTCA;RSEQ=GGGGCCATCACAGGAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18.7:1:30.3:1:1:0:60:6:1:0:1.7 1/1:1:1:0,1:0,0:1:0,0:13:0:32:0:1:0:60:2:1:0:2 -17 78898912 . G A 31 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=AGAATTGACTTGGGAGCTGT;RSEQ=CTGGGTCGGCCCTGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:10,0:0:0,0:23.7:1:33:1:1:0:60:20:1:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:31:1:1:0:60:4:1:0:1.5 -17 78899307 . T A 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17707;SOR=5.04769;LSEQ=CCGGGGTGTGGGGTTCAGAG;RSEQ=AGAGTCCTAGCGAACATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:1:1,0:149,248:0.0025:2,0:1:0:28:0:0.37688:0:60:2:0.0026:0:1 0/1:318:4:3,1:119,194:0.0126:2,2:11.5:1:25.8:1:0.16073:4.87:60:8:0.0127:0:1 -17 78899365 . G C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5111;SOR=0;LSEQ=AGCATAAACGCTCAAGGCTT;RSEQ=TGGCTGTGGGAGCGTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:10,124:0.0147:2,2:7:0:33:0:0.15577:11.87:60:4:0.0149:0:1.5 0/0:98:0:0,0:16,82:0:2,0:25.1:1:30.9:1:1:0:60:48:1:0:0.1 -17 78914245 . G T 255 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATACCCCATTGATACCAAGA;RSEQ=ACAACCCTGTTTCATCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:345:345:260,85:0,0:1:0,2:24.7:1:30.3:1:1:0:59.9:114:1:0:1.1 0/1:266:85:67,18:133,48:0.3195:2,2:19.8:1:29.8:1:0.36606:1.34:60:84:0.3243:0:1.1 -17 78914414 . G A 87 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54007;SOR=0.54684;LSEQ=TCAGAAGGGTAAGGGCACCC;RSEQ=CACAGCCAGCCAGGGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:8:5,3:238,395:0.0125:2,2:15.4:1:29.3:1:0.16305:2.76:60:16:0.0128:0:1.1 0/0:438:3:2,1:158,277:0.0068:2,2:11.7:1:29:1:0.3024:3.50:60:6:0.007:0:1 -17 78914465 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13372;SOR=Inf;LSEQ=GGGGCCTGGGGCGAGGGTCC;RSEQ=CTGTGAGCAGGCCCCCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:31,237:0:2,0:23:1:31:1:1:0:60:43.667:1:0:0.1 0/1:155:2:1,1:24,128:0.0129:2,2:16:1:32:0:0.29921:5.25:60:4:0.0132:0:1 -17 78914493 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00393;SOR=Inf;LSEQ=CAGGCCCCCCGCGGCCCACG;RSEQ=ACAACCTTCTCCAGCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:4,146:0:1,0:25.5:1:32.2:1:1:0:60:49:1:0:0.1 0/1:76:5:1,4:0,71:0.0658:1,2:19.8:1:27:1:0.06579:0:60:4:0.0548:0:1.4 -17 78914545 . A G 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGACCCGCCCCGCACCCC;RSEQ=CCTCCCTTGCAGATAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:3,66:0:1,0:22.8:1:29.8:1:1:0:60:68:1:0:0.2 0/1:27:12:0,12:0,15:0.4444:1,0:23.6:1:32.1:1:1:0:60:24:0.4444:0:1.4 -17 78914553 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0713;SOR=Inf;LSEQ=GCCCCGCACCCCACCTCCCT;RSEQ=GCAGATAAGCACATCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:2,57:0:1,0:23:1:30.5:1:1:0:60:118:1:0:0.1 0/1:22:2:0,2:0,20:0.0909:1,0:29.5:1:28:1:1:0:60:4:0.0909:0:2 -17 78914748 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCAGGTGGAACTCATGGA;RSEQ=GCGGAACTTTGCATGTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:37:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78919162 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCACTTTGGGAGGCCGAG;RSEQ=CGGGCAGATCACAAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18.3:1:31.3:1:1:0:59.7:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78919285 . A G 156 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00954;SOR=0;LSEQ=ACCTGTAGTCCCAGCTACTC;RSEQ=GGAGGCTGAGGCAGGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:37,0:0,0:1:0,1:27.7:1:30.1:1:1:0:36.8:74:1:0:1.5 1/0:11:8:8,0:3,0:0.7273:0,0:31.5:1:28.9:1:1:0:48:16:0.7273:0:1.5 -17 78919324 . GGAGCTTGCAGTGAGC AGAG 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGTGTGAACCTGGGAGGC;RSEQ=CAAGATTGCACCACTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:83,0:0:1,0:23.7:1:29.2:1:1:0:40.1:19.75:1:0:1.7 0/1:45:15:15,0:30,0:0.3333:1,1:16.5:1:29.5:1:1:0:52:14:0.3333:0.1333:2.1 -17 78919329 . TTGCAGTGAGCCAA AG 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00543;SOR=Inf;LSEQ=GTGAACCTGGGAGGCGGAGC;RSEQ=GATTGCACCACTGCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:90,0:0:1,0:23.2:1:31.3:1:1:0:41:21.5:1:0:1.7 0/1:51:5:5,0:36,0:0.098:1,0:5:1:33:1:1:0:54:10:0.119:0.0784:1.8 -17 78919349 . A G 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01917;LSEQ=TTGCAGTGAGCCAAGATTGC;RSEQ=CCACTGCACTCCAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:120:119:119,0:1,0:0.9917:0,1:23.2:1:29.7:1:1:0:48:28.75:0.9914:0:1.9 1/0:68:47:47,0:21,0:0.6912:1,1:23.8:1:30.4:1:1:0:51.1:94:0.6912:0:2 -17 78919387 . G A 243 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01392;LSEQ=GGGCGACAGAGCGAGACTCC;RSEQ=TCTCAAAAAAAATAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:279:273:243,30:1,0:0.9785:0,2:20.7:1:30.1:1:1:0:57.5:53.6:0.9781:0:1.4 0/1:187:72:66,6:101,13:0.385:2,2:24.1:1:29.1:1:0.62221:1.41:56.5:23:0.3791:0:1.5 -17 78919391 . C CA 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14597;SOR=0;LSEQ=GACAGAGCGAGACTCCGTCT;RSEQ=AAAAAAAATAAATAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:4:4,0:267,40:0.0128:2,0:25.8:1:29.8:1:1:0:50.5:8:0.0131:0:1.5 0/0:221:0:0,0:193,27:0:2,0:20.4:1:30.6:1:1:0:58.2:30.429:0.9953:0:0.7 -17 78919396 . AAAAT A 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=1.15083;LSEQ=AGCGAGACTCCGTCTCAAAA;RSEQ=AAATAAATAAATAAGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:6:5,1:321,63:0.0154:2,2:28.5:1:30.1:1:1:1.019:59.8:12:0.0154:0.0026:1.3 0/1:283:5:5,0:234,44:0.0177:2,0:25.6:1:31.7:1:1:0:56:10:0.0178:0.0035:1.4 -17 78919466 . G T 157 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTGTGTGTTTCTTTTGACA;RSEQ=GCATTACGAGATTGGACGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1178:37:21,16:631,510:0.0314:2,2:29.2:1:30.2:1:1:1.06:60:74:0.0321:0:1.4 0/0:965:0:0,0:521,443:0:2,0:26.6:1:30.5:1:1:0:60:42.818:1:0:0.2 -17 78919546 . G A 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09046;SOR=4.06533;LSEQ=GTGAAATTCCACCCCTTCAC;RSEQ=CCGTGCATCGCCGTAGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:2:2,0:250,458:0.0028:2,0:1:0:26:0:0.12565:0:60:4:0.0029:0:1 0/1:616:7:5,2:237,370:0.0114:2,2:11.4:1:26:1:0.11875:3.89:60:14:0.0116:0:1.7 -17 78919558 . C T 282 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00222;LSEQ=CCCTTCACGCCGTGCATCGC;RSEQ=GTAGCCGACAAGGACAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:626:623:210,413:0,2:0.9952:0,2:24.9:1:30.4:1:0.55308:0:60:68.222:0.9968:0:1.1 0/1:523:164:59,105:129,230:0.3136:2,2:26:1:30.1:1:1:1.00:60:163:0.3135:0:1.1 -17 78919590 . C T 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGACAGCATCTGGTATGCAC;RSEQ=GCGCTGGTCAGGCCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:0:0,0:83,278:0:2,0:23.3:1:30:1:1:0:60:71.2:1:0:0.9 0/1:326:24:8,16:88,214:0.0736:2,2:28.5:1:30.4:1:0.64755:1.22:60:48:0.0738:0:1.2 -17 78919837 . G C 62 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCCTGCAGGTCAGAGG;RSEQ=GAGTGGCAGGGACTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:27:1:31.3:1:1:0:60:8:1:0:2.3 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:60:2:1:0:1 -17 78919859 . G C 80 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGCAGGGACTCCCCAGT;RSEQ=ACACTTGTAATAGAGGCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:17.5:1:31.3:1:1:0:60:12:1:0:2.2 1/1:1:1:1,0:0,0:1:0,0:1:0:29:0:1:0:60:2:1:0:3 -17 78919892 . A G 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCGTACACAGGGGGGCC;RSEQ=GCTTGCTGCCCTGCCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:43:1:29:1:1:0:60:6:1:0:2.3 1/1:2:2:1,1:0,0:1:0,2:22:1:28:1:1:0:60:4:1:0:2.5 -17 78919920 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.1;SOR=Inf;LSEQ=GCCCTGCCCGCAGAAGCAAG;RSEQ=ATGTGATAGACAAGCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:15:1:33:1:1:0:60:6:1:0:2.3 1/1:2:2:1,1:0,0:1:0,2:38.5:1:28:1:1:0:60:4:1:0:2.5 -17 78920172 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTTAACCGTTCTGAGTGC;RSEQ=CAGCCAGTGGCATTCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78920945 . G A 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00424;SOR=Inf;LSEQ=TGGTTTTTTGATAGCAGCCC;RSEQ=GTGGGTTTCAGGAGGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:251,32:0:2,0:24.3:1:30.1:1:1:0:60:282:1:0:0.1 0/1:193:6:5,1:160,27:0.0311:2,2:21.7:1:30:1:1:1.18406:60:12:0.0313:0:1 -17 78920947 . T C 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00155;SOR=Inf;LSEQ=GTTTTTTGATAGCAGCCCGG;RSEQ=GGGTTTCAGGAGGTATCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:256,42:0:2,0:24:1:29.6:1:1:0:60:148:1:0:0.1 0/1:199:7:6,1:163,29:0.0352:2,2:29.1:1:30.6:1:1:1.07:60:14:0.0357:0:1.1 -17 78921108 . G A 171 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=63.58828;LSEQ=ACGAGGGTCACTGCCATGGA;RSEQ=TATCTGAACGGCCAGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:866:1:1,0:398,467:0.0012:2,0:1:0:30:0:0.46074:0:60:2:0.0012:0:1 0/1:758:52:23,29:318,388:0.0686:2,2:23.7:1:30:1:1:1.03335:60:51:0.0684:0:1.2 -17 78921117 . C T 204 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=74.76126;LSEQ=ACTGCCATGGAGTATCTGAA;RSEQ=GGCCAGGACTGCTCGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:796:2:1,1:354,440:0.0025:2,2:12.5:1:19:1:1:1.24:60:1:0.0013:0:1 0/1:699:111:43,68:260,327:0.1588:2,2:24:1:30.1:1:0.29764:1.25697:60:110:0.1599:0:1.1 -17 78921211 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGGAGGAGTGGCGGGGAGG;RSEQ=TGTGTGATCCTGAGATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:40,239:0:2,0:25:1:31.8:1:1:0:60:92:0.9964:0:0.2 0/1:186:24:2,22:34,128:0.129:2,2:20.5:1:29:1:0.17511:2.90888:60:11:0.1215:0:1 -17 78921916 . CG AT 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCTGGGCGGGAGGCAGG;RSEQ=GGGGAGGCCAGCACGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:30:1:1:0:60:4:1:0:1 -17 78921988 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCTGTCCCTGTCGGCC;RSEQ=CAGCCCCTGGACACCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78922683 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCCCTGAAGAGCAGGGC;RSEQ=GTGCGTCCCTGCCCACGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78922952 . C G 104 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGAAGGGCAGCCCCGG;RSEQ=TCCCAGGGCAGCCAAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:21.5:1:30.3:1:1:0:60:10:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78923126 . T G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.11713;LSEQ=CCACGGGTAGTGAGTCAGGC;RSEQ=GGCCGCCCAGGGTCACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:54:53,1:92,0:0.3699:1,1:22.1:1:29.6:1:0.36986:0:60:26:0.3611:0:1.1 0/1:47:3:3,0:43,1:0.0638:1,0:21:1:32:0:1:0:60:6:0.0652:0:1 -17 78923151 . G A 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00214;SOR=Inf;LSEQ=GCCCAGGGTCACTGCAGCAC;RSEQ=TCTGCCAGGAAGGGCTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:209,15:0:2,0:23.5:1:29.8:1:1:0:60:36.333:1:0:0.8 0/1:95:5:5,0:84,6:0.0526:2,0:25.2:1:30.8:1:1:0:60:10:0.0543:0:1 -17 78923178 . C T 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01057;SOR=0.62452;LSEQ=AGGAAGGGCTCTTACCACCA;RSEQ=GCACAGAGCACAGGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:342:200:171,29:114,28:0.5848:2,2:23.2:1:30.9:1:0.23901:1.45:60:65.667:0.5811:0:1.1 0/1:186:87:69,18:80,19:0.4677:2,2:20.6:1:29.1:1:0.85497:1.09784:60:20.75:0.4611:0:1.1 -17 78923193 . C T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06983;SOR=6.68061;LSEQ=CACCACGCACAGAGCACAGG;RSEQ=CAGGCCATCGAGGGGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:1:1,0:317,100:0.0024:2,0:36:0:32:0:1:0:60:2:0.0024:0:2 0/1:253:4:2,2:183,66:0.0158:2,2:26:1:30:1:0.29309:2.7596:60:8:0.0162:0:1.5 -17 78923203 . G T 61 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0381;SOR=7.74813;LSEQ=AGAGCACAGGCCAGGCCATC;RSEQ=AGGGGCCTGGTTCACATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:1:0,1:354,139:0.002:2,0:1:0:23:0:0.2834:0:60:2:0.002:0:1 0/1:323:5:1,4:223,95:0.0155:2,2:16:1:26.4:1:0.03221:9.31999:60:10:0.0157:0:1.4 -17 78923325 . G A 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19994;SOR=0.3117;LSEQ=ACCGCGTGGCAGGGGCTCTC;RSEQ=GACATGCTGCCAACGACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:8:7,1:280,470:0.0106:2,2:8.6:1:24.9:1:0.00574:11.72:60:3:0.0081:0:1 0/0:604:2:2,0:256,346:0.0033:2,0:1:0:24.5:1:0.18205:0:60:4:0.0034:0:1 -17 78923355 . C T 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAACGACGCGAGGTGGGTC;RSEQ=GCCCGGCTCCTCCCCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:0:0,0:118,341:0:2,0:24.6:1:29.7:1:1:0:60:50:1:0:0.1 0/1:350:22:6,16:106,222:0.0629:2,2:17.5:1:28.4:1:0.81399:1.27247:60:10:0.0585:0:1.3 -17 78923388 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12723;SOR=Inf;LSEQ=CCCAGAGCAGAATGTGTTCC;RSEQ=GGGGCTGCGGACGCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:29,228:0:2,0:21.2:1:29.9:1:1:0:60:84.667:1:0:0.1 0/1:143:2:1,1:19,122:0.014:2,2:6.5:1:32:0:0.26101:6.28:60:4:0.0141:0:1 -17 78931260 . T G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08734;SOR=Inf;LSEQ=GGACGTGGGGCACACCAGGG;RSEQ=CCCTAGCGGGAGCTCATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:55,1:0:1,0:22.5:1:29.5:1:1:0:60:112:1:0:0 0/1:24:2:2,0:19,3:0.0833:2,0:30.5:1:33:0:1:0:60:4:0.087:0:1 -17 78931354 . G T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29864;SOR=3.53509;LSEQ=GCTGGCCAAATTGCTGCCCA;RSEQ=AGCAGGCCCCAAAGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:0,1:249,70:0.0031:2,0:1:0:25:0:0.22188:0:60:2:0.0032:0:1 0/1:182:2:1,1:136,44:0.011:2,2:25:1:25:1:0.4344:3.06745:60:4:0.0112:0:1.5 -17 78931414 . A G 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGATGCCATGTCCCACTGT;RSEQ=TCTCTCCAGGAGCTGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:756:0:0,0:448,308:0:2,0:25.3:1:28.9:1:1:0:60:38.789:1:0:0.2 0/1:541:36:22,14:305,198:0.0665:2,2:23.5:1:31.4:1:1:1.02:60:72:0.0672:0:1.3 -17 78932003 . C CA 26 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCCTCCCACCTCACCCCC;RSEQ=CCCCCCACCACCAAGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23.5:1:26.5:1:1:0:60:4:1:0.5:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78932006 . C G 48 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCCACCTCACCCCCCCC;RSEQ=CCCACCACCAAGTAGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:18.3:1:30.3:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 78933289 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAGTGCACAACCCAGCACC;RSEQ=CCCATCGTGCGTGGAAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:43.5:1:29.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:32:0:1:0:60:4:1:0:1.5 -17 78933424 . A G 65 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGACCCCTCCTGGACTC;RSEQ=TCCCATAGCTCATTAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:24.4:1:28:1:1:0:60:4:1:0:1.4 1/1:1:1:0,1:0,0:1:0,0:37:0:32:0:1:0:60:2:1:0:1 -17 78933756 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATAGAGAGAAAGGCCCCT;RSEQ=CAGCCAGGGAGGGTGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:140,4:0.0136:1,2:33:1:31:1:0.06755:31.41546:60:4:0.014:0:1 0/0:65:0:0,0:61,4:0:2,0:22.2:1:31.9:1:1:0:60:64:1:0:0.1 -17 78934034 . G C 142 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.30463;LSEQ=ACCCTGTCCTCTCCCTCCCC;RSEQ=AGTGCTGGCAGGGTACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:1:1,0:124,336:0.0022:2,0:1:0:11:0:0.27115:0:60:0:0:0:2 0/1:356:24:8,16:102,229:0.0674:2,2:25.4:1:31:1:0.82078:1.12:60:48:0.0684:0:1.3 -17 78934088 . G A 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGTGTCACTGCCATTTGGTT;RSEQ=GGTCCAGGTTTCTCAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:68:2,66:6,88:0.4198:2,1:24.3:1:31.8:1:0.46971:2.23975:60:136:0.4198:0:1.1 0/0:89:0:0,0:5,84:0:2,0:23.9:1:30.5:1:1:0:60:178:1:0:0.1 -17 78935071 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14338;LSEQ=ACTAGCCCCTCGTGGGGAGC;RSEQ=GACGGGCGAGGGCCTGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:110:65:64,1:45,0:0.5909:1,1:23.7:1:30.5:1:1:0:60:64:0.6095:0:1.1 0/1:53:9:9,0:44,0:0.1698:1,0:20.9:1:31.4:1:1:0:60:18:0.1765:0:1 -17 78935166 . C G 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACGTCCTTCAGGGAAGCCC;RSEQ=ACGCTGAGCGTGCCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:397,204:0:2,0:23.6:1:31.1:1:1:0:60:59.1:0.9983:0:0.7 0/1:415:30:19,11:241,144:0.0723:2,2:26.6:1:30.7:1:1:1.03:60:60:0.0735:0:1 -17 78935197 . C T 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21305;LSEQ=TGCCCCCTCCCCTACAGCCG;RSEQ=GTCATGACGTACCGGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:847:542:321,221:182,123:0.6399:2,2:26.3:1:29.9:1:0.94193:1.0187:60:76.429:0.6415:0:1.1 0/1:645:177:98,79:267,201:0.2744:2,2:26.9:1:29.6:1:0.72225:1.07071:60:176:0.2772:0:1.1 -17 78936118 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01266;SOR=Inf;LSEQ=GGGCAGCCCTCACTGGGGAC;RSEQ=CTGAGCATCCAGGCAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:124,1:0:1,0:24.8:1:29.5:1:1:0:60:30.25:1:0:0.1 0/1:39:3:3,0:35,1:0.0769:1,0:12:1:32:0:1:0:60:6:0.0769:0:1 -17 78936409 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.38175;SOR=2.37522;LSEQ=CCACCTCCCTGGCCTGCACC;RSEQ=CTCACCCGCCTCGGGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:2:1,1:92,342:0.0046:2,2:7.5:1:29.5:1:0.38149:3.70:60:4:0.0047:0:1 0/1:278:3:1,2:74,201:0.0108:2,2:36.3:1:28:1:1:1.36:60:6:0.0109:0:1 -17 78936652 . C T 89 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00094;SOR=15.50467;LSEQ=GTCTAGCCGGCCTGTCCCCG;RSEQ=GGTCTCGGCATCTGCGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:1:1,0:217,17:0.0043:2,0:18:0:32:0:1:0:60:2:0.0043:0:1 0/1:144:9:8,1:123,12:0.0625:2,2:18.1:1:28.2:1:0.58415:1.27884:60:18:0.0629:0:1 -17 78937925 . C T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09516;SOR=0.59738;LSEQ=TGGGACCGGCCCGGCATTTC;RSEQ=GGGCCTGAGGTGGGCGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:158:99:95,4:59,0:0.6266:1,1:24.1:1:31.2:1:0.29761:0:60:32:0.6358:0:1.4 1/0:62:31:31,0:31,0:0.5:1,1:19.1:1:31.4:1:1:0:60:62:0.5082:0:1.6 -17 78938011 . C A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCGCCCCCCCGCCCCCCG;RSEQ=AGTGTCTGCCCGCACCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:774:0:0,0:485,287:0:2,0:22.9:1:29.6:1:1:0:60:19.865:0.9986:0:1.3 0/1:550:59:33,26:287,203:0.1073:2,2:19.4:1:24.9:1:0.78011:1.11368:60:2.278:0.0804:0:2 -17 78938191 . G A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.28735;SOR=0;LSEQ=ACATAGTGAAGCTGTCACTC;RSEQ=CCGGGGCACGGGGCGTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:43,247:0.0102:2,2:17.7:1:27:1:0.06259:11.33:60:6:0.0103:0:1.3 0/0:185:0:0,0:38,145:0:2,0:19.7:1:30.8:1:1:0:60:182:1:0:0.2 -17 78938204 . G C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.36814;LSEQ=GTCACTCGCCGGGGCACGGG;RSEQ=CGTCGGCTGCTGCGGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:89:6,83:7,124:0.4027:2,2:23.4:1:30.8:1:0.77307:1.28:60:43.5:0.4009:0:1.1 0/1:126:25:5,20:13,86:0.1984:2,2:17.8:1:29.5:1:0.35918:1.65:60:24:0.1951:0:1.2 -17 78939414 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGGCGGTGAGAGGCCCA;RSEQ=GACCACGGGAGTGAGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 79088915 . G GT 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACTTCTTGTCTTGAGTC;RSEQ=TATTTGTGCATCAGCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:28.5:1:1:0:60:4:1:0:0 -17 79090448 . C A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.67603;SOR=1.84301;LSEQ=CTCCTGGGTGGACCTCCCCC;RSEQ=CCCACCTCCGCTGACTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:7,9:2,3:0.7619:2,2:24.8:1:30.4:1:1:1.16:60:32:0.7619:0:1.1 1/1:14:12:5,7:1,1:0.8571:2,2:24.1:1:27.6:1:1:1.36624:60:11:0.8462:0:1.6 -17 79913615 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCCCCTGCAGTGCCCCCCAC;RSEQ=CCAGGCTCAGAGTTCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:25.5:1:30.5:1:1:0:57.5:4:1:0:2 0/0:3:0:0,0:1,2:0:2,0:33:1:30:1:1:0:52.3:6:1:0:0.3 -17 79915629 . A G 64 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCCCACACCCCTTCCATGC;RSEQ=CCCTGCACACCGTCCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:11:0:31:0:1:0:60:2:1:0:0 1/1:5:4:2,2:0,1:0.8:0,2:31.3:1:32.3:1:1:0:60:8:0.8:0:2 -17 79915647 . A G 62 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCACCCTGCACACCGTCCTC;RSEQ=CCCCTCACCTCCAGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:31:0:1:0:60:2:1:0:0 1/1:5:4:2,2:0,1:0.8:0,2:31:1:31.3:1:1:0:60:8:0.8:0:2 -17 79988254 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGGTGCGCGTGGAGCT;RSEQ=CAGGAGCAGAACGGCCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:28.5:1:29.5:1:1:1.7321:60:4:0.4:0:1 0/0:2:0:0,0:1,1:0:2,0:31:1:33:1:1:0:60:4:1:0:0 -17 79988999 . G T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCGCGCGGCGGGGTTTG;RSEQ=AAATACAGCGCGTTTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:27.5:1:1:0:60:4:1:0:1 -17 79989619 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.15152;SOR=Inf;LSEQ=CGGCTCGCGGCCGCGCCCGC;RSEQ=GCCGCCCGGCCCGCGCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:6.9:1:29:1:1:0:60:6:1:0:0.1 0/1:5:2:1,1:2,1:0.4:2,2:29:0:32:1:1:1.7321:60:4:0.4:0:1.5 -17 79989710 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.11084;SOR=Inf;LSEQ=AGGCCGCTTGGCTGGGCTGG;RSEQ=CGGGAGGGGGGCTCGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:14.8:1:29.8:1:1:0:60:38:1:0:0.5 0/1:10:2:1,1:4,4:0.2:2,2:28:1:27.5:1:1:1:60:4:0.2:0:1 -17 79991603 . C T 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43628;SOR=2.02833;LSEQ=AAATACCTGGAGTGCTCAGC;RSEQ=CTGACCCAGCGGGGCCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:2,1:26,17:0.0652:2,2:30.3:1:31:1:1:1.30:60:6:0.0667:0:1 0/1:32:4:3,1:18,10:0.125:2,2:21.3:1:29.8:1:1:1.64:60:8:0.125:0:1 -17 79992613 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGTCGGGGTGTGGTGTGG;RSEQ=GAGTGAAGAGAGCAGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:40:1:30.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 79995436 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCTATACCTGCCGGGAGCG;RSEQ=GCTCAGTGAAGGCGTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:9:0:32:0:1:0:60:2:1:0:0 0/1:5:2:1,1:2,1:0.4:2,2:18.5:1:29.5:1:1:1.7321:60:4:0.4:0:1.5 -17 79996915 . T C 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTTCTTGTCCACTTCCA;RSEQ=GTTCCTCCCGTACTCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:38.2:1:31:1:1:0:58.2:12:1:0:1 1/1:3:3:3,0:0,0:1:0,0:10:1:32.7:1:1:0:53.3:6:1:0:1 -17 80759327 . C T 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15545;SOR=0.74274;LSEQ=GGCGTGTGCGTCGTGTGGCT;RSEQ=GGAGTCAGCGTGGCAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:65:42,23:108,77:0.259:2,2:25.1:1:28.9:1:0.46202:1.30:59.7:15.25:0.2542:0:1.3 0/1:301:62:41,21:141,98:0.206:2,2:24.2:1:29.1:1:0.38192:1.36:59.6:30:0.2048:0:1.5 -17 80759400 . G A 53 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.41193;SOR=0.38794;LSEQ=GTGGCAGGATGGCGGCATGT;RSEQ=TGTCGTCGTGTGGCTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:4:3,1:82,117:0.0197:2,2:14.3:1:26.8:1:0.31089:4.25:60:8:0.0215:0:1.5 0/0:259:2:2,0:101,155:0.0077:2,0:1:0:23.5:1:0.15845:0:60:4:0.0083:0:1.5 -17 80759416 . C A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25369;SOR=Inf;LSEQ=ATGTGTGTCGTCGTGTGGCT;RSEQ=AGGGTCAGCGTGGCAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:68,99:0:2,0:27.3:1:29.9:1:1:0:59.5:9.438:1:0:0.7 0/1:199:3:2,1:69,126:0.0151:2,2:22.3:1:22.3:1:0.29254:3.63:60:2:0.0112:0:2.7 -17 80759466 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24727;SOR=0;LSEQ=GCGTCGTGTGGCTCGGTCAG;RSEQ=GTGGCAGGAGGGTGGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:3:1,2:68,65:0.0219:2,2:5:1:22.7:1:0.61667:2.08135:60:2:0.0165:0:1.3 0/0:135:0:0,0:59,76:0:2,0:21.2:1:28.2:1:1:0:59.9:8:1:0:1 -17 80759521 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49853;SOR=0;LSEQ=AGAGTCAGCGTGGCAGGAGG;RSEQ=CGGCGTGTGCGTTGTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:104,65:0.0117:2,2:29:1:31.5:1:1:1.59539:60:4:0.0124:0:1 0/0:170:0:0,0:94,76:0:2,0:24.4:1:29.6:1:1:0:59.4:13.167:1:0:1.3 -17 80759523 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2479;SOR=Inf;LSEQ=AGTCAGCGTGGCAGGAGGGC;RSEQ=GCGTGTGCGTTGTGTGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:106,63:0:2,0:27:1:28.6:1:1:0:57.9:15.9:1:0:1.5 0/1:173:3:1,2:92,78:0.0173:2,2:19.3:1:27.7:1:0.59644:2.34759:60:6:0.0179:0:1.7 -17 80759541 . G C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26021;SOR=0.73094;LSEQ=GCGGCGTGTGCGTTGTGTGG;RSEQ=TCGGAGTCAGCGTGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:45:26,19:90,60:0.2261:2,2:21.5:1:26.7:1:0.86297:1.09563:52.2:3.091:0.2208:0:2.7 0/1:199:35:17,18:90,71:0.1759:2,2:30.9:1:28.5:1:0.45835:1.34013:57.5:4:0.1667:0:2.6 -17 80759544 . G A 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00041;SOR=0;LSEQ=GCGTGTGCGTTGTGTGGGTC;RSEQ=GAGTCAGCGTGGCAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:12:4,8:117,72:0.0594:2,2:9.4:1:28.7:1:0.06777:3.23042:45.8:5:0.0568:0:3.4 0/0:201:0:0,0:111,90:0:2,0:25.7:1:27.7:1:1:0:59.1:15.75:1:0:1.2 -17 80759562 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24829;SOR=Inf;LSEQ=TCGGAGTCAGCGTGGCAGGA;RSEQ=GGCGGCGTGTGCGTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:129,91:0:2,0:21.5:1:29.8:1:1:0:57:11.941:1:0:1.6 0/1:220:3:1,2:108,108:0.0136:2,2:19:1:23:1:1:1.9939:60:2:0.0095:0:1.3 -17 80759565 . C T 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95954;LSEQ=GAGTCAGCGTGGCAGGAGGG;RSEQ=GGCGTGTGCGTTGTGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:22:10,12:113,77:0.1014:2,2:9.5:1:25.4:1:0.25538:1.75617:53.2:3.4:0.0924:0:2.7 0/1:215:21:7,14:97,93:0.0977:2,2:14.5:1:28.5:1:0.16748:2.07896:56.9:9.5:0.1016:0:3.2 -17 80759568 . C T 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCAGCGTGGCAGGAGGGCGG;RSEQ=GTGTGCGTTGTGTGGCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:127,84:0:2,0:22.8:1:28.5:1:1:0:57.1:7.792:1:0:1.6 0/1:220:26:13,13:100,94:0.1182:2,2:28.3:1:26.6:1:1:1.0635:60:7.667:0.1117:0:2.3 -17 80759574 . C T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37379;SOR=3.76715;LSEQ=TGGCAGGAGGGCGGCGTGTG;RSEQ=GTTGTGTGGCTCGGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:1:0,1:133,86:0.0045:2,0:29:0:14:0:0.39545:0:60:0:0:0:2 0/1:237:4:1,3:121,111:0.0169:2,2:11.5:1:23:1:0.35552:3.25518:60:3:0.0136:0:1.5 -17 80759577 . T GATC 101 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00089;SOR=Inf;LSEQ=CAGGAGGGCGGCGTGTGCGT;RSEQ=GTGTGGCTCGGAGTCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:139,89:0:2,0:22.8:1:29.2:1:1:0:58:16.538:1:0:1.5 0/1:238:11:2,9:122,104:0.0462:2,2:11.6:1:29.3:1:0.02819:5.24547:58.2:22:0.0476:0.021:4 -17 80759584 . C G 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24839;SOR=Inf;LSEQ=GCGGCGTGTGCGTTGTGTGG;RSEQ=TCGGAGTCAGCGTGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:140,90:0:2,0:25:1:29.6:1:1:0:58.4:6.188:1:0:1.4 0/1:233:3:2,1:118,111:0.0129:2,2:21:1:25:1:1:1.88:60:2:0.0094:0:1.3 -17 80759587 . G A 76 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01495;SOR=Inf;LSEQ=GCGTGTGCGTTGTGTGGCTC;RSEQ=GAGTCAGCGTGGCAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:147,91:0:2,0:24.6:1:28.6:1:1:0:58.6:13:1:0:1.4 0/1:242:7:1,6:126,109:0.0289:2,2:9.4:1:27.3:1:0.05551:6.88968:59.3:2.5:0.0224:0:4.7 -17 80759610 . A G 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.06636;SOR=0.70393;LSEQ=GTCAGCGTGGCAGGAGGGTG;RSEQ=CGTGTGCGTGATCGTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:120:80,40:87,65:0.4348:2,2:26.5:1:29.2:1:0.13253:1.49:57.1:7:0.4709:0:2.3 0/1:225:79:51,28:73,68:0.3511:2,2:25.9:1:28.4:1:0.08877:1.69:59.1:5.583:0.3583:0:2.1 -17 80759687 . C T 129 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.25717;LSEQ=GTCGTGTGGCTCGGAGTCAG;RSEQ=GTGGCAGGAGGGCGGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:608:4:2,2:346,253:0.0066:2,2:17.3:1:20:1:1:1.36685:60:1:0.0039:0:3 0/1:518:33:21,12:295,188:0.0637:2,2:21.8:1:25.6:1:0.85468:1.12:59.5:5.6:0.0602:0:1.5 -17 80759701 . G A 112 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.52518;LSEQ=AGTCAGCGTGGCAGGAGGGC;RSEQ=GCGTGTGCGTCGTGTGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:1:1,0:371,295:0.0015:2,0:44:0:16:0:1:0:57:0:0:0:3 0/1:593:21:16,5:327,244:0.0354:2,2:27.2:1:25.7:1:0.11423:2.38:59.4:2.5:0.0269:0:2.2 -17 80759703 . C T 62 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.56455;SOR=1.57153;LSEQ=TCAGCGTGGCAGGAGGGCGG;RSEQ=GTGTGCGTCGTGTGGTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:681:5:2,3:372,292:0.0073:2,2:24.6:1:19.4:1:0.65907:1.90907:53.4:0.667:0.0035:0:1.4 0/1:609:7:1,6:347,252:0.0115:2,2:11.7:1:22.1:1:0.04586:8.23679:60:2.5:0.0095:0:2 -17 80759709 . C T 65 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36581;SOR=1.98252;LSEQ=TGGCAGGAGGGCGGCGTGTG;RSEQ=GTCGTGTGGTTCGGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:4:2,2:400,319:0.0055:2,2:34.5:1:21.3:1:1:1.25352:43.8:1:0.0032:0:3.8 0/1:644:7:1,6:357,276:0.0109:2,2:5.9:1:23.4:1:0.04786:7.73957:53.3:2.5:0.0089:0:1.3 -17 80759723 . G C 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTGTGCGTCGTGTGGTTCG;RSEQ=AGTCAGCGTGGCAGGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:0:0,0:433,347:0:2,0:26.8:1:30:1:1:0:58.9:14.6:1:0:0.8 0/1:734:26:18,8:379,325:0.0354:2,2:25.2:1:27.8:1:0.1601:1.93:58.9:4.2:0.0315:0:2 -17 80759801 . C T 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.51007;LSEQ=GAGGGCGGCGTGTGTGTCGT;RSEQ=GTGTGGCTCGGAGTCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:638:261:94,167:155,219:0.4091:2,2:25.6:1:28.1:1:0.1864:1.25695:59.7:7.7:0.3935:0:1.9 0/1:667:174:71,103:211,282:0.2609:2,2:25.7:1:27.9:1:0.65662:1.0853:60:9.875:0.2492:0:1.8 -17 80759836 . A G 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01774;SOR=0.71372;LSEQ=CAGCGTGGCAGCAGGGTGGC;RSEQ=TGTGTGTCGTGTGGCTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:188:48,140:79,180:0.4206:2,2:23.8:1:31.5:1:0.28822:1.27939:59.6:93:0.4266:0:2.1 0/1:425:145:50,95:95,184:0.3412:2,2:24.6:1:30:1:1:1.02:60:71.5:0.3446:0:1.8 -17 80759875 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.21292;SOR=Inf;LSEQ=GGGTCAGCTCAGCCTCCCTG;RSEQ=CGTGGCAGCGTGTGTGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:33,164:0:2,0:22.7:1:31.8:1:1:0:60:48.25:0.9948:0:0.9 0/1:171:2:1,1:38,130:0.0117:2,2:23.5:1:27.5:1:0.40724:3.39:60:4:0.0121:0:1 -17 80759915 . C T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36648;SOR=0.69645;LSEQ=CGTGTTGCTCAGAGGCGGTG;RSEQ=GGCCTCCCTGGTGTGGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:29:0,29:1,46:0.3816:1,1:22.9:1:30.1:1:1:0:60:58:0.3867:0:2.2 0/1:60:18:0,18:1,41:0.3:1,1:31.1:1:29.3:1:1:0:60:17:0.2931:0:2.1 -17 80759933 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.98292;LSEQ=TGCGGCCTCCCTGGTGTGGA;RSEQ=GCGCTGTGGGGGAAAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:20:0,20:1,37:0.3448:1,1:30.1:1:30:1:1:0:60:40:0.3509:0:2.4 0/1:44:15:0,15:1,28:0.3409:1,1:32.7:1:30.9:1:1:0:60:30:0.3488:0:2.1 -17 80782917 . G C 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00385;SOR=Inf;LSEQ=ATGGGTGAGCTATTGCAGAT;RSEQ=ACCTTTGGAGGAATTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:81,33:0:2,0:25.4:1:31.5:1:1:0:60:37:1:0:0.1 0/1:97:7:4,3:64,26:0.0722:2,2:26.9:1:31.1:1:0.42346:1.83352:60:14:0.0745:0:1.1 -17 80782949 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22667;SOR=Inf;LSEQ=AATTGTGTCGGAGTGTAGAA;RSEQ=TTTCACAGTGTAGCTCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:87,61:0:2,0:25.4:1:30.7:1:1:0:60:296:1:0:0.3 0/1:135:2:1,1:82,51:0.0148:2,2:18.5:1:30.5:1:1:1.60193:60:4:0.015:0:1 -17 80782978 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23999;SOR=Inf;LSEQ=TGTAGCTCGCCATGCATCAG;RSEQ=CACATGTAGCCTGTGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:85,79:0:2,0:24.8:1:31.5:1:1:0:60:328:1:0:0.4 0/1:158:2:1,1:86,70:0.0127:2,2:27:1:30.5:1:1:1.22696:60:4:0.0129:0:1 -17 80782994 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24318;SOR=Inf;LSEQ=TCAGGCACATGTAGCCTGTG;RSEQ=CACAACCATTGTGCTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:73,93:0:2,0:25.8:1:31.2:1:1:0:60:54.333:1:0:0.5 0/1:162:2:1,1:82,78:0.0123:2,2:42:1:28:1:1:1.05098:60:4:0.0126:0:2 -17 80783009 . T C 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00685;SOR=0.52221;LSEQ=CTGTGCCACAACCATTGTGC;RSEQ=TGGGCGGGGTTCTCCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:68:27,41:41,60:0.4024:2,2:27.6:1:32:1:1:1.03744:60:136:0.4048:0:1.1 0/1:154:40:21,19:54,60:0.2597:2,2:23.6:1:30.3:1:0.5873:1.23:60:39:0.2566:0:1.2 -17 80783030 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49844;SOR=0;LSEQ=TGGGCGGGGTTCTCCATGCT;RSEQ=CCCTGTTGCAGGAGGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:59,97:0.0127:2,2:8:1:28:1:1:1.64:60:4:0.0128:0:2 0/0:155:0:0,0:70,85:0:2,0:24.6:1:31.6:1:1:0:60:76.5:1:0:0.4 -17 80783045 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22174;SOR=Inf;LSEQ=ATGCTGCCCTGTTGCAGGAG;RSEQ=ATGCTCTGCCCCTGCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:52,98:0:2,0:25.3:1:31.1:1:1:0:60:74:1:0:0.4 0/1:134:2:1,1:52,80:0.0149:2,2:39.5:1:30:1:1:1.53:60:4:0.0149:0:2 -17 80783049 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49989;SOR=0;LSEQ=TGCCCTGTTGCAGGAGGATG;RSEQ=TCTGCCCCTGCTTCTCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:51,91:0.0139:2,2:22.5:1:27:1:1:1.78:60:4:0.014:0:1.5 0/0:128:0:0,0:50,78:0:2,0:24.2:1:31.7:1:1:0:60:127:1:0:0.4 -17 80783051 . C A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.5697;LSEQ=CCCTGTTGCAGGAGGATGCT;RSEQ=TGCCCCTGCTTCTCCCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:50,91:0.014:2,2:26.5:1:30.5:1:1:1.81:60:4:0.0144:0:2 0/0:125:1:1,0:49,75:0.008:2,0:1:0:23:0:0.4:0:60:2:0.008:0:1 -17 80807777 . T C 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00345;SOR=Inf;LSEQ=TGCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:25.6:1:27.2:1:1:0:56.4:5.667:1:0:1.1 0/1:21:8:4,4:6,7:0.381:2,2:18.4:1:32.1:1:1:1.16:59.8:16:0.381:0:1.5 -17 80807828 . C G 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27567;SOR=0.31409;LSEQ=TGTTGGCTGTGCTGTTGTTG;RSEQ=CTGTGCTGCTGTTGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:7:4,3:13,14:0.2059:2,2:17.1:1:24.3:1:1:1.42:37.9:1.333:0.1538:0:1.7 0/1:27:2:2,0:9,15:0.0741:2,0:9.5:1:32:1:0.16923:0:21:4:0.0909:0:1.5 -17 80807833 . G GCTCTT 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49653;SOR=0;LSEQ=GCTGTGCTGTTGTTGCCTGT;RSEQ=CTGCTGTTGGCTGTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:16,17:0.0571:2,2:18.5:1:30:1:1:1.06:31.5:4:0.0645:0:1 0/0:29:0:0,0:13,16:0:2,0:23.6:1:30.4:1:1:0:44.7:28:1:0:1.3 -17 80807837 . C T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.22675;LSEQ=TGCTGTTGTTGCCTGTGCTG;RSEQ=TGTTGGCTGTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:2,1:14,17:0.0857:2,2:8.7:1:24.3:1:0.59091:2.37:28.7:2:0.0645:0:2.7 0/1:29:3:2,1:11,15:0.1034:2,2:9:1:30.7:1:0.57307:2.63:27.7:6:0.1111:0:1.7 -17 80807843 . G C 40 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.27494;LSEQ=TGTTGCCTGTGCTGCTGTTG;RSEQ=CTGTGCTGCTGTTGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:1,2:16,16:0.0857:2,2:25.3:1:23.3:1:1:1.96199:45:2:0.0645:0:2 0/1:28:3:0,3:12,13:0.1071:2,0:31:1:25.3:1:0.2381:0:36.3:2:0.0769:0:1.3 -17 80807852 . C T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.10416;SOR=0.27516;LSEQ=TGCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:3,6:10,11:0.3:2,2:24.3:1:30.6:1:0.69075:1.78267:51.2:18:0.3214:0:1.2 0/1:29:3:1,2:12,14:0.1034:2,2:27:1:30:1:1:1.6838:45.7:6:0.1034:0:1.3 -17 80807859 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49153;SOR=Inf;LSEQ=GTTGGCTGTGCTGCTGTTGG;RSEQ=TGTGCTGCTGTTGGCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:13,17:0:2,0:29.3:1:32:1:1:0:40.8:29:1:0:1.5 0/1:30:2:1,1:12,16:0.0667:2,2:21:1:28.5:1:1:1.32:49.5:4:0.0714:0:2 -17 80807897 . T C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53713;SOR=1.55364;LSEQ=TGCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:3,4:5,6:0.3889:2,2:10:1:26.6:1:1:1.10463:35:2.5:0.3333:0:2.6 1/0:22:11:3,8:6,5:0.5:2,2:14.8:1:29.9:1:0.387:3.02714:36.2:10:0.5556:0:3 -17 80807912 . T C 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGCTGTTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:2,5:5,2:0.5:2,2:13.1:1:31.4:1:0.28613:5.37707:38.4:14:0.5385:0:3 1/0:16:8:3,5:5,3:0.5:2,2:17.5:1:30.6:1:0.61927:2.59867:32.4:16:0.5714:0:3 -17 80807927 . T C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54846;SOR=3.03008;LSEQ=TGCTGTTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:2,0:0.7143:0,2:22.6:1:28.6:1:0.42857:0:33.8:4:0.6667:0:3.8 1/1:18:16:10,6:0,2:0.8889:0,2:18.4:1:30.2:1:0.18301:0:41.3:7:0.875:0:2.8 -17 80807989 . C T 34 v4;q23;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.26154;SOR=Inf;LSEQ=CTGTGCTGCTGTTGGCTGTG;RSEQ=TGCTGTTGGCTGTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:26.8:1:29.3:1:1:0:50.1:9:1:0:2 0/1:16:3:1,2:8,5:0.1875:2,2:14.3:1:21.7:1:0.55:2.96927:32:2:0.1538:0:5.3 -17 80808004 . T C 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.25714;SOR=Inf;LSEQ=CTGTGCTGCTGTTGGCTGTG;RSEQ=TGTTGTTGGCTGTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:16.5:1:29:1:1:0:52.4:16:1:0:1.6 0/1:13:3:1,2:4,4:0.2308:2,2:25.3:1:33:0:1:1.87936:46:6:0.2727:0:4 -17 80808007 . T C 87 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.12797;SOR=0;LSEQ=TGCTGCTGTTGGCTGTGTTG;RSEQ=TGTTGGCTGTGCTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:18.2:1:30.7:1:1:0:49.8:12:1:0:1.8 1/0:13:8:4,4:3,2:0.6154:2,2:13.1:1:29:1:1:1.45385:47.5:7:0.6364:0:3.4 -17 80808022 . T C 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10131;SOR=Inf;LSEQ=TGTTGTTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:9.9:1:28.4:1:1:0:48.7:14:1:0:1.7 0/1:11:5:2,3:3,3:0.4545:2,2:8.4:1:25.2:1:1:1.44544:38.8:4:0.4:0:3.4 -17 80808037 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=TGCTGTTGTTGGCTGTGCTG;RSEQ=TGTTGCCTGTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:16.8:1:29.7:1:1:0:35.7:12:1:0:2.2 0/1:9:2:1,1:3,4:0.2222:2,2:14.5:1:30.5:1:1:1.29:31.5:4:0.25:0:3.5 -17 80808043 . C G 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28671;SOR=5.514;LSEQ=TGTTGGCTGTGCTGTTGTTG;RSEQ=CTGTGCTGCTGTTGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:2,3:0.1667:2,0:17:0:33:0:1:0:22:2:0.2:0:2 1/0:9:5:3,2:2,2:0.5556:2,2:14.2:1:30.4:1:1:1.43:31:10:0.625:0:2.8 -17 80808058 . G C 64 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05929;SOR=0.14757;LSEQ=TGTTGCCTGTGCTGCTGTTG;RSEQ=CTGTGCTGCTGTTGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:0.5:2,2:40.8:1:32.3:1:1:1:42:8:0.5714:0:2.3 0/1:17:2:1,1:8,7:0.1176:2,2:47.5:1:22.5:1:1:1.13389:43.5:1:0.0667:0:3 -17 80808082 . T C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73743;SOR=1.3668;LSEQ=TGCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:3,3:4,3:0.4615:2,2:37.7:1:30.3:1:1:1.30401:35.7:12:0.4615:0:2.2 1/0:24:13:6,7:6,5:0.5417:2,2:29.5:1:32.2:1:1:1.3804:41.5:26:0.5417:0:2.1 -17 80808088 . G C 38 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75591;LSEQ=TGTTGGCTGTGCTGTTGTTG;RSEQ=CTGTGCTGCTGTTGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:0.1538:2,2:37:1:31.5:1:1:1.18321:59:4:0.1538:0:2 0/1:25:3:2,1:10,12:0.12:2,2:43.3:1:24.3:1:0.59304:2.32:48.3:2:0.0833:0:1.7 -17 80808127 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63527;SOR=0.64525;LSEQ=TGCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:17.5:1:31.5:1:1:2.23609:52:4:0.25:0:2 0/1:26:4:2,2:12,10:0.1538:2,2:18.3:1:31:1:1:1.19157:28.5:8:0.16:0:2 -17 80808142 . T C 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.29038;SOR=Inf;LSEQ=TGCTGTTGTTGGCTGTGTTG;RSEQ=TGTTGGCTGTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:20.6:1:29.5:1:1:0:58.4:22:1:0:0.8 0/1:25:4:2,2:10,11:0.16:2,2:14.5:1:30:1:1:1.10:26.5:8:0.16:0:1.5 -17 80808156 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51232;SOR=Inf;LSEQ=GTGTTGTTGTTGGCTGTGCT;RSEQ=CTGTTGGCTGTGCTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:20.6:1:32.4:1:1:0:55.9:22:1:0:1.5 0/1:18:2:1,1:6,10:0.1111:2,2:30.5:1:27:1:1:1.62:60:4:0.1111:0:1 -17 80808207 . T C 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34058;SOR=3.8004;LSEQ=TTCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:4,5:0.0909:2,0:45:0:12:0:1:0:31:0:0:0:7 0/1:14:4:2,2:4,6:0.2857:2,2:29.5:1:28:1:1:1.46:30.5:3:0.2308:0:3 -17 80808218 . G C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04074;SOR=0;LSEQ=GCTGTGCTGTTGTTGGCTGT;RSEQ=CTGTTGTTGGCTGTCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:1,3:5,4:0.3077:2,2:13:1:25.8:1:0.55944:3.3873:60:3:0.3:0:1 0/0:14:0:0,0:7,7:0:2,0:20:0:13:0:1:0:60:0:0:0:5 -17 80808222 . T C 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09962;SOR=Inf;LSEQ=TGCTGTTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTCCTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,8:0:2,0:25.6:1:27.1:1:1:0:58.5:5.5:1:0:1.7 0/1:15:4:2,2:5,6:0.2667:2,2:14.5:1:32.5:1:1:1.19:30.5:8:0.2667:0:3 -17 80808233 . C G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59304;SOR=2.31861;LSEQ=GCTGTGCTGTTGTTGGCTGT;RSEQ=CTGTTGTTGGCTGTCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:4,7:0.0769:2,0:19:0:33:0:0.41667:0:31:2:0.1111:0:7 0/1:12:2:0,2:4,6:0.1667:2,0:7:1:30:1:0.51515:0:30.5:4:0.2:0:3.5 -17 80808263 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=GCTGTCCTGTTGTTGGCTGT;RSEQ=CTGTTGTTGGCTGTGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:3,4:0.2222:2,0:8:1:31:1:0.5:0:60:4:0.2857:0:1 0/0:8:0:0,0:5,3:0:2,0:34:1:31.8:1:1:0:60:16:1:0:0.8 -17 80808318 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=5;SSF=0.53333;SOR=Inf;LSEQ=TGGCTGTGCTGTTGTTGGCT;RSEQ=TGCTGTTTTGCTGTTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:15.3:1:28.6:1:1:0:60:6:1:0:1 0/1:14:2:1,1:6,6:0.1429:2,2:20:1:27.5:1:1:1:60:4:0.1667:0:1 -17 80808501 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1746;SOR=0;LSEQ=CTGTTGTTGGCTGTGCTGTT;RSEQ=TGCTGTTGGCTGTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:27.5:1:33:1:1:1:60:4:0.1667:0:1 0/0:16:0:0,0:8,8:0:2,0:31.4:1:29.6:1:1:0:59.1:32:1:0:0.4 -17 80808544 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.21429;SOR=0;LSEQ=GGCTGTGCTGTTGTTGGTTG;RSEQ=GTGTGCTGACCCCGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:36.5:1:31.5:1:1:1.58:60:4:0.2:0:1 0/0:11:0:0,0:5,6:0:2,0:23.5:1:28.7:1:1:0:60:22:1:0:0.1 -17 81073882 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACTGACAAGCCCTGCGT;RSEQ=GACATGAGGTGCTGTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:47.5:1:29:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -17 81075004 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCCAAAAGGTAGAGCCC;RSEQ=GTTCCTCTCCCCTGAACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29:1:1:0:60:4:1:0:1 -18 106555 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTGTCTAGGCTCTGCTT;RSEQ=CGGGGGTATTGTGACATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:33:0:1:0:42:4:1:0:6 -18 106557 . GGGGG TGGGCA 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=CTTGTCTAGGCTCTGCTTAC;RSEQ=TATTGTGACATAGCTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:32.9:1:1:0:42:4:1:0:6 -18 106577 . C A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGGTATTGTGACATAGCT;RSEQ=TGCACTGATCACCTAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:0:30.5:1:1:0:42:4:1:0:6 -18 106592 . A T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCTCTGCACTGATCACCT;RSEQ=AGTGATGTAACACTTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:0:29.5:1:1:0:42:4:1:0:6 -18 106618 . T G 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAACACTTGTGTAGGCTC;RSEQ=GCCTACATGGGCATTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:28:1:1:0:42:4:1:0:6 -18 106812 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCCAGGTGATGTAACTCTT;RSEQ=TGTTGGATCTGCCTATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:28.5:1:1:0:30:4:1:0:1.5 -18 107530 . G A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCACAGTGACATATCACT;RSEQ=CATTGATCACCGAGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:27:0:1:0:44.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 107682 . A G 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCTCTTTACTGATCAACCAG;RSEQ=TGATGTAACTCTTGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:1:30.5:1:1:0:43.5:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 107687 . G C 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTGATCAACCAGATGAT;RSEQ=TAACTCTTGTCTAGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:1:30.5:1:1:0:43.5:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 107691 . C G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATCAACCAGATGATGTAA;RSEQ=TCTTGTCTAGGCTCTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:31.5:1:1:0:43.5:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 107693 . C A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAACCAGATGATGTAACT;RSEQ=TTGTCTAGGCTCTGCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:29:1:1:0:43.5:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 107720 . A T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTCTGCCTACAGGGGGC;RSEQ=TTGTGGCATAACTCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:31.5:1:1:0:43.5:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 107892 . G C 33 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCACTGATCACCCAGGTGAT;RSEQ=TAACTCTGGTCTAAGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:33:0:1:0:31.5:4:1:0:4 0/0:2:0:0,0:2,0:0:0,0:9.5:1:33.5:1:1:0:33.5:4:1:0:3 -18 108008 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGCCTTGTCACATATGTCT;RSEQ=CACTGATCACCCAGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:4:0:32:0:1:0:40:2:1:0:5 1/1:2:2:1,1:0,0:1:0,2:12:1:28:1:1:0:43.5:4:1:0:6.5 -18 108075 . C A 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5;SOR=0.23975;LSEQ=GGGGGTATTGTGACATATCT;RSEQ=TGCACTGATCACCTAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:0.5:0,2:26.5:1:31.5:1:1:0:23:4:0.5:0:6.5 0/1:6:1:1,0:1,2:0.1667:2,0:16:0:30:0:1:0:35:2:0.2:0:8 -18 108090 . A T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.45385;LSEQ=TATCTCTGCACTGATCACCT;RSEQ=AGTGATGTAATACTTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:26.5:1:31:1:0.33333:0:23:4:0.3333:0:6.5 0/1:7:3:2,1:1,3:0.4286:2,2:24.7:1:30.7:1:0.48571:4.45:38.3:6:0.4286:0:7.7 -18 108101 . T C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TGATCACCTAAGTGATGTAA;RSEQ=ACTTGTGTAGGCTCTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:7,1:0,0:0.8:0,2:18.1:1:32.9:1:1:0:27.8:16:0.8889:0:5.4 1/1:6:6:3,3:0,0:1:0,2:36.7:1:32:1:1:0:36.5:12:1:0:6.5 -18 108106 . GT TG 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.34727;SOR=2.82876;LSEQ=ACCTAAGTGATGTAATACTT;RSEQ=GTAGGCTCTGCCTACAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,2:0.1667:2,2:10:1:32.3:1:0.49091:3.05504:22.5:4:0.1667:0:6 0/1:8:3:2,1:2,3:0.375:2,2:26.7:1:31.8:1:1:2.60:32:6:0.375:0.125:6.3 -18 108108 . G A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54348;SOR=3.3216;LSEQ=CTAAGTGATGTAATACTTGT;RSEQ=TAGGCTCTGCCTACAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:8,6:0.0667:2,0:3:0:28:0:1:0:37:2:0.0667:0:5 0/1:10:2:1,1:5,3:0.2:2,2:20:1:28:1:1:1.58108:37:4:0.2:0:5 -18 108116 . T G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13676;LSEQ=TGTAATACTTGTGTAGGCTC;RSEQ=GCCTACAGGGGCATTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:3,4:6,2:0.4667:2,2:13.7:1:29.7:1:0.31469:3.61926:23.1:14:0.4667:0:5.6 1/0:10:5:4,1:2,3:0.5:2,2:26.2:1:30.2:1:0.52381:4.92:32:10:0.5:0:6 -18 108125 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TGTGTAGGCTCTGCCTACAG;RSEQ=GGCATTTTGACATATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:7,6:0.1333:2,0:40.5:1:30:1:0.48571:0:32.5:4:0.1333:0:6 0/0:10:0:0,0:6,3:0:2,0:28.7:1:29.7:1:1:0:31.7:8:0.8889:0:5.7 -18 108126 . G A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54348;SOR=3.3216;LSEQ=GTGTAGGCTCTGCCTACAGG;RSEQ=GCATTTTGACATATCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:8,6:0.0667:2,0:21:0:31:0:1:0:37:2:0.0667:0:5 0/1:10:2:1,1:5,3:0.2:2,2:33.5:1:30:1:1:1.58108:37:4:0.2:0:5 -18 108127 . GC TA 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TGTAGGCTCTGCCTACAGGG;RSEQ=ATTTTGACATATCTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:0.1333:2,2:17.5:1:27.7:1:1:1.54914:23:4:0.1333:0.0667:5 0/0:10:0:0,0:6,4:0:2,0:27.5:1:30.4:1:1:0:32.5:9:1:0:5.7 -18 108128 . C A 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.67846;SOR=1.75558;LSEQ=GTAGGCTCTGCCTACAGGGG;RSEQ=ATTTTGACATATCTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:6,2:0.3571:2,2:27:1:29.4:1:0.29293:3.95135:23.2:10:0.3846:0:5.6 1/0:10:5:4,1:2,3:0.5:2,2:28.6:1:29.6:1:0.52381:4.92:32:10:0.5556:0:6 -18 108131 . T C 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.77977;LSEQ=GGCTCTGCCTACAGGGGCAT;RSEQ=TTGACATATCTCTGCACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:6,2:0.3571:2,2:30:1:31.6:1:0.29293:3.95135:23.2:10:0.3571:0:5.6 0/1:10:3:2,1:2,3:0.3:2,2:33.7:1:33.3:1:1:2.60:32:6:0.3333:0:6.3 -18 108134 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48667;SOR=0;LSEQ=TCTGCCTACAGGGGCATTTT;RSEQ=ACATATCTCTGCACTGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:37:1:29:0:1:1.36624:33.5:4:0.1429:0:4 0/0:11:0:0,0:6,5:0:2,0:24.2:1:31.5:1:1:0:31.5:22:1:0:5.5 -18 108141 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48667;SOR=0;LSEQ=ACAGGGGCATTTTGACATAT;RSEQ=TCTGCACTGTTAACCGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:6,6:0.1429:2,0:35.5:1:29.5:1:0.47253:0:42.5:4:0.1429:0:5 0/0:11:0:0,0:6,4:0:2,0:24.2:1:30.1:1:1:0:32:9:0.9:0:5.6 -18 108146 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5504;SOR=3.08979;LSEQ=GGCATTTTGACATATCTCTG;RSEQ=ACTGTTAACCGAGGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:7,6:0.0714:2,0:41:0:30:0:1:0:37:2:0.0714:0:5 0/1:10:2:1,1:4,4:0.2:2,2:33.5:1:28:1:1:1:37:4:0.2:0:5 -18 108164 . T C 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.3179;LSEQ=TGCACTGTTAACCGAGGTGA;RSEQ=GTAACTCTTGTCTAGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:42.5:1:31.5:1:1:1:31:4:0.1429:0:3.5 0/1:11:2:1,1:3,6:0.1818:2,2:25:1:28.5:1:1:1.87:37:4:0.1818:0:5 -18 108165 . G T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68875;SOR=1.71101;LSEQ=GCACTGTTAACCGAGGTGAT;RSEQ=TAACTCTTGTCTAGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:2,5:5,2:0.5:2,2:32:1:29.7:1:0.28613:5.37707:25.6:14:0.5:0:5 1/0:11:7:2,5:1,1:0.6364:2,2:22.3:1:28.6:1:1:2.23609:27:14:0.6364:0:4.3 -18 108169 . C T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08462;SOR=Inf;LSEQ=TGTTAACCGAGGTGATGTAA;RSEQ=TCTTGTCTAGGCTGTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:28.2:1:31.1:1:1:0:30.9:28:1:0:4.6 0/1:12:3:1,2:3,6:0.25:2,2:34.3:1:30:1:1:1:23.3:6:0.25:0:5.7 -18 108181 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19928;SOR=Inf;LSEQ=TGATGTAACTCTTGTCTAGG;RSEQ=TGTGCCCACAGGGGGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:19.7:1:31.2:1:1:0:30.2:26:1:0:4.5 0/1:11:2:1,1:2,7:0.1818:2,2:16.5:1:29:1:0.49091:3.06:21:4:0.1818:0:4 -18 108193 . G T 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.48;SOR=0;LSEQ=TGTCTAGGCTGTGCCCACAG;RSEQ=GGGATTGAGACATATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:2,8:0.1538:2,2:5:1:27.5:1:0.45455:3.46:33.5:4:0.1538:0:4 0/0:12:0:0,0:2,8:0:2,0:23.5:1:28.3:1:1:0:28.3:20:0.8333:0:3.1 -18 108196 . G A 44 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=CTAGGCTGTGCCCACAGGGG;RSEQ=ATTGAGACATATCTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:2,9:0.2143:2,2:19.3:1:28.3:1:1:2.11:39:6:0.2143:0:4.3 0/0:13:0:0,0:4,8:0:2,0:22.6:1:28.8:1:1:0:27.8:24:0.9231:0:3.7 -18 108198 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=AGGCTGTGCCCACAGGGGGA;RSEQ=TGAGACATATCTCTGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:2,10:0.1429:2,2:8.5:1:32:1:0.3956:4.28:32:4:0.1429:0:5 0/0:13:0:0,0:4,9:0:2,0:23:1:27.8:1:1:0:27.3:26:1:0:3.6 -18 108232 . C A 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31373;SOR=4.29556;LSEQ=TGCACTGATCCCGAGGTGAT;RSEQ=CAACTCTTGCCTGGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:0,7:0.125:0,0:49:0:29:0:1:0:25:2:0.125:0:3 0/1:10:4:1,3:1,5:0.4:2,2:31.8:1:31.5:1:1:1.58:26:8:0.4:0:2.8 -18 108238 . C G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.69794;LSEQ=GATCCCGAGGTGATCCAACT;RSEQ=TTGCCTGGTCTCTGCCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:0,6:0.125:0,0:24:0:34:0:1:0:40:2:0.125:0:3 0/1:10:2:0,2:2,6:0.2:2,0:19.5:1:32.5:1:1:0:32:4:0.2:0:3.5 -18 108260 . G T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26154;SOR=5.3196;LSEQ=TGCCTGGTCTCTGCCTACTG;RSEQ=GGACATTGTGACATATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:0,8:0.1111:0,0:24:0:32:0:1:0:25:2:0.1111:0:3 0/1:7:3:1,2:0,3:0.4286:0,2:19:1:30:1:1:0:27:6:0.5:0:3 -18 108305 . C A 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGATCTCCCAGGTGCTGTAA;RSEQ=TTTTGTCTAGGCTCTGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25:1:32.5:1:1:0:24.5:4:1:0:5.5 0/0:1:0:0,0:0,1:0:0,0:5:0:32:0:1:0:40:2:1:0:2 -18 108382 . G A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=4.17095;LSEQ=GGTGATATAACTCTTGTCTA;RSEQ=GCTCTGCCTACAGGGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:4,1:0.1667:2,0:8:0:31:0:1:0:24:2:0.1667:0:2 1/0:4:2:1,1:2,0:0.5:0,2:36.5:1:32.5:1:1:0:23.5:4:0.5:0:6.5 -18 108400 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47368;SOR=0;LSEQ=TAGGCTCTGCCTACAGGGGG;RSEQ=TTGTGACATATCTCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:8,0:0.2:0,2:28:1:29:1:0.2:0:24:4:0.2:0:3.5 0/0:9:0:0,0:6,2:0:2,0:18.3:1:31.8:1:1:0:27.8:16:1:0:3.5 -18 108408 . A C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22925;SOR=0;LSEQ=GCCTACAGGGGGCTTGTGAC;RSEQ=TATCTCTGCACTGATCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:8,1:0.2308:2,2:32.3:1:31.7:1:0.45455:3.4638:24:6:0.2308:0:3.3 0/0:10:0:0,0:7,3:0:2,0:23.9:1:31.3:1:1:0:27:20:1:0:3.7 -18 108411 . T C 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59627;SOR=0.34803;LSEQ=TACAGGGGGCTTGTGACATA;RSEQ=CTCTGCACTGATCACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:9,1:0.2308:2,2:35.3:1:32:1:0.42308:3.87298:24:6:0.2308:0:3.3 0/1:11:1:1,0:7,3:0.0909:2,0:3:0:30:0:1:0:23:2:0.0909:0:5 -18 108412 . C A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57609;SOR=2.56011;LSEQ=ACAGGGGGCTTGTGACATAT;RSEQ=TCTGCACTGATCACCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:10,2:0.0769:2,0:30:0:30:0:1:0:28:2:0.0769:0:5 0/1:11:2:1,1:7,2:0.1818:2,2:28.5:1:30:1:0.49091:3.05504:31:4:0.1818:0:2 -18 108413 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19928;SOR=Inf;LSEQ=CAGGGGGCTTGTGACATATC;RSEQ=CTGCACTGATCACCCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:11,2:0:2,0:29.8:1:31.7:1:1:0:27.8:26:1:0:2.6 0/1:11:2:1,1:7,2:0.1818:2,2:36.5:1:30.5:1:0.49091:3.05504:28.5:4:0.1818:0:6.5 -18 108427 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48768;SOR=0;LSEQ=CATATCTCTGCACTGATCAC;RSEQ=CAGGTGATATAACTCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:11,3:0.125:2,2:27.5:1:30:0:0.45:3.31654:24:4:0.125:0:2 0/0:13:0:0,0:8,5:0:2,0:27.8:1:31.1:1:1:0:26.3:26:1:0:4 -18 108444 . T C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06363;SOR=Inf;LSEQ=CACCCAGGTGATATAACTCT;RSEQ=CTCTAGGATCTGCCTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:32:1:30.1:1:1:0:28.1:36:1:0:2.5 0/1:13:3:2,1:6,4:0.2308:2,2:38.3:1:31:1:1:1.30:29.7:6:0.25:0:3 -18 108449 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51613;SOR=0;LSEQ=AGGTGATATAACTCTTCTCT;RSEQ=GGATCTGCCTACAGGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:11,7:0.1:2,0:18:1:31.5:1:0.52105:0:29.5:4:0.1:0:4 0/0:12:0:0,0:7,5:0:2,0:33.8:1:27.3:1:1:0:26.6:11:1:0:3.3 -18 108455 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52273;SOR=0;LSEQ=TATAACTCTTCTCTAGGATC;RSEQ=GCCTACAGGGTGCTTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:0.0952:2,2:15.5:1:30:1:1:1.66897:28:4:0.0952:0:5.5 0/0:12:0:0,0:7,5:0:2,0:32.4:1:29.2:1:1:0:26.6:24:1:0:3.3 -18 108457 . C A 46 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03676;SOR=Inf;LSEQ=TAACTCTTCTCTAGGATCTG;RSEQ=CTACAGGGTGCTTTGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:23.9:1:30.8:1:1:0:28.2:21:1:0:2.8 0/1:12:3:1,2:6,3:0.25:2,2:28.3:1:29.3:1:0.52273:3.53288:27.7:6:0.25:0:5.3 -18 108459 . T C 48 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03676;SOR=Inf;LSEQ=ACTCTTCTCTAGGATCTGCC;RSEQ=ACAGGGTGCTTTGTGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:23.5:1:28.7:1:1:0:28.2:21:1:0:2.8 0/1:12:3:1,2:6,3:0.25:2,2:29:1:30.7:1:0.52273:3.53288:27.7:6:0.25:0:5.3 -18 108465 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51337;SOR=0;LSEQ=CTCTAGGATCTGCCTACAGG;RSEQ=TGCTTTGTGACATATCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:0.0952:2,2:25:1:28:1:1:1.35399:24:4:0.0952:0:2.5 0/0:13:0:0,0:7,6:0:2,0:25.8:1:28.2:1:1:0:26.5:12:1:0:3.3 -18 108467 . G A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51337;SOR=0;LSEQ=CTAGGATCTGCCTACAGGGT;RSEQ=CTTTGTGACATATCCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:0.0952:2,2:15.5:1:27.5:1:1:1.35399:28:4:0.0952:0:5.5 0/0:13:0:0,0:7,6:0:2,0:24.8:1:30.5:1:1:0:26.5:26:1:0:3.3 -18 108469 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51337;SOR=0;LSEQ=AGGATCTGCCTACAGGGTGC;RSEQ=TTGTGACATATCCCTGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:0.0952:2,2:15.5:1:30.5:1:1:1.35399:28:4:0.1:0:5.5 0/0:13:0:0,0:7,6:0:2,0:23.8:1:28.5:1:1:0:26.5:12:1:0:3.3 -18 108473 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51954;SOR=0;LSEQ=TCTGCCTACAGGGTGCTTTG;RSEQ=GACATATCCCTGCAATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:24:1:32.5:1:1:1.11803:24:4:0.1053:0:1 0/0:11:0:0,0:4,6:0:2,0:25.1:1:29:1:1:0:25.6:20:0.9091:0:3 -18 108483 . C T 25 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57609;SOR=2.56011;LSEQ=GGGTGCTTTGTGACATATCC;RSEQ=TGCAATGATCACCCAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:4,7:0.0769:2,0:22:0:31:0:1:0:24:2:0.0769:0:3 0/1:11:2:1,1:3,6:0.1818:2,2:20.5:1:25:0:1:1.87:25:4:0.1818:0:2.5 -18 108485 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=GTGCTTTGTGACATATCCCT;RSEQ=CAATGATCACCCAGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:4,6:0.1667:2,0:38.5:1:30.5:1:0.51515:0:44.5:4:0.1667:0:3 0/0:11:0:0,0:4,7:0:2,0:18.1:1:29.7:1:1:0:25.4:22:1:0:3.4 -18 108488 . A C 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59006;SOR=0.31536;LSEQ=CTTTGTGACATATCCCTGCA;RSEQ=TGATCACCCAGGTGATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:4,5:0.25:2,0:16.7:1:33.3:1:0.49091:0:23.7:6:0.25:0:1.7 0/1:11:1:1,0:2,7:0.0909:2,0:17:0:26:0:0.3:0:23:2:0.0909:0:5 -18 108505 . G A 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1321;LSEQ=GCAATGATCACCCAGGTGAT;RSEQ=TACCACTTGTCAAGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:2,5:0,2:0.7778:0,2:21.6:1:28.7:1:1:0:26.3:14:0.7778:0:3.4 1/1:5:4:0,4:0,1:0.8:0,0:21.3:1:32:0:1:0:25.3:8:0.8:0:4.5 -18 108541 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CTCTGCCTACAGGGGCATTG;RSEQ=GATGTATCTCTGCACTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:13.5:1:31:0:1:0:34:4:0.3333:0:5 0/0:3:0:0,0:0,3:0:0,0:30:1:29:1:1:0:26.3:6:1:0:5 -18 109213 . AG A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTAGGATCTGCCTACAGG;RSEQ=GTATTGTGAAATATCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:30.3:1:1:0:21:4:1:0.5:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 109337 . C A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGATGTAACTCTTGCCTAGG;RSEQ=TTTGCCTACAGGGGACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:39:0:34:0:1:0:24:2:1:0:8 1/1:2:2:1,1:0,0:1:0,2:37:1:28:1:1:0:22:4:1:0:3.5 -18 109356 . TGT AG 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTTTGCCTACAGGGGACAT;RSEQ=GACATATCTCTGCACTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:41:0:13:0:1:0:24:0:0:0:8 1/1:2:2:1,1:0,0:1:0,2:31:1:29.5:0:1:0:22:4:1:0:3.5 -18 109366 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CAGGGGACATTGTGACATAT;RSEQ=TCTGCACTGATCACCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:29:1:1:0:22:4:1:0:3.5 -18 109803 . G A 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGATCACCCAGGTGATG;RSEQ=GACTCTTGTCTAGGCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:26.5:1:1:0:22:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 109926 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TGGCATATTTCTGCACTGAT;RSEQ=ACCCAGGTGATGGACTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:12.7:1:30.3:1:1:0:47.7:6:1:0:2.3 1/1:2:2:1,1:0,0:1:0,2:13:1:28.5:1:1:0:44:4:1:0:6 -18 109930 . C A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATATTTCTGCACTGATCACC;RSEQ=AGGTGATGGACTCTTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:17.5:1:30.5:1:1:0:59.5:4:0.6667:0:1.5 1/1:2:2:1,1:0,0:1:0,2:17:1:32:0:1:0:44:4:1:0:6 -18 109937 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TGCACTGATCACCCAGGTGA;RSEQ=GGACTCTTGTCTTGGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:23.7:1:30.7:1:1:0:47.7:6:1:0:2.3 1/1:2:2:1,1:0,0:1:0,2:24:1:32:0:1:0:44:4:1:0:6 -18 109947 . T C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACCCAGGTGATGGACTCTTG;RSEQ=CTTGGATCTGCCTATGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:34.5:1:31:1:1:0:59.5:4:0.6667:0:1.5 0/0:2:0:0,0:1,1:0:2,0:34:1:30.5:1:1:0:44:4:1:0:6 -18 109959 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GACTCTTGTCTTGGATCTGC;RSEQ=TATGGGGGCATAGTGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:36.5:1:31.5:1:1:0:45.8:8:1:0:3 1/1:2:2:1,1:0,0:1:0,2:40:1:30.5:1:1:0:44:4:1:0:6 -18 109988 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGTGACATATCTCTGCA;RSEQ=TGATCACTCATGTGATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:21.5:1:31:1:1:1.7321:24:4:0.4:0:5 0/0:2:0:0,0:1,1:0:2,0:24.5:1:30:1:1:0:44:4:1:0:6 -18 109998 . A T 28 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=TATCTCTGCACTGATCACTC;RSEQ=TGTGATGTAACGCTTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:24.4:1:30.6:1:1:0:41.4:10:1:0:3.4 1/1:2:2:1,1:0,0:1:0,2:14.5:1:28.5:1:1:0:44:4:1:0:6 -18 110007 . A C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGATCACTCATGTGATGT;RSEQ=ACGCTTGTCTAAGCTGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:21.5:1:30:1:1:1.7321:24:4:0.4:0:5 0/0:1:0:0,0:0,1:0:0,0:16:0:32:0:1:0:44:2:1:0:7 -18 110034 . C G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTAAGCTGCGCCTAAAGG;RSEQ=GAATTGTGACAGATATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:32:1:1:0:32:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 110261 . A C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCATTGTGAAATATCTCTGC;RSEQ=CTGATCACCCAGGTGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:11:1:31:0:1:0:24:4:1:0:2.5 0/1:6:2:2,0:4,0:0.3333:0,0:22:1:31:0:1:0:24:4:0.3333:0:7 -18 110269 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATATCTCTGCACTGATCA;RSEQ=CCAGGTGATGGGACTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:12:1:32.5:1:1:0:26.3:8:1:0:3.3 0/1:9:2:1,1:5,1:0.2222:2,2:20:1:28.5:1:0.46429:3.87298:24:4:0.2222:0:8 -18 110274 . G C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=TCTCTGCACTGATCACCCAG;RSEQ=TGATGGGACTCTTCTCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:12:1:31.5:1:1:0:29.5:12:1:0:4.2 0/1:9:2:1,1:6,1:0.2222:2,2:25:1:33:1:0.41667:4.58262:24:4:0.25:0:8 -18 110277 . A T 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CTGCACTGATCACCCAGGTG;RSEQ=TGGGACTCTTCTCTATACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:15:1:30.7:1:1:0:29.5:12:1:0:4.2 0/1:10:2:1,1:6,2:0.2:2,2:12:0:27:1:1:2.64575:28:4:0.2:0:5 -18 110286 . T C 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TCACCCAGGTGATGGGACTC;RSEQ=TCTCTATACTCTGCCTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:22:1:30.5:1:1:3.1622:24:4:0.2857:0:2 0/0:14:0:0,0:9,5:0:2,0:23.1:1:29:1:1:0:29.3:28:1:0:5.4 -18 110295 . CT TG 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGATGGGACTCTTCTCTATA;RSEQ=CTGCCTAGAGGGGGATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:30.1:1:32:1:1:0:28.7:14:1:0:3.7 0/1:15:2:1,1:9,4:0.1333:2,2:32.5:1:30.5:1:1:2.12136:24:4:0.1333:0:7 -18 110304 . G T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52696;SOR=Inf;LSEQ=TCTTCTCTATACTCTGCCTA;RSEQ=AGGGGGATTTGTGACATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,2:0:2,0:32:1:31.9:1:1:0:28.9:14:0.875:0:3.7 0/1:17:3:2,1:7,4:0.1765:2,2:28.7:1:29:1:1:1.13:32:6:0.1765:0:4.7 -18 110307 . GG TT 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCTATACTCTGCCTAGAG;RSEQ=GGATTTGTGACATATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:35:1:31.4:1:1:0:28.3:16:1:0:3.5 0/1:17:2:1,1:9,5:0.1176:2,2:37:1:28.8:1:1:1.73197:23:4:0.1176:0:3 -18 110310 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=CTATACTCTGCCTAGAGGGG;RSEQ=ATTTGTGACATATCTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,3:0.2:2,2:24:1:29.5:1:1:1.29098:24:4:0.2222:0:2.5 0/0:17:0:0,0:9,4:0:2,0:30.9:1:28.8:1:1:0:25.3:12:0.75:0:4.9 -18 110312 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=ATACTCTGCCTAGAGGGGGA;RSEQ=TTGTGACATATCTCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:30.9:1:30.1:1:1:0:27.4:20:1:0:3.3 0/1:18:2:1,1:10,6:0.1111:2,2:37:1:29.5:1:1:1.61828:23:4:0.1176:0:3 -18 110318 . A T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=TGCCTAGAGGGGGATTTGTG;RSEQ=CATATCTCTGCACTGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:33.2:1:29.4:1:1:0:27.4:20:1:0:3.3 0/1:18:2:1,1:10,6:0.1111:2,2:32:1:27.5:1:1:1.61828:24:4:0.1111:0:7 -18 110319 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11905;SOR=0;LSEQ=GCCTAGAGGGGGATTTGTGA;RSEQ=ATATCTCTGCACTGATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,3:0.2:2,2:27.5:1:28.5:1:1:1.29098:24:4:0.2:0:2.5 0/0:18:0:0,0:11,7:0:2,0:30.3:1:30.2:1:1:0:28.9:17:1:0:4.9 -18 110327 . T C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51232;SOR=Inf;LSEQ=GGGGATTTGTGACATATCTC;RSEQ=GCACTGATCACCCAGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:30.2:1:30.2:1:1:0:27.1:22:1:0:3.2 0/1:18:2:1,1:10,6:0.1111:2,2:41:0:31:1:1:1.61828:60:4:0.1111:0:4.5 -18 110329 . C T 55 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26778;SOR=Inf;LSEQ=GGATTTGTGACATATCTCTG;RSEQ=ACTGATCACCCAGGTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:30:1:31.7:1:1:0:27.1:22:1:0:3.2 0/1:18:4:2,2:9,5:0.2222:2,2:28.5:1:27.8:1:1:1.74002:22.5:8:0.2222:0:5.5 -18 110333 . G C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49754;SOR=Inf;LSEQ=TTGTGACATATCTCTGCACT;RSEQ=ATCACCCAGGTGATGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:8,4:0:2,0:27.2:1:31.4:1:1:0:27.3:24:1:0:3.4 0/1:17:2:1,1:9,6:0.1176:2,2:28:0:33:0:1:1.46382:28:4:0.1333:0:5 -18 110338 . C A 55 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.5163;LSEQ=ACATATCTCTGCACTGATCA;RSEQ=CCAGGTGATGGAAGTCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,3:0.1667:2,2:24:1:29.5:1:1:2.16028:24:4:0.1667:0:2.5 0/1:17:4:2,2:8,5:0.2353:2,2:26.3:1:27.5:1:1:1.55528:22.5:8:0.2353:0:5.5 -18 110342 . G C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49754;SOR=Inf;LSEQ=ATCTCTGCACTGATCACCCA;RSEQ=GTGATGGAAGTCTTGTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:8,4:0:2,0:25.7:1:31.3:1:1:0:27.3:24:1:0:3.4 0/1:17:2:1,1:9,6:0.1176:2,2:19:0:31.5:1:1:1.46382:28:4:0.1176:0:5 -18 110348 . G T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23793;SOR=Inf;LSEQ=GCACTGATCACCCAGGTGAT;RSEQ=GAAGTCTTGTCTAGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:23.5:1:31.5:1:1:0:29:26:1:0:3.5 0/1:17:3:1,2:9,5:0.1765:2,2:29.3:1:29:1:0.53676:3.32592:22.7:6:0.1765:0:6.3 -18 110349 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49195;SOR=Inf;LSEQ=CACTGATCACCCAGGTGATG;RSEQ=AAGTCTTGTCTAGGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:23.5:1:31.2:1:1:0:29:26:1:0:3.5 0/1:17:2:1,1:9,6:0.1176:2,2:19:0:31:1:1:1.46382:60:4:0.1176:0:4.5 -18 110352 . G C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.6838;LSEQ=TGATCACCCAGGTGATGGAA;RSEQ=TCTTGTCTAGGCTCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:6,6:0.0769:2,0:20:0:34:0:1:0:30:2:0.0769:0:6 0/1:16:2:1,1:6,8:0.125:2,2:16:0:33.5:1:1:1.31:60:4:0.125:0:4.5 -18 110353 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48768;SOR=Inf;LSEQ=GATCACCCAGGTGATGGAAG;RSEQ=CTTGTCTAGGCTCTGTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:23.2:1:28.5:1:1:0:29:12:1:0:3.5 0/1:16:2:1,1:6,7:0.125:2,2:8:0:31:1:1:1.15:28:4:0.125:0:5 -18 110355 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1746;SOR=0;LSEQ=TCACCCAGGTGATGGAAGTC;RSEQ=TGTCTAGGCTCTGTCTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:15.5:1:30.5:1:1:1:40.5:4:0.1667:0:6.5 0/0:16:0:0,0:7,9:0:2,0:21.6:1:30.3:1:1:0:30.2:32:1:0:4.7 -18 110359 . C T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50345;SOR=Inf;LSEQ=CCAGGTGATGGAAGTCTTGT;RSEQ=TAGGCTCTGTCTATGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:24:1:31.2:1:1:0:29.4:24:1:0:3.7 0/1:18:2:1,1:7,9:0.1111:2,2:14:1:32:0:1:1.27:21:4:0.1111:0:4 -18 110364 . C T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.83892;LSEQ=TGATGGAAGTCTTGTCTAGG;RSEQ=TCTGTCTATGGGGGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:5,5:0.0909:2,0:39:0:30:0:1:0:24:2:0.0909:0:3 0/1:19:3:2,1:6,10:0.1579:2,2:33:1:29.3:1:0.54592:3.12:27.7:6:0.1579:0:3.7 -18 110366 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13306;SOR=0;LSEQ=ATGGAAGTCTTGTCTAGGCT;RSEQ=TGTCTATGGGGGCATTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:15.5:1:28.5:1:1:1:40.5:4:0.1667:0:6.5 0/0:20:0:0,0:7,11:0:2,0:15:1:31.1:1:1:0:34.5:36:0.9:0:4.1 -18 110370 . C G 66 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2652;SOR=Inf;LSEQ=AAGTCTTGTCTAGGCTCTGT;RSEQ=TATGGGGGCATTGTGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,5:0:2,0:28.2:1:32:1:1:0:29.4:18:0.9:0:3.7 0/1:18:4:1,3:7,7:0.2222:2,2:16.8:1:33:1:0.58824:2.83009:36:8:0.2222:0:4.3 -18 110375 . G T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=TTGTCTAGGCTCTGTCTATG;RSEQ=GGGCATTGTGTCAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:26.5:1:31.9:1:1:0:29.4:20:1:0:3.4 0/1:18:2:0,2:8,7:0.1111:2,0:15.5:1:30.5:1:0.47059:0:22.5:4:0.1176:0:7 -18 110377 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=GTCTAGGCTCTGTCTATGGG;RSEQ=GCATTGTGTCAAATATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:3,5:0.2:2,0:25.5:1:31.5:1:0.44444:0:27.5:4:0.2:0:5.5 0/0:17:0:0,0:8,9:0:2,0:20.4:1:29.6:1:1:0:30.6:34:1:0:4.1 -18 110383 . G A 29 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11077;SOR=0;LSEQ=GCTCTGTCTATGGGGGCATT;RSEQ=TGTCAAATATCTGCACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:3,4:0.2222:2,0:15.5:1:29:0:0.44444:0:35:4:0.2222:0:4.5 0/0:17:0:0,0:7,6:0:2,0:20.3:1:30:1:1:0:33.3:26:0.7647:0:4 -18 110389 . A G 52 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07174;SOR=0;LSEQ=TCTATGGGGGCATTGTGTCA;RSEQ=ATATCTGCACTGATCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:5,3:0.2727:2,2:18.3:1:33:0:0.54545:2.97405:43:6:0.2727:0:4 0/0:14:0:0,0:6,7:0:2,0:29.2:1:29.4:1:1:0:32.8:26:0.9286:0:3.5 -18 110392 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48718;SOR=Inf;LSEQ=ATGGGGGCATTGTGTCAAAT;RSEQ=TCTGCACTGATCACCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:22.5:1:30.3:1:1:0:33.8:24:1:0:3.9 0/1:15:2:1,1:6,7:0.1333:2,2:30:1:30.5:1:1:1.15:44.5:4:0.1333:0:3.5 -18 110401 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48188;SOR=Inf;LSEQ=TTGTGTCAAATATCTGCACT;RSEQ=ATCACCCAGGTGATGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:23.8:1:33.5:1:1:0:34.6:22:1:0:4 0/1:13:2:1,1:5,6:0.1538:2,2:19:1:30:1:1:1.18:24.5:4:0.1538:0:4.5 -18 110406 . CC G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19928;SOR=0;LSEQ=TCAAATATCTGCACTGATCA;RSEQ=CAGGTGATGTAACTCTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:25:1:31.3:1:1:1.22474:45:4:0.1818:0.0909:4 0/0:13:0:0,0:4,7:0:2,0:32.3:1:31.1:1:1:0:34:22:0.8462:0:3.2 -18 110425 . G T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.73755;LSEQ=ACCCAGGTGATGTAACTCTT;RSEQ=TCTAGGCTCTGTCTACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,3:0.2:2,2:15.5:1:32:0:1:1:35:4:0.2:0:5 0/1:13:2:1,1:4,6:0.1538:2,2:38:1:29.5:1:1:1.45:25:4:0.1667:0:6 -18 110430 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=Inf;LSEQ=GGTGATGTAACTCTTGTCTA;RSEQ=GCTCTGTCTACAGGGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:27.8:1:29.8:1:1:0:37.9:9:1:0:4.6 0/1:12:2:1,1:4,6:0.1667:2,2:16:0:29.5:1:1:1.45:44.5:4:0.1667:0:3.5 -18 110437 . T C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=TAACTCTTGTCTAGGCTCTG;RSEQ=CTACAGGGATTTTTGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:29.2:1:29.4:1:1:0:38.8:18:1:0:4.6 0/1:12:2:1,1:3,7:0.1667:2,2:9:0:29.5:1:1:2.16:44.5:4:0.1667:0:3.5 -18 110438 . C T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=AACTCTTGTCTAGGCTCTGT;RSEQ=TACAGGGATTTTTGTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:28.9:1:31.3:1:1:0:38.8:18:1:0:4.6 0/1:13:2:1,1:4,5:0.1538:2,2:15.5:1:26.5:1:1:1.22:25:4:0.1667:0:7.5 -18 110447 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTAGGCTCTGTCTACAGGGA;RSEQ=TTTTGTGACATATCACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:28:1:29.5:1:1:0:39.5:16:1:0:4.8 0/1:8:2:1,1:2,4:0.25:2,2:15.5:1:30:1:1:1.83:25:4:0.25:0:7.5 -18 110452 . G C 63 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=CTCTGTCTACAGGGATTTTT;RSEQ=TGACATATCACTGCACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:2,1:0.5714:2,2:27.8:1:31.5:1:1:1.81007:36.5:8:0.5714:0:5 0/0:7:0:0,0:2,3:0:2,0:28.2:1:31.8:1:1:0:32.6:10:0.7143:0:4.8 -18 110458 . T C 63 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=CTACAGGGATTTTTGTGACA;RSEQ=ATCACTGCACTGATCACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:0.5:2,2:24.8:1:31.8:1:1:1:36.5:8:0.5:0:5 0/0:7:0:0,0:3,4:0:2,0:23.9:1:28.7:1:1:0:30.4:14:1:0:5.6 -18 110466 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=ATTTTTGTGACATATCACTG;RSEQ=ACTGATCACCTAGGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:22:1:30.3:1:1:0:37.3:14:1:0:5 0/1:5:2:1,1:1,1:0.4:2,2:32.5:1:29.5:1:1:1:27:4:0.4:0:5 -18 110467 . A C 60 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29293;SOR=0.21696;LSEQ=TTTTTGTGACATATCACTGC;RSEQ=CTGATCACCTAGGTGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:1,2:0.5714:2,2:20:1:30:1:1:1.81:36.5:8:0.5714:0:5 0/1:5:1:0,1:2,2:0.2:2,0:36:0:32:0:1:0:44:2:0.2:0:4 -18 110468 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=TTTTGTGACATATCACTGCA;RSEQ=TGATCACCTAGGTGATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:20.7:1:30:1:1:0:37.3:14:1:0:5 0/1:5:2:1,1:1,1:0.4:2,2:30.5:1:29.5:1:1:1:27:4:0.4:0:5 -18 110473 . C A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=2.97405;LSEQ=TGACATATCACTGCACTGAT;RSEQ=ACCTAGGTGATGTAAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:2,3:0.1667:2,0:20:0:26:0:1:0:30:2:0.1667:0:6 0/1:5:2:1,1:1,2:0.4:2,2:25.5:1:29.5:1:1:1.73:27:4:0.4:0:5 -18 110479 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=ATCACTGCACTGATCACCTA;RSEQ=GTGATGTAAACCTTGTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,3:0:2,0:24:1:30:1:1:0:35:8:0.8:0:5 0/1:5:2:1,1:1,2:0.4:2,2:19.5:1:31.5:1:1:1.73:27:4:0.4:0:5 -18 110489 . A G 81 d7;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01515;SOR=0;LSEQ=TGATCACCTAGGTGATGTAA;RSEQ=CCTTGTATGGGCTTTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:14.7:1:31.5:1:1:0:31.2:12:1:0:5.2 0/1:5:1:0,1:0,1:0.2:0,0:14:0:32:0:1:0:44:2:0.25:0:4 -18 110554 . T G 50 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGATCTCTGAGGTGAT;RSEQ=CAACTCTTGTCTAGGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:26.3:1:32:1:1:0:23.7:6:1:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 110584 . C G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCTAGGCACTGCCTACAGGG;RSEQ=ACATTGGTACATATCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:49:0:30:0:1:0:24:2:0.5:0:3 1/1:2:2:1,1:0,0:1:0,2:6:0:32.5:1:1:0:33:4:1:0:2 -18 110656 . T A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=AGATCTGCCTACATGGACAT;RSEQ=GTGACACATCTCTGAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:12:1:30.5:1:0.33333:0:31:4:0.6667:0:3.5 0/0:3:0:0,0:2,1:0:2,0:18.7:1:28:1:1:0:35.3:6:1:0:2.7 -18 110696 . C A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATCAACCAAGTGATGAAACT;RSEQ=TTGTCTAGGCTCTGCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:41.5:1:31.5:1:0.33333:0:31:4:0.6667:0:3.5 0/0:3:0:0,0:1,2:0:2,0:20.3:1:32:1:1:0:40:6:1:0:3.3 -18 110717 . G A 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTGTCTAGGCTCTGCCTACA;RSEQ=GGGCTTTGTGACACATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:28:1:32.5:1:0.33333:0:31:4:0.6667:0:3.5 0/0:2:0:0,0:0,1:0:0,0:41:0:32:0:1:0:40:2:0.5:0:4 -18 111715 . G A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTCAGCCAGAATTTCAC;RSEQ=GACAAACAAGGGCACAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:29:1:1:0:35:4:1:0:5.5 -18 111720 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCAGAATTTCACGGACA;RSEQ=ACAAGGGCACAGAGAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:31:1:1:0:35:4:1:0:5.5 -18 111763 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTCCCTTGCACGTCAGC;RSEQ=GGGGTGCGCACTGCGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:32.5:1:1:0:35:4:1:0:5.5 -18 111774 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGTCAGCCGGGGTGCGCA;RSEQ=TGCGCGCAGGTCTAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:31:1:1:0:35:4:1:0:5.5 -18 111777 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCAGCCGGGGTGCGCACTG;RSEQ=GCGCAGGTCTAGCCAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:31:1:1:0:35:4:1:0:5.5 -18 111887 . C T 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GGGCCCGGGCGGGCGGGCGA;RSEQ=GGTGGCGCGCAGGCGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:6:0:25:0:1:0:22:2:1:0:7 1/1:3:3:2,1:0,0:1:0,2:14.7:1:29.3:1:1:0:29:6:1:0:6 -18 111895 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCGGGCGGGCGACGGTGGCG;RSEQ=GCAGGCGCAGAGGAGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:14:0:29:0:1:0:22:2:1:0:7 1/0:3:2:1,1:1,0:0.6667:0,2:22.5:1:28:1:1:0:33:4:0.6667:0:6.5 -18 111897 . C G 49 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGGGCGACGGTGGCGCG;RSEQ=AGGCGCAGAGGAGGCGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:24.7:1:31:1:1:0:29:6:1:0:6 -18 111899 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCGGGCGACGGTGGCGCGCA;RSEQ=GCGCAGAGGAGGCGAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:18:0:27:0:1:0:22:2:1:0:6 0/1:6:2:1,1:2,2:0.3333:2,2:26.5:1:28.5:1:1:1:33:4:0.3333:0:6.5 -18 111902 . G A 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GGCGACGGTGGCGCGCAGGC;RSEQ=CAGAGGAGGCGAGCCGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:21:0:30:0:1:0:22:2:1:0:6 0/1:8:2:1,1:3,3:0.25:2,2:5:0:30:1:1:1:31:4:0.25:0:1.5 -18 111914 . A G 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=GCGCAGGCGCAGAGGAGGCG;RSEQ=GCCGCCGGAGGGTGTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:11.6:1:28:1:1:0:36.8:4:1:0:1.4 0/1:8:2:1,1:3,3:0.25:2,2:15:0:29:1:1:1:60:4:0.25:0:2 -18 111921 . G A 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1049;SOR=Inf;LSEQ=CGCAGAGGAGGCGAGCCGCC;RSEQ=GAGGGTGTCAGGCCTGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:18.6:1:30.4:1:1:0:36.8:10:1:0:1.4 1/0:8:4:2,2:2,2:0.5:2,2:27.5:1:30:1:1:1:46.5:8:0.5:0:4.3 -18 111923 . AG A 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=CAGAGGAGGCGAGCCGCCGG;RSEQ=GGTGTCAGGCCTGGACGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:14.5:1:33:0:1:1:21:4:0.4:0:0 0/0:8:0:0,0:4,4:0:2,0:21.5:1:31:1:1:0:36.3:16:1:0:3.1 -18 111925 . G GA 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=GAGGAGGCGAGCCGCCGGAG;RSEQ=GTGTCAGGCCTGGACGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:14.5:1:31.3:1:1:0:40.5:8:1:0:0.3 0/1:8:2:1,1:3,3:0.25:2,2:29:0:31:1:1:1:31:4:0.2857:0:1.5 -18 111940 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CGGAGGGTGTCAGGCCTGGA;RSEQ=GCTGCGCGGGCCCGGCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:29.5:1:30.5:1:1:0:60:4:0.6667:0:0.5 0/1:6:2:1,1:2,2:0.3333:2,2:13:0:31.5:1:1:1:33:4:0.4:0:6.5 -18 111941 . G A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GGAGGGTGTCAGGCCTGGAC;RSEQ=CTGCGCGGGCCCGGCGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:29:1:32:1:1:0:47.3:6:1:0:2.7 0/1:6:2:1,1:2,2:0.3333:2,2:17:1:32:0:1:1:31:4:0.3333:0:1.5 -18 111948 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GTCAGGCCTGGACGCTGCGC;RSEQ=GGCCCGGCGTTTCGCGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:31.3:1:31.7:1:1:0:47.3:6:1:0:2.7 0/1:6:2:1,1:2,2:0.3333:2,2:5:0:32:1:1:1:33:4:0.3333:0:6.5 -18 112211 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CCCACCTGCTGGTACCTGGG;RSEQ=CGGCTCTGGGATCCCCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:11.3:1:33:1:1:0:30.3:8:1:0:5 0/1:7:2:2,0:3,2:0.2857:2,0:15:1:31.5:1:1:0:37:4:0.2857:0:6 -18 112215 . C T 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23636;SOR=Inf;LSEQ=CCTGCTGGTACCTGGGCCGG;RSEQ=TCTGGGATCCCCGGGATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:15.3:1:33.8:1:1:0:30.3:8:1:0:5 0/1:7:3:2,1:3,1:0.4286:2,2:28.3:1:30.7:1:1:1.41418:21:6:0.4286:0:4 -18 112217 . C A 59 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22797;SOR=Inf;LSEQ=TGCTGGTACCTGGGCCGGCT;RSEQ=TGGGATCCCCGGGATGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:17.3:1:32.5:1:1:0:30.3:8:1:0:5 0/1:9:4:2,2:4,1:0.4444:2,2:10.8:1:29.8:1:0.52381:3.38757:33:8:0.4444:0:4.5 -18 112218 . T C 33 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=GCTGGTACCTGGGCCGGCTC;RSEQ=GGGATCCCCGGGATGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:22:1:33:0:1:0:23.5:4:0.5:0:4.5 0/0:9:0:0,0:6,3:0:2,0:19.2:1:30.9:1:1:0:29.9:18:1:0:4.2 -18 112224 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=ACCTGGGCCGGCTCTGGGAT;RSEQ=CCCGGGATGCCCAGGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:13.6:1:32.4:1:1:0:34.1:18:1:0:5.1 0/1:9:2:1,1:5,2:0.2222:2,2:36.5:1:30:0:1:2.23609:21:4:0.2222:0:3 -18 112227 . C T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=TGGGCCGGCTCTGGGATCCC;RSEQ=GGGATGCCCAGGAAAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:5,2:0.2222:2,0:13.5:1:32.5:1:1:0:37:4:0.2222:0:4 0/0:9:0:0,0:6,3:0:2,0:28.2:1:30.4:1:1:0:29.9:18:1:0:4.2 -18 112228 . G T 64 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08669;SOR=0;LSEQ=GGGCCGGCTCTGGGATCCCC;RSEQ=GGATGCCCAGGAAAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:3,1:3,1:0.4:2,2:25.5:1:32.3:1:1:1:28.3:8:0.4:0:5.5 0/0:9:0:0,0:4,2:0:2,0:31.2:1:30.5:1:1:0:25.8:12:0.6667:0:3.3 -18 112235 . C T 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.46629;LSEQ=CTCTGGGATCCCCGGGATGC;RSEQ=CAGGAAAGAATGGCAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:0.1818:2,2:19:1:30:1:1:1.87089:40:4:0.1818:0:6.5 0/1:11:1:1,0:7,3:0.0909:2,0:47:0:33:0:1:0:34:2:0.0909:0:6 -18 112246 . T G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=CCGGGATGCCCAGGAAAGAA;RSEQ=GGCAGTTCTCCGCTGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:0.1333:2,2:30:1:32:0:1:1.54914:40:4:0.1333:0:6.5 0/0:12:0:0,0:8,4:0:2,0:32.6:1:30.3:1:1:0:29.3:24:1:0:4.6 -18 112251 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=ATGCCCAGGAAAGAATGGCA;RSEQ=TTCTCCGCTGTGTGGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:22.8:1:32.1:1:1:0:36.9:38:1:0:4.5 0/1:13:2:1,1:7,4:0.1538:2,2:41:1:29.5:1:1:1.67325:40:4:0.1538:0:6 -18 112255 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50202;SOR=0;LSEQ=CCAGGAAAGAATGGCAGTTC;RSEQ=CCGCTGTGTGGAGTCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:37.5:1:30.5:1:1:1.11803:34:4:0.1053:0:4 0/0:13:0:0,0:8,5:0:2,0:32.6:1:30.5:1:1:0:28.8:26:1:0:4.8 -18 112256 . C A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50202;SOR=0;LSEQ=CAGGAAAGAATGGCAGTTCT;RSEQ=CGCTGTGTGGAGTCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:25:1:27.5:1:1:1.11803:40:4:0.1053:0:5.5 0/0:13:0:0,0:8,5:0:2,0:32.6:1:31.3:1:1:0:28.8:26:1:0:4.8 -18 112257 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49621;SOR=0;LSEQ=AGGAAAGAATGGCAGTTCTC;RSEQ=GCTGTGTGGAGTCTCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:39.5:1:30:1:1:1.11803:34:4:0.1053:0:4 0/0:14:0:0,0:8,6:0:2,0:30.3:1:30.1:1:1:0:29.6:28:1:0:4.9 -18 112258 . G A 78 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02721;SOR=0;LSEQ=GGAAAGAATGGCAGTTCTCC;RSEQ=CTGTGTGGAGTCTCTCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:3,3:5,5:0.3158:2,2:23.2:1:30.2:1:1:1:40:12:0.3158:0:4.8 0/0:14:0:0,0:7,5:0:2,0:32.6:1:30.4:1:1:0:30.8:24:0.8571:0:4.5 -18 112261 . G C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49621;SOR=0;LSEQ=AAGAATGGCAGTTCTCCGCT;RSEQ=TGTGGAGTCTCTCACCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:30:1:30.5:1:1:1.11803:40:4:0.1053:0:5.5 0/0:14:0:0,0:8,6:0:2,0:30.3:1:31.2:1:1:0:29.6:28:1:0:4.7 -18 112262 . T G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.49621;SOR=0;LSEQ=AGAATGGCAGTTCTCCGCTG;RSEQ=GTGGAGTCTCTCACCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:42.5:1:31:0:1:1.11803:40:4:0.1053:0:4.5 0/0:14:0:0,0:8,6:0:2,0:30.3:1:29.4:1:1:0:29.6:28:1:0:4.7 -18 112269 . T C 63 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.11918;SOR=0;LSEQ=CAGTTCTCCGCTGTGTGGAG;RSEQ=CTCTCACCGGGCCTAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:2,2:8,7:0.2105:2,2:26.5:1:31.8:1:1:1.13484:40:8:0.2105:0:5 0/0:14:0:0,0:7,5:0:2,0:29.4:1:28.6:1:1:0:27.8:24:0.8571:0:4.9 -18 112270 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49621;SOR=0;LSEQ=AGTTCTCCGCTGTGTGGAGT;RSEQ=TCTCACCGGGCCTAGACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:34.5:1:31:1:1:1.11803:40:4:0.1053:0:4.5 0/0:14:0:0,0:8,6:0:2,0:29.3:1:30.9:1:1:0:29.6:28:1:0:4.7 -18 112272 . CT TC 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49621;SOR=0;LSEQ=TTCTCCGCTGTGTGGAGTCT;RSEQ=CACCGGGCCTAGACCTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:32:1:32:1:1:1.11803:40:4:0.1053:0:3 0/0:14:0:0,0:7,6:0:2,0:27.8:1:31:1:1:0:28.8:26:0.9286:0:4.7 -18 112276 . C A 44 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24432;SOR=0;LSEQ=CCGCTGTGTGGAGTCTCTCA;RSEQ=CGGGCCTAGACCTAGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:2,1:8,8:0.1579:2,2:18.7:1:28.3:1:1:1.93:24.3:6:0.1579:0:4.7 0/0:14:0:0,0:8,6:0:2,0:27.6:1:30.7:1:1:0:29.6:28:1:0:4.7 -18 112277 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.49194;SOR=0;LSEQ=CGCTGTGTGGAGTCTCTCAC;RSEQ=GGGCCTAGACCTAGAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:27.5:1:30.5:1:1:1:40:4:0.1111:0:4.5 0/0:14:0:0,0:8,6:0:2,0:27.3:1:29.6:1:1:0:29.6:28:1:0:4.7 -18 112278 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18347;SOR=Inf;LSEQ=GCTGTGTGGAGTCTCTCACC;RSEQ=GGCCTAGACCTAGAAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:33.8:1:30.7:1:1:0:37.8:36:1:0:4.4 0/1:14:2:1,1:7,5:0.1429:2,2:24.5:1:28.5:1:1:1.36624:26:4:0.1429:0:3 -18 112279 . G T 60 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.36787;SOR=0.30227;LSEQ=CTGTGTGGAGTCTCTCACCG;RSEQ=GCCTAGACCTAGAAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:7,7:0.2222:2,2:31.5:1:30:1:1:1:40:8:0.2222:0:5 0/1:13:1:0,1:7,5:0.0769:2,0:19:0:32:0:0.46154:0:21:2:0.0769:0:4 -18 112283 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49677;SOR=0;LSEQ=GTGGAGTCTCTCACCGGGCC;RSEQ=AGACCTAGAAGGCAGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,7:0.1111:2,2:39:1:31.5:1:1:1:40:4:0.1111:0:4.5 0/0:13:0:0,0:6,5:0:2,0:27.7:1:29.7:1:1:0:31.9:22:0.8462:0:4.7 -18 112287 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.57434;LSEQ=AGTCTCTCACCGGGCCTAGA;RSEQ=CTAGAAGGCAGGAATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:16.5:1:29:1:1:1:26:4:0.1111:0:5 0/1:12:2:1,1:5,4:0.1667:2,2:24:1:31.5:1:1:1.22474:40:4:0.1667:0:6 -18 112288 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15172;SOR=Inf;LSEQ=GTCTCTCACCGGGCCTAGAC;RSEQ=TAGAAGGCAGGAATCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:30.7:1:31.6:1:1:0:37.8:36:1:0:4.4 0/1:12:2:1,1:5,5:0.1667:2,2:14.5:1:29:1:1:1:26:4:0.1667:0:3 -18 112289 . T A 59 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26778;SOR=0;LSEQ=TCTCTCACCGGGCCTAGACC;RSEQ=AGAAGGCAGGAATCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:7,7:0.2222:2,2:26.5:1:29.5:1:1:1:33:8:0.2222:0:5.3 0/0:11:0:0,0:5,6:0:2,0:28.5:1:29.4:1:1:0:30.7:22:1:0:4.7 -18 112290 . A G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62208;SOR=1.74124;LSEQ=CTCTCACCGGGCCTAGACCT;RSEQ=GAAGGCAGGAATCCCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:29:0:33:1:1:1:40:4:0.1111:0:3 0/1:11:2:1,1:4,5:0.1818:2,2:21:1:33:1:1:1.22:40:4:0.1818:0:6 -18 112292 . A C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=CTCACCGGGCCTAGACCTAG;RSEQ=AGGCAGGAATCCCAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:32.5:1:31.5:1:1:1:40:4:0.1111:0:4.5 0/0:11:0:0,0:5,6:0:2,0:26.5:1:29.5:1:1:0:30.7:22:1:0:4.7 -18 112295 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=ACCGGGCCTAGACCTAGAAG;RSEQ=CAGGAATCCCAGGCCGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:32.5:1:30.5:1:1:1.13:40:4:0.1176:0:5.5 0/0:11:0:0,0:5,6:0:2,0:24.6:1:31.2:1:1:0:30.7:22:1:0:4.7 -18 112297 . A C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=CGGGCCTAGACCTAGAAGGC;RSEQ=GGAATCCCAGGCCGGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:27.5:1:29.5:1:1:1.13:40:4:0.1176:0:4.5 0/0:11:0:0,0:5,6:0:2,0:23.4:1:30.2:1:1:0:30.7:22:1:0:4.7 -18 112301 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12;SOR=Inf;LSEQ=CCTAGACCTAGAAGGCAGGA;RSEQ=TCCCAGGCCGGTCAGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:20.6:1:30.9:1:1:0:38.4:32:1:0:4.1 0/1:9:2:1,1:3,4:0.2222:2,2:41.5:1:29.5:1:1:1.29:22:4:0.2222:0:6 -18 112309 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=TAGAAGGCAGGAATCCCAGG;RSEQ=CGGTCAGCCCGGTGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:5,6:0.1538:2,0:11:1:30.5:1:0.48718:0:30:4:0.1538:0:5 0/0:7:0:0,0:3,4:0:2,0:24.7:1:31.1:1:1:0:32.1:14:1:0:5.1 -18 112310 . C T 44 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0307;SOR=Inf;LSEQ=AGAAGGCAGGAATCCCAGGC;RSEQ=GGTCAGCCCGGTGGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:15.2:1:30.9:1:1:0:38.5:26:1:0:4.2 0/1:7:3:2,1:1,3:0.4286:2,2:27.7:1:28.3:1:0.48571:4.45:28:6:0.4286:0:5.7 -18 112311 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GAAGGCAGGAATCCCAGGCC;RSEQ=GTCAGCCCGGTGGAGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:4,6:0.2308:2,2:19:1:31:1:1:1.30472:38:6:0.2308:0:3.7 0/0:7:0:0,0:3,3:0:2,0:22.3:1:30:1:1:0:34:12:0.8571:0:5 -18 112324 . G A 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=CCAGGCCGGTCAGCCCGGTG;RSEQ=AGGGGGCGGGGCGGAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:7:0:28.5:1:0.46429:3.87:40:4:0.25:0:3 0/0:5:0:0,0:2,3:0:2,0:16.4:1:29.4:1:1:0:29:10:1:0:5.6 -18 112330 . G A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=CGGTCAGCCCGGTGGAGGGG;RSEQ=CGGGGCGGAGACACGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:2.8:1:31.3:1:1:0:40:8:1:0:4.3 1/0:4:2:1,1:0,2:0.5:0,2:12.5:1:27.5:1:1:0:22:4:0.5:0:6 -18 112336 . C G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCGGTGGAGGGGGCGGGG;RSEQ=GGAGACACGCCCCTCCGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:15.5:1:32:0:1:0:31:4:1:0:6 -18 112338 . G A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCGGTGGAGGGGGCGGGGCG;RSEQ=AGACACGCCCCTCCGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:13.5:1:31:0:1:0:31:4:1:0:6 -18 724180 . T C 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=TACCATGCTGTCACCCACAC;RSEQ=GTCATCAGTATCTTAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:21.7:1:29.1:1:1:0:60:8:1:0:0.3 1/0:3:2:1,1:1,0:0.6667:0,2:28:1:31:1:1:0:60:4:0.6667:0:1 -18 724330 . G A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02523;SOR=Inf;LSEQ=TACCATTAAAAACATGCAGA;RSEQ=TAAAGAAGATTTTCTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:105,7:0:2,0:25.7:1:32.4:1:1:0:60:224:1:0:0 0/1:105:5:4,1:91,9:0.0476:2,2:20.6:1:29.8:1:0.39996:2.49694:60:10:0.0476:0:1.8 -18 724360 . T C 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TTTTCTTCTTTTGATTCCTG;RSEQ=AGAAAATCTACACAAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:177,38:0:2,0:22.1:1:29.5:1:1:0:60:214:1:0:0.1 0/1:212:15:9,6:154,43:0.0708:2,2:19.7:1:31.1:1:0.11856:2.37596:60:14:0.0664:0:1.3 -18 724612 . A G 291 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCTCGCTCCACTTGTTCTA;RSEQ=TACTTCACGGTTCACCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:555:554:208,346:1,0:0.9982:0,2:25:1:32:1:0.37658:0:59.8:91.333:0.9982:0:1.1 1/1:537:537:213,324:0,0:1:0,2:24.4:1:31.3:1:1:0:59.9:133.25:1:0:1.1 -18 732812 . G C 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCACTCATGAGATAACCAA;RSEQ=AGCTATAAAATGCAAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:738:0:0,0:488,250:0:2,0:26.3:1:31.6:1:1:0:60:66.091:1:0:0.1 0/1:700:21:11,10:409,269:0.03:2,2:31:1:31.4:1:0.5019:1.38154:60:42:0.0304:0:1.2 -18 736907 . G A 150 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=16.35799;LSEQ=TACAAGAATATTAGCAGCCC;RSEQ=AAGATCTCGGTGAATATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:715:2:2,0:266,446:0.0028:2,0:1:0:26:1:0.14056:0:60:4:0.0028:0:1 0/1:797:35:15,20:314,448:0.0439:2,2:26.6:1:29.3:1:0.86204:1.07:59.3:70:0.0448:0:1.2 -18 739918 . AT A 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.75765;SOR=0.89802;LSEQ=ACAAAACTTCTTAGCTTTTC;RSEQ=TTTTTTTAAATTTTGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:47:0,47:1,46:0.5:1,1:24.9:1:31.4:1:1:0:60:94:0.5054:0.0532:0.1 0/1:74:35:3,32:0,39:0.473:1,2:24.1:1:30.2:1:0.10097:0:60:70:0.4795:0.0541:0 -18 742845 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.219;SOR=Inf;LSEQ=TAAATTAGAAAACAGTATAA;RSEQ=TCTATATGCATACAAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:151,11:0:2,0:22.4:1:32.7:1:1:0:60:324:1:0:0.6 0/1:143:2:1,1:128,13:0.014:2,2:14:1:28:1:0.18684:9.52499:60:4:0.0142:0:2 -18 742858 . C T 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02975;SOR=0.64585;LSEQ=AGTATAAGTCTATATGCATA;RSEQ=AAATCAAGACTCTTAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:122:103,19:74,7:0.601:2,2:23.5:1:30.5:1:0.1984:1.94405:60:244:0.601:0:1 0/1:209:103:83,20:90,16:0.4928:2,2:20.4:1:29.5:1:0.46571:1.35344:60:206:0.4952:0:1.1 -18 743226 . A G 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00046;SOR=0.68192;LSEQ=GCACTTTAATCCACAGCTAA;RSEQ=CAATGACAGAAAACAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:624:366:223,143:151,106:0.5865:2,2:24.8:1:31.9:1:0.61842:1.09:60:60:0.5844:0:1.1 0/1:777:382:229,153:235,159:0.4916:2,2:24.4:1:31.8:1:0.94174:1.01:60:94.5:0.4909:0:1.1 -18 743436 . T C 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01842;SOR=0.64418;LSEQ=CTAGATAAATGAATAAACTA;RSEQ=ACTGTAATATCAATTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:255:151:24,127:19,85:0.5922:2,2:24.4:1:32.3:1:0.61476:1.18205:60:302:0.5992:0:1 0/1:236:114:17,97:28,93:0.4831:2,2:23.6:1:31.2:1:0.13557:1.71395:60:56:0.4828:0:1.1 -18 745884 . A C 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAAAAATAAATACTTTCACT;RSEQ=TATCTTTCTCAAAATACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:0:0,0:200,236:0:2,0:23.2:1:29.8:1:1:0:60:108:1:0:0.1 0/1:381:24:10,14:189,168:0.063:2,2:17.9:1:31.5:1:0.29983:1.57311:60:48:0.0632:0:1.1 -18 745924 . A T 52 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02946;SOR=Inf;LSEQ=CCCCAAGAAATTTTATACTT;RSEQ=TACTAATATAACAATATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:208,180:0:2,0:25.9:1:29.4:1:1:0:60:54.429:1:0:0.1 0/1:381:5:0,5:212,164:0.0131:2,0:10.6:1:22.8:1:0.01661:0:60:4:0.0106:0:2.4 -18 746126 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49859;SOR=Inf;LSEQ=ACAGAAGTGTCAGTAAGAAT;RSEQ=GACTGGGATAGGTTTGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:7,104:0:2,0:25.7:1:30.9:1:1:0:60:36:0.9908:0:0 0/1:121:2:0,2:10,108:0.0165:2,0:10.5:1:26.5:1:1:0:60:4:0.0169:0:1.5 -18 747825 . A G 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0061;SOR=Inf;LSEQ=AGCTGTATTAAGACTGGTAT;RSEQ=TAATTCTGTGTGTGTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:104,1:0:1,0:26.4:1:28:1:1:0:60:34:1:0:0.2 0/1:101:7:7,0:91,3:0.0693:1,0:19.1:1:31.4:1:1:0:60:14:0.0693:0:1 -18 748360 . C CT 43 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTACTCAGTATTCTTTT;RSEQ=TTTTTTTTTTTTTTAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:21:1:27.3:1:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 751596 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50102;SOR=0;LSEQ=ATCGTTAAACACAGTGGGCA;RSEQ=CCCATGCCCTACCTCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:2,0:98,1:0.0198:1,0:26.5:1:31:1:1:0:60:4:0.02:0:1 0/0:85:0:0,0:83,2:0:1,0:23.9:1:31.8:1:1:0:60:41.5:1:0:0.1 -18 751858 . GA G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGCTAACTTAACAAAACA;RSEQ=AAAAAAGAACTATTGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:36,154:0:2,0:23.2:1:29.8:1:1:0:60:37:1:0:0.3 0/1:213:19:3,16:48,146:0.0892:2,2:24.9:1:31.5:1:0.57397:1.74937:60:38:0.0909:0:0 -18 751880 . C CA 154 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.00743;SOR=0.40331;LSEQ=AAAAAAGAACTATTGCCAGC;RSEQ=AAAAAAAAAAAAGCTTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:38:2,36:11,63:0.314:2,2:28.4:1:29.4:1:0.21263:3.11618:60:18:0.3103:0:0.3 0/1:103:16:1,15:11,70:0.1553:2,1:35.6:1:30.3:1:0.6838:2.34084:60:32:0.1616:0:0.7 -18 756282 . T TG 74 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTTCCCGGTGCCTACAG;RSEQ=GGGGGGGGGCTCAATAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:22.6:1:32.2:1:1:0:60:10:1:0.2:0.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 756505 . AC A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.2423;SOR=Inf;LSEQ=ACAAGCCTTAAGTATATATT;RSEQ=CCAAGGTGATGTTCTCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:166,14:0:2,0:21.5:1:31.8:1:1:0:60:89:1:0:0 0/1:175:2:1,1:152,21:0.0114:2,2:21.5:1:29.5:1:0.23626:7.09472:60:4:0.0117:0:0 -18 1784672 . A G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGATGAATGGGTTTCCCCCC;RSEQ=GAAAAACACACAAAGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:20.5:1:30:1:1:0:60:4:1:0:0 0/1:7:2:1,1:3,2:0.2857:2,2:14.5:1:28:1:1:1.41418:60:4:0.2857:0:1 -18 1785171 . C T 101 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00366;SOR=0;LSEQ=ATGATCACAATGTCTCTCCA;RSEQ=TGGGGCAGAGAACTGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:2,8:0,0:1:0,2:25.5:1:30.6:1:1:0:60:20:1:0:1 0/1:5:1:0,1:1,3:0.2:2,0:44:0:30:0:1:0:60:2:0.2:0:1 -18 2224625 . G A 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=ATGGTAAAATTTACTCATTA;RSEQ=GAATACGTTGAGGTCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:107,11:0:2,0:24.1:1:32.2:1:1:0:60:117:1:0:0.2 0/1:65:8:7,1:51,5:0.1231:2,2:13.1:1:30.9:1:0.56694:1.44757:60:16:0.1231:0:2 -18 2224631 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=4.06945;LSEQ=AAATTTACTCATTAGGAATA;RSEQ=GTTGAGGTCTTTTGGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:27:22,5:91,11:0.2093:2,2:22.6:1:30.3:1:0.32491:1.8698:60:26:0.2047:0:1 1/0:73:38:34,4:33,2:0.5205:2,2:20.5:1:29.8:1:0.67565:1.92416:60:76:0.5205:0:1.3 -18 2224638 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53468;SOR=0;LSEQ=CTCATTAGGAATACGTTGAG;RSEQ=TCTTTTGGGAAACAAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:134,19:0.0129:2,2:7.5:1:30:1:0.24214:6.8995:60:4:0.0129:0:1.5 0/0:89:0:0,0:76,13:0:2,0:20.8:1:31.2:1:1:0:60:88:1:0:0.6 -18 2224644 . TG T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.53025;SOR=0;LSEQ=AGGAATACGTTGAGGTCTTT;RSEQ=GGAAACAAAGCTAGTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:143,31:0.0114:2,2:8.5:1:30:1:0.33143:4.55612:60:4:0.0115:0.0057:1 0/0:105:0:0,0:84,20:0:2,0:21.4:1:31.7:1:1:0:60:208:0.9905:0:0.6 -18 2224646 . G T 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00245;SOR=Inf;LSEQ=GAATACGTTGAGGTCTTTTG;RSEQ=GAAACAAAGCTAGTAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:147,33:0:2,0:22.8:1:30.9:1:1:0:60:59:1:0:0.2 0/1:107:6:6,0:80,21:0.0561:2,0:12.5:1:29:1:0.59532:0:60:12:0.0566:0:1.8 -18 2224742 . T C 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTAGAAATCCATCCTTGA;RSEQ=GTAAACTACACTGGTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:242,262:0:2,0:28.5:1:30.2:1:1:0:60:35:1:0:0.2 0/1:403:95:49,46:154,154:0.2357:2,2:26.3:1:29.1:1:0.81515:1.07:60:30.667:0.2341:0:1.2 -18 2224790 . CT C 169 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.90134;SOR=0.94679;LSEQ=GGTGTAATTTTAAATGGGTT;RSEQ=TTTTTTTTTTAATTCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:41:15,26:86,178:0.1336:2,2:28.3:1:31.6:1:0.59785:1.19:59.8:82:0.1367:0.013:0.2 0/1:267:34:12,22:87,134:0.1273:2,2:25.8:1:30.6:1:0.70865:1.1895:60:33:0.1264:0.015:0.2 -18 2315063 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.46154;SOR=0;LSEQ=AATCAGATCCACAGTGTATT;RSEQ=TCTGTTCCGGTGGCCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:24.5:1:27.5:1:1:0:60:4:0.2857:0:1 0/0:7:0:0,0:6,1:0:2,0:17.7:1:30.9:1:1:0:60:14:1:0:0 -18 2547799 . A T 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCAGTAATTTTACTATT;RSEQ=ACAATATTTTTTTCTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:20.5:1:31.5:1:1:0:60:4:1:0:1 1/1:5:5:5,0:0,0:1:0,0:18.4:1:30.2:1:1:0:60:10:1:0:1.4 -18 2547832 . A G 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3007;SOR=0.22461;LSEQ=TCTCCAATTCAAAATTAAGC;RSEQ=AATATTGTTGTTTAGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:16.8:1:31.3:1:1:0:60:8:0.5:0:1 0/1:6:1:1,0:5,0:0.1667:0,0:43:0:30:0:1:0:60:2:0.1667:0:2 -18 2548101 . T C 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06086;SOR=1.24925;LSEQ=CCCACTGCATTTGCAACCCC;RSEQ=AATCTATCATCTTGCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:204:96,108:194,209:0.3355:2,2:24.5:1:31.7:1:0.86345:1.0442:60:408:0.3377:0:1.8 0/1:654:253:117,136:199,201:0.3869:2,2:26.8:1:30.2:1:0.42163:1.15058:60:62.25:0.3866:0:1.9 -18 2548128 . T C 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02304;SOR=1.3325;LSEQ=TCATCTTGCTTTTTGCCTTC;RSEQ=CAGTCAATTCCACTGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:175:74,101:168,204:0.3193:2,2:27.1:1:31:1:0.57993:1.12377:60:174:0.321:0:1.9 0/1:616:237:100,137:173,206:0.3847:2,2:25.7:1:30.1:1:0.40605:1.15027:59.9:38.5:0.385:0:2 -18 2548199 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49986;SOR=0;LSEQ=ACAAAATCTATAATCTTGTA;RSEQ=CTCCTGGCCATAGAGTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:37,150:0.0106:2,2:16.5:1:28:1:0.36255:4.01:60:4:0.0109:0:1.5 0/0:171:0:0,0:31,140:0:2,0:20.7:1:30.4:1:1:0:60:41.75:1:0:0.3 -18 2548202 . C A 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.14618;LSEQ=AAATCTATAATCTTGTACCT;RSEQ=CTGGCCATAGAGTATAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:2,0:29,143:0.0115:2,0:1:0:23:0:0.03089:0:60:4:0.0117:0:1.5 0/1:152:2:1,1:23,126:0.0132:2,2:9.5:1:26:1:0.29351:5.38:60:4:0.0137:0:1 -18 2548370 . C CA 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=CTATAACTCATCCACCTTTG;RSEQ=AAAAAAAAACCCTGTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:31:1:30.7:1:1:0:60:6:0.6:0:1 0/0:3:0:0,0:1,2:0:2,0:29:1:32.3:1:1:0:60:6:1:0:0 -18 3406566 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49776;SOR=Inf;LSEQ=TACGCACATTAATTCTTTTG;RSEQ=CAAGAATCTTGCCCTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:84,24:0:2,0:20.2:1:31.4:1:1:0:60:107:0.9907:0:0.2 0/1:111:2:1,1:90,19:0.018:2,2:19:1:31.5:1:0.32924:4.64251:60:4:0.0182:0:1 -18 3406591 . A G 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00487;SOR=0.31789;LSEQ=AATCTTGCCCTTGTTTGTTT;RSEQ=TGCAATGCCAACAGCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:23:14,9:108,65:0.1162:2,2:25.3:1:31.8:1:1:1.06777:58:46:0.1168:0:1.1 0/1:200:8:5,3:121,70:0.04:2,2:20.9:1:31.1:1:1:1.03698:57.1:16:0.04:0:1 -18 3406699 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24317;SOR=0;LSEQ=ACCCATTCCCTTGATGTCTA;RSEQ=AATGTCACCTTTCTTATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:44,80:0.0159:2,2:15:1:27.5:1:1:1.81:49:4:0.0161:0:1 0/0:129:0:0,0:37,92:0:2,0:22.7:1:31.9:1:1:0:50:258:1:0:0.1 -18 3406787 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21698;SOR=Inf;LSEQ=CCAGAGAACATATATCGGGT;RSEQ=CCTCTCCTCTTTCCTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:11,32:0:2,0:26.2:1:32:1:1:0:57.4:42:1:0:0.2 0/1:38:2:1,1:10,26:0.0526:2,2:39:1:30:1:0.50071:2.53:60:4:0.0541:0:1 -18 3406885 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16374;SOR=Inf;LSEQ=TTCTTTCTGCCATCTTCACT;RSEQ=ATCCAAAGGCAGGCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:31.3:1:32.1:1:1:0:60:22:1:0:0.1 0/1:8:2:1,1:1,5:0.25:2,2:5.5:1:28.5:1:0.46429:3.87:60:4:0.25:0:1 -18 4131501 . C G 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CTTTTCTAGAACAAAAGCAG;RSEQ=CACAGACAATACATAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:20.8:1:31.4:1:1:0:60:10:0.7143:0:1 0/0:2:0:0,0:2,0:0:0,0:24:1:30.5:1:1:0:60:4:1:0:0 -18 4459041 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CTCTAGTTACATCAAAATGG;RSEQ=GGCACTCCTAGACCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:21.8:1:31.3:1:1:0:60:8:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:17:1:29.5:1:1:0:60:4:1:0:1 -18 4459307 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2186;SOR=0;LSEQ=AATTGATATCATCTGATGGC;RSEQ=ATGAATTTATTGTAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:68,107:0.0113:2,2:29:1:30:1:1:1.57:57:4:0.0114:0:1 0/0:201:0:0,0:89,112:0:2,0:23.8:1:30.5:1:1:0:59.6:49.25:1:0:0.1 -18 4459310 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21708;SOR=0;LSEQ=TGATATCATCTGATGGCCAT;RSEQ=AATTTATTGTAAAAGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:65,101:0.0119:2,2:22:1:27.5:1:1:1.55:54.5:4:0.012:0:1 0/0:192:0:0,0:81,108:0:2,0:23.6:1:31.1:1:1:0:59.6:93.5:0.9842:0:0.1 -18 4459351 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23003;SOR=Inf;LSEQ=CATGCATTAACATCAGGCAC;RSEQ=ATAAAAGCCATGTTGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:20,63:0:2,0:23.7:1:31.1:1:1:0:58:166:1:0:0.2 0/1:77:2:1,1:22,53:0.026:2,2:30:1:28:1:0.51094:2.38:60:4:0.0263:0:1 -18 5090168 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52551;SOR=0;LSEQ=CCCCTTTCTAGGTCCTGTGA;RSEQ=AGCCATCTTGCTATTACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:12,17:0.0645:2,2:9.5:1:30:0:1:1.40:60:4:0.0645:0:1 0/0:18:0:0,0:9,9:0:2,0:17:1:31:1:1:0:59.8:36:1:0:0.2 -18 7023484 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11327;SOR=Inf;LSEQ=TCAGACGGACTCTGTTCCCT;RSEQ=AGATTTACTGTGAAAGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:58,10:0:2,0:25.2:1:31.8:1:1:0:60:67:1:0:0.2 0/1:35:2:1,1:26,7:0.0571:2,2:32:0:30.5:1:0.41008:3.5403:60:4:0.0571:0:1.5 -18 7023508 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16823;SOR=Inf;LSEQ=TTTACTGTGAAAGGGATATG;RSEQ=CTCCCCACTCGGGCATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:63,24:0:2,0:25.2:1:29.4:1:1:0:60:86:1:0:0.2 0/1:61:2:1,1:42,17:0.0328:2,2:23.5:1:30:1:0.50656:2.42941:60:4:0.0328:0:1 -18 7023556 . G C 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCACCTGTCGCGGTGAAG;RSEQ=GGGAGAGCATCCAAAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:109,84:0:2,0:21.8:1:31:1:1:0:60:95.5:0.9948:0:0.2 0/1:132:28:16,12:58,46:0.2121:2,2:30.4:1:30.7:1:1:1.06:60:56:0.2154:0:2.9 -18 7023565 . A G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=22.667;LSEQ=TCGCGGTGAAGGGGGAGAGC;RSEQ=TCCAAAATGAGGCATAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:10:6,4:114,88:0.0472:2,2:24.4:1:31:1:1:1.16:60:20:0.0472:0:1.6 1/0:143:76:43,33:37,30:0.5315:2,2:27.8:1:30.2:1:1:1.06:60:152:0.5352:0:2.4 -18 7023594 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=32.72263;LSEQ=GAGGCATAAATCCAGGGGAC;RSEQ=TGCACCTGTTTCCAGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:9:4,5:128,121:0.0349:2,2:27.6:1:30.9:1:0.74457:1.32088:60:18:0.035:0:1.7 1/0:182:99:55,44:45,37:0.544:2,2:25.7:1:30.5:1:1:1.03:60:198:0.55:0:2 -18 7023637 . T C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26571;SOR=0;LSEQ=TCTGACCCACCCCTGACCAC;RSEQ=CCGGATGCCGCACAGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:3:1,2:93,126:0.0135:2,2:12.7:1:25.7:1:1:1.4737:60:2:0.0097:0:2 0/0:163:0:0,0:79,84:0:2,0:25.8:1:28.9:1:1:0:60:31.6:1:0:0.7 -18 7023644 . GC G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50431;SOR=0;LSEQ=CACCCCTGACCACTCCGGAT;RSEQ=CGCACAGCCTCCTGCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:75,114:0.0105:2,2:13.5:1:31.5:1:1:1.52:60:4:0.0106:0:0.5 0/0:154:0:0,0:69,85:0:2,0:25:1:30.9:1:1:0:60:153:1:0:0.6 -18 7023652 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21799;SOR=Inf;LSEQ=ACCACTCCGGATGCCGCACA;RSEQ=CCTCCTGCAGGCTCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:59,98:0:2,0:24.6:1:31.3:1:1:0:60:38.25:1:0:0.3 0/1:138:2:1,1:59,77:0.0145:2,2:31.5:1:29.5:1:1:1.30:60:4:0.0147:0:1.5 -18 7023705 . C T 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47659;SOR=1.87746;LSEQ=AGACGCACACATAGGAAAGA;RSEQ=AGCACTGGCCTTCAGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:0,3:3,48:0.0556:2,0:15.3:1:29.3:1:1:0:60:6:0.0556:0:1.3 0/1:50:5:0,5:9,35:0.1:2,0:22.6:1:28:1:0.56866:0:60:10:0.102:0:2 -18 7023733 . G C 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=49.73235;LSEQ=GCCTTCAGGAGCCAGAAGAC;RSEQ=GCTACTAAAGCAAACCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:0,31:0.0313:1,0:5:0:30:0:1:0:60:2:0.0357:0:2 1/0:30:19:1,18:0,11:0.6333:0,1:24:1:28.9:1:1:0:60:18:0.6207:0:2 -18 7023748 . C A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGACGGCTACTAAAGCAAA;RSEQ=CACCTGTCATCTCCAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:0:1,0:24.7:1:30.7:1:1:0:60:22:1:0:0.1 1/0:21:14:1,13:0,7:0.6667:0,1:27.4:1:28.8:1:1:0:60:13:0.65:0:2.3 -18 7023987 . G A 25 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGCTAGGATTACAGGCACCC;RSEQ=CCGTCATGCCCGGCCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:17:0:14:0:1:0:40:0:0:0:7 1/1:2:2:1,1:0,0:1:0,2:19.5:1:25.5:1:1:0:60:4:1:0:1.5 -18 8412485 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20536;SOR=Inf;LSEQ=CCCCTCCCCTCTCCAACAGG;RSEQ=TCATCAACTCATATAAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:59,14:0:2,0:21.4:1:32.1:1:1:0:60:72:1:0:0 0/1:61:2:1,1:47,12:0.0328:2,2:23.5:1:27.5:1:0.38361:3.80283:60:4:0.0351:0:1 -18 8412561 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21311;SOR=Inf;LSEQ=TATGATTGAAGAGGCATACA;RSEQ=GACAAAATAAGGCCACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:130,84:0:2,0:28:1:30.8:1:1:0:60:52.5:1:0:0.1 0/1:184:2:1,1:110,72:0.0109:2,2:41.5:1:30:1:1:1.52412:60:4:0.011:0:2 -18 8412650 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17667;SOR=Inf;LSEQ=CCAAGTATAACTATGTTGTG;RSEQ=ACAATACTAACCATCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:189,82:0:2,0:25.3:1:31.3:1:1:0:60:134.5:1:0:0 0/1:197:2:1,1:114,81:0.0102:2,2:15.5:1:26.5:1:1:1.4049:60:4:0.0104:0:1.5 -18 8412855 . CAGA C 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0;SOR=2.20359;LSEQ=TCATGTTGGAGTTACTAGTT;RSEQ=AGAAGAAACAACTGGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:70:31,39:206,273:0.1275:2,2:27.7:1:31.3:1:0.89741:1.05:60:69:0.1273:0.0091:0.1 0/1:439:107:43,64:143,189:0.2437:2,2:25.8:1:31.4:1:0.65321:1.12582:59.9:214:0.2454:0.0205:0.1 -18 8413015 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07847;SOR=Inf;LSEQ=TAAAAGAGTGGAAGAAATGA;RSEQ=TGGCTTACACTCTCCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:172,194:0:2,0:24.5:1:31.9:1:1:0:60:72.2:1:0:0.1 0/1:275:3:1,2:133,139:0.0109:2,2:25.3:1:29:1:1:1.90933:60:6:0.011:0:1 -18 8413075 . C A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28002;SOR=0;LSEQ=TCAACTTGAAGCTCCTCCTG;RSEQ=ATCACACAGTAGTATTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:107,172:0.0106:2,2:6:1:21.3:1:0.56146:3.20:60:2:0.0072:0:1.7 0/0:186:0:0,0:72,114:0:2,0:24.2:1:31.4:1:1:0:60:45.5:1:0:0.2 -18 8413087 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.16731;SOR=Inf;LSEQ=TCCTCCTGCATCACACAGTA;RSEQ=TATTATGGATTCCACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:80,149:0:2,0:22.7:1:31.8:1:1:0:60:228:1:0:0.1 0/1:159:2:1,1:61,96:0.0126:2,2:22:1:28:1:1:1.57:60:4:0.0127:0:1.5 -18 8413097 . T A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69543;LSEQ=TCACACAGTAGTATTATGGA;RSEQ=TCCACAGAATATAGCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:60,122:0.0109:2,2:17:1:28.5:1:1:2.02:60:4:0.0112:0:1 0/0:132:1:1,0:46,85:0.0076:2,0:1:0:24:0:0.35606:0:60:2:0.0078:0:1 -18 8413099 . C T 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACACAGTAGTATTATGGATT;RSEQ=CACAGAATATAGCCAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:60,119:0:2,0:23.9:1:30.6:1:1:0:60:28.833:1:0:0.2 0/1:129:19:7,12:38,72:0.1473:2,2:27.1:1:28.3:1:1:1.10:60:38:0.1484:0:1.1 -18 8413193 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53226;SOR=0;LSEQ=TTAACATCAAAATTAAAATG;RSEQ=CCCACTGCTCATTTTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:78,67:0.0136:2,2:33.5:1:29:1:1:1.16297:60:4:0.0139:0:1 0/0:86:0:0,0:51,35:0:2,0:25.8:1:31.4:1:1:0:60:172:1:0:0.1 -18 8413202 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13449;SOR=Inf;LSEQ=AAATTAAAATGGCCCACTGC;RSEQ=CATTTTGAAGACCTGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:85,73:0:2,0:26.2:1:30.8:1:1:0:60:316:1:0:0.1 0/1:92:2:1,1:56,34:0.0217:2,2:8.5:1:28.5:1:1:1.63772:60:4:0.022:0:1.5 -18 8413255 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5159;SOR=0;LSEQ=TACAAGGTTGTCTCGTATCT;RSEQ=AGATGACAGTTGAACTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:87,82:0.0117:2,2:23:1:27:1:1:1.06064:60:4:0.0119:0:1 0/0:117:0:0,0:65,52:0:2,0:25.8:1:31.3:1:1:0:60:234:1:0:0.1 -18 8413300 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19435;SOR=Inf;LSEQ=ATTGGATGAACTTCAGAAAT;RSEQ=CTTGTCCAAGGTTACTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:64,65:0:2,0:25.7:1:32.4:1:1:0:60:258:1:0:0.1 0/1:103:2:2,0:46,54:0.0194:2,0:10:1:26:1:0.21899:0:60:4:0.0198:0:1.5 -18 8413344 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19591;SOR=Inf;LSEQ=AATCAATATGAACTTTAGCC;RSEQ=CATTATCATGCCCTAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:100,53:0:2,0:21.9:1:30.1:1:1:0:60:75.5:1:0:0.1 0/1:122:2:1,1:74,46:0.0164:2,2:13:1:27:1:1:1.60215:60:4:0.0164:0:1 -18 8413517 . G T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=7.46156;LSEQ=CATTACCGTGTGAATGAAAT;RSEQ=ACCTCAATTCCAAAATCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:90:53,37:287,204:0.1546:2,2:23.2:1:29.1:1:1:1.02:60:89:0.1556:0:1.1 1/0:431:249:158,91:119,63:0.5777:2,2:22.9:1:29:1:0.68555:1.08768:60:82:0.5748:0:1.1 -18 8413657 . G A 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GTCTAACAGGAGCGTGAGAA;RSEQ=AGGTGTTGAAGTGTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:39:21,18:266,342:0.0603:2,2:20.4:1:29.9:1:0.24612:1.50:60:38:0.0598:0:1.1 0/0:486:0:0,0:215,271:0:2,0:23.1:1:31.2:1:1:0:60:120.5:1:0:0.1 -18 8413804 . G A 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.89858;LSEQ=GTGCTGTGTTAAATTCAGCC;RSEQ=CTCTTCCAGATGCCATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:90:44,46:224,238:0.163:2,2:24.5:1:29.8:1:1:1.02:59.3:89:0.1657:0:1.1 0/1:540:195:89,106:155,190:0.3611:2,2:23.9:1:29.4:1:0.92831:1.03:59.9:194:0.3633:0:1.1 -18 8413833 . T C 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=Inf;LSEQ=GATGCCATTTGGCTTTTGGC;RSEQ=GTGCGGATCATTGTGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:245,276:0:2,0:22.5:1:30.3:1:1:0:60:56.889:1:0:0.2 0/1:433:11:4,7:187,234:0.0254:2,2:26.7:1:30.2:1:0.76167:1.39744:60:22:0.0255:0:1.1 -18 8413903 . G A 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.66145;LSEQ=AATCATGGTATTCAAAGGAC;RSEQ=CCAAAAAGCAGTCTCTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:117:66,51:280,277:0.1736:2,2:26.3:1:29.9:1:0.2631:1.28:60:38:0.1712:0:1.2 0/1:524:188:94,94:174,162:0.3588:2,2:26.9:1:29.6:1:0.71614:1.07392:60:187:0.3617:0:1.2 -18 8413996 . A G 274 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01432;LSEQ=AACACTGTGGAATGTAGGGA;RSEQ=ACTGTACTGCCTACATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:415:413:170,243:1,0:0.9952:0,2:23.6:1:31.6:1:0.41304:0:60:81.6:0.9976:0:1.1 1/0:308:230:101,129:36,42:0.7468:2,2:23.3:1:31.1:1:0.79235:1.09444:60:75.667:0.7467:0:1.2 -18 8414149 . T C 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTTTGCTAACTTTTAAGT;RSEQ=TGATACAGTCAAAAGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:242,258:0:2,0:26.1:1:30:1:1:0:60:61.5:0.998:0:0.1 0/1:460:17:9,8:237,206:0.037:2,2:30.2:1:30.2:1:1:1.02261:60:16:0.0354:0:1.3 -18 8414275 . A AG 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=GCTGATTGCTGCTAACAGTG;RSEQ=GGGTACAATTAAGGTGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:130,160:0:2,0:24.1:1:30.6:1:1:0:60:95.667:0.9965:0:0.3 0/1:241:12:5,7:99,130:0.0498:2,2:22:1:30.4:1:1:1.06589:60:24:0.0504:0.0124:0.1 -18 8414336 . TC T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26833;SOR=0;LSEQ=TCAACCCTAAATGTACTTGA;RSEQ=CTGCTGATATACCTCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:117,155:0.0109:2,2:9.3:1:28.9:1:1:1.50751:53:6:0.0111:0.0073:1.3 0/0:198:0:0,0:79,119:0:2,0:28.2:1:31:1:1:0:59.8:98:1:0:0.5 -18 8414345 . T A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05697;LSEQ=AATGTACTTGATCCTGCTGA;RSEQ=ATACCTCTGCAGCTGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:276:254:105,149:8,14:0.9203:2,2:24.1:1:29.9:1:0.82182:1.23:59:253:0.92:0:1.1 0/1:195:77:30,47:43,75:0.3949:2,2:28.8:1:29.8:1:0.76319:1.11:59.4:76:0.3958:0:1.1 -18 8414713 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAAATTATGTAGGTTA;RSEQ=AACATGCAGAAGTACAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 8785010 . G GT 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTCTTGGTTGGGCTCC;RSEQ=TTTTTTTTGTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:26.5:1:29:1:0.33333:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 8785069 . C T 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTGTTTCTTTTTCCTTT;RSEQ=TCCTGTCTTATTTTTAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:19:1:30:1:1:0:60:8:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 8786031 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=CGCGCGGGAGCTGCACCGCC;RSEQ=CGCAGACGGGGACACCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:22.1:1:27:1:1:0:60:6:1:0:0.1 1/0:3:2:2,0:0,1:0.6667:0,0:18.5:1:28.5:1:0.33333:0:60:4:0.6667:0:1.5 -18 8786053 . C T 43 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02064;SOR=Inf;LSEQ=GCAGACGGGGACACCGGGAG;RSEQ=CACGGGCTGGGAGGCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,5:0:2,0:25.5:1:30.8:1:1:0:60:24:1:0:0.1 1/0:6:3:1,2:2,1:0.5:2,2:15.3:1:27.3:1:1:3.10575:60:6:0.5:0:1.3 -18 8786117 . C CCCA 48 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAAGCAATCCCCCCCC;RSEQ=CCGCCCTCCCCCTCCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:6,3:0.2143:2,0:36:1:30.8:1:0.18182:0:60:6:0.2308:0:0 0/0:4:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 9708049 . CGGGGCCGGGA C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCGGGCCCTGCGGCCAGG;RSEQ=GGGGCGGATGCCGGAGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 9708081 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGGATGCCGGAGGGCGC;RSEQ=GGGGGAGGCCGACCCGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 9708582 . C T 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.1009;SOR=Inf;LSEQ=CCCCGTCCCCCTCGTCCGCG;RSEQ=GCCCCCTGGTTCCCCGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:4,1:0.5:2,2:23.4:1:30.4:1:1:1:60:10:0.5:0:1 1/1:5:5:4,1:0,0:1:0,2:18.8:1:28:1:1:0:60:10:1:0:1 -18 9709183 . A G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAGCAGCCAGAAACAAA;RSEQ=AAGCAGTCAATCCGTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:32.5:1:1:0:60:4:1:0:1 -18 9924309 . G T 50 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGTTTCTATTTTAATCAA;RSEQ=ATGTTAAATTATTAGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:12.3:1:32:1:1:0:60:6:0.5:0:1 1/1:1:1:1,0:0,0:1:0,0:36:0:27:0:1:0:60:2:1:0:1 -18 9924504 . T C 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06671;SOR=Inf;LSEQ=GTTAAGACTATTGTTTATTT;RSEQ=CTCTGCCTTGTTTTCAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:147,45:0:2,0:21.6:1:29.6:1:1:0:60:23:1:0:0.1 0/1:132:3:2,1:96,33:0.0227:2,2:15.7:1:29:1:1:1.45008:60:6:0.0229:0:1 -18 9924617 . G A 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00237;SOR=1.52712;LSEQ=CGTTTAAGGTAGTTTTTTAA;RSEQ=ATGAAATGTCAATAAAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:160:78,82:109,146:0.3846:2,2:26.1:1:30.3:1:0.26497:1.27:60:320:0.3865:0:1.1 0/1:434:212:97,115:103,119:0.4885:2,2:24.5:1:29.9:1:0.92341:1.02611:60:69.667:0.4883:0:1.1 -18 10004711 . T TTA 80 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=0.00078;SOR=Inf;LSEQ=TAGCAATAACCTTTCATCCT;RSEQ=TATATATATATATATATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:9,31:0:2,0:23.6:1:29.4:1:1:0:60:19:0.9744:0:0 0/1:32:8:1,7:4,18:0.25:2,2:29.8:1:26.8:1:1:1.53446:60:16:0.2581:0.0313:0 -18 10004836 . A C 57 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTGTCTGGACCAGAAAA;RSEQ=ATATATTATAGTAATGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:18.3:1:28.5:1:1:0:60:3:1:0:1.3 1/1:1:1:0,1:0,0:1:0,0:11:0:33:0:1:0:60:2:1:0:1 -18 10054446 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50136;SOR=0;LSEQ=GAACTGCCATTTCACAAGGA;RSEQ=TTGATATGGAAGGTGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:18,26:0.0435:2,2:31.5:1:31.5:1:1:1.43:60:4:0.0444:0:1 0/0:36:0:0,0:17,19:0:2,0:30.6:1:29.4:1:1:0:60:35:1:0:0.2 -18 10054466 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16517;SOR=Inf;LSEQ=ATTGATATGGAAGGTGAGAG;RSEQ=AGGAGTCAGCGTTTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:19,27:0:2,0:32.5:1:31:1:1:0:60:45:1:0:0.2 0/1:32:2:1,1:12,18:0.0625:2,2:34:1:28:1:1:1.48:60:4:0.0714:0:1 -18 10054484 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51213;SOR=0;LSEQ=AGGAGGAGTCAGCGTTTCCC;RSEQ=GGTTTTCCTGCCTTTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:15,26:0.0465:2,2:19.5:1:31:1:1:1.71:60:4:0.0465:0:1 0/0:29:0:0,0:10,19:0:2,0:22.2:1:29.7:1:1:0:60:28:1:0:0.3 -18 10056249 . G A 25 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGAGTGACAGTGAAAT;RSEQ=TAAGTAGAAAAAAAAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:25:0:1:0:60:4:1:0:1 -18 10151780 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51643;SOR=0;LSEQ=GCCTTTAGTGTATGGGCCTG;RSEQ=CCAGACCAGCACATGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:126,31:0.0126:2,2:10:1:26.5:1:0.36303:4.01635:60:4:0.0127:0:1 0/0:108:0:0,0:77,31:0:2,0:23:1:31.3:1:1:0:60:53:1:0:0.1 -18 10151807 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1979;SOR=Inf;LSEQ=CAGCACATGGGCATCTGTTT;RSEQ=CCAGGAAAAACCCAGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:149,73:0:2,0:25.7:1:31:1:1:0:60:110:0.991:0:0.1 0/1:180:2:1,1:113,65:0.0111:2,2:40:0:30.5:1:1:1.73277:60:4:0.0112:0:1 -18 10151838 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09807;SOR=Inf;LSEQ=CCCAGCAGTGGCTGTGGTGG;RSEQ=TGGATGTGGGATTGGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:185,134:0:2,0:25.1:1:32:1:1:0:59.9:105.333:1:0:0.2 0/1:274:3:1,2:156,115:0.0109:2,2:12:1:27.7:1:0.57748:2.70324:60:6:0.0111:0:2 -18 10151860 . A T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09271;SOR=Inf;LSEQ=GGATGTGGGATTGGATGGGC;RSEQ=CACAGAAAAACATAAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:190,168:0:2,0:24.4:1:30:1:1:0:59.9:178:1:0:0.3 0/1:297:3:1,2:165,129:0.0101:2,2:20:1:22.7:1:0.58494:2.55019:60:2:0.0068:0:1.3 -18 10151888 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.88115;LSEQ=AAACATAAAAACCATGGCAA;RSEQ=AGTAATCATAATAGTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:87:42,45:151,165:0.2153:2,2:21.2:1:29.1:1:1:1.02:60:42.5:0.2141:0:1.2 0/1:353:156:77,79:102,95:0.4419:2,2:25.3:1:28.1:1:0.66929:1.10127:60:51:0.4461:0:1.2 -18 10151994 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52723;SOR=0;LSEQ=TTTTTCTTAATGTCCTAGAT;RSEQ=GAACAGGATGATTGGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:32,115:0.0134:2,2:26.5:1:28.5:1:0.39507:3.55:60:4:0.0135:0:1 0/0:91:0:0,0:21,70:0:2,0:3:0:14:0:1:0:60:0:0:0:4 -18 10152122 . C CT 59 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0.7602;LSEQ=GCAACATTAGACTTTCTGGA;RSEQ=TTTTTTTTTTTTCTGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:0,9:0.3077:0,0:28.8:1:29.9:1:1:0:60:8:0.3333:0.0769:0 0/1:8:2:0,2:0,6:0.25:0,0:25.5:1:28:1:1:0:60:4:0.25:0:1 -18 10451547 . T C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04413;SOR=Inf;LSEQ=AATAGAGCGTTCTACTACTC;RSEQ=GTACTCACTAAAAATCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:67,8:0:2,0:22.1:1:31:1:1:0:60:74:1:0:0 0/1:42:3:2,1:32,7:0.0714:2,2:32:1:30.7:1:0.47875:2.23132:60:6:0.0714:0:1 -18 10451595 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57955;SOR=2.65705;LSEQ=CTAAGAAAATCAAGCTAAGG;RSEQ=GATCACCCAAGCTCTACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:1:1,0:116,36:0.0065:2,0:31:0:32:0:1:0:60:2:0.0065:0:1 0/1:116:2:1,1:83,31:0.0172:2,2:13.5:1:30:1:0.47736:2.65108:60:4:0.0174:0:1 -18 10451695 . A G 242 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAAGACAGGCGATTATAGA;RSEQ=GCTCATAGGGCAACTGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:0:0,0:223,189:0:2,0:25.7:1:30.6:1:1:0:60:81.4:1:0:0.1 1/0:405:237:119,118:88,79:0.5852:2,2:26.7:1:30.7:1:0.68612:1.10429:60:46.4:0.5873:0:1.2 -18 10451751 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21508;SOR=4.06854;LSEQ=GCTTGGTAGACACGTGACAG;RSEQ=CCTCGTGAGTTGGTAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:1,0:129,190:0.0031:2,0:1:0:26:0:0.40625:0:60:2:0.0032:0:1 0/1:317:4:3,1:132,181:0.0126:2,2:12.8:1:27:1:0.31596:4.10:60:8:0.0129:0:1 -18 10451769 . T A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10485;SOR=Inf;LSEQ=AGGCCTCGTGAGTTGGTAAC;RSEQ=GAACAAATCACAGGCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:94,166:0:2,0:24.8:1:30:1:1:0:60:64:1:0:0.1 0/1:233:3:2,1:87,143:0.0129:2,2:14.3:1:27:1:0.55969:3.27:60:6:0.0132:0:3 -18 10451796 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17021;SOR=Inf;LSEQ=ATCACAGGCGTTCCAAGAGG;RSEQ=GATGTGTTGTGTGGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:33,140:0:2,0:24.8:1:29.7:1:1:0:60:42.25:1:0:0.1 0/1:122:2:1,1:33,87:0.0164:2,2:22.5:1:29.5:1:0.48137:2.61:60:4:0.0165:0:1 -18 10451813 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14365;SOR=Inf;LSEQ=AGGCGATGTGTTGTGTGGCT;RSEQ=GGAACTTAGCTCCTTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:18,126:0:2,0:23.6:1:31.1:1:1:0:60:143:0.9931:0:0.1 0/1:89:2:0,2:14,73:0.0225:2,0:12.5:1:30:1:1:0:60:4:0.0227:0:1 -18 11751952 . T A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACCCCGGTGGCGCGCTC;RSEQ=GTCCTCCGCGCCACGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 11752482 . A T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78892;LSEQ=GACGGAAGACCAGGGCGTCG;RSEQ=TGAAAAAGAACGACGCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:0,2:57,46:0.019:2,0:1:0:25:1:0.20659:0:60:4:0.0196:0:1.5 0/1:199:3:1,2:101,95:0.0151:2,2:13:1:21.7:1:0.61378:2.11852:60:2:0.0104:0:3.3 -18 11752554 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49812;SOR=Inf;LSEQ=AGAGCGCCTGGCTTACAAGG;RSEQ=TACCCACCGCCTGCTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:39,77:0:2,0:29.1:1:32.3:1:1:0:60:232:1:0:0.1 0/1:122:2:1,1:40,80:0.0164:2,2:28:0:31.5:1:1:1.99:60:4:0.0168:0:1.5 -18 11879931 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGCCGCTGCACCGTCCA;RSEQ=TACAGAACCACTGGGCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 11881026 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50267;SOR=Inf;LSEQ=GGTGACGGCAAACATTACTG;RSEQ=TACCCGCACTTCACCTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:57,31:0:2,0:25.8:1:31.8:1:1:0:60:176:1:0:0.1 0/1:108:2:1,1:61,45:0.0185:2,2:44:1:28:1:1:1.35167:60:4:0.0187:0:1 -18 11881069 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50187;SOR=Inf;LSEQ=TGGACACAGAGAACATCCGC;RSEQ=GGGTGTTCAACGACTGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:49,58:0:2,0:25.1:1:30.7:1:1:0:60:214:1:0:0.1 0/1:128:2:1,1:58,68:0.0156:2,2:21.5:1:29:1:1:1.17:60:4:0.0163:0:1.5 -18 11881080 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50073;SOR=Inf;LSEQ=AACATCCGCAGGGTGTTCAA;RSEQ=GACTGCCGCGACATCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:44,57:0:2,0:24.3:1:29.9:1:1:0:60:32.667:1:0:0.2 0/1:118:2:1,1:53,63:0.0169:2,2:18.5:1:27.5:1:1:1.19:60:4:0.0172:0:1 -18 11881085 . G A 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60297;SOR=0.4431;LSEQ=CCGCAGGGTGTTCAACGACT;RSEQ=CCGCGACATCATCCAGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:41,57:0.02:2,2:19:1:27:1:1:1.39:60:4:0.02:0:1 0/0:112:1:1,0:48,63:0.0089:2,0:1:0:23:0:0.4375:0:60:2:0.009:0:1 -18 11881113 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25513;SOR=Inf;LSEQ=ATCATCCAGCGGATGCACCT;RSEQ=AAGCAGTATGAGCTCTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:20,39:0:2,0:29:1:31.2:1:1:0:60:28.5:1:0:0.2 0/1:75:3:2,1:26,46:0.04:2,2:14.3:1:27.3:1:0.55175:3.48:60:6:0.0405:0:1 -18 11881143 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49333;SOR=0;LSEQ=GAGCTCTTGTGAGGATGCTG;RSEQ=CGCCACCCTGCGACGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:5,31:0.0526:2,2:11:0:31.5:1:0.29445:5.75:60:4:0.0526:0:1.5 0/0:37:0:0,0:9,28:0:2,0:22.4:1:30.5:1:1:0:60:36:1:0:0.2 -18 12101808 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTCACAATTTCTTAGTC;RSEQ=TAATTCCTCTCAAACCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1:0,2:16.3:1:30.8:1:1:0:60:20:1:0:1 1/1:2:2:1,1:0,0:1:0,2:40:1:31.5:1:1:0:60:4:1:0:1 -18 12102156 . G C 317 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00279;LSEQ=TAACAACTTGTCCAAGGCCC;RSEQ=AGTAACTATGAAGAGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1160:1158:560,598:0,0:0.9983:0,2:26:1:31.2:1:1:0:59.7:63.333:0.9982:0:1.2 1/0:906:559:273,286:170,174:0.617:2,2:25.9:1:30.7:1:0.89105:1.02352:59.7:138.75:0.6194:0:1.5 -18 12102188 . G T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=5.68261;LSEQ=AGAGTGAGGGTTGCAGCAAG;RSEQ=AGTAGAGTCCGTCACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:86:38,48:357,474:0.0938:2,2:18.2:1:28.8:1:0.82029:1.05:60:172:0.0952:0:1.7 0/1:734:272:126,146:224,237:0.3706:2,2:22.9:1:28.4:1:0.59225:1.09503:60:271:0.3717:0:1.8 -18 12102407 . G A 236 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGTGTGACCACTGGGGTTC;RSEQ=CAGCAACAGAGCTCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:247:247:137,110:0,0:1:0,2:23.7:1:29.7:1:1:0:60:48.4:1:0:1.1 1/0:194:118:66,52:42,34:0.6082:2,2:22.7:1:29.5:1:1:1.03:60:236:0.6114:0:1.1 -18 12325864 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.6;SOR=2.25968;LSEQ=CGTGTGCGACATCCCGCCCC;RSEQ=CGGCCTGAAGATGGCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:1,0:12,11:0.0417:2,0:1:0:26:0:1:0:60:2:0.0455:0:1 0/1:22:2:1,1:9,11:0.0909:2,2:40.5:1:30.5:1:1:1.21:60:4:0.0909:0:1 -18 12911159 . C G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCGGGCCGCACTGCTG;RSEQ=CGCGTCTAGCCGCCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:33.5:1:1:0:60:4:1:0:2 -18 12911214 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCTCGCCCCCGGGACTT;RSEQ=CCAGCAGCGAGTGGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:28:1:1:0:60:4:1:0:2 -18 12912750 . C T 86 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01884;SOR=0;LSEQ=TGTTGGATCAGGAACTGTGT;RSEQ=TGCTCTTAAGTGCTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:7:7,0:95,2:0.0673:1,0:25.6:1:30.9:1:1:0:60:14:0.0686:0:1.4 0/0:81:0:0,0:80,1:0:1,0:24:1:31.5:1:1:0:60:80:1:0:0 -18 12912821 . G C 139 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTCTTTTCAGTTGGGTGTT;RSEQ=AGTGGTTTTCCAGATCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:22:18,4:308,90:0.0524:2,2:22.7:1:31.2:1:0.79529:1.31:60:44:0.0531:0:1.3 0/0:399:0:0,0:293,105:0:2,0:22.4:1:31:1:1:0:60:78.6:0.9975:0:0.1 -18 12912932 . T C 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCAACTGGGATGAGATTG;RSEQ=TGATAACTTTGATGATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:0:0,0:381,420:0:2,0:25.1:1:29.9:1:1:0:60:159.2:1:0:0.1 0/1:806:30:13,17:352,423:0.0372:2,2:20:1:32.1:1:0.85405:1.08812:59.8:60:0.0377:0:1.2 -18 12913743 . T C 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTATGATCCACCTACCAA;RSEQ=TGTGAAAACAACATTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:204,210:0:2,0:22.1:1:30.4:1:1:0:60:102.5:1:0:0.1 0/1:406:20:15,5:208,178:0.0493:2,2:19:1:31:1:0.06948:2.56:60:40:0.05:0:1 -18 13910706 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52962;SOR=0;LSEQ=GGTCCCTGGTCTAGTCCTGG;RSEQ=TGGGCTGAGGCTGCTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:99,79:0.0111:2,2:20:1:29:1:1:1.25157:60:4:0.0111:0:2 0/0:108:0:0,0:64,44:0:2,0:24.4:1:31.9:1:1:0:60:35:1:0:0.5 -18 13910713 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52974;SOR=0;LSEQ=GGTCTAGTCCTGGCTGGGCT;RSEQ=AGGCTGCTCCAGTTACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:103,90:0.0103:2,2:27.5:1:28:1:1:1.14365:60:4:0.0104:0:1.5 0/0:117:0:0,0:65,52:0:2,0:23.4:1:31.4:1:1:0:60:234:1:0:0.5 -18 13910730 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18911;LSEQ=GCTGAGGCTGCTCCAGTTAC;RSEQ=CTCAGCACTAGGGCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:202:172:85,87:13,17:0.8515:2,2:28.7:1:30.5:1:0.5595:1.28:60:56.333:0.8492:0:1.1 1/0:133:69:36,33:35,28:0.5188:2,2:23.9:1:30:1:0.72925:1.14465:60:33.5:0.5115:0:1.1 -18 13912411 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGTTATTCCAAAGAGCC;RSEQ=GAGAGGCTGAGTGTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28.5:1:1:0:60:4:1:0:1.5 -18 14152836 . C A 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5579;SOR=0;LSEQ=CACTTTTTTTACAGTTAAAA;RSEQ=AAGAAATTCTAATAATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:4,0:29,0:0.1212:1,0:14.3:1:28:1:1:0:60:8:0.1212:0:1 0/0:11:0:0,0:10,1:0:2,0:20.7:1:31.8:1:1:0:51.1:22:1:0:0 -18 14152953 . A G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=0.35039;LSEQ=TTCAAGACAAAAAATACAAA;RSEQ=TAAAATTTAAAAGTTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:152:123,29:77,11:0.6333:2,2:20.9:1:31.9:1:0.21199:1.64713:45.3:75:0.6329:0:1.1 0/1:178:67:55,12:81,30:0.3764:2,2:22.7:1:31.4:1:0.20323:1.69:45.8:66:0.375:0:1 -18 14152987 . T G 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00575;SOR=1.48744;LSEQ=TTGAATTTAAAAAATAAAAG;RSEQ=ACATATACCTAATCTCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:197:131,66:182,97:0.413:2,2:23.2:1:31:1:0.84457:1.06:43.5:64.667:0.4128:0:1.1 1/0:348:178:112,66:111,58:0.5115:2,2:26.9:1:30.5:1:0.65417:1.12738:44:88:0.5116:0:1.1 -18 14154854 . A AC 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTCTGACCTTATGATCC;RSEQ=CCACCTCAGCCTCCCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:41.3:1:31.7:1:1:0:51.3:6:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 14156143 . A G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTATCAAATATAATCACC;RSEQ=TGGAGAAATTTTCCTATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:16.9:1:31.1:1:1:0:27.5:26:1:0:1.1 1/1:4:4:4,0:0,0:1:0,0:8.5:1:29.3:1:1:0:30:8:1:0:1.3 -18 14156233 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50226;SOR=0;LSEQ=AAAGAAATATGCAAAGAAAA;RSEQ=AATGAAAATTTTTTTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:143,35:0.011:2,2:37:1:32:1:0.36089:4.04263:51.5:4:0.0114:0:2 0/0:153:0:0,0:122,31:0:2,0:20.8:1:28.9:1:1:0:42.4:24.5:1:0:1.2 -18 14156241 . A T 232 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.49729;SOR=0.71439;LSEQ=ATGCAAAGAAAATAATGAAA;RSEQ=TTTTTTTTTTTAGTAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:197:188:150,38:1,0:0.9543:0,2:25.1:1:30.8:1:1:0:43.6:93:0.9947:0:1.3 1/1:175:164:124,40:2,0:0.9371:0,2:22.9:1:29.9:1:1:0:41.9:81:0.9818:0:1.2 -18 14156368 . G GA 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.22411;SOR=4.34197;LSEQ=CAGGAAGATCTATAGAAAAA;RSEQ=AAAAAAAAGCAGATTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:1:0,1:45,177:0.0045:2,0:43:0:32:0:1:0:49:2:0.0045:0:0 0/1:260:5:2,3:71,183:0.0192:2,2:18.8:1:30.4:1:0.62276:1.71:47.2:10:0.0195:0.0038:0.2 -18 14156556 . G C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19547;SOR=Inf;LSEQ=CTAGTCTTTCCGTTTATAAA;RSEQ=GATAATGGCATCAGTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:129,18:0:2,0:24.1:1:32.1:1:1:0:56.9:294:1:0:0 0/1:117:2:1,1:97,18:0.0171:2,2:19:0:31:1:0.29959:5.27224:24.5:4:0.0172:0:1.5 -18 14156807 . A G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ATATGTAATAACATCAACAC;RSEQ=TTATCCATATAGATGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:56,225:0:2,0:22.4:1:30.4:1:1:0:45:45.833:1:0:0.1 0/1:223:13:4,9:56,153:0.0583:2,2:17.5:1:26.7:1:0.75236:1.21:47.2:5.5:0.0507:0:1.2 -18 14157291 . A T 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00099;SOR=1.63629;LSEQ=GAACTTTTTGTCAGCTGCCT;RSEQ=CTTCCTCCGTGGCCAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:194:48,146:68,135:0.4874:2,2:24.9:1:30.2:1:0.06094:1.53042:59.4:388:0.4899:0:1.2 1/0:358:218:67,151:54,86:0.6089:2,2:23.2:1:29:1:0.13747:1.4137:59.6:108:0.6085:0:1.3 -18 14157373 . T A 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATAGCGATAAGATAAT;RSEQ=TATGAAGTTTCTTCTATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:161:161:30,131:0,0:1:0,2:23.5:1:30.4:1:1:0:52.7:160:1:0:1.2 1/1:136:136:40,96:0,0:1:0,2:22.7:1:29.1:1:1:0:55.3:135:1:0:1.3 -18 14157521 . TA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTAAATGTTTCTCAAAT;RSEQ=AAAAAAAATCTTTTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:0,2:0,13:0.1333:1,0:28.5:1:30.5:1:1:0:55.5:4:0.1333:0:0 0/0:7:0:0,0:1,6:0:2,0:12.7:1:29.9:1:1:0:53.3:14:1:0:0 -18 18510913 . C A 61 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=NNNNNNGAATTCATTGGAAA;RSEQ=GGGAATATCTTCATATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:1,0:0.8:0,2:8:0:30.5:1:1:0:37:8:0.8:0:5 -18 18510923 . T G 78 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTGGAAACGGGAATATC;RSEQ=TCATATAAAATCTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:6:3,3:2,1:0.6667:2,2:15.3:1:30.2:1:1:1.8525:31.7:12:0.6667:0:5.3 -18 18510929 . T C 81 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACGGGAATATCTTCATA;RSEQ=AAAATCTAGACAGAGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:6:3,3:2,1:0.6667:2,2:21.3:1:31.5:1:1:1.8525:31.7:12:0.6667:0:5.3 -18 18510937 . A G 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATCTTCATATAAAATCT;RSEQ=GACAGAGGCATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:4,3:0.2222:2,2:24:0:30:1:1:1.29098:21:4:0.2222:0:6 -18 18510944 . G A 94 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATATAAAATCTAGACAGA;RSEQ=GCATTCTCAGAAACTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:10:8:4,4:1,1:0.8:2,2:34:1:31.5:1:1:1:28.8:16:0.8:0:4.5 -18 18510954 . G C 82 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGACAGAGGCATTCTCA;RSEQ=AAACTTCTTTGTGATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:6:3,3:2,2:0.6:2,2:33:0:32:1:1:1:31.7:12:0.6:0:5.3 -18 18510961 . C A 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGCATTCTCAGAAACTT;RSEQ=TTTGTGATGTGTGTCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:4,4:0.2:2,2:26:0:30:1:1:1:20:4:0.2:0:2 -18 18511035 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTTGGAAACACTCTTTTT;RSEQ=TAGAATCTGCCAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:34:0:1:0:37:2:1:0:6 1/0:3:2:2,0:0,1:0.6667:0,0:25.5:1:28:1:0.33333:0:36.5:4:0.6667:0:6.5 -18 18511046 . C A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTTTTTGTAGAATCTGC;RSEQ=AGTGGATATTTGCATAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:40:0:32:0:1:0:37:2:1:0:6 1/1:3:3:3,0:0,0:1:0,0:19.7:1:30:1:1:0:33.3:6:1:0:6.7 -18 18511055 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAGAATCTGCCAGTGGATA;RSEQ=TTGCATAGCTCTAATGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:49:0:33:0:1:0:37:2:1:0:6 1/0:3:2:2,0:1,0:0.6667:0,0:29:1:30.5:1:1:0:36.5:4:0.6667:0:6.5 -18 18511059 . C G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGCCAGTGGATATTTG;RSEQ=ATAGCTCTAATGATTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:30.5:1:1:0:37:4:1:0:5 1/1:3:3:3,0:0,0:1:0,0:24:1:30.7:1:1:0:33.3:6:1:0:6.7 -18 18511070 . T C 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77722;LSEQ=GGATATTTGCATAGCTCTAA;RSEQ=GATTTCTTTGGAAACGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,0:0.4:0,0:6.5:1:31.5:1:1:0:50:4:0.4:0:8 0/1:3:1:1,0:0,0:0.3333:0,0:25:0:33:0:1:0:27:2:0.3333:0:7 -18 18511077 . T G 85 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=TGCATAGCTCTAATGATTTC;RSEQ=TTGGAAACGGGAATACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:5,2:0,0:1:0,2:13.7:1:30.3:1:1:0:43.6:14:1:0:6.1 1/0:4:3:2,1:1,0:0.75:0,2:17.3:1:29.3:1:1:0:45:6:0.75:0:3.7 -18 18511079 . T A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=CATAGCTCTAATGATTTCTT;RSEQ=GGAAACGGGAATACCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:25.5:1:28.5:1:1:3.1622:37:4:0.2857:0:5 0/0:4:0:0,0:3,1:0:2,0:22:1:30:1:1:0:40.5:8:1:0:4.5 -18 18511097 . CATATA AGTAT 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=TTTGGAAACGGGAATACCTT;RSEQ=AAATCTAGACAGAGGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:28:1:30.4:1:1:0:43.6:6:1:0:6 0/1:5:2:1,1:2,1:0.4:2,2:21:1:27.5:1:1:1.7321:27:4:0.4:0.2:7 -18 18511112 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=ACCTTCATATAAAATCTAGA;RSEQ=AGAGGCACTCTCAGAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:43.7:1:30:1:1:0:44.7:5:1:0:6 0/1:5:2:1,1:2,1:0.4:2,2:20:1:31:1:1:1.7321:27:4:0.4:0:7.5 -18 18511115 . A T 68 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24242;SOR=0.16477;LSEQ=TTCATATAAAATCTAGACAG;RSEQ=GGCACTCTCAGAAACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:0,1:0.8333:0,2:45.2:1:29.6:1:0.33333:0:46.2:10:0.8333:0:6.4 0/1:5:2:1,1:1,2:0.4:2,2:21:0:30:1:1:1.73:51:4:0.4:0:2 -18 18511155 . T C 69 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TTGTGATATCTGCATTCAAG;RSEQ=CACACAGTTCAACATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:0,1:0.8333:0,2:11.4:1:29.8:1:0.33333:0:46.2:10:0.8333:0:6.4 0/0:2:0:0,0:0,2:0:0,0:43.5:1:31:0:1:0:33.5:4:1:0:7 -18 18511160 . C G 69 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATCTGCATTCAAGTCACA;RSEQ=AGTTCAACATTCCCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:6.4:1:30:1:1:0:46.2:10:1:0:6.4 1/1:2:2:0,2:0,0:1:0,0:43.5:1:33:0:1:0:33.5:4:1:0:7 -18 18511165 . C G 59 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATTCAAGTCACACAGTT;RSEQ=AACATTCCCTTTCTTAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:2.8:1:29.5:1:1:0:43.5:8:1:0:6.3 1/1:2:2:0,2:0,0:1:0,0:43:1:33:0:1:0:33.5:4:1:0:7 -18 18511178 . C A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACAGTTCAACATTCCCTTT;RSEQ=TTAGAGCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:10:0:27:0:1:0:57:2:1:0:8 1/1:2:2:0,2:0,0:1:0,0:30:1:32:0:1:0:33.5:4:1:0:7 -18 18511239 . G T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGACATTTGGAGCGCTTT;RSEQ=ACGCCTTTGGTGATAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:29:0:32:0:1:0:57:2:1:0:8 0/1:5:2:1,1:1,2:0.4:2,2:21.5:1:28:1:1:1.73:60:4:0.4:0:2.5 -18 18511283 . A C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTCACATAAAAACTAGA;RSEQ=AGAAGCATTCTAAGAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:32.5:1:1:0:60:4:1:0:2.5 -18 18511426 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCAGGATTTCGTTGGAA;RSEQ=CGGGATTACAAACAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:42:0:31.5:1:1:2.44949:39:4:0.3333:0:7.5 -18 18511432 . T A 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TACAAACAAAATGTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:36:0:28.5:1:1:2.44949:39:4:0.3333:0:7.5 -18 18511434 . A T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCGTTGGAAACGGGATT;RSEQ=CAAACAAAATGTAGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:34:0:29:1:1:2.44949:39:4:0.3333:0:7.5 -18 18511439 . C T 68 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGGAAACGGGATTACAAA;RSEQ=AAAATGTAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:5:3,2:1,0:0.8333:0,2:27.4:1:29.6:1:1:0:39:10:0.8333:0:7.6 -18 18511441 . A G 52 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAACGGGATTACAAACA;RSEQ=AATGTAGACAGCAGCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:2,1:2,1:0.5:2,2:28.3:1:33:0:1:1:39:6:0.5:0:7.7 -18 18511444 . T A 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACGGGATTACAAACAAAA;RSEQ=GTAGACAGCAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:2,1:1,0:0.5:0,2:31.3:1:30.7:1:1:0:39:6:0.5:0:7.7 -18 18511467 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGCAGCATTCTCAGAA;RSEQ=CTTCTTTGTGATGTTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:4,3:0.2222:2,2:19:0:33:1:1:1.29098:24:4:0.2222:0:4 -18 18511470 . T G 51 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAGCATTCTCAGAAACT;RSEQ=CTTTGTGATGTTTGCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:3:2,1:3,2:0.375:2,2:43.7:1:32.3:1:1:1.29:39:6:0.375:0:7.7 -18 18511486 . T A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTTCTTTGTGATGTTTGC;RSEQ=TTTAAGTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:6:0:33:0:1:0:36:2:1:0:8 0/1:7:3:2,1:1,1:0.4286:2,2:27.7:1:30:1:1:1.73:39:6:0.4286:0:7.7 -18 18511489 . T C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTGTGATGTTTGCTTT;RSEQ=AAGTCACAGAGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:9:0:32:0:1:0:36:2:1:0:8 0/1:7:3:2,1:2,2:0.4286:2,2:24.7:1:30.7:1:1:1.81:39:6:0.4286:0:7.7 -18 18511498 . G T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTTTGCTTTTAAGTCACA;RSEQ=AGTTGAACATTCCCTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:18:0:34:0:1:0:36:2:1:0:8 0/1:7:2:1,1:2,2:0.2857:2,2:16:1:27.5:1:1:1:42:4:0.4:0:7.5 -18 18511507 . A G 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTAAGTCACAGAGTTGAAC;RSEQ=TTCCCTTCCATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:27:0:30:0:1:0:36:2:1:0:8 0/1:7:2:1,1:3,2:0.2857:2,2:19:0:27.5:1:1:1.41418:24:4:0.2857:0:4 -18 18511515 . C T 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGAGTTGAACATTCCCTT;RSEQ=CATAGAGCAGTTTAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:33:0:1:0:36:2:1:0:8 1/0:5:3:1,2:1,1:0.6:2,2:8:1:28.7:1:1:1.7321:30:6:0.6:0:5.3 -18 18511529 . A T 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTTCCATAGAGCAGTTT;RSEQ=GAAACACTCTTTCTATAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25.5:1:31.5:1:1:0:34.5:4:1:0:8 1/0:2:1:1,0:0,1:0.5:0,0:39:0:32:0:1:0:31:2:0.5:0:7 -18 18511544 . A G 49 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTAGAAACACTCTTTCT;RSEQ=TAGTATCTGGAAGTGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27:1:34:0:1:0:34.5:4:1:0:8 1/0:4:3:2,1:0,1:0.75:0,2:16.7:1:31.3:1:1:0:39.3:6:0.75:0:7 -18 18511561 . A C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.44721;LSEQ=TCTATAGTATCTGGAAGTGG;RSEQ=CATTTCGAGCGATTTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:20:0:34:0:1:0:36:2:0.5:0:8 0/1:7:2:1,1:2,3:0.2857:2,2:19.5:1:31:1:1:1.41:31:4:0.2857:0:7.5 -18 18511570 . G T 44 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGGAAGTGGACATTTCGA;RSEQ=CGATTTCAGGCCTATGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27:1:32.5:1:1:0:34.5:4:1:0:8 1/0:5:3:1,2:1,1:0.6:2,2:25:1:28:1:1:1.7321:37.7:6:0.6:0:4 -18 18511582 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTTCGAGCGATTTCAGGC;RSEQ=TATGTTGAAAAACGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:46:0:33:0:1:0:33:2:1:0:8 0/1:5:2:1,1:1,2:0.4:2,2:38:1:31:1:1:1.73:48:4:0.4:0:6 -18 18511588 . T G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCGATTTCAGGCCTATGT;RSEQ=GAAAAACGAAATATCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:40:0:30:0:1:0:33:2:1:0:8 0/1:5:2:1,1:1,2:0.4:2,2:39.5:1:31:1:1:1.73:48:4:0.4:0:6 -18 18511595 . C G 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGGCCTATGTTGAAAAA;RSEQ=GAAATATCTTCCCATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:33:0:35:0:1:0:33:2:1:0:8 1/1:5:5:2,3:0,0:1:0,2:24.8:1:30.8:1:1:0:41.8:10:1:0:4.8 -18 18511624 . T A 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCATAAAAACTAGACAG;RSEQ=AGCATACTCAGAAGCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:4:0:27:0:1:0:33:2:1:0:7 1/0:5:3:1,2:1,1:0.6:2,2:13.3:1:28.3:1:1:1.7321:42.3:6:0.6:0:6 -18 18511626 . G C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCATAAAAACTAGACAGTA;RSEQ=CATACTCAGAAGCTTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:2:0:29:0:1:0:33:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:17:1:29:1:1:1:48:4:0.5:0:6 -18 18511652 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGAAGCTTCTTTGTGATG;RSEQ=TTGCTTTTAAGTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:16:0:32:0:1:0:47:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:14:1:31.5:1:1:1:40:4:0.5:0:7.5 -18 18511678 . A G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=TTTAAGTCACAGAGTTGAAC;RSEQ=TTCCCTTTCGTAGAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23.5:1:30.5:1:1:1:43.5:4:0.5:0:7 1/0:4:3:1,2:1,0:0.75:0,2:33.7:1:31:1:1:0:46.7:6:0.75:0:7 -18 18511687 . C G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CAGAGTTGAACATTCCCTTT;RSEQ=GTAGAGCAGGTTTCAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:24.5:1:32.3:1:1:0:51.8:8:1:0:3.8 0/1:5:2:1,1:1,2:0.4:2,2:17:1:29:1:1:1.73:39:4:0.4:0:7.5 -18 18511688 . G A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=AGAGTTGAACATTCCCTTTC;RSEQ=TAGAGCAGGTTTCAGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:32:1:31:1:1:1:43.5:4:0.5:0:7 1/0:5:3:1,2:1,1:0.6:2,2:38.7:1:30:1:1:1.7321:46.7:6:0.6:0:7 -18 18511703 . G A 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CTTTCGTAGAGCAGGTTTCA;RSEQ=ACACTCTTTCTGTAGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:32:1:29.5:1:1:1:43.5:4:0.5:0:7 1/1:5:5:2,3:0,0:1:0,2:34.6:1:29:1:1:0:43.6:10:1:0:7.2 -18 18511706 . A C 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCGTAGAGCAGGTTTCAGAC;RSEQ=CTCTTTCTGTAGTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:30.5:1:1:0:43.5:4:1:0:7 1/1:6:5:2,3:0,1:0.8333:0,2:34:1:30.2:1:1:0:43.6:10:0.8333:0:7.2 -18 18511711 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCAGGTTTCAGACACTCT;RSEQ=TCTGTAGTATCTGGAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:32:1:29.5:1:1:0:43.5:4:1:0:7 0/1:8:2:1,1:2,4:0.25:2,2:5:0:33:1:1:1.83:60:4:0.25:0:4 -18 18511716 . T C 73 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGTTTCAGACACTCTTTCTG;RSEQ=AGTATCTGGAAGTGGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:31:1:1:0:43.5:4:1:0:7 1/0:8:5:2,3:1,2:0.625:2,2:29:1:31.6:1:1:1.29:43.6:10:0.625:0:7.2 -18 18511742 . T C 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGAAGTGGACATTTCGAG;RSEQ=GTTTTCAGGCCTATGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:32:0:32:0:1:0:40:2:1:0:7 1/0:6:4:1,3:1,1:0.6667:2,2:22.8:1:30.3:1:1:2.44949:42:8:0.6667:0:7 -18 18511744 . T C 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGTGGACATTTCGAGTG;RSEQ=TTTCAGGCCTATGGTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:30:0:34:0:1:0:40:2:1:0:7 1/1:5:4:2,2:0,1:0.8:0,2:31.5:1:33.5:1:1:0:49.5:8:0.8:0:5.8 -18 18511754 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=ATTTCGAGTGTTTTCAGGCC;RSEQ=ATGGTGAACAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:20:0:34:0:1:0:40:2:1:0:7 0/1:7:2:1,1:2,3:0.2857:2,2:15:1:30.5:1:1:1.41:39:4:0.2857:0:7.5 -18 18511779 . C A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACAAGGAAATATCTTCC;RSEQ=ATAAAAACCAGACACAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:12.5:1:28.5:1:1:1:60:4:0.3333:0:4 -18 18511782 . AA GC 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGGAAATATCTTCCCAT;RSEQ=AAACCAGACACAAGCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:32:1:33.5:1:1:1.7321:28:4:0.4:0:4.5 -18 18511786 . A G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAATATCTTCCCATAAAA;RSEQ=CCAGACACAAGCATTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:5.5:1:29.5:1:1:1.7321:60:4:0.4:0:4 -18 18511788 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATCTTCCCATAAAAAC;RSEQ=AGACACAAGCATTTGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:32:0:30.5:1:1:1.7321:28:4:0.4:0:4.5 -18 18511794 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCATAAAAACCAGACA;RSEQ=AAGCATTTGCAGAAACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:26:0:33.5:1:1:0:28:4:0.6667:0:4.5 -18 18511802 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACCAGACACAAGCATT;RSEQ=GCAGAAACTTGTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:18:0:32.5:1:1:0:28:4:0.6667:0:4.5 -18 18511823 . C T 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAAACTTGTTTGTGATG;RSEQ=GTGTCCTCAACTCACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:22:1:30.3:1:1:0:52.7:6:1:0:7.7 -18 18511834 . CTC GCG 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTGATGCGTGTCCTCAA;RSEQ=ACAGAATAGAACATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:28.5:1:30.2:1:1:0:59:4:0.6667:0:5.5 -18 18511844 . A T 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCCTCAACTCACAGAAT;RSEQ=GAACATTTCGTTTGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:29:1:29.7:1:1:0:52.7:6:1:0:6 -18 18511854 . GT CA 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCACAGAATAGAACATTTC;RSEQ=TTGACAGAGCAGCTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:10:0:31:0:1:0:40:2:1:0:5 1/0:4:2:1,1:0,1:0.5:0,2:28:1:28.8:1:1:0:59:4:0.5:0:4.5 -18 18511868 . C T 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCGTTTGACAGAGCAG;RSEQ=TTGGAAACACGCTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:13:1:31:1:1:0:40:4:1:0:6 1/1:4:4:2,2:0,0:1:0,2:25.5:1:29.3:1:1:0:39.5:8:1:0:6 -18 18511880 . C A 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=CAGAGCAGCTTGGAAACACG;RSEQ=TTTTTGTAGAATCTGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,0:0.5:0,0:36:0:32:0:1:0:40:2:0.5:0:5 1/0:7:4:2,2:1,2:0.5714:2,2:15.8:1:29.5:1:1:1.81:28.5:8:0.5714:0:6 -18 18511899 . T G 64 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=GCTTTTTGTAGAATCTGCAA;RSEQ=TGGATATTTGGATAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:29.7:1:33.7:1:1:0:33.3:6:1:0:5.3 1/0:7:4:2,2:1,2:0.5714:2,2:34.8:1:32.3:1:1:1.81:28.5:8:0.5714:0:6 -18 18511913 . A G 55 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTGCAATTGGATATTTGGAT;RSEQ=GCTTTGTGGATTTCTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:38:1:34:0:0.33333:0:40:4:0.6667:0:6 1/0:6:4:2,2:1,1:0.6667:2,2:43:1:27.5:1:1:1:28.5:3:0.6:0:6 -18 18511928 . T G 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22619;SOR=7.11489;LSEQ=TGGATAGCTTTGTGGATTTC;RSEQ=TTGGAAACGGGAGTATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,0:0.3333:0,0:14:0:32:0:1:0:40:2:0.5:0:5 1/1:6:5:2,3:1,0:0.8333:0,2:27.4:1:31.2:1:1:0:36.6:10:1:0:4.4 -18 18511952 . T G 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46429;SOR=3.87298;LSEQ=GAAACGGGAGTATCTTCATA;RSEQ=AAAACCTAGACGGAAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:12:0:34:0:1:0:40:2:0.5:0:6 1/1:6:5:3,2:0,1:0.8333:0,2:10.2:1:27.8:1:1:0:33:4:0.8:0:4.4 -18 18512013 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGCATTCACGTCACAGA;RSEQ=TTGAACATTCCCTTTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:30.5:1:1:0:40:4:1:0:7 1/1:2:2:1,1:0,0:1:0,2:26:1:32.5:1:1:0:23.5:4:1:0:6.5 -18 18512050 . T A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGAGCAGGTTTGAAACAC;RSEQ=CTTTCCGAAGTATCTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:41.7:1:29.7:1:1:0:40:6:1:0:6.7 1/1:2:2:1,1:0,0:1:0,2:41.5:1:30:1:1:0:25:4:1:0:6 -18 18512056 . C T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTTTGAAACACTCTTTC;RSEQ=GAAGTATCTGGATGTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:42.3:1:30.7:1:1:0:40:6:1:0:6.7 1/1:2:2:1,1:0,0:1:0,2:41.5:1:30:1:1:0:25:4:1:0:6 -18 18512058 . A T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTTGAAACACTCTTTCCG;RSEQ=AGTATCTGGATGTGGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:41.7:1:29:1:1:0:40:6:1:0:6.7 1/1:2:2:1,1:0,0:1:0,2:41.5:1:28.5:1:1:0:25:4:1:0:6 -18 18512074 . A G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCGAAGTATCTGGATGTGG;RSEQ=CACTTGGAGCGCTTTGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:28.3:1:31.3:1:1:0:40:6:1:0:6.7 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30:1:1:0:25:4:1:0:6 -18 18512089 . T G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGACACTTGGAGCGCTT;RSEQ=GACGCTTACGGTGAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:13.3:1:32.7:1:1:0:40:6:1:0:6.7 1/1:2:2:1,1:0,0:1:0,2:12.5:1:29:1:1:0:25:4:1:0:6 -18 18512098 . C T 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAGCGCTTTGACGCTTA;RSEQ=GGTGAAAAGGAAATAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:32:0:1:0:40:4:1:0:7 1/1:1:1:0,1:0,0:1:0,0:9:0:32:0:1:0:25:2:1:0:6 -18 18512156 . G T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGCATTCTCACAAACTGGT;RSEQ=TGTGATGTATGTCCTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:28.5:1:1:0:48:4:1:0:4.5 -18 18512174 . G A 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTGATGTATGTCCTCA;RSEQ=CTAACAGAGTTAAACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:0:29.5:1:1:0:48:4:1:0:4.5 -18 18512186 . A G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCCTCAGCTAACAGAGTT;RSEQ=AACCTTTCTATTTACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:8.3:1:33:0:1:0:49:6:1:0:5 1/1:2:2:1,1:0,0:1:0,2:38.5:1:32:1:1:0:48:4:1:0:4.5 -18 18512208 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ACCTTTCTATTTACAGAGCA;RSEQ=TTTTCAAAGACTCTTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:29:0:32:1:1:0:60:4:0.5:0:3.5 1/0:4:2:1,1:2,0:0.5:0,2:16.5:1:31.5:1:1:0:48:4:0.5:0:4.5 -18 18512213 . C G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCTATTTACAGAGCAGTTTT;RSEQ=AAAGACTCTTTTTGGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:25.5:1:33:0:1:0:33.5:4:0.5:0:7.5 1/0:4:2:2,0:1,1:0.5:2,0:19.5:1:33.5:1:1:0:41.5:4:0.5:0:6 -18 18512221 . CT C 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CAGAGCAGTTTTCAAAGACT;RSEQ=TTTTGGAGAATCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:38.8:1:31.8:1:1:0:46.8:8:1:0:5.5 1/0:4:3:3,0:0,1:0.75:0,0:21.3:1:32.6:1:0.25:0:43.3:6:0.75:0.25:5.3 -18 18512231 . A T 73 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=TTCAAAGACTCTTTTTGGAG;RSEQ=ATCTGCAAGTGGATATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:40.3:1:30.5:1:1:0:46.8:8:1:0:5.5 1/1:6:5:4,1:0,1:0.8333:0,2:19.2:1:31.6:1:0.33333:0:34.4:10:0.8333:0:5 -18 18512238 . A T 74 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00794;SOR=Inf;LSEQ=ACTCTTTTTGGAGAATCTGC;RSEQ=AGTGGATATCTGGAGATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:36.8:1:30.3:1:1:0:46.8:8:1:0:5.5 1/1:5:5:4,1:0,0:1:0,2:25.8:1:32.2:1:1:0:34.4:10:1:0:5 -18 18512248 . C G 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.43179;LSEQ=GAGAATCTGCAAGTGGATAT;RSEQ=TGGAGATCTTTAAGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:0.3333:2,2:5.5:1:30:1:1:1:45:4:0.3333:0:6.5 0/1:6:1:1,0:0,0:0.1667:0,0:35:0:32:0:1:0:40:2:0.1667:0:7 -18 18512255 . T G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.6233;LSEQ=TGCAAGTGGATATCTGGAGA;RSEQ=CTTTAAGGATTTCATTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:1,1:0.75:2,2:10:1:29:1:1:1.83:49.5:5:0.7143:0:5.7 1/1:12:10:6,4:1,1:0.8333:2,2:19.5:1:32.4:1:1:1.45:44.3:20:0.8333:0:5.2 -18 18512260 . A T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80821;LSEQ=GTGGATATCTGGAGATCTTT;RSEQ=AGGATTTCATTGGAAACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:13.5:1:27.5:1:1:2.64575:60:4:0.25:0:3.5 0/1:12:2:1,1:6,4:0.1667:2,2:6:0:31:1:1:1.4491:60:4:0.1667:0:1.5 -18 18512269 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48413;SOR=Inf;LSEQ=TGGAGATCTTTAAGGATTTC;RSEQ=TTGGAAACCGGAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:14.1:1:28.5:1:1:0:48:26:1:0:5 0/1:15:2:1,1:8,5:0.1333:2,2:8.5:1:30:1:1:1.54914:60:4:0.1333:0:2.5 -18 18512270 . T C 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09565;SOR=0.19169;LSEQ=GGAGATCTTTAAGGATTTCA;RSEQ=TGGAAACCGGAATATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:3,3:4,3:0.4615:2,2:18:1:31.3:1:1:1.30401:44:12:0.4615:0:6 0/1:15:2:2,0:7,5:0.1333:2,0:9.5:1:32:0:0.50549:0:50:4:0.1333:0:6.5 -18 18512279 . G C 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14194;SOR=0;LSEQ=TAAGGATTTCATTGGAAACC;RSEQ=GAATATCTTCAGGTAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:0.1667:2,2:30:0:32:0:1:1.45:60:4:0.1667:0:4.5 0/0:19:0:0,0:10,8:0:2,0:19:1:28.8:1:1:0:49.2:17:0.9444:0:4.4 -18 18512297 . A C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15766;SOR=0;LSEQ=CCGGAATATCTTCAGGTAAA;RSEQ=TCTAGACAGAGGCATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:14.5:1:29.5:1:1:1.15:50:4:0.1333:0:5 0/0:22:0:0,0:11,11:0:2,0:25.4:1:29.1:1:1:0:51.1:44:1:0:4.5 -18 18512311 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49198;SOR=Inf;LSEQ=GGTAAAATCTAGACAGAGGC;RSEQ=TTCTCAGAAACTTCTTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,9:0:2,0:31.8:1:30.3:1:1:0:49.2:30:1:0:4.9 0/1:19:2:1,1:8,9:0.1053:2,2:15:0:32.5:1:1:1.12:60:4:0.1053:0:2.5 -18 18512328 . C T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4757;SOR=1.7891;LSEQ=GGCATTCTCAGAAACTTCTT;RSEQ=GTGATGTGCGTCCTCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:1,4:4,4:0.3846:2,2:25.2:1:29.2:1:0.56488:3.5981:40.6:10:0.3846:0:5.4 1/0:15:8:3,5:3,4:0.5333:2,2:31.4:1:30.3:1:1:1.23147:50.3:16:0.5333:0:5.3 -18 18512331 . G A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59556;SOR=2.29077;LSEQ=ATTCTCAGAAACTTCTTCGT;RSEQ=ATGTGCGTCCTCAACTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:5,6:0,2:0.8462:0,2:30.1:1:28.1:1:0.48718:0:48.3:10:0.8333:0:5 1/1:14:13:6,7:0,0:0.9286:0,2:33.5:1:29.2:1:1:0:53.9:26:0.9286:0:5.3 -18 18512335 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48148;SOR=Inf;LSEQ=TCAGAAACTTCTTCGTGATG;RSEQ=GCGTCCTCAACTAACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:27.3:1:30.4:1:1:0:47.5:26:1:0:4.9 0/1:14:2:1,1:5,7:0.1429:2,2:30:1:31:0:1:1.37:59.5:4:0.1429:0:5.5 -18 18512337 . C T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAACTTCTTCGTGATGTG;RSEQ=GTCCTCAACTAACAGAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:5,8:0,0:1:0,2:25.9:1:30:1:1:0:47.5:26:1:0:4.9 1/1:14:14:6,8:0,0:1:0,2:27:1:30.2:1:1:0:53.8:28:1:0:5.2 -18 18512353 . A T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.47619;SOR=Inf;LSEQ=TGTGCGTCCTCAACTAACAG;RSEQ=GTACAACCTGTCTTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:4,5:0,2:0.8182:0,2:19.6:1:29:1:0.49091:0:49:18:0.8182:0:4.7 1/1:10:10:5,5:0,0:1:0,2:17.1:1:30:1:1:0:54.2:20:1:0:5.3 -18 18512363 . G A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAACTAACAGAGTACAACCT;RSEQ=TCTTTTGATACATCAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:2,4:0,1:0.8571:0,2:18.2:1:29.2:1:1:0:44.5:12:0.8571:0:5.3 1/1:7:7:3,4:0,0:1:0,2:13.7:1:29.4:1:1:0:53.6:14:1:0:5.4 -18 18512376 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAACCTGTCTTTTGATACA;RSEQ=CAGTTTGGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:30.5:1:1:0:30.5:4:1:0:7.5 1/1:2:2:0,2:0,0:1:0,0:8:1:32.5:1:1:0:50:4:1:0:7 -18 18512379 . GT CG 28 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTGTCTTTTGATACATCA;RSEQ=TTGGAAACACTCTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:28.5:1:1:0:30.5:4:1:0:6.5 1/1:1:1:0,1:0,0:1:0,0:9:0:32.5:0:1:0:40:2:1:0:7 -18 18512815 . C G 84 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTATATTCATGTAAAATCTA;RSEQ=ACAGAAGCATTCTCAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:9:0:34:0:1:0:40:2:1:0:5 1/1:6:6:6,0:0,0:1:0,0:9:1:32.8:1:1:0:32.7:12:1:0:6.5 -18 18512831 . G C 102 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01977;SOR=14.86818;LSEQ=TCTACACAGAAGCATTCTCA;RSEQ=AATCTTCTTTGTGATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:0.1429:2,0:25:0:34:0:1:0:40:2:0.1429:0:5 1/0:12:9:8,1:3,0:0.75:0,2:20.8:1:32.2:1:1:0:32.9:18:0.75:0:5.4 -18 18512834 . T A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAGAAGCATTCTCAGAA;RSEQ=CTTCTTTGTGATGTGTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:1:0,2:11.4:1:31.6:1:1:0:42.9:16:1:0:5.1 1/1:13:13:12,1:0,0:1:0,1:20.4:1:31.2:1:1:0:36.1:26:1:0:5.6 -18 18512838 . C A 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03241;SOR=0.12413;LSEQ=AGAAGCATTCTCAGAATCTT;RSEQ=TTTGTGATGTGTGTCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:2,0:0.75:0,2:14.3:1:30.3:1:1:0:47:12:0.75:0:4.7 0/1:16:4:4,0:11,1:0.25:2,0:9.5:1:29.5:1:1:0:42.8:8:0.25:0:4.5 -18 18512853 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52367;SOR=Inf;LSEQ=ATCTTCTTTGTGATGTGTGT;RSEQ=CTCAACTAACAGAGTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:18.6:1:31.9:1:1:0:39.4:34:1:0:4.9 0/1:29:2:1,1:18,7:0.069:2,2:15:0:31:1:0.51282:2.47127:43:4:0.069:0:6.5 -18 18512858 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50508;SOR=Inf;LSEQ=CTTTGTGATGTGTGTCCTCA;RSEQ=CTAACAGAGTTCAACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:18.4:1:30.4:1:1:0:40.1:44:1:0:5 0/1:31:2:1,1:20,9:0.0645:2,2:20:0:33.5:1:1:2.16029:43:4:0.0645:0:6.5 -18 18512861 . A C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5681;SOR=0.62748;LSEQ=TGTGATGTGTGTCCTCAACT;RSEQ=ACAGAGTTCAACCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:5,4:7,6:0.3913:2,2:25.9:1:31.8:1:1:1.07:45.2:18:0.3913:0:4.7 0/1:35:10:7,3:16,9:0.2857:2,2:20.7:1:32:1:1:1.30:43.5:20:0.2857:0:4 -18 18512868 . T A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16393;SOR=0;LSEQ=TGTGTCCTCAACTAACAGAG;RSEQ=TCAACCTTTCTTTTGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:13,10:0.08:2,2:15:1:32.5:1:1:1.28628:37:4:0.0833:0:5 0/0:36:0:0,0:23,13:0:2,0:27.8:1:29.8:1:1:0:38.6:72:1:0:5.1 -18 18512869 . TC GG 31 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.40408;LSEQ=GTGTCCTCAACTAACAGAGT;RSEQ=AACCTTTCTTTTGATACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:1,0:13,11:0.04:2,0:9:0:32.5:0:1:0:40:2:0.04:0:7 0/1:36:2:1,1:22,12:0.0556:2,2:32:0:31.8:1:1:1.8009:43:4:0.0556:0:5.5 -18 18512870 . C G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43177;SOR=1.55958;LSEQ=TGTCCTCAACTAACAGAGTT;RSEQ=AACCTTTCTTTTGATACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:14:8,6:5,5:0.56:2,2:23.9:1:32.2:1:1:1.32:36.6:28:0.5833:0:5.2 1/0:36:24:15,9:7,3:0.6667:2,2:28.1:1:31.4:1:1:1.38648:36.1:48:0.7059:0:5.5 -18 18512874 . C T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2623;SOR=Inf;LSEQ=CTCAACTAACAGAGTTCAAC;RSEQ=TTTCTTTTGATACAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:27.9:1:31.5:1:1:0:39.8:24:1:0:5 0/1:36:3:2,1:21,12:0.0833:2,2:30.7:1:28.7:1:1:1.14:38:6:0.0833:0:7 -18 18512876 . T C 32 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.40408;LSEQ=CAACTAACAGAGTTCAACCT;RSEQ=TCTTTTGATACAGCAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:1,0:13,11:0.04:2,0:15:0:32:0:1:0:40:2:0.04:0:7 0/1:36:2:1,1:22,12:0.0556:2,2:38:0:32:1:1:1.8009:43:4:0.0556:0:5.5 -18 18512878 . C G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17462;SOR=0.42297;LSEQ=ACTAACAGAGTTCAACCTTT;RSEQ=TTTTGATACAGCAGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:12:6,6:8,5:0.48:2,2:29.3:1:32.7:1:0.6951:1.56986:43.2:24:0.48:0:4.6 0/1:36:10:7,3:16,10:0.2778:2,2:35.4:1:31.8:1:0.71605:1.44:43.5:20:0.2778:0:4 -18 18512885 . T C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04917;LSEQ=GAGTTCAACCTTTCTTTTGA;RSEQ=ACAGCAGTTTGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:12,9:0.16:2,2:44.3:1:33.3:1:1:1.3179:46.8:8:0.16:0:3.3 0/1:36:6:3,3:20,10:0.1667:2,2:31.5:1:32.3:1:0.6454:1.95962:39.3:12:0.1667:0:3.8 -18 18512886 . A G 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1929;SOR=2.19277;LSEQ=AGTTCAACCTTTCTTTTGAT;RSEQ=CAGCAGTTTGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:6,3:8,8:0.36:2,2:33.2:1:30:1:0.67662:1.95:32.3:8:0.3333:0:6.3 1/0:36:20:13,7:10,6:0.5556:2,2:28.9:1:31.8:1:1:1.11:35.9:40:0.5556:0:6 -18 18512892 . G A 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25847;SOR=Inf;LSEQ=ACCTTTCTTTTGATACAGCA;RSEQ=TTTGGAAACACTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:33.6:1:32.1:1:1:0:39.8:50:1:0:5 0/1:35:3:3,0:19,13:0.0857:2,0:19:1:32:0:0.27899:0:32:6:0.0857:0:6.3 -18 18512904 . T C 83 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5014;SOR=1.75531;LSEQ=ATACAGCAGTTTGGAAACAC;RSEQ=CTTTTTGTAGAATCTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:1,2:11,8:0.1364:2,2:40.3:1:30:1:0.57143:2.62608:28.3:6:0.1364:0:7.3 0/1:32:7:5,2:14,11:0.2188:2,2:16.6:1:29.7:1:0.67065:1.92:38.1:14:0.2188:0:6.9 -18 18512905 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.50804;SOR=Inf;LSEQ=TACAGCAGTTTGGAAACACT;RSEQ=TTTTTGTAGAATCTTCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:32.2:1:31:1:1:0:39.1:21:1:0:5.1 0/1:32:2:1,1:18,12:0.0625:2,2:37.5:1:32.5:1:1:1.48061:36:4:0.0625:0:7 -18 18512910 . T G 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31239;LSEQ=CAGTTTGGAAACACTCTTTT;RSEQ=GTAGAATCTTCAAGTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:1,2:11,8:0.1364:2,2:35.3:1:31:1:0.57143:2.62608:28.3:6:0.1364:0:7.3 0/1:29:5:3,2:13,11:0.1724:2,2:18:1:31.2:1:1:1.26:42.6:10:0.1724:0:6.8 -18 18512913 . A G 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=TTTGGAAACACTCTTTTTGT;RSEQ=GAATCTTCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:17.5:1:29.5:1:1:1.21106:42.5:4:0.0909:0:6 0/0:27:0:0,0:15,12:0:2,0:18.9:1:29.3:1:1:0:40.4:54:1:0:4.9 -18 18512917 . T A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8603;LSEQ=GAAACACTCTTTTTGTAGAA;RSEQ=CTTCAAGTGGATATTTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:5,3:6,6:0.4:2,2:32.5:1:29.6:1:0.66992:1.62:31.4:16:0.4:0:6.5 0/1:22:8:2,6:8,6:0.3636:2,2:23.9:1:29.6:1:0.20433:3.74834:36.8:16:0.3636:0:6.6 -18 18512920 . T A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23148;LSEQ=ACACTCTTTTTGTAGAATCT;RSEQ=CAAGTGGATATTTGGATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:6,6:0,0:0.6:0,2:13.8:1:29:1:1:0:43.1:24:0.6:0:4.3 1/0:20:13:7,6:0,0:0.65:0,2:13.5:1:29.8:1:1:0:39.6:26:0.65:0:4.1 -18 18512924 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.2836;LSEQ=TCTTTTTGTAGAATCTTCAA;RSEQ=TGGATATTTGGATAGCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:8,6:0.2632:2,2:11.6:1:31:1:0.62848:1.92739:42.2:10:0.2632:0:4.6 0/1:19:6:3,3:5,7:0.3158:2,2:11.5:1:30.3:1:1:1.37:38.2:12:0.3158:0:4.5 -18 18512925 . T A 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48649;SOR=0;LSEQ=CTTTTTGTAGAATCTTCAAG;RSEQ=GGATATTTGGATAGCTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:9:0:29.5:1:1:1.11803:37:4:0.1053:0:5 0/0:19:0:0,0:8,11:0:2,0:12.9:1:30.4:1:1:0:37.7:38:1:0:4.7 -18 18512935 . GA CT 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=AATCTTCAAGTGGATATTTG;RSEQ=TAGCTCTAACGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:0.1818:2,2:11:1:30.8:1:1:1.22:24:4:0.1818:0.0909:5 0/0:11:0:0,0:3,8:0:2,0:6.9:1:32.1:1:1:0:35.9:22:1:0:5.1 -18 18513005 . G A 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACAGAAGCACTCTCAGGA;RSEQ=CTACTTTGTGATATCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:16:0:31:0:1:0:40:2:1:0:6 1/1:4:4:3,1:0,0:1:0,2:7.3:1:30.8:1:1:0:58:8:1:0:5.3 -18 18513012 . T G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.05491;SOR=0.10472;LSEQ=AGCACTCTCAGGAGCTACTT;RSEQ=GTGATATCTGCATTCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:6.3:1:32:1:1:1.7321:44:6:0.6:0:5.7 0/1:17:2:2,0:10,5:0.1176:2,0:7:0:31.5:1:1:0:42.5:4:0.1176:0:7 -18 18513020 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGAGCTACTTTGTGATAT;RSEQ=TGCATTCAGGTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:13.8:1:32.3:1:1:0:40.1:16:1:0:5.9 0/1:20:2:1,1:13,5:0.1:2,2:21:0:33.5:1:0.52105:2.46307:60:4:0.1053:0:5.5 -18 18513029 . G A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGTGATATCTGCATTCA;RSEQ=GTCACAGAGTTGAACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:22.8:1:29.4:1:1:0:40.1:7:1:0:5.9 1/1:20:20:14,6:0,0:1:0,2:23.3:1:30:1:1:0:45.8:19:1:0:4.3 -18 18513034 . C A 32 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06417;SOR=0;LSEQ=TGATATCTGCATTCAGGTCA;RSEQ=AGAGTTGAACATTCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:2,5:0.2222:2,0:25.5:1:32:0:0.16667:0:35:4:0.25:0:6.5 0/0:25:0:0,0:16,9:0:2,0:22.9:1:31.1:1:1:0:45.4:50:1:0:4.7 -18 18513049 . C G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12447;SOR=3.64389;LSEQ=GGTCACAGAGTTGAACATTC;RSEQ=CTTTCTTAGAGCACGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:0.4545:2,2:30.4:1:29.2:1:1:1.30:37.8:10:0.4545:0:5.4 1/0:25:19:12,7:4,2:0.76:2,2:32.3:1:30.8:1:1:1.15957:46.7:38:0.76:0:3.8 -18 18513053 . T A 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12447;SOR=0.27443;LSEQ=ACAGAGTTGAACATTCCCTT;RSEQ=CTTAGAGCACGTTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:2,4:2,3:0.5455:2,2:32.5:1:30.2:1:1:1.29868:37.8:12:0.5455:0:6.7 0/1:25:6:4,2:12,7:0.24:2,2:30:1:25.8:1:1:1.16:41.2:5:0.2083:0:7.5 -18 18513057 . A T 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03904;SOR=0.16912;LSEQ=AGTTGAACATTCCCTTTCTT;RSEQ=GAGCACGTTTGAAACACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:2,4:2,3:0.5455:2,2:33.8:1:31:1:1:1.29868:37.8:12:0.6:0:6.7 0/1:25:4:3,1:12,7:0.16:2,2:33.8:1:31:1:1:1.71:36.8:8:0.16:0:7.3 -18 18513067 . T G 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40261;SOR=0.49532;LSEQ=TCCCTTTCTTAGAGCACGTT;RSEQ=GAAACACACTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:3,5:0.2727:2,2:38:1:30.3:1:1:1.18052:32.3:6:0.2727:0:5.7 0/1:26:4:3,1:13,9:0.1538:2,2:38.3:1:31.3:1:1:2.02:38.5:8:0.16:0:4.5 -18 18513075 . A T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTAGAGCACGTTTGAAACAC;RSEQ=CTTTTTGTAGTATCTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:3,7:0,0:1:0,2:32.6:1:30.3:1:1:0:37.1:20:1:0:6.2 1/1:22:20:13,7:1,1:0.9091:2,2:27.2:1:30.4:1:1:1.80:43.8:40:0.9091:0:5.2 -18 18513080 . T G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACGTTTGAAACACACTTT;RSEQ=TGTAGTATCTGGAAGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:30.3:1:30.9:1:1:0:37.1:20:1:0:6.2 0/1:22:2:1,1:13,7:0.0909:2,2:22.5:1:31:1:1:1.80284:39:4:0.0909:0:4.5 -18 18513081 . T G 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.38882;SOR=0.40427;LSEQ=CACGTTTGAAACACACTTTT;RSEQ=GTAGTATCTGGAAGTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:2,3:0.4444:2,2:35:1:32:1:1:1.8525:35.5:8:0.5:0:7.5 0/1:21:5:3,2:10,6:0.2381:2,2:38.2:1:29.8:1:1:1.10551:40.8:10:0.2381:0:7.8 -18 18513083 . T A 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.38882;SOR=0.40427;LSEQ=CGTTTGAAACACACTTTTTG;RSEQ=AGTATCTGGAAGTGGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:2,3:0.4444:2,2:34:1:31.5:1:1:1.8525:35.5:8:0.4444:0:7.5 0/1:21:5:3,2:9,5:0.2381:2,2:36.2:1:29.4:1:1:1.18839:40.8:10:0.2381:0:7.8 -18 18513086 . T A 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.38882;SOR=0.40427;LSEQ=TTGAAACACACTTTTTGTAG;RSEQ=ATCTGGAAGTGGACATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:2,3:0.4444:2,2:31:1:31.5:1:1:1.8525:35.5:8:0.4444:0:7.5 0/1:21:5:3,2:10,6:0.2381:2,2:33.2:1:29:1:1:1.10551:40.8:10:0.2381:0:7.8 -18 18513087 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80643;LSEQ=TGAAACACACTTTTTGTAGT;RSEQ=TCTGGAAGTGGACATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:2,3:1,4:0.5:2,2:27.6:1:31:1:1:2.41:37.8:10:0.5:0:5.4 0/1:18:8:6,2:5,5:0.4444:2,2:16.6:1:30.5:1:0.36652:2.82:44.1:16:0.4444:0:4.6 -18 18513089 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=AAACACACTTTTTGTAGTAT;RSEQ=TGGAAGTGGACATTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:24.3:1:30.5:1:1:0:35.8:9:1:0:6.2 0/1:18:2:1,1:10,6:0.1111:2,2:21:0:33:1:1:1.61828:39:4:0.1111:0:4.5 -18 18513095 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=ACTTTTTGTAGTATCTGGAA;RSEQ=TGGACATTTGGAGCGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:22.2:1:32.4:1:1:0:35.3:18:1:0:6.2 0/1:14:2:1,1:7,5:0.1429:2,2:15:0:31.5:1:1:1.36624:39:4:0.1667:0:4.5 -18 18513105 . G C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=GTATCTGGAAGTGGACATTT;RSEQ=GAGCGCTTTCACGCCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:14.4:1:31.8:1:1:0:35.3:18:1:0:6.2 0/1:12:2:1,1:5,5:0.1667:2,2:5:0:32.5:1:1:1:39:4:0.1667:0:4.5 -18 18513115 . C G 65 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGACATTTGGAGCGCTTT;RSEQ=ACGCCTTTGGTGAAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:19.8:1:32:1:1:0:30.5:8:1:0:6.3 1/1:4:4:1,3:0,0:1:0,2:15.8:1:32.5:1:1:0:38:8:1:0:7.3 -18 18513117 . C T 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACATTTGGAGCGCTTTCA;RSEQ=GCCTTTGGTGAAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:18.8:1:31:1:1:0:30.5:8:1:0:6.3 1/1:4:4:1,3:0,0:1:0,2:14.8:1:31:1:1:0:38:8:1:0:7.3 -18 18513127 . GA G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AGCGCTTTCACGCCTTTGGT;RSEQ=AAAAGGAAATGTCTTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:12.5:1:31.5:1:1:0:26:4:0.6667:0.3333:6.5 0/0:3:0:0,0:1,2:0:2,0:13:1:29.3:1:1:0:40.3:6:1:0:7 -18 18513231 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACCTTTCTCTTTATAGA;RSEQ=CAGTTTGAAATGCTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:9:0:33.5:1:1:0:59.5:4:0.6667:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18513261 . G C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATGCTCTTTTTGTGGAATCT;RSEQ=CAAGTGGATATTTGGATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:38.7:1:33.3:1:1:0:52:6:1:0:5 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29.5:1:1:0:46:4:1:0:4 -18 18513268 . G T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TTTTGTGGAATCTGCAAGTG;RSEQ=ATATTTGGATAGCTCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:34:1:31.7:1:1:0:52:6:1:0:4.7 1/1:2:2:1,1:0,0:1:0,2:21.5:1:27:1:1:0:46:4:1:0:4 -18 18513277 . A C 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCTGCAAGTGGATATTTGG;RSEQ=TAGCTCTGAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:26:1:32.5:1:1:0:59.5:4:0.6667:0:5.5 1/1:1:1:0,1:0,0:1:0,0:30:0:34:0:1:0:52:2:1:0:6 -18 18513281 . C G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAAGTGGATATTTGGATAG;RSEQ=TCTGAGGATTTCGTTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:22:1:32:1:1:0:59.5:4:0.6667:0:5.5 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18513283 . C T 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGTGGATATTTGGATAGCT;RSEQ=TGAGGATTTCGTTGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:20:1:30:1:1:0:59.5:4:0.6667:0:5.5 1/1:1:1:0,1:0,0:1:0,0:24:0:32:0:1:0:52:2:1:0:6 -18 18513612 . C G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATCTGCAAGCGGATATTT;RSEQ=GATAACTTTGAAGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:1:31:1:1:0:53.5:4:1:0:5.5 -18 18513638 . A G 34 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGAAGATTTCGTTGGAA;RSEQ=CGGGAATATCTTCATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:34:0:1:0:53.5:4:1:0:5.5 -18 18513654 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAAACGGGAATATCTTCAT;RSEQ=TACAATCTAGACAGAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:33.5:1:1:0:53.5:4:1:0:5.5 -18 18513657 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGGGAATATCTTCATATA;RSEQ=AATCTAGACAGAGGCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:31.5:1:1:0:53.5:4:1:0:5.5 -18 18513843 . C A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAAAAACTAGACAGAAGC;RSEQ=TTCTCACAAACTGCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:29:1:1:0:59:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18513865 . T C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCACAAACTGCTTTGTGA;RSEQ=GTATGTCCTCCACTAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31:1:1:0:59:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18513873 . C T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCTTTGTGATGTATGTC;RSEQ=TCCACTAACAGAGTTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:31:1:1:0:59:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18513876 . C A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTGTGATGTATGTCCTC;RSEQ=ACTAACAGAGTTGAACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30.5:1:1:0:59:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18513879 . T A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTGATGTATGTCCTCCAC;RSEQ=AACAGAGTTGAACCTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31:1:1:0:59:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18513893 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACTAACAGAGTTGAAC;RSEQ=TTTCTATTTACAGGGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:0:32:0:1:0:59:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18513907 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAACCTTTCTATTTACAG;RSEQ=GCAGTTTTGAAAGACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:32:0:1:0:59:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18514166 . C A 28 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAATCTAGACAGAAGCACT;RSEQ=TCAGGAGGTACTTTGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:28.5:1:1:0:42.5:4:1:0:6.5 1/1:1:1:1,0:0,0:1:0,0:42:0:28:0:1:0:46:2:1:0:8 -18 18514168 . C T 28 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTAGACAGAAGCACTCT;RSEQ=AGGAGGTACTTTGTGATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28.5:1:1:0:42.5:4:1:0:6.5 1/1:1:1:1,0:0,0:1:0,0:44:0:32:0:1:0:46:2:1:0:8 -18 18514171 . G A 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGACAGAAGCACTCTCAG;RSEQ=AGGTACTTTGTGATATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29.5:1:1:0:42.5:4:1:0:6.5 1/1:1:1:1,0:0,0:1:0,0:47:0:30:0:1:0:46:2:1:0:8 -18 18514173 . GG AC 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGAAGCACTCTCAGGA;RSEQ=TACTTTGTGATATCTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:30.8:1:1:0:42.5:4:1:0:5.5 1/1:1:1:1,0:0,0:1:0,0:47:0:23:0:1:0:46:2:1:0:7 -18 18514180 . T G 48 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.5;SOR=0;LSEQ=AGCACTCTCAGGAGGTACTT;RSEQ=GTGATATCTGCATTCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31.5:1:1:0:42.5:4:1:0:5.5 1/0:7:4:3,1:1,2:0.5714:2,2:14.8:1:24:1:0.48571:4.45:44.3:1:0.4:0:3.8 -18 18514207 . T A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGCATTCAAGTCACAGAG;RSEQ=TGAACATTCCCTTTCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14:0:31.5:1:1:0:42.5:4:1:0:5.5 0/1:7:2:1,1:3,2:0.2857:2,2:17:1:29.5:1:1:1.41418:53.5:4:0.2857:0:3.5 -18 18514212 . C G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCAAGTCACAGAGTTGAA;RSEQ=ATTCCCTTTCATAGAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:9:0:34:0:1:0:42.5:4:1:0:5.5 0/1:7:2:1,1:3,2:0.2857:2,2:9:0:32:0:1:1.41418:42:4:0.2857:0:2 -18 18514217 . C G 61 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=AGTCACAGAGTTGAACATTC;RSEQ=CTTTCATAGAGCTGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:4:0:32:0:1:0:42.5:4:1:0:5.5 1/0:7:4:2,2:2,1:0.5714:2,2:6.8:1:30.8:1:1:1.81007:49.3:8:0.5714:0:2.5 -18 18514636 . A T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAGCTCTAACGATTTCAT;RSEQ=GGAAATGGGAATACCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:28:1:1:0:50:4:1:0:6 -18 18514647 . A G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGATTTCATAGGAAATGGGA;RSEQ=TACCTTCATATAAAATCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:35:1:29.5:1:1:0:50:4:0.6667:0:6 -18 18514672 . A T 72 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATATAAAATCTAGACAG;RSEQ=GGCACTCTCAGAAACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:1:0,2:24:1:28.2:1:1:0:46:12:1:0:5 -18 18514706 . C T 58 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCTTTGTGATATCTGCA;RSEQ=TCAAGTCACAGAGTTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:1,3:1,1:0.6667:2,2:27.3:1:29.3:1:1:2.44949:39:8:0.6667:0:5.3 -18 18514712 . T C 72 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTGATATCTGCACTCAAG;RSEQ=CACAGAGTTGAACATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:1:0,2:20.5:1:28.2:1:1:0:42.7:5:1:0:5.5 -18 18514729 . C T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCACAGAGTTGAACATT;RSEQ=CCTTTCTTAGAGCAGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:31:1:30:1:1:0:30.5:4:1:0:8 -18 18514732 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAGAGTTGAACATTCCC;RSEQ=TTCTTAGAGCAGGTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:31:1:31.5:1:1:0:30.5:4:1:0:8 -18 18514736 . T C 34 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTTGAACATTCCCTTTC;RSEQ=TAGAGCAGGTTTGAGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:31:1:34:0:1:0:30.5:4:1:0:8 -18 18514739 . G A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGAACATTCCCTTTCTTA;RSEQ=AGCAGGTTTGAGACACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:30.5:1:30.5:1:1:0:30.5:4:1:0:8 -18 18514751 . G A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTCTTAGAGCAGGTTTGA;RSEQ=ACACTTTGTAGTATCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:18.5:1:31:1:1:0:30.5:4:1:0:8 -18 18514952 . A C 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GGAATCTGCAAGTGGATATT;RSEQ=GGATAGCTCTGAGGATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:15:0:29:0:1:0:59:2:1:0:5 1/1:3:3:1,2:0,0:1:0,2:30.3:1:30.3:1:1:0:55.7:6:1:0:7.3 -18 18514970 . T G 33 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TTAGGATAGCTCTGAGGATT;RSEQ=CCTTGGAAACGGGATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22:1:33:0:1:0:58:4:1:0:4.5 0/0:3:0:0,0:1,2:0:2,0:41.3:1:30:1:1:0:55.7:6:1:0:7.3 -18 18514972 . C G 48 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATAGCTCTGAGGATTTC;RSEQ=TTGGAAACGGGATTACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:31:0:1:0:58:4:1:0:4.5 1/0:4:3:2,1:0,1:0.75:0,2:30:1:30.3:1:1:0:50:6:0.75:0:7.7 -18 18514978 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GCTCTGAGGATTTCCTTGGA;RSEQ=ACGGGATTACATATAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:22:1:31.3:1:1:0:48:6:1:0:4.7 1/0:4:2:1,1:1,1:0.5:2,2:39:1:32:1:1:1:53.5:4:0.5:0:7.5 -18 18514985 . T A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GGATTTCCTTGGAAACGGGA;RSEQ=TACATATAAAAAGTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22:1:30:1:1:0:44.3:8:1:0:4.8 0/1:5:2:1,1:2,1:0.4:2,2:32:1:31:1:1:1.7321:53.5:4:0.4:0:7.5 -18 18514992 . T A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTTGGAAACGGGATTACATA;RSEQ=AAAAAGTAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:7.5:1:29:1:1:1.7321:33:4:0.4:0:5 0/1:5:2:1,1:2,1:0.4:2,2:25:1:31:0:1:1.7321:53.5:4:0.4:0:7.5 -18 18514994 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.44544;LSEQ=TGGAAACGGGATTACATATA;RSEQ=AAAGTAGACAGCAGCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,0:0.4:0,2:9.5:1:31:1:1:0:33:4:0.4:0:5 1/0:6:3:2,1:0,1:0.5:0,2:15.7:1:31.7:1:1:0:55.7:6:0.5:0:7.7 -18 18515016 . A G 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36146;SOR=3.14354;LSEQ=AAGTAGACAGCAGCATTCTC;RSEQ=GAACCTTCTTTGTGATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:16.5:1:32.5:1:1:1:43.5:4:0.2:0:7.5 0/1:11:5:2,3:3,3:0.4545:2,2:21.4:1:29.2:1:1:1.44544:53.8:10:0.4545:0:7.2 -18 18515018 . A G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.52135;LSEQ=GTAGACAGCAGCATTCTCAG;RSEQ=ACCTTCTTTGTGATGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:2,2:0.6:2,2:24.3:1:31.7:1:1:1:43.5:12:0.6:0:6.2 1/0:10:7:3,4:2,1:0.7:2,2:23.6:1:29.9:1:1:2.41422:47.9:6:0.6667:0:6.3 -18 18515020 . CC GA 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.65944;SOR=1.88324;LSEQ=AGACAGCAGCATTCTCAGAA;RSEQ=TTCTTTGTGATGTTTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:3,3:0,0:0.5455:0,2:27.3:1:31.6:1:1:0:43.5:12:0.5455:0:5.2 1/0:10:7:3,4:0,0:0.7:0,2:26.6:1:30.9:1:1:0:47.9:14:0.7:0:5.3 -18 18515028 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=GCATTCTCAGAACCTTCTTT;RSEQ=TGATGTTTGCTTTTAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:24.1:1:30.9:1:1:0:45.9:24:1:0:5.3 0/1:13:2:1,1:7,4:0.1538:2,2:34.5:1:29:1:1:1.67325:41.5:4:0.1538:0:7 -18 18515035 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=CAGAACCTTCTTTGTGATGT;RSEQ=TGCTTTTAAGTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:25.3:1:30.6:1:1:0:45.9:24:1:0:5.3 0/1:15:2:1,1:9,4:0.1333:2,2:23:0:31:1:1:2.12136:33:4:0.1333:0:3 -18 18515039 . T G 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.4104;LSEQ=ACCTTCTTTGTGATGTTTGC;RSEQ=TTTAAGTCACAGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:5,5:0.0909:2,0:20:0:33:0:1:0:28:2:0.0909:0:5 0/1:16:2:1,1:9,5:0.125:2,2:34.5:1:29.5:1:1:1.73197:41.5:4:0.125:0:7 -18 18515042 . T G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.70162;LSEQ=TTCTTTGTGATGTTTGCTTT;RSEQ=AAGTCACAGAGTTGAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:4,5:0.25:2,2:22:1:31.3:1:1:1.53983:42.3:6:0.25:0:6.3 0/1:16:3:1,2:9,4:0.1875:2,2:39.3:1:31.7:1:0.51786:4.05684:49.7:6:0.1875:0:6 -18 18515043 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49206;SOR=Inf;LSEQ=TCTTTGTGATGTTTGCTTTT;RSEQ=AGTCACAGAGTTGAATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:26.5:1:29.7:1:1:0:43.3:24:1:0:5.6 0/1:16:2:1,1:9,5:0.125:2,2:45:0:32.5:1:1:1.73197:60:4:0.125:0:6.5 -18 18515056 . G C 48 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29035;SOR=0.21955;LSEQ=TGCTTTTAAGTCACAGAGTT;RSEQ=AATATTCCCTTACATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:3,7:0.2308:2,2:29.3:1:30.3:1:0.51049:4.09:47.7:6:0.2308:0:6.3 0/1:17:1:1,0:10,6:0.0588:2,0:36:0:31:0:1:0:30:2:0.0625:0:7 -18 18515059 . TA CG 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TTTTAAGTCACAGAGTTGAA;RSEQ=TTCCCTTACATAGAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:31.2:1:29.7:1:1:0:46.5:20:1:0:6 0/1:15:2:1,1:8,4:0.1333:2,2:19.5:1:28.8:1:1:1.89743:41.5:4:0.1333:0:6 -18 18515068 . AC CA 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68284;SOR=0.57502;LSEQ=ACAGAGTTGAATATTCCCTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:2,6:0,0:0.7273:0,2:25.5:1:31.6:1:1:0:43.6:16:0.7273:0.0909:5.1 1/0:15:9:5,4:0,0:0.6:0,2:24.3:1:29.5:1:1:0:43.8:18:0.6429:0.0667:5.6 -18 18515077 . A C 42 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08152;SOR=0;LSEQ=AATATTCCCTTACATAGAGC;RSEQ=GGTTTGAAACACTATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:2,6:0.2727:2,2:29:1:26.7:1:1:1.44:38:2:0.2:0:7.3 0/0:13:0:0,0:9,4:0:2,0:26:1:28.2:1:1:0:41.7:12:1:0:5.9 -18 18515091 . A C 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.22794;SOR=Inf;LSEQ=TAGAGCAGGTTTGAAACACT;RSEQ=TTTCTGTAGTATCTGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:1,6:0,0:0.7:0,2:23.9:1:32:1:1:0:42.4:14:0.7778:0:5.4 1/1:7:7:6,1:0,0:1:0,2:35:1:28.1:1:1:0:30.9:14:1:0:5.9 -18 18515095 . C T 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22794;SOR=0;LSEQ=GCAGGTTTGAAACACTATTT;RSEQ=TGTAGTATCTGGACATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:1,6:0.3:2,2:23:1:30.3:1:1:2.65:38:6:0.3:0:7.3 0/0:7:0:0,0:6,1:0:2,0:32.1:1:26.7:1:1:0:30.9:6:1:0:5.9 -18 18515109 . CA AG 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.46667;SOR=0;LSEQ=CTATTTCTGTAGTATCTGGA;RSEQ=TGGACATTTCGAGCGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:1:0,2:21.5:1:31.1:1:1:0:38.5:16:1:0.375:5.6 1/1:7:6:5,1:0,0:0.8571:0,2:21.2:1:28:1:1:0:32.5:12:1:0.1429:5.2 -18 18515123 . G T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=TCTGGACATGGACATTTCGA;RSEQ=CGATTTCAGGCCTATGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:24:1:31.3:1:1:0:31.3:6:0.6:0:5.3 1/0:4:3:2,1:1,0:0.75:0,2:16.7:1:28.7:1:1:0:28.3:6:0.75:0:5 -18 18515147 . C A 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAGGCCTATGTTGAAAA;RSEQ=GGAAATATCTTCCCATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:17:1:33.3:1:1:0:31.7:6:1:0:5.7 1/1:2:2:1,1:0,0:1:0,2:7.5:1:30:1:1:0:32:4:1:0:6.5 -18 18515192 . TT CG 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAGAAGCATTCTCAGAAA;RSEQ=TCTTTGTGATGTGTGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:33:0:33:0:1:0:40:2:0.5:0:4 1/1:2:2:0,2:0,0:1:0,0:31:1:32.5:0:1:0:39.5:4:1:0:5 -18 18515229 . T A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCAACTAACAGAGTTCA;RSEQ=CCTTTCTTATGATACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:25:0:32:0:1:0:40:2:1:0:4 1/1:2:2:0,2:0,0:1:0,0:25.5:1:31.5:1:1:0:39.5:4:1:0:5 -18 18515465 . G T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGTGGACATGGACATTTCGA;RSEQ=CGATTTCAGGCCTATGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:13:0:34:0:1:0:40:2:1:0:2 1/1:2:2:2,0:0,0:1:0,0:19:1:32:0:1:0:35:4:1:0:7 -18 18515489 . C A 84 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAGGCCTATGTTGAAAA;RSEQ=GGAAATATCTTCCCATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:37:0:30:0:1:0:40:2:1:0:2 1/1:7:7:5,2:0,0:1:0,2:21:1:30:1:1:0:39.4:14:1:0:6.6 -18 18515497 . T C 72 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CTATGTTGAAAACGGAAATA;RSEQ=CTTCCCATAAAAACTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25:1:29.5:1:1:0:44:4:1:0:2.5 1/0:8:5:4,1:2,1:0.625:2,2:32.4:1:31.2:1:1:1.83:37:10:0.625:0:6.8 -18 18515501 . CC AA 90 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01818;SOR=Inf;LSEQ=GTTGAAAACGGAAATATCTT;RSEQ=CATAAAAACTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26:1:31.5:1:1:0:44:4:1:0:2.5 1/1:9:9:6,3:0,0:1:0,2:25:1:28.7:1:1:0:41.4:18:1:0.1111:5.2 -18 18515534 . T C 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00952;SOR=0;LSEQ=GACAGAAGCATTCTCAGAAA;RSEQ=TTCTTTGTGATGTGTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:30.5:1:1:0:44:4:1:0:2.5 0/0:13:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18515558 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGTGATGTGTGTCCTCAA;RSEQ=TAACAGAGTTCATCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:35:0:34:0:1:0:48:2:1:0:3 0/1:12:2:1,1:5,5:0.1667:2,2:34:1:29:1:1:1:44.5:4:0.1667:0:3.5 -18 18515571 . T A 101 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCAACTAACAGAGTTCA;RSEQ=CCTTTCTTATGATACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:22:0:30:0:1:0:48:2:1:0:3 1/1:10:10:5,5:0,0:1:0,2:24.7:1:30.6:1:1:0:45.6:20:1:0:3.9 -18 18515610 . G A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTGGAAACACTCTTTTT;RSEQ=TAGAATATGTAAGTGGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:7.5:1:31:1:1:0:40:4:1:0:4 -18 18515670 . AA TT 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTTGGAAACGGGAGTATC;RSEQ=CATAGAAAACCTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:22:0:32.5:0:1:0:40:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:23.3:1:31.5:0:1:0:42.3:6:1:0:7 -18 18515674 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAACGGGAGTATCAACA;RSEQ=AGAAAACCTAGACAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:25:0:33:0:1:0:40:2:1:0:7 1/0:3:2:1,1:0,1:0.6667:0,2:28:0:31:1:1:0:39.5:4:0.6667:0:7 -18 18515678 . A C 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AACGGGAGTATCAACATAGA;RSEQ=AACCTAGACAGAAACATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:32:0:1:0:40:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:30.3:1:32.7:1:1:0:42.3:6:1:0:7 -18 18515690 . A T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AACATAGAAAACCTAGACAG;RSEQ=AACATTCTCAGAAACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:41:0:32:0:1:0:40:2:0.5:0:7 1/1:3:3:1,2:0,0:1:0,2:41.3:1:29:1:1:0:42.3:6:1:0:7 -18 18515696 . T G 63 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=GAAAACCTAGACAGAAACAT;RSEQ=CTCAGAAACTGCTTTATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:27:1:31.5:1:1:0:33.5:4:1:0:7 1/1:4:4:1,3:0,0:1:0,2:32:1:31.5:1:1:0:41.8:8:1:0:7.3 -18 18515712 . A G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCTCAGAAACTGCTTT;RSEQ=TGATGTCTGCATTCACGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30.5:1:34:0:1:0:33.5:4:1:0:7 1/1:5:4:1,3:1,0:0.8:0,2:24:1:31.3:1:0.4:0:41.8:8:0.8:0:7.3 -18 18515717 . G A 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=CTCAGAAACTGCTTTATGAT;RSEQ=TCTGCATTCACGTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18:1:29:1:1:0:31.5:4:0.6667:0:7 1/1:5:5:2,3:0,0:1:0,2:19.2:1:26.4:1:1:0:39.4:4:1:0:7 -18 18515742 . T A 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CATTCACGTCACAGAGTTGA;RSEQ=CATTCCCTTTCATAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:14.7:1:31.7:1:1:0:34.3:6:0.75:0:7.3 1/1:5:5:3,2:0,0:1:0,2:27:1:27.4:1:1:0:36:4:1:0:7 -18 18515772 . C A 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATAGAGCAGGTTTGAAAC;RSEQ=CTCTTTCCGTAGTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:33:1:29.7:1:1:0:30:6:1:0:7 1/1:7:7:5,2:0,0:1:0,2:28.6:1:29.3:1:1:0:38.3:14:1:0:6.6 -18 18515774 . T A 77 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=3.05504;LSEQ=ATAGAGCAGGTTTGAAACCC;RSEQ=CTTTCCGTAGTATCTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:40.5:1:31.5:1:1:0:31.5:4:0.6667:0:7.5 1/1:8:7:4,3:1,0:0.875:0,2:26.3:1:27.7:1:1:0:42.9:14:0.875:0:6.9 -18 18515780 . C T 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTTTGAAACCCTCTTTC;RSEQ=GTAGTATCTGGATGTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:30.3:1:29.7:1:1:0:30:6:1:0:7 1/1:9:9:6,3:0,0:1:0,2:23.1:1:29.3:1:1:0:43.1:18:1:0:6.1 -18 18515798 . A G 89 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51648;SOR=0;LSEQ=TCCGTAGTATCTGGATGTGG;RSEQ=CACTTGGAGCGCTTTGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:19.3:1:31.3:1:1:0:35.8:8:1:0:7.5 1/0:11:7:4,3:3,1:0.6364:2,2:18.4:1:32:1:1:2.09375:46.1:14:0.6364:0:6.7 -18 18515809 . G T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53007;SOR=0.31868;LSEQ=TGGATGTGGACACTTGGAGC;RSEQ=CTTTGACGCTTACGGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:22.5:1:29:1:1:0:40:4:0.5:0:7.5 0/1:9:2:1,1:4,3:0.2222:2,2:26.5:1:30.5:1:1:1.29098:51.5:4:0.2222:0:7 -18 18515813 . T G 86 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGACACTTGGAGCGCTT;RSEQ=GACGCTTACGGTGCAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:19.3:1:30:1:1:0:35.8:8:1:0:7.5 1/0:9:7:3,4:2,0:0.7778:0,2:30:1:30.9:1:0.44444:0:50.4:14:0.7778:0:7.1 -18 18515822 . C T 84 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TTGGAGCGCTTTGACGCTTA;RSEQ=GGTGCAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:28:1:28.3:1:1:0:40:6:1:0:7.7 1/0:11:7:3,4:3,1:0.6364:2,2:32:1:30:1:0.54545:3.51553:50.4:14:0.6364:0:7.1 -18 18515827 . C A 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTTTGACGCTTACGGTG;RSEQ=AAAAGGAAATATCTTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:29.7:1:28:1:1:0:40:6:1:0:7.7 1/1:10:8:3,5:1,0:0.8:0,2:32.8:1:30:1:0.44444:0:50.1:16:1:0:5.9 -18 18515841 . T G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55944;SOR=0.36341;LSEQ=ACGGTGCAAAAGGAAATATC;RSEQ=TCCCATAAAAACTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:37.5:1:32.5:1:0.33333:0:40:4:0.6667:0:7.5 0/1:10:4:2,2:3,2:0.4:2,2:29.3:1:25:1:1:1.43328:55.8:3:0.3333:0:6.8 -18 18515852 . A C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2028;SOR=0.15349;LSEQ=GGAAATATCTTCCCATAAAA;RSEQ=CTAGACAGAAGCATTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:26.5:1:32:1:0.33333:0:40:4:0.6667:0:7.5 0/1:10:2:1,1:4,4:0.2:2,2:19:1:29:1:1:1:51.5:4:0.2:0:7 -18 18515858 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCTTCCCATAAAAACTAGA;RSEQ=AGAAGCATTCTCACAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:23.3:1:33.3:1:1:0:40:6:1:0:7.3 0/1:9:2:1,1:3,4:0.2222:2,2:30.5:1:29:1:1:1.29:60:4:0.2222:0:4 -18 18515880 . A T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCATTCTCACAAACTGG;RSEQ=TTGTGATGTTTGTCCTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:30:0:28:0:1:0:40:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:38.3:1:29.7:1:1:0:49.3:6:1:0:5 -18 18515890 . T A 45 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAACTGGATTGTGATGT;RSEQ=TGTCCTCAACTAACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:8:1:28.7:1:1:0:44.7:6:1:0:6 1/0:3:2:1,1:0,0:0.6667:0,2:39:1:29.5:1:1:0:44:4:0.6667:0:5 -18 18515899 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GATTGTGATGTTTGTCCTCA;RSEQ=CTAACAGAGTTGAAACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:11:0:31:1:1:0:50:4:0.6667:0:7 0/0:3:0:0,0:1,2:0:2,0:23.7:1:31.7:1:1:0:49.3:6:1:0:4.7 -18 18515907 . A C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14286;SOR=Inf;LSEQ=TGTTTGTCCTCAACTAACAG;RSEQ=GTTGAAACTTTCTATTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:11.5:1:30.5:1:1:0:40.3:8:1:0:6 1/0:3:2:1,1:0,1:0.6667:0,2:22:1:33:1:1:0:44:4:0.6667:0:5 -18 18515914 . A C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCAACTAACAGAGTTGAA;RSEQ=CTTTCTATTTACAGAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:18.7:1:32:1:1:0:51.3:6:0.75:0:6.3 1/1:2:2:1,1:0,0:1:0,2:15:1:33:0:1:0:44:4:1:0:5 -18 18515933 . C G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AACTTTCTATTTACAGAGCA;RSEQ=TTTTGAAAGACTCTTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:17.5:1:31:1:1:1.7321:27:4:0.4:0:5.5 1/1:4:4:2,2:0,0:1:0,2:8.5:1:31.3:1:1:0:52.8:8:1:0:4 -18 18515946 . CT C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=CAGAGCACTTTTGAAAGACT;RSEQ=TTTTGGAGAATCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,0:0.4:0,2:31.5:1:30.5:1:1:0:27:4:0.4:0:6 1/0:3:2:1,1:1,0:0.6667:0,2:21.5:1:32:1:1:0:60:4:0.6667:0:3.5 -18 18515956 . A T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=TTGAAAGACTCTTTTTGGAG;RSEQ=ATCTGCAAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:37:1:28:1:1:1.7321:27:4:0.4:0:6 1/0:3:2:1,1:1,0:0.6667:0,2:29.5:1:30:1:1:0:60:4:0.6667:0:3.5 -18 18515963 . A T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=ACTCTTTTTGGAGAATCTGC;RSEQ=AGTGGATATTTGGAGAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:37:1:29:1:1:1.7321:27:4:0.4:0:6 1/0:3:2:1,1:1,0:0.6667:0,2:36:0:31:1:1:0:60:4:0.6667:0:3.5 -18 18515978 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=AGCTTTAAGGATTTCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23:1:28.5:1:1:1:60:4:0.5:0:7.5 0/0:3:0:0,0:2,1:0:2,0:26:1:30.3:1:1:0:56:6:1:0:3.7 -18 18515989 . A T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=ATATTTGGAGAGCTTTAAGG;RSEQ=TTTCATTGGAAACGGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:12:1:30.5:1:1:1:60:4:0.5:0:7.5 0/0:3:0:0,0:2,1:0:2,0:15:1:28.7:1:1:0:56:6:1:0:3.7 -18 18516002 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAAGGATTTCATTGGAAA;RSEQ=GGGAATATCTTCATATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:0.4:2,0:8:0:31:0:0.4:0:40:4:0.4:0:6.5 0/0:1:0:0,0:1,0:0:0,0:12:0:26:0:1:0:48:2:1:0:4 -18 18516003 . G C 48 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTAAGGATTTCATTGGAAAC;RSEQ=GGAATATCTTCATATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:2,0:0.6:0,2:12.7:1:30.7:1:0.4:0:38:6:0.6:0:6.3 1/1:1:1:1,0:0,0:1:0,0:11:0:24:0:1:0:48:2:1:0:4 -18 18516018 . T C 30 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACGGGAATATCTTCATA;RSEQ=AAAATCTAGACAGAGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:24:0:30.5:1:0.33333:0:40:4:0.6667:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18516033 . G A 29 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATATAAAATCTAGACAGA;RSEQ=GCATTCTCAGAAACTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:39:0:29.5:1:1:0:40:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18516084 . T A 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCTCAACCAACGGAGTACA;RSEQ=CCTGTCTTTTGATACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,0:0.5:0,0:2:0:32:0:1:0:41:2:0.5:0:6 1/1:4:4:2,2:0,0:1:0,2:13:1:29.3:1:1:0:50.8:8:1:0:6 -18 18516098 . A G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72867;SOR=1.2884;LSEQ=AGTACATCCTGTCTTTTGAT;RSEQ=CAGCAGTTTGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:16,1:2,2:0.8095:2,1:9.1:1:32.8:1:0.0797:12.75:46.6:34:0.8095:0:4.9 1/1:39:33:25,8:4,2:0.8462:2,2:7.7:1:31.8:1:0.63601:1.54:42:66:0.8462:0:5.5 -18 18516104 . G A 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.105;LSEQ=TCCTGTCTTTTGATACAGCA;RSEQ=TTTGGAAACACTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:18,8:0.0714:2,0:9:0:31:0:1:0:56:4:0.0714:0:7 0/1:51:4:4,0:30,15:0.0784:2,0:16:0:30.8:1:0.29834:0:34.5:8:0.0784:0:7.5 -18 18516116 . T C 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71637;SOR=1.89063;LSEQ=ATACAGCAGTTTGGAAACAC;RSEQ=CTTTTTGTAGAATCTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:2,0:26,12:0.05:2,0:21:0:32:0:1:0:56:4:0.05:0:7 0/1:77:7:6,1:43,27:0.0909:2,2:26.1:1:31.6:1:0.41163:3.72:33.3:14:0.0946:0:7 -18 18516117 . C G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.17239;LSEQ=TACAGCAGTTTGGAAACACT;RSEQ=TTTTTGTAGAATCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:3,1:25,11:0.1:2,2:18.8:1:32.3:1:1:1.31:49:8:0.1:0:6 0/1:78:9:5,4:44,24:0.1154:2,2:15.3:1:31.9:1:0.71603:1.45906:52.9:18:0.1169:0:6.2 -18 18516121 . T C 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.1044;LSEQ=GCAGTTTGGAAACACTCTTT;RSEQ=TGTAGAATCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:29,13:0.0455:2,2:21:1:33:1:0.54017:2.18641:51:4:0.0455:0:8 0/1:80:4:3,1:47,29:0.05:2,2:24.8:1:31.5:1:1:1.84:49.5:8:0.05:0:7.5 -18 18516122 . T G 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49024;SOR=1.99682;LSEQ=CAGTTTGGAAACACTCTTTT;RSEQ=GTAGAATCTGCAAGTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:2,0:29,14:0.0444:2,0:27:0:34:0:1:0:56:4:0.0444:0:7 0/1:82:7:6,1:46,29:0.0854:2,2:32.1:1:32.1:1:0.41351:3.73:33.3:14:0.0854:0:7 -18 18516123 . G A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71812;SOR=0.64291;LSEQ=AGTTTGGAAACACTCTTTTT;RSEQ=TAGAATCTGCAAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:3,1:28,13:0.0889:2,2:28.8:1:30.5:1:1:1.38:46.8:8:0.0889:0:6.8 0/1:85:5:3,2:50,29:0.0588:2,2:26:1:28:1:1:1.14749:53.6:10:0.0595:0:6 -18 18516125 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11776;SOR=0;LSEQ=TTTGGAAACACTCTTTTTGT;RSEQ=GAATCTGCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:31,14:0.0426:2,2:37.5:1:31.5:1:0.54117:2.17347:45.5:4:0.0426:0:6 0/0:89:0:0,0:55,34:0:2,0:23.7:1:29.1:1:1:0:45.7:88:1:0:5.4 -18 18516127 . A C 34 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.04512;LSEQ=TGGAAACACTCTTTTTGTAG;RSEQ=ATCTGCAAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:1,0:31,15:0.0213:2,0:17:0:34:0:1:0:55:2:0.0217:0:8 0/1:90:2:1,1:54,33:0.0222:2,2:18:0:34:0:1:1.62691:59:4:0.0222:0:7 -18 18516128 . AT TA 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54326;SOR=Inf;LSEQ=GGAAACACTCTTTTTGTAGA;RSEQ=CTGCAAGTGGATATTTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:33,16:0:2,0:26:1:29.9:1:1:0:48.3:23.5:1:0:5.6 0/1:92:2:1,1:56,34:0.0217:2,2:31:0:30.3:1:1:1.63772:49:4:0.0217:0:3 -18 18516129 . T A 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47354;SOR=0.6176;LSEQ=GAAACACTCTTTTTGTAGAA;RSEQ=CTGCAAGTGGATATTTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:43:29,14:4,2:0.8776:2,2:26.4:1:30:1:1:1.03:48.3:86:0.8776:0:5.3 1/1:92:75:47,28:9,6:0.8152:2,2:27.2:1:30:1:1:1.12:45.7:74:0.8315:0:5.4 -18 18516130 . C T 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13857;SOR=0.18535;LSEQ=AAACACTCTTTTTGTAGAAT;RSEQ=TGCAAGTGGATATTTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:3:2,1:32,18:0.0566:2,2:40:1:31.7:1:1:1.12:42.7:6:0.0577:0:8 0/1:92:1:1,0:56,35:0.0109:2,0:42:0:32:0:1:0:31:2:0.0109:0:7 -18 18516132 . G A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52614;SOR=Inf;LSEQ=ACACTCTTTTTGTAGAATCT;RSEQ=CAAGTGGATATTTGGATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:37,21:0:2,0:25.1:1:32.1:1:1:0:49.2:116:1:0:5.6 0/1:95:2:1,1:57,36:0.0211:2,2:11.5:1:27.5:1:1:1.57538:39:4:0.0213:0:7 -18 18516133 . C T 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.13717;SOR=0.48637;LSEQ=CACTCTTTTTGTAGAATCTG;RSEQ=AAGTGGATATTTGGATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:53:33,20:5,2:0.8833:2,2:24.6:1:29:1:1:1.50519:49.5:106:0.8833:0:5.4 1/0:98:77:48,29:12,9:0.7857:2,2:29.7:1:28.8:1:0.80118:1.24:45.7:37.5:0.7813:0:5.4 -18 18516136 . G C 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.21074;LSEQ=TCTTTTTGTAGAATCTGCAA;RSEQ=TGGATATTTGGATAGCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:3,0:37,23:0.0476:2,0:39.3:1:33.3:1:0.29339:0:50.7:6:0.0476:0:6 0/1:105:6:5,1:57,41:0.0571:2,2:32.7:1:31.5:1:0.39733:3.56:34:12:0.0577:0:6.2 -18 18516138 . G T 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14363;SOR=0.19012;LSEQ=TTTTTGTAGAATCTGCAAGT;RSEQ=GATATTTGGATAGCTCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:3:2,1:38,23:0.0469:2,2:41:1:31.3:1:1:1.21:42.7:6:0.0469:0:8 0/0:109:1:1,0:62,46:0.0092:2,0:37:0:32:0:1:0:31:2:0.0092:0:7 -18 18516143 . TT CA 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36957;SOR=0.3997;LSEQ=GTAGAATCTGCAAGTGGATA;RSEQ=TGGATAGCTCTAACGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:3:2,1:40,25:0.0441:2,2:35:1:32.2:1:1:1.25:42.7:6:0.0448:0:7 0/1:111:2:1,1:57,42:0.018:2,2:18.5:1:29.5:1:1:1.35297:31:4:0.018:0:6.5 -18 18516146 . G T 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16034;SOR=Inf;LSEQ=GAATCTGCAAGTGGATATTT;RSEQ=GATAGCTCTAACGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:42,28:0:2,0:26.1:1:31.7:1:1:0:48.4:140:0.9859:0:5.5 0/1:113:4:2,2:63,46:0.0354:2,2:30:1:25.8:1:1:1.36568:38.5:3:0.0273:0:6.8 -18 18516147 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5166;SOR=Inf;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=ATAGCTCTAACGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:46,30:0:2,0:24.8:1:31.2:1:1:0:49:75:1:0:5.6 0/1:113:2:1,1:64,47:0.0177:2,2:30.5:1:29:1:1:1.35791:36:4:0.0177:0:6.5 -18 18516152 . C G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52139;SOR=Inf;LSEQ=GCAAGTGGATATTTGGATAG;RSEQ=TCTAACGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:46,31:0:2,0:26:1:32.1:1:1:0:48.9:76:1:0:5.6 0/1:120:2:1,1:68,49:0.0167:2,2:27.5:1:29.5:1:1:1.38385:27:4:0.0169:0:4.5 -18 18516153 . T C 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05816;SOR=0.20162;LSEQ=CAAGTGGATATTTGGATAGC;RSEQ=CTAACGATTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:6:3,3:43,29:0.0769:2,2:16.8:1:30:1:0.68488:1.47508:47.5:12:0.0779:0:6.5 0/1:122:2:1,1:70,50:0.0164:2,2:18.5:1:29:1:1:1.39605:31:4:0.0164:0:6.5 -18 18516155 . T A 62 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.65119;SOR=2.51478;LSEQ=AGTGGATATTTGGATAGCTC;RSEQ=AACGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:1:1,0:44,32:0.0128:2,0:36:0:32:0:1:0:59:2:0.0128:0:8 0/1:126:4:2,2:71,47:0.0317:2,2:33.3:1:31:1:1:1.50536:40.3:8:0.032:0:7.5 -18 18516157 . A G 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53454;SOR=1.73576;LSEQ=TGGATATTTGGATAGCTCTA;RSEQ=CGATTTCGTTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:3:2,1:43,34:0.0375:2,2:20:1:33.7:1:1:1.57:59.7:6:0.0385:0:6.3 0/1:126:8:5,3:68,50:0.0635:2,2:33.8:1:33:1:1:1.22:43.4:16:0.0635:0:6.8 -18 18516158 . C T 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.39862;SOR=0.78358;LSEQ=GGATATTTGGATAGCTCTAA;RSEQ=GATTTCGTTGGAAACGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:81:42:23,19:22,16:0.5185:2,2:29.2:1:30.8:1:0.82418:1.13406:47.9:84:0.525:0:5.5 0/1:129:59:35,24:39,28:0.4574:2,2:25.2:1:29.6:1:1:1.05:48.9:58:0.4531:0:5.6 -18 18516159 . G T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90841;LSEQ=GATATTTGGATAGCTCTAAC;RSEQ=ATTTCGTTGGAAACGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:7:4,3:42,32:0.0854:2,2:20.1:1:28.7:1:1:1.02:49.1:14:0.0864:0:6.7 0/1:128:10:6,4:67,47:0.0781:2,2:28.7:1:29.8:1:1:1.05:41.8:20:0.08:0:6.3 -18 18516162 . T A 56 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30062;SOR=Inf;LSEQ=ATTTGGATAGCTCTAACGAT;RSEQ=TCGTTGGAAACGGGAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:48,35:0:2,0:25.8:1:30.1:1:1:0:49.7:166:1:0:5.7 0/1:133:4:2,2:74,55:0.0301:2,2:28:1:28.3:1:1:1.3424:43.3:8:0.0303:0:5 -18 18516165 . G T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28867;SOR=Inf;LSEQ=TGGATAGCTCTAACGATTTC;RSEQ=TTGGAAACGGGAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:48,36:0:2,0:25.7:1:30.9:1:1:0:49.6:168:1:0:5.7 0/1:136:3:1,2:77,56:0.0221:2,2:33:1:30:1:0.57523:2.72969:45:6:0.0222:0:6.3 -18 18516168 . G C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53258;SOR=Inf;LSEQ=ATAGCTCTAACGATTTCGTT;RSEQ=GAAACGGGAATATCTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:47,37:0:2,0:25.8:1:31.5:1:1:0:49.7:83:1:0:5.7 0/1:144:2:1,1:81,61:0.0139:2,2:19:1:32:1:1:1.32521:41.5:4:0.0141:0:8 -18 18516171 . A C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52727;SOR=Inf;LSEQ=GCTCTAACGATTTCGTTGGA;RSEQ=ACGGGAATATCTTCATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:47,39:0:2,0:25:1:30.1:1:1:0:49.4:172:1:0:5.8 0/1:141:2:1,1:76,63:0.0142:2,2:24:0:33.5:1:1:1.20473:58:4:0.0144:0:8 -18 18516176 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53084;SOR=Inf;LSEQ=AACGATTTCGTTGGAAACGG;RSEQ=AATATCTTCATAAAAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:42,39:0:2,0:26:1:31:1:1:0:50:80:1:0:5.9 0/1:137:2:1,1:70,65:0.0146:2,2:11:1:31.5:1:1:1.07632:41.5:4:0.0146:0:8 -18 18516179 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52874;SOR=Inf;LSEQ=GATTTCGTTGGAAACGGGAA;RSEQ=ATCTTCATAAAAAATCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:41,39:0:2,0:25.9:1:29.3:1:1:0:50.1:79:1:0:5.9 0/1:133:2:1,1:67,64:0.015:2,2:13.5:1:29.5:1:1:1.04653:39:4:0.0152:0:8 -18 18516180 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53239;SOR=Inf;LSEQ=ATTTCGTTGGAAACGGGAAT;RSEQ=TCTTCATAAAAAATCTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:39,38:0:2,0:26.7:1:29.4:1:1:0:50.2:76:1:0:5.9 0/1:132:2:1,1:67,63:0.0152:2,2:24:1:28.5:1:1:1.06303:52.5:4:0.0154:0:6 -18 18516181 . T C 99 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09932;SOR=5.29327;LSEQ=TTTCGTTGGAAACGGGAATA;RSEQ=CTTCATAAAAAATCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:1,0:33,37:0.0139:2,0:22:0:29:0:0.47887:0:59:2:0.0139:0:3 0/1:129:9:5,4:58,58:0.0698:2,2:9:1:31.4:1:1:1.25:51.2:18:0.0714:0:4.2 -18 18516183 . T A 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22164;SOR=0.54905;LSEQ=TCGTTGGAAACGGGAATATC;RSEQ=TCATAAAAAATCTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:61:28,33:4,3:0.8841:2,2:27.8:1:30.7:1:0.69862:1.56097:51.1:60:0.8824:0:6.2 1/1:119:96:45,51:11,11:0.8067:2,2:25.6:1:29.6:1:0.81698:1.13213:49.4:192:0.8067:0:6.3 -18 18516186 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52765;SOR=Inf;LSEQ=TTGGAAACGGGAATATCTTC;RSEQ=TAAAAAATCTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:33,36:0:2,0:27.7:1:30.5:1:1:0:50.4:68:1:0:6.1 0/1:114:2:1,1:52,59:0.0175:2,2:8:0:32.5:1:1:1.13:60:4:0.0179:0:6.5 -18 18516187 . T C 51 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.15709;SOR=0.20117;LSEQ=TGGAAACGGGAATATCTTCA;RSEQ=AAAAAATCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:1,2:32,35:0.0429:2,2:41.7:1:32.3:1:1:1.81347:52.3:6:0.0441:0:6 0/0:113:1:1,0:51,59:0.0088:2,0:24:0:33:0:0.46847:0:32:2:0.0089:0:4 -18 18516188 . AA CT 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.39472;SOR=0.63317;LSEQ=GGAAACGGGAATATCTTCAT;RSEQ=AAAATCTAGACAGAAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:57:25,32:4,3:0.8769:2,2:27.3:1:30.6:1:0.69202:1.6923:50:114:0.8769:0.0615:5.3 1/1:110:90:40,50:9,9:0.8182:2,2:26.4:1:30:1:0.79654:1.2474:48.7:180:0.8333:0.0364:5.3 -18 18516189 . A T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.49515;SOR=1.51422;LSEQ=GAAACGGGAATATCTTCATA;RSEQ=AAAATCTAGACAGAAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:7:4,3:1,0:0.1129:0,2:35.1:1:30:1:1:0:46:14:0.875:0:5.1 0/1:105:17:9,8:0,0:0.1619:0,2:23.4:1:29.5:1:1:0:41.8:34:1:0:5.5 -18 18516193 . A C 71 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41553;SOR=2.99384;LSEQ=CGGGAATATCTTCATAAAAA;RSEQ=TCTAGACAGAAGCACTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:1:1,0:27,35:0.0159:2,0:27:0:34:0:0.44444:0:59:2:0.0161:0:8 0/1:108:5:3,2:46,55:0.0463:2,2:19:1:30.6:1:0.66046:1.78:44.8:10:0.0472:0:6 -18 18516194 . T C 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72871;SOR=0.73376;LSEQ=GGGAATATCTTCATAAAAAA;RSEQ=CTAGACAGAAGCACTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:4:1,3:27,31:0.0645:2,2:38.8:1:32:1:0.61986:2.57604:46:8:0.0645:0:5 0/1:104:5:3,2:45,52:0.0481:2,2:34.2:1:32:1:0.66409:1.72:35:10:0.0495:0:4.6 -18 18516195 . C G 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.79576;LSEQ=GGAATATCTTCATAAAAAAT;RSEQ=TAGACAGAAGCACTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:3:1,2:27,32:0.0484:2,2:24:1:33.3:1:1:1.67387:60:6:0.0484:0:5.3 0/1:103:4:2,2:45,54:0.0388:2,2:33.3:1:33.3:1:1:1.20:45.5:8:0.0392:0:6 -18 18516199 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52011;SOR=Inf;LSEQ=TATCTTCATAAAAAATCTAG;RSEQ=CAGAAGCACTCTCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:28,36:0:2,0:24.7:1:29.8:1:1:0:48.3:128:1:0:5.5 0/1:99:2:1,1:44,53:0.0202:2,2:38:1:32.5:1:1:1.20:27:4:0.0204:0:6 -18 18516200 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15269;SOR=0;LSEQ=ATCTTCATAAAAAATCTAGA;RSEQ=AGAAGCACTCTCAGAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:27,35:0.0313:2,2:34:1:31:1:1:1.29:59.5:4:0.0317:0:5.5 0/0:99:0:0,0:45,54:0:2,0:25.9:1:30.9:1:1:0:47.5:98:1:0:5.3 -18 18516205 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16271;SOR=0;LSEQ=CATAAAAAATCTAGACAGAA;RSEQ=CACTCTCAGAAACTACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:25,33:0.0333:2,2:9.5:1:28:1:1:1.31:22:4:0.0339:0:7 0/0:88:0:0,0:38,50:0:2,0:27.5:1:31:1:1:0:47.5:28.333:1:0:5.3 -18 18516207 . A C 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73514;SOR=0.88579;LSEQ=TAAAAAATCTAGACAGAAGC;RSEQ=CTCTCAGAAACTACTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:27:10,17:13,17:0.4655:2,2:23.1:1:30.2:1:0.78762:1.29401:46.6:54:0.4655:0:5.9 0/1:85:37:14,23:21,25:0.4353:2,2:28.6:1:29.7:1:0.50959:1.37463:48.7:17.5:0.4268:0:5.5 -18 18516210 . C A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.34047;SOR=0.6844;LSEQ=AAAATCTAGACAGAAGCACT;RSEQ=TCAGAAACTACTTTGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:19:7,12:14,19:0.3654:2,2:26.9:1:30:1:0.77436:1.25752:51:38:0.3654:0:6.1 0/1:78:22:9,13:23,33:0.2821:2,2:29:1:29.2:1:1:1.00665:49.5:44:0.2857:0:5.9 -18 18516212 . C T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43138;SOR=0.7171;LSEQ=AATCTAGACAGAAGCACTCT;RSEQ=AGAAACTACTTTGTGATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:17:6,11:14,19:0.34:2,2:28.8:1:28.8:1:0.76348:1.34283:50.2:34:0.34:0:6.1 0/1:78:21:9,12:23,34:0.2692:2,2:29.4:1:28.8:1:1:1.11:49:42:0.2727:0:6 -18 18516224 . T G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.82728;SOR=0.86747;LSEQ=AGCACTCTCAGAAACTACTT;RSEQ=GTGATATCGGCATTCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:12:4,8:11,18:0.2927:2,2:28.6:1:31.8:1:1:1.21632:50.7:24:0.2927:0:6.4 0/1:72:19:8,11:20,33:0.2639:2,2:23.4:1:30.8:1:0.78793:1.20:49.4:38:0.2676:0:6 -18 18516231 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53995;SOR=Inf;LSEQ=TCAGAAACTACTTTGTGATA;RSEQ=CGGCATTCAAGTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:11,23:0:2,0:21.3:1:30.5:1:1:0:46.8:68:1:0:6 0/1:63:2:1,1:25,36:0.0317:2,2:35.5:1:32:0:1:1.43:39:4:0.0328:0:7 -18 18516232 . CG GT 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0682;LSEQ=CAGAAACTACTTTGTGATAT;RSEQ=GCATTCAAGTCACAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:10,21:0.0313:2,0:43:0:30:0:1:0:45:2:0.0313:0:6 0/1:60:2:1,1:23,35:0.0333:2,2:26:0:32.8:1:1:1.51:43:4:0.0333:0:3 -18 18516233 . G T 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93179;LSEQ=AGAAACTACTTTGTGATATC;RSEQ=GCATTCAAGTCACAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:29:9,20:0,0:0.9667:0,2:22.1:1:30.8:1:1:0:46.4:58:1:0:6.1 1/1:56:54:21,33:0,0:0.9643:0,2:21.9:1:30.1:1:1:0:46.4:53:1:0:5.5 -18 18516235 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53457;SOR=Inf;LSEQ=AAACTACTTTGTGATATCGG;RSEQ=ATTCAAGTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:8,21:0:2,0:22.6:1:32.1:1:1:0:47.3:58:1:0:6.1 0/1:52:2:1,1:19,31:0.0385:2,2:31.5:1:29.5:1:1:1.62:39:4:0.0385:0:7 -18 18516246 . C A 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12911;SOR=0.17189;LSEQ=TGATATCGGCATTCAAGTCA;RSEQ=AGAGTTGAACATTCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:2,1:4,15:0.1364:2,2:9:1:31:1:0.16883:6.66:51.7:6:0.1364:0:7 0/1:39:1:0,1:14,24:0.0256:2,0:17:0:32:0:1:0:55:2:0.0256:0:7 -18 18516256 . C T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54234;SOR=Inf;LSEQ=ATTCAAGTCACAGAGTTGAA;RSEQ=ATTCCCTTTCATGGAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:4,12:0:2,0:20.8:1:32.3:1:1:0:42.3:32:0.9412:0:6.3 0/1:32:3:2,1:7,21:0.0938:2,2:9.3:1:30.7:1:0.19488:5.60:34:6:0.0938:0:6.7 -18 18516261 . C G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGTCACAGAGTTGAACATTC;RSEQ=CTTTCATGGAGCAGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:2,6:0,4:0.6667:0,2:27.1:1:31.9:1:0.51515:0:35.6:16:0.6667:0:6.8 1/0:27:18:4,14:3,6:0.6667:2,2:15.7:1:31.4:1:0.65266:1.71239:41.4:36:0.6667:0:5.6 -18 18516267 . A T 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTTGAACATTCCCTTTC;RSEQ=TGGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:2,6:0,0:1:0,2:24.8:1:31.3:1:1:0:35.1:16:1:0:7.1 1/1:9:8:2,6:1,0:0.8889:0,2:24.3:1:31.8:1:0.33333:0:37.1:16:0.8889:0:6.6 -18 18516269 . G A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGTTGAACATTCCCTTTCAT;RSEQ=GAGCAGGTTTGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:2,4:0,0:0.8571:0,2:26.3:1:30.5:1:1:0:32.7:12:0.8571:0:7.2 1/1:8:8:2,6:0,0:1:0,2:24.9:1:32:1:1:0:37:16:1:0:6.8 -18 18516275 . G C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCCCTTTCATGGAGCA;RSEQ=GTTTGAAACACTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:20:1:31.4:1:1:0:34.4:14:1:0:7.3 1/1:7:6:1,5:1,0:0.8571:0,2:23.2:1:32:1:0.28571:0:38.7:12:0.8571:0:6.8 -18 18516279 . T G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCCCTTTCATGGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:1,3:0.4286:2,2:17:1:31:1:1:1.41:35.7:6:0.4286:0:7.7 0/1:7:3:1,2:1,3:0.4286:2,2:23:1:32.3:1:1:1.41:42.3:6:0.4286:0:7.7 -18 18516285 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46154;SOR=Inf;LSEQ=TCATGGAGCAGGTTTGAAAC;RSEQ=CTCTTTTTGTAGTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:10:1:30.7:1:1:0:34.4:14:1:0:7.3 0/1:7:2:1,1:1,4:0.2857:2,2:20.5:1:29.5:1:1:3.16:24:4:0.2857:0:4 -18 18516294 . G A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGTTTGAAACACTCTTTTT;RSEQ=TAGTATCTGGAAGTGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:8:1:33:0:1:0:32:4:1:0:7.5 0/1:6:2:1,1:1,3:0.3333:2,2:21:1:27.5:1:1:2.45:24:4:0.3333:0:4 -18 18516299 . A G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAACACTCTTTTTGTAGT;RSEQ=TCTGGAAGTGGACCTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:6:0:33:0:1:0:42:2:1:0:8 0/1:5:2:1,1:1,2:0.4:2,2:8.5:1:32.5:1:1:1.73:41.5:4:0.4:0:6.5 -18 18516549 . A T 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAAACCTACACAGAAGC;RSEQ=TTCTCAGAAACTTCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:9:0:28:1:1:1:28:4:0.3333:0:5.5 -18 18516556 . G C 87 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CCTACACAGAAGCATTCTCA;RSEQ=AAACTTCTTTGTGATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:6.5:1:31.5:1:1:0:31:4:1:0:0.5 1/0:11:7:4,3:2,2:0.6364:2,2:10.6:1:31.3:1:1:1.30:49.3:14:0.6364:0:1.1 -18 18516560 . C A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACAGAAGCATTCTCAGAAA;RSEQ=TTCTTTGTGATGTGTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:31.5:1:1:0:31:4:1:0:0.5 0/1:12:2:1,1:5,5:0.1667:2,2:20:0:28.5:1:1:1:28:4:0.1667:0:5.5 -18 18516571 . T C 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCTCAGAAACTTCTTTGTGA;RSEQ=GTGTGTCCTCAACTAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:15.7:1:22.7:1:1:0:37.3:2:1:0:2 0/1:12:2:1,1:5,5:0.1667:2,2:31:0:29:1:1:1:28:4:0.1667:0:5.5 -18 18516586 . A G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGATGTGTGTCCTCAACT;RSEQ=ACAGAGTTGAACCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:16.4:1:29.4:1:1:0:38:10:1:0:1.8 0/1:12:2:1,1:5,5:0.1667:2,2:26:1:33:0:1:1:45.5:4:0.1818:0:3.5 -18 18516599 . C A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTCAACTAACAGAGTTGAAC;RSEQ=TTTCTTTTGACAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:32:0:30:0:1:0:50:2:0.2:0:5 0/1:10:2:1,1:4,4:0.2:2,2:13:1:31:1:1:1:45.5:4:0.2:0:3.5 -18 18516601 . T A 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09524;SOR=0;LSEQ=CAACTAACAGAGTTGAACCT;RSEQ=TCTTTTGACAGAGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:22.5:1:29.5:1:1:1.73:39:4:0.4:0:1.5 0/0:10:0:0,0:4,4:0:2,0:10.4:1:30.3:1:1:0:44.4:16:0.8:0:2.3 -18 18516880 . T G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATCTTCCCATAAAAAC;RSEQ=AGACAGAAGGATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:28.3:1:31:1:1:0:35.7:6:1:0:5.7 1/1:3:3:3,0:0,0:1:0,0:17.7:1:30.7:1:1:0:40:6:1:0:6.7 -18 18516896 . C G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56044;SOR=0.40284;LSEQ=AAACTAGACAGAAGGATTCT;RSEQ=AGAAACATGTTTGTGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:24.5:1:33.5:1:1:0:38.5:4:0.5:0:6 0/1:11:3:3,0:6,2:0.2727:2,0:21.7:1:33.3:1:1:0:34.3:6:0.2727:0:7.7 -18 18516900 . A G 34 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.62114;LSEQ=TAGACAGAAGGATTCTCAGA;RSEQ=ACATGTTTGTGATGTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:3,0:0.25:0,0:16:0:34:0:1:0:37:2:0.25:0:7 0/1:12:2:2,0:7,3:0.1667:2,0:31:1:34:0:1:0:40:4:0.1667:0:7.5 -18 18516904 . T A 109 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGGATTCTCAGAAACA;RSEQ=GTTTGTGATGTATGTACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:32.3:1:30.5:1:1:0:36:8:1:0:6 1/1:13:13:10,3:0,0:1:0,2:20.6:1:29.5:1:1:0:33.1:26:1:0:7.1 -18 18516916 . A G 126 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAACATGTTTGTGATGT;RSEQ=TGTACTCAGCTAAGAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:25.6:1:32.4:1:1:0:36.8:10:1:0:6.4 1/1:16:16:12,4:0,0:1:0,2:25.7:1:31.5:1:1:0:32.3:32:1:0:7.3 -18 18516930 . G C 126 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATGTATGTACTCAGCTAA;RSEQ=AGAGTGGAACCTTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:21.8:1:32.2:1:1:0:41.7:12:1:0:6.7 1/1:16:16:12,4:0,0:1:0,2:35.6:1:31.7:1:1:0:32.3:32:1:0:7.3 -18 18516966 . T A 138 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTACAGAGCAGCTTTGA;RSEQ=ACACTATTTTTGTAGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:34.7:1:29.7:1:1:0:48.3:12:1:0:7.5 1/1:25:25:15,10:0,0:1:0,2:26.8:1:29.8:1:1:0:40.6:50:1:0:7.7 -18 18516969 . A T 139 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTACAGAGCAGCTTTGATAC;RSEQ=CTATTTTTGTAGAATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:35.7:1:30.2:1:1:0:48.3:12:1:0:7.5 1/1:25:25:15,10:0,0:1:0,2:26.7:1:30:1:1:0:40.6:50:1:0:7.7 -18 18516975 . T G 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGCTTTGATACACTATT;RSEQ=TTGTAGAATCTGCAATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:37.7:1:29.5:1:1:0:48.3:12:1:0:7.5 0/1:25:2:1,1:14,9:0.08:2,2:25.5:1:28:1:1:1.52748:24.5:4:0.08:0:7.5 -18 18516980 . A G 139 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGATACACTATTTTTGT;RSEQ=GAATCTGCAATTTGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:43.2:1:32:1:1:0:50.6:10:1:0:7.6 1/1:24:24:14,10:0,0:1:0,2:27.1:1:30.4:1:1:0:40.6:48:1:0:7.7 -18 18516983 . A T 131 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATACACTATTTTTGTAGA;RSEQ=TCTGCAATTTGATATTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:40.2:1:31:1:1:0:50.6:10:1:0:7.6 1/1:21:21:11,10:0,0:1:0,2:30:1:29.9:1:1:0:41.5:42:1:0:7.8 -18 18516991 . T A 124 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTGTAGAATCTGCAA;RSEQ=TTGATATTTTGATTGCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:32.2:1:31.6:1:1:0:50.6:10:1:0:7.6 1/1:19:19:9,10:0,0:1:0,2:27.4:1:29.3:1:1:0:44:38:1:0:7.7 -18 18516993 . T G 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54629;SOR=Inf;LSEQ=TTTTTGTAGAATCTGCAATT;RSEQ=GATATTTTGATTGCTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:22.1:1:29.9:1:1:0:47.6:14:1:0:7.1 0/1:19:4:2,2:7,8:0.2105:2,2:34.5:1:31.5:1:1:1.13:57.8:8:0.2105:0:8 -18 18517001 . T A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTGCAATTTGATATTT;RSEQ=GATTGCTTTAAAGATATCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:18.7:1:31.3:1:1:0:47.6:14:1:0:7.1 1/1:17:17:8,9:0,0:1:0,2:21.9:1:29.2:1:1:0:46.6:34:1:0:7.6 -18 18517013 . A C 101 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATATTTTGATTGCTTTAA;RSEQ=GATATCGTTGGAAACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:16.7:1:31:1:1:0:48.8:12:1:0:7 1/1:14:12:5,7:0,0:0.8571:0,2:15.9:1:28.3:1:1:0:49.7:11:0.8462:0:7.5 -18 18517028 . CA AG 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAAAGATATCGTTGGAAA;RSEQ=GGAATATCTTCATATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:21:1:31.2:1:1:0:50:8:1:0.5:6 1/1:2:2:0,2:0,0:1:0,0:38.5:1:30.5:1:1:0:44.5:4:1:0:6 -18 18517038 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTTGGAAACAGGAATATC;RSEQ=TCATATAAAATCTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30:0:34:0:1:0:40:4:1:0:5 1/1:2:2:0,2:0,0:1:0,0:30:0:32.5:1:1:0:44.5:4:1:0:6 -18 18517044 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACAGGAATATCTTCATA;RSEQ=AAAATCTAGACAGAAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24:0:34.5:1:1:0:40:4:1:0:5 1/1:2:2:0,2:0,0:1:0,0:24:0:32.5:1:1:0:44.5:4:1:0:6 -18 18517062 . A C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATAAAATCTAGACAGAAGC;RSEQ=CTCTCGGAAACGACTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:6:0:33:0:1:0:40:4:1:0:5 0/1:6:2:2,0:2,2:0.3333:2,0:14:1:31.5:1:0.46667:0:31:4:0.3333:0:8 -18 18517063 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=ATAAAATCTAGACAGAAGCA;RSEQ=TCTCGGAAACGACTTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5:0:32:0:1:0:40:4:1:0:5 0/1:6:2:0,2:4,0:0.3333:0,0:5:0:31:1:0.06667:0:44.5:4:0.3333:0:6 -18 18517068 . G A 63 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTAGACAGAAGCACTCTC;RSEQ=GAAACGACTTTGTGATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:4,0:0,0:1:0,0:16.5:1:31.8:1:1:0:30.8:8:1:0:7.8 -18 18517074 . G T 83 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAAGCACTCTCGGAAAC;RSEQ=ACTTTGTGATATCTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:5:0:33:0:1:0:57:2:1:0:7 1/1:6:6:6,0:0,0:1:0,0:16.5:1:32.2:1:1:0:32.5:12:1:0:7.5 -18 18517100 . T A 122 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGATATCTGCATTCAAGTC;RSEQ=CAGAGTTGAACGTTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:31:0:30:0:1:0:57:2:1:0:7 1/1:16:16:13,3:0,0:1:0,2:24.4:1:30.6:1:1:0:35.4:32:1:0:6.4 -18 18517104 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATCTGCATTCAAGTCTCAG;RSEQ=GTTGAACGTTCCCTTTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:18:1:29.5:1:1:0:43:4:1:0:7 0/1:19:2:1,1:14,3:0.1053:2,2:13:1:29.5:1:0.38596:4.1833:51.5:4:0.1053:0:5 -18 18517112 . G A 141 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAGTCTCAGAGTTGAAC;RSEQ=TTCCCTTTCTTAGAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:18.7:1:29.7:1:1:0:48.7:6:1:0:7 1/1:26:26:19,7:0,0:1:0,2:21.8:1:30.1:1:1:0:38.9:52:1:0:6.5 -18 18517116 . C G 130 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.39448;SOR=0.32526;LSEQ=AGTCTCAGAGTTGAACGTTC;RSEQ=CTTTCTTAGAGCAGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:0.8333:0,2:14.2:1:31:1:1:0:43:10:0.8333:0:7 1/0:31:19:14,5:9,2:0.6129:2,2:23.5:1:30.7:1:1:1.5828:34.7:38:0.6129:0:7 -18 18517122 . T A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36303;SOR=0.28971;LSEQ=AGAGTTGAACGTTCCCTTTC;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:3,2:0.1667:2,0:7:0:33:0:1:0:22:2:0.1667:0:3 0/1:38:2:2,0:23,11:0.0526:2,0:7:0:31:1:1:0:31:4:0.0556:0:5 -18 18517123 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36303;SOR=0.28971;LSEQ=GAGTTGAACGTTCCCTTTCT;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:3,2:0.1667:2,0:9:0:27:0:1:0:30:2:0.1667:0:8 0/1:38:2:1,1:24,10:0.0526:2,2:32:1:32.5:1:0.52381:2.33552:51.5:4:0.0556:0:5 -18 18517130 . G C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2901;SOR=2.14774;LSEQ=ACGTTCCCTTTCTTAGAGCA;RSEQ=GTTTGAAACACTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:4,2:3,2:0.5455:2,2:21.2:1:26.8:1:1:1.30:42.3:5:0.5:0:6.5 1/0:47:34:22,12:10,3:0.7234:2,2:21.2:1:30.9:1:0.50331:1.79629:41.3:68:0.7391:0:6.5 -18 18517134 . T G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52342;SOR=1.74944;LSEQ=TCCCTTTCTTAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:3,2:4,3:0.4167:2,2:26.4:1:29:1:1:1.11:43:4:0.3636:0:7 1/0:52:29:16,13:17,6:0.5577:2,2:22.7:1:30.8:1:0.24683:2.26525:38.8:58:0.5577:0:6.5 -18 18517138 . A C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTCTTAGAGCAGGTTTGAA;RSEQ=CACTCTTTTTGTAGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:16.5:1:30.6:1:1:0:41.7:30:1:0:5.1 0/1:58:2:1,1:34,22:0.0345:2,2:38.5:1:31:1:1:1.53351:51.5:4:0.0345:0:5 -18 18517139 . CACTCT ACTCA 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTTAGAGCAGGTTTGAAA;RSEQ=TTTTGTAGTATCTGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:17.4:1:32.5:1:1:0:41.7:30:1:0:5.1 0/1:62:2:1,1:36,23:0.0323:2,2:45:1:30.4:1:1:1.55335:40:4:0.0323:0:3 -18 18517141 . C A 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTTAGAGCAGGTTTGAAACA;RSEQ=TCTTTTTGTAGTATCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,6:0:2,0:18.1:1:32.9:1:1:0:40.4:32:0.9412:0:5.3 0/1:63:3:2,1:36,24:0.0476:2,2:21.7:1:27.7:1:1:1.33:43.3:6:0.0476:0:6 -18 18517145 . T A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCAGGTTTGAAACACTCT;RSEQ=TTTGTAGTATCTGGAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:0:2,0:18.5:1:30.7:1:1:0:42.1:38:1:0:4.6 0/1:69:2:2,0:39,28:0.029:2,0:20:1:27.5:1:0.51066:0:52.5:4:0.0299:0:5.5 -18 18517147 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.29385;SOR=0.39153;LSEQ=GCAGGTTTGAAACACTCTTT;RSEQ=TGTAGTATCTGGAAGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:0.1053:2,2:20.5:1:32.5:1:1:1.77272:60:4:0.1053:0:3.5 0/1:69:3:2,1:39,27:0.0435:2,2:21.7:1:31:1:1:1.38:60:6:0.0435:0:4.3 -18 18517148 . T G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31269;SOR=0.41408;LSEQ=CAGGTTTGAAACACTCTTTT;RSEQ=GTAGTATCTGGAAGTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:12,6:0.1:2,2:15:1:33.5:1:1:1.92731:31.5:4:0.1:0:8 0/1:69:3:2,1:39,27:0.0435:2,2:31:1:33.3:1:1:1.38:40.7:6:0.0441:0:6.7 -18 18517150 . T A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.30216;SOR=0.402;LSEQ=GGTTTGAAACACTCTTTTTG;RSEQ=AGTATCTGGAAGTGGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:12,6:0.1:2,2:17:1:31:1:1:1.92731:31.5:4:0.1:0:8 0/1:71:3:2,1:39,29:0.0423:2,2:33:1:31.3:1:1:1.48:40.7:6:0.0423:0:6.7 -18 18517151 . A C 72 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0412;SOR=0.24006;LSEQ=GTTTGAAACACTCTTTTTGT;RSEQ=GTATCTGGAAGTGGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:3,2:10,6:0.2381:2,2:20.4:1:31:1:1:1.10551:57.6:10:0.2381:0:3.8 0/1:73:5:4,1:37,31:0.0685:2,2:22.8:1:31.4:1:0.37721:3.30:54.6:10:0.0685:0:4.4 -18 18517153 . T A 83 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1;LSEQ=TTGAAACACTCTTTTTGTAG;RSEQ=ATCTGGAAGTGGACATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:13,7:0.0909:2,2:20:1:31:1:1:1.80284:31.5:4:0.0909:0:8 0/1:77:7:4,3:39,31:0.0909:2,2:31.1:1:29.6:1:1:1.06:44.7:14:0.0909:0:5.6 -18 18517154 . A G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14788;SOR=2.05355;LSEQ=TGAAACACTCTTTTTGTAGT;RSEQ=TCTGGAAGTGGACATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:7,3:7,4:0.4545:2,2:28.3:1:32.6:1:1:1.32:34.3:20:0.4545:0:5.8 1/0:79:50:26,24:18,11:0.6329:2,2:26.3:1:30.9:1:0.48258:1.50261:43.9:100:0.6329:0:5.2 -18 18517160 . A T 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5728;SOR=Inf;LSEQ=ACTCTTTTTGTAGTATCTGG;RSEQ=AGTGGACATTTGGAGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:0:2,0:24:1:30.2:1:1:0:41.7:50:1:0:4.6 0/1:86:4:3,1:43,39:0.0465:2,2:16.3:1:29.3:1:0.61984:2.69:53:8:0.0476:0:5 -18 18517161 . A T 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCTTTTTGTAGTATCTGGA;RSEQ=GTGGACATTTGGAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:0:2,0:24.7:1:30.9:1:1:0:41.7:50:1:0:4.6 0/1:87:2:1,1:46,39:0.023:2,2:11:0:29:1:1:1.17724:48:4:0.023:0:5 -18 18517169 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05046;SOR=0;LSEQ=GTAGTATCTGGAAGTGGACA;RSEQ=TTGGAGCGCTTTGACGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:16,8:0.0769:2,2:28.5:1:32:1:1:1.94371:52:4:0.08:0:1.5 0/0:88:0:0,0:45,43:0:2,0:28.3:1:29.7:1:1:0:45.8:87:1:0:4.8 -18 18517176 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05136;SOR=0;LSEQ=CTGGAAGTGGACATTTGGAG;RSEQ=GCTTTGACGCCTTTGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:15,9:0.0769:2,2:19.5:1:32.5:1:1:1.63293:51.5:4:0.0769:0:1 0/0:87:0:0,0:42,41:0:2,0:29.4:1:30.9:1:1:0:46.1:82:0.9535:0:4.8 -18 18517177 . G A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00047;SOR=0.11835;LSEQ=TGGAAGTGGACATTTGGAGC;RSEQ=CTTTGACGCCTTTGGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:6,3:10,7:0.3462:2,2:26.6:1:30.8:1:1:1.38:50.8:18:0.3462:0:3.9 0/1:87:5:4,1:40,42:0.0575:2,2:42:1:30.4:1:0.36038:4.14:54.6:10:0.0581:0:4.4 -18 18517181 . T G 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGGACATTTGGAGCGCTT;RSEQ=GACGCCTTTGGTGAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:16,10:0:2,0:32.2:1:31:1:1:0:42.3:52:1:0:4.3 0/1:85:2:1,1:41,42:0.0235:2,2:31:0:31:1:1:1.02:48:4:0.0238:0:5 -18 18517184 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00266;SOR=4.21098;LSEQ=GGACATTTGGAGCGCTTTGA;RSEQ=GCCTTTGGTGAAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:7,5:9,5:0.4615:2,2:36.3:1:31.4:1:1:1.27328:31.4:24:0.4615:0:5.8 1/0:84:66:31,35:8,8:0.7857:2,2:29.2:1:30.4:1:1:1.12736:44.9:132:0.7857:0:4.8 -18 18517187 . C G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTTGGAGCGCTTTGACGC;RSEQ=TTTGGTGAAAAAGGAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:16,10:0:2,0:32.8:1:31.9:1:1:0:42.3:52:1:0:4.3 0/1:83:2:1,1:40,40:0.0241:2,2:29:0:32.5:1:1:1:60:4:0.0244:0:4.5 -18 18517189 . T C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55472;SOR=0.60551;LSEQ=TTTGGAGCGCTTTGACGCCT;RSEQ=TGGTGAAAAAGGAAATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:1,0:15,10:0.0385:2,0:32:0:32:0:1:0:60:2:0.04:0:3 0/1:85:2:1,1:41,42:0.0235:2,2:19.5:1:29:0:1:1.02:48:4:0.0238:0:3.5 -18 18517194 . GA G 79 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.98696;LSEQ=AGCGCTTTGACGCCTTTGGT;RSEQ=AAAAGGAAATGTCTTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:16,9:0.0741:2,2:39:1:32:1:1:1.73837:31.5:4:0.0741:0:8 0/1:82:6:3,3:36,40:0.0732:2,2:26.3:1:30.6:1:1:1.11:45.5:12:0.0741:0.0244:6 -18 18517202 . A G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02376;SOR=2.92714;LSEQ=GACGCCTTTGGTGAAAAAGG;RSEQ=AATGTCTTCCCATAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:5,4:11,6:0.3462:2,2:21.7:1:30.7:1:0.69245:1.44479:32.4:18:0.3462:0:5.2 1/0:77:47:21,26:13,15:0.6104:2,2:22.3:1:31.6:1:1:1.07201:44.3:94:0.6104:0:4.7 -18 18517203 . A C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06436;SOR=0;LSEQ=ACGCCTTTGGTGAAAAAGGA;RSEQ=ATGTCTTCCCATAAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:15,9:0.0769:2,2:25.5:1:32:1:1:1.63293:54:4:0.0769:0:4.5 0/0:75:0:0,0:33,42:0:2,0:23.5:1:29.6:1:1:0:47.3:74:1:0:4.7 -18 18517205 . T C 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77242;SOR=1.34686;LSEQ=GCCTTTGGTGAAAAAGGAAA;RSEQ=GTCTTCCCATAAAAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:3,1:12,9:0.1538:2,2:34.5:1:30.3:1:0.62648:2.18:26.5:8:0.1538:0:7.3 0/1:71:14:5,9:26,30:0.1972:2,2:27.6:1:31.2:1:0.55631:1.55027:44:28:0.2029:0:5.6 -18 18517206 . GTCTTC ATCTT 68 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32208;SOR=Inf;LSEQ=CCTTTGGTGAAAAAGGAAAT;RSEQ=CCATAAAAACTAGACAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:28.4:1:31.9:1:1:0:42:50:1:0:4.3 0/1:71:5:2,3:27,35:0.0704:2,2:40.4:1:29.3:1:1:1.15464:55.8:10:0.0704:0:4.8 -18 18517211 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTGAAAAAGGAAATGTCTT;RSEQ=CCATAAAAACTAGACAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:27.5:1:31.2:1:1:0:41.3:48:1:0:4.2 0/1:59:2:1,1:25,32:0.0339:2,2:20:1:31.5:1:1:1.27:55.5:4:0.0339:0:5.5 -18 18517213 . C A 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41719;SOR=0.53287;LSEQ=TGAAAAAGGAAATGTCTTCC;RSEQ=ATAAAAACTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:2,1:12,9:0.125:2,2:23.7:1:28.3:1:1:1.48:28.3:6:0.125:0:7.7 0/1:57:4:1,3:23,30:0.0702:2,2:21.3:1:29.5:1:0.63108:2.26952:48.5:8:0.0702:0:5.8 -18 18517214 . A T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAAAAGGAAATGTCTTCCC;RSEQ=TAAAAACTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,9:0:2,0:26.3:1:30.5:1:1:0:41:46:0.9583:0:4.1 0/1:56:2:1,1:22,30:0.0357:2,2:17:1:32.5:1:1:1.36:55.5:4:0.037:0:5.5 -18 18517216 . A C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20064;SOR=0.44608;LSEQ=AAAAGGAAATGTCTTCCCAT;RSEQ=AAAACTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:3,3:9,5:0.2609:2,2:24.7:1:31.3:1:0.64241:1.74629:48.7:12:0.2609:0:5.3 0/1:52:7:3,4:13,25:0.1346:2,2:25.9:1:30.9:1:0.68597:1.43:53:14:0.1346:0:4.4 -18 18517220 . A G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35922;SOR=0.40547;LSEQ=GGAAATGTCTTCCCATAAAA;RSEQ=CTAGACAGAAGCATTCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:12,8:0.1304:2,2:16.7:1:29.7:1:1:1.32:28.3:6:0.1304:0:7.7 0/1:53:3:1,2:22,28:0.0566:2,2:19:1:33:1:1:1.55859:50.3:6:0.0566:0:5.3 -18 18517222 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36706;SOR=0.42219;LSEQ=AAATGTCTTCCCATAAAAAC;RSEQ=AGACAGAAGCATTCTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:12,8:0.1304:2,2:14.7:1:28.7:1:1:1.32:28.3:6:0.1304:0:7.7 0/1:51:3:1,2:21,27:0.0588:2,2:17:1:32.3:1:1:1.54264:50.3:6:0.0588:0:5.3 -18 18517227 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTCCCATAAAAACTAGAC;RSEQ=GAAGCATTCTAAGAAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:19.5:1:30:1:1:0:42.3:44:1:0:4.1 0/1:49:2:1,1:19,28:0.0408:2,2:40:1:30:1:1:1.46:53.5:4:0.0417:0:5.5 -18 18517233 . A T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATAAAAACTAGACAGAAGC;RSEQ=TTCTAAGAAACTTCTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:19.8:1:29.4:1:1:0:41.3:36:1:0:4.4 0/1:41:2:1,1:16,23:0.0488:2,2:12:1:32:1:1:1.42:49.5:4:0.0488:0:7.5 -18 18517237 . T C 74 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1626;SOR=Inf;LSEQ=AAAACTAGACAGAAGCATTC;RSEQ=AAGAAACTTCTTTGGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:20.3:1:29.3:1:1:0:44.8:32:1:0:4.2 0/1:34:5:2,3:14,15:0.1471:2,2:16.4:1:32.2:1:1:1.38634:55.8:10:0.1563:0:4.8 -18 18517238 . A C 107 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49726;SOR=1.94347;LSEQ=AAACTAGACAGAAGCATTCT;RSEQ=AGAAACTTCTTTGGGATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:8,5:0.1875:2,2:8.7:1:29.7:1:1:1.23:23.7:6:0.1875:0:5.3 0/1:32:10:2,8:12,10:0.3125:2,2:9.1:1:32.4:1:0.12406:4.57201:35.5:20:0.3226:0:5.3 -18 18517243 . A T 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27991;SOR=Inf;LSEQ=AGACAGAAGCATTCTAAGAA;RSEQ=CTTCTTTGGGATATATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:18.2:1:29.7:1:1:0:47.2:32:1:0:4.1 0/1:26:4:1,3:10,12:0.1538:2,2:13.8:1:30:1:0.61371:2.41924:54.8:8:0.1538:0:4.8 -18 18517245 . T A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53323;SOR=0.64874;LSEQ=ACAGAAGCATTCTAAGAAAC;RSEQ=TCTTTGGGATATATGTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:5,3:3,4:0.5333:2,2:21.1:1:30.6:1:0.61927:2.10:46.6:16:0.5333:0:5 0/1:26:11:6,5:5,10:0.4231:2,2:34.8:1:29:1:0.42586:2.32:49:10:0.4:0:4.8 -18 18517247 . C T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74753;SOR=0.6651;LSEQ=AGAAGCATTCTAAGAAACTT;RSEQ=TTTGGGATATATGTACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:5,4:2,3:0.5625:2,2:18.4:1:30:1:1:1.79:48:18:0.5625:0:5.3 0/1:24:11:6,5:4,5:0.4583:2,2:34.5:1:30.1:1:1:1.47:49:22:0.4583:0:4.8 -18 18517248 . T C 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26387;SOR=Inf;LSEQ=GAAGCATTCTAAGAAACTTC;RSEQ=TTGGGATATATGTACTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:17.7:1:29.5:1:1:0:49.6:30:1:0:4.4 0/1:23:3:0,3:9,11:0.1304:2,0:11.7:1:32:1:0.25296:0:57.3:6:0.1364:0:5 -18 18517252 . G C 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27005;SOR=Inf;LSEQ=CATTCTAAGAAACTTCTTTG;RSEQ=GATATATGTACTCAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:19.6:1:30.7:1:1:0:51.4:26:1:0:4.4 0/1:21:3:1,2:9,7:0.1429:2,2:13.3:1:32.3:1:0.58204:2.44724:57.3:6:0.1429:0:5.7 -18 18517257 . T G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52941;SOR=Inf;LSEQ=TAAGAAACTTCTTTGGGATA;RSEQ=ATGTACTCAACTAACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:20.5:1:29.6:1:1:0:53.9:24:1:0:4.4 0/1:22:2:1,1:10,10:0.0909:2,2:14.5:1:31:1:1:1:53.5:4:0.0952:0:5.5 -18 18517270 . A T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGGATATATGTACTCAACT;RSEQ=ACAGAGTTGAACCTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:23.5:1:29.1:1:1:0:48.6:22:1:0:5.9 0/1:29:2:1,1:15,12:0.069:2,2:9:0:31:1:1:1.24034:33:4:0.0741:0:5.5 -18 18517272 . CA AG 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74631;SOR=0.75491;LSEQ=GGATATATGTACTCAACTAA;RSEQ=GAGTTGAACCTTTCTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:4,2:4,5:0.4:2,2:7.2:1:29.8:1:0.60839:2.35:50.3:12:0.4:0.2667:6.7 0/1:30:10:6,4:11,8:0.3333:2,2:11:0:31.2:1:1:1.09:44.6:20:0.3333:0:6.1 -18 18517273 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.72056;LSEQ=GATATATGTACTCAACTAAC;RSEQ=GAGTTGAACCTTTCTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:3,5:0.0909:2,0:43:0:29:0:0.44444:0:47:2:0.1111:0:8 0/1:30:2:1,1:10,8:0.0667:2,2:21:0:32:0:1:1.23603:59:4:0.1:0:6.5 -18 18517278 . T A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04897;LSEQ=ATGTACTCAACTAACAGAGT;RSEQ=GAACCTTTCTATTTATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:4,2:4,5:0.4:2,2:8.7:1:28.5:1:0.60839:2.35:50.3:12:0.4:0:6.7 0/1:34:14:8,6:11,9:0.4118:2,2:12.9:1:29:1:1:1.09:46.2:28:0.4242:0:6.2 -18 18517282 . C T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54512;SOR=Inf;LSEQ=ACTCAACTAACAGAGTTGAA;RSEQ=CTTTCTATTTATAGATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:20.8:1:31:1:1:0:49.6:15:1:0:6 0/1:37:3:2,1:19,13:0.0811:2,2:32:1:30:1:1:1.36:55.3:6:0.0811:0:7 -18 18517284 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAACTAACAGAGTTGAACC;RSEQ=TTCTATTTATAGATCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:20.5:1:30.7:1:1:0:49:34:1:0:6.1 0/1:37:2:1,1:21,14:0.0541:2,2:32:0:31.5:1:1:1.4832:59:4:0.0541:0:6.5 -18 18517286 . T C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89084;LSEQ=AACTAACAGAGTTGAACCTT;RSEQ=CTATTTATAGATCAGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:9,7:0.0588:2,0:20:0:33:0:0.47059:0:49:2:0.0588:0:6 0/1:38:2:1,1:21,15:0.0526:2,2:36:1:29.5:1:1:1.38742:53:4:0.0526:0:6.5 -18 18517289 . A C 113 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33317;SOR=2.29872;LSEQ=TAACAGAGTTGAACCTTTCT;RSEQ=TTTATAGATCAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:6,6:0.1765:2,2:25.3:1:31.7:1:1:1.91151:56:6:0.1875:0:6 0/1:36:12:7,5:12,10:0.3333:2,2:26.3:1:31.7:1:1:1.16:44.3:24:0.3333:0:5.8 -18 18517292 . T C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.11526;LSEQ=CAGAGTTGAACCTTTCTATT;RSEQ=ATAGATCAGTTTTGAAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:5,3:2,5:0.5:2,2:19.6:1:29:1:0.31469:3.76:48:7:0.4667:0:6.5 1/0:36:19:11,8:8,6:0.5278:2,2:23.3:1:31.8:1:1:1.03:45.3:38:0.5278:0:6.2 -18 18517298 . TC GA 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58171;SOR=1.52702;LSEQ=TGAACCTTTCTATTTATAGA;RSEQ=AGTTTTGAAACGCTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:7,5:2,5:0.5455:2,2:20.4:1:30.5:1:0.34985:3.27:45.9:24:0.5714:0.0909:5.2 1/0:37:24:14,10:7,4:0.6486:2,2:25.3:1:30.7:1:1:1.24211:45.9:48:0.6486:0.0541:5.2 -18 18517305 . T G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTATTTATAGATCAGTTT;RSEQ=GAAACGCTCTTTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:21.5:1:29.4:1:1:0:45.7:23:1:0:5.9 0/1:57:2:1,1:28,26:0.0351:2,2:28.5:1:32:0:1:1.07547:33:4:0.0351:0:5.5 -18 18517306 . G C 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57344;SOR=Inf;LSEQ=TCTATTTATAGATCAGTTTT;RSEQ=AAACGCTCTTTTTGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,12:0:2,0:22.3:1:31.6:1:1:0:44.9:44:0.9565:0:5.9 0/1:58:4:2,2:28,25:0.069:2,2:19.5:1:30:1:1:1.11777:48.5:8:0.069:0:5.8 -18 18517307 . A G 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.24209;LSEQ=CTATTTATAGATCAGTTTTG;RSEQ=AACGCTCTTTTTGTGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:9,13:0.0833:2,2:24.5:1:29.5:1:1:1.42:53:4:0.0833:0:8 0/1:59:6:4,2:27,26:0.1017:2,2:17.8:1:29.7:1:0.67318:1.91:47.3:12:0.1017:0:6.5 -18 18517310 . C A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76583;SOR=0.85278;LSEQ=TTTATAGATCAGTTTTGAAA;RSEQ=GCTCTTTTTGTGGAATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:1,4:8,10:0.2:2,2:28.8:1:31:1:0.61057:3.05567:53.2:10:0.2:0:7 0/1:57:10:6,4:23,24:0.1754:2,2:25.4:1:30.6:1:0.72973:1.55:47:20:0.1754:0:6.5 -18 18517312 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09033;SOR=0;LSEQ=TATAGATCAGTTTTGAAACG;RSEQ=TCTTTTTGTGGAATCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:9,14:0.08:2,2:19.5:1:30:1:1:1.53:24:4:0.08:0:6.5 0/0:57:0:0,0:29,28:0:2,0:21.3:1:32:1:1:0:44.9:114:1:0:4.8 -18 18517318 . T A 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.85362;LSEQ=TCAGTTTTGAAACGCTCTTT;RSEQ=TGTGGAATCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:9,14:0.0417:2,0:29:0:33:0:1:0:59:2:0.0435:0:8 0/1:56:2:1,1:27,26:0.0357:2,2:20:1:31:1:1:1.03776:41.5:4:0.0364:0:5.5 -18 18517320 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTTTGAAACGCTCTTTTT;RSEQ=TGGAATCTGCAAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:0:2,0:27.3:1:32.5:1:1:0:45:48:1:0:5.7 0/1:56:2:1,1:27,27:0.0357:2,2:22.5:1:28.5:1:1:1:59:4:0.0357:0:6.5 -18 18517328 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08734;SOR=0;LSEQ=AACGCTCTTTTTGTGGAATC;RSEQ=GCAAGTGGATATTTGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:9,13:0.0833:2,0:26:1:31.5:1:0.51087:0:50:4:0.0833:0:6.5 0/0:56:0:0,0:28,28:0:2,0:22.2:1:30.3:1:1:0:44.8:112:1:0:4.8 -18 18517329 . G C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80318;SOR=0.81874;LSEQ=ACGCTCTTTTTGTGGAATCT;RSEQ=CAAGTGGATATTTGGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:5,5:4,9:0.4167:2,2:31.8:1:31.1:1:0.41728:2.17:50.1:20:0.4167:0:6.1 0/1:57:21:10,11:18,18:0.3684:2,2:20.5:1:30.6:1:1:1.09816:46.1:42:0.3684:0:5.1 -18 18517345 . A C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60214;SOR=1.97168;LSEQ=ATCTGCAAGTGGATATTTGG;RSEQ=TGGCTTTGAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:5,11:0,2:0.8889:0,2:27.6:1:32.5:1:1:0:44.4:32:0.8889:0:5.6 1/1:34:32:15,17:0,2:0.9412:0,2:23.4:1:31.9:1:0.49198:0:44.5:31:0.9394:0:4.6 -18 18517347 . G A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAGTGGATATTTGGAT;RSEQ=GCTTTGAGGATTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:5,12:0,0:1:0,2:25.3:1:30.7:1:1:0:44.1:34:1:0:5.8 1/1:32:31:14,17:0,0:0.9688:0,2:22.8:1:29.3:1:1:0:43.3:62:0.9688:0:4.9 -18 18517349 . C T 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42308;SOR=2.11794;LSEQ=GCAAGTGGATATTTGGATGG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:13:4,9:0,1:0.7647:0,2:23.1:1:30.5:1:1:0:42.7:26:0.7647:0:5.3 1/1:32:28:13,15:1,3:0.875:2,2:22:1:29.8:1:0.61282:2.53:43.4:56:0.875:0:4.8 -18 18517369 . A G 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51613;SOR=0;LSEQ=CTTTGAGGATTTCGTTGGAA;RSEQ=CGGGATTATATATAAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:3,9:0,0:1:0,2:5.3:1:32.5:1:1:0:43.2:24:1:0:5.8 1/1:20:18:7,11:1,1:0.9:2,2:6.1:1:32.2:1:1:1.53525:42.6:36:0.9:0:4.9 -18 18517463 . A G 34 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAACATTCCCTTTCATA;RSEQ=AGCAGGTTTGAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:0,0:0.6667:0,0:17.5:1:34:0:1:0:47:4:0.6667:0:5.5 -18 18517513 . G T 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGGAAGTGGACATTTTGA;RSEQ=CGCTTTCTGGCCTATGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:34.7:1:30:1:1:0:53:6:0.75:0:6 -18 18517516 . C A 46 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGTGGACATTTTGAGCG;RSEQ=TTTCTGGCCTATGTTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:35.7:1:29.3:1:1:0:53:6:0.75:0:6 -18 18517521 . T A 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACATTTTGAGCGCTTTC;RSEQ=GGCCTATGTTGAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:0.5:2,0:32.5:1:32:0:1:0:37:4:0.5:0:7 -18 18517547 . T G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGAAAAAGGAAATATC;RSEQ=TTCCATAAAAAGTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:22:1:29:1:1:1:40:4:0.5:0:7 -18 18517549 . TC AA 46 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGAAAAAGGAAATATCTT;RSEQ=CATAAAAAGTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,0:0.75:0,2:25.7:1:29.2:1:1:0:46.3:6:0.75:0:5.3 -18 18517559 . G C 102 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATATCTTTCCATAAAAA;RSEQ=TAGACAGAAGCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:4:1:32:1:1:0:44.5:4:1:0:4.5 1/1:11:9:5,4:0,0:0.8182:0,2:7:1:32.2:1:1:0:45.7:18:0.8182:0:4.1 -18 18517573 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TAAAAAGTAGACAGAAGCAT;RSEQ=CTCAGAAACTTATTTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:12:1:28.8:1:1:0:41.2:20:1:0:3.4 0/1:38:2:1,1:20,16:0.0526:2,2:16:0:33:0:1:1.24262:28:4:0.0526:0:2 -18 18517608 . A C 107 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42129;SOR=3.37607;LSEQ=TGTGATGTGTGTCCTCAACT;RSEQ=ACAGAGCTGTACCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:5,5:0.0909:2,0:39:0:32:0:1:0:58:2:0.0909:0:4 0/1:43:11:4,7:17,15:0.2558:2,2:34:1:31.2:1:0.48761:1.95201:45.9:22:0.2558:0:6.6 -18 18517615 . C A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13184;SOR=0.16684;LSEQ=TGTGTCCTCAACTAACAGAG;RSEQ=TGTACCTTTCTTTTGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:6,4:0,0:0.9091:0,2:38.6:1:30.3:1:1:0:39.3:20:0.9091:0:3.6 1/0:34:21:11,10:0,0:0.6176:0,2:37.1:1:29.5:1:1:0:44.1:42:0.6176:0:4.1 -18 18517617 . GT CA 103 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04568;SOR=Inf;LSEQ=TGTCCTCAACTAACAGAGCT;RSEQ=ACCTTTCTTTTGATACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:37.7:1:31.5:1:1:0:39.4:22:1:0:3.6 0/1:33:10:3,7:12,10:0.303:2,2:38.6:1:31.1:1:0.26545:2.71067:46.7:20:0.3125:0:5.5 -18 18517618 . T A 133 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04568;SOR=0;LSEQ=GTCCTCAACTAACAGAGCTG;RSEQ=ACCTTTCTTTTGATACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:1:0,2:36.9:1:30:1:1:0:39.4:22:1:0:3.6 1/0:33:23:13,10:0,0:0.697:0,2:37.9:1:29.6:1:1:0:43.4:46:1:0:4.6 -18 18517621 . CT TG 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCAACTAACAGAGCTGTAC;RSEQ=TTCTTTTGATACAGCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:34.5:1:31.7:1:1:0:39.4:22:1:0:3.6 0/1:33:2:1,1:15,16:0.0606:2,2:39:0:31:1:1:1.06:42:4:0.0625:0:5 -18 18517625 . C G 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.53322;LSEQ=ACTAACAGAGCTGTACCTTT;RSEQ=TTTTGATACAGCAGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:6,4:0,1:0.9091:0,2:31:1:32.3:1:0.45455:0:39.3:20:0.9091:0:3.6 1/1:33:31:15,16:1,1:0.9394:2,2:34.8:1:31.4:1:1:1.06462:44.6:62:0.9394:0:4.8 -18 18517630 . G C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAGCTGTACCTTTCTTTT;RSEQ=ATACAGCAGTTTGGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:30.1:1:32:1:1:0:40:20:1:0:3.7 0/1:32:2:1,1:15,15:0.0625:2,2:31:0:31:1:1:1:42:4:0.0625:0:5 -18 18517665 . T C 106 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACTCTTTTTGTAGAAT;RSEQ=TGCAAGTGGATATTTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:16:0:33:0:1:0:21:2:1:0:6 1/1:10:10:2,8:0,0:1:0,2:12.6:1:32:1:1:0:39.6:20:1:0:6.7 -18 18517667 . G A 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTCTTTTTGTAGAATTT;RSEQ=CAAGTGGATATTTGGATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:14:0:30:0:1:0:21:2:1:0:6 1/1:9:9:2,7:0,0:1:0,2:12.2:1:28.7:1:1:0:39.2:18:1:0:7 -18 18517671 . G A 68 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=TCTTTTTGTAGAATTTGCAA;RSEQ=TGGATATTTGGATAACTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:7:1:33.5:1:1:0:40.5:4:1:0:5 1/0:7:5:1,4:0,2:0.7143:0,2:12.6:1:29.4:1:1:0:40:10:0.7143:0:7.4 -18 18517672 . T A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.63248;LSEQ=CTTTTTGTAGAATTTGCAAG;RSEQ=GGATATTTGGATAACTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:9:0:32:0:1:0:21:2:0.5:0:6 0/1:8:3:1,2:1,4:0.375:2,2:6.3:1:31:1:1:1.83:40:6:0.375:0:7.3 -18 18517681 . G T 71 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=GAATTTGCAAGTGGATATTT;RSEQ=GATAACTTCGAAGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:14:0:33:0:1:0:60:2:1:0:4 1/0:7:5:3,2:1,1:0.7143:2,2:6:1:30.8:1:1:1.41:41.8:10:0.7143:0:7.4 -18 18517684 . T G 75 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28571;SOR=Inf;LSEQ=TTTGCAAGTGGATATTTGGA;RSEQ=AACTTCGAAGATTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:17:0:33:0:1:0:60:2:1:0:4 1/1:6:5:3,2:0,0:0.8333:0,2:17.2:1:32.4:1:1:0:42.2:10:1:0:7.4 -18 18517686 . A G 78 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.28571;SOR=Inf;LSEQ=TGCAAGTGGATATTTGGATA;RSEQ=CTTCGAAGATTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:19:0:32:0:1:0:60:2:1:0:4 1/1:6:5:3,2:0,0:0.8333:0,2:11:1:33.6:1:1:0:41.8:10:0.8333:0:7.2 -18 18517688 . T A 73 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28571;SOR=Inf;LSEQ=CAAGTGGATATTTGGATAAC;RSEQ=TCGAAGATTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:21:0:33:0:1:0:60:2:1:0:4 1/1:6:5:3,2:0,1:0.8333:0,2:13:1:31.6:1:1:0:41.8:10:0.8333:0:7.2 -18 18517690 . C T 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGATATTTGGATAACTT;RSEQ=GAAGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:32:0:1:0:60:2:1:0:4 1/1:6:6:3,3:0,0:1:0,2:20.2:1:31.2:1:1:0:40.3:12:1:0:7.3 -18 18517694 . G A 73 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GATATTTGGATAACTTCGAA;RSEQ=ATTTCGTTGGAAACGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:27:0:34:0:1:0:60:2:1:0:4 1/1:6:6:3,3:0,0:1:0,2:21.7:1:28.5:1:1:0:40.3:5:1:0:7.3 -18 18517707 . A G 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.3738;LSEQ=CTTCGAAGATTTCGTTGGAA;RSEQ=CGGGAATATCTTCATATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:13:0:31.3:1:1:0:33.7:6:0.5:0:6.3 1/0:12:7:3,4:2,3:0.5833:2,2:7.3:1:32.4:1:1:1.11:39.7:14:0.5833:0:6.4 -18 18517714 . T A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59207;SOR=0.43037;LSEQ=GATTTCGTTGGAAACGGGAA;RSEQ=ATCTTCATATAAAATCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:20:0:30:1:1:0:33.7:6:0.5:0:6.3 0/1:7:2:0,2:2,3:0.2857:2,0:20:0:30.5:1:1:0:34.5:4:0.2857:0:4.5 -18 18517716 . T C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59207;SOR=0.43037;LSEQ=TTTCGTTGGAAACGGGAATA;RSEQ=CTTCATATAAAATCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:22:0:31:1:1:0:33.7:6:0.5:0:6.3 0/1:7:2:0,2:2,3:0.2857:2,0:22:0:32:1:1:0:34.5:4:0.2857:0:4.5 -18 18517723 . A G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.30401;LSEQ=GGAAACGGGAATATCTTCAT;RSEQ=TAAAATCTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:34:1:30.7:1:1:0:47.3:6:0.5:0:4 1/0:7:4:2,2:0,3:0.5714:0,2:26.5:1:31:1:0.42857:0:52:8:0.5714:0:6.3 -18 18517725 . A T 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=AAACGGGAATATCTTCATAT;RSEQ=AAATCTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:32.8:1:29.3:1:1:0:40.5:12:1:0:5.2 0/1:7:2:1,1:1,4:0.2857:2,2:31:0:28.5:1:1:3.16:59:4:0.2857:0:6.5 -18 18517731 . T G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.30401;LSEQ=GAATATCTTCATATAAAATC;RSEQ=AGACAGAAGCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:36.7:1:30:1:1:0:47.3:6:0.5:0:4 1/0:7:4:2,2:0,3:0.5714:0,2:34.5:1:25.3:1:0.42857:0:52:3:0.5:0:6.3 -18 18517738 . A C 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53029;LSEQ=TTCATATAAAATCTAGACAG;RSEQ=AGCATTCTCAGAAACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:31.3:1:33.3:1:1:0:33.7:6:0.5:0:6.3 0/1:6:2:0,2:2,2:0.3333:2,0:17:0:34:0:0.46667:0:34.5:4:0.3333:0:4.5 -18 18517745 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=AAAATCTAGACAGAAGCATT;RSEQ=TCAGAAACTGCTTTTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:32.7:1:33:1:1:0:40.5:12:1:0:5.2 0/1:6:2:1,1:1,3:0.3333:2,2:41.5:1:29:1:1:2.45:59:4:0.3333:0:6.5 -18 18517754 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=ACAGAAGCATTCTCAGAAAC;RSEQ=GCTTTTTGATGTCTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:23.8:1:31.3:1:1:0:40.5:12:1:0:5.2 0/1:6:2:1,1:1,3:0.3333:2,2:39:0:31.5:1:1:2.45:45:4:0.3333:0:6 -18 18517755 . G T 49 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CAGAAGCATTCTCAGAAACT;RSEQ=CTTTTTGATGTCTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:14.3:1:31.3:1:1:0:33.7:6:0.5:0:6.3 0/0:4:0:0,0:2,2:0:2,0:34.8:1:31.8:1:1:0:52:8:1:0:6.3 -18 18517760 . T G 85 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTCTCAGAAACTGCTTT;RSEQ=TGATGTCTGCATTCAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:17.8:1:33.2:1:1:0:40.5:12:1:0:5.2 1/1:4:4:2,2:0,0:1:0,2:29.8:1:31:1:1:0:52:8:1:0:6.3 -18 18517763 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=TTCTCAGAAACTGCTTTTTG;RSEQ=TGTCTGCATTCAAGTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:14.8:1:31.5:1:1:0:40.5:12:1:0:5.2 1/0:4:2:1,1:1,1:0.5:2,2:30:0:33:0:1:1:45:4:0.6667:0:6 -18 18517776 . A C 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTGATGTCTGCATTCA;RSEQ=GTCACAGAGTTGAACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:31.5:1:1:0:41:4:1:0:4 1/1:4:4:2,2:0,0:1:0,2:13.8:1:30.3:1:1:0:52:8:1:0:6.3 -18 18517871 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGCGCTTTGACGCCTAC;RSEQ=GTGAAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:32:1:1:0:31:4:1:0:5.5 1/1:1:1:1,0:0,0:1:0,0:12:0:30:0:1:0:24:2:1:0:5 -18 18517901 . G A 30 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GAAATATCTTCCCATAAAAA;RSEQ=TAGACAGAAGCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:0:32:1:1:0:31:4:1:0:5.5 1/0:4:2:1,1:1,1:0.5:2,2:27:1:30:1:1:1:24:4:0.5:0:4.5 -18 18517930 . T G 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCATTCTCAGAAACTTGTT;RSEQ=GTGATGTATGTCCTCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:31:1:1:0:31:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:28:1:27.5:1:1:0:24:4:1:0:4.5 -18 18517936 . G A 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTCAGAAACTTGTTTGTGAT;RSEQ=TATGTCCTCAACTAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29:1:1:0:31:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:22:1:26.5:1:1:0:24:4:1:0:4.5 -18 18517938 . A G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAACTTGTTTGTGATGT;RSEQ=TGTCCTCAACTAACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:31:1:1:0:31:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:24:4:1:0:4.5 -18 18518068 . A C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.54771;LSEQ=AACGGGAATATCCAAATATC;RSEQ=ACTTGCAGATTCTACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:11:0:32:0:1:0:59:2:0.5:0:8 0/1:6:2:2,0:3,1:0.3333:2,0:8.5:1:31:0:1:0:45.5:4:0.4:0:7 -18 18518070 . C T 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGAATATCCAAATATCAA;RSEQ=TTGCAGATTCTACAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:13.5:1:32:0:1:0:58:4:1:0:7 1/1:10:9:6,3:1,0:0.9:0,2:6.6:1:29:1:1:0:51.1:8:0.8889:0:5.8 -18 18518078 . T A 111 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAATATCAACTTGCAGA;RSEQ=TCTACAAAAATAGTGTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:13.8:1:31.8:1:1:0:49.3:8:1:0:5.8 1/1:13:12:9,3:1,0:0.9231:0,2:12.5:1:31.1:1:1:0:52.6:24:0.9231:0:5.5 -18 18518081 . T C 121 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATCAACTTGCAGATTC;RSEQ=ACAAAAATAGTGTATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:14:1:28.2:1:1:0:51.4:4:1:0:5.8 1/1:15:15:11,4:0,0:1:0,2:14.3:1:31.1:1:1:0:52.5:30:1:0:5.3 -18 18518092 . T A 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83796;LSEQ=TGCAGATTCTACAAAAATAG;RSEQ=GTATCAAAGCTGCTCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:6,2:0,0:0.8889:0,2:17:1:30.1:1:1:0:50.1:16:0.8889:0:5.8 1/1:23:20:12,8:0,0:0.8696:0,2:18:1:29.5:1:1:0:51:19:0.95:0:4.8 -18 18518093 . GTA T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCAGATTCTACAAAAATAGT;RSEQ=TCAAAGCTGCTCTGTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:16.1:1:32.4:1:1:0:48.2:18:1:0:5.7 0/1:23:2:1,1:13,8:0.087:2,2:22:0:32:1:1:1.58984:60:4:0.087:0:3.5 -18 18518095 . A T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTCTACAAAAATAGTGT;RSEQ=TCAAAGCTGCTCTGTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:8,3:0,0:1:0,2:16.7:1:29.5:1:1:0:47.6:22:1:0:5.8 1/1:23:22:14,8:0,0:0.9565:0,2:19.2:1:29.5:1:1:0:52.8:21:1:0:4.6 -18 18518116 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAAGCTGCTCTGTAAAAA;RSEQ=AAAGGTTCCACTCTGTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:18.3:1:31.8:1:1:0:49.6:52:1:0:5.3 0/1:73:2:1,1:37,34:0.0274:2,2:12.5:1:30:1:1:1.08696:60:4:0.0282:0:6.5 -18 18518118 . A G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6467;SOR=1.28466;LSEQ=AAAGCTGCTCTGTAAAAAGA;RSEQ=AGGTTCCACTCTGTTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:4,5:10,7:0.3462:2,2:7:0:30.8:1:0.68284:1.74571:50.6:8:0.32:0:5.8 0/1:74:30:17,13:22,22:0.4054:2,2:6.4:1:30.5:1:0.63945:1.30:44.8:9:0.3803:0:3.1 -18 18518120 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTGCTCTGTAAAAAGAAA;RSEQ=GTTCCACTCTGTTAGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:0:2,0:15.9:1:31.3:1:1:0:49.2:35:1:0:4.9 0/1:76:2:1,1:38,36:0.0263:2,2:16.5:1:30:1:1:1.05483:60:4:0.027:0:6.5 -18 18518134 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10744;SOR=0;LSEQ=AAGAAAGGTTCCACTCTGTT;RSEQ=GCTGAGTACACACATCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:19,19:0.05:2,2:29:0:33:0:1:1:60:4:0.05:0:2.5 0/0:81:0:0,0:42,39:0:2,0:23.6:1:29.3:1:1:0:49.4:162:1:0:3.8 -18 18518141 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54802;SOR=Inf;LSEQ=GTTCCACTCTGTTAGCTGAG;RSEQ=ACACACATCACAAACATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:20,20:0:2,0:28.7:1:29.5:1:1:0:49.5:80:1:0:4.9 0/1:78:2:1,1:39,37:0.0256:2,2:30:0:30:0:1:1.05337:51:4:0.026:0:5 -18 18518143 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.54802;SOR=Inf;LSEQ=TCCACTCTGTTAGCTGAGTA;RSEQ=ACACATCACAAACATGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:20,20:0:2,0:29.3:1:32.8:1:1:0:49.5:80:1:0:4.9 0/1:78:2:1,1:39,37:0.0256:2,2:39.5:1:30:0:1:1.05337:57.5:4:0.0256:0:5 -18 18518157 . A T 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTACACACATCACAAAC;RSEQ=TGTTTCTGAGAATCCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:18,21:0,0:1:0,2:28.8:1:31.1:1:1:0:48.9:78:1:0:4.9 1/1:62:62:30,32:0,0:1:0,2:23.8:1:30.5:1:1:0:48.4:124:1:0:4.4 -18 18518161 . T C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.97848;LSEQ=TACACACATCACAAACATGT;RSEQ=TCTGAGAATCCTTCTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:8:3,5:14,16:0.2105:2,2:26:1:32.9:1:0.70873:1.44409:52.9:16:0.2105:0:6.1 0/1:58:12:5,7:23,23:0.2069:2,2:22.5:1:32:1:0.74916:1.39192:49.4:24:0.2105:0:5.7 -18 18518165 . G C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.37483;SOR=0.61219;LSEQ=CACATCACAAACATGTTTCT;RSEQ=AGAATCCTTCTGTGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:24:10,14:6,6:0.6667:2,2:25.5:1:32.6:1:0.72948:1.38683:49.3:48:0.6667:0:5.3 1/0:51:28:13,15:11,11:0.549:2,2:21:1:31.7:1:1:1.15054:44.5:56:0.549:0:5 -18 18518170 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17647;SOR=0;LSEQ=CACAAACATGTTTCTGAGAA;RSEQ=CCTTCTGTGTAGTTTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:0.0556:2,2:18.5:1:30:1:1:1.26:50:4:0.0556:0:4 0/0:49:0:0,0:23,26:0:2,0:17.6:1:29:1:1:0:46.8:48:1:0:4.4 -18 18518179 . G C 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=GTTTCTGAGAATCCTTCTGT;RSEQ=TAGTTTTTATAGGAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:27:11,16:0,1:0.9643:0,2:16.5:1:31.6:1:1:0:47.6:26:0.963:0:5.6 1/1:28:27:10,17:0,1:0.9643:0,2:17.4:1:31.6:1:1:0:45.7:54:0.9643:0:5.8 -18 18518181 . A C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66874;SOR=0.61899;LSEQ=TTCTGAGAATCCTTCTGTGT;RSEQ=GTTTTTATAGGAAGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:25:10,15:1,1:0.9259:2,2:14.4:1:30.2:1:1:1.47706:49.1:50:0.9259:0:5.8 1/1:26:23:8,15:1,2:0.8846:2,2:17.7:1:29.7:1:1:1.06:44:46:0.8846:0:6 -18 18518190 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTCTGTGTAGTTTTTAT;RSEQ=GGAAGATATTTCCTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:4,9:0,0:1:0,2:17.5:1:32.3:1:1:0:45:26:1:0:6.1 1/1:11:11:3,8:0,0:1:0,2:20.1:1:30.9:1:1:0:38.8:22:1:0:6.2 -18 18518202 . C A 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTTATAGGAAGATATTT;RSEQ=CTTTTTCAGCATAGGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:1,8:0,0:1:0,2:10.8:1:30.2:1:1:0:44.4:18:1:0:6.2 1/1:11:11:3,8:0,0:1:0,2:8.1:1:27.1:1:1:0:38.8:10:1:0:6.2 -18 18518211 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGAAGATATTTCCTTTTTCA;RSEQ=CATAGGCATCAGAGCGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:32:0:1:0:36.5:4:1:0:8 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18518213 . A G 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATATTTCCTTTTTCAGC;RSEQ=TAGGCATCAGAGCGCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17.5:1:33.5:1:1:0:36.5:4:1:0:8 1/1:1:1:0,1:0,0:1:0,0:10:0:32:0:1:0:25:2:1:0:8 -18 18518376 . T C 63 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55379;SOR=Inf;LSEQ=TTTATATGTATATATTCCCG;RSEQ=TTCCAACGAAATCCTCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:12.5:1:29.5:1:1:0:28.8:8:1:0:3.8 0/1:18:4:2,2:8,6:0.2222:2,2:6.8:1:31.8:1:1:1.31198:32.8:8:0.2222:0:4.5 -18 18518393 . TA CC 96 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32174;SOR=0.19944;LSEQ=CCGTTTCCAACGAAATCCTC;RSEQ=AGCTATCCAAATATCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:21.8:1:28.5:1:1:0:30:8:0.8:0:2 0/1:21:9:5,4:1,0:0.4286:0,2:24.9:1:30.3:1:1:0:52.7:18:0.4286:0:2.6 -18 18518396 . G A 57 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.55518;SOR=Inf;LSEQ=TTTCCAACGAAATCCTCTAA;RSEQ=CTATCCAAATATCCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:22:1:32.6:1:1:0:28.4:10:1:0:2.8 0/1:21:4:2,2:8,8:0.1905:2,2:20.3:1:28.5:1:1:1:35.5:8:0.1905:0:5 -18 18518400 . T G 114 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6169;SOR=0.34632;LSEQ=CAACGAAATCCTCTAAGCTA;RSEQ=CCAAATATCCACTTGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:27.8:1:31.8:1:1:0:30:8:0.8:0:2 1/0:21:12:7,5:4,5:0.5714:2,2:30.5:1:31.8:1:0.66992:1.70:49.4:24:0.5714:0:2.9 -18 18518412 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTAAGCTATCCAAATATCCA;RSEQ=TTGCAGATTCCGCAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:37.5:1:33:1:1:0:30:8:1:0:2 0/1:21:2:1,1:10,9:0.0952:2,2:36:1:31:1:1:1.10554:48.5:4:0.1:0:4 -18 18518423 . C A 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATATCCACTTGCAGATTC;RSEQ=GCAAAAAGAGTGTTTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27:0:31:1:1:0:30:8:1:0:2 0/1:21:4:2,2:9,8:0.1905:2,2:29:1:31:1:1:1.1187:35.5:8:0.1905:0:5 -18 18518424 . G A 64 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54404;SOR=Inf;LSEQ=AATATCCACTTGCAGATTCC;RSEQ=CAAAAAGAGTGTTTCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:26:0:31.8:1:1:0:30:8:1:0:2 0/1:20:5:3,2:8,7:0.25:2,2:30.8:1:27.6:1:1:1.29:35.6:10:0.25:0:2.6 -18 18518425 . C G 63 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATCCACTTGCAGATTCCG;RSEQ=AAAAAGAGTGTTTCAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:25:0:32.8:1:1:0:30:8:1:0:2 0/1:20:4:2,2:9,7:0.2:2,2:27:1:31.5:1:1:1.26953:35.5:8:0.2:0:5 -18 18518432 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTTGCAGATTCCGCAAAAAG;RSEQ=GTGTTTCAAAACTGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18:0:30.8:1:1:0:30:8:1:0:2 0/1:20:2:1,1:10,8:0.1:2,2:18:0:31:1:1:1.23603:48.5:4:0.1053:0:4 -18 18518450 . TGTCAAAAGAAAGGTTCAA CTTCAAAACGATGGTTTAG 92 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGTTTCAAAACTGCTC;RSEQ=TTCTGTTAGTTGAGTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:10:9:4,5:0,0:0.9:0,2:13.2:1:29.3:1:1:0:50.1:18:0.9:0.9:3.4 -18 18518589 . G T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCAAACGTCCACTTCCA;RSEQ=ATACTACAAAAAGAGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:12:1:29:0:1:1:43:4:0.5:0:2.5 -18 18518598 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCACTTCCAGATACTACA;RSEQ=AAAGAGTGTTTCAAACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:21:0:32:1:1:1:24:4:0.5:0:4 -18 18518601 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACTTCCAGATACTACAAAA;RSEQ=GAGTGTTTCAAACCTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:24:0:30.5:1:1:1:24:4:0.5:0:4 -18 18518624 . G C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTCAAACCTGCTCTAT;RSEQ=AAAGAGAATGTTCAATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:27:0:32.5:1:1:1:24:4:0.5:0:4 -18 18518629 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAAACCTGCTCTATGAAAG;RSEQ=GAATGTTCAATTCTGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:22:0:32:0:1:1:24:4:0.5:0:4 -18 18518640 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGAAAGAGAATGTTCAA;RSEQ=TCTGTGACTTGAAGGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:20.5:1:31:1:1:1:43:4:0.5:0:2.5 -18 18518732 . C T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGTTTCCAACGAAATC;RSEQ=TAAAATCTATCCAAATATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:16.5:1:32.5:1:1:0:33:4:0.6667:0:2.5 -18 18518755 . T C 51 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCTATCCAAATATCCAC;RSEQ=TGCAGATTCTACAAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:2,0:0.6:0,2:7:1:32.3:1:1:0:35.3:6:0.6:0:3 -18 18518765 . T C 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATCCACTTGCAGATTC;RSEQ=ACAAAAAGAGTGTTTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:26.7:1:30:1:1:0:35:6:1:0:4.7 -18 18518793 . GTGAAAAGAAAGCTTCAACTCTGTTAGCTGAGTACACACATCACAG CTATCAATGGCAAAGTTCAACTCTGTTAGTTGAGGACACATATCACCA 133 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=GAGTGTTTCAAAACTGCTCT;RSEQ=ACAAGTTTCTGAGAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:27:22:15,7:5,0:0.8148:0,2:11:1:29.9:1:0.28335:0:47.5:44:0.8148:0.8148:3.3 -18 18518805 . C G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCTCTGTGAAAAGAAAG;RSEQ=TTCAACTCTGTTAGCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:20:1:30:1:1:0:40:4:1:0:6 -18 18518820 . C T 110 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAGCTTCAACTCTGTTAG;RSEQ=TGAGTACACACATCACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9:1:30.5:1:1:0:40:4:1:0:6.5 1/1:13:12:12,0:1,0:0.9231:0,0:22.8:1:30.7:1:1:0:42.8:24:0.9231:0:6.8 -18 18518825 . T G 121 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAACTCTGTTAGCTGAG;RSEQ=ACACACATCACAGACAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14:1:32.5:1:1:0:40:4:1:0:6.5 1/1:17:15:14,1:2,0:0.8824:0,1:21.6:1:31.1:1:1:0:43.1:30:0.8824:0:6.9 -18 18518831 . C T 121 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTGTTAGCTGAGTACACA;RSEQ=ATCACAGACAAGTTTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:20:1:32:0:1:0:40:4:1:0:6.5 1/1:20:17:15,2:3,0:0.85:0,2:24.6:1:29.8:1:1:0:44.9:34:0.85:0:6.8 -18 18518837 . AG CA 124 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCTGAGTACACACATCAC;RSEQ=ACAAGTTTCTGAGAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18.3:1:30.7:1:1:0:46.7:6:1:0.3333:5.3 1/1:23:19:16,3:4,0:0.8261:0,2:26.3:1:29.4:1:1:0:44.4:18:0.8182:0:5.7 -18 18518838 . G A 69 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGAGTACACACATCACA;RSEQ=ACAAGTTTCTGAGAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:24:5:3,2:0,0:0.2083:0,2:10.8:1:29.8:1:1:0:50.4:10:1:0:5.6 -18 18518841 . AA TG 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGTACACACATCACAGAC;RSEQ=GTTTCTGAGAATGCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:12:1:31.3:1:1:0:49.8:12:1:0:4.3 0/1:50:2:2,0:31,17:0.04:2,0:28:1:33:1:0.54204:0:43.5:4:0.04:0:5 -18 18518848 . T G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACATCACAGACAAGTTTC;RSEQ=GAGAATGCTTCTGTCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:12.3:1:31.2:1:1:0:51.3:24:1:0:3.9 0/1:55:2:1,1:36,17:0.0364:2,2:9.5:1:28:1:1:2.08642:60:4:0.0364:0:6.5 -18 18518857 . TTCTG T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACAAGTTTCTGAGAATGC;RSEQ=TCTATTTTTTATGGGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:12,3:0:2,0:18.7:1:29.5:1:1:0:50.6:14:1:0:4 0/1:59:3:2,1:36,20:0.0508:2,2:22.7:1:31.7:1:1:1.11:33.7:6:0.0508:0:3.7 -18 18518866 . T G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.19994;SOR=0.32328;LSEQ=TCTGAGAATGCTTCTGTCTA;RSEQ=TTTTTATGGGAAGATATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:4,0:9,6:0.2105:2,0:17.8:1:33.3:1:0.25542:0:41:8:0.2105:0:4 0/1:64:5:4,1:35,22:0.0781:2,2:14.4:1:32:1:0.64269:2.48:39.2:10:0.0794:0:6.2 -18 18518869 . T G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGAATGCTTCTGTCTATTT;RSEQ=TTATGGGAAGATATTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:14,6:0:2,0:22.3:1:30.8:1:1:0:51.8:40:1:0:4.2 0/1:66:2:1,1:40,24:0.0303:2,2:15:1:29.5:1:1:1.65321:40:4:0.0303:0:8 -18 18518873 . T C 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGCTTCTGTCTATTTTTTA;RSEQ=GGGAAGATATTTCCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:16,6:0:2,0:23.4:1:30.7:1:1:0:52.5:21:1:0:4.3 0/1:68:2:1,1:41,25:0.0294:2,2:19:1:28:1:1:1.62758:40:4:0.0299:0:8 -18 18518886 . C A 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57775;SOR=Inf;LSEQ=TTTTTTATGGGAAGATATTT;RSEQ=CTTTTTCACCATAGGCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:18,8:0:2,0:27.5:1:31.8:1:1:0:52.3:52:1:0:4.4 0/1:97:4:2,2:55,38:0.0412:2,2:18:1:29.3:1:1:1.44171:56.8:8:0.0421:0:7 -18 18518895 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAGATATTTCCTTTTTCA;RSEQ=CATAGGCGTCAAAGCGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:20,9:0:2,0:27:1:31.5:1:1:0:52.3:28:1:0:4.7 0/1:105:2:1,1:59,44:0.019:2,2:33:1:33.5:1:1:1.3371:52.5:4:0.0194:0:6 -18 18518897 . A G 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71873;SOR=1.25419;LSEQ=AAGATATTTCCTTTTTCACC;RSEQ=TAGGCGTCAAAGCGCTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:26:17,9:2,0:0.8966:0,2:26.9:1:30.7:1:1:0:52.2:52:0.9286:0:4.7 1/1:107:98:58,40:4,5:0.9159:2,2:23.6:1:29.9:1:0.4878:1.80:50.6:48:0.9143:0:5.2 -18 18518903 . G C 101 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01346;SOR=0.26682;LSEQ=TTTCCTTTTTCACCATAGGC;RSEQ=TCAAAGCGCTCGAAATGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:8:6,2:15,8:0.2581:2,2:27.9:1:31.3:1:1:1.58:42.5:16:0.2667:0:4.8 0/1:119:10:6,4:54,48:0.084:2,2:19.1:1:30.6:1:0.74919:1.33:41.8:20:0.0847:0:5.3 -18 18518908 . A G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00134;SOR=4.69395;LSEQ=TTTTTCACCATAGGCGTCAA;RSEQ=GCGCTCGAAATGTCCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:23:15,8:8,5:0.6389:2,2:26.5:1:31.8:1:1:1.17:55.5:46:0.6389:0:4.8 1/1:113:101:54,47:7,5:0.8938:2,2:24.6:1:31.1:1:1:1.2164:51.4:100:0.8929:0:5.4 -18 18518912 . C A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00158;SOR=3.50338;LSEQ=TCACCATAGGCGTCAAAGCG;RSEQ=TCGAAATGTCCACTTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:24:16,8:11,7:0.5714:2,2:25.5:1:30.1:1:0.75401:1.27:56.4:23:0.561:0:4.9 1/1:120:99:53,46:14,7:0.825:2,2:25.6:1:29.4:1:0.33694:1.72808:52.1:98:0.8235:0:5.5 -18 18518914 . C T 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCATAGGCGTCAAAGCGCT;RSEQ=GAAATGTCCACTTCCACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:30,18:0:2,0:19.2:1:31.3:1:1:0:50.9:96:1:0:4.9 0/1:130:2:1,1:70,58:0.0154:2,2:21:0:32:0:1:1.20514:60:4:0.0156:0:6.5 -18 18518915 . G C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00022;SOR=0.19281;LSEQ=CCATAGGCGTCAAAGCGCTC;RSEQ=AAATGTCCACTTCCACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:16:9,7:20,11:0.3404:2,2:18.4:1:30.9:1:0.75264:1.40354:48.6:32:0.3478:0:4 0/1:134:12:8,4:63,59:0.0896:2,2:18:1:30.1:1:0.3762:1.86:40.8:24:0.0909:0:5.8 -18 18518925 . C T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52264;SOR=0.60825;LSEQ=CAAAGCGCTCGAAATGTCCA;RSEQ=TTCCACATACTACAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:3,2:29,18:0.0962:2,2:14.2:1:31:1:1:1.07259:42.4:10:0.0962:0:7 0/1:132:8:6,2:62,62:0.0606:2,2:13.4:1:31.1:1:0.27563:2.98:47.5:16:0.0606:0:7.1 -18 18518926 . T A 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09696;SOR=0.27708;LSEQ=AAAGCGCTCGAAATGTCCAC;RSEQ=TCCACATACTACAAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:4:4,0:28,20:0.0769:2,0:12.8:1:31.3:1:0.15072:0:25.8:8:0.0769:0:7.5 0/1:134:3:3,0:65,66:0.0224:2,0:19:1:32:0:0.24453:0:35.3:6:0.0226:0:7.7 -18 18518931 . C G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35545;SOR=0.59395;LSEQ=GCTCGAAATGTCCACTTCCA;RSEQ=ATACTACAAAAAGAGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:5,0:27,20:0.0962:2,0:15.8:1:33.4:1:0.1431:0:29.2:10:0.1:0:7.4 0/1:135:8:6,2:62,65:0.0593:2,2:11.5:1:31.8:1:0.2742:3.12:47.5:16:0.0593:0:6.4 -18 18518932 . ATACTACAA G 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGAAATGTCCACTTCCAC;RSEQ=AAAGAGTGTTTCAAACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:33,20:0:2,0:22.5:1:30.4:1:1:0:47.6:106:1:0:5.3 0/1:135:2:1,1:67,66:0.0148:2,2:20:0:29:1:1:1.01504:47:4:0.0148:0:6.5 -18 18518933 . T A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00251;SOR=2.75417;LSEQ=TCGAAATGTCCACTTCCACA;RSEQ=ACTACAAAAAGAGTGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:24:15,9:18,11:0.4528:2,2:25.4:1:30:1:1:1.02:53.5:23:0.4423:0:5.5 1/0:135:94:44,50:23,16:0.6963:2,2:27.7:1:29.6:1:0.25371:1.62745:52.6:46:0.7023:0:5.8 -18 18518937 . A C 114 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.02583;SOR=0.33713;LSEQ=AATGTCCACTTCCACATACT;RSEQ=CAAAAAGAGTGTTTCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:12:9,3:23,19:0.2222:2,2:20.8:1:31.8:1:0.32015:2.44:35.6:24:0.2222:0:7 0/1:126:11:7,4:55,58:0.0873:2,2:22.2:1:31.4:1:0.52954:1.84:45.8:22:0.0887:0:7.2 -18 18518940 . A G 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13741;SOR=0.48003;LSEQ=GTCCACTTCCACATACTACA;RSEQ=AAAGAGTGTTTCAAACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:10:8,2:21,19:0.1818:2,2:14.7:1:32.2:1:0.16044:3.53:36.4:20:0.1852:0:6.8 0/1:125:12:9,3:49,54:0.096:2,2:12.5:1:31.6:1:0.12473:3.27:47.3:24:0.0976:0:6.8 -18 18518943 . A C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CACTTCCACATACTACAAAA;RSEQ=GAGTGTTTCAAACCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:35,24:0:2,0:23.2:1:30.6:1:1:0:47.3:58:1:0:5.5 0/1:130:2:2,0:62,64:0.0154:2,0:30.5:1:32:1:0.49606:0:32.5:4:0.0154:0:8 -18 18518945 . A T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56271;SOR=0.66149;LSEQ=CTTCCACATACTACAAAAAG;RSEQ=GTGTTTCAAACCTTCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:6:3,3:34,21:0.0984:2,2:30.3:1:29.8:1:0.67171:1.60583:39:12:0.1:0:7.2 0/1:134:9:7,2:59,62:0.0672:2,2:33:1:29.8:1:0.16473:3.64:44.6:18:0.0677:0:7.3 -18 18518948 . G A 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50795;SOR=2.20603;LSEQ=CCACATACTACAAAAAGAGT;RSEQ=TTTCAAACCTTCTCTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:36,25:0.0317:2,2:7.5:1:31.5:1:1:1.43149:32.5:4:0.0323:0:7.5 0/1:133:9:5,4:62,62:0.0677:2,2:9.1:1:27.6:1:1:1.25:54.1:18:0.0682:0:6.9 -18 18518949 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1022;SOR=0;LSEQ=CACATACTACAAAAAGAGTG;RSEQ=TTCAAACCTTCTCTATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:36,25:0.0317:2,2:31.5:1:30.5:1:1:1.43149:26:4:0.0317:0:6 0/0:133:0:0,0:67,66:0:2,0:25.3:1:29.7:1:1:0:50:132:1:0:5.9 -18 18518956 . C A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.10348;SOR=0;LSEQ=TACAAAAAGAGTGTTTCAAA;RSEQ=CTTCTCTATGAAAGGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:36,27:0.0308:2,2:24.5:1:27.5:1:1:1.32735:26:4:0.0313:0:6 0/0:136:0:0,0:71,65:0:2,0:24.7:1:31:1:1:0:51.3:67:1:0:6.1 -18 18518957 . C G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.53234;SOR=0.66286;LSEQ=ACAAAAAGAGTGTTTCAAAC;RSEQ=TTCTCTATGAAAGGGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:5:3,2:34,26:0.0769:2,2:43.2:1:31.6:1:1:1.14:42.4:10:0.0781:0:7 0/1:134:7:5,2:64,59:0.0522:2,2:41.6:1:29.9:1:0.44664:2.29:46.9:14:0.0526:0:7.3 -18 18518959 . T G 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55296;SOR=0;LSEQ=AAAAAGAGTGTTTCAAACCT;RSEQ=CTCTATGAAAGGGAATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:63:36,27:0,0:1:0,2:26.5:1:32.5:1:1:0:47.6:126:1:0:5.9 1/1:136:133:70,63:0,1:0.9779:0,2:24.1:1:31.8:1:0.47761:0:51.1:65.5:0.9776:0:6.1 -18 18518961 . T C 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.01329;LSEQ=AAAGAGTGTTTCAAACCTTC;RSEQ=CTATGAAAGGGAATGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:4:2,2:33,26:0.0635:2,2:17.3:1:32.8:1:1:1.26439:34.3:8:0.0645:0:7.3 0/1:140:9:4,5:68,63:0.0643:2,2:20:1:28.1:1:0.7398:1.34632:51.3:18:0.0647:0:7.6 -18 18518962 . C G 133 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.0402;SOR=0.42838;LSEQ=AAGAGTGTTTCAAACCTTCT;RSEQ=TATGAAAGGGAATGTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:16:7,9:28,19:0.254:2,2:37.4:1:32.5:1:0.38341:1.87522:47.1:32:0.2667:0:5.4 0/1:142:18:9,9:64,60:0.1268:2,2:36.3:1:31.9:1:1:1.06615:50.3:36:0.1277:0:4.9 -18 18518964 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTGTTTCAAACCTTCTCT;RSEQ=TGAAAGGGAATGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:36,28:0:2,0:26.3:1:29:1:1:0:47:31:1:0:6 0/1:145:2:1,1:73,70:0.0138:2,2:20.5:1:30:1:1:1.04257:51.5:4:0.0138:0:6 -18 18518966 . G T 39 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1703;SOR=0.2877;LSEQ=GTGTTTCAAACCTTCTCTAT;RSEQ=AAAGGGAATGTTCAACTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:2,1:34,26:0.0476:2,2:15.7:1:24.7:1:1:1.52:60:2:0.0323:0:5 0/1:142:2:1,1:71,69:0.0141:2,2:7.5:1:27:1:1:1.02878:60:4:0.0142:0:6 -18 18518968 . A T 97 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17804;SOR=4.66656;LSEQ=GTTTCAAACCTTCTCTATGA;RSEQ=AGGGAATGTTCAACTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:1:0,1:35,26:0.0161:2,0:33:0:27:0:0.43548:0:49:2:0.0164:0:5 0/1:140:10:5,5:67,63:0.0714:2,2:28.6:1:29.4:1:1:1.06306:35.6:20:0.0725:0:6.1 -18 18518969 . AG CC 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCAAACCTTCTCTATGAA;RSEQ=GGAATGTTCAACTCTATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:36,27:0:2,0:26.7:1:30.4:1:1:0:46.6:62:1:0:6 0/1:140:2:1,1:71,67:0.0143:2,2:25:0:32.5:0:1:1.05929:52.5:4:0.0144:0:4.5 -18 18518972 . GA CC 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12271;SOR=1.84177;LSEQ=CAAACCTTCTCTATGAAAGG;RSEQ=ATGTTCAACTCTATGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:12:7,5:26,23:0.1935:2,2:17.4:1:31.1:1:1:1.23:49:24:0.1967:0.0161:5.7 0/1:140:43:21,22:47,44:0.3071:2,2:15.4:1:31.1:1:0.85362:1.11811:52.1:86:0.3071:0.05:5.8 -18 18518976 . G C 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01351;SOR=0.43803;LSEQ=CCTTCTCTATGAAAGGGAAT;RSEQ=TTCAACTCTATGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:28:17,11:18,19:0.4308:2,2:28.6:1:31.9:1:0.45177:1.62:43.7:56:0.4308:0:5.6 0/1:133:33:19,14:49,51:0.2481:2,2:26.4:1:31.8:1:0.42738:1.41:52.2:66:0.2481:0:5.9 -18 18518977 . T C 64 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30558;SOR=Inf;LSEQ=CTTCTCTATGAAAGGGAATG;RSEQ=TCAACTCTATGAGTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:35,30:0:2,0:25.8:1:30.4:1:1:0:45.9:64:1:0:5.8 0/1:134:4:2,2:66,64:0.0299:2,2:27.8:1:32.3:1:1:1.03102:51.5:8:0.0299:0:7.5 -18 18518978 . T G 34 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTCTATGAAAGGGAATGT;RSEQ=CAACTCTATGAGTTGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:35,30:0:2,0:25.8:1:30.4:1:1:0:45.9:64:1:0:5.8 0/1:133:2:1,1:66,65:0.015:2,2:17:0:34:0:1:1.01527:52.5:4:0.0152:0:4.5 -18 18518979 . C G 102 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33974;SOR=2.37323;LSEQ=TCTCTATGAAAGGGAATGTT;RSEQ=AACTCTATGAGTTGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:0,2:35,28:0.0308:2,0:22:0:33.5:1:0.20913:0:48:4:0.0308:0:6 0/1:128:9:4,5:58,61:0.0703:2,2:19.6:1:32.4:1:1:1.18693:35.1:18:0.0714:0:6.2 -18 18518981 . A T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25733;SOR=1.65528;LSEQ=TCTATGAAAGGGAATGTTCA;RSEQ=CTCTATGAGTTGAATGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:10:6,4:28,24:0.1613:2,2:20:1:30.2:1:1:1.28:49.8:20:0.1613:0:6 0/1:124:30:11,19:46,45:0.2419:2,2:15.6:1:29.7:1:0.21102:1.7574:50:29:0.2397:0:6 -18 18518982 . CT AC 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.34402;SOR=2.29893;LSEQ=CTATGAAAGGGAATGTTCAA;RSEQ=CTATGAGTTGAATGCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:0,2:34,26:0.0323:2,0:18:0:32:1:0.19989:0:48:4:0.0323:0:5 0/1:126:9:4,5:55,62:0.0714:2,2:15.6:1:31.3:1:1:1.10795:35.1:18:0.072:0:5.2 -18 18518992 . T C 51 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55291;SOR=Inf;LSEQ=GAATGTTCAACTCTATGAGT;RSEQ=GAATGCAAACATCAGAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:33,29:0:2,0:25.1:1:30.5:1:1:0:46.2:124:1:0:5.8 0/1:114:3:1,2:55,56:0.0263:2,2:6:0:32.3:1:1:1.95311:41:6:0.0268:0:5.7 -18 18518996 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11941;SOR=0;LSEQ=GTTCAACTCTATGAGTTGAA;RSEQ=GCAAACATCAGAACGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:29,26:0.0351:2,2:6:1:30:1:1:1.11325:54:4:0.0351:0:4.5 0/0:107:0:0,0:52,55:0:2,0:24:1:30.6:1:1:0:49.5:214:1:0:5.7 -18 18518998 . C G 95 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.74624;SOR=1.56961;LSEQ=TCAACTCTATGAGTTGAATG;RSEQ=AAACATCAGAACGAAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:1,2:26,23:0.0577:2,2:27.7:1:31.3:1:0.60294:2.22657:41:6:0.0577:0:7.3 0/1:91:8:4,4:42,41:0.0879:2,2:18.8:1:31.8:1:1:1.02412:45.4:16:0.0879:0:6.8 -18 18519000 . A G 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.03483;LSEQ=AACTCTATGAGTTGAATGCA;RSEQ=ACATCAGAACGAAATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:34:20,14:4,11:0.6939:2,2:33:1:31.9:1:0.06222:3.82:44.2:33:0.6875:0:6 1/0:87:61:32,29:11,14:0.7011:2,2:34.5:1:32.1:1:0.63535:1.40:50:122:0.7093:0:6.1 -18 18519002 . C T 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15664;LSEQ=CTCTATGAGTTGAATGCAAA;RSEQ=ATCAGAACGAAATTTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:3:1,2:23,20:0.0638:2,2:23.7:1:29.7:1:0.6:2.25968:41:6:0.0638:0:7.3 0/1:82:6:4,2:36,34:0.0732:2,2:23:1:30.5:1:0.67732:1.87:40.5:12:0.0741:0:6.7 -18 18519005 . C T 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1394;SOR=0;LSEQ=TATGAGTTGAATGCAAACAT;RSEQ=AGAACGAAATTTCTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:23,19:0.0455:2,2:17:0:30.5:1:1:1.20525:33:4:0.0455:0:6 0/0:73:0:0,0:39,33:0:2,0:32:1:32.1:1:1:0:49.4:71:0.9861:0:6 -18 18519006 . A C 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70832;SOR=1.89936;LSEQ=ATGAGTTGAATGCAAACATC;RSEQ=GAACGAAATTTCTGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:23,19:0.0455:2,2:16.5:1:31:1:1:1.20525:50.5:4:0.0455:0:7 0/1:72:6:4,2:35,31:0.0833:2,2:21:1:31.2:1:0.68086:1.76:40.5:12:0.0833:0:6.7 -18 18519007 . G C 34 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12958;SOR=0;LSEQ=TGAGTTGAATGCAAACATCA;RSEQ=AACGAAATTTCTGAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:22,17:0.0488:2,2:15:0:34:0:1:1.28591:33:4:0.0488:0:6 0/0:72:0:0,0:39,33:0:2,0:31:1:32.1:1:1:0:49.4:144:1:0:6 -18 18519010 . C A 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGAATGCAAACATCAGAA;RSEQ=GAAATTTCTGAGAATGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:21,18:0,0:1:0,2:27.3:1:31.1:1:1:0:44.5:78:1:0:6 1/1:68:67:35,32:0,0:0.9853:0,2:31.4:1:31:1:1:0:50.2:66:0.9851:0:6.1 -18 18519013 . A T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13252;SOR=0;LSEQ=GAATGCAAACATCAGAACGA;RSEQ=ATTTCTGAGAATGCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:20,18:0.05:2,2:26.5:1:28.5:1:1:1.10818:60:4:0.05:0:5 0/0:69:0:0,0:36,33:0:2,0:28.6:1:30.6:1:1:0:50.1:138:1:0:6.1 -18 18519014 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13678;SOR=0;LSEQ=AATGCAAACATCAGAACGAA;RSEQ=TTTCTGAGAATGCTGCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:20,19:0.0488:2,2:8:0:33.5:1:1:1.05134:33:4:0.0488:0:6 0/0:69:0:0,0:36,33:0:2,0:27.9:1:30.5:1:1:0:50.1:138:1:0:6.1 -18 18519021 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11008;LSEQ=ACATCAGAACGAAATTTCTG;RSEQ=GAATGCTGCTGTCCACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:4:1,3:17,18:0.1026:2,2:7.3:1:30.3:1:0.60937:2.7643:52.3:8:0.1026:0:7.8 0/1:71:8:5,3:33,30:0.1127:2,2:10.5:1:30.5:1:0.71609:1.51:44.6:16:0.1127:0:7 -18 18519035 . C T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35897;SOR=Inf;LSEQ=TTTCTGAGAATGCTGCTGTC;RSEQ=ACTTTTTATATGAATGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:27:12,15:0,0:0.9643:0,2:15.8:1:29.5:1:1:0:45.9:54:0.9643:0:7.3 1/1:50:50:27,23:0,0:1:0,2:16.9:1:29.5:1:1:0:50.6:49:1:0:7.1 -18 18519037 . C G 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.7619;SOR=0.7531;LSEQ=TCTGAGAATGCTGCTGTCCA;RSEQ=TTTTTATATGAATGCGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:3,3:9,10:0.24:2,2:17.7:1:32.7:1:1:1.11:51.8:12:0.24:0:7.7 0/1:47:9:6,3:19,19:0.1915:2,2:18.4:1:32.3:1:0.47032:1.97:49.6:18:0.1915:0:7.7 -18 18519038 . T C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.28286;SOR=1.81355;LSEQ=CTGAGAATGCTGCTGTCCAC;RSEQ=TTTTATATGAATGCGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:17:8,9:4,5:0.6538:2,2:17.1:1:31.5:1:1:1.11:44.2:34:0.6538:0:7.4 1/0:49:38:19,19:6,5:0.7755:2,2:15.4:1:30.4:1:1:1.19554:50.2:76:0.7755:0:6.9 -18 18519039 . T G 53 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.58669;LSEQ=TGAGAATGCTGCTGTCCACT;RSEQ=TTTATATGAATGCGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:12,13:0.0385:2,0:15:0:34:0:1:0:40:2:0.0385:0:8 0/1:50:3:3,0:22,25:0.06:2,0:17:1:34:0:0.23469:0:41.3:6:0.06:0:8 -18 18519045 . A T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58935;SOR=1.46095;LSEQ=TGCTGCTGTCCACTTTTTAT;RSEQ=TGAATGCGCGCTTTCAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:14:6,8:4,5:0.6087:2,2:15.5:1:29.5:1:1:1.06367:42.7:28:0.6087:0:7.6 1/0:46:32:17,15:7,7:0.6957:2,2:11.3:1:29.2:1:1:1.13:50.7:64:0.6957:0:7.1 -18 18519046 . T C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40656;SOR=0.57395;LSEQ=GCTGCTGTCCACTTTTTATA;RSEQ=GAATGCGCGCTTTCAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:4,5:6,7:0.4091:2,2:20.8:1:31:1:1:1.06805:47.9:18:0.4091:0:7.1 0/1:46:13:7,6:17,16:0.2826:2,2:21.2:1:30.6:1:1:1.10:47.5:26:0.2889:0:7.2 -18 18519051 . G T 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTCCACTTTTTATATGAAT;RSEQ=CGCGCTTTCAACGAAATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:8,10:0,0:1:0,2:22.6:1:30.1:1:1:0:45.1:36:1:0:7.6 1/1:34:34:16,18:0,0:1:0,2:16.1:1:28.9:1:1:0:47.5:33:1:0:7.2 -18 18519053 . G C 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCACTTTTTATATGAATGC;RSEQ=CGCTTTCAACGAAATCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:7,9:0,0:1:0,2:26.2:1:31.1:1:1:0:45.7:32:1:0:7.5 1/1:28:28:12,16:0,0:1:0,2:19.5:1:30.3:1:1:0:45:56:1:0:7.3 -18 18519059 . T C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATATGAATGCGCGCTT;RSEQ=CAACGAAATCCTCAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:8,16:0,0:1:0,2:21:1:30.9:1:1:0:44.5:48:1:0:6.2 1/1:50:48:17,31:0,0:0.96:0,2:13.7:1:30.1:1:1:0:41.1:96:0.96:0:5.6 -18 18519064 . G T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGAATGCGCGCTTTCAAC;RSEQ=AAATCCTCAAAGCAATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,17:0:2,0:22.7:1:30.6:1:1:0:44.7:52:1:0:5.8 0/1:55:2:1,1:20,33:0.0364:2,2:9:1:31:1:1:1.63:50:4:0.0364:0:5 -18 18519073 . A C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.02824;LSEQ=GCGCTTTCAACGAAATCCTC;RSEQ=AAGCAATCCAAATATCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:1,4:8,13:0.1923:2,2:35.6:1:31.8:1:0.62785:2.38576:34.8:10:0.2:0:6 0/1:61:12:0,12:20,29:0.1967:2,0:21:1:29.4:1:0.00565:0:34.6:24:0.1967:0:5.1 -18 18519076 . G A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTCAACGAAATCCTCAAA;RSEQ=CAATCCAAATATCCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:26.3:1:32.3:1:1:0:45.6:56:1:0:5.3 0/1:63:2:2,0:19,42:0.0317:2,0:23:0:28.5:1:0.10753:0:35:4:0.0323:0:5.5 -18 18519078 . A T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59474;SOR=1.432;LSEQ=TTCAACGAAATCCTCAAAGC;RSEQ=ATCCAAATATCCACTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:1,4:9,14:0.1786:2,2:34.6:1:28.2:1:0.62637:2.4947:34.8:10:0.1786:0:6 0/1:63:15:2,13:19,29:0.2381:2,2:23.8:1:26.6:1:0.06921:4.17474:35:30:0.2381:0:5.1 -18 18519080 . T G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAACGAAATCCTCAAAGCAA;RSEQ=CCAAATATCCACTTGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:27.7:1:30.1:1:1:0:45.6:56:1:0:5.3 0/1:64:2:2,0:19,43:0.0313:2,0:27:0:30:0:0.10417:0:35:4:0.0313:0:5.5 -18 18519093 . T C 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGCAATCCAAATATCCAC;RSEQ=TGCAGATTCCACAAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:28.8:1:30.6:1:1:0:45.6:56:1:0:5.3 0/1:66:2:0,2:21,43:0.0303:2,0:22:1:28.5:1:1:0:40:4:0.0308:0:5 -18 18519096 . C G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55274;SOR=Inf;LSEQ=GCAATCCAAATATCCACTTG;RSEQ=AGATTCCACAAAAAGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:28.4:1:30.5:1:1:0:45.6:8.333:1:0:5.3 0/1:67:3:2,1:20,44:0.0448:2,2:14.3:1:30.7:1:0.24914:4.29:47:6:0.0448:0:7 -18 18519098 . GA TT 68 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31702;SOR=Inf;LSEQ=AATCCAAATATCCACTTGCA;RSEQ=TTCCACAAAAAGAGTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:28:1:31.5:1:1:0:45.6:27:1:0:5.3 0/1:68:5:0,5:22,41:0.0735:2,0:30.2:1:29.3:1:0.1663:0:40:10:0.0735:0:4 -18 18519100 . T A 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21258;SOR=0.45802;LSEQ=TCCAAATATCCACTTGCAGA;RSEQ=TCCACAAAAAGAGTGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:23:9,14:1,4:0.8214:2,2:28.6:1:28.8:1:0.62637:2.49:48:6.667:0.8:0:5.1 1/0:68:46:18,28:4,18:0.6765:2,2:33.9:1:30.3:1:0.10266:2.85:43.4:92:0.6765:0:4.9 -18 18519114 . T C 84 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18419;SOR=Inf;LSEQ=TGCAGATTCCACAAAAAGAG;RSEQ=GTTTCAAAACTCCTCTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,15:0:2,0:24.1:1:30.3:1:1:0:44.9:46:0.9583:0:4.8 0/1:69:7:4,3:18,44:0.1014:2,2:23.6:1:30:1:0.19803:3.20:40.4:14:0.1029:0:7 -18 18519126 . C G 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18974;SOR=0;LSEQ=AAAAAGAGTGTTTCAAAACT;RSEQ=CTCTATCAATAGAAAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:3,10:0,0:1:0,2:26:1:32.5:1:1:0:44.9:26:1:0:4.2 1/1:54:44:11,33:0,0:0.8148:0,2:22.8:1:32.9:1:1:0:40.7:88:0.8627:0:4.4 -18 18519133 . C G 90 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32658;SOR=Inf;LSEQ=GTGTTTCAAAACTCCTCTAT;RSEQ=AATAGAAAGTTTCAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:22.6:1:32.4:1:1:0:47.3:22:1:0:4.1 0/1:47:7:3,4:10,30:0.1489:2,2:34.3:1:32.4:1:0.3769:2.21:40.1:14:0.1489:0:7.4 -18 18519136 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCAAAACTCCTCTATCAA;RSEQ=AGAAAGTTTCAACTCTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:19.6:1:27.5:1:1:0:47.3:10:1:0:4.1 0/1:45:2:1,1:12,31:0.0444:2,2:38.5:1:30:0:0.49899:2.52:30.5:4:0.0444:0:8 -18 18519137 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAAAACTCCTCTATCAAT;RSEQ=GAAAGTTTCAACTCTGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:18.6:1:30.8:1:1:0:47.3:22:1:0:4.1 0/1:44:2:0,2:13,29:0.0455:2,0:34.5:1:31.5:1:1:0:40:4:0.0455:0:6.5 -18 18519139 . A C 34 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAAACTCCTCTATCAATAG;RSEQ=AAGTTTCAACTCTGTTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:16.6:1:29.3:1:1:0:47.3:10:1:0:4.1 0/1:41:2:0,2:12,27:0.0488:2,0:32.5:1:34:0:1:0:40:4:0.0488:0:6.5 -18 18519142 . GT AG 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTCCTCTATCAATAGAAA;RSEQ=TTCAACTCTGTTAGTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:13.6:1:31.3:1:1:0:47.3:22:1:0:4.1 0/1:33:2:0,2:10,21:0.0606:2,0:28.5:1:33:0:1:0:40:4:0.0606:0:5.5 -18 18519143 . T G 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.10834;LSEQ=ACTCCTCTATCAATAGAAAG;RSEQ=TTCAACTCTGTTAGTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:2,7:0,0:0.9:0,2:15.3:1:32.3:1:1:0:46.4:18:0.9:0:4.4 1/1:33:30:10,20:0,1:0.9091:0,2:19.6:1:31.7:1:1:0:42.1:60:0.9677:0:5.3 -18 18519147 . A T 85 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30743;SOR=Inf;LSEQ=CTCTATCAATAGAAAGTTTC;RSEQ=ACTCTGTTAGTTGAGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:0:2,0:13:1:30.1:1:1:0:47.1:16:1:0:4.5 0/1:30:7:3,4:5,18:0.2333:2,2:28.6:1:30.4:1:0.3446:2.60:40.1:14:0.2414:0:7.4 -18 18519152 . TG CT 89 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29644;SOR=Inf;LSEQ=TCAATAGAAAGTTTCAACTC;RSEQ=TTAGTTGAGGACACACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:11.2:1:30.7:1:1:0:49.5:12:1:0:4.5 0/1:26:7:3,4:5,14:0.2692:2,2:23.3:1:32:1:0.63529:2.04:40.1:14:0.28:0:6.4 -18 18519153 . G T 120 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14987;SOR=0;LSEQ=CAATAGAAAGTTTCAACTCT;RSEQ=TTAGTTGAGGACACACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:10.2:1:29.8:1:1:0:49.5:12:1:0:4.5 1/0:26:17:5,12:0,2:0.6538:0,2:11.4:1:29.4:1:1:0:43.4:16:0.8889:0:4.9 -18 18519163 . G T 89 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47895;SOR=0;LSEQ=TTTCAACTCTGTTAGTTGAG;RSEQ=ACACACATCACAAATAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5.5:1:28.5:1:1:0:52:4:1:0:5 1/0:18:9:4,5:3,6:0.5:2,2:7:1:28.3:1:1:1.56:41.4:18:0.5:0:5.2 -18 18519274 . T C 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AAATATCCACTTGCAGATTC;RSEQ=ACAAAAAGAGTGTTTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:30:1:1:0:45:4:1:0:7 0/0:3:0:0,0:1,2:0:2,0:10.7:1:31:1:1:0:40.3:6:1:0:2.7 -18 18519278 . A G 29 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.55247;LSEQ=ATCCACTTGCAGATTCTACA;RSEQ=AAAGAGTGTTTCAAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:10.5:1:29.5:1:1:1:45:4:0.5:0:7 0/1:3:1:0,1:1,1:0.3333:2,0:22:0:33:0:1:0:23:2:0.3333:0:1 -18 18519282 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=ACTTGCAGATTCTACAAAAA;RSEQ=AGTGTTTCAAAACTGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:14.5:1:30.5:1:1:1.7321:45:4:0.4:0:7 0/0:5:0:0,0:2,3:0:2,0:12.6:1:31.2:1:1:0:36.2:10:1:0:4.2 -18 18519285 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TGCAGATTCTACAAAAAGAG;RSEQ=GTTTCAAAACTGCTCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:17.5:1:30:1:1:1.7321:45:4:0.4:0:7 0/0:5:0:0,0:2,3:0:2,0:15.6:1:30.4:1:1:0:36.2:10:1:0:4.2 -18 18519291 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=TTCTACAAAAAGAGTGTTTC;RSEQ=AAACTGCTCTGTAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:14.3:1:29.7:1:1:0:30.6:14:1:0:7 0/1:7:2:1,1:3,2:0.2857:2,2:12.5:1:29.5:1:1:1.41418:30:4:0.2857:0:6.5 -18 18519294 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.175;SOR=0;LSEQ=TACAAAAAGAGTGTTTCAAA;RSEQ=CTGCTCTGTAAAAAGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:26.5:1:31:1:1:3.1622:45:4:0.2857:0:7 0/0:9:0:0,0:6,3:0:2,0:15.3:1:30.6:1:1:0:34.3:18:1:0:5.4 -18 18519302 . G A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61451;SOR=0.39984;LSEQ=GAGTGTTTCAAAACTGCTCT;RSEQ=TAAAAAGAAAGGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:1,1:0.5714:2,0:20:1:29.5:1:0.33333:0:25.5:8:0.5714:0:6.8 0/1:9:3:3,0:3,3:0.3333:2,0:11.3:1:30:0:0.46429:0:31:6:0.3333:0:7.3 -18 18519304 . A C 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.63719;SOR=0.52127;LSEQ=GTGTTTCAAAACTGCTCTGT;RSEQ=AAAAGAAAGGTTCAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:1,1:0.5:2,0:22:1:32.3:1:0.33333:0:25.5:8:0.5:0:6.8 0/1:9:3:3,0:1,2:0.3333:2,0:13.3:1:33:0:0.4:0:31:6:0.3333:0:7.3 -18 18519305 . AAAAGAAAG TCAATGGCAAA 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.20588;SOR=0;LSEQ=TGTTTCAAAACTGCTCTGTA;RSEQ=GTTCAACTCTGTTAGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,1:0.25:2,0:33:1:30.3:1:1:0:22.5:4:0.25:0.125:5.5 0/0:9:0:0,0:1,2:0:2,0:40:1:30.3:1:1:0:40.3:6:0.3333:0:2.7 -18 18519307 . A T 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.36185;SOR=0.31991;LSEQ=TTTCAAAACTGCTCTGTAAA;RSEQ=AGAAAGGTTCAACTCTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:1,1:0.625:2,0:20.4:1:32.4:1:0.28571:0:27.8:10:0.7143:0:6.8 0/1:12:4:4,0:5,3:0.3333:2,0:13:1:30.8:1:0.49091:0:33.3:8:0.3333:0:7.5 -18 18519310 . A G 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23;SOR=Inf;LSEQ=CAAAACTGCTCTGTAAAAAG;RSEQ=AAGGTTCAACTCTGTTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,2:0:2,0:21:1:30.7:1:1:0:33.8:20:1:0:6.6 0/1:14:3:2,1:9,2:0.2143:2,2:28:1:31.7:1:1:2.10574:31.7:6:0.2143:0:6.3 -18 18519311 . A G 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24786;SOR=Inf;LSEQ=AAAACTGCTCTGTAAAAAGA;RSEQ=AGGTTCAACTCTGTTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,2:0:2,0:22:1:31:1:1:0:33.8:20:1:0:6.6 0/1:16:3:3,0:10,3:0.1875:2,0:5:1:32.3:1:1:0:40:6:0.1875:0:7.7 -18 18519318 . A C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25134;SOR=Inf;LSEQ=CTCTGTAAAAAGAAAGGTTC;RSEQ=ACTCTGTTAGTTGAGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,5:0:2,0:25.1:1:30.1:1:1:0:32:28:1:0:6.4 0/1:20:3:3,0:14,3:0.15:2,0:12:1:31.3:1:1:0:40:6:0.15:0:7.7 -18 18519324 . G T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74421;SOR=0.7334;LSEQ=AAAAAGAAAGGTTCAACTCT;RSEQ=TTAGTTGAGTACACACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:7,2:2,3:0.6:2,2:27.8:1:30.1:1:0.26573:4.58:30.7:18:0.6:0:6.4 1/0:23:12:12,0:7,4:0.5217:2,0:16.7:1:29.7:1:0.03727:0:36.4:11:0.5:0:7.5 -18 18519329 . T C 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27782;SOR=Inf;LSEQ=GAAAGGTTCAACTCTGTTAG;RSEQ=TGAGTACACACATCACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:30.3:1:30.6:1:1:0:33.9:30:1:0:5.9 0/1:25:4:3,1:16,2:0.16:2,2:17.3:1:31.8:1:0.47013:2.52306:31:8:0.1739:0:7 -18 18519333 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63901;LSEQ=GGTTCAACTCTGTTAGTTGA;RSEQ=TACACACATCACAAACAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:14,5:0.0952:2,2:35.5:1:32:0:0.5:2.64575:45:4:0.0952:0:7 0/1:32:2:1,1:25,5:0.0625:2,2:31.5:1:29.5:1:0.34476:4.65478:49:4:0.0625:0:3.5 -18 18519334 . T G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14141;SOR=0;LSEQ=GTTCAACTCTGTTAGTTGAG;RSEQ=ACACACATCACAAACAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:14,4:0.0952:2,0:30:1:32.5:1:0.07895:0:22.5:4:0.0952:0:5.5 0/0:34:0:0,0:28,6:0:2,0:19.8:1:29.7:1:1:0:35.2:68:1:0:6.6 -18 18519340 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.11795;SOR=0;LSEQ=CTCTGTTAGTTGAGTACACA;RSEQ=ATCACAAACAAGTTTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:0,2:16,5:0.087:2,0:30:1:29.5:1:0.083:0:22.5:4:0.087:0:5.5 0/0:43:0:0,0:31,12:0:2,0:19.6:1:31.5:1:1:0:35:86:1:0:6.5 -18 18519341 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11795;SOR=0;LSEQ=TCTGTTAGTTGAGTACACAC;RSEQ=TCACAAACAAGTTTCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:15,6:0.087:2,2:27.5:1:32.5:1:0.52569:2.39047:45:4:0.087:0:7 0/0:43:0:0,0:31,12:0:2,0:20.3:1:29.6:1:1:0:35:42:1:0:6.5 -18 18519343 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54229;SOR=Inf;LSEQ=TGTTAGTTGAGTACACACAT;RSEQ=ACAAACAAGTTTCTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:16,7:0:2,0:25.6:1:32.2:1:1:0:35.2:46:1:0:6.3 0/1:44:2:1,1:30,12:0.0455:2,2:21.5:1:30.5:1:0.50846:2.44164:49:4:0.0455:0:3.5 -18 18519344 . A T 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02291;LSEQ=GTTAGTTGAGTACACACATC;RSEQ=CAAACAAGTTTCTGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:15,7:0.0435:2,0:32:0:33:0:1:0:37:2:0.0435:0:6 0/1:45:2:2,0:29,14:0.0444:2,0:15:1:31.5:1:1:0:31.5:4:0.0444:0:6.5 -18 18519346 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.76758;SOR=0.8121;LSEQ=TAGTTGAGTACACACATCAC;RSEQ=AACAAGTTTCTGAGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:4,2:12,3:0.2609:2,2:24.2:1:30.5:1:0.59752:1.9297:29.3:12:0.2609:0:7.5 0/1:45:10:6,4:25,10:0.2222:2,2:22.8:1:29.4:1:0.69997:1.64673:35.1:20:0.2222:0:7.9 -18 18519349 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54902;SOR=Inf;LSEQ=TTGAGTACACACATCACAAA;RSEQ=AAGTTTCTGAGAATGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:15,7:0:2,0:27:1:33:1:1:0:35.1:44:0.9565:0:6.3 0/1:46:2:1,1:28,13:0.0435:2,2:19:0:33.5:1:1:2.11228:30:4:0.0435:0:6.5 -18 18519350 . AA TT 105 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19385;SOR=3.25109;LSEQ=TGAGTACACACATCACAAAC;RSEQ=GTTTCTGAGAATGCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:15,6:0.087:2,2:19:0:32:0:0.52569:2.39047:47:4:0.087:0:5 0/1:46:11:7,4:25,10:0.2391:2,2:26.8:1:30.4:1:0.71301:1.41716:33.5:22:0.2391:0:4.6 -18 18519351 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54608;SOR=Inf;LSEQ=GAGTACACACATCACAAACA;RSEQ=GTTTCTGAGAATGCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,7:0:2,0:27.4:1:30.6:1:1:0:33.6:21:1:0:6.3 0/1:47:2:1,1:24,10:0.0426:2,2:17:0:33:1:0.52381:2.33552:30:4:0.0556:0:6.5 -18 18519354 . T C 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.75319;LSEQ=TACACACATCACAAACAAGT;RSEQ=TCTGAGAATGCTTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:15,7:0.0833:2,2:22:0:33.5:1:1:2.07024:47:4:0.0833:0:5 0/1:47:3:2,1:30,14:0.0638:2,2:29.3:1:33.3:1:1:1.06984:31.7:6:0.0638:0:4.7 -18 18519358 . G C 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.31996;SOR=2.44814;LSEQ=CACATCACAAACAAGTTTCT;RSEQ=AGAATGCTTCTGTCTCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:15,7:0.0833:2,2:26:0:33.5:1:1:2.07024:47:4:0.087:0:5 0/1:49:9:6,3:26,14:0.1837:2,2:33.1:1:31.3:1:1:1.08:34:18:0.1875:0:5.2 -18 18519364 . G C 108 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12034;SOR=3.56634;LSEQ=ACAAACAAGTTTCTGAGAAT;RSEQ=CTTCTGTCTCGTTTTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:15,10:0.0741:2,2:32:0:32.5:1:1:1.47706:47:4:0.0741:0:5 0/1:49:11:7,4:24,13:0.2245:2,2:31.1:1:31.3:1:1:1.05376:33.5:22:0.2245:0:4.6 -18 18519374 . C G 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87671;LSEQ=TTCTGAGAATGCTTCTGTCT;RSEQ=GTTTTTATGGGAAGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:15:9,6:3,2:0.6818:2,2:28.2:1:31:1:1:1:31.1:30:0.6818:0:7.2 1/0:46:30:19,11:7,4:0.6522:2,2:34.3:1:30.3:1:1:1.01284:36.4:60:0.6522:0:7.5 -18 18519376 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.58818;SOR=0.62911;LSEQ=CTGAGAATGCTTCTGTCTCG;RSEQ=TTTTATGGGAAGATATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:10,6:4,2:0.7273:2,2:27.4:1:31.4:1:1:1.19021:31.7:32:0.7273:0:7 1/0:48:30:19,11:12,6:0.625:2,2:34.7:1:30.9:1:1:1.15438:36.4:60:0.625:0:7.5 -18 18519381 . AT TA 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGCTTCTGTCTCGTTTTT;RSEQ=GGGAAGATATTTCCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:29.2:1:28.4:1:1:0:36.9:42:1:0:6 0/1:48:2:1,1:30,16:0.0417:2,2:33.5:1:29.8:1:1:1.84915:45:4:0.0426:0:3.5 -18 18519383 . G T 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.79189;SOR=0.83552;LSEQ=TGCTTCTGTCTCGTTTTTAT;RSEQ=GGAAGATATTTCCTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:8,6:5,2:0.6667:2,2:30.1:1:29.4:1:0.65566:1.82076:31.6:28:0.6667:0:7.2 1/0:48:30:19,11:12,6:0.625:2,2:35:1:28.4:1:1:1.15438:36.4:60:0.625:0:7.5 -18 18519390 . TA CG 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76897;SOR=1.31208;LSEQ=GTCTCGTTTTTATGGGAAGA;RSEQ=TTTCCTTTTTCACCAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:5,6:3,2:0.6111:2,2:30.3:1:30.3:1:1:1.73457:32.1:22:0.6111:0:6.2 1/0:43:29:18,11:8,5:0.6744:2,2:33.1:1:28.3:1:1:1.02:36.8:13.5:0.6585:0.0465:6.6 -18 18519395 . C A 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1403;LSEQ=GTTTTTATGGGAAGATATTT;RSEQ=CTTTTTCACCAAAGTCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:11:0:28.5:1:1:1.26772:47:4:0.1111:0:5 0/1:40:5:3,2:21,14:0.125:2,2:11:0:30.6:1:1:1:29.8:10:0.1282:0:5.4 -18 18519396 . CT C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.7766;SOR=1.17838;LSEQ=TTTTTATGGGAAGATATTTC;RSEQ=TTTTCACCAAAGTCGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:5,6:5,2:0.6111:2,2:30.3:1:31.3:1:0.36652:2.8187:32.4:22:0.6111:0:7.2 1/0:40:26:15,11:9,5:0.65:2,2:32.3:1:30.2:1:0.74621:1.31092:36.8:52:0.65:0:7.5 -18 18519410 . T G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.30796;SOR=2.81755;LSEQ=TATTTCCTTTTTCACCAAAG;RSEQ=CGTCAAAGCGCTCCAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:5,5:1,1:0.8333:2,2:25.6:1:30.2:1:1:1:34:20:0.8333:0:7.1 1/1:31:29:15,14:0,0:0.9355:0,2:22.3:1:30.8:1:1:0:37:58:0.9355:0:7.1 -18 18519412 . G A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.24295;LSEQ=TTTCCTTTTTCACCAAAGTC;RSEQ=TCAAAGCGCTCCAAATGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:5,5:1,1:0.8333:2,2:24:1:28.9:1:1:1:34:20:0.8333:0:7.1 1/1:29:25:12,13:2,2:0.8621:2,2:22.2:1:28.7:1:1:1.08033:36.1:24:0.8571:0:7.4 -18 18519443 . A T 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0.68659;LSEQ=CCAAATGTCCACTTCCAGAT;RSEQ=CTACAAAAAGAATGTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:25.5:1:32:0:1:0:40:4:0.5:0:7.5 0/1:10:4:0,4:0,0:0.4:0,0:22.8:1:29:1:1:0:32.5:8:0.4:0:7.5 -18 18519446 . A T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.57143;SOR=2.68677;LSEQ=AATGTCCACTTCCAGATACT;RSEQ=CAAAAAGAATGTTTCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:26:0:32:0:1:0:40:2:0.25:0:7 1/0:6:3:0,3:0,3:0.5:0,0:28.7:1:29:1:1:0:30:6:0.5:0:7.3 -18 18519448 . A C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGTCCACTTCCAGATACTAC;RSEQ=AAAAGAATGTTTCAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:25.5:1:34:0:1:0:40:4:0.5:0:7.5 1/0:6:3:0,3:0,3:0.5:0,0:28:1:32.7:1:1:0:30:6:0.5:0:7.3 -18 18519455 . A G 90 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41667;SOR=Inf;LSEQ=TTCCAGATACTACAAAAAGA;RSEQ=TGTTTCAAACCTGCTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:24.5:1:32.5:1:1:0:36.3:8:0.8:0:7.3 1/1:7:7:0,7:0,0:1:0,0:24.1:1:32.3:1:1:0:32.1:14:1:0:6.6 -18 18519466 . C G 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.58251;LSEQ=ACAAAAAGAATGTTTCAAAC;RSEQ=TGCTCCATGAAAGGGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:17.7:1:32.3:1:1:0:36:6:0.75:0:7.7 1/0:8:5:1,4:0,3:0.625:0,2:16.6:1:32:1:1:0:37.4:10:0.625:0:7.6 -18 18519472 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=AGAATGTTTCAAACCTGCTC;RSEQ=ATGAAAGGGAATGTTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:15.5:1:30:1:1:0:32:4:0.5:0:6 0/1:6:2:0,2:0,0:0.3333:0,0:28.5:1:29.5:1:1:0:29:4:0.3333:0:5 -18 18519474 . T A 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=AATGTTTCAAACCTGCTCCA;RSEQ=GAAAGGGAATGTTCAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,1:0.5:0,2:16.5:1:30:1:1:0:27.5:4:0.6667:0:7 1/0:6:4:1,3:0,1:0.6667:0,2:26.3:1:32.5:1:1:0:38.5:8:0.6667:0:7.5 -18 18519476 . A T 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.60839;SOR=2.34872;LSEQ=TGTTTCAAACCTGCTCCATG;RSEQ=AAGGGAATGTTCAACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:2,3:0.2857:2,0:23.5:1:28:1:1:0:34:4:0.2857:0:7 1/0:8:4:1,3:1,3:0.5:2,2:27.3:1:29:1:1:1:38.5:8:0.5:0:7.5 -18 18519480 . G C 47 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.05455;SOR=0;LSEQ=TCAAACCTGCTCCATGAAAG;RSEQ=GAATGTTCAACTCTGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:2,4:0.3333:2,2:5:1:30:1:1:1:37:6:0.3333:0:5.7 0/0:13:0:0,0:3,9:0:2,0:15.3:1:31.8:1:1:0:36.9:24:0.9231:0:6.3 -18 18519485 . G A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.19206;LSEQ=CCTGCTCCATGAAAGGGAAT;RSEQ=TTCAACTCTGTGACTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:2,7:0.1:2,0:11:0:29:0:0.3:0:39:2:0.1:0:8 0/1:17:2:1,1:5,10:0.1176:2,2:11:0:28.5:1:1:1.91:25:4:0.1176:0:7.5 -18 18519495 . G C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94324;LSEQ=GAAAGGGAATGTTCAACTCT;RSEQ=TGACTTGAATGCCGATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:2,5:0.1111:2,0:21:0:33:0:0.375:0:39:2:0.1111:0:8 0/1:19:2:1,1:6,10:0.1053:2,2:21:0:32.5:1:1:1.62:25:4:0.1053:0:7.5 -18 18519499 . CT TA 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.8796;LSEQ=GGGAATGTTCAACTCTGTGA;RSEQ=TGAATGCCGATATCACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:2,5:0.125:2,0:26:0:30.5:0:0.375:0:39:2:0.125:0:7 0/1:18:2:1,1:6,10:0.1111:2,2:26:0:29.5:1:1:1.62:25:4:0.1111:0:6.5 -18 18519502 . G C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.78507;LSEQ=AATGTTCAACTCTGTGACTT;RSEQ=AATGCCGATATCACAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:2,5:0.125:2,0:28:0:33:0:0.375:0:39:2:0.125:0:7 0/1:20:2:1,1:7,11:0.1:2,2:28:0:32.5:1:1:1.54:25:4:0.1:0:6.5 -18 18519508 . C A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTCTGTGACTTGAATGC;RSEQ=GATATCACAAAGTAGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:3,5:0,0:1:0,2:31.9:1:30.6:1:1:0:38.5:16:1:0:6.1 1/1:20:20:9,11:0,0:1:0,2:23.7:1:30.8:1:1:0:40.7:40:1:0:5.9 -18 18519517 . A C 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67219;SOR=2.02915;LSEQ=GACTTGAATGCCGATATCAC;RSEQ=AAGTAGTTTCTGAGAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:3,3:0.25:2,0:26.5:1:33:1:0.46429:0:43:4:0.25:0:7.5 0/1:22:9:3,6:7,6:0.4091:2,2:29.7:1:31.4:1:0.41486:2.24368:48.3:18:0.4091:0:6.3 -18 18519529 . G A 92 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20401;SOR=4.65935;LSEQ=GATATCACAAAGTAGTTTCT;RSEQ=AGAGTGCTTCTGTCTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:3,3:0.1429:2,0:37:0:31:0:1:0:58:2:0.1429:0:7 0/1:20:9:4,5:6,5:0.45:2,2:28.1:1:29.1:1:1:1.46966:46.7:18:0.45:0:6 -18 18519531 . G T 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20401;SOR=4.65935;LSEQ=TATCACAAAGTAGTTTCTGA;RSEQ=AGTGCTTCTGTCTAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:3,3:0.1429:2,0:35:0:27:0:1:0:58:2:0.1429:0:7 0/1:20:9:4,5:6,5:0.45:2,2:27:1:28.8:1:1:1.46966:46.7:18:0.45:0:6 -18 18519534 . T G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14452;SOR=0.20225;LSEQ=CACAAAGTAGTTTCTGAGAG;RSEQ=GCTTCTGTCTAGATTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:2,1:0.5714:2,2:34.3:1:32.5:1:0.48571:4.4496:39:8:0.5714:0:5.3 0/1:20:4:2,2:8,8:0.2:2,2:33.3:1:31.8:1:1:1:39:8:0.2:0:5.3 -18 18519541 . G C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGTTTCTGAGAGTGCTTCT;RSEQ=TCTAGATTTTATATGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:26.6:1:32.4:1:1:0:40:14:1:0:5.9 0/1:19:2:1,1:9,8:0.1053:2,2:27.5:1:32:1:1:1.11803:33:4:0.1053:0:6 -18 18519542 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTTCTGAGAGTGCTTCTG;RSEQ=CTAGATTTTATATGAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:25.6:1:30.1:1:1:0:40:14:1:0:5.9 0/1:19:2:1,1:9,8:0.1053:2,2:25:0:33.5:1:1:1.11803:43:4:0.1053:0:4 -18 18519547 . A G 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62878;SOR=2.67506;LSEQ=CTGAGAGTGCTTCTGTCTAG;RSEQ=TTTTATATGAAGATATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:2,4:0.1429:2,0:19:0:27:0:0.42857:0:39:2:0.1429:0:7 0/1:19:6:3,3:7,6:0.3158:2,2:14.7:1:31.3:1:1:1.15722:39.3:12:0.3158:0:4 -18 18519553 . T G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.64002;LSEQ=GTGCTTCTGTCTAGATTTTA;RSEQ=ATGAAGATATTCTCATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:2,0:0.7143:0,2:14.8:1:33.2:1:0.14286:0:42.8:10:0.7143:0:5.6 1/0:18:11:5,6:4,3:0.6111:2,2:13.9:1:32.3:1:1:1.55841:40.1:22:0.6111:0:5.9 -18 18519558 . A T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88488;LSEQ=TCTGTCTAGATTTTATATGA;RSEQ=GATATTCTCATTTCCAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:2,0:0.7143:0,2:9.8:1:31.4:1:0.14286:0:42.8:10:0.7143:0:5.6 1/0:16:11:5,6:3,2:0.6875:2,2:8.9:1:30.3:1:1:1.73457:40.1:22:0.6875:0:5.9 -18 18519566 . T C 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATTTTATATGAAGATATTC;RSEQ=CATTTCCAATGAAATCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:1:30.5:1:1:0:26:4:1:0:6.5 1/1:6:6:4,2:0,0:1:0,2:7:1:30.3:1:1:0:37.2:12:1:0:5.7 -18 18519568 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATATGAAGATATTCTC;RSEQ=TTTCCAATGAAATCGTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:8:0:33:0:1:0:25:2:1:0:7 1/0:3:2:2,0:1,0:0.6667:0,0:17.5:1:31.5:1:1:0:35.5:4:0.6667:0:7 -18 18519576 . T C 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAGATATTCTCATTTCCAA;RSEQ=GAAATCGTTAGAGCTATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:8:0:32:0:1:0:40:2:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:8:0:29:1:1:0:31.5:4:0.6667:0:6.5 -18 18519608 . G A 54 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=3.1622;LSEQ=AGCTATCCAAATATCCACTT;RSEQ=CAGATTCTACAAAAAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:40:0:28:0:1:0:40:2:0.5:0:5 1/1:5:4:3,1:1,0:0.8:0,2:28:1:27.3:1:1:0:30.8:8:0.8:0:5.5 -18 18519612 . A T 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=3.1622;LSEQ=ATCCAAATATCCACTTGCAG;RSEQ=TTCTACAAAAAGAGTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:44:0:30:0:1:0:40:2:0.5:0:5 1/1:5:4:3,1:1,0:0.8:0,2:32:1:29.8:1:1:0:30.8:8:0.8:0:5.5 -18 18519636 . AC CG 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=0.45719;LSEQ=TACAAAAAGAGTGTTTCCAA;RSEQ=TGCTGTATCAAAAGAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:6:0:32.5:0:1:1:45:4:0.5:0:7 0/1:10:3:2,1:3,4:0.3:2,2:17:1:32.5:0:1:2.41:55.7:6:0.3333:0:6.3 -18 18519643 . T C 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24476;SOR=5.98921;LSEQ=AGAGTGTTTCCAAACTGCTG;RSEQ=ATCAAAAGAAAGGTTGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,2:0.25:2,0:16:0:28:0:1:0:40:2:0.25:0:5 1/0:10:7:3,4:2,1:0.7:2,2:29.6:1:31:1:1:2.41422:31.1:14:0.7:0:5.6 -18 18519653 . A T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53007;SOR=0.31868;LSEQ=CAAACTGCTGTATCAAAAGA;RSEQ=AGGTTGAACTTTGTTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,1:0.5:0,2:22:0:31.5:1:1:0:45:4:0.5:0:7 0/1:9:2:1,1:3,4:0.2222:2,2:35:0:30.5:1:1:1.29:60:4:0.2222:0:6.5 -18 18519659 . G C 87 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=GCTGTATCAAAAGAAAGGTT;RSEQ=AACTTTGTTAGTTGAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:30:1:33.7:1:1:0:43:6:1:0:6.7 1/0:9:7:3,4:1,1:0.7778:2,2:27.3:1:31:1:1:1.29098:31.1:14:0.7778:0:5.6 -18 18519660 . A T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23636;SOR=0.17439;LSEQ=CTGTATCAAAAGAAAGGTTG;RSEQ=ACTTTGTTAGTTGAGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:29:0:30.5:1:1:0:45:4:0.6667:0:7 0/1:9:2:1,1:3,4:0.2222:2,2:37.5:1:30:0:1:1.29:60:4:0.25:0:6.5 -18 18519663 . TT AC 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23636;SOR=0.17439;LSEQ=TATCAAAAGAAAGGTTGAAC;RSEQ=TGTTAGTTGAGGACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:33:0:32.3:1:1:0:45:4:0.6667:0:6 0/1:9:2:1,1:3,4:0.2222:2,2:33.5:1:31.8:1:1:1.29:60:4:0.2222:0:5.5 -18 18519664 . T C 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=ATCAAAAGAAAGGTTGAACT;RSEQ=TGTTAGTTGAGGACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,0:0.3333:0,0:29:0:34:0:1:0:39:2:1:0:6 1/0:9:7:3,4:0,0:0.7778:0,2:26.6:1:29.4:1:1:0:31.1:6:1:0:5.6 -18 18519685 . T C 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33781;SOR=3.73352;LSEQ=TGTTAGTTGAGGACACACAT;RSEQ=ACAAAGAAGTTTCTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:4,3:0.125:2,0:8:0:33:0:1:0:39:2:0.125:0:6 0/1:11:4:1,3:4,3:0.3636:2,2:29.3:1:32.3:1:0.54545:3.51553:29.5:8:0.3636:0:5.8 -18 18519688 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49474;SOR=Inf;LSEQ=TAGTTGAGGACACACATTAC;RSEQ=AAGAAGTTTCTGAGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:13.3:1:28.9:1:1:0:39.5:7:1:0:3.9 0/1:12:2:1,1:4,6:0.1667:2,2:9.5:1:29:1:1:1.45:60:4:0.1667:0:5.5 -18 18519698 . C G 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10604;SOR=Inf;LSEQ=CACACATTACAAAGAAGTTT;RSEQ=TGAGAATGCTTCTGTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:18.7:1:29.3:1:1:0:39.6:6:1:0:3.6 0/1:12:5:1,4:4,3:0.4167:2,2:19:1:31.4:1:0.29293:4.60906:30.4:10:0.4167:0:5.4 -18 18519708 . T C 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12281;SOR=0;LSEQ=AAAGAAGTTTCTGAGAATGC;RSEQ=TCTGTCTAGATTTTATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:10.5:1:30:1:1:1.41418:45:4:0.2857:0:6 0/0:12:0:0,0:5,7:0:2,0:21.1:1:31.5:1:1:0:41.2:24:1:0:3.3 -18 18519710 . C G 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12281;SOR=0;LSEQ=AGAAGTTTCTGAGAATGCTT;RSEQ=TGTCTAGATTTTATATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:8.5:1:30.5:1:1:1.41418:45:4:0.2857:0:6 0/0:12:0:0,0:5,7:0:2,0:21.5:1:32.5:1:1:0:41.2:24:1:0:3.3 -18 18519723 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=Inf;LSEQ=AATGCTTCTGTCTAGATTTT;RSEQ=TATGAAGATTTTCCCGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:30:0:29.8:1:1:0:37.4:10:1:0:2.6 0/1:9:2:1,1:4,3:0.2222:2,2:24:0:31:1:1:1.29098:28.5:4:0.2222:0:5 -18 18519729 . A C 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TCTGTCTAGATTTTATATGA;RSEQ=GATTTTCCCGTTTCCAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:24:0:30.8:1:1:0:37.4:10:1:0:2.6 0/1:9:2:1,1:4,3:0.2222:2,2:18:0:29.5:1:1:1.29098:28.5:4:0.2222:0:5 -18 18519731 . A G 85 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TGTCTAGATTTTATATGAAG;RSEQ=TTTTCCCGTTTCCAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:22:0:32.4:1:1:0:37.4:10:1:0:2.6 1/0:9:7:4,3:1,1:0.7778:2,2:13.3:1:30.6:1:1:1.29:48.9:14:0.7778:0:1.9 -18 18519733 . T A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TCTAGATTTTATATGAAGAT;RSEQ=TTCCCGTTTCCAATGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:20:0:26.8:1:1:0:37.4:4:1:0:2.6 0/1:9:2:1,1:4,3:0.2222:2,2:14:0:29.5:1:1:1.29098:28.5:4:0.2222:0:5 -18 18519739 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=TTTTATATGAAGATTTTCCC;RSEQ=TTTCCAATGAAATCCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:14:0:30:1:1:0:37.4:10:1:0:2.6 0/1:7:2:1,1:3,2:0.2857:2,2:8:0:31:1:1:1.41418:28.5:4:0.2857:0:5 -18 18519747 . T C 61 d7;MAF0.05;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=GAAGATTTTCCCGTTTCCAA;RSEQ=GAAATCCTTAAAGCTATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:6:0:26.6:1:1:0:37.4:4:1:0:2.6 1/0:2:1:1,0:0,0:0.5:0,0:6:0:25:0:1:0:60:2:0.5:0:2 -18 18519825 . TG AA 61 d7;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=AAACTGCTCTGTAAAAAGAA;RSEQ=GTTCAACTCTGTTAGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:6:1:30.9:1:1:0:44.3:8:1:0.5:5 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 18519830 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GCTCTGTAAAAAGAATGGTT;RSEQ=AACTCTGTTAGTTGAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:5:1:30.5:1:1:0:41.1:7:1:0:4.6 0/1:9:2:1,1:2,4:0.2222:2,2:5:0:33.5:1:1:1.83:39:4:0.2222:0:3 -18 18519835 . C G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01522;SOR=0.04673;LSEQ=GTAAAAAGAATGGTTCAACT;RSEQ=TGTTAGTTGAGGACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:0,1:0.8889:0,2:10:1:33:1:1:0:41.1:16:0.8889:0:4.6 0/1:9:2:1,1:3,4:0.2222:2,2:6:0:33.5:1:1:1.29:25:4:0.2222:0:5 -18 18519853 . C T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10446;SOR=Inf;LSEQ=CTCTGTTAGTTGAGGACACA;RSEQ=ATCACAAACAAGTTTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:25.8:1:33.8:1:1:0:38.1:20:1:0:4.8 0/1:13:4:1,3:7,2:0.3077:2,2:24.8:1:28.8:1:0.21678:8.36696:34:8:0.3077:0:3.3 -18 18519858 . C G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00398;SOR=0.06714;LSEQ=TTAGTTGAGGACACACATCA;RSEQ=AAACAAGTTTCTGAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:4,4:2,1:0.7273:2,2:31.6:1:32.3:1:1:1.87936:41.1:16:0.7273:0:4.6 0/1:15:2:1,1:7,6:0.1333:2,2:29:0:33.5:1:1:1.1547:25:4:0.1333:0:5 -18 18519859 . A C 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11338;SOR=Inf;LSEQ=TAGTTGAGGACACACATCAC;RSEQ=AACAAGTTTCTGAGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:28.1:1:31:1:1:0:38.3:22:1:0:5.1 0/1:15:4:1,3:7,4:0.2667:2,2:27.3:1:32.3:1:0.28205:4.676:34:8:0.2667:0:3.3 -18 18519862 . C G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.51401;LSEQ=TTGAGGACACACATCACAAA;RSEQ=AAGTTTCTGAGAATGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:6,4:0.0909:2,0:32:0:33:0:0.45455:0:27:2:0.0909:0:4 0/1:15:2:1,1:7,6:0.1333:2,2:37:0:32.5:1:1:1.1547:39:4:0.1333:0:3 -18 18519863 . A T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00411;SOR=0.07079;LSEQ=TGAGGACACACATCACAAAC;RSEQ=AGTTTCTGAGAATGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:4,4:0,1:0.6667:0,2:32.6:1:30.3:1:1:0:41.1:16:0.6667:0:4.6 0/1:18:2:1,1:2,4:0.1111:2,2:34:0:30.5:1:1:1.83:25:4:0.1111:0:5 -18 18519873 . G T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52273;SOR=Inf;LSEQ=CATCACAAACAAGTTTCTGA;RSEQ=AATGCTTCTGTCTAGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:27.8:1:32.3:1:1:0:37.2:24:1:0:5.1 0/1:21:2:1,1:9,10:0.0952:2,2:23.5:1:30.5:1:1:1.11:25:4:0.0952:0:6.5 -18 18519877 . G C 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04253;SOR=4.58878;LSEQ=ACAAACAAGTTTCTGAGAAT;RSEQ=CTTCTGTCTAGTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:4,5:0.3077:2,2:18.5:1:31.5:1:1:1.23:33.3:8:0.3077:0:7 1/0:22:15:9,6:2,5:0.6818:2,2:18.9:1:30.2:1:0.36146:3.52:40.2:30:0.6818:0:7.3 -18 18519883 . G C 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53333;SOR=Inf;LSEQ=AAGTTTCTGAGAATGCTTCT;RSEQ=TCTAGTTTTTGTGGGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:0:2,0:20.6:1:31.6:1:1:0:38.1:28:1:0:5.4 0/1:26:2:1,1:12,12:0.0769:2,2:19:0:28:0:1:1:47:4:0.0769:0:8 -18 18519887 . A C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00651;SOR=6.81268;LSEQ=TTCTGAGAATGCTTCTGTCT;RSEQ=GTTTTTGTGGGAAGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:4,5:0.3571:2,2:24.6:1:31.8:1:1:1.18452:35.4:10:0.3571:0:7 1/1:30:24:13,11:2,4:0.8:2,2:19.6:1:30.3:1:0.65134:2.30:39.5:48:0.8:0:7 -18 18519888 . G T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGAGAATGCTTCTGTCTA;RSEQ=TTTTTGTGGGAAGATATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:0:2,0:19.2:1:31.6:1:1:0:38.1:28:1:0:5.4 0/1:33:2:0,2:16,15:0.0606:2,0:20:1:30.5:1:0.48485:0:34.5:4:0.0606:0:4 -18 18519891 . T G 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00096;SOR=0.05448;LSEQ=GAGAATGCTTCTGTCTAGTT;RSEQ=TTGTGGGAAGATATTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:2,4:2,3:0.5455:2,2:19:1:31.8:1:1:1.29868:35.2:12:0.5455:0:5.2 0/1:36:2:1,1:16,18:0.0556:2,2:8.5:1:29.5:1:1:1.12:25:4:0.0556:0:5 -18 18519894 . G A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55967;SOR=1.67861;LSEQ=AATGCTTCTGTCTAGTTTTT;RSEQ=TGGGAAGATATTTCCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:4,6:0,0:0.9091:0,2:22.6:1:28.6:1:1:0:34.9:9:0.9:0:6.5 1/1:36:34:16,18:0,0:0.9444:0,2:20.5:1:28.7:1:1:0:38.9:68:0.9444:0:6.7 -18 18519904 . A T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTAGTTTTTGTGGGAAGAT;RSEQ=TTTCCTTTTTCACTGTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:19.3:1:29.9:1:1:0:35.1:26:1:0:6.4 0/1:35:2:1,1:15,18:0.0571:2,2:35:1:30:1:1:1.19:43:4:0.0571:0:7.5 -18 18519908 . C A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25207;SOR=2.71418;LSEQ=GTTTTTGTGGGAAGATATTT;RSEQ=CTTTTTCACTGTAGGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:3,6:2,3:0.6429:2,2:24.7:1:30.1:1:1:1.30579:37.4:18:0.6429:0:6.9 1/1:36:30:13,17:3,3:0.8333:2,2:29:1:28.6:1:1:1.29788:41.2:29:0.8286:0:7 -18 18519914 . T C 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39805;SOR=0.50252;LSEQ=GTGGGAAGATATTTCCTTTT;RSEQ=CACTGTAGGCATCAAAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:4,6:0.2143:2,2:17.7:1:33:0:1:1.30472:40:6:0.2143:0:7.7 0/1:42:5:2,3:15,22:0.119:2,2:37.8:1:31.6:1:1:1.02218:42.6:10:0.122:0:7.2 -18 18519918 . T C 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATATTTCCTTTTTCAC;RSEQ=GTAGGCATCAAAGCGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:6,8:0,0:1:0,2:20.9:1:30.4:1:1:0:41.2:28:1:0:5.8 1/1:47:45:18,27:0,0:0.9574:0,2:25.9:1:29.6:1:1:0:39.4:90:0.9574:0:6.6 -18 18519948 . A T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGCGCTCCAAATGTCCAC;RSEQ=TTCAGATACTACAAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:22.4:1:30.7:1:1:0:40.8:15:1:0:6 0/1:46:2:1,1:15,29:0.0435:2,2:27:1:30:1:1:1.90:37:4:0.0435:0:7 -18 18519950 . T C 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0678;SOR=Inf;LSEQ=AGCGCTCCAAATGTCCACAT;RSEQ=CAGATACTACAAAAAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:6,8:1,1:0.875:2,2:20:1:30.6:1:1:1.30929:38:13:0.8667:0:6.3 1/1:44:44:14,30:0,0:1:0,2:28.9:1:31.2:1:1:0:39.3:43:1:0:6.6 -18 18519956 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CCAAATGTCCACATTCAGAT;RSEQ=CTACAAAAAGAGTGTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,9:0:2,0:20.2:1:30.2:1:1:0:40.8:30:1:0:5.9 0/1:43:2:1,1:13,28:0.0465:2,2:32.5:1:29:1:1:2.11:37:4:0.0465:0:7 -18 18519959 . A C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=1.08913;LSEQ=AATGTCCACATTCAGATACT;RSEQ=CAAAAAGAGTGTTTCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:3,8:2,1:0.7857:2,2:17.5:1:31.9:1:0.50549:4.64888:42.9:22:0.7857:0:5.9 1/1:40:32:10,22:3,3:0.8:2,2:25.5:1:31.5:1:0.3924:2.15129:38.1:64:0.8:0:6.5 -18 18519961 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTCCACATTCAGATACTAC;RSEQ=AAAAGAGTGTTTCAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:20:1:31.8:1:1:0:42.1:26:1:0:6.1 0/1:38:2:1,1:12,24:0.0526:2,2:32.5:1:30:1:1:1.96:37:4:0.0526:0:7 -18 18519962 . A G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.31423;SOR=0;LSEQ=GTCCACATTCAGATACTACA;RSEQ=AAAGAGTGTTTCAAACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:5,7:0,0:1:0,2:21.1:1:32.5:1:1:0:42.3:24:1:0:6.3 1/1:37:31:10,21:1,1:0.8378:2,2:27.5:1:31.5:1:1:2.04944:39.4:62:0.8378:0:6.9 -18 18519965 . A C 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11462;SOR=0.12212;LSEQ=CACATTCAGATACTACAAAA;RSEQ=GAGTGTTTCAAACCTGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:14.5:1:30:1:1:1.58:40:4:0.2:0:7.5 0/1:36:1:0,1:13,22:0.0278:2,0:41:0:32:0:1:0:24:2:0.0278:0:8 -18 18519967 . A T 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04348;SOR=0;LSEQ=CATTCAGATACTACAAAAAG;RSEQ=GTGTTTCAAACCTGCTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:2,6:0.2:2,0:31.5:1:30.5:1:0.13333:0:34.5:4:0.2:0:7 0/0:36:0:0,0:13,23:0:2,0:24.3:1:30.6:1:1:0:38.8:72:1:0:6.6 -18 18519970 . G A 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.1222;LSEQ=TCAGATACTACAAAAAGAGT;RSEQ=TTTCAAACCTGCTCGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:4,5:0.1:2,0:47:0:33:0:1:0:31:2:0.1:0:7 0/1:36:4:2,2:11,21:0.1111:2,2:21.5:1:29:1:0.60915:1.87:48:8:0.1111:0:6.8 -18 18519979 . C G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAAAAAGAGTGTTTCAAAC;RSEQ=TGCTCGATGAAAGGGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:27.3:1:31.8:1:1:0:43.3:12:0.8571:0:6.2 0/1:30:2:1,1:7,20:0.0667:2,2:26:1:29:1:0.48276:2.74:37:4:0.0667:0:7 -18 18519985 . G T 113 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54644;SOR=0;LSEQ=AGAGTGTTTCAAACCTGCTC;RSEQ=ATGAAAGGGAATGTTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:23.3:1:29.7:1:1:0:43.3:12:1:0:6.2 1/1:18:15:1,14:1,1:0.8333:2,1:21.4:1:29.1:1:0.22794:10.24702:37.5:30:0.8333:0:7.5 -18 18519994 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAACCTGCTCGATGAAAGG;RSEQ=AATGTTCAACTCTGTGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:35:1:30.3:1:1:0:33.3:6:1:0:7 0/1:13:2:1,1:0,11:0.1538:0,2:23:1:28:1:0.15385:0:49:4:0.1538:0:7.5 -18 18519998 . G C 105 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0625;SOR=Inf;LSEQ=CCTGCTCGATGAAAGGGAAT;RSEQ=TTCAACTCTGTGACTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:31:1:30.7:1:1:0:33.3:6:1:0:7 1/0:13:9:0,9:0,2:0.6923:0,0:14.4:1:33.2:1:1:0:36:18:0.6923:0:7.4 -18 18520008 . G A 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13122;SOR=7.0072;LSEQ=GAAAGGGAATGTTCAACTCT;RSEQ=TGACTTGAATGCAGACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:4,0:0.2:0,0:16:0:33:0:0.2:0:31:2:0.2:0:7 1/0:12:8:0,8:2,2:0.6667:2,0:7.1:1:30.6:1:0.09091:0:35.5:16:0.6667:0:7.6 -18 18520013 . T G 57 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11888;SOR=0.12696;LSEQ=GGAATGTTCAACTCTGTGAC;RSEQ=TGAATGCAGACATCACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:0,1:0.8:0,0:16.3:1:28.5:1:0.2:0:44.5:8:0.8:0:6 0/1:10:3:2,1:0,7:0.3:0,2:29.3:1:30:1:0.06667:0:46.7:6:0.3:0:7.7 -18 18520019 . G A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.87936;LSEQ=TTCAACTCTGTGACTTGAAT;RSEQ=CAGACATCACAAAGCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:3,1:0.2:2,0:21:0:30:0:1:0:60:2:0.2:0:5 0/1:6:2:1,1:2,2:0.3333:2,2:40.5:1:28.5:1:1:1:49:4:0.3333:0:7.5 -18 18520024 . C T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=CTCTGTGACTTGAATGCAGA;RSEQ=ATCACAAAGCAGTTTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:15:0:26:0:1:0:40:2:0.3333:0:6 1/0:6:3:3,0:1,2:0.5:2,0:9.3:1:30.7:1:0.4:0:50:6:0.5:0:7.3 -18 18520035 . A C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.87936;LSEQ=GAATGCAGACATCACAAAGC;RSEQ=GTTTCTGAGAATGTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:4,0:0.2:0,0:9:0:32:0:1:0:57:2:0.2:0:7 0/1:6:2:2,0:3,1:0.3333:2,0:11:1:32:0:1:0:37.5:4:0.3333:0:7.5 -18 18520051 . T A 77 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.45647;LSEQ=AAGCAGTTTCTGAGAATGTT;RSEQ=CTGTCTAGATTTTATATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:2,0:0.6667:0,2:15.3:1:30.5:1:1:0:39.3:8:0.6667:0:6.5 1/0:8:6:5,1:1,1:0.75:2,2:25.8:1:30:1:0.46429:3.87:40.5:12:0.75:0:7.2 -18 18520054 . G T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.60839;LSEQ=CAGTTTCTGAGAATGTTTCT;RSEQ=TCTAGATTTTATATGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:4,1:0.1667:2,0:45:0:32:0:1:0:60:2:0.1667:0:5 0/1:8:2:1,1:5,1:0.25:2,2:18:1:32:0:0.46429:3.87298:49:4:0.25:0:7.5 -18 18520060 . A G 96 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGAATGTTTCTGTCTAG;RSEQ=TTTTATATGAAGATACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:29.5:1:32.7:1:1:0:44.3:12:1:0:6 1/1:8:8:6,2:0,0:1:0,2:27.9:1:32:1:1:0:42.6:16:1:0:7.3 -18 18520063 . T G 41 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60784;SOR=0.43816;LSEQ=AGAATGTTTCTGTCTAGATT;RSEQ=TATATGAAGATACTCCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:4,1:0.375:2,2:32:1:26.3:1:1:1.8258:41.3:2:0.2857:0:6.3 0/1:10:2:2,0:4,4:0.2:2,0:41.5:1:33:1:0.46667:0:51:4:0.2:0:7 -18 18520065 . A C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11765;SOR=7.85771;LSEQ=AATGTTTCTGTCTAGATTTT;RSEQ=TATGAAGATACTCCCGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:3,1:3,1:0.5:2,2:29.3:1:31.8:1:1:1:39.3:8:0.5:0:6.5 1/1:10:9:6,3:0,1:0.9:0,2:25.9:1:32:1:0.4:0:38.7:18:0.9:0:6.6 -18 18520076 . CT TA 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=CTAGATTTTATATGAAGATA;RSEQ=CCCGTTTCCAATGAAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:17:0:31.3:1:1:2.64575:60:4:0.2222:0:5.5 0/0:11:0:0,0:7,4:0:2,0:27:1:32.3:1:1:0:40.4:22:1:0:6.5 -18 18520079 . C G 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21739;SOR=0;LSEQ=GATTTTATATGAAGATACTC;RSEQ=CGTTTCCAATGAAATCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:0.1818:2,2:19:0:32.5:1:0.49091:3.05504:60:4:0.2:0:5.5 0/0:12:0:0,0:7,5:0:2,0:25.7:1:30.4:1:1:0:39:24:1:0:6.3 -18 18520089 . T C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14861;SOR=7.5535;LSEQ=GAAGATACTCCCGTTTCCAA;RSEQ=GAAATCCACAAAGCTATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:5,1:1,1:0.5455:2,2:31.7:1:31.8:1:0.46429:3.87:44:12:0.5455:0:5.8 1/1:11:10:6,4:1,0:0.9091:0,2:30:1:30.6:1:1:0:35.9:20:0.9091:0:6.3 -18 18520103 . CT GC 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48276;SOR=0;LSEQ=TTCCAATGAAATCCACAAAG;RSEQ=ATCCAAATATCCACTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:0.1333:2,2:29.5:1:32.8:1:1:1.1547:60:4:0.1333:0:4.5 0/0:15:0:0,0:10,5:0:2,0:22.8:1:30.3:1:1:0:43.5:30:1:0:6.1 -18 18520104 . T C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.38985;SOR=2.88932;LSEQ=TCCAATGAAATCCACAAAGC;RSEQ=ATCCAAATATCCACTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:6,4:1,2:0.6667:2,2:22.1:1:30.3:1:0.55944:2.75:49.1:9:0.75:0:5.4 1/1:14:12:7,5:2,0:0.8571:0,2:27.9:1:29.1:1:0.50549:0:41.4:24:0.8571:0:5.8 -18 18520106 . T C 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.51173;LSEQ=CAATGAAATCCACAAAGCTA;RSEQ=CCAAATATCCACTTGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:0.1333:2,2:14.5:1:32:1:1:1.1547:54:4:0.1333:0:4.5 0/1:14:1:0,1:9,4:0.0714:2,0:29:0:29:0:0.35714:0:24:2:0.0714:0:5 -18 18520111 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48589;SOR=Inf;LSEQ=AAATCCACAAAGCTATCCAA;RSEQ=TATCCACTTGCAGATTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:23.7:1:30.5:1:1:0:51.1:30:1:0:5.1 0/1:17:2:1,1:9,6:0.1176:2,2:24.5:1:30:1:1:1.46382:27:4:0.1176:0:7.5 -18 18520115 . C G 34 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49198;SOR=Inf;LSEQ=CCACAAAGCTATCCAAATAT;RSEQ=CACTTGCAGATTCTACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:23.9:1:31.2:1:1:0:51.1:30:1:0:5.1 0/1:19:2:1,1:10,7:0.1053:2,2:7:0:34:0:1:1.40151:50.5:4:0.1053:0:5.5 -18 18520118 . C A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50925;SOR=Inf;LSEQ=CAAAGCTATCCAAATATCCA;RSEQ=TTGCAGATTCTACAGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:24.1:1:31.7:1:1:0:51.1:30:1:0:5.1 0/1:23:2:2,0:10,11:0.087:2,0:19:1:32:0:0.47826:0:57:4:0.087:0:6.5 -18 18520122 . C T 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55014;SOR=0.30545;LSEQ=GCTATCCAAATATCCACTTG;RSEQ=AGATTCTACAGAAAGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:0.1333:2,2:11.5:1:28.5:1:1:1.1547:60:4:0.1429:0:4.5 0/1:23:1:1,0:10,10:0.0435:2,0:1:0:31:0:1:0:60:2:0.0435:0:7 -18 18520133 . G A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5254;SOR=0;LSEQ=ATCCACTTGCAGATTCTACA;RSEQ=AAAGCGTGTTTCCAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:6,7:0,0:1:0,2:26.4:1:29.9:1:1:0:51.7:26:1:0:4.9 1/1:23:21:11,10:0,0:0.913:0,2:20.9:1:30.1:1:1:0:47.7:42:0.913:0:5.4 -18 18520137 . G T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67798;SOR=1.4831;LSEQ=ACTTGCAGATTCTACAGAAA;RSEQ=CGTGTTTCCAAACTGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:4,6:1,2:0.7692:2,2:22.8:1:29.4:1:1:1.30:51.4:20:0.7692:0:5.4 1/1:24:20:9,11:3,1:0.8333:2,2:22.8:1:28.7:1:0.59006:3.4803:47.3:19:0.8261:0:5 -18 18520143 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5122;SOR=Inf;LSEQ=AGATTCTACAGAAAGCGTGT;RSEQ=TCCAAACTGCTCTGTCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:0:2,0:21.8:1:30.1:1:1:0:53:32:1:0:4.9 0/1:25:2:2,0:11,12:0.08:2,0:13.5:1:31:1:0.48:0:44.5:4:0.08:0:6.5 -18 18520147 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.5122;SOR=Inf;LSEQ=TCTACAGAAAGCGTGTTTCC;RSEQ=AACTGCTCTGTCAAACGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:0:2,0:21.8:1:30:1:1:0:53:32:1:0:4.9 0/1:25:2:1,1:12,11:0.08:2,2:21.5:1:32:1:1:1.0871:50.5:4:0.08:0:5.5 -18 18520161 . A C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54177;SOR=Inf;LSEQ=GTTTCCAAACTGCTCTGTCA;RSEQ=ACGAAATGTTCAACTCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:3,10:0:2,0:24.8:1:29.8:1:1:0:53.8:26:1:0:5.1 0/1:30:3:3,0:12,15:0.1:2,0:37.3:1:31.3:1:0.22414:0:58:6:0.1:0:6.7 -18 18520163 . C G 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54357;SOR=Inf;LSEQ=TTCCAAACTGCTCTGTCAAA;RSEQ=GAAATGTTCAACTCCGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:3,9:0:2,0:24.8:1:30.5:1:1:0:53.3:24:0.9231:0:5.2 0/1:31:3:3,0:11,14:0.0968:2,0:36.7:1:32.3:1:0.22222:0:58:6:0.0968:0:6.7 -18 18520164 . G C 48 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02245;SOR=0;LSEQ=TCCAAACTGCTCTGTCAAAC;RSEQ=AAATGTTCAACTCCGTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:3,8:0.2143:2,2:30.7:1:30.7:1:1:1.31:49.3:6:0.2143:0:5.7 0/0:33:0:0,0:19,14:0:2,0:22.3:1:30.5:1:1:0:51.8:32:1:0:5.2 -18 18520170 . T G 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08245;SOR=0;LSEQ=CTGCTCTGTCAAACGAAATG;RSEQ=TCAACTCCGTTAGTTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:0.1538:2,2:14.5:1:30.5:1:1:2.45:43.5:4:0.1538:0:7 0/0:31:0:0,0:17,14:0:2,0:25.1:1:30.1:1:1:0:51.2:62:1:0:5.3 -18 18520174 . A C 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.07879;SOR=0;LSEQ=TCTGTCAAACGAAATGTTCA;RSEQ=CTCCGTTAGTTGAGGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:0.1538:2,2:14.5:1:30.5:1:1:2.45:43.5:4:0.1538:0:7 0/0:32:0:0,0:17,15:0:2,0:25.1:1:30.2:1:1:0:50.8:64:1:0:5.3 -18 18520177 . CC GT 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65689;SOR=2.32013;LSEQ=GTCAAACGAAATGTTCAACT;RSEQ=GTTAGTTGAGGACACACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:2,9:0.0833:2,0:15:0:32.5:0:0.25:0:40:2:0.0833:0:5 0/1:34:6:3,3:14,14:0.1765:2,2:11:1:31:1:1:1:41.3:12:0.1818:0.0588:5.8 -18 18520178 . C T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05493;SOR=0.24103;LSEQ=TCAAACGAAATGTTCAACTC;RSEQ=GTTAGTTGAGGACACACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:2,8:0,2:0.7692:0,2:27.5:1:29.4:1:1:0:49.7:20:0.8333:0:5.6 0/1:32:14:7,7:7,7:0.4375:2,2:31.9:1:30.2:1:1:1:47:28:0.5:0:6 -18 18520181 . T G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06519;LSEQ=AACGAAATGTTCAACTCCGT;RSEQ=AGTTGAGGACACACATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:1,8:2,2:0.6923:2,2:36:1:31.6:1:0.2028:6.5151:53.8:18:0.6923:0:5.4 1/0:34:24:11,13:6,4:0.7059:2,2:28.1:1:30.7:1:0.70799:1.74291:52.7:11:0.6875:0:4.9 -18 18520182 . A G 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56386;SOR=Inf;LSEQ=ACGAAATGTTCAACTCCGTT;RSEQ=GTTGAGGACACACATCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:3,10:0:2,0:27.8:1:30.7:1:1:0:48.6:26:1:0:5.2 0/1:34:4:3,1:14,16:0.1176:2,2:22.8:1:31.8:1:0.60117:3.31:53.5:8:0.1176:0:6.8 -18 18520200 . G C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29381;SOR=2.1062;LSEQ=TTAGTTGAGGACACACATCA;RSEQ=AAACAAGTTTCTGCGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:3,6:2,3:0.6429:2,2:26.7:1:32.9:1:1:1.30579:52.1:18:0.6429:0:6 1/0:34:27:13,14:3,4:0.7941:2,2:24:1:31.5:1:1:1.23:50.7:54:0.7941:0:5.5 -18 18520203 . A T 75 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16698;SOR=Inf;LSEQ=GTTGAGGACACACATCAGAA;RSEQ=CAAGTTTCTGCGAATGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:24.6:1:30.6:1:1:0:45.1:28:1:0:6 0/1:36:6:3,3:14,16:0.1667:2,2:27.8:1:29.2:1:1:1.14:60:12:0.1667:0:4.8 -18 18520205 . A T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27768;SOR=0.44255;LSEQ=TGAGGACACACATCAGAAAC;RSEQ=AGTTTCTGCGAATGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:3,6:0.3571:2,2:24.8:1:29:1:1:1.31:32.6:10:0.3571:0:6 0/1:36:7:3,4:14,15:0.1944:2,2:34.4:1:29.6:1:1:1.23694:41.1:14:0.2:0:6 -18 18520214 . C A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48111;SOR=0.55688;LSEQ=ACATCAGAAACAAGTTTCTG;RSEQ=GAATGCTTCTGTGTAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:4,7:0.3125:2,2:31.4:1:31.4:1:1:1.16:32.6:10:0.3125:0:6 0/1:35:7:3,4:14,13:0.2:2,2:39.3:1:30.4:1:1:1.42069:41.1:14:0.2:0:6 -18 18520227 . G C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTCTGCGAATGCTTCTGT;RSEQ=TAGTTTTTATGGGAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:7,8:0,0:1:0,2:21.1:1:33.1:1:1:0:46.3:30:1:0:6.2 1/1:29:28:13,15:0,0:0.9655:0,2:25.2:1:31.7:1:1:0:50.5:56:0.9655:0:5.8 -18 18520233 . T G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2847;SOR=0.45506;LSEQ=GCGAATGCTTCTGTGTAGTT;RSEQ=TTATGGGAAGATATTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:2,3:4,2:0.4167:2,2:31:1:33.6:1:0.5671:2.69977:32.6:10:0.4167:0:6 0/1:29:7:3,4:10,12:0.2414:2,2:32.9:1:31.3:1:1:1.10709:41.1:14:0.2414:0:6 -18 18520234 . TT GC 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.71992;SOR=0.70713;LSEQ=CGAATGCTTCTGTGTAGTTT;RSEQ=ATGGGAAGATATTTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:4,1:2,5:0.4167:2,2:30:1:33.6:1:0.24242:7.96:51.2:10:0.4167:0:6.2 0/1:24:8:4,4:7,9:0.3333:2,2:29.4:1:32.6:1:1:1.27:49.9:16:0.3333:0:5.9 -18 18520241 . A G 70 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14287;SOR=Inf;LSEQ=TTCTGTGTAGTTTTTATGGG;RSEQ=AGATATTTCCTTTTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:17.4:1:31.4:1:1:0:43.1:40:1:0:5.4 0/1:31:5:1,4:13,13:0.1613:2,2:29:1:30.4:1:0.34446:3.84037:55.4:10:0.1613:0:4.8 -18 18520246 . A G 93 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00652;SOR=0.07685;LSEQ=TGTAGTTTTTATGGGAAGAT;RSEQ=TTTCCTTTTCCACCATAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:5,2:7,10:0.2917:2,2:6.7:1:33.3:1:0.37071:3.38:51.6:14:0.2917:0:3.7 0/1:34:1:0,1:14,19:0.0294:2,0:7:0:25:0:1:0:22:2:0.0294:0:4 -18 18520254 . T G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56873;SOR=0.65322;LSEQ=TTATGGGAAGATATTTCCTT;RSEQ=TCCACCATAGGCCTGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:5,4:7,7:0.3913:2,2:28.1:1:31.8:1:1:1.24:42.8:18:0.3913:0:6.1 0/1:34:10:5,5:9,15:0.2941:2,2:26.9:1:31.7:1:0.70412:1.64:42.9:20:0.2941:0:6.2 -18 18520255 . TC CT 46 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.03913;LSEQ=TATGGGAAGATATTTCCTTT;RSEQ=CACCATAGGCCTGAAAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:12,10:0.0435:2,0:17:0:32.5:0:0.47826:0:60:2:0.0435:0:7 0/1:35:3:1,2:13,19:0.0857:2,2:13.3:1:29.5:1:1:1.35659:58.7:6:0.0857:0:7 -18 18520256 . C T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91901;LSEQ=ATGGGAAGATATTTCCTTTT;RSEQ=CACCATAGGCCTGAAAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:17:11,6:1,3:0.7391:2,2:22.2:1:30.5:1:0.27218:5.05:47.5:34:0.7727:0:4.8 1/0:36:26:10,16:3,4:0.7222:2,2:22.8:1:28.2:1:1:1.1933:45:25:0.7813:0:4.8 -18 18520259 . C A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3926;SOR=0.47075;LSEQ=GGAAGATATTTCCTTTTCCA;RSEQ=CATAGGCCTGAAAGCGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:11,9:0.1304:2,0:21.7:1:30.7:1:0.21739:0:40.7:6:0.1304:0:7 0/1:46:3:0,3:17,24:0.0652:2,0:19.3:1:31:1:0.2722:0:46.3:6:0.0667:0:6.3 -18 18520261 . A G 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97899;LSEQ=AAGATATTTCCTTTTCCACC;RSEQ=TAGGCCTGAAAGCGCTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:0,2:11,10:0.08:2,0:29.5:1:34:0:0.47826:0:37.5:4:0.08:0:8 0/1:51:4:1,3:18,23:0.0784:2,2:13.3:1:31.8:1:0.627:2.30735:47.8:8:0.0816:0:5.3 -18 18520263 . A G 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32308;SOR=0.5277;LSEQ=GATATTTCCTTTTCCACCAT;RSEQ=GGCCTGAAAGCGCTCGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:2,3:10,13:0.1724:2,2:24.6:1:31.4:1:1:1.14801:52.2:10:0.1786:0:5.6 0/1:61:6:1,5:23,31:0.0984:2,2:29.3:1:30.3:1:0.3866:3.642:54.5:12:0.1017:0:5 -18 18520269 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCTTTTCCACCATAGGCCT;RSEQ=AAAGCGCTCGAAATGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:15,18:0:2,0:20.8:1:31.8:1:1:0:48.7:66:1:0:4.4 0/1:70:2:1,1:28,40:0.0286:2,2:8.5:1:30.5:1:1:1.42:42:4:0.0294:0:5.5 -18 18520271 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTCCACCATAGGCCTGA;RSEQ=AGCGCTCGAAATGTCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:15,18:0:2,0:22:1:30.5:1:1:0:48.7:66:1:0:4.4 0/1:70:2:1,1:28,40:0.0286:2,2:19.5:1:30.5:1:1:1.42:60:4:0.029:0:5.5 -18 18520274 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10692;SOR=0;LSEQ=TTCCACCATAGGCCTGAAAG;RSEQ=GCTCGAAATGTCCACTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:14,19:0.0571:2,2:9.5:1:30.5:1:1:1.35:60:4:0.0571:0:2.5 0/0:71:0:0,0:30,41:0:2,0:18.8:1:30.5:1:1:0:49.7:70:1:0:4 -18 18520275 . G A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCCACCATAGGCCTGAAAGC;RSEQ=CTCGAAATGTCCACTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:15,20:0:2,0:23.1:1:31.3:1:1:0:48:70:1:0:4.3 0/1:71:2:1,1:30,37:0.0282:2,2:17:0:29.5:1:1:1.23:60:4:0.029:0:5 -18 18520276 . C A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10692;SOR=0;LSEQ=CCACCATAGGCCTGAAAGCG;RSEQ=TCGAAATGTCCACTTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:0,2:15,18:0.0571:2,0:14.5:1:32.5:1:0.4958:0:37.5:4:0.0571:0:8 0/0:71:0:0,0:31,39:0:2,0:20.2:1:31.6:1:1:0:49.9:34:1:0:3.9 -18 18520278 . C T 139 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00074;SOR=9.08931;LSEQ=ACCATAGGCCTGAAAGCGCT;RSEQ=GAAATGTCCACTTCCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:14,20:0.0556:2,2:17:0:32:0:1:1.41:52.5:4:0.0556:0:5 0/1:71:25:12,13:19,27:0.3521:2,2:18.5:1:30.1:1:0.62375:1.31:52.6:24:0.3478:0:3 -18 18520279 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11109;SOR=0;LSEQ=CCATAGGCCTGAAAGCGCTC;RSEQ=AAATGTCCACTTCCAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:15,19:0.0556:2,0:11.5:1:31.5:1:0.5:0:37.5:4:0.0556:0:8 0/0:71:0:0,0:31,39:0:2,0:22.2:1:30.4:1:1:0:49.9:34:0.9855:0:3.9 -18 18520284 . GT AC 75 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41849;SOR=3.25201;LSEQ=GGCCTGAAAGCGCTCGAAAT;RSEQ=CCACTTCCAGATACTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:0,1:15,20:0.0278:2,0:45:0:32.5:0:1:0:60:2:0.0278:0:6 0/1:70:6:1,5:28,33:0.0857:2,2:24.3:1:29.3:1:0.2235:4.16569:42.5:12:0.0896:0:4.3 -18 18520285 . T G 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29551;SOR=Inf;LSEQ=GCCTGAAAGCGCTCGAAATG;RSEQ=CCACTTCCAGATACTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,20:0:2,0:27:1:29.9:1:1:0:47.4:70:1:0:4.1 0/1:68:4:2,2:26,31:0.0588:2,2:43:1:31.5:1:1:1.19:35.8:8:0.0656:0:6 -18 18520288 . A T 32 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGAAAGCGCTCGAAATGTCC;RSEQ=CTTCCAGATACTACAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:0,1:15,19:0.0286:2,0:46:0:32:0:1:0:20:2:0.0286:0:6 0/1:70:2:1,1:30,38:0.0286:2,2:21:0:32:1:1:1.26:60:4:0.029:0:4.5 -18 18520298 . A C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CGAAATGTCCACTTCCAGAT;RSEQ=CTACAGAAAGAGTGTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,18:0:2,0:29.7:1:29.7:1:1:0:47.9:64:1:0:3.8 0/1:67:2:1,1:29,36:0.0299:2,2:36.5:1:31.5:1:1:1.24:60:4:0.0303:0:6 -18 18520299 . C G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00144;SOR=0.23273;LSEQ=GAAATGTCCACTTCCAGATA;RSEQ=TACAGAAAGAGTGTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:18:8,10:5,8:0.5625:2,2:31.1:1:32.3:1:1:1.27:49:36:0.5625:0:3.2 0/1:66:15:7,8:19,26:0.2273:2,2:24.5:1:31.7:1:0.77299:1.19:49:30:0.2273:0:2.3 -18 18520300 . T G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATGTCCACTTCCAGATAC;RSEQ=ACAGAAAGAGTGTTTCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:12,18:0:2,0:31.9:1:29.6:1:1:0:47.6:60:1:0:3.7 0/1:66:2:0,2:28,34:0.0303:2,0:36.5:1:29.5:1:0.5:0:49.5:4:0.0323:0:5.5 -18 18520301 . A G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.1855;SOR=0.41108;LSEQ=AATGTCCACTTCCAGATACT;RSEQ=CAGAAAGAGTGTTTCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:2,4:10,14:0.2:2,2:34:1:31.8:1:1:1.41207:40.3:12:0.2:0:5.2 0/1:65:6:3,3:24,33:0.0923:2,2:27.8:1:32.2:1:1:1.37:52.2:12:0.0938:0:4 -18 18520303 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTCCACTTCCAGATACTAC;RSEQ=GAAAGAGTGTTTCAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:12,18:0:2,0:30.1:1:31.1:1:1:0:47.6:60:1:0:3.7 0/1:65:2:1,1:27,36:0.0308:2,2:6:0:32:0:1:1.33:60:4:0.0317:0:4.5 -18 18520307 . A T 80 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17197;SOR=Inf;LSEQ=CACTTCCAGATACTACAGAA;RSEQ=GAGTGTTTCAAACCTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:12,18:0:2,0:27.1:1:31.1:1:1:0:47.6:60:1:0:3.7 0/1:65:6:3,3:25,34:0.0923:2,2:34.2:1:31.2:1:1:1.35:60:12:0.0938:0:5.2 -18 18520308 . G C 94 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2627;SOR=4.16897;LSEQ=ACTTCCAGATACTACAGAAA;RSEQ=AGTGTTTCAAACCTGCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:0,1:12,17:0.0333:2,0:22:0:34:0:1:0:60:2:0.0333:0:6 0/1:63:8:2,6:25,30:0.127:2,2:30.5:1:31.4:1:0.44835:2.46634:46.4:16:0.129:0:5 -18 18520311 . T G 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3576;SOR=0.56394;LSEQ=TCCAGATACTACAGAAAGAG;RSEQ=GTTTCAAACCTGCTCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:2,4:10,14:0.2:2,2:24.3:1:31.7:1:1:1.41207:40.3:12:0.2:0:5.2 0/1:57:7:3,4:21,29:0.1228:2,2:22.7:1:30.4:1:1:1.04:50.4:14:0.1228:0:4.1 -18 18520313 . T A 89 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15015;SOR=4.86606;LSEQ=CAGATACTACAGAAAGAGTG;RSEQ=TTCAAACCTGCTCTATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:0,1:12,17:0.0333:2,0:17:0:33:0:1:0:60:2:0.0333:0:6 0/1:55:8:2,6:20,26:0.1455:2,2:25.5:1:29.9:1:0.44913:2.27461:46.4:16:0.1509:0:5 -18 18520315 . T G 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00207;SOR=0.06026;LSEQ=GATACTACAGAAAGAGTGTT;RSEQ=CAAACCTGCTCTATGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:2,5:9,12:0.2414:2,2:21:1:33:1:0.66834:1.83476:49.1:14:0.2414:0:3.6 0/1:55:1:0,1:23,30:0.0182:2,0:18:0:34:0:1:0:22:2:0.0182:0:4 -18 18520316 . C G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.77257;SOR=0.81688;LSEQ=ATACTACAGAAAGAGTGTTT;RSEQ=AAACCTGCTCTATGAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:2,4:9,11:0.2143:2,2:19.3:1:32.7:1:1:1.6063:40.3:12:0.2222:0:5.2 0/1:55:10:5,5:18,27:0.1818:2,2:15.5:1:29.8:1:0.72565:1.49:45.6:9:0.1667:0:4.8 -18 18520319 . A C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.54146;SOR=Inf;LSEQ=CTACAGAAAGAGTGTTTCAA;RSEQ=CCTGCTCTATGAAAGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:17.4:1:30.5:1:1:0:48.1:54:1:0:3.6 0/1:51:2:1,1:20,29:0.0392:2,2:24:0:33:0:1:1.44:60:4:0.04:0:6 -18 18520321 . C G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53862;SOR=Inf;LSEQ=ACAGAAAGAGTGTTTCAAAC;RSEQ=TGCTCTATGAAAGGGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:15.4:1:32.4:1:1:0:48.1:54:1:0:3.6 0/1:50:2:1,1:19,29:0.04:2,2:10:0:32.5:1:1:1.51:42:4:0.04:0:4.5 -18 18520325 . T A 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70127;SOR=1.80129;LSEQ=AAAGAGTGTTTCAAACCTGC;RSEQ=CTATGAAAGGGAATGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:8,15:0.08:2,2:16.5:1:29.5:1:1:1.83:52.5:4:0.08:0:5 0/1:44:6:3,3:14,24:0.1364:2,2:10.7:1:27.3:1:0.66188:1.69:52.3:5:0.1282:0:3.5 -18 18520327 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12163;SOR=0;LSEQ=AGAGTGTTTCAAACCTGCTC;RSEQ=ATGAAAGGGAATGTTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:7,14:0.087:2,2:12:0:33.5:1:1:1.94:33:4:0.087:0:6 0/0:42:0:0,0:17,25:0:2,0:11.1:1:29:1:1:0:46.9:41:1:0:4.1 -18 18520328 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53558;SOR=Inf;LSEQ=GAGTGTTTCAAACCTGCTCT;RSEQ=TGAAAGGGAATGTTTTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:0:2,0:10.5:1:30.5:1:1:0:46:46:1:0:3.9 0/1:42:2:1,1:16,23:0.0476:2,2:13.5:1:30.5:1:1:1.42:49:4:0.05:0:4.5 -18 18520330 . G A 44 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.79254;LSEQ=GTGTTTCAAACCTGCTCTAT;RSEQ=AAAGGGAATGTTTTATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:7,13:0.0909:2,2:11.5:1:28.5:1:1:1.80:52.5:4:0.0909:0:5 0/1:41:3:2,1:12,20:0.0732:2,2:1:0:28.3:1:0.5508:3.22:46.3:6:0.0769:0:4 -18 18520333 . A C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00935;SOR=0.16756;LSEQ=TTTCAAACCTGCTCTATGAA;RSEQ=GGGAATGTTTTATATTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:4,6:3,6:0.5263:2,2:7.9:1:31.1:1:1:1.31:43.3:20:0.5263:0:3.4 0/1:33:5:3,2:10,18:0.1515:2,2:9.4:1:29.8:1:0.35996:2.62:47.4:10:0.1515:0:2.6 -18 18520334 . G A 59 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=1.10136;LSEQ=TTCAAACCTGCTCTATGAAA;RSEQ=GGAATGTTTTATATTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:7.5:1:30:1:1:1.62:52.5:4:0.1111:0:5 0/1:33:4:2,2:11,18:0.1212:2,2:4.3:1:29.8:1:1:1.61:50.8:8:0.1212:0:4 -18 18520335 . G T 78 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07119;SOR=Inf;LSEQ=TCAAACCTGCTCTATGAAAG;RSEQ=GAATGTTTTATATTTGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:6,11:0:2,0:5.4:1:31.9:1:1:0:43.5:34:1:0:4 0/1:29:6:3,3:9,14:0.2069:2,2:6.2:1:30.2:1:0.66932:1.53:60:12:0.2143:0:5.2 -18 18699289 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GGCTTCTTTCTTTTTCTGAT;RSEQ=ATTTTCTTTCACGCGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:15,3:0.0952:2,2:29:1:30.5:1:0.36842:4.47215:60:4:0.1:0:1 0/0:15:0:0,0:14,1:0:1,0:18.5:1:31.3:1:1:0:60:30:1:0:0 -18 18699370 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19779;SOR=0;LSEQ=ACGCACATTAATTCTCTTGG;RSEQ=AAGAATCTTGCCCTTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:67,14:0.0241:2,2:27:1:29:0:0.33059:4.65785:60:4:0.0247:0:1 0/0:103:0:0,0:83,19:0:2,0:23.8:1:31.6:1:1:0:59.8:204:0.9903:0:0 -18 18699380 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50302;SOR=Inf;LSEQ=ATTCTCTTGGCAAGAATCTT;RSEQ=CCCTTAACTTGTTTGTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:77,24:0:2,0:22.7:1:31.7:1:1:0:59.6:100:1:0:0.1 0/1:124:2:1,1:88,34:0.0161:2,2:17.5:1:26.5:1:0.48649:2.56545:60:4:0.0167:0:1 -18 18699671 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.50545;SOR=Inf;LSEQ=CCGGCCAAAAGGAAGGGAGT;RSEQ=TTTTGTTTGTTTGTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:51,78:0:2,0:22.1:1:29.6:1:1:0:60:128:1:0:0.1 0/1:164:2:1,1:70,92:0.0122:2,2:12.5:1:27:1:1:1.31:60:4:0.0123:0:1 -18 18699672 . TTTTG T 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.19435;SOR=3.21948;LSEQ=CGGCCAAAAGGAAGGGAGTT;RSEQ=TTTGTTTGTTTGTTTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:48,78:0.0156:2,2:14:1:23.8:1:1:1.62:60:4:0.0157:0.0078:0 0/1:164:8:3,5:66,89:0.0488:2,2:39.4:1:30.5:1:1:1.23438:60:16:0.0491:0:0 -18 19020856 . T C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.29479;SOR=0.54601;LSEQ=CAATTGTAAATATACTGGTT;RSEQ=TAAGACATAAATGAGTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:9:8,1:46,6:0.1475:2,2:20.7:1:31.2:1:1:1.04:60:18:0.15:0:1 0/1:93:8:7,1:73,12:0.086:2,2:24.6:1:32.3:1:1:1.15:60:16:0.0879:0:1 -18 19020950 . G A 196 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAATAATTATGCCAGTCT;RSEQ=TCACTATGGTTGCTTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:174,126:0:2,0:28.1:1:32.2:1:1:0:60:299:1:0:0.1 0/1:388:116:54,62:145,127:0.299:2,2:26.1:1:28.7:1:0.26726:1.30995:60:115:0.2987:0:1.1 -18 19021022 . C G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49948;SOR=Inf;LSEQ=TCACACTTTTCTATACCTTT;RSEQ=AAAATGTATGTAATGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:52,120:0:2,0:23.5:1:31.4:1:1:0:60:85:1:0:0.1 0/1:187:2:1,1:65,120:0.0107:2,2:21:1:33.5:1:1:1.84:60:4:0.0107:0:2 -18 19756974 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.25257;SOR=Inf;LSEQ=AACTGCGGCTCCATCCAGAC;RSEQ=CCGCTGTGGCGGCGGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:68,35:0:2,0:26.6:1:30:1:1:0:60:50.5:1:0:0.1 0/1:123:3:1,2:72,48:0.0244:2,2:23.3:1:27.7:1:0.56579:2.97302:60:6:0.025:0:1 -18 19757048 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24691;SOR=Inf;LSEQ=CTACAGCAAGATGAACGGCC;RSEQ=CAGCCGGCCCCTCATCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:43,79:0:2,0:24.8:1:30:1:1:0:60:60:1:0:0.1 0/1:121:2:1,1:47,72:0.0165:2,2:19:1:29:1:1:1.53:60:4:0.0165:0:1 -18 21337438 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26281;SOR=Inf;LSEQ=CCTCCCCAGTCCCCTCCCCA;RSEQ=CCCCCACCCTCACTGCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:126,52:0:2,0:21:1:28:1:1:0:60:3.944:1:0:0.8 0/1:237:3:2,1:156,76:0.0127:2,2:14.7:1:25.3:1:1:1.02622:60:2:0.0108:0:1.7 -18 21337563 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24068;SOR=Inf;LSEQ=CTTCTGTGGAGTGGTGGCGC;RSEQ=ATCTTAGGTGAGAGAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:36,112:0:2,0:21.1:1:30.3:1:1:0:60:73:1:0:0.1 0/1:144:2:1,1:31,111:0.0139:2,2:17.5:1:29:1:0.39627:3.54:60:4:0.014:0:1 -18 22265718 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=AGTGGGGCAGGGCAAGGAGT;RSEQ=GGGGGCGTGGACATTCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:29.4:1:32:1:1:0:60:14:1:0:0 1/0:4:2:1,1:2,0:0.5:0,2:38:1:30:0:1:0:60:4:0.5:0:1 -18 22265894 . C T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21288;SOR=Inf;LSEQ=CTCTTTAGCTGTAGCTCAAC;RSEQ=CTGTGGATAGGTGATGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:111,32:0:2,0:23.4:1:30.9:1:1:0:60:46.667:1:0:0.2 0/1:123:2:1,1:86,35:0.0163:2,2:6.5:1:23.5:1:0.5014:2.43684:60:4:0.0163:0:1.5 -18 22265897 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=90.53229;LSEQ=TTTAGCTGTAGCTCAACCCT;RSEQ=TGGATAGGTGATGGGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:9:8,1:108,32:0.0604:2,2:30.4:1:27:1:0.68425:2.36:60:8:0.0544:0:1.1 1/1:140:120:87,33:11,7:0.8571:2,2:19.9:1:27.9:1:0.40344:1.67:60:39:0.8603:0:1.1 -18 22266007 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TGATGGGCATGTTGGAACAT;RSEQ=GTGGTGAATATCAGGATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:55,114:0.0117:2,2:31.5:1:29.5:1:0.54902:2.06:60:4:0.0118:0:1 0/0:153:0:0,0:49,103:0:2,0:21.8:1:30.6:1:1:0:60:151:0.9934:0:0.1 -18 22266010 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23046;SOR=Inf;LSEQ=TGGGCATGTTGGAACATGGT;RSEQ=GTGAATATCAGGATACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:51,112:0:2,0:24.2:1:31.5:1:1:0:60:326:1:0:0.1 0/1:151:2:1,1:46,103:0.0132:2,2:11.5:1:28.5:1:0.52706:2.23:60:4:0.0132:0:1 -18 22266046 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49796;SOR=Inf;LSEQ=CCACTTTGCACAGGTATTTT;RSEQ=AAATGATGCAGGACTCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:38,85:0:2,0:26.8:1:32:1:1:0:60:122:1:0:0.1 0/1:123:2:1,1:48,73:0.0163:2,2:31.5:1:28.5:1:1:1.52:60:4:0.0163:0:1 -18 22266143 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49209;SOR=Inf;LSEQ=TCATATTCTGTCATCCAGTT;RSEQ=TATCCCTTGAGCCCAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:2,27:0:2,0:27.7:1:32.1:1:1:0:60:58:1:0:0 0/1:31:2:0,2:4,25:0.0645:2,0:14.5:1:31:1:1:0:60:4:0.0667:0:1 -18 23784839 . A G 108 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00205;SOR=0.04814;LSEQ=CACGCCTCCACCCCATGGGA;RSEQ=ATTCGATGGACATGGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:8,2:5,1:0.625:2,2:22.4:1:32.8:1:1:1.23302:60:20:0.625:0:1 0/1:15:1:1,0:9,5:0.0667:2,0:15:0:33:0:1:0:60:2:0.0667:0:1 -18 23785015 . C A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14223;SOR=0.46378;LSEQ=TTGAATTGCACATTGTTGAA;RSEQ=CTGAGGCAATGAATTTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:12:3,9:22,27:0.1967:2,2:26.6:1:29.6:1:0.32766:2.41091:60:24:0.2:0:1.1 0/1:69:7:3,4:24,38:0.1014:2,2:18.1:1:29.4:1:1:1.18:60:14:0.1014:0:1.3 -18 23785060 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49327;SOR=Inf;LSEQ=ATCCCATTAAAGTAACACCG;RSEQ=CAACTTGAAGTGTATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:0:2,0:27.3:1:30.8:1:1:0:60:14.5:1:0:0.5 0/1:34:2:1,1:7,25:0.0588:2,2:8.5:1:27:1:0.42068:3.41:60:4:0.0606:0:1 -18 23785095 . C T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16651;SOR=0.43082;LSEQ=TATACAGCCAACGGCTTCCC;RSEQ=TGGGAGCTTTGAAATAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:12:6,6:10,6:0.4286:2,2:26.4:1:29.3:1:0.70217:1.63612:60:11:0.4074:0:1.4 0/1:29:7:3,4:9,13:0.2414:2,2:10.7:1:29.6:1:1:1.08:60:14:0.2414:0:1.1 -18 23785115 . C G 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.64567;SOR=0.50652;LSEQ=CTGGGAGCTTTGAAATAACA;RSEQ=CCCTCCATGGTCTTACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:9,12:0.125:2,0:34.7:1:33.7:1:0.21739:0:60:6:0.125:0:2 0/1:30:2:1,1:15,13:0.0667:2,2:22.5:1:34:0:1:1.14834:60:4:0.0667:0:1.5 -18 23785309 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53662;SOR=Inf;LSEQ=TCAGAAGATGAAGAAGAGGA;RSEQ=GATGTGAAACTCTTAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:30,41:0:2,0:20:1:31.4:1:1:0:60:142:1:0:0 0/1:126:2:1,1:46,78:0.0159:2,2:11.5:1:27:1:1:1.69:56.5:4:0.0159:0:1 -18 23785313 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54618;SOR=Inf;LSEQ=AAGATGAAGAAGAGGAGGAT;RSEQ=TGAAACTCTTAAGTATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:25,39:0:2,0:20.3:1:32.2:1:1:0:60:128:1:0:0 0/1:122:2:1,1:45,75:0.0164:2,2:25:1:27.5:1:1:1.66:60:4:0.0167:0:1 -18 23785328 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54298;SOR=Inf;LSEQ=AGGATGTGAAACTCTTAAGT;RSEQ=TATCTGGAAAGCAATCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:13,29:0:2,0:23.8:1:30.1:1:1:0:60:84:1:0:0 0/1:79:2:0,2:28,49:0.0253:2,0:15:1:32.5:1:0.53651:0:60:4:0.0253:0:1 -18 23785648 . A G 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04915;SOR=0.1623;LSEQ=AAAGACTCAAAACCATCAAC;RSEQ=CCAAGATAAAAAAGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:3,4:4,4:0.4667:2,2:7:1:30.9:1:1:1.30792:60:14:0.4667:0:1.3 0/1:17:2:1,1:10,5:0.1176:2,2:25.5:1:31.5:1:1:1.91491:60:4:0.1176:0:1.5 -18 23785705 . CA C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5298;SOR=Inf;LSEQ=GAAAAAAACTCCTAAAACAC;RSEQ=AAAGACCTAGTTCTGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:27.2:1:30.3:1:1:0:60:36:1:0:0.5 0/1:32:2:1,1:20,10:0.0625:2,2:24:1:29.3:1:1:1.95408:60:4:0.0645:0.0313:0 -18 23785855 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49024;SOR=Inf;LSEQ=CTATTCAAGATCTCTGGCAG;RSEQ=GGAGGAAGCCTCTTGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:24.2:1:31:1:1:0:60:38:1:0:0.5 0/1:22:2:1,1:5,15:0.0909:2,2:29:1:28:1:0.48052:2.83:60:4:0.0909:0:1 -18 23812488 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCCTGAAGGCGAGTAATAG;RSEQ=AAGATGGCTGTCACAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:9,2:0:2,0:23.3:1:31.6:1:1:0:60:22:1:0:0.3 0/1:28:2:1,1:18,8:0.0714:2,2:25:0:31:1:1:2.17949:31:4:0.0714:0:2 -18 23812504 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAGCAAGATGGCTGTCACA;RSEQ=GACCTAGAAAGGGGAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:22.1:1:32.3:1:1:0:60:32:1:0:0.4 0/1:37:2:1,1:23,12:0.0541:2,2:24:0:31.5:1:1:1.88115:31:4:0.0541:0:2 -18 23812510 . A T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15583;SOR=0.34036;LSEQ=AGATGGCTGTCACAGGACCT;RSEQ=GAAAGGGGAGAAGCCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:4,2:7,5:0.3333:2,2:22.3:1:30.2:1:1:1.40:60:12:0.3333:0:1.2 0/1:42:6:4,2:21,15:0.1429:2,2:21.3:1:30.3:1:1:1.42:56.2:12:0.1429:0:1.2 -18 24173336 . G A 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GAGGAGGAAGAGGAGGAGGA;RSEQ=GAAGAGGAGGAGGAAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:15:1:31.7:1:1:0:52.7:6:0.75:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 24173846 . TAAG T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAAGGAGGAAGAGGAAGA;RSEQ=GAGGAGGAGGAGGAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,7:0:2,0:24.5:1:29.1:1:1:0:60:40:0.9524:0:0.2 1/0:36:23:13,10:7,4:0.6389:2,2:21.3:1:31.4:1:1:1.33452:60:46:0.6571:0.1944:0.2 -18 24173847 . AAGG A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.1908;SOR=0;LSEQ=ACAAGGAGGAAGAGGAAGAT;RSEQ=AGGAGGAGGAGGAAGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:13,8:0.087:2,0:6.5:1:30.5:1:0.52569:0:60:4:0.087:0.0435:0 0/0:29:0:0,0:7,4:0:2,0:22.3:1:30:1:1:0:60:22:1:0:0.1 -18 26620725 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49799;SOR=Inf;LSEQ=TTAATACATTTATGTAAGAA;RSEQ=AGCTTCATAAACACCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:96,23:0:2,0:21.5:1:31.7:1:1:0:60:28.75:1:0:0.6 0/1:122:2:1,1:95,25:0.0164:2,2:29:0:31:1:0.3822:3.74587:60:4:0.0165:0:1.5 -18 26620796 . A G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2058;LSEQ=TCTCAGCTCCTATGCATTCT;RSEQ=TGATAATGGACATTAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:281:213:130,83:36,32:0.758:2,2:24.5:1:31.5:1:0.25878:1.39:60:70:0.7581:0:1.9 0/1:368:144:85,59:116,108:0.3913:2,2:26.7:1:31:1:0.19818:1.34:60:47:0.3895:0:2 -18 26620819 . A G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0.25211;LSEQ=ATAATGGACATTAAAGGAGC;RSEQ=TTTTTTTAGGAGCCAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:309:225:124,101:40,41:0.7282:2,2:25.8:1:30.5:1:0.43589:1.26:60:44:0.7237:0:1.9 0/1:457:184:99,85:136,136:0.4026:2,2:25:1:29.9:1:0.44581:1.16:60:91:0.4018:0:1.9 -18 26620907 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24765;LSEQ=TTTTTAGGTAAGAAGACTTC;RSEQ=ACTTCTGACCTAGGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:119:20,99:7,22:0.8041:2,2:24.4:1:28.8:1:0.42126:1.56974:60:238:0.8041:0:1.4 1/0:173:87:24,63:23,63:0.5029:2,2:20.4:1:28.1:1:1:1.04:60:174:0.5029:0:1.4 -18 26620985 . A C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00209;SOR=0.13202;LSEQ=TTTAAACTAGAAAAACAGAC;RSEQ=AAATATAAGAAATGATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:0,29:0,4:0.8788:0,1:15.8:1:32.7:1:1:0:60:58:0.8788:0:1.6 0/1:23:11:0,11:0,12:0.4783:0,0:24.6:1:32.7:1:1:0:60:22:0.4783:0:1.5 -18 28787355 . T A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00307;SOR=0.11065;LSEQ=TCATTTTATAAATTCTTTCC;RSEQ=AATTACCTCAAATCACAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:14:14,0:21,0:0.4:1,1:28:1:29.6:1:1:0:60:13:0.3939:0:1.1 0/1:30:2:2,0:26,2:0.0667:2,0:28.5:1:28.5:1:1:0:60:4:0.0667:0:1 -18 28787426 . G T 29 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.61827;SOR=2.06752;LSEQ=AGTCTGTCCTCATAGACAGA;RSEQ=CACTCTGATGACAATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:1:0,1:86,26:0.0088:2,0:1:0:25:0:0.23894:0:60:2:0.0089:0:1 0/1:110:2:1,1:78,30:0.0182:2,2:40:0:29.5:1:0.48607:2.57407:60:4:0.0182:0:1 -18 28787475 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21207;SOR=0;LSEQ=ACAGCTAGACACTCGGTTAG;RSEQ=TCAGCTCCTTAGGTCTTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:107,81:0.0105:2,2:22:1:30:1:1:1.31902:60:4:0.0109:0:1.5 0/0:222:0:0,0:129,93:0:2,0:26.1:1:30.6:1:1:0:60:73:1:0:0.4 -18 28787479 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20701;SOR=0;LSEQ=CTAGACACTCGGTTAGGTCA;RSEQ=CTCCTTAGGTCTTGCGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:108,80:0.0105:2,2:27.5:1:28.5:1:1:1.34782:60:4:0.0107:0:2 0/0:227:0:0,0:127,99:0:2,0:26.6:1:31.6:1:1:0:60:112:0.9956:0:0.4 -18 28787520 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16048;SOR=0;LSEQ=TGCCTCATGTAAATGCTGCA;RSEQ=GATATCCATTCGAGTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:85,114:0.01:2,2:25:1:29.5:1:1:1.34:60:4:0.0101:0:2 0/0:300:0:0,0:140,158:0:2,0:23.9:1:30:1:1:0:60:98.333:0.9933:0:0.6 -18 28787524 . A G 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=0.4525;LSEQ=TCATGTAAATGCTGCACGAT;RSEQ=TCCATTCGAGTGCAGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:200:126:51,75:33,41:0.63:2,2:22:1:31.7:1:0.65645:1.18264:60:62:0.6263:0:1.2 0/1:299:130:57,73:82,87:0.4348:2,2:23.9:1:31.1:1:0.483:1.20633:60:129:0.4329:0:1.1 -18 28787593 . G T 29 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.54275;LSEQ=GCACTCATTTCTTTATGGTA;RSEQ=TCATAATAATCGCAATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:0,1:39,90:0.0077:2,0:34:0:16:0:1:0:60:0:0:0:3 0/1:169:2:1,1:61,105:0.0118:2,2:13:0:29.5:1:1:1.72:60:4:0.012:0:1.5 -18 28787634 . G T 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=0;LSEQ=ATAATAACTTCCATTTATTG;RSEQ=TCTAGAAATCACTGTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:11:2,9:9,37:0.193:2,2:24.7:1:29.9:1:1:1.09289:60:22:0.193:0:1.1 0/0:63:0:0,0:14,49:0:2,0:13:0:14:0:1:0:60:0:0:0:2 -18 28787710 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21773;SOR=0.26369;LSEQ=AAGAACCCTTTGAAGGTAGG;RSEQ=ATTTTTAGAGTAAACAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:0.5:0,0:25.1:1:29.1:1:1:0:60:16:0.5:0:1.1 0/1:10:2:0,2:1,6:0.2:2,0:29:1:30:0:1:0:60:4:0.2222:0:1 -18 29691526 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5311;SOR=Inf;LSEQ=TAATTGTTCAAATATTCCCA;RSEQ=CTAGTCCAGTTATCAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:40,12:0:2,0:22.8:1:30.3:1:1:0:60:25:1:0:0.3 0/1:89:2:1,1:59,28:0.0225:2,2:15:1:29.5:1:0.54801:2.08802:60:4:0.0225:0:1.5 -18 29691607 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.30542;LSEQ=ATTTATGTACATATGAGTAG;RSEQ=CTAACTTATTTAATATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:57:25,32:13,14:0.6786:2,2:23.7:1:29:1:0.81552:1.18612:60:114:0.6786:0:1.1 0/1:151:59:27,32:42,50:0.3907:2,2:23.8:1:29:1:1:1.00:60:58:0.3919:0:1.2 -18 29691678 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50129;SOR=Inf;LSEQ=TTATAGAGATGAAGAGAGTA;RSEQ=TTTTTTTGTAATTAATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:10,33:0:2,0:24.9:1:30.5:1:1:0:60:86:1:0:0.3 0/1:54:2:1,1:11,41:0.037:2,2:33:1:28.5:1:0.39832:3.61:60:4:0.037:0:0 -18 30089439 . T G 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAATCTTCCCTTCTTCCCT;RSEQ=GGATGTCATCATTTCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:199,202:0:2,0:26.8:1:30:1:1:0:60:199.5:1:0:0.6 0/1:512:24:9,15:254,234:0.0469:2,2:29:1:29.7:1:0.20982:1.80703:60:11:0.0435:0:1.3 -18 30089478 . T C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.17128;LSEQ=TGAGTTTTAATCCTTACTTC;RSEQ=TTCCCCTGTAGAAAACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:332:270:107,163:27,34:0.8133:2,2:24.8:1:31.5:1:0.56406:1.20902:60:53:0.8179:0:1.1 0/1:443:189:81,108:118,134:0.4266:2,2:26.7:1:30.8:1:0.43969:1.1737:60:188:0.4273:0:1.1 -18 30089518 . CT C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16242;SOR=0;LSEQ=CCTCACGAGAGGAGGCAAAT;RSEQ=TTTTTTGAATTTCTGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:49,123:0.0115:2,2:22.5:1:29.5:1:0.49332:2.50:60:4:0.0116:0:0 0/0:257:0:0,0:87,167:0:2,0:22.7:1:30:1:1:0:60:62.5:0.9881:0:0.5 -18 30089578 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2385;SOR=0;LSEQ=CCATAGTAACTTAATTATTC;RSEQ=TCCAATTCCAGCTAAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:12,60:0.027:2,2:11:0:32:1:0.32247:4.84:60:4:0.0274:0:1.5 0/0:77:0:0,0:12,65:0:2,0:22:1:31.4:1:1:0:60:154:1:0:0.2 -18 31418065 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24943;SOR=Inf;LSEQ=ATAATAAATAAGTAAATTGA;RSEQ=GAAGAGAGAGAAAGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:204,67:0:2,0:22.8:1:31.9:1:1:0:60:44.167:1:0:0.1 0/1:289:3:1,2:195,91:0.0104:2,2:11.7:1:28.3:1:0.2432:4.26196:60:6:0.0106:0:1 -18 31418131 . T C 233 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGAATTGACATGTAGCTC;RSEQ=GAGCCTTCTGTCAACAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:243,214:0:2,0:24.9:1:30.2:1:1:0:60:56.125:1:0:0.1 0/1:502:237:126,111:141,121:0.4721:2,2:25.6:1:29.6:1:0.92845:1.02652:60:58.25:0.4707:0:1.2 -18 31418248 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19038;SOR=Inf;LSEQ=TTAACATATGAACTTCTTTT;RSEQ=CTTTCACAATTGCCCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:21,114:0:2,0:22.6:1:29.5:1:1:0:60:66.5:1:0:0.1 0/1:105:2:1,1:13,90:0.019:2,2:5:1:30.5:1:0.25:6.71:60:4:0.019:0:1 -18 31418249 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50414;SOR=0;LSEQ=TAACATATGAACTTCTTTTA;RSEQ=TTTCACAATTGCCCTATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:19,107:0.0155:2,2:18:1:30:1:0.28912:5.51:60:4:0.0156:0:1 0/0:103:0:0,0:13,90:0:2,0:20.3:1:31.4:1:1:0:60:33.333:1:0:0.1 -18 31705614 . A G 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34409;SOR=1.21316;LSEQ=ATAGTATAAATATTTTCTTT;RSEQ=TTAATGTTCGGAGTAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:217:116:53,63:45,55:0.5346:2,2:22.8:1:31.2:1:1:1.03:60:37.667:0.5305:0:1.2 1/0:237:138:63,75:39,59:0.5823:2,2:25.7:1:31.3:1:0.42418:1.27:60:276:0.5823:0:1.1 -18 31705717 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.23142;SOR=Inf;LSEQ=TCATATTAAAAGCATTTTTT;RSEQ=AAAAAAAGAGACAATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:4,44:0:2,0:22.7:1:28.9:1:1:0:60:96:1:0:0.1 0/1:45:2:0,2:4,39:0.0444:2,0:36:1:30.5:1:1:0:60:4:0.0455:0:1 -18 34882741 . T C 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5467;SOR=0.36007;LSEQ=CCCAGACCAGCAGGGTGAGC;RSEQ=TTCAGGAGGCAGAGGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:9,0:2,0:0.8182:0,0:28.3:1:30.9:1:1:0:60:18:0.8182:0:1 1/0:5:3:3,0:2,0:0.6:0,0:26.3:1:31.3:1:1:0:60:6:0.6:0:1 -18 34882891 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23262;SOR=Inf;LSEQ=TGAGGGACAGGGTGCACAGC;RSEQ=AGGCCAGGCACAGAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:80,59:0:2,0:25.2:1:29.4:1:1:0:60:68.5:1:0:0.7 0/1:130:2:1,1:70,58:0.0154:2,2:7:0:33:1:1:1.20514:60:4:0.0157:0:1.5 -18 34882899 . G A 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05402;SOR=Inf;LSEQ=AGGGTGCACAGCTAGGCCAG;RSEQ=CACAGAGGAGGGGTGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:87,65:0:2,0:24.3:1:30.8:1:1:0:60:24.333:1:0:0.7 0/1:143:4:2,2:73,66:0.028:2,2:33:1:29.8:1:1:1.10528:60:8:0.0286:0:1.3 -18 34882932 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00035;SOR=0.40235;LSEQ=GTGGGAGAGGAGAGTGGGAA;RSEQ=GGGGCTCCATCTCCTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:151:115:59,56:16,19:0.7616:2,2:27:1:30.7:1:0.6998:1.25:60:230:0.7616:0:1.2 1/0:146:82:36,46:30,34:0.5616:2,2:27.1:1:29.7:1:0.74022:1.12652:60:26.333:0.5524:0:1.2 -18 34883082 . T G 131 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10526;SOR=0;LSEQ=GTACCATTGTTCTCAGCACT;RSEQ=CCTTTGGCTCATTTGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:0,17:0,1:0.9444:0,1:21.6:1:32.2:1:1:0:60:34:0.9444:0:1 0/0:1:0:0,0:0,1:0:0,0:19:0:29:0:1:0:60:2:1:0:0 -18 35069156 . C T 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01767;SOR=0;LSEQ=ATCCGATGCAGCGGCTGACA;RSEQ=GCCAGCATGGCAGATTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:8,2:0.375:2,0:20.3:1:31.8:1:0.5:0:60:12:0.375:0:1 0/0:16:0:0,0:12,4:0:2,0:28.1:1:30.3:1:1:0:60:32:1:0:0.2 -18 35070733 . C T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGGCCCTCCCAGCTGTG;RSEQ=GACTCTGACGGGACATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:32:0:1:0:60:4:1:0:1 -18 35071242 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTCACCTGAGAGGGACG;RSEQ=CGTGCCCACCTCCTCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:30:1:1:0:60:4:1:0:1 -18 36969660 . C T 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CACACAGGGCAGGGGAGCCC;RSEQ=CACCCCCCAAGCCAAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:26.5:1:32.5:1:1:0:60:4:1:0:0 1/1:3:3:2,1:0,0:1:0,2:10:1:29.7:1:1:0:60:6:1:0:1.3 -18 36970447 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GGTGAGACCCTCCAAAAGGG;RSEQ=TTGTCAGACACCCTATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:22.4:1:30.9:1:1:0:60:16:1:0:0.1 0/1:9:2:1,1:3,4:0.2222:2,2:25.5:1:30.5:1:1:1.29:60:4:0.25:0:1.5 -18 36970621 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15852;SOR=0;LSEQ=AATAGGGCCTGAAGTGAACC;RSEQ=CCAGCAAACTGCAGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:8,13:0.087:2,2:30:1:29.5:1:1:1.59:60:4:0.087:0:1 0/0:34:0:0,0:16,18:0:2,0:26.8:1:29.3:1:1:0:59.9:33:1:0:0.1 -18 38529854 . C CT 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATTTGTCCTTTGTGTTCA;RSEQ=TGCCATAGGAGGGGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:159,34:0:2,0:25.1:1:32.1:1:1:0:60:386:1:0:0.1 0/1:129:17:15,2:93,19:0.1318:2,2:23.5:1:30.9:1:0.73761:1.53:60:34:0.1339:0.0233:0.2 -18 38529883 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24893;SOR=0;LSEQ=GAGGGGAATAAAATGAAAGA;RSEQ=AGGGAGAGTCAGGCCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:198,96:0.0101:2,2:6.3:1:25:1:0.25402:4.10357:60:6:0.0102:0:1 0/0:287:0:0,0:195,92:0:2,0:23:1:31.2:1:1:0:60:46.833:1:0:0.3 -18 38529971 . A C 242 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54488;SOR=1.09413;LSEQ=TTGAAAGTGACAAGAAGGTC;RSEQ=AATGAAGTTAACAGGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:191:84,107:97,112:0.4775:2,2:25.6:1:31.4:1:0.68761:1.10294:60:94.5:0.4749:0:1.1 1/0:494:247:111,136:109,138:0.5:2,2:25.2:1:30.5:1:0.92788:1.03:60:122.5:0.498:0:1.2 -18 38530035 . G C 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAATGGAATCCAGTTCAT;RSEQ=GGTGTGGGCATATCACGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:48,145:0:2,0:24.6:1:31.4:1:1:0:60:95.5:1:0:0.4 0/1:193:40:12,28:41,112:0.2073:2,2:24.6:1:29.3:1:0.69384:1.17:60:19:0.2:0:1.6 -18 38530039 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23707;SOR=Inf;LSEQ=ATGGAATCCAGTTCATGGGT;RSEQ=TGGGCATATCACGGTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:43,143:0:2,0:23.5:1:32.2:1:1:0:60:185:1:0:0.3 0/1:177:2:1,1:44,131:0.0113:2,2:14:1:26.5:1:0.44492:2.96:60:4:0.0113:0:2.5 -18 38530053 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22767;SOR=Inf;LSEQ=ATGGGTGTGGGCATATCACG;RSEQ=TGTTCAATGAACATACGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:26,117:0:2,0:22.7:1:32:1:1:0:60:70.5:1:0:0.2 0/1:131:2:1,1:26,103:0.0153:2,2:21:0:32:0:0.37099:3.91:60:4:0.0155:0:2.5 -18 38530160 . A G 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCCTTCTTTCCTTCCTC;RSEQ=TTTCTCTTTCTTTCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:2,34:0,0:1:0,2:20.9:1:31.8:1:1:0:58.8:72:1:0:1.1 1/1:16:16:0,16:0,0:1:0,1:21.4:1:31:1:1:0:60:15:1:0:1.3 -18 38530881 . A T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTTTTCCAAGTGCTTAGA;RSEQ=TAAAATTCAAACTACTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:1:28.5:1:1:0:60:4:1:0:1 -18 38531882 . C T 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACAGGCGTGAGCCACTG;RSEQ=GCCCAGCTCCTTAGTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:48:0:29:1:1:0:60:4:1:0:1 -18 39535169 . T TC 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGGGGGCGGAACCGGAAGT;RSEQ=CCGTGTTGTGGGGCTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:125,34:0:2,0:23.7:1:29.9:1:1:0:60:78.5:1:0:0.2 0/1:181:29:24,5:118,34:0.1602:2,2:18.7:1:29.9:1:0.62962:1.38:60:58:0.1629:0.0552:0.1 -18 39535420 . C G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01425;SOR=Inf;LSEQ=GAGGCAGAAAGTACGTGACT;RSEQ=GTCTCAAGGCCCAGATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:3,76:0:1,0:21.6:1:29:1:1:0:60:25.333:1:0:0.1 0/1:86:7:0,7:6,73:0.0814:2,0:31.1:1:31.3:1:1:0:60:14:0.0814:0:1 -18 39537688 . G C 245 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAGCCTTTGGCCTTGCCAGT;RSEQ=AGAACATCCTACAAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:220:90,130:117,163:0.44:2,2:24.5:1:31.6:1:0.85534:1.03675:60:72.333:0.4393:0:1.1 0/0:622:0:0,0:268,354:0:2,0:25.4:1:30.9:1:1:0:60:61.2:1:0:0.1 -18 39537777 . TG T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50184;SOR=0;LSEQ=ACTGTTCTTACCTTTCTTTA;RSEQ=GATGCTGCAAGTATAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:25,143:0.0118:2,2:15.5:1:29:1:0.28326:5.63:60:4:0.0118:0.0059:1 0/0:144:0:0,0:26,118:0:2,0:21.1:1:30.2:1:1:0:60:47:1:0:0.1 -18 39542407 . GAT G 202 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0;SOR=42.66667;LSEQ=GTTTGTTAATTTAAAAGAAA;RSEQ=ATATATATATGTATTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:3,0:152,21:0.0169:2,0:24.7:1:31.9:1:1:0:60:6:0.0172:0.0056:0 0/1:202:86:72,14:98,18:0.4257:2,2:24.5:1:31.5:1:1:1.05832:59.7:172:0.4279:0.099:0.1 -18 39542645 . C A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12771;SOR=Inf;LSEQ=GGAGTGTAGCAGCTTTCTGA;RSEQ=CCTTTTCTTTTTCGGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:85,250:0:2,0:22.4:1:30.9:1:1:0:60:26.917:1:0:0.1 0/1:386:4:3,1:102,279:0.0104:2,2:5.5:1:28.5:1:0.06354:8.15:60:8:0.0106:0:1.3 -18 39550227 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49946;SOR=Inf;LSEQ=TTCTCTTTATTTTTAGGAAT;RSEQ=TAAAATTTCCTGTAATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:155,31:0:2,0:24:1:31.4:1:1:0:60:185:1:0:0.1 0/1:201:2:1,1:158,40:0.01:2,2:15:1:26:1:0.36879:3.91386:60:4:0.0101:0:3.5 -18 39550244 . G T 40 v4;q23;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3759;SOR=3.64771;LSEQ=AATCTAAAATTTCCTGTAAT;RSEQ=AACTGTATTAATTTACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:0,1:204,61:0.0038:2,0:1:0:24:0:0.23308:0:60:2:0.0038:0:1 0/1:294:4:0,4:205,85:0.0136:2,0:8.5:1:20.3:1:0.00801:0:60:3:0.0103:0:1.8 -18 39550271 . A T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0676;SOR=Inf;LSEQ=ATTAATTTACTTCTACCCTG;RSEQ=ACATTCTCTTTTTCCCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:286,123:0:2,0:25.1:1:30:1:1:0:60:101.25:1:0:0.1 0/1:496:5:1,4:307,184:0.0101:2,2:10:1:25.2:1:0.07089:6.64948:60:10:0.0102:0:1 -18 39570304 . T C 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16481;LSEQ=AATAAAATAAAAATGTGTTA;RSEQ=GTTTTGACTTGTATTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:6,0:41,1:0.125:1,0:23.8:1:32.3:1:1:0:60:12:0.1277:0:1 0/1:49:7:7,0:42,0:0.1429:1,0:22.6:1:31.1:1:1:0:60:14:0.1429:0:1 -18 39570409 . A AT 137 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.27347;SOR=0.69052;LSEQ=AATCATTTTTCATGAAAATC;RSEQ=TTTTTTTTTTCAGAGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:24:16,8:266,114:0.0593:2,2:22.5:1:29.9:1:0.81901:1.16619:60:48:0.0596:0.0148:0.3 0/1:456:19:12,7:298,139:0.0417:2,2:20.5:1:29.7:1:0.62374:1.24993:59.7:38:0.042:0.0132:0.2 -18 39570536 . GT G 74 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=1.26755;LSEQ=AAGGTATTTCCCTTGGAACT;RSEQ=TTTTGGTCTCTAAAGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:3:1,2:117,255:0.008:2,2:37:1:31:1:1:1.09:60:6:0.0081:0:0 0/1:494:5:2,3:161,327:0.0101:2,2:12.8:1:32:1:0.66742:1.35:60:10:0.0102:0:0 -18 39570683 . A G 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01348;SOR=Inf;LSEQ=AATCAAATCATATAACTACA;RSEQ=CAAGATTACAAAAGCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:0:1,0:22.4:1:30.8:1:1:0:60:52:1:0:0 0/1:15:4:0,4:0,11:0.2667:0,0:22.8:1:33:1:1:0:60:8:0.2667:0:1 -18 39571373 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTTTGAAACCACATAAA;RSEQ=TATCTTCTATTATTGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:31:1:28.5:1:1:0:60:4:0.6667:0:1.5 -18 39575790 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4978;SOR=0;LSEQ=TAAGTACCTTTTCTATTTAT;RSEQ=AATAGCTTTTGAAATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:2,0:107,5:0.0175:1,0:28.5:1:32:0:1:0:60:4:0.0175:0:1 0/0:113:0:0,0:110,3:0:1,0:20.3:1:32:1:1:0:60:226:1:0:0 -18 39576759 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19732;SOR=Inf;LSEQ=TTTGTTATTAATGATCAAGA;RSEQ=GAGGAAAATGCCATGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:8,124:0:2,0:22.9:1:30.5:1:1:0:60:264:1:0:0.1 0/1:106:2:1,1:6,98:0.0189:2,2:32:1:31.5:1:0.1283:15.20:60:4:0.019:0:1 -18 39584264 . C T 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00513;SOR=Inf;LSEQ=GTGGAACTCTGCCTAGTCAA;RSEQ=TTCTCTATCCCAGGAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:75,7:0:2,0:22.9:1:31.9:1:1:0:60:81:1:0:0.2 0/1:76:7:6,1:62,7:0.0921:2,2:21.6:1:30.4:1:0.55656:1.46764:60:14:0.0921:0:1 -18 39584319 . G T 40 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33824;SOR=0.28168;LSEQ=TTAAATATTTTCTGATTTTA;RSEQ=GCCTTGACAAAATTCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:232,59:0.0102:2,2:14.7:1:25.7:1:0.49712:1.96083:60:2:0.007:0:1.7 0/0:346:1:0,1:252,92:0.0029:2,0:1:0:26:0:0.26957:0:60:2:0.0029:0:1 -18 39584412 . T C 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=GGAAAATGGAAGCCGATGGA;RSEQ=GTAGAGGACTCCTTGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:0:0,0:357,338:0:2,0:24.1:1:30.3:1:1:0:60:56.917:1:0:0.1 0/1:882:79:42,37:419,384:0.0896:2,2:20.9:1:29.9:1:0.90637:1.04:60:78:0.0897:0:1.2 -18 39593363 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=ATTATGTCTGTAATAATTTT;RSEQ=CATTCTTTTCCTAATATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:125,18:0:2,0:23.6:1:31.9:1:1:0:60:70.5:1:0:0 0/1:143:2:1,1:127,14:0.014:2,2:46:1:29.5:1:0.19945:8.79957:60:4:0.0141:0:1 -18 39593388 . CT C 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00858;SOR=0;LSEQ=CTTTTCCTAATATTACTTTA;RSEQ=TTTTTTTGTTTTCCAGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:6:5,1:171,42:0.0274:2,2:30.8:1:33.2:1:1:1.23:60:12:0.0274:0:0 0/0:262:0:0,0:202,60:0:2,0:24.1:1:30.7:1:1:0:60:261:1:0:0.1 -18 39595382 . C T 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=44.13184;LSEQ=CTGTTCCATAAAAAATTGTG;RSEQ=GTTCTCTTATGGACAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:2:0,2:274,102:0.0053:2,0:1:0:27.5:1:0.07517:0:60:4:0.0053:0:1 0/1:378:72:56,16:225,81:0.1905:2,2:19.2:1:29.5:1:0.54909:1.26:60:71:0.1898:0:1.1 -18 39600527 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20947;SOR=0;LSEQ=TACAGATGAAAACTGATAGG;RSEQ=AAATGTAAACTTACTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:114,17:0.015:2,2:17:1:30:1:0.25325:6.54547:60:4:0.0152:0:1 0/0:157:0:0,0:137,20:0:2,0:22.1:1:32.3:1:1:0:60:314:1:0:0.1 -18 39600755 . A G 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAACACAAAGATGATTTAAA;RSEQ=TAAGATATGAGCAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:1,90:0:1,0:25.6:1:31.9:1:1:0:60:182:1:0:0 0/1:54:11:0,11:1,42:0.2037:1,0:15.7:1:30:1:1:0:60:10:0.1923:0:1.2 -18 39617591 . A T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.22209;SOR=Inf;LSEQ=ATATATCAACATTTTCTTGT;RSEQ=TGTATAGTACAATTTTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:143,18:0:2,0:23.7:1:28.3:1:1:0:60:79.5:1:0:0.1 0/1:144:2:1,1:126,16:0.0139:2,2:7:1:23.5:1:0.2229:7.67002:60:4:0.0141:0:1 -18 39617865 . C CAG 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.00067;SOR=Inf;LSEQ=TTCATTTGCTGTTTATGGAA;RSEQ=AGAAGTATTTGTAACATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:12,171:0:2,0:23.6:1:32.3:1:1:0:60:90.5:1:0:0.1 0/1:150:9:0,9:14,127:0.06:2,0:26.6:1:31.1:1:1:0:60:18:0.0608:0.0067:0 -18 39620446 . TA T 28 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.57434;LSEQ=CAGACTAAATCAGCTTAATT;RSEQ=AAAAAAAAAAGTTTTCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:16,0:0.1111:1,0:29.5:1:30.5:1:1:0:60:4:0.1111:0:0 0/1:12:2:2,0:9,1:0.1667:2,0:29.5:1:28:1:1:0:60:4:0.1667:0:0 -18 39620557 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22631;SOR=Inf;LSEQ=ATGGAATGCATTTATTCAGA;RSEQ=ATGAGGATTATTCTTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:118,17:0:2,0:22.8:1:32.4:1:1:0:60:270:1:0:0.1 0/1:123:2:1,1:106,15:0.0163:2,2:11:1:27.5:1:0.24417:6.87422:60:4:0.0163:0:1 -18 39623621 . C T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10202;SOR=0;LSEQ=TATGCTAGACACTTGCTGGT;RSEQ=ACTATTTATAGTTTCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:3:1,2:139,16:0.019:2,2:8:1:26.7:1:0.03448:16.73835:60:6:0.0196:0:1 0/0:179:0:0,0:157,22:0:2,0:21.7:1:30.9:1:1:0:60:43.75:1:0:0 -18 39623865 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18808;SOR=Inf;LSEQ=GCCATAATCATATACATTTA;RSEQ=AACATGTTAATATTTAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:8,182:0:1,0:22.3:1:31.3:1:1:0:60:46.5:1:0:0.2 0/1:146:2:1,1:17,127:0.0137:2,2:30.5:1:27.5:1:0.23212:7.29:60:4:0.0139:0:1 -18 39623942 . A G 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGTCATTGATGCTTTGAC;RSEQ=TAATAGTATTAACAAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:55:1,54:0,0:1:0,1:25.4:1:32.3:1:1:0:60:110:1:0:1 1/1:26:26:0,26:0,0:1:0,1:26.8:1:31.3:1:1:0:60:52:1:0:1 -18 39629423 . C T 106 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00111;SOR=13.71388;LSEQ=TATTAAAGTTGCACAAACTG;RSEQ=TTTTATATTCAGTAGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:154,15:0.0059:2,0:1:0:25:0:0.09412:0:60:2:0.006:0:1 0/1:159:12:12,0:130,17:0.0755:2,0:28:1:29.7:1:0.36591:0:60:24:0.0764:0:1.2 -18 39629472 . AT A 92 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06749;SOR=0.28957;LSEQ=GTTTGCATTTGTTTTCACAT;RSEQ=TTTTTTTAACTGTTACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:8:5,3:266,108:0.0209:2,2:22.4:1:30.8:1:0.6959:1.47616:60:16:0.0211:0.0052:0.1 0/0:488:3:2,1:314,171:0.0061:2,2:24.3:1:30.3:1:1:1.09:60:6:0.0062:0.002:0 -18 39637814 . C A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07583;SOR=Inf;LSEQ=CCCAGTTCTTTAAGATAATT;RSEQ=TGGAAACAAATGAGTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:218,76:0:2,0:25.7:1:31.1:1:1:0:60:48:1:0:0.1 0/1:398:5:3,2:270,123:0.0126:2,2:16.2:1:24.8:1:0.65128:1.46195:60:4:0.0102:0:2.4 -18 39638072 . CA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49863;SOR=Inf;LSEQ=ATTTATTTTATTTTATAGAA;RSEQ=AGAGAATTTGTTTAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:18,142:0:2,0:24.5:1:29.9:1:1:0:60:159:1:0:0 0/1:166:2:1,1:21,143:0.012:2,2:30:1:30.5:1:0.24819:6.68:60:4:0.0123:0:0 -18 39638115 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.02711;SOR=Inf;LSEQ=GCATTCTTTAGCATTGATCA;RSEQ=TTTTTCAAAATGACAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:0,71:0:1,0:24:1:32.8:1:1:0:60:142:1:0:0 0/1:50:4:0,4:2,44:0.08:1,0:36.3:1:31.3:1:1:0:60:8:0.08:0:1 -18 39644675 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62365;SOR=2.88316;LSEQ=TGCAGAATTCTTAATCGTTG;RSEQ=TATTTTTTTCTTTTCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:0,1:176,33:0.0048:2,0:1:0:26:0:0.1619:0:60:2:0.0048:0:1 0/1:220:3:1,2:184,33:0.0136:2,2:20.3:1:26.7:1:0.06662:10.95198:60:6:0.0139:0:1 -18 39647276 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12112;SOR=0;LSEQ=CATGTTACCTTATAATGTCT;RSEQ=CATCAGTTTGATTCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:1,2:193,41:0.0126:2,2:8.7:1:28:1:0.0856:9.28078:60:6:0.0128:0:1 0/0:242:0:0,0:196,44:0:2,0:23.3:1:31.3:1:1:0:60:29:0.9915:0:0.2 -18 39660959 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49573;SOR=Inf;LSEQ=TAATTGCAATCCTCTTGGTA;RSEQ=CATTTAGCAAACTAATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:55,3:0:2,0:25.7:1:31.7:1:1:0:60:28:1:0:0.2 0/1:59:2:1,1:49,8:0.0339:2,2:20:1:28.5:1:0.28404:5.83337:60:4:0.0339:0:1 -18 39661005 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.2182;SOR=0;LSEQ=TTTTATTTTATTAGTAGTCT;RSEQ=TTTTAAAACTATAGACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:118,19:0.0144:2,2:18.5:1:30.5:1:0.26796:6.07889:60:4:0.0144:0:1 0/0:158:0:0,0:120,38:0:2,0:25.1:1:30.2:1:1:0:60:157:1:0:0.1 -18 42288477 . A T 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGAAATTTTGTTTCCTG;RSEQ=TAGATTTCTCTCTGATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:89,104:0:2,0:26.9:1:30.2:1:1:0:60:31.167:1:0:0.1 0/1:306:39:16,23:130,137:0.1275:2,2:24.8:1:29.7:1:0.39565:1.36267:60:78:0.1296:0:1.1 -18 42288703 . AAAAAGAAAAG A 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAGCTTCTACATGTTCAAA;RSEQ=AAAAGAAAAGAAAAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:42.2:1:29.8:1:1:0:55.8:12:0.75:0:0.8 1/1:3:3:0,3:0,0:1:0,0:19.7:1:28.8:1:1:0:60:6:1:0.3333:0 -18 43015532 . C T 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00155;SOR=0.55622;LSEQ=AGACAATTTTGGCAAGACTG;RSEQ=TGTTCTTATTTTTACACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:242:132:63,69:51,58:0.5455:2,2:24:1:29.9:1:0.89758:1.04:60:264:0.5477:0:1.1 0/1:250:100:47,53:69,81:0.4:2,2:24.5:1:29.2:1:0.89758:1.04:60:99:0.4024:0:1.1 -18 43015609 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50624;SOR=0;LSEQ=GCTGAAGAGTTTGCCTTTGG;RSEQ=TGGGACATAAACTCCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:33,91:0.0159:2,2:21.5:1:28.5:1:0.46844:2.73:60:4:0.0159:0:1.5 0/0:97:0:0,0:31,66:0:2,0:20.1:1:32.1:1:1:0:60:194:1:0:0.3 -18 44240423 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2073;SOR=Inf;LSEQ=GAGGATCCTGCACATAGCTG;RSEQ=CTGTGAACGGGTGCTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:111,20:0:2,0:22.8:1:31.3:1:1:0:60:42.667:1:0:0.1 0/1:110:2:1,1:79,29:0.0182:2,2:19.5:1:28:1:0.47289:2.69525:60:4:0.0185:0:1 -18 44240426 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50155;SOR=0;LSEQ=GATCCTGCACATAGCTGGCT;RSEQ=TGAACGGGTGCTCAGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:114,19:0.0148:2,2:22:1:29:1:0.27529:5.8737:60:4:0.0152:0:1 0/0:114:0:0,0:83,31:0:2,0:21.7:1:31.4:1:1:0:60:228:1:0:0.1 -18 44240453 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49903;SOR=Inf;LSEQ=GGTGCTCAGGGCATGCTTTG;RSEQ=AGACCCACTTCTCATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:143,43:0:2,0:26.8:1:32.1:1:1:0:60:185:1:0:0.4 0/1:196:2:1,1:136,58:0.0102:2,2:22:0:31:1:0.51251:2.33343:60:4:0.0103:0:1.5 -18 44240526 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33577;LSEQ=AGGCCTCAGTAGGCATAGCA;RSEQ=AAGGCCCTGAACTGTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:434:298:153,145:73,63:0.6866:2,2:27.1:1:29.3:1:0.67944:1.09791:60:58.6:0.6846:0:1.1 0/1:484:205:110,95:149,130:0.4236:2,2:24.5:1:28.8:1:1:1.01:60:204:0.4232:0:1.2 -18 45368374 . G T 48 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.2486;SOR=Inf;LSEQ=AATTCAAGTCCACAGGCAGG;RSEQ=AAAATGGCTATGTTTAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:39,229:0:2,0:23.7:1:31.4:1:1:0:60:133:1:0:0.1 0/1:268:3:1,2:48,217:0.0112:2,2:12:0:30.7:1:0.45571:2.25:60:6:0.0112:0:1.3 -18 45371509 . C T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16976;SOR=2.34715;LSEQ=CGTTAAAATGCACGCCTGTG;RSEQ=ATGTTTTAATATCTTCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:18:18,0:25,0:0.4186:1,1:31.2:1:30.3:1:1:0:60:36:0.4186:0:1 1/0:19:12:12,0:6,1:0.6316:2,0:23.8:1:30.3:1:0.36842:0:60:24:0.6316:0:1 -18 45371686 . T C 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=ATAATTACACTGTGGAAATT;RSEQ=AAGAACCAAATATGTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:593:0:0,0:350,243:0:2,0:24.7:1:29.2:1:1:0:60:295.5:1:0:0.1 0/1:710:15:6,9:395,299:0.0211:2,2:23.3:1:32.5:1:0.20084:1.9797:60:30:0.0212:0:1.1 -18 45374776 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.52035;LSEQ=GCACACAAGCTCTTGATGTG;RSEQ=CACACCATGCAATGCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:0,1:106,12:0.0084:2,0:47:0:32:0:0.10924:0:60:2:0.0085:0:1 0/1:157:2:2,0:130,24:0.0127:2,0:14:1:30:1:1:0:60:4:0.0129:0:1 -18 45374802 . A T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08791;SOR=0;LSEQ=CATGCAATGCCTACATTATG;RSEQ=GTATACAGCATTTATTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:1,2:182,53:0.0126:2,2:7.7:1:22:1:0.13431:6.79581:60:2:0.0085:0:1.7 0/0:296:0:0,0:210,86:0:2,0:23.2:1:29.4:1:1:0:60:295:1:0:0.1 -18 45377602 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26075;SOR=Inf;LSEQ=ATTTTTATTATTAAGTAGGT;RSEQ=ATACAGTATAAAAATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:134,59:0:2,0:24.5:1:31.8:1:1:0:60:192:1:0:0.1 0/1:250:3:1,2:160,87:0.012:2,2:24.7:1:27.7:1:0.28917:3.65795:60:6:0.012:0:1 -18 45377744 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18087;SOR=0;LSEQ=ATGAAGTATTTCCAGAACTT;RSEQ=TGATCAAGTAATCATAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:25,103:0.0154:2,2:31:1:30:1:0.36124:4.06:60:4:0.0155:0:1 0/0:175:0:0,0:53,122:0:2,0:23.2:1:31.5:1:1:0:60:174:1:0:0.1 -18 45391419 . AT A 103 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.11506;SOR=0.39667;LSEQ=ACTGAGGAATTTTCAAAGAC;RSEQ=TTTTTTTACCTGTGTCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:10:5,5:298,203:0.0196:2,2:30.6:1:31.1:1:0.53749:1.46682:60:20:0.0197:0:0 0/0:637:5:3,2:374,258:0.0078:2,2:19.6:1:29.6:1:1:1.03:60:10:0.0079:0.0016:0.2 -18 45394601 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.49806;SOR=Inf;LSEQ=AAAAACTCAAAAGCATTTTT;RSEQ=AAAAAGTGAAACCACAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:67,1:0:1,0:23.4:1:28.6:1:1:0:60:67:1:0:0 0/1:76:2:2,0:70,4:0.0263:2,0:5:1:30.5:1:1:0:60:4:0.027:0:1 -18 45394634 . A T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25248;SOR=Inf;LSEQ=CACAATTTACTAAAACTTGA;RSEQ=TGCTTATGAACAAAATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:123,27:0:2,0:22.6:1:30.4:1:1:0:60:74:1:0:0.1 0/1:176:3:1,2:139,34:0.017:2,2:10:1:22.7:1:0.10674:8.0406:60:2:0.0116:0:2.3 -18 45394919 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19937;SOR=Inf;LSEQ=TTCAACAAGAAGAGAAGTTG;RSEQ=AGCTTAATTTTTAAAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:0:1,0:23:1:28.1:1:1:0:60:21:1:0:0.1 0/1:36:2:0,2:0,34:0.0556:1,0:15.5:1:29.5:1:1:0:60:4:0.0571:0:1 -18 45397062 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23065;SOR=Inf;LSEQ=AGAAAATATACAATTGCTTC;RSEQ=CTTTTTCACAGGCATGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:0:1,0:21.3:1:29.1:1:1:0:60:15.5:1:0:0.2 0/1:31:2:1,1:0,29:0.0645:1,2:31:0:31.5:1:0.06452:0:60:4:0.0667:0:1.5 -18 45423757 . CAT C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGAGAGAAATTTTTTAACA;RSEQ=GTTTTTTTCATTTTCATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30.5:1:1:0:60:4:1:0:0.5 -18 46385146 . C G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=10.74891;LSEQ=CAGTTTGTATTTCTCTCCCC;RSEQ=ACTTCCTGTCACAAGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:5,0:39,2:0.1087:1,0:27.4:1:30.4:1:1:0:60:10:0.1111:0:1.2 1/0:47:27:21,6:20,0:0.5745:1,2:19.3:1:29:1:0.03118:0:60:26:0.5652:0:1 -18 46385291 . A T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.5017;LSEQ=ATGTAATAATGACTAAGCTC;RSEQ=TTGCCAGAGAGACGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:19:8,11:110,132:0.0728:2,2:29.8:1:30.6:1:0.81566:1.14524:60:18:0.0706:0:1.3 0/1:248:118:53,65:66,64:0.4758:2,2:27.4:1:30.8:1:0.37532:1.26353:60:236:0.4777:0:1.2 -18 46385334 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.2364;SOR=Inf;LSEQ=AGTGAAAATGACCACAGGGC;RSEQ=CCCTGATCACCAAGGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:61,116:0:2,0:26.4:1:30.3:1:1:0:60:28.5:1:0:0.2 0/1:168:2:1,1:63,101:0.0119:2,2:42.5:1:29.5:1:1:1.60:60:4:0.012:0:1.5 -18 46996347 . C T 134 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00042;SOR=16.58424;LSEQ=GCTTTCCCCCCAGGTGGACG;RSEQ=CCTCATCCTGTGCCACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:2,9:0.1538:2,0:25.5:1:28.5:1:1:0:60:4:0.1538:0:1 1/0:30:23:7,16:3,4:0.7667:2,2:27.5:1:29.7:1:0.65729:1.68229:60:46:0.7667:0:1.3 -18 46996404 . A G 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00281;SOR=0;LSEQ=GGGTCCCTACCTTCCTCCAT;RSEQ=CCCACCACCTGCCCCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:0.6:0,2:21.7:1:32.8:1:1:0:60:12:0.6:0:1.3 0/0:12:0:0,0:3,9:0:2,0:21.8:1:28.2:1:1:0:60:24:1:0:0.8 -18 48190440 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGTTTGGTGCTGTCGGCC;RSEQ=TGGACAGCCGGGCCTGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 48190685 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.78215;LSEQ=GCACGCCTGCTGGAGCAGGG;RSEQ=ACGCTGGCAGAAGAGCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:124,42:0.006:2,0:1:0:27:0:0.25749:0:60:2:0.006:0:1 0/1:188:2:1,1:134,52:0.0106:2,2:9.5:1:27.5:1:0.48544:2.56201:60:4:0.0108:0:1 -18 48190817 . G A 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10694;LSEQ=ATCAGCACAGAGGACCTCGT;RSEQ=CTCAAGATTGGGGATTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:80:22,58:26,59:0.4848:2,2:18.6:1:28.7:1:0.73266:1.16073:60:25.667:0.4753:0:1.2 0/1:209:19:8,11:56,134:0.0909:2,2:17.5:1:28.8:1:0.29807:1.74:60:38:0.0927:0:1.2 -18 48573268 . CT C 50 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.66188;SOR=1.69253;LSEQ=AAATGTGTTCTGATGTGTGT;RSEQ=TTTTTTTTTTTCTTTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:3,0:24,0:0.1111:1,0:21:1:30.8:1:1:0:60:6:0.1111:0.0741:1 0/1:17:3:3,0:14,0:0.1765:1,0:30:1:31.7:1:1:0:60:6:0.1765:0:1 -18 48573728 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49925;SOR=0;LSEQ=ATTTAAAAACTTGCTACGTT;RSEQ=CCTTTCAAGCTACTACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:6,58:0.0303:2,2:22.5:1:29.5:1:0.20233:9.03:60:4:0.0308:0:1 0/0:56:0:0,0:6,50:0:2,0:18.5:1:29.4:1:1:0:60:27:1:0:0.2 -18 48575389 . T C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00336;SOR=0.09892;LSEQ=TATACGTATTTAAATTTGAA;RSEQ=TTAGGAACAAACTTATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:28:6,22:2,1:0.9032:2,2:18.9:1:32.7:1:0.15573:6.74669:60:56:0.9032:0:1.3 0/1:13:6:0,6:2,5:0.4615:2,0:28.8:1:32.8:1:0.46154:0:60:12:0.4615:0:1 -18 48575746 . G GT 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02709;SOR=0;LSEQ=TGTTTTGTCCTATCCTCTCT;RSEQ=TTTTTTTGTTGACCTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:4:2,2:107,240:0.0114:2,2:25.3:1:28.6:1:0.59097:2.24:60:8:0.0116:0.0028:0 0/0:512:0:0,0:191,321:0:2,0:25.2:1:31:1:1:0:60:84.333:1:0:0.1 -18 48575929 . TA T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.05728;SOR=0.10257;LSEQ=ATTTATGAACTAAAGTACTG;RSEQ=AAAAAATATGATAGAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:1,8:0,1:0.9:0,2:34.2:1:31.1:1:1:0:60:18:0.9:0:0.8 0/1:9:4:0,4:0,5:0.4444:0,0:18.5:1:31.8:1:1:0:60:8:0.4444:0:0 -18 48581415 . C A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.77379;LSEQ=TTGAGTTTTCCTAATCATTG;RSEQ=TTATTTATGTGTAGTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:1,0:18,116:0.0074:2,0:1:0:25:0:0.14074:0:60:2:0.0075:0:1 0/1:231:3:2,1:37,191:0.013:2,2:29.7:1:28.3:1:0.07467:10.16:60:6:0.0132:0:1.3 -18 48581601 . C A 71 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22619;SOR=0.14055;LSEQ=TACTTTACTATTACATGTAG;RSEQ=AGTAAGTAGCCTCTTAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:21.6:1:30.6:1:1:0:60:10:0.8333:0:1 0/1:3:1:0,1:0,2:0.3333:0,0:22:0:32:0:1:0:60:2:0.3333:0:1 -18 48584855 . A TTT 94 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.03621;SOR=0.44095;LSEQ=CTTGTTTTTGTTGTAAGGGC;RSEQ=TTTTTTTTTTTTTTTTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:18:0,18:136,213:0.0452:2,1:30.1:1:22.7:1:0.00024:0:60:17:0.0528:0:2.8 0/1:587:12:0,12:200,349:0.0204:2,0:33.3:1:22.4:1:0.00561:0:58:3:0.0191:0:2.9 -18 48584872 . G T 63 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0237;SOR=Inf;LSEQ=GCTATTTTTTTTTTTTTTTT;RSEQ=GTAGGGCTTTGTTTTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:36,247:0:2,0:21.1:1:29.7:1:1:0:58.4:13.15:1:0:1.4 0/1:395:8:6,2:77,310:0.0203:2,2:9.1:1:21.1:1:0.00144:11.98:60:1.667:0.0136:0:1.6 -18 48586141 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49898;SOR=Inf;LSEQ=TGTTTTAAACAATTCCTAAC;RSEQ=TATAATAGTTATATTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:87,15:0:2,0:24.1:1:30.9:1:1:0:60:24.5:1:0:0.1 0/1:113:2:1,1:97,14:0.0177:2,2:5.5:1:28:1:0.24889:6.72937:60:4:0.018:0:1.5 -18 48593133 . G A 67 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTAGAATAATAGTACTT;RSEQ=TTGAGTTGTAAGGGTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:15:1:29:1:1:0:60:10:1:0:1 1/1:1:1:1,0:0,0:1:0,0:2:0:30:0:1:0:60:2:1:0:1 -18 48593582 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=GTTACAATTTTATTTGAATA;RSEQ=TTTAGACTTAAAGCTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:35,135:0:2,0:24.6:1:30.2:1:1:0:60:55.667:1:0:0.1 0/1:186:2:1,1:50,134:0.0108:2,2:12:1:26:1:0.47428:2.66:60:4:0.0109:0:1 -18 48593600 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50155;SOR=Inf;LSEQ=TATTTTAGACTTAAAGCTCT;RSEQ=TTTGTTGTCAAAAGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:17,97:0:2,0:26.6:1:30.9:1:1:0:60:228:1:0:0.1 0/1:135:2:1,1:33,100:0.0148:2,2:21:1:33:1:0.44168:3.00:60:4:0.0148:0:1 -18 48603212 . T A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50376;SOR=Inf;LSEQ=TTTTATCTTGATTTACTCAG;RSEQ=TGATTAGTTTCTTTGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:6,76:0:2,0:24.8:1:30.4:1:1:0:60:81:1:0:0.1 0/1:103:2:1,1:5,96:0.0194:1,2:16.5:1:24:1:0.11365:17.61:60:4:0.0194:0:1 -18 48603247 . G GT 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.16449;LSEQ=GAGCAGTAATAGAAATTAAA;RSEQ=TTTTTTTTTACTGGGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:0,3:1,34:0.0789:1,0:12.7:1:30.7:1:1:0:60:6:0.0789:0.0263:0.3 0/1:44:4:0,4:1,38:0.0909:1,0:17.8:1:30.8:1:1:0:57.5:8:0.0909:0.0227:0.5 -18 48603403 . T C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=ATTATTATATTATACTGTTC;RSEQ=ATCTCCTCCTTTTTTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:16:1:33.7:1:1:0:60:6:1:0:1 0/0:2:0:0,0:0,2:0:0,0:27.5:1:28:1:1:0:60:4:1:0:0 -18 48604582 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.5023;SOR=Inf;LSEQ=AATGTAGGGAGGATGGGAAG;RSEQ=GATCACCCTGTCCCTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:121,31:0:2,0:24:1:30.2:1:1:0:60:75:1:0:0 0/1:181:2:1,1:149,29:0.011:2,2:5.5:1:30.5:1:0.30633:5.06864:60:4:0.0112:0:1 -18 48604586 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50284;SOR=Inf;LSEQ=TAGGGAGGATGGGAAGAGAT;RSEQ=ACCCTGTCCCTCTGATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:130,33:0:2,0:24.3:1:31.5:1:1:0:60:80.5:1:0:0 0/1:196:2:1,1:159,35:0.0102:2,2:17:1:26:1:0.33438:4.4934:60:4:0.0103:0:1 -18 48604591 . T C 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13157;SOR=Inf;LSEQ=AGGATGGGAAGAGATCACCC;RSEQ=GTCCCTCTGATGTCTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:137,35:0:2,0:25.4:1:31.2:1:1:0:60:344:1:0:0 0/1:213:4:2,2:167,42:0.0188:2,2:24.5:1:23:1:0.18956:3.94193:60:3:0.0142:0:1 -18 49294155 . A T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03492;SOR=Inf;LSEQ=TCATACCTTATTCCCAGCAA;RSEQ=GGGTTTCCTGCTTTGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:14,1:0:1,0:20.7:1:29.7:1:1:0:60:14:1:0:0.1 0/1:13:4:4,0:9,0:0.3077:0,0:33.5:1:30.5:1:1:0:60:8:0.3077:0:1 -18 49294236 . A G 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00078;SOR=Inf;LSEQ=TCTAGAAACCAGTTGCCAGC;RSEQ=CCTGCTGCTGCTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:40,17:0:2,0:20.3:1:30:1:1:0:59.8:114:1:0:0.2 0/1:82:13:8,5:46,22:0.1585:2,2:22.7:1:29.9:1:0.75137:1.30234:60:26:0.1585:0:1.3 -18 49294237 . CCTG C 82 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.32012;SOR=0.44949;LSEQ=CTAGAAACCAGTTGCCAGCA;RSEQ=CTGCTGCTGCTGCTGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:6:4,2:38,19:0.0952:2,2:16.8:1:31.8:1:1:1:58.3:12:0.0984:0.0476:0.3 0/1:89:4:3,1:54,30:0.0449:2,2:23.8:1:30.1:1:1:1.66:53.8:8:0.0471:0.0225:1.3 -18 49294253 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.64022;SOR=2.19914;LSEQ=AGCACCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:1:0,1:48,30:0.0127:2,0:1:0:26:0:0.39241:0:60:2:0.0133:0:1 0/1:109:3:2,1:61,45:0.0275:2,2:27:1:30.7:1:1:1.47:60:6:0.0278:0:1.7 -18 49294256 . C T 78 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.08321;SOR=Inf;LSEQ=ACCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGCTGCTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:50,30:0:2,0:23.8:1:31.1:1:1:0:59.9:25.667:1:0:0.2 0/1:123:6:4,2:65,50:0.0488:2,2:32.3:1:30.5:1:0.69872:1.53:51.5:12:0.0504:0:3.2 -18 49294265 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51674;SOR=Inf;LSEQ=TGCTGCTGCTGCTGTTGCTG;RSEQ=TGTTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:55,34:0:2,0:25.3:1:31.1:1:1:0:59.9:21.25:1:0:0.2 0/1:132:2:2,0:68,61:0.0152:2,0:41.5:1:30:0:0.49853:0:60:4:0.0157:0:4 -18 51274616 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.69183;LSEQ=CAAAAAAAATTCCACAACAG;RSEQ=TGTTGTGAATCTTTTAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:43.3:1:30.3:1:1:0:60:6:0.5:0:1 0/1:5:2:2,0:3,0:0.4:0,0:49:1:27:1:1:0:60:4:0.4:0:1 -18 51274758 . C A 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8965;SOR=0.94623;LSEQ=TTCTTAGTTCAGAAGTGAAA;RSEQ=AGCTATTTTTTTTACACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:61:45,16:26,18:0.581:2,2:24.2:1:30:1:0.14044:1.93:60:122:0.5865:0:1.1 1/0:141:80:50,30:40,21:0.5674:2,2:26.7:1:29.6:1:0.72709:1.14178:60:160:0.5714:0:1.3 -18 51274763 . AT A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.38461;SOR=3.2801;LSEQ=AGTTCAGAAGTGAAACAGCT;RSEQ=TTTTTTTACACTTTCCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:1:1,0:76,45:0.0082:2,0:17:0:33:0:1:0:60:2:0.0082:0:1 0/1:151:4:2,2:88,59:0.0265:2,2:21.3:1:24.7:1:1:1.48744:60:3:0.0201:0.0132:0.8 -18 51274836 . T C 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41065;SOR=1.24869;LSEQ=GATTTGAGAATTTCTCTCAT;RSEQ=CAGTGCTTAATAAACTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:42:18,24:52,65:0.2642:2,2:28:1:31.5:1:1:1.06627:60:84:0.2642:0:1.2 0/1:197:61:24,37:66,68:0.3096:2,2:27.6:1:30.9:1:0.21781:1.49322:60:122:0.3112:0:1.3 -18 51274843 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50403;SOR=Inf;LSEQ=GAATTTCTCTCATTCAGTGC;RSEQ=TAATAAACTGAGGGGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:67,92:0:2,0:24.2:1:30.5:1:1:0:60:158:1:0:0.5 0/1:196:2:1,1:87,107:0.0102:2,2:29.5:1:31:1:1:1.23:60:4:0.0104:0:2.5 -18 51274997 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTCTAATGAAAATGTAAGCG;RSEQ=GTTGGCCTCATATTGACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:29.5:1:29.9:1:1:0:60:7:1:0:0.8 0/1:8:2:1,1:0,6:0.25:0,2:29.5:1:28.5:1:0.25:0:60:4:0.2857:0:1 -18 51275014 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=GCGGGTTGGCCTCATATTGA;RSEQ=TAGCAGTTACTGCCACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:28.8:1:30:1:1:0:60:8:0.5714:0:1.5 0/0:6:0:0,0:0,6:0:0,0:28.5:1:31:1:1:0:60:12:1:0:0.5 -18 52896000 . A G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TCTACTGTCTGCCACTGCTC;RSEQ=AGACTGGCGTGCCCATCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:43,1:0:1,0:26.2:1:30.8:1:1:0:60:88:1:0:0.1 0/1:29:10:9,1:19,0:0.3448:1,2:30.3:1:25.9:1:0.34483:0:60:4:0.2963:0:2.1 -18 52896003 . A G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ACTGTCTGCCACTGCTCAAG;RSEQ=CTGGCGTGCCCATCTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:45,1:0:1,0:26.5:1:30.3:1:1:0:60:45:1:0:0.1 0/1:32:11:10,1:21,0:0.3438:1,2:28.8:1:31.4:1:0.34375:0:60:22:0.3438:0:2 -18 52896063 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23554;SOR=Inf;LSEQ=TCACGAGCTCTGCAAGGAGG;RSEQ=TGGCCTGCACTGACCTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:110,4:0:1,0:21.7:1:31.5:1:1:0:60:27.5:1:0:0.1 0/1:108:2:1,1:97,9:0.0185:2,2:14:1:32:0:0.1774:10.27733:60:4:0.0189:0:1.5 -18 52896509 . G A 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAAGATATTTGGTTTTCTC;RSEQ=CAGACATTAAACCCAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:25.2:1:28.8:1:1:0:60:10:0.8333:0:1 1/1:2:2:1,1:0,0:1:0,2:28.5:1:28.5:1:1:0:60:4:1:0:1 -18 53303101 . C G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGGAGAGGCACCTGTG;RSEQ=TATTTTCTCCAGCCTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:27.2:1:32.3:1:1:0:60:18:1:0:1 1/1:21:21:17,4:0,0:1:0,2:29.1:1:31:1:1:0:60:42:1:0:1.1 -18 53303583 . T TA 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AATAAAGACCTTGGGATGGT;RSEQ=AAAAAAAAAAAGAAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31.5:1:32:0:1:0:60:4:1:0:0 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 53630757 . A G 47 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGCTAGATTAGGCCAC;RSEQ=GGATAAGGCTTGGAAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:32.3:1:23.5:1:1:0:60:3:1:0:1 1/1:2:2:2,0:0,0:1:0,0:11:1:31.5:1:1:0:60:4:1:0:2 -18 53631042 . C G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19729;LSEQ=GGCAGATTCATATTTTTGAG;RSEQ=TAAAAGCATAACTGTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:413:365:159,206:24,24:0.8838:2,2:26.9:1:31.5:1:0.44113:1.29477:60:72:0.8824:0:1.5 1/0:552:331:145,186:90,131:0.5996:2,2:25.6:1:30.9:1:0.48349:1.13:60:164.5:0.6004:0:1.4 -18 53631064 . AT A 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.25022;SOR=0.31019;LSEQ=AAAAGCATAACTGTGGCAGC;RSEQ=TTTTTCTTTCTTTGAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:5:2,3:79,118:0.0138:2,2:32.4:1:30.8:1:1:1.00422:60:10:0.014:0:0.6 0/0:463:2:1,1:136,241:0.0043:2,2:15.5:1:28.5:1:1:1.77:60:4:0.0044:0:0 -18 53631065 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0;SOR=0.28663;LSEQ=AAAGCATAACTGTGGCAGCA;RSEQ=TTTTTCTTTCTTTGAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:158:60,98:79,118:0.4365:2,2:25.2:1:32.1:1:0.74295:1.09323:60:157:0.4385:0:2 0/1:463:84:33,51:136,241:0.1814:2,2:28.6:1:31:1:0.61719:1.15:60:83:0.182:0:2 -18 54917169 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50089;SOR=Inf;LSEQ=CATCCAAAGAAGTTGGCTGA;RSEQ=AAACAATATTGTTAAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:99,66:0:2,0:23.7:1:31.5:1:1:0:60:54:1:0:0.5 0/1:189:2:1,1:97,90:0.0106:2,2:29:1:28.5:1:1:1.07733:60:4:0.0109:0:1.5 -18 54917232 . G C 230 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.57084;SOR=1.14447;LSEQ=GTAAAATGTGTGCTCAGAGA;RSEQ=AGCGGGGCCATCCATCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:207:154:79,75:26,27:0.744:2,2:25.9:1:31.9:1:0.87365:1.09:60:76:0.7415:0:1.2 1/0:212:163:69,94:22,27:0.7689:2,2:25.9:1:31.3:1:0.74554:1.10949:60:53.333:0.7656:0:1.2 -18 54917264 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49852;SOR=Inf;LSEQ=CCATCATGAGTGAGAAGCCT;RSEQ=ATTTACAGAGACAACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:68,98:0:2,0:24.2:1:31.2:1:1:0:60:54.333:1:0:0.7 0/1:168:2:1,1:69,97:0.0119:2,2:16.5:1:31:1:1:1.40:60:4:0.0121:0:2 -18 55178817 . TA T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAACTTAAAGTATAATAA;RSEQ=AAAAAAAAGAATTCATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:34:1:32.5:1:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 55178937 . T C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00915;SOR=10.66038;LSEQ=TGAAAGGGCAAGAGTTTCTA;RSEQ=GGAAAAGGCCCCCAAATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:6,0:14,0:0.3:1,0:25.5:1:32.3:1:1:0:60:12:0.3:0:2 1/1:12:10:9,1:2,0:0.8333:0,2:26.3:1:31.6:1:1:0:60:20:0.8333:0:2.7 -18 55178959 . A G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=17.44582;LSEQ=GAAAAGGCCCCCAAATTAGA;RSEQ=GGAGCATGAGGTTTAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:4,0:20,0:0.1667:1,0:35.8:1:33.5:1:1:0:60:8:0.1667:0:2.5 1/0:24:19:18,1:5,0:0.7917:0,1:23.8:1:32.2:1:1:0:60:38:0.7917:0:2.4 -18 55179004 . G A 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.97219;LSEQ=GGAAACATGAGAATGGGAAG;RSEQ=GTCAATCCCAGGGAGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:8:6,2:46,5:0.1356:2,2:15.6:1:29.5:1:0.23831:2.98981:60:16:0.1379:0:1.5 1/0:73:48:42,6:21,4:0.6575:2,2:22:1:28.4:1:0.72744:1.33:60:23:0.6765:0:1.5 -18 55179042 . C T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51535;SOR=Inf;LSEQ=GGGATCCAGGGACCATCCCA;RSEQ=AAAGAGCAACGAGGTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:85,25:0:2,0:27.4:1:32:1:1:0:60:109:1:0:0.1 0/1:160:2:1,1:117,41:0.0125:2,2:39:0:26.5:1:0.45731:2.83151:60:4:0.0128:0:1.5 -18 55179134 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08916;SOR=0;LSEQ=GGGACCTGAGCCTCTGTTTT;RSEQ=AGTCTTGTAGACCTAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:123,135:0.0115:2,2:11:1:28.7:1:1:1.8182:60:6:0.0116:0:1.3 0/0:322:0:0,0:141,180:0:2,0:23:0:14:0:1:0:60:0:0:0:3 -18 55179142 . T G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.73949;LSEQ=AGCCTCTGTTTTGAGTCTTG;RSEQ=AGACCTAGCTTTCTGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:26:10,16:112,127:0.0981:2,2:24.5:1:31.3:1:0.5351:1.40921:60:52:0.0992:0:1.3 1/0:311:219:97,122:38,54:0.7042:2,2:26.3:1:30.3:1:0.7071:1.13:60:30.286:0.6974:0:1.2 -18 55179209 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.23654;SOR=0;LSEQ=TGATGATGAGTGAGGTGGAG;RSEQ=AGCAAGGATGCCCCTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:45,105:0.0132:2,2:41:1:29.5:1:0.51507:2.32:60:4:0.0133:0:2.5 0/0:160:0:0,0:45,115:0:2,0:21.8:1:30.5:1:1:0:60:39:1:0:0.9 -18 55179225 . T C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=13.66121;LSEQ=GGAGGAGCAAGGATGCCCCT;RSEQ=CTCATGGGAAAGCTCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:12:4,8:24,84:0.0992:2,2:22.4:1:31.3:1:0.47152:1.74:60:24:0.1008:0:1.7 1/0:96:58:10,48:10,28:0.6042:2,2:22.8:1:31:1:0.31283:1.7043:60:116:0.6105:0:1.4 -18 55179231 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50988;SOR=0;LSEQ=GCAAGGATGCCCCTTCTCAT;RSEQ=GGAAAGCTCTGAGACATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:20,84:0.0189:2,2:43:1:29.5:1:0.35849:4.12:60:4:0.019:0:1 0/0:77:0:0,0:15,62:0:2,0:23.8:1:30.2:1:1:0:60:154:1:0:0.8 -18 55179269 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCAGACACCGTGTCCCCT;RSEQ=AGTGCTCATGCTGCTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:5,48:0.0364:2,2:10:1:28.5:1:0.20808:8.86:60:4:0.037:0:1 0/0:27:0:0,0:2,25:0:2,0:23.1:1:30.6:1:1:0:60:26:1:0:0.7 -18 55466451 . C G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.13994;LSEQ=ATGAGGCCTGCGTTCCAACC;RSEQ=AGGTCAAAAGACTCCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:25:23,2:21,0:0.5435:1,2:17.9:1:29.5:1:0.49275:0:60:24:0.5333:0:1.9 0/1:50:7:6,1:42,1:0.14:1,2:21.1:1:30.6:1:0.26286:6.55744:60:14:0.14:0:1.9 -18 55466490 . T A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.10472;LSEQ=GCTGGCAACCTCTGTTTCAC;RSEQ=GCTGCCTCTGGACTGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:58:46,12:30,6:0.617:2,2:26.6:1:30.8:1:0.78899:1.30074:60:116:0.617:0:1.5 0/1:133:19:16,3:85,29:0.1429:2,2:21.6:1:30.9:1:0.56251:1.81:60:38:0.1462:0:1.3 -18 55466495 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50891;SOR=Inf;LSEQ=CAACCTCTGTTTCACTGCTG;RSEQ=CTCTGGACTGCTTGCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:84,23:0:2,0:26.3:1:31.9:1:1:0:60:214:1:0:0.8 0/1:144:2:1,1:106,34:0.0139:2,2:10.5:1:29.5:1:0.43352:3.08701:60:4:0.0143:0:1 -18 55466510 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25658;SOR=Inf;LSEQ=TGCTGCCTCTGGACTGCTTG;RSEQ=AGGGACCAGTTATGAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:106,42:0:2,0:24.2:1:31.9:1:1:0:60:73:1:0:0.8 0/1:184:3:1,2:128,53:0.0163:2,2:15:1:26.3:1:0.21324:4.78318:60:6:0.0165:0:1.3 -18 55466516 . C T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32146;SOR=0.25423;LSEQ=CTCTGGACTGCTTGCAGGGA;RSEQ=CAGTTATGAAACATATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:1,2:116,51:0.0175:2,2:18.7:1:30:1:0.22954:4.50381:60:6:0.0178:0:1.7 0/0:222:1:0,1:147,73:0.0045:2,0:1:0:24:0:0.33484:0:60:2:0.0045:0:2 -18 55466518 . A G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18635;SOR=0;LSEQ=CTGGACTGCTTGCAGGGACC;RSEQ=GTTATGAAACATATTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:121,55:0.0112:2,2:46:0:31.5:1:0.53145:2.1893:60:4:0.0115:0:2 0/0:235:0:0,0:157,77:0:2,0:23.8:1:30:1:1:0:60:57.5:0.9957:0:0.4 -18 55466550 . T C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0576;SOR=0;LSEQ=TATTTCTCATTGTGGAAGGG;RSEQ=TGGGCAACAATTTATTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:2,1:147,113:0.0114:2,2:29.7:1:25.3:1:1:1.54:60:2:0.0077:0:2 0/0:418:0:0,0:242,175:0:2,0:23.5:1:29.2:1:1:0:60:68.5:1:0:0.5 -18 55466596 . A G 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.08572;LSEQ=AGTGCATTTATAAGTATCAA;RSEQ=GAAAGTACCAATATGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:291:258:116,142:14,19:0.8866:2,2:27.7:1:31.4:1:0.85366:1.11:60:63.5:0.8881:0:1.2 0/1:477:191:85,106:139,146:0.4004:2,2:26.5:1:31:1:0.39935:1.18684:60:190:0.4034:0:1.2 -18 55466664 . C A 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16628;SOR=Inf;LSEQ=GTTTTTTAAGAAAATGAGGC;RSEQ=GGGTGCGGTGGCTCACGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:22,68:0:2,0:22.7:1:30.5:1:1:0:60:180:1:0:0.6 0/1:168:5:3,2:48,113:0.0298:2,2:25.8:1:25.8:1:0.16955:3.50:60:4:0.0245:0:3.4 -18 55466668 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5323;SOR=Inf;LSEQ=TTTAAGAAAATGAGGCCGGG;RSEQ=GCGGTGGCTCACGCCTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:19,64:0:2,0:22.4:1:30:1:1:0:60:82:1:0:0.5 0/1:142:2:1,1:41,99:0.0141:2,2:37.5:1:31:0:0.50554:2.40:60:4:0.0146:0:6 -18 55466670 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53353;SOR=Inf;LSEQ=TAAGAAAATGAGGCCGGGTG;RSEQ=GGTGGCTCACGCCTATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:19,62:0:2,0:22:1:29.9:1:1:0:60:39.5:1:0:0.5 0/1:140:2:1,1:40,98:0.0143:2,2:35.5:1:31:1:0.50144:2.43:60:4:0.0146:0:6 -18 55466680 . C T 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29054;SOR=Inf;LSEQ=AGGCCGGGTGCGGTGGCTCA;RSEQ=GCCTATAATCCCAGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:12,58:0:2,0:20.6:1:30:1:1:0:60:69:1:0:0.4 0/1:115:3:2,1:28,84:0.0261:2,2:26.7:1:31.7:1:0.1662:5.89:57.3:6:0.0265:0:6 -18 55466682 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52706;SOR=Inf;LSEQ=GCCGGGTGCGGTGGCTCACG;RSEQ=CTATAATCCCAGCACTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:11,54:0:2,0:21.4:1:30.7:1:1:0:60:64:1:0:0.3 0/1:107:2:1,1:27,78:0.0187:2,2:23.5:1:31:1:0.45671:2.85:60:4:0.0196:0:6 -18 55466685 . A G 67 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15523;SOR=Inf;LSEQ=GGGTGCGGTGGCTCACGCCT;RSEQ=TAATCCCAGCACTTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:11,55:0:2,0:19.9:1:30:1:1:0:60:132:1:0:0.3 0/1:102:4:2,2:23,74:0.0392:2,2:22:1:33.5:1:0.25532:3.17:55:8:0.0404:0:4.3 -18 55466751 . G GTA 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0054;SOR=0;LSEQ=CAGGAGTTTGAGACTAGCCT;RSEQ=GCCAACATGGTGAAACCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:0,9:0,14:0.375:1,0:25.8:1:29.7:1:1:0:60:18:0.375:0.0417:0.4 0/0:18:0:0,0:0,18:0:1,0:26.2:1:30.9:1:1:0:60:36:1:0:0.2 -18 56338678 . A C 79 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GCGCGGCTGGCGCGGCCAGC;RSEQ=GGCCAGGCTCCCCTCGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:13:0:31:0:1:0:60:2:1:0:0 1/1:6:6:4,2:0,0:1:0,2:13.7:1:30.7:1:1:0:60:12:1:0:1.2 -18 56338743 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGCTTCCTCCTCTGAGGG;RSEQ=CGTGCCGCGCTGCCAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:19.6:1:29.4:1:1:0:60:4:1:0:0.2 0/1:12:2:1,1:7,3:0.1667:2,2:38.5:1:30:1:1:2.16028:60:4:0.1818:0:1 -18 56338878 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59925;SOR=0.48092;LSEQ=GGGTCGCCGGCGAGGGCCAT;RSEQ=TCGCTGTTGGGGGACCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:66,66:0.0149:2,2:32.5:1:29:0:1:1:60:4:0.0153:0:1 0/0:277:2:1,1:136,139:0.0072:2,2:34.5:1:28:1:1:1.02:60:4:0.0072:0:1 -18 56338909 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11389;SOR=0;LSEQ=GGGACCCGCTACAGGCCCTG;RSEQ=CGCCCTCGGCCGCCCCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:64,70:0.0147:2,2:31:1:30:1:1:1.09:60:4:0.015:0:2 0/0:266:0:0,0:131,134:0:2,0:24:1:31.3:1:1:0:60:52:0.9962:0:0.4 -18 56338918 . G A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14272;SOR=0.19116;LSEQ=TACAGGCCCTGCCGCCCTCG;RSEQ=CCGCCCCCACGGGGCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:2,1:66,63:0.0227:2,2:11.7:1:28.7:1:1:1.90:60:6:0.0236:0:1 0/0:227:1:1,0:113,112:0.0044:2,0:1:0:26:0:1:0:60:2:0.0046:0:1 -18 56338920 . C G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13065;SOR=0;LSEQ=CAGGCCCTGCCGCCCTCGGC;RSEQ=GCCCCCACGGGGCCGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:65,62:0.0155:2,2:7:0:32:0:1:1.04802:60:4:0.0157:0:1.5 0/0:227:0:0,0:114,113:0:2,0:23.6:1:29.3:1:1:0:60:55.75:1:0:0.4 -18 56338924 . C A 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.36607;SOR=0.39236;LSEQ=CCCTGCCGCCCTCGGCCGCC;RSEQ=CCACGGGGCCGCTGCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:3:2,1:65,60:0.0234:2,2:11.3:1:30.3:1:1:1.84:60:6:0.024:0:1 0/0:215:2:1,1:109,104:0.0093:2,2:11.5:1:26.5:1:1:1.04787:60:4:0.0096:0:1.5 -18 56338946 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11614;SOR=0;LSEQ=CACGGGGCCGCTGCTCGCCC;RSEQ=TCCGGCCGGCGCGACCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:61,43:0.0187:2,2:24.5:1:29.5:1:1:1.41382:60:4:0.0189:0:2 0/0:206:0:0,0:113,90:0:2,0:17.1:1:30.7:1:1:0:60:202:0.9902:0:0.3 -18 56338983 . G A 57 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71685;SOR=0.63712;LSEQ=CTCAACCGCCTGCGGGAGCC;RSEQ=CTGCTGCGGAGGCTCAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:4:3,1:94,58:0.0253:2,2:23:1:17.8:1:1:1.84:60:0.333:0.0066:0:0.8 0/1:246:4:3,1:138,103:0.0163:2,2:20.3:1:28.5:1:0.6391:2.23:60:8:0.0164:0:1 -18 56338990 . C T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.93926;LSEQ=GCCTGCGGGAGCCGCTGCTG;RSEQ=GGAGGCTCAGCGAGCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:0,1:106,72:0.0056:2,0:1:0:26:0:0.40782:0:60:2:0.0056:0:1 0/1:278:3:1,2:155,120:0.0108:2,2:13:1:28:1:0.58361:2.57465:60:6:0.0109:0:1 -18 56339018 . C T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65363;SOR=2.54139;LSEQ=CAGCGAGCTCCTGGATCAGG;RSEQ=GCCCGAGGGCCGGGGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:0,1:128,118:0.004:2,0:1:0:15:0:0.48178:0:60:0:0:0:1 0/1:397:4:1,3:206,187:0.0101:2,2:11.3:1:27.3:1:0.35295:3.29566:60:8:0.0103:0:1 -18 56339066 . G A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41662;SOR=3.06813;LSEQ=GGCGGAGCTGGCGGGGAGTC;RSEQ=CGGGCGCCTCCGCCTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:97,131:0.0044:2,0:1:0:26:0:0.42795:0:60:2:0.0045:0:1 0/1:376:5:5,0:167,204:0.0133:2,0:10:1:23.2:1:0.0194:0:60:4:0.0109:0:1.2 -18 56339103 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52062;SOR=Inf;LSEQ=AGGTGAGCTCAGGGCCGCGG;RSEQ=AGGCCGGGCGCGCGGGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:43,71:0:2,0:19.2:1:31.8:1:1:0:60:27.5:1:0:0.3 0/1:175:2:1,1:69,103:0.0114:2,2:29:0:29:1:1:1.49:60:4:0.0121:0:2 -18 56339139 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.53939;SOR=Inf;LSEQ=GTCGAGCGGGGTGGGCTGCG;RSEQ=TGGGGAGGTGGGGGCGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:13.6:1:31.2:1:1:0:60:38:1:0:0.2 0/1:36:2:1,1:10,24:0.0556:2,2:9:0:30:1:0.52381:2.34:60:4:0.0571:0:1 -18 56348161 . CAAA C 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=26.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GACAGAGCGAGACTCCGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:9.2:1:30.2:1:1:0:42:10:1:0:2.2 1/0:4:2:2,0:1,1:0.5:2,0:18.5:1:30.3:1:1:0:50:4:0.5:0.25:1.5 -18 56348181 . A T 27 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=26.000;MSILEN=1;SSF=0.07143;SOR=Inf;LSEQ=CAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAAATAATCATGGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:0:1,0:11.9:1:31.5:1:1:0:54:30:1:0:1.7 0/1:6:2:2,0:3,1:0.3333:2,0:24.5:1:27.5:1:1:0:60:4:0.3333:0:1.5 -18 56348724 . A G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11986;SOR=0.46205;LSEQ=GGTTGAAGCAAATGCAATGC;RSEQ=TGAATATTGGTTGGATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:16:0,16:0,49:0.2462:1,1:19.5:1:32.3:1:1:0:60:32:0.25:0:1 0/1:69:9:0,9:0,60:0.1304:1,0:24.6:1:30.7:1:1:0:60:18:0.1304:0:1.1 -18 56363494 . A T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=GATTTATGACAAAGATAAAT;RSEQ=TGCAAGTTATTTCTAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:52,0:0:1,0:19.5:1:28.5:1:1:0:60:51:1:0:0 0/1:39:11:11,0:28,0:0.2821:1,0:17.3:1:30.3:1:1:0:60:22:0.2821:0:1 -18 56363765 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25193;SOR=Inf;LSEQ=TTCTTCCAAGGAGAGAGAAT;RSEQ=ATAGAGAATTAATTAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:43,201:0:2,0:23.6:1:30.6:1:1:0:60:19.333:1:0:0.1 0/1:279:3:2,1:59,215:0.0108:2,2:12:1:27.3:1:0.12308:7.22:60:6:0.0109:0:1 -18 56363908 . A C 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03492;SOR=Inf;LSEQ=CAGAATTGTCTCATGAAAAC;RSEQ=TTGTAAACAATAATGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:0,15:0:1,0:18.3:1:31.3:1:1:0:60:30:1:0:0.4 0/1:13:4:0,4:0,9:0.3077:0,0:18.8:1:33.5:1:1:0:60:8:0.3077:0:1.3 -18 56367946 . TCATC T 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.18765;SOR=Inf;LSEQ=CAAAATTTCACATAGGTACT;RSEQ=CATTATAATGTCAACCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:0,70:0:1,0:26.2:1:31.7:1:1:0:60:22.333:1:0:0 0/1:54:2:0,2:2,50:0.037:1,0:34:1:34:0:1:0:60:4:0.037:0:0 -18 56368000 . CT C 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.87198;LSEQ=GATCCATGTGTTTTGTCTTT;RSEQ=TTTTTTTTTAATTTAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:0,4:0,29:0.1212:1,0:37:1:33:1:1:0:60:8:0.125:0:0 0/1:28:3:2,1:2,23:0.1071:2,2:22.3:1:33.3:1:0.04518:18.20:60:6:0.1071:0:0.3 -18 56377000 . A G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.70476;SOR=0.59575;LSEQ=GGCTTATATGTAAAATGTCA;RSEQ=ATAGTATTGCATGAAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:7:3,4:19,12:0.1842:2,2:20.1:1:31.7:1:0.42501:2.06868:60:14:0.1892:0:1 0/1:17:2:0,2:9,6:0.1176:2,0:23:1:32:0:0.20588:0:60:4:0.1176:0:1 -18 56378058 . AT A 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00062;SOR=0.42534;LSEQ=GCATGTGTTGGTTTGCCAAC;RSEQ=TATCTCTATGATATTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:52:43,9:149,21:0.2342:2,2:27.3:1:31.4:1:0.36024:1.4822:60:104:0.2374:0.027:0 0/1:261:30:25,5:202,29:0.1149:2,2:24.9:1:30.5:1:0.56303:1.39116:60:60:0.1163:0.0307:0.1 -18 56378529 . C T 74 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAGAAAGATAGGTGGCTA;RSEQ=GTGATCATGGATATTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:14.5:1:28.8:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 56383323 . T C 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.22866;SOR=1.39488;LSEQ=CATTGGGACCAAATGTTTTA;RSEQ=TTTTTTGTATCTGTAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:31:0,31:1,95:0.2441:1,1:23.6:1:32:1:1:0:60:30:0.2419:0:1.1 0/1:148:46:1,45:1,101:0.3108:1,1:24:1:32.6:1:0.52648:2.23:60:45:0.3061:0:1.2 -18 56390265 . C CT 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.88614;SOR=1.08315;LSEQ=CTTCTTTAAACACCCCCTTT;RSEQ=TTTTTTTTTCAAAGCGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:22:16,6:415,174:0.0359:2,2:23.6:1:30.7:1:1:1.12:60:44:0.0365:0.0114:0.3 0/1:747:29:22,7:473,245:0.0388:2,2:24.4:1:30.3:1:0.31992:1.63:60:58:0.0394:0.0054:0.2 -18 56390553 . A G 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATACAAGTTAGGTTAAGA;RSEQ=TTGAAAATCAGATAAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:205:205:14,191:0,0:1:0,2:27.2:1:31.8:1:1:0:60:67.333:1:0:1.1 1/1:209:209:19,190:0,0:1:0,2:24.4:1:31.2:1:1:0:60:103.5:1:0:1 -18 56400351 . C T 64 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGTTTCACCACGTTGGC;RSEQ=AGGCTGGTTTCGAACCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:29.5:1:32:1:1:0:54:8:0.3636:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 56400547 . T G 168 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04521;SOR=0.56686;LSEQ=AAAATTAAAGTCAAGGTTTT;RSEQ=CTACAAAAAGTTATGCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:41:39,2:146,7:0.2113:1,1:23.7:1:31.5:1:1:1.06923:60:19.5:0.2063:0:1.1 0/1:205:27:25,2:170,8:0.1317:1,2:28.3:1:31.9:1:0.62401:1.69478:60:54:0.133:0:1.1 -18 56400826 . T C 246 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24279;SOR=1.16015;LSEQ=GGTAAGTTTTCTAATCTTTA;RSEQ=TAAAGAATTGTTGGAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:152:40,112:132,285:0.2671:2,2:25.6:1:32.2:1:0.25649:1.29626:60:304:0.2695:0:1.1 0/1:757:225:72,153:188,342:0.2972:2,2:23.1:1:31.6:1:0.40248:1.16789:60:224:0.2979:0:1.1 -18 56400852 . G A 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=AATTGTTGGAGTTAAATATC;RSEQ=ACCATGACAAACTAGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:64,284:0:2,0:25.6:1:30.8:1:1:0:60:86:0.9971:0:0.3 0/1:432:18:5,13:88,326:0.0417:2,2:16.1:1:29.6:1:0.55736:1.42:60:36:0.0421:0:1.1 -18 56401758 . C T 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06827;SOR=Inf;LSEQ=TCACTGCTCCTGGGCTCAAG;RSEQ=GATCCTCCTGCCTCAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:0,84:0:1,0:21.6:1:30:1:1:0:60:83:1:0:0 0/1:107:5:0,5:2,100:0.0467:1,0:15.2:1:30.4:1:1:0:60:10:0.0472:0:1 -18 56402297 . ACC A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=9.000;MSILEN=1;SSF=1;SOR=1.48109;LSEQ=ACAGTCCCCACGCTGTCCCC;RSEQ=CCCCCCCAGCCTCTGGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:43:43,0:2,0:0.9556:0,1:25.9:1:32.5:1:1:0:60:86:0.9556:0.1333:0 1/1:33:32:32,0:0,0:0.9697:0,1:24.6:1:31.9:1:1:0:60:64:1:0.1515:0 -18 56406968 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTGCAGGTTTCAGACT;RSEQ=GCACCGCCACAATTCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 56409002 . A C 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.85006;SOR=0.90748;LSEQ=GTGAATAAATGATACTGAGA;RSEQ=TATAACCTGATAATGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:27:26,1:80,1:0.25:1,1:26.1:1:31.7:1:0.43925:3.03816:60:54:0.25:0:1.2 0/1:56:13:12,1:43,0:0.2321:1,1:23.2:1:31:1:0.23214:0:60:26:0.2321:0:1 -18 56409291 . G A 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00889;SOR=Inf;LSEQ=AGATCTACAATATACTTAAC;RSEQ=TTAAATCATAAAGTTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:103,312:0:2,0:22.5:1:31.2:1:1:0:60:50.875:1:0:0.1 0/1:485:8:3,5:125,352:0.0165:2,2:19:1:28.9:1:0.4404:1.69:60:16:0.0165:0:1 -18 56411493 . A T 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAAGCAAAAGAAATGCTA;RSEQ=CTATATTCTCCTCCATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:219,20:0:2,0:23.1:1:30.3:1:1:0:60:118.5:1:0:0 0/1:289:59:53,6:195,35:0.2042:2,2:23.4:1:30.7:1:0.40546:1.58:60:118:0.2049:0:1.1 -18 56411823 . A AAT 25 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.4983;SOR=0;LSEQ=TTGATGGTAAATATAAAGGA;RSEQ=ATATATATATTTATATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:0,2:0,139:0.0142:1,0:38:0:25.3:1:1:0:60:4:0.0143:0:3 0/0:137:0:0,0:0,137:0:1,0:22.4:1:30.6:1:1:0:60:136:1:0:0 -18 56412690 . G A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0.37796;LSEQ=AGAGCTCACTTTACTTTTTA;RSEQ=ATGGCTTAGTACAGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:14,0:1,0:0.9333:0,1:19.6:1:30.8:1:1:0:60:28:0.9333:0:1.2 1/1:6:5:5,0:1,0:0.8333:0,0:26.8:1:31:1:1:0:60:10:0.8333:0:1 -18 56412784 . C T 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04474;SOR=0.40013;LSEQ=TTTGGGATTACCAAAATTCA;RSEQ=GAGAGGCCAGAATTCACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:30:30,0:48,1:0.3797:1,1:24.3:1:31.5:1:1:0:60:60:0.3896:0:1.2 0/1:46:9:8,1:36,1:0.1957:1,2:31.6:1:30:1:0.35652:4.30117:60:18:0.1957:0:1 -18 56412882 . A AT 178 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.09967;SOR=1.43374;LSEQ=TTCATTATTAACAGTCCCTA;RSEQ=TTTTTTTTTTTACAGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:38:31,7:276,87:0.0931:2,2:27.8:1:31.4:1:0.5482:1.39:60:76:0.096:0:0.3 0/1:553:71:55,16:355,122:0.1284:2,2:23.9:1:29:1:0.66139:1.18:59.6:34.5:0.1283:0.0217:0.2 -18 56412894 . A T 47 q23 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01393;SOR=0;LSEQ=AGTCCCTAATTTTTTTTTTT;RSEQ=CAGGATCTAGATATTGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:3,2:341,151:0.01:2,2:10.6:1:20.4:1:0.64578:1.5042:60:1.5:0.0062:0:1.8 0/0:670:0:0,0:459,211:0:2,0:23.4:1:27.6:1:1:0:60:36.222:1:0:0.1 -18 56413121 . G C 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04882;SOR=0.50462;LSEQ=TATGCTGCCTTATTATTAAA;RSEQ=TAGAGATAACCAGTCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:28:0,28:3,108:0.2014:1,1:26:1:33.1:1:1:0:60:56:0.2014:0:1 0/1:142:16:1,15:1,125:0.1127:1,1:25.6:1:32.1:1:0.21337:8.10:60:32:0.1127:0:1.3 -18 56413217 . G T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73966;SOR=0.69636;LSEQ=TTATGTGTGCTTACCCTCCA;RSEQ=AATGCTAAAAAATTAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:11:0,11:1,32:0.25:1,0:27.4:1:28.7:1:1:0:60:22:0.2558:0:1 0/1:16:3:0,3:0,13:0.1875:1,0:14.7:1:29.7:1:1:0:60:6:0.1875:0:1.3 -18 56413237 . CATT C 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.26412;LSEQ=GAATGCTAAAAAATTAGTAA;RSEQ=AGAGTATATTCTTTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:22:0,22:0,4:0.8462:0,1:22.6:1:32:1:1:0:60:21:0.84:0.1538:0.4 1/1:8:7:0,7:0,1:0.875:0,0:18.7:1:31.9:1:1:0:60:14:0.875:0.25:0.1 -18 57560606 . T G 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01213;SOR=0.72243;LSEQ=ACTTTCTTGGCTGACAGAGG;RSEQ=TCTAAGCCTATTCCCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:145:62,83:219,313:0.2142:2,2:25:1:31.7:1:0.77564:1.07:60:71.5:0.2138:0:1.1 0/1:991:163:74,89:374,454:0.1645:2,2:24.2:1:31:1:1:1.01:60:80.5:0.165:0:1.2 -18 57567451 . C T 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AAGAACGCTCAACCGAGCCC;RSEQ=GCGCGGGCTCCAGCAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:0:0,0:207,353:0:2,0:26:1:29.8:1:1:0:60:45.667:0.9982:0:0.1 0/1:829:58:25,33:316,453:0.07:2,2:22.5:1:29.9:1:0.78323:1.09:60:116:0.0713:0:1.1 -18 57567510 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17201;SOR=0;LSEQ=GAAGACCCAGGCCGGGCGGG;RSEQ=TCGGGGCCGGGGTCGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:29,158:0.0106:2,2:35.5:1:27.5:1:0.29298:5.37:60:4:0.0107:0:1 0/0:266:0:0,0:54,212:0:2,0:20.6:1:30.9:1:1:0:60:65.5:1:0:0.3 -18 57568601 . C T 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68653;SOR=1.05449;LSEQ=TCAGGGCTTCCAGTGTCGGA;RSEQ=GCTGAATGGTATTTGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:233:95,138:106,151:0.4745:2,2:23.7:1:30.5:1:0.92697:1.01969:60:232:0.4754:0:1.1 0/1:779:380:150,230:168,230:0.4878:2,2:24.3:1:29.8:1:0.46589:1.11984:60:94:0.4896:0:1.1 -18 57568693 . A G 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08835;SOR=1.78616;LSEQ=ATGTAAATACTTCCCAACAT;RSEQ=TTTGATCTTGTAGCCCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:22:1,21:1,60:0.2651:1,1:28:1:32.2:1:0.46224:2.81:60:44:0.275:0:1.2 0/1:107:42:1,41:2,62:0.3925:1,1:21.2:1:31:1:1:1.31921:60:84:0.4:0:1.1 -18 57570044 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51678;SOR=Inf;LSEQ=AGTTTTCTCAGGAGGTGCAC;RSEQ=TTTCATCAATTTGAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:15,85:0:2,0:22.3:1:31.4:1:1:0:60:99:1:0:0.1 0/1:148:2:1,1:23,123:0.0135:2,2:31:1:28.5:1:0.29895:5.26:60:4:0.0135:0:1 -18 57571885 . A T 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51999;SOR=1.23779;LSEQ=ACCTCTGCCTCCTGGGTCTA;RSEQ=GTGATTCTCGTGCTAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:30:0,30:0,39:0.4348:1,1:26.2:1:27.3:1:1:0:59:6.5:0.4:0:1.1 0/1:84:41:2,39:1,42:0.4881:1,1:26.8:1:29.2:1:0.61145:2.13:60:12.667:0.475:0:1.2 -18 57571922 . A C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19814;SOR=Inf;LSEQ=AGCCTCCCCCACACGCCACC;RSEQ=CACTGGGTAATTTTTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,43:0:1,0:21.4:1:29.3:1:1:0:60:42:1:0:0.6 0/1:35:2:0,2:2,31:0.0571:2,0:14.5:1:28:1:1:0:60:4:0.0588:0:2 -18 57572213 . A G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGATTGCTTCATCTGAGGTT;RSEQ=GTCATGTGCAAAAGTAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:28:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:32:0:1:0:60:4:1:0:1 -18 59254083 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50013;SOR=0;LSEQ=GGGAAAAGTCAAGTTATTAT;RSEQ=AATACATTTCCTGATTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:118,56:0.0114:2,2:26.5:1:30.5:1:0.54409:2.09746:60:4:0.0114:0:1 0/0:157:0:0,0:99,58:0:2,0:27.1:1:28.4:1:1:0:60:51.333:1:0:0.4 -18 59254138 . C G 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10558;SOR=1.35598;LSEQ=TCTGAAGCTAAATTACAGAG;RSEQ=TTATATTTTGGATAAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:85:45,40:82,75:0.3512:2,2:26.9:1:31.2:1:1:1.03:60:170:0.3527:0:1.4 0/1:281:119:67,52:83,79:0.4235:2,2:23:1:30.9:1:0.46789:1.23:60:238:0.4281:0:1.7 -18 59254190 . A T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.18117;LSEQ=TATAAACAATGATTTGGCAC;RSEQ=TTTGTTTAATTCCCCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:93:32,61:34,69:0.4745:2,2:25.5:1:30.4:1:0.8803:1.06:60:92:0.4718:0:2.4 0/1:257:36:13,23:96,125:0.1401:2,2:30.1:1:30.5:1:0.4696:1.35718:60:72:0.1412:0:2.6 -18 59254198 . A C 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=33.8671;LSEQ=ATGATTTGGCACATTTGTTT;RSEQ=ATTCCCCTTTGTGTCTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:172:151:44,107:4,17:0.8779:2,2:25.1:1:32.2:1:0.44033:1.74:60:302:0.8779:0:2.4 1/1:246:245:99,146:0,0:0.9959:0,2:24.4:1:31.2:1:1:0:60:121.5:0.9959:0:2 -18 59254211 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57824;SOR=0.37161;LSEQ=TTTGTTTAATTCCCCTTTGT;RSEQ=TCTAAGTAAGGGCAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:33,113:0.0135:2,2:27.5:1:30:1:0.40789:3.39:60:4:0.0137:0:3.5 0/0:198:1:1,0:72,125:0.0051:2,0:1:0:23:0:0.36869:0:60:2:0.0051:0:3 -18 59254213 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17933;SOR=0;LSEQ=TGTTTAATTCCCCTTTGTGT;RSEQ=TAAGTAAGGGCAACAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:32,109:0.014:2,2:15.5:1:29.5:1:0.40953:3.37:60:4:0.0141:0:1.5 0/0:194:0:0,0:69,125:0:2,0:21.9:1:31.1:1:1:0:60:63.667:1:0:2.1 -18 59254227 . C T 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00035;SOR=17.40004;LSEQ=TTGTGTCTAAGTAAGGGCAA;RSEQ=AGAAAAAAGATCTTCAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:113:100:18,82:2,11:0.885:2,2:23.2:1:28.7:1:1:1.21:60:99:0.8839:0:2.5 1/1:136:135:41,94:0,0:0.9926:0,2:22.6:1:27.9:1:1:0:60:32.75:0.9924:0:2.4 -18 59254309 . G A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3532;SOR=3.90045;LSEQ=TGGGGGCATTTGGCTTTTCC;RSEQ=TGCATTCTACCCTGATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:22:3,19:0,4:0.8462:0,2:21.4:1:31.3:1:1:0:60:44:0.8462:0:1.5 1/1:23:22:0,22:0,0:0.9565:0,1:16.5:1:29.9:1:1:0:60:44:1:0:1.6 -18 59254399 . T G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15385;SOR=8.0749;LSEQ=TACAAATATTCACAAAATGC;RSEQ=TTTCCTGCACCAGGCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:0,10:0.0909:0,0:34:0:32:0:1:0:60:2:0.0909:0:1 1/0:4:2:0,2:0,2:0.5:0,0:24:1:30.5:1:1:0:60:4:0.5:0:1.5 -18 59899349 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=AATGGTATTTTAAATCTGTT;RSEQ=CTAGCCCAAAGAAATATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:32,12:0:2,0:23.6:1:30.3:1:1:0:60:88:1:0:0.2 0/1:52:2:1,1:35,15:0.0385:2,2:33.5:1:30.5:1:0.52489:2.29131:60:4:0.0385:0:1 -18 59899398 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.23448;SOR=Inf;LSEQ=GGAGCACTGTTGCTGTTGTT;RSEQ=CTGCTGCTGCTGCTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:50,40:0:2,0:26.1:1:31.6:1:1:0:59.4:29:1:0:0.2 0/1:85:2:1,1:43,40:0.0235:2,2:15.5:1:31.5:1:1:1.07406:60:4:0.0235:0:1 -18 59899410 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=1.03728;LSEQ=CTGTTGTTGCTGCTGCTGCT;RSEQ=CTGTTGTTGTTGTTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:43,40:0.0235:2,2:14:1:27.5:1:1:1.07406:31:4:0.0238:0:1.5 0/1:82:2:1,1:39,41:0.0244:2,2:14:1:31:1:1:1.05:31:4:0.0244:0:1.5 -18 60646484 . G A 27 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=TTTGCTGCCCCGGCTCAGCC;RSEQ=GATCCTGATGATCAGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:15.5:1:27.5:1:0.4:0:60:4:0.4:0:1 0/0:6:0:0,0:5,1:0:2,0:15.7:1:29.3:1:1:0:60:12:1:0:0.2 -18 60795696 . TTG T 28 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.57432;SOR=2.72629;LSEQ=TGCCTGAAGACTGTTAATTG;RSEQ=TGTGTGTGTGTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:50,1:0.0192:1,0:15:0:31:0:1:0:60:2:0.0204:0:0 0/1:39:2:1,1:35,2:0.0513:2,2:25.5:1:28.8:1:0.1498:14.49018:60:4:0.0526:0.0256:0 -18 60796065 . GA G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49735;SOR=0;LSEQ=AGAGAATGCCACCCCACAGA;RSEQ=AAGAGGCATCCTGCCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:7,85:0.0211:2,2:33:1:30.5:1:0.16381:11.43:60:4:0.0217:0:0 0/0:95:0:0,0:12,83:0:2,0:22.1:1:29.2:1:1:0:60:22.75:1:0:0.1 -18 60847763 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCCCACCCCAGACCGCCCA;RSEQ=CCCACCCCAGGCTTAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:23:0:27:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:26:1:29.5:1:1:0:60:4:1:0:1 -18 60849930 . G A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AGGCTTCATTGGCCCATTCT;RSEQ=CAAATCAACTCTGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:212,47:0:2,0:23:1:32.1:1:1:0:60:63.75:1:0:0.1 0/1:297:18:13,5:224,55:0.0606:2,2:22.7:1:28.3:1:0.3762:1.56379:60:36:0.061:0:1.1 -18 60850071 . TG T 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAAACCTCATGTCCCTACC;RSEQ=GGGTATTTGCCTGAAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:760:0:0,0:367,391:0:2,0:24.3:1:31.1:1:1:0:60:49.533:0.9973:0:0.1 0/1:962:44:21,23:430,485:0.0457:2,2:30.2:1:31:1:1:1.03:60:88:0.0468:0.0021:0.1 -18 60850310 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.82767;LSEQ=AGATGCATGTCACACTGATG;RSEQ=TGGGGCTCAGACCCACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:0,15:0,4:0.7895:0,1:25.7:1:31.9:1:1:0:60:30:0.7895:0:1.1 1/1:8:7:0,7:0,1:0.875:0,0:21.6:1:30.3:1:1:0:60:14:0.875:0:1 -18 60850631 . A G 39 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AGCAGGCTTCATGGAAGTTG;RSEQ=GCTATTATGGCGAAGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:29:0:32:0:1:0:60:2:1:0:3 1/1:3:3:1,2:0,0:1:0,2:27.3:1:25:1:1:0:60:2:1:0:3 -18 60850642 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAGTTGAGCTATTATGG;RSEQ=GAAGAGGGTGAGGTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:18:0:30:0:1:0:60:2:1:0:3 1/0:3:2:1,1:0,1:0.6667:0,2:27.5:1:28:1:1:0:60:4:0.6667:0:2 -18 60851849 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16118;SOR=0;LSEQ=CTGAAGATAAGTGCAACTCA;RSEQ=TGCAAAAGGATTCCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:94,95:0.0105:2,2:20:1:33.5:1:1:1.01:60:4:0.0109:0:1 0/0:284:0:0,0:133,151:0:2,0:28.8:1:29.7:1:1:0:60:70:1:0:0.4 -18 60851880 . G A 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0219;SOR=1.79518;LSEQ=TTCCTGCTGTAATACAGACT;RSEQ=TAGCCCATCAGGGGAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:29:15,14:57,90:0.1648:2,2:25.4:1:28.1:1:0.2188:1.69:60:28:0.1618:0:1.2 0/1:233:61:25,36:71,101:0.2618:2,2:27.2:1:29:1:1:1.01223:60:122:0.2641:0:1.2 -18 60852085 . T C 90 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGGCCACTTCTTGAATTTC;RSEQ=ACCCTTCTTCTTGAATGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:1,6:0,2:0.7778:0,2:24.6:1:32.4:1:1:0:60:14:0.7778:0:1.7 1/1:1:1:0,1:0,0:1:0,0:40:0:31:0:1:0:60:2:1:0:1 -18 60909860 . T C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.44444;SOR=0;LSEQ=ACAATCCCTTATTACCAGTC;RSEQ=CTCCTCATTAAAACATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:20,0:0,0:1:0,1:31.7:1:31.2:1:1:0:60:40:1:0:1.1 1/1:16:15:15,0:1,0:0.9375:0,1:16.6:1:29.1:1:1:0:60:14:0.9333:0:1.2 -18 60910012 . G T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13516;SOR=Inf;LSEQ=ATTAGATAAAATTTCAAATT;RSEQ=CTGAAAATGCATGTGGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:195,95:0:2,0:26.1:1:32.2:1:1:0:60:144:1:0:0.1 0/1:371:4:1,3:232,134:0.0108:2,2:6.8:1:27.5:1:0.14541:5.17081:60:8:0.011:0:1 -18 60910135 . C T 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GAGAAGACAATGAAAGGGAA;RSEQ=GGAGAGGCGCTGGAATATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:85,197:0:2,0:23.5:1:30.3:1:1:0:60:69.5:0.9964:0:0.1 0/1:332:18:7,11:101,211:0.0542:2,2:29.7:1:29.7:1:0.60874:1.33:60:36:0.0545:0:1.1 -18 60910163 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24852;SOR=Inf;LSEQ=CGCTGGAATATTGTGAAATG;RSEQ=CCCAAAAAGTTGTTTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:32,117:0:2,0:23:1:31.5:1:1:0:60:148:1:0:0.1 0/1:160:3:2,1:34,123:0.0188:2,2:18:1:28.3:1:0.12727:7.12:60:6:0.0194:0:1.3 -18 60910366 . G A 70 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTGATAGACTGGATAAA;RSEQ=AAAATTTGGTACATATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:22.8:1:30.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 60950140 . A T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0936;SOR=0;LSEQ=GATTCCATTCCATTTTGTAA;RSEQ=TTACTGATCTGTACCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:3:1,2:193,52:0.0121:2,2:14.3:1:22:1:0.12041:7.34263:60:2:0.0083:0:1 0/0:297:0:0,0:240,57:0:2,0:22.6:1:30:1:1:0:60:296:1:0:0 -18 60950363 . T A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17254;SOR=0;LSEQ=TTCCCCTCTTTTGAAAAATT;RSEQ=CTAGTTATTTTTTTCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:28,146:0.0114:2,2:22:1:25.5:1:0.30318:5.14:60:4:0.0114:0:1 0/0:247:0:0,0:57,190:0:2,0:22.8:1:29.3:1:1:0:60:81.333:1:0:0.1 -18 60985601 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.39242;LSEQ=GGCGGGAGAAGTCGTCGCCG;RSEQ=CCTGGCGGAGGGTCAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:2:1,1:41,233:0.0072:2,2:24:1:27.5:1:0.28166:5.63:60:4:0.0075:0:1 0/1:298:3:1,2:71,224:0.0101:2,2:28:1:29:1:0.56522:1.57:60:6:0.0102:0:1.7 -18 60985622 . AC A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24868;SOR=Inf;LSEQ=CCTGGCGGAGGGTCAGGTGG;RSEQ=CACAGGTGGCACCGGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:27,163:0:2,0:26.2:1:31.2:1:1:0:60:22.75:1:0:0.1 0/1:202:3:2,1:49,150:0.0149:2,2:9.3:1:26:1:0.15764:6.05:60:6:0.0155:0.0099:0.7 -18 60985637 . G A 45 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05798;SOR=Inf;LSEQ=GGTGGACCACAGGTGGCACC;RSEQ=GGCTGAGCGCAGGCCCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:21,130:0:2,0:23.5:1:31.3:1:1:0:60:150:1:0:0.2 0/1:147:4:3,1:38,105:0.0272:2,2:5.8:1:22.5:1:0.06594:8.15:60:3:0.0221:0:1 -18 60985671 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.80056;LSEQ=CCCCGCGGCGGCGCCGGGGG;RSEQ=AGCCGGGGTCTGCAGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:52,59:0.0089:2,0:1:0:23:0:1:0:60:2:0.0092:0:1 0/1:125:2:1,1:59,63:0.016:2,2:9.5:1:27:1:1:1.07:60:4:0.0168:0:1 -18 60985689 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51095;SOR=Inf;LSEQ=GGCAGCCGGGGTCTGCAGCG;RSEQ=CGAGGTCCTGGCGACCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:81,55:0:2,0:20.6:1:31.4:1:1:0:60:33:1:0:0.2 0/1:187:2:1,1:106,79:0.0107:2,2:6.5:1:28.5:1:1:1.33962:60:4:0.0109:0:1.5 -18 60985691 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17351;SOR=0;LSEQ=CAGCCGGGGTCTGCAGCGGC;RSEQ=AGGTCCTGGCGACCGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:86,56:0.0139:2,2:38.5:1:29:1:1:1.53096:60:4:0.0141:0:1 0/0:201:0:0,0:117,84:0:2,0:20.2:1:30:1:1:0:60:32.5:1:0:0.3 -18 60985879 . T C 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.55206;LSEQ=ATCTCCCGGTTATCGTACCC;RSEQ=GTTCTCCCAGCGTGCGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1001:630:310,320:179,191:0.6294:2,2:25.8:1:30.2:1:0.84421:1.03:60:104:0.6303:0:1.1 0/1:1358:657:317,340:349,349:0.4838:2,2:25.5:1:29.6:1:0.54986:1.0725:60:108.5:0.4833:0:1.1 -18 61199883 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25298;SOR=Inf;LSEQ=TCTTCAAGAGCAGGTTGTTT;RSEQ=AGATTAAAGAGGTTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:159,89:0:2,0:24.9:1:31.5:1:1:0:60:123:1:0:0.5 0/1:289:3:1,2:175,109:0.0104:2,2:26.3:1:22.7:1:0.56157:3.19766:60:2:0.0071:0:3.7 -18 61199950 . G C 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.02318;LSEQ=TTCAGTAGGAGTTTGCTGAG;RSEQ=GGTTGCTAACCTCTCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:334:332:155,177:1,0:0.994:0,2:26.8:1:30.8:1:0.46847:0:60:82:0.997:0:1.1 1/0:392:311:146,165:39,38:0.7934:2,2:26.2:1:30.4:1:0.61092:1.15943:60:61.2:0.7969:0:1.1 -18 66080132 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.12539;SOR=0;LSEQ=GAGATTTTGGAATAGATATT;RSEQ=TTATGTACAATGGTTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:42,18:0.0317:2,2:17.5:1:30:1:0.52247:2.298:60:4:0.0323:0:1 0/0:114:0:0,0:70,44:0:2,0:27:1:29.4:1:1:0:60:56:1:0:0.3 -18 66080181 . C A 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=TTTTACTCAAAAACACAAAT;RSEQ=TTTTAATATAAATATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:38,35:0:2,0:28.1:1:31.7:1:1:0:60:72:1:0:0.8 0/1:145:21:10,11:62,62:0.1448:2,2:21.2:1:28.7:1:1:1.09928:60:42:0.1458:0:1.2 -18 66080203 . T C 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTAATATAAATATGAAATG;RSEQ=TTATTTTCACATATACTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:85:40,45:0,0:1:0,2:21.5:1:31.6:1:1:0:60:27.333:1:0:1 1/0:137:76:36,40:25,36:0.5547:2,2:23.7:1:31.5:1:0.49231:1.29:60:75:0.5515:0:1.2 -18 66204582 . A G 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATGTTTAAGCACCACTGG;RSEQ=TGAGGGGGGGCTCCAATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:22.7:1:33.3:1:1:0:25.7:6:0.75:0:1 1/1:3:3:0,3:0,0:1:0,0:26.7:1:30:1:1:0:26.3:6:1:0:1.3 -18 66533736 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19355;SOR=0;LSEQ=ATGTCAACATGTAGACTTTT;RSEQ=TCCAGGCCGGACACAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:26,0:0.0714:1,2:8:1:29:0:0.07143:0:60:4:0.0741:0:1 0/0:35:0:0,0:28,7:0:2,0:20.1:1:30.9:1:1:0:60:70:1:0:0.1 -18 66533842 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1316;SOR=Inf;LSEQ=TATCAGAAAAGCTGCTCCTT;RSEQ=GGAACCTTAGTCAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:64,36:0:2,0:23.8:1:31.5:1:1:0:60:99:0.99:0:0.1 0/1:58:2:1,1:26,30:0.0345:2,2:16:1:29:1:1:1.15:60:4:0.0364:0:0 -18 66533990 . G T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10824;SOR=0;LSEQ=TGGGTCTGGTATTGCTTTGA;RSEQ=TGCACGGGTCTGTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:205,88:0.0101:2,2:25.3:1:22.7:1:1:1.16414:60:2:0.0068:0:1.7 0/0:324:0:0,0:226,98:0:2,0:23.3:1:31.2:1:1:0:60:80:1:0:0.1 -18 66534049 . T A 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=2.88923;LSEQ=TCCCTGGGAACTTTGAGTCT;RSEQ=ATTTGAAACTTGTGAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:17:7,10:318,271:0.0281:2,2:17.8:1:29.5:1:0.33145:1.67488:59.7:34:0.0286:0:3.4 0/1:740:57:27,30:354,328:0.077:2,2:15.1:1:28.8:1:0.58159:1.19889:59.8:56:0.0761:0:2.8 -18 66534055 . A G 170 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00087;SOR=2.67922;LSEQ=GGAACTTTGAGTCTTATTTG;RSEQ=AACTTGTGAAGTCCCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:15:7,8:321,291:0.0239:2,2:16.4:1:31.4:1:0.79515:1.26021:60:30:0.0245:0:3.7 0/1:746:46:22,24:354,346:0.0617:2,2:12.6:1:30.8:1:0.76218:1.11597:60:92:0.0626:0:3.2 -18 66534060 . TG CC 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00125;SOR=3.02455;LSEQ=TTTGAGTCTTATTTGAAACT;RSEQ=TGAAGTCCCTGTGTCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:637:10:5,5:323,301:0.0157:2,2:16.5:1:30.4:1:1:1.07294:60:20:0.0158:0:3.4 0/1:760:35:18,17:360,362:0.0461:2,2:10.4:1:30.5:1:0.86469:1.06:60:70:0.0464:0.0118:2.8 -18 66534270 . CT TG 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03925;LSEQ=GCTGGCAGCCATGTGAAGAG;RSEQ=GACGTTCCCAGCGTCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:7:7,0:21,57:0.0814:2,0:14.3:1:29.6:1:0.00024:0:38:14:0.0824:0.0233:2 0/1:83:7:7,0:28,48:0.0843:2,0:17.7:1:27.7:1:0.00162:0:37.4:14:0.0854:0.012:2.4 -18 66534274 . C A 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.76498;SOR=1.23306;LSEQ=GCAGCCATGTGAAGAGCTGA;RSEQ=GTTCCCAGCGTCATCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:5:5,0:17,54:0.0658:2,0:14.2:1:29.4:1:0.00143:0:37.2:10:0.0667:0:2.8 0/1:75:6:6,0:24,45:0.08:2,0:16:1:26.8:1:0.00295:0:37:12:0.0811:0:2.8 -18 66534284 . G A 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73759;SOR=1.3738;LSEQ=GAAGAGCTGACGTTCCCAGC;RSEQ=TCATCTTTCCACACACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:4:4,0:17,48:0.058:2,0:5.3:1:28:1:0.00692:0:36.8:8:0.058:0:3 0/1:64:5:5,0:18,41:0.0781:2,0:7.2:1:26.4:1:0.00441:0:36.4:10:0.0781:0:3 -18 66534313 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50096;SOR=0;LSEQ=CCACACACTATTAAGGTCAC;RSEQ=TATCCTCCCATTTGTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:8,38:0.0417:2,2:16:1:28.5:1:0.34309:4.54:60:4:0.0426:0:1 0/0:38:0:0,0:8,30:0:2,0:19.4:1:32.3:1:1:0:60:76:1:0:0.1 -18 66534344 . T C 84 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41528;SOR=0.33921;LSEQ=TTTGTCACTCTTGTCTCCAG;RSEQ=CTGGACAAAGTTCTCCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:4,2:4,26:0.1667:2,2:5.2:1:32.5:1:0.0144:11.63:58.5:12:0.1667:0:8 0/1:16:1:1,0:3,12:0.0625:2,0:7:0:30:0:0.25:0:60:2:0.0625:0:8 -18 66534349 . A G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47115;SOR=0.47281;LSEQ=CACTCTTGTCTCCAGTCTGG;RSEQ=CAAAGTTCTCCTGATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:8:4,4:4,23:0.2222:2,2:8.6:1:31.9:1:0.05958:5.39:51.4:16:0.2286:0:7.8 0/1:17:2:1,1:3,12:0.1176:2,2:8.5:1:32:1:0.42647:3.61:45:4:0.1176:0:7.5 -18 66534362 . G C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19752;LSEQ=AGTCTGGACAAAGTTCTCCT;RSEQ=ATTTATTTAGATCCTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:8:4,4:4,21:0.2424:2,2:21.6:1:33.5:1:0.07367:4.93:51.4:16:0.25:0:7.8 0/1:18:5:1,4:3,10:0.2778:2,2:12.8:1:27.4:1:1:1.18824:48.2:10:0.2778:0:6.6 -18 66534366 . TA AG 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.43177;SOR=1.55958;LSEQ=TGGACAAAGTTCTCCTGATT;RSEQ=TTTAGATCCTTTTGGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:14:4,10:4,20:0.3684:2,2:16.5:1:30.6:1:0.43318:1.96:48.4:28:0.3784:0.1579:5.4 0/1:23:11:1,10:3,9:0.4783:2,2:11.9:1:28.3:1:0.59006:3.17098:49.6:22:0.4783:0.2609:4.2 -18 66534382 . G T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4431;SOR=1.60893;LSEQ=GATTTATTTAGATCCTTTTG;RSEQ=GCTTTCAGATCCCCTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:19:4,15:4,18:0.4634:2,2:22.3:1:28.5:1:1:1.19:48.2:18:0.45:0:4.7 1/0:24:14:1,13:3,7:0.5833:2,1:20.3:1:29.3:1:0.27207:5.17077:46.6:28:0.5833:0:3.9 -18 66534389 . A T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60077;SOR=1.4086;LSEQ=TTAGATCCTTTTGGGCTTTC;RSEQ=GATCCCCTGGAGCTCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:20:4,16:1,16:0.5405:1,2:22.5:1:29.7:1:0.34792:3.87:47.8:40:0.5405:0:4.6 1/0:24:15:1,14:3,6:0.625:2,1:23:1:29.7:1:0.13043:6.39931:46.2:30:0.625:0:3.8 -18 66534393 . CCCC ACCCT 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.79633;SOR=1.25488;LSEQ=ATCCTTTTGGGCTTTCAGAT;RSEQ=TGGAGCTCAGTAGCAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:24:4,20:1,15:0.5854:1,2:20:1:30:1:0.63089:2.93:47.3:48:0.5854:0.122:4 1/0:25:16:0,16:3,5:0.64:2,1:21.7:1:30.6:1:0.02767:0:44.5:32:0.6667:0.08:3.4 -18 66534396 . C T 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39241;SOR=2.28548;LSEQ=CTTTTGGGCTTTCAGATCCC;RSEQ=TGGAGCTCAGTAGCAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:1,14:0.0556:1,0:12:1:26:0:1:0:33:4:0.125:0:2 0/1:25:3:1,2:3,5:0.12:2,2:8.3:1:27.3:1:1:1.18052:50.7:6:0.2727:0:3.3 -18 66534584 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TTCCCTTTTCCTGCCCACAG;RSEQ=TTGCCTACTCTGGGAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:15:0:32:0:1:0:41:4:0.5:0:8 0/0:5:0:0,0:2,3:0:2,0:29.6:1:32.2:1:1:0:60:10:1:0:0 -18 66534593 . TC CG 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=CCTGCCCACAGCTTGCCTAC;RSEQ=TGGGAATAGAAGCACTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:25:0:33:0:1:0:41:4:0.4:0:7 0/0:5:0:0,0:2,3:0:2,0:35:1:29.8:1:1:0:60:10:1:0:0 -18 66534599 . AA CC 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=CACAGCTTGCCTACTCTGGG;RSEQ=TAGAAGCACTTATTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:31:0:33.5:0:1:0:41:4:0.4:0:6 0/0:5:0:0,0:2,3:0:2,0:37.6:1:29.8:1:1:0:60:10:1:0:0 -18 66534615 . C T 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10714;SOR=0;LSEQ=TGGGAATAGAAGCACTTATT;RSEQ=TCTCTCCATATTGGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:18:0:32:0:1:0:41:4:0.6667:0:6 0/0:5:0:0,0:2,3:0:2,0:33.2:1:31.6:1:1:0:60:10:1:0:0 -18 66534621 . CC AT 30 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TAGAAGCACTTATTCTCTCT;RSEQ=ATATTGGGCTCTGATTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:11:0:30.5:0:1:0:41:4:1:0:5 0/0:4:0:0,0:2,2:0:2,0:36.3:1:30.8:1:1:0:60:8:1:0:0 -18 67870203 . CTT C 52 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TAACAGGTTAAGCATCAAAA;RSEQ=TTTTTTTTTTTTTTTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:21.7:1:32.9:1:1:0:60:6:1:0.3333:0 0/0:3:0:0,0:3,0:0:0,0:24.3:1:32.3:1:1:0:60:6:1:0:1 -18 67870440 . C CT 28 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CGATTCTATGAGAAAGTGTT;RSEQ=TTTTTTTTTTTTCGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:31.5:1:28.5:1:1:0:60:4:0.3333:0:0.5 0/0:3:0:0,0:0,3:0:0,0:29.7:1:22.3:1:1:0:60:2:1:0:1.7 -18 67870507 . C A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAATGGAGTGATCTCAG;RSEQ=TCACCGTTGCAACCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:8:0:32:0:1:0:60:2:1:0:1 1/1:2:2:0,2:0,0:1:0,0:25.5:1:31:1:1:0:60:4:1:0:1.5 -18 68060541 . T C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCCTGACCTCAGGTAAT;RSEQ=CGCCCACCTTGGCCTCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:27,0:0,0:1:0,1:21.6:1:32.1:1:1:0:59.4:54:1:0:1.1 1/1:16:16:16,0:0,0:1:0,1:28.1:1:31.4:1:1:0:60:32:1:0:1.1 -18 68060723 . C G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.15931;LSEQ=ACACACAATGCGGATGTAAT;RSEQ=GATCGTATCCCCCTGCGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:545:309:170,139:124,112:0.567:2,2:25.8:1:31.3:1:0.60307:1.10:60:60.8:0.5682:0:2.1 0/1:934:161:84,77:381,388:0.1724:2,2:26.8:1:30.5:1:0.60315:1.11:60:79.5:0.1719:0:2 -18 68060733 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.16558;LSEQ=CGGATGTAATCGATCGTATC;RSEQ=CCCTGCGTAGTTGCTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:545:303:158,145:121,121:0.556:2,2:26.9:1:30.3:1:0.66644:1.09:60:42.286:0.5574:0:2.1 0/1:962:165:88,77:377,420:0.1715:2,2:26.3:1:29.5:1:0.17119:1.27:60:54:0.1709:0:2 -18 69372730 . A G 84 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGCATTTAAAAAAATTATT;RSEQ=TCTATGCCTAGTTTCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:25.7:1:32.5:1:1:0:60:12:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 69372908 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21886;SOR=0;LSEQ=ATGTCAATACTCAAGCCAAT;RSEQ=TTCTTACTAACACCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:7,17:0.0769:2,2:25.5:1:30:1:0.52923:2.34:60:4:0.0769:0:2 0/0:29:0:0,0:7,22:0:2,0:24.9:1:30:1:1:0:60:58:1:0:0.2 -18 69372974 . T C 78 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTTTGATTTTGAAGGA;RSEQ=ATGTTTTGTGTAATAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:32:1:33.8:1:1:0:60:10:1:0:2.2 1/1:1:1:0,1:0,0:1:0,0:11:0:34:0:1:0:60:2:1:0:2 -18 69372976 . T A 76 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTTGATTTTGAAGGATA;RSEQ=GTTTTGTGTAATAGTAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:31.2:1:32.8:1:1:0:60:10:1:0:2.2 1/1:1:1:0,1:0,0:1:0,0:9:0:33:0:1:0:60:2:1:0:2 -18 69373446 . T G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACATGTTAAACTGCTTT;RSEQ=CTAAACAAAAATGCTCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:33.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 69373493 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGAATTGAGCTCCCCAGC;RSEQ=TCCAGTCACCATTATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 70571137 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.197;SOR=0;LSEQ=AAGTGTACAATGTGCTCTTG;RSEQ=GCATACTAATCACAATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:90,33:0.016:2,2:24:1:29.5:1:0.47161:2.70175:60:4:0.0164:0:1 0/0:156:0:0,0:110,46:0:2,0:21.4:1:30.1:1:1:0:60:30.2:1:0:0.2 -18 70571152 . A G 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTTGGGCATACTAATCACA;RSEQ=TTCAATTGACTCAGTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:110,49:0:2,0:23.5:1:30.3:1:1:0:60:78.5:1:0:0.3 0/1:209:20:12,8:127,62:0.0957:2,2:29.3:1:31.6:1:0.6191:1.36353:60:40:0.0976:0:1 -18 70571238 . T G 242 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00464;LSEQ=TTTTACTACAAACCAAATAC;RSEQ=ATGCTAATAAAATTGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:262:261:124,137:0,1:0.9962:0,2:24.6:1:30.2:1:1:0:60:64.25:0.9961:0:1.1 1/0:313:171:78,93:70,71:0.5463:2,2:23:1:30.2:1:0.49604:1.1749:60:84.5:0.5469:0:1.1 -18 71915176 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAGACCACCAGCCCTCG;RSEQ=CTACTCTTTCGGCCCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:28:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:33:0:32.5:1:1:0:60:4:1:0:1 -18 71915587 . A G 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.18657;LSEQ=TACAACAGATGTCTTCCGGA;RSEQ=AGAGAAGGTGTTTTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:28:13,15:74,45:0.1905:2,2:30.7:1:31.5:1:0.13975:1.88894:60:56:0.1931:0:1.1 0/1:215:9:5,4:132,74:0.0419:2,2:23.6:1:31.7:1:0.72612:1.42452:60:18:0.0421:0:1 -18 71915673 . C G 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00049;SOR=2.81049;LSEQ=ACAATACTTTCAGATTTAGT;RSEQ=ATTCCAACTTACAGTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:250:214:102,112:17,18:0.856:2,2:25.1:1:31.2:1:1:1.0369:60:52.5:0.8571:0:1.1 1/1:337:318:148,170:7,9:0.9436:2,2:23.9:1:31.2:1:1:1.12:60:105:0.9488:0:1.1 -18 71915785 . T A 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29668;SOR=Inf;LSEQ=TTTCAACTCAAAACCTTGAA;RSEQ=GTTTCTGTGAGCCAGGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:5,40:0:2,0:22.2:1:30:1:1:0:60:44:1:0:0 0/1:72:4:0,4:10,58:0.0556:2,0:26.8:1:31.5:1:1:0:60:8:0.0556:0:1 -18 72515764 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16731;SOR=0;LSEQ=CTGTGTGTCAGCTGTGAATG;RSEQ=CAGAGATAATGTGGTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:111,55:0.0119:2,2:24.5:1:33:0:1:2.00913:60:4:0.012:0:1 0/0:242:0:0,0:165,77:0:2,0:24.4:1:28.4:1:1:0:60:47.4:1:0:0.1 -18 72515839 . G A 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.35662;LSEQ=AAGGTCAGGAATGACGGAGC;RSEQ=AAAAATGTTCACGAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:70:37,33:128,130:0.2134:2,2:30.8:1:30.2:1:0.68668:1.14:60:140:0.2147:0:1.1 0/1:488:43:20,23:218,227:0.0881:2,2:26.7:1:30.2:1:0.8733:1.10418:60:86:0.0885:0:1.1 -18 72515919 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17903;SOR=0;LSEQ=CTTGATTGTCCTTGGCTTCA;RSEQ=AGTAAAGGTTGCATATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:44,121:0.012:2,2:16:0:31:1:0.4675:2.73:60:4:0.012:0:1.5 0/0:227:0:0,0:69,158:0:2,0:23.2:1:31:1:1:0:60:74.667:1:0:0.2 -18 72516095 . C CT 50 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=2.16028;LSEQ=AGTTAGACATATTTCATTGT;RSEQ=TTTTTTTTTTTCCTTTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:21.3:1:31.7:1:1:0:60:6:0.3333:0:1 1/0:2:1:0,1:0,1:0.5:0,0:35:0:31:0:1:0:60:2:0.5:0:0 -18 73601806 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=AGCTAGGAGAGGAAGCCACA;RSEQ=GTCCGTCCCAGAAGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:19.5:1:33:1:1:0:60:4:0.5:0:1 0/1:5:2:2,0:3,0:0.4:0,0:48:0:31.5:1:1:0:60:4:0.4:0:1.5 -18 73601954 . G A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00077;SOR=0.43912;LSEQ=GAGCCTCCCCTCCTTGGCAT;RSEQ=AAAGGCTTTGGAAGTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:121:69:43,26:31,21:0.5702:2,2:24.6:1:28.2:1:0.85105:1.12:60:33.5:0.5678:0:1.6 0/1:166:61:36,25:60,45:0.3675:2,2:25.4:1:27.9:1:0.87121:1.08:60:29.5:0.362:0:1.6 -18 73602003 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51361;SOR=Inf;LSEQ=GGCAGGTGAATTTGTCAGCT;RSEQ=TTGTTGGTTGCTCAGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:70,63:0:2,0:27.3:1:30:1:1:0:60:43.333:1:0:1.2 0/1:189:2:1,1:87,100:0.0106:2,2:16:1:30.5:1:1:1.15:60:4:0.0107:0:1 -18 73602007 . T C 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11022;SOR=0.68834;LSEQ=GGTGAATTTGTCAGCTTTTG;RSEQ=TGGTTGCTCAGCCCAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:80:43,37:26,28:0.5926:2,2:27.6:1:31.8:1:0.59812:1.25:60:39:0.5909:0:2.1 1/0:178:89:40,49:41,46:0.5:2,2:28.3:1:32:1:0.87985:1.0913:60:88:0.5:0:1.9 -18 73602031 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19151;SOR=0;LSEQ=TTGCTCAGCCCAGGCCAGCT;RSEQ=GTGTGGTGCGCTGTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:54,61:0.0169:2,2:28:1:29:1:1:1.13:60:4:0.0171:0:2.5 0/0:151:0:0,0:65,86:0:2,0:24.3:1:30.5:1:1:0:60:150:1:0:1.1 -18 73602051 . A G 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.88497;SOR=1.05023;LSEQ=GGTGTGGTGCGCTGTGCTGC;RSEQ=GAGCATCCTGTCCTTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:56:21,35:14,22:0.6087:2,2:28.1:1:30.3:1:1:1.05992:60:55:0.6111:0:1.9 1/0:108:67:25,42:15,26:0.6204:2,2:23.9:1:28.9:1:1:1.03:60:21.333:0.6154:0:1.7 -18 73984673 . CA C 80 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.14266;SOR=0.31803;LSEQ=ACGACAGAGGAAGACTGTTT;RSEQ=AAAAAAAAAAAAAAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:5,1:3,1:0.4615:2,2:38.7:1:31.2:1:1:1.58:60:12:0.4615:0:0.5 0/1:24:5:4,1:8,2:0.2083:2,2:24.2:1:32:1:1:1:60:10:0.2083:0:1.8 -18 74386967 . T C 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCTTCAGGTCTCAGCT;RSEQ=CAACGTTCTCCCTCATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:14.7:1:26.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 74387215 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29757;SOR=Inf;LSEQ=TGGCCTCAGACAGGAGCCGG;RSEQ=AGAACAGCCCACACAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:33,18:0:2,0:24:1:31.5:1:1:0:60:50:1:0:0.4 0/1:94:4:1,3:58,32:0.0426:2,2:20.8:1:26.5:1:0.1438:5.33842:60:8:0.044:0:1.5 -18 74387275 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51492;SOR=Inf;LSEQ=CAGCTGCCATGTCACACTCA;RSEQ=CTCCCAGCCTGTGCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:65,54:0:2,0:26.7:1:32:1:1:0:60:38.667:1:0:0.9 0/1:172:2:1,1:93,77:0.0116:2,2:17:0:31:1:1:1.20646:60:4:0.012:0:1.5 -18 74387296 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5016;SOR=Inf;LSEQ=CTCCCAGCCTGTGCTGCCTC;RSEQ=GGTCTGCTCTCCCGGGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:68,67:0:2,0:24.5:1:30.3:1:1:0:60:66.5:0.9925:0:1 0/1:160:2:1,1:82,76:0.0125:2,2:24.5:1:29:1:1:1.07841:60:4:0.0128:0:2 -18 74387299 . T C 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01687;SOR=0.55376;LSEQ=CCAGCCTGTGCTGCCTCGGG;RSEQ=CTGCTCTCCCGGGATACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:88:43,45:22,22:0.6667:2,2:26.1:1:31.3:1:1:1.04618:60:28.333:0.6589:0:1.5 1/0:160:84:46,38:37,39:0.525:2,2:28.8:1:31.1:1:0.52654:1.27:60:83:0.5287:0:1.4 -18 74387326 . T G 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00617;SOR=0.40272;LSEQ=TCCCGGGATACAGTGTCCCA;RSEQ=TGCCAGCCCCCGCCCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:30:13,17:36,47:0.2655:2,2:27:1:32:1:1:1.00162:60:60:0.2655:0:2 0/1:150:19:9,10:59,72:0.1267:2,2:21.1:1:30.8:1:1:1.10:60:38:0.1293:0:1.8 -18 74387332 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50904;SOR=Inf;LSEQ=GATACAGTGTCCCATTGCCA;RSEQ=CCCCCGCCCCACACTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:43,60:0:2,0:28.9:1:31.9:1:1:0:60:50.5:1:0:0.9 0/1:139:2:1,1:57,79:0.0144:2,2:31:0:30.5:1:1:1.38:60:4:0.0147:0:2.5 -18 74387341 . C T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13027;SOR=Inf;LSEQ=TCCCATTGCCAGCCCCCGCC;RSEQ=CACACTGCTGCCCCTACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:37,63:0:2,0:27.2:1:30.7:1:1:0:60:99:1:0:0.9 0/1:124:4:2,2:46,74:0.0323:2,2:25.5:1:28.5:1:0.6403:1.60:60:8:0.0333:0:2 -18 74387348 . G A 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18426;SOR=0;LSEQ=GCCAGCCCCCGCCCCACACT;RSEQ=CTGCCCCTACGCCCATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:33,55:0.0222:2,2:37:0:28.5:1:1:1.66:60:4:0.023:0:1 0/0:119:0:0,0:42,77:0:2,0:22.8:1:30.8:1:1:0:60:18.833:1:0:0.7 -18 74463123 . G T 61 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGAAGACTTCCAGCAGTTT;RSEQ=TTTTTCTTTTTTTTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:0,0:0.8:0,0:12:1:30.8:1:1:0:60:8:1:0:1.3 1/1:3:3:3,0:0,0:1:0,0:27.7:1:29.7:1:1:0:60:6:1:0:1 -18 74463129 . C CT 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=ACTTCCAGCAGTTTGTTTTT;RSEQ=TTTTTTTTTTTCTTTTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:14.8:1:31.6:1:1:0:60:10:1:0:1.2 1/0:4:2:2,0:2,0:0.5:0,0:15.5:1:31.9:1:1:0:60:4:0.6667:0.25:0.5 -18 74463340 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50525;SOR=Inf;LSEQ=TGCCTGGATCGCTACCTGTC;RSEQ=AGCATCTCCACCCAATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:59,55:0:2,0:25.3:1:31.1:1:1:0:60:113:1:0:0.1 0/1:145:2:1,1:67,76:0.0138:2,2:15:1:28:1:1:1.13:60:4:0.0141:0:1 -18 74463373 . C G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01481;SOR=Inf;LSEQ=CAATGGCACAGTTGCAGCTC;RSEQ=TGGGTGCAGTCCACATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:42,44:0:2,0:24:1:31.1:1:1:0:60:42:1:0:0.1 0/1:96:7:4,3:42,47:0.0729:2,2:25.7:1:31:1:0.7067:1.49:60:14:0.0737:0:1 -18 74463394 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17717;SOR=0;LSEQ=TGGGTGCAGTCCACATCCTG;RSEQ=TGGCCTCCAAGCTGGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:42,43:0.023:2,2:14.5:1:28.5:1:1:1.02:60:4:0.0235:0:1 0/0:119:0:0,0:62,57:0:2,0:20.8:1:31.8:1:1:0:60:238:1:0:0.2 -18 74463468 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17444;SOR=0;LSEQ=TGCACCAACCACGCTGTCTC;RSEQ=CCTCGCCAGTTGTGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:35,51:0.0227:2,2:31.5:1:30.5:1:1:1.45:60:4:0.0233:0:1 0/0:122:0:0,0:54,68:0:2,0:24:1:29.6:1:1:0:60:244:1:0:0.1 -18 75379986 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATATTGAATATAATTTCA;RSEQ=ATTTGTCATTTATCTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:24:0:28:0:1:0:60:2:1:0:1 1/0:3:2:2,0:1,0:0.6667:0,0:22:1:32.5:1:1:0:60:4:0.6667:0:2 -18 75380032 . G A 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=3.1622;LSEQ=TTTAGTGCAGATATTTTCAC;RSEQ=TTTCTGTCAATGTATTACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:19:0:32:0:1:0:60:2:0.5:0:1 1/1:5:4:4,0:1,0:0.8:0,0:36:1:29.8:1:1:0:60:8:0.8:0:1.5 -18 75380175 . A C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.9304;LSEQ=CCTTCTCCCTGGGTCTCAGC;RSEQ=GGGAGCACTGGCTGGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:6,6:3,3:0.6667:2,2:29.1:1:28.9:1:1:1:60:11:0.6471:0:1.1 1/0:20:13:5,8:3,4:0.65:2,2:30.7:1:29.8:1:1:1.18903:60:26:0.65:0:1.2 -18 75381671 . T G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCCTTATAAAAGGGAAC;RSEQ=TTGGACACAGAGACACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -18 75381780 . G T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GACTGGCATGGGGCAGAGAC;RSEQ=GGCATGGGGCAGAGACTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:30:0:1:0:43:4:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:47:0:26:0:1:0:60:2:1:0:2 -19 806673 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGTCTGCGCCTCTGCCC;RSEQ=GGCAGCCCCTCTGCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:30:1:1:0:60:4:0.6667:0:1.5 -19 872802 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGGGCAGCAGCAGCAG;RSEQ=AGCAAGGCGAACCGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 872969 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGGCTCCGAGGTGGGG;RSEQ=AGGGCTCCGAGGTGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:1:33:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 872987 . G C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGGCTCCGAGGTGGGG;RSEQ=AGGGCTCCGAGGTGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:34:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 874449 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGCCTGCCAGGCACAGTG;RSEQ=CTCACGCCTGTAATCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:18.5:1:30.9:1:1:0:60:16:1:0:0.1 0/1:24:2:1,1:11,11:0.0833:2,2:10:1:27:1:1:1:60:4:0.0833:0:1 -19 874457 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGGCACAGTGGCTCACGC;RSEQ=TGTAATCCCAGCGCTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:18.5:1:29.8:1:1:0:60:16:1:0:0.1 0/1:24:2:1,1:10,12:0.0833:2,2:36:1:31:1:1:1.19:60:4:0.0833:0:1 -19 875389 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGGTAGTCGCACACGCG;RSEQ=GTCACCGTGCAGGGCGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29:1:1:0:60:4:1:0:1 -19 1206796 . C CT 84 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.75933;LSEQ=CCTTTTGGGGTTTTTGTTGC;RSEQ=TTTTTTTTTTCTTTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:7,0:52,0:0.1167:1,0:19.4:1:30.2:1:1:0:60:14:0.1167:0.05:0 0/1:33:3:3,0:29,1:0.0909:1,0:17.3:1:32.2:1:1:0:60:6:0.0909:0.0303:0 -19 1206863 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16955;SOR=Inf;LSEQ=GAACACAAGGAAGGACCGCT;RSEQ=ACCCGCGGACTCAGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:142,33:0:2,0:26.2:1:30.9:1:1:0:60:57.333:1:0:0.1 0/1:123:2:1,1:93,27:0.0163:2,2:44.5:1:29:1:0.4078:3.40043:60:4:0.0167:0:1 -19 1206890 . G T 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0434;SOR=Inf;LSEQ=GGACTCAGGGCTGGCGGCGG;RSEQ=ACTCCAGGACCCTGGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:160,74:0:2,0:25.2:1:30.6:1:1:0:60:77:1:0:0.1 0/1:198:4:1,3:123,71:0.0202:2,2:22:1:25.3:1:0.14793:5.15381:60:8:0.0206:0:1 -19 1206942 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02835;SOR=Inf;LSEQ=GTGGACCCGCAGCAGCTGGG;RSEQ=ATGTTCACGGAGGGCGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:184,159:0:2,0:25.8:1:32.2:1:1:0:60:84.75:1:0:0.1 0/1:332:5:1,4:186,141:0.0151:2,2:14.8:1:26.2:1:0.17194:5.25315:60:10:0.0153:0:1 -19 1207217 . C A 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32081;SOR=3.96477;LSEQ=GAAGAAGTAAGTATGGCTTG;RSEQ=TGGGGTCGGGGCCGGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:1:0,1:113,271:0.0026:2,0:11:0:14:0:1:0:60:0:0:0:3 0/1:293:3:2,1:82,208:0.0102:2,2:16.3:1:20.7:1:0.19855:5.04:60:2:0.0069:0:1 -19 1207238 . G T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.374;LSEQ=TGGGGTCGGGGCCGGGCCGG;RSEQ=CCAGTCACGGTGCTGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:258:143:34,109:26,88:0.5543:2,2:25:1:29.7:1:0.883:1.06:60:34.75:0.5605:0:1.4 0/1:183:58:14,44:26,99:0.3169:2,2:25.2:1:28.8:1:0.70105:1.21:60:116:0.3169:0:1.4 -19 1207280 . C T 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02671;SOR=0.47377;LSEQ=CTGTCTTCCTTCCTTCTCTC;RSEQ=TCCCTCCCTCCCTTACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:61:1,60:3,56:0.5083:2,1:21.7:1:30:1:0.36034:3.18557:60:29.5:0.5043:0:1.7 0/1:61:20:1,19:3,38:0.3279:2,1:22.4:1:30.1:1:1:1.49072:60:40:0.3333:0:2 -19 1218219 . C T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.12995;LSEQ=GACTAGAGGGCGCTGTGCTC;RSEQ=CACCCCCTACCGCCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:15,0:16,1:0.4688:1,1:27.1:1:32.3:1:1:0:60:30:0.5:0:1 1/0:10:5:4,1:5,0:0.5:0,2:19.8:1:30.4:1:1:0:60:10:0.5556:0:1.2 -19 1218384 . C T 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATCATCCTGACGTTGGGT;RSEQ=GGCTGATACACCCCTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:285,163:0:2,0:25.5:1:30.4:1:1:0:60:63:1:0:0.1 0/1:465:35:20,15:274,156:0.0753:2,2:24.1:1:29.5:1:0.46841:1.31647:60:34:0.0747:0:1.2 -19 1218523 . G T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28372;LSEQ=TCCTTTCCGGTGTTGGGACC;RSEQ=CGGGGCCTCCGTGGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:330:175:58,117:49,106:0.5303:2,2:24:1:30.2:1:0.81411:1.07:60:86.5:0.5356:0:1.1 0/1:322:78:24,54:86,158:0.2422:2,2:28.3:1:29:1:0.49592:1.22392:60:77:0.2414:0:1.1 -19 1219274 . G A 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02552;SOR=0.71225;LSEQ=TCTGGCCCCCGTGCTCCCTG;RSEQ=GCCTGTGAGTGGGGCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:426:228:166,62:142,54:0.5352:2,2:23:1:30.1:1:1:1.02:60:75:0.5383:0:1.1 0/1:313:141:98,43:119,53:0.4505:2,2:22.4:1:28.4:1:1:1.02:60:27.2:0.4474:0:1.2 -19 1219411 . G A 71 v4;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18023;SOR=3.30412;LSEQ=TCCCAGTGTGCCAGGCCCAC;RSEQ=GGTGCGTGCGCGGGGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:653:2:2,0:259,391:0.0031:2,0:1:0:27.5:1:0.15988:0:60:4:0.0031:0:1 0/1:696:7:7,0:307,382:0.0101:2,0:6.9:1:25.6:1:0.00367:0:60:14:0.0102:0:1.1 -19 1219443 . G GCGGGGGC 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00335;SOR=0.58758;LSEQ=GGGGCAGGGGCCAGGGTGGG;RSEQ=CGGGGGCCGGGGGCCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:100:24,76:73,194:0.2674:2,2:25.8:1:30.5:1:0.59536:1.19101:59.3:99:0.2683:0.0481:0.3 0/1:357:63:16,47:90,203:0.1765:2,2:31:1:30.6:1:0.45019:1.3014:59.7:126:0.1805:0.0168:0.1 -19 1219553 . G T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00059;SOR=0.21346;LSEQ=TTGTTTTTTTGTTTTTTTGT;RSEQ=TTTTTTTTCGAGATGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:39:0,39:1,4:0.7358:2,1:17.5:1:31.1:1:0.11364:0:60:78:0.8864:0:1.1 0/1:38:14:0,14:1,18:0.3684:1,1:24.1:1:30.2:1:1:0:60:28:0.4:0:1.1 -19 1220321 . T C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.28268;LSEQ=GCAGCTGCAAAGGGGACCCC;RSEQ=GTGAGGGGCAGGGAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:203:156,47:103,39:0.5884:2,2:25.4:1:30.1:1:0.37815:1.26:60:39.6:0.5875:0:1.1 0/1:261:75:48,27:125,61:0.2874:2,2:23.1:1:29.3:1:0.66508:1.15202:60:74:0.2891:0:1.1 -19 1220600 . G A 126 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=25.27868;LSEQ=GCACTGCACCCGTTCGCGGC;RSEQ=GACGACACCTGCCGGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:1:1,0:419,362:0.0013:2,0:47:0:32:0:1:0:60:2:0.0013:0:1 0/1:637:20:11,9:328,288:0.0314:2,2:21.6:1:29.2:1:1:1.07:60:19:0.0304:0:1.2 -19 1220654 . T A 150 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=45.41803;LSEQ=GCTTTCCAGCCGCCCGAGAT;RSEQ=GCCAACGGCCTGGACACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:952:1:1,0:464,487:0.0011:2,0:1:0:24:0:0.48845:0:60:2:0.0011:0:1 0/1:832:38:20,18:395,398:0.0457:2,2:23.1:1:28.7:1:0.74333:1.12:60:37:0.045:0:1.2 -19 1221125 . G T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33802;SOR=3.55379;LSEQ=TGGTCCAGCAGCCACGGGAC;RSEQ=CCTCTGTCCCTGGGGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:1:0,1:263,48:0.0032:2,0:1:0:26:0:0.15705:0:60:2:0.0033:0:1 0/1:265:3:1,2:220,42:0.0113:2,2:15.3:1:26.3:1:0.07249:10.32853:60:6:0.0115:0:1 -19 1221161 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09565;LSEQ=TAGAGCTGGGGCTCCTAGGG;RSEQ=GTCAACCACCTTGACTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:605:207:133,74:257,141:0.3421:2,2:24.4:1:29.7:1:1:1.01411:60:68:0.3406:0:1.1 0/1:613:29:18,11:346,238:0.0473:2,2:23.2:1:29.1:1:0.84781:1.13:60:28:0.0462:0:1.1 -19 1221403 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16117;SOR=Inf;LSEQ=CTTTTGTGCAGAAATGTAGG;RSEQ=TTGGGGGTGTCAGGTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:26,179:0:2,0:24:1:31.7:1:1:0:60:204:1:0:0.2 0/1:138:2:1,1:17,119:0.0145:2,2:12.5:1:28:1:0.24468:6.83:60:4:0.0149:0:1.5 -19 1221484 . C T 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26539;SOR=0.46394;LSEQ=AGTGGAGAGGCCGACCTCCC;RSEQ=GCAGGGCCTGGTTTGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:0,24:0,22:0.5217:1,1:23.5:1:31.1:1:1:0:60:48:0.5333:0:1.1 0/1:18:6:1,5:0,12:0.3333:0,2:21.2:1:31.5:1:0.33333:0:60:12:0.3333:0:1.2 -19 1221545 . C T 94 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.46249;LSEQ=TCTGGGCCCTGTTCACCCTC;RSEQ=GAACTCCCACCCCAGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:3,6:1,7:0.5294:2,2:29.7:1:29.7:1:0.57647:3.26:60:18:0.5294:0:1.3 0/1:3:1:0,1:1,1:0.3333:2,0:50:0:29:0:1:0:60:2:0.3333:0:1 -19 1221991 . G A 104 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02271;SOR=0.19111;LSEQ=AAGAGGTTCTCCATCCGGCA;RSEQ=ATCCGGCAGCACAGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:909:11:6,5:365,532:0.0121:2,2:17.9:1:30.3:1:0.3711:1.75:60:22:0.0123:0:1.3 0/0:857:2:1,1:366,489:0.0023:2,2:9:1:19:1:1:1.34:60:1:0.0012:0:3.5 -19 1222012 . G C 191 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=113.74426;LSEQ=ATCCGGCAGCACAGGTGAGC;RSEQ=GCCCCTGGGGGCAGTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:1:1,0:260,422:0.0015:2,0:3:0:14:0:0.38214:0:60:0:0:0:1 0/1:666:95:39,56:218,350:0.1426:2,2:25.5:1:29.2:1:0.64976:1.12:60:46.5:0.1413:0:1.2 -19 1222268 . A G 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTAGGCATGGAGATGCGCC;RSEQ=GGAAGGGCACAGCTGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:30.7:1:31.9:1:1:0:60:14:0.875:0:1 1/1:3:3:0,3:0,0:1:0,0:37.3:1:30.7:1:1:0:60:6:1:0:1.3 -19 1222951 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10411;SOR=Inf;LSEQ=TGGACCGCCCTGGTGCCAGC;RSEQ=TGACAGGCGCCACTGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:168,29:0:2,0:23.6:1:31.1:1:1:0:60:97.5:1:0:0.1 0/1:176:3:1,2:133,40:0.017:2,2:18:1:23:1:0.14202:6.55867:60:2:0.0116:0:1 -19 1223224 . C A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28031;SOR=0;LSEQ=CTGACTCGGCCAGGATGTCC;RSEQ=ACGGGAGCAGGGTGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:2,1:36,224:0.0114:2,2:5:1:21.7:1:0.05558:12.24:60:2:0.0078:0:3 0/0:173:0:0,0:24,149:0:2,0:23.2:1:31.5:1:1:0:60:85.5:1:0:0.1 -19 1226675 . G A 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15866;SOR=Inf;LSEQ=GCCTGCAGGTGGGGCGCGGC;RSEQ=GGGCCCGGGTGGGGCATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:25,153:0:2,0:24.2:1:30.6:1:1:0:60:58.333:0.9943:0:0.2 0/1:119:2:1,1:18,99:0.0168:2,2:10:1:23:1:0.29497:5.38:60:4:0.0168:0:1 -19 1226772 . C T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.41032;SOR=2.60072;LSEQ=TGGTGACCGTCACGTGGCTG;RSEQ=GCGTGGTTGCCATGTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:1,14:1,15:0.4839:1,1:28.9:1:29.9:1:1:1.07:60:30:0.5:0:1 1/0:7:5:0,5:0,2:0.7143:0,0:18.6:1:32:0:1:0:60:10:0.7143:0:1 -19 1226901 . G T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGGCGGGGCTCTGGGGG;RSEQ=GCGTGCCGTCCTCACAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:27.5:1:28:1:1:0:60:4:0.6667:0:2.5 0/0:1:0:0,0:0,1:0:0,0:40:0:32:0:1:0:60:2:1:0:0 -19 1271910 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49091;SOR=Inf;LSEQ=GGCTGGCATGGGGGCTGGCG;RSEQ=CTCAGCCTGTTGTGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:26,2:0:2,0:29.8:1:30.9:1:1:0:60:56:1:0:0 0/1:28:2:1,1:25,1:0.0714:1,2:12:1:25.5:1:0.14021:18.02309:60:4:0.0714:0:1 -19 1272040 . T C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.71205;LSEQ=GGGTCCTACAGAGACAGTTA;RSEQ=GACAGTTACGGTAAGTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:16:3,13:10,20:0.3404:2,2:28.3:1:30:1:0.49291:2.13232:60:32:0.3404:0:1.1 1/0:68:53:21,32:4,11:0.7794:2,2:23.4:1:30.3:1:0.54527:1.79:60:106:0.7794:0:1.1 -19 1272143 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CAAGCACTTTAGGCTGGACA;RSEQ=TCAGACCTTGTCACTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:28.8:1:34:0:1:0:60:8:1:0:0 0/1:7:2:1,1:0,5:0.2857:0,2:18.5:1:28:1:0.28571:0:60:4:0.2857:0:1 -19 1611547 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCAGTGTCACCTTGGCC;RSEQ=CCCCCATCACTCCGAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:83,2:0.023:1,2:11.5:1:29.5:1:0.06816:34.10659:60:4:0.0235:0:1 0/0:41:0:0,0:34,7:0:2,0:22.4:1:29.9:1:1:0:60:40:1:0:0.2 -19 1611647 . G A 151 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=46.43769;LSEQ=GCCCGGGGTCTCGAGTGGCC;RSEQ=TTCTGGGGCCAGAGCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:1:1,0:416,131:0.0018:2,0:1:0:27:0:1:0:60:2:0.0018:0:1 0/1:485:38:28,10:332,115:0.0784:2,2:22.2:1:28.8:1:1:1.03099:60:11.667:0.0732:0:1.3 -19 1611856 . G A 166 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01696;LSEQ=TTCAGGTTCCGCTCTGGAGG;RSEQ=AGGGGGGAGAGCTCTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:49:17,32:390,561:0.049:2,2:24.9:1:29.6:1:0.45654:1.30824:60:23.5:0.0482:0:1.2 0/0:1147:1:1,0:490,656:9e-04:2,0:1:0:23:0:0.42807:0:60:2:9e-04:0:3 -19 1611917 . G T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01729;SOR=Inf;LSEQ=AAGATGTGAGGTGGGAGTGG;RSEQ=GGGTAGGATGTCGGGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:31,101:0:2,0:11.3:1:30.8:1:1:0:60:32:1:0:0.3 0/1:159:7:1,6:33,118:0.044:2,2:10.7:1:30:1:1:1.67316:60:14:0.0452:0:1 -19 1611929 . CG C 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.51953;SOR=0;LSEQ=GGGAGTGGGGGGTAGGATGT;RSEQ=GGGGGGGGGGTGGGGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:2,0:12,70:0.0235:2,0:32.5:1:30:1:0.0261:0:60:4:0.026:0:0 0/0:55:0:0,0:11,43:0:2,0:5.5:1:26.6:1:1:0:60:9.8:0.98:0:0.7 -19 1612144 . C T 44 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03637;SOR=Inf;LSEQ=CAAGCACAGGAGGACCCCAG;RSEQ=ATCTGCACCTGGGTGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:226,21:0:2,0:23.2:1:32.2:1:1:0:60:60.75:1:0:0.1 0/1:193:4:1,3:163,26:0.0207:2,2:9.3:1:22:1:0.01112:18.31979:60:3:0.0156:0:1.8 -19 1612178 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43115;SOR=2.21993;LSEQ=TGTGGGGAAGGGAGAGGGTG;RSEQ=TGGGGCAGCCCTGGCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:2:1,1:321,69:0.0051:2,2:21:1:28.5:1:0.32563:4.62604:60:4:0.0052:0:1.5 0/1:355:4:2,2:253,97:0.0113:2,2:19.5:1:27.8:1:0.31223:2.60009:60:8:0.0115:0:1.3 -19 1615203 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69754;SOR=1.40164;LSEQ=GAGGGCTGGCTCCAGGAAGG;RSEQ=GGGCGGGGAAGGAGAACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:3:2,1:302,36:0.0088:2,2:14.3:1:25.3:1:0.29223:4.16593:60:2:0.006:0:1 0/1:244:3:2,1:201,40:0.0123:2,2:11.3:1:29.7:1:0.42558:2.50016:60:6:0.0127:0:1 -19 1615796 . G A 174 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=21.79796;LSEQ=GCTTGATCTCGCTGGCGGCC;RSEQ=CCGTGGCACCTGCTCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1328:3:3,0:595,728:0.0023:2,0:1:0:25.3:1:0.09147:0:60:6:0.0023:0:1 0/1:1445:68:32,36:634,741:0.0471:2,2:26.6:1:28.6:1:0.90132:1.04:60:21.667:0.0459:0:1.3 -19 1615852 . C T 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05496;SOR=1.57052;LSEQ=CTAGGGTCAGGGGCCTGCGT;RSEQ=GGCCTCCAGGGCCAACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:35:10,25:135,427:0.0586:2,2:26:1:29.5:1:0.54461:1.26:60:70:0.0599:0:1 0/1:561:50:18,32:131,380:0.0891:2,2:18.9:1:29.1:1:0.13075:1.63:60:100:0.0901:0:1.2 -19 1618982 . C T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00249;SOR=Inf;LSEQ=CCTGAAGTTGCTGACTGGGG;RSEQ=GCCCATGTCACCAGGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:79,2:0:1,0:27.1:1:31.7:1:1:0:60:39.5:1:0:0.1 0/1:37:5:5,0:32,0:0.1351:1,0:28.2:1:29.4:1:1:0:60:10:0.1351:0:1 -19 1619333 . G A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.27001;SOR=0.73676;LSEQ=ACCAGGCCTGCGTGCCGCCC;RSEQ=CCCAGTGACATGGGGCCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:43:24,19:450,424:0.0469:2,2:20.9:1:30.1:1:0.64057:1.19:60:86:0.0473:0:2 0/1:772:27:17,10:391,354:0.035:2,2:21.9:1:28.4:1:0.3297:1.54:60:12.5:0.033:0:3.2 -19 1619339 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.05605;LSEQ=CCTGCGTGCCGCCCGCCCAG;RSEQ=GACATGGGGCCGGTGAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:947:42:25,17:468,436:0.0444:2,2:21:1:31.2:1:0.34713:1.37:60:84:0.0454:0:2 0/1:802:198:105,93:319,284:0.2469:2,2:24.7:1:30.7:1:1:1.01:60:98:0.2472:0:1.5 -19 1619348 . G A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.16802;LSEQ=CGCCCGCCCAGTGACATGGG;RSEQ=CCGGTGAAACCTGAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:956:1:0,1:492,463:0.001:2,0:40:0:32:0:0.48536:0:60:2:0.0011:0:2 0/1:850:21:15,6:430,398:0.0247:2,2:26.2:1:27.7:1:0.11952:2.31:60:20:0.0238:0:3.6 -19 1619350 . C T 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=22.13052;LSEQ=CCCGCCCAGTGACATGGGGC;RSEQ=GGTGAAACCTGAGGCCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:964:1:0,1:495,466:0.001:2,0:1:0:27:0:0.48545:0:60:2:0.0011:0:1 0/1:845:19:13,6:432,394:0.0225:2,2:29.4:1:30.7:1:0.24473:1.97:60:38:0.0228:0:3.8 -19 1619749 . A AGGGTG 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=4.000;MSILEN=1;SSF=0;SOR=2.76838;LSEQ=CCTGCAAATTCTGTCGGGGA;RSEQ=GGGTGGGGTGGGGCGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1186:37:31,6:689,423:0.0312:2,2:30.6:1:31:1:0.00565:3.17:60:74:0.0417:0.0034:0.4 0/1:1148:94:76,18:616,400:0.0819:2,2:26.9:1:29.5:1:8e-05:2.74:60:30.333:0.1035:0.0244:0.4 -19 1619753 . T TGGGGG 95 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=9.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CAAATTCTGTCGGGGAAGGG;RSEQ=GGGGTGGGGCGGGGCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1242:0:0,0:735,460:0:2,0:27.5:1:26:1:1:0:60:3.107:1:0:0.4 0/1:1239:15:1,14:720,453:0.0121:2,1:31.3:1:24.5:1:2e-05:22.20817:60:14:0.0148:0.0097:0.8 -19 1619757 . G C 201 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTGTCGGGGAAGGGTGGG;RSEQ=TGGGGCGGGGCAGGCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1295:0:0,0:753,535:0:2,0:27.6:1:29.2:1:1:0:60:9.915:0.9983:0:0.5 0/1:1291:113:67,46:674,500:0.0875:2,2:28.7:1:29.5:1:0.76517:1.08:60:6.063:0.0833:0:1.3 -19 1619792 . C T 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=31.00966;LSEQ=CACTCACCAGGCCGTGGAGA;RSEQ=CCCCGTCGTAGCTGGGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1639:2:0,2:808,827:0.0012:2,0:1:0:28.5:1:0.49978:0:60:4:0.0012:0:1 0/1:1725:63:31,32:824,835:0.0365:2,2:24.2:1:28.4:1:1:1.01865:60:30.5:0.0361:0:1.4 -19 1619992 . C T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14769;SOR=Inf;LSEQ=GGCCATTCCGGGGCACCCCA;RSEQ=ACTGATGCAAAGCTGCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:5,148:0:1,0:24:1:32.3:1:1:0:60:50:1:0:0.1 0/1:96:2:1,1:3,91:0.0208:1,2:32:0:27:1:0.08202:26.41:60:4:0.0215:0:1.5 -19 1621800 . C T 49 Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.13219;SOR=0;LSEQ=CCCTGCCTGGAGCCCAGTGT;RSEQ=CCCTCGGAGAGGCCGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:4:0,4:278,108:0.0103:2,0:8.3:1:24.8:1:0.00654:0:60:3:0.0078:0:1.8 0/0:316:0:0,0:223,92:0:2,0:23.3:1:30.4:1:1:0:60:44:0.9968:0:0.2 -19 1622012 . C T 78 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09886;SOR=2.70764;LSEQ=GGTGGGTTAGATGGGCACTG;RSEQ=CACCCTCCGCCCACCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1025:4:2,2:494,526:0.0039:2,2:13:1:28:1:1:1.06:60:8:0.004:0:1 0/1:857:9:3,6:419,429:0.0105:2,2:14.4:1:24.9:1:0.50596:1.9519:60:8:0.0095:0:1.7 -19 1622115 . C T 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCCACTGCTGCCCACCGGGC;RSEQ=GCTACCGGGCGGGAGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1122:33:14,19:523,566:0.0294:2,2:23.5:1:30.6:1:0.59752:1.25379:60:32:0.029:0:1.1 0/0:950:0:0,0:466,482:0:2,0:24.9:1:29.9:1:1:0:60:93.8:0.9989:0:0.5 -19 1622116 . G A 241 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACTGCTGCCCACCGGGCC;RSEQ=CTACCGGGCGGGAGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1112:0:0,0:536,576:0:2,0:23.6:1:30.8:1:1:0:60:73.133:1:0:0.2 0/1:945:299:146,153:322,324:0.3164:2,2:26.5:1:29.4:1:0.78004:1.04145:60:48.833:0.314:0:1.2 -19 1623850 . G C 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01644;SOR=Inf;LSEQ=ACAGGGGGCCTGTCCACTCA;RSEQ=GGCCCACCCCGCCATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:291,67:0:2,0:22.8:1:31.7:1:1:0:60:118.333:1:0:0.1 0/1:283:5:4,1:225,51:0.0177:2,2:18.6:1:31.2:1:1:1.10257:60:10:0.0182:0:1 -19 1624007 . A G 209 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGGCTGCGTGTCTGTTAG;RSEQ=AGCAAAAGGGGTGAGAACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1386:0:0,0:673,713:0:2,0:25:1:29.8:1:1:0:60:34.538:1:0:0.2 0/1:1561:114:65,49:713,729:0.073:2,2:26.1:1:30.6:1:0.14418:1.36:60:56:0.0731:0:1.1 -19 1624263 . C T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0117;SOR=Inf;LSEQ=AAAGTAGCCGGGCGTGGTGG;RSEQ=GGGTGCCTATAATTCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:0:1,0:25.5:1:29.5:1:1:0:60:26:1:0:0 1/0:8:4:0,4:0,4:0.5:0,0:8.5:1:30.5:1:1:0:60:8:0.5:0:1 -19 1625558 . G A 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGAAGCCCCCGATGCCCC;RSEQ=GCCAGACCCCGCTCACCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:934:0:0,0:574,359:0:2,0:25:1:29.9:1:1:0:60:50.833:1:0:0.2 0/1:871:46:30,16:473,351:0.0528:2,2:25.3:1:30.2:1:0.35795:1.39:60:45:0.0526:0:1.2 -19 1625791 . G A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28507;SOR=0;LSEQ=AAGAAAAAACTGCAAAGGCC;RSEQ=AAGCCACTCAGACCCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:2,1:22,254:0.0108:2,2:14.7:1:26.7:1:0.02022:22.47:60:6:0.0109:0:1 0/0:178:0:0,0:23,155:0:2,0:24:1:31.1:1:1:0:60:356:1:0:0.1 -19 1625811 . T C 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=GAAGCCACTCAGACCCGCCC;RSEQ=GCAGTGGGTGATGCCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:6,173:0:1,0:24.1:1:30.4:1:1:0:60:43.75:1:0:0.1 0/1:110:8:0,8:7,95:0.0727:2,0:22.5:1:30.8:1:1:0:60:16:0.0727:0:1 -19 1627422 . T C 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGCGCCCCGCTCACCGCTC;RSEQ=TGCCTGCAAGGGGAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1047:0:0,0:511,535:0:2,0:25:1:30.1:1:1:0:60:36.357:0.999:0:0.2 0/1:936:30:14,16:404,501:0.0321:2,2:30:1:30.2:1:0.85363:1.08:60:29:0.0315:0:1.2 -19 1627619 . G A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCAGTATGCCCATCTCCC;RSEQ=CAGAGCCCTGCCCTCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:1,2:1,47:0.0588:1,2:21:1:30.3:1:0.11529:19.40:60:6:0.06:0:1 0/0:16:0:0,0:1,15:0:1,0:28.6:1:31.8:1:1:0:60:32:1:0:0.1 -19 1628047 . A G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAGGGGACAGCAGAGCTC;RSEQ=CAGGGGGTGAGGCGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:18:0:27:0:1:0:26:2:1:0:7 1/0:3:2:1,1:0,1:0.6667:0,2:14:0:33:1:1:0:25:4:0.6667:0:1.5 -19 1631811 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1215;SOR=Inf;LSEQ=GAACGGCCTCCCTGCCTCTA;RSEQ=GCTCAGGCGGGGAAGCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:164,7:0:1,0:25.8:1:32.3:1:1:0:60:170:1:0:0.1 0/1:92:2:1,1:85,5:0.0217:2,2:31:1:31.5:1:0.12685:15.60585:60:4:0.0217:0:1 -19 1632160 . G GC 175 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=34.03774;LSEQ=GAGGTGCTGGGGCTTCACAG;RSEQ=CCCCCCCTCCACCCCGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:917:2:1,1:351,563:0.0022:2,2:33.5:1:32:1:1:1.60:60:4:0.0022:0:0.5 0/1:750:52:13,39:283,411:0.0693:2,2:29.6:1:30.7:1:0.02725:2.06383:60:51:0.0701:0.004:0.1 -19 1646161 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04416;SOR=Inf;LSEQ=GGGCTCAGGGGCTCGGGCTC;RSEQ=CAAGGCAGGTCACACGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:63,1:0:1,0:24.8:1:31.2:1:1:0:60:128:1:0:0 0/1:36:3:3,0:32,1:0.0833:1,0:29:1:31:1:1:0:60:6:0.0833:0:1.7 -19 1646221 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.39576;LSEQ=GTCTTCAGGCTCGCTGCCCC;RSEQ=GACCCGGCCTGTGTGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:8:8,0:172,4:0.0435:1,0:24.9:1:31.4:1:1:0:60:16:0.0437:0:1.1 0/1:143:43:40,3:98,2:0.3007:1,2:19.2:1:30.9:1:0.16022:3.63713:60:86:0.3028:0:1.2 -19 1646229 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19642;SOR=Inf;LSEQ=GCTCGCTGCCCCCGACCCGG;RSEQ=CTGTGTGGCCCTTTCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:219,4:0:1,0:23:1:32.1:1:1:0:60:43.6:1:0:0.1 0/1:178:2:2,0:169,7:0.0112:1,0:32:1:27:1:1:0:60:4:0.0115:0:1.5 -19 1646471 . C A 45 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04893;SOR=Inf;LSEQ=GAGCGGGGCGGGTGGCAAAC;RSEQ=AAACCCTACAGTCCCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:105,318:0:2,0:23.5:1:31.2:1:1:0:60:34.25:0.9976:0:0.2 0/1:378:4:3,1:105,269:0.0106:2,2:13.3:1:22.8:1:0.07224:7.64:60:3:0.0081:0:2.3 -19 1646644 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACCCTGGACACCCACGC;RSEQ=CAGAGTGAGAAAACTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:1,17:0.1:1,0:17:1:31.5:1:1:0:60:4:0.1:0:1 0/0:6:0:0,0:1,5:0:2,0:24.3:1:32.5:1:1:0:60:12:1:0:0.3 -19 1650134 . A G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.87141;LSEQ=AACCTTCCCGTGAACTGTGG;RSEQ=GGCAAAGGGGTGTCGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:783:38:26,12:481,263:0.0485:2,2:24.7:1:30.2:1:0.72902:1.18:60:18:0.0477:0:1.1 0/1:707:237:170,67:290,178:0.3352:2,2:23.3:1:30.1:1:0.01193:1.56:60:38.5:0.3353:0:1.1 -19 1650432 . CG C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50695;SOR=0;LSEQ=CCAGCAGAGCCCTGGGGGCA;RSEQ=GGGAGCCCTGGGAGCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:0,2:1,62:0.0308:1,0:28.5:1:32:0:1:0:60:4:0.0308:0:0 0/0:48:0:0,0:2,46:0:1,0:21.3:1:30.5:1:1:0:60:96:1:0:0.2 -19 2164109 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22986;SOR=Inf;LSEQ=GCCCCTCCCTCCCGCCCGCC;RSEQ=TCCTCCGCCCACCGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:53,4:0:2,0:10.8:1:31.8:1:1:0:59.6:114:1:0:0.9 0/1:53:2:2,0:42,9:0.0377:2,0:6:1:27.5:1:1:0:60:4:0.0377:0:2 -19 2164138 . C A 24 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.49927;SOR=0;LSEQ=CCACCGGCGGCCCCGCCCCT;RSEQ=CCCCAACCGCCCGCCTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:169,26:0.0102:2,2:30:1:24.5:1:0.25593:6.39734:60:4:0.0104:0:4 0/0:184:0:0,0:144,40:0:2,0:19.9:1:30.9:1:1:0:60:45:1:0:0.3 -19 2164139 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.11572;SOR=Inf;LSEQ=CACCGGCGGCCCCGCCCCTC;RSEQ=CCCAACCGCCCGCCTAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:174,28:0:2,0:19.9:1:31.3:1:1:0:59.9:66.333:1:0:0.4 0/1:193:3:1,2:148,42:0.0155:2,2:7:1:25.7:1:0.13072:6.95437:60:6:0.0158:0:2 -19 2164167 . C T 44 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19584;SOR=0.22397;LSEQ=GCCCGCCTAGCATGGTGCGG;RSEQ=GGCCGCGCGCGCGGACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:4:1,3:306,92:0.01:2,2:8.3:1:22.3:1:0.04261:9.90432:60:3:0.0076:0:1.3 0/0:446:1:0,1:294,151:0.0022:2,0:1:0:26:0:0.34081:0:60:2:0.0023:0:1 -19 2164351 . T A 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.78064;LSEQ=CAAACCCCCCCAAGCCGCGC;RSEQ=CACCGGTCCCCCCTGCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:38:4,34:36,231:0.1242:2,2:24.8:1:29.1:1:0.79885:1.32354:60:18:0.1259:0:1.3 0/1:226:64:9,55:24,136:0.2832:2,2:19.9:1:29:1:1:1.07808:60:15:0.2871:0:1.2 -19 2164363 . C A 29 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.5655;SOR=3.05467;LSEQ=AGCCGCGCTCACCGGTCCCC;RSEQ=CTGCGGAACGGAGACCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:1:1,0:13,229:0.0041:2,0:1:0:27:0:0.05761:0:60:2:0.0042:0:1 0/1:160:2:1,1:12,146:0.0125:2,2:5:0:29.5:1:0.15637:11.73:60:4:0.0128:0:0 -19 2164394 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15469;SOR=Inf;LSEQ=GAGACCCTGGACTCCACTGT;RSEQ=GCTGCTCCACCCCCGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:0,118:0:1,0:22.3:1:30.1:1:1:0:60:117:1:0:0.3 0/1:77:2:1,1:2,73:0.026:1,2:7.5:1:29.5:1:0.0769:30.00:60:4:0.0263:0:1.5 -19 2186237 . G A 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGACGGCCAGAAGTCCGC;RSEQ=TTCCTGCCTGAGGCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:33.8:1:31.5:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 2189588 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGGAAAGCGAGGCTTCT;RSEQ=CCAGAAGGGTCTTGGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:2,0:118,1:0.0165:1,0:20:1:27.5:1:1:0:60:4:0.0168:0:1 0/0:50:0:0,0:47,3:0:2,0:22.5:1:31.5:1:1:0:60:49:1:0:0 -19 2189631 . G T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55384;SOR=0;LSEQ=GCTGGTGGCTGTCCAGGCAG;RSEQ=GACCACACCTTGGAGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:3:3,0:231,13:0.0121:2,0:27.7:1:22.3:1:1:0:60:2:0.0083:0:1.7 0/0:120:0:0,0:111,9:0:2,0:22.7:1:30.9:1:1:0:60:59:1:0:0.1 -19 2190774 . T A 30 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84709;LSEQ=GAGAGGCCCGTGGCAGGAGG;RSEQ=GGAGCCTCCTAGGACCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:39:1:30:1:1:0:60:4:0.2857:0:1 0/1:4:1:1,0:2,1:0.25:2,0:20:0:31:0:1:0:60:2:0.25:0:1 -19 2190919 . C G 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00867;SOR=Inf;LSEQ=GAGGCCATGCAGCCGACTCC;RSEQ=TGCTTCCGCTGGGAAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:111,9:0:2,0:25:1:31.2:1:1:0:60:240:1:0:0.2 0/1:102:6:5,1:84,12:0.0588:2,2:9.2:1:29.8:1:0.56845:1.39485:60:12:0.0588:0:1.3 -19 2190947 . TTGG T 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.00058;SOR=2.67841;LSEQ=GCTGGGAAAGGTCCCGGGTC;RSEQ=TGGTGGAGGGGCTGGGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:23:17,6:145,35:0.1127:2,2:18.8:1:30.5:1:0.42088:1.45921:59.6:46:0.115:0.0441:0.2 0/1:169:43:32,11:90,36:0.2544:2,2:23.1:1:30.4:1:0.84419:1.16:60:86:0.2575:0.0828:0.1 -19 2190994 . C T 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6863;SOR=2.00857;LSEQ=GTTTATGTGACATGGCCGGG;RSEQ=CACCCTCCGTCCGCAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:2:1,1:283,106:0.0051:2,2:20.5:1:29:1:0.47294:2.662:60:4:0.0052:0:1 0/1:392:4:1,3:245,142:0.0102:2,2:11.8:1:25.5:1:0.14608:5.15422:60:3:0.0079:0:1.3 -19 2191338 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53041;SOR=0;LSEQ=AAGAGTTTATCAGGGACTTG;RSEQ=GACGTTGGCGTGGACAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:5,156:0.0123:1,2:14:1:30:1:0.07248:28.59:60:4:0.0126:0:1 0/0:97:0:0,0:6,91:0:2,0:18.7:1:29.6:1:1:0:60:47.5:1:0:0.2 -19 2193925 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGACGTCTTGGTTGCCTG;RSEQ=AGCGTGTGCCTGTGAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:4,66:0.0278:2,2:23.5:1:27.5:1:0.13498:14.87:60:4:0.0278:0:1 0/0:25:0:0,0:0,24:0:1,0:20.9:1:31.6:1:1:0:60:48:1:0:0.2 -19 2194437 . C T 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25431;SOR=3.04896;LSEQ=TCCTCAGCCTCCCAAAGTGC;RSEQ=GGGATTACAGGCGTGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:2:1,1:358,117:0.0042:2,2:4.5:1:29:1:0.43395:3.05102:60:4:0.0043:0:1.5 0/1:394:5:3,2:281,106:0.0127:2,2:13.6:1:28.4:1:0.61881:1.76441:60:10:0.0128:0:2 -19 2194657 . C T 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=2.57412;LSEQ=TGTCAGCCCCTCCTTTCTTG;RSEQ=CGATGTTGGCACATGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:37:5,32:36,247:0.1156:2,2:23.7:1:29.4:1:0.79841:1.07:59.5:17.5:0.1133:0:1.3 0/1:234:59:10,49:33,142:0.2521:2,2:24.2:1:28.5:1:0.84711:1.13813:60:28.5:0.2511:0:1.1 -19 2194660 . A ATGTTGGCACATGGC 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=1.929;MSILEN=1;SSF=0.00927;SOR=2.28159;LSEQ=CAGCCCCTCCTTTCTTGCCG;RSEQ=TGTTGGCACATGGCTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:19:1,18:29,246:0.0646:2,1:28.2:1:29.4:1:0.70439:2.11778:58.7:38:0.066:0.0136:1.2 0/1:220:30:0,30:35,154:0.1364:2,1:33.5:1:30.8:1:0.00589:0:60:60:0.1408:0.0227:0.9 -19 2194769 . A G 75 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02627;SOR=9.87065;LSEQ=CAGCAGGCGCCTCTGTTGGT;RSEQ=CCGTCCCTCTCGTCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:0,31:0.0313:1,0:45:0:34:0:1:0:60:2:0.0323:0:1 0/1:20:5:0,5:1,14:0.25:1,0:26.6:1:32.4:1:1:0:60:10:0.25:0:1 -19 2194896 . T C 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GGACAGGCTGGGTTCTGGGC;RSEQ=GGCTGCGGCATCCTTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:20.5:1:29.5:1:1:0:60:12:1:0:1.3 0/0:2:0:0,0:1,1:0:2,0:1:0:30.5:1:1:0:60:4:1:0:0.5 -19 2196170 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCCCTCCGCACTGTCCCACA;RSEQ=CACAAGTGAAGGCCGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:31.3:1:32.7:1:1:0:60:6:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:35:1:29:1:1:1:60:4:0.5:0:1.5 -19 2199748 . TG T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.53113;SOR=0;LSEQ=GCTCCCAGGGCTGCAGCCGG;RSEQ=GGGCCTGGGCCTCCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:126,1:0.0155:1,2:9.5:1:30.5:1:0.03089:89.65831:60:4:0.0165:0.0078:0.5 0/0:76:0:0,0:74,2:0:1,0:23.6:1:31.6:1:1:0:60:37:1:0:0.2 -19 2199950 . G A 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.48209;LSEQ=CAACACGAGGTATGGCCAGC;RSEQ=TGGGGCATGCAGGGCATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:727:1:1,0:315,411:0.0014:2,0:1:0:26:0:0.43466:0:60:2:0.0014:0:1 0/1:699:37:16,21:280,381:0.0529:2,2:27.9:1:29.4:1:1:1.04:60:36:0.0525:0:1.2 -19 2199993 . G A 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1773;SOR=5.04059;LSEQ=GTGTGCGCTCACAGGCGGGC;RSEQ=GTGGCCATGGCACCGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:1:1,0:138,329:0.0021:2,0:1:0:26:0:0.29701:0:60:2:0.0022:0:1 0/1:374:4:3,1:119,251:0.0107:2,2:13:1:26.3:1:0.10369:6.29:60:3:0.0084:0:2.3 -19 2200022 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17474;SOR=Inf;LSEQ=GGCACCGGGGACCGGGAGCG;RSEQ=CCCCTCGCTCCTGTGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:54,214:0:2,0:24.6:1:31.9:1:1:0:60:267:1:0:0.1 0/1:193:2:1,1:44,147:0.0104:2,2:13:1:30.5:1:0.41289:3.31:60:4:0.0105:0:1.5 -19 2200037 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51929;SOR=0;LSEQ=GAGCGGCCCCTCGCTCCTGT;RSEQ=CTGGCTGTGGCAGGAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:0,2:26,173:0.01:2,0:38.5:1:32:0:1:0:60:4:0.0103:0:1 0/0:133:0:0,0:20,111:0:2,0:24.8:1:31.7:1:1:0:60:64.5:0.9847:0:0.2 -19 2202887 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12571;SOR=Inf;LSEQ=CAGCTCAGACTTGGGGTCTT;RSEQ=AGTCCCCTTGGAGCCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:9,214:0:1,0:27.6:1:32.4:1:1:0:60:222:1:0:0 0/1:123:2:1,1:6,115:0.0163:1,2:11.5:1:27:1:0.11102:17.82:60:4:0.0167:0:1 -19 2202921 . C CT 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.55438;SOR=0;LSEQ=CCAGGTGGTCTTCCTTTATG;RSEQ=TTTTTTTTCTTTTTTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:3:0,3:2,121:0.0238:1,0:22.7:1:30.9:1:1:0:60:6:0.0238:0.0079:0 0/0:55:0:0,0:1,54:0:1,0:20.1:1:32.8:1:1:0:60:110:1:0:0.1 -19 2206520 . CA C 68 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=23.000;MSILEN=1;SSF=0.12043;SOR=3.46488;LSEQ=TGAGCCGGGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:4,0:21,0:0.1481:1,0:14.5:1:32:1:1:0:60:8:0.1481:0.037:1 0/1:13:5:5,0:6,0:0.3846:0,0:25.2:1:29.3:1:1:0:55.2:10:0.3846:0.1538:2.6 -19 2206575 . G T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37686;SOR=0.47816;LSEQ=AATAGGCTTCAACTTGGAAG;RSEQ=TGTTTCCTAGTGTTGCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:10:10,0:108,0:0.0847:1,0:25.4:1:30.9:1:1:0:60:20:0.0862:0:1.1 0/1:71:3:3,0:68,0:0.0423:1,0:13.3:1:26.3:1:1:0:60:2:0.0323:0:1 -19 2206610 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51168;SOR=0;LSEQ=GCTTGTAGGCAGGTGGACAG;RSEQ=ACCCGGAGCCCAGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:179,5:0.0108:1,2:19.5:1:27.5:1:0.06364:32.7567:60:4:0.0109:0:1 0/0:134:0:0,0:128,5:0:1,0:26.9:1:30.6:1:1:0:60:18:1:0:0.3 -19 2206622 . AGT A 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1.09297;LSEQ=GTGGACAGGACCCGGAGCCC;RSEQ=GTGTGTGTGTTCCGTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:6:6,0:229,15:0.024:2,0:25.7:1:31.3:1:1:0:60:12:0.0241:0.004:0 0/1:191:5:4,1:170,16:0.0262:2,2:20.8:1:31.4:1:0.3758:2.63665:60:10:0.0267:0:0 -19 2207041 . A G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07368;SOR=Inf;LSEQ=GCACTGTGTGCCATGGGGGT;RSEQ=GAATCACTCCTCGGGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:21.8:1:31.7:1:1:0:60:22:1:0:0.2 0/1:9:3:1,2:1,5:0.3333:2,2:17.7:1:31:1:1:2.24:60:6:0.3333:0:1 -19 2207269 . A G 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGTGCCTGTGTTGCTGG;RSEQ=TGCTGGCCGTTCTTGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:5,0:0.2857:0,2:15.5:1:32:0:0.28571:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 2207386 . G C 113 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15565;SOR=0;LSEQ=GGTTGGAGGGGCCCAGGCCA;RSEQ=GTGGTGTTGAATGGTGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:12:12,0:23,0:0.3429:1,0:24.3:1:31.7:1:1:0:60:24:0.3429:0:1.4 0/0:6:0:0,0:6,0:0:0,0:18.5:1:33.8:1:1:0:60:12:1:0:0.2 -19 2207517 . T C 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15257;SOR=Inf;LSEQ=GCCCTGGGGTGGGTGAGGTC;RSEQ=GCATGGAGGGGCTGTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:254,51:0:2,0:25.5:1:31.1:1:1:0:60:100.667:1:0:0.1 0/1:196:2:1,1:159,35:0.0102:2,2:30:1:24.5:1:0.33438:4.4934:60:4:0.0105:0:2 -19 2207536 . C T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17738;SOR=5.03499;LSEQ=CTGCATGGAGGGGCTGTGGG;RSEQ=AGGCGCAGGCCCCGGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:1:0,1:301,94:0.0025:2,0:1:0:24:0:0.2399:0:60:2:0.0026:0:1 0/1:318:4:1,3:227,87:0.0126:2,2:9.5:1:24.8:1:0.07018:7.76926:60:8:0.0127:0:1 -19 2207549 . C T 88 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05134;SOR=4.67482;LSEQ=CTGTGGGCAGGCGCAGGCCC;RSEQ=GGCCTCACCTGTGGCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:2:0,2:345,135:0.0041:2,0:1:0:25:0:0.08037:0:60:4:0.0042:0:1 0/1:419:8:5,3:280,131:0.0191:2,2:22:1:29.6:1:0.71446:1.28161:60:16:0.0193:0:1 -19 2207797 . GC G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCTCAGAGCCCTCAAC;RSEQ=CCCCCGGCCCCTGAGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:0,2:2,119:0.0163:1,0:15:1:32:1:1:0:60:4:0.0168:0.0081:0.5 0/0:58:0:0,0:3,55:0:2,0:23.6:1:30.9:1:1:0:60:28:1:0:0.1 -19 2208410 . T G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGGAGCGCTGGTGCCG;RSEQ=CTGGGGACCGACAGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 2208859 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.83612;LSEQ=CACTGTCCAGGTTGCTGTTG;RSEQ=TACCTGGGTGTCCAGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:34:23,11:261,134:0.0793:2,2:22.7:1:31.1:1:1:1.07:60:33:0.0778:0:1 0/1:379:164:109,55:138,77:0.4327:2,2:23.3:1:31.9:1:0.66468:1.11:60:163:0.4324:0:1.2 -19 2209142 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17157;SOR=Inf;LSEQ=CTCCTTCCTGCTCCTCCCCA;RSEQ=TGTCACTCCTGGTCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:1,69:0:1,0:26.3:1:32.3:1:1:0:60:140:1:0:0.1 0/1:50:2:1,1:0,48:0.04:1,2:20:1:28.5:1:0.04:0:60:4:0.04:0:1 -19 2210357 . C T 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.63759;SOR=0.43779;LSEQ=CGGTGCAGGAGGGCCGTGGG;RSEQ=AGCGCTGGGGCTTCCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:2,1:197,60:0.0115:2,2:31.7:1:22.7:1:0.55322:1.63815:60:2:0.0079:0:2.3 0/0:197:1:0,1:138,58:0.0051:2,0:1:0:23:0:0.29949:0:60:2:0.0051:0:1 -19 2210736 . C T 164 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=28.7236;LSEQ=AAGATGGCTGGCCGCAAGCG;RSEQ=GGGCGCCCCAAGAAGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:904:2:1,1:438,463:0.0022:2,2:17:1:30.5:1:1:1.06:60:4:0.0023:0:1 0/1:901:54:26,28:401,446:0.0599:2,2:24.2:1:28.6:1:1:1.03:60:108:0.0605:0:1.1 -19 2210778 . G A 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGCGAACCCCGAGCGGAA;RSEQ=CCCAAGAAGAACCAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:687:0:0,0:297,390:0:2,0:25:1:31.7:1:1:0:60:41.938:1:0:0.2 0/1:674:31:16,15:274,368:0.046:2,2:25:1:28.8:1:0.35655:1.43:60:30:0.0451:0:1.3 -19 2211050 . C T 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43526;LSEQ=ATGCTGACGCCTCTGCCCAC;RSEQ=GCTCTCCCGACCCGCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:602:272:171,101:225,105:0.4518:2,2:23.7:1:30.3:1:0.19543:1.26515:60:53.4:0.4503:0:1.1 0/1:504:133:89,44:244,127:0.2639:2,2:23.5:1:29.9:1:0.83179:1.05:60:43.333:0.261:0:1.1 -19 2211220 . G T 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGAAGCTTCTAGGTGAGCCC;RSEQ=TGTGAGGCGTCCGGCGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:24:7,17:182,344:0.0434:2,2:21.7:1:30.3:1:0.6653:1.28434:60:48:0.0442:0:1.1 0/0:535:0:0,0:195,340:0:2,0:22.5:1:30.2:1:1:0:60:88.167:1:0:0.2 -19 2211221 . T C 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=GAAGCTTCTAGGTGAGCCCG;RSEQ=GTGAGGCGTCCGGCGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:0:0,0:188,359:0:2,0:24.2:1:29.5:1:1:0:60:41.077:1:0:0.2 0/1:526:15:5,10:181,327:0.0285:2,2:22.7:1:30:1:1:1.10684:60:30:0.0294:0:1 -19 2211638 . T C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50196;SOR=0;LSEQ=TCTGCTGAGCTCCTGCCTCA;RSEQ=GAGTGCCTGACACCTGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:2,0:179,9:0.0105:1,0:34.5:1:34:0:1:0:60:4:0.0106:0:1 0/0:162:0:0,0:153,9:0:2,0:24.4:1:29.9:1:1:0:60:80:1:0:0.1 -19 2211951 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52293;SOR=0;LSEQ=TGGAGCGCAGGCCTGAGTGG;RSEQ=CTCCCTCCTCTGCTCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:0,2:1,111:0.0175:1,0:19:1:31.5:1:1:0:60:4:0.018:0:1 0/0:72:0:0,0:2,69:0:1,0:21.4:1:31.6:1:1:0:60:22.667:0.9855:0:0.2 -19 2212683 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAAGCGGGGGCAGGGGAGG;RSEQ=TGACAAGCAGGCATCAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:12:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:29.5:1:1:0:60:4:1:0:1.5 -19 2213298 . G T 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGGCTGAGTCCAGGTG;RSEQ=GGTGGCAGGTGCAGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,1:0.2:1,0:20.8:1:31.2:1:1:0:60:10:0.2083:0:1 0/0:2:0:0,0:2,0:0:0,0:4:1:30:1:1:0:60:4:1:0:0 -19 2213563 . C T 89 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03064;SOR=5.04677;LSEQ=GAACGCCCAGCTCCTGGGTG;RSEQ=GGCTCAGCAGCTCCTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:863:2:1,1:500,361:0.0023:2,2:14:1:28.5:1:1:1.38449:60:4:0.0024:0:1 0/1:776:9:3,6:417,350:0.0116:2,2:21.7:1:28.2:1:0.31435:2.38026:60:18:0.0117:0:1.1 -19 2213721 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1483;SOR=Inf;LSEQ=GTCCGTCGGTATGGCTTCCT;RSEQ=TGGCTTCCTGTCTATGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:74,219:0:2,0:23.9:1:32:1:1:0:60:72.25:1:0:0.1 0/1:184:2:1,1:36,146:0.0109:2,2:33:1:28:1:0.36262:4.01:60:4:0.0109:0:1 -19 2213885 . A G 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01273;SOR=Inf;LSEQ=GACCTACAACGACCTGATTC;RSEQ=AGCGCAGAAGGAGATCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:577:0:0,0:303,274:0:2,0:26.2:1:30:1:1:0:60:81.429:1:0:0.1 0/1:542:6:4,2:290,246:0.0111:2,2:34.2:1:27.5:1:0.69255:1.69:60:5:0.0094:0:1.5 -19 2214057 . C T 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0909;SOR=0.58024;LSEQ=GGGCGGGTGTGTCCTCTGTG;RSEQ=GGGTGGGAGGCTCTGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:59:10,49:7,32:0.602:2,2:25.6:1:28.7:1:1:1.07111:60:10.8:0.587:0:1.2 0/1:75:35:5,30:8,32:0.4667:2,2:24.1:1:28.9:1:0.55709:1.49199:60:34:0.4658:0:1.2 -19 2214242 . G A 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGAGGTGTGGGGTCATGC;RSEQ=AGCATCCCACCATCGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:5,1:7,5:0.3333:2,2:20.8:1:27.7:1:0.60003:3.34:60:5:0.3125:0:2 0/0:1:0:0,0:1,0:0:0,0:9:0:24:0:1:0:60:2:1:0:0 -19 2214423 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.156;SOR=Inf;LSEQ=CTGAGAGTGTGGGGTGTGCT;RSEQ=GGCAGGCAGCCAGCCAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:226,75:0:2,0:24.9:1:31.7:1:1:0:60:74.25:1:0:0.1 0/1:197:2:1,1:141,54:0.0102:2,2:29:1:29:1:0.48146:2.59643:60:4:0.0103:0:1 -19 2214634 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09546;SOR=Inf;LSEQ=TGCACTCCGTGGTGTCCGAG;RSEQ=CTCTCCCATCAGCCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:55,223:0:2,0:25.1:1:31.3:1:1:0:60:54.6:1:0:0.1 0/1:235:3:2,1:55,177:0.0128:2,2:23:1:27:1:0.14674:6.37:60:6:0.0129:0:1 -19 2216175 . C A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03791;SOR=Inf;LSEQ=GTTTTTCCATCCCACACAAG;RSEQ=AGCGGGGGTCCTGGCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:77,6:0:2,0:24.5:1:31.4:1:1:0:60:26.667:1:0:0.1 0/1:43:3:3,0:36,4:0.0698:2,0:15.3:1:30:1:1:0:60:6:0.0698:0:1 -19 2216738 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24878;SOR=Inf;LSEQ=GACCACACGGTGCCCGGCAG;RSEQ=CCGGCTGCCAGTGAGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:107,190:0:2,0:25.5:1:31.7:1:1:0:60:98:1:0:0.1 0/1:301:3:2,1:114,184:0.01:2,2:11.3:1:27:1:0.56126:3.22:60:6:0.0101:0:1 -19 2216750 . T A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24858;SOR=Inf;LSEQ=CCCGGCAGGCCGGCTGCCAG;RSEQ=GAGCTGCATTCGAGGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:98,163:0:2,0:24.8:1:29.8:1:1:0:60:51.2:1:0:0.1 0/1:263:3:2,1:97,163:0.0114:2,2:28.7:1:26.3:1:0.55854:3.34:60:6:0.0116:0:1 -19 2216784 . TG T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.09477;SOR=Inf;LSEQ=GGTGAGTGCCCTGGTGGGGC;RSEQ=GGGGTCTGCAGCTGGTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:74,105:0:2,0:22.7:1:31.4:1:1:0:60:43.75:1:0:0.1 0/1:151:3:1,2:47,101:0.0199:2,2:11.3:1:30.3:1:1:1.07:60:6:0.0201:0:0.3 -19 2216789 . G C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20271;SOR=Inf;LSEQ=GTGCCCTGGTGGGGCTGGGG;RSEQ=TCTGCAGCTGGTACCTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:71,103:0:2,0:22.6:1:31.7:1:1:0:60:57:1:0:0.1 0/1:143:2:1,1:41,100:0.014:2,2:5:0:32.5:1:0.50261:2.42:60:4:0.0142:0:0.5 -19 2216794 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50676;SOR=0;LSEQ=CTGGTGGGGCTGGGGGTCTG;RSEQ=AGCTGGTACCTGCCGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:2,0:73,95:0.0118:2,0:24.5:1:28:1:0.19318:0:60:4:0.0119:0:2.5 0/0:131:0:0,0:41,90:0:2,0:23.2:1:31.8:1:1:0:60:31.75:1:0:0.2 -19 2216810 . A T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5106;SOR=0;LSEQ=TCTGCAGCTGGTACCTGCCG;RSEQ=CTCTGCCTGGTGTGCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:90,70:0.0123:2,2:18:0:32:0:1:1.28369:60:4:0.0127:0:1.5 0/0:118:0:0,0:50,68:0:2,0:23.4:1:29.5:1:1:0:60:117:1:0:0.2 -19 2216827 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15219;SOR=Inf;LSEQ=CCGACTCTGCCTGGTGTGCT;RSEQ=AGGCTGTCGGGTTCTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:113,66:0:2,0:24.5:1:31.2:1:1:0:60:43.75:1:0:0.2 0/1:115:2:1,1:65,48:0.0174:2,2:35:0:30.5:1:1:1.35053:60:4:0.0174:0:1 -19 2216894 . G T 126 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=8.74555;LSEQ=GTGGGGAGGTGCTGGGCCAG;RSEQ=CCGCTGCCTCTGAGTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:3:0,3:304,138:0.0067:2,0:12.7:1:23:1:0.03135:0:60:2:0.0046:0:2 0/1:374:21:13,8:231,121:0.0561:2,2:19.3:1:28.8:1:0.81407:1.1743:60:42:0.0572:0:1.1 -19 2216896 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18412;SOR=4.79273;LSEQ=GGGGAGGTGCTGGGCCAGGC;RSEQ=GCTGCCTCTGAGTGCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:1:0,1:309,147:0.0022:2,0:11:0:14:0:0.32385:0:60:0:0:0:4 0/1:384:4:1,3:247,133:0.0104:2,2:5.5:1:29.3:1:0.1293:5.54591:60:8:0.0106:0:1 -19 2217123 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18023;SOR=Inf;LSEQ=CCCCTGCCCCGGGCTCAGGG;RSEQ=GGTGCTCAGCAGAGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:66,199:0:2,0:24.1:1:30.5:1:1:0:60:52:1:0:0.1 0/1:196:2:1,1:64,130:0.0102:2,2:21.5:1:29:1:1:2.02:60:4:0.0104:0:1 -19 2217203 . G A 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04334;SOR=0;LSEQ=TTGGGGCACGGTGAGGTACT;RSEQ=GGGCTGACCTGGAGTAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:7:1,6:1,51:0.1186:1,2:24.9:1:30.6:1:0.22501:7.95:60:14:0.1207:0:1 0/0:35:0:0,0:2,33:0:2,0:18.3:1:30.8:1:1:0:60:70:1:0:0.2 -19 2217659 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15225;SOR=Inf;LSEQ=AAGGTTGCAGGGCCTTGGCA;RSEQ=CGTGGGGGCCGCCTTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:137,6:0:1,0:26.6:1:32.2:1:1:0:60:70.5:1:0:0.2 0/1:92:2:1,1:85,5:0.0217:2,2:21.5:1:28.5:1:0.12685:15.60585:60:4:0.0217:0:1 -19 2217754 . C T 118 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00058;SOR=6.57089;LSEQ=GTTGACCCACGACTGGGGGT;RSEQ=GGGCCTTCGTCTGCAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:3:1,2:410,226:0.0047:2,2:7.7:1:29:1:0.29077:3.62061:60:6:0.0048:0:1 0/1:598:18:10,8:347,233:0.0301:2,2:22.1:1:28.3:1:0.80855:1.19106:60:17:0.0289:0:1.3 -19 2217970 . C T 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=CCACGTTGAGGCAAAACAGT;RSEQ=TGGGGTGCTCGAGACCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:59,270:0:2,0:23.9:1:31.9:1:1:0:60:64.8:0.9969:0:0.1 0/1:257:12:2,10:55,190:0.0467:2,2:18.4:1:30.3:1:1:1.44545:60:24:0.0476:0:1 -19 2219783 . G A 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGCTTGGAGAACACAGCC;RSEQ=CTTCCCGGTGAGGGCGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:30:1:32:0:1:0:60:4:0.4:0:1 1/1:1:1:1,0:0,0:1:0,0:6:0:32:0:1:0:60:2:1:0:1 -19 2220254 . TCTG T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.05927;SOR=2.42308;LSEQ=CTGTGCCCTACCCTCAGGAC;RSEQ=CTGCTGCTGCTGCTCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:8:3,5:110,345:0.0172:2,2:30.6:1:31.4:1:0.41047:1.88:60:16:0.0175:0:0.1 0/1:392:16:3,13:123,253:0.0408:2,2:31.2:1:33:1:0.28773:2.10327:60:32:0.0417:0:0.2 -19 2220642 . C A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTTCCTTGAGAAGGTGCCGC;RSEQ=TGAGCAGTCTCTGCTGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:18:1:32.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:28.5:1:1:0:60:4:1:0:1.5 -19 2221792 . T C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01081;SOR=Inf;LSEQ=CACAGGGTCAGCCCTGAGCC;RSEQ=TGAGCTTGCCCACAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:26,2:0:2,0:26.9:1:29.7:1:1:0:60:13:1:0:0.2 0/1:9:3:3,0:3,3:0.3333:2,0:17.7:1:30.3:1:0.46429:0:60:6:0.3333:0:1.3 -19 2221892 . C A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=CTCTCCTGGAGCCCACAGAG;RSEQ=TCCTAGGGGGTGGTGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:142,21:0:2,0:21.8:1:32.6:1:1:0:60:326:1:0:0.2 0/1:68:8:7,1:52,8:0.1176:2,2:19:1:28.4:1:1:1.08:60:7:0.1061:0:1 -19 2221918 . A T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28928;SOR=0;LSEQ=GGGGGTGGTGCTCCCACAGC;RSEQ=AGGCTTTCTCTTTGGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:202,59:0.0114:2,2:17.3:1:21:1:0.1344:6.78275:60:2:0.0077:0:1.7 0/0:164:0:0,0:119,45:0:2,0:19.9:1:29.8:1:1:0:60:81:1:0:0.1 -19 2222393 . T A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.082;SOR=Inf;LSEQ=GCCAGCGCCCGTGGGGACTG;RSEQ=GTGCCGAGCCACGGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:135,236:0:2,0:23.5:1:29.7:1:1:0:60:52:1:0:0.1 0/1:286:3:2,1:112,171:0.0105:2,2:10.3:1:27.7:1:0.56547:3.04:60:6:0.0106:0:1 -19 2222429 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07447;SOR=Inf;LSEQ=CAGGACAGTCGCAGGCGCGG;RSEQ=CGGCGGAAGCGAGCATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:104,181:0:2,0:24.3:1:31:1:1:0:60:34.625:1:0:0.1 0/1:208:3:1,2:101,104:0.0144:2,2:29.3:1:31:1:1:1.93635:60:6:0.0144:0:1.3 -19 2222530 . C A 45 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.37384;SOR=3.86879;LSEQ=TGGCCTTTTCACACAGCCTT;RSEQ=GGGGTCTCCCCTCAACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:1:1,0:174,198:0.0027:2,0:1:0:24:0:0.46917:0:60:2:0.0027:0:1 0/1:388:4:3,1:178,205:0.0103:2,2:7.3:1:22.5:1:0.34378:3.44:60:3:0.0079:0:2 -19 2222567 . G A 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.435;SOR=2.16837;LSEQ=CTCAACTCCATGGTAAGGAT;RSEQ=GGGACCGGCAGGGCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:2:2,0:92,161:0.0078:2,0:1:0:24:1:0.13497:0:60:4:0.0079:0:1 0/1:237:4:3,1:93,140:0.0169:2,2:23.5:1:26:1:0.30623:4.49:60:8:0.0169:0:1 -19 2222588 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.219;SOR=Inf;LSEQ=GGGACCGGCAGGGCTGGGGA;RSEQ=CGCGGCCTGTGAAAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:45,117:0:2,0:20.5:1:31.5:1:1:0:60:53:1:0:0.1 0/1:143:2:1,1:45,96:0.014:2,2:35.5:1:28.5:1:0.54142:2.12:60:4:0.0143:0:1 -19 2222590 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22558;SOR=Inf;LSEQ=GACCGGCAGGGCTGGGGAGC;RSEQ=CGGCCTGTGAAAGAAAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:43,109:0:2,0:20.6:1:30.6:1:1:0:60:37:1:0:0.1 0/1:138:2:1,1:44,92:0.0145:2,2:14.5:1:32:1:0.54745:2.08:60:4:0.0147:0:1 -19 2222654 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12867;SOR=Inf;LSEQ=TCACGCCTGTAATCCCAGCA;RSEQ=TTTGGGAGGCCGAGGCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:0,42:0:1,0:23.2:1:30.3:1:1:0:60:84:1:0:0.1 0/1:24:2:0,2:0,22:0.0833:1,0:8:1:32.5:1:1:0:60:4:0.0833:0:1.5 -19 2223327 . G A 203 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=39.51146;LSEQ=ATTACAGCCATCTCGTCCCC;RSEQ=GAGACCTCCCTGAAGAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1346:3:3,0:684,658:0.0022:2,0:12.3:1:22.3:1:0.24979:0:60:2:0.0015:0:3.7 0/1:1317:107:56,51:615,594:0.0812:2,2:23.7:1:30.2:1:0.84022:1.06:60:106:0.0815:0:1.3 -19 2223511 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.56282;SOR=3.14771;LSEQ=TCCAGGGGCCCGGAGGGGGG;RSEQ=GGGGCCTGGCAGCAGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:23,162:0.0053:2,0:2:0:30:0:1:0:60:2:0.0055:0:1 0/1:121:2:0,2:17,102:0.0165:2,0:23.5:1:30.5:1:1:0:60:4:0.0169:0:1 -19 2223514 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15274;SOR=Inf;LSEQ=AGGGGCCCGGAGGGGGGCGG;RSEQ=GCCTGGCAGCAGGGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:18,148:0:2,0:23.2:1:31.4:1:1:0:59.9:54.333:1:0:0.3 0/1:107:2:1,1:14,91:0.0187:2,2:28.5:1:31:0:0.26186:6.31:60:4:0.0189:0:1.5 -19 2223548 . T C 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0.04997;SOR=Inf;LSEQ=GGCAGGAGGTGCCTGCTCAC;RSEQ=GTGTGTGTGTGGGTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:0,56:0:1,0:17.5:1:28.4:1:1:0:59:4.6:0.9787:0:1.1 0/1:36:3:0,3:1,32:0.0833:1,0:10.7:1:25.7:1:1:0:60:2:0.0667:0:1.7 -19 2223560 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTGCTCACTGTGTGTGTGTG;RSEQ=GTGGGTGGGTGGGGAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:0,2:0,52:0.0364:1,0:28.5:1:31.5:1:1:0:60:4:0.0392:0:3 0/0:24:0:0,0:1,21:0:1,0:11.8:1:28.5:1:1:0:59.1:21:0.9545:0:2 -19 2225371 . CT C 94 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.59963;SOR=0.72154;LSEQ=GGGTTTCAAGCATTAATGAC;RSEQ=TTTTTTCTTAACAGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:663:8:4,4:368,287:0.0121:2,2:28:1:31.4:1:0.73535:1.28174:60:16:0.0122:0:0.1 0/0:687:6:3,3:378,303:0.0087:2,2:15.2:1:28:1:1:1.24711:60:5:0.0074:0.0044:1 -19 2225535 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50474;SOR=0;LSEQ=GCTGCTGACCCACCTGCTGG;RSEQ=CCGCTGCATCGTGTCCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:0,2:30,168:0.01:2,0:35.5:1:28:1:1:0:60:4:0.0103:0:1 0/0:161:0:0,0:30,131:0:2,0:22.5:1:30.8:1:1:0:60:52.667:1:0:0.1 -19 2225871 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGACCTCAGCATTTTCCC;RSEQ=AGAGCTCATCCCGCATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:21:1:32.5:1:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:0:0,0:3:0:30:0:1:0:60:2:1:0:0 -19 2226041 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCCTGTCCTCTCCCATC;RSEQ=TGTCCCGCTTGGCATCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:2,0:88,5:0.0211:2,0:7:1:32:0:1:0:60:4:0.0213:0:1.5 0/0:41:0:0,0:39,2:0:1,0:23.7:1:30:1:1:0:60:40:1:0:0.3 -19 2226092 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51573;SOR=0;LSEQ=CCAGCCCTGCCTGCAGAGTT;RSEQ=CCCGGGCCGTGGCAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:169,14:0.0108:2,2:14:1:29.5:1:0.15599:11.69678:60:4:0.011:0:1 0/0:127:0:0,0:109,18:0:2,0:23.6:1:31.8:1:1:0:60:62.5:1:0:0.2 -19 2226104 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15423;SOR=Inf;LSEQ=GCAGAGTTGCCCGGGCCGTG;RSEQ=CAGCAGCCCCGGTTAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:206,36:0:2,0:23.1:1:31:1:1:0:60:39.333:1:0:0.2 0/1:157:2:1,1:125,30:0.0127:2,2:14.5:1:27:1:0.35693:4.11528:60:4:0.0132:0:1 -19 2226128 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08878;SOR=Inf;LSEQ=CAGCCCCGGTTAGCCTCATG;RSEQ=GTAGCCCGGGCAGGTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:0:0,0:268,101:0:2,0:24.3:1:31:1:1:0:60:122:1:0:0.1 0/1:299:3:1,2:212,84:0.01:2,2:15:1:27:1:0.19972:5.016:60:6:0.0103:0:1 -19 2226676 . G A 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.53071;LSEQ=TGAAGGGCGAGGGCAGCCGC;RSEQ=GCAAGGAGGCAGGGGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:62:32,30:283,259:0.1023:2,2:24.5:1:30.3:1:1:1.02434:60:30:0.1008:0:1.1 0/1:484:139:73,66:178,165:0.2872:2,2:25:1:29.8:1:0.92012:1.03:60:68.5:0.2866:0:1.2 -19 2226705 . G A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00385;SOR=Inf;LSEQ=GCAGGGGAGGGCGGCCTACC;RSEQ=CTGTGCGGGCCCACGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:656:0:0,0:332,323:0:2,0:24.1:1:30.5:1:1:0:60:58.545:0.9984:0:0.2 0/1:544:7:4,3:287,250:0.0129:2,2:27.3:1:26.4:1:1:1.16:60:6:0.0113:0:1.3 -19 2226772 . G C 217 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAGGCCCGGGACCGCGAG;RSEQ=TCGACCTCAAGAATGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:793:0:0,0:316,476:0:2,0:25:1:31.5:1:1:0:60:98:0.9987:0:0.2 0/1:730:119:55,64:270,340:0.163:2,2:25.2:1:31.6:1:0.76243:1.08:60:118:0.1646:0:1.2 -19 2226826 . G A 62 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01504;SOR=Inf;LSEQ=CTGCGGCGGCCGTGCCTCCC;RSEQ=GAAGCCTCCTCAGCGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:178,337:0:2,0:25.8:1:30.5:1:1:0:60:38.615:1:0:0.2 0/1:511:6:6,0:197,306:0.0117:2,0:9.2:1:24.2:1:0.00385:0:60:5:0.0099:0:1.3 -19 2226847 . G T 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGCCTCCTCAGCGGCCCC;RSEQ=GCCTGGCCCCGGCGGCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:138,247:0:2,0:22.1:1:30.3:1:1:0:60:41.778:1:0:0.2 0/1:350:23:10,13:129,196:0.0657:2,2:29.9:1:29.2:1:0.8263:1.17:60:10.5:0.0618:0:1.4 -19 2226879 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.62757;SOR=2.60621;LSEQ=GCGGCGTCCTCCGCAGGCGG;RSEQ=GCGGCGTCCTCCGCCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:1:0,1:118,130:0.004:2,0:1:0:28:0:1:0:60:2:0.0041:0:1 0/1:288:3:1,2:138,147:0.0104:2,2:8.7:1:26.7:1:1:1.8736:60:6:0.0105:0:1 -19 2226945 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22007;SOR=4.59988;LSEQ=CCGCCGGGACCGCAGTTCGC;RSEQ=CTCGGCCCCATGTCCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:1:0,1:263,167:0.0023:2,0:13:0:12:0:0.38979:0:60:0:0:0:1 0/1:475:5:3,2:269,201:0.0105:2,2:29.4:1:29.8:1:1:1.12:60:10:0.0107:0:1.6 -19 2226997 . G A 47 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06046;SOR=0;LSEQ=GCTCCGTGGCCGGCTCCTCC;RSEQ=TGCTGCAGTCGCTGTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:3,1:203,184:0.0102:2,2:11:1:23.8:1:0.62525:2.71:60:3:0.0078:0:1.3 0/0:396:0:0,0:194,201:0:2,0:25.4:1:29.8:1:1:0:60:64.833:0.9974:0:0.2 -19 2227064 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24857;SOR=0;LSEQ=GCACGTGTCGTCCGCTGCCA;RSEQ=CAGACTGACCAACTCGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:0,3:101,142:0.0122:2,0:12:1:22.7:1:0.27103:0:60:2:0.0083:0:1 0/0:240:0:0,0:93,147:0:2,0:23.7:1:31:1:1:0:60:119:1:0:0.2 -19 2227080 . G T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35329;SOR=3.29131;LSEQ=GCCACCAGACTGACCAACTC;RSEQ=CACGCCATGGGCAGCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:0,1:103,150:0.0039:2,0:1:0:28:0:1:0:60:2:0.004:0:1 0/1:234:3:1,2:93,138:0.0128:2,2:19.7:1:26:1:1:1.34617:60:6:0.0129:0:1 -19 2227115 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09598;SOR=Inf;LSEQ=CTTTTCCGGGGTGGCAGGCG;RSEQ=CACAGTTGGAGGTAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:95,143:0:2,0:29.3:1:31.3:1:1:0:60:25.444:1:0:0.2 0/1:202:3:2,1:82,117:0.0149:2,2:14:1:28.7:1:0.57156:2.84:60:6:0.0149:0:1.3 -19 2227146 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.32427;SOR=3.85094;LSEQ=GGTAGGCAGGGCGGCCGTCC;RSEQ=TCCGCCCCCCGCCCCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:1,0:64,110:0.0057:2,0:1:0:26:0:0.37143:0:60:2:0.0058:0:1 0/1:138:3:2,1:51,82:0.0217:2,2:17.3:1:27:1:0.56014:3.19:60:6:0.0222:0:1 -19 2227150 . G A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.26474;SOR=0;LSEQ=GGCAGGGCGGCCGTCCGTCC;RSEQ=CCCCCCGCCCCGGCCCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:2,1:60,108:0.0175:2,2:21.7:1:27.7:1:0.29792:3.57:60:6:0.0182:0:1 0/0:126:0:0,0:47,77:0:2,0:25.5:1:30.9:1:1:0:60:123:0.984:0:0.3 -19 2227161 . C G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50755;SOR=0;LSEQ=CGTCCGTCCGCCCCCCGCCC;RSEQ=GGCCCCCGCCGGAGGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:43,95:0.0143:2,2:10:0:32:0:0.53135:2.20:60:4:0.0145:0:1.5 0/0:106:0:0,0:37,69:0:2,0:22.6:1:29.3:1:1:0:60:105:1:0:0.2 -19 2227621 . C A 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00058;SOR=Inf;LSEQ=CGCTGCTTGTGCTTGGTGCC;RSEQ=GCACACGCCTGGCGGCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:89,1:0:1,0:26.5:1:31.3:1:1:0:60:89:1:0:0 0/1:62:8:8,0:54,0:0.129:1,0:29.5:1:30.6:1:1:0:60:16:0.1311:0:1.1 -19 2227669 . G T 46 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78398;LSEQ=TCCCTTTTTGTGAGCCTGCG;RSEQ=CTGCTGCTCTGCGCTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:1,2:186,62:0.012:2,2:9.3:1:29.3:1:0.16077:5.94732:60:6:0.0122:0:1 0/0:213:2:0,2:152,59:0.0094:2,0:1:0:23:1:0.08105:0:60:4:0.0094:0:1 -19 2227849 . G A 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.34424;SOR=3.43805;LSEQ=CGAGCCCGCTGCAGGCGGCG;RSEQ=CCAGCGCCTCGGCCTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:0,1:73,174:0.004:2,0:20:0:30:0:1:0:60:2:0.0041:0:1 0/1:218:3:2,1:67,147:0.0138:2,2:18.3:1:23.7:1:0.23792:4.36:60:2:0.0093:0:1 -19 2227861 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60174;SOR=2.27996;LSEQ=AGGCGGCGGCCAGCGCCTCG;RSEQ=CCTCTTCCTTTCAGGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:1:0,1:70,155:0.0044:2,0:44:0:11:0:1:0:60:0:0:0:2 0/1:199:2:1,1:65,131:0.0101:2,2:23:1:27.5:1:1:2.01:60:4:0.0102:0:1 -19 2227873 . C T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24852;SOR=0;LSEQ=GCGCCTCGGCCTCTTCCTTT;RSEQ=AGGCCCCGGCCTCGGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:60,144:0.0144:2,2:22.7:1:26:1:1:1.20:60:6:0.0148:0:1 0/0:199:0:0,0:70,129:0:2,0:21.9:1:31.8:1:1:0:60:198:1:0:0.3 -19 2227899 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24194;SOR=0;LSEQ=CCGGCCTCGGTTGAGACCCG;RSEQ=CCGCCCCCTCCGCCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:57,107:0.012:2,2:40.5:1:31:1:1:1.87:60:4:0.012:0:1 0/0:172:0:0,0:76,96:0:2,0:25.3:1:31.8:1:1:0:59.9:56.333:1:0:0.5 -19 2227902 . G C 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.92401;LSEQ=GCCTCGGTTGAGACCCGGCC;RSEQ=CCCCCTCCGCCTCCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:1:1,0:63,96:0.0062:2,0:30:0:8:0:0.4:0:60:0:0:0:3 0/1:168:2:1,1:76,90:0.0119:2,2:42.5:1:30.5:1:1:1.18:60:4:0.0121:0:1.5 -19 2227905 . CCCTCCG C 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12289;SOR=Inf;LSEQ=TCGGTTGAGACCCGGCCGCC;RSEQ=CCTCCGCCTCCGCCTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:78,97:0:2,0:21.6:1:31.1:1:1:0:59.5:57.333:1:0:0.7 0/1:177:4:2,2:86,87:0.0226:2,2:33:1:31.5:1:1:1.01:60:8:0.0227:0:0.3 -19 2227919 . C T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.24949;SOR=Inf;LSEQ=GCCGCCCCCTCCGCCTCCGC;RSEQ=TCCGCCTCCCCCGCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:111,77:0:2,0:19.8:1:31.6:1:1:0:59.6:36.6:1:0:1.1 0/1:205:3:1,2:119,83:0.0146:2,2:5:1:21.7:1:0.57107:2.85273:60:2:0.01:0:1.7 -19 2227928 . C T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.62506;SOR=2.7465;LSEQ=TCCGCCTCCGCCTCCGCCTC;RSEQ=CCCGCTGCCCCCGCCTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:1:0,1:142,80:0.0045:2,0:1:0:26:0:0.36323:0:60:2:0.0045:0:1 0/1:245:3:1,2:149,92:0.0122:2,2:9.7:1:25.7:1:0.56075:3.22315:60:6:0.0123:0:1 -19 2227935 . G A 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.12217;SOR=0;LSEQ=CCGCCTCCGCCTCCCCCGCT;RSEQ=CCCCCGCCTGCGCACCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:3:2,1:175,81:0.0115:2,2:17.7:1:23.7:1:1:1.07992:60:6:0.0127:0:1.3 0/0:265:0:0,0:167,95:0:2,0:17.4:1:29.9:1:1:0:59.8:9.077:0.9874:0:0.8 -19 2227944 . T A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12373;SOR=Inf;LSEQ=CCTCCCCCGCTGCCCCCGCC;RSEQ=GCGCACCTGGGCCGGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:212,81:0:2,0:18.6:1:29.7:1:1:0:59.9:8.452:1:0:1.2 0/1:296:4:3,1:194,96:0.0135:2,2:10:1:26.8:1:1:1.48:60:8:0.0142:0:1 -19 2228273 . C T 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15764;SOR=3.40646;LSEQ=ACAGGCCAGCGCCACGGGGC;RSEQ=GTCCGCGGTGTGGGTGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:2:0,2:315,284:0.0033:2,0:1:0:27:0:0.22604:0:60:4:0.0034:0:1 0/1:533:6:1,5:271,254:0.0113:2,2:7.2:1:26.7:1:0.11461:5.32025:60:5:0.0096:0:2.3 -19 2229679 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10465;SOR=Inf;LSEQ=ATGGTGCTGGCCCCAGGTGG;RSEQ=GTGTGTGCTCGTGGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:293,38:0:2,0:25.6:1:32:1:1:0:60:164.5:1:0:0.1 0/1:296:3:2,1:251,42:0.0101:2,2:23.3:1:25.7:1:0.37665:2.97263:60:6:0.0104:0:1 -19 2229864 . C T 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCGCGGCATGGTGCCCGC;RSEQ=GGCCTGCCGGGCTCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:0:0,0:166,377:0:2,0:22.6:1:29.4:1:1:0:60:44.25:0.9962:0:0.1 0/1:500:38:10,28:157,305:0.076:2,2:24.3:1:30.1:1:0.37599:1.44032:60:76:0.0771:0:1.1 -19 2229892 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04357;SOR=Inf;LSEQ=CGGGCTCCCACCCCTGGACG;RSEQ=CAGAGGCAAGGACGGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:46,272:0:2,0:23.2:1:31.7:1:1:0:60:62.6:1:0:0.1 0/1:269:4:2,2:58,207:0.0149:2,2:15.3:1:29.3:1:0.21615:3.55:60:8:0.0151:0:1.3 -19 2230029 . CTT C 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02956;SOR=Inf;LSEQ=AAAAGTATAAACAATTCTGA;RSEQ=ATTTTATTCCATCTAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:0,20:0:1,0:25.4:1:31:1:1:0:60:40:1:0:0.1 0/1:10:3:0,3:0,7:0.3:0,0:9.3:1:31.2:1:1:0:60:6:0.3333:0.2:0 -19 2250803 . C T 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.04329;SOR=Inf;LSEQ=GGGAGCCGGGTCGACTGCCC;RSEQ=CGGGCCCCCAGCCCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:0:2,0:20.2:1:31.1:1:1:0:60:34:1:0:0.1 0/1:5:2:1,1:2,1:0.4:2,2:30.5:1:30.5:1:1:1.7321:60:4:0.4:0:1.5 -19 3094613 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.2111;SOR=0;LSEQ=GGCCGGGGGCCGGGGGGCGG;RSEQ=GGCGGGCAGGCGGCCGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:61,14:0.026:2,2:8.5:1:27:1:0.35373:4.24377:60:4:0.026:0:1 0/0:90:0:0,0:64,26:0:2,0:9.6:1:29.8:1:1:0:60:21.5:1:0:0.4 -19 3094624 . C T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.24891;SOR=Inf;LSEQ=GGGGGGCGGCGGCGGGCAGG;RSEQ=GGCCGCGTCGGCCGGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:109,34:0:2,0:14.7:1:31.5:1:1:0:60:70.5:1:0:0.1 0/1:156:3:0,3:101,52:0.0192:2,0:5:1:22.3:1:0.04227:0:60:2:0.0132:0:1.7 -19 3094633 . C T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68455;SOR=1.52004;LSEQ=CGGCGGGCAGGCGGCCGCGT;RSEQ=GGCCGGGGCCGGGACGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:2:0,2:159,53:0.0093:2,0:1:0:26:0:0.06516:0:60:4:0.0095:0:1 0/1:212:3:1,2:136,73:0.0142:2,2:23.7:1:21.7:1:0.28596:3.70164:58:2:0.0097:0:1.3 -19 3094793 . C T 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3515;SOR=0.30126;LSEQ=CTGCTGCTGCTCGGTGAGTG;RSEQ=GGCCCCCGGGCCTGCCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:3:1,2:63,203:0.0111:2,2:23.7:1:32:0:0.55896:1.61:60:6:0.0113:0:1.3 0/0:297:1:0,1:95,200:0.0034:2,0:44:0:28:0:1:0:60:2:0.0035:0:1 -19 3094811 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98813;LSEQ=TGCGGCCCCCGGGCCTGCCG;RSEQ=CTGCGGGCCCTGCCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:42,124:0.0119:2,2:32.5:1:30.5:1:0.44753:2.93:60:4:0.0121:0:1.5 0/1:170:2:1,1:47,121:0.0118:2,2:18.5:1:29.5:1:0.48618:2.56:60:4:0.0123:0:1 -19 3094847 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23217;SOR=0;LSEQ=TGCCTGTGCCTGCCCTGCCT;RSEQ=TCCGGGTCGGGCCGGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:15,30:0.0426:2,2:33:1:29.5:1:1:1.97:60:4:0.0435:0:1 0/0:50:0:0,0:18,32:0:2,0:15:1:30.7:1:1:0:60:49:1:0:0.4 -19 3095927 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTGTAAAGTGTTGTCAC;RSEQ=CCAAATAAGGGCCCCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:1:32.5:1:1:0:60:4:1:0:1 -19 3109758 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTGTGCTGTCCCTCTGG;RSEQ=GAGCATTGGTCATGAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 3110098 . G A 190 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.24304;LSEQ=GTAAGAGGGGGCAGCAGCAC;RSEQ=AGAGTCAGGCCCCGGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:142:80:70,10:60,2:0.5634:1,2:23.3:1:30.2:1:0.06749:4.24851:60:79:0.5603:0:1.1 0/1:101:24:23,1:72,4:0.2376:2,1:24:1:29.3:1:1:1.27:60:11:0.2245:0:1.3 -19 3110126 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20346;SOR=Inf;LSEQ=GGCCCCGGCTGCCGCCCGCC;RSEQ=TCACGTGCCCCGTCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:196,48:0:2,0:22:1:31.2:1:1:0:60:243:1:0:0.3 0/1:201:2:1,1:151,48:0.01:2,2:28.5:1:32.5:1:0.42905:3.12401:60:4:0.0102:0:1 -19 3110349 . T G 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10183;SOR=1.30209;LSEQ=AAGGTGAGCCCGCGGGCGCC;RSEQ=GGGGAGGGGAGCGCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:106:28,78:72,184:0.2912:2,2:23.1:1:30.8:1:0.79689:1.08983:60:212:0.3003:0:1.9 0/1:393:137:39,98:82,174:0.3486:2,2:26:1:29.4:1:0.49311:1.1837:60:136:0.3532:0:1.2 -19 3110361 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07767;LSEQ=CGGGCGCCTGGGGAGGGGAG;RSEQ=GCCTGGGCAGCTGTGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:86:19,67:43,164:0.2935:2,2:25.6:1:29.8:1:0.87532:1.08:60:85:0.2951:0:2.1 0/1:321:10:2,8:82,228:0.0312:2,2:21.9:1:29.3:1:1:1.43705:60:20:0.0321:0:2 -19 3110487 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72224;SOR=0.72114;LSEQ=TTCCTGTCATGGACATGGAA;RSEQ=CAGCAACCGCTGACTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:19:0,19:0,17:0.5278:1,1:25.7:1:33.3:1:1:0:60:38:0.5278:0:1 0/1:9:4:0,4:0,5:0.4444:0,0:15.3:1:32.8:1:1:0:60:8:0.4444:0:1 -19 3110515 . A G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CGCTGACTTCCTGGGGGCCA;RSEQ=CTGGAGAGTTGTGATGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:0,11:0,11:0.5:0,0:17.8:1:31.5:1:1:0:60:10:0.4762:0:1.5 1/0:6:3:0,3:0,3:0.5:0,0:19.7:1:32.7:1:1:0:60:6:0.5:0:1 -19 3110585 . A G 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CCAAGTAGCTGTGGGCGCCC;RSEQ=CATCCTGTGGGTGGGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:39.7:1:32.5:1:1:0:60:12:1:0:1.2 0/0:1:0:0,0:0,1:0:0,0:14:0:30:0:1:0:60:2:1:0:0 -19 3112793 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGATAAGCATTTTTCGGA;RSEQ=GAAAGAGAGAAGCCGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:11:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 3113176 . C T 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00334;SOR=0;LSEQ=GGCCTCGCGTTTTTCTGACA;RSEQ=GTGTTCACACGGAACTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:71:70,1:0,0:1:0,1:23:1:31.1:1:1:0:60:70:1:0:1.1 1/1:24:20:19,1:4,0:0.8333:0,1:24:1:29.3:1:1:0:60:9:0.8182:0:1.3 -19 3113305 . G C 284 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCCCAGCGAGCTCTCGAC;RSEQ=TCTCCCCTGCCCGCCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:554:554:362,192:0,0:1:0,2:25.3:1:31.2:1:1:0:60:137.5:1:0:1.1 1/1:519:442:291,151:42,33:0.8516:2,2:24:1:30.6:1:0.11737:1.51:60:109.5:0.8555:0:1.2 -19 3113516 . CGGCAGCTGCGGGCCG C 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCGCTGGCGGCCTGGGGA;RSEQ=GTGCCTGGGACCCTTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:60,272:0:2,0:24.9:1:31:1:1:0:60:331:0.997:0:0.1 0/1:288:25:8,17:57,206:0.0868:2,2:25.6:1:31.2:1:0.31436:1.70:60:50:0.088:0.0208:0.1 -19 3113574 . GC G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52746;SOR=0;LSEQ=GCCTCCGCGGCGTCTGTGGT;RSEQ=CCCCTGCCTGCTCGCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:0,2:1,85:0.0227:1,0:38.5:1:34:0:1:0:60:4:0.0233:0:0 0/0:53:0:0,0:3,50:0:2,0:20.9:1:31.2:1:1:0:60:25.5:1:0:0.1 -19 3114545 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGACTCTCCTAATGATGCGC;RSEQ=TGTTTGTGAAGCCTCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:41:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 3114864 . C T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1508;LSEQ=CTGGTGGCTTTCCGTCCTCC;RSEQ=GCTGGTTTGGGTGCTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:47:40,7:117,19:0.2554:2,2:23.2:1:31.3:1:1:1.07718:60:94:0.2626:0:1.1 0/1:143:7:5,2:117,19:0.049:2,2:19.7:1:31:1:0.27337:2.44297:60:14:0.0493:0:1 -19 3115124 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1974;LSEQ=CACTGAGAGGCTCATTTGCC;RSEQ=GGTGTGCCGGCTCATGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:271:168:50,118:33,68:0.6199:2,2:23:1:30.5:1:0.68291:1.14471:60:336:0.6222:0:1.1 0/1:284:69:18,51:67,146:0.243:2,2:20.3:1:29.4:1:0.45216:1.29905:60:68:0.2429:0:1.2 -19 3115141 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23005;SOR=Inf;LSEQ=GCCCGGTGTGCCGGCTCATG;RSEQ=CTGCGCACCCAGTGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:34,164:0:2,0:21.4:1:30.9:1:1:0:60:48.5:1:0:0.6 0/1:183:2:1,1:33,147:0.0109:2,2:22.5:1:28:1:0.33957:4.40:60:4:0.0113:0:1 -19 3115402 . C T 63 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGGGAGACCCTGTTT;RSEQ=GTCTTATTAAACAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:15.3:1:31.8:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 3118851 . G T 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=GGCAGGAGGGGCTTGGGTGG;RSEQ=AGCCGTCCTGGGATTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:20:18,2:208,19:0.081:2,2:27.9:1:29.2:1:0.68184:1.21534:60:40:0.0823:0:1.3 0/0:143:0:0,0:125,18:0:2,0:20.9:1:31:1:1:0:60:142:1:0:0.2 -19 3119184 . T G 282 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02344;LSEQ=GGAGGGCCCCTCTGATTCCC;RSEQ=CTGCCTTCGCTCCCGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:658:655:388,267:0,1:0.9954:0,2:24.7:1:30.2:1:0.40854:0:60:49.385:0.9969:0:1.3 1/1:605:506:291,215:52,46:0.8364:2,2:25:1:30:1:0.43672:1.20:60:35.143:0.8367:0:1.4 -19 3119239 . C T 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01878;SOR=1.26051;LSEQ=AGCAAAGCCCTGTTCCGGAC;RSEQ=ATCATCACCTACCCCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1002:278:141,137:382,340:0.2774:2,2:25.1:1:29.8:1:0.57197:1.09156:60:138:0.2802:0:1.6 0/1:978:319:173,146:355,304:0.3262:2,2:23.3:1:29.4:1:0.94548:1.01:60:105.333:0.3264:0:1.6 -19 3119365 . G C 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCGAGTTCGATGGTGCGCC;RSEQ=GGCTGCGGCATGGGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:557:0:0,0:192,364:0:2,0:24.6:1:30.1:1:1:0:60:41.769:0.9982:0:0.6 0/1:564:52:21,31:180,331:0.0922:2,2:24.8:1:29.6:1:0.4522:1.25:60:104:0.0937:0:1.5 -19 3119405 . T G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.33859;LSEQ=GCTCGCGGGCAGGGCCTTAC;RSEQ=GGGGGGAGGGGGCTGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:249:178:27,151:0,0:0.7149:0,2:24.4:1:30.9:1:1:0:60:88:0.7213:0:1.2 0/1:229:105:14,91:5,41:0.4585:2,2:25.4:1:29.7:1:0.7938:1.26:60:51.5:0.4578:0:1.3 -19 3119441 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5079;SOR=0;LSEQ=ATATGGGAGAGGGGCTCATA;RSEQ=AGGCCGGGAGCTCTAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:0,2:5,135:0.0141:1,0:29.5:1:28:1:1:0:60:4:0.0143:0:2 0/0:107:0:0,0:4,103:0:1,0:21.5:1:32:1:1:0:60:214:1:0:0.8 -19 3120511 . C T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCCGGTGGGAAGCAGCG;RSEQ=CCCTGCTGGAGCCCCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:16:0:16:0:1:0:60:0:0:0:1 1/1:3:3:1,2:0,0:1:0,2:19:1:30.3:1:1:0:60:6:1:0:1.3 -19 3120739 . T G 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=CTGAGCAGAGGGAGCAGCGG;RSEQ=GGGTGCAGAGCCCCAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:24.4:1:30.2:1:1:0:60:10:0.5:0:1 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30:1:1:0:60:4:1:0:1 -19 3121246 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52661;SOR=0;LSEQ=TTCCACGGAGCCTGCGGCTG;RSEQ=CGGGCGGGTGGCGCTGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:0,2:13,138:0.0131:2,0:22:1:31.5:1:1:0:60:4:0.0135:0:1 0/0:94:0:0,0:10,84:0:2,0:27.3:1:29.6:1:1:0:60:14.667:1:0:0.2 -19 3121260 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52841;SOR=0;LSEQ=CGGCTGCCGGGCGGGTGGCG;RSEQ=TGCCGAGTCCGGGCCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:8,121:0.0153:2,2:22:1:29.5:1:0.13318:14.31:60:4:0.0156:0:1 0/0:79:0:0,0:5,73:0:2,0:27.8:1:31.1:1:1:0:60:18.5:1:0:0.1 -19 3121299 . AT A 74 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01651;LSEQ=GCCTCTGCCCGCGGGAGGAG;RSEQ=TTTTTTTTTTCATATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:5:0,5:1,60:0.0758:1,0:25.8:1:32.2:1:1:0:60:10:0.0758:0:0.4 0/1:39:3:0,3:1,35:0.0769:1,0:24.7:1:28.7:1:1:0:60:6:0.0811:0.0256:0 -19 3121609 . T C 69 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCCCCACACCGCAGCCCCC;RSEQ=GTGGCTGTCCTTCCAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:30.2:1:29.8:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 3148552 . C G 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGTCGGGGGTGGGAGTCC;RSEQ=GTGGAGGGCTGAGCGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:68,5:0:2,0:25.2:1:31.1:1:1:0:60:72:1:0:0.1 0/1:62:21:20,1:39,2:0.3387:1,1:20.8:1:30.1:1:1:1.03:60:42:0.3443:0:1 -19 3148577 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24485;SOR=Inf;LSEQ=AGGGCTGAGCGGTTCTGCTG;RSEQ=TCCATCCCCAGGCCCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:86,36:0:2,0:23.1:1:31.7:1:1:0:60:39.667:1:0:0 0/1:120:2:1,1:87,31:0.0167:2,2:27:1:29.5:1:0.46387:2.77808:60:4:0.0168:0:1 -19 3148593 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22922;SOR=0;LSEQ=GCTGCTCCATCCCCAGGCCC;RSEQ=GGCGAGAGCGGGAAGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:103,59:0.0122:2,2:27:1:31.5:1:1:1.73945:60:4:0.0125:0:1 0/0:178:0:0,0:114,64:0:2,0:23:1:29.7:1:1:0:60:43.5:1:0:0.3 -19 3148631 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12898;SOR=Inf;LSEQ=CACCTTCATCAAGCAGATGC;RSEQ=GATCATCCACGGCGCCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:148,120:0:2,0:25.1:1:30:1:1:0:60:52.6:1:0:0.2 0/1:317:4:1,3:169,144:0.0126:2,2:27:1:29.5:1:0.34016:3.50786:60:8:0.0127:0:1 -19 3148656 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09666;SOR=0;LSEQ=ATCCACGGCGCCGGCTACTC;RSEQ=GAGGAGGAGCGCAAGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:1,2:132,151:0.0105:2,2:23:1:24.7:1:1:1.74507:60:2:0.0071:0:1 0/0:336:0:0,0:159,176:0:2,0:25.8:1:29.6:1:1:0:59.9:110.667:0.997:0:0.2 -19 3148708 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23663;SOR=Inf;LSEQ=TCTACCAGAACATCTTCGTG;RSEQ=CCATGCGGGCCATGATCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:60,119:0:2,0:23.9:1:29.3:1:1:0:60:34.8:1:0:0.2 0/1:171:2:1,1:59,110:0.0117:2,2:17:1:32:0:1:1.86:60:4:0.012:0:1 -19 3148740 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22583;SOR=Inf;LSEQ=ATGATCGAGGCCATGGAGCG;RSEQ=CTGCAGATTCCATTCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:19,71:0:2,0:22.6:1:31.7:1:1:0:60:44:1:0:0.1 0/1:82:2:1,1:13,67:0.0244:2,2:14:0:28:1:0.31406:5.00:60:4:0.0247:0:1 -19 3148746 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49664;SOR=Inf;LSEQ=GAGGCCATGGAGCGGCTGCA;RSEQ=ATTCCATTCAGCAGGCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:11,64:0:2,0:23.8:1:31.5:1:1:0:60:74:1:0:0.2 0/1:75:2:1,1:12,60:0.0267:2,2:29.5:1:30.5:1:0.32247:4.84:60:4:0.0267:0:1 -19 3148819 . G T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0017;SOR=22.00852;LSEQ=CCAGGGCAGGCAGGGGCCCA;RSEQ=GGCAGGGTTCCCCAGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:43.8:1:30.6:1:1:0:60:10:0.2632:0:1 1/1:10:9:1,8:0,1:0.9:0,2:17.3:1:29.6:1:1:0:60:18:0.9:0:1.1 -19 3150418 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCTCCAGGATGAGGTC;RSEQ=TTCCAGGGGGACCCTAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:25.5:1:30:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 3779127 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50041;SOR=0;LSEQ=GACCAGGATGTTGCGGGCGG;RSEQ=CAGGTCGCGGTGCACAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:28,31:0.0328:2,2:26:1:29:1:1:1.11:60:4:0.0339:0:1 0/0:50:0:0,0:24,26:0:2,0:29.2:1:31.2:1:1:0:60:49:1:0:0.1 -19 3780533 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCCAGGTCACGCCATTC;RSEQ=CCTGCCTCAGCCTCCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29:1:1:0:60:4:1:0:2.5 -19 4025041 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAATGCTGGGATTACAGG;RSEQ=GTGAGCCACTGCGCCTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 4025484 . C T 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCATGGCAGGGCTGGGC;RSEQ=GGGCGCCCCCATTTAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14:1:31.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:26:0:27:0:1:0:60:2:1:0:1 -19 4025616 . G A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21041;SOR=0;LSEQ=GTAAGGGTTCAGATCCAGCC;RSEQ=AGCCAGGCTTGGCCATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:15,8:0,0:1:0,2:23.4:1:29:1:1:0:60:46:1:0:1.2 1/1:20:18:12,6:1,1:0.9:2,2:24.8:1:30.2:1:1:1.93:59.7:36:0.9:0:1.1 -19 4025686 . C CGTCTTTCTCAGCCTT 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.45652;SOR=0;LSEQ=GACCTCGTCTTTCTCAGCCT;RSEQ=GTCTTCCTTGTCTATGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:8,17:0,0:1:0,2:27.1:1:30.7:1:1:0:60:50:1:0.32:0.4 1/1:21:20:7,13:1,0:0.9524:0,2:23.8:1:30:1:0.38095:0:59.5:40:0.9524:0.4762:0.6 -19 4090113 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTCTCCTTCCTTTTGG;RSEQ=GAGAGCCGCCATCGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 4090422 . G T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.70494;LSEQ=AGAGGCACCCCGGCCAGGAC;RSEQ=GGCAGGAGAGGAGACCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:8:8,0:26,2:0.2222:2,0:18.5:1:31.5:1:1:0:60:16:0.2222:0:1.3 0/1:12:2:1,1:8,2:0.1667:2,2:45.5:1:32.5:1:0.45455:3.4638:60:4:0.1667:0:1 -19 4090572 . G A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=ACGGTGGGCAGGTCACCAGC;RSEQ=GGACGCAGGGAGCCCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:250,108:0:2,0:24.4:1:30.3:1:1:0:59.5:50.143:1:0:0.2 0/1:366:14:11,3:245,105:0.0383:2,2:24.4:1:30.4:1:0.76592:1.57:59.3:28:0.0392:0:1 -19 4090622 . C T 74 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.35349;SOR=2.04227;LSEQ=GGCGGTGCGCGTGGGTGTGC;RSEQ=GGGCTGGTTCAGCCGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:3:0,3:347,244:0.005:2,0:1:0:23:1:0.07139:0:60:2:0.0034:0:1 0/1:683:7:1,6:390,286:0.0102:2,2:11.6:1:26.6:1:0.04616:8.15986:60:14:0.0104:0:1 -19 4094110 . G T 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAGGGAAAGGAGCCTG;RSEQ=GGGGCTGAGAGCTGCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:32:1:30:1:1:0:60:8:0.6667:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 4094555 . G A 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01689;SOR=Inf;LSEQ=GAGACAAGACAGGGCAGTCA;RSEQ=CTGGTGGCCCCGGGGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:159,241:0:2,0:25.7:1:31.8:1:1:0:60:56.143:1:0:0.2 0/1:461:7:6,1:178,276:0.0152:2,2:6.3:1:23.4:1:0.0179:9.26:60:6:0.0133:0:1.1 -19 4094587 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12341;SOR=Inf;LSEQ=GGGGCACCCGCGTGTGGGCC;RSEQ=TGGTCGGAGGGGGCCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:57,178:0:2,0:23.9:1:31.3:1:1:0:60:77.333:0.9957:0:0.1 0/1:235:3:2,1:56,176:0.0128:2,2:14.7:1:28:1:0.15146:6.22:60:6:0.013:0:1 -19 4094775 . G A 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GGTGGGTCAGAAGCCTGGAC;RSEQ=CAACCCCAGCTAACTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:0.625:0,2:22:1:31.2:1:1:0:60:10:0.625:0:1.2 0/0:1:0:0,0:0,1:0:0,0:47:0:34:0:1:0:60:2:1:0:0 -19 4095290 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50928;SOR=0;LSEQ=TAACGCTGCACTGGGATTCT;RSEQ=GATGGGCAGGCTGGGCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:152,21:0.0114:2,2:23:1:30:1:0.23626:7.09472:60:4:0.0116:0:1 0/0:130:0:0,0:114,16:0:2,0:25:1:31.5:1:1:0:60:64:1:0:0.2 -19 4095506 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.22825;SOR=Inf;LSEQ=TCGTCAGGGACCCTCGGCTG;RSEQ=AGCCCTCTCTACCCCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:32,150:0:2,0:23.2:1:31.8:1:1:0:60:44.5:1:0:0.1 0/1:167:2:1,1:33,132:0.012:2,2:36:0:28.5:1:0.36671:3.96:60:4:0.0121:0:1 -19 4099187 . T C 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=23.74988;LSEQ=TCCAGACCGGAAGTTGCAGA;RSEQ=TCAGGCCGTACCGCTGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:177:117,60:179,98:0.3899:2,2:23.9:1:31.6:1:0.76281:1.07:60:43.25:0.3923:0:1.2 1/1:406:381:231,150:18,6:0.9384:2,2:25.1:1:30.6:1:0.19707:1.94511:60:26.214:0.9386:0:1.2 -19 4100970 . A G 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12237;SOR=Inf;LSEQ=GGGTGGGGAGAGCTTGGGGG;RSEQ=GAGCAGCAGGGAGGAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:215,69:0:2,0:24.2:1:29.7:1:1:0:60:30.556:0.9964:0:0.3 0/1:282:3:2,1:207,72:0.0106:2,2:29:1:24:1:1:1.4355:60:2:0.0074:0:1.3 -19 4101062 . G T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.9836;LSEQ=AAGGAGTTGGCCATGGAGTC;RSEQ=ATGAGCTGGCCGCTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:702:278:148,130:238,186:0.396:2,2:25.3:1:29.7:1:0.48528:1.12376:52:138:0.3988:0:1.1 1/0:676:489:241,248:92,94:0.7234:2,2:26.4:1:28.9:1:1:1.00714:52.9:96.8:0.7246:0:1.1 -19 4101212 . C T 90 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3869;SOR=1.92422;LSEQ=CCCCGGGGCTCTGGGGAGGG;RSEQ=GGGCTGGGCCTTACCTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:4:2,2:322,321:0.0062:2,2:9:1:28.8:1:1:1.00311:60:8:0.0064:0:1 0/1:676:8:3,5:338,330:0.0118:2,2:24:1:30.3:1:0.50172:1.70573:60:16:0.0122:0:1.3 -19 4102132 . A C 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02098;SOR=0;LSEQ=GGGACCAGTGTGGCAAACAG;RSEQ=GGATACTAAGAGTGAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:22.6:1:29.3:1:1:0:60:6:0.75:0:2 0/0:4:0:0,0:4,0:0:0,0:25.5:1:28.3:1:1:0:60:8:1:0:0 -19 4102294 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18967;SOR=Inf;LSEQ=ACCCCCACCACACTGTGAGT;RSEQ=GCTCCCGGAACCCTGGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:138,13:0:2,0:24.2:1:31.5:1:1:0:60:20.571:1:0:0.2 0/1:117:2:1,1:100,14:0.0171:2,2:9.5:1:28.5:1:0.24288:6.93504:60:4:0.0179:0:1.5 -19 4102310 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49937;SOR=0;LSEQ=GAGTGGCTCCCGGAACCCTG;RSEQ=CCGTGTGGAAGAGGTCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:153,28:0.0109:2,2:27:1:30.5:1:0.29256:5.38686:60:4:0.0114:0:1 0/0:169:0:0,0:140,29:0:2,0:23.4:1:30.9:1:1:0:60:32.8:1:0:0.2 -19 4102313 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11109;SOR=Inf;LSEQ=TGGCTCCCGGAACCCTGGCC;RSEQ=TGTGGAAGAGGTCCGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:167,35:0:2,0:23.8:1:29.6:1:1:0:60:39.4:1:0:0.2 0/1:188:3:1,2:149,36:0.016:2,2:17:1:28.3:1:0.1045:8.14739:60:6:0.0161:0:1 -19 4102330 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24868;SOR=0;LSEQ=GCCGTGTGGAAGAGGTCCGT;RSEQ=CAGAGTGCGGTGGGGGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:213,68:0.0106:2,2:17:1:28:1:0.1513:6.21404:60:6:0.0106:0:1 0/0:282:0:0,0:211,71:0:2,0:23.2:1:31.8:1:1:0:60:55.4:1:0:0.2 -19 4102338 . C T 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49404;SOR=0.5631;LSEQ=GAAGAGGTCCGTGCAGAGTG;RSEQ=GGTGGGGGCGCGATGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:5:2,3:225,91:0.0156:2,2:17:1:28.2:1:0.15205:3.69164:60:10:0.0158:0:1.2 0/0:340:3:1,2:240,97:0.0088:2,2:15.3:1:26.3:1:0.20421:4.9217:60:6:0.0089:0:1 -19 4102449 . G A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03883;LSEQ=ACCTGGTCCAGGGAGCCGCC;RSEQ=TCCTAGAGGGCACACAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:641:399:171,228:109,132:0.6225:2,2:26:1:30.2:1:0.56588:1.10084:59.9:56:0.6252:0:1.1 0/1:700:42:17,25:288,370:0.06:2,2:29.7:1:28.9:1:0.74941:1.14444:60:20:0.0581:0:1.2 -19 4102486 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06065;SOR=Inf;LSEQ=AGGAGTGAGTGCAGGCTCTG;RSEQ=GCAGGTGGCCGGGAAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:100,271:0:2,0:23.9:1:30.3:1:1:0:60:122.667:1:0:0.6 0/1:367:4:2,2:112,250:0.0109:2,2:25:1:29.3:1:0.5915:2.23:60:8:0.011:0:1.3 -19 4102623 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07338;SOR=Inf;LSEQ=TCTTCTGACAGTTCTGCCTT;RSEQ=GGGTCTGAACACCCACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:2,37:0:2,0:23.8:1:29.2:1:1:0:60:18.5:1:0:0.3 0/1:15:2:0,2:2,11:0.1333:2,0:18.5:1:32:0:1:0:60:4:0.1333:0:1 -19 4110318 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=GCCTCTCAAAAAAACAAAAA;RSEQ=AAAACAAAACAAAACCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:15,1:0.1111:1,0:22.5:1:30.5:1:1:0:60:4:0.1111:0:1 0/0:11:0:0,0:11,0:0:0,0:19.3:1:33.7:1:1:0:60:22:1:0:0 -19 4110408 . T C 101 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00971;SOR=4.66143;LSEQ=CCCTGGAAGCCAGCGCACTG;RSEQ=TGCCTCTGAGGAAAGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:4:4,0:82,1:0.046:1,0:22.8:1:32.3:1:1:0:60:8:0.046:0:1 0/1:54:10:10,0:43,1:0.1852:1,0:25.6:1:30.5:1:1:0:60:9:0.1698:0:1.2 -19 4112080 . T G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGGAGCAGCCTGAGGCT;RSEQ=TGGGACGGCACCCTGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:30.5:1:1:0:60:4:1:0:1 -19 4116162 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGTGATTAACCTTTAAAT;RSEQ=GGCAGACTCTGAGCAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 4117290 . T C 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00115;SOR=0;LSEQ=TCAGGACCTAGAGTCCCTGG;RSEQ=GGGGATGAGGGACAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:83:83:83,0:0,0:1:0,1:24.4:1:32:1:1:0:60:40.5:1:0:1.1 1/1:54:47:46,1:7,0:0.8704:0,1:22.7:1:32.8:1:1:0:60:94:0.8704:0:1.2 -19 4117528 . G A 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2644;LSEQ=TCATCGTCTTTGAGTTCGCC;RSEQ=ACCTTGGCTTTCTGGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1011:249:129,120:393,369:0.2463:2,2:25.4:1:30:1:1:1.01:59:40.5:0.2445:0:1.2 0/1:1082:86:47,39:501,495:0.0795:2,2:21.3:1:30:1:0.50029:1.19:59.8:172:0.0804:0:1.1 -19 4117681 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19717;SOR=Inf;LSEQ=CTAGGGAGACTCCATCTGGC;RSEQ=GTTTGCTATGTGGCCGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:18,213:0:2,0:24.2:1:30:1:1:0:60:45.2:1:0:0.7 0/1:185:2:0,2:31,152:0.0108:2,0:30.5:1:26.5:1:1:0:60:4:0.011:0:2 -19 4117690 . T A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.035;SOR=Inf;LSEQ=CTCCATCTGGCCGTTTGCTA;RSEQ=GTGGCCGTGGTGCATCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:13,191:0:2,0:23.5:1:30.4:1:1:0:60:50:1:0:0.8 0/1:157:4:2,2:20,133:0.0255:2,2:13.5:1:24.5:1:0.09461:6.52:60:3:0.0196:0:2.5 -19 4117695 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50946;SOR=0;LSEQ=TCTGGCCGTTTGCTATGTGG;RSEQ=CGTGGTGCATCGGCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:8,174:0.0108:1,2:18:1:27:0:0.09569:20.56:60:4:0.011:0:2 0/0:138:0:0,0:15,123:0:2,0:21.4:1:30.3:1:1:0:60:18.714:1:0:0.9 -19 4117705 . T C 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03024;LSEQ=TGCTATGTGGCCGTGGTGCA;RSEQ=CGGCCCCCAGGAGGACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:147:1,146:0,0:0.9932:0,1:24.2:1:31.1:1:1:0:60:23.5:1:0:1.1 1/1:108:88:2,86:1,19:0.8148:1,1:21.3:1:29.8:1:0.46249:2.24198:60:13.667:0.8039:0:1.3 -19 4122876 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCATTATTGAGGGACCCT;RSEQ=ACCCCGTCTTTTCCTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:30:1:1:0:60:4:1:0:1 -19 4123543 . TCCGAGGGCCCCCTGCCCCGTCCTCCC T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCACCCTTCGCCCCGTCC;RSEQ=CCGAGGGCCCCCTGCCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:3,0:15,0:0.1667:1,0:8.3:1:31.7:1:1:0:60:6:0.1765:0.1667:1.7 0/0:5:0:0,0:4,1:0:2,0:21.8:1:30.8:1:1:0:60:10:1:0:1.6 -19 4123656 . C T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07144;SOR=Inf;LSEQ=GCCCCGTGCACCACTCACCC;RSEQ=GTCCTCCCCCGTGACCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:85,1:0:1,0:20.6:1:30.8:1:1:0:59.4:42:1:0:1.5 0/1:62:3:3,0:58,1:0.0484:1,0:26.7:1:32.3:1:1:0:60:6:0.0484:0:1 -19 4123680 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20796;SOR=Inf;LSEQ=CTCCCCCGTGACCCCCCTGC;RSEQ=TCGTGCACTCCTCGCGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:122,11:0:2,0:23.5:1:31:1:1:0:59.9:65.5:1:0:0.8 0/1:112:2:1,1:100,10:0.0179:2,2:12.5:1:28.5:1:0.18758:9.58219:60:4:0.018:0:1 -19 4123693 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50503;SOR=0;LSEQ=CCCCTGCCTCGTGCACTCCT;RSEQ=GCGAACCCCCGTCCCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:150,28:0.0111:2,2:24:1:27.5:1:0.29702:5.2816:60:4:0.0115:0:3 0/0:143:0:0,0:122,21:0:2,0:23.2:1:29.4:1:1:0:60:13.3:1:0:0.5 -19 5159183 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09952;SOR=0;LSEQ=GGCAAGTAATAGCAAGATGG;RSEQ=TGTCACGGGACCTAGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:1,2:123,84:0.0143:2,2:18:1:29:1:0.56896:2.91352:60:6:0.0144:0:1 0/0:242:0:0,0:139,102:0:2,0:24.3:1:31.4:1:1:0:59.8:79.333:0.9958:0:0.2 -19 5159187 . C T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.30743;LSEQ=AGTAATAGCAAGATGGCTGT;RSEQ=ACGGGACCTAGAAAGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:2:0,2:128,97:0.0088:2,0:1:0:24.5:1:0.18912:0:60:4:0.0089:0:1.5 0/1:261:3:1,2:146,112:0.0115:2,2:7.7:1:21.3:1:0.58238:2.59771:60:2:0.0078:0:1.3 -19 5159191 . G T 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.10023;LSEQ=ATAGCAAGATGGCTGTCACG;RSEQ=GACCTAGAAAGGGGAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:136,105:0.0123:2,2:15.3:1:27.7:1:0.58318:2.58052:60:6:0.0124:0:1 0/1:296:4:0,4:158,132:0.0135:2,0:1:0:26.3:1:0.0447:0:60:8:0.014:0:1 -19 5159196 . T C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08566;SOR=0;LSEQ=AAGATGGCTGTCACGGGACC;RSEQ=AGAAAGGGGAAAAGCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:140,115:0.0116:2,2:22.3:1:31.7:1:0.59181:2.42658:60:6:0.0118:0:1.3 0/0:326:0:0,0:174,152:0:2,0:23.6:1:29:1:1:0:60:64.2:1:0:0.2 -19 5159288 . G A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92544;LSEQ=AGAAGCCTTTTCCTGTAAAC;RSEQ=CCAGGCGGCGTCTCCTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:43,93:0.0145:2,2:26.5:1:29:1:0.53761:2.15:60:4:0.0145:0:1 0/1:149:2:1,1:56,91:0.0134:2,2:26.5:1:30:1:1:1.62:60:4:0.0135:0:1 -19 5174025 . A G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05387;SOR=Inf;LSEQ=TGAGGCAGGAGAATGGCGTG;RSEQ=ATCCAGGAGGCGGAGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:56,0:0:1,0:23.5:1:30.3:1:1:0:55.3:112:1:0:0.6 0/1:35:3:3,0:32,0:0.0857:1,0:19:1:32:1:1:0:56.3:6:0.0909:0:2 -19 5174030 . A G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9512;LSEQ=CAGGAGAATGGCGTGAATCC;RSEQ=GGAGGCGGAGCTTGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:37:37,0:23,0:0.6167:1,1:23.1:1:30.1:1:1:0:53.7:74:0.6167:0:1.1 1/0:43:26:26,0:17,0:0.6047:1,1:22:1:28.7:1:1:0:56.6:12:0.5854:0:1.2 -19 5174086 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.59361;LSEQ=CTGCACTCCAGCCTGGGCGA;RSEQ=ACTCCGTCTAAAAAACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:125,54:0.011:2,2:37.5:1:29.5:1:0.51657:2.30286:60:4:0.0111:0:1.5 0/0:152:1:0,1:106,45:0.0066:2,0:1:0:23:0:0.30263:0:60:2:0.0067:0:1 -19 5174098 . AAAAC A 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.19455;SOR=4.49602;LSEQ=CTGGGCGAGACTCCGTCTAA;RSEQ=AAACAAACAAACAAAACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:0,1:161,96:0.0039:2,0:45:0:32:0:0.37597:0:60:2:0.0039:0:0 0/1:232:4:3,1:149,79:0.0172:2,2:16.8:1:31.5:1:1:1.59:60:8:0.0175:0.0086:0.3 -19 5174101 . A T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.25078;SOR=0;LSEQ=GGCGAGACTCCGTCTAAAAA;RSEQ=CAAACAAACAAACAAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:3:0,3:164,102:0.0111:2,0:8:1:22.7:1:0.05843:0:60:2:0.0075:0:1.3 0/0:242:0:0,0:157,83:0:2,0:20.3:1:29.6:1:1:0:60:119:1:0:0.5 -19 5174132 . CT C 74 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.12002;SOR=5.14898;LSEQ=AACAAAACACGTATAAGCAC;RSEQ=TTTTCCAGGAATGCCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:1,0:217,174:0.0026:2,0:47:0:33:0:1:0:60:2:0.0026:0:0 0/1:384:5:2,3:204,174:0.013:2,2:15.8:1:32:1:0.66571:1.75602:60:10:0.0133:0.0026:1 -19 5174155 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00758;SOR=Inf;LSEQ=TTTCCAGGAATGCCAACATC;RSEQ=TTCCAAGGGAAAAGAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:213,219:0:2,0:26.4:1:31.7:1:1:0:60:60.714:1:0:0.6 0/1:440:8:3,5:216,216:0.0182:2,2:27:1:29.6:1:0.72407:1.66476:60:16:0.0185:0:2 -19 5174180 . C T 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=0.5865;LSEQ=AAGGGAAAAGAGCAAAGTCT;RSEQ=GTCACCACGGTCCAGCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:365:235:98,137:58,71:0.6438:2,2:26.1:1:29.8:1:0.58062:1.14157:60:77.333:0.6427:0:1.1 1/0:381:196:84,112:81,102:0.5144:2,2:24.2:1:29.4:1:0.83589:1.05864:60:195:0.5145:0:1.2 -19 5174221 . T A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.52588;LSEQ=CCTACAGCTGATGAGGGTGA;RSEQ=GGAGCTGCTGTAATGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:50,139:0.0105:2,2:8.5:1:30:1:0.46376:2.76:60:4:0.0106:0:2 0/0:181:1:1,0:49,131:0.0055:2,0:1:0:25:0:0.27624:0:60:2:0.0056:0:1 -19 5174304 . G A 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0069;SOR=0;LSEQ=TTTGCTGAATAAAGCAGTGT;RSEQ=GGATTTGTGGTTCCCGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:9:0,9:0,22:0.2903:1,0:28.3:1:28.7:1:1:0:60:8:0.2667:0:1.7 0/0:22:0:0,0:2,20:0:2,0:19.5:1:28.8:1:1:0:60:10:1:0:0.1 -19 5206724 . C A 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTCCAGGCCTCAGGAGGTC;RSEQ=GCCCGGGAGGGGCAGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:101:77,24:180,36:0.3186:2,2:24:1:30.2:1:0.1656:1.55619:60:202:0.3248:0:1.7 0/0:303:0:0,0:233,70:0:2,0:24:1:29.5:1:1:0:60:49.5:1:0:0.7 -19 5206775 . A G 290 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09057;LSEQ=GTGGTGTCGGGCCTGGGGGG;RSEQ=ACCATGGCTTTAGGTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:735:724:424,300:0,0:0.985:0,2:26.7:1:30.6:1:1:0:60:33.476:0.9874:0:1.2 1/1:744:637:361,276:55,51:0.8562:2,2:26.1:1:30.6:1:0.39817:1.21:60:44.5:0.8569:0:1.2 -19 5207183 . T C 100 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGGCTCCCTGCAACCTCTG;RSEQ=CTCCTGGGTTCAAGTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:26.8:1:31.6:1:1:0:59.6:18:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 5207878 . T A 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAGGAGGAAACTGGAGCT;RSEQ=AGGGGCAGTCGGGGCGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:295,108:0:2,0:21.7:1:29.4:1:1:0:60:66.167:1:0:0.1 0/1:365:23:16,7:259,82:0.063:2,2:23.6:1:28.5:1:0.46154:1.38055:60:46:0.0635:0:1.1 -19 5208110 . C T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09188;SOR=Inf;LSEQ=CAGCCATTCAGGGGCAGGTG;RSEQ=TGGGGAGCCCTGATCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:113,219:0:2,0:24.4:1:31.5:1:1:0:60:24.538:1:0:0.1 0/1:274:3:1,2:90,181:0.0109:2,2:16:1:31.7:1:1:1.01:60:6:0.0112:0:1 -19 5208115 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08262;SOR=Inf;LSEQ=ATTCAGGGGCAGGTGCTGGG;RSEQ=AGCCCTGATCTGACCACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:114,210:0:2,0:24.2:1:30.6:1:1:0:60:23.923:1:0:0.1 0/1:251:3:2,1:82,166:0.012:2,2:8.7:1:26.3:1:0.26014:4.02:60:6:0.0122:0:1 -19 5208202 . A G 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0478;SOR=Inf;LSEQ=GGCTGTCCCCACCAGGCCTC;RSEQ=GTTTCCCCAGCAGGGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:258,165:0:2,0:23.2:1:30.3:1:1:0:60:51.875:1:0:1.1 0/1:373:4:2,2:251,118:0.0107:2,2:34.3:1:29:1:0.59672:2.12245:60:8:0.0108:0:1 -19 5208216 . G A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.0703;LSEQ=GGCCTCAGTTTCCCCAGCAG;RSEQ=GCCAAAAGCTGGGACACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:487:249:151,98:139,95:0.5113:2,2:24.8:1:30:1:0.85257:1.05:60:40.5:0.5127:0:2 0/1:483:33:21,12:284,164:0.0683:2,2:23.2:1:28.4:1:1:1.01:60:66:0.0689:0:1.8 -19 5208236 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18649;LSEQ=GGCCAAAAGCTGGGACACTC;RSEQ=AGGGAGCTCACCTGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:636:331:192,139:174,130:0.5204:2,2:23.9:1:29.6:1:0.87242:1.03:60:54.167:0.5192:0:1.8 0/1:684:115:69,46:331,237:0.1681:2,2:19.7:1:29.8:1:0.75645:1.07:60:230:0.1701:0:1.3 -19 5208257 . A T 170 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01618;LSEQ=AGGGAGCTCACCTGCAGTGG;RSEQ=CAGAGATGGGGCCGTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:798:54:33,21:396,348:0.0677:2,2:25.8:1:29.6:1:0.32256:1.38:60:108:0.0691:0:1.1 0/0:854:1:0,1:459,394:0.0012:2,0:1:0:26:0:0.46253:0:60:2:0.0012:0:1 -19 5208471 . C T 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0036;SOR=Inf;LSEQ=GGGGTTTTTCTCCATCCTCC;RSEQ=TATCTTCACCCCCATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:33,188:0:2,0:22.5:1:31.7:1:1:0:60:54.25:0.9954:0:0.1 0/1:221:8:2,6:42,170:0.0362:2,2:15.8:1:31.3:1:0.66178:1.35:60:16:0.0364:0:1.3 -19 5208488 . TTTTG T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.21668;SOR=Inf;LSEQ=TCCCTATCTTCACCCCCATT;RSEQ=TTTGTTTGTTTGTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:17,134:0:2,0:23.3:1:30:1:1:0:60:150:1:0:0.1 0/1:132:2:0,2:12,118:0.0152:2,0:10.5:1:31:1:1:0:60:4:0.0153:0.0076:0.5 -19 5208514 . TG T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1036;LSEQ=TTGTTTGTTTGTTTTTGAGA;RSEQ=GAGTTTCACTCTTGTCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:44:0,44:1,53:0.449:1,1:26.8:1:31.4:1:1:0:60:88:0.4536:0.0816:0.2 0/1:65:5:1,4:0,60:0.0769:1,2:28.4:1:31.6:1:0.07692:0:60:10:0.0769:0.0154:0.2 -19 5208588 . G A 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00489;SOR=Inf;LSEQ=CTGCAACCTCCACCTCCAGT;RSEQ=ATTCAAGTAATTCTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:0:1,0:24.6:1:31.1:1:1:0:60:28:1:0:0.2 0/1:12:4:0,4:0,8:0.3333:0,0:22.8:1:31.3:1:1:0:60:8:0.3333:0:1 -19 5210622 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22986;LSEQ=TCTCCTGTGGAGGAGATGGC;RSEQ=GCCGTGGTCAGCGCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:211:128,83:115,98:0.4976:2,2:22.7:1:30.5:1:0.17068:1.31:60:69.333:0.4988:0:1.1 0/1:405:75:37,38:172,157:0.1852:2,2:21.9:1:30.6:1:0.70143:1.12482:60:74:0.1845:0:1.1 -19 5210782 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22741;LSEQ=GTCTTCCGTGGTCTCCGCCA;RSEQ=CGGCCCCTGTGTCGCGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:775:401:171,230:161,212:0.5174:2,2:25.8:1:29.1:1:0.88474:1.02144:60:27.643:0.5119:0:1.2 0/1:919:180:79,101:323,416:0.1959:2,2:25.5:1:29.2:1:1:1.01:60:59:0.1945:0:1.2 -19 5211335 . T A 28 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.64575;LSEQ=GTACTCATGAAAATAAGAAA;RSEQ=ATCCTCAGGGTGTCAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:28.5:1:28.5:1:1:1.8258:60:4:0.25:0:1 1/0:2:1:1,0:1,0:0.5:0,0:16:0:32:0:1:0:60:2:0.5:0:1 -19 5211551 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22953;SOR=Inf;LSEQ=ACTGGAGGCCTCTTGAGAGT;RSEQ=GAGATGGGCTCCTTCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:176,42:0:2,0:24.3:1:28.5:1:1:0:60:108:1:0:0.4 0/1:201:2:1,1:148,51:0.01:2,2:43:0:31:0:0.45144:2.88361:60:4:0.01:0:1.5 -19 5211552 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22497;SOR=Inf;LSEQ=CTGGAGGCCTCTTGAGAGTA;RSEQ=AGATGGGCTCCTTCTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:177,43:0:2,0:24.4:1:31.9:1:1:0:60:72.333:1:0:0.4 0/1:199:2:1,1:146,51:0.0101:2,2:28.5:1:29:0:0.45531:2.84478:60:4:0.0104:0:1 -19 5211568 . G A 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.30728;SOR=1.19892;LSEQ=AGTAGAGATGGGCTCCTTCT;RSEQ=GGGCCCTGAGGTGGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:126:90,36:122,50:0.4228:2,2:21.5:1:28.1:1:1:1.02:60:30.5:0.4192:0:1.1 0/1:263:123:81,42:92,45:0.4677:2,2:22.7:1:28.6:1:0.89541:1.05982:60:60.5:0.4727:0:1.2 -19 5211870 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52028;SOR=0;LSEQ=GGTGGATAGGTAGGTAGGGG;RSEQ=ACCCTGCCACCACCTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:75,120:0.0102:2,2:25:1:28:1:1:1.60:60:4:0.0102:0:1 0/0:129:0:0,0:54,75:0:2,0:22.3:1:32:1:1:0:60:42:1:0:0.1 -19 5211884 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16911;SOR=Inf;LSEQ=TAGGGGCACCCTGCCACCAC;RSEQ=TCTAGTCCCCATTGCTCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:98,96:0:2,0:24.3:1:31:1:1:0:60:193:1:0:0.1 0/1:136:2:1,1:74,60:0.0147:2,2:12:1:30:1:1:1.23141:60:4:0.0148:0:0 -19 5211967 . C T 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.38585;LSEQ=GCCCACAGCAGCCTCCACCC;RSEQ=GCTGGCACCTTGAACTCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:1:0,1:240,155:0.0025:2,0:45:0:13:0:0.39394:0:60:0:0:0:1 0/1:392:28:17,11:220,144:0.0714:2,2:28.9:1:30.4:1:1:1.01:60:56:0.072:0:1.1 -19 5212209 . G A 76 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07253;SOR=6.33838;LSEQ=TGTCTTCTCTGGCTTGATCC;RSEQ=CTCAAGCATGGCGTCGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:1,0:216,318:0.0019:2,0:21:0:26:0:0.40561:0:60:2:0.0019:0:1 0/1:596:7:5,2:265,323:0.0117:2,2:13.3:1:27.4:1:0.25399:3.04:60:14:0.0119:0:1 -19 5212230 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03085;SOR=Inf;LSEQ=CTCAAGCATGGCGTCGATGA;RSEQ=GATAAAGCAGCCTGTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:200,257:0:2,0:23.6:1:30.6:1:1:0:60:64.286:1:0:0.1 0/1:471:6:2,4:207,258:0.0127:2,2:31:1:24.2:1:0.69739:1.6031:60:2:0.0086:0:2.2 -19 5212311 . G A 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGCTGGGCTGCGGGGACC;RSEQ=GGGGGAAGCGGATGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:225,180:0:2,0:21.8:1:30:1:1:0:60:80:1:0:0.3 0/1:364:38:21,17:165,158:0.1044:2,2:20.4:1:29.4:1:0.73202:1.18:60:37:0.1036:0:1.5 -19 5212380 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.30525;LSEQ=ACGATGGGGCCGGCATCTGG;RSEQ=GGGTTGCAGGTCTTGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:722:395:214,181:162,164:0.5471:2,2:26:1:29.6:1:0.23202:1.20:60:48.375:0.5474:0:1.2 0/1:780:210:112,98:308,262:0.2692:2,2:25:1:28.7:1:0.87167:1.0286:60:41:0.2701:0:1.3 -19 5212482 . G A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03134;LSEQ=AACTGGAACTGGCGGACCTC;RSEQ=CGTTTCTCACTGGAGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:720:419:194,225:145,156:0.5819:2,2:25.9:1:29.9:1:0.64995:1.0779:60:82.8:0.5823:0:1.2 0/1:767:32:16,16:343,392:0.0417:2,2:25.3:1:29.5:1:0.72149:1.14:60:64:0.0422:0:1.2 -19 5212571 . G A 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00174;SOR=Inf;LSEQ=CATGTGCTGAAGATGCCCAA;RSEQ=TGGCCGGGTGTGGTGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:39,192:0:2,0:21.9:1:31.6:1:1:0:60:32:1:0:0.6 0/1:194:8:3,5:37,148:0.0412:2,2:18.6:1:27.3:1:0.36593:2.39:60:7:0.0368:0:1 -19 5212584 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1915;SOR=Inf;LSEQ=TGCCCAAGTGGCCGGGTGTG;RSEQ=TGGCTCATGCCTGTTATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:13,156:0:2,0:22.5:1:31.9:1:1:0:59.7:55.333:1:0:0.6 0/1:132:2:1,1:12,118:0.0152:2,2:25:1:30:1:0.18795:9.49:60:4:0.0153:0:2 -19 5212586 . G T 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05642;LSEQ=CCCAAGTGGCCGGGTGTGGT;RSEQ=GCTCATGCCTGTTATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:161:85:4,81:5,71:0.528:2,1:22.1:1:30.4:1:0.73618:1.4229:59.2:170:0.5313:0:1.1 0/1:119:7:1,6:8,104:0.0588:2,2:18.9:1:31.1:1:0.43193:2.15:58.4:14:0.0603:0:1.4 -19 5212680 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1145;SOR=0.3069;LSEQ=GCCTGACCAACATGGAGAAA;RSEQ=CTCGTCTCAACTAAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:19:0,19:0,19:0.5:1,1:18.8:1:30.4:1:1:0:55.8:38:0.5:0:1.4 0/1:13:3:0,3:0,10:0.2308:0,0:18.3:1:28.3:1:1:0:56.3:6:0.2308:0:1.3 -19 5212808 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTGCAGTGAGCTGAGAT;RSEQ=GCGCCACTGTACTCCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26:1:31.5:1:1:0:45.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 5212853 . C CA 26 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAAACTCCATCT;RSEQ=AAAAAAAAAAACACCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:26:1:1:0:60:4:1:0:2 -19 5212923 . T C 43 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGACTTGGGCTCTAGC;RSEQ=GGCCCTGGACGGTTTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:33.7:1:27.7:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:1:0,0:8:0:29:0:1:0:60:2:1:0:2 -19 5214116 . A G 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.11111;SOR=0;LSEQ=GGGCATGAGTAAAGGCAAGA;RSEQ=GAAATCAGGCTCATTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:23.9:1:33:1:1:0:60:16:1:0:1.8 0/0:1:0:0,0:0,1:0:0,0:10:0:32:0:1:0:60:2:1:0:0 -19 5214158 . T C 132 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04135;SOR=0.04344;LSEQ=TTGGGCTCTGCCGGCTTTGT;RSEQ=CTCCTGCCGTGGGTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:17,0:1,0:0.9444:0,1:28.1:1:32.3:1:1:0:60:34:0.9444:0:1.4 0/1:3:1:1,0:2,0:0.3333:0,0:30:0:33:0:1:0:60:2:0.3333:0:1 -19 5214258 . C T 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=GTAGTCAGCCTGGGTAGACA;RSEQ=GCTCCGCTTTCTCTCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:99,2:0:1,0:23.4:1:31.8:1:1:0:60:49.5:1:0:0.1 0/1:59:7:7,0:48,4:0.1186:2,0:27:1:30.7:1:1:0:60:14:0.1207:0:2.1 -19 5214264 . G A 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=AGCCTGGGTAGACACGCTCC;RSEQ=CTTTCTCTCTGTCCCATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:119,3:0:1,0:22.8:1:30.1:1:1:0:60:121:1:0:0.1 0/1:71:8:8,0:59,4:0.1127:2,0:26:1:30:1:1:0:60:16:0.1127:0:2 -19 5214533 . A G 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14389;LSEQ=GTGTCAGCAGGGACAGGCTG;RSEQ=CTGGCAGGGGCTTGAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:680:646:342,304:16,17:0.95:2,2:24.8:1:31.1:1:0.7214:1.20:60:28.364:0.9483:0:1.1 1/0:720:527:271,256:98,94:0.7319:2,2:23.4:1:30.9:1:0.93301:1.02:60:39.538:0.7301:0:1.2 -19 5214689 . G A 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGCGTGGCAATGTACGC;RSEQ=TTCTGACACCGGTAGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:753:0:0,0:336,416:0:2,0:23.4:1:30.8:1:1:0:60:74.2:0.9987:0:1 0/1:776:43:20,23:326,407:0.0554:2,2:22.2:1:29.6:1:0.87489:1.09:60:42:0.055:0:2 -19 5214697 . A G 291 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11753;SOR=5.21931;LSEQ=GGCAATGTACGCGTTCTGAC;RSEQ=CCGGTAGCCGTCCACGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:695:690:296,394:4,0:0.9928:0,2:24.3:1:30.8:1:0.03452:0:60:56.5:0.9927:0:1.1 1/1:722:721:309,412:1,0:0.9986:0,2:24.7:1:30.7:1:0.42936:0:60:54.462:0.9986:0:1.2 -19 5214873 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08649;SOR=Inf;LSEQ=TCCCCAAGGTGACCATGGGA;RSEQ=GTGTACTTCACAGTTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:2,76:0:1,0:24:1:29.6:1:1:0:60:38:1:0:0.4 0/1:33:2:0,2:0,31:0.0606:1,0:21:1:28.5:1:1:0:60:4:0.0645:0:1 -19 5214904 . C T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00035;SOR=0;LSEQ=CAGTTTCTCCCCCTCAGCGC;RSEQ=ATCACCATTTGGGGCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:20:1,19:1,19:0.5:1,1:18.6:1:28.6:1:1:1:60:40:0.5128:0:1.1 0/0:15:0:0,0:0,15:0:1,0:27.3:1:32.1:1:1:0:60:30:1:0:0.2 -19 5214986 . G A 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03251;SOR=0;LSEQ=GAGCAGCATCCCTGGCCTCC;RSEQ=CCCACTCCACGCCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:5,4:1,4:0.6429:2,2:30.2:1:29.9:1:0.3007:4.45:60:18:0.75:0:1.1 0/0:5:0:0,0:1,4:0:2,0:26:1:32.2:1:1:0:60:10:1:0:0.4 -19 5215040 . T G 74 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGTTGTGACAACCAAAGATG;RSEQ=CCCTGGACATTGCCAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:4,1:6,3:0.3571:2,2:31.6:1:32.2:1:1:1.91:60:10:0.3571:0:1 1/1:1:1:1,0:0,0:1:0,0:33:0:33:0:1:0:60:2:1:0:1 -19 5215472 . C T 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=87.32772;LSEQ=CAGGGTAGGTGCCTGTGAGG;RSEQ=CGAGGTGATGAGGGTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:1:0,1:272,275:0.0018:2,0:30:0:31:0:1:0:60:2:0.0019:0:1 0/1:610:84:44,40:285,240:0.1377:2,2:26.2:1:28.6:1:0.81377:1.07941:60:41:0.1383:0:1.1 -19 5215474 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07874;LSEQ=GGGTAGGTGCCTGTGAGGCC;RSEQ=AGGTGATGAGGGTGGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:555:285:142,143:138,132:0.5135:2,2:24.4:1:29.8:1:0.79905:1.05269:60:34.625:0.5111:0:1.1 0/1:627:48:28,20:313,265:0.0766:2,2:25.9:1:30.5:1:0.65182:1.18:60:47:0.0768:0:1.1 -19 5215662 . C A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12169;SOR=0;LSEQ=CTTGGGGGGCCAGCCGGGGA;RSEQ=TCGGGGGAGGGGGGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:3:2,1:30,135:0.0179:2,2:12:1:21.7:1:0.09329:8.83:60:2:0.0127:0:2.7 0/0:170:0:0,0:30,136:0:2,0:37:0:17:0:1:0:60:0:0:0:6 -19 5215826 . T G 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGCAGCAGGTTTGAGGCCC;RSEQ=CTGCTCCGTGCAGAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:1,9:0,1:0.9091:0,2:24.3:1:32.9:1:1:0:60:20:0.9091:0:1.2 1/1:2:2:0,2:0,0:1:0,0:37:1:32:1:1:0:60:4:1:0:1 -19 5216248 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTATCCTTTCAAGCCCCC;RSEQ=AGGATGGCTGCCGAAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:34.7:1:30.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 5216514 . ACACATACACAC A 99 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=CTCACCCACATCCCTGACAC;RSEQ=CACACACACAGCAGTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:49,4:0:2,0:24.3:1:32.2:1:1:0:60:106:1:0:0 0/1:26:9:9,0:16,1:0.3462:1,0:29.6:1:31.4:1:1:0:60:18:0.36:0:0.2 -19 5216574 . C A 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00188;SOR=Inf;LSEQ=CTGAGGGCCCAATGGACCAA;RSEQ=CCCCTGCCCTCTTCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:111,5:0:1,0:24.2:1:31.8:1:1:0:60:115:1:0:0.2 0/1:83:7:5,2:73,2:0.0843:1,2:26.4:1:31.1:1:0.03484:13.51722:60:14:0.0854:0:1.1 -19 5216632 . G T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12383;SOR=Inf;LSEQ=GGCAAAGGCCGGTGATGGGT;RSEQ=GGCGTGTGGACAGAGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:256,58:0:2,0:22.1:1:31.6:1:1:0:60:38.25:1:0:0.2 0/1:317:4:2,2:253,60:0.0126:2,2:22:1:27.8:1:0.17305:4.19049:60:8:0.0127:0:1 -19 5216635 . C T 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37317;SOR=0.24899;LSEQ=AAAGGCCGGTGATGGGTGGG;RSEQ=GTGTGGACAGAGACAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:4:1,3:266,72:0.0117:2,2:5.5:1:27.5:1:0.03436:10.97733:60:8:0.0121:0:1 0/0:341:1:0,1:264,75:0.0029:2,0:1:0:26:0:0.22353:0:60:2:0.003:0:1 -19 5216821 . TA T 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGAAAACATGCAGGGGG;RSEQ=GGGGGGGGTCCCACCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:39,175:0:2,0:23.3:1:30.1:1:1:0:59.9:22.778:1:0:0.3 0/1:245:36:10,26:49,154:0.1469:2,2:23.5:1:29.7:1:0.6762:1.21:60:35:0.1458:0.0327:0.3 -19 5216822 . AG A 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.76222;SOR=0.73327;LSEQ=AATGAAAACATGCAGGGGGT;RSEQ=GGGGGGGTCCCACCTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:6:1,5:35,169:0.0286:2,2:27.7:1:31.3:1:1:1.03534:60:12:0.029:0.0048:0.2 0/1:237:5:2,3:54,176:0.0211:2,2:33:1:29.6:1:0.59526:2.16:59:10:0.0216:0:0.2 -19 5216896 . C CG 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.09552;SOR=2.15406;LSEQ=GGGCAGAGCAACGCGGACAA;RSEQ=GGGGGGTATGTACAGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:20:0,20:1,32:0.3704:1,1:29.6:1:31.5:1:1:0:60:40:0.3846:0.037:0.1 1/0:41:23:0,23:0,18:0.561:1,1:23.1:1:30.9:1:1:0:59.8:46:0.561:0.0488:0.3 -19 5217759 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGAACCCATAAGGAGAA;RSEQ=AGCAGCCATCAGTAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:60:4:1:0:1 -19 5218214 . A T 47 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGGTTAAATGTTAACTTT;RSEQ=AAAAAAAAAAAGCCTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:3,0:15,0:0.1579:1,0:7.3:1:29.7:1:1:0:60:6:0.1579:0:1.3 0/0:3:0:0,0:3,0:0:0,0:12:1:24:1:1:0:60:2:1:0:0.3 -19 5218659 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12737;SOR=Inf;LSEQ=CCATGGACCCGTATGACTAG;RSEQ=GTTTCCAGGACCAAGTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:139,134:0:2,0:23.7:1:31.4:1:1:0:60:67.25:1:0:0.3 0/1:152:2:1,1:88,62:0.0132:2,2:7.5:1:28:1:1:1.416:60:4:0.0132:0:1 -19 5218684 . G A 198 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CCAGGACCAAGTACAGCTAC;RSEQ=TGTACAAGCTGTGGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:88:60,28:132,67:0.3056:2,2:28.3:1:30.7:1:0.78714:1.09:60:176:0.3088:0:1 0/0:194:0:0,0:137,57:0:2,0:22.5:1:29.6:1:1:0:60:193:1:0:0.1 -19 5218836 . G A 163 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=51.02659;LSEQ=CCGAAAGCAGACACAGGTGA;RSEQ=AAGGGGGAAAAAAAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:1:1,0:281,398:0.0015:2,0:1:0:29:0:0.41471:0:60:2:0.0015:0:1 0/1:743:52:22,30:298,393:0.07:2,2:23.3:1:28.6:1:1:1.03396:60:51:0.0699:0:1.1 -19 5219493 . G T 50 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.05644;SOR=0;LSEQ=AAAGGTCTGCAGGGAAAGGA;RSEQ=GGGGGTCTCCATCAGTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:4:2,2:97,275:0.0106:2,2:22.5:1:25.3:1:0.28386:2.83:60:3:0.0081:0:1.3 0/0:397:0:0,0:118,279:0:2,0:24.2:1:30.4:1:1:0:60:131.333:1:0:0.1 -19 5219803 . T C 112 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=35.57984;LSEQ=AAGAAACCTTCGTTTCAGGA;RSEQ=CCCTCCGCTCCCAAGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:2,0:39,3:0.0455:2,0:34:0:33:0:1:0:60:4:0.0513:0:2 1/0:20:13:12,1:7,0:0.65:0,1:23.1:1:30.4:1:1:0:60:26:0.65:0:1.8 -19 5219829 . T G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.32148;LSEQ=CGCTCCCAAGTCTTCCCCTC;RSEQ=GCCCAGCTCTGACCACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:5:5,0:63,2:0.0714:1,0:20.4:1:26.2:1:1:0:60:4:0.058:0:1.4 1/0:35:18:18,0:15,2:0.5143:2,1:26.2:1:29.2:1:0.22857:0:60:17:0.5152:0:1.6 -19 5219852 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52174;SOR=0;LSEQ=CCAGCTCTGACCACAGGGAG;RSEQ=TGCCTGTGACTGACCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:89,8:0.0202:2,2:24.5:1:26.5:1:0.1744:10.54764:60:4:0.0204:0:1 0/0:63:0:0,0:54,9:0:2,0:20.8:1:31.3:1:1:0:60:62:1:0:0.4 -19 5219891 . TG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49862;SOR=0;LSEQ=GAGGTCAGGGCCCTGGGGAA;RSEQ=GGGTCTGCCTCATTCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:129,47:0.0112:2,2:41:1:31:1:0.46772:2.72645:60:4:0.0115:0:1 0/0:175:0:0,0:124,47:0:2,0:22.2:1:31.3:1:1:0:60:342:0.9771:0:0.1 -19 5219897 . C T 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.5089;LSEQ=AGGGCCCTGGGGAATGGGGT;RSEQ=TGCCTCATTCAGAGGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:0,2:135,55:0.0104:2,0:17.5:1:26:1:0.08704:0:60:4:0.0106:0:1 0/0:188:1:0,1:134,53:0.0053:2,0:1:0:26:0:0.28723:0:60:2:0.0053:0:1 -19 5220003 . G A 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03432;SOR=Inf;LSEQ=GAGGACATAGCGGTGGCCGG;RSEQ=CTCCAGGCCCCGGTTATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:246,195:0:2,0:24.8:1:31:1:1:0:60:32.923:1:0:0.1 0/1:525:6:4,2:275,244:0.0114:2,2:11.5:1:27.5:1:0.68944:1.77:60:12:0.0117:0:1 -19 5220134 . C T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01908;SOR=0;LSEQ=GACGCGAGTGCCGCAGGCTG;RSEQ=GCCTCTGTAGCCGTGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:5:2,3:146,174:0.0154:2,2:19.6:1:24.4:1:1:1.25774:60:4:0.0125:0:1 0/0:390:0:0,0:177,213:0:2,0:24.8:1:30.4:1:1:0:60:64:1:0:0.1 -19 5220406 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50025;SOR=0;LSEQ=TCAGAGGGGCTGTCGATAGG;RSEQ=ATGACCAAGGGATGCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:0,2:33,162:0.0102:2,0:12.5:1:27:1:1:0:60:4:0.0102:0:1 0/0:176:0:0,0:24,151:0:2,0:23.7:1:30.9:1:1:0:60:42.75:0.9942:0:0.2 -19 5220436 . C T 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATGCTTCATGGGGGCAAA;RSEQ=GGGGGAAGCCGTTTCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:5,121:0:1,0:24.2:1:29.2:1:1:0:60:17:1:0:0.2 0/1:78:13:0,13:0,64:0.1667:1,1:19.2:1:31.2:1:1:0:60:26:0.1688:0:1.2 -19 5220441 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52907;SOR=0;LSEQ=CTTCATGGGGGCAAACGGGG;RSEQ=AAGCCGTTTCTCTGAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:2,112:0.0171:1,2:24:1:27.5:1:0.05127:45.93:60:4:0.0177:0:1 0/0:70:0:0,0:0,70:0:1,0:20:1:30.8:1:1:0:60:16.5:1:0:0.3 -19 5220900 . T C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=5.41897;LSEQ=GAACTAGGGCTGATAGGGTC;RSEQ=GTGTTTCATAGGCAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:41:38,3:35,1:0.5325:1,2:24.9:1:30.3:1:0.61826:2.73025:60:82:0.5395:0:1.1 1/1:58:50:49,1:6,1:0.8621:2,1:25.6:1:30.4:1:0.23246:7.64:60:49:0.875:0:1.1 -19 5221408 . CTGATCCCAGG C 94 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00827;SOR=9.18057;LSEQ=AATCTAACACTGACTGATCC;RSEQ=CTGAGTCCCCAACTCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:0,22:0.0833:1,0:31.5:1:34.5:1:1:0:60:4:0.087:0:0 0/1:17:8:3,5:1,8:0.4706:2,2:25.4:1:31.6:1:0.29412:4.37:60:16:0.4706:0.1176:0.4 -19 5222047 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50302;SOR=0;LSEQ=AGCCCTGATCCCTCACTTCA;RSEQ=ACCAACTCCAAACTGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:119,3:0.0161:1,2:20:0:31.5:1:0.06373:34.50252:60:4:0.0163:0:1.5 0/0:101:0:0,0:96,5:0:1,0:26.1:1:31.1:1:1:0:60:49.5:1:0:0.9 -19 5222071 . G C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.88557;LSEQ=AACTCCAAACTGAGCCTTAA;RSEQ=CCCTGCTGAACTACAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:181:101:95,6:74,6:0.558:2,2:23:1:32.1:1:0.76747:1.28:60:202:0.5611:0:1.9 1/1:160:133:119,14:26,1:0.8313:1,2:24.3:1:30.8:1:0.46981:3.04352:60:266:0.8313:0:1.1 -19 5222073 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21561;SOR=Inf;LSEQ=CTCCAAACTGAGCCTTAAGC;RSEQ=CTGCTGAACTACAACCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:171,13:0:2,0:25.1:1:31.1:1:1:0:60:91:1:0:1.1 0/1:160:2:1,1:144,14:0.0125:2,2:21:1:28:1:0.17925:9.97142:60:4:0.0126:0:2 -19 5222088 . C G 225 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAGCCCTGCTGAACTACAA;RSEQ=CCCTGACCCTGCCTGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:128:108,20:99,19:0.5182:2,2:21.9:1:32.2:1:1:1.04:60:127:0.5184:0:1.7 0/0:216:0:0,0:182,34:0:2,0:22.7:1:30.8:1:1:0:60:107:1:0:0.7 -19 5222095 . CCCTG C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=5.000;MSILEN=4;SSF=0.2285;SOR=0.40868;LSEQ=TGCTGAACTACAACCCCTGA;RSEQ=CCTGCCTGCCTGCCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:8:6,2:226,56:0.0274:2,2:23:1:31.6:1:0.66243:1.34375:60:16:0.0277:0.0068:1.1 0/1:264:3:2,1:197,58:0.0114:2,2:34.3:1:32.7:1:0.54271:1.69432:60:6:0.0114:0:0.3 -19 5222655 . G A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20922;SOR=4.18043;LSEQ=GGGCTGGGGTGGGGGTGGGC;RSEQ=CAAGGCCCGGTCCGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:100,70:0.0058:2,0:8:0:32:0:1:0:60:2:0.0059:0:1 0/1:167:4:3,1:100,63:0.024:2,2:16.3:1:26.5:1:1:1.88:60:8:0.0248:0:1.5 -19 5222836 . C T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.16257;LSEQ=GTGAGCGCGTTCTCCGCGCC;RSEQ=GGCTCAGCCGCTGCCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:3:1,2:173,134:0.0097:2,2:13.3:1:28:1:0.58372:2.57431:60:6:0.0099:0:1 0/1:267:3:1,2:153,111:0.0112:2,2:21:1:29.3:1:0.5756:2.74635:60:6:0.0114:0:1 -19 5223018 . G A 183 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAATCTGCGGGTGGCCAC;RSEQ=GGGCGTGTCCTCCGGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:0:0,0:296,236:0:2,0:25.3:1:30.4:1:1:0:60:87.667:1:0:0.1 0/1:439:66:36,30:209,163:0.1503:2,2:22.3:1:30.4:1:0.8931:1.06834:60:65:0.1515:0:1.3 -19 5223279 . G A 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.30512;SOR=4.64151;LSEQ=CAGGCTGCCCTCGGGGGTCT;RSEQ=CTGCACCGACAGGGTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:1,0:52,198:0.004:2,0:1:0:23:0:0.21116:0:60:2:0.0041:0:1 0/1:164:3:2,1:41,120:0.0183:2,2:18:1:22.7:1:0.16848:5.78:60:6:0.0185:0:1.3 -19 5225558 . G C 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00055;SOR=0;LSEQ=AAAGGAGGAGGCAGGGGCGG;RSEQ=GGGGGCCAAGCTGGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:21:21,0:25,1:0.4468:1,1:27.3:1:32.5:1:1:0:60:42:0.4468:0:1 0/0:16:0:0,0:15,1:0:1,0:19.4:1:30.7:1:1:0:60:15:1:0:0.3 -19 5225611 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51395;SOR=0;LSEQ=AGCAGCCCTCACACCTTTGT;RSEQ=TCACTGTTCCAGCTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:96,2:0.02:1,2:8.5:1:31:1:0.05939:39.3701:60:4:0.0204:0:1.5 0/0:69:0:0,0:64,5:0:2,0:21.9:1:31.4:1:1:0:60:68:1:0:0.2 -19 5225676 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10533;SOR=Inf;LSEQ=GCTCAAGGACTCTGGAGTCA;RSEQ=GCTCTGGTGCCAGTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:254,79:0:2,0:23.7:1:31:1:1:0:60:32.3:1:0:0.1 0/1:299:3:1,2:207,89:0.01:2,2:27:1:29.3:1:0.22066:4.62475:60:6:0.0102:0:1.3 -19 5225686 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44182;SOR=2.09938;LSEQ=TCTGGAGTCACGCTCTGGTG;RSEQ=CAGTGGGGGCAAAGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:2:0,2:285,108:0.0051:2,0:19.5:1:17.5:1:0.07704:0:60:1:0.0026:0:1 0/1:379:4:2,2:250,125:0.0106:2,2:22.5:1:24.3:1:0.60444:1.99611:60:3:0.0081:0:1 -19 5225802 . G A 189 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=80.38476;LSEQ=TCGCCCTTCATGGTGTAGGC;RSEQ=GCTACCGTGATGGAGTACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:864:1:1,0:394,469:0.0012:2,0:1:0:26:0:0.45718:0:60:2:0.0012:0:1 0/1:879:75:36,39:371,433:0.0853:2,2:26.8:1:30.4:1:0.80905:1.08:60:150:0.086:0:1.2 -19 5225931 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17719;SOR=Inf;LSEQ=ACCCCCACTCCCCGTGCTGA;RSEQ=AACAAGCAAGGAGGATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:6,135:0:1,0:24.5:1:31.4:1:1:0:60:69.5:1:0:0.1 0/1:103:2:0,2:7,94:0.0194:2,0:14:1:29:1:1:0:60:4:0.0198:0:1 -19 5225981 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09987;SOR=Inf;LSEQ=CAGGGGTGGAGACGTGCACA;RSEQ=GAGCTCATGCAGAGACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:3,63:0:1,0:23.7:1:29.8:1:1:0:60:32:1:0:0 0/1:31:2:0,2:1,28:0.0645:1,0:14:1:31.5:1:1:0:60:4:0.0667:0:1 -19 5228988 . A G 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGACATACTCACAGGAG;RSEQ=AATGACTACGGGCAGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:11.5:1:30.3:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 5229490 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.24779;SOR=0;LSEQ=CGTCCCCGGCCCCGCCCCGG;RSEQ=CCCCCGCCCACCTGGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:3:0,3:66,84:0.0196:2,0:11:1:28.3:1:0.25929:0:60:6:0.0196:0:1.7 0/0:147:0:0,0:62,85:0:2,0:23.3:1:30.7:1:1:0:60:23.5:1:0:0.3 -19 5229495 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24613;SOR=0;LSEQ=CCGGCCCCGCCCCGGCCCCC;RSEQ=GCCCACCTGGGCATCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:76,82:0.0125:2,2:8:0:32:0:1:1.08:60:4:0.0127:0:1.5 0/0:162:0:0,0:75,87:0:2,0:22.7:1:29.9:1:1:0:60:53:1:0:0.3 -19 5229510 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67922;SOR=0.63486;LSEQ=CCCCCCGCCCACCTGGGCAT;RSEQ=GGCCAGCATGACGTCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:1,2:100,95:0.0152:2,2:13.3:1:28:1:0.61556:2.09762:60:6:0.0155:0:1 0/0:207:2:0,2:97,108:0.0097:2,0:5.5:1:20:1:0.49955:0:60:1:0.005:0:1.5 -19 5229511 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23383;SOR=0;LSEQ=CCCCCGCCCACCTGGGCATC;RSEQ=GCCAGCATGACGTCCTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:101,96:0.0101:2,2:9:1:29.5:1:1:1.05184:60:4:0.0104:0:1 0/0:212:0:0,0:100,112:0:2,0:22.1:1:29.5:1:1:0:60:41.4:1:0:0.3 -19 5229601 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25606;SOR=0;LSEQ=TGGTAGCCGCGGATCTGGCC;RSEQ=TGCTGCCGGCCGGGCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:104,143:0.012:2,2:7.3:1:30:1:1:1.45245:60:6:0.0124:0:1.3 0/0:204:0:0,0:90,114:0:2,0:26.5:1:30:1:1:0:60:50:1:0:0.3 -19 5229604 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.24289;LSEQ=TAGCCGCGGATCTGGCCGTG;RSEQ=TGCCGGCCGGGCGCGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:2:0,2:101,139:0.0083:2,0:6:1:19:1:0.51164:0:60:1:0.0042:0:1.5 0/1:195:2:1,1:86,107:0.0103:2,2:43.5:1:30.5:1:1:1.24:60:4:0.0104:0:1.5 -19 5229617 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49915;SOR=0;LSEQ=GGCCGTGCTGCCGGCCGGGC;RSEQ=CGGGCGAGCGCCACAGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:75,99:0.0113:2,2:22:0:32.5:1:1:1.32:60:4:0.0116:0:1.5 0/0:165:0:0,0:74,91:0:2,0:28.3:1:30.2:1:1:0:60:40.25:1:0:0.3 -19 5229622 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.49839;SOR=0;LSEQ=TGCTGCCGGCCGGGCGCGGG;RSEQ=GAGCGCCACAGCACGCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:69,85:0.0128:2,2:25.5:1:27:1:1:1.23:60:4:0.0131:0:1.5 0/0:155:0:0,0:69,85:0:2,0:27.9:1:29.8:1:1:0:60:37.5:0.9934:0:0.3 -19 5229623 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24751;SOR=0;LSEQ=GCTGCCGGCCGGGCGCGGGC;RSEQ=AGCGCCACAGCACGCGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:68,80:0.0133:2,2:17:0:32:0:1:1.18:60:4:0.0134:0:1.5 0/0:151:0:0,0:70,81:0:2,0:27.9:1:30:1:1:0:60:302:1:0:0.3 -19 5229633 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49886;SOR=Inf;LSEQ=GGGCGCGGGCGAGCGCCACA;RSEQ=CACGCGGATGGCCGTGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:64,74:0:2,0:20.7:1:32.2:1:1:0:60:276:1:0:0.4 0/1:148:2:1,1:69,77:0.0135:2,2:19:1:25:0:1:1.12:60:4:0.0135:0:2 -19 5229644 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5858;SOR=0.39504;LSEQ=AGCGCCACAGCACGCGGATG;RSEQ=CCGTGGCGTTGAGCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:49,62:0.0177:2,2:46:1:30.5:1:1:1.26:60:4:0.018:0:1 0/0:142:1:1,0:67,74:0.007:2,0:1:0:23:0:0.47887:0:60:2:0.0072:0:1 -19 5229647 . G A 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75971;LSEQ=GCCACAGCACGCGGATGGCC;RSEQ=TGGCGTTGAGCGCCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:49,58:0.0183:2,0:1:0:26:0:0.21662:0:60:4:0.0185:0:1.5 0/1:143:2:1,1:68,73:0.014:2,2:27:0:32:0:1:1.07:60:4:0.0142:0:1.5 -19 5229662 . T A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.482;LSEQ=TGGCCGTGGCGTTGAGCGCC;RSEQ=CCGCCTCCACCTTCCGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:33,42:0.0132:2,0:1:0:31:0:0.44737:0:60:2:0.0137:0:1 0/1:103:2:1,1:44,57:0.0194:2,2:11:1:29.5:1:1:1.29:60:4:0.0202:0:1 -19 5229719 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49126;SOR=Inf;LSEQ=GCGGGCGGGAGGGGAGGGGA;RSEQ=GGGCGGGCGGAGCCGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:18.6:1:31.1:1:1:0:60:25:1:0:0.5 0/1:28:2:1,1:15,11:0.0714:2,2:20.5:1:32.5:1:1:1.34838:60:4:0.0714:0:1 -19 5229728 . G A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00199;SOR=0;LSEQ=AGGGGAGGGGAGGGGCGGGC;RSEQ=GAGCCGTTACCAGGGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:5,2:8,7:0.3182:2,2:22.7:1:29.1:1:0.64783:2.11:60:14:0.3684:0:1.1 0/0:27:0:0,0:15,12:0:2,0:14.2:1:28.5:1:1:0:60:26:1:0:0.4 -19 5229739 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=Inf;LSEQ=GGGGCGGGCGGAGCCGTTAC;RSEQ=AGGGCGCCCGGCCCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:15.5:1:29.5:1:1:0:60:13:1:0:0.6 0/1:13:2:1,1:6,5:0.1538:2,2:14.5:1:28:1:1:1.18321:60:4:0.1538:0:1 -19 5231135 . T C 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37652;SOR=2.52553;LSEQ=TGCAGAGCTAAGCCTGCCCA;RSEQ=GTCTAGAATCGCCAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:7,1:0.2727:2,0:18.3:1:33.3:1:1:0:60:6:0.2727:0:1 1/0:8:4:4,0:4,0:0.5:0,0:19.3:1:32.3:1:1:0:60:8:0.5:0:1.3 -19 5231264 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17795;SOR=Inf;LSEQ=GTTTCCAGATGGAAGGCTTC;RSEQ=AGGCGGGGGCCGGGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:154,18:0:2,0:22.8:1:29.6:1:1:0:60:33.4:1:0:0.2 0/1:126:2:1,1:109,15:0.0159:2,2:12.5:1:28:1:0.23873:7.06799:60:4:0.016:0:1 -19 5231289 . C T 37 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.64649;SOR=0.47402;LSEQ=GGGGGCCGGGCTGGGGCCTG;RSEQ=GGGGGGTCCCGGGCCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:3,0:209,47:0.0115:2,0:22:1:23.7:1:1:0:60:2:0.0079:0:1 0/0:182:1:0,1:132,49:0.0055:2,0:1:0:24:0:0.27473:0:60:2:0.0056:0:1 -19 5231316 . C T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04925;SOR=Inf;LSEQ=TCCCGGGCCTGGGGCAGGTA;RSEQ=TTACCATCCTCGTCGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:274,124:0:2,0:24.9:1:31.5:1:1:0:60:32.167:1:0:0.2 0/1:356:4:2,2:234,118:0.0112:2,2:7.3:1:28:1:0.60556:1.979:60:8:0.0115:0:1.3 -19 5231584 . C T 50 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05612;SOR=0;LSEQ=TTACCAAAATGGCCGTGGAG;RSEQ=GCACGCTGACACATTTAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:4:2,2:76,224:0.0132:2,2:31.5:1:25.3:1:0.27221:2.93:60:3:0.0103:0:2.5 0/0:319:0:0,0:87,230:0:2,0:24.7:1:29.9:1:1:0:60:25.417:0.9935:0:0.3 -19 5231610 . A AG 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.6227;SOR=2.9521;LSEQ=CTGACACATTTAACGTCTTG;RSEQ=GGGGGGGCTGACGGTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:31,119:0.0065:2,0:18:0:33:0:1:0:60:2:0.007:0:0 0/1:158:3:1,2:48,103:0.019:2,2:24.3:1:32.3:1:1:1.07:60:6:0.0203:0:0.3 -19 5238771 . G A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03162;SOR=Inf;LSEQ=GGGATACTGAGGCACAGCGC;RSEQ=GGTAGATGGATCCGAGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:14,1:0:1,0:22.9:1:29.6:1:1:0:60:14:1:0:0.4 0/1:8:3:3,0:4,1:0.375:2,0:25.3:1:30.7:1:1:0:60:6:0.4286:0:1 -19 5238944 . C T 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06426;SOR=0;LSEQ=ACCTACTGGACTGCAGCGTG;RSEQ=GCTGCCGCACCACGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:5:3,2:356,94:0.011:2,2:31:1:29.4:1:0.28501:2.51844:60:10:0.0112:0:1.2 0/0:401:0:0,0:278,122:0:2,0:24:1:30.9:1:1:0:60:39:1:0:0.1 -19 5239140 . GGA G 128 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.26501;SOR=1.6204;LSEQ=GAGAGAGACAGAAACAAAGG;RSEQ=GAGAGAGAGAGACAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:12:4,8:116,349:0.025:2,2:26.7:1:31.7:1:0.50738:1.50:59.6:24:0.026:0:0.9 0/1:451:18:4,14:118,314:0.0399:2,2:29.4:1:30.9:1:0.79003:1.3145:59.4:36:0.041:0.0022:0.8 -19 5239171 . AGG A 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.05484;SOR=6.93029;LSEQ=GAGACAGAAACAGAGGGGGG;RSEQ=GGGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:1:0,1:13,204:0.0046:2,0:48:0:30:0:1:0:60:2:0.0048:0:0 0/1:194:6:0,6:14,174:0.0309:2,0:38.7:1:28:1:1:0:60:12:0.0317:0.0052:0.3 -19 5239175 . G GGA 175 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=13.000;MSILEN=2;SSF=1e-05;SOR=0.34055;LSEQ=CAGAAACAGAGGGGGGAGGG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:70:1,69:9,101:0.3415:2,1:33.6:1:28.7:1:0.09108:6.10389:58:22.333:0.3702:0.0146:1.3 0/1:187:28:3,25:3,72:0.1497:1,2:34.5:1:29:1:0.34069:2.85:59.1:27:0.1688:0.0053:0.8 -19 5239200 . C G 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.26053;SOR=0;LSEQ=GAGAGAGAGAGAGAGAGAGA;RSEQ=AGAGAAATAGAGACAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:0,3:4,135:0.0208:1,0:13.7:1:22:1:1:0:56.7:2:0.0154:0:2.7 0/0:110:0:0,0:5,105:0:1,0:28:0:16:0:1:0:60:0:0:0:4 -19 5239214 . CA C 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=GAGAGACAGAGAAATAGAGA;RSEQ=GGGGTGCGGCAGAGAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:5,104:0:1,0:22.5:1:30.4:1:1:0:59:17.167:1:0:1.1 0/1:80:10:2,8:3,58:0.125:1,2:23.6:1:28.8:1:0.14226:4.67:59:9:0.1216:0.0125:0.5 -19 5240115 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14704;SOR=Inf;LSEQ=GAGCAGAATCCGCAGCACAC;RSEQ=TAGGGACAAAGAGGGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:119,4:0:1,0:27.3:1:30.4:1:1:0:60:122:1:0:0.1 0/1:77:2:1,1:68,7:0.026:2,2:24:1:29:1:0.19822:9.15346:60:4:0.0263:0:1 -19 5240392 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.06494;LSEQ=GTCGGGGAGCGTCCACCCCA;RSEQ=AAAGGGGGCCCCACCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:115:32,83:37,132:0.4049:2,2:25.3:1:28.6:1:0.26262:1.37:60:56.5:0.4036:0:1.1 0/1:261:11:3,8:70,180:0.0421:2,2:21.3:1:26.9:1:1:1.03686:60:22:0.0423:0:1.2 -19 5240416 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23253;SOR=Inf;LSEQ=GGGGGCCCCACCTGCTGAGT;RSEQ=TCCCCACTAAAAGATGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:24,158:0:2,0:24.6:1:32.2:1:1:0:60:59.667:1:0:0.5 0/1:170:2:1,1:28,140:0.0118:2,2:32:1:29:1:0.31291:4.93:60:4:0.012:0:1 -19 5240432 . G T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=GAGTGTCCCCACTAAAAGAT;RSEQ=CCAGCTCTGGGTGCTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:8,133:0:2,0:23.2:1:31.9:1:1:0:60:34.25:1:0:0.4 0/1:118:2:1,1:7,109:0.0169:2,2:11:0:27.5:1:0.13154:14.63:60:4:0.0171:0:1 -19 5240463 . T A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02719;SOR=Inf;LSEQ=GTGCTTCTAGAATGTTCTTT;RSEQ=ATTTTCCTGGGGACCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:4,83:0:1,0:24:1:28.4:1:1:0:60:174:1:0:0.3 0/1:61:4:0,4:3,54:0.0656:2,0:19.5:1:29.8:1:1:0:60:8:0.0667:0:2 -19 5240636 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGGCGGGCAGATCACGAG;RSEQ=TCAGGAGATCGAGACCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:28:1:31:1:1:0:41:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 5243702 . C T 29 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=CATGTTGGCCATGCTGGTCT;RSEQ=GAACTCCTGACCTCCGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:12,0:0.0769:0,0:13:0:32:0:1:0:60:2:0.0769:0:1 1/1:2:2:2,0:0,0:1:0,0:27:1:29.5:1:1:0:60:4:1:0:1 -19 5243846 . C T 52 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14766;SOR=0;LSEQ=ACAAACCGCTCTGCGGCTTC;RSEQ=AGGGAGCATGCAAAGAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:4:1,3:156,35:0.0205:2,2:11:1:26.3:1:0.02394:13.11975:60:8:0.0208:0:1.3 0/0:135:0:0,0:93,42:0:2,0:23.8:1:30.2:1:1:0:60:66.5:1:0:0.1 -19 5243864 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1895;SOR=Inf;LSEQ=TCCAGGGAGCATGCAAAGAA;RSEQ=CAAGCCGCACGGCCGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:186,65:0:2,0:26.1:1:31.7:1:1:0:60:124.5:1:0:0.1 0/1:194:2:1,1:125,67:0.0103:2,2:28.5:1:28:1:1:1.85937:60:4:0.0105:0:1 -19 5244506 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49989;SOR=0;LSEQ=GGGGAGAGCTGTGGGCAGGA;RSEQ=GCAGCTGTGTCACGCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:23,101:0.0159:2,2:26.5:1:31.5:1:0.3459:4.32:60:4:0.0163:0:1 0/0:111:0:0,0:22,89:0:2,0:22.5:1:30.7:1:1:0:60:222:1:0:0.1 -19 5244554 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52532;SOR=0;LSEQ=GGTTGAGGACCCTGAAGGCT;RSEQ=TGTGACTTTTCACCATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:0,48:0.04:1,0:8:0:31:0:1:0:60:4:0.0408:0:1 0/0:30:0:0,0:1,28:0:1,0:19:1:31.3:1:1:0:60:58:0.9667:0:0 -19 5245630 . A G 130 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00036;SOR=11.46047;LSEQ=ATTTATAACCAATAAATAAT;RSEQ=CCTGTTCAAAGAACAACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:32,0:0.0588:1,0:25.5:1:33:0:1:0:60:4:0.0588:0:1 0/1:40:17:16,1:22,1:0.425:1,1:22.8:1:32:1:1:1.36391:60:34:0.425:0:1.1 -19 5245665 . T G 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01585;SOR=Inf;LSEQ=AACCGTCCCCTTCCTAGCCA;RSEQ=GAATGACTGAAGCCAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:78,2:0:1,0:23.6:1:31:1:1:0:60:39:1:0:0.1 0/1:64:5:5,0:55,4:0.0781:2,0:31.4:1:32.2:1:1:0:60:10:0.0794:0:1 -19 5245699 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19658;SOR=Inf;LSEQ=CAAGAGGGTAACTCGGAGGT;RSEQ=CTCCCACGCTGCCTCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:134,11:0:2,0:24.4:1:32:1:1:0:60:35.25:1:0:0.1 0/1:116:2:1,1:103,11:0.0172:2,2:19:0:27.5:1:0.197:9.00842:60:4:0.0174:0:1.5 -19 5245732 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.32573;SOR=3.82144;LSEQ=CTCCCACCTGTGCCTGAAGT;RSEQ=GGGGATCGACTCCAGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:0,1:203,41:0.0041:2,0:1:0:25:0:0.17143:0:60:2:0.0042:0:1 0/1:194:3:0,3:146,45:0.0155:2,0:7.7:1:27:1:0.01444:0:60:6:0.0157:0:1 -19 5245971 . G A 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGGCATGGGCGAGCCCAC;RSEQ=GCCACGCAGGTGATGTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:874:0:0,0:378,494:0:2,0:24.9:1:30.1:1:1:0:60:71.667:0.9977:0:0.1 0/1:742:61:29,32:310,369:0.0822:2,2:24.4:1:30.1:1:0.78995:1.08:60:29.5:0.081:0:1.2 -19 5245977 . G A 189 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=111.5428;LSEQ=ATGGGCGAGCCCACGGCCAC;RSEQ=CAGGTGATGTTCACGTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:845:1:0,1:367,475:0.0012:2,0:15:0:21:0:1:0:60:2:0.0012:0:1 0/1:727:85:34,51:292,348:0.1169:2,2:25.1:1:29.6:1:0.35453:1.25822:60:170:0.1182:0:1.2 -19 5246041 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.198;SOR=4.41341;LSEQ=TGGGCAGGATGGAGAAGCGC;RSEQ=GGGCCACGCGGCGGACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:1:1,0:118,302:0.0024:2,0:1:0:28:0:0.28266:0:60:2:0.0024:0:1 0/1:384:4:2,2:135,245:0.0104:2,2:25.5:1:28.8:1:0.61888:1.81:60:8:0.0105:0:1 -19 5246058 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11362;SOR=Inf;LSEQ=CGCGGGGCCACGCGGCGGAC;RSEQ=GGGGAGGGGGCGGCAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:65,215:0:2,0:24.5:1:30.1:1:1:0:60:45.667:1:0:0.1 0/1:264:3:3,0:78,183:0.0114:2,0:11.3:1:21:1:0.02814:0:60:2:0.0079:0:1.7 -19 5246097 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.16201;SOR=Inf;LSEQ=GCGGCGGGAGGGAGATGCGA;RSEQ=GGGTGAGGTGGGGTGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:25,142:0:2,0:22.8:1:30.8:1:1:0:60:54.667:1:0:0.1 0/1:113:2:1,1:17,94:0.0177:2,2:20.5:1:27.5:1:0.29441:5.40:60:4:0.0177:0:1 -19 5246125 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGTGAGGTTGGGAGGG;RSEQ=AAGACAGGATGCGGAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:7,109:0.0169:2,2:40:1:29.5:1:0.13154:14.63:60:4:0.0174:0:1 0/0:58:0:0,0:7,51:0:2,0:25:1:31.1:1:1:0:60:57:1:0:0.1 -19 5246158 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGAGAAAAAGAAAAGCA;RSEQ=GAAGGAAGAAAGAAAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:0,2:3,70:0.0267:1,0:25.5:1:31:1:1:0:60:4:0.0267:0:1 0/0:36:0:0,0:4,32:0:2,0:23.5:1:29.7:1:1:0:60:35:1:0:0.2 -19 5246194 . G GA 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.10145;SOR=Inf;LSEQ=GAAGGAAAGAAAGAAAAAAA;RSEQ=AAAAAAAAAGGAAAACCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:0,31:0:1,0:20.4:1:31.8:1:1:0:60:62:1:0:0.2 0/1:15:2:0,2:0,13:0.1333:1,0:26:1:32:0:1:0:60:4:0.1429:0:0 -19 5255992 . A AT 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00285;SOR=0.24673;LSEQ=AAATTGTTGTTCATTTTTCT;RSEQ=TTTTTTTTCCGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:18:18,0:16,0:0.5294:1,1:25.7:1:31.8:1:1:0:60:36:0.5294:0.0588:0.1 0/1:56:12:12,0:38,4:0.2143:2,0:29.8:1:31:1:0.5644:0:60:24:0.2143:0:0 -19 5256056 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51133;SOR=Inf;LSEQ=ACATGTGTTTTGTGTGTGTG;RSEQ=GTGTCATTTTCAGAATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:114,11:0:2,0:26.6:1:32:1:1:0:60:124:1:0:0.1 0/1:173:2:1,1:143,28:0.0116:2,2:16:0:32:0:0.30797:5.03598:60:4:0.012:0:1 -19 5256073 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18122;SOR=0;LSEQ=GTGCGTGTCATTTTCAGAAT;RSEQ=TAAAAATGTGGGTAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:151,38:0.0105:2,2:9.5:1:29:1:0.36754:3.93538:60:4:0.0106:0:1 0/0:257:0:0,0:183,74:0:2,0:21.9:1:30.9:1:1:0:60:50.4:1:0:0.1 -19 5256251 . G GT 143 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=4e-04;SOR=0.33041;LSEQ=AAAAGCTGCAATAGTTTGTT;RSEQ=TTTTTTTTTTCTTTAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:46:1,45:3,69:0.368:1,1:27.3:1:25.9:1:1:1.94643:60:3.6:0.3636:0:1.2 0/1:112:18:1,17:8,82:0.1607:2,1:24.9:1:29.7:1:1:1.65181:58.3:17:0.1789:0.0089:1.6 -19 5256270 . CA C 103 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.14885;SOR=0.35846;LSEQ=TGTTTTTTTTTTCTTTAAAC;RSEQ=AAAAAAAAAATTAAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:10:0,10:0,76:0.1163:1,0:23.3:1:31.2:1:1:0:57:20:0.1176:0.0116:1.3 0/1:67:3:0,3:2,60:0.0448:1,0:37:1:31.3:1:1:0:60:6:0.0455:0:2.3 -19 5257811 . C A 41 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2451;SOR=6.606;LSEQ=ACGGGGCATCTCTCGCAAGG;RSEQ=ACGAGGAAGGGAATTTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:9,1:0.0909:2,0:7:0:31:0:1:0:60:2:0.0909:0:1 0/1:7:3:3,0:4,0:0.4286:0,0:16.7:1:26.3:1:1:0:60:6:0.4286:0:2.3 -19 5257926 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52457;SOR=0;LSEQ=GGGAGGGGCCTTCCTGCTTG;RSEQ=GTGTGCAGGGGACGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:82,5:0.0225:2,2:8.5:1:28.5:1:0.131:15.06193:60:4:0.0233:0:1 0/0:55:0:0,0:55,0:0:1,0:23.2:1:31.5:1:1:0:60:54:1:0:0.2 -19 5257982 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11038;SOR=0;LSEQ=CCCGAGGAGGGAGGGGGATG;RSEQ=GACGGGGCGGGTCCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:3:1,2:179,67:0.012:2,2:23:1:29.7:1:0.18672:5.3009:60:6:0.0123:0:1.3 0/0:269:0:0,0:194,75:0:2,0:23.4:1:30.2:1:1:0:60:52.8:1:0:0.2 -19 5258309 . C T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13845;SOR=0;LSEQ=CTTGGCCAGGCCTTGTATAA;RSEQ=CTCCACCCCCACATCTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:0,4:0,19:0.1739:1,0:26.3:1:28.8:1:1:0:60:8:0.1818:0:1 0/0:15:0:0,0:1,14:0:1,0:16.1:1:31.3:1:1:0:60:30:1:0:0.1 -19 5258490 . G A 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGCTCTCCTGGCCAGAA;RSEQ=GAAAGAGTGGGTTGGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31:1:33:0:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 5260674 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01696;SOR=Inf;LSEQ=CAGACACAGACGCAGAGACC;RSEQ=GACTAACACTGGGTGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:38,1:0:1,0:19.4:1:30.3:1:1:0:60:78:1:0:0.2 0/1:33:5:3,2:25,3:0.1515:2,2:24.2:1:26:1:0.15455:5.14903:60:4:0.125:0:1.2 -19 5260718 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=1.92487;LSEQ=GTGGTGGCAGGGTGGACACG;RSEQ=ATGGAAGGGGGCCTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:0,1:72,13:0.0116:2,0:1:0:24:0:0.16279:0:60:2:0.0119:0:1 0/1:90:2:1,1:72,15:0.0222:2,2:21:1:29.5:1:0.32891:4.67978:60:4:0.0225:0:1 -19 5260731 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49798;SOR=0;LSEQ=GGACACGCATGGAAGGGGGC;RSEQ=TGGGGGCAGGCCCTGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:99,23:0.0161:2,2:29.5:1:31:0:0.3509:4.23495:60:4:0.0164:0:1 0/0:123:0:0,0:96,27:0:2,0:2:0:15:0:1:0:60:0:0:0:2 -19 5260761 . C T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25095;SOR=Inf;LSEQ=GCCCTGTGGAGCCTGAGGGG;RSEQ=TGAGTGGGCAGCAAGAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:137,68:0:2,0:24.2:1:31.9:1:1:0:60:204:1:0:0.1 0/1:231:3:1,2:148,80:0.013:2,2:10.7:1:20.7:1:0.2877:3.67787:60:2:0.0087:0:1.7 -19 5260878 . TGT CG 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33449;SOR=1.19646;LSEQ=GGTGAATGTCACAAGGCGGT;RSEQ=TGGGGGGCCGGGGGGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:311:192:78,114:53,65:0.6174:2,2:24.4:1:30.1:1:0.47903:1.19103:59.9:31:0.6179:0.135:1.4 1/0:255:168:62,106:33,49:0.6588:2,2:23.6:1:29.7:1:0.6775:1.15076:59.9:41:0.6667:0.149:1.3 -19 5260879 . GT G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.85967;SOR=1.10344;LSEQ=GTGAATGTCACAAGGCGGTT;RSEQ=TGGGGGGCCGGGGGGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:22:15,7:51,69:0.1549:2,2:6.2:1:29:1:0.03577:2.88:59.5:44:0.1571:0.1408:1.3 0/1:101:17:10,7:33,49:0.1683:2,2:6.9:1:29.3:1:0.18612:2.10:59.4:34:0.1717:0.1386:1.2 -19 5260895 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07832;SOR=Inf;LSEQ=GGTTGTTGGGGGGCCGGGGG;RSEQ=CCCCAGGGAAGCTGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:82,148:0:2,0:24:1:31.3:1:1:0:60:31.857:1:0:1 0/1:173:3:2,1:53,116:0.0173:2,2:14.7:1:27.3:1:0.23997:4.34:60:6:0.0175:0:2.3 -19 5260912 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16142;SOR=Inf;LSEQ=GGGGCCCCAGGGAAGCTGGG;RSEQ=TGGGCCGTAAGCCAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:46,122:0:2,0:22:1:32:1:1:0:60:167:0.994:0:1 0/1:114:2:1,1:24,88:0.0175:2,2:20.5:1:27:1:0.39202:3.61:60:4:0.0175:0:2.5 -19 5260933 . A T 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31419;SOR=0.68503;LSEQ=TGGGCCGTAAGCCAGGCCTC;RSEQ=GCACTCTGCCCCAGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:101:60:3,57:3,38:0.5941:2,2:23.5:1:30.2:1:0.68449:1.4938:60:59:0.59:0:1.8 1/0:56:28:2,26:6,22:0.5:2,2:22.1:1:30.2:1:0.25156:3.46949:59.8:56:0.5091:0:1.9 -19 5260935 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53996;SOR=0;LSEQ=GGCCGTAAGCCAGGCCTCAG;RSEQ=ACTCTGCCCCAGGGAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:4,91:0.0206:1,2:16:1:31:1:0.10095:20.46:60:4:0.0208:0:1 0/0:53:0:0,0:7,46:0:2,0:20.6:1:31.9:1:1:0:59.9:106:1:0:1.1 -19 5261506 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGAAAAGGCGGCTCGG;RSEQ=GCTGGAACGTTACTCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:28.5:1:1:0:60:4:1:0:1.5 -19 5262853 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21681;SOR=Inf;LSEQ=GAGGGCGTTAGTAAACATAC;RSEQ=AGGCAGAGTGGGTCACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:182,23:0:2,0:23.3:1:30.5:1:1:0:60:24.625:0.9949:0:0.1 0/1:180:2:2,0:147,30:0.0111:2,0:23:1:31.5:1:1:0:60:4:0.0114:0:1 -19 5262856 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2124;SOR=Inf;LSEQ=GGCGTTAGTAAACATACCAG;RSEQ=CAGAGTGGGTCACAGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:188,29:0:2,0:23.5:1:31.2:1:1:0:60:35.167:1:0:0.1 0/1:186:2:2,0:150,34:0.0108:2,0:14:1:31:1:1:0:60:4:0.011:0:1 -19 5262979 . G C 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGAAATCAGACTTACCAAA;RSEQ=GTTTCTGAACGTTTACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:788:0:0,0:378,408:0:2,0:27.4:1:31.5:1:1:0:60:195.5:0.9987:0:0.2 0/1:948:81:37,44:414,453:0.0854:2,2:26.7:1:30:1:0.72896:1.08669:60:162:0.0871:0:1.3 -19 5263061 . G T 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36578;SOR=1.20484;LSEQ=CAAAGAATCCTATGTCCTCA;RSEQ=CGAGGAGGGGAGGGCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:167:30,137:19,59:0.6761:2,2:22.7:1:27.4:1:0.30342:1.46825:60:6.591:0.6713:0:1.5 1/0:218:156:28,128:8,48:0.7156:2,2:19.9:1:26.9:1:0.67886:1.31:60:7.667:0.7302:0:1.5 -19 5263077 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07455;SOR=Inf;LSEQ=CTCAGCGAGGAGGGGAGGGC;RSEQ=GGGGAGGGGAGGGGGACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:23,160:0:2,0:21.8:1:30.5:1:1:0:59.8:60:1:0:1.5 0/1:134:3:1,2:12,119:0.0224:2,2:17.3:1:27.3:1:0.26551:4.86:60:6:0.0226:0:3 -19 5264967 . A G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.00063;SOR=2.00568;LSEQ=GGGCCCTGGAGATGCTCCCC;RSEQ=CCCCCTGCTGCCCTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:212:160,52:81,21:0.673:2,2:22.7:1:30.2:1:0.4782:1.25269:60:211:0.6806:0:1.1 1/1:231:186:128,58:36,9:0.8052:2,2:23.4:1:30:1:0.14839:1.8082:60:45.5:0.8018:0:1.1 -19 5265222 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36929;LSEQ=GGTCCTCTGAGGGCAGAGAC;RSEQ=TGAGAGAAATGGGCATGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:335:206:60,146:41,87:0.6149:2,2:23.4:1:30.6:1:0.62447:1.14627:60:205:0.6193:0:1.1 0/1:340:126:37,89:68,146:0.3706:2,2:23.8:1:29.9:1:0.71568:1.11995:60:125:0.3709:0:1.2 -19 5265318 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCAGCTCCTCCCTGGCTG;RSEQ=GTGACCTCAGCCATGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:1,69:0.0278:1,0:45.5:1:31:1:1:0:60:4:0.0286:0:1 0/0:27:0:0,0:0,27:0:1,0:25.4:1:29.9:1:1:0:60:26:1:0:0.1 -19 5265414 . T A 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGGCTGGAGTACAGTGGC;RSEQ=CGATCATAGCTCACCGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:29.3:1:30.7:1:1:0:60:12:0.75:0:1.7 1/1:3:3:0,3:0,0:1:0,0:22.3:1:32:0:1:0:60:6:1:0:1.7 -19 5265429 . C T 50 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGCTCGATCATAGCTCAC;RSEQ=GCAGTCTCAACAACCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:34.3:1:25:1:1:0:60:3:0.75:0:2 1/1:2:2:0,2:0,0:1:0,0:27.5:1:31.5:1:1:0:60:4:1:0:2 -19 5273331 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13598;SOR=Inf;LSEQ=ACTGGTTGGATAAGGGAGAT;RSEQ=AAGGTCCTCCCAAAAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:93,2:0:1,0:26.3:1:31.4:1:1:0:60:94:1:0:0.1 0/1:56:2:2,0:52,2:0.0357:1,0:15.5:1:29:1:1:0:60:4:0.0364:0:1 -19 5273571 . T G 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=0.59915;LSEQ=TGGATCCTCAGCACTGCCCC;RSEQ=GCACTCTCATCAAACTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:146:53,93:119,272:0.2714:2,2:25.6:1:30.2:1:0.21266:1.30:60:72:0.2748:0:1.1 0/1:658:120:50,70:211,324:0.1824:2,2:24.7:1:29.9:1:0.68041:1.10:60:119:0.1836:0:1.2 -19 5273650 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2187;SOR=Inf;LSEQ=CTGGGGTCCCAGGAAGGTTC;RSEQ=TGTCTAGGCTGGGCTAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:19,125:0:2,0:23:1:32.1:1:1:0:60:143:1:0:0.2 0/1:127:2:1,1:12,112:0.0157:2,2:15:1:28.5:1:0.19644:9.01:60:4:0.016:0:1 -19 5273746 . G C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.56504;SOR=1.40159;LSEQ=GCTGCAGGCTGAATGTGCAC;RSEQ=TGTGTCGGTGTCCAGTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:1,8:2,27:0.2368:2,2:27:1:32.7:1:1:1.66:60:18:0.2432:0:1 0/1:23:7:0,7:0,16:0.3043:1,0:15:1:30.9:1:1:0:60:14:0.3043:0:1 -19 5274089 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10085;SOR=Inf;LSEQ=AGGCTGCGCAGCCATGCTTG;RSEQ=TTGGCCACAGATGATGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:126,4:0:1,0:24.5:1:32.3:1:1:0:60:64:1:0:0.1 0/1:61:2:2,0:58,1:0.0328:1,0:14.5:1:30:1:1:0:60:4:0.0333:0:1 -19 5274384 . C T 175 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=37.64414;LSEQ=ACAGTGGAAAGAAGGGGGGG;RSEQ=GCTGATGGGTCCAGGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:0,3:88,207:0.0101:2,0:23:1:14.7:1:0.55771:0:60:0:0:0:3.7 0/1:270:75:27,48:58,136:0.2778:2,2:23.5:1:28.2:1:0.38065:1.32:60:11.5:0.2828:0:1.3 -19 5285985 . CCA C 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.73703;SOR=0.74056;LSEQ=GGAGGAGGTGGGGAGTGTGC;RSEQ=CACACACACAGCCATAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:5:4,1:235,66:0.0163:2,2:31:1:32.6:1:1:1.12:60:10:0.0166:0:0.2 0/1:247:3:2,1:184,59:0.0121:2,2:28.7:1:30.3:1:0.56946:1.55621:60:6:0.0123:0:0 -19 5286192 . GC G 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.57238;SOR=2.84177;LSEQ=CTCCGCCCTGGAGGGGGATG;RSEQ=CCCCCGGTCCCTCACAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:1:0,1:46,226:0.0037:2,0:18:0:33:0:1:0:60:2:0.0037:0:0 0/1:193:2:0,2:33,158:0.0104:2,0:21:1:33:1:1:0:60:4:0.0106:0:0 -19 5286222 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5207;SOR=0;LSEQ=CCCTCACAGAGAGGCCTCGA;RSEQ=CCGAGCGTCAGATGGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:7,148:0.0127:1,2:12:1:29:1:0.09962:19.85:60:4:0.0127:0:1 0/0:102:0:0,0:6,96:0:2,0:23.3:1:32.2:1:1:0:60:101:1:0:0.1 -19 5286348 . G A 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.27018;SOR=0.22752;LSEQ=GGAGCAGGGGAGGGTCCTGC;RSEQ=GGGGCTGGTCATGGGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:0,12:0,1:0.9231:0,0:16.7:1:28.8:1:1:0:60:5:0.9091:0:1.4 1/0:7:5:1,4:0,2:0.7143:0,2:26:1:32:1:1:0:60:10:0.7143:0:1 -19 5299547 . C A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTACTGTCACCTGAAATT;RSEQ=TCTGTCTTTACTCACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 5301061 . C A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAAGCAAAAGCCACATTG;RSEQ=TGGGCTTTGAACCTGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:10:1:30:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:0:0,0:36:0:28:0:1:0:60:2:1:0:0 -19 5301160 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15172;SOR=Inf;LSEQ=ACTTGGAAAAGGCTTCCAGG;RSEQ=CACAGCCGGAGTCAGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:28.4:1:32.1:1:1:0:60:36:1:0:0.1 0/1:12:2:1,1:5,5:0.1667:2,2:25:1:28.5:1:1:1:60:4:0.1667:0:1 -19 5301281 . G GCCCA 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCTGGGCCCCTGCCAG;RSEQ=CCGTCTCCCACCTTGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:29.5:1:32.5:1:1:0:60:4:0.6667:0:0 0/0:1:0:0,0:0,1:0:0,0:48:0:31:0:1:0:60:2:1:0:0 -19 6494915 . C G 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGTGCGGTTTCCAGAGT;RSEQ=AGAAGGGGTGAAGCGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:27:1:1:0:60:4:1:0:1 -19 6495736 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGCAGGCGAGGAAAGGG;RSEQ=ACCATGTTGACGGCCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:9:1:30.5:1:1:0:60:4:0.6667:0:1 -19 6554160 . A G 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTGTATTTTTAGTAGAG;RSEQ=CGGGGTTTCACTGTGTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:15.5:1:32:0:1:0:40:8:1:0:1 1/1:2:2:2,0:0,0:1:0,0:49:1:32.5:1:1:0:40:4:1:0:1 -19 6554328 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5003;SOR=Inf;LSEQ=TGACACTTGATGGTGAGTGA;RSEQ=AGTGCGGTTGTGGCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:55,38:0:2,0:29:1:31.5:1:1:0:60:45.5:1:0:0.1 0/1:108:2:1,1:54,51:0.0185:2,2:22.5:1:25.5:1:1:1.05828:60:4:0.0189:0:1.5 -19 6554418 . C T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=TCTATGAGACCTGGGCCAGG;RSEQ=GACGGCTTCATAGTAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:15,33:0:2,0:21:1:29.6:1:1:0:60:47:1:0:0.1 0/1:46:9:4,5:12,25:0.1957:2,2:21.4:1:28.4:1:0.69819:1.65:60:8:0.1778:0:1.1 -19 7116778 . TG T 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.11111;SOR=0;LSEQ=TTCCATCTGCTGGGGGCGGG;RSEQ=GGGGGAACGAAAAAACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:32.5:1:32.8:1:1:0:60:16:1:0:0.1 0/0:1:0:0,0:1,0:0:0,0:38:0:33:0:1:0:60:2:1:0:0 -19 7116843 . G A 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24451;SOR=0;LSEQ=GCCCCAAAGGAGCAGCAACT;RSEQ=TGGAAACCCCTTGCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:17.8:1:29:1:1:0:60:10:0.4167:0:1 0/0:5:0:0,0:5,0:0:0,0:14.2:1:33.2:1:1:0:60:10:1:0:0 -19 7116963 . T C 220 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGAACGATCTCTGAACTCCA;RSEQ=TGGACATGGTAGAGTCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:119:119:116,3:0,0:1:0,1:23.5:1:32:1:1:0:60:58.5:1:0:1.1 1/0:108:85:80,5:22,1:0.787:1,2:23.5:1:31.6:1:1:1.37126:60:84:0.7925:0:1.1 -19 7117487 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00101;SOR=Inf;LSEQ=CACGCATCCTCCCAAACCCC;RSEQ=ACTCTTGTCCCTGCAGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:7,107:0:2,0:23.1:1:31.9:1:1:0:60:37:1:0:0.1 0/1:103:9:1,8:10,83:0.0874:2,2:17.6:1:27.9:1:1:1.04:60:18:0.0882:0:1.7 -19 7117506 . G A 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00224;SOR=Inf;LSEQ=CCACTCTTGTCCCTGCAGCC;RSEQ=ACACCCACGGACCACATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:4,78:0:1,0:25.8:1:30.3:1:1:0:60:19.5:1:0:0.1 0/1:62:7:1,6:4,51:0.1129:2,2:30:1:28.7:1:0.46241:2.09:60:14:0.1129:0:1.9 -19 7119636 . GAC G 110 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.12106;SOR=2.53168;LSEQ=AGTAACAAAGAAGCCATTTA;RSEQ=ACACACACACACGCGCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:4:0,4:62,209:0.0145:2,0:29.8:1:32.3:1:0.57769:0:60:8:0.0146:0:0 0/1:306:11:1,10:90,204:0.0359:2,2:26.6:1:31.8:1:0.1834:4.39731:59.1:22:0.0364:0:0.2 -19 7119649 . A G 50 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.67704;SOR=0.62426;LSEQ=CCATTTAGACACACACACAC;RSEQ=CGCGCGCGCGCAAACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:1,2:40,190:0.0128:2,2:15.7:1:32:1:0.442:2.36:60:6:0.0133:0:1 0/0:250:2:0,2:63,184:0.008:2,0:21.5:1:33.5:1:1:0:57.5:4:0.0082:0:1 -19 7119651 . G A 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATTTAGACACACACACACAC;RSEQ=CGCGCGCGCAAACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:18:3,15:33,171:0.0811:2,2:20.9:1:29.7:1:1:1.04:59.2:36:0.0833:0:2.2 0/0:247:0:0,0:40,156:0:2,0:23.1:1:30.7:1:1:0:60:27:1:0:0.1 -19 7119653 . G A 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.0826;SOR=1.78234;LSEQ=TTAGACACACACACACACGC;RSEQ=CGCGCGCAAACACACACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:15:3,12:26,166:0.0725:2,2:20.2:1:29.1:1:0.44716:1.59:59.3:30:0.0735:0:2.4 0/1:237:29:13,16:43,164:0.1224:2,2:21:1:28.1:1:0.00878:3.08:60:58:0.1239:0:2.1 -19 7119659 . GCA G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=0.50489;SOR=Inf;LSEQ=ACACACACACACGCGCGCGC;RSEQ=AACACACACACGCAAACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:14,140:0:2,0:25:1:32.1:1:1:0:59.9:37.5:1:0:0.3 0/1:193:2:1,1:38,152:0.0104:2,2:17:0:31.5:1:0.36584:3.96:60:4:0.0106:0:0 -19 7119775 . A AAACACG 58 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.36341;SOR=0.2895;LSEQ=GCACACACATGCAAATACAC;RSEQ=CAAACACGCATGCGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:0,4:0,18:0.1818:1,0:26.8:1:29.4:1:1:0:60:8:0.1905:0.0455:0.8 0/1:17:1:0,1:0,16:0.0588:1,0:31:0:28.3:0:1:0:60:2:0.0588:0:2 -19 7119783 . G A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85311;LSEQ=ATGCAAATACACACAAACAC;RSEQ=CATGCGCACACATGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:0,14:0.1765:1,0:21:1:29:1:1:0:60:6:0.1765:0:1 0/1:13:2:0,2:0,11:0.1538:0,0:24.5:1:26:0:1:0:60:4:0.1538:0:2 -19 7119834 . CACACAA C 77 d7;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.28571;SOR=0;LSEQ=AACACACAAACACATATACA;RSEQ=ACACACACACCCAAACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:23.8:1:33.2:1:1:0:60:10:1:0.2:0 1/0:2:1:0,1:0,1:0.5:0,0:21:0:33:0:1:0:60:2:0.5:0:0 -19 7119865 . GCA G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACACCCAAACACACACAC;RSEQ=CACACATGCAAACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:11:1:32.5:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7121011 . C CT 28 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAAGAAGCTACATTTTT;RSEQ=TTTTTTTTTTTCTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:1,8:0.1667:2,0:9:1:28.8:1:1:0:60:4:0.1818:0.0833:0 0/0:2:0:0,0:0,2:0:0,0:12.5:1:33.5:1:1:0:60:4:1:0:0 -19 7121115 . T A 50 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCTCCCTGATTCAAGCAAT;RSEQ=CTCTTGCCTCAGCCTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:30:1:25:1:1:0:57.5:3:0.6:0:2.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7121192 . T C 42 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATGTTTTGTATTTTGAG;RSEQ=AGAGACAGGGTTTCACCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:11:1:26.7:1:1:0:56.7:6:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7122322 . C T 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTAGCCAGGCATGGTGG;RSEQ=GCACACCTGTAGTCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:31.3:1:30:1:1:0:56.3:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7122389 . G T 85 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02424;SOR=0;LSEQ=ACTTGAACCTGGGAGGTGGA;RSEQ=GTTGCAGTGAGCTGAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:18.3:1:30.4:1:1:0:56.1:14:1:0:1.6 0/1:4:1:1,0:3,0:0.25:0,0:21:0:32:0:1:0:60:2:0.25:0:1 -19 7122430 . GGCA ATG 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19886;SOR=Inf;LSEQ=CACCACTGCACTCCAGCCTG;RSEQ=ACAGACAGAGTAAGACTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:18,0:0:1,0:22.2:1:31.3:1:1:0:60:36:1:0:0.2 0/1:15:2:1,1:13,0:0.1333:1,2:30:1:26.8:1:0.13333:0:60:4:0.1333:0:1.5 -19 7122481 . CA C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.91322;LSEQ=AACAAAAAGACAAAACAAAA;RSEQ=AAAAAAACCCCACAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:51,0:0.0192:1,0:24:0:34:0:1:0:60:2:0.02:0:0 0/1:55:2:2,0:51,2:0.0364:1,0:7:1:32.3:1:1:0:60:4:0.0377:0.0182:0 -19 7122495 . C CA 93 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.36783;SOR=0.4948;LSEQ=ACAAAACAAAAAAAACCCCA;RSEQ=AAAAAAAAAAGAAGTATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:8:8,0:65,0:0.1096:1,0:19.6:1:31.1:1:1:0:59.4:16:0.1127:0.0274:0.1 0/1:70:4:4,0:61,2:0.0571:1,0:27.5:1:31.8:1:1:0:60:8:0.0615:0:0 -19 7122511 . AT A 199 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06701;LSEQ=CCCACAAAAAAAAAAGAAGT;RSEQ=CTTGCCCCTTTATATTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:90:86:83,3:4,0:0.9556:0,1:25.6:1:31.1:1:1:0:59.9:42:0.9655:0.1222:0.3 1/0:92:54:53,1:36,2:0.587:2,1:26.3:1:30.5:1:0.56699:2.91:60:53:0.5889:0.1087:0.3 -19 7123031 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.06548;LSEQ=AGCAACCAGGGTTCTTGGAG;RSEQ=AGGGTCCGTGATTCGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:179:52,127:119,211:0.3503:2,2:25.5:1:29.8:1:0.11669:1.37655:60:43.75:0.3507:0:1.1 0/1:529:18:5,13:196,315:0.034:2,2:21.8:1:29.6:1:0.46269:1.6164:60:36:0.0342:0:1.3 -19 7123073 . G A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11648;SOR=Inf;LSEQ=CAGGGTTCTCCTCCCTCCCT;RSEQ=GTGTCTATGTCACACACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:43,199:0:2,0:20.8:1:30.7:1:1:0:60:25.889:1:0:0.5 0/1:232:3:2,1:44,185:0.0129:2,2:14.7:1:21.3:1:0.1011:8.30:60:2:0.0088:0:1 -19 7123192 . T A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00812;SOR=0.19373;LSEQ=CCTTTGTATTTTTTTTTTTT;RSEQ=AATTTTCGAGACGGAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:25:0,25:0,6:0.7813:0,1:16.8:1:30.8:1:1:0:60:50:0.7813:0:1.4 0/1:20:8:1,7:0,10:0.4:0,2:19.3:1:29:1:0.44444:0:60:16:0.4:0:1.9 -19 7124986 . C T 83 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3;SOR=0;LSEQ=TGGAAAATGATGGAAGATTC;RSEQ=GGAAAGTGGTGGAAGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:35.1:1:29.6:1:1:0:60:6:1:0:1.3 1/0:3:2:1,1:1,0:0.6667:0,2:12.5:1:28.5:1:1:0:60:4:0.6667:0:1 -19 7125225 . C T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62332;SOR=2.99341;LSEQ=GTGTCCTCTGTCGCTCTGTG;RSEQ=AGGAGGAGGAGGCAGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:1:1,0:166,54:0.0045:2,0:29:0:31:0:1:0:60:2:0.0046:0:1 0/1:223:3:2,1:158,62:0.0135:2,2:23:1:26:1:1:1.27277:60:6:0.0138:0:1 -19 7125267 . C T 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12456;SOR=5.72364;LSEQ=GGAAGGGTCAGGAAAGCCAG;RSEQ=CCATGTCCCACCCCCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:1:0,1:278,151:0.0023:2,0:1:0:26:0:0.35349:0:60:2:0.0024:0:1 0/1:455:6:3,3:274,175:0.0132:2,2:26.2:1:29.2:1:0.68285:1.56407:60:12:0.0135:0:1 -19 7125297 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCCCCACTGGACTCACCAC;RSEQ=TGATGGCAGGTGAAGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:0:0,0:348,232:0:2,0:25.5:1:30.6:1:1:0:60:81.857:0.9983:0:0.1 0/1:640:25:14,11:363,251:0.0391:2,2:27.2:1:29.7:1:0.83651:1.13608:60:24:0.0379:0:1.2 -19 7125518 . C T 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00196;SOR=7.04371;LSEQ=CACCTCCCACTCGTCCGGCA;RSEQ=GTACACAGAGCATGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:649:2:0,2:232,415:0.0031:2,0:18.5:1:29:1:0.53992:0:60:4:0.0031:0:1 0/1:797:17:6,11:325,455:0.0213:2,2:25:1:29.9:1:0.80439:1.30909:60:34:0.0215:0:1.1 -19 7125519 . G A 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCCCACTCGTCCGGCAC;RSEQ=TACACAGAGCATGGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:0:0,0:229,404:0:2,0:25.9:1:31.2:1:1:0:60:78.125:1:0:0.1 0/1:785:85:31,54:296,404:0.1083:2,2:24.4:1:29.9:1:0.35162:1.27588:60:84:0.1085:0:1.1 -19 7125900 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGGGATGGAAGACAGG;RSEQ=TGTAATAGGTTGGGGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7126218 . A G 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTGGGACCACCCAGCCT;RSEQ=CTGACCACCAGACATGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:39.3:1:26.7:1:1:0:60:2:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7126324 . T C 61 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCAAGACCAGAAGAAC;RSEQ=GCCCAGCTGAGCCCAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:28.3:1:30.5:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:1:0,0:31:0:32:0:1:0:60:2:1:0:1 -19 7126505 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11208;SOR=Inf;LSEQ=CTTTTCTTGGCCTCCCTGGG;RSEQ=AACCCATCCTTCACTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:171,31:0:2,0:22.2:1:30.9:1:1:0:60:32.667:1:0:0.1 0/1:190:3:1,2:142,45:0.0158:2,2:12.7:1:26:1:0.1518:6.23456:60:6:0.0161:0:1 -19 7126889 . G GT 28 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCATCCCTCCCTGGGTG;RSEQ=TTTTTTTTTTGTTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:0,11:0.1538:0,0:37.5:1:28.5:1:1:0:60:4:0.1667:0:0.5 0/0:3:0:0,0:0,3:0:0,0:20.3:1:32.7:1:1:0:60:6:1:0:0 -19 7128815 . C T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24871;SOR=Inf;LSEQ=ATATCAAGGCATGTTTTCCC;RSEQ=CAGAGAACCAACTGTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:208,74:0:2,0:24.9:1:30.9:1:1:0:60:55.4:1:0:0.1 0/1:286:3:2,1:195,87:0.0105:2,2:15:1:21:1:1:1.12023:60:2:0.0071:0:1.7 -19 7128928 . G C 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAAGACAAAGATGAGGGG;RSEQ=CCGATGATAATTTTTGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:0:0,0:202,318:0:2,0:28.2:1:31.5:1:1:0:60:56.778:1:0:0.1 0/1:606:21:11,10:253,329:0.0347:2,2:31.3:1:30.7:1:0.5036:1.43:60:20:0.0333:0:1.1 -19 7128950 . T A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06319;SOR=Inf;LSEQ=CGATGATAATTTTTGCAATA;RSEQ=TTGACGGGACGTCTACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:157,295:0:2,0:26.1:1:30.5:1:1:0:60:149.667:1:0:0.1 0/1:496:5:5,0:197,293:0.0101:2,0:6.2:1:23:1:0.01099:0:60:4:0.0081:0:1.2 -19 7128977 . T A 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95006;LSEQ=GGACGTCTACTGAAATAGAA;RSEQ=AAGAAAATATATGTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:80,205:0.0104:2,2:9.7:1:21.7:1:0.19612:5.09:60:2:0.0071:0:1.7 0/0:303:3:3,0:107,193:0.0099:2,0:1:0:21.7:1:0.04701:0:60:2:0.0067:0:1.7 -19 7128994 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49873;SOR=Inf;LSEQ=GAATAAGAAAATATATGTTT;RSEQ=ATATCAATGTGTTTCCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:44,154:0:2,0:22.1:1:31.7:1:1:0:60:65:1:0:0.1 0/1:198:2:1,1:50,146:0.0101:2,2:31:1:32.5:1:0.44978:2.90:60:4:0.0102:0:1 -19 7129086 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49291;SOR=0;LSEQ=TCCTTCCCTCCCTTGTCCAT;RSEQ=AACCTCTCTGCTGCTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:1,21:0,0:1:0,1:23.6:1:31.4:1:1:0:60:44:1:0:1 1/1:26:24:0,24:0,2:0.9231:0,1:20.3:1:30.8:1:1:0:60:23:0.92:0:1.2 -19 7132081 . C T 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00365;SOR=Inf;LSEQ=AAGGCCAGGGCCAGCACCTG;RSEQ=GGCCTCTCCAAGTCATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:145,5:0:1,0:25.8:1:32:1:1:0:60:49:1:0:0.1 0/1:125:7:6,1:111,7:0.056:2,2:15:1:28.3:1:0.37805:2.61323:60:14:0.0569:0:1.1 -19 7132173 . G C 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=51.97858;LSEQ=TGCCATGGAGACTTACAATA;RSEQ=TCTGTCACGTAGAAATAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:701:1:1,0:389,310:0.0014:2,0:7:0:14:0:1:0:60:0:0:0:3 0/1:896:62:30,32:467,367:0.0692:2,2:25.6:1:31.2:1:0.28942:1.35683:60:124:0.0703:0:1.2 -19 7132343 . G A 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCTCCTGGGAGGAAGAGA;RSEQ=GAGGAGAAGGAGGGTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:82:21,61:31,126:0.3431:2,2:24.4:1:30.4:1:0.32377:1.40:60:40:0.3433:0:1.1 0/0:241:0:0,0:56,185:0:2,0:24.2:1:30.5:1:1:0:60:59.25:1:0:0.2 -19 7132570 . T C 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTTCCTAAGCCAGAAGC;RSEQ=GAGCATTAAACCCTGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23.5:1:27.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7132655 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGTTGCCCAGGCTGGAG;RSEQ=GCAATGGCTTAATCTCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23:1:32:0:1:0:58:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7141858 . G A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23892;SOR=3.91659;LSEQ=AGGAAGTGAGAGGCAGGGAT;RSEQ=TAACTCTTGGATGAGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:1:1,0:104,267:0.0027:2,0:1:0:23:0:0.28226:0:60:2:0.0027:0:1 0/1:478:5:4,1:164,309:0.0105:2,2:6:1:24.4:1:0.0539:7.51:60:10:0.0106:0:1.2 -19 7141976 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23557;SOR=Inf;LSEQ=CGGACATCTAAAACTCATCC;RSEQ=ACAAGATTGTTAGGAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:0:1,0:28.3:1:32.3:1:1:0:60:43:1:0:0.4 0/1:42:2:0,2:2,38:0.0476:2,0:25.5:1:31.5:1:1:0:60:4:0.0476:0:1 -19 7142064 . C T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23352;SOR=0;LSEQ=GTCTTGCTCTGTCACCCAGG;RSEQ=GGGAGTGCAGTGGTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:0,4:0,6:0.4:0,0:31.5:1:28.3:1:1:0:60:3:0.375:0:1 0/0:6:0:0,0:1,4:0:2,0:26.6:1:27.2:1:1:0:60:4:1:0:0 -19 7142773 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21661;SOR=0;LSEQ=AGGGTGGAGAATCTGTCCTT;RSEQ=GTCAGCCTTGATGTCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:156,41:0.0101:2,2:44:0:30.5:1:0.37841:3.77137:60:4:0.0103:0:1.5 0/0:228:0:0,0:159,69:0:2,0:25.1:1:30.7:1:1:0:60:37:1:0:0.1 -19 7143098 . T A 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03405;SOR=0;LSEQ=AGGGACCTGCGTTTCCGAGA;RSEQ=GGCCTGGAACGACAGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:4:2,2:77,169:0.016:2,2:18:1:26.8:1:0.59287:2.19:60:8:0.0162:0:1 0/0:330:0:0,0:114,216:0:2,0:25.4:1:29.5:1:1:0:60:46.143:1:0:0.1 -19 7149959 . G A 31 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=12.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AAAAAGAAAGAAGGAAGGAA;RSEQ=GAAGGAAGGAAGGAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14:1:31.5:1:1:0:60:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7149975 . G A 31 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=12.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GGAAGGAAGGAAGGAAGGAA;RSEQ=GAAGGAAGGAAGGAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30:1:31.5:1:1:0:60:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7150418 . C G 237 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CCGCCGCATGCAAAAAGCCA;RSEQ=AGAAACCCCTGGGTTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:164:164:150,14:0,0:1:0,2:23.8:1:32.3:1:1:0:60:163:1:0:1.1 1/0:178:136:119,17:37,5:0.764:2,2:22:1:31.8:1:1:1.05682:60:67:0.7614:0:1.1 -19 7151049 . T C 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTCTTTCCTTCCTTCTT;RSEQ=TTTTCATTTTCTTTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:34.5:1:32:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:34:0:32:0:1:0:60:2:1:0:2 -19 7151171 . TTC T 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=14.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCTCTCTTTCCTTTCTTTCT;RSEQ=TCTTTCTTTCTTTCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:21.5:1:31:1:1:0:60:4:1:0:0.5 -19 7152211 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGGTTAGAGACCAGCCT;RSEQ=GCCAACATGGCAAAACCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:14:0:28:0:1:0:44:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:42.5:1:31.5:1:1:0:60:4:1:0:1 -19 7152389 . CAAA C 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGATAGAGTGAGACTCTGT;RSEQ=AAAAAAAAAAAAAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,0:0.5:0,0:12:1:32.3:1:1:0:60:4:0.5:0.25:2.5 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7152404 . A G 68 d7;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCAAAAAAAAAAAAAA;RSEQ=AGAGAGAGAGAGAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:26.3:1:34:1:1:0:60:8:1:0:2 1/1:2:2:2,0:0,0:1:0,0:16.5:1:34:0:1:0:60:4:1:0:2 -19 7152417 . A AG 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAGAGAGAGAGAG;RSEQ=AAAAAAAAAATGTTAATCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:20.5:1:32.6:1:1:0:60:4:0.3333:0.1667:0.5 0/0:2:0:0,0:2,0:0:0,0:29.5:1:29:0:1:0:60:4:1:0:2 -19 7152418 . A G 69 d7;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAAAAGAGAGAGAGAGA;RSEQ=AAAAAAAAATGTTAATCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:25.8:1:34.5:1:1:0:60:8:0.6667:0:2 1/1:2:2:2,0:0,0:1:0,0:30.5:1:32.5:1:1:0:60:4:1:0:2 -19 7153006 . A C 205 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=3e-05;SOR=0.17764;LSEQ=ACACATACACACACACACAC;RSEQ=CCCCACACACACACACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:99:12,87:1,3:0.9252:2,2:20.8:1:31:1:0.42207:2.38919:58.9:48.5:0.9417:0:2.1 1/0:89:61:5,56:3,25:0.6854:2,2:19.6:1:30:1:0.70282:1.33939:59:14.25:0.6706:0:2.2 -19 7153011 . A C 186 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TACACACACACACACACCCC;RSEQ=CACACACACACACCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:0,4:0:0,0:19:1:24:1:1:0:52.3:3:1:0:2.5 1/1:73:69:6,63:0,4:0.9452:0,2:20.3:1:30.6:1:1:0:58:33.5:0.9437:0:2.2 -19 7153013 . A C 68 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.50678;SOR=1.64143;LSEQ=CACACACACACACACCCCAC;RSEQ=CACACACACACCACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:4:1,3:7,76:0.046:2,2:21.8:1:26:1:0.32499:3.54:55:3:0.037:0:2.5 0/1:68:5:1,4:5,58:0.0735:2,2:22.4:1:29.4:1:0.37923:2.84:55:10:0.0769:0:2.8 -19 7153022 . CACCACA C 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.02664;SOR=Inf;LSEQ=ACACACCCCACACACACACA;RSEQ=CACACACACCACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:2,69:0:1,0:20.9:1:27.3:1:1:0:58:7.875:0.9844:0:2.3 0/1:51:4:0,4:1,45:0.0784:1,0:7.5:1:26.9:1:1:0:60:8:0.0851:0.0588:2 -19 7153026 . A C 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.15764;SOR=6.04784;LSEQ=ACCCCACACACACACACACC;RSEQ=CACACACACACCACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:1:0,1:1,64:0.0149:1,0:14:0:11:0:1:0:40:0:0:0:3 0/1:47:4:1,3:0,42:0.0851:1,2:15.3:1:25.5:1:0.08696:0:56.3:3:0.0714:0:2.8 -19 7153028 . A ACACACAC 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.25644;SOR=0;LSEQ=CCCACACACACACACACCAC;RSEQ=CACACACACCACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:3:0,3:1,53:0.0508:1,0:29.3:1:29.3:1:1:0:53.3:6:0.0556:0.0339:2.3 0/0:45:0:0,0:0,42:0:1,0:18.2:1:28.6:1:1:0:56.8:84:1:0:2.2 -19 7153044 . C CACCACACAT 157 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=7.000;MSILEN=2;SSF=0.07696;SOR=0.26634;LSEQ=CCACACACACACACCACACA;RSEQ=ACACACACCACACACCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:44:0,44:0,2:0.9362:0,1:22.2:1:28.8:1:1:0:55.3:21:0.9333:0.383:2.5 1/0:29:23:0,23:0,3:0.7931:0,1:20.3:1:29:1:1:0:53.9:22:0.8462:0.4138:2.4 -19 7153064 . CCA C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=7.000;MSILEN=1;SSF=0.29506;SOR=0.44818;LSEQ=CACACACACCACACACCCCC;RSEQ=CACACACACACCACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:19:0,19:0,10:0.6552:0,1:26.7:1:31.6:1:1:0:50.5:38:0.6552:0.1034:2.1 0/1:11:5:0,5:0,5:0.4545:0,0:21:1:26.5:1:1:0:58:4:0.4:0.2727:2.4 -19 7153065 . CA C 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.16301;SOR=4.17663;LSEQ=ACACACACCACACACCCCCC;RSEQ=CACACACACACCACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:0,3:0,5:0.1154:0,0:18.3:1:32.7:1:1:0:51.7:6:0.3:0.0385:2 0/1:11:4:0,4:0,3:0.3636:0,0:26.3:1:32.5:1:1:0:50:8:0.5714:0:2 -19 7162789 . T C 81 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGATGAGCCAAGGTCGCG;RSEQ=CATTGCACTCCAGCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:11.7:1:31.5:1:1:0:60:12:0.8571:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7162912 . G T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03964;SOR=Inf;LSEQ=GTTTTCATATGAGATAGAAT;RSEQ=GAGTGTGTGTGTGTGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:85,0:0:1,0:24.9:1:31.9:1:1:0:60:41.5:1:0:0.1 0/1:70:4:4,0:66,0:0.0571:1,0:13.8:1:27:1:1:0:60:8:0.0597:0:1 -19 7162914 . AGT A 139 v4;MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0;SOR=15.99157;LSEQ=TTTCATATGAGATAGAATGG;RSEQ=GTGTGTGTGTGTGCCTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:2,0:85,0:0.023:1,0:48.5:1:32.5:1:1:0:60:4:0.0235:0:0 0/1:76:21:21,0:55,0:0.2763:1,1:23.2:1:31.7:1:1:0:60:42:0.2763:0.0526:0 -19 7162968 . C T 75 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10488;SOR=0.17588;LSEQ=CAGGAAGAGATAGCTGCTTC;RSEQ=CTAGAGGTGAAGCAAAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:5:5,0:144,18:0.0299:2,0:31.2:1:32.4:1:1:0:60:10:0.0299:0:1 0/0:186:1:0,1:153,32:0.0054:2,0:1:0:24:0:0.17742:0:60:2:0.0056:0:1 -19 7163065 . G A 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGAGGCAATAATCCAGCTC;RSEQ=AACAGCTCACTGTCTTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:0:0,0:365,289:0:2,0:24.3:1:30.2:1:1:0:60:92.429:1:0:0.2 0/1:914:63:40,23:471,380:0.0689:2,2:21.7:1:29:1:0.23742:1.40:60:30.5:0.0677:0:1.3 -19 7163140 . T G 225 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGCCATTGGGGTCGGAGGG;RSEQ=GGTTTCCACTTCAGAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:886:0:0,0:435,451:0:2,0:24.8:1:29.7:1:1:0:60:67.154:1:0:0.2 0/1:1182:178:81,97:479,519:0.1506:2,2:25.4:1:30.2:1:0.56897:1.10514:60:43.5:0.1488:0:2.2 -19 7163154 . G A 220 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=154.06151;LSEQ=GGAGGGTGGTTTCCACTTCA;RSEQ=AATAATCTGGGATGATGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:811:1:1,0:395,415:0.0012:2,0:1:0:26:0:0.48829:0:60:2:0.0013:0:1 0/1:1038:166:73,93:409,463:0.1599:2,2:27.6:1:29.9:1:0.49829:1.12526:60:165:0.1603:0:2.5 -19 7163214 . T C 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGGCACAGAGGGGTCTG;RSEQ=CAGGGAGAAAGGAAATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:0:0,0:139,307:0:2,0:24:1:29.4:1:1:0:60:48.556:1:0:0.1 0/1:483:80:23,57:134,268:0.1656:2,2:23.6:1:29.9:1:0.51381:1.23858:60:15:0.1576:0:3 -19 7163230 . T C 219 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGTCAGGGAGAAAGGAAA;RSEQ=GGGTCCATCATGAGAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:87,254:0:2,0:23.4:1:30:1:1:0:60:67.2:0.9941:0:0.1 0/1:370:178:51,127:56,134:0.4811:2,2:23.7:1:29.4:1:0.90875:1.04058:60:88:0.4796:0:1.6 -19 7163326 . T C 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02453;SOR=Inf;LSEQ=TGAGGGCACCCATCCCAGCA;RSEQ=TTTGGGCGGCCAAGGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:0,45:0:1,0:25.5:1:30.4:1:1:0:59.9:44:1:0:0 0/1:31:4:0,4:0,27:0.129:1,0:32.3:1:33.5:1:1:0:60:8:0.1333:0:1 -19 7165788 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCTGAGGTGGGAGAAT;RSEQ=ACTTGAACCTGGGAGGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23.5:1:32:1:1:0:36:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7166006 . T C 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0087;SOR=Inf;LSEQ=GCCATGATCACCCCACTGCA;RSEQ=TGCACTCTAGCCTGGGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:21,0:0:1,0:21.3:1:30.8:1:1:0:55.7:42:1:0:0.5 0/1:16:5:5,0:11,0:0.3125:0,0:23.2:1:31.8:1:1:0:59.8:10:0.3125:0:3.6 -19 7166014 . T C 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00384;SOR=Inf;LSEQ=CACCCCACTGCATTGCACTC;RSEQ=AGCCTGGGTGACAAAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:0:1,0:21:1:31.3:1:1:0:55.4:50:1:0:1.1 0/1:19:6:6,0:13,0:0.3158:1,0:21.3:1:30.3:1:1:0:59.8:12:0.3158:0:3.5 -19 7166036 . C A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=GCCTGGGTGACAAAGTAAGA;RSEQ=CCTGTCTAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:35,0:0:1,0:18.5:1:31.7:1:1:0:55.4:34:1:0:1.9 0/1:43:11:11,0:32,0:0.2558:1,0:22.1:1:30.8:1:1:0:56.2:22:0.2619:0:3.5 -19 7166109 . A G 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77037;SOR=1.08842;LSEQ=CAACCTCACTGCATCAGCCT;RSEQ=TTAAAAGCAAGAGGTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:171:145:129,16:24,1:0.848:1,2:26.4:1:31.5:1:0.47281:2.96309:60:17.125:0.8616:0:1.8 1/1:198:170:132,38:19,4:0.8586:2,2:23.6:1:30.5:1:0.78895:1.36531:59.9:14.455:0.8785:0:1.4 -19 7166138 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14753;LSEQ=AAGAGGTCTGATTCACATAC;RSEQ=AATTCACATTCCCAAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:154:123,31:116,42:0.4936:2,2:23.9:1:29.9:1:0.18431:1.43:60:153:0.4968:0:1.6 0/1:343:43:31,12:195,103:0.1254:2,2:24.3:1:29.3:1:0.49052:1.36:60:42:0.1254:0:1.7 -19 7166376 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11947;LSEQ=GTCCAACTGTTGGAACCACA;RSEQ=GCATCCTGCCCGTCGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:646:338:146,192:130,175:0.5232:2,2:25.5:1:30.8:1:0.93643:1.02:60:337:0.5266:0:1.1 0/1:864:100:45,55:354,410:0.1157:2,2:24.3:1:29.5:1:0.83165:1.05524:60:32.333:0.114:0:1.1 -19 7166388 . G A 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02394;SOR=1.28494;LSEQ=GAACCACACGCATCCTGCCC;RSEQ=TCGAACTCCGTCACATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:217:89,128:166,213:0.3635:2,2:25.2:1:30.3:1:0.54727:1.12064:60:71.333:0.3627:0:1.1 0/1:808:342:148,194:210,256:0.4233:2,2:24.9:1:29.9:1:0.61675:1.07517:60:84.5:0.422:0:1.2 -19 7166541 . A G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=0.19744;LSEQ=TCACCCAACAATCTAATGCC;RSEQ=CAAGAAAAAATAACTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:45:0,45:0,8:0.8491:0,1:28.2:1:32.5:1:1:0:60:90:0.8491:0:1.1 1/0:46:24:0,24:0,22:0.5217:1,1:28:1:32.3:1:1:0:60:48:0.5217:0:1 -19 7167601 . AT A 27 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTCAAAAAAAAAAAAAAA;RSEQ=TGGGGATAAAAAAGAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:14:1:27.5:1:1:0:60:4:0.6667:0.25:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7167715 . A G 51 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACACAGGCAAGGCAAAAT;RSEQ=GAATATTGCCCCAGGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:18.7:1:32.3:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7167817 . C A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01511;SOR=0.18173;LSEQ=GACACTATTGACTTTGCATG;RSEQ=CATCGACTGGTGAGATTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:18:15,3:11,0:0.6207:0,2:26.1:1:30.1:1:0.26847:0:60:36:0.6429:0:1.1 0/1:18:4:4,0:14,0:0.2222:1,0:22.3:1:29.8:1:1:0:60:8:0.2222:0:1 -19 7167951 . T G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.14234;LSEQ=GCCAGCCAGCCCTCGCCTCC;RSEQ=CAGCGTCTCTCTAACTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:283:142:98,44:98,43:0.5018:2,2:25.2:1:30.2:1:1:1.02318:60:70:0.5128:0:1.2 0/1:352:44:28,16:212,96:0.125:2,2:22.8:1:29.9:1:0.49276:1.26101:60:21:0.121:0:1.2 -19 7168159 . C G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50194;SOR=Inf;LSEQ=TATTTCAGTGTAGTTTCAGA;RSEQ=CAAAGCCTGGGACCCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:17,117:0:2,0:25.8:1:31.2:1:1:0:60:66:1:0:0.2 0/1:159:2:1,1:27,130:0.0126:2,2:19:1:34:0:0.32211:4.75:60:4:0.0127:0:1 -19 7168213 . C G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0.1266;LSEQ=CCGTGAGAAGGCAGAGGTGA;RSEQ=GCTGCTATTCCCTTAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:29:0,29:0,26:0.5273:1,1:23.8:1:30.8:1:1:0:60:13.5:0.5094:0:1 0/1:33:4:1,3:0,23:0.1212:1,2:26.8:1:31.8:1:0.14815:0:60:8:0.129:0:1.3 -19 7168240 . C G 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03778;SOR=0;LSEQ=ATTCCCTTAAGGGTCTCCTC;RSEQ=CCATGTGCCTGGCTGAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:0,9:0,18:0.3333:1,0:27.4:1:33.4:1:1:0:60:18:0.3462:0:1 0/0:11:0:0,0:0,11:0:0,0:26.5:1:32:1:1:0:60:22:1:0:0.3 -19 7170241 . C T 60 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACTGTGTACATGAGGTA;RSEQ=CTAGACTGCACACTCCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:27.5:1:30.3:1:1:0:58.5:8:1:0:1.3 1/1:1:1:1,0:0,0:1:0,0:5:0:29:0:1:0:60:2:1:0:1 -19 7170450 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19935;SOR=Inf;LSEQ=TAAATGTAATGCACTTGAAT;RSEQ=ATGCTGAAACCATCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:74,1:0:1,0:23.6:1:31.4:1:1:0:60:74:1:0:0.7 0/1:61:2:2,0:58,1:0.0328:1,0:14.5:1:31.5:1:1:0:60:4:0.0328:0:1.5 -19 7170505 . C A 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.91539;SOR=0.97005;LSEQ=GGAAAAACCATCTTCCACTA;RSEQ=ACCGGTCCCTCATGCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:72:66,6:104,19:0.3692:2,2:22.1:1:30.4:1:0.18601:2.00:60:144:0.3692:0:2 0/1:185:67:56,11:101,17:0.3622:2,2:22.3:1:29.4:1:0.83134:1.16602:60:66:0.3587:0:2 -19 7170517 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18432;LSEQ=TTCCACTACACCGGTCCCTC;RSEQ=TGCCAAAAAGGTTGGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:254:221:182,39:28,4:0.8701:2,2:22.3:1:29.9:1:0.61741:1.49779:60:72.667:0.8685:0:1.4 1/0:252:139:106,33:83,29:0.5516:2,2:21.6:1:29.3:1:0.76879:1.12:60:45.333:0.5462:0:1.5 -19 7172209 . C T 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CTGGGATTACAGGCATCAGC;RSEQ=ACCACACCTGGCCAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:122,20:0:2,0:23.1:1:30.9:1:1:0:60:141:1:0:0.1 0/1:159:42:33,9:97,20:0.2642:2,2:24.2:1:29.9:1:0.64155:1.32033:60:41:0.2611:0:1.1 -19 7172469 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25753;SOR=Inf;LSEQ=AGGAAAGGAGAGAATATCCA;RSEQ=TGGGTTTCTATAGACATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:45,165:0:2,0:24.1:1:32.4:1:1:0:60:420:1:0:0.2 0/1:262:3:2,1:75,184:0.0115:2,2:27.3:1:27.7:1:0.20736:4.87:60:6:0.0116:0:1 -19 7172526 . C A 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCCATGGTGAGAAGATAA;RSEQ=CCTCAGGCTGCAAATGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:26:0,26:0,40:0.3939:1,1:27:1:31:1:1:0:60:52:0.4:0:1.1 0/0:68:0:0,0:3,65:0:1,0:23.5:1:31.4:1:1:0:60:67:1:0:0.1 -19 7174490 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17907;SOR=Inf;LSEQ=ACGACCATCCTAAAAGTGCT;RSEQ=TAGGAGCACGCAGCAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:116,5:0:1,0:22.8:1:32.4:1:1:0:60:242:1:0:0 0/1:90:2:2,0:85,3:0.0222:1,0:25.5:1:31.5:1:1:0:60:4:0.0225:0:1.5 -19 7174755 . CAG C 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.63155;SOR=0.747;LSEQ=ACAGCAAGCTAAGGACGGAG;RSEQ=AGAGAGAGAGAAAGAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:9:1,8:75,204:0.0311:2,2:27.8:1:32.6:1:0.4533:2.93262:60:18:0.0318:0:0.1 0/1:384:9:3,6:102,273:0.0234:2,2:26:1:32.3:1:0.7097:1.34:60:18:0.0239:0.0026:0.2 -19 7184154 . A G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00323;SOR=0.19678;LSEQ=GAAAAAGGTAGTCAACTCCC;RSEQ=CTCCCAAGCCCAGGACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:26:25,1:21,0:0.5532:1,1:27.2:1:30.2:1:1:0:60:52:0.5532:0:1.6 0/1:26:5:4,1:21,0:0.1923:1,2:17.4:1:31.2:1:0.19231:0:60:10:0.2:0:1.4 -19 7184238 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06618;LSEQ=AGCCAATTAACCCTGGGTTT;RSEQ=CACACAGTTTTAACAAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:164:85:75,10:67,12:0.5183:2,2:23.6:1:28.6:1:0.64761:1.34:60:170:0.5247:0:2.2 0/1:182:12:9,3:145,23:0.0659:2,2:19.5:1:28:1:0.38522:2.09072:60:24:0.0674:0:2 -19 7184243 . C G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.04718;LSEQ=ATTAACCCTGGGTTTGCACA;RSEQ=AGTTTTAACAAGCGGCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:90:77,13:76,18:0.4891:2,2:24.6:1:32.3:1:0.43521:1.40:60:180:0.4891:0:2.1 0/1:210:9:6,3:165,36:0.0429:2,2:20.4:1:31.1:1:0.37274:2.28049:60:18:0.0429:0:2.3 -19 7184275 . C T 170 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=5.06813;LSEQ=GCGGCATCGTCACAACCAAC;RSEQ=CCACGTTCCTTCTCCTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:9:8,1:227,92:0.0274:2,2:28.4:1:31.7:1:0.45421:3.23:60:18:0.028:0:1.1 0/1:407:51:36,15:242,113:0.1253:2,2:24.2:1:30:1:0.87209:1.12:60:50:0.1241:0:1.1 -19 7184490 . G A 225 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.00535;LSEQ=GTCCTGGAAGTGGTAGTACG;RSEQ=GGGCGGGCAGGTCTCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:174:65,109:122,191:0.3566:2,2:25:1:30.3:1:0.77081:1.07094:60:57:0.3563:0:1.1 0/0:679:2:2,0:290,387:0.0029:2,0:1:0:25.5:1:0.18458:0:60:4:0.003:0:1 -19 7184518 . G A 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=2.37129;LSEQ=CAGGTCTCCACACACCTGCC;RSEQ=TCCAGGTAGAAGTTGCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:24:10,14:116,225:0.0658:2,2:26.8:1:31:1:0.50667:1.38:60:48:0.0667:0:1 0/1:496:71:30,41:165,260:0.1431:2,2:23.1:1:29.4:1:0.60128:1.15:60:70:0.1431:0:1.2 -19 7184545 . G A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13913;SOR=Inf;LSEQ=TAGAAGTTGCGGCAGGCCAC;RSEQ=CACTTGGTGGGGTCGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:88,195:0:2,0:25.4:1:31.5:1:1:0:60:69.75:1:0:0.4 0/1:377:4:1,3:147,226:0.0106:2,2:33.5:1:30.3:1:1:1.94819:60:8:0.0107:0:1.3 -19 7184560 . G A 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13417;SOR=Inf;LSEQ=GCCACGCACTTGGTGGGGTC;RSEQ=TCGGGCTGAGAACAGTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:72,170:0:2,0:24:1:31.2:1:1:0:60:47.4:1:0:0.3 0/1:307:4:3,1:111,192:0.013:2,2:18.8:1:28:1:0.14626:5.16:60:8:0.0131:0:1 -19 7184618 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50285;SOR=Inf;LSEQ=AACAGAGGCCTTCGGCGGTG;RSEQ=AGCCGTGTGACTTACAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:28,97:0:2,0:29:1:31.8:1:1:0:60:40.667:1:0:0.2 0/1:154:2:1,1:42,110:0.013:2,2:26.5:1:30.5:1:0.48179:2.60:60:4:0.0135:0:1.5 -19 7184651 . GGA G 151 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=10.000;MSILEN=2;SSF=0.00034;SOR=0.19582;LSEQ=TACAGATGGTCGGGCAAACT;RSEQ=GAGAGAGAGAGAGAGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:26:5,21:10,54:0.2737:2,2:27.2:1:32.3:1:0.75725:1.28:60:52:0.2796:0.0105:0.4 0/1:88:6:1,5:19,63:0.0682:2,2:20.3:1:28.8:1:1:1.50155:58.8:12:0.069:0.0114:0.2 -19 7184721 . C T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.44737;SOR=0.40419;LSEQ=ATAAATAAATAAATAAATGG;RSEQ=TTTGTCCAATTCCTGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:0,8:0,19:0.2963:1,0:25.5:1:31.1:1:1:0:60:16:0.3077:0:2 0/1:14:2:0,2:0,12:0.1429:0,0:26.5:1:31.5:1:1:0:47.5:4:0.1429:0:2 -19 7184762 . A G 91 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.40825;LSEQ=ATATGCAGCAATTCTGGATC;RSEQ=GACAGTGAAAGCCAACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:0.7273:0,0:25.1:1:30.4:1:1:0:60:16:0.7273:0:2.1 1/0:2:1:0,1:0,1:0.5:0,0:1:0:31:0:1:0:60:2:0.5:0:1 -19 7184801 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACTAACAGTAAAAGCGG;RSEQ=ACGTCTACATCATTACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:31.5:1:28.5:1:1:0:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 7267253 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18492;SOR=Inf;LSEQ=CCACCACCCACTATTCCCCG;RSEQ=CCCCTACCTAATGACCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:53,2:0:1,0:21:1:31.1:1:1:0:60:110:1:0:0.1 0/1:42:2:1,1:39,1:0.0476:1,2:15:1:26.5:1:0.09408:27.93708:60:4:0.0476:0:1 -19 7267267 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49645;SOR=Inf;LSEQ=TCCCCGGCCCCTACCTAATG;RSEQ=CCATTTAACATTTTTAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:60,10:0:2,0:20.6:1:29.2:1:1:0:60:16.5:1:0:0.1 0/1:71:2:2,0:61,8:0.0282:2,0:23.5:1:31.5:1:1:0:60:4:0.0282:0:1 -19 7267277 . AT A 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.02652;SOR=0.4782;LSEQ=CTACCTAATGACCATTTAAC;RSEQ=TTTTAAGCCATAAAACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:36:29,7:45,5:0.4186:2,2:22.4:1:30.7:1:0.22747:2.1523:60:72:0.4286:0.0698:0 0/1:94:24:20,4:60,10:0.2553:2,2:24.7:1:30.2:1:0.7487:1.19757:60:48:0.2581:0.0213:0 -19 7267332 . T G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00254;SOR=Inf;LSEQ=ACAAGGCACGAGACACTGCT;RSEQ=AGAACCCTGTATCCCCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:174,71:0:2,0:25.5:1:29.6:1:1:0:60:121.5:0.9959:0:0.1 0/1:296:10:6,4:200,86:0.0338:2,2:21.7:1:29.7:1:0.49864:1.54793:60:9:0.0309:0:1.2 -19 7267523 . C T 79 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21876;SOR=0.41154;LSEQ=CCTCCACGGAATCCAGGATA;RSEQ=GGGACCAGTCGATAGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:7:1,6:314,304:0.0112:2,2:16.4:1:28.4:1:0.06688:6.18265:60:14:0.0113:0:1 0/0:864:4:1,3:435,424:0.0046:2,2:18.5:1:30.5:1:0.36898:3.07431:60:8:0.0047:0:1 -19 7267746 . A G 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGACCCGGAAGAGCAGCA;RSEQ=GTAATCAGTGATCATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:184,196:0:2,0:24.6:1:30.3:1:1:0:60:41.222:0.9973:0:0.1 0/1:491:32:16,16:200,259:0.0652:2,2:24.7:1:30.5:1:0.58122:1.29:60:64:0.0657:0:1.1 -19 7267980 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49613;SOR=Inf;LSEQ=TGCATCAGAAGGATCAGGGG;RSEQ=AGAGCCGGCTTCATGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:6,40:0:2,0:24.6:1:32.3:1:1:0:60:92:1:0:0 0/1:51:2:1,1:5,44:0.0392:2,2:19:1:27.5:1:0.22353:8.12:60:4:0.0417:0:1 -19 7293734 . AT A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.19779;SOR=0;LSEQ=AGTCCACAAGCGGGGGCTCG;RSEQ=TTTGGCTTGGGTGGGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:60,21:0.0241:2,2:18:1:29.9:1:0.46224:2.81462:60:4:0.0244:0.012:0 0/0:103:0:0,0:72,31:0:2,0:22.3:1:29.5:1:1:0:60:33.333:1:0:0.2 -19 7293748 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50104;SOR=Inf;LSEQ=GGCTCGATTTTGGCTTGGGT;RSEQ=GGGTCCTCTCCCCATCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:73,47:0:2,0:21.2:1:31.3:1:1:0:60:119:1:0:0.1 0/1:140:2:1,1:79,59:0.0143:2,2:32.5:1:30:1:1:1.33614:60:4:0.0143:0:1 -19 7293765 . G T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59618;SOR=0.42371;LSEQ=GGTGGGGTCCTCTCCCCATC;RSEQ=CGGCGCTCCCCGCCCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:76,77:0.0129:2,2:11.5:1:30:1:1:1.01:60:4:0.0134:0:1.5 0/0:182:1:0,1:89,92:0.0055:2,0:1:0:23:0:1:0:60:2:0.0056:0:1 -19 7293788 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.20414;SOR=0;LSEQ=GCGCTCCCCGCCCACGCCCG;RSEQ=GCCCCCAGACTCACCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:70,109:0.011:2,2:5:0:31.5:1:1:1.55:60:4:0.0113:0:0.5 0/0:219:0:0,0:95,124:0:2,0:28:1:30.1:1:1:0:60:108.5:1:0:0.2 -19 7293818 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22271;SOR=0;LSEQ=CTCACCCTCTCCGGGGTACA;RSEQ=GTGGCCCGCGGCGCCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:50,104:0.0128:2,2:8.5:1:29.5:1:0.54839:2.07:60:4:0.0129:0:1.5 0/0:174:0:0,0:64,110:0:2,0:25.6:1:31.1:1:1:0:60:173:1:0:0.3 -19 7293823 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50008;SOR=Inf;LSEQ=CCTCTCCGGGGTACAGGTGG;RSEQ=CCGCGGCGCCCAGTAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:47,98:0:2,0:25:1:30.7:1:1:0:60:15.111:1:0:0.2 0/1:163:2:1,1:56,105:0.0123:2,2:12.5:1:29:1:1:1.87:60:4:0.0125:0:1 -19 7293838 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21285;SOR=0;LSEQ=GGTGGCCCGCGGCGCCCAGT;RSEQ=GCAGCGCGGCCACCGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:24,73:0.0202:2,2:9.5:1:31:1:0.44321:3.00:60:4:0.0213:0:1 0/0:115:0:0,0:34,81:0:2,0:17.4:1:30.6:1:1:0:60:230:1:0:0.3 -19 7293898 . G C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCCGCCGGCCCCCGGTG;RSEQ=CCATGGCTGCGGGAGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:25.5:1:32.8:1:1:0:60:16:1:0:1.4 1/1:10:10:6,4:0,0:1:0,2:15.2:1:30.3:1:1:0:60:9:1:0:1.3 -19 7805128 . G A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10832;SOR=6.25391;LSEQ=TAACTCAGTCCCTGTTCCTC;RSEQ=GTCTGAGCACTTAGGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:15,0:14,0:0.5172:1,1:29.9:1:29.3:1:1:0:60:14:0.5:0:1.3 1/1:8:7:7,0:1,0:0.875:0,0:25.9:1:31.3:1:1:0:60:14:0.875:0:1 -19 7805278 . C T 134 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=11.45129;LSEQ=ACCAGATTGGGCTGAATCTG;RSEQ=GGTTACAATGTTTACCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:2:0,2:272,96:0.0054:2,0:8:1:19:1:0.06963:0:60:1:0.0028:0:2.5 0/1:426:25:20,5:288,113:0.0587:2,2:24:1:28.9:1:0.4919:1.57:60:50:0.059:0:1.1 -19 7805296 . G T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.88389;LSEQ=TGCGGTTACAATGTTTACCA;RSEQ=TTTATTATAAAGGATACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:523:110:74,36:292,121:0.2103:2,2:23.8:1:30.4:1:0.48467:1.17362:60:35.667:0.2078:0:1.2 1/0:627:406:274,132:145,76:0.6475:2,2:24:1:29.7:1:0.65756:1.09:60:405:0.648:0:1.1 -19 7805664 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01998;SOR=Inf;LSEQ=AGTTAAAGGAACAATGGGAA;RSEQ=AACAGCAGAGGAAAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:458:0:0,0:219,239:0:2,0:24.5:1:31.7:1:1:0:60:75.333:1:0:0.1 0/1:581:7:5,2:261,313:0.012:2,2:16.1:1:25.1:1:0.25568:2.99:60:6:0.0105:0:1 -19 7805951 . A T 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00512;LSEQ=CATGTTTACAGTGTTTGGAA;RSEQ=GGAGCAGTGCAGGAGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1026:965:502,463:36,24:0.9405:2,2:24.9:1:30.5:1:0.28647:1.38303:60:73.231:0.9407:0:1.1 0/1:1239:92:50,42:582,565:0.0743:2,2:22.5:1:30.3:1:0.51757:1.16:60:91:0.0742:0:1.2 -19 7806219 . A G 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAGAATTAGCTGGGCGC;RSEQ=GTGGTGCACGCCCAGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:61:11,50:0,0:1:0,2:24.4:1:31.2:1:1:0:60:60:1:0:1.4 1/1:39:39:3,36:0,0:1:0,2:25.5:1:31.1:1:1:0:60:78:1:0:1.4 -19 7806229 . GC G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=44.87195;LSEQ=AGCTGGGCGCAGTGGTGCAC;RSEQ=CCAGCTAATTTTTGTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:10:2,8:12,36:0.1724:2,2:23.2:1:31.9:1:1:1.32709:59.5:20:0.1818:0.069:1.7 1/1:33:30:4,26:0,3:0.9091:0,2:23.1:1:32.5:1:1:0:60:60:0.9091:0.1515:1.5 -19 7806255 . G A 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATTTTTGTACTTTTAGT;RSEQ=GAGTCCCAGCTACTCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:18,23:0,0:1:0,2:25.6:1:30.2:1:1:0:59.6:82:1:0:1.7 1/1:18:18:7,11:0,0:1:0,2:18.9:1:29.9:1:1:0:60:17:1:0:1.9 -19 7806377 . T TA 57 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.19733;LSEQ=ACAGAGCAAGACCCCATCTT;RSEQ=AAAAAAAAATAGTAATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:4:4,0:120,10:0.0292:2,0:32.5:1:29.5:1:1:0:60:8:0.0294:0:0.3 0/1:115:4:4,0:99,5:0.0348:1,0:25.8:1:28.5:1:1:0:60:8:0.0351:0.0087:0.3 -19 7806723 . G A 282 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83803;LSEQ=GCTCCAAGGGGAGAGAGAGG;RSEQ=TGGGCCACCACGATGAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:745:742:383,359:1,0:0.996:0,2:25.1:1:30.2:1:1:0:60:56.077:0.9986:0:1.1 1/1:833:829:450,379:0,0:0.9952:0,2:24.4:1:29.1:1:1:0:60:62.769:0.9951:0:1.1 -19 7806868 . T A 276 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.69238;SOR=0.58344;LSEQ=CAGGAGAGGCACAATTCACC;RSEQ=AGCAGAGGAAGAAATAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:513:511:208,303:0,0:0.9961:0,2:26.9:1:30.1:1:1:0:60:62.875:0.998:0:1.1 1/1:600:596:271,325:0,0:0.9933:0,2:26.1:1:30:1:1:0:60:118.2:0.9966:0:1.2 -19 7807027 . A G 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04781;LSEQ=GTTCAGAGTCCCAAATCCCA;RSEQ=TAAACCTGTTTTATTCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:315:311:99,212:3,0:0.9873:0,2:26:1:32:1:0.0336:0:60:61.2:0.9903:0:1.1 1/0:452:356:133,223:37,57:0.7876:2,2:24.1:1:31.4:1:0.72138:1.08817:59.7:117.667:0.7915:0:1.2 -19 7807066 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51112;SOR=Inf;LSEQ=ACAAAAAATAATAGGCCAGG;RSEQ=GCGGTGGCTCACACCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:35,97:0:2,0:20.9:1:29.6:1:1:0:60:25.4:1:0:0.9 0/1:182:2:1,1:52,127:0.011:2,2:29.5:1:27:1:0.50104:2.43:60:4:0.0112:0:2 -19 7807084 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50641;SOR=Inf;LSEQ=GGCGCGGTGGCTCACACCTG;RSEQ=AATCCCAGCAATTTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:8,80:0:2,0:21.3:1:28.4:1:1:0:58.9:176:1:0:0.7 0/1:115:2:1,1:19,94:0.0174:2,2:7.5:1:30.5:1:0.31884:4.85:60:4:0.0174:0:2 -19 7807115 . G A 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01777;SOR=Inf;LSEQ=ATTTTGGGAGGCCGAGGCGG;RSEQ=CAGATCATCTGAGGTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:0:1,0:28.4:1:32.6:1:1:0:57.6:96:1:0:0.4 0/1:62:7:0,7:0,55:0.1129:1,0:21.1:1:30.1:1:1:0:59.9:14:0.1129:0:1.9 -19 7807171 . A G 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78218;LSEQ=GACCAACACGGAGAAACCCC;RSEQ=TCTGTACTAAAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:0,18:0,1:0.9:0,1:25:1:32.6:1:1:0:56:36:0.9474:0:1.4 1/1:24:21:0,21:0,3:0.875:0,1:26.6:1:31.4:1:1:0:60:42:0.875:0:1.8 -19 7807203 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50476;SOR=0;LSEQ=AATACAAAAAATTAGCCGGG;RSEQ=CTGGTGGCGCCTGCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:27.3:1:31.6:1:1:0:56.5:16:1:0:2.1 1/1:13:11:0,11:0,2:0.8462:0,0:17.1:1:31.5:1:1:0:60:22:0.8462:0:2.3 -19 7808679 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTAGGGATCTGTGT;RSEQ=TATGAGAAGCTATTCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:30:1:1:0:60:4:1:0:4 -19 7808692 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTGTATATGAGAAGCTA;RSEQ=TCACAATGGCAGGTGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:30.5:1:1:0:60:4:1:0:4 -19 7808709 . C A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTCACAATGGCAGGTGT;RSEQ=TCCTGAGCTGGTGGCCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38.5:1:29:0:1:0:60:4:1:0:4 -19 7815543 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50375;SOR=Inf;LSEQ=AGAGGTGCCTTTTGGCCGTA;RSEQ=CTGCCATCTTCCAGTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:34,28:0:2,0:26.9:1:29.9:1:1:0:59.9:124:1:0:0.8 0/1:79:2:1,1:41,36:0.0253:2,2:25:1:30.5:1:1:1.13701:60:4:0.0253:0:1 -19 7815572 . G C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.5064;SOR=Inf;LSEQ=TTCCAGTAATTTGCCAAAAT;RSEQ=ATGAACGCAAAGGGGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:28,37:0:2,0:28.6:1:31.6:1:1:0:59.9:64:1:0:0.9 0/1:86:2:1,1:39,45:0.0233:2,2:22:0:33.5:1:1:1.15:60:4:0.0233:0:1.5 -19 7815587 . G C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07265;LSEQ=AAAATGATGAACGCAAAGGG;RSEQ=AAGAGGAGAGGCACCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:38:13,25:12,15:0.5846:2,2:21.7:1:32.6:1:0.44632:1.5281:59.9:76:0.5938:0:1.3 0/1:77:7:3,4:32,38:0.0909:2,2:26.3:1:32.7:1:1:1.12112:60:14:0.0909:0:1.1 -19 7815594 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50222;SOR=Inf;LSEQ=TGAACGCAAAGGGGAAGAGG;RSEQ=GAGGCACCCAATATATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:23,33:0:2,0:23.1:1:30:1:1:0:59.6:27:1:0:1 0/1:70:2:1,1:30,38:0.0286:2,2:23:1:29:1:1:1.26:60:4:0.0286:0:1 -19 7815690 . G T 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=GTAAGAAAGGTGATATTGTA;RSEQ=ACATCAAGGGAATGGGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:15:11,4:30,14:0.2542:2,2:28.5:1:31:1:1:1.28:60:30:0.2632:0:1 0/0:56:0:0,0:39,17:0:2,0:21.8:1:31.3:1:1:0:59.6:27:1:0:0.3 -19 7815732 . A G 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01026;SOR=Inf;LSEQ=TTCAAAAAGGAATGGACCAC;RSEQ=AGGGTTACCGTGGCAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:50,30:0:2,0:25.6:1:30.1:1:1:0:59.9:79:1:0:0.3 0/1:104:8:6,2:59,37:0.0769:2,2:13.1:1:30.5:1:0.70693:1.87:60:16:0.0769:0:1 -19 7815800 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51903;SOR=Inf;LSEQ=GCTGTTGGCATTGTTGTAAA;RSEQ=AAACAAGGGCAAGATTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:22,40:0:2,0:24.8:1:31.5:1:1:0:60:61:1:0:0.1 0/1:95:2:1,1:37,56:0.0211:2,2:35:1:27.5:1:1:1.51:60:4:0.0215:0:1.5 -19 7815817 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19263;SOR=0;LSEQ=AAACAAACAAGGGCAAGATT;RSEQ=ATGCCGAGAGAATTAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:12,35:0.0408:2,2:22:1:27.5:1:0.46429:2.84:60:4:0.0417:0:1 0/0:62:0:0,0:21,41:0:2,0:21.6:1:30.7:1:1:0:59.2:61:1:0:0.2 -19 7815954 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=ACCTGGGTTCAACTGAAGCA;RSEQ=CAGCCTGCTCCACCCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:19.2:1:29.5:1:1:0:60:10:1:0:0.1 0/1:6:2:1,1:1,3:0.3333:2,2:28.5:1:32:1:1:2.45:40:4:0.3333:0:3.5 -19 7815958 . C AGG 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.11029;SOR=Inf;LSEQ=GGGTTCAACTGAAGCACCAG;RSEQ=CTGCTCCACCCAGAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:19.1:1:30.5:1:1:0:60:10:1:0:0.1 0/1:6:2:1,1:1,3:0.3333:2,2:30.5:1:31.2:1:1:2.45:40:4:0.3333:0:3.5 -19 7815975 . AGCAT A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=CAGCCTGCTCCACCCAGAGA;RSEQ=GCTTTGTGAGAACCAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:2,8:0:2,0:19.1:1:30.5:1:1:0:60:9:1:0:0.2 0/1:6:2:1,1:1,3:0.3333:2,2:32.5:1:30.5:1:1:2.45:40:4:0.3333:0:3.5 -19 7815994 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=AAGCATGCTTTGTGAGAACC;RSEQ=ATGGGAAGGAGGCTGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:32.4:1:30.7:1:1:0:60:14:1:0:0.3 0/1:5:2:1,1:0,3:0.4:0,2:22.5:1:28:1:0.4:0:40:4:0.4:0:3.5 -19 7816004 . AG A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=TGTGAGAACCAATGGGAAGG;RSEQ=GCTGAGCTGCTGGAAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:29.6:1:31.6:1:1:0:60:14:1:0:0.3 0/1:5:2:1,1:0,3:0.4:0,2:12.5:1:29.7:1:0.4:0:40:4:0.4:0.2:3.5 -19 8463260 . C A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TTGCATCTTGGCAAGCTGCT;RSEQ=TGCTGTGCACCCCCCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10:1:30:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:33.5:1:30:0:1:0:60:4:1:0:1 -19 8464809 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49061;SOR=0;LSEQ=TGTCGCGCTTCACCCGCAAC;RSEQ=AGTTCAACCTGGAGAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:23,1:0.0769:1,2:18.5:1:27.5:1:0.15077:16.61257:60:4:0.0769:0:1 0/0:24:0:0,0:23,1:0:1,0:24.8:1:29.2:1:1:0:60:23:1:0:0.1 -19 8464838 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22435;SOR=0;LSEQ=CTGGAGAGCAAGAGCACCAT;RSEQ=GGCGTGGAGTTCGCCACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:37,2:0.0488:2,2:30.5:1:29:1:0.14268:15.3059:60:4:0.0488:0:1 0/0:45:0:0,0:43,2:0:1,0:22.5:1:31:1:1:0:60:44:1:0:0 -19 8465005 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20216;SOR=0;LSEQ=CGTGGGCTTGCAGCGCGTGG;RSEQ=CTTGGAAGGATGTGTAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:1,31:0.0588:1,2:28:1:31.5:1:0.11586:22.27:60:4:0.0588:0:1.5 0/0:41:0:0,0:3,38:0:2,0:22.8:1:32.4:1:1:0:60:82:1:0:0.1 -19 8465083 . G A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGTGAGGCTGGAAGAAC;RSEQ=CTTTAGCCATGCGCCGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:3,12:0,0:1:0,2:20:1:30.8:1:1:0:60:30:1:0:1.4 1/1:8:8:2,6:0,0:1:0,2:26.3:1:27.4:1:1:0:60:7:1:0:1.8 -19 8465102 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTTAGCCATGCGCCGTG;RSEQ=GACCCTCAGGCTGACCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:2,9:0.1538:2,2:22:0:32.5:1:0.42308:3.87:60:4:0.1538:0:2 0/0:6:0:0,0:1,5:0:2,0:39:1:30.5:1:1:0:60:12:1:0:2 -19 8988233 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTAGCTGGGACCACAGGC;RSEQ=TGCACCACCACACCTGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:30:0:1:0:60:4:1:0:1 -19 8989995 . A G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAGGCTGGCAGTGACCCAC;RSEQ=GAGAGAAGGAAGAGCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:7,7:0,0:1:0,2:19.6:1:28.6:1:1:0:60:13:1:0:1.1 1/1:8:8:4,4:0,0:1:0,2:30:1:29.8:1:1:0:60:16:1:0:1.1 -19 8990077 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16256;SOR=Inf;LSEQ=CCCCTCCTTCCAGCCAAGGG;RSEQ=GGTGGTGAGTGAGCGGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:21.1:1:30.3:1:1:0:60:34:1:0:0.3 0/1:12:2:1,1:6,4:0.1667:2,2:34:1:31.5:1:1:1.4491:60:4:0.1667:0:1 -19 8990129 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=GAAACTGTGCTTTTTCCACG;RSEQ=AACTGTGCAACTCACAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:26:1:28:1:1:1.13389:60:4:0.1176:0:1 0/0:17:0:0,0:10,7:0:2,0:29.6:1:31.4:1:1:0:60:34:1:0:0.2 -19 8990409 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAATAGCTCCAGGCTGT;RSEQ=CTTTTCCCCTGCTAGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:5,7:0,0:1:0,2:22.2:1:31.4:1:1:0:60:24:1:0:1 1/1:10:10:4,6:0,0:1:0,2:23.4:1:32.9:1:1:0:60:20:1:0:1.3 -19 8990627 . A G 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCCCTGGGCTTGGGCCCCT;RSEQ=GTGGGAGGGATGGCTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:25.5:1:32:1:1:0:60:4:0.6667:0:2 1/1:1:1:0,1:0,0:1:0,0:16:0:32:0:1:0:60:2:1:0:2 -19 8990629 . T C 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCTGGGCTTGGGCCCCTAG;RSEQ=GGGAGGGATGGCTGTAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:25.5:1:32:1:1:0:60:4:0.6667:0:2 1/1:1:1:0,1:0,0:1:0,0:18:0:32:0:1:0:60:2:1:0:2 -19 8990761 . C A 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CTCCACCAGGGGACAAAGTG;RSEQ=TTCATTAAATGGGTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:41.5:1:33:0:1:0:60:4:0.6667:0:1 0/0:4:0:0,0:2,2:0:2,0:28:1:33.3:1:1:0:60:8:1:0:0 -19 8991073 . T A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.42857;SOR=Inf;LSEQ=TGACAATAACATCATCATCA;RSEQ=CAACAACAACAACCAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:27.3:1:28.7:1:1:0:60:6:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:25.5:1:28:1:1:1:60:4:0.5:0:1 -19 8991200 . G A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04727;LSEQ=GCTGAAAACCCAAAAGGCCA;RSEQ=AGTGCCTCTTTTCCTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:3,0:0.625:0,2:16.4:1:29.4:1:0.46429:0:60:10:0.625:0:1 1/0:11:7:4,3:2,2:0.6364:2,2:18.9:1:29.9:1:1:1.30:60:14:0.6364:0:1 -19 9291308 . G A 46 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGCATCTGTTGTCAACAT;RSEQ=AGATTAATTTGCAGATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:27.3:1:29.3:1:1:0:60:6:1:0:1 -19 9291693 . CA TG 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCTGTAGTCATAGCTACT;RSEQ=GGAGGCTGAGGTGGGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5.5:1:29:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 9293025 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16605;SOR=0;LSEQ=CTGAAATGAGTTAACAGTTT;RSEQ=TTATAATTTATTGTATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:126,41:0.0118:2,2:14.5:1:29:1:0.43639:3.04831:60:4:0.0123:0:1 0/0:245:0:0,0:177,68:0:2,0:24.6:1:28.2:1:1:0:59.9:80.667:1:0:0.1 -19 9293144 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16513;SOR=0;LSEQ=CTGTTAGCGTAGCGAACCTT;RSEQ=TACATAAAATACATGCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:0,2:39,118:0.0125:2,0:11:1:28:1:1:0:60:4:0.0126:0:1 0/0:233:0:0,0:65,168:0:2,0:21.2:1:30.9:1:1:0:60:57.25:1:0:0.1 -19 9293159 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28208;SOR=Inf;LSEQ=ACCTTGTACATAAAATACAT;RSEQ=CATACTTTATTTATTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:18,82:0:2,0:24.4:1:31.9:1:1:0:59.9:32.333:1:0:0.2 0/1:155:3:2,1:20,132:0.0194:2,2:7:1:26.3:1:0.053:12.82:60:6:0.0196:0:1 -19 9293164 . C CTTTATTTATTTATTTA 131 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=10.000;MSILEN=4;SSF=0.00926;SOR=0.37418;LSEQ=GTACATAAAATACATGCATA;RSEQ=TTTATTTATTTATTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:22:4,18:10,62:0.234:2,2:34.7:1:29.6:1:0.73294:1.37:59.5:44:0.2366:0.0426:0.1 0/1:137:14:2,12:14,98:0.1022:2,2:20.9:1:28.9:1:0.69215:1.17:59.6:28:0.1053:0.0584:0.1 -19 9293193 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20434;SOR=0;LSEQ=TTTATTTATTTATTTATTAT;RSEQ=ATTATTATTATTATTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:6,42:0.04:2,2:12.5:1:29.5:1:0.26286:6.56:60:4:0.0408:0:1 0/0:60:0:0,0:6,54:0:2,0:22.2:1:31.6:1:1:0:60:120:1:0:0.1 -19 9293518 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49317;SOR=Inf;LSEQ=CATGCATATACTTTTGATAG;RSEQ=ACATGTGAAGGGATCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:22,12:0:2,0:23:1:31.5:1:1:0:60:33:1:0:0.1 0/1:36:2:1,1:23,11:0.0556:2,2:28:0:31.5:1:1:2.045:60:4:0.0556:0:1 -19 9293524 . T TG 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0611;SOR=0.2618;LSEQ=TATACTTTTGATAGCACATG;RSEQ=GAAGGGATCTCTCTAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:5,4:19,8:0.25:2,2:23.9:1:32.2:1:0.44283:1.8645:60:18:0.25:0.0278:0.1 0/1:38:3:2,1:24,11:0.0789:2,2:28:1:33.3:1:1:1.08838:60:6:0.0789:0:0 -19 9293701 . G A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58462;SOR=0.39042;LSEQ=TCAGGGCCTTCACAGCCACC;RSEQ=TAGGTTTTCTTCTCACCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:86,101:0.0106:2,2:35:1:31.5:1:1:1.17:60:4:0.0108:0:1 0/0:241:1:0,1:108,132:0.0041:2,0:40:0:27:0:1:0:60:2:0.0042:0:1 -19 9293747 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24619;SOR=Inf;LSEQ=TGTTCTTACGAAATTCTACT;RSEQ=TGCTTCCCCAGGAACTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:28,68:0:2,0:22:1:30.3:1:1:0:60:192:1:0:0.3 0/1:98:3:2,1:29,66:0.0306:2,2:5.7:1:28:1:0.23439:4.47:60:6:0.0313:0:1 -19 9293782 . G C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65824;SOR=0.80224;LSEQ=CTTTAGTAGTTTCTCGTCAG;RSEQ=CCCACAGCCAGCGCAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:20:1,19:0,22:0.4762:1,1:21.9:1:32:1:0.47619:0:60:40:0.4762:0:1.1 0/1:38:16:2,14:1,21:0.4211:1,2:21.6:1:31.1:1:0.56188:2.91:60:32:0.4324:0:1.2 -19 9425404 . G T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=CATTTGTAAGACCCTCTGTA;RSEQ=CTTGATGGCCTCGATCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:23.2:1:33.6:1:1:0:60:10:1:0:0.2 0/1:8:2:1,1:4,2:0.25:2,2:32:1:27.5:1:1:1.8258:60:4:0.25:0:1 -19 9425482 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20964;SOR=0;LSEQ=CCCAAAGGCAAGTAATAGCA;RSEQ=GATGGCTGTCCTGAGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,8:0.08:2,2:22:1:30.5:1:1:1.82581:60:4:0.08:0:1 0/0:29:0:0,0:17,12:0:2,0:21.9:1:29.9:1:1:0:60:58:1:0:0.1 -19 10244476 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21533;SOR=Inf;LSEQ=GGACCATCAGGAAACATTAA;RSEQ=GTACTGATGTTAACAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:20,170:0:2,0:24:1:30.2:1:1:0:60:94:1:0:0.1 0/1:165:2:1,1:21,142:0.0121:2,2:28.5:1:28.5:1:0.24959:6.63:60:4:0.0123:0:1 -19 10244554 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0402;SOR=0.192;LSEQ=AGACTGAACACTCCTCAAAC;RSEQ=GTCCCCAGAGGGTTCTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:20:2,18:5,27:0.3846:2,2:28.1:1:30.5:1:0.69358:1.65118:60:19:0.38:0:1.3 0/1:19:2:1,1:1,16:0.1053:1,2:14.5:1:31:0:0.20468:11.66:60:4:0.1053:0:1 -19 10244805 . A G 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09573;SOR=Inf;LSEQ=GTGACCCGCCTGAGTCCCAG;RSEQ=GCCCAAAACGGTGGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:291,46:0:2,0:23:1:30:1:1:0:60:41.125:1:0:0.1 0/1:286:3:1,2:237,45:0.0105:2,2:8.7:1:24.3:1:0.07164:10.39431:60:2:0.0071:0:1.3 -19 10246029 . G A 43 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATGAAAATACACTTAACT;RSEQ=AGACTAACTCATAGACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:24:1:27.7:1:1:0:60:6:0.3333:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 10246947 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25113;SOR=Inf;LSEQ=TTGAACTGCCTGGCTGCGGG;RSEQ=TCGCAGGCTTTGCCGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:84,167:0:2,0:23.7:1:31.4:1:1:0:59.9:124.5:1:0:0.1 0/1:282:3:2,1:106,173:0.0106:2,2:7:1:27:1:0.56043:3.25:60:6:0.0109:0:1 -19 10246979 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49909;SOR=Inf;LSEQ=GCCGGCTGGAAGACAGGACA;RSEQ=TGATGAGGCTGCAGTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:52,129:0:2,0:26.7:1:32.1:1:1:0:60:362:1:0:0.1 0/1:192:2:1,1:57,133:0.0104:2,2:34.5:1:28.5:1:0.51402:2.32:60:4:0.0105:0:1 -19 10246990 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21778;SOR=0;LSEQ=GACAGGACAGTGATGAGGCT;RSEQ=CAGTTGTGGGATGGGGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:40,109:0.0132:2,2:18:1:29:1:0.47064:2.70:60:4:0.0134:0:1 0/0:172:0:0,0:49,123:0:2,0:24.5:1:31.8:1:1:0:60:56.333:1:0:0.1 -19 10247043 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21776;SOR=Inf;LSEQ=TGGCTCTTAGAGCTTTGGGA;RSEQ=GCAGAGATGGCACCTCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:8,51:0:2,0:22.1:1:31.1:1:1:0:60:58:1:0:0.1 0/1:53:2:1,1:7,44:0.0377:2,2:26.5:1:28:1:0.28157:5.95:60:4:0.0377:0:1 -19 10247946 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24895;SOR=Inf;LSEQ=GCATGCGGGCAGCCACCAAT;RSEQ=CACTCATGTCCTGAAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:72,203:0:2,0:22.3:1:31.1:1:1:0:60:24:1:0:0.1 0/1:286:3:1,2:87,196:0.0105:2,2:14.7:1:22.3:1:1:1.13:60:2:0.0072:0:1 -19 10247971 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.10095;SOR=Inf;LSEQ=CATGTCCTGAAAGAGTGTGG;RSEQ=GGGCCCAGCTGTCACCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:20,151:0:2,0:25.2:1:30.1:1:1:0:60:27.5:1:0:0.1 0/1:150:3:2,1:27,120:0.02:2,2:7.3:1:27:1:0.09574:8.70:60:6:0.02:0:1.7 -19 10247979 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19309;SOR=Inf;LSEQ=GAAAGAGTGTGGGGGGCCCA;RSEQ=CTGTCACCTCATGTGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:16,139:0:2,0:25.9:1:31.4:1:1:0:60:30:1:0:0.1 0/1:122:2:1,1:16,104:0.0164:2,2:21:1:26:1:0.26026:6.34:60:4:0.0165:0:1 -19 10249340 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18785;SOR=Inf;LSEQ=GACACTCCCAACTGGACTGG;RSEQ=CAGACCCAGGCCCAGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:7,93:0:2,0:26.2:1:31.1:1:1:0:60:32.333:1:0:0.2 0/1:77:2:1,1:9,66:0.026:2,2:29:0:31:0:0.24436:7.01:60:4:0.0263:0:1.5 -19 10250311 . G T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60058;SOR=2.29389;LSEQ=GGCTGCTGGCCGGGTCACGT;RSEQ=CTGGCCACATCTGTCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:0,1:140,21:0.0062:2,0:1:0:26:0:0.1358:0:60:2:0.0064:0:1 0/1:142:2:1,1:118,22:0.0141:2,2:24:1:26.5:1:0.29867:5.26803:60:4:0.0143:0:1 -19 10250332 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10735;SOR=Inf;LSEQ=CTGGCCACATCTGTCTGCCC;RSEQ=CCCCAGCCCCAGGGCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:196,48:0:2,0:23.1:1:29.6:1:1:0:60:29.5:1:0:0.1 0/1:222:3:2,1:166,53:0.0135:2,2:7:1:26.7:1:0.56851:1.56254:60:6:0.0137:0:1 -19 10250515 . G A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03558;SOR=Inf;LSEQ=TGTAGGGGGCAGGAGAGACT;RSEQ=CAGGAGTCACCTCCACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:0:0,0:159,310:0:2,0:25.1:1:31.9:1:1:0:60:66:1:0:0.1 0/1:574:6:5,1:204,363:0.0105:2,2:12.2:1:25:1:0.02632:8.87:60:12:0.0106:0:1 -19 10250567 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19969;SOR=Inf;LSEQ=ACGACCCACTGTGCCGGAAG;RSEQ=CCCTCACGAATGTTATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:47,143:0:2,0:23.1:1:30.8:1:1:0:60:22.75:1:0:0.2 0/1:154:2:1,1:34,118:0.013:2,2:34:1:27:1:0.40404:3.44:60:4:0.0137:0:1 -19 10250613 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1891;SOR=Inf;LSEQ=TCCCTGGTGAGAGCTGAGCT;RSEQ=TGAGCTTCCGGGGGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:89,64:0:2,0:25.9:1:32.4:1:1:0:60:75.5:1:0:0.2 0/1:119:2:1,1:74,43:0.0168:2,2:33:1:32:0:1:1.71264:60:4:0.0169:0:1 -19 10250687 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.202;SOR=4.32374;LSEQ=CATGCGGCACAGCCCCGGGC;RSEQ=GTCTGGCAACACTGGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:1:0,1:275,117:0.0025:2,0:1:0:25:0:0.30025:0:60:2:0.0026:0:1 0/1:366:4:1,3:236,126:0.0109:2,2:8.8:1:27.5:1:0.12759:5.59185:60:8:0.0111:0:1 -19 10251396 . G T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09436;SOR=0;LSEQ=CGGGGTTGGAAGTCGTTTCA;RSEQ=GTAGCACCTGCCCGGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:235,52:0.0103:2,2:14:1:32:1:0.45545:2.25168:60:6:0.0105:0:1.3 0/0:347:0:0,0:265,82:0:2,0:21.6:1:31.1:1:1:0:60:172.5:1:0:0.1 -19 10251709 . C T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24888;SOR=Inf;LSEQ=TAACACCAGAGGTGGTTTTA;RSEQ=ACTGAGGGATTCACAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:178,90:0:2,0:24.8:1:31.7:1:1:0:60:32.5:0.9962:0:0.5 0/1:279:3:1,2:187,89:0.0108:2,2:8:1:25:1:0.24892:4.17858:60:6:0.0108:0:2 -19 10251717 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0615;SOR=Inf;LSEQ=GAGGTGGTTTTACACTGAGG;RSEQ=ATTCACAGGCAGCCTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:204,108:0:2,0:23.8:1:31.1:1:1:0:60:51:1:0:0.5 0/1:311:4:2,2:204,102:0.0129:2,2:14:1:24:1:0.60433:1.99523:60:3:0.0099:0:2 -19 10251747 . A G 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00295;SOR=1.4592;LSEQ=CAGCCTCCAAGTTACAGAAG;RSEQ=ATAACTTGAAAAGAAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:216:144,72:150,88:0.4737:2,2:22.7:1:30.9:1:0.43271:1.17:60:71:0.4733:0:1.1 1/0:553:314:201,113:141,95:0.5678:2,2:23.7:1:30.6:1:0.32896:1.20:60:43.857:0.5633:0:1.1 -19 10252620 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51875;SOR=Inf;LSEQ=AGCTGAAACCCTGCAGCCAA;RSEQ=CCGCCTTGTGTATAACCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:91,11:0:2,0:23.3:1:31.5:1:1:0:60:33:1:0:0.1 0/1:154:2:1,1:125,26:0.013:2,2:17.5:1:28:1:0.32276:4.7367:60:4:0.0133:0:1 -19 10252760 . G A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03107;SOR=Inf;LSEQ=GTACACCTGGACGCACTCGG;RSEQ=CAGGTCCTCCCCATACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:0:0,0:266,228:0:2,0:26.7:1:31.5:1:1:0:60:69.571:1:0:0.1 0/1:519:6:5,1:268,245:0.0116:2,2:12.7:1:27:1:0.21985:4.56:60:12:0.0118:0:1.2 -19 10252936 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2267;SOR=0;LSEQ=CGTTAGGAGCTCTCCTTTGT;RSEQ=GTGAGCTTATGCTGAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:43,140:0.0108:2,2:21.5:1:30:1:0.42009:3.23:60:4:0.011:0:1 0/0:203:0:0,0:59,144:0:2,0:25:1:30.4:1:1:0:60:100.5:1:0:0.1 -19 10253099 . T G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=1;SOR=1.39581;LSEQ=TGGGGAACTGCAAGGTAGAC;RSEQ=CCCCCCCATTTAGGGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:0.5833:0,0:24:1:29.7:1:1:0:60:6:0.5455:0:1.7 1/0:3:2:0,2:0,1:0.6667:0,0:37:1:34:0:1:0:60:4:0.6667:0:1.5 -19 10254733 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22791;SOR=0;LSEQ=GTCAGTCAGGCATGACTGAC;RSEQ=AGTGAAAATAACCATTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:9,111:0.0164:2,2:12:0:31:1:0.15784:11.75:60:4:0.0165:0:1 0/0:133:0:0,0:16,116:0:2,0:23:1:31.2:1:1:0:60:32:1:0:0.1 -19 10256889 . CCA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10476;SOR=Inf;LSEQ=CGATTTATGTTGTCTGTTTG;RSEQ=CCTATGCCAACGTGACGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:45,2:0:1,0:25.4:1:31.3:1:1:0:60:94:1:0:0.2 0/1:23:2:1,1:21,0:0.087:1,2:43.5:1:30.5:1:0.08696:0:60:4:0.0909:0:0 -19 10256971 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=AGGAGGGGGACACCACAAAG;RSEQ=CAGCCTGGCTCAGCCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:146,26:0.0115:2,2:7:1:26.5:1:0.28702:5.52933:60:4:0.0116:0:1 0/0:168:0:0,0:143,25:0:2,0:23:1:32:1:1:0:60:167:1:0:0.1 -19 10257245 . G A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=0.40264;LSEQ=CATAAGGCCCTGAGGTGGCC;RSEQ=GCAGTGGCCGCAGCAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:146:81:15,66:13,52:0.5548:2,2:23.7:1:30.8:1:0.83552:1.09928:60:162:0.5664:0:1.1 0/1:123:41:9,32:22,60:0.3333:2,2:23.1:1:30.5:1:0.66177:1.30096:60:40:0.3279:0:1 -19 10257412 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46553;LSEQ=GAGAGAACATAGCAAGAAAA;RSEQ=CAGGCAACTTTTGAGTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:0.25:0,0:22.7:1:32.7:1:1:0:60:6:0.25:0:1.3 0/1:6:2:0,2:1,3:0.3333:2,0:25.5:1:27.5:1:1:0:60:4:0.3333:0:1 -19 10259732 . G A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62917;SOR=0.3967;LSEQ=GTGTCAGGCCAGGCGCAGTG;RSEQ=CTCATGCCTGTATTCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:2,1:28,181:0.0142:2,2:17:1:27.7:1:0.05316:12.66:60:6:0.0146:0:1 0/0:177:1:1,0:35,141:0.0056:2,0:1:0:22:0:0.20339:0:60:2:0.0057:0:1 -19 10259739 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19913;SOR=Inf;LSEQ=GCCAGGCGCAGTGGCTCATG;RSEQ=CTGTATTCCCAGCACTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:20,168:0:2,0:24.2:1:31:1:1:0:60:36.6:1:0:0.1 0/1:152:2:1,1:27,123:0.0132:2,2:30:1:28:1:0.33548:4.49:60:4:0.0133:0:1 -19 10260006 . C CA 94 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.8049;SOR=1.17338;LSEQ=AGCGAAACTCAGTCTCAAAA;RSEQ=AAAAAAAAAAACAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:9:9,0:69,3:0.1084:1,0:16.6:1:30.8:1:1:0:59.4:18:0.1111:0.0361:2.8 0/1:72:9:9,0:61,1:0.125:1,0:25.1:1:29.7:1:1:0:56.2:18:0.1268:0:1.9 -19 10260018 . C CA 66 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.74389;SOR=1.32655;LSEQ=TCTCAAAACAAAAAAAAAAA;RSEQ=AAAAAAAAAACCAAATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:4:4,0:104,4:0.0325:1,0:23.8:1:30.8:1:1:0:60:8:0.04:0:2.3 0/1:117:5:4,1:99,3:0.0427:1,2:16.8:1:28.6:1:0.17654:7.87682:60:10:0.0532:0.0085:2.6 -19 10260030 . C A 121 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02269;SOR=2.8857;LSEQ=AAAAAAAACAAAAAAAAAAC;RSEQ=AAATTAAAAAAAAATACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:7:6,1:137,6:0.0464:1,2:25.6:1:24.3:1:0.28937:3.74791:54:1.333:0.0331:0:2.4 0/1:154:19:17,2:127,8:0.1234:2,2:23.9:1:28.6:1:0.35619:1.85833:59.3:18:0.1333:0:2.3 -19 10260035 . T TA 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.72407;SOR=1.59504;LSEQ=AAACAAAAAAAAAACCAAAT;RSEQ=AAAAAAAAATACAAATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:3:3,0:143,9:0.0183:2,0:22.7:1:29:1:1:0:60:6:0.0252:0:2.7 0/1:173:5:5,0:148,16:0.0289:2,0:31.8:1:28.2:1:1:0:60:10:0.0365:0:1.6 -19 10260362 . A G 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11491;SOR=Inf;LSEQ=AGAAGACGGGCATGGGGAGA;RSEQ=AGTTCTGACTTGGCCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:66,157:0:2,0:25.7:1:30.1:1:1:0:60:110.5:1:0:0.1 0/1:212:3:2,1:79,130:0.0142:2,2:40:1:26.3:1:0.55946:3.27:60:2:0.0096:0:1 -19 10260400 . T C 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01473;SOR=0;LSEQ=CAGATATGTGACCAAGTCTA;RSEQ=GCAGGAGCACTCGTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:7:2,5:43,105:0.0452:2,2:25:1:30.9:1:1:1.02367:60:14:0.0467:0:1 0/0:148:0:0,0:60,88:0:2,0:23.8:1:29.9:1:1:0:60:73:1:0:0.1 -19 10260543 . C T 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03867;SOR=4.77451;LSEQ=GCAAACCTTGCTAGATACAG;RSEQ=GGTTTTGAGGAATCATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:694:2:1,1:424,268:0.0029:2,2:7:1:28:1:1:1.58095:60:4:0.0029:0:1 0/1:734:10:2,8:401,323:0.0136:2,2:17.6:1:28.2:1:0.0492:4.95681:60:20:0.0138:0:1 -19 10262651 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00033;SOR=Inf;LSEQ=TTGCAGACCAGCCTGGCCAA;RSEQ=GTGGTGAAACCCCATCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:0,56:0:1,0:23.8:1:30:1:1:0:60:27:1:0:0.1 0/1:36:8:0,8:0,28:0.2222:1,0:21:1:29.6:1:1:0:60:16:0.2222:0:1.1 -19 10264885 . CAG C 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.77391;SOR=1.20345;LSEQ=GCAGCCAGAGTCTCAAGCCA;RSEQ=AGAGAAAGATGGAGCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:6:6,0:101,5:0.0536:1,0:39.8:1:32.3:1:1:0:60:12:0.0536:0:0 0/1:94:6:5,1:84,4:0.0638:1,2:19.5:1:30.8:1:0.2863:4.09141:60:12:0.0652:0.0106:0.2 -19 10265248 . T C 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50841;LSEQ=CCAGTCTTCACTCTGGTCCC;RSEQ=GCCGCATCCTTACCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:499:276:155,121:129,92:0.5531:2,2:25.7:1:30.6:1:0.6489:1.0944:59.9:275:0.5556:0:1.6 0/1:632:244:123,121:200,188:0.3861:2,2:23.3:1:29.6:1:0.80657:1.04648:60:121:0.3878:0:1.6 -19 10265312 . T C 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03239;SOR=0;LSEQ=ATCAGGTCCCGCATGCAGGG;RSEQ=GTCAGGAAGATGGGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:637:637:322,315:0,0:1:0,2:26.1:1:30.5:1:1:0:60:56.909:1:0:1.3 1/1:713:707:346,361:2,2:0.9916:2,2:24.4:1:30.5:1:1:1.04331:60:116.833:0.9929:0:1.3 -19 10265593 . G T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38002;LSEQ=TCTCTTACCTCGATCTTGTT;RSEQ=ATCAGGTCCTCATAGGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:639:271:155,116:215,151:0.4241:2,2:25.6:1:29.3:1:0.74536:1.06548:60:270:0.4265:0:1.1 0/1:723:158:85,73:313,251:0.2185:2,2:23.7:1:28.9:1:0.71809:1.07086:60:316:0.2207:0:1.1 -19 10266418 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16646;SOR=Inf;LSEQ=TAAGGTTCCCAGTCACATGG;RSEQ=CTTCTGCAAGCCTGCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:107,4:0:1,0:23.4:1:31.7:1:1:0:60:36:1:0:0.1 0/1:77:2:2,0:71,4:0.026:2,0:16.5:1:30:1:1:0:60:4:0.0263:0:1 -19 10266681 . G A 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.90215;LSEQ=ACATCCCAAACCCAGGAGGC;RSEQ=CTCTAAGCGCCCACTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:1,2:51,179:0.0129:2,2:23:1:28.7:1:0.53297:1.75:60:6:0.0133:0:1 0/1:258:3:2,1:57,198:0.0116:2,2:9:1:26.7:1:0.13185:6.88:60:6:0.0118:0:1 -19 10267011 . C A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.82477;SOR=1.18945;LSEQ=AGGATTACAGATGTGAGCCA;RSEQ=CCTGCCTGGCTGTTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:9:7,2:162,95:0.0338:2,2:33.7:1:29.6:1:0.49379:2.05:60:18:0.035:0:1.4 0/1:300:12:11,1:196,92:0.04:2,2:22.3:1:30.3:1:0.1129:5.14:60:24:0.0412:0:1.5 -19 10267077 . T C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.42391;LSEQ=TATTCCTTACCTTCAAGAGA;RSEQ=GGGTCATCATCATAGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:524:302:153,149:118,104:0.5763:2,2:26.6:1:31.1:1:0.59621:1.10474:60:150:0.5758:0:1.2 0/1:744:272:149,123:251,220:0.3656:2,2:27.9:1:30.2:1:0.70322:1.06:60:89.667:0.368:0:1.2 -19 10267223 . C T 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=CACATGCTTACCAGCTAAGC;RSEQ=GTGAAGGCGGGTCTTCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:78,169:0:2,0:24.3:1:29.5:1:1:0:60:48.4:1:0:0.1 0/1:314:16:5,11:95,203:0.051:2,2:23.2:1:29.1:1:1:1.02946:60:32:0.0519:0:1.2 -19 10267252 . G T 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19751;SOR=1.84635;LSEQ=GGGTCTTCGTGCAGACTTCA;RSEQ=ATCAGGCACGAGGCAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:8:0,8:19,128:0.0516:2,0:19.1:1:28.5:1:0.59677:0:60:16:0.0523:0:1.9 0/1:164:15:3,12:17,132:0.0915:2,2:21.3:1:28.1:1:0.39876:1.93:60:30:0.0926:0:1.7 -19 10267266 . C A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4534;SOR=1.59002;LSEQ=ACTTCAGATCAGGCACGAGG;RSEQ=AATGAGAGAATGTACAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:7:0,7:11,115:0.0526:2,0:31:1:31.4:1:1:0:60:14:0.0538:0:2 0/1:123:10:2,8:6,107:0.0813:2,2:22.6:1:29.8:1:0.12812:4.37:60:20:0.0826:0:2.1 -19 10267318 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10833;SOR=Inf;LSEQ=TTTTGTTTGTTTTTGAGACA;RSEQ=AGTCTTGCTCTATCCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:2,52:0:1,0:26.4:1:31.5:1:1:0:59.8:53:1:0:0.4 0/1:27:2:0,2:0,25:0.0741:1,0:16.5:1:28:1:1:0:60:4:0.0741:0:2 -19 10270593 . G A 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0;SOR=56.66497;LSEQ=CACTGAATGCACTTGGGAGG;RSEQ=TGGGTCTGTGGGAGCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:1:1,0:298,252:0.0018:2,0:1:0:27:0:1:0:60:2:0.0018:0:1 0/1:620:58:30,28:297,263:0.0935:2,2:19.2:1:27.7:1:0.89057:1.05393:60:8.667:0.0852:0:1.2 -19 10270746 . GA G 254 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.04433;SOR=0.75282;LSEQ=TTTTTTTCTCCGTTCTGGGG;RSEQ=AAAAAAAAAATCACAAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:406:278:101,177:48,49:0.6847:2,2:30.4:1:31.3:1:0.02978:1.71421:59.9:277:0.6873:0.0172:0.1 1/0:519:322:110,212:69,85:0.6204:2,2:29.3:1:30.5:1:0.02649:1.56292:59.9:106.333:0.6304:0.0308:0.2 -19 10270801 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50033;SOR=Inf;LSEQ=TTTCAGAAAATATCAAAATC;RSEQ=CCCCTGTGAGGTTTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:22,106:0:2,0:23.9:1:31.3:1:1:0:60:31:1:0:0.3 0/1:146:2:0,2:18,126:0.0137:2,0:22.5:1:26.5:1:1:0:60:4:0.0142:0:1.5 -19 10270942 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49794;SOR=Inf;LSEQ=TGGTCCTATGTTCACCAACC;RSEQ=GATCCAAAATGAGCCTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:101,20:0:2,0:23.9:1:31.1:1:1:0:60:242:1:0:0.1 0/1:122:2:2,0:101,19:0.0164:2,0:46.5:1:29.5:1:1:0:60:4:0.0164:0:1 -19 10271034 . C G 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.59562;LSEQ=TTAACATTACCATCTGCTTT;RSEQ=GATAATGTCAAGAATAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:25:14,11:266,210:0.0498:2,2:24.3:1:30.8:1:1:1.00:60:50:0.0506:0:1.1 0/1:701:84:47,37:358,255:0.1198:2,2:24.2:1:31.1:1:0.72385:1.10505:60:168:0.1214:0:1.1 -19 10271141 . A C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12895;SOR=1.78003;LSEQ=AAAGGCTAAGAGAGTGTTTT;RSEQ=CACCCAGATAGTGCTTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:11:2,9:100,199:0.0355:2,2:29:1:31.6:1:0.35044:2.25625:60:22:0.0358:0:1 0/1:439:27:8,19:129,283:0.0615:2,2:24.5:1:30.2:1:1:1.08241:60:26:0.0599:0:1.2 -19 10271159 . G A 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31034;SOR=0.22998;LSEQ=TTACACCCAGATAGTGCTTC;RSEQ=GTGTTAAGAACTTTGTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:2,1:53,161:0.0138:2,2:13.7:1:29.7:1:0.15885:6.01:60:6:0.0142:0:1 0/0:312:1:1,0:78,233:0.0032:2,0:1:0:24:0:0.25321:0:60:2:0.0032:0:1 -19 10273372 . T C 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.91213;SOR=1.04482;LSEQ=CTCGTCTTTTTCATCAGAAA;RSEQ=CTGTGGATTTACTTTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:823:36:20,16:423,363:0.0437:2,2:30.1:1:30.5:1:0.866:1.07:59:35:0.0443:0:1.5 0/1:1140:52:26,26:571,516:0.0456:2,2:29.8:1:30.6:1:0.77696:1.10649:60:51:0.0461:0:1.5 -19 10277204 . C T 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11633;SOR=3.50748;LSEQ=GAACCCAGAGCCCCACCCTG;RSEQ=GCACTCCCGCCCAAGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:2:1,1:298,162:0.0043:2,2:22:1:30:1:1:1.837:60:4:0.0044:0:1 0/1:532:8:3,5:351,173:0.015:2,2:12.1:1:26.4:1:0.12503:3.37305:60:7:0.0134:0:1.1 -19 10277266 . G A 170 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=41.84939;LSEQ=AGTTCAGAAACAAATAACCC;RSEQ=CCTTTACTTTCTCGTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:981:1:1,0:504,475:0.001:2,0:25:0:14:0:1:0:60:0:0:0:1 0/1:1342:55:28,27:674,612:0.041:2,2:24:1:29.5:1:0.89066:1.06189:60:110:0.0415:0:1.3 -19 10277400 . C CG 90 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.13392;SOR=2.8477;LSEQ=CACACACAGGCTGGTCAGCT;RSEQ=GGGGGGGGCCCTGCACCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:3:1,2:75,245:0.0092:2,2:22.3:1:31.3:1:0.5541:1.63:60:6:0.0094:0.0031:0.3 0/1:310:8:3,5:78,223:0.0258:2,2:30.6:1:30.1:1:0.43624:1.71:60:16:0.0265:0.0032:0.5 -19 10277421 . G A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10486;SOR=Inf;LSEQ=GGGGGGGGCCCTGCACCGGG;RSEQ=CCAACAGCTCCTAAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:38,185:0:2,0:26:1:31.7:1:1:0:57.6:30.857:1:0:0.1 0/1:200:3:1,2:44,153:0.015:2,2:26.3:1:29.3:1:0.53656:1.73:60:6:0.0152:0:1.7 -19 10278859 . G T 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53377;SOR=0.57126;LSEQ=TCAGCCTTCACTTCAGGGTG;RSEQ=TCTCACCTTTCACAAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:8:8,0:114,3:0.064:1,0:24.6:1:30.9:1:1:0:60:16:0.0645:0:1.1 0/1:80:3:3,0:76,1:0.0375:1,0:15.7:1:31.3:1:1:0:60:6:0.0385:0:1 -19 10278953 . T G 209 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTATTTTACCAAGATACTTA;RSEQ=GTTAGCAATTCAGTTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:93:64,29:228,150:0.1975:2,2:26.5:1:32:1:0.15254:1.45:60:186:0.2009:0:1.1 0/0:585:0:0,0:357,227:0:2,0:22.6:1:29.4:1:1:0:60:63.889:1:0:0.1 -19 10279189 . T C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2113;SOR=0.51799;LSEQ=CCAGTGGGCACAGTAGCTCA;RSEQ=GCCTGTAATCTCAGAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:27:0,27:0,18:0.6:1,1:23.5:1:29.7:1:1:0:60:54:0.6:0:1.1 0/1:23:10:0,10:0,13:0.4348:1,0:33.3:1:28:1:1:0:60:9:0.4091:0:1.2 -19 10279454 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAGGAATGAAATAGGATG;RSEQ=CCCAATCTGAAAAGTAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:29.5:1:31:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 10283932 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.91446;LSEQ=TTTTCATAAAGCTCCTCTTT;RSEQ=CCCCAAAAGCAATCTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:8:1,7:22,144:0.0457:2,2:22.9:1:29.8:1:1:1.06906:60:16:0.0471:0:1.3 0/1:143:6:1,5:16,121:0.042:2,2:23.8:1:27.5:1:0.5388:1.51:60:5:0.0357:0:1 -19 10284415 . A G 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.3805;SOR=1.74234;LSEQ=TGACCTCAAGTGATTCGCCC;RSEQ=TCTTGGCCTCCCAAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:5:4,1:63,2:0.0714:1,2:16.6:1:30.6:1:0.20205:7.39874:60:10:0.0714:0:1 0/1:59:7:7,0:52,0:0.1186:1,0:24.7:1:30.4:1:1:0:60:14:0.1186:0:1 -19 10284422 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.4966;SOR=0;LSEQ=AAGTGATTCGCCCATCTTGG;RSEQ=CTCCCAAAGTGCTGAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:69,3:0.027:1,0:33.5:1:27.5:1:1:0:60:4:0.0274:0:2 0/0:73:0:0,0:70,3:0:1,0:22.8:1:32.4:1:1:0:60:146:1:0:0.2 -19 10284461 . C T 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=0.39934;LSEQ=TACAGGCATGAGTCACCGTG;RSEQ=CCGGCCTTAAACTTTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:72:51,21:82,29:0.3934:2,2:18.9:1:30:1:0.73462:1.16332:60:71:0.3966:0:1 0/1:224:46:35,11:141,36:0.2054:2,2:17.7:1:29.6:1:0.68497:1.2298:60:92:0.2063:0:1.1 -19 10284622 . G T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22455;SOR=4.34306;LSEQ=ACAAAAAAGATTAGAATACT;RSEQ=GTTTCAAGGGAAGGTCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:1:0,1:95,220:0.0032:2,0:14:0:15:0:1:0:60:0:0:0:7 0/1:367:5:1,4:124,238:0.0136:2,2:25.6:1:24.6:1:0.66509:2.08043:60:1.5:0.0082:0:2 -19 10284778 . A G 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27785;SOR=0.38119;LSEQ=CCCACCAACCCCAAAACAAA;RSEQ=GCAGGTCCGAGAAGTAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:15:0,15:0,13:0.5357:1,1:21.3:1:31.5:1:1:0:60:30:0.5556:0:1 0/1:10:3:0,3:0,7:0.3:0,0:30:1:31.3:1:1:0:60:6:0.3:0:1 -19 10286416 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23591;SOR=Inf;LSEQ=AGTTTAATGTTTCTCTGAAT;RSEQ=ACGGGTTTAGAATGTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:1,80:0:1,0:25.7:1:31:1:1:0:60:26:1:0:0.1 0/1:77:2:0,2:1,74:0.026:1,0:13.5:1:29.5:1:1:0:60:4:0.0263:0:1 -19 10286465 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17187;SOR=Inf;LSEQ=TGTAAGTCCTAAGAAATCAC;RSEQ=GGTCTAAACACCGATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:2,34:0:2,0:20.9:1:31.3:1:1:0:60:72:1:0:0.1 0/1:26:2:0,2:1,23:0.0769:1,0:11.5:1:29:1:1:0:60:4:0.08:0:1 -19 10287635 . A T 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.44444;SOR=0;LSEQ=CTAGAAATATACTAAACTAT;RSEQ=TATGGACAAAGTAATCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:18.2:1:29.2:1:1:0:60:10:0.625:0:1 0/0:2:0:0,0:1,1:0:2,0:8.5:1:30.5:1:1:0:60:4:1:0:0 -19 10288072 . G GA 122 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.57878;SOR=1.26445;LSEQ=AGAAGAAAAAGCATTAAAAA;RSEQ=AAAAAAAAAAGCCACTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:12:3,9:98,205:0.037:2,2:25.8:1:31.6:1:0.7579:1.43261:60:24:0.0423:0:0.1 0/1:388:18:4,14:131,233:0.0464:2,2:28.6:1:29.4:1:0.31494:1.9647:60:36:0.0495:0:0.3 -19 10291064 . C T 77 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.192;SOR=2.97519;LSEQ=ACTTGCTCCTCCTGGGCGTG;RSEQ=GAGGTTTGGAAAGGGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:2:1,1:375,178:0.0036:2,2:44:0:26.5:1:0.54142:2.1037:60:4:0.0037:0:1 0/1:657:7:2,5:408,241:0.0107:2,2:18.1:1:27.7:1:0.10949:4.22285:60:14:0.0108:0:1 -19 10291298 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24895;SOR=Inf;LSEQ=GAATGTAAACAAGTGTCAGA;RSEQ=AACAAGGAAACACATGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:90,125:0:2,0:24.7:1:31.8:1:1:0:60:70.667:1:0:0.1 0/1:228:3:1,2:78,147:0.0132:2,2:18:1:22.3:1:1:1.06095:60:2:0.0091:0:2.7 -19 10292523 . C CA 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=TCAAAAAACAAAAACAACAA;RSEQ=AAAAAAAAACACCACCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:19,1:0:1,0:26.4:1:33:1:1:0:60:40:1:0:0.3 0/1:20:2:2,0:18,0:0.1:1,0:15:1:31.9:1:1:0:60:4:0.1:0.05:0 -19 10292608 . C A 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00478;SOR=0;LSEQ=TCCAAATTATCTTTGAAACT;RSEQ=CATGGGAAAAAATGCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:7:7,0:68,4:0.0886:2,0:25.9:1:27.9:1:1:0:60:14:0.0886:0:1 0/0:87:0:0,0:79,8:0:2,0:23.1:1:30.6:1:1:0:60:86:1:0:0.1 -19 10292826 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23413;SOR=0;LSEQ=TTGCCTGTAAGAATATCACA;RSEQ=TTCTAAAGAAGTTTTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:33,138:0.0116:2,2:23.5:1:30:0:0.35536:4.13:60:4:0.0117:0:1 0/0:184:0:0,0:42,142:0:2,0:22.6:1:31.1:1:1:0:60:368:1:0:0 -19 10292901 . C T 86 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06512;SOR=0.15027;LSEQ=TAAGCTGGCTTTTGTCTCCC;RSEQ=GCAAGAGTCTAGAGTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:7:0,7:1,33:0.1707:1,0:23.4:1:30.9:1:1:0:60:14:0.175:0:1 0/1:34:1:0,1:1,32:0.0294:1,0:50:0:29:0:1:0:60:2:0.0294:0:1 -19 10305282 . G A 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.8165;LSEQ=CTAGCCACCAGGGAGCTACG;RSEQ=GGGAATCCACGGTCCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:40:0:28:0:1:0:60:2:0.5:0:1 0/1:9:4:2,2:3,2:0.4444:2,2:25.8:1:30.5:1:1:1.43328:60:8:0.4444:0:1.3 -19 10305389 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23619;SOR=Inf;LSEQ=GCCGCACCACCCCACGCATG;RSEQ=GCGCCCGTCTGTCAGCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:144,12:0:2,0:27:1:32.4:1:1:0:60:77:1:0:0.2 0/1:148:2:1,1:129,17:0.0135:2,2:16.5:1:28:1:0.22918:7.4034:60:4:0.0143:0:1.5 -19 10305434 . C T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00435;SOR=0;LSEQ=CCGGCCACCCCGAGGGGAAG;RSEQ=GACCCCCCACCCAGCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:7:1,6:325,151:0.0144:2,2:8:1:27.1:1:0.00563:12.84973:60:14:0.0147:0:1.1 0/0:566:0:0,0:371,195:0:2,0:23.1:1:30.1:1:1:0:60:25.952:1:0:0.4 -19 10305615 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12371;SOR=Inf;LSEQ=GCGGCGGCGGCAGCGCAGGC;RSEQ=CCCCGGCTTTTCGCGCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:82,186:0:2,0:23.4:1:31.1:1:1:0:60:133:1:0:0.2 0/1:274:4:4,0:84,185:0.0146:2,0:7.8:1:23.8:1:0.0103:0:60:3:0.0113:0:2.3 -19 10305639 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2334;SOR=Inf;LSEQ=CGGCTTTTCGCGCGGAAACC;RSEQ=ATGGGGAGGGGCGATGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:32,144:0:2,0:23.5:1:30.9:1:1:0:60:57.667:1:0:0.2 0/1:165:2:1,1:36,127:0.0121:2,2:5:0:31:1:0.39926:3.49:60:4:0.0123:0:1.5 -19 10305664 . C T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62758;SOR=0.39457;LSEQ=GGAGGGGCGATGAGCGGAGG;RSEQ=GGCGTCTACCACCCCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:3:1,2:10,102:0.0261:2,2:30.3:1:29.7:1:0.26245:4.97:60:6:0.027:0:1.3 0/1:96:1:0,1:10,85:0.0104:2,0:1:0:25:0:1:0:60:2:0.0108:0:1 -19 10472221 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22727;SOR=0;LSEQ=ACACAGACGCCATGCACGAA;RSEQ=GCCAGGTGCGTGTGGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:0.125:2,2:32.5:1:27.5:1:1:1.30929:60:4:0.125:0:1 0/0:17:0:0,0:9,8:0:2,0:22.5:1:29.8:1:1:0:60:16:1:0:0.1 -19 10597746 . T A 73 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAAATGGCCAGGC;RSEQ=TGGTAGCTCACGCCTATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:16.8:1:31.6:1:1:0:52:10:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 10599685 . G A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.11974;SOR=2.88153;LSEQ=GGAGGCTGAGGCAGGAGGAT;RSEQ=GCTGGAGCCCAGGCTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:6,0:16,0:0.2727:1,0:26.5:1:26.7:1:1:0:60:5:0.3846:0:1.8 1/0:19:10:10,0:9,0:0.5263:0,0:22.3:1:27.9:1:1:0:60:20:0.7143:0:1.8 -19 10599797 . G A 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96162;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=GAAAGCAAAAGCAAAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:3:2,1:107,42:0.0196:2,2:13.7:1:26.7:1:1:1.27172:48:2:0.015:0:1.7 0/1:212:4:4,0:119,85:0.0189:2,0:18.8:1:18:1:0.14656:0:37.5:0.333:0.0052:0:4.5 -19 10599836 . G C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19805;LSEQ=AGTCCACAAAAGATGGGCTA;RSEQ=TCAGGACTCTTCCCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:161:100,61:200,121:0.3326:2,2:27.9:1:31.4:1:1:1.00825:60:31.2:0.3319:0:1.3 0/1:613:55:32,23:311,245:0.0897:2,2:24.2:1:31.4:1:0.77758:1.10:60:54:0.09:0:1.3 -19 10600052 . G A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12857;SOR=Inf;LSEQ=AGGACGCAGACGCCTAAAGG;RSEQ=CACCATGCAGAGAAGGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:117,212:0:2,0:25.4:1:31.4:1:1:0:60:40.125:1:0:0.1 0/1:385:4:3,1:122,259:0.0104:2,2:18:1:25.8:1:0.10242:6.34:60:8:0.0107:0:1 -19 10600094 . AC A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.08104;SOR=Inf;LSEQ=CTGGGGGTCTGGCTTTGGGA;RSEQ=CCCAGCCATCACCTCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:50,144:0:2,0:22.7:1:31.2:1:1:0:60:193:1:0:0.1 0/1:149:3:2,1:36,110:0.0201:2,2:12.3:1:26.7:1:0.16005:6.02:60:6:0.0207:0.0067:0.3 -19 10600442 . G C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.36609;LSEQ=AAGCCCCCCACGGCATAAAG;RSEQ=AGACGATTGAGGACAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:739:477:225,252:123,137:0.6455:2,2:26.2:1:31.9:1:1:1.00554:60:58.625:0.6469:0:1.1 0/1:918:367:171,196:255,293:0.3998:2,2:24.5:1:31.7:1:1:1.00:60:90.75:0.3993:0:1.2 -19 10600615 . C CT 78 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.03983;SOR=0;LSEQ=GCCAGATACTCTTTTTTTTC;RSEQ=TTTTTTTTTTCCCCCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:0,6:1,60:0.0896:1,0:21.3:1:30.5:1:1:0:60:12:0.0909:0:0.3 0/0:48:0:0,0:1,47:0:1,0:17:0:12:0:1:0:60:0:0:0:1 -19 10600654 . G A 90 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0536;SOR=0.12276;LSEQ=AAGAGACAGGTTCATCCGGC;RSEQ=CGATGGCTCATGCCTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:0,8:0,15:0.3478:1,0:19.1:1:30:1:1:0:57.9:16:0.3478:0:1.1 0/1:17:1:0,1:0,16:0.0588:1,0:44:0:28:0:1:0:60:2:0.0667:0:1 -19 10600753 . A C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=GCCTGGCCAACATGGTAAAA;RSEQ=CCTGTCTCTACTAAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,3:0.3333:0,0:28.5:1:33:0:1:0:60:4:0.4:0:1.5 1/0:2:1:0,1:0,1:0.5:0,0:13:0:32:0:1:0:46:2:0.5:0:1 -19 10602180 . A C 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=0;LSEQ=GAAACAGCCTCAGGAAGAAT;RSEQ=CCCGGATCTCAGTGTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:139:121,18:0,0:1:0,2:24.9:1:31.1:1:1:0:60:26.8:1:0:1.2 1/1:116:104:86,18:7,5:0.8966:2,2:24.8:1:31:1:0.05961:3.37:60:208:0.8966:0:1.1 -19 10602767 . C T 79 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.76295;SOR=0.70603;LSEQ=CGTCAACGAGTGGCAGCGCA;RSEQ=GGCCCGCAGCAGCGCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:6:3,3:280,268:0.0108:2,2:26.3:1:30.8:1:1:1.04471:60:12:0.011:0:1.2 0/0:652:5:2,3:319,326:0.0077:2,2:22:1:27.2:1:1:1.46693:60:10:0.0077:0:1.2 -19 10602989 . T C 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13084;SOR=Inf;LSEQ=TCTCCAGTCACCCCCACACC;RSEQ=CACCAAGCAGGACCGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:46,172:0:2,0:22.7:1:29.5:1:1:0:60:23.222:1:0:0.1 0/1:266:4:2,2:78,182:0.015:2,2:18.8:1:30.8:1:0.58696:2.32:60:8:0.0156:0:1 -19 10603024 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50232;SOR=0;LSEQ=GGGACAAGTAACTTATCACT;RSEQ=CCGCTGACAGTCTCAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:8,125:0.0148:2,2:17:1:27:0:0.12935:14.79:60:4:0.015:0:2 0/0:112:0:0,0:11,101:0:2,0:28:0:15:0:1:0:60:0:0:0:2 -19 10603059 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14577;SOR=Inf;LSEQ=AGCTTCCTTATCTGCTAAAT;RSEQ=GGGATTCAAATAATAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:1,84:0:1,0:27.4:1:31.2:1:1:0:60:84:1:0:0.1 0/1:53:2:0,2:5,46:0.0377:2,0:26:1:29.5:1:1:0:60:4:0.0392:0:1 -19 10603115 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10476;SOR=Inf;LSEQ=GACTAAATGAGTTAATCCTG;RSEQ=CGGGCGCGGTGGCTCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,24:0:1,0:22.9:1:31.1:1:1:0:60:23:1:0:0 0/1:12:2:1,1:1,9:0.1667:2,2:31:1:29.5:1:0.31818:6.71:60:4:0.1667:0:1 -19 10610011 . G T 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62547;SOR=2.73025;LSEQ=TCAAGGGGAGACAGTGATGA;RSEQ=CACTCGTCCATCCCTGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:0,1:187,71:0.0039:2,0:1:0:15:0:0.27799:0:60:0:0:0:1 0/1:286:3:1,2:203,80:0.0105:2,2:12.7:1:23.7:1:0.19855:5.0416:60:2:0.007:0:1.3 -19 10610017 . G C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07154;LSEQ=GGAGACAGTGATGAGCACTC;RSEQ=TCCATCCCTGGTCCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:120:81,39:118,46:0.4225:2,2:22.1:1:30.3:1:0.43381:1.23417:60:23:0.4152:0:1.1 0/1:323:16:10,6:211,96:0.0495:2,2:20.6:1:30.4:1:0.59035:1.31762:60:32:0.0497:0:1.2 -19 10610236 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16694;LSEQ=TCGATCTGGTACATGACAGC;RSEQ=CCGTTCATGACGTGGAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:248:125,123:201,194:0.3857:2,2:24.8:1:30.4:1:0.93549:1.01948:60:34.429:0.3819:0:1.2 0/1:897:85:42,43:418,391:0.0948:2,2:26.9:1:30.8:1:0.73281:1.0944:60:84:0.0944:0:1.2 -19 10610644 . C T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12855;SOR=Inf;LSEQ=TCCCCTGCCCCCTCAGGGCA;RSEQ=TGTGACTGCAGGGGCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:94,162:0:2,0:24.7:1:31.9:1:1:0:60:63:1:0:0.1 0/1:301:4:2,2:122,174:0.0133:2,2:14.5:1:28.3:1:1:1.42:60:8:0.0134:0:1 -19 10610648 . G T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04535;SOR=0;LSEQ=CTGCCCCCTCAGGGCACTGT;RSEQ=ACTGCAGGGGCAGGAATCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:4:2,2:80,159:0.0164:2,2:29.8:1:28.3:1:0.60503:1.98:60:8:0.0167:0:1 0/0:283:0:0,0:114,168:0:2,0:23.9:1:31:1:1:0:60:69.5:0.9964:0:0.2 -19 10610657 . G A 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.62661;SOR=2.64476;LSEQ=CAGGGCACTGTGACTGCAGG;RSEQ=GCAGGAATCGGCAGCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:1,0:69,143:0.0047:2,0:1:0:26:0:0.32864:0:60:2:0.0048:0:1 0/1:243:3:3,0:89,151:0.0123:2,0:8:1:26.3:1:0.05317:0:60:6:0.0126:0:1 -19 10610681 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49939;SOR=Inf;LSEQ=GGAATCGGCAGCAGGCCCCA;RSEQ=CCCCGCTAGGCCTGGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:47,108:0:2,0:24:1:31.9:1:1:0:60:37.75:0.9934:0:0.1 0/1:170:2:1,1:54,114:0.0118:2,2:6:1:29:1:0.54368:2.10:60:4:0.0122:0:1 -19 10610682 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49893;SOR=Inf;LSEQ=GAATCGGCAGCAGGCCCCAG;RSEQ=CCCGCTAGGCCTGGGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:45,111:0:2,0:23.5:1:31.1:1:1:0:60:30.2:1:0:0.1 0/1:166:2:1,1:51,113:0.012:2,2:16.5:1:28.5:1:0.52968:2.20:60:4:0.0128:0:1.5 -19 10610759 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52301;SOR=0;LSEQ=CCTCTGGCACTCAGGGACCT;RSEQ=GAGGGGAGAGAGCACAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:7,54:0.0317:2,2:15.5:1:28:1:0.23963:7.28:60:4:0.0323:0:1 0/0:39:0:0,0:5,34:0:2,0:22.7:1:29.9:1:1:0:60:78:1:0:0.1 -19 11095896 . T C 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGCAGCGCATAGCTGCGC;RSEQ=GCCACCTCACGTTCCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:225,46:0:2,0:23.4:1:30.8:1:1:0:60:66.75:1:0:0.1 0/1:228:32:26,6:151,44:0.1404:2,2:24.7:1:29.3:1:0.81842:1.26:60:15:0.1333:0:1.1 -19 11096829 . C T 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06263;SOR=0;LSEQ=GTAAAAATCACAGACATATG;RSEQ=TGCCGAGTGACCAGTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:1,4:341,152:0.01:2,2:15.6:1:27.8:1:0.03534:8.93213:60:10:0.0102:0:1.2 0/0:464:0:0,0:301,163:0:2,0:24.7:1:31.8:1:1:0:60:76.333:1:0:0.2 -19 11096851 . A G 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGAGTGACCAGTGGGCTG;RSEQ=CCTTTCTCTGCAGGTTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:0:0,0:411,257:0:2,0:25.2:1:29.9:1:1:0:60:132.6:1:0:0.1 0/1:623:47:27,20:346,228:0.0754:2,2:24.7:1:31.1:1:0.7574:1.12389:60:46:0.0749:0:1.2 -19 11096912 . C G 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCATGCCTCTAGTCCAGTT;RSEQ=CAGCCAGTGGCCCGTCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:926:0:0,0:475,451:0:2,0:24.5:1:31:1:1:0:60:60.733:1:0:0.2 0/1:1009:62:30,32:483,464:0.0614:2,2:25.1:1:32.1:1:0.69656:1.11023:60:124:0.0624:0:1.2 -19 11097098 . C T 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCCAGGGGGCAGCCCCTC;RSEQ=CCGACCACCTGCAGATGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:698:0:0,0:318,379:0:2,0:24.4:1:30.9:1:1:0:60:115.167:1:0:0.1 0/1:678:21:7,14:294,362:0.031:2,2:18:1:27.9:1:0.3746:1.62319:60:9.5:0.0283:0:1.2 -19 11097205 . T C 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.13552;SOR=0;LSEQ=TCCGCAACAGGACCCGGCCC;RSEQ=GGCCCTGGCCCTGGCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:4:2,2:151,220:0.0107:2,2:12.5:1:28.8:1:1:1.46:60:8:0.0108:0:1 0/0:292:0:0,0:119,172:0:2,0:23.1:1:29.8:1:1:0:60:35.375:0.9965:0:0.2 -19 11097207 . G T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.08379;SOR=Inf;LSEQ=CGCAACAGGACCCGGCCCTG;RSEQ=CCCTGGCCCTGGCCCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:148,216:0:2,0:24.9:1:31.2:1:1:0:60:35.4:0.9972:0:0.1 0/1:285:3:1,2:116,165:0.0105:2,2:14.3:1:20.7:1:1:1.40444:60:2:0.0074:0:1 -19 11097450 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00628;SOR=Inf;LSEQ=AATGCTGCTTCCCCAGCTCC;RSEQ=CGCTTCCCCTGGGGCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:144,16:0:2,0:23:1:31.7:1:1:0:60:79:1:0:0.1 0/1:123:6:6,0:114,3:0.0488:1,0:15.8:1:32.5:1:1:0:60:12:0.0488:0:1.2 -19 11097509 . C T 51 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11329;SOR=5.35906;LSEQ=TGTGTCCCCTGGAGCCAGGG;RSEQ=TGCCCACGGGGCTGGGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:1:0,1:353,144:0.002:2,0:1:0:25:0:0.29116:0:60:2:0.002:0:1 0/1:468:5:2,3:315,147:0.0107:2,2:18:1:22.2:1:0.33378:3.20537:60:1.5:0.0065:0:1.2 -19 11097744 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19529;SOR=Inf;LSEQ=CATCTCAAGCTTGGGTCCTT;RSEQ=AGATGAGCTTTGTCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:18,191:0:2,0:24.1:1:31.4:1:1:0:60:103.5:1:0:0.1 0/1:166:2:1,1:29,135:0.012:2,2:32:1:28:1:0.32968:4.59:60:4:0.0123:0:1 -19 11098455 . G A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00664;SOR=0;LSEQ=TCCCACCCGCCGCCTCGCCC;RSEQ=TGATGCCACCGCAGACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:7:4,3:305,332:0.0109:2,2:17.6:1:25.6:1:0.71549:1.45:60:2.5:0.0079:0:1.7 0/0:671:0:0,0:315,353:0:2,0:1:0:15:0:1:0:60:0:0:0:1 -19 11098651 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.24845;SOR=Inf;LSEQ=TGCCCTGTGTCCCCCATGTC;RSEQ=CCCTGGGGAAGCCACTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:60,177:0:2,0:24.4:1:30.6:1:1:0:60:25.333:1:0:0.1 0/1:240:3:1,2:59,178:0.0125:2,2:9.7:1:27:1:1:1.51:60:6:0.0127:0:1.3 -19 11098666 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50018;SOR=0;LSEQ=ATGTCCCCCTGGGGAAGCCA;RSEQ=TCAACTTTCTCCCCCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:31,154:0.0107:2,2:33:1:30:0:0.31373:4.91:60:4:0.0109:0:1 0/0:167:0:0,0:28,139:0:2,0:23.2:1:32:1:1:0:60:82.5:1:0:0.1 -19 11098724 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54362;SOR=0;LSEQ=GCCCACCACTGCCACTTGGC;RSEQ=TACACCTCCTTCCTCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:3,67:0.0278:1,2:20.5:1:28:1:0.10876:19.49:60:4:0.0286:0:1 0/0:38:0:0,0:3,35:0:2,0:21.4:1:32.2:1:1:0:60:37:1:0:0.2 -19 11100147 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35559;SOR=3.25728;LSEQ=CTGGCATGGCCGCAGCTTTC;RSEQ=GAAAAGGGCCTTTGTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:1:1,0:68,242:0.0032:2,0:14:0:14:0:0.22186:0:60:0:0:0:7 0/1:288:3:2,1:80,203:0.0104:2,2:9.7:1:27:1:0.19855:5.04:60:6:0.0106:0:1.7 -19 11100224 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50815;SOR=0;LSEQ=CTAGTATTACACCTGCCTGG;RSEQ=CTGTGAAAAGCAGCCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:0,2:0,64:0.0303:1,0:36:1:32:0:1:0:60:4:0.0303:0:1 0/0:48:0:0,0:1,47:0:1,0:27.5:1:32.5:1:1:0:60:96:1:0:0.1 -19 11101993 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCGCAAGCGCCGGCAGAA;RSEQ=CACCAGGTACGCTCCGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:117,193:0:2,0:24:1:31.9:1:1:0:60:61:1:0:0.1 0/1:348:25:8,17:128,195:0.0718:2,2:23.7:1:29.6:1:0.52752:1.39358:60:50:0.0731:0:1.4 -19 11102076 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51591;SOR=0;LSEQ=CCAGCGGTTGCCACGGGGCT;RSEQ=TGTTTGCTTTGTTCCTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:9,94:0.019:2,2:16.5:1:26:1:0.18223:9.96:60:4:0.0194:0:1 0/0:71:0:0,0:7,64:0:2,0:22.7:1:31:1:1:0:60:142:1:0:0.1 -19 11105449 . G T 22 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.342;LSEQ=TTAAACAAGCCTTGCGGGGA;RSEQ=ATGTGTCCACCATGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:145,35:0.011:2,2:16:1:27.5:1:0.35736:4.09898:60:4:0.0111:0:1.5 0/1:136:2:0,2:102,32:0.0147:2,0:1:0:22.5:1:0.06111:0:60:4:0.0149:0:1 -19 11105468 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20235;SOR=Inf;LSEQ=AGATGTGTCCACCATGCTGC;RSEQ=GAAGGGTCAGCCTTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:182,62:0:2,0:25.1:1:31:1:1:0:60:121:1:0:0.1 0/1:200:2:1,1:139,59:0.01:2,2:34:1:29:1:0.51106:2.34463:60:4:0.0101:0:1 -19 11105593 . A G 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCAGAAGCTGACCAAGGC;RSEQ=GTGGCCACGTACCATGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:0:0,0:216,265:0:2,0:26.3:1:30.6:1:1:0:60:159.333:1:0:0.1 0/1:560:41:18,23:249,270:0.0732:2,2:23.2:1:28.9:1:0.63055:1.17805:60:12.667:0.0688:0:1.9 -19 11105608 . T C 230 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCAGTGGCCACGTACCA;RSEQ=GCCAACACGGAGCGGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:204,281:0:2,0:24.4:1:30.4:1:1:0:60:120.25:1:0:0.1 0/1:532:188:84,104:161,183:0.3534:2,2:25.7:1:30.5:1:0.65024:1.08908:60:187:0.3542:0:1.3 -19 11105714 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50065;SOR=Inf;LSEQ=TTGACGTGCGCTCTTCTACA;RSEQ=GTGTAGCTGGTACTGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:46,123:0:2,0:21:1:30.5:1:1:0:60:338:1:0:0.1 0/1:192:2:1,1:66,123:0.0104:2,2:30:1:27:1:1:1.86:60:4:0.0106:0:1 -19 11106790 . T C 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCACGGCACCCGCGTGAGC;RSEQ=ACGCGTGCCCTCAGTGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:116,3:0:1,0:24.2:1:31.4:1:1:0:60:118:1:0:0.2 1/0:69:38:38,0:31,0:0.5507:1,1:25:1:30.3:1:1:0:60:76:0.5507:0:1.1 -19 11106814 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17979;SOR=Inf;LSEQ=CGTGCCCTCAGTGCGCTTCT;RSEQ=GATTGACTGGCCATGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:185,14:0:2,0:23.2:1:32.1:1:1:0:60:48.75:1:0:0.1 0/1:147:2:1,1:129,16:0.0136:2,2:25.5:1:29:0:0.21862:7.85179:60:4:0.0137:0:1 -19 11107081 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09868;SOR=Inf;LSEQ=GCTGGGCCTGGCATGGTGCC;RSEQ=GCCGCGGGTGGGATGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:172,119:0:2,0:24.8:1:30.3:1:1:0:60:47.5:1:0:0.1 0/1:251:3:1,2:141,106:0.012:2,2:8.7:1:28:1:0.57979:2.65008:60:6:0.0123:0:1.7 -19 11107085 . G A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GGCCTGGCATGGTGCCCGCC;RSEQ=CGGGTGGGATGGGAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:186,105:0:2,0:25.5:1:30.2:1:1:0:60:35.375:0.9965:0:0.1 0/1:258:34:17,17:134,89:0.1318:2,2:25.3:1:29.9:1:0.26937:1.50313:60:68:0.1344:0:1.6 -19 11107133 . T C 232 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=352.21326;LSEQ=CGTGTGTGGCCTCAGCCTTG;RSEQ=GGGTCAGGGCCTGACCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:1:0,1:249,181:0.0023:2,0:36:0:28:0:0.42227:0:60:2:0.0023:0:1 0/1:432:195:105,90:137,98:0.4514:2,2:25.4:1:30.6:1:0.38012:1.19774:60:194:0.4543:0:1.3 -19 11107295 . G A 112 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00154;SOR=13.39726;LSEQ=TGTTTCAGACTTTAAAACCT;RSEQ=TGTTCTTTTAAAATTACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:1:1,0:30,146:0.0056:2,0:1:0:27:0:0.17514:0:60:2:0.0057:0:2 0/1:183:13:3,10:43,127:0.071:2,2:15.1:1:30.4:1:1:1.12788:60:26:0.071:0:1.1 -19 11107297 . G A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12071;SOR=0;LSEQ=TTTCAGACTTTAAAACCTGT;RSEQ=TTCTTTTAAAATTACGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:3:2,1:26,143:0.0174:2,2:5:1:26.7:1:0.06925:10.75:60:6:0.0176:0:1 0/0:175:0:0,0:41,134:0:2,0:20.4:1:31.1:1:1:0:60:350:1:0:0.2 -19 11111535 . CAAAAA C 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAGTCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:24.5:1:31:1:1:0:55:4:0.6667:0:0 -19 11113651 . T C 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCACCTTGGCCTCTGTAAG;RSEQ=GTTTGGTCTGGAGGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:223,77:0:2,0:22.1:1:29.9:1:1:0:60:99:1:0:0.1 0/1:319:45:31,14:190,84:0.1411:2,2:25:1:31.2:1:1:1.02145:60:90:0.142:0:1 -19 11113902 . G A 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGGCCTTGTTCCAGGGA;RSEQ=GTGGCAGCCAGGAGCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:123,138:0:2,0:22.9:1:31.1:1:1:0:60:42.5:1:0:0.1 0/1:200:40:20,20:69,91:0.2:2,2:21.7:1:29.5:1:0.47918:1.32:60:19:0.1949:0:1.1 -19 11113997 . G T 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=18.40394;LSEQ=CTGAGCAGATTTGTATGAAA;RSEQ=CCCTTACATTTTTTCTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:2:1,1:296,242:0.0037:2,2:17:1:29.5:1:1:1.22268:60:4:0.0038:0:1 0/1:577:37:24,13:312,227:0.0641:2,2:27.2:1:29.5:1:0.49148:1.34:60:74:0.0648:0:1 -19 11114206 . C T 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=CAGCAGGGCCCAGGCCTGCC;RSEQ=GAAGTCGGTGCTTTAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:1,75:0:1,0:24.2:1:30.2:1:1:0:60:75:1:0:0 0/1:41:8:1,7:0,33:0.1951:1,2:29.4:1:30.9:1:0.19512:0:60:16:0.1951:0:1 -19 11118575 . TAGG T 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.73085;SOR=0.69253;LSEQ=GACATGGGCTTGTCTCTTGG;RSEQ=AGGAGGAGGAAGAGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:5:4,1:256,96:0.014:2,2:29.4:1:30.6:1:1:1.50:60:10:0.0141:0:0.2 0/0:309:3:2,1:217,88:0.0097:2,2:9:1:27.3:1:1:1.23204:60:6:0.0099:0.0032:0.7 -19 11118711 . C T 164 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=19.58651;LSEQ=CATCATTGAGTAAGGGGTCC;RSEQ=GACACAGGTTGTTCTGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:2:1,1:281,379:0.003:2,2:21.5:1:15.5:1:1:1.35:60:0:0:0:2 0/1:732:41:17,24:308,381:0.056:2,2:24.2:1:30.7:1:0.74784:1.14106:60:82:0.0566:0:1.2 -19 11120937 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01823;SOR=Inf;LSEQ=CTGCACCTCTATGTGTCTTA;RSEQ=AGTGCTGGCCACAGGTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:108,3:0:1,0:27.4:1:32.6:1:1:0:60:222:1:0:0.1 0/1:66:4:3,1:62,0:0.0606:1,2:25.3:1:29.8:1:0.06061:0:60:8:0.0606:0:1 -19 11121234 . G A 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05303;SOR=7.08852;LSEQ=TAGGGGGTGGGGAGGCCACC;RSEQ=CCACGTAGCTGCCTCGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:1:1,0:155,322:0.0021:2,0:1:0:30:0:0.32636:0:60:2:0.0021:0:1 0/1:409:6:4,2:144,259:0.0147:2,2:8.7:1:26:1:0.19516:3.59:60:12:0.0147:0:1 -19 11123738 . C T 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCGCGCTCATCACGTACCT;RSEQ=ATGGAGCACAAACGCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:689:0:0,0:318,371:0:2,0:24.9:1:31.6:1:1:0:60:97.429:1:0:0.1 0/1:757:55:30,25:337,363:0.0727:2,2:22.7:1:28.6:1:0.40174:1.29:60:110:0.074:0:1.2 -19 11123859 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24489;SOR=Inf;LSEQ=GTTTGTTTCCTAAGTTTGCC;RSEQ=CAGTAGAATACCACAAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:20,152:0:2,0:24.6:1:32:1:1:0:60:85:1:0:0.1 0/1:169:2:1,1:27,140:0.0118:2,2:5:1:24.5:1:0.30473:5.11:60:4:0.0122:0:1 -19 11123888 . A G 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=TACCACAAACGAGGTGGCTT;RSEQ=ATTACAGAAATTTGTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:0,2:0,93:0.0211:1,0:15:1:25.5:1:1:0:60:4:0.0211:0:1 0/0:86:0:0,0:3,83:0:1,0:22.3:1:29.6:1:1:0:60:42:1:0:0.1 -19 11129429 . C G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54587;SOR=0.60392;LSEQ=TTTTCCCAGTGGCCTCCCTT;RSEQ=TGTCCTCTGAGGCAGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:23,0:11,0:0.6765:0,1:25.3:1:32.4:1:1:0:60:46:0.6765:0:1 1/0:18:10:9,1:6,2:0.5556:2,2:18.9:1:32.5:1:0.55882:2.82:60:20:0.5556:0:1.1 -19 11129600 . C T 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.69827;SOR=0.95015;LSEQ=GTGAGCCATTGATGAGAGAC;RSEQ=GGCACTTGACTCTCATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:153:92,61:286,207:0.2361:2,2:24.4:1:30.6:1:0.70727:1.09:60:75.5:0.2359:0:1.1 0/1:696:158:99,59:310,228:0.227:2,2:25.7:1:30.3:1:0.27116:1.23:60:157:0.2285:0:1.1 -19 11130114 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09684;SOR=Inf;LSEQ=GTGGTGAGGTCTGGGGACGC;RSEQ=CCAGCGGCCCTGCCAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:48,4:0:2,0:23:1:28.8:1:1:0:60:16.333:1:0:0.2 0/1:24:2:1,1:20,1:0.0833:1,2:34.5:1:29:1:0.16996:14.49116:60:4:0.087:0:1 -19 11130190 . AG A 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.19888;SOR=Inf;LSEQ=CCGTGTCACTGGGCAGTTGC;RSEQ=GGGGTGCCTGTGCCCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:168,14:0:2,0:22.5:1:31.8:1:1:0:59.9:29.333:1:0:0.1 0/1:147:2:1,1:129,16:0.0136:2,2:19:1:33:0:0.21862:7.85179:60:4:0.0138:0:0.5 -19 11130195 . G A 82 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.013;SOR=9.9744;LSEQ=TCACTGGGCAGTTGCAGGGG;RSEQ=TGCCTGTGCCCCTCTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:1,0:173,20:0.0052:2,0:44:0:13:0:1:0:60:0:0:0:1 0/1:162:8:7,1:135,19:0.0494:2,2:25.5:1:27.5:1:1:1.01494:60:7:0.044:0:1.1 -19 11130431 . G A 210 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00549;LSEQ=GGCCGAGTGCTCACACGTGG;RSEQ=TCACGCTGCCCGTCTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:115:30,85:82,213:0.2805:2,2:24.1:1:30.7:1:0.8054:1.09056:60:114:0.2808:0:1.1 0/0:470:1:1,0:143,326:0.0021:2,0:1:0:24:0:0.30638:0:60:2:0.0022:0:1 -19 11130477 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=CCCTACAAGTTTCTTCCCGG;RSEQ=GTCCCACCTGCATGTGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:4,140:0:1,0:25.6:1:31:1:1:0:60:27.8:1:0:0.4 0/1:153:2:0,2:5,146:0.0131:1,0:32.5:1:32:0:1:0:60:4:0.0133:0:1 -19 11132080 . G A 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTCTTCTGCCAGAACGT;RSEQ=CTCGGCATTTTTCTGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:114,4:0:1,0:23.5:1:32:1:1:0:60:58:1:0:0.1 0/1:92:27:26,1:65,0:0.2935:1,1:23.6:1:28.6:1:0.29348:0:60:54:0.2967:0:1 -19 11132244 . G A 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.79995;LSEQ=GTGTGGCTCCAACTCGGTGA;RSEQ=TCAGCCCCGGGGCAGGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:744:2:2,0:382,359:0.0027:2,0:25.5:1:20:1:0.49989:0:60:1:0.0014:0:2.5 0/1:715:38:18,20:330,347:0.0531:2,2:25.3:1:30.3:1:1:1.05662:60:76:0.0538:0:1.1 -19 11132315 . G A 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCCACCTGGAGCCTTCCTG;RSEQ=CTGCTGGGCGCAGAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:707:0:0,0:358,348:0:2,0:23.9:1:31.4:1:1:0:60:77.444:0.9986:0:0.1 0/1:654:58:32,26:324,270:0.0887:2,2:26.1:1:28:1:1:1.03:60:28:0.0871:0:1.2 -19 11132687 . G A 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71174;SOR=0.65999;LSEQ=TGCTGACGGTTCCAGGTGCG;RSEQ=CTGGCTTTGCTGGTTGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:3,1:129,258:0.0102:2,2:15.3:1:27.8:1:0.11379:5.97:60:8:0.0104:0:1 0/0:443:3:2,1:162,278:0.0068:2,2:17:1:28:1:0.55807:3.42:60:6:0.0069:0:1 -19 11134090 . A G 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAAGGGCAAGATCACCCC;RSEQ=GGGGACCCCGTCCACCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:141,1:0:1,0:27.9:1:30.3:1:1:0:60:46.333:1:0:0.1 0/1:96:20:19,1:73,3:0.2083:1,1:23.7:1:27.6:1:1:1.27719:60:19:0.2021:0:1.3 -19 11134270 . G A 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19041;SOR=3.00568;LSEQ=GCGGCCCTTCTTGCTCCGAC;RSEQ=ACTCAAGAAGGAAGTCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:2:2,0:243,338:0.0034:2,0:1:0:27.5:1:0.17618:0:60:4:0.0035:0:1 0/1:683:7:6,1:293,382:0.0102:2,2:7.6:1:26.9:1:0.04756:7.80:60:14:0.0104:0:1 -19 11134301 . C T 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTCGAGGCCCAGTTGCC;RSEQ=GAAAAGGTGATGGAGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:160,250:0:2,0:24.7:1:29.9:1:1:0:60:67.333:0.9975:0:0.1 0/1:476:37:12,25:162,275:0.0777:2,2:24.1:1:29.1:1:0.72278:1.22673:60:11.333:0.0734:0:1.4 -19 11135163 . C A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07602;SOR=Inf;LSEQ=CCCCACTGGGTGTCCAAGGC;RSEQ=GGCAGCGTGGCAGGCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:41,159:0:2,0:24.1:1:30:1:1:0:60:99:1:0:0.1 0/1:148:3:2,1:37,108:0.0203:2,2:20.3:1:30.3:1:0.16983:5.75:60:6:0.0204:0:1.3 -19 11135164 . G A 25 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68735;LSEQ=CCCACTGGGTGTCCAAGGCC;RSEQ=GCAGCGTGGCAGGCAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:40,155:0.0102:2,2:12.5:1:25.5:1:0.37377:3.84:60:4:0.0103:0:1 0/0:143:1:1,0:37,105:0.007:2,0:1:0:26:0:0.26573:0:60:2:0.0071:0:1 -19 11136006 . A C 170 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00739;SOR=0.45714;LSEQ=TTCCCCACTAGAGCGTCCCC;RSEQ=TGGCCCTTCTCCCAACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:48:43,5:190,20:0.1853:2,2:22.4:1:30.6:1:0.791:1.10423:60:47:0.185:0:1.2 0/1:202:19:17,2:153,29:0.0941:2,2:26.4:1:29.9:1:0.74373:1.61:60:38:0.0955:0:1.3 -19 11136215 . C G 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74373;SOR=1.06655;LSEQ=CGCGGCTGGGACGGCTCAGG;RSEQ=CCTGCTGTCTGCTGAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:105:28,77:56,185:0.3035:2,2:24.3:1:31.1:1:0.49805:1.20:60:34:0.3036:0:1.1 0/1:353:112:33,79:79,160:0.3173:2,2:22.7:1:30.2:1:0.54045:1.18145:60:15:0.3088:0:1.1 -19 11136315 . C T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.64409;SOR=0.72094;LSEQ=GGTAATGCCTGTACATCTGT;RSEQ=TCTCATTTGGTCTTCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:16:0,16:1,45:0.2581:1,1:25.2:1:30.2:1:1:0:60:32:0.2581:0:1 0/1:45:9:0,9:1,35:0.2:1,0:15.3:1:29.3:1:1:0:60:8:0.1818:0:1 -19 11136857 . C T 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=TCTCAGAGCCGCCGTGGGCC;RSEQ=GTGCCGAGCACACAGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:116,6:0:1,0:21.5:1:31:1:1:0:60:121:1:0:0.1 0/1:78:8:8,0:66,4:0.1026:2,0:26.8:1:31.1:1:1:0:60:16:0.1053:0:1.1 -19 11137135 . T C 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAATTTCAAAGGCAGAAAAT;RSEQ=AGAAAATACAGAAGAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:7,171:0:1,0:27.1:1:28:1:1:0:59.6:58.333:1:0:0.5 0/1:158:26:3,23:8,124:0.1646:2,2:22.5:1:30.5:1:0.39141:2.01:60:7.667:0.1503:0:1.5 -19 11138292 . A G 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00107;SOR=0;LSEQ=GCTTATTTCAGTTGGGGGAA;RSEQ=TGGCTTTGCTGAAGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:19:19,0:24,0:0.4419:1,1:22.1:1:33.1:1:1:0:60:38:0.4524:0:1.1 0/0:15:0:0,0:13,2:0:2,0:19.5:1:29.2:1:1:0:60:14:1:0:0.4 -19 11141724 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50619;SOR=0;LSEQ=CCCATATCTCCATAGGTCAT;RSEQ=AGGGAGAAAAGAGGCGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:1,84:0.023:1,2:25:1:28:1:0.04571:59.74:60:4:0.0238:0:1 0/0:66:0:0,0:6,60:0:2,0:20.9:1:30.4:1:1:0:60:15.5:1:0:0.1 -19 11143811 . C G 113 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15518;SOR=0.17968;LSEQ=CATGGCGGCCCAGGCTCCAC;RSEQ=AGCTCTGTTTTCATGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:14:14,0:30,1:0.3043:1,1:31.5:1:29.7:1:1:0:60:28:0.3043:0:1.1 0/1:14:1:1,0:12,1:0.0714:1,0:43:0:28:0:1:0:60:2:0.0714:0:1 -19 11143895 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16134;SOR=Inf;LSEQ=ACAGCACACCTCTCCAGCTA;RSEQ=TGTCAGAGGCCACCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:145,33:0:2,0:24:1:31.8:1:1:0:60:177:1:0:0.1 0/1:120:2:1,1:88,30:0.0167:2,2:21.5:1:29:1:0.45154:2.90217:60:4:0.0172:0:1.5 -19 11143914 . CT C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.19514;SOR=Inf;LSEQ=AGTGTCAGAGGCCACCTTCC;RSEQ=TTTATGACCTCCTGGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:175,67:0:2,0:25.9:1:30.6:1:1:0:60:120:1:0:0.1 0/1:192:2:2,0:137,53:0.0104:2,0:25:1:28:1:1:0:60:4:0.0107:0.0052:0.5 -19 11144243 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19695;SOR=Inf;LSEQ=CCAGCGTGAATGGTGGACGC;RSEQ=TGAGCGGCTTTCATTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:42,193:0:2,0:23.9:1:31.6:1:1:0:60:46:1:0:0.1 0/1:188:2:1,1:32,154:0.0106:2,2:15:1:29.5:1:0.32103:4.75:60:4:0.0107:0:1 -19 11144287 . AT A 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.07859;SOR=0;LSEQ=TTTACCTTTTTTGCACTCTT;RSEQ=TTTTTTTGCATCCCTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:5:4,1:64,74:0.035:2,2:31:1:32:1:0.19117:4.58:60:10:0.0355:0:0 0/0:101:0:0,0:47,54:0:2,0:20.9:1:30.1:1:1:0:60:100:1:0:0.2 -19 11144367 . G GT 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08185;SOR=0.43562;LSEQ=CTTGCTTTTTCTTTGAAGTG;RSEQ=TTTTTTTTTCTAAACTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:15:9,6:181,66:0.0573:2,2:17.8:1:29.4:1:0.36993:1.82353:59.7:30:0.0579:0.0229:0.1 0/1:272:7:4,3:180,83:0.0257:2,2:21:1:22.9:1:0.68309:1.62338:60:2.5:0.0188:0.0037:0.7 -19 11144610 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12419;SOR=Inf;LSEQ=GGCTGAGACGGCCAGCAAGG;RSEQ=CCCTGGTCCCACGGAGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:116,229:0:2,0:22.7:1:31.5:1:1:0:60:42.125:1:0:0.1 0/1:358:4:3,1:132,221:0.0112:2,2:12.5:1:25:1:0.15365:5.00:60:8:0.0116:0:1.3 -19 11144616 . G T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1238;SOR=Inf;LSEQ=GACGGCCAGCAAGGGCCCTG;RSEQ=TCCCACGGAGCGTGCGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:99,210:0:2,0:21.8:1:31.7:1:1:0:60:153.5:1:0:0.1 0/1:311:4:2,2:105,202:0.0129:2,2:15.8:1:28.8:1:0.6098:1.92:60:8:0.0132:0:1.3 -19 11144928 . C A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62339;SOR=0.34044;LSEQ=GGCATCCCACTCTGCTGCCA;RSEQ=CAGGAGCAAAGCAGACGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:1,2:47,166:0.0138:2,2:30.3:1:27.3:1:0.53137:1.76:60:6:0.0143:0:2.7 0/0:211:1:1,0:44,166:0.0047:2,0:1:0:28:0:0.21327:0:60:2:0.0048:0:1 -19 11144945 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24105;SOR=Inf;LSEQ=CCACCAGGAGCAAAGCAGAC;RSEQ=TCCTAGTGCCCATGGTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:20,135:0:2,0:25.3:1:31.7:1:1:0:60:76.5:1:0:0.2 0/1:150:2:1,1:21,126:0.0133:2,2:20:1:32:0:0.27435:5.89:60:4:0.0133:0:1 -19 11145547 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18144;SOR=Inf;LSEQ=GGCTCTAGCGTGCCCCTGGT;RSEQ=CCTGCATGCTGATGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:154,34:0:2,0:24.2:1:31.8:1:1:0:60:61.667:1:0:0.1 0/1:140:2:1,1:109,29:0.0143:2,2:21:0:27.5:1:0.38386:3.71257:60:4:0.0145:0:1.5 -19 11145691 . C T 167 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=16.19534;LSEQ=TCGTGGATCATCAAGGACGA;RSEQ=GCGGAGGTGGAGCGGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:692:3:0,3:375,313:0.0043:2,0:1:0:27.3:1:0.09514:0:60:6:0.0044:0:1 0/1:819:54:29,25:414,351:0.0659:2,2:21.7:1:29.1:1:1:1.01678:60:108:0.0666:0:1.2 -19 11145715 . TGAG T 133 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.02741;SOR=2.80593;LSEQ=GAGGTGGAGCGGCTGACCTG;RSEQ=GAGGAGGAGGAGAAGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:743:6:4,2:380,355:0.0081:2,2:24.8:1:30.7:1:0.68748:1.87:60:12:0.0082:0.0027:0.2 0/1:895:20:10,10:441,429:0.0223:2,2:25.4:1:31:1:1:1.02795:60:40:0.0227:0.0045:0.2 -19 11145842 . G A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20507;SOR=4.25933;LSEQ=AGGCCCAGCAGCTGCCGCAG;RSEQ=CCAGCGCCAGGCAGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:1:1,0:77,241:0.0031:2,0:1:0:25:0:0.24451:0:60:2:0.0032:0:1 0/1:302:4:2,2:82,216:0.0132:2,2:20.3:1:29.5:1:0.30951:2.62:60:8:0.0133:0:1.3 -19 11145848 . G A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34718;SOR=3.38886;LSEQ=AGCAGCTGCCGCAGGCCAGC;RSEQ=CCAGGCAGGGCTGGGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:1:0,1:55,228:0.0035:2,0:36:0:31:0:1:0:60:2:0.0035:0:1 0/1:253:3:2,1:61,189:0.0119:2,2:28.3:1:21:1:0.15402:6.14:60:2:0.0081:0:1 -19 11145853 . G A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCCGCAGGCCAGCGCCAG;RSEQ=CAGGGCTGGGGAGACAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:49,221:0:2,0:23.2:1:31.7:1:1:0:60:53:1:0:0.1 0/1:233:16:4,12:52,165:0.0687:2,2:28.1:1:29.6:1:1:1.06:60:32:0.069:0:1.1 -19 11150013 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14589;SOR=Inf;LSEQ=GCACTCCAGCCTGGGCGACA;RSEQ=AATGAGACCCTGTCTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:71,1:0:1,0:22.4:1:32.6:1:1:0:60:71:1:0:0.1 0/1:45:2:2,0:42,1:0.0444:1,0:21:1:33:0:1:0:60:4:0.0455:0:1 -19 11150067 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25038;SOR=Inf;LSEQ=ACCTAAATGCCCAAGAACAA;RSEQ=GGGAGGCTAAATTAGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:155,50:0:2,0:24.9:1:31.5:1:1:0:60:67.333:1:0:0.1 0/1:228:3:1,2:164,61:0.0132:2,2:20.7:1:27:1:0.18567:5.33021:60:6:0.0135:0:1 -19 11150265 . C T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0945;SOR=0;LSEQ=GTGGTGGGTGGCGCTGAGGG;RSEQ=TGCACAACACTGGGGACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:3:1,2:74,185:0.0115:2,2:19:1:23.7:1:1:1.25:60:2:0.0078:0:2 0/0:312:0:0,0:92,220:0:2,0:23.6:1:31.7:1:1:0:60:311:1:0:0.1 -19 11151997 . C A 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04337;SOR=0;LSEQ=CTGAAGGCCATCGAGGAGGG;RSEQ=ACGCTGGAGGAGATCGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:4:2,2:189,130:0.0124:2,2:11.3:1:30.8:1:1:1.45209:60:8:0.0125:0:1 0/0:383:0:0,0:228,154:0:2,0:24.9:1:31.6:1:1:0:60:62.667:1:0:0.1 -19 11152282 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49914;SOR=0;LSEQ=GGGCTGTAGGGGTCCCCGTG;RSEQ=GAGCAGGCCTGGCATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:23,139:0.0122:2,2:12.5:1:30.5:1:0.27203:5.94:60:4:0.0124:0:1 0/0:152:0:0,0:33,119:0:2,0:23.4:1:29.7:1:1:0:60:24.333:1:0:0.1 -19 11167071 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAAGGGTATGTGCTCCC;RSEQ=TGCTGGACCGGCTGGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:32.5:1:1:0:60:4:1:0:1.5 -19 11168798 . G A 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00076;SOR=Inf;LSEQ=GTCTCAAAAAAAAAAAAAGC;RSEQ=CATGTGCAAGAAATAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:49,1:0:1,0:20.7:1:26.5:1:1:0:59.1:6.143:1:0:0.6 0/1:31:7:7,0:23,0:0.2258:1,0:19:1:27:1:1:0:59.7:6:0.2222:0:1.3 -19 11168896 . A G 213 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGGCTCCCGGGTGGGCGG;RSEQ=CTCGGGGGTGATAGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:201,88:0:2,0:24.1:1:29.3:1:1:0:60:56.8:1:0:0.1 0/1:332:140:95,45:133,59:0.4217:2,2:25.5:1:30:1:0.81127:1.06758:60:19:0.4118:0:1.2 -19 11169305 . T C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.07935;LSEQ=GCTGGGCCTCAGTCATGCAG;RSEQ=TCCCATGCCTAGTGAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:30:26,4:37,11:0.3846:2,2:26.9:1:32.3:1:0.38274:1.92:60:60:0.3846:0:1.4 0/1:43:2:2,0:36,4:0.0465:2,0:21.5:1:27:1:1:0:60:4:0.0476:0:1 -19 11169401 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06396;SOR=Inf;LSEQ=GTGGGGTCTCCAGCACACAG;RSEQ=CAGGCCTGCGGGCAGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:239,90:0:2,0:24.2:1:31.5:1:1:0:60:64.8:1:0:0.1 0/1:372:5:1,4:256,111:0.0134:2,2:5:1:25.4:1:0.0334:9.16678:60:10:0.0136:0:1 -19 11169514 . C T 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAACGACCTAGAGAAGGA;RSEQ=GTCATGCTCCTGTGCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:0:0,0:440,442:0:2,0:24.9:1:30.7:1:1:0:60:62:1:0:0.1 0/1:973:29:14,15:452,491:0.0298:2,2:25.6:1:29.8:1:1:1.01:60:28:0.0289:0:1.4 -19 11169785 . TA T 49 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATAACAAGACCCTGTCTT;RSEQ=AAAAAAAAAAAGAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:0,3:1,17:0.1364:1,0:26.7:1:31.3:1:1:0:60:6:0.1364:0.0455:1 0/0:2:0:0,0:0,2:0:0,0:26:1:32:0:1:0:60:4:1:0:0 -19 11170589 . G A 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05126;SOR=Inf;LSEQ=CCGGGGGGGTTCAGGACGCC;RSEQ=GGGTTCACGCTGGCCCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:133,111:0:2,0:26:1:29.9:1:1:0:60:39.667:1:0:0.2 0/1:223:4:2,2:114,104:0.0179:2,2:13:1:32.5:1:1:1.0957:60:8:0.0186:0:1.5 -19 11170839 . T C 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCCGGTCGTGAGTGACGA;RSEQ=GACAGTGAGGAGGAACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:81,190:0:2,0:26.4:1:29.8:1:1:0:60:29.111:1:0:0.2 0/1:283:71:24,47:71,140:0.2509:2,2:25:1:29.5:1:1:1.01:60:34.5:0.2509:0:1.1 -19 11170909 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20201;SOR=Inf;LSEQ=GAGCTGGCATGTGGCAGGAG;RSEQ=CATCCCGGGGCCCTGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:17,111:0:2,0:24.7:1:32.2:1:1:0:60:63:1:0:0.1 0/1:105:2:1,1:19,84:0.019:2,2:28:1:30.5:1:0.34615:4.33:60:4:0.0196:0:1 -19 11170916 . G C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08482;SOR=Inf;LSEQ=CATGTGGCAGGAGGCATCCC;RSEQ=GGGCCCTGATGGGACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:13,98:0:2,0:24.4:1:30.4:1:1:0:60:21.2:1:0:0.1 0/1:88:3:1,2:12,73:0.0341:2,2:28.7:1:31.7:1:0.38466:2.99:60:6:0.0345:0:1 -19 11172299 . G A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=CCTGACCTCGTGATCCGCCC;RSEQ=CCTTGGCCTTCCAAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:55,0:0:1,0:23.9:1:30.2:1:1:0:55.3:110:1:0:0.1 0/1:49:10:10,0:38,1:0.2041:1,0:24.5:1:31.8:1:1:0:60:20:0.2041:0:1 -19 11172439 . C T 79 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.02795;SOR=0.12147;LSEQ=GGGTGGCCAACGCACACTCT;RSEQ=TCCTCCTGTCCCCTCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:7:3,4:373,241:0.0113:2,2:21.6:1:28.3:1:0.4427:2.06117:60:14:0.0114:0:1.1 0/0:724:1:0,1:423,300:0.0014:2,0:1:0:25:0:0.41575:0:60:2:0.0014:0:1 -19 11446366 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50988;SOR=0;LSEQ=CTGCACAGCGGCAAAGGATT;RSEQ=CTGATTGGCGATGTCATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:90,13:0.0189:2,2:20.5:1:30.5:1:0.25:6.70931:60:4:0.0192:0:1 0/0:77:0:0,0:62,15:0:2,0:18.1:1:30.5:1:1:0:59.7:76:1:0:0.1 -19 11446520 . T G 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11611;SOR=1.67958;LSEQ=TTCCCAGTCCACCCCTGTCT;RSEQ=AGAGGGGCACTGCCCTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:21:3,18:4,61:0.2442:2,2:22.6:1:32.1:1:0.35436:2.51:60:42:0.2471:0:1.1 0/1:105:37:6,31:14,53:0.3524:2,2:22.8:1:30.5:1:0.61422:1.36082:60:17.5:0.3431:0:1.2 -19 12984252 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55751;SOR=2.97834;LSEQ=TCCAGCGATAGTCTCCCGGG;RSEQ=TCGCCTACGCACGGGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:13,4:0.0556:2,0:1:0:25:0:0.27778:0:60:2:0.0588:0:1 0/1:13:2:1,1:8,3:0.1538:2,2:25:1:28:1:1:2.4495:60:4:0.1667:0:1 -19 12984358 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19886;SOR=0;LSEQ=GCACCTGCGCGGGGACCGAG;RSEQ=AGCGCGGGGTGGCCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:3,10:0.1333:2,2:29:1:30:1:0.47619:3.03:60:4:0.1429:0:1 0/0:18:0:0,0:5,13:0:2,0:25.4:1:30.7:1:1:0:60:17:1:0:0.5 -19 13049423 . G T 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.31546;SOR=4.13927;LSEQ=CAAGGCGGGCGGCGGCGTCC;RSEQ=TCCGTACTGCAGAGCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:1:1,0:306,48:0.0028:2,0:31:0:28:0:1:0:60:2:0.0029:0:1 0/1:259:3:0,3:200,55:0.0116:2,0:12.3:1:25:0:0.01091:0:60:6:0.0118:0:1 -19 13049895 . T TG 95 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10856;SOR=0.25962;LSEQ=CTCTCGGCAGATGTTTGGTG;RSEQ=GGGGGGGGATTAGCACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:8:6,2:371,102:0.0166:2,2:15.3:1:31.7:1:0.68491:1.21191:59.4:16:0.0168:0.0083:0.3 0/0:460:2:1,1:353,105:0.0043:2,2:14.5:1:25.5:1:0.40816:3.3507:60:4:0.0044:0:0 -19 13050526 . AT A 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19029;SOR=4.60721;LSEQ=CATTGACTTTCTTAATAATG;RSEQ=TTTTTTTGGAAGGGGAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:1:0,1:56,288:0.0029:2,0:47:0:30:0:1:0:60:2:0.0029:0:1 0/1:302:4:0,4:61,237:0.0132:2,0:36.8:1:30.8:1:0.58633:0:60:8:0.0134:0:0 -19 13050675 . AT A 86 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.50874;SOR=1.66653;LSEQ=TTTTGAGTTCTAGAGCACTG;RSEQ=TTTTTTTTTTTCTCCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:7:5,2:42,19:0.1029:2,2:21:1:30.8:1:1:1.13:60:14:0.1045:0.0294:0.9 0/1:31:5:5,0:18,6:0.1613:2,0:29.4:1:29.3:1:0.55261:0:60:10:0.1613:0.0323:0 -19 13051554 . G T 261 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00312;LSEQ=TCGGTTTCCTTCTCCCTTCT;RSEQ=CAGGGTGAGTGGAAGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1333:418:204,214:448,467:0.3136:2,2:23.5:1:30:1:1:1.00634:60:51.25:0.3123:0:1.1 0/0:1401:2:0,2:733,660:0.0014:2,0:1:0:27.5:1:0.22502:0:60:4:0.0014:0:1 -19 13052115 . AT A 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTATCTCTACAAAAAAA;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:13.5:1:32:1:1:0:60:4:0.4:0.2:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 13054649 . TGAGGATGAG T 224 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGATGATGAGGACAAAGA;RSEQ=GAGGATGAGGAGGACAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1738:0:0,0:863,870:0:2,0:25.4:1:31.8:1:1:0:60:77.773:0.9971:0:0.2 0/1:2067:141:67,74:957,965:0.0682:2,2:26.8:1:31.4:1:0.66278:1.09526:59.9:282:0.0689:0.0106:0.2 -19 13054781 . G T 261 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00363;LSEQ=AGCGCTCCTGCCGCAGAGCT;RSEQ=GCCGCGCCAAATAATGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:390:388:34,354:0,1:0.9949:0,2:24.1:1:30.4:1:1:0:60:193:0.9948:0:1.1 0/1:360:148:18,130:37,175:0.4111:2,2:21.9:1:29.8:1:0.18319:1.52524:60:147:0.4118:0:1.1 -19 13056829 . G T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGATCCGCATGGAGCCTGAC;RSEQ=AGACGGTGCGGGCCGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30:1:1:0:60:4:1:0:2 -19 13519178 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.24144;LSEQ=TGGGCAACAGAGTGAGACCC;RSEQ=GTTTCAAAAATATATATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:39:29,10:61,6:0.3645:2,2:19.7:1:30.2:1:0.02648:3.46057:60:78:0.3645:0:1.1 0/1:91:11:9,2:61,19:0.1209:2,2:20.2:1:30.9:1:1:1.40:60:22:0.1209:0:1.1 -19 13519199 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4986;SOR=Inf;LSEQ=GTTTCAAAAATATATATGTG;RSEQ=TGAAACAAAAGAACTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:125,44:0:2,0:21.6:1:31.4:1:1:0:60:168:1:0:0.3 0/1:173:2:1,1:124,47:0.0116:2,2:20:1:28:1:0.4791:2.62118:60:4:0.0116:0:1 -19 13519205 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23549;SOR=0;LSEQ=AAAATATATATGTGGTGAAA;RSEQ=AAAAGAACTAATGAATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:136,51:0.0105:2,2:23.5:1:31.5:1:0.47563:2.6506:60:4:0.0107:0:1.5 0/0:201:0:0,0:143,58:0:2,0:20.9:1:30.8:1:1:0:60:200:1:0:0.2 -19 13519258 . A G 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATACTTTGAGCAGGGTAT;RSEQ=AGGAACCTGGGTAAGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:0:0,0:252,178:0:2,0:26:1:29:1:1:0:60:214:1:0:0.4 0/1:470:33:19,14:240,197:0.0702:2,2:27.8:1:31.9:1:0.85678:1.11:60:66:0.0707:0:1.2 -19 13519303 . C T 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00099;SOR=0.60861;LSEQ=TTCCAAGATCTTCAAAGGTA;RSEQ=CTTTCTAGGCACTAAGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:142:71,71:143,150:0.3257:2,2:25.1:1:30.4:1:0.83841:1.05:60:284:0.3272:0:1.1 0/1:458:104:50,54:160,193:0.2271:2,2:26.7:1:29.4:1:0.65504:1.12:60:103:0.2289:0:1.1 -19 14581049 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22938;SOR=Inf;LSEQ=CCCCTGAGGTGCTGACGGAC;RSEQ=CGTCGTACACGCGAGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:26.3:1:29.6:1:1:0:60:30:1:0:0.1 0/1:29:2:1,1:11,15:0.069:2,2:39.5:1:28:1:1:1.35:60:4:0.0714:0:1 -19 14627050 . G A 309 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01045;LSEQ=TCAGCTCTTGCCCAGAGGCC;RSEQ=TCTGCCATAGATAAGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1145:1141:580,561:0,0:0.9965:0,2:24.7:1:30.5:1:1:0:60:125.778:0.9982:0:1.2 1/0:1296:970:514,456:169,156:0.7485:2,2:24.8:1:29.9:1:0.7974:1.04:60:106.778:0.7484:0:1.2 -19 14627093 . T C 239 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=270.19005;LSEQ=AGGCCTCTGCAGCTAAGACC;RSEQ=GGCCCCCAAATCTACACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1360:1:0,1:746,612:7e-04:2,0:1:0:31:0:0.45107:0:60:2:7e-04:0:2 0/1:1649:275:161,114:736,637:0.1668:2,2:24:1:29.5:1:0.14454:1.22:60:33.375:0.1646:0:1.6 -19 14627140 . C T 263 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00127;LSEQ=ACGAAAGCTCCACAACAGCG;RSEQ=CCTGGTCAGTCCTGTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1567:464:243,221:588,513:0.2961:2,2:23:1:29.8:1:0.73938:1.04242:60:153.667:0.2986:0:1.2 0/0:1895:1:1,0:978,915:5e-04:2,0:2:0:27:0:1:0:60:2:5e-04:0:1 -19 14627215 . T C 224 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=125.05335;LSEQ=CAACACATTGGTTCAGCAAA;RSEQ=ACTAAACTGCTTCAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1632:1:0,1:782,848:6e-04:2,0:27:0:34:0:1:0:60:2:6e-04:0:1 0/1:1979:141:70,71:899,935:0.0712:2,2:23.3:1:31.5:1:0.93041:1.03:60:46:0.0706:0:1.2 -19 14628083 . G A 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=37.06591;LSEQ=AGTGGAAAAGGACTCATGCG;RSEQ=TTAGGTGTTCACCTCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1417:2:1,1:748,667:0.0014:2,2:38.5:1:30:1:1:1.12135:60:4:0.0014:0:1 0/1:1586:79:43,36:790,717:0.0498:2,2:20.5:1:29:1:0.81738:1.08:60:38.5:0.0492:0:1.3 -19 14628242 . G A 312 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0601;LSEQ=GGGCTAATGGTGCGTAGGAA;RSEQ=AGAAGAAAAAAAAAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1456:1303:648,655:72,74:0.8949:2,2:23.5:1:30.2:1:0.9307:1.02:60:117.455:0.9016:0:1.3 0/1:1779:602:305,297:580,591:0.3384:2,2:23.4:1:29.5:1:0.65214:1.05:59.9:65.889:0.348:0:1.3 -19 14628247 . G GA 213 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.29166;SOR=0.87513;LSEQ=AATGGTGCGTAGGAAGAGAA;RSEQ=AAAAAAAAAAACAAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1412:138:64,74:654,587:0.0977:2,2:28.5:1:29.9:1:0.1779:1.28798:59.9:137:0.1034:0:1.4 0/1:1744:151:71,80:801,752:0.0866:2,2:29.4:1:29.5:1:0.30655:1.20005:60:302:0.0924:0:0.8 -19 14628259 . C A 195 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=5.98472;LSEQ=GAAGAGAAGAAAAAAAAAAA;RSEQ=AAAAATAAATAGGGAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1519:19:19,0:786,712:0.0125:2,1:16.3:1:16.9:1:1e-05:0:56.8:0.583:0.005:0:3.4 0/1:1759:124:73,51:824,793:0.0705:2,2:22.8:1:28.1:1:0.09385:1.38:59.8:7.857:0.0667:0:2.1 -19 14628261 . A T 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGAAGAAAAAAAAAAACA;RSEQ=AAATAAATAGGGAGTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1520:0:0,0:814,705:0:2,0:21.4:1:30.1:1:1:0:59.9:115.846:0.9993:0:1 0/1:1757:83:45,38:851,802:0.0472:2,2:24.2:1:28:1:0.65383:1.12:59.9:19.75:0.0456:0:2.1 -19 14628524 . C T 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03676;SOR=1.43372;LSEQ=CCCAAGCCCACGAACGGGGT;RSEQ=GGCTCCTGCATTCACAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:839:63:23,40:259,517:0.0751:2,2:23.1:1:28.9:1:0.67759:1.15:60:20:0.0729:0:1.2 0/1:911:95:34,61:308,504:0.1043:2,2:26.4:1:29.3:1:0.73777:1.09632:60:94:0.105:0:1.1 -19 14628541 . A G 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTCGGCTCCTGCATTCACA;RSEQ=CCCCTCGCCCCGCAGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:681:0:0,0:211,468:0:2,0:25.2:1:29:1:1:0:60:28.522:1:0:0.3 0/1:705:98:35,63:217,389:0.139:2,2:25.4:1:31.1:1:1:1.00411:60:31.667:0.1381:0:1.1 -19 14628557 . C A 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11008;SOR=5.47295;LSEQ=CACAACCCCTCGCCCCGCAG;RSEQ=TGAGCCGGAGGCGCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:1:1,0:136,365:0.002:2,0:1:0:26:0:0.27291:0:60:2:0.002:0:1 0/1:462:5:3,2:146,311:0.0108:2,2:9.8:1:27.8:1:0.33425:3.19:60:10:0.011:0:1.6 -19 14628629 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52835;SOR=Inf;LSEQ=CGGGTCCGCAGCGGGCTCCG;RSEQ=CGCGCCGTCCCCGTCGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:20,16:0:2,0:21.7:1:32:1:1:0:60:35:1:0:0.3 0/1:61:2:1,1:30,29:0.0328:2,2:33.5:1:29.5:1:1:1.03392:60:4:0.0333:0:1.5 -19 14628633 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13729;SOR=0;LSEQ=TCCGCAGCGGGCTCCGCCGC;RSEQ=CCGTCCCCGTCGTCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:21,14:0.0541:2,2:16.5:1:29:1:1:1.4832:60:4:0.0556:0:1.5 0/0:62:0:0,0:33,29:0:2,0:24.5:1:31:1:1:0:60:61:1:0:0.3 -19 14628649 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53976;SOR=Inf;LSEQ=CCGCGCCGTCCCCGTCGTCA;RSEQ=CCCCGGCTCCCCCACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:29,14:0:2,0:26.9:1:32.5:1:1:0:60:86:1:0:0.3 0/1:79:2:1,1:42,35:0.0253:2,2:24:0:31:1:1:1.19722:60:4:0.0253:0:1.5 -19 14628720 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51197;SOR=Inf;LSEQ=CGGGAGGAGGCGCCCGGGGA;RSEQ=GGGCAGCCCCAGACATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:45,30:0:2,0:24.4:1:31.4:1:1:0:60:150:1:0:0.1 0/1:106:2:1,1:58,46:0.0189:2,2:31.5:1:29.5:1:1:1.25808:60:4:0.0192:0:1 -19 14628765 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49769;SOR=Inf;LSEQ=CTTCTGGCCGAGCGGCTGGG;RSEQ=CAAGGCTCCTCCTCCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:39,53:0:2,0:25:1:31:1:1:0:60:29.667:1:0:0.2 0/1:97:2:1,1:43,52:0.0206:2,2:27:1:30:0:1:1.21:60:4:0.0211:0:1 -19 14628803 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21178;SOR=Inf;LSEQ=CCGCGCGGCCGCCAATCCGA;RSEQ=GGCGGAGGCCCGCGAGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:42,36:0:2,0:21.9:1:31.6:1:1:0:60:77:1:0:0.2 0/1:67:2:1,1:36,29:0.0299:2,2:20.5:1:28.5:1:1:1.23734:60:4:0.0303:0:1 -19 14628828 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GAGGCCCGCGAGGCCGGAGG;RSEQ=CGGGGCAGCTCGGCCCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:114,37:0.0131:2,2:18:1:31:0:0.43627:3.05348:60:4:0.0137:0:1 0/0:120:0:0,0:98,22:0:2,0:16.7:1:31.3:1:1:0:60:29:1:0:0.2 -19 14628840 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49882;SOR=Inf;LSEQ=GCCGGAGGGCGGGGCAGCTC;RSEQ=GCCCCACGGCCCGGGGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:155,41:0:2,0:19.8:1:30.4:1:1:0:60:97:1:0:0.1 0/1:201:2:1,1:159,40:0.01:2,2:24.5:1:28:1:0.36716:3.93855:60:4:0.0102:0:1 -19 14628890 . C T 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00405;SOR=Inf;LSEQ=GGGCCGCCGAGAGGGGCCAG;RSEQ=GTGCCTCAGTTTCCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:483,226:0:2,0:23.4:1:31.1:1:1:0:60:53.538:1:0:0.2 0/1:771:9:1,8:503,259:0.0117:2,2:7.4:1:26.2:1:0.00121:15.48798:60:18:0.0118:0:1 -19 14629138 . C T 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.94818;LSEQ=GCGCCGCGGGCCAGGCCCAA;RSEQ=GTCTGGTAGTAGTCTTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1253:2:0,2:582,667:0.0016:2,0:1:0:26.5:1:0.50202:0:60:4:0.0016:0:1 0/1:1553:71:32,39:669,813:0.0457:2,2:22.8:1:30.1:1:1:1.00288:60:142:0.0462:0:1.1 -19 14629150 . G A 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=2.65569;LSEQ=AGGCCCAACGTCTGGTAGTA;RSEQ=TCTTTACCCATGACCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1164:107:43,64:470,586:0.0919:2,2:23.2:1:30.2:1:0.41496:1.19356:60:52.5:0.0915:0:1.2 0/1:1458:309:134,175:503,645:0.2119:2,2:23.1:1:29.8:1:0.89738:1.01844:59.9:76.25:0.2117:0:1.2 -19 14629171 . C T 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCTTTACCCATGACCCCCTC;RSEQ=TGCGGCCCGCCGACCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:936:0:0,0:388,547:0:2,0:27.1:1:31.6:1:1:0:60:132.571:0.9989:0:0.3 0/1:1125:137:55,82:409,577:0.1218:2,2:28.2:1:30:1:0.78205:1.05678:60:44.667:0.121:0:1.1 -19 14629296 . CG C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.63299;SOR=1.66669;LSEQ=CCAGAACCTTCCGCCCCGCC;RSEQ=CCCCCGCGGCGCCGGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:0,2:0,0:0.0183:0,0:36.5:1:33:0:1:0:60:4:0.0202:0:0 0/1:66:2:0,2:0,11:0.0303:0,0:26.5:1:30.5:1:1:0:60:4:0.0357:0:0.5 -19 14629297 . G C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=2e-05;SOR=0.14886;LSEQ=CAGAACCTTCCGCCCCGCCC;RSEQ=CCCCCGCGGCGCCGGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:109:102:0,102:0,0:0.9358:0,1:24.1:1:31:1:1:0:60:19.4:0.9798:0:1.4 1/0:66:45:0,45:0,11:0.6818:0,1:23.8:1:30.5:1:1:0:60:21.5:0.7679:0:1.7 -19 14629336 . G A 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00404;SOR=0;LSEQ=ATCGCCGCCGCCCTTTCAGC;RSEQ=ACACGCGACATCCGGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:0,11:0,23:0.3235:1,0:11.5:1:31.1:1:1:0:60:22:0.3333:0:2 0/0:20:0:0,0:0,20:0:1,0:14.2:1:31.8:1:1:0:60:40:1:0:1.5 -19 15271135 . T G 76 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAAAAAAAAAAGAAAAA;RSEQ=AAAAATAATAATAATTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:23.5:1:29.5:1:1:0:59.5:5:0.8333:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15271771 . G A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.68815;LSEQ=GGCTGCTGTGTGCCCCAGCC;RSEQ=CCGGGTACTCCTCGCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:672:259:97,162:161,252:0.3854:2,2:25.5:1:30.1:1:0.74453:1.06687:60:258:0.3891:0:1.1 1/0:567:356:137,219:84,127:0.6279:2,2:23.8:1:29.4:1:0.78949:1.05719:60:70.2:0.6268:0:1.2 -19 15271934 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02353;LSEQ=CAGCCGGGCCCAATCGAGGG;RSEQ=CACAGCCACAGGGTTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:3:2,1:140,164:0.0098:2,2:10.3:1:29.3:1:0.59767:2.34:60:6:0.0099:0:1.3 0/1:300:3:1,2:143,154:0.01:2,2:19:1:28:1:1:1.85346:60:6:0.0101:0:1 -19 15272001 . C T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.04456;SOR=Inf;LSEQ=GGGGGCTGGCGCCCTAGACC;RSEQ=GCCCGGCCTGGGCCACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:121,128:0:2,0:22.1:1:30.1:1:1:0:60:61.25:1:0:0.1 0/1:214:4:2,2:110,100:0.0187:2,2:14.8:1:28.3:1:1:1.09951:60:8:0.0189:0:1 -19 15272045 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.25033;SOR=0;LSEQ=TGCCAGAGACACTGCAGTGG;RSEQ=AGTGGCAGCTGCATAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:1,2:131,133:0.0112:2,2:43:1:28:1:1:1.96511:60:6:0.0115:0:1 0/0:243:0:0,0:114,129:0:2,0:26.3:1:31.3:1:1:0:60:80:1:0:0.1 -19 15272116 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.2555;SOR=0;LSEQ=GGGGCCCACCGAAAGGCCGC;RSEQ=GGGAGTCCAGCGAGTCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:1,2:118,120:0.0124:2,2:7.7:1:27.7:1:1:1.96135:60:6:0.0127:0:1 0/0:198:0:0,0:83,115:0:2,0:23.1:1:29.7:1:1:0:60:65:1:0:0.2 -19 15272125 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17;SOR=Inf;LSEQ=CGAAAGGCCGCGGGGAGTCC;RSEQ=GCGAGTCCACGGGCGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:125,128:0:2,0:21.3:1:30.4:1:1:0:60:83.333:1:0:0.1 0/1:178:2:1,1:76,100:0.0112:2,2:33:1:31:1:1:1.31:60:4:0.0114:0:1 -19 15272127 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16863;SOR=Inf;LSEQ=AAAGGCCGCGGGGAGTCCAG;RSEQ=GAGTCCACGGGCGACAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:123,126:0:2,0:21.7:1:30.4:1:1:0:60:30.125:1:0:0.1 0/1:174:2:1,1:75,97:0.0115:2,2:23.5:1:28.5:1:1:1.29:60:4:0.0116:0:1 -19 15272146 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5665;SOR=3.01751;LSEQ=GCGAGTCCACGGGCGACAGC;RSEQ=TGACCGAGCTGTCAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:1,0:112,118:0.0043:2,0:10:0:14:0:0.48918:0:60:0:0:0:2 0/1:154:2:1,1:80,72:0.013:2,2:27.5:1:31:1:1:1.11035:60:4:0.0132:0:1.5 -19 15272225 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25549;SOR=0;LSEQ=CCGGGGCCCCTGCGGCCCCA;RSEQ=CCCCGCCTTCCCGGGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:142,134:0.0108:2,2:21.3:1:29:1:0.61438:2.11388:60:6:0.0109:0:1 0/0:230:0:0,0:121,109:0:2,0:24.9:1:31.6:1:1:0:60:31.857:1:0:0.1 -19 15272336 . C CG 84 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02064;SOR=8.14965;LSEQ=AGGCCCCAGGCCGTGGGGAC;RSEQ=GGGGGGGCTGCGGGGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:1:1,0:304,197:0.002:2,0:29:0:29:0:1:0:60:2:0.002:0:0 0/1:500:8:5,3:281,209:0.016:2,2:25.5:1:28.3:1:1:1.24:60:16:0.0164:0.002:0.5 -19 15272943 . C T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGACTACAGGTGTGCA;RSEQ=CACTACGCCCAGCTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,1:0.75:0,0:37:1:29.3:1:0.25:0:58.7:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15273047 . C T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAGTAATCCACCCATCTCGA;RSEQ=CTCCCAAAGTGCTGGGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:0.6667:0,0:26.1:1:32:1:1:0:60:16:0.6667:0:1 1/0:3:2:2,0:1,0:0.6667:0,0:16.5:1:31:1:1:0:60:4:0.6667:0:1 -19 15273221 . T C 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01449;SOR=1.48081;LSEQ=ACTCTGTTGCCCAGGCTGGA;RSEQ=TGCAATGGCACTGTGCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:468:336:271,65:106,26:0.7179:2,2:25.5:1:31.9:1:1:1.02:59.9:167:0.7183:0:2.9 1/0:396:313:241,72:61,22:0.7904:2,2:23.3:1:30.9:1:0.56174:1.21:60:77.25:0.7883:0:3 -19 15273231 . A G 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00105;SOR=1.63656;LSEQ=CCAGGCTGGATTGCAATGGC;RSEQ=CTGTGCCACTGCTGACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:545:387:295,92:116,37:0.7101:2,2:25.5:1:29.9:1:0.91129:1.02:59.9:63.5:0.7108:0:2.9 1/1:476:381:272,109:66,28:0.8004:2,2:23.6:1:29.8:1:0.80089:1.06:60:53.429:0.8009:0:2.8 -19 15273248 . A C 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00513;SOR=1.43445;LSEQ=GGCACTGTGCCACTGCTGAC;RSEQ=CCCAGTGGACCAAGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:703:513:339,174:127,63:0.7297:2,2:24:1:30.4:1:0.92844:1.03465:59.9:41.75:0.7271:0:2.4 1/0:658:523:323,200:78,53:0.7948:2,2:24.7:1:29.7:1:0.68843:1.10:60:57.111:0.7932:0:2.3 -19 15273381 . A G 280 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00034;SOR=1.54737;LSEQ=AAGGCTGATTTCCCTGGAGG;RSEQ=TGAAGGGGAGAGAGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:754:530:194,336:86,137:0.7029:2,2:26.3:1:31.6:1:0.62099:1.08709:60:105:0.7038:0:1.1 1/0:718:564:237,327:63,89:0.7855:2,2:24.4:1:30.7:1:0.9264:1.02:60:36.6:0.7821:0:1.2 -19 15273401 . G A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10119;SOR=5.85547;LSEQ=ATGAAGGGGAGAGAGGTCAG;RSEQ=ACCAGGCACCTGTCCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:1:1,0:176,393:0.0018:2,0:3:0:14:0:0.31053:0:60:0:0:0:4 0/1:491:5:4,1:172,314:0.0102:2,2:15:1:23.8:1:0.05793:7.27:60:4:0.0083:0:2 -19 15273525 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13066;SOR=Inf;LSEQ=GTGTCTGGATCCATGTGTGT;RSEQ=CAAATCTGCAAAATGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:1,67:0:1,0:24.4:1:32.2:1:1:0:59.9:67:1:0:0.3 0/1:39:2:1,1:0,37:0.0513:1,2:34.5:1:30.5:1:0.05128:0:60:4:0.0526:0:1.5 -19 15273576 . GTGTGTGTT G 116 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=13.000;MSILEN=2;SSF=0.05882;SOR=0;LSEQ=GAAGCACTTTGTGTCTGTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:0,13:0,10:0.5:0,1:19.9:1:31.5:1:1:0:58.5:26:0.5909:0.2692:1.7 0/0:6:0:0,0:0,6:0:0,0:12.8:1:27.5:1:1:0:60:5:1:0:1.5 -19 15273605 . C T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GTGCATGTGCATGACTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:0,11:0,3:0.7857:0,0:31.5:1:29.2:1:1:0:57.3:22:0.7857:0:2.3 1/1:2:2:0,2:0,0:1:0,0:21:1:28.5:1:1:0:60:4:1:0:2.5 -19 15273624 . T C 114 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGTGCATGTGCATGACTGT;RSEQ=TATACACAGGGGGTGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:1:0,0:19.4:1:31.9:1:1:0:59.2:24:1:0:2.1 1/1:1:1:0,1:0,0:1:0,0:49:0:30:0:1:0:60:2:1:0:4 -19 15273749 . C T 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGAGGTAGTGTCTTGTT;RSEQ=TGTCACCCAGGCTGGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:24:1:28.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15276007 . C A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56142;SOR=1.6083;LSEQ=TTTTCTAAATCCCTGAGGCA;RSEQ=CCTAAGGACTAGTGGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:13,0:19,0:0.4063:1,1:15.1:1:30.8:1:1:0:60:26:0.4194:0:1.9 1/0:19:10:10,0:9,0:0.5263:0,0:32.4:1:29.9:1:1:0:60:20:0.5263:0:1.9 -19 15276055 . C G 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66768;SOR=0.80323;LSEQ=ACCCTGCAGGCTTCATGAAG;RSEQ=CTGGTTATGTGTGCGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:59:59,0:15,0:0.7973:1,1:29:1:31.2:1:1:0:60:28.5:0.7917:0:1.5 1/0:54:41:41,0:13,0:0.7593:1,1:20.8:1:31.1:1:1:0:60:82:0.7736:0:1.6 -19 15276143 . C T 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.87616;SOR=0.97324;LSEQ=CCTCAGGGCCCAGGTGACAC;RSEQ=AACCCAGCTTAGACTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:445:336:225,111:71,38:0.7551:2,2:26.5:1:30:1:0.7274:1.08:60:83:0.7545:0:1.2 1/0:436:327:221,106:65,44:0.75:2,2:24.3:1:29.9:1:0.1323:1.41:60:108:0.7517:0:1.2 -19 15276386 . AC A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18558;SOR=Inf;LSEQ=GGAACAGAGGAATCAGGAGC;RSEQ=CCCTAAGTCCCATGAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:37,109:0:2,0:22.8:1:30.4:1:1:0:60:23.333:1:0:0.2 0/1:111:2:1,1:16,93:0.018:2,2:17:1:28:1:0.28403:5.67:60:4:0.0185:0.009:0.5 -19 15276523 . C T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12366;SOR=Inf;LSEQ=GAAAAAATGAGTCTGAAAGG;RSEQ=AGAACTGGGGCTCAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:184,55:0:2,0:24.4:1:31.8:1:1:0:60:46.8:1:0:0.1 0/1:247:4:1,3:186,57:0.0162:2,2:11:1:25.5:1:0.0455:9.67487:60:8:0.0165:0:1 -19 15276919 . G A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00172;SOR=1.94202;LSEQ=CCATCTGCAGGGACAGGAGT;RSEQ=TGTCAGCAGGAAGGTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:335:252:68,184:27,55:0.7522:2,2:24.1:1:30.1:1:0.325:1.32722:60:251:0.756:0:2.1 1/1:283:242:80,162:14,26:0.8551:2,2:23.6:1:29.1:1:0.85692:1.09004:60:241:0.8546:0:2.1 -19 15276923 . C T 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00602;SOR=1.83018;LSEQ=CTGCAGGGACAGGAGTGTGT;RSEQ=AGCAGGAAGGTAAACACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:237:63,174:22,51:0.7596:2,2:23.4:1:28.1:1:0.55151:1.1907:60:32.857:0.7591:0:2.2 1/1:258:220:69,151:12,25:0.8527:2,2:23.5:1:28.3:1:1:1.05023:60:35.667:0.8492:0:2.2 -19 15277006 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00647;SOR=Inf;LSEQ=TAATGGGACACATGGAAAAA;RSEQ=GACAATTAGCAGATCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:33:1,32:0,19:0.6346:1,1:25.5:1:29.6:1:1:0:60:32:0.6275:0:4.1 1/1:14:14:0,14:0,0:1:0,1:24.6:1:29.4:1:1:0:60:28:1:0:3.9 -19 15277009 . CA TG 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00561;SOR=Inf;LSEQ=TGGGACACATGGAAAAATGA;RSEQ=ATTAGCAGATCCTCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:29:1,28:0,18:0.5918:1,1:26.3:1:30.2:1:1:0:60:28:0.6087:0.0204:3.1 1/1:13:13:0,13:0,0:1:0,1:24.3:1:29.6:1:1:0:60:26:1:0.1538:2.8 -19 15277010 . A G 30 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACACATGGAAAAATGAC;RSEQ=ATTAGCAGATCCTCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:0,2:0,18:0.0417:1,0:22.5:1:30:0:1:0:60:4:0.1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15277027 . G A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18294;SOR=3.2352;LSEQ=GACAATTAGCAGATCCTCCT;RSEQ=TCTGCACACCCACACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:25:1,24:0,13:0.625:1,1:23.9:1:30.1:1:1:0:60:24:0.6316:0:2.8 1/1:13:11:0,11:1,1:0.8462:2,0:19.8:1:29.9:1:0.15385:0:60:22:0.8462:0:2.5 -19 15277317 . AG A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCATTTGAGTGTTTTAAA;RSEQ=GGGGGGGGAAAAAAAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:32.5:1:1:0:60:4:1:0.5:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15277336 . GC AA 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGGGGGGGAAAAAAAGA;RSEQ=TGCCCCCAGGGACATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:21:1:29:1:1:0:60:6:1:0.3333:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15277429 . T A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTACAGGCCATTTGGAGCA;RSEQ=AAGCAAAATGAAGCTAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:29.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15277601 . T C 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAAGCCCTGGGTAGAGAC;RSEQ=GACCTCCCCGCTCCACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:32.3:1:29:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15277610 . C T 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTAGAGACTGACCTCCC;RSEQ=GCTCCACCAGCAGACCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:29.3:1:29.7:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15277620 . G C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACCTCCCCGCTCCACCA;RSEQ=CAGACCCGACCCCCACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:26:1:31.3:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15277765 . T TG 90 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATGCATCCTGAGACTTT;RSEQ=CTGGAGCATTAAGAAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:18.9:1:32.1:1:1:0:60:14:1:0.2857:0 1/1:1:1:1,0:0,0:1:0,0:18:0:26:0:1:0:60:2:1:0:0 -19 15277938 . C T 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.27218;SOR=1.37627;LSEQ=ACCAAGAGTGTTGCTGAATA;RSEQ=ACACACCCTTCACAGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:157:108:108,0:48,1:0.6879:1,1:21.8:1:31:1:0.3121:0:60:53:0.6883:0:1.2 1/0:109:82:80,2:27,0:0.7523:1,1:22.9:1:30.3:1:1:0:60:164:0.7523:0:1.1 -19 15278057 . A G 302 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=1.53261;LSEQ=TTGGGAGGGGCACTGTCACT;RSEQ=ACCTGGGCCACGCACATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1016:729:410,319:153,133:0.7175:2,2:26.1:1:31.8:1:0.44059:1.12:60:144.8:0.7175:0:1.1 1/0:876:697:379,318:93,84:0.7957:2,2:26.2:1:31.3:1:0.67362:1.08:60:76.444:0.7972:0:1.2 -19 15278373 . A ATTTG 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0.58737;SOR=0.67086;LSEQ=TACCATCTGTTTGGTGTTTT;RSEQ=TTTGTTTTTGAGACAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:0,24:0,22:0.5217:1,1:24.8:1:31.4:1:1:0:59.6:48:0.5217:0.1087:0 0/1:19:8:0,8:0,11:0.4211:0,0:23.4:1:29.9:1:1:0:60:16:0.4211:0.0526:0 -19 15280765 . A G 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10453;SOR=1.99349;LSEQ=AGGGTTGCAAAGCTGGGACT;RSEQ=TTCTCTGGAGCTAGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:133:98:96,2:35,0:0.7368:1,1:21.3:1:32.5:1:1:0:60:97:0.7348:0:1.1 1/1:66:56:54,2:10,0:0.8485:0,1:24.8:1:32.6:1:1:0:60:112:0.8485:0:1.1 -19 15280794 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25463;SOR=4.09127;LSEQ=AGCTAGGGAGGTGGGGACAG;RSEQ=GGTGCCATCCCCTGATCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:1:1,0:214,10:0.0044:1,0:17:0:32:0:1:0:60:2:0.0045:0:1 0/1:111:2:1,1:104,5:0.018:1,2:5.5:1:27:1:0.10565:19.08943:60:4:0.0182:0:1.5 -19 15280830 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0596;SOR=Inf;LSEQ=TCACGCCCATCATCCACTGG;RSEQ=GACCCCACCCAGTACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:332,58:0:2,0:25.3:1:30.5:1:1:0:60:29:1:0:0.3 0/1:251:3:1,2:203,45:0.012:2,2:25:1:25.3:1:0.09091:8.90884:60:2:0.0084:0:3.3 -19 15281359 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08791;SOR=Inf;LSEQ=GGGTTCTGGAGGCTCCAGCG;RSEQ=CTCCCCTAAGAGCAGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:137,179:0:2,0:24.5:1:31.7:1:1:0:60:44.143:1:0:0.4 0/1:254:3:1,2:105,146:0.0118:2,2:25.3:1:24.3:1:1:1.43638:60:2:0.0081:0:2.7 -19 15281386 . C A 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=3.38636;LSEQ=TAAGAGCAGGAAGCAGAGGG;RSEQ=GGGGCTTCAGCCGAGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:103:55,48:94,97:0.3503:2,2:24.1:1:30.8:1:0.54161:1.18:60:102:0.3542:0:1.1 1/0:201:130:70,60:36,34:0.6468:2,2:22.7:1:29.6:1:0.76808:1.10:60:31.5:0.6495:0:1.2 -19 15281459 . C G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.35072;SOR=1.35914;LSEQ=CCAGCTCCGCCCCCGCCACC;RSEQ=CCTCCCCAAGGCAGGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:20:14,6:318,201:0.0371:2,2:23.1:1:28.9:1:0.49072:1.47:60:9:0.0342:0:1.2 0/1:462:23:12,11:259,179:0.0498:2,2:28.6:1:28.5:1:0.52169:1.3255:60:10.5:0.0465:0:1.2 -19 15282138 . T C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCGTGAGCCGCCACTGTGCC;RSEQ=GGCCTGTTTTTTTTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:49:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:7.5:1:29:1:1:0:60:4:1:0:1.5 -19 15284546 . AAAAAAAGAAAAGAAGAAGGAGAAGGAGAAGGAGAAGG A 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCGTCTCAAAAAAAAAA;RSEQ=AGAAGGAGAAGGAGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16.5:1:31.3:1:1:0:58.5:4:1:1:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15284589 . G A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=6;SSF=1;SOR=0;LSEQ=AGGAGAAGGAGAAGGAGAAG;RSEQ=AGAAGGAGAAGAAGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:6:0:31.5:1:1:0:58.5:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15284595 . G A 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=6;SSF=1;SOR=0;LSEQ=AGGAGAAGGAGAAGGAGAAG;RSEQ=AGAAGAAGAAGAAGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,0:0.6:0,0:10:1:31.7:1:1:0:59:6:0.75:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15284611 . A C 75 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GAAGGAGAAGAAGAAGAAGA;RSEQ=GAAGAAAAAAACCCTACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:2,0:0.6667:0,0:18.7:1:29.3:1:1:0:59.5:5:0.7143:0:2.3 1/1:1:1:1,0:0,0:1:0,0:9:0:32:0:1:0:60:2:1:0:1 -19 15284855 . G T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20724;SOR=4.21482;LSEQ=TCCTCTCCCCAGCCACCACG;RSEQ=CTTTTCCAGGTGGGGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:1:0,1:281,137:0.0024:2,0:1:0:27:0:0.32936:0:60:2:0.0025:0:1 0/1:401:4:2,2:248,148:0.01:2,2:21.5:1:24:1:0.63269:1.67335:60:3:0.0077:0:1.3 -19 15285052 . T C 254 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=1.90401;LSEQ=CTGGAACGCAGTAGCTCCTC;RSEQ=GGCGGCAGCAGCACTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:475:326:160,166:80,69:0.6863:2,2:26.9:1:30.5:1:0.37423:1.20243:60:64.2:0.6859:0:1.2 1/1:398:321:158,163:36,41:0.8065:2,2:25.6:1:29.6:1:0.70556:1.10:60:106:0.8071:0:1.1 -19 15285272 . T C 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08389;SOR=1.55912;LSEQ=GTCAGAGGAGACAATCCCCT;RSEQ=CCATGCATTCACACCGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:208:154:27,127:6,47:0.7404:2,2:20.8:1:30.9:1:0.38511:1.66:60:37.5:0.75:0:1.1 1/1:169:138:33,105:6,25:0.8166:2,2:18.2:1:30.4:1:0.81365:1.31:60:68:0.8193:0:1.1 -19 15285382 . ATTTT A 87 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=18.000;MSILEN=1;SSF=0.69152;SOR=1.59543;LSEQ=ATCTTGCCATTCACTGGATA;RSEQ=TTTTTTTTTTTTTTGAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:0,7:0,14:0.2917:1,0:28.7:1:31.3:1:1:0:59.3:14:0.2917:0:0.3 0/1:10:4:0,4:0,6:0.4:0,0:33.8:1:29.5:1:1:0:60:8:0.4:0:0 -19 15288062 . G GGA 107 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=AGAGCAAGACTCCATCTCGG;RSEQ=AAAAAAAAAAAAAAGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:11,0:7,0:0.5789:0,0:18.8:1:31:1:1:0:60:22:0.5789:0.2632:1.2 0/0:2:0:0,0:2,0:0:0,0:20:1:31:0:1:0:57:4:1:0:4.5 -19 15288072 . A T 109 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=0.05854;SOR=0;LSEQ=TCCATCTCGGGAAAAAAAAA;RSEQ=AAAAGTAATTATTGGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:12:12,0:13,0:0.48:1,0:21.6:1:30.6:1:1:0:60:11:0.4583:0:1.2 0/0:6:0:0,0:6,0:0:0,0:11.3:1:30:1:1:0:59:12:1:0:1.5 -19 15288518 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08458;SOR=Inf;LSEQ=CCGTCCCAGCCGCAGCCTGG;RSEQ=CTGTTGCACTCGCGGTCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:64,175:0:2,0:23.3:1:32.2:1:1:0:60:78.667:1:0:0.3 0/1:188:3:2,1:56,129:0.016:2,2:19:1:26.3:1:0.22549:4.57:60:6:0.0161:0:1 -19 15288572 . G A 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.24476;SOR=0;LSEQ=CGCTTGGCCTGGCAGGCGGC;RSEQ=CGCGGGCACCGCGGCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:14,19:0.0833:2,0:11:1:23.7:1:0.09524:0:60:2:0.0571:0:1.3 0/0:30:0:0,0:14,16:0:2,0:26.2:1:31.2:1:1:0:60:60:1:0:0.5 -19 15288655 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20653;SOR=Inf;LSEQ=GGTCCAGCCCTGCGCGCAAG;RSEQ=GCAGCGGAAGAAGGGCGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:19:1:30.8:1:1:0:60:26:1:0:0.3 0/1:23:2:1,1:10,10:0.087:2,2:15:0:32:0:1:1:60:4:0.087:0:1.5 -19 15288677 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10213;SOR=Inf;LSEQ=CAGCGGAAGAAGGGCGCGAG;RSEQ=GGCGCGGGGCGGCAGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:24,17:0:2,0:23.7:1:31:1:1:0:60:19.5:1:0:0.4 0/1:37:3:2,1:20,14:0.0811:2,2:12:1:29.7:1:1:1.39:60:6:0.0811:0:1.3 -19 15288689 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49669;SOR=0;LSEQ=GGCGCGAGCGGCGCGGGGCG;RSEQ=CAGGAGCCCCCGTGGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:38,23:0.0317:2,2:30.5:1:31.5:1:1:1.63846:60:4:0.0323:0:1.5 0/0:58:0:0,0:37,20:0:2,0:15.9:1:31.6:1:1:0:60:114:0.9828:0:0.4 -19 15288720 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24567;SOR=0;LSEQ=CGTGGAGACAGGGGGCGGCC;RSEQ=CGCAGCTGGCGTTGCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:74,66:0.014:2,2:22.5:1:29:1:1:1.12031:60:4:0.0143:0:1 0/0:145:0:0,0:74,70:0:2,0:21.7:1:30.5:1:1:0:60:143:0.9931:0:0.4 -19 15288722 . G T 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37198;SOR=3.82932;LSEQ=TGGAGACAGGGGGCGGCCGC;RSEQ=CAGCTGGCGTTGCTGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:0,1:79,69:0.0067:2,0:1:0:29:0:0.4698:0:60:2:0.0068:0:1 0/1:158:4:1,3:80,74:0.0253:2,2:7.3:1:25.8:1:0.3578:3.22105:60:8:0.0258:0:1.3 -19 15288735 . C T 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62433;SOR=2.78528;LSEQ=CGGCCGCGCAGCTGGCGTTG;RSEQ=TGGCCCCCGGCGGCGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:103,85:0.0053:2,0:1:0:26:0:0.45503:0:60:2:0.0054:0:1 0/1:205:3:1,2:110,91:0.0146:2,2:17.7:1:23:1:0.59277:2.40737:60:2:0.0099:0:1.7 -19 15288758 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24994;SOR=Inf;LSEQ=GCCCCCGGCGGCGACCCCGG;RSEQ=AAGCTGCGGCAGGAGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:149,116:0:2,0:23.6:1:31.1:1:1:0:60:65.25:0.9962:0:0.3 0/1:289:3:1,2:160,126:0.0104:2,2:25.7:1:26.3:1:0.5859:2.53164:60:6:0.0106:0:1.3 -19 15288787 . C A 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.35188;SOR=0.30178;LSEQ=GCAGGAGGGTCCCGACAACC;RSEQ=TGGGGGGCAGGCGCAGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:3,0:154,137:0.0102:2,0:13.3:1:22.7:1:0.25092:0:60:2:0.007:0:1.7 0/0:323:1:1,0:170,152:0.0031:2,0:1:0:25:0:1:0:60:2:0.0031:0:1 -19 15288788 . TG T 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.4287;SOR=0.4445;LSEQ=CAGGAGGGTCCCGACAACCC;RSEQ=GGGGGCAGGCGCAGCGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:4:2,2:151,133:0.0138:2,2:44.8:1:30.8:1:1:1.13484:60:8:0.0142:0:0 0/0:323:2:1,1:167,153:0.0062:2,2:43.5:1:30:1:1:1.0912:60:4:0.0063:0:0 -19 15288928 . G A 104 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.00297;SOR=12.56922;LSEQ=GTCGGGTTTGGGGAGGGAGG;RSEQ=ATAAAAATGAGGGTGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:1,0:75,126:0.005:2,0:1:0:25:0:0.37624:0:60:2:0.005:0:1 0/1:203:12:6,6:79,112:0.0591:2,2:23.6:1:29.1:1:0.56257:1.42:60:24:0.06:0:1.2 -19 15289366 . T G 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50893;SOR=0;LSEQ=CCACTACGCCCGGCTAATTT;RSEQ=TATATTTTTAGTAGAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:23.6:1:31:1:1:0:60:10:0.3846:0:1 0/0:3:0:0,0:3,0:0:0,0:23:1:30.7:1:1:0:60:6:1:0:0 -19 15289613 . A T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.38671;LSEQ=ACGCCCCTACTCCTCCTCCA;RSEQ=AGGCCGCCACCCACACCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:983:392:214,178:325,263:0.3988:2,2:26.9:1:29.3:1:0.84436:1.02784:60:55:0.4048:0:1.2 1/0:863:529:292,237:185,146:0.613:2,2:25.9:1:28.3:1:0.88789:1.02843:60:30.118:0.6103:0:1.2 -19 15290125 . G A 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.97491;LSEQ=AACGAGGGGTGGTCAAGAGG;RSEQ=AATGAAGACAGCCTCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:245:129,116:185,140:0.4283:2,2:22.8:1:30.2:1:0.34952:1.18789:60:48:0.4278:0:1.1 1/0:449:268:143,125:94,87:0.5969:2,2:21.2:1:29.4:1:0.77342:1.06:60:267:0.6:0:1.1 -19 15290236 . G T 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTCAATGCATGAACCCCC;RSEQ=TGCTGGCAGGGCTGGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1195:0:0,0:613,581:0:2,0:26.1:1:30.8:1:1:0:60:73.625:0.9992:0:0.2 0/1:1114:45:22,23:549,517:0.0404:2,2:26.2:1:30.4:1:0.76249:1.11006:60:90:0.0409:0:1.2 -19 15290380 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12102;SOR=Inf;LSEQ=CTGGACATACCCATGAAGAC;RSEQ=CAAAGAACCCCAGCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:16,238:0:2,0:23.3:1:31.8:1:1:0:60:41.333:1:0:0.4 0/1:136:2:1,1:11,123:0.0147:2,2:11.5:1:30:1:0.16928:10.75:60:4:0.0148:0:1.5 -19 15290412 . G A 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35779;SOR=0.74799;LSEQ=AGCACAAAAGGACACACACA;RSEQ=ATGTTCAGCGCACTACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:96:1,95:3,40:0.6857:2,1:24:1:30.2:1:0.08784:7.01412:59.8:31:0.694:0:1.2 1/0:71:44:1,43:2,25:0.6197:2,1:21.7:1:30.4:1:0.55311:3.37829:60:43:0.6143:0:1.1 -19 15290491 . G A 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01606;SOR=0;LSEQ=TCACCTGAGATCAGGAGTTC;RSEQ=AGACCAGCCTGGCCAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:13:2,11:3,13:0.4483:2,2:20.9:1:29.5:1:1:1.25893:57.2:12:0.4286:0:2.2 0/0:10:0:0,0:0,10:0:0,0:24.3:1:31:1:1:0:60:20:1:0:0.8 -19 15290648 . C T 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.28323;SOR=0;LSEQ=AGGTTGCAGTGAGCTGAGAT;RSEQ=GCGCCACTGCACTCGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:7,1:15,1:0.3333:1,2:30.1:1:31.3:1:1:2.07024:60:16:0.3333:0:1 0/0:5:0:0,0:4,1:0:2,0:11.6:1:30:1:1:0:60:10:1:0:0 -19 15291428 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16722;SOR=Inf;LSEQ=CCCCATTCGGCTCACACTAG;RSEQ=AGGAGGTACGTGCATGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:183,62:0:2,0:23.2:1:32:1:1:0:60:80.667:1:0:0.1 0/1:170:2:1,1:126,42:0.0118:2,2:8:0:30.5:1:0.44302:2.97664:60:4:0.012:0:1.5 -19 15291576 . C G 256 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGGGGACAAAGGCAATAGG;RSEQ=CCCAGTCTGGACGCAGCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:284:139,145:286,282:0.3326:2,2:25.7:1:31.5:1:0.71668:1.05786:60:46.333:0.3337:0:1.1 0/0:808:0:0,0:416,388:0:2,0:23.8:1:31.1:1:1:0:60:66:0.9975:0:0.2 -19 15291675 . TG T 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.03648;SOR=0;LSEQ=TCAGAGTCAGTACTGTGGGG;RSEQ=GGGGGTAGTCTGGGAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:6:2,4:159,253:0.0143:2,2:36.8:1:32:1:1:1.25623:55.8:12:0.0146:0:1.3 0/0:335:0:0,0:116,216:0:2,0:22.4:1:30.1:1:1:0:60:40.5:0.9908:0:0.2 -19 15291699 . T C 208 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GGGTAGTCTGGGAGAAACTG;RSEQ=GCCCCGACTTGGCTTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:108:55,53:108,152:0.2935:2,2:18.7:1:30.8:1:0.10749:1.46:60:107:0.2972:0:1.1 0/0:251:0:0,0:106,144:0:2,0:22.4:1:29.9:1:1:0:60:249:1:0:0.1 -19 15292055 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54897;SOR=0;LSEQ=TCCTGAGTCCCGCTGTTAGC;RSEQ=CTGGGGACGTCCCACTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:0,2:4,105:0.018:1,0:16.5:1:30:1:1:0:60:4:0.0187:0:1 0/0:57:0:0,0:4,52:0:2,0:23.3:1:32.3:1:1:0:60:55:0.9821:0:0.4 -19 15292088 . G C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39839;SOR=1.83873;LSEQ=CACTCCCTGACCCTTATCTC;RSEQ=GCAAGAAGCTGCAGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:39:2,37:1,16:0.6964:1,2:27.9:1:30.3:1:1:1.15317:60:38:0.7037:0:1.2 1/1:21:17:0,17:0,4:0.8095:0,1:30.7:1:30.8:1:1:0:60:34:0.8095:0:1.6 -19 15292271 . C T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00117;SOR=4.22153;LSEQ=CCCCATCAGTCATCAGAGTC;RSEQ=GCAGTGGGTACCAAGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:32:31,1:40,4:0.4211:2,1:27:1:30.9:1:0.39046:3.06:60:15:0.411:0:1.4 1/0:37:28:27,1:8,0:0.7568:0,1:27.7:1:31.6:1:1:0:60:56:0.7568:0:1.1 -19 15292366 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.63041;LSEQ=CAAGCCAGAGTCCCTGCTCT;RSEQ=CAAGCAGAGGCCCCGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:148:106,42:154,60:0.4088:2,2:27.1:1:29.8:1:1:1.01694:60:36:0.4045:0:1.5 1/1:277:233:149,84:30,14:0.8412:2,2:25.4:1:29.3:1:0.73128:1.20724:60:76.667:0.8425:0:1.6 -19 15292437 . T C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=5.96079;LSEQ=CAGTGGAAGCCTCCGTAGCC;RSEQ=GGCGGGCAGGTGCAGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:719:306:168,138:220,191:0.4256:2,2:23.6:1:29.7:1:0.7619:1.06:60:29.6:0.4235:0:1.3 1/1:564:460:259,201:57,45:0.8156:2,2:23.9:1:29.6:1:1:1.02:60:64.714:0.8177:0:1.4 -19 15292440 . C T 78 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36452;SOR=0.47339;LSEQ=TGGAAGCCTCCGTAGCCTGG;RSEQ=GGGCAGGTGCAGGTGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:8:1,7:385,342:0.0109:2,2:13.5:1:26:1:0.03042:7.86246:60:7:0.0099:0:1.4 0/0:580:3:0,3:320,256:0.0052:2,0:4.3:1:29.7:1:0.08893:0:60:6:0.0052:0:2.3 -19 15292632 . G A 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04933;SOR=Inf;LSEQ=TCTGCGGACAGGAGGAAGGC;RSEQ=GTCTGGTCACCTACCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:73,217:0:2,0:23.6:1:30.4:1:1:0:60:57:1:0:0.2 0/1:260:4:2,2:72,184:0.0154:2,2:12.5:1:27:1:0.32078:2.54:60:3:0.0118:0:1.5 -19 15292853 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAAAGGTCCCTTTAAGCT;RSEQ=CCAAGCAAACGCTGCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:0,8:0.2:0,2:15:0:30.5:1:0.2:0:60:4:0.2:0:1.5 0/0:3:0:0,0:1,2:0:2,0:13.7:1:33.3:1:1:0:60:6:1:0:0 -19 15294991 . C T 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15749;SOR=1.92607;LSEQ=CAGTTTCCATATAAATAAAA;RSEQ=GGGAAAAGTAAGATAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:79:78,1:24,1:0.7524:1,1:20.8:1:30.8:1:0.42476:3.20:60:25.333:0.7525:0:1.1 1/1:55:47:47,0:8,0:0.8545:0,1:19:1:30.5:1:1:0:60:46:0.8679:0:1.1 -19 15295027 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=ACTGTGAAGATGAAATGACA;RSEQ=CACAGTGCCAGGCACACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:207,26:0:2,0:25.7:1:32.1:1:1:0:60:37.833:1:0:0.4 0/1:189:2:1,1:156,31:0.0106:2,2:21:1:27.5:1:0.31071:4.96899:60:4:0.0106:0:2 -19 15295082 . C A 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20623;SOR=0.68644;LSEQ=TGTGTTCCCCAGAGCAGCAC;RSEQ=CCCAAGAGCTCCCCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:33:24,9:376,171:0.0568:2,2:24.4:1:29.9:1:0.70234:1.21:60:66:0.0575:0:1.9 0/1:504:20:10,10:308,176:0.0397:2,2:29.1:1:29.6:1:0.24101:1.74787:60:40:0.0404:0:1.8 -19 15295134 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.51896;LSEQ=CAGTCATTGATGTCCTGATC;RSEQ=CAGGAAGGGCCAGTGTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:897:344:186,158:288,265:0.3835:2,2:25.6:1:30:1:0.58248:1.08:60:113.667:0.3836:0:1.3 1/0:814:497:264,233:160,155:0.6106:2,2:24.8:1:29.6:1:0.56417:1.10:60:123.25:0.6132:0:1.2 -19 15295902 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13844;SOR=Inf;LSEQ=ATCCCATCTCCCCCCACCTC;RSEQ=CCCAACCCCAGGGTCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:147,187:0:2,0:23.4:1:30.5:1:1:0:59.9:40.75:0.9969:0:0.2 0/1:199:2:1,1:89,108:0.0101:2,2:15:1:28.5:1:1:1.21:60:4:0.0103:0:1 -19 15296513 . C T 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=0;LSEQ=GGGGAGTACACAAGCAATCT;RSEQ=ATCTCAGAACAAAGTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:153:48,105:101,245:0.306:2,2:24.8:1:28.2:1:0.67151:1.11:60:37.25:0.3028:0:1.1 0/0:434:0:0,0:135,298:0:2,0:23.3:1:31:1:1:0:60:85.6:1:0:0.1 -19 15296917 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTGCGTGTTTATCTAC;RSEQ=TATTGACTAATCTGGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:36:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15297576 . C T 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06125;SOR=0.52462;LSEQ=CACAGACTCAGGGCAAAGCA;RSEQ=GGACAACCTCGTTGGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:44:44,0:88,0:0.3333:1,1:28.4:1:31.7:1:1:0:60:43:0.3282:0:1 0/1:82:17:16,1:64,1:0.2073:1,1:24.7:1:30.4:1:0.37368:3.91077:60:34:0.2073:0:1.1 -19 15298031 . C T 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TGGCTCTCGCAGCGTGTGCC;RSEQ=GTGTAGCCAGGAGCACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:684:0:0,0:329,355:0:2,0:25.1:1:30:1:1:0:60:61.182:1:0:0.1 0/1:588:15:8,7:280,293:0.0255:2,2:16.3:1:30.1:1:0.79769:1.20:60:30:0.0259:0:1.2 -19 15298159 . C A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05272;SOR=Inf;LSEQ=GCCCTCAAAGCCTGTGGGGC;RSEQ=AAGAGGGTCAGGCTCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:150,269:0:2,0:25.3:1:31.6:1:1:0:60:68.833:1:0:0.1 0/1:387:4:3,1:151,232:0.0103:2,2:5.3:1:27.3:1:0.30567:4.59:60:8:0.0105:0:1 -19 15298171 . G A 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22626;SOR=0.23399;LSEQ=TGTGGGGCCAAGAGGGTCAG;RSEQ=CTCCGCCCACTTGCCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:353:5:3,2:111,237:0.0142:2,2:21.4:1:25.6:1:0.33362:3.19:60:4:0.0114:0:1.4 0/0:299:1:1,0:101,197:0.0033:2,0:1:0:22:0:0.34114:0:60:2:0.0034:0:1 -19 15298270 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0015;SOR=4.18516;LSEQ=CATCAAGCTGTCAGGAGGCG;RSEQ=GCTCAATACAGGCCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:22:1,21:1,35:0.3793:1,1:22.3:1:31.3:1:1:1.65:60:44:0.3793:0:1.1 1/0:36:26:1,25:0,10:0.7222:0,1:25.5:1:30.8:1:1:0:60:52:0.7222:0:1.6 -19 15298604 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.56126;SOR=3.23409;LSEQ=TGCCTTGCTACAACCCCGCC;RSEQ=CCAAGCTCTCCCCAAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:218,35:0.0039:2,0:24:0:17:0:1:0:60:0:0:0:5 0/1:158:2:1,1:130,26:0.0127:2,2:11.5:1:28.5:1:0.31347:4.92548:60:4:0.0128:0:1.5 -19 15298632 . C T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32854;SOR=3.75841;LSEQ=CTCCCCAAGTCTGTTATTGG;RSEQ=CCTGTCGCCCACAAGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:1:0,1:269,94:0.0027:2,0:1:0:28:0:0.26099:0:60:2:0.0028:0:1 0/1:293:3:1,2:203,87:0.0102:2,2:14:1:29:1:0.21989:4.63901:60:6:0.0106:0:1 -19 15298952 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1433;SOR=Inf;LSEQ=ACATATGGTTTCTATTGTAA;RSEQ=TTATCCGCTAACGTGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:187,65:0:2,0:24.3:1:32.1:1:1:0:60:62:1:0:0.2 0/1:154:2:1,1:129,23:0.013:2,2:18:0:32:0:0.28826:5.51192:60:4:0.0135:0:1 -19 15299048 . G A 237 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCTCCTGAGGTCCTCACCC;RSEQ=AGGGGCAGGTGCAGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:254:151,103:320,205:0.3261:2,2:23.9:1:29.7:1:0.69652:1.06468:60:62.5:0.3255:0:1.1 0/0:718:0:0,0:403,315:0:2,0:24.4:1:29.8:1:1:0:60:78.778:1:0:0.2 -19 15299051 . G A 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTGAGGTCCTCACCCGAG;RSEQ=GGCAGGTGCAGCTGAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:804:0:0,0:486,317:0:2,0:24.1:1:30.9:1:1:0:60:65.917:0.9987:0:0.4 0/1:739:19:12,7:398,320:0.0257:2,2:22.1:1:28.8:1:0.64155:1.38:60:38:0.0259:0:1.2 -19 15299217 . G A 42 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0436;SOR=Inf;LSEQ=CCCTATGGTGTGAACGGGGT;RSEQ=CAAGGAAGGAGGTACTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:73,277:0:2,0:24.6:1:32.2:1:1:0:60:115.667:1:0:0.1 0/1:296:4:3,1:64,228:0.0135:2,2:8.5:1:21.3:1:0.03745:10.57:60:3:0.0105:0:2.3 -19 15299648 . T C 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5756;SOR=0.72566;LSEQ=AGAATCACACAGTATTCCCT;RSEQ=CTGGTCCTGACCCCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:36:35,1:13,1:0.72:1,1:25.8:1:31.3:1:0.48571:2.63:60:72:0.7347:0:1.1 1/0:20:13:13,0:7,0:0.65:0,1:24.5:1:31.9:1:1:0:60:26:0.65:0:1 -19 15300069 . T C 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.05854;LSEQ=CCCAGCCCATTCACAGACGA;RSEQ=GGAGCTCCCCTCACCGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:599:412:235,177:105,82:0.6878:2,2:23.9:1:30.4:1:0.85901:1.04:60:57.857:0.6888:0:1.1 1/1:432:354:201,153:45,33:0.8194:2,2:23.9:1:30.2:1:0.90023:1.03791:60:117:0.8201:0:1.2 -19 15300136 . A G 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCCACCCGTGAAGCCGGG;RSEQ=GGACAGGTGCAAATGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:864:0:0,0:450,413:0:2,0:25.7:1:30.2:1:1:0:60:40.095:1:0:0.3 0/1:814:44:23,21:431,338:0.0541:2,2:23.8:1:29.8:1:0.64238:1.16404:60:43:0.0544:0:1.4 -19 15301796 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCTTGGCCTCCCAAAG;RSEQ=GCTGGGATTACAGGCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42.5:1:31.5:1:1:0:60:4:1:0:1.5 -19 15301857 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCTTTTTTTTATTTTTT;RSEQ=AATTTGAGAAGGAGTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:23.5:1:31.5:1:1:0:49.5:4:0.5:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 15302146 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20844;SOR=Inf;LSEQ=GAGCCACTGTGCCCAGCCTA;RSEQ=CATAATCTTTCTAACACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:154,18:0:2,0:21.6:1:32:1:1:0:60:56.333:1:0:0.1 0/1:145:2:1,1:123,20:0.0138:2,2:19.5:1:29:1:0.26954:6.02616:60:4:0.014:0:1 -19 15302370 . C T 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03053;SOR=3.90693;LSEQ=TGTCCAGCCATTGACACACA;RSEQ=GCAGCTGTGGCCACCCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:935:3:0,3:462,470:0.0032:2,0:1:0:25.3:1:0.2493:0:60:6:0.0032:0:1 0/1:885:11:2,9:433,441:0.0124:2,2:11.8:1:27:1:0.06421:4.41184:60:10:0.0114:0:1.1 -19 15302733 . G A 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48337;SOR=1.9252;LSEQ=GGCTGGCCTGCTGTCCCCAC;RSEQ=CCCACCCCTCTGACTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:3:3,0:189,330:0.0057:2,0:1:0:27:1:0.04927:0:60:6:0.0059:0:1 0/1:454:5:4,1:150,299:0.011:2,2:5:1:27.8:1:0.0473:7.94:60:10:0.0111:0:1.2 -19 15302844 . T C 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=1.76078;LSEQ=CCGTTACGGCATGGTGAGGG;RSEQ=GCACAGGGCACCGCGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:473:324:170,154:73,76:0.685:2,2:25.6:1:31.1:1:0.48999:1.15:60:648:0.6864:0:1.1 1/0:401:318:166,152:41,39:0.793:2,2:26.8:1:30.4:1:0.90089:1.04:60:38.75:0.7969:0:1.2 -19 15303225 . G A 221 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=104.12926;LSEQ=CACCGGCATGAGAATCGGGC;RSEQ=GTGCCAGCCACCACTGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:769:2:2,0:412,355:0.0026:2,0:1:0:26:1:0.5023:0:60:4:0.0026:0:1 0/1:748:160:87,73:300,288:0.2139:2,2:26.4:1:30.2:1:0.47603:1.14:60:320:0.2177:0:1.2 -19 15303359 . G A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04024;SOR=Inf;LSEQ=AGAGATGGCTTGGTTGGGCA;RSEQ=CACAGGGCAGGATGGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:113,287:0:2,0:25.9:1:31.7:1:1:0:60:65.667:1:0:0.2 0/1:326:4:2,2:113,209:0.0123:2,2:23.3:1:24:1:0.6158:1.85:60:3:0.0093:0:2.5 -19 15308068 . T C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28677;SOR=Inf;LSEQ=TGCAGACCATGACACTGAGA;RSEQ=GTAAAGAGTTTAATTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:17:17,0:5,0:0.7727:0,1:25.6:1:32.6:1:1:0:60:34:0.7727:0:1.2 1/1:8:8:7,1:0,0:1:0,2:26.5:1:31.4:1:1:0:60:16:1:0:1.3 -19 15308096 . G A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02631;SOR=Inf;LSEQ=GTTTAATTCCTAGCCGGTCA;RSEQ=CAACATGATGTGGGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:0:1,0:28:1:32.5:1:1:0:60:66:1:0:0.5 0/1:15:3:2,1:11,1:0.2:2,2:25:1:30.3:1:0.37143:4.69047:60:6:0.2:0:1.3 -19 15308179 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51802;SOR=0;LSEQ=TGGGGAAACACGAGAGGTTG;RSEQ=CCAAGCCACACACATGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:119,1:0.0164:1,0:23:1:29:1:1:0:60:4:0.0171:0:1 0/0:81:0:0,0:79,2:0:1,0:24.1:1:32.8:1:1:0:60:80:1:0:0.1 -19 15308287 . G C 230 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCACACACAGGGCCCACT;RSEQ=GTGGCTCTGAGCCAGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:759:230:134,96:299,226:0.303:2,2:26.1:1:29.4:1:0.74977:1.05:60:16.692:0.3091:0:1.5 0/0:700:0:0,0:394,306:0:2,0:24.4:1:29:1:1:0:60:10.864:1:0:0.5 -19 15308541 . CCA C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCCCCCATCCACAGTTC;RSEQ=CGCCCCCCCCCCCCCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:0,2:1,65:0.0294:1,0:46:1:30.5:1:1:0:60:4:0.0323:0:6.5 0/0:28:0:0,0:0,27:0:1,0:20.4:1:30.6:1:1:0:59.6:54:1:0:0.8 -19 15308545 . G A 119 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=1e-04;SOR=0.0489;LSEQ=CCCCCATCCACAGTTCCCAC;RSEQ=CCCCCCCCCCCCCCGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:28:0,28:1,21:0.4667:1,1:19.3:1:24.9:1:0.44:0:60:2.5:0.5405:0:1.9 0/1:25:1:0,1:0,23:0.04:1,0:42:0:26:0:1:0:60:2:0.0455:0:1 -19 15308555 . C CCA 117 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=0.25385;SOR=2.09598;LSEQ=CAGTTCCCACGCCCCCCCCC;RSEQ=CCCCGCCCCAGCCCCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:14:0,14:1,25:0.2979:1,1:27.8:1:30.9:1:1:0:60:13:0.2826:0.0426:2.2 0/1:19:9:0,9:0,3:0.4737:0,0:16.8:1:30.8:1:1:0:58.9:18:0.4737:0.2105:0.8 -19 15310866 . C CG 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAGGAGAGGAGGAGGGG;RSEQ=GGGGGCCCCTGGCCGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:0:32:0:1:0:60:4:1:0:0.5 -19 15311535 . C T 28 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02554;LSEQ=GAACCCCCGCCAGCCCCGGC;RSEQ=TTGGGGGTTCTTGCACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:0,2:73,47:0.0164:2,0:1.5:1:27.5:1:0.15933:0:60:4:0.0168:0:1 0/1:119:2:1,1:76,40:0.0168:2,2:14:0:28.5:1:1:1.88906:60:4:0.0171:0:1 -19 15311552 . TC T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50055;SOR=0;LSEQ=GGCCTTGGGGGTTCTTGCAC;RSEQ=CCCCTCTGCCGCCCTCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:88,83:0.0116:2,2:20:1:29.5:1:1:1.05991:60:4:0.0116:0:0 0/0:152:0:0,0:82,70:0:2,0:23.5:1:30.4:1:1:0:60:151:1:0:0.2 -19 15311566 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25426;SOR=0;LSEQ=TTGCACTCCCCCTCTGCCGC;RSEQ=CTCGTCCCATCCGCCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:1,2:99,107:0.0143:2,2:25:1:28.3:1:1:1.84524:60:6:0.0143:0:1 0/0:175:0:0,0:82,93:0:2,0:25.7:1:29.7:1:1:0:60:86.5:1:0:0.2 -19 15311594 . C G 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19058;SOR=Inf;LSEQ=CATCCGCCAGGTCCCGGCCC;RSEQ=TCACCTGCAGCCCCCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:95,147:0:2,0:26.2:1:31.4:1:1:0:60:47.4:1:0:0.3 0/1:188:2:1,1:70,114:0.0106:2,2:46:0:29.5:1:1:1.62:60:4:0.0108:0:1 -19 15311604 . GC G 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.06948;SOR=0;LSEQ=GTCCCGGCCCCTCACCTGCA;RSEQ=CCCCGGCCCCGCTAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:5:2,3:86,139:0.0217:2,2:30:1:32.6:1:1:1.08:60:10:0.0221:0:0 0/0:182:0:0,0:66,116:0:2,0:26.8:1:31.1:1:1:0:60:90:1:0:0.2 -19 15311616 . G A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33568;SOR=3.59549;LSEQ=CACCTGCAGCCCCCGGCCCC;RSEQ=CTAGCAGCAGCAGCAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:1,0:69,126:0.0051:2,0:1:0:25:0:0.35714:0:60:2:0.0052:0:1 0/1:166:3:1,2:56,107:0.0181:2,2:31.3:1:30:1:1:1.04645:60:6:0.0183:0:1 -19 15311618 . TAGC T 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.08658;SOR=4.21132;LSEQ=CCTGCAGCCCCCGGCCCCGC;RSEQ=AGCAGCAGCAGGGGCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:0,2:65,121:0.0106:2,0:16.5:1:28.5:1:0.54517:0:60:4:0.0109:0.0053:0.5 0/1:161:7:3,4:51,103:0.0435:2,2:36:1:32.4:1:0.68791:1.51:60:14:0.0435:0:0.1 -19 15311669 . C T 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11775;SOR=0;LSEQ=GGTGGCGGTGGCGGTGGCGG;RSEQ=GACATCGGGCGACGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:4:2,2:13,34:0.0769:2,2:16:1:31.5:1:0.57143:2.56:60:8:0.08:0:1.3 0/0:51:0:0,0:18,33:0:2,0:15.5:1:30.5:1:1:0:60:50:1:0:0.3 -19 15349342 . C T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.30021;SOR=0;LSEQ=TACCCGCTACCAGCAGTCAG;RSEQ=CCCGTAGCCCTCCCCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:4:0,4:35,138:0.0226:2,0:13:1:29.5:1:0.5863:0:60:8:0.023:0:1 0/0:103:0:0,0:16,87:0:2,0:23:1:31.1:1:1:0:60:102:1:0:0.1 -19 15349501 . TC T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08005;SOR=Inf;LSEQ=TCCAGTCCCCCTTTCCCAGC;RSEQ=CCTCAGGAGCTAATCCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:223,82:0:2,0:25.4:1:31.2:1:1:0:60:304:1:0:0.1 0/1:232:3:2,1:155,74:0.0129:2,2:22.3:1:30:1:1:1.04709:60:6:0.0132:0.0043:0.3 -19 15349507 . A T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32239;SOR=3.91629;LSEQ=CCCCCTTTCCCAGCTCCCTC;RSEQ=GGAGCTAATCCTTAGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:1:0,1:234,97:0.003:2,0:3:0:27:0:0.29518:0:60:2:0.003:0:1 0/1:256:3:1,2:168,84:0.0117:2,2:17.3:1:22:1:0.26364:3.97647:60:2:0.0081:0:1.7 -19 15349680 . TTGC T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.7052;SOR=1.69729;LSEQ=GCCACCGCAGCTGCTTGCTG;RSEQ=TGCTGCTGCTGTTGCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:3:0,3:129,201:0.009:2,0:27:1:30.7:1:0.2859:0:60:6:0.0091:0.003:0.3 0/1:263:4:2,2:110,149:0.0152:2,2:28.3:1:30.5:1:1:1.35:60:8:0.0153:0:0 -19 15349705 . CGCT C 51 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=1;SOR=0.75405;LSEQ=GCTGCTGCTGTTGCTCCTGG;RSEQ=GCTGCTGCTGCTGCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:0,3:104,155:0.0114:2,0:38.3:1:32.7:1:0.27911:0:60:6:0.0115:0:0 0/0:232:2:1,1:92,138:0.0086:2,2:38.5:1:31:1:1:1.50:60:4:0.0087:0:0 -19 15349752 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25768;SOR=0;LSEQ=CGACGTGCCTCCTCATGGGC;RSEQ=CGCCGGGCCTGCTCCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:1,2:139,145:0.0105:2,2:11.7:1:28.3:1:1:1.91306:60:6:0.0109:0:1 0/0:230:0:0,0:102,127:0:2,0:23.5:1:29.9:1:1:0:60:44.8:0.9956:0:0.2 -19 15349754 . G A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08527;SOR=Inf;LSEQ=ACGTGCCTCCTCATGGGCCC;RSEQ=CCGGGCCTGCTCCAGCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:145,145:0:2,0:24.5:1:30.8:1:1:0:60:95.667:1:0:0.2 0/1:229:3:1,2:101,125:0.0131:2,2:12.7:1:29.3:1:1:1.61275:60:6:0.0133:0:1 -19 15349811 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16051;SOR=Inf;LSEQ=CCTGGGCAGAGGGTCCCAGT;RSEQ=AGCCTGGGGACTGGTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:147,135:0:2,0:26:1:31.6:1:1:0:60:93:1:0:0.1 0/1:189:2:1,1:88,99:0.0106:2,2:21:0:31:1:1:1.12:60:4:0.0107:0:1.5 -19 15349813 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06299;SOR=Inf;LSEQ=TGGGCAGAGGGTCCCAGTCA;RSEQ=CCTGGGGACTGGTGTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:147,139:0:2,0:25.4:1:31.7:1:1:0:60:27.6:1:0:0.1 0/1:190:3:2,1:90,97:0.0158:2,2:5:1:26:1:0.61137:2.15:60:6:0.016:0:1 -19 15349848 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15032;SOR=Inf;LSEQ=TGGCCCCAAGAGTCCCCATG;RSEQ=CCCACCCAGACACCCGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:144,130:0:2,0:23.6:1:31.3:1:1:0:60:53.8:1:0:0.1 0/1:174:2:1,1:94,78:0.0115:2,2:43.5:1:30:1:1:1.20383:60:4:0.0119:0:1 -19 15350428 . C CG 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.10082;SOR=Inf;LSEQ=CTTATGTCCAACACGGGCCT;RSEQ=GGGGGGCCTGAGCCCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:135,182:0:2,0:22.7:1:29.8:1:1:0:60:51.833:1:0:0.1 0/1:277:3:1,2:117,157:0.0108:2,2:26:1:29.7:1:1:1.48838:60:6:0.011:0:0 -19 15350433 . G A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.10983;SOR=Inf;LSEQ=GTCCAACACGGGCCTCGGGG;RSEQ=GCCTGAGCCCTGGCTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:145,175:0:2,0:23.5:1:30.6:1:1:0:60:39:0.9968:0:0.1 0/1:296:3:2,1:130,163:0.0101:2,2:18.3:1:25:1:0.58765:2.50:60:2:0.0069:0:1.7 -19 15350575 . TCTC T 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=GATGATGGGTGAGTGGATCT;RSEQ=CTCCTTCACCACCACGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:562:0:0,0:327,230:0:2,0:24.5:1:31.7:1:1:0:60:91.833:0.991:0:0.2 0/1:541:13:7,6:292,237:0.024:2,2:22.5:1:30:1:1:1.05592:60:26:0.0242:0.0018:0.8 -19 15350594 . G A 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.40851;LSEQ=TTCTCCTCCTTCACCACCAC;RSEQ=AGGGGCTGGGGCTGGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:591:29:17,12:336,226:0.0491:2,2:25.3:1:29.1:1:1:1.04934:60:28:0.0481:0:1.1 0/1:521:78:44,34:247,196:0.1497:2,2:26.8:1:29.6:1:1:1.03:60:38:0.1487:0:1.3 -19 15353850 . C T 85 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2221;SOR=2.0127;LSEQ=TGGCCCTGGGGTGGCGGGGG;RSEQ=TGTTGGATGTGGGTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:799:6:0,6:314,474:0.0075:2,0:5.8:1:16.3:1:0.08655:0:60:0.2:0.0014:0:3.3 0/1:733:11:1,10:293,429:0.015:2,2:8:1:24.7:1:0.05769:6.81639:60:4.5:0.0132:0:1.5 -19 15353935 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47878;SOR=2.03119;LSEQ=GCTGCTGGGGTGGAGGCTGG;RSEQ=GCTGGGGTGGTGGGGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:3:3,0:221,223:0.0067:2,0:1:0:26.3:1:0.24832:0:60:6:0.0069:0:1 0/1:369:5:4,1:174,188:0.0136:2,2:10.4:1:24.6:1:0.20291:4.31:60:4:0.0111:0:1.4 -19 15353963 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.57395;SOR=2.79463;LSEQ=TGGTGGGGGTGGTGGCGGCT;RSEQ=CTGCTGCAGCTGCTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:1,0:101,105:0.0048:2,0:1:0:25:0:0.49275:0:60:2:0.005:0:1 0/1:149:2:1,1:64,83:0.0134:2,2:8.5:1:29:1:1:1.29:60:4:0.0135:0:1.5 -19 15353976 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.5119;SOR=0;LSEQ=GGCGGCTGCTGCTGCAGCTG;RSEQ=TGCTGCACAGAGGGGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:2,0:79,69:0.0132:2,0:10:1:27.5:1:0.49987:0:60:4:0.0143:0:3.5 0/0:108:0:0,0:53,55:0:2,0:14.1:1:32:1:1:0:59.8:107:1:0:1.4 -19 15354023 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51027;SOR=0;LSEQ=CGGCAGGGGGGGTGGGGGCT;RSEQ=GGACTGCACCTTCACGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:84,87:0.0114:2,2:36.5:1:30:1:1:1.04:60:4:0.012:0:4 0/0:129:0:0,0:75,54:0:2,0:19.4:1:30.1:1:1:0:59.5:42:1:0:0.5 -19 15354026 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51195;SOR=0;LSEQ=CAGGGGGGGTGGGGGCTGGG;RSEQ=CTGCACCTTCACGGAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:91,95:0.0106:2,2:18.5:1:29:1:1:1.04:60:4:0.0113:0:1 0/0:135:0:0,0:79,56:0:2,0:20.4:1:28.3:1:1:0:59.5:26:1:0:0.5 -19 15354033 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.185;SOR=Inf;LSEQ=GGTGGGGGCTGGGACTGCAC;RSEQ=TCACGGAAGGGAGTAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:104,106:0:2,0:20.9:1:29.5:1:1:0:59.8:18.091:1:0:0.6 0/1:159:2:1,1:92,65:0.0126:2,2:17.5:1:30.5:1:1:1.41221:60:4:0.0128:0:0.5 -19 15354041 . A T 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.3272;SOR=3.7841;LSEQ=CTGGGACTGCACCTTCACGG;RSEQ=AGGGAGTAGCGGCGTAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:1:0,1:115,113:0.0043:2,0:1:0:24:0:0.49782:0:60:2:0.0045:0:1 0/1:184:3:1,2:103,78:0.0163:2,2:13.3:1:20.7:1:0.58049:2.62726:60:2:0.0116:0:1.7 -19 15354093 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09729;SOR=Inf;LSEQ=TGCAGCTGCTGCAGGTACAG;RSEQ=TGCATCTGCATGGAGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:185,124:0:2,0:27.2:1:31.6:1:1:0:60:21.071:1:0:0.4 0/1:265:3:2,1:142,120:0.0113:2,2:41:1:30.7:1:1:1.69:60:6:0.0119:0:1 -19 15354334 . G A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25162;SOR=0;LSEQ=ACCGAGGCGGTGAGGCCTGA;RSEQ=CACCTGTGGCCCCAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:1,2:91,202:0.0101:2,2:18.3:1:27.7:1:1:1.11:60:6:0.0102:0:1.7 0/0:261:0:0,0:84,177:0:2,0:25.2:1:31.4:1:1:0:60:42.5:1:0:0.1 -19 15354369 . C A 23 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58941;SOR=2.46848;LSEQ=GCCTGGCCTTTCTGCTCCAT;RSEQ=CTGACCTCATCTGGACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:1,0:17,139:0.0064:2,0:1:0:23:0:0.11465:0:60:2:0.0065:0:1 0/1:128:2:1,1:21,105:0.0156:2,2:7:1:23:0:0.31533:4.91:60:4:0.0159:0:1 -19 15354998 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.58776;SOR=2.50267;LSEQ=CACCACATGGGTAAACCGAG;RSEQ=CAGGAAGGGGTCTCAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:1:1,0:192,43:0.0042:2,0:48:0:14:0:1:0:60:0:0:0:5 0/1:191:2:1,1:145,43:0.0105:2,2:28:1:28.5:1:0.41047:3.34498:60:4:0.0108:0:1 -19 15354999 . C T 43 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04032;SOR=Inf;LSEQ=ACCACATGGGTAAACCGAGG;RSEQ=AGGAAGGGGTCTCAACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:196,46:0:2,0:22.4:1:31.9:1:1:0:60:120:1:0:0.1 0/1:198:4:1,3:149,45:0.0202:2,2:8.5:1:21.8:1:0.0449:9.78708:60:3:0.0155:0:2.5 -19 15355214 . G T 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.05583;SOR=6.84479;LSEQ=GGCTCCAGGACGGGCACCTG;RSEQ=GTGGCAATGAAGGGTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:635:1:0,1:230,404:0.0016:2,0:1:0:29:0:1:0:60:2:0.0016:0:1 0/1:561:6:2,4:222,333:0.0107:2,2:17.7:1:30.8:1:1:1.33267:60:12:0.0109:0:1.2 -19 15355248 . G A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48662;SOR=1.87017;LSEQ=GTGGGGGCGAGGACTTCATC;RSEQ=CCGGGGCTGCCTGCTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:3:3,0:185,281:0.0064:2,0:1:0:27.3:1:0.06379:0:60:6:0.0068:0:1 0/1:420:5:3,2:175,237:0.0119:2,2:9.6:1:28:1:0.65494:2.03:60:10:0.0128:0:1.2 -19 15355257 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04087;SOR=Inf;LSEQ=AGGACTTCATCGCCGGGGCT;RSEQ=CCTGCTGCGGCATGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:184,233:0:2,0:22.6:1:30.8:1:1:0:60:11.636:1:0:0.6 0/1:343:4:2,2:144,189:0.0117:2,2:19:1:23.5:1:1:1.31:60:3:0.0098:0:2.5 -19 15355286 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.06419;SOR=Inf;LSEQ=GGCATGGAGGGTGGGGGAGG;RSEQ=GGGGGTGGCGGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:171,121:0:2,0:25.3:1:29.2:1:1:0:60:9.069:0.9962:0:0.7 0/1:200:3:1,2:106,86:0.015:2,2:13.3:1:27.3:1:0.58989:2.45396:60:6:0.0169:0:1 -19 15355423 . GAGAC G 100 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.60023;SOR=0.71653;LSEQ=ATGATGGTGCTGCAGACAGA;RSEQ=AGACAGACAGACAGGCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:9:6,3:470,226:0.0128:2,2:25.9:1:31.6:1:1:1.03975:58.9:18:0.013:0.0028:0.3 0/0:544:5:1,4:338,198:0.0092:2,2:22.6:1:29.8:1:0.06724:6.80494:60:10:0.0094:0.0018:0 -19 15356795 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGCAGCATGCCACCAAA;RSEQ=GGGATGGGGAAGGACCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:27.5:1:32.5:1:1:1:60:4:0.5:0:1 0/0:1:0:0,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 -19 15359971 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49902;SOR=Inf;LSEQ=GGACAGGCCCAGGGCTCTGA;RSEQ=GAATTCCATAACTTGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:136,17:0:2,0:23.8:1:31.9:1:1:0:60:75.5:1:0:0.1 0/1:164:2:1,1:137,25:0.0122:2,2:19:1:28:1:0.29276:5.39325:60:4:0.0123:0:1 -19 15360009 . G T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45715;SOR=2.21968;LSEQ=GGAGTCCTGTCCCTTTCACG;RSEQ=AAGAAAATGGACTTAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:2:1,1:228,84:0.0064:2,2:35.5:1:28:1:0.46875:2.70418:60:4:0.0065:0:1 0/1:356:5:2,3:242,109:0.014:2,2:5:1:24.8:1:0.18147:3.31784:60:10:0.0142:0:1.2 -19 15360216 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16756;SOR=Inf;LSEQ=TCCTGCGCCCTGGTGGCTGA;RSEQ=GGGCACAAGAACGGCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:10,148:0:2,0:24.6:1:30:1:1:0:60:30.6:1:0:0.1 0/1:110:2:1,1:5,103:0.0182:1,2:13:1:28.5:1:0.10659:18.89:60:4:0.0182:0:1 -19 15364464 . C T 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31354;SOR=2.45273;LSEQ=CCAGCAGCAGACTGGCGATG;RSEQ=GGCTGGCCAGCTGCAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:651:3:0,3:347,301:0.0046:2,0:1:0:26:1:0.10129:0:60:6:0.0047:0:1 0/1:534:6:1,5:301,227:0.0112:2,2:17.3:1:27.8:1:0.09023:6.60869:60:12:0.0114:0:1 -19 15364655 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16885;SOR=Inf;LSEQ=CCCCACGCCCACAGTCCTCA;RSEQ=GGCCCAGCTTCCCCGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:50,235:0:2,0:23.4:1:29.8:1:1:0:60:22.75:0.9964:0:0.1 0/1:200:2:1,1:46,151:0.01:2,2:34.5:1:29.5:1:0.41749:3.26:60:4:0.0103:0:1 -19 15364669 . C G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18021;SOR=Inf;LSEQ=TCCTCATGGCCCAGCTTCCC;RSEQ=GCCCACCATCCAGGGCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:27,196:0:2,0:23.9:1:29.9:1:1:0:60:73.333:1:0:0.1 0/1:165:2:1,1:27,136:0.0121:2,2:21.5:1:27.5:1:0.31146:4.96:60:4:0.0121:0:1 -19 15364683 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17099;SOR=Inf;LSEQ=CTTCCCCGCCCACCATCCAG;RSEQ=GCTCCGCAGTGTCAACGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:12,166:0:2,0:23.6:1:31:1:1:0:60:43.5:1:0:0.1 0/1:126:2:1,1:14,110:0.0159:2,2:29:1:28:1:0.22476:7.62:60:4:0.0161:0:1 -19 15364894 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50059;SOR=0;LSEQ=GGCTCTAGCATCCTGGACAC;RSEQ=GGACCGAGCTAGTGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:152,41:0.0102:2,2:24:1:29.5:1:0.38525:3.67526:60:4:0.0104:0:1 0/0:173:0:0,0:129,44:0:2,0:24.2:1:29.7:1:1:0:60:42.25:1:0:0.1 -19 15366000 . GA G 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.66742;SOR=0.3615;LSEQ=GAACACAGATATTATAATTG;RSEQ=AAAAAAAAAGGGGGGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:5:5,0:123,3:0.0382:1,0:16:1:31.9:1:1:0:60:10:0.04:0.0153:0 0/1:71:1:1,0:64,6:0.0141:2,0:17:0:33:0:1:0:60:2:0.0147:0:0 -19 15366010 . A AG 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.12516;LSEQ=ATTATAATTGGAAAAAAAAA;RSEQ=GGGGGGGGGCGCAGAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:71:69,2:63,0:0.4641:1,1:23.4:1:32.2:1:0.49804:0:60:22.667:0.5:0.1307:0.7 0/1:103:10:9,1:65,9:0.0971:2,2:27.4:1:31.8:1:1:1.24:60:20:0.1053:0:0.8 -19 15366029 . A T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27018;SOR=0;LSEQ=AAGGGGGGGGGCGCAGAAAG;RSEQ=GTGGACTGAGCAAGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:3:2,1:209,22:0.0127:2,2:18.3:1:22.3:1:0.26787:4.69533:60:2:0.0099:0:1 0/0:167:0:0,0:142,24:0:2,0:21.5:1:26.9:1:1:0:60:5.385:1:0:0.4 -19 15366449 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20809;SOR=Inf;LSEQ=TCAAGAACGGGCCCCCTGAG;RSEQ=AAGCCAGGCACTCATTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:37,146:0:2,0:21.3:1:30.9:1:1:0:60:90.5:1:0:0.1 0/1:154:2:1,1:37,115:0.013:2,2:20:1:28:1:0.43383:3.08:60:4:0.013:0:1 -19 15366663 . G A 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01284;SOR=0;LSEQ=ATCCTCCCCAACCAAACATG;RSEQ=TGAGCTCCGAAGGCTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:18:16,2:27,4:0.3673:2,2:26.4:1:29.7:1:1:1.18:60:17:0.3542:0:1.2 0/0:13:0:0,0:11,2:0:2,0:25.6:1:30.8:1:1:0:60:26:1:0:0 -19 15367141 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14249;SOR=Inf;LSEQ=TCCTGTCACCCAAGACCCAG;RSEQ=CGTCTGCTCCAAAAAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:9,132:0:2,0:22.2:1:31.9:1:1:0:60:46:1:0:0.1 0/1:86:2:1,1:6,78:0.0233:2,2:31:1:27:1:0.15705:12.11:60:4:0.0238:0:1 -19 15367720 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58878;SOR=2.48446;LSEQ=TCTTAGAAACTTCTGGGGAG;RSEQ=CCACCCTGGTCCACGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:1:1,0:184,55:0.0042:2,0:4:0:31:0:1:0:60:2:0.0043:0:1 0/1:194:2:2,0:131,59:0.0103:2,0:18.5:1:31:0:1:0:60:4:0.0105:0:1 -19 15367734 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25204;SOR=0;LSEQ=GGGGAGGCCACCCTGGTCCA;RSEQ=GGACTCTGGGGATTAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:2,1:213,77:0.0102:2,2:28.7:1:24.7:1:1:1.38148:60:2:0.0069:0:1 0/0:256:0:0,0:168,88:0:2,0:22.9:1:30.1:1:1:0:60:255:1:0:0.2 -19 15374138 . G GA 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58254;SOR=0.60175;LSEQ=TTATCCCAAGGAAAGTGACA;RSEQ=AAAAAAAAACTCTGCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:11:11,0:144,3:0.0696:1,0:20.5:1:30.2:1:1:0:60:22:0.0705:0.019:0.1 0/1:93:4:4,0:85,0:0.043:1,0:25.3:1:30:1:1:0:60:8:0.044:0:0 -19 15374435 . G T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28559;SOR=0;LSEQ=GTGGCTGGCAGCAGACGAAA;RSEQ=GGATGCCTAGAAGAGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:1,2:14,237:0.0118:2,2:15.3:1:32:1:0.16753:8.30:60:6:0.0119:0:1 0/0:162:0:0,0:15,146:0:2,0:22.7:1:30.3:1:1:0:60:79.5:0.9938:0:0 -19 15374491 . T TG 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.8669;LSEQ=CAGTTTGGTCAAGACTCTAG;RSEQ=GGGGGGACAGGCCATCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:0,2:2,69:0.0274:1,0:25.5:1:33:0:1:0:60:4:0.0278:0:0 0/1:42:1:0,1:1,40:0.0238:1,0:25:0:32:0:1:0:60:2:0.0238:0:1 -19 15376011 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54801;SOR=0;LSEQ=GACCTTTGAGTCAGTGGGGC;RSEQ=GCTGTTTCTGGGCTGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:3,0:56,1:0.05:1,0:33:1:28.3:1:1:0:60:6:0.0526:0:1 0/0:29:0:0,0:28,1:0:1,0:24.1:1:29.9:1:1:0:60:58:1:0:0 -19 15376087 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17685;SOR=Inf;LSEQ=GTGCCCGGGACCCAGGACAG;RSEQ=CTCTGTGTAAAGCACGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:162,44:0:2,0:21.7:1:31.1:1:1:0:60:102:1:0:0.1 0/1:150:2:1,1:116,30:0.0133:2,2:30.5:1:28.5:1:0.37617:3.82015:60:4:0.0135:0:1 -19 15376099 . G T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31133;SOR=4.29121;LSEQ=CAGGACAGGCTCTGTGTAAA;RSEQ=CACGGGCAAGGACAGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:0,1:186,68:0.0039:2,0:7:0:32:0:0.27059:0:60:2:0.004:0:1 0/1:180:3:2,1:131,46:0.0167:2,2:24.7:1:25.7:1:1:1.4209:60:6:0.0167:0:1 -19 15378434 . GCCAC G 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=7e-05;SOR=5.9886;LSEQ=CTGTAGACAGGGCACCCCAT;RSEQ=CCACCCCCTGCCCCCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:7:0,7:4,123:0.0522:1,0:21.4:1:32.6:1:1:0:60:14:0.0526:0:0 0/1:72:18:1,17:6,48:0.25:2,1:30.1:1:32.9:1:0.67154:2.10633:60:36:0.25:0:0.1 -19 15379563 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16093;SOR=Inf;LSEQ=AGTCACAGGAACAACCACAG;RSEQ=TCTCATTACCTCTACCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:49,1:0:1,0:24.2:1:31.3:1:1:0:60:24:1:0:0.1 0/1:34:2:1,1:29,3:0.0588:2,2:21.5:1:25:0:0.2246:8.51255:60:4:0.0588:0:1 -19 15379632 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20689;SOR=Inf;LSEQ=CAGCCACACCCAACACCCCT;RSEQ=CCCACGGGCTCCTGACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:150,9:0:2,0:24.5:1:32.1:1:1:0:60:30.8:1:0:0.1 0/1:134:2:1,1:120,12:0.0149:2,2:14.5:1:27:1:0.18528:9.64765:60:4:0.0153:0:1 -19 15379640 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50464;SOR=0;LSEQ=CCCAACACCCCTGCCCACGG;RSEQ=CTCCTGACATGCCCACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:177,18:0.0102:2,2:25:1:29:0:0.18404:9.59807:60:4:0.0106:0:1 0/0:158:0:0,0:140,18:0:2,0:22.9:1:30.8:1:1:0:60:78:1:0:0.2 -19 15379660 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66169;SOR=1.83725;LSEQ=GCTCCTGACATGCCCACTGC;RSEQ=GTCGCCTCCCCTCCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:2:0,2:217,43:0.0076:2,0:1:0:28:1:0.02895:0:60:4:0.0078:0:1 0/1:215:3:1,2:174,38:0.014:2,2:15.3:1:27.7:1:0.08962:9.01732:60:6:0.0142:0:1 -19 15379908 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20054;SOR=Inf;LSEQ=AGGCAGCCAGGCAGCACAAA;RSEQ=GCTGGGCTGGCCAGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:21,188:0:2,0:24.2:1:30.2:1:1:0:60:103.5:1:0:0.1 0/1:170:2:1,1:25,143:0.0118:2,2:32:1:32.5:1:0.28326:5.63:60:4:0.0119:0:1 -19 15383516 . C T 88 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03675;SOR=4.23297;LSEQ=AAGGGCCCTGCAGCTCTCAC;RSEQ=ATGATTCCAAATGCATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:4:4,0:90,3:0.0412:1,0:38:1:32:1:1:0:60:8:0.0421:0:1.3 0/1:45:7:7,0:35,3:0.1556:2,0:31:1:31.6:1:1:0:60:14:0.1591:0:1.9 -19 15383542 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.17313;SOR=Inf;LSEQ=TCCAAATGCATCTCCTACCC;RSEQ=CCCCCCAGGAACTGCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:120,7:0:2,0:26.9:1:30.8:1:1:0:60:24.4:1:0:0.1 0/1:91:2:2,0:76,13:0.022:2,0:22.5:1:31:0:1:0:60:4:0.0227:0:2 -19 15383582 . C A 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=13.50849;LSEQ=ACCAGGAGACATGCAGGAGA;RSEQ=GACCTCCAGGACGGCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:4:4,0:187,64:0.0157:2,0:20.3:1:32.3:1:0.5748:0:60:8:0.0159:0:1.3 0/1:225:40:33,7:124,58:0.1778:2,2:25.6:1:30.3:1:0.08466:2.20:60:80:0.1794:0:1.2 -19 15383958 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21864;SOR=Inf;LSEQ=AGGCACTCTACAAAGGAAGA;RSEQ=AAGAGCCCCCGTGAGATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:24,169:0:2,0:22.9:1:30.9:1:1:0:60:47.25:1:0:0.1 0/1:170:2:1,1:31,137:0.0118:2,2:32.5:1:27.5:1:0.34194:4.37:60:4:0.0118:0:1 -19 15383972 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22324;SOR=Inf;LSEQ=GGAAGAGAAGAGCCCCCGTG;RSEQ=GATATCAGTCAGCAGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:13,126:0:2,0:26.5:1:30.5:1:1:0:60:26.8:1:0:0.1 0/1:125:2:1,1:19,104:0.016:2,2:38:1:30:1:0.29548:5.36:60:4:0.0163:0:1 -19 15449749 . T TA 30 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.6233;LSEQ=AGACAGAGCAAGACTCCGTT;RSEQ=AAAAAAAAAAACAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:7,3:0.1667:2,0:24.5:1:27.5:1:1:0:60:4:0.1667:0.0833:0.5 0/1:8:2:2,0:4,2:0.25:2,0:24:1:30:1:1:0:60:4:0.25:0.125:0 -19 15449967 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=GCTGTTGGGATTCTTCTAAA;RSEQ=GGACAAGTTAAGGGCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:6,11:0:2,0:22.1:1:29.9:1:1:0:60:34:1:0:0.1 0/1:13:2:1,1:6,5:0.1538:2,2:26:1:28.5:1:1:1.18321:60:4:0.1538:0:1 -19 15888953 . T A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=ACTACAGAGGAATGAGTGAG;RSEQ=GAGGAGAGGAGTGAGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:43:0:31:0:1:0:60:2:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:36.5:1:30:0:1:1:60:4:0.5:0:1 -19 15889924 . G A 28 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GTGAGTGAGTGAGTGAGGAG;RSEQ=GGAGTGCGTGAGTGAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19:0:31.5:1:1:0:24:4:1:0:3.5 0/1:5:2:1,1:1,2:0.4:2,2:15.5:1:28.5:1:1:1.73:60:4:0.4:0:2 -19 15889945 . G GGAGT 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=4.000;MSILEN=4;SSF=0.44444;SOR=Inf;LSEQ=GGAGTGCGTGAGTGAGGAGA;RSEQ=GAGTGAGTGAGTGCATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:30.5:1:32:1:1:0:26.5:8:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:37.5:1:30.1:1:1:1.73:60:4:0.4:0:2 -19 15889963 . G A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GAGGAGTGAGTGAGTGCATG;RSEQ=GTAGAGGAGTGAGTGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:30.5:1:30.5:1:1:1:24:4:0.5:0:3.5 0/0:5:0:0,0:2,3:0:2,0:19.2:1:31:1:1:0:48.8:10:1:0:1 -19 15889969 . GGAGT G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.42857;SOR=0;LSEQ=TGAGTGAGTGCATGGGTAGA;RSEQ=GAGTGAGTGAGGAGAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:31.5:1:32.5:1:1:1:29:4:0.5:0:0.5 0/0:3:0:0,0:1,2:0:2,0:20.7:1:32.7:1:1:0:51.3:6:1:0:1.3 -19 15890075 . C T 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGTGAGTGAGGAGAGGAGTG;RSEQ=GTGAGTGAGGAGAGGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28:1:17.5:1:1:0:25:1:1:0:3 1/0:3:2:1,1:0,1:0.6667:0,2:37:1:26:1:1:0:49:4:0.6667:0:1 -19 15890088 . A G 27 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AGGAGTGCGTGAGTGAGGAG;RSEQ=GGAGTGAGTGAGTGCATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:27:1:1:0:25:4:1:0:3 0/0:3:0:0,0:1,2:0:2,0:39:1:29.3:1:1:0:41:6:1:0:1.3 -19 15890134 . AGAG A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAGTGAGTGAGTGCATGGGT;RSEQ=GAGTGAGTGAGTGCATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:8.5:1:34:0:1:0:42.5:4:1:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:36.5:1:32:1:1:0:55:4:0.6667:0:0.5 -19 15890316 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=4.000;MSILEN=1;SSF=0.03126;SOR=0.29219;LSEQ=GGGAGTGAGTGAGTGAGGAG;RSEQ=GGAGTGAGTGCATGGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:40:38,2:6,0:0.8696:0,2:20.9:1:29.6:1:1:0:58.7:19:0.8837:0:1.7 1/0:35:23:22,1:10,2:0.6571:2,1:23.3:1:28.3:1:0.26555:4.20:60:10.5:0.6563:0:1.9 -19 15890386 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23421;SOR=0;LSEQ=GCATGGGTAGAGGAGTGAGT;RSEQ=AATGAGCCGCCTCCCTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:146,41:0.0106:2,2:34.5:1:29.5:1:0.39598:3.53014:60:4:0.0108:0:2 0/0:201:0:0,0:158,43:0:2,0:21.5:1:31.3:1:1:0:60:32.5:1:0:1.1 -19 15890388 . A G 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00044;SOR=0.06593;LSEQ=ATGGGTAGAGGAGTGAGTGA;RSEQ=TGAGCCGCCTCCCTCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:198:197:152,45:0,0:0.9949:0,2:22.7:1:31.7:1:1:0:60:38.4:0.9948:0:1.2 1/1:209:194:150,44:10,5:0.9282:2,2:21.6:1:31.5:1:0.35089:1.70:60:47.5:0.9268:0:1.2 -19 15890517 . A C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.47562;LSEQ=CAGAGTCATCCTGCTGCCAC;RSEQ=CTCACGAGGTCCTGGTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:114:48,66:108,171:0.2886:2,2:24.9:1:30.4:1:0.5706:1.15:60:21.8:0.2861:0:1.2 1/0:384:265:104,161:49,70:0.6901:2,2:22.2:1:30.2:1:0.73629:1.08343:60:65.25:0.6941:0:1.1 -19 15890568 . G T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11358;SOR=Inf;LSEQ=TTTCTGTTTTGGGGGTTGTG;RSEQ=AAAGTACTGAAGGCGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:95,184:0:2,0:25.5:1:30.8:1:1:0:60:26.9:1:0:0.7 0/1:263:3:1,2:99,161:0.0114:2,2:24.7:1:21.7:1:1:1.22884:60:2:0.0078:0:1.7 -19 15890625 . CG GA 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01285;LSEQ=ATAGGTCCAGGCCAGGAAGC;RSEQ=GCCAGGAGCCGGGAGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:80:24,56:0,1:0.6107:0,2:21.8:1:30.7:1:1:0:60:160:0.6299:0.0763:1 0/1:103:2:1,1:10,19:0.0194:2,2:17:1:26.3:1:1:1.86:60:4:0.0198:0.0097:0.5 -19 15890626 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25444;SOR=0;LSEQ=TAGGTCCAGGCCAGGAAGCC;RSEQ=GCCAGGAGCCGGGAGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:0,3:10,34:0.0254:2,0:24:1:31.3:1:1:0:60:6:0.0625:0:3 0/0:96:0:0,0:28,67:0:2,0:23.4:1:30:1:1:0:60:30.667:1:0:0.9 -19 15890725 . G T 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00255;SOR=0;LSEQ=AGGCTCAGCTGCGGCATCCT;RSEQ=CAGGGCAGACAGGATGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:0,10:0,6:0.625:0,0:17.3:1:29.8:1:1:0:60:20:0.625:0:1 0/0:10:0:0,0:0,10:0:0,0:26.3:1:31.3:1:1:0:60:20:1:0:0.6 -19 15890771 . T G 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.45385;LSEQ=ATCCTGAGGCCCAGGGAAAG;RSEQ=CTCAGGGAGCTCCAGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:20.8:1:33.3:1:1:0:60:8:0.5:0:2.3 1/0:5:3:0,3:0,2:0.6:0,0:18.7:1:33.7:1:1:0:60:6:0.6:0:2 -19 15890777 . G T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=AGGCCCAGGGAAAGTCTCAG;RSEQ=GAGCTCCAGGGACAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:25:1:30.7:1:1:0:60:6:0.4286:0:2.7 1/0:4:2:0,2:0,2:0.5:0,0:19:1:31:1:1:0:60:4:0.5:0:2.5 -19 15890800 . A G 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=GCTCCAGGGACAGTGGAGAG;RSEQ=AGCAGGGAAGGGGTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:25.3:1:31:1:1:0:60:6:0.4286:0:2.3 1/0:2:1:0,1:0,1:0.5:0,0:9:0:33:0:1:0:60:2:0.5:0:3 -19 16044035 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAGGAATGAGTGAGTGAG;RSEQ=AGAGGAATGAGTGAGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:29.5:1:1:0:59:4:1:0:1.5 -19 16044722 . A G 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=ATGAGTGAGTGGGCAGAGGA;RSEQ=TGAGTGAGCGGGGAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:9:0:33.5:1:1:1:34:4:0.3333:0:3.5 0/0:3:0:0,0:2,1:0:2,0:9.7:1:28.7:1:1:0:37.7:6:1:0:1.3 -19 16044742 . A G 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52689;LSEQ=ATGAGTGAGCGGGGAGAGGA;RSEQ=TGAGTGAGCGGGGAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:29:0:32:1:1:1.41:34:4:0.2857:0:3.5 0/1:6:1:0,1:4,1:0.1667:2,0:14:0:14:0:0.33333:0:60:0:0:0:6 -19 16044762 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=ATGAGTGAGCGGGGAGAGGA;RSEQ=TGAGTGAGCGGGGAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:29.1:1:30.9:1:1:0:42.4:16:1:0:1.9 0/1:6:2:1,1:3,1:0.3333:2,2:33:1:30.5:1:1:2.44949:53.5:4:0.3333:0:6 -19 16044775 . G C 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.62174;LSEQ=GAGAGGAATGAGTGAGCGGG;RSEQ=AGAGGAATGAGTGAGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:33:0:33:0:1:1:46:4:0.25:0:2.5 0/1:6:1:1,0:3,2:0.1667:2,0:35:0:33:0:1:0:53:2:0.25:0:6 -19 16044782 . A G 64 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02098;SOR=Inf;LSEQ=ATGAGTGAGCGGGGAGAGGA;RSEQ=TGAGTGAGCGGGGAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:23.3:1:28:1:1:0:39.9:6:1:0:2.4 1/0:6:4:2,2:2,0:0.6667:0,2:32.3:1:32:1:0.46667:0:41.3:8:0.6667:0:4 -19 16044793 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=GGGAGAGGAATGAGTGAGCG;RSEQ=GGAGAGGAATGAGTGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:15:0:31:1:1:1.41:46:4:0.2857:0:2.5 0/0:7:0:0,0:4,3:0:2,0:23.7:1:29.7:1:1:0:46.6:14:1:0:3.6 -19 16044795 . G C 38 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19231;SOR=Inf;LSEQ=GAGAGGAATGAGTGAGCGGG;RSEQ=AGAGGAATGAGTGAGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:19:1:28.9:1:1:0:39.9:6:1:0:2.4 0/1:7:3:1,2:3,1:0.4286:2,2:28:1:24.3:1:0.48571:4.4496:55.3:2:0.3333:0:5 -19 16044802 . A G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=ATGAGTGAGCGGGGAGAGGA;RSEQ=TGAGTGAGTGGGCAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:23:1:31.2:1:1:0:42.2:10:1:0:2 0/1:5:2:1,1:2,1:0.4:2,2:24.5:1:30:1:1:1.7321:53.5:4:0.5:0:6 -19 16044811 . T C 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=CGGGGAGAGGAATGAGTGAG;RSEQ=GGGCAGAGGAATGAGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,2:0.3333:0,0:50:0:34:0:0.33333:0:55:2:0.5:0:2 0/1:5:2:1,1:2,1:0.4:2,2:15.5:1:28:1:1:1.7321:53.5:4:0.5:0:6 -19 16044851 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=TGGGCAGAGGAATGAGTGAG;RSEQ=GGGGAGAGGAATGAGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:0.4286:2,0:13.7:1:24.7:1:1:0:60:2:0.3333:0:1.7 0/0:3:0:0,0:2,1:0:2,0:25.7:1:26.3:1:1:0:57.7:2:1:0:2.3 -19 16044871 . T C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.45647;LSEQ=CGGGGAGAGGAATGAGTGAG;RSEQ=GGGCAGAGGAATGAGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:0.25:2,2:15.5:1:33:1:0.46429:3.87298:49:4:0.2857:0:2.5 0/1:6:2:1,1:3,1:0.3333:2,2:25:1:30:1:1:2.44949:56.5:4:0.3333:0:3.5 -19 16044875 . C G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52527;SOR=3.62203;LSEQ=GAGAGGAATGAGTGAGTGGG;RSEQ=AGAGGAATGAGTGAGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:6,2:0.1111:2,0:29:0:33:0:1:0:60:2:0.125:0:2 0/1:6:2:2,0:3,1:0.3333:2,0:26:1:31:1:1:0:60:4:0.3333:0:2.5 -19 16045035 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15455;SOR=Inf;LSEQ=ACTCACCAGGCCCTGGTGTC;RSEQ=CCAAAACCAGTTCTGTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:0:2,0:27.2:1:30.9:1:1:0:60:54:1:0:0 0/1:18:2:1,1:9,7:0.1111:2,2:36.5:1:28:1:1:1.26772:60:4:0.1111:0:1 -19 16045141 . T C 91 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=0;LSEQ=CGGGCCAGGAGCCAGGAGCC;RSEQ=CCAACCAGCAGCAGAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:26.7:1:32.6:1:1:0:60:14:1:0:1 1/0:5:3:0,3:1,1:0.6:2,0:13:1:33:0:0.4:0:60:6:0.6:0:1 -19 16045817 . G C 29 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGCTGGGTGCAGAGGAGCCA;RSEQ=CTCAGGGTGACACAGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5:0:29.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:37:0:33.5:1:1:0:60:4:1:0:0.5 -19 16126203 . T G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGTTGGGGCCTGGTCAG;RSEQ=GAGGATCAGATCAGTGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 16133219 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTGGAGTTTCCTTTTCC;RSEQ=GCCCTGGAGCAGGCAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:32:0:1:0:60:4:1:0:1.5 -19 16133428 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49758;SOR=0;LSEQ=AGCCCCAAGGACCTCTGCTG;RSEQ=TCCCATTAGGACAAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:17,7:0.0769:2,2:24.5:1:30.5:1:0.52923:2.3376:60:4:0.08:0:1 0/0:20:0:0,0:11,9:0:2,0:17:1:30.9:1:1:0:60:40:1:0:0.3 -19 16133492 . C A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49392;SOR=Inf;LSEQ=TTACGCTGACTCCTCCAGTG;RSEQ=CTCATCAATGAAGTAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,15:0:2,0:26.6:1:30.9:1:1:0:60:28:1:0:0.2 0/1:33:2:1,1:13,18:0.0606:2,2:26:0:27:1:1:1.37:60:4:0.0606:0:1.5 -19 16133647 . T C 52 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGACCCTCCTGCCCCA;RSEQ=ACTCCCCAGATCCCCCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:18:1:33:0:1:0:60:6:1:0:1.7 1/1:1:1:0,1:0,0:1:0,0:22:0:34:0:1:0:60:2:1:0:1 -19 16435563 . T A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCCATCCGGGACGCGTT;RSEQ=CCGCCGCCGCCGCTTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 16435911 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGACGCGAAGGCGGGGACTG;RSEQ=AGACTCAGGAGAGGAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:12:0:27:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:27.5:1:1:0:60:4:1:0:1 -19 16436765 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCCGCAAACGCACCGCCACT;RSEQ=ACACCTGCAGCTACGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:45,25:0:2,0:23.3:1:31.2:1:1:0:60:34:1:0:0.1 0/1:141:2:1,1:86,52:0.0142:2,2:38.5:1:30:1:1:1.6476:60:4:0.0143:0:1 -19 16436817 . T C 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5524;SOR=Inf;LSEQ=CTACACCAAGAGTTCGCATC;RSEQ=GAAGGCGCATCTGCGCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:30,40:0:2,0:26:1:30.5:1:1:0:60:69:1:0:0.1 0/1:142:3:1,2:62,75:0.0211:2,2:20:1:22.7:1:1:1.64765:60:2:0.0146:0:1 -19 16436824 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGAGTTCGCATCTGAAGGC;RSEQ=CATCTGCGCACGCACACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:24,37:0:2,0:26.1:1:31.2:1:1:0:60:60:1:0:0.1 0/1:125:2:1,1:52,71:0.016:2,2:12:1:24.5:1:1:1.36:60:4:0.0163:0:1 -19 16437671 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCCCTCCCTGCAGGTGA;RSEQ=AAGCCCTACCACTGCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:27.5:1:1:0:60:4:1:0:1 -19 17193435 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.4983;SOR=Inf;LSEQ=TTTCCTGGTGAATGTGCCAT;RSEQ=GGGGGCAAGGGGTAGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:121,16:0:2,0:26.3:1:32.1:1:1:0:60:274:1:0:0.3 0/1:141:2:1,1:124,15:0.0142:2,2:17.5:1:28.5:1:0.21479:8.03591:60:4:0.0144:0:1.5 -19 17193518 . A G 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19747;LSEQ=GGAGATGCTGTTTATTGGGT;RSEQ=GGCACAAGAACAAGAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:468:426:231,195:22,20:0.9103:2,2:26.9:1:31.2:1:0.87176:1.08:60:37.727:0.9081:0:1.9 1/0:588:392:207,185:104,91:0.6667:2,2:26.7:1:30.7:1:0.93017:1.02136:60:129.667:0.6684:0:1.9 -19 17193551 . A G 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29173;LSEQ=AGAGAGGCGGAGAAAGTGTG;RSEQ=TCGTACTTATTTGGCCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:531:487:229,258:21,23:0.9171:2,2:25.1:1:31.5:1:1:1.02862:60:120.75:0.9165:0:1.8 1/0:655:500:237,263:75,80:0.7634:2,2:25.5:1:30.9:1:0.85425:1.0403:60:99:0.7627:0:1.8 -19 17193654 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49864;SOR=0;LSEQ=GCAGGGAAGGGAGAAGGTAA;RSEQ=GGTTGGGGTGTCCTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:21,125:0.0135:2,2:11:1:30:1:0.27606:5.84:60:4:0.014:0:1 0/0:140:0:0,0:19,121:0:2,0:21.1:1:30.5:1:1:0:60:280:1:0:0.1 -19 17700442 . A T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGGAAGAGGTTCCAGCAGCT;RSEQ=AGGCTCCTTCCCACTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:14.3:1:29.3:1:1:0:60:6:1:0:0 1/0:4:2:1,1:2,0:0.5:0,2:40:1:28.5:1:1:0:60:4:0.5:0:1 -19 17700634 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11659;SOR=Inf;LSEQ=CACATCAATTCTCTTGGCAA;RSEQ=GATCTTGCCCTCGTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:50,17:0:2,0:21.4:1:31.7:1:1:0:60:134:1:0:0.1 0/1:65:3:1,2:47,15:0.0462:2,2:21.7:1:29.3:1:0.16502:6.05045:60:6:0.0462:0:1.3 -19 17700647 . G A 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTGGCAAGGATCTTGCCCTC;RSEQ=TTTGTTTACAACAATGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:59,35:0:2,0:20:1:30:1:1:0:60:46:1:0:0.1 0/1:83:15:11,4:47,21:0.1807:2,2:19.1:1:30:1:1:1.23:60:30:0.1829:0:1 -19 17700751 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51554;SOR=Inf;LSEQ=CTTTTTGAACAGTACCTTCT;RSEQ=TTGATGTCTACAATATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:23,35:0:2,0:22.8:1:31.1:1:1:0:59.7:57:1:0:0.1 0/1:86:2:1,1:31,53:0.0233:2,2:19.5:1:29:1:1:1.70:60:4:0.0235:0:1.5 -19 17700770 . C T 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00111;SOR=Inf;LSEQ=TCTTGATGTCTACAATATCA;RSEQ=CTTTCTTATAGATTCACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:17,34:0:2,0:23.9:1:31.1:1:1:0:59.6:50:1:0:0.1 0/1:64:11:3,8:17,35:0.1719:2,2:22.8:1:27.9:1:1:1.2901:59.8:10:0.1587:0:1 -19 17700822 . TA T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.03172;SOR=2.45846;LSEQ=AGGAACAACTTCATGTTTTC;RSEQ=AAAAAGCCTAGAGAACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:29:16,13:13,12:0.537:2,2:24.3:1:30.7:1:1:1.13:57:28:0.5283:0.1296:0.3 1/0:62:46:27,19:12,4:0.7419:2,2:26.4:1:30.8:1:0.36883:2.08697:59.9:92:0.7419:0.1129:0.2 -19 17700893 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49844;SOR=0;LSEQ=TTTGTCATCTTGGCAAATTA;RSEQ=TGGAAGATGGCGGTTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:88,71:0.0124:2,0:35.5:1:30:1:0.50388:0:60:4:0.0125:0:1 0/0:160:0:0,0:88,72:0:2,0:29.7:1:31:1:1:0:60:159:1:0:0.2 -19 17700902 . G A 22 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49847;SOR=Inf;LSEQ=TTGGCAAATTACTGGAAGAT;RSEQ=GCGGTTCTGGCCGAAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:87,77:0:2,0:29.1:1:31.4:1:1:0:60:81:1:0:0.2 0/1:164:2:2,0:81,81:0.0122:2,0:6.5:1:22.5:1:0.49701:0:60:4:0.0123:0:1 -19 17700904 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4985;SOR=0;LSEQ=GGCAAATTACTGGAAGATGG;RSEQ=GGTTCTGGCCGAAAAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:85,77:0.0122:2,2:38:0:31.5:1:1:1.10323:60:4:0.0123:0:1.5 0/0:161:0:0,0:80,81:0:2,0:29.3:1:30.2:1:1:0:60:160:1:0:0.2 -19 17700920 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24749;SOR=Inf;LSEQ=ATGGCGGTTCTGGCCGAAAA;RSEQ=CCCCACTGGTATCCTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:74,76:0:2,0:23.5:1:32:1:1:0:60:300:1:0:0.3 0/1:149:2:1,1:69,78:0.0134:2,2:31.5:1:28.5:1:1:1.13:60:4:0.0134:0:1.5 -19 17700980 . T C 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11503;SOR=2.57282;LSEQ=ACTCCAAGTCACTCCAATCC;RSEQ=TTCAATGCTATGTATTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:35:0,35:0,13:0.7292:1,1:21.3:1:31.3:1:1:0:60:34:0.7234:0:1.5 1/1:40:35:0,35:0,5:0.875:0,1:24.5:1:32.7:1:1:0:60:70:0.875:0:1.4 -19 17701011 . T C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01121;SOR=Inf;LSEQ=TGTATTCACCTAACCTCTTG;RSEQ=CTCCCTCTTCTAAGGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:0:1,0:27.6:1:30.2:1:1:0:60:58:1:0:1.3 0/1:22:5:0,5:0,17:0.2273:1,0:23.2:1:32.6:1:1:0:60:10:0.2273:0:2.6 -19 17701030 . T C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91903;LSEQ=GTCTCCCTCTTCTAAGGACA;RSEQ=TTGTGATTACATTTAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:16:0,16:0,4:0.8:0,1:31.3:1:32.9:1:1:0:60:32:0.8:0:1.9 1/0:14:11:0,11:0,3:0.7857:0,0:23.5:1:32.8:1:1:0:60:22:0.7857:0:1.9 -19 17937429 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=3.65424;LSEQ=GCCCCCCCAAATGCAATGTC;RSEQ=TGGGGGTGTTCCTGAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:20:20,0:134,5:0.1258:1,1:25.7:1:30:1:1:0:60:40:0.1266:0:1.2 0/1:107:37:35,2:70,0:0.3458:1,2:23.3:1:30.1:1:0.11744:0:60:74:0.3458:0:1.1 -19 17937434 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51041;SOR=0;LSEQ=CCCAAATGCAATGTCATGGG;RSEQ=GTGTTCCTGAAGTAGAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:169,4:0.0114:1,2:29:1:29:1:0.05649:37.88902:60:4:0.0117:0:1 0/0:128:0:0,0:125,3:0:1,0:20.2:1:30.7:1:1:0:60:41.667:1:0:0.4 -19 17937479 . A G 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATAAGGCCTCTGAGGCCCAG;RSEQ=GAGGGGCAGCTCCGGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:0:0,0:314,119:0:2,0:22.4:1:29.9:1:1:0:60:53.125:1:0:0.2 0/1:383:17:12,5:258,107:0.0444:2,2:21.4:1:28.9:1:1:1.00466:60:16:0.0428:0:1 -19 17937749 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5072;SOR=0;LSEQ=GGGGGACAGATAATGGGGTC;RSEQ=TGCCTGAGCAGTCCAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:32,155:0.0106:2,2:42:1:30.5:1:0.31949:4.79:60:4:0.0108:0:1 0/0:145:0:0,0:41,104:0:2,0:26.1:1:30.2:1:1:0:60:71.5:1:0:0.5 -19 17937758 . C T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.989;LSEQ=ATAATGGGGTCGTGCCTGAG;RSEQ=AGTCCAAAGGACACAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:11:2,9:22,132:0.0667:2,2:19.8:1:28.2:1:0.66304:1.33:60:22:0.0679:0:1 0/1:126:46:14,32:20,60:0.3651:2,2:23.5:1:27.8:1:0.53663:1.31:60:45:0.3659:0:1.7 -19 17937786 . C T 138 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=55.94822;LSEQ=AGGACACAACTCCCATTCAG;RSEQ=GTATTTGTTTTTGTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:1:0,1:4,101:0.0094:1,0:14:0:32:0:1:0:60:2:0.0096:0:1 0/1:71:25:5,20:10,36:0.3521:2,2:20.6:1:29.8:1:1:1.10951:60:50:0.3676:0:2.2 -19 17940705 . C T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01781;SOR=Inf;LSEQ=CCTCACCCTATAAGGCATTA;RSEQ=TATTCTCATTTTGGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:45,2:0:1,0:21.3:1:32:1:1:0:60:94:1:0:0 0/1:40:5:4,1:31,4:0.125:2,2:16.8:1:29.4:1:0.50664:1.89953:60:10:0.1316:0:1.2 -19 17940758 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22666;SOR=Inf;LSEQ=TCTGAAAGTGCTCTGACTTG;RSEQ=CACACAGTGAGAGAGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:120,6:0:1,0:24.7:1:31.4:1:1:0:60:17:1:0:0.4 0/1:115:2:1,1:95,17:0.0174:2,2:24:1:31:0:0.29204:5.45938:60:4:0.0183:0:2 -19 17940765 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49987;SOR=0;LSEQ=GTGCTCTGACTTGCCACACA;RSEQ=TGAGAGAGTAGCCAAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:132,12:0.0137:2,2:17:1:29.5:1:0.17071:10.60856:60:4:0.0139:0:1 0/0:130:0:0,0:107,23:0:2,0:25.8:1:31.4:1:1:0:60:42.333:1:0:0.5 -19 17940785 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22548;SOR=Inf;LSEQ=GTGAGAGAGTAGCCAAGTGG;RSEQ=GGCCAGGATCCTCATCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:176,38:0:2,0:24.2:1:30.9:1:1:0:60:41.8:1:0:0.5 0/1:194:2:1,1:139,53:0.0103:2,2:22:1:29:1:0.48026:2.60758:60:4:0.0105:0:2.5 -19 17940816 . G C 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05289;SOR=1.38491;LSEQ=CTCATCGGCCTCACACTCTA;RSEQ=CCTTTCTTCTCAGTACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:95:63,32:164,91:0.2707:2,2:25.5:1:31.4:1:0.80151:1.09:60:190:0.2802:0:1.9 0/1:374:127:81,46:144,102:0.3396:2,2:21.2:1:30.9:1:0.3719:1.25:60:254:0.3451:0:2 -19 17940842 . G A 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01224;SOR=1.44597;LSEQ=CTTCTCAGTACAGAGACTCA;RSEQ=GCGCCAGCTGGCTTGCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:114:65,49:180,140:0.2627:2,2:27.3:1:30.1:1:0.91276:1.03:60:113:0.2665:0:1.9 0/1:494:168:93,75:174,152:0.3401:2,2:27.4:1:30.1:1:0.70366:1.08:60:83:0.3437:0:1.9 -19 17941060 . A G 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27129;SOR=2.70534;LSEQ=AGGAGCGCATGTGGTGGGGG;RSEQ=GGAGCCTCCGTGGGTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:2:0,2:141,222:0.0055:2,0:10:1:21:1:0.52455:0:60:1:0.0029:0:1.5 0/1:340:5:2,3:139,196:0.0147:2,2:31.2:1:26.8:1:1:1.06359:60:4:0.0123:0:1.4 -19 17941079 . G T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01856;SOR=Inf;LSEQ=GAGGAGCCTCCGTGGGTGGA;RSEQ=GGGGAGGGGCCACCCGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:82,179:0:2,0:23.6:1:30.9:1:1:0:60:51.2:1:0:0.2 0/1:216:5:2,3:71,140:0.0231:2,2:14.2:1:29.6:1:1:1.31:60:10:0.0235:0:1.2 -19 17941084 . A G 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25754;SOR=0;LSEQ=GCCTCCGTGGGTGGAGGGGG;RSEQ=GGGGCCACCCGTGGTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:0,3:66,169:0.0125:2,0:36:1:23.7:1:0.56253:0:60:2:0.0092:0:2.3 0/0:192:0:0,0:60,131:0:2,0:21.9:1:28.5:1:1:0:60:11.733:1:0:0.3 -19 17941102 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.1786;SOR=Inf;LSEQ=GGAGGGGCCACCCGTGGTGG;RSEQ=GGTAGGGGCCATCTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:32,134:0:2,0:22:1:30.9:1:1:0:60:54.333:1:0:0.3 0/1:122:2:1,1:19,101:0.0164:2,2:11:1:28.5:1:0.30213:5.21:60:4:0.0167:0:1 -19 17941143 . A C 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCGGGGAGGGGCTGCCTG;RSEQ=ACCGTGAAGGGGTCAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:22,67:0:2,0:25.8:1:30.1:1:1:0:60:43.5:1:0:0.3 0/1:48:11:2,9:4,33:0.2292:2,2:19.6:1:30.1:1:0.60927:1.81:60:10:0.2128:0:2.1 -19 17941173 . C G 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00075;SOR=18.53233;LSEQ=GGGTCAGAAAGGTGAGGAAG;RSEQ=GTCCTCCCCACTGGGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:1,0:29,47:0.013:2,0:17:0:11:0:0.38961:0:60:0:0:0:2 0/1:40:8:4,4:13,19:0.2:2,2:27.9:1:31.1:1:0.70247:1.45:60:16:0.2:0:2.1 -19 17941181 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1111;SOR=Inf;LSEQ=AAGGTGAGGAAGCGTCCTCC;RSEQ=CACTGGGGCCTATGATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:39,42:0:2,0:22.4:1:31:1:1:0:60:26:1:0:0.3 0/1:41:2:1,1:18,21:0.0488:2,2:23.5:1:32:1:1:1.16:60:4:0.05:0:2.5 -19 17941254 . T C 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00913;SOR=Inf;LSEQ=AGGCGCAGACAGGTTGGAGA;RSEQ=TGGCCACGAGGGGCGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:104,25:0:2,0:23.7:1:30.4:1:1:0:60:63.5:1:0:0.1 0/1:112:6:4,2:86,20:0.0536:2,2:23.3:1:30.8:1:0.33561:2.13236:60:12:0.055:0:1.3 -19 17941294 . T C 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGAAGAAGGCTGGGGGC;RSEQ=CTGGGAAGCCGACTCACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:182,91:0:2,0:23.5:1:30.4:1:1:0:60:44.5:1:0:0.1 0/1:250:73:50,23:120,56:0.292:2,2:24.2:1:29.4:1:1:1.01:60:17.25:0.2851:0:1.1 -19 17941477 . GAAGAG AAAGA 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27422;SOR=Inf;LSEQ=CGAGGGTGTAGAAAGGACAG;RSEQ=GGGGGCAGCCTTGGAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:27,114:0:2,0:22.4:1:30.7:1:1:0:60:34.25:1:0:0.1 0/1:206:3:2,1:43,159:0.0146:2,2:17.3:1:26.9:1:0.12198:7.30:60:6:0.0148:0.0049:1 -19 17941927 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02138;SOR=Inf;LSEQ=CCAAAGCTGCAGCGGAGGAA;RSEQ=GGCGGGGCTAAGGCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:86,2:0:1,0:21.7:1:31.8:1:1:0:60:43:1:0:0.3 0/1:56:4:4,0:52,0:0.0714:1,0:21:1:30.3:1:1:0:60:8:0.0741:0:1 -19 17941937 . A G 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AGCGGAGGAAGGGCGGGGCT;RSEQ=AGGCTGGGGAGCAAAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:108,2:0:1,0:22:1:28.4:1:1:0:60:54:1:0:0.2 0/1:72:11:11,0:60,1:0.1528:1,0:24.2:1:32.5:1:1:0:60:22:0.1594:0:1.6 -19 17941998 . G T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.04705;SOR=Inf;LSEQ=CTGGGGGCGGAGCCAGAGCC;RSEQ=TGGGGAATAGGGGCGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:266,120:0:2,0:24.5:1:30.1:1:1:0:60:772:1:0:0.3 0/1:338:4:1,3:221,113:0.0118:2,2:11.8:1:23.8:1:0.11873:5.83534:60:3:0.0091:0:1.5 -19 17942005 . A G 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGAGCCAGAGCCGTGGGGA;RSEQ=TAGGGGCGGAGCCTAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:0:0,0:289,147:0:2,0:24.3:1:29.5:1:1:0:60:28.067:0.9976:0:0.3 0/1:376:121:79,42:159,95:0.3218:2,2:25.6:1:30.7:1:0.64747:1.12:60:59.5:0.3278:0:1.3 -19 17942180 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01915;SOR=Inf;LSEQ=GCGGCCAGGTCGCGGTGCAC;RSEQ=CAGCGGCGGGAGCCCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:0:0,0:172,326:0:2,0:25.2:1:30.7:1:1:0:60:34.571:1:0:0.2 0/1:415:5:3,2:144,266:0.012:2,2:14.6:1:27.4:1:0.35147:2.76:60:10:0.0124:0:1.2 -19 17942298 . C G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57005;SOR=2.86512;LSEQ=CTGGCACCCCAACCCAGACC;RSEQ=CAACTATAACCCTACCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:1,0:26,62:0.0112:2,0:40:0:9:0:0.30337:0:60:0:0:0:3 0/1:63:2:1,1:21,40:0.0317:2,2:18:1:30:1:1:1.88:60:4:0.0317:0:1 -19 17942370 . T C 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTAAGCCAACCCCACCAC;RSEQ=CCCGAGACCTGGACCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:82,22:0:2,0:25.5:1:31:1:1:0:60:103:1:0:0 0/1:104:26:22,4:66,12:0.25:2,2:24.9:1:29:1:1:1:60:25:0.2475:0:1 -19 17942411 . C T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25268;SOR=Inf;LSEQ=CCACTCCTCAGCCTTCACCG;RSEQ=GACCTCCAAGCAGACCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:145,61:0:2,0:23:1:30.8:1:1:0:60:40.2:1:0:0.1 0/1:240:3:0,3:165,72:0.0125:2,0:11.3:1:25:1:0.02968:0:60:6:0.0128:0:1 -19 17942412 . G A 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CACTCCTCAGCCTTCACCGC;RSEQ=ACCTCCAAGCAGACCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:151,65:0:2,0:22.4:1:29.7:1:1:0:60:53:1:0:0.1 0/1:246:17:11,6:158,71:0.0691:2,2:24.9:1:30.1:1:0.78754:1.21282:60:34:0.0702:0:1.1 -19 17942451 . A G 98 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04033;SOR=7.30846;LSEQ=GCCCAGGCCGTGCCAGCTGA;RSEQ=TCCCCACAAGTCCCGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:1:1,0:216,162:0.0026:2,0:5:0:33:0:1:0:60:2:0.0026:0:0 0/1:421:8:5,3:222,191:0.019:2,2:18.4:1:32.9:1:0.73075:1.43:60:16:0.0193:0:1.5 -19 17942604 . C T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01221;SOR=Inf;LSEQ=TGACCAGCCGCAGGCTCTGG;RSEQ=GGCCTGGAGAAGGCAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:120,183:0:2,0:25.7:1:30.2:1:1:0:60:49.5:1:0:0.1 0/1:283:6:1,5:104,173:0.0212:2,2:21:1:29.8:1:0.41751:2.99625:60:12:0.0217:0:1.2 -19 17942609 . T C 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24952;SOR=0;LSEQ=AGCCGCAGGCTCTGGCGGCC;RSEQ=GGAGAAGGCAGGATCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:1,2:113,175:0.0103:2,2:28:1:24.3:1:1:1.29032:60:2:0.007:0:1.3 0/0:272:0:0,0:101,171:0:2,0:25.6:1:29.9:1:1:0:60:67:1:0:0.2 -19 17942637 . GC G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49956;SOR=0;LSEQ=GCAGGATCTGTCACAGCAGG;RSEQ=CCAGCCCTGCTCGTCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:60,138:0.01:2,2:7.5:1:30.9:1:0.51804:2.29:60:4:0.0101:0.005:0 0/0:185:0:0,0:52,133:0:2,0:24:1:30.8:1:1:0:60:36:1:0:0.2 -19 17943383 . G A 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.49703;LSEQ=AAATCACTGTGCAGTGCTTT;RSEQ=AGGATCTGAATCTCCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:981:1:1,0:506,473:0.001:2,0:1:0:25:0:1:0:60:2:0.001:0:1 0/1:960:29:14,15:476,452:0.0302:2,2:21.5:1:28.4:1:0.85099:1.12818:60:28:0.0295:0:1.3 -19 17943771 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0908;SOR=Inf;LSEQ=CATGGGCAGTGGTAAGCAGC;RSEQ=CCTCTCATCCTGGGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:59,196:0:2,0:24.2:1:31.1:1:1:0:60:62.75:0.996:0:0.1 0/1:210:3:2,1:54,153:0.0143:2,2:6:1:27:1:0.17409:5.61:60:6:0.0145:0:1.7 -19 17943897 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGTGGAGACTGGAAAAA;RSEQ=GTGTCTCCCACTCTGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:0,2:0,27:0.069:1,0:18:1:32:0:1:0:60:4:0.0769:0:1 0/0:10:0:0,0:0,10:0:0,0:15.3:1:28.9:1:1:0:57.4:9:1:0:0.5 -19 17945471 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGCACTGTTGAATCAGCAG;RSEQ=GCCAGCTCTGTCCACTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:0:0,0:294,356:0:2,0:25:1:30.5:1:1:0:60:35.111:0.9984:0:0.2 0/1:684:27:13,14:292,365:0.0395:2,2:20.2:1:27.9:1:0.69885:1.16:60:26:0.0392:0:1.1 -19 17945546 . G A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1931;SOR=4.53312;LSEQ=AGTTTCTGAGGGTGAGAGGA;RSEQ=CAGTCGGTAATCCCCAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:1:1,0:172,222:0.0025:2,0:1:0:29:0:0.43797:0:60:2:0.0026:0:1 0/1:351:4:3,1:163,184:0.0114:2,2:13.3:1:28:1:0.34784:3.38:60:8:0.0116:0:1.3 -19 17945636 . C T 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28755;SOR=2.96747;LSEQ=TCAAAGTGGGGGTTCGGAGA;RSEQ=CGATGCCGGGTGAGGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:591:2:0,2:322,267:0.0034:2,0:1:0:27.5:1:0.20675:0:60:4:0.0034:0:1 0/1:601:6:2,4:344,251:0.01:2,2:17.8:1:27.7:1:0.40944:2.73647:60:12:0.0101:0:1 -19 17946054 . G A 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGACACAGGAAAATGCCC;RSEQ=GGAGGGTTTGATGAATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:53,235:0:2,0:23.5:1:30.4:1:1:0:60:47:1:0:0.1 0/1:242:39:9,30:55,148:0.1612:2,2:25.4:1:29.9:1:0.69452:1.23772:60:38:0.1597:0:1.2 -19 17946206 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTACACTGACCTGGCTAT;RSEQ=TCCCTCCCCTTCTCAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:2,20:0.0833:2,2:20:1:28.5:1:0.23913:8.36:60:4:0.0833:0:1 0/0:6:0:0,0:0,6:0:0,0:25.7:1:29:1:1:0:60:5:1:0:0.5 -19 17946662 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.62301;SOR=2.01777;LSEQ=TGCATACTACAGAGCCCACT;RSEQ=CCAATTCCTCTTCCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:156,33:0.0053:2,0:1:0:25:0:0.17895:0:60:2:0.0054:0:1 0/1:189:2:1,1:149,38:0.0106:2,2:10.5:1:29:1:0.37099:3.88342:60:4:0.0109:0:1 -19 17946900 . C A 48 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27934;SOR=2.60097;LSEQ=GGCGGGGTTGGGAGACTGAA;RSEQ=TGCACTTGTGTTGAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:2:2,0:82,216:0.0067:2,0:4.5:1:20:1:0.07773:0:60:1:0.0036:0:1.5 0/1:291:5:4,1:75,211:0.0172:2,2:11.8:1:21:1:0.0203:11.15:60:1.5:0.0109:0:2.6 -19 17947194 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCCTCCCGGGTTCAAG;RSEQ=GATTCTCCTGTCTCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:33:1:30.5:1:1:0:59.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 17947911 . T G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.77209;SOR=1.35043;LSEQ=AGACTTGGGTGAGGCAGGGG;RSEQ=GGGGTGGGTGGGTGGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:5:0,5:215,3:0.022:1,0:6.6:1:24.2:1:0:0:60:4:0.019:0:3.8 0/1:237:7:2,5:224,4:0.0295:1,2:8:1:23.1:1:0:122.84991:60:2.5:0.023:0:3.1 -19 17947916 . T G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18669;SOR=1.89967;LSEQ=TGGGTGAGGCAGGGGTGGGG;RSEQ=GGGTGGGTGGGGGGCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:7:2,5:224,7:0.0292:1,2:16.9:1:23.9:1:0:73.53464:60:2.5:0.0224:0:3.3 0/1:259:14:1,13:237,6:0.0541:1,1:9.1:1:25.1:1:0:451.53727:60:6:0.0486:0:3.3 -19 17947920 . T G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08674;SOR=1.87156;LSEQ=TGAGGCAGGGGTGGGGTGGG;RSEQ=GGGTGGGGGGCTCTCACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:12:1,11:238,14:0.0455:2,2:11.5:1:23.2:1:0:176.16842:60:3:0.0363:0:2.8 0/1:293:24:2,22:255,13:0.0819:1,2:8.6:1:25.9:1:0:203.22839:60:11:0.0794:0:2.8 -19 17947924 . T G 103 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.03936;SOR=1.89087;LSEQ=GCAGGGGTGGGGTGGGTGGG;RSEQ=GGGGGGCTCTCACTGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:17:0,17:253,20:0.0584:2,1:7.2:1:23.7:1:0:0:60:3.25:0.0474:0:2 0/1:314:33:2,31:263,16:0.1051:2,2:9.3:1:20.5:1:0:242.06674:60:1.75:0.0727:0:2.4 -19 17948131 . CT C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.28123;SOR=0;LSEQ=AACACCTGGCCACAGGTCAC;RSEQ=TTGGCCCTGGAGTCTGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:1,2:3,130:0.0221:1,2:15.7:1:31.3:1:0.08628:19.85:60:6:0.0224:0.0074:0 0/0:88:0:0,0:1,87:0:1,0:24.8:1:30.5:1:1:0:60:176:1:0:0.1 -19 17948732 . T C 221 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCAAAAGTCTGGTCCACAT;RSEQ=GCTCTCACCTCCATGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:0:0,0:457,264:0:2,0:25.8:1:29.9:1:1:0:60:59.083:1:0:0.1 0/1:731:160:90,70:349,222:0.2189:2,2:25.4:1:30.3:1:0.27426:1.22237:60:159:0.2211:0:1.1 -19 17950172 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14626;SOR=Inf;LSEQ=ACAAATCACCTTTTCTTCCC;RSEQ=AACCCACCTTGACCTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:172,134:0:2,0:24.4:1:29.9:1:1:0:60:42.714:1:0:0.1 0/1:190:2:2,0:102,86:0.0105:2,0:9:1:32:0:0.50187:0:60:4:0.0108:0:1 -19 17950457 . C A 45 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05257;SOR=Inf;LSEQ=GATGAGGCAGCCCTTATAAT;RSEQ=AGGACCAAGGGGGTTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:106,245:0:2,0:24.5:1:31.5:1:1:0:60:69.2:1:0:0.1 0/1:324:4:3,1:108,212:0.0123:2,2:21.3:1:22.8:1:0.11811:5.86:60:3:0.0094:0:1.8 -19 17950500 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.222;SOR=Inf;LSEQ=GAAGAGTGGCCCCTGAGTGG;RSEQ=ACTGAGCGACAGACACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:29,159:0:2,0:28.7:1:31.4:1:1:0:59.9:187:1:0:0.4 0/1:168:2:1,1:33,133:0.0119:2,2:17:0:31:1:0.36477:3.99:60:4:0.012:0:1.5 -19 17950514 . C A 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.34217;SOR=3.47047;LSEQ=GAGTGGGACTGAGCGACAGA;RSEQ=ACTCTCCTTCTCAGTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:0,1:20,131:0.0066:2,0:21:0:13:0:1:0:60:0:0:0:1 0/1:133:3:1,2:23,107:0.0226:2,2:25.7:1:24.3:1:0.45231:2.31:60:2:0.0169:0:3 -19 17950520 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50303;SOR=0;LSEQ=GACTGAGCGACAGACACTCT;RSEQ=CTTCTCAGTCCTTCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:0,2:18,124:0.0139:2,0:30:1:31:1:1:0:60:4:0.0152:0:1 0/0:118:0:0,0:18,100:0:2,0:23.9:1:29.5:1:1:0:59.5:8.833:1:0:0.7 -19 17950528 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49922;SOR=0;LSEQ=GACAGACACTCTCCTTCTCA;RSEQ=TCCTTCTTCCTTTTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:11,100:0.0175:2,2:21:1:32:0:0.20196:8.75:60:4:0.0189:0:1 0/0:102:0:0,0:16,86:0:2,0:20.6:1:30.2:1:1:0:59.4:16:1:0:0.8 -19 17951178 . G A 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16905;SOR=0.82697;LSEQ=GGAAGGTGAGAGGGAATGGG;RSEQ=AGGAGTCAGAGATAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:159:52,107:115,180:0.3495:2,2:24:1:29.8:1:0.22083:1.31385:60:78.5:0.3504:0:1.1 0/1:504:155:55,100:128,221:0.3075:2,2:25.1:1:29.1:1:0.8412:1.05297:60:76.5:0.3066:0:1.1 -19 17951229 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49873;SOR=Inf;LSEQ=CCTGGGCTCAAATTCAGGTA;RSEQ=CTCTGTAGCCCTGGGATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:13,140:0:2,0:25.8:1:31.5:1:1:0:60:152:1:0:0.3 0/1:162:2:1,1:16,144:0.0123:2,2:35:1:26.5:1:0.19945:8.76:60:4:0.0123:0:1 -19 17951234 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23842;SOR=Inf;LSEQ=GCTCAAATTCAGGTACCTCT;RSEQ=TAGCCCTGGGATCCTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:10,132:0:2,0:26:1:32:1:1:0:60:46.333:1:0:0.3 0/1:136:2:1,1:11,123:0.0147:2,2:11:1:27:1:0.16928:10.75:60:4:0.0147:0:1 -19 17952156 . C T 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.32492;SOR=3.83879;LSEQ=CATAGAGAAGGGGAGGGGCC;RSEQ=TGAGTGGCCACAGAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:1,0:143,65:0.0048:2,0:47:0:16:0:1:0:60:0:0:0:7 0/1:165:3:1,2:118,44:0.0182:2,2:10.3:1:23.7:1:0.18819:5.2994:60:6:0.0186:0:2.3 -19 17952185 . G T 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45272;SOR=0.86438;LSEQ=CACAGAGGCCGGGAATGGGG;RSEQ=ACAGGTCCTTACGTGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:83:57,26:140,91:0.2643:2,2:24.3:1:29:1:0.23364:1.42:60:40.5:0.2656:0:1.2 0/1:287:68:45,23:135,84:0.2369:2,2:25.6:1:29.1:1:0.56671:1.22:60:136:0.2411:0:1.2 -19 17952209 . G A 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01552;SOR=Inf;LSEQ=GGTCCTTACGTGATGGGGCC;RSEQ=TGGCACTGCTCGGCCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:216,150:0:2,0:25.8:1:30.5:1:1:0:60:44.75:0.9972:0:0.4 0/1:391:7:3,4:220,164:0.0179:2,2:29.9:1:29:1:0.46896:1.78588:60:14:0.0182:0:1.6 -19 17952607 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12427;SOR=Inf;LSEQ=AGTACCGAAGTGGGGGCCCA;RSEQ=CTGGACCCCGCCAAACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:74,165:0:2,0:25.3:1:31.7:1:1:0:60:58.75:1:0:0.5 0/1:255:4:1,3:85,166:0.0157:2,2:13:1:29:1:1:1.53376:60:8:0.0162:0:1 -19 17952609 . T G 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01215;LSEQ=TACCGAAGTGGGGGCCCAGC;RSEQ=GGACCCCGCCAAACCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:78:25,53:46,106:0.3362:2,2:25.3:1:30.7:1:0.88025:1.09:60:156:0.3436:0:1.1 0/1:239:81:26,55:52,106:0.3389:2,2:26.4:1:29.4:1:1:1.03758:60:39.5:0.3362:0:1.1 -19 17952639 . AC A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50263;SOR=0;LSEQ=CAAACCACGCCCATGAACCC;RSEQ=CCCCAAGCCACACCATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:22,120:0.0139:2,2:15.5:1:30.3:1:0.29487:5.36:60:4:0.0141:0.0069:0 0/0:119:0:0,0:17,102:0:2,0:21.8:1:30.8:1:1:0:60:118:1:0:0.5 -19 17952647 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18422;SOR=Inf;LSEQ=GCCCATGAACCCACCCCCAA;RSEQ=CCACACCATCCACTCCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:14,113:0:2,0:22.4:1:31.8:1:1:0:60:41.333:1:0:0.4 0/1:96:2:1,1:10,84:0.0208:2,2:22:1:25.5:1:0.21711:8.06:60:4:0.0217:0:1 -19 17953044 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50546;SOR=0;LSEQ=TCTTTCGTTTTGGCTCCGCC;RSEQ=CACATCCCCTACCACTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:112,8:0.0164:2,0:20:1:32:1:1:0:60:4:0.0165:0:1 0/0:95:0:0,0:84,11:0:2,0:23.7:1:30:1:1:0:60:94:1:0:0.3 -19 17953067 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.20051;SOR=Inf;LSEQ=CATCCCCTACCACTCTCCGG;RSEQ=CCCTCCCCGAGCCCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:163,30:0:2,0:23.5:1:31.5:1:1:0:60:37.6:1:0:0.2 0/1:157:2:1,1:112,42:0.0127:2,2:23:0:28:1:0.47659:2.64722:60:4:0.0132:0:2 -19 17953088 . C T 120 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.64027;LSEQ=CCCTCCCCGAGCCCCGCCCC;RSEQ=ACGTTGGCCCCGCCCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:1:0,1:198,68:0.0037:2,0:24:0:9:0:0.25843:0:60:0:0:0:2 0/1:235:20:10,10:138,77:0.0851:2,2:22.6:1:27.9:1:0.23144:1.78761:60:9:0.0776:0:1.8 -19 17953254 . C T 89 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58182;SOR=1.50382;LSEQ=GCGGCCCCGGCTGGATCCAG;RSEQ=CGCTCCAGGTCCATGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:618:5:2,3:304,308:0.0081:2,2:24.4:1:26.8:1:1:1.47958:60:4:0.0066:0:1.6 0/1:660:8:4,4:338,313:0.0121:2,2:27.4:1:29.9:1:1:1.07973:60:16:0.0123:0:1.4 -19 17953355 . T G 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03881;SOR=7.72116;LSEQ=CACCGTCCTCCGAATACGCC;RSEQ=CCGCGTCACGAAGCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:1:1,0:277,325:0.0017:2,0:3:0:10:0:0.46103:0:60:0:0:0:3 0/1:632:8:2,6:310,314:0.0127:2,2:22.1:1:29.6:1:0.28625:2.95733:60:7:0.0113:0:1.3 -19 17953472 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.65881;LSEQ=CAGCGTCGGGAGGGGTCCCC;RSEQ=CGGGGACACACACAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:1:1,0:17,133:0.0065:2,0:1:0:25:0:0.11921:0:60:2:0.0068:0:1 0/1:185:2:1,1:38,145:0.0108:2,2:34.5:1:27.5:1:0.37808:3.78:60:4:0.0109:0:1 -19 17953864 . G A 86 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39595;SOR=1.78255;LSEQ=CTTCAGCAGCTCTCCCGGCC;RSEQ=CTGGGCCTGCTCTCGCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:4:3,1:350,299:0.0061:2,2:13:1:28:1:0.6288:2.56:60:8:0.0062:0:1 0/1:737:8:5,3:390,336:0.0109:2,2:23.5:1:28.8:1:0.73146:1.44:60:7:0.0097:0:1 -19 17953950 . G C 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTTGAGACTGAGGCCCACG;RSEQ=GGAGGCGCCCACTCACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:35:11,24:203,317:0.0631:2,2:24:1:30:1:0.47356:1.39638:60:34:0.0622:0:1.1 0/0:586:0:0,0:252,333:0:2,0:29:0:12:0:1:0:60:0:0:0:5 -19 17954008 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36057;SOR=3.18541;LSEQ=GGCCGCCACAGGGAGCATCA;RSEQ=CTGAGGCCACCCAACTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:1,0:74,175:0.004:2,0:1:0:28:0:0.3:0:60:2:0.0041:0:1 0/1:237:3:2,1:73,160:0.0127:2,2:11:1:27.3:1:0.23778:4.35:60:6:0.013:0:1 -19 17954107 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.34567;SOR=3.41306;LSEQ=CCACAGGGAGGGTCAGACGA;RSEQ=GCCCCACCTGATTGCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:0,1:171,56:0.0044:2,0:1:0:25:0:0.25:0:60:2:0.0045:0:1 0/1:202:3:2,1:146,52:0.0149:2,2:33.7:1:28:1:1:1.4013:60:6:0.0155:0:1.3 -19 17954485 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21357;SOR=Inf;LSEQ=TGTTTCCTCATCTGAGAAAT;RSEQ=GGTAGTGACCATACCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:77,26:0:2,0:24.8:1:32.3:1:1:0:60:206:1:0:0.1 0/1:89:2:2,0:74,13:0.0225:2,0:19:1:26:0:1:0:60:4:0.0225:0:1 -19 17954947 . G A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16663;SOR=1.47886;LSEQ=TCCCCCAAAGCCCCAGCTCC;RSEQ=ATGCTGACTTCTGCAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:45:35,10:84,5:0.3333:2,2:24.2:1:30.4:1:0.00728:4.73662:60:90:0.3409:0:2.7 0/1:94:40:36,4:46,8:0.4255:2,2:20.8:1:30.5:1:0.54838:1.56:60:80:0.4348:0:3 -19 17955001 . C T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.5467;LSEQ=CAATCTTGGCCCCACACAGC;RSEQ=CCATCCTTCCCTCTGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:71:54,17:157,58:0.2483:2,2:25.2:1:30.4:1:0.64465:1.17:60:22.667:0.242:0:3.4 0/1:269:123:83,40:99,46:0.4572:2,2:24:1:29.8:1:0.89633:1.03707:60:23.6:0.4521:0:3.3 -19 17955003 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.6192;LSEQ=ATCTTGGCCCCACACAGCCC;RSEQ=ATCCTTCCCTCTGGCCCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:73:55,18:161,61:0.2475:2,2:24.9:1:30.2:1:0.76077:1.16:60:35.5:0.2465:0:3.3 0/1:285:132:88,44:102,51:0.4632:2,2:23.2:1:29.6:1:1:1:60:65:0.4659:0:3.2 -19 17955021 . G A 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.31683;LSEQ=CCCATCCTTCCCTCTGGCCC;RSEQ=ATCCACTAGGGATGCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:108:71,37:181,98:0.2791:2,2:21.4:1:29.9:1:0.90581:1.04:60:107:0.2801:0:2.5 0/1:427:202:126,76:133,92:0.4731:2,2:23.3:1:29.5:1:0.55175:1.15:60:66.333:0.4738:0:2.4 -19 18266640 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10877;SOR=Inf;LSEQ=TCAACCAATGGGGCCAGTGG;RSEQ=GCTCCAAGCAGCCACCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:176,101:0:2,0:24.4:1:30.5:1:1:0:60:33.625:1:0:0.2 0/1:254:3:1,2:160,91:0.0118:2,2:32:1:28.3:1:0.55619:3.49832:60:6:0.012:0:1 -19 18266694 . C T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22164;SOR=4.50006;LSEQ=CCCCACTCACGCGGCCATGG;RSEQ=GGGCCCTGAGGGCTTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:1:0,1:231,207:0.0023:2,0:1:0:27:0:0.4738:0:60:2:0.0023:0:1 0/1:491:5:2,3:257,229:0.0102:2,2:22.2:1:27.2:1:0.67083:1.68162:60:4:0.0082:0:1.6 -19 18266861 . C T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06176;SOR=Inf;LSEQ=CACAGAGCGTGGGCTGGATG;RSEQ=CCGGCCTCAACGAGCGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:192,226:0:2,0:25.5:1:31.4:1:1:0:60:51.25:1:0:0.1 0/1:420:5:1,4:191,224:0.0119:2,2:11.6:1:27:1:0.38124:3.40205:60:10:0.0122:0:1.2 -19 18266882 . C T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02956;SOR=0;LSEQ=CCGGCCTCAACGAGCGCACA;RSEQ=GGCAGCGAGGTGACTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:5:1,4:186,258:0.0111:2,2:9.6:1:24.8:1:0.4069:2.87788:60:4:0.009:0:1 0/0:458:0:0,0:204,254:0:2,0:25.4:1:30:1:1:0:60:75.333:1:0:0.3 -19 18266964 . GC G 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.12278;SOR=0;LSEQ=GCCCGGCCCTCGCCCACGGG;RSEQ=CCCCGCCCACTGCCCGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:4:2,2:43,105:0.0263:2,2:18:1:33.3:1:0.58212:2.43:60:8:0.0272:0:0.5 0/0:146:0:0,0:59,87:0:2,0:20.2:1:30.1:1:1:0:60:28.2:1:0:0.3 -19 18266977 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49765;SOR=0;LSEQ=CCACGGGGCCCCCGCCCACT;RSEQ=CCCGCCAGGCCCCGTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:33,72:0.0187:2,2:9:1:29:1:0.53659:2.16:60:4:0.0192:0:1.5 0/0:107:0:0,0:38,67:0:2,0:20.2:1:30.9:1:1:0:60:34:0.9808:0:0.3 -19 18266983 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50258;SOR=Inf;LSEQ=GGCCCCCGCCCACTGCCCGC;RSEQ=AGGCCCCGTGATGGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:22,55:0:2,0:20.5:1:31.6:1:1:0:60:37.5:1:0:0.2 0/1:95:2:1,1:36,57:0.0211:2,2:15.5:1:31.5:1:1:1.58:60:4:0.0215:0:1 -19 18271576 . C T 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=TGACCAGGCCACTGCATGTG;RSEQ=TGTGCCCTCTCCCAGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:17:12,5:37,13:0.2537:2,2:32.5:1:30.9:1:0.76166:1.1828:60:34:0.2615:0:1 0/0:45:0:0,0:37,8:0:2,0:21.3:1:32.1:1:1:0:60:90:1:0:0.2 -19 18271645 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24796;SOR=Inf;LSEQ=CTGGGCAGCAAAGGGAGACT;RSEQ=CAGGGGGGTTGAGCGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:148,35:0:2,0:24.6:1:32:1:1:0:60:35.6:0.9944:0:0.1 0/1:183:2:1,1:132,49:0.0109:2,2:16.5:1:26.5:1:0.47289:2.67689:60:4:0.011:0:1 -19 18271987 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20474;SOR=Inf;LSEQ=CTCGGCCGAGGCGCGCCGGG;RSEQ=CCTGCGGGGTGAGCCTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:48,143:0:2,0:22.8:1:31.3:1:1:0:60:30.833:0.9893:0:0.1 0/1:160:2:1,1:38,120:0.0125:2,2:16:0:31.5:1:0.42925:3.13:60:4:0.0129:0:1.5 -19 18271988 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20781;SOR=Inf;LSEQ=TCGGCCGAGGCGCGCCGGGC;RSEQ=CTGCGGGGTGAGCCTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:45,143:0:2,0:22.7:1:31.5:1:1:0:60:187:1:0:0.1 0/1:158:2:1,1:37,119:0.0127:2,2:5:0:30:1:0.42433:3.19:60:4:0.0132:0:1.5 -19 18272037 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.214;SOR=Inf;LSEQ=GGGGAAGGAGGGGGCTGTAG;RSEQ=GGGTGGGAGGGCCCAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:39,58:0:2,0:22:1:30.3:1:1:0:60:31.333:1:0:0.1 0/1:84:2:1,1:31,51:0.0238:2,2:6:0:31:1:1:1.63:60:4:0.0244:0:1.5 -19 18272107 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49802;SOR=Inf;LSEQ=AGAGGCCGCGGGGCCCGTGG;RSEQ=GCCGGCGCTGGAGCCACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:39,51:0:2,0:27.1:1:30.7:1:1:0:60:44:1:0:0.2 0/1:97:2:1,1:44,51:0.0206:2,2:27:1:28.5:1:1:1.16:60:4:0.0217:0:1 -19 18272147 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17673;SOR=0;LSEQ=ACGCTGCCGCTGCACCGCGC;RSEQ=CTCACGCTGCGCTTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:20,30:0.0385:2,2:39.5:1:28.5:1:1:1.49:60:4:0.0392:0:1.5 0/0:71:0:0,0:31,40:0:2,0:21.4:1:31.3:1:1:0:60:70:1:0:0.7 -19 18272190 . A C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00118;SOR=Inf;LSEQ=AGCACCTGGGCCGCGTGGCC;RSEQ=GCCGCGCCCCGGCCCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:6,7:3,3:0.6842:2,2:26.2:1:30.9:1:1:1.15722:60:26:0.6842:0:1.4 1/1:34:34:17,17:0,0:1:0,2:20.5:1:29.8:1:1:0:60:68:1:0:1.4 -19 18272252 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.51304;SOR=Inf;LSEQ=GCCACCTTTGGGCCGCTGCT;RSEQ=CTGCGCGCGCCGCCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:26.3:1:33:1:1:0:60:36:1:0:0.4 0/1:28:2:1,1:13,13:0.0714:2,2:35.5:1:30.5:1:1:1:60:4:0.0769:0:1 -19 18272683 . A AC 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.50347;SOR=0;LSEQ=GCACATACTGTCTCGTATAT;RSEQ=CCCCCAGGCGTGCAAGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:2,0:158,22:0.011:2,0:21:1:31:1:1:0:60:4:0.0112:0:0 0/0:149:0:0,0:133,16:0:2,0:22.1:1:28.2:1:1:0:60:148:1:0:0.1 -19 18272695 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20288;SOR=Inf;LSEQ=TCGTATATACCCCCAGGCGT;RSEQ=CAAGCGCACGCACAATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:197,31:0:2,0:23.3:1:31.4:1:1:0:60:24.333:0.991:0:0.1 0/1:189:2:2,0:159,28:0.0106:2,0:5.5:1:31:1:1:0:60:4:0.0109:0:1 -19 18273013 . G A 217 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=87.90917;LSEQ=TTGTTTTCCTGTCCCCCAGC;RSEQ=CTGCCGCCTAAACCCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:876:2:2,0:443,429:0.0023:2,0:11.5:1:28:1:0.4996:0:60:4:0.0023:0:3.5 0/1:978:164:81,83:407,406:0.1677:2,2:23.8:1:29.5:1:0.93181:1.02719:60:40:0.1668:0:1.8 -19 18273047 . T C 294 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.14498;LSEQ=CCCCCAAGGCAAAGCCGGCC;RSEQ=CCACAGTCCTGGCCAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:821:817:413,404:0,2:0.9951:0,2:25.7:1:30.8:1:0.24544:0:60:50.063:0.9975:0:1.2 1/1:887:858:425,433:15,13:0.9673:2,2:25.8:1:30.2:1:0.70493:1.17535:60:46.667:0.9677:0:1.3 -19 18273410 . A G 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0057;SOR=0;LSEQ=ATGTGCGGTTTCAAGAATGG;RSEQ=GGGCCAGGCACGGTGGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:99:99:5,94:0,0:1:0,2:21.1:1:31.4:1:1:0:60:98:1:0:1.1 1/1:75:69:2,67:0,6:0.92:0,1:20.8:1:30.5:1:1:0:60:138:0.9324:0:1 -19 18273537 . AT A 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.54404;SOR=1.83231;LSEQ=AACCCCGTCTCTACTAAAAA;RSEQ=TAAAAAAAAAAATTAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:7,7:0.15:2,0:16.7:1:32.3:1:0.22794:0:60:6:0.1579:0.05:0.3 0/1:4:1:0,1:2,1:0.25:2,0:34:0:31:0:1:0:60:2:0.25:0:0 -19 18273539 . T A 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=1.06826;LSEQ=CCCCGTCTCTACTAAAAAAT;RSEQ=AAAAAAAAAAATTAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:7,7:3,0:0.7368:0,2:26.5:1:29.6:1:0.22794:0:58.9:28:0.8235:0:1.3 1/0:4:3:2,1:0,1:0.75:0,2:15:1:27.3:1:1:0:60:6:0.75:0:1 -19 18273632 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.18208;SOR=Inf;LSEQ=ATTGCTTGAACCCGGGAGGT;RSEQ=GAGGTTGCAGTGAGCCGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:39,6:0:2,0:23.6:1:31.5:1:1:0:59.3:44:1:0:0.2 0/1:34:2:2,0:32,0:0.0588:1,0:31.5:1:26.5:1:1:0:60:4:0.0588:0:1 -19 18273668 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.21277;SOR=Inf;LSEQ=CGAAATCGCACCACTGCACT;RSEQ=CAGCCTGGACAACAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:76,4:0:2,0:19.7:1:32.4:1:1:0:59.7:79:1:0:0.2 0/1:69:2:1,1:66,1:0.029:1,2:18:1:25.5:1:0.05754:47.02217:60:4:0.0299:0:1.5 -19 18273702 . C CA 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.96818;LSEQ=AGAGCAGCAAGACTCTGTCT;RSEQ=AAAAAAAAAGGGGACAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:8:8,0:145,11:0.0488:2,0:26.5:1:31.1:1:1:0:60:16:0.0488:0:0 0/1:148:7:7,0:121,20:0.0473:2,0:21.4:1:30:1:0.59406:0:60:14:0.0486:0.0135:0.3 -19 18274631 . C CTAAAAACAAA 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGGGCACGACCTTGTCT;RSEQ=TAAAAACAGAAATAAGCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20.3:1:30.4:1:1:0:60:6:1:0.6667:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 18275984 . T G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTAAGGAGTTCAAGACCAG;RSEQ=CTGGCCAACATGGTGAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:46:1:31.5:1:1:0:60:4:1:0:1 -19 18276856 . T C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGTTAGAAGAATGACACTC;RSEQ=GATAGAGGGACCAGCTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:51,2:0,0:1:0,1:23.7:1:30.9:1:1:0:60:52:1:0:1 1/1:39:39:39,0:0,0:1:0,1:24.2:1:31.1:1:1:0:60:78:1:0:1.1 -19 18277175 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22916;SOR=Inf;LSEQ=GGTGCAGTACAAGCCAGGGA;RSEQ=GGAAGGAAGCAGAAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:33,120:0:2,0:21.1:1:31.2:1:1:0:60:152:1:0:0.4 0/1:141:2:0,2:25,114:0.0142:2,0:27:1:27.5:1:1:0:60:4:0.0145:0:1.5 -19 18277206 . G A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.18458;LSEQ=AGAAGGAGGCCAGCCACTTG;RSEQ=AGGCAAAGAGTAGTCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:80:68:0,68:1,11:0.85:2,1:23.6:1:30.6:1:0.15:0:60:136:0.85:0:1 1/0:63:32:2,30:1,30:0.5079:1,2:20.8:1:30.9:1:1:1.98:60:64:0.5161:0:1.1 -19 18277820 . C G 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0028;SOR=0;LSEQ=GCCAGACATGGTGGTGCACA;RSEQ=CTGTGGTCCCAGCTACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:11:10,1:90,0:0.1089:1,2:23.3:1:32.9:1:0.10891:0:60:22:0.11:0:1.1 0/0:73:0:0,0:72,1:0:1,0:26.6:1:31.3:1:1:0:60:72:1:0:0.1 -19 18279467 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24875;SOR=0;LSEQ=GGGAGGAAAAGTTGTCCAGG;RSEQ=AGCTGGGGAGCCTCGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:199,95:0.0101:2,2:8.3:1:28.3:1:0.24955:4.16737:60:6:0.0103:0:1 0/0:294:0:0,0:189,105:0:2,0:24.2:1:31.9:1:1:0:60:97:1:0:0.1 -19 18279638 . T C 280 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03959;LSEQ=CAGGCAGAGGAGATGCTGAG;RSEQ=GGCAAGCGGGATGGCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:564:562:231,331:1,0:0.9965:0,2:25.1:1:30.6:1:0.41208:0:60:92.667:0.9964:0:1.1 1/1:666:611:251,360:20,35:0.9174:2,2:23.5:1:30.3:1:0.56741:1.22:60:54.545:0.9174:0:1.1 -19 18279736 . G A 51 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02407;SOR=Inf;LSEQ=CCGCAGCGGTGGGGATTCCC;RSEQ=CGTCCCTCCCAGAGCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:52,134:0:2,0:23.8:1:31.9:1:1:0:60:185:1:0:0.3 0/1:170:5:4,1:56,109:0.0294:2,2:11.4:1:22.2:1:0.053:7.69:60:1.5:0.0183:0:1 -19 18279737 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21372;SOR=Inf;LSEQ=CGCAGCGGTGGGGATTCCCG;RSEQ=GTCCCTCCCAGAGCTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:52,137:0:2,0:23.1:1:30.7:1:1:0:60:93.5:1:0:0.3 0/1:163:2:1,1:55,106:0.0123:2,2:13:1:30:1:1:1.92:60:4:0.0125:0:1.5 -19 18279816 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.06097;LSEQ=CTGGTGGGGTCATCCGGGAC;RSEQ=GGGGAGCACGCGGCCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:185:173:127,46:6,5:0.9351:2,2:22.7:1:29.9:1:0.18113:2.29:60:56.667:0.9341:0:1.1 0/1:144:67:45,22:57,19:0.4653:2,2:23.2:1:29.7:1:0.35565:1.46268:60:134:0.4653:0:1.1 -19 18279852 . C T 50 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.70787;SOR=1.58855;LSEQ=CTGGAACGGGGAAAGCTTGG;RSEQ=GGGGAGGCCAGCCTTCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:0,3:201,84:0.0104:2,0:14.7:1:22.7:1:0.0269:0:60:2:0.0071:0:1.3 0/1:243:4:0,4:160,79:0.0165:2,0:1:0:25:1:0.01297:0:60:8:0.0167:0:1 -19 18279861 . C T 96 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00696;SOR=0.10003;LSEQ=GGAAAGCTTGGCGGGGAGGC;RSEQ=AGCCTTCCGACTCCCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:11:6,5:221,105:0.0325:2,2:19.3:1:28:1:0.34764:1.75087:60:22:0.0327:0:1.2 0/0:299:1:0,1:192,106:0.0033:2,0:1:0:24:0:0.35786:0:60:2:0.0034:0:1 -19 18280044 . C T 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67278;SOR=1.24412;LSEQ=CAGCACAACGACGCGCTCAC;RSEQ=GTCACCCTGGCGCACCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:10:2,8:51,174:0.0426:2,2:27.1:1:31:1:1:1.17165:60:20:0.0431:0:1.2 0/1:248:13:3,10:61,172:0.0524:2,2:23.5:1:30.3:1:1:1.18139:60:26:0.0535:0:1 -19 18280080 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49943;SOR=Inf;LSEQ=CCAGTGCGCGCCCCGGGCCC;RSEQ=GGCCCGCCGCCTGCCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:22,86:0:2,0:21:1:30.4:1:1:0:60:53:1:0:0.5 0/1:121:2:1,1:37,82:0.0165:2,2:38:0:32:0:0.53127:2.20:60:4:0.0168:0:1 -19 18280082 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24925;SOR=Inf;LSEQ=AGTGCGCGCCCCGGGCCCCG;RSEQ=CCCGCCGCCTGCCGCCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:22,79:0:2,0:20.7:1:32.4:1:1:0:60:100:1:0:0.5 0/1:114:3:2,1:36,75:0.0263:2,2:10.3:1:26:1:0.25727:4.11:60:6:0.0265:0:1 -19 18280089 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.65567;LSEQ=GCCCCGGGCCCCGGCCCGCC;RSEQ=CCTGCCGCCCGCTGAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:1:0,1:21,62:0.0119:2,0:25:0:32:0:1:0:60:2:0.012:0:2 0/1:102:2:1,1:32,68:0.0196:2,2:11.5:1:29:1:0.54455:2.11:60:4:0.02:0:1 -19 18280096 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05158;LSEQ=GCCCCGGCCCGCCGCCTGCC;RSEQ=CCCGCTGAGCACCGAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:23:7,16:14,35:0.3194:2,2:19.3:1:29.5:1:1:1.09:60:22:0.3099:0:1.5 0/1:86:2:0,2:30,54:0.0233:2,0:11:1:31.5:1:0.54036:0:60:4:0.0238:0:1 -19 18280110 . G A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03968;SOR=Inf;LSEQ=CCTGCCGCCCGCTGAGCACC;RSEQ=AGGACCCGCCCCAAGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:13,27:0:2,0:14.5:1:30.8:1:1:0:60:39:1:0:0.9 0/1:60:7:3,4:23,30:0.1167:2,2:23.3:1:31.6:1:1:1.02185:60:14:0.1273:0:1.3 -19 18280114 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.15714;SOR=0;LSEQ=CCGCCCGCTGAGCACCGAGG;RSEQ=CCCGCCCCAAGCAGAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:10,22:0.0588:2,2:11.5:1:30:1:1:2.14:60:4:0.0606:0:2.5 0/0:51:0:0,0:24,27:0:2,0:18.7:1:28.5:1:1:0:60:16:1:0:0.4 -19 18280187 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GCGGGAGCCACGGACCAGAC;RSEQ=AGCCACATCCAGGGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:13:1:28.5:1:1:0:60:8:1:0:0.8 0/1:10:2:1,1:4,4:0.2:2,2:19.5:1:28:1:1:1:60:4:0.2:0:1 -19 18391999 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49231;SOR=Inf;LSEQ=GGCGCTCGAGCTCGGGGGAG;RSEQ=CCAGCTTCAGCAGCCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:4,14:0:2,0:18.4:1:29.4:1:1:0:60:8:1:0:0.3 0/1:22:2:1,1:6,14:0.0909:2,2:44.5:1:29:1:1:2.24:60:4:0.0909:0:1 -19 18758169 . C A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21567;LSEQ=GAATGTCATCCCACCTCCCC;RSEQ=ACGGCGATTACTTTTTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:469:248:153,95:132,89:0.5288:2,2:26.2:1:29.6:1:0.705:1.09:60:40.333:0.5284:0:1.1 0/1:442:86:52,34:218,138:0.1946:2,2:23.7:1:29.3:1:0.90246:1.03283:60:85:0.1959:0:1.1 -19 18758255 . C T 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.66094;SOR=1.05928;LSEQ=CTCCAGCCCTTTGGTTTTTT;RSEQ=CTTTTTCTGATATTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:195:70,125:122,182:0.3908:2,2:25:1:29.9:1:0.3478:1.19658:59.9:390:0.3971:0:1.1 0/1:566:229:90,139:132,202:0.4046:2,2:25.9:1:28.9:1:1:1.00923:60:75.333:0.405:0:1.1 -19 18758348 . AGAG A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.50312;SOR=0;LSEQ=AGAGGCCCTGGAGGAGGAAG;RSEQ=GAGGAGGAGGAAGAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:0,75:0.026:1,0:25.5:1:27.4:1:1:0:60:4:0.026:0.013:0 0/0:61:0:0,0:1,60:0:1,0:22.7:1:30.9:1:1:0:60:29.5:1:0:0.1 -19 19256537 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61303;SOR=2.1251;LSEQ=TCTCTGAAGAGGCCTGGAGG;RSEQ=AGGTGGGGTCCCCACGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:1:1,0:63,16:0.0125:2,0:41:0:31:0:1:0:60:2:0.0133:0:1 0/1:76:2:1,1:54,20:0.0263:2,2:12.5:1:27:1:0.47895:2.65922:60:4:0.0263:0:1.5 -19 19256584 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07567;SOR=Inf;LSEQ=GTACCTGGCGAGCGCTCTGG;RSEQ=CTGGTGCCACCGGGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:147,59:0:2,0:25:1:31.1:1:1:0:60:33.333:1:0:0.2 0/1:152:3:1,2:102,47:0.0197:2,2:28.3:1:28.3:1:0.24321:4.2943:60:6:0.0197:0:1.3 -19 19256596 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58626;SOR=2.52998;LSEQ=CGCTCTGGGCTGGTGCCACC;RSEQ=GGTGATCTCCTACCGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:1,0:159,72:0.0043:2,0:28:0:15:0:1:0:60:0:0:0:6 0/1:185:2:1,1:121,62:0.0108:2,2:18.5:1:31:1:1:1.94411:60:4:0.0109:0:1 -19 19256633 . C T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05031;SOR=Inf;LSEQ=GGCCAGCCGTCGGCCAAGGG;RSEQ=AGCCGGCGCAGGGCGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:228,125:0:2,0:22.7:1:31.7:1:1:0:60:34.3:1:0:0.2 0/1:320:4:1,3:193,122:0.0125:2,2:6:1:27.8:1:0.3036:4.72317:60:8:0.0127:0:1.3 -19 19256637 . C T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1108;SOR=5.44848;LSEQ=AGCCGTCGGCCAAGGGCAGC;RSEQ=GGCGCAGGGCGGGCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:1:0,1:226,129:0.0028:2,0:1:0:26:0:0.36517:0:60:2:0.0029:0:1 0/1:331:5:1,4:199,127:0.0151:2,2:5.2:1:27:1:0.08222:6.235:60:10:0.0153:0:1 -19 19256768 . TG T 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06176;SOR=0;LSEQ=CGCTCAGACTTGATGCTGAC;RSEQ=GGGGGGTCGGCGGGGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:5:2,3:156,247:0.0122:2,2:30.6:1:31.8:1:1:1.06:60:10:0.0123:0:0 0/0:404:0:0,0:180,224:0:2,0:23.6:1:30.7:1:1:0:60:201:1:0:0.3 -19 19256855 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49858;SOR=0;LSEQ=CAGGGGGAAAGAGAGAGGGA;RSEQ=GCCGTGAGCTCAGCGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:2,0:38,99:0.0144:2,0:17:1:32.5:1:0.08133:0:60:4:0.0149:0:1.5 0/0:131:0:0,0:43,88:0:2,0:26:1:30.7:1:1:0:60:130:1:0:0.4 -19 19256870 . G A 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.06809;SOR=0.58972;LSEQ=AGGGAGGCCGTGAGCTCAGC;RSEQ=AGGAAGGGAAGGAAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:43:17,26:27,44:0.3772:2,2:21.9:1:29.6:1:1:1.06:60:42:0.375:0:1.2 0/1:118:31:14,17:25,62:0.2627:2,2:19.3:1:29.4:1:0.12035:2.03:60:62:0.2627:0:1.2 -19 19257036 . C T 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25719;SOR=2.96633;LSEQ=CACCAGGGGTCAGCAGCGGC;RSEQ=GGGGCTTTGGAGGACTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:2:0,2:260,195:0.0044:2,0:1:0:26:1:0.18529:0:60:4:0.0045:0:1 0/1:388:5:2,3:212,171:0.0129:2,2:23.8:1:27.8:1:0.66053:1.85665:60:4:0.0106:0:1.6 -19 19257037 . G T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01993;SOR=Inf;LSEQ=ACCAGGGGTCAGCAGCGGCC;RSEQ=GGGCTTTGGAGGACTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:0:0,0:264,203:0:2,0:25.5:1:30:1:1:0:60:92.4:1:0:0.2 0/1:395:5:2,3:215,173:0.0127:2,2:24.2:1:30:1:0.66035:1.86118:60:10:0.0128:0:1.2 -19 19257152 . G T 44 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03245;SOR=Inf;LSEQ=GGGGGCCAGGGTGGGGGGCT;RSEQ=CAACAAGCCAGGGGGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:0:0,0:216,219:0:2,0:21.6:1:29.6:1:1:0:60:7.056:1:0:0.6 0/1:323:4:0,4:158,158:0.0124:2,0:12.3:1:22:1:0.12277:0:60:3:0.0105:0:2.3 -19 19257160 . C T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01713;SOR=Inf;LSEQ=GGGTGGGGGGCTGCAACAAG;RSEQ=CAGGGGGCGGTGGAGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:221,230:0:2,0:23:1:29.9:1:1:0:60:10.275:1:0:0.6 0/1:362:5:1,4:178,177:0.0138:2,2:11:1:23.6:1:0.37154:4.00877:60:4:0.0122:0:1.8 -19 19257315 . A T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18615;SOR=4.72743;LSEQ=GTGTGGAACCCCCAGAGGGC;RSEQ=GGAGTGCGGACGCTTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:0,1:300,130:0.0023:2,0:36:0:14:0:0.30394:0:60:0:0:0:1 0/1:368:4:1,3:239,125:0.0109:2,2:9.8:1:24.3:1:0.12318:5.70789:60:3:0.0084:0:2 -19 19257383 . G A 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGGGGGCCTCCGGGGAG;RSEQ=AAGGGGAAGCTCCCCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:859:0:0,0:497,362:0:2,0:23.6:1:30.7:1:1:0:60:38.045:1:0:0.2 0/1:899:74:38,36:449,371:0.0823:2,2:25:1:28.8:1:0.62641:1.14637:60:73:0.0831:0:1.3 -19 19257803 . G T 71 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02789;SOR=8.24319;LSEQ=AGCCAAGATGCACCCAAACA;RSEQ=CCCCTCAGGACCTCACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:1:0,1:372,266:0.0016:2,0:1:0:27:0:0.41784:0:60:2:0.0016:0:1 0/1:548:7:3,4:305,235:0.0128:2,2:31.6:1:25.3:1:0.70465:1.72871:60:2.5:0.0093:0:1.6 -19 19258018 . GAGGACCCCAGGCCAGATGGGGGTGCCAAGTCCAAGGGAGAAAATCCTGATGAGTTCAGGGGCCCAGCTCTACCTTCAGGAAGCCTTTGCTCCACCTCCCACCAGGCTCCCTACCTGCTCCTCCCCCTGCCCTAACCCTACAGGCTGGGGGAGCTTCTGTCTGGCTCTGCCTGTCCTTGACAGGTAGGTCCAGAGCCAAGACCTCTCACTTAGTGTAGAGTTGGCACTGAGGGGGCTGCACAGAGTGTTTGATGAATCAAAGATGAAATGAAGGA G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.00507;SOR=0.63115;LSEQ=GGTAGAGAAGGGATGGGTCA;RSEQ=AGGAACTGTTTGCCTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:143:38,105:56,197:0.3602:2,2:24.7:1:31.6:1:0.32755:1.27:59.9:286:0.3657:0.0856:0.1 0/1:332:87:22,65:73,171:0.262:2,2:25.2:1:30.8:1:0.49042:1.26043:59.4:86:0.2638:0.0602:0.2 -19 19258656 . G A 205 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=73.96215;LSEQ=CAGCGTCTATGGGGACAGGA;RSEQ=ACAACAGGGTAGACCCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:2:2,0:168,379:0.0036:2,0:1:0:25:0:0.0955:0:60:4:0.0037:0:1 0/1:553:118:37,81:134,301:0.2134:2,2:25.1:1:29.9:1:0.91095:1.03:60:236:0.2161:0:1.1 -19 19258697 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.58764;SOR=2.50512;LSEQ=CCCTACCCCACCCAGGGAAC;RSEQ=CAGTTCTATGGGAGAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:1:0,1:39,207:0.004:2,0:28:0:26:0:1:0:60:2:0.0041:0:1 0/1:198:2:1,1:45,151:0.0101:2,2:9.5:1:28:1:0.41158:3.33:60:4:0.0103:0:1.5 -19 19259489 . CTTAT C 30 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=42;MSI=11.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CCCAGTGAAGACTCCTCTGT;RSEQ=TTATTTATTTATTTATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:0.5 -19 19259945 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20761;SOR=Inf;LSEQ=CACAAAGCCAGATGAAGACA;RSEQ=TCATCTTTTGTGCAAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:157,23:0:2,0:23.6:1:31.9:1:1:0:60:44:1:0:0.1 0/1:152:2:1,1:116,34:0.0132:2,2:29.5:1:27.5:1:0.40868:3.37707:60:4:0.0132:0:1 -19 19259952 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49982;SOR=0;LSEQ=CCAGATGAAGACACTCATCT;RSEQ=TTGTGCAAACCAAGAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:166,28:0.0102:2,2:36:0:33:1:0.27467:5.84302:60:4:0.0107:0:1.5 0/0:178:0:0,0:136,42:0:2,0:21.8:1:29.6:1:1:0:60:58.333:1:0:0.1 -19 19259975 . G T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.1002;SOR=Inf;LSEQ=GTGCAAACCAAGAGTCCCTG;RSEQ=GCTCTGAGAAAGCAGCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:222,87:0:2,0:24.2:1:30.2:1:1:0:60:22.769:1:0:0.1 0/1:269:3:1,2:185,81:0.0112:2,2:17.3:1:21.3:1:0.22594:4.53903:60:2:0.0076:0:1 -19 19260105 . T C 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTACTTCAGCAGCACACGG;RSEQ=CCATGTCCGTGCTGGCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:24:9,15:333,321:0.0353:2,2:27.2:1:31.8:1:0.21768:1.72759:60:48:0.036:0:1.1 0/0:642:0:0,0:332,310:0:2,0:23.2:1:28.8:1:1:0:60:52.5:1:0:0.2 -19 19260386 . C T 31 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0238;SOR=Inf;LSEQ=ATTCTCATGTCACAACCTGG;RSEQ=AAACTCCTACTGGAGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:1,51:0:1,0:25.2:1:32.6:1:1:0:60:51:1:0:0.1 0/1:10:2:1,1:0,8:0.2:0,2:12:0:31:1:0.2:0:60:4:0.2222:0:1.5 -19 19260760 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTAGCCTAGCCAGGCGTGGT;RSEQ=GTGGGCGCCTGTAATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:29:1:1:0:60:4:1:0:1.5 -19 19261065 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAACACTGACAGACCAGGC;RSEQ=CGGTGGCTCACGCCTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:3:0:30:1:1:0:60:4:1:0:1.5 1/1:3:3:1,2:0,0:1:0,2:13.3:1:30.3:1:1:0:60:6:1:0:1 -19 19261367 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13263;SOR=Inf;LSEQ=AAAAAAGAAAGGCTGACATG;RSEQ=CATCAGGACTCCTCATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:152,4:0:1,0:16.8:1:29.7:1:1:0:59.6:7.211:1:0:0.5 0/1:91:2:2,0:86,3:0.022:1,0:7.5:1:30.5:1:1:0:60:4:0.0238:0:1 -19 19261634 . G A 34 v4;q23;Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62379;SOR=0.35141;LSEQ=GAGTGGGGAGGGGTACCCCA;RSEQ=CCTCACACCTCTCCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:3:3,0:29,174:0.0146:2,0:7.3:1:21.7:1:0.00345:0:60:2:0.01:0:1 0/0:194:1:1,0:32,161:0.0052:2,0:1:0:24:0:0.1701:0:60:2:0.0052:0:1 -19 19261833 . A G 26 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACTTTGGGAGGCCAAGGC;RSEQ=GGAGGATCACTTGAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:27.5:1:26:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:1:0,0:18:0:32:0:1:0:60:2:1:0:1 -19 19850027 . A G 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCACACAGATGTTCACCCAC;RSEQ=CGGGATGCTCACATGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:52,23:0:2,0:23.5:1:29.5:1:1:0:60:36.5:1:0:0.2 0/1:80:28:19,9:42,10:0.35:2,2:25.3:1:29.5:1:0.27083:1.97147:60:56:0.35:0:1.1 -19 19850032 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23431;SOR=0;LSEQ=CAGATGTTCACCCACACGGG;RSEQ=TGCTCACATGCACAGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:54,27:0.0238:2,2:26.5:1:31:1:1:1.98212:60:4:0.0253:0:1.5 0/0:89:0:0,0:66,23:0:2,0:23.2:1:27.7:1:1:0:60:11.714:1:0:0.4 -19 20100284 . C A 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAGGGGTTGTCGGACACC;RSEQ=TATACAGGAGCAATCATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:11:1:32:0:1:1.7321:60:4:0.4:0:1 0/0:2:0:0,0:1,1:0:2,0:23.5:1:33:1:1:0:60:4:1:0:0 -19 20101636 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66685;SOR=0.54001;LSEQ=TTGGTGTTAAGCCCAAGCAC;RSEQ=TCTAATATATGCTGGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:0.7273:0,0:31.3:1:30.5:1:1:0:60:16:0.7273:0:1 1/0:12:7:7,0:5,0:0.5833:0,0:17.4:1:30.4:1:1:0:60:14:0.5833:0:1 -19 20101766 . G A 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.97678;LSEQ=TAGGAGGTGGGGTCATAAAA;RSEQ=GAATAGCAAAGTACCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:1:1,0:58,55:0.0088:2,0:1:0:14:0:1:0:51:0:0:0:1 0/1:116:2:1,1:53,61:0.0172:2,2:12:1:32.5:1:1:1.15:60:4:0.0175:0:1 -19 20101780 . C A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05541;SOR=Inf;LSEQ=ATAAAAGGAATAGCAAAGTA;RSEQ=CTTGTTCAAAAGGATCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:52,61:0:2,0:25.6:1:31.7:1:1:0:59.9:226:1:0:0.2 0/1:108:4:1,3:45,59:0.037:2,2:28.8:1:28.8:1:0.63479:2.27227:60:8:0.0374:0:1 -19 20101792 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49904;SOR=0;LSEQ=GCAAAGTACCTTGTTCAAAA;RSEQ=GATCAGATATAGTTACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:45,54:0.0198:2,2:33:1:30:1:1:1.20:60:4:0.0198:0:1 0/0:90:0:0,0:34,55:0:2,0:24.9:1:30.6:1:1:0:60:43.5:0.9886:0:0.2 -19 27731893 . A T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGATATCTTCGTATAAAAAC;RSEQ=AGACAGAATGATTTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7.5:1:28.5:1:1:0:60:4:1:0:1.5 1/1:2:2:2,0:0,0:1:0,0:23:1:32.5:1:1:0:33.5:4:1:0:5.5 -19 27731907 . T C 50 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AAAAACAAGACAGAATGATT;RSEQ=TCAGAAACTGCTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:22:0:26:0:1:0:60:2:1:0:1 1/0:4:3:3,0:0,0:0.75:0,0:27.3:1:32:1:1:0:32.3:6:0.75:0:5.3 -19 27731917 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAATGATTTTCAGAAACT;RSEQ=CTTTGTGATGTGTGCGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:32:0:29:0:1:0:60:2:1:0:1 1/0:4:2:2,0:2,0:0.5:0,0:35:1:30.5:1:1:0:33.5:4:0.5:0:4 -19 27731918 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAATGATTTTCAGAAACTG;RSEQ=TTTGTGATGTGTGCGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:33:0:29:0:1:0:60:2:1:0:1 1/0:4:2:2,0:2,0:0.5:0,0:29.5:1:31:1:1:0:35:4:0.5:0:5.5 -19 27731951 . C A 119 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GCGTTCAACTCACAGAGTTT;RSEQ=AACTTTCTTTTCATAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:0,1:0.6667:0,0:14.5:1:27.8:1:0.2:0:28.5:8:0.8:0:5.3 1/0:27:18:18,0:0,0:0.6667:0,1:17.1:1:28.7:1:1:0:34.4:36:1:0:4.7 -19 27731953 . A C 118 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9639;LSEQ=GTTCAACTCACAGAGTTTCA;RSEQ=CTTTCTTTTCATAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:1,0:0.4286:0,2:25.7:1:32.7:1:1:0:36:6:0.4286:0:4 0/1:31:13:13,0:2,0:0.4194:0,1:18.2:1:32:1:1:0:35.5:26:0.5652:0:5 -19 27731960 . T G 34 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17595;SOR=0.17297;LSEQ=TCACAGAGTTTCAACTTTCT;RSEQ=TTCATAGAGCAGTTAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:11,3:0.125:2,0:13.5:1:34:0:1:0:25.5:4:0.125:0:5.5 0/1:43:1:1,0:42,0:0.0233:1,0:20:0:34:0:1:0:39:2:0.0233:0:4 -19 27731961 . T C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.70212;LSEQ=CACAGAGTTTCAACTTTCTT;RSEQ=TCATAGAGCAGTTAGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:12,3:0.0625:2,0:4:0:32:0:1:0:42:2:0.0625:0:3 0/1:45:2:2,0:43,0:0.0444:1,0:7.5:1:32.5:1:1:0:40:4:0.0444:0:3.5 -19 27731965 . T A 63 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.6562;LSEQ=GAGTTTCAACTTTCTTTTCA;RSEQ=AGAGCAGTTAGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:16,3:0.0476:2,0:6:0:32:0:1:0:40:2:0.05:0:3 0/1:52:4:4,0:48,0:0.0769:1,0:19.5:1:31.8:1:1:0:37.8:8:0.0769:0:4.5 -19 27731970 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10104;SOR=0;LSEQ=TCAACTTTCTTTTCATAGAG;RSEQ=AGTTAGGAAACACTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:21,4:0.0714:2,0:12:1:31.5:1:1:0:38.5:4:0.0714:0:4 0/0:59:0:0,0:59,0:0:1,0:17.1:1:33.1:1:1:0:37.4:118:1:0:3.9 -19 27731975 . A G 76 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16756;SOR=Inf;LSEQ=TTTCTTTTCATAGAGCAGTT;RSEQ=GGAAACACTCTGTTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:27,5:0:2,0:17:1:29.2:1:1:0:33.5:64:1:0:4.1 0/1:65:5:5,0:58,0:0.0769:1,0:26.6:1:32.8:1:1:0:37:10:0.0781:0:4.2 -19 27731977 . G T 105 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16593;SOR=5.10682;LSEQ=TCTTTTCATAGAGCAGTTAG;RSEQ=AAACACTCTGTTTGTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:27,4:0.0313:2,0:24:0:24:0:0.15625:0:40:2:0.0313:0:5 0/1:70:10:10,0:60,0:0.1429:1,0:20.2:1:31.9:1:1:0:39.3:20:0.1429:0:5.1 -19 27731991 . G A 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=2.07775;LSEQ=AGTTAGGAAACACTCTGTTT;RSEQ=TAAAGTCTACAAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:5:3,2:42,7:0.0893:2,2:22:1:29.8:1:0.18966:3.85924:41:10:0.0926:0:4 0/1:106:18:15,3:84,2:0.1698:1,2:23.6:1:29.3:1:0.03539:8.1342:40.4:36:0.1698:0:4.7 -19 27731995 . A T 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.552;SOR=Inf;LSEQ=AGGAAACACTCTGTTTGTAA;RSEQ=GTCTACAAGTGGATATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:47,13:0:2,0:21.4:1:29.8:1:1:0:35:19:0.9828:0:4 0/1:125:3:2,1:110,12:0.024:2,2:5.3:1:27.7:1:0.28271:4.49039:46.3:6:0.0242:0:5.3 -19 27731996 . G C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46359;SOR=1.6104;LSEQ=GGAAACACTCTGTTTGTAAA;RSEQ=TCTACAAGTGGATATTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:5:4,1:44,12:0.0806:2,2:27:1:32.4:1:1:1.09:33.6:10:0.082:0:4.8 0/1:129:16:13,3:103,10:0.124:2,2:21.9:1:31.9:1:0.20477:2.35659:37.4:32:0.124:0:4.6 -19 27731997 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10442;SOR=0;LSEQ=GAAACACTCTGTTTGTAAAG;RSEQ=CTACAAGTGGATATTCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:50,12:0.0313:2,2:26.5:1:30:1:0.36756:4.04304:37:4:0.0317:0:3.5 0/0:133:0:0,0:116,16:0:2,0:23:1:29.8:1:1:0:38.7:65:0.9924:0:4.1 -19 27732000 . A G 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66612;SOR=0.39855;LSEQ=ACACTCTGTTTGTAAAGTCT;RSEQ=CAAGTGGATATTCAGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:70:56,14:0,0:0.9859:0,2:22.3:1:32.5:1:1:0:37.3:140:0.9859:0:3.9 1/1:144:139:117,22:2,0:0.9653:0,2:23.4:1:32.2:1:1:0:39.6:278:0.972:0:4.1 -19 27732003 . A C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55356;SOR=Inf;LSEQ=CTCTGTTTGTAAAGTCTACA;RSEQ=GTGGATATTCAGACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:66,19:0:2,0:21.1:1:30.2:1:1:0:38.2:27.333:1:0:3.8 0/1:181:3:3,0:142,36:0.0166:2,0:17.7:1:30:1:1:0:48.7:6:0.0169:0:3.7 -19 27732004 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGTTTGTAAAGTCTACAA;RSEQ=TGGATATTCAGACCTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:71,22:0:2,0:20.1:1:32.1:1:1:0:38.4:92:1:0:3.7 0/1:196:2:1,1:154,40:0.0102:2,2:25:1:30:1:0.37546:3.81509:50:4:0.0103:0:4.5 -19 27732007 . G C 34 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24939;SOR=0.24005;LSEQ=GTTTGTAAAGTCTACAAGTG;RSEQ=ATATTCAGACCTCTTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:2,0:81,27:0.0182:2,0:42.5:1:34:0:1:0:32:4:0.0189:0:4.5 0/0:227:1:1,0:168,57:0.0044:2,0:45:0:33:0:1:0:40:2:0.0044:0:4 -19 27732013 . C G 64 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58114;SOR=Inf;LSEQ=AAAGTCTACAAGTGGATATT;RSEQ=AGACCTCTTTGAGGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:85,34:0:2,0:22:1:31.3:1:1:0:39.5:118:0.9916:0:3.5 0/1:303:4:2,2:206,91:0.0132:2,2:18.5:1:32.3:1:0.58992:2.25694:33:8:0.0133:0:6 -19 27732015 . G A 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19255;SOR=0.19424;LSEQ=AGTCTACAAGTGGATATTCA;RSEQ=ACCTCTTTGAGGCCTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:87,34:0.016:2,2:33.5:1:29:1:0.4898:2.53646:24:4:0.0164:0:4 0/0:319:1:1,0:218,100:0.0031:2,0:25:0:32:0:1:0:31:2:0.0032:0:7 -19 27732017 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07278;SOR=0;LSEQ=TCTACAAGTGGATATTCAGA;RSEQ=CTCTTTGAGGCCTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:2,0:87,35:0.016:2,0:21.5:1:31.5:1:1:0:53:4:0.0163:0:4 0/0:337:0:0,0:221,111:0:2,0:19:1:30.7:1:1:0:43.9:65.4:0.9849:0:3.7 -19 27732018 . C A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49597;SOR=1.58499;LSEQ=CTACAAGTGGATATTCAGAC;RSEQ=TCTTTGAGGCCTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:5:4,1:86,33:0.0394:2,2:26:1:31:1:1:1.53:31.8:10:0.0403:0:6.2 0/1:344:21:16,5:193,99:0.061:2,2:16.3:1:29.9:1:0.47307:1.64:37.1:42:0.0616:0:4.9 -19 27732019 . T C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21335;SOR=1.70178;LSEQ=TACAAGTGGATATTCAGACC;RSEQ=CTTTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:8:4,4:89,31:0.0625:2,2:27.9:1:30.9:1:0.21294:2.84352:41.1:16:0.0635:0:3.5 0/1:353:36:21,15:209,103:0.102:2,2:27.6:1:30.3:1:0.35279:1.44781:43.8:72:0.1034:0:4.1 -19 27732020 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06964;SOR=0;LSEQ=ACAAGTGGATATTCAGACCT;RSEQ=TTTGAGGCCTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:92,36:0.0153:2,2:28.5:1:26:1:0.4898:2.53446:50:4:0.0157:0:2.5 0/0:364:0:0,0:233,124:0:2,0:19.5:1:30.8:1:1:0:44.4:88.25:0.9833:0:3.6 -19 27732021 . T C 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61777;SOR=1.16162;LSEQ=CAAGTGGATATTCAGACCTC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:25:22,3:71,35:0.1894:2,2:26.4:1:32.1:1:0.0489:3.59:32.5:50:0.1923:0:3.6 0/1:370:79:56,23:183,104:0.2135:2,2:18.7:1:30.5:1:0.28588:1.38:45.7:78:0.2137:0:3.6 -19 27732024 . G C 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16731;SOR=0.17443;LSEQ=GTGGATATTCAGACCTCTTT;RSEQ=AGGCCTTCGTTGGAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:93,46:0.0142:2,2:22.5:1:32:1:1:2.0109:24.5:4:0.0142:0:3.5 0/0:401:1:1,0:248,151:0.0025:2,0:37:0:33:0:1:0:40:2:0.0025:0:4 -19 27732028 . C T 106 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02611;SOR=Inf;LSEQ=ATATTCAGACCTCTTTGAGG;RSEQ=CTTCGTTGGAAACGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:95,53:0:2,0:26:1:31.5:1:1:0:39.8:36:1:0:3.4 0/1:425:14:8,6:246,163:0.0329:2,2:15.4:1:27.9:1:1:1.13156:46.1:28:0.0333:0:4.1 -19 27732029 . C T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12426;LSEQ=TATTCAGACCTCTTTGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:7:6,1:88,53:0.0473:2,2:23.3:1:31.6:1:0.42297:3.59:31.3:14:0.0476:0:5.6 0/1:435:23:13,10:240,168:0.0529:2,2:17.2:1:29.4:1:0.83097:1.09866:39.9:46:0.0532:0:5.2 -19 27732033 . G T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08259;SOR=0.32293;LSEQ=CAGACCTCTTTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:6:4,2:90,54:0.0397:2,2:28.2:1:30:1:1:1.20:40.2:12:0.0403:0:4.2 0/1:456:6:3,3:252,193:0.0132:2,2:18.8:1:28:1:1:1.30491:40.3:12:0.0132:0:3.8 -19 27732034 . T G 76 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33933;SOR=Inf;LSEQ=AGACCTCTTTGAGGCCTTCG;RSEQ=TGGAAACGGGATTTCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:95,59:0:2,0:28.1:1:29.8:1:1:0:40.1:153:1:0:3.4 0/1:465:5:3,2:254,203:0.0108:2,2:24.6:1:32.8:1:1:1.20:49.6:10:0.0108:0:5.6 -19 27732040 . A G 155 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03577;SOR=3.34934;LSEQ=CTTTGAGGCCTTCGTTGGAA;RSEQ=CGGGATTTCTTTATATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:3:2,1:97,69:0.0178:2,2:36.7:1:33.7:1:1:1.42:49:6:0.018:0:5.7 0/1:490:28:15,13:249,212:0.0571:2,2:27.8:1:32.4:1:1:1.01789:41.5:56:0.058:0:5.1 -19 27732041 . C A 57 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65056;SOR=0.69162;LSEQ=TTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTTATATTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:2,0:97,72:0.0117:2,0:42.5:1:32:0:0.5096:0:44:4:0.0118:0:4 0/0:493:4:2,2:258,226:0.0081:2,2:24.8:1:28.8:1:1:1.14128:45.5:8:0.0081:0:5 -19 27732042 . G A 60 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00443;SOR=0;LSEQ=TTGAGGCCTTCGTTGGAAAC;RSEQ=GGATTTCTTTATATTATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:4:2,2:95,70:0.023:2,2:26.5:1:30:1:1:1.35464:41.5:8:0.0233:0:4.8 0/0:496:0:0,0:261,231:0:2,0:27:1:29.4:1:1:0:44.8:163:0.9959:0:3.4 -19 27732043 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.75694;LSEQ=TGAGGCCTTCGTTGGAAACG;RSEQ=GATTTCTTTATATTATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:1:1,0:98,73:0.0057:2,0:15:0:25:0:1:0:40:2:0.0058:0:5 0/1:497:5:3,2:258,232:0.0101:2,2:28:1:30:1:1:1.35:45.8:10:0.0101:0:3.4 -19 27732045 . A T 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.04443;LSEQ=AGGCCTTCGTTGGAAACGGG;RSEQ=TTTCTTTATATTATGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:98,74:0.0115:2,2:33.5:1:31.5:1:1:1.32215:41:4:0.0116:0:4 0/1:500:6:3,3:253,235:0.012:2,2:19:1:27.8:1:1:1.07641:32.5:12:0.0122:0:3.7 -19 27732050 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0669;SOR=0;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TTATATTATGCTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:97,77:0.0114:2,2:27.5:1:30:1:1:1.25807:50:4:0.0114:0:4 0/0:503:0:0,0:255,245:0:2,0:30.5:1:30:1:1:0:44.5:99:0.994:0:3.5 -19 27732052 . T C 275 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2909;SOR=0.56136;LSEQ=CGTTGGAAACGGGATTTCTT;RSEQ=ATATTATGCTAGACAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:174:169:94,75:0,0:0.9713:0,2:30.9:1:31.4:1:1:0:39.9:83.5:0.9824:0:3.5 1/1:499:474:237,237:1,2:0.9499:2,2:31.6:1:31:1:1:2.00:44.4:117.5:0.9651:0:3.5 -19 27732055 . A G 106 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.16064;LSEQ=TGGAAACGGGATTTCTTTAT;RSEQ=TTATGCTAGACAGAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:2,1:93,76:0.0172:2,2:43.7:1:33:1:1:1.63:47:6:0.0176:0:6.3 0/1:501:10:5,5:243,244:0.02:2,2:42.6:1:32:1:1:1.00:52.6:20:0.0202:0:5.5 -19 27732056 . T C 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88518;SOR=1.07664;LSEQ=GGAAACGGGATTTCTTTATA;RSEQ=TATGCTAGACAGAAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:17:9,8:87,70:0.0977:2,2:32.4:1:31.8:1:1:1.10413:43.6:34:0.0983:0:3.4 0/1:498:52:25,27:221,223:0.1044:2,2:34.1:1:31.2:1:0.88384:1.07014:45.3:104:0.1068:0:3.8 -19 27732058 . A C 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00986;SOR=0.61059;LSEQ=AAACGGGATTTCTTTATATT;RSEQ=TGCTAGACAGAAGAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:68:41,27:52,50:0.3977:2,2:32.6:1:30.9:1:0.27195:1.46:37.1:21.667:0.3892:0:4.2 0/1:498:143:69,74:164,163:0.2871:2,2:37.6:1:31.1:1:0.76371:1.07886:41.5:46.667:0.2851:0:4.4 -19 27732061 . C A 49 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01722;SOR=0;LSEQ=CGGGATTTCTTTATATTATG;RSEQ=TAGACAGAAGAATTCTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:3,0:89,78:0.0173:2,0:13.7:1:31:1:0.25068:0:44.7:6:0.0178:0:5.7 0/0:494:0:0,0:237,247:0:2,0:33.6:1:31.7:1:1:0:44.6:120:0.9796:0:3.4 -19 27732062 . T G 36 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01755;SOR=0;LSEQ=GGGATTTCTTTATATTATGC;RSEQ=AGACAGAAGAATTCTCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:1,2:96,79:0.0168:2,2:30:1:23.3:1:0.59192:2.41854:27.3:2:0.0114:0:5 0/0:507:0:0,0:253,254:0:2,0:32.8:1:29.2:1:1:0:44.5:83.5:1:0:3.5 -19 27732064 . G T 106 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37637;SOR=2.28339;LSEQ=GATTTCTTTATATTATGCTA;RSEQ=ACAGAAGAATTCTCAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:2,0:89,82:0.0114:2,0:35.5:1:31.5:1:0.49845:0:46.5:4:0.0117:0:6 0/1:505:13:5,8:241,246:0.0257:2,2:41.2:1:28.8:1:0.5766:1.56609:37.7:26:0.0258:0:5.7 -19 27732066 . C A 61 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11929;SOR=0.33733;LSEQ=TTTCTTTATATTATGCTAGA;RSEQ=AGAAGAATTCTCAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:4:2,2:87,80:0.0233:2,2:32.3:1:30:1:1:1.08695:31.5:8:0.0234:0:5 0/0:503:4:2,2:240,252:0.008:2,2:44:1:30.5:1:1:1.05:28.5:8:0.008:0:5 -19 27732070 . A T 135 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21077;LSEQ=TTTATATTATGCTAGACAGA;RSEQ=GAATTCTCAGTAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:24:12,12:67,66:0.1437:2,2:27.8:1:29.6:1:1:1.01506:41:23:0.1411:0:3.3 0/1:499:17:7,10:222,242:0.0341:2,2:32.5:1:29.5:1:0.62979:1.30978:45.6:34:0.0343:0:3 -19 27732071 . G T 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01267;SOR=2.13134;LSEQ=TTATATTATGCTAGACAGAA;RSEQ=AATTCTCAGTAACTTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:13:6,7:80,74:0.0778:2,2:27.9:1:26.7:1:0.77686:1.2595:42.8:5.5:0.0675:0:3.1 0/1:498:76:32,44:207,214:0.1526:2,2:32.4:1:28.5:1:0.26469:1.32926:46.7:75:0.1524:0:3.2 -19 27732077 . T C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18322;SOR=0.62911;LSEQ=TATGCTAGACAGAAGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:13:9,4:75,76:0.0788:2,2:13.2:1:31:1:0.24901:2.27:53.5:26:0.0798:0:5.4 0/1:490:25:16,9:215,249:0.051:2,2:14.5:1:30.8:1:0.10095:2.06:43.6:50:0.0515:0:5.4 -19 27732081 . T A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98303;LSEQ=CTAGACAGAAGAATTCTCAG;RSEQ=AACTTCCTTGTGTTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:12:8,4:73,77:0.0732:2,2:23.6:1:30.3:1:0.36904:2.10:41:24:0.0741:0:6 0/1:486:35:16,19:208,240:0.072:2,2:30.6:1:29.7:1:1:1.02911:39.6:34:0.0704:0:6 -19 27732083 . A T 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83882;LSEQ=AGACAGAAGAATTCTCAGTA;RSEQ=CTTCCTTGTGTTGTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:78,80:0.0124:2,2:29:1:32:0:1:1.03:31:4:0.0126:0:7 0/1:479:5:3,2:215,256:0.0104:2,2:24.6:1:31:1:0.6644:1.78:34.2:10:0.0106:0:5.2 -19 27732086 . T G 74 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.66896;LSEQ=CAGAAGAATTCTCAGTAACT;RSEQ=CCTTGTGTTGTGTGTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:1,0:76,81:0.0063:2,0:16:0:34:0:0.48734:0:27:2:0.0064:0:5 0/1:475:5:2,3:211,259:0.0105:2,2:28.6:1:32.2:1:1:1.2215:32.2:10:0.0107:0:5.6 -19 27732093 . G A 95 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4641;SOR=2.93364;LSEQ=ATTCTCAGTAACTTCCTTGT;RSEQ=TTGTGTGTATTCAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:1,0:65,76:0.007:2,0:14:0:30:0:0.46479:0:28:2:0.0071:0:4 0/1:441:9:3,6:186,244:0.0204:2,2:22.3:1:30.2:1:0.73804:1.52318:42.7:18:0.0207:0:2.8 -19 27732097 . T G 22 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.27062;SOR=0.34072;LSEQ=TCAGTAACTTCCTTGTGTTG;RSEQ=GTGTATTCAACTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:63,74:0.0143:2,2:25:1:29.5:1:1:1.17:50:4:0.0144:0:4.5 0/0:408:2:1,1:167,236:0.0049:2,2:15.5:1:22.5:1:1:1.41:22.5:1:0.0025:0:4.5 -19 27732098 . G A 48 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01677;SOR=0;LSEQ=CAGTAACTTCCTTGTGTTGT;RSEQ=TGTATTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:2,1:63,74:0.0214:2,2:9.3:1:30.7:1:0.597:2.34:57:6:0.0217:0:5 0/0:404:0:0,0:167,233:0:2,0:18.6:1:31.3:1:1:0:45.7:399:0.9925:0:3.5 -19 27732099 . T A 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.57674;SOR=Inf;LSEQ=AGTAACTTCCTTGTGTTGTG;RSEQ=GTATTCAACTCACAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:58,75:0:2,0:21.1:1:29.9:1:1:0:42.4:132:0.9851:0:3.7 0/1:391:4:3,1:157,227:0.0102:2,2:15.5:1:26:1:0.3105:4.32:48:8:0.0103:0:3.3 -19 27732100 . G T 60 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.04087;SOR=0.16998;LSEQ=GTAACTTCCTTGTGTTGTGT;RSEQ=TATTCAACTCACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:4:1,3:59,71:0.0299:2,2:21.8:1:30.3:1:0.62769:2.47753:50:8:0.0299:0:4.3 0/0:386:2:1,1:157,227:0.0052:2,2:15.5:1:32:0:1:1.44:55.5:4:0.0052:0:5.5 -19 27732101 . T C 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05662;SOR=0.58623;LSEQ=TAACTTCCTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:25:14,11:46,60:0.188:2,2:27:1:32.5:1:0.27329:1.65:51.6:50:0.1894:0:5.2 0/1:377:45:24,21:128,201:0.1194:2,2:26.8:1:31.2:1:0.07541:1.79:46.4:90:0.1206:0:5.2 -19 27732102 . A T 137 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00838;SOR=8.89047;LSEQ=AACTTCCTTGTGTTGTGTGT;RSEQ=TTCAACTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:0,1:55,71:0.0078:2,0:11:0:31:0:1:0:49:2:0.0079:0:6 0/1:366:24:8,16:139,203:0.0656:2,2:14:1:29.9:1:0.52603:1.36832:42.8:23:0.0634:0:6.1 -19 27732105 . C A 64 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34362;SOR=Inf;LSEQ=TTCCTTGTGTTGTGTGTATT;RSEQ=AACTCACAGAGTTGAACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:43,66:0:2,0:21.4:1:31.8:1:1:0:42.5:108:1:0:3.9 0/1:332:6:3,3:123,202:0.0181:2,2:13.7:1:24.8:1:0.67758:1.64:41:5:0.0152:0:5 -19 27732108 . C A 54 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.57621;SOR=Inf;LSEQ=CTTGTGTTGTGTGTATTCAA;RSEQ=TCACAGAGTTGAACGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:37,65:0:2,0:21.1:1:32:1:1:0:42.5:50:1:0:4 0/1:296:4:2,2:105,184:0.0135:2,2:5:1:27.3:1:0.62468:1.75:50.5:8:0.0135:0:5.5 -19 27732109 . T A 76 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34635;SOR=Inf;LSEQ=TTGTGTTGTGTGTATTCAAC;RSEQ=CACAGAGTTGAACGGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:36,64:0:2,0:21:1:30.6:1:1:0:42.9:99:1:0:4 0/1:283:6:3,3:96,181:0.0212:2,2:17.7:1:29.5:1:0.42503:1.88:43.7:12:0.0216:0:4.2 -19 27732110 . C G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.34239;SOR=1.79067;LSEQ=TGTGTTGTGTGTATTCAACT;RSEQ=ACAGAGTTGAACGGTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:4:2,2:33,61:0.0408:2,2:8.3:1:30.5:1:0.61523:1.84:41.8:8:0.0412:0:3.3 0/1:268:19:6,13:82,166:0.0709:2,2:7.7:1:31:1:1:1.07002:46.9:38:0.0709:0:2.6 -19 27732114 . G C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30741;SOR=0.379;LSEQ=TTGTGTGTATTCAACTCACA;RSEQ=AGTTGAACGGTTCTTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:30,58:0.0222:2,2:41:1:31.5:1:1:1.92:31:4:0.0222:0:7 0/0:235:2:1,1:70,158:0.0085:2,2:24.5:1:31.5:1:0.52303:2.25:28:4:0.0085:0:7 -19 27732119 . G A 57 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26054;SOR=0.44181;LSEQ=TGTATTCAACTCACAGAGTT;RSEQ=AACGGTTCTTTACACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:4:1,3:29,56:0.0449:2,2:24:1:29.5:1:1:1.54646:29.3:8:0.0455:0:5.3 0/1:197:4:2,2:59,132:0.0203:2,2:5:0:28.8:1:0.59053:2.23:46:8:0.0204:0:2 -19 27732122 . C T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08374;SOR=0.60637;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=GGTTCTTTACACAGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:34:19,15:8,32:0.4595:2,2:26.2:1:30.6:1:0.00178:4.95:52.7:33:0.4648:0:5.7 0/1:159:54:30,24:17,87:0.3396:2,2:27.6:1:29.6:1:0:6.31:48.4:53:0.3376:0:5.2 -19 27732123 . GGTTCTTTACAC TTTCATTTAGAG 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.23991;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=AGAGCAGATTTGAGACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:27,43:0.0278:2,0:14.5:1:31.1:1:0.52465:0:39:4:0.0278:0.0278:3.5 0/1:146:5:1,4:43,97:0.0342:2,2:6.9:1:29.3:1:1:1.767:38.8:4:0.0341:0.0338:2.8 -19 27732124 . G A 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACTCACAGAGTTGAACG;RSEQ=TTCTTTACACAGAGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:64:27,37:0,0:1:0,2:22.6:1:31.1:1:1:0:44.6:128:1:0:5.3 1/1:110:109:37,72:0,0:0.9909:0,2:21.7:1:29.8:1:1:0:44.2:108:1:0:5 -19 27732126 . T C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0419;LSEQ=AACTCACAGAGTTGAACGGT;RSEQ=CTTTACACAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:23:4,19:23,14:0.3594:2,2:14.3:1:31.7:1:0.00114:7.51895:33.6:46:0.3651:0:4.7 0/1:103:38:2,36:31,27:0.3689:2,2:13.9:1:32.2:1:0:20.07453:37.4:76:0.3725:0:4.7 -19 27732127 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15212;SOR=0;LSEQ=ACTCACAGAGTTGAACGGTT;RSEQ=TTTACACAGAGCAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:27,36:0.0299:2,2:28:1:31:1:1:1.33:31:4:0.0308:0:7 0/0:104:0:0,0:33,67:0:2,0:21.9:1:31.8:1:1:0:44.1:200:1:0:5 -19 27732130 . T C 32 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.30575;LSEQ=CACAGAGTTGAACGGTTCTT;RSEQ=ACACAGAGCAGATTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:1:0,1:30,38:0.0145:2,0:20:0:14:0:1:0:58:0:0:0:8 0/1:106:2:1,1:37,67:0.0189:2,2:18:1:32.5:1:1:1.80:34.5:4:0.0192:0:7.5 -19 27732134 . C G 50 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.64985;SOR=2.03335;LSEQ=GAGTTGAACGGTTCTTTACA;RSEQ=AGAGCAGATTTGAGACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:1:0,1:30,36:0.0149:2,0:5:0:33:0:1:0:40:2:0.0149:0:5 0/1:100:3:0,3:42,55:0.03:2,0:15:1:32:1:0.26182:0:33.7:6:0.03:0:6.3 -19 27732143 . T C 114 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01724;SOR=8.35669;LSEQ=GGTTCTTTACACAGAGCAGA;RSEQ=TTGAGACACTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:0,1:25,25:0.0196:2,0:50:0:34:0:1:0:40:2:0.0196:0:3 0/1:83:12:4,8:36,35:0.1446:2,2:8.4:1:31.8:1:0.35416:2.03974:35.8:24:0.1446:0:3.9 -19 27732148 . G A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25995;SOR=0.50111;LSEQ=TTTACACAGAGCAGATTTGA;RSEQ=ACACTCTTTTTGTGGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:8:0,8:22,19:0.1633:2,0:10.5:1:29.1:1:0.00563:0:35.5:16:0.1633:0:5.1 0/1:79:7:2,5:36,36:0.0886:2,2:8.7:1:28.3:1:0.43383:2.47264:28.7:14:0.0886:0:6 -19 27732154 . C G 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20583;SOR=0.30161;LSEQ=CAGAGCAGATTTGAGACACT;RSEQ=TTTTTGTGGAATTTGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:4:0,4:23,23:0.08:2,0:20.8:1:31:1:0.11465:0:36.5:8:0.08:0:5 0/1:79:2:1,1:37,40:0.0253:2,2:4.3:1:31:1:1:1.08:40:8:-0.0193:0:6 -19 27732156 . T A 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.28444;SOR=Inf;LSEQ=GAGCAGATTTGAGACACTCT;RSEQ=TTTGTGGAATTTGTAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:23,27:0:2,0:23.1:1:29.7:1:1:0:50:49:1:0:5.2 0/1:80:3:2,1:36,40:0.0375:2,2:5.3:1:27.3:1:0.60596:2.20:37.7:6:0.038:0:6.3 -19 27732159 . T G 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.83946;SOR=0.86342;LSEQ=CAGATTTGAGACACTCTTTT;RSEQ=GTGGAATTTGTAAGTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:37:21,16:2,10:0.74:2,2:24.9:1:31.8:1:0.02102:6.32:52.2:74:0.7551:0:5.3 1/0:76:54:24,30:10,12:0.7105:2,2:24:1:31:1:1:1.04113:45.7:53:0.7067:0:5 -19 27732160 . G C 48 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29981;SOR=0.21031;LSEQ=AGATTTGAGACACTCTTTTT;RSEQ=TGGAATTTGTAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:0,3:24,23:0.0588:2,0:27.7:1:30.7:1:0.23592:0:35.7:6:0.0588:0:5 0/1:78:1:0,1:35,42:0.0128:2,0:13:0:34:0:1:0:21:2:0.0128:0:6 -19 27732168 . T G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14244;SOR=0;LSEQ=GACACTCTTTTTGTGGAATT;RSEQ=GTAAGTGGAGATTTCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:20,26:0.0408:2,2:14.5:1:30:1:1:1.29:26:4:0.0408:0:6 0/0:80:0:0,0:37,43:0:2,0:22.5:1:30:1:1:0:42.5:160:1:0:4.8 -19 27732170 . T C 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99859;LSEQ=CACTCTTTTTGTGGAATTTG;RSEQ=AAGTGGAGATTTCAGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:11:3,8:18,19:0.2292:2,2:23.9:1:31.9:1:0.30432:2.4796:40.5:22:0.2292:0:4.9 0/1:83:19:10,9:28,36:0.2289:2,2:15.2:1:32.2:1:0.60236:1.42:32:38:0.2289:0:5.2 -19 27732171 . A T 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98694;LSEQ=ACTCTTTTTGTGGAATTTGT;RSEQ=AGTGGAGATTTCAGCCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:3:2,1:18,27:0.0625:2,2:33.3:1:29.7:1:0.5629:2.93:42.7:6:0.0625:0:5.7 0/1:81:5:2,3:35,41:0.0617:2,2:29.8:1:28.4:1:1:1.27663:48.6:10:0.0625:0:5.8 -19 27732173 . G T 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29519;SOR=Inf;LSEQ=TCTTTTTGTGGAATTTGTAA;RSEQ=TGGAGATTTCAGCCGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:21,29:0:2,0:26.7:1:31.8:1:1:0:46.6:100:1:0:5.1 0/1:85:3:1,2:40,42:0.0353:2,2:35.7:1:31:1:1:1.89091:45:6:0.0361:0:6.7 -19 27732180 . T A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11028;SOR=0.54859;LSEQ=GTGGAATTTGTAAGTGGAGA;RSEQ=TTCAGCCGCTTTGAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:37:19,18:4,12:0.6981:2,2:25.8:1:30.4:1:0.13019:3.10:49.5:74:0.6981:0:5.3 1/0:86:48:22,26:21,15:0.5581:2,2:24.6:1:29.2:1:0.27863:1.64452:47.2:23:0.5476:0:4.9 -19 27732186 . C A 46 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.73786;LSEQ=TTTGTAAGTGGAGATTTCAG;RSEQ=CGCTTTGAGGTCAGTGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:0,1:23,26:0.0196:2,0:40:0:32:0:1:0:40:2:0.0196:0:6 0/1:89:3:1,2:45,40:0.0337:2,2:22:1:29.3:1:0.60387:2.22993:40:6:0.0337:0:5.3 -19 27732187 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14045;SOR=0.38622;LSEQ=TTGTAAGTGGAGATTTCAGC;RSEQ=GCTTTGAGGTCAGTGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:8:4,4:19,26:0.1509:2,2:28:1:30.6:1:0.71525:1.36:56.6:16:0.1509:0:6.1 0/1:94:6:2,4:46,39:0.0638:2,2:23.8:1:28.2:1:0.41618:2.33727:50.5:5:0.0549:0:6 -19 27732195 . G T 71 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00307;SOR=0;LSEQ=GGAGATTTCAGCCGCTTTGA;RSEQ=GTCAGTGGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:2,3:20,26:0.0962:2,2:32.8:1:31:1:1:1.15064:38.2:10:0.0962:0:5.4 0/0:109:0:0,0:51,51:0:2,0:22.6:1:30.8:1:1:0:44.6:101:0.9352:0:4.3 -19 27732196 . G T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59515;SOR=0.4697;LSEQ=GAGATTTCAGCCGCTTTGAG;RSEQ=TCAGTGGTAGAAAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:0,2:22,28:0.0385:2,0:16.5:1:26:1:0.50226:0:33.5:4:0.0385:0:5.5 0/1:109:2:1,1:54,52:0.0183:2,2:8.5:1:28.5:1:1:1.03811:60:4:0.0183:0:7.5 -19 27732199 . AG CA 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00304;SOR=Inf;LSEQ=ATTTCAGCCGCTTTGAGGTC;RSEQ=TGGTAGAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:23,30:0:2,0:26.2:1:30.3:1:1:0:46.4:106:1:0:5 0/1:114:15:9,6:49,50:0.1316:2,2:18.5:1:31.2:1:0.58178:1.52:52.4:30:0.1327:0:2.5 -19 27732200 . GT AC 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03368;SOR=0.49279;LSEQ=TTTCAGCCGCTTTGAGGTCA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:31:16,15:2,2:0.5636:2,2:24.3:1:30.3:1:1:1.06:50.3:62:0.5636:0.0182:4.3 0/1:116:45:20,25:3,1:0.3879:2,2:24.6:1:29.7:1:0.32968:3.65513:48.3:44:0.449:0.0431:3.7 -19 27732202 . G A 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44502;SOR=0.48978;LSEQ=TCAGCCGCTTTGAGGTCAGT;RSEQ=GTAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:4:1,3:27,33:0.0625:2,2:36.5:1:31.3:1:0.6252:2.42328:46.5:8:0.0625:0:5.5 0/1:127:4:2,2:56,63:0.0315:2,2:21.8:1:31:1:1:1.12:30.5:8:0.032:0:5.8 -19 27732205 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCGCTTTGAGGTCAGTGGT;RSEQ=GAAAAGGAAATATCTTCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:31,37:0:2,0:20.7:1:29.9:1:1:0:44.9:136:0.9855:0:4.1 0/1:143:2:1,1:66,74:0.014:2,2:26:1:29:1:1:1.12:45.5:4:0.014:0:6 -19 27732206 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCGCTTTGAGGTCAGTGGTA;RSEQ=AAAAGGAAATATCTTCGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:32,36:0:2,0:20.9:1:31.7:1:1:0:44.8:136:1:0:4 0/1:150:2:1,1:69,77:0.0133:2,2:23:1:31:1:1:1.12:51.5:4:0.0136:0:5.5 -19 27732209 . A T 94 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11628;SOR=4.86004;LSEQ=CTTTGAGGTCAGTGGTAGAA;RSEQ=AGGAAATATCTTCGTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:0,1:33,38:0.0139:2,0:20:0:24:0:1:0:27:2:0.0139:0:6 0/1:171:11:2,9:78,82:0.0643:2,2:22.4:1:27.2:1:0.06291:4.24884:38.2:22:0.0647:0:5.5 -19 27732212 . G T 86 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06285;SOR=Inf;LSEQ=TGAGGTCAGTGGTAGAAAAG;RSEQ=AAATATCTTCGTATAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:33,41:0:2,0:20.5:1:31.4:1:1:0:44.6:148:1:0:3.7 0/1:182:9:4,5:79,92:0.0495:2,2:9:1:27.2:1:1:1.07297:45.3:18:0.0503:0:4.6 -19 27732213 . A C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08211;SOR=0;LSEQ=GAGGTCAGTGGTAGAAAAGG;RSEQ=AATATCTTCGTATAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:32,40:0.027:2,2:13:0:33:1:1:1.25:45:4:0.0274:0:6 0/0:183:0:0,0:86,97:0:2,0:19.9:1:29.1:1:1:0:43.7:90.5:1:0:3.3 -19 27732214 . A C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGTCAGTGGTAGAAAAGGA;RSEQ=ATATCTTCGTATAAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:33,42:0:2,0:20.8:1:30.1:1:1:0:44.6:74:1:0:3.7 0/1:181:2:0,2:84,95:0.011:2,0:47:1:32:1:0.49982:0:40:4:0.011:0:6.5 -19 27732215 . A AC 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58027;SOR=Inf;LSEQ=GGTCAGTGGTAGAAAAGGAA;RSEQ=TATCTTCGTATAAAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:32,41:0:2,0:21.6:1:30.7:1:1:0:44.4:146:0.9865:0:3.7 0/1:186:4:2,2:83,97:0.0215:2,2:19.5:1:30.5:1:1:1.17:35:8:0.0215:0:3.8 -19 27732217 . A T 30 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.80069;LSEQ=TCAGTGGTAGAAAAGGAAAT;RSEQ=TCTTCGTATAAAAACTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:1:0,1:32,42:0.0133:2,0:1:0:26:0:1:0:33:2:0.0133:0:3 0/1:187:2:0,2:87,98:0.0107:2,0:48.5:1:30.5:1:0.49974:0:40:4:0.0107:0:6.5 -19 27732218 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTGGTAGAAAAGGAAATA;RSEQ=CTTCGTATAAAAACTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:33,44:0:2,0:21.4:1:30.5:1:1:0:43.7:154:1:0:3.6 0/1:187:2:1,1:85,100:0.0107:2,2:27:1:30.5:1:1:1.18:33:4:0.0108:0:4 -19 27732223 . G C 148 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02778;SOR=3.77182;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:3:0,3:34,40:0.038:2,0:31:1:32.3:1:0.25051:0:35.7:6:0.038:0:4.7 0/1:200:26:10,16:74,88:0.13:2,2:24.8:1:31.5:1:0.53085:1.34336:37.3:52:0.13:0:4.1 -19 27732225 . AT GG 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19979;SOR=0.19933;LSEQ=AGAAAAGGAAATATCTTCGT;RSEQ=AAAAACTAGACAGAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:32,47:0.0244:2,2:37:1:32.5:1:1:1.46:53.5:4:0.0244:0:4.5 0/0:203:1:1,0:88,111:0.0049:2,0:30:0:33.5:0:0.445:0:21:2:0.005:0:5 -19 27732226 . T G 105 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.56589;SOR=1.66401;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGACAGAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:3:1,2:31,45:0.0361:2,2:16:1:31.7:1:1:1.37239:35.3:6:0.037:0:6 0/1:204:12:6,6:84,107:0.0588:2,2:23.5:1:29.3:1:0.76874:1.27:41.9:11:0.0547:0:3.4 -19 27732228 . A G 88 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.44425;SOR=2.96108;LSEQ=AAAGGAAATATCTTCGTATA;RSEQ=AAACTAGACAGAATGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:1:0,1:35,49:0.0118:2,0:39:0:29:0:1:0:27:2:0.0118:0:6 0/1:205:7:1,6:90,108:0.0341:2,2:40.1:1:31.4:1:0.13517:4.96888:33.9:14:0.0345:0:6.9 -19 27732229 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.08377;SOR=0;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACTAGACAGAATGATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:34,48:0.0238:2,2:29:0:33:1:1:1.41:45:4:0.0238:0:5 0/0:205:0:0,0:90,113:0:2,0:25.8:1:30.1:1:1:0:43.9:202:0.9902:0:3.1 -19 27732230 . A G 119 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.41104;SOR=1.96091;LSEQ=AGGAAATATCTTCGTATAAA;RSEQ=ACTAGACAGAATGATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:3:1,2:33,47:0.0361:2,2:21.3:1:31.3:1:1:1.39872:37:6:0.0361:0:2.7 0/1:204:14:6,8:83,105:0.0686:2,2:24.9:1:31.4:1:1:1.05371:43.3:28:0.0697:0:4.4 -19 27732232 . C G 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32743;SOR=Inf;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATGATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:34,49:0:2,0:24.1:1:32.5:1:1:0:44.5:166:1:0:3.3 0/1:204:4:2,2:88,112:0.0196:2,2:31.3:1:31.3:1:1:1.27:48.5:8:0.02:0:6 -19 27732233 . TA T 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08292;SOR=0;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=GACAGAATGATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:33,48:0.0241:2,2:21.5:1:33.5:1:1:1.45:33:4:0.0241:0:6.5 0/0:204:0:0,0:87,114:0:2,0:27.8:1:29.7:1:1:0:44.1:66:0.9851:0:3.1 -19 27732237 . C A 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.79862;LSEQ=ATCTTCGTATAAAAACTAGA;RSEQ=AGAATGATTCTCAGAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:32,47:0.0247:2,2:31.5:1:29.5:1:1:1.46:48.5:4:0.0247:0:4 0/1:202:4:2,2:85,111:0.0198:2,2:16.5:1:28.5:1:1:1.30:53:8:0.0201:0:4.5 -19 27732241 . A G 33 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80675;LSEQ=TCGTATAAAAACTAGACAGA;RSEQ=TGATTCTCAGAAACTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:1:0,1:32,47:0.0125:2,0:8:0:33:0:1:0:27:2:0.0125:0:7 0/1:198:2:1,1:83,113:0.0101:2,2:26:0:33.5:1:1:1.36:46:4:0.0102:0:2.5 -19 27732242 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08538;SOR=0;LSEQ=CGTATAAAAACTAGACAGAA;RSEQ=GATTCTCAGAAACTGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:31,48:0.0247:2,2:35:1:31:1:1:1.54:46.5:4:0.0247:0:3 0/0:195:0:0,0:84,111:0:2,0:35:0:8:0:1:0:45:0:0:0:3 -19 27732247 . C A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAACTAGACAGAATGATT;RSEQ=TCAGAAACTGCTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:32,44:0:2,0:29.5:1:32.3:1:1:0:44.2:152:1:0:3.2 0/1:196:2:1,1:82,112:0.0102:2,2:27:0:28:1:1:1.36:60:4:0.0103:0:4 -19 27732248 . T G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07848;SOR=0;LSEQ=AAAACTAGACAGAATGATTC;RSEQ=CAGAAACTGCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:31,43:0.0263:2,2:38.5:1:30:1:1:1.38:42:4:0.0263:0:4.5 0/0:194:0:0,0:82,108:0:2,0:31.4:1:29.7:1:1:0:44.3:46.5:0.9841:0:3 -19 27732251 . GA TT 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1881;SOR=0.18988;LSEQ=ACTAGACAGAATGATTCTCA;RSEQ=AACTGCTTTGTGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:30,42:0.027:2,2:34.5:1:30.3:1:1:1.39:60:4:0.027:0:2 0/0:192:1:0,1:82,106:0.0052:2,0:28:0:30:0:1:0:57:2:0.0053:0:6 -19 27732254 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0757;SOR=0;LSEQ=AGACAGAATGATTCTCAGAA;RSEQ=CTGCTTTGTGATGTGTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:29,42:0.0274:2,2:8:0:33.5:1:1:1.44:45:4:0.0274:0:5 0/0:191:0:0,0:81,107:0:2,0:29.9:1:29.8:1:1:0:44.3:93:0.9841:0:3 -19 27732255 . C A 74 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32652;SOR=Inf;LSEQ=GACAGAATGATTCTCAGAAA;RSEQ=TGCTTTGTGATGTGTGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:30,43:0:2,0:29.8:1:32.7:1:1:0:44.3:146:1:0:3.2 0/1:190:5:2,3:78,105:0.0263:2,2:22.2:1:32:0:1:1.11369:35:10:0.0267:0:4.4 -19 27732257 . G C 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14411;SOR=1.57445;LSEQ=CAGAATGATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:19:7,12:12,19:0.2676:2,2:24.4:1:31.7:1:1:1.08097:42.1:38:0.2714:0:2.9 0/1:186:68:28,40:25,40:0.3656:2,2:29.8:1:31.5:1:0.85958:1.12:41.1:33:0.3607:0:3.1 -19 27732258 . C T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05217;SOR=0.55427;LSEQ=AGAATGATTCTCAGAAACTG;RSEQ=TTTGTGATGTGTGCGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:30:11,19:18,23:0.4225:2,2:30.8:1:30.2:1:0.62818:1.34605:49.1:29:0.4143:0:2.9 0/1:184:53:20,33:55,71:0.288:2,2:30.1:1:29:1:0.50953:1.27643:49.8:25.5:0.2881:0:2.9 -19 27732259 . T A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76329;LSEQ=GAATGATTCTCAGAAACTGC;RSEQ=TTGTGATGTGTGCGTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:1:0,1:28,41:0.0143:2,0:28:0:32:0:1:0:25:2:0.0145:0:4 0/1:183:2:1,1:76,105:0.0109:2,2:42.5:1:30:1:1:1.38:30:4:0.011:0:3.5 -19 27732261 . T G 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07576;SOR=0;LSEQ=ATGATTCTCAGAAACTGCTT;RSEQ=GTGATGTGTGCGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:27,41:0.0286:2,2:36:0:31.5:1:1:1.51:33:4:0.0286:0:6.5 0/0:183:0:0,0:75,104:0:2,0:27.2:1:30:1:1:0:45.1:43.75:0.9777:0:2.9 -19 27732263 . T G 51 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01931;SOR=0;LSEQ=GATTCTCAGAAACTGCTTTG;RSEQ=GATGTGTGCGTTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:3:1,2:26,38:0.0448:2,2:35.7:1:32.3:1:1:1.36224:39.7:6:0.0448:0:3.3 0/0:180:0:0,0:76,103:0:2,0:26.3:1:29.9:1:1:0:45.5:178:0.9944:0:3 -19 27732265 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTCAGAAACTGCTTTGTG;RSEQ=TGTGTGCGTTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:27,39:0:2,0:27.6:1:31.1:1:1:0:44.9:132:1:0:3 0/1:178:2:1,1:74,102:0.0112:2,2:22.5:1:31:1:1:1.38:48:4:0.0114:0:5.5 -19 27732269 . G T 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.56865;SOR=Inf;LSEQ=CAGAAACTGCTTTGTGATGT;RSEQ=TGCGTTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:23,36:0:2,0:27.7:1:32.7:1:1:0:44.8:118:1:0:3 0/1:166:3:1,2:69,93:0.0181:2,2:9.7:1:29.3:1:1:1.48046:54.3:6:0.0183:0:4 -19 27732271 . G C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56891;SOR=Inf;LSEQ=GAAACTGCTTTGTGATGTGT;RSEQ=CGTTCAACTCACAGAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:23,34:0:2,0:27.2:1:32.4:1:1:0:45:56:1:0:3 0/1:161:3:1,2:67,91:0.0186:2,2:38.7:1:31.3:1:1:1.46913:55:6:0.0191:0:3 -19 27732272 . C T 86 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.49405;LSEQ=AAACTGCTTTGTGATGTGTG;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:22,33:0.0351:2,2:30:1:28.5:1:1:1.49:42:4:0.0351:0:4.5 0/1:155:8:4,4:58,88:0.0516:2,2:17.1:1:28.8:1:0.71482:1.51:37.4:7:0.0455:0:4.3 -19 27732273 . G T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29983;SOR=0.36873;LSEQ=AACTGCTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:21,33:0.0351:2,2:38.5:1:30:1:1:1.56:46:4:0.0351:0:4 0/1:152:2:1,1:58,90:0.0132:2,2:16:1:31:1:1:1.55:60:4:0.0132:0:3.5 -19 27732274 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07365;SOR=0;LSEQ=ACTGCTTTGTGATGTGTGCG;RSEQ=TCAACTCACAGAGTTTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:21,33:0.0357:2,2:38.5:1:31:1:1:1.56:39:4:0.0357:0:3 0/0:149:0:0,0:58,91:0:2,0:21.8:1:30:1:1:0:45.4:298:1:0:2.9 -19 27732276 . C A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62101;SOR=0.57789;LSEQ=TGCTTTGTGATGTGTGCGTT;RSEQ=AACTCACAGAGTTTAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:20,33:0.0364:2,2:13.5:1:28:1:1:1.63:45:4:0.037:0:3.5 0/1:141:3:1,2:52,84:0.0213:2,2:12:1:31.3:1:1:1.23622:46:6:0.0214:0:5 -19 27732279 . C A 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08184;SOR=0;LSEQ=TTTGTGATGTGTGCGTTCAA;RSEQ=TCACAGAGTTTAACCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:19,33:0.0364:2,2:18:0:29:1:1:1.72:33:4:0.037:0:6.5 0/0:136:0:0,0:51,85:0:2,0:19.3:1:31.8:1:1:0:46.1:272:1:0:2.9 -19 27732281 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTGATGTGTGCGTTCAACT;RSEQ=ACAGAGTTTAACCTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:21,33:0:2,0:20.6:1:32.1:1:1:0:43.7:108:1:0:3 0/1:131:2:1,1:49,80:0.0153:2,2:6.5:1:30:1:1:1.63:48:4:0.0155:0:5.5 -19 27732284 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09051;SOR=0;LSEQ=GATGTGTGCGTTCAACTCAC;RSEQ=GAGTTTAACCTTCCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:20,31:0.0377:2,2:18:1:29:1:1:1.54:42:4:0.0377:0:4.5 0/0:122:0:0,0:44,76:0:2,0:16.9:1:30.5:1:1:0:45:119:0.9835:0:2.8 -19 27732286 . A T 28 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08289;SOR=0;LSEQ=TGTGTGCGTTCAACTCACAG;RSEQ=GTTTAACCTTCCTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:17,28:0.0426:2,2:11:0:28.5:1:1:1.63:33:4:0.0426:0:6.5 0/0:115:0:0,0:41,74:0:2,0:15.8:1:29.8:1:1:0:45.1:37.333:1:0:2.8 -19 27732292 . ACCTTC A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55311;SOR=Inf;LSEQ=CGTTCAACTCACAGAGTTTA;RSEQ=CTTTTCATAGAGCAGTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:14,24:0:2,0:16.5:1:31.8:1:1:0:41.5:76:1:0:3.2 0/1:88:3:2,1:26,59:0.0341:2,2:8.3:1:25.6:1:0.23653:4.45:43.3:6:0.0341:0.0341:3.3 -19 27732294 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22859;SOR=0.21995;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTCCTTTTCATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:0,2:14,22:0.0526:2,0:21.5:1:30.5:1:0.52205:0:45:4:0.0526:0:3.5 0/1:84:1:0,1:25,55:0.0119:2,0:7:0:31:0:1:0:60:2:0.0123:0:3 -19 27732297 . C T 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04663;SOR=0;LSEQ=AACTCACAGAGTTTAACCTT;RSEQ=CTTTTCATAGAGCAGTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:9,21:0,0:1:0,2:16.2:1:30.3:1:1:0:41.9:60:1:0:3.2 1/1:54:47:10,37:2,2:0.8704:2,2:17:1:29.2:1:0.23202:3.58237:43.1:46:0.92:0:3.2 -19 27732299 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13356;SOR=0;LSEQ=CTCACAGAGTTTAACCTTCC;RSEQ=TTTCATAGAGCAGTTAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:6,19:0.0741:2,2:5:0:33.5:1:0.45869:3.01:33:4:0.0769:0:3.5 0/0:46:0:0,0:10,36:0:2,0:17.2:1:30.3:1:1:0:44.2:92:1:0:3.1 -19 27732304 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53634;SOR=Inf;LSEQ=AGAGTTTAACCTTCCTTTTC;RSEQ=TAGAGCAGTTAGGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:4,16:0:2,0:15.7:1:31.1:1:1:0:44:40:1:0:3.3 0/1:37:2:1,1:7,28:0.0541:2,2:10:1:27.5:1:0.39039:3.81:53:4:0.0556:0:3.5 -19 27732305 . T A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GAGTTTAACCTTCCTTTTCA;RSEQ=AGAGCAGTTAGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:2,6:2,8:0.4:2,2:15.6:1:31.4:1:1:1.31:44.4:16:0.4:0:3.6 0/1:35:14:5,9:3,15:0.4:2,2:17.8:1:30.1:1:0.25167:2.69:45.8:28:0.4:0:3.6 -19 27732336 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=GGAAACACTCTGTTTGTAAA;RSEQ=TCTGCAATTGGATATTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,0:0.6667:0,0:7:1:33.5:1:1:0:33:4:0.6667:0:4 1/0:4:3:0,3:0,0:0.75:0,0:18.7:1:32:0:1:0:23:6:0.75:0:4 -19 27732392 . T C 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTGCAAACGGGATTTCTT;RSEQ=ATGTTATGCTACACAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:32.5:1:1:0:30:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 27732398 . A C 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACGGGATTTCTTTATGTT;RSEQ=TGCTACACAGAAGAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:33:0:1:0:30:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 27732421 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACACAGAAGAATTCTCAG;RSEQ=AACTTTCTTGTGTTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:31.5:1:1:0:30:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 27732427 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGAATTCTCAGTAACTT;RSEQ=CTTGTGTTGTGTGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:32.5:1:1:0:30:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 27732607 . T C 128 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTGATGTGTGCGTTCAA;RSEQ=TCACAGAGTTTAACCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:20:1:33.5:1:1:0:35.8:12:1:0:5.7 1/1:19:17:14,3:1,1:0.8947:2,2:13.6:1:31.5:1:0.38596:4.18:42.9:34:0.8947:0:5.7 -19 27732614 . A G 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03977;SOR=0;LSEQ=TGTGTGCGTTCAATTCACAG;RSEQ=GTTTAACCTTTCTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:29.5:1:32:0:1:3.1622:44.5:4:0.3333:0:7.5 0/0:26:0:0,0:20,6:0:2,0:16.4:1:29.7:1:1:0:44.2:52:1:0:5.3 -19 27732631 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAGTTTAACCTTTCTTTT;RSEQ=ATAGAGCAGTTAGGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:34:1:29.6:1:1:0:32.6:7:1:0:5.5 0/1:34:2:1,1:23,9:0.0588:2,2:18:1:30:1:0.50802:2.47657:45:4:0.0588:0:5 -19 27732633 . T C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69982;SOR=1.58276;LSEQ=GAGTTTAACCTTTCTTTTCA;RSEQ=AGAGCAGTTAGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:3,2:2,2:0.5556:2,2:32.2:1:32.8:1:1:1.43:35.8:10:0.5556:0:6.4 1/0:36:24:18,6:7,4:0.6667:2,2:28.1:1:32:1:0.68892:1.69:44.6:48:0.6667:0:6 -19 27732634 . A G 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGTTTAACCTTTCTTTTCAT;RSEQ=GAGCAGTTAGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:28.2:1:28.9:1:1:0:36.9:9:1:0:5.4 0/1:38:3:2,1:25,10:0.0789:2,2:15:1:29.7:1:1:1.24235:46.3:6:0.0789:0:5.3 -19 27732643 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCTTTTCATAGAGCAGTT;RSEQ=GGAAACACTCTGTTTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:27.2:1:28.9:1:1:0:36:24:1:0:5.2 0/1:40:2:1,1:27,11:0.05:2,2:30:1:29:1:0.51538:2.39319:45:4:0.05:0:5 -19 27732661 . A G 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74409;SOR=1.37735;LSEQ=TTAGGAAACACTCTGTTTGT;RSEQ=ATGTCTGCAAGTGGATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:7,3:2,3:0.6667:2,2:23.9:1:31.7:1:0.32867:3.20:37.2:20:0.7143:0:6.1 1/0:49:36:27,9:7,6:0.7347:2,2:31.6:1:31.8:1:0.17812:2.52:44.1:72:0.7347:0:5.8 -19 27732663 . T A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=1.71157;LSEQ=AGGAAACACTCTGTTTGTAA;RSEQ=GTCTGCAAGTGGATATTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:7,3:2,3:0.6667:2,2:24.3:1:30.2:1:0.32867:3.20:37.2:20:0.7143:0:6.1 1/0:49:38:28,10:5,4:0.7755:2,2:30.6:1:30.3:1:0.41884:2.20:43.5:76:0.7755:0:5.9 -19 27732665 . T C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7719;SOR=0.71169;LSEQ=GAAACACTCTGTTTGTAATG;RSEQ=CTGCAAGTGGATATTCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:7,5:2,3:0.7059:2,2:20.8:1:31.3:1:0.61991:2.01:38.3:24:0.7059:0:5.8 1/0:54:34:24,10:12,7:0.6296:2,2:28.8:1:30.8:1:0.75974:1.39:44.7:16:0.6154:0:5.9 -19 27732670 . A C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9285;LSEQ=ACTCTGTTTGTAATGTCTGC;RSEQ=AGTGGATATTCGGACCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:8,5:2,3:0.7222:2,2:20.8:1:30.5:1:0.60784:2.28:38:26:0.7222:0:5.6 1/0:58:41:27,14:9,7:0.7069:2,2:26.7:1:29.7:1:0.55064:1.49:45.2:40:0.7018:0:5.4 -19 27732671 . A C 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05095;SOR=0;LSEQ=CTCTGTTTGTAATGTCTGCA;RSEQ=GTGGATATTCGGACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:24:1:28.5:1:1:1.26772:40:4:0.1111:0:4.5 0/0:60:0:0,0:38,21:0:2,0:25.2:1:30.1:1:1:0:44.7:118:1:0:5 -19 27732673 . T G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTTTGTAATGTCTGCAAG;RSEQ=GGATATTCGGACCTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:22.6:1:28.4:1:1:0:37:36:1:0:5.2 0/1:64:2:1,1:40,22:0.0313:2,2:26.5:1:30:1:1:1.80021:47:4:0.0313:0:6.5 -19 27732675 . G C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTGTAATGTCTGCAAGTG;RSEQ=ATATTCGGACCTCTTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:24.2:1:28.8:1:1:0:37.9:7.5:1:0:5.4 0/1:67:2:1,1:41,24:0.0299:2,2:39:1:33:1:1:1.69403:45:4:0.0299:0:5 -19 27732679 . T A 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96013;LSEQ=GTAATGTCTGCAAGTGGATA;RSEQ=TCGGACCTCTTTGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:24.5:1:29:1:1:1.12:59:4:0.1111:0:5 0/1:69:7:3,4:37,25:0.1014:2,2:19.7:1:29.1:1:0.44287:1.95352:46.4:14:0.1014:0:5.7 -19 27732681 . C T 28 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04467;SOR=0;LSEQ=AATGTCTGCAAGTGGATATT;RSEQ=GGACCTCTTTGAGGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:16.5:1:28:1:1:1.12:40:4:0.1111:0:4.5 0/0:69:0:0,0:40,29:0:2,0:23.3:1:30:1:1:0:46.5:68:1:0:4.7 -19 27732682 . G A 123 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17687;SOR=4.88271;LSEQ=ATGTCTGCAAGTGGATATTC;RSEQ=GACCTCTTTGAGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:8,8:0.0556:2,0:48:0:31:0:1:0:50:2:0.0625:0:4 0/1:71:16:9,7:31,23:0.2254:2,2:22.1:1:30.9:1:1:1.04757:44.8:32:0.2319:0:3.9 -19 27732686 . C A 99 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11261;SOR=Inf;LSEQ=CTGCAAGTGGATATTCGGAC;RSEQ=TCTTTGAGGCCTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,9:0:2,0:23:1:30.2:1:1:0:41.6:18:0.9474:0:4.7 0/1:74:10:6,4:36,28:0.1351:2,2:25:1:30.1:1:1:1.16:40.1:20:0.1351:0:4.3 -19 27732689 . T C 97 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19791;SOR=Inf;LSEQ=CAAGTGGATATTCGGACCTC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:22.6:1:28.9:1:1:0:42.4:9.5:1:0:4.5 0/1:77:9:5,4:37,31:0.1169:2,2:18:1:30.7:1:1:1.05:35.9:18:0.12:0:5 -19 27732692 . G C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14793;SOR=0.15493;LSEQ=GTGGATATTCGGACCTCTTT;RSEQ=AGGCCTTCGTTGGAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:0.08:2,2:33:1:31:1:1:1.0871:52.5:4:0.08:0:6 0/1:77:1:1,0:40,36:0.013:2,0:49:0:33:0:1:0:40:2:0.013:0:7 -19 27732696 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATTCGGACCTCTTTGAGG;RSEQ=CTTCGTTGGAAACGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:20.6:1:31.8:1:1:0:43.9:52:1:0:4 0/1:80:2:1,1:41,37:0.025:2,2:28.5:1:28.5:1:1:1.10668:39:4:0.025:0:5 -19 27732697 . C T 94 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.72677;SOR=1.65963;LSEQ=TATTCGGACCTCTTTGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:14,10:0.0769:2,0:19.5:1:23:1:0.20308:0:35.5:1:0.04:0:4.5 0/1:82:10:5,5:38,34:0.122:2,2:27.2:1:28.5:1:1:1.11613:36.6:20:0.122:0:5.3 -19 27732700 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06542;SOR=0;LSEQ=TCGGACCTCTTTGAGGCCTT;RSEQ=GTTGGAAACGGGATTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:14,12:0.0714:2,2:29:1:31:1:1:1.16024:59:4:0.0769:0:5 0/0:80:0:0,0:43,37:0:2,0:22.1:1:29.9:1:1:0:47.5:79:1:0:4 -19 27732710 . G C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGAGGCCTTCGTTGGAAAC;RSEQ=GGATTTCTTCATATTATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:0:2,0:22:1:30.1:1:1:0:47.7:68:1:0:3.4 0/1:77:2:1,1:39,36:0.026:2,2:35:0:30.5:1:1:1.08219:46:4:0.0263:0:3.5 -19 27732721 . A G 29 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27606;SOR=0.25953;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TATTATGCTAGAAAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:23,17:0.0476:2,2:41:0:29:1:1:1.34309:48:4:0.0476:0:3 0/1:79:1:0,1:39,39:0.0127:2,0:43:0:33:0:1:0:48:2:0.013:0:5 -19 27732724 . T C 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05086;LSEQ=GGAAACGGGATTTCTTCATA;RSEQ=TATGCTAGAAAGAAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:1:0,1:24,17:0.0238:2,0:6:0:34:0:0.42857:0:50:2:0.0238:0:4 0/1:80:2:1,1:39,39:0.025:2,2:30.5:1:30:0:1:1:60:4:0.0253:0:2.5 -19 27732726 . A C 104 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20875;SOR=3.04829;LSEQ=AAACGGGATTTCTTCATATT;RSEQ=TGCTAGAAAGAAGAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:24,19:0.0444:2,2:23:0:33.5:1:1:1.25655:45:4:0.0444:0:3 0/1:80:10:5,5:34,34:0.125:2,2:31.7:1:31.4:1:1:1:35.4:20:0.1282:0:4.7 -19 27732728 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53431;SOR=Inf;LSEQ=ACGGGATTTCTTCATATTAT;RSEQ=CTAGAAAGAAGAATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:26,20:0:2,0:23.7:1:32.1:1:1:0:49.5:92:1:0:3.3 0/1:81:2:1,1:39,40:0.0247:2,2:36.5:1:29:1:1:1.03:50:4:0.026:0:5.5 -19 27732732 . GAA TTC 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05944;SOR=0.13531;LSEQ=GATTTCTTCATATTATGCTA;RSEQ=AGAAGAATTCTCAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:3,1:23,18:0.0889:2,2:22.8:1:30.8:1:0.627:2.31:47.8:8:0.0889:0.0222:2.5 0/1:78:1:1,0:36,40:0.0128:2,0:38:0:30:0:0.48052:0:60:2:0.0132:0:3 -19 27732734 . A C 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10041;SOR=0.40449;LSEQ=TTTCTTCATATTATGCTAGA;RSEQ=AGAAGAATTCTCAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:38:21,17:1,1:0.8837:2,2:28.4:1:32.5:1:1:1.23:49.6:76:0.95:0:3.2 1/0:77:58:29,29:6,7:0.7532:2,2:27.5:1:31.6:1:1:1.16:50.4:116:0.7733:0:3.3 -19 27732741 . A T 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04051;SOR=0.25455;LSEQ=ATATTATGCTAGAAAGAAGA;RSEQ=TTCTCAGTAACTTCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:42:23,19:1,2:0.9333:2,2:29.1:1:30.9:1:0.59154:2.37:50.3:84:0.9333:0:3.3 1/0:77:60:29,31:8,9:0.7792:2,2:26.9:1:30.1:1:1:1.05:50.1:120:0.7792:0:3.4 -19 27732749 . T A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55148;SOR=Inf;LSEQ=CTAGAAAGAAGAATTCTCAG;RSEQ=AACTTCTTTGTGTTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:0:2,0:32.1:1:29:1:1:0:50.4:40:1:0:3.1 0/1:74:3:1,2:32,39:0.0405:2,2:11.7:1:29:1:1:1.63051:40.3:6:0.0405:0:3.7 -19 27732754 . T A 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.29651;SOR=Inf;LSEQ=AAGAAGAATTCTCAGTAACT;RSEQ=CTTTGTGTTGTGTGTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:0:2,0:31.9:1:29.9:1:1:0:50.4:40:1:0:3.1 0/1:77:4:2,2:30,43:0.0519:2,2:16:1:25.3:1:1:1.43:38:8:0.0519:0:6.8 -19 27732755 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53715;SOR=Inf;LSEQ=AGAAGAATTCTCAGTAACTT;RSEQ=TTTGTGTTGTGTGTATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:0:2,0:31.7:1:31.3:1:1:0:49.9:40:1:0:3.1 0/1:74:2:1,1:29,43:0.027:2,2:10:1:27.5:1:1:1.47:53:4:0.0278:0:3.5 -19 27732756 . T C 90 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25512;SOR=4.24244;LSEQ=GAAGAATTCTCAGTAACTTC;RSEQ=TTGTGTTGTGTGTATGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:1:0,1:23,18:0.0238:2,0:31:0:32:0:0.45238:0:21:2:0.0238:0:3 0/1:74:7:1,6:28,38:0.0946:2,2:13:1:32.3:1:0.23189:4.34865:35:14:0.0959:0:5 -19 27732760 . T G 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.15457;SOR=Inf;LSEQ=AATTCTCAGTAACTTCTTTG;RSEQ=GTTGTGTGTATGCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:23,21:0:2,0:29:1:30.3:1:1:0:48.4:88:1:0:3.3 0/1:70:5:3,2:26,37:0.0714:2,2:29.8:1:31.4:1:0.64405:2.11:57.4:10:0.0714:0:4.2 -19 27732772 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15143;SOR=0;LSEQ=CTTCTTTGTGTTGTGTGTAT;RSEQ=CAACTCACAGAGTTCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:20,17:0.05:2,2:22:1:30:0:1:1.17156:55.5:4:0.05:0:3 0/0:62:0:0,0:26,32:0:2,0:25.6:1:31.6:1:1:0:47.3:116:0.9355:0:3.8 -19 27732774 . A C 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.5135;SOR=Inf;LSEQ=TCTTTGTGTTGTGTGTATGC;RSEQ=ACTCACAGAGTTCAACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:21,19:0:2,0:25.4:1:30.5:1:1:0:48.4:80:1:0:3.4 0/1:59:2:1,1:24,33:0.0339:2,2:35:1:28:1:1:1.37:26:4:0.0339:0:8 -19 27732809 . C G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCTTCCTTTAGACAGAGCA;RSEQ=ATCGGAAACACTCTTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:4,8:0,0:1:0,2:29.3:1:31.9:1:1:0:34.8:24:1:0:5.8 1/1:24:23:9,14:0,0:0.9583:0,2:31.6:1:31.7:1:1:0:35.1:46:0.9583:0:6.1 -19 27732812 . CG TT 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=2.04944;LSEQ=TTCCTTTAGACAGAGCACAT;RSEQ=GAAACACTCTTTCTGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:3,7:1,0:0.9091:0,2:31.1:1:30.6:1:0.36364:0:31.8:20:0.9091:0:5.3 1/1:22:21:8,13:0,0:0.9545:0,2:32.4:1:30.2:1:1:0:33:42:1:0:5.5 -19 27732826 . C T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1567;SOR=Inf;LSEQ=GCACATCGGAAACACTCTTT;RSEQ=TGAGGGATTTGCAAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:3,6:1,1:0.8182:2,2:20.1:1:30.2:1:1:1.87089:30.9:18:0.8182:0:5.4 1/1:16:16:7,9:0,0:1:0,2:27.8:1:30.4:1:1:0:32:32:1:0:5.9 -19 27732829 . A T 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14229;SOR=Inf;LSEQ=CATCGGAAACACTCTTTCTG;RSEQ=GGGATTTGCAAGTGGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:2,5:1,1:0.7778:2,2:22.3:1:30.1:1:1:2.23609:30:14:0.7778:0:5.6 1/1:14:14:6,8:0,0:1:0,2:28.6:1:30.3:1:1:0:31.9:28:1:0:5.7 -19 27732832 . G A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14229;SOR=Inf;LSEQ=CGGAAACACTCTTTCTGAGG;RSEQ=ATTTGCAAGTGGAGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:2,5:1,1:0.7778:2,2:19.3:1:30:1:1:2.23609:30:14:0.7778:0:5.6 1/1:14:14:6,8:0,0:1:0,2:25.6:1:30.6:1:1:0:31.9:28:1:0:5.7 -19 27732992 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCAGCAGTTTGGAAACACT;RSEQ=TGTTTGTCAAGTCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:23.5:1:32.5:1:1:0:36:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 27733020 . C G 33 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=CAAGTCTGCAAGTGGATATT;RSEQ=GGACCTCTTTGAGGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:0:33.5:1:1:0:36:4:1:0:3 0/0:4:0:0,0:3,1:0:2,0:14.3:1:30.8:1:1:0:47.8:8:1:0:6.5 -19 27733021 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AAGTCTGCAAGTGGATATTC;RSEQ=GACCTCTTTGAGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:0:32.5:1:1:0:36:4:1:0:3 1/0:4:2:2,0:1,1:0.5:2,0:12.5:1:31:1:1:0:38.5:4:0.5:0:6 -19 27733032 . A T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TGGATATTCGGACCTCTTTG;RSEQ=GGCCTTCGTTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:8:1:31.8:1:1:0:39.8:10:1:0:3 0/1:5:2:1,1:3,0:0.4:0,2:29:0:29.5:1:0.4:0:57:4:0.4:0:7 -19 27733043 . G T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=ACCTCTTTGAGGCCTTCGTT;RSEQ=GAAACGGGATTTCTTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15:1:33:1:1:0:38.5:8:1:0:3.3 0/1:5:2:1,1:3,0:0.4:0,2:40:0:30:1:0.4:0:57:4:0.4:0:7 -19 27733048 . C A 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCATATTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23:0:32.5:1:1:1:50:4:0.5:0:2.5 0/0:5:0:0,0:4,1:0:2,0:38.2:1:31:1:1:0:43.6:10:1:0:6.6 -19 27733050 . GG TT 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TGAGGCCTTCGTTGGAAACG;RSEQ=ATTTCTTCATATTACACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22:1:32.8:1:1:0:38.5:8:1:0:3.3 0/1:5:2:1,1:3,0:0.4:0,2:46:1:29:1:0.4:0:57:4:0.4:0:6 -19 27733059 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CGTTGGAAACGGGATTTCTT;RSEQ=ATATTACACTAGACAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:31:1:33.3:1:1:0:38.5:8:1:0:3.3 0/1:5:2:1,1:3,0:0.4:0,2:38:1:27.5:1:0.4:0:57:4:0.4:0:6 -19 27733064 . T A 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0.23975;LSEQ=GAAACGGGATTTCTTCATAT;RSEQ=ACACTAGACAGAAGAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:31.5:1:30.5:1:1:1:50:4:0.5:0:2.5 0/1:6:1:1,0:2,1:0.1667:2,0:38:0:29:0:1:0:27:2:0.1667:0:7 -19 27733066 . CA TG 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AACGGGATTTCTTCATATTA;RSEQ=CTAGACAGAAGAATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:36:1:32.5:0:1:1:27:4:0.5:0:3 1/0:6:3:2,1:1,0:0.5:0,2:29:1:30.3:1:1:0:38:6:0.5:0:4.7 -19 27733076 . A G 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07609;SOR=0;LSEQ=CTTCATATTACACTAGACAG;RSEQ=AGAATTCTCAGTAACTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:45:1:32:1:1:3.1622:27:4:0.2857:0:3 0/0:17:0:0,0:13,4:0:2,0:14.9:1:28.8:1:1:0:41:34:1:0:4.8 -19 27733081 . T A 107 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08087;SOR=7.63012;LSEQ=TATTACACTAGACAGAAGAA;RSEQ=TCTCAGTAACTTCCTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:0.1429:2,0:14:0:32:0:1:0:40:2:0.1429:0:5 1/0:19:11:10,1:5,3:0.5789:2,2:15:1:31:1:0.26213:5.43:39.8:22:0.5789:0:4.5 -19 27733095 . C T 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26923;SOR=0.29428;LSEQ=GAAGAATTCTCAGTAACTTC;RSEQ=TTTTGTTGTGTGTATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,1:0.2857:2,0:27.5:1:32.5:1:1:0:40:4:0.2857:0:5 0/1:20:2:2,0:14,4:0.1:2,0:19:1:33:0:1:0:31:4:0.1:0:6 -19 27733098 . T G 127 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60605;SOR=1.82435;LSEQ=GAATTCTCAGTAACTTCCTT;RSEQ=TGTTGTGTGTATTCAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:2,0:0.6667:0,2:26.5:1:32.3:1:1:0:30.8:8:0.6667:0:4.5 1/0:19:15:12,3:3,1:0.7895:2,2:24.7:1:32.7:1:1:1.31:38.2:30:0.7895:0:4.3 -19 27733102 . T G 34 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20427;SOR=0.22715;LSEQ=TCTCAGTAACTTCCTTTTGT;RSEQ=GTGTGTATTCAACTGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:34.5:1:33.5:1:1:0:40:4:0.3333:0:5 0/1:21:2:2,0:14,5:0.0952:2,0:26:1:34:0:1:0:31:4:0.0952:0:6 -19 27733107 . GT AC 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTAACTTCCTTTTGTTGTGT;RSEQ=ATTCAACTGACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:30.8:1:32.3:1:1:0:33.8:12:1:0:4.7 0/1:23:2:1,1:16,5:0.087:2,2:25.5:1:30:1:0.46245:3.01096:40:4:0.0909:0:4.5 -19 27733117 . G C 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25618;SOR=0.32084;LSEQ=TTTGTTGTGTGTATTCAACT;RSEQ=ACAGAGTTGAACCTTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:49.5:1:32:1:1:0:40:4:0.3333:0:5 0/1:30:4:3,1:18,8:0.1333:2,2:33.3:1:30.8:1:1:1.32:35.5:8:0.1333:0:5.3 -19 27733134 . CC TT 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGACAGAGTTGAACCTTC;RSEQ=TTAGACAGAGCAGATTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:25.8:1:29.5:1:1:0:36.3:12:1:0:6 0/1:30:2:2,0:18,10:0.0667:2,0:32:0:31:1:0.54023:0:42:4:0.0667:0:3.5 -19 27733135 . C T 140 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACAGAGTTGAACCTTCC;RSEQ=TTAGACAGAGCAGATTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:25.8:1:28.8:1:1:0:36.3:12:1:0:6 1/1:31:28:18,10:0,1:0.9032:0,2:26:1:29.2:1:0.37931:0:36.4:27:0.9643:0:5.6 -19 27733145 . G T 29 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03636;SOR=0;LSEQ=TGAACCTTCCCTTAGACAGA;RSEQ=CAGATTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:13:1:29:1:1:2.23609:40:4:0.2222:0:6.5 0/0:36:0:0,0:21,15:0:2,0:22.1:1:31.3:1:1:0:37.5:72:1:0:5.6 -19 27733152 . T C 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02489;SOR=6.11667;LSEQ=TCCCTTAGACAGAGCAGATT;RSEQ=GAAACACTCTTTTTGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:4,1:0.4444:2,2:20.5:1:29.8:1:0.52381:3.38757:34.5:8:0.4444:0:7 1/1:37:31:17,14:4,2:0.8378:2,2:22.3:1:29.5:1:0.67963:1.6256:38.1:62:0.8378:0:5.8 -19 27733158 . A T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01992;SOR=0.11866;LSEQ=AGACAGAGCAGATTTGAAAC;RSEQ=CTCTTTTTGTGGGGTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:3,2:0.4444:2,2:16.8:1:30:1:1:1.85:37.8:8:0.4444:0:5.8 0/1:37:3:2,1:18,16:0.0811:2,2:12:1:27.7:1:1:1.75:30:6:0.0811:0:6.7 -19 27733167 . G C 134 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17797;SOR=3.64083;LSEQ=AGATTTGAAACACTCTTTTT;RSEQ=TGGGGTTTGCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:3,1:0.4286:2,2:28:1:31.7:1:0.48571:4.4496:32.7:6:0.4286:0:7.7 1/0:27:20:7,13:5,2:0.7407:2,2:32.9:1:31.2:1:0.18502:4.36956:36.7:40:0.7407:0:7.3 -19 27733170 . GGG CAA 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.6545;SOR=1.76506;LSEQ=TTTGAAACACTCTTTTTGTG;RSEQ=TTTGCAAGTGGAGATTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:0.625:2,2:22.4:1:31:1:1:2.60168:31:10:0.625:0.25:5.2 1/0:24:18:7,11:5,1:0.75:2,2:35.7:1:30.5:1:0.15495:7.21316:35.8:36:0.75:0.0417:5.7 -19 27733171 . GG AA 95 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.66446;SOR=0.62006;LSEQ=TTGAAACACTCTTTTTGTGG;RSEQ=TTTGCAAGTGGAGATTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:0,0:0.5:0,2:35.7:1:31:1:1:0:37:6:1:0:4.7 0/1:29:11:8,3:0,0:0.3793:0,2:9.6:1:27.7:1:1:0:36.6:22:0.9167:0.3103:4.5 -19 27733183 . G A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.07137;SOR=0;LSEQ=TTTTGTGGGGTTTGCAAGTG;RSEQ=AGATTTAAAGCGCTTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:0.1429:2,2:26:1:28.5:1:1:1.37:44.5:4:0.1429:0:4.5 0/0:37:0:0,0:19,18:0:2,0:22.6:1:30.6:1:1:0:38.2:74:1:0:5.4 -19 27733187 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17732;SOR=2.79979;LSEQ=GTGGGGTTTGCAAGTGGAGA;RSEQ=TTAAAGCGCTTTGAGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:2,4:3,4:0.4615:2,2:25:1:32.7:1:1:1.45385:28:12:0.4615:0:4.8 1/0:38:27:12,15:8,3:0.7105:2,2:25.9:1:31.3:1:0.15957:3.22875:37.1:54:0.7105:0:5.3 -19 27733190 . A C 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24074;SOR=Inf;LSEQ=GGGTTTGCAAGTGGAGATTT;RSEQ=AAGCGCTTTGAGGCCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:4,8:0,0:0.9231:0,2:28.3:1:32.2:1:1:0:33.1:24:0.9231:0:5.2 1/1:41:41:22,19:0,0:1:0,2:22:1:30.8:1:1:0:38:82:1:0:5.4 -19 27733201 . A G 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59118;SOR=0.46365;LSEQ=TGGAGATTTAAAGCGCTTTG;RSEQ=GGCCAAAGGCAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:9,13:0.0833:2,2:5:0:33:0:1:1.42:49.5:4:0.0833:0:2.5 0/1:50:2:1,1:26,22:0.04:2,2:10:0:28.5:1:1:1.17786:49:4:0.04:0:3 -19 27733208 . A C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52295;SOR=0.66058;LSEQ=TTAAAGCGCTTTGAGGCCAA;RSEQ=GGCAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:2,3:10,13:0.1786:2,2:24:1:30.8:1:1:1.14801:34:10:0.1786:0:6.2 0/1:56:7:5,2:26,23:0.125:2,2:24.7:1:31.4:1:0.44277:2.18:38.1:14:0.1273:0:6.4 -19 27733209 . G A 40 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03317;SOR=0;LSEQ=TAAAGCGCTTTGAGGCCAAA;RSEQ=GCAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:1,2:11,13:0.1071:2,2:23.3:1:25.3:1:1:1.66075:48.3:2:0.0769:0:4 0/0:57:0:0,0:30,25:0:2,0:21:1:30.3:1:1:0:40:26.5:0.9636:0:4.4 -19 27733216 . A G 47 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12783;SOR=0.1736;LSEQ=CTTTGAGGCCAAAGGCAGAA;RSEQ=AGGAAATATCTTCGTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:1,2:12,15:0.1:2,2:26.3:1:30:1:1:1.57599:48.3:6:0.1:0:4 0/1:54:1:0,1:30,23:0.0185:2,0:35:0:27:0:0.44444:0:43:2:0.0185:0:7 -19 27733219 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51513;SOR=Inf;LSEQ=TGAGGCCAAAGGCAGAAAAG;RSEQ=AAATATCTTCGTATAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,18:0:2,0:24:1:31.7:1:1:0:40.8:64:0.9697:0:4.2 0/1:50:2:1,1:26,22:0.04:2,2:46:1:31:1:1:1.17786:59.5:4:0.04:0:3.5 -19 27733221 . A T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51429;SOR=Inf;LSEQ=AGGCCAAAGGCAGAAAAGGA;RSEQ=ATATCTTCGTATAAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,19:0:2,0:23.6:1:30.7:1:1:0:40.6:68:1:0:4 0/1:51:2:1,1:27,22:0.0392:2,2:30:0:29:1:1:1.22232:49:4:0.0392:0:3 -19 27733226 . C T 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05453;SOR=0;LSEQ=AAAGGCAGAAAAGGAAATAT;RSEQ=TTCGTATAAAAACTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:1,2:14,17:0.0882:2,2:40.3:1:30:1:1:1.62392:48.3:6:0.0882:0:4 0/0:54:0:0,0:30,24:0:2,0:28.9:1:32:1:1:0:40.8:108:1:0:4.1 -19 27733230 . G C 51 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04804;SOR=0;LSEQ=GCAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:1,2:14,16:0.0909:2,2:40.7:1:32.3:1:1:1.7216:48.3:6:0.0909:0:4 0/0:56:0:0,0:31,25:0:2,0:28.4:1:30.7:1:1:0:40.2:55:1:0:4.1 -19 27733232 . A T 45 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.68864;LSEQ=AGAAAAGGAAATATCTTCGT;RSEQ=TAAAAACTAGACAGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:14,16:0.0323:2,0:43:0:30:0:1:0:49:2:0.0323:0:6 0/1:56:3:2,1:29,24:0.0536:2,2:42:1:29:1:1:1.64:42:6:0.0536:0:5.3 -19 27733233 . T G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.76219;SOR=0.72749;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGACAGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:3,3:11,14:0.1935:2,2:27.7:1:32.3:1:1:1.26:33:12:0.1935:0:6.5 0/1:54:8:5,3:25,21:0.1481:2,2:35.5:1:32.8:1:0.72012:1.39:37.1:16:0.1481:0:6 -19 27733234 . A C 48 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.72067;LSEQ=AAAAGGAAATATCTTCGTAT;RSEQ=AAAACTAGACAGAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:14,16:0.0323:2,0:41:0:31:0:1:0:49:2:0.0323:0:6 0/1:55:3:2,1:28,23:0.0545:2,2:42.7:1:30.3:1:1:1.63:42:6:0.0545:0:5.3 -19 27733239 . C A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76275;SOR=0.74348;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:3,3:11,14:0.1935:2,2:28:1:31:1:1:1.26:33:12:0.1935:0:6.5 0/1:53:8:5,3:26,19:0.1509:2,2:30:1:30.9:1:1:1.21:37.1:16:0.1538:0:6 -19 27733240 . TA CC 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.80499;SOR=1.2273;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=GACAGAATCATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:8:4,4:9,11:0.2667:2,2:30.4:1:31.8:1:1:1.21:25.4:16:0.2667:0:3.3 0/1:55:17:11,6:21,16:0.3091:2,2:27.5:1:30.9:1:0.76667:1.39:34.8:34:0.3091:0.0182:4.1 -19 27733243 . A T 30 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27838;SOR=0.25927;LSEQ=TATCTTCGTATAAAAACTAG;RSEQ=CAGAATCATTCTCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:12,15:0.069:2,2:24:0:30.5:1:1:1.24:60:4:0.069:0:3 0/1:54:1:0,1:32,21:0.0185:2,0:24:0:27:0:0.40741:0:43:2:0.0185:0:7 -19 27733245 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.76122;SOR=0.83664;LSEQ=TCTTCGTATAAAAACTAGAC;RSEQ=GAATCATTCTCAGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:2,3:11,13:0.1724:2,2:32:1:31.8:1:1:1.25893:33.4:10:0.1724:0:6.6 0/1:54:8:5,3:27,19:0.1481:2,2:24:1:30.8:1:1:1.17:37.1:16:0.1481:0:6 -19 27733248 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53982;SOR=Inf;LSEQ=TCGTATAAAAACTAGACAGA;RSEQ=TCATTCTCAGAAACTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:13,16:0:2,0:27.2:1:30.6:1:1:0:41.4:28:1:0:3.6 0/1:54:2:1,1:31,21:0.037:2,2:16:0:33.5:1:1:1.46529:52:4:0.037:0:1.5 -19 27733267 . G C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26649;SOR=2.09781;LSEQ=AATCATTCTCAGAAACTGCT;RSEQ=TGTGATGTGTGCTTTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:2,4:5,5:0.2857:2,2:12.8:1:33.5:1:0.63287:1.91506:29.7:12:0.2857:0:4.2 0/1:37:17:14,3:8,7:0.4595:2,2:15.9:1:31.3:1:0.12828:3.90:38.2:34:0.4595:0:3.9 -19 27733268 . T C 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.78593;SOR=0.82786;LSEQ=ATCATTCTCAGAAACTGCTG;RSEQ=GTGATGTGTGCTTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:5,5:4,7:0.4762:2,2:11.7:1:31.4:1:0.66992:1.70:51.7:20:0.4762:0:2 0/1:35:15:8,7:16,4:0.4286:2,2:17.9:1:30.1:1:0.14405:3.368:40.9:14:0.4118:0:2.7 -19 27733270 . T G 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.25498;SOR=0.38094;LSEQ=CATTCTCAGAAACTGCTGTG;RSEQ=GATGTGTGCTTTCAACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:6,7:0.2632:2,2:10:1:32.8:1:1:1.26799:33.4:10:0.2632:0:6.6 0/1:34:4:3,1:18,7:0.1176:2,2:7.3:1:32.8:1:1:1.16:43:8:0.1176:0:7 -19 27733280 . T G 142 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5585;SOR=1.63856;LSEQ=AACTGCTGTGTGATGTGTGC;RSEQ=TTCAACTCAGAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,0:0.8333:0,2:9.6:1:30:1:1:0:42.8:10:0.8333:0:3.6 1/1:28:25:17,8:1,1:0.8929:2,2:12:1:30.6:1:1:2.06:37.4:50:0.8929:0:3.8 -19 27733289 . AG TC 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.55309;SOR=Inf;LSEQ=GTGATGTGTGCTTTCAACTC;RSEQ=AGAGTTTAACTTTTCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:6.6:1:28.6:1:1:0:44:16:1:0:4.4 0/1:27:4:2,2:15,7:0.1481:2,2:12:1:28.8:1:0.59064:2.07641:36.5:8:0.1481:0.0741:2 -19 27733290 . G C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55484;SOR=0;LSEQ=TGATGTGTGCTTTCAACTCA;RSEQ=AGAGTTTAACTTTTCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:6.9:1:31.5:1:1:0:44:16:1:0:4.4 1/1:24:21:14,7:0,0:0.875:0,2:16:1:30.4:1:1:0:35.7:42:1:0:3.9 -19 27733332 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTCAGCAGTTTGGAAACACT;RSEQ=TGTTTGTAAAGTCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:39.8:1:31.4:1:1:0:38.5:16:1:0:4.4 0/1:39:2:1,1:19,18:0.0513:2,2:34:1:30.5:1:1:1.05412:31:4:0.0513:0:5 -19 27733335 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGTTTGGAAACACTCTG;RSEQ=TTGTAAAGTCTGCAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:40.1:1:29.4:1:1:0:38.5:16:1:0:4.4 0/1:39:2:1,1:17,17:0.0513:2,2:28.5:1:31:1:1:1:60:4:0.0571:0:5.5 -19 27733359 . A C 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.57103;SOR=0;LSEQ=TAAAGTCTGCAAGTGGATAT;RSEQ=TTGACCTCTTAGGGTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:25.5:1:31:1:1:0:38.5:16:1:0:4.4 1/1:39:33:15,18:3,2:0.8462:2,2:23.1:1:32:1:0.65251:1.77231:36:66:0.8462:0:4.4 -19 27733363 . A G 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGCAAGTGGATATATTG;RSEQ=CCTCTTAGGGTCCTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:21.5:1:31.3:1:1:0:38.5:16:1:0:4.4 1/1:37:33:15,18:3,1:0.8919:2,2:22.4:1:32:1:0.33977:3.48361:37:66:0.8919:0:4.5 -19 27733370 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGGATATATTGACCTCTT;RSEQ=GGGTCCTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:14.5:1:29.4:1:1:0:38.5:16:1:0:4.4 0/1:32:2:1,1:14,16:0.0625:2,2:23:1:28:1:1:1.14:60:4:0.0625:0:5.5 -19 27733372 . G A 140 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATATATTGACCTCTTAG;RSEQ=GTCCTTCGTTGGAAACGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:20.2:1:30.8:1:1:0:40.8:10:1:0:5 1/1:23:23:8,15:0,0:1:0,2:25.9:1:31:1:1:0:36.3:46:1:0:5.3 -19 27733374 . T G 142 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATATTGACCTCTTAGGG;RSEQ=CCTTCGTTGGAAACGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:18.2:1:32.2:1:1:0:40.8:10:1:0:5 1/1:22:21:8,13:0,1:0.9545:0,2:25:1:32.4:1:1:0:34.4:42:0.9545:0:5.2 -19 27733380 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGACCTCTTAGGGTCCTTC;RSEQ=TTGGAAACGGGTTTTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:11:1:31.2:1:1:0:41.5:12:1:0:4.7 0/1:27:2:0,2:10,15:0.0741:2,0:23.5:1:31:1:0.51567:0:45.5:4:0.0769:0:6.5 -19 27733387 . ACGGGTT GCGGG 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTAGGGTCCTTCGTTGGAA;RSEQ=TTTTTTCATGTAAGGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:14.3:1:24.3:1:1:0:37:2:1:0:3.7 0/1:26:3:2,1:8,15:0.1154:2,2:14.7:1:31.4:1:0.53846:3.55:45.7:6:0.1154:0.0769:6 -19 27733391 . GTT G 133 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTCCTTCGTTGGAAACGG;RSEQ=TTTTTTCATGTAAGGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:11.7:1:32.2:1:1:0:37:6:1:0.3333:3.7 1/0:28:22:8,14:1,2:0.7857:2,2:16.4:1:29.9:1:1:1.14:38.2:44:0.8462:0.3929:4.6 -19 27733407 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGGGTTTTTTTTCATGTAA;RSEQ=GCTAGACAGAAGAATTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:16:1:23:1:1:0:42:1:1:0:3.5 0/1:23:2:1,1:7,14:0.087:2,2:30:0:31:1:1:1.94:33:4:0.0909:0:5 -19 27733409 . C T 106 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43478;SOR=Inf;LSEQ=GGGTTTTTTTTCATGTAAGG;RSEQ=TAGACAGAAGAATTCCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:22:13:5,8:1,2:0.5909:2,2:23.5:1:28.9:1:1:1.23:39.6:26:0.5909:0:4.7 -19 27733418 . A G 123 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATGTAAGGCTAGACAGA;RSEQ=GAATTCCCAATAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:41:0:32:0:1:0:45:2:1:0:3 1/1:19:17:6,11:1,1:0.8947:2,2:28.5:1:30.3:1:1:1.77272:39.2:34:0.8947:0:5 -19 27733428 . A G 123 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAGACAGAAGAATTCCCA;RSEQ=TAACTTCCTTGTGTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:42:0:34:0:1:0:45:2:1:0:3 1/1:17:15:4,11:0,0:0.8824:0,2:30.7:1:31.5:1:1:0:36.9:30:0.8824:0:4.7 -19 27733492 . CG TC 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTTAGACAGAGCAGAT;RSEQ=GAAACAATCTTTTTGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:30.5:1:1:0:24:4:1:0:3 -19 27733500 . A C 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGCAGATCGGAAACA;RSEQ=TCTTTTTGTGCAATTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:4:0:34:0:1:0:43:2:1:0:4 1/1:5:4:2,2:0,0:0.8:0,2:12:1:33:1:1:0:39:8:0.8:0:3.5 -19 27733508 . G C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGATCGGAAACAATCTTTTT;RSEQ=TGCAATTTGCAGGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10:1:33:1:1:0:43:4:1:0:4 0/1:8:2:1,1:3,3:0.25:2,2:12:0:32:1:1:1:24:4:0.25:0:3 -19 27733511 . C G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGGAAACAATCTTTTTGTG;RSEQ=AATTTGCAGGTGGAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13:1:26.5:1:1:0:43:1:1:0:4 0/1:8:2:1,1:3,3:0.25:2,2:13:1:30.5:1:1:1:60:4:0.25:0:2.5 -19 27733516 . T G 65 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=AACAATCTTTTTGTGCAATT;RSEQ=GCAGGTGGAGATTTCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:33:0:1:0:43:4:1:0:4 0/1:10:4:2,2:3,3:0.4:2,2:18:1:32.8:1:1:1:48:8:0.4:0:3 -19 27733520 . G A 64 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ATCTTTTTGTGCAATTTGCA;RSEQ=GTGGAGATTTCAAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:32:1:1:0:43:4:1:0:4 1/0:8:4:2,2:2,2:0.5:2,2:22:1:32:1:1:1:48:8:0.5:0:3 -19 27733521 . G C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTTTTGTGCAATTTGCAG;RSEQ=TGGAGATTTCAAGCGCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23:1:33:1:1:0:43:4:1:0:4 0/1:8:2:1,1:3,3:0.25:2,2:22:1:32.5:1:1:1:60:4:0.25:0:2.5 -19 27733545 . T A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGATTTCAAGCGCTTTAAGG;RSEQ=CAATGGCAGAAAAAGATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:17:0:30.5:1:1:0:43:4:1:0:4 1/0:4:2:1,1:1,1:0.5:2,2:17:0:30:1:1:1:54:4:0.5:0:4 -19 27733859 . T C 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=CACTCTTTTTGTGGAATTTG;RSEQ=AAGTGGAGATTTCAGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:19.5:1:30.5:1:1:0:33:4:0.6667:0:6 1/1:5:5:3,2:0,0:1:0,2:22.8:1:32.4:1:1:0:39.8:10:1:0:5.8 -19 27733867 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46429;SOR=Inf;LSEQ=TTGTGGAATTTGTAAGTGGA;RSEQ=ATTTCAGCCGCTTTGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:33.3:1:26:1:1:0:35:2:1:0:6 0/1:5:2:1,1:2,1:0.4:2,2:38.5:1:28:1:1:1.7321:27:4:0.4:0:7 -19 27733884 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=GGAGATTTCAGCCGCTTTGA;RSEQ=GTCAATGGCAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:23.3:1:31.9:1:1:0:42.4:14:1:0:4.6 0/1:5:2:1,1:2,1:0.4:2,2:40:1:30.5:1:1:1.7321:27:4:0.4:0:7 -19 27733890 . TG AA 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06993;SOR=Inf;LSEQ=TTCAGCCGCTTTGAGGTCAA;RSEQ=GCAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:26.5:1:31.2:1:1:0:43:12:1:0:4.3 1/0:6:3:1,2:1,0:0.5:0,2:29:1:28.3:1:1:0:49:6:0.5:0.1667:5.7 -19 27733891 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=TCAGCCGCTTTGAGGTCAAT;RSEQ=GCAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,2:0.2857:2,2:20:0:31.5:1:1:1.73:47:4:0.3333:0:4.5 0/0:5:0:0,0:2,1:0:2,0:42.3:1:32.3:1:1:0:26.3:6:1:0:6 -19 27733893 . C T 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59207;SOR=0.32855;LSEQ=AGCCGCTTTGAGGTCAATGG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:0.625:2,2:21.2:1:29.4:1:1:2.60168:46.2:10:0.7143:0:4 0/1:6:2:1,1:2,2:0.3333:2,2:36.5:1:29.5:1:1:1:27:4:0.3333:0:7 -19 27733901 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TGAGGTCAATGGCAGAAAAG;RSEQ=AAATATCTTCGTATAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:26.6:1:32:1:1:0:42:16:1:0:4.3 0/1:7:2:1,1:2,3:0.2857:2,2:22.5:1:28:1:1:1.41:25:4:0.2857:0:5.5 -19 27733904 . A AC 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GGTCAATGGCAGAAAAGGAA;RSEQ=TATCTTCGTATAAAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:31:0:33.5:1:1:1:49:4:0.25:0:2.5 0/0:7:0:0,0:3,4:0:2,0:23.7:1:29:1:1:0:35.9:14:1:0:6 -19 27733908 . C T 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07692;SOR=Inf;LSEQ=AATGGCAGAAAAGGAAATAT;RSEQ=TTCGTATAAAAACTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:23.9:1:30.9:1:1:0:42:7:1:0:4.3 0/1:7:3:1,2:2,2:0.4286:2,2:22:1:27.7:1:1:1.81007:49:6:0.4286:0:5.7 -19 27733912 . G C 71 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02098;SOR=Inf;LSEQ=GCAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:22.7:1:31.4:1:1:0:42.4:14:1:0:4 1/0:7:5:2,3:1,1:0.7143:2,2:19.4:1:30.8:1:1:1.41418:40.2:10:0.7143:0:6.2 -19 27733915 . T G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGACAGAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:22.5:1:32.5:1:1:1.41418:47:4:0.2857:0:4.5 0/0:7:0:0,0:3,4:0:2,0:19:1:27.1:1:1:0:35.9:14:1:0:6 -19 27733918 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACTAGACAGAATGATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:20:1:31:1:1:1.41418:33:4:0.2857:0:6 0/0:7:0:0,0:3,4:0:2,0:17.7:1:28.4:1:1:0:35.9:14:1:0:6 -19 27733919 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=AGGAAATATCTTCGTATAAA;RSEQ=ACTAGACAGAATGATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:16:0:33.5:1:1:1.41418:49:4:0.3333:0:2.5 0/0:6:0:0,0:1,3:0:2,0:19:1:28.8:1:1:0:43.5:8:0.6667:0:5.8 -19 27733921 . C G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATGATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:16.5:1:33:1:1:1.41418:47:4:0.3333:0:4.5 0/0:6:0:0,0:2,4:0:2,0:19.5:1:30.5:1:1:0:37.3:12:1:0:5.7 -19 27733922 . T C 33 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=AGACAGAATGATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:16:1:33.5:1:1:1:33:4:0.3333:0:6 0/0:6:0:0,0:2,4:0:2,0:19.2:1:28:1:1:0:37.3:12:1:0:5.7 -19 27733929 . A G 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=TTCGTATAAAAACTAGACAG;RSEQ=ATGATTCTCAGAAACTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:9:1:28.5:1:1:1:33:4:0.3333:0:6 0/0:6:0:0,0:2,4:0:2,0:16.8:1:27.8:1:1:0:37.3:12:1:0:5.7 -19 27734160 . C G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGATTTGAAAGATCCTTTA;RSEQ=ACAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:1:33:0:1:0:41:4:1:0:6 1/1:3:3:3,0:0,0:1:0,0:10:1:33:1:1:0:51.7:6:1:0:6 -19 27734204 . C G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTGGAATTTGCAAGTG;RSEQ=AGATTTCAAGCGCTTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:9,7:0,0:1:0,2:28.7:1:31.6:1:1:0:44.9:32:1:0:5.4 1/1:23:22:18,4:0,0:0.9565:0,2:29.6:1:31.6:1:1:0:48.3:44:1:0:6 -19 27734220 . G C 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCAGATTTCAAGCGCTT;RSEQ=GAGGCCAATTGTAGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:10,12:0,0:1:0,2:28.8:1:30.4:1:1:0:47:44:1:0:5.9 1/1:29:28:21,7:0,0:0.9655:0,2:32.1:1:30.7:1:1:0:48.5:56:0.9655:0:6.2 -19 27734223 . G T 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGATTTCAAGCGCTTGGA;RSEQ=GCCAATTGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:10,12:0,0:1:0,2:29.5:1:30.3:1:1:0:47:44:1:0:5.9 1/1:32:32:24,8:0,0:1:0,2:29.8:1:29.9:1:1:0:49.4:64:1:0:6.2 -19 27734230 . T G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGCGCTTGGAGGCCAAT;RSEQ=GTAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:12,14:0,0:1:0,2:25.9:1:31.3:1:1:0:47.6:52:1:0:5.9 1/1:40:39:25,14:1,0:0.975:0,2:25.8:1:30.7:1:1:0:49.6:78:0.975:0:6 -19 27734254 . T G 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05877;SOR=0;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACAAGACAAAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:2,1:17,16:0.0833:2,2:21.3:1:31.3:1:1:1.85:46.7:6:0.0833:0:6.7 0/0:55:0:0,0:32,23:0:2,0:24.6:1:28.4:1:1:0:50.5:110:1:0:5.8 -19 27734269 . A C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30928;SOR=Inf;LSEQ=TCGTATAAAAACAAGACAAA;RSEQ=TCATTCCCAGAAACTGCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:29:13,16:1,0:0.9667:0,2:31.3:1:32.8:1:0.46667:0:45.7:58:0.9667:0:6.4 1/1:67:67:37,30:0,0:1:0,2:24.4:1:31.3:1:1:0:48:134:1:0:6.2 -19 27734272 . A G 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12355;LSEQ=TATAAAAACAAGACAAAATC;RSEQ=TTCCCAGAAACTGCGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:28:13,15:1,0:0.9655:0,2:32.7:1:32:1:0.48276:0:46.5:56:0.9655:0:6.5 1/1:65:63:35,28:1,1:0.9692:2,2:26.2:1:30.5:1:1:1.25:47.9:126:0.9692:0:6.3 -19 27734281 . A C 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29897;SOR=Inf;LSEQ=AAGACAAAATCATTCCCAGA;RSEQ=ACTGCGTAGTGAGGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:28:14,14:1,0:0.9655:0,2:33.2:1:33.1:1:1:0:46.3:56:0.9655:0:6.5 1/1:68:68:38,30:0,0:1:0,2:26.1:1:31.9:1:1:0:46.9:136:1:0:6.3 -19 27734294 . G T 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAGAAACTGCGTAGTGA;RSEQ=GTGTGTGTTTAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:16,14:0,0:1:0,2:28.1:1:31:1:1:0:46.8:60:1:0:6.2 1/1:65:65:34,31:0,0:1:0,2:27.4:1:30.3:1:1:0:47.2:64:1:0:6.1 -19 27734316 . T A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGTGTTTAACTCACAGAG;RSEQ=TTAACCTTTCGTTTCATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:16,10:0:2,0:22.2:1:29.3:1:1:0:44.1:52:1:0:5.6 0/1:64:2:1,1:36,26:0.0313:2,2:17.5:1:27.5:1:1:1.37745:50:4:0.0313:0:6 -19 27734319 . A C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46606;SOR=0.66843;LSEQ=GTGTTTAACTCACAGAGTTT;RSEQ=ACCTTTCGTTTCATACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:5,6:11,4:0.4231:2,2:23.5:1:31.2:1:0.22797:3.14133:46.1:22:0.4231:0:6.4 0/1:61:20:11,9:23,18:0.3279:2,2:25.9:1:31.9:1:1:1.04472:39.4:40:0.3279:0:6.5 -19 27734327 . G T 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACAGAGTTTAACCTTTC;RSEQ=TTTCATACAGCATTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:16,10:0,0:1:0,2:19.4:1:30.1:1:1:0:43.3:52:1:0:5.7 1/1:61:61:38,23:0,0:1:0,2:23.6:1:31:1:1:0:43.7:122:1:0:5.8 -19 27734342 . T C 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23171;SOR=Inf;LSEQ=CTTTCGTTTCATACAGCATT;RSEQ=TGGAAACACTCTGTTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:18:13,5:0,1:0.9474:0,2:26.1:1:31.6:1:0.31579:0:40.3:36:0.9474:0:5.1 1/1:63:63:42,21:0,0:1:0,2:21.3:1:31.6:1:1:0:42.1:126:1:0:5.7 -19 27734350 . A C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55693;SOR=0;LSEQ=TCATACAGCATTTTGGAAAC;RSEQ=CTCTGTTTGTAAAGTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:14,9:0,0:1:0,2:22.3:1:30.7:1:1:0:43:46:1:0:4.5 1/1:60:57:37,20:2,1:0.95:2,2:23.6:1:30.7:1:1:1.0797:43.3:114:0.95:0:5.4 -19 27734353 . C G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.44955;SOR=1.56689;LSEQ=TACAGCATTTTGGAAACACT;RSEQ=TGTTTGTAAAGTCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:4,2:10,8:0.25:2,2:29.8:1:32.2:1:1:1.57:40:12:0.2609:0:5.3 0/1:61:21:14,7:25,15:0.3443:2,2:25.8:1:31.9:1:0.78669:1.20:44.9:42:0.3443:0:6 -19 27734360 . T G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTGGAAACACTCTGTTTG;RSEQ=AAAGTCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:21.5:1:28.8:1:1:0:45.4:54:1:0:4.1 0/1:57:2:1,1:35,20:0.0351:2,2:12.5:1:29:1:1:1.73197:27:4:0.0351:0:5 -19 27734371 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5429;SOR=Inf;LSEQ=CTCTGTTTGTAAAGTCTGCA;RSEQ=GTGGATATTTGGATCTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:0:2,0:22.7:1:30.5:1:1:0:47:60:1:0:3.7 0/1:57:2:1,1:34,21:0.0351:2,2:23.5:1:29:1:1:1.60486:27:4:0.0351:0:5 -19 27734374 . G C 30 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0366;LSEQ=TGTTTGTAAAGTCTGCAAGT;RSEQ=GATATTTGGATCTCTTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:1,0:13,15:0.0345:2,0:12:0:31:0:0.48276:0:60:2:0.0345:0:3 0/1:56:2:1,1:35,19:0.0357:2,2:47:1:30:1:1:1.821:36.5:4:0.0357:0:5 -19 27734375 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54774;SOR=Inf;LSEQ=GTTTGTAAAGTCTGCAAGTG;RSEQ=ATATTTGGATCTCTTAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,15:0:2,0:24.9:1:30.2:1:1:0:47.2:13.5:1:0:3.6 0/1:57:2:1,1:35,20:0.0351:2,2:33:0:28.5:1:1:1.73197:60:4:0.0351:0:3 -19 27734382 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54826;SOR=Inf;LSEQ=AAGTCTGCAAGTGGATATTT;RSEQ=GATCTCTTAGATGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:14,17:0:2,0:25.5:1:30.7:1:1:0:47.2:30:1:0:3.4 0/1:61:2:1,1:39,20:0.0328:2,2:34.5:1:29:1:1:1.92731:27:4:0.0328:0:5 -19 27734385 . T C 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54826;SOR=0;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=CTCTTAGATGCCTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:14,17:0,0:1:0,2:26.7:1:30.8:1:1:0:47.8:30:1:0:3.4 1/1:61:59:39,20:1,1:0.9672:2,2:25.6:1:31.3:1:1:1.93:45.2:118:0.9672:0:4.1 -19 27734401 . G T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGATCTCTTAGATGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:14,18:0:2,0:30.4:1:30.6:1:1:0:48:64:1:0:3.3 0/1:65:2:2,0:34,27:0.0308:2,0:17.5:1:32:1:0.5023:0:36.5:4:0.0308:0:5.5 -19 27734405 . G C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65012;SOR=0.68252;LSEQ=TCTCTTAGATGCCTTCGTTG;RSEQ=AAACGGGATTTCTTCATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:12,17:0.0645:2,2:38:1:31.5:1:1:1.40:41.5:4:0.0667:0:3 0/1:67:3:2,1:36,28:0.0448:2,2:33:1:31.3:1:1:1.55:49.7:6:0.0455:0:4 -19 27734418 . T C 70 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66071;SOR=2.63992;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TCATATAATGCTACAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:16,17:0.0294:2,0:28:0:33:0:1:0:39:2:0.0303:0:4 0/1:67:5:2,3:36,24:0.0746:2,2:28.8:1:30.2:1:0.64152:2.22139:47.4:10:0.0758:0:4 -19 27734419 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.54891;SOR=Inf;LSEQ=TCGTTGGAAACGGGATTTCT;RSEQ=CATATAATGCTACAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:16,18:0:2,0:28.8:1:30.1:1:1:0:46.3:68:1:0:3.2 0/1:67:2:2,0:37,28:0.0299:2,0:10.5:1:29.5:1:0.50611:0:26:4:0.0299:0:5 -19 27734428 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53873;SOR=Inf;LSEQ=ACGGGATTTCTTCATATAAT;RSEQ=CTACAGGGAAGAATTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:16,20:0:2,0:25.9:1:32.5:1:1:0:46:72:1:0:3.4 0/1:66:2:1,1:35,29:0.0303:2,2:41:1:29:1:1:1.20344:60:4:0.0303:0:3 -19 27734432 . C G 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTCTTCATATAATGCTA;RSEQ=AGGGAAGAATTCTTAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:14,21:0,0:1:0,2:26.2:1:32:1:1:0:46.2:70:1:0:3.5 1/1:60:60:31,29:0,0:1:0,2:25:1:31.7:1:1:0:42.2:120:1:0:4 -19 27734473 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTTTGTGTTGTGTGTATT;RSEQ=AACTGTCAGATTTGAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:0:2,0:25.3:1:31.5:1:1:0:40.4:46:1:0:4.4 0/1:52:2:1,1:24,26:0.0385:2,2:30.5:1:30:1:1:1.08:53.5:4:0.0385:0:6 -19 27734479 . T A 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTGTGTGTATTCAACTG;RSEQ=CAGATTTGAACCTTCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:8,14:0,0:1:0,2:24.3:1:29.1:1:1:0:41:21:1:0:4.5 1/1:48:48:22,26:0,0:1:0,2:29.4:1:29.6:1:1:0:40.7:96:1:0:5.1 -19 27734484 . T G 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTATTCAACTGTCAGA;RSEQ=TTGAACCTTCATTTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:7,12:0,0:1:0,2:25.7:1:30.7:1:1:0:37.9:18:1:0:4.9 1/1:48:48:21,27:0,0:1:0,2:28.1:1:31.6:1:1:0:40.4:96:1:0:5.2 -19 27734495 . A C 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTCAGATTTGAACCTTC;RSEQ=TTTAGACAGAGCAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:7,9:0,0:1:0,2:24.9:1:29.8:1:1:0:36.7:15:1:0:5.3 1/1:50:49:20,29:0,0:0.98:0,2:23.8:1:30.4:1:1:0:40.5:48:0.9796:0:5.6 -19 27734508 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACCTTCATTTAGACAGAGC;RSEQ=GATTTGAAACACTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:3,9:0:2,0:22.8:1:29.9:1:1:0:38:11:1:0:5.7 0/1:39:2:1,1:15,22:0.0513:2,2:8.5:1:27.5:1:1:1.45:39:4:0.0526:0:3.5 -19 27734518 . CA GT 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.54359;LSEQ=TAGACAGAGCAGATTTGAAA;RSEQ=CTCTTTTTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:2,7:0,0:0.9:0,2:23.1:1:31.7:1:1:0:39.8:18:1:0.1:5.2 1/1:35:29:12,17:1,5:0.8286:2,2:23.9:1:30.2:1:0.37713:3.42:43.7:58:0.8286:0:5.4 -19 27734541 . A G 127 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTTGTGGAATTTGCAA;RSEQ=TGCAGATTTCAAGCCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:31:1:32:1:1:0:30.7:6:1:0:6.7 1/1:19:17:5,12:1,1:0.8947:2,2:28.9:1:31.2:1:1:2.28037:43.1:34:0.9444:0:6.4 -19 27734544 . C G 129 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTGGAATTTGCAAATG;RSEQ=AGATTTCAAGCCCTTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:28:1:31:1:1:0:30.7:6:1:0:6.7 1/1:18:18:6,12:0,0:1:0,2:27.7:1:31.1:1:1:0:42.8:36:1:0:6.1 -19 27734556 . C G 115 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAATGCAGATTTCAAGC;RSEQ=CTTTGAGGCCAAACGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:16:1:30.7:1:1:0:30.7:6:1:0:6.7 1/1:14:13:3,10:0,0:0.9286:0,2:21.5:1:31.1:1:1:0:41.8:12:0.9231:0:6 -19 27734570 . C A 105 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGCCCTTTGAGGCCAAA;RSEQ=GCAGAAAAGCAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:6:0:33:0:1:0:22:2:1:0:6 1/1:10:10:2,8:0,0:1:0,2:13.9:1:31.8:1:1:0:40.2:20:1:0:6.5 -19 27734580 . C G 88 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGCCAAACGCAGAAAAG;RSEQ=AAATATCTTCGTATAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:2,5:0,0:1:0,2:8.4:1:31.4:1:1:0:41:14:1:0:6.7 -19 27734587 . C T 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACGCAGAAAAGCAAATAT;RSEQ=TTCGTATAAAAACTAGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:1:32:0:1:0:35.5:4:1:0:7.5 -19 27734591 . G C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAAAAGCAAATATCTTC;RSEQ=TATAAAAACTAGACTGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:1:33:1:1:0:35.5:4:1:0:7.5 -19 27734602 . A C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATCTTCGTATAAAAACT;RSEQ=GACTGAATCATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:28.5:1:1:0:36:4:1:0:7 -19 27734606 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCGTATAAAAACTAGAC;RSEQ=GAATCATTCTCAGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:29:1:1:0:36:4:1:0:7 -19 27734633 . C A 26 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCAGAAACTGCTCTGTG;RSEQ=TGTGTGCGTTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39.5:1:26.5:1:1:0:36:4:1:0:7 -19 27734661 . G C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCAACTCACAGAGTTTAA;RSEQ=TTTTCTTTTCATTCAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:29.5:1:1:0:36:4:1:0:7 -19 27734798 . C T 94 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATTCTTAGTAACTTCTT;RSEQ=GTGTTGTGTGTATTCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:9:9:5,4:0,0:1:0,2:34:1:29.7:1:1:0:37.2:18:1:0:2.9 -19 27734819 . T A 85 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTGTGTGTATTCAACTG;RSEQ=CAGAGTTGAACCATCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:8:8:4,4:0,0:1:0,2:14.8:1:28.4:1:1:0:38.1:16:1:0:3.1 -19 27734831 . C G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACTGTCAGAGTTGAAC;RSEQ=ATCATTTAGACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:29:1:1:1:47.5:4:0.5:0:5 -19 27734835 . A C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTCAGAGTTGAACCATC;RSEQ=TTTAGACAGAGCAGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:28.5:1:1:0:47.5:4:1:0:5 -19 27735216 . T G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACTCTTTTTGTGCAATT;RSEQ=GCAAGTGGAGATTTCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:31.5:1:1:0:60:4:1:0:2.5 -19 27735289 . A C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGCATAAAAACTAGACAAA;RSEQ=TCATTCCCAGAAACTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:11.3:1:33.3:1:1:0:37.7:6:1:0:7 1/1:3:3:1,2:0,0:1:0,2:5.3:1:32:1:1:0:43:6:1:0:6.7 -19 27735292 . A G 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAAACTAGACAAAATC;RSEQ=TTCCCAGAAACTGCATAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:11:1:31.8:1:1:0:40:8:1:0:7 1/1:5:4:1,3:1,0:0.8:0,2:6.8:1:31.5:1:0.4:0:44:8:0.8:0:6.5 -19 27735300 . A T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=CTAGACAAAATCATTCCCAG;RSEQ=AACTGCATAGTGATGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:14.3:1:29.9:1:1:0:43.3:14:1:0:6 0/1:9:2:1,1:2,5:0.2222:2,2:6:0:31:1:1:2.24:21:4:0.2222:0:4 -19 27735301 . A C 90 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=TAGACAAAATCATTCCCAGA;RSEQ=ACTGCATAGTGATGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:15.3:1:32.1:1:1:0:43.3:14:1:0:6 1/0:9:7:2,5:1,1:0.7778:2,2:12.9:1:32.4:1:1:2.23609:44.3:14:0.7778:0:5.4 -19 27735307 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCATTCCCAGAAACTGC;RSEQ=TAGTGATGTGTGTGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:21.3:1:31.4:1:1:0:43.3:14:1:0:6 1/1:10:10:3,7:0,0:1:0,2:16.4:1:29.4:1:1:0:38.2:9:1:0:4.9 -19 27735320 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.53623;SOR=Inf;LSEQ=AAACTGCATAGTGATGTGTG;RSEQ=GTTTAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:29.9:1:30.1:1:1:0:40.5:16:1:0:5.9 0/1:16:2:1,1:2,10:0.125:2,2:26:0:32.5:1:0.3956:4.28:21:4:0.125:0:4 -19 27735335 . G T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53623;SOR=Inf;LSEQ=GTGTGTGTTTAACTCACAGA;RSEQ=TTTAACCTTTCTTTTCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:38.3:1:32.6:1:1:0:40.5:16:1:0:5.9 0/1:16:2:1,1:3,11:0.125:2,2:22.5:1:30.5:1:0.45:3.32:60:4:0.1333:0:4.5 -19 27735336 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53623;SOR=Inf;LSEQ=TGTGTGTTTAACTCACAGAG;RSEQ=TTAACCTTTCTTTTCATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:38:1:30.6:1:1:0:40.5:16:1:0:5.9 0/1:16:2:1,1:3,11:0.125:2,2:24:0:30.5:1:0.45:3.32:21:4:0.125:0:4 -19 27735339 . A C 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67335;SOR=0.61321;LSEQ=GTGTTTAACTCACAGAGTTT;RSEQ=ACCTTTCTTTTCATACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:0.5:2,2:35:1:31.8:1:1:1:34:8:0.5:0:6.5 0/1:16:6:1,5:3,7:0.375:2,2:30.3:1:30.7:1:1:2.04824:42.2:5:0.3333:0:6 -19 27735357 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52569;SOR=Inf;LSEQ=TTAACCTTTCTTTTCATACA;RSEQ=CATTTTGGAAACACTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:22.4:1:33:1:1:0:40.5:16:1:0:5.9 0/1:15:2:1,1:2,11:0.1333:2,2:27:0:31.5:1:0.37143:4.69:60:4:0.1333:0:4.5 -19 27735362 . T C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=CTTTCTTTTCATACAGCATT;RSEQ=TGGAAACACTCTGTTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:17.8:1:31.6:1:1:0:40.5:16:1:0:5.9 1/1:11:9:0,9:1,1:0.8182:2,0:21.3:1:30.2:1:0.18182:0:46.7:8:0.8:0:4.6 -19 27735370 . A C 89 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46154;SOR=0;LSEQ=TCATACAGCATTTTGGAAAC;RSEQ=CTCTGTTTGTAAATTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:12:1:31.9:1:1:0:43.3:14:1:0:5.6 1/0:7:5:0,5:1,1:0.7143:2,0:27.2:1:28.2:1:0.28571:0:46.6:4:0.6667:0:5.4 -19 27735371 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.46154;SOR=Inf;LSEQ=CATACAGCATTTTGGAAACA;RSEQ=TCTGTTTGTAAATTCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:11:1:32:1:1:0:43.3:14:1:0:5.6 0/1:7:2:1,1:0,5:0.2857:0,2:13:0:33.5:1:0.28571:0:60:4:0.3333:0:4.5 -19 27735373 . C G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.55811;LSEQ=TACAGCATTTTGGAAACACT;RSEQ=TGTTTGTAAATTCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:17.3:1:33.3:1:1:1.81007:38.3:6:0.4286:0:6 0/1:7:2:0,2:1,4:0.2857:2,0:36:0:31.5:1:1:0:48:4:0.3333:0:4.5 -19 27735384 . T G 42 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAACACTCTGTTTGTAAA;RSEQ=TCTGCAAGTGGATATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:25:0:34:0:1:0:21:2:1:0:5 1/1:3:3:0,3:0,0:1:0,0:24.3:1:26.7:1:1:0:46.3:2:1:0:4.7 -19 27735507 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATTCAACTGACAGAGTT;RSEQ=AACCTTCCTTTAGACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:0:33.5:1:1:0:21:4:1:0:5.5 -19 27735538 . CC GT 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACAGAGCAGATTTGAAA;RSEQ=CTCCTTCTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29.8:1:1:0:21:4:1:0:4.5 -19 27735543 . C T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCAGATTTGAAACCCTC;RSEQ=TTCTGTGGAATTTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:30:1:1:0:21:4:1:0:4.5 -19 27735565 . C A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTGGAATTTGCAAGTGG;RSEQ=GATTTCAAGCGCTTTAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:28:1:1:0:21:4:1:0:4.5 -19 27735920 . A C 60 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTGGAAGTTTCAAGCGCTT;RSEQ=GAGGCCAATGGTAGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:7.3:1:30.3:1:1:0:41.3:8:1:0:2.3 -19 27735923 . G T 56 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGTTTCAAGCGCTTAGA;RSEQ=GCCAATGGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:10.3:1:28.3:1:1:0:41.3:8:1:0:2.3 -19 27735967 . A AACTCGTTCCCAG 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCGTATAAAAACAAGACA;RSEQ=AATCATTCTCAGAAACTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:27.3:1:1:0:35:4:1:0.5:2 -19 27736207 . G C 78 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01786;SOR=0;LSEQ=GAACCTTCCTTTAGACAGAG;RSEQ=AGATTTAAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:15.8:1:33.6:1:1:0:35.2:10:1:0:6.6 0/0:3:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 27736211 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CTTCCTTTAGACAGAGGAGA;RSEQ=TTAAAACACTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:19.8:1:32.2:1:1:0:35.2:10:1:0:6.6 0/1:6:2:1,1:2,2:0.3333:2,2:9:0:33.5:1:1:1:33:4:0.3333:0:5.5 -19 27736214 . A G 87 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTAGACAGAGGAGATTT;RSEQ=AAACACTCTTTTTGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:22.8:1:33.6:1:1:0:35.2:10:1:0:6.6 1/1:7:7:4,3:0,0:1:0,2:10.4:1:31:1:1:0:39.7:14:1:0:4.6 -19 27736218 . CA GT 51 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=TAGACAGAGGAGATTTAAAA;RSEQ=CTCTTTTTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:2,1:0.5:2,2:30:1:32.7:1:1:3.10575:35:6:0.5:0:6.3 0/0:10:0:0,0:6,4:0:2,0:11:1:31.1:1:1:0:44.1:20:1:0:4.1 -19 27736219 . A T 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28006;SOR=0.24597;LSEQ=AGACAGAGGAGATTTAAAAC;RSEQ=CTCTTTTTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:0,0:0.5:0,2:17.3:1:31:1:1:0:38:6:1:0:6 0/1:11:2:0,2:6,3:0.1818:2,0:5.5:1:27:1:0.18182:0:27.5:4:0.1818:0:5 -19 27736220 . C A 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50476;SOR=Inf;LSEQ=GACAGAGGAGATTTAAAACA;RSEQ=TCTTTTTGTGGAATTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:18.8:1:32.8:1:1:0:37.3:16:1:0:5.9 0/1:13:2:1,1:6,5:0.1538:2,2:18:0:32:0:1:1.18321:33:4:0.1538:0:5.5 -19 27736231 . G T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48387;SOR=Inf;LSEQ=TTTAAAACACTCTTTTTGTG;RSEQ=AATTTGCAAGTAGAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:18.9:1:31.9:1:1:0:39.6:30:1:0:6.5 0/1:16:2:1,1:7,7:0.125:2,2:20.5:1:31:1:1:1:33:4:0.125:0:5.5 -19 27736241 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48485;SOR=Inf;LSEQ=TCTTTTTGTGGAATTTGCAA;RSEQ=TAGAGATTTCAAGCGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:26.3:1:33:1:1:0:39.1:32:1:0:6.4 0/1:17:2:1,1:7,8:0.1176:2,2:32.5:1:27.5:1:1:1.13:60:4:0.1176:0:3.5 -19 27736243 . A G 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17484;SOR=0.16841;LSEQ=TTTTTGTGGAATTTGCAAGT;RSEQ=GAGATTTCAAGCGCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:8,7:0,1:0.9375:0,2:27.8:1:32.5:1:1:0:39.3:30:0.9375:0:6.3 1/0:17:12:5,7:3,2:0.7059:2,2:23.9:1:30.4:1:0.61991:2.00863:38.9:24:0.8:0:4.7 -19 27736260 . TG CT 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51052;SOR=Inf;LSEQ=AGTAGAGATTTCAAGCGCTT;RSEQ=AGGCCAATGGCAGAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,8:0:2,0:31.9:1:31:1:1:0:39.3:32:1:0:6.3 0/1:26:2:1,1:10,14:0.0769:2,2:17.5:1:32:1:1:1.38:41:4:0.0833:0:2.5 -19 27736267 . A T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.32471;LSEQ=ATTTCAAGCGCTTTGAGGCC;RSEQ=ATGGCAGAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:8,8:0.0588:2,0:44:0:30:0:1:0:36:2:0.0588:0:6 0/1:26:2:1,1:10,14:0.0769:2,2:23.5:1:31:1:1:1.38:41:4:0.0769:0:2.5 -19 27736269 . TG AA 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00818;SOR=0.15313;LSEQ=TTCAAGCGCTTTGAGGCCAA;RSEQ=GCAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:5,5:1,1:0.5556:2,2:30.6:1:31:1:1:1:40.1:20:0.5556:0.0556:5.7 0/1:26:4:1,3:4,6:0.1538:2,2:37.8:1:30.8:1:1:1.90754:38:8:0.1667:0:5.5 -19 27736271 . GC AT 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22927;SOR=4.8283;LSEQ=CAAGCGCTTTGAGGCCAATG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:7,10:0.0556:2,0:22:0:32.5:0:0.44444:0:42:2:0.0556:0:7 0/1:31:7:1,6:12,11:0.2258:2,2:20.1:1:29.4:1:0.10375:6.18497:48.9:14:0.2414:0:5.7 -19 27736272 . C T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27878;SOR=Inf;LSEQ=AAGCGCTTTGAGGCCAATGG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,10:0:2,0:29.3:1:32.6:1:1:0:39:36:1:0:5.9 0/1:31:3:3,0:10,11:0.0968:2,0:12:1:28.7:1:0.22283:0:48.7:6:0.1429:0:5.3 -19 27736286 . T C 95 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13301;SOR=5.49117;LSEQ=CAATGGCAGAAAAGGAAATA;RSEQ=CTTCGTATAAAAACTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:1,0:8,11:0.05:2,0:8:0:34:0:0.45:0:42:2:0.05:0:7 0/1:35:8:2,6:13,14:0.2286:2,2:29.8:1:31.8:1:0.41928:2.70886:50.3:16:0.2353:0:6 -19 27736287 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3882;SOR=0.53823;LSEQ=AATGGCAGAAAAGGAAATAT;RSEQ=TTCGTATAAAAACTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:5,5:3,6:0.5263:2,2:22.9:1:30.6:1:0.64992:1.93:40.1:20:0.5263:0:6 0/1:35:13:6,7:9,13:0.3714:2,2:15.9:1:29.4:1:1:1.23:36.8:26:0.3714:0:6.5 -19 27736291 . G C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23784;SOR=0.47096;LSEQ=GCAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:5,4:3,5:0.5294:2,2:23.9:1:31.2:1:0.63719:1.99:41.8:18:0.5294:0:6 0/1:35:12:5,7:9,13:0.3429:2,2:17.2:1:31.3:1:1:1.03:38.2:24:0.3636:0:6.3 -19 27736294 . T G 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.41048;SOR=0.51681;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGACAGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:6,7:0.1875:2,2:22:1:32.3:1:1:1.659:38:6:0.1875:0:6.3 0/1:38:4:1,3:16,18:0.1053:2,2:12.8:1:33:1:0.61309:2.60412:42:8:0.1081:0:5 -19 27736297 . A T 88 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.08836;SOR=Inf;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACTAGACAGAATCATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:20.6:1:30.3:1:1:0:38.8:32:1:0:6 0/1:37:8:2,6:14,15:0.2162:2,2:24.5:1:29.6:1:0.42271:2.72671:50.3:16:0.2222:0:6 -19 27736300 . C A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59726;SOR=0.4915;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATCATTTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:8,7:0.1176:2,0:24.5:1:33:0:0.47059:0:37:4:0.1176:0:6.5 0/1:33:2:0,2:11,12:0.0606:2,0:15.5:1:31.5:1:0.48667:0:24:4:0.0606:0:6.5 -19 27736301 . TA CC 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28307;SOR=0.25788;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=GACAGAATCATTTTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:8,7:0.1176:2,0:26:1:32.3:1:0.47059:0:32:4:0.1176:0:3.5 0/1:31:1:1,0:11,19:0.0323:2,0:28:0:32:0:0.3871:0:27:2:0.0357:0:4 -19 27736302 . A C 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35494;SOR=0.51869;LSEQ=AATATCTTCGTATAAAAACT;RSEQ=GACAGAATCATTTTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:6,2:2,5:0.4706:2,2:17.5:1:31.1:1:0.13193:6.40:39.3:16:0.5333:0:6.9 0/1:32:10:5,5:6,15:0.3125:2,2:19.2:1:30.9:1:0.42322:2.42:34.5:20:0.3333:0:7.2 -19 27736306 . A G 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46059;SOR=2.36209;LSEQ=TCTTCGTATAAAAACTAGAC;RSEQ=GAATCATTTTCAGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:8,7:0.1176:2,0:18.5:1:32.5:1:0.47059:0:37:4:0.1176:0:6.5 0/1:33:8:1,7:12,13:0.2424:2,2:18.4:1:30.6:1:0.1077:6.15201:44.5:16:0.2581:0:6.6 -19 27736312 . A T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.74504;SOR=0.6824;LSEQ=TATAAAAACTAGACAGAATC;RSEQ=TTTTCAGAAACTGCTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:6,1:0,6:0.5385:0,2:22.3:1:31.6:1:0.00466:0:36.6:14:0.5385:0:7.1 0/1:34:15:7,8:5,14:0.4412:2,2:24.6:1:30.3:1:0.28827:2.38:34.9:30:0.4688:0:7.3 -19 27736315 . T C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACTAGACAGAATCATT;RSEQ=TCAGAAACTGCTCTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:6,6:0,0:1:0,2:23.3:1:32.8:1:1:0:36.1:24:1:0:6.3 1/1:36:36:13,23:0,0:1:0,2:21.2:1:30.3:1:1:0:37:17:1:0:6 -19 27736323 . C G 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAGAATCATTTTCAGAAA;RSEQ=TGCTCTGTGATGTGTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:24.7:1:32.4:1:1:0:34.3:22:1:0:6.1 0/1:39:2:1,1:14,23:0.0513:2,2:21:0:31.5:1:1:1.62:31:4:0.0526:0:5.5 -19 27736331 . T G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28902;SOR=0.41659;LSEQ=CATTTTCAGAAACTGCTCTG;RSEQ=GATGTGTGTGTTCAACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:0,3:0.6667:0,2:31.5:1:32.2:1:0.04762:0:33.2:12:0.6667:0:7 0/1:40:18:8,10:7,12:0.45:2,2:30.8:1:30.2:1:0.74314:1.36:35.4:36:0.4737:0:7 -19 27736340 . T C 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0.97028;LSEQ=AAACTGCTCTGTGATGTGTG;RSEQ=GTTCAACTCAGAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:5,1:0,2:0.75:0,2:33.3:1:33:1:0.10714:0:33.2:12:0.75:0:7 1/0:43:32:15,17:5,6:0.7442:2,2:29.5:1:30.7:1:1:1.06:32:64:0.7805:0:5.9 -19 27736349 . C A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGATGTGTGTGTTCAACT;RSEQ=AGAGAGTTTAACTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:24.5:1:31.9:1:1:0:34.9:20:1:0:5.8 0/1:44:2:1,1:19,23:0.0455:2,2:19.5:1:27.5:1:1:1.21:24:4:0.0465:0:6 -19 27736351 . G C 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATGTGTGTGTTCAACTCA;RSEQ=AGAGTTTAACTTTTCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:6,4:0,0:1:0,2:23.8:1:30.1:1:1:0:34.9:9:1:0:5.8 1/1:45:43:19,24:1,1:0.9556:2,2:29.8:1:30.7:1:1:1.25655:33.3:13.333:0.9524:0:5.5 -19 27736361 . CT C 119 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.10504;SOR=Inf;LSEQ=GTTCAACTCAGAGAGTTTAA;RSEQ=TTTCTTTTCATTCCGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:18.8:1:30.3:1:1:0:36.4:24:1:0:5.6 0/1:58:13:7,6:19,26:0.2241:2,2:22.8:1:32.2:1:0.53517:1.58:41.9:26:0.2241:0.0345:3.8 -19 27736370 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=AGAGAGTTTAACTTTTCTTT;RSEQ=CATTCCGCAGTTTGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:21.1:1:29.4:1:1:0:34.7:22:1:0:5 0/1:58:2:1,1:23,33:0.0345:2,2:29.5:1:33:0:1:1.43:47:4:0.0351:0:5 -19 27736376 . C A 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17808;SOR=Inf;LSEQ=TTTAACTTTTCTTTTCATTC;RSEQ=GCAGTTTGGAAACACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:7,5:0,1:0.9231:0,2:20.8:1:28.8:1:0.46154:0:34.2:11:1:0:5 1/1:60:60:24,36:0,0:1:0,2:25.2:1:30.2:1:1:0:37.6:59:1:0:4.7 -19 27736379 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTTTTCTTTTCATTCCGC;RSEQ=GTTTGGAAACACTCTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:17.1:1:28.1:1:1:0:35.6:15:1:0:4.8 0/1:60:2:2,0:23,35:0.0333:2,0:6:1:29:1:0.16949:0:22.5:4:0.0345:0:6.5 -19 27736400 . T G 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.7886;LSEQ=GTTTGGAAACACTCTGTTTG;RSEQ=AAAGTCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:13:8,5:3,1:0.7647:2,2:26.4:1:29.8:1:1:1.81053:31.1:12:0.75:0:3.9 1/0:64:46:21,25:8,10:0.7188:2,2:29.6:1:30.5:1:1:1.05:40.4:22:0.7097:0:4.2 -19 27736411 . A C 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.14378;LSEQ=CTCTGTTTGTAAAGTCTGCA;RSEQ=GTGGATATTTTGACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:11,5:1,1:0.8889:2,2:29.7:1:31.1:1:1:2.10:33.3:32:0.8889:0:4.1 1/1:61:55:26,29:2,2:0.9016:2,2:27.5:1:30.4:1:1:1.11332:37:110:0.9016:0:4.4 -19 27736417 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTAAAGTCTGCAAGTGGA;RSEQ=ATTTTGACCTCTTTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:0:2,0:29.8:1:28.1:1:1:0:33.9:9:1:0:4 0/1:66:2:1,1:32,32:0.0303:2,2:31.5:1:30:1:1:1:23:4:0.0303:0:6.5 -19 27736419 . T A 78 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.67622;SOR=2.05146;LSEQ=GTAAAGTCTGCAAGTGGATA;RSEQ=TTTGACCTCTTTGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:1,0:12,9:0.0455:2,0:42:0:15:0:1:0:57:0:0:0:7 0/1:67:6:4,2:29,30:0.0896:2,2:16.3:1:30.3:1:0.67237:2.05:27.7:12:0.0909:0:5.2 -19 27736420 . T C 52 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TAAAGTCTGCAAGTGGATAT;RSEQ=TTGACCTCTTTGAGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:13,8:0.0455:2,0:30:0:33:0:0.40909:0:40:2:0.05:0:4 0/1:66:3:1,2:31,30:0.0455:2,2:33.7:1:33:1:1:2.0441:27:6:0.0469:0:5.7 -19 27736422 . T G 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15619;SOR=0.1605;LSEQ=AAGTCTGCAAGTGGATATTT;RSEQ=GACCTCTTTGAGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,8:0.0909:2,2:17:1:30.5:1:1:1.35399:35.5:4:0.1:0:5.5 0/1:65:1:1,0:31,33:0.0154:2,0:5:0:31:0:0.49231:0:37:2:0.0154:0:4 -19 27736424 . A G 33 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76433;LSEQ=GTCTGCAAGTGGATATTTTG;RSEQ=CCTCTTTGAGGCCTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:12,12:0.04:2,0:26:0:34:0:1:0:40:2:0.0455:0:4 0/1:65:2:1,1:31,31:0.0308:2,2:35:0:33:0:1:1:27:4:0.0308:0:4.5 -19 27736425 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGCAAGTGGATATTTTGA;RSEQ=CTCTTTGAGGCCTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:26.3:1:29.5:1:1:0:33.4:7.333:1:0:3.8 0/1:63:2:1,1:30,31:0.0317:2,2:36:1:28:1:1:1.03:25:4:0.0317:0:7 -19 27736427 . T A 111 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05796;SOR=6.89475;LSEQ=TGCAAGTGGATATTTTGACC;RSEQ=CTTTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:1,0:12,13:0.0385:2,0:50:0:16:0:1:0:57:0:0:0:7 0/1:64:14:8,6:23,27:0.2188:2,2:30.6:1:29.4:1:0.55165:1.55:26.6:28:0.2222:0:5.6 -19 27736431 . T A 124 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02729;SOR=5.2221;LSEQ=AGTGGATATTTTGACCTCTT;RSEQ=GAGGCCTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:0.0769:2,2:33:1:30:1:1:1:48.5:4:0.0833:0:5.5 0/1:62:19:10,9:20,23:0.3065:2,2:29.1:1:29.2:1:0.78445:1.27:29.1:38:0.3065:0:5.4 -19 27736440 . C G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGACCTCTTTGAGGCCTT;RSEQ=GTTGGAAACGGGTTTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:14,16:0:2,0:23.1:1:29.4:1:1:0:33.5:29:1:0:3.8 0/1:67:2:1,1:28,35:0.0299:2,2:28:0:30:1:1:1.25:31:4:0.0303:0:4 -19 27736448 . A G 34 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTGAGGCCTTCGTTGGAA;RSEQ=CGGGTTTTTTTCTTGTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:13,15:0:2,0:24.6:1:28.6:1:1:0:32.8:56:1:0:3.8 0/1:59:2:1,1:26,31:0.0339:2,2:11:0:34:0:1:1.19:27:4:0.0345:0:4.5 -19 27736452 . GT G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGGCCTTCGTTGGAAACGG;RSEQ=TTTTTTCTTGTAAGGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:26.1:1:28.7:1:1:0:31.7:25:1:0:3.7 0/1:56:2:0,2:25,29:0.0357:2,0:37:1:33:0:0.49675:0:33:4:0.0357:0:6 -19 27736461 . T A 151 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04576;SOR=0.12852;LSEQ=GTTGGAAACGGGTTTTTTTC;RSEQ=TGTAAGGCTAGACAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:26:11,15:1,0:0.963:0,2:25.4:1:30.2:1:0.44444:0:30.7:52:1:0:3.7 1/0:47:36:15,21:0,1:0.766:0,2:27.5:1:29.3:1:1:0:36.5:72:0.766:0:4.5 -19 27736472 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52074;SOR=Inf;LSEQ=GTTTTTTTCTTGTAAGGCTA;RSEQ=ACAGAAGAATTCTCAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:0:2,0:27.5:1:31:1:1:0:31.3:48:1:0:4 0/1:39:2:1,1:15,22:0.0513:2,2:18:1:31.5:1:1:1.45:25:4:0.0513:0:7 -19 27736474 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51921;SOR=Inf;LSEQ=TTTTTTCTTGTAAGGCTAGA;RSEQ=AGAAGAATTCTCAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:27.9:1:31.3:1:1:0:31.3:46:1:0:4 0/1:37:2:1,1:14,21:0.0541:2,2:34:0:32.5:1:1:1.48:49:4:0.0541:0:3 -19 27736478 . A G 73 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14652;SOR=Inf;LSEQ=TTCTTGTAAGGCTAGACAGA;RSEQ=GAATTCTCAGTAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:29.8:1:28.9:1:1:0:30.8:9:1:0:3.9 0/1:35:5:2,3:11,19:0.1429:2,2:33.4:1:31.6:1:1:1.15:32.6:10:0.1429:0:5.4 -19 27736482 . T A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38874;SOR=0.56014;LSEQ=TGTAAGGCTAGACAGAAGAA;RSEQ=TCTCAGTAACTTCCTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:5,8:2,4:0.6842:2,2:30.4:1:30.5:1:1:1.24:29.8:26:0.6842:0:3.6 1/0:33:18:6,12:5,10:0.5455:2,2:29.8:1:30.3:1:1:1:38.6:36:0.5455:0:4.2 -19 27736485 . T C 96 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03872;SOR=Inf;LSEQ=AAGGCTAGACAGAAGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:0:2,0:29.3:1:29.2:1:1:0:31.1:17:1:0:4 0/1:32:8:2,6:8,16:0.25:2,2:17.5:1:32.1:1:1:1.48185:37:16:0.25:0:4.6 -19 27736518 . C G 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62848;SOR=0.51884;LSEQ=TGTGTTGTGTGTATTCAACT;RSEQ=ACGGAGTTGAACGTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:1,7:1,1:0.8:2,2:18:1:32.1:1:0.37778:5.29155:33.8:16:0.8:0:4.5 1/0:9:6:1,5:1,2:0.6667:2,2:17.7:1:32.8:1:1:2.23609:38.7:12:0.6667:0:5.5 -19 27736521 . G A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GTTGTGTGTATTCAACTCAC;RSEQ=GAGTTGAACGTTCCTTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:1,6:1,1:0.7778:2,2:17.4:1:31.1:1:0.41667:4.58262:35.6:14:0.7778:0:4.7 1/1:9:9:2,7:0,0:1:0,2:13.3:1:32.1:1:1:0:37.1:18:1:0:5.2 -19 27736531 . G C 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03966;LSEQ=TTCAACTCACGGAGTTGAAC;RSEQ=TTCCTTTAGAGAGAGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:1,1:0.375:2,2:7:1:32:1:1:1.7321:34.7:6:0.375:0:5 0/1:13:5:1,4:0,1:0.3846:0,2:6.6:1:31.2:1:1:0:38.4:10:0.3846:0:5.6 -19 27736535 . C A 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12281;SOR=0;LSEQ=ACTCACGGAGTTGAACGTTC;RSEQ=TTTAGAGAGAGCAGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:3,2:0.2857:2,0:18.5:1:32.5:1:0.42857:0:32.5:4:0.2857:0:5 0/0:12:0:0,0:5,7:0:2,0:10.2:1:30.5:1:1:0:42.3:24:1:0:6.2 -19 27736542 . G A 86 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.08891;SOR=12.49706;LSEQ=GAGTTGAACGTTCCTTTAGA;RSEQ=AGAGCAGACTTGAAACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:1,3:0.2:2,0:14:0:31:0:0.4:0:50:2:0.2:0:6 1/1:10:8:4,4:0,0:0.8:0,2:19.6:1:28.9:1:1:0:47.4:16:0.8889:0:6.3 -19 27736544 . G C 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.11813;SOR=6.81901;LSEQ=GTTGAACGTTCCTTTAGAGA;RSEQ=AGCAGACTTGAAACTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:9:1:32:1:1:2.45:45:4:0.3333:0:6.5 1/1:10:8:4,4:1,1:0.8:2,2:21.6:1:30.5:1:1:1:47.4:16:0.8:0:6.3 -19 27736551 . C T 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61451;SOR=0.39984;LSEQ=GTTCCTTTAGAGAGAGCAGA;RSEQ=TTGAAACTCTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:1,2:0.5714:2,2:11.5:1:32.3:1:1:1.81:40.5:8:0.5714:0:5.3 0/1:9:3:2,1:0,0:0.3333:0,2:22.3:1:24:1:1:0:25:2:0.25:0:6.3 -19 27736591 . CA C 64 d7;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02098;SOR=0;LSEQ=GAATTTGCAAGTGGAGATTT;RSEQ=AGAGCTTTGTTGCCAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:42:1:32:1:1:0:40.5:8:1:0:5.3 0/1:9:2:1,1:4,3:0.2222:2,2:29:1:32.5:1:1:1.29098:53:4:0.25:0:6 -19 27736593 . AG A 81 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06993;SOR=Inf;LSEQ=ATTTGCAAGTGGAGATTTCA;RSEQ=AGCTTTGTTGCCAATGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:41.3:1:31.8:1:1:0:40.5:8:1:0:5.3 1/0:9:6:3,3:2,1:0.6667:2,2:27.5:1:31.5:1:1:1.8525:45.5:12:0.6667:0.1111:6.3 -19 27736602 . TT AG 90 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGATTTCAAGAGCTTTG;RSEQ=GCCAATGGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:32.3:1:30.8:1:1:0:40.5:8:1:0:4.3 1/1:8:7:3,4:0,0:0.875:0,2:23.1:1:32.3:1:1:0:48.4:14:1:0:5.1 -19 27736608 . A G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TTTCAAGAGCTTTGTTGCCA;RSEQ=TGGTAGAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27.3:1:30:1:1:0:40.5:8:1:0:4.3 0/1:8:2:1,1:3,3:0.25:2,2:19.5:1:33.5:1:1:1:27:4:0.25:0:5.5 -19 27736632 . C T 44 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAAAAGGAAATATCTTCG;RSEQ=ATAAAAACTAGACAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:5:1:28.3:1:1:0:37.3:6:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 27736686 . T A 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGTAGTGATGTGTGTGTTTA;RSEQ=CTCCCAGAGTTTAACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34:1:31.5:1:1:0:32.5:4:1:0:6 1/0:2:1:0,1:1,0:0.5:0,0:2:0:25:0:1:0:21:2:0.5:0:6 -19 27736690 . C A 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATGTGTGTGTTTATCTC;RSEQ=CAGAGTTTAACCTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:38:1:31.5:1:1:0:32.5:4:1:0:6 1/1:3:3:1,2:0,0:1:0,2:10:1:27.3:1:1:0:47:6:1:0:3.3 -19 27736716 . C A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAACCTTTCTTTTCATAC;RSEQ=GCATTCTGGAAACACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:19.6:1:30:1:1:0:38:16:1:0:4.6 1/1:9:9:1,8:0,0:1:0,2:21.3:1:30:1:1:0:47.2:18:1:0:3.3 -19 27736730 . A C 99 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21053;SOR=0;LSEQ=TCATACCGCATTCTGGAAAC;RSEQ=CTCTGTTTGTAAAGTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:5,4:0,0:1:0,2:25:1:31.3:1:1:0:36.1:18:1:0:4.4 1/0:10:7:0,7:1,2:0.7:2,0:29:1:30.9:1:0.3:0:47.4:14:0.7:0:3.7 -19 27736733 . C G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09228;SOR=0.18056;LSEQ=TACCGCATTCTGGAAACACT;RSEQ=TGTTTGTAAAGTCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:4,3:1,1:0.7778:2,2:28.3:1:32.7:1:1:1.29:32.1:14:0.7778:0:4.4 0/1:11:4:0,4:1,6:0.3636:2,0:30.8:1:30.5:1:1:0:43.5:8:0.3636:0:4.3 -19 27736781 . G T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TGGACCTCTTAGATGCCTTC;RSEQ=TTGGAAATGGGATTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:3,3:0.25:2,0:33:0:32:0:0.46429:0:45.5:4:0.25:0:4 0/0:7:0:0,0:0,7:0:0,0:21.3:1:32.4:1:1:0:45.3:14:1:0:3.7 -19 27736789 . T C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGATGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCATATAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:16.4:1:31.4:1:1:0:38:14:1:0:4 1/1:4:4:0,4:0,0:1:0,0:18.8:1:31:1:1:0:44:8:1:0:3.5 -19 27736884 . CA GT 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTGAACGTTCCTTTAGACA;RSEQ=GCAGATTTGAAACACTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:14.5:1:29.8:1:1:0:45:4:0.6667:0:3.5 -19 27736899 . A T 59 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGACACAGCAGATTTGAAAC;RSEQ=CTCTATTTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:13:1:29.8:1:1:1:43:8:0.6667:0:3.3 -19 27736902 . CTATT TGTC 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACAGCAGATTTGAAACACT;RSEQ=TGTGGAATTTGCAAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:47:0:32:0:1:0:21:2:1:0:6 0/1:6:2:1,1:2,2:0.3333:2,2:31.5:1:31.1:1:1:1:45:4:0.3333:0:2.5 -19 27736904 . A T 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAGATTTGAAACACTCT;RSEQ=TTTGTGGAATTTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:45:0:29:0:1:0:21:2:1:0:6 1/1:4:4:2,2:0,0:1:0,2:18:1:30.5:1:1:0:43:8:1:0:3.3 -19 27736952 . T C 34 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCGCTTTGAGGCCAACGG;RSEQ=AAAAAAGGTAATAAATTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:34:0:1:0:40:4:1:0:4.5 -19 27736954 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTTTGAGGCCAACGGTA;RSEQ=AAAAGGTAATAAATTCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:33.5:1:1:0:40:4:1:0:4.5 -19 27737211 . GT TG 83 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACTCACAGAGGTGAAC;RSEQ=TCCTTTAGACAGACAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:18:1:31.9:1:1:0:23:8:1:0:2.5 1/1:6:6:3,3:0,0:1:0,2:20.3:1:32.3:1:1:0:28.3:12:1:0:2.7 -19 27737226 . CAGATT GCAGATG 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TGAACGTTCCTTTAGACAGA;RSEQ=TGAAACACTCTTTTTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30.3:1:1:0:23:4:1:0:5 1/1:5:5:2,3:0,0:1:0,2:20.6:1:31.1:1:1:0:28:10:1:0.2:4 -19 27737238 . A C 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAGACAGACAGATTTGAAAC;RSEQ=CTCTTTTTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29.5:1:1:0:23:4:1:0:5 1/1:5:4:1,3:1,0:0.8:0,2:12:1:31:1:0.4:0:28.8:8:1:0:4.5 -19 27737428 . T C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCTGTTTATAAAGTCTG;RSEQ=AAGTGGATATTTTGACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:33:0:1:0:60:4:1:0:6 -19 27737436 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATAAAGTCTGTAAGTGGA;RSEQ=ATTTTGACCTCTTTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:33:1:1:0:60:4:1:0:6 -19 27737440 . TT CA 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTCTGTAAGTGGATATT;RSEQ=GACCTCTTTGAGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:32:0:1:0:60:4:1:0:5 -19 27737446 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAGTGGATATTTTGACC;RSEQ=CTTTGAGGCCTTCGTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:60:4:1:0:5 -19 27737486 . G C 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=AACGGGTTTTTTTCATGTAA;RSEQ=GCTAGACAGAAGAATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:22.5:1:31:1:1:1.73:60:4:0.4:0:2 0/0:11:0:0,0:6,5:0:2,0:20.2:1:32:1:1:0:38:22:1:0:3.6 -19 27737501 . T A 70 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09341;SOR=0;LSEQ=TGTAAGGCTAGACAGAAGAA;RSEQ=TCTCAGTAACTTCCTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:24.8:1:31.4:1:1:0:49.8:10:1:0:3.4 0/1:11:5:3,2:3,3:0.4545:2,2:35.4:1:30.4:1:1:1.45:35:10:0.4545:0:4 -19 27737504 . T C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGGCTAGACAGAAGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:25.4:1:31.6:1:1:0:49.8:10:1:0:3.4 0/1:11:2:1,1:5,4:0.1818:2,2:10:0:32.5:1:1:1.22474:30:4:0.2:0:1.5 -19 27737537 . C G 68 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49091;SOR=0;LSEQ=TGTGTTGTGTGTATTCAACT;RSEQ=ACAGATTTGAACGTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24:1:33.3:1:1:0:43:6:1:0:4.3 1/0:9:5:3,2:2,2:0.5556:2,2:23.4:1:29.6:1:1:1.43:35:10:0.5556:0:4 -19 27737539 . C G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTTGTGTGTATTCAACTCA;RSEQ=AGATTTGAACGTTCCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:22:1:34:0:1:0:43:6:1:0:4.3 0/1:9:2:1,1:4,3:0.2222:2,2:26:1:33.5:1:1:1.29098:44.5:4:0.2222:0:4.5 -19 27737541 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTGTGTATTCAACTCACA;RSEQ=ATTTGAACGTTCCTTTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:20:1:33:1:1:0:43:6:1:0:4.3 0/1:9:2:1,1:4,3:0.2222:2,2:21.5:1:30.5:1:1:1.29098:47:4:0.2222:0:4 -19 27737543 . T G 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTATTCAACTCACAGA;RSEQ=TTGAACGTTCCTTTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:18:1:33.7:1:1:0:43:6:1:0:4.3 1/1:9:9:5,4:0,0:1:0,2:18.9:1:30.6:1:1:0:39.8:18:1:0:4.1 -19 27737550 . G C 65 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=TTCAACTCACAGATTTGAAC;RSEQ=TTCCTTTAGACAGAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:11:1:33:0:1:0:43:6:1:0:4.3 1/0:9:5:3,2:2,2:0.5556:2,2:10.4:1:28:1:1:1.43:35:10:0.5556:0:4 -19 27737551 . T A 59 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=TCAACTCACAGATTTGAACG;RSEQ=TCCTTTAGACAGAGGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:10:1:31.7:1:1:0:43:6:1:0:4.3 0/1:9:4:2,2:3,2:0.4444:2,2:12.8:1:29.5:1:1:1.43328:45.8:8:0.4444:0:4.3 -19 27737559 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGATTTGAACGTTCCTTTA;RSEQ=ACAGAGGAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:0:32:1:1:0:48:4:1:0:4.5 0/1:7:2:1,1:2,1:0.2857:2,2:6:1:29.5:1:1:1.7321:44.5:4:0.2857:0:4.5 -19 27737604 . GAT AGAC 50 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=ATTGCGGAATTTGCAAGTGG;RSEQ=TTCAAGCGCTTTGAGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:0,0:0.6:0,2:10:1:31.6:1:1:0:48.3:6:0.6:0.4:3.3 -19 27737613 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAAGTGGGATTTCAAG;RSEQ=GCTTTGAGGCCAACGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:7:0:32:0:1:2.45:60:4:0.3333:0:1 -19 27737709 . C A 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGTGTGCGTTCACCTCA;RSEQ=GGACCTTAACCTTTCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:0:28:1:1:0:31:4:1:0:6.5 -19 27737713 . CC GT 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGCGTTCACCTCACGGA;RSEQ=TTAACCTTTCTTTTCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:0:31:1:1:0:31:4:1:0:5.5 -19 27737736 . C T 26 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACCTTTCTTTTCATAGAG;RSEQ=AGTTTGGAAACACTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:26:1:1:0:31:4:1:0:5.5 -19 27737889 . A T 72 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=TTCAACCCACAGAGATGAAC;RSEQ=TTCCTTTAGACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:10.6:1:31.4:1:1:0:45.6:10:1:0:6.4 -19 27737899 . AC A 73 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28571;SOR=Inf;LSEQ=AGAGATGAACATTCCTTTAG;RSEQ=AGAGCAGATTTCAAACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:14:0:33:0:1:0:60:2:1:0:5 1/1:6:5:3,2:0,1:0.8333:0,2:21.6:1:31.6:1:1:0:45.6:10:0.8333:0:6.4 -19 27737910 . T G 100 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=TTCCTTTAGACAGAGCAGAT;RSEQ=TCAAACACACTTTTTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14:1:29.5:1:1:0:59:4:1:0:4.5 1/0:12:8:6,2:1,3:0.6667:2,2:22.9:1:33.4:1:0.22222:7.22:44.9:16:0.6667:0:6.6 -19 27737912 . C T 93 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=CCTTTAGACAGAGCAGATTT;RSEQ=AAACACACTTTTTGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:16:1:33.5:1:1:0:59:4:1:0:4.5 1/0:12:8:6,2:0,0:0.6667:0,2:24.9:1:31:1:1:0:44.9:16:0.6667:0:6.6 -19 27737916 . C G 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TAGACAGAGCAGATTTCAAA;RSEQ=ACACTTTTTGTGGAATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:20:1:34:1:1:0:59:4:1:0:4.5 0/1:14:2:1,1:7,4:0.1429:2,2:13:0:29.5:1:1:1.67325:45:4:0.1429:0:7 -19 27737917 . A T 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.00833;SOR=0;LSEQ=AGACAGAGCAGATTTCAAAC;RSEQ=CACTTTTTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:32:0:1:0:59:4:1:0:4.5 0/0:14:0:0,0:8,5:0:2,0:23.5:1:30.8:1:1:0:44.5:26:1:0:6 -19 27737919 . A T 59 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.09804;SOR=0;LSEQ=ACAGAGCAGATTTCAAACAC;RSEQ=CTTTTTGTGGAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:32:0:1:0:59:4:1:0:4.5 0/1:16:4:1,3:1,1:0.25:2,2:12.3:1:29.5:1:1:2.44949:37.3:8:0.25:0:5 -19 27737927 . T G 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTTCAAACACACTTTTTG;RSEQ=GGAATTTGCAAGTGGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:22.3:1:31.3:1:1:0:54.7:6:1:0:5.7 0/1:20:2:1,1:10,8:0.1:2,2:24:0:29.5:1:1:1.23603:45:4:0.1:0:7 -19 27737932 . T G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAACACACTTTTTGTGGAA;RSEQ=TTGCAAGTGGAGATTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:17.2:1:31.4:1:1:0:50:10:1:0:5.4 0/1:22:2:1,1:11,9:0.0909:2,2:14:1:31:1:1:1.21106:60:4:0.0909:0:6.5 -19 27737938 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13504;SOR=0.15852;LSEQ=CACTTTTTGTGGAATTTGCA;RSEQ=GTGGAGATTTCAAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:8:0:33:0:1:1:43:4:0.4:0:5 0/1:23:2:1,1:1,3:0.087:2,2:8:0:33:1:1:2.45:48:4:0.087:0:4.5 -19 27737943 . A G 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGTGGAATTTGCAAGTGG;RSEQ=GATTTCAAGCGCTTTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:25.6:1:31.8:1:1:0:50:10:1:0:5.2 0/1:28:2:1,1:13,13:0.0714:2,2:40:0:30.5:1:1:1:45:4:0.0714:0:7 -19 27737959 . G T 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57018;SOR=0.40423;LSEQ=GTGGAGATTTCAAGCGCTTT;RSEQ=AGGCCAATTGTAGAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:29:0:30.5:1:1:1.73:43:4:0.4:0:5 0/1:29:6:3,3:11,12:0.2069:2,2:23.2:1:29.3:1:1:1.09:54:12:0.2069:0:2.8 -19 27737960 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAGATTTCAAGCGCTTTG;RSEQ=GGCCAATTGTAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:32.4:1:30.8:1:1:0:50:10:1:0:5.2 0/1:28:2:1,1:13,13:0.0714:2,2:37:0:31:1:1:1:60:4:0.0714:0:6.5 -19 27737963 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGATTTCAAGCGCTTTGAGG;RSEQ=CAATTGTAGAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:33:1:32:1:1:0:50:10:1:0:5.2 0/1:24:2:1,1:10,12:0.0833:2,2:27.5:1:30:1:1:1.19:48:4:0.0833:0:4.5 -19 27737965 . A T 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6169;SOR=2.88746;LSEQ=ATTTCAAGCGCTTTGAGGCC;RSEQ=ATTGTAGAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:43:0:30:0:1:0:46:2:0.2:0:7 0/1:21:9:4,5:5,7:0.4286:2,2:17:1:30.6:1:1:1.11:38.3:18:0.4286:0:6.2 -19 27737966 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCAAGCGCTTTGAGGCCA;RSEQ=TTGTAGAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:33.4:1:30.4:1:1:0:50:10:1:0:5.2 0/1:19:2:1,1:7,10:0.1053:2,2:31:0:33:1:1:1.40:60:4:0.1053:0:6.5 -19 27737967 . TT CG 86 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61462;SOR=0.40522;LSEQ=TTCAAGCGCTTTGAGGCCAA;RSEQ=GTAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,0:0.6:0,2:29.7:1:30.7:1:1:0:54.7:6:0.6:0:4.3 0/1:19:7:3,4:1,3:0.3684:2,2:22.9:1:30.9:1:1:2.09:40.7:14:0.3684:0:6.4 -19 27737968 . T G 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54404;SOR=Inf;LSEQ=TCAAGCGCTTTGAGGCCAAT;RSEQ=GTAGAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,1:0:2,0:38:0:32:0:1:0:43:4:1:0:5 0/1:19:4:1,3:3,3:0.2105:2,2:22.3:1:32:1:0.57143:2.68677:44:8:0.4:0:5.5 -19 27737977 . G T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGAGGCCAATTGTAGAAAA;RSEQ=GAAATATCTTCGTATAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:24.6:1:31.6:1:1:0:50:10:1:0:4.6 0/1:18:2:1,1:7,9:0.1111:2,2:20:0:32:0:1:1.27:60:4:0.1111:0:6.5 -19 27737982 . T C 77 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.77078;LSEQ=GCCAATTGTAGAAAAGGAAA;RSEQ=ATCTTCGTATAAAAGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:27:0:34:0:1:0:46:2:0.2:0:6 0/1:16:5:1,4:5,6:0.3125:2,2:26.2:1:33.2:1:0.58791:3.10368:38.6:10:0.3571:0:6.4 -19 27737989 . G T 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=0.26046;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=TATAAAAGCTAGACAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:19:1:31:1:1:0:44:6:0.75:0:5.3 0/1:12:5:1,4:3,4:0.4167:2,2:21.2:1:32.2:1:0.57576:2.74155:38.6:10:0.4167:0:6.4 -19 27737990 . T A 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=Inf;LSEQ=TAGAAAAGGAAATATCTTCG;RSEQ=ATAAAAGCTAGACAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:15.3:1:29.5:1:1:0:47.5:8:1:0:4.8 0/1:10:3:2,1:2,5:0.3:2,2:5:1:29:1:0.5:4.17:46:6:0.3:0:5.7 -19 27737997 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GGAAATATCTTCGTATAAAA;RSEQ=CTAGACAGAATGATTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:10.5:1:29:1:1:0:43:4:0.6667:0:5 0/0:3:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 27738009 . G C 52 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATAAAAGCTAGACAGAAT;RSEQ=ATTCCCAGAAACTGCGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:1:0,0:14:0:33.3:1:1:0:36.3:6:1:0:7 -19 27738014 . C A 50 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCTAGACAGAATGATTC;RSEQ=CAGAAACTGCGTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:1:0,0:9:0:31.7:1:1:0:36.3:6:1:0:7 -19 27738034 . T G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCAGAAACTGCGTTGTGATG;RSEQ=GTGCGTTCAAGTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:6:0:32:0:1:0:36:2:1:0:8 1/0:3:2:1,1:0,1:0.6667:0,2:9:0:32.5:1:1:0:41:4:0.6667:0:4.5 -19 27738045 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGTGATGTGTGCGTTCAA;RSEQ=TCACAGAGTTTAACTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:20:0:33:1:1:0:41:4:1:0:4.5 -19 27738051 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTGTGCGTTCAAGTCACA;RSEQ=AGTTTAACTTTTCTTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:23:0:33:0:1:0:36:2:1:0:7 1/0:3:2:1,1:0,1:0.6667:0,2:26:0:31.5:1:1:0:41:4:0.6667:0:4.5 -19 27738072 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTTAACTTTTCTTTTCAT;RSEQ=GAGCAGTTTGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:8.5:1:29:1:1:0:41:4:0.6667:0:4.5 -19 27738359 . T A 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACAGAATCATTCCCACA;RSEQ=AGTGCGTTGTTATGTGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:29.5:1:1:0:60:4:1:0:1.5 -19 27738400 . TA CT 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0119;SOR=0;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTCTTTTCATAGAGCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:6:1:31.8:1:1:0:43:6:1:0.6667:3.3 0/0:6:0:0,0:2,2:0:2,0:19.3:1:28:1:1:0:41.5:8:0.6667:0:2.8 -19 27738401 . A T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACTCACAGAGTTTAACT;RSEQ=TTCTTTTCATAGAGCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:1,1:0.3333:2,2:19:1:28.5:1:1:1:23:4:0.5:0:4 -19 27738411 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10417;SOR=0;LSEQ=GAGTTTAACTATTCTTTTCA;RSEQ=AGAGCAGTTAGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,0:0.1818:0,2:10.5:1:31:1:0.22222:0:54.5:4:0.1818:0:3 0/0:22:0:0,0:17,5:0:2,0:10.4:1:29.3:1:1:0:43.6:44:1:0:3.1 -19 27738417 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53131;SOR=Inf;LSEQ=AACTATTCTTTTCATAGAGC;RSEQ=GTTAGGAAACACTCTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:12,4:0:2,0:10.6:1:29.8:1:1:0:45.9:15:1:0:3.9 0/1:29:2:1,1:20,7:0.069:2,2:35:1:29:1:0.48276:2.73861:23:4:0.069:0:4 -19 27738426 . A T 51 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17969;SOR=0.25549;LSEQ=TTTCATAGAGCAGTTAGGAA;RSEQ=CACTCTGTTTGTAAAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:16,5:0.16:2,2:17.3:1:25.5:1:0.54846:3.03008:50.5:3:0.125:0:4.8 0/1:44:2:0,2:30,12:0.0455:2,0:1:0:24.5:1:0.09619:0:40.5:4:0.0455:0:4 -19 27738433 . G C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54133;SOR=Inf;LSEQ=GAGCAGTTAGGAAACACTCT;RSEQ=TTTGTAAAGTCTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:22,9:0:2,0:17.5:1:32.2:1:1:0:47.5:62:0.9688:0:3.8 0/1:60:2:1,1:36,21:0.0333:2,2:24:1:33.5:1:1:1.6979:46.5:4:0.0339:0:4 -19 27738434 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5461;SOR=Inf;LSEQ=AGCAGTTAGGAAACACTCTG;RSEQ=TTGTAAAGTCTGCAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:23,9:0:2,0:18.6:1:29.6:1:1:0:46.7:31:1:0:3.9 0/1:62:2:2,0:35,24:0.0323:2,0:30:1:33.5:1:0.51475:0:43:4:0.0333:0:5 -19 27738437 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTAGGAAACACTCTGTTT;RSEQ=TAAAGTCTGCAAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:23,9:0:2,0:21.6:1:32:1:1:0:46.7:31:1:0:3.9 0/1:71:2:1,1:41,28:0.0282:2,2:11.5:1:29.5:1:1:1.45623:48:4:0.0286:0:4.5 -19 27738438 . T G 69 v4;Bias;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32152;SOR=Inf;LSEQ=GTTAGGAAACACTCTGTTTG;RSEQ=AAAGTCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:23,10:0:2,0:22:1:29.3:1:1:0:46.2:32:1:0:3.8 0/1:73:5:0,5:43,25:0.0685:2,0:9.4:1:29.8:1:0.00949:0:42.6:10:0.0694:0:2.8 -19 27738445 . T C 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81103;LSEQ=AACACTCTGTTTGTAAAGTC;RSEQ=GCAAGTGGATATTTTGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:0,1:25,9:0.0286:2,0:26:0:24:0:0.28571:0:45:2:0.0286:0:4 0/1:86:2:1,1:50,34:0.0233:2,2:19:1:29:1:1:1.46382:50:4:0.0233:0:4 -19 27738449 . A C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30206;SOR=0.59704;LSEQ=CTCTGTTTGTAAAGTCTGCA;RSEQ=GTGGATATTTTGACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:8:4,4:23,7:0.2105:2,2:23.4:1:29.9:1:0.19496:3.16866:46.4:16:0.2222:0:3.9 0/1:95:13:4,9:52,29:0.1368:2,2:21.8:1:29.4:1:0.03257:3.97192:37.8:26:0.1413:0:3.8 -19 27738455 . T G 32 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78567;LSEQ=TTGTAAAGTCTGCAAGTGGA;RSEQ=ATTTTGACCTCTTTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:0,1:28,12:0.0244:2,0:36:0:30:0:0.31707:0:45:2:0.0244:0:4 0/1:104:2:1,1:58,42:0.0192:2,2:29:1:32.5:1:1:1.3765:50:4:0.0196:0:4 -19 27738457 . T A 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57737;SOR=Inf;LSEQ=GTAAAGTCTGCAAGTGGATA;RSEQ=TTTGACCTCTTTGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:28,13:0:2,0:32.8:1:30.9:1:1:0:45:40:1:0:4 0/1:104:4:2,2:58,42:0.0385:2,2:25.8:1:29.5:1:1:1.37658:36:8:0.0388:0:4.8 -19 27738458 . T C 106 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50984;SOR=2.06552;LSEQ=TAAAGTCTGCAAGTGGATAT;RSEQ=TTGACCTCTTTGAGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:26,11:0.0488:2,2:8:0:33:1:0.52632:2.30614:45:4:0.0488:0:4.5 0/1:104:10:5,5:54,38:0.0962:2,2:26.7:1:32.2:1:0.73895:1.41605:32.6:20:0.099:0:5.1 -19 27738459 . TT CA 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.85365;SOR=0.90849;LSEQ=AAAGTCTGCAAGTGGATATT;RSEQ=GACCTCTTTGAGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:30:24,6:6,8:0.6667:2,2:33.2:1:31.4:1:0.03409:5.10:43.4:60:0.6667:0.0889:3.1 1/0:107:69:45,24:12,19:0.6449:2,2:28.3:1:30.8:1:0.01684:2.93:42.3:138:0.6571:0.028:3.3 -19 27738461 . G C 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.27586;LSEQ=AGTCTGCAAGTGGATATTTT;RSEQ=ACCTCTTTGAGGCCTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:0,1:31,14:0.0213:2,0:42:0:14:0:0.32609:0:45:0:0:0:4 0/1:111:3:1,2:63,45:0.027:2,2:37:1:32.7:1:0.57283:2.77416:44.3:6:0.0275:0:3.7 -19 27738462 . A G 107 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.512;SOR=2.21814;LSEQ=GTCTGCAAGTGGATATTTTG;RSEQ=CCTCTTTGAGGCCTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:31,14:0.0426:2,2:12:0:33:1:0.54117:2.17347:45:4:0.0435:0:4.5 0/1:111:10:5,5:57,40:0.0901:2,2:30.7:1:32.3:1:0.73933:1.42018:32.6:20:0.0901:0:5.1 -19 27738465 . T A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02924;LSEQ=TGCAAGTGGATATTTTGACC;RSEQ=CTTTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:3,3:31,14:0.1176:2,2:38.3:1:29.7:1:0.38713:2.17709:46.3:12:0.125:0:4.2 0/1:116:14:7,7:62,40:0.1207:2,2:26.6:1:28.9:1:0.56348:1.54395:40.6:13:0.115:0:3.7 -19 27738469 . T A 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.67029;SOR=1.30877;LSEQ=AGTGGATATTTTGACCTCTT;RSEQ=GAGGCCTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:8:4,4:30,15:0.1509:2,2:36.5:1:30.4:1:0.43631:1.97245:46:16:0.1538:0:4.3 0/1:127:24:12,12:62,40:0.189:2,2:32.4:1:29.3:1:0.36359:1.54444:37.3:23:0.184:0:4.3 -19 27738470 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGATATTTTGACCTCTTT;RSEQ=AGGCCTTCGTTGGAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:34,19:0:2,0:30.7:1:32.4:1:1:0:44.5:106:1:0:3.3 0/1:129:2:1,1:75,52:0.0155:2,2:30.5:1:29:1:1:1.4381:53.5:4:0.0156:0:4.5 -19 27738474 . C T 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20149;SOR=0.19973;LSEQ=ATATTTTGACCTCTTTGAGG;RSEQ=CTTCGTTGGAAACGGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:2,0:33,20:0.0364:2,0:35:0:32:0:0.52862:0:40.5:4:0.037:0:5.5 0/0:135:1:1,0:77,57:0.0074:2,0:9:0:29:0:1:0:40:2:0.0076:0:6 -19 27738477 . T G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08806;SOR=0;LSEQ=TTTTGACCTCTTTGAGGCCT;RSEQ=CGTTGGAAACGGGTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:35,23:0.0333:2,2:24.5:1:33:1:1:1.51079:54.5:4:0.0339:0:3 0/0:141:0:0,0:80,61:0:2,0:27.7:1:29.5:1:1:0:43.2:69.5:1:0:3.5 -19 27738479 . G A 51 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02507;SOR=0;LSEQ=TTGACCTCTTTGAGGCCTTC;RSEQ=TTGGAAACGGGTTTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:2,1:34,24:0.0492:2,2:13.3:1:32.7:1:1:1.40:36.3:6:0.05:0:5.7 0/0:145:0:0,0:82,61:0:2,0:27.1:1:30.4:1:1:0:43.3:70.5:0.986:0:3.5 -19 27738480 . T C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08501;SOR=0;LSEQ=TGACCTCTTTGAGGCCTTCG;RSEQ=TGGAAACGGGTTTTTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:35,24:0.0328:2,2:32:1:33.5:1:1:1.44911:50.5:4:0.0339:0:4 0/0:147:0:0,0:83,62:0:2,0:27.1:1:29.3:1:1:0:43.1:290:0.9864:0:3.5 -19 27738481 . T C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.82839;LSEQ=GACCTCTTTGAGGCCTTCGT;RSEQ=GGAAACGGGTTTTTTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:36,24:0.0164:2,0:31:0:10:0:0.40984:0:59:0:0:0:4 0/1:147:2:1,1:83,62:0.0136:2,2:35.5:1:29:1:1:1.336:48.5:4:0.0139:0:3.5 -19 27738486 . ACGGGT GCGGG 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTGAGGCCTTCGTTGGAA;RSEQ=TTTTTTCATGTAAGGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:37,27:0:2,0:24.6:1:29.4:1:1:0:43.6:63:1:0:3.7 0/1:156:2:1,1:86,68:0.0128:2,2:35.5:1:30.5:1:1:1.26278:31:4:0.013:0:7 -19 27738490 . GT G 124 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.28511;SOR=2.23095;LSEQ=GAGGCCTTCGTTGGAAACGG;RSEQ=TTTTTTCATGTAAGGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:3:2,1:36,27:0.0448:2,2:28.7:1:31.7:1:1:1.49:44.3:6:0.0469:0:4.7 0/1:158:15:7,8:80,59:0.0949:2,2:25.6:1:31.9:1:0.42764:1.54513:37:30:0.098:0:4.1 -19 27738493 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTTCGTTGGAAACGGGTT;RSEQ=TTTTCATGTAAGGCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:37,29:0:2,0:23.4:1:29.8:1:1:0:43.1:65:1:0:3.7 0/1:161:2:1,1:89,70:0.0124:2,2:37:1:32:1:1:1.26951:25:4:0.0125:0:5.5 -19 27738497 . T G 34 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08109;SOR=0;LSEQ=TCGTTGGAAACGGGTTTTTT;RSEQ=CATGTAAGGCTAGACAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:35,28:0.0308:2,2:16:0:34:0:1:1.24568:46:4:0.0317:0:5.5 0/0:162:0:0,0:89,72:0:2,0:23.7:1:29.5:1:1:0:43.3:79.5:0.9938:0:3.8 -19 27738498 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08109;SOR=0;LSEQ=CGTTGGAAACGGGTTTTTTT;RSEQ=ATGTAAGGCTAGACAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:35,28:0.0308:2,2:24:0:31:1:1:1.24568:44:4:0.0317:0:5.5 0/0:162:0:0,0:90,72:0:2,0:23.5:1:31:1:1:0:43.4:39.5:1:0:3.8 -19 27738499 . A C 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57965;SOR=Inf;LSEQ=GTTGGAAACGGGTTTTTTTC;RSEQ=TGTAAGGCTAGACAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:36,29:0:2,0:22.5:1:29:1:1:0:43.2:12:1:0:3.7 0/1:164:4:2,2:89,69:0.0244:2,2:20:1:31.3:1:1:1.2878:42.3:8:0.025:0:5 -19 27738501 . G A 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24207;SOR=1.47111;LSEQ=TGGAAACGGGTTTTTTTCAT;RSEQ=TAAGGCTAGACAGAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:45:27,18:6,10:0.6923:2,2:23.8:1:28:1:0.15081:2.46:42.1:90:0.7031:0:3.7 1/0:164:126:76,50:15,22:0.7683:2,2:24.4:1:28.2:1:0.03921:2.22:44.3:41:0.7688:0:3.8 -19 27738503 . A C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.76946;SOR=0.80358;LSEQ=GAAACGGGTTTTTTTCATGT;RSEQ=AGGCTAGACAGAAGAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:5:3,2:30,29:0.0781:2,2:27.4:1:28.4:1:1:1.44:46.2:4:0.0645:0:4.4 0/1:157:10:5,5:80,63:0.0637:2,2:25.7:1:28.8:1:0.7517:1.26783:44.1:9:0.0596:0:4.2 -19 27738505 . G A 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.83517;LSEQ=AACGGGTTTTTTTCATGTAA;RSEQ=GCTAGACAGAAGAATTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:32,31:0.0308:2,2:38.5:1:30:1:1:1.03176:39:4:0.0308:0:5 0/1:155:4:2,2:84,65:0.0258:2,2:24.8:1:30.8:1:1:1.29011:43.5:8:0.0261:0:5 -19 27738507 . C T 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72677;SOR=1.73031;LSEQ=CGGGTTTTTTTCATGTAAGG;RSEQ=TAGACAGAAGAATTCTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:31,31:0.0313:2,2:9.5:1:30:1:1:1:45:4:0.0313:0:4.5 0/1:151:8:4,4:78,60:0.053:2,2:8.1:1:31.1:1:0.73014:1.29763:33:16:0.0544:0:4.6 -19 27738512 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTTTCATGTAAGGCTAGA;RSEQ=AGAAGAATTCTTAGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:29,29:0:2,0:22.7:1:30.9:1:1:0:42.2:18.333:1:0:4.1 0/1:141:2:1,1:75,64:0.0142:2,2:31:1:32:1:1:1.17055:50:4:0.0144:0:5 -19 27738516 . A G 62 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.5713;LSEQ=TTCATGTAAGGCTAGACAGA;RSEQ=GAATTCTTAGTAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:0,1:24,26:0.0196:2,0:1:0:31:0:1:0:45:2:0.02:0:5 0/1:131:4:2,2:68,59:0.0305:2,2:8.8:1:31.3:1:1:1.15129:39:8:0.0308:0:6.3 -19 27738518 . A G 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32419;SOR=Inf;LSEQ=CATGTAAGGCTAGACAGAAG;RSEQ=ATTCTTAGTAACTTCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:0:2,0:25.7:1:29.5:1:1:0:41.3:48:1:0:4.3 0/1:128:5:2,3:65,58:0.0391:2,2:23.6:1:31.2:1:0.66864:1.67425:39.8:10:0.0397:0:4.4 -19 27738523 . TT CC 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41045;SOR=0.53539;LSEQ=AAGGCTAGACAGAAGAATTC;RSEQ=AGTAACTTCCTTGTGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:39:18,21:0,1:0.9286:0,2:27.7:1:30.8:1:1:0:40.1:78:0.9286:0.119:3.7 1/1:127:111:58,53:2,2:0.874:2,2:24.4:1:30.1:1:1:1.09:41.8:222:0.888:0.1811:3.8 -19 27738524 . T C 82 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6759;SOR=2.19392;LSEQ=AGGCTAGACAGAAGAATTCT;RSEQ=AGTAACTTCCTTGTGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:1:0,1:0,0:0.027:0,0:45:0:31:0:1:0:40:2:1:0:4 0/1:104:6:3,3:1,1:0.0577:2,2:14:1:32:1:1:1:35.3:12:0.75:0:4 -19 27738530 . C A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAGAAGAATTCTTAGTAA;RSEQ=TTCCTTGTGTTGTGTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:15,23:0:2,0:28.3:1:31.7:1:1:0:39.4:76:0.9744:0:4 0/1:122:2:1,1:58,62:0.0164:2,2:31.5:1:28.5:1:1:1.07:42:4:0.0165:0:7 -19 27738531 . T C 61 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29714;LSEQ=ACAGAAGAATTCTTAGTAAC;RSEQ=TCCTTGTGTTGTGTGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:1:1,0:14,24:0.0256:2,0:42:0:33:0:0.38462:0:26:2:0.0263:0:5 0/1:121:4:1,3:58,59:0.0331:2,2:19.3:1:30.5:1:0.61915:2.9253:36.5:8:0.0339:0:6 -19 27738546 . GTG ACA 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTAACTTCCTTGTGTTGTGT;RSEQ=TTCAACTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:12,25:0:2,0:23.5:1:32.4:1:1:0:39.6:74:0.9737:0:4.2 0/1:116:2:1,1:53,61:0.0172:2,2:29.5:1:28.5:1:1:1.15:36:4:0.0177:0:4.5 -19 27738556 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTGTTGTGTGTGTTCAACT;RSEQ=ACAGAGTTGAACGTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:10,27:0:2,0:19.3:1:31.7:1:1:0:38.5:74:0.9737:0:4.4 0/1:103:2:1,1:45,55:0.0194:2,2:18.5:1:30:1:1:1.22:38.5:4:0.0194:0:4 -19 27738557 . A T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55997;SOR=Inf;LSEQ=GTGTTGTGTGTGTTCAACTC;RSEQ=CAGAGTTGAACGTTTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:11,28:0:2,0:18.2:1:29.7:1:1:0:38.2:78:1:0:4.5 0/1:101:3:1,2:44,54:0.0297:2,2:8:1:28.7:1:1:1.62208:50:6:0.0297:0:4.3 -19 27738561 . A T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTGTGTGTTCAACTCACAG;RSEQ=GTTGAACGTTTCTTTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:7,25:0:2,0:20.3:1:31.4:1:1:0:37.4:64:1:0:4.8 0/1:94:2:1,1:40,52:0.0213:2,2:8:0:31.5:1:1:1.30:45:4:0.0217:0:5 -19 27738569 . G T 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.39723;SOR=2.01988;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTTCTTTAGACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:18:4,14:0,2:0.8571:0,2:29.8:1:30.3:1:1:0:37.3:36:0.8571:0:6.2 1/1:53:49:19,30:0,2:0.9245:0,2:33.3:1:30.2:1:0.52314:0:34.8:48:0.9412:0:6 -19 27738572 . TC CA 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78691;SOR=1.21872;LSEQ=AACTCACAGAGTTGAACGTT;RSEQ=TTTAGACAGAGCAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:2,10:1,0:0.6:0,2:32.1:1:31.2:1:0.23077:0:37.6:24:0.6316:0:5.2 1/0:51:33:11,22:0,1:0.6471:0,2:33.2:1:31.1:1:1:0:33.9:66:0.66:0:5.3 -19 27738578 . G C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17702;SOR=5.70401;LSEQ=CAGAGTTGAACGTTTCTTTA;RSEQ=ACAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:17:3,14:1,1:0.8947:2,2:30.4:1:32.5:1:0.38596:4.1833:38:34:0.8947:0:5.4 1/1:51:50:18,32:0,0:0.9804:0,2:30.6:1:31.3:1:1:0:33.8:49:0.98:0:5.2 -19 27738580 . C A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTTGAACGTTTCTTTAGA;RSEQ=AGAGCAGATTTGAAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:3,16:0:2,0:27.7:1:32.2:1:1:0:37.8:38:0.95:0:5.4 0/1:51:2:1,1:16,32:0.0392:2,2:37:1:32:0:1:1.97:22:4:0.04:0:5.5 -19 27738591 . T G 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22682;LSEQ=TTCTTTAGACAGAGCAGATT;RSEQ=GAAACACTGTTTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:3,13:0.1111:2,0:39:1:31:1:1:0:22:4:0.1111:0:5 0/1:45:6:2,4:11,28:0.1333:2,2:22:1:29.5:1:1:1.27:29.3:12:0.1333:0:6.2 -19 27738600 . G C 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGCAGATTTGAAACACT;RSEQ=TTTTTGTGGAATTTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:3,15:0,0:1:0,2:22:1:32.2:1:1:0:36.4:36:1:0:5.5 1/1:41:40:9,31:0,0:0.9756:0,2:22:1:32.3:1:1:0:33.9:80:1:0:5.2 -19 27738619 . G A 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16541;SOR=0.24089;LSEQ=TGTTTTTGTGGAATTTGCAA;RSEQ=TGGAGATTTCAAGCGATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:0,4:1,6:0.3333:2,0:18.8:1:31.5:1:1:0:42:8:0.3333:0:5.8 0/1:29:3:0,3:5,21:0.1034:2,0:11.7:1:30.7:1:1:0:41.7:6:0.1034:0:5.7 -19 27738635 . A C 114 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07353;SOR=Inf;LSEQ=GCAAGTGGAGATTTCAAGCG;RSEQ=TTTAAGGTCAATGGCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:1,1:0.6:2,0:35.3:1:34:1:0.4:0:36.7:6:0.6:0:5.3 1/1:12:12:1,11:0,0:1:0,2:24.3:1:31.8:1:1:0:33.5:24:1:0:5.8 -19 27738639 . A G 100 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAGATTTCAAGCGATTT;RSEQ=AGGTCAATGGCAGAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:34.8:1:32.8:1:1:0:36.5:8:1:0:5.5 1/1:9:9:0,9:0,0:1:0,0:29.9:1:31.8:1:1:0:34.7:18:1:0:6.1 -19 27738643 . T C 83 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36364;SOR=Inf;LSEQ=AGATTTCAAGCGATTTAAGG;RSEQ=CAATGGCAGAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:41:1:33:1:1:0:35.3:6:0.75:0:5.3 1/1:7:7:0,7:0,0:1:0,0:35.6:1:29.7:1:1:0:33.1:6:1:0:6 -19 27738647 . T A 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36364;SOR=Inf;LSEQ=TTCAAGCGATTTAAGGTCAA;RSEQ=GGCAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:37:1:32.7:1:1:0:35.3:6:0.75:0:5.3 1/1:7:7:0,7:0,0:1:0,0:31.7:1:32.1:1:1:0:33.1:14:1:0:6 -19 27738863 . T C 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=AAGGCACGACAGAAGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:14:0:33:0:1:0:21:2:0.3333:0:6 0/1:9:3:2,1:4,2:0.3333:2,2:8.3:1:29:1:1:1:27:6:0.3333:0:5.7 -19 27738868 . A G 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55944;SOR=0.36341;LSEQ=ACGACAGAAGAATTCTCAGT;RSEQ=ACTTCCTTGTGTTGTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:19:0:33:0:1:0:39:4:0.6667:0:6 0/1:10:4:2,2:4,2:0.4:2,2:22.8:1:33:1:1:1.86195:54.5:8:0.4:0:7 -19 27738870 . C A 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55944;SOR=0.36341;LSEQ=GACAGAAGAATTCTCAGTAA;RSEQ=TTCCTTGTGTTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21:0:32:1:1:0:39:4:0.6667:0:6 0/1:10:4:2,2:4,2:0.4:2,2:24.8:1:31.5:1:1:1.86195:54.5:8:0.4:0:7 -19 27738874 . C T 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.15267;LSEQ=GAAGAATTCTCAGTAACTTC;RSEQ=TTGTGTTGTGTGTATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:25:0:32:0:1:0:39:4:0.6667:0:6 1/0:10:7:4,3:2,1:0.7:2,2:24:1:32.1:1:1:1.44135:47.6:14:0.7:0:7 -19 27738877 . G C 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.68659;LSEQ=GAATTCTCAGTAACTTCCTT;RSEQ=TGTTGTGTGTATTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:0:33:1:1:1:39:4:0.5:0:6 0/1:10:4:2,2:4,2:0.4:2,2:30.5:1:32.8:1:1:1.86195:54.5:8:0.4:0:7 -19 27738880 . T TG 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68659;LSEQ=TTCTCAGTAACTTCCTTGTG;RSEQ=TGTGTGTATTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:32:0:33.5:1:1:1:39:4:0.5:0:6 0/1:10:4:2,2:2,1:0.4:2,2:32.5:1:32.5:1:1:1.81007:54.5:8:0.4:0:7.3 -19 27738888 . A T 28 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10145;SOR=0;LSEQ=AACTTCCTTGTGTTGTGTGT;RSEQ=TTCAACTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:26.5:1:28.5:1:1:1:21:4:0.2857:0:5.5 0/0:16:0:0,0:6,7:0:2,0:21:1:28.8:1:1:0:47.7:26:0.8125:0:5.6 -19 27738898 . C T 57 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26893;SOR=Inf;LSEQ=TGTTGTGTGTATTCAACTCA;RSEQ=AGAGTTGAACGTTCCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:27.1:1:32:1:1:0:26.4:16:1:0:5.4 0/1:17:4:2,2:6,7:0.2353:2,2:33.3:1:28.5:1:1:1.16:36.5:8:0.2353:0:7 -19 27738909 . G T 84 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40179;SOR=2.56643;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTCCTTTAGACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,2:0.25:2,2:36:1:30.5:1:1:1.41418:21:4:0.25:0:5.5 0/1:17:8:4,4:4,5:0.4706:2,2:32.9:1:28.3:1:1:1.23:31.8:7:0.4375:0:6.1 -19 27738913 . C A 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.92606;LSEQ=ACTCACAGAGTTGAACGTTC;RSEQ=TTTAGACAGAGCAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:36:1:30.5:1:1:1:21:4:0.25:0:5.5 0/1:17:4:2,2:6,7:0.2353:2,2:27.3:1:28:1:1:1.16:27:8:0.25:0:5.3 -19 27738918 . G C 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92606;LSEQ=CAGAGTTGAACGTTCCTTTA;RSEQ=ACAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:36:1:32.5:1:1:1:21:4:0.25:0:5.5 0/1:17:4:2,2:6,7:0.2353:2,2:24.8:1:28.5:1:1:1.16:27:8:0.2353:0:5.3 -19 27738919 . AC A 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26893;SOR=Inf;LSEQ=AGAGTTGAACGTTCCTTTAG;RSEQ=AGAGCAGATTTGAAACACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,3:0:2,0:29.3:1:31:1:1:0:26.6:14:0.875:0:5 0/1:17:4:2,2:6,7:0.2353:2,2:34.8:1:30:1:1:1.16:36.5:8:0.2353:0:7 -19 27738925 . C T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67919;SOR=0.6129;LSEQ=GAACGTTCCTTTAGACAGAG;RSEQ=AGATTTGAAACACGCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:0.625:2,2:22.2:1:27.4:1:1:2.60:28.8:10:0.625:0:4.8 1/0:16:8:3,5:4,4:0.5:2,2:24.6:1:28.3:1:1:1.61372:54.3:16:0.5:0:4.6 -19 27738930 . T G 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.26219;SOR=Inf;LSEQ=TTCCTTTAGACAGAGCAGAT;RSEQ=TGAAACACGCTTTTTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:24:1:30.3:1:1:0:26.4:16:1:0:5.4 0/1:16:4:2,2:5,7:0.25:2,2:30.3:1:31:1:1:1.37:36.5:8:0.25:0:7 -19 27738931 . T G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40032;SOR=0.41677;LSEQ=TCCTTTAGACAGAGCAGATT;RSEQ=GAAACACGCTTTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:0.625:2,2:16.2:1:31.6:1:1:2.60:28.8:10:0.625:0:4.8 0/1:15:6:2,4:4,4:0.4:2,2:24.7:1:28.8:1:0.62704:1.90258:54.7:5:0.3846:0:5.7 -19 27738932 . G T 56 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25359;SOR=Inf;LSEQ=CCTTTAGACAGAGCAGATTT;RSEQ=AAACACGCTTTTTGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:22:1:31.1:1:1:0:26.4:16:1:0:5.4 0/1:14:4:2,2:4,6:0.2857:2,2:29:1:28.3:1:1:1.46:36.5:8:0.2857:0:7 -19 27738939 . G T 89 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2451;SOR=0;LSEQ=ACAGAGCAGATTTGAAACAC;RSEQ=CTTTTTGTGGAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:21.2:1:30.2:1:1:0:22.2:5:1:0:5.2 1/0:12:8:3,5:0,0:0.6667:0,2:18.9:1:29.8:1:1:0:47.8:16:0.6667:0:5.5 -19 27738945 . T A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.52941;SOR=Inf;LSEQ=CAGATTTGAAACACGCTTTT;RSEQ=GTGGAATTTGCAAGTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:15.2:1:26.8:1:1:0:22.2:5:1:0:5.2 0/1:12:2:1,1:4,6:0.1667:2,2:10:0:30.5:1:1:1.45:59:4:0.1667:0:4 -19 27739268 . A T 30 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=CGTTCCTTTAGACAGAGCAG;RSEQ=TTTGAAACACTCTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:7:0:30.5:1:1:1:37:4:0.5:0:2.5 0/0:8:0:0,0:4,4:0:2,0:16.8:1:28:1:1:0:40:16:1:0:2.5 -19 27739271 . T G 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=TCCTTTAGACAGAGCAGATT;RSEQ=GAAACACTCTTTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:14:1:29.5:1:1:1:29.5:4:0.5:0:2 1/1:8:8:4,4:0,0:1:0,2:19.8:1:28.6:1:1:0:40:7:1:0:2.5 -19 27739284 . T G 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07353;SOR=0;LSEQ=GCAGATTTGAAACACTCTTT;RSEQ=TGTGGAATTTGCAAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:23:0:31.5:1:1:1.73:37:4:0.4:0:2.5 0/0:12:0:0,0:6,6:0:2,0:20.8:1:28.1:1:1:0:46.7:5:1:0:2.7 -19 27739285 . T G 65 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2605;SOR=Inf;LSEQ=CAGATTTGAAACACTCTTTT;RSEQ=GTGGAATTTGCAAGTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:18:1:30:1:1:0:33.6:10:1:0:1.8 0/1:12:4:2,2:4,4:0.3333:2,2:9.3:1:32.5:1:1:1:60:8:0.3636:0:3 -19 27739296 . C T 71 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.2605;SOR=Inf;LSEQ=CACTCTTTTTGTGGAATTTG;RSEQ=AAGTGGAGAATTCAGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:13.8:1:32.5:1:1:0:36:8:1:0:1.5 0/1:13:5:3,2:4,4:0.3846:2,2:16.4:1:30.6:1:1:1.45:58.4:10:0.3846:0:3.4 -19 27739321 . A G 72 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAATTCAGCCGCTTTGA;RSEQ=GACAATGTTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:8:5:2,3:0,0:0.625:0,2:6:1:31.4:1:1:0:56.6:10:0.625:0:3.8 -19 27739323 . A T 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATTCAGCCGCTTTGAAG;RSEQ=CAATGTTAGAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:0,0:0.8:0,2:21:1:30.3:1:1:0:51.8:8:0.8:0:4.5 -19 27739327 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGCCGCTTTGAAGACAA;RSEQ=GTTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:24:0:32.5:1:1:1.7321:52:4:0.4:0:4.5 -19 27739328 . GT AG 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGCCGCTTTGAAGACAAT;RSEQ=TAGAAAAGGAAATATCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:20.5:1:31.5:1:1:1.7321:51.5:4:0.4:0:3.5 -19 27739329 . T G 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCGCTTTGAAGACAATG;RSEQ=TAGAAAAGGAAATATCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:0,0:0.6:0,2:17:1:30.7:1:1:0:43.7:6:1:0:5 -19 27739480 . G T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCTGCAAGTGGATATTC;RSEQ=GACCTCTTTGAGGCCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:32.5:1:30.5:1:1:0:43:4:0.6667:0:2.5 -19 27739484 . C T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGCAAGTGGATATTCGGAC;RSEQ=TCTTTGAGGCCTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:36.5:1:32:1:1:0:43:4:0.6667:0:2.5 -19 27739585 . G C 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTATGCAACTCACCGAGTT;RSEQ=AACCTTCCTTTATACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:5:1:30:0:1:0:35:4:0.6667:0:6.5 1/1:1:1:0,1:0,0:1:0,0:6:0:25:0:1:0:40:2:1:0:6 -19 27739598 . T G 79 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCGAGTTGAACCTTCCTTTA;RSEQ=ACAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:15.2:1:34.2:1:1:0:38.6:10:1:0:5.4 1/1:1:1:0,1:0,0:1:0,0:19:0:26:0:1:0:40:2:1:0:6 -19 27739636 . T C 65 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTCTTTTTGTGGAATTTG;RSEQ=AAGTGGAGATTTCAAGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:47:1:32.8:1:1:1:35:8:0.6667:0:5.8 1/1:1:1:0,1:0,0:1:0,0:42:0:30:0:1:0:40:2:1:0:6 -19 27739655 . A C 81 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAGTGGAGATTTCAAGCG;RSEQ=TTTGAGGCCAATGGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:29.3:1:31.5:1:1:0:38.8:12:1:0:4.8 1/1:1:1:0,1:0,0:1:0,0:23:0:34:0:1:0:40:2:1:0:6 -19 27739658 . T C 55 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGGAGATTTCAAGCGATT;RSEQ=GAGGCCAATGGTAGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:25.8:1:27.8:1:1:1:35:8:0.6667:0:5.8 1/1:1:1:0,1:0,0:1:0,0:20:0:30:0:1:0:40:2:1:0:6 -19 27739661 . G T 57 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGATTTCAAGCGATTTGA;RSEQ=GCCAATGGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:22.8:1:28.8:1:1:1:35:8:0.6667:0:5.8 1/1:1:1:0,1:0,0:1:0,0:17:0:31:0:1:0:40:2:1:0:6 -19 27739667 . T C 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAGCGATTTGAGGCCAA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:19:1:29.5:1:1:1:46.5:4:0.3333:0:3 0/0:1:0:0,0:0,1:0:0,0:11:0:30:0:1:0:40:2:1:0:6 -19 27740011 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGAGGCCAGTGTTAGAA;RSEQ=AGGAAATATCTTCGTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:6:0:32.5:1:1:0:42:4:0.6667:0:2 -19 27740053 . G C 49 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAGACAGAATCATTCCCA;RSEQ=AAACTGCGTTGTGATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,1:0.75:0,2:15:1:31:1:1:0:35.3:6:1:0:1.7 -19 27740171 . G C 49 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTGGACCTCCTTGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:16.3:1:31:1:1:0:42.3:6:1:0:4.7 -19 27740178 . G T 26 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTCCTTGAGGCGTTCGTT;RSEQ=GAAACGGGATTTCTTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:2,3:0.2857:2,2:5.5:1:26.5:1:1:1.41:34:4:0.2857:0:7 -19 27740182 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGAGGCGTTCGTTGGAA;RSEQ=CGGGATTTCTTCATATAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:1,2:0.2857:2,2:19:0:31:1:1:1.73:41:4:0.2857:0:4 -19 27740185 . G T 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGCGTTCGTTGGAAACG;RSEQ=GATTTCTTCATATAAGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:2,3:0.2857:2,2:12.5:1:27:1:1:1.41:34:4:0.2857:0:7 -19 27740206 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTTCTTCATATAAGGCTA;RSEQ=ACAGAAGAATTCTCAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:2:0:33:0:1:0:60:2:1:0:0 0/1:12:2:1,1:4,6:0.1667:2,2:16:1:31:1:1:1.45:50:4:0.1667:0:7 -19 27740213 . G T 55 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATATAAGGCTAGACAGAA;RSEQ=AATTCTCAGTAACTTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7.5:1:30:1:1:0:60:4:1:0:0 0/1:12:4:2,2:3,5:0.3333:2,2:30:1:27.5:1:1:1.60:44.5:8:0.3333:0:3.5 -19 27740216 . T G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATAAGGCTAGACAGAAGAA;RSEQ=TCTCAGTAACTTCCTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:28.5:1:1:0:60:4:1:0:0 0/1:14:2:1,1:5,7:0.1429:2,2:26:1:32.5:1:1:1.37:50:4:0.1429:0:7 -19 27740219 . T C 84 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.475;SOR=Inf;LSEQ=AAGGCTAGACAGAAGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13.5:1:29:1:1:0:60:4:1:0:0 1/0:14:7:3,4:3,4:0.5:2,2:22.7:1:30.1:1:1:1:33.6:14:0.5:0:5.9 -19 27740242 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTAACTTCCTTGTGTTGTGT;RSEQ=TATTCAACTCACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:36.5:1:32:1:1:0:60:4:1:0:0 0/1:13:2:1,1:5,6:0.1538:2,2:47.5:1:32:1:1:1.18:23:4:0.1538:0:8 -19 27740244 . A G 66 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTTCCTTGTGTTGTGTGT;RSEQ=TTCAACTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:38.5:1:29.5:1:1:0:60:4:1:0:0 0/1:13:4:2,2:4,5:0.3077:2,2:28.3:1:33:1:1:1.23:32:8:0.3077:0:6 -19 27740246 . T G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTCCTTGTGTTGTGTGTAT;RSEQ=CAACTCACAGAGTTGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:40.5:1:30:1:1:0:60:4:1:0:0 0/1:13:2:1,1:5,6:0.1538:2,2:32.5:1:31.5:1:1:1.18:31:4:0.1538:0:5.5 -19 27740249 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTGTGTTGTGTGTATTCA;RSEQ=CTCACAGAGTTGAACCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:43.5:1:30.5:1:1:0:60:4:1:0:0 0/1:13:2:1,1:5,6:0.1538:2,2:35:1:31:1:1:1.18:50:4:0.1538:0:7 -19 27740261 . G C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTATTCAACTCACAGAGTT;RSEQ=AACCCTCCTTTAGACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:45.5:1:32.5:1:1:0:60:4:1:0:0 0/1:11:2:1,1:4,5:0.1818:2,2:47:0:32:1:1:1.22:31:4:0.1818:0:5.5 -19 27740265 . CC TT 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TCCTTTAGACAGAGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:41.5:1:32:1:1:0:60:4:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:23.5:1:32.3:1:1:1:23:4:0.3333:0:7 -19 27740266 . C T 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=Inf;LSEQ=TCAACTCACAGAGTTGAACC;RSEQ=TCCTTTAGACAGAGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:40.5:1:32.5:1:1:0:60:4:1:0:0 1/0:6:4:2,2:0,0:0.6667:0,2:30.3:1:30:1:1:0:40.5:8:1:0:6.3 -19 27740269 . C A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCACAGAGTTGAACCCTC;RSEQ=TTTAGACAGAGCAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:37.5:1:33:0:1:0:60:4:1:0:0 0/1:6:2:1,1:1,1:0.3333:2,2:20.5:1:32:0:1:1:23:4:0.3333:0:7 -19 27740274 . G C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAGTTGAACCCTCCTTTA;RSEQ=ACAGAGCAGATTTGATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:32.5:1:33:1:1:0:60:4:1:0:0 0/1:5:2:1,1:1,2:0.4:2,2:15.5:1:33.5:1:1:1.73:23:4:0.4:0:7 -19 27740290 . T G 52 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TTTAGACAGAGCAGATTTGA;RSEQ=ACACTCTTTTTGTGGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:16.5:1:31:1:1:0:60:4:1:0:0 1/1:3:3:1,2:0,0:1:0,2:13.7:1:33.3:1:1:0:34:6:1:0:5.7 -19 28778454 . T C 117 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11688;SOR=0.10983;LSEQ=GCATTTGCGACGATCATCAT;RSEQ=GTCATCATCATCATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:16:9,7:1,0:0.8421:0,2:32.1:1:29.4:1:1:0:60:15:0.9375:0:3.6 0/1:3:1:0,1:1,1:0.3333:2,0:44:0:32:0:1:0:60:2:0.3333:0:4 -19 28778470 . ATCATCATCG GTCA 26 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=7.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCATTGTCATCATCATCATC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:29:1:26.1:1:1:1.40151:60:4:0.1053:0:3 0/0:5:0:0,0:2,3:0:2,0:21.8:1:31.2:1:1:0:60:10:1:0:0.8 -19 28778476 . A G 112 NM4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.11586;SOR=0.11685;LSEQ=TCATCATCATCATCATCATC;RSEQ=TCGTCATCATCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:6,6:2,1:0.7059:2,2:31.6:1:31.3:1:1:1.91151:60:24:0.8571:0:4.1 0/1:5:1:0,1:2,2:0.2:2,0:22:0:33:0:1:0:60:2:0.2:0:4 -19 28778494 . A G 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.00296;SOR=0;LSEQ=TCATCGTCATCATCATCATC;RSEQ=TCATCGTCAACATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:7,8:2,2:0.7895:2,2:23:1:29.9:1:1:1.13484:60:30:0.8333:0:3.7 0/0:5:0:0,0:1,1:0:2,0:11.5:1:27:1:1:0:60:4:0.4:0:0 -19 28780326 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGAGAGAGTTTTTCCAC;RSEQ=CTGGGTACTGGCAAAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:28,1:0.0645:1,0:8.5:1:31.5:1:1:0:60:4:0.0645:0:1 0/0:12:0:0,0:11,1:0:2,0:21.6:1:29.3:1:1:0:60:11:1:0:0 -19 28780398 . G T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0.78894;LSEQ=TGGGGAGGGGCAGTGCAGGG;RSEQ=GCTCCAGCCCTCAGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:84,20:0.0189:2,2:33:1:31:1:0.35849:4.12311:60:4:0.0194:0:1 0/1:67:1:0,1:54,12:0.0149:2,0:1:0:27:0:0.19403:0:60:2:0.0152:0:1 -19 28780443 . G A 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50151;SOR=0;LSEQ=GGCGGACAGGGCAGGACACA;RSEQ=CTGCCTGATTCCAGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:98,81:0.011:2,2:27:0:29.5:1:1:1.20859:60:4:0.0111:0:2 0/0:155:0:0,0:92,63:0:2,0:23.3:1:31.1:1:1:0:60:50.667:1:0:0.5 -19 28780457 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22212;SOR=Inf;LSEQ=GACACAGCTGCCTGATTCCA;RSEQ=CCCAGCATCAAAGCACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:103,95:0:2,0:26:1:31.9:1:1:0:60:65:1:0:1 0/1:177:2:1,1:98,77:0.0113:2,2:14.5:1:28.5:1:1:1.27097:60:4:0.0114:0:1 -19 28780462 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=0.04407;LSEQ=AGCTGCCTGATTCCAGCCCA;RSEQ=CATCAAAGCACCCACATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:203:190:96,94:8,5:0.936:2,2:26.9:1:30.1:1:0.56978:1.56325:60:380:0.936:0:1.1 0/1:190:74:43,31:61,54:0.3895:2,2:25.1:1:29.4:1:0.55016:1.23:60:73:0.3925:0:1.1 -19 28780531 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09914;SOR=Inf;LSEQ=TGACAGAAAGTTGCTTTTAT;RSEQ=TGAATGCACCCAAGCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:54,105:0:2,0:25.6:1:31.3:1:1:0:60:18.875:1:0:0.5 0/1:138:3:2,1:49,86:0.0217:2,2:22:1:26.3:1:0.55478:3.48:60:6:0.0222:0:1 -19 28780545 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57689;SOR=2.71137;LSEQ=TTTTATGTGAATGCACCCAA;RSEQ=CCATGTTGGATCACTGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:1:0,1:43,85:0.0078:2,0:8:0:12:0:1:0:60:0:0:0:1 0/1:96:2:1,1:27,67:0.0208:2,2:6.5:1:28:1:0.50044:2.45:60:4:0.0215:0:1 -19 28780552 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51246;SOR=0;LSEQ=TGAATGCACCCAAGCCATGT;RSEQ=GGATCACTGTTTAGAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:34,83:0.0168:2,2:34:1:29:1:0.50349:2.42:60:4:0.0174:0:1 0/0:84:0:0,0:22,62:0:2,0:22.2:1:29.6:1:1:0:60:83:1:0:0.3 -19 28780554 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18045;SOR=Inf;LSEQ=AATGCACCCAAGCCATGTTG;RSEQ=ATCACTGTTTAGAATGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:30,79:0:2,0:25.2:1:30.1:1:1:0:59.8:11.111:1:0:0.3 0/1:81:2:1,1:20,59:0.0247:2,2:22.5:1:24:1:0.4537:2.90:60:4:0.0253:0:1.5 -19 28780590 . GT G 79 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.67418;SOR=0.48535;LSEQ=GATTTGGTATTTCTTTTATT;RSEQ=TTTTTTTTTTTATTTAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:6:0,6:5,47:0.1034:2,0:30.2:1:30.8:1:1:0:60:12:0.1071:0:1 0/1:19:1:0,1:1,17:0.0526:1,0:33:0:33:0:1:0:60:2:0.0588:0:0 -19 28788849 . G T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26436;SOR=0;LSEQ=CTGCACATAATCCGTGCAGT;RSEQ=AGGGGTGAGCCACTCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:1,2:119,18:0.0214:2,2:25.7:1:29.3:1:0.05349:12.79711:60:6:0.0214:0:2.3 0/0:103:0:0,0:90,13:0:2,0:24.8:1:31.7:1:1:0:60:102:1:0:0.9 -19 28788858 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20524;LSEQ=ATCCGTGCAGTGAGGGGTGA;RSEQ=CCACTCGGCTGGTCTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:161:131:109,22:23,7:0.8137:2,2:25.3:1:30.1:1:0.43195:1.50:60:130:0.8125:0:1.7 0/1:121:57:48,9:52,12:0.4711:2,2:22.7:1:29.5:1:0.81084:1.23:60:56:0.4706:0:1.9 -19 28788918 . A C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17419;LSEQ=CCCATTGCCCTGGCAGGCAG;RSEQ=CTGGATGGCAGAGGAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:394:301:164,137:49,39:0.764:2,2:25.4:1:31.2:1:0.90329:1.04945:60:59.2:0.7789:0:1.4 0/1:314:113:59,54:102,97:0.3599:2,2:26.6:1:30:1:0.90648:1.04:60:21.6:0.3649:0:1.4 -19 28789135 . A T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07742;SOR=Inf;LSEQ=CCAGACTGGAGTGCAGCAGC;RSEQ=TGATCATAGCTCACTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:0,22:0:1,0:18.3:1:31.3:1:1:0:59.1:44:1:0:0.4 0/1:9:2:0,2:0,7:0.2222:0,0:20.5:1:32:0:1:0:60:4:0.2222:0:1 -19 28789169 . G A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.09491;SOR=0.10512;LSEQ=CTGCAGCCTCAACTTCGGGG;RSEQ=CTCAAGTGATCCTCCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:0,1:0.8889:0,0:31:1:30.9:1:1:0:60:16:0.8889:0:1 0/1:5:2:0,2:0,3:0.4:0,0:26:1:29:0:1:0:60:4:0.4:0:1 -19 29401768 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGAATGTCAGCAAAACA;RSEQ=ACCTGCCTGCAAGTGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:30:1:1:0:60:4:1:0:2.5 -19 29403570 . C A 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23575;SOR=3.18952;LSEQ=TTGGTGAGGGCTGCTTCTGA;RSEQ=GTGTGCAAGAATGGCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:8,2:0.1667:2,0:16:1:32:0:1:0:60:4:0.1667:0:1 0/1:15:6:3,3:5,4:0.4:2,2:28.5:1:30.2:1:1:1.23147:60:12:0.4:0:1 -19 29403630 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16121;SOR=Inf;LSEQ=GGAGTTGCAGATGTTGACTG;RSEQ=CGGCGACTCTGACTTCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:17,21:0:2,0:29.9:1:30.1:1:1:0:60:76:1:0:0.2 0/1:26:2:1,1:10,14:0.0769:2,2:23:1:27:1:1:1.38:60:4:0.0769:0:1 -19 29403700 . T G 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09874;SOR=8.45755;LSEQ=CTCATTAGGGCTCCACCTCC;RSEQ=TCATTGCCATCTCATGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:2,8:0.0909:2,0:34:0:34:0:1:0:60:2:0.1:0:1 1/0:6:3:1,2:1,2:0.5:2,2:15.7:1:28.7:1:1:1:60:6:0.5:0:1.3 -19 29917584 . T C 53 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23482;SOR=0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGTTTGTTGTTGTTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:6,11:0.1429:2,0:31:1:34:0:0.07368:0:60:6:0.1429:0:4 0/0:18:0:0,0:8,10:0:2,0:26.8:1:29.4:1:1:0:57:36:1:0:0.5 -19 29917587 . TTTGTTG T 56 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=44;MSI=16.000;MSILEN=3;SSF=0.04145;SOR=Inf;LSEQ=TGCTGCTGCTGCTGCTGTTG;RSEQ=TTGTTGTTGTTGTTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:7,5:0:2,0:24:1:31:1:1:0:60:24:0.6316:0:1.2 0/1:18:4:1,3:6,7:0.2222:2,2:31.5:1:28:1:0.60294:2.43937:60:8:0.2222:0:0 -19 29918435 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGGCATTTGAGCTTTA;RSEQ=CTTGAAGGATGGTTAGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:37:1:30.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 29918979 . G T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTATCCTCCCCACCACCAA;RSEQ=GTCTCCCCTCTCCTCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 30303379 . GA G 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13239;SOR=3.87494;LSEQ=GCCGCCCGCGCGCAAAGGGG;RSEQ=AGGGGTACTGGGCCCGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:2,0:11,8:0.0909:2,0:33:1:31.5:1:0.50476:0:60:4:0.0909:0:0.5 0/1:21:6:4,2:8,5:0.2857:2,2:7.5:1:29.6:1:1:1.24:58.3:12:0.2857:0.2381:0.5 -19 30303399 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.87389;LSEQ=GAAGGGGTACTGGGCCCGCG;RSEQ=CCTGACCCCGCCGCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:1:0,1:35,29:0.0154:2,0:1:0:25:0:0.46154:0:60:2:0.0159:0:1 0/1:70:2:1,1:36,32:0.0286:2,2:19:1:28:1:1:1.1231:60:4:0.0303:0:1 -19 30303409 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.4973;SOR=Inf;LSEQ=TGGGCCCGCGGCCTGACCCC;RSEQ=CCGCCGCCTCACCCCGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:54,39:0:2,0:17.6:1:29.5:1:1:0:60:17.6:1:0:0.3 0/1:93:2:1,1:52,39:0.0215:2,2:9:1:32.5:1:1:1.32915:60:4:0.0222:0:1 -19 30303421 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01553;SOR=Inf;LSEQ=CTGACCCCGCCGCCGCCTCA;RSEQ=CCCGCGCCGCCCCGCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:77,53:0:2,0:20:1:31.5:1:1:0:60:129:1:0:0.3 0/1:146:7:2,5:82,57:0.0479:2,2:14.6:1:26:1:0.13505:3.56545:60:6:0.0417:0:1.6 -19 30303425 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.73609;LSEQ=CCCCGCCGCCGCCTCACCCC;RSEQ=CGCCGCCCCGCAGGCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:82,58:0.0071:2,0:28:0:14:0:0.41844:0:60:0:0:0:1 0/1:163:2:1,1:91,70:0.0123:2,2:11.5:1:29.5:1:1:1.29788:60:4:0.0127:0:1 -19 30303435 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09724;SOR=0;LSEQ=GCCTCACCCCGCGCCGCCCC;RSEQ=CAGGCCTCAGGCCGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:3:1,2:108,77:0.0158:2,2:22.3:1:25:1:0.57334:2.78986:60:2:0.0109:0:1.3 0/0:222:0:0,0:127,95:0:2,0:22.8:1:30.5:1:1:0:60:73:1:0:0.4 -19 30303484 . C T 73 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30391;SOR=2.50628;LSEQ=TGCCGAGGGAGCGCAGGGAG;RSEQ=GGTGAGTGCCCGCGCCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:2:1,1:229,214:0.0045:2,2:27:1:28.5:1:1:1.0699:60:4:0.0046:0:1 0/1:537:6:2,4:271,260:0.0112:2,2:25:1:28.5:1:0.44332:2.08185:60:12:0.0116:0:1.2 -19 30303508 . CGGACG C 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=5.000;MSILEN=5;SSF=1;SOR=1.1553;LSEQ=GAGTGCCCGCGCCGCGGGGC;RSEQ=GGACGGGACGGGACGGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:4,1:281,208:0.01:2,2:17.2:1:32.6:1:0.40193:2.96:60:10:0.0102:0:0.2 0/1:518:6:3,3:280,228:0.0116:2,2:24.7:1:29:1:1:1.22757:60:12:0.0118:0.0039:0.3 -19 30303714 . T TC 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=2.51978;LSEQ=AAGAGACAGGTTGGGGAGCA;RSEQ=CCCCCCCATCTCACCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:195:65,130:144,211:0.3533:2,2:26.5:1:30.4:1:0.09916:1.36415:60:31.5:0.352:0.0344:0.1 1/0:447:259:86,173:74,112:0.5794:2,2:26.7:1:30.6:1:0.16194:1.32823:60:50.8:0.5786:0.0157:0.1 -19 30303950 . T A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12148;SOR=5.10866;LSEQ=CAGTGTGGGAGCCAGGTAGG;RSEQ=CCGCCCGGGGTTGGGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:1:1,0:116,228:0.0029:2,0:1:0:26:0:0.33913:0:60:2:0.0029:0:1 0/1:341:5:4,1:125,211:0.0147:2,2:5.6:1:23.8:1:0.06994:6.72:60:4:0.0119:0:1 -19 30303995 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20475;SOR=Inf;LSEQ=AGGTCCTTCTCCCCCTGGGT;RSEQ=ACATGGGGTTTCATGCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:36,134:0:2,0:23.4:1:31.8:1:1:0:60:84:1:0:0.1 0/1:141:2:1,1:30,109:0.0142:2,2:6:0:31:1:0.3926:3.59:60:4:0.0143:0:1.5 -19 30304011 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50993;SOR=0;LSEQ=GGGTCACATGGGGTTTCATG;RSEQ=TGTCTTGTCTCTTGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:22,109:0.0149:2,2:24.5:1:31.5:1:0.31704:4.87:60:4:0.015:0:1 0/0:98:0:0,0:17,81:0:2,0:21.9:1:32:1:1:0:60:196:1:0:0.1 -19 30304013 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50761;SOR=0;LSEQ=GTCACATGGGGTTTCATGCT;RSEQ=TCTTGTCTCTTGCTGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:20,104:0.0159:2,2:14.5:1:29:1:0.30667:5.10:60:4:0.0161:0:1 0/0:95:0:0,0:15,80:0:2,0:21.3:1:31.1:1:1:0:60:190:1:0:0.1 -19 30304018 . G T 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00155;SOR=Inf;LSEQ=ATGGGGTTTCATGCTGTCTT;RSEQ=TCTCTTGCTGGAGACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:16,101:0:2,0:21.7:1:31.3:1:1:0:60:57.5:1:0:0.1 0/1:80:7:3,4:10,63:0.0875:2,2:20.1:1:29.4:1:0.08072:4.59:60:14:0.0875:0:1.1 -19 30304028 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52317;SOR=0;LSEQ=ATGCTGTCTTGTCTCTTGCT;RSEQ=GAGACACTCTGGTGAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:4,85:0.022:1,2:9:1:29:1:0.10745:19.13:60:4:0.0225:0:1 0/0:57:0:0,0:5,52:0:2,0:22.1:1:30.4:1:1:0:60:114:1:0:0.1 -19 30306546 . TTG T 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTTTTTTTTTTTTTTTT;RSEQ=GGGGGGGGACAGAGTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:30:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 30308385 . T C 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTTAAGGGATCAGCACTT;RSEQ=CTTGAGCAACACCCTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:827:0:0,0:386,438:0:2,0:24.7:1:30.1:1:1:0:60:136.333:0.9976:0:0.1 0/1:811:47:24,23:360,402:0.058:2,2:22.6:1:31:1:0.65328:1.16:60:94:0.0583:0:1.1 -19 30311454 . C CA 73 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.80333;LSEQ=GGTGACAGAATAAGGCACCT;RSEQ=AAAAAAAAAACAAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:5:5,0:33,3:0.122:2,0:26.8:1:31.6:1:1:0:60:10:0.125:0:0.6 0/1:10:1:1,0:9,0:0.1:0,0:33:0:31:0:1:0:60:2:0.1:0:0 -19 30311542 . G GT 174 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.45013;SOR=1.22916;LSEQ=CTTCACCAAAGTCATTACAA;RSEQ=TTTTTTTTTTTTCCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:58:51,7:103,7:0.3187:2,2:27.8:1:29.8:1:0.24385:2.01061:59.7:57:0.3202:0:0.3 0/1:115:42:39,3:55,9:0.3652:2,2:26.2:1:29.2:1:0.35606:2.11:59.3:84:0.3684:0.0783:0.5 -19 30311555 . CCCCT TC 115 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=2e-04;SOR=0;LSEQ=ATTACAAGTTTTTTTTTTTT;RSEQ=CCCTCAAGTAAAACTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:17:15,2:188,30:0.0714:2,2:18.5:1:28.3:1:1:1.20:59.1:16:0.0727:0.0336:1.2 0/0:153:0:0,0:127,24:0:2,0:21.8:1:29.3:1:1:0:59.6:12.727:0.9929:0:0.4 -19 30312542 . G T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2524;SOR=0;LSEQ=CTCTCTCTTTCCATGCCAGG;RSEQ=TACTGAGAAGTCATTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:3:2,1:143,23:0.0178:2,2:40:1:31.3:1:0.37027:3.07923:60:6:0.0182:0:1 0/0:144:0:0,0:117,27:0:2,0:23.7:1:30.7:1:1:0:60:47:1:0:0.2 -19 30312874 . C T 245 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00495;LSEQ=GAACTTCTTTTCTCAATCAT;RSEQ=GGTCTCTTTTCTCTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:297:187,110:299,193:0.3764:2,2:24.5:1:29.9:1:0.54666:1.10:60:58.4:0.3763:0:1.1 0/0:673:2:0,2:407,264:0.003:2,0:1:0:25.5:1:0.15586:0:60:4:0.003:0:1 -19 30313523 . CCTT C 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=1.92005;LSEQ=ATTTGCTGGTCAGTGCTGCT;RSEQ=CTTTCAGTCCTTCTTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:89:22,67:153,325:0.1561:2,2:24.1:1:31.5:1:0.21117:1.43284:59.9:43.5:0.1559:0.0281:0.4 0/1:469:123:43,80:117,228:0.2623:2,2:25:1:31.3:1:0.8258:1.05:60:122:0.2641:0.0384:0.4 -19 30313576 . C T 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=3.27605;LSEQ=AACTGCCTAAATAGGCCAGC;RSEQ=GCGGTGGTTCAGGCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:21:2,19:16,142:0.1167:2,2:24:1:30.4:1:1:1.07005:59.8:20:0.1124:0:1.6 0/1:142:43:6,37:15,84:0.3028:2,2:17.5:1:29.8:1:1:1.10047:60:86:0.305:0:1.6 -19 30313603 . C G 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00505;SOR=2.91285;LSEQ=GTTCAGGCCTGTAAACCCAG;RSEQ=ACTTTGGGAGGCCGAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:13:1,12:4,97:0.114:1,1:19.5:1:31.5:1:0.46044:2.01:59.6:26:0.115:0:2 0/1:84:23:0,23:2,59:0.2738:1,1:27:1:31.4:1:1:0:60:46:0.2738:0:1.9 -19 30313622 . G T 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01107;SOR=0;LSEQ=GCACTTTGGGAGGCCGAGGT;RSEQ=GGCCGATCACTTGAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:0,9:1,78:0.1023:1,0:26.7:1:29.9:1:1:0:60:18:0.1059:0:1.2 0/0:60:0:0,0:0,60:0:1,0:27.7:1:30.6:1:1:0:60:120:1:0:0.6 -19 30313850 . CA C 50 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGCGAAACTATGTCT;RSEQ=AAAAAAAAAAAACTGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:21:1:32:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 30314457 . A AG 34 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.34432;LSEQ=GAAAGCAAGTCTCCATCTTG;RSEQ=GAAAAAAAAAAAATTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:2,0:174,8:0.0108:1,0:27:1:33.3:1:1:0:60:4:0.0109:0.0054:0 0/1:138:2:2,0:134,2:0.0145:1,0:26.5:1:34:0:1:0:60:4:0.0149:0:0 -19 30314459 . A G 176 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0;SOR=3.80491;LSEQ=AAGCAAGTCTCCATCTTGAG;RSEQ=AAAAAAAAAAATTTAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:23:23,0:174,10:0.1036:2,1:23.9:1:32.1:1:0.60648:0:60:46:0.105:0:1.4 0/1:160:49:49,0:97,3:0.3063:1,1:22.4:1:31.4:1:0.55106:0:60:48:0.3038:0:1.1 -19 30314471 . T A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22652;SOR=2.99348;LSEQ=ATCTTGAGAAAAAAAAAAAA;RSEQ=TTAAAAATTAAAAAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:2:2,0:284,19:0.0066:2,0:27.5:1:11.5:1:1:0:60:0:0:0:2 0/1:206:4:3,1:195,7:0.0194:1,2:29.3:1:29.8:1:0.14754:9.02164:60:8:0.0198:0:2.5 -19 30314666 . C T 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.35572;LSEQ=AGCGGTAAGAAGCAGAGCAG;RSEQ=GGGCCGGAAATGGCGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:772:91:27,64:248,433:0.1179:2,2:25.1:1:30:1:0.2439:1.35711:60:182:0.1194:0:1.1 0/1:665:206:79,127:173,285:0.3098:2,2:25.4:1:29.6:1:0.93115:1.02:60:50.5:0.3079:0:1.2 -19 30315112 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGCTGGGCAGGGGGCTG;RSEQ=CCTCTCCACATTATCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:37.5:1:30.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 31301619 . T TCA 71 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTAGACTTCAGCTCTTTGT;RSEQ=CAGTTATCTCCATTACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:9.8:1:30.6:1:1:0:60:10:1:0.6:0 1/1:3:3:3,0:0,0:1:0,0:41:1:30.7:1:1:0:60:6:1:0:0 -19 31301718 . T C 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00348;SOR=0;LSEQ=TGATCCTTTTATCACCTCAA;RSEQ=ACCCTGCACTACAATGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:63:62,1:0,0:1:0,1:26.7:1:32.4:1:1:0:60:126:1:0:1.1 1/1:32:27:26,1:5,0:0.8438:0,1:17.5:1:31.1:1:1:0:60:54:0.8438:0:1.1 -19 31301886 . C T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17312;LSEQ=AGGTTTCCAGCCCGCTGAGT;RSEQ=CTGCCTTTCTTTCTGTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:482:406:192,214:38,38:0.8423:2,2:25.2:1:29.6:1:0.70814:1.11433:60:39.6:0.8498:0:1.1 0/1:373:179:86,93:93,101:0.4799:2,2:25.1:1:28.8:1:1:1.00:60:58.667:0.4783:0:1.1 -19 31301979 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51312;SOR=0;LSEQ=ATTTAATAATCTTTTTTGTG;RSEQ=TTTGTCTTTAATGCCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:38,116:0.0128:2,2:19:1:28.5:1:0.43871:3.03:60:4:0.0131:0:1.5 0/0:110:0:0,0:25,85:0:2,0:22.4:1:30.8:1:1:0:60:220:1:0:0.2 -19 31706411 . A G 277 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03397;LSEQ=TTAAAAAACTAAAACTCTGA;RSEQ=GATAGCTGGTCCCAATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:493:473:180,293:8,12:0.9594:2,2:26.3:1:31.2:1:1:1.085:60:66.571:0.9608:0:1.1 0/1:470:209:88,121:108,152:0.4447:2,2:25.3:1:30.7:1:0.92513:1.02:60:103.5:0.4471:0:1.1 -19 32988213 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18525;SOR=Inf;LSEQ=GGAGGGTGAGTCGTCCAAGT;RSEQ=ATTGATAAGGTCAAGCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:70,63:0:2,0:29.4:1:31.6:1:1:0:60:43.333:1:0:0.1 0/1:101:2:1,1:50,49:0.0198:2,2:28.5:1:29.5:1:1:1.02021:60:4:0.0208:0:1 -19 33185013 . A G 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.06713;LSEQ=CCTTGATTCTAGAGGAAACA;RSEQ=ATTTGACAAGGAGGTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:0.4:2,0:7:0:30:1:0.4:0:60:4:0.4:0:1 0/1:12:5:3,2:5,2:0.4167:2,2:39.4:1:31.2:1:1:1.59564:60:10:0.4545:0:1 -19 33185051 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AAAATACAGGGCCCGAAGGC;RSEQ=AGTAATAGTAAAACGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:17,4:0:2,0:15.2:1:29.6:1:1:0:60:20:1:0:0.3 0/1:28:2:1,1:19,7:0.0714:2,2:8.5:1:29:1:0.49735:2.60494:60:4:0.0714:0:1.5 -19 33782249 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGACCCCTCCAGCCCTG;RSEQ=ATCGGCCTTGAGATCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:11:0:31:1:1:1:60:4:0.5:0:1.5 -19 33782794 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=3.51553;LSEQ=CACGCTGACCTCCTGGGCCC;RSEQ=AGCTGGGTTGGGCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:1,3:0.2:2,0:47:0:30:0:0.4:0:60:2:0.2:0:1 1/0:6:3:1,2:1,2:0.5:2,2:35:1:30.3:1:1:1:60:6:0.5:0:1.3 -19 33784339 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08308;SOR=Inf;LSEQ=AAACACACATTTCCTAACAG;RSEQ=GAGTAGACACCGTGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:99,1:0:1,0:25:1:32.2:1:1:0:60:99:1:0:0.1 0/1:41:2:2,0:38,1:0.0488:1,0:39:1:29:1:1:0:60:4:0.0488:0:1 -19 33784657 . T C 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCGGGAGGGCATGGCATTC;RSEQ=TGGGGGGTGCTGGGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:838:0:0,0:276,561:0:2,0:24:1:29.9:1:1:0:60:37.045:0.9988:0:0.1 0/1:581:22:9,13:198,360:0.0379:2,2:23.3:1:30.2:1:0.65231:1.26:60:44:0.0389:0:1.1 -19 33784680 . T A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00723;SOR=Inf;LSEQ=GGGGGTGCTGGGGAGGGTGC;RSEQ=CTGGTTGGCTGGAGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:573:0:0,0:122,450:0:2,0:24.1:1:30:1:1:0:60:51:1:0:0.1 0/1:343:5:4,1:80,256:0.0146:2,2:8.6:1:24.6:1:0.01412:12.68:60:4:0.012:0:1.2 -19 33789010 . G A 100 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=21.68768;LSEQ=CCCAGTGCCCCATCTTTGGC;RSEQ=CAGGCCCTGGCATACAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:1:1,0:366,32:0.0025:2,0:29:0:32:0:1:0:60:2:0.0026:0:1 0/1:212:11:10,1:182,18:0.0519:2,2:32.2:1:29:1:1:1.01106:60:10:0.0476:0:1.5 -19 33789248 . G GC 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.25296;SOR=0.70112;LSEQ=CCTTCCTCCCCTCTACTTTG;RSEQ=CCCCCCCCGGGGGCCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1286:34:11,23:460,784:0.0264:2,2:32.6:1:31.4:1:0.71914:1.22658:60:33:0.0261:0:0.2 0/1:910:17:5,12:364,525:0.0187:2,2:30.4:1:29.9:1:0.45685:1.66312:60:16:0.018:0.0011:0.5 -19 33789251 . CC T 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCCCCTCTACTTTGGCC;RSEQ=CCCCGGGGGCCTCGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1273:0:0,0:465,802:0:2,0:24.8:1:31.2:1:1:0:60:56.591:0.9952:0:0.2 0/1:897:47:15,32:339,491:0.0524:2,2:25.5:1:30.6:1:0.28473:1.47229:59.9:94:0.0535:0.0123:0.4 -19 33789397 . A G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20612;SOR=1.77658;LSEQ=TTCCGGGAGCCATCAGCTTT;RSEQ=AAAGAGGAAGCCCCTAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:44:1,43:0,48:0.4783:1,1:20.4:1:30.3:1:0.47826:0:60:21:0.4719:0:1.2 1/0:29:18:1,17:0,11:0.6207:0,1:28.4:1:31.4:1:1:0:60:36:0.6207:0:1 -19 33792302 . C T 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00116;SOR=6.41028;LSEQ=CTGGCAGCTGGCGGAAGATG;RSEQ=CCCGCAGCGTGTCCAGTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1681:3:1,2:883,792:0.0018:2,2:13.7:1:24.7:1:0.60576:2.22878:60:2:0.0012:0:1 0/1:1323:15:6,9:668,639:0.0113:2,2:28.4:1:28.2:1:0.4442:1.56754:60:30:0.0115:0:1.2 -19 33792520 . G A 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04963;SOR=0.13997;LSEQ=GCCTTGCCCGCGCCGCTGCC;RSEQ=CCACTCGCGCGGAGGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:793:9:6,3:240,544:0.0113:2,2:17.1:1:30:1:0.02911:4.52:60:18:0.0116:0:1.3 0/0:624:1:1,0:215,408:0.0016:2,0:1:0:25:0:0.34615:0:60:2:0.0016:0:1 -19 33792620 . C T 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40487;SOR=0.34419;LSEQ=GCGCGGGCGCGGGGTGCGGG;RSEQ=TGGGCACGGGCGTGGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:4:1,3:129,88:0.0181:2,2:8.3:1:28.3:1:0.30837:4.36931:60:8:0.0183:0:1.3 0/0:159:1:0,1:94,64:0.0063:2,0:1:0:29:0:0.40881:0:60:2:0.0063:0:1 -19 33792623 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19174;SOR=Inf;LSEQ=CGGGCGCGGGGTGCGGGCTG;RSEQ=GCACGGGCGTGGGCGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:136,97:0:2,0:15.8:1:31:1:1:0:60:57.25:1:0:0.3 0/1:182:2:1,1:104,76:0.011:2,2:6:0:31.5:1:1:1.36601:60:4:0.0112:0:1 -19 33792625 . C T 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.27154;LSEQ=GGCGCGGGGTGCGGGCTGGG;RSEQ=ACGGGCGTGGGCGGCGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:1,2:137,105:0.0122:2,2:11.3:1:24:1:0.58222:2.59945:60:2:0.0082:0:1.3 0/1:194:3:1,2:108,83:0.0155:2,2:8:1:27:1:0.58243:2.58977:60:6:0.0155:0:1 -19 33792631 . C A 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTGCGGGCTGGGCACGGG;RSEQ=GTGGGCGGCGGCGTGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:163,130:0:2,0:19.2:1:31.3:1:1:0:60:292:0.9932:0:0.3 0/1:246:19:11,8:122,102:0.0772:2,2:14.6:1:29.5:1:0.81496:1.15:60:38:0.0802:0:1.3 -19 33792637 . C T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.66236;SOR=1.82836;LSEQ=GGGCTGGGCACGGGCGTGGG;RSEQ=GGCGGCGTGGGGTGACCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:2:0,2:174,153:0.0061:2,0:1:0:26.5:1:0.2212:0:60:4:0.0062:0:1 0/1:271:3:1,2:145,123:0.0111:2,2:21:1:28.7:1:0.59666:2.35046:60:6:0.0113:0:1.3 -19 33792731 . G GGCGGGT 148 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=4.000;MSILEN=6;SSF=0;SOR=0;LSEQ=GGGCGGCCAGGTGCGCGGGC;RSEQ=GCGGGTGCGGGTGCGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:28:16,12:134,142:0.0918:2,2:15.7:1:30.9:1:0.4315:1.41:59.3:56:0.093:0.0492:0.3 0/0:253:0:0,0:121,132:0:2,0:14:1:29.9:1:1:0:59.6:83.333:1:0:0.3 -19 33792740 . G A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32482;SOR=3.84734;LSEQ=GGTGCGCGGGCGGCGGGTGC;RSEQ=GGTGCGGGTGCGAGGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:1:1,0:147,130:0.0036:2,0:1:0:26:0:1:0:60:2:0.0036:0:1 0/1:220:3:2,1:112,105:0.0136:2,2:17.7:1:31.7:1:1:1.87:60:6:0.0139:0:1.3 -19 33792751 . C T 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.08048;SOR=0;LSEQ=GGCGGGTGCGGGTGCGGGTG;RSEQ=GAGGGCGGCGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:5:2,3:149,122:0.0179:2,2:6:1:28:1:0.66126:1.82793:60:10:0.0182:0:1.2 0/0:196:0:0,0:106,88:0:2,0:13.2:1:30.2:1:1:0:59.8:31.333:0.9895:0:0.3 -19 33792754 . GGGC G 108 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.81462;SOR=1.18111;LSEQ=GGGTGCGGGTGCGGGTGCGA;RSEQ=GGCGGCGGCGGCGGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:10:6,4:141,114:0.0376:2,2:23.3:1:32.6:1:1:1.21:60:20:0.0383:0:0.1 0/1:204:9:5,4:109,83:0.0441:2,2:22.6:1:30.9:1:1:1.05031:60:18:0.0464:0.0049:0.4 -19 33792759 . G T 51 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.03383;SOR=Inf;LSEQ=CGGGTGCGGGTGCGAGGGCG;RSEQ=CGGCGGCGGCGGCGGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:150,109:0:2,0:15.6:1:31.6:1:1:0:59.9:128.5:1:0:0.3 0/1:196:4:1,3:112,79:0.0204:2,2:5.3:1:25.5:1:0.31151:4.22292:60:8:0.0207:0:1.3 -19 33792772 . C T 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=1;SOR=0.71379;LSEQ=GAGGGCGGCGGCGGCGGCGG;RSEQ=GGCTGGTAAGGGAAGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:4:1,3:212,129:0.0116:2,2:11.3:1:28.3:1:0.1584:4.90765:60:8:0.0117:0:1 0/0:241:2:0,2:144,95:0.0083:2,0:1:0:28:0:0.161:0:60:4:0.0084:0:1 -19 33792865 . C T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0309;SOR=Inf;LSEQ=ACCAGCGGCCGCAGCGCCGG;RSEQ=GCCCCGACGCGCTCGTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:0:0,0:234,305:0:2,0:25.5:1:30.5:1:1:0:60:76:1:0:0.2 0/1:554:6:2,4:252,294:0.0108:2,2:11.8:1:27.2:1:0.69178:1.71268:60:12:0.011:0:1.2 -19 33792894 . G A 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44026;SOR=0.47315;LSEQ=GCGCTCGTACAGGGGCTCCA;RSEQ=CCTGCCGTCCAGGTAGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:4:3,1:98,195:0.0135:2,2:7.5:1:28:1:0.11567:5.93:60:8:0.0137:0:1 0/0:312:2:2,0:118,192:0.0064:2,0:1:0:25.5:1:0.14717:0:60:4:0.0065:0:1 -19 33792938 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50387;SOR=Inf;LSEQ=CCGCGCAGCCGTAGCCGGGC;RSEQ=GGGGCCCGTGCGCTCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:15,27:0:2,0:18.9:1:30.5:1:1:0:60:41:1:0:0.4 0/1:55:2:1,1:18,34:0.0364:2,2:16.5:1:25.5:1:1:1.87:60:4:0.0364:0:1.5 -19 33793007 . TCGC T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.65918;SOR=1.89087;LSEQ=GCGCGCCCGGGTAGTCAAAG;RSEQ=CGCCGCCGCCGCCGCCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:2:2,0:183,43:0.0088:2,0:33:0:32.5:1:1:0:60:4:0.0089:0:0 0/1:182:3:2,1:135,44:0.0165:2,2:14.7:1:29.4:1:1:1.53013:60:6:0.0166:0.0055:0 -19 33793011 . C T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=3;SSF=0.13519;SOR=0;LSEQ=GCCCGGGTAGTCAAAGTCGC;RSEQ=GCCGCCGCCGCCGCCCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:4:1,3:212,54:0.0148:2,2:15.8:1:28.5:1:0.0306:11.6279:60:8:0.0149:0:1.3 0/0:210:0:0,0:153,56:0:2,0:14.6:1:30.3:1:1:0:60:40.8:0.9951:0:0.3 -19 33793016 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=1;SOR=1.28571;LSEQ=GGTAGTCAAAGTCGCCGCCG;RSEQ=CGCCGCCGCCCGTGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:3:1,2:251,68:0.0093:2,2:13.3:1:29.3:1:0.12033:7.3209:60:6:0.0093:0:1 0/1:251:3:1,2:180,68:0.012:2,2:12:1:30:1:0.18888:5.25282:60:6:0.0122:0:1 -19 33793372 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16435;SOR=Inf;LSEQ=CCTCGGCGGCCTCCAGCCTG;RSEQ=GCGGGGCGTCGCCGCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:49,160:0:2,0:21:1:30.6:1:1:0:60:103.5:1:0:0.1 0/1:143:2:1,1:35,105:0.014:2,2:19:0:28.5:1:0.44411:2.97:60:4:0.0142:0:1 -19 33795172 . C A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16767;SOR=5.57091;LSEQ=TGCTGAGCCAAATGCAGGAC;RSEQ=CATTCATATAGCATTCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:1:0,1:106,406:0.0019:2,0:3:0:27:0:1:0:60:2:0.002:0:1 0/1:371:4:3,1:96,269:0.0108:2,2:10.5:1:25:1:0.06068:8.35:60:8:0.011:0:1 -19 33795241 . G A 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00044;SOR=Inf;LSEQ=AAGCACCAAGAGCGATTTGC;RSEQ=TTTTTTTCTGCGGTGCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:1,126:0:1,0:23.1:1:32.2:1:1:0:60:62.5:1:0:0.1 0/1:66:7:0,7:0,58:0.1061:1,0:16:1:29.3:1:1:0:60:14:0.1077:0:1.1 -19 33796867 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54926;SOR=0;LSEQ=GAAGCCTAAAAGTGTACCTC;RSEQ=GGATGAGGAGGAAATGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:2,0:181,1:0.0109:1,0:17:1:29.5:1:1:0:60:4:0.0112:0:1 0/0:95:0:0,0:90,5:0:2,0:23.5:1:30:1:1:0:60:190:1:0:0.1 -19 33796881 . A T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10994;SOR=Inf;LSEQ=TACCTCGGGATGAGGAGGAA;RSEQ=TGGTTTTGAGGGCAAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:251,2:0:1,0:23.9:1:30.1:1:1:0:60:41.167:1:0:0.1 0/1:126:2:1,1:120,4:0.0159:1,2:12.5:1:26.5:1:0.0781:26.94449:60:4:0.016:0:1 -19 33797172 . A G 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGAAGTGGCTCTGGCTC;RSEQ=TGTGCAACTGAGACAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:857:0:0,0:226,630:0:2,0:23.2:1:30.8:1:1:0:60:213:1:0:0.1 0/1:660:43:17,26:196,421:0.0652:2,2:25.4:1:29.5:1:0.31305:1.40:60:42:0.0645:0:1.1 -19 33797283 . TG T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGTACACAGGCCCAGTG;RSEQ=GGGGGTTGAGCGTGAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:0,2:2,86:0.0222:1,0:13.5:1:26.5:1:1:0:60:4:0.0227:0.0111:0.5 0/0:43:0:0,0:0,43:0:1,0:20.9:1:28.8:1:1:0:60:9.75:1:0:0.1 -19 33798450 . CCCTT C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=5.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTTTCTTTTTCTTTTCTTTT;RSEQ=CCTTCCTTCCTTCCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:1:32:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 33798509 . C T 32 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTCTTTCTCTCTCTCTCT;RSEQ=TCTTTCTTTCTTTCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:15:0:32:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 33905969 . G A 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00832;SOR=0;LSEQ=CCACATGGCAAGCCCTGTGC;RSEQ=CCAGGCCAGACAGGCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:8,1:24,2:0.2571:2,2:27.4:1:30.8:1:1:1.48133:60:18:0.2571:0:1.1 0/0:23:0:0,0:19,4:0:2,0:25:1:28.3:1:1:0:60:22:1:0:0.6 -19 33905985 . A G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00101;SOR=6.5112;LSEQ=GTGCGCCAGGCCAGACAGGC;RSEQ=GCCTCAGAAGCCACTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:5:4,1:40,3:0.1042:2,2:21.2:1:31.8:1:0.36576:3.21397:60:10:0.1042:0:1 0/1:32:14:10,4:14,4:0.4375:2,2:25.4:1:27.5:1:0.70349:1.38516:60:13:0.4194:0:1.1 -19 33906015 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59713;SOR=2.33509;LSEQ=GCCACTTCACACCTCTGTGG;RSEQ=GCCCTCCCAGAAAGCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:1:0,1:69,12:0.0122:2,0:1:0:25:0:0.15854:0:60:2:0.0125:0:1 0/1:71:2:1,1:46,23:0.0282:2,2:17.5:1:27.5:1:1:1.97912:60:4:0.0286:0:1.5 -19 33906052 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21818;SOR=Inf;LSEQ=CGAGAAGAGGCCTGACCCAC;RSEQ=CCGTGGAACAGGGGTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:104,61:0:2,0:24.9:1:30:1:1:0:60:40.25:1:0:0.6 0/1:146:2:1,1:87,57:0.0137:2,2:38:1:29:1:1:1.52173:60:4:0.0137:0:1 -19 33906063 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.20705;SOR=Inf;LSEQ=CTGACCCACGCCGTGGAACA;RSEQ=GGGTGCTCCCTTGGCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:126,77:0:2,0:24.9:1:31.3:1:1:0:60:66.667:1:0:0.7 0/1:170:2:1,1:100,68:0.0118:2,2:30:1:27.5:1:1:1.46714:60:4:0.012:0:1 -19 33906068 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2049;SOR=Inf;LSEQ=CCACGCCGTGGAACAGGGGT;RSEQ=CTCCCTTGGCTTTGTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:126,85:0:2,0:25.8:1:31.3:1:1:0:60:22.444:1:0:0.7 0/1:175:2:1,1:103,70:0.0114:2,2:32:0:28.5:1:1:1.46807:60:4:0.0118:0:1 -19 33906102 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.99936;LSEQ=GTGAGATGTGGTCCTGCACC;RSEQ=ACAGAAGCGAACCTCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:34:19,15:124,104:0.1293:2,2:27.6:1:30.1:1:1:1.06:60:33:0.1289:0:3 0/1:185:79:42,37:57,49:0.427:2,2:24.4:1:30:1:1:1.02465:60:158:0.4341:0:2.8 -19 33906110 . C T 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.28176;LSEQ=TGGTCCTGCACCAACAGAAG;RSEQ=GAACCTCAGAGGTCACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:35:19,16:121,114:0.1292:2,2:27.3:1:29.4:1:0.85663:1.12:60:16.5:0.1231:0:3 0/1:184:81:41,40:53,50:0.4402:2,2:23.1:1:29.5:1:1:1.03397:60:80:0.4469:0:2.9 -19 33906123 . T C 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02081;SOR=1.57627;LSEQ=ACAGAAGCGAACCTCAGAGG;RSEQ=CACATGGTCATTCTCGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:128:62,66:63,77:0.4758:2,2:26.2:1:30.8:1:0.62444:1.15:60:31:0.4679:0:1.6 1/0:180:106:50,56:35,39:0.5889:2,2:22.4:1:30.8:1:1:1.0051:60:105:0.5899:0:2.3 -19 33906150 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56272;SOR=3.16252;LSEQ=GTCATTCTCGACGTGATGGC;RSEQ=ACAGCGGACCTCTGTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:0,1:102,128:0.0043:2,0:45:0:12:0:1:0:60:0:0:0:1 0/1:147:2:2,0:61,84:0.0136:2,0:8:1:31.5:1:0.182:0:60:4:0.0138:0:1 -19 33906191 . C T 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00106;SOR=Inf;LSEQ=AAGTGACCTGCAGACAACCA;RSEQ=GGGCTGCGCTGGGACTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:45,111:0:2,0:23.2:1:29.8:1:1:0:60:38:1:0:0.4 0/1:97:7:3,4:26,63:0.0722:2,2:18.1:1:30.7:1:0.42823:1.80:60:14:0.0722:0:2.7 -19 33906196 . TG T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71329;SOR=0.55689;LSEQ=ACCTGCAGACAACCACGGGC;RSEQ=CGCTGGGACTGGCCGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:6:1,5:38,97:0.0426:2,2:21.7:1:29.7:1:1:1.9508:60:12:0.0429:0.0142:0.2 0/1:83:2:1,1:26,55:0.0241:2,2:32.5:1:29:1:0.54746:2.09:60:4:0.0241:0:0.5 -19 34080051 . TAC T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTACTGAATATATATATA;RSEQ=ACATATATATATTTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23.5:1:31.5:1:1:0:48.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 34080228 . C G 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.90552;LSEQ=CTTCAGTTGAACCCAGGTAC;RSEQ=TTTCTCTTTGGCTTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:6,3:0.3571:2,0:20.6:1:31.2:1:0.25824:0:60:10:0.3571:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:2:0:29:0:1:0:60:2:0.3333:0:1 -19 34080254 . T C 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGCTTCTTTCTTTTTC;RSEQ=GATCATTTTCCTTCATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:15,5:0.0909:2,2:20:0:31.5:1:0.48052:2.82843:60:4:0.0909:0:1.5 0/0:5:0:0,0:5,0:0:0,0:21.4:1:32.8:1:1:0:58:10:1:0:0.2 -19 34080443 . CC TT 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGACACTTGTGAGGCATT;RSEQ=TTTTTGAACAGTGCCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:39:14,25:26,39:0.3679:2,2:27.5:1:30.5:1:0.8353:1.18849:59.5:78:0.3786:0:1.3 0/0:81:0:0,0:39,42:0:2,0:20.4:1:30.6:1:1:0:59.7:80:1:0:0.3 -19 34080511 . G C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.82713;SOR=0.89057;LSEQ=TTATAGATTCGCATATACGT;RSEQ=GCCAAAGGAACAACTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:13:7,6:21,17:0.2549:2,2:17.8:1:30.6:1:1:1.05761:60:26:0.26:0:1 0/1:60:14:7,7:26,20:0.2333:2,2:16.8:1:30.1:1:0.76307:1.29427:58.6:28:0.2333:0:1.1 -19 34080517 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49589;SOR=Inf;LSEQ=ATTCGCATATACGTGGCCAA;RSEQ=GGAACAACTCCATGTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:32,23:0:2,0:22.3:1:30.6:1:1:0:58.1:54:1:0:0.6 0/1:58:2:1,1:34,22:0.0345:2,2:25.5:1:29:1:1:1.53351:60:4:0.0351:0:1.5 -19 34080579 . C G 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64356;SOR=0.85369;LSEQ=TCGGGTGCCTCTCCTCTTTC;RSEQ=CTTTGTCTTCGTCATTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:34:18,16:34,23:0.3696:2,2:27.2:1:31.1:1:0.66191:1.31002:59.7:68:0.3778:0:1.1 0/1:90:30:16,14:33,27:0.3333:2,2:22:1:31.5:1:1:1.06864:59.7:60:0.3409:0:1.3 -19 34080659 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20376;SOR=Inf;LSEQ=TTTACTGAATATTTTAAACC;RSEQ=ACTGTTGAGACCTACTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:15,33:0:2,0:22.7:1:30.4:1:1:0:59.5:11:1:0:0.4 0/1:40:2:1,1:14,24:0.05:2,2:29:1:27.5:1:1:1.69:60:4:0.0513:0:1 -19 34113746 . C A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAACTCTCCAGGGCACCGGC;RSEQ=TGTGAGTGCTGGAGGCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:48:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:30:1:1:0:60:4:1:0:1 -19 34115267 . G A 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTTGGTAGAACATCCCCCTC;RSEQ=GACTGTAACCGACGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:4,1:10,0:0.3333:0,2:17.6:1:30.8:1:0.33333:0:60:10:0.3333:0:1.2 0/1:3:1:1,0:2,0:0.3333:0,0:11:0:32:0:1:0:60:2:0.3333:0:2 -19 34115326 . A T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03527;SOR=4.9005;LSEQ=CTGCTGTTAGAGATGCCTTT;RSEQ=TAATCTTGTAGCCAGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:4,0:22,1:0.1481:1,0:39.8:1:30.8:1:1:0:60:8:0.1481:0:1.3 0/1:17:8:8,0:9,0:0.4706:0,0:26.8:1:30.3:1:1:0:60:16:0.4706:0:1.1 -19 34115396 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53153;SOR=0;LSEQ=TGTTTCCATAATGAACATTT;RSEQ=CTGATTACAGGGTATCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:94,5:0.0198:2,2:17:1:30.5:1:0.11584:17.25167:60:4:0.0198:0:1 0/0:59:0:0,0:59,0:0:1,0:24.2:1:28.4:1:1:0:60:118:1:0:0.1 -19 34115548 . T C 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.19224;LSEQ=TGGGCTACTCTCAGAATTTG;RSEQ=CTTCAGTTCTCTTAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:114:48,66:166,210:0.2327:2,2:24.4:1:31.5:1:0.74686:1.0867:60:113:0.234:0:1.1 0/1:398:159:72,87:89,150:0.3995:2,2:27:1:31.1:1:0.11849:1.39:60:52:0.398:0:1.1 -19 34115930 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCCACACTGGAGAAAC;RSEQ=TGGGGCAGCGGGGAACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:42:1:31:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 34115967 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGTGAGCAGGAAAGAGGAC;RSEQ=CAGGATTATGGCAGCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:18.5:1:31:0:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 34116248 . G A 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCCACCTTGGCCTCCCA;RSEQ=AGTGTTGGGATTACAGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:28.5:1:1:0:54:4:1:0:1 -19 34356388 . GG AA 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00185;SOR=Inf;LSEQ=TAACGTATCCTCTCTGCTGC;RSEQ=TGCTGGACGGACTTAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:35,48:0:2,0:24.6:1:29.7:1:1:0:60:40.5:1:0:0.7 0/1:73:8:3,5:27,38:0.1096:2,2:26.4:1:30.2:1:1:1.18151:60:16:0.1111:0.0137:0.9 -19 34356389 . G A 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41494;SOR=1.32556;LSEQ=AACGTATCCTCTCTGCTGCG;RSEQ=TGCTGGACGGACTTAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:43:18,25:16,23:0.5244:2,2:24.6:1:29.8:1:1:1.03:60:42:0.525:0:1.1 1/0:69:41:17,24:8,13:0.5942:2,2:27.2:1:29.1:1:1:1.15:60:40:0.6557:0:1.1 -19 34357872 . G A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGTGAGAACCCAGGGTC;RSEQ=GCGAGCAGGCAGGCAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:40:1:31.3:1:1:0:60:6:1:0:1 1/1:2:2:1,1:0,0:1:0,2:9.5:1:30:1:1:0:60:4:1:0:1 -19 36227688 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CATCTGCGCTTCGAGATCAG;RSEQ=AGTGAGGATGGGTTCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13.5:1:31.5:1:1:0:60:4:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:28:1:1:1:60:4:0.5:0:1 -19 36228954 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGTTCCCTGTTCATCCT;RSEQ=CCCTGCAGATCAGCCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 36229192 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48908;SOR=0;LSEQ=CATCCCTGCAGGGCATCGGG;RSEQ=GCTATATGTTCCGCATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:15,2:0.1053:2,2:25.5:1:30:1:0.29825:6.32456:60:4:0.1053:0:1.5 0/0:16:0:0,0:12,4:0:2,0:28.6:1:28.6:1:1:0:60:32:1:0:0.1 -19 36229256 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.12848;SOR=Inf;LSEQ=GATGCATGGCAATGCCGCCC;RSEQ=CTTCATCAACCACTCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:33,18:0:2,0:24.9:1:30.8:1:1:0:60:102:1:0:0.2 0/1:29:2:1,1:14,13:0.069:2,2:28:1:28.5:1:1:1.07415:60:4:0.069:0:1 -19 36229296 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GAGCCCAACTGCTTCTCTCG;RSEQ=GTCATCCACGTGGAGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:45,21:0.0294:2,2:26:1:30.5:1:0.54565:2.11677:60:4:0.0313:0:1 0/0:43:0:0,0:30,13:0:2,0:25.5:1:31.3:1:1:0:60:42:1:0:0.1 -19 36229351 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=0;LSEQ=TCTTCGCCCTGCGCCGCATC;RSEQ=TGCGTGGTGAGGAGCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:86,48:0.0147:2,2:12.5:1:29:1:1:1.78348:60:4:0.015:0:1.5 0/0:124:0:0,0:78,46:0:2,0:20.1:1:30.3:1:1:0:60:123:1:0:0.1 -19 36229471 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50141;SOR=0;LSEQ=TTAACTGAGGCCGTGGCTGC;RSEQ=CACCACGACCCCTCACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:28,73:0.0194:2,2:15.5:1:29.5:1:0.48582:2.58:60:4:0.0202:0:2 0/0:86:0:0,0:28,58:0:2,0:23.5:1:28.6:1:1:0:60:13.333:1:0:0.1 -19 36229477 . C T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18035;SOR=4.89002;LSEQ=GAGGCCGTGGCTGCCCACCA;RSEQ=GACCCCTCACACCTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:1,0:23,67:0.011:2,0:18:0:15:0:0.26374:0:60:0:0:0:1 0/1:77:4:1,3:22,51:0.0519:2,2:31.8:1:30.3:1:1:1.28996:60:8:0.0519:0:1 -19 36229524 . C T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1124;SOR=Inf;LSEQ=GCTGCCATCTTGCCCCTAGC;RSEQ=TGGGGGCTCCCTAGCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:0:1,0:22.1:1:32.5:1:1:0:60:29:1:0:0 0/1:30:4:0,4:0,26:0.1333:1,0:28.5:1:31:1:1:0:60:8:0.1379:0:1 -19 36234762 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16131;SOR=Inf;LSEQ=CTGGAGGTTCTGGGAAATGG;RSEQ=CCGCAGATGCATGAAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:15,20:0:2,0:28.7:1:30.5:1:1:0:60:16.5:1:0:0.1 0/1:24:2:1,1:12,10:0.0833:2,2:14:0:30:0:1:1.19087:60:4:0.087:0:1.5 -19 36833695 . C CAG 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.14993;LSEQ=TATTATTAATTTTCTTAAAA;RSEQ=GGGTGAAAGGGCTCCTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:162:130:95,35:27,5:0.8025:2,2:21.2:1:30.7:1:0.25314:1.98195:60:260:0.8075:0.2407:0.1 0/1:138:52:34,18:60,24:0.3768:2,2:21.5:1:29.5:1:0.56703:1.32074:59.9:25:0.3731:0.0942:0.1 -19 36833798 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.20836;LSEQ=AGCTAGCTCCACTGGACTAG;RSEQ=AAAATTACTCATAAGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:251:108,143:56,54:0.6953:2,2:26:1:30.8:1:0.17051:1.37188:60:34.857:0.6912:0:2 0/1:373:120:62,58:131,122:0.3217:2,2:25.4:1:30.7:1:1:1.00448:60:59:0.3198:0:2 -19 36833811 . A G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19209;LSEQ=GGACTAGAAAAATTACTCAT;RSEQ=AGCCAATCATCTACATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:340:234:95,139:51,55:0.6882:2,2:26.9:1:31.3:1:0.23687:1.35549:60:45.8:0.6898:0:2 0/1:360:107:51,56:122,131:0.2972:2,2:27.5:1:31.1:1:1:1.02254:60:214:0.2997:0:2.1 -19 36833881 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24212;SOR=Inf;LSEQ=GTGTACCATGGGACAGATTG;RSEQ=ACTCTCATCATTTTGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:34,110:0:2,0:23.1:1:32:1:1:0:60:71:1:0:0.7 0/1:140:2:1,1:41,97:0.0143:2,2:7.5:1:28.5:1:0.51151:2.35:60:4:0.0145:0:1 -19 36834637 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGGGACTGCATCTGGTGAG;RSEQ=GCCTTCTTGCTGGTGACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 38205212 . A AAACAACAAC 86 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=31;MSI=13.000;MSILEN=3;SSF=0.4757;SOR=0.55894;LSEQ=CAGAGCAAGACTCCGTCTCA;RSEQ=AACAACAACAACAACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:4,4:6,0:0.5333:0,2:21.3:1:28.8:1:0.08492:0:50.1:16:0.5333:0.2667:0.6 0/1:13:5:1,4:0,1:0.3846:0,2:15.4:1:30:1:1:0:56.2:10:0.3846:0.2308:0.2 -19 38205244 . G A 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=3;SSF=0.05709;SOR=0.20122;LSEQ=CAACAACAACAACAACAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:18:9,9:2,4:0.75:2,2:20.9:1:26.9:1:0.6494:1.94:55.5:8:0.8:0:1.8 0/1:11:4:2,2:2,5:0.3636:2,2:28.3:1:26.8:1:0.57576:2.29:48.8:8:0.3636:0:1.5 -19 39103257 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=CCACGCCTGCCTACCTGAGA;RSEQ=GGTGCACATCAAAGAGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:0.1538:2,2:15.5:1:29.5:1:1:2.4495:60:4:0.1667:0:1 0/0:14:0:0,0:9,5:0:2,0:16.5:1:32.1:1:1:0:60:28:1:0:0.1 -19 39350370 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24299;SOR=0;LSEQ=GGGGGCAGGGTAAGGAGGGT;RSEQ=AATCCTCTAAGTGATTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:29,21:0.0377:2,2:23.5:1:28:1:1:1.37225:60:4:0.0385:0:1 0/0:54:0:0,0:31,23:0:2,0:26:1:30:1:1:0:58.6:9.8:1:0:0.5 -19 39350412 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50413;SOR=Inf;LSEQ=GGTGAAGCAAGTCACGTGAT;RSEQ=ATAGGACGGGGGTGGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:27,28:0:2,0:26.7:1:30.1:1:1:0:60:12.75:1:0:0.5 0/1:71:2:1,1:36,33:0.0282:2,2:13:0:31:1:1:1.08956:51.5:4:0.0294:0:1.5 -19 39350421 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AGTCACGTGATCATAGGACG;RSEQ=GGGTGGGGGGCCCTTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:27,28:0:2,0:23.9:1:30.1:1:1:0:60:26.5:1:0:0.5 0/1:66:2:1,1:32,32:0.0303:2,2:48:0:30.5:1:1:1:60:4:0.0308:0:2 -19 39350452 . A G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00143;SOR=6.10624;LSEQ=CCCTTCCCTTTTAGGTAGCC;RSEQ=AAGCAGAGAGAGAAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:4:3,1:10,20:0.1176:2,2:25.3:1:30.8:1:0.27398:5.68:60:8:0.1212:0:1.3 0/1:44:20:8,12:11,13:0.4545:2,2:26.4:1:29.6:1:0.76618:1.26236:58.4:40:0.4545:0:1 -19 39350462 . G T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.50311;SOR=Inf;LSEQ=TTAGGTAGCCAAAGCAGAGA;RSEQ=AGAAGGCAGCATACGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:11,19:0:2,0:20.3:1:31:1:1:0:59.7:29:1:0:0.4 0/1:40:2:1,1:13,25:0.05:2,2:7:0:26.5:1:1:1.89:60:4:0.0513:0:2 -19 39538324 . C T 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCCTGACCTCAAGTGAGC;RSEQ=GCCCGTCTTGGCCTTCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:12.3:1:32.7:1:1:0:60:6:0.4286:0:2.3 1/1:1:1:1,0:0,0:1:0,0:9:0:32:0:1:0:60:2:1:0:2 -19 39538403 . G A 49 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68562;SOR=1.40133;LSEQ=GTGTCAGAACTGAACTGAAT;RSEQ=AGAAAACACCCAAGTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:17,0:0.1905:1,0:23.8:1:24.8:1:1:0:60:3:0.15:0:3 0/1:12:3:3,0:9,0:0.25:0,0:21.7:1:28.3:1:1:0:60:6:0.25:0:2 -19 39538417 . G C 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18608;LSEQ=CTGAATGAGAAAACACCCAA;RSEQ=TGGTGTCTGCTGTCAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:7,0:25,0:0.2188:1,0:16.1:1:28.9:1:1:0:60:6:0.1935:0:2.1 0/1:16:4:4,0:12,0:0.25:0,0:18.8:1:32.8:1:1:0:60:8:0.25:0:1.5 -19 39538478 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51961;SOR=0;LSEQ=CCCCCTATACACCCAGAGTC;RSEQ=CTGAAGTATTCTGTGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:80,24:0.0189:2,2:12.5:1:26.5:1:0.41779:3.28631:60:4:0.0198:0:2 0/0:69:0:0,0:56,13:0:2,0:21.1:1:29.9:1:1:0:60:33.5:1:0:0.8 -19 39538536 . G T 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66244;SOR=0.89953;LSEQ=ACTGGATTTGTTTTTCTTGT;RSEQ=TGGGGGGACAGGAGGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:58:32,26:118,80:0.2266:2,2:28.3:1:29.6:1:0.54869:1.19758:60:57:0.2253:0:2.1 0/1:235:49:30,19:115,69:0.2085:2,2:28.4:1:29.9:1:0.86979:1.0553:60:98:0.2103:0:2.2 -19 39538538 . G T 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.8265;SOR=0.93336;LSEQ=TGGATTTGTTTTTCTTGTGT;RSEQ=GGGGGACAGGAGGAAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:57:30,27:119,84:0.2192:2,2:28.8:1:29.8:1:0.45072:1.27378:60:56:0.2179:0:2.2 0/1:236:49:30,19:117,70:0.2076:2,2:29:1:29.9:1:0.8698:1.05831:60:98:0.2094:0:2.2 -19 39538545 . C T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.48991;LSEQ=GTTTTTCTTGTGTGGGGGGA;RSEQ=AGGAGGAAGTAAGGAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:66:41,25:117,97:0.2357:2,2:26.2:1:29.7:1:0.32167:1.36:60:32:0.237:0:1.8 1/0:258:150:91,59:63,45:0.5814:2,2:24.9:1:28.6:1:0.79705:1.10:60:36.5:0.5771:0:1.8 -19 39538592 . G T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.61663;LSEQ=AGGATGCTGCTCAGAGACAG;RSEQ=TGAGACAGGAGGGTGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:90:47,43:116,112:0.283:2,2:24:1:29.6:1:0.90101:1.06:60:89:0.2825:0:1.6 1/0:316:186:92,94:63,67:0.5886:2,2:27.2:1:29.7:1:0.90913:1.04:60:372:0.5886:0:1.7 -19 39538623 . G A 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01535;SOR=0.61889;LSEQ=GGGTGGACCAGCCCAGGACC;RSEQ=GGGCATAGGAGCCAGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:87:44,43:74,112:0.3187:2,2:29.2:1:30.4:1:0.11553:1.55:60:42.5:0.3148:0:1.4 0/1:263:59:22,37:88,115:0.2243:2,2:24.2:1:30.5:1:0.45532:1.28573:60:58:0.2214:0:1.3 -19 39538678 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19261;SOR=Inf;LSEQ=ATAGATTTGAGGGTGCCCAC;RSEQ=GGATTTGCTGAAGAATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:28,112:0:2,0:23.6:1:30.7:1:1:0:60:69:1:0:0.8 0/1:110:2:1,1:27,81:0.0182:2,2:32:1:29:1:0.44604:2.96:60:4:0.0183:0:2 -19 39538680 . G A 131 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGATTTGAGGGTGCCCACAG;RSEQ=ATTTGCTGAAGAATTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:21:6,15:18,93:0.1591:2,2:22.3:1:30:1:0.21631:2.05:60:42:0.1603:0:2.1 0/0:108:0:0,0:28,80:0:2,0:23.2:1:30.9:1:1:0:60:216:1:0:0.7 -19 39538706 . T A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=3.86425;LSEQ=CTGAAGAATTGGGCATGGGA;RSEQ=GCTGGGCCACACAGAACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:20:2,18:4,59:0.241:2,2:20.5:1:31.6:1:0.62756:1.63:60:40:0.2439:0:1 1/0:56:31:5,26:6,19:0.5536:2,2:24.2:1:30.3:1:0.51389:1.62737:60:30:0.5455:0:1.3 -19 39538726 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02052;SOR=0.285;LSEQ=TGCTGGGCCACACAGAACAC;RSEQ=TTCAGGATATCAGGCGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:22:0,22:1,32:0.4:1,1:24.5:1:30:1:1:0:60:21:0.3889:0:1.4 0/1:38:6:1,5:2,30:0.1579:2,2:22.8:1:31:1:0.41204:2.89:60:12:0.1579:0:1 -19 40739513 . A G 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00202;SOR=0;LSEQ=TTGTGTGGATTAAAACCTGA;RSEQ=TCTCCAACCGCCCAACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:29.1:1:31.5:1:1:0:60:16:1:0:1 0/0:4:0:0,0:3,1:0:2,0:27.5:1:31.5:1:1:0:60:8:1:0:0 -19 40739701 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16615;SOR=Inf;LSEQ=TGGGGACACAAACCAAAAAG;RSEQ=CTAAGTAAAAAGTTAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:174,36:0:2,0:22.5:1:31.5:1:1:0:60:209:1:0:1 0/1:145:2:2,0:121,22:0.0138:2,0:12.5:1:27:1:1:0:60:4:0.0144:0:1.5 -19 40739715 . T C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26456;SOR=0;LSEQ=AAAAAGGCTAAGTAAAAAGT;RSEQ=AGGGGGAAAAAACCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:218,57:0.0108:2,2:8.3:1:32.3:1:0.50581:1.90694:60:6:0.0111:0:2.3 0/0:207:0:0,0:165,42:0:2,0:23.2:1:29:1:1:0:60:24.875:1:0:0.6 -19 40739721 . G T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=0.08537;LSEQ=GCTAAGTAAAAAGTTAGGGG;RSEQ=AAAAAACCACCCAGCGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:308:280:220,60:18,10:0.9091:2,2:23.6:1:29.3:1:0.09866:2.03:60:139:0.9205:0:1.1 0/1:233:107:84,23:98,28:0.4592:2,2:25.1:1:27.9:1:1:1.04:60:20.4:0.4513:0:1.1 -19 40739765 . C T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCGAGCGTGCGTCCTCTG;RSEQ=GTGGGCAGACTGCTCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:638:0:0,0:422,216:0:2,0:25.3:1:31:1:1:0:60:44.571:1:0:0.5 0/1:524:27:15,12:305,192:0.0515:2,2:25.5:1:30:1:0.54958:1.27022:60:54:0.0521:0:1.3 -19 40739942 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12763;SOR=Inf;LSEQ=CTCCCTGGGGAAACGGCCCC;RSEQ=GCTGGCGGGGGCTGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:10,187:0:2,0:25.5:1:31.5:1:1:0:60:196:1:0:0.1 0/1:110:2:1,1:12,96:0.0182:2,2:22:1:28:1:0.22335:7.73:60:4:0.0183:0:1 -19 40741297 . G A 78 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.31724;SOR=0.39224;LSEQ=AGCACCTGCCTCCCGGAGCA;RSEQ=CTGGGTTCGGGCAGACGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:7:5,2:162,410:0.0121:2,2:9.6:1:28.1:1:0.02354:6.30:60:14:0.0124:0:1.1 0/0:419:2:0,2:123,294:0.0048:2,0:37:1:32:0:1:0:60:4:0.0049:0:1 -19 40741338 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17521;SOR=Inf;LSEQ=TTTCGGAGCAGGCAGGCCCT;RSEQ=TATGGCCCTTAATGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:24,242:0:2,0:22.8:1:32:1:1:0:60:43.333:1:0:0.1 0/1:192:2:1,1:16,174:0.0104:2,2:12.5:1:29.5:1:0.16967:10.58:60:4:0.0105:0:1 -19 40741684 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TTTCAGGGGCTGTGTGGGGA;RSEQ=GACACACTGCGACCCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:61,4:0:2,0:25.9:1:31.6:1:1:0:60:31.5:1:0:0.2 0/1:40:2:2,0:35,3:0.05:2,0:17.5:1:30.5:1:1:0:60:4:0.05:0:3 -19 40741694 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01273;SOR=Inf;LSEQ=TGTGTGGGGACGACACACTG;RSEQ=GACCCTACAAGCGAGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:78,4:0:1,0:23.8:1:31.7:1:1:0:60:40:1:0:0.2 0/1:43:4:4,0:36,3:0.093:2,0:21:1:31.3:1:1:0:60:8:0.0952:0:2.5 -19 40741707 . G T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.056;SOR=7.55029;LSEQ=CACACTGCGACCCTACAAGC;RSEQ=AGCACCCTTGTGGACGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:1,0:87,3:0.011:1,0:33:0:16:0:1:0:60:0:0:0:8 0/1:51:4:4,0:41,6:0.0784:2,0:22.5:1:31.3:1:1:0:60:8:0.0784:0:2.8 -19 40741988 . G A 83 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10657;SOR=2.49896;LSEQ=CCCCACCAGTCCACGGCCCG;RSEQ=CCATAGTCATTGTCCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1137:5:3,2:509,621:0.0044:2,2:19.6:1:29.6:1:0.66278:1.83:60:10:0.0045:0:1.2 0/1:824:9:8,1:346,467:0.0109:2,2:11.7:1:26.3:1:0.00633:10.77:60:18:0.0111:0:1 -19 40742105 . T C 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.64878;LSEQ=CTGGGCTGGAAACACACAGG;RSEQ=CTGGGGGATCCCCCTACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:651:48:31,17:333,270:0.0737:2,2:27.2:1:31.4:1:0.22943:1.48:60:23:0.072:0:1.1 0/1:395:89:53,36:173,129:0.2253:2,2:21.7:1:31:1:0.71615:1.10:60:43.5:0.226:0:1.1 -19 40742320 . T C 285 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01449;LSEQ=AAAAGTCAACGGATCTCAGG;RSEQ=GCATGCTCCCAAGGCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:699:695:223,472:1,1:0.9943:2,2:24.5:1:30.2:1:0.53978:2.11415:60:62.182:0.9942:0:1.1 1/0:534:382:136,246:55,96:0.7154:2,2:25.5:1:30.3:1:0.92019:1.03626:60:126.333:0.7178:0:1.1 -19 40742428 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51128;SOR=0;LSEQ=GCTGGGCCCAGCACACACAG;RSEQ=CTCACCCTCTGAGGCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:0,2:1,94:0.0206:1,0:45:1:31:1:1:0:60:4:0.0211:0:1 0/0:69:0:0,0:2,67:0:1,0:25.3:1:30.6:1:1:0:60:22:1:0:0.2 -19 40743523 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCACACCACTGCACTCAA;RSEQ=AGAGTAAGACTCCTCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 40744160 . T TA 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.57011;LSEQ=AGGCAGAGCGCAGAAGCTCA;RSEQ=AAGTGACACAGAGCTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:0,4:3,40:0.0851:2,0:22.3:1:31.8:1:1:0:60:8:0.0889:0.0426:0.3 0/1:20:1:0,1:1,18:0.05:1,0:41:0:30:0:1:0:60:2:0.05:0:1 -19 40744677 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53899;SOR=0;LSEQ=AAATGGAGACGAAGCCGCCT;RSEQ=CCTCAAGGGAGAGGGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:157,3:0.0123:1,2:33:0:31.5:1:0.04892:45.46662:60:4:0.0127:0:1.5 0/0:90:0:0,0:87,3:0:1,0:22.7:1:31.5:1:1:0:60:29:1:0:0.3 -19 40744697 . T C 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTCAAGGGAGAGGGGCAC;RSEQ=AGATGACACTGAAATTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:238,12:0:1,0:22.1:1:31.3:1:1:0:60:124:1:0:0.2 0/1:135:24:22,2:101,10:0.1778:2,2:26:1:30.7:1:1:1.09:60:48:0.1791:0:1 -19 40744970 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11329;SOR=Inf;LSEQ=GCCCTGGCCCTGCTTATTCT;RSEQ=CACACACACACCCTGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:9,195:0:1,0:25.8:1:32:1:1:0:60:33:1:0:0.1 0/1:104:2:1,1:5,96:0.0192:1,2:21.5:1:30:1:0.11365:17.61:60:4:0.0194:0:1 -19 40745621 . CA C 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.65162;SOR=0.49499;LSEQ=AGCATATCTGAAAACAAAAA;RSEQ=AAAAAAATAATGTTTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:3:2,1:157,3:0.0184:1,2:23.3:1:31.7:1:0.07226:23.95072:60:6:0.0185:0:0 0/0:109:1:1,0:107,1:0.0092:1,0:16:0:31:0:1:0:60:2:0.0092:0:0 -19 40746088 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5241;SOR=0;LSEQ=ACTCCGCCCCGACGAAGGGG;RSEQ=GCAAGGCCTTGTGAAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:9,173:0.0109:1,2:31.5:1:32:1:0.10602:18.28:60:4:0.0112:0:1 0/0:116:0:0,0:13,103:0:2,0:21.1:1:30.1:1:1:0:60:28:1:0:0.1 -19 40747717 . T G 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03772;SOR=Inf;LSEQ=CAGGCTCCCCCTTTTCTGAC;RSEQ=AGGGGGAATTTGTGGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:101,6:0:2,0:24.9:1:30.7:1:1:0:60:52.5:1:0:0.1 0/1:55:3:3,0:50,2:0.0545:1,0:19:1:29:0:1:0:60:6:0.0556:0:1 -19 40748022 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02153;SOR=Inf;LSEQ=CAGTCAGCGCCTGGCTCATG;RSEQ=CCCGTGGGAGGAAATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:0:0,0:148,402:0:2,0:24:1:31.5:1:1:0:60:60.111:1:0:0.1 0/1:343:4:3,1:93,246:0.0117:2,2:5:1:27.5:1:0.06814:7.88:60:8:0.0118:0:1 -19 40748026 . G A 66 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02629;SOR=8.84436;LSEQ=CAGCGCCTGGCTCATGGCCC;RSEQ=TGGGAGGAAATTTTAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:1:1,0:134,389:0.0019:2,0:10:0:15:0:0.25763:0:60:0:0:0:1 0/1:300:5:3,2:73,221:0.0167:2,2:9.2:1:28.8:1:0.10618:4.51:60:10:0.0167:0:1 -19 40748648 . C T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=GGAGTCCTGGGCCTCAGAGT;RSEQ=GAACAGCTGAGTGCCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:21,256:0:2,0:23.3:1:29.9:1:1:0:60:38.571:1:0:0.1 0/1:186:9:1,8:23,153:0.0484:2,2:19.1:1:28.1:1:1:1.20149:60:8:0.0444:0:1.1 -19 40760939 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.003;SOR=Inf;LSEQ=GCCCCAGCTGGAGAGACCCC;RSEQ=CAACCAGAAGCGCAGATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:78,1:0:1,0:26.3:1:31.2:1:1:0:60:158:1:0:0.1 0/1:38:5:5,0:33,0:0.1316:1,0:20.6:1:31.2:1:1:0:60:10:0.1316:0:1.6 -19 40761026 . C A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTCCTCACACCAGGCTTG;RSEQ=TCCCTCTCAAGGGCAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:318,101:0:2,0:25.5:1:32.1:1:1:0:60:103.75:1:0:0.1 0/1:320:18:14,4:220,78:0.0563:2,2:19.2:1:28:1:1:1.24:60:17:0.0538:0:1.2 -19 40761212 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACAGACAGCAGGGGGCTGAG;RSEQ=GGATAGCCCTGCTAGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:416:0:0,0:93,323:0:2,0:22.7:1:30.9:1:1:0:60:58.429:1:0:0.1 0/1:347:14:7,7:90,243:0.0403:2,2:18.9:1:30:1:0.07189:2.69:60:28:0.0413:0:1.1 -19 40761345 . AGT A 53 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCACAGGGCTCAGGGTCT;RSEQ=GTGTGTGTGTGTGGAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:0,3:1,31:0.0857:1,0:19:1:33.7:1:1:0:60:6:0.0857:0:0 0/0:11:0:0,0:0,11:0:0,0:15:1:32:1:1:0:60:22:1:0:0.1 -19 40762720 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03474;SOR=Inf;LSEQ=GGGTGAAAACAGATCCAAGG;RSEQ=CAAGCAGGCCCAGGACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:125,3:0:1,0:26:1:31.2:1:1:0:60:24.6:1:0:0.1 0/1:63:3:3,0:58,2:0.0476:1,0:18:1:28.7:1:1:0:60:6:0.0484:0:1 -19 40770737 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGCCCCACCCCCACTGGAAT;RSEQ=TAAGCTCCATCAGGGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:24:1:33.5:1:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:23.5:1:28.5:1:1:0:60:4:0.6667:0:1.5 -19 40770860 . G A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15485;SOR=0.17482;LSEQ=CACTGTGTTAGTTCAGTGAC;RSEQ=TGACTTCCCCTCTCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:18,1:2,0:0.9048:0,1:20.5:1:31.4:1:1:0:60:38:0.9048:0:1.1 1/0:5:3:3,0:2,0:0.6:0,0:33.7:1:29.7:1:1:0:60:6:0.75:0:1 -19 40770982 . T C 232 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACTGAAGGAGTCCACGAAA;RSEQ=GGGGGCATAAGCAGCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:158:158:156,2:0,0:1:0,1:23:1:31.8:1:1:0:60:51.667:1:0:1.1 1/0:76:56:52,4:19,1:0.7368:1,2:26.1:1:31.7:1:1:1.4549:60:112:0.7368:0:1.1 -19 40771024 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14248;SOR=Inf;LSEQ=CCTGGGGCTGCGGAATGCTG;RSEQ=CTCCTCAGGCTGGTAAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:229,37:0:2,0:25:1:30.8:1:1:0:60:43.333:0.9962:0:0.5 0/1:163:2:1,1:130,30:0.0123:2,2:24.5:1:26.5:1:0.34706:4.27924:60:4:0.0124:0:1.5 -19 40771042 . A T 43 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02887;SOR=Inf;LSEQ=TGGCTCCTCAGGCTGGTAAG;RSEQ=CCCTCCGCCTCTGCCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:276,114:0:2,0:22.2:1:29.3:1:1:0:60:64:1:0:0.3 0/1:275:4:0,4:182,88:0.0145:2,0:9.8:1:21.5:1:0.01216:0:60:3:0.0112:0:2 -19 41073996 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.51567;SOR=Inf;LSEQ=GCCTGAGCGGCAAGAGTCAG;RSEQ=CGATCAATCCGAGGAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:0:2,0:28.8:1:30:1:1:0:60:20:1:0:0 0/1:17:2:1,1:8,7:0.1176:2,2:32.5:1:28:1:1:1.13389:60:4:0.1176:0:1 -19 41073998 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51567;SOR=Inf;LSEQ=CTGAGCGGCAAGAGTCAGTC;RSEQ=ATCAATCCGAGGAGGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:0:2,0:29.2:1:29.1:1:1:0:60:20:1:0:0 0/1:17:2:1,1:8,7:0.1176:2,2:26:1:29:1:1:1.13389:60:4:0.1176:0:1 -19 41173874 . TTGC T 63 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=1;SOR=0.77038;LSEQ=ACTGAGGCTGCTTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:4:2,2:54,46:0.0385:2,2:29.3:1:31.8:1:1:1.17209:60:8:0.0392:0:0 0/1:67:2:1,1:31,34:0.0299:2,2:25:0:32:0:1:1.10:53.5:4:0.0303:0:0.5 -19 41173880 . C T 151 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0;SOR=11.18799;LSEQ=GCTGCTTGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:11:6,5:52,45:0.1019:2,2:17.6:1:29.9:1:1:1.04:60:22:0.1028:0:1 1/0:71:40:19,21:15,16:0.5634:2,2:23:1:28.5:1:1:1.03568:58.6:19:0.5507:0:1.5 -19 41173889 . CTGCTGCTGT C 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.00768;SOR=Inf;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:61,56:0:2,0:24.2:1:30.3:1:1:0:59.8:28.25:1:0:0.2 0/1:73:5:2,3:33,35:0.0685:2,2:36:1:31.2:1:1:1.40766:60:10:0.0704:0:1 -19 41173892 . CTGCTGT C 152 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0;SOR=9.95025;LSEQ=TGTTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:6:2,4:59,56:0.05:2,2:23.7:1:31.7:1:0.43922:2.09458:60:12:0.0531:0.0083:0.8 0/1:75:26:14,12:20,24:0.3467:2,2:24.6:1:32.4:1:0.62177:1.39:57.8:52:0.3768:0.12:1.6 -19 41173904 . TTGC T 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.04835;SOR=0;LSEQ=TGCTGCTGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:7:2,5:50,52:0.0642:2,2:28.9:1:30.3:1:0.44118:2.38569:60:14:0.0667:0:0 0/0:63:0:0,0:28,35:0:2,0:25.3:1:29.7:1:1:0:58.7:62:1:0:0.9 -19 41723887 . G T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGAGCAGAGGGATAGAC;RSEQ=CCCAGCCTCCTCCTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:43:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:27.5:1:29:1:1:0:60:4:1:0:1 -19 41724687 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=4;SSF=0.33333;SOR=Inf;LSEQ=TGTGCGTGCGTGCGTGCGTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:31:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29:1:1:0:60:4:1:0:2 -19 41724694 . G A 27 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=11.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GCGTGCGTGCGTGCGTGTGT;RSEQ=TGTGTGTGTGTGTGTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:38:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:25.5:1:27:1:1:0:60:4:1:0:2 -19 41725271 . A G 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.3583;SOR=1.12079;LSEQ=CCTCCCCCGCTGGGAGCCCA;RSEQ=CAACTTCTGAGGAAAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:817:212:128,84:368,236:0.2595:2,2:23.5:1:31.7:1:0.93486:1.02329:60:69.667:0.2596:0:1.1 0/1:578:163:99,64:250,162:0.282:2,2:24.7:1:30.7:1:1:1.00:60:22.286:0.2756:0:1.2 -19 41726492 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17058;SOR=Inf;LSEQ=ACAGGGTGGAACTGAGGGCC;RSEQ=GAAGGAGCTGGGGGGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:226,49:0:2,0:22.4:1:30:1:1:0:60:274:1:0:0.1 0/1:194:2:1,1:143,49:0.0103:2,2:35.5:1:29.5:1:0.45003:2.89925:60:4:0.0106:0:1 -19 41726531 . T C 72 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02761;SOR=8.293;LSEQ=CTAAGCTAACTCTTCCCATC;RSEQ=CCCCTCCAGGCACGCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:1:0,1:386,167:0.0018:2,0:20:0:11:0:0.30325:0:60:0:0:0:3 0/1:473:7:3,4:301,165:0.0148:2,2:25.3:1:26:1:0.25467:2.42746:60:2.5:0.0109:0:1.4 -19 41726903 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12351;SOR=Inf;LSEQ=GAACCTCTAGGTTTCGTTTT;RSEQ=CTCTTCTGCAAAATGAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:139,52:0:2,0:24.2:1:31.5:1:1:0:60:190:1:0:0.1 0/1:104:2:2,0:77,25:0.0192:2,0:21:1:29:1:1:0:60:4:0.0194:0:1 -19 41727143 . G C 222 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCCCAGCCTGGCTATGTTG;RSEQ=GCTGGAGGGTGAGCTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:845:154:63,91:276,415:0.1822:2,2:26.8:1:30.6:1:0.8559:1.04:60:153:0.1841:0:1.1 0/0:749:0:0,0:313,432:0:2,0:25.1:1:30:1:1:0:60:42.824:0.9945:0:0.2 -19 41727197 . C T 192 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGGGTCAGAGGACATGTGG;RSEQ=GCTCATAGGTTGTGGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:87:16,71:46,240:0.2332:2,2:22.7:1:29.9:1:0.62336:1.18:59.9:86:0.2356:0:1.1 0/0:274:0:0,0:65,209:0:2,0:23.3:1:29.4:1:1:0:60:29.444:1:0:0.1 -19 41727231 . GGGTCAA G 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGAAGTCAGGAATCCTGAG;RSEQ=GGTCAAAGGGTGCTGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:39:3,36:6,142:0.2074:1,2:27.4:1:31.1:1:0.39773:1.96:60:38:0.2077:0.0266:0.9 0/0:119:0:0,0:8,111:0:2,0:21.1:1:29.9:1:1:0:60:58.5:1:0:0.1 -19 41727951 . G A 73 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57699;SOR=1.50978;LSEQ=CACGGCCCCCAGCGCAGCCT;RSEQ=CATGTTCCAGGTGAGTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:872:6:5,1:340,525:0.0069:2,2:9.3:1:25.7:1:0.03867:7.70:60:12:0.007:0:1 0/1:676:7:3,4:285,384:0.0104:2,2:23.9:1:26.1:1:1:1.01:60:6:0.009:0:1 -19 41728211 . G GTC 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.55128;SOR=0;LSEQ=TTCTGTCTCTCTTTGTATGT;RSEQ=TCTCTCTCTCTGTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:1,17:0.1429:1,0:26:1:30.9:1:1:0:60:6:0.1429:0.0476:0 0/0:7:0:0,0:3,4:0:2,0:26.3:1:31.7:1:1:0:60:14:1:0:0.1 -19 41736788 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15022;SOR=Inf;LSEQ=ACTGCCCCTGGTCAGGCAGG;RSEQ=CATGGTAGGAGTGGCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:234,67:0:2,0:24.2:1:31.8:1:1:0:60:149.5:1:0:0.1 0/1:191:2:1,1:143,46:0.0105:2,2:17.5:1:27.5:1:0.43257:3.08596:60:4:0.0106:0:1 -19 41737344 . C T 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0075;SOR=0.24069;LSEQ=GGGGGGTTAAGCCAGATGTC;RSEQ=TGGGTTCGAATCCTAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:25:0,25:0,44:0.3623:1,1:22.5:1:30.2:1:1:0:60:50:0.3623:0:1.3 0/1:42:5:0,5:2,35:0.119:2,0:20.8:1:31.4:1:1:0:60:10:0.122:0:1.2 -19 41737410 . C T 88 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.60825;LSEQ=GGTAGGTGGCTTAATCTGTC;RSEQ=GGGGCTCAGCTCTCTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:0,7:0,21:0.25:1,0:31.1:1:31.6:1:1:0:60:14:0.2593:0:1.9 0/1:6:1:0,1:1,4:0.1667:2,0:23:0:32:0:1:0:60:2:0.1667:0:2 -19 41743454 . C A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCGTGCCCAGTCTATTTG;RSEQ=GTTATTATTGTCATCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:34.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 41743861 . A G 319 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.88722;LSEQ=CTCCTCAGGCTGTGCTGTCA;RSEQ=ACGATGGGATGGGCATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1165:1161:670,491:1,0:0.9966:0,2:26.1:1:31.4:1:1:0:60:60.105:0.9983:0:1.2 1/1:1034:1030:573,457:1,0:0.9961:0,2:25.1:1:31.2:1:1:0:60:53.211:0.9961:0:1.2 -19 41744134 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.28113;SOR=3.73995;LSEQ=ATCAGTGCCACCCCCATTGT;RSEQ=CCCTTTCACTCCTTTACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:1:1,0:49,238:0.0035:2,0:44:0:13:0:0.17361:0:60:0:0:0:2 0/1:155:2:1,1:21,132:0.0129:2,2:19:1:29:1:0.26452:6.16:60:4:0.0131:0:1 -19 41744285 . C T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28191;SOR=0;LSEQ=ACGAGTTGCCCACGTGTGTG;RSEQ=CCTTGGCACCCTGCACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:1,2:243,34:0.0107:2,2:7.3:1:22:1:0.04444:14.04215:60:2:0.0072:0:1 0/0:183:0:0,0:156,27:0:2,0:24:1:31.7:1:1:0:60:182:1:0:0.1 -19 41744831 . C T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28397;SOR=0.33285;LSEQ=TGATTTTCACAAAGGCACTC;RSEQ=TATCAGGGCTAGCAATACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:15:10,5:20,2:0.4054:2,2:24.3:1:29.9:1:0.09526:4.77126:60:14:0.3889:0:1.2 0/1:11:2:2,0:9,0:0.1818:0,0:20:1:32.5:1:1:0:60:4:0.1818:0:1 -19 41744906 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10493;SOR=Inf;LSEQ=AAGGGGATGGAGGGATACAG;RSEQ=TTAAAGGATGAGGATGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:115,5:0:1,0:22.4:1:31.2:1:1:0:59.8:29:1:0:0.2 0/1:58:2:1,1:53,2:0.0345:1,2:34.5:1:27.5:1:0.10338:21.8405:60:4:0.0357:0:1.5 -19 41745414 . C T 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.85198;SOR=0.88372;LSEQ=CACGGCCTCACTCCTTTACC;RSEQ=GTGCCACACCCTCACTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:25:14,11:52,30:0.2336:2,2:26.9:1:30.8:1:0.63896:1.35787:60:50:0.2381:0:1.2 0/1:66:14:9,5:36,16:0.2121:2,2:21:1:29.5:1:0.75336:1.24565:60:13:0.2031:0:1.1 -19 41745493 . C A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10082;SOR=Inf;LSEQ=CCTTCACTCCCTTACTCGTG;RSEQ=CACACCCTCACTCCCTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:253,64:0:2,0:22.5:1:31.4:1:1:0:60:38.625:1:0:0.2 0/1:277:3:1,2:207,66:0.0108:2,2:33.3:1:23:1:0.15116:6.22047:60:2:0.0075:0:1.7 -19 41745680 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00289;SOR=Inf;LSEQ=ACCCTCAACACCTAGTGGGG;RSEQ=CACTGTCACCATGCATACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:800:0:0,0:258,539:0:2,0:24.4:1:31.4:1:1:0:60:36.952:0.9961:0:0.1 0/1:616:7:4,3:211,398:0.0114:2,2:10.7:1:24.3:1:0.24566:2.51:60:6:0.0098:0:1.7 -19 41746281 . G GTGGA 62 d7;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=7.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ATATATGGATGGGTAGATGG;RSEQ=TGGATGGATGGATGGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:30.8:1:31.4:1:1:0:60:8:0.8:0.2:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 41748753 . T C 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29863;LSEQ=CAGAGAGCTGGATCCAAGGC;RSEQ=TCATCCATGACCTGTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:897:579:362,217:188,125:0.6455:2,2:25.4:1:31.1:1:0.47171:1.11:60:63.333:0.6426:0:1.1 0/1:713:251:144,107:254,208:0.352:2,2:23.6:1:30.1:1:0.58062:1.10:60:26.889:0.3492:0:1.2 -19 41748982 . G A 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07602;SOR=0;LSEQ=GAGAGGCTGGAGGCAGGGAG;RSEQ=CCAGTGAGGAGGCTGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:5:3,2:74,305:0.013:2,2:16:1:28.6:1:0.05711:6.14:60:10:0.0133:0:1 0/0:283:0:0,0:58,225:0:2,0:22.4:1:31.7:1:1:0:60:93.333:1:0:0.1 -19 41749325 . CA C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGTGAGATCCTGTTTT;RSEQ=AAAAAAAGAATGAGGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:2,0:59,8:0.029:2,0:23:1:31.8:1:1:0:60:4:0.029:0.0145:3.5 0/0:26:0:0,0:23,3:0:2,0:19.8:1:30.6:1:1:0:60:52:1:0:0 -19 41749397 . C T 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=0;LSEQ=GTAGCTGCCCAAGGCATGCT;RSEQ=AGCAAATGTTAGCACAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:17:17,0:219,5:0.0705:1,1:25.9:1:30.9:1:1:0:60:34:0.0723:0:1.1 0/0:146:0:0,0:141,5:0:1,0:26.8:1:31.6:1:1:0:60:72:1:0:0.1 -19 41749511 . TC T 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00022;SOR=0;LSEQ=CTGCCCTCACCTACTCCCCC;RSEQ=CCCCCCAGAGAAGTGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1347:14:9,5:706,626:0.0104:2,2:20.6:1:30.4:1:0.43436:1.60:60:28:0.0106:0.0015:0.1 0/0:1118:0:0,0:594,523:0:2,0:24.6:1:30.6:1:1:0:60:43.68:1:0:0.2 -19 41754190 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCAGGGTGCCCACTGGAG;RSEQ=AAGAGCGTGGCCAGGCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:4,0:19,1:0.1667:1,0:14:1:30:1:1:0:60:8:0.1667:0:1 0/0:3:0:0,0:3,0:0:0,0:23:1:32:1:1:0:60:6:1:0:0.7 -19 41754217 . G T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45767;SOR=0.4627;LSEQ=GTGGCCAGGCTTTACCCCTT;RSEQ=AGTTCCCTTTGAGGGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:10,1:19,1:0.3548:1,2:21.8:1:30.5:1:1:1.85871:60:22:0.3667:0:1.4 0/1:10:2:2,0:8,0:0.2:0,0:16.5:1:31.5:1:1:0:60:4:0.2:0:1 -19 41754537 . C T 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAGTCCCCCGGCAGCATACA;RSEQ=ACATCCTTCTGAACTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1175:0:0,0:530,644:0:2,0:24.7:1:31.9:1:1:0:60:57.7:0.9991:0:0.2 0/1:974:60:23,37:406,506:0.0616:2,2:26.3:1:29.1:1:0.42093:1.29044:60:120:0.0622:0:1.2 -19 41755660 . GA G 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGCAAGACTCCGTCT;RSEQ=AAAAAAAAAAAAATTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:28:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 41758016 . TA T 58 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACAGAGTGAGACTCCATC;RSEQ=AAAAAAAAAAAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:0.2857:0,0:20:1:29.4:1:1:0:60:8:0.2857:0.1429:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 41758044 . ATT A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAAGAAAATATAT;RSEQ=TTATATATATATATATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:2,0:22,1:0.0833:1,0:17:1:31:1:1:0:60:4:0.087:0.0417:0.5 0/0:3:0:0,0:3,0:0:0,0:5.7:1:29.7:1:1:0:60:6:1:0:0 -19 41758880 . G C 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGACCAGCCAGTGGTAAGGG;RSEQ=CGTTTAATCATTCAGTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:876:0:0,0:317,556:0:2,0:24.8:1:31.4:1:1:0:60:40.571:0.9965:0:0.1 0/1:769:37:13,24:285,445:0.0481:2,2:22.4:1:29.8:1:0.73069:1.18209:60:11.333:0.045:0:1.2 -19 41758945 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18229;SOR=Inf;LSEQ=GTACCCAGTGCTGCTCAGAC;RSEQ=CTGGGAAGACCACGGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:23,229:0:2,0:22.6:1:30.7:1:1:0:60:24.2:0.9959:0:0.1 0/1:189:2:1,1:33,154:0.0106:2,2:25:1:25.5:1:0.32821:4.61:60:4:0.0108:0:1 -19 41759474 . C T 175 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGCATCAAGGACTCTGTTGA;RSEQ=CTCTCCTCCCACCTGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:55:38,17:410,181:0.0851:2,2:21.6:1:30.3:1:1:1.01336:60:26.5:0.0837:0:1.1 0/0:516:0:0,0:328,188:0:2,0:23.2:1:30.9:1:1:0:60:128:1:0:0.2 -19 41759631 . AC A 212 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.88748;SOR=1.02417;LSEQ=CATGTGAGTGCCTTTCAGGG;RSEQ=CCCCCCCCCCCAACTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:132:52,80:189,248:0.1575:2,2:30.8:1:30.2:1:0.48196:1.17213:60:15.5:0.168:0.0095:0.9 0/1:672:108:48,60:194,194:0.1607:2,2:32.3:1:29:1:0.32848:1.24943:60:11:0.1698:0:1.1 -19 41759634 . CCCC T 234 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=12.000;MSILEN=1;SSF=0.00025;SOR=0.60926;LSEQ=ATGTGAGTGCCTTTCAGGGA;RSEQ=CCCCCCAACTGCTCCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:192:77,115:189,248:0.2291:2,2:26.6:1:30.9:1:0.48405:1.13796:60:63:0.2561:0.0382:0.2 0/1:672:103:42,61:194,194:0.1533:2,2:26.5:1:30.6:1:0.09783:1.45127:60:206:0.1767:0.0357:0.4 -19 41759637 . C T 71 q23;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.46035;SOR=1.48173;LSEQ=AGTGCCTTTCAGGGACCCCC;RSEQ=CCCCCCAACTGCTCCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:7:1,6:236,390:0.0111:2,2:28.9:1:23.6:1:0.26556:3.62502:60:1.333:0.0066:0:1.1 0/1:552:9:2,7:228,314:0.0163:2,2:21.9:1:22.4:1:0.31648:2.5376:60:2:0.0113:0:1.1 -19 41762263 . G C 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=ACCCGCAGCCAGGACAGTGA;RSEQ=GGGAGGAGGTGCAGATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:238,14:0:2,0:26:1:32.1:1:1:0:60:62:0.996:0:0.1 0/1:174:9:9,0:155,9:0.0517:2,0:26.4:1:32:1:1:0:60:18:0.052:0:1 -19 41762525 . A G 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03609;SOR=1.49627;LSEQ=AAGAGCGATGTGGTAGGTGC;RSEQ=CTCCCGCCAAGAGTGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:63:20,43:84,270:0.1507:2,2:22.6:1:31:1:0.20563:1.49:60:62:0.1512:0:1 0/1:343:72:22,50:78,193:0.2099:2,2:21.1:1:30.5:1:0.77191:1.09:60:23:0.2041:0:1.1 -19 41762601 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGGTGGCTGTGGATGC;RSEQ=AGGGTCACAGGGACATGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:0,2:7,111:0.0165:2,0:20.5:1:31.5:1:1:0:60:4:0.0175:0:1 0/0:55:0:0,0:5,50:0:2,0:23.4:1:30.1:1:1:0:60:54:1:0:0.4 -19 41762670 . T C 112 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08084;SOR=0.15232;LSEQ=GGGCTGGGCATGTCTTGGGG;RSEQ=ATGGTGGGCATCTCTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:13:1,12:0,27:0.325:1,1:17.8:1:30.5:1:0.325:0:60:12:0.3243:0:1.5 0/1:15:1:0,1:2,12:0.0667:2,0:7:0:34:0:1:0:60:2:0.0667:0:1 -19 41762699 . TA T 72 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.55824;LSEQ=CATCTCTGAATAGTGGTGTG;RSEQ=CATGCCCAGGATAAATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:0,5:1,21:0.1852:1,0:27:1:31.2:1:1:0:60:10:0.1852:0:0.8 0/1:9:1:0,1:1,7:0.1111:2,0:17:0:26:0:1:0:60:2:0.1111:0:0 -19 41763269 . A T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16004;SOR=0;LSEQ=AAAGTATTATGTTTCTATGA;RSEQ=TACTTGTGATGCTCCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:5:5,0:152,1:0.0316:1,0:26.2:1:31:1:1:0:60:10:0.0318:0:1 0/0:102:0:0,0:100,2:0:1,0:19.2:1:30.5:1:1:0:60:101:1:0:0.2 -19 41765229 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31732;SOR=3.23194;LSEQ=CATCAGAATACTACTCCATA;RSEQ=ACAGACAGGTTTCCCGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:18,0:0.1:1,0:14:1:33:1:1:0:60:4:0.1:0:1 0/1:11:3:2,1:8,0:0.2727:0,2:24.3:1:31.7:1:0.27273:0:60:6:0.3:0:1.3 -19 41765368 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57804;SOR=2.69986;LSEQ=CCTCTAAAATGCCCCCAGTC;RSEQ=CCTGAGTGTCCTAAAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:220,33:0.0039:2,0:32:0:16:0:1:0:60:0:0:0:1 0/1:189:2:1,1:162,25:0.0106:2,2:5.5:1:29.5:1:0.25684:6.37375:60:4:0.0107:0:1 -19 41765407 . A C 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00845;SOR=1.59014;LSEQ=TCCCCAGGCTTCCAGAATGC;RSEQ=CCCCTTCTGAGTCCCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:73:48,25:302,153:0.1383:2,2:20:1:30.4:1:0.89488:1.02802:60:35.5:0.1363:0:1.1 0/1:418:85:54,31:216,116:0.2033:2,2:24.4:1:29.6:1:0.80016:1.06879:60:41.5:0.2029:0:1.1 -19 41765806 . C A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06987;SOR=Inf;LSEQ=CCAGGGCAGGAGGATGGTGC;RSEQ=TGAGACAACCCTCCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:92,245:0:2,0:25.3:1:31.5:1:1:0:60:47.143:1:0:0.1 0/1:237:3:2,1:61,173:0.0127:2,2:22.3:1:30.3:1:0.17325:5.62:60:6:0.0129:0:1 -19 41765858 . C A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.56002;SOR=3.26068;LSEQ=AGGATCCAAGCTAAGCACTG;RSEQ=CACTGGGGAAAACTCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:0,1:19,135:0.0065:2,0:20:0:12:0:1:0:60:0:0:0:6 0/1:96:2:1,1:13,81:0.0208:2,2:37:1:29:1:0.27171:6.04:60:4:0.0215:0:1 -19 42382729 . C G 89 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCAGAGTACAAAGTG;RSEQ=GTATGCGGGAGGGGGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:17.4:1:32:1:1:0:60:14:1:0:1.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 42382745 . A G 64 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCGTATGCGGGAGGGGG;RSEQ=CAAGAGATGGCGCTGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:26.2:1:27.8:1:1:0:60:4:0.5:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 42383511 . TG T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.12719;SOR=Inf;LSEQ=CCTCTGCAGAGTGGGGTCTC;RSEQ=GGGGGTCTGGGGCCTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:223,99:0:2,0:25:1:32:1:1:0:60:63.4:1:0:0.1 0/1:179:2:2,0:129,48:0.0112:2,0:20.5:1:31:1:1:0:60:4:0.0114:0.0056:0.5 -19 42383810 . G GT 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00207;SOR=Inf;LSEQ=GTAGCCCTCTAGAGCCTGAG;RSEQ=TTCCCCATCCAAAACTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:12,314:0:1,0:25.6:1:32:1:1:0:60:64.2:1:0:0 0/1:233:7:0,7:16,210:0.03:2,0:30.1:1:31.8:1:1:0:60:14:0.0303:0.0043:0 -19 42383918 . G T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01947;SOR=0.26038;LSEQ=ACTGGCGCTGAGCCCAGGGG;RSEQ=TGTCTTCAATTTAGTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:30:0,30:0,23:0.566:1,1:24.3:1:30.7:1:1:0:60:60:0.566:0:1.1 0/1:20:5:0,5:1,14:0.25:1,0:18.6:1:25.8:1:1:0:60:4:0.2105:0:1.8 -19 42384461 . AAGAG A 66 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=15.000;MSILEN=2;SSF=1;SOR=2.2361;LSEQ=AAGAAAGAGAGAGAGAGAGA;RSEQ=AGAGAGAGAGAGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:6,0:9,0:0.3:0,0:22.3:1:25.9:1:1:0:60:5:0.2778:0.05:0.8 1/0:2:1:1,0:1,0:0.5:0,0:28:0:30:0:1:0:60:2:1:0:1 -19 42384525 . AG A 113 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=12.000;MSILEN=4;SSF=0.32033;SOR=1.88708;LSEQ=GAGGGAAGGAAGGGAAGGGA;RSEQ=GGAAGGAAGGAAGGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:14:14,0:36,1:0.2258:1,1:18.1:1:29.8:1:1:0:60:13:0.2203:0.0806:0.7 0/1:14:5:5,0:7,0:0.3571:0,0:16.4:1:33.2:1:1:0:60:10:0.3571:0.0714:0.4 -19 42384526 . G GGAA 103 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.44657;SOR=0.36044;LSEQ=AGGGAAGGAAGGGAAGGGAA;RSEQ=GGAAGGAAGGAAGGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:11:11,0:36,1:0.1774:1,0:15.7:1:30:1:1:0:60:22:0.1864:0.1129:0.1 0/1:14:1:1,0:7,0:0.0714:0,0:25:0:31.3:0:1:0:60:2:0.0714:0:0 -19 42578291 . CA C 32 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAATTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:32:1:1:0:60:4:1:0:1 -19 42579984 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15796;SOR=Inf;LSEQ=TGGCGCCCGCGGCCGCGCTC;RSEQ=GCCGCCTAACGTCATCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:24:1:29.1:1:1:0:60:24:1:0:0.2 0/1:17:2:1,1:6,9:0.1176:2,2:35:1:28:1:1:1.46:60:4:0.1176:0:1 -19 42579985 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55575;SOR=3.11044;LSEQ=GGCGCCCGCGGCCGCGCTCC;RSEQ=CCGCCTAACGTCATCGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:12,12:0.04:2,0:27:0:32:0:1:0:60:2:0.0417:0:1 0/1:17:2:1,1:6,9:0.1176:2,2:27.5:1:28.5:1:1:1.46:60:4:0.1176:0:1 -19 42787490 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATGAGGATGCGGGTTGGCGA;RSEQ=GCATGTGTGACAGGGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:32:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:33:0:33:0:1:0:60:2:1:0:0 -19 42788752 . TC T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49194;SOR=0;LSEQ=ATGCGGCGACGGCCTCCCGC;RSEQ=CCCCCGGGCCCAAGCGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:12,4:0.1111:2,2:12.5:1:30:1:0.4902:2.79285:60:4:0.1111:0:0.5 0/0:14:0:0,0:11,3:0:2,0:11.3:1:31.2:1:1:0:60:28:1:0:0.3 -19 42788786 . G T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3254;SOR=3.82093;LSEQ=AGCGGCGACGGCCGAGGAGC;RSEQ=GGCTGCGGGCGGAGCGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:1:0,1:118,47:0.006:2,0:1:0:25:0:0.28916:0:60:2:0.0062:0:1 0/1:132:3:2,1:92,37:0.0227:2,2:24.7:1:29.7:1:1:1.24115:60:6:0.0229:0:1 -19 42788791 . G T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17556;SOR=5.09163;LSEQ=CGACGGCCGAGGAGCGGGCT;RSEQ=CGGGCGGAGCGGCGTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:0,1:140,53:0.0052:2,0:1:0:25:0:0.27835:0:60:2:0.0053:0:1 0/1:155:4:2,2:106,45:0.0258:2,2:22:1:27.8:1:0.58516:2.34102:60:8:0.0258:0:1 -19 42790821 . G C 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00124;SOR=0;LSEQ=GGTGTTGGGGGTGGGGGGTA;RSEQ=ACAAAAGGGGTGGGGCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:13:13,0:310,10:0.0388:1,1:17.5:1:31.3:1:1:0:60:26:0.0405:0:1 0/0:226:0:0,0:213,12:0:2,0:17:0:14:0:1:0:60:0:0:0:8 -19 42791015 . C A 172 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04928;LSEQ=GCCAGCCTGACCCCTCCGTG;RSEQ=AGCCGAGCGAGGCCCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1164:55:24,31:474,635:0.0473:2,2:23.6:1:29.9:1:0.89003:1.04:60:54:0.0469:0:1.1 0/0:821:2:2,0:345,472:0.0024:2,0:1:0:25:0:0.17921:0:60:4:0.0024:0:1 -19 42792901 . G GT 108 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.21944;SOR=0.3567;LSEQ=TGGACTGGTGGTGGGTGGTG;RSEQ=TTTTTTTTTTTCACCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:12:11,1:50,1:0.1846:1,2:22.1:1:30.2:1:0.34716:4.39525:60:24:0.1905:0.0462:0.4 0/1:27:2:2,0:22,0:0.0741:1,0:18.5:1:28:1:1:0:60:4:0.0741:0:0 -19 42792980 . C G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.57404;SOR=2.79798;LSEQ=AATATCTATGGGTTGTTGGG;RSEQ=CAGTCTAGGTGCTGGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:1:1,0:232,40:0.0037:2,0:2:0:15:0:1:0:60:0:0:0:3 0/1:196:2:1,1:155,37:0.0102:2,2:12:1:30:1:0.3542:4.14702:60:4:0.0103:0:1 -19 42793590 . G A 256 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26266;SOR=1.13948;LSEQ=AGGGCCCAGAATCTTGCCCA;RSEQ=GACCCAGCAGGCCAAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:326:111,215:125,243:0.4691:2,2:26.4:1:30.7:1:1:1.00:60:325:0.4731:0:1.1 1/0:590:296:109,187:112,181:0.5017:2,2:24.9:1:30.1:1:0.73429:1.06145:60:147:0.5026:0:1.1 -19 42793920 . G T 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.38222;SOR=2.37045;LSEQ=TGCCGGTTTGGAGCAGAGCT;RSEQ=AGATCCAGGCTCCAGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:2:1,1:322,90:0.0048:2,2:34.5:1:28.5:1:0.39171:3.56332:60:4:0.0049:0:1 0/1:264:3:1,2:197,64:0.0114:2,2:7.3:1:25:1:0.15518:6.10359:60:6:0.0116:0:1.7 -19 42794080 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01055;SOR=Inf;LSEQ=GCGAGAGTGGGGACAGCTCT;RSEQ=GGGAGGACCCAGAGGGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:675:0:0,0:244,431:0:2,0:24.4:1:31.4:1:1:0:60:111.5:1:0:0.1 0/1:597:6:5,1:233,358:0.0101:2,2:12.8:1:27.3:1:0.03958:7.66:60:12:0.0101:0:1.2 -19 42794913 . T C 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.67477;SOR=1.72303;LSEQ=GGGCCCCAGCAGCTCCCCTG;RSEQ=CCCGTCCTGCCGCCACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:3:1,2:230,258:0.0061:2,2:19.7:1:17.3:1:1:1.78093:60:0.5:0.0021:0:2.3 0/1:286:3:2,1:143,140:0.0105:2,2:12.3:1:26.7:1:1:1.95:60:2:0.0071:0:1 -19 42794925 . G A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4278;SOR=0.35451;LSEQ=CTCCCCTGTCCCGTCCTGCC;RSEQ=CCACCATGGTCACCAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:5:2,3:252,242:0.01:2,2:29.4:1:27:1:0.68075:1.56059:60:4:0.0082:0:1.8 0/0:280:1:1,0:148,131:0.0036:2,0:1:0:23:0:1:0:60:2:0.0036:0:1 -19 42795554 . T C 227 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCAACGGCAAAGTCCTGGC;RSEQ=GCCACTGCACCCACTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:198:109,89:583,550:0.1486:2,2:25.9:1:29.8:1:0.35613:1.16:60:32:0.1468:0:1.1 0/0:1079:0:0,0:549,528:0:2,0:23:0:9:0:1:0:60:0:0:0:7 -19 42795961 . C CT 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.68669;SOR=1.51875;LSEQ=GTACCCCATCATTTCTTTGT;RSEQ=TTTTTTTTCAGTCTTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:3:0,3:55,368:0.007:2,0:19:1:31.3:1:1:0:60:6:0.0071:0.0023:0.3 0/1:282:3:0,3:55,224:0.0106:2,0:27.3:1:30.6:1:1:0:60:6:0.0108:0.0035:0 -19 42796287 . C T 189 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.49751;LSEQ=CACACCCAGCGGCCTGGTGC;RSEQ=GCCCCTGAGCCCAGCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1384:4:1,3:722,656:0.0029:2,2:6:1:28:1:0.35291:3.29924:60:8:0.0029:0:1 0/1:1137:84:38,46:526,526:0.0739:2,2:27.5:1:29.7:1:0.42858:1.21032:60:41:0.0734:0:1.1 -19 42797603 . C T 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04102;SOR=0;LSEQ=CTCCTCTCCCATCTGAGGCC;RSEQ=CTGTCTTGGCCTTCCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:15:7,8:56,37:0.1389:2,2:28.2:1:31.1:1:0.40085:1.72069:60:30:0.1429:0:1.2 0/0:30:0:0,0:23,7:0:2,0:23.9:1:30.6:1:1:0:60:60:1:0:0 -19 42798740 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09346;SOR=6.34228;LSEQ=GCTGCAGCCTTGCCATGCTG;RSEQ=CTGTGCCCTGCACAGGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:607:1:1,0:389,217:0.0016:2,0:1:0:31:0:1:0:60:2:0.0017:0:1 0/1:482:5:1,4:281,195:0.0104:2,2:5.6:1:25:1:0.16509:5.74502:60:10:0.0105:0:1 -19 42799049 . C T 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=1.81043;LSEQ=GTTTGTCTGCAGTTGAAGAT;RSEQ=CGTGAGGTGCGCCAGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:96:40,56:290,404:0.1215:2,2:25.9:1:29.7:1:1:1.00494:60:95:0.1226:0:1.1 0/1:579:116:58,58:207,255:0.2003:2,2:23.8:1:29.3:1:0.34861:1.23:60:57:0.2:0:1.2 -19 42799230 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.08501;SOR=Inf;LSEQ=ACTCTGGCACGGCCCAGGCT;RSEQ=CCCCGCCACTGCCTCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:147,234:0:2,0:23.4:1:30.4:1:1:0:60:13.654:1:0:0.5 0/1:300:3:2,1:123,172:0.01:2,2:11:1:25.7:1:0.57407:2.79:60:6:0.0106:0:1 -19 42799296 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08213;SOR=Inf;LSEQ=GCTGGGAGGGGGCTCCCCAG;RSEQ=CCTCCCCCCCACCCCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:57,164:0:2,0:26.9:1:29.1:1:1:0:60:6.893:0.9897:0:0.7 0/1:174:3:2,1:64,104:0.0172:2,2:33.7:1:28.7:1:0.5599:3.23:60:6:0.02:0:1 -19 42799299 . TC T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=1.2908;LSEQ=GGGAGGGGGCTCCCCAGCCC;RSEQ=CCCCCCACCCCCAGGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:2:0,2:58,159:0.0091:2,0:35:1:27.5:1:1:0:60:4:0.0102:0:0 0/1:170:2:2,0:60,105:0.0118:2,0:19:1:30.5:1:0.13643:0:60:4:0.0132:0.0059:0.5 -19 42799314 . G C 20 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98282;LSEQ=AGCCCTCCCCCCCACCCCCA;RSEQ=GTCCCTCCACAGCTGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:3,0:28,142:0.0172:2,0:16:1:13:1:0.0053:0:60:0:0:0:4 0/1:118:2:2,0:26,87:0.0169:2,0:6:0:23.5:1:0.05767:0:50:4:0.0211:0:5 -19 42799347 . A G 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.37752;SOR=2.41543;LSEQ=CTGCCACAGGCAGGTGAGGG;RSEQ=CCCCTGAGAAGATGCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:10,91:0.0192:2,0:42:0:13:1:1:0:60:0:0:0:1.5 0/1:66:3:1,2:7,56:0.0455:2,2:25.7:1:24.7:1:0.3257:3.87:60:2:0.0317:0:1.3 -19 43941594 . C T 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16506;SOR=0.2341;LSEQ=TGCAGAGAAGAAAACGCTGA;RSEQ=GTACGTTGCCTTCCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:6,2:0.3333:2,0:22:1:32.5:1:0.51515:0:60:8:0.3333:0:2 0/1:20:2:1,1:13,5:0.1:2,2:16:1:28.5:1:0.52105:2.46307:60:4:0.1:0:2.5 -19 43941596 . T C 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1587;SOR=0.22199;LSEQ=CAGAGAAGAAAACGCTGACG;RSEQ=ACGTTGCCTTCCCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:6,2:0.3333:2,0:23:1:33.8:1:0.51515:0:60:8:0.3333:0:2 0/1:21:2:1,1:14,5:0.0952:2,2:16:1:31:1:0.5:2.64575:60:4:0.0952:0:2.5 -19 43941641 . GC G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.29054;SOR=Inf;LSEQ=AGGCTACCCAAGAGGGAAGG;RSEQ=CCCCGTCCTATGATCACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:17,10:0:2,0:27.1:1:31:1:1:0:59.9:26:1:0:0.3 0/1:49:4:2,2:22,23:0.0816:2,2:31.8:1:31.3:1:1:1.04:60:8:0.0816:0:0.3 -19 43948553 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49671;SOR=Inf;LSEQ=TAACTGGGATTACAGGCATG;RSEQ=GCCACCATGCCCGGCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:25,20:0:2,0:28.4:1:29.9:1:1:0:60:90:1:0:0.1 0/1:51:2:1,1:27,22:0.0392:2,2:15:0:32:1:1:1.22232:60:4:0.0392:0:3.5 -19 43948561 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50318;SOR=Inf;LSEQ=ATTACAGGCATGTGCCACCA;RSEQ=GCCCGGCTAATTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:27,23:0:2,0:29.6:1:31:1:1:0:60:100:1:0:0.1 0/1:64:2:1,1:33,28:0.0313:2,2:23:0:32.5:1:1:1.17549:60:4:0.0323:0:3.5 -19 43948565 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50746;SOR=Inf;LSEQ=CAGGCATGTGCCACCATGCC;RSEQ=GGCTAATTTGTTGTTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:26,24:0:2,0:30.5:1:30.9:1:1:0:60:100:1:0:0.1 0/1:68:2:1,1:36,30:0.0294:2,2:27:0:31.5:1:1:1.19677:60:4:0.0299:0:3.5 -19 43948586 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.17933;SOR=0;LSEQ=GGCTAATTTGTTGTTGTTGT;RSEQ=GCTGTTGCTGCTGCTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:30,28:0.0333:2,2:40.5:1:29.5:1:1:1.07017:60:4:0.0333:0:1 0/0:81:0:0,0:43,38:0:2,0:27:1:30:1:1:0:59.7:80:1:0:0.4 -19 43948600 . CTGT C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.16403;SOR=0;LSEQ=TGTTGTTGCTGTTGCTGCTG;RSEQ=TGTTGTTGTTGAGACGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:26,29:0.0351:2,2:12.5:1:32.6:1:1:1.11:57.5:4:0.0351:0.0175:0.5 0/0:83:0:0,0:41,42:0:2,0:23.3:1:30.3:1:1:0:59.7:40.5:1:0:0.4 -19 43948630 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51265;SOR=Inf;LSEQ=TGTTGAGACGGAGTCTCACT;RSEQ=TGTCATCCAGGCTGGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:0:2,0:23.5:1:31.8:1:1:0:60:62:1:0:0.1 0/1:46:2:1,1:20,24:0.0435:2,2:6.5:1:29:1:1:1.20:60:4:0.0476:0:1 -19 45854503 . CCCTCA C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGTGGATGTAACACTTGC;RSEQ=CCTCCCCTCCAACCATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:22.5:1:30.5:1:1:0:60:4:0.5:0:0 0/0:1:0:0,0:1,0:0:0,0:16:0:32:0:1:0:60:2:1:0:0 -19 45854919 . T G 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1711;LSEQ=AGCAATCTGCTCTATCCTCT;RSEQ=CAGCGTCTCCTCTGATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1029:556:229,327:196,276:0.5403:2,2:25.6:1:31.9:1:0.94934:1.01404:60:60.778:0.5389:0:1.1 0/1:1028:172:68,104:362,490:0.1673:2,2:26.3:1:31.8:1:0.49879:1.12975:60:171:0.1685:0:1.1 -19 45855055 . A AC 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.35208;SOR=1.60293;LSEQ=GCTGCTGCACTTCCCCAACC;RSEQ=CCCCCCCGAATGGCCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:13:1,12:14,128:0.0839:2,1:23.9:1:31.5:1:1:1.3104:59.2:26:0.0861:0.0129:0.2 0/1:78:10:2,8:9,58:0.1282:2,2:22.1:1:29:1:0.62884:1.60:59.5:9:0.1216:0.0128:0.1 -19 45855060 . C G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0.11608;LSEQ=TGCACTTCCCCAACCACCCC;RSEQ=CCGAATGGCCAGTAGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:72:6,66:3,62:0.5255:1,2:22.7:1:31.6:1:0.49836:1.87:60:23:0.5227:0:1.1 0/1:62:7:0,7:5,50:0.1129:2,0:21.1:1:32.9:1:1:0:60:14:0.1167:0:1.1 -19 45855262 . G T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74878;SOR=1.30946;LSEQ=CCAACTTCTCTCACCCTGCC;RSEQ=TGCCTGGGCCACCTGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:15,2:10,3:0.5484:2,2:29.4:1:30:1:0.62781:2.19:60:16:0.5517:0:1.6 1/0:13:8:6,2:4,1:0.6154:2,2:22.4:1:29.8:1:1:1.30472:60:16:0.6154:0:1.4 -19 45855318 . A G 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05042;SOR=4.38875;LSEQ=AATCTCCCCCTTCCCCCCAG;RSEQ=GCCTGGCACGTAGATGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:3,0:62,5:0.0429:2,0:19:1:31:1:1:0:60:6:0.0435:0:1.7 0/1:30:5:5,0:23,2:0.1667:2,0:30.2:1:31.4:1:1:0:60:10:0.1667:0:1.2 -19 45855524 . G A 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16437;LSEQ=TTGGCCACCTGGACACCCTC;RSEQ=TCCACGGTCAGGTTGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1163:653:341,312:257,250:0.5615:2,2:24.9:1:30.2:1:0.63572:1.06:60:53.417:0.5603:0:1.1 0/1:1013:176:89,87:405,431:0.1737:2,2:25.1:1:29.7:1:0.61955:1.09:60:87:0.1745:0:1.1 -19 45856014 . C T 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1248;SOR=5.7318;LSEQ=AGCTACTCACCTTGAGAATG;RSEQ=GGCTCTGTGTGTAGACGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:572:1:0,1:285,286:0.0017:2,0:1:0:24:0:1:0:60:2:0.0018:0:1 0/1:603:6:3,3:304,293:0.01:2,2:29.8:1:28:1:1:1.03749:60:12:0.0101:0:1 -19 45856141 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00028;SOR=Inf;LSEQ=GTGGGACAGGGACAGCCTCA;RSEQ=GCGACCCAGGATGCTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:92,173:0:2,0:23.4:1:30:1:1:0:60:43.167:0.9962:0:0.6 0/1:184:9:2,7:45,130:0.0489:2,2:17.7:1:31.6:1:1:1.21032:60:18:0.0506:0:1.1 -19 45856144 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20482;LSEQ=GGACAGGGACAGCCTCACGC;RSEQ=ACCCAGGATGCTGTGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:144:59,85:33,71:0.5806:2,2:23.3:1:29.8:1:0.14523:1.49:60:35:0.5761:0:1.1 0/1:168:37:13,24:31,100:0.2202:2,2:22.1:1:29.2:1:0.20349:1.74:60:36:0.2182:0:1.1 -19 45856221 . GC G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12851;SOR=Inf;LSEQ=GGGACAGAGGGGAGGGGAGG;RSEQ=CCCTCTGTGCACCTAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:181,40:0:2,0:24.6:1:31.7:1:1:0:60:35.833:1:0:0.3 0/1:124:2:1,1:96,26:0.0161:2,2:16.5:1:30:1:0.38946:3.64248:60:4:0.0169:0:0 -19 45856260 . G A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGGGTGGGTGGTTCCCC;RSEQ=CGGGAGCAGACAGCAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:27:19,8:249,94:0.073:2,2:22.3:1:29.8:1:0.82419:1.115:60:54:0.074:0:1.3 0/0:276:0:0,0:196,80:0:2,0:23.6:1:29.9:1:1:0:60:68:1:0:0.2 -19 45856267 . C T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41497;SOR=2.5117;LSEQ=TGGGTGGTTCCCCGCGGGAG;RSEQ=AGACAGCAGAGCGGGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:2:0,2:297,132:0.0046:2,0:1:0:24:1:0.09616:0:60:4:0.0048:0:1 0/1:346:4:1,3:235,107:0.0116:2,2:11.3:1:24.8:1:0.09663:6.55003:60:8:0.0118:0:1 -19 45856468 . G C 291 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49058;LSEQ=CTCCTCAGAGCCACCTCCCC;RSEQ=ACCCCTCTCCACGCTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:731:632:338,294:53,44:0.8646:2,2:23.9:1:31.3:1:0.913:1.04769:60:69.222:0.8677:0:1.1 1/0:603:457:242,215:82,62:0.7579:2,2:23.8:1:30.4:1:0.44341:1.1747:60:90.4:0.7571:0:1.2 -19 45856630 . G A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41617;SOR=2.48343;LSEQ=GAGGTCAGGGTGGGTTCAGG;RSEQ=CACAGCCATCCTGGTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:2:2,0:138,347:0.0041:2,0:1:0:20.5:1:0.08222:0:60:1:0.0021:0:1 0/1:395:4:2,2:117,274:0.0101:2,2:19.3:1:25:1:0.58712:2.34:60:8:0.0102:0:1.3 -19 45856926 . C G 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGACTTCCCATATGACA;RSEQ=TACAATAGAGACAGTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:33:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:8:0:33:0:1:0:60:2:1:0:1 -19 45857049 . T C 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTGGAGCAAGTGGATTT;RSEQ=CAAATGGAACCAAAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:35:1:29:0:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:6:0:33:0:1:0:60:2:1:0:1 -19 45857820 . G A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00173;SOR=7.59711;LSEQ=AGCCTGATGTACTGGGGGCG;RSEQ=GGCATGGGGGTGTGTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:8,0:29,0:0.2162:1,0:22.8:1:31.1:1:1:0:60:16:0.2286:0:1.9 1/0:16:11:9,2:5,0:0.6875:0,2:29.5:1:28.8:1:1:0:60:22:0.7333:0:1.8 -19 45857867 . A G 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.31193;SOR=0;LSEQ=CCCATTCCTACATGCTGCAC;RSEQ=CACTCTCCTGTCACACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:75:75:74,1:0,0:1:0,1:26.5:1:29.7:1:1:0:60:36.5:1:0:1.2 1/1:34:33:31,2:0,0:0.9706:0,2:23.3:1:29.7:1:1:0:60:32:0.9697:0:1.3 -19 45857920 . A T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27694;SOR=0;LSEQ=TCAGAGTGTGAGAGGAATGA;RSEQ=GCTGACATAGCGGTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:3:1,2:161,24:0.016:2,2:13.3:1:22.3:1:0.0507:13.08781:60:2:0.011:0:1.7 0/0:126:0:0,0:101,25:0:2,0:23.2:1:29.7:1:1:0:60:62:1:0:0.3 -19 45858228 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.1399;SOR=Inf;LSEQ=GTCAGGCTTTTCACACATAT;RSEQ=CCCCTCCTCCTCCTCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:1,121:0:1,0:23:1:31.2:1:1:0:60:29.5:0.9916:0:0.3 0/1:74:2:0,2:4,68:0.027:2,0:24.5:1:25.5:1:1:0:60:4:0.027:0:2.5 -19 45858245 . C T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3427;SOR=1.44973;LSEQ=TATCCCCCTCCTCCTCCTCC;RSEQ=GGGCGTGTCTGAGGACCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:26:0,26:1,62:0.2921:1,1:24:1:30.1:1:1:0:60:25:0.2841:0:1.1 0/1:48:18:1,17:2,27:0.375:2,1:27.1:1:29.8:1:1:1.25325:60:36:0.383:0:1.3 -19 45858605 . ACT A 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCTAGGCAACAGAGCAAG;RSEQ=CTGTCTCAAAAAAAGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:7,1:0.2727:2,2:17.3:1:33.3:1:0.49091:3.05504:60:6:0.2727:0.0909:0 0/0:1:0:0,0:0,1:0:0,0:50:0:31:0:1:0:60:2:1:0:0 -19 45858784 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13573;SOR=Inf;LSEQ=CCTACCAGCTCACAGTGGAC;RSEQ=TGTACCACGGGCAAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:148,2:0:1,0:22.4:1:30.1:1:1:0:60:74:1:0:0.1 0/1:88:2:1,1:82,4:0.0227:1,2:22:0:32.5:1:0.11102:18.441:60:4:0.023:0:1 -19 45859092 . A T 59 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64959;SOR=0.36286;LSEQ=CTTTTTTTTTTTTTTTTTTT;RSEQ=AAGAGAGACAGGGTGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:4:0,4:4,99:0.037:1,0:10.8:1:29.5:1:1:0:60:8:0.0381:0:5.3 0/1:73:1:0,1:6,66:0.0137:2,0:20:0:30:0:1:0:60:2:0.0143:0:1 -19 45860158 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGTTACAGAGACGGAGAC;RSEQ=GAGAGGAAGGCTCACTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:32.5:1:30:1:1:0:60:4:0.3333:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 45861345 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAGCCTCGCGCTGTCGC;RSEQ=CAGGCTAGAGTGCAGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:22.5:1:28:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 45862016 . A AT 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.73398;SOR=0.71993;LSEQ=ATATTCCAACACAACAATGT;RSEQ=TTTTTTTTCATGATAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:5:5,0:259,23:0.0174:2,0:23.4:1:31.4:1:1:0:60:10:0.0177:0.0069:0 0/1:239:3:2,1:211,25:0.0126:2,2:33:1:30.3:1:0.29324:4.17882:60:6:0.0127:0:0 -19 45862022 . T C 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAACACAACAATGTATTTTT;RSEQ=TTCATGATAACTGTCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:290,36:0:2,0:23.1:1:30.3:1:1:0:60:107.667:1:0:0.1 0/1:277:20:18,2:212,45:0.0722:2,2:19.1:1:31.7:1:0.54349:1.91:60:40:0.0725:0:1.1 -19 45862194 . A G 200 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TTTGTTGAAGAAATAAATGA;RSEQ=TGAATGAATTTACATATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:0:0,0:192,438:0:2,0:22.9:1:30.5:1:1:0:60:56.273:1:0:0.1 0/1:588:84:28,56:169,335:0.1429:2,2:24.2:1:31.3:1:1:1.00894:60:83:0.1446:0:1.1 -19 45862449 . A G 87 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATCTCTACTAAGCTGAGA;RSEQ=CCTAAGGATGAGGGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:25.9:1:31.3:1:1:0:60:14:0.875:0:1 1/1:1:1:0,1:0,0:1:0,0:23:0:34:0:1:0:60:2:1:0:1 -19 45864751 . G T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01497;SOR=Inf;LSEQ=CTGATTCCAGCTGCTAGGAG;RSEQ=CCCAGCAGGGACAGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:605:0:0,0:400,204:0:2,0:24.2:1:31.4:1:1:0:60:85.286:0.9983:0:0.1 0/1:599:6:2,4:385,208:0.01:2,2:14.3:1:26.5:1:0.19232:3.69336:60:12:0.0102:0:1 -19 45865002 . C A 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42316;LSEQ=TCACGTGCCTGTCTCCCCAG;RSEQ=CAATGAGCACTCAGTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:606:479:224,255:62,63:0.7904:2,2:25.7:1:29.7:1:0.61537:1.12011:60:118.75:0.7917:0:1.1 1/0:493:303:139,164:91,99:0.6146:2,2:24:1:29:1:0.71078:1.08433:60:74.75:0.6152:0:1.2 -19 45865094 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41849;SOR=2.42339;LSEQ=TGTCACAAATAGCCATTGCC;RSEQ=CATAATGGCACAGACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:2:1,1:136,251:0.0051:2,2:22.5:1:28:1:1:1.84:60:4:0.0052:0:1 0/1:323:4:2,2:126,193:0.0124:2,2:19.3:1:28.8:1:0.65009:1.53:60:8:0.0126:0:1 -19 45865100 . T A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09409;SOR=Inf;LSEQ=AAATAGCCATTGCCGCATAA;RSEQ=GGCACAGACAGAGCAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:118,238:0:2,0:23.5:1:29.9:1:1:0:60:58.333:1:0:0.2 0/1:298:3:2,1:115,180:0.0101:2,2:10:1:22.3:1:0.56349:3.12:60:2:0.0068:0:3.3 -19 45865191 . CTTTT C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.48463;SOR=0.6828;LSEQ=CCTAAGTGGGTTCTTTTTTT;RSEQ=TCTTTTTTTTCTTTGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:18:0,18:1,55:0.2432:1,1:18.9:1:33.1:1:1:0:60:36:0.2571:0.0405:0.5 0/1:39:7:0,7:0,32:0.1795:1,0:20.6:1:29.2:1:1:0:60:6:0.1667:0.0256:0.6 -19 45865217 . T C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12981;SOR=0.36435;LSEQ=CTTTTTTTTCTTTGTTCAGA;RSEQ=GGAGTCTTGCCCTGTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:28:0,28:0,9:0.7568:0,1:20.4:1:29.5:1:1:0:60:27:0.75:0:1.2 1/0:19:10:0,10:0,9:0.5263:0,0:25.3:1:27.9:1:1:0:60:9:0.5:0:1.1 -19 45867026 . C T 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.34937;SOR=0.29819;LSEQ=GGGCTTGCGCTGGATGCACA;RSEQ=GCGCTGGGCCAGGCCGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:165,127:0.0102:2,2:40:1:30.3:1:1:1.54:60:6:0.0103:0:2 0/0:328:1:0,1:177,150:0.003:2,0:1:0:28:0:0.46037:0:60:2:0.0031:0:2 -19 45867190 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16742;SOR=5.54258;LSEQ=CTGCGAGGAGACGCTATCAG;RSEQ=GGCGACGGGGAGGCGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:0,1:123,136:0.0038:2,0:12:0:19:0:1:0:60:0:0:0:2 0/1:191:4:2,2:91,96:0.0209:2,2:20:1:24.3:1:1:1.05:60:3:0.0167:0:1.8 -19 45867216 . T TG 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.02178;SOR=1.72489;LSEQ=CGGGGAGGCGGGAAAGGGAC;RSEQ=GGGGGGCAGCGGGGGGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:40:21,19:87,98:0.1762:2,2:24:1:31.4:1:0.60178:1.24:60:80:0.1778:0.0132:0.1 0/1:215:58:33,25:78,79:0.2698:2,2:28.8:1:30:1:0.36094:1.34:60:28:0.2679:0.0186:0.2 -19 45867259 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1534;LSEQ=CTCACCCTGCAGCACTTCGT;RSEQ=GGGCAGCACGGGGTTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:263:176:103,73:44,43:0.6692:2,2:23.7:1:30.2:1:0.23695:1.38:60:57.667:0.6758:0:1.2 0/1:233:55:27,28:97,81:0.2361:2,2:25.5:1:29.4:1:0.53746:1.24072:60:110:0.2402:0:1.3 -19 45867301 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08078;SOR=Inf;LSEQ=GTGGGCGTCCGTCTCCCGGG;RSEQ=GGCGCTGGCCTCCCGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:166,140:0:2,0:25.8:1:30.3:1:1:0:60:37.25:1:0:0.5 0/1:234:3:1,2:110,121:0.0128:2,2:23.3:1:29.7:1:1:1.81373:60:6:0.0132:0:1.3 -19 45868006 . A T 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00274;SOR=0.46704;LSEQ=CAGACAGGCAGACTCACAGC;RSEQ=AGCAACAGACAGACATGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:185:142:124,18:35,8:0.7676:2,2:23.5:1:30.4:1:0.325:1.57:60:46.333:0.7637:0:1.6 1/0:132:80:67,13:45,7:0.6061:2,2:22.7:1:30.9:1:0.80524:1.24528:60:160:0.6061:0:1.5 -19 45868038 . G A 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.47018;LSEQ=GACATGGGCAGACAGGAGAC;RSEQ=GGCGGGCAGCCCACACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:319:166:123,43:115,37:0.5204:2,2:22.8:1:29.8:1:0.79646:1.08628:60:54.333:0.5175:0:1.6 0/1:240:81:52,29:117,42:0.3375:2,2:22.2:1:29.5:1:0.13781:1.55069:60:80:0.339:0:1.6 -19 45868309 . T G 296 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3859;LSEQ=CCTCCAGTAACCTCATAGAA;RSEQ=CGGCAGTGGGGCAGGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:800:630:339,291:93,76:0.7875:2,2:25.2:1:31.9:1:0.79482:1.05037:60:41:0.7905:0:1.2 1/0:634:373:210,163:142,119:0.5883:2,2:23.9:1:31.8:1:0.68482:1.08:60:123.333:0.5949:0:1.1 -19 45868478 . T A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33088;LSEQ=CCCAACCACTCTTCAAACCC;RSEQ=GGTCTCCACACCTCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:276:229:36,193:3,43:0.8297:2,2:23.3:1:30.6:1:0.16157:2.67:60:37.167:0.8352:0:1.1 1/0:193:119:21,98:13,61:0.6166:2,2:23:1:30.8:1:1:1.01:60:238:0.6198:0:1.1 -19 45868487 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16712;SOR=Inf;LSEQ=TCTTCAAACCCTGGTCTCCA;RSEQ=ACCTCCCAGCTGGCTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:23,211:0:2,0:24.5:1:32:1:1:0:60:45.8:1:0:0.9 0/1:163:2:1,1:25,135:0.0123:2,2:27:1:29:1:0.29607:5.31:60:4:0.0124:0:1 -19 45868647 . G A 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01084;SOR=0;LSEQ=CACTTTGTGAGGCTGAGGTG;RSEQ=GCAGATCACGAGGTCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:0,10:0,4:0.7143:0,0:27.2:1:31.2:1:1:0:54.4:20:0.7143:0:2 0/0:6:0:0,0:0,6:0:0,0:20.3:1:30.5:1:1:0:58:12:1:0:0.3 -19 45868649 . C G 109 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0031;SOR=0;LSEQ=CTTTGTGAGGCTGAGGTGGG;RSEQ=AGATCACGAGGTCAGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:1:0,1:27.3:1:28.8:1:1:0:53.3:6:1:0:2 0/1:6:2:0,2:0,4:0.3333:0,0:14.5:1:32.5:1:1:0:60:4:0.3333:0:1 -19 45871606 . T C 97 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15385;SOR=0.12384;LSEQ=AAATGCCTCTCCATAAATAC;RSEQ=GGGCTAGTAAGTTTCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:0.8333:0,0:25.1:1:29.3:1:1:0:60:9:0.8182:0:1.6 0/1:3:1:1,0:1,0:0.3333:0,0:1:0:29:0:1:0:60:2:0.3333:0:1 -19 45872036 . C T 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02039;SOR=0.6481;LSEQ=GGGGGCAGGGGGAGCTTGTG;RSEQ=TCATTGGAGGCACAAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:234:79,155:30,62:0.7178:2,2:22.4:1:30:1:0.89662:1.05:60:233:0.7169:0:1.1 1/0:225:140:46,94:18,67:0.6222:2,2:22.7:1:29.7:1:0.06817:1.82:60:139:0.6261:0:1.1 -19 45872446 . G A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09839;SOR=Inf;LSEQ=GGGCAACACACAGGGTCTCA;RSEQ=AACCTTGGGCACACAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:87,257:0:2,0:25.8:1:31.2:1:1:0:60:85:1:0:0.1 0/1:296:3:2,1:84,209:0.0101:2,2:9.3:1:21.7:1:0.20331:4.95:60:2:0.0069:0:2.7 -19 45873366 . C T 66 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72636;SOR=0.63399;LSEQ=AGCCCCACCGGTCGAGTGGG;RSEQ=GGGTCGGGCCCACCGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:5:1,4:298,191:0.0101:2,2:16:1:28.8:1:0.08199:6.21909:60:10:0.0103:0:1.8 0/0:466:3:1,2:273,189:0.0064:2,2:9:1:25.3:1:0.57094:2.88228:60:6:0.0065:0:1 -19 45873531 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15936;SOR=Inf;LSEQ=GTCAGTTCCCGTCCCCTCAG;RSEQ=CCCTCTCCCGCCTCCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:53,172:0:2,0:24.1:1:31.3:1:1:0:60:55.25:1:0:0.1 0/1:150:2:1,1:34,114:0.0133:2,2:22.5:1:31:1:0.41342:3.32:60:4:0.0133:0:1 -19 45873591 . GC G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGGTGACGGGCCCGGC;RSEQ=CCCCGGTAACCCTCAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:67,70:0.0144:2,2:28:1:33:1:1:1.04:60:4:0.0146:0:0 0/0:52:0:0,0:19,33:0:2,0:24.8:1:31.2:1:1:0:60:51:1:0:0.4 -19 45873942 . G C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00125;SOR=0.20428;LSEQ=CCCGTCAATCCGCTAGGGCA;RSEQ=AGCCAATCGGGATACTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:88:81:1,80:1,6:0.9205:2,1:20.2:1:32.1:1:0.15361:12.42128:60:80:0.9195:0:1 1/0:50:35:0,35:0,14:0.7:1,1:22.8:1:32.7:1:1:0:60:70:0.7:0:1.3 -19 45873959 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14605;SOR=Inf;LSEQ=GCAGAGCCAATCGGGATACT;RSEQ=CGCGTGCGCACGGAAAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:1,58:0:1,0:26.2:1:32.1:1:1:0:60:58:1:0:0.9 0/1:37:2:0,2:0,35:0.0541:1,0:13:1:29:1:1:0:60:4:0.0571:0:1.5 -19 46373526 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCTCCACCTTCCGGGTT;RSEQ=ACGCCATTCTCCTGCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:31:1:1:0:60:4:1:0:1 -19 46375666 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1937;SOR=Inf;LSEQ=TGGCCATCCAGCAGGCGCCG;RSEQ=GCAAGATGCTGACCTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:145,49:0:2,0:22.5:1:30.9:1:1:0:60:47.5:1:0:0.1 0/1:153:2:1,1:111,40:0.0131:2,2:30.5:1:29:1:0.46543:2.75327:60:4:0.0134:0:1 -19 46375779 . C T 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCCACTCGCTGTCTTTCAA;RSEQ=GACTGCTTCGTCAAGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:150,199:0:2,0:24.6:1:30.4:1:1:0:60:57.167:0.9971:0:0.1 0/1:352:101:44,57:113,138:0.2869:2,2:24.4:1:29.4:1:0.81385:1.06062:59.9:32.667:0.2849:0:1.2 -19 46375844 . A T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19495;SOR=Inf;LSEQ=GGGCTCCTACTGGGCCCTAC;RSEQ=CCCCAGCTCAGGGAACATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:30,129:0:2,0:23.4:1:29.9:1:1:0:60:158:1:0:0.1 0/1:127:2:1,1:30,95:0.0157:2,2:5:0:28.5:1:0.43007:3.13:60:4:0.0161:0:0 -19 46375850 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1958;SOR=Inf;LSEQ=CTACTGGGCCCTACACCCCA;RSEQ=CTCAGGGAACATGTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:26,117:0:2,0:23.5:1:32:1:1:0:60:70.5:1:0:0.1 0/1:114:2:1,1:25,87:0.0175:2,2:9.5:1:30:1:0.40568:3.43:60:4:0.0177:0:1 -19 46375973 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAACGGGACAGGGTCTG;RSEQ=TGCCTCGACCACCACCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:3,24:0.069:2,2:20:1:26.5:1:0.26108:7.07:60:4:0.069:0:1 0/0:8:0:0,0:1,7:0:2,0:14.9:1:31.9:1:1:0:60:16:1:0:0.1 -19 46376217 . C A 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06619;SOR=0;LSEQ=GAACAGACACCAGCACCTCC;RSEQ=AAACTGGACGTGGGGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:2,3:10,19:0.1471:2,2:24.8:1:30:1:1:1.26:60:10:0.1471:0:1 0/0:25:0:0,0:11,14:0:2,0:25.7:1:28.7:1:1:0:60:24:1:0:0.1 -19 47724690 . CCT C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCGAGAGGAGAGCCCCCC;RSEQ=CCCAGTGTCACCCCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:11,1:0.1538:2,2:25:1:31:1:0.27473:8.12278:60:4:0.1818:0.0769:0.5 0/0:1:0:0,0:1,0:0:0,0:20:0:32:0:1:0:60:2:1:0:0 -19 47725036 . G A 134 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.91897;LSEQ=CTGCCCCCCGAGTCCCTGAC;RSEQ=TCCACCGGGCGGGTGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:884:1:1,0:417,465:0.0011:2,0:1:0:25:0:0.47339:0:60:2:0.0012:0:1 0/1:910:25:12,13:444,441:0.0275:2,2:25.3:1:29:1:0.84259:1.09058:60:24:0.0268:0:1.2 -19 47726220 . CAAAA C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=21.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGAGCAAAACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:28.5:1:32:1:1:0:45.5:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 47726823 . C CA 31 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.03752;LSEQ=AACAGAGCAAGACTCCGTGT;RSEQ=AAAAAAAAAATTTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:2,0:26,1:0.069:1,0:20.5:1:31.5:1:1:0:60:4:0.069:0:0 0/1:14:1:1,0:13,0:0.0714:1,0:43:0:32:0:1:0:60:2:0.0714:0:0 -19 47729764 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12382;SOR=Inf;LSEQ=CATCTGGCGGGGGCCGCCTG;RSEQ=CGCCCCCTCCTCCGGCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:263,56:0:2,0:23.2:1:31.4:1:1:0:60:34.444:1:0:0.2 0/1:319:4:1,3:246,69:0.0125:2,2:7.3:1:26.5:1:0.03722:10.58981:60:8:0.0127:0:1.5 -19 47731304 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50311;SOR=0;LSEQ=GCCACACCCTCCCAGTGGCC;RSEQ=GGCTGGGCCCGCCACCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:50,0:0.0385:1,2:19.5:1:27:1:0.03846:0:60:4:0.0392:0:1 0/0:40:0:0,0:39,1:0:1,0:25.2:1:29.8:1:1:0:60:39:1:0:0.3 -19 47731354 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22929;SOR=0;LSEQ=TCCCACTTCTCCAGTTCCTC;RSEQ=GAGTCTCCAGCCCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:87,53:0.0141:2,2:6:1:29.5:1:1:1.63549:60:4:0.0143:0:1 0/0:154:0:0,0:91,63:0:2,0:22:1:29.2:1:1:0:60:76:1:0:0.3 -19 47731359 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22782;SOR=0;LSEQ=CTTCTCCAGTTCCTCCGAGT;RSEQ=TCCAGCCCTCTCTCTTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:88,63:0.0131:2,2:20:1:28:1:1:1.3937:60:4:0.0135:0:1 0/0:167:0:0,0:98,69:0:2,0:23.5:1:30.4:1:1:0:60:26.833:1:0:0.3 -19 47731444 . C T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15914;SOR=0.20495;LSEQ=GCGGGCCTCGGGGCCGGCTG;RSEQ=GGGGACCCCCAGGCCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:0,3:66,132:0.0149:2,0:6.7:1:28.7:1:0.55226:0:60:6:0.0153:0:1.3 0/0:324:1:0,1:142,181:0.0031:2,0:1:0:27:0:1:0:60:2:0.0032:0:1 -19 47731480 . G T 31 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25873;SOR=0.24822;LSEQ=AGCGGGAACCCCCCAGGGCG;RSEQ=CGGTGACGGCGGGTGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:63,76:0.0142:2,2:17:0:31:1:1:1.20:60:4:0.0147:0:1.5 0/0:282:1:0,1:135,143:0.0035:2,0:1:0:25:0:1:0:60:2:0.0037:0:1 -19 47731544 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.55297;SOR=Inf;LSEQ=GGGCAGCAGGGTGGGGGCGG;RSEQ=GGGGGCGGCAGCCAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:37,35:0:2,0:22.1:1:27.6:1:1:0:60:5.545:1:0:0.5 0/1:142:3:1,2:67,70:0.0211:2,2:6.3:1:26:1:1:1.90576:60:6:0.0222:0:1.7 -19 47731549 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.54557;SOR=Inf;LSEQ=GCAGGGTGGGGGCGGCGGGG;RSEQ=CGGCAGCCAGGCCGGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:37,38:0:2,0:23.7:1:31.1:1:1:0:60:24:1:0:0.6 0/1:142:2:1,1:70,70:0.0141:2,2:45.5:1:29:1:1:1:60:4:0.0144:0:1.5 -19 47731560 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52299;SOR=Inf;LSEQ=GCGGCGGGGGCGGCAGCCAG;RSEQ=CCGGGCTCGCAGAGGCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:47,44:0:2,0:21.5:1:31.1:1:1:0:60:29.333:0.9888:0:0.5 0/1:145:2:1,1:74,69:0.0138:2,2:42:1:29:1:1:1.07192:60:4:0.014:0:3 -19 47731594 . G T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15949;SOR=Inf;LSEQ=GGCCGCAGGACACTGCCGAG;RSEQ=GCACCAGGCGGCCGAGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:93,71:0:2,0:21.6:1:31.2:1:1:0:60:53.667:1:0:0.3 0/1:256:4:1,3:135,115:0.0156:2,2:6.5:1:27:1:0.34015:3.50554:60:8:0.0162:0:1 -19 47731606 . C T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63168;SOR=2.4414;LSEQ=CTGCCGAGGGCACCAGGCGG;RSEQ=CGAGCGGGAAGGGGCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:0,1:118,85:0.0049:2,0:1:0:28:0:0.42157:0:60:2:0.005:0:1 0/1:252:3:2,1:134,113:0.0119:2,2:13.3:1:28.3:1:1:1.68:60:6:0.0124:0:1 -19 47731632 . G T 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62527;SOR=2.74877;LSEQ=GGGAAGGGGCGCGGGCCGTC;RSEQ=CGGGCCAGGCCCTCTACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:1:0,1:174,94:0.0037:2,0:1:0:27:0:0.35316:0:60:2:0.0038:0:1 0/1:295:3:0,3:176,116:0.0102:2,0:9:1:22.7:1:0.06465:0:60:2:0.0069:0:2.3 -19 47731653 . C T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37852;SOR=3.52887;LSEQ=CGGGCCAGGCCCTCTACGGG;RSEQ=TCCGGGGAGCTGCCCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:1:1,0:192,112:0.0033:2,0:30:0:12:0:1:0:60:0:0:0:2 0/1:348:4:1,3:206,138:0.0115:2,2:14.3:1:26.3:1:0.30759:4.45958:60:3:0.0088:0:2.3 -19 47731692 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09039;SOR=0;LSEQ=TGGCGTGCGCGGGCCATGGC;RSEQ=CTCCCTGGGGCCTGCGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:2,1:171,125:0.01:2,2:31:1:28.7:1:1:1.46:60:6:0.0103:0:1.7 0/0:366:0:0,0:200,164:0:2,0:26.6:1:30:1:1:0:60:59.667:0.9944:0:0.2 -19 47731744 . C A 27 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.77302;LSEQ=AGCAGGTCAGCAGGGAAGTA;RSEQ=CAGGGCCCACTGTACCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:61,118:0.011:2,2:7:0:31.5:1:1:1.93:60:4:0.0112:0:1 0/0:235:2:2,0:97,136:0.0085:2,0:1:0:27.5:1:0.17643:0:60:4:0.0088:0:1 -19 47731758 . A C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50297;SOR=Inf;LSEQ=GAAGTACCAGGGCCCACTGT;RSEQ=CCTCCAGCCTACCCGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:38,110:0:2,0:24.4:1:29.2:1:1:0:60:147:1:0:0.1 0/1:179:2:1,1:65,112:0.0112:2,2:5:0:29:1:1:1.72:60:4:0.0114:0:0 -19 47731829 . C T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10656;SOR=0.44893;LSEQ=TGTGCATGCGGAGGGGGTGA;RSEQ=GGCCCCACAGAGACACGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:1,17:2,22:0.4286:2,1:24.1:1:30.6:1:1:1.5301:60:36:0.4286:0:1 0/1:40:10:1,9:3,27:0.25:2,2:23.9:1:28.8:1:1:1:60:20:0.2632:0:1 -19 47735745 . G A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCCCACTGCACACACGTC;RSEQ=GAGCATGCACACCTGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:0:0,0:360,211:0:2,0:25.2:1:29.9:1:1:0:60:56.1:1:0:0.1 0/1:698:28:18,10:404,264:0.0401:2,2:28.4:1:30.4:1:0.84393:1.18:60:56:0.0406:0:1.1 -19 47735875 . T C 197 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCATCCTGTCTCATAGCTT;RSEQ=CCATTCCGTTTCTTTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:278,449:0:2,0:27.1:1:29.9:1:1:0:60:37.263:0.9986:0:0.1 0/1:993:82:35,47:383,528:0.0826:2,2:29.1:1:31:1:0.90763:1.03:59.8:40:0.0818:0:1.2 -19 48922772 . CT C 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTGGGAATTGTAGTTCTTT;RSEQ=TTTTTTTTTTTTCCCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:7:0:32:0:1:0:60:2:1:0:0 1/1:2:2:2,0:0,0:1:0,0:14:1:31:1:1:0:60:4:1:0.5:0 -19 48923101 . C A 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12874;SOR=5.91384;LSEQ=GGCCCAGGGCTGGGCTGGAG;RSEQ=TGGGGCTGGGGCTGGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:1,9:0.1667:2,0:39:1:32.5:1:1:0:60:4:0.1667:0:1 1/0:7:4:0,4:0,3:0.5714:0,0:17.3:1:30.3:1:1:0:60:8:0.5714:0:1 -19 48945339 . T TC 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14773;SOR=Inf;LSEQ=AAGGGGCTAAGGGCCTACAT;RSEQ=CCCACATCACAGACAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:18,2:0:2,0:25:1:30.3:1:1:0:60:40:1:0:0.1 0/1:13:2:2,0:11,0:0.1538:0,0:11:1:28.1:1:1:0:60:4:0.1538:0.0769:0 -19 48945528 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.501;SOR=0;LSEQ=GTCTTCTACATGCTCCTGGT;RSEQ=GCCATGGGCCTGTCCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:70,110:0.0109:2,2:32.5:1:29:1:1:1.57:60:4:0.0111:0:1.5 0/0:159:0:0,0:54,105:0:2,0:25.1:1:29.7:1:1:0:60:30.8:1:0:0.2 -19 49004919 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20085;SOR=0;LSEQ=ACCCCTCCCATGACCCTGCC;RSEQ=CGCCACACTGACTCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,6:0.1:2,2:47:0:31:1:1:1.77272:60:4:0.1:0:1.5 0/0:24:0:0,0:12,12:0:2,0:24.1:1:29.8:1:1:0:60:48:1:0:0.4 -19 49256974 . AG A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50435;SOR=Inf;LSEQ=TATTTATTGTATACAAGACA;RSEQ=GGGGGGCAGGATAAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:0:2,0:19.8:1:31.5:1:1:0:60:38:1:0:0 0/1:27:2:2,0:19,6:0.0741:2,0:27.5:1:30:1:1:0:60:4:0.0769:0.037:0 -19 49535186 . A T 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49624;SOR=0;LSEQ=CCCCTGGAGGGAGGAAGGGG;RSEQ=ACTGTATCTGAGAGAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:37,28:0.0299:2,2:19.5:1:24.5:1:1:1.31586:56:4:0.0303:0:3.5 0/0:66:0:0,0:37,28:0:2,0:30.5:1:29:1:1:0:54.2:130:1:0:0.1 -19 49535205 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50136;SOR=Inf;LSEQ=GAACTGTATCTGAGAGAGAG;RSEQ=AGCCAATTGGGTCCGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:45,34:0:2,0:26.7:1:32:1:1:0:55.2:78:1:0:0.2 0/1:95:2:1,1:48,45:0.0211:2,2:41.5:1:29.5:1:1:1.06598:60:4:0.0213:0:1 -19 49535232 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50072;SOR=Inf;LSEQ=TTGGGTCCGCTGACTCCGGC;RSEQ=GGGTTCCCGTGCCGCGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:38,44:0:2,0:27.4:1:29.7:1:1:0:56.5:81:1:0:0.2 0/1:97:2:1,1:46,49:0.0206:2,2:13.5:1:32.5:1:1:1.06:60:4:0.0208:0:1 -19 49535279 . C A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.60638;SOR=2.20032;LSEQ=CTCACTCCCTGTCTCACTCC;RSEQ=CCACGGAGACTCAATTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:16,35:0.0192:2,0:1:0:27:0:0.32692:0:60:2:0.02:0:1 0/1:48:2:1,1:16,30:0.0417:2,2:33:1:30.5:1:1:1.85:54.5:4:0.0426:0:1 -19 49535281 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60982;SOR=2.15746;LSEQ=CACTCCCTGTCTCACTCCCC;RSEQ=ACGGAGACTCAATTTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:1,0:15,34:0.0196:2,0:2:0:17:0:0.32:0:60:0:0:0:2 0/1:48:2:1,1:16,30:0.0417:2,2:31.5:1:28:1:1:1.85:51:4:0.0426:0:2 -19 49535284 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23059;SOR=Inf;LSEQ=TCCCTGTCTCACTCCCCCAC;RSEQ=GAGACTCAATTTACTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:15,31:0:2,0:25.2:1:30.8:1:1:0:55.9:92:1:0:0.1 0/1:43:2:1,1:13,27:0.0465:2,2:32:1:29:1:1:2.04:51:4:0.0465:0:2 -19 49610389 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGTGAGCGTGGGGACAC;RSEQ=GGGAAAGGCCTGGGACACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29:1:1:0:60:4:1:0:1.5 -19 49611319 . C T 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00036;SOR=Inf;LSEQ=CGCAAGGAGGAGCTGCGTGG;RSEQ=GGCGGTGGCGACATGGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:0:2,0:28.7:1:30.8:1:1:0:60:54:1:0:0.1 0/1:16:7:2,5:4,5:0.4375:2,2:32.1:1:30.4:1:0.63287:1.91506:60:14:0.4375:0:1.4 -19 49611329 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13289;SOR=Inf;LSEQ=AGCTGCGTGGCGGCGGTGGC;RSEQ=ACATGGCGGAGCCCTCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:0:2,0:25.9:1:29.9:1:1:0:60:26:1:0:0.1 0/1:16:2:1,1:5,9:0.125:2,2:30.5:1:28.5:1:1:1.73:60:4:0.125:0:1.5 -19 50143171 . G C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.49854;SOR=0;LSEQ=AGGGCTCAGTTCTGGGTCCC;RSEQ=GGGGACACCCTCCCGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:20,11:0.0606:2,2:21:1:28.5:1:1:1.78367:60:4:0.0606:0:1 0/0:26:0:0,0:18,8:0:2,0:21.3:1:27.4:1:1:0:60:25:1:0:0.2 -19 50143214 . G C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50279;SOR=Inf;LSEQ=GCCCACTACCTGGATGAACT;RSEQ=GATGGTCAGCGCGCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:0:2,0:31.9:1:31.4:1:1:0:60:35:1:0:0.3 0/1:47:2:1,1:19,26:0.0426:2,2:48:1:27:1:1:1.36:60:4:0.0426:0:1 -19 50143225 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.1897;SOR=0;LSEQ=GGATGAACTGGATGGTCAGC;RSEQ=CGCTCTTGCCCACGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:12,22:0.0556:2,2:46.5:1:30.5:1:1:1.80:60:4:0.0556:0:1 0/0:46:0:0,0:17,29:0:2,0:31.2:1:29.8:1:1:0:60:22:1:0:0.2 -19 50902014 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15519;SOR=Inf;LSEQ=CCAGTCCAGAGTAGGAAAAG;RSEQ=CTCGTGGTCATGGTGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:202,8:0:1,0:23.9:1:31.2:1:1:0:60:69:1:0:0.1 0/1:137:2:2,0:126,9:0.0146:2,0:23:1:29:1:1:0:60:4:0.0148:0:1 -19 50902265 . CAGG C 138 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.30164;SOR=0.66951;LSEQ=CAGAACACAGGCTGCAGGAG;RSEQ=AGGAGGAGGAGCTGCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1750:20:11,9:826,901:0.0114:2,2:27.5:1:32:1:0.65384:1.33:60:40:0.0116:0.0034:0.4 0/0:1823:14:5,9:878,927:0.0077:2,2:21.6:1:31.8:1:0.42495:1.70436:60:28:0.0077:0.0022:0.1 -19 50902843 . G A 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGCTCCTGGGGCAGAGGCC;RSEQ=GGCCAGGTCAGCCCCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:4,224:0:1,0:25.4:1:31.3:1:1:0:60:227:1:0:0.1 0/1:185:16:0,16:8,161:0.0865:1,1:21.7:1:31.9:1:1:0:60:32:0.0865:0:1.1 -19 50905412 . A G 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=77.72266;LSEQ=CCCCAGGATCAGCGGGTTGG;RSEQ=GGGTCCCCTCGGGAGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1486:1:1,0:723,762:7e-04:2,0:47:0:30:0:0.48721:0:60:2:7e-04:0:1 0/1:1386:69:33,36:640,675:0.0498:2,2:20.5:1:30.3:1:0.9024:1.03433:60:68:0.0501:0:1.2 -19 50905655 . G A 195 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=113.57039;LSEQ=GGCCTCTGCCTCACTTCTCC;RSEQ=GCCTCTATCCCCACCCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1350:1:1,0:660,689:7e-04:2,0:1:0:27:0:0.48963:0:60:2:8e-04:0:1 0/1:1248:97:47,50:559,590:0.0777:2,2:24.1:1:29.6:1:1:1.00793:60:96:0.0781:0:1.2 -19 50905762 . T C 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTGGCTGGAGCTCCCAGC;RSEQ=GGGAAATACGCCCTGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1395:0:0,0:709,685:0:2,0:24.7:1:30.5:1:1:0:60:65.381:0.9993:0:0.2 0/1:1431:83:44,39:665,679:0.058:2,2:23.5:1:29.5:1:0.5725:1.15:60:166:0.059:0:1.2 -19 50906159 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13417;SOR=Inf;LSEQ=GCACAGAGGGTGTGGAGATG;RSEQ=CCTGGAGGTGAGAGCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:68,73:0:2,0:26.9:1:31.3:1:1:0:60:22.5:1:0:0.1 0/1:82:2:2,0:38,42:0.0244:2,0:23:1:32:0:0.23487:0:60:4:0.0256:0:1 -19 50906179 . CAGGAGCCAGGGTGA GCCGTACCGGATCTCAAAGTCGACGTTG 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.55447;SOR=0;LSEQ=GCCTGGAGGTGAGAGCAGAG;RSEQ=GCCACGTAGGGCCGGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:2,1:92,70:0.0182:2,2:21:1:30.1:1:1:1.52:60:6:0.0186:0.0182:0 0/0:91:0:0,0:55,36:0:2,0:22.4:1:31.6:1:1:0:60:21.75:1:0:0.3 -19 50906239 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13638;SOR=Inf;LSEQ=GGACAGCCCCGGGGAGATGG;RSEQ=AGGTGCAGCCTCCCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:277,62:0:2,0:22.9:1:32:1:1:0:60:55.5:1:0:0.1 0/1:199:2:1,1:164,33:0.0101:2,2:23.5:1:26:1:0.31323:4.91108:60:4:0.0102:0:1 -19 50906507 . C T 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCACGCCCCACACCATTT;RSEQ=CCGGGGTCCCCGCCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:719:63:20,43:275,381:0.0876:2,2:24.1:1:29.6:1:0.1401:1.55092:60:62:0.0879:0:1.1 0/0:692:0:0,0:272,419:0:2,0:21:0:16:0:1:0:60:0:0:0:7 -19 50906519 . G A 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03415;SOR=7.43749;LSEQ=CACCATTTCCCGGGGTCCCC;RSEQ=CCAGCCTCCGCGTCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:1:1,0:233,366:0.0017:2,0:1:0:25:0:0.39:0:60:2:0.0017:0:1 0/1:570:7:5,2:213,350:0.0123:2,2:24.1:1:28.7:1:0.11244:4.10:60:14:0.0125:0:1 -19 50906529 . G A 138 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=35.62065;LSEQ=CGGGGTCCCCGCCAGCCTCC;RSEQ=CGTCCTGAGCCATCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:1:1,0:206,334:0.0018:2,0:1:0:26:0:0.38262:0:60:2:0.0019:0:1 0/1:485:30:12,18:165,287:0.0619:2,2:16.3:1:28.3:1:0.6997:1.16:60:29:0.0614:0:1.1 -19 50909389 . T G 281 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07302;SOR=1.321;LSEQ=CAATCTCCGTTCTTCAGGCT;RSEQ=ATGTGACGGGGACCCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:614:485:357,128:92,35:0.7899:2,2:24.8:1:31.6:1:0.8218:1.06:60:68.286:0.7888:0:1.1 1/1:555:462:318,144:68,24:0.8324:2,2:23.2:1:31.2:1:0.38518:1.28244:60:76:0.8367:0:1.2 -19 50909405 . G A 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTTATGTGACGGGGACCC;RSEQ=CAGCCTGCTGCACACCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:817:0:0,0:528,285:0:2,0:24.1:1:30.1:1:1:0:60:46.824:0.995:0:0.7 0/1:751:47:30,17:437,266:0.0626:2,2:25.1:1:30:1:0.87746:1.07:60:94:0.0639:0:1.9 -19 50909765 . C T 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01313;SOR=1.36786;LSEQ=GTGCAGCACAGCATCATCAC;RSEQ=GACCTGCAGGTGCCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1293:130:58,72:586,577:0.1005:2,2:24.2:1:30.7:1:0.22968:1.26051:60:129:0.1008:0:1.2 0/1:1244:165:83,82:545,530:0.1326:2,2:25.9:1:30.2:1:0.93356:1.0159:60:330:0.1336:0:1.2 -19 50910079 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11546;SOR=Inf;LSEQ=CTCCCTGGCCCCCAACCCTA;RSEQ=CTCCATCCCCACCCAGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:89,13:0:2,0:26.3:1:31.7:1:1:0:60:33:1:0:0.3 0/1:53:2:1,1:47,4:0.0377:2,2:36.5:1:27:1:0.18142:10.62088:60:4:0.0385:0:1 -19 50910196 . A G 176 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.02128;LSEQ=CTTCTCCTGCTCCACCTCCC;RSEQ=CCCCCAACCCCTGGTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:792:81:60,21:469,240:0.1023:2,2:26.8:1:27.9:1:0.17081:1.46:60:12.5:0.1015:0:1.1 0/0:829:2:1,1:513,307:0.0024:2,2:25.5:1:11.5:1:1:1.66985:60:0:0:0:4 -19 50911847 . C A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01023;SOR=Inf;LSEQ=ATAGGGTTTTGCCATGTTGC;RSEQ=CAGGCTGATCTGAAACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:114,0:0:1,0:26.1:1:31.2:1:1:0:60:56:1:0:0.1 0/1:78:5:5,0:73,0:0.0641:1,0:26:1:29.2:1:1:0:60:10:0.0649:0:1 -19 50911947 . AT A 177 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.51361;SOR=0.88358;LSEQ=CTGCTCCCAGCCAATGAATG;RSEQ=TTTTTTTTTTTAAAGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:61:46,15:372,172:0.0995:2,2:29:1:31.1:1:0.30734:1.42:60:122:0.1017:0.0016:0.4 0/1:742:66:41,25:433,232:0.0889:2,2:20.6:1:29.4:1:0.68541:1.13783:60:132:0.0905:0.0283:0.3 -19 50911960 . A T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.87956;SOR=0.95146;LSEQ=ATGAATGATTTTTTTTTTTT;RSEQ=AAGGGTGAGGCCACAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:782:21:14,7:490,265:0.0269:2,2:25.3:1:28.8:1:1:1.08:60:20:0.0266:0:1.7 0/1:899:23:9,14:528,343:0.0256:2,2:17.5:1:28:1:0.0507:2.39216:60:46:0.0262:0:1 -19 50912211 . T C 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCCATCTGGGCCTTCCCT;RSEQ=GGGGGGCTCAGTCTGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:839:0:0,0:361,478:0:2,0:25.2:1:29.4:1:1:0:60:26.065:1:0:0.2 0/1:677:45:22,23:252,378:0.0665:2,2:26.2:1:29.4:1:0.27228:1.43:60:44:0.0664:0:1.1 -19 50912821 . G C 219 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGACCCCCTCCGGCGCCA;RSEQ=GTCCTGGATGGACGGCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1184:136:68,68:545,502:0.1149:2,2:25:1:31:1:0.71535:1.08558:60:135:0.1152:0:1.1 0/0:1116:0:0,0:544,567:0:2,0:23.5:1:30.8:1:1:0:60:68.438:0.9955:0:0.2 -19 50916571 . A G 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00244;SOR=Inf;LSEQ=GGAGGGGCAGAGTGGCTTGT;RSEQ=CATAAGCCTATGCCACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:128,0:0:1,0:25.1:1:28:1:1:0:59.9:24.6:1:0:0.3 0/1:97:7:7,0:89,1:0.0722:1,0:25.9:1:31.6:1:1:0:60:14:0.0745:0:1.3 -19 50916597 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61841;SOR=2.06885;LSEQ=GCCTATGCCACTGGGAAATG;RSEQ=CAGAGGCGGGACCCCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:1,0:185,15:0.005:2,0:22:0:16:0:1:0:45:0:0:0:8 0/1:195:2:1,1:186,7:0.0103:1,2:12:1:27.5:1:0.08057:24.92238:60:4:0.0105:0:1 -19 50916772 . T C 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGAATGGCTACAGCACCAG;RSEQ=GCCAAGGTCGGGGGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1048:0:0,0:465,581:0:2,0:24.6:1:29.7:1:1:0:60:64.375:0.999:0:0.2 0/1:1128:78:36,42:466,581:0.0691:2,2:25.4:1:30.5:1:0.81385:1.07:60:77:0.0691:0:1.2 -19 50916902 . TG T 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CCACTCTCCTGTTGCATCCT;RSEQ=GGTCCCGTTGGCATTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:153,136:0:2,0:24.6:1:31.6:1:1:0:60:47.167:1:0:0.1 0/1:198:12:9,3:105,81:0.0606:2,2:15.4:1:30.5:1:0.24354:2.31:60:24:0.0619:0.0202:0 -19 50918969 . A G 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=23.05439;LSEQ=CCTCACCCACCCGCCACCCC;RSEQ=TCTCCACGCAGGATGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:970:3:1,2:429,503:0.0031:2,2:45.3:1:25.3:1:1:1.70483:60:2:0.0026:0:2 0/1:883:59:29,30:404,397:0.0668:2,2:26.4:1:27.6:1:0.89315:1.05268:60:7.429:0.0688:0:1.5 -19 50919530 . G GC 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.2705;LSEQ=CGACCCCATCCCAGACCCAG;RSEQ=CCCCCCCCATGTCACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:3,0:139,6:0.0203:1,0:32.3:1:32.3:1:1:0:60:6:0.0214:0:0 0/1:78:2:2,0:69,6:0.0256:2,0:4.1:1:29.3:1:1:0:60:6:0.0257:0.0221:0 -19 50919797 . C T 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.5752;LSEQ=TGCTACTGCGTACGGGGGCA;RSEQ=CAGGGGACTGGGGGCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:730:567:283,284:74,82:0.7767:2,2:24.1:1:29.9:1:0.58893:1.10:60:24.773:0.7752:0:1.2 1/0:693:462:232,230:115,114:0.6667:2,2:22.8:1:28.8:1:1:1.00006:60:41:0.6652:0:1.2 -19 50919828 . A G 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCACCCTGGGGGGGCAG;RSEQ=GGAGATCACCGGCCCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:0:0,0:365,354:0:2,0:22.7:1:30:1:1:0:60:24.679:0.9986:0:0.7 0/1:707:45:28,17:339,323:0.0636:2,2:22.8:1:30.8:1:0.16735:1.57:60:90:0.0648:0:1.1 -19 50919865 . AG A 104 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.11275;SOR=0.38712;LSEQ=CCACCTGCCTCCTCTCCTGC;RSEQ=GGGGGGACCACACGCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:929:10:5,5:477,440:0.0108:2,2:26.4:1:31.6:1:1:1.08398:60:20:0.0109:0.0011:0.5 0/0:954:4:3,1:506,441:0.0042:2,2:30.5:1:33:1:0.62794:2.61:60:8:0.0042:0:0.3 -19 50919929 . G A 91 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02206;SOR=5.49031;LSEQ=TGGGCGGCCTCCTGGCCTTC;RSEQ=CCAAACGCCGCAACTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:977:2:1,1:453,522:0.002:2,2:19:1:29:1:1:1.15:60:4:0.0021:0:1 0/1:987:11:8,3:463,511:0.0111:2,2:6.1:1:26.4:1:0.13019:2.94:60:22:0.0112:0:1 -19 50920100 . T C 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGGCCCAGGGCCCCTGGG;RSEQ=GGGTGGCCCCTGTCTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:37,82:0:2,0:26.8:1:30.1:1:1:0:60:238:1:0:0.1 0/1:59:14:5,9:9,35:0.2373:2,2:25.5:1:29.6:1:0.29068:2.13:60:13:0.2321:0:1 -19 50920410 . C T 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGCGGGGGCGCCCTGCT;RSEQ=AGCCGCTGCCGTCCCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1006:0:0,0:444,562:0:2,0:23.7:1:31.5:1:1:0:60:54.889:1:0:0.2 0/1:1008:66:24,42:424,517:0.0655:2,2:20.7:1:28.4:1:0.20018:1.4347:60:132:0.0665:0:1.1 -19 50920536 . A G 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCTGCACCAGGTGTGTGCC;RSEQ=TGTCCCGACCCTGGGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:713:0:0,0:303,410:0:2,0:25.2:1:30.3:1:1:0:60:100.857:1:0:0.2 0/1:670:36:14,22:295,339:0.0537:2,2:27.1:1:29.6:1:0.39544:1.36684:60:17:0.0515:0:1.9 -19 50920558 . C T 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCCGACCCTGGGCTGCCC;RSEQ=GCCCCTTCCCAGCTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:0:0,0:235,345:0:2,0:25.6:1:29.8:1:1:0:60:63.444:0.9983:0:0.2 0/1:512:26:11,15:213,270:0.0508:2,2:25.8:1:29.9:1:1:1.07563:60:25:0.0498:0:2.1 -19 50920581 . T C 53 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.064;SOR=0;LSEQ=CCCTTCCCAGCTCCCAGGCC;RSEQ=GTGGGTTGTGGACCCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:5:3,2:127,287:0.0119:2,2:13.6:1:23.2:1:0.17567:3.38:60:1.5:0.0074:0:1.6 0/0:373:0:0,0:142,227:0:2,0:24.4:1:29.7:1:1:0:60:40:0.989:0:0.2 -19 50920902 . C T 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAGCCATGGCCCTGCAC;RSEQ=TCGCCAGGCACCCGCTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:31,2:0.0833:2,0:21.7:1:32.7:1:1:0:60:6:0.0857:0:1.7 0/0:10:0:0,0:9,1:0:2,0:16.8:1:29.8:1:1:0:59:20:1:0:0.7 -19 50920928 . TC T 73 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.48997;LSEQ=AGGCACCCGCTGTTATCGGC;RSEQ=CCCCCCCCCACCCCCCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:6:5,1:29,0:0.1714:1,2:20.7:1:28.4:1:0.17143:0:59.2:5:0.1429:0.0286:2.3 0/1:11:1:0,1:10,0:0.0909:0,0:50:0:33:0:0.09091:0:60:2:0.0909:0:0 -19 50920939 . A C 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0.92493;LSEQ=GTTATCGGCTCCCCCCCCCC;RSEQ=CCCCCCCCGTGCCTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:24:24,0:14,1:0.5581:1,1:9.8:1:27.4:1:0.38462:0:57:7:0.6364:0:1.2 1/0:13:7:7,0:4,1:0.5385:2,0:9:0:27.9:1:0.41667:0:49.4:6:0.5455:0:1 -19 50921074 . A ACCCTGC 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGGCCTTGGCTGGTCCTG;RSEQ=CCCTGCCCCTGCCCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:786:0:0,0:494,290:0:2,0:25.5:1:29.2:1:1:0:60:29.154:0.9974:0:0.2 0/1:693:36:23,13:415,238:0.0519:2,2:25.7:1:31.2:1:1:1.01:59.7:72:0.0533:0.0115:0.1 -19 50921272 . T C 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AAAGTTCTGGACTTTTGCTA;RSEQ=ATGGTGCTTTGTGGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:59,281:0:2,0:20.7:1:28.5:1:1:0:60:67:0.997:0:0.2 0/1:300:40:7,33:52,207:0.1333:2,2:19.6:1:31.3:1:0.83249:1.18361:60:39:0.1345:0:1.3 -19 50921317 . C A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07553;SOR=Inf;LSEQ=ACACTGTCTGGTTTCATAAG;RSEQ=CCTGGCCTTGGCTGGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:0,127:0:1,0:22.2:1:31.4:1:1:0:60:126:1:0:0.1 0/1:94:3:0,3:1,90:0.0319:1,0:19.3:1:32:0:1:0:60:6:0.0337:0:1.3 -19 51108018 . T C 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00078;SOR=Inf;LSEQ=GGAGTGAGGGGTGTTGGACG;RSEQ=GGCACGGGAACCCGGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:25,15:0:2,0:27.4:1:30.1:1:1:0:57.7:80:1:0:0.2 0/1:88:18:11,7:37,33:0.2045:2,2:32.9:1:31.6:1:0.60241:1.40:51.7:36:0.2093:0:1.1 -19 51108208 . G C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=AGATCAAAGGGAAGAAAGGA;RSEQ=AGCCCCGACAGCCGGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:9:0:27:0:1:0:60:2:1:0:1 0/1:6:2:0,2:0,4:0.3333:0,0:8.5:1:33:1:1:0:60:4:0.3333:0:2 -19 51231068 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCCAGCATCGCCTGGCA;RSEQ=ATGGGAGCCCTTTGAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:33:1:32.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 51231314 . CAG C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.21189;SOR=Inf;LSEQ=CAGGGCCAGCTGTGGGCATG;RSEQ=AGAGAGAGGTCTGAAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:83,36:0:2,0:24.5:1:30.3:1:1:0:60:58.5:1:0:0.3 0/1:102:2:1,1:62,38:0.0196:2,2:29:1:32.5:1:1:1.6234:60:4:0.02:0:0 -19 51231337 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09637;SOR=Inf;LSEQ=AGAGAGAGGTCTGAAGTGGG;RSEQ=AGTGGCGTGCCTGCAAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:96,67:0:2,0:25.3:1:30.4:1:1:0:60:39.75:1:0:0.5 0/1:139:3:1,2:74,62:0.0216:2,2:18.7:1:26.3:1:0.59451:2.37254:60:6:0.0222:0:1.7 -19 51231339 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50027;SOR=0;LSEQ=AGAGAGGTCTGAAGTGGGGA;RSEQ=TGGCGTGCCTGCAAGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:96,66:0.0122:2,2:25:0:32.5:1:1:1.45112:60:4:0.0123:0:1.5 0/0:145:0:0,0:80,65:0:2,0:25.5:1:30.9:1:1:0:60:71.5:1:0:0.6 -19 51231363 . A T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24826;SOR=Inf;LSEQ=CGTGCCTGCAAGGACGGTTT;RSEQ=TGCATCAGAACAGCACGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:92,81:0:2,0:27.7:1:29.4:1:1:0:60:85.5:1:0:0.6 0/1:181:3:1,2:90,88:0.0166:2,2:38.7:1:23.7:1:0.62082:2.03766:60:2:0.0112:0:2.7 -19 51231391 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10931;SOR=Inf;LSEQ=GAACAGCACGCCTATATGTG;RSEQ=CATTCGGCGCTGATTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:84,107:0:2,0:24.4:1:31.8:1:1:0:60:190:1:0:0.7 0/1:176:3:2,1:84,89:0.017:2,2:13.3:1:25.3:1:0.61439:2.11:60:6:0.0171:0:2 -19 51231399 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.81414;LSEQ=CGCCTATATGTGGCATTCGG;RSEQ=GCTGATTCCTGACTCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:189:113:48,65:30,45:0.5979:2,2:22.9:1:29.4:1:0.76422:1.11:60:36.667:0.5914:0:1.1 1/1:174:148:69,79:15,11:0.8506:2,2:26.2:1:29.3:1:0.39517:1.55724:60:48.333:0.8529:0:1.2 -19 51231451 . G GC 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50293;SOR=0;LSEQ=CCTACTCTCTCCTCCAGGAA;RSEQ=CCCCCCCAGACTTCCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:46,84:0.0152:2,2:33.5:1:31:1:1:1.82:60:4:0.0154:0:1.5 0/0:108:0:0,0:43,65:0:2,0:23.1:1:31.4:1:1:0:60:107:1:0:0.8 -19 51231465 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51155;SOR=0;LSEQ=CAGGAAGCCCCCCCAGACTT;RSEQ=CTGCGGGCCAGAGTTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:34,79:0.0174:2,2:27.5:1:31:1:0.51793:2.30:60:4:0.0179:0:1.5 0/0:82:0:0,0:30,52:0:2,0:24.1:1:30.4:1:1:0:60:81:1:0:0.6 -19 51322211 . T C 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTGTTCTGGCGTCCCTGACT;RSEQ=GCCCTTTGGGATCTGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:25:0:26:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:28:1:1:0:60:4:1:0:1 -19 51805209 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50239;SOR=Inf;LSEQ=TTTAGCTATCTTCAGTTTGA;RSEQ=ACTTGCATAAATGAAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:103,27:0:2,0:24.1:1:31.8:1:1:0:60:260:1:0:0.1 0/1:156:2:1,1:103,51:0.0128:2,2:27.5:1:26.5:1:1:2.00984:60:4:0.013:0:1 -19 51805318 . G A 256 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00169;LSEQ=GAAATTGCTGGATCATAGGA;RSEQ=TGCTCAGCTTTAGTAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:351:350:165,185:0,0:0.9972:0,2:24.6:1:30.4:1:1:0:60:174:1:0:1.1 0/1:370:137:67,70:115,118:0.3703:2,2:24.2:1:30.3:1:1:1.01817:60:274:0.3733:0:1.1 -19 51805440 . T C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1675;SOR=Inf;LSEQ=AGTCCTTTTCATTTTAGTCA;RSEQ=TCTGGCAGCAGAGTAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:4,66:0:2,0:25.2:1:30.2:1:1:0:60:69:1:0:0.2 0/1:49:2:0,2:2,45:0.0408:1,0:32:1:34:0:1:0:60:4:0.0417:0:1 -19 52693277 . T C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.08704;SOR=Inf;LSEQ=CCACGCCCGCCCTTCCTTCT;RSEQ=CTCCCAGCATTGCCCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:112,35:0:2,0:22.4:1:29.1:1:1:0:60:23.5:1:0:0.2 0/1:118:3:3,0:93,22:0.0254:2,0:16.3:1:31.3:1:1:0:53.3:6:0.0263:0:3.3 -19 52693289 . G GC 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=7.15263;LSEQ=TTCCTTCTTCTCCCAGCATT;RSEQ=CCCCCCCCACGTTTCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:7:4,3:124,44:0.0395:2,2:17.3:1:30.4:1:0.38757:2.1034:60:14:0.0409:0.0169:0.1 0/1:140:32:27,5:79,24:0.2286:2,2:27.6:1:31.3:1:0.46303:1.63:59.1:31:0.2348:0:0.5 -19 52693295 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.20924;SOR=Inf;LSEQ=CTTCTCCCAGCATTGCCCCC;RSEQ=CCACGTTTCAGCACAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:133,52:0:2,0:24.4:1:30.7:1:1:0:60:36:0.9945:0:0.2 0/1:159:2:1,1:123,34:0.0126:2,2:35:1:27.5:1:0.39288:3.57976:60:4:0.0127:0:1 -19 52693297 . C CT 173 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCCCAGCATTGCCCCCCC;RSEQ=ACGTTTCAGCACAGCGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:55:39,16:98,41:0.2821:2,2:24.4:1:30:1:1:1.02:60:110:0.288:0.0564:0.3 0/0:166:0:0,0:128,38:0:2,0:22.8:1:29.6:1:1:0:59.5:32.2:1:0:0.4 -19 52693298 . A G 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0936;SOR=Inf;LSEQ=CTCCCAGCATTGCCCCCCCC;RSEQ=CGTTTCAGCACAGCGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:139,56:0:2,0:24.8:1:28.9:1:1:0:60:31.5:1:0:0.2 0/1:164:3:2,1:122,37:0.0183:2,2:27:1:27:1:0.55411:1.64294:56.7:6:0.0194:0:2 -19 52693540 . C T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCGGAAGGGGGCGACGGC;RSEQ=AATCAGCGTGCGTCTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:134,222:0:2,0:25.3:1:31.4:1:1:0:60:38.556:1:0:0.2 0/1:503:32:10,22:205,265:0.0636:2,2:23.1:1:28.5:1:0.19872:1.70016:60:64:0.0643:0:1.2 -19 52693613 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=CTCCCGATTGGGTGTCGGCC;RSEQ=AGTGGAGGGCGGGGGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:18,97:0.0171:2,2:16.5:1:29:1:0.29959:5.27:60:4:0.0172:0:1.5 0/0:104:0:0,0:20,83:0:2,0:20.4:1:30.5:1:1:0:60:24.75:1:0:0.2 -19 52695551 . C CT 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAACAGATATGTAATGGC;RSEQ=TTTTTTTTTTTTTCTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 52704961 . T C 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.68385;LSEQ=CAACTGAGTAGGTGTCACCT;RSEQ=CATAAGACCCAAGGGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:34:1:31.3:1:1:0:60:8:0.3636:0:1 1/0:4:2:2,0:1,1:0.5:2,0:30:1:31:1:1:0:60:4:0.5:0:1 -19 52705523 . GCAGCTCCAA G 63 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.08492;SOR=Inf;LSEQ=GGTAGAACGAGGTTTGAGTT;RSEQ=CAGTTGGAAGCTGGTGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:29.7:1:32.5:1:1:0:60:12:1:0:0 1/0:8:4:0,4:0,4:0.5:0,0:27:1:31.5:1:1:0:60:8:0.5:0.125:0 -19 52705688 . G T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATGCTTACTGTATGCCA;RSEQ=GTGGTGTTCTACACCGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:36.5:1:31:1:0.4:0:60:4:0.4:0:1.5 0/0:1:0:0,0:0,1:0:0,0:39:0:27:0:1:0:60:2:1:0:0 -19 52709064 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05652;SOR=Inf;LSEQ=CCTGTACCTTAATATCTGTG;RSEQ=CAGCCCAGGTGGAGAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:60,1:0:1,0:25.4:1:31.1:1:1:0:60:29.5:1:0:0.2 0/1:39:3:3,0:35,1:0.0769:1,0:38.7:1:29.7:1:1:0:60:6:0.0789:0:1 -19 52709171 . C T 139 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.03488;LSEQ=TTCTGAGCTTGGGCTGGGGT;RSEQ=AGAGTTGAGATGGGATAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:1:1,0:197,95:0.0034:2,0:43:0:9:0:1:0:60:0:0:0:7 0/1:379:30:20,10:224,125:0.0792:2,2:32.6:1:28.4:1:0.84506:1.12:60:60:0.0806:0:1.1 -19 52714298 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACCTTTGTGGAAGGCAC;RSEQ=CTGACAGAGACCTTCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:44.5:1:30.5:1:1:0:60:4:0.1818:0:1 0/0:5:0:0,0:5,0:0:0,0:20.4:1:30.4:1:1:0:60:10:1:0:0 -19 52714719 . C T 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTGCTACCCCCGAGTGTC;RSEQ=AGTGCTGTGAAGGCGGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:232,334:0:2,0:25.5:1:31.3:1:1:0:60:39.429:1:0:0.2 0/1:645:40:14,26:254,351:0.062:2,2:21.3:1:29:1:0.41264:1.34331:60:80:0.0632:0:1.2 -19 52714742 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28748;SOR=2.92846;LSEQ=TGCTGTGAAGGCGGAACTTC;RSEQ=ACAGTGAGTCTCTGCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:2:2,0:171,298:0.0042:2,0:1:0:27.5:1:0.13442:0:60:4:0.0043:0:1 0/1:486:6:5,1:177,303:0.0123:2,2:13:1:26.8:1:0.02959:8.53:60:12:0.0125:0:1.3 -19 52714917 . G A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.06636;SOR=0;LSEQ=GAGAGTTGGTCTCTGGACAC;RSEQ=GCCACGTGTCAGTTTACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:0.375:0,0:15.3:1:31.7:1:1:0:60:12:0.375:0:2.3 0/0:8:0:0,0:0,8:0:0,0:23.5:1:29.4:1:1:0:60:16:1:0:0 -19 52716301 . C T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01596;SOR=Inf;LSEQ=CCCTGGTGATGCCCACTCTG;RSEQ=GCCAGGCCGCTGAAGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:280,328:0:2,0:25.3:1:30.6:1:1:0:60:42.429:0.9983:0:0.1 0/1:663:7:2,5:313,342:0.0106:2,2:15.9:1:27.6:1:0.4545:2.28524:60:14:0.0107:0:1.1 -19 52718799 . C T 99 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.21106;LSEQ=ATTTTTAATGCTGACAACAC;RSEQ=GTGAGGTAGGTGCCCTCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:9,0:11,0:0.45:0,0:24.2:1:31.4:1:1:0:60:18:0.45:0:1.1 1/0:2:1:1,0:1,0:0.5:0,0:45:0:33:0:1:0:60:2:0.5:0:2 -19 52718884 . T A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00234;SOR=0.18562;LSEQ=GAGCCTTGCCCCGGGGCCAG;RSEQ=CTTGGCACTCGAATTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:27:26,1:32,0:0.4576:1,1:26.2:1:30:1:0.45763:0:60:26:0.4561:0:1.1 0/1:30:4:4,0:25,1:0.1333:1,0:32.8:1:30.3:1:1:0:60:8:0.1379:0:1 -19 52719190 . A G 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAAGTGGGGTGGGTATCC;RSEQ=AGGGGCTGGAGGTGGAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:536:0:0,0:302,234:0:2,0:23.5:1:29.9:1:1:0:60:75.571:1:0:0.1 0/1:595:33:16,17:296,264:0.0555:2,2:22.4:1:29.6:1:0.72055:1.19093:60:32:0.0546:0:1.2 -19 52719416 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51411;SOR=0;LSEQ=GCTTTGGGGATAGTCAGCTG;RSEQ=AAACTAGGTTCCCAGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:13,146:0.0123:2,2:9.5:1:28:1:0.16685:10.86:60:4:0.0126:0:1 0/0:113:0:0,0:15,98:0:2,0:21.9:1:31.8:1:1:0:60:226:1:0:0.1 -19 52719436 . C T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00137;SOR=Inf;LSEQ=CAAACTAGGTTCCCAGCCCT;RSEQ=TGGGACCAGGCAGCTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:8,109:0:2,0:21.5:1:31.7:1:1:0:60:28.25:1:0:0.1 0/1:61:6:0,6:1,54:0.0984:1,0:23.2:1:31.2:1:1:0:60:12:0.0984:0:1.2 -19 52719690 . A G 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27663;SOR=0;LSEQ=TGAATGAGAGGGGCAGAAGC;RSEQ=GGTTATTGTCTCTTAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:2,1:210,19:0.0129:2,2:15.3:1:21.7:1:0.2379:5.4501:60:2:0.0088:0:2.7 0/0:157:0:0,0:151,6:0:1,0:24.4:1:30.2:1:1:0:60:51.333:1:0:0.1 -19 52723571 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34587;SOR=3.40896;LSEQ=GCAGGATGGATTGGCTGGGG;RSEQ=TGTGGCGGGCAGTGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:1:0,1:42,162:0.0049:2,0:24:0:26:0:1:0:60:2:0.005:0:1 0/1:182:3:1,2:38,141:0.0165:2,2:21.3:1:27.3:1:0.51714:1.85:60:6:0.017:0:1 -19 52723584 . T C 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00195;SOR=Inf;LSEQ=GCTGGGGCTGTGGCGGGCAG;RSEQ=GGAGGAGGCTAGAGTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:17,143:0:2,0:24.8:1:29.9:1:1:0:60:31:1:0:0.1 0/1:139:8:0,8:17,113:0.0576:2,0:31.3:1:30.8:1:0.59542:0:60:16:0.0584:0:1.1 -19 52723865 . G A 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTGCCTTGGGGCCATTAT;RSEQ=AGAATGGCTCATTGTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:41:0:30:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 52723930 . C T 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATATTTATCTCTGTGAAG;RSEQ=CCTGTTTGAAGTAATAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:33.7:1:30.7:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 52724095 . T C 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.54143;SOR=1.50119;LSEQ=ATATAGCACATAGTAAGTCC;RSEQ=TTTTTCTCTCTTTGGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:5,0:54,0:0.0847:1,0:25.2:1:31.8:1:1:0:60:10:0.0847:0:1 0/1:49:6:6,0:43,0:0.1224:1,0:22.3:1:28.5:1:1:0:60:5:0.1042:0:1 -19 52724448 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61751;SOR=2.07782;LSEQ=GGAGCGCGTGGGAGAGGAGG;RSEQ=ATGCTAGAGGGTTCCCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:0,1:14,137:0.0066:2,0:35:0:32:0:1:0:60:2:0.0068:0:1 0/1:147:2:1,1:19,126:0.0136:2,2:13:1:27:1:0.2544:6.49:60:4:0.0137:0:1 -19 52724461 . TC T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.22892;SOR=Inf;LSEQ=GAGGAGGGATGCTAGAGGGT;RSEQ=CCCAAGGGAGACACCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:5,110:0:1,0:22.8:1:31.4:1:1:0:60:56.5:1:0:0.1 0/1:106:2:1,1:11,93:0.0189:2,2:25.5:1:29.8:1:0.21456:8.14:60:4:0.0192:0.0094:0.5 -19 52724465 . C CT 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22955;SOR=Inf;LSEQ=AGGGATGCTAGAGGGTTCCC;RSEQ=AAGGGAGACACCTGGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:3,103:0:1,0:23.2:1:32.5:1:1:0:60:105:1:0:0 0/1:98:2:1,1:8,88:0.0204:2,2:21:1:25.6:1:0.1761:10.43:60:4:0.0206:0.0102:0 -19 52725271 . A G 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0357;SOR=Inf;LSEQ=TGGGGCCTGATGATCACCAG;RSEQ=GTGGCCTGGTCAGAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:126,19:0:2,0:25.7:1:29.9:1:1:0:60:19.714:1:0:0.1 0/1:113:4:4,0:94,15:0.0354:2,0:19:1:31.3:1:1:0:60:8:0.0374:0:1.5 -19 52725338 . T C 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCATACTCACCCCTGCCAC;RSEQ=CACTGGCCCCCAGGTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:283,147:0:2,0:25.6:1:30.5:1:1:0:60:70.667:1:0:0.1 0/1:419:22:16,6:259,138:0.0525:2,2:27.7:1:30.6:1:0.64539:1.42:60:44:0.053:0:1.2 -19 52728890 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05222;SOR=Inf;LSEQ=GTGTCTGTGTACACTCTCTT;RSEQ=CCCAAGAGCCCTGTGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:172,36:0:2,0:22.6:1:32.4:1:1:0:60:207:1:0:0.1 0/1:192:4:2,2:151,37:0.0208:2,2:22.3:1:29.8:1:0.18401:4.041:60:8:0.0212:0:1 -19 52729082 . A C 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAAGACCTAGAAAGCACGG;RSEQ=GCCCTAGCAGGAGGGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:0:0,0:246,275:0:2,0:23.6:1:30.3:1:1:0:60:56.889:1:0:0.1 0/1:587:34:16,18:256,297:0.0579:2,2:27.4:1:30.5:1:1:1.03:60:68:0.0591:0:1.2 -19 53081621 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCCTTGTCCTATGATCAC;RSEQ=TGACTTGCTTCACCTTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:14,7:0:2,0:24.3:1:31.5:1:1:0:59.3:42:1:0:0 0/1:47:2:1,1:20,25:0.0426:2,2:25:1:28:1:1:1.24:60:4:0.0426:0:1 -19 53081658 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAATCACTTAGAAGATTC;RSEQ=CCCTCCTTACCCTGCCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:21.9:1:30.6:1:1:0:59.5:30:1:0:0.2 0/1:41:2:1,1:16,23:0.0488:2,2:9.5:1:29:1:1:1.42:60:4:0.05:0:1 -19 53081735 . C T 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01409;SOR=0;LSEQ=TTTGGGGCCACTACCTGTCT;RSEQ=CGCGTCTTGATGGTAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:1,5:1,4:0.5455:2,2:27.8:1:29.8:1:1:1.22474:60:12:0.5455:0:1 0/0:9:0:0,0:3,6:0:2,0:24.1:1:31.3:1:1:0:60:18:1:0:0.1 -19 53082892 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCAGTAATTTGGGAGGC;RSEQ=GAGGTGGGCAGATCACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:1:28:1:1:0:60:4:1:0:1 -19 53792794 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCACCACGCCTGGCTT;RSEQ=CATTTTTTTTTTCTACTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:19.5:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 53792953 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23547;SOR=Inf;LSEQ=CTTTGCTTGAAATCAATAAC;RSEQ=GCGCTGCACATGGGACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:66,30:0:2,0:26.4:1:30.5:1:1:0:60:47:1:0:0.2 0/1:91:2:1,1:52,36:0.022:2,2:28:1:32:1:1:1.4384:60:4:0.0222:0:1 -19 53792954 . GC AT 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00596;SOR=Inf;LSEQ=TTTGCTTGAAATCAATAACC;RSEQ=GCTGCACATGGGACATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:66,30:0:2,0:26.8:1:30:1:1:0:60:23:1:0:0.2 0/1:92:7:5,2:48,37:0.0761:2,2:21.9:1:29.4:1:0.69453:1.91:60:14:0.0761:0.0109:0.9 -19 53793007 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24742;SOR=Inf;LSEQ=GCACATTGTTTACAAGTGAC;RSEQ=AGATGTCCACAAGGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:86,60:0:2,0:24.4:1:31.2:1:1:0:60:47.667:1:0:0.5 0/1:145:2:1,1:68,75:0.0138:2,2:26:1:31:1:1:1.10:60:4:0.014:0:1 -19 53793014 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2187;SOR=Inf;LSEQ=GTTTACAAGTGACCAGATGT;RSEQ=CACAAGGAATAAAAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:82,62:0:2,0:25.6:1:31.1:1:1:0:60:143:1:0:0.5 0/1:127:2:1,1:58,67:0.0157:2,2:17:1:31.5:1:1:1.15:60:4:0.0159:0:2 -19 53793032 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17586;SOR=Inf;LSEQ=GTCCACAAGGAATAAAAACA;RSEQ=CAGCGATATGTCTGTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:84,69:0:2,0:24.9:1:29.6:1:1:0:60:37.25:1:0:0.6 0/1:111:2:1,1:54,54:0.018:2,2:34:0:33.5:1:1:1:60:4:0.0183:0:1.5 -19 53793039 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20018;SOR=Inf;LSEQ=AGGAATAAAAACAACAGCGA;RSEQ=ATGTCTGTCCATGCAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:84,71:0:2,0:24.8:1:29.4:1:1:0:60:76.5:1:0:0.6 0/1:126:2:1,1:63,61:0.0159:2,2:46:1:26.5:1:1:1.03253:60:4:0.016:0:2 -19 53793042 . G A 179 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00253;SOR=2.12269;LSEQ=AATAAAAACAACAGCGATAT;RSEQ=TCTGTCCATGCAGATTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:76:42,34:43,36:0.4903:2,2:23.9:1:29.6:1:1:1.03:60:152:0.4903:0:1.1 1/0:128:86:46,40:20,21:0.6719:2,2:22.7:1:28:1:0.70501:1.21:60:27.667:0.6694:0:1.1 -19 53793048 . C A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50219;SOR=0;LSEQ=AACAACAGCGATATGTCTGT;RSEQ=CATGCAGATTTTACAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:78,73:0.0131:2,2:22:1:25:1:1:1.068:60:4:0.0134:0:2 0/0:128:0:0,0:66,62:0:2,0:23.3:1:30.8:1:1:0:60:127:1:0:0.9 -19 53793055 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58664;SOR=2.51692;LSEQ=GCGATATGTCTGTCCATGCA;RSEQ=ATTTTACAAAGCTTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:1:1,0:76,73:0.0067:2,0:1:0:26:0:1:0:60:2:0.0067:0:1 0/1:120:2:1,1:61,57:0.0167:2,2:23:1:29.5:1:1:1.06954:60:4:0.0167:0:2 -19 53793084 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17192;SOR=Inf;LSEQ=AAGCTTCTCCTCTTGCAGAC;RSEQ=CCTTAGCGGCTCTTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:62,70:0:2,0:27.2:1:30.3:1:1:0:60:21:1:0:0.4 0/1:94:2:1,1:42,50:0.0213:2,2:27.5:1:31:1:1:1.19:60:4:0.0217:0:1 -19 53793162 . C T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0493;SOR=Inf;LSEQ=TTCTGTAGTGTCTTTCTGAG;RSEQ=GCTCACTAGATCTGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:74,50:0:2,0:25.3:1:31.5:1:1:0:60:248:1:0:0 0/1:112:4:2,2:66,42:0.0357:2,2:12.8:1:28.8:1:0.64496:1.56484:60:8:0.0364:0:1.3 -19 53793528 . C A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.56299;LSEQ=AAAGCACTGTACTTTATCCT;RSEQ=TTGACCTATAGCATAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:69,121:0.0104:2,2:28:1:28.5:1:1:1.75:60:4:0.0105:0:1 0/0:170:1:1,0:67,102:0.0059:2,0:1:0:22:0:0.4:0:60:2:0.0061:0:1 -19 53793533 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22072;SOR=Inf;LSEQ=ACTGTACTTTATCCTCTTGA;RSEQ=CTATAGCATAAAATCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:65,115:0:2,0:22.7:1:31:1:1:0:60:59:1:0:0.3 0/1:160:2:0,2:61,97:0.0125:2,0:22.5:1:27:1:0.52524:0:60:4:0.0126:0:2.5 -19 53793555 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22217;SOR=Inf;LSEQ=TATAGCATAAAATCCAGCTC;RSEQ=TGCAAGCTGCTCTTTGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:54,89:0:2,0:25.1:1:30.2:1:1:0:60:34.75:1:0:0.4 0/1:128:2:1,1:48,78:0.0156:2,2:33:1:29:1:1:1.62:60:4:0.0159:0:2 -19 53793574 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.63492;LSEQ=CTTGCAAGCTGCTCTTTGTT;RSEQ=ACGGAGTACATCCATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:46:18,28:35,48:0.3566:2,2:26.7:1:32.3:1:0.85211:1.13315:60:92:0.3622:0:1.1 1/0:112:85:31,54:10,17:0.7589:2,2:27:1:31.5:1:1:1.02446:60:170:0.7658:0:1 -19 53793583 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50148;SOR=0;LSEQ=TGCTCTTTGTTAACGGAGTA;RSEQ=ATCCATGTCCCAAAAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:52,74:0.0156:2,0:24:1:28:1:0.17606:0:60:4:0.0159:0:2 0/0:108:0:0,0:43,65:0:2,0:26.8:1:31.7:1:1:0:60:216:1:0:0.7 -19 53793798 . C T 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCCCAGTTTTTCAGTTTTC;RSEQ=GCCACAACAGAAGCACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:252,264:0:2,0:27.4:1:30:1:1:0:60:45.909:1:0:0.2 0/1:497:39:18,21:220,237:0.0785:2,2:26.4:1:29.5:1:0.86831:1.08278:60:38:0.0772:0:1.2 -19 53793874 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5052;SOR=0;LSEQ=CTGGCCAGCTCTCTCGGGGT;RSEQ=AAGTGGGCAGAGGCTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:21,160:0.0109:2,2:30.5:1:29:1:0.22657:7.47:60:4:0.0109:0:1 0/0:145:0:0,0:19,126:0:2,0:31:0:14:0:1:0:60:0:0:0:1 -19 53793888 . C A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01369;SOR=Inf;LSEQ=CGGGGTCAAGTGGGCAGAGG;RSEQ=TGGCCAGTTGTGAAACGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:21,138:0:2,0:24.1:1:32.6:1:1:0:60:158:1:0:0.3 0/1:119:5:0,5:12,102:0.042:2,0:22.8:1:30.4:1:1:0:60:10:0.0424:0:1.8 -19 53793911 . T A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.22769;LSEQ=GCCAGTTGTGAAACGACTGT;RSEQ=ATCTAGCTTCTTCACTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:35:8,27:14,68:0.2991:2,2:23.1:1:29.6:1:0.45198:1.43:60:16.5:0.2895:0:1.1 1/0:93:60:9,51:6,27:0.6452:2,2:23.4:1:29.5:1:0.77093:1.25605:60:59:0.6413:0:1.2 -19 53793969 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18846;SOR=Inf;LSEQ=GTGTATGGAGTCTGATCTAT;RSEQ=CACCACCTGTCCAGCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:14,44:0:2,0:25.4:1:30.7:1:1:0:60:28:1:0:0.6 0/1:45:2:1,1:10,32:0.0444:2,2:46:1:29.5:1:0.44186:3.10:60:4:0.0476:0:1 -19 53793995 . C T 79 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12964;SOR=0.18206;LSEQ=CCTGTCCAGCTCTCAAAAGC;RSEQ=GGTCTGCACGAGTCTCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:7:2,5:3,32:0.1667:2,2:29:1:28.4:1:0.18752:4.07:60:6:0.1579:0:2 0/1:29:1:0,1:7,21:0.0345:2,0:44:0:32:0:1:0:60:2:0.037:0:2 -19 53794353 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19962;SOR=Inf;LSEQ=TGATGTCTGCAGACACATAC;RSEQ=TTTTAGATCCTTCGAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:34,31:0:2,0:25.4:1:30.3:1:1:0:60:130:1:0:0.1 0/1:53:2:1,1:28,23:0.0377:2,2:6:1:25:1:1:1.21285:60:4:0.0385:0:1 -19 53794385 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21406;SOR=Inf;LSEQ=TCGAAACTGTTCAAAGTTAT;RSEQ=TTCTCTTGAATATAGGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:24,30:0:2,0:26.1:1:31.2:1:1:0:60:108:1:0:0.1 0/1:47:2:1,1:20,25:0.0426:2,2:39:1:29.5:1:1:1.24:60:4:0.0426:0:1 -19 53794388 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49907;SOR=0;LSEQ=AAACTGTTCAAAGTTATCTT;RSEQ=TCTTGAATATAGGACTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:22,30:0.037:2,2:17.5:1:28.5:1:1:1.36:60:4:0.0385:0:1 0/0:45:0:0,0:19,26:0:2,0:27.7:1:30.7:1:1:0:60:44:1:0:0.2 -19 53812461 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49773;SOR=Inf;LSEQ=AGTGTGCTTTCAGCGATATC;RSEQ=GCATTTCTAGAACAGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:55,39:0:2,0:25.3:1:30.2:1:1:0:60:93:1:0:0.2 0/1:99:2:1,1:56,41:0.0202:2,2:24:1:29:1:1:1.36147:60:4:0.0204:0:1 -19 53812496 . A G 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0024;SOR=Inf;LSEQ=GCATTTATTTTTGCATATGC;RSEQ=TGTAGGACACAGATACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:70,60:0:2,0:25.4:1:30.6:1:1:0:60:260:1:0:0.2 0/1:157:10:6,4:74,73:0.0637:2,2:26.3:1:31.2:1:0.74619:1.48:60:20:0.0641:0:1.1 -19 53812507 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50304;SOR=Inf;LSEQ=TGCATATGCATGTAGGACAC;RSEQ=GATACACAGGGCGGGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:72,63:0:2,0:25.7:1:30.3:1:1:0:60:44:1:0:0.2 0/1:164:2:1,1:85,77:0.0122:2,2:17:0:32:0:1:1.10323:60:4:0.0126:0:1.5 -19 53812523 . T C 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00024;SOR=4.02764;LSEQ=ACACAGATACACAGGGCGGG;RSEQ=TTGGGGCGGGACCTCGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:8:4,4:70,64:0.0563:2,2:27.3:1:32.9:1:1:1.09306:60:16:0.0576:0:1.1 0/1:180:35:18,17:75,70:0.1944:2,2:25.1:1:31.5:1:1:1.01184:60:34:0.1954:0:1.4 -19 53812535 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50666;SOR=Inf;LSEQ=AGGGCGGGTTTGGGGCGGGA;RSEQ=CTCGTGCGGTGCAGGCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:70,62:0:2,0:26.3:1:31.8:1:1:0:60:65:1:0:0.2 0/1:171:2:1,1:86,83:0.0117:2,2:13:1:29:1:1:1.03594:60:4:0.0121:0:2 -19 53812552 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19336;SOR=0;LSEQ=GGACCTCGTGCGGTGCAGGC;RSEQ=CTGTGGGAAGCGTTGCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:62,66:0.0154:2,2:32:1:31:1:1:1.06:60:4:0.0157:0:1 0/0:165:0:0,0:81,84:0:2,0:25.3:1:30.1:1:1:0:60:32:1:0:0.4 -19 53812559 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50296;SOR=Inf;LSEQ=GTGCGGTGCAGGCGCTGTGG;RSEQ=AAGCGTTGCCCTAACGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:59,66:0:2,0:25.3:1:30.6:1:1:0:60:30.25:1:0:0.2 0/1:152:2:1,1:73,77:0.0132:2,2:26.5:1:28.5:1:1:1.05:60:4:0.0132:0:1.5 -19 53812582 . C G 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=GCGTTGCCCTAACGGCTGGT;RSEQ=TCCAGGGCTGCAGGTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:39,57:0:2,0:25.8:1:30.9:1:1:0:60:23:0.9892:0:0.2 0/1:126:14:4,10:51,60:0.1111:2,2:24.9:1:30.9:1:0.26299:2.1129:60:28:0.1129:0:1.6 -19 53812688 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06363;SOR=Inf;LSEQ=TAGCTGTCCCTCTCATCCCC;RSEQ=CCCCTGCAACCTGAGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:1,17:0:1,0:28.4:1:30.9:1:1:0:60:17:1:0:0.2 0/1:13:3:0,3:0,10:0.2308:0,0:43.7:1:30:1:1:0:60:6:0.2308:0:1 -19 54380850 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21041;SOR=0;LSEQ=AGGGTGCCCTTCCCTCTTAG;RSEQ=TAGCCGAAGCAGAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,10:0.1:2,2:14.5:1:30:1:1:1.40:60:4:0.1053:0:1 0/0:23:0:0,0:9,14:0:2,0:23.7:1:30.5:1:1:0:60:46:1:0:0.1 -19 56007371 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGTCTTGGCCTCCCTAA;RSEQ=TGCTGGGATTATAGGCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 56172495 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=CCGGTGCCCGTGGTCGGGAG;RSEQ=CAGATGACCAGACAAGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:36.3:1:31.7:1:1:0:60:18:1:0:0 0/1:14:2:1,1:6,6:0.1429:2,2:19.5:1:29:1:1:1:60:4:0.1429:0:1.5 -19 56709003 . CGAGAAAATAAATGCAT C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24819;SOR=Inf;LSEQ=CGCTGCCTTCACAAAGTCTC;RSEQ=GAGAAAATAAACCCAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:39,39:0:2,0:26.8:1:30.2:1:1:0:59.6:77:1:0:0.2 0/1:88:3:1,2:45,40:0.0341:2,2:15.3:1:30.8:1:0.60387:2.22993:60:6:0.0349:0.0341:0 -19 56709008 . A G 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.88819;LSEQ=CCTTCACAAAGTCTCCGAGA;RSEQ=AATAAATGCATGAGAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:33,38:0.0274:2,2:25:0:17.5:1:1:1.15:60:1:0.0143:0:1.5 0/1:82:2:1,1:37,40:0.0244:2,2:21:1:29.5:1:1:1.08:60:4:0.0256:0:1 -19 56709052 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.49462;SOR=0;LSEQ=CCAAACTTTCTGAAACCAAC;RSEQ=CCCCGCATGCCAGCTCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:0,2:12,33:0.0426:2,0:5:0:31:1:1:0:45:4:0.0444:0:0 0/0:46:0:0,0:9,37:0:2,0:23.4:1:30.9:1:1:0:60:92:1:0:0.4 -19 56709105 . C T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72095;SOR=0.62325;LSEQ=TCGCCGCTGGACACTCACCT;RSEQ=CTTCCCGGCTTCTGCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:13:1,12:0,4:0.7647:0,1:21.8:1:28.7:1:1:0:56.9:12:0.8:0:1.2 1/0:21:14:1,13:0,7:0.6667:0,1:22.2:1:28.9:1:1:0:58.6:28:0.7:0:1.1 -19 56709176 . T A 28 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=CGGCCTGGAGCTGAACTGCG;RSEQ=CTATTTATGGAGAAGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:15.5:1:28.5:1:1:0:50:4:0.5:0:2.5 0/1:4:1:0,1:0,3:0.25:0,0:7:0:32:0:1:0:49:2:0.25:0:1 -19 56739528 . GA G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51443;SOR=Inf;LSEQ=TGCCTTCACAAAGTCTCCGA;RSEQ=AAACGCACGAAAAAATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:22,36:0:2,0:25.3:1:29.7:1:1:0:60:57:1:0:0.2 0/1:85:2:1,1:28,55:0.0235:2,2:15.5:1:29.5:1:1:1.95:60:4:0.0238:0:3.5 -19 56739565 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50834;SOR=Inf;LSEQ=TAAACCCAAACTTTCTGAAA;RSEQ=CAACCCCCGACATGCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:5,23:0:2,0:27.1:1:30.6:1:1:0:60:27:1:0:0.1 0/1:40:2:1,1:7,31:0.05:2,2:17:1:28.5:1:0.3641:4.21:60:4:0.0513:0:1 -19 56751782 . T C 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAACCAATCATGGGGCAG;RSEQ=GCAGGAACTGGAAATGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:23.8:1:32.3:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 56751951 . G T 212 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01363;LSEQ=TGGGGTTTAGGAGCTGGCAT;RSEQ=CAGGGGGGTTAGTTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:130:104,26:1,0:0.9924:0,2:25.7:1:30.2:1:1:0:60:260:1:0:1.3 1/0:135:86:59,27:36,13:0.637:2,2:23.7:1:29.6:1:0.6954:1.26508:59.9:172:0.637:0:1.2 -19 56752018 . AG A 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00985;LSEQ=TTGCTTGGAGACCTTGTGAA;RSEQ=CATCGGGTCTCCTTTGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:279:277:147,130:1,1:0.9928:2,2:25.4:1:31.7:1:1:1.13:59.9:554:0.9928:0.1541:1.2 1/0:358:206:108,98:80,72:0.5754:2,2:25.3:1:30.6:1:1:1.00821:60:412:0.5787:0.1089:1.2 -19 56752041 . C T 252 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00505;LSEQ=ATCGGGTCTCCTTTGCACCC;RSEQ=GTGATTAACTCTGGCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:311:310:142,168:0,1:0.9968:0,2:26.2:1:30.5:1:1:0:59.9:154:0.9968:0:1.2 1/0:381:232:107,125:72,77:0.6089:2,2:26.4:1:30:1:0.67571:1.09211:60:231:0.6095:0:1.2 -19 56752069 . C A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12923;SOR=Inf;LSEQ=ACTCTGGCTTGTTATGAAAC;RSEQ=CTTATGTAAACTAGGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:109,176:0:2,0:27.6:1:31.2:1:1:0:59.9:284:1:0:0.9 0/1:338:4:3,1:135,199:0.0118:2,2:21.3:1:27:1:0.30859:4.40:60:8:0.012:0:1.5 -19 56752143 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20472;SOR=Inf;LSEQ=TAGAGACGGGGGTCTCACTC;RSEQ=TTGCCCAGGCTGGCTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:11,61:0:2,0:23.6:1:30.8:1:1:0:60:144:1:0:0 0/1:60:2:1,1:9,49:0.0333:2,2:13.5:1:30:1:0.30791:5.22:60:4:0.0339:0:1.5 -19 56752381 . T A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCACCTTGCCGGCCGCAC;RSEQ=CCACTTGTTAAAAAGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 56754157 . T TA 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTTCTTTCTTTCTCTCTT;RSEQ=TTTTTTTGAGACGGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:27.5:1:1:0:60:4:1:0:0 -19 57396817 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=Inf;LSEQ=GGTCACTGGAGCTGTGACCT;RSEQ=CAAATTAGGATACTTGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:21.6:1:29.5:1:1:0:60:16:1:0:0.3 0/1:10:2:1,1:4,4:0.2:2,2:34.5:1:30:1:1:1:60:4:0.2:0:1 -19 57396818 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18301;SOR=0;LSEQ=GTCACTGGAGCTGTGACCTT;RSEQ=AAATTAGGATACTTGTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:22.5:1:27.5:1:1:1.83:60:4:0.25:0:1 0/0:10:0:0,0:5,5:0:2,0:23.8:1:32:1:1:0:60:20:1:0:0.3 -19 57742472 . G C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCGAAGCCTGTGTAGCA;RSEQ=TGAGACATCAGTGAGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:36:1:34:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 57742489 . CTGCAGGACGAGCAGGATTGGAAGCG TTGCAGGAAGCGC 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGAGACATCAGTGAGG;RSEQ=CCCCGGCCAGAAAGTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:28.3:1:30.5:1:1:0:60:8:1:0.5:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -19 57743039 . T C 47 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCTCTACTGTTCTCCTC;RSEQ=CCTCTCTTTCTCTCCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:30.3:1:30:1:1:0:60:6:1:0:1.3 -19 57744965 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.47895;SOR=0;LSEQ=TTTGGCTGGTCTGTGCACAC;RSEQ=CCCTCCCTGAGGTAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:0.1818:2,2:27:0:32:0:1:1.87:60:4:0.1818:0:1 0/0:9:0:0,0:4,5:0:2,0:31.8:1:30.1:1:1:0:60:18:1:0:0 -19 57746302 . A T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27007;SOR=Inf;LSEQ=CTTGCCGCCAGAAATGATTG;RSEQ=GGGGAGAACATATGATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:76,43:0:2,0:26.5:1:29.9:1:1:0:60:58.5:1:0:0 0/1:169:3:1,2:103,63:0.0178:2,2:7.7:1:28:1:0.55945:3.24634:60:6:0.0181:0:1 -19 58288034 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50505;SOR=Inf;LSEQ=CCTTGACACTTATATCCTCC;RSEQ=TGGGTAAGGTACTCATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:57,11:0:2,0:21.1:1:30.9:1:1:0:60:136:1:0:0 0/1:88:2:1,1:73,13:0.0227:2,2:22:1:29:1:0.29441:5.44814:60:4:0.023:0:1 -19 58288169 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38642;LSEQ=GGAGAGGTTCTGTTGTTGGT;RSEQ=GGACTGAGGTGTACGTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:341:184:85,99:84,73:0.5396:2,2:24.9:1:30:1:0.19322:1.33903:60:91:0.5417:0:1.2 0/1:472:147:65,82:152,172:0.3114:2,2:23.9:1:29.5:1:0.6186:1.11459:60:146:0.3133:0:1.1 -19 58288210 . G T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02904;SOR=0;LSEQ=CCCTGTCCTTTCCTTGAGCA;RSEQ=CCCCAACCTGCTTTGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:4:1,3:87,139:0.0174:2,2:36:1:26.3:1:1:1.87303:60:3:0.0132:0:1 0/0:325:0:0,0:123,202:0:2,0:26.4:1:31.5:1:1:0:60:39.625:1:0:0.4 -19 58288231 . G T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18567;SOR=0;LSEQ=CCCCAACCTGCTTTGTTGCA;RSEQ=GCTTCCAGGGAAGGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:61,123:0.0108:2,2:24:0:29:1:1:2.01:60:4:0.011:0:2 0/0:245:0:0,0:80,165:0:2,0:22.1:1:30.2:1:1:0:60:29.625:1:0:0.4 -19 58288238 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20171;SOR=0;LSEQ=CTGCTTTGTTGCAGGCTTCC;RSEQ=GGGAAGGAGTCAGGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:51,113:0.012:2,2:8.5:1:29.5:1:0.52968:2.20:60:4:0.0123:0:1 0/0:203:0:0,0:64,139:0:2,0:21.9:1:30:1:1:0:60:32.833:1:0:0.3 -19 58288257 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24696;SOR=Inf;LSEQ=CAGGGAAGGAGTCAGGGTCA;RSEQ=GAGTCTTAAAGTCACCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:28,96:0:2,0:22.8:1:31:1:1:0:60:61:1:0:0.2 0/1:123:2:1,1:25,96:0.0163:2,2:45.5:1:30.5:1:0.37945:3.79:60:4:0.0167:0:1 -2 740424 . G A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGCCCAGCCAGGAGAGCT;RSEQ=GAGAGGCAGCCAGGATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:1:27.5:1:1:0:46.5:4:1:0:4.5 -2 740456 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=AGGATCTTCCCTCAGAGCCT;RSEQ=GCGAGGGGGCGCGGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:10.2:1:32.2:1:1:0:59.8:10:1:0:1.8 1/0:3:2:1,1:1,0:0.6667:0,2:46:1:29.5:1:1:0:46.5:4:0.6667:0:4.5 -2 740482 . G T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.46429;SOR=0;LSEQ=GGGGCGCGGCCCAGCCAGGA;RSEQ=AGCTGGAGAGGCAGCGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:33.5:1:30.5:1:1:1.7321:60:4:0.4:0:1.5 0/0:3:0:0,0:2,1:0:2,0:35.3:1:33.3:1:1:0:51:6:1:0:3.7 -2 740483 . A G 32 d7;v4;MAF0.05;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.77722;LSEQ=GGGCGCGGCCCAGCCAGGAG;RSEQ=GCTGGAGAGGCAGCGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:34:0:32.5:1:1:1.7321:60:4:0.4:0:1.5 0/1:3:1:1,0:1,1:0.3333:2,0:49:0:33:0:1:0:60:2:0.3333:0:2 -2 740498 . G C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=AGGAGAGCTGGAGAGGCAGC;RSEQ=AGGATCTTCCCTCAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:32:1:31:1:1:0:59.8:10:1:0:1.4 1/0:3:2:1,1:1,0:0.6667:0,2:13:1:33:1:1:0:46.5:4:0.6667:0:4.5 -2 740678 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=Inf;LSEQ=GGCCCAGCCAGGAGAGCTGG;RSEQ=GAGGCAGCGAGGATCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:30:1:1:0:36:4:1:0:3.5 1/0:3:2:1,1:1,0:0.6667:0,2:21:0:32:0:1:0:48:4:0.6667:0:4.5 -2 740696 . C G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GGAGAGGCAGCGAGGATCTT;RSEQ=CCTCAGAGCCTGGCGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:30:1:1:0:36:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:39:0:32.5:1:1:1:48:4:0.5:0:4.5 -2 740697 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GAGAGGCAGCGAGGATCTTC;RSEQ=CTCAGAGCCTGGCGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:30:1:1:0:36:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:28.5:1:1:1:50:4:0.5:0:7 -2 740698 . C G 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGAGGCAGCGAGGATCTTCC;RSEQ=TCAGAGCCTGGCGAGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:30:1:1:0:36:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:41:0:30.5:1:1:1:48:4:0.5:0:4.5 -2 740700 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGGCAGCGAGGATCTTCCCT;RSEQ=AGAGCCTGGCGAGGGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:30:1:1:0:36:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:40.5:1:28.5:1:1:1:48:4:0.5:0:4.5 -2 740717 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCTCAGAGCCTGGCGAGGGG;RSEQ=CGCGGCCCAGCCAGGAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:42:0:34:0:1:0:36:2:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:29:1:1:1:50:4:0.5:0:7 -2 740727 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGCGAGGGGGCGCGGCCCA;RSEQ=CCAGGAGAGCTGGAGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:32:0:34:0:1:0:36:2:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:30:1:1:1:50:4:0.5:0:7 -2 741921 . G T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01494;SOR=0.10522;LSEQ=TTACTGCTGTACCTGCTGTG;RSEQ=AATCTAGTGAGATTCTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:7,5:2,1:0.8:2,2:20.4:1:28.3:1:1:1.39581:60:24:0.8:0:1.8 0/1:11:3:2,1:5,3:0.2727:2,2:26.3:1:28.7:1:1:1.18:60:6:0.2727:0:1.7 -2 741946 . C G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00893;SOR=0.14146;LSEQ=TAGTGAGATTCTAAGTAGTC;RSEQ=TATTTAATTGTGAGTCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:15:8,7:2,1:0.8333:2,2:28.3:1:30.1:1:1:1.69794:60:30:0.8333:0:1.7 0/1:20:8:4,4:8,4:0.4:2,2:14.6:1:31:1:0.64792:1.92981:60:16:0.4211:0:1.5 -2 742090 . T G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAGGGAACGTGAGAATTAGG;RSEQ=CAACCAGAGTGTTTTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24:1:33.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:48:0:30:0:1:0:60:2:1:0:1 -2 1107063 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19119;SOR=Inf;LSEQ=GCTGGAAGCAGGAAGGGGAG;RSEQ=CAGCGTACGGCCGGGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:34,40:0:2,0:28.3:1:29.4:1:1:0:60:73:1:0:0.3 0/1:58:2:1,1:24,32:0.0345:2,2:37.5:1:27.5:1:1:1.33:60:4:0.0345:0:2.5 -2 1107122 . G A 110 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06107;SOR=0.20319;LSEQ=CTGCTGTTGAGATTAGGACC;RSEQ=CAGGTGTGCAGCAGAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:14:3,11:7,18:0.359:2,2:28:1:29.1:1:0.72115:1.41332:60:13:0.3611:0:1.1 0/1:20:2:1,1:5,13:0.1:2,2:4.5:1:28.5:1:0.52105:2.46:60:4:0.1:0:2.5 -2 1826996 . A G 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=CAGGCAGACCCAGCAGGGGC;RSEQ=CCCAGCTGGTGGTGCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:4,0:9,2:0.2667:2,0:21.8:1:30.5:1:1:0:60:8:0.3077:0:2 0/0:4:0:0,0:4,0:0:0,0:24:1:31.3:1:1:0:60:8:1:0:0 -2 1827040 . A G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08005;SOR=0.27603;LSEQ=ATAGTCGTGGTGGTTGTGGT;RSEQ=GTGAGGGCTGTTGCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:18:11,7:15,11:0.4091:2,2:25.6:1:31.1:1:1:1.15:60:36:0.4091:0:1.4 0/1:19:3:2,1:10,6:0.1579:2,2:18.3:1:31.7:1:1:1.19:60:6:0.1579:0:2.3 -2 2526697 . A C 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0061;SOR=Inf;LSEQ=AGCCGGAGTTCAGCGCCAGG;RSEQ=AGCCCGGTGGCCCCCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:0:2,0:23:1:30.2:1:1:0:60:60:1:0:0.2 0/1:19:5:2,3:7,7:0.2632:2,2:24.2:1:29:1:1:1.46843:60:4:0.2222:0:1 -2 4561867 . T C 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24482;SOR=0.33497;LSEQ=TCCAGAAGCCATTATTCACG;RSEQ=AATTGATGAACTTGGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:3,2:15,3:0.2174:2,2:29.8:1:31:1:0.29068:3.1287:60:10:0.2174:0:1 0/1:24:2:2,0:17,5:0.0833:2,0:35.5:1:32.5:1:1:0:60:4:0.0833:0:1 -2 4562125 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.50416;SOR=0;LSEQ=CACCTTTTCTTCAGTTTCCT;RSEQ=ATCATCAAAATTATCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:46,40:0.0227:2,2:22.5:1:27.5:1:1:1.14817:60:4:0.0227:0:1 0/0:69:0:0,0:36,33:0:2,0:22.6:1:31.2:1:1:0:60:68:1:0:0.1 -2 4562144 . GTCA G 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.25225;SOR=0;LSEQ=TCATCATCAAAATTATCATT;RSEQ=TCATCATCATCATCTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:2,1:49,41:0.0323:2,2:39.7:1:33:1:1:1.66:60:6:0.0326:0:0 0/0:77:0:0,0:40,37:0:2,0:25:1:29.5:1:1:0:60:154:1:0:0.1 -2 4562168 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51039;SOR=0;LSEQ=TCATCATCATCATCTTCATC;RSEQ=GCAGCAAGTTTTACTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:55,47:0.0192:2,2:27.5:1:30.5:1:1:1.16844:60:4:0.0194:0:1 0/0:75:0:0,0:37,38:0:2,0:27.4:1:30.7:1:1:0:60:150:1:0:0.1 -2 4562203 . TACC T 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.45298;SOR=0.59047;LSEQ=TTGTTTCCATGGAAACTTGC;RSEQ=ACCCCCTGGGGCAGATTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:13:8,5:38,27:0.1667:2,2:24.1:1:31.1:1:1:1.13:60:26:0.1688:0.0256:0.1 0/1:57:6:3,3:25,26:0.1053:2,2:35.2:1:30:1:1:1.04:60:12:0.1053:0:0 -2 4562211 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=ATGGAAACTTGCTACCACCC;RSEQ=CTGGGGCAGATTGCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:2,0:44,31:0.026:2,0:6.5:1:26:1:0.51265:0:60:4:0.026:0:1.5 0/0:56:0:0,0:28,28:0:2,0:21.9:1:29.9:1:1:0:60:55:1:0:0.1 -2 4562266 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13513;SOR=Inf;LSEQ=TTTCACATCCTCCTCCTCTT;RSEQ=ATCTCCTGACTCTGCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:98,25:0:2,0:25.3:1:31.5:1:1:0:60:60.5:1:0:0.1 0/1:72:2:1,1:52,18:0.0278:2,2:47:1:29:0:0.46088:2.83875:60:4:0.0278:0:1 -2 4562410 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07411;SOR=Inf;LSEQ=CATTGCTGTACAGACATTTT;RSEQ=AAAGTTACCAGTGTTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:104,168:0:2,0:23.5:1:31.4:1:1:0:59.9:37.857:1:0:0.1 0/1:198:3:2,1:76,119:0.0152:2,2:14.7:1:26.3:1:0.56292:3.11:60:6:0.0153:0:1 -2 4562511 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17513;SOR=Inf;LSEQ=ACCAACCACTAAACTGACTG;RSEQ=TTTTAAAGATAACTTGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:13,53:0:2,0:25.1:1:30:1:1:0:60:65:1:0:0.1 0/1:48:2:1,1:10,36:0.0417:2,2:5:0:33.5:1:0.40957:3.48:60:4:0.0426:0:0 -2 4562591 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09729;SOR=Inf;LSEQ=TGGCCTTTAGTTCACAACTG;RSEQ=AAAGGTAATTCTGGGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:0:2,0:21.7:1:30.1:1:1:0:60:86:1:0:0.1 0/1:20:2:1,1:10,8:0.1:2,2:43:1:31:1:1:1.23603:60:4:0.1:0:1 -2 4562621 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15892;SOR=Inf;LSEQ=TCTGGGGCCTCAGGGTGCTC;RSEQ=TGTCCATGTCCATCGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:23,23:0:2,0:23.3:1:31:1:1:0:60:92:1:0:0.1 0/1:31:2:1,1:14,15:0.0645:2,2:16.5:1:27:1:1:1.07:60:4:0.0645:0:1 -2 4562657 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49425;SOR=0;LSEQ=AATCTTCCATGAGGTGGTGG;RSEQ=ATGTACTTAGGTGGGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:21,21:0.0455:2,2:47.5:1:30.5:1:1:1:60:4:0.0476:0:1 0/0:43:0:0,0:20,23:0:2,0:25.3:1:31.6:1:1:0:60:42:1:0:0.3 -2 4562775 . G A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=TAAAGAGCAGGTAAGCTCCC;RSEQ=CAGTGTCGCACAGCCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:25.7:1:31.3:1:1:0:60:6:0.4286:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:23:1:32:0:1:0:60:4:1:0:1 -2 4716777 . T G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTAAAACTCATCTTTGCT;RSEQ=TACCTTTTGAGAACAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:42.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 4717009 . A G 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20546;SOR=Inf;LSEQ=TAGTATATATGTTAATAATT;RSEQ=TTTGATAATTATTATTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:141,54:0:2,0:22.3:1:28.6:1:1:0:60:64:0.9948:0:0.4 0/1:163:2:1,1:116,45:0.0123:2,2:19:0:27:1:0.48603:2.56058:60:4:0.0125:0:1 -2 4717038 . C T 154 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.20204;LSEQ=TTATTATTTGATTAGCCAAA;RSEQ=GCCATGAGAAAGTCTCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:2:0,2:218,118:0.0059:2,0:1:0:26.5:1:0.12537:0:60:4:0.006:0:2 0/1:285:36:23,13:144,105:0.1263:2,2:24.8:1:29.9:1:0.58813:1.29:60:35:0.1246:0:1 -2 4717057 . TA T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.41484;SOR=2.51258;LSEQ=ACGCCATGAGAAAGTCTCAG;RSEQ=AAGAACATTTTGGAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:2:1,1:240,160:0.005:2,2:26:1:31.5:1:1:1.49841:60:4:0.0051:0:1 0/1:322:4:1,3:171,147:0.0124:2,2:20.8:1:27.8:1:0.34186:3.47724:60:8:0.0125:0.0062:1 -2 4717089 . C A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33617;LSEQ=TGGAAAAAGCAGTTTCATAT;RSEQ=TATACGCATCACACATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:452:345:182,163:64,42:0.7633:2,2:25.8:1:29.4:1:0.18184:1.36379:60:68:0.764:0:1.1 1/0:379:197:97,100:87,95:0.5198:2,2:25.2:1:28.9:1:0.83712:1.06:60:196:0.5213:0:1.1 -2 4717156 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17339;SOR=Inf;LSEQ=ATTGCACTCATCAAAACTCA;RSEQ=AGAACCTTATGATTTTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:78,195:0:2,0:25.8:1:28.8:1:1:0:60:90:0.9963:0:0.4 0/1:196:2:1,1:64,130:0.0102:2,2:23:1:28:1:1:2.02:60:4:0.0103:0:1 -2 4717162 . C A 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.57189;SOR=2.85332;LSEQ=CTCATCAAAACTCATAGAAC;RSEQ=TTATGATTTTAAGACATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:1:1,0:64,182:0.004:2,0:1:0:25:0:0.26316:0:60:2:0.0041:0:1 0/1:174:2:1,1:51,121:0.0115:2,2:25:1:26.5:1:0.5096:2.36:60:4:0.0116:0:1 -2 4717192 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.529;SOR=0;LSEQ=TAAGACATTTTGAGCTCTCT;RSEQ=ATAACACTTGTAGATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:18,127:0.0135:2,2:22.5:1:27:0:0.24257:6.89:60:4:0.0138:0:1 0/0:89:0:0,0:12,77:0:2,0:23.6:1:32:1:1:0:60:178:1:0:0.1 -2 4717291 . T C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64446;SOR=0.67517;LSEQ=TTGACTGTAAAATTATTGAG;RSEQ=AAATGGATTAACAGGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:21:0,21:0,7:0.75:0,1:26.6:1:32.8:1:1:0:60:42:0.75:0:1 1/0:6:4:0,4:0,2:0.6667:0,0:23:1:31.3:1:1:0:60:8:0.6667:0:1 -2 4900640 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATACACCATCTAAGGCC;RSEQ=GCCCTAGGAGGATAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:35.5:1:31:1:1:0:60:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 4900652 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAGGCCTGCCCTAGGAGG;RSEQ=TAAGAGAATGATTTGTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:40:1:31:1:1:0:60:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 4900678 . A C 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGATTTGTAATGTGAAA;RSEQ=TGGCAAAGAAGCCACCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:26.5:1:31.3:1:1:0:60:8:0.8:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 4901103 . A C 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.60931;LSEQ=AGAGTTGCGCTCAAATGGTG;RSEQ=CTACATGTTGTAATGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:649:395:196,199:116,137:0.6086:2,2:25.1:1:31.1:1:0.37565:1.16:60:31.917:0.6051:0:1.1 0/1:479:233:117,116:110,133:0.4864:2,2:26.2:1:31.4:1:0.31276:1.22:59.9:57.25:0.4883:0:1.1 -2 4901179 . AAAT A 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00082;SOR=0.53836;LSEQ=GCTATTATGTGAGATACAGA;RSEQ=AATAACCTGGAAAAGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:306:183:32,151:35,88:0.598:2,2:25.9:1:30.4:1:0.02485:1.87282:60:182:0.5967:0.0588:0.4 0/1:207:92:17,75:34,80:0.4444:2,2:27.9:1:29.7:1:0.07424:1.86935:60:91:0.4527:0.029:0.4 -2 4901307 . G A 127 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19652;SOR=0.2076;LSEQ=AATATATAAATTGTACTATA;RSEQ=TGGTACCTATAGTAGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:0,16:0,16:0.5:1,1:23.6:1:31.8:1:1:0:60:32:0.5:0:1 0/1:6:1:0,1:0,5:0.1667:0,0:49:0:32:0:1:0:60:2:0.1667:0:1 -2 4901589 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCAAAGAATTAGAAAA;RSEQ=TGGAAATATGTAAGACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 5429063 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTCTATTTAAAAAATAC;RSEQ=CCTAATGAAACAATGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:18,0:0,0:1:0,1:24.4:1:31.1:1:1:0:60:36:1:0:1 1/1:9:9:8,1:0,0:1:0,2:31:1:30:1:1:0:60:18:1:0:1 -2 5429187 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15252;SOR=Inf;LSEQ=CTGGGTCCACTCTGAGGGAC;RSEQ=CTCCCATCATGTGGATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:112,62:0:2,0:25.1:1:30.7:1:1:0:60:173:1:0:0.4 0/1:112:2:1,1:68,42:0.0179:2,2:13:0:32:0:1:1.61177:60:4:0.018:0:3 -2 5429197 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=10.83728;LSEQ=TCTGAGGGACGCTCCCATCA;RSEQ=GTGGATGCTTCTTCATAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:40:21,19:96,61:0.203:2,2:26.1:1:29.7:1:0.36862:1.42125:60:12.333:0.1947:0:2 1/0:125:92:54,38:20,13:0.736:2,2:27.4:1:30.3:1:1:1.0819:60:184:0.736:0:1.7 -2 5429215 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15039;SOR=Inf;LSEQ=CATGTGGATGCTTCTTCATA;RSEQ=GCAAGGGCAGAGCTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:124,112:0:2,0:24.6:1:31.5:1:1:0:60:58:1:0:0.5 0/1:150:2:1,1:83,65:0.0133:2,2:37:0:31.5:1:1:1.27482:60:4:0.0134:0:1.5 -2 5429237 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55574;SOR=0;LSEQ=CAAGGGCAGAGCTCCAAGGA;RSEQ=CACCTCCTCCTCACCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:138,138:0.0108:2,2:14.3:1:25.7:1:1:1.99521:60:2:0.0073:0:1.3 0/0:155:0:0,0:81,74:0:2,0:25.3:1:31.8:1:1:0:60:76.5:1:0:1.7 -2 5429260 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.65429;LSEQ=CCTCCTCCTCACCTTCTGCA;RSEQ=GTAGTGGGGGAGATCGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:51:24,27:102,126:0.1821:2,2:25.6:1:29.5:1:0.87646:1.10:60:11.75:0.1728:0:2.6 1/1:161:130:66,64:15,16:0.8075:2,2:24.4:1:29.1:1:0.84383:1.10:60:17.571:0.7987:0:2.7 -2 5429279 . G A 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=28.99916;LSEQ=ACGTAGTGGGGGAGATCGCC;RSEQ=GTACCAACATCCTTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:39:20,19:94,124:0.1518:2,2:28.2:1:30:1:0.38391:1.39:60:18.5:0.1468:0:2.8 1/1:144:121:59,62:10,13:0.8403:2,2:26.8:1:30:1:0.65758:1.24:60:120:0.8392:0:2.8 -2 5429284 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13672;SOR=Inf;LSEQ=GTGGGGGAGATCGCCGGTAC;RSEQ=AACATCCTTGGAGTGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:107,141:0:2,0:26.4:1:31.7:1:1:0:60:247:1:0:0.5 0/1:146:2:1,1:67,77:0.0137:2,2:20:0:31:1:1:1.15:60:4:0.014:0:4 -2 5429303 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14339;SOR=Inf;LSEQ=CCAACATCCTTGGAGTGGAG;RSEQ=TGAAGACTTTTTGAAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:81,120:0:2,0:24.4:1:31.8:1:1:0:60:99.5:1:0:0.4 0/1:123:2:1,1:47,74:0.0163:2,2:13:0:30.5:1:1:1.57:60:4:0.0168:0:3.5 -2 5429313 . T C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=28.17397;LSEQ=TGGAGTGGAGCTGAAGACTT;RSEQ=TTGAAGCTGTTCATGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:25:10,15:53,98:0.142:2,2:14:1:30.2:1:0.65693:1.23:60:50:0.1429:0:2.7 1/1:115:95:34,61:7,13:0.8261:2,2:25.1:1:31.3:1:1:1.03:60:94:0.8246:0:2.6 -2 5429341 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15311;SOR=Inf;LSEQ=TGTTCATGCCAGCTCATGGA;RSEQ=CTCTTCATGCCACACTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:23,82:0:2,0:22.9:1:31.9:1:1:0:60:210:1:0:0.1 0/1:68:2:1,1:17,48:0.0294:2,2:34:1:30.5:1:0.46811:2.77:60:4:0.0303:0:1 -2 5429475 . T G 47 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAAGATGTCAGCTTGCAT;RSEQ=GCTCCTCCATGCCCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:0.25:0,0:31.7:1:30:1:1:0:60:6:0.25:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 5429486 . G A 45 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTGCATTGCTCCTCCAT;RSEQ=CCCACACACATAGCTAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:0.25:0,0:20.7:1:29:1:1:0:60:6:0.25:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 5429997 . G C 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCTTCTCTTGCCCTTG;RSEQ=GCTTCAGTGTTCCTGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 5490556 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CAGCAAAATGAATCTACATA;RSEQ=CCTGTATAAATGTGACATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:24.5:1:31:1:1:0:60:4:0.5:0:1 0/0:3:0:0,0:3,0:0:0,0:35.3:1:34:0:1:0:60:6:1:0:0 -2 6635870 . TA T 105 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0.95274;LSEQ=TCATACAGAAATAACTAGTG;RSEQ=AAAAAAAAAAAAGGTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:13:13,0:28,1:0.2826:1,1:35:1:28.5:1:1:0:60:12:0.2667:0.0435:1.1 0/1:11:3:3,0:8,0:0.2727:0,0:18.3:1:30:1:1:0:60:6:0.3:0.0909:0 -2 6635991 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19159;SOR=Inf;LSEQ=GCGGCTGCCTCCTCTCGGGC;RSEQ=GGGGCAGGGAGGAGCCGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:207,47:0:2,0:21.4:1:30.4:1:1:0:60:30.75:0.996:0:0.2 0/1:199:2:1,1:144,52:0.0101:2,2:23.5:1:29:1:0.4647:2.75249:60:4:0.0102:0:1 -2 6636076 . G GGCTTCGTTAAACTTCACTCGGAAGTGCTTCGTTAAACTTCACTCGGAAGTGCTTCTTTAAACTTCACTCGGAAGT 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.50742;LSEQ=GGTTTCCAGCTCTCGCGGAG;RSEQ=GCTTCGTTAAACTTCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:950:269:138,131:336,248:0.2832:2,2:30.1:1:30.1:1:0.10274:1.28572:54.7:268:0.2872:0.2716:0.5 0/1:677:113:61,52:299,260:0.1669:2,2:29:1:29.1:1:1:1.02:53.9:226:0.1702:0.1595:0.4 -2 6636082 . G T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60191;SOR=1.2541;LSEQ=CAGCTCTCGCGGAGGGCTTC;RSEQ=TTAAACTTCACTCGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:19:15,4:528,460:0.0188:2,2:6.3:1:31.1:1:0.03481:3.26:27.9:18:0.0181:0:1.3 0/1:680:16:10,6:343,307:0.0235:2,2:7.1:1:31.1:1:0.61359:1.49:32:32:0.0243:0:1.2 -2 6636094 . T A 110 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14819;SOR=0.41822;LSEQ=AGGGCTTCGTTAAACTTCAC;RSEQ=CGGAAGTGCTTCGTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:965:14:4,10:498,451:0.0145:2,2:17.4:1:28.9:1:0.1047:2.75778:35.2:28:0.0149:0.001:1.9 0/0:654:4:2,2:332,305:0.0061:2,2:9.5:1:25.8:1:1:1.08837:43.5:8:0.0065:0:1.5 -2 6636107 . G T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47213;SOR=0.73993;LSEQ=ACTTCACTCGGAAGTGCTTC;RSEQ=TTAAACTTCACTCGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:915:21:6,15:465,426:0.023:2,2:29.6:1:31:1:0.04483:2.72603:32:42:0.0232:0.0011:1.7 0/1:644:11:7,4:321,312:0.0171:2,2:29.8:1:31:1:0.54609:1.70:41.7:22:0.0173:0:1.4 -2 6636414 . G A 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATGGGACACGCTGACGGTT;RSEQ=ATTCCAAACGTGGTCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:982:54:22,32:447,481:0.055:2,2:25.3:1:29.4:1:0.32763:1.35131:60:108:0.0558:0:2 0/0:706:0:0,0:349,356:0:2,0:24.8:1:31.3:1:1:0:59.9:77.333:0.9986:0:0.6 -2 6636424 . G T 267 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72668;SOR=1.03759;LSEQ=GCTGACGGTTGATTCCAAAC;RSEQ=TGGTCTTGAAATTCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:943:452:210,242:221,269:0.4793:2,2:26.1:1:30.3:1:0.69478:1.06:60:55.5:0.4779:0:1.2 0/1:698:341:171,170:167,189:0.4885:2,2:24.6:1:30.3:1:0.40508:1.14:59.8:340:0.4906:0:1.2 -2 6636578 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08191;SOR=6.20496;LSEQ=AGAGGGTGAACTCTTCGTTG;RSEQ=CTCCATCCATGTTGCGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:1:0,1:199,254:0.0022:2,0:1:0:27:0:1:0:60:2:0.0022:0:1 0/1:296:4:1,3:133,159:0.0135:2,2:17.3:1:25.3:1:0.62922:2.50232:60:3:0.0103:0:1.5 -2 6636622 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07204;SOR=Inf;LSEQ=AGTTGGATGTTGGCGATGGT;RSEQ=TCTGGGTGGAGTAGCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:231,190:0:2,0:25.4:1:32.1:1:1:0:60:59.143:1:0:0.1 0/1:301:3:2,1:172,126:0.01:2,2:9:1:26.7:1:1:1.46:60:6:0.0101:0:1 -2 6636735 . G A 131 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=CCACAGGACGTCCATGAGCC;RSEQ=GATCGTCTGCATGGTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:20:10,10:306,322:0.0308:2,2:31.2:1:30.4:1:1:1.05:60:19:0.0299:0:2.1 0/0:443:0:0,0:217,226:0:2,0:26.5:1:29.6:1:1:0:60:62.286:1:0:1 -2 6636747 . T C 282 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06533;SOR=0;LSEQ=CATGAGCCGGATCGTCTGCA;RSEQ=GGTCAGCATGTCCTGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:608:608:292,316:0,0:1:0,2:25.1:1:30.5:1:1:0:60:75:1:0:1.1 1/1:411:408:203,205:1,1:0.9927:2,2:24.8:1:30.3:1:1:1.00983:60:203:0.9927:0:1.1 -2 6636940 . C T 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08505;SOR=0.6659;LSEQ=GACTGCAGGTGTAAGTGGCT;RSEQ=TGGGTGAGTGAGTGAGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:91:10,81:23,101:0.4233:2,2:25.9:1:30.2:1:0.17955:1.83951:60:182:0.4252:0:1.6 0/1:125:41:5,36:18,66:0.328:2,2:25.6:1:30.2:1:0.32514:1.95387:60:40:0.3226:0:1.6 -2 6636974 . T C 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19379;SOR=0.63265;LSEQ=GAGGGTATTACTTAAAATAC;RSEQ=CTTTCTATGTTTAGAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:61:6,55:13,64:0.442:2,2:23.3:1:30.5:1:0.32087:1.8539:60:19.333:0.4296:0:1.9 0/1:54:18:1,17:3,33:0.3333:2,1:19.8:1:31.3:1:1:1.5339:60:17:0.3208:0:2.1 -2 6636996 . C CA 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTATGTTTAGAAAGAGT;RSEQ=AAAAAAAATTTTAAGTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:0,2:1,71:0.0267:1,0:27:1:29.5:1:1:0:60:4:0.0278:0:0 0/0:25:0:0,0:1,24:0:1,0:17.8:1:31.6:1:1:0:60:50:1:0:0.6 -2 6637065 . G GA 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.51088;LSEQ=TTAATTTATAATTGACAAAA;RSEQ=AAAAAAATTCATAAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:0,3:0,20:0.1154:1,0:29.7:1:31.3:1:1:0:60:6:0.1154:0:0 0/1:6:1:0,1:0,4:0.1667:0,0:21:0:32:0:1:0:60:2:0.1667:0:0 -2 6851114 . GC G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1979;SOR=0.44118;LSEQ=AAGACATGAGGCTGGATAAG;RSEQ=AAGTAAATTGGGTAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:19:19,0:51,1:0.2676:1,1:31.4:1:32.6:1:1:0:60:38:0.2676:0:0.1 0/1:29:4:4,0:24,1:0.1379:1,0:23.8:1:32.3:1:1:0:60:8:0.1429:0:0 -2 6851238 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.831;LSEQ=AAATTTAAATAGTATACTAC;RSEQ=GTAAATCCAGAAATATCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:94:52,42:246,192:0.1767:2,2:24.9:1:30.5:1:0.90912:1.03481:60:188:0.179:0:1.8 0/1:349:132:83,49:127,90:0.3782:2,2:23.7:1:30.3:1:0.4324:1.20:60:65:0.3768:0:1.9 -2 6851269 . T C 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.41643;LSEQ=AAATATCACTGGGTGGGTAG;RSEQ=GTGGAAAAAATGTTTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:108:56,52:238,257:0.1782:2,2:25.6:1:30.8:1:0.52419:1.16:60:107:0.1786:0:1.8 0/1:404:139:72,67:126,137:0.3441:2,2:26.9:1:30.1:1:0.46501:1.17:60:68.5:0.3434:0:1.8 -2 7541706 . TA T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.15111;LSEQ=TTATAAAATTCACAGATTCA;RSEQ=AAAAAAAAAGCAAAATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:47:40,7:93,18:0.2938:2,2:27:1:31.2:1:1:1.11:60:94:0.2994:0.0563:2.4 0/1:153:9:7,2:115,29:0.0588:2,2:21.6:1:30:1:1:1.13207:60:18:0.0596:0.0131:1.4 -2 7541718 . C G 181 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGATTCATAAAAAAAAAAG;RSEQ=AAAATGTTCTCTCTTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:59:49,10:104,29:0.3026:2,2:24.4:1:30.8:1:0.56038:1.36:60:28.5:0.3167:0:2.9 0/0:193:0:0,0:146,46:0:2,0:23.3:1:31.1:1:1:0:60:23:1:0:1.3 -2 7541750 . A C 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03872;SOR=1.44636;LSEQ=TCTTTTCTATCCAAGAGAGG;RSEQ=AAATCTATATATAGCACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:286:184,102:67,44:0.7204:2,2:24.2:1:31.4:1:0.48754:1.18:60:30.778:0.7195:0:2.3 1/0:331:261:154,107:42,28:0.7885:2,2:25.5:1:31:1:1:1.04209:60:36.286:0.7864:0:2 -2 7541769 . A G 267 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.75638;SOR=1.05563;LSEQ=GAAAATCTATATATAGCACT;RSEQ=AAATCCTAAGGAGGACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:498:370:209,161:70,57:0.743:2,2:26.2:1:31.3:1:0.83598:1.06:60:40.111:0.7398:0:2 1/0:393:296:158,138:53,42:0.7532:2,2:27.8:1:30.7:1:0.72341:1.1019:60:58.2:0.7539:0:2 -2 7541865 . G A 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47858;SOR=0.83746;LSEQ=GTTTTAAAGTCCTGTTTTAC;RSEQ=CAATATTCTTCTACTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:187:44,143:13,38:0.7792:2,2:22.3:1:30.1:1:0.8533:1.11133:60:186:0.7782:0:1.2 1/0:170:127:36,91:12,31:0.7471:2,2:21.7:1:29.6:1:1:1.02:60:126:0.7456:0:1.1 -2 8822446 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52164;SOR=0;LSEQ=CCAAGCTCAAGGAGCTGGTG;RSEQ=CCAGCATCCCCCAGAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:55,19:0.0263:2,2:23:1:28.5:1:0.45965:2.84697:54.5:4:0.0274:0:1 0/0:48:0:0,0:36,12:0:2,0:24.3:1:31.6:1:1:0:57.3:96:1:0:0.1 -2 8822551 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49746;SOR=Inf;LSEQ=TGGACTCGCATCCCACTATT;RSEQ=TCAGCCTGCATCACCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:28,54:0:2,0:20.6:1:31:1:1:0:59.6:26.333:1:0:0.1 0/1:87:2:1,1:32,53:0.023:2,2:17.5:1:26.5:1:1:1.65:60:4:0.0235:0:1 -2 8822912 . A C 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=25.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAACCCTTTCTACTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 9036068 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.52266;SOR=0;LSEQ=GCCCAACTCCAGAGGTTGGT;RSEQ=TAAGAGTTGTGAAAGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:24,26:0.0385:2,2:36.5:1:33:1:1:1.08:60:4:0.04:0:1 0/0:32:0:0,0:18,14:0:2,0:30.7:1:28.8:1:1:0:59.4:64:1:0:0.3 -2 9036089 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13356;SOR=Inf;LSEQ=TAAGAGTTGTGAAAGGGAGC;RSEQ=GGGCACGGTGGCTCATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:19,27:0:2,0:22.7:1:29.7:1:1:0:60:92:1:0:0.3 0/1:27:2:1,1:12,13:0.0741:2,2:20.5:1:29.5:1:1:1.08:60:4:0.0741:0:1.5 -2 11805745 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGTTCTACATACCTATG;RSEQ=AACTCCCAGTGGTCATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:46:1:32.5:1:1:0:60:4:1:0:1 -2 11805999 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.20376;SOR=Inf;LSEQ=CTTGGCTTTGTAGACACGAC;RSEQ=CCAAGTGCCTCAGCCTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:27,21:0:2,0:28.6:1:30.7:1:1:0:60:47:1:0:0.1 0/1:40:2:1,1:20,18:0.05:2,2:47:0:30.5:1:1:1.10818:60:4:0.0513:0:1.5 -2 11806057 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05343;SOR=Inf;LSEQ=AACAGGTCCTCAAGCGGCTC;RSEQ=CACTTGCTGGACAGCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:18,25:0:2,0:23.8:1:30.3:1:1:0:60:42:1:0:0.1 0/1:27:3:2,1:8,16:0.1111:2,2:11:1:30.3:1:0.53504:3.79:60:6:0.12:0:1.3 -2 12737845 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52869;SOR=0;LSEQ=ATGCTTGGTTCAATTGCAAA;RSEQ=GAAAAGGACAGCCAAAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:33,18:0.0377:2,2:18.5:1:29:1:1:1.81117:60:4:0.0385:0:1 0/0:31:0:0,0:21,10:0:2,0:21.1:1:31.1:1:1:0:60:62:1:0:0.4 -2 12737918 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5326;SOR=0;LSEQ=AGAGCTGACTCCGGCCAATG;RSEQ=CCAAGTTGTAAACTAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:35,48:0.0235:2,2:29:0:31.5:1:1:1.37:60:4:0.0238:0:1.5 0/0:49:0:0,0:20,29:0:2,0:23.8:1:29.8:1:1:0:60:15.333:1:0:0.1 -2 14528016 . C T 261 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.94818;SOR=0.98355;LSEQ=CTTTTCTATTTAAAAAATAG;RSEQ=GGTCCAGGAGAAAACCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:610:425:227,198:86,98:0.6967:2,2:23.7:1:30:1:0.13441:1.31:60:850:0.699:0:1.1 1/0:515:357:180,177:78,80:0.6932:2,2:25.1:1:29.6:1:0.84881:1.04:60:118:0.6928:0:1.1 -2 14528089 . C T 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TCATCCTCCTTTCTCTTTCC;RSEQ=TCTCTTTCTCTCATCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:42:13,29:119,250:0.1019:2,2:24.9:1:29.6:1:1:1.0617:60:20:0.1003:0:1.2 0/0:308:0:0,0:106,201:0:2,0:23.7:1:31.1:1:1:0:59.9:152.5:0.9967:0:0.6 -2 14528108 . C TTCTTTCCTCTCTCTCTCTCTT 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.23384;LSEQ=CTTTCCCTCTCTTTCTCTCA;RSEQ=TCTCCTCCTTCCCTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:346:240:60,180:38,45:0.6936:2,2:20.8:1:29.8:1:0.00053:2.52515:59.7:47:0.6932:0.4393:0.9 0/1:272:94:15,79:62,98:0.3456:2,2:30.5:1:29.9:1:0.00012:3.317:59.6:30.333:0.3396:0.0956:1.1 -2 16079871 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCTCCTCCGCAGTGGT;RSEQ=AGGACGCGTGGACAGTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 16080157 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTGCACCTTCGGACTA;RSEQ=CCTTCTTTCGTAATTACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 16080895 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCTTGCAAACCGCCCGG;RSEQ=GCCCAGGGAAGCGACGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:155,4:0.0124:1,0:24.5:1:31.5:1:1:0:60:4:0.0126:0:1 0/0:76:0:0,0:73,3:0:1,0:25.2:1:32:1:1:0:60:75:1:0:0 -2 16080911 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12792;SOR=Inf;LSEQ=CCGGCGCCCAGGGAAGCGAC;RSEQ=AGCGCCGGGGCAAGGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:204,16:0:2,0:24.3:1:29.6:1:1:0:60:43:1:0:0.1 0/1:123:2:1,1:102,19:0.0163:2,2:8:1:31.5:1:0.29988:5.25819:60:4:0.0164:0:1 -2 16080936 . G T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15813;SOR=4.89585;LSEQ=CCGGGGCAAGGCAAGCCCTG;RSEQ=ACGGGATTGCGACGTGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:1:0,1:280,80:0.0028:2,0:1:0:23:0:0.22438:0:60:2:0.0028:0:1 0/1:223:3:1,2:164,56:0.0135:2,2:5.7:1:25.7:1:0.1665:5.80061:60:6:0.0136:0:1 -2 16081186 . AC A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.25753;SOR=0;LSEQ=CGGAGAGCCGGTGCGTCCCC;RSEQ=CCCAGGCTGGGGTTCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:2,1:36,212:0.012:2,2:8.3:1:30.7:1:0.06074:11.58:60:6:0.0123:0.004:0.3 0/0:201:0:0,0:35,164:0:2,0:19.6:1:30.5:1:1:0:60:65.333:0.9949:0:0.1 -2 16081233 . AG A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGCCCCTGGAGGAAGAAG;RSEQ=GGGGGGATTAGGCAGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:2,113:0.0171:1,0:18.5:1:32.5:1:1:0:60:4:0.0172:0:0 0/0:48:0:0,0:0,48:0:1,0:22.5:1:31:1:1:0:60:96:1:0:0 -2 16082313 . AC A 99 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.07735;SOR=3.48584;LSEQ=ACTTCGGCGGCCCCGACTCG;RSEQ=CCCCCCGGGGGAGGACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1018:3:2,1:476,538:0.0029:2,2:16:1:29:1:0.6035:2.26:60:6:0.003:0:0 0/1:882:9:5,4:419,453:0.0102:2,2:17.4:1:31.3:1:0.74488:1.35:60:18:0.0105:0.0011:0.6 -2 16082393 . G A 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAGCCGTGGCTTCGCGGA;RSEQ=CACAGCTCCGAGCCCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:0:0,0:317,369:0:2,0:24.5:1:31.9:1:1:0:60:67.6:1:0:0.1 0/1:550:34:18,16:241,274:0.0618:2,2:19.7:1:29.3:1:0.59529:1.28:60:68:0.0626:0:1.1 -2 16082706 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49652;SOR=0;LSEQ=GAGCCGGCCGCGCCGGGGCC;RSEQ=CCCTGCCCGCCGAGCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:28,13:0.0465:2,2:18:0:32:0:1:2.11228:60:4:0.0465:0:1 0/0:37:0:0,0:21,16:0:2,0:9:1:28.8:1:1:0:60:11.333:1:0:0.3 -2 16082734 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62286;SOR=0.35644;LSEQ=CGCCGAGCTCGCCCACCCGG;RSEQ=CGCCGAGTGCGTGGATCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:1,2:64,51:0.0254:2,2:19:1:28:1:0.58699:2.49063:60:6:0.0256:0:1 0/0:109:1:0,1:58,50:0.0092:2,0:1:0:26:0:0.46789:0:60:2:0.0097:0:1 -2 16082775 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26021;SOR=0;LSEQ=CCGTGGTCTTCCCCTTTCCC;RSEQ=TGAACAAGCGCGAGCCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:2,1:89,87:0.0168:2,2:29.3:1:29:1:1:1.95:60:6:0.0169:0:1 0/0:138:0:0,0:69,69:0:2,0:28.6:1:30.2:1:1:0:60:68:1:0:0.4 -2 16082778 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50664;SOR=0;LSEQ=TGGTCTTCCCCTTTCCCGTG;RSEQ=ACAAGCGCGAGCCAGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:88,86:0.0114:2,2:26:1:30:1:1:1.02313:60:4:0.0116:0:1 0/0:136:0:0,0:68,68:0:2,0:28.5:1:28.8:1:1:0:60:26.2:1:0:0.4 -2 16082784 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50638;SOR=0;LSEQ=TCCCCTTTCCCGTGAACAAG;RSEQ=GCGAGCCAGCGCCCGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:83,84:0.0118:2,2:24:1:31.5:1:1:1.01:60:4:0.0121:0:1 0/0:131:0:0,0:64,66:0:2,0:2:0:13:0:1:0:60:0:0:0:1 -2 16082881 . CG C 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1032;SOR=Inf;LSEQ=TGCCGCCCCAGCCGGGGCCC;RSEQ=GGGGTCGCCCCTCCGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:42,1:0:1,0:18:1:30.3:1:1:0:60:42:1:0:0.1 0/1:39:3:1,2:31,5:0.0769:2,2:10:1:27:1:0.07736:11.162:60:6:0.0769:0.0256:0.7 -2 16083525 . C CT 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTATTCTTTTTCTTTTT;RSEQ=TTTTTTTTTTTTTTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:0,2:0.3333:0,0:36.5:1:31.5:1:0.33333:0:60:4:0.3333:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 16083861 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTTGAAGGTGAGGGCAG;RSEQ=CACTCAGCAGCCTCTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:138,2:0.0141:1,0:22.5:1:30:1:1:0:60:4:0.0146:0:1 0/0:58:0:0,0:58,0:0:1,0:25.3:1:31.1:1:1:0:60:28:1:0:0.1 -2 16084202 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15501;SOR=Inf;LSEQ=TCTGTCCCTTTAATGTCTGT;RSEQ=CCTTGACAGCTTTTGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:21,220:0:2,0:24.2:1:32.4:1:1:0:60:240:1:0:0.1 0/1:157:2:0,2:16,139:0.0127:2,0:24:1:32:0:1:0:60:4:0.013:0:1 -2 16084594 . T C 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGTTAAATGAAAAACTG;RSEQ=TTATTGTATAAAACTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:22.5:1:28:1:1:0:60:3:0.75:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 16085519 . C T 94 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10683;SOR=0;LSEQ=AGCAGTCTGCCAGGGTCTGC;RSEQ=GGAAGAGACAGATAAGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:8:8,0:83,1:0.087:1,0:19:1:31.5:1:1:0:60:16:0.0879:0:1.1 0/0:34:0:0,0:34,0:0:1,0:22.4:1:30.1:1:1:0:60:16:1:0:0.2 -2 16085563 . G T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08886;SOR=Inf;LSEQ=ATTAACATGGATATATATGT;RSEQ=AATTTCATTCAAATGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:148,22:0:2,0:25.2:1:32.2:1:1:0:60:169:1:0:0.1 0/1:138:3:1,2:117,17:0.0217:2,2:17.3:1:22:1:0.05044:13.29618:60:2:0.015:0:1 -2 16086264 . AT A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.32913;SOR=0.47361;LSEQ=CTGCCACTTTGCACATTTTG;RSEQ=TTTTTTTTTAAACAAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:6:0,6:25,130:0.0373:2,0:28.5:1:32.2:1:0.59124:0:60:12:0.0387:0.0062:0 0/1:167:3:1,2:29,135:0.018:2,2:24.3:1:27.3:1:0.4501:2.31:60:6:0.018:0:0 -2 16086469 . C T 73 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGCGCTAAACGTTGGTGA;RSEQ=GGTTGGGAGCCTCTGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:30.8:1:31.6:1:1:0:60:10:0.8333:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 16087661 . G T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1664;SOR=5.64956;LSEQ=AGAATAAACAGATGGAAATG;RSEQ=GTTCCTCCCTTCAATGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:1:0,1:69,284:0.0028:2,0:19:0:14:0:1:0:60:0:0:0:8 0/1:254:4:2,2:56,193:0.0157:2,2:22.8:1:28:1:0.22621:3.43:60:8:0.0161:0:1 -2 16087781 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10448;SOR=Inf;LSEQ=GGGTCACAATGGAGACCCCA;RSEQ=ATGGGTGGCATGGCTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:0,45:0:1,0:25.2:1:28.2:1:1:0:60:44:1:0:0.2 0/1:22:2:0,2:0,19:0.0909:1,0:25.5:1:32.5:1:1:0:60:4:0.0952:0:1 -2 16797699 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52074;SOR=0;LSEQ=CCAGCCTTCCCTGGCTCCCC;RSEQ=GGGCTCCTGCTTCCACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:19,18:0.0513:2,2:38:0:32:1:1:1.05412:60:4:0.0526:0:1.5 0/0:24:0:0,0:13,11:0:2,0:28.2:1:29.7:1:1:0:60:48:1:0:0.2 -2 17626751 . G C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGGCGAGGCCAAGATGGC;RSEQ=GACTAGAAGCAGTGGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:35.4:1:30.7:1:1:0:60:14:1:0:1.6 1/1:2:2:1,1:0,0:1:0,2:19.5:1:31.5:1:1:0:60:4:1:0:1 -2 17626983 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49057;SOR=Inf;LSEQ=AGGTGAGTGAGTATGCTACC;RSEQ=AGCCTGGGAAACCATGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:26.1:1:31.6:1:1:0:60:52:1:0:0.3 0/1:27:2:1,1:15,10:0.0741:2,2:29:1:29:1:1:1.47706:60:4:0.0769:0:1.5 -2 17627057 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60041;SOR=0.68179;LSEQ=ATCCCACTCAGAAGCCCATG;RSEQ=AACCAGGGCCTTGGGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:6,6:8,9:0.4138:2,2:21.2:1:28.8:1:1:1.12:60:24:0.4138:0:1.2 0/1:34:11:4,7:11,12:0.3235:2,2:16.2:1:26.1:1:0.71521:1.58211:60:22:0.3333:0:1.3 -2 17627857 . C G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAATCAATGAAAAAATG;RSEQ=TGAAAACTCAAAAGGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:18:1:30:1:1:1.7321:60:4:0.4:0:1 0/0:2:0:0,0:1,1:0:2,0:15:1:30:1:1:0:60:4:1:0:0 -2 17675597 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15696;SOR=Inf;LSEQ=CCATTCTAACTGGTGTGAGA;RSEQ=AGTATCTCATTGTGGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:47,1:0:1,0:23.8:1:30.6:1:1:0:48.9:47:1:0:0.4 0/1:32:2:1,1:28,2:0.0625:2,2:8.5:1:33.5:1:0.18145:11.63346:53:4:0.0645:0:7.5 -2 17675599 . G A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14002;SOR=Inf;LSEQ=ATTCTAACTGGTGTGAGATA;RSEQ=TATCTCATTGTGGTTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:49,2:0:1,0:23.1:1:32:1:1:0:49.9:50:1:0:0.4 0/1:31:2:1,1:27,2:0.0645:2,2:10.5:1:32:0:0.1871:11.22521:53:4:0.0645:0:7.5 -2 17675612 . G A 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26579;SOR=4.00114;LSEQ=TGAGATAGTATCTCATTGTG;RSEQ=TTTTGATTTGCATTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:1:1,0:61,6:0.0147:2,0:22:0:14:0:1:0:40:0:0:0:3 0/1:35:2:1,1:31,2:0.0571:2,2:23.5:1:31.5:1:0.16639:12.85824:53:4:0.0606:0:7.5 -2 17675625 . T G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16057;SOR=Inf;LSEQ=CATTGTGGTTTTGATTTGCA;RSEQ=TTCTCTGATGGCCAGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:69,14:0:2,0:22.6:1:30.7:1:1:0:55.3:82:1:0:0.5 0/1:56:2:1,1:42,12:0.0357:2,2:36.5:1:33:0:0.41364:3.40239:53:4:0.0357:0:7.5 -2 17675636 . GC AT 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18976;SOR=Inf;LSEQ=TGATTTGCATTTCTCTGATG;RSEQ=CAGTGATGATGACCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:80,23:0:2,0:22.9:1:31.3:1:1:0:57.1:50.5:1:0:0.5 0/1:80:2:1,1:52,26:0.025:2,2:48.5:1:30:1:1:1.98146:53:4:0.025:0:6.5 -2 17675640 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18681;SOR=Inf;LSEQ=TTGCATTTCTCTGATGGCCA;RSEQ=TGATGATGACCATTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:84,27:0:2,0:23.4:1:32.2:1:1:0:57.9:110:1:0:0.5 0/1:85:2:1,1:56,27:0.0235:2,2:49:1:30.5:1:1:2.05486:53:4:0.0238:0:6.5 -2 17675655 . TTTTCA T 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03383;SOR=0;LSEQ=GGCCAGTGATGATGACCATT;RSEQ=TGCCTGACACCCTATTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:6:4,2:97,44:0.0405:2,2:32.5:1:31.2:1:1:1.10153:60:12:0.0408:0:0 0/0:122:0:0,0:73,49:0:2,0:22.4:1:29.6:1:1:0:59.4:121:1:0:0.6 -2 17675662 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5762;SOR=2.73431;LSEQ=GATGATGACCATTTTTTCAT;RSEQ=CCTGACACCCTATTCTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:1,0:112,54:0.006:2,0:9:0:32:0:1:0:60:2:0.0061:0:2 0/1:123:2:1,1:71,50:0.0163:2,2:19.5:1:28:1:1:1.41585:60:4:0.0165:0:1.5 -2 17675684 . T A 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12352;SOR=0.72245;LSEQ=CTGACACCCTATTCTTGATA;RSEQ=TTATGGGGTCTTCAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:111:64,47:68,48:0.489:2,2:24.9:1:30.1:1:0.89377:1.04021:60:36:0.4865:0:1.1 0/1:164:67:34,33:52,45:0.4085:2,2:26.8:1:30:1:0.75213:1.12078:60:66:0.4074:0:1.1 -2 17675722 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16661;SOR=Inf;LSEQ=AGAAGAAAGTGTGAATATGG;RSEQ=ATATGAGATGGAGCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:136,146:0:2,0:25.4:1:31.4:1:1:0:60:564:1:0:0.6 0/1:195:2:1,1:89,104:0.0103:2,2:38.5:1:29.5:1:1:1.17:60:4:0.0104:0:2.5 -2 17675735 . G T 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=2.45156;LSEQ=AATATGGGATATGAGATGGA;RSEQ=CAAAGAATTCTTGAACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:34:15,19:107,120:0.1303:2,2:25.2:1:29.7:1:0.85423:1.12892:60:33:0.1289:0:1.5 0/1:171:46:20,26:60,65:0.269:2,2:26.4:1:29.5:1:0.60963:1.19872:60:92:0.2722:0:1.5 -2 17675745 . C A 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28347;SOR=0;LSEQ=ATGAGATGGAGCAAAGAATT;RSEQ=TTGAACATGGAGAGTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:3:3,0:108,135:0.0121:2,0:8:1:20.3:1:0.0905:0:60:2:0.0083:0:3.3 0/0:159:0:0,0:67,92:0:2,0:25.2:1:31.6:1:1:0:60:158:1:0:0.7 -2 17675754 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13563;SOR=Inf;LSEQ=AGCAAAGAATTCTTGAACAT;RSEQ=GAGAGTCTCACTCCTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:95,134:0:2,0:26.1:1:31.4:1:1:0:60:228:1:0:0.6 0/1:134:2:1,1:55,77:0.0149:2,2:20:1:31.5:1:1:1.40:60:4:0.0152:0:1 -2 17675774 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53255;SOR=0;LSEQ=GGAGAGTCTCACTCCTGTGA;RSEQ=GTGCAGATGCACTGCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:64,110:0.0114:2,2:42:1:31.5:1:1:1.71:60:4:0.0115:0:1 0/0:103:0:0,0:40,63:0:2,0:26:1:30.6:1:1:0:60:33.333:1:0:0.5 -2 17675779 . A T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12894;SOR=1.70089;LSEQ=GTCTCACTCCTGTGAGGTGC;RSEQ=GATGCACTGCCCCAAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:23:7,16:49,90:0.142:2,2:27.3:1:29.4:1:0.81382:1.2428:60:10.5:0.1338:0:1.8 0/1:100:22:8,14:32,46:0.22:2,2:22.2:1:30.6:1:0.80731:1.21502:60:44:0.22:0:1.9 -2 17675959 . G A 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTAGGTGACTTCAAGTAC;RSEQ=GGACAAAGTGGGAACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:28.3:1:33:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 17986417 . A G 52 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=TAAATACCCAGCCTGTGAAA;RSEQ=TCATCTGTTCACACATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:25.5:1:28.5:1:1:0:60:8:1:0:0 1/1:3:3:3,0:0,0:1:0,0:29.7:1:33.3:1:1:0:60:6:1:0:1 -2 17986612 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06988;SOR=Inf;LSEQ=ACACAGGCTTTGCTGAAACT;RSEQ=TCACAGGCTTGACAGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:188,89:0:2,0:24.8:1:31.7:1:1:0:60:91.333:1:0:0.2 0/1:195:3:1,2:128,64:0.0154:2,2:17:1:29:1:0.265:3.96923:60:6:0.0155:0:1.3 -2 17986683 . G T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.49264;LSEQ=CACCACTTTCAGTTCTCTTT;RSEQ=CTAACTCAAGGACACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:60:28,32:162,209:0.1392:2,2:23.7:1:29.2:1:0.67646:1.13:60:59:0.1382:0:1.1 0/1:357:129:59,70:105,123:0.3613:2,2:28.6:1:29.7:1:1:1.01278:60:258:0.3665:0:1.1 -2 17986739 . T TAC 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.16423;SOR=1.38171;LSEQ=TTAGTTGTTTTCTTCACACA;RSEQ=ACACACACACCTATATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:48:14,34:72,135:0.1868:2,2:26.7:1:31:1:0.50199:1.29396:60:96:0.1882:0.0156:0 0/1:195:47:17,30:51,97:0.241:2,2:28.9:1:29.5:1:0.86151:1.08:60:94:0.2448:0.0256:0.1 -2 17986837 . A G 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09488;SOR=5.13317;LSEQ=GTGGCAGTGTGAAAGGGCCC;RSEQ=GGTTTTTAACTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:0,2:0,45:0.0417:1,0:27.5:1:20.5:1:1:0:50:1:0.0286:0:2 0/1:16:3:0,3:0,13:0.1875:1,0:8.3:1:25.3:1:1:0:46.7:6:0.2143:0:1 -2 17987407 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGCAGGGATGGGCGAGA;RSEQ=TACTGCAGCTGGCTCTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 20614873 . G C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAGCAGGGCAGTGACGT;RSEQ=GACTCTGTGTAGGTCGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:48:1:30.5:1:1:0:60:4:1:0:1 -2 20616307 . G T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1638;SOR=5.84919;LSEQ=CTAAAGGAAAGAGGCTTATT;RSEQ=GTGGACTGTCAGAAAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:199,33:0.0043:2,0:1:0:25:0:0.14592:0:60:2:0.0043:0:2 0/1:162:4:3,1:134,24:0.0247:2,2:29.3:1:30.5:1:0.49203:1.85243:60:8:0.0247:0:2 -2 20616374 . G C 296 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.3808;LSEQ=CTAGTCATTTGCAATAAAGG;RSEQ=AGATACTTTGGGACCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:669:615:380,235:35,18:0.9193:2,2:25.8:1:32:1:0.65827:1.20214:60:101.5:0.9199:0:1.4 1/1:528:429:250,179:54,45:0.8125:2,2:26.2:1:31.5:1:0.50095:1.16:60:38:0.8101:0:1.5 -2 20616425 . C T 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11023;SOR=1.18794;LSEQ=TCTTGGTTGAAAAAACTTCA;RSEQ=AGGTTGCAGCTTTTTGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:819:423:212,211:201,194:0.5165:2,2:25.7:1:29.2:1:0.83405:1.03117:60:83.6:0.516:0:1.6 1/0:624:349:167,182:135,139:0.5593:2,2:25.3:1:28.4:1:0.74704:1.05834:60:68.8:0.5621:0:1.6 -2 20616665 . C T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTTGCCATATGTTGAGC;RSEQ=CAGAATGTTTCTGAAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:0,4:0,25:0.1379:1,0:27:1:29.8:1:1:0:60:8:0.1429:0:1.8 0/0:3:0:0,0:0,3:0:0,0:21.7:1:30.7:1:1:0:60:6:1:0:0.7 -2 20616708 . G C 99 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTAAGTGAGTTCTATAAT;RSEQ=TGAAACTGGTTCATCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:0.7273:0,0:24.5:1:33.3:1:1:0:60:16:0.7273:0:1.5 1/1:1:1:0,1:0,0:1:0,0:20:0:33:0:1:0:60:2:1:0:1 -2 20647241 . C T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28327;SOR=0;LSEQ=CCGCTCATGGCGGCCATCCG;RSEQ=AAGAAGCTGGTGGTGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:13,0:0.2353:1,0:31.5:1:29.5:1:1:0:60:8:0.2353:0:1 0/0:7:0:0,0:7,0:0:0,0:14.6:1:33.3:1:1:0:60:14:1:0:0 -2 20764031 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCTCACCACCTCTCAGG;RSEQ=GGTCTACTGCAGGGTGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29:1:1:0:60:4:1:0:1.5 -2 21058065 . C G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08809;SOR=0.30485;LSEQ=AAATAAGTTAATCAGTGTTG;RSEQ=TGGAGATCAAGGTTCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:15:15,0:28,1:0.3333:1,1:25.9:1:32.7:1:1:0:60:30:0.3488:0:2 0/1:23:3:3,0:20,0:0.1304:1,0:20.7:1:32.3:1:1:0:60:6:0.1304:0:2 -2 21058088 . A G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03505;SOR=0.36507;LSEQ=GAGATCAAGGTTCTGGAGTG;RSEQ=GGAAAGGCACAGAAGGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:44:44,0:17,0:0.7213:1,1:29:1:31.5:1:1:0:60:88:0.7213:0:1.5 0/1:29:14:14,0:15,0:0.4828:1,1:25.9:1:29.5:1:1:0:60:13:0.4643:0:1.2 -2 21058264 . G A 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00051;SOR=0.59446;LSEQ=TCCAATGGTAAAAGTGAGAG;RSEQ=TTTTGAAAACTTTAATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:403:278:131,147:58,66:0.6898:2,2:27.3:1:30.2:1:1:1.01:60:68.5:0.6937:0:1.1 1/0:383:218:108,110:73,92:0.5692:2,2:24.7:1:29:1:0.35235:1.24:60:217:0.5711:0:1.2 -2 21059930 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=GGGCTGGATTTGAAGACTGA;RSEQ=ATGTGTAAATGCATTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:29.5:1:28.5:1:1:0:60:5:1:0:0 0/1:5:2:1,1:1,2:0.4:2,2:23:1:28:1:1:1.73:60:4:0.4:0:1 -2 21324937 . G C 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51921;SOR=Inf;LSEQ=AAGGCGGCGCGGACCCAAAG;RSEQ=CGAGTAACAGCAAGATGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:16,7:0:2,0:27:1:30:1:1:0:56:22:1:0:0.2 0/1:37:2:1,1:21,14:0.0541:2,2:5:0:28:1:1:1.4832:49:4:0.0571:0:2 -2 21324980 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21934;SOR=0;LSEQ=CACGGGACCTAGAAAGGGGA;RSEQ=AAGCCATGTTGCCCAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:30,24:0.0357:2,2:20.5:1:28:1:1:1.24498:60:4:0.0357:0:1 0/0:63:0:0,0:31,32:0:2,0:28.4:1:30.8:1:1:0:52.2:126:1:0:0.3 -2 21324997 . C A 71 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02735;SOR=0;LSEQ=GGAGAAGCCATGTTGCCCAA;RSEQ=TCCAGAGGTTGGTATAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:5:3,2:26,27:0.0862:2,2:22.8:1:30.8:1:1:1.55:23:10:0.0862:0:5 0/0:59:0:0,0:25,34:0:2,0:30.2:1:30.5:1:1:0:51.7:28.5:1:0:0.3 -2 21325009 . G A 77 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02743;SOR=0;LSEQ=TTGCCCAACTCCAGAGGTTG;RSEQ=TATAAGAGTTTGAAAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:6:3,3:22,29:0.1053:2,2:31:1:29.8:1:1:1.31:23:12:0.1053:0:5 0/0:54:0:0,0:22,32:0:2,0:28.8:1:30.3:1:1:0:50.9:26:1:0:0.3 -2 21325028 . A T 77 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02717;SOR=0;LSEQ=GGTATAAGAGTTTGAAAGGT;RSEQ=TTGTCTGATTTCAGAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:6:3,3:19,28:0.1132:2,2:36.2:1:29.8:1:0.6834:1.46:23:12:0.1132:0:5 0/0:50:0:0,0:20,30:0:2,0:19.1:1:28.4:1:1:0:52.4:49:1:0:0.3 -2 21325039 . T C 80 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03015;SOR=0;LSEQ=TTGAAAGGTATTGTCTGATT;RSEQ=CAGAAGCCTTTTCCTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:6:3,3:15,21:0.1429:2,2:34.2:1:31.2:1:1:1.39:23:12:0.1429:0:5 0/0:34:0:0,0:11,23:0:2,0:19.9:1:28.8:1:1:0:55.7:68:1:0:0.1 -2 21325064 . A G 51 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23482;SOR=0;LSEQ=AGCCTTTTCCTGTAAATGCC;RSEQ=GGTGGCATCTCATACTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:6,12:0.1429:2,0:25.3:1:32.7:1:0.52632:0:23:6:0.1429:0:5 0/0:18:0:0,0:4,14:0:2,0:20.9:1:30:1:1:0:59.4:36:1:0:0.1 -2 21325188 . A T 40 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTCTAGGGGAGGGAGGTA;RSEQ=CCACTGGGCGGAGGCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:24.7:1:30:1:1:0:60:6:0.75:0:1.3 1/1:3:3:1,2:0,0:1:0,2:18.3:1:25.7:1:1:0:60:6:1:0:1 -2 22412449 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26056;SOR=0;LSEQ=TGACAGAGATGCATCAAATC;RSEQ=GGATCTTAATACTGGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:2,1:25,14:0.0714:2,2:13.3:1:31.3:1:1:1.12:60:6:0.0714:0:1 0/0:30:0:0,0:17,13:0:2,0:23.5:1:28.2:1:1:0:60:14:1:0:0.1 -2 22412483 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5186;SOR=0;LSEQ=GGTTTAAGTGAGCATTCAGG;RSEQ=GACTGGTGGGATCAGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:31,32:0.0308:2,2:19:1:29:1:1:1.03:60:4:0.0308:0:1 0/0:42:0:0,0:22,20:0:2,0:27.3:1:29.5:1:1:0:60:84:1:0:0.1 -2 22412715 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18301;SOR=0;LSEQ=TTTATTAAATGAAATTAATC;RSEQ=TCCTCTTCTAGGCCATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:8:1:26.5:1:1:1.8258:60:4:0.25:0:1 0/0:10:0:0,0:5,5:0:2,0:25.2:1:29.7:1:1:0:60:20:1:0:0 -2 24166747 . TG T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19791;SOR=0;LSEQ=CTTGCTGAGACATGTTGGAG;RSEQ=GTCATTGCCTCCGAGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:112,58:0.0116:2,2:22:1:30:1:1:1.92319:60:4:0.0119:0:0.5 0/0:214:0:0,0:132,81:0:2,0:24.9:1:30.7:1:1:0:60:105.5:0.9953:0:0.1 -2 24166761 . G A 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59873;SOR=0.43046;LSEQ=TTGGAGTGGTCATTGCCTCC;RSEQ=AGCGCACTTTAGCCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:2,0:113,69:0.0108:2,0:8.5:1:32:0:0.52869:0:30.5:4:0.0109:0:4 0/0:214:1:1,0:124,89:0.0047:2,0:13:0:32:0:1:0:25:2:0.0048:0:5 -2 24166765 . G C 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59993;SOR=0.43374;LSEQ=AGTGGTCATTGCCTCCGAGC;RSEQ=CACTTTAGCCCTCAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:111,76:0.0106:2,0:12.5:1:32:0:0.5166:0:30.5:4:0.0108:0:4 0/0:217:1:1,0:123,92:0.0046:2,0:17:0:32:0:1:0:25:2:0.0047:0:5 -2 24166783 . T C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.84067;LSEQ=GCGCACTTTAGCCCTCAGCT;RSEQ=TGTATCAGAAATGCTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:2,1:108,92:0.0148:2,2:22:1:31:1:1:1.70:27.3:6:0.0149:0:5 0/1:241:3:1,2:121,117:0.0124:2,2:13:1:30.3:1:0.61877:2.06235:27:6:0.0126:0:5.7 -2 24166802 . C CTGATGGTTG 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39614;SOR=0.59495;LSEQ=TTTGTATCAGAAATGCTGTT;RSEQ=CTTTGGGAATCATGGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:7:2,5:106,102:0.0326:2,2:23:1:30.3:1:0.2798:2.58718:31.1:14:0.0335:0.0047:5 0/1:255:5:1,4:123,126:0.0196:2,2:22.4:1:27.4:1:0.37074:3.88633:31:10:0.0198:0.0039:5.4 -2 24166812 . T C 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56038;SOR=0.622;LSEQ=AAATGCTGTTCCTTTGGGAA;RSEQ=CATGGCCAAAGAAGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:7:2,5:110,103:0.0317:2,2:28.1:1:31.3:1:0.27362:2.65866:31.1:14:0.0323:0:5 0/1:251:5:1,4:120,126:0.0199:2,2:29.8:1:28.8:1:0.3716:3.79172:31:10:0.0205:0:5.4 -2 24166826 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.10153;SOR=0;LSEQ=TGGGAATCATGGCCAAAGAA;RSEQ=AGATGGAATGGTTCTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:1,2:104,110:0.0138:2,2:33.3:1:28.3:1:1:1.88558:60:6:0.0139:0:1 0/0:247:0:0,0:111,136:0:2,0:27:1:31.2:1:1:0:59.4:122.5:1:0:0.2 -2 24166832 . G A 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84679;LSEQ=TCATGGCCAAAGAAGAGATG;RSEQ=AATGGTTCTGGAATAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:5:0,5:98,106:0.0239:2,0:31.6:1:31.4:1:0.06192:0:31.4:10:0.0244:0:5.4 0/1:246:5:1,4:109,132:0.0203:2,2:25.4:1:28.6:1:0.38398:3.28918:31:10:0.0206:0:5.4 -2 24166834 . ATG GCA 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73881;SOR=0.68392;LSEQ=ATGGCCAAAGAAGAGATGGA;RSEQ=GTTCTGGAATAAGAACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:5:0,5:99,106:0.0238:2,0:28:0:33:1:0.06156:0:31.4:10:0.0239:0:3.4 0/1:244:4:0,4:107,133:0.0164:2,0:28:0:31.7:1:0.13329:0:32.5:8:0.0168:0:3.5 -2 24166853 . A G 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25054;SOR=Inf;LSEQ=AATGGTTCTGGAATAAGAAC;RSEQ=CAGGTTCAAACCGTCCCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:104,103:0:2,0:25.3:1:30.3:1:1:0:59.3:206:1:0:0.2 0/1:231:3:2,1:96,132:0.013:2,2:34:1:29.3:1:0.57577:2.74:60:6:0.013:0:1.7 -2 24166869 . C T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00741;SOR=Inf;LSEQ=GAACACAGGTTCAAACCGTC;RSEQ=CGTATCTCCCCACGTCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:106,89:0:2,0:23.3:1:31:1:1:0:60:96.5:1:0:0.1 0/1:205:8:3,5:91,106:0.039:2,2:29.9:1:29.1:1:0.7289:1.42837:60:16:0.0398:0:1.3 -2 24167053 . GGA TCT 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42145;SOR=1.27513;LSEQ=TGTCTGGGGCCAGCACTGAT;RSEQ=CACAACTAAGTTTGCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:27:25,2:484,268:0.0347:2,2:14.1:1:31.6:1:0.00157:6.91:40:54:0.0351:0.0193:6.4 0/1:708:31:26,5:399,276:0.0438:2,2:12.9:1:30.7:1:0.00756:3.59:38.2:62:0.0445:0.0297:6.2 -2 24167060 . A G 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38254;SOR=1.26593;LSEQ=GGCCAGCACTGATGGACACA;RSEQ=CTAAGTTTGCACTCGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:816:31:27,4:491,293:0.038:2,2:13.5:1:33.3:1:0.00416:4.02:39.9:62:0.0384:0:6.4 0/1:756:36:28,8:426,294:0.0476:2,2:12.1:1:32.6:1:0.03502:2.41:37.7:72:0.0478:0:6.3 -2 24167075 . G A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09382;SOR=1.51799;LSEQ=ACACAACTAAGTTTGCACTC;RSEQ=TCTTCCCTCTCATGTATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:941:31:27,4:541,365:0.0329:2,2:28.5:1:31.5:1:0.00221:4.55:39.9:62:0.0336:0:6.4 0/1:854:42:31,11:474,337:0.0492:2,2:25:1:30.3:1:0.05357:2.00:40.3:41:0.0485:0:6.3 -2 24167100 . G A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1335;SOR=1.44623;LSEQ=CCCTCTCATGTATCATACCT;RSEQ=GAATGGGATCCAACACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1133:33:29,4:618,482:0.0291:2,2:34.5:1:28.2:1:0.00023:5.65:41.1:66:0.0295:0:6.3 0/1:1082:45:33,12:574,463:0.0416:2,2:34.8:1:28.9:1:0.02063:2.22:41.6:90:0.0422:0:6.2 -2 24167110 . C T 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18286;SOR=1.35957;LSEQ=TATCATACCTGGAATGGGAT;RSEQ=CAACACTTGATGTGGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1207:37:28,9:636,534:0.0307:2,2:24.5:1:29.1:1:0.01126:2.61:42.5:74:0.0312:0:5.9 0/1:1140:47:32,15:599,494:0.0412:2,2:27.6:1:28.9:1:0.09835:1.76:41.3:22.5:0.0403:0:6.4 -2 24167121 . T C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07531;SOR=1.50865;LSEQ=GAATGGGATCCAACACTTGA;RSEQ=GTGGGACCTAGGAAAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1268:35:27,8:645,587:0.0276:2,2:17.3:1:30.2:1:0.00524:3.07:40.8:70:0.028:0:6.7 0/1:1193:49:32,17:612,530:0.0411:2,2:19.2:1:30:1:0.14253:1.63:41.4:48:0.0411:0:6.6 -2 24167129 . C A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14348;SOR=1.51368;LSEQ=TCCAACACTTGATGTGGGAC;RSEQ=TAGGAAAAGGCCTGAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1269:24:17,7:652,593:0.0189:2,2:17.1:1:28.8:1:0.09745:2.21:45.6:48:0.0191:0:6.7 0/1:1199:34:19,15:623,540:0.0284:2,2:18.7:1:29.4:1:0.86242:1.10:45.8:68:0.029:0:7 -2 24167132 . G T 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08991;SOR=1.64949;LSEQ=AACACTTGATGTGGGACCTA;RSEQ=GAAAAGGCCTGAAGATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1276:20:14,6:655,599:0.0157:2,2:18.3:1:28.9:1:0.17434:2.13:45.8:40:0.0159:0:7.4 0/1:1211:31:17,14:641,539:0.0256:2,2:18.5:1:28.8:1:1:1.02:47.5:30:0.025:0:7.2 -2 24167134 . A G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11784;SOR=1.58456;LSEQ=CACTTGATGTGGGACCTAGG;RSEQ=AAAGGCCTGAAGATTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1290:20:14,6:660,605:0.0155:2,2:17.1:1:29.3:1:0.12122:2.14:45.8:40:0.0159:0:7.4 0/1:1232:30:17,13:645,556:0.0244:2,2:17.9:1:30.9:1:0.8536:1.13:47.1:60:0.0248:0:7.4 -2 24167267 . A G 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTACACATTATTGTATTC;RSEQ=CCCATCTTTCAGTTTGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:0:0,0:255,413:0:2,0:26.2:1:30.1:1:1:0:60:50.385:0.997:0:0.8 0/1:746:23:11,12:301,421:0.0308:2,2:22.4:1:30.9:1:0.66862:1.28:60:46:0.0315:0:1.1 -2 24167268 . C T 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.42824;LSEQ=CCTACACATTATTGTATTCA;RSEQ=CCATCTTTCAGTTTGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:671:468:172,296:83,118:0.6975:2,2:25.6:1:30.3:1:0.29752:1.21012:60:65.857:0.6985:0:1.1 0/1:745:370:147,223:165,210:0.4966:2,2:25:1:29.2:1:0.26531:1.19165:60:184:0.5007:0:1.1 -2 24167385 . G A 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=AGTACCTTGTAGACCGTAAT;RSEQ=GTGGAAAAGGGTCTAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:6,142:0:1,0:23.9:1:31.2:1:1:0:60:48.333:1:0:0.1 0/1:130:12:2,10:8,110:0.0923:2,2:25.8:1:30.1:1:0.23144:2.72:60:24:0.0952:0:1.5 -2 24167445 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=9e-04;SOR=Inf;LSEQ=GGGTGGCTGCAAAAACTCCC;RSEQ=TTTTTTTGCCCACAGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:2,60:0:1,0:23.3:1:32.4:1:1:0:59.9:61:0.9839:0:0.1 0/1:31:6:1,5:0,25:0.1935:1,2:19:1:28:1:0.19355:0:60:12:0.2069:0:1.8 -2 24167751 . C A 77 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCCCAGCTAGAGAGAG;RSEQ=TAAAGAGGACTAGTTAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:28.3:1:30:1:1:0:60:12:1:0:1 1/1:2:2:1,1:0,0:1:0,2:21.5:1:28:1:1:0:60:4:1:0:1 -2 25100674 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10112;SOR=Inf;LSEQ=ACCAGACAGAGAGGGAAGAG;RSEQ=CTCCTTGGCCTGGGGCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:62,32:0:2,0:27.7:1:31.3:1:1:0:60:46:1:0:0.2 0/1:83:3:1,2:52,28:0.0361:2,2:30.3:1:29:1:0.29511:3.65262:60:6:0.0361:0:1.7 -2 25100707 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4978;SOR=Inf;LSEQ=GGGCGAGACAGCTGGCGCTC;RSEQ=AAGCCTTACTTCTGGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:64,49:0:2,0:23.7:1:29.7:1:1:0:60:55.5:1:0:0.4 0/1:114:2:1,1:62,50:0.0175:2,2:6.5:1:28.5:1:1:1.23764:60:4:0.0175:0:1.5 -2 25100723 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22665;SOR=0;LSEQ=GCTCGAAGCCTTACTTCTGG;RSEQ=CCCAAGGGCAACAGCTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:48,55:0.019:2,2:7:1:26:1:1:1.14:60:4:0.0192:0:1 0/0:115:0:0,0:55,60:0:2,0:43:0:14:0:1:0:60:0:0:0:2 -2 25100738 . C A 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68729;SOR=1.14242;LSEQ=TCTGGGCCCAAGGGCAACAG;RSEQ=TGTACCTGGGAGCTGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:50:22,28:22,29:0.495:2,2:28:1:30.3:1:1:1.04:60:100:0.5051:0:1.1 1/0:123:65:29,36:28,30:0.5285:2,2:27:1:29.7:1:0.71985:1.15723:60:130:0.5285:0:1.2 -2 25100902 . C G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33591;SOR=0.2973;LSEQ=GGCTCTGTGGTGACAGAGGT;RSEQ=CACAGCCCCTGGGGTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:0,9:0,5:0.6429:0,0:27:1:32:1:1:0:60:18:0.6429:0:1.7 0/1:6:2:0,2:0,4:0.3333:0,0:6.5:1:31:1:1:0:60:4:0.3333:0:1 -2 25458067 . T C 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCTCTTTTTTTTTTTTT;RSEQ=CCCTTTGAGATGGAATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:0,0:0.6667:0,0:27.5:1:30.5:1:1:0:60:8:0.8:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 25458100 . C A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTCTCTGTTGCACAGG;RSEQ=TGGAGCACAGTGGCGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:33.5:1:28.5:1:1:0:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 25458379 . G A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30492;SOR=1.78589;LSEQ=ACTCCTCTTACTTGGGACCA;RSEQ=CCTTAAAATACCCAGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:25:25,0:27,1:0.4545:1,1:22.7:1:30.2:1:1:0:60:50:0.4808:0:1.1 1/0:20:12:12,0:8,0:0.6:0,0:22:1:30.5:1:1:0:60:24:0.6:0:1.3 -2 25458424 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14229;SOR=Inf;LSEQ=GTGTCAGGAGTCCACCCCAG;RSEQ=AGTCTGCCATGTTGGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:120,3:0:1,0:26.2:1:31.1:1:1:0:60:23.6:1:0:0.3 0/1:75:2:2,0:71,1:0.0267:1,0:5:1:29:1:1:0:60:4:0.0282:0:1 -2 25458546 . C T 280 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.59802;LSEQ=AGCAATCAGAACAGCCACAC;RSEQ=GCAGCCAGATGCCAGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1050:591:363,228:267,188:0.5629:2,2:25.9:1:30.5:1:0.37316:1.12:60:117.2:0.5651:0:1.1 0/1:938:408:230,178:294,236:0.435:2,2:26.8:1:30.2:1:0.79115:1.04:60:101:0.4344:0:1.1 -2 25458853 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAGCAGAGTTCGCAGGGC;RSEQ=GGAGCCTCCACAGACCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:0,38:0.05:1,0:8:1:31.5:1:1:0:60:4:0.05:0:1 0/0:12:0:0,0:0,12:0:0,0:25.1:1:31.2:1:1:0:60:24:1:0:0 -2 25459718 . C T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5677;SOR=2.98158;LSEQ=ACACTAGCTGGAGAAGCAGG;RSEQ=GGGACAAGGCCCTGGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:201,68:0.0037:2,0:1:0:26:0:0.25556:0:60:2:0.0038:0:1 0/1:182:2:1,1:137,43:0.011:2,2:20.5:1:26:1:0.42608:3.1611:60:4:0.0112:0:1 -2 25462138 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08334;SOR=Inf;LSEQ=AGGAGGAGCATGAAACAGCG;RSEQ=CGGCATGCTGCTGGGGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:49,254:0:2,0:25.6:1:31.3:1:1:0:60:59.6:1:0:0.1 0/1:236:3:2,1:49,184:0.0127:2,2:16.3:1:28:1:0.11868:7.42:60:6:0.0128:0:1.3 -2 25463077 . TC T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.27418;SOR=0;LSEQ=TGCAAAGCAGAAGTCACCAG;RSEQ=CCCAGCTCCACAATGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:212,24:0.0126:2,2:23:1:29.3:1:0.03197:17.22491:60:6:0.0127:0.0042:0.3 0/0:164:0:0,0:146,18:0:2,0:23.1:1:30.9:1:1:0:59.9:163:1:0:0.1 -2 25463090 . A G 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26672;SOR=0;LSEQ=TCACCAGTCCCCAGCTCCAC;RSEQ=ATGCAGATGAGACAGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:2,1:249,49:0.01:2,2:16.3:1:22.3:1:0.4213:2.53042:60:2:0.0067:0:1 0/0:220:0:0,0:180,40:0:2,0:21.8:1:29.6:1:1:0:60:72.333:1:0:0.1 -2 25463116 . C T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.45856;SOR=1.87852;LSEQ=GATGAGACAGGATGAAGCAG;RSEQ=AGTCCAAGGTAGAAGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:3:2,1:341,137:0.0062:2,2:21.3:1:28.3:1:1:1.24398:60:6:0.0064:0:1 0/1:343:4:2,2:230,109:0.0117:2,2:27:1:27.3:1:0.5976:2.10512:60:8:0.0119:0:1 -2 25463399 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12425;SOR=Inf;LSEQ=CTCGGGCACGGGGAGGGCAC;RSEQ=GGAAGACAGGGTCATCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:173,120:0:2,0:23.3:1:30:1:1:0:60:40.857:1:0:0.2 0/1:160:2:1,1:102,56:0.0125:2,2:28:1:32:0:1:1.81411:60:4:0.0127:0:1 -2 25463483 . G A 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00146;SOR=1.41004;LSEQ=GCGGAAGCACCAGCTGAGAA;RSEQ=GTGGAGGGGACAGGATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:841:296:188,108:349,196:0.352:2,2:25:1:30.2:1:0.88083:1.02289:60:73:0.3522:0:1.1 0/1:634:275:167,108:223,136:0.4338:2,2:25.6:1:29.9:1:0.74224:1.0603:60:54:0.4348:0:1.2 -2 25463748 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12167;SOR=Inf;LSEQ=GCAGGCTCACGACCCTAGCT;RSEQ=CAACCATGGACAAGTCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:0,70:0:1,0:26.9:1:31.4:1:1:0:60:13:1:0:0.2 0/1:38:2:1,1:0,36:0.0526:1,2:42:1:29:1:0.05263:0:60:4:0.0541:0:1 -2 25463871 . C T 40 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGGAAGGTGACCCAAGTGGA;RSEQ=GGCTGAGTCTGAAGGTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:14:1:25.7:1:1:0:60:2:0.2857:0:2 1/1:1:1:0,1:0,0:1:0,0:24:0:32:0:1:0:60:2:1:0:1 -2 25464631 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08349;SOR=Inf;LSEQ=GCCATCTCCCTGGCACCCTG;RSEQ=TCTCGGCAGGTGAGCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:56,265:0:2,0:23.7:1:31.2:1:1:0:60:28.182:1:0:0.2 0/1:251:3:2,1:60,188:0.012:2,2:15.3:1:26:1:0.15177:6.21:60:6:0.0121:0:1 -2 25464653 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.184;SOR=Inf;LSEQ=CTCGGCAGGTGAGCCTGCTG;RSEQ=CCAACAGGACCCATGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:17,193:0:2,0:25.7:1:31.8:1:1:0:60:29:0.9951:0:0.2 0/1:159:2:1,1:20,136:0.0126:2,2:21.5:1:28.5:1:0.24889:6.66:60:4:0.0128:0:1 -2 25466810 . C T 159 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02818;LSEQ=GACAGCACCCGGATGGGCTT;RSEQ=CTCTTCTCAGCTGGGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1076:40:18,22:479,556:0.0372:2,2:26.1:1:29.9:1:1:1.05292:60:80:0.0384:0:1.2 0/0:921:1:0,1:425,492:0.0011:2,0:1:0:28:0:1:0:60:2:0.0011:0:1 -2 25466888 . G T 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14496;SOR=0.79588;LSEQ=ACAGGTCAGATGCAGGCCCA;RSEQ=CGGTGTCCCAAGCTCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:465:305:119,186:54,105:0.6559:2,2:23.2:1:30.3:1:0.31239:1.24:60:75.25:0.663:0:1.1 1/0:302:182:64,118:44,76:0.6026:2,2:21.4:1:29:1:0.80711:1.0672:60:59.667:0.6007:0:1.1 -2 25467285 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12815;SOR=Inf;LSEQ=GTGTGCTACCTGGAATGGAA;RSEQ=GACCGGGTCTGGAGCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:154,202:0:2,0:22.3:1:30.9:1:1:0:60:43.5:1:0:0.2 0/1:199:2:1,1:82,115:0.0101:2,2:23:1:30:1:1:1.40:60:4:0.0101:0:1.5 -2 25467290 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12997;SOR=Inf;LSEQ=CTACCTGGAATGGAAAGACC;RSEQ=GGTCTGGAGCATGGCTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:165,180:0:2,0:22.6:1:30.6:1:1:0:60:56.5:1:0:0.2 0/1:195:2:1,1:90,103:0.0103:2,2:19:1:28:1:1:1.14:60:4:0.0104:0:1 -2 25467308 . G A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11423;SOR=0.3887;LSEQ=CCGGGTCTGGAGCATGGCTA;RSEQ=GGGGTGGAGGGTCTGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:19:10,9:207,123:0.0544:2,2:30.6:1:31.3:1:0.46653:1.51271:60:38:0.0549:0:1.4 0/1:183:4:2,2:108,71:0.0219:2,2:16:1:30.8:1:1:1.5175:60:8:0.0221:0:1 -2 25467591 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15941;SOR=Inf;LSEQ=GGCCAGGACGAAGGGAGGCT;RSEQ=CACACCTGGCCTCACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:32,214:0:2,0:24.2:1:30.8:1:1:0:60:26.333:1:0:0.1 0/1:164:2:1,1:24,138:0.0122:2,2:22.5:1:26:0:0.28243:5.65:60:4:0.0123:0:1.5 -2 25467986 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCATCAGGACTCTGCTTC;RSEQ=AGAGGAAGCTCTGAAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:2,0:149,5:0.0127:1,0:30.5:1:32:0:1:0:60:4:0.0129:0:1 0/0:63:0:0,0:61,2:0:1,0:22:1:30.7:1:1:0:60:126:1:0:0.1 -2 25468012 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09645;SOR=Inf;LSEQ=AAGCTCTGAAGTCTACATCA;RSEQ=ACGCACACCGGGTGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:200,11:0:2,0:24.9:1:32.3:1:1:0:60:104.5:1:0:0.1 0/1:96:2:2,0:90,4:0.0208:1,0:12.5:1:31.5:1:1:0:60:4:0.0213:0:1 -2 25468034 . G A 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCACACCGGGTGTCACCCT;RSEQ=TACATGCCCAGAAGCGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:269,31:0:2,0:23.5:1:32.3:1:1:0:60:299:1:0:0.1 0/1:174:13:11,2:147,14:0.0747:2,2:20.3:1:27.5:1:0.34039:1.90033:60:12:0.0698:0:1.2 -2 25468251 . C A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.35805;SOR=2.66357;LSEQ=GTACCACCGAAGGGCCTCTC;RSEQ=CTCCCCGGGCCGGAGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:2:2,0:125,346:0.0042:2,0:1:0:27.5:1:0.07168:0:60:4:0.0043:0:1 0/1:269:3:2,1:69,197:0.0112:2,2:24.7:1:28.3:1:0.17119:5.67:60:6:0.0113:0:1 -2 25468763 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGACAGTGCACGAAGCAC;RSEQ=GTGAAGGTGGTGTGACACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:179,2:0.0109:1,2:7.5:1:30:1:0.03261:73.29687:60:4:0.0111:0:1 0/0:84:0:0,0:80,4:0:1,0:26.7:1:29.9:1:1:0:60:168:1:0:0.1 -2 25468793 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14805;SOR=Inf;LSEQ=GTGTGACACGCAGGACGTGG;RSEQ=CCCTGGTCCCATGTCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:266,37:0:2,0:22.7:1:31.6:1:1:0:60:36.875:1:0:0.1 0/1:190:2:1,1:151,37:0.0105:2,2:27.5:1:28.5:1:0.36085:4.04034:60:4:0.0108:0:1 -2 25468820 . C T 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02906;SOR=Inf;LSEQ=TCCCATGTCATTCAAACCTT;RSEQ=CTAAGTGCCTCTGCTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:487:0:0,0:331,155:0:2,0:23.7:1:30.9:1:1:0:60:68.429:1:0:0.1 0/1:344:4:1,3:222,118:0.0116:2,2:11.3:1:27.5:1:0.12682:5.6149:60:8:0.0117:0:1 -2 25468969 . G A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01341;SOR=Inf;LSEQ=AGCTGGCGTCAGAGGAGGCC;RSEQ=CGCCTGCTCCTCGGATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:0:0,0:351,332:0:2,0:23.5:1:30.6:1:1:0:60:67.3:1:0:0.1 0/1:501:5:5,0:260,235:0.01:2,0:10.6:1:23.2:1:0.0635:0:60:4:0.0082:0:1.2 -2 25469405 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09112;SOR=Inf;LSEQ=CTCTGTGGAGGCCTTGGCAG;RSEQ=CCTCCCTAAGCATGGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:235,46:0:2,0:23.3:1:31.6:1:1:0:60:45.833:1:0:0.1 0/1:122:2:1,1:97,23:0.0164:2,2:8:1:28:1:0.35605:4.14982:60:4:0.0167:0:1 -2 25469502 . C T 207 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=216.38339;LSEQ=CATTTACCTTCTGGTGGCTC;RSEQ=AGGCCCTTAGGGCCAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:988:1:0,1:576,411:0.001:2,0:1:0:25:0:0.417:0:60:2:0.001:0:1 0/1:733:132:73,59:357,244:0.1801:2,2:22.2:1:29.4:1:0.43499:1.18224:60:131:0.1814:0:1.2 -2 25469628 . C T 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CACACCGGGAACAGCTTCCC;RSEQ=GCGCGGCTGCTGGCCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:954:0:0,0:388,566:0:2,0:23.2:1:30.1:1:1:0:60:94.4:1:0:0.1 0/1:722:78:36,42:283,358:0.108:2,2:26.6:1:30.3:1:0.80943:1.08:59.9:38:0.1063:0:1.3 -2 25469714 . C A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29574;SOR=0;LSEQ=CAGATGGGTCAGGCTCAAGG;RSEQ=CAGACTCTGAGTAGTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:53,228:0.0106:2,2:17.3:1:23.3:1:0.09697:8.51:60:2:0.0072:0:1 0/0:170:0:0,0:24,143:0:2,0:25.2:1:30.6:1:1:0:60:26.833:0.9817:0:0.2 -2 25469715 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13744;SOR=Inf;LSEQ=AGATGGGTCAGGCTCAAGGC;RSEQ=AGACTCTGAGTAGTGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:54,232:0:2,0:23.7:1:31.9:1:1:0:60:94.333:1:0:0.1 0/1:169:2:1,1:22,145:0.0118:2,2:17:1:30.5:1:0.25437:6.47:60:4:0.0122:0:1 -2 25469913 . C T 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=1.64472;LSEQ=CTCCGAGCTCCCAGCAGGGA;RSEQ=ACTCACCTGCAGGACCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:627:374:241,133:150,103:0.5965:2,2:24.2:1:29.5:1:0.20786:1.24:60:40.556:0.5945:0:1.2 1/0:508:360:222,138:89,59:0.7087:2,2:23.6:1:28.8:1:0.76434:1.07:60:71:0.7086:0:1.2 -2 25469945 . C T 90 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02597;SOR=0.13163;LSEQ=GGACCTCGTAGATGGCTTTG;RSEQ=GGTACATGGGCTGCTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:9:2,7:467,396:0.0103:2,2:11:1:28.4:1:0.08922:4.12164:60:18:0.0105:0:1.2 0/0:731:1:1,0:391,336:0.0014:2,0:47:0:29:0:1:0:60:2:0.0014:0:2 -2 25470667 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68427;SOR=1.54967;LSEQ=CACAGTGGTCACGAGGCCCT;RSEQ=CCACCCTGATCCCCCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:3:3,0:97,300:0.0075:2,0:7.3:1:25:1:0.01527:0:60:6:0.0077:0:1.3 0/1:259:3:2,1:69,187:0.0116:2,2:15:1:27.7:1:0.18319:5.38:60:6:0.0118:0:1 -2 25470803 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.27064;SOR=3.86974;LSEQ=CCGGGGTCAGGTGGAGAGAG;RSEQ=GAGCGGCCCGTGGGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:1:0,1:244,53:0.0034:2,0:40:0:32:0:0.18121:0:60:2:0.0034:0:1 0/1:155:2:2,0:130,22:0.0129:2,0:11.5:1:30.5:1:1:0:60:4:0.0131:0:1 -2 25471158 . T A 47 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03313;SOR=Inf;LSEQ=CAAAAAGTCACCTTGACCTC;RSEQ=CCAGGAATTAGCAAGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:95,367:0:2,0:22.2:1:29.8:1:1:0:60:37.5:1:0:0.1 0/1:346:4:4,0:83,259:0.0116:2,0:6.8:1:23.5:1:0.00379:0:60:8:0.0118:0:1 -2 25471169 . GC G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1406;LSEQ=CTTGACCTCTCCAGGAATTA;RSEQ=AAGGCCACCTGACACTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:118:18,100:33,208:0.3278:2,2:20.1:1:31.4:1:0.74801:1.13:60:117:0.3296:0.0694:0.2 0/1:250:16:4,12:40,194:0.064:2,2:18.4:1:30.8:1:0.4938:1.61:60:32:0.0643:0.012:0.4 -2 25471246 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11538;SOR=Inf;LSEQ=AAGGTCAAGGGCTGGAGAGA;RSEQ=CCAACCAGCTGCCTTGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:1,103:0:1,0:24:1:32.5:1:1:0:60:103:1:0:0.1 0/1:54:2:0,2:1,51:0.037:1,0:33.5:1:30:1:1:0:60:4:0.0377:0:1 -2 25472666 . G A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2957;SOR=0;LSEQ=TTACTGAATCTAGGAAACAC;RSEQ=GCCCTCTGACTTCAAGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:29,242:0.0109:2,2:17:1:22.7:1:0.03465:16.34:60:2:0.0074:0:1 0/0:164:0:0,0:24,140:0:2,0:22.4:1:30.2:1:1:0:60:81:1:0:0.1 -2 25472784 . C T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.24211;LSEQ=TGGGCCTAGAGCTGCGAATG;RSEQ=AAACCCATCCTCAAGGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:1,13:0,10:0.5833:0,1:25.9:1:27.4:1:1:0:60:28:0.6087:0:1.4 1/0:11:7:0,7:1,3:0.6364:2,0:23.6:1:28.4:1:0.36364:0:60:14:0.6364:0:1.4 -2 25474918 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.53487;SOR=0;LSEQ=TAAGTCAGCATCTCCAGAAC;RSEQ=CGGGCCAGGCCGGGACGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:111,1:0.0175:1,2:20:1:29.5:1:0.03493:78.80349:60:4:0.0179:0:1 0/0:65:0:0,0:63,1:0:1,0:21.9:1:31.1:1:1:0:60:63:1:0:0.1 -2 25475126 . T A 56 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00484;SOR=Inf;LSEQ=GAGCCGCGGCCCTGAAGCTC;RSEQ=GGAAGTAGCTGCCCGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:815:0:0,0:305,501:0:2,0:25.1:1:29.3:1:1:0:60:13.393:1:0:0.3 0/1:572:6:6,0:226,337:0.0105:2,0:8:1:21.8:1:0.00442:0:60:2:0.0075:0:1.2 -2 25475140 . C A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08039;SOR=6.25078;LSEQ=AAGCTCTGGAAGTAGCTGCC;RSEQ=GTCTTGGGGGAGGGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:624:1:1,0:225,393:0.0016:2,0:1:0:25:0:0.36511:0:60:2:0.0018:0:1 0/1:402:4:3,1:148,250:0.01:2,2:19:1:24.8:1:0.15111:5.05:60:8:0.0106:0:1.5 -2 25475155 . G A 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07037;SOR=6.65482;LSEQ=CTGCCCGTCTTGGGGGAGGG;RSEQ=AAGGGGGCGATGGGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:1:0,1:122,323:0.0022:2,0:48:0:13:0:1:0:60:0:0:0:2 0/1:272:4:2,2:87,180:0.0147:2,2:19:1:24.3:1:0.59982:2.06:60:3:0.0118:0:2 -2 25475189 . A C 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57056;SOR=0;LSEQ=GGCTGGGGGCGGAGGGGGCC;RSEQ=CTGGGAGGGGAGGGGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:3:0,3:18,139:0.0186:2,0:10.3:1:26.3:1:1:0:52:2:0.0138:0:3.7 0/0:56:0:0,0:6,50:0:2,0:8:0:14:0:1:0:60:0:0:0:1 -2 25497684 . A AC 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.1556;LSEQ=GAGCAGATGAACCAGTCATC;RSEQ=TGACTAGAGATTAAGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:140:112:110,2:27,1:0.8:1,1:24.5:1:31.7:1:0.49077:2.02:60:111:0.8102:0.1857:0.1 0/1:97:37:36,1:58,2:0.3814:1,1:28.3:1:31.8:1:1:1.24:60:74:0.3814:0.0515:0 -2 25498504 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.506;SOR=0;LSEQ=CCTTGTGCCTGGGGTCCCTG;RSEQ=CACAGGGGATGGGGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:18,143:0.0123:2,2:8.5:1:27:1:0.22018:7.76:60:4:0.0127:0:1 0/0:127:0:0,0:19,108:0:2,0:23.1:1:30.6:1:1:0:60:20.167:1:0:0.1 -2 25505793 . T C 89 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63948;SOR=0.34368;LSEQ=CCCTTGAAATCACGAGTCTG;RSEQ=GGACTCCAGCTTCAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:0,8:0,16:0.3333:1,0:17.8:1:29.8:1:1:0:60:16:0.3478:0:1.1 0/1:7:1:0,1:0,6:0.1429:0,0:30:0:32:0:1:0:60:2:0.1429:0:1 -2 25521806 . AC A 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACCTCCAGGAACTCACC;RSEQ=CCCCCCCGCCTCTACTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:32.5:1:1:0:60:4:1:0:0.5 -2 25522795 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00641;SOR=0.1282;LSEQ=GGGCAACAGAGTGAGACTCC;RSEQ=TCTCAGTAAAAAAGTAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:26:26,0:21,0:0.5532:1,1:24.1:1:30.2:1:1:0:60:52:0.5652:0:1 0/1:15:2:2,0:13,0:0.1333:1,0:13:1:29:1:1:0:60:4:0.1333:0:1 -2 25522925 . G T 49 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01493;SOR=Inf;LSEQ=AATGTCTCCAGGTCCCTGCA;RSEQ=GACATACATCACTGCCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:0:0,0:443,143:0:2,0:21.7:1:31.3:1:1:0:60:52.273:1:0:0.1 0/1:448:5:1,4:333,109:0.0112:2,2:14.8:1:21.4:1:0.01575:12.13864:60:1.5:0.0069:0:1 -2 25523196 . T C 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00879;SOR=0.50242;LSEQ=TGTCTGGGGCTGGCCCTGGC;RSEQ=TCCCTTCCAGCCCCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:91:3,88:7,93:0.4691:2,1:24.7:1:31.7:1:0.33623:2.19923:60:44.5:0.4709:0:1.1 0/1:101:31:2,29:5,65:0.3069:2,2:21.3:1:32.1:1:1:1.1142:60:62:0.31:0:1.1 -2 25535032 . G T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATCCGACAGAGAAAGCAA;RSEQ=CCAGGCCCAAGAAGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 25536827 . G A 177 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=51.46989;LSEQ=GCAGAGCTGCTGGTGTCCCC;RSEQ=GGGCCGCTGGAGGGCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1002:2:2,0:440,559:0.002:2,0:1:0:26.5:1:0.19473:0:60:4:0.002:0:1 0/1:748:70:34,36:308,369:0.0936:2,2:24.3:1:28.9:1:0.70567:1.13:60:13:0.0889:0:1.2 -2 25536863 . G A 81 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01049;SOR=9.99982;LSEQ=ATGGCGGGCATCTGGGCGCC;RSEQ=GGAGGCAGGCTGGGGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:715:1:1,0:236,477:0.0014:2,0:47:0:14:0:0.33193:0:60:0:0:0:1 0/1:506:7:5,2:188,311:0.0138:2,2:12.6:1:28.9:1:0.1117:4.12:60:14:0.014:0:1.1 -2 25966872 . TG T 104 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.21373;SOR=0.48836;LSEQ=ACGGCAGGTGTTGGAGGCAC;RSEQ=GGGGGGTTTGCTGTAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1070:11:6,5:585,474:0.0103:2,2:23.8:1:30.1:1:1:1.02846:60:10:0.0095:0.0028:0.4 0/0:991:5:3,2:527,457:0.005:2,2:31.2:1:30.5:1:1:1.30:60:10:0.0051:0.001:0 -2 25967169 . T TGCGGCG 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=4.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ACTGAGGCGGCTGCAGCAGC;RSEQ=GCGGCGGCAGCGGCAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:526:0:0,0:275,251:0:2,0:22.3:1:30.4:1:1:0:60:39.462:1:0:0.1 0/1:498:21:13,8:245,231:0.0422:2,2:30.4:1:29.1:1:0.38059:1.53:59.8:20:0.0412:0.006:0.2 -2 25972936 . C T 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTCTCAGATTCCTGTTCAG;RSEQ=AGAGGTGACTGGCTTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:991:73:34,39:467,448:0.0737:2,2:22.3:1:28.6:1:0.46872:1.19549:60:72:0.0735:0:1.1 0/0:785:0:0,0:374,409:0:2,0:24.1:1:31.8:1:1:0:60:77.3:0.9974:0:0.1 -2 25973309 . C T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37395;SOR=1.2724;LSEQ=AGGGGAAAAAAGAAATATTC;RSEQ=AGTTGAAAAATAGCCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:54:7,47:24,127:0.2621:2,2:22.9:1:29:1:0.66552:1.26747:60:53:0.2585:0:1.1 0/1:122:38:8,30:18,66:0.3115:2,2:16.7:1:27.9:1:1:1.02254:60:37:0.3109:0:1.1 -2 25973405 . G A 94 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42031;SOR=0.33566;LSEQ=CTGACACAGCAGGTATTCAT;RSEQ=TATTATCTTCACTATTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:0,29:0.2162:1,0:21.4:1:31.6:1:1:0:60:16:0.2286:0:1.1 0/1:12:1:0,1:0,11:0.0833:0,0:3:0:28:0:1:0:60:2:0.0833:0:2 -2 25976268 . C CA 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.674;SOR=1.24792;LSEQ=CTAAAGAAGAATCAGTGAGA;RSEQ=AAAAAAAAAAACAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:19:19,0:119,1:0.1338:1,1:21.4:1:31.2:1:1:0:59.5:38:0.1348:0.0352:0.4 0/1:68:11:11,0:56,1:0.1618:1,0:27.1:1:30.5:1:1:0:60:22:0.1618:0:0.7 -2 25978827 . G T 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64732;SOR=0.47686;LSEQ=ACTGCGTAATTACCTGATGA;RSEQ=GAAGAGAGGTGCTCTGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:1,2:228,52:0.0106:2,2:22:1:24.7:1:0.09431:8.67272:60:2:0.0072:0:1 0/0:197:1:0,1:150,45:0.0051:2,0:1:0:24:0:0.23469:0:60:2:0.0051:0:1 -2 25990640 . T C 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=7e-05;SOR=0.26345;LSEQ=GACTGGTAGCACTGAGATTA;RSEQ=AGACAGAATCAATTAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:46:7,39:36,160:0.1893:2,2:23.1:1:31.6:1:0.8303:1.25243:60:92:0.1909:0:1 0/1:173:10:1,9:33,130:0.0578:2,2:26.7:1:32:1:0.68893:2.27593:60:20:0.0585:0:1 -2 25991534 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=Inf;LSEQ=ATTTAAAAATAAATGATGTC;RSEQ=TAAACAAATCAGGAAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:150,25:0:2,0:22.8:1:30.6:1:1:0:60:174:1:0:0.1 0/1:179:2:1,1:145,32:0.0112:2,2:7.5:1:28:1:0.33557:4.47744:60:4:0.0112:0:1 -2 25991793 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5047;SOR=0;LSEQ=AATCAGTTTTTTAGTAATAA;RSEQ=ATAAATTACTTCTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:12,154:0.0119:2,2:17.5:1:31.5:1:0.1492:12.37:60:4:0.0123:0:1 0/0:134:0:0,0:18,116:0:2,0:19.9:1:28.5:1:1:0:60:133:1:0:0.1 -2 25991820 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.14094;SOR=Inf;LSEQ=TACTTCTTTTTTAAATGGCA;RSEQ=GAAGCATGCTGATCGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:1,88:0:1,0:25.6:1:31:1:1:0:60:43.5:1:0:0.2 0/1:54:2:1,1:2,50:0.037:1,2:24:1:29:1:0.10901:20.61:60:4:0.037:0:1 -2 25994220 . A C 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAAGGGCCCAATGTAAAA;RSEQ=ATTTTCAAAAAATATCCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:182,11:0:2,0:22.1:1:30.3:1:1:0:60:192:1:0:0.1 0/1:153:15:13,2:125,13:0.098:2,2:19.1:1:30.5:1:0.64368:1.475:60:14:0.0927:0:1.1 -2 25994298 . G T 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00489;SOR=Inf;LSEQ=TACTTGATAAATACAGACTA;RSEQ=CAATGCTTACCTGCTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:772:0:0,0:530,241:0:2,0:24.9:1:31.9:1:1:0:60:54.071:1:0:0.1 0/1:681:7:1,6:419,255:0.0103:2,2:6.4:1:27.4:1:0.01447:9.82795:60:14:0.0104:0:1.1 -2 25994412 . A AG 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0.44776;LSEQ=GCGGGGAGGACGACGATACT;RSEQ=GGGAAAAAAAAGTGACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:829:127:44,83:249,453:0.1532:2,2:25.6:1:31.4:1:0.91977:1.03683:60:126:0.1546:0.0241:0.2 0/1:761:57:26,31:275,429:0.0749:2,2:27.6:1:31:1:0.32866:1.31:60:56:0.0746:0.0105:0.3 -2 26022303 . ACTG A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.80006;SOR=1.09435;LSEQ=TCCTTGTTGCTGCCACCATC;RSEQ=CTGCTGCTGCTGTTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1148:29:13,16:562,557:0.0253:2,2:33.5:1:32.7:1:0.5793:1.24158:60:58:0.0256:0:0 0/1:1269:35:18,17:607,623:0.0276:2,2:28.5:1:31:1:0.86483:1.09:60:70:0.0279:0.0039:0 -2 26022461 . TA T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50736;SOR=0;LSEQ=CCATTTAAGCAAACAGAAAT;RSEQ=AAACTTCTGATATGCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:8,182:0.0104:1,2:6:1:27:1:0.09179:21.51:60:4:0.0106:0.0052:0 0/0:147:0:0,0:15,132:0:2,0:24.8:1:29.8:1:1:0:60:72.5:1:0:0 -2 26029255 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=0;LSEQ=GAACACAACAATTAATTTCT;RSEQ=TCTCTGAATATCCTATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:25,170:0.0102:2,2:9.5:1:26.5:1:0.24713:6.69:60:4:0.0103:0:1 0/0:198:0:0,0:31,167:0:2,0:24.9:1:31.2:1:1:0:60:48.5:1:0:0.1 -2 26029407 . A C 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.67843;LSEQ=AATCATTTCCATGTATCTAC;RSEQ=AAATAGTAATTCCTTAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:42.3:1:32.8:1:1:0:60:12:0.3333:0:1 0/1:4:1:0,1:0,3:0.25:0,0:38:0:33:0:1:0:60:2:0.25:0:1 -2 26068509 . C T 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44211;SOR=0.77778;LSEQ=ATATATATTTCTTATAATTA;RSEQ=GTCTTAAAAGCTAAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:40:0,40:0,101:0.2837:1,1:25.2:1:30.9:1:1:0:60:80:0.2837:0:1 0/1:85:20:0,20:1,64:0.2353:1,1:29.2:1:30.6:1:1:0:60:40:0.2353:0:1 -2 26101168 . CT C 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.04714;SOR=Inf;LSEQ=GCCTGCTCTGCCCTGCGCTG;RSEQ=TTTCCCGCGGTGCCGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:62,342:0:2,0:23.3:1:30:1:1:0:60:30.077:1:0:0.2 0/1:354:4:1,3:67,283:0.0113:2,2:21.8:1:31.6:1:0.57569:1.41:60:8:0.0115:0.0028:0 -2 26836683 . T C 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAGAGGAGAAGGAATGTCC;RSEQ=CAACAGGTCTCTCTGTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:35:0:33:0:1:0:60:2:0.5:0:1 1/1:2:2:1,1:0,0:1:0,2:32:1:28:1:1:0:60:4:1:0:1 -2 26836738 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=CCTGTCCTGCCTCTCTGCAC;RSEQ=TGGGTGAATGTGTCCCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:19.8:1:28.7:1:1:0:60:5:1:0:0.2 0/1:9:2:1,1:4,3:0.2222:2,2:23.5:1:27.5:1:1:1.29098:60:4:0.25:0:1 -2 26837395 . A G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACCTCAGACACATGAAC;RSEQ=GTTTTCCCAGGAGGCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:0:31:1:1:0:60:4:1:0:1.5 -2 26838050 . A G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACAGTAACAGTCTGAATGCT;RSEQ=CTTCCCAGTAAGATGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:31:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:25.5:1:28.5:1:1:0:60:4:1:0:0 -2 26838128 . A T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGAAAGCAGAATGCCTCTCC;RSEQ=TCCCCTGCCCCCAGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:29.5:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:0:2,0:13.5:1:29:1:1:0:60:4:1:0:0 -2 27009046 . G A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66013;SOR=1.87432;LSEQ=AGCCGTGGGACCGGGCGCCA;RSEQ=CACCCTCTGCGGCGTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:2:1,1:127,152:0.0071:2,2:29:1:28.5:1:1:1.20:60:4:0.0072:0:1 0/1:226:3:1,2:103,118:0.0133:2,2:40.7:1:31.3:1:1:1.7416:60:6:0.0137:0:1 -2 27009059 . C T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.7106;SOR=1.53083;LSEQ=GGCGCCAGCACCCTCTGCGG;RSEQ=GTGTCATGGGCCCGCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:3:0,3:145,179:0.0092:2,0:15.7:1:28.7:1:0.25733:0:60:6:0.0093:0:1.3 0/1:286:4:2,2:130,151:0.014:2,2:20.3:1:30:1:1:1.16:60:8:0.0145:0:1.3 -2 27009070 . C T 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26314;SOR=2.83501;LSEQ=CCTCTGCGGCGTGTCATGGG;RSEQ=CCGCGCCGCCGGAGCCGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:2:1,1:168,192:0.0055:2,2:23:1:23.5:1:1:1.14:60:4:0.0057:0:1.5 0/1:322:5:2,3:149,168:0.0155:2,2:28.8:1:28:1:1:1.32919:60:10:0.016:0:1.2 -2 27009338 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCGAGGGGCTGGAGCAGG;RSEQ=GGTTCCGAAAGCGGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:0,37:0.0513:1,0:18.5:1:26:1:1:0:60:4:0.0513:0:1 0/0:19:0:0,0:0,19:0:1,0:23.4:1:28.2:1:1:0:60:18:1:0:0.1 -2 27009478 . C T 43 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGTGCGTTATCTCAGCTT;RSEQ=ATATTGTGCCCATTTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:15.3:1:27.7:1:1:0:60:6:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 27014522 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAGTCTCTCAGATTCTTT;RSEQ=CAGCTGTAAAAAACAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:35:1:30:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 27014808 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05553;SOR=Inf;LSEQ=AAAATTACTATATATCAGGT;RSEQ=GGTGCAAAAGTATTGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:45,2:0:1,0:20.8:1:30.9:1:1:0:60:94:1:0:0.1 0/1:15:2:1,1:13,0:0.1333:1,2:30.5:1:29:1:0.13333:0:60:4:0.1429:0:1 -2 27014885 . G A 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01523;SOR=0;LSEQ=TAAAACAGACAAAAATCCCT;RSEQ=CTCTGTGGAGGGTAGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:10:10,0:163,3:0.0568:1,0:30.8:1:27.8:1:1:0:60:20:0.0575:0:1.6 0/0:108:0:0,0:107,1:0:1,0:20.5:1:31.5:1:1:0:60:35:1:0:0.2 -2 27014901 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06373;SOR=Inf;LSEQ=CCCTGCTCTGTGGAGGGTAG;RSEQ=CACATAGATATAGTCTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:217,1:0:1,0:24.4:1:31.3:1:1:0:60:35.333:1:0:0.3 0/1:146:3:3,0:142,1:0.0205:1,0:35:1:24.3:1:1:0:60:2:0.0139:0:2.3 -2 27014980 . T C 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00195;SOR=0.73261;LSEQ=CCACCTATTTTCCACTGAAC;RSEQ=TACCTTTCTTTTGCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:868:341:216,125:342,185:0.3929:2,2:25.6:1:31.3:1:0.66372:1.06974:60:112.667:0.3935:0:1.1 0/1:877:282:185,97:363,232:0.3216:2,2:22.5:1:30.2:1:0.20456:1.22:60:93:0.3218:0:1.1 -2 27015118 . G A 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00051;SOR=0.73193;LSEQ=TCAGCCGCCTGGTAAGCTCC;RSEQ=GGAGCTTCCCACCAACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1083:466:179,287:240,376:0.4303:2,2:27.7:1:30.6:1:0.89972:1.0234:60:57.25:0.4288:0:1.2 0/1:1031:367:143,224:283,379:0.356:2,2:26.1:1:30.2:1:0.26141:1.16948:60:90.75:0.3566:0:1.2 -2 27015141 . G GC 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.55988;LSEQ=AGCTTCCCACCAACCCCTAT;RSEQ=CCACCCTCCTTTTTTTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:858:338:108,230:164,353:0.3939:2,2:24.3:1:31.3:1:0.94031:1.01:60:168:0.3962:0.0513:1.1 0/1:761:203:61,142:197,356:0.2668:2,2:27.7:1:31:1:0.16642:1.28775:60:39.6:0.2658:0.0079:1.1 -2 27015610 . CCA C 274 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.49811;LSEQ=ACTCCTACTCCTCCCCTTCC;RSEQ=CTCCTTCACAGGCAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1450:421:246,175:566,464:0.2903:2,2:28:1:31.5:1:0.24394:1.15:60:420:0.2949:0.0303:0.1 0/1:1477:250:132,118:667,559:0.1693:2,2:26.5:1:30.6:1:0.67621:1.06659:60:124:0.1699:0.0217:0.2 -2 27015827 . C T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAAGAACAATGAGGTAA;RSEQ=CTCTGAGGGTTTGGAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:73,222:0:2,0:24.1:1:31.6:1:1:0:60:58:1:0:0.1 0/1:152:19:2,17:24,109:0.125:2,2:25.2:1:29.3:1:0.5317:1.86511:60:38:0.1258:0:1.1 -2 27015903 . T C 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55209;SOR=1.13648;LSEQ=GTTCAGTCTCATTCTGTGAA;RSEQ=AGTTTCCTACAATCCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:125:99,26:155,38:0.3931:2,2:24.2:1:31.9:1:0.88628:1.07101:60:30.25:0.3891:0:1.5 0/1:158:67:60,7:82,9:0.4241:2,2:22.3:1:31.1:1:1:1.06254:60:134:0.4295:0:1.6 -2 27015953 . C CA 87 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.52753;SOR=0.55448;LSEQ=GATTAAGTTTAGCAGGTTTC;RSEQ=AAAAAAAAGCAGCCCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:7:6,1:473,147:0.0111:2,2:35.9:1:31.3:1:1:1.86:60:14:0.0112:0.0016:0.9 0/0:484:3:3,0:372,107:0.0062:2,0:28:1:28.7:1:1:0:60:6:0.0063:0:0 -2 27015963 . C T 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20093;SOR=2.77575;LSEQ=AGCAGGTTTCCAAAAAAAAG;RSEQ=AGCCCGTGGCCCTTCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:3:1,2:528,196:0.0041:2,2:13.7:1:28.7:1:0.18175:5.37295:60:6:0.0043:0:1.7 0/1:616:7:2,5:438,171:0.0114:2,2:15:1:25.1:1:0.02261:6.38046:60:14:0.0116:0:1.3 -2 27015969 . G A 247 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.87467;SOR=0.98058;LSEQ=TTTCCAAAAAAAAGCAGCCC;RSEQ=TGGCCCTTCATCTGTGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:846:303:212,91:379,162:0.3582:2,2:23.5:1:30:1:1:1.00422:60:74.75:0.3594:0:1.3 0/1:738:261:179,82:330,145:0.3537:2,2:22.6:1:29.6:1:0.80296:1.04249:60:129.5:0.3533:0:1.3 -2 27016259 . A G 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.48928;SOR=0.80078;LSEQ=GTAATTTCCTTTCTCCATCC;RSEQ=TAGTCCCTTGTCACCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:55:3,52:1,79:0.4074:1,2:25.9:1:31.7:1:0.3039:4.51:60:54:0.4154:0:1.1 0/1:93:33:0,33:2,58:0.3548:1,1:21.6:1:31.2:1:0.53717:0:60:32:0.3556:0:1.3 -2 27016302 . G GT 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.62405;SOR=1.35512;LSEQ=CCCTTTGTTCTCTAGTAAAG;RSEQ=TTGATCTAGTTTTGACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:30:1,29:0,34:0.4688:1,1:26.8:1:30.2:1:0.46875:0:60:29:0.4603:0.0625:1.1 1/0:22:12:0,12:0,10:0.5455:0,0:31:1:30.8:1:1:0:60:24:0.5714:0.0455:1.3 -2 27016351 . G A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00308;SOR=Inf;LSEQ=TGTGGTTTGTGCCCTTTTGT;RSEQ=CAATGTTAGATAAAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:0,9:0,20:0.3103:1,0:16.9:1:30:1:1:0:60:18:0.3103:0:1.1 1/1:6:6:1,5:0,0:1:0,2:16:1:30.5:1:1:0:60:12:1:0:1.5 -2 27016988 . C T 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01025;LSEQ=CTGTGGTATGGGAGAAAAGG;RSEQ=TATGTACTTATTATTTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:684:683:406,277:0,0:0.9985:0,2:25.3:1:29.5:1:1:0:60:55.917:0.9985:0:1.1 1/1:559:489:288,201:40,30:0.8748:2,2:25.1:1:29:1:0.79627:1.07:60:53.333:0.8743:0:1.1 -2 27017552 . CT TC 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGCCACAATTTTTTTTT;RSEQ=TTTTTTTTTTTTTGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:11.5:1:32:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 27247832 . T C 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81204;LSEQ=GCCTGCCCCACTCGCCCGCC;RSEQ=GCTTGCTTTGCACTAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:2,2:0.5556:2,2:13.2:1:28.8:1:0.52381:3.39:60:10:0.5556:0:1 1/0:6:3:3,0:3,0:0.5:0,0:15:1:31:1:1:0:60:6:0.5:0:2 -2 27249245 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCCCTGGCTGACTGCAC;RSEQ=GCTTCCCCGTGCCTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:29.5:1:1:0:60:4:1:0:1 -2 28539745 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15554;SOR=Inf;LSEQ=CACTTTAGAAATGAAACAAG;RSEQ=GAGAATTCTGCCCAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:150,12:0:2,0:25:1:30.9:1:1:0:60:31.4:1:0:0.1 0/1:106:2:1,1:91,12:0.0189:2,2:8.5:1:30.5:1:0.23333:7.32702:60:4:0.0196:0:1 -2 28539774 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16229;SOR=Inf;LSEQ=TGCCCAAGGTCACAGATTTT;RSEQ=AGTCTGAATTCAGGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:220,52:0:2,0:24.1:1:31.8:1:1:0:60:89.667:1:0:0.1 0/1:184:2:1,1:147,35:0.0109:2,2:23.5:1:27.5:1:0.35388:4.15532:60:4:0.0109:0:1 -2 28539877 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.28144;LSEQ=CTTGTTGGTTGGTTTCTGGG;RSEQ=ATTTTCACTGGATTACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:765:142:77,65:300,322:0.1856:2,2:25.5:1:28.9:1:0.22655:1.27:60:284:0.1868:0:1.1 0/1:605:259:121,138:168,176:0.4281:2,2:25.3:1:28.7:1:0.62198:1.0885:60:258:0.4293:0:1.2 -2 28539937 . G A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0327;SOR=Inf;LSEQ=CACTTGGCTGCATGTCCTTC;RSEQ=GCACTGCCGTGCTCAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:0:0,0:163,308:0:2,0:24.6:1:30.1:1:1:0:60:41.818:1:0:0.2 0/1:350:4:4,0:123,223:0.0114:2,0:5.5:1:23:1:0.01682:0:60:3:0.0087:0:1.3 -2 28539946 . G A 106 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=17.27984;LSEQ=GCATGTCCTTCGGCACTGCC;RSEQ=TGCTCAGCTTTATGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:1:1,0:120,283:0.0025:2,0:1:0:28:0:0.2995:0:60:2:0.0025:0:1 0/1:291:12:6,6:85,194:0.0412:2,2:29.2:1:29.7:1:0.20191:2.28:60:24:0.0418:0:1.4 -2 28736687 . T C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATCCTCTTTTGAGCCC;RSEQ=ATTAAAACCTTTGAATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:11,9:0,0:1:0,2:27.8:1:31.4:1:1:0:60:40:1:0:1.1 1/1:15:15:10,5:0,0:1:0,2:23.3:1:30.6:1:1:0:60:30:1:0:1.1 -2 29414782 . A G 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTATGTGTGTAAAATTAA;RSEQ=CAGATTCCCAATGCGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:34.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29415792 . G A 92 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAGAGCACACACAATTT;RSEQ=AAAGAAGCATAAGGAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:26:1:26.6:1:1:0:60:10:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29416025 . C CATTG 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=3e-05;SOR=0.34313;LSEQ=TCTCTGGTTTGTGAAGGAGC;RSEQ=ATTGCCTCTCTCTCCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:93:77,16:69,22:0.5054:2,2:24.9:1:31:1:0.27711:1.53:60:186:0.5082:0.125:0.1 0/1:112:29:23,6:64,19:0.2589:2,2:21.5:1:30:1:1:1.14:60:58:0.2613:0.0804:0.1 -2 29416366 . G C 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27433;LSEQ=TCCAGCCCCAGGTTACCCCT;RSEQ=TCGTGTGGCTCCTTCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1525:900:412,488:293,328:0.5902:2,2:26.5:1:31.6:1:0.60117:1.05802:60:68.231:0.5905:0:1.1 0/1:1187:336:151,185:399,448:0.2831:2,2:26.1:1:31.4:1:0.51841:1.09108:60:83:0.2823:0:1.2 -2 29416481 . T C 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22155;LSEQ=TGTTTCTGGATCCGTGGACC;RSEQ=TGTGCAACTCCGAAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1392:809:384,425:277,303:0.5812:2,2:25.6:1:31.4:1:0.95656:1.01179:60:66.417:0.5796:0:1.2 0/1:1268:298:148,150:466,504:0.235:2,2:26.7:1:30.6:1:0.64305:1.07:60:58.6:0.2331:0:1.2 -2 29416572 . T C 312 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04869;LSEQ=TCTAGGGACTCGAACAGAGA;RSEQ=CTCTGCAGCTGTGGGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1017:1014:487,527:0,3:0.9971:0,2:24.9:1:31.3:1:0.2506:0:60:47.286:0.998:0:1.2 1/1:837:789:353,436:23,25:0.9427:2,2:25.6:1:30.5:1:0.76536:1.13614:60:40.526:0.9448:0:1.2 -2 29416791 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15918;SOR=Inf;LSEQ=GTTGATTACATCCGGGTCCT;RSEQ=CCGTAGGGGAAATTATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:73,219:0:2,0:21.4:1:31.8:1:1:0:60:57.4:0.9965:0:0.1 0/1:195:2:1,1:65,127:0.0103:2,2:25.5:1:27:1:1:1.95:60:4:0.0104:0:2 -2 29416794 . G A 124 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=31.84596;LSEQ=GATTACATCCGGGTCCTGCC;RSEQ=TAGGGGAAATTATTAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:1:1,0:65,198:0.0038:2,0:1:0:27:0:0.25:0:60:2:0.0038:0:1 0/1:175:19:10,9:49,107:0.1086:2,2:12.5:1:29.3:1:0.07552:2.41:60:38:0.1092:0:1.2 -2 29416946 . T C 106 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.22188;SOR=0.18655;LSEQ=AGGCACTGGGGCATACAAAA;RSEQ=GAATGGGAAGTCATCCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:0,12:0,4:0.75:0,0:24.3:1:29.6:1:1:0:60:24:0.8:0:1.1 0/1:3:1:0,1:0,2:0.3333:0,0:47:0:31:0:1:0:60:2:0.3333:0:1 -2 29419252 . C T 38 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTATATGCAATTAATTA;RSEQ=TTCACATGTTGTTATTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:26.3:1:24:1:1:0:60:2:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29419413 . T C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTCCCCAGTTTTTACTGTG;RSEQ=GTCTGGCACTGTGCTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:19.3:1:32.2:1:1:0:60:26:1:0:1 1/1:2:2:2,0:0,0:1:0,0:12:1:30:1:1:0:60:4:1:0:1 -2 29419591 . G T 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=1.96496;LSEQ=TATTTGCCATCTTTAAGACT;RSEQ=TTTCATATAGAGTAAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:156:111,45:153,72:0.4084:2,2:27:1:30.1:1:0.57257:1.16:60:77:0.4096:0:1.1 1/0:323:186:134,52:84,52:0.5759:2,2:25.3:1:29.6:1:0.0546:1.59:60:61:0.5737:0:1.1 -2 29420315 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.26298;LSEQ=AGGGAGGGCAGCCATCTGCC;RSEQ=CTTCATCTTAAAGAAGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:204:123:116,7:77,4:0.6029:1,2:25.4:1:31.5:1:1:1.16077:60:246:0.6119:0:1.1 0/1:116:33:31,2:80,3:0.2845:1,2:22.9:1:30.6:1:0.62191:1.71159:60:32:0.2807:0:1.2 -2 29420595 . TCA T 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.77791;SOR=0.7401;LSEQ=ATAGACACACCCACCCACAT;RSEQ=CACACACACACAGGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:10:2,8:25,195:0.0435:2,2:28.7:1:30.8:1:0.33204:1.94:60:20:0.0444:0.0043:0.2 0/1:123:4:0,4:16,103:0.0325:2,0:28:1:31.3:1:1:0:60:8:0.0325:0:0 -2 29429642 . GGTGT G 49 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=12.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTAAAAGACTCCCTTTATT;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:32.7:1:31.3:1:1:0:60:6:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29429741 . C CTT 71 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=GTGGCTGTTAATGTGTGGTC;RSEQ=CAGCCAGCAATGGCAGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:28.8:1:30.6:1:1:0:60:10:0.8333:0.1667:0.4 0/0:1:0:0,0:1,0:0:0,0:21:0:32:0:1:0:60:2:1:0:0 -2 29429888 . G A 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40114;SOR=1.38885;LSEQ=GAATTCTGATAGATGCTCAC;RSEQ=TTTGAGAACCACTGTTGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:141:97:95,2:43,1:0.6879:1,1:25.1:1:30.6:1:1:1.10:60:96:0.6857:0:1 1/0:61:46:45,1:14,0:0.7541:1,1:23.9:1:29.7:1:1:0:60:92:0.7667:0:1.1 -2 29429948 . C T 177 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02378;LSEQ=TTTCCCTCCCTACTAACACA;RSEQ=GGGCTCCCGGCTTAGAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:57:48,9:267,37:0.1579:2,2:24.1:1:30.5:1:0.51498:1.35182:60:56:0.1569:0:1.1 0/0:226:1:1,0:180,45:0.0044:2,0:2:0:28:0:1:0:60:2:0.0045:0:1 -2 29430195 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13943;SOR=Inf;LSEQ=GAGATGGCATTAAGCATCTG;RSEQ=CCTGCTGGGAAAGTTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:23,248:0:2,0:23.1:1:31:1:1:0:60:29.111:1:0:0.1 0/1:162:2:1,1:17,143:0.0123:2,2:22.5:1:31.5:1:0.21049:8.20:60:4:0.0126:0:1 -2 29430519 . G T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAATGCAAGATCCAAAAT;RSEQ=GGAGAACTGAGAGCAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:25:1:30.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29432408 . CAAAAA C 49 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=21.000;MSILEN=1;SSF=0.10395;SOR=7.29785;LSEQ=ACAAGAGCGAAACTCCGTCT;RSEQ=AAAAAAAAAAAAAAAAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:1,0:12,0:0.0588:0,0:20:0:33:0:1:0:60:2:0.0588:0:0 0/1:9:3:2,1:5,0:0.3333:0,2:15:1:31.4:1:0.375:0:60:6:0.3333:0.1111:0.3 -2 29432776 . T C 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=GGAAATGCATTTCCTAATTT;RSEQ=ATCCCTAGGAAGATGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:0:0,0:166,463:0:2,0:23.6:1:28.4:1:1:0:60:68.889:0.9968:0:0.1 0/1:460:10:3,7:146,303:0.0217:2,2:21.5:1:30.8:1:1:1.12403:60:20:0.022:0:1.3 -2 29432803 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02524;SOR=Inf;LSEQ=AGGAAGATGAGTGTACAACG;RSEQ=CCATCACTAGGATTTTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:66,321:0:2,0:23.7:1:31.7:1:1:0:60:54.286:1:0:0.1 0/1:258:4:3,1:56,198:0.0155:2,2:8.3:1:27.5:1:0.03839:10.48:60:8:0.0157:0:1 -2 29432814 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15476;SOR=Inf;LSEQ=TGTACAACGGCCATCACTAG;RSEQ=ATTTTATCTCCAAGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:32,270:0:2,0:24.7:1:31.3:1:1:0:60:49.333:1:0:0.1 0/1:197:2:1,1:33,162:0.0102:2,2:8.5:1:26:1:0.31612:4.85:60:4:0.0103:0:1.5 -2 29432982 . C T 100 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61794;LSEQ=AAAAATGTTTAATGGGGCAA;RSEQ=CATAATGAAATGCATCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:1,9:0,6:0.625:0,2:29.8:1:30.3:1:1:0:60:20:0.625:0:1 1/0:2:1:0,1:0,1:0.5:0,0:17:0:31:0:1:0:60:2:0.5:0:1 -2 29433205 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGGTACAAACCACGGG;RSEQ=TGGTTTCTGCCAGTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29436633 . G T 145 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02779;SOR=0.07132;LSEQ=GCCAAGGTGGGAGGATTACT;RSEQ=GAGCCCAGAAATTCGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:31:31,0:0,0:0.9688:0,1:24.1:1:29.3:1:1:0:59.6:30:1:0:1.3 1/0:9:6:6,0:3,0:0.6667:0,0:16.8:1:27.5:1:1:0:60:5:0.625:0:1.2 -2 29437182 . T C 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04396;SOR=0;LSEQ=GTATTTGTACATTTGAAGTC;RSEQ=TCCCAGGTAATATGATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:1,8:0,3:0.75:0,2:21.8:1:32.1:1:1:0:60:18:0.75:0:1.3 0/0:3:0:0,0:0,3:0:0,0:14:1:32:0:1:0:60:6:1:0:0 -2 29443373 . G A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=1.10921;LSEQ=AGCCTTGCACAAGCTCCTTG;RSEQ=GGCTGGGGCTCAGCCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:30:30,0:25,0:0.5455:1,1:30.9:1:29.3:1:1:0:60:14:0.5714:0:1.2 1/0:7:4:4,0:3,0:0.5714:0,0:24.3:1:29.8:1:1:0:60:8:0.5714:0:1.3 -2 29443758 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16731;SOR=Inf;LSEQ=AGCTGAGTCTGGGCAAATCT;RSEQ=AAACTGGGAGGAACAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:22,246:0:2,0:23.9:1:28.4:1:1:0:60:66:1:0:0.1 0/1:186:2:1,1:23,160:0.0108:2,2:28.5:1:29.5:1:0.24324:6.83:60:4:0.0109:0:1 -2 29444076 . G T 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGCCTCAGGCAGAAGGT;RSEQ=AAGCAAAACAACTGCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:43.3:1:28.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29444095 . C T 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGCAAAACAACTGCTTC;RSEQ=AAGAGAGACTGGGTGAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:26.7:1:29:0:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29445113 . C T 98 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=9e-05;SOR=20.54953;LSEQ=AGGGGACATGCTAGGGACAA;RSEQ=ACGATTTCCCTTGGAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:1:1,0:346,61:0.0025:2,0:46:0:33:0:1:0:60:2:0.0025:0:1 0/1:228:11:9,2:178,39:0.0482:2,2:18.6:1:28.6:1:1:1.01418:60:22:0.0487:0:1.1 -2 29445458 . G T 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2432;LSEQ=TCATACACCTCCCCAAAGGC;RSEQ=CCATGGCCCAGACCCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1348:791:352,439:235,317:0.5868:2,2:25.1:1:30:1:0.50249:1.08:59.9:27.25:0.5851:0:1.2 0/1:1025:263:106,157:352,408:0.2566:2,2:25.7:1:29.6:1:0.09814:1.27753:60:36.571:0.2545:0:1.1 -2 29445798 . T C 106 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTTTCCCCGGGGGAGG;RSEQ=TCATGCTCCTTGGGGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:6,6:0,0:1:0,2:25.1:1:29.8:1:1:0:60:11:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29446112 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10877;SOR=Inf;LSEQ=TGCCCATAGGGAGGGCTCTG;RSEQ=CGGCCTTTTGTGGCTAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:178,12:0:2,0:25.6:1:32.1:1:1:0:60:62.333:1:0:0.4 0/1:94:2:1,1:90,2:0.0213:1,2:16:1:28:1:0.06314:36.93876:60:4:0.0215:0:1 -2 29446138 . G T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.296;SOR=3.56492;LSEQ=TTTTGTGGCTAGAGGAGTCT;RSEQ=CGGTGCTGTGATAACATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:1:1,0:258,53:0.0032:2,0:49:0:13:0:1:0:60:0:0:0:3 0/1:176:2:1,1:138,36:0.0114:2,2:6:1:25:1:0.37721:3.79485:60:4:0.0117:0:1 -2 29446141 . G T 43 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04647;SOR=Inf;LSEQ=TGTGGCTAGAGGAGTCTGCG;RSEQ=TGCTGTGATAACATTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:268,57:0:2,0:23.4:1:31.2:1:1:0:60:53.167:1:0:0.6 0/1:184:3:2,1:140,40:0.0163:2,2:28:1:27.3:1:0.53502:1.74389:60:2:0.0112:0:3 -2 29446184 . C G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.26718;LSEQ=TACACTGCACCCCTCTCCTC;RSEQ=CAGGACGGCAGCAGGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:658:392:287,105:178,86:0.5957:2,2:25.9:1:30.2:1:0.1153:1.32:60:42.556:0.5938:0:1.1 0/1:496:140:92,48:230,126:0.2823:2,2:25:1:30:1:0.83519:1.05:60:139:0.2837:0:1.1 -2 29446202 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.22813;LSEQ=TCCCAGGACGGCAGCAGGGC;RSEQ=CTCACCGAATGAGGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:54:36,18:521,262:0.0644:2,2:21.9:1:30.3:1:1:1.01:60:108:0.0654:0:1.1 0/1:619:186:122,64:262,170:0.3005:2,2:24.8:1:30:1:0.27804:1.24:60:92:0.2992:0:1.2 -2 29446701 . T C 302 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07338;SOR=0.88769;LSEQ=AGATGGGATTAGACCCAATA;RSEQ=GGTCTGCAGATTTTATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2661:907:463,444:890,859:0.3408:2,2:23.9:1:30.8:1:0.96736:1.01:60:180.4:0.3414:0:1.9 0/1:1780:560:267,293:625,594:0.3146:2,2:24.4:1:30.1:1:0.16817:1.15455:60:111:0.315:0:1.8 -2 29446721 . A G 353 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01279;LSEQ=TGGTCTGCAGATTTTATTAG;RSEQ=AGAAATGCCCATGAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2651:2645:1334,1311:1,0:0.9977:0,2:23:1:31.1:1:1:0:60:100.731:0.9985:0:1.4 1/1:1789:1519:753,766:133,129:0.8491:2,2:24.3:1:30.9:1:0.73832:1.0488:60:167.778:0.8502:0:1.4 -2 29447064 . C A 177 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=101.6525;LSEQ=TCCTATAGTTGGAGAACTGC;RSEQ=AAGCCACAGAGTTGGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2739:1:1,0:1311,1423:4e-04:2,0:1:0:26:0:0.47971:0:60:2:4e-04:0:1 0/1:1870:67:31,36:885,912:0.0358:2,2:23.2:1:29.2:1:0.70924:1.12684:60:66:0.0358:0:1.9 -2 29447108 . G A 311 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00103;SOR=1.23731;LSEQ=CACATCATGAAAAGATCTCT;RSEQ=AATTGGTGTCTGGGGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2646:1686:823,863:473,482:0.6372:2,2:23.3:1:29.1:1:0.74592:1.02902:60:87.737:0.6375:0:1.1 1/0:1796:1230:590,640:271,291:0.6849:2,2:23.5:1:28.9:1:0.95937:1.01019:60:71.353:0.6865:0:1.2 -2 29447253 . A G 349 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06574;LSEQ=CCTGCCCTGTTTCCCTAACC;RSEQ=CTGCCACTCCCCACCCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2673:2454:1160,1294:101,110:0.9181:2,2:25.5:1:31:1:0.8859:1.02424:60:67.167:0.9176:0:1.1 0/1:1823:773:390,383:536,509:0.424:2,2:24:1:30.5:1:0.73988:1.03414:60:84.889:0.4235:0:1.2 -2 29447615 . T C 218 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=105.83983;LSEQ=ATGCAACAAGTGTTAGCTCC;RSEQ=ATTATCCTGTCCCTTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2629:2:1,1:1347,1280:8e-04:2,2:14.5:1:31:0:1:1.05234:60:4:8e-04:0:1.5 0/1:1755:131:71,60:792,829:0.0746:2,2:25.5:1:31:1:0.27562:1.24:60:130:0.0749:0:1.2 -2 29448760 . C T 38 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGGAAGAGATGTGGGGGC;RSEQ=GCAGGTGACCAAACAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:1,5:0.3333:2,0:26.3:1:24:1:1:0:60:2:0.25:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29449344 . CAAAAAAAAAA C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=24.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAACAGTGAAACTCCGCCT;RSEQ=AAAAAAAAAAAAAAGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:20.5:1:32:1:1:0:60:4:0.6667:0.3333:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29449423 . G A 80 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACATGCACAGCTGCTGCT;RSEQ=TAAGGAAACCTAGGAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:9,0:5,0:0.6429:0,0:21.3:1:25.4:1:1:0:57.6:8:0.6154:0:1.9 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29449526 . C T 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAAGATCCCTGTCACTGGG;RSEQ=ATGTTTAAGTGGAGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:5.3:1:29.7:1:1:0:60:6:0.5:0:1 1/1:1:1:1,0:0,0:1:0,0:15:0:32:0:1:0:60:2:1:0:1 -2 29449819 . C T 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.05812;LSEQ=ACGCCATCCTCAGCCAGCAC;RSEQ=GTCCCGTGGTCACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1237:81:42,39:639,517:0.0655:2,2:24.6:1:30.2:1:0.56513:1.14756:60:80:0.0657:0:1.1 0/1:909:238:134,104:365,306:0.2618:2,2:24.4:1:30:1:0.64938:1.08:60:476:0.2647:0:1.2 -2 29450072 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCCCATAGCCACTGGAA;RSEQ=CACAACTGTGTAGAAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:10,165:0.0113:2,2:22.5:1:32:0:0.12076:15.77:60:4:0.0115:0:1 0/0:72:0:0,0:4,68:0:2,0:22.1:1:32.7:1:1:0:60:71:1:0:0 -2 29450286 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06469;SOR=Inf;LSEQ=AGCACACATCCTGACTTCTG;RSEQ=AAAATGTGGTGACCTGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:103,4:0:1,0:26.8:1:31.3:1:1:0:60:34.667:1:0:0.1 0/1:37:2:2,0:34,1:0.0541:1,0:12.5:1:32:0:1:0:60:4:0.0556:0:1 -2 29450383 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGAGACTCTGAGGTTTTA;RSEQ=CTTGGTGGGAGGACTGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:425,95:0:2,0:23.3:1:32:1:1:0:60:85.667:0.9981:0:0.1 0/1:296:24:18,6:211,59:0.0811:2,2:18.5:1:30:1:0.79735:1.19138:60:48:0.0816:0:1.1 -2 29450592 . AAC A 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=0.88372;LSEQ=GGGGTGGGTGCCAAAATCTT;RSEQ=ACACACACACGTCAGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:2,2:55,330:0.0102:2,2:20:1:28.8:1:0.10411:5.96:60:8:0.0104:0.0026:0.3 0/0:221:2:0,2:49,169:0.009:2,0:23:1:32:0:1:0:60:4:0.0093:0:0 -2 29450684 . G A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.66055;LSEQ=GGATGCGGGGAGGGAAGGGA;RSEQ=GCTCAGGGCACAGAGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:9:0,9:0,80:0.1011:1,0:19.3:1:31.8:1:1:0:60:18:0.1071:0:1 0/1:29:2:0,2:0,27:0.069:1,0:26.5:1:31.5:1:1:0:60:4:0.0714:0:1 -2 29451354 . A G 88 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGGAAGCTGGTGGGCTG;RSEQ=GGTAGGGAGCAGGAGTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1:0,2:16.4:1:31.7:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29451511 . C G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07269;SOR=4.20037;LSEQ=TTATCATCGACTTTGGGGGA;RSEQ=ATCAAGAATCACATGGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:14:14,0:25,1:0.35:1,1:19:1:32.2:1:1:0:60:28:0.359:0:1.1 1/0:10:7:7,0:3,0:0.7:0,0:17.1:1:32.4:1:1:0:60:14:0.7:0:1 -2 29451557 . GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G 77 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.33914;SOR=0;LSEQ=GCTGTCGCTGAGGAAGCCTG;RSEQ=AGGCAGGTCGAGAGGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:6:6,0:64,0:0.0857:1,0:28.8:1:30:1:1:0:60:12:0.0896:0.0857:0.5 0/0:18:0:0,0:18,0:0:1,0:26.3:1:29.4:1:1:0:60:17:1:0:0.4 -2 29451670 . AGGGGA G 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.03551;SOR=0;LSEQ=TGGGCAGGCCAGGGGAGGGC;RSEQ=GGGCAGGGCAGGGAGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:10:6,4:440,101:0.0181:2,2:5.7:1:29.4:1:0.10292:2.8969:60:20:0.0185:0.0163:0.1 0/0:264:0:0,0:206,57:0:2,0:22.6:1:29.3:1:1:0:60:31.875:1:0:0.2 -2 29451675 . A AGGGCG 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=AGGCCAGGGGAGGGCAGGGG;RSEQ=GGGCAGGGCAGGGAGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:590:25:23,2:430,128:0.0424:2,2:27:1:31.6:1:0.0884:3.42:60:50:0.0441:0.0051:0.1 0/0:300:0:0,0:218,81:0:2,0:22.3:1:28.6:1:1:0:60:32.222:1:0:0.1 -2 29451679 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.18936;SOR=3.84206;LSEQ=CAGGGGAGGGCAGGGGAGGG;RSEQ=AGGGCAGGGAGGTGAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:635:2:0,2:473,158:0.0031:2,0:1:0:24:0:0.06359:0:60:4:0.0032:0:1 0/1:333:4:1,3:232,97:0.012:2,2:15.3:1:25:1:0.08267:7.12799:60:8:0.0123:0:1 -2 29451986 . C T 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=0;LSEQ=GCTGGCAAGGTTCAATTAGC;RSEQ=ATGCTGGCCAGAGAAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:19:2,17:45,302:0.0519:2,2:24.5:1:28.5:1:1:1.2658:60:38:0.0528:0:1.1 0/0:189:0:0,0:29,160:0:2,0:21:1:31.3:1:1:0:60:62:1:0:0.2 -2 29454701 . A G 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCCATTAATGAGGGAGGAG;RSEQ=GCTCAGCCGTGGAGAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:28.3:1:30.3:1:1:0:60:6:1:0:1 -2 29454901 . G GCAAGTTGGTAAAACC 103 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGGAGGCTCTAACAATT;RSEQ=CAGGGAGGGCCAGCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:11,0:6,1:0.6111:2,0:17.2:1:29.8:1:0.38889:0:58.2:22:0.6471:0.3889:0.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29454985 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCCAAGCTCCAGGTCAG;RSEQ=AAGATGGCCTGCAGGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:68,1:0.0282:1,2:19.5:1:29.5:1:0.05594:48.43646:57.5:4:0.0282:0:1.5 0/0:14:0:0,0:14,0:0:1,0:16.5:1:33.4:1:1:0:60:28:1:0:0.6 -2 29455016 . C T 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=4.70357;LSEQ=GCAGGGCTCCCAGGGTGCTG;RSEQ=CTGCCCTCCCTCCCTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:27:26,1:90,0:0.2308:1,1:26.6:1:30.4:1:0.23077:0:60:54:0.2328:0:1.1 1/0:34:20:20,0:14,0:0.5882:1,1:25.2:1:30.7:1:1:0:60:40:0.625:0:1.1 -2 29455107 . C T 49 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04744;SOR=7.88355;LSEQ=TGCCCTCAGGCATGCGATGG;RSEQ=ATCGGGGCCCAGCTGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:637:1:0,1:481,155:0.0016:2,0:1:0:24:0:0.2449:0:60:2:0.0016:0:1 0/1:326:4:1,3:241,81:0.0123:2,2:9.5:1:24.5:1:0.05409:8.85273:60:8:0.0125:0:1 -2 29455267 . A G 276 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.60601;LSEQ=TTGGCCCCGTAGGCCCTGCC;RSEQ=CCACCTCCGGCTGCAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1189:501:218,283:287,401:0.4214:2,2:24.8:1:30.8:1:0.55269:1.08:60:82.5:0.4209:0:1.1 1/0:805:434:191,243:164,205:0.5391:2,2:26.4:1:30.4:1:0.94318:1.01778:60:71.333:0.5384:0:1.1 -2 29455738 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACCCCCAAAGATTCAAG;RSEQ=TTAAGCCCTCAGCATCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:36:1:30.5:1:0.33333:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29455767 . G C 39 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCAGCATCACAGTCCTGTGG;RSEQ=AGGACCTAGCAGGTGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:1,0:0.75:0,0:12.7:1:25:1:0.25:0:60:2:0.6667:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29456180 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05121;SOR=Inf;LSEQ=CACCAAAACTGGCTAATTTT;RSEQ=AAATTTTTTTTGGTAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:28,1:0:1,0:14.4:1:30.9:1:1:0:60:58:1:0:0 0/1:9:2:2,0:7,0:0.2222:0,0:30:1:28.5:1:1:0:60:4:0.2222:0:1 -2 29456336 . G T 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03873;SOR=Inf;LSEQ=TCATCTTTACACGGGGATAA;RSEQ=AGCATCTGAGGTGTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:472,55:0:2,0:23.8:1:32:1:1:0:60:74.286:1:0:0.2 0/1:271:3:2,1:224,44:0.0111:2,2:22:1:23:1:0.4213:2.53385:60:2:0.0075:0:2 -2 29456384 . T C 261 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGTCATGAGGCTCTGACAT;RSEQ=GCAGATGCACAGGAACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1305:371:240,131:602,332:0.2843:2,2:24.9:1:30.6:1:0.94895:1.01:60:184.5:0.2856:0:1.1 0/0:813:0:0,0:437,297:0:2,0:37:0:17:0:1:0:60:0:0:0:2 -2 29456865 . T TG 71 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAGGATAGGGAGTTTTT;RSEQ=TTTGTTTGTTTTTGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:0.4545:0,0:29.2:1:30.6:1:1:0:60:10:0.4545:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29456882 . T C 72 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTGTTTGTTTTTGTT;RSEQ=TTTTCACAGAGAGTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:32.6:1:31.4:1:1:0:60:10:0.5556:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29462271 . G A 59 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGCTTCAGGTGAGGGAG;RSEQ=GGGGGAGCCTGGCCCAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:13.3:1:29.5:1:1:0:60:8:0.3636:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29462298 . T A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGCCCAACCAGGAGAT;RSEQ=CACCTGGCAGGGTGCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:0.25:0,0:39.7:1:29.3:1:1:0:60:6:0.25:0:2 0/0:2:0:0,0:2,0:0:0,0:9.5:1:31.5:1:1:0:60:4:1:0:0 -2 29462405 . A G 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03588;SOR=0.44016;LSEQ=GGGGTGCTGGGAGTTTGCAA;RSEQ=GCTGCTGTTTAATTACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:42:41,1:67,2:0.3784:1,1:24.9:1:31.5:1:1:1.22:60:20:0.3774:0:1.1 0/1:57:12:12,0:42,3:0.2105:2,0:20.3:1:32.7:1:1:0:60:24:0.2143:0:1.5 -2 29462520 . G A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21304;LSEQ=GGGCCTGACAGAGTGCAGAC;RSEQ=AGAAACCCCTGCTCTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:825:227:151,76:399,199:0.2752:2,2:25.4:1:29.9:1:1:1.00914:60:112.5:0.2774:0:1.1 0/1:602:45:24,21:341,216:0.0748:2,2:26.7:1:29.5:1:0.3418:1.38057:60:44:0.0747:0:1.2 -2 29472936 . T G 56 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCCAGGAGGCCCAGGATGT;RSEQ=GTGGATCCCGGAGGCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:7.3:1:28.3:1:1:0:60:8:1:0:1.5 -2 29473851 . G T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00381;SOR=0.33733;LSEQ=TATACCCCCTATGGGCCTGA;RSEQ=TCTGTTGCCTTTGAACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:56:55,1:106,5:0.3353:1,1:23.4:1:31.6:1:0.66476:2.58:60:112:0.3394:0:1 0/1:69:10:9,1:58,1:0.1449:1,2:17.2:1:30.6:1:0.27067:6.16623:60:20:0.1493:0:1.1 -2 29473898 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06561;SOR=Inf;LSEQ=CTGGGCACCCCAGGAACATG;RSEQ=ACCCATAGGCAAGACTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:251,36:0:2,0:24:1:32.1:1:1:0:60:94.667:1:0:0.2 0/1:195:3:2,1:153,38:0.0154:2,2:13.3:1:27.3:1:0.49198:2.00456:60:6:0.0158:0:1 -2 29474176 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.13296;SOR=Inf;LSEQ=GTCACTCATGTGGCCAGGCC;RSEQ=TCCCTCCTCCAGGGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:37,281:0:2,0:25.5:1:31.6:1:1:0:60:23.462:1:0:0.1 0/1:183:2:1,1:31,150:0.0109:2,2:35.5:1:31.5:1:0.31994:4.78:60:4:0.0112:0:1 -2 29497967 . G A 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGAGCTGAACCCTTACCT;RSEQ=TAGGGTCAAAGATGGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1180:0:0,0:735,442:0:2,0:25.7:1:31.9:1:1:0:60:60.947:0.9983:0:0.1 0/1:921:49:29,20:525,345:0.0532:2,2:23.1:1:28.1:1:0.88161:1.0494:60:48:0.0526:0:1.1 -2 29498181 . ACAGT A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=CACTGAGGGAGGTGGGAGAG;RSEQ=CAGGCTTAGGCTGAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:243,199:0:2,0:23.9:1:32:1:1:0:60:62.143:1:0:0.8 0/1:278:12:6,6:162,104:0.0432:2,2:28.5:1:32:1:0.54947:1.55508:60:24:0.0438:0.0036:0.9 -2 29498210 . A G 291 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.1112;LSEQ=CTTAGGCTGAGGAGGGGACA;RSEQ=TGAGGCCATGGGCCATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:547:544:338,206:0,1:0.9945:0,2:22.6:1:32.1:1:0.37982:0:60:180.333:0.9963:0:1.1 1/1:359:342:216,126:8,9:0.9526:2,2:23.7:1:31.1:1:0.20462:1.92:60:113:0.9549:0:1.1 -2 29498217 . C T 43 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02336;SOR=Inf;LSEQ=TGAGGAGGGGACAATGAGGC;RSEQ=ATGGGCCATGGGGGTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:364,234:0:2,0:22.5:1:30.8:1:1:0:60:26.182:1:0:1 0/1:386:4:1,3:235,147:0.0104:2,2:9.3:1:21.5:1:0.30346:4.77675:60:3:0.0079:0:1.5 -2 29499956 . A G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGTGTCAAGAGCAGAAAACC;RSEQ=GAGCAGGGTGGCACTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45.5:1:31.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29.5:1:1:0:60:4:1:0:1.5 -2 29519622 . C T 193 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGTGTGCACGTGCGTGCACG;RSEQ=GCACATATCGGTGTGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:89:89:89,0:0,0:1:0,1:21.8:1:29.9:1:1:0:60:43.5:1:0:1.2 1/0:48:33:32,1:15,0:0.6875:1,1:24.8:1:30:1:1:0:60:66:0.7174:0:1 -2 29519631 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.13335;SOR=Inf;LSEQ=GTGCGTGCACGCGCACATAT;RSEQ=GGTGTGTGGGCACATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:93,0:0:1,0:24.8:1:31.6:1:1:0:60:92:1:0:1.1 0/1:54:2:2,0:51,1:0.037:1,0:26:1:29.5:1:1:0:60:4:0.0392:0:1 -2 29519715 . T C 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTTTTCATTTTAGCTGA;RSEQ=AGAGGAGAAGGGTATTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:0:0,0:374,140:0:2,0:22.8:1:29.6:1:1:0:60:33.267:1:0:0.2 0/1:381:16:10,6:250,115:0.042:2,2:24.1:1:31.3:1:0.59353:1.30345:60:32:0.0423:0:1.3 -2 29519851 . C A 171 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02259;LSEQ=CATCCTGCCTTGCTCCTTCC;RSEQ=GGTTTTGTTCTCCACTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1148:51:22,29:524,573:0.0444:2,2:25.6:1:30.2:1:0.56769:1.20526:60:50:0.0438:0:1.1 0/0:954:1:1,0:439,512:0.001:2,0:1:0:26:0:0.46218:0:60:2:0.0011:0:1 -2 29519934 . G A 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08075;SOR=4.02408;LSEQ=ACATTCGGAGCTGTGAGGGC;RSEQ=AGAAGAGTCAGAGGACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:2:2,0:172,427:0.0033:2,0:1:0:27:1:0.08348:0:60:4:0.0034:0:1 0/1:452:6:3,3:151,295:0.0133:2,2:21.7:1:26.3:1:0.41431:1.95:60:5:0.0113:0:1.2 -2 29519951 . A G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03157;SOR=Inf;LSEQ=GGCGAGAAGAGTCAGAGGAC;RSEQ=AGGTATGATTGCTGAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:92,329:0:2,0:23.4:1:30.1:1:1:0:60:104.25:1:0:0.1 0/1:309:4:2,2:83,222:0.0129:2,2:31.5:1:30:1:0.30418:2.66:60:8:0.0131:0:2 -2 29520085 . G A 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCTCACCAAGAGGCTTTCA;RSEQ=TGAAGTTCAAGTATCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:35:0,35:0,0:0.9722:0,1:26.9:1:32.2:1:1:0:60:70:0.9722:0:1.1 1/1:14:14:0,14:0,0:1:0,1:20.6:1:31.1:1:1:0:60:28:1:0:1 -2 29540686 . C CCA 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGGGCGCCAGTCCCTCCAC;RSEQ=CACACCAATGAGATAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30:1:32:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29541104 . C T 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00698;LSEQ=AGCTAGGCTACTTTCTTAAT;RSEQ=TGGGTTCCGGAAGTGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:294:293:242,51:0,0:0.9966:0,2:22.1:1:29.9:1:1:0:60:72.25:1:0:1.1 1/0:218:146:114,32:51,21:0.6697:2,2:19.4:1:29.2:1:0.24516:1.46:60:28.2:0.6682:0:1.1 -2 29543663 . T C 330 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02454;LSEQ=TTTAGGGTCCTGACCTGCCA;RSEQ=TGAGGAGTGTGGGGTGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1371:1364:696,668:0,3:0.9949:0,2:26.3:1:31.7:1:0.118:0:60:47.714:0.9948:0:1.1 1/1:1086:898:466,432:98,88:0.8269:2,2:25.8:1:31.2:1:0.87207:1.03236:60:88.8:0.8299:0:1.2 -2 29543699 . G A 153 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.16938;LSEQ=GACAGTGTGCCTTGGGTCCA;RSEQ=CCACAGAAGCCATCTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1264:4:3,1:555,705:0.0032:2,2:16:1:28.5:1:0.3268:3.81:60:8:0.0032:0:1.8 0/1:971:39:20,19:451,481:0.0402:2,2:18.9:1:29:1:0.74621:1.12:60:78:0.0408:0:1.9 -2 29543829 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14184;SOR=Inf;LSEQ=TGCCAAGTCGAATTAGCCAG;RSEQ=CATGACCAAATTATCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:11,205:0:2,0:22.1:1:32.4:1:1:0:60:107:1:0:0.1 0/1:131:2:1,1:5,124:0.0153:1,2:33:0:29:1:0.08984:22.73:60:4:0.0156:0:1 -2 29544336 . C T 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCCTTTCTCTCCCAACC;RSEQ=GCTTGCAGTTAAGTGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:31.3:1:30:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29544512 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGGGTGACACTATATTGA;RSEQ=GGAGGAGCCTCTGCCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29550841 . G C 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGCCGGAGCTGGGGTGCATG;RSEQ=AGGAGGGAGAGGATGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:26:1:32:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:0:0,0:12:0:33:0:1:0:60:2:1:0:0 -2 29551161 . G A 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0.43609;LSEQ=CCTGGGATAATGGGGACAAC;RSEQ=GGGTTATGAGCATGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:146:113,33:254,81:0.3029:2,2:25.5:1:30.3:1:0.72831:1.09:60:72:0.3013:0:1.1 0/1:289:46:32,14:171,72:0.1592:2,2:27.8:1:29.3:1:1:1.03891:60:14.333:0.1503:0:1.2 -2 29551401 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.1275;SOR=Inf;LSEQ=TTTGCATGGCCCCAGGCAGC;RSEQ=GCTGGCCTGATGGGTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:55,279:0:2,0:23:1:31.1:1:1:0:60:65.8:1:0:0.1 0/1:186:2:1,1:37,147:0.0108:2,2:18.5:1:28.5:1:0.36774:3.93:60:4:0.0109:0:1 -2 29551493 . G C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78453;SOR=1.13472;LSEQ=AAGGCCTGATTGAGACATCT;RSEQ=CATCTCCATCTGGCCAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:12:0,12:0,50:0.1935:1,0:21.8:1:31.8:1:1:0:60:24:0.1935:0:1 0/1:28:6:0,6:0,22:0.2143:1,0:34.5:1:30.8:1:1:0:60:12:0.2143:0:1 -2 29606520 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29194;SOR=0;LSEQ=CATAAGTGTGCACATTCCCA;RSEQ=CCAAACATGGTTGCAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:2,1:155,13:0.0175:2,2:17.3:1:29.3:1:0.22728:5.8417:60:6:0.0176:0:1 0/0:104:0:0,0:93,11:0:2,0:23.5:1:31.4:1:1:0:60:19.8:1:0:0.2 -2 29606533 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1589;SOR=Inf;LSEQ=ATTCCCAGCCAAACATGGTT;RSEQ=CAGGTTATTGACACATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:190,28:0:2,0:24:1:31.8:1:1:0:60:35.333:1:0:0.1 0/1:145:2:1,1:119,24:0.0138:2,2:8.5:1:27:1:0.31609:4.87862:60:4:0.0141:0:1 -2 29606824 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02469;SOR=Inf;LSEQ=TGTCCTTGCAGGGACTTCAG;RSEQ=ACTCACATTCTTCATGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:1,128:0:1,0:26.2:1:31.7:1:1:0:60:128:1:0:0.1 0/1:54:3:0,3:0,51:0.0556:1,0:22.7:1:29:1:1:0:60:6:0.0556:0:1 -2 29754721 . T C 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGTCACAGACTCTGGAAATG;RSEQ=GTAACCAAAAGCCAAATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:336,84:0:2,0:23.2:1:29.8:1:1:0:60:419:1:0:0.1 0/1:276:39:26,13:170,66:0.1413:2,2:20.2:1:30.8:1:0.56682:1.28669:60:38:0.1387:0:1.1 -2 29755018 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26458;SOR=0;LSEQ=GAAAACGAATCTGCAGATGT;RSEQ=TTCAGGTAAGACCAGCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:45,189:0.0127:2,2:18.3:1:30:1:0.47818:2.09:60:6:0.013:0:1 0/0:176:0:0,0:46,130:0:2,0:21.8:1:31:1:1:0:60:175:1:0:0.1 -2 29917150 . C A 54 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACCACAGGAAGCATCACA;RSEQ=CAAGCAAATGTGTCGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:29.8:1:27.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 29917621 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29916;SOR=3.53723;LSEQ=AGGTTTCAAAGTAAACAGAG;RSEQ=AGAACAGGAGTGAAGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:1,0:197,9:0.0048:1,0:24:0:31:0:1:0:60:2:0.005:0:1 0/1:118:2:2,0:111,5:0.0169:1,0:10.5:1:29:0:1:0:60:4:0.0171:0:1 -2 29917940 . C G 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00039;SOR=2.36614;LSEQ=CCAAACGTGACTTTTCAGCC;RSEQ=CCTCCACTCCACACTAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:366:281:53,228:19,65:0.7678:2,2:23.3:1:31.6:1:0.43872:1.25669:60:92.667:0.768:0:1.1 1/1:212:188:45,143:6,18:0.8868:2,2:22.6:1:30.8:1:1:1.05897:60:46:0.8846:0:1.1 -2 29918087 . C T 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03252;SOR=Inf;LSEQ=TCTTTCTGTAACTCATATTA;RSEQ=GGGAGATGTTCTCAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:0,34:0:1,0:20.8:1:30.2:1:1:0:60:68:1:0:0.2 0/1:8:2:0,2:0,6:0.25:0,0:26.5:1:32:0:1:0:60:4:0.25:0:1 -2 29940332 . A G 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00842;SOR=0;LSEQ=GAAAGACTTCTTTTGCATAT;RSEQ=GGGAGCTGAGGGAATGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:12:12,0:83,1:0.125:1,0:27.6:1:31.3:1:1:0:60:11:0.1209:0:1.2 0/0:52:0:0,0:51,1:0:1,0:18.7:1:29.1:1:1:0:60:104:1:0:0.1 -2 29940400 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09243;SOR=Inf;LSEQ=TCACAGAGTCCTTATTATGA;RSEQ=ATAGTGACAGTGTATCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:273,59:0:2,0:23.2:1:31.5:1:1:0:60:26.667:1:0:0.1 0/1:275:3:1,2:209,63:0.0109:2,2:8:1:25.7:1:0.14015:6.57646:60:6:0.011:0:1 -2 29940529 . A T 294 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30881;SOR=1.12962;LSEQ=AAATAATCAGGAGAAGGAGA;RSEQ=GGCATGTTTGTTGGTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1153:912:414,498:120,120:0.791:2,2:27.4:1:30:1:0.21646:1.2027:60:56:0.7894:0:1.1 1/1:844:684:313,371:72,87:0.8104:2,2:25.7:1:29.7:1:0.92979:1.02:60:96.714:0.8118:0:1.2 -2 29940820 . C T 107 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGATCTCTGGGAGATGAA;RSEQ=TAGAAGCCAGGGCACTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:0,12:0,1:0.9231:0,0:26.9:1:30:1:1:0:60:24:0.9231:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 30142798 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16428;SOR=Inf;LSEQ=GAAGTGAAGATTATTTAATG;RSEQ=TTGCATATCAATGTGACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:173,17:0:2,0:23.1:1:31.3:1:1:0:60:46.5:1:0:0.1 0/1:130:2:1,1:110,18:0.0154:2,2:20.5:1:31.5:1:0.27191:5.97512:60:4:0.0157:0:1 -2 30142801 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51786;SOR=0;LSEQ=GTGAAGATTATTTAATGGTT;RSEQ=CATATCAATGTGACTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:180,19:0.01:2,2:5.5:1:29.5:1:0.18955:9.25942:60:4:0.01:0:1 0/0:135:0:0,0:114,20:0:2,0:22.5:1:31.2:1:1:0:60:32.5:0.9924:0:0.2 -2 30142817 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.13866;SOR=Inf;LSEQ=GGTTGCATATCAATGTGACT;RSEQ=AAAACACTAAATCCCGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:241,43:0:2,0:23.2:1:28.7:1:1:0:60:283:1:0:0.1 0/1:169:2:1,1:132,35:0.0118:2,2:32.5:1:29.5:1:0.38166:3.73289:60:4:0.0121:0:1.5 -2 30142837 . C T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.38362;SOR=2.35651;LSEQ=AAAAACACTAAATCCCGGCA;RSEQ=ACTCAGGCGGGAGCTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:2:0,2:314,84:0.005:2,0:1:0:23.5:1:0.0458:0:60:4:0.0051:0:1 0/1:256:3:1,2:177,76:0.0117:2,2:16.3:1:25.7:1:0.22095:4.62637:60:6:0.012:0:1 -2 30143420 . G A 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14332;SOR=5.19936;LSEQ=CTCCCGGGGCTGCAGCGGCG;RSEQ=CCCCGCAGCTGGGGAGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:1,0:123,268:0.0026:2,0:1:0:26:0:0.31633:0:60:2:0.0026:0:1 0/1:228:3:3,0:74,151:0.0132:2,0:29:1:26.3:1:0.03752:0:60:6:0.0133:0:1.3 -2 30143450 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13332;SOR=5.44027;LSEQ=TGGGGAGCCCGCGCGCTGGC;RSEQ=GGTCCCCATCCCGGAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:1:0,1:88,196:0.0035:2,0:1:0:25:0:1:0:60:2:0.0036:0:2 0/1:159:3:1,2:46,110:0.0189:2,2:24.3:1:30:1:1:1.19:60:6:0.0194:0:1.7 -2 30143499 . G C 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGGAAAGCAGCAGCGGCAG;RSEQ=AGCCACAGGAGCCCGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:218:79,139:0,0:1:0,2:25.9:1:32.3:1:1:0:60:217:1:0:1.1 1/1:136:122:48,74:6,8:0.8971:2,2:26.5:1:31.6:1:0.78195:1.155:60:244:0.8971:0:1.1 -2 30143519 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16117;SOR=Inf;LSEQ=GAGCCACAGGAGCCCGATGG;RSEQ=TCCCATCCCGCCGGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:76,129:0:2,0:25:1:32.1:1:1:0:60:101.5:1:0:0.9 0/1:138:2:1,1:54,82:0.0145:2,2:18.5:1:28.5:1:1:1.51:60:4:0.0149:0:1.5 -2 30143539 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51461;SOR=0;LSEQ=CTCCCATCCCGCCGGAGGAG;RSEQ=CCGTTTACACTGCTCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:61,107:0.0118:2,2:37:1:29.5:1:1:1.75:60:4:0.0118:0:2 0/0:118:0:0,0:48,70:0:2,0:27.8:1:30.9:1:1:0:60:38.333:1:0:0.8 -2 30433204 . T G 73 LongAT STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12131;SOR=0;LSEQ=TTATGATGGGGAACATTTCA;RSEQ=TCTCAAAAAAAAAAAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:7,4:0.3125:2,2:40.8:1:31.8:1:1:1.15538:60:10:0.3333:0:1.6 0/0:10:0:0,0:6,4:0:2,0:24.1:1:29.1:1:1:0:60:20:1:0:0.1 -2 30433208 . C CA 93 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0.83876;LSEQ=GATGGGGAACATTTCATTCT;RSEQ=AAAAAAAAAAAAAATCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:4,4:7,3:0.4444:2,2:25.3:1:31.1:1:0.63047:2.22221:60:16:0.4706:0.1111:1 0/1:10:4:3,1:2,2:0.4:2,2:39.5:1:28.5:1:1:2.60:60:8:0.4:0:0 -2 30433791 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGGAGGCCGAGGTGGG;RSEQ=GGATCACGAGGTCAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:1:27.5:1:1:0:52:4:1:0:1 -2 31513661 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=Inf;LSEQ=TTGGCTGGAACTGCCATCTT;RSEQ=CAGTAATTTGCCAAAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:33.3:1:31.4:1:1:0:60:22:1:0:0.1 0/1:13:2:1,1:6,5:0.1538:2,2:23:1:27.5:1:1:1.18321:60:4:0.1818:0:1 -2 31513677 . A C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.48;SOR=Inf;LSEQ=TCTTCCAGTAATTTGCCAAA;RSEQ=TAATGAACACAAAGGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:0:2,0:34.5:1:30.1:1:1:0:60:26:1:0:0.2 0/1:13:2:1,1:5,6:0.1538:2,2:30:1:26.5:1:1:1.18:60:4:0.1667:0:1 -2 31514140 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22414;SOR=0;LSEQ=AATGGGTACTGTTCAGAAAG;RSEQ=AAGGCCCTACAAGTGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:14:0:30:1:1:1.36624:60:4:0.1429:0:1.5 0/0:15:0:0,0:9,6:0:2,0:22.3:1:30.7:1:1:0:60:30:1:0:0.2 -2 34654129 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16475;LSEQ=TACTTATTAAAGGCAGCAAT;RSEQ=CTAGCAGTGTACTTAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:210:108,102:76,75:0.5817:2,2:28.7:1:30.9:1:0.91504:1.04:60:34:0.5746:0:1.1 0/1:328:61:31,30:135,132:0.186:2,2:26.5:1:30.5:1:1:1.01:60:122:0.1865:0:1.1 -2 34654198 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20711;SOR=Inf;LSEQ=GATTAAATTTTCATTTTTGG;RSEQ=CAGGTGCAGTGGCTCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:57,121:0:2,0:23.5:1:31.1:1:1:0:60:88:0.9944:0:0.4 0/1:150:2:1,1:51,97:0.0133:2,2:25.5:1:29:1:1:1.89:60:4:0.0135:0:1 -2 36353114 . A G 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.627;LSEQ=ACACTTACCCTAAACAGAGC;RSEQ=CAGTCTTTTCATCCACCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:149:77,72:142,176:0.3184:2,2:27.5:1:30.6:1:0.16477:1.32:60:73.5:0.3161:0:1.1 1/0:439:332:160,172:54,53:0.7563:2,2:25.9:1:30.8:1:0.73893:1.09506:60:82:0.754:0:1.2 -2 36526768 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19718;SOR=Inf;LSEQ=TCTTGGCAAGAATCTTGCCC;RSEQ=TACCTTGTTTATTTACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:157,79:0:2,0:21:1:31:1:1:0:60:472:1:0:0.1 0/1:189:2:1,1:125,61:0.0106:2,2:14.5:1:28.5:1:0.552:2.04076:60:4:0.0106:0:1 -2 36526875 . C A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20926;LSEQ=CTTCCTTTTTGGACAGTACC;RSEQ=ATTCCCTTGATGTCTACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:3:2,1:117,183:0.0099:2,2:9.7:1:27.7:1:0.56356:3.12:60:6:0.0103:0:1.3 0/1:251:3:2,1:96,152:0.012:2,2:11.7:1:27.7:1:0.56241:3.15:60:6:0.0121:0:1.7 -2 38467056 . C T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00175;SOR=Inf;LSEQ=GGGTTTTTCTAGACCTCCCC;RSEQ=ATCCCCAAGGGTCTGACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:27,0:0:1,0:24.4:1:30.4:1:1:0:60:26:1:0:0.1 0/1:17:6:6,0:11,0:0.3529:0,0:25.3:1:31.2:1:1:0:60:12:0.3529:0:2.2 -2 38467073 . C G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=CCCCATCCCCAAGGGTCTGA;RSEQ=GCAGGGCCCTGGTTTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:0:1,0:24.3:1:32.3:1:1:0:60:76:1:0:0.1 0/1:22:8:8,0:14,0:0.3636:1,0:27.9:1:32.3:1:1:0:60:16:0.3636:0:1.9 -2 38467176 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17306;SOR=Inf;LSEQ=GAGGGATGCTGGGTCCCAAG;RSEQ=GTCCAAAGGTGCCCTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:174,85:0:2,0:26:1:31:1:1:0:60:36:1:0:0.1 0/1:185:2:1,1:124,59:0.0108:2,2:17:1:25.5:1:0.54465:2.09254:60:4:0.0109:0:1.5 -2 38467256 . G A 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATCTCAACTCTTTCTTGAGC;RSEQ=CGTTGAGATGAATTTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:172,209:0:2,0:25.8:1:30.9:1:1:0:60:380:0.9974:0:0.1 0/1:367:54:23,31:147,166:0.1471:2,2:25.9:1:29.6:1:0.65787:1.19298:60:108:0.1484:0:1.1 -2 38467258 . G A 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTCAACTCTTTCTTGAGCGC;RSEQ=TTGAGATGAATTTTGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:170,207:0:2,0:25.8:1:30.8:1:1:0:60:124.667:1:0:0.1 0/1:366:16:6,10:162,188:0.0437:2,2:29.3:1:30.3:1:0.61098:1.43478:60:32:0.0442:0:1.3 -2 38978149 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGCTTTAGGCTGGATTGGG;RSEQ=CACAAAAATGCCCAAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:0:2,0:17.7:1:29.3:1:1:0:60:9:1:0:0 0/1:22:2:1,1:18,2:0.0909:2,2:24.5:1:25.5:1:0.25974:7.54971:60:4:0.0909:0:1 -2 39095413 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.4929;SOR=Inf;LSEQ=TTTCTGTTGCCGCCACCTCC;RSEQ=CCACCACCACCACCGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:0:2,0:22.7:1:29.4:1:1:0:60:58:1:0:0.2 0/1:32:2:1,1:15,14:0.0625:2,2:34:1:28.5:1:1:1.06901:60:4:0.0645:0:1 -2 39841994 . G C 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31866;SOR=1.36435;LSEQ=ATTTCAGCGTGTACACATAC;RSEQ=CAGATCTGGTTAATTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:43:41,2:86,7:0.3139:2,1:25.7:1:31.4:1:0.71895:1.66:60:86:0.3185:0:1 0/1:91:35:34,1:55,1:0.3846:1,1:23.8:1:30.3:1:1:1.60874:60:34:0.382:0:1.1 -2 39842140 . G C 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-04;SOR=1.49616;LSEQ=AGGGTTGGGCTGTCCGTGAC;RSEQ=ATTTTTCCTGTGATGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:710:214:97,117:227,266:0.3014:2,2:28.9:1:31.3:1:0.86987:1.0293:60:213:0.3034:0:1.1 0/1:655:257:118,139:187,201:0.3924:2,2:25.1:1:30.7:1:0.57406:1.09576:60:127.5:0.3929:0:1.2 -2 39842175 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01963;SOR=Inf;LSEQ=GTGAACAGGGTCCATCTATG;RSEQ=CAAGAGAGAATGAGGTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:0:0,0:195,368:0:2,0:24.7:1:31.8:1:1:0:60:280.5:0.9982:0:0.3 0/1:474:5:4,1:187,282:0.0105:2,2:13.8:1:26:1:0.16296:6.01:60:10:0.0108:0:1 -2 39842241 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.51073;SOR=0;LSEQ=ACAGAAAGAAGTAGATCTGA;RSEQ=AGAGGCAGAGAAAAAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:13,154:0.0118:2,2:31:1:28.5:1:0.15927:11.45:60:4:0.0121:0:1 0/0:123:0:0,0:16,106:0:2,0:24:1:30.7:1:1:0:60:19.333:0.9915:0:0.1 -2 39842288 . CAGATAGAG C 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=2;SSF=0.46645;SOR=0.66727;LSEQ=AGATAGAGATGATAGATAGA;RSEQ=AGATAGACAGATAGACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:16:0,16:1,40:0.2807:1,1:22.9:1:31.4:1:1:0:60:15:0.2679:0.0877:0.9 0/1:34:7:0,7:0,27:0.2059:1,0:25.6:1:31.4:1:1:0:60:14:0.2121:0.0588:1 -2 39842361 . T G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25167;SOR=2.68681;LSEQ=AGAAAGTGAGAATGAGCCCT;RSEQ=GTGAATAGTTTGAGATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:0,9:0,15:0.375:1,0:31.2:1:30.9:1:1:0:60:18:0.375:0:1.1 1/0:8:5:1,4:0,3:0.625:0,2:22.6:1:31.8:1:1:0:60:10:0.625:0:1.8 -2 40904504 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21429;SOR=0;LSEQ=ATGCACCTTCTTAGGGGAAG;RSEQ=GTGTTCTTTTTACACTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:16.5:1:33:0:1:2.64575:60:4:0.2:0:1 0/0:11:0:0,0:9,2:0:2,0:17.7:1:30.2:1:1:0:58.4:22:1:0:0.2 -2 40904636 . A T 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00954;SOR=0;LSEQ=GAGTTGGGCGACATGGCTTC;RSEQ=CCCCTTTCTAGGTCCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:72:34,38:0,0:1:0,2:28.1:1:30.5:1:1:0:58.4:144:1:0:1.2 1/1:64:58:29,29:1,5:0.9063:2,2:25.8:1:28.8:1:0.20182:4.89:59.4:18.333:0.9016:0:1.1 -2 40904919 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAAGTAGCTAAAGCGGTCAT;RSEQ=GCCCAATTCCCGACAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:5:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:27.5:1:1:0:60:4:1:0:1 -2 41449888 . A G 49 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03497;SOR=0;LSEQ=GCTGGAATCTGCTTAAGCCT;RSEQ=CCAAACTCCCAGTGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:34:1:31:1:1:0:60:6:1:0:1 0/1:10:2:1,1:5,3:0.2:2,2:22:1:31:1:1:1.58108:60:4:0.2:0:1 -2 41450141 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51087;SOR=0;LSEQ=GCCCAAAATACACCAGCTGT;RSEQ=GCAGTCTGTGGTGAGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:38:0:32:1:1:1.15:60:4:0.1333:0:1.5 0/0:9:0:0,0:5,4:0:2,0:35.7:1:32:1:1:0:60:18:1:0:0.2 -2 41450292 . A G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31373;SOR=0.2328;LSEQ=GAGCCACTAGCGGGAGGAGC;RSEQ=GCTGCAGTCTCTGCAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:1,0:0.875:0,0:24:1:31.3:1:1:0:60:14:0.875:0:1 1/0:10:6:4,2:3,1:0.6:2,2:18.8:1:26.2:1:1:1.44135:60:5:0.5556:0:1 -2 41450618 . A T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTAGGCACAGGAGCAAG;RSEQ=CAGATGAACAGGGGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:6,4:0,0:1:0,2:20.8:1:29.4:1:1:0:60:20:1:0:1 1/1:4:4:2,2:0,0:1:0,2:31:1:28.5:1:1:0:60:8:1:0:1.5 -2 41450696 . A AAAAC 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.17037;SOR=Inf;LSEQ=GAAGGACCTGACTATTGAAA;RSEQ=AAACAAACAAACAAGCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:27,5:0:2,0:20.8:1:29.4:1:1:0:60:15:1:0:0.3 0/1:23:2:2,0:20,1:0.087:1,0:17.5:1:32.1:1:1:0:60:4:0.087:0:1 -2 41450721 . T A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04579;SOR=Inf;LSEQ=AAACAAACAAGCTGAAAGTG;RSEQ=CAACAACAGCATCACCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:37,17:0:2,0:23.5:1:29.2:1:1:0:60:26:1:0:0.1 0/1:48:4:3,1:33,11:0.0833:2,2:31.5:1:27.8:1:1:1:60:8:0.0833:0:1 -2 41450758 . G A 69 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28678;SOR=2.72525;LSEQ=ACCACCAACAACAAAAGGCC;RSEQ=CACAAAAACGCCATTCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:47,37:0.0233:2,2:16:0:29:1:1:1.2667:60:4:0.0235:0:1 0/1:98:6:3,3:49,43:0.0612:2,2:16.7:1:26.7:1:1:1.13801:60:12:0.0645:0:1.2 -2 41450783 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.5004;SOR=Inf;LSEQ=AAAACGCCATTCAAGGGTCA;RSEQ=CAGCCTCAAAGACCAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:44,46:0:2,0:28:1:31.8:1:1:0:60:89:1:0:0.2 0/1:105:2:1,1:51,52:0.019:2,2:38:1:27:1:1:1.02:60:4:0.0194:0:1 -2 41764773 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14622;SOR=Inf;LSEQ=TTATTTGACATTCTCCTGCT;RSEQ=TAGCTCCATCTTATGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:192,22:0:2,0:23.2:1:31.8:1:1:0:60:29.571:1:0:0 0/1:133:2:1,1:105,26:0.015:2,2:13.5:1:26.5:1:0.36603:3.9818:60:4:0.0153:0:1 -2 41764905 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.27329;LSEQ=TGACTCTCCGAATCAAAACC;RSEQ=TCATCCAAATAACCATACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:478:217:84,133:97,163:0.454:2,2:26:1:29.2:1:0.77671:1.06:60:11.765:0.4566:0:1.4 0/1:465:86:38,48:172,207:0.1849:2,2:24.9:1:29.3:1:0.90464:1.04949:60:20.5:0.1834:0:1.3 -2 42758255 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGGGATTACATGTGTGAG;RSEQ=TACCATGCCCGGCCCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:31.5:1:1:0:60:4:1:0:1 -2 42760158 . G T 40 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24808;SOR=0;LSEQ=CCTTGTTTGTTTACAGCAAT;RSEQ=CCAACAGCATGCTGGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:1,2:94,73:0.0175:2,2:11.7:1:25.7:1:0.58372:2.56125:60:2:0.0128:0:4.7 0/0:164:0:0,0:99,64:0:2,0:24.6:1:30.8:1:1:0:60:19.375:1:0:0.6 -2 42760199 . C T 39 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24835;SOR=0;LSEQ=ATTGCAGACTTCCACTTTTG;RSEQ=CATGGTAACACTTGTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:1,2:87,89:0.0168:2,2:27.3:1:25:1:1:1.94802:51.3:2:0.0132:0:4.3 0/0:170:0:0,0:94,74:0:2,0:28.4:1:30.5:1:1:0:59.8:17.667:1:0:0.8 -2 42760201 . A G 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79992;SOR=1.0883;LSEQ=TGCAGACTTCCACTTTTGCC;RSEQ=TGGTAACACTTGTGGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:40:21,19:65,66:0.226:2,2:34.5:1:27.2:1:0.85695:1.12:58.4:4:0.2133:0:2 0/1:170:41:21,20:73,53:0.2412:2,2:31.3:1:27.2:1:0.47328:1.3096:59:5.833:0.2258:0:1.9 -2 42760390 . G A 25 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=CTGCGCCCGCCACCATGCCC;RSEQ=GCTAATTTTTCTATTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:45:0:33:0:1:0:60:2:0.3333:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:21.5:1:25.5:1:1:0:60:4:0.6667:0:2 -2 43081218 . CGT C 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.15097;SOR=0;LSEQ=TGTGTGTTTACATGTGTCTG;RSEQ=GTGTGTGTGTTGTGCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:3,2:20,15:0.125:2,2:37:1:30.6:1:1:1.12:60:10:0.125:0:0.2 0/0:22:0:0,0:13,9:0:2,0:32.1:1:29.9:1:1:0:60:44:1:0:0.1 -2 43082062 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGACCCGGGTCCAGAGGA;RSEQ=GGGAAAAGAGGCGGCTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:43:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:23:0:31.5:1:1:0:60:4:1:0:1.5 -2 43083070 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGTGGATTATTCTAGCC;RSEQ=GTGAATGTGGGGCCGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 43451509 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGGCAGGCGGCGGCCAGG;RSEQ=TCGAGGCTGGGAGACTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:31:1:1:0:60:4:1:0:1 -2 43452183 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCTGAGGCTGTGGTGCA;RSEQ=CTTGGGCCGCGGCTCCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:18:0:34:0:1:0:60:2:1:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:23.5:1:31:1:1:0:60:4:0.6667:0:1 -2 43951871 . A G 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.86565;SOR=1.03574;LSEQ=ACAATATTTTTCTTTTCAAT;RSEQ=AGCAGTTTTGAGACTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:137:96,41:115,62:0.4349:2,2:23.6:1:31.7:1:0.3964:1.26:60:136:0.4359:0:1.8 0/1:257:114:78,36:94,47:0.4436:2,2:26.4:1:31.6:1:0.78944:1.08:60:228:0.4471:0:1.7 -2 43951922 . T A 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73275;SOR=1.05644;LSEQ=CTTTTGATCCAATAACTTAA;RSEQ=CAAATTGCTGATCAATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:217:112,105:135,131:0.4493:2,2:27.4:1:30.1:1:0.85536:1.04:60:216:0.4491:0:1.5 0/1:391:181:93,88:108,102:0.4629:2,2:25.9:1:29.2:1:1:1.00189:60:89.5:0.4674:0:1.5 -2 43952068 . G A 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0017;SOR=0;LSEQ=TTCTTGTTCTCAAGGACAAG;RSEQ=AGATCTGGGTCATGGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:10:1,9:1,51:0.1613:1,2:18.2:1:29.7:1:0.29878:5.43:60:20:0.1639:0:1 0/0:53:0:0,0:2,51:0:1,0:20.4:1:31.2:1:1:0:60:52:1:0:0.1 -2 44311676 . C A 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26749;SOR=0;LSEQ=ATTCTCTGCTTGGCCAAACT;RSEQ=TAGTCAGCCTTCTGAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:8,2:0.375:2,2:22.5:1:29:1:0.6044:1.91107:60:12:0.375:0:1 0/0:4:0:0,0:2,2:0:2,0:19.8:1:31.8:1:1:0:60:8:1:0:0.3 -2 44312262 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAGCTGGGACTACAGGC;RSEQ=TGCACCACCATGCCCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 44561412 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21325;SOR=Inf;LSEQ=TTAGATACCTGAGAGAAACA;RSEQ=GTTCAGTTTTAGCACTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:74,7:0:2,0:27:1:32.2:1:1:0:60:162:1:0:0.1 0/1:70:2:2,0:64,4:0.0286:2,0:11:1:30.5:1:1:0:60:4:0.029:0:1 -2 44561532 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23161;LSEQ=TCTAAATAAAACTGATGTTA;RSEQ=CATACAGCAAAAAACGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:386:348:178,170:18,20:0.9016:2,2:26.7:1:29.9:1:0.73356:1.16:60:173:0.9058:0:1.1 1/0:399:271:133,138:61,65:0.6792:2,2:25.2:1:29.6:1:0.91451:1.03:60:66.75:0.6811:0:1.2 -2 44561591 . C CA 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.20672;SOR=0.23655;LSEQ=ATCATAACTTCTTTTTGTGA;RSEQ=AAAAAAAAATACTTCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:4:0,4:68,147:0.0181:2,0:29.8:1:29.8:1:0.3131:0:60:8:0.0189:0:0.8 0/0:231:1:1,0:82,146:0.0043:2,0:49:0:32:0:0.36245:0:60:2:0.0044:0:0 -2 44561607 . C A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTGACAAAAAAAAATACTTC;RSEQ=AGAAAATACTGATGGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:2,0:41,142:0.0108:2,0:9:1:20:1:0.05306:0:60:1:0.0055:0:3 0/1:185:2:1,1:53,130:0.0108:2,2:5.5:1:29.5:1:0.49971:2.44:60:4:0.0109:0:2 -2 44561616 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24128;SOR=Inf;LSEQ=AAAAATACTTCCAGAAAATA;RSEQ=TGATGGCATGGTGACCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:34,125:0:2,0:23.3:1:31.9:1:1:0:60:158:1:0:1.1 0/1:154:2:1,1:34,117:0.013:2,2:17.5:1:27.5:1:0.40635:3.41:60:4:0.0132:0:2 -2 44561627 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.22498;LSEQ=CAGAAAATACTGATGGCATG;RSEQ=TGACCAAGGATACGAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:114:16,98:3,7:0.9194:2,2:25.5:1:30.6:1:0.18112:2.59854:60:56:0.918:0:1.2 1/0:110:79:11,68:7,24:0.7182:2,2:23.3:1:29.8:1:0.26828:1.79265:60:38.5:0.713:0:1.1 -2 45237593 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22067;SOR=Inf;LSEQ=GGCAGCTGCGACGCAGAACC;RSEQ=CGGACGGCGCAGACCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:0:2,0:26.4:1:31.1:1:1:0:60:44:1:0:0.1 0/1:20:2:1,1:8,10:0.1:2,2:27.5:1:29.5:1:1:1.24:60:4:0.1:0:1.5 -2 46128389 . C G 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00213;SOR=Inf;LSEQ=AAAACCGTCTGTGTTGAGTA;RSEQ=TCCTAATCGGTTGCTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:291,158:0:2,0:24.1:1:31.7:1:1:0:60:63.143:1:0:0.3 0/1:322:7:6,1:196,118:0.0217:2,2:34.6:1:31.6:1:0.2657:3.60:60:14:0.022:0:1.6 -2 46128458 . G T 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=1.68201;LSEQ=TGTTTCAGAATGTTAAAATG;RSEQ=TTCTTACCCAAGGCCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:720:195:92,103:256,269:0.2708:2,2:24.1:1:29.3:1:0.73743:1.06534:60:26.857:0.2674:0:1.1 0/1:520:200:87,113:157,163:0.3846:2,2:27.1:1:29.5:1:0.24054:1.25049:60:99:0.3845:0:1.2 -2 46128526 . C A 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GTAAGGTATTAGCCTGTTCA;RSEQ=ATATTTCTCATGTAATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:40:10,30:115,256:0.0973:2,2:24.2:1:30.6:1:0.47553:1.34673:60:80:0.098:0:1 0/0:240:0:0,0:79,160:0:2,0:24.8:1:31.5:1:1:0:60:78.667:1:0:0.3 -2 46128576 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10429;SOR=Inf;LSEQ=AGATCCAATAAAGTTTGCCC;RSEQ=GGGCCTTCTTGGAAAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:18,134:0:2,0:23.7:1:30.3:1:1:0:60:75:1:0:0.2 0/1:73:2:1,1:8,62:0.0274:2,2:25:1:29:1:0.23592:7.37:60:4:0.0278:0:1 -2 46128729 . G A 29 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04412;SOR=Inf;LSEQ=CTGTGAGTGTAAAGTTTGAA;RSEQ=GATTTTTTTATAATTCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:0:1,0:25.5:1:29.2:1:1:0:60:12:1:0:0.1 1/0:4:2:1,1:0,2:0.5:0,2:43:0:29.5:1:1:0:60:4:0.5:0:1 -2 47257865 . C T 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.48111;LSEQ=CCCGCCTGTTCCCCCTCCAT;RSEQ=CTGGCCTAGGCAGGTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:208:86,122:126,187:0.3985:2,2:25.3:1:29.5:1:0.85557:1.05:60:25:0.3922:0:1.1 0/1:265:64:26,38:88,113:0.2415:2,2:29.2:1:28.9:1:0.77206:1.13764:60:128:0.2462:0:1.2 -2 47257887 . T C 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03756;SOR=Inf;LSEQ=TGGCCTAGGCAGGTCCCCAC;RSEQ=GCTCACAGCCAGGTGTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:157,268:0:2,0:24.2:1:30:1:1:0:60:41.5:1:0:0.5 0/1:215:3:1,2:86,126:0.014:2,2:26.7:1:25.3:1:1:1.36317:60:6:0.0144:0:1.3 -2 47257977 . T C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76113;SOR=0.88418;LSEQ=CCCTGATTCTGAGCCTTGCC;RSEQ=CAGCAGCATTCAAGAGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:46:3,43:9,49:0.4381:2,2:24.5:1:31.5:1:0.21941:2.61017:60:92:0.4466:0:1.1 0/1:76:31:9,22:12,33:0.4079:2,2:21.7:1:30.6:1:1:1.12:60:62:0.4247:0:1.3 -2 47257989 . A C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00068;SOR=Inf;LSEQ=GCCTTGCCTCAGCAGCATTC;RSEQ=AGAGACTACTAAAGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:6,78:0:2,0:20.5:1:29.8:1:1:0:60:27:1:0:0.5 0/1:60:8:2,6:11,41:0.1333:2,2:27.8:1:31.4:1:1:1.24:60:16:0.1356:0:2 -2 47413836 . C G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=8.2064;LSEQ=TGCTGCTTTGTGCCGCCTTT;RSEQ=TGGGAGGCAGAGAAGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:19:7,12:12,16:0.4043:2,2:24.8:1:31.5:1:0.76724:1.27887:60:18:0.3913:0:1.2 1/1:47:40:15,25:3,4:0.8511:2,2:27.9:1:31.3:1:1:1.24396:60:80:0.8511:0:1.1 -2 47596597 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18014;SOR=Inf;LSEQ=CTCCCGGCGCACGCCCTCCC;RSEQ=CGAGTCCCGGGCCCCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:107,32:0:2,0:16:1:30.2:1:1:0:60:68.5:1:0:0.2 0/1:103:2:1,1:71,30:0.0194:2,2:20.5:1:29.5:1:0.51342:2.34454:60:4:0.02:0:1 -2 47596649 . C T 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TCGGCGCGCGCGCAGCATGG;RSEQ=GCCCCCGCAGGTCCTCGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:271,131:0:2,0:27.5:1:31.2:1:1:0:60:35.545:1:0:0.2 0/1:360:13:9,4:219,128:0.0361:2,2:18.2:1:29.4:1:0.7751:1.31:60:26:0.0368:0:1.1 -2 47596653 . C T 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.04528;SOR=Inf;LSEQ=CGCGCGCGCAGCATGGCGCC;RSEQ=CCGCAGGTCCTCGCGTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:294,148:0:2,0:26.4:1:30.9:1:1:0:60:54.25:1:0:0.2 0/1:380:4:1,3:238,138:0.0105:2,2:9.8:1:26.3:1:0.14626:5.15147:60:8:0.0107:0:1.3 -2 47596694 . C T 82 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23011;SOR=0.40872;LSEQ=GCTTCTGCTTGCCGCGGCGA;RSEQ=GGCGACTTTTGCCGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:8:3,5:413,271:0.0116:2,2:13.8:1:27.5:1:0.27675:2.53648:60:7:0.0103:0:1 0/0:631:3:1,2:344,284:0.0048:2,2:22:1:28:1:0.59277:2.41922:60:6:0.0048:0:1.3 -2 47596775 . GC G 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.7055;SOR=1.71218;LSEQ=GGCTGGGCTGGGGGGCAGCG;RSEQ=CCCCGGCCCTCGGCCCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:3:1,2:203,283:0.0061:2,2:18.7:1:30.4:1:1:1.43361:60:6:0.0063:0.002:0 0/1:383:4:1,3:150,228:0.0104:2,2:28:1:33:1:1:1.9705:60:8:0.0106:0:0 -2 47596853 . C CG 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07254;SOR=Inf;LSEQ=TTTCCAGCGTGGAGACCGGA;RSEQ=GGTGCGGCCGTGCTCCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:1,117:0:1,0:25.8:1:29.9:1:1:0:60:58:1:0:0.1 0/1:44:2:0,2:1,41:0.0455:1,0:15.5:1:32:0:1:0:60:4:0.0476:0:0.5 -2 47596866 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07037;SOR=Inf;LSEQ=GACCGGACGGTGCGGCCGTG;RSEQ=TCCGGCTCAGGCCCTCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:0,90:0:1,0:28.5:1:32.3:1:1:0:60:29:1:0:0.1 0/1:33:2:0,2:0,31:0.0606:1,0:21.5:1:32.5:1:1:0:60:4:0.0625:0:1 -2 47600555 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26046;SOR=0;LSEQ=AACTTAGCTGGGACATGAGA;RSEQ=TTAATAGATCCACATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:3:2,1:195,17:0.014:2,2:16.3:1:24.7:1:0.23171:5.6474:60:2:0.0095:0:1.3 0/0:166:0:0,0:147,19:0:2,0:22.2:1:32.1:1:1:0:60:332:1:0:0.1 -2 47600581 . AT A 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.85345;SOR=0.91572;LSEQ=AGATCCACATTTTAAAGTAG;RSEQ=TTTTTTTTTAATTTTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:17:14,3:288,76:0.0446:2,2:21.8:1:31.3:1:1:1.23:60:34:0.0452:0.0105:0.2 0/1:317:13:11,2:238,66:0.041:2,2:31.4:1:30.8:1:0.74207:1.52:60:26:0.0414:0:0.6 -2 47600782 . T C 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06908;SOR=Inf;LSEQ=TTAATTGATGTGCCTTGAGT;RSEQ=GGAAAGAGTTTTATTGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:56,230:0:2,0:23.3:1:30.2:1:1:0:60:285:1:0:0.1 0/1:200:3:1,2:39,158:0.015:2,2:27.3:1:29:1:0.48993:2.02:60:6:0.0152:0:1 -2 47600881 . A AT 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.9993;LSEQ=ACCCTGGAACTTTAGAGTTA;RSEQ=TTTTTTTTTTCCCGTAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:14:9,5:163,75:0.0553:2,2:25:1:31.3:1:0.77126:1.20645:60:28:0.0567:0.004:0.1 0/1:217:12:8,4:132,72:0.0553:2,2:26.8:1:28.8:1:1:1.09:60:24:0.0561:0:0.7 -2 47601106 . T C 248 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06707;SOR=0.79129;LSEQ=GCAGTGCAACGGCACCTCCA;RSEQ=GTGCTGGTGTGTGAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:507:277:123,154:107,123:0.5464:2,2:24.6:1:30.6:1:0.65481:1.08898:60:137.5:0.5478:0:1.1 0/1:496:242:113,129:114,140:0.4879:2,2:24:1:29.7:1:0.71871:1.08:60:47.4:0.4857:0:1.1 -2 47601257 . T C 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00109;SOR=Inf;LSEQ=TAATTAAATTTATTTTTGAT;RSEQ=ATGTAATATGATTTCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:12,95:0:2,0:23.1:1:28.5:1:1:0:60:106:1:0:0.1 0/1:83:8:2,6:8,67:0.0964:2,2:20.6:1:32:1:0.24612:2.75:60:16:0.0964:0:1.1 -2 47602178 . A T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00252;SOR=0.10309;LSEQ=TGTCCAGAGAACAGAGGGTC;RSEQ=ATATTAGAAAAGGTGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:19:19,0:15,0:0.5588:1,1:25.5:1:31.9:1:1:0:60:38:0.5588:0:1 0/1:18:2:2,0:16,0:0.1111:1,0:10.5:1:33:0:1:0:60:4:0.1111:0:1 -2 47602241 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16796;SOR=Inf;LSEQ=GGATGTGTAAGGGAAGAAAT;RSEQ=ATAGGAATAGCTACTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:90,0:0:1,0:23.1:1:30.5:1:1:0:60:44:1:0:0.2 0/1:63:2:2,0:59,2:0.0317:1,0:15:1:29:1:1:0:60:4:0.0333:0:1 -2 47604118 . A AT 146 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00088;SOR=3.05108;LSEQ=TACTGTTGTGTGGTACAAAC;RSEQ=TTTTTTTTTAATACAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:596:12:8,4:399,182:0.0201:2,2:24.4:1:31:1:1:1.09598:59.6:24:0.0204:0.005:0.1 0/1:525:31:15,16:308,184:0.059:2,2:29.2:1:29.5:1:0.12901:1.78337:60:62:0.0597:0.0057:0.6 -2 47604148 . T C 158 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=37.59738;LSEQ=AATACAGATTTTAAATTCTT;RSEQ=ACAGTGCACTTCAGAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:803:1:0,1:480,322:0.0012:2,0:40:0:14:0:0.40224:0:60:0:0:0:4 0/1:803:36:19,17:435,332:0.0448:2,2:23.1:1:30.6:1:0.73142:1.17208:60:35:0.0439:0:1.1 -2 47604368 . G GT 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.18253;SOR=3.9568;LSEQ=AATGTGAATTTCCTGTTACT;RSEQ=TTTTTTTTTGTTTGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:0,2:1,87:0.0222:1,0:35:1:32:0:1:0:60:4:0.0233:0:0 0/1:48:4:0,4:1,42:0.0833:1,0:20.3:1:29.3:1:1:0:60:8:0.0851:0:0 -2 47605839 . C T 114 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTCAATATAAGAAAAT;RSEQ=CTCTTAGGAAAAATTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:16.3:1:30.9:1:1:0:60:26:1:0:1 1/1:1:1:1,0:0,0:1:0,0:2:0:30:0:1:0:60:2:1:0:1 -2 47606239 . C A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10012;SOR=Inf;LSEQ=TGTTCAGGAATGTAGTCTAT;RSEQ=ATGCCTCAATGAATTAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:65,228:0:2,0:22.2:1:31.8:1:1:0:60:57.6:1:0:0.1 0/1:255:3:2,1:56,196:0.0118:2,2:9:1:25.7:1:0.13053:6.93:60:6:0.0119:0:1 -2 47606774 . A G 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.83825;SOR=0.8651;LSEQ=AGTTTTTTAAAGTTCCAATA;RSEQ=ATTAGATTGTTATCACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:50:49,1:27,0:0.6494:1,1:25.2:1:32.5:1:1:0:60:49:0.6447:0:1 1/0:39:24:24,0:15,0:0.6154:1,1:25.6:1:32.1:1:1:0:60:48:0.6154:0:1 -2 47606829 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20002;SOR=Inf;LSEQ=TGGCAGCGGTTCTTTTGGCA;RSEQ=ACAATTTGTATGTAATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:143,22:0:2,0:22.2:1:30.8:1:1:0:60:330:1:0:0.2 0/1:134:2:1,1:114,18:0.0149:2,2:26.5:1:29:1:0.26439:6.1914:60:4:0.0156:0:1 -2 47606851 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11953;SOR=Inf;LSEQ=CAATTTGTATGTAATTATAT;RSEQ=TGGCCATGGTTGGTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:187,53:0:2,0:23.9:1:31.6:1:1:0:60:29:1:0:0.2 0/1:234:3:2,1:172,59:0.0128:2,2:28.3:1:29.3:1:1:1.45508:60:6:0.013:0:1.3 -2 47607186 . T C 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TAGTGGCTGGGCGCGGTGGC;RSEQ=CACCACACCTGTTATCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:7,117:0:2,0:24.2:1:30:1:1:0:60:40.333:1:0:0.1 0/1:90:11:1,10:2,77:0.1222:1,2:19.4:1:31.3:1:0.32687:3.76:60:22:0.1222:0:1.1 -2 47612198 . G GT 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.19831;SOR=Inf;LSEQ=ATGGATAGATGTTAAAATTA;RSEQ=TTTTTTTTCAGATCAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:230,16:0:2,0:24.7:1:32.6:1:1:0:60:245:1:0:0.4 0/1:198:2:2,0:174,22:0.0101:2,0:24:1:27:1:1:0:60:4:0.0102:0:0 -2 47612224 . C T 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.51084;LSEQ=TTTCAGATCAAAATTATGTC;RSEQ=ATTAAAAGCATATATGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:158:131,27:195,57:0.3854:2,2:24.5:1:30.6:1:0.20887:1.42:60:316:0.3901:0:1.1 0/1:330:80:64,16:187,62:0.2424:2,2:23.7:1:30.8:1:0.45035:1.33:60:160:0.2469:0:1 -2 47613635 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50372;SOR=0;LSEQ=TTCCTTTAATTTCATTTTTA;RSEQ=TTAATACTATTTTCAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:2,0:159,35:0.0102:2,0:15:1:33.5:1:1:0:60:4:0.0103:0:1 0/0:160:0:0,0:127,33:0:2,0:22.9:1:29.6:1:1:0:59.9:79:1:0:0 -2 47613870 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05745;LSEQ=TTTGTTAGTTTAACATCATA;RSEQ=ATTTGTAATAGTGAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:33:3,30:1,38:0.4583:1,2:22.5:1:32.5:1:0.32655:3.73:60:66:0.4648:0:1.2 0/1:44:2:0,2:1,41:0.0455:1,0:27:1:34:0:1:0:60:4:0.0455:0:1 -2 47630213 . T C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06602;LSEQ=AACGCAGCCCTGGAAGCTGA;RSEQ=TGGGTGTGGTCGCCGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:53:51,2:70,4:0.4141:2,1:24.2:1:31.8:1:1:1.45:60:52:0.4228:0:1.1 0/1:68:3:2,1:61,3:0.0441:1,2:25:1:30.3:1:0.17105:9.36402:60:6:0.0448:0:1 -2 47630314 . G T 161 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGCATTTTCTTCAACCAGGA;RSEQ=GTGAGGAGGTTTCGACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:40:20,20:302,266:0.0658:2,2:25.3:1:30.4:1:0.74462:1.1351:60:39:0.0653:0:1.2 0/0:492:0:0,0:274,218:0:2,0:26.4:1:30.7:1:1:0:60:43.727:1:0:0.2 -2 47630371 . C T 74 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03863;SOR=0;LSEQ=GACGCTGCAGTTGGAGAGCG;RSEQ=GGCCGAGGTCGGCTTCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:6:2,4:262,307:0.0104:2,2:26.3:1:28.7:1:0.69216:1.70532:60:12:0.0106:0:1 0/0:444:0:0,0:210,233:0:2,0:24.7:1:30.2:1:1:0:60:109.75:0.9977:0:0.2 -2 47630550 . C G 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01866;SOR=1.38944;LSEQ=TGGGGCCGGCAGGTGAGGGC;RSEQ=GGGACGGCGCGTGCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:176:56,120:104,172:0.3885:2,2:23.7:1:30.3:1:0.22653:1.29494:60:57.667:0.3896:0:1.2 0/1:403:189:80,109:84,130:0.469:2,2:24.9:1:29.7:1:0.5436:1.14:60:188:0.4724:0:1.3 -2 47630592 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19647;SOR=Inf;LSEQ=GGACCCGGGGCCTTGTGGCG;RSEQ=GGCTCCTTTCCCGCCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:45,188:0:2,0:24.9:1:29.6:1:1:0:60:37.833:1:0:0.5 0/1:186:2:0,2:52,132:0.0108:2,0:25:1:25.5:1:1:0:60:4:0.011:0:3 -2 47630620 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12898;SOR=Inf;LSEQ=TTCCCGCCTCAGAGAGTGGG;RSEQ=GGTGAGCAGCCTCTCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:12,137:0:2,0:22.3:1:29.8:1:1:0:60:36.25:1:0:0.6 0/1:84:2:1,1:7,75:0.0238:2,2:24:1:27.5:1:0.18244:10.09:60:4:0.0238:0:1 -2 47630639 . T C 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.72921;SOR=1.19423;LSEQ=GCGGTGAGCAGCCTCTCCAG;RSEQ=GCGGAGGCACGGGGGCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:46:0,46:1,54:0.4554:1,1:24:1:30.3:1:1:0:60:92:0.4554:0:1.3 1/0:50:25:0,25:2,23:0.5:2,1:19.4:1:30.3:1:0.4898:0:60:50:0.5:0:1.4 -2 47635566 . C T 51 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4966;SOR=0.57031;LSEQ=AGAATCTGCAGAGTGTTGTG;RSEQ=TTAGTAAAATGAATTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:5:3,2:272,126:0.0124:2,2:27.6:1:22:1:0.65463:1.4378:60:1.5:0.0085:0:2.4 0/0:422:3:3,0:258,161:0.0071:2,0:20.3:1:14.3:1:0.29043:0:60:0:0:0:4.3 -2 47637065 . C T 80 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTGCAGTGAGTTGAGAT;RSEQ=GCACCATTGCACTCTAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:13,0:0.3158:1,0:30.7:1:31.3:1:1:0:60:12:0.3158:0:1 0/0:2:0:0,0:2,0:0:0,0:12:1:32:1:1:0:60:4:1:0:0.5 -2 47638795 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCCTGACCTTGTGATCC;RSEQ=CCCGCCTTGGCCTCCCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:42.5:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47639329 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=AAAGAGTTGTTACCGTTGGG;RSEQ=CTATTTTTTGAAAGCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:25.5:1:33:0:1:0:60:4:0.2222:0:1 0/0:6:0:0,0:6,0:0:0,0:22.2:1:28.7:1:1:0:60:12:1:0:0 -2 47639493 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1951;SOR=Inf;LSEQ=AGTTATCAATGTTATAATTT;RSEQ=CATTTTTGCTTTTCTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:138,32:0:2,0:22.5:1:30.1:1:1:0:60:55.667:1:0:0.1 0/1:135:2:1,1:111,22:0.0148:2,2:30.5:1:28:1:0.31277:4.95686:60:4:0.0152:0:1 -2 47641295 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21645;SOR=Inf;LSEQ=TTTGGATTGGGAAGGAACAC;RSEQ=AAGGAAAATGAGGGACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:148,2:0:1,0:26.4:1:30.8:1:1:0:60:29:1:0:0.1 0/1:131:2:1,1:128,1:0.0153:1,2:5.5:1:29:1:0.03042:91.02182:60:4:0.0156:0:1 -2 47641587 . G A 62 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05577;SOR=0.22849;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=GGTTAAAAATGTTGAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:542:8:6,2:174,357:0.0148:2,2:9.1:1:20.9:1:0.01909:6.13:55:1.667:0.0101:0:2 0/0:587:2:2,0:188,394:0.0034:2,0:24:1:13:1:0.10547:0:49:0:0:0:3.5 -2 47641746 . CT C 186 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.92626;SOR=0.97279;LSEQ=TCCTCCACTCCACTTTTTAA;RSEQ=TTTTTTTTTTTAAGTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:64:23,41:193,309:0.1111:2,2:26.6:1:31.8:1:0.78506:1.11323:60:128:0.1137:0.0139:0.5 0/1:618:67:23,44:196,348:0.1084:2,2:28.3:1:30.8:1:0.89273:1.07734:60:32.5:0.1078:0.0065:0.3 -2 47641758 . T A 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=CTTTTTAACTTTTTTTTTTT;RSEQ=AAGTCAGAGTCTCACTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:0:0,0:167,306:0:2,0:21.2:1:28.4:1:1:0:59.9:38.417:0.9957:0:0.5 0/1:492:11:5,6:158,323:0.0224:2,2:7.1:1:26.7:1:0.51772:1.70:60:22:0.0226:0:1.1 -2 47641781 . C A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70167;LSEQ=GTCAGAGTCTCACTTGTTCC;RSEQ=TAGGCCAGAGTGCAGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:2,1:56,208:0.0112:2,2:16:1:27.3:1:0.11997:7.35:60:6:0.0115:0:1.7 0/0:253:2:2,0:45,205:0.0079:2,0:1:0:24.5:1:0.03418:0:60:4:0.0082:0:1 -2 47643274 . C T 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64265;SOR=0.43609;LSEQ=GAAATGTACAGTTGAACATA;RSEQ=GGATTAAGAGGTTGAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:4,0:24,0:0.1429:1,0:22.5:1:31:1:1:0:60:8:0.1429:0:1.5 0/1:15:1:1,0:14,0:0.0667:1,0:19:0:32:0:1:0:60:2:0.0667:0:1 -2 47643457 . G A 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTGTTGAAGATACCACTG;RSEQ=CTCTCAGTCTCTGGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:417,185:0:2,0:25.9:1:31.3:1:1:0:60:65.889:1:0:0.1 0/1:561:34:24,10:332,195:0.0606:2,2:20.6:1:29:1:0.46352:1.41:60:68:0.0612:0:1.1 -2 47643746 . GT G 74 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.67563;SOR=1.58463;LSEQ=GAACTCATTTTTTTAAATAA;RSEQ=TTTTTTTTTTTCACTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:5:0,5:0,32:0.1351:1,0:38.6:1:32.2:1:1:0:60:10:0.1351:0:0 0/1:15:3:0,3:0,12:0.2:0,0:44.3:1:32:1:1:0:60:6:0.2:0:0 -2 47656801 . G A 168 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04858;SOR=0.46949;LSEQ=TGGAATTTTGAGCTGATTTA;RSEQ=TTGAGACTTACGTGCTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:48:47,1:28,0:0.6316:1,1:23:1:30.1:1:1:0:60:96:0.6316:0:1.1 0/1:54:24:22,2:27,3:0.4444:2,2:24.9:1:30.5:1:1:1.22:60:48:0.4528:0:1.2 -2 47656871 . T C 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTACATTAATTCAAGTTAA;RSEQ=TTATTTCAGATTGAATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:257,78:0:2,0:24.2:1:30.6:1:1:0:60:29.455:1:0:0.2 0/1:304:35:25,10:190,79:0.1151:2,2:23.5:1:30.9:1:1:1.04:60:70:0.1163:0:1.1 -2 47657117 . T A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62559;SOR=0.37122;LSEQ=TTTTTTTGTTTTCCTTCAAC;RSEQ=CATACAATATATACTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:3:1,2:29,181:0.0141:2,2:11:1:29:1:0.36729:3.10:60:6:0.0146:0:1 0/0:190:1:1,0:41,148:0.0053:2,0:1:0:25:0:0.22105:0:60:2:0.0054:0:1 -2 47657134 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17993;SOR=Inf;LSEQ=AACTCATACAATATATACTT;RSEQ=GCAATGTGCTGTCCTCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:7,142:0:1,0:27:1:30.4:1:1:0:60:20.286:1:0:0.2 0/1:111:2:1,1:10,99:0.018:2,2:16.5:1:29:1:0.18919:9.49:60:4:0.0187:0:1 -2 47672475 . T A 102 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63153;SOR=0.46572;LSEQ=GTGTATTATTAGTGGGAAGC;RSEQ=TTGAGTGCTACATCATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:11,0:14,1:0.4231:1,0:19:1:29.5:1:1:0:60:10:0.4:0:1.3 0/1:4:1:1,0:3,0:0.25:0,0:25:0:32:0:1:0:60:2:0.25:0:1 -2 47672569 . G A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00185;SOR=0.29785;LSEQ=AATAGTAACTTTGGAGACCT;RSEQ=CTGTACTATTTGTACCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:69:68,1:26,0:0.7263:1,1:24.5:1:28.5:1:1:0:60:68:0.7234:0:1.1 0/1:41:18:17,1:23,0:0.439:1,1:20.2:1:29:1:0.43902:0:60:36:0.439:0:1.1 -2 47673515 . T C 27 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTTTTCCATGTAGAGTTCTT;RSEQ=GCAGGAGGAGGTTAGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:1:27.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:20.5:1:27:0:1:0:60:4:1:0:0 -2 47690404 . T C 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0271;SOR=0.35502;LSEQ=CTGTCCCCAAGATGATGACT;RSEQ=CACATCTCTGTCAAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:49:0,49:1,30:0.6125:1,1:27.2:1:31.4:1:0.3875:0:60:48:0.6076:0:2.9 0/1:28:10:0,10:1,17:0.3571:1,0:17.2:1:30.2:1:1:0:60:20:0.3571:0:2.4 -2 47690408 . A G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02977;SOR=0.32531;LSEQ=CCCCAAGATGATGACTTCAC;RSEQ=TCTCTGTCAAACAGAAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:45:0,45:1,30:0.5921:1,1:27.7:1:32.4:1:0.40789:0:60:44:0.5867:0:3.1 0/1:22:7:0,7:1,14:0.3182:1,0:22:1:30.9:1:1:0:60:14:0.3182:0:3 -2 47690411 . T C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04629;SOR=0.34128;LSEQ=CAAGATGATGACTTCACATC;RSEQ=CTGTCAAACAGAAATCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:43:0,43:1,28:0.5972:1,1:27.7:1:31.9:1:0.40278:0:60:86:0.5972:0:3.1 0/1:21:7:0,7:1,13:0.3333:1,0:21.1:1:30:1:1:0:60:14:0.3333:0:2.9 -2 47693706 . G T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.85934;SOR=1.1131;LSEQ=TTGTCATATAATAACAGTAT;RSEQ=TTTTTCACTATTTAAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:39:39,0:50,0:0.4333:1,1:24.9:1:30.2:1:1:0:60:38:0.427:0:1.3 0/1:50:23:22,1:27,0:0.46:1,1:23.9:1:30.8:1:0.46:0:60:46:0.46:0:1.1 -2 47693788 . A T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10365;LSEQ=TACTTTTTCTTTTCTTCTTG;RSEQ=TTATCAAGGCTTGGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:210:150,60:248,97:0.3784:2,2:21:1:29.4:1:0.9228:1.02265:60:51.5:0.378:0:1.2 0/1:422:25:19,6:276,121:0.0592:2,2:19:1:29.7:1:0.65389:1.39:60:50:0.0601:0:1.1 -2 47693959 . G A 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.51012;LSEQ=TACCAACAGGTTTGCAAGTC;RSEQ=TTATTATATTTTTAACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:686:326:112,214:133,227:0.4752:2,2:24.6:1:30.6:1:0.52339:1.11931:60:652:0.4766:0:1.1 0/1:649:205:77,128:170,273:0.3159:2,2:25.1:1:29.5:1:0.86229:1.03511:60:204:0.3168:0:1.1 -2 47694037 . T C 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTATGATAAGTTTTACTAA;RSEQ=GTAGTCATCAGGTAAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:2,152:0:1,0:25.3:1:30.4:1:1:0:60:153:1:0:0.2 0/1:118:39:2,37:1,78:0.3305:1,2:23.9:1:30.5:1:0.25356:4.16:60:78:0.3333:0:1.1 -2 47694252 . C G 57 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTATTAGAGCTAGTTCCC;RSEQ=CTCATATCTCTGCTTTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:0,4:0,6:0.4:0,0:21:1:28.5:1:1:0:60:3:0.3333:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47694312 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTTTTTTTTTTTGGAGA;RSEQ=GGAGTCTCGCTCTGTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:37:1:31:0:1:0:54:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47698254 . A T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08494;SOR=Inf;LSEQ=GTCACCTGGCTTTTGGTAAC;RSEQ=GAAGAAAAATCATGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:29,189:0:2,0:23.3:1:31:1:1:0:60:217:1:0:0.3 0/1:172:3:0,3:24,145:0.0174:2,0:18.7:1:31.3:1:1:0:60:6:0.0176:0:1 -2 47698308 . A G 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1544;SOR=0.58901;LSEQ=TTATTTTCGCAAGCCATTAC;RSEQ=TTCTGACTATTTAATATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:50:0,50:0,36:0.5814:1,1:23.7:1:32.4:1:1:0:60:100:0.5814:0:1.2 0/1:49:22:0,22:0,27:0.449:1,1:22.5:1:31.7:1:1:0:60:44:0.449:0:1 -2 47698384 . G A 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66533;SOR=0.64874;LSEQ=AGTAGGACACATAACTGGAA;RSEQ=TTACTCTTGCACATAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:0.6111:0,0:18.4:1:32.5:1:1:0:60:22:0.6111:0:1.7 1/0:6:3:0,3:0,3:0.5:0,0:34.3:1:30.7:1:1:0:60:6:0.5:0:1 -2 47701705 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCTGGGTTCATGCAATT;RSEQ=TGGTGCCTCAGCCTCCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:10.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47702102 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16498;SOR=Inf;LSEQ=GGGATTAAATGTATTTTTAC;RSEQ=GCTTATATCTGTTTATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:138,6:0:1,0:26.3:1:30.1:1:1:0:60:288:1:0:0.1 0/1:99:2:2,0:89,8:0.0202:2,0:37.5:1:28.5:1:1:0:60:4:0.0202:0:1 -2 47702446 . G T 36 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.88066;LSEQ=TTGGGCTTTGTGGGGGTAAC;RSEQ=TTTTGTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:5:0,5:26,144:0.0272:2,0:22.8:1:15.6:1:1:0:53:0.25:0.0074:0:3.8 0/1:125:3:0,3:24,91:0.024:2,0:15.3:1:21.3:1:1:0:39:2:0.0204:0:2.7 -2 47702493 . T TA 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.19501;SOR=Inf;LSEQ=TCTTGGAGTAGAAATATATT;RSEQ=AAAATTGATGGAGAAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:0,55:0:1,0:24.6:1:28.3:1:1:0:60:54:1:0:1 0/1:44:2:0,2:4,38:0.0455:2,0:37.5:1:32:0:1:0:60:4:0.0488:0:0 -2 47703241 . A G 108 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTCTAGGCCACAGTCA;RSEQ=ATTACAGGTATATTTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:12,0:4,0:0.75:0,0:29.2:1:30.3:1:1:0:60:11:0.7333:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47703290 . G A 87 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATGAAAGGCCCAGTATC;RSEQ=GTTTGTCTGAAGATATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:7,0:9,0:0.4375:0,0:21.7:1:31.3:1:1:0:60:14:0.4375:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47703379 . C T 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAGGCTGTGGTTCTGC;RSEQ=TTTATATGCTATGTCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:108:108:107,1:0,0:1:0,1:24.1:1:31.3:1:1:0:60:35:1:0:1.1 1/1:51:51:51,0:0,0:1:0,1:24:1:31.9:1:1:0:60:102:1:0:1 -2 47703500 . T C 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.28195;SOR=1.18859;LSEQ=GCTTTCTGATATAATTTGTT;RSEQ=TGTAGGCCCCAATATGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:793:103:63,40:426,264:0.1299:2,2:24.5:1:31.2:1:0.91386:1.02451:60:102:0.1293:0:1.1 0/1:637:96:72,24:315,226:0.1507:2,2:23.9:1:31.5:1:0.00208:2.15:60:192:0.1531:0:1.1 -2 47703766 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15356;SOR=Inf;LSEQ=GTATGTCTCTGTCCTGTGAG;RSEQ=AGGAAAAGTATATTTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:34,198:0:2,0:24:1:30.1:1:1:0:60:57:1:0:0 0/1:150:2:1,1:25,123:0.0133:2,2:31.5:1:29.5:1:0.31758:4.84:60:4:0.0134:0:1 -2 47703885 . G A 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23465;SOR=0.34815;LSEQ=TCTTAAAAGAGTGATTGATG;RSEQ=TAGCTACGGAAAACTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:19:0,19:1,7:0.7037:2,1:28.7:1:31.7:1:0.2963:0:60:38:0.7037:0:1.1 0/1:9:4:0,4:0,5:0.4444:0,0:8.8:1:31.5:1:1:0:60:8:0.4444:0:1 -2 47703984 . T G 62 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATCTCCACTACCATGTT;RSEQ=TTGCTTGGACTGTTCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:16.5:1:31:1:1:0:60:8:0.5:0:2.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47704027 . G C 86 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGAATGGTCCTTCTTGCC;RSEQ=TTTATCCAACTTCTTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:17.4:1:30.7:1:1:0:60:14:1:0:2.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47708066 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18665;SOR=Inf;LSEQ=CTCTATTATTACATAAACAG;RSEQ=ACACTAAGATGAAGGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:34,176:0:2,0:22.2:1:31.2:1:1:0:60:104:0.9952:0:0.2 0/1:161:2:1,1:33,126:0.0124:2,2:14.5:1:25:1:0.3788:3.78:60:4:0.0124:0:1.5 -2 47709704 . T C 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52688;SOR=1.93621;LSEQ=GCACACATAAATAATAAATA;RSEQ=GTTCTTCAAATATTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:27.7:1:32.7:1:1:0:60:6:0.1429:0:1 0/1:4:1:1,0:3,0:0.25:0,0:16:0:33:0:1:0:60:2:0.25:0:1 -2 47709796 . T TA 81 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.69626;LSEQ=GTCTCTAAAAATATGAAAAA;RSEQ=AAAAAAAAAATTTTTTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:7:7,0:107,0:0.0614:1,0:27.7:1:28.9:1:1:0:60:14:0.0619:0:0.3 0/1:46:2:2,0:44,0:0.0435:1,0:20.5:1:25.5:1:1:0:60:4:0.0435:0:0 -2 47709807 . T A 132 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.01542;SOR=0.19343;LSEQ=TATGAAAAATAAAAAAAAAA;RSEQ=TTTTTAAATGTGTGATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:21:21,0:109,0:0.1591:1,1:20.5:1:30.1:1:1:0:60:20:0.1563:0:1 0/1:57:2:1,1:54,0:0.0351:1,2:18.5:1:31:1:0.03571:0:60:4:0.0357:0:1 -2 47710121 . AT A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14249;SOR=Inf;LSEQ=ATGGAATGAAGGTAATATTG;RSEQ=AAGCTATTGTCTGTAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:91,237:0:2,0:23.4:1:28.9:1:1:0:60:108.333:0.9969:0:0.1 0/1:200:2:1,1:52,146:0.01:2,2:5:1:30:1:0.46075:2.79:60:4:0.0102:0.005:0.5 -2 47739551 . A G 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.38543;LSEQ=TCGGCCAGAGAGACAGAACC;RSEQ=GGGCAGTGGTGAGCTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:455:301:84,217:43,110:0.6615:2,2:27.4:1:30.5:1:1:1.00983:60:74.25:0.6659:0:1.1 0/1:361:155:55,100:68,136:0.4294:2,2:24.7:1:29.6:1:0.73641:1.10:60:37.75:0.4302:0:1.3 -2 47739567 . C T 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=31.38285;LSEQ=AACCAGGGCAGTGGTGAGCT;RSEQ=TCATGACCTGGTGTCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:1:0,1:84,284:0.0027:2,0:21:0:13:0:1:0:60:0:0:0:3 0/1:267:21:6,15:67,177:0.0787:2,2:26.2:1:29.7:1:1:1.06:60:42:0.0811:0:2.1 -2 47740566 . T C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTCTTGGTTTTCTCCCA;RSEQ=ATCTCTGACCCTCTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:45:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 47887915 . TC T 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18528;SOR=0.20944;LSEQ=TTTGACATCTTTGATAGGTT;RSEQ=CCCAGCATCAAAATACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:3,1:16,1:0.1905:1,2:17:1:29.8:1:0.35238:4.76102:60:8:0.1905:0.0952:0.3 0/1:22:1:1,0:18,3:0.0455:2,0:13:0:32:0:1:0:60:2:0.0476:0:0 -2 47888014 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03158;LSEQ=CTTCAAAGAATGTATCTCTC;RSEQ=TCCTGTAGAGATATTAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:100:55,45:14,9:0.8065:2,2:26.7:1:30.4:1:0.64867:1.27026:60:99:0.8049:0:1.1 0/1:114:13:6,7:53,48:0.114:2,2:26.2:1:30.8:1:0.77178:1.28533:60:26:0.1161:0:1.1 -2 47888018 . T C 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=AAAGAATGTATCTCTCATCC;RSEQ=GTAGAGATATTAAATGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:67,56:0.016:2,2:25:1:26.5:1:1:1.1947:60:4:0.0163:0:2 0/0:117:0:0,0:58,58:0:2,0:22.9:1:29.9:1:1:0:60:57:1:0:0.4 -2 47888022 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21674;SOR=Inf;LSEQ=AATGTATCTCTCATCCTGTA;RSEQ=AGATATTAAATGATTAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:67,61:0:2,0:25.9:1:30.6:1:1:0:60:20.333:1:0:0.9 0/1:112:2:1,1:54,55:0.0179:2,2:13.5:1:27:1:1:1.02:60:4:0.0182:0:1 -2 47888040 . A C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00206;SOR=Inf;LSEQ=TAGAGATATTAAATGATTAG;RSEQ=CTTATTTGGTAAATTGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:60,63:0:2,0:27.3:1:28.8:1:1:0:60:23.6:1:0:0.8 0/1:109:8:4,4:49,52:0.0734:2,2:33:1:31.1:1:1:1.06:60:16:0.0762:0:1 -2 47888091 . CT C 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.82288;SOR=1.13255;LSEQ=TATTTTTTCTTTTTCTTTTT;RSEQ=TTTTTTTTTTTGAGACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:11:9,2:45,39:0.1146:2,2:28.6:1:28.9:1:0.10723:3.85:60:10:0.1064:0.0208:0.5 0/1:86:11:5,6:42,30:0.1279:2,2:22.4:1:32.3:1:0.51972:1.66929:60:22:0.1279:0.0116:0.3 -2 47888189 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22218;SOR=Inf;LSEQ=TCTGCCTCCTGGACTCAAGC;RSEQ=ATCCTCCTACCTCAACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:161,19:0:2,0:21.1:1:30.2:1:1:0:59.9:360:1:0:0.1 0/1:161:2:1,1:137,22:0.0124:2,2:19.5:1:27.5:1:0.26607:6.1126:60:4:0.0124:0:3 -2 47888212 . A T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62379;SOR=2.96506;LSEQ=CCTCCTACCTCAACCTCCCA;RSEQ=GTAGCTGGGACCACAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:0,1:205,90:0.0034:2,0:1:0:26:0:0.30743:0:60:2:0.0034:0:1 0/1:301:3:1,2:200,98:0.01:2,2:5:1:21.3:1:0.25704:4.06092:60:2:0.0068:0:2.7 -2 47888224 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37449;SOR=3.79265;LSEQ=ACCTCCCAAGTAGCTGGGAC;RSEQ=ACAGACTCATGCCACCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:1:0,1:235,142:0.0026:2,0:1:0:26:0:0.37831:0:60:2:0.0027:0:1 0/1:401:4:2,2:242,154:0.01:2,2:8.5:1:27.5:1:0.64495:1.56954:60:8:0.0102:0:1.3 -2 47888366 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50441;SOR=0;LSEQ=AATGTTATAAAAATCTAAAA;RSEQ=GTTATCAGTCATAATTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:15,184:0.01:2,2:15.5:1:33:1:0.15323:11.91:60:4:0.0101:0:1 0/0:162:0:0,0:20,142:0:2,0:18.9:1:30:1:1:0:60:161:1:0:0 -2 47905390 . C A 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTGCTTCATTTCCTAGGC;RSEQ=TGAAATTCATTGCTTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:832:0:0,0:414,417:0:2,0:26.2:1:31.3:1:1:0:60:82.1:1:0:0.3 0/1:806:38:21,17:393,375:0.0471:2,2:25.6:1:29.3:1:0.73999:1.18:60:76:0.0476:0:1.3 -2 47905398 . C A 214 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00473;LSEQ=CATTTCCTAGGCCTGAAATT;RSEQ=ATTGCTTGTGTACCCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:170:79,91:308,330:0.2104:2,2:26.3:1:29:1:0.72978:1.07498:60:55.667:0.2093:0:1.1 0/0:795:1:1,0:394,400:0.0013:2,0:1:0:25:0:0.49686:0:60:2:0.0013:0:2 -2 48010214 . C T 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54404;SOR=0;LSEQ=GGGGCCTGGCGCGCACCGCC;RSEQ=GCGCACGGCGAGGCGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:0.2632:1,0:21.8:1:33:0:1:0:60:10:0.2632:0:1 0/0:5:0:0,0:5,0:0:0,0:18:1:31.6:1:1:0:60:10:1:0:0.2 -2 48010481 . G A 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.06106;SOR=Inf;LSEQ=AAGGCGGCCGTGCCGCCGCT;RSEQ=CCCCCGGGGCCTCTCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:391:0:0,0:166,225:0:2,0:23.9:1:32:1:1:0:60:38.1:1:0:0.2 0/1:388:4:3,1:152,232:0.0103:2,2:9.8:1:26.3:1:0.30612:4.56:60:8:0.0106:0:1.3 -2 48010488 . G A 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=2.69339;LSEQ=CCGTGCCGCCGCTGCCCCCG;RSEQ=GGCCTCTCCTTCCCCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:32:17,15:145,199:0.0851:2,2:20.9:1:30.5:1:0.26467:1.55:60:64:0.0867:0:1.1 0/1:354:71:31,40:111,172:0.2006:2,2:24.8:1:30:1:0.50143:1.20:60:70:0.2023:0:1.2 -2 48010501 . C A 43 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18345;SOR=4.81239;LSEQ=GCCCCCGGGGCCTCTCCTTC;RSEQ=CCAGGCGGGGATGCGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:1:1,0:166,180:0.0029:2,0:1:0:26:0:0.48127:0:60:2:0.0029:0:1 0/1:291:4:3,1:130,157:0.0137:2,2:6.8:1:21.8:1:0.33489:3.61:60:3:0.0105:0:2.3 -2 48010548 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04703;SOR=Inf;LSEQ=GGCTGGGCCTGGGCCCAGGC;RSEQ=CTTGGCGCGCTCCGCGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:272,160:0:2,0:24.5:1:30.5:1:1:0:60:35:1:0:0.2 0/1:378:4:2,2:215,158:0.0106:2,2:20.8:1:29.8:1:1:1.35961:60:8:0.011:0:1.8 -2 48010555 . G T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.04257;SOR=Inf;LSEQ=CCTGGGCCCAGGCCCTTGGC;RSEQ=CGCTCCGCGTCACCGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:284,184:0:2,0:24.8:1:30.2:1:1:0:60:57.5:1:0:0.2 0/1:391:4:2,2:221,166:0.0102:2,2:33:1:28.3:1:1:1.33032:60:8:0.0106:0:2.3 -2 48010558 . C A 187 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCCAGGCCCTTGGCGCG;RSEQ=TCCGCGTCACCGCCCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:300,190:0:2,0:24.6:1:31.5:1:1:0:60:36.692:1:0:0.2 0/1:395:96:54,42:172,125:0.243:2,2:24.9:1:28.5:1:0.8127:1.07004:60:47:0.2442:0:1.3 -2 48010654 . C G 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGCGGGGTGGGGGTGGGGT;RSEQ=GAAGGCGGGGGCATAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:159,243:0:2,0:23.2:1:29.8:1:1:0:60:49.25:1:0:0.2 0/1:282:57:17,40:92,132:0.2021:2,2:20.6:1:30.5:1:0.13029:1.63714:60:114:0.2096:0:1.4 -2 48010676 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.26907;SOR=0;LSEQ=AAGGCGGGGGCATAGCGGCG;RSEQ=GGCGCTTGGAACCCGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:2,1:70,183:0.0117:2,2:16.3:1:24:1:0.19176:5.19:60:2:0.0079:0:2.7 0/0:183:0:0,0:52,131:0:2,0:22.7:1:29.6:1:1:0:60:60:1:0:0.4 -2 48010872 . C T 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46429;SOR=0;LSEQ=GAAGAGGGCTGCAGGGGAGA;RSEQ=GCGGAGAGTTCGGGCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:17:1:30.3:1:1:0:60:6:0.5:0:1 0/0:2:0:0,0:0,2:0:0,0:25.5:1:27.5:1:1:0:60:4:1:0:0 -2 48018081 . A G 219 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=91.53997;LSEQ=AACAGTTGTGACTTCTCACC;RSEQ=GGAGATTTGGTTTGGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:793:3:2,1:470,320:0.0038:2,2:21.3:1:26.7:1:1:1.36:60:6:0.0038:0:1 0/1:704:182:98,84:302,218:0.2585:2,2:27:1:29.2:1:0.33924:1.18712:60:35.4:0.2547:0:1.2 -2 48018281 . ATG A 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.68662;SOR=0.52302;LSEQ=AGGTAAGAGTCACTACTGCC;RSEQ=TGTGTGTGTTTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:4:1,3:81,243:0.0122:2,2:34.8:1:32:1:1:1:60:8:0.0128:0:0.5 0/0:313:2:1,1:112,199:0.0064:2,2:31:1:32:0:1:1.77:60:4:0.0066:0:0.5 -2 48018288 . T A 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=0.36443;SOR=3.13323;LSEQ=AGTCACTACTGCCATGTGTG;RSEQ=GTGTTTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:1:1,0:61,231:0.0034:2,0:1:0:29:0:0.2116:0:60:2:0.0034:0:1 0/1:284:3:2,1:100,181:0.0106:2,2:27:1:23.7:1:0.29363:3.60:60:2:0.0072:0:1.7 -2 48018314 . T A 191 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=2;SSF=0.31785;SOR=0.79017;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GAGAGAAACAGACAGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:69:10,59:18,121:0.3317:2,2:22.7:1:31.3:1:0.82988:1.14:60:138:0.3366:0:1.2 0/1:174:49:13,36:36,87:0.2816:2,2:25.1:1:29.7:1:0.85188:1.14497:60:48:0.2857:0:1.4 -2 48018322 . A C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1961;SOR=Inf;LSEQ=TGTGTGTGTGTGTGAGAGAA;RSEQ=CAGACAGACAGGCAGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:14,159:0:2,0:22.6:1:30.2:1:1:0:60:85.5:1:0:0.5 0/1:138:2:1,1:26,110:0.0145:2,2:12:0:29:1:0.35417:4.17:60:4:0.0148:0:2 -2 48022875 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52577;SOR=0;LSEQ=CCACCTAAGCCTCCCAAAAT;RSEQ=CTGGGATTACAGGCGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:2,0:45,0:0.0426:1,0:28.5:1:29:1:1:0:60:4:0.0426:0:1 0/0:28:0:0,0:28,0:0:1,0:22.5:1:31.9:1:1:0:60:56:1:0:0.7 -2 48022900 . A G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00031;SOR=4.89444;LSEQ=GATTACAGGCGTGAGCCACC;RSEQ=CACCTGGCATATATATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:34:34,0:45,0:0.4304:1,1:25.2:1:30.6:1:1:0:60:68:0.4359:0:1.2 1/0:38:30:30,0:8,0:0.7895:0,1:26.4:1:30.2:1:1:0:60:60:0.7895:0:1.1 -2 48022981 . G T 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00927;SOR=1.68425;LSEQ=TTGAACTGCTGGGATTACAG;RSEQ=CGTGAGCCTCTGCACCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:55:42,13:275,64:0.1396:2,2:25.1:1:29.7:1:0.46289:1.32896:60:110:0.1429:0:1.2 0/1:312:67:47,20:178,67:0.2147:2,2:23.7:1:28.5:1:0.75866:1.13006:60:32.5:0.2117:0:1.1 -2 48023000 . G T 50 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09864;SOR=5.99266;LSEQ=GGCGTGAGCCTCTGCACCCG;RSEQ=CCCTTATTGTTTATAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:1:0,1:398,153:0.0018:2,0:1:0:25:0:0.27899:0:60:2:0.0019:0:1 0/1:464:5:1,4:303,156:0.0108:2,2:6.2:1:21.8:1:0.05025:7.73488:60:4:0.0088:0:1.4 -2 48023115 . T C 274 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00226;SOR=0.77188;LSEQ=AGAGCAATGCAACGTGCAGA;RSEQ=GAAGCCTTAAATAAAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1533:473:253,220:577,480:0.3085:2,2:23:1:30.9:1:0.69783:1.04529:60:117.25:0.3098:0:1.1 0/1:1296:332:174,158:514,450:0.2562:2,2:22.8:1:30.4:1:0.79882:1.03718:60:82:0.2553:0:1.2 -2 48025694 . C T 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=0.23839;LSEQ=TCATAAGTTGAACTGTCTTA;RSEQ=ATTATGGTTTTCCAAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:41:39,2:96,10:0.2789:2,1:24.3:1:31.1:1:0.51094:2.02:60:82:0.2808:0:1.6 0/1:119:10:9,1:94,15:0.084:2,2:20.9:1:30.2:1:1:1.43:60:20:0.0855:0:1.1 -2 48025729 . T C 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24858;SOR=Inf;LSEQ=AATTTTGATTTGTTTTTAAA;RSEQ=ACTCTTTCCTTGCCTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:216,42:0:2,0:24.1:1:30.7:1:1:0:60:257:1:0:0.5 0/1:261:3:2,1:196,61:0.0115:2,2:25.3:1:28.7:1:0.55996:1.60329:60:6:0.0116:0:2.3 -2 48025764 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13647;LSEQ=TGGCAGGTAGGCACAACTTA;RSEQ=GTAACAGATAAGAGTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:122:86,36:231,102:0.2681:2,2:23.6:1:30.5:1:0.90841:1.05:60:121:0.2695:0:1.3 0/1:526:25:17,8:321,180:0.0475:2,2:21.5:1:29.1:1:0.83162:1.19:60:24:0.046:0:1.4 -2 48026289 . C T 144 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=33.78723;LSEQ=AGGAGGAGGCCTGATCACCC;RSEQ=GATTTTGATGCATCTACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:653:1:0,1:315,337:0.0015:2,0:1:0:25:0:1:0:60:2:0.0016:0:1 0/1:588:29:13,16:270,289:0.0493:2,2:25:1:29.8:1:0.84928:1.14958:60:58:0.0495:0:1.1 -2 48027216 . G A 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05262;SOR=7.13008;LSEQ=AAAAAATGCCTTATTGATCA;RSEQ=GAGCTTTTATCAATGGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:665:1:1,0:305,359:0.0015:2,0:1:0:25:0:0.46015:0:60:2:0.0015:0:1 0/1:564:6:5,1:288,270:0.0106:2,2:6.5:1:24.8:1:0.2184:4.68:60:5:0.009:0:1.3 -2 48028337 . T C 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=TCTCAGGCTTTGATAAGTAG;RSEQ=GCTGTTTGCCAGCTGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:80,238:0:2,0:24.7:1:29.9:1:1:0:60:52:1:0:0.2 0/1:308:12:4,8:75,221:0.039:2,2:23.9:1:31.9:1:0.51191:1.47:60:24:0.039:0:1.1 -2 48028465 . C T 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14877;SOR=0;LSEQ=AATTTAAGTTACTTGAAACT;RSEQ=GCTTTTATCTTAGTAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:0,21:0.1923:1,0:23.4:1:31.8:1:1:0:60:10:0.1923:0:1 0/0:13:0:0,0:0,13:0:1,0:28.6:1:29.3:1:1:0:60:12:1:0:0 -2 48030458 . G C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.66976;LSEQ=GGACTGTAATTGAAAGTTAT;RSEQ=TCTTATAATGAAATGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:108:99,9:99,9:0.4977:2,2:21.5:1:31.3:1:1:1:60:216:0.5023:0:1 1/0:168:122:112,10:41,5:0.7262:2,2:22.2:1:31.3:1:0.55751:1.36:60:60:0.7229:0:1.1 -2 48030629 . G T 180 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTCGCCCAGTAATTCTGTT;RSEQ=CCGGAAGATACCCCCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:73:30,43:599,691:0.0536:2,2:24.7:1:29.1:1:0.4:1.2423:60:23.333:0.0524:0:1.1 0/0:1439:0:0,0:678,760:0:2,0:25.4:1:31.4:1:1:0:60:48.586:1:0:0.2 -2 48030639 . AC A 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.67404;SOR=1.1006;LSEQ=TAATTCTGTTGCCGGAAGAT;RSEQ=CCCCCCCTTCTTAGAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1336:43:17,26:583,710:0.0322:2,2:31.2:1:30.5:1:0.53459:1.25563:60:42:0.032:0.0022:0.4 0/1:1416:50:22,28:630,732:0.0353:2,2:31:1:30.2:1:0.77484:1.09528:60:49:0.0354:0.0021:0.1 -2 48030838 . A T 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGACAGGTAACTGATTCTT;RSEQ=AAGTTTTGTTATCAGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:54,151:0:2,0:25.1:1:29.4:1:1:0:60:101.5:1:0:0.1 0/1:214:85:25,60:38,91:0.3972:2,2:24.4:1:27.9:1:1:1.00219:60:41.5:0.3934:0:1.1 -2 48031975 . G A 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=3e-04;SOR=Inf;LSEQ=TGCCTAGCTCTTACGTAAGG;RSEQ=TTCATAAGAAAGACAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:197,40:0:2,0:21.9:1:31.3:1:1:0:60:78:1:0:0.1 0/1:194:10:8,2:145,39:0.0515:2,2:16.6:1:26.2:1:1:1.08:60:9:0.0474:0:1.4 -2 48032312 . G A 124 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=47.31831;LSEQ=CACTTTTTAAGAACTGCATA;RSEQ=TCTCTCTCTCTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:1:0,1:1,46:0.0208:1,0:31:0:29:0:1:0:60:2:0.0256:0:2 1/0:37:19:0,19:1,17:0.5135:1,1:16.7:1:29.3:1:0.48649:0:60:18:0.6207:0:1.3 -2 48032572 . C T 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02696;SOR=0;LSEQ=GGTGATCTGCTTGCCTCGGC;RSEQ=TCCCAAAGTGCTGGGATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:5,1:11,3:0.3:2,2:22:1:28.7:1:1:1.34:56.7:5:0.2632:0:2 0/0:15:0:0,0:14,1:0:1,0:22.7:1:30.9:1:1:0:60:30:1:0:0.8 -2 48032613 . G A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=12.53454;LSEQ=AGGCGTGAGCCACCGTGCCC;RSEQ=GCCAATAATTGCATAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:7,2:19,1:0.3103:1,2:19.6:1:31.3:1:0.22003:5.07055:57.8:18:0.3103:0:1.7 1/1:21:18:17,1:3,0:0.8571:0,1:30.1:1:29.4:1:1:0:60:36:0.8571:0:1.1 -2 48032874 . ACTAT A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0;SOR=3.97713;LSEQ=ATTAAACTTCTCATTTGAAG;RSEQ=CTATCTTAAAAACATTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:134:35,99:119,249:0.2669:2,2:26.3:1:31.8:1:0.19102:1.35102:60:133:0.2671:0.0259:0.4 1/0:495:293:90,203:80,119:0.5919:2,2:26.4:1:31.8:1:0.03368:1.51498:60:586:0.5955:0.0202:0.3 -2 48032937 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.93354;LSEQ=GAAGATTATCTGAAGTACAT;RSEQ=TAAACAATATGAATGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:56:3,53:4,99:0.3522:1,2:21.8:1:32.2:1:0.69763:1.40:60:55:0.3548:0:1 1/0:126:86:1,85:3,36:0.6825:2,1:23.4:1:32.6:1:0.08959:6.9615:59.9:85:0.68:0:1.1 -2 48032955 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.17891;SOR=Inf;LSEQ=ATTTAAACAATATGAATGTT;RSEQ=TTAGAGCACGCACTCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:4,114:0:1,0:23.4:1:30.8:1:1:0:60:117:1:0:0.3 0/1:87:2:0,2:1,84:0.023:1,0:7.5:1:32.5:1:1:0:60:4:0.023:0:2 -2 48033195 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07498;SOR=Inf;LSEQ=ATGGGCTGCTAAGCAGACTC;RSEQ=TGTAGCTAAACAAGGCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:55,2:0:1,0:23.8:1:30.3:1:1:0:60:56:1:0:0.1 0/1:22:2:2,0:20,0:0.0909:1,0:37:1:29.5:1:1:0:60:4:0.0909:0:1 -2 48033271 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21001;SOR=Inf;LSEQ=ATGTTGCTTTTCTGTCCTAG;RSEQ=ATTTTTGTTTTAATTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:157,15:0:2,0:24:1:32.3:1:1:0:60:171:1:0:0 0/1:146:2:1,1:125,19:0.0137:2,2:18:1:26:1:0.25602:6.43797:60:4:0.0139:0:1 -2 48033272 . ATTTTTGTTTTAATTCCT A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=6.000;MSILEN=1;SSF=0;SOR=0.04894;LSEQ=TGTTGCTTTTCTGTCCTAGC;RSEQ=TTTTTGTTTTAATTCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:52:46,6:119,14:0.2796:2,2:24:1:31:1:0.79802:1.10806:60:51:0.2757:0.0538:0.1 0/1:162:3:3,0:135,24:0.0185:2,0:34.3:1:32:0:1:0:60:6:0.0186:0:0 -2 48033502 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCCTAGGACATATGGTAT;RSEQ=TGCAAATTGTTTTTTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:134,267:0:2,0:23.6:1:32:1:1:0:60:99.25:1:0:0.2 0/1:340:17:7,10:106,217:0.05:2,2:15.9:1:28.1:1:0.59791:1.43:60:34:0.0509:0:1.3 -2 48033549 . CTC TCTG 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.06211;LSEQ=TCGGTTTTTTGAGAGGGCAC;RSEQ=TTGCTAGCACATGTATCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:79:35,44:78,128:0.2743:2,2:24.4:1:31.1:1:0.34521:1.30:60:78:0.2766:0.066:1 0/1:175:4:1,3:73,98:0.0229:2,2:17:1:32.1:1:0.6387:2.22541:60:8:0.0237:0.0057:1 -2 48033551 . C G 218 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTTGAGAGGGCACTTCT;RSEQ=TTGCTAGCACATGTATCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:82,124:0:2,0:21.3:1:32:1:1:0:60:205:1:0:0.1 1/0:176:118:50,68:25,29:0.6705:2,2:25.6:1:31.8:1:0.7406:1.17132:60:117:0.6842:0:1.1 -2 48033791 . GTAAC G 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=3.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=CAGTCACTACGATTATTTCG;RSEQ=TAACTAACTATAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:0:0,0:207,317:0:2,0:23.2:1:28.7:1:1:0:60:523:1:0:0.1 0/1:474:17:7,10:173,284:0.0359:2,2:28.9:1:31.2:1:0.80272:1.15:60:34:0.0362:0.0042:0.3 -2 48033829 . C G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TGGAATTATAACTAACTGAC;RSEQ=TTAAGTTTCAAAGAAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:116,228:0:2,0:27.5:1:31.3:1:1:0:59.9:42:1:0:0.2 0/1:273:12:2,10:99,162:0.044:2,2:32.8:1:30.4:1:0.22049:3.04526:60:24:0.0441:0:1 -2 48033846 . CAGTAAA C 215 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACCTTAAGTTTCAAAGAAA;RSEQ=AGGGGAAGGGATGATGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:107:42,65:67,128:0.3531:2,2:24.7:1:32:1:0.45254:1.23:59.7:52.5:0.3559:0.0462:0.3 0/0:206:0:0,0:84,122:0:2,0:25.1:1:30.5:1:1:0:60:40.2:1:0:0.3 -2 48033909 . A T 58 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91087;LSEQ=ACTTTTTTTTTTTTTTTTTT;RSEQ=ATTTTAAGGGAAGTTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:9:6,3:232,138:0.0234:2,2:11.7:1:18.3:1:1:1.19:59.2:0.8:0.0119:0:1.3 0/1:374:8:4,4:220,143:0.0214:2,2:7.6:1:20.8:1:0.71754:1.53658:60:3:0.0195:0:1.6 -2 49394705 . T G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.68644;LSEQ=TAGCTGACAAGAAAGACAGG;RSEQ=AGAGGATATACAGAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:510:72:37,35:227,210:0.1412:2,2:25.6:1:30.6:1:1:1.02248:60:71:0.1406:0:1.1 0/1:368:178:96,82:90,99:0.4837:2,2:25.9:1:31.1:1:0.25099:1.29:60:356:0.4917:0:1.1 -2 49394735 . A G 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00046;SOR=2.48031;LSEQ=ACAGAGAAAAATAGTCTACT;RSEQ=AAGTCTTTGTACGGACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:26:12,14:221,277:0.0496:2,2:28.7:1:32:1:1:1.07:60:52:0.0501:0:1.2 0/1:366:42:17,25:141,181:0.1148:2,2:29.4:1:31.4:1:0.74235:1.14517:60:84:0.1157:0:1.1 -2 50178087 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26364;SOR=0;LSEQ=GACCATAAATCAGCTGTCTG;RSEQ=TTGGGAAAAAGGCAGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:1,2:167,103:0.011:2,2:21.7:1:29:1:0.56083:3.2284:60:6:0.0113:0:1 0/0:205:0:0,0:124,81:0:2,0:25:1:31.5:1:1:0:60:50.25:1:0:0.4 -2 50178130 . AT A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.13708;SOR=0;LSEQ=AGCCATTCAATTTTCTTCGA;RSEQ=TTTTTTCAGCTGTTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:4:2,2:190,182:0.0106:2,2:27.8:1:30.5:1:1:1.04385:60:8:0.0107:0:0 0/0:288:0:0,0:143,145:0:2,0:26.1:1:29.7:1:1:0:60:71:1:0:0.7 -2 50178151 . A T 221 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTTTCAGCTGTTTAAAA;RSEQ=GTATGCAATGGTTCCAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:185,195:0:2,0:25.4:1:30.5:1:1:0:60:189:1:0:0.1 1/0:291:181:86,95:55,55:0.622:2,2:25.2:1:29.6:1:0.71749:1.10427:60:59.333:0.6202:0:1.2 -2 50178165 . C A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0915;SOR=Inf;LSEQ=TTAAAAAGTATGCAATGGTT;RSEQ=CAGAACCACTAAAGTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:165,191:0:2,0:25.5:1:30.6:1:1:0:60:43.5:1:0:0.1 0/1:293:3:3,0:136,154:0.0102:2,0:10:1:20.3:1:0.10555:0:60:2:0.0069:0:2 -2 50178197 . ACT A 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00372;SOR=Inf;LSEQ=AAGTGGGTTTGAGTAGAAGA;RSEQ=CTGCCGTGGTAAAGAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:99,164:0:2,0:24.2:1:32.1:1:1:0:60:130.5:1:0:0.1 0/1:218:7:1,6:87,124:0.0321:2,2:26:1:32.8:1:0.24588:4.18791:60:14:0.0327:0.0092:0.9 -2 51288299 . T C 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TTTGATTAAATCAACAACTT;RSEQ=TTAAATAAAAGTACCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:164,1:0:1,0:23.7:1:30:1:1:0:60:26.5:1:0:0.1 0/1:93:10:10,0:81,2:0.1075:1,0:22.9:1:32:1:1:0:60:20:0.1075:0:1 -2 51288348 . C CA 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.70222;SOR=1.36143;LSEQ=ATTAAAGACAACTTTCTCAA;RSEQ=AAAAAAAAGGACATTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:3:3,0:327,68:0.0075:2,0:33.7:1:29.3:1:1:0:60:6:0.0076:0:0 0/1:293:3:2,1:223,66:0.0102:2,2:17:1:28.7:1:0.5439:1.68596:60:6:0.0104:0:0.7 -2 51288460 . C G 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22121;LSEQ=CAGGATGCCTGCCTTTAACA;RSEQ=TGCTATTCAACATTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:392:188,204:318,297:0.3889:2,2:24:1:31.7:1:0.27188:1.16165:60:34.636:0.3837:0:1.3 0/1:738:91:41,50:332,315:0.1233:2,2:26.4:1:30.1:1:0.31361:1.28488:60:10.375:0.115:0:1.4 -2 51288569 . A G 232 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=CACACATATTTTATAGATAG;RSEQ=TAGATGGTATCCAAGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1337:0:0,0:810,524:0:2,0:24:1:30:1:1:0:59.2:48.407:0.9977:0:0.4 0/1:1126:227:139,88:515,382:0.2016:2,2:24.6:1:29.7:1:0.32761:1.17:59.9:9.81:0.1902:0:1.3 -2 51288710 . A C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10605;LSEQ=GCAAAGTTGCGGGGTACAAG;RSEQ=TTGATACTCAAAAATCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1202:485:153,332:222,494:0.4035:2,2:25.5:1:31.7:1:0.84924:1.03:60:47.5:0.4022:0:1.1 0/1:957:64:22,42:315,578:0.0669:2,2:24.2:1:31.5:1:1:1.04038:60:63:0.0669:0:1.2 -2 52993022 . G T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=AGCAGCTGTGGAAGTCTGCA;RSEQ=CCAGAGTGCCTCTTCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:36:0:29.5:1:1:1.22474:60:4:0.1818:0:1 0/0:8:0:0,0:4,4:0:2,0:30.5:1:33.1:1:1:0:60:16:1:0:0.1 -2 52993507 . G C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=GAATCAGATGAATAGGGCCT;RSEQ=AAGTGAATCCCCAGCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:31:1:32.2:1:1:0:60:10:1:0:0.2 0/1:10:2:1,1:4,4:0.2:2,2:18.5:1:32.5:1:1:1:60:4:0.2:0:1 -2 52993657 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16471;SOR=Inf;LSEQ=CCAAAACTAGACAAACTCAC;RSEQ=ATAATGAGAAAGAGTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:14,16:0:2,0:25.8:1:29.5:1:1:0:60:29:1:0:0.6 0/1:21:2:2,0:8,9:0.0952:2,0:21:1:25.5:1:0.47368:0:60:4:0.1111:0:1.5 -2 52993660 . A G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.77016;SOR=1.30853;LSEQ=AAACTAGACAAACTCACGAT;RSEQ=ATGAGAAAGAGTCAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:5,8:7,7:0.4815:2,2:32.5:1:30.2:1:0.70357:1.57214:60:12:0.4615:0:1.2 1/0:20:11:5,6:4,5:0.55:2,2:26.5:1:27.9:1:1:1.04:60:4.5:0.5:0:1.6 -2 52993673 . C CA 49 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.60386;SOR=0.32306;LSEQ=TCACGATAATGAGAAAGAGT;RSEQ=AAAAAAAAAAATGCTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:6,10:0.1579:2,2:39.3:1:31:1:1:1.18873:60:6:0.1765:0:0.7 0/1:18:1:0,1:9,8:0.0556:2,0:19:0:32:0:1:0:60:2:0.0625:0:0 -2 52994119 . G A 28 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=ACGAAGCCTTCAAGAAATAT;RSEQ=GGACTTTATAAAAAGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:30:1:32.2:1:1:0:60:12:1:0:0.2 1/1:2:2:1,1:0,0:1:0,2:33.5:1:28:1:1:0:60:4:1:0:1 -2 54256901 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23142;SOR=Inf;LSEQ=GCCAACAGCATGCTGGGGAA;RSEQ=ATTGTAGGCTCTTCCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:26,22:0:2,0:32.1:1:31.6:1:1:0:60:47:1:0:0.3 0/1:45:2:1,1:21,22:0.0444:2,2:35:1:29:1:1:1.05:60:4:0.0444:0:1 -2 54257795 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.175;SOR=Inf;LSEQ=GAATATCTACCCAGCGCCTC;RSEQ=CCTCTCTCCCTTTGTGTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:22.6:1:29.6:1:1:0:60:18:1:0:0.3 0/1:7:2:1,1:3,2:0.2857:2,2:47.5:1:30:1:1:1.41418:60:4:0.2857:0:1 -2 54257826 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=TTTGTGTTCGTTATTTTGGC;RSEQ=AATTACTGGAAGACGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:43.5:1:30.5:1:1:1.41:60:4:0.2857:0:1 0/0:5:0:0,0:2,3:0:2,0:17.8:1:29:1:1:0:60:10:1:0:0.4 -2 54652827 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.21142;SOR=Inf;LSEQ=CAACAGCAGCACCAGCAGCA;RSEQ=CAAGATGAGAAGGCTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:27.4:1:31.3:1:1:0:60:36:1:0:0.2 0/1:32:2:1,1:12,18:0.0625:2,2:41.5:1:26:0:1:1.48:60:4:0.0645:0:1 -2 54652923 . C T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=CTCAGAAATAACTGATGGGA;RSEQ=AGTGACAGTAGCTGATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:15.5:1:27:1:1:0:60:4:0.2222:0:1 1/1:1:1:0,1:0,0:1:0,0:3:0:28:0:1:0:60:2:1:0:1 -2 54659980 . C G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGAACAGCCCATTCCCT;RSEQ=TTTGTTTCAACTTTGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:10.3:1:31:1:1:0:60:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 54660456 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24189;LSEQ=CCTAAATGTTTCCTTCCAAT;RSEQ=CTTTCATGTATGATGTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:96:75,21:116,29:0.3967:2,2:23.8:1:28.2:1:0.74744:1.11947:60:95:0.4008:0:1.3 0/1:190:26:18,8:116,46:0.1368:2,2:21.2:1:28:1:0.81752:1.12007:60:52:0.1376:0:1.4 -2 54660484 . G A 148 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.03505;LSEQ=GTATGATGTTAGGGATCTGC;RSEQ=TGTTCATAGGCTTCACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:31:22,9:242,95:0.0842:2,2:26.1:1:30:1:1:1.04199:60:30:0.0843:0:1.3 0/0:312:1:1,0:194,117:0.0032:2,0:36:0:28:0:1:0:60:2:0.0033:0:1 -2 54660542 . C T 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04567;SOR=0.7758;LSEQ=CAGCCATTCCCTGGGGCCCA;RSEQ=GACCAGTGACTACTAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:609:411:222,189:106,92:0.6749:2,2:26.1:1:30.3:1:0.931:1.02:60:57.714:0.6722:0:1.2 1/0:522:322:176,146:97,102:0.6169:2,2:26:1:29.7:1:0.2066:1.27:60:79.5:0.6139:0:1.2 -2 55685927 . C A 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGTCAGGAGATCGAGAC;RSEQ=AGCCTATCCAACATGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:30:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:38:0:27:0:1:0:60:2:1:0:1 -2 55687290 . G C 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TTTCTGTATCGTGATTCCTC;RSEQ=GTCTCGAGAAATGGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:19:1:30.3:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:0:0,0:10:0:31:0:1:0:60:2:1:0:0 -2 55687526 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49903;SOR=0;LSEQ=TCTACTGACAAAATAAATGT;RSEQ=AAAGGTAACTGTCTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:123,41:0.012:2,2:11.5:1:31:1:0.44315:2.97608:60:4:0.0123:0:2 0/0:155:0:0,0:109,46:0:2,0:23.4:1:28.2:1:1:0:60:310:1:0:0.5 -2 55687597 . C T 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0;LSEQ=GCCAGAGTTAAAGCAAGATT;RSEQ=AGCCTAGGAGACACAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:304:304:152,152:0,0:1:0,2:26.1:1:29:1:1:0:60:151:1:0:1.8 1/1:303:290:138,152:7,5:0.9571:2,2:25.7:1:28.6:1:0.56131:1.53981:60:95.667:0.9599:0:1.6 -2 55687618 . T C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18838;LSEQ=AGCCTAGGAGACACAGAGAC;RSEQ=TGGTAGTTTCTGGATAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:307:262:120,142:18,27:0.8534:2,2:25.9:1:31.6:1:0.51882:1.27:60:130:0.8553:0:1.9 1/0:291:152:70,82:65,74:0.5223:2,2:26.5:1:30.7:1:0.90696:1.02887:60:75:0.5282:0:2 -2 55687681 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25082;SOR=0;LSEQ=TAGATACATTTTTGGAAACA;RSEQ=TTTTATTCTAGTTCTACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:1,2:56,127:0.0161:2,2:13:1:24:1:1:1.13:60:2:0.0108:0:2.7 0/0:164:0:0,0:50,114:0:2,0:24.8:1:31.2:1:1:0:60:163:1:0:0.6 -2 55844445 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGCTGTCTCCACCGCTC;RSEQ=AGCCGCCGCCTCCTCGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 55844521 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.54282;SOR=Inf;LSEQ=AGGCAGTAGTGGCGGTGGCG;RSEQ=CGGCGGCGGCTTCGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:31.7:1:31.8:1:1:0:60:36:1:0:0.2 0/1:35:2:1,1:18,15:0.0571:2,2:23:0:30.5:1:1:1.19373:60:4:0.0606:0:1.5 -2 55844616 . A AG 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGAGGCCTCTCCGCCCGG;RSEQ=GCCCCGTTACCTCTCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:25:1:30.2:1:1:0:60:12:0.8571:0.1429:0 1/1:6:6:0,6:0,0:1:0,0:18:1:29.3:1:1:0:60:12:1:0.5:0.3 -2 57016125 . T G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.13484;LSEQ=AATGAGAAATGAATCAATGA;RSEQ=TTTGTCAATTAAAATATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:0.4667:0,0:15.6:1:32.7:1:1:0:60:14:0.4667:0:1 1/0:4:2:2,0:2,0:0.5:0,0:8.5:1:32:1:1:0:60:4:0.5:0:1 -2 57016218 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07649;SOR=Inf;LSEQ=ATGGAATGCAGAGAATTATA;RSEQ=TTGGTAGGAATGAATGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:84,1:0:1,0:24.1:1:32.5:1:1:0:60:170:1:0:0.1 0/1:33:2:2,0:31,0:0.0606:1,0:32.5:1:32:0:1:0:60:4:0.0625:0:1 -2 57016287 . G T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14028;SOR=Inf;LSEQ=AGACAGCTGTGTGTTTGTGA;RSEQ=CCACTTACACTTGGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:198,55:0:2,0:23.6:1:32.2:1:1:0:60:125.5:1:0:0.2 0/1:152:2:1,1:117,33:0.0132:2,2:10:1:23.5:1:0.39848:3.50763:60:4:0.0132:0:1.5 -2 57016366 . G A 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03076;SOR=0.76432;LSEQ=GGAAAGAAAGTACTGTTGAA;RSEQ=TCTGTTCAGTAATTAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:652:305:147,158:168,179:0.4678:2,2:26.8:1:30.3:1:1:1.00877:60:100.667:0.4675:0:1.9 0/1:448:180:92,88:129,139:0.4018:2,2:25.7:1:29.5:1:0.56377:1.13:60:89:0.4:0:1.8 -2 57016392 . A G 260 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11499;SOR=0.80987;LSEQ=TCAGTAATTAACAGGTGTTT;RSEQ=TATACACATCATTTTATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:609:275:116,159:147,187:0.4516:2,2:27:1:32.1:1:0.68138:1.07736:60:90.667:0.4511:0:1.9 0/1:385:154:68,86:105,126:0.4:2,2:25.9:1:31.4:1:0.83472:1.05381:60:153:0.3984:0:1.9 -2 57016409 . T C 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTATATACACATCATTTTA;RSEQ=TCCATCTATGTCTTTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:0:0,0:204,320:0:2,0:25.3:1:30.5:1:1:0:60:261:1:0:0.9 0/1:322:13:5,8:123,185:0.0404:2,2:26.1:1:31.3:1:1:1.06359:60:26:0.0411:0:1.4 -2 57016461 . G A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16218;SOR=6.01566;LSEQ=TCAAGATTTACAAAGGTTGG;RSEQ=ATGAACAGAAGTCTCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:1,0:34,161:0.0051:2,0:1:0:25:0:0.17857:0:60:2:0.0051:0:1 0/1:133:4:1,3:29,100:0.0301:2,2:12.8:1:28:1:1:1.15:60:8:0.0305:0:2 -2 58496276 . G A 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.73864;LSEQ=CAAAACCTTTCTCAAAACTC;RSEQ=TCTCCAAAATCATCCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:201:73,128:181,283:0.3:2,2:26.6:1:30:1:0.54349:1.12126:60:17.273:0.3016:0:1.3 0/1:576:246:103,143:122,200:0.4271:2,2:26.4:1:29.4:1:0.34236:1.18:60:19.5:0.4262:0:1.3 -2 58496321 . A T 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCTAATTTTAATCCATCCTT;RSEQ=ATCTAGCACTGTATGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:584:0:0,0:222,359:0:2,0:26.6:1:29.1:1:1:0:60:71.625:0.9965:0:0.4 0/1:484:14:4,10:195,275:0.0289:2,2:29.6:1:27.6:1:0.41585:1.77076:60:13:0.0273:0:2 -2 58496397 . T A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACTATGTTTTTACTTGTT;RSEQ=CATTGTTCTGTTTCATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:3,122:0:1,0:23.3:1:30.1:1:1:0:60:124:1:0:0.1 0/1:93:19:2,17:6,68:0.2043:2,2:25.1:1:29.4:1:0.66426:1.33:60:38:0.2043:0:1 -2 59093379 . A G 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0799;SOR=Inf;LSEQ=AGTCCCATTGAAAAGGCGAG;RSEQ=GCTGCCTGCTGAGCTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:161,106:0:2,0:22.3:1:29.8:1:1:0:60:28.667:1:0:0.1 0/1:203:3:1,2:123,77:0.0148:2,2:28:1:25.3:1:0.56144:3.17614:60:2:0.01:0:1.3 -2 59093487 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50192;SOR=0;LSEQ=TGTGGGTTCTGACTCGCTCT;RSEQ=GATGATATTGGAGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:53,121:0.0114:2,2:26:1:29.5:1:0.52071:2.27:60:4:0.0115:0:1 0/0:149:0:0,0:49,98:0:2,0:20.3:1:29.3:1:1:0:60:48:0.9863:0:0.1 -2 59093502 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.50663;SOR=0;LSEQ=GCTCTTGATGATATTGGAGT;RSEQ=TGTGTTTGTGGCACTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:27,99:0.0156:2,2:23:1:30:1:0.39099:3.62:60:4:0.0156:0:1 0/0:98:0:0,0:28,70:0:2,0:28:0:14:0:1:0:60:0:0:0:5 -2 59093686 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTTAGGAAGGGAGATTT;RSEQ=GGGCTTTTTTTCCCCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:19:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 59400645 . T C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71643;SOR=1.41551;LSEQ=AAAGGGAAGGGCCCCCCGTC;RSEQ=TGTGATCACGTGACTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:8,6:3,2:0.7368:2,2:31.5:1:31:1:1:1.11808:59.3:28:0.7368:0:1.2 1/1:20:16:8,8:2,2:0.8:2,2:28.8:1:31.5:1:1:1:60:32:0.8:0:1.3 -2 60170649 . CTG C 81 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=9.000;MSILEN=2;SSF=0.6494;SOR=0.46079;LSEQ=TAGTAAATATATGTGTGTGT;RSEQ=TGTGTGTGTGTGTGTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:27.3:1:31.7:1:1:0:60:12:0.4286:0.0714:0 0/1:8:2:2,0:5,1:0.25:2,0:32.5:1:30.5:1:1:0:60:4:0.2857:0:1 -2 60170678 . G A 23 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.12644;SOR=Inf;LSEQ=TGTGTGTGTGGTGTGTGTGT;RSEQ=TGTTTCTGTAGATATTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:0:1,0:21.8:1:31.8:1:1:0:60:38:1:0:0 0/1:11:2:2,0:8,1:0.1818:2,0:29:1:23.5:1:1:0:60:4:0.1818:0:1 -2 60170875 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36306;LSEQ=TGGTCTTATCTCTAAAATAA;RSEQ=ATGATCAACTCTCTGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:179:82,97:92,74:0.5188:2,2:24.6:1:29:1:0.0849:1.46898:60:178:0.5205:0:1.1 0/1:242:68:35,33:88,85:0.281:2,2:24.5:1:28.8:1:1:1.02:60:136:0.281:0:1 -2 60170956 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16076;SOR=Inf;LSEQ=GTTGAAGAAAAACTTTCTTA;RSEQ=ACAACAGCAAGAAAGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:48,141:0:2,0:24.1:1:29.1:1:1:0:60:378:1:0:0.6 0/1:127:2:1,1:36,89:0.0157:2,2:22:0:31.5:1:0.49944:2.45:60:4:0.016:0:2.5 -2 60170973 . A G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=0.33185;LSEQ=TTATACAACAGCAAGAAAGT;RSEQ=TTTGTAGCATGAATTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:145:75:17,58:10,60:0.5172:2,2:20.7:1:32.1:1:0.20879:1.75:60:150:0.5172:0:1.1 0/1:88:23:6,17:13,52:0.2614:2,2:25.5:1:31:1:0.56359:1.41:60:46:0.2614:0:1.2 -2 60171126 . T C 34 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0.76645;LSEQ=TGCAGTTGTCAAAGTGAATG;RSEQ=ATGTACTGGGGACAAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:27:1:34:0:1:0:60:4:0.2857:0:1 0/1:5:1:0,1:0,4:0.2:0,0:8:0:33:0:1:0:60:2:0.2:0:1 -2 60902384 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=CCTGATTCTGATCCAGTAGG;RSEQ=CCAAGTTGAGGCCTGATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:11,4:0.1176:2,2:10.5:1:31:1:0.51471:2.56905:60:4:0.1176:0:1 0/0:17:0:0,0:10,7:0:2,0:18.7:1:28.3:1:1:0:60:34:1:0:0.4 -2 60902408 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13564;SOR=Inf;LSEQ=AGTTGAGGCCTGATAGCCCA;RSEQ=ACCTGTAACAGGCTTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:18,12:0:2,0:23.8:1:32:1:1:0:60:60:1:0:0.2 0/1:18:2:1,1:8,8:0.1111:2,2:45:1:30.5:1:1:1:60:4:0.1111:0:1 -2 60902430 . G A 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.00113;SOR=18.94817;LSEQ=CCTGTAACAGGCTTCCAGCT;RSEQ=CTGCTGCTGCTGGTGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:1,0:22,13:0.0278:2,0:8:0:23:0:1:0:60:2:0.0278:0:1 0/1:22:8:5,3:7,7:0.3636:2,2:26.9:1:29.4:1:0.67492:1.63:60:16:0.3636:0:1 -2 60902510 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGTTATTCGGGGTCCACA;RSEQ=CCTCAGCTGTAGCCTTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:5,14:0.0952:2,2:18.5:1:29.5:1:0.5:2.65:60:4:0.1:0:1.5 0/0:7:0:0,0:2,5:0:2,0:21.7:1:29.3:1:1:0:60:14:1:0:0.1 -2 61079090 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTGCATGTGTGTGTGT;RSEQ=TTAAAAAATAATTTATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:30.5:1:1:0:60:4:1:0:1 -2 61079440 . C A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23729;SOR=Inf;LSEQ=CGCAACCCGTGTTCTCTAGG;RSEQ=CTTTTAGAAAACATGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:0:2,0:27.8:1:31.9:1:1:0:60:58:1:0:0.2 0/1:30:3:2,1:15,12:0.1:2,2:24:1:23.3:1:1:1.58:60:2:0.0769:0:1 -2 61079589 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=CTGGAAGAGTCTACAGTGTT;RSEQ=CACAGCATGCTGTTGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:8:1:31.1:1:1:0:60:16:1:0:0.4 0/1:7:2:1,1:2,3:0.2857:2,2:7.5:1:26:1:1:1.41:60:4:0.2857:0:1.5 -2 61079674 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAATGTGGGTATTTATTGAG;RSEQ=ACAGCCACCATAGCATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:23.5:1:32:0:1:1.13389:60:4:0.1176:0:1 0/0:5:0:0,0:3,2:0:2,0:20.2:1:31.4:1:1:0:60:10:1:0:0.6 -2 61079678 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGTATTTATTGAGCACA;RSEQ=CCACCATAGCATTATTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:22:1:29:1:1:1.13389:60:4:0.1176:0:1 0/0:5:0:0,0:3,2:0:2,0:19.4:1:30.4:1:1:0:60:10:1:0:0.6 -2 61108829 . G A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08773;SOR=0.50036;LSEQ=GAGCCGCAAACCCAGCGGAG;RSEQ=GCGGGAAGAAGGAGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:32:31,1:25,0:0.5614:1,1:23.5:1:29.8:1:1:0:60:64:0.5714:0:1 0/1:54:21:19,2:29,4:0.3889:2,2:26.4:1:28.4:1:1:1.30:60:20:0.3846:0:1.1 -2 61108891 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4989;SOR=Inf;LSEQ=GGGGCCCCGCCGGCAGAGGT;RSEQ=CCTCGGCCTCCTGACTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:148,22:0:2,0:24.1:1:31.5:1:1:0:60:169:1:0:0.5 0/1:179:2:1,1:138,39:0.0112:2,2:34.5:1:24:1:0.39797:3.5064:60:4:0.0114:0:2 -2 61108894 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49883;SOR=Inf;LSEQ=GCCCCGCCGGCAGAGGTCCC;RSEQ=CGGCCTCCTGACTGACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:155,28:0:2,0:23.4:1:31.2:1:1:0:60:90.5:1:0:0.5 0/1:190:2:1,1:143,45:0.0105:2,2:27.5:1:30:1:0.42657:3.15401:60:4:0.0109:0:2 -2 61108896 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24827;SOR=Inf;LSEQ=CCCGCCGGCAGAGGTCCCTC;RSEQ=GCCTCCTGACTGACTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:160,35:0:2,0:22.7:1:29.9:1:1:0:60:64:1:0:0.5 0/1:201:3:2,1:148,50:0.0149:2,2:19:1:30.7:1:1:1.47686:60:6:0.0152:0:1.7 -2 61108926 . C G 216 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGACTGACTGCGGCCGCCT;RSEQ=CGGCCAGGACGCTGGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:122:71,51:134,68:0.3742:2,2:24.7:1:31.3:1:0.1544:1.41391:60:60:0.3715:0:1.1 0/0:381:0:0,0:231,150:0:2,0:23.4:1:30.4:1:1:0:60:33.636:1:0:0.3 -2 61108996 . A T 189 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=70.90866;LSEQ=ATGGCCTCCGGTGAGTGTTC;RSEQ=TGGGGCGCGGGCCTGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:1:1,0:216,251:0.0021:2,0:38:0:16:0:0.46368:0:60:0:0:0:7 0/1:583:77:36,41:241,264:0.1321:2,2:24.9:1:30.3:1:0.90299:1.03961:60:24.667:0.1298:0:1.4 -2 61109147 . A G 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69452;SOR=0.64412;LSEQ=TTAAAAAAGTTACCTGCTTC;RSEQ=GGGTTTGCGTGCAGAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:0,4:0,41:0.0889:1,0:11.8:1:30.8:1:1:0:60:8:0.0909:0:1.3 0/1:34:2:0,2:1,31:0.0588:1,0:33:1:31:1:1:0:60:4:0.0588:0:1.5 -2 61109544 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGGCCGGGCGCGGTGGC;RSEQ=CATGCCTGTATTCCCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 61118738 . TA T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49796;SOR=0;LSEQ=TTTGTTTTAGTCTGCTGTTA;RSEQ=AAAAAAACAGAATGTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:2,0:109,12:0.0163:2,0:39:1:32:1:1:0:60:4:0.0165:0:0 0/0:123:0:0,0:75,7:0:2,0:22.5:1:28.1:1:1:0:60:81:0.6639:0:0 -2 61119075 . C T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACAGGTTTATCTTTTT;RSEQ=TTTTTTCCTTTTTTTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:0,2:2,112:0.0172:1,0:6:0:28:1:1:0:60:4:0.0194:0:1.5 0/0:46:0:0,0:0,46:0:1,0:23.7:1:30.1:1:1:0:60:8.2:1:0:0.1 -2 61119083 . C CT 99 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.83246;LSEQ=GTTTATCTTTTTCTTTTTTC;RSEQ=TTTTTTTTTTTAAACGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:10:0,10:2,95:0.0935:1,0:27.2:1:30:1:1:0:60:20:0.0971:0.0093:0.8 0/1:38:3:0,3:0,35:0.0789:1,0:15.3:1:28.7:1:1:0:60:6:0.0789:0:0 -2 61121472 . G C 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62188;SOR=0.49265;LSEQ=GTAAATTGAATTCTCATTTA;RSEQ=TAGATCAGTTTATAATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:0,2:148,30:0.0111:2,0:13:1:29.5:1:0.03079:0:60:4:0.0111:0:2 0/0:182:1:1,0:140,41:0.0055:2,0:3:0:30:0:1:0:60:2:0.0056:0:2 -2 61121492 . G A 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.07765;LSEQ=GTAGATCAGTTTATAATGCA;RSEQ=TCTATTTGGATCATGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:258:257:189,68:0,0:0.9961:0,2:24:1:30.4:1:1:0:60:84.667:1:0:1.1 1/1:278:277:194,83:0,0:0.9964:0,2:24.9:1:29.8:1:1:0:60:68.25:0.9964:0:1.1 -2 61128034 . C T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.11319;SOR=0;LSEQ=GCTTTGGTATGTACAACTGA;RSEQ=AGCATGATAACTTCAGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:3:1,2:102,15:0.025:2,2:5.7:1:26.3:1:0.0523:13.08025:60:6:0.0254:0:1 0/0:127:0:0,0:110,17:0:2,0:20.4:1:31.3:1:1:0:60:62.5:1:0:0.1 -2 61128268 . G A 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATTTGGGTGTTGATTTCT;RSEQ=TTTCTTTTTTCTTTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:16,72:0:2,0:17.1:1:31.1:1:1:0:59.8:13.667:1:0:0.6 0/1:102:39:14,25:12,49:0.3824:2,2:18.2:1:29:1:0.10129:2.27:60:78:0.398:0:1.7 -2 61128279 . C T 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.20666;LSEQ=TTGATTTCTGTTTCTTTTTT;RSEQ=TTTCTCTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:0,2:10,48:0.0333:2,0:38:1:30.5:1:1:0:33.5:4:0.037:0:5 0/1:75:3:0,3:19,53:0.04:2,0:26.3:1:17.7:1:0.56668:0:46.7:0.5:0.0143:0:4.7 -2 61128284 . T C 162 LongAT STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00868;SOR=3.34129;LSEQ=TTCTGTTTCTTTTTTCTTTC;RSEQ=CTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:26:5,21:2,17:0.5652:2,2:8.8:1:31.1:1:0.68077:1.99:60:52:0.6047:0:1.3 1/1:54:44:14,30:0,8:0.8148:0,2:8.4:1:29.7:1:0.09041:0:60:88:0.88:0:1.7 -2 61143965 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20634;SOR=Inf;LSEQ=GGAGGACCTAGCAAGTCTTT;RSEQ=GGTCTATGTGACTATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:159,11:0:2,0:26:1:28.1:1:1:0:60:41.5:1:0:0.1 0/1:142:2:1,1:129,11:0.0141:2,2:15:1:28.5:1:0.16242:11.27173:60:4:0.0142:0:1 -2 61143993 . A AT 112 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.67273;SOR=1.27468;LSEQ=GTGACTATTACATTTAAAAA;RSEQ=TTTTTTTTTTCTATTCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:10:6,4:244,60:0.0314:2,2:27.5:1:30:1:0.12427:2.70009:60:20:0.0318:0:0.1 0/1:327:13:13,0:244,69:0.0398:2,1:18.9:1:30.5:1:0.07825:0:60:26:0.0401:0.0122:0.3 -2 61145241 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14792;SOR=Inf;LSEQ=AAAACTTTTATTCTGTGAAT;RSEQ=CTTTTCCTCAAATTCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:119,5:0:1,0:22.6:1:32.5:1:1:0:60:248:1:0:0.1 0/1:78:2:1,1:71,5:0.0256:2,2:19.5:1:26.5:1:0.14885:13.05378:60:4:0.0263:0:1 -2 61147110 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49987;SOR=Inf;LSEQ=TATATGTGAATAAAATATTT;RSEQ=TTTATTAAAGGAGAGGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:141,29:0:2,0:22.9:1:32.4:1:1:0:60:169:1:0:0 0/1:188:2:1,1:148,38:0.0106:2,2:32:1:25.5:1:0.37274:3.85745:60:4:0.0108:0:1 -2 61147323 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.5062;SOR=0;LSEQ=AGTTTTTCAAATTTTATTAT;RSEQ=TTTGTTTTGTTTTGTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:10,149:0.0124:2,2:11:1:33:0:0.13238:14.25:60:4:0.0124:0:1 0/0:125:0:0,0:15,110:0:2,0:22:1:29.9:1:1:0:60:124:1:0:0.1 -2 61147590 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.22963;SOR=Inf;LSEQ=AGGTGATCCACCCACCTTGG;RSEQ=CTCCCAAAGTGCTGGGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:139,30:0:2,0:25.9:1:31.4:1:1:0:59.7:32.8:1:0:0.1 0/1:156:2:1,1:127,27:0.0128:2,2:27.5:1:27.5:1:0.32771:4.63712:60:4:0.0131:0:1 -2 61147604 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.23482;SOR=0;LSEQ=CCTTGGCCTCCCAAAGTGCT;RSEQ=GGATTACAGGTGGGAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:0,2:148,47:0.0102:2,0:21:1:31:1:0.06091:0:56:4:0.0103:0:3 0/0:209:0:0,0:153,56:0:2,0:23:1:30.8:1:1:0:60:51.25:1:0:0.1 -2 61705919 . G T 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6264;SOR=0.37435;LSEQ=TGCTGTTTTCCTCTGCTAAC;RSEQ=AGTTGCAGAGAAAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:247,49:0.01:2,2:5.7:1:25:1:0.07641:9.961:60:6:0.0102:0:1 0/0:265:1:0,1:202,62:0.0038:2,0:1:0:23:0:0.23774:0:60:2:0.0038:0:1 -2 61706131 . G A 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37328;SOR=0.25432;LSEQ=CAGATAGTTGAAATGTCAAC;RSEQ=CAATAAACTTCAACTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:4:2,2:77,252:0.012:2,2:13.8:1:29.3:1:0.23965:3.26:60:8:0.0121:0:1 0/0:326:1:1,0:91,234:0.0031:2,0:1:0:30:0:0.28221:0:60:2:0.0031:0:1 -2 61708575 . GT G 32 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.7113;LSEQ=TGCCTCAGCGTCCCAATAAT;RSEQ=TTTTTTTTTTTAATCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:0,24:0.0769:1,0:37.5:1:32.5:1:1:0:60:4:0.0769:0:0 0/1:18:1:0,1:0,17:0.0556:1,0:35:0:32:0:1:0:60:2:0.0588:0:0 -2 61709349 . C A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.09871;SOR=2.66411;LSEQ=ATGCATACCACTTCTGACTA;RSEQ=TTTTTTTTTTGTAGAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:13:13,0:29,0:0.2889:1,1:19.9:1:30.9:1:1:0:60:26:0.2889:0:1.1 1/0:21:11:11,0:9,0:0.5238:0,0:26.7:1:29.3:1:1:0:60:22:0.5238:0:1.2 -2 61709447 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23976;SOR=Inf;LSEQ=CCTTAGGCTTCCCAAAGTGC;RSEQ=GGATTACAGGTGTGAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:155,30:0:2,0:22.8:1:31.3:1:1:0:60:19.556:1:0:0.1 0/1:178:2:1,1:147,29:0.0112:2,2:9:1:29.4:1:0.30946:5.00084:60:4:0.0116:0.0056:0 -2 61709715 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11403;SOR=Inf;LSEQ=ATTAACTCCAAAATGTAATA;RSEQ=AACTATAGATCTTAGCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:31,172:0:2,0:24.6:1:27:1:1:0:60:10.941:0.9947:0:0.3 0/1:194:3:2,1:43,148:0.0155:2,2:12:1:21.3:1:0.13496:6.79:60:2:0.0114:0:2.7 -2 61709732 . G GT 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.59608;SOR=2.35918;LSEQ=ATATAACTATAGATCTTAGC;RSEQ=TTTTTTTTTGTTTTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:1:0,1:14,127:0.007:2,0:13:0:31:0:1:0:60:2:0.0074:0:0 0/1:122:2:0,2:14,102:0.0164:2,0:32.5:1:31.5:1:1:0:60:4:0.0183:0:0 -2 61709736 . T G 114 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00794;SOR=2.97933;LSEQ=AACTATAGATCTTAGCGTTT;RSEQ=TTTTTGTTTTGTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:10:1,9:9,112:0.0763:2,2:21.1:1:28.1:1:0.56131:1.38:60:4:0.0625:0:1.8 0/1:116:23:2,21:9,84:0.1983:2,2:20:1:25.3:1:1:1.12389:59.6:1.875:0.1485:0:2.3 -2 61709742 . G T 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00147;SOR=3.32924;LSEQ=AGATCTTAGCGTTTTTTTTT;RSEQ=TTTTGTTTTTTTTTTTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:12:1,11:4,92:0.1101:1,2:19:1:25.7:1:0.45165:2.07:58.3:3:0.1:0:2.8 0/1:99:29:0,29:5,64:0.2929:2,1:20:1:30.7:1:0.3176:0:58.3:58:0.3494:0:2.9 -2 61709747 . GT G 147 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.04268;SOR=2.02217;LSEQ=TTAGCGTTTTTTTTTGTTTT;RSEQ=TTTTTTTTTTTAGACGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:18:0,18:1,73:0.1895:1,1:28.4:1:32:1:1:0:60:36:0.1957:0.0316:0.6 0/1:87:28:0,28:3,51:0.3218:2,1:24.8:1:30.7:1:0.54756:0:59.6:56:0.3457:0.0345:1.7 -2 61710077 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=TGGCACTTAACATTTAAATC;RSEQ=TATTAAATTCTTACCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:141,53:0:2,0:24.4:1:30.2:1:1:0:60:37.8:1:0:0.1 0/1:194:2:1,1:134,58:0.0103:2,2:19:1:29:1:0.51685:2.29924:60:4:0.0103:0:1 -2 61710320 . T A 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0396;SOR=0;LSEQ=AAGTATTCTGAATCTAACCC;RSEQ=GTTCTCCCTTTTTTTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:6:0,6:1,86:0.0645:1,0:26.7:1:32.5:1:1:0:60:12:0.0659:0:1 0/0:68:0:0,0:0,68:0:1,0:24:1:30.1:1:1:0:60:136:1:0:0.1 -2 61710328 . CT C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.35404;LSEQ=TGAATCTAACCCTGTTCTCC;RSEQ=TTTTTTTGGGATGATGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:0,2:0,76:0.0256:1,0:31:1:34:0:1:0:60:4:0.0256:0:0.5 0/1:58:2:0,2:0,56:0.0345:1,0:28:1:31.5:1:1:0:60:4:0.0351:0:0 -2 61711293 . G C 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06106;SOR=Inf;LSEQ=TCAGTGTCTTTGTTGTGCTA;RSEQ=ACAGGAGGGGAAAAGCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:21,138:0:2,0:21.1:1:31.4:1:1:0:60:318:1:0:0.1 0/1:168:5:1,4:25,138:0.0298:2,2:16.6:1:30.8:1:0.57335:1.38:60:10:0.0299:0:1.2 -2 61711440 . G A 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03024;SOR=Inf;LSEQ=AACTGTCCCGTTACGCACAT;RSEQ=AGTTATCAAATTGAAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:0:1,0:30.4:1:30.3:1:1:0:60:12:1:0:0.1 0/1:6:2:0,2:0,4:0.3333:0,0:24.5:1:30.5:1:1:0:60:4:0.3333:0:1 -2 61711815 . G T 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTCTGTCACCCAGGCTGGA;RSEQ=TGCGTGGCGCGATCTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:34:0:33:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:23.5:1:32:0:1:0:60:4:0.6667:0:2 -2 61713110 . GA G 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06482;SOR=0;LSEQ=TCAGCGACCTGTTGGGGAGG;RSEQ=AAAAAAAGTTATGTTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:5:1,4:67,293:0.0137:2,2:25.6:1:30.5:1:1:1.09:60:10:0.0139:0.0027:0.6 0/0:316:0:0,0:89,227:0:2,0:22.2:1:29.5:1:1:0:60:157:1:0:0.1 -2 61713210 . GAAAATCTTGT TAGG 119 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.70737;LSEQ=TGATCATCTACTGAAAACAG;RSEQ=GTTTGTATTAGGGTTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:0,2:0,49:0.0392:1,0:39.5:1:31:1:1:0:60:4:0.04:0:0 0/1:32:15:0,15:0,15:0.4688:1,1:19.5:1:30.6:1:1:0:60:30:0.4688:0.0938:0.1 -2 61713218 . T A 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04973;SOR=Inf;LSEQ=TACTGAAAACAGGAAAATCT;RSEQ=GTGTTTGTATTAGGGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:0:1,0:23:1:30.5:1:1:0:60:94:1:0:0.2 0/1:14:2:0,2:0,12:0.1429:0,0:25.5:1:29:1:1:0:60:4:0.1429:0:2 -2 61713220 . T G 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04407;SOR=Inf;LSEQ=CTGAAAACAGGAAAATCTTG;RSEQ=GTTTGTATTAGGGTTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:0:1,0:22.1:1:30.4:1:1:0:60:94:1:0:0.2 0/1:13:2:0,2:0,11:0.1538:0,0:27:1:28:1:1:0:60:4:0.1538:0:2 -2 61713320 . CT C 34 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=GGACACACTGTCATTCAAGA;RSEQ=TTTTTTTTTTGAGACAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:15.5:1:34:0:1:0:60:4:0.4:0:0 1/0:2:1:0,1:0,1:0.5:0,0:27:0:32:0:1:0:60:2:1:0:1 -2 61713526 . C G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCAGTGGGTGTCTCCAA;RSEQ=TTAGGTGGCAGAATCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:18.7:1:33.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 61715159 . GACT G 122 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0466;SOR=2.4502;LSEQ=TATTAGTATATTAACGTAAG;RSEQ=ACAATAAATAAAATGCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:12:12,0:73,2:0.1379:1,0:20.8:1:31.4:1:1:0:60:24:0.1446:0.0575:0.1 0/1:53:15:15,0:38,0:0.283:1,1:18.1:1:31.3:1:1:0:60:30:0.283:0.1321:0.1 -2 61715436 . T A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02732;SOR=Inf;LSEQ=AGAATCAAATGGAATCTAAT;RSEQ=TTACCACTAAACTTATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:112,294:0:2,0:23.7:1:29.7:1:1:0:60:49.75:1:0:0.1 0/1:387:5:3,2:97,285:0.0129:2,2:9.2:1:26.6:1:0.11118:4.39:60:10:0.0131:0:1 -2 61715955 . G A 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-04;SOR=Inf;LSEQ=ATCATATAAGAATTATCCAC;RSEQ=GCTGGGAACAGTGGCTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:12,137:0:2,0:22.7:1:30.9:1:1:0:60:148:1:0:0 0/1:125:9:3,6:10,106:0.072:2,2:19.2:1:31.2:1:0.05157:5.18:60:18:0.072:0:1.1 -2 61717338 . A ATT 29 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CCGGCCCAGATTTTTCATTT;RSEQ=TTTTTTTTTTTTTGAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:3,0:0.25:0,0:15:0:32:0:1:0:60:2:0.3333:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:29.3:1:1:0:60:4:1:0:1.5 -2 61719969 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15287;SOR=Inf;LSEQ=ATTTAGAAAATATTTAGAAA;RSEQ=TACAAGTACATTTCCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:149,101:0:2,0:22.8:1:32.2:1:1:0:59.9:61.5:1:0:0.1 0/1:161:2:1,1:99,60:0.0124:2,2:5.5:1:27.5:1:1:1.6446:60:4:0.0125:0:1.5 -2 61719985 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.1469;SOR=Inf;LSEQ=GAAACTACAAGTACATTTCC;RSEQ=AAAATGTATTTCCACCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:188,96:0:2,0:23:1:30.4:1:1:0:59.9:141:1:0:0.1 0/1:177:2:1,1:126,49:0.0113:2,2:29.5:1:31.5:1:0.48633:2.55567:60:4:0.0114:0:1.5 -2 61722519 . G GA 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=5.98146;LSEQ=CAAAAGGTACATACATTTTA;RSEQ=AAAAAGGCACTTTTAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:46:37,9:118,23:0.246:2,2:24.1:1:30.4:1:0.65363:1.24645:60:92:0.246:0.0374:0 1/0:160:106:87,19:44,10:0.6625:2,2:25:1:29.1:1:1:1.04:60:105:0.6604:0.1375:0.2 -2 61722778 . G A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34671;SOR=0.29435;LSEQ=TTAAAAGGGACGATCAGTTC;RSEQ=CATTTTATAAAACAACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:2,1:47,243:0.0102:2,2:17.3:1:27.7:1:0.07359:10.21:60:6:0.0103:0:1 0/0:330:1:1,0:87,242:0.003:2,0:1:0:27:0:0.26667:0:60:2:0.0031:0:1 -2 61722904 . C T 94 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=21.92972;LSEQ=GCAGCCTCCACCTCCTAGGC;RSEQ=CAATCAGTCCTCCTCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:0,3:0,25:0.1071:1,0:11.7:1:29.7:1:1:0:60:6:0.1154:0:1.3 1/0:12:9:0,9:0,3:0.75:0,0:24.8:1:29.9:1:1:0:60:18:0.75:0:1 -2 61725501 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATTATCAGTTAAAAGAT;RSEQ=AACTTTTCATTTTTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:14.5:1:28:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 61726050 . TA T 164 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.72572;SOR=0.9181;LSEQ=TGAGAATTCATTGCACATGC;RSEQ=AAAAAAAAAACACACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:43:17,26:151,232:0.1009:2,2:30.4:1:30.4:1:1:1.00:60:86:0.1019:0.0047:0.1 0/1:396:37:16,21:145,214:0.0934:2,2:33.1:1:30.2:1:0.72911:1.12:59.6:74:0.0941:0:0.3 -2 61726086 . G A 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00531;SOR=5.22497;LSEQ=CAAAAATATCAGATTTAGAA;RSEQ=ACACAGAAATAAGTATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:3,0:46,191:0.0125:2,0:22.3:1:13.3:1:0.0081:0:60:0:0:0:4 0/1:225:14:6,8:48,162:0.0622:2,2:24.4:1:29.1:1:0.10803:2.52:60:28:0.0707:0:2.1 -2 61727056 . G A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36282;SOR=0.317;LSEQ=CAAGACATGAAATGTTAATC;RSEQ=CACTTCATTTCTCAAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:2,1:38,204:0.0122:2,2:18.7:1:28.3:1:0.07013:10.57:60:6:0.0124:0:1 0/0:256:1:1,0:53,200:0.0039:2,0:1:0:27:0:0.2126:0:60:2:0.004:0:2 -2 61727215 . G A 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=GGTAGAAAACAAAACACAAA;RSEQ=TCTTTTATCTTAATCACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:0.2308:0,0:19.7:1:32.7:1:1:0:60:6:0.2308:0:1 1/1:2:2:0,2:0,0:1:0,0:12.5:1:31:1:1:0:60:4:1:0:1 -2 61728900 . C CAT 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51354;SOR=1.53734;LSEQ=AAAGATAAATAAGAATCCAA;RSEQ=AGAGTCCAGTCCACACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:10:10,0:28,1:0.2439:1,0:15:1:30.8:1:1:0:59.5:20:0.2778:0.0976:0.1 0/1:15:5:5,0:9,1:0.3333:2,0:22.8:1:31:1:1:0:60:10:0.3846:0.0667:0 -2 61729258 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.62931;LSEQ=CAATCCTAACAAATGATTAC;RSEQ=GCTCTACTGTAAATGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:93:41,52:79,152:0.287:2,2:24.2:1:30.7:1:0.10007:1.51:60:186:0.2906:0:1.9 1/0:244:145:56,89:40,49:0.5943:2,2:22.4:1:30.1:1:0.34247:1.2959:60:144:0.595:0:1.9 -2 61729268 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.38803;LSEQ=AAATGATTACAGCTCTACTG;RSEQ=AAATGACTGACTGTGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:94:44,50:90,142:0.2883:2,2:24:1:32:1:0.21413:1.39:60:188:0.2892:0:1.9 1/0:231:148:66,82:39,44:0.6407:2,2:22.3:1:32.1:1:0.78347:1.10078:60:147:0.6476:0:1.9 -2 61729641 . TC AA 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59993;LSEQ=ACGCTTGTAATCCCAGCAAT;RSEQ=TTTGGGAGGCTGAGGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:0,6:0,7:0.4615:0,0:28.2:1:31.3:1:1:0:60:12:0.4615:0.0769:1.2 0/1:6:2:0,2:0,4:0.3333:0,0:27:1:31.5:1:1:0:60:4:0.3333:0:1 -2 61729695 . A C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GCCAGGAATTCGAGACCAGC;RSEQ=TGACCAACATGGTGAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,5:0.1667:0,0:15:0:33:0:1:0:60:2:0.1667:0:2 1/1:2:2:0,2:0,0:1:0,0:27.5:1:31.5:1:1:0:60:4:1:0:1 -2 61749472 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTGTTAGGATTACAGGC;RSEQ=TGGGCCACTGTGCCATAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:23:1:28:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 61749690 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.11472;LSEQ=CCCCCTCAAACAGTCAACTA;RSEQ=AATAAAAATGCCAGGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:89:60,29:189,80:0.2486:2,2:27.3:1:30.3:1:0.69031:1.14144:60:178:0.25:0:2 1/0:329:207:137,70:83,39:0.6292:2,2:22.8:1:28.8:1:0.80856:1.0871:60:40.4:0.6254:0:2.1 -2 61749716 . C T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.48847;LSEQ=AAATGCCAGGAAAAACAAAA;RSEQ=TCTGAATTTATAATTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:116:73,43:218,137:0.2463:2,2:27.3:1:30.8:1:0.82608:1.07:60:232:0.2489:0:1.7 1/0:475:323:183,140:89,63:0.68:2,2:25.6:1:29.6:1:0.76559:1.08056:60:106.667:0.678:0:1.7 -2 61753513 . G T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12413;SOR=Inf;LSEQ=TTCCTCAAAGTTTATGACTG;RSEQ=AAGAAAAGAAATAACAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:276,108:0:2,0:25.2:1:31.1:1:1:0:60:191:1:0:0.1 0/1:393:4:1,3:274,115:0.0102:2,2:16:1:26.3:1:0.08283:7.10801:60:8:0.0104:0:1 -2 61753669 . T TA 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.72584;SOR=1.57104;LSEQ=ATTCTTTGCTAAAATATTAT;RSEQ=AAAAAAAACAAAACTTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:0,3:63,219:0.0105:2,0:33.3:1:31.7:1:1:0:60:6:0.0106:0:0 0/1:305:5:2,3:76,224:0.0164:2,2:30.4:1:26.4:1:0.60514:1.96:60:10:0.0167:0.0033:0.4 -2 61753696 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23377;SOR=Inf;LSEQ=AACAAAACTTAAGCTAATGT;RSEQ=TTCTTTTGAATCATTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:25,155:0:2,0:23.8:1:30.8:1:1:0:60:179:1:0:0.1 0/1:169:2:1,1:22,145:0.0118:2,2:15:1:29:1:0.25437:6.47:60:4:0.012:0:1.5 -2 61753786 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00136;SOR=6.31396;LSEQ=ATTATTGATGTTCAGAAATA;RSEQ=TCAAAAATTAGACCTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:11:0,11:0,27:0.2895:1,0:19.9:1:30.2:1:1:0:60:22:0.2895:0:1 1/0:22:16:0,16:0,6:0.7273:0,1:22:1:30.4:1:1:0:60:32:0.7273:0:1.1 -2 61760756 . A C 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0046;SOR=6.04692;LSEQ=AACATGCAATTTCTTTCTCC;RSEQ=AACCAATTTTCATTATGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:4,0:69,0:0.0548:1,0:24.5:1:31.8:1:1:0:60:8:0.0548:0:1 0/1:38:10:9,1:28,0:0.2632:1,2:22.6:1:29.8:1:0.26316:0:60:20:0.2632:0:1 -2 61760814 . C T 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAATGCAAACTATGGAATAT;RSEQ=TTTTTTAAAGGTGATAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:27:23,4:172,8:0.1304:1,2:22.3:1:30.1:1:0.05474:3.70438:60:54:0.1311:0:1 0/0:150:0:0,0:138,12:0:2,0:22.7:1:31.6:1:1:0:60:149:1:0:0.1 -2 61761050 . G GA 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.25592;SOR=0;LSEQ=CATAGATTACTGAAAATAAA;RSEQ=AAAAAAAATTGAAGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:3:1,2:33,192:0.0132:2,2:10.3:1:29.3:1:0.3854:2.89:60:6:0.0136:0.0044:0.3 0/0:186:0:0,0:29,157:0:2,0:22.5:1:31.1:1:1:0:60:185:1:0:0.1 -2 61761169 . G A 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAGAGACTTTAATTACA;RSEQ=AAAACTGAGATAGTAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:0,30:0,0:1:0,1:30.4:1:30.2:1:1:0:60:29:1:0:1 1/1:9:9:0,9:0,0:1:0,0:22.4:1:28.9:1:1:0:60:8:1:0:1 -2 62759659 . CT C 31 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTTTTTGCTACTTCATT;RSEQ=TTTTTTTTTTTTTTACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31:1:31:1:1:0:60:4:1:0:0 1/1:1:1:1,0:0,0:1:0,0:29:0:33:0:1:0:60:2:1:0:3 -2 62759886 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1876;SOR=Inf;LSEQ=CTTCATGCGTTTCAGGAAGC;RSEQ=ATCTCAGCTCTTAGAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:45,8:0:2,0:25:1:30.4:1:1:0:58.5:52:1:0:0.2 0/1:41:2:1,1:34,5:0.0488:2,2:25:1:32:0:0.27439:6.29815:60:4:0.0488:0:1 -2 62759961 . G C 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00038;SOR=Inf;LSEQ=AAGAATCTTGCCCTTAATTT;RSEQ=TTTGTTTACAACAATGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:147,67:0:2,0:24.9:1:32.4:1:1:0:44.4:213:1:0:0.1 0/1:183:10:5,5:108,64:0.0546:2,2:20.5:1:27.8:1:0.50752:1.68238:49.5:4:0.0452:0:1.1 -2 62759976 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19742;SOR=Inf;LSEQ=AATTTGTTTGTTTACAACAA;RSEQ=GCCAACAGCATGCTGGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:154,93:0:2,0:28.3:1:30.8:1:1:0:42.2:494:1:0:0.1 0/1:198:2:1,1:114,82:0.0101:2,2:16.5:1:27.5:1:1:1.38787:50:4:0.0101:0:1 -2 62760131 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50679;SOR=0;LSEQ=TGGCCAAAGAACAACTCCAT;RSEQ=TTTTCTAAAAGGCCTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:110,72:0.0109:2,2:9.5:1:30:1:1:1.52412:60:4:0.0112:0:1 0/0:142:0:0,0:90,52:0:2,0:23.5:1:31.4:1:1:0:57.8:141:1:0:0.1 -2 62760259 . T A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09581;SOR=Inf;LSEQ=TCATTCTTTTACAGTCCTTT;RSEQ=CTCCAAGTCATAAACTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:73,170:0:2,0:21.1:1:29.5:1:1:0:60:47.6:1:0:0.1 0/1:206:3:2,1:75,128:0.0146:2,2:7.7:1:21.7:1:0.55725:3.39:60:2:0.0099:0:1 -2 66015029 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48413;SOR=0;LSEQ=GGTAATGTCTGATCACCCTG;RSEQ=CATCTATCTTCAGCAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:11,2:0.1333:2,2:24.5:1:29:1:0.37143:4.69047:60:4:0.1333:0:1 0/0:13:0:0,0:8,5:0:2,0:21.1:1:30.1:1:1:0:60:26:1:0:0.2 -2 66015141 . T C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74903;LSEQ=TGCTCCTCGGCTATAAATTC;RSEQ=GAGTTGCCCACACTGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:5,9:3,10:0.5185:2,2:19.4:1:30.7:1:0.67762:1.81:60:28:0.5185:0:1.1 0/1:9:4:1,3:1,4:0.4444:2,2:22:1:29:1:1:1.29:60:8:0.4444:0:1 -2 66352599 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04341;LSEQ=CAAAGCTGGAATTTGTTTGT;RSEQ=TGGTTCCTCCACAGCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:55:55,0:19,0:0.7432:1,1:26.2:1:28.8:1:1:0:60:110:0.7432:0:1 0/1:37:4:4,0:33,0:0.1081:1,0:19.5:1:28.5:1:1:0:60:8:0.1081:0:1 -2 66352795 . C G 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12655;LSEQ=AAATGATAACCCAGATTGAG;RSEQ=TGGGTTTGGTTTCATTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:551:514:184,330:15,21:0.9328:2,2:26.3:1:31.5:1:0.47827:1.28044:60:41.833:0.9331:0:1.1 1/0:562:358:145,213:74,129:0.637:2,2:25.3:1:30.7:1:0.36846:1.19:60:88.5:0.6378:0:1.2 -2 67047320 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16435;SOR=Inf;LSEQ=TGTGTCACTACCTCAGTTTG;RSEQ=CCCCATGTCCCTTACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:147,106:0:2,0:26.8:1:30.6:1:1:0:59.9:17.071:1:0:0.5 0/1:173:2:1,1:102,69:0.0116:2,2:18:1:26:1:1:1.47481:60:4:0.0122:0:2 -2 67047340 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15541;SOR=Inf;LSEQ=CCCCCATGTCCCTTACACAC;RSEQ=AGCAAAATACCCCTTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:138,124:0:2,0:28.9:1:28.1:1:1:0:59.9:8.034:1:0:0.4 0/1:171:2:1,1:93,75:0.0117:2,2:30:0:32.5:1:1:1.23841:60:4:0.0126:0:1.5 -2 67047383 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14935;SOR=Inf;LSEQ=GGGAAGAATTGGCAAGTGAC;RSEQ=GCTATGCTCCATGACTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:106,98:0:2,0:20.6:1:30.1:1:1:0:60:101:1:0:0.1 0/1:129:2:1,1:57,70:0.0155:2,2:26:1:27.5:1:1:1.23:60:4:0.0155:0:1 -2 67047384 . G T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14957;SOR=Inf;LSEQ=GGAAGAATTGGCAAGTGACT;RSEQ=CTATGCTCCATGACTCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:103,96:0:2,0:20.7:1:31.5:1:1:0:60:98.5:1:0:0.1 0/1:126:2:1,1:55,69:0.0159:2,2:7:0:27:1:1:1.25:60:4:0.016:0:1 -2 67047403 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51714;SOR=0;LSEQ=TGCTATGCTCCATGACTCAC;RSEQ=CAACAGTCTCTGCCTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:57,75:0.0149:2,2:5.5:1:26.5:1:1:1.31:60:4:0.0155:0:1 0/0:90:0:0,0:28,62:0:2,0:25.1:1:30.6:1:1:0:60:29:1:0:0.1 -2 67047640 . A G 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00218;SOR=0.48797;LSEQ=TGCAGCTCCAGCTTACATTC;RSEQ=TAGTGAATGCCAATGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:83:23,60:38,79:0.415:2,2:24.3:1:31.6:1:0.53411:1.2534:60:166:0.4256:0:1.1 0/1:148:38:9,29:38,72:0.2568:2,2:21.3:1:31.2:1:0.23341:1.69481:60:76:0.2603:0:1.1 -2 67047656 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18521;SOR=Inf;LSEQ=ATTCATAGTGAATGCCAATG;RSEQ=CCTGCTCTTACTGGGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:48,133:0:2,0:21.4:1:31.8:1:1:0:60:89.5:0.9944:0:0.5 0/1:138:2:1,1:42,94:0.0145:2,2:8:0:29:0:0.52766:2.22:60:4:0.0148:0:2.5 -2 67047717 . C T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=3.78048;LSEQ=TGGTGTGCAGCTGACACTTC;RSEQ=TTGGCATTAATCATCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:43:17,26:28,57:0.3359:2,2:28.2:1:30.7:1:0.55705:1.33:60:42:0.3387:0:1.1 1/0:79:52:21,31:9,18:0.6582:2,2:26.1:1:30:1:0.62874:1.35:60:25:0.6494:0:1.1 -2 67047766 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12416;SOR=Inf;LSEQ=AAAAAAATTGTGAGATGTCT;RSEQ=TCTTTTGACTAGTGCCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:40,62:0:2,0:21.8:1:31.6:1:1:0:60:50:1:0:0.4 0/1:56:2:1,1:26,28:0.0357:2,2:34.5:1:31:1:1:1.08:60:4:0.0364:0:1 -2 67047812 . A G 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.46001;SOR=0.73845;LSEQ=CACACTCTCAAGGAGCCACA;RSEQ=GAAGGGTGATCATCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:30:12,18:20,36:0.3488:2,2:28.4:1:31.4:1:0.81555:1.20:60:60:0.3488:0:1.3 0/1:53:15:8,7:20,18:0.283:2,2:26.1:1:30.9:1:1:1.03:60:30:0.283:0:1 -2 67047831 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52544;SOR=0;LSEQ=AAGAAGGGTGATCATCTCCC;RSEQ=CCTTGGGCTGTGCATGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:28,47:0.026:2,2:26.5:1:32:1:1:1.67:60:4:0.0267:0:2.5 0/0:47:0:0,0:25,22:0:2,0:25:1:29.8:1:1:0:60:94:1:0:0.3 -2 67048002 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12058;SOR=Inf;LSEQ=GTATCCCTGATGTGCATGAT;RSEQ=CTCCCCTGGTGCCACAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:69,56:0:2,0:25.3:1:30.8:1:1:0:60:61.5:1:0:0.1 0/1:67:2:1,1:41,24:0.0299:2,2:12:0:31:1:1:1.69403:60:4:0.0303:0:1.5 -2 67048161 . G A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61397;SOR=0.73467;LSEQ=TGGGCGGCTTCCTTTTCTCA;RSEQ=CTGGGACAGGCGAGTAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:10:2,8:71,77:0.0633:2,2:25.9:1:30.3:1:0.10838:3.66132:60:20:0.0637:0:1 0/1:127:6:4,2:52,69:0.0472:2,2:23:1:29:1:0.40406:2.63:60:12:0.0484:0:1 -2 67048329 . G GCAA 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01814;LSEQ=CTTCCTTAATGGTCACCTGG;RSEQ=CAACCTCTGGCCCAACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:46:27,19:85,50:0.2541:2,2:22:1:30.2:1:0.60348:1.19509:60:45:0.2557:0.0552:0.2 0/1:132:34:19,15:61,37:0.2576:2,2:25.9:1:30.2:1:0.54557:1.29891:60:68:0.2656:0.0455:0.1 -2 67048418 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11956;SOR=Inf;LSEQ=ATGAGCACCTCGTGCCCACA;RSEQ=CAGCAGATGGTGCAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:121,177:0:2,0:28.9:1:31.9:1:1:0:60:48.667:1:0:0.1 0/1:158:2:1,1:62,94:0.0127:2,2:8:1:29:1:1:1.51:60:4:0.0127:0:1 -2 67048433 . G A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64557;LSEQ=CCACAGCAGCAGATGGTGCA;RSEQ=CAGAACTGATAGCCTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:3:2,1:97,170:0.0111:2,2:18:1:27.7:1:0.55644:3.49:60:6:0.0113:0:1 0/0:139:1:1,0:47,91:0.0072:2,0:1:0:29:0:0.34532:0:60:2:0.0072:0:1 -2 67048521 . G A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.34059;SOR=0.44379;LSEQ=ATATTCCTAGCATGAAGAGG;RSEQ=GCTGTTCCAGAGTGACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:15:0,15:1,17:0.4545:1,1:24.3:1:31.2:1:1:0:60:30:0.4545:0:1.1 0/1:15:4:0,4:0,11:0.2667:0,0:25.8:1:32.5:1:1:0:60:8:0.2667:0:1.3 -2 67048595 . T C 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56923;SOR=3.83897;LSEQ=TTCTGGCACTTCTTCCTCAC;RSEQ=TTGTACACTAACTACTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:1,6:0.4167:2,0:20:1:30.8:1:1:0:60:10:0.4167:0:1.8 1/0:4:3:0,3:0,1:0.75:0,0:41.7:1:32.3:1:1:0:60:6:0.75:0:1 -2 67048932 . T A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53623;SOR=0;LSEQ=CAAGGTGCTGGGATTACAGG;RSEQ=GTGAGCTACTGTGCCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:24,4:0.0667:2,2:17.5:1:32:1:0.31034:5.47729:60:4:0.069:0:3 0/0:16:0:0,0:12,4:0:2,0:20.3:1:28.8:1:1:0:60:32:1:0:0 -2 67048934 . T A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5461;SOR=0;LSEQ=AGGTGCTGGGATTACAGGTG;RSEQ=GAGCTACTGTGCCTGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:26,4:0.0625:2,2:19.5:1:32:1:0.29234:5.92455:60:4:0.0645:0:3 0/0:16:0:0,0:12,4:0:2,0:21.1:1:28.3:1:1:0:60:32:1:0:0 -2 67049133 . T C 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03552;LSEQ=GAACCCCCCAAAGGTCCATC;RSEQ=GAATATCTGCTTGCTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:109,36:0.0136:2,2:7:1:28.5:1:0.44134:3.00025:60:4:0.0136:0:1 0/1:71:1:1,0:54,16:0.0141:2,0:38:0:32:0:1:0:60:2:0.0143:0:1 -2 67049224 . C T 123 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=30.71315;LSEQ=AACAGCTCCCCTGTACACTG;RSEQ=TGGCCACCGGCAGGACTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:1:0,1:180,127:0.0032:2,0:1:0:25:0:0.41558:0:60:2:0.0033:0:1 0/1:219:20:9,11:115,84:0.0913:2,2:22.2:1:28.6:1:0.345:1.66924:60:40:0.0922:0:1.1 -2 67049232 . C T 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCCTGTACACTGCTGGCCAC;RSEQ=GGCAGGACTTCGTAGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:191,142:0:2,0:22.9:1:29.9:1:1:0:60:36:1:0:0.2 0/1:257:14:8,6:132,110:0.0545:2,2:23.6:1:31.2:1:1:1.11:60:28:0.0558:0:1.3 -2 67049237 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08329;SOR=Inf;LSEQ=TACACTGCTGGCCACCGGCA;RSEQ=GACTTCGTAGATGGCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:203,153:0:2,0:22.8:1:31:1:1:0:60:28.667:1:0:0.2 0/1:277:3:1,2:149,125:0.0108:2,2:19.7:1:27:1:0.59498:2.37672:60:6:0.011:0:1 -2 67049381 . T C 190 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCAAGCCACATGACACAG;RSEQ=GGGTGCCTTCAGCTGCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:71:46,25:199,165:0.1632:2,2:27:1:31:1:0.11917:1.52:60:70:0.162:0:1.1 0/0:278:0:0,0:156,122:0:2,0:23.8:1:29.3:1:1:0:60:45.333:1:0:0.1 -2 67049554 . C T 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04375;SOR=Inf;LSEQ=CTTGTTCCCAGCCTCAGTCC;RSEQ=CACAGGCTCAGGTGTGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:122,139:0:2,0:22.5:1:30.6:1:1:0:60:28:1:0:0.1 0/1:143:3:1,2:70,70:0.021:2,2:6.7:1:28.7:1:1:1.99067:60:6:0.0214:0:1 -2 67049598 . C T 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3028;SOR=0;LSEQ=CAGTGGGGGATGTGGGGTTG;RSEQ=TGGGCTGCCGCACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:4:1,3:168,189:0.0111:2,2:10.5:1:27.5:1:0.62598:2.65998:60:8:0.0113:0:1 0/0:220:0:0,0:122,98:0:2,0:27.5:1:31.7:1:1:0:60:54:1:0:0.1 -2 67049643 . G A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06261;SOR=Inf;LSEQ=TGGCCTCCTCCACCTTTGCA;RSEQ=ACTCCTCTGAGCCCTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:160,212:0:2,0:27.2:1:31.6:1:1:0:60:73.4:1:0:0.1 0/1:246:3:2,1:117,126:0.0122:2,2:16.7:1:25:1:0.61154:2.15:60:6:0.0122:0:1.3 -2 67049699 . CT C 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1604;SOR=0;LSEQ=ATTACTGCAGTGACCTCGGC;RSEQ=TTCTTCTCAGCCCATGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:4:1,3:61,135:0.02:2,2:14.5:1:31:1:1:1.35366:60:8:0.0205:0.01:0 0/0:127:0:0,0:35,92:0:2,0:24.3:1:29.8:1:1:0:60:62.5:1:0:0.2 -2 67049832 . CT C 99 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.64822;SOR=0.46002;LSEQ=ACCCCTATGAGATGCGATGC;RSEQ=TTTTTTTTTCTTTCTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:0,8:2,16:0.3077:2,0:26.4:1:33.1:1:1:0:60:16:0.32:0:0 0/1:6:1:0,1:1,4:0.1667:2,0:23:0:33:0:1:0:60:2:0.1667:0:0 -2 67673780 . G A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80563;SOR=0.87125;LSEQ=CCTCTATAATTAATTTCCTT;RSEQ=AGTCACTGAATACCTTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:22,1:23,3:0.4694:2,1:22.7:1:27.9:1:0.61192:2.81:60:46:0.4694:0:1.9 0/1:23:10:10,0:13,0:0.4348:1,0:16.2:1:29:1:1:0:60:20:0.4348:0:2 -2 67673823 . A T 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.65678;SOR=1.18164;LSEQ=CCTTCTGCCATAAACGTCTC;RSEQ=TTTTCTCTAATATCCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:41:33,8:53,13:0.3832:2,2:27.3:1:31.3:1:1:1.01:60:82:0.3868:0:1.5 0/1:85:36:28,8:34,15:0.4235:2,2:24.5:1:30.6:1:0.46356:1.54:60:72:0.4235:0:1.3 -2 67673875 . T C 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00711;SOR=Inf;LSEQ=AACCAGAATTGAGCACAACA;RSEQ=GGCTTTTCCTTTCAATGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:126,64:0:2,0:24.3:1:30.2:1:1:0:60:26.143:1:0:0.5 0/1:188:7:3,4:114,67:0.0372:2,2:20.6:1:28:1:0.42887:2.25831:60:6:0.0328:0:1.4 -2 67673881 . T A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62126;SOR=2.0371;LSEQ=AATTGAGCACAACATGGCTT;RSEQ=TCCTTTCAATGGCGCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:1,0:130,71:0.005:2,0:1:0:23:0:1:0:60:2:0.005:0:1 0/1:199:2:1,1:119,78:0.0101:2,2:18:1:27.5:1:1:1.52227:60:4:0.0101:0:2 -2 67673930 . C G 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00151;SOR=1.75053;LSEQ=TCTGACTCATGCTCTGCACA;RSEQ=TGAGCAGTGACAGGACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:132:72,60:85,78:0.4475:2,2:24.5:1:31.9:1:0.72537:1.10:60:131:0.4471:0:1.1 1/0:254:149:79,70:58,47:0.5866:2,2:23.2:1:30.9:1:0.79844:1.09307:60:48.667:0.5863:0:1.2 -2 67673938 . T C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10251;SOR=Inf;LSEQ=ATGCTCTGCACACTGAGCAG;RSEQ=GACAGGACAGTCTGTGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:143,148:0:2,0:27.3:1:30.1:1:1:0:60:582:1:0:0.5 0/1:257:3:1,2:128,126:0.0117:2,2:12.3:1:29.7:1:0.62206:2.02634:60:6:0.0118:0:2.7 -2 67674042 . G A 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78505;SOR=0.92593;LSEQ=TCTGCTCTCTGTTAAGCCTT;RSEQ=TTATCATTTGAGGCTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:57:15,42:17,60:0.4254:2,2:23.5:1:29.5:1:0.68248:1.26:60:27.5:0.4198:0:1.1 0/1:91:37:7,30:13,41:0.4066:2,2:23.3:1:29.4:1:0.61508:1.35438:60:36:0.4:0:1 -2 67977367 . G GT 117 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00028;SOR=0.0802;LSEQ=ATCAAGGAGTCAATAGGGTT;RSEQ=TTTTTTTTTTTCCTAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:16:13,3:15,4:0.4103:2,2:22.6:1:29.3:1:1:1.15:60:32:0.4324:0.1538:0.6 0/1:39:2:2,0:27,10:0.0513:2,0:12:1:32:0:1:0:60:4:0.0526:0:0 -2 67977405 . A T 76 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15631;SOR=3.38204;LSEQ=GCTGAGACAGGATCTGTTTC;RSEQ=TGTCTCCCTTCTAGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:2,0:52,32:0.0233:2,0:23:1:16:0:0.52722:0:60:0:0:0:5 0/1:80:6:4,2:39,35:0.075:2,2:20.5:1:29.7:1:0.6809:1.78:60:12:0.0759:0:1 -2 67977433 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=0;LSEQ=CTTCTAGCTTCTGGGGGTTT;RSEQ=CCGGCAAGCTTTGGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:55,49:0.0189:2,2:22.5:1:29.5:1:1:1.12122:60:4:0.02:0:1.5 0/0:93:0:0,0:45,48:0:2,0:30.6:1:31.2:1:1:0:60:92:1:0:0.2 -2 67977529 . G T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06073;SOR=0.21;LSEQ=ACATGCTTGTCTGTCTCTGC;RSEQ=TCCAGATTTCTTCCTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:0,20:0,4:0.8333:0,1:33.1:1:30.8:1:1:0:60:40:0.8333:0:1.1 1/0:14:7:0,7:0,7:0.5:0,0:21.1:1:30.9:1:1:0:60:14:0.5:0:1 -2 68104810 . A T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25542;SOR=Inf;LSEQ=AATTAGCTAAACAGTTCCTC;RSEQ=TTTAGAGCTTTCCTGGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:9,0:3,1:0.6923:2,0:23.3:1:31.9:1:0.30769:0:60:18:0.6923:0:1.3 1/1:6:6:5,1:0,0:1:0,2:18:1:28.7:1:1:0:60:12:1:0:1.3 -2 68104870 . C A 26 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52962;SOR=0;LSEQ=TCCAGGCAGCATCTTCAGGA;RSEQ=CAAAGGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:20:0:26:0:1:1.0801:60:4:0.0741:0:1.5 0/0:15:0:0,0:9,6:0:2,0:31.6:1:31.7:1:1:0:60:30:1:0:0.3 -2 68104885 . ACAG A 31 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.59215;SOR=2.10626;LSEQ=CAGGACCAAAGGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:14,16:0.0625:2,2:29:0:34:0:1:1.14:60:4:0.0625:0:0.5 0/1:16:2:1,1:8,6:0.125:2,2:41:1:31:1:1:1.30929:60:4:0.125:0:0 -2 68104888 . G A 28 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.11101;SOR=Inf;LSEQ=GACCAAAGGCAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,16:0:2,0:24.8:1:31.4:1:1:0:60:28:1:0:0.3 0/1:16:2:1,1:7,5:0.125:2,2:30.5:1:28.5:1:1:1.36624:60:4:0.1429:0:1.5 -2 69741609 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18301;SOR=Inf;LSEQ=TGGTTGATTCTTACCGCTGG;RSEQ=TCCTGGGCAGGGGCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:0:2,0:34.8:1:32.9:1:1:0:60:20:1:0:0.1 0/1:8:2:1,1:5,1:0.25:2,2:25.5:1:29:1:0.46429:3.87298:60:4:0.25:0:1 -2 69741731 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49666;SOR=0;LSEQ=CAGCTGTTGTTGATGCAGGG;RSEQ=TGTGGCCAGCTGTTGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:35,35:0.0278:2,2:39:1:31:1:1:1:60:4:0.0286:0:1 0/0:69:0:0,0:35,33:0:2,0:27.5:1:31.4:1:1:0:60:33:0.9851:0:0.3 -2 69741753 . CTGT C 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTGGCCAGCTGTTGCTGTTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:45,43:0:2,0:26.8:1:30.3:1:1:0:60:176:1:0:0.4 0/1:81:27:15,12:25,29:0.3333:2,2:30:1:32.3:1:0.48517:1.44:60:54:0.3333:0.0741:0.3 -2 69741762 . TTGC T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.21854;SOR=Inf;LSEQ=TGTTGCTGTTGCTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:42,44:0:2,0:26.4:1:29.9:1:1:0:60:172:1:0:0.5 0/1:76:2:1,1:35,39:0.0263:2,2:24.5:1:29.5:1:1:1.11:60:4:0.0263:0:0.5 -2 69741765 . C T 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.12217;SOR=0;LSEQ=TGCTGTTGCTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:4:2,2:38,42:0.0476:2,2:29.8:1:29.3:1:1:1.10:60:8:0.0482:0:1 0/0:76:0:0,0:35,39:0:2,0:26.8:1:32.1:1:1:0:60:73:1:0:0.3 -2 69741801 . C T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00119;SOR=0.22147;LSEQ=TGGTAGAAATTCTGCATTAG;RSEQ=TGCTGTTGAGAGCCTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:26:9,17:10,12:0.5417:2,2:21.1:1:30.5:1:0.55702:1.55905:60:52:0.5417:0:1.3 0/1:44:9:4,5:13,22:0.2045:2,2:26.2:1:29:1:0.71607:1.34:60:18:0.2045:0:1.1 -2 69741805 . T C 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4953;SOR=0;LSEQ=AGAAATTCTGCATTAGCTGC;RSEQ=GTTGAGAGCCTCCTTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:18,26:0.0435:2,2:30:1:24.5:1:1:1.43:60:4:0.0444:0:2 0/0:42:0:0,0:15,27:0:2,0:23:1:29.7:1:1:0:60:41:1:0:0.5 -2 69741854 . T G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACTGAGCAATTGCTGGTT;RSEQ=CTGGGTTGCTGGATGTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:3,18:0,0:1:0,2:27:1:32.5:1:1:0:60:42:1:0:1.3 1/1:11:11:0,11:0,0:1:0,0:25.9:1:32.6:1:1:0:60:22:1:0:1.2 -2 69746137 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.49677;SOR=Inf;LSEQ=AACGTGCCTGCCGGCTGCTG;RSEQ=TGTGCTGGCGGTGGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:35,25:0:2,0:25.1:1:31.4:1:1:0:60:59:1:0:0.1 0/1:65:2:1,1:41,22:0.0308:2,2:29.5:1:31.5:1:1:1.84484:60:4:0.0308:0:1 -2 69746188 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24914;SOR=Inf;LSEQ=TGCTGCTTGAGGAAGAGTTG;RSEQ=TGCTGGTGCTGGGGTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:31,36:0:2,0:29.5:1:32:1:1:0:60:66:1:0:0.1 0/1:78:3:2,1:33,42:0.0385:2,2:15.3:1:28.3:1:0.58456:2.52:60:6:0.04:0:1 -2 69746199 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49646;SOR=Inf;LSEQ=GAAGAGTTGCTGCTGGTGCT;RSEQ=GGGTGTGGCCTGGGCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:26,34:0:2,0:27.6:1:31.5:1:1:0:60:59:1:0:0.1 0/1:64:2:1,1:26,36:0.0313:2,2:17:1:27.5:1:1:1.38:60:4:0.0313:0:1 -2 69746224 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58116;SOR=2.58244;LSEQ=GTGGCCTGGGCCTGAGCGGG;RSEQ=AGACCCTGGGCCTGAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:1:0,1:17,30:0.0208:2,0:1:0:31:0:1:0:60:2:0.0208:0:1 0/1:38:2:1,1:10,26:0.0526:2,2:21.5:1:28:1:0.50071:2.53:60:4:0.0526:0:1 -2 69746296 . C T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52632;SOR=0;LSEQ=GGCTGCTTGGCCTGAGTTTG;RSEQ=GGCAGAGGCTGGCTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:0,12:0.2:0,0:21:1:32:1:1:0:60:6:0.2:0:1 0/0:6:0:0,0:0,6:0:0,0:14.7:1:29:1:1:0:60:12:1:0:0 -2 69747759 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACCCGCCTTAGCCTCCC;RSEQ=AAGTGTTGGGATTACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 69751151 . T A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00622;SOR=0.14642;LSEQ=GGGCATTTCCCCAAATAACA;RSEQ=CTTCGTTTAATCCTCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:4,8:7,10:0.4138:2,2:25.8:1:29.6:1:0.71669:1.3839:60:24:0.4444:0:1.4 0/1:33:3:1,2:11,19:0.0909:2,2:26.3:1:31.3:1:1:1.15289:60:6:0.0909:0:1.3 -2 69751203 . C T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81119;LSEQ=TTGGAAGAACCTAGGTTGAA;RSEQ=AGACTGTGATTAGCTAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:21.7:1:28.3:1:1:0:60:6:0.3333:0:1.7 0/1:7:2:0,2:0,5:0.2857:0,0:21:1:29:1:1:0:60:4:0.2857:0:1 -2 70165296 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17134;SOR=Inf;LSEQ=CTGGACTGGAGCAGCAGCAG;RSEQ=GTGAGCGACTCTGACGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:31,32:0:2,0:26.3:1:30.2:1:1:0:60:126:1:0:0.2 0/1:45:2:1,1:21,22:0.0444:2,2:27:1:28.5:1:1:1.05:60:4:0.0444:0:1 -2 70166936 . C A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCGACCTAAGGGCTCAA;RSEQ=GGCTGACTCGGCAGCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:38.5:1:30.5:1:1:1:60:4:0.5:0:1.5 -2 70585033 . G C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.78786;SOR=0.84636;LSEQ=AAAGAAGTGGGATGTGAGCT;RSEQ=TCAAATGTCACAGAAGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:10,2:5,4:0.5714:2,2:20.5:1:30.4:1:0.33105:3.72:60:11:0.55:0:1.2 1/0:34:18:11,7:9,7:0.5294:2,2:23.7:1:31:1:1:1.22:60:36:0.5294:0:1.1 -2 71182900 . T C 79 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52273;SOR=0.28305;LSEQ=GCTAGGCAAAAAAACAAATC;RSEQ=GCTTTGCAGTGAACTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:3,0:0.6667:0,2:13.8:1:30.7:1:1:0:60:12:0.6667:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:11:0:31:0:1:0:60:2:0.3333:0:1 -2 71183017 . A AT 63 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.64823;SOR=0.39808;LSEQ=AGAGTTAACAGTTTATTATA;RSEQ=TTTTTTTTTTCACAATCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:4:4,0:52,16:0.0556:2,0:21:1:31.8:1:0.56889:0:60:8:0.0556:0:0 0/1:44:1:1,0:34,9:0.0227:2,0:31:0:31:0:1:0:60:2:0.0233:0:0 -2 71183397 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18801;SOR=Inf;LSEQ=AAATCCTCCTTTGCTTCCCA;RSEQ=GGAACTTGAGAAGTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:54,187:0:2,0:22.6:1:30.7:1:1:0:60:47.2:1:0:0.1 0/1:185:2:1,1:55,127:0.0108:2,2:9.5:1:28.5:1:0.51722:2.30:60:4:0.011:0:1 -2 71183445 . C T 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03374;SOR=Inf;LSEQ=CACAGCCACCATAGCCGGGT;RSEQ=CCCATGTACTGCCATAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:1,110:0:1,0:25.1:1:31.1:1:1:0:60:36:1:0:0.1 0/1:54:3:0,3:1,50:0.0556:1,0:19:1:29:1:1:0:60:6:0.0566:0:3 -2 71210606 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=AGCAGGTGTAATTACATAGG;RSEQ=TGCAAAACCCAGAAAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:17:1:31:1:1:1:60:4:0.2:0:1 0/0:11:0:0,0:7,4:0:2,0:22:1:29.4:1:1:0:60:22:1:0:0.1 -2 71734021 . T C 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTCCCTGTGGCTCTCTGA;RSEQ=GGGCAGCTAGAAGACAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:30:1:1:0:60:4:1:0:1.5 -2 71735047 . A G 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCGCCTCAGCCTCCTGA;RSEQ=TAGCTGGGACTACAAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:24.8:1:31.3:1:1:0:60:12:1:0:1 1/1:2:2:2,0:0,0:1:0,0:18.5:1:33.5:1:1:0:60:4:1:0:1 -2 71735178 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50404;SOR=0;LSEQ=CCTCATGCTAATCTTGGAGG;RSEQ=CCGGAGTCAGCATGGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:29,29:0.0333:2,2:19:1:29.5:1:1:1:60:4:0.0339:0:1 0/0:46:0:0,0:26,20:0:2,0:20.9:1:31.4:1:1:0:60:92:1:0:0.2 -2 72126420 . G A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.85534;SOR=0.96242;LSEQ=CTGGGGGAAAAAGTGCCAAC;RSEQ=GCGGTGTTTCAGACACCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:100:47,53:126,139:0.274:2,2:22.4:1:29.8:1:1:1.02214:60:24:0.2682:0:1.1 0/1:259:69:35,34:98,92:0.2664:2,2:27:1:29.9:1:1:1.03466:60:138:0.2727:0:1.1 -2 72126508 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.53647;SOR=0;LSEQ=ACAGAGAAGGAAAGGACGGA;RSEQ=AAGAAGAAAGAGCGCTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:34,109:0.0138:2,2:11:0:31:0:0.42577:3.17:60:4:0.0138:0:1.5 0/0:82:0:0,0:19,63:0:2,0:21.7:1:31.1:1:1:0:60:81:1:0:0.2 -2 74317094 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50548;SOR=0;LSEQ=TCTCCTTTGGTTGTTCCTGG;RSEQ=GCATGTACTTCAACGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:26,27:0.0364:2,2:27:1:32.5:1:1:1.04:60:4:0.037:0:1 0/0:41:0:0,0:16,25:0:2,0:24.4:1:29.5:1:1:0:60:19.5:1:0:0.2 -2 74317132 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18937;SOR=Inf;LSEQ=TGCAAGTATGCTCGGAGCAA;RSEQ=ACACCTCGCAAGTTCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:20.7:1:30.5:1:1:0:60:48:1:0:0.2 0/1:19:2:1,1:7,10:0.1053:2,2:6.5:1:27:1:1:1.40:60:4:0.1053:0:1.5 -2 75399893 . T A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.52746;SOR=0.65816;LSEQ=AAATAGAAATTTATTTATAG;RSEQ=TTTGGAGGCTAGAAGTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:23:12,11:5,4:0.7188:2,2:21.3:1:29:1:1:1.14098:60:22:0.7097:0:1.1 1/0:16:10:6,4:3,3:0.625:2,2:22:1:27.9:1:1:1.46:60:20:0.625:0:1 -2 75660748 . G A 50 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.28205;SOR=0.21386;LSEQ=CTGCTAGTTCTGAGTAATCC;RSEQ=GGCAACTCAGACGAGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:0.4286:2,0:25:1:31.7:1:1:0:60:6:0.4286:0:2 0/1:8:1:1,0:5,2:0.125:2,0:31:0:32:0:1:0:60:2:0.125:0:1 -2 75660828 . G T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11196;SOR=0.30697;LSEQ=CCAAAGTGCTTTGTTAAATG;RSEQ=GTCCTGCTCCCCGTGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:6,6:5,5:0.5455:2,2:26:1:29.5:1:1:1:60:24:0.5455:0:1.3 0/1:19:5:3,2:7,7:0.2632:2,2:22.6:1:30.6:1:1:1.47:60:10:0.2632:0:1.2 -2 75660834 . G T 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.002;SOR=0;LSEQ=TGCTTTGTTAAATGGGTCCT;RSEQ=CTCCCCGTGCCACCCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:5,4:5,8:0.4091:2,2:19.6:1:30.3:1:0.66563:1.94:56.2:18:0.4091:0:1 0/0:18:0:0,0:9,9:0:2,0:24.7:1:31.3:1:1:0:60:36:1:0:0.6 -2 75660847 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1417;SOR=Inf;LSEQ=GGGTCCTGCTCCCCGTGCCA;RSEQ=CCAACTGGGTGAGACCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:31.8:1:31.5:1:1:0:58.6:48:1:0:0.9 0/1:15:2:1,1:6,7:0.1333:2,2:28:0:28.5:1:1:1.15:60:4:0.1333:0:1 -2 76787924 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.34836;LSEQ=CTTTTTTATTGTTACTATAA;RSEQ=GGAGGTTTTAAAATAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:242:136,106:164,122:0.4583:2,2:24.8:1:30.6:1:0.7922:1.04761:60:241:0.4582:0:1.1 0/1:466:106:62,44:198,162:0.2275:2,2:21.7:1:30.2:1:0.57842:1.15:60:212:0.2299:0:1.1 -2 79227376 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GGTGCCAACACCTGTGCTCT;RSEQ=TGCAGTTGAAGGGCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:13.5:1:32:1:1:0:60:8:0.4:0:3 1/1:2:2:2,0:0,0:1:0,0:8:1:33.5:1:1:0:60:4:1:0:3 -2 79227379 . C T 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53846;SOR=3.18702;LSEQ=GCCAACACCTGTGCTCTATG;RSEQ=AGTTGAAGGGCCAGGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:16.5:1:30.5:1:1:0:60:8:0.3636:0:3 1/0:3:2:2,0:1,0:0.6667:0,0:11:1:31:1:1:0:60:4:0.6667:0:3 -2 79227405 . A G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91372;LSEQ=AAGGGCCAGGAGTGTGGATC;RSEQ=GGGATCCCACACCAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:11:11,0:5,0:0.6875:0,0:24.2:1:28.5:1:1:0:60:10:0.6667:0:1.8 1/0:3:2:2,0:1,0:0.6667:0,0:37:1:30.5:1:1:0:60:4:0.6667:0:3 -2 79227455 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13788;SOR=Inf;LSEQ=TGCAACCATGTGAACTTCAT;RSEQ=CCAAGGTCCTCTTTCGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:0:1,0:23.3:1:30.6:1:1:0:60:15.5:1:0:0.6 0/1:20:2:2,0:17,1:0.1:1,0:36.5:1:33:0:1:0:60:4:0.1053:0:1 -2 79227583 . A G 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGAAGCTTTCCCTGCTGC;RSEQ=GCCTTCAAAATGTCCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:285,125:0:2,0:24.7:1:30.4:1:1:0:60:135.667:1:0:0.4 0/1:275:69:48,21:132,73:0.2509:2,2:25.6:1:29.2:1:0.46665:1.26:60:68:0.2509:0:1.1 -2 79227650 . G C 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3592;LSEQ=TCTTCCCTCTGGTTTTCCCT;RSEQ=ATCTTCTCATCTCCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:703:457:252,205:140,105:0.6501:2,2:23.5:1:31.5:1:0.63289:1.08452:60:90.4:0.6485:0:1.1 0/1:520:208:109,99:168,144:0.4:2,2:23.4:1:31:1:0.788:1.0595:60:207:0.4019:0:1.1 -2 79227759 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32458;LSEQ=CATTGTTTTCTACTTATTCA;RSEQ=CTTTCCCATAGTCTGAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:356:239:55,184:22,95:0.6713:2,2:23.4:1:31.2:1:0.41227:1.29:59.9:478:0.6751:0:1.1 0/1:221:88:26,62:34,99:0.3982:2,2:23.7:1:30.6:1:0.53917:1.22:60:176:0.4018:0:1.2 -2 79227772 . C CTG 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00215;SOR=0.53841;LSEQ=TTATTCATCTTTCCCATAGT;RSEQ=TGAGCATTTTTCAGTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:139:15,124:26,105:0.511:2,2:31.1:1:30.9:1:0.04268:2.0416:59.9:68.5:0.5131:0.0184:1.1 0/1:164:59:11,48:21,84:0.3598:2,2:26:1:30.8:1:1:1.09036:60:118:0.362:0.0244:1.1 -2 79227782 . T C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00562;SOR=Inf;LSEQ=TTCCCATAGTCTGAGCATTT;RSEQ=TCAGTCATAGACCACTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:26,205:0:2,0:25.1:1:30.2:1:1:0:59.9:76:1:0:0.6 0/1:129:5:1,4:16,108:0.0388:2,2:16.4:1:32.6:1:0.51258:1.68:60:10:0.0388:0:1.8 -2 79227813 . G GT 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.17744;SOR=0.60842;LSEQ=ACCACTCCTTCATTTTATTT;RSEQ=TTTTTTTATAGAAAGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:55:2,53:0,71:0.4297:1,1:28.5:1:30.5:1:0.18857:0:60:110:0.4331:0:0.7 0/1:51:16:1,15:0,35:0.3137:1,1:27.6:1:31.4:1:0.31373:0:60:32:0.3137:0.0196:0.8 -2 79228733 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAATAACATGGTGAAAAA;RSEQ=AAAAGCATAGGCAATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22:1:31.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 79228861 . A ATATTTATT 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=4;SSF=0.04762;SOR=0;LSEQ=AGGGACACAGATGCACATTT;RSEQ=TATTTATTTATTGGATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19.5:1:31.3:1:1:0:60:4:1:0.5:3.5 0/0:5:0:0,0:5,0:0:0,0:31:1:28.2:1:1:0:60:10:1:0:0 -2 79228890 . G A 63 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00699;SOR=0;LSEQ=TATTGGATGCCATCCACATG;RSEQ=CAAATGAGTAGGCTAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,1:0.7143:2,2:22.4:1:27.2:1:1:3.16:60:4:0.6667:0:3.2 0/0:8:0:0,0:5,3:0:2,0:22.6:1:31.1:1:1:0:60:16:1:0:0 -2 79228904 . T C 63 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01923;SOR=0;LSEQ=CACATGGCAAATGAGTAGGC;RSEQ=AAACGGAAGGTAGCACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:1,1:0.5714:2,2:27.8:1:31.8:1:1:2.45:60:8:0.6667:0:3 0/0:9:0:0,0:5,4:0:2,0:23.3:1:29.3:1:1:0:60:18:1:0:0 -2 79228925 . T A 89 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00191;SOR=0.03262;LSEQ=AAACGGAAGGTAGCACAGAA;RSEQ=TGTCTCTGTCCTCAACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:6,3:1,1:0.8182:2,2:23.8:1:28.3:1:1:1.87:60:8:0.8:0:2.6 0/1:10:1:1,0:4,5:0.1:2,0:18:0:32:0:1:0:60:2:0.1:0:2 -2 79229006 . A G 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28613;SOR=0.18597;LSEQ=TTCCAGAAAACAAAGCCCCT;RSEQ=CCTTCCTCTGGTTATTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:1,1:0.7143:2,0:25:1:33:1:0.28571:0:60:10:0.7143:0:1.6 0/1:7:2:1,1:2,3:0.2857:2,2:26:1:31.5:1:1:1.41:60:4:0.2857:0:1.5 -2 79422965 . C G 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4672;SOR=0.88794;LSEQ=CTGAATCAATACATATCACT;RSEQ=AATGAAAGTTCTAGACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:148:73,75:71,88:0.4821:2,2:24.6:1:31.4:1:0.42527:1.21:60:73:0.4834:0:1.1 0/1:305:138:65,73:78,89:0.4525:2,2:26.5:1:30.7:1:1:1.02:60:33.5:0.4482:0:1.2 -2 79423056 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51678;SOR=0;LSEQ=TGGAAAGTAGGGGGATGAAC;RSEQ=CAGTTTTTTGTTTGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:25,92:0.0168:2,2:9.5:1:29:1:0.39069:3.63:60:4:0.0171:0:1.5 0/0:80:0:0,0:19,61:0:2,0:24.2:1:29.2:1:1:0:60:79:1:0:0.2 -2 79423062 . TTTTG T 106 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.03318;SOR=0.1254;LSEQ=GTAGGGGGATGAACTCAGTT;RSEQ=TTTGTTTGTTTTATGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:12:4,8:17,79:0.1101:2,2:25.3:1:29.7:1:0.2432:2.30:60:24:0.1121:0.0092:0 0/1:66:1:0,1:14,51:0.0152:2,0:48:0:28:0:1:0:60:2:0.0152:0:0 -2 79524985 . C T 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13075;SOR=0;LSEQ=CTTGAAGTCAAATTCTGAGG;RSEQ=AGATTATCCACACTCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:4:1,3:217,125:0.0115:2,2:20.3:1:27:1:0.14499:5.18305:60:8:0.0119:0:2 0/0:287:0:0,0:162,125:0:2,0:26:1:31.9:1:1:0:60:142.5:1:0:0.5 -2 79524994 . C T 228 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAATTCTGAGGCAGATTATC;RSEQ=ACACTCATTGGAAACAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:209:125,84:104,65:0.5529:2,2:27.7:1:29.7:1:0.75173:1.07498:60:103.5:0.5535:0:1.1 0/0:315:0:0,0:172,143:0:2,0:25.9:1:30.8:1:1:0:60:314:1:0:0.5 -2 79524996 . C T 69 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03483;SOR=0;LSEQ=ATTCTGAGGCAGATTATCCA;RSEQ=ACTCATTGGAAACAAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:6:3,3:226,154:0.0155:2,2:38.2:1:26.8:1:0.69065:1.46601:60:5:0.0131:0:2 0/0:319:0:0,0:174,145:0:2,0:26:1:31.3:1:1:0:60:158.5:1:0:0.5 -2 79525033 . T A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.38565;LSEQ=TAACTGCAAATAGTTACTCA;RSEQ=CTATCTCTCATTTGATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:147:74,73:142,149:0.3349:2,2:27.5:1:29.6:1:0.76263:1.06:60:72.5:0.3356:0:1.1 1/0:381:208:107,101:90,82:0.5459:2,2:25.3:1:29.3:1:0.91793:1.03594:60:51:0.544:0:1.1 -2 79525176 . C T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.01303;SOR=0.34399;LSEQ=TATGGTACCACATGTCTTGG;RSEQ=CCATTTTGCATTGCTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:47:1,46:0,28:0.6267:1,1:25.6:1:30.6:1:1:0:60:46:0.6301:0:1 0/1:33:12:1,11:0,21:0.3636:1,2:19.2:1:30:1:0.36364:0:60:24:0.3636:0:1 -2 79600541 . CG GT 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATACAGAATACTATTAAA;RSEQ=TAGTGATTCATACCTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 79601273 . A T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=1;SOR=1.16426;LSEQ=GTCCCTGATTATTCATCATC;RSEQ=TCACCAGCAACAACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:36:19,17:4,2:0.8571:2,2:28.8:1:29.9:1:0.67286:1.76554:60:35:0.8537:0:1.9 1/1:32:28:14,14:3,1:0.875:2,2:24.6:1:29.9:1:0.60289:2.90535:60:56:0.875:0:2.1 -2 79601323 . T G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09812;LSEQ=AGCAGAAATAGAGAATTACT;RSEQ=GTTCAAGTAGTAAAACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:25:8,17:2,3:0.8333:2,2:27.2:1:30.2:1:1:1.39974:60:11.5:0.8214:0:2.6 1/1:26:22:7,15:2,2:0.8462:2,2:29.5:1:30.8:1:0.59064:2.07641:60:44:0.8462:0:2.8 -2 79601338 . A G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.71606;LSEQ=TTACTTGTTCAAGTAGTAAA;RSEQ=CCTTCTGTGGAAGTCTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:5,14:1,2:0.8636:2,2:27.9:1:32.2:1:1:1.37755:60:38:0.8636:0:2.8 1/1:22:18:6,12:2,2:0.8182:2,2:23.6:1:31.6:1:0.60191:1.93443:60:36:0.8182:0:2.9 -2 79601392 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14286;SOR=0;LSEQ=ACCTTCCCCTGTCTCTAACC;RSEQ=TCTTGTTTTCTAAAATTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:23:1:30:1:1:0:60:6:0.75:0:3 0/0:4:0:0,0:0,4:0:0,0:16.5:1:32:1:1:0:60:8:1:0:1.3 -2 80688324 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49754;SOR=Inf;LSEQ=AATCCTGTTAAGTCAGTTTA;RSEQ=TAAGAACCACCCACCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:21.5:1:32.2:1:1:0:60:24:1:0:0.1 0/1:17:2:1,1:5,10:0.1176:2,2:11.5:1:29:1:1:1.91:60:4:0.1176:0:1.5 -2 81267146 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TTGTTTCCTCTAGGATCAAG;RSEQ=CCATCAAGCTACAGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:0:2,0:26.6:1:32.6:1:1:0:55.8:16:1:0:0 0/1:7:2:1,1:1,4:0.2857:2,2:12:1:31.5:1:1:3.16:60:4:0.2857:0:1 -2 81267220 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=AACTTCTACTGAGGACCCCT;RSEQ=GACTCACCCGCTGGCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:23.5:1:30.5:1:1:0:60:8:1:0:0 0/1:7:2:1,1:2,3:0.2857:2,2:23:1:27.5:1:1:1.41:60:4:0.2857:0:1 -2 81420681 . G A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAGTTATTTACAACTGTGCA;RSEQ=TAATGTGTTGCAAACTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:17:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:42:0:31:1:1:0:60:4:1:0:1.5 -2 81421230 . C G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06757;SOR=Inf;LSEQ=GCCCCCGGCATGGTCTTCTC;RSEQ=TCCCGCCGGGGCCGGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:7,1:27,0:0.2286:1,2:31.8:1:31:1:0.22857:0:60:16:0.2286:0:1 1/1:2:2:2,0:0,0:1:0,0:30.5:1:30:1:1:0:60:4:1:0:1 -2 81421702 . C T 238 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=309.39854;LSEQ=ATGAACTGGCTGGTGTTGAG;RSEQ=CGGTCGCGCACTGACTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1051:2:0,2:521,528:0.0019:2,0:12.5:1:26.5:1:0.49956:0:60:4:0.0019:0:1 0/1:864:321:179,142:284,258:0.3715:2,2:27.4:1:28.7:1:0.35885:1.14:60:28.182:0.3682:0:1.1 -2 81421951 . A G 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.08611;LSEQ=ACAGCTAGTTCAGGGACTCC;RSEQ=CCAGCGAGGGAGGGGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:976:162:79,83:428,386:0.166:2,2:25.1:1:30.7:1:0.3901:1.16477:60:53:0.1668:0:1.1 1/0:740:523:271,252:108,108:0.7068:2,2:23.5:1:30.2:1:0.68606:1.08:60:64.375:0.7113:0:1.2 -2 81422135 . G T 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=11.19505;LSEQ=GTGCAGGAATTCGAAGTAGG;RSEQ=GTTGGCCCTGTCGCTGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1820:318:162,156:776,725:0.1747:2,2:24.4:1:29.9:1:0.85303:1.0307:60:158:0.1763:0:1.1 1/0:1430:1006:507,499:219,205:0.7035:2,2:24.9:1:29.2:1:0.68538:1.05143:60:51.947:0.7025:0:1.2 -2 81422297 . G A 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=21.60926;LSEQ=GCGCGGATGCTGGGCTGGGC;RSEQ=TAGTCCTCCTCCGAGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1029:2:1,1:443,584:0.0019:2,2:1:0:29:1:1:1.32:60:4:0.002:0:1.5 0/1:742:30:10,20:309,403:0.0404:2,2:21.9:1:29.6:1:0.34745:1.53265:60:60:0.0408:0:1 -2 81422395 . C T 64 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01695;SOR=9.33039;LSEQ=TCTGCCGGTTCCTGGTGATG;RSEQ=AGTGAGGGATCTACCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:898:1:0,1:474,423:0.0011:2,0:1:0:23:0:0.47216:0:60:2:0.0011:0:1 0/1:582:6:1,5:321,255:0.0103:2,2:12.2:1:24.8:1:0.09409:6.27634:60:12:0.0105:0:1 -2 81422495 . C T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGCCGCAGGGAGGGCCTT;RSEQ=GGCTGGGGCGGCAGCACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:662:0:0,0:225,436:0:2,0:24.5:1:29.9:1:1:0:60:49.846:0.9985:0:0.1 0/1:464:29:10,19:154,278:0.0625:2,2:20.4:1:29.4:1:1:1.05241:60:58:0.0637:0:1.2 -2 81422590 . G A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08753;SOR=1.90095;LSEQ=CAGTGTCCATGGGGGGCAAG;RSEQ=GGTGTCGGGGGCACAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:23:9,14:36,93:0.1513:2,2:20.8:1:30.8:1:0.3232:1.65:60:46:0.1513:0:1.9 0/1:67:17:6,11:10,40:0.2537:2,2:20.2:1:29.4:1:0.20899:2.15:60:34:0.2656:0:1.8 -2 81422631 . T G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.35887;LSEQ=ATGCGGCAGGGGGTAGGAGG;RSEQ=GTTCAGCCTCGGCCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:28:14,14:61,56:0.1931:2,2:26.5:1:32:1:1:1.08864:60:56:0.1958:0:2.1 1/0:68:52:32,20:11,5:0.7647:2,2:23.6:1:30.2:1:0.76894:1.36872:60:25:0.7576:0:2 -2 81422682 . C G 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.2402;LSEQ=CCAGTTGGCACTGTTCAGGG;RSEQ=GAACGGGTGTGGGCTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:42:28,14:123,44:0.201:2,2:25:1:30.8:1:0.44069:1.39541:60:84:0.2049:0:1.7 1/0:108:78:53,25:24,6:0.7222:2,2:23.8:1:30.7:1:0.24465:1.87639:60:77:0.7196:0:1.7 -2 81422771 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.52355;LSEQ=TCCGTAGCTTCTAGAGCCAC;RSEQ=TCCAGCTTTGGCTCCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:63:45,18:285,149:0.1268:2,2:21.8:1:30.5:1:0.39523:1.31:60:62:0.127:0:1.1 1/0:318:216:128,88:62,38:0.6792:2,2:24.2:1:29.8:1:0.71131:1.1213:60:107:0.6772:0:1.2 -2 81423100 . GTCC T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTAGACAGGCTGTGGCTGTT;RSEQ=AGGAGGCTATTTTCCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:314,288:0:2,0:25.3:1:31.8:1:1:0:60:42:0.9983:0:0.2 0/1:320:11:5,6:141,166:0.0344:2,2:23.5:1:30.2:1:1:1.01922:60:22:0.0347:0:0 -2 81423277 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.24718;LSEQ=GGTAGAGATGGTGGCGGGGA;RSEQ=GGCTTCCACCCTGTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:504:104:39,65:139,260:0.2063:2,2:21.7:1:30.5:1:0.6457:1.12:60:33.667:0.2061:0:1.3 1/0:354:279:116,163:31,44:0.7881:2,2:23.1:1:29.3:1:1:1.01:59.9:45.5:0.7867:0:1.2 -2 81423349 . C T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30225;SOR=0;LSEQ=AGTGTTCTGGGAGAGAGAGG;RSEQ=GGAAAGGGGGGGGCGGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:4:2,2:246,152:0.01:2,2:6.5:1:28.5:1:0.6392:1.61635:60:8:0.0104:0:2.3 0/0:230:0:0,0:134,95:0:2,0:22:1:29.8:1:1:0:60:24.444:1:0:0.7 -2 81423354 . A AG 122 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00018;SOR=6.91094;LSEQ=TCTGGGAGAGAGAGGCGGAA;RSEQ=GGGGGGGGCGGGTATGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:4:3,1:272,148:0.0094:2,2:18:1:33.2:1:1:1.63:60:8:0.0099:0.0024:0 0/1:259:16:9,7:150,93:0.0618:2,2:22.2:1:30.7:1:0.79191:1.25334:60:32:0.0632:0.0039:0.9 -2 81423356 . G A 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.01685;SOR=1.57911;LSEQ=TGGGAGAGAGAGGCGGAAAG;RSEQ=GGGGGGCGGGTATGGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:79:51,28:231,119:0.1837:2,2:19.8:1:29.9:1:0.79462:1.06558:60:18.75:0.1807:0:1.8 0/1:263:69:36,33:128,66:0.2624:2,2:19.5:1:29.5:1:0.04446:1.77379:60:33.5:0.2597:0:1.7 -2 81423424 . G A 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07552;SOR=1.2744;LSEQ=CAGAGTGGAGGGAGTCCGCG;RSEQ=AGCAGAAGTATTCTGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:985:148:87,61:514,321:0.1503:2,2:24.9:1:29.6:1:0.52337:1.12258:60:73:0.1513:0:1.4 0/1:647:119:72,47:295,231:0.1839:2,2:23.8:1:28.8:1:0.4129:1.20:60:118:0.1844:0:1.3 -2 81423752 . T C 293 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=611.18451;LSEQ=GGGAAGGTTTTGCTTGTAAA;RSEQ=TTGAGAAGACGCCCTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2153:2:1,1:1129,1021:9e-04:2,2:16.5:1:31:1:1:1.10573:60:4:9e-04:0:1 0/1:1788:654:346,308:569,562:0.3658:2,2:25.3:1:31.4:1:0.30224:1.11:59.3:58.455:0.367:0:1.2 -2 81424068 . G A 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=53.50043;LSEQ=TTGGCAGGAGCCTGGCTGGC;RSEQ=TTTTCCAAAAGCCCACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1389:2:1,1:724,663:0.0014:2,2:15:1:20:1:1:1.09193:60:1:7e-04:0:2.5 0/1:1101:79:45,34:540,481:0.0718:2,2:24.7:1:29.5:1:0.55874:1.18:60:78:0.0715:0:1.2 -2 81424158 . G T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=13.64386;LSEQ=CAGTGGGCACGGGCGTGGAG;RSEQ=GCGGGGAGTGGGCGCAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1134:202:104,98:455,477:0.1781:2,2:27:1:29.7:1:0.53473:1.11:60:49.5:0.1787:0:1.1 1/0:832:622:294,328:107,102:0.7476:2,2:23.3:1:29.4:1:0.3378:1.17011:60:68.111:0.7467:0:1.2 -2 81424517 . C T 269 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=135.47571;LSEQ=CGTCGTCTGCTGGCTTCGCC;RSEQ=TCTCCTTGAGGTTGGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2591:7:3,4:1363,1219:0.0027:2,2:20.4:1:30.1:1:0.71373:1.4906:60:14:0.0027:0:2 0/1:1737:467:237,230:645,621:0.2689:2,2:24.9:1:30.4:1:0.95685:1.00797:59.6:115.75:0.2692:0:1.2 -2 81424736 . T C 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGATACTTTATCATCCCCT;RSEQ=TGCTCATCTTCACAGAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1846:0:0,0:926,917:0:2,0:25:1:29.9:1:1:0:60:64.821:0.9994:0:0.2 0/1:1376:82:49,33:659,634:0.0596:2,2:22.5:1:30.8:1:0.13869:1.43:60:81:0.0598:0:1.2 -2 81424759 . C T 233 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01707;LSEQ=CTCATCTTCACAGAGTCGTC;RSEQ=TTTTCTTTTTCTGCACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1862:204:107,97:826,832:0.1096:2,2:26.9:1:30.4:1:0.50459:1.11:60:39.8:0.1086:0:1.2 0/0:1432:3:0,3:725,704:0.0021:2,0:1:0:26:1:0.12009:0:60:6:0.0021:0:1 -2 81425140 . T C 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=77.83328;LSEQ=ATCTTCTATGACAGCTTTCA;RSEQ=GTTGTAAGAAACTCCATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1902:1:1,0:1015,885:5e-04:2,0:8:0:33:0:1:0:60:2:5e-04:0:1 0/1:1473:58:25,33:695,719:0.0394:2,2:24.4:1:30.9:1:0.42193:1.27573:60:116:0.0395:0:1.1 -2 81425437 . C A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=18.54364;LSEQ=GCTCCTGCCCTCAGTCTGTG;RSEQ=AGCTGTCAGAGGAGACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1206:177:102,75:600,427:0.1468:2,2:22.8:1:29.8:1:0.86904:1.03319:60:87.5:0.1468:0:1.1 1/0:722:550:325,225:107,62:0.7618:2,2:24.5:1:29:1:0.36927:1.19449:60:54:0.7595:0:1.2 -2 81425558 . C T 135 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=0.11201;LSEQ=ACTTCTCAAGGACTTCCTCT;RSEQ=CTTGGAATATTCTTTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2041:24:16,8:1008,1007:0.0118:2,2:21.5:1:29.6:1:0.14927:2.00:60:48:0.012:0:1.1 0/0:1503:2:0,2:764,735:0.0013:2,0:1:0:24:0:0.24092:0:60:4:0.0013:0:1 -2 81425585 . C T 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11149;LSEQ=ATATTCTTTATCTGACTTCT;RSEQ=TTTGTGTTTGCTGTTAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1956:595:302,293:676,677:0.3042:2,2:24.5:1:30.1:1:0.76795:1.03:60:73.375:0.3048:0:1.1 0/1:1464:68:39,29:713,682:0.0464:2,2:22.6:1:29.4:1:0.32346:1.29:60:67:0.0463:0:1.1 -2 81425899 . G A 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCATAGGCCTCCCGCCCTTC;RSEQ=TCCTTCTCCTAGAGGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:825:0:0,0:359,466:0:2,0:25.3:1:31.1:1:1:0:60:102.125:1:0:0.1 0/1:552:26:11,15:240,286:0.0471:2,2:22.7:1:29.7:1:0.84118:1.14403:60:52:0.0474:0:1.2 -2 81426046 . A AT 203 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.70153;SOR=1.06127;LSEQ=TTCTCCTTGCCTTTCTTGTC;RSEQ=TTTTTTTTTTCAGAGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1794:103:56,47:905,768:0.0574:2,2:31:1:30.4:1:1:1.01:60:33.333:0.0574:0:0.1 0/1:1334:81:40,41:652,594:0.0607:2,2:31.4:1:29.6:1:0.64692:1.12498:59.9:39.5:0.0612:0:0.3 -2 81426131 . C CT 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.75846;SOR=0.89613;LSEQ=CTTGGTCAAGAGACACTTTC;RSEQ=TTTTTTTTGTCTTTGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1794:26:13,13:904,862:0.0145:2,2:25.8:1:30.5:1:1:1.04871:60:52:0.0147:0.0017:0.2 0/1:1307:17:11,6:674,610:0.013:2,2:23.5:1:28.9:1:0.34084:1.66:60:16:0.0124:0.0023:0.5 -2 81426483 . C A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.70132;LSEQ=GGCCCTGCAGTCCCTGTGCT;RSEQ=CTTGGAGCTCTGGAGGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:516:97:58,39:237,180:0.188:2,2:25.4:1:28.8:1:0.64898:1.13:60:47.5:0.187:0:1.1 1/0:329:211:127,84:72,46:0.6413:2,2:22.4:1:28.3:1:0.90686:1.03516:60:69.333:0.644:0:1.1 -2 81426529 . G A 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTCCTGGCTGGCCTCTAC;RSEQ=GACTCTCTCTCCTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:0:0,0:474,229:0:2,0:22.5:1:30:1:1:0:60:57.583:0.9971:0:0.2 0/1:450:29:19,10:283,138:0.0644:2,2:26.3:1:30.3:1:0.84029:1.07914:60:58:0.0649:0:1.5 -2 81426638 . G A 177 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=93.29062;LSEQ=CAAATAGTCCTTGTCCTTTT;RSEQ=GAAGAAGGGCTCTCTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2023:1:1,0:1113,906:5e-04:2,0:1:0:26:0:1:0:60:2:5e-04:0:1 0/1:1495:66:36,30:768,656:0.0441:2,2:25.6:1:29.3:1:1:1.02:60:132:0.0446:0:1.2 -2 81426909 . C T 271 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=0.00317;LSEQ=CTGATTTTTATTAAAATATT;RSEQ=ATCAAAAGCAGAATCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2349:619:333,286:869,859:0.2635:2,2:24.2:1:29.3:1:0.14632:1.15:59.7:205.333:0.2646:0:1.1 0/0:1777:2:0,2:895,877:0.0011:2,0:1:0:23.5:1:0.24537:0:57.5:4:0.0011:0:1 -2 81427036 . C T 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.39593;LSEQ=TTCTTTTTCTCTAATTTTGA;RSEQ=GGCCCGTCTTTTCACTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2208:388:191,197:878,940:0.1757:2,2:23.8:1:30.6:1:0.7797:1.04:59.9:387:0.1769:0:1.1 1/0:1613:1143:539,604:215,252:0.7086:2,2:24.5:1:30:1:0.70026:1.05:60:284.75:0.7092:0:1.1 -2 81427187 . C T 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=12.16944;LSEQ=TGCTGATATCTTTGTTCATG;RSEQ=CTTTGATTCTCTTCAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1298:240:117,123:528,530:0.1849:2,2:24.5:1:30:1:0.77506:1.0473:60:480:0.1878:0:1.1 1/0:956:702:358,344:131,122:0.7343:2,2:25.4:1:29.3:1:0.88339:1.03176:60:233:0.735:0:1.1 -2 81427308 . G A 259 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTTTTTTAAAGTGGTCTC;RSEQ=ATCAAGCTATAACACTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1283:379:181,198:462,441:0.2954:2,2:24:1:30.3:1:0.27119:1.14589:60:188.5:0.2959:0:1.1 0/0:963:0:0,0:472,490:0:2,0:25:1:30.3:1:1:0:60:67.714:0.9989:0:0.1 -2 81427526 . C T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.42144;LSEQ=CTCCTTGTTCAGCTTGGGGA;RSEQ=GGTGCCCTCTGCGCTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1272:206:84,122:473,593:0.1619:2,2:22.8:1:30.5:1:0.35796:1.15834:60:205:0.1639:0:1.1 1/0:822:566:232,334:105,150:0.6886:2,2:23.7:1:29.8:1:1:1.00775:60:55.6:0.6847:0:1.1 -2 81428037 . A AT 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.89564;SOR=0.95132;LSEQ=TTTTCCTTCACTTCTTTTTC;RSEQ=TTTTTTTTTCCTTCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1125:34:22,12:723,365:0.0302:2,2:24.7:1:29.9:1:0.85462:1.08037:59:16:0.0295:0.0036:0.4 0/1:903:26:18,8:546,324:0.0288:2,2:28.3:1:30.8:1:0.54455:1.33:59.8:52:0.0295:0:1 -2 81428075 . C T 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=13.90951;LSEQ=TGCTTGGCATTAGAAGCCTC;RSEQ=CATTTCTTACTACCAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1701:255:153,102:876,569:0.1499:2,2:26.9:1:30.5:1:0.88951:1.02636:60:50:0.1489:0:1.1 1/0:1296:921:502,419:211,162:0.7106:2,2:25.6:1:29.6:1:0.5373:1.08704:59.9:91.1:0.7128:0:1.1 -2 81428378 . C A 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00141;SOR=2.32746;LSEQ=AAAATAAAAAATAATGCCTT;RSEQ=GATGGCTTCCTCTACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:41:1,40:3,193:0.173:1,1:27.5:1:31.6:1:0.53473:1.60:60:40:0.1702:0:1.1 0/1:125:41:3,38:3,80:0.328:1,2:20.5:1:31.2:1:0.39598:2.09:60:82:0.328:0:1 -2 82017107 . T C 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.64818;SOR=1.27263;LSEQ=TAGACATTTTCATGGCTTTT;RSEQ=AAAAACATTTTTATAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:17:17,0:30,1:0.3542:1,1:26.4:1:31.4:1:1:0:60:16:0.3404:0:1.1 0/1:34:14:14,0:19,1:0.4118:1,1:25.6:1:31.4:1:1:0:60:28:0.4242:0:1 -2 82017114 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.05877;SOR=Inf;LSEQ=TTTCATGGCTTTTTAAAAAC;RSEQ=TTTTTATAAAATCTGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:54,1:0:1,0:21.5:1:30.6:1:1:0:60:54:1:0:0.4 0/1:36:3:3,0:32,1:0.0833:1,0:36.3:1:30.7:1:1:0:60:6:0.0857:0:1 -2 82017237 . C G 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCATATTAGTTGGGTTTGAG;RSEQ=TCTTTGTGAACTTCAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:275,212:0:2,0:26.6:1:31.8:1:1:0:60:59.875:0.9958:0:0.3 0/1:404:25:14,11:215,163:0.0619:2,2:31.1:1:30.5:1:1:1.0363:60:24:0.0605:0:1.2 -2 82017300 . T A 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00391;SOR=1.54651;LSEQ=AGGAAAAATAAATGTATTGG;RSEQ=TCAGATATTTTAGTTACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:145:58,87:90,158:0.369:2,2:27.2:1:30.6:1:0.51759:1.17:60:144:0.3721:0:1.2 0/1:360:171:71,100:76,113:0.475:2,2:24.9:1:29.6:1:0.83042:1.06:60:84.5:0.4761:0:1.2 -2 82017339 . AATC A 48 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.69328;SOR=0.59903;LSEQ=TGTAAAATAATAATAATAGT;RSEQ=ATCATCATCATCACTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:4:3,1:44,163:0.019:2,2:7.8:1:24:1:0.03536:10.94:60:8:0.0194:0.0142:1 0/1:175:2:1,1:43,129:0.0114:2,2:25.5:1:28.5:1:0.44289:2.98:60:4:0.0118:0.0057:1.5 -2 82017373 . C A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06615;SOR=1.80731;LSEQ=TCACTCCAAATGGCTTAAGC;RSEQ=ACAAAGTAAGTTTCAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:39:1,38:4,63:0.3679:2,1:23.3:1:30.1:1:0.64972:2.39543:60:78:0.39:0:1.5 1/0:74:38:4,34:3,33:0.5135:2,2:22.2:1:30.4:1:1:1.29:60:76:0.5205:0:1.6 -2 83593573 . G T 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=1.00712;LSEQ=TGGATGGGCAAGTGCTTTGA;RSEQ=ATATCCCCTGCATTCGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:106:51,55:182,207:0.2141:2,2:27.4:1:29.4:1:0.82692:1.05:60:105:0.2143:0:1.2 0/1:339:73:37,36:132,133:0.2153:2,2:26:1:28.9:1:1:1.04:60:146:0.2179:0:1.2 -2 83738306 . C A 49 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.31815;SOR=3.42481;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGATGATGAAGGAGGGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:2,0:19,23:0.0455:2,0:33:1:31:1:0.22199:0:60:4:0.0465:0:1 0/1:21:3:1,2:9,9:0.1429:2,2:30.3:1:31.3:1:1:1.93674:60:6:0.1429:0:1 -2 85408298 . G A 29 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GAAAGAGGTGCGGAGAGCAG;RSEQ=GAGCACCTGAGAGAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:11,1:0.1429:2,0:28:1:29:1:1:0:60:4:0.1429:0:1 0/1:7:1:1,0:6,0:0.1429:0,0:8:0:29:0:1:0:60:2:0.1667:0:2 -2 85408364 . G A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01311;SOR=Inf;LSEQ=GCCCAATGAGAGTAGCCAGC;RSEQ=TGTGCATGTGAGGGGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:37,3:0:2,0:24:1:30.6:1:1:0:60:39:1:0:0.1 0/1:22:4:4,0:18,0:0.1818:1,0:23.5:1:28.8:1:1:0:60:8:0.1818:0:1.3 -2 85408551 . A G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.42886;LSEQ=GGTGTGCCTCCCTGCTGGGC;RSEQ=TGGGCCCGCCTGCTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:115:42,73:77,102:0.3912:2,2:27.4:1:30.8:1:0.27627:1.31087:60:56.5:0.391:0:1.1 1/0:223:136:60,76:40,47:0.6099:2,2:25.8:1:30.4:1:0.89027:1.07765:60:272:0.6154:0:1.1 -2 85408559 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03607;SOR=Inf;LSEQ=TCCCTGCTGGGCATGGGCCC;RSEQ=CCTGCTGGGGGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:106,173:0:2,0:26.7:1:30.9:1:1:0:60:138.5:1:0:0.5 0/1:217:4:3,1:90,123:0.0184:2,2:21.8:1:27.5:1:0.31597:4.07:60:8:0.0185:0:1.5 -2 85408601 . G GA 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05719;SOR=Inf;LSEQ=AGGAAGCAAGTAGCCCGGAG;RSEQ=AAAAAAAGAACTATGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:63,134:0:2,0:22.7:1:31.3:1:1:0:60:196:1:0:0.3 0/1:191:4:2,2:71,114:0.0209:2,2:32.5:1:30.8:1:0.64069:1.60:60:8:0.0212:0:0 -2 85408621 . T C 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.24756;SOR=0;LSEQ=GAAAAAAAGAACTATGTGTG;RSEQ=GACTGTGTGGTGGCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:1,2:46,104:0.0195:2,2:18.3:1:25:1:1:1.13:60:2:0.0132:0:1.3 0/0:154:0:0,0:55,99:0:2,0:23.9:1:29.9:1:1:0:60:153:1:0:0.4 -2 85408669 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07991;SOR=Inf;LSEQ=GAGGGTTCAGCACACACAGG;RSEQ=AACCCCAGGCAGCTCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:14,60:0:2,0:24.6:1:30.9:1:1:0:60:36:1:0:0.1 0/1:57:3:0,3:13,41:0.0526:2,0:28:1:32:0:1:0:60:6:0.0526:0:1 -2 85531579 . C A 23 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCTCACCCTCCCCCCA;RSEQ=CTCTCTTTGATCAAGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:23.5:1:1:0:60:4:1:0:1 -2 85533450 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08425;SOR=Inf;LSEQ=TGGTGGCTGAGTGCACCCTG;RSEQ=AGGAAAGTGCAGCCATTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:20,35:0:2,0:25.1:1:30.3:1:1:0:60:110:1:0:0.1 0/1:23:2:1,1:3,18:0.087:2,2:15.5:1:29.5:1:0.32411:5.34:60:4:0.087:0:1 -2 85533634 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24727;SOR=0;LSEQ=GAGCTGGCCCGGAAGGAGCG;RSEQ=CAGCTTCACTCGCAGCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:3:1,2:44,45:0.0326:2,2:32.3:1:29:1:1:1.94186:60:6:0.0326:0:1 0/0:84:0:0,0:43,41:0:2,0:28.9:1:31.5:1:1:0:60:168:1:0:0.1 -2 85533668 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50086;SOR=0;LSEQ=AGCTCTACCCAACCTGGTCA;RSEQ=CCCGGGACAACTATGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:24,49:0.0267:2,2:30:1:29:1:1:2.02:60:4:0.027:0:1 0/0:62:0:0,0:27,35:0:2,0:24.7:1:31.2:1:1:0:60:124:1:0:0.1 -2 85533678 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50276;SOR=0;LSEQ=AACCTGGTCAGCCCGGGACA;RSEQ=CTATGTAAGTGCACACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:19,52:0.0274:2,2:10.5:1:28.5:1:0.47565:2.69:60:4:0.0282:0:1.5 0/0:58:0:0,0:24,34:0:2,0:21.1:1:28.7:1:1:0:60:116:1:0:0.1 -2 85960749 . C T 65 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=TGGGGCCTTGGCCATCTCTC;RSEQ=CCTCCCCGCTGGGCCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:39.8:1:32.5:1:1:0:60:8:0.6667:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:28:0:27:0:1:0:60:2:0.3333:0:1 -2 86184026 . CA TG 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGAAATGACACTCCCCA;RSEQ=GGAAGTCCTTGGTTAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:34.8:1:32.9:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 86184199 . C T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.39581;LSEQ=CAGGTGGCATTTATGAAATG;RSEQ=AATCCTTTGGGAAAAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:7,0:5,0:0.5833:0,0:27.6:1:30:1:1:0:60:14:0.5833:0:1.1 1/0:3:2:2,0:1,0:0.6667:0,0:17:1:31.5:1:1:0:60:4:0.6667:0:1 -2 86184354 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18814;SOR=Inf;LSEQ=CTGATATCATAGCTGGTGCG;RSEQ=TATGAAGCAATGTTATAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:134,22:0:2,0:22.1:1:30.9:1:1:0:60:51:1:0:0.3 0/1:120:2:1,1:98,20:0.0167:2,2:13:1:28.5:1:0.32059:4.80631:60:4:0.0168:0:1 -2 86184441 . A G 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00073;SOR=1.5642;LSEQ=TTTGGATACCAATGGTCCAA;RSEQ=AGGAAGGTCCTGATTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:637:422:238,184:117,97:0.6625:2,2:26.8:1:31.9:1:0.73543:1.07:60:421:0.664:0:1.7 1/0:513:387:214,173:70,56:0.7544:2,2:25.8:1:31.2:1:1:1.01049:60:76.4:0.752:0:1.7 -2 86184486 . T G 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00354;SOR=1.46447;LSEQ=TTGGGGAGGAATGTCACAAC;RSEQ=TGCTACAAGCTCACCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:678:441:213,228:114,123:0.6504:2,2:24.7:1:31.1:1:1:1.01:60:219.5:0.6513:0:1.7 1/0:503:368:173,195:65,69:0.7316:2,2:24:1:30:1:0.83992:1.06167:60:91:0.7309:0:1.7 -2 86184565 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15359;SOR=Inf;LSEQ=GTTGTGGGAATTGCTCTCAG;RSEQ=CTTCCCCAGGGTAGTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:80,228:0:2,0:23.8:1:31.6:1:1:0:60:101.667:1:0:0.3 0/1:199:2:1,1:51,146:0.0101:2,2:32:1:27.5:1:0.45531:2.84:60:4:0.0101:0:1 -2 86184608 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.1428;SOR=Inf;LSEQ=CCAAGCTATTTCAAACCAAT;RSEQ=TTTTTTTCTTCTTTTTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:7,114:0:2,0:24.9:1:32.2:1:1:0:60:59.5:1:0:0.1 0/1:74:2:1,1:5,67:0.027:2,2:17:0:28.5:1:0.15661:12.32:60:4:0.0274:0:1 -2 86650358 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50958;SOR=Inf;LSEQ=GTTCCCGAAGAGGGTGATGA;RSEQ=GCACAGCAGAAAAACATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:42,26:0:2,0:25.5:1:30.6:1:1:0:60:67:0.9853:0:0.2 0/1:95:2:1,1:56,37:0.0211:2,2:25.5:1:29.5:1:1:1.5067:60:4:0.0213:0:1.5 -2 86650379 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51253;SOR=Inf;LSEQ=GCACAGCAGAAAAACATGGA;RSEQ=AAGTTAGCAACAGCAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:57,40:0:2,0:27.3:1:31.6:1:1:0:60:47.5:1:0:0.3 0/1:137:2:1,1:75,60:0.0146:2,2:13:0:27:1:1:1.24794:60:4:0.015:0:1 -2 86650444 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17865;SOR=0;LSEQ=TGAAGTATGTTGCCAGCACC;RSEQ=GAATGCTGCAGTCATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:26,34:0.0323:2,2:18.5:1:32.5:1:1:1.30:60:4:0.0328:0:2 0/0:84:0:0,0:35,49:0:2,0:24.1:1:29.7:1:1:0:60:41:1:0:0.4 -2 86650474 . T G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16927;SOR=2.32679;LSEQ=AGTCATTCCTTTGAATAGTT;RSEQ=GACAGGCTAATTCAGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:20:4,16:4,7:0.6452:2,2:25.1:1:31.3:1:0.40549:2.22149:60:40:0.6667:0:1.1 1/1:37:30:5,25:1,6:0.8108:2,2:17.7:1:29.3:1:1:1.19:60:14:0.8:0:1 -2 89852137 . C CGGTTCCATTCCATTCGACTCCACTCCATTCGAGTCTTTTCTATTG 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=CCATCCAATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:16.5:1:32.5:1:1:0:50:4:0.6667:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:36.5:1:27.5:1:1:1:43:4:0.5:0.5:4 -2 89852158 . A T 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=3.1622;LSEQ=CATTCCATTCCATTCCGTTC;RSEQ=GTTCGATTCCAATCCGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:33:0:32:0:1:0:20:2:0.5:0:8 1/1:5:4:2,2:0,1:0.8:0,2:20.3:1:29.5:1:1:0:46.5:8:0.8:0:5.3 -2 89852174 . G A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=GTTCAGTTCGATTCCAATCC;RSEQ=TTTGATTCCATTTTGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:2,0:0.3333:0,0:43:0:33:0:0.33333:0:20:2:0.3333:0:8 0/1:5:2:1,1:1,2:0.4:2,2:34:1:28.5:1:1:1.73:50:4:0.4:0:6.5 -2 89852204 . A T 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=ATTTTGTTCCAGTCCATTCC;RSEQ=TTCGAGTCCATTCCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:19.7:1:26.3:1:1:0:40:2:1:0:7.7 1/0:5:3:1,2:0,2:0.6:0,2:19.3:1:28.7:1:1:0:41.3:6:0.6:0:6.7 -2 89852214 . A T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGTCCATTCCATTCGAGTCC;RSEQ=TTCCAATCCACTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:30:1:1:0:40:4:1:0:8 1/0:4:2:1,1:0,2:0.5:0,2:15:1:31.5:1:1:0:50:4:0.5:0:6.5 -2 89852359 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCGTTCCATTGCATTCCA;RSEQ=TTGATTACATTCCATTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:1:29.5:1:1:0:56:4:1:0:6.5 -2 89852377 . G T 28 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CACTTGATTACATTCCATTC;RSEQ=ATTCCAATCCATTCGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:31:1:1:0:58.5:4:1:0:5.5 0/1:5:2:1,1:1,2:0.4:2,2:24:1:28:1:1:1.73:56:4:0.4:0:6.5 -2 89852384 . A T 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=TTACATTCCATTCGATTCCA;RSEQ=TCCATTCGAATCAATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:16.7:1:32:1:1:0:59:6:1:0:3.7 1/0:5:3:1,2:1,1:0.6:2,2:18.7:1:29.7:1:1:1.7321:42.3:6:0.6:0:4 -2 89852393 . A T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=ATTCGATTCCAATCCATTCG;RSEQ=ATCAATTACATTGCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:31:1:30:0:1:0:58.5:4:0.6667:0:5.5 0/1:5:2:1,1:1,2:0.4:2,2:39:1:28.5:1:1:1.73:56:4:0.4:0:6.5 -2 89852405 . T A 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=TCCATTCGAATCAATTACAT;RSEQ=GCAATCCATTACATTCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:36.7:1:31:1:1:0:59:6:1:0:3.7 1/0:5:3:1,2:1,1:0.6:2,2:31.3:1:30.3:1:1:1.7321:42.3:6:0.6:0:4 -2 89852421 . C G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=ACATTGCAATCCATTACATT;RSEQ=GAGTCTGTTCTATTGCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:36:1:31:1:1:0:58.5:4:0.6667:0:5.5 0/1:5:2:1,1:1,2:0.4:2,2:26.5:1:32.5:1:1:1.73:56:4:0.4:0:6.5 -2 89852428 . G A 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=AATCCATTACATTCGAGTCT;RSEQ=TTCTATTGCAGTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:36:1:31.3:1:1:0:59:6:1:0:3.7 1/0:5:3:1,2:1,1:0.6:2,2:8.3:1:29:1:1:1.7321:42.3:6:0.6:0:4 -2 89852436 . G C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATTCGAGTCTGTTCTATT;RSEQ=CAGTCCATTCCATTCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21:1:29.5:1:1:0:58.5:4:0.6667:0:5.5 1/1:2:2:0,2:0,0:1:0,0:12:1:31:1:1:0:51.5:4:1:0:6 -2 89852439 . G T 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGAGTCTGTTCTATTGCA;RSEQ=TCCATTCCATTCTGGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18:1:29:1:1:0:58.5:4:0.6667:0:5.5 1/1:1:1:0,1:0,0:1:0,0:20:0:32:0:1:0:60:2:1:0:8 -2 89853177 . T G 71 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CATTCCGTTGCATTCCATTC;RSEQ=ATTCCATTCCATTGTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:8:0:32:0:1:0:60:2:1:0:4 1/0:10:6:5,1:3,0:0.6:0,2:9.8:1:27.5:1:1:0:39.3:5:0.5556:0:7.5 -2 89853192 . TT CA 116 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24871;SOR=3.95518;LSEQ=CATTCTATTCCATTCCATTG;RSEQ=TTCCATTCCATTCCATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,0:0.6:0,0:10.7:1:32.2:1:1:0:36.7:6:0.6:0:5.7 1/1:15:13:10,3:0,0:0.8667:0,2:19.1:1:31.5:1:1:0:39.4:26:0.8667:0.0667:5.4 -2 89853196 . C G 137 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15958;SOR=3.41353;LSEQ=CTATTCCATTCCATTGTTTT;RSEQ=CATTCCATTCCATTTGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:0.2222:2,0:15:1:33.5:1:1:0:37.5:4:0.2222:0:5 1/0:38:19:13,6:11,8:0.5:2,2:14.6:1:32.4:1:0.73743:1.56:45.5:38:0.5:0:5.7 -2 89853211 . T G 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01522;LSEQ=GTTTTCCATTCCATTCCATT;RSEQ=GATTACATTCCATTCGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:7,6:3,1:0.5417:2,2:17:1:31.8:1:0.60294:2.43937:50:26:0.5417:0:4.2 1/0:66:36:18,18:1,2:0.5455:2,2:20.4:1:31.3:1:1:1.97:42.5:72:0.5455:0:4.6 -2 89853214 . T C 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56912;SOR=Inf;LSEQ=TTCCATTCCATTCCATTTGA;RSEQ=TACATTCCATTCGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:0:2,0:20.7:1:31:1:1:0:50.4:48:1:0:4.5 0/1:71:3:2,1:32,36:0.0423:2,2:23.3:1:33:1:0.60381:2.23:57.7:6:0.0423:0:5.3 -2 89853216 . A G 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34201;SOR=0.57906;LSEQ=CCATTCCATTCCATTTGATT;RSEQ=CATTCCATTCGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:9,7:6,2:0.6667:2,2:22.3:1:32.9:1:0.65702:2.25451:48.8:32:0.6667:0:4.6 1/0:71:38:18,20:15,16:0.5352:2,2:24.7:1:32.3:1:1:1.04107:42.6:76:0.5429:0:4.6 -2 89853223 . A T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.067;SOR=0;LSEQ=ATTCCATTTGATTACATTCC;RSEQ=TTCGATTCCATTCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:15,9:0.0769:2,2:26:0:32.5:1:1:1.63293:59:4:0.0769:0:4 0/0:73:0:0,0:34,39:0:2,0:27.2:1:30.3:1:1:0:44.2:72:1:0:4.2 -2 89853224 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTTGATTACATTCCA;RSEQ=TCGATTCCATTCCATTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:16,10:0:2,0:28.5:1:31.2:1:1:0:50.3:52:1:0:4.3 0/1:73:2:1,1:33,38:0.0274:2,2:24.5:1:31.5:1:1:1.15:33:4:0.0274:0:4 -2 89853225 . T G 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.34282;SOR=1.77885;LSEQ=TCCATTTGATTACATTCCAT;RSEQ=CGATTCCATTCCATTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:5,2:11,8:0.2692:2,2:29.3:1:32.4:1:0.66798:1.78:52.6:14:0.2692:0:4.3 0/1:73:29:14,15:20,24:0.3973:2,2:26.9:1:32.4:1:1:1.12:47.7:58:0.3973:0:4.2 -2 89853227 . G A 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05439;SOR=0.1095;LSEQ=CATTTGATTACATTCCATTC;RSEQ=ATTCCATTCCATTCGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:2,1:13,8:0.1154:2,2:34.3:1:31:1:1:1.22:43.7:6:0.1154:0:6 0/1:73:1:0,1:34,37:0.0137:2,0:31:0:27:0:1:0:31:2:0.0139:0:6 -2 89853236 . CCA AAT 48 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0528;SOR=0.10814;LSEQ=ACATTCCATTCGATTCCATT;RSEQ=TTCGAATCAATTACATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:2,1:9,7:0.1111:2,2:29.3:1:30.6:1:1:1.52:43.7:6:0.1111:0:4 0/1:77:1:0,1:21,23:0.013:2,0:34:0:28.3:0:1:0:31:2:0.013:0:4 -2 89853237 . CAT GAAA 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.3592;SOR=1.68062;LSEQ=CATTCCATTCGATTCCATTC;RSEQ=TCGAATCAATTACATTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:5,3:9,7:0.2963:2,2:29.5:1:30.5:1:1:1.28:51:16:0.2963:0.037:4.9 0/1:77:32:14,18:21,23:0.4156:2,2:29.3:1:29.9:1:0.81735:1.17144:47:64:0.4156:0.0519:4.6 -2 89853246 . C T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGATTCCATTCCATTCGAAT;RSEQ=AATTACATTGCAATCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:16,11:0:2,0:24.1:1:32.2:1:1:0:49.9:54:1:0:4.2 0/1:76:2:1,1:33,41:0.0263:2,2:24:1:27.5:1:1:1.24:43.5:4:0.027:0:5 -2 89853247 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCCATTCGAATC;RSEQ=ATTACATTGCAATCCATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:16,11:0:2,0:23.2:1:30.7:1:1:0:49.9:54:1:0:4.2 0/1:75:2:1,1:33,40:0.0267:2,2:12.5:1:31:1:1:1.21:33:4:0.0267:0:4 -2 89853255 . T A 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82004;SOR=1.16479;LSEQ=TCCATTCGAATCAATTACAT;RSEQ=GCAATCCATTACATTCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:6,6:9,5:0.4615:2,2:20:1:30.5:1:0.69217:1.75912:49.2:24:0.4615:0:4.4 1/0:70:35:16,19:15,20:0.5:2,2:14.3:1:29.3:1:1:1.12:44.1:70:0.5147:0:4.6 -2 89853260 . T A 25 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGAATCAATTACATTGCAA;RSEQ=CCATTACATTCACGTCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:11.9:1:30.9:1:1:0:49.5:52:1:0:4.3 0/1:64:2:1,1:27,35:0.0313:2,2:11:1:25.5:1:1:1.29:44.5:4:0.0323:0:6 -2 89853265 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08877;SOR=0;LSEQ=TCAATTACATTGCAATCCAT;RSEQ=ACATTCACGTCCGTTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:13,8:0.087:2,2:8:0:33:0:1:1.58984:49:4:0.087:0:2 0/0:53:0:0,0:21,31:0:2,0:8:1:28.4:1:1:0:43.6:51:0.9808:0:4.6 -2 89853268 . ATTCAC TATTGA 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38779;SOR=3.25055;LSEQ=ATTACATTGCAATCCATTAC;RSEQ=GTCCGTTCTATTCCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:8,6:0.0667:2,0:29:0:32.4:0:0.46667:0:40:2:0.0667:0:8 0/1:26:5:1,4:6,15:0.1923:2,2:30.8:1:29.5:1:1:1.57335:37:10:0.1923:0:7.6 -2 89853272 . AC CA 27 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=0;LSEQ=CATTGCAATCCATTACATTC;RSEQ=GTCCGTTCTATTCCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,1:0.2857:2,2:14:0:27.5:1:1:1.7321:60:4:0.3333:0:5 0/0:10:0:0,0:0,1:0:0,0:1:0:32:0:1:0:33:2:0.2:0:3 -2 89853277 . C T 31 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=CAATCCATTACATTCACGTC;RSEQ=GTTCTATTCCACTCCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,1:0.5:0,2:10:0:31.5:1:1:0:60:4:0.5:0:5 0/0:8:0:0,0:1,4:0:2,0:36.2:1:29.8:1:1:0:37:10:0.625:0:7.6 -2 89853281 . C T 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=4.34109;LSEQ=CCATTACATTCACGTCCGTT;RSEQ=TATTCCACTCCATTGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:0.25:2,0:42:0:32:0:1:0:40:2:0.3333:0:8 1/0:8:5:1,4:1,2:0.625:2,2:38.6:1:30.2:1:1:1.8258:37:10:0.625:0:7.6 -2 89853289 . C G 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACGTCCGTTCTATTCCA;RSEQ=TCCATTGAATTCCAGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:34:0:34:0:1:0:40:2:1:0:8 1/1:5:5:1,4:0,0:1:0,2:33:1:32.2:1:1:0:37:10:1:0:7.6 -2 89853294 . T C 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCGTTCTATTCCACTCCA;RSEQ=TGAATTCCAGTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:29:0:34:0:1:0:40:2:1:0:8 1/1:5:4:1,3:0,1:0.8:0,2:33.5:1:33.5:1:1:0:36.3:8:0.8:0:7.5 -2 89853297 . A C 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTCTATTCCACTCCATTG;RSEQ=ATTCCAGTCCATTCCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:26:0:34:0:1:0:40:2:1:0:8 1/1:5:5:1,4:0,0:1:0,2:25:1:32.4:1:1:0:37:10:1:0:7.6 -2 89853302 . CA TG 50 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTCCACTCCATTGAATTC;RSEQ=GTCCATTCCATTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:11.5:1:30.6:1:1:0:40:4:1:0.5:4.5 1/0:4:3:1,2:0,0:0.75:0,2:25.7:1:31.8:1:1:0:35:6:0.75:0:6.3 -2 89853563 . A GTCCATT 26 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TTCGAGTCCATTACATTTGG;RSEQ=TCCATTCCTTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:43.5:1:26.6:1:1:0:21:4:0.6667:0:4.5 -2 89853572 . T G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACATTTGGATCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:39:1:29.5:1:1:0:21:4:0.6667:0:4.5 -2 89853780 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCCATTAGGTTCCATT;RSEQ=CGTTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33:0:32:1:1:0:60:4:1:0:4.5 -2 89853782 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTAGGTTCCATTTC;RSEQ=TTCCATTCCATTCCATTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:30:1:1:0:60:4:1:0:4.5 -2 89853801 . GT CA 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTCCATTCCATTCCATTC;RSEQ=TTCCATTCCAATCGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:31.5:1:1:0:60:4:1:0:3.5 -2 89854790 . C G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATCCGATATACTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:32:0:1:0:43.5:4:1:0:8 -2 89854794 . CC TT 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=GATATACTTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:30:1:1:0:43.5:4:1:0:7 -2 89854801 . AC CT 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATCCGATAT;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:31.5:1:1:0:43.5:4:1:0:6 -2 89854825 . CT AG 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=ATTCGACTCCATTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:0:29:1:1:0:43.5:4:1:0:5 -2 89854850 . C G 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGACTCCATTCCATTCGAGT;RSEQ=CATTCCATTCCATTCGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:29:1:1:0:43.5:4:1:0:5 -2 89854853 . T TTCCACTCGAA 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTCCATTCCATTCGAGTCCA;RSEQ=TCCATTCCATTCGACATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:1:28:1:1:0:43.5:4:1:1:8 -2 89870063 . T C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAATCCATTCCATTCCTTT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:16:0:31.5:1:1:0:37:4:0.6667:0:2 -2 89870070 . G T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCTTTTCACTCG;RSEQ=GTTGATTCCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:23:0:31:1:1:0:37:4:0.6667:0:2 -2 89870381 . A T 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAATTTCATTCCATTCCA;RSEQ=TCCTTTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:6:1:29.7:1:1:0:40:6:1:0:5 -2 89870398 . C G 65 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAATCCTTTCCATTCCATT;RSEQ=CACTCGGGTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:21.5:1:32.5:1:1:0:40.5:8:1:0:4.8 -2 89870402 . T A 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTTCCATTCCATTCCAC;RSEQ=CGGGTTCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:25.5:1:30:1:1:0:40.5:8:1:0:4.8 -2 89870435 . A C 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:13:0:32.5:1:1:1:42:4:0.5:0:4.5 -2 89870438 . C A 30 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:10:0:30.5:1:1:1:42:4:0.5:0:4.5 -2 89870453 . C T 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTGCATTCTAGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:28:1:1:0:39:4:1:0:5 -2 89870458 . G C 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCTAGTTGATTCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:29.5:1:1:0:39:4:1:0:5 -2 89870460 . ATTCTAGTTGATTCAATTCCATTTGT A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTGC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:27.6:1:1:1:39:4:0.5:0.5:5 -2 89870668 . C G 34 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:0:34:0:1:0:33:4:1:0:1.5 0/0:2:0:0,0:1,1:0:2,0:3.5:1:27.5:1:1:0:20:4:1:0:3.5 -2 89870683 . CCATTCACTTGGGTTG GTATTCGGGTTA 29 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:29:0:32.5:1:1:0:33:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29.8:1:1:0:20:4:1:0:1.5 -2 89870688 . C CCCCTGT 31 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=ACTTGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:0:31.8:1:1:0:33:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 89870969 . T C 32 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCAACTCGGTTTGATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:32:0:32.5:1:1:0:60:4:0.6667:0:3 -2 89870981 . C T 31 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:29:0:31.5:1:1:0:60:4:0.6667:0:3 -2 89871001 . T G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:9:0:33:1:1:0:60:4:0.6667:0:3 -2 89871220 . T A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAC;RSEQ=CGGGTTGATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:2:0:31:0:1:0:29:2:1:0:3 1/0:3:2:1,1:0,1:0.6667:0,2:27.5:1:27:1:1:0:29:4:0.6667:0:3 -2 89871246 . CCATTGTATT C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCCATTCCATTTCATT;RSEQ=CTTTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:40:0:32.5:1:1:0:29:4:0.6667:0:3 -2 89871288 . C G 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCACTCGG;RSEQ=TTGATTCCATTCCATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:30.5:1:1:0:29:4:1:0:3 -2 89872079 . A T 112 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.75022;SOR=1.49317;LSEQ=ATTCCGCTTCTTTCCATTCC;RSEQ=TTCCATTCCATTCCTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:8,6:0.1667:2,2:10.7:1:29.7:1:0.57647:2.51691:44.7:6:0.1875:0:3 0/1:65:15:8,7:27,23:0.2308:2,2:7.9:1:28.9:1:1:1.02676:38.9:14:0.2222:0:4.8 -2 89872080 . T A 31 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.213;SOR=0.27129;LSEQ=TTCCGCTTCTTTCCATTCCA;RSEQ=TCCATTCCATTCCTGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,10:0.0909:2,2:11:0:27:0:1:1:41.5:4:0.0909:0:4.5 0/1:77:2:1,1:37,37:0.026:2,2:1:0:31.5:1:1:1:21:4:0.0263:0:4 -2 89872083 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CGCTTCTTTCCATTCCATTC;RSEQ=ATTCCATTCCTGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:11.7:1:30.3:1:1:0:39.2:21:1:0:3.7 0/1:79:2:1,1:39,38:0.0253:2,2:12:1:31.5:1:1:1.02598:36:4:0.0253:0:3 -2 89872084 . A T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.2059;SOR=0.2643;LSEQ=GCTTCTTTCCATTCCATTCC;RSEQ=TTCCATTCCTGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,10:0.0909:2,2:14:1:31.5:1:1:1:44:4:0.0952:0:4 0/1:79:2:1,1:39,38:0.0253:2,2:12:0:31:1:1:1.02598:27:4:0.0256:0:2 -2 89872088 . C A 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CTTTCCATTCCATTCCATTC;RSEQ=ATTCCTGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:16.2:1:31.6:1:1:0:38.3:46:1:0:3.6 0/1:81:2:1,1:40,39:0.0247:2,2:19:0:32:0:1:1.02533:37:4:0.025:0:5 -2 89872092 . C A 111 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.34938;SOR=2.56524;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CTGTTGATTCCATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:0.087:2,2:22.5:1:19:1:1:1.09544:39:1:0.0455:0:4 0/1:81:16:9,7:32,33:0.1975:2,2:20:1:27.9:1:0.78127:1.32:37.1:15:0.1899:0:4.4 -2 89872093 . CT AA 103 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93954;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=GTTGATTCCATTCCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:1,2:11,8:0.1304:2,2:15:0:29.2:1:0.57143:2.62608:38.7:6:0.1429:0:3.3 0/1:81:10:4,6:36,32:0.1235:2,2:16:1:31.1:1:0.51235:1.67623:38.2:20:0.1235:0:3.9 -2 89872094 . T G 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87828;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=GTTGATTCCATTCCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:11,7:0,1:0.7826:0,2:23.5:1:29.4:1:0.42105:0:38.3:17:0.8947:0:3.3 1/0:79:60:32,28:3,4:0.7595:2,2:23.1:1:30.4:1:0.70137:1.51:35.3:120:0.8824:0:4.2 -2 89872096 . T A 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08355;SOR=2.42112;LSEQ=TCCATTCCATTCCATTCCTG;RSEQ=TGATTCCATTCCATTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:6,5:1,3:0.4783:2,2:25.5:1:30.4:1:0.56923:3.31:38.1:22:0.5:0:3.4 1/0:81:56:30,26:5,8:0.6914:2,2:24.5:1:29.4:1:0.37065:1.83:37.5:55:0.7051:0:4 -2 89872100 . T A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49647;SOR=0.65013;LSEQ=TTCCATTCCATTCCTGTTGA;RSEQ=TCCATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:1,3:12,9:0.16:2,2:21:0:29.8:1:0.32174:3.78956:38.8:8:0.1739:0:4.3 0/1:82:9:3,6:38,33:0.1098:2,2:22.6:1:30.6:1:0.30557:2.27955:37.6:18:0.1125:0:4.1 -2 89872112 . G CCCCTGTACTCGGGTTGATTC 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.5852;SOR=Inf;LSEQ=CCTGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:24.7:1:29.9:1:1:0:37.4:24:1:0:3.2 0/1:87:5:4,1:41,40:0.0575:2,2:22.2:1:29:1:0.36286:3.85:27.2:10:0.0575:0.0575:2.2 -2 89872119 . A G 111 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.29331;SOR=3.77531;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:12,14:0.037:2,0:15:0:30:0:0.48148:0:40:2:0.0385:0:5 0/1:94:12:7,5:41,40:0.1277:2,2:27.7:1:31.2:1:0.76006:1.36:34.3:24:0.129:0:5 -2 89872123 . C G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTGCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:0:2,0:16.6:1:31.3:1:1:0:38:54:1:0:3.3 0/1:96:2:1,1:48,46:0.0208:2,2:45.5:1:29.5:1:1:1.04303:48.5:4:0.0208:0:6 -2 89872124 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTGCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:0:2,0:15.9:1:30:1:1:0:38:26:1:0:3.3 0/1:96:2:1,1:47,45:0.0208:2,2:10:0:32.5:1:1:1.04398:45:4:0.0215:0:3 -2 89872127 . C A 96 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.1174;SOR=Inf;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:0:2,0:13.7:1:29.1:1:1:0:38:8:1:0:3.3 0/1:99:10:6,4:44,43:0.101:2,2:20.5:1:29.1:1:0.74158:1.46:29.2:20:0.102:0:5.1 -2 89872128 . C G 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.0981;LSEQ=CATTGCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:0,2:13,12:0.0741:2,0:34.5:1:32:1:0.48148:0:40.5:4:0.0741:0:6.5 0/1:99:8:3,5:47,42:0.0808:2,2:30:1:30.4:1:0.47804:1.85323:45:16:0.0833:0:5.8 -2 89872130 . T A 114 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.35784;SOR=2.39588;LSEQ=TTGCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCACTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:12,13:0.0741:2,2:18:0:23.5:1:1:1.08:41.5:1:0.04:0:2.5 0/1:99:16:9,7:41,40:0.1616:2,2:15.5:1:28.7:1:0.78712:1.25:30.9:15:0.1579:0:4.3 -2 89872132 . C A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCACTCGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:11:1:30.6:1:1:0:38.8:24:1:0:3.4 0/1:99:2:1,1:48,46:0.0202:2,2:41:0:29:1:1:1.04303:40:4:0.0208:0:8 -2 89872134 . ATTCCATTC CCTG 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.7219;SOR=0.73246;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=CACTCGTGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:1,3:2,4:0.4:2,2:30:1:32.8:1:1:1.44135:35.5:8:0.4444:0:4.5 0/1:52:17:9,8:16,14:0.3269:2,2:28.9:1:30.7:1:1:1.01554:39.4:34:0.3469:0.0385:4.3 -2 89872136 . T G 126 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.47566;SOR=2.1006;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCACTCGTGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:1,3:0.2:2,2:24:0:30.5:1:1:2.45:41.5:4:0.5:0:2.5 0/1:49:17:9,8:5,7:0.3469:2,2:20.3:1:30.9:1:0.71038:1.55:31.4:16:0.5714:0:4.4 -2 89872138 . C G 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.29573;SOR=0.40574;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCACTCGTGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:1,2:0.2222:2,0:24.5:1:32:1:1:0:40.5:4:0.4:0:6.5 0/1:49:5:2,3:12,12:0.102:2,2:23.8:1:29.4:1:1:1.47932:38.8:10:0.1724:0:5.8 -2 89872139 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGTGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,3:0:2,0:25.3:1:30.5:1:1:0:41:8:0.8:0:4.5 0/1:49:2:1,1:13,14:0.0408:2,2:34:0:32:0:1:1.07:40:4:0.0714:0:8 -2 89872142 . C G 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.14377;SOR=0.2333;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCGTGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:1,1:0.6:2,0:22:1:27:1:0.4:0:38.3:2:1:0:6.7 0/1:32:8:3,5:10,9:0.25:2,2:23:1:30:1:0.67762:1.81002:40:7:0.2593:0:6.6 -2 89872149 . T G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00955;SOR=0.13149;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:1,5:1,1:0.6667:2,2:23.8:1:31:1:0.46429:3.87298:38.2:12:0.6667:0:6.2 0/1:45:9:4,5:14,12:0.2:2,2:16.3:1:29.9:1:0.71119:1.44261:37.2:18:0.2143:0:5.2 -2 89872155 . T A 31 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02612;SOR=0;LSEQ=TTCCATTCCACTCGTGTTGA;RSEQ=TCCATTCCATTCCATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:1,6:0.2222:2,2:42.5:1:31:1:0.41667:4.58:34:4:0.25:0:6.5 0/0:44:0:0,0:21,21:0:2,0:22.9:1:29.8:1:1:0:35.7:41:1:0:5.2 -2 89872159 . A ATTCT 122 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.46256;SOR=2.17377;LSEQ=ATTCCACTCGTGTTGATTCC;RSEQ=TTCCATTCCATTCAACTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:1,6:0.2222:2,2:33.5:1:26.5:1:0.41667:4.58:41.5:4:0.2222:0:2.5 0/1:44:17:9,8:12,13:0.3864:2,2:35.8:1:30:1:1:1.21:31.4:34:0.4048:0:4.4 -2 89872161 . T G 34 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCACTCGTGTTGATTCCAT;RSEQ=CCATTCCATTCAACTCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:0:2,0:20.8:1:28.6:1:1:0:37.6:7:1:0:5 0/1:42:2:1,1:20,18:0.0476:2,2:12:0:34:0:1:1.10818:40:4:0.0526:0:8 -2 89872164 . A C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ACTCGTGTTGATTCCATTCC;RSEQ=TTCCATTCAACTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:21.1:1:26:1:1:0:37:2.5:1:0:4.9 0/1:42:2:1,1:20,18:0.0476:2,2:9.5:1:32.5:1:1:1.10818:48.5:4:0.05:0:6 -2 89872167 . C G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CGTGTTGATTCCATTCCATT;RSEQ=CATTCAACTCCGTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:32.5:1:30.8:1:1:0:37.8:8:1:0:4.5 0/1:39:2:1,1:19,16:0.0513:2,2:7:1:32.5:1:1:1.18197:41:4:0.0541:0:5.5 -2 89872170 . T C 33 d7;v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.01686;SOR=0.03102;LSEQ=GTTGATTCCATTCCATTCCA;RSEQ=TCAACTCCGTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:37:1:33:1:1:1:34:4:0.5:0:6.5 0/1:42:1:1,0:15,15:0.0238:2,0:3:0:27:0:1:0:43:2:0.025:0:6 -2 89872173 . A C 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06621;SOR=0.08951;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=ACTCCGTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:34:1:33:0:1:1:34:4:0.5:0:6.5 0/1:28:2:2,0:8,7:0.0714:2,0:1.6:1:27:1:0.48529:0:49.5:4:-0.1364:0:6.5 -2 89872175 . C T 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01379;SOR=0;LSEQ=TTCCATTCCATTCCATTCAA;RSEQ=TCCGTTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:32:1:31.5:1:1:0:34:4:0.5:0:6.5 0/0:26:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 89872177 . CCG TGA 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCAACT;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:30:1:32.5:1:1:0:34:4:1:0:6.5 0/1:21:3:1,2:0,0:0.1429:0,2:31.3:1:28.8:1:1:0:38.3:6:1:0:6 -2 89872192 . C G 108 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.54592;SOR=3.12168;LSEQ=CAACTCCGTTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:17:0:34:0:1:0:44:2:0.3333:0:3 1/0:16:10:4,6:2,3:0.625:2,2:20.6:1:32.6:1:1:1:34.2:20:0.625:0:4.4 -2 89872208 . C G 69 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:2.5:1:32.5:1:1:0:39:4:1:0:5 0/1:14:5:2,3:3,6:0.3571:2,2:10:1:30:1:1:1.31:36.6:10:0.3571:0:5.4 -2 89872218 . C G 30 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCACTCAGATTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:20.5:1:30:1:1:1.73:36:4:0.4:0:5.5 -2 89872219 . AT CC 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCAGATTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:37:0:31.8:1:1:1.73:37:4:0.4:0:6 -2 89872222 . C G 52 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCAGATTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,0:0.75:0,2:38.7:1:33.3:1:1:0:35.3:6:0.75:0:6 -2 89872246 . TT CC 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGATTGATTCCATTCCAT;RSEQ=CATTCCATTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:17:0:32.8:1:1:0:37:4:0.6667:0:5 -2 89872296 . TG GC 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTTCCACTCGGGTTGAT;RSEQ=CATTCCATTTCATTCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:30.8:1:1:0:23:4:1:0:4.5 -2 89872307 . T G 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGTTGATTGCATTCCATT;RSEQ=CATTCCATTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:31.5:1:1:0:23:4:1:0:4.5 -2 89872325 . T G 33 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.46667;SOR=0;LSEQ=TTTCATTCCATTTCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:33.5:1:1:0:42.5:4:1:0:5.5 1/0:4:2:1,1:1,1:0.5:2,2:6:0:33:0:1:1:43.5:4:0.5:0:6.5 -2 89872343 . C A 30 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:21:1:1:0:42.5:1:1:0:5.5 0/1:5:2:1,1:2,1:0.4:2,2:24:0:30.5:1:1:1.7321:43.5:4:0.4:0:6.5 -2 89872345 . T A 28 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:0:29.5:1:1:0:42.5:4:1:0:5.5 0/1:5:2:1,1:2,1:0.4:2,2:26:0:28.5:1:1:1.7321:43.5:4:0.4:0:6.5 -2 89872354 . A G 32 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCACTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:37:0:24.5:1:1:0:42.5:1:1:0:5.5 0/1:5:2:1,1:2,1:0.4:2,2:16.5:1:32:1:1:1.7321:23:4:0.4:0:4.5 -2 89872359 . A G 32 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCACTAGGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:42:0:28.5:1:1:0:42.5:4:1:0:5.5 0/1:5:2:1,1:2,1:0.4:2,2:11.5:1:32.5:1:1:1.7321:23:4:0.4:0:4.5 -2 89872360 . T C 32 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCACTAGGATTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41.5:1:24.5:1:1:0:42.5:1:1:0:5.5 0/1:5:2:1,1:2,1:0.4:2,2:36.5:1:32.5:1:1:1.7321:43.5:4:0.4:0:6.5 -2 89872383 . C A 28 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCACTAGGATTGATTC;RSEQ=ATTCCATTCCATTCCATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:28.5:1:1:0:42.5:4:1:0:5.5 1/0:3:2:1,1:1,0:0.6667:0,2:14.5:1:28.5:1:1:0:43.5:4:0.6667:0:6.5 -2 89872499 . A G 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTTCAGTTGATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:3.5:1:28.5:1:1:0:41:4:1:0:4 1/0:4:3:2,1:0,1:0.75:0,2:6.7:1:28.7:1:1:0:49:6:0.75:0:4.3 -2 89872512 . C T 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=3.1622;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCAGATTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:14:0:25:0:1:0:41:2:0.5:0:4 1/1:5:4:2,2:0,1:0.8:0,2:17.3:1:30.3:1:1:0:43.8:8:0.8:0:3.8 -2 89872517 . C A 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=3.1622;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCAGATTGATTCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:19:0:26:0:1:0:41:2:0.5:0:4 1/1:5:4:2,2:0,1:0.8:0,2:21.8:1:29.8:1:1:0:43.8:8:0.8:0:3.8 -2 89872538 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCAGATTGATTCTATTC;RSEQ=ATTCCCTTCAATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9:0:29:1:1:0:41:4:1:0:4 1/0:3:2:1,1:0,1:0.6667:0,2:9:0:31:1:1:0:59.5:4:0.6667:0:5 -2 89872672 . C G 32 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCGTTCTATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:2,0:1,2:0.4:2,0:7:1:32:1:0.4:0:34:4:0.4:0:6 -2 89872684 . A G 29 d7;v4;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12:0:32.5:1:1:0:48:4:1:0:4 0/1:5:2:2,0:1,2:0.4:2,0:19:1:29:0:0.4:0:34:4:0.6667:0:6 -2 89872692 . C A 31 pSTD;NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:0:31:1:1:0:48:4:1:0:4 0/0:3:0:0,0:2,1:0:2,0:26:1:31:1:1:0:42.7:6:1:0:4 -2 89872702 . C A 26 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCGTATTGATTCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:0:30.5:1:1:0:48:4:1:0:4 1/0:3:2:2,0:0,1:0.6667:0,0:31:1:26.5:1:0.33333:0:34:4:0.6667:0:6 -2 89872723 . C A 30 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCGTATTGATTCTATTC;RSEQ=ATTCCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:30.5:1:1:0:48:4:1:0:4 1/0:2:1:1,0:0,0:0.5:0,0:6:0:24:0:1:0:26:2:0.5:0:4 -2 89872834 . T C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGCATGCCTTTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:33:1:1:0:40:4:1:0:1 -2 89873268 . CATTCT C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCCATTCCCTTCCATTA;RSEQ=ATTCCATTCCACTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:1:29.7:1:1:0:38:4:1:1:2 -2 89873313 . A C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTGATTCCATTCCATTG;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:31:1:1:0:38:4:1:0:2 -2 89873373 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCAATTC;RSEQ=ATTCCACTCGTGTTGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:28:1:1:0:27:4:1:0:2 -2 89873831 . A TTCGATCCATTACACT 46 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TCCACTCCATTCCATTCCAT;RSEQ=CAATTCCACTCTGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:1,2:2,1:0.5:2,2:17.3:1:29.6:1:1:3.10575:35:6:0.5:0.5:3.3 -2 89873838 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATACAATTC;RSEQ=ACTCTGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:23.5:1:30:1:1:1:38:4:0.3333:0:3.5 -2 89873846 . T G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATACAATTCCACTCTGG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:31.5:1:32.5:1:1:1:38:4:0.3333:0:3.5 -2 89873851 . T C 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAATTCCACTCTGGTTGAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:1,1:0.3333:2,2:19:0:30:1:1:1:29:4:0.3333:0:3.5 -2 89873857 . CC GG 31 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCACTCTGGTTGATTCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:27:0:31:1:1:1:38:4:0.3333:0:3 -2 89873859 . A T 29 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ACTCTGGTTGATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:11:0:29.5:1:1:1:29:4:0.3333:0:3.5 -2 89873868 . C CACTCGAATACATTCCCTCCTATTCCACTCGGAACG 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:46:1:31.2:1:1:1:29:4:0.3333:0.3333:3.5 -2 89873888 . C A 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCTATTCCACTGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:6:0:28:1:1:0:38:4:0.6667:0:3 -2 91883968 . CA C 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGACCCTGTCTCCCAAC;RSEQ=AAAAAAAAAAAAAAATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:31:1:1:0:55.5:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 91884263 . C G 89 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54612;SOR=0;LSEQ=TATGGTGCTCCTTGAGATTT;RSEQ=TGTAAGGTAGGTCTGTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:7,0:16,2:0.28:2,0:32.4:1:31.9:1:1:0:29.1:14:0.2917:0:1.4 0/0:4:0:0,0:3,1:0:2,0:26.8:1:30:1:1:0:39.3:8:1:0:0 -2 91884390 . T C 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55793;SOR=0.86772;LSEQ=TAAGTCAGTGTGATTTACCC;RSEQ=TTGGTAAATCATACACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:93:81,12:96,11:0.465:2,2:22.1:1:30.8:1:0.65844:1.29125:32.9:45.5:0.4691:0:1.1 0/1:114:49:44,5:60,5:0.4298:2,2:22.4:1:31.3:1:0.74286:1.35986:32.4:98:0.4298:0:1 -2 91884532 . T G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26933;SOR=0.7105;LSEQ=TCTGATTGGATGTCTGGAGG;RSEQ=GTCTGAAGGACGGCCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:831:37:18,19:447,347:0.0445:2,2:17.2:1:31.2:1:0.399:1.35923:24.4:74:0.045:0:1.1 0/1:593:19:7,12:317,257:0.032:2,2:20.4:1:30.5:1:0.15878:2.11187:25.6:18:0.0306:0:1.1 -2 91884576 . T C 260 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.95924;SOR=1.0084;LSEQ=TCTGATTTATAATCTTCAAT;RSEQ=TCAGTTTTGGTTTTGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1151:293:220,73:438,418:0.2546:2,2:12.6:1:31.8:1:0:2.87:39.4:145.5:0.2571:0:1.1 0/1:894:229:184,45:357,307:0.2562:2,2:12.4:1:31.4:1:0:3.51:41.6:113.5:0.2568:0:1.1 -2 91884897 . T A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89839;LSEQ=CCTTGGATTATAGGCAGAAA;RSEQ=GTTACATGTTTTTAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:29:5,24:1,12:0.6905:1,2:29.6:1:31.4:1:0.64684:2.45:40.9:58:0.6905:0:2 1/0:12:8:1,7:2,2:0.6667:2,2:14.1:1:30:1:0.23636:5.73436:35.3:16:0.6667:0:1.8 -2 91884911 . A T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.24937;SOR=0.36659;LSEQ=CAGAAATGTTACATGTTTTT;RSEQ=AAAAATGGTCTTCCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:29:4,25:1,12:0.6905:1,2:27.6:1:28.2:1:1:1.89:45.2:28:0.6829:0:2 0/1:9:4:1,3:2,3:0.4444:2,2:21.3:1:28:1:1:1.8525:43.5:8:0.4444:0:2 -2 91884937 . C T 42 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04261;SOR=8.55185;LSEQ=TGGTCTTCCTGGGCCCGTTG;RSEQ=GGGGGCTCATGCCTGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:3,28:0.0606:2,2:15.5:1:29:1:0.23106:8.23:50:4:0.0625:0:1 0/1:8:3:1,2:2,3:0.375:2,2:31.7:1:26.7:1:1:1.28664:27:6:0.375:0:1.3 -2 91885008 . C T 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81102;LSEQ=AGATCACGAGGTCAGGAGAT;RSEQ=GAGACCATCCTGGCAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:1,4:1,7:0.3846:2,2:33.8:1:30.6:1:1:1.67:39.8:10:0.3846:0:1.6 0/1:3:1:0,1:0,2:0.3333:0,0:21:0:32:0:1:0:34:2:0.3333:0:1 -2 91885040 . G T 47 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAAACACAGTGAAACCCT;RSEQ=TCTCTTCTAAAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:22.3:1:29.7:1:1:0:41.7:6:0.5:0:2 0/0:1:0:0,0:0,1:0:0,0:23:0:33:0:1:0:27:2:1:0:1 -2 91885725 . T C 89 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61462;SOR=0.35794;LSEQ=CAAAGCAAGTATGGCATTAA;RSEQ=GGTTATTCTAAGAGCTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:11,0:0.4211:0,0:18.6:1:29.9:1:1:0:28.5:7:0.3889:0:1.1 0/1:5:1:1,0:4,0:0.2:0,0:40:0:33:0:1:0:24:2:0.2:0:1 -2 91885842 . G A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.21192;LSEQ=GAAATGATTACCAACATTAC;RSEQ=GAATTTGGATAGAACACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:3,0:204,27:0.0128:2,0:18.7:1:28:1:1:0:38.7:6:0.013:0:1.3 0/1:129:2:2,0:111,16:0.0155:2,0:18:1:29:1:1:0:38:4:0.0156:0:1.5 -2 91885859 . C A 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14212;SOR=0.69375;LSEQ=TACGGAATTTGGATAGAACA;RSEQ=CCATATGATTGAAGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:79:60,19:183,28:0.2724:2,2:19.9:1:29:1:0.03211:2.06391:28.5:78:0.2727:0:1.7 0/1:165:34:29,5:111,20:0.2061:2,2:21.8:1:28.4:1:1:1.04:29.2:33:0.2012:0:1.6 -2 91885883 . T C 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08623;SOR=0.6518;LSEQ=TATGATTGAAGCAGATTTTA;RSEQ=AAGTGGTAAGCCAATTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:69:51,18:229,67:0.189:2,2:25:1:32.3:1:0.53059:1.20564:30.5:138:0.1896:0:1.9 0/1:220:29:27,2:145,46:0.1318:2,2:25.4:1:31.4:1:0.05064:4.26:29.6:58:0.1324:0:1.8 -2 91885946 . T C 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.80877;SOR=0.9652;LSEQ=ATTAAATTAAGTAAAGCATT;RSEQ=CAAATTTTAACTAGCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:825:259:226,33:396,168:0.3139:2,2:27.8:1:31.9:1:0:2.90:29.5:85.333:0.3164:0:1.2 0/1:519:159:144,15:244,116:0.3064:2,2:28.2:1:31.8:1:0:4.55:31.4:318:0.3075:0:1.1 -2 91886030 . GAA G 257 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.05097;SOR=1.22875;LSEQ=TCTGAGGAAGGCACTGAAAT;RSEQ=AAAAAAAAAATCCAGGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1064:304:62,242:260,479:0.2857:2,2:29.7:1:31.2:1:0:2.11723:31.3:303:0.2875:0.0132:0.5 0/1:707:233:50,183:171,289:0.3296:2,2:31:1:30.7:1:2e-05:2.1633:34:466:0.3338:0.0057:0.5 -2 91886070 . A G 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08886;SOR=0.76294;LSEQ=AATTCTTTTCAGAAAAGGTA;RSEQ=AGTGTATTTACATACTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:155:11,144:18,406:0.2672:1,2:27.8:1:31.6:1:0.1955:1.72:44.9:37.75:0.2654:0:1.1 0/1:363:79:7,72:16,268:0.2176:2,2:24.2:1:31.4:1:0.30075:1.63:42.6:78:0.2167:0:1.3 -2 91886089 . C T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25313;SOR=1.22647;LSEQ=AAAGTGTATTTACATACTTA;RSEQ=ATATGATTAAAATTTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:138:0,138:16,236:0.3538:2,1:26.4:1:29.1:1:0.00095:0:28.9:276:0.3557:0:1 0/1:214:86:1,85:6,122:0.4019:1,1:21:1:28.8:1:0.24628:4.15842:31.6:85:0.3991:0:1.2 -2 91886661 . A AT 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03776;SOR=0;LSEQ=TAAAAAGACCATATTTGTAC;RSEQ=TTTTTTTTTAAAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:6:0,6:41,221:0.0224:2,0:22.7:1:30.8:1:0.59498:0:34.3:12:0.0231:0.0037:0.2 0/0:208:0:0,0:45,161:0:2,0:23.5:1:29.2:1:1:0:34.3:33.333:0.995:0:0.1 -2 91886670 . T A 173 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATATTTGTACATTTTTTTT;RSEQ=AAAAATGGAATATACTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:52:5,47:34,161:0.2105:2,2:19.7:1:30.4:1:0.20321:1.98034:33.1:104:0.2122:0:1.1 0/0:188:0:0,0:37,149:0:2,0:23.7:1:28:1:1:0:35.2:92:0.9892:0:0.1 -2 91886771 . T C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTCCTCCTACCTTGCCC;RSEQ=TTTCTCCTAACTATCCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:0,2:6,58:0.0303:2,0:28:1:34:0:1:0:24:4:0.0308:0:1 0/0:31:0:0,0:2,29:0:2,0:24.2:1:29.3:1:1:0:38.5:30:1:0:0.1 -2 91887704 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GGAGTTTGCAGTGAGCCGAG;RSEQ=TAGCGCCGATGCACTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:26.3:1:29.9:1:1:0:41:16:1:0:0.5 0/1:8:2:2,0:5,1:0.25:2,0:30.5:1:33:0:1:0:32:4:0.25:0:5 -2 91887709 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08235;SOR=0;LSEQ=TTGCAGTGAGCCGAGATAGC;RSEQ=CCGATGCACTCCAGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:5,0:0.4444:0,2:22:1:31.3:1:0.44444:0:46.5:8:0.4444:0:1.3 0/0:8:0:0,0:7,1:0:2,0:24.8:1:30.8:1:1:0:42.3:16:1:0:1.3 -2 91887713 . A C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14737;SOR=Inf;LSEQ=AGTGAGCCGAGATAGCGCCG;RSEQ=TGCACTCCAGCCTGGCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:11,1:0:2,0:18.4:1:30.3:1:1:0:47.3:24:1:0:0.5 0/1:8:2:2,0:5,1:0.25:2,0:39.5:1:33.5:1:1:0:32:4:0.25:0:5 -2 91887736 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=CACTCCAGCCTGGCGACAGA;RSEQ=CAAGACTCTGTCTGTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:0:1,0:22.5:1:32.1:1:1:0:53.2:16:1:0:0.5 0/1:13:2:2,0:10,1:0.1538:2,0:38.5:1:30:1:1:0:32:4:0.1538:0:5 -2 91887750 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.11628;SOR=Inf;LSEQ=GACAGAGCAAGACTCTGTCT;RSEQ=TAAATTTAAAAACAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:26,2:0:2,0:20.2:1:32.9:1:1:0:54.8:56:1:0:0.4 0/1:15:2:2,0:11,2:0.1333:2,0:24.5:1:30.5:1:1:0:32:4:0.1333:0:5 -2 91887802 . A G 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.79458;LSEQ=ACTTTAGTCTGGAGTTGAGA;RSEQ=TTCAAAACAGGAAATCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:6:5,1:120,7:0.0451:2,2:24.3:1:30.3:1:0.31589:3.37738:56.7:12:0.0458:0:1.2 0/1:83:3:3,0:72,8:0.0361:2,0:38:1:30.3:1:1:0:50.3:6:0.0361:0:1 -2 91887842 . T C 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.27566;SOR=1.26594;LSEQ=TCTGTAAGTTTCTAGGTGAC;RSEQ=AAAAATCTACAAGGCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:126:116,10:105,9:0.525:2,2:27.8:1:31:1:1:1.00572:34.2:62:0.521:0:1.1 1/0:180:105:95,10:65,10:0.5833:2,2:25.1:1:30.6:1:0.47511:1.46:41.2:104:0.5843:0:1.2 -2 91887867 . T C 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04083;SOR=Inf;LSEQ=ATCTACAAGGCAAAAAGCTC;RSEQ=GTACCTAAAACTTGTGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:278,30:0:2,0:25.4:1:31:1:1:0:38.8:50.333:1:0:0.5 0/1:253:4:4,0:224,25:0.0158:2,0:18.8:1:29.8:1:1:0:44:8:0.0162:0:2 -2 91887961 . G A 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.72678;SOR=1.06017;LSEQ=TTTAAAAAGATGAAAAAATA;RSEQ=CACAATACCTATCACATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:124:54,70:175,229:0.2335:2,2:26.4:1:28.6:1:1:1.01:38.8:23.8:0.2419:0:1.3 0/1:598:146:70,76:181,267:0.2441:2,2:28:1:28.3:1:0.12279:1.36:41.5:145:0.2627:0:1.3 -2 91888009 . C T 119 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01155;SOR=0.21093;LSEQ=GCAGAATAAGATCTTCTTCT;RSEQ=TATAGTTTCAATAGCAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:14:0,14:2,270:0.049:1,1:31.3:1:31.4:1:1:0:35.9:28:0.0495:0:1 0/1:280:3:0,3:0,277:0.0107:1,0:15.3:1:31.7:1:1:0:40:6:0.0108:0:1 -2 91888069 . T G 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30037;SOR=0;LSEQ=CACAAGGAGCGCACTGTGTG;RSEQ=AATTGTTCTGCCATTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:4:0,4:10,157:0.0234:2,0:22.8:1:32.8:1:1:0:32:8:0.0234:0:1.5 0/0:102:0:0,0:1,101:0:1,0:21.6:1:28.5:1:1:0:36.7:101:1:0:0.2 -2 91888125 . C T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.85128;SOR=1.11636;LSEQ=GTTGCTCCACAGTGTCTGCA;RSEQ=CAAACACACCTGAAATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:121:70:23,47:8,43:0.5785:2,2:24.1:1:30.8:1:0.03676:2.61:32.5:140:0.5833:0:1.1 1/0:38:23:4,19:3,12:0.6053:2,2:27.4:1:28.9:1:1:1.18207:35.7:22:0.5946:0:1.1 -2 91888217 . C T 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01516;LSEQ=TTCAGGAAGCTACATACGAA;RSEQ=ATAATGGGGCAAATGATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:75:68,7:132,8:0.3488:2,2:22.4:1:30.9:1:0.40068:1.69418:27.7:36.5:0.3493:0:1.1 0/1:88:31:30,1:56,1:0.3523:1,1:23.1:1:30.6:1:1:1.85271:28:62:0.3563:0:1 -2 91888374 . A G 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0;SOR=1.40338;LSEQ=TTGAAAGACTAACAAGGCAA;RSEQ=CAAACCCTAGAGAACCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3469:607:359,248:1716,1141:0.175:2,2:27.5:1:31.9:1:0.6817:1.03895:38.3:85.714:0.1742:0:1.1 0/1:2886:662:376,286:1276,943:0.2294:2,2:28:1:31.8:1:0.75412:1.02924:40.2:109.333:0.2292:0:1.1 -2 91888456 . C A 327 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=0.83469;LSEQ=CTAGGCAGTAGGTGTGATAA;RSEQ=TTATGTCACAATCATCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3759:1746:872,874:997,1006:0.4645:2,2:22.5:1:30.4:1:0.92179:1.01:36.2:78.364:0.4638:0:1.1 0/1:2929:1230:619,611:863,835:0.4199:2,2:21.5:1:29.7:1:0.79335:1.02017:37.7:204:0.4203:0:1.1 -2 91888488 . T C 198 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCATCACACAGCAGGAGTCT;RSEQ=CCTGGGTCAGTTGCCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3395:88:42,46:1441,1865:0.0259:2,2:28.2:1:30.8:1:0.44786:1.18:28.8:43:0.0257:0:1.1 0/0:2553:0:0,0:1146,1405:0:2,0:15:0:10:0:1:0:40:0:0:0:2 -2 91888700 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07568;LSEQ=TCAACTAACATTTATTGAGC;RSEQ=CCTACGGAGGCCCAATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:6:0,6:14,99:0.0504:2,0:15.3:1:30.2:1:1:0:23.3:12:0.0526:0:1.2 0/1:37:2:0,2:5,30:0.0541:2,0:6:0:31:1:1:0:23:4:0.0556:0:1 -2 91888973 . CA C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATCAATAGAAAAAATAC;RSEQ=AAAAAATTAATGTAAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:24:1:30.6:1:1:0:25.5:4:0.5:0.25:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 91890415 . C T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCCTCAAGTGATCCACC;RSEQ=GCCTCGGCCTCCCAAAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:0:32:0:1:0:29:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 91890444 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCAAAGTGCTGGGATGA;RSEQ=AGGTGTGAGGCACCACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:30:1:1:0:29:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 91893730 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11084;SOR=Inf;LSEQ=TTTAAAGTACTTAAATACGG;RSEQ=CACATATGTTTAATAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:18,1:0:1,0:24.1:1:30.3:1:1:0:36.5:38:1:0:0.1 0/1:10:2:2,0:8,0:0.2:0,0:19.5:1:31.5:1:1:0:37:4:0.2:0:1 -2 91893801 . A C 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09871;SOR=1.60602;LSEQ=GTTACTACTAAAACCAAATA;RSEQ=AAATTCAATACATATTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:71:71,0:92,1:0.4329:1,1:21.9:1:32.7:1:1:0:25:142:0.4329:0:1 1/0:78:43:43,0:35,0:0.5513:1,1:26.9:1:31.7:1:1:0:25:86:0.5513:0:1 -2 91894045 . T C 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00365;SOR=0;LSEQ=TCTTAACTAATATAGCTCTA;RSEQ=AGCTAAATATTGGATCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:11:8,3:379,121:0.0215:2,2:20.8:1:32.5:1:0.73281:1.17416:25.7:22:0.0219:0:1 0/0:360:0:0,0:291,69:0:2,0:22.6:1:29.8:1:1:0:25.5:119:1:0:0.2 -2 91894137 . A G 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5099;SOR=1.06425;LSEQ=GACAGTAAATTGTCAAGTTC;RSEQ=AACCTGATTCAAAGTGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2144:257:160,97:1097,790:0.1199:2,2:26.7:1:30.4:1:0.22446:1.19:37.5:63.25:0.119:0:1.9 0/1:2030:257:158,99:1007,761:0.1266:2,2:24.9:1:30.2:1:0.17729:1.21:40.5:256:0.127:0:1.9 -2 91894194 . C T 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=1.80038;LSEQ=CAACACAACCATATCGAGCA;RSEQ=AGAGTTTTCTTCATCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2213:452:196,256:733,1024:0.2042:2,2:25.8:1:29.2:1:0.55683:1.07:36:149.667:0.2048:0:1.5 0/1:2164:684:281,403:636,844:0.3161:2,2:27.1:1:28.4:1:0.42651:1.08066:39.2:113:0.3156:0:1.4 -2 91894266 . A G 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00341;SOR=0;LSEQ=TAAAAAGCAAAATACACAAA;RSEQ=TACGAAGTTATATTTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:527:11:0,11:32,483:0.0209:2,0:30.5:1:32:1:1:0:26:22:0.0214:0:1.3 0/0:388:0:0,0:16,372:0:1,0:22.7:1:29.9:1:1:0:26.8:28.846:1:0:0.5 -2 91894273 . G A 161 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.31644;LSEQ=CAAAATACACAAAATACGAA;RSEQ=TTATATTTTTCACTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:14:1,13:30,417:0.0303:2,1:29.9:1:31.9:1:1:1.07:26.9:28:0.031:0:1.3 0/1:336:40:1,39:14,282:0.119:1,1:24.2:1:30.3:1:1:1.93315:26.3:39:0.1185:0:1.5 -2 91894294 . A G 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.10348;SOR=0.73986;LSEQ=TTATATTTTTCACTTGTTTT;RSEQ=CACTTAACTGGAAAGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:318:162:6,156:18,138:0.5094:2,1:25.2:1:32.4:1:0.01008:3.37909:26.4:161:0.5079:0:1.1 0/1:198:86:4,82:7,104:0.4343:2,1:24:1:32.1:1:0.75883:1.37761:26.7:42:0.4308:0:1.1 -2 91894305 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.19503;LSEQ=ACTTGTTTTACACTTAACTG;RSEQ=AAAGCTTCAGAAAATTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:3:3,0:16,253:0.011:2,0:16:1:30.7:1:0.00029:0:24.3:6:0.0111:0:1.3 0/1:152:2:2,0:8,142:0.0132:2,0:16:1:27.5:1:0.00392:0:27:4:0.0132:0:1 -2 91894361 . CA TG 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.32097;SOR=0;LSEQ=TTTGCTAAGGTCTAGAATAA;RSEQ=ATTCCAAATATTAATGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:4:2,2:13,98:0.0348:2,2:25:1:30.4:1:0.08196:7.31:23.3:8:0.0348:0.0087:1.8 0/0:48:0:0,0:7,41:0:2,0:21.7:1:31.3:1:1:0:27:47:1:0:0.5 -2 91894362 . A G 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67518;SOR=0.38127;LSEQ=TTGCTAAGGTCTAGAATAAC;RSEQ=ATTCCAAATATTAATGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:6:2,4:11,93:0.0531:2,2:26.8:1:28:1:0.14748:4.14:25.8:12:0.055:0:1.8 0/1:48:1:1,0:6,41:0.0208:2,0:10:0:30:0:0.14583:0:27:2:0.0208:0:2 -2 91894393 . C T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.85744;SOR=0.89089;LSEQ=TTAATGCTAAGATACTACAG;RSEQ=AAAATGGAGTCATGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:41:5,36:6,66:0.3596:2,2:24.5:1:26.9:1:0.52394:1.52:29:19.5:0.3514:0:1.4 0/1:48:16:3,13:3,29:0.3333:2,2:23.9:1:27.8:1:0.3858:2.19:31.3:32:0.3404:0:1.1 -2 91894423 . A C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGACATTTTATTATTCA;RSEQ=CTCATTCTCTCTTTAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:0,2:6,81:0.0225:2,0:13.5:1:32:0:1:0:27:4:0.0225:0:3 0/0:37:0:0,0:5,31:0:2,0:34.9:1:29:1:1:0:30:35:1:0:0.4 -2 91894426 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACATTTTATTATTCAACT;RSEQ=ATTCTCTCTTTAGAGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:0,2:5,79:0.0233:2,0:10.5:1:31:0:1:0:27:4:0.0235:0:3 0/0:36:0:0,0:5,31:0:2,0:34.2:1:31.4:1:1:0:30.7:17:1:0:0.4 -2 91894459 . C G 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57569;SOR=0;LSEQ=GAGGTAGAATTCCTTTAGAC;RSEQ=AAGAAGTAATGAGAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:4:1,3:4,62:0.0571:2,2:28:1:30.8:1:0.26159:4.95:27:8:0.0588:0:2 0/0:28:0:0,0:2,26:0:2,0:13.4:1:31.8:1:1:0:34.1:56:1:0:0.4 -2 91894464 . A G 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17461;SOR=0;LSEQ=AGAATTCCTTTAGACCAAGA;RSEQ=GTAATGAGAAAATATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:6:0,6:3,52:0.0984:2,0:8.3:1:31.8:1:1:0:27:12:0.1017:0:1 0/0:25:0:0,0:2,23:0:2,0:10.7:1:30:1:1:0:34:50:1:0:0.4 -2 91894486 . G C 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86316;LSEQ=TAATGAGAAAATATAATAAA;RSEQ=CTGTCTTAGTAAGACTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:1,7:0.4667:2,0:20.9:1:32.1:1:1:0:26.1:14:0.4667:0:1.6 0/1:7:3:1,2:0,4:0.4286:0,2:6.3:1:31:1:0.42857:0:22.3:6:0.4286:0:1 -2 91898520 . G A 27 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGAAGCTGGAGTTATGCT;RSEQ=ATACCAAAACCAGATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 91898572 . C A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGTAAGACTACAGGCTGGGG;RSEQ=ATGGTGACTCACGCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25:0:33.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:13:0:31.5:1:1:0:30:4:1:0:2.5 -2 91899415 . A G 85 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATATTTGCTAGTAGTTA;RSEQ=CAAATATATTTGTAATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:2,2:0.6:2,2:34.7:1:33:1:1:1.86:33.3:12:0.6:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 91899419 . A C 85 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATTTGCTAGTAGTTAACAA;RSEQ=TATATTTGTAATACACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:2,2:0.6:2,2:38.7:1:33.2:1:1:1.86:33.3:12:0.6:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 91899421 . A G 84 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGCTAGTAGTTAACAAAT;RSEQ=TATTTGTAATACACATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:2,2:0.6:2,2:39.7:1:32.7:1:1:1.86:33.3:12:0.6:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 91899505 . C G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13504;SOR=6.3085;LSEQ=ATTTTTTAAATAAAAGAGCA;RSEQ=CTATATTACATACTGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:2,1:17,4:0.125:2,2:26:1:31.3:1:0.52125:2.04831:31:6:0.1429:0:1 1/0:4:2:1,1:1,1:0.5:2,2:37:1:31:1:1:1:27:4:0.5:0:1 -2 91899684 . A G 82 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.811;LSEQ=ACATTTTGACCTATTTATAT;RSEQ=ACTTTTAAGTTCAAAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:6:2,4:169,32:0.029:2,2:19.5:1:31.8:1:0.00908:10.37364:28:12:0.03:0:1.7 0/1:127:3:2,1:100,22:0.0236:2,2:28.3:1:15.7:1:0.45964:2.25419:29:0:0:0:2.3 -2 91899746 . G T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.30135;SOR=0;LSEQ=TAACTGACATTTAGATTAGA;RSEQ=AAAATATACATGAAGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:4:2,2:127,124:0.0157:2,2:30.5:1:31.3:1:1:1.0241:25.3:8:0.0159:0:1.8 0/0:149:0:0,0:71,78:0:2,0:23.6:1:29.8:1:1:0:46.2:73.5:1:0:0.1 -2 91899807 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12394;SOR=Inf;LSEQ=AGCTCCGATTCCACTTTTCA;RSEQ=CTTTGACCTGCCTCGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:31,119:0:2,0:26.1:1:32.2:1:1:0:37.8:49:1:0:0.2 0/1:82:2:0,2:15,65:0.0244:2,0:36.5:1:31.5:1:1:0:40:4:0.0244:0:1 -2 91899815 . C T 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68536;LSEQ=TTCCACTTTTCAGCTTTGAC;RSEQ=TGCCTCGGCCACCTCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:5:4,1:27,103:0.037:2,2:32:1:31.8:1:0.00993:14.86:24.8:10:0.0373:0:2.4 0/1:78:2:2,0:14,62:0.0256:2,0:27:1:31.5:1:0.03996:0:27.5:4:0.026:0:2.5 -2 91899835 . C T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84634;LSEQ=CTGCCTCGGCCACCTCGCCC;RSEQ=GACAGTCCTGCACCTCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:6:5,1:35,80:0.0496:2,2:24.7:1:31.2:1:0.01487:11.19:25:12:0.0504:0:2.3 0/1:71:3:3,0:21,47:0.0423:2,0:23.7:1:30.3:1:0.03541:0:25.3:6:0.0429:0:2.3 -2 91899860 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52506;SOR=0;LSEQ=GTCCTGCACCTCGAGGTCTC;RSEQ=GCTTTCCTGGAAATCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:2,0:50,50:0.0196:2,0:10.5:1:26:0:0.49524:0:24:4:0.0196:0:3 0/0:63:0:0,0:34,29:0:2,0:23.9:1:29.7:1:1:0:37.9:30.5:1:0:0.2 -2 91899884 . T C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98126;LSEQ=TTCCTGGAAATCCAGACCCA;RSEQ=GGCCCTATGTAACAGATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:6:6,0:45,32:0.0714:2,0:29.5:1:32.5:1:0.07732:0:28.2:12:0.0732:0:2 0/1:57:4:4,0:33,20:0.0702:2,0:19.8:1:32.5:1:0.28625:0:24.3:8:0.0702:0:2.3 -2 91899924 . A T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0155;LSEQ=GGAAAAGTCAACATTCTGTG;RSEQ=CAGCCCAAAATAATTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:16:6,10:28,22:0.2424:2,2:12:1:27.7:1:0.25506:2.09696:24.6:32:0.2424:0:1.5 0/1:53:13:6,7:23,17:0.2453:2,2:17.5:1:26.9:1:0.5335:1.56468:23.8:26:0.2453:0:1.4 -2 91902433 . G A 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30406;SOR=0;LSEQ=GACTTCTCCCTCATAAAACC;RSEQ=GTAGTAATCACAACAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:5,0:16,2:0.2174:2,0:27.2:1:31.6:1:1:0:26.4:10:0.2174:0:1.6 0/0:7:0:0,0:6,1:0:2,0:22.4:1:31.1:1:1:0:41.1:14:1:0:0.3 -2 91902472 . G C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20879;SOR=0.32442;LSEQ=GGAATTAACCATAAAAAGAG;RSEQ=TATTAAAAATGTATACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:16:13,3:39,2:0.2807:1,2:26.9:1:32.9:1:0.12853:4.35831:30.7:32:0.2807:0:1.1 0/1:18:2:2,0:14,2:0.1111:2,0:48:1:32.5:1:1:0:42:4:0.1176:0:1 -2 91902876 . CAT C 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00012;SOR=0;LSEQ=ACAGCAAAAACAAATGCAAA;RSEQ=ATGGAAATTTAGGACAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:21:2,19:2,24:0.4375:2,2:25.1:1:31.2:1:1:1.26:32.7:20:0.4348:0.0208:0.4 0/0:21:0:0,0:4,17:0:2,0:26:1:29.7:1:1:0:36.1:42:1:0:0 -2 92145244 . C T 31 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=GAAGAGGTCGTGAATGATGT;RSEQ=CCAGCAGCAGGAGACAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:15,1:0:1,0:22.7:1:32.8:1:1:0:48.6:32:1:0:0.2 0/1:5:2:1,1:3,0:0.4:0,2:16:0:31.5:1:0.4:0:47:4:0.5:0:1 -2 92145399 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16386;SOR=Inf;LSEQ=GATGGTGACCTGTTAATCCT;RSEQ=GCATACTATTACTGATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:193,43:0:2,0:24.7:1:31.7:1:1:0:57:58:1:0:0.1 0/1:161:2:1,1:121,37:0.0124:2,2:32:1:28.5:1:0.41973:3.24025:60:4:0.0127:0:1 -2 92145401 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07181;SOR=Inf;LSEQ=TGGTGACCTGTTAATCCTGG;RSEQ=ATACTATTACTGATAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:195,43:0:2,0:25:1:32:1:1:0:56.7:78.333:0.9958:0:0.1 0/1:171:3:1,2:129,39:0.0175:2,2:20:1:27.7:1:0.14321:6.52236:52:6:0.0176:0:1 -2 92145555 . G A 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01537;SOR=Inf;LSEQ=CCGTGGCTTCAGGTGGGTGT;RSEQ=GGACAGTGCCTGCAAGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:0:0,0:246,384:0:2,0:25.9:1:31.2:1:1:0:49:69:1:0:0.1 0/1:634:7:3,4:292,334:0.011:2,2:28:1:30:1:1:1.16539:37.4:14:0.0112:0:1.3 -2 92145582 . T A 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0562;SOR=1.74488;LSEQ=TGCCTGCAAGCATAAAATAC;RSEQ=TGGGAAGCCCTGCTGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:22:2,20:136,278:0.0505:2,2:23.5:1:31.8:1:0.01823:4.87901:26.9:44:0.0509:0:1 0/1:424:36:3,33:159,229:0.0849:2,2:25.1:1:29.7:1:5e-05:7.61153:26.7:35:0.0835:0:1.1 -2 92145637 . C G 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83887;LSEQ=AGGACAGAAACATGTTTAGT;RSEQ=TGTTTAATCTAATTGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:3:0,3:20,146:0.0178:2,0:17:1:28.3:1:1:0:35.7:6:0.0185:0:4 0/1:134:2:1,1:15,117:0.0149:2,2:28:1:29:1:0.22534:7.58:26:4:0.0153:0:4 -2 92145660 . T A 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00727;SOR=0;LSEQ=TTTAATCTAATTGTTTTAGA;RSEQ=GTATGGGGGGTATCTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:8:0,8:8,90:0.0755:2,0:28.9:1:29.3:1:1:0:50.6:7:0.0667:0:1.5 0/0:96:0:0,0:11,85:0:2,0:22.3:1:29:1:1:0:46.1:12.714:1:0:0.5 -2 92145667 . G A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.19063;SOR=Inf;LSEQ=TAATTGTTTTAGATGTATGG;RSEQ=GGGTATCTTGGAGGATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:7,93:0:2,0:28.3:1:30.9:1:1:0:43.8:32.333:1:0:0.5 0/1:78:2:1,1:9,67:0.0256:2,2:35.5:1:27:1:0.24143:7.11:23:4:0.027:0:4.5 -2 92145670 . G T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4431;SOR=1.56023;LSEQ=TTGTTTTAGATGTATGGGGG;RSEQ=TATCTTGGAGGATGGGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:8:0,8:7,82:0.0825:2,0:24.4:1:28.5:1:1:0:32.9:7:0.0769:0:3 0/1:73:9:2,7:8,56:0.1233:2,2:34.3:1:28.9:1:0.60107:1.98:25.4:18:0.1286:0:2.6 -2 92145696 . GTC G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28167;SOR=0;LSEQ=TGGAGGATGGGTTACAACCT;RSEQ=TTTTTTTTTTTTCTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:0,3:6,55:0.0462:2,0:32:1:31.7:1:1:0:28.7:6:0.05:0:3.3 0/0:41:0:0,0:5,30:0:2,0:28.6:1:27.8:1:1:0:49.4:16.5:0.8462:0:0.8 -2 92145698 . CT C 77 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.41465;SOR=0.34019;LSEQ=GAGGATGGGTTACAACCTGT;RSEQ=TTTTTTTTTTTCTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:5:1,4:5,53:0.0781:2,2:36.4:1:33.2:1:0.4043:2.59:40.8:10:0.0833:0:0.4 0/1:36:1:0,1:5,29:0.0278:2,0:18:0:32:0:1:0:40:2:0.0294:0:0 -2 92145736 . G C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0881;LSEQ=TTGAGACAGGTTCTCATTCT;RSEQ=TCACCCTGGCTGGAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:2,16:0.1429:2,0:7:1:32.3:1:1:0:39.7:6:0.1429:0:4.3 0/1:13:2:0,2:1,10:0.1538:2,0:23:1:34:0:1:0:23:4:0.1538:0:3 -2 92150176 . A C 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47608;SOR=1.67343;LSEQ=GAAGGTAGAGGGGGCAACAC;RSEQ=TAATGCCTTCGCTGTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:5:5,0:56,5:0.0758:2,0:4.8:1:32:1:1:0:23.4:10:0.0769:0:3.4 0/1:33:4:4,0:27,2:0.1212:2,0:6.8:1:31:1:1:0:23.8:8:0.1212:0:3 -2 92150223 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47535;SOR=1.70013;LSEQ=CAAGGGGATGATTCTTGGAC;RSEQ=GACATCTTTTCCTCCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:5:5,0:105,8:0.0424:2,0:47.2:1:31:1:1:0:23.4:10:0.0427:0:3.4 0/1:57:4:4,0:46,7:0.0702:2,0:47.3:1:31:1:1:0:23.8:8:0.0714:0:3 -2 92150253 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28546;SOR=0;LSEQ=TCCTCCCTCTTTCCACAGGG;RSEQ=CATGCCACCCCTGTCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:3,0:166,22:0.0157:2,0:15.3:1:29.3:1:1:0:60:6:0.0164:0:1 0/0:121:0:0,0:95,26:0:2,0:21.9:1:30.4:1:1:0:57.9:23.2:1:0:0.2 -2 92150259 . C T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.74404;SOR=1.22632;LSEQ=CTCTTTCCACAGGGGCATGC;RSEQ=ACCCCTGTCATTCTAGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:5:5,0:174,30:0.0239:2,0:13.2:1:30.4:1:1:0:23.4:10:0.0246:0:3.4 0/1:137:4:4,0:104,29:0.0292:2,0:11.3:1:31:1:0.57843:0:23.8:8:0.0296:0:3 -2 92150264 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16236;SOR=Inf;LSEQ=TCCACAGGGGCATGCCACCC;RSEQ=TGTCATTCTAGGATTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:186,37:0:2,0:23.8:1:30.9:1:1:0:59:54.75:1:0:0.2 0/1:151:2:1,1:114,35:0.0132:2,2:22:1:29:1:0.42119:3.22563:60:4:0.0134:0:1 -2 92150362 . G C 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=1.59744;LSEQ=AGAAAGTTTCAAGATCTTCT;RSEQ=TCTGAGGAAAATGAATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:886:165:131,34:382,337:0.1862:2,2:17.7:1:31.7:1:0:3.39:29.9:164:0.1874:0:1.1 0/1:788:211:154,57:301,276:0.2678:2,2:15.8:1:31.4:1:0:2.47:32.8:69.333:0.2663:0:1.1 -2 92150414 . G A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AGGTTCTAGCCCAGGTATTC;RSEQ=TATTCCTGATGATCACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:825:0:0,0:351,474:0:2,0:28.3:1:30.8:1:1:0:36.7:116.857:1:0:0.4 0/1:750:15:6,9:336,399:0.02:2,2:19.1:1:29.9:1:0.79561:1.26277:35.8:30:0.0202:0:1 -2 92150470 . G A 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.06162;SOR=1.40479;LSEQ=AGGAGCTGATAAGCAAAGAT;RSEQ=ATGAAATTCAAGATTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:117:10,107:9,197:0.3622:1,2:23.2:1:30.1:1:0.14326:2.04:26.4:116:0.3636:0:1 0/1:223:99:10,89:7,117:0.4439:2,2:22.5:1:29.6:1:0.30975:1.87:27.2:48.5:0.4429:0:1.1 -2 92150496 . G A 24 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13411;SOR=Inf;LSEQ=ATTCAAGATTTTCCTGAGTA;RSEQ=CAATTGCTTAACATTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:6,206:0:1,0:23:1:31.8:1:1:0:30.1:25.5:1:0:0.4 0/1:123:2:0,2:5,116:0.0163:1,0:10:0:24:0:1:0:24.5:4:0.0165:0:2 -2 92150575 . A T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.00097;SOR=6.06715;LSEQ=ACTCCAGCACCCTTAGATTT;RSEQ=AAAATGCAGGATATGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:1,7:2,27:0.2162:2,2:18.5:1:28.6:1:0.52973:1.89:24:16:0.2162:0:1 1/0:30:19:0,19:4,7:0.6333:2,1:23.7:1:29.5:1:0.01204:0:24.6:38:0.6333:0:1.2 -2 92150621 . A G 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.83749;LSEQ=AACACATAATAGACAGATAA;RSEQ=CACAGCTAGGGATTGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:0,6:1,19:0.2308:1,0:25.2:1:31.8:1:1:0:22:12:0.2308:0:1 0/1:10:2:0,2:3,5:0.2:2,0:31:1:34:0:1:0:22:4:0.2:0:1 -2 92151406 . G C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38713;SOR=2.17709;LSEQ=GCTACAGTGAGGACTCAGTT;RSEQ=TCAATTATGACAACCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:2,1:29,2:0.0882:2,2:14:1:31.3:1:0.24883:6.51127:44:6:0.0882:0:2 0/1:17:3:3,0:11,3:0.1765:2,0:9.7:1:32:1:1:0:30.7:6:0.1875:0:4.3 -2 92151412 . T G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74051;SOR=1.38163;LSEQ=GTGAGGACTCAGTTGTCAAT;RSEQ=ATGACAACCAGTAATTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:7:4,3:32,3:0.1667:2,2:9.4:1:30.9:1:0.04778:7.40508:32.7:14:0.1667:0:2.7 0/1:23:5:5,0:15,3:0.2174:2,0:10.2:1:32.6:1:1:0:34.2:10:0.2174:0:4.2 -2 92151432 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17394;SOR=Inf;LSEQ=TATGACAACCAGTAATTTTT;RSEQ=GTACTAGAATTTCACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:50,8:0:2,0:24.5:1:31.9:1:1:0:51.6:57:1:0:0.7 0/1:42:2:1,1:33,7:0.0476:2,2:28:0:32:0:0.34843:4.47614:60:4:0.0488:0:1.5 -2 92151462 . C G 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1421;SOR=3.83253;LSEQ=TTTCACATCAAATACCCCCA;RSEQ=TTTACTGGAAGTACATTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:74,11:0.023:2,2:30.5:1:32:0:0.25822:6.48425:49:4:0.023:0:4 0/1:72:6:4,2:52,14:0.0833:2,2:36.7:1:31.2:1:0.60882:1.83891:40.8:12:0.0833:0:4.5 -2 92151474 . T C 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.011;SOR=0;LSEQ=TACCCCCACTTTACTGGAAG;RSEQ=ACATTGAGGAACTTTGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:9:8,1:85,17:0.0811:2,2:25.7:1:31:1:1:1.59:41.8:8:0.0727:0:3.1 0/0:81:0:0,0:61,20:0:2,0:28.8:1:28.7:1:1:0:41:80:1:0:1.2 -2 92151486 . C T 153 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01955;SOR=1.99602;LSEQ=ACTGGAAGTACATTGAGGAA;RSEQ=TTTGATAATCTTAAAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:29:19,10:87,15:0.2214:2,2:25.6:1:31:1:0.02945:3.02156:34.9:58:0.2266:0:3 0/1:102:37:24,13:51,14:0.3627:2,2:28.7:1:29.5:1:0.16381:1.95947:32.4:74:0.3627:0:3 -2 92151492 . T C 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02618;SOR=1.90078;LSEQ=AGTACATTGAGGAACTTTGA;RSEQ=AATCTTAAAGAAGCCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:35:22,13:90,19:0.2431:2,2:23.1:1:31.9:1:0.01987:2.77594:34.1:70:0.2431:0:2.9 0/1:108:41:24,17:52,15:0.3796:2,2:26.6:1:30.6:1:0.05018:2.43396:32:82:0.3832:0:3 -2 92151504 . A G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13968;SOR=2.63803;LSEQ=AACTTTGATAATCTTAAAGA;RSEQ=GCCAGTGATTTTCTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:4:3,1:130,42:0.0227:2,2:22.8:1:32:1:1:1.03156:36.5:8:0.0227:0:4 0/1:138:8:4,4:97,33:0.058:2,2:20.4:1:29.5:1:0.21002:2.91232:39:16:0.0593:0:4.4 -2 92151517 . C A 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=4.000;MSILEN=1;SSF=0.00896;SOR=Inf;LSEQ=TTAAAGAAGCCAGTGATTTT;RSEQ=TTTTGAACATTTCTCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:164,57:0:2,0:23.6:1:31.7:1:1:0:46.4:220:1:0:0.4 0/1:143:5:3,2:102,36:0.035:2,2:28.4:1:28.4:1:0.60877:1.87935:34:10:0.0357:0:3.8 -2 92151564 . C G 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44066;SOR=1.28281;LSEQ=ATTTTCAGCCTTCTACTAGT;RSEQ=GAAAGCGGCCTCGTGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:24:15,9:223,120:0.0654:2,2:17.2:1:32.4:1:0.8269:1.11466:33.5:48:0.0654:0:3 0/1:267:22:10,12:164,81:0.0824:2,2:18.1:1:30.6:1:0.05993:2.42091:29:44:0.0833:0:3.3 -2 92151590 . T C 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03093;SOR=0.48478;LSEQ=CGGCCTCGTGAAGGGGAAGC;RSEQ=GAGGGTGCTGAGACCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:32:23,9:249,185:0.0687:2,2:18.2:1:30.3:1:0.13705:1.90:38.3:31:0.067:0:3.1 0/1:377:13:10,3:213,150:0.0345:2,2:18.9:1:30.3:1:0.25475:2.34:28.7:26:0.0349:0:3.2 -2 92151599 . T C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90109;SOR=0.94484;LSEQ=GAAGGGGAAGCTGAGGGTGC;RSEQ=GAGACCACAAAGCACCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:38:29,9:256,204:0.0763:2,2:22.5:1:31.1:1:0.01614:2.56:37.4:76:0.0769:0:3 0/1:442:32:27,5:233,177:0.0724:2,2:13.3:1:30.6:1:0.00237:4.09:33.6:64:0.0729:0:3.2 -2 92151616 . C T 91 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06951;SOR=6.87398;LSEQ=TGCTGAGACCACAAAGCACC;RSEQ=GGCTGTGTGTGCTGCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:1:1,0:278,253:0.0019:2,0:16:0:33:0:1:0:40:2:0.0019:0:3 0/1:548:7:6,1:291,250:0.0128:2,2:16.3:1:32.6:1:0.13187:5.14:32.6:14:0.013:0:3.6 -2 92151667 . A G 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01346;SOR=1.47825;LSEQ=GTGGTTTGAACATGAAAGAA;RSEQ=TGTACCTTCTTTCACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:87:37,50:140,239:0.1867:2,2:20.7:1:31.3:1:0.33068:1.26:35.3:174:0.1875:0:2.7 0/1:509:129:62,67:159,221:0.2534:2,2:28.4:1:31.1:1:0.21965:1.29:38.8:258:0.2539:0:2.4 -2 92151689 . A T 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0016;SOR=1.79432;LSEQ=GTACCTTCTTTCACTCTGTC;RSEQ=TCTTTCTTTTCTTTGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:55:18,37:90,190:0.1642:2,2:27.9:1:29.9:1:1:1.03:29.8:54:0.1627:0:2.7 0/1:395:103:44,59:106,186:0.2608:2,2:22.2:1:29.7:1:0.28798:1.31:36.4:102:0.2609:0:2.6 -2 92151761 . G A 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56193;SOR=0.67786;LSEQ=ATAATTGCTTTTTCACAGTC;RSEQ=CTGATGTACAATTAAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:7:0,7:7,64:0.0897:2,0:36.9:1:30:1:1:0:24.6:14:0.0897:0:1.9 0/1:80:5:0,5:11,64:0.0625:2,0:22.6:1:30.4:1:1:0:26.6:10:0.0633:0:2.6 -2 92279357 . A C 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTAGACAGAAGTATTCTC;RSEQ=TAAACTAGGTTGTGATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:29:0:1:0:27:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92280748 . G C 104 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAGTTTGTGATGTGTGT;RSEQ=CTCAACTAACAGAGCTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:12:0:33:0:1:0:40:2:1:0:8 1/1:10:10:7,3:0,0:1:0,2:12:0:31.6:1:1:0:38.4:20:1:0:7.4 -2 92280758 . CA AG 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGTGTGTGCTCAACTAA;RSEQ=GAGCTGAACCTTTCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:33:0:1:0:40:2:1:0:7 1/1:10:9:7,2:0,0:0.9:0,2:23:0:30.6:1:1:0:38.8:18:1:0:6.4 -2 92280763 . CT TA 97 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGCTCAACTAACAGAG;RSEQ=GAACCTTTCTTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:28:0:31:0:1:0:40:2:1:0:6 1/1:10:10:7,3:0,0:1:0,2:28:0:29.5:1:1:0:38.4:20:1:0:5.5 -2 92280785 . T A 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACCTTTCTTTTCATAGAG;RSEQ=AGTTTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:22.7:1:29.3:1:1:0:36.7:14:1:0:5.4 1/1:17:17:9,8:0,0:1:0,2:27.4:1:29.1:1:1:0:39:34:1:0:5.4 -2 92280797 . A G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07609;SOR=Inf;LSEQ=TCATAGAGTAGTTTTGAAAC;RSEQ=CTCTTTTTGTGGAATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:0,0:0.7143:0,2:30.6:1:30.8:1:1:0:41:10:0.7143:0:6.6 1/1:17:17:9,8:0,0:1:0,2:23.9:1:29.6:1:1:0:39:16:1:0:5.4 -2 92280818 . T A 89 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTTTTTGTGGAATCTGCA;RSEQ=GTGGATATTTGGAAAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:31.6:1:30.8:1:1:0:41:10:1:0:6.6 1/1:9:8:3,5:0,0:0.8889:0,2:22.9:1:29.8:1:1:0:39.9:16:0.8889:0:5.9 -2 92280831 . AA CT 71 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCATGTGGATATTTGG;RSEQ=AGTTTTGAGGATTTCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:25:1:31.9:1:1:0:41.3:8:1:0:5.8 1/1:5:5:1,4:0,0:1:0,2:19.8:1:30.9:1:1:0:39.8:10:1:0:5.4 -2 92280841 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GGATATTTGGAAAGTTTTGA;RSEQ=GATTTCTTTGGAAAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:16:1:32.8:1:1:0:41.3:8:1:0:5.8 0/1:5:2:1,1:0,3:0.4:0,2:6:1:29:1:0.4:0:32:4:0.4:0:5.5 -2 92280848 . T G 65 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAGTTTTGAGGATTTC;RSEQ=TTGGAAAAGGGAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:9:1:32.5:1:1:0:41.3:8:1:0:5.8 1/1:3:3:0,3:0,0:1:0,0:8.7:1:32.3:1:1:0:42.3:6:1:0:6 -2 92281273 . G A 49 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=0.26566;LSEQ=GTTAGCATTCGAGTCACAGA;RSEQ=TTGAACATTCCCTTTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:8:1:31.3:1:1:0:35.3:6:0.6:0:6 0/1:4:1:1,0:2,1:0.25:2,0:25:0:32:0:1:0:27:2:0.25:0:8 -2 92281281 . T C 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24629;SOR=0.34288;LSEQ=TCGAGTCACAGAGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:4,4:3,0:0.7273:0,2:8.8:1:30.9:1:0.23636:0:33.9:16:0.7273:0:5.6 0/1:15:7:4,3:5,3:0.4667:2,2:7.9:1:30.1:1:1:1.23147:34.9:14:0.4667:0:5.4 -2 92281284 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49195;SOR=Inf;LSEQ=AGTCACAGAGTTGAACATTC;RSEQ=CTTTCATAGAGCAGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,4:0:2,0:10.8:1:30.4:1:1:0:36.8:24:0.9231:0:5.4 0/1:17:2:1,1:9,6:0.1176:2,2:21.5:1:30.5:1:1:1.46382:60:4:0.1176:0:4.5 -2 92281290 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4958;SOR=Inf;LSEQ=AGAGTTGAACATTCCCTTTC;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:14.9:1:29.3:1:1:0:38.8:30:1:0:5.4 0/1:20:2:1,1:10,7:0.1:2,2:27.5:1:31:1:1:1.40151:60:4:0.1053:0:4.5 -2 92281291 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2381;SOR=0;LSEQ=GAGTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:9,7:0,0:1:0,2:15:1:31.5:1:1:0:40.1:32:1:0:5.4 1/1:20:17:10,7:2,1:0.85:2,2:12.7:1:30.2:1:1:1.37728:36.3:16:0.8421:0:6.1 -2 92281298 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53846;SOR=Inf;LSEQ=ACATTCCCTTTCATAGAGCA;RSEQ=GTTTGAAACACTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:20.1:1:31.7:1:1:0:42.1:36:1:0:5.4 0/1:34:2:1,1:19,13:0.0588:2,2:35.5:1:31.5:1:1:1.44493:60:4:0.0588:0:4.5 -2 92281302 . T G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05774;LSEQ=TCCCTTTCATAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:10,8:0.0526:2,0:8:0:33:0:1:0:60:2:0.0526:0:7 0/1:36:2:1,1:20,14:0.0556:2,2:39.5:1:32:1:1:1.41419:60:4:0.0556:0:4.5 -2 92281326 . GG AT 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19257;SOR=3.14931;LSEQ=ACACTCTTTTTGTAGTGTCT;RSEQ=AAGTGGACATTTGGATTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:12,11:0.08:2,0:30.5:1:28.8:1:0.48667:0:36.5:4:0.08:0:5 0/1:46:10:6,4:18,17:0.2174:2,2:31.5:1:29.6:1:0.72888:1.41:40.3:20:0.2174:0:5.6 -2 92281327 . G T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03855;SOR=0.20265;LSEQ=CACTCTTTTTGTAGTGTCTG;RSEQ=AAGTGGACATTTGGATTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:23:12,11:0,0:0.92:0,2:34.3:1:29.4:1:1:0:44.4:46:1:0:5.2 1/0:46:32:16,16:2,2:0.6957:2,2:30.5:1:27.6:1:1:1:46.9:15:0.9091:0:4.9 -2 92281333 . G A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54686;SOR=0;LSEQ=TTTTGTAGTGTCTGGAAGTG;RSEQ=ACATTTGGATTGCTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:14,11:0,0:1:0,2:34.6:1:30.4:1:1:0:43.8:50:1:0:5.2 1/1:47:44:22,22:2,1:0.9362:2,2:32.2:1:28.5:1:1:1.97168:45.2:13.667:0.9318:0:5.2 -2 92281338 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12367;SOR=0;LSEQ=TAGTGTCTGGAAGTGGACAT;RSEQ=TGGATTGCTTTCAGGCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:13,11:0.0769:2,2:38:0:30.5:1:1:1.17422:60:4:0.08:0:5 0/0:47:0:0,0:24,23:0:2,0:31:1:29.6:1:1:0:45.4:22.5:1:0:5.2 -2 92281342 . AT CG 85 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04159;SOR=Inf;LSEQ=GTCTGGAAGTGGACATTTGG;RSEQ=TGCTTTCAGGCTTAAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,12:0:2,0:33.2:1:30.9:1:1:0:44.2:48:1:0:5.2 0/1:43:7:4,3:17,17:0.1628:2,2:33.3:1:30.6:1:1:1.32:43.7:14:0.1667:0:5.9 -2 92281355 . T C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.79828;LSEQ=CATTTGGATTGCTTTCAGGC;RSEQ=TAAGGTGAAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:10,12:1,0:0.9167:0,2:26.6:1:32:1:0.47826:0:43.4:44:0.9167:0:5 1/1:39:35:17,18:0,0:0.8974:0,2:30.1:1:30.7:1:1:0:46.1:34:0.8947:0:5 -2 92281359 . G C 85 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23723;SOR=4.79551;LSEQ=TGGATTGCTTTCAGGCTTAA;RSEQ=GTGAAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:1,0:10,11:0.0455:2,0:14:0:30:0:1:0:46:2:0.0455:0:7 0/1:37:7:4,3:14,16:0.1892:2,2:17.3:1:30.6:1:0.6928:1.51:43.7:14:0.1892:0:5.9 -2 92281374 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52715;SOR=Inf;LSEQ=CTTAAGGTGAAAAAGGAAAT;RSEQ=TCTTCCCACAAAAACTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:15:1:29.7:1:1:0:43.9:38:1:0:5 0/1:33:2:1,1:15,16:0.0606:2,2:16:0:33.5:1:1:1.06:60:4:0.0625:0:5 -2 92281382 . AC GT 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAAAAGGAAATATCTTCCC;RSEQ=AAAAACTACACAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:17.9:1:29.6:1:1:0:48.9:20:1:0:5.3 0/1:21:2:1,1:9,10:0.0952:2,2:16.5:1:31.8:1:1:1.11:49:4:0.1053:0:5 -2 92281383 . C T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54023;SOR=0;LSEQ=AAAAAGGAAATATCTTCCCA;RSEQ=AAAAACTACACAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:5,5:0,0:1:0,2:16.9:1:28.7:1:1:0:48.9:20:1:0:5.3 1/1:20:18:8,10:0,0:0.9:0,2:14.3:1:28.2:1:1:0:49.3:17:1:0:5.1 -2 92281392 . C G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATCTTCCCACAAAAACTA;RSEQ=ACAGAAGCATTCTCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:11:1:30.8:1:1:0:46.6:16:1:0:5.4 1/1:12:12:5,7:0,0:1:0,2:12.5:1:30:1:1:0:43.5:11:1:0:5.4 -2 92281414 . AC TG 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGCATTCTCAGAAACT;RSEQ=TTTGTGATGTGTTTACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:8.5:1:31.9:1:1:0:39.5:4:1:0.5:4.5 1/1:2:2:0,2:0,0:1:0,0:11.5:1:29.5:1:1:0:36.5:4:1:0:6 -2 92281450 . A C 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCAACTTCAGAGTTGAAC;RSEQ=TTTCTTTTGATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:8.5:1:31:1:1:0:33:4:1:0:5 1/1:3:3:1,2:0,0:1:0,2:12:0:29.3:1:1:0:33.3:6:1:0:4 -2 92281458 . TG GC 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TCAGAGTTGAACATTTCTTT;RSEQ=ATAGAGCAGTTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17.5:1:30.5:1:1:0:33:4:1:0:4 0/1:3:1:0,1:1,1:0.3333:2,0:21:0:30:0:1:0:40:2:0.3333:0:4 -2 92281459 . G C 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTTGAACATTTCTTTT;RSEQ=ATAGAGCAGTTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:21:0:30:1:1:0:30:4:1:0:3.5 -2 92281461 . T A 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GAGTTGAACATTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:29.5:1:1:0:33:4:1:0:4 0/1:3:1:0,1:1,1:0.3333:2,0:23:0:28:0:1:0:40:2:0.3333:0:4 -2 92281511 . G C 84 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18182;SOR=Inf;LSEQ=AATCTGCAAGAGGATATTTG;RSEQ=AGAGCTTTGAGGATTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:13.5:1:32.5:1:1:0:33:4:1:0:4 1/0:9:6:3,3:1,2:0.6667:2,2:15:1:32.8:1:1:1.85:35.7:12:0.6667:0:3.5 -2 92281513 . G T 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGCAAGAGGATATTTGGA;RSEQ=AGCTTTGAGGATTTCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:11.5:1:28.5:1:1:0:33:4:1:0:4 1/1:8:8:3,5:0,0:1:0,2:17.3:1:30.5:1:1:0:33.8:16:1:0:2.6 -2 92282156 . T A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGATAGAGCACTCTTGA;RSEQ=ACACTCTTTTTGTAGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:32:0:1:0:46.5:4:1:0:3.5 -2 92282164 . T C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCACTCTTGATACACTCT;RSEQ=TTTGTAGACTCTGCAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:33.5:1:1:0:46.5:4:1:0:3.5 -2 92282208 . T A 30 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGATAGCTTTGAGGATT;RSEQ=CTTTGGAAACGGGAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:0:30.5:1:1:0:31:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92282210 . TT GG 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATAGCTTTGAGGATTTC;RSEQ=TGGAAACGGGAATATCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:0:32.5:1:1:0:31:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92282232 . T G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGAAACGGGAATATCTTAA;RSEQ=ATGAAATCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:0:29.5:1:1:0:31:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:6.5:1:29.5:1:1:0:25:4:1:0:6 -2 92282264 . A T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAAGCATTCTCAGAAAC;RSEQ=TCTTTGGGATATTTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38.5:1:30.5:1:1:0:25:4:1:0:6 -2 92282275 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGAAACATCTTTGGGAT;RSEQ=TTTGCATTCAAGTCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36:0:32.5:1:1:0:25:4:1:0:6 -2 92282291 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGATATTTGCATTCAAGTCA;RSEQ=AGAGTTGAACATTCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:33.5:1:1:0:25:4:1:0:6 -2 92282297 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCATTCAAGTCAGAGAGT;RSEQ=GAACATTCCCTTTCATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:31.5:1:1:0:25:4:1:0:6 -2 92284267 . A G 34 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGAGGATTTCGTTGGAA;RSEQ=CGGGATATCTTCATATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:6:0:34:0:1:0:27:4:1:0:1.5 -2 92284320 . G T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCCTCAGAAACATCTTTG;RSEQ=GATGTTTGCATTCAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:12,4:0,0:1:0,2:14:0:30.8:1:1:0:39.8:32:1:0:5.9 1/1:30:29:16,13:0,0:0.9667:0,2:13.1:1:29.9:1:1:0:45.8:58:1:0:5.5 -2 92284328 . GC TT 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52128;SOR=Inf;LSEQ=GAAACATCTTTGGGATGTTT;RSEQ=ATTCAAGTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:13,5:0:2,0:20.3:1:32.7:1:1:0:40.3:36:1:0:5.9 0/1:30:2:1,1:16,12:0.0667:2,2:20:0:29.8:1:1:1.32044:54.5:4:0.0667:0:5 -2 92284329 . C T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82681;LSEQ=AAACATCTTTGGGATGTTTG;RSEQ=ATTCAAGTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:12,5:0,0:0.9444:0,2:21.2:1:29.8:1:1:0:40.3:34:0.9444:0:5.9 1/1:30:28:16,12:0,0:0.9333:0,2:22.3:1:29.5:1:1:0:45.4:56:1:0:5.5 -2 92284335 . A G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGGATGTTTGCATTCA;RSEQ=GTCACAGAGTTGAACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:13,6:0,0:1:0,2:25.5:1:31.6:1:1:0:39.6:38:1:0:5.9 1/1:30:30:17,13:0,0:1:0,2:27.3:1:31.9:1:1:0:46:60:1:0:5.5 -2 92284337 . T A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGGATGTTTGCATTCAAG;RSEQ=CACAGAGTTGAACATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:13,6:0,0:1:0,2:26.7:1:29.8:1:1:0:39.6:38:1:0:5.9 1/1:30:30:17,13:0,0:1:0,2:28.4:1:29.8:1:1:0:46:60:1:0:5.5 -2 92284363 . G A 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTGAACATTCCCTATCAT;RSEQ=GAGCAGGTTTGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:10,6:0,0:1:0,2:19.1:1:28.7:1:1:0:38.4:32:1:0:6.3 1/1:27:27:14,13:0,0:1:0,2:15.6:1:28.9:1:1:0:44.6:54:1:0:5.5 -2 92284367 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51923;SOR=Inf;LSEQ=GAACATTCCCTATCATGGAG;RSEQ=AGGTTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:16.8:1:31.4:1:1:0:38.9:30:1:0:6.3 0/1:25:2:1,1:12,11:0.08:2,2:15:0:33:0:1:1.0871:48:4:0.08:0:4 -2 92284373 . T G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52688;SOR=Inf;LSEQ=TCCCTATCATGGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:16.9:1:29.5:1:1:0:39.7:22:1:0:6.8 0/1:20:2:1,1:9,9:0.1:2,2:9:0:33:1:1:1:48:4:0.1:0:4 -2 92284377 . A T 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATCATGGAGCAGGTTTGAA;RSEQ=CACTCTTTTTGTGGAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:7,4:0,0:1:0,2:12.9:1:29.2:1:1:0:39.7:22:1:0:6.8 1/1:14:14:7,7:0,0:1:0,2:7.9:1:29.9:1:1:0:37:28:1:0:5.9 -2 92284383 . T C 95 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCAGGTTTGAAACACTC;RSEQ=TTTTGTGGAATCTGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:5,4:0,0:1:0,2:8.8:1:30.4:1:1:0:42:18:1:0:7 1/1:9:9:5,4:0,0:1:0,2:4.1:1:30:1:1:0:37.7:18:1:0:7 -2 92284390 . G A 59 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGAAACACTCTTTTTGT;RSEQ=GAATCTGGAAGTGGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:7.5:1:29.5:1:1:0:52:8:1:0:7.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92289803 . T G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGCGTTCGAGTCACAGAG;RSEQ=TGATCACTCCCTTTCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:31.5:1:1:0:27:4:1:0:2.5 -2 92289807 . T A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTCGAGTCACAGAGTTGA;RSEQ=CACTCCCTTTCATAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:31:1:1:0:27:4:1:0:2.5 -2 92289940 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAGAAGCATTCTCAGAA;RSEQ=TTTATTTGTGATGTGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:4,4:0.2:2,2:14.5:1:29.5:1:1:1:43:4:0.2:0:3 -2 92289956 . C T 93 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAATTTATTTGTGATGTG;RSEQ=GCCCTCAACTAACAGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:10:8:4,4:0,0:0.8:0,2:31.1:1:31:1:1:0:46.6:16:0.8:0:2.6 -2 92289972 . T A 98 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCGCCCTCAACTAACAG;RSEQ=GTTGAACCTTTCTTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:10:10:5,5:0,0:1:0,2:38.3:1:29.7:1:1:0:45.6:20:1:0:2.6 -2 92290081 . T G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGGAAACGGGATTGTCTTCA;RSEQ=ATAAACTCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,0:0.5:0,0:30:0:34:0:1:0:40:2:0.5:0:3 1/1:2:2:2,0:0,0:1:0,0:34:1:33:1:1:0:35:4:1:0:3.5 -2 92290116 . A T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCATTCTCAGAAACTTC;RSEQ=TTGGGATGTTTCTATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:11.5:1:32.5:1:1:0:31.5:4:1:0:3.5 1/1:2:2:2,0:0,0:1:0,0:11.5:1:32.5:1:1:0:35:4:1:0:3.5 -2 92290212 . T G 29 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTGGAAGTGGACATTTG;RSEQ=AGCGCTTTCAGGGCTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:40:1:29:0:1:0:31.5:4:1:0:5 1/0:2:1:0,1:0,0:0.5:0,0:49:0:30:0:1:0:30:2:0.5:0:3 -2 92290225 . G C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTTGTAGCGCTTTCAGG;RSEQ=CTATGTTGAAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:45.5:1:31.5:1:1:0:31.5:4:1:0:5 1/1:2:2:0,2:0,0:1:0,0:44:1:31:1:1:0:35:4:1:0:5.5 -2 92290382 . T G 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTGCAAGTGGATATTT;RSEQ=GCTGGCTTTGAGGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:30.5:1:1:0:43.5:4:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92290386 . G A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAGTGGATATTTTGCT;RSEQ=GCTTTGAGGATTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29.5:1:1:0:43.5:4:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92290408 . A G 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGAGGATTTCGTTGGAA;RSEQ=CGGGAATACATACAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38.5:1:33:1:1:0:43.5:4:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92290511 . G T 76 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTATCATAGAGCAGGTT;RSEQ=GAAACACGCCTTTTGTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:13:1:29.7:1:1:0:46.5:12:1:0:4.3 1/1:5:5:3,2:0,0:1:0,2:9.2:1:31.6:1:1:0:29.4:10:1:0:4.6 -2 92290519 . G T 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.60277;LSEQ=ATAGAGCAGGTTGGAAACAC;RSEQ=CCTTTTGTCATATCTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:19:1:32:1:1:1.29098:39:4:0.25:0:4 0/1:7:1:0,1:4,2:0.1429:2,0:23:0:31:0:0.42857:0:45:2:0.1429:0:7 -2 92290529 . A G 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.45774;LSEQ=TTGGAAACACGCCTTTTGTC;RSEQ=TATCTGGAAGTGTCCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:22:0:32:1:1:1.29098:39:4:0.25:0:4 0/1:9:1:0,1:5,3:0.1111:2,0:33:0:33:0:0.44444:0:45:2:0.1111:0:7 -2 92290548 . T C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.18465;LSEQ=CATATCTGGAAGTGTCCATT;RSEQ=GGAGTGCATTCAGGCTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:4,3:1,1:0.7778:2,2:27.7:1:31.1:1:1:1.29:52.3:14:0.7778:0:3.9 1/1:9:8:5,3:0,1:0.8889:0,2:32.8:1:31.5:1:0.44444:0:41:16:0.8889:0:3.1 -2 92290553 . T C 100 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01923;SOR=Inf;LSEQ=CTGGAAGTGTCCATTTGGAG;RSEQ=GCATTCAGGCTTGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:0,0:0.4286:0,2:18.7:1:30.7:1:1:0:46:6:0.4286:0:5.3 1/1:9:9:5,4:0,0:1:0,2:29.4:1:31.7:1:1:0:41.4:18:1:0:3.6 -2 92290599 . A T 25 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACCTTCCCATAGAAAC;RSEQ=AGACAGAAGCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:2.5:1:31.5:1:1:0:24:4:1:0:7.5 1/1:2:2:1,1:0,0:1:0,2:7:1:25:0:1:0:30:4:1:0:6.5 -2 92290626 . T C 66 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28205;SOR=0.18851;LSEQ=AAGCATTCTCAGAAACTTAT;RSEQ=TGTGATGTGTGTACTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,0:0.8:0,2:24.3:1:33.3:1:1:0:28:8:0.8:0:6.3 0/1:10:4:2,2:6,0:0.4:0,2:16.5:1:33:1:0.13333:0:28.5:8:0.4444:0:6.5 -2 92290629 . T A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=Inf;LSEQ=CATTCTCAGAAACTTATTTG;RSEQ=GATGTGTGTACTCAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:28:1:31.6:1:1:0:27.2:10:1:0:6.4 0/1:10:3:3,0:5,2:0.3:2,0:22.3:1:29.7:1:1:0:22.7:6:0.3:0:7 -2 92290635 . G A 78 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.10131;SOR=0;LSEQ=CAGAAACTTATTTGTGATGT;RSEQ=TGTACTCAACTAACAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:34:1:30.4:1:1:0:27.2:10:1:0:6.4 0/1:13:6:4,2:6,0:0.4615:0,2:18.3:1:30.3:1:0.45455:0:32:12:0.4615:0:6.7 -2 92290637 . G T 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.52105;SOR=Inf;LSEQ=GAAACTTATTTGTGATGTGT;RSEQ=TACTCAACTAACAGAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:30.3:1:33.7:1:1:0:27.7:12:1:0:6.3 0/1:14:3:3,0:8,3:0.2143:2,0:30.3:1:30.3:1:1:0:22.7:6:0.2143:0:7.3 -2 92290639 . A G 52 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=Inf;LSEQ=AACTTATTTGTGATGTGTGT;RSEQ=CTCAACTAACAGAATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:32.3:1:30:1:1:0:27.7:12:1:0:6.3 0/1:14:3:3,0:8,3:0.2143:2,0:32.3:1:33:1:1:0:22.7:6:0.2143:0:7.3 -2 92290649 . C G 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53202;SOR=Inf;LSEQ=TGATGTGTGTACTCAACTAA;RSEQ=AGAATTCAACAATCGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:30.3:1:33.4:1:1:0:30.8:18:1:0:6.9 0/1:20:3:3,0:10,7:0.15:2,0:42.3:1:31.7:1:0.52105:0:22.7:6:0.15:0:7 -2 92290652 . A G 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07421;LSEQ=TGTGTGTACTCAACTAACAG;RSEQ=ATTCAACAATCGTTTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:5,1:0.3333:2,2:12:1:33.3:1:1:2.23609:37:6:0.3333:0:8 0/1:20:7:4,3:9,4:0.35:2,2:25.3:1:32.1:1:0.65135:1.64262:27.7:14:0.3684:0:7.7 -2 92290654 . T C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45427;SOR=0.51203;LSEQ=TGTGTACTCAACTAACAGAA;RSEQ=TCAACAATCGTTTTGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:2,1:0.6667:2,2:41:1:33.2:1:1:2.24:27.7:12:0.6667:0:6.3 1/0:20:10:6,4:7,3:0.5:2,2:27.7:1:33.3:1:1:1.52135:33.4:20:0.5:0:6.5 -2 92290656 . C A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45427;SOR=0.51203;LSEQ=TGTACTCAACTAACAGAATT;RSEQ=AACAATCGTTTTGAAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:0,0:0.6667:0,2:40.3:1:29:1:1:0:27.7:12:0.6667:0:6.3 1/0:20:10:6,4:0,0:0.5:0,2:29.3:1:30:1:1:0:33.4:20:0.5263:0:6.5 -2 92290660 . A C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAACTAACAGAATTCAAC;RSEQ=ATCGTTTTGAAGGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:7,3:0,0:1:0,2:29.8:1:32.1:1:1:0:30.3:20:1:0:6.8 1/1:24:24:13,11:0,0:1:0,2:28.6:1:30.7:1:1:0:29.6:48:1:0:7 -2 92290662 . T C 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28231;SOR=Inf;LSEQ=CAACTAACAGAATTCAACAA;RSEQ=CGTTTTGAAGGAGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:25.2:1:31.2:1:1:0:29.3:24:1:0:6.8 0/1:25:4:3,1:10,11:0.16:2,2:34.5:1:26:1:0.59304:3.15:22.5:3:0.125:0:7.3 -2 92290691 . C G 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09577;SOR=0.31728;LSEQ=AGGAGCAGTTTTGAAACACT;RSEQ=TTTTTGTGGAATCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:3,4:4,2:0.5385:2,2:33.4:1:31.3:1:0.59207:2.46629:30.6:14:0.5385:0:7.1 0/1:34:9:4,5:12,13:0.2647:2,2:33.2:1:30.3:1:1:1.14901:26.8:18:0.2647:0:7.3 -2 92290696 . T C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.46702;SOR=0.5121;LSEQ=CAGTTTTGAAACACTCTTTT;RSEQ=GTGGAATCTGCAAGTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:2,3:4,3:0.4167:2,2:39.4:1:30:1:1:1.88578:33.2:10:0.4167:0:7 0/1:34:9:4,5:12,13:0.2647:2,2:31.6:1:29.6:1:1:1.14901:26.8:18:0.2647:0:7.3 -2 92290697 . G C 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17139;SOR=Inf;LSEQ=AGTTTTGAAACACTCTTTTT;RSEQ=TGGAATCTGCAAGTGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:27:1:30.5:1:1:0:29.7:24:1:0:6.7 0/1:33:6:4,2:12,15:0.1818:2,2:21:1:27.8:1:0.39832:2.43:28.3:5:0.1563:0:7.5 -2 92290698 . T C 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51363;SOR=0.6022;LSEQ=GTTTTGAAACACTCTTTTTG;RSEQ=GGAATCTGCAAGTGCATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:4,3:2,3:0.5833:2,2:17.9:1:30:1:1:1.89:27.1:14:0.5833:0:6.4 0/1:33:15:6,9:9,7:0.4545:2,2:29.3:1:30.2:1:0.47949:1.88746:32.5:30:0.4545:0:6.9 -2 92290713 . C G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTGGAATCTGCAAGTG;RSEQ=ATATTTAGCTAGATTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:3,5:0,0:1:0,2:33.1:1:30.3:1:1:0:30.5:16:1:0:6.9 1/1:25:24:9,15:0,0:0.96:0,2:32.7:1:30.3:1:1:0:33.3:48:0.96:0:6.8 -2 92290720 . A G 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTGCAAGTGCATATTT;RSEQ=GCTAGATTTGAGGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:3,5:0,0:1:0,2:26.1:1:30.5:1:1:0:30.5:16:1:0:6.9 1/1:25:24:9,15:0,0:0.96:0,2:26.8:1:30:1:1:0:33.3:48:0.96:0:6.8 -2 92290726 . A C 117 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.29447;SOR=0;LSEQ=GCAAGTGCATATTTAGCTAG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:23:1:31.7:1:1:0:30.6:14:1:0:7 1/0:18:14:2,12:1,1:0.7778:2,2:29.5:1:30.9:1:0.35:5.09912:30.3:13:0.7647:0:7.4 -2 92290728 . TT GG 94 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67839;SOR=1.63642;LSEQ=AAGTGCATATTTAGCTAGAT;RSEQ=GAGGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:2,3:0.2857:2,0:27.5:1:32.5:1:1:0:24:4:0.2857:0:6 0/1:20:8:1,7:4,8:0.4:2,2:25.1:1:31.4:1:0.60268:3.3021:35.6:16:0.4:0.1:6.3 -2 92290731 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCATATTTAGCTAGATTTG;RSEQ=GGATTTCGTTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:18:1:30.4:1:1:0:30.6:14:1:0:6.7 0/1:20:2:1,1:4,14:0.1:2,2:30.5:1:30:1:0.44737:3.24:40:4:0.1:0:8 -2 92290740 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTAGATTTGAGGATTTCG;RSEQ=TGGAAACGGGATTACATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:14.6:1:31.4:1:1:0:29.2:10:1:0:6.2 0/1:18:2:1,1:3,13:0.1111:2,2:21.5:1:31:1:0.40523:3.89:40:4:0.1176:0:8 -2 92290745 . A C 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTTGAGGATTTCGTTGGA;RSEQ=ACGGGATTACATATAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:12.5:1:31.5:1:1:0:25.8:8:1:0:5.8 0/1:17:2:1,1:3,12:0.1176:2,2:9:0:30.5:1:0.42647:3.61:42:4:0.125:0:4 -2 92290746 . A G 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGAGGATTTCGTTGGAA;RSEQ=CGGGATTACATATAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:11.5:1:31.5:1:1:0:25.8:8:1:0:5.8 0/1:17:3:2,1:2,12:0.1765:2,2:12.3:1:29:1:0.12059:9.64:34.3:6:0.1875:0:7 -2 92290752 . T A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TACATATAAAAAGCAGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:7.7:1:31.7:1:1:0:26.3:6:1:0:6 0/1:15:2:1,1:2,11:0.1333:2,2:9.5:1:27:1:0.37143:4.69:40:4:0.1333:0:8 -2 92290759 . T C 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.87089;LSEQ=GTTGGAAACGGGATTACATA;RSEQ=AAAAAGCAGGCCGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:3:0:30:0:1:0:24:2:0.5:0:7 1/0:9:6:1,5:1,2:0.6667:2,2:13.7:1:31.8:1:1:2.23609:36.8:12:0.6667:0:6.2 -2 92290769 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTACATATAAAAAGCAG;RSEQ=CCGCAGCATTCTCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:0:30.5:1:1:0:48:4:1:0:6 -2 92290771 . C A 64 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACATATAAAAAGCAGGC;RSEQ=GCAGCATTCTCAGAAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:22.5:1:32:1:1:0:38.5:8:1:0:4.3 -2 92290796 . T G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CATTCTCAGAAACTTCTTTG;RSEQ=GATGTTTGCATTCAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25:0:31.5:1:1:0:21:4:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:25:0:32.5:1:1:1:24:4:0.3333:0:6 -2 92290809 . C G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTTTGTGATGTTTGCATT;RSEQ=AAGTCACAGAGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:20:0:33.5:1:1:0:21:4:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:19.5:1:32.5:1:1:1:29:4:0.3333:0:2.5 -2 92290815 . A G 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GTGATGTTTGCATTCAAGTC;RSEQ=CAGAGTTGAACATTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:0:32.5:1:1:0:21:4:1:0:1 0/0:6:0:0,0:3,3:0:2,0:18.8:1:29.8:1:1:0:33.7:12:1:0:4.8 -2 92290817 . AG CT 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GATGTTTGCATTCAAGTCAC;RSEQ=AGTTGAACATTCCCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:12:0:32:0:1:0:21:4:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:7.5:1:28:1:1:1:48:4:0.3333:0:5 -2 92290822 . T A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGCATTCAAGTCACAGAGT;RSEQ=GAACATTCCCTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7:0:31.5:1:1:0:21:4:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:25.5:1:30:1:1:1:24:4:0.3333:0:6 -2 92290836 . CA GG 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTTGAACATTCCCTTT;RSEQ=TAGAGCAGGATTGAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:30:1:1:0:24:4:1:0:5 -2 92290890 . G T 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=2.44949;LSEQ=TCTGGATGTGGACATTTGGA;RSEQ=CGCTTTCAGGCCTATGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:4:0:31:0:1:0:20:2:0.5:0:3 1/0:4:3:3,0:1,0:0.75:0,0:11.7:1:31.7:1:1:0:31.3:6:0.75:0:2.7 -2 92290902 . C G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81093;LSEQ=CATTTGGAGCGCTTTCAGGC;RSEQ=TATGGTGAAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:3,1:0.2:2,0:1:0:31:0:1:0:38:2:0.2:0:6 0/1:12:2:1,1:8,2:0.1667:2,2:11:0:32.5:1:0.45455:3.4638:40:4:0.1818:0:5 -2 92290929 . C A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55096;SOR=0.63461;LSEQ=GAAAAAGGAAATATCTTCCC;RSEQ=TGAAAACTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:7,5:0,0:0.6316:0,2:13.8:1:30.2:1:1:0:44.3:24:0.6316:0:3.1 1/0:27:14:10,4:0,0:0.5185:0,2:24.4:1:29.9:1:1:0:40.7:13:0.5:0:3.2 -2 92290931 . G A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56164;SOR=1.4681;LSEQ=AAAAGGAAATATCTTCCCCT;RSEQ=AAAACTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:5,3:6,5:0.4211:2,2:26.6:1:29.8:1:1:1.37:38.6:16:0.4211:0:4.9 1/0:27:14:8,6:9,4:0.5185:2,2:28.8:1:29.1:1:0.69458:1.65488:35.9:28:0.5185:0:4.9 -2 92290958 . AC GT 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15157;SOR=2.75668;LSEQ=AGACAGAAGCATTCTCAGAA;RSEQ=TTATTTGTGATGTGTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:2,2:11,9:0.1667:2,2:36.5:1:31.4:1:1:1.21199:38.8:8:0.1667:0:4.5 0/1:39:14:7,7:15,10:0.359:2,2:30.6:1:29.4:1:0.73765:1.48425:36:28:0.359:0:3.9 -2 92290959 . C T 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4666;SOR=0.57677;LSEQ=GACAGAAGCATTCTCAGAAA;RSEQ=TTATTTGTGATGTGTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:2,2:9,7:0.1667:2,2:32.5:1:31:1:1:1.26953:39.5:8:0.2:0:4.3 0/1:39:4:2,2:13,8:0.1026:2,2:33.3:1:29.3:1:1:1.59276:31.5:8:0.1667:0:3.8 -2 92290985 . A G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41211;SOR=0.58277;LSEQ=TGTGATGTGTGCCCTCAACT;RSEQ=ACAATGTTGAACCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:13:7,6:5,4:0.5909:2,2:21.6:1:32.8:1:1:1.06805:49.3:26:0.5909:0:3.8 0/1:33:15:8,7:9,9:0.4545:2,2:32.6:1:30.3:1:1:1.14:51.7:14:0.4375:0:4.5 -2 92290989 . A G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54305;SOR=0.63155;LSEQ=ATGTGTGCCCTCAACTAACA;RSEQ=TGTTGAACCTTTCTTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:6,6:0,0:0.6667:0,2:20.4:1:33.4:1:1:0:51.8:24:0.6667:0:3.8 1/0:27:15:8,7:1,0:0.5556:0,2:30.7:1:30.8:1:1:0:51.7:14:0.5385:0:4.5 -2 92291002 . C G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.32078;LSEQ=ACTAACAATGTTGAACCTTT;RSEQ=TTTTGATAGAGCAGTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:2,2:0.6:2,2:17.8:1:33.2:1:1:1:46.8:12:0.6:0:4.7 1/0:21:14:7,7:3,4:0.6667:2,2:20:1:31.3:1:1:1.32:51.1:28:0.6667:0:4.4 -2 92291008 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGTTGAACCTTTCTTTTG;RSEQ=TAGAGCAGTTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:14.3:1:31.2:1:1:0:46.1:18:1:0:4.1 0/1:21:2:1,1:9,10:0.0952:2,2:15.5:1:31.5:1:1:1.11:60:4:0.0952:0:5 -2 92291016 . G C 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27273;SOR=Inf;LSEQ=ACCTTTCTTTTGATAGAGCA;RSEQ=TTTTGAAACACTATTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:7.4:1:31:1:1:0:46.3:7:1:0:4.1 0/1:14:3:2,1:5,6:0.2143:2,2:8.3:1:31.7:1:1:2.26:47.3:6:0.2143:0:5.3 -2 92291019 . T C 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.33054;LSEQ=TTTCTTTTGATAGAGCAGTT;RSEQ=TGAAACACTATTTTGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:1,2:0.625:2,2:3.8:1:32.4:1:1:1.29:52:10:0.625:0:4.6 1/0:13:9:5,4:1,3:0.6923:2,2:6.9:1:31.4:1:0.55944:3.39:54.9:18:0.6923:0:4.8 -2 92291058 . G C 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08009;SOR=16.60315;LSEQ=AATCTGCAAGAGGATATTTG;RSEQ=ATAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:4,0:0.1667:0,0:18:0:34:0:1:0:40:2:0.1667:0:7 1/1:6:5:5,0:0,1:0.8333:0,0:14.2:1:33.8:1:0.16667:0:28.2:10:0.8333:0:6.4 -2 92291076 . G T 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55338;SOR=0.33645;LSEQ=TGGATAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGATTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:10:1:32:0:1:0:26:4:0.2222:0:5 0/1:12:1:0,1:7,4:0.0833:2,0:12:0:32:0:0.41667:0:40:2:0.0833:0:5 -2 92291078 . T G 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.3804;LSEQ=GATAGCTTTGAGGATTTCGT;RSEQ=GGAAACGGGATTGTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:4,1:5,2:0.4167:2,2:16.8:1:32.6:1:1:1.54:31:10:0.4167:0:5.6 1/0:12:6:5,1:2,4:0.5:2,2:30.8:1:33.2:1:0.24242:7.96:30.2:12:0.5:0:6.2 -2 92291089 . T A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43315;SOR=0.42867;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:6,6:3,0:0.8:0,2:22.1:1:29.8:1:0.22857:0:28.4:24:0.8:0:4.8 1/0:16:10:5,5:5,0:0.625:0,2:20:1:30.3:1:0.1009:0:47.7:20:0.625:0:5.4 -2 92291098 . T G 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.3049;SOR=0.46731;LSEQ=TGGAAACGGGATTGTCTTCA;RSEQ=ATAAACTCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:3,3:4,4:0.3529:2,2:26.8:1:30:1:1:1:27.7:12:0.3529:0:4.7 0/1:25:5:2,3:7,8:0.2:2,2:12.6:1:25.4:1:1:1.29489:38:1.5:0.1304:0:3 -2 92291099 . A G 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.92488;LSEQ=GGAAACGGGATTGTCTTCAT;RSEQ=TAAACTCTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:4,4:3,3:0.5:2,2:30.6:1:32.1:1:1:1:27.8:16:0.5714:0:5.5 0/1:25:12:6,6:3,5:0.48:2,2:21.5:1:31.8:1:0.66992:1.62:47.4:24:0.6316:0:5.7 -2 92291100 . T G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50639;SOR=Inf;LSEQ=GAAACGGGATTGTCTTCATA;RSEQ=AAACTCTAGACAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:29.5:1:27.6:1:1:0:29.9:16:1:0:5.3 0/1:25:2:1,1:13,10:0.08:2,2:7:1:30.5:1:1:1.28628:60:4:0.08:0:7.5 -2 92291104 . C A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.21783;LSEQ=CGGGATTGTCTTCATATAAA;RSEQ=TCTAGACAGAAGCATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:3,2:6,7:0.2778:2,2:24.8:1:29:1:1:1.70:36.4:10:0.2778:0:6.6 0/1:25:8:6,2:8,9:0.32:2,2:31.6:1:29.9:1:0.23368:3.22:35.1:16:0.3478:0:5.9 -2 92291108 . A G 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69439;SOR=0.61568;LSEQ=ATTGTCTTCATATAAACTCT;RSEQ=GACAGAAGCATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:7,7:0.2222:2,2:31.5:1:27.3:1:1:1:25:3:0.1765:0:6.3 0/1:27:4:2,2:12,11:0.1481:2,2:20.5:1:32.8:1:1:1.08739:41:8:0.1538:0:5.8 -2 92291109 . G C 87 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03388;SOR=Inf;LSEQ=TTGTCTTCATATAAACTCTA;RSEQ=ACAGAAGCATTCTCAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:31.6:1:30.3:1:1:0:30.4:36:1:0:5.4 0/1:29:7:4,3:11,11:0.2414:2,2:21.3:1:31.3:1:1:1.32:59.3:14:0.25:0:5.4 -2 92291129 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08148;LSEQ=GACAGAAGCATTCTCAGAAA;RSEQ=TTCTTTGGGATGTTTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:8,8:0,0:0.8889:0,2:32.6:1:30.7:1:1:0:29.6:15:0.8824:0:5.5 1/1:29:26:13,13:0,0:0.8966:0,2:29.8:1:31.7:1:1:0:41.7:52:0.8966:0:5.3 -2 92291131 . T G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16285;LSEQ=CAGAAGCATTCTCAGAAATT;RSEQ=CTTTGGGATGTTTCAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:4,4:5,5:0.4444:2,2:30.6:1:31.1:1:1:1:27.8:16:0.4444:0:5.5 0/1:29:14:7,7:8,7:0.4828:2,2:30.2:1:32.9:1:1:1.1376:49.2:28:0.5:0:5.4 -2 92291145 . CA GC 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63571;SOR=2.49479;LSEQ=GAAATTTCTTTGGGATGTTT;RSEQ=ATTGAAGTCACAGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:6,8:0.0667:2,0:45:0:31:0:1:0:40:2:0.0667:0:7 0/1:26:4:2,2:10,12:0.1538:2,2:21.3:1:30.6:1:1:1.19:25.3:8:0.1538:0.0769:6.3 -2 92291146 . A C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1417;SOR=0;LSEQ=AAATTTCTTTGGGATGTTTC;RSEQ=ATTGAAGTCACAGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,7:0.1333:2,2:30:1:32.5:1:1:1.37:40:4:0.1429:0:6 0/0:24:0:0,0:10,12:0:2,0:25.5:1:30:1:1:0:46.5:44:1:0:5 -2 92291150 . G C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33668;SOR=0.3439;LSEQ=TTCTTTGGGATGTTTCAATT;RSEQ=AAGTCACAGTGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:4,7:0.2143:2,2:34:1:32:1:1:1.1321:40:6:0.2143:0:6.3 0/1:24:2:0,2:10,12:0.0833:2,0:44.5:1:32:1:0.49275:0:26:4:0.0909:0:6.5 -2 92291154 . TCA T 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.11092;SOR=0;LSEQ=TTGGGATGTTTCAATTGAAG;RSEQ=CAGTGTTGAACATTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:2,8:0.1667:2,2:17.5:1:33.5:1:0.45455:3.46:29:4:0.1667:0:4 0/0:23:0:0,0:9,13:0:2,0:22:1:31.4:1:1:0:44.8:44:0.9565:0:5.2 -2 92291156 . A C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47641;SOR=1.95965;LSEQ=GGGATGTTTCAATTGAAGTC;RSEQ=CAGTGTTGAACATTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:0,4:2,4:0.3333:2,0:27:1:32.8:1:0.46667:0:27.8:8:0.4:0:6.5 1/0:22:11:5,6:3,6:0.5:2,2:12.4:1:30.2:1:0.66992:1.62:51.8:22:0.5:0:5.4 -2 92291160 . T A 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05695;LSEQ=TGTTTCAATTGAAGTCACAG;RSEQ=GTTGAACATTCCCTTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:2,7:0.1818:2,0:38:1:31.5:1:1:0:40:4:0.1818:0:6.5 0/1:21:4:1,3:8,9:0.1905:2,2:38.3:1:30.5:1:0.60301:2.55208:26.5:8:0.1905:0:6.5 -2 92291162 . TT CA 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51232;SOR=Inf;LSEQ=TTTCAATTGAAGTCACAGTG;RSEQ=GAACATTCCCTTTGTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:2,9:0:2,0:19.4:1:30.4:1:1:0:30.5:22:1:0:5.5 0/1:18:2:1,1:6,10:0.1111:2,2:32:1:30.3:1:1:1.62:27:4:0.1111:0:5.5 -2 92291163 . T A 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62208;SOR=0.5743;LSEQ=TTCAATTGAAGTCACAGTGT;RSEQ=GAACATTCCCTTTGTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:2,7:0.1818:2,0:35:1:32:0:1:0:40:4:0.1818:0:6.5 0/1:18:2:0,2:6,8:0.1111:2,0:41.5:1:32:1:0.5:0:26:4:0.125:0:6.5 -2 92291164 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54023;SOR=Inf;LSEQ=TCAATTGAAGTCACAGTGTT;RSEQ=AACATTCCCTTTGTTAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:0:2,0:19.1:1:32.2:1:1:0:31.2:20:1:0:5.5 0/1:20:2:1,1:7,11:0.1:2,2:30:1:30.5:1:1:1.54:60:4:0.1:0:7.5 -2 92291177 . GT CA 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29293;SOR=0.25308;LSEQ=CAGTGTTGAACATTCCCTTT;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:8.3:1:31.7:1:1:0:29:6:0.6:0.2:6.3 0/1:8:2:1,1:2,4:0.25:2,2:16:1:32.8:1:1:1.83:60:4:0.25:0:6.5 -2 92291178 . T G 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGTGTTGAACATTCCCTTTG;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,0:0.5:0,0:20:1:34:0:1:0:40:4:1:0:6.5 1/0:8:4:1,3:1,1:0.5:2,2:29.3:1:32:1:1:2.44949:26.5:8:0.6667:0:6 -2 92291202 . C T 59 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGTTTGAAACACTCTT;RSEQ=TTGTAGTATCTGGAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:24.8:1:29.8:1:1:0:30.8:8:1:0:4.5 -2 92291205 . G T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTTGAAACACTCTTCTT;RSEQ=TAGTATCTGGAAGTGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:29:1:28.5:1:1:0:36:4:0.5:0:4 -2 92291212 . C A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACTCTTCTTGTAGTAT;RSEQ=TGGAAGTGGACATTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:22:1:27.5:1:1:0:36:4:0.6667:0:4 -2 92291400 . T G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77001;LSEQ=AATATGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:9.5:1:31.5:1:1:0:21:4:0.5:0:5 0/1:7:3:3,0:3,0:0.4286:0,0:15.7:1:32.7:1:1:0:27.3:6:0.4286:0:5 -2 92291407 . TT GG 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.46561;LSEQ=AAGTGGATATTTGTCTAGCT;RSEQ=GAGGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:5,0:0.1429:0,0:24:0:33.5:0:1:0:22:2:0.1429:0:4 0/1:10:2:2,0:8,0:0.2:0,0:26.5:1:32.8:1:1:0:31:4:0.2:0:4.5 -2 92291426 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=TTTGAGGATTTCGTTGGAAA;RSEQ=GGGATTACATATAAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:29:1:33:1:1:0:20.6:14:1:0:3.7 0/1:11:2:1,1:9,0:0.1818:0,2:12.5:1:29.5:1:0.18182:0:21:4:0.1818:0:4.5 -2 92291438 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.43333;LSEQ=GTTGGAAACGGGATTACATA;RSEQ=AAAAAGCAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:28.5:1:33:1:1:2.64575:22:4:0.2:0:3 0/1:15:4:3,1:7,4:0.2667:2,2:37:1:31.3:1:1:1.66:26:8:0.2667:0:3.8 -2 92291445 . C G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60147;SOR=0.51333;LSEQ=ACGGGATTACATATAAAAAG;RSEQ=AGACAGCAGCATTCCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,2:0.2:2,2:33.5:1:30:1:1:2.23609:20:4:0.2:0:5 0/1:18:2:1,1:9,7:0.1111:2,2:31.5:1:32:1:1:1.26772:21:4:0.1176:0:4.5 -2 92291460 . C T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23646;SOR=0.28631;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTTCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:5,2:2,1:0.7:2,2:37.6:1:30.3:1:1:1.22:20.9:14:0.7:0:4.7 0/1:18:7:4,3:6,5:0.3889:2,2:29.6:1:29.6:1:1:1.10:23.7:14:0.3889:0:3.7 -2 92291467 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11084;SOR=0;LSEQ=GACAGCAGCATTCCCAGAAA;RSEQ=TTCTTTGTGATGTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:5,3:0.2:2,0:36.5:1:30:0:1:0:21:4:0.2:0:5 0/0:19:0:0,0:10,9:0:2,0:28.6:1:29.2:1:1:0:22.6:18:1:0:1.7 -2 92291480 . T A 26 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11905;SOR=0;LSEQ=CCAGAAACTTCTTTGTGATG;RSEQ=TTGCATTCAAGTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:5,3:0.2:2,0:23.5:1:26:0:1:0:21:4:0.2:0:5 0/0:18:0:0,0:9,9:0:2,0:27.8:1:27.9:1:1:0:21.7:36:1:0:1.6 -2 92291481 . T C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.60147;SOR=0.51333;LSEQ=CAGAAACTTCTTTGTGATGT;RSEQ=TGCATTCAAGTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:31.5:1:32.5:1:1:2.64575:20:4:0.2222:0:5 0/1:18:2:1,1:8,8:0.1111:2,2:33.5:1:30:1:1:1:21:4:0.1111:0:4.5 -2 92291490 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52;SOR=Inf;LSEQ=CTTTGTGATGTTTGCATTCA;RSEQ=GTCACAGAGTTGAACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:20.2:1:29.8:1:1:0:20.4:18:1:0:3.7 0/1:16:2:1,1:5,9:0.125:2,2:21.5:1:32:1:1:1.73:20:4:0.125:0:1 -2 92291491 . G T 31 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13043;SOR=0;LSEQ=TTTGTGATGTTTGCATTCAA;RSEQ=TCACAGAGTTGAACATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:21.5:1:31.5:1:1:1.29098:20:4:0.2222:0:5 0/0:15:0:0,0:5,10:0:2,0:27.5:1:30.3:1:1:0:21.7:30:1:0:1.4 -2 92291584 . T A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAGCGCTTTCAGGCCTA;RSEQ=GGTGAAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,0:0.6667:0,0:9.5:1:32.5:1:1:0:20.5:4:0.6667:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92295905 . T G 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCATTCTCAGCAACTTC;RSEQ=TTGTGATGTTTCCATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:1:31:0:1:0:33:4:1:0:6.5 1/0:2:1:0,1:0,1:0.5:0,0:19:0:26:0:1:0:47:2:0.5:0:7 -2 92295909 . T G 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATTCTCAGCAACTTCTTTG;RSEQ=GATGTTTCCATTGAAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12:1:31:1:1:0:33:4:1:0:6.5 1/0:2:1:0,1:0,1:0.5:0,0:23:0:25:0:1:0:47:2:0.5:0:7 -2 92295918 . C G 48 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=CAACTTCTTTGTGATGTTTC;RSEQ=ATTGAAGTCCCAGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:31.5:1:1:0:33:4:1:0:6.5 1/0:6:3:1,2:1,2:0.5:2,2:16.7:1:30.7:1:1:1:42.3:6:0.5:0:5 -2 92295945 . A C 50 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GTCCCAGTGTTGAACATTCC;RSEQ=TTTGATAGAGCAGGTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19:0:33:0:1:0:33:4:1:0:6.5 1/0:6:3:1,2:1,2:0.5:2,2:25:0:32:1:1:1:42.3:6:0.5:0:5 -2 92295949 . G T 47 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=CAGTGTTGAACATTCCATTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:30.5:1:1:0:33:4:1:0:6.5 1/0:6:3:1,2:1,2:0.5:2,2:21:0:29.7:1:1:1:42.3:6:0.5:0:5 -2 92295962 . T G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTTGATAGAGCAGGTT;RSEQ=GAAACACGCCTTTTGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:2:0:33:1:1:0:33:4:1:0:6.5 1/0:5:3:1,2:0,1:0.6:0,2:8:0:31.7:1:1:0:42.3:6:0.6:0:5 -2 92296224 . C A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=TTACATATAAAAGCAGACAG;RSEQ=AGCATTCCCAGAAACTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:12:0:33:0:1:0:45:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:6:1:27:1:1:0:38:4:1:0:7.5 -2 92296232 . C T 40 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTTCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:20:0:33:0:1:0:45:2:1:0:0 1/1:3:3:1,2:0,0:1:0,2:9.7:1:25.7:1:1:0:38.7:6:1:0:7.3 -2 92296238 . A C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGACAGCAGCATTCCCAGAA;RSEQ=CTTCTTTGTGATGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:9.3:1:31.7:1:1:0:55:6:1:0:3.3 1/0:3:2:1,1:0,1:0.6667:0,2:13:1:29:1:1:0:40:4:0.6667:0:7 -2 92296250 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TCCCAGAAACTTCTTTGTGA;RSEQ=GTTTGCATTCAAGTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:13:0:32:1:1:0:60:4:0.6667:0:5 0/0:3:0:0,0:1,2:0:2,0:27.7:1:26.7:1:1:0:38.7:6:1:0:7.3 -2 92296251 . G A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CCCAGAAACTTCTTTGTGAT;RSEQ=TTTGCATTCAAGTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:22.3:1:33.3:1:1:0:55:6:1:0:3.3 1/0:3:2:1,1:0,1:0.6667:0,2:26:1:27.5:1:1:0:40:4:0.6667:0:7 -2 92296253 . T G 34 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CAGAAACTTCTTTGTGATGT;RSEQ=TGCATTCAAGTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:16:0:34:0:1:1:60:4:0.5:0:5 0/0:3:0:0,0:0,1:0:0,0:36:0:27:0:1:0:36:2:0.3333:0:8 -2 92296257 . A T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=AACTTCTTTGTGATGTTTGC;RSEQ=TTCAAGTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22.8:1:31.8:1:1:0:51.8:8:1:0:2.5 1/0:3:2:1,1:0,1:0.6667:0,2:32:1:28.5:1:1:0:40:4:0.6667:0:7 -2 92296287 . CA TG 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CAGAGTTTAACATTCCCTTT;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:27:0:33:0:1:1:49:4:0.3333:0:2.5 0/0:3:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92296288 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=AGAGTTTAACATTCCCTTTC;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:0.3333:2,2:29.5:1:31.5:1:1:1:60:4:0.5:0:5 0/0:3:0:0,0:1,1:0:2,0:38:1:29.5:1:1:0:40:4:1:0:7 -2 92296300 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TCCCTTTCATAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:17.5:1:29.5:1:1:1:60:4:0.3333:0:5 0/0:3:0:0,0:1,2:0:2,0:22.7:1:31.7:1:1:0:38.7:6:1:0:6.7 -2 92296306 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5;SOR=0;LSEQ=TCATAGAGCAGGTTTGAAAC;RSEQ=CTCTTTTTGTAGTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:11.5:1:29.5:1:1:1:60:4:0.3333:0:5 0/0:3:0:0,0:1,2:0:2,0:16.7:1:32:0:1:0:38.7:6:1:0:6.7 -2 92296327 . T A 29 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTCTTTTTGTAGTATCTGGA;RSEQ=GTGGACATTTGGAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:14.5:1:29.5:1:1:0:49:4:0.6667:0:2.5 1/1:1:1:0,1:0,0:1:0,0:5:0:31:0:1:0:40:2:1:0:7 -2 92296660 . G C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=TATCTGGAAGTGGACATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:25.5:1:32.5:1:1:0:40:4:1:0:5.5 -2 92296688 . C T 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTGGACATTTGGAGCGCT;RSEQ=TCAGGACTACTGTGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16:1:31.5:1:1:0:37:4:1:0:6.5 1/1:3:3:3,0:0,0:1:0,0:31.3:1:32:0:1:0:36.3:6:1:0:6.3 -2 92296694 . A T 48 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTTGGAGCGCTCTCAGG;RSEQ=CTACTGTGAAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22:1:31.5:1:1:0:37:4:1:0:6.5 1/0:4:3:3,0:1,0:0.75:0,0:33.3:1:30.7:1:1:0:36.3:6:1:0:6.3 -2 92296699 . T G 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGAGCGCTCTCAGGACTAC;RSEQ=GTGAAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27:1:31.5:1:1:0:37:4:1:0:6.5 1/1:4:4:4,0:0,0:1:0,0:27.8:1:30.3:1:1:0:35.5:8:1:0:6.3 -2 92296711 . A G 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGACTACTGTGAAAAAGGA;RSEQ=ATATCTTCCAATAAAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29.7:1:34:0:1:0:31.3:6:1:0:6 1/1:4:4:4,0:0,0:1:0,0:27.8:1:33.8:1:1:0:35.5:8:1:0:6.3 -2 92296728 . G A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAATATCTTCCAATAAAA;RSEQ=CTAGATAGAAGCAATGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:35.3:1:31.7:1:1:0:31.3:6:1:0:6 1/1:3:3:3,0:0,0:1:0,0:31:1:31.3:1:1:0:34:6:1:0:6.7 -2 92296751 . A CT 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AGATAGAAGCAATGTCAGAA;RSEQ=TTTTTCATGATGTATCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:26:1:32.3:1:1:0:31.3:8:1:0:5.3 1/1:2:2:2,0:0,0:1:0,0:27.5:1:32:1:1:0:31:4:1:0:7 -2 92296776 . T A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TCATGATGTATCTACTCAGC;RSEQ=AACAGAGTTGAACCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:1:0,2:14:1:29.5:1:1:0:28.4:16:1:0:5.8 1/1:7:6:6,0:1,0:0.8571:0,0:13.2:1:31.7:1:1:0:39.7:12:0.8571:0:5.2 -2 92296805 . C G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACCTTTCTTTTGAGAGA;RSEQ=CAGTTTTAAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:8,5:0,0:1:0,2:20.9:1:31.8:1:1:0:34.2:26:1:0:5.5 1/1:22:22:15,7:0,0:1:0,2:24.3:1:31.5:1:1:0:35.5:44:1:0:4.9 -2 92296812 . TA CG 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16844;SOR=0;LSEQ=TTCTTTTGAGAGACCAGTTT;RSEQ=AAACACTCTTTTTGGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,7:0.1:2,2:46:1:30.8:1:1:1.53525:24:4:0.1:0:6 0/0:28:0:0,0:17,11:0:2,0:25:1:29.3:1:1:0:36.1:56:1:0:5.1 -2 92296813 . A G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1424;SOR=6.90392;LSEQ=TCTTTTGAGAGACCAGTTTT;RSEQ=AAACACTCTTTTTGGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:9,6:0,0:0.7895:0,2:16.7:1:31.7:1:1:0:38.9:30:0.8824:0:5.3 1/1:28:27:16,11:0,0:0.9643:0,2:26.6:1:30.9:1:1:0:36.1:54:0.9643:0:5 -2 92296823 . T G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.53247;SOR=Inf;LSEQ=GACCAGTTTTAAAACACTCT;RSEQ=TTTGGGGAATATGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:25.5:1:30.6:1:1:0:35.4:40:1:0:5.5 0/1:36:2:1,1:19,15:0.0556:2,2:12.5:1:30.5:1:1:1.2583:37:4:0.0556:0:6.5 -2 92296825 . T C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12338;SOR=0;LSEQ=CCAGTTTTAAAACACTCTTT;RSEQ=TGGGGAATATGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,7:0.1:2,2:43:1:33:1:1:1.53525:24:4:0.1:0:6 0/0:36:0:0,0:20,16:0:2,0:28.9:1:29.6:1:1:0:35.9:72:1:0:4.9 -2 92296828 . G T 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTAAAACACTCTTTTTG;RSEQ=GGAATATGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:12,8:0,0:1:0,2:28:1:30.5:1:1:0:35.4:40:1:0:5.5 1/1:37:37:20,17:0,0:1:0,2:30:1:29.2:1:1:0:36.1:74:1:0:5 -2 92296844 . A G 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.34684;SOR=2.78786;LSEQ=TTTGGGGAATATGCAAGTGG;RSEQ=TATTAGGCCAGCTTGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:26:14,12:2,1:0.8966:2,2:23.5:1:31.7:1:1:1.6838:40.6:52:0.8966:0:5.2 1/1:51:49:24,25:1,1:0.9608:2,2:25.8:1:30.7:1:1:1.04085:38.8:98:0.9608:0:4.9 -2 92296852 . C G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36432;SOR=0.39129;LSEQ=ATATGCAAGTGGATATTAGG;RSEQ=CAGCTTGGAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:2,1:14,15:0.0938:2,2:38:1:32.3:1:1:2.09:25.3:6:0.0938:0:6 0/1:52:2:1,1:24,26:0.0385:2,2:39.5:1:32.5:1:1:1.08:37:4:0.0385:0:6.5 -2 92296855 . GC G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5263;SOR=Inf;LSEQ=TGCAAGTGGATATTAGGCCA;RSEQ=TTGGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:27.8:1:32.6:1:1:0:39.2:62:1:0:5.3 0/1:52:2:1,1:23,27:0.0385:2,2:19:1:29.5:1:1:1.17:43.5:4:0.0385:0:5.5 -2 92296859 . G T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62718;SOR=0.58402;LSEQ=AGTGGATATTAGGCCAGCTT;RSEQ=GAGGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:13,15:0.0645:2,2:37:1:31:1:1:1.15:27:4:0.0645:0:5.5 0/1:52:2:1,1:23,27:0.0385:2,2:34:0:31.5:1:1:1.17:37:4:0.0385:0:6.5 -2 92296883 . TC AA 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52214;SOR=Inf;LSEQ=GATTTCGTTGGAAACGGGAA;RSEQ=CATATAAAAAGCAGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:31.1:1:29.5:1:1:0:40.3:50:1:0:5.2 0/1:41:2:1,1:15,24:0.0488:2,2:25:1:32:0:1:1.58:45:4:0.0488:0:5 -2 92296884 . C A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52565;SOR=0;LSEQ=ATTTCGTTGGAAACGGGAAT;RSEQ=CATATAAAAAGCAGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:10,13:0,0:1:0,2:33.3:1:29.3:1:1:0:41.6:46:1:0:5.3 1/1:39:37:14,23:0,0:0.9487:0,2:28.8:1:29.3:1:1:0:38.6:74:1:0:5.1 -2 92296886 . A G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.6282;SOR=1.69847;LSEQ=TTCGTTGGAAACGGGAATCC;RSEQ=TATAAAAAGCAGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:21:9,12:1,1:0.913:2,2:33.1:1:31.2:1:1:1.31655:43.2:42:0.913:0:5.1 1/1:38:36:14,22:1,1:0.9474:2,2:29.4:1:30.8:1:1:1.55221:39.2:72:0.9474:0:5 -2 92296888 . A G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.6282;SOR=0.58877;LSEQ=CGTTGGAAACGGGAATCCAT;RSEQ=TAAAAAGCAGACAGCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,12:0.087:2,2:24:1:31.5:1:1:1.32:24.5:4:0.087:0:6.5 0/1:38:2:1,1:14,22:0.0526:2,2:5:0:33:1:1:1.55:37:4:0.0526:0:6.5 -2 92296905 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50046;SOR=Inf;LSEQ=CATATAAAAAGCAGACAGCA;RSEQ=CATTGTCAGAAACTTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:9,11:0:2,0:20.1:1:31.3:1:1:0:41.8:40:1:0:5.2 0/1:27:2:1,1:7,18:0.0741:2,2:17:1:29:1:0.51282:2.47:60:4:0.0741:0:5.5 -2 92296920 . T A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAGCATTGTCAGAAACT;RSEQ=CTTTGTCATGTTTGCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:3,7:0,0:1:0,2:18.5:1:29.2:1:1:0:42.1:20:1:0:5.2 1/1:15:15:3,12:0,0:1:0,2:14.7:1:30:1:1:0:38.8:30:1:0:5.5 -2 92296927 . C G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTCAGAAACTTCTTTGT;RSEQ=ATGTTTGCATTGAAGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:2,7:0,0:1:0,2:12.8:1:31.3:1:1:0:40.1:18:1:0:5.3 1/1:13:13:3,10:0,0:1:0,2:9.5:1:32.1:1:1:0:38.2:26:1:0:5.5 -2 92296939 . G C 75 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTGTCATGTTTGCATT;RSEQ=AAGTCCCAGAGTTCAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:5.2:1:32.4:1:1:0:34.2:10:1:0:5.4 1/1:4:4:0,4:0,0:1:0,0:5.8:1:31.5:1:1:0:42.8:8:1:0:6.5 -2 92297055 . C T 62 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=GTCTTGAAAAAGGAAATATC;RSEQ=TCCCATAAAAACTAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:17:1:32.7:1:1:0:29:6:1:0:6.7 1/0:8:4:2,2:2,2:0.5:2,2:8:1:31.3:1:1:1:53:8:0.5:0:5.5 -2 92297059 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAAAAGGAAATATCCTCC;RSEQ=ATAAAAACTAGATAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:21:1:33:0:1:0:29:6:1:0:6.7 0/1:8:2:1,1:3,3:0.25:2,2:17:1:28.5:1:1:1:36:4:0.25:0:6 -2 92297064 . AAACTAG CAA 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGAAATATCCTCCCATAA;RSEQ=ATAGAAGCATTCTCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:26:1:31.7:1:1:0:29:6:1:0:6.7 0/1:10:2:1,1:4,4:0.2:2,2:25:0:31:1:1:1:46:4:0.2:0:4.5 -2 92297072 . TA CG 61 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19231;SOR=0;LSEQ=ATCCTCCCATAAAAACTAGA;RSEQ=GAAGCATTCTCAGAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:35:1:32.7:1:1:0:29:6:1:0:5.7 0/1:10:4:2,2:1,1:0.4:2,2:16.5:1:30.8:1:1:1:52.3:8:0.4:0:4.8 -2 92297095 . T C 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25497;SOR=Inf;LSEQ=AAGCATTCTCAGAAACTTAT;RSEQ=TGTGATGTGTGTACTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:29.3:1:31.3:1:1:0:41.3:14:1:0:3.9 0/1:14:4:2,2:5,5:0.2857:2,2:40.8:1:31.8:1:1:1:39:8:0.2857:0:5.5 -2 92297098 . T A 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=CATTCTCAGAAACTTATTTG;RSEQ=GATGTGTGTACTCAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:22:0:31:0:1:3.1622:50:4:0.2857:0:2 0/1:14:4:2,2:5,5:0.2857:2,2:28.5:1:28.3:1:1:1:47.5:8:0.2857:0:3.5 -2 92297104 . G A 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.25497;SOR=Inf;LSEQ=CAGAAACTTATTTGTGATGT;RSEQ=TGTACTCAACTAACAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:30.3:1:32.6:1:1:0:41.3:14:1:0:3.9 0/1:14:4:2,2:5,5:0.2857:2,2:31.8:1:29.3:1:1:1:39:8:0.2857:0:5.5 -2 92297106 . G T 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.36146;SOR=0.31811;LSEQ=GAAACTTATTTGTGATGTGT;RSEQ=TACTCAACTAACAGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,1:0.7143:2,2:29.2:1:30.8:1:1:3.16:37.8:10:0.7143:0:4.6 0/1:14:6:3,3:4,4:0.4286:2,2:30.2:1:30.8:1:1:1:51.3:12:0.4286:0:4.5 -2 92297108 . A G 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36146;SOR=0.31811;LSEQ=AACTTATTTGTGATGTGTGT;RSEQ=CTCAACTAACAGAATTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,1:0.7143:2,2:27.2:1:33:1:1:3.16:37.8:10:0.7143:0:4.6 0/1:14:6:3,3:4,4:0.4286:2,2:28.3:1:33:1:1:1:51.3:12:0.4615:0:4.5 -2 92297118 . C G 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8401;LSEQ=TGATGTGTGTACTCAACTAA;RSEQ=AGAATTGAACCATCGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:18:0:32.5:1:1:3.1622:50:4:0.2857:0:2 0/1:16:4:2,2:6,6:0.25:2,2:15.8:1:29.3:1:1:1:47.5:8:0.25:0:3.5 -2 92297121 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75944;LSEQ=TGTGTGTACTCAACTAACAG;RSEQ=ATTGAACCATCGTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:2,1:0.5714:2,2:14:1:32.5:1:1:1.41:37.3:8:0.6667:0:4.3 1/0:16:8:4,4:4,4:0.5:2,2:13.9:1:30.8:1:1:1:48.5:16:0.5:0:5.3 -2 92297123 . T C 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27273;SOR=Inf;LSEQ=TGTGTACTCAACTAACAGAA;RSEQ=TGAACCATCGTTGTGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:12.4:1:30.9:1:1:0:41.3:14:1:0:3.9 0/1:16:4:2,2:6,6:0.25:2,2:12.8:1:31.5:1:1:1:39:8:0.25:0:5.5 -2 92297125 . G A 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27273;SOR=Inf;LSEQ=TGTACTCAACTAACAGAATT;RSEQ=AACCATCGTTGTGGAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:10.4:1:32.3:1:1:0:41.3:14:1:0:3.9 0/1:16:4:2,2:6,6:0.25:2,2:10.8:1:29:1:1:1:39:8:0.2667:0:5.5 -2 92297131 . T C 46 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63916;LSEQ=CAACTAACAGAATTGAACCA;RSEQ=CGTTGTGGAAGAGCAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:5:0:33:0:1:3.1622:50:4:0.2857:0:2 0/1:15:3:1,2:6,6:0.2:2,2:4:1:29.3:1:1:1.91151:48.3:6:0.2:0:3.3 -2 92297136 . G T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAATTGAACCATCGTT;RSEQ=TGGAAGAGCAGTTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:2:0:27:0:1:0:25:2:1:0:6 1/1:3:3:1,2:0,0:1:0,2:17:1:29:1:1:0:46.7:6:1:0:7 -2 92297139 . G A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATTGAACCATCGTTGTG;RSEQ=AAGAGCAGTTTGGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:28.5:1:1:0:40:4:1:0:7.5 -2 92297141 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATTGAACCATCGTTGTGGA;RSEQ=GAGCAGTTTGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:30.5:1:1:0:40:4:1:0:7.5 -2 92297151 . G T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTTGTGGAAGAGCAGTTT;RSEQ=GAAACACTCTTTTTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:10:0:31:0:1:0:22:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:39.5:1:30:1:1:0:40:4:1:0:7.5 -2 92297160 . C G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAGCAGTTTGGAAACACT;RSEQ=TTTTTGTGGAATCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:7:0:27:0:1:0:22:2:0.5:0:7 1/1:2:2:1,1:0,0:1:0,2:48.5:1:32:1:1:0:40:4:1:0:7.5 -2 92297190 . T G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:42:1:32:1:1:0:22:4:1:0:6.5 0/0:2:0:0,0:1,1:0:2,0:19:0:30.5:1:1:0:40:4:1:0:7.5 -2 92297345 . T A 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.57733;LSEQ=CTCTTTTTGTAGTATCTGGA;RSEQ=GTGGACATTTGGAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:34:1:29.5:1:0.33333:0:25:4:0.6667:0:7.5 1/0:2:1:0,1:1,0:0.5:0,0:28:0:33:0:1:0:37:2:0.5:0:7 -2 92297469 . T G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CAAGTAACAGTGTTGAACCT;RSEQ=TCTTTTGATAGAGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:31.5:1:1:0:23:4:1:0:2 1/0:3:2:1,1:0,1:0.6667:0,2:30:1:30:1:1:0:45:4:0.6667:0:1 -2 92297569 . A G 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAAACGGGATTGTCTTCAT;RSEQ=TAAACTCTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:33.5:1:1:0:23:4:1:0:6.5 -2 92297595 . T G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGACAGAAGCATTCTCA;RSEQ=AAATTTCTTTGGGATGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42:1:32:1:1:0:23:4:1:0:6.5 -2 92297599 . T C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAAGCATTCTCATAAA;RSEQ=TTCTTTGGGATGTTTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42.5:1:32:1:1:0:23:4:1:0:6.5 -2 92297601 . T G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGCATTCTCATAAATT;RSEQ=CTTTGGGATGTTTTAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42.5:1:32:1:1:0:23:4:1:0:6.5 -2 92297626 . A C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATGTTTTAATTGAAGTC;RSEQ=CAGTGTTGAACATTCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:29:1:1:0:23:4:1:0:6.5 -2 92297644 . TG AT 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAGTGTTGAACATTCCC;RSEQ=TCATAGAGCAGGTTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:29.5:1:1:0:23:4:1:0.5:6 -2 92297717 . A G 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGCGCTCTCAGGACTAC;RSEQ=GTGAAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:37.5:1:30:1:1:0:25.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92297980 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTCACAGAGTTGAACATTC;RSEQ=CTTTCATAGAGCAGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:5:0:30:0:1:0:23:2:1:0:5 1/0:3:2:1,1:0,1:0.6667:0,2:34.5:1:30:1:1:0:21:4:0.6667:0:4 -2 92297986 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTTGAACATTCCCTTTC;RSEQ=TAGAGCAGCTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:34:0:30:1:1:0:21:4:0.6667:0:4 -2 92298002 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTCATAGAGCAGCTTTGAA;RSEQ=CACTCTTTTTGTAGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:32.5:1:1:0:21:4:1:0:4 -2 92305371 . AA TG 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTGTAAAATCTGCAAG;RSEQ=GATATTTGGATAGCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:28:1:1:0:28:4:1:0:2.5 -2 92305597 . A C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAAATATCTTCCCATAA;RSEQ=AACTAGACAGAAGCATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:17.7:1:33.3:1:1:0:44.6:18:1:0:6.7 1/1:19:19:18,1:0,0:1:0,1:11.1:1:31.5:1:1:0:45.1:38:1:0:7.1 -2 92305618 . T A 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53571;SOR=2.20075;LSEQ=AACTAGACAGAAGCATTCTC;RSEQ=GAACCTAGTTTCTGAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:13,4:1,0:0.9444:0,2:23.5:1:30.4:1:1:0:43:34:0.9444:0:6.6 1/1:39:38:25,13:1,0:0.9744:0,2:22.7:1:30.5:1:1:0:46.4:76:0.9744:0:6.8 -2 92305622 . C A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29412;SOR=Inf;LSEQ=AGACAGAAGCATTCTCTGAA;RSEQ=CTAGTTTCTGAGATGTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:14,5:0,0:0.95:0,2:26.4:1:30.1:1:1:0:42.8:38:0.95:0:6.5 1/1:48:48:31,17:0,0:1:0,2:22:1:29.9:1:1:0:48.4:47:1:0:6.8 -2 92305634 . GA TG 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17941;SOR=5.59178;LSEQ=TCTCTGAACCTAGTTTCTGA;RSEQ=TGTGTCCTCAACTAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:15,7:0,0:0.9167:0,2:28.9:1:31.4:1:1:0:43.6:44:0.9167:0:5.4 1/1:64:63:38,25:0,0:0.9844:0,2:26.4:1:30.5:1:1:0:48.5:126:0.9844:0.0469:5.5 -2 92305649 . A G 62 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.43108;LSEQ=TCTGAGATGTGTCCTCAACT;RSEQ=ACAGAGTTGAACATTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:1,0:19,14:0.0294:2,0:14:0:34:0:1:0:40:2:0.0303:0:7 0/1:96:4:2,2:51,41:0.0417:2,2:26:1:31:1:1:1.24105:59.5:8:0.0417:0:5.5 -2 92305650 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGAGATGTGTCCTCAACTA;RSEQ=CAGAGTTGAACATTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:0:2,0:26.2:1:29.4:1:1:0:45.6:33:1:0:5 0/1:97:2:1,1:53,42:0.0206:2,2:15:1:29:1:1:1.25885:50:4:0.0208:0:7 -2 92305653 . G C 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.526;SOR=1.59743;LSEQ=AGATGTGTCCTCAACTAACA;RSEQ=AGTTGAACATTTCTTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:29:16,13:4,1:0.8529:2,2:28.1:1:31.7:1:0.37863:3.15126:46.2:58:0.8529:0:4.9 1/1:103:93:50,43:6,4:0.9029:2,2:27.7:1:30.9:1:0.75163:1.28685:49.3:186:0.9029:0:5.3 -2 92305659 . A T 122 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06507;SOR=4.1456;LSEQ=GTCCTCAACTAACAGAGTTG;RSEQ=ACATTTCTTTTGACAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:19,16:0.0541:2,2:23:1:28.5:1:1:1.18197:50:4:0.0556:0:6 0/1:109:21:10,11:46,40:0.1927:2,2:29.2:1:28:1:0.63655:1.26221:47.9:42:0.1927:0:5.1 -2 92305662 . A T 110 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56393;SOR=1.61617;LSEQ=CTCAACTAACAGAGTTGAAC;RSEQ=TTTCTTTTGACAGAACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:1,2:18,15:0.0833:2,2:32.7:1:31:1:0.59286:2.34335:41.7:6:0.0857:0:6.7 0/1:109:14:7,7:49,46:0.1284:2,2:32.3:1:29.1:1:1:1.06457:46.9:13:0.1226:0:6 -2 92305668 . T A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.24844;SOR=0.31154;LSEQ=TAACAGAGTTGAACATTTCT;RSEQ=TTGACAGAACAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:16,17:0.0571:2,2:31.5:1:31:1:1:1.06:50.5:4:0.0571:0:6.5 0/1:109:2:1,1:54,53:0.0183:2,2:33:0:30:0:1:1.0187:60:4:0.0183:0:2 -2 92305670 . T A 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16121;SOR=2.44451;LSEQ=ACAGAGTTGAACATTTCTTT;RSEQ=GACAGAACAGTTTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:29:13,16:2,0:0.8529:0,2:29.1:1:29:1:0.22581:0:44.3:28:0.8485:0:5 1/1:107:100:50,50:1,2:0.9346:2,2:30.6:1:28.9:1:1:1.99:50:49:0.9333:0:5.2 -2 92305673 . C G 64 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00323;SOR=0;LSEQ=GAGTTGAACATTTCTTTTGA;RSEQ=AGAACAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:4:3,1:14,17:0.1143:2,2:31.8:1:32:1:0.33766:3.52:50:8:0.1143:0:6.8 0/0:107:0:0,0:52,55:0:2,0:30.8:1:30.9:1:1:0:48.5:52.5:1:0:5.2 -2 92305676 . A T 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35538;SOR=0.39152;LSEQ=TTGAACATTTCTTTTGACAG;RSEQ=ACAGTTTTGAAACACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:2,1:13,17:0.0909:2,2:43.3:1:29.7:1:0.57936:2.54:48.3:6:0.0938:0:6 0/1:107:4:2,2:49,53:0.0374:2,2:29.5:1:29.8:1:1:1.08:26.3:8:0.0377:0:6.3 -2 92305677 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05427;SOR=0;LSEQ=TGAACATTTCTTTTGACAGA;RSEQ=CAGTTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:13,18:0.0606:2,0:24.5:1:32.5:1:0.19886:0:40:4:0.0625:0:7 0/0:107:0:0,0:52,55:0:2,0:30.1:1:29.5:1:1:0:48.5:214:1:0:5.2 -2 92305678 . C T 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0492;SOR=0;LSEQ=GAACATTTCTTTTGACAGAA;RSEQ=AGTTTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:14,17:0.0606:2,2:41.5:1:30.5:1:1:1.21:60:4:0.0606:0:6.5 0/0:114:0:0,0:58,55:0:2,0:27.8:1:31.3:1:1:0:48.1:112:0.9912:0:5.3 -2 92305690 . A T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGACAGAACAGTTTTGAAAC;RSEQ=CTCTTTTTGTGGAATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,19:0:2,0:24:1:29.5:1:1:0:44.2:33:1:0:5.4 0/1:106:3:1,2:50,53:0.0283:2,2:22:1:30.7:1:1:1.87595:37.3:6:0.0288:0:7.3 -2 92305692 . T G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGAACAGTTTTGAAACAC;RSEQ=CTTTTTGTGGAATCTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,19:0:2,0:23.8:1:30.4:1:1:0:44.2:66:1:0:5.3 0/1:106:2:1,1:50,54:0.0189:2,2:23.5:1:32.5:1:1:1.08:50:4:0.0192:0:6 -2 92305693 . C G 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.1421;SOR=0.15171;LSEQ=CAGAACAGTTTTGAAACACT;RSEQ=TTTTTGTGGAATCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:13,18:0.0606:2,2:23:0:32.5:1:1:1.37:60:4:0.0606:0:3 0/0:105:1:0,1:49,53:0.0095:2,0:27:0:33:0:1:0:32:2:0.0096:0:7 -2 92305695 . T C 49 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0.97974;LSEQ=GAACAGTTTTGAAACACTCT;RSEQ=TTTGTGGAATCTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:1:0,1:14,18:0.0303:2,0:24:0:34:0:1:0:52:2:0.0303:0:3 0/1:101:3:1,2:46,52:0.0297:2,2:41:1:31.3:1:1:1.75966:50:6:0.0297:0:6.3 -2 92305697 . T C 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15185;SOR=0.15911;LSEQ=ACAGTTTTGAAACACTCTTT;RSEQ=TGTGGAATCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:2,0:11,19:0.0625:2,0:24.5:1:30.5:1:0.15726:0:40:4:0.0625:0:7 0/1:97:1:1,0:43,53:0.0103:2,0:20:0:29:0:0.45361:0:42:2:0.0104:0:5 -2 92305699 . G C 83 v4;pSTD;NM4;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67565;SOR=2.17076;LSEQ=AGTTTTGAAACACTCTTTTT;RSEQ=TGGAATCTGCAAGTGGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:1:1,0:12,20:0.0303:2,0:20:0:33:0:0.39394:0:50:2:0.0313:0:8 0/1:94:6:6,0:35,53:0.0638:2,0:22:0:32.3:1:0.00552:0:38.5:12:0.0652:0:7.3 -2 92305704 . A G 75 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03129;SOR=0.24758;LSEQ=TGAAACACTCTTTTTGTGGA;RSEQ=TCTGCAAGTGGATACTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:3,3:7,17:0.2:2,2:19.2:1:29.3:1:0.37171:2.35:35.5:12:0.2:0:6.2 0/1:87:5:2,3:35,46:0.0575:2,2:23:1:32:1:1:1.13955:35.6:10:0.0575:0:4.6 -2 92305705 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10573;SOR=0.21526;LSEQ=GAAACACTCTTTTTGTGGAA;RSEQ=CTGCAAGTGGATACTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:2,1:8,19:0.1:2,2:18.7:1:31.3:1:0.25123:4.48:40:6:0.1:0:7 0/1:87:2:1,1:36,48:0.023:2,2:15.5:1:30:1:1:1.33:41.5:4:0.0235:0:6 -2 92305707 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACACTCTTTTTGTGGAATC;RSEQ=GCAAGTGGATACTTTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:10,19:0:2,0:18.4:1:30.6:1:1:0:43.1:58:1:0:5.3 0/1:84:2:1,1:35,47:0.0238:2,2:9:0:32:0:1:1.34:55:4:0.0244:0:3.5 -2 92305716 . A C 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36084;SOR=0.5749;LSEQ=TTTGTGGAATCTGCAAGTGG;RSEQ=TACTTTGCTGGCTTTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:5,6:0.3529:2,0:30.2:1:33.7:1:0.10229:0:43:12:0.3529:0:6.7 0/1:59:14:4,10:20,22:0.2373:2,2:25.9:1:31.1:1:0.35004:2.24055:46.8:13:0.2321:0:6.5 -2 92305719 . C T 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTGGAATCTGCAAGTGGATA;RSEQ=TTTGCTGGCTTTGAGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:2,9:0,0:0.9167:0,2:32.5:1:31.2:1:1:0:39.3:22:0.9167:0:7.1 1/1:48:44:18,26:2,1:0.9167:2,2:23.4:1:30.1:1:0.56707:2.82401:42.8:88:0.9167:0:6.8 -2 92305722 . T G 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTGCAAGTGGATACTT;RSEQ=GCTGGCTTTGAGGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:2,8:0,0:1:0,2:34.5:1:32.3:1:1:0:39.7:20:1:0:7.2 1/1:39:39:17,22:0,0:1:0,2:24.6:1:30.6:1:1:0:41.7:38:1:0:6.8 -2 92305726 . G A 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70123;SOR=1.32565;LSEQ=CTGCAAGTGGATACTTTGCT;RSEQ=GCTTTGAGGATTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:2,7:1,2:0.75:2,2:24:1:31.3:1:1:1.66417:43.2:18:0.75:0:7.3 1/1:40:32:14,18:3,5:0.8:2,2:23.7:1:29.7:1:1:1.29:42.2:31:0.7949:0:7.1 -2 92305728 . C A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.92427;LSEQ=GCAAGTGGATACTTTGCTGG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:5,3:0.4667:2,0:28.4:1:32.1:1:0.02564:0:38.1:14:0.5:0:7.1 0/1:47:21:5,16:13,13:0.4468:2,2:21.1:1:30.5:1:0.07964:3.12003:43.6:42:0.4468:0:7 -2 92305733 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58643;SOR=1.42142;LSEQ=TGGATACTTTGCTGGCTTTG;RSEQ=GGATTTCGTTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:5,2:2,8:0.4118:2,2:12.7:1:31:1:0.05841:8.43:47.4:14:0.4118:0:7.4 1/0:54:27:16,11:7,20:0.5:2,2:13.6:1:29.7:1:0.0267:4.04:47.3:54:0.5:0:7.1 -2 92305734 . G C 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.04024;LSEQ=GGATACTTTGCTGGCTTTGA;RSEQ=GATTTCGTTGGAAACGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:36.5:1:30.5:1:1:1.12:40:4:0.1053:0:7 0/1:55:6:2,4:22,27:0.1091:2,2:19.3:1:28.8:1:0.68617:1.61569:50.5:12:0.1111:0:6.2 -2 92305742 . T C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45873;SOR=1.47082;LSEQ=TGCTGGCTTTGAGGATTTCG;RSEQ=TGGAAACGGGAATACATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:9,2:2,9:0.5:2,2:14.4:1:32.4:1:0.00892:16.65:40.4:22:0.5:0:7 1/0:57:34:18,16:5,18:0.5965:2,2:15.2:1:30.9:1:0.0276:3.95:48.8:33:0.6:0:6.9 -2 92305748 . A G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59009;SOR=1.49857;LSEQ=CTTTGAGGATTTCGTTGGAA;RSEQ=CGGGAATACATATAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:9,2:2,7:0.55:2,2:19.3:1:29.5:1:0.02155:13.05:40.4:4.5:0.5:0:7 1/0:54:35:18,17:4,14:0.6481:2,2:18.6:1:31:1:0.0759:3.62:49.1:34:0.6667:0:6.9 -2 92305754 . A T 47 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71947;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TACATATAAAAAGCAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:0,2:13,7:0.087:2,0:6.5:1:30.5:1:0.15584:0:30.5:4:0.0909:0:8 0/1:47:3:0,3:21,23:0.0638:2,0:4:1:29.7:1:0.24237:0:38.7:6:0.0638:0:6.7 -2 92305765 . AA T 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54536;SOR=Inf;LSEQ=GAAACGGGAATACATATAAA;RSEQ=GCAGACAGCAGCGTTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:23.9:1:28.6:1:1:0:42.9:21:1:0:6.4 0/1:42:3:1,2:17,22:0.0714:2,2:39:1:31.5:1:1:1.5301:58.3:6:0.0732:0:5 -2 92305770 . G C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.7846;SOR=1.26482;LSEQ=GGGAATACATATAAAAAGCA;RSEQ=ACAGCAGCGTTGTGAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:13:9,4:3,4:0.619:2,2:33.3:1:31:1:0.35635:2.83:44.6:12:0.6316:0:6.5 1/0:49:33:13,20:7,9:0.6735:2,2:31.1:1:30.8:1:1:1.19217:49.7:32:0.6667:0:6.5 -2 92305773 . A T 94 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09451;SOR=Inf;LSEQ=AATACATATAAAAAGCAGAC;RSEQ=GCAGCGTTGTGAGAAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:32:1:30.7:1:1:0:44:19:1:0:6.2 0/1:50:8:4,4:16,26:0.16:2,2:7:0:31.4:1:0.6974:1.61:35.9:16:0.1667:0:8 -2 92305782 . G C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAGCAGACAGCAGCGTT;RSEQ=TGAGAAACTTCTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:11,7:0,0:1:0,2:34.5:1:32.2:1:1:0:45:36:1:0:6.1 1/1:47:47:17,30:0,0:1:0,2:27.4:1:31.2:1:1:0:48.8:22.5:1:0:6.6 -2 92305789 . A G 34 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07589;SOR=0;LSEQ=AGACAGCAGCGTTGTGAGAA;RSEQ=CTTCTTTGTGATGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:0.1111:2,2:24:0:34:0:1:1.61828:60:4:0.1111:0:5.5 0/0:46:0:0,0:17,29:0:2,0:25.2:1:30.1:1:1:0:48.6:92:1:0:6.6 -2 92305791 . T A 98 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0274;SOR=Inf;LSEQ=ACAGCAGCGTTGTGAGAAAC;RSEQ=TCTTTGTGATGTTTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:27.6:1:31.1:1:1:0:45:36:1:0:6.1 0/1:44:10:4,6:12,22:0.2273:2,2:23.9:1:29.7:1:1:1.22:35.6:20:0.2326:0:7.9 -2 92305792 . T G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88562;LSEQ=CAGCAGCGTTGTGAGAAACT;RSEQ=CTTTGTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:8,3:2,1:0.6111:2,2:24.9:1:32.6:1:1:1.31:40.1:22:0.6111:0:6.5 1/0:43:25:9,16:4,7:0.5814:2,2:26:1:32.4:1:1:1.01543:50.4:50:0.5814:0:6.4 -2 92305796 . T G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31275;SOR=0.51173;LSEQ=AGCGTTGTGAGAAACTTCTT;RSEQ=GTGATGTTTGCATTCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:9,4:0.2778:2,2:28.4:1:31.8:1:0.32598:3.13525:49.8:10:0.2941:0:5.4 0/1:43:7:2,5:13,23:0.1628:2,2:20.9:1:32.3:1:1:1.40215:54.4:14:0.1628:0:5.7 -2 92305797 . G C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55981;SOR=0.59324;LSEQ=GCGTTGTGAGAAACTTCTTT;RSEQ=TGATGTTTGCATTCAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:9,4:2,3:0.7222:2,2:19.3:1:30.8:1:0.32598:3.14:43.2:12:0.7059:0:6.4 1/0:43:26:9,17:6,11:0.6047:2,2:21:1:31.6:1:1:1.0296:50.8:25:0.5952:0:6.4 -2 92305805 . T C 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19662;SOR=0.18927;LSEQ=AGAAACTTCTTTGTGATGTT;RSEQ=GCATTCAAGTCACAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:10,5:0.1176:2,2:8:0:32:1:1:1.91491:60:4:0.125:0:5.5 0/1:42:1:0,1:15,26:0.0238:2,0:13:0:32:0:1:0:60:2:0.0238:0:7 -2 92305807 . C T 94 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04937;SOR=Inf;LSEQ=AAACTTCTTTGTGATGTTTG;RSEQ=ATTCAAGTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:12.7:1:32.5:1:1:0:45.3:34:1:0:6.1 0/1:42:10:4,6:11,21:0.2381:2,2:39:1:28.5:1:1:1.27:35.6:20:0.2381:0:7.9 -2 92305813 . A G 101 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04812;SOR=Inf;LSEQ=CTTTGTGATGTTTGCATTCA;RSEQ=GTCACAGAGTTGAACGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:0:2,0:8.8:1:30.2:1:1:0:40.8:26:1:0:6 0/1:38:10:4,6:9,19:0.2632:2,2:39.3:1:30.6:1:0.70918:1.39:35.6:20:0.2778:0:7.9 -2 92305815 . T A 97 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04812;SOR=Inf;LSEQ=TTGTGATGTTTGCATTCAAG;RSEQ=CACAGAGTTGAACGTTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:0:2,0:6.8:1:29.4:1:1:0:40.8:26:1:0:6 0/1:38:10:4,6:9,19:0.2632:2,2:37.5:1:29.4:1:0.70918:1.39:35.6:20:0.2703:0:7.9 -2 92305818 . CAG AA 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATGTTTGCATTCAAGTCA;RSEQ=AGTTGAACGTTCCGTATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:12.8:1:32:1:1:0:52.3:8:1:0:5 0/1:16:2:1,1:5,9:0.125:2,2:6:1:29.5:1:1:1.73:60:4:0.125:0.0625:7 -2 92305822 . G A 60 d7;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00275;SOR=0;LSEQ=GTTTGCATTCAAGTCACAGA;RSEQ=TTGAACGTTCCGTATCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:8.8:1:30.3:1:1:0:52.3:8:1:0:5 0/1:12:1:0,1:4,7:0.0833:2,0:7:0:31:0:1:0:60:2:0.0833:0:5 -2 92305824 . T G 52 d7;v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02692;SOR=0.04568;LSEQ=TTGCATTCAAGTCACAGAGT;RSEQ=GAACGTTCCGTATCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:6.7:1:33:1:1:0:60:6:0.75:0:5.3 0/1:12:1:0,1:4,7:0.0833:2,0:5:0:31:0:1:0:60:2:0.0833:0:5 -2 92305829 . G A 84 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=3.4638;LSEQ=TTCAAGTCACAGAGTTGAAC;RSEQ=TTCCGTATCATAGAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:2:0:28:0:1:0:29:2:0.5:0:4 1/1:10:8:3,5:0,0:0.8:0,2:24.6:1:28.3:1:1:0:34.1:7:0.7778:0:8 -2 92305834 . G C 104 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACAGAGTTGAACGTTCC;RSEQ=TATCATAGAGCAGGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:10:10:4,6:0,0:1:0,2:18.5:1:31.6:1:1:0:35.6:20:1:0:7.9 -2 92306081 . T G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=GCTAGATTTGACGATTTCGT;RSEQ=GGAAACGGGATTACATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:5.8:1:29:1:1:0:31.2:10:1:0:6.6 0/1:8:2:1,1:4,2:0.25:2,2:5:0:32:0:1:1.8258:47:4:0.25:0:3 -2 92306095 . C A 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12281;SOR=0;LSEQ=TTTCGTTGGAAACGGGATTA;RSEQ=ATATAAAAAGCAGACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:20:1:31:1:1:1.41418:25:4:0.2857:0:7.5 0/0:12:0:0,0:7,5:0:2,0:15.9:1:32.5:1:1:0:40.8:24:1:0:4.3 -2 92306097 . T A 87 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01282;SOR=0;LSEQ=TCGTTGGAAACGGGATTACA;RSEQ=ATAAAAAGCAGACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:18.3:1:31.3:1:1:0:28.9:14:1:0:6.4 0/1:12:4:3,1:4,4:0.3333:2,2:14.8:1:30.8:1:0.57576:2.74:30.5:8:0.3636:0:5.5 -2 92306098 . A G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26316;SOR=Inf;LSEQ=CGTTGGAAACGGGATTACAT;RSEQ=TAAAAAGCAGACAGCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:19.3:1:31.4:1:1:0:28.9:14:1:0:6.4 0/1:12:3:2,1:5,4:0.25:2,2:22.7:1:30.7:1:1:1.54:60:6:0.25:0:4.3 -2 92306099 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=GTTGGAAACGGGATTACATA;RSEQ=AAAAAGCAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:20.3:1:30.6:1:1:0:28.9:14:1:0:6.4 0/1:12:2:1,1:6,4:0.1667:2,2:23:0:33.5:1:1:1.4491:47:4:0.1667:0:3 -2 92306101 . A G 92 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00472;SOR=0;LSEQ=TGGAAACGGGATTACATATA;RSEQ=AAAGCAGACAGCAGCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:22.3:1:33:1:1:0:28.9:14:1:0:6.4 0/1:13:4:3,1:2,3:0.3077:2,2:18.8:1:33.8:1:0.52381:3.76:30.5:8:0.3333:0:5.5 -2 92306106 . C T 85 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00458;SOR=0;LSEQ=ACGGGATTACATATAAAAAG;RSEQ=AGACAGCAGCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:27.3:1:30.3:1:1:0:28.9:14:1:0:6.4 0/1:16:5:3,2:6,5:0.3125:2,2:20:1:31.2:1:1:1.23:32.6:10:0.3125:0:5.2 -2 92306122 . C G 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18803;SOR=0.17121;LSEQ=AAAGCAGACAGCAGCATTCT;RSEQ=AGAAACTCCTTTGTGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:38:1:31:1:1:1:25:4:0.25:0:7.5 0/1:20:1:0,1:10,9:0.05:2,0:36:0:31:0:1:0:22:2:0.05:0:8 -2 92306127 . A G 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27679;SOR=Inf;LSEQ=AGACAGCAGCATTCTCAGAA;RSEQ=CTCCTTTGTGATGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:40.1:1:29.9:1:1:0:27.8:16:1:0:6.1 0/1:18:4:2,2:6,7:0.2222:2,2:29:1:32.5:1:1:1.16:48:8:0.2222:0:5.8 -2 92306130 . C G 100 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02612;SOR=0;LSEQ=CAGCAGCATTCTCAGAAACT;RSEQ=CTTTGTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:40:1:32:1:1:0:27.8:16:1:0:6.1 1/0:17:9:4,5:0,0:0.5294:0,2:37:1:31.7:1:1:0:29.7:18:0.5294:0:4.8 -2 92306135 . G A 68 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13043;SOR=Inf;LSEQ=GCATTCTCAGAAACTCCTTT;RSEQ=TGATGTTTGCATTCAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:38.8:1:31.6:1:1:0:27.8:16:1:0:6.1 0/1:16:5:3,2:5,5:0.3125:2,2:32.6:1:29.4:1:1:1.46:48.8:10:0.3125:0:5.8 -2 92306140 . G A 28 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10145;SOR=0;LSEQ=CTCAGAAACTCCTTTGTGAT;RSEQ=TTTGCATTCAAGTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:26.5:1:28:1:1:1:25:4:0.25:0:7.5 0/0:16:0:0,0:8,8:0:2,0:34.1:1:31.6:1:1:0:37.8:32:1:0:4.9 -2 92306146 . A G 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13043;SOR=Inf;LSEQ=AACTCCTTTGTGATGTTTGC;RSEQ=TTCAAGTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:31.5:1:29.6:1:1:0:27.8:16:1:0:6.1 0/1:16:5:3,2:5,6:0.3125:2,2:31.2:1:30.8:1:1:1.73:48.8:10:0.3125:0:5.8 -2 92306157 . AG CT 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.05728;SOR=0.08594;LSEQ=GATGTTTGCATTCAAGTCAC;RSEQ=AGTTGAACATTCCCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:0,1:0.8571:0,2:24.3:1:30:1:1:0:28.7:12:0.8571:0:4.7 0/1:13:4:2,2:5,4:0.3077:2,2:24:1:29.5:1:1:1.22862:41.3:8:0.3077:0:3.8 -2 92306158 . G T 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61262;SOR=2.54896;LSEQ=ATGTTTGCATTCAAGTCACA;RSEQ=AGTTGAACATTCCCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:0,0:0.1429:0,0:21:0:30:0:1:0:25:2:1:0:8 0/1:13:4:2,2:3,2:0.3077:2,2:31.3:1:29.3:1:1:1.43328:20:8:0.4444:0:4 -2 92306167 . A G 69 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1235;SOR=Inf;LSEQ=TTCAAGTCACAGAGTTGAAC;RSEQ=TTCCCTTTCATAGAGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:14.9:1:30.1:1:1:0:28.1:14:1:0:5.1 0/1:14:5:3,2:4,5:0.3571:2,2:10.8:1:29.8:1:1:1.79:48.8:10:0.3571:0:5.8 -2 92306187 . A T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCCTTTCATAGAGCAGG;RSEQ=TTGAAAAACTCTTTTTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:6:0:31:0:1:0:20:2:1:0:3 1/1:2:2:0,2:0,0:1:0,0:6:0:32:0:1:0:20:4:1:0:3 -2 92306698 . C T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCTTTTGAGAGAGCAG;RSEQ=TTTGAAACACTCTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:15:0:31:0:1:0:22:2:1:0:8 1/1:2:2:2,0:0,0:1:0,0:16:0:32:0:1:0:22.5:4:1:0:8 -2 92306738 . T A 24 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=GGAATATGCAAGTGGATATT;RSEQ=GTCTAGCTTTGAGGATTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:46:0:27:0:1:0:22:2:0.3333:0:8 0/1:5:2:2,0:3,0:0.4:0,0:45:0:24.5:1:1:0:22.5:4:0.4:0:8 -2 92306740 . T G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:28.3:1:31.3:1:1:0:21:6:1:0:7.7 1/1:5:4:4,0:0,0:0.8:0,0:18.8:1:31.3:1:1:0:22.5:8:0.8:0:6.3 -2 92306743 . A G 34 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=ATGCAAGTGGATATTTGTCT;RSEQ=GCTTTGAGGATTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:20.5:1:34:0:1:0:20.5:4:0.6667:0:7.5 0/0:7:0:0,0:7,0:0:0,0:18:1:25.1:1:1:0:22.4:6:1:0:6.1 -2 92306745 . C A 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.22183;LSEQ=GCAAGTGGATATTTGTCTAG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:20.5:1:31:0:1:0:20.5:4:0.6667:0:7.5 1/0:7:5:5,0:2,0:0.7143:0,0:11.2:1:29:1:1:0:22.4:10:0.7143:0:5.8 -2 92306771 . T A 55 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10702;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TACATATAAAAAGCAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:5,0:0.1667:0,0:13:0:25:0:1:0:22:2:0.1667:0:8 0/1:22:4:2,2:14,4:0.1818:2,2:13:1:27.5:1:0.29187:3.2706:22.5:8:0.1818:0:6.3 -2 92306774 . CA GG 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07563;SOR=0;LSEQ=TTTCGTTGGAAACGGGATTA;RSEQ=TATAAAAAGCAGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:7,1:0.2:2,2:29:1:30.2:1:0.37778:5.29155:26.5:4:0.2:0.1:7.5 0/0:25:0:0,0:18,7:0:2,0:16.1:1:31:1:1:0:30.2:50:1:0:5 -2 92306775 . A G 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58748;SOR=0.47206;LSEQ=TTCGTTGGAAACGGGATTAC;RSEQ=TATAAAAAGCAGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,1:0.2:2,2:5:1:27.5:1:0.41667:4.58262:21.5:4:0.2222:0:7 0/1:29:3:2,1:18,8:0.1034:2,2:6.7:1:29.3:1:1:1.12035:28.7:6:0.1034:0:7 -2 92306777 . A G 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58548;SOR=0.45372;LSEQ=CGTTGGAAACGGGATTACAT;RSEQ=TAAAAAGCAGACAGCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:9,3:0.1429:2,2:5.5:1:30.5:1:0.50549:2.73861:43:4:0.1429:0:5 0/1:29:2:1,1:19,8:0.069:2,2:16.5:1:29:1:0.53202:2.29737:23:4:0.069:0:5 -2 92306788 . A T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7992;SOR=1.30185;LSEQ=GGATTACATATAAAAAGCAG;RSEQ=CAGCAGCATTCCCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:6,2:8,10:0.3077:2,2:13.4:1:31.3:1:0.21638:3.56:37.6:16:0.3077:0:5.1 0/1:49:18:12,6:17,14:0.3673:2,2:18.9:1:28.9:1:0.5495:1.63:36.8:36:0.3673:0:5.7 -2 92306799 . CC GT 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59356;SOR=0.4699;LSEQ=AAAAAGCAGACAGCAGCATT;RSEQ=CAGAAACTTCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:0,2:15,12:0.069:2,0:22:1:30.3:1:0.22414:0:21.5:4:0.0714:0:4.5 0/1:60:2:0,2:33,25:0.0333:2,0:29.5:1:28.5:1:0.19831:0:22.5:4:0.0333:0:5 -2 92306800 . C T 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.59356;SOR=2.12812;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTTCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:27:15,12:0,0:0.931:0,2:22.4:1:31:1:1:0:37:54:1:0:4.7 1/1:60:58:33,25:0,0:0.9667:0,2:23.4:1:30.1:1:1:0:37.9:116:1:0:5 -2 92306804 . A C 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13123;SOR=0.32449;LSEQ=GCAGACAGCAGCATTCCCAG;RSEQ=AACTTCTTTGTGATGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:1,4:14,10:0.1724:2,2:24.8:1:30:1:0.16858:5.28917:22.8:10:0.1724:0:4.8 0/1:64:4:2,2:32,28:0.0625:2,2:17.3:1:32:1:1:1.14047:44:8:0.0635:0:5 -2 92306805 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGACAGCAGCATTCCCAGA;RSEQ=ACTTCTTTGTGATGTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:25.2:1:30.5:1:1:0:35.3:62:1:0:4.5 0/1:64:2:1,1:33,29:0.0313:2,2:22.5:1:28:1:1:1.13563:25:4:0.0313:0:7 -2 92306807 . C G 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34733;SOR=1.64028;LSEQ=GACAGCAGCATTCCCAGAAA;RSEQ=TTCTTTGTGATGTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:19:12,7:4,8:0.6129:2,2:29.2:1:33.4:1:0.14888:3.29:39.9:38:0.6129:0:4.9 1/0:65:47:26,21:7,9:0.7231:2,2:27.4:1:31.6:1:0.56392:1.58:36.3:94:0.7231:0:5 -2 92306809 . T A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59239;SOR=0.46441;LSEQ=CAGCAGCATTCCCAGAAACT;RSEQ=CTTTGTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:0,2:16,12:0.0645:2,0:31:1:30:1:0.2092:0:21.5:4:0.0667:0:4.5 0/1:65:2:0,2:34,29:0.0308:2,0:38.5:1:28.5:1:0.22356:0:22.5:4:0.0308:0:5 -2 92306811 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAGCATTCCCAGAAACTTC;RSEQ=TTGTGATGTTTGCATTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,15:0:2,0:29.9:1:31:1:1:0:35.8:60:0.9677:0:4.4 0/1:65:2:1,1:33,30:0.0308:2,2:17:0:32.5:1:1:1.09839:37:4:0.0308:0:8 -2 92306814 . G T 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54856;SOR=Inf;LSEQ=GCATTCCCAGAAACTTCTTT;RSEQ=TGATGTTTGCATTCAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:16,16:0:2,0:32:1:32.6:1:1:0:34.8:64:1:0:4.6 0/1:65:3:2,1:32,30:0.0462:2,2:31.7:1:31.3:1:1:1.86:48.7:6:0.0462:0:6.3 -2 92306815 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CATTCCCAGAAACTTCTTTG;RSEQ=GATGTTTGCATTCAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:16,16:0:2,0:32.9:1:30.3:1:1:0:34.8:64:1:0:4.6 0/1:65:2:1,1:33,30:0.0308:2,2:21:0:32.5:1:1:1.09839:37:4:0.0308:0:8 -2 92306820 . T A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00957;SOR=3.74078;LSEQ=CCAGAAACTTCTTTGTGATG;RSEQ=TTGCATTCAAGTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:20:12,8:3,7:0.625:2,2:39.2:1:31.1:1:0.24508:3.35:39.5:40:0.625:0:4.9 1/1:66:57:31,26:3,6:0.8636:2,2:34.9:1:29.3:1:0.29714:2.35:37.4:114:0.8636:0:4.9 -2 92306823 . GC CG 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACTTCTTTGTGATGTTT;RSEQ=ATTCAAGTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:16,16:0:2,0:38.3:1:32.7:1:1:0:34.8:64:1:0:4.5 0/1:68:2:1,1:33,33:0.0294:2,2:30:0:32.5:0:1:1:37:4:0.0294:0:7 -2 92306824 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACTTCTTTGTGATGTTTG;RSEQ=ATTCAAGTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:16,16:0:2,0:38.6:1:32.6:1:1:0:34.8:64:1:0:4.5 0/1:69:2:1,1:32,33:0.029:2,2:28.5:1:28.5:1:1:1.03:23:4:0.0299:0:7 -2 92306828 . C G 50 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.38037;LSEQ=TTCTTTGTGATGTTTGCATT;RSEQ=AAGTCACAGAGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:15,15:0.0323:2,0:38:0:32:0:1:0:32:2:0.0323:0:8 0/1:68:3:1,2:32,33:0.0441:2,2:30.3:1:31.7:1:1:1.92126:32.3:6:0.0441:0:6 -2 92306833 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTGATGTTTGCATTCAAGT;RSEQ=ACAGAGTTGAACATTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:38.6:1:32.2:1:1:0:35.2:62:1:0:4.4 0/1:67:2:1,1:31,34:0.0299:2,2:37:1:30:0:1:1.10:42.5:4:0.0299:0:5 -2 92306838 . AG TA 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTTTGCATTCAAGTCACAG;RSEQ=TTGAACATTCCCTTTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:35.6:1:30.5:1:1:0:35.2:62:1:0:4.4 0/1:66:2:1,1:30,34:0.0303:2,2:46.5:1:29.3:1:1:1.13:54:4:0.0308:0:4.5 -2 92306839 . G A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.70241;LSEQ=GTTTGCATTCAAGTCACAGA;RSEQ=TTGAACATTCCCTTTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:30:14,16:1,0:0.9677:0,2:35.6:1:31:1:0.48387:0:35.7:60:1:0:4.5 1/1:66:63:30,33:0,1:0.9545:0,2:34.6:1:29.6:1:1:0:37:126:0.9844:0:4.9 -2 92306841 . T G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGCATTCAAGTCACAGAGT;RSEQ=GAACATTCCCTTTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:33.4:1:30.6:1:1:0:35.2:62:1:0:4.4 0/1:66:2:1,1:29,35:0.0303:2,2:40.5:1:29.5:1:1:1.20:41:4:0.0303:0:6.5 -2 92306847 . T C 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67915;SOR=0.62552;LSEQ=TCAAGTCACAGAGTTGAACA;RSEQ=TCCCTTTCACAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:1,2:14,14:0.0968:2,2:23:1:26.7:1:1:1.9571:21.3:2:0.0667:0:4 0/1:64:4:1,3:27,33:0.0625:2,2:24:1:32.5:1:0.6252:2.42328:29.8:8:0.0625:0:6 -2 92306849 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGTCACAGAGTTGAACATT;RSEQ=CCTTTCACAGAGCAGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:26.5:1:31.2:1:1:0:35.2:62:1:0:4.4 0/1:64:2:1,1:26,34:0.0313:2,2:37:0:33:1:1:1.30:31:4:0.0317:0:5.5 -2 92306879 . T A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCAGGTTTGAAACACTCT;RSEQ=TTTGTAATATCTGGATGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:0:2,0:7.1:1:29.8:1:1:0:33.3:24:1:0:3.7 0/1:33:2:1,1:11,20:0.0606:2,2:6.5:1:26.5:1:1:1.78:54:4:0.0606:0:4.5 -2 92306886 . A G 94 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=TATCTGGATGTGGACATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:32.5:1:1:0:38.5:4:1:0:6.5 1/1:8:8:0,8:0,0:1:0,0:15.3:1:31.4:1:1:0:41.1:16:1:0:6.6 -2 92306888 . A G 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAAACACTCTTTTTGTAAT;RSEQ=TCTGGATGTGGACATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:25:0:34:0:1:0:20:2:1:0:8 1/1:5:4:0,4:0,1:0.8:0,0:26.8:1:33:0:1:0:35.3:8:0.8:0:7 -2 92306890 . C G 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACTCTTTTTGTAATAT;RSEQ=TGGATGTGGACATTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:23:0:34:0:1:0:20:2:1:0:8 1/1:4:4:0,4:0,0:1:0,0:24.8:1:33:0:1:0:35.3:8:1:0:7 -2 92306893 . G T 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCTTTTTGTAATATCTG;RSEQ=ATGTGGACATTTGGAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:20:0:30:0:1:0:20:2:1:0:8 1/1:4:4:0,4:0,0:1:0,0:21.8:1:30:0:1:0:35.3:8:1:0:7 -2 92306895 . T A 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTTTTTGTAATATCTGGA;RSEQ=GTGGACATTTGGAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:18:0:33:0:1:0:20:2:1:0:8 1/1:4:4:0,4:0,0:1:0,0:19.8:1:33:0:1:0:35.3:8:1:0:7 -2 92307078 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCTGCAAGAGGATATTTG;RSEQ=ATAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:40:0:32:0:1:0:39:2:1:0:4 1/0:3:2:1,1:1,0:0.6667:0,2:17.5:1:30.5:1:1:0:21:4:0.6667:0:5 -2 92307180 . T A 63 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGTTTCAATTGAAGTCACAG;RSEQ=GTTGAACATTCCCTGTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:32:0:1:0:39:2:1:0:5 1/1:5:4:2,2:0,1:0.8:0,2:6:0:31.8:1:1:0:33:8:0.8:0:4.5 -2 92307195 . G A 60 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACAGTGTTGAACATTCCCT;RSEQ=TCATAGAGCAGGTTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:0,1:0.8:0,2:21:0:30.3:1:1:0:33:8:0.8:0:4.5 -2 92307214 . A T 59 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22797;SOR=Inf;LSEQ=TGTCATAGAGCAGGTTTGAA;RSEQ=CACTCTTTTTGTAGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:3:1:29.3:1:1:0:26.5:8:1:0:4 0/1:9:4:2,2:3,2:0.4444:2,2:38.8:1:29.5:1:1:1.43328:33:8:0.4444:0:4.5 -2 92307220 . T C 61 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.4965;SOR=Inf;LSEQ=AGAGCAGGTTTGAAACACTC;RSEQ=TTTTGTAGTATCTGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:9.7:1:26.7:1:1:0:22.3:2:1:0:3.7 0/1:10:4:2,2:4,2:0.4:2,2:36:1:30.8:1:1:1.86195:33:8:0.4:0:4.5 -2 92307256 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.57471;LSEQ=AAGTGGACATTTGGAGCGCT;RSEQ=TCAGGACTACAGTGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,1:0.2857:2,0:34:1:32.5:1:1:0:20:4:0.3333:0:6 0/1:11:2:1,1:7,1:0.1818:2,2:12:1:31.5:1:0.37778:5.29155:22.5:4:0.1818:0:6 -2 92307261 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=GACATTTGGAGCGCTCTCAG;RSEQ=ACTACAGTGAAAAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:29:1:28.9:1:1:0:22.7:6:1:0:3.3 0/1:11:2:1,1:6,2:0.1818:2,2:21.5:1:28:1:1:2.64575:43:4:0.1818:0:3.5 -2 92307265 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=TTTGGAGCGCTCTCAGGACT;RSEQ=CAGTGAAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:30.3:1:25.6:1:1:0:22.7:6:1:0:3.3 0/1:10:2:2,0:6,2:0.2:2,0:41:1:32:1:1:0:37:4:0.2:0:1 -2 92307267 . A G 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.684;LSEQ=TGGAGCGCTCTCAGGACTAC;RSEQ=GTGAAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,1:0.5:2,0:42.3:1:30.3:1:1:0:21.3:6:0.5:0:4.3 0/1:10:4:4,0:4,2:0.4:2,0:40.3:1:30.5:1:0.46667:0:21.3:8:0.4:0:3.5 -2 92307272 . A T 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.35749;SOR=0.32196;LSEQ=CGCTCTCAGGACTACAGTGA;RSEQ=AAAGGAAATATCTTCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:3,1:7,1:0.3333:2,2:18.3:1:29.5:1:1:2.16028:22.5:8:0.3333:0:1 0/1:15:2:2,0:10,3:0.1333:2,0:22.5:1:28:0:1:0:22:4:0.1333:0:2.5 -2 92307279 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.29082;LSEQ=AGGACTACAGTGAAAAAGGA;RSEQ=ATATCTTCCAATAAAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:11,2:0.0714:2,0:35:0:34:0:1:0:20:2:0.0714:0:6 0/1:22:2:1,1:17,3:0.0909:2,2:24:1:32.5:1:0.33766:5.04987:20:4:0.0909:0:6 -2 92307280 . A G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.32357;LSEQ=GGACTACAGTGAAAAAGGAA;RSEQ=TATCTTCCAATAAAAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:11,3:0.0667:2,0:11:0:33:0:1:0:20:2:0.0667:0:1 0/1:23:2:1,1:16,4:0.087:2,2:25.5:1:31:1:0.41126:3.6879:20:4:0.087:0:2 -2 92307291 . T G 34 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.84584;LSEQ=AAAAAGGAAATATCTTCCAA;RSEQ=AAAAGCTAGATAGAAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:13,3:0.1111:2,2:23:1:30.5:1:0.40523:3.89444:20:4:0.1111:0:6 0/1:21:2:2,0:15,4:0.0952:2,0:20.5:1:34:0:1:0:20:4:0.0952:0:7.5 -2 92307296 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95111;LSEQ=GGAAATATCTTCCAATAAAA;RSEQ=CTAGATAGAAGCAATGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:13,4:0.0952:2,2:16:1:28.5:1:0.46784:3.01641:20:4:0.0952:0:5.5 0/1:22:2:1,1:15,3:0.0909:2,2:33.5:1:29:1:0.36842:4.47215:20:4:0.0909:0:6 -2 92307307 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4898;SOR=0;LSEQ=CCAATAAAAGCTAGATAGAA;RSEQ=CAATGTCAGAAACTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,8:0.08:2,2:33.5:1:29.5:1:1:1.82581:22:4:0.08:0:3.5 0/0:25:0:0,0:19,6:0:2,0:25.7:1:31.7:1:1:0:24.8:50:1:0:2.4 -2 92307319 . AC CT 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.0574;LSEQ=AGATAGAAGCAATGTCAGAA;RSEQ=TTTTTCATGATGTATCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:15,8:0.04:2,0:38:0:29:0:0.375:0:20:2:0.04:0:4 0/1:25:2:1,1:17,6:0.08:2,2:33.5:1:29.3:1:0.49:2.69921:20:4:0.08:0:5 -2 92307320 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.48605;LSEQ=GATAGAAGCAATGTCAGAAA;RSEQ=TTTTTCATGATGTATCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,7:0.08:2,2:33.5:1:29:1:1:2.07024:22:4:0.087:0:3.5 0/1:25:1:0,1:17,5:0.04:2,0:39:0:31:0:0.26087:0:43:2:0.0435:0:3 -2 92307323 . T G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.4898;SOR=0;LSEQ=AGAAGCAATGTCAGAAACTT;RSEQ=TTCATGATGTATCTACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,8:0.08:2,2:31:1:30.5:1:1:1.82581:22:4:0.08:0:3.5 0/0:24:0:0,0:17,7:0:2,0:33.8:1:30.5:1:1:0:23.8:48:1:0:2.1 -2 92307325 . TCA ATG 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60984;SOR=0.46685;LSEQ=AAGCAATGTCAGAAACTTTT;RSEQ=TGATGTATCTACTCAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,8:0.08:2,2:26.5:1:28.9:1:1:1.82581:20:4:0.08:0.04:5 0/1:26:1:1,0:16,8:0.0385:2,0:41:0:32:0:1:0:20:2:0.0385:0:5 -2 92307333 . T G 50 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61098;SOR=3.06075;LSEQ=TCAGAAACTTTTTCATGATG;RSEQ=ATCTACTCAGCTAACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:16,10:0.037:2,0:47:0:31:0:0.40741:0:20:2:0.037:0:4 0/1:28:3:2,1:16,9:0.1071:2,2:28:1:31.7:1:1:1.12:20:6:0.1071:0:5 -2 92307334 . A G 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.97579;LSEQ=CAGAAACTTTTTCATGATGT;RSEQ=TCTACTCAGCTAACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:15,11:0.037:2,0:27:0:34:0:1:0:21:2:0.037:0:3 0/1:28:2:2,0:16,10:0.0714:2,0:38.5:1:31:1:0.52381:0:21:4:0.0714:0:2.5 -2 92307348 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49269;SOR=Inf;LSEQ=TGATGTATCTACTCAGCTAA;RSEQ=AGAGTTGAACCTTTCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:0:2,0:30.1:1:31.3:1:1:0:21.3:13:1:0:1.5 0/1:31:2:2,0:18,11:0.0645:2,0:8.5:1:31:1:0.52688:0:23:4:0.0645:0:3 -2 92307358 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49392;SOR=Inf;LSEQ=ACTCAGCTAACAGAGTTGAA;RSEQ=CTTTCTTTTGAGAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:17,12:0:2,0:25.8:1:30.8:1:1:0:21.2:28:1:0:1.6 0/1:33:2:2,0:18,13:0.0606:2,0:29:1:32:0:0.50758:0:27.5:4:0.0606:0:2 -2 92307362 . TCT CC 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.85922;LSEQ=TCAGCTAACAGAGTTGAACC;RSEQ=TTTGAGAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:3,3:11,10:0.2:2,2:27:1:30.8:1:1:1.09612:20.3:12:0.2143:0.0667:0.7 0/1:34:6:4,2:15,11:0.1765:2,2:19.3:1:31.6:1:1:1.45:28:12:0.1818:0.0588:0.3 -2 92307364 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18857;SOR=0;LSEQ=CTAACAGAGTTGAACCTTTC;RSEQ=TTTGAGAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:33.5:1:29.5:1:1:1.21106:30.5:4:0.1:0:2 0/0:28:0:0,0:15,12:0:2,0:23.3:1:29.6:1:1:0:22.2:54:1:0:2 -2 92307365 . T A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09662;SOR=0;LSEQ=TAACAGAGTTGAACCTTTCT;RSEQ=TTGAGAGAGCAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:2,1:14,12:0.1034:2,2:21:1:28:1:1:1.68:20.7:6:0.1111:0:1.7 0/0:33:0:0,0:20,13:0:2,0:23.2:1:29.4:1:1:0:23.2:66:1:0:1.8 -2 92307376 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23529;SOR=0;LSEQ=AACCTTTCTTTTGAGAGAGC;RSEQ=GTTTTGAAACACTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:9,12:0.08:2,2:28.5:1:31:1:1:1.32:31:4:0.08:0:1.5 0/0:26:0:0,0:13,13:0:2,0:28.3:1:30:1:1:0:23.1:52:1:0:1.5 -2 92307383 . A C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4898;SOR=Inf;LSEQ=CTTTTGAGAGAGCAGTTTTG;RSEQ=AACACTCTTTTTGTGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:22.4:1:29.7:1:1:0:21.7:48:1:0:1.2 0/1:25:2:0,2:10,13:0.08:2,0:35:0:31.5:1:0.5:0:20:4:0.08:0:5 -2 92307391 . T G 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.32228;SOR=0.26317;LSEQ=AGAGCAGTTTTGAAACACTC;RSEQ=TTTTGTGGAATCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:7,13:0.1304:2,2:21:1:30.3:1:0.53755:3.50:22:6:0.1304:0:2 0/1:27:1:1,0:9,17:0.037:2,0:38:0:25:0:0.37037:0:21:2:0.037:0:2 -2 92307403 . C A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50435;SOR=Inf;LSEQ=AAACACTCTTTTTGTGGAAT;RSEQ=TGCAAGTGGATATTTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:24.5:1:31.4:1:1:0:22.1:38:1:0:1.4 0/1:27:2:0,2:7,18:0.0741:2,0:30.5:1:31:1:1:0:20:4:0.0741:0:5 -2 92307419 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17436;SOR=0;LSEQ=GAATCTGCAAGTGGATATTT;RSEQ=TCTAGCTTTGAGGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:4,11:0.1176:2,2:20:1:31.5:1:0.51471:2.57:23:4:0.1176:0:2 0/0:23:0:0,0:6,17:0:2,0:25:1:30.4:1:1:0:26.4:46:1:0:1.2 -2 92307438 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48589;SOR=Inf;LSEQ=TGTCTAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGATTACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:3,12:0:2,0:25.1:1:30.9:1:1:0:21.5:30:1:0:1.6 0/1:17:2:1,1:1,14:0.1176:1,2:24.5:1:29:1:0.22794:10.25:22:4:0.125:0:2 -2 92307465 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49275;SOR=Inf;LSEQ=ACGGGATTACATATAAAAAG;RSEQ=AGACAGCAGCATTCCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:0:2,0:26.2:1:31.7:1:1:0:21.4:20:1:0:1.7 0/1:14:2:1,1:0,12:0.1429:0,2:10.5:1:30.5:1:0.14286:0:43.5:4:0.1429:0:4.5 -2 92307472 . C A 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51087;SOR=Inf;LSEQ=TACATATAAAAAGCAGACAG;RSEQ=AGCATTCCCAGAAACTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:0:2,0:25.2:1:31.7:1:1:0:21.1:18:1:0:1.8 0/1:15:2:1,1:1,11:0.1333:2,2:7:0:27.5:1:0.27473:8.12:21:4:0.1333:0:6 -2 92307480 . C T 56 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24871;SOR=Inf;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTTCTTTGTGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:27.6:1:30.9:1:1:0:21:14:1:0:2 0/1:13:4:2,2:0,9:0.3077:0,2:20.3:1:28.3:1:0.07692:0:32.3:8:0.3077:0:5.3 -2 92307487 . C G 31 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2451;SOR=0.20301;LSEQ=GACAGCAGCATTCCCAGAAA;RSEQ=TTCTTTGTGACGTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,4:0.3333:0,2:23:1:31.5:1:0.33333:0:20:4:0.3333:0:3 0/1:12:1:0,1:2,9:0.0833:2,0:50:0:33:0:1:0:24:2:0.0833:0:4 -2 92307495 . T G 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49091;SOR=Inf;LSEQ=CATTCCCAGAAACTTCTTTG;RSEQ=GACGTTTGCATTCAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:28.8:1:31.3:1:1:0:20.8:8:1:0:2.8 0/1:7:2:1,1:1,4:0.2857:2,2:30:0:27.5:1:1:3.16:21:4:0.2857:0:6 -2 92307498 . C A 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=0;LSEQ=TCCCAGAAACTTCTTTGTGA;RSEQ=GTTTGCATTCAAGTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,0:0.5:0,0:27:1:32:0:1:0:21.5:4:0.5:0:2.5 0/0:7:0:0,0:2,2:0:2,0:38:1:25.8:1:1:0:32.3:3:0.5:0:5.3 -2 92307501 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CAGAAACTTCTTTGTGACGT;RSEQ=TGCATTCAAGTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:22.8:1:31.5:1:1:0:20.8:8:1:0:2.5 0/1:7:2:1,1:1,4:0.2857:2,2:43:1:31.5:1:1:3.16:43.5:4:0.2857:0:4.5 -2 92307521 . T A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=TTGCATTCAAGTCACAGAGT;RSEQ=GAACATTCCCTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:11:1:31:0:1:0:20:4:1:0:2.5 1/0:6:3:1,2:1,2:0.5:2,2:31.7:1:30:1:1:1:20.7:6:0.5:0:4.7 -2 92307524 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCAAGTCACAGAGTTGA;RSEQ=CATTCCCTTTCATAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:8:1:31:0:1:0:20:4:1:0:2.5 0/1:6:2:1,1:1,3:0.3333:2,2:31.5:1:31:1:1:2.45:43.5:4:0.3333:0:4.5 -2 92307535 . CA GG 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTTGAACATTCCCTTT;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:16.5:1:30.8:1:1:2.45:21:4:0.3333:0:5 -2 92307713 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAACCTTTCTTTTCATAGAG;RSEQ=AGTTTTTAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:4:0:33:0:1:0:22:2:1:0:6 0/1:8:2:1,1:3,3:0.25:2,2:22.5:1:28.5:1:1:1:29:4:0.25:0:7 -2 92307720 . T G 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTCATAGAGCAGTTTT;RSEQ=AAACACTCTTTTTCTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:11:0:34:0:1:0:22:2:1:0:6 1/1:8:7:3,4:0,0:0.875:0,2:29.7:1:30.3:1:1:0:41.9:14:1:0:6.1 -2 92307725 . A G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCATAGAGCAGTTTTTAAAC;RSEQ=CTCTTTTTCTAAAATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:16:0:32:0:1:0:22:2:1:0:6 0/1:8:2:1,1:3,3:0.25:2,2:34.5:1:30.5:1:1:1:29:4:0.25:0:7 -2 92307734 . C G 100 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AGTTTTTAAACACTCTTTTT;RSEQ=TAAAATCTGCAAGAGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:25:0:33:0:1:0:22:2:1:0:6 1/1:11:10:6,4:0,1:0.9091:0,2:31.8:1:30.2:1:0.45455:0:40.7:20:0.9091:0:6.1 -2 92307737 . A G 103 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTAAACACTCTTTTTCTA;RSEQ=AATCTGCAAGAGGATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:17:10:6,4:4,1:0.5882:2,2:33.3:1:31.2:1:0.6004:2.5065:40.8:20:0.625:0:6.2 -2 92307741 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACACTCTTTTTCTAAAAT;RSEQ=TGCAAGAGGATATTTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:11.7:1:32:1:1:0:23:6:1:0:4.3 0/1:22:2:1,1:11,9:0.0909:2,2:46:1:30:1:1:1.21106:60:4:0.0909:0:7 -2 92307747 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTTTTCTAAAATCTGCAA;RSEQ=AGGATATTTGGATAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:10.2:1:31.2:1:1:0:27.8:12:1:0:5.2 0/1:27:2:1,1:15,10:0.0741:2,2:49:1:29.5:1:1:1.47706:60:4:0.0769:0:7 -2 92307758 . GA CC 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13462;SOR=0.24498;LSEQ=AATCTGCAAGAGGATATTTG;RSEQ=TAGCTTTGAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,0:0.4286:0,2:19.3:1:29.4:1:0.4:0:23:6:0.5:0.1429:5.7 0/1:27:4:1,3:10,4:0.1481:2,2:16.3:1:30.1:1:0.2451:6.606:23:8:0.1481:0:6 -2 92307764 . T C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07916;SOR=0.17219;LSEQ=CAAGAGGATATTTGGATAGC;RSEQ=TTGAGGATTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:3,1:0.4286:2,2:19.7:1:29.3:1:0.48571:4.4496:23:6:0.5:0:5.7 0/1:28:3:1,2:14,11:0.1071:2,2:24:1:29.7:1:0.58333:2.46268:24:6:0.1111:0:6.3 -2 92307766 . T G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGGATATTTGGATAGCTT;RSEQ=GAGGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:22.4:1:29.3:1:1:0:27.4:14:1:0:5.1 0/1:28:2:1,1:14,12:0.0714:2,2:32:1:32.5:1:1:1.16024:28:4:0.0741:0:6 -2 92307776 . G T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGATAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGATTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:29.6:1:27:1:1:0:27.4:6:1:0:5.1 0/1:29:2:1,1:14,13:0.069:2,2:39.5:1:31:0:1:1.07415:27:4:0.069:0:5 -2 92307778 . T G 104 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.56049;LSEQ=GATAGCTTTGAGGATTTCGT;RSEQ=GGAAACGGGATTGTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:33.5:1:32:1:1:1:38:4:0.25:0:5.5 0/1:29:10:4,6:11,8:0.3448:2,2:24.7:1:31.5:1:0.44973:2.01071:41.8:20:0.3448:0:5.8 -2 92307780 . G C 112 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23231;SOR=4.13988;LSEQ=TAGCTTTGAGGATTTCGTTG;RSEQ=AAACGGGATTGTCTTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:3,4:0.125:2,0:40:0:33:0:1:0:20:2:0.1429:0:4 0/1:29:11:7,4:8,10:0.3793:2,2:34.5:1:32.4:1:0.44973:2.13:39.1:22:0.3793:0:4.6 -2 92307788 . AT TA 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGATTTCGTTGGAAACGGG;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:34.8:1:29.8:1:1:0:27.4:16:1:0:5.4 0/1:28:2:1,1:13,13:0.0714:2,2:43.5:1:29:1:1:1:28:4:0.0714:0:5 -2 92307789 . T A 119 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22848;SOR=3.84981;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:2,4:0.25:2,0:49.5:1:30.5:1:0.42857:0:23.5:4:0.25:0:4 1/0:28:16:10,6:3,7:0.5714:2,2:38.8:1:29.8:1:0.22619:3.68:35.5:32:0.6154:0:4.8 -2 92307792 . T G 112 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10937;SOR=6.54088;LSEQ=TTTCGTTGGAAACGGGATTG;RSEQ=CTTCATATAAACTCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:3,5:0.1111:2,0:46:0:31:0:0.44444:0:20:2:0.1111:0:4 0/1:26:12:7,5:7,7:0.4615:2,2:36.8:1:31.3:1:0.71269:1.38:38.9:24:0.4615:0:4.8 -2 92307798 . T G 95 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68547;SOR=0.70914;LSEQ=TGGAAACGGGATTGTCTTCA;RSEQ=ATAAACTCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:2,1:0.375:2,0:35.7:1:31.3:1:0.4:0:24.7:6:0.375:0:6.7 0/1:27:8:3,5:9,8:0.2963:2,2:36.8:1:31.8:1:0.67277:1.82828:25.3:16:0.3077:0:5.5 -2 92307799 . A G 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.60211;SOR=0.53269;LSEQ=GGAAACGGGATTGTCTTCAT;RSEQ=TAAACTCTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,3:0.25:2,2:25:1:29:1:1:2.45:27:4:0.3333:0:4.5 0/1:27:4:2,2:10,11:0.1481:2,2:21.5:1:30.8:1:1:1.10:23.5:8:0.16:0:5 -2 92307801 . A C 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.21082;LSEQ=AAACGGGATTGTCTTCATAT;RSEQ=AACTCTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:3,4:0.125:2,0:44:0:33:0:1:0:22:2:0.1429:0:6 0/1:27:4:1,3:12,11:0.1481:2,2:35.3:1:32.8:1:0.59556:3.1395:23:8:0.1481:0:6 -2 92307804 . C A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09616;SOR=0.23992;LSEQ=CGGGATTGTCTTCATATAAA;RSEQ=TCTAGACAGAAGCATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:1,4:2,2:0.5556:2,2:34.2:1:31.6:1:0.52381:3.38757:30:10:0.5556:0:5.8 0/1:27:6:2,4:11,10:0.2222:2,2:31.2:1:31.8:1:0.64831:2.13731:28.7:12:0.2222:0:5.5 -2 92307813 . G T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTCATATAAACTCTAGACA;RSEQ=AAGCATTCTCAGAAACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,5:0:2,0:25.1:1:31.8:1:1:0:27.1:16:0.8889:0:5.3 0/1:27:2:1,1:12,13:0.0741:2,2:19.5:1:27.5:1:1:1.08:28:4:0.0741:0:5 -2 92307831 . T G 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59084;SOR=0.48906;LSEQ=CAGAAGCATTCTCAGAAACT;RSEQ=CATTGGGATGTTTCAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:25:1:31.5:1:1:2.24:27:4:0.2222:0:4.5 0/1:25:3:1,2:11,11:0.12:2,2:28.7:1:30:1:1:1.94684:22.7:6:0.12:0:5.3 -2 92307833 . A T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40652;SOR=0.45221;LSEQ=GAAGCATTCTCAGAAACTTC;RSEQ=TTGGGATGTTTCAATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:0,0:0.5714:0,2:21.3:1:30.8:1:1:0:25.3:8:0.6667:0:5.5 0/1:19:7:2,5:0,0:0.3684:0,2:15.1:1:29.9:1:1:0:23.9:14:0.3684:0:5.6 -2 92307846 . A G 68 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=4.17095;LSEQ=AAACTTCATTGGGATGTTTC;RSEQ=ATTGAAGTCACAGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,1:0.3333:0,0:44:0:33:0:1:0:20:2:0.5:0:7 1/0:7:5:1,4:0,2:0.7143:0,2:30.6:1:29.6:1:1:0:38.6:10:0.7143:0:6.6 -2 92307856 . A C 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATGTTTCAATTGAAGTC;RSEQ=CAGTGTTGAACAGTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:41:1:24.5:1:1:0:23.5:1:1:0:6 1/1:7:7:1,6:0,0:1:0,2:26:1:31.1:1:1:0:34.3:14:1:0:6.4 -2 92307869 . G T 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGTCACAGTGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28:1:31:1:1:0:23.5:4:1:0:6 1/1:5:5:1,4:0,0:1:0,2:19.2:1:31:1:1:0:32.4:10:1:0:6.6 -2 92307874 . T A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TCACAGTGTTGAACAGTCCC;RSEQ=TTCATAGAGCAGGTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:23:1:31:0:1:0:23.5:4:1:0:6 1/0:4:2:0,2:0,2:0.5:0,0:21.5:1:31.5:1:1:0:23.5:4:0.5:0:6 -2 92307877 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAGTGTTGAACAGTCCCTTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:26:0:29:0:1:0:20:2:0.5:0:7 1/0:4:2:0,2:0,2:0.5:0,0:12.5:1:30:0:1:0:37.5:4:0.5:0:7 -2 92307976 . G A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAATATTCTCCAATAAAA;RSEQ=CTAGATAGAAGCAATGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:5:0:33:0:1:0:20:2:1:0:4 1/0:3:2:2,0:0,0:0.6667:0,0:7:1:30:1:1:0:22.5:4:0.6667:0:4 -2 92307999 . AC CT 110 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8083;LSEQ=AGATAGAAGCAATGTCAGAA;RSEQ=TTTTTCATGATGTATCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:20.7:1:32.7:1:1:0:28:6:0.75:0:2.7 1/0:17:12:9,3:5,0:0.7059:0,2:11.3:1:30.8:1:0.51471:0:38:24:0.7059:0.2941:2.8 -2 92308005 . TCA ATG 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83843;LSEQ=AAGCAATGTCAGAAACTTTT;RSEQ=TGATGTATCTACTCAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:3,1:0.5:2,2:11:1:29.6:1:1:2.60168:34:8:0.5:0.375:3.8 0/1:22:10:9,1:9,3:0.4545:2,2:12.8:1:30.4:1:0.59398:2.86:42.1:20:0.4545:0.2273:3 -2 92308013 . T G 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70027;SOR=1.43879;LSEQ=TCAGAAACTTTTTCATGATG;RSEQ=ATCTACTCAGCTAACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:3,1:0.5:2,2:13.5:1:31:1:1:2.60168:34:8:0.5:0:3.8 1/0:27:16:13,3:8,3:0.5926:2,2:12.5:1:31.6:1:0.66184:1.60:43.7:32:0.5926:0:2.8 -2 92308024 . CT GA 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCATGATGTATCTACTCAG;RSEQ=AACAGAGTTGAACCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:26.4:1:32.4:1:1:0:30.8:20:1:0:3.2 0/1:33:2:1,1:22,9:0.0606:2,2:28.5:1:31.8:1:0.52083:2.37114:46.5:4:0.0606:0:2.5 -2 92308025 . T A 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15781;SOR=0.34259;LSEQ=TCATGATGTATCTACTCAGC;RSEQ=AACAGAGTTGAACCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:2,2:0.6:2,2:28.3:1:31:1:1:1:28.7:12:0.6:0:2.8 0/1:33:11:7,4:15,5:0.3333:2,2:29.8:1:29.8:1:0.68277:1.68366:34.9:22:0.3548:0:3.1 -2 92308039 . C T 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05141;SOR=0;LSEQ=CTCAGCTAACAGAGTTGAAC;RSEQ=TTTCTTTTGAGAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:32:0:30.5:1:1:1:44:4:0.1429:0:5 0/0:46:0:0,0:26,20:0:2,0:26.8:1:30.6:1:1:0:39.2:92:1:0:3.7 -2 92308050 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GAGTTGAACCTTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:26.8:1:31.6:1:1:0:35.9:36:1:0:3.9 0/1:60:2:1,1:29,29:0.0333:2,2:10.5:1:31.5:1:1:1:21:4:0.0333:0:3 -2 92308051 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGTTGAACCTTTCTTTTGAG;RSEQ=GAGCAGTTTTGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:27.3:1:30.3:1:1:0:35.9:36:1:0:3.9 0/1:61:2:1,1:29,29:0.0328:2,2:39.5:1:29.5:1:1:1:42:4:0.0333:0:4.5 -2 92308057 . G C 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04722;SOR=0;LSEQ=ACCTTTCTTTTGAGAGAGCA;RSEQ=TTTTGAAACACTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:36.5:1:31.5:1:1:1:45:4:0.1111:0:2.5 0/0:63:0:0,0:31,32:0:2,0:27.2:1:31.3:1:1:0:39.7:126:1:0:3.6 -2 92308058 . T A 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04722;SOR=0;LSEQ=CCTTTCTTTTGAGAGAGCAG;RSEQ=TTTGAAACACTCTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:31:1:30:1:1:1:43.5:4:0.1111:0:4 0/0:63:0:0,0:31,32:0:2,0:27.4:1:29.2:1:1:0:39.7:126:1:0:3.6 -2 92308063 . A C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.78527;SOR=1.29571;LSEQ=CTTTTGAGAGAGCAGTTTTG;RSEQ=AACACTCTTTTTGTGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:5,5:4,4:0.5556:2,2:27.6:1:32.1:1:1:1:39.5:20:0.5556:0:4 1/0:63:39:19,20:12,12:0.619:2,2:29.4:1:31.8:1:1:1.05174:41.4:78:0.619:0:4.2 -2 92308079 . GA TT 30 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04211;SOR=0;LSEQ=TTTGAAACACTCTTTTTGTG;RSEQ=ATATGCAAGTGGATATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,8:0.125:2,2:18:0:30.8:1:1:1.31:44:4:0.1333:0:4 0/0:60:0:0,0:28,32:0:2,0:25.7:1:30.8:1:1:0:40.6:120:1:0:3.6 -2 92308082 . T C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACACTCTTTTTGTGGAA;RSEQ=ATGCAAGTGGATATTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,9:0:2,0:23.1:1:30:1:1:0:38.8:30:1:0:4 0/1:60:2:1,1:27,31:0.0333:2,2:47:0:32:1:1:1.15:42:4:0.0333:0:6 -2 92308093 . A G 127 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.2901;LSEQ=TTTGTGGAATATGCAAGTGG;RSEQ=TATTTGTCTAGCTTTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:3,5:0.2727:2,0:11.7:1:33.7:1:0.49091:0:29.3:6:0.2727:0:3 0/1:52:17:6,11:15,20:0.3269:2,2:11.9:1:31.3:1:0.765:1.36667:37.9:34:0.3333:0:2.6 -2 92308098 . T A 140 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATATGCAAGTGGATATT;RSEQ=GTCTAGCTTTGAGGATTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:37.5:1:30.8:1:1:0:37.3:12:1:0:6.7 1/1:26:24:5,19:0,2:0.9231:0,2:33.4:1:30.7:1:1:0:39.3:48:0.9231:0:5.8 -2 92308100 . TCT GGC 134 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76665;LSEQ=AATATGCAAGTGGATATTTG;RSEQ=AGCTTTGAGGATTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:0,0:0.8333:0,2:37:1:32.2:1:1:0:40.8:10:0.8333:0:4.8 1/0:24:19:4,15:0,0:0.7917:0,2:31.2:1:31.7:1:1:0:40.3:38:0.7917:0:3.9 -2 92308102 . T C 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TATGCAAGTGGATATTTGTC;RSEQ=AGCTTTGAGGATTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,0:0.1667:0,0:16:0:34:0:1:0:20:2:1:0:6 0/1:24:4:0,4:0,1:0.1667:0,0:31.5:1:32.5:1:1:0:32.3:8:0.8:0:6.3 -2 92308108 . T G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGTGGATATTTGTCTAGCTT;RSEQ=GAGGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:2,3:0.1667:2,0:10:0:32:0:1:0:20:2:0.1667:0:6 0/1:24:4:0,4:4,16:0.1667:2,0:25.5:1:31.3:1:1:0:32.3:8:0.1667:0:6.3 -2 92308131 . T A 109 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TACATATAAAAAGCAGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:10.5:1:30.3:1:1:0:40.5:8:1:0:5 1/1:12:12:1,11:0,0:1:0,2:10.2:1:30.5:1:1:0:39.1:24:1:0:4.9 -2 92308135 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTCGTTGGAAACGGGATTAC;RSEQ=TATAAAAAGCAGACCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:6.5:1:29.3:1:1:0:40.5:8:1:0:5 0/1:9:2:0,2:0,7:0.2222:0,0:9:1:32.5:1:1:0:31:4:0.25:0:7 -2 92308137 . A G 75 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49091;SOR=0;LSEQ=CGTTGGAAACGGGATTACAT;RSEQ=TAAAAAGCAGACCCCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:4.5:1:31.3:1:1:0:40.5:8:1:0:5 1/0:7:5:0,5:0,2:0.7143:0,0:9.6:1:32.4:1:1:0:40.6:10:0.7143:0:5 -2 92308217 . C G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGTTGAACATTCCTTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:29.5:1:1:0:35:4:1:0:8 -2 92308220 . A T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGAACATTCCTTTTCACAG;RSEQ=GCAGGTTTGAAACACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:28.5:1:1:0:35:4:1:0:8 -2 92308239 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAGGTTTGAAACACTCT;RSEQ=TTTGTAGTATCTGGATGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30.5:1:1:0:35:4:1:0:8 -2 92308255 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTTTTTGTAGTATCTGGA;RSEQ=GTGGACATTTGGAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:48:0:31:1:1:0:35:4:1:0:8 -2 92308262 . A T 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGTATCTGGATGTGGAC;RSEQ=TTTGGAGCGCTTTCAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31.5:1:1:0:35:4:1:0:8 -2 92308276 . CA GG 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGACATTTGGAGCGCTTT;RSEQ=GGCCTATGGTGAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:32:1:1:0:35:4:1:0:7 -2 92308282 . T A 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGGAGCGCTTTCAGGCC;RSEQ=ATGGTGAAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:32:0:1:0:35:4:1:0:7 -2 92308427 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTTGTAAAATCTGCAA;RSEQ=AATATATTTGGATAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:1:30:1:1:0:40.5:4:1:0:7 -2 92308438 . GA CC 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AATCTGCAAAAATATATTTG;RSEQ=TAGCTTTGAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:5.5:1:31.5:1:1:0:30:4:1:0:5 1/1:2:2:1,1:0,0:1:0,2:19:1:29.8:1:1:0:40.5:4:1:0:6 -2 92308444 . T C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAAAATATATTTGGATAGC;RSEQ=TTGAGGATTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:11.5:1:32.5:1:1:0:30:4:1:0:5 0/1:7:2:1,1:5,0:0.2857:0,2:24:1:29.5:1:0.28571:0:40.5:4:0.2857:0:6 -2 92308456 . G T 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.37796;LSEQ=TGGATAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGATTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:26:0:33:0:1:0:40:2:0.5:0:5 0/1:8:2:2,0:5,1:0.25:2,0:14.5:1:33:0:1:0:20.5:4:0.25:0:5 -2 92308458 . T G 53 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATAGCTTTGAGGATTTCGT;RSEQ=GGAAACGGGATTGTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:25.5:1:32:0:1:0:30:4:1:0:5 0/1:8:3:3,0:4,1:0.375:2,0:17:1:34:0:1:0:26:6:0.375:0:6 -2 92308469 . T A 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84709;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:19.5:1:32:1:1:0:30:4:1:0:6 1/0:8:5:5,0:2,1:0.625:2,0:26.6:1:30.6:1:0.375:0:20.8:10:0.625:0:5.6 -2 92308478 . T G 76 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.89792;LSEQ=TGGAAACGGGATTGTCTTCA;RSEQ=ATAAACTCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:46:0:34:0:1:0:40:2:0.3333:0:4 1/0:10:5:4,1:4,0:0.5:0,2:32:1:33:1:1:0:28.8:10:0.5556:0:5 -2 92308484 . C A 50 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52797;SOR=Inf;LSEQ=CGGGATTGTCTTCATATAAA;RSEQ=TCTAGACAGAAGCATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:36.3:1:26:1:1:0:33.3:2:1:0:5.3 0/1:10:3:2,1:7,0:0.3:0,2:37.3:1:31.7:1:0.3:0:39.3:6:0.3:0:6.3 -2 92308511 . T G 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18421;SOR=0.16053;LSEQ=CAGAAGCATTCTCAGAAACT;RSEQ=CATTGGGATGTTTCAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:35.5:1:31.5:1:1:2.44949:43.5:4:0.4:0:6.5 0/1:15:1:1,0:8,6:0.0667:2,0:33:0:29:0:1:0:22:2:0.0714:0:5 -2 92308513 . A T 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63106;SOR=1.93219;LSEQ=GAAGCATTCTCAGAAACTTC;RSEQ=TTGGGATGTTTCAATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,0:0.5:0,2:28.7:1:30.7:1:1:0:42.3:6:0.5:0:5.7 1/0:15:10:7,3:1,1:0.6667:2,2:24.1:1:28.9:1:1:2.16:26.5:9:0.6429:0:5 -2 92308526 . A G 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61262;SOR=0.56336;LSEQ=AAACTTCATTGGGATGTTTC;RSEQ=ATTGAAGTCACAGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:19.5:1:29:1:1:1.7321:20:4:0.4:0:5.5 0/1:15:4:2,2:5,5:0.2667:2,2:26.5:1:29:1:1:1:20.5:8:0.2857:0:6.3 -2 92308536 . A C 68 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30341;SOR=0.24062;LSEQ=GGGATGTTTCAATTGAAGTC;RSEQ=CAGTGTTGAACAGTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:39:1:32:1:1:0:35.7:6:0.75:0:6.3 0/1:15:6:3,3:5,4:0.4:2,2:21.5:1:26.5:1:1:1.23147:21:5:0.3571:0:5.5 -2 92308538 . A T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATGTTTCAATTGAAGTCAC;RSEQ=GTGTTGAACAGTCCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:36.5:1:31.8:1:1:0:36.8:8:1:0:5 0/1:14:2:1,1:6,6:0.1429:2,2:39.5:1:30:1:1:1:34:4:0.1429:0:2.5 -2 92308549 . G T 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.44461;LSEQ=TGAAGTCACAGTGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:29.7:1:31.3:1:1:0:35.7:6:0.75:0:6.3 1/0:9:5:0,5:2,2:0.5556:2,0:35.8:1:30.6:1:0.16667:0:20.8:10:0.5556:0:4.2 -2 92308554 . T A 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=TCACAGTGTTGAACAGTCCC;RSEQ=TTCATAGAGCAGGTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22.5:1:31.5:1:1:1:43.5:4:0.5:0:6.5 0/0:9:0:0,0:2,7:0:2,0:32.2:1:31:1:1:0:24:18:1:0:3.4 -2 92308557 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86755;LSEQ=CAGTGTTGAACAGTCCCTTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:26:0:30:0:1:0:20:2:0.25:0:6 0/1:9:2:0,2:2,5:0.2222:2,0:26:0:28.5:1:1:0:20.5:4:0.2222:0:6 -2 92308559 . T C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGTTGAACAGTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27:1:31:1:1:0:36.8:8:1:0:5 0/1:9:2:0,2:2,5:0.2222:2,0:31:0:33.5:1:1:0:20.5:4:0.2222:0:3 -2 92308563 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAACAGTCCCTTTCATAGA;RSEQ=CAGGTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:23.8:1:32.8:1:1:0:36.8:8:0.8:0:5 0/1:11:2:1,1:2,7:0.1818:2,2:26:1:31.5:1:0.49091:3.06:34:4:0.2:0:2.5 -2 92308570 . T G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89556;LSEQ=TCCCTTTCATAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:13:0:33:0:1:0:20:2:0.2:0:6 0/1:11:2:0,2:3,6:0.1818:2,0:13:0:31.5:1:1:0:20.5:4:0.1818:0:6 -2 92308571 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCTTTCATAGAGCAGGTTT;RSEQ=AAACACTCTTTTTGTAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:17.2:1:32.6:1:1:0:37.4:10:1:0:4 0/1:11:2:1,1:2,7:0.1818:2,2:23.5:1:30.5:1:0.49091:3.06:22:4:0.1818:0:2.5 -2 92308592 . C G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=AAACACTCTTTTTGTAGTAT;RSEQ=TGGACGTGGACATTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:29.5:1:33:1:1:0:40:4:0.6667:0:3.5 0/1:5:2:1,1:0,3:0.4:0,2:33:0:33:0:0.4:0:40:4:0.4:0:4.5 -2 92308597 . C A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=CTCTTTTTGTAGTATCTGGA;RSEQ=GTGGACATTTGGAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:14:0:31:0:1:0:40:2:0.3333:0:1 0/1:5:2:0,2:1,1:0.4:2,0:13.5:1:31.5:1:1:0:28:4:0.4:0:3 -2 92308618 . C G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTGGACATTTGGAGCGCTTT;RSEQ=AGGCCTATGGTGAAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:12:0:33.5:1:1:0:40:4:0.6667:0:3.5 1/0:3:2:1,1:0,1:0.6667:0,2:26.5:1:31.5:1:1:0:40:4:0.6667:0:4.5 -2 92308626 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGGAGCGCTTTCAGGCCTA;RSEQ=GGTGAAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:4:0:31:1:1:0:40:4:0.6667:0:3.5 1/1:2:2:1,1:0,0:1:0,2:18.5:1:30:1:1:0:40:4:1:0:4.5 -2 92308930 . G C 64 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAGACACTCTTCTTGTA;RSEQ=TATCTGGAAGTGGACATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:3,1:1,1:0.6667:2,2:6.3:1:32:1:1:2.45:31:8:0.6667:0:6.5 -2 92308958 . G T 112 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGGACATTTGGAGCGCT;RSEQ=TCAGGACTACGGTGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:0:31.5:1:1:0:44:4:1:0:4 1/1:14:14:7,7:0,0:1:0,2:25.4:1:29.5:1:1:0:36.6:13:1:0:5.4 -2 92308964 . A T 96 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=ACATTTGGAGCGCTGTCAGG;RSEQ=CTACGGTGAAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:31:0:31:1:1:0:44:4:1:0:4 1/0:14:10:5,5:2,2:0.7143:2,2:32.7:1:29.1:1:1:1:34:20:0.7143:0:5.5 -2 92308966 . T G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2451;SOR=0.20301;LSEQ=ATTTGGAGCGCTGTCAGGAC;RSEQ=ACGGTGAAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:33:0:31:1:1:0:44:4:0.6667:0:4 0/1:15:4:2,2:6,5:0.2667:2,2:30:1:31.3:1:1:1.18545:43:8:0.2857:0:5 -2 92308977 . A T 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2451;SOR=0.20301;LSEQ=TGTCAGGACTACGGTGAAAA;RSEQ=GGAAATATCTTCCAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:42:1:30.5:1:1:0:44:4:0.6667:0:4 0/1:15:4:2,2:6,5:0.2667:2,2:41:1:31:1:1:1.18545:43:8:0.2667:0:5 -2 92308981 . A G 105 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06863;SOR=Inf;LSEQ=AGGACTACGGTGAAAAAGGA;RSEQ=ATATCTTCCAATAAAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:31:1:30.7:1:1:0:36.7:6:1:0:3.7 1/0:15:10:5,5:3,2:0.6667:2,2:39.2:1:31.7:1:1:1.46001:34:20:0.6667:0:5.5 -2 92308983 . T A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACTACGGTGAAAAAGGAAA;RSEQ=ATCTTCCAATAAAAGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:30.3:1:30.7:1:1:0:36.7:6:1:0:3.7 0/1:15:2:1,1:7,6:0.1333:2,2:38:0:29.5:1:1:1.1547:40:4:0.1333:0:7.5 -2 92308991 . A C 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAAAAGGAAATATCTTCC;RSEQ=ATAAAAGCTAGATAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:27.7:1:30.3:1:1:0:36.7:6:1:0:3.7 0/1:15:2:1,1:7,6:0.1333:2,2:30:0:30:1:1:1.1547:40:4:0.1429:0:7.5 -2 92308993 . T G 65 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAGGAAATATCTTCCAA;RSEQ=AAAAGCTAGATAGAAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:27:1:30:1:1:0:36.7:6:1:0:3.7 0/1:15:4:2,2:5,5:0.2667:2,2:28:0:32.5:1:1:1:43:8:0.2857:0:5 -2 92308998 . G T 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2451;SOR=0.20301;LSEQ=GGAAATATCTTCCAATAAAA;RSEQ=CTAGATAGAAGCAATGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21:1:29.5:1:1:0:44:4:0.6667:0:4 0/1:15:4:2,2:1,0:0.2667:0,2:23:0:30.3:1:1:0:43:8:0.2667:0:5 -2 92309026 . G T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCAATGTCAGAAAATTT;RSEQ=TCATGATGTATCTACTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:39:0:32:0:1:0:22:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:26.5:1:31.5:1:1:0:21.5:4:1:0:4 -2 92309060 . C T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACTCAGCTAACAGAGTTGAA;RSEQ=CTTTCTTTTGAGAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:28.5:1:1:0:22:4:1:0:3.5 0/0:2:0:0,0:1,1:0:2,0:14:1:27.5:1:1:0:22:4:1:0:1.5 -2 92309129 . TT GG 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGTGGATATTTGTCTAGCT;RSEQ=GAGGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:22:2:1:0:4 1/0:3:2:1,1:0,1:0.6667:0,2:40.5:1:29:1:1:0:39:4:0.6667:0:5.5 -2 92309143 . G T 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGCTTTGAGGATTTCGTT;RSEQ=GAAACGGGATTACATATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:27.5:1:1:0:39:4:1:0:5.5 -2 92309160 . T CA 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=GTTGGAAACGGGATTACATA;RSEQ=AAAAGCAGAGAGCAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:30.5:1:1:0:39:4:1:0:6.5 -2 92309450 . T G 70 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTGTGGAATATGCAAGT;RSEQ=GATATTAAGCCAGCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:4,1:0,0:1:0,2:8:1:30.4:1:1:0:33.4:10:1:0:6.2 -2 92309458 . A G 82 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATATGCAAGTTGATATTA;RSEQ=GCCAGCTTTGAGGATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:5,1:0,0:1:0,2:14.3:1:32:1:1:0:34.5:12:1:0:6 -2 92309460 . C G 88 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGCAAGTTGATATTAAG;RSEQ=CAGCTTTGAGGATTTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:6,1:0,0:1:0,2:14.3:1:31.4:1:1:0:33.1:14:1:0:6.1 -2 92309477 . C G 91 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGAATGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:8:8:7,1:0,0:1:0,2:28.8:1:30.4:1:1:0:34:16:1:0:6 -2 92309492 . G A 89 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCCTTGGAAACGGGAAT;RSEQ=CATATAAAAAGCAGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:10.3:1:29:0:1:0:40:6:1:0:6 1/1:9:9:8,1:0,0:1:0,2:38:1:28.2:1:1:0:34.7:18:1:0:6 -2 92309496 . A G 105 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTTGGAAACGGGAATGCAT;RSEQ=TAAAAAGCAGACAGCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:10:1:32.6:1:1:0:40:10:1:0:5.6 1/1:12:10:9,1:2,0:0.8333:0,2:35.4:1:31.9:1:1:0:35.2:20:0.8333:0:5.9 -2 92309553 . C A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATGTTTGCATTGAAGTC;RSEQ=CAGATTTGAACATTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:12,7:0,0:1:0,2:29.1:1:30.1:1:1:0:45.2:38:1:0:5.2 1/1:30:30:17,13:0,0:1:0,2:30:1:29.8:1:1:0:43.5:60:1:0:4.9 -2 92309558 . T G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCATTGAAGTCCCAGA;RSEQ=TTGAACATTCCCTTTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:12,8:0,0:1:0,2:29.3:1:30.9:1:1:0:45.1:19:1:0:5.1 1/1:32:32:18,14:0,0:1:0,2:29.8:1:31.2:1:1:0:43.4:64:1:0:4.9 -2 92309565 . A G 29 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56531;SOR=0.34446;LSEQ=TTGAAGTCCCAGATTTGAAC;RSEQ=TTCCCTTTCATAGAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:14,9:0.08:2,2:5:0:29.5:1:1:1.52748:57:4:0.08:0:4 0/1:35:1:1,0:19,14:0.0286:2,0:5:0:32:0:1:0:33:2:0.0286:0:6 -2 92309574 . C G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75318;LSEQ=CAGATTTGAACATTCCCTTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:24:14,10:1,1:0.9231:2,2:25.4:1:30.4:1:1:1.38:43.4:23:0.92:0:5.1 1/1:40:36:19,17:1,1:0.9:2,2:27.6:1:31.1:1:1:1.11:43:72:0.9:0:4.6 -2 92309576 . T G 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37483;SOR=2.44298;LSEQ=GATTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:23:14,9:1,2:0.8846:2,2:26:1:31.3:1:0.55577:2.98:43.8:46:0.8846:0:5 1/1:40:38:20,18:0,0:0.95:0,2:27:1:31.2:1:1:0:42.6:76:0.95:0:4.6 -2 92309578 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14534;SOR=0;LSEQ=TTTGAACATTCCCTTTCATA;RSEQ=AGCAGGTTTGAAACACGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:15,10:0.0741:2,2:33.5:1:30:1:1:1.47706:43:4:0.0741:0:6.5 0/0:43:0:0,0:21,22:0:2,0:24.5:1:31.2:1:1:0:43.5:86:1:0:4.5 -2 92309580 . G A 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36015;SOR=0.38407;LSEQ=TGAACATTCCCTTTCATAGA;RSEQ=CAGGTTTGAAACACGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:1,2:15,10:0.1071:2,2:15.7:1:26.7:1:0.56044:2.88294:49:6:0.1111:0:5 0/1:46:2:1,1:22,22:0.0435:2,2:14:1:32:0:1:1:36.5:4:0.0435:0:6.5 -2 92309584 . G C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11107;SOR=0;LSEQ=CATTCCCTTTCATAGAGCAG;RSEQ=TTTGAAACACGCCTTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:0.08:2,2:24:0:33:1:1:1.0871:57:4:0.08:0:4 0/0:49:0:0,0:24,25:0:2,0:22:1:31:1:1:0:45:98:1:0:4.4 -2 92309593 . A T 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52918;SOR=Inf;LSEQ=TCATAGAGCAGGTTTGAAAC;RSEQ=CGCCTTTTGTCATATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:24.9:1:30.3:1:1:0:46.3:52:1:0:4.6 0/1:45:2:1,1:19,24:0.0444:2,2:24:0:32:1:1:1.26:49:4:0.0444:0:5.5 -2 92309595 . G T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65818;SOR=0.51679;LSEQ=ATAGAGCAGGTTTGAAACAC;RSEQ=CCTTTTGTCATATCTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:1,2:10,12:0.12:2,2:30.7:1:29.7:1:1:1.63407:49:6:0.12:0:5 0/1:46:3:1,2:19,24:0.0652:2,2:24.3:1:31:0:1:1.56818:35.3:6:0.0652:0:6.3 -2 92309600 . T C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11404;SOR=0;LSEQ=GCAGGTTTGAAACACGCCTT;RSEQ=TGTCATATCTGGAAGTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:10,14:0.0769:2,2:11.5:1:29.5:1:1:1.38:43:4:0.0769:0:6.5 0/0:50:0:0,0:21,29:0:2,0:22.7:1:30:1:1:0:47:100:1:0:4.2 -2 92309605 . A G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.85415;LSEQ=TTTGAAACACGCCTTTTGTC;RSEQ=TATCTGGAAGTTGTCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:11,14:0.0741:2,2:30:0:31.5:1:1:1.26:57:4:0.0741:0:4 0/1:47:3:1,2:18,26:0.0638:2,2:34.3:1:31.3:1:1:1.37537:35.3:6:0.0638:0:6.3 -2 92309615 . GT G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26851;SOR=4.0023;LSEQ=GCCTTTTGTCATATCTGGAA;RSEQ=TGTCCATTTGGAGCGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:23:10,13:1,1:0.92:2,2:25.8:1:32.4:1:1:1.28628:47.8:46:0.92:0.08:4.3 1/1:48:47:19,28:0,1:0.9792:0,2:25:1:31.4:1:1:0:49:94:0.9792:0.1667:4.3 -2 92309625 . T C 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37619;SOR=2.27086;LSEQ=ATATCTGGAAGTTGTCCATT;RSEQ=GGAGCGCATTCCGGCTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:20:10,10:1,2:0.8696:2,2:25.5:1:31.2:1:1:1.94:47.1:40:0.8696:0:4.3 1/1:49:46:20,26:1,2:0.9388:2,2:23.2:1:30:1:1:1.53:48.8:92:0.9388:0:4.2 -2 92309630 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12072;SOR=0;LSEQ=TGGAAGTTGTCCATTTGGAG;RSEQ=GCATTCCGGCTTGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:11,12:0.08:2,2:46.5:1:30.5:1:1:1.09:39:4:0.08:0:3.5 0/0:46:0:0,0:20,26:0:2,0:26:1:30.8:1:1:0:48.5:92:1:0:4.3 -2 92309632 . C T 41 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54897;SOR=Inf;LSEQ=GAAGTTGTCCATTTGGAGCG;RSEQ=ATTCCGGCTTGTGTTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,15:0:2,0:21.2:1:32.3:1:1:0:46.5:54:1:0:4.4 0/1:48:3:1,2:20,25:0.0625:2,2:20.7:1:26:1:1:1.58499:53.3:6:0.0638:0:4.3 -2 92309637 . C A 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCCATTTGGAGCGCATTC;RSEQ=GGCTTGTGTTGAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:11,13:0,0:1:0,2:24.2:1:31.3:1:1:0:44.7:48:1:0:4.3 1/1:45:45:19,26:0,0:1:0,2:26.2:1:30.1:1:1:0:48.2:44:1:0:4.2 -2 92309649 . A G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54609;SOR=Inf;LSEQ=GCGCATTCCGGCTTGTGTTG;RSEQ=AAAAGGAAATATCCTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:0:2,0:26.3:1:30.7:1:1:0:45.9:44:1:0:4.1 0/1:47:3:1,2:18,26:0.0638:2,2:19:1:30.7:1:1:1.37537:35.3:6:0.0652:0:6.3 -2 92309655 . G A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCGGCTTGTGTTGAAAAAG;RSEQ=AAATATCCTCCCATAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:30.3:1:31.7:1:1:0:46.4:38:1:0:3.9 0/1:47:2:1,1:18,27:0.0426:2,2:33:1:26:1:1:1.49:53.5:4:0.0426:0:4.5 -2 92309663 . C T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.21067;LSEQ=GTGTTGAAAAAGGAAATATC;RSEQ=TCCCATAAAAACTAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:7,10:0.0556:2,0:12:0:31:0:1:0:33:2:0.0556:0:7 0/1:45:3:1,2:17,25:0.0667:2,2:11.3:1:31:1:1:1.35103:32.3:6:0.0698:0:6.3 -2 92309669 . T G 51 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02871;SOR=0;LSEQ=AAAAAGGAAATATCCTCCCA;RSEQ=AAAAACTAGATAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:7,10:0.15:2,2:36:1:32.7:1:1:1.37728:46:6:0.15:0:5 0/0:43:0:0,0:15,25:0:2,0:28.3:1:28.5:1:1:0:47.9:39:0.9512:0:3.8 -2 92309675 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09586;SOR=0;LSEQ=GAAATATCCTCCCATAAAAA;RSEQ=TAGATAGAAGCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:12:0:32:0:1:1.62:30:4:0.1111:0:3.5 0/0:39:0:0,0:16,21:0:2,0:27.5:1:31.5:1:1:0:45.9:74:0.9487:0:3.8 -2 92309678 . G T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.54717;SOR=Inf;LSEQ=ATATCCTCCCATAAAAACTA;RSEQ=ATAGAAGCATTCTCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:29.3:1:31.8:1:1:0:45.8:36:1:0:3.7 0/1:36:2:1,1:14,20:0.0556:2,2:14.5:1:27.5:1:1:1.41:55.5:4:0.0556:0:5.5 -2 92309680 . T C 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTCCCATAAAAACTAGA;RSEQ=AGAAGCATTCTCAGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:7,11:0,0:1:0,2:28.6:1:32.6:1:1:0:45.8:36:1:0:3.7 1/1:35:35:15,20:0,0:1:0,2:26.8:1:31.4:1:1:0:46.7:70:1:0:3.9 -2 92309695 . A T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10204;SOR=0;LSEQ=CTAGATAGAAGCATTCTCAG;RSEQ=AACTTATTTGTGATGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:32:0:30.5:1:1:1:30:4:0.125:0:3.5 0/0:33:0:0,0:15,18:0:2,0:18.7:1:29.1:1:1:0:44:32:1:0:4.5 -2 92309701 . A G 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54296;SOR=Inf;LSEQ=AGAAGCATTCTCAGAAACTT;RSEQ=TTTGTGATGTGTGTACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,8:0:2,0:19.8:1:29.2:1:1:0:43.5:32:0.9412:0:3.8 0/1:31:3:2,1:13,15:0.0968:2,2:15:1:31:1:0.59956:2.25:41.7:6:0.0968:0:8 -2 92309703 . T C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.75145;SOR=1.46197;LSEQ=AAGCATTCTCAGAAACTTAT;RSEQ=TGTGATGTGTGTACTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:2,3:5,3:0.3333:2,2:23.8:1:31.2:1:0.59207:2.32357:41.8:10:0.3333:0:4.6 0/1:33:14:5,9:11,8:0.4242:2,2:14.3:1:31.4:1:0.296:2.40603:45.6:28:0.4516:0:4.6 -2 92309704 . T G 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54117;SOR=Inf;LSEQ=AGCATTCTCAGAAACTTATT;RSEQ=GTGATGTGTGTACTCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:20.9:1:30.4:1:1:0:41:30:1:0:4.1 0/1:32:3:2,1:13,15:0.0938:2,2:18:1:31:1:0.59956:2.25:41.7:6:0.1:0:8 -2 92309706 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CATTCTCAGAAACTTATTTG;RSEQ=GATGTGTGTACTCAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:19.9:1:30.1:1:1:0:41:30:1:0:4.1 0/1:33:2:1,1:15,16:0.0606:2,2:21.5:1:28.5:1:1:1.06:50:4:0.0606:0:6 -2 92309710 . G A 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.07699;SOR=Inf;LSEQ=CTCAGAAACTTATTTGTGAT;RSEQ=TGTGTACTCAACTAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:15.2:1:32.5:1:1:0:39.5:38:1:0:3.5 0/1:34:6:4,2:12,16:0.1765:2,2:14.2:1:28:1:0.3872:2.59:41.2:12:0.1765:0:7.2 -2 92309712 . G A 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.7787;SOR=1.20865;LSEQ=CAGAAACTTATTTGTGATGT;RSEQ=TGTACTCAACTAACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:3,5:7,4:0.4211:2,2:14.9:1:29.1:1:0.36985:2.74899:41.4:16:0.4211:0:4.1 0/1:32:15:6,9:9,8:0.4688:2,2:9.5:1:28.7:1:0.50226:1.65989:42.3:30:0.4839:0:4.3 -2 92309716 . A C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08025;SOR=3.21896;LSEQ=AACTTATTTGTGATGTGTGT;RSEQ=CTCAACTAACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:3,1:7,9:0.2:2,2:23.8:1:32.8:1:0.58204:3.61:43.3:8:0.2:0:4.3 0/1:31:14:8,6:7,10:0.4516:2,2:24.3:1:30.6:1:0.47949:1.86:35.9:28:0.4516:0:5.6 -2 92309721 . A G 34 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56243;SOR=0.34207;LSEQ=ATTTGTGATGTGTGTACTCA;RSEQ=CTAACAGAGTTGAACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:23.5:1:34:0:1:1:59:4:0.1111:0:3.5 0/1:25:1:1,0:10,14:0.04:2,0:24:0:34:0:0.44:0:20:2:0.04:0:3 -2 92309724 . A G 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43066;SOR=2.60853;LSEQ=TGTGATGTGTGTACTCAACT;RSEQ=ACAGAGTTGAACCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:7,9:0.1111:2,0:37:1:34:0:0.47059:0:27.5:4:0.1111:0:5 0/1:24:6:3,3:7,11:0.25:2,2:26.7:1:29.5:1:0.66533:1.54:29.7:12:0.25:0:4 -2 92309728 . G C 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55304;SOR=0.31382;LSEQ=ATGTGTGTACTCAACTAACA;RSEQ=AGTTGAACCTTTCTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:30.5:1:33.5:1:1:1:59:4:0.125:0:3.5 0/1:24:1:1,0:9,14:0.0417:2,0:31:0:33:0:0.41667:0:20:2:0.0417:0:3 -2 92309737 . C A 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67572;SOR=2.09486;LSEQ=CTCAACTAACAGAGTTGAAC;RSEQ=TTTCTTTTGAGAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:5,5:0.1667:2,0:47.5:1:32:0:0.4697:0:27.5:4:0.1667:0:5 0/1:20:6:3,3:3,4:0.3:2,2:31:1:29:1:1:1.30:29.7:12:0.3:0:4 -2 92309739 . T A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11902;SOR=0.26243;LSEQ=CAACTAACAGAGTTGAACCT;RSEQ=TCTTTTGAGAGAGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:3,3:3,2:0.5:2,2:30.8:1:30.3:1:1:1.44544:37.7:12:0.5:0:2.5 0/1:20:4:2,2:8,7:0.2:2,2:28.3:1:28.3:1:1:1.13484:44.5:8:0.2:0:2 -2 92309740 . T G 91 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02876;SOR=Inf;LSEQ=AACTAACAGAGTTGAACCTT;RSEQ=CTTTTGAGAGAGCAGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:31.5:1:30.5:1:1:0:38.3:24:1:0:3.3 0/1:20:7:4,3:6,7:0.35:2,2:40.3:1:32.7:1:1:1.52:43.6:14:0.35:0:7.3 -2 92309742 . TT CA 86 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02876;SOR=Inf;LSEQ=CTAACAGAGTTGAACCTTTC;RSEQ=TTGAGAGAGCAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:32.3:1:31.3:1:1:0:38.3:24:1:0:3.3 0/1:20:7:4,3:6,7:0.35:2,2:39.7:1:30.9:1:1:1.52:43.6:14:0.35:0:6.3 -2 92309746 . G GAT 84 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06372;SOR=Inf;LSEQ=CAGAGTTGAACCTTTCTTTT;RSEQ=AGAGAGCAGTTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:39.5:1:32.8:1:1:0:39.9:20:1:0:3.2 0/1:20:7:4,3:6,6:0.35:2,2:38:1:30:1:1:1.31:43.6:14:0.35:0:7.3 -2 92309748 . G C 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.18131;SOR=0.27844;LSEQ=GAGTTGAACCTTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:4,2:0.4:2,2:33.8:1:32.8:1:1:1.86195:33.5:8:0.4:0:2 0/1:20:3:1,2:9,7:0.15:2,2:38:1:31:1:0.58204:2.44724:37:6:0.15:0:2.3 -2 92309772 . T C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.67628;LSEQ=GCAGTTTTGAAACACTCTTT;RSEQ=TGTGGAATCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:34:1:30.5:1:1:1:46:4:0.1667:0:3.5 0/1:17:2:1,1:6,9:0.1176:2,2:26:0:33:0:1:1.46:45:4:0.1176:0:2 -2 92309779 . A G 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.54711;LSEQ=TGAAACACTCTTTTTGTGGA;RSEQ=TCTGCAAGTGGATATTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:6,5:0.0833:2,0:27:0:29:0:1:0:33:2:0.0833:0:8 0/1:16:2:1,1:5,9:0.125:2,2:13.5:1:29.5:1:1:1.73:40:4:0.125:0:7.5 -2 92309798 . T G 63 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,0:0.8:0,0:28.3:1:31.8:1:1:0:42.8:8:0.8:0:6.3 1/1:1:1:0,1:0,0:1:0,0:31:0:32:0:1:0:57:2:1:0:7 -2 92309805 . TT GG 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGGATATTTGTCTAGCT;RSEQ=GAGGATTTCGTTGCAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:40.5:1:31.8:1:1:0:40:4:0.5:0:5.5 0/0:1:0:0,0:0,1:0:0,0:24:0:30:0:1:0:57:2:1:0:7 -2 92309820 . C G 51 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TAGCTTTGAGGATTTCGTTG;RSEQ=AAACGGGATTACATATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:38:1:32.3:1:1:0:37.7:6:1:0:6.3 0/0:1:0:0,0:0,1:0:0,0:9:0:32:0:1:0:57:2:1:0:7 -2 92309836 . T C 34 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAAACGGGATTACATA;RSEQ=AAAAAGCAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:29:1:34:0:1:0:40:4:0.6667:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92311411 . G C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACTTCTTTGTGATGTTT;RSEQ=CATTCAAGTCACAGAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:33:0:1:0:23:4:1:0:4 -2 92311422 . A T 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATGTTTGCATTCAAGTC;RSEQ=CAGAGTTCTACATTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:32:1:1:0:23:4:1:0:4 -2 92311424 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATGTTTGCATTCAAGTCAC;RSEQ=GAGTTCTACATTCCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:31.5:1:1:0:23:4:1:0:4 -2 92311431 . T A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTCAAGTCACAGAGTTC;RSEQ=ACATTCCCTTTCATAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:31.5:1:1:0:23:4:1:0:4 -2 92312618 . T C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTACTCAACTAACAGAA;RSEQ=TCAACAATCGTTTTGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:24.5:1:33:0:1:0:26:4:0.6667:0:5.5 -2 92312620 . C A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTACTCAACTAACAGAATT;RSEQ=AACAATCGTTTTGAAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:0,0:0.6667:0,0:26.5:1:30:0:1:0:26:4:0.6667:0:5.5 -2 92312624 . A C 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAACTAACAGAATTCAAC;RSEQ=ATCGTTTTGAAGGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:33.7:1:32:0:1:0:25.3:6:1:0:6 -2 92312662 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTGAAACACTCTTTTTG;RSEQ=GGAATCTGCAAGTGCATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:2,0:3,1:0.3333:2,0:20:0:31.5:1:1:0:26:4:0.3333:0:5.5 -2 92312677 . C G 71 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTGGAATCTGCAAGTG;RSEQ=ATATGTAGCTAGATTTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:4,1:0,0:1:0,2:20.6:1:30.6:1:1:0:32.2:10:1:0:5.8 -2 92312682 . G T 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCTGCAAGTGCATAT;RSEQ=TAGCTAGATTTGAGCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:36:1:30.3:1:1:0:36.3:6:1:0:6 -2 92312684 . A G 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTGCAAGTGCATATGT;RSEQ=GCTAGATTTGAGCATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:38:1:31.7:1:1:0:36.3:6:1:0:6 -2 92312723 . T C 49 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGGAAACGGGATTACATA;RSEQ=AAAAAGCAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:1,2:1,2:0.5:2,2:20.3:1:31:1:1:1:36:6:0.5:0:4.7 -2 92312738 . A G 61 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ACATATAAAAAGCAGACAGC;RSEQ=GCATTCCCAGAAACTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:1:0:32:0:1:0:50:2:1:0:6 1/0:7:4:2,2:0,3:0.5714:0,2:17.5:1:30.5:1:0.42857:0:33.5:8:0.5714:0:5.8 -2 92312745 . C T 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTTCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:8:0:32:0:1:0:50:2:1:0:6 1/1:8:8:2,6:0,0:1:0,2:16.8:1:27.6:1:1:0:31.3:16:1:0:5.1 -2 92312786 . T A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TTGCATTCAAGTCACAGAGT;RSEQ=GAACATTCCCTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:48:0:27:0:1:0:50:2:1:0:6 0/1:6:2:1,1:0,4:0.3333:0,2:44:1:29:1:0.33333:0:32:4:0.3333:0:6 -2 92312789 . A G 34 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCAAGTCACAGAGTTGA;RSEQ=CATTCCCTTTCATAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:47:0:29:0:1:0:50:2:1:0:6 0/1:5:2:0,2:1,2:0.4:2,0:36:1:34:0:1:0:26.5:4:0.4:0:5 -2 92312813 . T G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TCCCTTTCATAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:20:1:29:1:1:0:36:4:1:0:4 1/0:4:2:0,2:1,1:0.5:2,0:16.5:1:32:0:1:0:26.5:4:0.5:0:5 -2 92312907 . A G 84 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCCTGAAAACTAGACA;RSEQ=AAGCATTCTCAGAAACTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:13.3:1:32.8:1:1:0:31.7:12:1:0:2.3 1/1:5:5:5,0:0,0:1:0,0:16.2:1:32.2:1:1:0:27.2:10:1:0:2.6 -2 92312942 . C T 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17351;SOR=4.03863;LSEQ=ACTTATTTGTGATGTGCGCC;RSEQ=TCAACTAACAGTGTTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:12,5:0.1053:2,0:30.5:1:33:0:1:0:36:4:0.1053:0:2.5 0/1:12:4:3,1:7,1:0.3333:2,2:36.3:1:28.5:1:1:2.16028:24.3:8:0.3333:0:2.8 -2 92312963 . T A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0848;SOR=3.01477;LSEQ=TCAACTAACAGTGTTGAAGC;RSEQ=TTCTTTTGATAGAGCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:8,2:8,5:0.4348:2,2:35.2:1:30.5:1:0.40503:2.40:44:20:0.4762:0:2.1 1/0:27:19:12,7:6,2:0.7037:2,2:16:1:29.4:1:0.67582:1.71542:35.9:38:0.7037:0:1.8 -2 92312967 . T C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24548;SOR=Inf;LSEQ=CTAACAGTGTTGAAGCTTTC;RSEQ=TTTGATAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:16,7:0:2,0:30.9:1:29.3:1:1:0:38:10.5:1:0:1.3 0/1:29:3:2,1:17,9:0.1034:2,2:21.7:1:30:1:1:1.06:37.3:6:0.1111:0:2.7 -2 92312979 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49503;SOR=Inf;LSEQ=AAGCTTTCTTTTGATAGAGC;RSEQ=GTTTTGAAACACTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:16,11:0:2,0:26.4:1:29.6:1:1:0:37.1:54:1:0:1.4 0/1:32:2:1,1:18,12:0.0625:2,2:25:1:29:1:1:1.48061:43.5:4:0.0645:0:2.5 -2 92312982 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22186;SOR=0;LSEQ=CTTTCTTTTGATAGAGCAGT;RSEQ=TTGAAACACTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:15,12:0.069:2,2:39.5:1:30:1:1:1.24034:46.5:4:0.0714:0:2 0/0:32:0:0,0:18,14:0:2,0:25.7:1:28.8:1:1:0:37.2:31:1:0:1.9 -2 92312987 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49327;SOR=Inf;LSEQ=TTTTGATAGAGCAGTTTTGA;RSEQ=ACACTCTTTTTGTGGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:23.1:1:28.7:1:1:0:37.5:30:1:0:1.2 0/1:34:2:1,1:18,14:0.0588:2,2:38.5:1:29:1:1:1.27615:46:4:0.0606:0:2.5 -2 92312994 . T G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.49392;SOR=Inf;LSEQ=AGAGCAGTTTTGAAACACTC;RSEQ=TTTTGTGGAATCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:0:2,0:24.5:1:30.1:1:1:0:37.1:58:1:0:1.4 0/1:33:2:1,1:17,14:0.0606:2,2:26:1:28:1:1:1.20712:22:4:0.0625:0:2 -2 92313000 . T C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.35314;LSEQ=GTTTTGAAACACTCTTTTTG;RSEQ=GGAATCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:13,16:0.0645:2,0:17:1:33:0:0.22581:0:21.5:4:0.0645:0:5.5 0/1:35:3:2,1:17,15:0.0857:2,2:26:1:30.7:1:1:1.74:22:6:0.0857:0:6 -2 92313023 . T G 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74246;SOR=0.67608;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:3,3:9,16:0.1935:2,2:25.8:1:32.7:1:0.65256:1.74:24.3:12:0.1935:0:4.8 0/1:36:5:2,3:14,17:0.1389:2,2:34.4:1:31.4:1:1:1.22813:25.6:10:0.1429:0:5.2 -2 92313030 . TT GG 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72076;SOR=0.6446;LSEQ=AAGTGGATATTTGTCTAGCT;RSEQ=GAGGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:3,2:7,17:0.1724:2,2:29:1:32.3:1:0.30643:3.47:21.2:10:0.1786:0:4.2 0/1:34:4:2,2:12,18:0.1176:2,2:34.8:1:30.6:1:1:1.48:22:8:0.1176:0:4.8 -2 92313052 . G C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1908;SOR=0;LSEQ=GAGGATTTCGTTGGAAACGG;RSEQ=ATTACATATAAAAAGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:6,15:0.087:2,2:43:0:32.5:1:0.52569:2.39:20:4:0.087:0:1 0/0:29:0:0,0:8,21:0:2,0:21.3:1:30.6:1:1:0:30.1:28:1:0:1.9 -2 92313061 . T C 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.71859;SOR=0.71193;LSEQ=GTTGGAAACGGGATTACATA;RSEQ=AAAAAGCAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:3,2:3,12:0.25:2,2:37.8:1:31.6:1:0.13132:5.37:21.2:10:0.25:0:4.2 0/1:21:4:2,2:4,13:0.1905:2,2:20.8:1:31.3:1:0.54386:3.04:22:8:0.1905:0:4.8 -2 92313083 . C T 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.66087;SOR=0.56853;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTTCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:3,7:0.2857:2,2:22.8:1:30.8:1:0.58042:2.19:21:8:0.2857:0:4.3 0/1:11:2:0,2:2,7:0.1818:2,0:14.5:1:31:0:1:0:22:4:0.1818:0:5 -2 92313089 . A T 30 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6387;LSEQ=AGACAGCAGCATTCCCAGAA;RSEQ=CTTCTTTGTGATGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:5,5:0.1667:2,0:8.5:1:30:1:0.4697:0:30.5:4:0.1667:0:1.5 0/1:9:1:0,1:1,7:0.1111:2,0:10:0:30:0:1:0:24:2:0.125:0:1 -2 92315332 . T A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTCAGTTGAAGTCGCAG;RSEQ=GTTGAACAGTCCCTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:7:1:30:1:1:0:26:4:1:0:5.5 -2 92315335 . T A 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TTCAGTTGAAGTCGCAGTGT;RSEQ=GAACAGTCCCTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:2.3:1:31.5:1:1:0:24.3:8:1:0:5.3 1/0:6:3:3,0:3,0:0.5:0,0:7.7:1:28.7:1:1:0:25.7:6:0.5:0:6.3 -2 92315341 . G T 117 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGTCGCAGTGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:8.3:1:27.8:1:1:0:24.3:3:1:0:5.3 1/1:15:14:13,1:0,0:0.9333:0,1:6.8:1:30.8:1:1:0:24.6:28:0.9333:0:5.8 -2 92315346 . T A 73 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.28871;SOR=Inf;LSEQ=TCGCAGTGTTGAACAGTCCC;RSEQ=TTCATAGAGCAGGTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:10:1:30:1:1:0:30.8:5:1:0:5 0/1:19:5:5,0:12,2:0.2632:2,0:13:1:31.8:1:1:0:31:10:0.2632:0:4 -2 92315347 . T A 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03285;SOR=0.08457;LSEQ=CGCAGTGTTGAACAGTCCCT;RSEQ=TCATAGAGCAGGTTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:5,2:1,0:0.875:0,2:9.3:1:24.6:1:1:0:30.4:2.5:0.8333:0:5 0/1:20:7:5,2:13,0:0.35:1,2:10.4:1:30.1:1:0.11053:0:32:14:0.35:0:5.3 -2 92315349 . CA GG 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38577;SOR=3.38531;LSEQ=CAGTGTTGAACAGTCCCTTT;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:6,2:0.1111:2,0:6:0:33:0:1:0:44:2:0.125:0:4 0/1:23:7:5,2:12,2:0.3043:2,2:9.4:1:31.6:1:0.57427:2.29323:24.3:14:0.3043:0.087:6.1 -2 92315351 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGTTGAACAGTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:10,3:0:2,0:8.3:1:30.3:1:1:0:33.5:26:1:0:4.3 0/1:34:2:1,1:26,6:0.0588:2,2:8:1:32:1:0.37433:4.08831:25:4:0.0588:0:7 -2 92315359 . G A 96 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.71954;SOR=1.87695;LSEQ=CAGTCCCTTTCATAGAGCAG;RSEQ=TTTGAAACACTCTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:14,7:0.087:2,0:7:1:30:1:1:0:49:4:0.087:0:2 0/1:59:9:8,1:36,14:0.1525:2,2:16.8:1:30.4:1:0.42418:3.06:31.8:18:0.1525:0:3.3 -2 92315361 . T G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCCCTTTCATAGAGCAGGT;RSEQ=TGAAACACTCTTTTTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:17,7:0:2,0:12.4:1:30.8:1:1:0:35.9:48:1:0:4.4 0/1:62:2:2,0:43,17:0.0323:2,0:8.5:1:33:1:1:0:32:4:0.0323:0:5.5 -2 92315362 . T G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45292;SOR=0.53061;LSEQ=TCCCTTTCATAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:3,1:14,6:0.1667:2,2:17:1:32.5:1:1:1.27:37.8:8:0.1667:0:5.3 0/1:63:6:5,1:40,17:0.0952:2,2:20.2:1:33.3:1:0.66449:2.10:39.3:12:0.0952:0:5.2 -2 92315366 . A T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01591;SOR=0.31577;LSEQ=TTTCATAGAGCAGGTTTGAA;RSEQ=CACTCTTTTTGTAGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:14:8,6:11,4:0.4828:2,2:18.2:1:29.4:1:0.44973:2.01071:33.1:13:0.4643:0:4.9 0/1:71:16:12,4:36,19:0.2254:2,2:17.9:1:31.1:1:0.55629:1.57:38.3:32:0.2286:0:5.2 -2 92315368 . A C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56235;SOR=Inf;LSEQ=TCATAGAGCAGGTTTGAAAC;RSEQ=CTCTTTTTGTAGTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:19,10:0:2,0:16:1:30.4:1:1:0:36.1:58:1:0:4.7 0/1:79:3:2,1:47,29:0.038:2,2:8.3:1:31:1:1:1.23:32.3:6:0.0395:0:6 -2 92315369 . C T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06898;SOR=0;LSEQ=CATAGAGCAGGTTTGAAACA;RSEQ=TCTTTTTGTAGTATCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:18,9:0.069:2,2:12:0:32:0:1:1.94942:40:4:0.069:0:5 0/0:80:0:0,0:50,30:0:2,0:16.7:1:31.2:1:1:0:33.1:79:1:0:5 -2 92315372 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.13416;SOR=0.52168;LSEQ=AGAGCAGGTTTGAAACACTC;RSEQ=TTTTGTAGTATCTGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:8,7:12,5:0.4688:2,2:21.2:1:31.9:1:0.46701:2.05071:34.1:30:0.4688:0:4.9 0/1:86:27:17,10:36,23:0.314:2,2:14.3:1:31.3:1:1:1.09:36:54:0.314:0:4.9 -2 92315377 . G T 131 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05028;SOR=3.43604;LSEQ=AGGTTTGAAACACTCTTTTT;RSEQ=TAGTATCTGGAAGTGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:2,1:19,15:0.0811:2,2:17.3:1:30:1:1:1.56:31.7:6:0.0833:0:5.7 0/1:94:22:13,9:38,30:0.234:2,2:25:1:29.5:1:1:1.14:31.8:44:0.2391:0:6 -2 92315379 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTGAAACACTCTTTTTGT;RSEQ=GTATCTGGAAGTGGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:21,16:0:2,0:21.1:1:29:1:1:0:35.7:36:1:0:4.9 0/1:100:2:1,1:55,42:0.02:2,2:28:1:28.5:1:1:1.30591:27:4:0.0204:0:4 -2 92315380 . G T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07402;SOR=0;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=TATCTGGAAGTGGACATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:20,17:0.0513:2,2:9:0:32:0:1:1.17156:25:4:0.0541:0:6 0/0:103:0:0,0:58,45:0:2,0:21.9:1:31.4:1:1:0:33.8:206:1:0:4.9 -2 92315382 . A G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61242;SOR=0.54672;LSEQ=TGAAACACTCTTTTTGTAGT;RSEQ=TCTGGAAGTGGACATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:20,17:0.0513:2,2:31.5:1:32:1:1:1.17156:20:4:0.0541:0:5.5 0/1:105:3:1,2:58,44:0.0286:2,2:31.3:1:32:1:0.58015:2.61237:25.7:6:0.0288:0:7.3 -2 92315384 . C A 131 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02051;SOR=4.06954;LSEQ=AAACACTCTTTTTGTAGTAT;RSEQ=TGGAAGTGGACATTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:2,1:18,16:0.0769:2,2:24.3:1:28.3:1:1:1.75:31.7:6:0.0811:0:5.7 0/1:106:27:17,10:41,34:0.2547:2,2:30.5:1:27.6:1:0.50343:1.41:31.7:26:0.2476:0:6 -2 92315387 . G T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.61717;SOR=0.56494;LSEQ=CACTCTTTTTGTAGTATCTG;RSEQ=AAGTGGACATTTGGAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:20,19:0.0488:2,2:36:0:29:1:1:1.05134:20:4:0.0488:0:5.5 0/1:107:3:1,2:58,46:0.028:2,2:36:1:29.7:1:0.58623:2.50037:25.7:6:0.028:0:7.3 -2 92315390 . G A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56668;SOR=Inf;LSEQ=TCTTTTTGTAGTATCTGGAA;RSEQ=TGGACATTTGGAGCGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:20,20:0:2,0:28.3:1:32.1:1:1:0:36.2:80:1:0:5 0/1:112:3:2,1:58,49:0.0268:2,2:23:1:29.7:1:1:1.68:36.3:6:0.027:0:5.3 -2 92315392 . G A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56615;SOR=Inf;LSEQ=TTTTTGTAGTATCTGGAAGT;RSEQ=GACATTTGGAGCGCTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:20,21:0:2,0:29.2:1:31.3:1:1:0:36.3:40:1:0:5.1 0/1:114:3:2,1:59,52:0.0263:2,2:26.3:1:29.7:1:1:1.75:35.3:6:0.0268:0:5 -2 92315405 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGGAAGTGGACATTTGGAGC;RSEQ=CTTTCAGGCCTATGTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:20,22:0:2,0:35.2:1:30.5:1:1:0:35.8:41:1:0:5 0/1:117:2:1,1:59,56:0.0171:2,2:35.5:1:29:1:1:1.05312:25:4:0.0172:0:7 -2 92315407 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAGTGGACATTTGGAGCGC;RSEQ=TTCAGGCCTATGTTGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:20,22:0:2,0:35.6:1:30.7:1:1:0:35.8:84:1:0:5 0/1:117:2:1,1:59,56:0.0171:2,2:35:0:30.5:1:1:1.05312:33:4:0.0172:0:5 -2 92315411 . A T 58 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41302;LSEQ=TGGACATTTGGAGCGCTTTC;RSEQ=GGCCTATGTTGAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:0,1:19,21:0.0244:2,0:48:0:32:0:1:0:30:2:0.025:0:6 0/1:117:4:2,2:57,54:0.0342:2,2:35.5:1:29:1:1:1.05508:45.8:8:0.0342:0:5.5 -2 92315415 . C T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTTGGAGCGCTTTCAGGC;RSEQ=TATGTTGAAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:19,22:0:2,0:35.9:1:31.1:1:1:0:36.1:40:1:0:5 0/1:117:2:1,1:59,56:0.0171:2,2:33.5:1:27.5:1:1:1.05312:27:4:0.0177:0:6 -2 92315416 . T C 119 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56239;SOR=1.7164;LSEQ=ATTTGGAGCGCTTTCAGGCC;RSEQ=ATGTTGAAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:3:2,1:17,21:0.0732:2,2:34.7:1:32.3:1:0.58827:2.42:35.7:6:0.0732:0:6 0/1:117:14:7,7:53,50:0.1197:2,2:33.8:1:31.4:1:1:1.0595:32.4:28:0.1207:0:5.4 -2 92315418 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30527;SOR=1.68449;LSEQ=TTGGAGCGCTTTCAGGCCTA;RSEQ=GTTGAAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:4,4:15,18:0.1951:2,2:32.5:1:30.3:1:1:1.19:33.4:16:0.1951:0:5.5 0/1:117:34:19,15:39,40:0.2906:2,2:29.7:1:29.8:1:0.54556:1.30:30.2:33:0.2895:0:5.7 -2 92315419 . G T 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57325;SOR=Inf;LSEQ=TGGAGCGCTTTCAGGCCTAT;RSEQ=TTGAAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:19,22:0:2,0:34.4:1:31.8:1:1:0:36.1:82:1:0:5 0/1:117:4:2,2:57,54:0.0342:2,2:26.5:1:30:1:1:1.05508:28:8:0.036:0:4.8 -2 92315423 . A G 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22278;SOR=0.55061;LSEQ=GCGCTTTCAGGCCTATGTTG;RSEQ=AAAAGGAAATATCTTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:32:15,17:3,5:0.8:2,2:32.6:1:31.3:1:0.70894:1.46:35.8:64:0.8:0:5.4 1/0:115:79:41,38:17,19:0.687:2,2:29.2:1:30.4:1:0.69063:1.20:33.9:78:0.6842:0:5.2 -2 92315427 . A G 135 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03231;SOR=0.41266;LSEQ=TTTCAGGCCTATGTTGAAAA;RSEQ=GGAAATATCTTCCCATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:15:8,7:10,16:0.3659:2,2:31.6:1:32.5:1:0.51485:1.80:35.7:30:0.375:0:5.6 0/1:115:22:11,11:45,48:0.1913:2,2:26.4:1:30.4:1:1:1.07:36:21:0.1875:0:5.5 -2 92315442 . A G 116 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02884;SOR=0.36326;LSEQ=GAAAAAGGAAATATCTTCCC;RSEQ=TAAAAACAAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:5,7:8,17:0.3243:2,2:21.3:1:31.1:1:0.71613:1.50:36.2:24:0.3333:0:6.4 0/1:95:14:6,8:28,46:0.1474:2,2:16.9:1:30.7:1:0.76994:1.23:37.1:28:0.1474:0:6.4 -2 92315446 . A C 154 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGGAAATATCTTCCCATAA;RSEQ=AACAAGACAGAAGCATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:9,20:2,2:0.8788:2,2:17.1:1:31.8:1:0.58602:2.16451:35.3:58:0.9063:0:6.1 0/0:82:0:0,0:3,8:0:2,0:18.4:1:30.1:1:1:0:32.8:22:1:0:2.8 -2 92315448 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAATATCTTCCCATAAAA;RSEQ=CAAGACAGAAGCATTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:10,20:0:2,0:16.7:1:28.8:1:1:0:36:29:1:0:5.7 0/1:80:2:1,1:29,49:0.025:2,2:19.5:1:30.5:1:1:1.68:28:4:0.0253:0:5 -2 92315450 . A T 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATCTTCCCATAAAAAC;RSEQ=AGACAGAAGCATTCTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:10,20:0,0:1:0,2:15:1:28.5:1:1:0:36:60:1:0:5.7 1/1:68:66:23,43:2,0:0.9706:0,2:14.4:1:29.2:1:0.13169:0:34:132:0.9706:0:5.2 -2 92315453 . A G 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03434;SOR=0.27937;LSEQ=TATCTTCCCATAAAAACAAG;RSEQ=CAGAAGCATTCTCTGAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:3,6:5,13:0.3333:2,2:14.6:1:31.9:1:1:1.29:37.8:18:0.3333:0:6.8 0/1:58:7:2,5:16,35:0.1207:2,2:14:1:30.7:1:1:1.1403:40.7:6:0.1053:0:7 -2 92315455 . A G 97 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48729;SOR=2.27879;LSEQ=TCTTCCCATAAAAACAAGAC;RSEQ=GAAGCATTCTCTGAAACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:0,2:6,17:0.08:2,0:15:1:32:1:1:0:40:4:0.08:0:2.5 0/1:54:9:2,7:12,33:0.1667:2,2:12.1:1:30.7:1:1:1.26732:34:18:0.1667:0:3 -2 92315456 . G C 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48767;SOR=2.383;LSEQ=CTTCCCATAAAAACAAGACA;RSEQ=AAGCATTCTCTGAAACCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:0,2:6,17:0.08:2,0:12.5:1:33.5:1:1:0:25:4:0.08:0:6 0/1:52:9:3,6:9,34:0.1731:2,2:8.6:1:31.3:1:0.41471:1.86:31.8:18:0.1731:0:5 -2 92315467 . T A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAAGACAGAAGCATTCTC;RSEQ=GAAACCGGTTTCTGAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:1,12:0,0:1:0,1:13:1:31.7:1:1:0:36.1:26:1:0:6.6 1/1:23:23:2,21:0,0:1:0,2:10.7:1:31.1:1:1:0:32.2:46:1:0:5.4 -2 92315473 . CG TA 71 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=ACAGAAGCATTCTCTGAAAC;RSEQ=GTTTCTGAGGTGTGTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:33.3:1:30.3:1:1:0:33.5:8:1:0:7 1/0:8:6:0,6:0,0:0.75:0,0:19.5:1:27.8:1:1:0:27:12:0.75:0.25:6.8 -2 92315483 . G T 81 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTGAAACCGGTTTCTGA;RSEQ=GTGTGTCCTCAACTAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:31:1:31:1:1:0:33.5:8:1:0:7 1/1:8:8:0,8:0,0:1:0,0:20:1:27.3:1:1:0:29.8:7:1:0:6.5 -2 92315502 . G C 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTGTGTCCTCAACTAACA;RSEQ=AGTTGAACATTTCTTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:28.3:1:33.7:1:1:0:31.3:6:1:0:7 1/1:6:5:0,5:0,1:0.8333:0,0:27.6:1:31.2:1:1:0:24.6:10:0.8333:0:6.6 -2 92315519 . T A 62 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGTTGAACATTTCTTT;RSEQ=GACAGAACAGTTTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17:1:32.5:1:1:0:27:4:1:0:7 1/0:6:4:0,4:0,1:0.6667:0,0:29.5:1:31.3:1:1:0:24.5:8:0.6667:0:6.8 -2 92315543 . A T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACAGTTTTGAAACACTC;RSEQ=TTTTGTGGTATCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:24:1:30.5:1:1:0:26:4:1:0:6.5 -2 92315552 . T A 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAACACTCATTTTGTGG;RSEQ=ATCTGCAAGTGAATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:15:1:32:0:1:0:26:4:1:0:6.5 -2 92315970 . C T 47 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTTCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:10:1:30:1:1:0:27.3:6:1:0:6.7 0/1:6:2:2,0:2,2:0.3333:2,0:1:0:30:1:0.46667:0:45:4:0.3333:0:6 -2 92315979 . T G 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06593;SOR=0;LSEQ=CAGCAGCATTCCCAGAAACT;RSEQ=CTTTGTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:16.5:1:30.5:1:1:1:21:4:0.5:0:6 0/0:10:0:0,0:6,4:0:2,0:15:1:27:1:1:0:44.1:4:1:0:3.8 -2 92315985 . T G 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.68659;LSEQ=CATTCCCAGAAACTTCTTTG;RSEQ=GATGTTTGCATTCAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:20:1:30.5:1:1:1:43.5:4:0.5:0:7 0/1:10:4:3,1:3,3:0.4:2,2:14.8:1:32.3:1:0.57143:2.69:44.5:8:0.4444:0:5.5 -2 92315990 . T C 33 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05714;SOR=0;LSEQ=CCAGAAACTTCTTTGTGATG;RSEQ=TTGCATTCAAGTCACACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:25:1:33:1:1:1:43.5:4:0.5:0:7 0/0:11:0:0,0:6,4:0:2,0:18.2:1:30.2:1:1:0:42.5:20:0.9091:0:3.5 -2 92316006 . AC CT 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09804;SOR=0;LSEQ=GATGTTTGCATTCAAGTCAC;RSEQ=AGTTGAACATTCCCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:39:1:30.5:1:1:1:21:4:0.3333:0:5 0/0:12:0:0,0:6,6:0:2,0:25.1:1:30.2:1:1:0:46.8:24:1:0:5.2 -2 92316007 . C G 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.61991;SOR=2.64037;LSEQ=ATGTTTGCATTCAAGTCACA;RSEQ=AGTTGAACATTCCCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:0.3333:2,2:32:0:31:1:1:1:43.5:4:0.5:0:7 1/0:12:7:4,3:2,3:0.5833:2,2:29.7:1:31.3:1:1:1.89:42:14:0.5833:0:5.4 -2 92316011 . T A 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63801;SOR=1.9247;LSEQ=TTGCATTCAAGTCACACAGT;RSEQ=GAACATTCCCTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:32:1:29.5:1:1:1:43.5:4:0.3333:0:7 1/0:12:6:3,3:3,3:0.5:2,2:33.3:1:28.8:1:1:1:43:12:0.5:0:5.5 -2 92316016 . A T 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=TTCAAGTCACACAGTTGAAC;RSEQ=TTCCCTTTCATAGAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:30:1:31.2:1:1:0:41.5:12:1:0:4.7 0/1:12:3:2,1:3,4:0.25:2,2:20.3:1:29.7:1:1:2.41:42.3:6:0.25:0:2.7 -2 92316021 . C A 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.09804;SOR=0;LSEQ=GTCACACAGTTGAACATTCC;RSEQ=TTTCATAGAGCAGGTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:23:0:32.5:1:1:1:60:4:0.3333:0:2 0/0:12:0:0,0:6,6:0:2,0:34.3:1:31.2:1:1:0:46.8:24:1:0:5.2 -2 92316025 . CA GG 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61991;SOR=2.27808;LSEQ=CACAGTTGAACATTCCCTTT;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:0.3333:2,2:31.5:1:30.8:1:1:1:43.5:4:0.3333:0:6 1/0:11:6:3,3:2,2:0.5455:2,2:41.3:1:30.5:1:1:1:43:12:0.5455:0:4.5 -2 92316039 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=CCCTTTCATAGAGCAGGTTT;RSEQ=AAACACTCTTTTTGTAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:17.2:1:33.2:1:1:0:41.8:10:1:0:3.8 0/1:10:2:1,1:4,4:0.2:2,2:34:1:32:1:1:1:60:4:0.2:0:6.5 -2 92316042 . A T 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24176;SOR=0.19209;LSEQ=TTTCATAGAGCAGGTTTGAA;RSEQ=CACTCTTTTTGTAGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:16.5:1:32:1:1:1.73:21:4:0.4:0:5 0/1:10:1:0,1:5,4:0.1:2,0:27:0:31:0:1:0:56:2:0.1:0:8 -2 92316044 . A C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCATAGAGCAGGTTTGAAAC;RSEQ=CTCTTTTTGTAGTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:20.3:1:31.3:1:1:0:29.7:6:1:0:5 0/1:10:2:1,1:4,4:0.2:2,2:29:1:31:1:1:1:60:4:0.2:0:6.5 -2 92316051 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.45455;SOR=0.2887;LSEQ=GCAGGTTTGAAACACTCTTT;RSEQ=TGTAGTATCTGGAAGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:19:0:33:0:1:0:21:2:0.5:0:7 0/1:10:2:1,1:4,4:0.2:2,2:22:1:31.5:1:1:1:60:4:0.2:0:6.5 -2 92316054 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGTTTGAAACACTCTTTTTG;RSEQ=AGTATCTGGAAGTGGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:19:1:30.5:1:1:0:34:4:1:0:6 0/1:10:2:1,1:4,4:0.2:2,2:19:1:32:1:1:1:60:4:0.2:0:6.5 -2 92316076 . A G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTATCTGGAAGTGGACATTT;RSEQ=GAGCGCTCTCAGGACTACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:13.5:1:32:0:1:0:40:4:1:0:4.5 -2 92316084 . C T 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTGGACATTTAGAGCGCT;RSEQ=TCAGGACTACGGTGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:5.5:1:32:0:1:0:40:4:1:0:4.5 -2 92316195 . T A 57 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=ACAGAGTTCAACCTTTCTTT;RSEQ=GAGAGAGCAGTTTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:8:0:29:0:1:0:27:2:0.5:0:6 1/0:6:4:4,0:1,1:0.6667:2,0:7.5:1:28.5:1:0.33333:0:34.3:8:0.6667:0:5 -2 92316198 . G C 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGTTCAACCTTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:11:0:33:0:1:0:26:4:1:0:5.5 1/1:10:8:6,2:1,0:0.8:0,2:6.9:1:30.8:1:1:0:36.1:16:0.8:0:4.6 -2 92316202 . G A 98 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84158;LSEQ=TCAACCTTTCTTTTGAGAGA;RSEQ=CAGTTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,0:0.8:0,2:5.5:1:29.5:1:1:0:39.5:8:0.8:0:3.5 1/0:13:10:7,3:2,1:0.7692:2,2:9.3:1:29.7:1:1:1.15:35.4:20:0.7692:0:4.4 -2 92316214 . CA TG 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGAGAGAGCAGTTTTGAAA;RSEQ=CTCTTTTTGTGGAATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:11.6:1:32.5:1:1:0:42.1:28:1:0:3.4 0/1:46:2:1,1:26,18:0.0435:2,2:18.5:1:33:0:1:1.43267:46.5:4:0.0435:0:2.5 -2 92316215 . AC TT 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGAGAGAGCAGTTTTGAAAC;RSEQ=TCTTTTTGTGGAATCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:0:2,0:11.4:1:30.2:1:1:0:43.2:26:0.9286:0:3.2 0/1:47:2:1,1:25,18:0.0426:2,2:10.5:1:30.4:1:1:1.3786:21:4:0.0444:0.0213:3.5 -2 92316218 . C G 34 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.08593;SOR=0;LSEQ=GAGAGCAGTTTTGAAACACT;RSEQ=TTTTTGTGGAATCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:0.1:2,2:8:0:34:0:1:1.23603:50:4:0.1:0:6 0/0:47:0:0,0:27,20:0:2,0:16.3:1:31.8:1:1:0:39.4:94:1:0:3.2 -2 92316229 . A G 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71322;SOR=1.80493;LSEQ=TGAAACACTCTTTTTGTGGA;RSEQ=TCTGCAAGTGGATATTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:19:0:33:0:1:1.21106:50:4:0.0909:0:6 0/1:52:8:4,4:23,20:0.1538:2,2:21.9:1:31:1:1:1.14684:38:16:0.1569:0:5.8 -2 92316238 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTTGTGGAATCTGCAAG;RSEQ=GGATATTTGTCTAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:30:1:29.5:1:1:0:40.5:21:1:0:3.4 0/1:53:2:1,1:26,25:0.0377:2,2:33:0:32.5:1:1:1.03924:42:4:0.0377:0:3 -2 92316241 . A C 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.30521;SOR=0.5633;LSEQ=TTTGTGGAATCTGCAAGTGG;RSEQ=TATTTGTCTAGATTTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:6,5:6,5:0.5:2,2:31:1:32.9:1:1:1:37.9:22:0.5:0:3.5 0/1:53:19:9,10:18,16:0.3585:2,2:34.3:1:32.2:1:0.77855:1.24473:34.9:38:0.3585:0:3.4 -2 92316246 . T G 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71427;SOR=1.72765;LSEQ=GGAATCTGCAAGTGGATATT;RSEQ=GTCTAGATTTGAGGATTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:39:0:32:1:1:1.21106:44:4:0.0909:0:2.5 0/1:54:8:4,4:23,23:0.1481:2,2:35.8:1:30:1:1:1:40:16:0.1481:0:3.6 -2 92316248 . T G 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=CTAGATTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:12,10:0,0:1:0,2:38.2:1:32.4:1:1:0:40.5:44:1:0:3.4 1/1:54:52:26,26:1,1:0.963:2,2:34.2:1:31.4:1:1:1:38.4:51:0.9623:0:3.5 -2 92316251 . A G 93 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09599;SOR=Inf;LSEQ=CTGCAAGTGGATATTTGTCT;RSEQ=GATTTGAGGATTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:40.4:1:30:1:1:0:40.5:44:1:0:3.4 0/1:54:8:4,4:23,23:0.1481:2,2:35.6:1:31.3:1:1:1:38:16:0.1481:0:5.8 -2 92316274 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGAGGATTTCGTTGGAAA;RSEQ=GGGATTACATATAAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:25.7:1:30.9:1:1:0:40.4:50:1:0:3.8 0/1:57:2:1,1:28,27:0.0351:2,2:34:0:31.5:1:1:1.03639:43:4:0.0351:0:4 -2 92316275 . G A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGAGGATTTCGTTGGAAAC;RSEQ=GGATTACATATAAAAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:24.9:1:29:1:1:0:40.4:11.5:1:0:3.8 0/1:57:2:1,1:28,27:0.0351:2,2:16.5:1:32.5:1:1:1.03639:41:4:0.0357:0:5.5 -2 92316276 . G C 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30578;SOR=Inf;LSEQ=TGAGGATTTCGTTGGAAACG;RSEQ=GATTACATATAAAAAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:24.2:1:31.1:1:1:0:40.4:50:1:0:3.8 0/1:56:4:2,2:26,26:0.0714:2,2:18.5:1:31:1:1:1:32.5:8:0.0714:0:6.5 -2 92316279 . T A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5138;SOR=0.63228;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TACATATAAAAAGCAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:2,3:12,10:0.1852:2,2:7:1:29.6:1:0.64831:1.76109:43:10:0.1923:0:7.4 0/1:56:7:5,2:24,25:0.125:2,2:12.4:1:30.3:1:0.42394:2.56:40.4:14:0.1296:0:6.7 -2 92316280 . T A 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47799;SOR=2.06518;LSEQ=GATTTCGTTGGAAACGGGAT;RSEQ=ACATATAAAAAGCAGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:18.5:1:28:1:1:1.0801:50:4:0.08:0:6 0/1:49:7:2,5:21,20:0.1429:2,2:21.3:1:31:1:0.41912:2.57471:39.4:14:0.1458:0:6.3 -2 92316282 . CA GG 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70416;SOR=1.55334;LSEQ=TTTCGTTGGAAACGGGATTA;RSEQ=TATAAAAAGCAGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:15.5:1:30.3:1:1:1.0801:50:4:0.0741:0:5 0/1:45:5:1,4:21,19:0.1111:2,2:15.6:1:32.1:1:0.34625:4.29064:38:10:0.1136:0:6.2 -2 92316283 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.56989;SOR=1.48181;LSEQ=TTCGTTGGAAACGGGATTAC;RSEQ=TATAAAAAGCAGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:2,3:10,9:0.1923:2,2:11:1:30:1:1:1.63159:43:10:0.2083:0:7.4 0/1:42:11:7,4:12,14:0.2619:2,2:18.4:1:30.4:1:0.47563:2.00:36.2:22:0.2973:0:5.6 -2 92316296 . A T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06259;SOR=0.28207;LSEQ=GGATTACATATAAAAAGCAG;RSEQ=CAGCAGCATTCCCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:5,4:8,10:0.3333:2,2:8.9:1:28.8:1:0.69458:1.54:40.3:18:0.3333:0:3.3 0/1:33:4:0,4:14,15:0.1212:2,0:16.3:1:29.8:1:0.11918:0:26.5:8:0.1212:0:4.3 -2 92316307 . CC GT 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30698;SOR=0.39058;LSEQ=AAAAAGCAGACAGCAGCATT;RSEQ=CAGAAACTACTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:4,5:2,2:0.6923:2,2:29.1:1:31.8:1:1:1.22862:43.1:18:0.6923:0:4.8 0/1:26:12:7,5:4,10:0.4615:2,2:33.9:1:31:1:0.23286:3.32:38.8:24:0.4615:0:5 -2 92316308 . C T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.31719;SOR=2.27738;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTACTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:2,2:1,1:0.2667:2,2:7:1:28:1:1:1:32.8:3:0.6:0:3.5 0/1:24:11:3,8:0,1:0.4583:0,2:15.4:1:28.9:1:1:0:29.9:22:0.9167:0:4 -2 92316312 . A T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GCAGACAGCAGCATTCCCAG;RSEQ=AACTACTTTGTGATGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:5:0:30.5:1:1:1.15:40:4:0.1333:0:2.5 0/0:21:0:0,0:8,13:0:2,0:29.3:1:30:1:1:0:34:42:1:0:4.5 -2 92316315 . C G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.90433;LSEQ=GACAGCAGCATTCCCAGAAA;RSEQ=TACTTTGTGATGTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:5,6:0.0833:2,0:1:0:31:0:1:0:42:2:0.0833:0:5 0/1:20:3:0,3:8,9:0.15:2,0:12:1:32.7:1:0.24211:0:25.7:6:0.15:0:5.3 -2 92316317 . A T 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26935;SOR=Inf;LSEQ=CAGCAGCATTCCCAGAAACT;RSEQ=CTTTGTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:33:1:30.2:1:1:0:42.5:22:1:0:4.4 0/1:20:4:0,4:8,7:0.2:2,0:14.5:1:31:0:0.1032:0:25:8:0.2105:0:4.3 -2 92316345 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20308;SOR=0;LSEQ=ATGTTTGCATTCAAGTCACA;RSEQ=AGTTGAACATTCCCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:0.1667:2,2:38:0:31.5:1:1:1.45:40:4:0.1667:0:2.5 0/0:14:0:0,0:7,7:0:2,0:27.7:1:31.7:1:1:0:38:28:1:0:4.9 -2 92316347 . G A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20308;SOR=Inf;LSEQ=GTTTGCATTCAAGTCACAGA;RSEQ=TTGAACATTCCCTTTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:4,6:1,1:0.8333:2,2:20:1:30.6:1:1:1.4491:41.3:20:0.8333:0:5 1/1:14:14:7,7:0,0:1:0,2:26.3:1:30:1:1:0:38:28:1:0:4.9 -2 92316355 . T C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30021;SOR=4.22767;LSEQ=TCAAGTCACAGAGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:3,5:1,2:0.7273:2,2:13.9:1:32.4:1:1:1.18:44.6:16:0.7273:0:5.1 1/1:13:12:6,6:0,1:0.9231:0,2:20.9:1:30.9:1:1:0:40.3:24:0.9231:0:5.2 -2 92316364 . AT GC 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=AGAGTTGAACATTCCCTTTC;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:8.5:1:32:1:1:1.29:50.5:4:0.2222:0:6 0/0:9:0:0,0:4,5:0:2,0:18:1:28.8:1:1:0:40.3:18:1:0:5.1 -2 92316365 . T C 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13122;SOR=7.0072;LSEQ=GAGTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:1,1:0.5:2,2:14.5:1:31:1:1:2.44949:34.8:8:0.6667:0:6.3 1/1:9:8:3,5:0,0:0.8889:0,2:16.8:1:30.3:1:1:0:41:16:0.8889:0:5.3 -2 92316526 . T A 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55728;SOR=0.38591;LSEQ=TCAACTAACAGTGTTGAAGC;RSEQ=TTCTTTTGATAGAGCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:27.5:1:29:1:1:0:34:4:0.5:0:1.5 0/1:15:4:2,2:5,6:0.2667:2,2:15.8:1:29.3:1:1:1.19:30.5:8:0.2667:0:1.8 -2 92316635 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GATTACATATTAAAAGCAGA;RSEQ=AGCAGCATTCCCAGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:4:0:35:0:1:0:30:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:14.5:1:28.5:1:1:0:20:4:1:0:2 -2 92317235 . T C 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGAGCAGTTTTGAAACAC;RSEQ=CTTTTTGTGGAATCTGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:10.5:1:30.5:1:1:0:42:4:0.6667:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92317243 . T C 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTGAAACACTCTTTTTG;RSEQ=GGAATCTGCAACTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18.5:1:29.5:1:1:0:42:4:0.6667:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92317266 . T G 50 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGCAACTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:35.7:1:31.7:1:1:0:41.3:6:1:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92317274 . T G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGATATTTGTCTAGCTT;RSEQ=GAGGATTTCGTTGGAAACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:41:1:32:1:1:0:42:4:0.6667:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92317294 . T G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGATTTCGTTGGAAACG;RSEQ=GATTACATACAAAAAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:32.5:1:1:0:42:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92317304 . C T 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=GTTGGAAACGTGATTACATA;RSEQ=AAAAAGCAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:7:0:32:0:1:0:27:2:0.3333:0:8 1/1:6:6:4,2:0,0:1:0,2:6.5:1:28.7:1:1:0:43.7:12:1:0:8 -2 92317313 . G C 102 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04096;SOR=18.0326;LSEQ=GTGATTACATACAAAAAGCA;RSEQ=ACAGCAGCATTCCCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:16:0:34:0:1:0:27:2:0.25:0:8 1/1:10:9:5,4:0,0:0.9:0,2:11.4:1:32.2:1:1:0:44.2:18:0.9:0:7.7 -2 92317322 . A G 103 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09341;SOR=13.74787;LSEQ=TACAAAAAGCAGACAGCAGC;RSEQ=TTCCCAGAAACTTCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:25:0:32:0:1:0:27:2:0.3333:0:8 1/1:11:10:6,4:0,1:0.9091:0,2:20.9:1:31.3:1:0.45455:0:45.8:20:0.9091:0:7.7 -2 92317326 . CC TG 102 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51648;SOR=3.98567;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=AGAAACTTCTTTCTGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:0.5:0,2:17.5:1:30.7:1:1:0:43.5:4:0.5:0.25:7 1/1:11:9:5,4:0,0:0.8182:0,2:25.4:1:32.4:1:1:0:48.6:18:0.9:0:6.7 -2 92317333 . C T 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50435;SOR=0.46197;LSEQ=GACAGCAGCATTCCCAGAAA;RSEQ=TTCTTTCTGATGTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:22:0:33:0:1:0:26:2:0.3333:0:7 0/1:22:4:2,2:11,7:0.1818:2,2:5.8:1:30.8:1:1:1.53863:40:8:0.1818:0:6.3 -2 92317335 . T G 140 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12308;SOR=5.01083;LSEQ=CAGCAGCATTCCCAGAAACT;RSEQ=CTTTCTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:23:1:30.5:1:1:1.7321:43.5:4:0.4:0:7 1/0:23:18:11,7:2,3:0.7826:2,2:22.3:1:33.6:1:0.61752:2.27:50.1:36:0.7826:0:6.9 -2 92317347 . T C 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.56882;SOR=0.40973;LSEQ=CAGAAACTTCTTTCTGATGT;RSEQ=TGCATTCAAGTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:14:0:33:1:1:1.7321:40:4:0.4:0:7 0/1:24:5:2,3:11,8:0.2083:2,2:18.6:1:32:1:0.62992:2.00028:40:10:0.2083:0:6.2 -2 92317354 . C A 30 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02463;SOR=0;LSEQ=TTCTTTCTGATGTTTGCATT;RSEQ=AAGTCACAGAGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:21:0:30.5:1:1:1.7321:40:4:0.4:0:7 0/0:24:0:0,0:13,11:0:2,0:29.1:1:31.8:1:1:0:48.1:48:1:0:6.8 -2 92317357 . G C 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11188;SOR=0.18927;LSEQ=TTTCTGATGTTTGCATTCAA;RSEQ=TCACAGAGTTGAACATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:21.7:1:34:0:1:1.73:35.3:6:0.6:0:7 0/1:24:5:2,3:11,8:0.2083:2,2:28.6:1:32.2:1:0.62992:2.00028:40:10:0.2083:0:6.2 -2 92317361 . C T 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30025;SOR=0.27764;LSEQ=TGATGTTTGCATTCAAGTCA;RSEQ=AGAGTTGAACATTCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:0,0:0.5:0,2:23:1:31.7:1:1:0:35.3:6:0.5:0:7 0/1:24:5:2,3:0,0:0.2083:0,2:32.6:1:28.8:1:1:0:40:10:0.2083:0:6.2 -2 92317371 . C G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5705;SOR=0.4146;LSEQ=ATTCAAGTCACAGAGTTGAA;RSEQ=ATTCCCTTTCATAGAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:38:0:33:0:1:1:40:4:0.3333:0:7 0/1:24:4:2,2:11,8:0.1667:2,2:34:1:31.3:1:1:1.35584:40:8:0.1667:0:5.8 -2 92317373 . T C 128 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30025;SOR=3.60185;LSEQ=TCAAGTCACAGAGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:2,1:0.5:2,2:24.3:1:33:1:1:3.10575:42.3:6:0.5:0:7.7 1/0:24:19:11,8:2,3:0.7917:2,2:28.7:1:30.3:1:0.62992:2.00:50.3:18:0.7826:0:7.4 -2 92317391 . GT TC 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.9469;LSEQ=CATTCCCTTTCATAGAGCAG;RSEQ=TTGAAACACTCTTTTTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,1:0.25:2,0:29:0:32:0:1:0:60:2:0.25:0:6 0/1:20:8:4,4:2,3:0.4:2,2:29.4:1:30.7:1:1:1.45:54.6:16:0.4:0:6.1 -2 92317402 . T C 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=3.83897;LSEQ=ATAGAGCAGGTTTGAAACAC;RSEQ=CTTTTTGTAGTATCTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:0.25:2,0:19:0:33:0:1:0:60:2:0.25:0:6 1/0:12:7:4,3:2,3:0.5833:2,2:17:1:30.4:1:1:1.89:54.7:14:0.5833:0:6 -2 92317404 . T C 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.11813;SOR=7.63506;LSEQ=AGAGCAGGTTTGAAACACTC;RSEQ=TTTTGTAGTATCTGGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,1:0.25:2,0:41:0:34:0:1:0:40:2:0.25:0:6 1/0:12:9:5,4:1,2:0.75:2,2:17.1:1:30.3:1:1:2.32:55.2:18:0.75:0:6 -2 92317407 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51648;SOR=0.2509;LSEQ=GCAGGTTTGAAACACTCTTT;RSEQ=TGTAGTATCTGGATGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:27:0:31:1:1:0:40:4:0.5:0:7 0/1:11:2:1,1:5,4:0.1818:2,2:22.5:1:33.5:1:1:1.22474:40:4:0.1818:0:6.5 -2 92317410 . T G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51648;SOR=0.2509;LSEQ=GGTTTGAAACACTCTTTTTG;RSEQ=AGTATCTGGATGTGGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:24:0:30:1:1:0:40:4:0.5:0:7 0/1:11:2:1,1:5,4:0.1818:2,2:19.5:1:33:0:1:1.22474:40:4:0.1818:0:6.5 -2 92317421 . TG AC 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=CTCTTTTTGTAGTATCTGGA;RSEQ=TGGACATTTGGAGCGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:13:1:31.8:1:1:0:50:4:0.5:0.25:6 1/0:8:4:2,2:2,2:0.5:2,2:7.8:1:30:1:1:1:49.8:8:0.5:0.375:6.8 -2 92317751 . G T 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGGTTTGAAACACTCTTTTT;RSEQ=TAGTATATGGAAGTGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:7:0:33:0:1:0:40:2:1:0:2 1/1:5:4:2,2:1,0:0.8:0,2:16.5:1:31:1:1:0:50.8:8:0.8:0:4.5 -2 92317774 . C G 71 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATATGGAAGTGGACATTT;RSEQ=GAGCGCTCTCAGGACTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:13.7:1:27.3:1:1:0:41.3:6:1:0:1.3 1/0:7:5:2,3:0,0:0.7143:0,2:12:1:31:1:1:0:32.4:10:0.7143:0:2.8 -2 92317777 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=Inf;LSEQ=TATGGAAGTGGACATTTCGA;RSEQ=CGCTCTCAGGACTGCGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:13:1:27.5:1:1:0:46:3:1:0:1 0/1:8:2:1,1:3,2:0.25:2,2:34:0:31:1:1:1.41418:41.5:4:0.25:0:8 -2 92317782 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=Inf;LSEQ=AAGTGGACATTTCGAGCGCT;RSEQ=TCAGGACTGCGGTGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18:1:28.3:1:1:0:46:3:1:0:1 0/1:8:2:1,1:3,3:0.25:2,2:29:0:32:0:1:1:41.5:4:0.25:0:8 -2 92317783 . T A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=Inf;LSEQ=AGTGGACATTTCGAGCGCTC;RSEQ=CAGGACTGCGGTGAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:19:1:30.8:1:1:0:46:8:1:0:1 0/1:8:2:1,1:3,3:0.25:2,2:20.5:1:29:1:1:1:43:4:0.25:0:2.5 -2 92317788 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=ACATTTCGAGCGCTCTCAGG;RSEQ=CTGCGGTGAAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:24:1:30.8:1:1:0:46:8:1:0:1 0/1:8:2:1,1:3,3:0.25:2,2:23:0:33.5:1:1:1:41.5:4:0.25:0:8 -2 92317791 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TTTCGAGCGCTCTCAGGACT;RSEQ=CGGTGAAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27:1:29.3:1:1:0:46:3:1:0:1 0/1:8:2:1,1:3,3:0.25:2,2:20:0:31:1:1:1:41.5:4:0.25:0:8 -2 92317794 . G T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=CGAGCGCTCTCAGGACTGCG;RSEQ=TGAAAAAGGAAATATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:30:1:32.5:1:1:0:46:8:1:0:1 0/1:8:2:1,1:3,3:0.25:2,2:17:0:32:0:1:1:41.5:4:0.25:0:8 -2 92317797 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=GCGCTCTCAGGACTGCGGTG;RSEQ=AAAAGGAAATATCTTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:31.8:1:31:1:1:0:46:8:1:0:1 0/1:8:2:1,1:3,3:0.25:2,2:14:0:33:0:1:1:41.5:4:0.25:0:8 -2 92317888 . TCT CA 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTAACAGAGTTGAACCTT;RSEQ=TTTGAGAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:0,1:0.6667:0,0:28.5:1:31.9:1:1:0:32:4:0.6667:0:0.5 -2 92317974 . G T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGATTTCGTTGGAAACG;RSEQ=GATTACATATAAAAAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29.5:1:1:0:43.5:4:1:0:5 -2 92318000 . GC AT 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CATATAAAAAGCAGACAGCA;RSEQ=ATTCCCACAAACTTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:38:1:30:1:1:1.7321:43.5:4:0.4:0:4 -2 92318014 . T A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGCAGCATTCCCACAAAC;RSEQ=TCTTTGTGATGTTTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:20.5:1:28.5:1:1:1.7321:44:4:0.4:0:2 -2 92318020 . GT AC 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTCCCACAAACTTCTTT;RSEQ=GATGTTTGCATTCAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:38:1:28.8:1:1:1.7321:43.5:4:0.4:0:3 -2 92318021 . T C 49 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATTCCCACAAACTTCTTTG;RSEQ=GATGTTTGCATTCAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:0,0:0.6:0,2:26.3:1:31.3:1:1:0:36:6:1:0:2 -2 92318231 . TG GC 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTGTTGAACCTTTCTTT;RSEQ=ATAGAGCAGTTTTGAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:1:33.8:1:1:0:25:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92318234 . T A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTGAACCTTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:1:31.5:1:1:0:25:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92318253 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATAGAGCAGTTTTGAAACCC;RSEQ=CTTTTTGTAAAATCTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:32.5:1:1:0:25:4:1:0:7 0/0:2:0:0,0:2,0:0:0,0:16:1:33:0:1:0:29:4:1:0:7 -2 92318263 . A G 32 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAAACCCTCTTTTTGTA;RSEQ=AATCTGCAAGAGGATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:1:33:0:1:0:25:4:1:0:7 1/0:3:2:2,0:0,0:0.6667:0,0:13:1:32.5:1:1:0:21:4:1:0:7.5 -2 92318292 . T G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGAGGATATTTGGATAGCTT;RSEQ=GAGGATTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:27.3:1:30.3:1:1:0:30:6:1:0:5.7 1/0:3:2:2,0:1,0:0.6667:0,0:39.5:1:32.5:1:1:0:21:4:0.6667:0:7.5 -2 92318302 . G T 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TGGATAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGATTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:20:1:29.5:1:1:0:25:4:0.6667:0:7 0/0:4:0:0,0:3,1:0:2,0:25.3:1:29.8:1:1:0:29.5:8:1:0:7 -2 92318304 . T G 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=GATAGCTTTGAGGATTTCGT;RSEQ=GGAAACGGGATTGTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18:1:30.5:1:1:0:25:4:0.6667:0:7 0/0:5:0:0,0:3,2:0:2,0:20.6:1:28.6:1:1:0:29.2:10:1:0:7.2 -2 92318314 . AT TA 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=AGGATTTCGTTGGAAACGGG;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15.5:1:29.5:1:1:0:34:8:1:0:5.3 0/1:5:2:2,0:1,2:0.4:2,0:36:1:28:1:0.4:0:21:4:0.4:0:6.5 -2 92318315 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:7:1:29:1:1:1:25:4:0.5:0:7 0/0:5:0:0,0:1,2:0:2,0:11.7:1:27.3:1:1:0:34.7:6:1:0:7 -2 92318324 . T G 41 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=Inf;LSEQ=TGGAAACGGGATTGTCTTCA;RSEQ=ATAAACTCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:29.5:1:28:1:1:0:43:4:1:0:3.5 1/0:4:3:1,2:0,0:0.75:0,2:20.3:1:26.3:1:1:0:28.7:6:0.75:0:7.3 -2 92318328 . A C 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=AACGGGATTGTCTTCATATA;RSEQ=ACTCTAGACAGAAGCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:29.5:1:31:1:1:0:43:4:0.5:0:3.5 0/0:6:0:0,0:2,4:0:2,0:17.3:1:27.8:1:1:0:25:12:1:0:7 -2 92318330 . C A 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.53707;LSEQ=CGGGATTGTCTTCATATAAA;RSEQ=TCTAGACAGAAGCATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:29.5:1:29.5:1:1:0:43:4:0.5:0:3.5 0/1:6:2:0,2:2,2:0.3333:2,0:28.5:1:26:0:0.46667:0:33:4:0.3333:0:8 -2 92318367 . G T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CTCAGAAGCTTCATTGGGAT;RSEQ=TTTCAATTGAAGTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:33.4:1:32.2:1:1:0:35.6:10:1:0:5.6 0/1:6:2:1,1:0,4:0.3333:0,2:5.5:1:27.5:1:0.33333:0:49:4:0.3333:0:7.5 -2 92318370 . TCAATTG GCATTC 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5671;SOR=0.3704;LSEQ=AGAAGCTTCATTGGGATGTT;RSEQ=AAGTCACAGAGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:43:1:32.1:1:1:1.73:30.7:6:0.6:0:6 0/1:6:2:0,2:1,3:0.3333:2,0:45.5:1:30.9:1:1:0:21:4:0.3333:0:6 -2 92318371 . CA GC 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GAAGCTTCATTGGGATGTTT;RSEQ=ATTGAAGTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,1:0:0,0:42:0:32:0:1:0:46:2:1:0:4 0/1:6:2:0,2:1,1:0.3333:2,0:30.5:1:33.3:1:1:0:33:4:0.5:0:7 -2 92318376 . G C 34 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTCATTGGGATGTTTCAATT;RSEQ=AAGTCACAGAGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,1:0:0,0:37:0:32:0:1:0:46:2:1:0:4 0/1:6:2:0,2:1,1:0.3333:2,0:26.5:1:34:0:1:0:33:4:0.5:0:7 -2 92318384 . AG CT 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45455;SOR=Inf;LSEQ=GATGTTTCAATTGAAGTCAC;RSEQ=AGTTGAACATTCCCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:33.6:1:30.2:1:1:0:34.8:10:1:0:5.8 0/1:6:2:1,1:0,4:0.3333:0,2:23.5:1:30.3:1:0.33333:0:49:4:0.3333:0:6.5 -2 92318389 . T A 65 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.5321;LSEQ=TTCAATTGAAGTCACAGAGT;RSEQ=GAACATTCCCTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:34:1:28.8:1:1:0:32:8:0.8:0:6.3 1/0:6:4:0,4:1,1:0.6667:2,0:24.3:1:32.5:1:0.33333:0:27:8:0.6667:0:7 -2 92318400 . T A 58 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.24242;SOR=0.1553;LSEQ=TCACAGAGTTGAACATTCCC;RSEQ=TTCATAGAGCAGGTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:28.5:1:29.3:1:1:0:32:8:0.8:0:6.3 0/1:6:2:0,2:1,3:0.3333:2,0:24:1:32:0:1:0:21:4:0.3333:0:7 -2 92318413 . G A 59 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CATTCCCTTTCATAGAGCAG;RSEQ=TTTGAAACACTCTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:22:1:29.5:1:1:0:32:8:1:0:6.3 1/0:4:2:0,2:1,1:0.5:2,0:11:1:31.5:1:1:0:21:4:0.5:0:7 -2 92318420 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14286;SOR=Inf;LSEQ=TTTCATAGAGCAGGTTTGAA;RSEQ=CACTCTTTTTGTAGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.5:1:29:1:1:0:32:8:1:0:6.3 1/0:3:2:1,1:0,1:0.6667:0,2:22:0:31.5:1:1:0:49:4:0.6667:0:6.5 -2 92318425 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TAGAGCAGGTTTGAAACACT;RSEQ=TTTTTGTAGTATCTGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15.3:1:31:1:1:0:32:8:1:0:6.3 1/0:3:2:1,1:0,1:0.6667:0,2:17:0:33.5:1:1:0:49:4:0.6667:0:6.5 -2 92318429 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCAGGTTTGAAACACTCTTT;RSEQ=TGTAGTATCTGGATGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:25.5:1:22:1:1:0:32:1:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:13:0:33.5:1:1:0:49:4:1:0:6.5 -2 92318433 . A C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTTTGAAACACTCTTTTTGT;RSEQ=GTATCTGGATGTGGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:21.5:1:31.5:1:1:0:32:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:9:0:32.5:1:1:0:49:4:1:0:6.5 -2 92318585 . T G 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTTTTGATAGAGCAGT;RSEQ=TTGAAACTCTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:11:0:31:1:1:2.44949:24:4:0.3333:0:2 0/0:1:0:0,0:1,0:0:0,0:20:0:31:0:1:0:34:2:1:0:5 -2 92318593 . T A 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.375;SOR=Inf;LSEQ=TGATAGAGCAGTTTTGAAAC;RSEQ=CTCTTTTTGTGGAATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:0.2857:2,0:21:1:32:0:1:0:34:4:0.2857:0:4.5 1/1:1:1:1,0:0,0:1:0,0:28:0:30:0:1:0:34:2:1:0:5 -2 92318596 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGCAGTTTTGAAACTCT;RSEQ=TTTTTGTGGAATCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:15.5:1:30.5:1:1:3.1622:33:4:0.2857:0:6.5 0/0:1:0:0,0:1,0:0:0,0:31:0:31:0:1:0:34:2:1:0:5 -2 92318600 . T C 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02778;SOR=Inf;LSEQ=GCAGTTTTGAAACTCTCTTT;RSEQ=TGTGGAATCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:25:1:30.4:1:1:0:29.9:14:1:0:4.6 1/1:2:2:2,0:0,0:1:0,0:18:1:29.5:1:1:0:40.5:4:1:0:3.5 -2 92318607 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAACTCTCTTTTTGTGGA;RSEQ=TCTGCAAGTGGATATTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:0.25:2,2:26.5:1:31.5:1:0.46429:3.87298:33:4:0.25:0:6.5 0/0:2:0:0,0:2,0:0:0,0:25:1:29.5:1:1:0:40.5:4:1:0:3.5 -2 92318615 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTTGTGGAATCTGCAA;RSEQ=TGGATATTTGTCTAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:34.5:1:30:1:1:2.64575:33:4:0.2:0:6.5 0/0:4:0:0,0:2,2:0:2,0:15.5:1:29:1:1:0:37.8:8:1:0:3.3 -2 92318616 . T C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51648;SOR=0;LSEQ=CTTTTTGTGGAATCTGCAAG;RSEQ=GGATATTTGTCTAGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:4,2:0.2727:2,2:9.3:1:32.7:1:1:1:36:6:0.2727:0:2.3 0/0:4:0:0,0:2,1:0:2,0:20.3:1:27.7:1:1:0:43.3:6:0.75:0:2.7 -2 92318626 . T G 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4965;SOR=0;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:3,1:0.3333:2,2:39.3:1:31:1:1:1.41418:31:6:0.3333:0:6.3 0/0:4:0:0,0:2,1:0:2,0:23.7:1:26.7:1:1:0:43.3:6:0.75:0:2.7 -2 92318631 . C A 46 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GCAAGTGGATATTTGTCTAG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:3,3:0.3:2,2:37.7:1:29.3:1:1:1.85:31:6:0.3:0:6.3 0/0:4:0:0,0:2,2:0:2,0:23.5:1:30.8:1:1:0:37.8:8:1:0:3 -2 92318638 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16374;SOR=Inf;LSEQ=GATATTTGTCTAGCTTTGAG;RSEQ=ATTTCGTTGGAAACGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:26.4:1:30.4:1:1:0:40.2:22:1:0:3.1 0/1:8:2:1,1:4,2:0.25:2,2:35:1:28.5:1:1:1.8258:48:4:0.2857:0:1.5 -2 92318660 . CA AT 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07792;SOR=Inf;LSEQ=TTTCGTTGGAAACGGGATTA;RSEQ=TATAAAAAGCAGACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,5:0:2,0:29.3:1:29.4:1:1:0:41.7:10:0.9091:0:1.9 0/1:10:3:1,2:4,3:0.3:2,2:31.3:1:30:1:1:2.41422:34:6:0.3:0:4.3 -2 92318664 . T TA 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.21739;SOR=Inf;LSEQ=GTTGGAAACGGGATTACATA;RSEQ=AAAAAGCAGACAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:29.3:1:28.8:1:1:0:41:24:1:0:2.3 0/1:11:2:1,1:4,5:0.1818:2,2:27:1:26.5:1:1:1.22:40.5:4:0.1818:0:6 -2 92318666 . A T 43 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.59006;SOR=0.28733;LSEQ=TGGAAACGGGATTACATATA;RSEQ=AAAGCAGACAGCAGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:5,4:0.25:2,2:36.7:1:27.7:1:1:2.31595:58.3:6:0.25:0:2 0/1:12:1:0,1:6,5:0.0833:2,0:34:0:30:0:1:0:34:2:0.0909:0:2 -2 92318680 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.48308;SOR=0;LSEQ=CATATAAAAAGCAGACAGCA;RSEQ=CATTCCCAGAATCTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:0.1429:2,2:36:1:32:1:1:1.37:60:4:0.1429:0:2.5 0/0:12:0:0,0:5,5:0:2,0:32.4:1:32.7:1:1:0:46.9:20:0.9091:0:1 -2 92318709 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=GAATCTTGTTTGTGATGTTT;RSEQ=CATTCAAGTCACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:5,9:0.125:2,2:28.5:1:32.5:1:1:1.73:46.5:4:0.125:0:1.5 0/0:12:0:0,0:6,6:0:2,0:22.9:1:31.9:1:1:0:47.8:24:1:0:1.7 -2 92318718 . TCA T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49351;SOR=0;LSEQ=TTGTGATGTTTGCATTCAAG;RSEQ=CAGAGTTGAACATTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:4,7:0.1538:2,2:30.5:1:29.5:1:1:1.67:23:4:0.1538:0:1.5 0/0:9:0:0,0:5,4:0:2,0:21.7:1:31:1:1:0:50.6:18:1:0:1.9 -2 92318747 . C G 86 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACATTCCCTTTCAGAGA;RSEQ=CAGGTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:20.5:1:33.3:1:1:0:25.3:12:1:0:1.7 1/1:1:1:1,0:0,0:1:0,0:2:0:29:0:1:0:60:2:1:0:1 -2 92318769 . G A 32 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGTTTGAAACACTCTTTTT;RSEQ=TAGTATCTGGATGTGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:16:1:32.5:1:0.33333:0:31.5:4:0.6667:0:2 1/1:1:1:0,1:0,0:1:0,0:3:0:23:0:1:0:40:2:1:0:6 -2 92318832 . C T 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=GTGAAAAAGGAAATATCTTC;RSEQ=CCTGAAAACTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:14.3:1:32.3:1:1:0:20.7:6:1:0:0.7 1/0:5:3:1,2:2,0:0.6:0,2:36.7:1:30:1:0.4:0:40:6:0.6:0:3 -2 92318939 . T C 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09023;SOR=Inf;LSEQ=CAGTTTTGAAACACTCTTTT;RSEQ=GTAAAATCTGCAAGAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:32.8:1:28.8:1:1:0:21.5:10:1:0:0.8 0/1:11:4:3,1:3,4:0.3636:2,2:31.8:1:31:1:0.54545:3.52:29.3:8:0.3636:0:1.8 -2 92318944 . A T 59 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.63512;SOR=0.40612;LSEQ=TTGAAACACTCTTTTTGTAA;RSEQ=ATCTGCAAGAGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:3,4:0.3636:2,2:24:1:29.5:1:1:1.30:21.5:8:0.3636:0:1.5 0/1:11:2:1,1:5,4:0.1818:2,2:29.5:1:21.5:1:1:1.22474:20.5:1:0.1:0:2 -2 92318963 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22078;SOR=Inf;LSEQ=AAATCTGCAAGAGGATATTT;RSEQ=GATAGCTTTGAGGATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:26.5:1:32.2:1:1:0:21.5:20:1:0:0.7 0/1:12:3:3,0:3,6:0.25:2,0:6.7:1:26:1:0.18182:0:32.3:2:0.2:0:2.3 -2 92318964 . G C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=AATCTGCAAGAGGATATTTG;RSEQ=ATAGCTTTGAGGATTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:25.7:1:31.4:1:1:0:21.5:20:1:0:0.7 0/1:11:2:1,1:4,5:0.1818:2,2:14:0:30:1:1:1.22:22.5:4:0.2:0:2 -2 92318982 . A T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGATAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGATTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,1:0.4:2,0:24:1:31:1:1:0:21:4:0.4:0:1.5 0/1:5:2:1,1:1,2:0.4:2,2:24.5:1:32:1:1:1.73:22:4:0.4:0:1.5 -2 92319034 . G A 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACAGAAGCATTCTCAGAA;RSEQ=CTTCATTGGGATGTTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:18.5:1:31:1:1:0:22.5:4:1:0:0 0/1:12:2:1,1:6,4:0.1667:2,2:9:1:26:1:1:1.4491:21:4:0.1818:0:2 -2 92319053 . A G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTTCATTGGGATGTTTCA;RSEQ=TTGAAGTCACAGTGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:28.7:1:30.7:1:1:0:21.7:6:1:0:0.3 0/1:16:2:0,2:9,5:0.125:2,0:44:1:29:0:0.175:0:23:4:0.125:0:1.5 -2 92319115 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TTGAAACACTCTTTTTGTAG;RSEQ=ATCTGGAAGTGGACATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:26.3:1:28:1:1:0:30.4:28:1:0:3 0/1:32:2:1,1:15,15:0.0625:2,2:45:1:31:1:1:1:45:4:0.0645:0:3 -2 92319123 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCTTTTTGTAGTATCTGGA;RSEQ=GTGGACATTTGGAGAGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:28.9:1:30:1:1:0:30.6:28:1:0:3.2 0/1:32:2:1,1:14,16:0.0625:2,2:14.5:1:31.5:1:1:1.14:24:4:0.0625:0:4 -2 92319144 . CT TA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14444;SOR=0;LSEQ=GTGGACATTTGGAGAGATCT;RSEQ=GGACTACGGTGAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:39.5:1:30.3:1:1:1:24:4:0.1429:0:3 0/0:22:0:0,0:7,15:0:2,0:22.2:1:30.9:1:1:0:35.4:44:1:0:2.6 -2 92319145 . T A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=TGGACATTTGGAGAGATCTC;RSEQ=GGACTACGGTGAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:6,6:0,0:0.8571:0,2:30.8:1:31.3:1:1:0:32.1:24:1:0:3.3 1/1:21:21:6,15:0,0:1:0,2:22.8:1:29.8:1:1:0:35.2:20:1:0:2.8 -2 92319149 . C A 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3547;SOR=0.27938;LSEQ=CATTTGGAGAGATCTCTGGA;RSEQ=TACGGTGAAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:6,7:1,0:0.9286:0,2:30.5:1:31:1:1:0:31.5:26:0.9286:0:3.2 1/0:18:14:4,10:1,3:0.7778:2,2:25.7:1:29.4:1:1:1.19:34.6:28:0.7778:0:3.1 -2 92319158 . A T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.09138;SOR=0.14611;LSEQ=AGATCTCTGGACTACGGTGA;RSEQ=AAAGGAAATATCTTCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:4,7:1,0:0.9167:0,2:29.9:1:29.5:1:0.41667:0:30.9:22:0.9167:0:3.4 1/0:15:9:2,7:2,4:0.6:2,2:32.3:1:28.4:1:1:1.68385:31:18:0.6:0:3.4 -2 92319173 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=GGTGAAAAAGGAAATATCTT;RSEQ=CAATAAAAGCTAGATAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:0.1818:2,2:18.5:1:31.5:1:1:1.22:46:4:0.1818:0:4 0/0:11:0:0,0:2,9:0:2,0:23.7:1:30.5:1:1:0:31.7:22:1:0:3.3 -2 92319244 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=ACTCAGCTAACAGAGTTGAA;RSEQ=ATTTCTTTTGAGAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:14.5:1:32.2:1:1:0:24.5:12:1:0:4.8 0/1:5:2:1,1:2,1:0.4:2,2:35.5:1:30:1:1:1.7321:45:4:0.4:0:5 -2 92319247 . T G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=CAGCTAACAGAGTTGAACAT;RSEQ=TCTTTTGAGAGAGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:8.5:1:31:1:1:1:32:4:0.2857:0:5 0/0:5:0:0,0:3,2:0:2,0:24.2:1:30.4:1:1:0:30.6:10:1:0:3.4 -2 92319249 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=GCTAACAGAGTTGAACATTT;RSEQ=TTTTGAGAGAGCAGTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:15.5:1:32:1:1:0:23.4:16:1:0:5.1 0/1:5:2:1,1:2,1:0.4:2,2:40.5:1:30:1:1:1.7321:45:4:0.4:0:5 -2 92319252 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=AACAGAGTTGAACATTTCTT;RSEQ=TGAGAGAGCAGTTTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:17.8:1:27.5:1:1:0:23.4:7:1:0:5.1 0/1:6:2:1,1:2,2:0.3333:2,2:43:1:31.5:1:1:1:45:4:0.3333:0:5 -2 92319253 . T A 66 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03097;SOR=0;LSEQ=ACAGAGTTGAACATTTCTTT;RSEQ=GAGAGAGCAGTTTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:0.625:2,2:14.8:1:28.8:1:1:2.60:20.6:10:0.625:0:6 0/0:6:0:0,0:3,3:0:2,0:23:1:29.5:1:1:0:29:12:1:0:2.8 -2 92319256 . G C 75 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13753;SOR=0.14176;LSEQ=GAGTTGAACATTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:0.625:2,2:17.8:1:32.4:1:1:2.60:20.6:10:0.625:0:6 0/1:6:1:1,0:2,3:0.1667:2,0:25:0:27:0:1:0:20:2:0.1667:0:4 -2 92319260 . G A 69 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03097;SOR=0;LSEQ=TGAACATTTCTTTTGAGAGA;RSEQ=CAGTTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:0.625:2,2:21.8:1:30:1:1:2.60:20.6:10:0.625:0:6 0/0:6:0:0,0:2,3:0:2,0:24.2:1:30.8:1:1:0:30.8:10:1:0:2.6 -2 92319280 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=GCAGTTTTGAAACACTCTTT;RSEQ=TGTGGAATCTGCAAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:36:0:33:0:1:1.29:32:4:0.25:0:5 0/0:6:0:0,0:3,3:0:2,0:21.8:1:28.8:1:1:0:28.7:12:1:0:3.8 -2 92319288 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GAAACACTCTTTTTGTGGAA;RSEQ=CTGCAAGTGGATATTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:28:0:33:1:1:1.29:32:4:0.2222:0:5 0/0:5:0:0,0:2,3:0:2,0:24.4:1:28.8:1:1:0:30.4:10:1:0:4 -2 92319294 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=Inf;LSEQ=CTCTTTTTGTGGAATCTGCA;RSEQ=GTGGATATTTGTCTAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:32.4:1:28.7:1:1:0:23.3:8:1:0:4.9 0/1:5:2:1,1:1,2:0.4:2,2:15.5:1:29:1:1:1.73:45:4:0.4:0:5 -2 92319299 . A C 64 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.1049;SOR=0;LSEQ=TTTGTGGAATCTGCAAGTGG;RSEQ=TATTTGTCTAGCTTTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:0.5:2,2:40:1:32.3:1:1:1:20:8:0.5:0:6 0/0:5:0:0,0:2,3:0:2,0:22.2:1:29.6:1:1:0:30.4:10:1:0:4 -2 92319304 . T G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=GGAATCTGCAAGTGGATATT;RSEQ=GTCTAGCTTTGAGGATTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:33:1:31:1:1:1:23:4:0.25:0:4.5 0/0:4:0:0,0:1,3:0:2,0:25.8:1:29.8:1:1:0:26.8:8:1:0:3.8 -2 92319306 . T G 96 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05455;SOR=0;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:27.3:1:32.1:1:1:0:23.8:16:1:0:5.4 0/1:3:1:0,1:0,2:0.3333:0,0:42:0:34:0:1:0:20:2:0.3333:0:8 -2 92319309 . A G 33 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.44322;LSEQ=CTGCAAGTGGATATTTGTCT;RSEQ=GCTTTGAGGATTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:7:0:33:1:1:1:32:4:0.25:0:5 0/1:3:1:0,1:0,2:0.3333:0,0:45:0:32:0:1:0:20:2:0.3333:0:8 -2 92319311 . C A 77 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=0.20187;LSEQ=GCAAGTGGATATTTGTCTAG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:1,1:0.75:2,2:29.7:1:30:1:1:1:21:12:0.75:0:5.5 0/1:3:1:0,1:0,2:0.3333:0,0:47:0:32:0:1:0:20:2:0.3333:0:8 -2 92319793 . T A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTTTGAAACACTCTTTTTGT;RSEQ=GTATCTGGAAGTGGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23.5:1:29:1:1:0:30:4:1:0:2.5 1/1:2:2:2,0:0,0:1:0,0:28:1:30:0:1:0:24.5:4:1:0:4 -2 92319822 . C T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.44135;LSEQ=AAGTGGACATTTGGAGCGCT;RSEQ=TCAGGACTACGGTGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:22:0:32:0:1:0:40:2:0.3333:0:4 0/1:7:3:3,0:4,0:0.4286:0,0:17.3:1:30.3:1:1:0:34.3:6:0.4286:0:4.3 -2 92319828 . A C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=ACATTTGGAGCGCTCTCAGG;RSEQ=CTACGGTGAAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:28:0:34:0:1:0:40:2:0.3333:0:4 0/1:7:3:3,0:4,0:0.4286:0,0:23.3:1:32.7:1:1:0:34.3:6:0.4286:0:4.3 -2 92319831 . A G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGGAGCGCTCTCAGGACT;RSEQ=CGGTGAAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:26:1:27.3:1:1:0:33.3:6:1:0:3 0/1:7:2:2,0:5,0:0.2857:0,0:23:1:33:1:1:0:33:4:0.2857:0:2.5 -2 92319832 . C T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.41421;LSEQ=TTGGAGCGCTCTCAGGACTA;RSEQ=GGTGAAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:36:1:32.5:1:1:0:40:4:0.6667:0:3 0/1:7:3:3,0:4,0:0.4286:0,0:26.3:1:30.7:1:1:0:34.3:6:0.4286:0:4.3 -2 92319872 . A G 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01894;SOR=0;LSEQ=TCCAATAAAAGCTACATAGA;RSEQ=GCAATGTCAGAAACTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:16:1:30:1:0.4:0:45:4:0.4:0:1 0/0:28:0:0,0:17,11:0:2,0:23.3:1:29.3:1:1:0:35.5:27:1:0:1.5 -2 92319885 . A T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATAGAAGCAATGTCAGAA;RSEQ=CTTTTTCATGATGTATCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:21.6:1:29.7:1:1:0:36.3:14:1:0:2 0/1:27:2:1,1:15,10:0.0741:2,2:19:1:24.5:1:1:1.47706:33:4:0.0741:0:3 -2 92319894 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CAATGTCAGAAACTTTTTCA;RSEQ=GATGTATCTACTCAGCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:24.3:1:30.1:1:1:0:36.3:14:1:0:1.7 0/1:29:2:1,1:15,12:0.069:2,2:34:0:31.5:1:1:1.24034:45:4:0.069:0:2 -2 92319900 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAAACTTTTTCATGATGT;RSEQ=TCTACTCAGCTAACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:26.9:1:29:1:1:0:36.3:14:1:0:1.7 0/1:29:2:0,2:15,12:0.069:2,0:25.5:1:30:1:0.22414:0:33:4:0.069:0:3.5 -2 92319928 . TCT CC 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.56203;SOR=Inf;LSEQ=AGCTAACAGAGTTGAACCTT;RSEQ=TTTGAGAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:32.4:1:30.6:1:1:0:33.4:14:1:0:1.6 0/1:28:4:1,3:10,14:0.1429:2,2:36.5:1:30.7:1:1:2.0895:39:8:0.1429:0:1.8 -2 92319930 . T C 115 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08293;SOR=7.87281;LSEQ=CTAACAGAGTTGAACCTTTC;RSEQ=TTTGAGAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:2,4:0.1429:2,0:45:0:34:0:1:0:40:2:0.1429:0:1 1/0:24:14:7,7:3,7:0.5833:2,2:18.3:1:30.4:1:0.42122:2.25:34.9:28:0.5833:0:1.1 -2 92319934 . G A 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03977;SOR=0;LSEQ=CAGAGTTGAACCTTTCTTTT;RSEQ=AGAGAGCAGTTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:22.5:1:28.5:1:1:3.16:22:4:0.2857:0:2.5 0/0:26:0:0,0:9,17:0:2,0:22.3:1:31.1:1:1:0:34.9:52:1:0:1.2 -2 92320067 . T C 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTAACTTCCTTGTGATGT;RSEQ=TGCATTCAAGTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:11:0:32:0:1:0:40:2:1:0:5 1/1:7:7:5,2:0,0:1:0,2:7:1:32.6:1:1:0:38.6:14:1:0:4.6 -2 92320077 . G T 102 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24451;SOR=4.40909;LSEQ=CTTGTGATGTTTGCATTCAA;RSEQ=TCACAGAGTTGAACATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:11.5:1:30.5:1:1:1:31:4:0.5:0:5 1/1:12:10:5,5:2,0:0.8333:0,2:11.8:1:30.9:1:0.4697:0:40.2:20:0.8333:0:4.2 -2 92320090 . A G 131 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=CATTCAAGTCACAGAGTTGA;RSEQ=CATTCCCTTTCATAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,0:0.8:0,2:20.8:1:32.3:1:1:0:40.8:8:0.8:0:3.3 1/1:15:15:9,6:0,0:1:0,2:20.8:1:33.7:1:1:0:39.6:30:1:0:3.9 -2 92320110 . G C 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATTCCCTTTCATAGAGCA;RSEQ=GTTTGAAACACTCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:26.1:1:31.4:1:1:0:40.2:20:1:0:2.4 0/1:32:2:1,1:17,13:0.0625:2,2:49:0:30.5:1:1:1.29665:40:4:0.0645:0:5 -2 92320114 . T G 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.65317;SOR=0.40105;LSEQ=TCCCTTTCATAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:5,6:1,0:0.9167:0,2:27:1:31:1:1:0:40.2:22:0.9167:0:2.5 1/1:32:26:14,12:4,2:0.8125:2,2:28.4:1:31.5:1:0.67223:1.68636:40.3:52:0.8125:0:3.3 -2 92320125 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCAGGTTTGAAACACTCT;RSEQ=TTTGTAGTATCTGGATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:31.2:1:30.2:1:1:0:40.2:26:1:0:2.5 0/1:42:2:1,1:20,20:0.0476:2,2:26.5:1:31:1:1:1:40:4:0.0488:0:2 -2 92320135 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACACTCTTTTTGTAGTA;RSEQ=CTGGATGAGGACATTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:29.8:1:30.5:1:1:0:40.1:14:1:0:2.2 0/1:44:2:1,1:21,21:0.0455:2,2:19:1:29.5:1:1:1:30:4:0.0476:0:6 -2 92320145 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTGTAGTATCTGGATGAG;RSEQ=ACATTTGGAGCGCTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:28.9:1:32:1:1:0:40.1:30:1:0:2.2 0/1:44:2:1,1:21,21:0.0455:2,2:19:1:28:1:1:1:30:4:0.0488:0:6 -2 92320167 . C G 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=23.3137;LSEQ=CATTTGGAGCGCTTTCAGGC;RSEQ=TATGGTGAAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:4,5:0.3571:2,2:22.8:1:31.4:1:1:1.18452:36.8:10:0.3571:0:3.2 1/1:31:29:13,16:0,1:0.9355:0,2:22.6:1:30.4:1:1:0:39.4:58:0.9667:0:3 -2 92320194 . C G 108 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAAGGAAATATCTTCCC;RSEQ=TGAAAACTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:16.5:1:31.8:1:1:0:40:8:1:0:3 1/1:11:11:4,7:0,0:1:0,2:14.5:1:31.5:1:1:0:37.5:22:1:0:3.6 -2 92320196 . G A 91 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGAAATATCTTCCCCT;RSEQ=AAAACTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:14.5:1:29.5:1:1:0:40:8:1:0:3 1/1:8:8:3,5:0,0:1:0,2:17.1:1:30.6:1:1:0:36.3:16:1:0:4 -2 92320303 . A G 53 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=AATCTGCAAGAGGATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:20.7:1:34:0:1:0:20.3:6:1:0:5 -2 92320342 . A T 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGATTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:41:1:28.7:1:1:0:20.3:6:1:0:5 -2 92320344 . T G 46 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAGCTTTGAGGATTTCAT;RSEQ=GGAAACGGGATTGTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:3,0:1,0:0.75:0,0:39.3:1:29.3:1:1:0:20.3:6:0.75:0:5 -2 92320355 . T A 78 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTTCATTGGAAACGGGA;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:6,1:0,0:1:0,2:18.7:1:27.9:1:1:0:24:14:1:0:5.4 -2 92320358 . T G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCATTGGAAACGGGATTG;RSEQ=CTTCATATAAACTCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:2,0:7,1:0.2:2,0:9.5:1:32:1:1:0:22.5:4:0.2:0:7 -2 92320364 . T G 73 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51471;SOR=Inf;LSEQ=TGGAAACGGGATTGTCTTCA;RSEQ=ATAAACTCTAGACAGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:3.5:1:31.5:1:1:0:24:4:1:0:5.5 0/1:15:6:4,2:9,0:0.4:0,2:17.2:1:28.5:1:0.14286:0:23.8:12:0.4:0:4.5 -2 92320365 . A G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05848;SOR=0;LSEQ=GGAAACGGGATTGTCTTCAT;RSEQ=TAAACTCTAGACAGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:4.5:1:32:1:1:0:24:4:1:0:5.5 0/1:17:3:3,0:11,2:0.1765:2,0:7:1:33:1:1:0:31:6:0.1765:0:5.3 -2 92320374 . A G 53 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGTCTTCATATAAACTCT;RSEQ=GACAGAAGCATTCTCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:6.4:1:30:1:1:0:33.7:14:1:0:3.9 0/1:23:3:3,0:16,4:0.1304:2,0:17.3:1:34:0:1:0:38:6:0.1304:0:6 -2 92320394 . G A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19164;SOR=5.51539;LSEQ=AGACAGAAGCATTCTCAGAA;RSEQ=CTTCATTGGGATGTTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:9,1:1,0:0.8333:0,2:20.8:1:31.2:1:1:0:34.4:20:0.8333:0:4.2 1/1:30:29:20,9:1,0:0.9667:0,2:25.6:1:30:1:1:0:36.9:58:0.9667:0:4.8 -2 92320397 . T G 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48893;SOR=0.53187;LSEQ=CAGAAGCATTCTCAGAAGCT;RSEQ=CATTGGGATGTTTCAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:5,1:5,0:0.5:0,2:28.2:1:33.7:1:1:0:37.2:12:0.5455:0:4.8 0/1:32:11:9,2:13,8:0.3438:2,2:29.1:1:32.8:1:0.42502:2.69:38.1:22:0.3438:0:5.4 -2 92320399 . A T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65629;SOR=0.37847;LSEQ=GAAGCATTCTCAGAAGCTTC;RSEQ=TTGGGATGTTTCAATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:9,1:1,0:0.9091:0,2:25.8:1:32.8:1:1:0:34.4:20:0.9091:0:4.2 1/0:33:26:17,9:1,0:0.7879:0,2:25.2:1:30.8:1:1:0:37.7:52:0.7879:0:4.2 -2 92320407 . G A 29 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04969;SOR=0;LSEQ=CTCAGAAGCTTCATTGGGAT;RSEQ=TTTCAATTGAAGTCACAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:10,3:0.125:2,0:22.5:1:29.5:1:1:0:41:4:0.125:0:3.5 0/0:54:0:0,0:32,22:0:2,0:22.6:1:31.4:1:1:0:39.1:108:1:0:3.8 -2 92320412 . A G 97 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10269;SOR=Inf;LSEQ=AAGCTTCATTGGGATGTTTC;RSEQ=ATTGAAGTCACAGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:14,6:0:2,0:25.4:1:30.7:1:1:0:38.6:40:1:0:4 0/1:60:9:6,3:27,23:0.15:2,2:27.2:1:30.9:1:0.71763:1.69:39.3:18:0.1525:0:5.2 -2 92320422 . A C 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47285;SOR=1.55376;LSEQ=GGGATGTTTCAATTGAAGTC;RSEQ=CAGTGTTGAACATTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:6,5:9,4:0.4583:2,2:27.6:1:28.8:1:0.67517:1.82559:37.1:10:0.4348:0:4.5 1/0:65:37:21,16:13,15:0.5692:2,2:28.1:1:30.4:1:0.45917:1.50:39.2:74:0.5692:0:4.4 -2 92320440 . T A 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.378;SOR=0.45619;LSEQ=TCACAGTGTTGAACATTCCC;RSEQ=TTCATAGAGCAGGTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:2,1:13,8:0.125:2,2:31.7:1:29.3:1:1:1.22:27.7:6:0.125:0:5.3 0/1:66:4:2,2:32,30:0.0606:2,2:21:1:28.5:1:1:1.06559:22:8:0.0606:0:5.8 -2 92320443 . C T 86 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10205;SOR=Inf;LSEQ=CAGTGTTGAACATTCCCTTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:0:2,0:28.2:1:31.3:1:1:0:36.8:48:1:0:3.9 0/1:65:8:5,3:28,29:0.1231:2,2:22:1:28.8:1:0.70847:1.71:41.3:16:0.125:0:5.1 -2 92320445 . T C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33223;SOR=0.58898;LSEQ=GTGTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:8,4:7,5:0.5:2,2:28.3:1:32.8:1:1:1.41:37.5:24:0.5:0:3.5 0/1:65:24:11,13:22,18:0.3692:2,2:29.6:1:31.6:1:0.60661:1.43609:40.7:48:0.3692:0:2.7 -2 92320453 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCCTTTCATAGAGCAG;RSEQ=TTTGAAACACTCTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:14,8:0:2,0:26.3:1:30.6:1:1:0:38:44:1:0:4.1 0/1:65:2:1,1:32,31:0.0308:2,2:17.5:1:30:1:1:1.03176:47:4:0.0308:0:4 -2 92320456 . T G 90 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1035;SOR=Inf;LSEQ=TCCCTTTCATAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:0:2,0:23.7:1:29.4:1:1:0:37.5:46:1:0:4 0/1:64:8:5,3:27,29:0.125:2,2:9.9:1:30.3:1:0.70785:1.77:41.3:16:0.125:0:5.1 -2 92320462 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06816;SOR=0;LSEQ=TCATAGAGCAGGTTTGAAAC;RSEQ=CTCTTTTTGTAGTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:0.0952:2,2:16:1:31.5:1:1:1.66897:42:4:0.0952:0:3 0/0:58:0:0,0:27,31:0:2,0:19:1:29.6:1:1:0:40.2:116:1:0:3.4 -2 92320471 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07432;SOR=0;LSEQ=AGGTTTGAAACACTCTTTTT;RSEQ=TAGTATCTGGATGTGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:7:1:29:1:1:1.13389:42:4:0.1176:0:3 0/0:44:0:0,0:18,26:0:2,0:16.3:1:31.7:1:1:0:39:88:1:0:3.1 -2 92320474 . G C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54931;SOR=1.70571;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=TATCTGGATGTGGACATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:6,5:0.3125:2,2:26.2:1:32.2:1:1:1.73457:39.4:10:0.3125:0:4.4 0/1:41:18:5,13:11,12:0.439:2,2:21.3:1:32:1:0.21788:2.33282:39.9:36:0.439:0:4 -2 92320476 . A G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14933;SOR=0.23462;LSEQ=TGAAACACTCTTTTTGTAGT;RSEQ=TCTGGATGTGGACATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:2,5:0.3:2,0:22.3:1:33:1:1:0:45.3:6:0.3:0:6.7 0/1:23:2:0,2:7,14:0.087:2,0:35:1:33:0:1:0:31:4:0.087:0:8 -2 92320480 . GG AT 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55458;SOR=0.34886;LSEQ=ACACTCTTTTTGTAGTATCT;RSEQ=ATGTGGACATTTGGAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,5:0.25:2,0:26.5:1:31.3:1:1:0:47.5:4:0.25:0:7 0/1:20:2:0,2:5,13:0.1:2,0:30:1:31:0:1:0:31:4:0.1:0:7 -2 92320483 . T A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.76929;LSEQ=CTCTTTTTGTAGTATCTGGA;RSEQ=GTGGACATTTGGAGCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:1,6:0,1:0.875:0,2:25.3:1:32.6:1:1:0:40:14:0.875:0:5 1/1:19:16:3,13:2,1:0.8421:2,2:19.3:1:30.9:1:0.1548:7.43427:36.6:32:0.8421:0:4.4 -2 92320487 . G A 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56334;SOR=0.39125;LSEQ=TTTTGTAGTATCTGGATGTG;RSEQ=ACATTTGGAGCGCTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,5:0.25:2,0:20.5:1:31.5:1:1:0:47.5:4:0.25:0:7 0/1:18:2:0,2:5,11:0.1111:2,0:24:1:32:0:1:0:31:4:0.1111:0:7 -2 92320496 . A C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61603;LSEQ=ATCTGGATGTGGACATTTGG;RSEQ=GCGCTTTCAGGCCTATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,5:0.25:2,0:11.5:1:31:0:1:0:47.5:4:0.25:0:7 0/1:12:2:0,2:3,7:0.1667:2,0:15:1:32:0:1:0:31:4:0.1667:0:7 -2 92320498 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76221;LSEQ=CTGGATGTGGACATTTGGAG;RSEQ=GCTTTCAGGCCTATGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,5:0.25:2,0:9.5:1:31:0:1:0:47.5:4:0.25:0:7 0/1:10:2:0,2:3,5:0.2:2,0:13:1:31.5:1:1:0:31:4:0.2:0:7 -2 92320508 . C T 57 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.43179;LSEQ=ACATTTGGAGCGCTTTCAGG;RSEQ=CTATGGTGAAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:11.5:1:31:0:1:0:32.5:4:0.6667:0:5 0/1:9:4:1,3:2,3:0.4444:2,2:9.3:1:28.5:1:1:1.8525:30.5:8:0.4444:0:4.8 -2 92320512 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=TTGGAGCGCTTTCAGGCCTA;RSEQ=GGTGAAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:7.5:1:28.5:1:1:0:32.5:4:0.6667:0:5 0/1:5:2:0,2:2,1:0.4:2,0:11.5:1:30.5:1:0.4:0:32:4:0.4:0:5.5 -2 92320666 . G C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AATCTGCAAGAGGATATTTG;RSEQ=ATAGATTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:11.5:1:31.5:1:1:0:40:4:0.6667:0:3.5 0/0:2:0:0,0:0,1:0:0,0:2:0:31:0:1:0:20:2:1:0:3 -2 92320670 . GA G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAGAGGATATTTGGATA;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:21:1:30.9:1:1:1:21:4:0.5:0.25:1 0/0:1:0:0,0:1,0:0:0,0:45:0:25:0:1:0:22:2:1:0:3 -2 92320684 . G T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATAGATTTGAGGATTTC;RSEQ=TTGGAAACGGGATTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:29.5:1:31.5:1:1:1:40:4:0.5:0:3.5 0/0:1:0:0,0:1,0:0:0,0:32:0:26:0:1:0:22:2:1:0:3 -2 92320712 . C A 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=CGGGATTGTCTTCATATAAA;RSEQ=TCTAGACAGAAGCATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:20:0:32.5:1:1:0:40:4:0.6667:0:3.5 0/0:2:0:0,0:1,1:0:2,0:14.5:1:29.5:1:1:0:22:4:1:0:2 -2 92320794 . G T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTCCCTTTCATAGAGCA;RSEQ=GTTTGAAACAATCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:29:1:1:1:25:4:0.5:0:1.5 -2 92320953 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TAACAGAGTTGAACCTTTCT;RSEQ=TTGAGAGAGCAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:30:1:1:0:43:4:1:0:4 0/0:1:0:0,0:1,0:0:0,0:27:0:33:0:1:0:22:2:1:0:4 -2 92320963 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACCTTTCTTTTGAGAGAG;RSEQ=AGTTTTGAAACCCTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:31:1:30.5:1:1:0:43:4:0.6667:0:4 0/0:1:0:0,0:1,0:0:0,0:37:0:33:0:1:0:22:2:1:0:4 -2 92320983 . T G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=CAGTTTTGAAACCCTCTTTT;RSEQ=GTGGAATCTGCAAGTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:31:1:31:1:1:1:43:4:0.5:0:4 0/0:3:0:0,0:1,1:0:2,0:27.5:1:30:1:1:0:35.5:4:0.6667:0:4 -2 92320994 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCCTCTTTTTGTGGAATCTG;RSEQ=AAGTGGATATTTGTCTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:27:1:28.5:1:1:1:43:4:0.5:0:4 0/0:3:0:0,0:2,1:0:2,0:24.3:1:32.3:1:1:0:30.3:6:1:0:5 -2 92321008 . T G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:22:1:30:1:1:0:38.8:10:1:0:1.8 1/0:4:2:1,1:1,0:0.5:0,2:31.5:1:33.5:1:1:0:34.5:4:0.5:0:5.5 -2 92321053 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGGGATTACATATAAAAAG;RSEQ=AGACAGCAGCATTCCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:19.4:1:32.6:1:1:0:32.8:10:1:0:0.6 0/1:11:2:1,1:4,5:0.1818:2,2:29.5:1:30.5:1:1:1.22:20:4:0.1818:0:6 -2 92321068 . C T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.3127;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGTAACTTCTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:3,3:0.1429:2,0:1:0:29:0:1:0:23:2:0.1429:0:2 0/1:11:2:1,1:4,5:0.1818:2,2:29.5:1:30.5:1:1:1.22:20:4:0.1818:0:6 -2 92321071 . G T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49474;SOR=Inf;LSEQ=AGCAGACAGCAGCATTCCCA;RSEQ=TAACTTCTTTGTGATGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:16.5:1:32.1:1:1:0:31.9:16:1:0:1.1 0/1:12:2:1,1:5,5:0.1667:2,2:27:1:30:1:1:1:20:4:0.1667:0:6 -2 92321080 . T C 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13725;SOR=0;LSEQ=CAGCATTCCCAGTAACTTCT;RSEQ=TGTGATGTTTGCATTCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:12.5:1:32.5:1:1:1.41418:23:4:0.2857:0:1.5 0/0:11:0:0,0:5,6:0:2,0:34.2:1:30.9:1:1:0:36.9:22:1:0:1.3 -2 92321091 . G T 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13725;SOR=0;LSEQ=GTAACTTCTTTGTGATGTTT;RSEQ=CATTCAAGTCACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:33:0:31.5:1:1:1.41418:44.5:4:0.2857:0:1.5 0/0:11:0:0,0:5,6:0:2,0:26.8:1:32.6:1:1:0:36.9:22:1:0:1.3 -2 92321303 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTTTCTTTTGATAGAGCA;RSEQ=TTTTGAAACACACTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:4:0:32:0:1:0:22:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:30:1:1:1:43:4:0.5:0:2.5 -2 92321351 . A C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGAGGATATTTGGATAG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:44.5:1:32.5:1:1:0:30.5:4:1:0:3 -2 92321487 . G C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGCAGGTTTGAAACACT;RSEQ=TTTTTGTAGTATCTGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:33:1:1:0:46:4:1:0:4 -2 92321522 . T A 68 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGTGGACATTTTGAGAG;RSEQ=TCTCAGGAATACGGTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:1:0,2:32.6:1:29.6:1:1:0:43.8:10:1:0:2.8 -2 92321539 . AA TT 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTCTCAGGAATACGGTG;RSEQ=AAAGGAAATATCTTCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:17:1:28:1:1:1.7321:46:4:0.4:0:3 -2 92321540 . A T 45 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTCTCAGGAATACGGTGA;RSEQ=AAAGGAAATATCTTCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:0,0:0.6:0,2:28.7:1:29:1:1:0:42.3:6:1:0:2 -2 92321617 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATGTATCTACTCAGCTAAC;RSEQ=GAGTTGAACCTTTCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:34.5:1:29.5:1:1:0:45:4:0.6667:0:2.5 -2 92321632 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAACAGAGTTGAACCTTTC;RSEQ=TTTCAGAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:27:0:32.5:1:1:0:45:4:0.6667:0:2.5 -2 92321678 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTGTGGAATCTGCAAG;RSEQ=GGATATTTGTCTAGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:32:1:1:0:44:4:1:0:4.5 -2 92321688 . TC GA 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=TAGCTTTGAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:21:0:32.3:1:1:1:44:4:0.5:0:3.5 -2 92321722 . C A 61 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCGTTGGAAACGGGATTA;RSEQ=TTATAAAAAGCAGACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:29.3:1:30.5:1:1:0:35:8:1:0:2.8 -2 92322002 . GTG CCT 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTTGAAACACTCTTTTT;RSEQ=GAATCTGCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:11.5:1:30:1:1:0:60:4:0.6667:0.3333:2.5 -2 92322014 . A G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTCTTTTTGTGGAATCTGCA;RSEQ=GTGGATATTTGTCTAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:2.5:1:30.5:1:1:0:45:4:1:0:4.5 1/0:3:2:1,1:0,1:0.6667:0,2:15.5:1:32:1:1:0:60:4:0.6667:0:2.5 -2 92322030 . A C 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TGCAAGTGGATATTTGTCTA;RSEQ=GTTTGAGGATTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:32:1:1:0:45:4:1:0:4.5 0/0:3:0:0,0:0,1:0:0,0:29:0:32:0:1:0:47:2:0.3333:0:3 -2 92322057 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TACATATGAAAAGCAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:32:0:1:0:45:4:1:0:4.5 0/0:1:0:0,0:0,1:0:0,0:2:0:31:0:1:0:47:2:1:0:3 -2 92322065 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAAACGGGATTACATAT;RSEQ=AAAAGCAGACAGCAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:30:1:1:0:45:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92322072 . A C 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGATTACATATGAAAAGC;RSEQ=GACAGCAGCATTCCCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:32:0:1:0:45:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92322111 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTCTTTGTGATGTTTGC;RSEQ=TTCAAGTCACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:32.5:1:1:0:49:4:1:0:3 -2 92322114 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTGTGATGTTTGCATT;RSEQ=AAGTCACAGAGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:31:1:1:0:49:4:1:0:3 -2 92322132 . A G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAGTCACAGAGTTGAAC;RSEQ=TTCCCTTTCATAGAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:32:1:1:0:49:4:1:0:3 -2 92322302 . G C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAACTTACCGTGTTGAA;RSEQ=CTTTCTTTTGATAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:29.5:1:1:0:24:4:1:0:6.5 -2 92322309 . T A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACCGTGTTGAAGCTTTCT;RSEQ=TTGATAGAGCAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:27.5:1:1:0:24:4:1:0:6.5 -2 92322314 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTGAAGCTTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:30:1:1:0:24:4:1:0:6.5 -2 92322343 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=AATCTGCAAGAGGATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:1:31.5:1:1:0:24:4:1:0:6.5 -2 92322348 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACTCTTTTTGTAAAATC;RSEQ=GCAAGAGGATATTTGGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41.5:1:30.5:1:1:0:24:4:1:0:6.5 -2 92322364 . G C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGCAAGAGGATATTTG;RSEQ=ATAGCATTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:33.5:1:1:0:24:4:1:0:6.5 -2 92323161 . T G 33 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GAGTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:39:1:33:1:1:0:21.5:4:1:0:2.5 0/1:5:2:2,0:2,0:0.4:0,0:8:1:33.5:1:1:0:20:4:0.4:0:2 -2 92323213 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18182;SOR=0;LSEQ=TCTGGATGTGGACATTTGGA;RSEQ=CGCTTTCAGGCCTATGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:16.5:1:29:1:1:1.73:21:4:0.4:0:2.5 0/0:6:0:0,0:3,3:0:2,0:34:1:30.2:1:1:0:20:12:1:0:1.2 -2 92323250 . C T 57 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=GTGAAAAAGGAAATATCTTC;RSEQ=CCTGAAAACTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:27.5:1:29.8:1:1:0:30.8:8:1:0:1.8 1/0:7:4:1,3:1,2:0.5714:2,2:27.5:1:28.5:1:1:1.41418:20:8:0.5714:0:2.8 -2 92323454 . T G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAAGCATTCTCAGAAGC;RSEQ=TCATTGGGATGTTTCAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:0:32.5:1:1:0:45:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 92323559 . C T 69 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTGGAAATTTTGAGAGA;RSEQ=CTCAGGAATACGGTGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:5.6:1:29.8:1:1:0:41.6:10:1:0:1.8 1/1:2:2:2,0:0,0:1:0,0:7.5:1:32:0:1:0:24.5:4:1:0:1.5 -2 92323655 . C A 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77722;LSEQ=TGTATCTACTCAGCTAACAG;RSEQ=GTTGAACCTTTCTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,0:0.6667:0,0:20.5:1:32:1:1:0:33.5:4:0.6667:0:1.5 1/0:5:3:0,3:1,1:0.6:2,0:11.3:1:32:1:0.4:0:26.7:6:0.6:0:1 -2 92323703 . G A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGAAACACTCTTTTTGTG;RSEQ=AATCTGCAAGTGGATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:26.3:1:30.7:1:1:0:29.7:6:1:0:0.3 0/1:9:2:1,1:5,2:0.2222:2,2:25.5:1:30:1:1:2.23609:23:4:0.2222:0:2 -2 92323728 . G C 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCAAGTGGATATTTGTCTA;RSEQ=CTTTGAGGATTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:28.8:1:31.8:1:1:0:28:8:1:0:0.3 0/1:12:2:1,1:5,5:0.1667:2,2:31:0:30:1:1:1:23:4:0.1667:0:2 -2 92323757 . A T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTCGTTGGAAACGGGATT;RSEQ=CATATAAAAAGCAGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:25.8:1:28:1:1:0:28:8:1:0:0.3 0/1:12:2:1,1:6,4:0.1667:2,2:27.5:1:27.5:1:1:1.4491:23:4:0.1667:0:1 -2 92323794 . C G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGCATTCCCAGTAACTT;RSEQ=TTTGTGATGTTTGCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13:1:30:1:1:0:24.5:4:1:0:0 0/1:8:2:1,1:0,6:0.25:0,2:37:1:32:1:0.25:0:40.5:4:0.25:0:3 -2 92323807 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAACTTCTTTGTGATGTTT;RSEQ=CATTCAAGTGTCAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:7:0:34:0:1:0:23:2:1:0:0 0/1:6:2:1,1:0,4:0.3333:0,2:37:1:30.5:1:0.33333:0:40.5:4:0.3333:0:3 -2 92323818 . T A 45 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATGTTTGCATTCAAGTG;RSEQ=CAGAGTTGAACATTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:39.7:1:29:1:1:0:34.3:6:1:0:2.7 -2 92324216 . C G 52 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACTCTTTTTGTAGTTT;RSEQ=TGGAAGTGGACATTTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,1:0.75:0,2:14.7:1:33:1:1:0:47.3:6:0.75:0:1 -2 92324262 . A T 44 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTAATACGGTGATAAAGG;RSEQ=AATATCTTCCAATAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:25:1:28.3:1:1:0:28.3:6:1:0:3 -2 92324281 . G C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATATCTTCCAATAAAAG;RSEQ=TAGATAGAAGCAATGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:0:32:1:1:0:30:4:1:0:3 -2 92324348 . T C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTAACAGAGTTGAACCTTTC;RSEQ=TTTGAGAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:33:0:1:0:21:4:1:0:3 0/0:1:0:0,0:1,0:0:0,0:13:0:33:0:1:0:20:2:1:0:0 -2 92324712 . C G 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TAGAGTAGTTTTGAAACACT;RSEQ=TTTTTGTGGAATCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:4:1:29.5:1:1:0:31:4:1:0:2.5 1/0:3:2:1,1:0,1:0.6667:0,2:14:1:28:1:1:0:50:4:0.6667:0:4 -2 92324717 . T C 59 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14286;SOR=Inf;LSEQ=TAGTTTTGAAACACTCTTTT;RSEQ=GTGGAATCTGCAAGTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:9:1:28.5:1:1:0:31:4:1:0:2.5 1/1:5:4:2,2:0,1:0.8:0,2:11:1:29.8:1:1:0:49:8:0.8:0:3 -2 92324742 . T G 68 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28571;SOR=Inf;LSEQ=AATCTGCAAGTGGATATTTG;RSEQ=CTAGCTTTGAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:25:0:30:0:1:0:40:2:0.5:0:3 1/1:5:5:2,3:0,0:1:0,2:31:1:29.4:1:1:0:47.2:4:1:0:3.2 -2 92324979 . T A 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AGACAGAAGCATTCTCAGAA;RSEQ=CTTATTTGTGATGTGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:43:1:31:1:1:0:21:4:1:0:0.5 1/0:5:3:2,1:2,0:0.6:0,2:38:1:29:1:1:0:21.3:6:0.6:0:2.7 -2 92324993 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCAGAATCTTATTTGTGATG;RSEQ=GCGCCCTCAACTAACAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:29:1:29.5:1:1:0:21:4:1:0:0.5 0/1:5:2:1,1:3,0:0.4:0,2:44:1:30.5:1:0.4:0:21:4:0.4:0:3.5 -2 92324996 . G A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=GAATCTTATTTGTGATGTGC;RSEQ=CCCTCAACTAACAGTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:30:0:27:0:1:0:22:2:0.5:0:1 0/1:5:2:1,1:3,0:0.4:0,2:44:1:30:1:0.4:0:21:4:0.4:0:3.5 -2 92325030 . A T 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.53981;LSEQ=GTGTTGAAGCTTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:20:1:33:0:1:0:20.5:4:0.6667:0:2 1/0:6:3:3,0:2,1:0.5:2,0:31.3:1:31:1:1:0:23:6:0.5:0:2 -2 92325055 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTTTTGAAACACTCTTTT;RSEQ=GTAAAATCTGCAAGAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:26.9:1:30.4:1:1:0:21.4:16:1:0:1.6 0/1:17:2:2,0:14,1:0.1176:1,0:27:1:29.5:1:1:0:20:4:0.1176:0:3 -2 92325060 . A T 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.67572;SOR=1.89001;LSEQ=TTGAAACACTCTTTTTGTAA;RSEQ=ATCTGCAAGAGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:5,4:0.1818:2,0:32.5:1:32.5:1:0.49091:0:21.5:4:0.1818:0:2 0/1:20:6:6,0:13,1:0.3:1,0:16.7:1:31.3:1:1:0:25.8:12:0.3:0:1.3 -2 92325098 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1551;SOR=0;LSEQ=TGGATAGCTTTGAGGATTTC;RSEQ=TTGGAAACGGGATTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:12,6:0.1:2,2:24:1:29:1:1:1.92731:22:4:0.1:0:6 0/0:30:0:0,0:21,9:0:2,0:33.3:1:30.2:1:1:0:22.1:60:1:0:1.2 -2 92325100 . T G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15837;SOR=0;LSEQ=GATAGCTTTGAGGATTTCGT;RSEQ=GGAAACGGGATTGTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:0.0952:2,2:24:1:30:1:1:1.66897:22:4:0.0952:0:6 0/0:31:0:0,0:21,10:0:2,0:32.3:1:29.6:1:1:0:22:62:1:0:1.3 -2 92325111 . T A 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56007;SOR=0.32954;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:13,7:0.0909:2,2:24:1:31:1:1:1.80284:22:4:0.0909:0:6 0/1:32:1:1,0:20,11:0.0313:2,0:45:0:30:0:1:0:27:2:0.0313:0:5 -2 92325112 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51234;SOR=Inf;LSEQ=GATTTCGTTGGAAACGGGAT;RSEQ=GTCTTCATATAAACTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:28.2:1:31:1:1:0:25.3:42:1:0:1.3 0/1:32:2:1,1:20,10:0.0625:2,2:19:1:29.5:1:1:1.95408:20:4:0.0625:0:1.5 -2 92325114 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51234;SOR=Inf;LSEQ=TTTCGTTGGAAACGGGATTG;RSEQ=CTTCATATAAACTCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:28.5:1:30.7:1:1:0:25.3:42:1:0:1.3 0/1:32:2:1,1:20,10:0.0625:2,2:40.5:1:26.5:1:1:1.95408:20:4:0.0625:0:2.5 -2 92325123 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12704;SOR=0;LSEQ=AAACGGGATTGTCTTCATAT;RSEQ=AACTCTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:11,8:0.0952:2,0:25.5:1:31:0:0.50476:0:24:4:0.0952:0:3.5 0/0:37:0:0,0:23,14:0:2,0:24.5:1:27.9:1:1:0:23.5:36:1:0:1.1 -2 92325124 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52995;SOR=Inf;LSEQ=AACGGGATTGTCTTCATATA;RSEQ=ACTCTAGACAGAAGCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:28:1:30.4:1:1:0:25.3:42:1:0:1.3 0/1:37:2:1,1:21,13:0.0541:2,2:24.5:1:30.5:1:1:1.5932:22:4:0.0541:0:2 -2 92325126 . C A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54673;SOR=Inf;LSEQ=CGGGATTGTCTTCATATAAA;RSEQ=TCTAGACAGAAGCATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:28:1:32:1:1:0:25.3:20:1:0:1.3 0/1:37:3:2,1:21,13:0.0811:2,2:27:1:30.3:1:1:1.23:22:6:0.0857:0:2 -2 92325127 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12704;SOR=0;LSEQ=GGGATTGTCTTCATATAAAC;RSEQ=CTAGACAGAAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:11,8:0.0952:2,0:29.5:1:32:1:0.50476:0:24:4:0.1053:0:3.5 0/0:37:0:0,0:23,14:0:2,0:23.1:1:29.2:1:1:0:23.5:74:1:0:1.1 -2 92325136 . A T 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84085;LSEQ=TTCATATAAACTCTAGACAG;RSEQ=AGCATTCTCAGAAGCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:10,9:0.0952:2,0:38:1:30.5:1:0.48571:0:24:4:0.1:0:3.5 0/1:37:3:1,2:20,13:0.0811:2,2:18.7:1:26.7:1:0.55882:2.98068:21.3:6:0.0882:0:1.7 -2 92325150 . G A 45 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.94747;LSEQ=AGACAGAAGCATTCTCAGAA;RSEQ=CTTCATTGGGATGTTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:14,7:0.0455:2,0:12:0:31:0:0.36364:0:22:2:0.0455:0:6 0/1:35:3:3,0:13,18:0.0857:2,0:17.3:1:29:1:0.09358:0:24.7:6:0.0909:0:6 -2 92325151 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14474;SOR=0;LSEQ=GACAGAAGCATTCTCAGAAG;RSEQ=TTCATTGGGATGTTTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:2,0:12,8:0.0909:2,0:22.5:1:30.5:1:0.51515:0:25:4:0.0909:0:3 0/0:35:0:0,0:15,20:0:2,0:21.9:1:31.6:1:1:0:24:70:1:0:1.5 -2 92325153 . T G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27632;SOR=Inf;LSEQ=CAGAAGCATTCTCAGAAGCT;RSEQ=CATTGGGATGTTTCAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:14,8:0:2,0:25.1:1:29.5:1:1:0:25.4:21:1:0:1.5 0/1:35:3:3,0:12,20:0.0857:2,0:18.3:1:30.7:1:0.06952:0:24.7:6:0.0857:0:6 -2 92325155 . A T 48 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.03913;LSEQ=GAAGCATTCTCAGAAGCTTC;RSEQ=TTGGGATGTTTCAATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:14,8:0.0435:2,0:7:0:31:0:0.3913:0:22:2:0.0435:0:6 0/1:35:3:3,0:12,20:0.0857:2,0:19:1:30.7:1:0.06952:0:24.7:6:0.0882:0:6 -2 92325162 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13959;SOR=0;LSEQ=TCTCAGAAGCTTCATTGGGA;RSEQ=GTTTCAATTGAAGTCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:11,6:0.1053:2,0:33.5:1:32:1:1:0:40:4:0.1053:0:1.5 0/0:31:0:0,0:11,20:0:2,0:26:1:29.1:1:1:0:23.7:30:1:0:1.5 -2 92325170 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50101;SOR=Inf;LSEQ=GCTTCATTGGGATGTTTCAA;RSEQ=TGAAGTCACAGTGTTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:0:2,0:25.8:1:29.3:1:1:0:25.3:18:1:0:1.6 0/1:26:2:0,2:10,14:0.0769:2,0:18:1:31:1:0.50769:0:21:4:0.08:0:3 -2 92325178 . A C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=GGGATGTTTCAATTGAAGTC;RSEQ=CAGTGTTGAACAGTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:24.3:1:29.7:1:1:0:26.1:40:1:0:1.6 0/1:25:2:2,0:7,16:0.08:2,0:39.5:1:32:0:0.12:0:23.5:4:0.0833:0:6.5 -2 92325191 . G T 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12556;SOR=Inf;LSEQ=TGAAGTCACAGTGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:9,11:0:2,0:23.5:1:31.6:1:1:0:26.1:40:1:0:1.7 0/1:27:4:3,1:6,17:0.1481:2,2:29.3:1:29.3:1:0.09333:7.75:25.3:8:0.1481:0:5 -2 92325193 . C T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91095;LSEQ=AAGTCACAGTGTTGAACAGT;RSEQ=CCTTTCATAGAGCAGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:1,3:7,9:0.2:2,2:23.5:1:28:1:0.61858:2.24244:26.5:8:0.2:0:2.3 0/1:27:5:1,4:8,14:0.1852:2,2:28.6:1:27.2:1:0.63612:2.22344:26.8:10:0.1852:0:2.8 -2 92325196 . T A 75 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.03118;SOR=Inf;LSEQ=TCACAGTGTTGAACAGTCCC;RSEQ=TTCATAGAGCAGGTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:23:1:29.6:1:1:0:25.2:40:1:0:1.7 0/1:27:6:3,3:6,15:0.2222:2,2:18:1:29.3:1:0.36735:2.41:24:12:0.24:0:4.7 -2 92325200 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15455;SOR=0;LSEQ=AGTGTTGAACAGTCCCTTTC;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:22:1:28.5:1:1:1.62:22:4:0.1111:0:3 0/0:27:0:0,0:9,18:0:2,0:24.6:1:28.1:1:1:0:25.5:12.5:1:0:2 -2 92325205 . G A 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72096;SOR=0.7655;LSEQ=TGAACAGTCCCTTTCATAGA;RSEQ=CAGGTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:1,3:5,9:0.2222:2,2:23.5:1:28:1:1:1.62241:26.5:8:0.2353:0:2.3 0/1:28:5:1,4:8,15:0.1786:2,2:26.2:1:27.4:1:1:2.08182:26.8:10:0.1786:0:2.8 -2 92325217 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50166;SOR=Inf;LSEQ=TTCATAGAGCAGGTTTGAAA;RSEQ=ACTCTTTTTGTAGTATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:4,14:0:2,0:26.7:1:31.6:1:1:0:26.6:36:1:0:1.8 0/1:25:2:0,2:6,17:0.08:2,0:12.5:1:28.5:1:1:0:31:4:0.08:0:2.5 -2 92325230 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19615;SOR=0;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=TATCTGGAAGTGGACATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:3,13:0.1111:2,2:22:1:27.5:1:0.40523:3.89:22:4:0.1111:0:3 0/0:22:0:0,0:2,16:0:2,0:19.6:1:29.9:1:1:0:26.6:36:0.8182:0:1.7 -2 92325231 . T C 65 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.02894;SOR=0;LSEQ=TTGAAACACTCTTTTTGTAG;RSEQ=ATCTGGAAGTGGACATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:1,3:3,10:0.2353:2,2:29.3:1:32.8:1:1:1.10:24.5:8:0.2353:0:2.3 0/0:22:0:0,0:3,19:0:2,0:21:1:26.9:1:1:0:26.2:44:1:0:2.5 -2 92325256 . C T 50 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08152;SOR=0;LSEQ=GGAAGTGGACATTTGGAGCG;RSEQ=TCTCAGGACTACGGTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:0.2727:0,0:33:1:31.7:1:1:0:22.7:6:0.2727:0:2.3 0/0:13:0:0,0:0,13:0:1,0:34.1:1:32.2:1:1:0:28.8:26:1:0:2.7 -2 92325258 . C T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22283;SOR=Inf;LSEQ=AAGTGGACATTTGGAGCGCT;RSEQ=TCAGGACTACGGTGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:0:0,0:29.5:1:33.4:1:1:0:29.4:22:1:0:2.2 0/1:13:3:0,3:0,10:0.2308:0,0:37.7:1:30.3:1:1:0:24.7:6:0.2308:0:5.3 -2 92325264 . A T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23913;SOR=Inf;LSEQ=ACATTTGGAGCGCTCTCAGG;RSEQ=CTACGGTGAAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:0:0,0:26.1:1:31:1:1:0:30.1:20:1:0:2.1 0/1:14:3:0,3:0,11:0.2143:0,0:31.7:1:30.3:1:1:0:24.7:6:0.2143:0:5.3 -2 92325267 . A G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.5977;LSEQ=TTTGGAGCGCTCTCAGGACT;RSEQ=CGGTGAAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:31.5:1:34:0:1:0:31.5:4:0.2222:0:2 0/1:14:2:0,2:0,11:0.1429:0,0:32.5:1:31.5:1:1:0:31.5:4:0.1429:0:1.5 -2 92325268 . C T 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.11388;LSEQ=TTGGAGCGCTCTCAGGACTA;RSEQ=GGTGAAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:0,8:0.1111:0,0:23:0:32:0:1:0:22:2:0.1111:0:4 0/1:14:3:0,3:0,11:0.2143:0,0:12.3:1:32:0:1:0:30.3:6:0.2143:0:2.3 -2 92325274 . A T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.54416;SOR=0.30916;LSEQ=CGCTCTCAGGACTACGGTGA;RSEQ=AAAGGAAATATCTTCCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:18.5:1:29.5:1:1:0:40:4:0.2222:0:1.5 0/1:13:1:0,1:0,12:0.0769:0,0:50:0:30:0:1:0:21:2:0.0769:0:4 -2 92325281 . A G 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24211;SOR=Inf;LSEQ=AGGACTACGGTGAAAAAGGA;RSEQ=ATATCTTCCAATAAAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:13.8:1:31:1:1:0:29.5:16:1:0:2.1 0/1:12:3:0,3:0,9:0.25:0,0:14.7:1:32.3:1:1:0:24.7:6:0.25:0:5.3 -2 92325302 . C G 32 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=ATATCTTCCAATAAAAGCTA;RSEQ=ATAGAAGCAATGTCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:6.5:1:32.5:1:1:0:40:4:1:0:2.5 0/1:6:2:0,2:0,4:0.3333:0,0:18:1:32:1:1:0:30.5:4:0.3333:0:4 -2 92325772 . T G 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATTTGTCTAGCTTTGAG;RSEQ=ATTTCGTTGGAAACGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31:1:1:0:23.5:4:1:0:1.5 1/1:5:5:5,0:0,0:1:0,0:26.8:1:32.4:1:1:0:21.6:10:1:0:2 -2 92325804 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=AACGGGATTACATATAAAAA;RSEQ=CAGACAGCAGCATTCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:12.7:1:31.3:1:1:0:22.3:6:1:0:1.3 0/1:5:2:1,1:2,1:0.4:2,2:22:1:30:1:1:1.7321:20:4:0.4:0:2 -2 92325877 . T G 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:13:0:29:0:1:0:20:2:1:0:1 0/1:5:2:0,2:0,3:0.4:0,0:27.5:1:27:0:1:0:23:4:0.4:0:1.5 -2 95490959 . T TTGC 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.12156;SOR=Inf;LSEQ=GGTTGTTGCTGCTGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:32,37:0:2,0:26.8:1:30.2:1:1:0:59.3:138:1:0:0.3 0/1:76:4:2,2:39,33:0.0526:2,2:26.5:1:31.9:1:1:1.17921:60:8:0.0526:0:0.3 -2 95490970 . G A 116 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.01046;SOR=0.27682;LSEQ=CTGCTGTTGTTGCTGCTGCT;RSEQ=CTGCTGTTGTTGTTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:16:8,8:21,28:0.2462:2,2:28.2:1:29.1:1:0.77326:1.33:60:32:0.2462:0:1.1 0/1:73:6:3,3:36,31:0.0822:2,2:14.3:1:29.3:1:1:1.1589:60:12:0.0822:0:1.3 -2 95490973 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=0.89926;LSEQ=CTGTTGTTGCTGCTGCTGCT;RSEQ=CTGTTGTTGTTGTTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:28,34:0.0313:2,2:16:0:31:1:1:1.21:44:4:0.0313:0:2 0/1:71:2:1,1:37,32:0.0282:2,2:17:1:31:1:1:1.15388:26:4:0.0286:0:3.5 -2 95490974 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.49759;SOR=Inf;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGTTGTTGTTGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:28,34:0:2,0:26:1:32.4:1:1:0:59.5:124:1:0:0.4 0/1:69:2:1,1:35,32:0.029:2,2:18:1:28.5:1:1:1.09232:60:4:0.029:0:1 -2 95491693 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACCCATACTCATAGTGC;RSEQ=TGATTATCCATTAAGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:29:1:1:0:49.5:4:1:0:1.5 -2 95849529 . C T 165 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00169;SOR=0.07108;LSEQ=CAGGTGCCCGCCAACACGCC;RSEQ=GGCTAATTTTTTGTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:45:0,45:0,2:0.9574:0,1:21.6:1:30.1:1:1:0:48.4:44:0.9565:0:1 1/0:15:9:0,9:0,6:0.6:0,0:15.9:1:30.3:1:1:0:51.8:18:0.6:0:1.2 -2 95849653 . T C 100 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGATTACAGACGTAAG;RSEQ=CACCGTGCCCGGCCTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:1,10:0,0:1:0,2:22:1:29.1:1:1:0:51.5:10:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 96028398 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=GCTCCTATGAGAATTTAATG;RSEQ=CGCTGCTCATCTGACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:25.4:1:33.2:1:1:0:60:18:1:0:0 0/1:12:2:1,1:6,4:0.1667:2,2:24.5:1:26.5:1:1:1.4491:60:4:0.1667:0:1 -2 96918481 . C A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGTTCCTAAACTGAGGC;RSEQ=AGGTTCCATCTCAGTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:7.5:1:29.5:1:1:0:60:4:0.6667:0:1.5 0/0:1:0:0,0:0,1:0:0,0:3:0:29:0:1:0:60:2:1:0:0 -2 96919642 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.15457;LSEQ=ATCTCTGAGAGCAGCTCCAG;RSEQ=GCCTGCTCCTCTTCCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1023:76:39,37:456,489:0.0743:2,2:24.2:1:30:1:0.63458:1.13:60:75:0.0746:0:1.1 0/1:778:284:131,153:240,253:0.365:2,2:23.5:1:29.4:1:0.50293:1.10778:60:46.333:0.3629:0:1.1 -2 96919780 . ATGC A 116 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03363;SOR=2.66612;LSEQ=TGGGATCCATGGTACTTCTT;RSEQ=TGCTGCTGCTGGGCCAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:817:7:3,4:350,459:0.0086:2,2:26.6:1:32.3:1:1:1.01668:60:14:0.0088:0.0012:0.3 0/1:710:16:7,9:317,377:0.0225:2,2:26.5:1:29.1:1:1:1.081:59.7:32:0.0227:0.0042:0.2 -2 96920501 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5841;SOR=2.56823;LSEQ=AGAGAAACCAGAGCCCCCAC;RSEQ=GGCAACTCAGACAGGATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:154,34:0.0053:2,0:1:0:22:0:0.18519:0:60:2:0.0053:0:2 0/1:148:2:1,1:112,34:0.0135:2,2:7:1:28:1:0.41828:3.26116:60:4:0.0135:0:1 -2 96920728 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01699;SOR=Inf;LSEQ=AGCACTGTCTGGGGATTCAT;RSEQ=CAGAAATCTGTAGAGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:612:0:0,0:239,373:0:2,0:26.1:1:32.1:1:1:0:60:101:1:0:0.1 0/1:488:5:3,2:183,300:0.0102:2,2:18:1:26:1:0.37421:2.45:60:10:0.0103:0:1 -2 96920793 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15153;SOR=Inf;LSEQ=ACACTTGGTGCAGGAAGTCC;RSEQ=CACCTAGAAGGAGTTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:33,189:0:2,0:22.3:1:31.1:1:1:0:60:54.5:1:0:0.1 0/1:142:2:1,1:23,116:0.0141:2,2:39.5:1:31:0:0.31246:4.96:60:4:0.0145:0:1.5 -2 96920893 . T G 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07555;SOR=5.04481;LSEQ=CTCCTGGGTGGTCTGCAGGG;RSEQ=AGCTGGAGCAAATTCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:1,33:0.0556:1,0:20:1:32:0:1:0:60:4:0.0571:0:1 0/1:17:4:0,4:1,12:0.2353:1,0:19.3:1:30:1:1:0:60:8:0.2353:0:1 -2 96921693 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACTCCAGCCTGGATGAC;RSEQ=GAGAGAGACCCTGTCTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:31.5:1:1:0:49:4:1:0:3 -2 96921697 . AG CA 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCCAGCCTGGATGACCGAG;RSEQ=AGACCCTGTCTCTTAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:32:1:1:0:49:4:1:0:2 -2 96924666 . A C 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=CCAGGCAGTTGGAGTAAGAA;RSEQ=AGTAATATGTGCAGGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:33,235:0:2,0:24.1:1:30:1:1:0:60:43.667:1:0:0.1 0/1:175:9:0,9:26,140:0.0514:2,0:29.7:1:30.9:1:0.35924:0:60:8:0.0465:0:1.1 -2 96927965 . C T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05252;SOR=3.18091;LSEQ=TGAGATGGCGCCGCTGCACT;RSEQ=CAGCCTGGGTGACAGAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:8:8,0:40,0:0.1667:1,0:19.1:1:31.4:1:1:0:60:16:0.1702:0:2.1 0/1:28:11:11,0:17,0:0.3929:1,0:22.4:1:29.6:1:1:0:58.6:22:0.3929:0:1.8 -2 96931025 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05955;SOR=Inf;LSEQ=GGGCGCCAGGCAGGGCCGAG;RSEQ=CCAGGCTACGCTCCGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:84,312:0:2,0:25.7:1:32:1:1:0:60:65:0.9949:0:0.1 0/1:256:3:1,2:65,188:0.0117:2,2:13.3:1:28.3:1:1:1.44:60:6:0.0118:0:1.3 -2 96931044 . G A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26782;SOR=2.32004;LSEQ=GGCCAGGCTACGCTCCGGCT;RSEQ=CTTGGGCAGAGCGCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:2,1:50,222:0.0109:2,2:15.3:1:27.3:1:0.0927:8.78:60:6:0.011:0:1.3 0/1:160:4:3,1:36,120:0.025:2,2:8.3:1:23.5:1:0.04518:9.82:60:3:0.0189:0:1.5 -2 96931061 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55677;SOR=3.48069;LSEQ=GCTGCTTGGGCAGAGCGCTG;RSEQ=CTCCCGGGCTCCTCCGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:1:0,1:29,165:0.0051:2,0:1:0:26:0:1:0:60:2:0.0052:0:1 0/1:113:2:1,1:25,86:0.0177:2,2:44.5:1:28.5:1:0.40882:3.39:60:4:0.0179:0:2 -2 96931077 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13724;SOR=Inf;LSEQ=GCTGCCTCCCGGGCTCCTCC;RSEQ=CCGGCGCCCGCCGGGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:16,97:0:2,0:18.3:1:32.3:1:1:0:60:112:1:0:0.2 0/1:67:2:1,1:17,48:0.0299:2,2:9:0:32:1:0.46811:2.77:60:4:0.0299:0:1.5 -2 96931591 . G T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAGACCCTCCCCACGCC;RSEQ=CCCACTGTTCCTCACCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:10.5:1:29.5:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 97569926 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5013;SOR=Inf;LSEQ=AGAGGCACTAGAAGGTTTGC;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:0:2,0:29.5:1:29.5:1:1:0:60:23:1:0:0 0/1:32:2:1,1:17,12:0.0625:2,2:38.5:1:30:1:1:1.40053:60:4:0.0645:0:1 -2 98354139 . G T 28 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=1.56622;LSEQ=CTACTACACTGTAAGCCTCT;RSEQ=CCCCTGTGATGCCCGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:14,2:0.1111:2,0:28:1:28.5:1:1:0:60:4:0.1176:0:1 0/1:6:1:1,0:5,0:0.1667:0,0:6:0:30:0:1:0:60:2:0.1667:0:1 -2 98354171 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGACTGGATGGGCTGGGT;RSEQ=GGTAGAGGGTCCCTGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:27,2:0.0645:2,0:17:1:28.5:1:1:0:60:4:0.0667:0:1.5 0/0:14:0:0,0:14,0:0:1,0:23.4:1:30.9:1:1:0:60:13:1:0:0.1 -2 98354224 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22505;SOR=Inf;LSEQ=ATCTCCCCCTCCCCAGGCCC;RSEQ=CTCAGCAGGGAAGTGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:53,24:0:2,0:23.5:1:30.5:1:1:0:60:154:1:0:0.1 0/1:70:2:1,1:44,24:0.0286:2,2:20.5:1:29:1:1:1.81649:60:4:0.029:0:1 -2 98354290 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09959;SOR=Inf;LSEQ=CAACTTCCGCAAGTTCTCCA;RSEQ=CCGCAGCGATGTCTGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:43,60:0:2,0:26.1:1:31.1:1:1:0:60:24.75:1:0:0.1 0/1:90:3:1,2:36,50:0.0333:2,2:15.3:1:25.7:1:1:1.43433:60:2:0.0235:0:3 -2 98445370 . T C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48308;SOR=Inf;LSEQ=TTTGGGCCCTGTATTTTTAA;RSEQ=CTCCTTGTCAAATTTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:0:2,0:25.4:1:30.3:1:1:0:59.4:24:1:0:0.4 0/1:14:2:1,1:7,5:0.1429:2,2:44:0:31:1:1:1.36624:34:4:0.1429:0:4 -2 98445397 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCAAATTTGTTTCCTCTAC;RSEQ=ATCGAGGCCATCAAGCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:34.1:1:31.1:1:1:0:60:14:1:0:0.1 0/1:17:2:1,1:7,8:0.1176:2,2:22.5:1:28.5:1:1:1.13:34:4:0.1176:0:4 -2 98445404 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTTTCCTCTACGATCGAG;RSEQ=CCATCAAGCTACAGATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:30.7:1:32.7:1:1:0:60:14:1:0:0.1 0/1:17:2:1,1:7,8:0.1176:2,2:15.5:1:28:1:1:1.13:34:4:0.1176:0:4 -2 98445407 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCCTCTACGATCGAGGCC;RSEQ=TCAAGCTACAGATGGTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:28.6:1:31.6:1:1:0:60:14:1:0:0.1 0/1:16:2:1,1:6,8:0.125:2,2:12.5:1:28.5:1:1:1.31:34:4:0.125:0:4 -2 99117251 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19476;SOR=Inf;LSEQ=TGAGGAGGGGAGGTTTTTGC;RSEQ=AAACTGGCTCAGCAGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:34,16:0:2,0:26.2:1:30.1:1:1:0:60:100:1:0:0.1 0/1:40:2:1,1:24,14:0.05:2,2:23:1:30:1:1:1.69023:60:4:0.05:0:1 -2 99117310 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22125;SOR=0;LSEQ=TACAAAGAAGTGCACAGATG;RSEQ=GCCTAGAAGGTTCAGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:30,36:0.0294:2,2:41:1:30:1:1:1.20:60:4:0.0294:0:1 0/0:76:0:0,0:36,40:0:2,0:26.7:1:29.7:1:1:0:60:37:1:0:0.1 -2 99117369 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1908;SOR=Inf;LSEQ=GCAGAAAATCTTTGTTACTG;RSEQ=CACTGGTGGAATGGCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:6,23:0:2,0:22.1:1:31.5:1:1:0:60:58:1:0:0 0/1:23:2:1,1:3,18:0.087:2,2:15.5:1:27.5:1:0.32411:5.34:60:4:0.087:0:1 -2 99117526 . T C 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCCTATAATCCCAGCAC;RSEQ=GGGATATTTTTGGGAGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 99136704 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15893;SOR=Inf;LSEQ=GCAGTGCTGGCAGGTACCCA;RSEQ=TGATTCCCCATGACTACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:8,127:0:2,0:23.1:1:30.7:1:1:0:60:44:1:0:0.1 0/1:90:2:1,1:2,86:0.0222:1,2:22.5:1:31:0:0.06592:35.31:60:4:0.0225:0:1 -2 99137272 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24153;SOR=Inf;LSEQ=AAAAACACTACCACCAGTGC;RSEQ=TGGGCTTGTCTCAGAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:7,127:0:2,0:24.1:1:31.3:1:1:0:60:66:1:0:0 0/1:130:2:0,2:7,121:0.0154:2,0:37.5:1:32:0:1:0:60:4:0.0155:0:1 -2 99149946 . G A 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.66674;LSEQ=TGGACGAAGCATGCACAGAC;RSEQ=GAGATCATTGAGGTGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:55:27,28:261,331:0.085:2,2:23.5:1:30.1:1:0.48198:1.22:60:54:0.0844:0:1.2 0/1:750:149:65,84:252,346:0.1987:2,2:26.1:1:30.5:1:0.7813:1.06:60:298:0.1995:0:1.2 -2 99150118 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54869;SOR=0;LSEQ=TACATTGATATTTTTCATCA;RSEQ=ATTTACTCATCTGGGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:3:0,3:2,42:0.0638:1,0:19.7:1:28.3:1:1:0:60:6:0.0652:0:1 0/0:20:0:0,0:1,19:0:1,0:20.7:1:31.1:1:1:0:60:40:1:0:0.1 -2 99152383 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14441;SOR=Inf;LSEQ=AATCGTTTGAATGAGAGATG;RSEQ=ACACAGATTGACTTCACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:58,243:0:2,0:23.2:1:30.4:1:1:0:60:74.25:1:0:0.1 0/1:185:2:1,1:32,151:0.0108:2,2:25.5:1:27.5:1:0.32573:4.66:60:4:0.0109:0:1 -2 99152770 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06505;SOR=Inf;LSEQ=TATACTGAGAGAGCACCCTT;RSEQ=CCTTCCCAGAAGCCAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:12,208:0:2,0:24.6:1:31.4:1:1:0:60:72.333:1:0:0.1 0/1:149:3:1,2:6,140:0.0201:1,2:30.3:1:24.3:1:0.13529:11.14:60:2:0.0138:0:1.7 -2 99154229 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11855;SOR=1.8518;LSEQ=CAGCTCGGCCCTGCTGCCCC;RSEQ=AGGACCCTGATGACCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:15:12,3:94,6:0.1304:2,2:23.3:1:31.3:1:0.09354:3.84923:60:30:0.1304:0:1.1 0/1:78:17:16,1:59,2:0.2179:1,1:23.6:1:31.6:1:0.52692:1.82707:60:34:0.2179:0:1 -2 99154610 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACCTTGAAGCAGGAAAA;RSEQ=GGGCTCCTGCCTGTAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:0,2:0,47:0.0408:1,0:29:1:33:0:1:0:60:4:0.0408:0:1.5 0/0:19:0:0,0:0,19:0:1,0:29.5:1:31.2:1:1:0:60:38:1:0:0.4 -2 99155491 . C A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0914;SOR=Inf;LSEQ=TTGCCTCTCTAGTGAGTATC;RSEQ=ACTTGGGCCCGCAGTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:103,263:0:2,0:23.9:1:31.7:1:1:0:60:121:1:0:0.1 0/1:301:3:3,0:91,207:0.01:2,0:12:1:22:1:0.02979:0:60:2:0.0067:0:2.3 -2 99155520 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1615;SOR=Inf;LSEQ=CCGCAGTCCCCTTTGCTCCC;RSEQ=ACCTGCTGCGATTGTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:25,199:0:2,0:21.5:1:31.9:1:1:0:60:55:1:0:0.1 0/1:151:2:1,1:20,129:0.0132:2,2:32.5:1:28:1:0.2596:6.32:60:4:0.0133:0:1 -2 99155881 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1405;SOR=Inf;LSEQ=TAATTCCCATGAGATGAACA;RSEQ=TGAGAGGACTTGAGGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:223,8:0:1,0:23.3:1:32.4:1:1:0:60:76:1:0:0.1 0/1:139:2:2,0:133,4:0.0144:1,0:14:1:31:1:1:0:60:4:0.0147:0:1 -2 99155895 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16153;SOR=Inf;LSEQ=TGAACAGTGAGAGGACTTGA;RSEQ=GTGTCACCATCCCTGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:261,21:0:2,0:25.4:1:32.2:1:1:0:60:93:1:0:0.1 0/1:190:2:1,1:168,20:0.0105:2,2:13:1:29.5:1:0.20936:8.2211:60:4:0.0109:0:1 -2 99156212 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14894;SOR=Inf;LSEQ=TCCTTTCTGAGATATAGCGG;RSEQ=CAGAGCACTGGCATCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:16,128:0:2,0:22:1:31.9:1:1:0:60:35:1:0:0.1 0/1:91:2:1,1:12,77:0.022:2,2:27:1:27.5:1:0.26667:6.21:60:4:0.0222:0:1 -2 99160361 . G C 174 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGTGTGAGCTGGAGGAGCT;RSEQ=GGAGAGCTGTCCCCTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:55:34,21:485,361:0.061:2,2:25.7:1:30.1:1:0.57452:1.20:60:54:0.0609:0:1.2 0/0:785:0:0,0:440,339:0:2,0:24.8:1:30.5:1:1:0:60:40:0.9922:0:0.2 -2 99160528 . T A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17436;SOR=5.15873;LSEQ=GCACACACACACACACACAC;RSEQ=CTCACTCTCACTCAGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:1:0,1:47,251:0.0033:2,0:14:0:31:0:1:0:60:2:0.0035:0:2 0/1:236:4:1,3:38,194:0.0169:2,2:10.5:1:24.5:1:0.51693:1.70:60:3:0.0133:0:1.5 -2 99162189 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTTTGAAGCCGGTTCTC;RSEQ=CTGGCACCATTCACCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:6:1:32.5:1:1:0:60:4:0.2222:0:1 0/0:4:0:0,0:4,0:0:0,0:11.5:1:26.5:1:1:0:60:3:1:0:0.3 -2 99162384 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07795;SOR=Inf;LSEQ=TCTACTTGCAACTCGTGAAT;RSEQ=CAGCATGTATGCTGATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:270,84:0:2,0:23.6:1:32:1:1:0:60:69.8:1:0:0.1 0/1:265:3:2,1:189,71:0.0113:2,2:30:1:22.3:1:1:1.32945:60:2:0.0076:0:1.7 -2 99162585 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08219;SOR=Inf;LSEQ=AATCACATTTCGCTGCTTTT;RSEQ=TCTGTGGGTACTTGGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:95,256:0:2,0:23.1:1:31.6:1:1:0:60:49.143:1:0:0.1 0/1:271:3:2,1:80,187:0.0111:2,2:5.3:1:26.3:1:0.21975:4.64:60:6:0.0112:0:1 -2 99163213 . T C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07959;SOR=Inf;LSEQ=GCTTTCTGATGCTTCTTTTC;RSEQ=CAGTTTAAAATAAAATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:33,224:0:2,0:20.9:1:29.8:1:1:0:60:41.833:1:0:0.1 0/1:195:3:1,2:35,157:0.0154:2,2:17.7:1:30:1:0.45979:2.23:60:6:0.0157:0:1 -2 99163261 . T A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.08516;SOR=3.23769;LSEQ=CGCAAAAACACCCAGCCATC;RSEQ=GATCTGCTTTTGCGTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:4:0,4:1,84:0.0449:1,0:27.5:1:31:1:1:0:60:8:0.0449:0:1 0/1:45:6:0,6:1,38:0.1333:1,0:19.7:1:31.8:1:1:0:60:12:0.1333:0:1 -2 99165588 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54356;SOR=0;LSEQ=ACAGTCCTCCCTTCCAACTG;RSEQ=AATGTTCTTTAATAATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:0,81:0.0241:1,2:21.5:1:29:1:0.0241:0:60:4:0.0241:0:1 0/0:44:0:0,0:1,43:0:1,0:22.7:1:31.5:1:1:0:60:21:1:0:0.1 -2 99168953 . T C 115 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACGATCATTTGGGTGATTA;RSEQ=GGGATATGATTGTTCAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:22.4:1:32.3:1:1:0:60:24:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 99170727 . C T 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03824;SOR=1.66985;LSEQ=GCAGCCTTGGTTTGTGTGCA;RSEQ=CTGCAGACACGGCAGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:34:25,9:281,114:0.0793:2,2:25.1:1:30.4:1:0.84564:1.13:60:68:0.081:0:1.1 0/1:334:42:29,13:201,91:0.1257:2,2:25.8:1:29.9:1:1:1.01:60:84:0.1288:0:1.1 -2 99171929 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54835;SOR=0;LSEQ=AGTGTGGAAGCCTAGGGCAG;RSEQ=GGATCAGTGGAGGGCGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:141,17:0.0125:2,2:34.5:1:29.5:1:0.21297:8.08842:60:4:0.0131:0:1 0/0:83:0:0,0:71,12:0:2,0:25.7:1:30.5:1:1:0:60:26.667:1:0:0.2 -2 99171949 . T C 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56184;SOR=3.20099;LSEQ=GGGATCAGTGGAGGGCGATT;RSEQ=GGTTTGTGTTATGTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:187,41:0.0044:2,0:32:0:15:0:1:0:60:0:0:0:5 0/1:144:2:1,1:105,37:0.0139:2,2:23.5:1:24:1:0.4595:2.81355:60:4:0.0144:0:1 -2 99171957 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16363;SOR=Inf;LSEQ=TGGAGGGCGATTTGGTTTGT;RSEQ=TTATGTTTGTGTTTCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:202,49:0:2,0:25.8:1:31.9:1:1:0:60:61.75:1:0:0.2 0/1:171:2:1,1:125,44:0.0117:2,2:24.5:1:27.5:1:0.4582:2.82038:60:4:0.0118:0:1 -2 99171963 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17295;SOR=Inf;LSEQ=GCGATTTGGTTTGTGTTATG;RSEQ=TTGTGTTTCTGTTCGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:210,66:0:2,0:25.8:1:29.9:1:1:0:60:552:1:0:0.1 0/1:197:2:1,1:142,53:0.0102:2,2:24.5:1:30.5:1:0.4741:2.66365:60:4:0.0105:0:1 -2 99172243 . C T 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.45569;LSEQ=TGCCCCTCCACCATGCCCTC;RSEQ=ACTGCATGCCATCCTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1319:183:71,112:482,654:0.1387:2,2:24.5:1:29.3:1:0.37528:1.16246:60:366:0.141:0:1.2 0/1:1214:83:34,49:511,618:0.0684:2,2:23.4:1:28.5:1:0.49352:1.19148:60:82:0.0684:0:1.1 -2 99172244 . A G 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.25752;LSEQ=GCCCCTCCACCATGCCCTCC;RSEQ=CTGCATGCCATCCTCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1305:88:31,57:516,699:0.0674:2,2:28.9:1:30.4:1:0.21846:1.35702:60:16.6:0.0655:0:1.1 0/1:1206:230:105,125:437,535:0.1907:2,2:26.8:1:30.1:1:0.88291:1.03:60:31.857:0.1904:0:1.1 -2 99172299 . G A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.80588;LSEQ=TGCATCCATGCTTCCCATAT;RSEQ=CTGCCTCCATTTCACCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:6:4,2:137,454:0.0101:2,2:16:1:24.2:1:0.03007:6.60:60:5:0.0086:0:1.5 0/0:493:4:4,0:124,365:0.0081:2,0:13.3:1:23.8:1:0.00439:0:60:8:0.0083:0:1.8 -2 99172368 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATGCCCTCCTCCCCCAT;RSEQ=CAGACTGCAGGGAGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:0,2:2,145:0.0134:1,0:12:1:26.5:1:1:0:60:4:0.0139:0:1 0/0:70:0:0,0:2,68:0:1,0:24.2:1:32.5:1:1:0:60:140:1:0:0.1 -2 99175795 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18752;SOR=Inf;LSEQ=GGAAGAGGCAGCCAGGCACC;RSEQ=AGACCTCTTTTCTGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:157,6:0:1,0:22.4:1:31.3:1:1:0:60:162:1:0:0.1 0/1:125:2:1,1:117,6:0.016:1,2:48.5:1:30.5:1:0.10929:18.12619:60:4:0.016:0:1.5 -2 99179756 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=8;SSF=0.5524;SOR=3.56451;LSEQ=GCTGGAAAGAGCTGGGGCTA;RSEQ=AGGGCTAGAGGGCTAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:1:1,0:62,3:0.0152:1,0:13:0:32:0:1:0:60:2:0.0154:0:1 0/1:38:2:1,1:34,2:0.0526:2,2:24:1:27.5:1:0.15363:14.08907:60:4:0.0526:0:1 -2 99179971 . C G 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGCTGCTGACCACTCTCAC;RSEQ=GACTGCGTGGCCATGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1146:0:0,0:593,551:0:2,0:25.4:1:30.3:1:1:0:60:80.714:0.9982:0:0.1 0/1:1041:45:21,24:494,500:0.0432:2,2:21.2:1:29.4:1:0.76129:1.12901:60:44:0.0428:0:1.1 -2 99180947 . GC G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCCATGGCCAGGGCAT;RSEQ=CCCACCTGGGCTTCTCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:61,4:0.0299:2,2:21:1:30.5:1:0.14473:13.75137:60:4:0.0308:0:0 0/0:26:0:0,0:26,0:0:1,0:23.5:1:32.6:1:1:0:60:52:1:0:0.2 -2 99181315 . AT A 119 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04192;SOR=2.74442;LSEQ=CTTTTCTCACTATACCAGTA;RSEQ=GCGTGCTTATTGAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:8:0,8:2,101:0.0721:1,0:15.5:1:30.1:1:1:0:60:16:0.0748:0.027:0.3 0/1:85:15:0,15:2,68:0.1765:1,1:10.7:1:30.6:1:1:0:60:30:0.1807:0.0941:0.2 -2 99182040 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51847;SOR=0;LSEQ=CCTGGGCTTGGCTGCCTTCT;RSEQ=CTGAGACTGGGGAGAGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:167,20:0.0106:2,0:7.5:1:31.5:1:1:0:60:4:0.0107:0:1 0/0:126:0:0,0:102,24:0:2,0:23.6:1:31.2:1:1:0:60:62:1:0:0.1 -2 99182079 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03081;SOR=Inf;LSEQ=GCAGGGCCCTCTGCCTGACA;RSEQ=CCCTGCCCCTCTCTCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:310,102:0:2,0:24.1:1:32:1:1:0:60:57.857:0.9951:0:0.1 0/1:300:4:2,2:200,95:0.0133:2,2:20.3:1:30.3:1:0.59777:2.09959:60:8:0.0137:0:1.5 -2 99182085 . C T 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01449;SOR=Inf;LSEQ=CCCTCTGCCTGACAGCCCTG;RSEQ=CCCTCTCTCATGTCCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:324,125:0:2,0:25:1:31.7:1:1:0:60:48.889:1:0:0.1 0/1:339:5:2,3:218,116:0.0147:2,2:12.6:1:23.2:1:0.34866:2.80973:60:1.5:0.0091:0:1.8 -2 99182258 . C A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22971;SOR=0.24012;LSEQ=TTGGTTTAAAATTCTCTGAG;RSEQ=CAGAGAGCGGTTTTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:493:5:3,2:149,338:0.0101:2,2:16.2:1:26.8:1:0.17404:3.39:60:4:0.0082:0:2 0/0:408:1:1,0:132,275:0.0025:2,0:1:0:23:0:0.32598:0:60:2:0.0025:0:1 -2 99182393 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17988;SOR=Inf;LSEQ=TTAAAGGTCTGTGGTTGGCA;RSEQ=TTTGGCCATCACTAAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:186,35:0:2,0:25.1:1:32.3:1:1:0:60:109.5:0.9955:0:0.1 0/1:164:2:1,1:143,17:0.0122:2,2:22:1:29:1:0.21049:8.20252:60:4:0.0123:0:1 -2 99184905 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGCTCGGAAGAGGGAGA;RSEQ=TGGCTTAGAATTTAGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:2,0:107,1:0.0182:1,0:16:1:32:1:1:0:60:4:0.0183:0:1 0/0:48:0:0,0:48,0:0:1,0:18.7:1:32.6:1:1:0:60:96:1:0:0 -2 99185227 . G A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.27963;SOR=0;LSEQ=CCCTGCCTCTGTGAGTGCAT;RSEQ=CCTGTGCATGTGTGTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:3:2,1:3,175:0.0166:1,2:12.3:1:25:1:0.00182:97.85:60:6:0.0166:0:1 0/0:119:0:0,0:4,115:0:1,0:22.8:1:32.4:1:1:0:60:118:1:0:0.1 -2 99185276 . CAG C 86 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=1.14847;LSEQ=TCTCCCTAAACACACACACG;RSEQ=AGAGAGAGAGAGAAGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:6:0,6:0,68:0.08:1,0:33.5:1:33.3:1:1:0:60:12:0.0811:0:0 0/1:33:3:0,3:0,30:0.0909:1,0:26.3:1:34:0:1:0:60:6:0.0909:0:0 -2 99185423 . C G 88 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCATGCATTGTGCACCT;RSEQ=CTGGTAGGACTTGGGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:21.1:1:31.6:1:1:0:60:14:1:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 99189424 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0317;SOR=Inf;LSEQ=AGAGGAAAAGGAGGCTATTG;RSEQ=GGTGCCCACAGCTGAACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:113,273:0:2,0:24.7:1:30.2:1:1:0:60:95.5:0.9974:0:0.1 0/1:284:4:1,3:94,186:0.0141:2,2:37:1:31.3:1:1:1.51407:60:8:0.0143:0:1.3 -2 99193007 . A G 83 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTACCTTCCAGGGAGACCT;RSEQ=GAGACCTGGCCCAGGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:26.8:1:32.3:1:1:0:60:12:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 99193496 . C T 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.38671;LSEQ=CGGTTCACCAGCTGCAAGAG;RSEQ=GCTAAGGACCGTACAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1324:99:48,51:587,636:0.0748:2,2:25.9:1:29.6:1:1:1.02:60:48.5:0.075:0:1.2 0/1:1149:247:120,127:432,467:0.215:2,2:23.5:1:29.5:1:0.88595:1.02:60:122.5:0.2176:0:1.1 -2 99193650 . G A 50 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65186;SOR=0.37687;LSEQ=CGCCCCGCCTGCCCCGGCCC;RSEQ=TGTAAACTGCAGATGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:4:2,2:29,171:0.0196:2,2:19:1:25.3:1:0.1103:5.82:60:3:0.0149:0:1.5 0/0:134:1:0,1:13,120:0.0075:2,0:8:0:31:0:1:0:60:2:0.0075:0:1 -2 99197896 . AT A 51 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.50336;LSEQ=TTCTATTGTGACTTCATTTC;RSEQ=TTTTTTTTAACCTTATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:3,0:52,2:0.0526:1,0:20:1:32.3:1:1:0:60:6:0.0536:0:0 0/1:37:1:1,0:34,2:0.027:2,0:47:0:30:0:1:0:60:2:0.027:0:0 -2 99197971 . T C 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=7.000;MSILEN=1;SSF=0.08202;SOR=Inf;LSEQ=AATCCATCGCATGTGTCTTC;RSEQ=TTTTTTCTTTATTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:230,16:0:2,0:24.4:1:31.4:1:1:0:60:492:1:0:0.1 0/1:190:3:3,0:171,16:0.0158:2,0:10:1:27.3:1:1:0:60:6:0.0158:0:1 -2 99203871 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21527;SOR=0;LSEQ=AAAATGATCAGTTCATTTCA;RSEQ=CTTAGTTTAAGTCTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:160,22:0.0109:2,2:29.5:1:31:1:0.23497:7.13472:60:4:0.0111:0:1 0/0:212:0:0,0:179,33:0:2,0:23:1:29.9:1:1:0:60:105:1:0:0.1 -2 99204138 . T C 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27192;SOR=0;LSEQ=CCTCTAGTGTCATATATGAA;RSEQ=TCTTCAAGAAGACCTGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:1,2:14,153:0.0176:2,2:24.7:1:26.3:1:0.24334:5.36:60:2:0.0123:0:2 0/0:118:0:0,0:12,105:0:2,0:23.2:1:29.6:1:1:0:60:18.5:0.9911:0:0.1 -2 99373720 . T C 284 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42518;LSEQ=GATTTCTGTTGACTTACCCC;RSEQ=CACTTCCCCCTATCTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:768:576:308,268:104,87:0.75:2,2:26.4:1:31:1:0.86707:1.04012:60:114.2:0.7523:0:1.1 1/0:869:487:237,250:195,185:0.5604:2,2:26.7:1:30:1:0.45202:1.11173:60:47.7:0.5585:0:1.1 -2 100441349 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00425;SOR=0.11081;LSEQ=CCAATGAAATAATGGCTCAT;RSEQ=TTCAAAAAACAGTTAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:3,16:0,2:0.9048:0,2:21.9:1:30.9:1:1:0:60:38:0.9048:0:1 1/0:24:12:3,9:3,9:0.5:2,2:21.3:1:28.6:1:1:1:60:24:0.5:0:1 -2 100515319 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50879;SOR=Inf;LSEQ=TGCCTGGGGCTCTCTCGCTT;RSEQ=GGCCAACGCTGACTCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:46,52:0:2,0:27.5:1:29.3:1:1:0:60:48:1:0:0.1 0/1:132:2:1,1:68,62:0.0152:2,2:34:1:29.5:1:1:1.096:60:4:0.0152:0:1 -2 100515321 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1842;SOR=0;LSEQ=CCTGGGGCTCTCTCGCTTTG;RSEQ=CCAACGCTGACTCCCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:44,53:0.0202:2,2:35:0:30.5:1:1:1.20:60:4:0.0211:0:1.5 0/0:131:0:0,0:68,63:0:2,0:26.6:1:30.9:1:1:0:60:42.667:1:0:0.3 -2 100515343 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50145;SOR=Inf;LSEQ=CAACGCTGACTCCCACTTTG;RSEQ=CCTGCCCTCACAGGGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:35,57:0:2,0:26.3:1:30.7:1:1:0:60:45:1:0:0.1 0/1:111:2:2,0:47,62:0.018:2,0:17.5:1:28:1:0.19263:0:60:4:0.0183:0:1 -2 100515353 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TCCCACTTTGCCCTGCCCTC;RSEQ=CAGGGCCTGTCCTGCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:26,52:0:2,0:27.8:1:29.3:1:1:0:60:77:1:0:0.1 0/1:101:2:1,1:38,61:0.0198:2,2:44:0:32:0:1:1.60:60:4:0.02:0:1.5 -2 100801091 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18415;SOR=Inf;LSEQ=TTCGTGAATCAAGAGAAATT;RSEQ=TGTCACAGGTCCAAATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:116,31:0:2,0:26.1:1:31.7:1:1:0:60:35.75:1:0:0.1 0/1:111:2:1,1:78,31:0.018:2,2:19.5:1:32:0:0.49533:2.49234:60:4:0.0183:0:1 -2 100801198 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32688;LSEQ=CTTTCATGGACTCTTCTCAA;RSEQ=TCTGCTTTGAACTGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:295:200:96,104:47,46:0.678:2,2:25.7:1:31.9:1:0.70786:1.1065:60:99:0.6804:0:1.1 0/1:307:125:65,60:90,91:0.4072:2,2:26:1:30.7:1:0.72794:1.10:59.8:30.25:0.4033:0:1.3 -2 101852256 . T C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=0;LSEQ=CTAACCAGTAAGGGATAGTA;RSEQ=GAGATGCTGCCCAGAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:1:0,2:27.8:1:31.9:1:1:0:60:18:1:0:1 1/1:13:11:8,3:1,1:0.8462:2,2:21.3:1:30.4:1:1:2.45:60:22:0.8462:0:1 -2 101992072 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14936;SOR=0;LSEQ=GAGGTGGCTGAGTGCCCTCT;RSEQ=TGGCACCCCAGGAGGCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:0.1333:2,2:25:1:29.5:1:1:1.54914:60:4:0.1333:0:1.5 0/0:23:0:0,0:15,8:0:2,0:22.3:1:30.8:1:1:0:60:46:1:0:0.9 -2 101992105 . A G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCGAGCTCTGCTTCTCC;RSEQ=AACTCCAGTGGTCAGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:13,11:0,0:1:0,2:27.5:1:31.1:1:1:0:60:48:1:0:1.5 1/1:39:39:21,18:0,0:1:0,2:26.8:1:30.1:1:1:0:60:78:1:0:1.3 -2 101992167 . C T 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.44236;SOR=2.52567;LSEQ=GGGACCACCCTACCCCAGGA;RSEQ=GGGGTGGGGTGCGGCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:7,7:0.125:2,0:12.5:1:30:1:0.475:0:60:4:0.125:0:2 0/1:26:7:2,5:9,10:0.2692:2,2:22.4:1:29.4:1:0.65761:2.18265:60:14:0.2692:0:1.7 -2 101992173 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50166;SOR=Inf;LSEQ=ACCCTACCCCAGGACGGGGT;RSEQ=GGGTGCGGCACATTCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:21.1:1:30.2:1:1:0:60:17:1:0:0.9 0/1:25:2:1,1:9,14:0.08:2,2:25.5:1:28.5:1:1:1.53:60:4:0.08:0:2 -2 101992225 . T C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.66075;LSEQ=CCATTCTGGCTCCAAGGCTG;RSEQ=GTCTCTCCCCTGAACTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:5,6:0.0833:2,0:41:0:32:0:1:0:60:2:0.0833:0:2 0/1:15:2:2,0:5,8:0.1333:2,0:40.5:1:32:1:0.2:0:60:4:0.1333:0:1 -2 101992329 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14675;SOR=Inf;LSEQ=CAAGGGCCTATGCTGCGGCT;RSEQ=CACCCCTTCCTCTCCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:21,12:0:2,0:25.8:1:31.9:1:1:0:60:66:1:0:0 0/1:21:2:1,1:9,10:0.0952:2,2:16.5:1:27:1:1:1.11:60:4:0.1:0:1 -2 101992383 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24352;SOR=Inf;LSEQ=GACAAGTCGTTACTGACTGT;RSEQ=TTCAAGGGGGTGGATCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:16,22:0:2,0:26.3:1:31.9:1:1:0:60:76:1:0:0.2 0/1:43:3:2,1:20,20:0.0698:2,2:35.7:1:30:1:1:1.97:60:6:0.0698:0:1.3 -2 101992421 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49675;SOR=Inf;LSEQ=CAGAAGGCTGTCAAGGCAGG;RSEQ=CTGTCGGCAGTTTCAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:6,19:0:2,0:20.7:1:31.5:1:1:0:60:50:1:0:0.5 0/1:31:2:1,1:12,17:0.0645:2,2:28:1:29:1:1:1.40:60:4:0.0645:0:1 -2 101992445 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=TCGGCAGTTTCAGCTTTCAG;RSEQ=TTTGCTGGGCTGTGCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:2,12:0.125:2,2:21:1:29.5:1:0.35:5.10:60:4:0.125:0:1 0/0:15:0:0,0:4,11:0:2,0:22.6:1:30.5:1:1:0:60:14:1:0:0.7 -2 101992474 . A G 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47432;LSEQ=GCTGTGCTGTTTCAACTGTC;RSEQ=CGACATGGGCATCTGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:0,2:0.8:0,0:25.3:1:32.1:1:1:0:60:16:0.8:0:1 1/1:14:12:3,9:1,1:0.8571:2,2:26.4:1:30.9:1:0.50549:2.73861:60:11:0.8462:0:1.1 -2 102578173 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24194;SOR=Inf;LSEQ=GTGCCATTTGCTGGTGCTGG;RSEQ=CCTTGGTCAAATCCACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:21,26:0:2,0:26.3:1:31.4:1:1:0:60:46:1:0:0.2 0/1:47:3:1,2:19,25:0.0638:2,2:13:1:25.7:1:1:1.50701:60:6:0.0638:0:1.3 -2 106021437 . C T 168 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCGTCGGATACAGTTTCCA;RSEQ=TGTGGCTTTGATACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:47:33,14:186,111:0.1366:2,2:26.8:1:30.3:1:0.33351:1.41:60:22.5:0.1331:0:1.1 0/0:312:0:0,0:187,125:0:2,0:24.5:1:31.4:1:1:0:60:61.4:1:0:0.4 -2 106021465 . ACT A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TTGATACCTCTTTAAGAAAG;RSEQ=CTGTTTGGTACATTAATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:22:12,10:231,176:0.0513:2,2:21.7:1:31.7:1:0.82947:1.09352:60:44:0.0516:0.0093:1 0/0:411:0:0,0:231,177:0:2,0:25.5:1:31.4:1:1:0:60:101:0.9975:0:0.6 -2 106021488 . C G 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00656;SOR=0.68885;LSEQ=CTGTTTGGTACATTAATGAC;RSEQ=AATAGAATGAAACTATTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:276:132,144:90,69:0.6301:2,2:26.4:1:30.4:1:0.09046:1.42174:60:137:0.6299:0:1.1 1/0:452:244:129,115:108,96:0.5398:2,2:26.5:1:30.1:1:1:1.0029:60:243:0.5412:0:1.1 -2 106021547 . G A 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CCAGTAAATGTTGCTGGATG;RSEQ=TTTCAGATGAAAAGTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:120,219:0:2,0:25.6:1:31.7:1:1:0:60:168.5:1:0:0.4 0/1:333:13:5,8:127,193:0.039:2,2:21.8:1:30.2:1:1:1.05269:60:26:0.0395:0:1.2 -2 106021801 . G C 33 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGCTTCCCTAAAATACCT;RSEQ=AAATGGGAGATTCTTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:12.5:1:33:0:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:1:0,0:47:0:16:0:1:0:60:0:0:0:2 -2 106678447 . G A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09693;SOR=Inf;LSEQ=AAAATGAAGCCCTCTCGGCT;RSEQ=TCGAATCTCTCTTACTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:37,3:0:2,0:21.1:1:31:1:1:0:60:19:1:0:1.3 0/1:35:3:3,0:31,1:0.0857:1,0:19:1:29.3:1:1:0:60:6:0.0882:0:2 -2 106678449 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10097;SOR=Inf;LSEQ=AATGAAGCCCTCTCGGCTGT;RSEQ=GAATCTCTCTTACTGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:36,3:0:2,0:22.2:1:30.4:1:1:0:60:38:1:0:1.4 0/1:35:3:3,0:30,2:0.0857:2,0:21:1:31.3:1:1:0:60:6:0.0857:0:2 -2 106678450 . G A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.64822;SOR=1.24953;LSEQ=ATGAAGCCCTCTCGGCTGTC;RSEQ=AATCTCTCTTACTGCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:24:21,3:16,0:0.5854:1,2:21.7:1:29:1:0.26154:0:60:11:0.5789:0:1.9 1/0:36:23:22,1:11,2:0.6389:2,1:21.4:1:29.2:1:0.53936:3.84:60:10.5:0.6176:0:1.9 -2 106678497 . T C 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26055;SOR=0.68367;LSEQ=AGGCAGAGTCAAGATGGACC;RSEQ=GGCCTTGCTGTGGTTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:47:32,15:22,7:0.6184:2,2:26.3:1:28.6:1:0.60433:1.46585:60:10.75:0.5972:0:1.5 1/0:80:42:31,11:27,11:0.525:2,2:26.2:1:29:1:0.80702:1.15:60:41:0.519:0:1.5 -2 106678555 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24453;SOR=0;LSEQ=ATCAAAGGCAGCTCCGTCTT;RSEQ=GACCCTGCCCCCTTTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:90,66:0.0127:2,2:20.5:1:31:1:1:1.3609:60:4:0.013:0:2 0/0:161:0:0,0:85,76:0:2,0:26:1:28.9:1:1:0:60:79.5:1:0:0.6 -2 106678562 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24777;SOR=0;LSEQ=GCAGCTCCGTCTTAGACCCT;RSEQ=CCCCCTTTCCCCTGTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:94,72:0.0119:2,2:29:1:30.5:1:1:1.30345:60:4:0.0123:0:1 0/0:169:0:0,0:83,86:0:2,0:25.6:1:31.2:1:1:0:60:23.143:1:0:0.6 -2 106678595 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50122;SOR=0;LSEQ=TGTGTGCATTCAGCTCACGG;RSEQ=ACGCTCGCAGAGTGATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:93,88:0.0109:2,2:32.5:1:30.5:1:1:1.05652:60:4:0.011:0:2 0/0:158:0:0,0:72,86:0:2,0:27.3:1:31.7:1:1:0:60:316:1:0:0.7 -2 106678604 . A T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25408;SOR=0;LSEQ=TCAGCTCACGGCACGCTCGC;RSEQ=GAGTGATGGCACTTCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:2,1:96,93:0.0156:2,2:16.7:1:28.7:1:1:1.93:60:6:0.0161:0:2 0/0:160:0:0,0:69,91:0:2,0:26.3:1:29.9:1:1:0:60:52.333:1:0:0.8 -2 106678606 . A G 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.91195;SOR=0.9622;LSEQ=AGCTCACGGCACGCTCGCAG;RSEQ=GTGATGGCACTTCCTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:191:119:62,57:35,37:0.623:2,2:24.3:1:30:1:0.657:1.15:60:18.833:0.6209:0:1.1 1/0:158:97:43,54:26,35:0.6139:2,2:25.4:1:29.6:1:0.87022:1.07:60:31.333:0.6184:0:1.2 -2 106678644 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20633;SOR=Inf;LSEQ=AGTCCTCTATCTGCTATTGC;RSEQ=AGGTATCTGTGAATTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:68,96:0:2,0:27.2:1:31.2:1:1:0:60:40:1:0:0.7 0/1:137:2:1,1:54,81:0.0146:2,2:27:1:28:1:1:1.50:60:4:0.015:0:1.5 -2 106678692 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51072;SOR=0;LSEQ=GGGAGGACCACTGAGGCCCC;RSEQ=GAGTCACGTGGAGGAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:27,66:0.0211:2,2:18:1:29.5:1:0.50482:2.42:60:4:0.0211:0:1 0/0:68:0:0,0:19,47:0:2,0:26.1:1:29.8:1:1:0:60:65:0.9701:0:0.5 -2 106678715 . A G 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53778;SOR=0.72216;LSEQ=GTCACGTGGAGGAAGGGAAC;RSEQ=CCATGTCTGGACTGTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:37:12,25:3,19:0.6271:2,2:18.2:1:31:1:0.13309:2.99:60:74:0.6379:0:1.2 1/0:42:23:5,18:7,12:0.5476:2,2:23.2:1:31.3:1:0.32267:2.06232:60:22:0.5366:0:1.1 -2 106678755 . G A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.13937;SOR=0.27827;LSEQ=GAGAAGGTCAGTCTGACAAT;RSEQ=TGTGACAATGGTATGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:2,14:1,9:0.6154:2,2:29.9:1:30.4:1:1:1.27:60:15:0.625:0:1.9 0/1:10:3:0,3:0,7:0.3:0,0:26.7:1:32:0:1:0:60:6:0.3:0:1.7 -2 106678977 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGATAATATTGCCCCCAT;RSEQ=TTACCTCTGGCCTAGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:10:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 108622946 . G A 77 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGTCTCCCAAAGTGCTGG;RSEQ=ATTATAGGTGTGAGCTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:17.2:1:29.8:1:1:0:55.3:12:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 108623227 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08347;SOR=Inf;LSEQ=TGTTCTTTTAAAACCCCTAG;RSEQ=TGAGTTGAGAGCCAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:218,77:0:2,0:25.3:1:31.2:1:1:0:60:146.5:1:0:0.1 0/1:230:3:1,2:159,68:0.013:2,2:5.7:1:28:1:0.22041:4.64113:60:6:0.0131:0:1.3 -2 108623322 . T G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00536;SOR=1.46371;LSEQ=CACTTTGAACTTGAGATTTC;RSEQ=GCTTTACACCTTTAGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:478:198:81,117:118,161:0.4142:2,2:24.6:1:30.5:1:0.77811:1.0585:60:396:0.4168:0:1.1 1/0:401:204:91,113:90,107:0.5087:2,2:27.3:1:29.9:1:0.8415:1.04438:60:203:0.5088:0:1.1 -2 108623340 . G T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02128;SOR=Inf;LSEQ=TCTGCTTTACACCTTTAGTA;RSEQ=TTTTTAATTAGGGGTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:162,252:0:2,0:23.9:1:32.1:1:1:0:60:137:1:0:0.5 0/1:359:5:2,3:150,203:0.0139:2,2:14:1:30.4:1:1:1.10809:60:10:0.014:0:1.8 -2 108623538 . T C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTAATTAAATGTATTAA;RSEQ=TACTCCTGACCTTTATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:0.2143:0,0:27:1:31.3:1:1:0:60:6:0.2143:0:1 0/0:4:0:0,0:0,4:0:0,0:12.8:1:30:1:1:0:60:8:1:0:0 -2 108623666 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTAAAGTTCACCTTTTG;RSEQ=CCTGTGGTATTCTGTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:21:1:30.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 108623876 . GA G 33 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTATGTAGTGTTTGTCTCT;RSEQ=AAAAAAAAAAGATAGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:33.5:1:1:0:60:4:1:0:0.5 -2 109004001 . C T 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=CCAGTTATCAGAATAGTTTA;RSEQ=TGTGTTTGCTCTTATTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:25.3:1:32.8:1:1:0:60:8:1:0:0 0/1:10:3:2,1:5,2:0.3:2,2:11.7:1:29:1:1:1.22183:60:6:0.3333:0:1 -2 109004506 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACCCCATGATCCACCCGC;RSEQ=TCGGCCTCCCAAAGTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:30.5:1:1:0:57:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:13:0:33:1:1:0:60:4:1:0:1.5 -2 109201157 . A G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=CAGGTTTTCTGAGTTGTTTG;RSEQ=GGATGTGAGCATTAGCGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:27,11:0.05:2,2:8.5:1:27.5:1:0.51538:2.39319:60:4:0.0513:0:1.5 0/0:28:0:0,0:20,8:0:2,0:18.5:1:29.1:1:1:0:60:56:1:0:0.1 -2 109201345 . C T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GGGCCTGGAGCAGTAGCTCA;RSEQ=GCTTGTAATCCCAGCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:30.5:1:31:1:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:0,2:0:0,0:11.5:1:28.5:1:1:0:60:4:1:0:0 -2 110053094 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49834;SOR=Inf;LSEQ=TGTGGTATAAAAGATTTCGT;RSEQ=CAGCTCATTCCTCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:118,33:0:2,0:22.6:1:30.1:1:1:0:60:74.5:1:0:0.1 0/1:151:2:2,0:114,35:0.0132:2,0:19:1:26:1:1:0:60:4:0.0133:0:1 -2 110053209 . T G 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05946;SOR=0.74131;LSEQ=CTTCTGCCCAGTGACGGGCA;RSEQ=TGTTTTAGGACCTCGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:144:63,81:85,109:0.426:2,2:26.5:1:32:1:1:1.00261:60:143:0.4256:0:1.1 0/1:341:121:58,63:96,124:0.3548:2,2:24.2:1:30.7:1:0.49534:1.19:60:39.333:0.3522:0:1.3 -2 110053248 . C T 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCAGATCAGTTGGCCTTCAT;RSEQ=TCTTAAAGCCAGCAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:84,166:0:2,0:26.3:1:31.8:1:1:0:60:61.5:1:0:0.4 0/1:216:16:6,10:61,139:0.0741:2,2:22.9:1:30.1:1:0.58042:1.37:60:32:0.0755:0:2 -2 111726228 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51019;SOR=Inf;LSEQ=GTCCCAAAATGTCCATTGCC;RSEQ=AGAAGAAAGATCAGATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:27,25:0:2,0:27.2:1:31:1:1:0:60:51:1:0:0.2 0/1:73:2:1,1:37,34:0.0274:2,2:18:1:28:1:1:1.08696:60:4:0.0294:0:1 -2 111727161 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTGGGAGGCCGAGGTGG;RSEQ=CAGCTTACCTGAGGTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39.5:1:29:1:1:0:60:4:1:0:1 -2 111881124 . CA C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTGGGGGTACCCTCTAC;RSEQ=AAAAAAAATTACACCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:2,0:22,0:0.0833:1,0:26.5:1:31.4:1:1:0:60:4:0.087:0.0417:1.5 0/0:5:0:0,0:5,0:0:0,0:24.4:1:31:1:1:0:60:10:1:0:0 -2 111881156 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCTTTATTATTTTAGGT;RSEQ=CAATTTTTTTATTTGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:40,0:0.0476:1,0:23.5:1:29.5:1:1:0:60:4:0.0488:0:1 0/0:13:0:0,0:13,0:0:1,0:19.7:1:31:1:1:0:60:12:1:0:0.3 -2 111881263 . AT A 148 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01159;LSEQ=GCTAATTTGTTTATTCATCG;RSEQ=TTTTTTTTTTGCTTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:27:20,7:177,20:0.1195:2,2:23.9:1:31.2:1:0.02755:3.07649:60:54:0.1211:0.0265:0.1 0/1:174:21:16,5:130,21:0.1207:2,2:25.6:1:29.7:1:0.32431:1.92583:60:42:0.1214:0.0172:0.4 -2 111881275 . G T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25255;SOR=0;LSEQ=ATTCATCGATTTTTTTTTTT;RSEQ=CTTAAAATAATCTTAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:2,1:221,47:0.0111:2,2:16:1:21:1:0.44414:2.34166:60:2:0.0079:0:2.3 0/0:234:0:0,0:175,57:0:2,0:20.7:1:30.1:1:1:0:59.9:22.2:1:0:0.2 -2 111881810 . C T 128 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00247;SOR=0.19651;LSEQ=AAAATCCCCTTTTAAAACCC;RSEQ=GTAACTGATTTATTCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:18:0,18:1,55:0.2432:1,1:27.8:1:30.8:1:1:0:60:36:0.2535:0:1.1 0/1:68:4:1,3:2,61:0.0588:1,2:23.8:1:30.8:1:0.17105:9.36:60:8:0.0625:0:1.3 -2 111883066 . T C 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12327;SOR=0;LSEQ=AGGAAACCCAGTACAGAGTC;RSEQ=ATTATAATTTAGATTGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:136,77:0.0139:2,2:28:1:26:1:1:1.13:60:2:0.0094:0:1 0/0:217:0:0,0:130,87:0:2,0:24.3:1:29.5:1:1:0:60:107.5:1:0:0.1 -2 111883077 . A T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24843;SOR=0;LSEQ=TACAGAGTCTATTATAATTT;RSEQ=GATTGTACCTCATGATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:142,94:0.0126:2,2:7:1:26.7:1:0.5662:3.00716:60:6:0.0129:0:1 0/0:237:0:0,0:141,96:0:2,0:26.3:1:28.9:1:1:0:60:58.25:1:0:0.1 -2 111883196 . G A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.6236;SOR=0.33269;LSEQ=GCTTCAGTGAGGTAAATCAG;RSEQ=CAGGCCTTTGCCCATGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:116,150:0.0112:2,2:18:1:28.3:1:0.58344:2.58:60:6:0.0114:0:1 0/0:268:1:1,0:110,156:0.0037:2,0:1:0:22:0:0.41573:0:60:2:0.0039:0:1 -2 111883400 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49916;SOR=0;LSEQ=GGGCTGGAAGTTTTATTATT;RSEQ=CTGTTACTACTGCTCGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:94,85:0.011:2,2:22.5:1:26.5:1:1:1.10527:60:4:0.0114:0:1 0/0:169:0:0,0:88,81:0:2,0:24.6:1:31.2:1:1:0:60:27.167:1:0:0.2 -2 111883401 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23529;SOR=Inf;LSEQ=GGCTGGAAGTTTTATTATTG;RSEQ=TGTTACTACTGCTCGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:94,87:0:2,0:26.4:1:31.7:1:1:0:60:29.167:1:0:0.2 0/1:171:2:1,1:88,81:0.0117:2,2:27.5:1:26:1:1:1.08588:60:4:0.012:0:1.5 -2 111883407 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49987;SOR=0;LSEQ=AAGTTTTATTATTGCTGTTA;RSEQ=TACTGCTCGTGAACTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:98,88:0.0106:2,2:7.5:1:27.5:1:1:1.113:60:4:0.0106:0:1 0/0:170:0:0,0:88,82:0:2,0:24:1:31.3:1:1:0:60:169:1:0:0.2 -2 111883412 . G A 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61092;SOR=2.15742;LSEQ=TTATTATTGCTGTTACTACT;RSEQ=CTCGTGAACTCATTTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:1,0:99,88:0.0053:2,0:10:0:11:0:1:0:60:0:0:0:5 0/1:175:2:1,1:91,82:0.0114:2,2:29.5:1:24:0:1:1.10909:60:4:0.0116:0:1 -2 111883494 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21502;SOR=Inf;LSEQ=ATGCTCCCCCATATATATGA;RSEQ=CATTCTCGCTTACTATAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:94,87:0:2,0:24:1:30.6:1:1:0:60:180:1:0:0.1 0/1:157:2:1,1:89,66:0.0127:2,2:27.5:1:28:1:1:1.34587:60:4:0.0129:0:1.5 -2 111883499 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49949;SOR=0;LSEQ=CCCCCATATATATGATCATT;RSEQ=TCGCTTACTATAACATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:95,83:0.0111:2,2:26:1:32.5:1:1:1.14372:60:4:0.0113:0:2 0/0:165:0:0,0:94,71:0:2,0:22.3:1:31.1:1:1:0:60:81.5:1:0:0.1 -2 111883682 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21933;SOR=Inf;LSEQ=GTTCCCTTTCAAGCAAAATG;RSEQ=ATACATTGGTCTCTGTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:108,106:0:2,0:25.3:1:31.9:1:1:0:60:52.5:1:0:0.1 0/1:189:2:1,1:89,98:0.0106:2,2:12:1:29.5:1:1:1.10:60:4:0.0108:0:1 -2 111883779 . T A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24906;SOR=Inf;LSEQ=AGATAGTGTATTTTTTAATG;RSEQ=AAAGACAGGCACAAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:109,116:0:2,0:26.4:1:29.3:1:1:0:60:450:1:0:0.1 0/1:239:3:2,1:111,125:0.0126:2,2:6.3:1:26.7:1:0.60394:2.24:60:6:0.0126:0:1 -2 111883806 . T A 86 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03708;SOR=7.21465;LSEQ=AGGCACAAATGCTTTTTTTG;RSEQ=TGATAAATACTATTTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:1:1,0:92,118:0.0047:2,0:1:0:28:0:0.44076:0:60:2:0.0047:0:1 0/1:210:7:4,3:93,110:0.0333:2,2:29.3:1:30.9:1:0.7061:1.57:60:14:0.0338:0:1.3 -2 111883823 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24683;SOR=Inf;LSEQ=TTGTTGATAAATACTATTTT;RSEQ=CAAGCTAATTATAAGTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:90,108:0:2,0:23:1:29.2:1:1:0:60:197:1:0:0.1 0/1:196:2:1,1:80,114:0.0102:2,2:18:1:30.5:1:1:1.42:60:4:0.0105:0:1 -2 111883855 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19706;SOR=Inf;LSEQ=TAAGTTAAGCACTGTTACTT;RSEQ=AGATGAAATATACAGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:87,89:0:2,0:23.4:1:31.7:1:1:0:60:175:1:0:0.1 0/1:141:2:1,1:56,82:0.0142:2,2:25:1:27.5:1:1:1.46:60:4:0.0144:0:1 -2 111884280 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15312;SOR=Inf;LSEQ=GGTTCTCTTGACTTTGTTTA;RSEQ=TATTCTTTACTCAACCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:86,89:0:2,0:24.9:1:32.1:1:1:0:60:86.5:1:0:0 0/1:113:2:1,1:52,58:0.0177:2,2:21.5:1:27:0:1:1.11:60:4:0.0177:0:1 -2 111884464 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50133;SOR=0;LSEQ=CAAAGCAGTTTTTTGCTCAG;RSEQ=AACTTGGGGTAGAGATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:67,72:0.0142:2,2:29.5:1:29.5:1:1:1.07:60:4:0.0145:0:1 0/0:120:0:0,0:58,61:0:2,0:25.6:1:31.9:1:1:0:60:238:0.9917:0:0 -2 111884472 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50062;SOR=0;LSEQ=TTTTTTGCTCAGCAACTTGG;RSEQ=GTAGAGATCAGTGTGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:67,76:0.0138:2,2:8.5:1:27:1:1:1.13:60:4:0.0139:0:1 0/0:126:0:0,0:57,69:0:2,0:24.4:1:30.3:1:1:0:60:252:1:0:0.1 -2 111884592 . CT C 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00965;SOR=1.91222;LSEQ=AACACTGTTTTCATATTTTC;RSEQ=TTTATGTCTCTGATTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:56:24,32:56,58:0.3275:2,2:24.3:1:31.8:1:0.51393:1.28544:60:112:0.3275:0.0292:0.1 0/1:116:56:28,28:32,28:0.4828:2,2:22.7:1:31:1:0.85263:1.14154:60:112:0.487:0.069:0.4 -2 111884658 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50335;SOR=0;LSEQ=TCTCTGTGGGGCAACAGATA;RSEQ=AGTTTTTTCACTTTTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:61,76:0.0144:2,2:13:0:31:1:1:1.24:60:4:0.0145:0:1 0/0:113:0:0,0:61,52:0:2,0:22.5:1:31.1:1:1:0:60:36.667:1:0:0.2 -2 111884689 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22047;SOR=Inf;LSEQ=CTTTTCCTCAATTTTAGTCT;RSEQ=CTTACACTCTGGGAGGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:71,64:0:2,0:25.9:1:31.4:1:1:0:60:66.5:1:0:0.1 0/1:120:2:1,1:68,50:0.0167:2,2:33:1:31:1:1:1.35645:60:4:0.0169:0:1 -2 111884802 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49899;SOR=Inf;LSEQ=GTGCCTTTTTGGATGAGTGT;RSEQ=TTATGCCATATGTGTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:80,94:0:2,0:25.8:1:29.7:1:1:0:60:33.8:1:0:0.1 0/1:184:2:1,1:86,96:0.0109:2,2:21.5:1:30:1:1:1.12:60:4:0.011:0:1 -2 111884909 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23748;SOR=Inf;LSEQ=AAGTCAGGATATGGAGGAAT;RSEQ=CTCCCTAGTGTCATGTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:36,55:0:2,0:21.6:1:32:1:1:0:60:90:1:0:0.1 0/1:87:2:1,1:31,54:0.023:2,2:12:0:30.5:1:1:1.73:60:4:0.0233:0:1 -2 111884937 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50105;SOR=Inf;LSEQ=GTGTCATGTTAGTAAATGTC;RSEQ=TAAATTTTATACTTGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:34,42:0:2,0:27.7:1:30.6:1:1:0:60:75:1:0:0.2 0/1:91:2:1,1:39,50:0.022:2,2:28.5:1:31:1:1:1.28:60:4:0.022:0:1 -2 111885058 . C A 31 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63148;LSEQ=CTCTTATAGCTGGTACTTGT;RSEQ=TGACCCCTCCTTTAGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:71,47:0.0163:2,2:22:0:31.5:1:1:1.50527:60:4:0.0185:0:1 0/1:97:1:0,1:48,46:0.0103:2,0:2:0:28:0:0.49474:0:60:2:0.0112:0:1 -2 111885088 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19236;SOR=Inf;LSEQ=CTTTAGTTTGTGAGCTCCCT;RSEQ=GGCGGGGAATAATGGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:89,55:0:2,0:26.7:1:30.7:1:1:0:60:17:1:0:0.3 0/1:113:2:1,1:57,54:0.0177:2,2:29:0:27.5:1:1:1.05507:60:4:0.0185:0:1.5 -2 111885134 . A G 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22045;SOR=Inf;LSEQ=CTAGCGAGTGCCTGACAAAG;RSEQ=GGAGAAGCCCAGGAGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:85,76:0:2,0:24.7:1:29.4:1:1:0:60:15.1:1:0:0.2 0/1:143:2:1,1:71,70:0.014:2,2:8:0:28:1:1:1.01419:60:4:0.0148:0:1 -2 111885189 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50238;SOR=0;LSEQ=CTCTGCCTGTTAGCCTTTCA;RSEQ=ACAAATAAAGTTGAAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:80,112:0.0103:2,2:28:1:30:1:1:1.40:60:4:0.0105:0:1 0/0:163:0:0,0:78,85:0:2,0:24.4:1:30.8:1:1:0:60:39.75:1:0:0.2 -2 111885199 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58341;SOR=2.58187;LSEQ=TAGCCTTTCAGACAAATAAA;RSEQ=TTGAAGAAGGCAGGTAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:76,113:0.0053:2,0:12:0:13:0:1:0:60:0:0:0:6 0/1:148:2:1,1:67,79:0.0135:2,2:5:1:30:1:1:1.18:60:4:0.0135:0:1 -2 111885210 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51168;SOR=0;LSEQ=ACAAATAAAGTTGAAGAAGG;RSEQ=AGGTAGCAAGAAAAAGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:78,106:0.0108:2,2:8:0:30.5:1:1:1.36:60:4:0.011:0:1.5 0/0:134:0:0,0:60,74:0:2,0:26:1:31.4:1:1:0:60:66:1:0:0.2 -2 111885244 . G T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02808;SOR=Inf;LSEQ=AAGATCCTGACCTCTGCTCT;RSEQ=CCAAAGTGTTTTTAATTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:61,84:0:2,0:25.3:1:31.7:1:1:0:60:23.167:1:0:0.2 0/1:102:4:1,3:46,52:0.0392:2,2:25.3:1:28.8:1:0.62225:2.6307:60:8:0.0396:0:1 -2 111885270 . C A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28352;SOR=0;LSEQ=GTGTTTTTAATTACCTGGAT;RSEQ=TAGCTGTAAGGTTTGCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:1,2:63,52:0.0254:2,2:27.7:1:25:1:0.59214:2.40535:60:2:0.0172:0:1.3 0/0:75:0:0,0:40,35:0:2,0:26.8:1:31.4:1:1:0:60:74:1:0:0.1 -2 111885392 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16764;SOR=Inf;LSEQ=CTGAACTGAGTTGTGCTGTC;RSEQ=TTATTGATACACACTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:95,99:0:2,0:26.4:1:30.6:1:1:0:60:193:1:0:0.1 0/1:135:2:1,1:66,67:0.0148:2,2:38:1:31.5:1:1:1.02:60:4:0.0148:0:1 -2 111885507 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18411;SOR=Inf;LSEQ=TATATAGGTTAAATAAAATA;RSEQ=AAACTTGTATTGCAGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:97,62:0:2,0:25.1:1:30.1:1:1:0:60:318:1:0:0.2 0/1:120:2:1,1:70,48:0.0167:2,2:24.5:1:29.5:1:1:1.45362:60:4:0.0167:0:1 -2 111885515 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18073;SOR=Inf;LSEQ=TTAAATAAAATATAAACTTG;RSEQ=ATTGCAGTTAAACACAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:102,65:0:2,0:24.9:1:29.3:1:1:0:60:334:1:0:0.2 0/1:124:2:1,1:75,47:0.0161:2,2:12:1:26.5:1:1:1.58947:60:4:0.0161:0:1 -2 111885554 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22366;SOR=Inf;LSEQ=GCGTAAAATTTACCATCTGA;RSEQ=CCATTTATTTCTAAGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:130,89:0:2,0:24.7:1:29.2:1:1:0:60:26.375:1:0:0.3 0/1:197:2:1,1:120,75:0.0102:2,2:23:1:31:0:1:1.59599:60:4:0.0104:0:1 -2 111885565 . C T 168 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCATCTGAACCATTTATTT;RSEQ=TAAGTGTACTGTTCAGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:47:27,20:108,82:0.1983:2,2:26.4:1:30.4:1:1:1.02:60:94:0.2009:0:1.1 0/0:218:0:0,0:133,85:0:2,0:24.9:1:30.8:1:1:0:60:26.25:1:0:0.1 -2 111885578 . T C 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11863;SOR=0;LSEQ=TTTATTTCTAAGTGTACTGT;RSEQ=CAGTAGTGTTAAGTGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:1,2:138,116:0.0117:2,2:32:1:26:1:0.59525:2.37149:60:2:0.008:0:1.7 0/0:265:0:0,0:155,110:0:2,0:23.9:1:29.1:1:1:0:60:52:1:0:0.1 -2 111885684 . TC T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.12352;SOR=0;LSEQ=AACAACTCCCCATTTCCCCC;RSEQ=CCCCCAGCTTCTGACAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:4:2,2:98,118:0.0181:2,2:26.8:1:30.3:1:1:1.20:60:8:0.0184:0.0045:0.3 0/0:213:0:0,0:88,125:0:2,0:23.3:1:30.4:1:1:0:60:41.6:1:0:0.1 -2 111885697 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24547;SOR=0;LSEQ=TTCCCCCTCCCCCCAGCTTC;RSEQ=GACAACCACCATTCTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:83,106:0.0105:2,2:13.5:1:29.5:1:1:1.28:60:4:0.0106:0:1 0/0:194:0:0,0:77,117:0:2,0:23.8:1:29.8:1:1:0:60:47.5:1:0:0.2 -2 111885720 . G T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24889;SOR=0;LSEQ=CAACCACCATTCTATTTTCT;RSEQ=TCTATTAATTTGACAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:1,2:68,104:0.0171:2,2:22.7:1:31.3:1:1:1.30575:60:6:0.0171:0:2 0/0:162:0:0,0:56,106:0:2,0:24.8:1:30.9:1:1:0:60:53:1:0:0.1 -2 111885727 . A T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5969;SOR=2.34828;LSEQ=CATTCTATTTTCTGTCTATT;RSEQ=ATTTGACAACTTCAGATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:66,100:0.006:2,0:10:0:11:0:1:0:60:0:0:0:5 0/1:143:2:1,1:48,93:0.014:2,2:20:1:26:1:1:1.93:60:4:0.0147:0:1.5 -2 111885947 . T C 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24893;SOR=0;LSEQ=ATACTTGGGTTGCTTCCACT;RSEQ=TTTGGCTATTGTGAGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:2,1:75,29:0.028:2,2:29.3:1:26.3:1:1:1.28987:60:2:0.0194:0:1.3 0/0:95:0:0,0:63,32:0:2,0:21.1:1:28.6:1:1:0:60:30.667:1:0:0.1 -2 111885951 . G C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50057;SOR=0;LSEQ=TTGGGTTGCTTCCACTTTTT;RSEQ=GCTATTGTGAGTAGTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:84,37:0.0163:2,2:15:1:27.5:1:0.52419:2.25353:60:4:0.0164:0:1 0/0:106:0:0,0:67,39:0:2,0:21.1:1:30.2:1:1:0:60:52:1:0:0.1 -2 111886041 . G A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68659;SOR=1.8804;LSEQ=TTTTGGATATATACTTGGAA;RSEQ=TGGAATTGCTGGATCATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:2:2,0:108,117:0.0088:2,0:1:0:20:1:0.23371:0:60:1:0.0045:0:1 0/1:243:4:3,1:114,125:0.0165:2,2:14:1:26.5:1:0.35421:3.27:60:8:0.0167:0:1 -2 111886066 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=ATTGCTGGATCATATGGTAA;RSEQ=TCTATTTTTAATTTTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:70,79:0:2,0:20.9:1:30.2:1:1:0:60:36.25:1:0:0.1 0/1:154:2:1,1:75,77:0.013:2,2:10:0:33.5:1:1:1.03:60:4:0.013:0:1.5 -2 111886332 . C T 253 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAGGATTTCTCATGATAC;RSEQ=TTTTTATAGCCACAGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:996:0:0,0:410,586:0:2,0:25.6:1:31.5:1:1:0:60:75.615:1:0:0.1 0/1:940:328:152,176:254,356:0.3489:2,2:26.5:1:30.3:1:0.16781:1.21:60:163:0.3517:0:1.2 -2 111886444 . T C 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.08367;SOR=Inf;LSEQ=TTTCTCTGTTTCTTTCTACC;RSEQ=TTTTAAACATGGCTACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:94,207:0:2,0:24.5:1:30.6:1:1:0:60:59.2:1:0:0.1 0/1:235:3:0,3:75,156:0.0128:2,0:10.3:1:33.7:1:0.55313:0:60:6:0.0129:0:1 -2 111886914 . C T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGGAAACTTTTTAGGTC;RSEQ=TAAGTGGGGAGAGAAAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:31.3:1:30.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 111887368 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22206;SOR=Inf;LSEQ=CTTTCTGTCTCTTCCTTACC;RSEQ=ATGATAACCACTCATCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:62,153:0:2,0:20.9:1:31.4:1:1:0:60:70.667:1:0:0.1 0/1:193:2:1,1:62,129:0.0104:2,2:28.5:1:28.5:1:0.54744:2.07:60:4:0.0105:0:1 -2 111887384 . C A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11975;SOR=Inf;LSEQ=TACCCATGATAACCACTCAT;RSEQ=TGATCTACATATCTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:24,119:0:2,0:21.9:1:32.2:1:1:0:60:142:1:0:0.1 0/1:140:3:2,1:36,101:0.0214:2,2:13:1:24.7:1:0.17906:5.53:60:6:0.0214:0:1 -2 111887564 . C T 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36328;SOR=3.14836;LSEQ=ATAGTATTCCATAGATGATG;RSEQ=ACCACAGTTTGCTTAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:1,0:163,81:0.0041:2,0:12:0:30:0:1:0:60:2:0.0042:0:1 0/1:235:3:1,2:166,65:0.0128:2,2:7:1:24.7:1:0.19787:5.0664:60:6:0.013:0:2 -2 111887621 . C T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06403;SOR=Inf;LSEQ=ACTGTGTTTGCATGTTCTGG;RSEQ=AAGGCCCTGGCACAGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:0:0,0:206,226:0:2,0:28:1:31.6:1:1:0:59.9:23:0.9976:0:0.3 0/1:491:5:2,3:238,246:0.0102:2,2:30.4:1:28.4:1:1:1.45012:60:10:0.0105:0:1 -2 111887703 . T A 180 LongAT STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00064;SOR=2.34455;LSEQ=TCTCTTTTTTTTTTTTTTTG;RSEQ=GACAGTCTCACTCTGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:42:5,37:25,70:0.3043:2,2:18.7:1:29.6:1:0.07394:2.62617:56.6:6:0.2791:0:2 1/0:140:71:13,58:14,55:0.5071:2,2:20.5:1:29.4:1:0.83209:1.13463:57.1:13.2:0.5:0:1.9 -2 111899787 . A T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52373;SOR=0;LSEQ=CTTAACTTGCACTTGTGCTA;RSEQ=TGAAGACTCTACCTCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:151,7:0.0125:1,2:5:1:25.5:1:0.0978:20.24495:60:4:0.0127:0:1 0/0:101:0:0,0:95,6:0:2,0:23.8:1:30:1:1:0:60:100:1:0:0.1 -2 111899881 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21215;LSEQ=TATTTATACAACATTTTTAT;RSEQ=GCTTGCAGATGACTCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:195:114,81:268,182:0.3019:2,2:24.1:1:29.1:1:0.79429:1.04617:60:194:0.3046:0:1.1 0/1:560:47:29,18:296,216:0.0839:2,2:21.8:1:30:1:0.64579:1.18:60:94:0.0848:0:1.2 -2 111901935 . GGT G 88 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.14474;SOR=0.18843;LSEQ=GAGAAATAGACCTGGAGGGA;RSEQ=GTGTGTGTGTGTTGTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:7:5,2:166,14:0.0374:2,2:25.4:1:31.4:1:0.11203:4.67441:60:14:0.0378:0.0053:0.1 0/0:138:1:1,0:121,14:0.0072:2,0:20:0:34:0:1:0:60:2:0.0075:0:0 -2 111907691 . T C 296 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=2.02366;LSEQ=GCCCAAGAGTTGCGGCGTAT;RSEQ=GGAGACGAGTTTAACGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1325:706:340,366:299,320:0.5328:2,2:26.5:1:30.3:1:1:1.00582:60:63.182:0.5309:0:1.1 1/0:1254:875:423,452:183,190:0.6978:2,2:26.8:1:30.3:1:0.8528:1.02918:60:124:0.6983:0:1.2 -2 111907770 . T A 53 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05137;SOR=7.26285;LSEQ=TTCTGCTCACACCCTCCCCT;RSEQ=CCACACTATATTTTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:1:1,0:165,423:0.0017:2,0:1:0:23:0:0.28183:0:60:2:0.0017:0:1 0/1:491:6:5,1:142,342:0.0122:2,2:7.5:1:20.8:1:0.0105:11.98:60:5:0.0106:0:2 -2 111909247 . A G 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACACTATCAGTTCTTCAGT;RSEQ=TGGAATTTCTGTAAGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:149,0:0:1,0:26.9:1:28.6:1:1:0:60:73.5:1:0:0.1 0/1:96:39:38,1:56,1:0.4063:1,1:22.2:1:32.1:1:1:1.46757:60:78:0.4105:0:1 -2 111909271 . A T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07052;SOR=Inf;LSEQ=AATTTCTGTAAGAGTCAAGA;RSEQ=AACACACATCGGATCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:215,8:0:1,0:23.4:1:30.2:1:1:0:60:446:1:0:0.1 0/1:158:3:1,2:141,14:0.019:2,2:15.3:1:26:1:0.02729:19.29977:60:6:0.0194:0:1 -2 111909542 . CT C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18065;SOR=Inf;LSEQ=ATTCCCTCCAGTTCCTCTGC;RSEQ=TGGTTTACCTAAAGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:26,229:0:2,0:21.9:1:30.2:1:1:0:60:62.75:1:0:0.1 0/1:189:2:1,1:20,167:0.0106:2,2:21.5:1:29.5:1:0.2104:8.17:60:4:0.0106:0:0 -2 111909610 . A G 90 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.25755;SOR=0.22351;LSEQ=GGCTGTCTCTATTGACTAGG;RSEQ=AGAACTGGTGAGAAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:7:0,7:1,75:0.0843:1,0:22.1:1:32.3:1:1:0:60:14:0.0843:0:1.1 0/1:50:1:0,1:1,48:0.02:1,0:7:0:32:0:1:0:60:2:0.0204:0:1 -2 111911182 . ATCC A 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00037;SOR=0;LSEQ=GCTGTCTTCACAAGGGAATT;RSEQ=TCTCTTGGCAAGCGAGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:23:23,0:32,2:0.4035:2,1:27:1:31.6:1:0.51003:0:60:46:0.4107:0.0175:0 0/0:20:0:0,0:19,1:0:1,0:26.3:1:30.1:1:1:0:60:40:1:0:0.4 -2 111911251 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=0;LSEQ=TATTAACCTTTTAAATGTTG;RSEQ=GTGTCTTTATTTGCTTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:125,19:0.0137:2,2:22.5:1:29:1:0.25602:6.43797:60:4:0.014:0:1 0/0:133:0:0,0:110,23:0:2,0:19.5:1:29.2:1:1:0:60:43.333:1:0:0.1 -2 111911418 . G T 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.05544;SOR=Inf;LSEQ=CAGTCCACTTAAGGGCAGTG;RSEQ=GGAAGCGTTTGAGACGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:144,231:0:2,0:24.5:1:31:1:1:0:60:92.75:1:0:0.1 0/1:355:4:2,2:140,210:0.0113:2,2:8.5:1:32:0:1:1.50:60:8:0.0115:0:1.5 -2 111918842 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17391;SOR=Inf;LSEQ=CAGCCCATAAAGAGGAAGAT;RSEQ=CCCAGAAGTTTCAGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:65,0:0:1,0:21.5:1:28.2:1:1:0:60:31.5:1:0:0.1 0/1:47:2:1,1:44,1:0.0426:1,2:40:1:32:1:0.08418:31.46141:60:4:0.0435:0:1 -2 111921438 . CTTTT C 34 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=22.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=TTCAAACATTTTTTTGAGTG;RSEQ=TTTTTTTTTTTTTTTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,1:0.2857:2,0:29.5:1:34:0:1:0:50.5:4:0.2857:0:3.5 0/0:4:0:0,0:3,0:0:0,0:8.7:1:32.3:1:1:0:51.3:6:0.75:0:1.3 -2 113103646 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.181;SOR=Inf;LSEQ=GGGTGCCCACCCAGCACTCC;RSEQ=TCGCCCTCCCTGTCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:60,19:0:2,0:22:1:30.5:1:1:0:60:25.333:1:0:0.1 0/1:59:2:1,1:45,12:0.0339:2,2:33:0:32:0:0.39509:3.64304:60:4:0.0339:0:1.5 -2 113103670 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50105;SOR=0;LSEQ=CCCTCCCTGTCCCCTGGCAG;RSEQ=CACGAGGAAGACAGGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:65,43:0.0182:2,2:19:1:28:1:1:1.50576:60:4:0.0182:0:1 0/0:93:0:0,0:59,34:0:2,0:24.8:1:31.1:1:1:0:60:186:1:0:0.1 -2 113103716 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24254;SOR=Inf;LSEQ=TGGATGACCACCTGTCCAGG;RSEQ=TCCTCAAGACCCCTGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:72,80:0:2,0:26.4:1:31.3:1:1:0:60:49.667:1:0:0.2 0/1:148:2:1,1:76,70:0.0135:2,2:13.5:1:28.5:1:1:1.0851:60:4:0.0136:0:1.5 -2 113103726 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49838;SOR=0;LSEQ=CCTGTCCAGGGTCCTCAAGA;RSEQ=CCCTGGCTGCCAGTCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:65,85:0.0132:2,2:25:0:31.5:1:1:1.31:60:4:0.0133:0:1.5 0/0:149:0:0,0:71,78:0:2,0:26.4:1:30.6:1:1:0:59.8:28.8:1:0:0.1 -2 113103819 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49336;SOR=Inf;LSEQ=ACCACCACCACCATCACCAC;RSEQ=AACATCACCATCACCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:1,24:0:1,0:23.3:1:32.2:1:1:0:60:50:1:0:0.8 0/1:29:2:1,1:0,27:0.069:1,2:34.5:1:31:1:0.06897:0:60:4:0.069:0:1 -2 113608823 . A G 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATAGCCTGGGGTTCCTTA;RSEQ=AGAAAATGGAGAAGGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:33.5:1:1:0:60:4:1:0:1 -2 113609886 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTACCTTATCAGTTAAT;RSEQ=GGACTCTTTGATATGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:24.5:1:29.5:1:1:1:60:4:0.5:0:1 -2 113610950 . TCATC T 126 v4;MSI6 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=37;MSI=10.000;MSILEN=4;SSF=0;SOR=14.77001;LSEQ=CAAGAAATCAATCCATCCAT;RSEQ=CATCCATCCATCCATCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:3:3,0:104,15:0.0244:2,0:14.3:1:31.7:1:1:0:60:6:0.0259:0.0163:0 0/1:66:18:17,1:40,9:0.2727:2,1:22.1:1:30.4:1:0.26658:3.77:60:36:0.2727:0.0909:0.4 -2 113611639 . T A 43 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0379;SOR=Inf;LSEQ=AAACAATGTGCTGAAGTGGT;RSEQ=GACAAATGTCTCAAGTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:157,316:0:2,0:25.4:1:29.9:1:1:0:60:117.25:1:0:0.1 0/1:375:4:3,1:133,238:0.0107:2,2:5.8:1:21.5:1:0.13767:5.34:60:3:0.008:0:1.3 -2 113611747 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20535;SOR=Inf;LSEQ=TCGTATTATCCTGATTGAAT;RSEQ=TGTGATGTGAACTGACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:12,96:0:2,0:23.8:1:31.9:1:1:0:59.8:216:1:0:0 0/1:90:2:1,1:23,65:0.0222:2,2:9.5:1:27.5:1:0.46442:2.79:60:4:0.0233:0:1 -2 113687740 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGCTCATGCCTGTAATCCC;RSEQ=CACTTTGGGAGGCTGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:31:1:1:0:60:4:1:0:1.5 -2 113688731 . A G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGATGCCTGGAGTTCTGGC;RSEQ=TGTCTTCTAGCACAATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:0.6667:0,0:14.5:1:29.4:1:1:0:60:16:0.6667:0:1.3 1/0:3:2:2,0:1,0:0.6667:0,0:36:1:29:1:1:0:60:4:0.6667:0:1 -2 113688869 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=3.56432;LSEQ=ACAGATTAAAGATGGCTGCA;RSEQ=ATCCTTTGGTCCAGGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:127:68:67,1:53,6:0.5354:2,1:25:1:30.4:1:0.04896:7.48:60:33:0.528:0:2.9 1/1:77:62:57,5:13,2:0.8052:2,2:20.5:1:30.2:1:0.61655:1.74:60:61:0.8026:0:2.8 -2 113688885 . G T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.10826;LSEQ=TGCAGATCCTTTGGTCCAGG;RSEQ=TTGGGATACAGGCAGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:169:97:90,7:63,9:0.574:2,2:23.5:1:29.1:1:0.29283:1.83:60:31.333:0.5732:0:2.7 1/1:105:89:75,14:13,3:0.8476:2,2:21.4:1:28.6:1:0.72061:1.23:60:43.5:0.8529:0:2.6 -2 113688894 . C T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=3.26865;LSEQ=TTTGGTCCAGGGTTGGGATA;RSEQ=AGGCAGCATTTGTATTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:207:125:107,18:71,11:0.6039:2,2:22.5:1:30.5:1:1:1.08541:60:61.5:0.6:0:2.3 1/1:120:100:83,17:16,4:0.8333:2,2:24.1:1:29.8:1:0.75083:1.22:60:99:0.8319:0:2.5 -2 113688949 . C T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04516;SOR=0;LSEQ=GGCCATGAAAAGTCCACCTG;RSEQ=AGTAGTGGTAGGAGGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:6:2,4:308,183:0.0121:2,2:22:1:27.7:1:0.20443:3.35761:60:12:0.0122:0:1.7 0/0:350:0:0,0:218,132:0:2,0:24.4:1:31.3:1:1:0:60:69:1:0:0.6 -2 113689223 . C A 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05198;SOR=Inf;LSEQ=GAGAAATTCTAAGCTGCCCC;RSEQ=TTAAGAGGCCCACATGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:1,7:0.5:2,0:25.4:1:31.6:1:1:0:60:16:0.5:0:1.1 1/1:7:7:0,7:0,0:1:0,0:16:1:30.4:1:1:0:60:14:1:0:1 -2 113689329 . T G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCGAGTGAACCACTTAG;RSEQ=ACTGTATACTCCAGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:25:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 113690077 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00307;SOR=Inf;LSEQ=AAACTTCTAGGGCTGGTCCC;RSEQ=TGGAAGCCTCACACATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:17:17,0:9,0:0.6296:0,1:16.1:1:29.6:1:1:0:60:16:0.6154:0:1.1 1/1:18:18:18,0:0,0:1:0,1:18.8:1:30.1:1:1:0:60:17:1:0:1.1 -2 113690132 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.2106;SOR=Inf;LSEQ=TGAAAAGAAACGTAAGTGTG;RSEQ=TTTTTGGTTTAATAAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:55,1:0:1,0:23:1:29.8:1:1:0:60:112:1:0:0.4 0/1:48:2:2,0:46,0:0.0417:1,0:5.5:1:32:1:1:0:60:4:0.0417:0:1 -2 113690289 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25815;SOR=0;LSEQ=GGCATTATACCAAAGCTATT;RSEQ=ATAGTTGGGCTTATAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:1,2:157,136:0.0101:2,2:21.7:1:28:1:0.59997:2.30249:60:6:0.0103:0:1.3 0/0:236:0:0,0:123,113:0:2,0:22.1:1:31.2:1:1:0:60:77.667:1:0:0.3 -2 113690316 . T C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15516;LSEQ=GGGCTTATAGGGTGTATGTT;RSEQ=GAAGAACTACTAATGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:105:57,48:110,80:0.3559:2,2:24.2:1:30.9:1:0.62375:1.15731:60:104:0.3574:0:1 0/1:254:20:10,10:118,115:0.0787:2,2:19.2:1:31.2:1:1:1.02599:60:40:0.0803:0:1.2 -2 113690350 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.36135;LSEQ=TGTCAAAACCAATATTTCAC;RSEQ=GTCGACAAGAGGACATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:60:36,24:170,128:0.1671:2,2:27.5:1:30.7:1:0.77491:1.13:60:120:0.1709:0:1.2 0/1:305:123:69,54:101,79:0.4033:2,2:26.6:1:30.1:1:1:1.00055:60:23.6:0.396:0:1.2 -2 113690442 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.50438;LSEQ=GGATTTCCTGCAAATAAAGA;RSEQ=GGGGAAGATATAAAAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:70:36,34:206,171:0.1566:2,2:25.3:1:29.4:1:0.69548:1.13742:60:22.333:0.1526:0:2.1 0/1:397:181:94,87:115,100:0.4559:2,2:24.2:1:29:1:0.7629:1.06418:59.6:17.1:0.443:0:2.1 -2 113690452 . A G 280 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.93733;LSEQ=CAAATAAAGACGGGGAAGAT;RSEQ=TAAAAAAGATGCCTGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:463:462:253,209:0,0:0.9978:0,2:25:1:31.7:1:1:0:60:50.333:1:0:1.2 1/1:434:433:228,205:0,0:0.9977:0,2:25.8:1:31.1:1:1:0:59.8:60.857:0.9977:0:1.5 -2 113690661 . G A 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGAAGACCCACTTCCTAC;RSEQ=TCAGACGTTTTCACCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:210:210:131,79:0,0:1:0,2:23.5:1:30.6:1:1:0:60:69:1:0:1.5 1/1:145:145:79,66:0,0:1:0,2:21.6:1:30.4:1:1:0:60:290:1:0:1.4 -2 113690670 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18336;SOR=Inf;LSEQ=CCACTTCCTACGTCAGACGT;RSEQ=TTCACCAGTTGTCAAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:148,77:0:2,0:24.4:1:30:1:1:0:60:36.5:1:0:1.4 0/1:169:2:1,1:104,63:0.0118:2,2:24:1:27.5:1:1:1.64563:60:4:0.0119:0:3 -2 113690675 . C A 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00573;SOR=0.56071;LSEQ=TCCTACGTCAGACGTTTTCA;RSEQ=CAGTTGTCAAATCCCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:108:68,40:81,40:0.4696:2,2:24.4:1:29.9:1:0.57953:1.19026:60:35:0.4688:0:1.8 0/1:172:57:38,19:76,38:0.3314:2,2:23.6:1:30.2:1:1:1:60:114:0.3373:0:1.8 -2 113690935 . C T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.67388;LSEQ=ACATGCTGCCTATATCCCAA;RSEQ=CCTGGACCAAGCACATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:946:72:31,41:376,498:0.0761:2,2:26:1:29.3:1:1:1.00:60:23:0.074:0:1.2 0/1:770:179:79,100:264,327:0.2325:2,2:26.6:1:27.8:1:0.93171:1.02192:60:12.769:0.2216:0:1.1 -2 113691060 . T C 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05127;SOR=0.63328;LSEQ=GGAATCTTGTCCGTGCACTG;RSEQ=TGTGAATGCTGCAGGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:96:14,82:16,93:0.4683:2,2:24.3:1:31.8:1:1:1.00764:60:47:0.47:0:1.1 0/1:123:44:9,35:19,59:0.3577:2,2:23.2:1:31.6:1:0.66143:1.25008:60:43:0.3583:0:1.1 -2 113691072 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53019;SOR=0;LSEQ=GTGCACTGTTGTGAATGCTG;RSEQ=AGGGCTGACTGTGCAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:18,146:0.012:2,2:23:1:27.5:1:0.21643:7.92:60:4:0.0123:0:2 0/0:99:0:0,0:19,80:0:2,0:21.5:1:31.7:1:1:0:60:48.5:1:0:0.5 -2 113691404 . A G 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCCAGTGTAACAACATT;RSEQ=TCTGACCAATAGTACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:15.3:1:28.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 113977454 . G A 29 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGAAGCAGGAGGGAAAC;RSEQ=AATGCCTGGAAGCCTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:35:1:29.5:1:1:0:60:4:0.25:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 113977703 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60717;SOR=2.20554;LSEQ=TTGGGGAAGCGCCAGGCCTC;RSEQ=CTGTAGGAGGAGTAGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:0,1:143,56:0.005:2,0:1:0:17:0:0.285:0:60:0:0:0:1 0/1:183:2:1,1:122,58:0.0109:2,2:9.5:1:28.5:1:0.54447:2.09413:60:4:0.0111:0:1 -2 113977862 . T G 288 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0.91891;LSEQ=TGGGCAAGCTCAGGAATGGT;RSEQ=GGGGAGACAGTTGGAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:580:579:320,259:0,0:0.9983:0,2:25.4:1:31.4:1:1:0:60:56.9:0.9982:0:1.3 1/1:533:532:281,251:0,0:0.9981:0,2:24.6:1:30.7:1:1:0:60:75:1:0:1.3 -2 113977936 . C T 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50056;LSEQ=TCATCCCTTTTGGAACCCAT;RSEQ=GATCTGGAAAATTTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:745:421:198,223:147,177:0.5651:2,2:26.2:1:29.9:1:0.65738:1.07:60:69.167:0.5654:0:1.3 0/1:731:288:154,134:219,223:0.394:2,2:25.2:1:29.6:1:0.32491:1.17:60:47:0.39:0:1.4 -2 113978183 . A G 151 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=24.30354;LSEQ=CTGCTGCCTGGACCTTCTGG;RSEQ=GAAGGGCTCTTCTGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:2:1,1:220,262:0.0041:2,2:33:1:29.5:1:1:1.19:60:4:0.0043:0:1 0/1:403:37:16,21:176,190:0.0918:2,2:23.5:1:29:1:0.60813:1.2152:60:11.333:0.0876:0:1.2 -2 113978293 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08968;SOR=Inf;LSEQ=AGGTATGAGTGTGTGTGTTT;RSEQ=TGTGCATGGGGGGCTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:0:0,0:208,158:0:2,0:24.4:1:32.1:1:1:0:60:72.2:0.9918:0:0.1 0/1:300:3:1,2:168,129:0.01:2,2:16.7:1:27.3:1:0.58257:2.59646:60:6:0.01:0:1 -2 113978650 . C T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.55715;LSEQ=ATACATTATGATCTTTTATT;RSEQ=TCAAGACTACCCCATGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:92:44,48:156,126:0.2453:2,2:23.7:1:30.2:1:0.2298:1.34954:60:45:0.2426:0:1.2 0/1:339:154:81,73:98,86:0.4543:2,2:22.7:1:29.6:1:0.9133:1.02692:60:153:0.454:0:1.1 -2 113978894 . G A 228 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00428;LSEQ=AATGTCCACCCAGCCTTTCA;RSEQ=AAACTCACCTACGATTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:568:190:102,88:187,189:0.3345:2,2:24.5:1:30.2:1:0.42302:1.17:60:189:0.3351:0:1.1 0/0:467:1:1,0:230,236:0.0021:2,0:1:0:26:0:0.49465:0:60:2:0.0022:0:1 -2 113978906 . C T 165 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=67.95495;LSEQ=GCCTTTCAGAAACTCACCTA;RSEQ=GATTGGGAGCTATGTGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:1:1,0:271,277:0.0018:2,0:35:0:32:0:0.49545:0:60:2:0.0019:0:1 0/1:461:51:22,29:205,204:0.1106:2,2:21.8:1:29.1:1:0.3754:1.32383:60:50:0.1092:0:1.8 -2 113978940 . C G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.10238;LSEQ=GTGGTTCTGAGTCTCCTTCC;RSEQ=CAGACTCTTTGGAGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:124:53,71:213,232:0.2175:2,2:23.5:1:30.7:1:0.3598:1.22946:60:40.333:0.2157:0:1.2 0/1:451:209:101,108:113,128:0.4634:2,2:25.6:1:31:1:0.77712:1.06:60:418:0.4655:0:1.3 -2 113979073 . C A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29003;SOR=0;LSEQ=CTCTCTGAGTGAGTGACTTA;RSEQ=AGGTGAACCTTGGTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:118,173:0.0102:2,2:14.7:1:23:1:0.56918:2.92:60:2:0.0069:0:3.3 0/0:182:0:0,0:78,104:0:2,0:24.4:1:31.2:1:1:0:60:364:1:0:0.1 -2 113979081 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14359;SOR=Inf;LSEQ=GTGAGTGACTTACAGGTGAA;RSEQ=CTTGGTTTCCTTATCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:117,169:0:2,0:23.3:1:31.4:1:1:0:60:56.2:1:0:0.1 0/1:175:2:1,1:73,99:0.0114:2,2:15:1:28:1:1:1.35:60:4:0.0116:0:1 -2 113979098 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15662;SOR=Inf;LSEQ=GAACCTTGGTTTCCTTATCT;RSEQ=TAAAATGGGCCAAATAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:105,137:0:2,0:24.4:1:32.2:1:1:0:60:484:1:0:0.2 0/1:159:2:1,1:71,86:0.0126:2,2:37.5:1:28.5:1:1:1.21:60:4:0.0127:0:1 -2 113979129 . A T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06934;SOR=Inf;LSEQ=CAAATAATTATCCCTATCTC;RSEQ=TTTGGTTTAATGAGAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:131,130:0:2,0:22.8:1:30.6:1:1:0:60:129.5:1:0:0.2 0/1:183:3:1,2:91,89:0.0164:2,2:18.3:1:23.7:1:0.62087:2.03724:60:2:0.0111:0:1.7 -2 113979133 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17277;SOR=Inf;LSEQ=TAATTATCCCTATCTCATTT;RSEQ=GTTTAATGAGAATTAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:136,129:0:2,0:22.8:1:31.6:1:1:0:60:264:1:0:0.2 0/1:189:2:1,1:96,91:0.0106:2,2:7.5:1:28:1:1:1.05467:60:4:0.0108:0:1.5 -2 113979160 . A G 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=8e-05;SOR=0.3282;LSEQ=TGAGAATTAAATGACAAAAT;RSEQ=TGTATTAAATGCTTAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:59:26,33:128,116:0.1947:2,2:24.4:1:31.5:1:0.30978:1.39896:60:28.5:0.1894:0:1.1 0/1:218:16:7,9:106,96:0.0734:2,2:24:1:31.5:1:0.60629:1.41735:60:32:0.0741:0:1.1 -2 113979230 . T C 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.65409;SOR=2.10339;LSEQ=AAATCTAAGCTTTTATTATT;RSEQ=TCCCATTAAACAGGTGCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:2:0,2:188,161:0.0057:2,0:16.5:1:22:1:0.21495:0:60:1:0.0029:0:2 0/1:253:3:1,2:129,120:0.0119:2,2:21.7:1:29.3:1:0.61185:2.14368:60:6:0.012:0:1 -2 113979352 . A T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGACAAGTAGGCATTTAT;RSEQ=CAGGAAGAAGAGAGATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:0:0,0:254,226:0:2,0:25.1:1:28.9:1:1:0:60:95:1:0:0.2 0/1:416:16:8,8:220,180:0.0385:2,2:18.3:1:29.9:1:0.79965:1.22162:60:15:0.0364:0:1.3 -2 113979364 . G A 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.12278;LSEQ=GCATTTATACAGGAAGAAGA;RSEQ=AGATGAAGAGGAGCAGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:70:34,36:209,198:0.1468:2,2:24.6:1:30.3:1:0.69911:1.11739:60:140:0.1471:0:1.1 0/1:436:9:5,4:233,194:0.0206:2,2:15:1:28.7:1:1:1.04:60:18:0.0207:0:1.1 -2 113979446 . C T 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCAATGACGGACTGAGAACA;RSEQ=AGTAAGAAAGTTCCTTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:576:0:0,0:292,283:0:2,0:24:1:31.8:1:1:0:60:94.833:0.9982:0:0.1 0/1:509:50:22,28:239,219:0.0982:2,2:24.9:1:28.7:1:0.29889:1.38805:60:100:0.0996:0:1.2 -2 113979545 . G GA 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.8794;SOR=0.94235;LSEQ=TAAAGAAGTAAAAAAGCAAA;RSEQ=AAAAAAAAACCTAAGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:24:10,14:199,243:0.0508:2,2:30.5:1:30.3:1:0.83475:1.14617:60:48:0.0525:0.0021:0.2 0/1:437:21:10,11:184,227:0.0481:2,2:27.9:1:29.1:1:0.8252:1.12:60:42:0.0495:0:0.1 -2 113979580 . T A 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAATAATCTAATCGAAACA;RSEQ=CTATTTAACAGATGAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:186,196:0:2,0:27.2:1:30.2:1:1:0:60:33.727:1:0:0.1 0/1:381:29:16,13:162,190:0.0761:2,2:25.8:1:28.6:1:0.43919:1.44:60:58:0.0773:0:1 -2 113979653 . T C 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=CAGATAACACAGCTGTGACA;RSEQ=AGGGAAGTAAAGACATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:191,190:0:2,0:24.9:1:29.5:1:1:0:60:126:1:0:0.1 0/1:378:11:7,4:187,179:0.0291:2,2:20.1:1:32.5:1:0.54472:1.67:60:22:0.0294:0:1.1 -2 113980189 . G A 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.09373;LSEQ=ACCTTTCCAAGGATTTGGCC;RSEQ=CTCCAATGATCCCGTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:764:3:3,0:404,357:0.0039:2,0:6.3:1:21.7:1:0.25223:0:60:2:0.0027:0:2.3 0/1:728:75:38,37:342,311:0.103:2,2:22.7:1:29.2:1:0.80796:1.07062:60:150:0.1045:0:1.2 -2 113980203 . G A 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=37.94882;LSEQ=TTGGCCGCTCCAATGATCCC;RSEQ=TTTTCTGTTTCATCAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:792:1:1,0:422,367:0.0013:2,0:1:0:29:0:1:0:60:2:0.0013:0:1 0/1:741:34:17,17:359,348:0.0459:2,2:23.7:1:29.4:1:1:1.03157:60:68:0.0464:0:1.2 -2 113980645 . C G 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00487;SOR=0.6183;LSEQ=CAATGGCTGAAATTTATACT;RSEQ=TAGTCAGGATTCTTTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:125:63,62:162,157:0.2809:2,2:22:1:32.4:1:1:1.01544:60:124:0.2831:0:1.1 0/1:360:70:34,36:144,146:0.1944:2,2:22.7:1:31:1:0.89471:1.04421:60:22.333:0.1882:0:1.1 -2 113980736 . C T 185 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=25.64914;LSEQ=TAGGCATCTCAATCATAACA;RSEQ=GGCCCAAAAAACTCTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:790:4:3,1:420,366:0.0051:2,2:35:1:26.8:1:0.62783:2.61:60:3:0.0038:0:1.3 0/1:666:77:39,38:324,265:0.1156:2,2:24.9:1:29.6:1:0.54315:1.19097:60:154:0.1165:0:1.1 -2 113981022 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.2815;LSEQ=GTCCCCTAACTGGTCTTTGT;RSEQ=CTTTCTCTCTTGACTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:110:50,60:152,200:0.2381:2,2:23.6:1:28.7:1:0.74129:1.10:60:54:0.2358:0:1.1 1/0:375:190:87,103:87,98:0.5067:2,2:23.5:1:28.7:1:0.83635:1.05085:60:94:0.5054:0:1.1 -2 113981137 . T C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=2.65647;LSEQ=AAACTAGTTCCTGCCTTAGG;RSEQ=CCTTTGCCCTTGCTGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:719:161:88,73:318,240:0.2239:2,2:24.7:1:31.5:1:0.65202:1.099:60:52.667:0.2219:0:1.2 0/1:569:247:129,118:170,148:0.4341:2,2:24.7:1:30.9:1:0.79908:1.05058:60:40.167:0.4342:0:1.1 -2 113981691 . T A 147 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06931;LSEQ=ATGGATGATGAAAGGATAGA;RSEQ=GGAAAGACAGATTAAAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:27:14,13:328,332:0.0393:2,2:30.6:1:31.1:1:0.84699:1.09:60:54:0.0398:0:1 0/0:708:2:1,1:381,325:0.0028:2,2:24.5:1:15.5:1:1:1.17204:60:0:0:0:1 -2 113981810 . A G 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=1.85711;LSEQ=AGATGGATGATAGATAACTG;RSEQ=AAAGACAGATGAATTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:662:267:103,164:165,230:0.4033:2,2:25.2:1:31:1:0.42076:1.14202:60:65.75:0.4046:0:1.1 1/0:670:373:154,219:118,178:0.5567:2,2:25.6:1:30.8:1:0.7514:1.06:60:92.25:0.5574:0:1.1 -2 113982039 . AC GA 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04307;SOR=0.21216;LSEQ=GAGGCTGAGGCAGGAGAATC;RSEQ=TTGAACCCGGGAGGCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:18:9,9:0,0:0.6207:0,2:24.8:1:30.6:1:1:0:60:36:0.6429:0:1.1 0/1:12:3:2,1:0,0:0.25:0,2:13:1:30.7:1:1:0:56:6:0.3:0:1 -2 113982143 . G A 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=2.38545;LSEQ=CCAAAAAAAAAAAAAAAAAA;RSEQ=GAAAGATGGATGGAAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:37:23,14:125,43:0.1762:2,2:12.3:1:27.7:1:0.15654:1.76423:58.2:6.4:0.186:0:1.6 0/1:201:68:36,32:78,32:0.3383:2,2:11.6:1:28.9:1:0.01679:2.15687:59:33:0.3952:0:1.6 -2 113982413 . A T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12635;SOR=Inf;LSEQ=TAAAAAAATAAAATAAAATA;RSEQ=AATATAAAATAAAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:167,65:0:2,0:26.1:1:30.4:1:1:0:59.4:115:1:0:0.1 0/1:129:2:2,0:83,44:0.0155:2,0:26:1:32:0:0.547:0:60:4:0.0155:0:2 -2 113982414 . AATAT A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00583;SOR=Inf;LSEQ=AAAAAAATAAAATAAAATAA;RSEQ=AAAATAAAATAAAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:167,65:0:2,0:26.8:1:30.4:1:1:0:59.4:45.4:1:0:0.2 0/1:131:5:4,1:82,43:0.0382:2,2:6.2:1:29.2:1:0.66178:2.09:60:10:0.0388:0.0305:0 -2 113982416 . TATAAAATAAAATAAA T 235 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=9.000;MSILEN=5;SSF=0;SOR=0.26322;LSEQ=AAAAATAAAATAAAATAAAA;RSEQ=ATAAAATAAAATAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:268:188:145,43:26,31:0.7015:2,2:25.6:1:31.2:1:1e-05:3.99:59.4:376:0.7041:0.1343:0.2 0/1:139:53:37,16:31,20:0.3813:2,2:30.5:1:30.2:1:0.41071:1.49:59.4:106:0.3897:0.0432:0.2 -2 113982428 . TAAA T 82 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04936;SOR=3.85635;LSEQ=AAATAAAATATAAAATAAAA;RSEQ=ATAAAATAAAATAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:3:0,3:43,24:0.0135:2,0:11:1:33:0:0.05343:0:60:6:0.0429:0:0 0/1:139:7:4,3:42,20:0.0504:2,2:11.6:1:29.4:1:0.67856:1.56413:60:14:0.1014:0:0 -2 113982584 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=3.29108;LSEQ=TATGGTGTAGAGGAAAGAGC;RSEQ=TTAGACTTGAAATTGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:130:54,76:186,243:0.2321:2,2:24.4:1:31.6:1:0.7619:1.0771:60:42.333:0.2292:0:1.8 0/1:517:258:120,138:129,130:0.499:2,2:24.5:1:30.8:1:0.48177:1.14086:60:63.5:0.499:0:1.4 -2 113982608 . G A 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18279;SOR=0.8035;LSEQ=GACTTGAAATTGAAAAATCC;RSEQ=TGTTTGCATAACTCAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:113:50,63:192,211:0.2186:2,2:26:1:30.7:1:0.59398:1.14624:60:55.5:0.2189:0:1.9 0/1:496:91:48,43:192,212:0.1835:2,2:26.6:1:30.2:1:0.4167:1.23:60:90:0.1829:0:1.9 -2 113982769 . C G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07591;SOR=Inf;LSEQ=TACATATTTGAATGGCTAGA;RSEQ=ATGCAAAAGTACATAATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:188,196:0:2,0:24:1:32:1:1:0:60:95:1:0:0.1 0/1:283:3:2,1:140,140:0.0106:2,2:7.7:1:32.3:1:1:2.00:60:6:0.0106:0:1.3 -2 113983156 . G A 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04843;SOR=Inf;LSEQ=GCAGTCAGTGTCCTAGTTGT;RSEQ=CTATTTTTTTTCTTTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:167,163:0:2,0:22.9:1:32:1:1:0:60:81.5:1:0:0.1 0/1:294:4:2,2:130,159:0.0136:2,2:23.3:1:27.3:1:1:1.22:60:8:0.0139:0:1 -2 113983157 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.34345;SOR=3.45354;LSEQ=CAGTCAGTGTCCTAGTTGTG;RSEQ=TATTTTTTTTCTTTTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:1:1,0:166,165:0.003:2,0:1:0:25:0:1:0:60:2:0.003:0:1 0/1:290:3:2,1:128,158:0.0103:2,2:6:1:27:1:0.58985:2.46:60:6:0.0105:0:1 -2 113983159 . A AT 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02317;SOR=Inf;LSEQ=GTCAGTGTCCTAGTTGTGCT;RSEQ=TTTTTTTTCTTTTTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:165,163:0:2,0:22.9:1:29.3:1:1:0:60:64.6:1:0:0.1 0/1:294:5:2,3:132,157:0.017:2,2:37.6:1:25.6:1:1:1.26016:60:4:0.0138:0:0 -2 113983367 . G A 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.0628;LSEQ=TCCTCCTCCTCTAAGCAGGC;RSEQ=GCAGGGGAAGGTGGAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:1:1,0:289,219:0.002:2,0:1:0:26:0:1:0:60:2:0.002:0:1 0/1:420:19:12,7:210,191:0.0452:2,2:24.2:1:30:1:0.48169:1.56:60:38:0.0453:0:1.2 -2 113983522 . AAGGG A 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.55585;SOR=1.47021;LSEQ=ATTTCACGCTCCAGAAGAGG;RSEQ=AGGGAGGGAGGGAGTCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:423:5:2,3:222,195:0.0118:2,2:33.4:1:30.6:1:0.66902:1.70552:60:10:0.0121:0:0 0/1:347:6:2,4:194,146:0.0173:2,2:35.3:1:29.3:1:0.4093:2.65011:60:12:0.0177:0:0 -2 113983689 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17616;SOR=Inf;LSEQ=CCCTCCCTCTTTCTCTCCCT;RSEQ=CCTTCCCTCTGCCCAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:108,154:0:2,0:23.5:1:31:1:1:0:60:64.5:1:0:0.1 0/1:190:2:1,1:71,117:0.0105:2,2:6.5:1:27.5:1:1:1.64:60:4:0.0108:0:1 -2 113983708 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.17799;SOR=Inf;LSEQ=TCCCTTCCCTCTGCCCAGGA;RSEQ=ATCCCAGCCCACCTGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:97,138:0:2,0:24.1:1:31.6:1:1:0:60:116.5:1:0:0.1 0/1:172:2:1,1:79,91:0.0116:2,2:29:1:29.5:1:1:1.15:60:4:0.012:0:1 -2 113983815 . T A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08618;SOR=Inf;LSEQ=CTAGGTAAATACGCCAAGTC;RSEQ=CTGGGGTCACAGCCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:208,132:0:2,0:24.8:1:30.6:1:1:0:60:36.778:1:0:0.1 0/1:270:3:2,1:145,122:0.0111:2,2:14:1:21.7:1:1:1.68:60:2:0.0077:0:1.3 -2 113983840 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03456;SOR=Inf;LSEQ=GGTCACAGCCAGAGAGGCTG;RSEQ=CCTAGGGCTGGCATGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:207,138:0:2,0:25.3:1:31.3:1:1:0:60:48.286:1:0:0.1 0/1:263:4:3,1:153,106:0.0152:2,2:28:1:28.3:1:0.64809:2.07:60:8:0.0156:0:1.3 -2 113983869 . C A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0344;SOR=Inf;LSEQ=TGGCATGGGGGTCACAGATG;RSEQ=CTTGTGTTCAGAGCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:255,170:0:2,0:23.5:1:31.4:1:1:0:60:46.222:1:0:0.1 0/1:323:4:3,1:187,132:0.0124:2,2:21:1:23:1:0.64594:2.11:60:3:0.0096:0:1 -2 113983937 . T C 222 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACCAGTGACAATGGCTCAA;RSEQ=TATGTCTCATCCATCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:636:0:0,0:314,322:0:2,0:25.6:1:30.3:1:1:0:60:105:1:0:0.1 0/1:556:148:74,74:211,197:0.2662:2,2:25.6:1:30.8:1:0.77351:1.07092:60:28.6:0.2624:0:1.2 -2 113984033 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33793;LSEQ=TCTTCATTTGTCCAGACCTT;RSEQ=TCATCTTGAATCATCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:309:199:77,122:44,66:0.644:2,2:23.1:1:29.7:1:0.90318:1.05608:60:48.75:0.6436:0:1.1 0/1:285:108:37,71:72,104:0.3789:2,2:23.3:1:29.3:1:0.31477:1.32715:60:107:0.3794:0:1.1 -2 113984239 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.09128;SOR=Inf;LSEQ=ATATATTTCATCATCATCAT;RSEQ=GTCATCGTCATCATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:177,138:0:2,0:24.4:1:30.5:1:1:0:59.9:62:1:0:0.2 0/1:259:3:2,1:141,114:0.0116:2,2:19.3:1:28:1:1:1.61:60:6:0.0117:0:1 -2 113984246 . G GTCA 188 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=9.000;MSILEN=3;SSF=0.27583;SOR=1.24109;LSEQ=TCATCATCATCATCGTCATC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:73:43,30:144,100:0.2296:2,2:27.3:1:30.5:1:1:1.00464:59.8:72:0.2308:0.044:0.7 0/1:237:64:36,28:95,64:0.27:2,2:31.4:1:30.8:1:0.65412:1.15376:60:128:0.2735:0.0211:0.6 -2 113984303 . T C 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=2.14187;LSEQ=TTCAGATTTTACAGAACGGG;RSEQ=AAACTGGGATTCATCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:118:73,45:182,112:0.285:2,2:24:1:31.5:1:1:1.00171:60:38.333:0.284:0:1.1 0/1:332:153:86,67:103,76:0.4608:2,2:26.3:1:31:1:0.82475:1.05565:60:37.25:0.4571:0:1.2 -2 113984503 . C T 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATCATGGAGGGTAATGTAG;RSEQ=AGGCCTGGGAAGAAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:216,168:0:2,0:25.4:1:31.8:1:1:0:60:41.667:1:0:0.1 0/1:326:42:25,17:160,124:0.1288:2,2:23.8:1:28.2:1:0.74097:1.14:60:41:0.1269:0:1.2 -2 113984515 . G T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04341;SOR=Inf;LSEQ=TAATGTAGCAGGCCTGGGAA;RSEQ=AAGGAGGCCGAGCTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:233,182:0:2,0:24.9:1:31.5:1:1:0:60:58.286:1:0:0.1 0/1:350:4:2,2:191,154:0.0114:2,2:33:1:24.3:1:1:1.23948:60:3:0.0088:0:2.3 -2 113984562 . TG T 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGGGAGTCAGGACTGCAC;RSEQ=GGACATCGTCTCCAGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:276,254:0:2,0:25:1:31.5:1:1:0:60:264:1:0:0.2 0/1:440:29:15,14:201,209:0.0659:2,2:28.1:1:31.2:1:0.84873:1.11:60:58:0.0668:0.0068:0.4 -2 113984594 . T C 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.41757;LSEQ=TCCAGGCATTTACAAGGAGA;RSEQ=GCCCTCTTTGGTCCATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:87:44,43:245,239:0.1524:2,2:24.5:1:31:1:1:1.0018:60:86:0.1522:0:1.2 0/1:473:33:14,19:208,232:0.0698:2,2:28.3:1:30.7:1:0.71817:1.21625:60:66:0.0705:0:1.2 -2 113985170 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.52718;LSEQ=GAGGTTATGTCTTCTGTTTT;RSEQ=TGTTACCCCCAACAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:96:54,42:172,192:0.2087:2,2:25.1:1:30.5:1:0.13577:1.43:60:47:0.2084:0:1.9 0/1:396:191:87,104:91,114:0.4823:2,2:25.3:1:29.6:1:0.84022:1.05:60:94.5:0.4859:0:1.3 -2 113985186 . C G 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00749;SOR=0.5977;LSEQ=TTTTCTGTTACCCCCAACAG;RSEQ=AGCCAGCAGAGCAGTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:94:53,41:156,193:0.2122:2,2:24.9:1:31.3:1:0.04824:1.60:60:46:0.2125:0:1.9 0/1:368:51:25,26:148,168:0.1386:2,2:27.5:1:30.5:1:0.88:1.09:60:50:0.1385:0:1.9 -2 113985902 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08311;SOR=Inf;LSEQ=AGGTGATGACCAGTATCCCA;RSEQ=CATATTTGTTAATAATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:125,224:0:2,0:24:1:31.8:1:1:0:60:48.857:0.9971:0:0.1 0/1:272:3:1,2:105,163:0.011:2,2:32.3:1:28:1:1:1.28717:60:6:0.0112:0:1 -2 113985910 . G T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32262;SOR=3.91017;LSEQ=ACCAGTATCCCAGCATATTT;RSEQ=TTAATAATGCCCATTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:1:0,1:126,211:0.003:2,0:20:0:26:0:1:0:60:2:0.003:0:1 0/1:261:3:1,2:103,155:0.0115:2,2:27.3:1:28.7:1:1:1.32763:60:6:0.0116:0:1 -2 113986019 . G A 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63692;SOR=0.43552;LSEQ=TCTCAGTCTCAGCAACATTG;RSEQ=CATGTTAGGCTGCACAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:2,1:104,119:0.0133:2,2:21.7:1:25:1:0.60133:2.28:60:2:0.0091:0:3 0/0:172:1:1,0:73,98:0.0058:2,0:1:0:25:0:0.43023:0:60:2:0.0059:0:1 -2 113986031 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16114;SOR=Inf;LSEQ=CAACATTGGCATGTTAGGCT;RSEQ=CACAATTCTTTGCTGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:102,109:0:2,0:24.4:1:32:1:1:0:60:69.333:1:0:0.1 0/1:142:2:2,0:56,84:0.0141:2,0:24.5:1:25:1:0.16512:0:60:4:0.0144:0:1 -2 113986071 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52365;SOR=0;LSEQ=AGGCTGTCCTGTGCATTGTA;RSEQ=GATGTTTAGCAGCATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:83,78:0.0123:2,2:8.5:1:29.5:1:1:1.06373:60:4:0.0123:0:1 0/0:103:0:0,0:62,41:0:2,0:19.8:1:31.1:1:1:0:60:102:1:0:0.1 -2 113986086 . T C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52566;SOR=0;LSEQ=TTGTAGGATGTTTAGCAGCA;RSEQ=TTCTGGCCTCCATCCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:93,71:0.012:2,2:17:1:34:0:1:1.30769:60:4:0.0123:0:1 0/0:103:0:0,0:71,32:0:2,0:20.7:1:30.1:1:1:0:60:102:1:0:0.1 -2 113986629 . C T 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02241;SOR=0.67502;LSEQ=GGATGCTAAATTAGCAAGGC;RSEQ=GGGCACTAAATCAAGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:128:73,55:245,196:0.225:2,2:24.7:1:30.6:1:0.83983:1.06:60:41.667:0.2256:0:1.1 0/1:403:66:36,30:170,166:0.1638:2,2:26.8:1:30.1:1:0.59177:1.17:60:32:0.1624:0:1.1 -2 113986858 . G GA 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.70934;SOR=1.20215;LSEQ=GTTTCTTCATATGCAAAATG;RSEQ=AAAAAAAAACATAGCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:17:9,8:211,192:0.0405:2,2:28.1:1:29.4:1:1:1.02:59.7:16:0.039:0.0071:0.1 0/1:290:14:7,7:139,133:0.0483:2,2:30.9:1:29.6:1:1:1.04497:60:28:0.0495:0:0.1 -2 113986881 . A G 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25514;LSEQ=AAAAAAACATAGCTGTAGGC;RSEQ=CCTTATTACAATTTCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:72:42,30:199,157:0.1678:2,2:22.8:1:31.2:1:0.79466:1.10:59.9:144:0.1718:0:1.1 0/1:307:15:11,4:152,139:0.0489:2,2:25.1:1:29.9:1:0.12127:2.51:60:30:0.0492:0:1.1 -2 113987465 . C T 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13078;SOR=0;LSEQ=GTGATGGAAGAAGGTGGTGG;RSEQ=GGATTCAGGCCTGCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:4:3,1:188,185:0.0106:2,2:19.5:1:30.5:1:0.62313:2.94:60:8:0.0107:0:1.5 0/0:312:0:0,0:151,161:0:2,0:25.3:1:30.8:1:1:0:60:61.4:1:0:0.2 -2 113987699 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08361;SOR=Inf;LSEQ=CTCCTGGCACCCAGTGTTGA;RSEQ=AAGGATTCTGAGGCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:120,203:0:2,0:25.4:1:31.5:1:1:0:60:106.667:1:0:0.1 0/1:252:3:3,0:107,142:0.0119:2,0:14:1:27.3:1:0.08189:0:60:6:0.012:0:1 -2 113987725 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17429;SOR=Inf;LSEQ=TTCTGAGGCAGCCTGTGTCT;RSEQ=CCATGATCGGGGTGGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:97,173:0:2,0:24:1:31.9:1:1:0:60:44:1:0:0.1 0/1:194:2:1,1:75,117:0.0103:2,2:19.5:1:29:0:1:1.56:60:4:0.0104:0:1 -2 113987800 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5004;SOR=0;LSEQ=TTGCTGGTGCTGGCCTTGTG;RSEQ=CCTGCAGGGCTGCTTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:96,85:0.0109:2,2:17.5:1:29:1:1:1.12866:60:4:0.0114:0:1 0/0:162:0:0,0:76,85:0:2,0:23.7:1:30.9:1:1:0:60:52.667:1:0:0.1 -2 113987825 . C T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62612;SOR=0.37752;LSEQ=CAGGGCTGCTTCTGGCCTGG;RSEQ=AGCCTGTGGCCCCGCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:2,1:108,75:0.0161:2,2:25:1:29.7:1:1:1.39:60:6:0.0167:0:1 0/0:163:1:0,1:86,76:0.0061:2,0:1:0:22:0:0.47239:0:60:2:0.0062:0:1 -2 113987835 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.21726;SOR=Inf;LSEQ=TCTGGCCTGGCAGCCTGTGG;RSEQ=CCCGCACTCCCCTTCCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:116,77:0:2,0:24.4:1:31:1:1:0:60:23.125:1:0:0.1 0/1:169:2:1,1:86,81:0.0118:2,2:28:1:26.5:1:1:1.06138:60:4:0.0123:0:1.5 -2 113987856 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21381;SOR=Inf;LSEQ=CCCGCACTCCCCTTCCCCCT;RSEQ=CCTTCATCCTGTTCCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:138,80:0:2,0:24.7:1:32:1:1:0:60:30.143:1:0:0.1 0/1:188:2:1,1:98,88:0.0106:2,2:16:1:27.5:1:1:1.113:60:4:0.0109:0:1 -2 113987892 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08544;SOR=Inf;LSEQ=TTCTCGTTCTATTACCTGAA;RSEQ=CTGCTGCCTCTCGAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:152,97:0:2,0:26.4:1:31.9:1:1:0:60:248:1:0:0.1 0/1:197:3:2,1:107,87:0.0152:2,2:14.7:1:28:1:1:1.62:60:6:0.0154:0:1.3 -2 113988252 . A G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACAATAAACTCTCCCAAC;RSEQ=GCCCTACAAAACTCTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:0:0,0:332,371:0:2,0:26.9:1:30.6:1:1:0:60:99.429:1:0:0.1 0/1:562:19:11,8:281,262:0.0338:2,2:26.4:1:30.7:1:0.64688:1.28:60:38:0.0344:0:1.1 -2 113988492 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.49232;LSEQ=TCCAACGTGGTCCTATTTTA;RSEQ=GAAGTTGACAGAAAGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:112:49,63:178,166:0.2456:2,2:24.3:1:30:1:0.15769:1.37767:60:36.333:0.2455:0:1.1 1/0:323:172:77,95:67,84:0.5325:2,2:24.4:1:30.1:1:1:1.02:60:171:0.5377:0:1.1 -2 113988729 . T C 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00684;SOR=0.59118;LSEQ=AATTCCTTATCTCGTTCTGA;RSEQ=AGCAAGGAGAATTTATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:88:38,50:246,300:0.1388:2,2:25.7:1:32.3:1:0.8175:1.07885:60:176:0.141:0:1.1 0/1:506:44:23,21:207,255:0.087:2,2:22.6:1:30.4:1:0.34729:1.35:60:88:0.0885:0:1 -2 113989082 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07481;SOR=Inf;LSEQ=AATCACACTATCAGAGCCAC;RSEQ=AGGCGGAAATAAGTGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:200,190:0:2,0:23.1:1:31.7:1:1:0:60:96.5:1:0:0.1 0/1:285:3:3,0:147,135:0.0105:2,0:5.3:1:27.7:1:0.24944:0:60:6:0.0107:0:1 -2 113989122 . A AG 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.29896;LSEQ=AGAGAAAAACGCTATGAAGT;RSEQ=GTGAAGGAGTTGCAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:93:60,33:199,128:0.2214:2,2:26.1:1:31.5:1:0.54772:1.17:59.9:92:0.2222:0.0405:0.1 0/1:364:144:88,56:131,87:0.3956:2,2:23.3:1:30.8:1:0.91261:1.04:60:288:0.4045:0.0879:0.1 -2 113989236 . C T 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.90581;SOR=0.9802;LSEQ=GAATGAAAACTCACTGTGTC;RSEQ=TCTCTCCTCTCTCCTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:983:195:91,104:368,419:0.1984:2,2:28.1:1:30:1:1:1.00375:60:38:0.1981:0:2 0/1:835:163:75,88:322,347:0.1952:2,2:25.7:1:29.9:1:0.66232:1.08868:60:80.5:0.1983:0:1.8 -2 113989267 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.26024;LSEQ=CTCCTGGTCTGCAGCATTAC;RSEQ=TAGGAATAATGTGGCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:849:185:71,114:255,409:0.2179:2,2:27.1:1:31.8:1:1:1.00107:60:184:0.2185:0:2.2 0/1:693:330:138,192:155,207:0.4762:2,2:27:1:30.9:1:0.81746:1.04176:60:109:0.4788:0:1.6 -2 113989327 . T C 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.39618;LSEQ=TATTTTTTTCTTTTTTGAGA;RSEQ=GGAGTTTCGCTCTTGTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:70:16,54:37,175:0.2473:2,2:23.9:1:30.3:1:0.37737:1.40:60:140:0.2509:0:1.9 0/1:195:86:13,73:23,83:0.441:2,2:21.3:1:29.9:1:0.2696:1.55254:58.9:85:0.4427:0:1.9 -2 113989558 . G A 183 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGTGATCCACCCACCTTG;RSEQ=CCTCCCAAAGTGCTGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:245,86:0:2,0:22.7:1:30.9:1:1:0:55.7:54.167:1:0:0.1 0/1:267:80:55,25:140,47:0.2996:2,2:19.9:1:29.1:1:0.36642:1.35244:56.8:160:0.303:0:1.2 -2 113989968 . A G 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07802;SOR=Inf;LSEQ=GCCTCTGTGCTGAATTGTCA;RSEQ=CCCTTGGGCTAGGGGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:171,152:0:2,0:26.2:1:29.8:1:1:0:60:52.833:1:0:0.1 0/1:242:3:1,2:110,128:0.0124:2,2:25.7:1:22:1:1:1.71505:60:2:0.0086:0:1.7 -2 113990078 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04685;SOR=Inf;LSEQ=CACCAGCCTGAAAGATATGC;RSEQ=GGTGCTGCATATTTGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:181,192:0:2,0:24.5:1:30.2:1:1:0:60:73.6:1:0:0.2 0/1:326:4:1,3:169,153:0.0123:2,2:22.3:1:24.8:1:0.35245:3.30252:60:3:0.0094:0:1 -2 113990101 . G A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.12404;SOR=0;LSEQ=TGCTGCATATTTGGCTGCCT;RSEQ=CTTCCTACATGACTACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:4:2,2:166,178:0.0115:2,2:21.5:1:29.5:1:1:1.07:60:8:0.0117:0:1 0/0:339:0:0,0:178,160:0:2,0:26.4:1:31.6:1:1:0:60:55.333:1:0:0.2 -2 113990242 . T C 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46263;SOR=0.88346;LSEQ=GTTGGAGGCGTCACCTCTGA;RSEQ=TGACTGCATGTTGACAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:120:74,46:234,137:0.2444:2,2:22.4:1:31.9:1:0.82823:1.06162:60:119:0.2459:0:1.9 0/1:360:80:44,36:157,123:0.2222:2,2:22.7:1:31:1:0.89879:1.04425:60:79:0.2219:0:1.9 -2 113990261 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.18937;LSEQ=ATTGACTGCATGTTGACAGG;RSEQ=GATGCTAACAGGATGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:120:72,48:267,191:0.2073:2,2:25.1:1:30:1:0.7558:1.07:60:119:0.2073:0:1.9 1/0:411:215:119,96:109,87:0.5231:2,2:24.2:1:29.4:1:1:1.0107:60:34.833:0.5186:0:1.4 -2 113990393 . C A 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.47557;LSEQ=ATACATCTATCCACTTCCAG;RSEQ=TGCCCTACATCCTTCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:133:64,69:186,232:0.2409:2,2:26.4:1:30.3:1:0.485:1.16:60:132:0.244:0:1.1 0/1:477:210:100,110:130,136:0.4403:2,2:27:1:29:1:0.85347:1.05133:60:69:0.4376:0:1.2 -2 113990440 . C T 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGGTCTTGCCAAGCTTCT;RSEQ=CGCGGCTTCCACAGCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:204,260:0:2,0:25:1:31.1:1:1:0:60:65.286:1:0:0.3 0/1:425:45:21,24:159,221:0.1059:2,2:26.3:1:29:1:0.63261:1.22:60:44:0.1055:0:1.6 -2 113990504 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07396;SOR=Inf;LSEQ=CACACCCTCACCCCTTGCCT;RSEQ=CCCCATGACCGCCGCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:98,184:0:2,0:25.5:1:31.5:1:1:0:60:39.286:1:0:0.1 0/1:205:3:0,3:71,130:0.0146:2,0:23:1:26:1:0.55298:0:60:2:0.0101:0:1 -2 113990509 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17875;SOR=Inf;LSEQ=CCTCACCCCTTGCCTGCCCC;RSEQ=TGACCGCCGCCAGCTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:93,178:0:2,0:25.3:1:30.3:1:1:0:60:89.333:1:0:0.1 0/1:199:2:1,1:69,128:0.0101:2,2:28:1:31.5:1:1:1.85:60:4:0.0102:0:1 -2 113990552 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.53157;SOR=0;LSEQ=GCCATTCTCAGAAGACATGC;RSEQ=GGCTTGCGTAACTCCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:74,122:0.0101:2,2:26:1:32:0:1:1.64:60:4:0.0102:0:1 0/0:117:0:0,0:41,76:0:2,0:25:1:30.4:1:1:0:60:234:1:0:0.5 -2 113990597 . CCCCCT C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=5.000;MSILEN=5;SSF=0.24917;SOR=4.18046;LSEQ=ACATGAACCTCTTCTCCTCA;RSEQ=CCCCTCCCCTCCCCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:1:1,0:81,80:0.0061:2,0:27:0:33:0:1:0:60:2:0.0066:0:8 0/1:79:2:1,1:34,43:0.0253:2,2:25:1:29:1:1:1.26:60:4:0.0267:0.0127:1.5 -2 113990602 . T TC 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.66654;SOR=0.39359;LSEQ=AACCTCTTCTCCTCACCCCC;RSEQ=CCCCTCCCCTCCCCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:5:5,0:72,75:0.0316:2,0:49.4:1:25.6:1:0.05851:0:60:4:0.0342:0.019:3.4 0/1:79:1:1,0:31,44:0.0127:2,0:35:0:31:0:0.42105:0:60:2:0.0167:0:4 -2 113990621 . C T 47 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.15474;SOR=0;LSEQ=CTCCCCTCCCCTCCCCTCCC;RSEQ=TCCCTTCCCTTCCCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:4:2,2:91,77:0.0233:2,2:21:1:23.8:1:1:1.18066:60:3:0.0183:0:2 0/0:113:0:0,0:65,47:0:2,0:15.5:1:29.9:1:1:0:59.6:27:1:0:0.8 -2 113990872 . G A 62 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23751;SOR=2.14876;LSEQ=GGATGTCCCTCTCTTCTAAG;RSEQ=AAACTTCTCACATTAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:4:2,2:268,489:0.0052:2,2:10.5:1:17.5:1:0.61814:1.82:60:0.333:0.0014:0:4 0/1:624:7:4,3:249,368:0.0112:2,2:7:1:22.1:1:0.44968:1.97:60:2.5:0.0085:0:2.3 -2 113990907 . G GA 204 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.0279;SOR=0.68463;LSEQ=AGGTGCTGGGATGTACGGAG;RSEQ=AAAAAAAAAAAAAAACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:119:23,96:84,128:0.2946:2,2:26.2:1:29.6:1:0.00014:2.73112:60:118:0.3233:0.052:1.3 0/1:324:72:11,61:89,121:0.2222:2,2:31.6:1:28.9:1:3e-05:4.0607:59.5:35:0.2333:0:1.7 -2 113990922 . A C 99 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03668;SOR=4.01427;LSEQ=CGGAGGAAAAAAAAAAAAAA;RSEQ=CCCGGGTGCCAGCCAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:3:1,2:84,269:0.0084:2,2:8.3:1:18:1:0.56005:1.60:60:0.5:0.0029:0:5 0/1:273:9:3,6:75,176:0.033:2,2:8.4:1:31.3:1:1:1.17:57.2:18:0.034:0:1.1 -2 113990923 . C A 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGAAAAAAAAAAAAAAA;RSEQ=CCGGGTGCCAGCCAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:53,248:0:2,0:21.8:1:29.7:1:1:0:59.6:9.75:1:0:0.9 0/1:244:15:9,6:48,181:0.0615:2,2:8.9:1:24.8:1:0.00182:5.60:57:4:0.0536:0:2.9 -2 113990941 . A G 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCCGGGTGCCAGCCAGAA;RSEQ=GAAAATGTAGAGCCAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:42,186:0:2,0:25.7:1:30.8:1:1:0:60:31.571:1:0:0.9 0/1:188:19:2,17:36,133:0.1011:2,2:24.7:1:29.8:1:0.37321:2.29258:58.9:18:0.1006:0:1.9 -2 113990961 . TA T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.50495;SOR=0;LSEQ=AGAAAATGTAGAGCCAGTTA;RSEQ=AAAAAGGGTCCATGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:36,154:0.0104:2,2:26:1:30:1:0.34909:4.23:59.5:4:0.0107:0:4 0/0:153:0:0,0:33,120:0:2,0:26.5:1:29.5:1:1:0:59.8:152:1:0:0.8 -2 113990977 . G T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50263;SOR=0;LSEQ=GTTATAAAAAAGGGTCCATG;RSEQ=GCTGGGTGCAGTGGCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:32,110:0.0139:2,2:14:0:28:1:0.40705:3.40:60:4:0.0146:0:1.5 0/0:119:0:0,0:29,90:0:2,0:27:1:30.2:1:1:0:59.7:58.5:1:0:0.6 -2 113990984 . TG CC 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50423;SOR=0;LSEQ=AAAAGGGTCCATGGGCTGGG;RSEQ=CAGTGGCTCACACCTGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:30,95:0.0156:2,2:45.5:1:32.3:1:0.43007:3.13:59.5:4:0.0171:0:3 0/0:102:0:0,0:24,76:0:2,0:27.6:1:29.3:1:1:0:59.8:24:1:0:0.4 -2 113990988 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50333;SOR=0;LSEQ=GGGTCCATGGGCTGGGTGCA;RSEQ=TGGCTCACACCTGTAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:29,89:0.0167:2,2:43.5:1:31.5:1:0.43908:3.03:59.5:4:0.0174:0:3 0/0:97:0:0,0:26,71:0:2,0:26.1:1:30.8:1:1:0:59.7:23.25:1:0:0.5 -2 113991005 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50207;SOR=0;LSEQ=GCAGTGGCTCACACCTGTAA;RSEQ=CCCAGCACTTTGGGAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:17,66:0.0233:2,2:26.5:1:32:1:0.38067:3.80:59.5:4:0.0247:0:3 0/0:70:0:0,0:15,55:0:2,0:21.3:1:31.3:1:1:0:60:140:1:0:0.2 -2 113991184 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14125;SOR=Inf;LSEQ=AGAATCACTTGAACCCAGGA;RSEQ=GTGGAGGTTGCAGTGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:40,4:0:2,0:25:1:31.8:1:1:0:58.9:13.667:1:0:0.4 0/1:27:2:2,0:25,0:0.0741:1,0:41.5:1:32:0:1:0:60:4:0.087:0:1.5 -2 113991259 . AAC A 81 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.7374;SOR=0.65009;LSEQ=AGTGAGATTCCATCTCAAAA;RSEQ=AAAAAAACAAAAAAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:6:6,0:164,48:0.0274:2,0:20.7:1:31.7:1:0.34279:0:53:12:0.0278:0:1.8 0/1:167:3:2,1:130,34:0.018:2,2:18:1:28.7:1:0.50855:1.90297:56.7:6:0.018:0:1.3 -2 113991261 . C A 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.03605;SOR=2.01301;LSEQ=TGAGATTCCATCTCAAAAAA;RSEQ=AAAAAAACAAAAAAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:196:151,45:0,0:0.8376:0,2:15.3:1:30.5:1:1:0:57:195:0.8628:0:2.1 1/1:171:156:123,33:0,0:0.9123:0,2:17.8:1:30:1:1:0:57.4:155:0.9281:0:2.3 -2 113991269 . CA C 118 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00108;SOR=4.91948;LSEQ=CATCTCAAAAAACAAAAAAA;RSEQ=AAAAAAAAAGGGTCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:5:3,2:201,80:0.0168:2,2:19.2:1:27.4:1:0.62684:1.6717:60:4:0.015:0:2 0/1:206:16:12,4:143,43:0.0777:2,2:19.6:1:29.6:1:1:1.10796:60:32:0.0821:0.0243:0.8 -2 113991518 . G A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03186;SOR=Inf;LSEQ=GATGGACTGTCTGACTCTGG;RSEQ=CTGCCTCTGTGACAGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:137,215:0:2,0:24.2:1:31.3:1:1:0:60:69.4:1:0:0.1 0/1:259:4:2,2:93,160:0.0154:2,2:26.8:1:29.5:1:0.62787:1.72:60:8:0.0157:0:1 -2 113991554 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13129;SOR=Inf;LSEQ=GTCTCACACACCCCACCCAC;RSEQ=CACTGGTCTCTGCTCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:133,201:0:2,0:25.4:1:31.2:1:1:0:60:82.5:0.991:0:0.1 0/1:192:2:1,1:84,106:0.0104:2,2:6:0:31:1:1:1.26:60:4:0.0107:0:1 -2 113991561 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13581;SOR=Inf;LSEQ=ACACCCCACCCACGCACTGG;RSEQ=CTCTGCTCCAGCATTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:132,203:0:2,0:25.7:1:29.9:1:1:0:60:66:1:0:0.1 0/1:196:2:1,1:85,109:0.0102:2,2:8:1:32:1:1:1.28:60:4:0.0104:0:1 -2 113991567 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05052;SOR=Inf;LSEQ=CACCCACGCACTGGTCTCTG;RSEQ=TCCAGCATTTCAAGGTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:138,202:0:2,0:25.4:1:32.4:1:1:0:60:112.333:0.997:0:0.1 0/1:201:3:1,2:88,110:0.0149:2,2:8:1:28:1:1:1.59641:60:6:0.0151:0:1.3 -2 113991570 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29995;SOR=3.51923;LSEQ=CCACGCACTGGTCTCTGCTC;RSEQ=AGCATTTCAAGGTCGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:1:0,1:144,207:0.0028:2,0:1:0:23:0:1:0:60:2:0.0029:0:1 0/1:201:2:1,1:87,112:0.01:2,2:26.5:1:28.5:1:1:1.29:60:4:0.0102:0:1 -2 113991793 . T A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CTTGAGGTATCTGAAGACCA;RSEQ=ATGGGTCTCTGCTTCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:138,168:0:2,0:24.8:1:29.5:1:1:0:60:75.5:1:0:0.1 0/1:221:12:5,7:108,101:0.0543:2,2:20.8:1:30.2:1:0.56291:1.4943:60:24:0.0545:0:1 -2 113991841 . C T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2631;SOR=0;LSEQ=CATCTCAGGCCCTCTCCAAC;RSEQ=CAAGCCAAGCGCTTGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:140,156:0.01:2,2:28.3:1:29.3:1:1:1.7915:60:6:0.0102:0:1.7 0/0:226:0:0,0:109,117:0:2,0:25.3:1:30.2:1:1:0:60:112:1:0:0.2 -2 113991871 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17082;SOR=Inf;LSEQ=CGCTTGACTCTCAGCCATTC;RSEQ=TCAGGCCCTGGCTGGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:134,135:0:2,0:24.7:1:31.3:1:1:0:60:52.8:1:0:0.2 0/1:190:2:1,1:85,103:0.0105:2,2:6.5:1:30.5:1:1:1.21:60:4:0.0106:0:1.5 -2 113991948 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19197;SOR=Inf;LSEQ=GAGGTCTGACTCATGCAGTG;RSEQ=AGGCCCAGGCCTCAACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:163,80:0:2,0:27.2:1:32.2:1:1:0:60:59.75:1:0:0.3 0/1:190:2:1,1:127,61:0.0105:2,2:15:1:29:1:0.54731:2.07328:60:4:0.0106:0:3 -2 113991970 . A G 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.28478;LSEQ=GGCCCAGGCCTCAACCAGCT;RSEQ=CAGATGGTGCTCCTGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:69:46,23:146,76:0.2371:2,2:23.9:1:31.9:1:1:1.04:60:68:0.2353:0:1.1 0/1:243:101:65,36:91,50:0.4156:2,2:25.2:1:31.2:1:1:1.00797:60:100:0.4132:0:1.2 -2 113992201 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78118;SOR=0.7663;LSEQ=TATGCCTCCTGGGTTCAAGC;RSEQ=ATTCTCCTGCCTCGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:16:2,14:16,28:0.2667:2,2:21.6:1:31.2:1:0.11206:3.92072:60:32:0.2712:0:1 0/1:23:5:4,1:3,15:0.2174:2,2:21.8:1:29.2:1:0.01727:16.56:60:10:0.2174:0:1 -2 113992344 . C T 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00061;SOR=Inf;LSEQ=TGACCTTGTGATCCACCTGC;RSEQ=TCGGCCTCCCAAACTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:156,34:0:2,0:22.1:1:30.8:1:1:0:59.8:30.667:1:0:0.5 0/1:178:10:8,2:130,38:0.0562:2,2:26.7:1:31.2:1:1:1.17:60:20:0.0565:0:2 -2 113992358 . C G 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.07155;LSEQ=ACCTGCCTCGGCCTCCCAAA;RSEQ=TGCTGGAATTACAGGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:2,1:184,69:0.0117:2,2:20.7:1:20.3:1:1:1.33174:56:0.5:0.0039:0:4.7 0/1:240:3:2,1:169,67:0.0125:2,2:13.7:1:30:1:1:1.25995:60:6:0.0128:0:4.3 -2 113992360 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11506;SOR=Inf;LSEQ=CTGCCTCGGCCTCCCAAACT;RSEQ=CTGGAATTACAGGGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:189,75:0:2,0:21.5:1:31.9:1:1:0:59.9:131:1:0:0.5 0/1:251:3:1,2:172,74:0.012:2,2:14.3:1:26:1:0.22161:4.61637:60:6:0.0122:0:1.7 -2 113992365 . A G 80 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01489;SOR=Inf;LSEQ=TCGGCCTCCCAAACTGCTGG;RSEQ=ATTACAGGGGTGAGCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:195,87:0:2,0:22.3:1:29.7:1:1:0:59.9:93:0.9964:0:0.5 0/1:281:6:4,2:186,89:0.0214:2,2:16.7:1:31:1:1:1.04478:59:12:0.0217:0:4.8 -2 113992374 . G C 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00072;SOR=1.69473;LSEQ=CAAACTGCTGGAATTACAGG;RSEQ=GTGAGCCACCTCGCCCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:136:84,52:142,67:0.3919:2,2:23.4:1:30.2:1:0.24839:1.31094:60:26.2:0.391:0:1.1 1/0:337:176:115,61:100,52:0.5223:2,2:24.5:1:30.5:1:1:1.02001:59.9:43:0.5228:0:1.4 -2 113992515 . G T 133 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.15259;LSEQ=AGATGTCTGACTGTCCTCCC;RSEQ=GTGATGCTGTTAAGCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:573:2:1,1:311,259:0.0035:2,2:23.5:1:31:1:1:1.20038:60:4:0.0036:0:1 0/1:476:21:11,10:239,215:0.0441:2,2:22.9:1:30.5:1:1:1.01055:60:42:0.0451:0:1.2 -2 113992624 . T C 228 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=260.96486;LSEQ=AAATGGGCTCCAAAAGCCAA;RSEQ=TCCTTTTTCCCTCCAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:809:1:0,1:359,448:0.0012:2,0:1:0:31:0:1:0:60:2:0.0013:0:1 0/1:683:167:80,87:247,267:0.2445:2,2:26.6:1:30.9:1:1:1.00603:60:32.4:0.2411:0:1.1 -2 113992792 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31615;SOR=4.10911;LSEQ=ACAGCATCCGCCCCTTCCGA;RSEQ=CATGTCTTCCCCGTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:1:0,1:108,189:0.0033:2,0:1:0:26:0:1:0:60:2:0.0034:0:1 0/1:220:3:1,2:85,132:0.0136:2,2:19:1:28.3:1:1:1.28644:60:6:0.014:0:1.3 -2 113992800 . TCC T 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=2e-04;SOR=2.05077;LSEQ=CGCCCCTTCCGAGCATGTCT;RSEQ=CCGTCACAGAGAACTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:75:27,48:77,135:0.2613:2,2:23.7:1:30.9:1:1:1.01394:60:74:0.2671:0.0453:0.1 0/1:221:93:37,56:52,76:0.4208:2,2:24.4:1:30.9:1:1:1.03541:60:186:0.4247:0.0407:0.2 -2 113992872 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50474;SOR=0;LSEQ=TAGGGAACAGGGTGGGGGTG;RSEQ=ATGAGACTGAGGCCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:64,106:0.0116:2,2:34.5:1:28.5:1:1:1.65:60:4:0.012:0:1 0/0:138:0:0,0:54,84:0:2,0:23.7:1:30.3:1:1:0:60:26.6:1:0:0.2 -2 113993073 . A G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTTGCTGCAGATCCAAAA;RSEQ=GGCGGAGCTAGATAAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:0:0,0:282,189:0:2,0:25:1:30.4:1:1:0:60:93.2:1:0:0.2 0/1:364:25:14,11:193,145:0.0687:2,2:33:1:31.3:1:1:1.04571:60:50:0.0691:0:1.2 -2 113993235 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16334;SOR=Inf;LSEQ=ACACGCACAAGCCAAGCCGT;RSEQ=GGATGTGGAGGGTGCGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:94,150:0:2,0:23.2:1:31.4:1:1:0:60:80.333:1:0:0.2 0/1:166:2:1,1:68,96:0.012:2,2:31.5:1:28:1:1:1.41:60:4:0.0121:0:2 -2 113993252 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16697;SOR=Inf;LSEQ=CGTGGGATGTGGAGGGTGCG;RSEQ=GCGGGGCGCGGGGCAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:77,122:0:2,0:24.5:1:30.7:1:1:0:60:48.75:1:0:0.2 0/1:138:2:1,1:59,77:0.0145:2,2:31.5:1:28:1:1:1.30:60:4:0.0146:0:2 -2 113993253 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51336;SOR=0;LSEQ=GTGGGATGTGGAGGGTGCGG;RSEQ=CGGGGCGCGGGGCAGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:74,118:0.0103:2,2:19:1:27:1:1:1.59:60:4:0.0105:0:1 0/0:137:0:0,0:60,77:0:2,0:24.1:1:31.4:1:1:0:60:67.5:1:0:0.2 -2 113993331 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.50584;SOR=0;LSEQ=CACGAGGCGTGGCAAGGCGG;RSEQ=GAGAGAGAAGCTAGACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:42,70:0.0175:2,2:30:1:28.5:1:1:1.66:60:4:0.0179:0:1 0/0:88:0:0,0:37,51:0:2,0:24.1:1:30.7:1:1:0:60:176:1:0:0.6 -2 113993344 . A C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=3.61364;LSEQ=AAGGCGGGGAGAGAGAAGCT;RSEQ=GACCTCCCTGCTGCGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:20:6,14:34,57:0.1802:2,2:21.4:1:27.8:1:0.61418:1.3878:60:5.667:0.1574:0:1.7 0/1:81:36:16,20:19,26:0.4444:2,2:23.2:1:30.2:1:1:1.09:60:72:0.4444:0:1.5 -2 113993385 . C G 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01817;SOR=2.3971;LSEQ=GCAGCGAAAATGGAGAGACC;RSEQ=GGAAGGCGTGTGTGCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:19:6,13:29,37:0.2235:2,2:26:1:29.9:1:0.43098:1.68791:60:18:0.2169:0:1.7 0/1:61:25:14,11:15,21:0.4098:2,2:28:1:29.6:1:0.30665:1.76:60:24:0.4138:0:1.8 -2 113993526 . G T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11874;SOR=0;LSEQ=ACCCCTGGGCCCACCTTGAG;RSEQ=CCCGGCCTAGGACTGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:3:1,2:42,43:0.0341:2,2:30.7:1:22.3:1:1:1.93921:47:2:0.0241:0:1 0/0:90:0:0,0:44,46:0:2,0:25.8:1:30.7:1:1:0:48.5:44:1:0:0.1 -2 113993527 . C T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24586;SOR=0;LSEQ=CCCCTGGGCCCACCTTGAGG;RSEQ=CCGGCCTAGGACTGGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:3:1,2:45,43:0.033:2,2:22:1:27:1:0.61662:2.07665:60:2:0.0227:0:3 0/0:90:0:0,0:45,45:0:2,0:26:1:30.6:1:1:0:48.4:29:1:0:0.2 -2 113993539 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49738;SOR=0;LSEQ=CCTTGAGGCCCGGCCTAGGA;RSEQ=TGGAGGCGCGACCCCTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:47,47:0.0208:2,2:5.5:1:29.5:1:1:1:30:4:0.0227:0:1 0/0:95:0:0,0:47,48:0:2,0:26.5:1:31.3:1:1:0:48.3:94:1:0:0.2 -2 113993549 . G C 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24623;SOR=0;LSEQ=CGGCCTAGGACTGGAGGCGC;RSEQ=ACCCCTCGGCCCACCTTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:3:2,1:46,50:0.0303:2,2:32.7:1:22:1:0.60982:2.16:35:2:0.0215:0:1.3 0/0:97:0:0,0:48,49:0:2,0:26.7:1:29.7:1:1:0:48.4:47.5:1:0:0.2 -2 113993570 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20786;SOR=Inf;LSEQ=ACCCCTCGGCCCACCTTGCG;RSEQ=GAGCCGCCTAGGACCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:50,58:0:2,0:24.1:1:30.4:1:1:0:51.4:20.6:1:0:0.3 0/1:91:2:1,1:38,51:0.022:2,2:46:0:30:0:1:1.34:54:4:0.022:0:2 -2 113993573 . G T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09681;SOR=Inf;LSEQ=CCTCGGCCCACCTTGCGGGA;RSEQ=CCGCCTAGGACCGGAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:48,58:0:2,0:24.6:1:31.9:1:1:0:51.5:52:1:0:0.3 0/1:91:3:1,2:37,50:0.033:2,2:26.3:1:21.3:1:1:1.47381:43:2:0.023:0:1 -2 113993581 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1794;SOR=Inf;LSEQ=CACCTTGCGGGAGCCGCCTA;RSEQ=GACCGGAGGCGCGACCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:51,64:0:2,0:23.1:1:30.5:1:1:0:52.7:27.75:1:0:0.3 0/1:85:2:1,1:38,45:0.0235:2,2:35:0:30.5:1:1:1.18:54:4:0.0247:0:2 -2 113993583 . A G 86 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.022;SOR=5.57531;LSEQ=CCTTGCGGGAGCCGCCTAGG;RSEQ=CCGGAGGCGCGACCCCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:50,61:0.0177:2,2:1:0:22.5:1:1:1.22:44:1:0.009:0:2 0/1:87:8:5,3:35,44:0.092:2,2:19.1:1:28.8:1:0.46168:2.08:47.9:3:0.0714:0:2 -2 113993592 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50223;SOR=0;LSEQ=AGCCGCCTAGGACCGGAGGC;RSEQ=CGACCCCTCGGCCCAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:50,62:0.0175:2,2:14:1:28.5:1:1:1.24:60:4:0.018:0:1 0/0:94:0:0,0:44,50:0:2,0:21.6:1:29.4:1:1:0:54.2:14.667:1:0:0.4 -2 113993608 . G A 90 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02754;SOR=5.30764;LSEQ=AGGCGCGACCCCTCGGCCCA;RSEQ=CTTGAGGCCCGGCCTAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:47,54:0.0194:2,2:15.5:1:31.5:1:1:1.15:56:4:0.0202:0:1.5 0/1:94:9:6,3:44,41:0.0957:2,2:33.9:1:28.6:1:0.49446:1.85:44.3:8:0.092:0:1.9 -2 113993631 . G A 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06589;SOR=0;LSEQ=TGAGGCCCGGCCTAGGACCG;RSEQ=AGGCGCGACCCCTCGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:2,3:56,53:0.0439:2,2:33.6:1:30.2:1:0.67631:1.57857:49.8:10:0.0439:0:1.2 0/0:93:0:0,0:50,43:0:2,0:26.2:1:30.3:1:1:0:51.2:45.5:1:0:0.4 -2 113993734 . G C 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.26318;SOR=2.68165;LSEQ=GGACCGGAGGCGCGACCCCT;RSEQ=GGCCCACCTTGAGGCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:0,3:34,39:0.0395:2,0:24.7:1:32:0:0.24842:0:35:6:0.0411:0:1 0/1:50:5:3,2:22,23:0.1:2,2:15:1:28.6:1:1:1.55:35.8:10:0.1:0:2 -2 113993747 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1514;SOR=Inf;LSEQ=GACCCCTGGGCCCACCTTGA;RSEQ=GCCCGGCCTAGGACTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:31,42:0:2,0:25.1:1:31.5:1:1:0:43.1:35.5:1:0:0.1 0/1:47:2:1,1:22,23:0.0426:2,2:44:1:31:1:1:1.04:50.5:4:0.0435:0:1 -2 113993757 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.18459;SOR=Inf;LSEQ=CCCACCTTGAGGCCCGGCCT;RSEQ=GGACTGGAGGCGCGACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:36,39:0:2,0:25.2:1:30.2:1:1:0:43.8:74:1:0:0.2 0/1:57:2:1,1:28,27:0.0351:2,2:19:1:29:1:1:1.03639:41:4:0.0364:0:1 -2 113993789 . A G 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31882;SOR=3.96523;LSEQ=GCGACCCCTCGGCCCACCTT;RSEQ=CGGGAGCCGCCTAGGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:1:0,1:48,36:0.0118:2,0:27:0:13:0:0.43529:0:40:0:0:0:1 0/1:66:3:1,2:32,31:0.0455:2,2:32.7:1:26.7:1:1:2.04269:35.7:2:0.0317:0:2 -2 113993818 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21448;SOR=Inf;LSEQ=GCCTAGGGCCGGAGGCGCGA;RSEQ=CCCTCGGCCCAGCTTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:52,39:0:2,0:22.4:1:30.5:1:1:0:52.1:21.75:1:0:0.2 0/1:79:2:1,1:39,38:0.0253:2,2:27.5:1:29.5:1:1:1.02598:28:4:0.027:0:2.5 -2 113993830 . G A 61 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0205;SOR=Inf;LSEQ=AGGCGCGACCCCTCGGCCCA;RSEQ=CTTGAGGCCCGGCCTAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:45,41:0:2,0:24.4:1:31.3:1:1:0:51.3:20.5:1:0:0.2 0/1:76:5:2,3:36,34:0.0658:2,2:39.4:1:26.4:1:0.67447:1.57854:30.8:4:0.0556:0:4 -2 113993839 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21064;SOR=Inf;LSEQ=CCCTCGGCCCAGCTTGAGGC;RSEQ=CGGCCTAGGACCGGAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:47,42:0:2,0:24.6:1:30.8:1:1:0:50.4:88:1:0:0.2 0/1:76:2:0,2:39,35:0.0263:2,0:15:1:29:1:0.23368:0:42:4:0.027:0:1 -2 113993867 . C G 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.12058;SOR=Inf;LSEQ=GGACCGGAGGCGCGACCCCT;RSEQ=GGCCCACCTTGAGGCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:43,41:0:2,0:27.8:1:29.9:1:1:0:43.4:83:1:0:0.3 0/1:85:4:2,2:40,41:0.0471:2,2:10.3:1:30.8:1:1:1.02:56.5:8:0.0494:0:1 -2 113993895 . T C 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10224;SOR=Inf;LSEQ=CTTGAGGCCCGGCCTAGGAC;RSEQ=GGAGGCGCGACCCCTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:34,39:0:2,0:25:1:28:1:1:0:40.7:6.3:0.9844:0:0.3 0/1:66:3:2,1:32,31:0.0455:2,2:14:1:23.7:1:1:1.92:24.7:2:0.0313:0:1.7 -2 113993947 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.49515;SOR=Inf;LSEQ=CCGGCCTAGGACCGGAGGCG;RSEQ=GACCCCTGGGCCCACCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:16,33:0:2,0:23:1:29.5:1:1:0:31:23.5:1:0:0.6 0/1:51:2:1,1:20,29:0.0392:2,2:19:1:28:1:1:1.44:37:4:0.0408:0:1 -2 113993983 . T C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61661;SOR=0.72768;LSEQ=CTTGAGGCCCGGCCTAGGAC;RSEQ=GGAGGCGCGACCCCTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:12:5,7:30,20:0.1905:2,2:33.4:1:31.3:1:0.33505:2.07438:33.4:24:0.1935:0:1.1 0/1:48:7:3,4:19,21:0.1458:2,2:27.6:1:28.9:1:1:1.20157:30.7:14:0.1556:0:1.7 -2 113994069 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52799;SOR=0;LSEQ=ACCTGGCGGCCCGGCCGGCA;RSEQ=AGCCCGCCTCTCCTCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:117,65:0.0109:2,2:23:1:28.5:1:1:1.79383:60:4:0.0112:0:1 0/0:112:0:0,0:68,44:0:2,0:23.2:1:30.6:1:1:0:59.9:27:1:0:0.4 -2 113994074 . C T 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84094;LSEQ=GCGGCCCGGCCGGCACAGCC;RSEQ=GCCTCTCCTCTCCAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:120,75:0.0102:2,2:19:1:32.5:1:1:1.59599:60:4:0.0103:0:1 0/0:117:1:0,1:69,47:0.0085:2,0:2:0:27:0:0.41026:0:60:2:0.0088:0:2 -2 113994079 . C T 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCGGCCGGCACAGCCCGCCT;RSEQ=TCCTCTCCAGGCCAGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:124,79:0:2,0:23.3:1:31.2:1:1:0:60:66.667:1:0:0.2 0/1:120:26:16,10:56,38:0.2167:2,2:23.3:1:28.8:1:1:1.09:60:12:0.2069:0:1.2 -2 113994082 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14277;SOR=Inf;LSEQ=GCCGGCACAGCCCGCCTCTC;RSEQ=TCTCCAGGCCAGGGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:125,80:0:2,0:23.6:1:30.9:1:1:0:60:40:1:0:0.2 0/1:125:2:1,1:73,50:0.016:2,2:24.5:1:31:1:1:1.45545:60:4:0.0164:0:1.5 -2 113994118 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5866;SOR=2.52294;LSEQ=CCCACACCTTCCGCCTGACA;RSEQ=CCAGCCAAGCTCTTCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:1:0,1:103,117:0.0045:2,0:50:0:29:0:1:0:60:2:0.0047:0:1 0/1:176:2:1,1:93,81:0.0114:2,2:32.5:1:27:1:1:1.14724:60:4:0.0116:0:1 -2 113994119 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20119;SOR=Inf;LSEQ=CCACACCTTCCGCCTGACAG;RSEQ=CAGCCAAGCTCTTCAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:100,117:0:2,0:27.6:1:31.2:1:1:0:60:42.4:1:0:0.2 0/1:177:2:1,1:94,81:0.0113:2,2:35:1:28:1:1:1.15951:60:4:0.0115:0:2 -2 113994145 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19794;SOR=Inf;LSEQ=AAGCTCTTCAGTCCCCCGCC;RSEQ=TCCACCTGCCAGGGAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:79,120:0:2,0:26.1:1:31.3:1:1:0:60:65.333:1:0:0.2 0/1:160:2:1,1:75,83:0.0125:2,2:13:1:28:1:1:1.11:60:4:0.0125:0:1 -2 114000920 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCTGACATCTTCAACTT;RSEQ=AGCCTACCTTGTGCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:44:1:28.5:1:1:0:60:4:1:0:1 -2 114002052 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13894;SOR=Inf;LSEQ=TGTCATTGTCACAGACGCCC;RSEQ=CAGCCAGGAGCCGGTCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:33,20:0:2,0:31.2:1:30.9:1:1:0:60:106:1:0:0.2 0/1:32:2:1,1:18,12:0.0625:2,2:37:1:31:1:1:1.48061:60:4:0.0645:0:1 -2 114256607 . A AG 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGGGAAGAAGGGTTATAA;RSEQ=GGGGGGAGTCCACCACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:44:1:32.5:1:0.33333:0:23.5:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 114257227 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23325;SOR=0;LSEQ=ACAAGCGCCTCACGCTCAGC;RSEQ=GCATCTGCGCCTTCATTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:13,21:0.0556:2,2:13:1:31:1:1:1.59:44.5:4:0.0556:0:1 0/0:38:0:0,0:17,21:0:2,0:26.5:1:29.5:1:1:0:42.1:37:1:0:0.1 -2 114257266 . C T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.35955;LSEQ=GTGGCCGCTTCCCCTACTAC;RSEQ=GCCGCAAGTTCCCCGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:8,18:0.0714:2,2:25.5:1:24.5:1:1:2.18:35:1:0.0385:0:1 0/1:21:2:1,1:5,14:0.0952:2,2:22:1:27:1:0.5:2.65:46:4:0.0952:0:1 -2 114258384 . G A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTTCGGCTGTGGCTTCT;RSEQ=TGGCTTTCCGGATTTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 115200297 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=AAGTCCAATAGAGGAGACTT;RSEQ=ATCTCTAGTTCATTCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:28.2:1:31.1:1:1:0:60:22:1:0:0 0/1:17:2:1,1:5,10:0.1176:2,2:9.5:1:26.5:1:1:1.91:60:4:0.1176:0:1 -2 117045275 . C A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATAGACTCTTTGACAG;RSEQ=AGTGACTTTCCAAAACCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:11:0:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 117045438 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21601;SOR=0;LSEQ=GCTTCTGAACTCAGGCAATG;RSEQ=CTTTCAAACTCTTATACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:27,21:0.04:2,2:14.5:1:28:1:1:1.2792:60:4:0.04:0:1 0/0:57:0:0,0:33,24:0:2,0:23.4:1:30.7:1:1:0:58.9:27.5:1:0:0.4 -2 117045503 . C T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38722;SOR=0.65486;LSEQ=TCTCTCCTTTCTAGGTCCCA;RSEQ=GACAGCCATCTTGCTACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:20:7,13:9,18:0.4255:2,2:18.5:1:30.8:1:1:1.08:59.6:40:0.4348:0:1.2 0/1:43:14:6,8:11,18:0.3256:2,2:19.4:1:30:1:1:1.22:60:28:0.3256:0:1.1 -2 119592580 . GA G 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGGCTCACCTGGTGCAG;RSEQ=AAAGTTCAGTTGGCAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,0:0.8:0,2:33.3:1:30.3:1:1:0:60:8:1:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 119592934 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50913;SOR=0;LSEQ=TACCAGGGGAAGGGCGCTCC;RSEQ=CTTTTCCCTGGTAATACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:82,67:0.0132:2,2:39:1:29.5:1:1:1.22223:60:4:0.0137:0:2 0/0:112:0:0,0:59,53:0:2,0:24.3:1:30.1:1:1:0:60:55:1:0:0.6 -2 119592943 . T G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50845;SOR=0;LSEQ=AAGGGCGCTCCCCTTTTCCC;RSEQ=GGTAATACTCCGGGAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:86,72:0.0125:2,2:38:1:30:1:1:1.19311:60:4:0.0128:0:2 0/0:120:0:0,0:65,55:0:2,0:24.7:1:30.2:1:1:0:60:240:1:0:0.7 -2 119592977 . A G 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14343;LSEQ=GAGCCCCTACTCGGAAGCCC;RSEQ=AGAGTCAAAGGGATACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:175:162:82,80:5,8:0.9257:2,2:26.6:1:30.4:1:0.56604:1.64:60:161:0.9253:0:1.2 1/0:136:87:42,45:22,27:0.6397:2,2:25.9:1:30.4:1:0.72408:1.14:60:86:0.637:0:1.2 -2 119594426 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAATTGCCTGCACTCTGC;RSEQ=AAATGGACAAGTCCTGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 119594504 . C G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGCTGTGGTCGTTACTGGGA;RSEQ=TCGCTTTTGTTTTCTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:11:0:27:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:36:1:30.5:1:1:0:60:4:1:0:1 -2 119641913 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GCCAGCGGGTCGGTCCAAGG;RSEQ=TCCTCACTAGAAATTGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:20.5:1:31.5:1:1:0:60:4:0.5:0:3.5 1/1:2:2:1,1:0,0:1:0,2:24:1:30.5:1:1:0:60:4:1:0:3.5 -2 119641921 . T C 41 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=GTCGGTCCAAGGATCCTCAC;RSEQ=AGAAATTGTTAGTTGAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:15.7:1:26.3:1:1:0:60:2:0.5:0:3.3 1/0:4:2:1,1:2,0:0.5:0,2:32:1:31:1:1:0:60:4:0.5:0:3.5 -2 119641926 . A G 67 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=TCCAAGGATCCTCACTAGAA;RSEQ=TTGTTAGTTGAGCTCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:14.3:1:33.5:1:1:0:60:8:0.6667:0:3 1/0:4:2:1,1:2,0:0.5:0,2:37:1:31.5:1:1:0:60:4:0.5:0:3.5 -2 119641974 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48768;SOR=Inf;LSEQ=ATTTGTAAGATCATCTGTAG;RSEQ=TTGATGGCCTCAATCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:12,1:0:1,0:21.9:1:29.4:1:1:0:60:26:1:0:0.8 0/1:16:2:1,1:11,3:0.125:2,2:11:1:30.5:1:0.45:3.31654:60:4:0.125:0:1.5 -2 119641993 . G A 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16087;LSEQ=GTTTGATGGCCTCAATCCTA;RSEQ=AGGAAACAAATTTTACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:8,1:0.4:2,0:22.7:1:30.8:1:1:0:60:12:0.4:0:2 0/1:16:7:5,2:8,1:0.4375:2,2:30.4:1:30:1:0.55:2.96927:60:14:0.4375:0:1.4 -2 119642126 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49635;SOR=0;LSEQ=GTTGGTATAAGAGTTTGAAA;RSEQ=GCGTTGTCTGATTTCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:27,39:0.029:2,2:35.5:1:32:0:1:1.44:43:4:0.029:0:2.5 0/0:68:0:0,0:29,39:0:2,0:22.2:1:31:1:1:0:57.9:136:1:0:0.2 -2 119642149 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.49985;SOR=0;LSEQ=GTTGTCTGATTTCAGAAGCC;RSEQ=TTTCCTGTAAACGCCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:19,25:0.0435:2,2:12.5:1:30.5:1:1:1.31:43:4:0.0444:0:2.5 0/0:37:0:0,0:13,24:0:2,0:21:1:30.9:1:1:0:57.7:74:1:0:0.2 -2 119642167 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14474;SOR=Inf;LSEQ=CCTTTTCCTGTAAACGCCGG;RSEQ=CAGCATCTCTTACTATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:14,21:0:2,0:23.7:1:31:1:1:0:58.1:70:1:0:0.1 0/1:22:2:1,1:6,14:0.0909:2,2:22:1:30:1:1:2.24:60:4:0.0952:0:1 -2 120048537 . G A 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1321;LSEQ=AGCTATCAGACGCCAAGGCT;RSEQ=ACTTACAGGGGGACAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:0.6364:0,0:12.9:1:26.3:1:1:0:60:6:0.6:0:1.7 1/0:3:2:2,0:1,0:0.6667:0,0:40.5:1:26.5:1:1:0:60:4:0.6667:0:2 -2 120048550 . A T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68017;SOR=1.94206;LSEQ=CAAGGCTGACTTACAGGGGG;RSEQ=CAAACCTATTGAACACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:18.3:1:29.8:1:1:0:60:12:0.4286:0:2 1/0:10:6:6,0:4,0:0.6:0,0:14.7:1:30.3:1:1:0:60:12:0.6:0:2.2 -2 120048632 . G A 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0144;SOR=2.43896;LSEQ=AGGCCCAGACAGACTCTGCT;RSEQ=CCACCTGGTGGCTGAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:44:33,11:27,2:0.6027:2,2:23.4:1:28.1:1:0.06302:4.42108:60:88:0.6197:0:1.2 1/0:85:67:44,23:12,6:0.7882:2,2:24.2:1:28:1:1:1.04492:60:66:0.7857:0:1.3 -2 120048649 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4999;SOR=Inf;LSEQ=GCTGCCACCTGGTGGCTGAA;RSEQ=GGTAGGCAAAGGCGGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:74,21:0:2,0:21.2:1:31.2:1:1:0:60:22.75:1:0:0.8 0/1:109:2:1,1:68,39:0.0183:2,2:30.5:1:28.5:1:1:1.73419:60:4:0.0183:0:1 -2 120048677 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49899;SOR=Inf;LSEQ=AAAGGCGGACAAGTGCAGAG;RSEQ=CACTCCACCTGACCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:90,46:0:2,0:25.3:1:31.1:1:1:0:60:18.429:1:0:0.8 0/1:147:2:1,1:87,58:0.0136:2,2:30.5:1:30:1:1:1.49572:60:4:0.014:0:2.5 -2 120048729 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=3.82227;LSEQ=CGCGTAACGAGGCTCTGCTA;RSEQ=TATGGCAGGAAAGGTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:114:55,59:62,58:0.4851:2,2:25:1:31.7:1:0.69488:1.14603:60:113:0.485:0:1.2 1/0:226:177:98,79:25,24:0.7832:2,2:25.5:1:31.5:1:0.62884:1.19:60:354:0.7832:0:1.2 -2 120048774 . A T 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AGGAGAAGCTGCTCGGCAAG;RSEQ=TGTAAAGATGAACGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:99,141:0:2,0:25.8:1:30.6:1:1:0:60:119:1:0:0.5 0/1:221:16:7,9:97,108:0.0724:2,2:21.9:1:28.4:1:0.80207:1.15401:60:32:0.0748:0:1.8 -2 120048803 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5019;SOR=0;LSEQ=TGAACGGCTGGGCATTAATC;RSEQ=GCTGGTGCCTGGCAGGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:74,117:0.0104:2,2:6.5:1:29:1:1:1.58:60:4:0.0105:0:3 0/0:164:0:0,0:66,98:0:2,0:24:1:29.5:1:1:0:60:40:1:0:0.4 -2 120048808 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21333;SOR=Inf;LSEQ=GGCTGGGCATTAATCGGCTG;RSEQ=TGCCTGGCAGGTATCTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:70,110:0:2,0:26.9:1:31.6:1:1:0:59.9:89:1:0:0.3 0/1:155:2:1,1:59,94:0.0129:2,2:20.5:1:28:1:1:1.59:60:4:0.0132:0:1.5 -2 121107321 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15408;SOR=Inf;LSEQ=CGCATGCGGGGTCTGAACCC;RSEQ=GGCACGGTGAACTCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:25,16:0:2,0:25.1:1:30.5:1:1:0:60:82:1:0:0.1 0/1:27:2:1,1:16,9:0.0741:2,2:33:1:30:1:1:1.73837:60:4:0.0741:0:1 -2 121107864 . A G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCGCCTTCCGAGCACACAT;RSEQ=AAAGCACAAAGACAGAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:27:0:27:0:1:0:60:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:35.5:1:30.5:1:1:1:60:4:0.5:0:1 -2 121726310 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50184;SOR=0;LSEQ=TGTCCCGTTTCTCCAGCCCG;RSEQ=GGGTGACGCCCCGCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:2,0:121,22:0.0138:2,0:20.5:1:27.5:1:1:0:60:4:0.0138:0:1.5 0/0:122:0:0,0:99,23:0:2,0:23.2:1:31.5:1:1:0:60:60:1:0:0.1 -2 121726338 . G T 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33389;SOR=3.6361;LSEQ=GCCCCGCCTGAGCCGCAAGC;RSEQ=GGCGCTGTCCATCTCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:1:0,1:186,90:0.0036:2,0:1:0:26:0:0.32852:0:60:2:0.0036:0:1 0/1:231:3:1,2:138,89:0.013:2,2:10.7:1:23:1:0.56393:3.08563:60:2:0.0089:0:1 -2 121726353 . C T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08882;SOR=Inf;LSEQ=CAAGCGGGCGCTGTCCATCT;RSEQ=CCCACTCTCAGACGCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:208,146:0:2,0:25.4:1:30.9:1:1:0:60:58:1:0:0.2 0/1:287:3:1,2:159,125:0.0105:2,2:7.7:1:22.3:1:0.58567:2.53587:60:2:0.007:0:2.3 -2 121726439 . A G 52 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16042;SOR=0;LSEQ=CCTACATCAACAACTCCCGA;RSEQ=GCAGCTCGGCGGCCAGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:4:2,2:54,156:0.0187:2,2:18.8:1:26:1:0.2807:2.87:60:3:0.0144:0:1.5 0/0:136:0:0,0:40,96:0:2,0:47:0:16:0:1:0:60:0:0:0:2 -2 121726447 . G A 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00321;SOR=0;LSEQ=AACAACTCCCGAAGCAGCTC;RSEQ=GCGGCCAGCGGTTCCTACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:166:166:31,135:0,0:1:0,2:20.8:1:30.7:1:1:0:60:40.5:1:0:1.1 1/1:106:100:24,76:1,5:0.9434:2,2:17.7:1:29.3:1:1:1.57:60:13.286:0.949:0:1.2 -2 121726469 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54113;SOR=0;LSEQ=CGGCCAGCGGTTCCTACGGG;RSEQ=ATCTGTCAGCGGGTGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:0,2:2,83:0.023:1,0:25.5:1:29:0:1:0:60:4:0.0238:0:2 0/0:47:0:0,0:0,47:0:1,0:21.7:1:31.7:1:1:0:60:46:1:0:1 -2 121726496 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13426;SOR=Inf;LSEQ=CAGCGGGTGCCCTCAGGTGA;RSEQ=CCCCGCCTGCAAGCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:2,48:0:1,0:24.9:1:31.8:1:1:0:60:24:1:0:0.6 0/1:30:2:0,2:0,28:0.0667:1,0:40:1:30:1:1:0:60:4:0.0667:0:2 -2 121726571 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCGCTGGCTTTTCAGTG;RSEQ=GCGCTTTTGACCCGAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:1,19:0.0909:1,2:28:1:30:1:0.17749:13.79:60:4:0.0952:0:1 0/0:9:0:0,0:1,8:0:2,0:27:1:30.4:1:1:0:60:18:1:0:0 -2 121735497 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCATGTGTTATTTTTCTA;RSEQ=TGAAACAAAATATGTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 121735983 . C T 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGCCTCTGGCCCTGCTTAC;RSEQ=CTCTTCTGGGCATGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:19:13,6:187,96:0.0629:2,2:23.5:1:29.4:1:1:1.11:60:18:0.061:0:1.2 0/0:268:0:0,0:177,91:0:2,0:22.2:1:30:1:1:0:60:133:1:0:0.2 -2 121736077 . G T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01562;SOR=Inf;LSEQ=CCGCTGGCAGGCCTGCACGC;RSEQ=GGAGCAGAAGCCCTTCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:0:0,0:326,302:0:2,0:23.6:1:30.2:1:1:0:60:77.5:1:0:0.1 0/1:486:5:2,3:251,230:0.0103:2,2:18:1:27.6:1:0.6743:1.6353:60:4:0.0084:0:1.2 -2 121736194 . CA C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10477;SOR=Inf;LSEQ=CCCCACCCCCGCCGCAGCAT;RSEQ=AGACTGGCCTGTCAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:34,151:0:2,0:23.6:1:29.8:1:1:0:60:25.429:1:0:0.2 0/1:166:3:0,3:33,130:0.0181:2,0:19:1:32.3:1:1:0:60:6:0.0183:0.006:0 -2 121740190 . C T 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATGCTTCTGAGTGCGCTGA;RSEQ=GGGTTGGAGCAGAGCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:35:35,0:0,0:0.9722:0,1:26.1:1:31.6:1:1:0:60:70:1:0:2.1 1/1:12:12:11,1:0,0:1:0,2:26.1:1:30.3:1:1:0:60:24:1:0:2.1 -2 121740194 . T G 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTGAGTGCGCTGACGGG;RSEQ=TGGAGCAGAGCAGAGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:37,0:0,0:1:0,1:27.2:1:31.9:1:1:0:60:74:1:0:2.2 1/1:13:13:11,2:0,0:1:0,2:28:1:31.3:1:1:0:60:26:1:0:2 -2 121740348 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.09775;SOR=Inf;LSEQ=AACCTGAAGACACACCTGCG;RSEQ=TCCCACACCGGGGAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:213,116:0:2,0:27:1:31.2:1:1:0:60:53.833:1:0:0.1 0/1:282:3:1,2:175,104:0.0106:2,2:17.7:1:27:1:0.55857:3.35042:60:6:0.0109:0:1.3 -2 121740454 . G A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05129;SOR=Inf;LSEQ=AGAATCGCACCCACTCCAAC;RSEQ=AGGTACCTCTGCGGGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:44,168:0:2,0:21.7:1:30.6:1:1:0:60:52:1:0:0.4 0/1:194:4:2,2:53,137:0.0206:2,2:12.3:1:26.5:1:0.31865:2.57:60:8:0.0208:0:1 -2 121740505 . C T 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=0;LSEQ=GCACACTGGGGCCCCACTGA;RSEQ=GCCCCATGGCTTCCAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:83:83:4,79:0,0:1:0,1:25.1:1:29:1:1:0:60:9.375:1:0:1.1 1/1:44:36:2,34:1,7:0.8182:2,2:23.5:1:28:1:0.46089:2.36808:60:6.2:0.7949:0:1.1 -2 121740609 . CTT C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54592;SOR=0.32034;LSEQ=CTCAGATACAGACCAGGACT;RSEQ=TGAGACCTAGACAGACCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:0.9091:0,0:25:1:31.9:1:1:0:57.5:20:0.9091:0.0909:1 1/0:8:6:0,6:0,2:0.75:0,0:16.3:1:31.9:1:1:0:60:12:0.75:0.375:0.5 -2 121740743 . C T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAATAAATATAATAGTG;RSEQ=CCTCCCCAAAGGCCATCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:18.3:1:29.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 122466245 . C A 30 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.75669;LSEQ=TCTTTTCCATTCTGATTTGA;RSEQ=TTTTGTGCATTTTTGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:94,61:0.0127:2,2:10:0:32:1:1:1.53657:48:4:0.0128:0:1.5 0/0:207:2:1,1:113,92:0.0097:2,2:5.5:1:30.5:1:1:1.22703:52:4:0.0098:0:1 -2 122466253 . C T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1319;SOR=Inf;LSEQ=ATTCTGATTTGACTTTTGTG;RSEQ=ATTTTTGGCTGGAGTATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:94,74:0:2,0:24.4:1:32.1:1:1:0:59.6:83:1:0:0.1 0/1:209:4:2,2:112,93:0.0191:2,2:23.5:1:28.8:1:1:1.20322:60:8:0.0194:0:1.3 -2 122466270 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21762;SOR=0;LSEQ=GTGCATTTTTGGCTGGAGTA;RSEQ=CTCGTATGGATTTCTTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:91,92:0.0108:2,2:14:1:28.5:1:1:1.01:60:4:0.011:0:1 0/0:211:0:0,0:99,112:0:2,0:26.7:1:29.2:1:1:0:59.1:210:1:0:0.1 -2 122466293 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12375;SOR=Inf;LSEQ=CGTATGGATTTCTTCACCGG;RSEQ=GCTTTTTCTTCAGCTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:85,89:0:2,0:27.2:1:30.9:1:1:0:60:173:1:0:0.1 0/1:186:4:2,2:85,95:0.0215:2,2:12.5:1:29.8:1:1:1.12:60:8:0.0219:0:1 -2 122466446 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22822;SOR=Inf;LSEQ=AAGAGTTTCACATCCTCCTC;RSEQ=TCTTCATCTTCTGACTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:101,69:0:2,0:24.5:1:31.6:1:1:0:49.9:340:1:0:0.1 0/1:156:2:1,1:85,69:0.0128:2,2:23.5:1:28.5:1:1:1.23022:36:4:0.0128:0:1 -2 122466458 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49887;SOR=0;LSEQ=TCCTCCTCCTCTTCATCTTC;RSEQ=GACTCTGCATCTTCCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:103,68:0.0116:2,2:39.5:1:31.5:1:1:1.51093:24:4:0.0116:0:1 0/0:164:0:0,0:88,76:0:2,0:25.7:1:29.9:1:1:0:48.6:53.667:1:0:0.1 -2 122466505 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23343;SOR=0;LSEQ=TAAGTGCTGTCCACTAATAT;RSEQ=CACTGGCCCTGAACCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:90,102:0.0103:2,2:43:1:31.5:1:1:1.13:50.5:4:0.0106:0:1 0/0:207:0:0,0:96,108:0:2,0:27.4:1:31.6:1:1:0:50.3:50:0.9901:0:0.2 -2 122466514 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22884;SOR=0;LSEQ=TCCACTAATATGCACTGGCC;RSEQ=TGAACCACACTTCAACCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:2,0:78,103:0.0109:2,0:18:1:29:1:0.18976:0:46:4:0.0111:0:1 0/0:199:0:0,0:88,111:0:2,0:28:1:30.8:1:1:0:51.4:48.75:1:0:0.2 -2 122466563 . T C 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=GGTGGTGTGATTTCAAAGCC;RSEQ=CCAAGGGAATCCTTTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:45,83:0:2,0:21.2:1:30:1:1:0:60:24.6:1:0:0.1 0/1:111:10:5,5:35,66:0.0901:2,2:27.3:1:30.1:1:0.49112:1.87:59.1:20:0.0943:0:1.2 -2 122466739 . G GT 49 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.27296;SOR=0;LSEQ=ACACCAGGTTTTTTTTTGTT;RSEQ=TTTTTTTTTTGAGATAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:1,2:6,21:0.1:2,2:34:1:31.3:1:1:1.71:60:6:0.1034:0:1 0/0:19:0:0,0:4,10:0:2,0:24.1:1:31:1:1:0:60:28:0.7778:0:0.6 -2 123421479 . TTGC T 66 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=11.000;MSILEN=3;SSF=0.05106;SOR=Inf;LSEQ=GTCACCACATCAAAAAAGCT;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:23:1:29.8:1:1:0:57.4:40:1:0:0.4 0/1:23:5:3,2:11,6:0.2174:2,2:27.2:1:28.8:1:1:1.21094:60:10:0.2273:0.0435:0.8 -2 123421570 . A G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23821;SOR=0.42883;LSEQ=GCTGCTGCTGAGCCCAACTT;RSEQ=TCCTTGGTGCTGCTCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:4,7:4,7:0.5:2,2:32.7:1:33.5:1:1:1:60:22:0.5238:0:1.5 0/1:27:8:4,4:6,13:0.2963:2,2:30.5:1:30.3:1:0.41467:2.10:58.3:16:0.3077:0:1.6 -2 123421606 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.05766;SOR=0;LSEQ=TGGCCTGAGTCCGGGTTCCC;RSEQ=GGGCCCTGCCATGCATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:4,6:0.2308:2,2:21.3:1:30:1:1:1.30472:60:6:0.2308:0:1 0/0:19:0:0,0:6,13:0:2,0:22.6:1:28.7:1:1:0:60:38:1:0:0.4 -2 125301057 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACAGGCTGAGTAGTGAA;RSEQ=GCTTGTAAAGTTGGCGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 125301394 . C T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01921;LSEQ=AATGCCATCTAAAGCCTCTT;RSEQ=ATTTAATAAAAAGGAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:40:31,9:41,5:0.4651:2,2:20.7:1:29.1:1:0.24097:2.35658:60:80:0.4651:0:1.5 0/1:83:39:31,8:34,10:0.4699:2,2:27.4:1:29.1:1:1:1.14:60:78:0.4699:0:1.4 -2 125301476 . C A 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.87869;SOR=1.02481;LSEQ=GTTTCTACAGTGGATTCTAA;RSEQ=TAGAATCACCTAGGTTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:170:99,71:113,83:0.4645:2,2:25.6:1:30.3:1:0.91591:1.02:60:169:0.4656:0:2 0/1:323:152:82,70:92,79:0.4706:2,2:28.7:1:29.4:1:1:1.01:60:37:0.4684:0:2 -2 125301502 . G T 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82414;SOR=1.04002;LSEQ=TCACCTAGGTTTACTAAAAT;RSEQ=CAACAATTGGACCAGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:171:84,87:101,99:0.4597:2,2:27.1:1:29.7:1:0.83521:1.05646:60:84.5:0.4617:0:1.9 0/1:360:169:88,81:94,96:0.4694:2,2:26.2:1:28.5:1:0.67258:1.11:60:32.8:0.4686:0:1.9 -2 125301528 . G GT 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.23758;SOR=0.81337;LSEQ=ATTGGACCAGATGCTAGCTA;RSEQ=TTTTTTTTTCCTGCTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:117:41,76:81,104:0.3703:2,2:29:1:29.9:1:0.14917:1.44195:60:116:0.373:0.0285:1.4 0/1:303:98:41,57:87,95:0.3234:2,2:29.1:1:29.4:1:0.37941:1.27207:60:48:0.3265:0.0033:1.3 -2 125301538 . C T 56 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02851;SOR=Inf;LSEQ=ATGCTAGCTAGTTTTTTTTT;RSEQ=CTGCTAATTTTCTTGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:93,182:0:2,0:25.9:1:30.9:1:1:0:60:90.667:1:0:0.7 0/1:272:5:3,2:108,159:0.0184:2,2:10.8:1:24.2:1:0.40112:2.20:60:4:0.0154:0:4.2 -2 125301638 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.81019;SOR=0.7947;LSEQ=GACACTGAGGTTCACAGGTA;RSEQ=GAAATTACTTTCCCAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:19:0,19:0,26:0.4222:1,1:31.7:1:29.1:1:1:0:60:18:0.4091:0:1.2 0/1:30:11:0,11:1,18:0.3667:1,0:28:1:29.5:1:1:0:60:22:0.3667:0:1.1 -2 125301742 . C T 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=AAGTTAAACTAACCATCTAA;RSEQ=AGGTCTTAAGGGATCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:1,6:0,3:0.7:0,2:17.7:1:27.4:1:1:0:60:6:0.6667:0:1.6 0/0:1:0:0,0:0,1:0:0,0:33:0:34:0:1:0:60:2:1:0:0 -2 125301795 . T A 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTATCCATGCAAGGCTAG;RSEQ=TAGTGCTTGGACTAAGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:18.3:1:31:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 125424512 . T TG 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00465;SOR=0.39996;LSEQ=AAGATGTTCAGGATGGTGCA;RSEQ=AACTACAGCAAAGAACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:90:75,15:15,6:0.8036:2,2:23.6:1:31.8:1:0.22426:1.99:60:89:0.8091:0.1696:0.9 1/0:92:57:46,11:29,6:0.6196:2,2:20.6:1:31.2:1:1:1.15399:60:114:0.6196:0.1522:0.9 -2 125424553 . A G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00278;SOR=0.50967;LSEQ=GGGAGACTATTACTCTGGAC;RSEQ=TTAAATACACATTTTATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:254:205:141,64:30,19:0.8071:2,2:22.3:1:30.4:1:0.31425:1.39:60:410:0.8071:0:1.8 1/0:194:132:93,39:41,21:0.6804:2,2:26:1:30.3:1:0.61776:1.22:60:131:0.6788:0:1.8 -2 125424600 . TG T 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.03908;SOR=0.71844;LSEQ=ATGTGCTTTAAGAAGAACGA;RSEQ=GGGGAAACATGAGCAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:410:301:159,142:58,50:0.7341:2,2:28.2:1:31.5:1:0.91079:1.0359:60:602:0.7396:0.0707:1.5 1/0:352:234:122,112:68,50:0.6648:2,2:27.3:1:30.3:1:0.3654:1.24773:60:468:0.6667:0.0653:1.5 -2 125424612 . G T 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00755;SOR=0.65533;LSEQ=AAGAACGATGGGGGAAACAT;RSEQ=AGCAATGATTGGGCAGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:421:319:168,151:50,52:0.7577:2,2:26.6:1:29:1:0.56972:1.16:60:62.8:0.7566:0:1.5 1/0:378:254:128,126:65,59:0.672:2,2:26.1:1:28.5:1:0.74303:1.08425:60:253:0.6711:0:1.5 -2 125424686 . G A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19921;SOR=4.3867;LSEQ=CTTTAAACATCTTGGTAGCT;RSEQ=GGAAAGATTAACCAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:1,0:60,137:0.0051:2,0:1:0:24:0:0.30808:0:60:2:0.0051:0:1 0/1:183:4:2,2:59,120:0.0219:2,2:25.8:1:24.8:1:0.60167:2.03:60:3:0.0165:0:1.3 -2 125424690 . A C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02392;SOR=Inf;LSEQ=AAACATCTTGGTAGCTGGGA;RSEQ=AGATTAACCAAGGAATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:52,130:0:2,0:24.2:1:30:1:1:0:60:59.667:1:0:0.3 0/1:166:5:1,4:51,110:0.0301:2,2:27:1:32.6:1:1:1.84849:60:10:0.0301:0:1.4 -2 127721295 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21187;SOR=Inf;LSEQ=GCATGGTTCTGGGGTTGGGG;RSEQ=TCTAGGCCCCCGTGGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:28,23:0:2,0:27.2:1:32:1:1:0:60:102:1:0:0.1 0/1:44:2:1,1:24,18:0.0455:2,2:26:1:31.5:1:1:1.32452:60:4:0.0476:0:1 -2 127773880 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52367;SOR=Inf;LSEQ=GGAATTGGCTGCCAGCCTCA;RSEQ=CCCTGAGGACGTGCCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:24.5:1:32.8:1:1:0:60:34:1:0:0 0/1:29:2:1,1:18,9:0.069:2,2:30.5:1:30.5:1:1:1.94942:60:4:0.0714:0:2 -2 127773898 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.54839;SOR=Inf;LSEQ=CAGCCCTGAGGACGTGCCCG;RSEQ=GCAGGGTTTATCTGCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,8:0:2,0:31.1:1:30.1:1:1:0:60:19:0.95:0:0 0/1:42:2:1,1:23,17:0.0476:2,2:38:1:29.5:1:1:1.34309:60:4:0.0476:0:2 -2 127773985 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23729;SOR=0;LSEQ=TCTACCCCCAGAGGGAGCTA;RSEQ=GGGTGTGTGGCCCCAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:10,17:0.069:2,2:13.5:1:31.5:1:1:1.67:60:4:0.069:0:2 0/0:30:0:0,0:10,19:0:2,0:26.6:1:29.5:1:1:0:60:28:0.9655:0:0.3 -2 127774020 . T C 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01686;SOR=Inf;LSEQ=AGGCCCACCCTCCCCAACAG;RSEQ=AGGCTCCTTCTGGGCCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:4,11:0:2,0:25.2:1:26.9:1:1:0:60:30:1:0:0.2 0/1:14:5:1,4:2,7:0.3571:2,2:17.8:1:31.4:1:1:1.1321:60:10:0.3846:0:1.2 -2 127965811 . A C 34 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CTGGCATAACCCACGGAGAG;RSEQ=AGGAAGAACAGTGTAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:23:1:34:0:1:0:60:4:0.5:0:1.5 0/0:4:0:0,0:2,2:0:2,0:32.3:1:28.8:1:1:0:60:8:1:0:0.5 -2 127965845 . A G 32 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.51811;LSEQ=TAGTGCAGTGGCCCACCTGG;RSEQ=AGCCACACGGGGAAGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:22.5:1:32.5:1:1:2.64575:60:4:0.2:0:1 0/1:9:1:1,0:5,3:0.1111:2,0:29:0:26:0:1:0:60:2:0.1111:0:1 -2 127965922 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49675;SOR=Inf;LSEQ=GGCTACCCAGCTGGGGAAAC;RSEQ=GTGCTTTTTCCACAGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:18.8:1:30:1:1:0:60:50:1:0:0.1 0/1:31:2:1,1:21,8:0.0645:2,2:29:1:30.5:1:0.50323:2.53312:60:4:0.0645:0:1 -2 127966823 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=AAGTGAACCCCCAGCAAACT;RSEQ=CAGCAGCCCTACAGAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:0.1538:2,2:40.5:1:29:1:1:1.18:60:4:0.1538:0:1 0/0:7:0:0,0:4,3:0:2,0:19:1:31:1:1:0:60:14:1:0:0.1 -2 128014913 . C T 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCAGAACGGTAACATAAATA;RSEQ=ACCTTAAATATTAACATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:0.6154:0,0:27.5:1:27.6:1:1:0:60:7:0.5833:0:1.3 0/0:1:0:0,0:1,0:0:0,0:40:0:31:0:1:0:60:2:1:0:0 -2 128015066 . A G 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00175;SOR=Inf;LSEQ=TCCTCAGCACAATTTGGCCA;RSEQ=CGCTGGAGGGAAGGTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:93,2:0:1,0:23.7:1:29.9:1:1:0:60:46.5:1:0:0.2 0/1:82:8:8,0:69,5:0.0976:2,0:19:1:29.4:1:1:0:60:7:0.0864:0:1.1 -2 128015350 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24205;SOR=Inf;LSEQ=GTTAGTCTCCAGAAGAAAAG;RSEQ=TACTCCTTTTATAATACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:26,180:0:2,0:24.6:1:30.6:1:1:0:60:40.2:1:0:0.6 0/1:200:2:1,1:33,165:0.01:2,2:20.5:1:29.5:1:0.31181:4.94:60:4:0.0101:0:1.5 -2 128015356 . CT C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.21292;SOR=Inf;LSEQ=CTCCAGAAGAAAAGATACTC;RSEQ=TTTATAATACTTATAATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:22,170:0:2,0:22.9:1:30:1:1:0:60:63:1:0:0.7 0/1:165:2:0,2:26,137:0.0121:2,0:29.5:1:32:1:1:0:60:4:0.0121:0:0 -2 128015367 . C T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.028;SOR=0.50635;LSEQ=AAGATACTCCTTTTATAATA;RSEQ=TTATAATCACAGCAAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:146:121:7,114:0,25:0.8288:1,2:23.9:1:30.2:1:0.6037:0:60:120:0.8333:0:1.1 1/0:124:88:7,81:4,32:0.7097:2,2:23.7:1:29.8:1:0.72862:1.44187:60:176:0.7097:0:1.1 -2 128015370 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50404;SOR=0;LSEQ=ATACTCCTTTTATAATACTT;RSEQ=TAATCACAGCAAATTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:4,135:0.0141:1,2:24:1:31:1:0.06991:30.29:60:4:0.0143:0:2 0/0:114:0:0,0:8,106:0:2,0:22.7:1:29.7:1:1:0:60:113:1:0:0.8 -2 128016761 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.13314;SOR=Inf;LSEQ=TCCGTGTTTTCCAACATTTC;RSEQ=AAAAAAATCCCATGGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:160,1:0:1,0:24.1:1:31.2:1:1:0:60:39.25:1:0:0.1 0/1:93:2:1,1:90,1:0.0215:1,2:31:1:29:1:0.04278:63.9884:60:4:0.022:0:1 -2 128018460 . GGAGGCAAACT G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGATAGCTCTGATGTCTG;RSEQ=GAGGCAAACTAAGGCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:27.5:1:32.5:1:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 128018710 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1982;SOR=Inf;LSEQ=TAATCTCCTAATGCTTGGTG;RSEQ=CTGCCTGCTGACAGTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:190,15:0:2,0:24.6:1:32.2:1:1:0:60:101.5:1:0:0 0/1:165:2:1,1:140,23:0.0121:2,2:12.5:1:31.5:1:0.27051:5.98006:60:4:0.0123:0:1 -2 128018973 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22488;SOR=Inf;LSEQ=GAAGACAACATTAGCCATTA;RSEQ=AATGCCAAGAGCTAAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:30,178:0:2,0:22.4:1:31.4:1:1:0:60:68.333:1:0:0.1 0/1:189:2:1,1:20,167:0.0106:2,2:41:1:28.5:1:0.2104:8.17:60:4:0.0108:0:1 -2 128019178 . G C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATAAGGGATTTGTATCTA;RSEQ=GTTATACAAAGAACTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:37.5:1:28:0:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 128028792 . T C 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.96541;LSEQ=AGGTCTTTGCTTTGGGATTC;RSEQ=CTCCCTCCAGAGTCTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:145:121:118,3:24,0:0.8345:1,1:26.1:1:31.5:1:1:0:60:242:0.8403:0:1.1 1/1:88:73:72,1:15,0:0.8295:1,1:23.1:1:30.2:1:1:0:60:23.333:0.8235:0:1.1 -2 128029065 . GA G 198 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.01056;SOR=0.58188;LSEQ=GGAAGGTTTTTATATATGAG;RSEQ=AAAAAAAAAAGTCAACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:82:15,67:42,129:0.3154:2,2:29.7:1:31.3:1:0.33486:1.45219:59.9:164:0.3228:0.0077:0.1 0/1:232:49:11,38:53,127:0.2112:2,2:26.2:1:30.3:1:0.37404:1.43947:60:48:0.2115:0.0086:0.2 -2 128029082 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21984;SOR=Inf;LSEQ=GAGGAAAAAAAAAAAGTCAA;RSEQ=TGATCCAGAATTTAAATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:34,174:0:2,0:24.4:1:32:1:1:0:60:40.6:1:0:0.3 0/1:185:2:1,1:41,142:0.0108:2,2:41:1:30:1:0.40347:3.43:60:4:0.0112:0:1 -2 128030377 . T C 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3115;LSEQ=AATTCACTGTCCAGGAATCA;RSEQ=AGTGTACCCCCCAGGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:76:55,21:338,107:0.1459:2,2:22.8:1:32.2:1:0.5641:1.20563:60:152:0.1467:0:1.1 0/1:436:22:13,9:293,121:0.0505:2,2:28.4:1:30.6:1:0.24098:1.67426:60:44:0.0507:0:1.2 -2 128036654 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20106;SOR=Inf;LSEQ=GGAGCCCAAGAAGTTCCTGA;RSEQ=AGAAAAACAAAAAAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:143,4:0:1,0:21.8:1:31.6:1:1:0:60:23.5:1:0:0.2 0/1:120:2:1,1:101,17:0.0167:2,2:35.5:1:27.5:1:0.27857:5.80234:60:4:0.0167:0:1 -2 128036662 . C CA 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20017;SOR=Inf;LSEQ=AGAAGTTCCTGAGAGAAAAA;RSEQ=AAAAAAACAAAACAACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:166,10:0:2,0:20.5:1:31.3:1:1:0:60:24.143:1:0:0.1 0/1:143:2:2,0:122,19:0.014:2,0:15:1:31:1:1:0:60:4:0.014:0.007:0 -2 128036701 . G T 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06576;SOR=0;LSEQ=CCACCTTCTGCACTCTCAAT;RSEQ=GGGAAGAGAAACTGGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:5:3,2:295,93:0.0127:2,2:9.6:1:28.8:1:0.59829:2.11004:60:10:0.0128:0:1 0/0:334:0:0,0:232,102:0:2,0:23.2:1:30.9:1:1:0:60:54.667:1:0:0.1 -2 128037201 . G A 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52857;SOR=0;LSEQ=TACAAAAATTAGCTGGGTGT;RSEQ=GTAGTGCATGTCTGTAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:0,9:0.3077:0,0:33.5:1:32:1:1:0:60:8:0.3077:0:1 0/0:3:0:0,0:0,3:0:0,0:5:1:31:0:1:0:60:6:1:0:0 -2 128037478 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGATTTTTAAATGCAATCA;RSEQ=ATCCAGGGAGTTATTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:7:1:27:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 128037942 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50883;SOR=0;LSEQ=TAAGTCCTGACCTGTGTCTG;RSEQ=CCATGAGGAATCGATCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:149,19:0.0118:2,2:17:1:27.5:1:0.22207:7.66904:60:4:0.012:0:1.5 0/0:127:0:0,0:112,15:0:2,0:23.5:1:31.6:1:1:0:60:41.333:1:0:0.1 -2 128037999 . C T 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=31.31059;LSEQ=GGAGGAGGCCCTTTCCCAGA;RSEQ=GCCCCCAGCCCAGGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:1:0,1:318,138:0.0022:2,0:1:0:29:0:0.30416:0:60:2:0.0022:0:1 0/1:466:30:20,10:286,148:0.0644:2,2:25.6:1:29.9:1:1:1.03:60:60:0.0652:0:1.1 -2 128038005 . C A 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCCTTTCCCAGACGCCCC;RSEQ=AGCCCAGGCCCAGCTACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:25:19,6:325,168:0.0483:2,2:21.2:1:29.4:1:0.38715:1.64:59.7:11.5:0.0451:0:1.3 0/0:512:0:0,0:327,184:0:2,0:25.5:1:30.1:1:1:0:60:38.308:0.998:0:0.3 -2 128038065 . C T 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=47.30686;LSEQ=ATGTAGCCATTATTCTGCAG;RSEQ=TCCATCCAGTTGGCTTCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:780:1:0,1:390,387:0.0013:2,0:1:0:27:0:0.49871:0:60:2:0.0013:0:1 0/1:820:47:27,20:391,382:0.0573:2,2:23.9:1:30:1:0.37208:1.32:60:94:0.058:0:1.2 -2 128044048 . G T 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGAACTGCTTGAACCTG;RSEQ=GAGGTGGAAGTTGTGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:28.2:1:29.8:1:1:0:60:10:0.5556:0:1.2 0/0:1:0:0,0:1,0:0:0,0:28:0:33:0:1:0:60:2:1:0:0 -2 128044121 . C CA 78 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.25207;SOR=2.71418;LSEQ=GACAGAGTGAGACTCCCTCT;RSEQ=AAAAAAAAAAAAAAGAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:5,1:28,1:0.1667:1,2:27.2:1:30.3:1:0.31765:5.20267:54.5:12:0.1667:0:1.8 0/1:14:5:5,0:8,1:0.3571:2,0:20:1:30.6:1:1:0:57:10:0.3571:0.1429:1 -2 128044217 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58054;SOR=2.64024;LSEQ=ACAGCAGTCCCTTTCCCAAC;RSEQ=TAACAACTGGAAATTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:1,0:170,17:0.0053:2,0:9:0:14:0:1:0:60:0:0:0:1 0/1:144:2:1,1:119,23:0.0139:2,2:20.5:1:28:1:0.30653:5.08635:60:4:0.014:0:1 -2 128044653 . G A 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.82974;LSEQ=TGAAATGAAGGACAGGGACA;RSEQ=GCAGAATGACTCACAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:2,1:57,208:0.0112:2,2:15:1:22:1:0.12297:7.23:60:2:0.0076:0:2.7 0/0:215:2:2,0:55,158:0.0093:2,0:1:0:24:0:0.06938:0:60:4:0.0094:0:1 -2 128044930 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACCTGGCTGAGCCACC;RSEQ=TGCCACGGTGGCTCATACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29:1:1:0:60:4:1:0:1.5 -2 128046548 . C A 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06725;SOR=1.99527;LSEQ=GTGGCATTCTATCTAAACTT;RSEQ=TACAAGATTTTAGATCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:36:2,34:3,46:0.4186:2,2:21.4:1:31.2:1:1:1.1074:60:72:0.4337:0:1 1/0:44:26:0,26:0,18:0.5909:1,1:26.3:1:30.7:1:1:0:60:52:0.5909:0:1 -2 128046943 . CTCT C 109 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.24735;SOR=1.91158;LSEQ=TCAAAAGACACTGTCTGTGT;RSEQ=TCTTCTTCTTCTTCATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:847:7:4,3:482,358:0.0083:2,2:28:1:31.1:1:1:1.00977:60:14:0.0083:0:0 0/1:765:12:6,6:393,355:0.0157:2,2:15.3:1:30.5:1:1:1.10689:58.8:24:0.016:0.0065:0.2 -2 128047685 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51487;SOR=0;LSEQ=TCTTGTTTCTCTTCTCTTAT;RSEQ=TGTGCTTCACAGAAAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:149,28:0.0112:2,2:16.5:1:28.5:1:0.29854:5.24651:60:4:0.0113:0:1 0/0:124:0:0,0:102,22:0:2,0:20.6:1:31.3:1:1:0:60:123:1:0:0.1 -2 128047998 . C T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02014;SOR=Inf;LSEQ=TCCTAAAGTGGTCAGATGTG;RSEQ=CTAAACTGAGCTTTTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:2,108:0:1,0:24.5:1:31.6:1:1:0:60:54:1:0:0.1 0/1:68:4:0,4:0,64:0.0588:1,0:23.5:1:30.8:1:1:0:60:8:0.0597:0:1 -2 128050000 . A G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.65665;SOR=0.54199;LSEQ=TGTAGCGGCTCATGAGAAGC;RSEQ=TGGCCTCACCCAGAACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:24,1:4,0:0.8621:0,1:21.9:1:29.4:1:1:0:60:24:0.8571:0:1.3 1/0:13:10:10,0:3,0:0.7692:0,0:19.5:1:30.1:1:1:0:60:20:0.7692:0:1.1 -2 128050068 . C T 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=GTAATCAGTCGTTATGCTCC;RSEQ=CACAGGAAATCTGAATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:91,0:0:1,0:22.9:1:31.2:1:1:0:60:44.5:1:0:0.7 0/1:48:8:7,1:40,0:0.1667:1,2:17.5:1:30.5:1:0.16667:0:60:16:0.1702:0:1 -2 128050125 . A T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07532;SOR=Inf;LSEQ=ACAGGCTGACAACATGGAGC;RSEQ=CCTATGCCTATTGTTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:208,56:0:2,0:22.8:1:29.7:1:1:0:60:51.8:1:0:0.9 0/1:194:3:1,2:140,51:0.0155:2,2:23.7:1:28.3:1:0.18172:5.43295:60:6:0.0155:0:2 -2 128050134 . T C 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34105;LSEQ=CAACATGGAGCACCTATGCC;RSEQ=ATTGTTACATTAGCAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:257:198,59:31,8:0.8653:2,2:23.1:1:30.7:1:0.83915:1.15412:60:35.714:0.8711:0:1.1 1/0:239:164:121,43:47,28:0.6862:2,2:25.5:1:30.3:1:0.09397:1.67:60:53.667:0.6851:0:1.2 -2 128050273 . G A 80 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11378;SOR=3.59666;LSEQ=TCACTGGTTTGCAGCCCAAC;RSEQ=CTGACAGCTGCATACAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:703:2:1,1:358,340:0.0028:2,2:15.5:1:21.5:1:1:1.05289:60:1:0.0015:0:1 0/1:787:8:5,3:394,382:0.0102:2,2:25.5:1:26.8:1:0.72551:1.61:60:7:0.009:0:1 -2 128050416 . C T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01034;SOR=Inf;LSEQ=TTCCAAGAAGATATGGCCAT;RSEQ=GGGAGCCTGAGAGATACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:0:0,0:172,321:0:2,0:25.5:1:30.2:1:1:0:60:97.6:1:0:0.1 0/1:434:6:3,3:161,267:0.0138:2,2:27.7:1:30.2:1:0.67714:1.66:60:12:0.014:0:1.2 -2 128050483 . T C 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=0.20896;LSEQ=AGTTGCAGAGACTACTGGGC;RSEQ=CTTGCCCATATCATTATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:31:5,26:16,143:0.1623:2,2:28.4:1:31.1:1:0.348:1.71:60:62:0.1649:0:1.1 0/1:129:5:1,4:20,104:0.0388:2,2:18.6:1:30:1:1:1.30:60:10:0.0394:0:1 -2 128051381 . G A 85 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.02915;SOR=5.89181;LSEQ=AGCATTTCACCTGCGCCGCC;RSEQ=CAAACTCCTAGCTAAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:12,85:0.0202:2,0:9:1:31:0:1:0:60:4:0.0211:0:1 0/1:64:7:1,6:6,51:0.1094:2,2:25.7:1:30.3:1:0.57441:1.41:60:14:0.1111:0:1.3 -2 128051487 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTCCAGCATCTCTCCC;RSEQ=CCCAAAGGCCTGTCCCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:64,16:0.0244:2,2:28:1:28.5:1:0.37368:3.91077:60:4:0.0256:0:1 0/0:36:0:0,0:28,8:0:2,0:24.1:1:29.1:1:1:0:60:11:1:0:0.1 -2 128051525 . C T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6363;SOR=0.43412;LSEQ=ACGGGGTGCGCGCGGGAGGG;RSEQ=CAGCAGGGTCGGCCGGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:3:1,2:138,40:0.0166:2,2:20:1:28.7:1:0.13494:6.80462:60:6:0.0171:0:1 0/0:138:1:0,1:110,27:0.0072:2,0:1:0:26:0:0.2029:0:60:2:0.0074:0:1 -2 128051542 . C T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13098;SOR=0;LSEQ=GGGCCAGCAGGGTCGGCCGG;RSEQ=GCAGAGGCCCGGAGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:4:1,3:224,78:0.0131:2,2:17.3:1:28:1:0.05824:8.54263:60:8:0.0133:0:1 0/0:251:0:0,0:187,64:0:2,0:20.6:1:30.8:1:1:0:60:30.375:1:0:0.1 -2 128051726 . G A 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCGGCATCCGCTCTGGGGG;RSEQ=ACTTCCGGCTCAATCCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:749:0:0,0:281,468:0:2,0:25.6:1:30.8:1:1:0:60:52.5:1:0:0.1 0/1:619:35:12,23:239,345:0.0565:2,2:23.7:1:28.8:1:0.48269:1.32719:60:70:0.0571:0:1.2 -2 128051821 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14914;SOR=Inf;LSEQ=CTGGAAGAGCGGAGAGCCAG;RSEQ=GACCGCCGATCTGTTAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:3,117:0:1,0:25:1:30.2:1:1:0:60:119:1:0:0.3 0/1:76:2:0,2:6,68:0.0263:2,0:22:1:31:1:1:0:60:4:0.0263:0:1 -2 128975123 . A G 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87218;LSEQ=AAAAAAATAAAGTAACTATA;RSEQ=CTTTTTCGGCTGGCACCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:11,2:0.1875:2,0:9.7:1:32.3:1:1:0:60:6:0.1875:0:1.3 0/1:6:1:1,0:3,2:0.1667:2,0:22:0:32:0:1:0:60:2:0.1667:0:1 -2 128975230 . C A 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.73843;SOR=1.34045;LSEQ=AGGCCTTTTGGAAAACATGC;RSEQ=GTTTTTCCTTTGGTCACGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:3,2:23,12:0.125:2,2:19.2:1:30.2:1:1:1.26973:60:10:0.125:0:1.8 0/1:31:5:3,2:24,2:0.1613:2,2:14.2:1:29.4:1:0.11171:7.19006:59.6:10:0.1613:0:2.2 -2 128975303 . C G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0713;SOR=0.49792;LSEQ=ACATCAAGGGAATGGGTACT;RSEQ=TTCAAAAAGGAGTGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:23:12,11:78,41:0.162:2,2:21.7:1:32.3:1:0.24366:1.73683:57.8:22:0.156:0:1.3 0/1:137:12:6,6:73,51:0.0876:2,2:17:1:31.6:1:0.5575:1.4275:59.8:24:0.0902:0:1.8 -2 128975331 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=AGGAGTGCCCACAAGTGTTA;RSEQ=CATGGCAAAACTGGAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:102,75:0:2,0:28.2:1:31.5:1:1:0:59.8:43.25:1:0:0.2 0/1:190:2:1,1:97,91:0.0105:2,2:25.5:1:29:1:1:1.06561:60:4:0.0108:0:1 -2 128975346 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49959;SOR=Inf;LSEQ=TGTTACCATGGCAAAACTGG;RSEQ=AGAGTTTACAATGTTACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:91,83:0:2,0:29.2:1:30.2:1:1:0:59.8:173:1:0:0.2 0/1:190:2:1,1:88,100:0.0105:2,2:45:0:32:1:1:1.14:60:4:0.0107:0:2 -2 128975378 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49828;SOR=0;LSEQ=TGTTACTCAGCATGCTGTTG;RSEQ=CATTGTTGTAAACAAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:60,77:0.0144:2,2:9.5:1:28.5:1:1:1.28:60:4:0.0145:0:1.5 0/0:135:0:0,0:55,80:0:2,0:25.4:1:31.4:1:1:0:60:66.5:1:0:0.2 -2 128975405 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50029;SOR=Inf;LSEQ=TGTAAACAAACAAGTTCAGG;RSEQ=CAAGATTCTTGCCAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:15,56:0:2,0:24:1:31.9:1:1:0:60:142:1:0:0.1 0/1:84:2:1,1:27,55:0.0238:2,2:6:1:31.5:1:1:2.02:60:4:0.025:0:1 -2 129053496 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13664;SOR=Inf;LSEQ=TGTGTTCCACCAAAACTCAT;RSEQ=TTGAAGTCCTAATCTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:24:1:31.3:1:1:0:60:46:1:0:0.2 0/1:14:2:1,1:6,6:0.1429:2,2:33.5:1:30.5:1:1:1:60:4:0.1429:0:1 -2 129521630 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTGCGTTTTTTTGCTTT;RSEQ=CATTTGTTTGGTAAATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:31:1:1:0:60:4:1:0:1 -2 129523137 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.9301;LSEQ=GGTGTCTGGCAACCCCTGTC;RSEQ=GAGGGTCTCATCCAGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:3,5:0.1111:2,0:8:0:32:0:1:0:60:2:0.1111:0:1 0/1:10:2:1,1:3,5:0.2:2,2:28:1:32:0:1:1.58:60:4:0.2:0:1 -2 129523348 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=GGCTCAGGCCCAGGGAGATC;RSEQ=GAATTCTGTCCCTGAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:0.1818:2,2:17:0:32.5:1:1:1.87089:60:4:0.2:0:1.5 0/0:6:0:0,0:5,1:0:2,0:28.8:1:28.3:1:1:0:60:5:1:0:0.7 -2 129523431 . T G 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06658;SOR=0.29023;LSEQ=TGAGGAAGGATGGATCAGGG;RSEQ=TAGGCCTGAAGAGGCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:6,6:4,2:0.6667:2,2:24.3:1:29.7:1:0.63801:1.9247:60:11:0.6875:0:1.6 0/1:25:9:4,5:9,6:0.36:2,2:25:1:32:1:0.67517:1.82559:60:18:0.36:0:1.8 -2 129523483 . C T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49053;SOR=0.4955;LSEQ=GCCACAGCTGGTGTGTTGGG;RSEQ=TGTGGGGACAAGTCTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:5,6:2,4:0.6471:2,2:24.5:1:30.2:1:1:1.62:60:22:0.6471:0:1.6 0/1:17:8:3,5:3,6:0.4706:2,2:17.9:1:29.8:1:1:1.19:60:16:0.5:0:1.9 -2 129523508 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=0;LSEQ=GGGACAAGTCTTGGGACCAA;RSEQ=CCGTTCAGCCTCCCTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:0.1538:2,2:27.5:1:29.5:1:1:1.18:60:4:0.1538:0:2 0/0:11:0:0,0:4,7:0:2,0:26.3:1:30.5:1:1:0:60:10:1:0:0.5 -2 129523511 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=0;LSEQ=ACAAGTCTTGGGACCAAGCC;RSEQ=TTCAGCCTCCCTGGCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:24.5:1:28.5:1:1:1:60:4:0.1667:0:2 0/0:10:0:0,0:4,6:0:2,0:27.5:1:29.9:1:1:0:60:20:1:0:0.5 -2 129737822 . A G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGAATAAGGGGGATTCT;RSEQ=GCTAAACCAACCTAACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:10,13:0,0:1:0,2:24:1:30.7:1:1:0:60:22:1:0:1.1 1/1:16:16:8,8:0,0:1:0,2:27.1:1:30.9:1:1:0:60:32:1:0:1.1 -2 129739742 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGATTTTGGAAGCACATA;RSEQ=CTTGTTTGGCTTCAAAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:28.5:1:1:0:60:4:1:0:1 -2 129739875 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGCTCCAGAGCTCATGCC;RSEQ=GTGCGAGTTTAGACCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 131495401 . C CG 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53964;SOR=0;LSEQ=GTCGCTGCAACACCATCCCC;RSEQ=GGGCAGCAGAGCCCCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:2,0:34,9:0.0444:2,0:23.5:1:31.5:1:1:0:60:4:0.0444:0:0 0/0:24:0:0,0:19,5:0:2,0:18.9:1:29.7:1:1:0:60:48:1:0:0.1 -2 131495488 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=CACCAAGGGTGGCACCGTGG;RSEQ=GACTCTGAGACCTACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:65,66:0.015:2,2:26.5:1:29:1:1:1.02:60:4:0.015:0:1 0/0:122:0:0,0:65,57:0:2,0:25.7:1:30.6:1:1:0:60:60:1:0:0.2 -2 131495494 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49851;SOR=0;LSEQ=GGGTGGCACCGTGGCGACTC;RSEQ=GAGACCTACCCAGGATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:60,67:0.0155:2,2:12:0:32:1:1:1.12:60:4:0.0157:0:1.5 0/0:121:0:0,0:64,57:0:2,0:24.7:1:30.1:1:1:0:60:59.5:1:0:0.2 -2 131946026 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.36471;SOR=3.12955;LSEQ=ATAGTATTTCTTACCCCGTG;RSEQ=AGCATAATAAAAAATAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:1:0,1:189,113:0.0033:2,0:1:0:23:0:0.37624:0:47:2:0.0033:0:1 0/1:292:3:1,2:182,107:0.0103:2,2:7.7:1:27:1:0.55803:3.38709:49:6:0.0106:0:1 -2 131947284 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12072;SOR=Inf;LSEQ=TTAGTGTCTTTACATATTTT;RSEQ=AACACAAAAGTTTTACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:45,1:0:1,0:20.5:1:32.8:1:1:0:42.9:92:1:0:0.1 0/1:25:2:1,1:23,0:0.08:1,2:27.5:1:26.5:1:0.08:0:25:4:0.0833:0:1 -2 131947395 . A AT 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.29403;SOR=1.83934;LSEQ=CCCACTAATATTGGAAAGTC;RSEQ=TTTTTTTTTACCTTGTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:5:2,3:157,110:0.0184:2,2:19.6:1:24.2:1:0.65209:2.13483:53.6:4:0.0148:0.0037:0.2 0/1:270:9:6,3:159,102:0.0333:2,2:35.7:1:30.6:1:1:1.28:56.1:18:0.0336:0:0.8 -2 131947526 . AT A 85 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.09186;SOR=0.25126;LSEQ=GAAAAGAGAAACAGCAAACA;RSEQ=TTTTTTGAAGTCACACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:7:2,5:124,185:0.0222:2,2:27.6:1:30.4:1:0.70675:1.67312:59.9:14:0.0227:0:0.1 0/0:354:2:1,1:150,202:0.0056:2,2:17:1:32:0:1:1.35:59.5:4:0.0057:0:0 -2 131947551 . C A 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.34592;SOR=0.29329;LSEQ=TTTGAAGTCACACCTCACCC;RSEQ=CACACACACACCTTTAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:2,1:79,151:0.0129:2,2:27:1:31:1:0.27763:3.80:60:6:0.0131:0:1 0/0:263:1:1,0:94,167:0.0038:2,0:44:0:29:0:0.3626:0:60:2:0.0039:0:6 -2 131947586 . C T 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGTCATGTAAGATTACTTA;RSEQ=AGTGCAAATAATTTGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:23,107:0:2,0:24.8:1:32.2:1:1:0:59.6:129:1:0:0.1 0/1:104:18:4,14:9,76:0.1731:2,2:24.2:1:27.3:1:0.23525:2.39:57.4:36:0.1765:0:1.4 -2 131947812 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51613;SOR=0;LSEQ=GGCACAAAGCTTAGGGAAAT;RSEQ=TGAGGAGAGACATAGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:16,2:0.1:2,0:8.5:1:31:1:1:0:34:4:0.1:0:3 0/0:12:0:0,0:7,5:0:2,0:15.8:1:31.3:1:1:0:59:24:1:0:0 -2 131947825 . T C 86 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07824;SOR=0;LSEQ=GGGAAATCTGAGGAGAGACA;RSEQ=AGAGAAAAACAAACATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:5,1:22,2:0.2:2,2:13.7:1:33.3:1:0.50148:2.13203:42.7:12:0.2:0:2.8 0/0:16:0:0,0:12,4:0:2,0:20.1:1:30.1:1:1:0:60:32:1:0:0 -2 131947893 . C G 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01074;SOR=0;LSEQ=TACCAGTAACCAGATATCTA;RSEQ=TCTATTTCTGTACTTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:8:6,2:76,4:0.0909:2,2:22.1:1:30:1:0.09062:6.09674:43.5:16:0.0952:0:2.9 0/0:66:0:0,0:59,7:0:2,0:24:1:31.2:1:1:0:60:132:1:0:0.1 -2 131947913 . G C 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14915;SOR=0;LSEQ=CTCTATTTCTGTACTTCATT;RSEQ=AACAAACTAAGATTTACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:4:3,1:111,6:0.0331:2,2:11.8:1:31.3:1:0.21453:5.97811:40:8:0.0339:0:3 0/0:82:0:0,0:74,7:0:2,0:25.8:1:31.9:1:1:0:59.7:162:0.9878:0:0.1 -2 131947920 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51432;SOR=0;LSEQ=TCTGTACTTCATTGAACAAA;RSEQ=TAAGATTTACAAGACCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:121,7:0.0154:2,2:15:1:32:1:0.11974:16.23671:46:4:0.0157:0:3 0/0:90:0:0,0:82,8:0:2,0:26:1:31.3:1:1:0:59.7:180:1:0:0.1 -2 131947925 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16934;SOR=Inf;LSEQ=ACTTCATTGAACAAACTAAG;RSEQ=TTTACAAGACCCTACATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:128,9:0:2,0:23.9:1:30.2:1:1:0:59.6:136:1:0:0.1 0/1:97:2:1,1:86,9:0.0206:2,2:8:1:30:1:0.19652:9.11775:60:4:0.0217:0:1 -2 131948173 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16342;SOR=Inf;LSEQ=AAGATAAGGCATTCAAAATA;RSEQ=TTTAATCATCAAATAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:23,130:0:2,0:24.6:1:32.8:1:1:0:59.4:306:0.9935:0:0.1 0/1:105:2:0,2:11,92:0.019:2,0:16:1:27:0:1:0:60:4:0.0192:0:1.5 -2 131948232 . G A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00874;SOR=Inf;LSEQ=AAACAGTAAGATATTTATTT;RSEQ=TAGGAGAGCATACACAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:25,51:0:2,0:24.9:1:32.3:1:1:0:60:152:1:0:0 0/1:35:4:3,1:9,22:0.1143:2,2:11:1:29.5:1:0.10609:6.88:60:8:0.1176:0:1.8 -2 131948248 . A T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0804;SOR=Inf;LSEQ=ATTTGTAGGAGAGCATACAC;RSEQ=ATTTCTGGTTACCTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:29,42:0:2,0:25.1:1:30.5:1:1:0:60:142:1:0:0 0/1:29:2:2,0:11,16:0.069:2,0:33:1:32:1:0.19212:0:60:4:0.069:0:2 -2 131948593 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21935;SOR=Inf;LSEQ=TCAATGCCCAGAAGACAGAT;RSEQ=CCTAGAGAGATGAAACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:44,145:0:2,0:22.2:1:30.6:1:1:0:35.6:30.5:1:0:0.1 0/1:167:2:1,1:40,125:0.012:2,2:17:1:27.5:1:0.43186:3.10:45.5:4:0.0123:0:1 -2 131948695 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17582;SOR=Inf;LSEQ=TATACACAGACACTCATACC;RSEQ=ATATACAAGGCACGTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:7,38:0:2,0:21.1:1:32.1:1:1:0:36.4:90:1:0:0 0/1:33:2:0,2:5,26:0.0606:2,0:48:1:26.5:1:1:0:46:4:0.0606:0:1 -2 131948847 . C G 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01305;SOR=Inf;LSEQ=AAATACTCTGAAAGAAACAG;RSEQ=CTTCATTATTTCAAACAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:33,11:0:2,0:26:1:31.3:1:1:0:54.2:21:1:0:0.3 0/1:24:4:3,1:17,3:0.1667:2,2:19.8:1:30.8:1:0.54404:1.83231:39.3:8:0.1667:0:1 -2 131949169 . G A 279 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00131;LSEQ=TGTTCACTGACCGGACCCAC;RSEQ=GGTGGGCTATAGGTTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:603:602:292,310:0,0:0.9983:0,2:28.2:1:30.3:1:1:0:52.8:74.25:1:0:1.1 0/1:670:299:133,166:171,199:0.4463:2,2:27.5:1:29.9:1:0.69631:1.07238:51.7:73.75:0.4456:0:1.1 -2 131949242 . C A 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCAAGGGCACAAAGGAAG;RSEQ=CAGTCATGTTGATCCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:25:11,14:130,182:0.0742:2,2:23.2:1:29.1:1:0.83573:1.10:51.3:24:0.0732:0:1.4 0/0:283:0:0,0:106,177:0:2,0:23.5:1:31.1:1:1:0:52.1:46.167:1:0:0.3 -2 131949318 . T C 78 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22148;SOR=0.2224;LSEQ=TCCTCCACTCACATGGGACA;RSEQ=TCGCCTCTTAACAATGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:5:5,0:198,195:0.0126:2,0:18.2:1:33.6:1:0.06118:0:35:10:0.0127:0:1 0/0:355:1:1,0:194,160:0.0028:2,0:4:0:30:0:1:0:40:2:0.0029:0:1 -2 131949409 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23235;SOR=0;LSEQ=TAAACCTAAATTAGTTGAGA;RSEQ=TTGACAAATTACTCGTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:44,149:0.0103:2,2:13.5:1:30.5:1:0.4092:3.36:24:4:0.0104:0:1 0/0:209:0:0,0:65,144:0:2,0:26.1:1:30.9:1:1:0:50.2:40.8:1:0:0.1 -2 131949439 . G T 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.76794;SOR=0.80979;LSEQ=TACTCGTTATCCAACATTTC;RSEQ=TCCGTGACAAAAGTACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:6:0,6:11,123:0.0429:2,0:9:1:29:1:1:0:39:12:0.0438:0:1 0/1:143:5:1,4:18,120:0.035:2,2:7.8:1:29.4:1:0.51508:1.66:48.4:10:0.036:0:1.2 -2 131950765 . C CAA 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGACAAAAGGCAACTTTA;RSEQ=AAACTTACCTGGCCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:276,126:0:2,0:22.9:1:31.8:1:1:0:57.1:99.5:0.9975:0:0.4 0/1:355:21:14,7:222,112:0.0592:2,2:25:1:30:1:1:1.01:59.5:42:0.06:0.0113:0.2 -2 131950767 . A G 221 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACAAAAGGCAACTTTACA;RSEQ=ACTTACCTGGCCATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:131:89,42:194,89:0.3164:2,2:24.9:1:31.5:1:0.90992:1.02861:51.3:64.5:0.3162:0:1 0/0:367:0:0,0:241,126:0:2,0:23:1:29.6:1:1:0:59.9:121.333:1:0:0.1 -2 131950965 . G A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATTAAGTACTCAGATATT;RSEQ=TACTTGCGATATGCACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:77,99:0:2,0:23.4:1:32.4:1:1:0:59.2:87:1:0:0.1 0/1:126:14:7,7:61,51:0.1111:2,2:26.4:1:28.5:1:0.78289:1.19437:40:13:0.1057:0:1.9 -2 131950973 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTCAGATATTGTACTTGC;RSEQ=ATATGCACATATCTTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:89,87:0:2,0:22.9:1:30.8:1:1:0:59.4:57.667:1:0:0.1 0/1:130:15:8,7:71,44:0.1154:2,2:25:1:29.4:1:0.58059:1.40806:44:30:0.1154:0:1.8 -2 131951015 . T C 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=ACTTCAAAAGCTATTCCTCA;RSEQ=CACACATATGTAACAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:161,72:0:2,0:24.1:1:30.6:1:1:0:59.6:115.5:1:0:0.1 0/1:226:12:11,1:163,51:0.0531:2,2:25.8:1:32.7:1:0.30463:3.43:60:24:0.0541:0:1 -2 131951231 . T A 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGCCAATGGAGAACCTGA;RSEQ=AAGCCCCACCCAAAAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:67,192:0:2,0:24.8:1:28.5:1:1:0:58.7:42.167:1:0:0.2 0/1:297:70:25,45:59,168:0.2357:2,2:24.2:1:29.2:1:0.12966:1.58:57.9:34:0.2345:0:1.4 -2 131951299 . C T 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTGATAAAGCCAAAAACTT;RSEQ=GTTCACTAACCTCACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:7,82:0:2,0:24.2:1:30.5:1:1:0:58.6:88:1:0:0 0/1:94:19:4,15:9,66:0.2021:2,2:22.8:1:30.2:1:0.29049:1.94:58.1:38:0.2021:0:1.7 -2 131951587 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23055;SOR=Inf;LSEQ=AATTTCCCCTGTAAACTTAC;RSEQ=GAATAGTAACCTTAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:57,2:0:1,0:26.2:1:30.7:1:1:0:60:118:1:0:0 0/1:55:2:1,1:48,5:0.0364:2,2:26:1:28:1:0.20808:8.85505:60:4:0.0364:0:1 -2 131951631 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=TCACAATCAGATGCCATGTG;RSEQ=TTCAGGCAGGTTGAGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:115,31:0:2,0:22.9:1:31.8:1:1:0:59.7:47.667:0.9931:0:0.1 0/1:123:2:1,1:94,27:0.0163:2,2:9.5:1:27.5:1:0.4049:3.43677:60:4:0.0167:0:2 -2 131951634 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20161;SOR=Inf;LSEQ=CAATCAGATGCCATGTGCTT;RSEQ=AGGCAGGTTGAGTAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:118,36:0:2,0:23.2:1:31.1:1:1:0:59.6:76:1:0:0.1 0/1:126:2:1,1:94,30:0.0159:2,2:12.5:1:26:1:0.43302:3.09901:60:4:0.0161:0:2 -2 131951647 . T TA 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=TGTGCTTCAGGCAGGTTGAG;RSEQ=AAAAAAACCACTATTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:134,53:0.0106:2,2:16:1:27:1:0.49088:2.51412:60:4:0.0109:0:0 0/0:176:0:0,0:125,51:0:2,0:22.8:1:28.2:1:1:0:60:34.2:1:0:0.2 -2 131951717 . G A 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAACTCCATGAATGTGTTA;RSEQ=AGTTGGGCAAGAGGTTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:238,193:0:2,0:27.2:1:31.9:1:1:0:59.5:142.667:0.9977:0:0.1 0/1:421:23:12,11:225,172:0.0546:2,2:28.7:1:29.7:1:0.67239:1.1986:59.5:46:0.0554:0:1.1 -2 131951961 . G A 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTATATTTGCAACTTGGGTA;RSEQ=TTTCATGTAAAAAACCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:88,247:0:2,0:22.9:1:31.5:1:1:0:60:36.222:1:0:0.2 0/1:329:69:23,46:72,187:0.2097:2,2:24.5:1:28.8:1:0.37342:1.30:60:16.25:0.205:0:1.2 -2 131951969 . TA T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.24889;SOR=0;LSEQ=GCAACTTGGGTAGTTTCATG;RSEQ=AAAAACCCAATGACGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:1,2:60,218:0.0107:2,2:24:1:28.3:1:0.52153:1.81:60:6:0.0108:0:0 0/0:271:0:0,0:73,198:0:2,0:24:1:29:1:1:0:60:89.333:1:0:0.4 -2 131952108 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18617;SOR=Inf;LSEQ=CAAACCCCAAAATATCTTGT;RSEQ=CAAATGAGAAATGAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:5,22:0:2,0:25.8:1:32.1:1:1:0:59.2:54:1:0:0 0/1:21:2:1,1:3,16:0.0952:2,2:12.5:1:27.5:1:0.35238:4.76:60:4:0.0952:0:1 -2 131953219 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22956;SOR=Inf;LSEQ=AGTTCATTCAGAAAACAAAT;RSEQ=GAGCACACGAGATGATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:107,24:0:2,0:23.2:1:28.8:1:1:0:42.7:262:1:0:0 0/1:121:2:1,1:99,20:0.0165:2,2:18.5:1:28.5:1:0.31818:4.85513:31:4:0.0165:0:2 -2 131953240 . G A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GAGCACACGAGATGATACAG;RSEQ=AAAATTACAAAAGAAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:143,45:0:2,0:24.4:1:31.1:1:1:0:48.8:187:1:0:0.1 0/1:175:16:12,4:109,50:0.0914:2,2:27.6:1:28.8:1:0.77861:1.37:45.9:32:0.092:0:1.3 -2 131953248 . C T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3643;SOR=0.31903;LSEQ=GAGATGATACAGGAAAATTA;RSEQ=AAAAGAAGCTGACCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:1,2:141,48:0.0156:2,2:25.7:1:27.7:1:0.16667:5.80904:47.7:6:0.0159:0:1 0/0:199:1:0,1:132,66:0.005:2,0:1:0:22:0:0.33668:0:60:2:0.005:0:1 -2 131953329 . C T 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGTGACACTTCAAGACCCA;RSEQ=GGACATTTGACTGGTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:158,171:0:2,0:26.9:1:30.8:1:1:0:60:328:1:0:0.1 0/1:351:78:44,34:126,147:0.2222:2,2:24.4:1:29.7:1:0.12382:1.51:54.6:77:0.2225:0:1.4 -2 131953403 . T C 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGGAGAAAGTGACAGGAA;RSEQ=TTCTATCTGCCTGCTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:85,184:0:2,0:24.6:1:30.1:1:1:0:59.9:52.8:0.9962:0:0.1 0/1:255:77:29,48:63,115:0.302:2,2:24.1:1:31:1:0.77696:1.10:54.3:76:0.3016:0:1.5 -2 131953444 . C A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.71915;LSEQ=AAAGAAAGAAATAAGCTTTA;RSEQ=TGATGCACTGACAACCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:1,0:23,95:0.0084:2,0:1:0:25:0:0.20168:0:60:2:0.0086:0:1 0/1:139:2:1,1:39,98:0.0144:2,2:12.5:1:29:1:0.49421:2.49:60:4:0.0144:0:1.5 -2 131954747 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCAACAGTGTGGTTTTA;RSEQ=GGCCAAAGTTTCAGAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:33:1:32.5:1:0.33333:0:60:4:0.3333:0:1 0/0:2:0:0,0:2,0:0:0,0:27:1:28.5:1:1:0:60:4:1:0:0 -2 131954927 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24731;SOR=0;LSEQ=TATTCTCCCATTTTTTAAAG;RSEQ=TGTCATTTTGCTTACCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:113,24:0.0144:2,2:10.5:1:30.5:1:0.32843:4.6336:60:4:0.0146:0:1 0/0:140:0:0,0:106,33:0:2,0:23.6:1:28.4:1:1:0:59.2:33.75:1:0:0.1 -2 131955091 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49883;SOR=0;LSEQ=AGTAACATAAAGTTCATTGT;RSEQ=ACTAGCATCAATAATAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:41,145:0.0106:2,2:33:1:31:1:0.39783:3.51:60:4:0.0106:0:1 0/0:182:0:0,0:49,132:0:2,0:23.2:1:28.5:1:1:0:59.9:180:0.9945:0:0.1 -2 131955247 . G C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05242;SOR=Inf;LSEQ=AAATGTTAAGAAATGGTAAG;RSEQ=GCAATTAAGAATCTGATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:24.5:1:31:1:1:0:51.5:19:1:0:0.1 0/1:13:3:0,3:5,5:0.2308:2,0:36.3:1:30.7:1:0.23077:0:60:6:0.2308:0:1 -2 131955336 . G A 94 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03937;SOR=0.12751;LSEQ=TTTCAGTTATGATCAGAAAG;RSEQ=ATCAGTAAGTGCTCTTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:9:9,0:40,4:0.1698:2,0:29.9:1:29.7:1:1:0:55.7:18:0.1698:0:1 0/1:40:1:1,0:39,0:0.025:1,0:38:0:30:0:1:0:60:2:0.025:0:1 -2 131955431 . T TA 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25191;SOR=0;LSEQ=GGTAATTTTGAGACATTTCA;RSEQ=AAAAAAACACTTACACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:2,1:187,90:0.0107:2,2:17.7:1:28.3:1:1:1.03873:60:6:0.0109:0:0 0/0:245:0:0,0:147,98:0:2,0:23.8:1:28.4:1:1:0:59.3:60.25:1:0:0.1 -2 132181483 . G T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29617;SOR=0.85018;LSEQ=GAAGTGGGAGTAGATAATTT;RSEQ=GTCACTGGGTTCAGGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:115:62,53:257,248:0.1849:2,2:24.6:1:30.2:1:0.60564:1.13:58.8:230:0.1879:0:1.1 0/1:631:102:51,51:246,280:0.1616:2,2:23.8:1:29.9:1:0.58858:1.14:57.7:204:0.1637:0:1.1 -2 132181860 . C G 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAATGACACTTTGTAAGT;RSEQ=AAAGGGGTATTCGACGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:831:0:0,0:420,409:0:2,0:23.9:1:31.3:1:1:0:59.8:45.056:0.9975:0:0.2 0/1:695:51:26,25:311,330:0.0734:2,2:22.8:1:30.5:1:0.77227:1.10:59.4:102:0.074:0:1.1 -2 132181872 . C T 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.87476;SOR=1.03097;LSEQ=TTGTAAGTCAAAGGGGTATT;RSEQ=GACGATCCCTGTGGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:817:98:58,40:364,353:0.12:2,2:25.3:1:30.3:1:0.13159:1.41:59.3:196:0.1214:0:1.1 0/1:698:86:39,47:298,312:0.1232:2,2:22.1:1:29.8:1:0.56608:1.15082:59.8:42:0.1224:0:1.1 -2 132182138 . G T 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.6053;SOR=1.10298;LSEQ=ACTTGTATGTGCTCATACTT;RSEQ=TATGGGATCTTGAGTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:87:51,36:280,258:0.139:2,2:26.4:1:29.7:1:0.29757:1.30:53:86:0.1389:0:2.5 0/1:483:73:37,36:203,207:0.1511:2,2:27.7:1:29.6:1:0.89923:1.05:53.4:23.333:0.1471:0:2.4 -2 132182159 . T C 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50873;SOR=1.12134;LSEQ=TATGGGATCTTGAGTGAGTC;RSEQ=ATGGCTCTGATCATGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:636:90:48,42:285,261:0.1415:2,2:27.2:1:31.3:1:0.90943:1.05:49.5:89:0.141:0:2.6 0/1:532:83:43,40:236,213:0.156:2,2:27.1:1:30.9:1:0.90541:1.03063:49.6:82:0.1553:0:2.5 -2 132182199 . C T 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.93356;SOR=0.97559;LSEQ=GCATGGCCGTGAAGATGTTC;RSEQ=GATACACCAGCTTGGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:721:90:47,43:317,314:0.1248:2,2:23.2:1:30.5:1:0.73674:1.08:42.4:89:0.1257:0:2.1 0/1:614:75:38,37:273,266:0.1221:2,2:25.7:1:29.9:1:1:1.00:42.4:74:0.1225:0:2.2 -2 132182448 . G A 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03741;SOR=0.55345;LSEQ=ACTCCAGAGTCATTCTTCCA;RSEQ=AGTGCCTCCGCTGCAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:666:42:5,37:193,431:0.0631:2,2:18.5:1:30.1:1:0.00826:3.30911:38.7:41:0.0627:0:1.4 0/1:585:21:3,18:212,352:0.0359:2,2:23.1:1:28.8:1:0.03628:3.60738:37.5:9.5:0.033:0:1.4 -2 132182489 . T G 143 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59985;SOR=0.81388;LSEQ=GCCGGCACCCCCTGCTCACA;RSEQ=CGCGCACACACGCCTTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:22:2,20:26,258:0.0717:2,2:29.9:1:32.2:1:1:1.00773:47.5:44:0.0738:0:2.1 0/1:220:13:1,12:30,177:0.0591:2,1:20.8:1:31.5:1:0.69915:2.02868:45.2:26:0.0594:0:2.1 -2 132182552 . G A 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55862;SOR=1.44848;LSEQ=GTGGCTGCCGAGCCCCCGCC;RSEQ=CCTGGGCGCGCGTCCGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:11:0,11:0,56:0.1642:1,0:20.6:1:27.4:1:1:0:57.6:4.5:0.1385:0:2.5 0/1:27:6:0,6:0,21:0.2222:1,0:21.5:1:31.2:1:1:0:60:12:0.2308:0:2.2 -2 132182587 . G A 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.58108;LSEQ=CGGGACGAGCTCCGGGAACC;RSEQ=CCGCGGGGGCGGCGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:10:1:26.7:1:1:0:54.3:2:0.2857:0:3.3 1/0:2:1:0,1:0,1:0.5:0,0:1:0:31:0:1:0:60:2:0.5:0:3 -2 132182592 . G C 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGCTCCGGGAACCGCCGC;RSEQ=GGGGCGGCGGCCAGGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:5:1:28.3:1:1:0:54.3:6:0.6:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 132184299 . G GAA 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGAGAAGGAAGAGGAGGA;RSEQ=AAAGAAGAGGAAGAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:28.3:1:1:0:60:4:1:0:0 -2 133317889 . C G 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3066;LSEQ=CTTTCCCACCTCTTTTTCCT;RSEQ=AACCATAAACCTGTTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:738:359:170,189:194,184:0.4864:2,2:26.7:1:31.5:1:0.30235:1.17193:60:50.286:0.4869:0:1.1 0/1:747:168:77,91:300,277:0.2249:2,2:25.2:1:31.1:1:0.16207:1.27951:60:167:0.2248:0:1.2 -2 133317891 . A T 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCCCACCTCTTTTTCCTCA;RSEQ=CCATAAACCTGTTTGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:737:0:0,0:358,379:0:2,0:26.7:1:29.6:1:1:0:60:66:1:0:0.6 0/1:740:32:13,19:360,347:0.0432:2,2:28:1:29.5:1:0.28175:1.51544:60:64:0.0439:0:1.1 -2 133317983 . C T 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=7e-05;SOR=Inf;LSEQ=CTTCCACTGCTCTCCAGTCT;RSEQ=TCCCCATCCTCACACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:34,211:0:2,0:24.7:1:31.5:1:1:0:60:34:1:0:0.2 0/1:233:13:2,11:43,177:0.0558:2,2:18.5:1:30.1:1:1:1.33462:60:26:0.0565:0:1 -2 133919324 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50016;SOR=0;LSEQ=AAACTCTCAACTGAGATTCA;RSEQ=GTTTCAAAGTAATGGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:88,23:0.0177:2,2:38.5:1:29:1:0.38116:3.76677:60:4:0.0182:0:1 0/0:98:0:0,0:67,31:0:2,0:25.9:1:30.4:1:1:0:60:97:1:0:0.1 -2 133919333 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20861;SOR=Inf;LSEQ=ACTGAGATTCACGTTTCAAA;RSEQ=TAATGGCATCCTGAAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:104,31:0:2,0:24.4:1:32.1:1:1:0:60:44:1:0:0.2 0/1:114:2:1,1:74,38:0.0175:2,2:5.5:1:30.5:1:1:1.93525:60:4:0.0177:0:1 -2 133919370 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21162;SOR=Inf;LSEQ=GCTCAGGCCTGTCCAAGGAA;RSEQ=GTTTATTTTATTCTTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:159,74:0:2,0:24.4:1:31.5:1:1:0:60:57.25:1:0:0.5 0/1:199:2:0,2:124,73:0.0101:2,0:7.5:1:27.5:1:0.14086:0:60:4:0.0102:0:1 -2 133919427 . C A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.36599;LSEQ=TATATAGGGCCCAGAACTGT;RSEQ=CACAAAGACATCTTCTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:332:180:87,93:77,75:0.5422:2,2:25.2:1:29:1:0.74113:1.09716:60:360:0.5505:0:1.1 0/1:298:90:44,46:106,102:0.302:2,2:26.3:1:28.6:1:0.8011:1.08615:60:180:0.3051:0:1.1 -2 133919631 . G A 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01806;SOR=0;LSEQ=ATTTGCACTTACTCATTCTT;RSEQ=GCCTTTTCTGTGCCCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:0.6154:0,0:27:1:30:1:1:0:60:7:0.5833:0:1.5 0/0:6:0:0,0:1,5:0:2,0:30.5:1:28.7:1:1:0:60:12:1:0:0.5 -2 133919662 . A G 53 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.79151;LSEQ=TGCCCTCTTGTATAGTTCAT;RSEQ=TATAGAACCTATAATTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:19:1:33.7:1:1:0:60:6:0.3:0:1 0/1:4:1:0,1:0,3:0.25:0,0:42:0:31:0:1:0:60:2:0.25:0:1 -2 134775183 . A T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10948;SOR=0.46159;LSEQ=TTAACCACTTTTTGAAGTTG;RSEQ=AAAGGGATTGTATACAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:22:21,1:17,0:0.5641:1,1:23.1:1:30:1:1:0:59.8:44:0.5641:0:1.1 0/1:35:13:13,0:21,1:0.3714:1,1:26.5:1:29.6:1:1:0:60:26:0.4063:0:1.1 -2 134775262 . CA C 186 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.31263;SOR=1.28483;LSEQ=CTACAAATGACTTTTTAAAC;RSEQ=AAAAAAAAAAAACAGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:73:56,17:53,12:0.4563:2,2:27.8:1:30.5:1:0.53506:1.33793:59.9:35.5:0.4581:0.0625:0.5 1/0:158:82:58,24:34,19:0.519:2,2:26.3:1:29.3:1:0.45344:1.35:60:81:0.5226:0.1013:0.7 -2 134775344 . T C 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00053;SOR=2.05507;LSEQ=CTGTGGCTTGTGTTCTCTTA;RSEQ=TAACAGATCAAAATCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:41:20,21:153,172:0.112:2,2:31.8:1:32.4:1:0.86929:1.07:60:82:0.1133:0:1 0/1:398:82:42,40:154,162:0.206:2,2:29.6:1:31.1:1:0.71137:1.10:59.9:40:0.2041:0:1.2 -2 134775446 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49775;SOR=0;LSEQ=TTAGTTTTATGTAAAAAAAG;RSEQ=CCTCACATTTTTCACGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:9,81:0.0217:2,2:22.5:1:29.5:1:0.20664:8.59:60:4:0.022:0:1 0/0:86:0:0,0:8,78:0:2,0:21.1:1:28.6:1:1:0:60:42:1:0:0.1 -2 134775529 . G A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36341;SOR=3.4542;LSEQ=ACTTTATAGCTTTATCAATG;RSEQ=AAGCTTCATATTCAAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:18:1,17:0,4:0.8182:0,1:22.5:1:31.1:1:1:0:60:36:0.8182:0:1 1/1:17:16:0,16:0,1:0.9412:0,1:20.8:1:30.3:1:1:0:60:15:0.9375:0:1 -2 134776262 . T C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCAAGAGAATTGCTTGAACC;RSEQ=AGGAGAGGGAGGTTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:13:0:27:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:32.5:1:1:0:60:4:1:0:1 -2 135069340 . T A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11851;SOR=0;LSEQ=AAAACTTTGTTTGTAGTAAG;RSEQ=GAATGTTTTATGATGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:2,1:49,5:0.0526:2,2:6:1:27.3:1:0.28828:4.67695:60:6:0.0536:0:2.7 0/0:58:0:0,0:50,7:0:2,0:24:1:29.2:1:1:0:60:114:1:0:0 -2 135069472 . G A 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01436;SOR=1.55294;LSEQ=TAGCCTTGTGTGACACCCAA;RSEQ=GCACCTAGCATCTGATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:276:168:86,82:53,55:0.6087:2,2:28:1:30.7:1:0.80529:1.09:60:167:0.6095:0:1.1 1/0:311:220:108,112:44,47:0.7074:2,2:26:1:30.3:1:1:1.03:60:219:0.7087:0:1.1 -2 135069544 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24479;SOR=Inf;LSEQ=TTAAGATTTTCTCCAGGCCG;RSEQ=GTACAGTGGCTTATGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:51,118:0:2,0:22.2:1:31:1:1:0:60:168:1:0:0.3 0/1:166:2:1,1:51,113:0.012:2,2:15:1:26.5:1:0.52968:2.20:60:4:0.0123:0:1 -2 135343919 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53131;SOR=Inf;LSEQ=TTCCTTCTACAGGCTGCAGA;RSEQ=GAAACTGGCCCCAGCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:0:2,0:24.3:1:31.4:1:1:0:60:32:1:0:0.3 0/1:29:2:1,1:15,12:0.069:2,2:22.5:1:29.5:1:1:1.24034:60:4:0.0714:0:1.5 -2 135343920 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54296;SOR=Inf;LSEQ=TCCTTCTACAGGCTGCAGAG;RSEQ=AAACTGGCCCCAGCCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:23.1:1:30:1:1:0:60:16:1:0:0.3 0/1:31:3:1,2:16,12:0.0968:2,2:11:1:28.7:1:0.57642:2.58395:60:6:0.1:0:2.3 -2 135343934 . C G 130 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00076;SOR=9.44872;LSEQ=GCAGAGGAAACTGGCCCCAG;RSEQ=CCTCTCTCTAGCTGCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:9,9:0.1429:2,0:21.7:1:32.3:1:0.22857:0:60:6:0.15:0:1 1/0:37:23:13,10:8,6:0.6216:2,2:26.9:1:28.8:1:1:1.02495:60:4.75:0.5758:0:1.3 -2 135894862 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51475;SOR=Inf;LSEQ=CGTATTCCACACATCTGTAC;RSEQ=ATTCTTGAGTATGATCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:0:2,0:28.9:1:29.6:1:1:0:60:48:1:0:0.1 0/1:37:2:1,1:23,12:0.0541:2,2:34.5:1:30:1:1:1.88115:60:4:0.0556:0:1.5 -2 135894904 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12049;SOR=0;LSEQ=GGGTGTCAAATTGAGAACCA;RSEQ=GCAGATCCACCACCTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:14,18:0.0588:2,2:20.5:1:29:1:1:1.28:60:4:0.0588:0:1 0/0:63:0:0,0:31,32:0:2,0:29:1:30.8:1:1:0:59.4:30.5:1:0:0.4 -2 136869825 . G A 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31091;SOR=0;LSEQ=TGGGAAGCCTGCAGTAGGGG;RSEQ=AGATAAATTTTCAAGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:4:4,0:50,0:0.0741:1,0:28:1:31.8:1:1:0:60:8:0.0769:0:1 0/0:23:0:0,0:23,0:0:1,0:22.4:1:31.2:1:1:0:60:46:1:0:0.1 -2 136869873 . G A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.73356;SOR=0.86826;LSEQ=AAAACAAAGGCTTTGCAAGA;RSEQ=AAAACATCCACTTTCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:25:25,0:94,0:0.2101:1,1:22.1:1:30.1:1:1:0:60:24:0.2051:0:1.2 0/1:96:18:18,0:78,0:0.1875:1,1:21:1:30.6:1:1:0:60:36:0.1895:0:1.1 -2 136872392 . TA T 83 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.22801;SOR=2.48993;LSEQ=TATCTGAAAAATGTGTAACT;RSEQ=AAAAAAAGTTATTTATCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:3:2,1:416,126:0.0055:2,2:19.7:1:28.3:1:0.54959:1.64908:60:6:0.0056:0.0018:0.3 0/1:588:8:4,4:419,161:0.0136:2,2:15.6:1:27.8:1:0.22935:2.5976:60:16:0.0136:0.0085:0.5 -2 136873084 . G A 200 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.71651;LSEQ=TGACTGTTGGTGGCGTGGAC;RSEQ=ATGGCCAGGTAGCGGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1924:3:1,2:935,984:0.0016:2,2:10.7:1:29.3:1:1:1.89979:60:6:0.0016:0:1.3 0/1:2175:118:62,56:999,1052:0.0543:2,2:23.5:1:29.2:1:0.44923:1.17:60:38.333:0.0533:0:1.2 -2 136873549 . A T 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.37991;LSEQ=CATTAACCCAGTTAAAAAAA;RSEQ=TTTTTAAAGCAATTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:759:435:114,321:92,232:0.5731:2,2:23.3:1:30.2:1:0.5102:1.11644:60:71.5:0.5712:0:1.1 0/1:853:288:90,198:186,378:0.3376:2,2:22.5:1:29.7:1:0.64275:1.08247:60:287:0.3376:0:1.1 -2 136874692 . T G 87 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01643;SOR=8.88445;LSEQ=AGCCAAACGGTTTCCCCACT;RSEQ=GCACCTGCCAGTCTTCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:1:0,1:64,360:0.0024:2,0:21:0:14:0:1:0:60:0:0:0:2 0/1:389:8:2,6:61,319:0.0206:2,2:16:1:29.3:1:0.62134:1.74:60:16:0.0207:0:1 -2 136874906 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGCGGCCGTGGGGAAGAGGC;RSEQ=CGCTTCGGACGGCGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:0,11:0.1538:0,2:30.5:1:29:1:0.15385:0:60:4:0.1538:0:1 0/0:3:0:0,0:0,3:0:0,0:18:1:31.3:1:1:0:60:6:1:0:0 -2 136874926 . GT G 101 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTTCGGACGGCGGGAAG;RSEQ=TTTCCCCCTCAAACCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:2,7:0,0:1:0,2:29.8:1:32:1:1:0:60:18:1:0:0.3 1/1:1:1:0,1:0,0:1:0,0:19:0:33:0:1:0:60:2:1:0:0 -2 136875448 . A C 54 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46877;SOR=0.44641;LSEQ=TCCAATCCTGCTCCCCCCCC;RSEQ=CCCACCCGCACTATATAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:6,0:19,3:0.2143:2,0:5:1:21:1:1:0:60:2:0.1905:0:1.3 0/1:28:3:3,0:24,1:0.1071:1,0:5:1:25.3:1:1:0:60:6:0.1154:0:1.3 -2 136875497 . CT C 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.01509;SOR=Inf;LSEQ=GAAAACTCCTTTCGGTGACC;RSEQ=TTTTTGGAGTACGGGTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:253,34:0:2,0:23.4:1:31.4:1:1:0:60:56.4:0.993:0:0.1 0/1:294:7:6,1:250,37:0.0238:2,2:17.4:1:32.1:1:1:1.12562:60:14:0.024:0.0068:0.3 -2 138749676 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTGGAAGATCCCACTCG;RSEQ=GAACCCACACCACCAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:31:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:33:1:30.5:1:1:0:60:4:1:0:1 -2 138750570 . A C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=CAGAAAGCAACAACAACAGC;RSEQ=TCAACAACAAGAACAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:29.1:1:31.1:1:1:0:60:16:1:0:0 0/1:14:2:1,1:6,6:0.1429:2,2:5:0:32.5:1:1:1:60:4:0.1538:0:0 -2 138750684 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51772;SOR=0;LSEQ=AAAGAATCAATGAAACAATG;RSEQ=TGAAAACCCAAAAGGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:17,19:0.0526:2,2:19:1:31.5:1:1:1.11:60:4:0.0526:0:1 0/0:24:0:0,0:11,13:0:2,0:24.3:1:32.2:1:1:0:60:48:1:0:0.3 -2 138750696 . A T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15239;SOR=Inf;LSEQ=AAACAATGCTGAAAACCCAA;RSEQ=AGGTCAGAGTGCCTTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:15,17:0:2,0:22.4:1:29.9:1:1:0:60:64:1:0:0.1 0/1:21:2:1,1:7,12:0.0952:2,2:9:0:29.5:1:1:1.67:60:4:0.0952:0:1.5 -2 139259201 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49621;SOR=Inf;LSEQ=CCGGCTGCGGAACCTGCCCC;RSEQ=CCGGGAGCCTAGTGCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:33.9:1:30:1:1:0:60:13:1:0:1 0/1:19:2:1,1:8,9:0.1053:2,2:12.5:1:27.5:1:1:1.12:60:4:0.1111:0:1.5 -2 139259220 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4949;SOR=Inf;LSEQ=CGCCGGGAGCCTAGTGCCAT;RSEQ=CAGCAGCGGCGGCGGTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:0:2,0:25.1:1:31.8:1:1:0:60:22:1:0:1 0/1:28:2:1,1:12,14:0.0714:2,2:27:0:31:1:1:1.16:60:4:0.0714:0:2.5 -2 139259222 . A G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.3908;LSEQ=CCGGGAGCCTAGTGCCATGC;RSEQ=GCAGCGGCGGCGGTGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:20:7,13:1,1:0.9091:2,2:25.9:1:30.7:1:1:1.80284:60:40:0.9091:0:1.2 1/1:30:28:13,15:1,1:0.9333:2,2:21.1:1:29.7:1:1:1.14834:60:56:0.9333:0:1.5 -2 139308127 . G A 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0094;SOR=0;LSEQ=CGAGAGGAAATGGGTGAAGT;RSEQ=TTAAAAAGTTCAACATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:5,4:4,4:0.5294:2,2:22.9:1:29.4:1:1:1.23:60:18:0.5294:0:1 0/0:9:0:0,0:5,4:0:2,0:29.6:1:31.8:1:1:0:60:18:1:0:0 -2 139316829 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49491;SOR=Inf;LSEQ=AATGCATTTATGCATAAAAT;RSEQ=ATGATACATAATCTTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:17.2:1:29.4:1:1:0:60:42:1:0:0.2 0/1:26:2:1,1:17,7:0.0769:2,2:13.5:1:29.5:1:0.52923:2.3376:60:4:0.0833:0:1 -2 139316917 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17421;SOR=0;LSEQ=AAAGCAAAAAGGTAAACATG;RSEQ=CTTAAAGGCTAATATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:0.0909:2,2:36.5:1:31:1:1:1.21:60:4:0.0909:0:1 0/0:30:0:0,0:9,21:0:2,0:23.7:1:31.3:1:1:0:60:60:1:0:0.2 -2 139316934 . G T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13892;SOR=Inf;LSEQ=ATGGCTTAAAGGCTAATATT;RSEQ=AATTTATATAAACGTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:0:2,0:20.3:1:31.7:1:1:0:60:24:1:0:0.6 0/1:19:4:1,3:3,12:0.2105:2,2:38:1:29.3:1:1:1.31:60:8:0.2105:0:1 -2 139318426 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11429;SOR=Inf;LSEQ=AAGTTTTTAAAGAAATGATG;RSEQ=GATTCATTTACACAGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:29,17:0:2,0:29.2:1:30.2:1:1:0:60:92:1:0:0.2 0/1:24:2:1,1:13,9:0.0833:2,2:40.5:1:31:1:1:1.42202:60:4:0.0833:0:1 -2 139690082 . C CA 85 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.29226;SOR=2.91172;LSEQ=CAGAGACACGAAAAAGCCTC;RSEQ=AAAAAAAAAAATTAATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:20,22:0.0455:2,2:39:1:30.5:1:1:1.10:60:4:0.0455:0:2 0/1:57:7:4,3:23,26:0.1228:2,2:37.7:1:30.4:1:0.70045:1.50:60:14:0.125:0:0.1 -2 141599025 . C G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19928;SOR=0;LSEQ=ATAGCACATCTTTCTAGTTA;RSEQ=GAGAAAGTACTTGTGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:25.3:1:32.2:1:1:0:60:12:1:0:1.1 1/1:11:9:9,0:2,0:0.8182:0,0:18.9:1:31.1:1:1:0:60:18:0.8182:0:1 -2 141599218 . G A 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=0.51336;LSEQ=TATTTTAACATCCCTTCAAC;RSEQ=TGGATTCTGCAGAAAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:153:69,84:45,42:0.6375:2,2:27.8:1:30.1:1:0.34846:1.30288:60:50:0.6383:0:1.1 0/1:329:156:78,78:83,90:0.4742:2,2:24.9:1:29.1:1:0.74117:1.08:60:38:0.4691:0:1.1 -2 141599395 . G GA 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.4873;SOR=Inf;LSEQ=TAAAAACTGCACCTTTTCAA;RSEQ=AAAAAAAATGAGGTGTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:0:1,0:27.6:1:31.4:1:1:0:60:34:1:0:0 0/1:19:2:1,1:0,17:0.1053:1,2:45:1:30:1:0.10526:0:60:4:0.1111:0:0 -2 141599495 . T TTACTC 73 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCAATTTATAGCATTTGA;RSEQ=TACCTTGATTTTGGTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,1:0.7143:0,0:30:1:31.8:1:1:0:60:10:0.8333:0.1429:0 1/1:1:1:0,1:0,0:1:0,0:16:0:32.2:0:1:0:60:2:1:0:0 -2 141641717 . C T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04792;SOR=Inf;LSEQ=ATTTCAACTTTGAGAGATTG;RSEQ=AAAAGTGCTACCTAGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:28,0:0:1,0:27.2:1:32.7:1:1:0:60:56:1:0:0.1 0/1:17:3:3,0:14,0:0.1765:1,0:36.3:1:30.7:1:1:0:60:6:0.1765:0:1 -2 141641859 . C A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTCTGAGGCTAATAACAA;RSEQ=GTTGAGGTTGCAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:136,91:0:2,0:26.4:1:31:1:1:0:60:74.667:0.9956:0:0.3 0/1:243:34:17,17:116,93:0.1399:2,2:28.1:1:30:1:0.58119:1.24616:60:33:0.1375:0:1.1 -2 141641870 . CA C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.80065;SOR=0.77814;LSEQ=TAATAACAACGTTGAGGTTG;RSEQ=AAAAAAAAGTTATTTCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:9:4,5:154,106:0.0335:2,2:25.6:1:32.9:1:0.49506:1.81186:60:18:0.0335:0.0074:0.4 0/1:267:7:4,3:135,124:0.0262:2,2:25.3:1:31.8:1:1:1.22:60:14:0.0264:0.0037:0.7 -2 141641896 . G T 49 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05335;SOR=0;LSEQ=AAAAGTTATTTCTTGTTCCT;RSEQ=ACTTTTTTATACAGAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:4:2,2:165,136:0.0131:2,2:20:1:24.5:1:1:1.21246:60:3:0.01:0:1.8 0/0:328:0:0,0:166,160:0:2,0:23.1:1:30.9:1:1:0:60:53.333:0.9938:0:0.5 -2 141641929 . C T 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.4498;LSEQ=AGAGCAAAGGATTTTGGAAA;RSEQ=AATAATGATATTCTGGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:295:177:90,87:52,66:0.6:2,2:26.5:1:29.5:1:0.285:1.31:60:87.5:0.5993:0:1.1 0/1:313:126:61,65:85,102:0.4026:2,2:29.5:1:28.6:1:0.64475:1.13:60:125:0.4019:0:1.2 -2 141641945 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24881;SOR=Inf;LSEQ=GAAACAATAATGATATTCTG;RSEQ=TTAAAATCAGTGCAACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:130,164:0:2,0:24.9:1:31.4:1:1:0:60:97:1:0:0.6 0/1:300:3:1,2:139,158:0.01:2,2:12.3:1:29.3:1:1:1.75632:60:6:0.0102:0:1.3 -2 141641999 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.24457;SOR=Inf;LSEQ=CTTCAAGAGTAGAATAAAAT;RSEQ=AAAAGAAAAAGCCCACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:42,119:0:2,0:26.3:1:31.9:1:1:0:60:160:0.9938:0:0.3 0/1:159:2:1,1:50,106:0.0126:2,2:8:0:30.5:1:0.54277:2.11:60:4:0.0128:0:1.5 -2 141642010 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23808;SOR=Inf;LSEQ=GAATAAAATCAAAAGAAAAA;RSEQ=CCCACCAGAGCTAAGATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:28,110:0:2,0:25:1:32:1:1:0:60:68:1:0:0.2 0/1:132:2:1,1:34,96:0.0152:2,2:8.5:1:28:1:0.46149:2.80:60:4:0.0155:0:2 -2 142098069 . A G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=0.3284;LSEQ=TCTTCTATACAATTCTTATA;RSEQ=AAGCAAAAATGCCTTTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:82:66,16:30,7:0.6833:2,2:22.6:1:32.2:1:1:1.03863:60:164:0.6891:0:1.2 0/1:104:43:36,7:45,16:0.4135:2,2:26.3:1:32.3:1:0.3374:1.82:60:86:0.4135:0:1.3 -2 142098098 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24357;SOR=Inf;LSEQ=ATGCCTTTAATAAATGCAGT;RSEQ=ACCCTGATAAAAATAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:122,54:0:2,0:25.8:1:31.9:1:1:0:60:87:1:0:0.7 0/1:172:2:1,1:111,59:0.0116:2,2:23:0:31:1:1:1.87407:60:4:0.0118:0:2 -2 142098153 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10232;SOR=Inf;LSEQ=CCATTACAAATGTTCTAAAA;RSEQ=GTTTCATGTAGTACTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:183,154:0:2,0:25.9:1:31.4:1:1:0:60:66.4:1:0:0.7 0/1:298:3:2,1:157,138:0.0101:2,2:5:1:27.7:1:1:1.75:60:6:0.0102:0:1.3 -2 142098162 . T C 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03409;SOR=0.71044;LSEQ=ATGTTCTAAAAGGTTTCATG;RSEQ=AGTACTTCACTAATTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:358:215:110,105:67,74:0.6006:2,2:25.7:1:32:1:0.51717:1.16:60:214:0.6045:0:1.2 1/0:306:158:79,79:74,74:0.5163:2,2:24.3:1:32.1:1:1:1:60:316:0.518:0:1.2 -2 142098235 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20887;SOR=Inf;LSEQ=ATTATCATAATTTTATTGCT;RSEQ=ACCCACCAAAGAAAAGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:58,141:0:2,0:24:1:31.5:1:1:0:60:98.5:1:0:0.4 0/1:168:2:1,1:53,113:0.0119:2,2:5.5:1:27:1:0.54085:2.12:60:4:0.0121:0:2 -2 142098325 . T C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26565;SOR=0.48267;LSEQ=TTTAAACAGTCAATACCCCT;RSEQ=GAAAAGTAGTCTTCTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:21:0,21:0,8:0.7241:0,1:25:1:30.3:1:1:0:60:42:0.7241:0:1 1/0:27:15:1,14:0,12:0.5556:0,1:26.7:1:30.4:1:1:0:60:30:0.5556:0:1.1 -2 142100281 . A T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACAAAGCCTTCAAGAAAT;RSEQ=TGGGACTATGTGAAAAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:44:0:31:1:1:0:60:4:1:0:2.5 -2 142100310 . A C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAAAAGACCAAACCTAC;RSEQ=TTGGAATGGTGTACCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:33:1:1:0:60:4:1:0:2.5 -2 147565133 . T TAAA 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTATGTTATTACAAAGT;RSEQ=AAAAAAAAAAAAAATTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:28.7:1:1:0:60:4:1:0:1 -2 147565661 . G T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGAGCTCCCTGAGCGGGG;RSEQ=GAAGGGCGGCACCCATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:45.5:1:31.5:1:1:0:60:4:1:0:0.5 0/1:7:2:1,1:3,2:0.2857:2,2:13.5:1:29.5:1:1:1.41418:60:4:0.2857:0:1 -2 147566461 . C G 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=GTGTCAGCAGCCTTGAAGAC;RSEQ=AAAACTAGAGAAACTCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:26.8:1:32:1:1:0:60:10:1:0:0.2 0/1:8:2:0,2:3,3:0.25:2,0:25:1:31.5:1:0.46429:0:60:4:0.25:0:2 -2 147566997 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50361;SOR=0;LSEQ=CTGGAGTACCAGAAGGAGAT;RSEQ=GGGAGAATGGAAACAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:24,30:0.0357:2,2:33:1:30.5:1:1:1.24:60:4:0.0364:0:1 0/0:43:0:0,0:19,24:0:2,0:28.8:1:31.1:1:1:0:59.4:86:1:0:0.2 -2 147568623 . C CA 32 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATACACAAAAAACCCTC;RSEQ=AAAAAAAAAAATCAATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:32:0:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 148075769 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AAAACTGCCAAGGCTTAGAC;RSEQ=TCCTCACTGCTGAGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:0.2222:2,0:25:1:30.5:1:1:0:60:4:0.2222:0:1 0/0:2:0:0,0:1,1:0:2,0:9:0:33:1:1:0:20:4:1:0:0.5 -2 148075953 . T G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05763;SOR=Inf;LSEQ=GGCAACATGGCTTCTCCCCT;RSEQ=TCTAGGTCCTGTGGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:27,27:0:2,0:31.2:1:28.5:1:1:0:56.5:12.5:1:0:0.1 0/1:35:3:2,1:16,16:0.0857:2,2:37.3:1:32.7:1:1:1.96:56.3:6:0.0857:0:1 -2 148076060 . A T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1455;SOR=Inf;LSEQ=TCAAGGCCATCAAGCTACAG;RSEQ=TGATCTTACAAATGGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:4,13:0:2,0:26.2:1:31.2:1:1:0:60:34:1:0:0 0/1:11:2:1,1:3,6:0.1818:2,2:8:0:30.5:1:1:1.87:60:4:0.1818:0:1.5 -2 148468930 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21394;SOR=0;LSEQ=TGCTGCTACTGCTGTTGCTG;RSEQ=TGCAGAGAACTCACTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:24,27:0.0377:2,2:25.5:1:29.5:1:1:1.12:60:4:0.0385:0:1 0/0:61:0:0,0:23,38:0:2,0:25.6:1:31.9:1:1:0:60:60:1:0:0.2 -2 148468933 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49648;SOR=Inf;LSEQ=TGCTACTGCTGTTGCTGCTG;RSEQ=AGAGAACTCACTTGATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:25,28:0:2,0:28.2:1:32.5:1:1:0:60:106:1:0:0.2 0/1:58:2:1,1:20,36:0.0345:2,2:32.5:1:29:1:1:1.78:60:4:0.0345:0:1 -2 148779023 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22967;SOR=0;LSEQ=TTAGCAACACAGACCCTTTG;RSEQ=TGCTGCTGTTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:29,33:0.0313:2,2:30.5:1:30:1:1:1.14:60:4:0.0313:0:1 0/0:69:0:0,0:33,35:0:2,0:29.3:1:31.5:1:1:0:60:136:1:0:0.2 -2 148779032 . TTGC T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.24485;SOR=Inf;LSEQ=CAGACCCTTTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:32,35:0:2,0:31.1:1:30:1:1:0:60:134:1:0:0.2 0/1:70:3:1,2:31,36:0.0429:2,2:40.7:1:31:1:1:1.70942:60:6:0.0429:0:0.3 -2 148779065 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.23997;SOR=Inf;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TACTGCTGCTGCTGCTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:26,37:0:2,0:20.5:1:30.9:1:1:0:60:30.5:1:0:0.2 0/1:61:2:1,1:24,35:0.0328:2,2:29.5:1:29:1:1:1.45:60:4:0.0328:0:1 -2 151649843 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGTGGGTTTCCCTCGAG;RSEQ=GAAGCACACCCCCTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:2:0:31:0:1:0:60:2:1:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:26.5:1:31:1:1:0:60:4:0.6667:0:1 -2 151649991 . A G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CATCAGGTTGGTGACCCTCA;RSEQ=GGTCAGAGGTTCCAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:31.8:1:31.3:1:1:0:60:8:1:0:0.3 1/0:3:2:1,1:1,0:0.6667:0,2:40:0:32:0:1:0:60:4:0.6667:0:1 -2 152156132 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18886;SOR=0;LSEQ=TTTTGCCATATTCTTTAATG;RSEQ=ACTGTACACGTAAGAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:44,6:0.0385:2,2:25:1:27.5:1:0.25339:6.86595:60:4:0.04:0:1 0/0:67:0:0,0:53,14:0:2,0:20.7:1:29.1:1:1:0:60:134:1:0:0.1 -2 152156169 . GT G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=AGATGGGTAATATTGAGTGG;RSEQ=TTTTTGTGATGTAGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:86,33:0:2,0:25.7:1:29.8:1:1:0:60:118:1:0:0.2 0/1:130:2:1,1:86,42:0.0154:2,2:39.5:1:29:1:1:2.03546:60:4:0.0154:0:0 -2 152156204 . C T 22 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.90663;LSEQ=GTCTCTGAAGATATACCAAG;RSEQ=AGCAATTGTTTTCTCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:0,2:115,69:0.0108:2,0:23:1:25:1:0.14443:0:60:4:0.0109:0:1 0/0:205:2:0,2:122,81:0.0098:2,0:1:0:22:0:0.16275:0:60:4:0.0099:0:1.5 -2 152156237 . CTT C 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00094;SOR=0.49946;LSEQ=CTCTGCTGCTCATACAGCCC;RSEQ=TTATGTGGCCACAAACCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:76:47,29:85,84:0.3102:2,2:25.6:1:31.6:1:0.09868:1.60:60:152:0.3154:0.0408:1.1 0/1:262:48:26,22:115,99:0.1832:2,2:27.1:1:31.1:1:1:1.02:60:96:0.186:0.042:1.1 -2 152156258 . A C 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00312;SOR=0.556;LSEQ=TTTTATGTGGCCACAAACCT;RSEQ=ATCTGGCCTCCTGCAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:82:43,39:66,82:0.3565:2,2:27.7:1:31.2:1:0.27236:1.37:60:40:0.3571:0:1.2 0/1:272:64:34,30:103,103:0.2353:2,2:26.1:1:31:1:0.67076:1.13:60:63:0.236:0:1.3 -2 152156338 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50584;SOR=Inf;LSEQ=TCAAAAATTCTGCCCAGTTT;RSEQ=ATTTCTCATGCCACAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:16,72:0:2,0:23.8:1:31.7:1:1:0:60:43:1:0:0.3 0/1:114:2:1,1:28,84:0.0175:2,2:14.5:1:27:1:0.44574:2.97:60:4:0.0179:0:2 -2 152771082 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11712;SOR=0;LSEQ=CACTCTTGCCTTTTGGGTTT;RSEQ=CAGCATTTTTCATTGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:9,2:0.1538:2,2:20:1:30:1:0.42308:3.87298:60:4:0.1538:0:1 0/0:24:0:0,0:15,9:0:2,0:28.4:1:30:1:1:0:60:48:1:0:0.1 -2 152771292 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48617;SOR=0;LSEQ=CGGGGGTTCACTTCAGGCCC;RSEQ=ATTCATCTGATTCACTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:2,9:0.1538:2,2:35.5:1:32.5:1:0.42308:3.87:60:4:0.1538:0:1.5 0/0:10:0:0,0:3,7:0:2,0:27.3:1:29.8:1:1:0:60:20:1:0:0 -2 152772103 . T C 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTGGCTCATGCATATAG;RSEQ=CCCAGCACTTTGGGAGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:0:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 154688399 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTATAGTTCTTGTTCTATA;RSEQ=TCGTGTGACATATTTCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 154688728 . G A 252 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAAAAATGAAGAAGGCATA;RSEQ=TGGAGACTAACAAAGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:309:309:120,189:0,0:1:0,2:27.2:1:30.5:1:1:0:60:76.25:1:0:1.1 1/0:360:259:115,144:41,60:0.7194:2,2:26.9:1:29.6:1:0.55482:1.17:60:85.333:0.7273:0:1.1 -2 158593900 . G A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03489;SOR=Inf;LSEQ=TGTCTCCCCAACACATGGCT;RSEQ=GGTACGACGTCTGCCTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:102,1:0:1,0:26.7:1:32.5:1:1:0:60:102:1:0:0.3 0/1:51:3:3,0:48,0:0.0588:1,0:8.3:1:29.3:1:1:0:60:6:0.06:0:2 -2 158593905 . C T 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.72719;SOR=1.16486;LSEQ=CCCCAACACATGGCTGGGTA;RSEQ=GACGTCTGCCTTGTCAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:33:32,1:81,0:0.2895:1,1:28.5:1:31.2:1:0.28947:0:60:66:0.2895:0:1 0/1:59:19:19,0:40,0:0.322:1,1:21.6:1:31.4:1:1:0:60:38:0.3333:0:1.2 -2 158617379 . A G 250 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTAAGACAATATTATATTAG;RSEQ=TTAGATACCTACCATTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1398:266:163,103:685,445:0.1903:2,2:25.3:1:31.1:1:0.88905:1.03:60:52.2:0.1901:0:1.1 0/0:1334:0:0,0:792,540:0:2,0:24.2:1:29.1:1:1:0:60:110:0.9985:0:0.1 -2 158617791 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACTAAATGTCAGAAACA;RSEQ=TCTAAGGCTATCAGGTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:0,26:0.0714:1,0:13:1:32.5:1:1:0:60:4:0.0741:0:1 0/0:8:0:0,0:0,8:0:0,0:24.4:1:31.4:1:1:0:60:16:1:0:0.1 -2 158622572 . C A 218 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00712;LSEQ=AGACCACTAGCTATGGACAG;RSEQ=ACTATTCGAAGGCAGCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1925:157:72,85:849,918:0.0816:2,2:26:1:30:1:0.61774:1.09175:60:77.5:0.0817:0:1.2 0/0:1582:1:1,0:757,819:6e-04:2,0:1:0:24:0:0.48066:0:60:2:6e-04:0:1 -2 158626980 . C T 323 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04156;LSEQ=AAGATCTTCACGGCAACATT;RSEQ=TCCCCTTGCCAGCTGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1809:1799:830,969:0,0:0.9945:0,2:24.9:1:29.9:1:1:0:60:61.034:0.9944:0:1.1 1/1:1830:1614:767,847:99,108:0.882:2,2:25.3:1:29.8:1:0.94121:1.01227:60:99.875:0.8829:0:1.2 -2 158627188 . A AT 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCACAACCTTTATTTTTT;RSEQ=TTTTTTTTGGCCTATAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:0,2:1,80:0.0238:1,0:21:1:28.5:1:1:0:60:4:0.025:0:0.5 0/0:32:0:0,0:1,31:0:1,0:19.9:1:29.7:1:1:0:60:31:1:0:0.3 -2 158630481 . A G 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00133;SOR=Inf;LSEQ=CAGAATAGAGACCACATCTC;RSEQ=TAAGTTTAATAAGGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:137,1:0:1,0:24.1:1:30.5:1:1:0:60:137:1:0:0.1 0/1:71:6:6,0:65,0:0.0845:1,0:19.7:1:28.8:1:1:0:60:12:0.0845:0:1.2 -2 158634289 . G A 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAAAGGTGCCTTTTTAAA;RSEQ=GAGCACTTTTATGGCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:26.5:1:30.4:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 158635051 . A G 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCAATTAGACACAACT;RSEQ=GAATTTGAAAAAATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:0,42:0,0:1:0,1:30:1:30.9:1:1:0:60:84:1:0:1 1/1:13:13:0,13:0,0:1:0,1:23.5:1:31.3:1:1:0:60:26:1:0:1 -2 158636320 . C T 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAACTACAGGGTTTGTG;RSEQ=GAAATCTCATCCTGCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:25.8:1:28.8:1:1:0:60:10:1:0:2.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 158636341 . A G 72 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATCTCATCCTGCTTCAA;RSEQ=TTTCAGTGATAGGGTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:21.6:1:31.2:1:1:0:60:10:1:0:2.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 158636510 . T C 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTACTAGCAGAATTGTT;RSEQ=CAGAAATTATGAATGACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:20.1:1:31.1:1:1:0:60:28:1:0:1.3 1/1:2:2:2,0:0,0:1:0,0:8.5:1:31.5:1:1:0:60:4:1:0:2 -2 158636910 . G A 333 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30299;LSEQ=TCCCCTTGGCAGCACTCCAC;RSEQ=GCTTGGCCAGGGGACGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2074:1914:929,985:78,78:0.9229:2,2:24.6:1:30.6:1:0.7396:1.06028:60:105.333:0.9258:0:1.1 1/0:1965:1540:789,751:203,217:0.7837:2,2:24.2:1:30.3:1:0.29609:1.12:60:84.556:0.7833:0:1.2 -2 158637132 . A AG 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00017;SOR=0.60589;LSEQ=TCTGCAAAGGAGAGAAAGGA;RSEQ=GGGGAAAAAAAAAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:154:52,102:453,711:0.1156:2,2:29.7:1:28.5:1:0.25151:1.24955:59.9:10:0.1106:0.009:0.7 0/1:1390:102:37,65:536,746:0.0734:2,2:32.8:1:27.9:1:0.29732:1.26202:60:9.2:0.0686:0:1 -2 158637137 . A G 290 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAGGAGAGAAAGGAAGGGG;RSEQ=AAAAAAAAAAAAAGAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1177:772:299,473:73,141:0.6559:2,2:20.8:1:30.3:1:0.23239:1.22:60:21.706:0.6554:0:1.4 0/0:1220:0:0,0:118,171:0:2,0:25.9:1:28:1:1:0:59.9:14.211:0.5556:0:0.7 -2 158637445 . A C 112 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCAGCGTGATTGGCTCT;RSEQ=AGATCCCAATTACTGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:29.2:1:32.6:1:1:0:60:22:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 158655838 . G C 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=CCAAATATTTATTATAAAAA;RSEQ=AGTGTTTTAAGTTTGATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:20:20,0:230,11:0.0766:1,1:26.2:1:33:1:1:0:58.8:40:0.0797:0:1.4 0/0:182:0:0,0:174,8:0:1,0:22.7:1:31.8:1:1:0:59.5:44.5:1:0:0.4 -2 158655883 . C CAA 248 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=0.00565;SOR=0.7018;LSEQ=AGAAGTAGTTTATAGTAAGC;RSEQ=AAAAAAAAAAATCACAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:537:308:246,62:53,12:0.5736:2,2:28.6:1:30.1:1:0.86481:1.11283:59.6:153:0.5763:0:0.6 0/1:482:234:180,54:75,23:0.4855:2,2:29.2:1:29.9:1:1:1.02:59.7:233:0.4895:0:0.5 -2 158739387 . A G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93661;LSEQ=GAAATTTTTTCAAAGAACTC;RSEQ=TAGAGCTTTGACTTGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:11:11,0:18,0:0.3793:1,0:29.1:1:27.7:1:1:0:60:10:0.3571:0:1.2 0/1:11:4:4,0:7,0:0.3636:0,0:24.8:1:28.8:1:1:0:60:8:0.4444:0:1 -2 158739584 . C T 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01567;SOR=0.68329;LSEQ=TTTAAAAGCTAGTCCCATGG;RSEQ=GGGAAGATCAAATTAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:334:196:94,102:65,73:0.5868:2,2:26.9:1:29.9:1:0.91165:1.03:60:195:0.5873:0:1.1 0/1:327:161:81,80:84,82:0.4924:2,2:25.1:1:29.6:1:1:1.01171:60:322:0.4939:0:1.2 -2 158739600 . A G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.86545;SOR=0.93534;LSEQ=ATGGCGGGAAGATCAAATTA;RSEQ=TTTCTTCCTCAAATTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:19:9,10:140,160:0.0596:2,2:26.9:1:32.1:1:1:1.03:60:38:0.0601:0:1.2 0/1:304:17:8,9:140,147:0.0559:2,2:30.5:1:31.5:1:1:1.07122:60:34:0.0567:0:1.2 -2 158739646 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2249;SOR=0;LSEQ=ATTTCAAATATAACTGTGTG;RSEQ=CTCTTGGTAGAACCCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:58,120:0.0111:2,2:5.5:1:29:1:0.54935:2.06:60:4:0.0111:0:1.5 0/0:199:0:0,0:73,125:0:2,0:26.6:1:31.7:1:1:0:60:396:0.995:0:0.4 -2 159559834 . T C 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23852;SOR=2.6266;LSEQ=CCAAACTTAGACGACATCTA;RSEQ=ATTTCCTTGTGTTCATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:3:3,0:41,1:0.0667:1,0:14.7:1:31.7:1:1:0:60:6:0.0667:0:1.3 0/1:25:4:4,0:21,0:0.16:1,0:7.3:1:30.3:1:1:0:60:8:0.16:0:1.3 -2 159560007 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.01109;LSEQ=TACACATGGGTAATTTGCTT;RSEQ=AATTATTTTTTCCCTCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:682:409:233,176:154,118:0.5997:2,2:26:1:29.4:1:0.93719:1.01:60:408:0.6018:0:1.2 1/1:546:447:248,199:49,50:0.8187:2,2:25.6:1:28.9:1:0.31578:1.27:60:88.4:0.8185:0:1.4 -2 159560048 . C A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.41585;LSEQ=TACTGTTTTTGAAATGTTTG;RSEQ=CCTTCCTGGTTATCTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:36:16,20:308,354:0.0514:2,2:22.4:1:29.4:1:0.86485:1.08741:60:17:0.0496:0:2.1 0/1:507:131:60,71:177,198:0.2584:2,2:27.4:1:28.9:1:0.83897:1.05774:60:130:0.26:0:2.2 -2 159560098 . C T 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.87707;SOR=0.97067;LSEQ=TAAGTTTGCTAAATTGGGGT;RSEQ=AAAAGGCTGATTTTAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:406:231:75,156:50,122:0.569:2,2:24.7:1:28.7:1:0.51403:1.17:60:462:0.5746:0:1.2 1/0:292:164:56,108:45,82:0.5616:2,2:25.9:1:28.3:1:0.90125:1.05814:60:163:0.566:0:1.5 -2 159560213 . GA G 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.80233;LSEQ=ATAAAGTATTGCTTATCATG;RSEQ=AAAAAAAAAGAACCTTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:11:0,11:0,44:0.2:1,0:22.3:1:31.6:1:1:0:60:22:0.2075:0.0182:0.1 0/1:18:3:0,3:0,15:0.1667:1,0:26.3:1:32.3:1:1:0:60:6:0.1667:0:0 -2 163928821 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14773;SOR=0;LSEQ=CAGGGATAGTACGAGATGCC;RSEQ=CCCAGCATTTACAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:0.1538:2,2:19:1:31:1:1:2.4495:60:4:0.1538:0:1 0/0:20:0:0,0:15,5:0:2,0:19.8:1:29.8:1:1:0:59.9:40:1:0:0.7 -2 163928850 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19808;SOR=0;LSEQ=TTACAAGAAAAGGCTTCTGA;RSEQ=ATCAGACAATACCTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:24,13:0.0513:2,2:7.5:1:28:1:1:1.81575:60:4:0.0513:0:3.5 0/0:48:0:0,0:28,20:0:2,0:19.1:1:30.1:1:1:0:59.8:96:1:0:1.1 -2 163928879 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50327;SOR=Inf;LSEQ=ATACCTTTCAAACTCTTATA;RSEQ=CAACCTCTGGACTTCGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:34,26:0:2,0:27.8:1:32:1:1:0:60:120:1:0:1.2 0/1:76:2:1,1:39,35:0.0263:2,2:20:0:28.5:1:1:1.1127:60:4:0.0263:0:3.5 -2 163928884 . C T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00037;SOR=0.2702;LSEQ=TTTCAAACTCTTATACCAAC;RSEQ=TCTGGACTTCGGCAACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:33:19,14:14,12:0.5593:2,2:32.5:1:30.7:1:0.79766:1.16:60:66:0.5593:0:2.2 0/1:75:19:9,10:29,25:0.2533:2,2:35.2:1:30.9:1:0.79032:1.28439:59.6:38:0.2533:0:2.1 -2 163928905 . A C 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.94401;LSEQ=TCTGGACTTCGGCAACATGG;RSEQ=TTTTCCCCTTTCTAGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:63:39:20,19:13,11:0.619:2,2:28.3:1:31.3:1:1:1.12067:60:18.5:0.6066:0:2 1/0:76:46:21,25:15,15:0.6053:2,2:28.1:1:31.6:1:0.81529:1.18774:59.8:45:0.6:0:1.7 -2 163928925 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2437;SOR=Inf;LSEQ=ATTTTCCCCTTTCTAGGTCC;RSEQ=ATGACAGCCATCTTGCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:27,30:0:2,0:22.9:1:31.3:1:1:0:60:56:1:0:1.2 0/1:59:3:2,1:24,32:0.0508:2,2:22.7:1:26.7:1:0.57772:2.62:60:6:0.0508:0:2.3 -2 163929071 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACTAACAACTTCTACCG;RSEQ=GGACCCCTGGACCAACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:24.5:1:32.5:1:1:2.24:60:4:0.25:0:1 0/0:3:0:0,0:1,2:0:2,0:23.3:1:27.7:1:1:0:60:6:1:0:0 -2 164133568 . A T 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTTTAAATAAAGTTCCTTA;RSEQ=GATGTTCATTTTTAAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:208,193:0:2,0:24.4:1:30.5:1:1:0:60:99.25:1:0:0.1 0/1:413:86:51,35:157,169:0.2082:2,2:25.7:1:29.7:1:0.07003:1.57:60:85:0.2078:0:1.1 -2 169205164 . T G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64917;SOR=1.1687;LSEQ=TGGGTATTGGGTGGCTCTAT;RSEQ=ATGCCATCATGGCGACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:27:25,2:91,15:0.203:2,2:25.3:1:33:1:0.52246:2.05:60:54:0.2061:0:1 0/1:122:28:23,5:76,18:0.2295:2,2:23.6:1:31.3:1:1:1.09:60:56:0.2295:0:1.1 -2 169205178 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49978;SOR=0;LSEQ=CTCTATTATGCCATCATGGC;RSEQ=ACTGTCACATTAAATAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:141,35:0.0112:2,2:8.5:1:28:1:0.3645:3.98629:60:4:0.0112:0:1 0/0:161:0:0,0:121,40:0:2,0:23.6:1:29.9:1:1:0:60:79.5:1:0:0.3 -2 169205230 . C T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04927;SOR=Inf;LSEQ=GAATTTAAGGGAATGTTTGA;RSEQ=CTGCCCCACAGTATATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:227,190:0:2,0:26.4:1:31.1:1:1:0:60:51.125:1:0:0.3 0/1:373:4:1,3:195,174:0.0107:2,2:5.5:1:25.8:1:0.34933:3.35199:60:8:0.0109:0:1.5 -2 169205282 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.20462;LSEQ=TAGGCCATAGGGAAAGTCAG;RSEQ=AAATGTTCAGGAGAGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:79:31,48:156,200:0.1812:2,2:24.1:1:28.3:1:0.53023:1.20722:60:38.5:0.1812:0:1.1 1/0:395:243:102,141:71,80:0.6152:2,2:24.6:1:28.4:1:0.34833:1.22619:60:80:0.6138:0:1.2 -2 169205353 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50822;SOR=0;LSEQ=AAGGACCTCCTGTAAGGAAG;RSEQ=CTGGGCTCAGGGAACTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:32,119:0.0131:2,2:32.5:1:29:1:0.38596:3.68:60:4:0.0135:0:1.5 0/0:115:0:0,0:30,84:0:2,0:23:1:30.9:1:1:0:60:37:0.9911:0:0.3 -2 169205451 . G A 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.2476;LSEQ=GAGTTGTCATTAGGATCAAC;RSEQ=GAATATATTGGTTGGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:0,5:0,23:0.1786:1,0:25.8:1:32:1:1:0:60:10:0.1786:0:1 0/1:14:3:0,3:0,11:0.2143:0,0:33.7:1:32.3:1:1:0:60:6:0.2143:0:1 -2 170170329 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52389;SOR=0;LSEQ=CTGTTCCTATTCGGCCATCT;RSEQ=GGAACCTCCCTCCTCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:107,45:0.013:2,2:31:1:31:1:0.50955:2.36278:60:4:0.0133:0:1 0/0:97:0:0,0:63,34:0:2,0:21.9:1:29.3:1:1:0:60:194:1:0:0.1 -2 170170404 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57174;SOR=2.85471;LSEQ=ATTCATGTTTTTGTCCATTA;RSEQ=TGGTCCGTGGGTATCTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:1:1,0:97,120:0.0045:2,0:1:0:27:0:0.44954:0:60:2:0.0047:0:1 0/1:155:2:1,1:69,84:0.0129:2,2:27.5:1:31.5:1:1:1.22:60:4:0.013:0:1 -2 170845304 . TA T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.24751;SOR=0;LSEQ=ATAGAGTAAGACCCTATCTT;RSEQ=AAAAAATTAAAAAAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:129,19:0.0133:2,2:9.5:1:29.5:1:0.24966:6.6432:60:4:0.0135:0.0067:0.5 0/0:151:0:0,0:127,24:0:2,0:19.2:1:28.3:1:1:0:60:74.5:1:0:0.3 -2 170845313 . T C 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00546;SOR=2.53494;LSEQ=GACCCTATCTTTAAAAAAAT;RSEQ=AAAAAAGAAAAAAAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:15:12,3:153,23:0.0785:2,2:18.2:1:32.1:1:0.4354:1.6579:60:30:0.0798:0:1 0/1:191:34:27,7:130,27:0.178:2,2:23.4:1:30.7:1:0.6259:1.24677:60:68:0.1799:0:1 -2 170845320 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.12252;SOR=Inf;LSEQ=TCTTTAAAAAAATTAAAAAA;RSEQ=AAAAAAAGAAACTGACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:195,32:0:2,0:22.6:1:32.2:1:1:0:60:44.4:1:0:0.2 0/1:225:3:2,1:176,46:0.0133:2,2:17:1:31.3:1:0.50663:1.90646:60:6:0.0135:0:1.3 -2 170845413 . A G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.53273;LSEQ=TGTTTCCTTCTTTACCATCT;RSEQ=AGCCTTATCCACCCATTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:53:29,24:376,358:0.0671:2,2:25.6:1:31.4:1:0.67085:1.15:60:106:0.0678:0:1.1 0/1:823:355:181,174:237,231:0.4313:2,2:25.6:1:31.3:1:0.94394:1.01:60:117.333:0.4335:0:1.2 -2 170845438 . TC A 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATCCACCCATTGATACTT;RSEQ=CCCCTTTTACCCCTTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:784:0:0,0:343,441:0:2,0:26.8:1:30.4:1:1:0:60:97:1:0:0.2 0/1:843:31:13,18:381,429:0.0368:2,2:28.5:1:30.1:1:0.71442:1.22939:60:62:0.0372:0.0047:1.2 -2 170845609 . T C 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01631;SOR=Inf;LSEQ=CTGGCTAATTTTATTTCATT;RSEQ=GTTCCCTCCTTATTAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:2,42:0:1,0:21:1:30:1:1:0:60:88:1:0:0.1 0/1:26:4:1,3:0,22:0.1538:1,2:33.5:1:29.8:1:0.15385:0:60:8:0.1538:0:1 -2 172443775 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18706;SOR=0;LSEQ=TGCCCCACAAATGTTAACCA;RSEQ=GGCAAAACTGGGAGAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:42,35:0.0253:2,2:28.5:1:32:1:1:1.19722:60:4:0.0256:0:1.5 0/0:103:0:0,0:52,51:0:2,0:31.1:1:29.1:1:1:0:60:33.333:1:0:0.1 -2 173022484 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52;SOR=0;LSEQ=GCATCACTCTAATCTCTGCT;RSEQ=CCATTGTCACATGGCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:3,11:0.125:2,2:18:1:28.5:1:0.45:3.32:60:4:0.125:0:1 0/0:9:0:0,0:3,6:0:2,0:27.7:1:32.1:1:1:0:60:18:1:0:0.2 -2 173022501 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=GCTGCCATTGTCACATGGCT;RSEQ=TCTTCTTCCTGTGTGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:2,7:0.1818:2,2:33:1:29:1:0.49091:3.06:60:4:0.1818:0:1 0/0:8:0:0,0:1,6:0:2,0:20.4:1:33:1:1:0:60:14:0.875:0:0 -2 173353511 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51446;SOR=Inf;LSEQ=GCCTCAAATGGCAAGCATGG;RSEQ=CCCACCTGACTCCGGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:18,23:0:2,0:27.4:1:31.9:1:1:0:60:40:1:0:0.1 0/1:61:2:1,1:29,30:0.0328:2,2:28.5:1:28.5:1:1:1.03:60:4:0.0333:0:1 -2 173914558 . G T 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GTTTTCATCTATTAATTTAC;RSEQ=TTGTGTTTAAAGATGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:0:1,0:23.5:1:29.9:1:1:0:60:58:1:0:0 1/0:14:7:7,0:7,0:0.5:0,0:33:1:30.7:1:1:0:60:14:0.5:0:1 -2 173914775 . T C 231 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAAATAATATGCTTTGTT;RSEQ=TATGAGCTTCTTTGGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:147,211:0:2,0:26:1:29.5:1:1:0:60:58.667:1:0:0.1 0/1:355:164:67,97:80,110:0.462:2,2:24.4:1:31.5:1:0.82944:1.0528:60:163:0.4631:0:1.1 -2 173915007 . G A 30 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=GTAATTACAGTATATTGTAC;RSEQ=TGTAGAGTACACTGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:42:1:32:1:1:0:60:4:1:0:1 1/0:4:2:0,2:0,2:0.5:0,0:13:1:30.5:1:1:0:60:4:0.5:0:1 -2 175584493 . AT A 81 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.12645;LSEQ=AGCCATTTGGGTTGCTTCTG;RSEQ=TTTTTTTTTTACTAGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:6:6,0:50,3:0.1017:2,0:28.3:1:32:1:1:0:60:12:0.1034:0:0 0/1:53:6:6,0:43,4:0.1132:2,0:33:1:31.5:1:1:0:60:12:0.1132:0:0 -2 175584534 . AGCC A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.50274;SOR=0;LSEQ=AAATGTTGGTATAGGTTCGC;RSEQ=GCCGCCGCGCCGCCGTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:121,5:0.0156:1,0:21:1:32.5:1:1:0:60:4:0.0163:0:0.5 0/0:105:0:0,0:93,11:0:2,0:22.8:1:31.5:1:1:0:58:103:1:0:0.2 -2 175584637 . T C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12064;LSEQ=GTAAGGAGGTCTCTGTACCA;RSEQ=GGCTCGTACAAAGCAGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:63,113:0.0112:2,2:28:1:29.5:1:1:1.79:31:4:0.0116:0:1 0/1:159:2:1,1:61,96:0.0126:2,2:27.5:1:31.5:1:1:1.57:31:4:0.0127:0:1.5 -2 175584721 . G C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.26031;LSEQ=TACAAAAGCCGCTCGCAAGA;RSEQ=TGCGCCCTCTACTGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:53:33,20:58,44:0.3419:2,2:24:1:31.8:1:0.6066:1.25:32.2:25.5:0.34:0:1.1 0/1:118:14:10,4:68,36:0.1186:2,2:19.7:1:31.4:1:0.77001:1.32:28.9:28:0.1197:0:1 -2 175584977 . T C 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74727;SOR=1.39186;LSEQ=ACCAACCTGTGTGCTATCCA;RSEQ=GCCAAACGTGTAACAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:5:2,3:86,84:0.0286:2,2:31.2:1:30.2:1:0.68205:1.53199:28:10:0.0286:0:2 0/1:127:5:0,5:74,48:0.0394:2,0:36.2:1:28.6:1:0.01129:0:24.2:10:0.0394:0:2 -2 175584979 . C G 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.64165;SOR=1.1418;LSEQ=CAACCTGTGTGCTATCCATG;RSEQ=CAAACGTGTAACAATTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:76:23,53:68,35:0.4246:2,2:27:1:32.1:1:0:4.43649:30.4:152:0.4246:0:1.1 0/1:129:59:16,43:60,10:0.4574:2,2:28.4:1:31.2:1:0:15.66491:28.2:118:0.4609:0:1.1 -2 175585001 . A T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07165;SOR=Inf;LSEQ=AAACGTGTAACAATTATGCC;RSEQ=AAAGACATCCAGCTAGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:113,108:0:2,0:26.3:1:30.1:1:1:0:32.9:72.667:1:0:0.4 0/1:158:3:1,2:95,60:0.019:2,2:11.7:1:25:1:0.56164:3.14314:32:6:0.0191:0:1.3 -2 175585011 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26549;SOR=0;LSEQ=CAATTATGCCAAAAGACATC;RSEQ=AGCTAGCACGCCGCATACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:1,2:117,143:0.0114:2,2:11:1:22.3:1:1:1.63343:49.3:2:0.008:0:1.3 0/0:194:0:0,0:97,97:0:2,0:24.3:1:29.8:1:1:0:35.4:31.333:1:0:0.5 -2 175585095 . T A 80 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4801;SOR=0.47524;LSEQ=TCTCAAAAAAAAAAAAAAAA;RSEQ=TTCTCTTCTTCCTGTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:6:0,6:53,178:0.0252:2,0:19:1:31:1:0.34231:0:37.2:12:0.0258:0:1.3 0/1:165:2:1,1:31,132:0.0121:2,2:34.5:1:20.5:1:0.35122:4.21:21:1:0.0061:0:4 -2 175585136 . T A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGTTCTGAACGTTAGATA;RSEQ=TTTTTTTCCATGGGGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:4,75:0.0244:2,0:7.5:1:32:0:1:0:44:4:0.0244:0:1 0/0:36:0:0,0:1,35:0:1,0:21.7:1:30.4:1:1:0:40.3:35:1:0:0.4 -2 175585567 . T TAAA 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTAAAATACATTAAACTA;RSEQ=AAAAAAAAAAAAAAGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18:1:31.7:1:1:0:60:4:1:0.5:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 175585616 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATATATGCATACACATTT;RSEQ=TGTGTGGGCATGTGTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 175586803 . CAT C 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGTTTACATAATTCTTGA;RSEQ=GTGGTAACTGCTGCTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:32.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 175898771 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20094;SOR=Inf;LSEQ=CATAATAACACTTGTGGGGC;RSEQ=TTCCTTTTTGAACAGTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:40,48:0:2,0:24.2:1:30.4:1:1:0:60:176:1:0:0.1 0/1:72:2:1,1:30,40:0.0278:2,2:32:1:31.5:1:1:1.33:60:4:0.0278:0:1 -2 175898881 . T G 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.10694;LSEQ=TGTTTTCTAAAAGACCAACA;RSEQ=ATATTGGGTGCCTCTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:1,7:0.2727:2,2:12:1:31.3:1:0.49091:3.06:60:6:0.2727:0:1 0/1:17:5:0,5:2,10:0.2941:2,0:21.2:1:32.2:1:1:0:60:10:0.2941:0:1 -2 177739275 . TTGC T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.51831;SOR=Inf;LSEQ=TTTATTAGATGCTGTTGCTG;RSEQ=TGCTGCTGCTGCAAAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:0:2,0:24.8:1:30.4:1:1:0:60:68:1:0:0.1 0/1:53:2:1,1:25,26:0.0377:2,2:30:0:32:0:1:1.04:60:4:0.0377:0:0 -2 178095441 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.24828;SOR=0;LSEQ=CTTATAAAGTATGAGCATTT;RSEQ=ACATCACAGTAGGAGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:2,1:178,26:0.0144:2,2:17.7:1:22.7:1:0.34392:3.39306:53.3:2:0.0098:0:2 0/0:203:0:0,0:159,44:0:2,0:22.6:1:30.9:1:1:0:60:202:1:0:0.1 -2 178095460 . TTAGTA T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00034;SOR=Inf;LSEQ=TCACATCACAGTAGGAGCTT;RSEQ=TAATAGTACAAAAAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:249,59:0:2,0:24:1:29.6:1:1:0:59.9:60.6:1:0:0.1 0/1:294:11:7,4:206,77:0.0374:2,2:29.8:1:29.1:1:0.50222:1.52637:60:22:0.0378:0:0 -2 178095536 . TCTTA T 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTTTCTTAACATCTGGCT;RSEQ=CTTTTGGGAACAAGGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:892:0:0,0:535,357:0:2,0:25.9:1:31.5:1:1:0:60:73.333:1:0:0.1 0/1:878:53:28,25:466,356:0.0604:2,2:24.5:1:31.2:1:0.66845:1.16853:60:106:0.0612:0.0103:0.2 -2 178097082 . T TA 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.62279;SOR=3.0091;LSEQ=ATGACTAAAGGCACTGAATA;RSEQ=AAAAAAAATCTCCAGTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:1,0:138,31:0.0059:2,0:16:0:24:0:1:0:60:2:0.0062:0:0 0/1:171:3:3,0:140,28:0.0175:2,0:9:1:29.4:1:1:0:60:6:0.0176:0.0117:0 -2 178097666 . C T 95 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=0;LSEQ=TGCCCAGCTGGCTCTTTACT;RSEQ=ACCAAACCTCTTAGATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:25.2:1:30:1:1:0:60:18:1:0:1.1 1/0:5:3:3,0:2,0:0.6:0,0:15.3:1:31.7:1:1:0:60:6:0.6:0:1 -2 178097778 . G GT 99 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.10242;SOR=2.66455;LSEQ=GGTTTTGTATTGTGTGAAGG;RSEQ=TTTTTTTTTTTCTTAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:7:6,1:61,2:0.0986:1,2:26.7:1:29.7:1:0.27455:4.88391:60:14:0.0986:0.0141:0 0/1:44:10:9,1:33,1:0.2273:1,2:21.6:1:30:1:0.40698:3.53056:60:20:0.2381:0.0455:0 -2 178098087 . CA C 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50705;SOR=1.29409;LSEQ=CCTGATAAAAGGGAATGACA;RSEQ=AAGGAAAACAAAAATGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:20:1,19:27,157:0.0976:2,1:23.8:1:33.1:1:0.3214:3.25444:60:40:0.0995:0.0195:0.1 0/1:171:21:6,15:30,120:0.1228:2,2:26.6:1:31.1:1:0.39396:1.60:60:42:0.1235:0.0234:0.1 -2 178098917 . C T 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=36.45457;LSEQ=TTTCCAGCTCATACTCTTTC;RSEQ=GTCGCTGACTGAAGTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:845:1:1,0:334,509:0.0012:2,0:14:0:16:0:0.39692:0:60:0:0:0:2 0/1:941:39:16,23:391,509:0.0414:2,2:23.9:1:30.2:1:0.86933:1.10417:60:78:0.0416:0:1.1 -2 178099012 . CA C 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.36107;SOR=0.31461;LSEQ=TCCATGTCCTATGTTTAAGA;RSEQ=AAAAAAGGAAGGAGAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:50,193:0.0122:2,2:21:1:31:1:0.11397:7.63:60:6:0.0123:0.0041:0.3 0/0:259:1:0,1:63,195:0.0039:2,0:24:0:34:0:1:0:60:2:0.0039:0:0 -2 178099031 . G A 29 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60909;SOR=2.18046;LSEQ=ACAAAAAAAGGAAGGAGAGA;RSEQ=CTCATGTTTTTTAAATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:1,0:29,159:0.0053:2,0:1:0:26:0:0.15873:0:60:2:0.0054:0:1 0/1:175:2:1,1:36,137:0.0114:2,2:6:0:29.5:1:0.37911:3.77:60:4:0.0116:0:1.5 -2 178099051 . A G 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59171;SOR=2.42631;LSEQ=GCTCATGTTTTTTAAATGAC;RSEQ=GATACCACATAAATTAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:1:0,1:10,113:0.0081:2,0:34:0:14:0:1:0:60:0:0:0:1 0/1:103:2:1,1:9,92:0.0194:2,2:17.5:1:28:1:0.18561:9.75:60:4:0.0198:0:1 -2 178129188 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24968;SOR=0;LSEQ=CCGGTTGCGGCTGTCCCTCC;RSEQ=GGGCCGCGGTTCCCTAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:3,0:165,9:0.0169:2,0:34.3:1:24.7:1:1:0:60:2:0.0115:0:2 0/0:160:0:0,0:144,16:0:2,0:22.5:1:30:1:1:0:60:39:1:0:0.4 -2 178129390 . TGGC T 136 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.00034;SOR=8.87515;LSEQ=CGCGGACAGGGCGGCTCTGG;RSEQ=GGCGGCGGCGGCGGTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:13,78:0.0215:2,2:24:0:33.5:1:0.2798:5.82:60:4:0.0215:0:0.5 0/1:134:22:2,20:27,73:0.1642:2,2:9.3:1:30.7:1:0.09779:3.66806:60:44:0.1654:0.0896:0.7 -2 178129402 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.54083;SOR=Inf;LSEQ=GGCTCTGGTGGCGGCGGCGG;RSEQ=GGCGGTGGCGGCTGCGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:3,33:0:2,0:7.2:1:30.4:1:1:0:60:72:1:0:0.3 0/1:67:2:1,1:12,53:0.0299:2,2:32:1:31.5:1:0.35278:4.28:60:4:0.0299:0:1.5 -2 178130037 . T G 42 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGGGGAGATGTGGACAGC;RSEQ=CCGGCAGCTCGTGTTCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:10:1:27:1:1:0:60:6:1:0:1.7 -2 178130073 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCAGTCACCCTGAACGCCC;RSEQ=CCTCTGAACTCCCACGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:30:1:1:0:60:4:1:0:2 -2 178209345 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34375;SOR=0;LSEQ=GAAGTCCATAAGCTTCTGAT;RSEQ=TGCAAACTTCCCTTCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:16,5:0,0:1:0,2:23:1:29.4:1:1:0:60:20:1:0:1.2 1/1:11:10:9,1:1,0:0.9091:0,2:22.3:1:31:1:1:0:60:20:0.9091:0:1.1 -2 178209494 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23296;SOR=0;LSEQ=GATAACAACCTATGTGTCCT;RSEQ=TATGCCAAATGTGTAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:50,39:0.022:2,2:34.5:1:30.5:1:1:1.27851:60:4:0.022:0:1.5 0/0:97:0:0,0:59,38:0:2,0:24.4:1:30.7:1:1:0:60:96:1:0:0.1 -2 178209507 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.50209;SOR=Inf;LSEQ=GTGTCCTCTATGCCAAATGT;RSEQ=TAACAATTATGGCAAAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:54,49:0:2,0:27.5:1:32.1:1:1:0:60:102:1:0:0.2 0/1:124:2:1,1:72,49:0.0161:2,2:24:1:27.5:1:1:1.46465:60:4:0.0163:0:1 -2 178209534 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20558;SOR=0;LSEQ=TTATGGCAAAAGACATCCAG;RSEQ=TAGCACACCACATATGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:45,63:0.0182:2,2:39.5:1:32:1:1:1.40:60:4:0.0183:0:1 0/0:132:0:0,0:61,71:0:2,0:28.3:1:31.3:1:1:0:60:65:1:0:0.2 -2 178209544 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50002;SOR=Inf;LSEQ=AGACATCCAGCTAGCACACC;RSEQ=CATATGTGAAGAACATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:39,65:0:2,0:26.8:1:29.6:1:1:0:60:208:1:0:0.1 0/1:119:2:1,1:49,68:0.0168:2,2:33:0:31:1:1:1.38:60:4:0.0169:0:1.5 -2 178209572 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50857;SOR=Inf;LSEQ=GAAGAACATGCTTAAGAATT;RSEQ=ACTGTGCTGGAAAACATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:20,53:0:2,0:23.9:1:31.5:1:1:0:60:72:1:0:0.2 0/1:99:2:1,1:38,59:0.0202:2,2:31.5:1:27.5:1:1:1.55:60:4:0.0202:0:1 -2 178209597 . TTC T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.51513;SOR=Inf;LSEQ=TGCTGGAAAACATTTCATTC;RSEQ=TCTCTCTCTCTTCTTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:3,30:0:2,0:25.5:1:30.1:1:1:0:60:32:1:0:0 0/1:50:2:0,2:9,39:0.04:2,0:32:1:32:0:1:0:60:4:0.0417:0:0 -2 178848343 . AAAAC A 79 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.39563;SOR=0.28412;LSEQ=GTGATAAATTAATTACTTAA;RSEQ=AAACAAACAAACAAACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:5,1:25,0:0.1935:1,2:17.2:1:30.8:1:0.19355:0:60:12:0.1935:0:0.3 0/1:16:1:1,0:15,0:0.0625:1,0:39:0:32:0:1:0:60:2:0.0625:0:1 -2 178848402 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20115;SOR=Inf;LSEQ=TGCTATTTGGTGGACTAAAG;RSEQ=AAACTTTTTTGTATGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:68,15:0:2,0:23.3:1:30.5:1:1:0:60:26.667:1:0:0.2 0/1:68:2:1,1:61,5:0.0294:2,2:28.5:1:30.5:1:0.16989:11.22821:60:4:0.0313:0:1 -2 178848433 . TA T 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00041;SOR=Inf;LSEQ=GTATGTTCTGGGTTTCTTAA;RSEQ=TTTTTTATTTTGAAATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:112,43:0:2,0:24.1:1:28.7:1:1:0:60:76.5:1:0:0.5 0/1:136:10:7,3:90,36:0.0735:2,2:20.4:1:29.2:1:1:1.07088:60:20:0.0746:0.0294:1 -2 178848447 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24398;SOR=Inf;LSEQ=TCTTAATATTTTTTATTTTG;RSEQ=AATACATGGCACTGATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:138,50:0:2,0:25.3:1:29.9:1:1:0:60:61.667:1:0:0.5 0/1:184:2:1,1:121,61:0.0109:2,2:25.5:1:29:1:1:1.97572:60:4:0.011:0:1 -2 178848451 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23716;SOR=0;LSEQ=AATATTTTTTATTTTGAAAT;RSEQ=CATGGCACTGATGAATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:139,55:0.0102:2,2:40:1:32:1:0.49084:2.51361:60:4:0.0102:0:1 0/0:207:0:0,0:135,72:0:2,0:22.8:1:28.4:1:1:0:60:68:1:0:0.4 -2 178848487 . T C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31884;LSEQ=TTTATCATTGAACTGCAAGA;RSEQ=AGCCAGAAAACTAAGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:139:78,61:96,68:0.4587:2,2:26.1:1:31.9:1:0.72681:1.10371:60:138:0.46:0:1.1 0/1:306:65:36,29:130,111:0.2124:2,2:28.1:1:31.4:1:0.88889:1.06:60:130:0.2138:0:1.2 -2 178882890 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19862;SOR=Inf;LSEQ=TGCCACCCAGCCGCCATTCT;RSEQ=TTTCCAAGGCTGCGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:99,26:0:2,0:22.4:1:32.1:1:1:0:60:124:1:0:0.1 0/1:101:2:2,0:82,17:0.0198:2,0:32:1:31.5:1:1:0:60:4:0.0202:0:1 -2 178882923 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22125;SOR=Inf;LSEQ=CGTCTGTCCACTGGACTGGT;RSEQ=ACGGGGTTGTCAGTGTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:141,78:0:2,0:25.8:1:31.6:1:1:0:60:108.5:1:0:0.1 0/1:195:2:1,1:129,64:0.0103:2,2:23:1:26:1:1:2.00786:60:4:0.0105:0:1 -2 178883022 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49859;SOR=0;LSEQ=CAGCCCTCACTCTCCTTAGT;RSEQ=ACTAAGACTTTGAACAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:56,120:0.0112:2,2:31.5:1:28:1:0.53914:2.13:60:4:0.0115:0:1 0/0:178:0:0,0:55,122:0:2,0:24.6:1:31.1:1:1:0:60:87.5:0.9943:0:0.1 -2 178883096 . T TTTGGCACACTTGACTTTAAC 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00063;SOR=5.20251;LSEQ=AAAGCTGCCAAGGCAGGCCT;RSEQ=TTGGCACACTTGACTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:10:1,9:4,39:0.1887:2,2:28.2:1:30.2:1:1:1.08:59.5:20:0.1923:0.0755:0.2 1/0:38:21:3,18:1,16:0.5526:1,2:20:1:30.9:1:0.61309:2.60:59.8:42:0.5526:0.3158:0.1 -2 178883104 . A ACTTGACTTTAACTTGGCACG 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=9e-04;SOR=0.20411;LSEQ=CAAGGCAGGCCTTTTGGCAC;RSEQ=CTTGACTTTAACCTTTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:32:3,29:1,19:0.6154:1,2:25.1:1:29.7:1:1:1.94:58.9:31:0.6078:0.2115:0.2 0/1:33:8:2,6:2,23:0.2424:2,2:33.4:1:29.9:1:0.2412:3.64:60:16:0.2424:0.0303:0 -2 178883193 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=CCATGCTGTGGAAGCTCTGA;RSEQ=CTTTTAGACTTAACACCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:0:2,0:24.8:1:32:1:1:0:60:18:1:0:0.4 0/1:12:2:1,1:3,7:0.1667:2,2:45.5:1:29:1:1:2.16:60:4:0.1667:0:1 -2 178883209 . C A 45 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26154;SOR=0.18798;LSEQ=CTGACCTTTTAGACTTAACA;RSEQ=CTTAAAAAGTAATTCTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:0,4:0.4286:0,2:22.3:1:29:1:0.42857:0:60:6:0.4286:0:1 0/1:9:1:0,1:2,6:0.1111:2,0:28:0:32:0:1:0:60:2:0.1111:0:1 -2 178883450 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCAGCTATTCTTTTTTA;RSEQ=TTTTTGTAGACACAGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 179632710 . T C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=5.25768;LSEQ=ATTCAGAGGAAACTGGGAAT;RSEQ=ACTGGAATGTAGCAAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:194:97,97:204,187:0.3316:2,2:24.9:1:31.2:1:0.66067:1.09075:60:63.667:0.331:0:1.1 1/0:495:358:194,164:74,62:0.7232:2,2:25.7:1:30.7:1:1:1.00896:60:43.75:0.7202:0:1.1 -2 180262226 . TAC T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATATATACACACATACGCA;RSEQ=ACACACATATACGTATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:28.6:1:1:0:60:4:1:0.5:0 -2 180264359 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22304;SOR=Inf;LSEQ=GATAAATCCTTAGCAATAAA;RSEQ=GTAATTCTTCACGAGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:118,20:0:2,0:19.6:1:31.8:1:1:0:60:68:1:0:0.1 0/1:124:2:1,1:103,19:0.0161:2,2:14:1:30:1:0.29767:5.30948:60:4:0.0164:0:1.5 -2 180264698 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11156;SOR=Inf;LSEQ=GCTTGACCACACCATCCCCT;RSEQ=CATCTGGAGTCACATCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:72,151:0:2,0:24.2:1:31.8:1:1:0:60:73.333:1:0:0.1 0/1:208:3:1,2:78,127:0.0144:2,2:10.7:1:26:1:1:1.22713:60:2:0.0097:0:1 -2 180264701 . T C 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACCACACCATCCCCTGCA;RSEQ=CTGGAGTCACATCCCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:64,146:0:2,0:24.8:1:30.1:1:1:0:60:104:1:0:0.1 0/1:205:20:9,11:68,117:0.0976:2,2:25.9:1:29.8:1:0.47584:1.41:60:19:0.0945:0:1 -2 180264797 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22418;SOR=Inf;LSEQ=GGACTTGCTGTTTCTCCATC;RSEQ=GCTCCCAGAACTGCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:78,55:0:2,0:24.8:1:30.9:1:1:0:60:132:0.9925:0:0.1 0/1:121:2:1,1:55,64:0.0165:2,2:36:1:29:1:1:1.16:60:4:0.0167:0:1 -2 180264857 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.18783;SOR=Inf;LSEQ=TCTGCTGGTTCGTGGCCTCT;RSEQ=TCACCAATAGTGGATGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:108,43:0:2,0:23.4:1:31.3:1:1:0:60:74.5:1:0:0.1 0/1:116:2:1,1:62,52:0.0172:2,2:9:0:32:0:1:1.19049:60:4:0.0174:0:1.5 -2 180265078 . AG A 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGAGGCAGCTGGCGTGGA;RSEQ=CTTGTTTAGTGACCTCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:220,179:0:2,0:25.6:1:32.1:1:1:0:60:78.8:0.9975:0:0.3 0/1:389:27:15,12:190,172:0.0694:2,2:27.9:1:32.5:1:0.84284:1.13:60:54:0.0705:0.0077:0.2 -2 180265135 . C T 194 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00986;LSEQ=TACAATTTCCAAGTGCGTTC;RSEQ=GAAAACTCCTGGGGGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:84:47,37:287,198:0.1476:2,2:24.6:1:30.5:1:0.63155:1.14082:60:168:0.1495:0:1.9 0/0:588:1:0,1:349,238:0.0017:2,0:1:0:25:0:0.40646:0:60:2:0.0017:0:2 -2 180265158 . T C 294 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04047;LSEQ=AAACTCCTGGGGGCTTGCTT;RSEQ=AGCCCGTCTGTCACCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:668:667:369,298:0,1:0.9985:0,2:25.9:1:31.6:1:0.4476:0:60:221.333:0.9985:0:1.4 1/1:755:728:395,333:13,14:0.9642:2,2:25.8:1:31:1:0.56025:1.28:59.9:51:0.9636:0:1.1 -2 180265174 . G A 210 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01123;LSEQ=GCTTTAGCCCGTCTGTCACC;RSEQ=CCTCCTTCCTTGCCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:776:133:66,67:350,293:0.1714:2,2:23.9:1:29.9:1:0.33986:1.21233:59.9:132:0.1719:0:1.8 0/0:865:2:1,1:446,416:0.0023:2,2:35.5:1:30.5:1:1:1.072:60:4:0.0023:0:2.5 -2 180265634 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1822;SOR=Inf;LSEQ=TTGACCTCTCTGGCACTGCA;RSEQ=AGTGCATGCAGGTAGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:28,162:0:2,0:24.3:1:32.3:1:1:0:60:37:1:0:0.1 0/1:142:2:1,1:31,109:0.0141:2,2:27.5:1:27.5:1:0.40116:3.48:60:4:0.0141:0:1.5 -2 180265684 . G T 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00085;SOR=Inf;LSEQ=TTTTGTTTATCCACTCACTT;RSEQ=TTAATGGTCATTTAAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:1,55:0:1,0:24.7:1:32.2:1:1:0:60:27:1:0:0.1 0/1:51:9:0,9:2,39:0.1765:1,0:26.2:1:30.7:1:1:0:60:18:0.1837:0:1 -2 180265720 . G C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06786;SOR=Inf;LSEQ=GTTGTTTCCACCTTTTGGCT;RSEQ=TTGTGCACAGCGCTCCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:0:1,0:23.1:1:31.8:1:1:0:60:58:1:0:0.1 0/1:21:3:0,3:0,18:0.1429:1,0:23:1:32.7:1:1:0:60:6:0.1429:0:3 -2 181049373 . A T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATCTTCACATGGTGTTC;RSEQ=TCCTCTGCACATCTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:4,8:0,0:1:0,2:21.5:1:30.3:1:1:0:60:24:1:0:1 1/1:3:3:1,2:0,0:1:0,2:17.7:1:28.7:1:1:0:60:6:1:0:1 -2 182275634 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=TCCTTCACCGGCAACAAAGG;RSEQ=ATCCAGGTTCCCTCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:34.6:1:28.6:1:1:0:60:16:1:0:0.1 0/1:5:2:1,1:2,1:0.4:2,2:25:0:31.5:1:1:1.7321:60:4:0.4:0:1.5 -2 182276161 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.175;SOR=Inf;LSEQ=GGGGTCCCAAGACTTTTCCC;RSEQ=ACAGCCCAACACACCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:30:1:31:1:1:0:60:18:1:0:0.1 0/1:7:2:1,1:3,2:0.2857:2,2:37.5:1:28.5:1:1:1.41418:60:4:0.2857:0:1 -2 182276675 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51588;SOR=0;LSEQ=AAATCAGATGAATAAGGCCT;RSEQ=AAATGAACTTCCAGCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:24,33:0.0339:2,2:11:1:31:1:1:1.37:60:4:0.0345:0:1 0/0:39:0:0,0:19,20:0:2,0:23.9:1:31.4:1:1:0:60:78:1:0:0.1 -2 182276873 . T TCAA 31 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.18347;SOR=0;LSEQ=CTCACGAAGATGAGAAAGAA;RSEQ=CAACAACAACAACAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:0.1429:2,2:42:0:31.7:1:1:1.37:60:4:0.1429:0:0.5 0/0:18:0:0,0:6,11:0:2,0:24.8:1:29.2:1:1:0:60:34:1:0:0.1 -2 183484910 . C CTTTA 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ACTTTAAAATGTATTTATTT;RSEQ=TTTATTTAATAAATAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:32:1:31.1:1:1:0:60:6:0.4286:0.1429:0.3 0/0:1:0:0,0:1,0:0:0,0:19:0:33:0:1:0:60:2:1:0:0 -2 183484981 . T C 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0634;SOR=0;LSEQ=CAACTATTAACACATTTCTA;RSEQ=ATTAATATGAATTTCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:6,0:17,0:0.2609:1,0:27.5:1:33:1:1:0:60:12:0.2727:0:1 0/0:15:0:0,0:15,0:0:1,0:17.1:1:30.7:1:1:0:60:30:1:0:0 -2 183485158 . A C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13561;LSEQ=ATATGTGTGGAATTATCCTG;RSEQ=CAAAAATATAAGTTGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:403:304:164,140:54,44:0.7543:2,2:25.8:1:31.4:1:0.90731:1.04757:60:42.429:0.75:0:1.1 0/1:375:110:64,46:143,121:0.2933:2,2:25.3:1:31:1:0.49535:1.18:60:35.667:0.2908:0:1.1 -2 183485213 . TC T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.66089;SOR=1.8631;LSEQ=AAATTTATCTTCTATTGTTA;RSEQ=CCCCATCCAAACTGGGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:2:1,1:155,213:0.0054:2,2:33.5:1:30:1:1:1.37:60:4:0.0054:0:0 0/1:299:3:1,2:116,178:0.01:2,2:32.7:1:31.3:1:1:1.30224:60:6:0.01:0:0 -2 184373031 . CT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.13732;SOR=0;LSEQ=CATTGTCTGATTTCAGAAGC;RSEQ=TTTCCTGTAAACGCCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:0,2:9,16:0.0741:2,0:20.5:1:33.5:1:0.53846:0:46.5:4:0.0741:0:0.5 0/0:45:0:0,0:20,25:0:2,0:27.6:1:30.2:1:1:0:53.5:90:1:0:0.2 -2 184373044 . C T 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=CAGAAGCCTTTTCCTGTAAA;RSEQ=GCCAGGTGGCAGTCGTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:5,9:0.3636:2,2:24.6:1:30.6:1:1:1.08:54.1:16:0.3636:0:1 0/0:41:0:0,0:17,24:0:2,0:24.2:1:30.2:1:1:0:55.3:82:1:0:0.2 -2 184756508 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCAGGAATAACAAAAT;RSEQ=TATCCTTGCTTTACAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:38:0:30:1:1:0:60:4:0.5:0:1 -2 184756657 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16471;SOR=Inf;LSEQ=ACACTAAACAGTCAGGGATA;RSEQ=TATGAGATGCTGCCCAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:25,5:0:2,0:26.3:1:32:1:1:0:60:60:1:0:0.1 0/1:21:2:1,1:15,4:0.0952:2,2:32.5:1:31.5:1:0.42857:3.46389:60:4:0.1:0:2.5 -2 184756669 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18012;SOR=Inf;LSEQ=CAGGGATAGTATGAGATGCT;RSEQ=CCCAGTATTTACAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:29,11:0:2,0:22.8:1:31.6:1:1:0:60:39:1:0:0.1 0/1:30:2:1,1:19,9:0.0667:2,2:27:0:31:1:1:2.05485:60:4:0.0667:0:2.5 -2 184756676 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19571;SOR=Inf;LSEQ=AGTATGAGATGCTGCCCAGT;RSEQ=TTTACAGGAAAAGGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:32,14:0:2,0:21.4:1:28.8:1:1:0:60:92:1:0:0.2 0/1:37:2:1,1:22,13:0.0541:2,2:26.5:1:33.5:1:1:1.66733:28:4:0.0556:0:2 -2 184756691 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49747;SOR=Inf;LSEQ=CCAGTATTTACAGGAAAAGG;RSEQ=TTCTGAAATCAGACAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:31,21:0:2,0:23.7:1:31.3:1:1:0:60:25:0.9804:0:0.2 0/1:60:2:1,1:34,24:0.0333:2,2:11.5:1:25.5:1:1:1.40828:60:4:0.0351:0:1.5 -2 184756721 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22798;SOR=0;LSEQ=CAGACAATGTCTTTCAAACT;RSEQ=TTTTACCAACCTCTGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:44,34:0.025:2,2:48:1:30:1:1:1.2899:60:4:0.0253:0:1 0/0:87:0:0,0:49,38:0:2,0:29:1:31:1:1:0:60:42.5:1:0:0.2 -2 184756785 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49624;SOR=0;LSEQ=CTAGGTCCCGTGGCAGCCAT;RSEQ=TTGCTGTTATTCCTCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:25,39:0.0303:2,2:34.5:1:30:1:1:1.55:60:4:0.0303:0:1 0/0:64:0:0,0:29,35:0:2,0:24.8:1:31.3:1:1:0:60:63:1:0:0.2 -2 184756811 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.54455;LSEQ=GTTATTCCTCTTTGGACCCT;RSEQ=TATTTTTAATCTCCTTGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:9,31:0.0476:2,2:28:1:28.5:1:0.42393:3.32:60:4:0.0476:0:1 0/1:38:1:1,0:12,25:0.0263:2,0:1:0:23:0:0.34211:0:60:2:0.0263:0:1 -2 184757074 . G A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAGCAGTTGGGGTGTCCT;RSEQ=TTTAGAGGGGGGATTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:4:0:31:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30:1:1:0:60:4:1:0:1.5 -2 185198135 . C A 59 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.31624;LSEQ=GCAGACAGAGAAGCAAGAAT;RSEQ=AATACTGTTGACTCCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:31:1:29.8:1:1:0:60:8:0.8:0:1 1/0:2:1:1,0:1,0:0.5:0,0:37:0:27:0:1:0:60:2:0.5:0:1 -2 185198375 . A G 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTAAGTAACAATGACCTA;RSEQ=GTGGAAAAATTAGAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:221,160:0:2,0:25.8:1:30.3:1:1:0:60:53.429:1:0:0.7 0/1:298:16:10,6:155,125:0.0537:2,2:25.3:1:30.1:1:0.61617:1.34:60:15:0.0517:0:1.2 -2 185198425 . T A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00058;SOR=0.56302;LSEQ=AGCCAGTAGCATATTCAGAC;RSEQ=TTCATTTAGCCTGGACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:425:343:158,185:38,44:0.8071:2,2:25.8:1:30.1:1:1:1.01119:60:41.875:0.8053:0:1.8 1/0:389:273:133,140:56,60:0.7018:2,2:25.6:1:29.9:1:1:1.02:60:44.5:0.7008:0:1.8 -2 185198456 . A C 261 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43447;SOR=1.1733;LSEQ=CTGGACACCTCTTGACTCCA;RSEQ=AGGGAAGCCACAAGTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:360:286:104,182:33,41:0.7944:2,2:24.5:1:32.1:1:0.22677:1.40712:60:142:0.7955:0:1.9 1/1:310:254:114,140:26,29:0.8194:2,2:25.6:1:31.2:1:0.76686:1.10068:60:62.5:0.8197:0:1.8 -2 185198788 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCAAATAAAATTATTC;RSEQ=CAGACTAGAGTTAGCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:25.5:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 186821397 . C G 41 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=GTATACTTCTTTGGGTAGAG;RSEQ=AGGCTGGCACTTCAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:18.5:1:33.5:1:1:0:60:8:1:0:0.3 1/1:3:3:2,1:0,0:1:0,2:26.3:1:26:1:1:0:60:2:1:0:1 -2 186821594 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49847;SOR=Inf;LSEQ=TGCCAACAGCATGCTGGGTA;RSEQ=ATTGTAGAATATTCCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:49,39:0:2,0:34.9:1:31.4:1:1:0:60:21:1:0:0.1 0/1:97:2:1,1:54,41:0.0206:2,2:26:0:28.5:1:1:1.31328:60:4:0.0208:0:1 -2 186821699 . C T 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01153;SOR=Inf;LSEQ=TCACCATTCTTACAGGTTCA;RSEQ=ATGTATATGGCCAAAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:3,22:0:2,0:23.7:1:32.1:1:1:0:60:24:1:0:0.1 0/1:29:7:1,6:5,17:0.2414:2,2:20.6:1:29:1:1:1.73356:60:14:0.2414:0:1 -2 186821709 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48986;SOR=Inf;LSEQ=TACAGGTTCACATGTATATG;RSEQ=CCAAAGGAGCACCTCCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:3,19:0:2,0:24:1:32:1:1:0:60:44:1:0:0.1 0/1:24:2:1,1:5,17:0.0833:2,2:21.5:1:28:1:0.44565:3.19:60:4:0.0833:0:1 -2 187558960 . G A 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20455;SOR=0;LSEQ=CTCGGCCTGGCCGTGGTGCT;RSEQ=CTGAAAGCGCGGCTGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:3,1:0.5556:2,0:34.6:1:28.8:1:0.44444:0:60:10:0.5556:0:1 0/0:3:0:0,0:3,0:0:0,0:43:1:32:1:1:0:60:6:1:0:0 -2 187559029 . A ACAG 75 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.48495;SOR=1.86941;LSEQ=TCCGACCTCAGCCTCATCCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:3,3:8,11:0.24:2,2:13.7:1:32.1:1:1:1.36:60:12:0.24:0.16:0.8 0/1:16:6:3,3:4,3:0.375:2,2:31.8:1:29.4:1:1:1.30401:60:12:0.375:0.0625:0.5 -2 187559047 . G GCAA 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=0.92998;LSEQ=CAACAGCAGCAGCAGCAGCA;RSEQ=CAACAACAACAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:14:6,8:3,4:0.56:2,2:32.9:1:30.4:1:1:1:60:28:0.56:0:0.1 1/0:24:13:7,6:4,7:0.5417:2,2:23.1:1:31:1:0.44419:1.98:59.6:26:0.5417:0.2083:0.6 -2 189541688 . A T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=16.68219;LSEQ=TTGCAAGGATTCCATTTACT;RSEQ=AATAAAAAATAGAGCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:342:188:88,100:68,86:0.5497:2,2:26.5:1:29.1:1:0.6631:1.11:60:376:0.5529:0:1 1/1:343:327:146,181:6,10:0.9534:2,2:26.9:1:28.5:1:0.61716:1.34:60:108:0.9529:0:1.1 -2 189541807 . C G 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=0;LSEQ=CATAAAACATTCAAAATTAT;RSEQ=TTGATTATTTGCTTTATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:13:0,13:2,34:0.2653:2,1:24.8:1:32.7:1:1:0:60:26:0.2708:0:1.2 0/0:39:0:0,0:0,39:0:1,0:22.1:1:32.3:1:1:0:60:38:1:0:0 -2 190656341 . CA C 49 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.07792;SOR=Inf;LSEQ=TGACAGCGAGATTTCATCTC;RSEQ=AAAAAAAAAAAAGAAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:10,1:0:2,0:16.9:1:30.2:1:1:0:60:22:0.9167:0:0.5 0/1:10:3:3,0:6,0:0.3:0,0:20:1:31:1:1:0:60:6:0.3:0:0 -2 190656484 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25014;SOR=Inf;LSEQ=TGTTGGTCAGGAATGCTTAA;RSEQ=AATTCTTACAAGTTGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:193,58:0:2,0:23.1:1:32.2:1:1:0:60:502:1:0:0.1 0/1:275:3:1,2:207,65:0.0109:2,2:7.3:1:27:1:0.14811:6.31521:60:6:0.011:0:1.3 -2 190656496 . G T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37581;SOR=3.6661;LSEQ=ATGCTTAACAATTCTTACAA;RSEQ=TTGCATTTTTATCTTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:1:0,1:216,87:0.0033:2,0:1:0:27:0:0.28947:0:60:2:0.0033:0:1 0/1:334:4:2,2:240,90:0.012:2,2:16.5:1:28.3:1:0.30485:2.65756:60:8:0.0122:0:1.3 -2 190670363 . GT G 88 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.20712;SOR=0.38601;LSEQ=AAGTGTTAGTTTTATTAGAT;RSEQ=TTTTTTCCCCCAGGTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:7:4,3:430,255:0.0101:2,2:22.3:1:31.5:1:0.71578:1.26425:60:14:0.0102:0.0014:0.3 0/0:764:3:1,2:442,319:0.0039:2,2:22.3:1:30.7:1:0.5755:2.76748:60:6:0.004:0.0013:0.7 -2 190670539 . T TA 141 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.42557;SOR=0.76325;LSEQ=TTCTGTCTTAATTGTTGGTT;RSEQ=AAAAAAAAAAAGTTACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:27:1,26:12,136:0.1517:2,1:29:1:29.7:1:0.69464:2.28576:60:12.5:0.1462:0.0112:0 0/1:150:18:2,16:18,112:0.12:2,2:22.3:1:30.3:1:1:1.28368:59.7:36:0.1241:0.0067:0.3 -2 190670808 . CAT C 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGATTAAAATTTTATTGAAA;RSEQ=ATAAAACATAATTGATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:39.8:1:31.5:1:1:0:60:8:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 190682613 . CT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.54167;SOR=0;LSEQ=AGTAGTTTGCAAAGTTGAGC;RSEQ=TTGGGTTTCTAGAATTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:40,0:0.0476:1,2:28:1:30.5:1:0.04762:0:60:4:0.05:0:0 0/0:22:0:0,0:22,0:0:1,0:18:1:30.4:1:1:0:60:44:1:0:0.1 -2 190682632 . G C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.3588;SOR=0.49813;LSEQ=CCTTTGGGTTTCTAGAATTG;RSEQ=AGGAGGAGACCTTCAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:9:9,0:42,1:0.1731:1,0:31.6:1:29.7:1:1:0:60:8:0.1569:0:1.1 0/1:32:3:3,0:29,0:0.0938:1,0:16:1:33.3:1:1:0:60:6:0.0938:0:1 -2 190682693 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50421;SOR=0;LSEQ=TGTATACGGATTTGAAGATC;RSEQ=GTGACGTTCCTTCCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:127,51:0.011:2,2:33:1:30.5:1:0.49547:2.47584:60:4:0.0112:0:1 0/0:146:0:0,0:103,43:0:2,0:25.9:1:30.6:1:1:0:60:145:1:0:0.1 -2 190682952 . T TAAAC 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.00087;SOR=Inf;LSEQ=TTTCTGGGTATATGATATAA;RSEQ=AAACAATGTATACTTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:21,117:0:2,0:23.7:1:29:1:1:0:60:276:1:0:0 0/1:149:11:4,7:27,110:0.0738:2,2:24.8:1:29.3:1:0.24302:2.31:60:22:0.0738:0.0134:0.1 -2 190708712 . G A 221 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTTATTTGGCAGAAAAGCA;RSEQ=AGTATCAGATCACAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:171:99,72:475,353:0.171:2,2:27.5:1:29.9:1:0.93241:1.02:60:56:0.169:0:1.1 0/0:838:0:0,0:453,384:0:2,0:26.1:1:31.4:1:1:0:60:103.625:0.9988:0:0.1 -2 190710798 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGTAACTTCCACAGAAAG;RSEQ=GGGGACATGAGAGGTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:30.5:1:1:0:60:4:1:0:1.5 -2 190717314 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTTTTTATACCTTTCAAA;RSEQ=TGTTATATATAGCCAGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:0,2:148,22:0.0116:2,0:24.5:1:29:1:0.01877:0:60:4:0.0118:0:1 0/0:83:0:0,0:73,10:0:2,0:21.4:1:32:1:1:0:60:82:1:0:0 -2 190717517 . G GA 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.02047;LSEQ=CTTAAAGGTAGTATGCTTTA;RSEQ=AAAAAAAAAATTATTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:21:10,11:89,203:0.0652:2,2:26.7:1:30.2:1:0.14264:2.07:60:42:0.0693:0.0031:0.1 0/1:331:22:5,17:104,200:0.0665:2,2:27.5:1:29.7:1:0.35205:1.76519:60:44:0.0688:0.0091:0.4 -2 190717528 . T A 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71377;SOR=0.67855;LSEQ=TATGCTTTAGAAAAAAAAAA;RSEQ=TATTTGAATTGGAAATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:4:1,3:73,191:0.0149:2,2:6.5:1:30.8:1:1:1.14603:60:8:0.0154:0:1 0/1:295:3:0,3:80,212:0.0102:2,0:5.6:1:29.6:1:0.56546:0:60:8:0.0093:0:1 -2 190717570 . T A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=Inf;LSEQ=ACATTGTAACAAGGACTGCT;RSEQ=CCAAGAATTTGCTCTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:7,106:0:2,0:23.4:1:30.3:1:1:0:60:226:1:0:0.1 0/1:127:2:1,1:8,117:0.0157:2,2:17:1:24.5:1:0.13723:13.85:60:4:0.016:0:3.5 -2 190717628 . T C 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01685;SOR=Inf;LSEQ=ATGTCATTTATTAAACATTA;RSEQ=GCATGATAGAAAGACATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:0:1,0:21.6:1:30.5:1:1:0:60:94:1:0:0.1 0/1:28:4:0,4:2,22:0.1429:2,0:14.3:1:31:1:1:0:60:8:0.1429:0:1 -2 190718940 . A C 194 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTATTTTCATAATTTCCCCT;RSEQ=ACATTTGTTAATTTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:71:49,22:109,55:0.3021:2,2:24.5:1:31.6:1:0.76324:1.12:60:142:0.3034:0:1 0/0:228:0:0,0:160,68:0:2,0:23.3:1:28.4:1:1:0:60:113:1:0:0.1 -2 190719922 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23647;SOR=Inf;LSEQ=TTCTATATGACTCACTGTTT;RSEQ=AAAAGAATTTTTTTCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:7,96:0:2,0:24.2:1:30.8:1:1:0:60:206:1:0:0.1 0/1:98:2:1,1:10,86:0.0204:2,2:22.5:1:31:1:0.21292:8.25:60:4:0.0208:0:1 -2 190720748 . A AT 35 v4;q23;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.26847;SOR=0;LSEQ=ACTACCTAGATACTTGACCA;RSEQ=TTTTTTTTTTCATTCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:0,3:1,14:0.1667:1,0:26:1:22.7:1:1:0:60:2:0.125:0:0 0/0:11:0:0,0:1,10:0:2,0:24.3:1:29.5:1:1:0:60:22:1:0:0.2 -2 190720880 . CT C 29 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=TCTTCAGCCTTTTTTGTCAT;RSEQ=TTTTTTTTTTTTAAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:25:0:32:0:1:0:60:2:0.25:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:27.5:1:29.5:1:1:2.45:60:4:0.4:0:0 -2 190728895 . T C 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GCCCTGCTATTTAAAAGACT;RSEQ=CTTGAGAATCATAAACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:126,158:0:2,0:25.7:1:29.7:1:1:0:60:55.8:1:0:0.1 0/1:323:19:5,14:138,166:0.0588:2,2:25.7:1:30.6:1:0.15203:2.32201:60:18:0.057:0:1.3 -2 190738206 . A AT 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24961;SOR=0;LSEQ=GAACTTAACTATGTGTTTTT;RSEQ=TTTTTTTTCTTTCAGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:159,54:0.0139:2,2:22.7:1:29:1:1:1.46936:58.3:6:0.014:0.0046:0.3 0/0:198:0:0,0:154,44:0:2,0:22.8:1:28:1:1:0:60:65:1:0:0.1 -2 190738435 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4973;SOR=0;LSEQ=ACAGGGGTCCCAACTCCCGG;RSEQ=CCAAGCCGGTTAGGAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:10,81:0.0215:2,2:9.5:1:28:1:0.2237:7.77:60:4:0.0215:0:1 0/0:92:0:0,0:15,77:0:2,0:24.7:1:32:1:1:0:60:91:1:0:0.1 -2 191848154 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGGAATCACTGACTGCCC;RSEQ=AGCTTACCCACATGGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:29.5:1:1:0:60:4:1:0:1 -2 191848312 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTTCAGAGATGCAGCAG;RSEQ=GAGAGCGTGGGGTCTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28:1:33.5:1:1:0:60:4:1:0:1 1/1:2:2:2,0:0,0:1:0,0:22.5:1:31.5:1:1:0:60:4:1:0:1 -2 191848392 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18586;SOR=0;LSEQ=GGTTCCGCCACCAGCATGTT;RSEQ=TACCAAAGGATGGAGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:14,8:0.0833:2,2:25.5:1:31.5:1:1:1.70775:60:4:0.0833:0:1 0/0:31:0:0,0:20,11:0:2,0:26.2:1:29.8:1:1:0:60:14.5:1:0:0.2 -2 191848434 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49875;SOR=Inf;LSEQ=CCGCTCGGGAGCTGGCTGAC;RSEQ=TTGGAGATCACCACAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:30.6:1:30.9:1:1:0:60:50:1:0:0.1 0/1:32:2:1,1:14,16:0.0625:2,2:31:1:32:1:1:1.14:60:4:0.0625:0:1 -2 191851586 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51607;SOR=0;LSEQ=ACTGATGTCCCTACCAGGTG;RSEQ=CGAAATTCAGCCGCCAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:23,11:0.0556:2,2:31:1:29.5:1:1:2.045:60:4:0.0588:0:1 0/0:23:0:0,0:15,8:0:2,0:23.8:1:31.9:1:1:0:60:46:1:0:0 -2 191869163 . G A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0829;SOR=1.3436;LSEQ=GGAAGGGGGTCCTTTCCAAT;RSEQ=GAGTGAGCAGTTGTCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:82:46,36:172,167:0.1943:2,2:24.2:1:29.2:1:0.39192:1.24:60:81:0.1938:0:1.1 0/1:433:106:53,53:164,163:0.2448:2,2:28.9:1:29.4:1:1:1.00612:60:212:0.2465:0:1.1 -2 192745796 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55388;SOR=0;LSEQ=GTACAAAAGCCCTCCCTGGG;RSEQ=CCTCCCACCCTCTCATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:2,1:246,9:0.0116:1,2:9.7:1:22.3:1:0.11225:13.24082:60:2:0.0079:0:2.3 0/0:126:0:0,0:117,8:0:2,0:24.1:1:31.7:1:1:0:59.7:40.667:0.9919:0:0.1 -2 192746182 . G A 324 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06425;LSEQ=CAGAACCATCTCTCTTAAAG;RSEQ=TATTGTGTGGCTTGTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1722:1715:943,772:0,0:0.9959:0,2:25.3:1:30.2:1:1:0:57.8:52.594:0.9976:0:1.1 1/1:1607:1511:861,650:47,44:0.9403:2,2:25:1:29:1:0.32862:1.24:57.4:47.742:0.9415:0:1.1 -2 192746735 . T C 319 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09106;LSEQ=TTAGGGCTTCCTCCCGGTAG;RSEQ=GGTCGAAGATCTCGCGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1304:1296:706,590:1,4:0.9939:2,2:24.6:1:30.9:1:0.18453:4.78:60:63.8:0.9961:0:1.1 1/1:1086:1017:579,438:37,31:0.9365:2,2:23.7:1:30.8:1:0.70575:1.11:59.9:112:0.9377:0:1.1 -2 193538630 . T C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08802;SOR=0.3259;LSEQ=ACTTGCTCTGATGGAGGCAG;RSEQ=CATTCTTGTGCAACATTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:34:34,0:24,0:0.5862:1,1:28.3:1:31.4:1:1:0:60:33:0.5789:0:1 0/1:16:5:5,0:11,0:0.3125:0,0:20.8:1:32.2:1:1:0:60:10:0.3125:0:1 -2 193538820 . C T 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0.65828;LSEQ=TCCTCCTAGAGTAACTGATA;RSEQ=CACACTATCTGCTTTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:772:359:182,177:197,216:0.465:2,2:26.7:1:30.1:1:0.42758:1.13:60:58.833:0.4626:0:1.1 0/1:742:270:134,136:237,232:0.3639:2,2:25.7:1:29.1:1:0.81918:1.03677:60:53:0.3615:0:1.2 -2 193538925 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18432;SOR=Inf;LSEQ=AGTTTTGTGGATGCTTTCTT;RSEQ=AGTAGGCATTCCAAACGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:25,191:0:2,0:24.7:1:28:1:1:0:59.9:53:1:0:0.2 0/1:163:2:1,1:21,140:0.0123:2,2:10:1:31.5:1:0.25244:6.54:60:4:0.0124:0:1 -2 193538931 . G A 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93956;LSEQ=GTGGATGCTTTCTTTAGTAG;RSEQ=CATTCCAAACGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:19,167:0.0159:2,2:19.7:1:29.3:1:0.28641:4.34:60:6:0.0167:0:1 0/1:134:2:1,1:13,119:0.0149:2,2:22:1:28:1:0.19874:8.86:60:4:0.0153:0:1 -2 193538936 . C A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5192;SOR=0;LSEQ=TGCTTTCTTTAGTAGGCATT;RSEQ=CAAACGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:15,163:0.0111:2,2:13.5:1:25.5:1:0.17033:10.55:60:4:0.0118:0:3.5 0/0:119:0:0,0:9,110:0:2,0:25.1:1:30.4:1:1:0:60:18.833:1:0:0.2 -2 193538963 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51328;SOR=0;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=CCGGTGCATCTGTTTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:0,2:3,104:0.0183:1,0:24:1:30:0:1:0:60:4:0.019:0:1 0/0:76:0:0,0:1,75:0:1,0:21.9:1:30.7:1:1:0:60:75:1:0:0.1 -2 193562102 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.5085;SOR=0;LSEQ=GGGTGAGGGAACAACATTTT;RSEQ=ATCAGGCTCAAAGAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:72,21:0.0211:2,2:17.5:1:27:1:0.41142:3.37286:60:4:0.0213:0:1 0/0:70:0:0,0:52,18:0:2,0:21.6:1:31:1:1:0:60:140:1:0:0 -2 193562104 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50931;SOR=0;LSEQ=GTGAGGGAACAACATTTTCA;RSEQ=CAGGCTCAAAGAATTATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:73,21:0.0208:2,2:27.5:1:32:1:0.40768:3.41935:60:4:0.0211:0:1 0/0:70:0:0,0:52,18:0:2,0:22.7:1:29.5:1:1:0:60:69:1:0:0 -2 193562208 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30555;LSEQ=ATACGTATTTATAATCTAAA;RSEQ=GACTGTTAAAAACAATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:95:43,52:31,42:0.5655:2,2:25.2:1:30.7:1:0.75546:1.12:60:190:0.5655:0:1.1 0/1:141:40:17,23:41,60:0.2837:2,2:26.8:1:29.3:1:0.85144:1.08:60:39:0.2806:0:1.2 -2 196859045 . C T 111 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=5e-05;SOR=19.221;LSEQ=AAAGATATCACTGATGCCTT;RSEQ=CTCCTCCCCAAGGCTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:1:1,0:306,159:0.0021:2,0:13:0:13:0:1:0:60:0:0:0:4 0/1:377:15:11,4:224,138:0.0398:2,2:21.8:1:28.6:1:0.42818:1.69:60:14:0.0375:0:1 -2 196859205 . G A 165 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.90475;LSEQ=GCCATAGAAATTGACCAATC;RSEQ=CCATGTCCTGTGTTGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:1:1,0:234,265:0.002:2,0:6:0:32:0:0.47:0:60:2:0.002:0:1 0/1:450:49:26,23:193,207:0.1089:2,2:25.2:1:29.5:1:0.54793:1.21:60:98:0.1104:0:1 -2 196860048 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21742;SOR=Inf;LSEQ=AGTTTTTCTGCCTTGTTCAA;RSEQ=TCCAAGACCCCATGGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:111,75:0:2,0:25.9:1:29.9:1:1:0:60:45.5:1:0:0.3 0/1:163:2:1,1:100,61:0.0123:2,2:43.5:1:31:1:1:1.63412:60:4:0.0124:0:1 -2 196860056 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21778;SOR=Inf;LSEQ=TGCCTTGTTCAAATCCAAGA;RSEQ=CCCATGGAGAGACTGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:114,74:0:2,0:26:1:31.3:1:1:0:60:93:1:0:0.3 0/1:165:2:1,1:104,59:0.0121:2,2:15.5:1:25:1:1:1.75626:60:4:0.0121:0:1 -2 196860059 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57615;LSEQ=CTTGTTCAAATCCAAGACCC;RSEQ=ATGGAGAGACTGGCTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:115,76:0.0104:2,2:37.5:1:29:1:1:1.50978:60:4:0.0106:0:1 0/0:167:1:1,0:104,62:0.006:2,0:1:0:25:0:1:0:60:2:0.0061:0:1 -2 196860081 . C A 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27494;SOR=0.76214;LSEQ=TGGAGAGACTGGCTCAGGAG;RSEQ=TGAATGAACTTCTTGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:53:31,22:82,65:0.2637:2,2:26.4:1:30:1:0.7496:1.12:60:52:0.2653:0:1.2 0/1:168:36:24,12:65,67:0.2143:2,2:24.1:1:27.9:1:0.08927:2.05:60:17:0.2073:0:1.1 -2 196860155 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20462;SOR=Inf;LSEQ=GAGGGAGATTTTTGGAGTTT;RSEQ=AGGACTATCTGGACTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:134,93:0:2,0:25.7:1:29.2:1:1:0:60:55.75:1:0:0.2 0/1:188:2:1,1:107,79:0.0106:2,2:31.5:1:30.5:1:1:1.3522:60:4:0.0108:0:1.5 -2 196860191 . T A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25331;SOR=0;LSEQ=TCATAGAGCAGCTCTTCTTT;RSEQ=GCCCTCAGGGGTTTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:3:2,1:161,106:0.0111:2,2:32.3:1:22.3:1:1:1.32:60:2:0.0075:0:1.7 0/0:230:0:0,0:141,89:0:2,0:22:0:11:0:1:0:60:0:0:0:6 -2 196860313 . G A 155 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=48.44129;LSEQ=CTGGCTCAGCAGGGGAAGAT;RSEQ=GGAGGCCAGCTAGAGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:1:1,0:123,206:0.003:2,0:1:0:23:0:0.37576:0:60:2:0.0031:0:1 0/1:326:42:16,26:112,172:0.1288:2,2:24.4:1:28.8:1:1:1.05797:60:20:0.1246:0:1 -2 196860410 . G T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.09245;LSEQ=ACTAGGGAGAGAAGATAAAG;RSEQ=GTGGTGGTGCTGGGCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:34:2,32:1,36:0.4789:1,2:25.4:1:30.5:1:0.60381:2.23:60:33:0.4714:0:1.1 0/1:39:3:0,3:1,35:0.0769:1,0:26.3:1:28:1:1:0:60:6:0.0769:0:1.3 -2 197719100 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22531;SOR=Inf;LSEQ=GTGATACTAGATCTTCTTTC;RSEQ=GTTATATTCATGTTATTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:23.1:1:30.2:1:1:0:60:25:1:0:0.1 0/1:24:2:1,1:9,13:0.0833:2,2:15.5:1:28:1:1:1.42:60:4:0.0833:0:1 -2 198244598 . G A 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23643;SOR=1.2299;LSEQ=TACAGAACTAGGTCCTTTTA;RSEQ=GTGTTTTAGGAGTTTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:89:50,39:183,115:0.23:2,2:21.8:1:30.5:1:0.38978:1.2405:55.3:88:0.2322:0:1.1 0/1:361:97:60,37:154,110:0.2687:2,2:26.2:1:30.2:1:0.62901:1.16:56.8:194:0.2694:0:1 -2 198244785 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4987;SOR=Inf;LSEQ=ATCAAAGTCATCATCATCAT;RSEQ=TTCATCATCGTGATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:71,112:0:2,0:26.2:1:32:1:1:0:60:182:1:0:0.1 0/1:187:2:1,1:81,104:0.0107:2,2:24.5:1:28:1:1:1.28:60:4:0.0108:0:1 -2 198244800 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49949;SOR=Inf;LSEQ=ATCATCTTCATCATCGTGAT;RSEQ=TTCGTCATCATCTTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:68,100:0:2,0:26.4:1:31.6:1:1:0:60:41:1:0:0.1 0/1:183:2:1,1:79,101:0.0109:2,2:32:1:27.5:1:1:1.28:60:4:0.0112:0:1 -2 198244885 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.87948;LSEQ=CAGACCACTTTCCTGATATA;RSEQ=GTAAGAGTTTCACATCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:0,1:63,51:0.0087:2,0:1:0:26:0:0.45217:0:60:2:0.009:0:1 0/1:123:2:1,1:69,52:0.0163:2,2:15:1:29:1:1:1.32382:60:4:0.0164:0:1 -2 198244927 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20858;SOR=0;LSEQ=CCTCTCATCTTCTGACTTTG;RSEQ=ATCTTCCTCCACAGCTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:120,71:0.0104:2,2:39:1:30:0:1:1.68527:60:4:0.0104:0:1 0/0:229:0:0,0:140,89:0:2,0:24.5:1:31.6:1:1:0:59.8:75.333:1:0:0.1 -2 198245064 . TTC T 30 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.61498;SOR=0.47499;LSEQ=GTACAGACATTTTCTTTTTT;RSEQ=TTTTCTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:0,2:35,71:0.0183:2,0:15.5:1:30.5:1:1:0:40:4:0.0196:0:1 0/0:114:1:0,1:27,86:0.0088:2,0:13:0:30:0:1:0:40:2:0.0093:0:2 -2 198245066 . C T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.803;SOR=0.83034;LSEQ=ACAGACATTTTCTTTTTTTT;RSEQ=TTTTCTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:9:0,9:35,60:0.0841:2,0:19.9:1:26.2:1:0.02699:0:44.9:3.5:0.0833:0:4.1 0/1:113:8:0,8:27,74:0.0708:2,0:15.9:1:21.9:1:0.19622:0:49.1:1.667:0.0495:0:3 -2 198245232 . C G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29945;SOR=0.27545;LSEQ=TACAGGCGCCCGCCACCATG;RSEQ=CTGGCTAATTTTTTTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:5,3:2,1:0.7273:2,2:25.3:1:31.3:1:1:1.18052:49.9:16:0.7273:0:1.6 0/1:5:2:2,0:1,2:0.4:2,0:25.5:1:33:0:0.4:0:43.5:4:0.5:0:1.5 -2 198245297 . G A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01684;SOR=0.10689;LSEQ=ATGTTAGCCAGGATGGTCTC;RSEQ=ATCTCCTGACCTTGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:12,0:4,0:0.75:0,0:31.2:1:29.9:1:1:0:56.8:11:0.7333:0:1.2 0/1:9:2:2,0:6,1:0.2222:2,0:21.5:1:27.5:1:1:0:50:4:0.25:0:1.5 -2 198245341 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49444;SOR=Inf;LSEQ=TGCCTCGGCTCGGCCTCCCA;RSEQ=AGTGCTGGGATTACAGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:34,4:0:2,0:22.6:1:31.9:1:1:0:59.4:76:1:0:0.4 0/1:42:2:1,1:34,6:0.0476:2,2:10:0:32:0:0.30894:5.323:60:4:0.0488:0:1 -2 198245413 . C A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12527;SOR=Inf;LSEQ=TGTTACTTTAATTGGACTGC;RSEQ=TTCATCATTCATGGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:103,48:0:2,0:22.2:1:31.2:1:1:0:59.6:150:0.9934:0:0.2 0/1:171:4:3,1:105,62:0.0234:2,2:28.3:1:24.8:1:1:1.77:60:3:0.0181:0:1.3 -2 198245464 . C A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24858;SOR=Inf;LSEQ=GTGCAGTTCATCCCTTGCAC;RSEQ=AGCCCCTAAACTGACCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:150,111:0:2,0:27.5:1:31.1:1:1:0:59.7:25.1:1:0:0.1 0/1:263:3:2,1:133,127:0.0114:2,2:29:1:30.3:1:1:1.91:60:6:0.0116:0:1 -2 198245481 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24919;SOR=0;LSEQ=CACCAGCCCCTAAACTGACC;RSEQ=TTCTTAAAGATAACTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:3:2,1:147,127:0.0108:2,2:22.7:1:28.7:1:1:1.72:56.3:6:0.0109:0:1 0/0:262:0:0,0:130,132:0:2,0:25.7:1:29.9:1:1:0:59.9:261:1:0:0.2 -2 198245588 . C T 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09734;SOR=Inf;LSEQ=AGTTCTGGGGCCTCAGGGGG;RSEQ=TCATGTCCATGTCCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:217,134:0:2,0:23.9:1:31.6:1:1:0:57.5:30.909:1:0:0.1 0/1:300:3:1,2:178,119:0.01:2,2:14.3:1:20:1:0.56732:2.98057:53.3:2:0.0068:0:3.3 -2 198245597 . A T 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.0497;SOR=Inf;LSEQ=GCCTCAGGGGGCTCATGTCC;RSEQ=TGTCCATTGAATCTTCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:232,152:0:2,0:23.5:1:30.3:1:1:0:57.7:127:1:0:0.1 0/1:345:4:1,3:202,138:0.0116:2,2:8.8:1:23:1:0.30923:4.37309:55:3:0.0089:0:2.8 -2 198245718 . C A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10834;SOR=0;LSEQ=GGAATCACACCAGGGATGTT;RSEQ=TGTATGCATTCTATCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:2,1:60,194:0.0117:2,2:19.3:1:26.7:1:0.1454:6.41:60:6:0.0119:0:2.3 0/0:281:0:0,0:78,202:0:2,0:22.6:1:31.1:1:1:0:60:39:1:0:0.1 -2 198245733 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49894;SOR=Inf;LSEQ=ATGTTCTGTATGCATTCTAT;RSEQ=CACATCCACAAGAGTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:17,162:0:2,0:24.5:1:31.7:1:1:0:60:88.5:1:0:0.1 0/1:188:2:1,1:33,153:0.0106:2,2:11:1:27.5:1:0.32979:4.58:60:4:0.0108:0:1 -2 198245734 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24109;SOR=0;LSEQ=TGTTCTGTATGCATTCTATC;RSEQ=ACATCCACAAGAGTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:16,160:0.0112:2,2:32.5:1:30:1:0.18238:9.73:60:4:0.0114:0:1.5 0/0:184:0:0,0:31,153:0:2,0:21.8:1:31.6:1:1:0:60:60.333:1:0:0.1 -2 198245740 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4984;SOR=0;LSEQ=GTATGCATTCTATCCACATC;RSEQ=ACAAGAGTTCAAATATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:10,145:0.0127:2,2:25:1:28.5:1:0.13564:13.87:60:4:0.0128:0:1 0/0:156:0:0,0:18,138:0:2,0:21.6:1:31.4:1:1:0:60:155:1:0:0.1 -2 198245965 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGAGGTGGGAGGATCACC;RSEQ=GACCAAGCCCAGGAGGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:20.5:1:31:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 198257008 . C G 214 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGAAGTAGCTGTGCATTAAA;RSEQ=ACAAAATAAACAATAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:110:80,30:120,54:0.3873:2,2:25.2:1:31.7:1:0.59362:1.20:60:220:0.3873:0:1.2 0/0:247:0:0,0:164,83:0:2,0:24.4:1:31.3:1:1:0:60:494:1:0:0.1 -2 198257075 . G A 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATAGGTGTTCTTATCATC;RSEQ=TTGTAGATTCTTGGGTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:623:0:0,0:356,267:0:2,0:26.3:1:30.6:1:1:0:60:102.833:1:0:0.2 0/1:571:29:17,12:303,237:0.0508:2,2:30.8:1:30.5:1:0.84947:1.11:60:58:0.0511:0:1.1 -2 198257294 . T TG 93 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00322;SOR=6.36146;LSEQ=AATTATTTCCCTTGGGGAGT;RSEQ=GGGGGGGGGGGAACCTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:4:0,4:4,20:0.1026:2,0:33.8:1:20:1:1:0:60:1:0.0606:0:0.8 0/1:28:12:0,12:1,14:0.4286:1,0:31.3:1:26.2:1:1:0:58.3:11:0.4583:0.0714:3.7 -2 198257299 . G GGC 45 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.07749;SOR=Inf;LSEQ=TTTCCCTTGGGGAGTTGGGG;RSEQ=GGGGGGAACCTACTAATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:5,34:0:2,0:20.5:1:30.9:1:1:0:58.1:78:1:0:1.5 0/1:30:3:0,3:1,26:0.1:1,0:7:1:29:1:1:0:60:6:0.1111:0.0667:0.7 -2 198257652 . T TA 195 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.00186;SOR=0.54137;LSEQ=CCAGAACTTAAAGTATTATT;RSEQ=AAAAAAAAAAAATCACCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:216:121:107,14:65,7:0.5602:2,2:24.7:1:28.3:1:0.81305:1.21374:60:39.333:0.5813:0.0694:0.6 0/1:206:84:72,12:83,18:0.4078:2,2:22.8:1:28.3:1:0.55362:1.30:59.8:83:0.4171:0.068:0.5 -2 198257673 . TA T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.13519;SOR=1.84945;LSEQ=AAAAAAAAAAAATCACCGAT;RSEQ=AAAAAAAAATCTTTAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:11:9,2:279,79:0.0297:2,2:19.2:1:31.1:1:1:1.27:60:22:0.0305:0.0108:0.3 0/1:354:19:12,7:238,97:0.0537:2,2:27:1:28.6:1:0.44786:1.42973:59.5:38:0.0544:0.0056:0.9 -2 198257795 . T C 310 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35236;LSEQ=ACATGAGGAGATGTCTCAAA;RSEQ=ACATTGGGCCATACATAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:964:813:422,391:77,74:0.8434:2,2:23.7:1:32.1:1:0.85953:1.04:60:115.143:0.8431:0:1.1 1/0:976:639:350,289:178,157:0.6547:2,2:24.7:1:31.2:1:0.63609:1.07:60:158.75:0.6567:0:1.1 -2 198258179 . C CT 49 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCATATTTTCTAATTAA;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:34.7:1:31:1:1:0:60:6:0.4286:0:0.3 0/0:1:0:0,0:0,1:0:0,0:6:0:34:0:1:0:60:2:1:0:1 -2 198260098 . A T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTATTAATGAATAACTT;RSEQ=AATCTGTACACAAAAGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 198261055 . G GA 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.12906;SOR=0;LSEQ=GCCAATACATCATGAGGGCT;RSEQ=AAAAAAACAAATGGGTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:4:3,1:90,256:0.0114:2,2:15.8:1:27.5:1:0.05901:8.47:60:8:0.0116:0.0057:0.5 0/0:297:0:0,0:74,223:0:2,0:23.7:1:31.1:1:1:0:60:296:1:0:0.1 -2 198262599 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50533;SOR=0;LSEQ=ATGAAGAGCTTTCTCAACTG;RSEQ=ATTATTCAGACCATGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:2,0:74,0:0.0263:1,0:39:1:30.5:1:1:0:60:4:0.0274:0:1 0/0:58:0:0,0:58,0:0:1,0:30.2:1:31.8:1:1:0:60:28:1:0:0.2 -2 198262606 . C G 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25562;SOR=0;LSEQ=GCTTTCTCAACTGCATTATT;RSEQ=AGACCATGCCTCAAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:3:3,0:82,0:0.0353:1,0:21:1:33:1:1:0:60:6:0.0357:0:3.3 0/0:67:0:0,0:66,0:0:1,0:28.4:1:30.8:1:1:0:60:32:1:0:0.1 -2 198262677 . A AT 111 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.01083;SOR=0.21846;LSEQ=AATGCATTTATTATAAAGTA;RSEQ=TTTTTTTTTAATGGAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:13:9,4:242,83:0.0385:2,2:18.9:1:30.1:1:0.74693:1.2948:59.6:26:0.0387:0.0089:0.5 0/0:347:3:2,1:229,111:0.0086:2,2:33.7:1:28.3:1:1:1.03147:60:6:0.0087:0:0.7 -2 198263146 . T C 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71401;SOR=1.06382;LSEQ=AAAGTGGCCAAATTTGAAAA;RSEQ=TGATACTGCTTATAAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:115:73,42:221,115:0.255:2,2:25.2:1:32.1:1:0.65203:1.10541:60:114:0.2533:0:1.1 0/1:517:138:83,55:237,142:0.2669:2,2:24.1:1:31.3:1:0.6823:1.10575:60:276:0.2685:0:1.1 -2 198264715 . G GA 138 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00804;SOR=2.49801;LSEQ=CTAAATAAGATTTTACTTAC;RSEQ=AAAAAAAAAAGAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:13:13,0:218,22:0.0512:2,1:28.5:1:31.3:1:0.61176:0:58.5:26:0.0522:0.0079:0.5 0/1:227:27:21,6:180,19:0.1189:2,2:22.4:1:29.1:1:0.09239:2.6911:60:54:0.1205:0.0044:0.1 -2 198264903 . AAAT A 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.44669;SOR=1.11515;LSEQ=AATTTTTCCTATAATAAAAC;RSEQ=AATGTTAAAATGTTACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:125:39,86:165,279:0.2197:2,2:27.2:1:30.3:1:0.24597:1.30351:60:124:0.2206:0.0299:0.1 0/1:611:146:69,77:188,277:0.239:2,2:26.1:1:29.6:1:0.15053:1.32:60:72:0.2384:0.0262:0.1 -2 198265167 . T A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1009;SOR=0;LSEQ=CATTACTGAGTCCTAAAAAA;RSEQ=AAATTTAAAAAAAAGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:81,194:0.0108:2,2:5.7:1:21.3:1:0.21327:4.76:60:2:0.0073:0:2.7 0/0:318:0:0,0:98,220:0:2,0:22.7:1:28.4:1:1:0:60:52:1:0:0.7 -2 198265170 . AT A 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.72833;SOR=1.49016;LSEQ=TACTGAGTCCTAAAAAATAA;RSEQ=TTAAAAAAAAGACATATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:0,3:71,184:0.0116:2,0:28.3:1:33:0:0.56354:0:60:6:0.0119:0:0 0/1:290:5:2,3:83,202:0.0172:2,2:30.6:1:29.2:1:0.63214:1.62:60:10:0.0175:0.0034:0.2 -2 198265173 . T A 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=4e-05;SOR=0.4132;LSEQ=TGAGTCCTAAAAAATAAATT;RSEQ=AAAAAAAAGACATATTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:247:208:59,149:5,27:0.8421:2,2:21.4:1:29.5:1:0.19606:2.13:60:33.667:0.8632:0:1.2 1/0:272:187:57,130:22,61:0.6875:2,2:22.1:1:29.5:1:0.56352:1.21:60:186:0.6966:0:1.1 -2 198265247 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55251;SOR=0;LSEQ=AGTCAACCTTTTCTAACCAC;RSEQ=CAAACATCTGTTGCTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:0,2:28,68:0.0204:2,0:14.5:1:30.5:1:1:0:60:4:0.0213:0:1.5 0/0:49:0:0,0:13,36:0:2,0:21.7:1:30.4:1:1:0:60:23.5:1:0:0.4 -2 198265350 . T C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.58802;LSEQ=AAAAATTACTTCAAATTCAA;RSEQ=TGCATTCTAGAAAAATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:15:14,1:134,20:0.0888:2,1:25.8:1:30.5:1:0.69674:2.08:60:14:0.0843:0:1.2 0/1:130:46:42,4:74,10:0.3538:2,2:17.1:1:31.3:1:0.76918:1.42:60:92:0.3538:0:1 -2 198265526 . A G 306 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41521;LSEQ=ATATCTGCTGCTCCCAAATT;RSEQ=CCCATAATTTTCTCAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:867:750:374,376:60,56:0.8651:2,2:25.4:1:32.1:1:0.7649:1.07704:60:124:0.8681:0:1.1 1/0:970:705:367,338:138,126:0.7268:2,2:26.9:1:31.6:1:1:1.00869:60:63.091:0.7244:0:1.1 -2 198265952 . CA C 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14086;SOR=0;LSEQ=TAAGTATTAATCCTCGAATC;RSEQ=AAATCAAAATGGAAGTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:5,0:17,7:0.1724:2,0:34.2:1:32.2:1:0.29649:0:60:10:0.1724:0:0 0/0:18:0:0,0:17,1:0:1,0:22.2:1:31.1:1:1:0:60:36:1:0:0.2 -2 198266043 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2193;SOR=Inf;LSEQ=GAGATAATCAAGGCAAAAAA;RSEQ=AATATACAACATGCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:111,19:0:2,0:22.5:1:30.4:1:1:0:60:42.333:1:0:0.1 0/1:115:2:1,1:89,24:0.0174:2,2:26.5:1:31:1:0.38902:3.65411:60:4:0.018:0:1.5 -2 198266602 . G A 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=ACCCAATAGCCTTCAAGAAA;RSEQ=CAGCCAAACCCTATTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:38:18,20:201,279:0.0731:2,2:22.4:1:30.3:1:0.60933:1.25:60:76:0.0738:0:1.1 0/0:506:0:0,0:230,275:0:2,0:24.1:1:31.9:1:1:0:60:100:1:0:0.1 -2 198266943 . C T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45926;SOR=0;LSEQ=CTCTCAATATATCAACTATT;RSEQ=AGCCAAACTGCAGAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:146:146:6,140:0,0:1:0,1:25.6:1:28.7:1:1:0:60:145:1:0:1.1 1/1:124:123:5,118:0,0:0.9919:0,1:23.3:1:28.5:1:1:0:60:122:0.9919:0:1.1 -2 198267770 . G GAA 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=2e-04;SOR=0.52926;LSEQ=CCACGAGGATCTGAAAAAGA;RSEQ=AAAAGAGAAGAAGCTACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:310:242:89,153:29,39:0.7806:2,2:26.6:1:30:1:0.39856:1.27725:60:484:0.7857:0.1161:0.2 1/0:415:271:111,160:62,80:0.653:2,2:27:1:29.4:1:0.60139:1.11681:59.9:66.75:0.6544:0.0916:0.1 -2 198267791 . T A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1377;SOR=Inf;LSEQ=AAAAGAGAAGAAGCTACACT;RSEQ=TCACATCAATTACTGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:70,160:0:2,0:23.2:1:29.6:1:1:0:60:37.333:1:0:0.1 0/1:303:4:2,2:105,194:0.0132:2,2:8.3:1:23:1:0.61594:1.84:60:3:0.0101:0:2.8 -2 198269717 . A T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10787;SOR=0;LSEQ=AGCCTGGGCAACATGGCAAA;RSEQ=CCCTGTCTCTACAAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:3:1,2:253,33:0.0104:2,2:8.3:1:21.3:1:0.0396:15.05367:60:2:0.007:0:1.7 0/0:317:0:0,0:250,67:0:2,0:19.6:1:29.5:1:1:0:60:157.5:1:0:0.1 -2 198272802 . G A 100 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00195;SOR=12.16294;LSEQ=ATCAATTTCTCTTTCCCACC;RSEQ=CCAAGCCTGAAGCTGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:737:1:1,0:292,444:0.0014:2,0:1:0:26:0:0.39756:0:60:2:0.0014:0:1 0/1:799:13:9,4:333,452:0.0163:2,2:14.3:1:27.2:1:0.08621:3.05:60:26:0.0166:0:1.1 -2 198273027 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19072;SOR=Inf;LSEQ=CATTAATAGTACACAGAATA;RSEQ=CACAAAGGAAAAAATTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:197,50:0:2,0:22.9:1:31.7:1:1:0:60:81.333:1:0:0.1 0/1:192:2:1,1:156,33:0.0104:2,2:9.5:1:29.5:1:0.3251:4.67217:60:4:0.0106:0:1 -2 198273347 . T C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19918;SOR=1.33457;LSEQ=AAAACCACAATTTTAATCAC;RSEQ=GTTAAAATAATATTCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:59:5,54:27,158:0.2408:2,2:20.8:1:30.1:1:0.27335:1.84149:60:118:0.2438:0:1.1 0/1:205:61:14,47:26,117:0.2976:2,2:21.6:1:29.2:1:0.44545:1.34:60:60:0.2941:0:1.2 -2 198273591 . C T 45 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGGGAGGCAGAGGTTGCAGT;RSEQ=AGCCGAGAGCGCACCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:20.7:1:28.7:1:1:0:60:6:0.6:0:1 0/0:2:0:0,0:0,2:0:0,0:37.5:1:33:1:1:0:60:4:1:0:0 -2 198274299 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.20538;SOR=Inf;LSEQ=TACTAACTTTACTTTTACCT;RSEQ=AGGTTCTTCCTTAAATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:0:1,0:22.2:1:27.8:1:1:0:60:37:1:0:0.1 0/1:32:2:1,1:27,3:0.0625:2,2:44.5:1:32:1:0.2379:7.93681:60:4:0.0667:0:1.5 -2 198274742 . C CA 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04252;SOR=Inf;LSEQ=GCCCAGGGGTCTTAAAAAAG;RSEQ=AAAAAAATTTTATTTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:76,254:0:2,0:24.8:1:32.1:1:1:0:60:65:1:0:0.1 0/1:276:4:2,2:83,189:0.0145:2,2:10.5:1:29.4:1:0.58925:2.27:60:8:0.015:0.0072:0.3 -2 198274758 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.18394;SOR=Inf;LSEQ=AAAGCAAAAAAATTTTATTT;RSEQ=ACACACCCACACAGAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:39,220:0:2,0:23.5:1:32:1:1:0:60:85.333:1:0:0.1 0/1:195:2:1,1:41,152:0.0103:2,2:39:1:29.5:1:0.38525:3.68:60:4:0.0105:0:1 -2 198274929 . G A 66 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.8165;LSEQ=ATGATTAAAAACAATGTAAA;RSEQ=TTTCAATCCGAAGCACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:16:1:28.6:1:1:0:60:4:0.5:0:2.4 1/0:2:1:0,1:0,1:0.5:0,0:17:0:32:0:1:0:60:2:0.5:0:1 -2 198281743 . T C 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07148;SOR=0.39651;LSEQ=TTTATACTTTGCTCATTCTC;RSEQ=TTTCTATGTACTGGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:42:0,42:0,9:0.8235:0,1:21.8:1:31.6:1:1:0:60:20:0.8163:0:1.5 1/0:51:33:0,33:0,18:0.6471:1,1:25.5:1:32.8:1:1:0:60:66:0.6471:0:1.5 -2 198281776 . C A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5293;SOR=0.59869;LSEQ=GGTGATCTCCTTTCTACGCT;RSEQ=GCTGGTTCCATAGTCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:19:0,19:0,6:0.76:0,1:24.6:1:31.4:1:1:0:60:18:0.7826:0:1.9 1/0:23:15:0,15:0,8:0.6522:0,1:18.5:1:32.4:1:1:0:60:30:0.6522:0:2 -2 198283305 . T C 296 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.32267;LSEQ=TTCATTTTAGGATCAGGGGT;RSEQ=TTCCCTCCTGCAGAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:767:669:270,399:43,55:0.8722:2,2:25.4:1:31.6:1:0.51116:1.15513:60:65.9:0.8728:0:1.1 1/0:669:460:202,258:89,120:0.6876:2,2:24.7:1:31.2:1:0.80081:1.06:60:64.714:0.6895:0:1.1 -2 198283516 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1888;SOR=Inf;LSEQ=TTTGAACACAAACATCTACA;RSEQ=CAGTTTAAAACAAATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:112,24:0:2,0:24.4:1:32.5:1:1:0:60:272:1:0:0.1 0/1:105:2:1,1:95,8:0.019:2,2:22.5:1:25.5:1:0.16484:11.25491:60:4:0.0194:0:1 -2 198285074 . C CA 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.7622;SOR=0.70635;LSEQ=AAGCAAATTCAGAAGCATGC;RSEQ=AAAAAAAATCAAAGGGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:6:4,2:220,95:0.0186:2,2:29.5:1:30.5:1:1:1.15734:60:12:0.019:0.0031:0.2 0/1:378:5:2,3:251,122:0.0132:2,2:22.4:1:29.2:1:0.3372:3.07597:60:10:0.0135:0.0026:0 -2 198285554 . C G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28421;SOR=0.14853;LSEQ=GAGGTTGAGACAGGAGGAAT;RSEQ=CTTGAGCCCAGGAGTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:8,8:0,1:0.9412:0,2:25.4:1:33:1:1:0:60:32:0.9412:0:1.3 1/0:3:2:2,0:1,0:0.6667:0,0:27:1:34:0:1:0:60:4:0.6667:0:1 -2 198285583 . G C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25296;SOR=0;LSEQ=CAGGAGTTTGGGATCAGCCT;RSEQ=AGCAAGACAGCAAAACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:7,4:0.2143:2,0:39.7:1:32:1:0.50549:0:60:6:0.2143:0:2.3 0/0:9:0:0,0:8,1:0:2,0:16.6:1:32:1:1:0:60:18:1:0:0.2 -2 198285697 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18712;SOR=Inf;LSEQ=TTATGGATTTCTATGGGAAC;RSEQ=CAGACATTCACTTTTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:139,23:0:2,0:24.3:1:30.7:1:1:0:60:26:1:0:0.1 0/1:124:2:1,1:99,23:0.0161:2,2:33:1:29.5:1:0.3509:4.23495:60:4:0.0161:0:1 -2 198285744 . A C 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAACTATGCTTTTAAAATG;RSEQ=AAGATCACCTGTTCTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:222,80:0:2,0:24.7:1:30:1:1:0:60:99.667:0.9967:0:0.1 0/1:302:37:27,10:178,86:0.1225:2,2:21.8:1:32.5:1:0.57509:1.30:60:74:0.1237:0:1.1 -2 198286004 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18733;SOR=Inf;LSEQ=TAAAACTTAGAAACACAATT;RSEQ=GTCTTCTTTCACTTCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:0,57:0:1,0:22.2:1:31.2:1:1:0:60:114:1:0:0.1 0/1:44:2:1,1:1,41:0.0455:1,2:33:1:28.5:1:0.08985:29.33:60:4:0.0465:0:1 -2 198288213 . T C 53 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACAGATGGCTATTTACAA;RSEQ=TAAGTCACTTCTCACACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:9.5:1:26.8:1:1:0:60:3:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 198288753 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21544;SOR=Inf;LSEQ=CTTTCCAAAAGAACTCCCAA;RSEQ=ACAATGCATTTCTTTACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:17,211:0:2,0:23.9:1:32.3:1:1:0:60:456:1:0:0.1 0/1:198:2:1,1:23,173:0.0101:2,2:8:1:28:1:0.22827:7.39:60:4:0.0103:0:1 -2 198299579 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49808;SOR=Inf;LSEQ=GAGGAGACGACCCTTGGCCC;RSEQ=GAAACGCGGGCTCAGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:69,3:0:1,0:24.8:1:31.7:1:1:0:60:144:1:0:0 0/1:80:2:1,1:69,9:0.025:2,2:15.5:1:28.5:1:0.23576:7.32689:60:4:0.025:0:1 -2 198299594 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19103;SOR=0;LSEQ=GGCCCCGAAACGCGGGCTCA;RSEQ=CTCCTACGAAAGAAACCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:78,16:0.0208:2,2:14:1:29:1:0.32434:4.75972:60:4:0.0215:0:1 0/0:123:0:0,0:97,26:0:2,0:20.3:1:31.5:1:1:0:60:122:1:0:0.1 -2 198299672 . C T 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08707;SOR=Inf;LSEQ=GGCTAGCAACGAAGAAAACA;RSEQ=GTAAGCAGGGAAAGACCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:214,151:0:2,0:26.3:1:31.1:1:1:0:60:90.25:1:0:0.1 0/1:571:6:2,4:316,249:0.0105:2,2:17:1:28.2:1:0.41372:2.53409:60:12:0.0106:0:1 -2 198299785 . G A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.67057;SOR=0.59442;LSEQ=AACTTCCGCTCGTCGCCGCC;RSEQ=CCACGGAGAAAAATAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:3:2,1:41,145:0.0158:2,2:15.3:1:28.7:1:0.13019:6.98:60:6:0.016:0:1.3 0/0:212:2:2,0:64,146:0.0094:2,0:1:0:26.5:1:0.0959:0:60:4:0.0097:0:1 -2 198299792 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24052;SOR=0;LSEQ=GCTCGTCGCCGCCGCCACGG;RSEQ=GAAAAATAGCTGGGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:29,136:0.012:2,2:18.5:1:29.5:1:0.3279:4.63:60:4:0.0121:0:1 0/0:173:0:0,0:45,128:0:2,0:24.6:1:29.9:1:1:0:60:56.667:1:0:0.1 -2 198299819 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49987;SOR=Inf;LSEQ=TAGCTGGGGGCTGCACTCTG;RSEQ=GCGTGCGCCAAACGGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:10,72:0:2,0:25:1:30.3:1:1:0:60:81:1:0:0.1 0/1:95:2:1,1:13,80:0.0211:2,2:14:1:30.5:1:0.27436:5.97:60:4:0.0215:0:1 -2 199565710 . AT A 69 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCCAAGGAATGTCAAGG;RSEQ=TTGCCAGAGCCACCAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:32.8:1:31.8:1:1:0:60:10:1:0.2:0.2 1/1:5:5:0,5:0,0:1:0,0:21.8:1:30:1:1:0:60:10:1:0:0 -2 200019363 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGGCCAAGATGGCCGA;RSEQ=TAGAAGAAGGGGCGTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:26.5:1:30.5:1:1:1.41:60:4:0.2857:0:1.5 0/0:1:0:0,0:1,0:0:0,0:24:0:32:0:1:0:60:2:1:0:0 -2 200020274 . T C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51049;SOR=0.24443;LSEQ=CTATACAGGAGCAATCCTAC;RSEQ=GGCATCAGGTTGGTGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:3,4:1,0:0.875:0,2:20.7:1:30.9:1:1:0:60:14:0.875:0:1 1/0:5:3:3,0:1,1:0.6:2,0:15.7:1:31.7:1:0.4:0:60:6:0.6:0:1 -2 200020501 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52425;SOR=Inf;LSEQ=ACAACACCAACAACAAAAAT;RSEQ=GGGCCCCCACAAAAACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:25.9:1:28.8:1:1:0:60:10:1:0:0.3 0/1:37:2:1,1:15,20:0.0541:2,2:8:0:32:1:1:1.32:60:4:0.0541:0:1.5 -2 202082459 . T A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96767;LSEQ=TGCCCCTGGATGCACTTTCA;RSEQ=TATAGCAGAGAGTTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:5,6:3,6:0.55:2,2:17.2:1:31.6:1:0.66992:1.62:60:22:0.55:0:1.1 1/0:24:13:5,8:4,7:0.5417:2,2:23.3:1:28.8:1:1:1.09:60:12:0.5217:0:1.2 -2 202122901 . G GT 77 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.1706;SOR=0.3414;LSEQ=CTCCTCCTTTTATCTTTTGT;RSEQ=TTTTTTTTCAAGCCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:6:4,2:234,66:0.0196:2,2:19.7:1:30:1:0.61782:1.76892:60:12:0.0199:0.0098:0.3 0/0:443:3:2,1:341,95:0.0068:2,2:18.7:1:29.7:1:0.52395:1.79197:60:6:0.0068:0.0023:0 -2 202122995 . A G 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.20991;LSEQ=CAGGGTGGTTATTGAAAGTA;RSEQ=AAGAAACTTCTTCCTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:800:640:313,327:79,79:0.8:2,2:26.2:1:31.6:1:0.85903:1.04469:60:90.429:0.8013:0:1.2 0/1:1245:568:269,299:329,348:0.4562:2,2:25.7:1:31.2:1:0.69026:1.05076:60:80.143:0.4554:0:1.2 -2 202129706 . G T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAACATGATCGCAGTGGG;RSEQ=TGGGAGTAGGGGATGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29.5:1:1:0:60:4:1:0:2.5 -2 202130133 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGAAAACTAAATACCGTA;RSEQ=GTTCTCACTTAAAAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:31.5:1:1:0:60:4:1:0:1 -2 202131130 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18871;SOR=0;LSEQ=AGTAGCCTTTGATGAACAAG;RSEQ=CAGCAAATGGTACTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:110,16:0.0156:2,2:13:1:30:1:0.24889:6.7009:60:4:0.0159:0:1 0/0:166:0:0,0:132,33:0:2,0:24.6:1:31.5:1:1:0:60:40.25:1:0:0.1 -2 202131541 . T A 35 v4;q23;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11334;SOR=0;LSEQ=GGAAACTCCCATTGTGGGAC;RSEQ=GGGAGGTGTGGGTTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:3,0:36,158:0.0152:2,0:9.7:1:22.7:1:0.00728:0:60:2:0.0103:0:2 0/0:209:0:0,0:51,158:0:2,0:25.6:1:29.6:1:1:0:60:51.25:1:0:0.2 -2 202131587 . T G 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=CTCTGAGCTGATTGGGGCTT;RSEQ=TTTTTGTGGTACCCTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:5,88:0:2,0:25.8:1:30.5:1:1:0:60:92:1:0:0.1 0/1:87:11:0,11:5,71:0.1264:2,0:25.5:1:30.5:1:1:0:60:22:0.1279:0:1 -2 202134144 . G T 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TAAGGCACTTATTCATTAAG;RSEQ=CGCCAGTTAGTCCTAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:154,43:0:2,0:21.6:1:31.2:1:1:0:60:48.25:1:0:0.1 0/1:217:30:21,9:141,46:0.1382:2,2:22.4:1:28.4:1:0.50606:1.31195:60:29:0.1362:0:1.1 -2 202136014 . G T 86 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.81547;LSEQ=TGAAATAAACTGAAAGAAAA;RSEQ=TTGATAGAACTTTAAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:6,1:17,0:0.2917:1,2:28.6:1:30.7:1:0.29167:0:60:14:0.2917:0:1.1 0/1:4:1:1,0:3,0:0.25:0,0:45:0:31:0:1:0:60:2:0.25:0:1 -2 202136190 . G T 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.25206;LSEQ=TGACTCCATATATCAAATGG;RSEQ=AAATTATTTGGGAAAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:2:0,2:176,67:0.0082:2,0:2.5:1:23.5:1:0.07849:0:60:4:0.0083:0:1 0/1:294:3:1,2:217,74:0.0102:2,2:9.3:1:20.3:1:0.16497:5.82179:60:2:0.0069:0:2 -2 202136272 . C T 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=11.47842;LSEQ=CAGATTTCAGAAGAAGTGAG;RSEQ=AGATCAGAATTGAGGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:2:1,1:352,334:0.0029:2,2:13.5:1:28:1:1:1.05383:60:4:0.0029:0:1 0/1:864:28:14,14:449,385:0.0324:2,2:23.9:1:28.7:1:0.70446:1.16602:60:56:0.0327:0:1.1 -2 202136398 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.4987;SOR=Inf;LSEQ=GAGACTTGGTTAGCCAGGGG;RSEQ=CATTTCTGAGACCAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:27,159:0:2,0:23.3:1:32:1:1:0:60:61:1:0:0 0/1:189:2:1,1:28,159:0.0106:2,2:23.5:1:28:0:0.28403:5.60:60:4:0.0108:0:1 -2 202136547 . CAG C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.125;SOR=Inf;LSEQ=GTTAATTATTGGGAGCAAGG;RSEQ=AGTCAGAGGCCGGGAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:0:0,0:21.8:1:32.3:1:1:0:60:20:1:0:0 0/1:6:2:0,2:0,4:0.3333:0,0:41:1:30:1:1:0:60:4:0.3333:0:0 -2 202137288 . TA T 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.51046;SOR=1.4074;LSEQ=TGGTTGGAGAAATTGGAAAT;RSEQ=AAAAAAAAAATCTAATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:9:8,1:73,14:0.0938:2,2:18:1:30.6:1:1:1.53:60:18:0.0947:0.0208:0.1 0/1:110:14:12,2:74,20:0.1273:2,2:17.8:1:29.4:1:0.73039:1.62:60:28:0.1296:0.0455:0.1 -2 202137321 . G T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26587;SOR=Inf;LSEQ=CTAATCTAAAAACCAGTAGG;RSEQ=CTCAATCCAGATTCCCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:124,40:0:2,0:25.7:1:31:1:1:0:60:22.429:1:0:0.2 0/1:225:3:1,2:157,65:0.0133:2,2:8.7:1:20.3:1:0.21207:4.79227:60:2:0.0091:0:1.3 -2 202139528 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49893;SOR=Inf;LSEQ=CATCTTAAAAAAGACCTTAT;RSEQ=TTGTCCTATGTGCTACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:168,24:0:2,0:24.5:1:32.2:1:1:0:60:95:1:0:0.1 0/1:201:2:1,1:166,33:0.01:2,2:9.5:1:32:0:0.3104:4.97082:60:4:0.01:0:2 -2 202139698 . CT C 88 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.78232;SOR=0.83213;LSEQ=TAGACGGAAACCTCCAAATC;RSEQ=TTTTTTTACATTACAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:543:6:4,2:187,349:0.011:2,2:29.3:1:31:1:0.19144:3.72:60:12:0.0114:0.0018:0.2 0/0:760:7:3,4:300,453:0.0092:2,2:26.4:1:31.6:1:1:1.13:60:14:0.0095:0:1.1 -2 202141718 . T A 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25057;SOR=Inf;LSEQ=TAGAACCCAAAAGAGAAAAG;RSEQ=AAAATATTTCTTATGCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:42,163:0:2,0:23.7:1:27.9:1:1:0:60:24.625:1:0:0.1 0/1:229:3:2,1:57,169:0.0131:2,2:16:1:20:1:0.16371:5.87:60:2:0.009:0:2.3 -2 202141737 . AT A 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10357;SOR=3.98107;LSEQ=GTAAAATATTTCTTATGCCT;RSEQ=TTTTTTTTAAATCAAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:0,2:16,110:0.0156:2,0:36:1:32:1:1:0:60:4:0.0163:0:0 0/1:134:8:1,7:25,100:0.0597:2,2:20.6:1:29.4:1:1:1.74368:60:16:0.062:0.0075:0.1 -2 202146409 . TTG T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=0.2308;SOR=Inf;LSEQ=TCTTTTATTCAAAAATTGTT;RSEQ=TTTTTTTCTGATTATGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:72,1:0:1,0:24.2:1:30:1:1:0:60:23.333:1:0:0.1 0/1:68:2:2,0:66,0:0.0294:1,0:42:1:28.5:1:1:0:60:4:0.0299:0:0 -2 202146653 . ATTC A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37659;SOR=3.59123;LSEQ=CTCTTGAATTTCTGGTTCAA;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:1:0,1:73,133:0.0046:2,0:33:0:32:0:1:0:60:2:0.0051:0:2 0/1:244:4:0,4:79,156:0.0164:2,0:42.3:1:28.3:1:0.30513:0:60:8:0.0185:0:2 -2 202146679 . A T 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10695;SOR=3.70125;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=TTGATCATTCTTGGGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:0,2:1,68:0.0282:1,0:21:1:30.5:1:1:0:40:4:0.0294:0:1 0/1:82:8:6,2:1,71:0.0976:1,2:8:1:21.3:1:0:158.98:60:1.667:0.0714:0:2.4 -2 202149392 . G GAGA 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05047;SOR=0.3039;LSEQ=CATGAGAGGGAGAGGGAGAC;RSEQ=GGGAGAGGGAGAGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:15,0:9,0:0.6:0,1:16.3:1:27.6:1:1:0:56.5:14:0.6364:0.04:0.9 0/1:26:8:8,0:13,0:0.3077:1,0:12.9:1:27.1:1:1:0:55:7:0.28:0.1154:0.3 -2 202149406 . G GGAGAC 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05099;SOR=2.84201;LSEQ=GGAGACGGGGAGAGGGAGAG;RSEQ=GAGAGGGAGACGGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:7:7,0:33,0:0.1707:1,0:24.4:1:32.1:1:1:0:55.1:14:0.1795:0.0244:1.1 0/1:43:16:16,0:27,0:0.3721:1,1:21.1:1:30.2:1:1:0:57.8:15:0.3659:0.0698:1.2 -2 202149416 . ACG A 166 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=6;SSF=0.03002;SOR=0.37092;LSEQ=AGAGGGAGAGGGAGAGGGAG;RSEQ=GGGAGAGGGAGAGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:43:43,0:3,0:0.8113:0,1:23.7:1:30.6:1:1:0:58.3:13.333:0.8333:0.1887:0.5 1/0:49:30:30,0:3,0:0.6122:0,1:21:1:30.7:1:1:0:57.8:29:0.6304:0.1224:0.3 -2 202149417 . C G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.05251;SOR=2.86874;LSEQ=GAGGGAGAGGGAGAGGGAGA;RSEQ=GGGGAGAGGGAGAGGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:7:7,0:3,0:0.1321:0,0:37:1:33.1:1:1:0:55.1:14:0.1458:0:1.1 0/1:49:15:15,0:3,0:0.3061:0,1:32.8:1:32.8:1:1:0:57.7:30:0.3261:0:1.1 -2 202149418 . G GGAGA 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13502;SOR=2.35255;LSEQ=AGGGAGAGGGAGAGGGAGAC;RSEQ=GGGAGAGGGAGAGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:7:7,0:2,0:0.1556:0,0:38.4:1:31.1:1:1:0:55.1:14:0.7:0:1.1 0/1:46:14:14,0:3,0:0.3043:0,1:33.4:1:30.3:1:1:0:57.9:28:0.8235:0:1.1 -2 202149589 . G C 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15456;LSEQ=ATTTTGAGATCAAGCCCCAC;RSEQ=ATGACTGCACAGTAGAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:91:39,52:264,265:0.1463:2,2:25.8:1:31.8:1:0.25623:1.32769:60:182:0.1472:0:1.1 0/1:776:20:11,9:389,365:0.0258:2,2:21.2:1:30.8:1:0.82353:1.15:60:40:0.026:0:1.1 -2 202149737 . A G 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGACAGGAGGCCCCCATCT;RSEQ=TGAGCTGACATCTCAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:0:0,0:350,376:0:2,0:25.8:1:29.4:1:1:0:60:79.667:1:0:0.1 0/1:848:32:13,19:403,410:0.0377:2,2:26.8:1:31.6:1:0.36969:1.43597:60:64:0.0382:0:1.2 -2 202151140 . T G 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.22296;LSEQ=GGAGACAGTTCATCAGTTGC;RSEQ=TTCCCCCACAGACAGTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:41:35,6:125,34:0.205:2,2:26.2:1:30.3:1:0.38896:1.58:60:82:0.205:0:1.9 0/1:203:11:10,1:159,33:0.0542:2,2:21.5:1:29.7:1:0.69484:2.07:60:22:0.0542:0:1.9 -2 202151163 . A G 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.08372;LSEQ=CCCCCACAGACAGTCACAAT;RSEQ=TTATGTGATGTATTTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:110:85,25:127,40:0.3971:2,2:24.2:1:32.5:1:0.88517:1.07:60:220:0.4:0:1.4 1/0:349:202:154,48:109,38:0.5788:2,2:21.5:1:31.3:1:0.70634:1.12:60:201:0.5809:0:1.1 -2 202151400 . G A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5285;SOR=0.8063;LSEQ=CCAGGCTGGAGTGCAGTGGC;RSEQ=TGATCTCGGCTCACCGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:24:0,24:0,74:0.2449:1,1:25.8:1:30.5:1:1:0:57.8:11:0.2292:0:1.2 0/1:140:29:0,29:1,109:0.2071:1,1:21.9:1:30.2:1:1:0:60:58:0.2086:0:1 -2 202151416 . G A 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00704;SOR=Inf;LSEQ=TGGCGTGATCTCGGCTCACC;RSEQ=CAAGCTCCGCCTCCCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:0,86:0:1,0:22.9:1:32.5:1:1:0:55.8:172:1:0:0.5 0/1:94:8:0,8:0,86:0.0851:1,0:26.4:1:30.6:1:1:0:54.3:16:0.086:0:1.4 -2 202151439 . G C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.84122;SOR=0.88198;LSEQ=AGCTCCGCCTCCCGGGTTCA;RSEQ=GCCATTCTCCTGCCTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:21:0,21:0,37:0.3621:1,1:20.7:1:30:1:1:0:46.3:42:0.3621:0:1 0/1:51:17:0,17:0,34:0.3333:1,1:24.7:1:31.1:1:1:0:43.9:34:0.34:0:1.1 -2 202151492 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12891;SOR=5.96095;LSEQ=GGGACTACAGGGGCCCGCCA;RSEQ=CACACCTGGCTAATTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:0,27:0.0357:1,0:7:0:14:0:1:0:60:0:0:0:7 0/1:16:3:0,3:0,13:0.1875:1,0:37:1:27:1:1:0:60:6:0.2:0:1 -2 202151746 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGAGCTAAAGTTAAATAGG;RSEQ=TATTAACAACAATAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:14,3:0:2,0:20.9:1:29.5:1:1:0:60:34:1:0:0 0/1:48:2:2,0:31,15:0.0417:2,0:30:1:33:0:1:0:60:4:0.0444:0:1 -2 202151826 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11921;SOR=0;LSEQ=AGCTGGTGGCAATAAATACC;RSEQ=GACACGTACAAAATCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:15,22:0.0513:2,2:36:1:31:1:1:1.45:60:4:0.0513:0:1 0/0:73:0:0,0:29,44:0:2,0:25.8:1:30.1:1:1:0:60:146:1:0:0.1 -2 202948109 . G C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCCTCCCACCCTGCCCC;RSEQ=ACCTCTACTCCAGTTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:11.5:1:21:1:1:0:60:1:1:0:1 1/1:2:2:1,1:0,0:1:0,2:23:1:31:1:1:0:60:4:1:0:1.5 -2 202948195 . C T 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CAACGACAATGATCAGTCAC;RSEQ=GTGTTCTAAGATTTGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:21,10:0:2,0:17.7:1:30:1:1:0:60:30:1:0:0.3 0/1:30:13:8,5:11,6:0.4333:2,2:28:1:30.6:1:1:1.14063:60:26:0.4333:0:1.1 -2 203369783 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=GGCATGATTGTTACACGTTT;RSEQ=GCATGGATAACATACAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:31.5:1:30.5:1:1:1:60:4:0.1:0:1 0/0:14:0:0,0:8,6:0:2,0:22.1:1:30.9:1:1:0:60:13:1:0:0 -2 203723989 . A T 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00159;SOR=2.24281;LSEQ=ATTATAATTGAATTCAGATT;RSEQ=TAAATATAAATCTTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:36:18,18:45,50:0.2748:2,2:22.8:1:29.9:1:0.846:1.11:60:72:0.2748:0:1.1 0/1:163:75:38,37:46,42:0.4601:2,2:22.7:1:29.7:1:0.87587:1.06599:60:150:0.463:0:1.1 -2 203724058 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=ATGATTTGGTTACTGAGATA;RSEQ=TGATCTAGTCCAGGACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:31,64:0:2,0:27.4:1:32.7:1:1:0:60:190:1:0:0.2 0/1:107:2:1,1:39,66:0.0187:2,2:27:1:30:1:1:1.68:60:4:0.0187:0:1 -2 203724085 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49624;SOR=Inf;LSEQ=AGTCCAGGACTACAGTAGTT;RSEQ=AAATTTACACACAGAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:22,45:0:2,0:21.4:1:31.1:1:1:0:60:66:1:0:0.1 0/1:67:2:1,1:17,48:0.0299:2,2:12:1:25:0:0.46811:2.77:60:4:0.0299:0:1 -2 204637162 . G T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCCATACCAAGCAAAG;RSEQ=GTGGAGTTCCATCTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:14:1:26.5:1:1:0:60:4:0.6667:0:1 -2 204637485 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.99161;LSEQ=ACCTTTTTCTATACTTACTT;RSEQ=CATTTTTGCTATAATGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:1:1,0:48,30:0.0127:2,0:20:0:30:0:1:0:60:2:0.013:0:1 0/1:80:2:1,1:50,28:0.025:2,2:26.5:1:27:1:1:1.77202:60:4:0.0256:0:1 -2 204637529 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2026;SOR=0;LSEQ=CAGAACTAGGTCCTTTTGGT;RSEQ=TTTTGGGAGTTTTTTCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:55,45:0.0196:2,2:29.5:1:28:1:1:1.2198:60:4:0.0198:0:1 0/0:124:0:0,0:71,53:0:2,0:23.5:1:30.9:1:1:0:59.7:123:1:0:0.1 -2 204637705 . TTCATCATCATCA T 177 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=11.000;MSILEN=3;SSF=0;SOR=0.06525;LSEQ=TCATCAAAATCATTATCATT;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:56:31,25:9,11:0.5385:2,2:26.6:1:30.5:1:0.44756:1.51:59.3:112:0.5385:0.125:0.2 0/1:86:6:5,1:7,8:0.0698:2,2:25.8:1:30.8:1:0.1778:5.28:55:12:0.0698:0.0233:0.3 -2 204637740 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50064;SOR=Inf;LSEQ=ATCATCATCATCATCATCAT;RSEQ=TTCATCAGCAGCAAGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:70,66:0:2,0:24.7:1:32:1:1:0:59.7:272:1:0:0.2 0/1:156:2:1,1:94,60:0.0128:2,2:12.5:1:28:1:1:1.56196:60:4:0.0129:0:1.5 -2 204637754 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50053;SOR=Inf;LSEQ=CATCATCTTCATCAGCAGCA;RSEQ=GTTTTCCTTTTTTCTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:85,79:0:2,0:24.1:1:30.4:1:1:0:59.7:40:0.9938:0:0.2 0/1:187:2:1,1:106,79:0.0107:2,2:44:1:31:1:1:1.33962:60:4:0.011:0:1 -2 204637901 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5197;SOR=Inf;LSEQ=AGCACTGTCTACTAATATGC;RSEQ=CTGGCCCTGAACCACACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:46,49:0:2,0:24.9:1:30:1:1:0:59.9:94:1:0:0.1 0/1:145:2:1,1:68,75:0.0138:2,2:38:1:32:1:1:1.10:60:4:0.0138:0:1 -2 204638147 . TG T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13317;SOR=Inf;LSEQ=CACCTTAAAGTGATCATCTT;RSEQ=TCGGCCTTTAGTTCACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:61,102:0:2,0:25.5:1:31.7:1:1:0:57.2:53.333:1:0:0.1 0/1:206:4:1,3:82,119:0.0194:2,2:21.3:1:30.3:1:0.64847:2.06061:60:8:0.0195:0:0 -2 204638150 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19074;SOR=0;LSEQ=CTTAAAGTGATCATCTTTGT;RSEQ=GGCCTTTAGTTCACAACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:59,100:0.0124:2,2:25:1:29.5:1:1:1.69:54.5:4:0.0127:0:1 0/0:207:0:0,0:83,124:0:2,0:25.1:1:29.8:1:1:0:57.7:33.5:1:0:0.2 -2 204638317 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51052;SOR=Inf;LSEQ=CACGCAGGATGGAATCACAC;RSEQ=AGTTTGCTAAGCATTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:1,16:0:1,0:30.1:1:32.2:1:1:0:60:34:1:0:0 0/1:26:2:0,2:5,19:0.0769:2,0:11:1:30:0:1:0:60:4:0.0769:0:1 -2 204729153 . C T 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89671;SOR=0.97746;LSEQ=AATTAAGGAATCTGGTAAGA;RSEQ=GTCTTTGAAAGTTCTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:460:252:173,79:145,63:0.5478:2,2:23.7:1:30.5:1:0.83966:1.05092:60:83:0.5485:0:1.1 1/0:498:270:183,87:154,74:0.5422:2,2:25.4:1:29.8:1:1:1.01:60:134:0.5436:0:1.1 -2 204729356 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12314;SOR=Inf;LSEQ=GGCAACTATTTTCCATGGAT;RSEQ=CCATAAACTCAACATACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:58,245:0:2,0:24.6:1:32.2:1:1:0:60:302:1:0:0.1 0/1:301:3:2,1:79,217:0.01:2,2:5:1:26:1:0.17949:5.46:60:6:0.0101:0:1 -2 204729357 . C T 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12372;SOR=0;LSEQ=GCAACTATTTTCCATGGATG;RSEQ=CATAAACTCAACATACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:4:2,2:53,236:0.0136:2,2:22.8:1:29.3:1:0.16111:4.42:60:8:0.0137:0:1.3 0/0:294:0:0,0:78,215:0:2,0:25.1:1:31.1:1:1:0:60:96.667:0.9966:0:0.1 -2 204732223 . T A 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCCTAGTAGTTTTGGAG;RSEQ=TGTCAATGAAATGAATTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:35.7:1:29:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 204732714 . A G 282 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.5541;LSEQ=AGGCTCAGCTGAACCTGGCT;RSEQ=CCAGGACCTGGCCCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:793:466:247,219:163,162:0.5876:2,2:25.6:1:31.9:1:0.4696:1.12:60:57.25:0.5842:0:1.1 0/1:943:416:210,206:271,252:0.4411:2,2:25.3:1:31.7:1:0.6938:1.05483:60:103:0.4392:0:1.2 -2 204732850 . A G 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTGTTTCAGCAGTCAA;RSEQ=GGCAGTGATTTATAGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:196:20,176:0,0:1:0,2:24.7:1:31.1:1:1:0:60:38.2:1:0:1.1 1/1:156:156:15,141:0,0:1:0,2:23.5:1:30.7:1:1:0:60:155:1:0:1 -2 204735238 . G T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11829;SOR=0;LSEQ=GGGGATGAAGCTAGAAGGCA;RSEQ=AAGGGCTTGCCTGGGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:3:1,2:70,8:0.0366:2,2:33.3:1:30.3:1:0.03885:16.29545:60:6:0.0375:0:1 0/0:84:0:0,0:63,21:0:2,0:21.9:1:31.1:1:1:0:60:83:1:0:0.2 -2 204735616 . C T 66 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07528;SOR=Inf;LSEQ=CTCATGTACCCACCGCCATA;RSEQ=TACCTGGGCATAGGCAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:90,187:0:2,0:24.9:1:32:1:1:0:60:54.4:1:0:0.1 0/1:373:5:1,4:138,228:0.0134:2,2:21.6:1:28.6:1:0.65437:2.41611:60:10:0.0134:0:1 -2 204735710 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49704;SOR=Inf;LSEQ=TTGCATTGCAGTCTTCTATG;RSEQ=ACAAAAACAGTTTTGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:12,73:0:2,0:24.6:1:32.4:1:1:0:60:84:1:0:0.1 0/1:85:2:1,1:18,65:0.0235:2,2:7.5:1:28:1:0.39916:3.54:60:4:0.0235:0:1 -2 204736887 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAGGCCAGCTTTGCCATT;RSEQ=CAAACTCTCCCTTCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 204737586 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=TCAATTTCCAAGAGCTGAGG;RSEQ=AATTCTAACTTTTTTGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:20,170:0.0104:2,2:14:1:32:0:0.2073:8.32:60:4:0.0105:0:1 0/0:179:0:0,0:24,155:0:2,0:22.5:1:31.6:1:1:0:60:88.5:1:0:0.1 -2 204836074 . A T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AAAACAGTACAAATTTATTT;RSEQ=CTTACAGTTCCGAAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 204836514 . C T 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77058;SOR=0.93367;LSEQ=CCACCTTCCTCACACGTTCA;RSEQ=GCTTCCAATGTGCACGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:83:51,32:70,37:0.4368:2,2:24.3:1:30.2:1:0.64864:1.18599:60:166:0.4392:0:1.3 0/1:250:105:65,40:89,56:0.42:2,2:27.1:1:30.1:1:1:1.02:60:210:0.4217:0:1.4 -2 204836598 . T C 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20113;SOR=1.248;LSEQ=ATTTGATTTCTAGCAAATAA;RSEQ=ATTATCTACTACATTACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:106:47,59:60,82:0.4257:2,2:27.3:1:31.8:1:0.79592:1.09:60:34.333:0.4221:0:1.3 0/1:310:149:67,82:68,93:0.4806:2,2:25.4:1:30.8:1:0.64792:1.12:60:73.5:0.4804:0:1.3 -2 204836610 . C T 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=GCAAATAATATTATCTACTA;RSEQ=ATTACACCTTGAGTTTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:110,137:0:2,0:23.1:1:32.2:1:1:0:60:494:1:0:0.5 0/1:289:14:5,9:118,157:0.0484:2,2:26.6:1:26.7:1:0.7832:1.35149:60:13:0.0458:0:1 -2 204836648 . TG T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49947;SOR=Inf;LSEQ=ACGAGAAAGTCACATTGAAA;RSEQ=GAGGCTTTGGGTGGGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:63,115:0:2,0:26.4:1:31.2:1:1:0:60:58.333:1:0:0.4 0/1:193:2:1,1:63,128:0.0104:2,2:26.5:1:32:1:1:2.02:60:4:0.0105:0:0 -2 204836654 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50006;SOR=Inf;LSEQ=AAGTCACATTGAAATGGAGG;RSEQ=TTTGGGTGGGGTGTGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:54,110:0:2,0:28.3:1:31.9:1:1:0:60:81:1:0:0.4 0/1:183:2:1,1:56,125:0.0109:2,2:36:1:31:0:0.52711:2.22:60:4:0.011:0:1 -2 204836692 . CT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51428;SOR=0;LSEQ=TGGAGAATCCCCTATGCACC;RSEQ=TCCTTCCACTCCCAACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:24,80:0.0189:2,2:23.5:1:30:1:0.41779:3.29:60:4:0.0192:0:0 0/0:73:0:0,0:17,56:0:2,0:23.6:1:29.9:1:1:0:60:35.5:1:0:0.2 -2 206545779 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCACTCTAAAATCCCGC;RSEQ=CCACCCCCCAACACAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 208229946 . T TA 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=2.10911;LSEQ=TGAGAAATACCCTAGAGCTC;RSEQ=AAATTCTTTCTTCCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:13,0:0.0714:1,0:50:0:30:0:1:0:60:2:0.0714:0:0 0/1:14:2:2,0:12,0:0.1429:0,0:27:1:29.5:1:1:0:60:4:0.1429:0:0 -2 208230026 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50494;SOR=Inf;LSEQ=GATAAATTATACTCTGACCC;RSEQ=ATTTTCTAAATTTCATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:63,10:0:2,0:22.2:1:31.3:1:1:0:60:72:1:0:0.2 0/1:94:2:1,1:73,19:0.0213:2,2:18:1:28:1:0.38206:3.77038:60:4:0.0213:0:1 -2 208230050 . A AT 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.11478;SOR=0.40549;LSEQ=TTCTAAATTTCATTAAAAAC;RSEQ=TTTTTTTTTCTGTATCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:10:6,4:93,37:0.0709:2,2:30.2:1:30.7:1:0.47864:1.66899:60:20:0.0714:0:0.2 0/1:167:5:4,1:115,47:0.0299:2,2:20.6:1:31.3:1:1:1.63:60:10:0.0303:0.012:0.2 -2 208230091 . A C 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=3.34198;LSEQ=AATGCCTCTCTCAACTCTTA;RSEQ=AAAGACACTCCTGGGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:23:14,9:157,96:0.083:2,2:23.7:1:32.3:1:1:1.05113:60:46:0.0842:0:1.5 0/1:374:87:53,34:176,111:0.2326:2,2:24.4:1:30.7:1:1:1.01713:60:86:0.2324:0:1.8 -2 208230143 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=17.84846;LSEQ=ATAAGTAACGTGCTACTGTG;RSEQ=GCACTGACTGTAATCAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:17:7,10:147,144:0.0552:2,2:25.4:1:31:1:0.61905:1.45655:60:34:0.0561:0:1.6 1/0:397:203:99,104:96,97:0.5113:2,2:25.2:1:30.5:1:0.91993:1.0396:60:100.5:0.5154:0:1.4 -2 209101905 . GA G 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03343;SOR=0.7015;LSEQ=CGTTGCACACTAACGGGAAG;RSEQ=AAAAAAAAAGAAAATTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:256:47,209:31,48:0.7574:2,2:26.7:1:31.4:1:0.00023:2.86122:60:255:0.7567:0.0325:0.1 1/0:405:278:49,229:44,78:0.6864:2,2:27.8:1:30.9:1:1e-04:2.62922:60:91.667:0.6875:0.037:0.1 -2 209102117 . A ACT 104 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTAGGCAACCGGCAGTAGAG;RSEQ=CAGCCATACATACTCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:1:0,2:24.1:1:31.4:1:1:0:60:20:1:0.2:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 209103013 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTGATCCACCCACCTCGG;RSEQ=CTCCCAAAGTGCTAGGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:28:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 209103095 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAATTTAAATTAAGAAA;RSEQ=ATGCAGTGACCAAGTATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:28.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 209103748 . G A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00052;SOR=Inf;LSEQ=CGATGCTCTGAGCCCAGTGA;RSEQ=GATAAGTGTTAATTTGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:294,108:0:2,0:24.6:1:31.6:1:1:0:60:56.429:0.9975:0:0.1 0/1:444:12:7,5:287,145:0.027:2,2:16.8:1:30.3:1:0.54954:1.41269:60:11:0.0252:0:1.2 -2 209103969 . G GA 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00398;SOR=0;LSEQ=AAATGGAAGCTAAAAGAGGG;RSEQ=AAAAAAAACACAACACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:9:3,6:99,238:0.0259:2,2:28.4:1:30.8:1:0.7264:1.20:60:18:0.0264:0:0.2 0/0:317:0:0,0:107,210:0:2,0:23.8:1:30.7:1:1:0:60:104.667:1:0:0.1 -2 209104230 . A G 65 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.31624;LSEQ=ATCTCTTCTATCTCTTGTCT;RSEQ=TATTGGTCTCCTTTTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:32.8:1:32.8:1:1:0:60:8:0.8:0:1 1/0:2:1:0,1:1,0:0.5:0,0:24:0:31:0:1:0:60:2:0.5:0:4 -2 209104740 . G C 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCATACCCTGTAAGTAGTG;RSEQ=AGCATGAAGCGTTGGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:74,254:0:2,0:24:1:31.2:1:1:0:60:163:1:0:0.1 0/1:351:24:5,19:84,242:0.0684:2,2:19.5:1:31.4:1:0.80838:1.31799:60:48:0.069:0:1 -2 209104798 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22627;SOR=Inf;LSEQ=GAGTCTCTCAGAGATGAGAG;RSEQ=ATAAATGACTCAATCTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:9,115:0:2,0:25.5:1:32.4:1:1:0:60:61:1:0:0.1 0/1:113:2:1,1:15,96:0.0177:2,2:7:1:27.5:1:0.26422:6.23:60:4:0.018:0:1 -2 209106589 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13948;SOR=Inf;LSEQ=TTAATTTCCTTAGCTGTCAG;RSEQ=TAAGACGGTGGACCTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:78,0:0:1,0:22.3:1:31.6:1:1:0:60:77:1:0:0.1 0/1:47:2:2,0:44,1:0.0426:1,0:22:1:28.5:1:1:0:60:4:0.0426:0:1 -2 209106897 . A G 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=7e-05;SOR=Inf;LSEQ=ACAAAAGGTAAAAGAGAATA;RSEQ=TAATAAAGAAAATTGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:59,178:0:2,0:23.2:1:30.6:1:1:0:60:78:1:0:0.1 0/1:314:17:6,11:88,209:0.0541:2,2:28.8:1:30.9:1:0.59582:1.29:60:34:0.0552:0:1.1 -2 209107912 . C A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TTATTTAAACATTAAAGAAC;RSEQ=TGGCTCTGAAAACAATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:25.5:1:31.5:1:1:0:60:4:0.3333:0:1 0/0:4:0:0,0:4,0:0:0,0:16.5:1:31:1:1:0:60:8:1:0:0.3 -2 209108118 . A T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0826;SOR=0;LSEQ=AAATGTCAGCTTACTTGAGA;RSEQ=TAAAGAAAAAGTTAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:207,78:0.0104:2,2:9.3:1:22.3:1:0.18768:5.27149:60:2:0.007:0:1 0/0:372:0:0,0:248,124:0:2,0:23.2:1:29.5:1:1:0:60:61:1:0:0.1 -2 209108317 . C T 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00211;SOR=0.61311;LSEQ=ATTATACATCCCCATGGCAA;RSEQ=ACCACCACCTTCTGTAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:109:36,73:170,294:0.1896:2,2:27.2:1:28.9:1:0.50741:1.1722:60:108:0.1915:0:1.2 0/1:662:83:35,48:223,356:0.1254:2,2:23.6:1:28.7:1:0.54843:1.16:60:166:0.1261:0:1.2 -2 209108497 . A G 78 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50749;LSEQ=CCAACAAATTTCTGAGGCAC;RSEQ=TAATGAGAGAAAAGCCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:0,5:0,25:0.1667:1,0:25:1:33.6:1:1:0:60:10:0.1667:0:1 0/1:11:1:0,1:0,10:0.0909:0,0:26:0:33:0:1:0:60:2:0.1:0:1 -2 209110006 . T TA 151 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.15298;SOR=0.70371;LSEQ=TATTATCTAAATCATTTGTT;RSEQ=AAAAAAAAAAGAAGCTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:46:38,8:203,68:0.1433:2,2:24.1:1:27.5:1:0.35006:1.59:60:22:0.141:0.028:0.3 0/1:323:34:28,6:210,77:0.1053:2,2:26.4:1:28.1:1:0.30384:1.71:60:33:0.1044:0:0.3 -2 209110175 . GA G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.10636;SOR=0.45833;LSEQ=AGAGGGGAAAAAGGTATAAA;RSEQ=AAAAAAAAATACCCTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:12:2,10:61,201:0.0436:2,2:29.6:1:30.3:1:0.73938:1.5153:60:24:0.044:0:0 0/1:391:8:1,7:106,276:0.0205:2,2:25.1:1:30.1:1:0.4547:2.68298:60:16:0.0208:0:0.4 -2 209110196 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2567;SOR=Inf;LSEQ=AAAAAAAAAATACCCTAGCA;RSEQ=GAATTGTAAGGAGAATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:33,165:0:2,0:25:1:31:1:1:0:60:197:0.9949:0:0.2 0/1:246:3:0,3:38,205:0.0122:2,0:27.3:1:24.7:1:1:0:60:2:0.0083:0:2.7 -2 209110216 . C A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24207;SOR=0;LSEQ=GGAATTGTAAGGAGAATATT;RSEQ=ATATAATATAGACCTAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:9,127:0.0144:2,2:7.5:1:27:1:0.14017:13.44:60:4:0.0155:0:4 0/0:143:0:0,0:11,132:0:2,0:24.7:1:31.8:1:1:0:60:27.6:1:0:0.3 -2 209110270 . C TTTTTTT 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.26851;SOR=0;LSEQ=TAGGGCAGTATGTCAAACTT;RSEQ=TTTTTTTTTTTTTTTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:0,3:0,28:0.0938:1,0:24.3:1:24.2:1:1:0:53.3:2:0.08:0.0625:3.7 0/0:21:0:0,0:1,19:0:1,0:10.9:1:29.2:1:1:0:60:5.667:0.9444:0:0.8 -2 209110386 . T C 66 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTTTTCTGAGCACTGAT;RSEQ=TGAAGAGGACAGAGAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:27.2:1:28.8:1:1:0:60:4:1:0:1.8 1/1:1:1:0,1:0,0:1:0,0:6:0:33:0:1:0:60:2:1:0:1 -2 209113048 . G GA 136 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.60357;SOR=0.78675;LSEQ=GTTGGAAATTTCTGGGCCAT;RSEQ=AAAAAAAAAACATGCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:21:19,2:191,44:0.0805:2,2:28.7:1:31:1:0.38539:2.18:58.8:42:0.082:0.0115:0.7 0/1:233:15:8,7:154,63:0.0644:2,2:31.5:1:29.8:1:0.15695:2.13115:60:30:0.0661:0.0086:0.7 -2 209113192 . G A 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9991;LSEQ=ATGGCTTCTCTGAAGACCGT;RSEQ=CCACCCAGAATATTTCGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:847:164:92,72:366,313:0.1936:2,2:25.4:1:29.2:1:0.66251:1.09:60:163:0.1947:0:1.1 0/1:1013:196:101,95:426,388:0.1935:2,2:25.8:1:28.4:1:0.87356:1.03269:60:64.333:0.1942:0:1.2 -2 209115941 . CT C 82 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.65809;SOR=0.36319;LSEQ=AAAATAATTCAGATTATATT;RSEQ=TTTTTTTTTTCCTGTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:6,0:30,0:0.1667:1,0:22:1:32:1:1:0:56.7:12:0.1667:0.0278:1.8 0/1:15:1:1,0:14,0:0.0667:1,0:45:0:33:0:1:0:60:2:0.0667:0:0 -2 209115978 . C CT 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.56595;SOR=1.55755;LSEQ=TTCTCCTTCCCTTTTTTTTC;RSEQ=TTTTTTTTTTAAAGTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:8:8,0:55,0:0.1194:1,0:28.1:1:29.5:1:1:0:60:7:0.1186:0.0448:1.8 0/1:40:7:7,0:33,0:0.175:1,0:28.3:1:31.2:1:1:0:60:14:0.1892:0.025:1.3 -2 209116049 . C T 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00938;LSEQ=AATTCCTGGTCTTGAGGGAT;RSEQ=CTCCTGCCTCTGCCTCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:29:28,1:133,5:0.1737:1,1:28.2:1:30.5:1:1:1.05:59.8:58:0.1801:0:1.2 0/1:160:28:27,1:126,5:0.175:1,1:25.4:1:29.9:1:1:1.07:60:56:0.1783:0:1 -2 209116097 . C T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.06986;SOR=Inf;LSEQ=GGACTTCACGTGTGCACCAC;RSEQ=ATGCCCAGCCAGATTATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:246,111:0:2,0:22.7:1:31.2:1:1:0:60:177.5:0.9972:0:0.1 0/1:450:5:1,4:295,150:0.0111:2,2:6.8:1:24.4:1:0.04885:7.83045:60:10:0.0113:0:1.2 -2 209116134 . C T 155 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.53612;LSEQ=TCCTTTCTGAGTTTGCTACA;RSEQ=GGAGGGGTAACTCATTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:645:4:0,4:362,279:0.0062:2,0:1:0:26.3:1:0.03662:0:60:8:0.0063:0:1 0/1:823:37:22,15:440,345:0.045:2,2:22.2:1:29.8:1:0.73678:1.15:60:74:0.0454:0:1.2 -2 209116299 . G GA 146 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.7883;SOR=0.92875;LSEQ=GACTTCAATAAACCTAAAAA;RSEQ=AAAAAAAAAATACATGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:27:6,21:86,235:0.0758:2,2:22.8:1:29.9:1:0.8204:1.27995:59.6:26:0.0762:0.0084:0.2 0/1:466:33:7,26:110,319:0.0708:2,2:29:1:29.1:1:0.68079:1.28011:60:32:0.0721:0:0.2 -2 209330917 . A AT 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.24041;SOR=0;LSEQ=AAAAGGAAGAAGAGCTTTTC;RSEQ=TTTTTTTTTCTTTGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:2,1:25,8:0.0833:2,2:23:1:30.5:1:1:1.54148:60:6:0.0882:0.0278:0 0/0:33:0:0,0:25,8:0:2,0:18.7:1:29.8:1:1:0:60:66:1:0:0.3 -2 209330966 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.20787;SOR=0;LSEQ=CCCATCATAGTGGATTGTCA;RSEQ=GCAAGTTCTCCATGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:32,24:0.0333:2,2:13.5:1:29:1:1:1.32664:60:4:0.0357:0:1 0/0:71:0:0,0:41,30:0:2,0:28.8:1:29.9:1:1:0:60:142:1:0:0.2 -2 209330985 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49664;SOR=0;LSEQ=AAGCAAGTTCTCCATGAATG;RSEQ=AGCATGGATGTCTTTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:37,36:0.0267:2,2:27:1:31.5:1:1:1.02741:60:4:0.0274:0:1 0/0:74:0:0,0:38,36:0:2,0:29:1:31.1:1:1:0:60:36:1:0:0.2 -2 209331070 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49061;SOR=Inf;LSEQ=CCAGAGAGGCCAACCTGATA;RSEQ=ACGTCACTTTTCTCCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:7,17:0:2,0:19.7:1:30.6:1:1:0:60:23:1:0:0.2 0/1:26:2:1,1:5,19:0.0769:2,2:9.5:1:25:1:0.41538:3.56:60:4:0.0769:0:1.5 -2 212248286 . G T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.21073;SOR=4.14782;LSEQ=ACCACCAGAGAAAGAGAGGG;RSEQ=GGTGGGGAAATTGGAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:1:0,1:251,96:0.0029:2,0:1:0:26:0:0.27874:0:60:2:0.0029:0:1 0/1:338:4:1,3:230,104:0.0118:2,2:11:1:26.3:1:0.09549:6.59443:60:8:0.0119:0:1 -2 212251070 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTAATTTTTGAAAAACGTC;RSEQ=TATAAGAACATAATATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:39:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212251864 . T C 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20695;SOR=1.25186;LSEQ=GCAAAACCTCCATCTCGGTA;RSEQ=ACAAACTGGTTCTGTTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:76:21,55:117,211:0.1881:2,2:28:1:31.9:1:0.22689:1.45098:60:152:0.1891:0:1.1 0/1:458:103:42,61:137,218:0.2249:2,2:27.1:1:31.1:1:0.73118:1.10:60:33.333:0.2227:0:1.1 -2 212251910 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15394;LSEQ=AACATATGTGGAGAGAAGGC;RSEQ=TTGTTAGAAATAGTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:55:13,42:29,132:0.2546:2,2:21.7:1:30.9:1:0.42992:1.41:60:110:0.2558:0:1.1 0/1:221:11:2,9:53,157:0.0498:2,2:19:1:30.7:1:0.73544:1.51644:60:22:0.0505:0:1.1 -2 212252384 . TA T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTAGTACATGACCAA;RSEQ=ATCAGGGAAGTAAAGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:16.5:1:31:1:1:0:60:4:0.5:0.25:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212252440 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATAATTTATGTGCCCAGG;RSEQ=AAATCCTTCAGATAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:0.1176:1,0:44:1:32:1:1:0:60:4:0.1176:0:1 0/0:8:0:0,0:7,1:0:2,0:24.3:1:29.9:1:1:0:60:16:1:0:0 -2 212252570 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=AAATTCTTAACTCACTGTTG;RSEQ=CAAAGGCAAAATGAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:123,19:0:2,0:26.6:1:31.1:1:1:0:60:34.5:1:0:0.1 0/1:143:2:1,1:119,21:0.014:2,2:33:1:28.5:1:0.28678:5.55967:60:4:0.0141:0:1 -2 212252809 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19528;LSEQ=CGAAAAAGAAAAGCCACATG;RSEQ=GTCGTATGAACCAAAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:61:5,56:1,26:0.6932:1,2:19.9:1:30.7:1:0.662:2.30:60:60:0.6977:0:1.2 0/1:79:24:2,22:8,47:0.3038:2,2:26.3:1:30.6:1:0.71491:1.85899:60:23:0.2949:0:1.2 -2 212284621 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTTCAAAACTTAAATCT;RSEQ=CTTCTTAAAAACAAAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:26:1:33:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212285103 . T C 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58908;SOR=0.84535;LSEQ=TTTTGAAATGTTAGTGCTTA;RSEQ=GAACTATTACATGATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:69:65,4:65,3:0.5036:1,2:24.9:1:32.1:1:1:1.33055:60:68:0.5113:0:1 0/1:91:42:35,7:46,3:0.4615:2,2:23.2:1:30.9:1:0.17769:3.02958:60:84:0.4615:0:1.1 -2 212285339 . AAAAG A 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCATACGATCATCACCCT;RSEQ=AAAGATTGCCCATCAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:0:0,0:165,328:0:2,0:25.2:1:29.9:1:1:0:60:48.3:1:0:0.1 0/1:513:34:11,23:176,303:0.0663:2,2:28.1:1:30.1:1:0.71358:1.21404:60:68:0.0673:0.0097:0.1 -2 212285785 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTCTATAGCATACTGACT;RSEQ=CATTATCAAAGTAGGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:19:1:31:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212286462 . G GTGTC 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=1;SOR=1.22474;LSEQ=AAATCAAGGTGCTAAAATAA;RSEQ=TGTCTGAGGATTAAGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:28.8:1:31:1:1:0:60:8:0.4444:0.1111:0 1/0:2:1:1,0:1,0:0.5:0,0:13:0:32.5:0:1:0:60:2:0.5:0:0 -2 212286805 . C A 83 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02478;SOR=7.77392;LSEQ=CCAGTTCCTTAAATTTAGGT;RSEQ=TACTGTCAGCATCAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:1:1,0:271,347:0.0016:2,0:1:0:25:0:0.43942:0:60:2:0.0016:0:1 0/1:726:9:7,2:321,395:0.0124:2,2:17.6:1:26.2:1:0.08673:4.30:60:18:0.0125:0:1.1 -2 212286934 . A T 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19852;SOR=0.59888;LSEQ=GTTTGAAAAATGTTGTTTTA;RSEQ=TCGTAATGATCTGAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:31:0,31:0,36:0.4627:1,1:20.5:1:30.7:1:1:0:60:62:0.4627:0:1.2 0/1:56:19:2,17:1,36:0.3393:1,2:25.5:1:30:1:0.2632:4.12:60:38:0.3393:0:1 -2 212287069 . T C 83 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAAATTTTTTCTCTGATG;RSEQ=GTATAGACGTGACTGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:25.3:1:29.9:1:1:0:60:14:1:0:1 1/1:1:1:0,1:0,0:1:0,0:30:0:32:0:1:0:60:2:1:0:1 -2 212288782 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50276;SOR=0;LSEQ=ATAATTGTTTTTGAACTGTC;RSEQ=TATTTTTCAATACAGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:95,3:0.02:1,2:17.5:1:27:1:0.07879:27.56815:60:4:0.0202:0:1 0/0:81:0:0,0:77,4:0:1,0:25.7:1:29.7:1:1:0:60:80:1:0:0.1 -2 212289142 . TA T 118 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.81858;SOR=1.19848;LSEQ=CAATCCAAACACCAATCAAT;RSEQ=AAAAAAAAAAAGCTCCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:14:0,14:0,52:0.2029:1,1:28.9:1:31:1:1:0:60:28:0.209:0:0.3 0/1:47:11:1,10:2,34:0.234:2,2:32.1:1:30.5:1:0.55967:1.68:60:22:0.234:0:0.3 -2 212292929 . G C 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=0;LSEQ=GCAGGTTCTGCATGTGTATC;RSEQ=CAGAACTTAAAATAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:27.8:1:30.3:1:1:0:60:8:0.3636:0:1.5 0/0:4:0:0,0:4,0:0:0,0:31.3:1:31.3:1:1:0:60:8:1:0:0 -2 212292968 . AT A 83 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.39378;SOR=0.2731;LSEQ=AAAATAAAATAAAATAAAAT;RSEQ=TTTTTTTTCATTGAGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:6,0:19,0:0.2:1,0:15:1:32.3:1:1:0:60:12:0.24:0.0333:0 0/1:16:1:1,0:15,0:0.0625:1,0:13:0:31:0:1:0:60:2:0.0667:0:1 -2 212292969 . T AAATAAAATA 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.07824;SOR=0;LSEQ=AAATAAAATAAAATAAAATA;RSEQ=TTTTTTTTCATTGAGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:7:7,0:23,0:0.2258:1,0:25.4:1:29.4:1:1:0:60:14:0.2258:0.0645:1.3 0/0:16:0:0,0:15,0:0:1,0:19.9:1:27.8:1:1:0:60:14:0.9333:0:0.6 -2 212295468 . GTA G 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.00585;SOR=0;LSEQ=ACGGAAGCTGGTAATATATG;RSEQ=TATATATATGTGTGTGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:13,0:13,0:0.5:1,1:26.8:1:32:1:1:0:60:26:0.5:0.0769:0 0/0:10:0:0,0:10,0:0:0,0:23:1:30:1:1:0:60:20:1:0:0.3 -2 212295492 . GATATAT ATATATC 139 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=2e-05;SOR=0;LSEQ=ATATATATGTGTGTGTATAT;RSEQ=ATATACACACACATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:24:24,0:19,0:0.5581:1,1:23.5:1:30.4:1:1:0:60:48:0.5714:0.186:0.1 0/0:17:0:0,0:17,0:0:1,0:23.6:1:32.4:1:1:0:60:34:1:0:0.2 -2 212295590 . G GT 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.11159;SOR=1.51061;LSEQ=CCTAAGCTTCAGGCTTATTG;RSEQ=TTTCTTGTATAAAATATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:51:44,7:94,21:0.3072:2,2:22.3:1:29.6:1:0.65358:1.40:60:50:0.3106:0.0843:0.1 0/1:132:53:44,9:66,13:0.4015:2,2:16.7:1:29.4:1:1:1.03819:60:106:0.4015:0.1591:0 -2 212295600 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50108;SOR=0;LSEQ=AGGCTTATTGGTTTCTTGTA;RSEQ=AAAATATAAGGAGATAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:154,44:0.01:2,2:24.5:1:31:1:0.40025:3.47197:60:4:0.01:0:1 0/0:174:0:0,0:132,42:0:2,0:18.3:1:29.2:1:1:0:60:348:1:0:0 -2 212295875 . C T 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08076;SOR=0.67594;LSEQ=TCAGTTAATGCCCAGGTTTT;RSEQ=CCATTTTTCTAAAACAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:191:31,160:6,37:0.8162:2,2:22.2:1:30:1:0.8202:1.19:60:94.5:0.8147:0:1.1 1/0:256:192:42,150:13,48:0.75:2,2:23.5:1:28.6:1:1:1.03:60:47:0.752:0:1.1 -2 212296094 . G C 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTATTTTTCCAAGTGACTT;RSEQ=ATATCCTTTTGCAAACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:19.7:1:32.7:1:1:0:60:6:0.4286:0:1 1/1:1:1:0,1:0,0:1:0,0:44:0:34:0:1:0:60:2:1:0:1 -2 212426466 . A C 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0059;SOR=Inf;LSEQ=ATATCACGCATTTAATCTGT;RSEQ=GTTTACCTAAAAGTACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:50,2:0:1,0:22.8:1:28.6:1:1:0:60:104:1:0:0.1 0/1:41:6:5,1:34,1:0.1463:1,2:17:1:30.2:1:0.27439:6.29815:60:12:0.1463:0:1 -2 212426554 . A T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35835;SOR=3.21696;LSEQ=TGGGAAGACAACATATTTTC;RSEQ=ATATGAAAACTGTTCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:0,1:223,66:0.0034:2,0:1:0:26:0:0.23103:0:60:2:0.0035:0:1 0/1:272:3:1,2:193,76:0.011:2,2:10:1:28.3:1:0.19857:5.04379:60:6:0.0112:0:1 -2 212426588 . C T 162 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01853;LSEQ=TCCAGGTTAGGAAATATTAA;RSEQ=CTAAAAATGTAATTTCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:41:31,10:272,146:0.0893:2,2:25.6:1:30.4:1:0.22631:1.66:60:40:0.0877:0:1 0/0:553:1:0,1:351,200:0.0018:2,0:1:0:25:0:0.36413:0:60:2:0.0018:0:1 -2 212483804 . T C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00129;SOR=Inf;LSEQ=TAATATTTCCATAAGAGAAA;RSEQ=TTGTAAGTTGTGGAGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:200,12:0:2,0:22.8:1:30.7:1:1:0:60:52:1:0:0 0/1:167:8:7,1:147,12:0.0479:2,2:13.8:1:31.6:1:0.48467:1.74276:60:16:0.05:0:1.1 -2 212485648 . T C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGACCAGCATAGGCAACA;RSEQ=AGAGACATTCCAACTCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:33.5:1:1:0:60:4:1:0:1 -2 212488815 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49985;SOR=Inf;LSEQ=TACTTTCAGTCCGATAGTCA;RSEQ=TCCTCTCTCTCTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:26,146:0:2,0:25.1:1:31.2:1:1:0:59.9:27.667:1:0:0.2 0/1:190:2:1,1:39,148:0.0105:2,2:24:1:31.5:1:0.37938:3.76:60:4:0.0106:0:1 -2 212488817 . CCT C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.21832;SOR=0;LSEQ=CTTTCAGTCCGATAGTCAGT;RSEQ=CTCTCTCTGTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:19,140:0.0124:2,2:38:1:31.5:1:0.2337:7.21:60:4:0.0126:0:0 0/0:183:0:0,0:33,150:0:2,0:21.8:1:30.7:1:1:0:60:19.333:1:0:0.3 -2 212488870 . G GC 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25561;SOR=0.61911;LSEQ=TTGGTTCTCTTTCTTACAAA;RSEQ=AAAAACACACCAACTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:63:45:0,45:0,18:0.7143:1,1:27.2:1:32.1:1:1:0:60:90:0.7377:0.0794:0.1 1/0:61:37:0,37:1,23:0.6066:1,1:24.9:1:32:1:0.39344:0:60:74:0.6167:0.1475:0.3 -2 212495336 . GA G 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.46593;SOR=0.72685;LSEQ=AGTTCTGACAACCAGAATGA;RSEQ=AAAAAAAAAATAAAAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:20:6,14:67,225:0.0639:2,2:22.1:1:30.6:1:0.42744:1.44:60:40:0.0643:0.0064:0.2 0/1:254:12:1,11:73,168:0.0472:2,2:24:1:30.5:1:0.18936:4.76006:60:24:0.0478:0.0039:0.5 -2 212495342 . A AT 158 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=11.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACAACCAGAATGAGAAAAA;RSEQ=AAAAATAAAAAGTATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:55,207:0:2,0:22.5:1:30.3:1:1:0:59.9:524:1:0:0.2 0/1:214:50:11,39:51,113:0.2336:2,2:20.6:1:28.1:1:0.28521:1.59683:60:100:0.2336:0.0561:0.2 -2 212522384 . A G 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.57327;SOR=0.35666;LSEQ=TTGATATATTATGAGTTACA;RSEQ=TATATTATAAATTTAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:96,12:0.0182:2,2:21.5:1:30.5:1:0.22335:7.72593:60:4:0.0185:0:1 0/0:153:1:1,0:134,17:0.0065:2,0:14:0:34:0:1:0:60:2:0.0067:0:1 -2 212522450 . C T 211 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00299;LSEQ=TAACTAGGAAAGGATTTGAG;RSEQ=GACAAAATGGAAACATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:143:94,49:154,81:0.3773:2,2:24.3:1:29.5:1:1:1.01:60:46.667:0.3794:0:1.1 0/0:556:1:0,1:324,230:0.0018:2,0:1:0:25:0:0.41622:0:60:2:0.0018:0:1 -2 212522651 . A G 232 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGAGCCTTGGAGGAAGAAC;RSEQ=TGGGAAGCAAGCACACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:187:99,88:225,242:0.2859:2,2:26.4:1:30.8:1:0.29917:1.21:60:92.5:0.2864:0:1.1 0/0:808:0:0,0:391,415:0:2,0:26.4:1:29.9:1:1:0:60:200.5:0.9975:0:0.1 -2 212522738 . TA T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.12495;SOR=Inf;LSEQ=ACCTGCAGAAAATGCAAATT;RSEQ=AAAAAATACAAGGGGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:99,273:0:2,0:25.6:1:29.5:1:1:0:60:371:1:0:0.1 0/1:399:4:2,2:127,268:0.01:2,2:29.3:1:28:1:0.59769:2.11:60:8:0.0101:0:0 -2 212529910 . C A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01021;SOR=Inf;LSEQ=AAATCATTCTCTCAGTATTT;RSEQ=TCTTAAAATCAGCATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:53,1:0:1,0:23.4:1:31.5:1:1:0:60:108:1:0:0.2 0/1:38:5:5,0:32,1:0.1316:1,0:29.2:1:29:1:1:0:60:10:0.1316:0:1 -2 212529962 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5103;SOR=0;LSEQ=AGTAGAGTTCTATGAGAATG;RSEQ=TATACATTTCAGAGATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:134,4:0.0143:1,2:8.5:1:29:1:0.0704:30.0704:60:4:0.0149:0:1 0/0:102:0:0,0:97,5:0:1,0:23.9:1:30.5:1:1:0:60:19.4:1:0:0.1 -2 212530218 . G GA 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1411;SOR=0.51148;LSEQ=GGACCCTGAAATGTGAAAAC;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:15:3,12:65,251:0.0448:2,2:28.9:1:28.9:1:1:1.03576:60:14:0.0433:0:0.3 0/1:342:8:2,6:80,254:0.0234:2,2:21.3:1:28.6:1:1:1.06:60:16:0.0238:0.0058:0.1 -2 212530340 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51919;SOR=0;LSEQ=ATTGGAGAACATTTTCAGCA;RSEQ=TGCAAATGTGGATGTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:0,26:0.0714:1,0:24.5:1:31.5:1:1:0:60:4:0.0714:0:1.5 0/0:17:0:0,0:0,17:0:1,0:23.4:1:29.4:1:1:0:60:16:1:0:0.1 -2 212530466 . C T 25 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGAAATATTTTCCTTTT;RSEQ=GACATAAGCAGTTCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:23:1:25.5:1:1:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212543560 . C T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00466;SOR=Inf;LSEQ=AAATTAGCCGGGCATGGTGG;RSEQ=GGGCGCCTGTAATCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,0:0:0,0:26.8:1:32.8:1:1:0:52.8:12:1:0:0.7 1/1:6:5:5,0:1,0:0.8333:0,0:21.6:1:24.6:1:1:0:43:4:0.8:0:1.8 -2 212543572 . A G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34985;SOR=3.26886;LSEQ=CATGGTGGCGGGCGCCTGTA;RSEQ=TCCCAGCTACTTGGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:7.8:1:24.6:1:1:0:56:1.5:0.3:0:1.6 1/0:7:5:5,0:2,0:0.7143:0,0:25:1:32.2:1:1:0:45.6:10:0.7143:0:1.8 -2 212543924 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=5.60202;LSEQ=CAGCAGCTGTGAAACACCAA;RSEQ=ATCAAGGGGAAATAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:86:23,63:94,195:0.2293:2,2:24:1:31.5:1:0.35435:1.31945:60:172:0.2312:0:1 1/0:390:244:80,164:45,101:0.6256:2,2:26.1:1:31:1:0.73711:1.09:60:80.333:0.6292:0:1.1 -2 212544024 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=8.57881;LSEQ=AAAAGAGATATATGGCAAAT;RSEQ=ACTTTGGTGGCCTATCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:8:0,8:1,44:0.1509:1,0:25:1:30.9:1:1:0:60:16:0.1538:0:1.3 1/0:36:22:1,21:0,13:0.6111:1,1:26.1:1:30.5:1:1:0:60:44:0.6111:0:1 -2 212544026 . CT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51163;SOR=0;LSEQ=AAGAGATATATGGCAAATGA;RSEQ=TTGGTGGCCTATCCCATCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:0,2:1,48:0.0392:1,0:34.5:1:33:0:1:0:60:4:0.04:0:0.5 0/0:35:0:0,0:2,33:0:2,0:21.9:1:30.5:1:1:0:60:34:1:0:0.6 -2 212544080 . T C 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00814;SOR=0;LSEQ=TACCCACAACTTCTTCTATA;RSEQ=TGCAGAGTCCTAGTAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:1,7:0.4667:2,0:26.6:1:33.6:1:1:0:60:14:0.4667:0:1 0/0:12:0:0,0:1,11:0:2,0:31.3:1:30.7:1:1:0:60:24:1:0:0.3 -2 212566481 . CAAAAAAAA C 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=28.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGCGAGACTCCGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:12.5:1:32:1:1:0:58:4:0.2857:0.1429:2.5 0/0:2:0:0,0:2,0:0:0,0:14:1:30:1:1:0:50:4:1:0:1 -2 212566935 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20257;SOR=Inf;LSEQ=CGGAACCATGAAACGCATTC;RSEQ=GGAGTAAAATAAGGCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:21,158:0:2,0:24.5:1:29.6:1:1:0:60:58.667:1:0:0.1 0/1:147:2:1,1:22,123:0.0136:2,2:21.5:1:32.5:1:0.28935:5.49:60:4:0.014:0:1 -2 212568257 . T C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCATAAATAAGAACATCA;RSEQ=ACAGATGACATCAGAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:11:1:33.5:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:0:0,0:12:0:32:0:1:0:60:2:1:0:0 -2 212569005 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51101;SOR=0;LSEQ=TTGAAATATGGTGAAAATGT;RSEQ=TTGAAAGTTGGGAAGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:3,116:0.0165:1,2:29:1:29:1:0.06529:33.66:60:4:0.0167:0:1 0/0:87:0:0,0:3,84:0:1,0:24.4:1:31.5:1:1:0:60:174:1:0:0.1 -2 212569828 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07407;SOR=Inf;LSEQ=AGCAGCTGGGATTACAGGCA;RSEQ=GCGCCACCACACCCAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:0:1,0:16.6:1:31.9:1:1:0:59.1:40:1:0:0.1 0/1:8:2:2,0:6,0:0.25:0,0:16.5:1:31:1:1:0:60:4:0.25:0:2 -2 212569879 . T C 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAGTAGAGACAGGGTTTC;RSEQ=CCATGTTGGCCAGGATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:39,0:0:1,0:24.8:1:31.8:1:1:0:59.8:78:1:0:0.1 1/0:33:17:17,0:16,0:0.5152:1,1:28.8:1:30:1:1:0:60:16:0.5:0:1.5 -2 212569924 . G A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=CCTGACCTCATGATCCACCC;RSEQ=CCTCAACCTCCCTAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:91,1:0:1,0:24.3:1:29.6:1:1:0:60:45:1:0:0.2 0/1:84:12:12,0:72,0:0.1429:1,0:21.4:1:30.3:1:1:0:60:24:0.15:0:2.1 -2 212569969 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49887;SOR=Inf;LSEQ=TTACTGGTGTGAGCCACGAT;RSEQ=CCCAGTCAATCTTGTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:156,34:0:2,0:22:1:32:1:1:0:60:189:1:0:0.2 0/1:197:2:1,1:159,36:0.0102:2,2:17.5:1:27.5:1:0.34114:4.37026:60:4:0.0103:0:2.5 -2 212569983 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=8.61053;LSEQ=CACGATGCCCAGTCAATCTT;RSEQ=TGTAATTTTTAAAAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:22:15,7:174,50:0.0894:2,2:25.4:1:29.1:1:0.30067:1.62047:60:44:0.0905:0:1.1 0/1:294:135:96,39:108,51:0.4592:2,2:23.8:1:28.3:1:0.61208:1.16:60:270:0.4639:0:1.1 -2 212576951 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4999;SOR=0;LSEQ=TTGAGAAACTTATTTTTGGC;RSEQ=AATAAATCATTGCATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:26,155:0.0109:2,2:27:1:28.5:1:0.274:5.87:60:4:0.0112:0:1 0/0:165:0:0,0:34,131:0:2,0:25.4:1:31.3:1:1:0:60:330:1:0:0.1 -2 212576980 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47801;SOR=1.42611;LSEQ=ATTGCATCTTCATTATAAAA;RSEQ=AGCAGAGTATTTTTAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:9:0,9:7,101:0.0769:2,0:33.2:1:32.1:1:1:0:60:18:0.0769:0:1 0/1:94:10:1,9:8,76:0.1064:2,2:17.9:1:32.7:1:1:1.05:60:20:0.1099:0:1 -2 212577264 . T G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTTTGAAAATATCATT;RSEQ=TTAATGATTTTGAAATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:27:1:33:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212578379 . TA T 198 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.0473;SOR=0.69606;LSEQ=CTACCACAAAGTTATCTGAT;RSEQ=AAAAAAAAAAAAAGGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:95:17,78:48,149:0.2819:2,2:28.1:1:30.2:1:0.2328:1.47619:59.8:30.667:0.2805:0.0178:0.6 0/1:317:68:15,53:76,148:0.2145:2,2:31:1:29.1:1:0.07332:1.81094:59.9:33:0.215:0.0095:1.1 -2 212578523 . C T 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03082;SOR=0;LSEQ=ACAACTCTTTGTTTAAATAT;RSEQ=TCAACCTGAAATTGTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:0,6:0,22:0.2143:1,0:21.5:1:30.3:1:1:0:60:12:0.2222:0:1 0/0:21:0:0,0:1,20:0:1,0:21.2:1:32.8:1:1:0:60:42:1:0:0 -2 212579599 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAGCAAATGGTTAAGAG;RSEQ=CCCCCATGCCATCCACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212587321 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25517;LSEQ=ATAATACTTGTTAATGAAAC;RSEQ=CTGCCAAAACAGGAGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:163:115:9,106:7,40:0.7055:2,2:22.5:1:30.4:1:0.24351:2.05096:60:114:0.7125:0:1.1 0/1:119:45:6,39:9,64:0.3782:2,2:22.1:1:28.9:1:1:1.09:60:21.5:0.3739:0:1.2 -2 212589742 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49996;SOR=Inf;LSEQ=GACAAAGATTCAGTATGCCT;RSEQ=AATCAAATAGGGAAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:138,20:0:2,0:23.2:1:32.3:1:1:0:60:78:1:0:0.1 0/1:176:2:1,1:144,30:0.0114:2,2:15:1:27.5:1:0.32208:4.73836:60:4:0.0116:0:1 -2 212589774 . A G 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGGAAAGGAGAGCAGGAT;RSEQ=ATAAAAGAGAGAAATCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:21:17,4:194,76:0.0722:2,2:30.2:1:32.7:1:0.45452:1.66:60:42:0.0724:0:1.1 0/0:346:0:0,0:243,103:0:2,0:24:1:28.2:1:1:0:60:85.5:1:0:0.1 -2 212589986 . T C 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25445;SOR=0.7598;LSEQ=GAAACTCATAAGCTGAGTTC;RSEQ=GGAGTGACAATTTCTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:152:96:6,90:7,48:0.6316:2,2:23.5:1:30:1:0.22858:2.17549:60:95:0.6376:0:1 1/0:168:95:15,80:7,66:0.5655:2,2:21.6:1:29:1:0.25926:1.76:60:30.667:0.5576:0:1.1 -2 212590067 . T G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24;SOR=Inf;LSEQ=TTACAACTAGATCAAAATTT;RSEQ=TATACAAAAATCTCCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:1,37:0:1,0:27.6:1:30.2:1:1:0:60:76:1:0:0.1 0/1:37:2:0,2:1,34:0.0541:1,0:26:1:33:0:1:0:60:4:0.0541:0:1 -2 212590228 . T TG 54 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCGTAATCCCAACTACT;RSEQ=GGAGACTGAGACAGGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:29:1:27.3:1:1:0:60:8:0.8:0.2:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212615284 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=0;LSEQ=GCTCATTTCATGTTTTAGAT;RSEQ=ACCAGAGGCATGAAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:156,28:0.0108:2,2:29.5:1:28.5:1:0.28823:5.49213:60:4:0.0108:0:1 0/0:170:0:0,0:140,30:0:2,0:21.9:1:31.4:1:1:0:60:169:1:0:0.1 -2 212615516 . T C 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0128;SOR=1.80238;LSEQ=CTCCTCAAAGGAAATACTCC;RSEQ=GCTCCTTTATGAGGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:177:99:16,83:8,70:0.5593:2,2:18.5:1:29.9:1:0.27807:1.68:60:48.5:0.5575:0:1 1/0:158:110:27,83:6,41:0.6962:2,2:19.8:1:29.4:1:0.13385:2.21:60:109:0.6987:0:1.1 -2 212652939 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23783;SOR=Inf;LSEQ=AAACTGCTTGTTGATGAAAA;RSEQ=GTAATCAACAAAAGTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:8,148:0:2,0:23.4:1:31.2:1:1:0:60:77:1:0:0.1 0/1:149:2:1,1:17,130:0.0134:2,2:13.5:1:29.5:1:0.22773:7.46:60:4:0.0137:0:1 -2 212698718 . C T 231 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77423;SOR=1.04939;LSEQ=CAGAGCATTTACTATGAAAA;RSEQ=GAGTGTAGTCGATCTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:180:88,92:92,89:0.4986:2,2:25:1:30.1:1:0.75254:1.08046:60:44:0.4958:0:1.2 1/0:421:215:97,118:99,104:0.5107:2,2:26.2:1:29.9:1:0.49281:1.1576:60:70.667:0.5072:0:1.2 -2 212698775 . T A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0616;LSEQ=TAATTTTATGTCTATGAAAC;RSEQ=GACAATATGTCATCCTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:129:46,83:45,74:0.5202:2,2:25.8:1:30.4:1:0.79226:1.09683:60:42:0.5207:0:1.7 0/1:241:15:7,8:82,144:0.0622:2,2:20.6:1:29.9:1:0.42147:1.53:60:30:0.0622:0:1.3 -2 212698795 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08374;SOR=Inf;LSEQ=TGACAATATGTCATCCTTCC;RSEQ=CAATTTGCTACCATGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:54,135:0:2,0:24.2:1:30.7:1:1:0:60:30.5:1:0:1.6 0/1:148:3:3,0:43,102:0.0203:2,0:7:1:26.3:1:0.02867:0:60:6:0.0204:0:1.7 -2 212698806 . C G 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATCCTTCCGCAATTTGCTA;RSEQ=CATGTCAGTTTGCTTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:166:166:39,127:0,0:1:0,2:23.1:1:31.5:1:1:0:60:32.2:1:0:1.6 1/1:122:104:26,78:4,14:0.8525:2,2:21.7:1:32.1:1:1:1.17:60:103:0.8512:0:1.3 -2 212811801 . G T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGCTTGGATATTACTAAGC;RSEQ=CTAATGATAGTTATCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:32:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212811923 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CAGAGCATTTCCAGAGTTTA;RSEQ=TCCTGTTCAGCTGAGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:33.3:1:32.4:1:1:0:60:18:1:0:0.1 0/1:6:2:1,1:3,1:0.3333:2,2:33.5:1:31:1:1:2.44949:60:4:0.3333:0:1.5 -2 212812057 . G A 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00015;SOR=0;LSEQ=TGATATTTAAATGCCTTAGA;RSEQ=TGTTCCTCAATGTAACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:17:17,0:117,1:0.1259:1,1:22.2:1:29.7:1:1:0:60:16:0.1203:0:1 0/0:88:0:0,0:84,4:0:1,0:25.2:1:32.3:1:1:0:60:176:1:0:0.4 -2 212812060 . T C 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTTAAATGCCTTAGAGTG;RSEQ=TCCTCAATGTAACAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:141,1:0:1,0:24.9:1:30.5:1:1:0:60:284:1:0:0.1 0/1:93:17:15,2:73,2:0.1828:1,2:28.2:1:32:1:0.15417:4.74882:60:34:0.1848:0:1.9 -2 212812097 . T C 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TATGACAGTAACCCTACATA;RSEQ=ACAATTGCCTTATATTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:214,35:0:2,0:24.2:1:30.5:1:1:0:60:123.5:1:0:0.1 0/1:221:34:26,8:150,37:0.1538:2,2:24:1:31.2:1:0.64492:1.24611:60:68:0.156:0:1.5 -2 212989308 . T C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77978;SOR=0.83965;LSEQ=AGTCATTATGGCTTTGTTAC;RSEQ=CTTGTTCTTTTCCTGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:23,0:11,0:0.6765:0,1:21.5:1:29.9:1:1:0:60:22:0.6667:0:1 1/0:22:14:14,0:7,1:0.6364:2,1:21.8:1:30.3:1:0.36364:0:60:28:0.6667:0:1.1 -2 212989396 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52418;LSEQ=CAGAAGAGCACCCCTTCCAG;RSEQ=TATCAGCACACAGGTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:165,15:0.011:2,2:31.5:1:28.5:1:0.16854:10.6831:60:4:0.0114:0:1 0/0:173:1:0,1:161,11:0.0058:2,0:1:0:25:0:0.06936:0:60:2:0.006:0:1 -2 212989410 . G C 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=TTCCAGGTATCAGCACACAG;RSEQ=TCTGCCTGTATGCATCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:194,33:0:2,0:24.2:1:31.4:1:1:0:60:44.4:0.9955:0:0 0/1:251:14:12,2:197,39:0.0558:2,2:33.1:1:31.4:1:1:1.19:60:28:0.0569:0:1 -2 212989698 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23439;SOR=Inf;LSEQ=TGCGCAATGATAATATCTTT;RSEQ=TCAAAACTCTCTATTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:6,116:0:1,0:23:1:32.2:1:1:0:60:60:1:0:0.1 0/1:115:2:1,1:17,96:0.0174:2,2:28:1:29.5:1:0.2897:5.52:60:4:0.0175:0:1 -2 212989940 . AT A 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTTACTTTTATTTAAAC;RSEQ=TTTTTTTTTTAGGACATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:30.5:1:28:1:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 212990868 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTATTCCTATGTGAGCACA;RSEQ=AAGTTTACACAAGTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:27:1:1:0:60:4:1:0:2 -2 212990921 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTGGCTGGGCATGGTG;RSEQ=CTCACACCTGTTATCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:30.5:1:1:0:60:4:1:0:2 -2 213402641 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGCGAGTTGCGTCTGAC;RSEQ=CCACAAGGCTCGGGCGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:32.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 213402705 . A G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACACAGGTGCAAAGCCCG;RSEQ=TTTTCTGAGCGCCGCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:1:31.5:1:1:0:60:4:1:0:2 1/1:2:2:1,1:0,0:1:0,2:17.5:1:32.5:1:1:0:60:4:1:0:1.5 -2 213402964 . A AC 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01457;SOR=0;LSEQ=AGGAGAGAAAAGAGGGACTC;RSEQ=GAGTGATTTTTCACGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:9,0:15,0:0.375:1,0:18.8:1:32.9:1:1:0:60:18:0.375:0.0833:0 0/0:13:0:0,0:11,2:0:2,0:24.8:1:31.1:1:1:0:60:26:1:0:0.1 -2 213403040 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51117;SOR=0;LSEQ=TGGAAAGAGGGGTGACCGAA;RSEQ=GCCCAGGGAAGAGGCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:101,2:0.019:1,2:25:1:28.5:1:0.05659:41.48291:60:4:0.0196:0:1 0/0:75:0:0,0:69,6:0:2,0:25.4:1:30.6:1:1:0:60:150:1:0:0.4 -2 213403091 . G A 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46393;SOR=0.8505;LSEQ=CCTCCACGCCTCCCGGGATG;RSEQ=GTGAAGAGGGCAGGGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:82:71,11:149,22:0.3241:2,2:24.2:1:29.7:1:1:1.04909:60:40:0.3252:0:1.2 0/1:183:53:47,6:109,20:0.2896:2,2:22.2:1:28.9:1:0.64146:1.43:60:106:0.2961:0:1 -2 213404504 . GC G 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCACCGCCCCGCCTCCC;RSEQ=CCCCAGTTATGCCATCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:0:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 214575258 . G T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63386;SOR=0.46614;LSEQ=ATTAGGATGGGAATCACATT;RSEQ=TATGGCTGTGTTGTAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:7,6:0.1875:2,0:21:1:30:1:0.25:0:60:6:0.1875:0:1 0/1:21:2:1,1:10,9:0.0952:2,2:45:1:30:1:1:1.10554:60:4:0.0952:0:1 -2 215145376 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49643;SOR=Inf;LSEQ=GGTTTAGCTCTCAGTAGCCT;RSEQ=CCCCTGAGCTGTGAGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:34,18:0:2,0:22.4:1:32.2:1:1:0:60:104:1:0:0.2 0/1:57:2:1,1:37,18:0.0351:2,2:31:1:28.5:1:1:2.02764:60:4:0.0357:0:1 -2 215145663 . G T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=GCTGATAATGTGCTTCCAGT;RSEQ=TACTTCTGCATTAAATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:17:1:33.8:1:1:0:60:8:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:33:0:30.5:1:1:0:60:4:1:0:1 -2 215593233 . T C 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17553;SOR=2.98875;LSEQ=CAGCTTCTAAATGGTAAACA;RSEQ=AACATGAATTCCTAATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:13,0:10,0:0.5652:0,1:25.5:1:32.7:1:1:0:59.6:26:0.5652:0:1.6 1/1:15:12:11,1:3,0:0.8:0,2:22.1:1:29.8:1:1:0:60:5:0.7692:0:2 -2 215593261 . C CTT 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=0.53687;SOR=1.51809;LSEQ=ATTCCTAATCTGGCATTAGA;RSEQ=TTTTTTTTTTTTTTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:6,0:8,0:0.2222:0,0:35.2:1:30.4:1:1:0:60:12:0.2308:0:1.3 0/1:23:7:7,0:9,1:0.3043:2,0:32.7:1:31.5:1:1:0:60:14:0.3043:0:2.1 -2 215593349 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58654;SOR=0.39597;LSEQ=AAAAACAGTACAATGACTGG;RSEQ=CTCTCACAAACCGTGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:166,30:0.0101:2,2:30.5:1:28.5:1:0.28929:5.45981:60:4:0.0105:0:1 0/0:249:1:1,0:178,70:0.004:2,0:5:0:28:0:1:0:60:2:0.0041:0:1 -2 215593851 . G C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31333;SOR=2.32624;LSEQ=CCTTACCTGAAACATTTGGA;RSEQ=GAGAAGCATTTCAGATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:17:0,17:0,11:0.6071:0,1:28.2:1:30.9:1:1:0:60:34:0.6071:0:1.7 1/0:14:11:0,11:1,2:0.7857:2,0:21.5:1:30.2:1:0.21429:0:60:22:0.7857:0:1.6 -2 215593871 . T G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.63781;SOR=2.55248;LSEQ=GGAGAAGCATTTCAGATTCA;RSEQ=AAATTTTTTGGGTTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:16:0,16:0,7:0.6957:0,1:19.6:1:31.4:1:1:0:60:32:0.6957:0:1.8 1/1:7:6:0,6:1,0:0.8571:0,0:14.3:1:32:1:0.14286:0:60:12:0.8571:0:2 -2 215595069 . T G 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTTGAAAGGGCAGAAGTTCT;RSEQ=CCTGATGGTGATAATAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:146,16:0:2,0:24.8:1:30.4:1:1:0:60:161:1:0:0.1 0/1:188:18:16,2:150,20:0.0957:2,2:27.9:1:32.9:1:1:1.07:60:36:0.0973:0:1 -2 215595203 . A G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATACTTTTCTTCCTGTTCAC;RSEQ=TACTTTTCTTCGTAGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:793:0:0,0:364,429:0:2,0:25.3:1:30.3:1:1:0:60:71.091:1:0:0.1 0/1:851:20:9,11:369,462:0.0235:2,2:24.9:1:30.8:1:1:1.02:60:40:0.0238:0:1.3 -2 215595440 . T A 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61637;LSEQ=AAGAAAATATTTTAAAAAAC;RSEQ=CTTTCTTTGGAGGATTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:0.3571:0,0:32.8:1:28.4:1:1:0:60:10:0.3846:0:1 0/1:4:1:0,1:0,3:0.25:0,0:1:0:31:0:1:0:60:2:0.25:0:1 -2 215595445 . C A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22794;SOR=Inf;LSEQ=AATATTTTAAAAAACTCTTT;RSEQ=TTTGGAGGATTAAGCCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:0,7:0,6:0.5:0,0:19.4:1:29.6:1:1:0:60:6:0.5455:0:1.3 1/1:3:3:0,3:0,0:1:0,0:21:1:30:1:1:0:60:6:1:0:1 -2 215595512 . C T 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATCTCCTTTCTGAAAAA;RSEQ=CTAAGCCAGGATACTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:21:1:30.7:1:1:0:60:6:0.375:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 215595645 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTTACCATCTATACTGCT;RSEQ=ATTTTGACAGTTATATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:31:0:29:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1 -2 215609504 . G A 29 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTGGGACTACAGGCGCCC;RSEQ=CCACCACGCCCGGCTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:15:1:29.5:1:1:0:50.5:4:0.4:0:1.5 1/1:1:1:1,0:0,0:1:0,0:4:0:28:0:1:0:60:2:1:0:2 -2 215609570 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55807;SOR=2.70217;LSEQ=CTTCACCGTGTTAGCCAGGA;RSEQ=GATCTCGATCTCCTGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:17,0:0.15:1,0:33:1:32.7:1:1:0:55.7:6:0.1579:0:1.3 0/1:6:2:2,0:4,0:0.3333:0,0:40:1:29.5:1:1:0:60:4:0.3333:0:1.5 -2 215609645 . A G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.68011;SOR=0.81296;LSEQ=GATTACAGGCTTGAGCCACC;RSEQ=CGCCCAGCCAGAAGCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:29:29,0:26,0:0.5273:1,1:19.2:1:28.1:1:1:0:59.7:6.25:0.4902:0:1.3 0/1:40:19:19,0:21,0:0.475:1,1:22.2:1:30.3:1:1:0:60:38:0.475:0:1.1 -2 215609913 . G T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09014;SOR=0;LSEQ=AAAAAAAGCAGTAAGAGAAA;RSEQ=AAAGATACAAGCCAAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:49,240:0.0103:2,2:19.3:1:21:1:0.43197:2.44:60:2:0.007:0:1.3 0/0:358:0:0,0:75,283:0:2,0:24.1:1:31:1:1:0:60:58.667:1:0:0.2 -2 215609960 . T C 114 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00098;SOR=14.25543;LSEQ=GGCCTGCTTCTTATAACTCA;RSEQ=CTATATTTTGTAAGCTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:1:0,1:5,116:0.0082:1,0:23:0:27:0:1:0:60:2:0.0083:0:1 0/1:113:12:0,12:2,99:0.1062:1,0:14.2:1:31.8:1:1:0:60:24:0.1081:0:1.9 -2 215610313 . G T 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56607;SOR=0.79116;LSEQ=TACTGAAAAAAAATTTAGAT;RSEQ=TATTACAAGATGCAAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:38:38,0:30,0:0.5588:1,1:26.1:1:30.5:1:1:0:60:76:0.5588:0:1.1 1/0:44:22:21,1:22,0:0.5:1,1:21.6:1:30.4:1:1:0:60:44:0.5:0:1 -2 215610740 . A T 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCCAGAACCTTTTAAATAA;RSEQ=TTTTTTCTCTTTATTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:34:0,34:0,0:0.9714:0,1:21.9:1:30.7:1:1:0:60:68:1:0:1.3 1/1:16:16:0,16:0,0:1:0,1:25.7:1:29.1:1:1:0:60:15:1:0:1.3 -2 215610777 . T C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.23779;LSEQ=TTCCCTCAAGAAAATGTCAA;RSEQ=TGTGATAGCTCTCTATACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:0.375:0,0:21:1:32.7:1:1:0:60:12:0.375:0:2.2 0/1:7:3:0,3:0,4:0.4286:0,0:24.3:1:27:1:1:0:60:2:0.3333:0:1.7 -2 215617082 . T G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04229;SOR=Inf;LSEQ=TGTTTGGTGAATGTAAGCAA;RSEQ=TGGTCAAATGGAAATTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:91,6:0:2,0:24.9:1:30.9:1:1:0:60:47.5:1:0:0.2 0/1:82:4:3,1:77,1:0.0488:1,2:13:1:31.8:1:0.09575:22.37217:60:8:0.0488:0:1 -2 215617500 . T C 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.31595;LSEQ=TGTTTTTACTGAATATAGTA;RSEQ=TATGAATTTTTCACAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:23.8:1:33.5:1:1:0:60:8:0.4444:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:27.5:1:31.5:1:1:0:60:4:0.6667:0:1 -2 215631932 . T C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATATATGTAACACATTTT;RSEQ=TTTATCCGATCTGTCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:21.7:1:32:1:1:0:60:6:0.4286:0:1.7 0/0:1:0:0,0:1,0:0:0,0:28:0:32:0:1:0:60:2:1:0:0 -2 215631987 . A G 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.28006;SOR=0.24597;LSEQ=TTTTGATCTGCAGTTGGCTG;RSEQ=ATCCTCAAGTGTAGAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:9,0:3,0:0.75:0,0:23.2:1:29.7:1:1:0:60:8:0.7273:0:2 0/1:5:2:2,0:3,0:0.4:0,0:18:1:31.5:1:1:0:60:4:0.4:0:2.5 -2 215632035 . A AAGAG 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.72102;SOR=1.53569;LSEQ=GAAGGACCAACTGTATCATA;RSEQ=AAAGGGCATGAAGGCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:9,0:14,0:0.3913:1,0:25.4:1:28.7:1:1:0:60:18:0.3913:0.1304:1.7 1/0:12:6:6,0:6,0:0.5:0,0:24.8:1:31.6:1:1:0:60:12:0.5:0.0833:1.5 -2 215632048 . G T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34703;SOR=1.969;LSEQ=TATCATAAAAAGGGCATGAA;RSEQ=GCTGATTATGAGTGCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:10:10,0:20,0:0.3333:1,0:17:1:31:1:1:0:60:20:0.3333:0:1.5 1/0:16:8:8,0:8,0:0.5:0,0:22.4:1:30.3:1:1:0:60:16:0.5:0:1.4 -2 215632124 . ATT A 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.31311;SOR=0.73358;LSEQ=AGAAAGCCATCAACTTGACT;RSEQ=TTAAAGTCTGCTTTATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:61:61,0:71,0:0.4656:1,1:28.4:1:31.6:1:1:0:60:122:0.4656:0.0687:1.6 0/1:77:30:28,2:41,2:0.3896:1,2:24.1:1:29.6:1:1:1.45645:60:60:0.3896:0.0519:1.6 -2 215632155 . T C 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00179;SOR=0.51015;LSEQ=TGCTTTATCACACACCTTGA;RSEQ=TCAAGAATATAGGTCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:108:94,14:99,13:0.4909:2,2:23.8:1:31.8:1:0.83838:1.13356:60:107:0.4954:0:1.8 0/1:167:55:49,6:91,21:0.3293:2,2:22.3:1:30.7:1:0.26431:1.88:60:110:0.3354:0:1.9 -2 215632192 . G A 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.55521;LSEQ=ATTTTAAAAATAATTTTTAC;RSEQ=TTGAACTACTTACACAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:207:146,61:183,52:0.4673:2,2:23.8:1:30.3:1:0.08146:1.46904:60:206:0.4682:0:2.5 0/1:446:146:106,40:211,88:0.3274:2,2:21.2:1:29.8:1:0.73807:1.10:60:72:0.3265:0:2.5 -2 215632255 . CA TG 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0028;SOR=0.75016;LSEQ=TAACAGCTTGACTATATCCA;RSEQ=TGCCCATTCTTGGCTGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:857:366:210,156:269,214:0.4271:2,2:26.1:1:31.3:1:0.67504:1.07:60:365:0.432:0.0128:1.4 0/1:1029:369:194,175:368,282:0.3586:2,2:25.7:1:30.5:1:0.21399:1.17696:60:738:0.3621:0.036:1.3 -2 215632256 . A G 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.62365;LSEQ=AACAGCTTGACTATATCCAC;RSEQ=TGCCCATTCTTGGCTGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:856:498:276,222:0,0:0.5818:0,2:25.9:1:30.3:1:1:0:60:54.333:0.998:0:1.1 0/1:999:464:261,203:113,88:0.4645:2,2:24.4:1:29.8:1:1:1.00:60:57:0.6962:0:1.2 -2 215632629 . G T 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTTGGGTCAAGCACTTTTCT;RSEQ=TTTTTTAGAAGAAAATGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:19.5:1:31.5:1:1:0:60:4:0.25:0:2 1/1:1:1:0,1:0,0:1:0,0:37:0:31:0:1:0:60:2:1:0:2 -2 215632659 . A T 43 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGAAAATGTAGTTTTAAACC;RSEQ=ACGGTAGCTCCTTAAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:36:1:27.7:1:1:0:60:6:0.5:0:1.7 1/0:2:1:0,1:0,1:0.5:0,0:7:0:30:0:1:0:60:2:0.5:0:2 -2 215632703 . G GA 60 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CAATAAATGTAACACATTAA;RSEQ=AAAAAAGTCTACATATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:28:1:30:1:1:0:60:8:0.6667:0:0.8 0/0:1:0:0,0:0,1:0:0,0:40:0:33:0:1:0:60:2:1:0:0 -2 215634055 . C T 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04036;SOR=0.75369;LSEQ=CCCTAGAAAAATGAACAAAA;RSEQ=GGAAATTAAAAAGCATTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:166:43,123:86,162:0.401:2,2:22.7:1:30.3:1:0.06592:1.51699:60:82:0.3981:0:1 0/1:522:175:58,117:132,211:0.3352:2,2:24.7:1:29.6:1:0.24838:1.26141:60:86.5:0.3353:0:1.2 -2 215634232 . A G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAACACTTTGAGAGGCC;RSEQ=AGGTGGGTGGATCACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:24.7:1:31.6:1:1:0:48.4:20:1:0:1.9 1/1:2:2:0,2:0,0:1:0,0:17:0:32:1:1:0:60:4:1:0:2 -2 215634236 . T C 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACTTTGAGAGGCCAAGG;RSEQ=GGGTGGATCACCTGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:30.4:1:30.8:1:1:0:45.5:16:1:0:2 1/1:2:2:0,2:0,0:1:0,0:13:0:28.5:1:1:0:60:4:1:0:2 -2 215634411 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCAGAGGTTGCAGTGA;RSEQ=CCAAGATCATGTCACTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:29:1:29.7:1:1:0:46:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 215645046 . C T 65 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTTGGCAAAATAAAAGC;RSEQ=GAAATATTCAAATATTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:25.5:1:32.5:1:1:0:60:8:0.4444:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 215645135 . A G 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72808;SOR=1.48429;LSEQ=GAAGTAGAGATGCTCTCCCT;RSEQ=TGAATCTGGCTTCTCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:15,0:10,0:0.6:0,1:27.1:1:31.5:1:1:0:60:14:0.6087:0:1.1 1/0:13:9:9,0:4,0:0.6923:0,0:29.6:1:33.2:1:1:0:60:18:0.6923:0:1 -2 215645464 . C G 306 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.49298;LSEQ=TCGGACATGTTACTGTTTTT;RSEQ=CTCCCTGATGTACCACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1115:611:287,324:249,253:0.548:2,2:25.8:1:32:1:0.39895:1.11096:60:100.833:0.55:0:1.1 1/0:1200:773:374,399:219,203:0.6442:2,2:24.8:1:31.9:1:0.25071:1.15079:60:192.25:0.6457:0:1.1 -2 215645545 . C G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30914;LSEQ=GGTATATTTTCTGAGGGCAC;RSEQ=GTTTGCTTAACAAAATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:285:123,162:163,198:0.4405:2,2:24.3:1:30.1:1:0.63274:1.08412:60:56:0.4403:0:1.1 0/1:772:151:61,90:289,328:0.1956:2,2:25.9:1:29.6:1:0.17168:1.29953:60:150:0.1966:0:1.1 -2 215646015 . C T 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04036;SOR=7.33659;LSEQ=TCTTGCAGAAGCCTTTTTAG;RSEQ=CCTCTCAGAAACATCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:662:1:0,1:301,360:0.0015:2,0:1:0:25:0:1:0:60:2:0.0015:0:1 0/1:728:8:4,4:320,400:0.011:2,2:30.1:1:28.4:1:1:1.25:60:16:0.0111:0:1.3 -2 215656919 . G T 38 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15203;SOR=5.09393;LSEQ=GATTTTAAAATCTGAAATAC;RSEQ=TATTCCAGAACTCCAGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:1,0:89,0:0.0109:1,0:1:0:31:0:1:0:60:2:0.013:0:2 0/1:56:3:3,0:50,3:0.0536:2,0:34.7:1:24.3:1:1:0:60:2:0.0426:0:5 -2 215656968 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20804;SOR=Inf;LSEQ=TATACTTTATGAATATGAAT;RSEQ=CATCAGTTTTTAACTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:190,30:0:2,0:24.2:1:29.7:1:1:0:60:30.429:1:0:0.1 0/1:185:2:1,1:152,31:0.0108:2,2:26.5:1:27.5:1:0.3168:4.84193:60:4:0.0111:0:1 -2 215657182 . TA T 184 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.11841;SOR=0.73166;LSEQ=CACAATTACTTTAAAATAAT;RSEQ=AAAAAAAAAAAAAAAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:73:13,60:55,84:0.316:2,2:27:1:29.3:1:0.00116:3.00706:58.8:72:0.3214:0.0216:0.9 0/1:297:75:10,65:84,111:0.2525:2,2:29.6:1:29.6:1:0:4.89311:59.7:74:0.2543:0.0168:0.9 -2 215657560 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACACTGGGAAAGACCTT;RSEQ=TGTTTTGTTTTGGGACTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:40:0:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 215661918 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23871;SOR=Inf;LSEQ=CACCCAATATTTCATCCAAG;RSEQ=CCCAACACTACCATATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:15,153:0:2,0:22.6:1:32.1:1:1:0:60:55:1:0:0.1 0/1:161:2:0,2:18,141:0.0124:2,0:27.5:1:27:1:1:0:60:4:0.0128:0:1.5 -2 215673937 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13915;SOR=0.29901;LSEQ=GATTCAGGGCAAGGGGAGGC;RSEQ=GGTAAGTCGCCCAAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:14,0:6,0:0.7:0,1:18.5:1:31.1:1:1:0:60:28:0.7:0:1.1 0/1:10:4:4,0:5,1:0.4:2,0:28.8:1:32:1:1:0:60:8:0.4:0:1 -2 215674052 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4989;SOR=0;LSEQ=GCGGGAACGGAAGGAGGAAA;RSEQ=GGAAGATTTGAAAAGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:138,17:0.0127:2,2:7.5:1:29.5:1:0.21681:7.91716:60:4:0.0128:0:2.5 0/0:148:0:0,0:126,22:0:2,0:23.2:1:30.2:1:1:0:60:23.667:1:0:0.7 -2 215674090 . T G 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00044;SOR=1.82125;LSEQ=TCTGCCGCCCCCAGAAACTG;RSEQ=GCGACCCGTGCCCTCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:289:157:122,35:100,32:0.5433:2,2:26.6:1:31.2:1:0.77981:1.12:60:51.333:0.5461:0:1.1 1/0:320:219:150,69:74,26:0.6844:2,2:22.7:1:29.9:1:0.35686:1.30814:60:23.333:0.6818:0:1.2 -2 215674224 . G A 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00058;SOR=0.69265;LSEQ=ACCATCCGGTTCCATGGCGG;RSEQ=CGCGGAACGAGGCTCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:714:335:145,190:166,212:0.4692:2,2:27:1:30:1:0.87994:1.026:60:110.667:0.4756:0:1.1 0/1:748:284:114,170:216,247:0.3797:2,2:24.3:1:28.9:1:0.09493:1.3036:60:39.571:0.3815:0:1.2 -2 215674275 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2188;SOR=4.70915;LSEQ=CCTCGGCTGCCGGTTCCTCG;RSEQ=CTGCCGATTATCCGGCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:1:1,0:152,296:0.0022:2,0:31:0:32:0:0.34076:0:60:2:0.0023:0:3 0/1:480:5:4,1:186,289:0.0104:2,2:9.4:1:26.2:1:0.08277:6.19:60:10:0.0106:0:2 -2 215674323 . C G 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00799;SOR=1.70523;LSEQ=TTCGGATGAAAGGCTCCTCG;RSEQ=AGAGCGGGAAGCAAGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:127:25,102:14,82:0.567:2,2:24.8:1:31.3:1:0.37537:1.43:60:126:0.5701:0:2.1 1/0:220:152:52,100:15,52:0.6909:2,2:24.4:1:30.8:1:0.11098:1.80:60:151:0.6927:0:2.1 -2 215674341 . A G 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05135;SOR=1.60512;LSEQ=CGCAGAGCGGGAAGCAAGGA;RSEQ=GCCTCGGGAAACCACAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:161:90:12,78:9,61:0.559:2,2:25.1:1:31.5:1:1:1.04:60:89:0.5669:0:2.6 1/0:161:108:31,77:6,47:0.6708:2,2:23.1:1:30.2:1:0.01627:3.13:60:107:0.6815:0:2.6 -2 215674353 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4981;SOR=Inf;LSEQ=AGCAAGGAAGCCTCGGGAAA;RSEQ=CACAGGGAAGCTGCAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:15,114:0:2,0:24.1:1:31.5:1:1:0:60:63.5:1:0:1.7 0/1:131:2:1,1:25,104:0.0153:2,2:8:0:31.5:1:0.35878:4.10:60:4:0.0153:0:3.5 -2 215674371 . C T 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.75397;SOR=1.15128;LSEQ=AACCACAGGGAAGCTGCAGG;RSEQ=CAGCGACTCGAAACCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:58:3,55:2,32:0.6304:2,2:21.7:1:30.7:1:1:1.14411:60:116:0.6304:0:2.9 1/0:86:57:6,51:4,25:0.6628:2,2:23.8:1:29.2:1:0.72717:1.35491:60:114:0.6706:0:3 -2 215674436 . C T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGCCGCCAGAGGGGCGGGG;RSEQ=GCGCGGGGAGGGGCGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:0,32:0,0:1:0,1:25.3:1:30.3:1:1:0:60:64:1:0:1.5 1/1:21:21:1,20:0,0:1:0,1:19:1:30:1:1:0:60:42:1:0:1.8 -2 215674466 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGCGGGGCACGGCGGCCG;RSEQ=AATGCTCCCAAAATAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:0,19:0.0952:1,2:13.5:1:29.5:1:0.09524:0:60:4:0.1:0:1 0/0:7:0:0,0:0,7:0:0,0:26.7:1:33.4:1:1:0:60:14:1:0:1 -2 216768578 . A G 76 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02777;SOR=Inf;LSEQ=AGAGTCTGAAAACTTCCAAC;RSEQ=TCCCACTGGCCCAGAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:16.7:1:29.7:1:1:0:60:6:0.3333:0:1 1/1:6:6:6,0:0,0:1:0,0:24:1:29.5:1:1:0:60:12:1:0:1 -2 216768702 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50128;SOR=0;LSEQ=TCACTCTGTGATTTTAGGTT;RSEQ=CTGTGTTTATTAGCGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:117,14:0.015:2,2:31:1:30.5:1:0.2136:8.1076:60:4:0.0153:0:1 0/0:113:0:0,0:92,20:0:2,0:23.1:1:32:1:1:0:60:224:0.9912:0:0.1 -2 216768707 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.50064;SOR=0;LSEQ=CTGTGATTTTAGGTTGCTGT;RSEQ=TTTATTAGCGACTTGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:122,20:0.0139:2,2:5:1:28.5:1:0.27127:5.97736:60:4:0.014:0:1 0/0:125:0:0,0:101,24:0:2,0:23.1:1:31.1:1:1:0:60:30.25:1:0:0.1 -2 216768797 . G T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06218;SOR=Inf;LSEQ=GCAGCTAATTAGGGAGCAGG;RSEQ=TGTCAAACTCAAGTAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:243,171:0:2,0:25.4:1:31.3:1:1:0:60:40.4:1:0:0.4 0/1:436:5:1,4:240,189:0.0115:2,2:14.2:1:26.8:1:0.17642:5.06287:60:10:0.0115:0:1 -2 216768824 . G T 52 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06215;SOR=Inf;LSEQ=ACTCAAGTAAACAAGACAGG;RSEQ=ATGCTTTTATCCTTGTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:245,217:0:2,0:23.7:1:30.8:1:1:0:60:65:1:0:0.5 0/1:483:5:1,4:247,230:0.0104:2,2:21.6:1:22.8:1:0.20393:4.28386:60:4:0.0084:0:1.8 -2 216768839 . G T 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=0.62516;LSEQ=ACAGGGATGCTTTTATCCTT;RSEQ=TATGATCCTTGGCCAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:226:110,116:128,127:0.4689:2,2:24.9:1:29.8:1:0.78416:1.0627:60:55.5:0.4693:0:1.1 0/1:481:171:91,80:153,157:0.3555:2,2:25.4:1:29.3:1:0.44653:1.17:60:84.5:0.355:0:1.1 -2 216768907 . A G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=4e-04;SOR=Inf;LSEQ=TATGGTAAATCTGTGCCTAA;RSEQ=GGGGAATCACTACAAATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:107,229:0:2,0:24.2:1:30.4:1:1:0:60:32.6:1:0:0.3 0/1:329:11:4,7:118,200:0.0334:2,2:23.1:1:31.3:1:1:1.0324:60:22:0.0338:0:1 -2 216826471 . G C 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=0.06091;LSEQ=CTCCTCCTTTTTGACCCAGA;RSEQ=CTATCTACTTGCCCTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:80:77,3:1,0:0.9877:0,1:25.6:1:32.4:1:1:0:60:79:0.9875:0:1.1 1/1:99:82:70,12:14,3:0.8283:2,2:22.3:1:30.5:1:0.71825:1.25:60:26.333:0.8229:0:1.1 -2 216826486 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17684;SOR=0;LSEQ=CCAGAGCTATCTACTTGCCC;RSEQ=TTCACTGAATCCCAGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:94,9:0.019:2,2:10.5:1:30.5:1:0.18223:9.96106:60:4:0.0194:0:2 0/0:144:0:0,0:102,42:0:2,0:23.4:1:30.4:1:1:0:60:143:1:0:0.8 -2 216826579 . T G 254 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00749;LSEQ=TCCCATCACCAGGCCCTAAG;RSEQ=TCCCACCCCAGATGCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:300:299:146,153:0,1:0.9967:0,2:26.9:1:31:1:1:0:60:22:0.9965:0:1.5 1/0:407:281:129,152:64,62:0.6904:2,2:26.5:1:30.7:1:0.3911:1.21571:60:69.25:0.6908:0:1.5 -2 216826606 . A G 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.68451;SOR=0.92753;LSEQ=CCCAGATGCTCTGATACTTA;RSEQ=AAGATTAATAAAGTGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:124:52,72:75,89:0.4291:2,2:25.5:1:30.9:1:0.55034:1.16618:60:19.667:0.4275:0:2 0/1:336:138:65,73:83,115:0.4107:2,2:23.3:1:30.9:1:0.37255:1.23:60:68:0.4096:0:1.9 -2 216826660 . C T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35724;SOR=3.23186;LSEQ=TCTCTATATACCATGCGGAG;RSEQ=CTCAAACCCCAAATCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:66,122:0.0053:2,0:24:0:12:0:1:0:60:0:0:0:1 0/1:177:3:1,2:60,114:0.0169:2,2:22:1:29:1:1:1.05233:60:6:0.0172:0:1.3 -2 216826690 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5054;SOR=0;LSEQ=CAAATCACACCTTGGAGTTA;RSEQ=TGCTTAGAGCACCTTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:33,98:0.015:2,2:19.5:1:28:1:0.44737:2.94:60:4:0.015:0:1 0/0:104:0:0,0:33,71:0:2,0:21.7:1:31.5:1:1:0:60:51:1:0:0.4 -2 216826707 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51959;SOR=0;LSEQ=TTACTGCTTAGAGCACCTTA;RSEQ=ACAGGCACATCCATAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:22,76:0.02:2,2:12.5:1:27.5:1:0.40889:3.40:60:4:0.0204:0:1 0/0:65:0:0,0:13,52:0:2,0:21.5:1:31.4:1:1:0:60:130:1:0:0.1 -2 216827773 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTAGGAGGATTGCTTGAG;RSEQ=CTGGGAGGTCAAGGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:1:29.5:1:1:0:60:4:1:0:1 -2 217736023 . A G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGTAAAGAGAGATCACAC;RSEQ=AACCCTGGACCTACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:144,25:0:2,0:22.1:1:30.4:1:1:0:60:168:1:0:0.1 0/1:142:32:29,3:95,15:0.2254:2,2:24.4:1:29.6:1:0.76365:1.52:60:31:0.2214:0:1.1 -2 217736131 . G A 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23929;SOR=1.18005;LSEQ=GGTCCCTATATGAAAAACAC;RSEQ=TGGGTTCTTGGAGTGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:124:63,61:217,230:0.2168:2,2:26.5:1:30.2:1:0.68536:1.09:60:61:0.2175:0:1.1 0/1:597:147:68,79:217,232:0.2462:2,2:25.2:1:29.9:1:0.70392:1.08649:60:294:0.2475:0:1.1 -2 218974191 . A G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCATTTGGGGTTCCACTT;RSEQ=TAAGACCATCTGTAGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:50:0:34:0:1:0:60:2:1:0:1 1/0:6:3:2,1:2,1:0.5:2,2:27:1:30.3:1:1:1:60:6:0.5:0:1 -2 219219875 . G A 66 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGAAGTTTGTAGTAGAT;RSEQ=GCGGTAGAAGAAATAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:21.3:1:28.5:1:1:0:60:8:1:0:1.5 1/1:5:5:4,1:0,0:1:0,2:29.6:1:28.8:1:1:0:60:10:1:0:1.2 -2 220431802 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.00855;SOR=Inf;LSEQ=AAGACGGCATCTTCCCCGTC;RSEQ=TATACCTGCACATCCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:56,0:0:1,0:21:1:29.4:1:1:0:60:27:1:0:0.1 0/1:26:4:4,0:22,0:0.1538:1,0:18.3:1:31.8:1:1:0:60:8:0.1538:0:1.3 -2 220431919 . A G 284 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5066;SOR=Inf;LSEQ=GCAGAGGCTGGCGGATGGCA;RSEQ=GCCTGTGAGAGGACCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:491:489:416,73:0,0:0.9959:0,2:23.5:1:31.8:1:1:0:60:60.125:1:0:1.2 1/1:386:386:310,76:0,0:1:0,2:22.4:1:31.3:1:1:0:60:76.2:1:0:1.2 -2 220431921 . C T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09561;SOR=6.17984;LSEQ=AGAGGCTGGCGGATGGCAAG;RSEQ=CTGTGAGAGGACCAGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:1:1,0:417,82:0.002:2,0:31:0:27:0:1:0:60:2:0.002:0:2 0/1:408:5:2,3:312,91:0.0123:2,2:11:1:27.4:1:0.08267:5.11608:60:10:0.0127:0:1.8 -2 220432014 . G A 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32142;LSEQ=CCAAGGTGAGCAGAACCGTG;RSEQ=AACACCACGTGGGGACTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1547:928:467,461:296,321:0.5999:2,2:25.6:1:30:1:0.37739:1.10:60:76.333:0.6038:0:1.2 0/1:1618:526:268,258:551,539:0.3251:2,2:26:1:29.6:1:0.91544:1.02:60:130.5:0.3263:0:1.2 -2 220432709 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGAGATGCGGACAGGA;RSEQ=TCCATCAACCTGGAATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:25.5:1:31.5:1:0.33333:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 220435034 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGATCCTTGGCCTGGCAGTA;RSEQ=AGCACCTTGAGCACGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:29.5:1:1:0:60:4:1:0:1 -2 220436108 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15158;SOR=Inf;LSEQ=GCCTCCCGCTCCCGGCTCGC;RSEQ=TCCTTACCCTCGGCCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:184,5:0:1,0:22.2:1:31.5:1:1:0:60:46.25:1:0:0.1 0/1:121:2:1,1:111,8:0.0165:2,2:31.5:1:29:1:0.1438:13.14031:60:4:0.0167:0:1 -2 220436138 . TGCG T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.81544;SOR=1.18807;LSEQ=TCGGCCCCGAGCTGCAGCTC;RSEQ=GCGGCGGCGGCGGCGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:10:10,0:314,59:0.026:2,0:30.5:1:32.7:1:0.3719:0:60:20:0.0265:0:0.1 0/1:293:9:6,3:214,69:0.0307:2,2:22.6:1:30.3:1:0.69408:1.54816:60:18:0.0313:0.0034:0.3 -2 220436696 . T TGTGA 46 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTCTGTGTGTGTGTGTG;RSEQ=GAGAGAGTGTGTGTGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:0,1:0.375:0,2:15:1:29.3:1:1:0:60:6:0.375:0.125:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 220436754 . TGTGA T 53 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=11.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGTGTGTGTGAGTGTGTG;RSEQ=GTGTGTGTGTGTGTAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,0:0.6:0,2:30:1:34:0:1:0:60:6:0.75:0:0.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 220436973 . A G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01539;SOR=0.57819;LSEQ=AAAGGACTGGGGAAGACTGG;RSEQ=TGAGAAGGGTAGAAGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:151:148,3:95,2:0.604:1,1:22.7:1:31.7:1:1:1.04:60:302:0.6138:0:1.1 0/1:126:59:58,1:63,4:0.4683:2,1:19.4:1:31.7:1:0.37007:3.65:60:118:0.4876:0:1.1 -2 220437081 . C T 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTGTGAGTTCCCCACTAG;RSEQ=AGGGCCAGGTGAGCTATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1236:0:0,0:687,549:0:2,0:26.7:1:31.9:1:1:0:60:52.739:1:0:0.1 0/1:1171:115:62,53:596,459:0.0982:2,2:23.5:1:27.9:1:0.62136:1.10989:60:37.333:0.097:0:1.2 -2 220437864 . T C 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTGTTCCACTGACTGAA;RSEQ=GGATAAGCCCTCCTGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:19.3:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 220439000 . CA C 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACAGTAAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:10.5:1:31.2:1:1:0:43.5:4:0.6667:0.3333:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 220439102 . G T 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTGAAGTCTAATACAAA;RSEQ=TCTTAGTGCTGGTGAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:28.8:1:32:1:1:0:60:10:0.7143:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 220439206 . T C 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGCAATGTCTTCTATTTT;RSEQ=TTAAGTCCCTTCATGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:14,0:0.125:1,2:29:0:31:1:0.125:0:60:4:0.125:0:1 0/0:1:0:0,0:1,0:0:0,0:28:0:32:0:1:0:60:2:1:0:0 -2 220439330 . G A 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.001;SOR=Inf;LSEQ=CCATCATTGGCTCATGACTG;RSEQ=TGGCCACATCCCTCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:101,6:0:2,0:24.7:1:31:1:1:0:60:34.667:1:0:0.1 0/1:52:6:5,1:44,2:0.1154:1,2:15.5:1:30.5:1:0.31312:4.20593:60:12:0.1154:0:1 -2 220439350 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51508;SOR=0;LSEQ=GTGGCCACATCCCTCCTGCT;RSEQ=AAGAGGAGGGGTGCCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:128,20:0.0132:2,2:43.5:1:29.5:1:0.26121:6.27012:60:4:0.0135:0:1 0/0:104:0:0,0:90,14:0:2,0:19.4:1:31.4:1:1:0:60:51:1:0:0.1 -2 220439364 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18333;SOR=Inf;LSEQ=CCTGCTGAAGAGGAGGGGTG;RSEQ=CAGGTCCTGCCAGTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:171,34:0:2,0:22.2:1:31.8:1:1:0:60:67.333:1:0:0.1 0/1:154:2:1,1:128,24:0.013:2,2:10.5:1:26.5:1:0.29921:5.24607:60:4:0.0132:0:1 -2 220439678 . C T 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=79.59795;LSEQ=CATGCTCCCCCTCACTGGGC;RSEQ=GTGCTGCACCTGGCCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1557:4:0,4:806,747:0.0026:2,0:1:0:27.5:1:0.0539:0:60:8:0.0026:0:1.3 0/1:1550:264:142,122:664,620:0.1703:2,2:23.3:1:30.5:1:0.54358:1.09:60:263:0.1719:0:1.2 -2 220439679 . G A 179 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=66.11248;LSEQ=ATGCTCCCCCTCACTGGGCC;RSEQ=TGCTGCACCTGGCCACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1564:1:1,0:815,745:6e-04:2,0:1:0:25:0:1:0:60:2:7e-04:0:1 0/1:1551:63:32,31:780,707:0.0406:2,2:23.5:1:30.1:1:0.79845:1.0687:60:126:0.041:0:1.1 -2 220439916 . G A 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGGCCTCCGGAGGAACCG;RSEQ=CTGCCCATGCCAACTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1442:0:0,0:736,705:0:2,0:25:1:31.3:1:1:0:60:39.028:0.9993:0:0.1 0/1:1517:34:18,16:743,737:0.0224:2,2:19:1:28.9:1:0.86268:1.12:60:68:0.0229:0:1.1 -2 220440431 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACACAGTGCATATGACT;RSEQ=GACATATGTTCTCCAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:2,72:0.0263:1,2:29.5:1:31:1:0.07789:29.59:60:4:0.0278:0:1 0/0:20:0:0,0:0,20:0:1,0:16.5:1:30.9:1:1:0:60:40:1:0:0.3 -2 220441405 . A C 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03694;SOR=Inf;LSEQ=TCCACCCCAGGGTCCCTGCT;RSEQ=TCAGCCACTGGTTCCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:35,1:0:1,0:23.1:1:28:1:1:0:59.7:35:1:0:0.3 0/1:19:3:3,0:15,1:0.1579:1,0:29:1:32:1:1:0:60:6:0.1765:0:1.3 -2 220441436 . C CGTGT 124 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=17.000;MSILEN=2;SSF=0.02568;SOR=0.1885;LSEQ=GTTCCATCCAGTCTCCAACA;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:17:17,0:19,0:0.2931:1,1:32.6:1:30.5:1:1:0:60:34:0.2931:0.0172:0.3 0/1:28:2:2,0:14,0:0.0714:1,0:46:1:29.1:1:1:0:60:4:0.0714:0:0.5 -2 220441467 . TTG T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.82274;LSEQ=GTGTGTGTGTGTGTGTGTGT;RSEQ=TGTGTGTGTGTTTAGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:118,2:0.0164:1,0:40:1:29:0:1:0:60:4:0.0172:0:0 0/1:74:1:1,0:72,1:0.0135:1,0:21:0:31:0:1:0:60:2:0.0139:0:0 -2 220441469 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.52854;SOR=0;LSEQ=GTGTGTGTGTGTGTGTGTTT;RSEQ=TGTGTGTGTGTTTAGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:2,0:116,2:0.0163:1,0:23:1:30.5:1:1:0:60:4:0.0171:0:1.5 0/0:74:0:0,0:70,1:0:1,0:21.2:1:31.8:1:1:0:58.9:142:1:0:0.5 -2 220441802 . G A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06903;SOR=Inf;LSEQ=TACACGCCCCAGTCTCTGTT;RSEQ=ACACTGAGTCCCCCAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:35,369:0:2,0:24.6:1:31.1:1:1:0:60:49.5:1:0:0.1 0/1:282:3:2,1:19,260:0.0106:2,2:6:1:24.7:1:0.01518:26.50:60:2:0.0072:0:1 -2 222085105 . CT C 33 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTTCTTTTTCTTTTT;RSEQ=TTTTTTTTTTGAGCCGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:33.5:1:1:0:60:4:1:0:0 -2 222085393 . C T 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84139;LSEQ=CAGGCGTGAGCCACCGCGCC;RSEQ=GGCCCACTTTTTTCTATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:6,0:4,0:0.6:0,0:22.2:1:29.2:1:1:0:60:5:0.625:0:1 1/0:9:5:5,0:4,0:0.5556:0,0:24.4:1:30.8:1:1:0:60:10:0.5556:0:1.2 -2 222085613 . G T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.30019;LSEQ=GGAAAGCATGTCAGCTATGG;RSEQ=CTCTTCTCCTTAAGCCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:62:30,32:124,139:0.1908:2,2:25.3:1:29.2:1:0.88826:1.05:60:61:0.1906:0:1 0/1:363:159:82,77:89,113:0.438:2,2:24.6:1:28.7:1:0.1684:1.35:60:158:0.4401:0:1.1 -2 222085727 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51753;SOR=Inf;LSEQ=GTCTGGTGAGCTGCACAGTG;RSEQ=CTAAGTTTCAGGACCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:9,56:0:2,0:21.3:1:32:1:1:0:60:130:1:0:0.2 0/1:98:2:1,1:18,78:0.0204:2,2:5.5:1:27.5:1:0.35178:4.24:60:4:0.0204:0:1.5 -2 222085787 . C T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75983;SOR=1.38865;LSEQ=AATCATGAGCTGTGCATCAA;RSEQ=CTGCTTTGATCTCAGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:0,6:0,22:0.2143:1,0:20.3:1:31:1:1:0:60:12:0.2143:0:1 0/1:29:8:1,7:0,21:0.2759:1,2:25.8:1:30.3:1:0.27586:0:60:16:0.2759:0:1.1 -2 222202431 . AAGAAAGAAAG A 29 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=17.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AAAGAAAGAAAGAAAGAAAG;RSEQ=AGAAAGAAAGAAAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:50:0:29.5:1:1:0:44:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 222202862 . C T 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00148;SOR=1.51855;LSEQ=TTTGAAAAACATCTGTGTGT;RSEQ=CCTGGTAAAAATTAGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:185:87,98:141,157:0.3822:2,2:25.4:1:29.8:1:1:1.01162:60:36:0.3789:0:1.1 0/1:485:235:105,130:120,130:0.4845:2,2:22.7:1:29.3:1:0.46788:1.14254:60:470:0.4906:0:1.1 -2 222202971 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11974;SOR=Inf;LSEQ=ACATAACTATGTTTTCGGTT;RSEQ=CAAGCACAACCACCCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:17,103:0:2,0:22.5:1:31.9:1:1:0:60:29:1:0:0.1 0/1:64:2:1,1:7,55:0.0313:2,2:9:1:26:1:0.23611:7.42:60:4:0.0323:0:1 -2 222298873 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16435;SOR=Inf;LSEQ=GAGACTTACATCTTGATTGG;RSEQ=CATATCCCAATAGGGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:88,33:0:2,0:21.3:1:29.4:1:1:0:60:29.25:1:0:0.2 0/1:83:2:1,1:63,18:0.0241:2,2:12.5:1:27:1:0.40758:3.43346:60:4:0.0247:0:1 -2 222298879 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18313;SOR=Inf;LSEQ=TACATCTTGATTGGACATAT;RSEQ=CCAATAGGGCCTCTCCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:89,40:0:2,0:23:1:30.8:1:1:0:60:63.5:1:0:0.2 0/1:97:2:1,1:68,27:0.0206:2,2:17.5:1:26:1:0.49613:2.49126:60:4:0.0208:0:1 -2 222298962 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49856;SOR=0;LSEQ=CACTTGCTGATGTGAATTTA;RSEQ=GATAGGCAATTGCTTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:58,97:0.0127:2,2:25:1:29.5:1:1:1.67:60:4:0.0129:0:1 0/0:151:0:0,0:58,91:0:2,0:25.8:1:30.1:1:1:0:60:148:0.9867:0:0.2 -2 222298986 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23895;SOR=0;LSEQ=AGGCAATTGCTTCTGGCGCA;RSEQ=TCCACCGGATAGGAATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:25,72:0.0202:2,2:13:1:32.5:1:0.45826:2.84:60:4:0.0206:0:1 0/0:103:0:0,0:30,73:0:2,0:23.4:1:30.4:1:1:0:60:33.333:1:0:0.1 -2 222301212 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48148;SOR=Inf;LSEQ=AAGTTGCTGTTCACCAGGAT;RSEQ=TTCCGTGCGGCCAGATCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:0:2,0:16.1:1:30.4:1:1:0:60:26:1:0:0.1 0/1:14:2:1,1:3,9:0.1429:2,2:23:1:27.5:1:0.50549:2.74:60:4:0.1429:0:1 -2 222301357 . T C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAAGGAGTGAGGAACAATC;RSEQ=CATTAGCATTAGGCCAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24:1:33:0:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:8:0:32:0:1:0:60:2:1:0:1 -2 222307534 . G T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.45612;SOR=1.5117;LSEQ=CTAGCTTGGCTTTGTAAAGG;RSEQ=GGTGACCCACGTACATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:9:8,1:35,6:0.18:2,2:26.8:1:30.3:1:1:1.36:60:18:0.1837:0:1.1 0/1:44:11:11,0:24,9:0.25:2,0:27.7:1:29.5:1:0.08488:0:60:22:0.2558:0:1.1 -2 222307572 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=TAGTGACCACGCCTTCCAAG;RSEQ=GAATGATGTTCGGATGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:71,38:0:2,0:23.7:1:29.6:1:1:0:60:218:1:0:0.2 0/1:116:2:1,1:61,53:0.0172:2,2:38.5:1:31.5:1:1:1.14954:60:4:0.0174:0:1.5 -2 222307614 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24493;SOR=0;LSEQ=ACTGTCCCATGATGCTGGCC;RSEQ=CACTCAGGAAGTCTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:56,64:0.0164:2,2:33:1:29.5:1:1:1.14:60:4:0.0165:0:1 0/0:124:0:0,0:56,68:0:2,0:29.1:1:29.6:1:1:0:60:123:1:0:0.2 -2 222428870 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49256;SOR=0;LSEQ=ACTGGTTCTCTCTGATGAAA;RSEQ=GCTCTTTGTCGTTGTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:11,20:0.0606:2,2:21:1:30:1:1:1.78:60:4:0.0625:0:1 0/0:31:0:0,0:10,21:0:2,0:23:1:29.6:1:1:0:60:62:1:0:0 -2 223360792 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTGTCACATAGTGCCCC;RSEQ=ACTCCCTTCGTGCAAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:14:1:32.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 223360949 . A G 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22236;SOR=0.2985;LSEQ=GTCTGTTAACACACGACAAC;RSEQ=TGAAACACAGATGTAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:18,0:2,0:0.9:0,1:25.1:1:29.8:1:1:0:60:36:0.9:0:1.8 1/0:18:13:13,0:5,0:0.7222:0,1:23.4:1:29.4:1:1:0:60:26:0.7222:0:1.8 -2 223361000 . T A 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ATGAGGTCTTCACTTCTCAG;RSEQ=TTGAGACGCTTTCCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:64,1:0,0:1:0,1:27.3:1:30.1:1:1:0:60:31.5:1:0:1.3 1/1:40:38:35,3:2,0:0.95:0,2:26.1:1:28.4:1:1:0:60:37:0.9487:0:1.4 -2 223361050 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49839;SOR=Inf;LSEQ=GTCTTATTCTCCAGGGAGCC;RSEQ=GGGTTGTTGCATTTATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:115,30:0:2,0:24.2:1:29.6:1:1:0:60:23.167:1:0:0.4 0/1:149:2:1,1:102,44:0.0134:2,2:22:1:29.5:1:0.5171:2.30352:60:4:0.0136:0:1.5 -2 223361058 . TG T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24904;SOR=Inf;LSEQ=CTCCAGGGAGCCAGGGTTGT;RSEQ=CATTTATTCATTTAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:132,46:0:2,0:22.5:1:31.7:1:1:0:60:34.6:1:0:0.4 0/1:192:3:1,2:123,66:0.0156:2,2:6.3:1:26.6:1:0.2864:3.70034:60:6:0.0159:0.0104:1 -2 223361065 . A T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24961;SOR=Inf;LSEQ=GAGCCAGGGTTGTTGCATTT;RSEQ=TTCATTTAATAAAGACTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:136,60:0:2,0:22.2:1:28.9:1:1:0:60:97:1:0:0.4 0/1:215:3:1,2:132,80:0.014:2,2:7:1:21.7:1:0.55931:3.28116:60:2:0.0096:0:1.3 -2 223361153 . G A 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06901;SOR=1.31001;LSEQ=TTCCCTCCATTCAGGCCTGC;RSEQ=TCATCTTTATTTTGCACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:165:78,87:113,123:0.4115:2,2:26.4:1:30.2:1:0.91938:1.02465:60:54:0.4112:0:1.4 0/1:366:175:82,93:93,97:0.4781:2,2:25.4:1:29.3:1:0.75318:1.08713:60:57.333:0.4738:0:1.4 -2 223361209 . G T 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0015;SOR=0.41393;LSEQ=CATCAGTCTCCCTCGAGCTA;RSEQ=TCTTATACCTTCAAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:216:192:53,139:10,12:0.8889:2,2:24.1:1:30.2:1:0.08935:2.17667:60:191:0.8884:0:1.4 1/0:198:152:48,104:18,28:0.7677:2,2:25:1:30.1:1:0.37429:1.39052:60:151:0.7704:0:1.5 -2 224504471 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14634;SOR=Inf;LSEQ=TGAAAGCATCAACTTATTTC;RSEQ=TAAGTCACAATAAGAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,8:0:2,0:23.2:1:31.8:1:1:0:60:48:0.96:0:0 0/1:16:2:1,1:11,3:0.125:2,2:30.5:1:28.5:1:0.45:3.31654:60:4:0.1333:0:1 -2 224504527 . CA C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.12707;LSEQ=ACAAAAAAAATCAACCCCCC;RSEQ=AAAAAAACTCAACTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:31:19,12:1,1:0.9394:2,2:32.3:1:31.8:1:1:1.56:60:62:0.9394:0.0303:0.1 1/1:37:35:17,18:2,0:0.9459:0,2:28:1:30.5:1:0.48649:0:60:34:0.9444:0.0811:0.4 -2 225069340 . C A 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCAAAGGATTTTTCAGTT;RSEQ=CATTTTTCTTATAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:19:8,11:97,102:0.0872:2,2:23.3:1:29.3:1:0.63691:1.306:60:38:0.0884:0:1.1 0/0:224:0:0,0:116,108:0:2,0:26.7:1:30.8:1:1:0:60:55:1:0:0.4 -2 225069368 . T C 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1451;SOR=0.74219;LSEQ=CTTATAGGAAAAGTTTTATA;RSEQ=CTAAGGTAATACAATCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:97:45,52:49,63:0.4641:2,2:24.2:1:31.2:1:0.7806:1.11:60:194:0.4732:0:1.1 0/1:225:88:41,47:64,73:0.3911:2,2:23.1:1:30.1:1:1:1.00499:60:28.333:0.3864:0:1.1 -2 225339145 . C A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61821;SOR=2.07105;LSEQ=AAACACATAAAAATTCGTAT;RSEQ=TTTGAACAGAACTGATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:1:0,1:24,170:0.0051:2,0:10:0:31:0:1:0:60:2:0.0052:0:3 0/1:189:2:0,2:23,164:0.0106:2,0:30:1:29.5:1:1:0:60:4:0.0106:0:1.5 -2 225339154 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49836;SOR=0;LSEQ=AAAATTCGTATCTTTGAACA;RSEQ=AACTGATATGTCATTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:0,2:6,145:0.0131:1,0:26:1:27.5:1:1:0:60:4:0.0132:0:1 0/0:152:0:0,0:9,143:0:2,0:23.1:1:30.9:1:1:0:60:37:1:0:0.1 -2 225342597 . A T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATGAAAGCATTTAATGA;RSEQ=TGGTAACCATTATTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:10.5:1:32:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 225343208 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09107;SOR=Inf;LSEQ=TTAATTCAAGTACGCATTCA;RSEQ=AAACTGTCTTAATGTTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:1,43:0:1,0:21.4:1:31.5:1:1:0:60:88:1:0:0 0/1:37:3:0,3:0,34:0.0811:1,0:8.7:1:31:1:1:0:60:6:0.0811:0:1 -2 225346548 . A AT 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0654;SOR=Inf;LSEQ=AAAGAAATCCAATAGATGAG;RSEQ=TTTTTTTTCTAAAGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:146,24:0:2,0:23.4:1:29.6:1:1:0:59.9:23.286:1:0:0.1 0/1:203:5:4,1:170,27:0.0246:2,2:15.2:1:29:1:0.52959:1.56996:60:10:0.0253:0.0049:0.2 -2 225346646 . T C 196 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGTAGTTTGGATGTGAA;RSEQ=TGATCATTAACTGTAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:746:0:0,0:425,320:0:2,0:27.4:1:30.7:1:1:0:60:92.125:0.9986:0:0.1 0/1:863:76:38,38:418,369:0.0881:2,2:28.7:1:31.4:1:0.63159:1.13263:60:75:0.0875:0:1.1 -2 225362392 . C T 23 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.58702;LSEQ=ACAGAAGTAAGTAATTTACC;RSEQ=AGGTCAACATAAATCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:97,26:0.016:2,2:9:1:23:1:0.38671:3.68014:60:4:0.0163:0:1 0/0:106:1:0,1:84,21:0.0094:2,0:1:0:21:0:0.20755:0:60:2:0.0094:0:1 -2 225362478 . C T 161 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.48163;LSEQ=ATCAATATTTACCTTTTTAA;RSEQ=TGGTCCATAAAATGTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:1:1,0:249,168:0.0024:2,0:23:0:33:0:1:0:60:2:0.0024:0:1 0/1:485:43:28,15:258,183:0.0887:2,2:24.3:1:29.8:1:0.42212:1.32:60:42:0.0884:0:1.1 -2 225362644 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49751;SOR=Inf;LSEQ=CAAACTACAGGATAACATCC;RSEQ=TTAAACATTTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:4,86:0:1,0:23.1:1:32.1:1:1:0:60:89:1:0:0.1 0/1:94:2:1,1:5,87:0.0213:2,2:25.5:1:32:0:0.12423:15.98:60:4:0.0225:0:1 -2 225365056 . A G 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACACTTACTTGTACACAGTG;RSEQ=TACAAAGTCTGATTTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:281,111:0:2,0:25.2:1:30:1:1:0:60:48:1:0:0.1 0/1:488:31:23,8:322,134:0.0635:2,2:25.5:1:31.1:1:0.83859:1.20:60:62:0.064:0:1 -2 225367669 . C T 173 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.06215;LSEQ=AATATCTAAGTAGAAATTAA;RSEQ=GCAGAATCTTACACCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:2:0,2:380,233:0.0033:2,0:1:0:25.5:1:0.14563:0:60:4:0.0033:0:1 0/1:714:58:34,24:381,275:0.0812:2,2:24:1:29.7:1:1:1.02:60:116:0.0819:0:1.1 -2 225368321 . A G 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.14469;LSEQ=CGTTGTCAGTACACAATCAT;RSEQ=ATAAACCTCAGTTAGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:74:50,24:154,54:0.2624:2,2:22:1:31.9:1:0.29286:1.36735:60:148:0.2624:0:1.1 0/1:381:165:108,57:141,75:0.4331:2,2:24.5:1:31.5:1:1:1.01:60:164:0.4362:0:1.1 -2 225368622 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23048;SOR=Inf;LSEQ=TCATTTACAGCTTAAAAACA;RSEQ=TATTGTTTGAAAACATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:5,119:0:1,0:24.5:1:32.6:1:1:0:60:248:1:0:0 0/1:115:2:1,1:7,105:0.0174:2,2:29:1:28:1:0.136:14.10:60:4:0.0175:0:1 -2 225370554 . C A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.82533;SOR=0.8715;LSEQ=TTTTTAATAGACCATGGCAC;RSEQ=CATTTAAGCACAGCAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:17:17,0:33,0:0.34:1,1:22.8:1:30.9:1:1:0:60:34:0.34:0:1.1 0/1:42:13:13,0:29,0:0.3095:1,1:28.3:1:30.6:1:1:0:60:26:0.3095:0:1 -2 225371505 . AAAGTGGCCTTTTT A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.22178;SOR=Inf;LSEQ=ACACAATACACAGCATGGTA;RSEQ=AGCACTTGTCAAAATGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:195,28:0:2,0:26.5:1:29.8:1:1:0:60:43.6:1:0:0.1 0/1:199:2:2,0:153,44:0.0101:2,0:9.5:1:30.1:1:1:0:60:4:0.0103:0.0101:0 -2 225371801 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50591;SOR=0;LSEQ=TGTTCACGCTATAATACTGA;RSEQ=AGAAGCTTATTTCTCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:0,2:7,155:0.0122:1,0:29:1:29.5:1:1:0:60:4:0.0123:0:1.5 0/0:128:0:0,0:6,122:0:1,0:22.5:1:31.3:1:1:0:60:127:1:0:0.1 -2 225376032 . G C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36795;LSEQ=TTAAAAATATCGATAAGGCA;RSEQ=AGTAAGGATTTAATTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:167:122,45:135,54:0.4691:2,2:23.4:1:31.8:1:0.81274:1.08:60:40.75:0.4644:0:1.1 0/1:408:100:71,29:197,110:0.2451:2,2:23.8:1:31.2:1:0.22662:1.37:60:99:0.2463:0:1.1 -2 225376034 . G A 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAATATCGATAAGGCAGA;RSEQ=TAAGGATTTAATTATTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:267,105:0:2,0:23.2:1:32.1:1:1:0:60:744:1:0:0.5 0/1:430:34:24,10:258,137:0.0791:2,2:23.4:1:29.5:1:0.57832:1.27:60:68:0.0798:0:1 -2 225378177 . TA T 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49865;SOR=0;LSEQ=GGTCAAAATAGTTAAATTAG;RSEQ=ACTATATTAAATAACATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:160,18:0.0111:2,2:5:1:24.5:1:0.2005:8.68078:60:4:0.0112:0.0056:0.5 0/0:176:0:0,0:157,18:0:2,0:21.8:1:28.1:1:1:0:60:42.75:0.9942:0:0.1 -2 225378382 . ATAAT A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32655;LSEQ=AAAAAAGTTATTATCACTTG;RSEQ=TAAATTACATTTAAAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:163:41,122:35,138:0.4851:2,2:27.3:1:30.8:1:0.29879:1.32:60:162:0.485:0.0446:0.1 0/1:417:98:31,67:91,228:0.235:2,2:28.6:1:29.8:1:0.61179:1.16:60:196:0.2356:0.0288:0.1 -2 225379531 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24882;SOR=Inf;LSEQ=TATGAGTACAGTTCTTGTGA;RSEQ=CATAATAATTATTGTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:42,159:0:2,0:23:1:31.9:1:1:0:60:66:0.995:0:0 0/1:214:3:1,2:48,163:0.014:2,2:27:1:23:1:0.54356:1.69:60:2:0.0095:0:2.3 -2 225400176 . C T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21758;SOR=0;LSEQ=GGATTACAGGCGTGAGCCAC;RSEQ=GTGCCCAGCCTTCAACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:2,0:129,19:0.0133:2,0:33.5:1:33:0:1:0:60:4:0.0134:0:1 0/0:171:0:0,0:125,46:0:2,0:21.6:1:29.8:1:1:0:60:170:1:0:0.1 -2 225400185 . CCTTCAA C 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.00094;SOR=Inf;LSEQ=GCGTGAGCCACCGTGCCCAG;RSEQ=CTTCAAATGCTTAACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:161,30:0:2,0:20.4:1:31.3:1:1:0:60:94.5:1:0:0.1 0/1:209:11:7,4:143,55:0.0526:2,2:25:1:32.3:1:0.50897:1.4827:60:22:0.0529:0:0 -2 225422080 . GA G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGATTAAATCATTTTAAG;RSEQ=AAAAAATTCCTTGTAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:47:1:29.5:1:1:0:60:4:0.2857:0:0.5 0/0:1:0:0,0:1,0:0:0,0:27:0:31:0:1:0:60:2:1:0:1 -2 225422239 . AT A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03068;SOR=2.63168;LSEQ=TAAATTTTTCATGAGTGCTT;RSEQ=TAACAGTCACGAATTAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:15:15,0:42,0:0.2632:1,1:31.5:1:30.4:1:1:0:60:14:0.2593:0:0.5 0/1:39:19:19,0:20,0:0.4872:1,1:18.7:1:30.5:1:1:0:60:38:0.4872:0.1795:0.3 -2 225422300 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49936;SOR=0;LSEQ=CCTTTAAAAAGAACACTTCC;RSEQ=GTCAAAGTGCAATATGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:168,19:0.0105:2,2:36:1:30:1:0.20095:8.64597:60:4:0.0107:0:1 0/0:176:0:0,0:156,20:0:2,0:22.8:1:29.3:1:1:0:60:43:1:0:0.1 -2 225422594 . AAG A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=1.87314;LSEQ=CTGTAATATCCAAGAGAGAG;RSEQ=AGACAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:1:0,1:32,133:0.006:2,0:29:0:26:0:1:0:60:2:0.0063:0:5 0/1:180:2:0,2:59,118:0.0111:2,0:36.5:1:27:0:1:0:60:4:0.0116:0:2 -2 225422598 . GAC G 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24987;SOR=Inf;LSEQ=AATATCCAAGAGAGAGAAGA;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:26,96:0:2,0:12.4:1:28.5:1:1:0:59.7:12.556:1:0:1 0/1:142:3:0,3:50,83:0.0211:2,0:39.7:1:24.3:1:0.29739:0:60:2:0.0157:0:0.3 -2 225423683 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGGAGGCTGTGGCAGGA;RSEQ=AATGGTGTGAGCCCGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29:1:1:0:60:4:1:0:1 -2 225434256 . C G 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72582;SOR=1.48338;LSEQ=CAGGATTACAATTTTCCCAT;RSEQ=AGAAAAGTATCAATAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:6,0:15,0:0.2857:1,0:17:1:33:1:1:0:60:12:0.2857:0:1 0/1:16:6:6,0:10,0:0.375:0,0:20.2:1:32.8:1:1:0:60:12:0.375:0:1 -2 225434445 . A G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-04;SOR=1.82169;LSEQ=ATTACTGAGAGAACTACATC;RSEQ=TGAGACAAATTAAAACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:91:41,50:136,144:0.2453:2,2:27:1:30.5:1:0.62921:1.15132:60:44.5:0.2432:0:1.1 0/1:465:173:91,82:136,155:0.372:2,2:28.1:1:30.4:1:0.24931:1.26:60:346:0.3745:0:1.1 -2 225434527 . G T 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=CAAGAAGTCTTTAGTCCTCT;RSEQ=TGAATAATTTTCTACAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:36,114:0:2,0:22.6:1:31.8:1:1:0:60:49:1:0:0.2 0/1:176:14:4,10:38,123:0.0795:2,2:23:1:29.6:1:0.74509:1.29:60:28:0.0795:0:1 -2 226701156 . C G 51 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACATCCTTCAATCCAAT;RSEQ=AAGTTGGCACTCAATATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:20.7:1:32.7:1:1:0:60:6:0.5:0:1 0/0:1:0:0,0:1,0:0:0,0:5:0:32:0:1:0:60:2:1:0:0 -2 226701301 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2236;SOR=0;LSEQ=TTTCATTTCCAATAAGAAGA;RSEQ=ATTACACCTCCAAGAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:75,15:0.0217:2,2:37:1:31:1:0.31916:4.87349:60:4:0.0217:0:1 0/0:102:0:0,0:79,23:0:2,0:23.1:1:30:1:1:0:60:101:1:0:0.1 -2 226701342 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22782;SOR=0;LSEQ=CATGGTCTGTTCAATCAGTG;RSEQ=TCTGTAATTATATAAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:106,66:0.0115:2,2:23.5:1:30:1:1:1.60147:60:4:0.0116:0:1.5 0/0:190:0:0,0:128,62:0:2,0:26:1:29.1:1:1:0:60:37:1:0:0.2 -2 226701408 . G A 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02554;SOR=0.61254;LSEQ=TGGTTCTTTTTAATAGAAAC;RSEQ=TATATTCAGCAATGTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:63:28,35:82,90:0.2681:2,2:21.4:1:30.3:1:0.76806:1.13826:60:126:0.2681:0:1.1 0/1:284:52:23,29:117,115:0.1831:2,2:29.4:1:29.4:1:0.44608:1.28167:60:51:0.1815:0:1.2 -2 226701471 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50551;SOR=Inf;LSEQ=TATCTCTTCTAAAATGACAC;RSEQ=TCTGTGTAAAAACTTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:42,99:0:2,0:25:1:30.2:1:1:0:60:69.5:1:0:0.2 0/1:179:2:1,1:61,116:0.0112:2,2:5:1:27.5:1:1:1.89:60:4:0.0114:0:1 -2 226701521 . C CA 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.40401;SOR=3.22528;LSEQ=TAAAACAAAAAGTCATTTCA;RSEQ=AAAAAAAAACTGTAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:1:0,1:1,40:0.0238:1,0:36:0:32:0:1:0:60:2:0.0244:0:0 0/1:68:5:1,4:7,54:0.0735:2,2:23.8:1:29:1:0.48728:1.91:60:10:0.0769:0.0147:0.2 -2 226701540 . A C 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.00773;SOR=0;LSEQ=ACAAAAAAAAACTGTAAAAC;RSEQ=AAAAGGTCATTATGTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:6:0,6:0,27:0.1818:1,0:30:1:33.7:1:1:0:60:12:0.1818:0:1 0/0:38:0:0,0:0,38:0:1,0:25:1:30.9:1:1:0:60:76:1:0:0.1 -2 227597887 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49816;SOR=0;LSEQ=CAGGGCTTCAGTATTGTAAA;RSEQ=TACTGTTTCTTACCATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:128,0:0.0154:1,2:10.5:1:31:1:0.01538:0:60:4:0.0156:0:1 0/0:126:0:0,0:124,2:0:1,0:23.6:1:29.9:1:1:0:60:41:1:0:0 -2 227598134 . G T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03074;SOR=Inf;LSEQ=CATTATTGACTCAGGTGGTT;RSEQ=ATCATTAATGGATTCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:140,314:0:2,0:24.3:1:31.3:1:1:0:60:74.667:0.9956:0:0.1 0/1:455:5:2,3:163,286:0.011:2,2:39.6:1:28.8:1:1:1.17:60:10:0.0111:0:1.2 -2 227651909 . C CT 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.5159;SOR=0;LSEQ=AAGATCCAAAGCAAAGATAT;RSEQ=TTTTTTCCTGCTTTTTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:128,7:0.0145:2,2:28.5:1:28.5:1:0.11378:17.17024:60:4:0.0148:0:0 0/0:94:0:0,0:90,4:0:1,0:23.3:1:31.5:1:1:0:60:188:1:0:0.1 -2 227651920 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51567;SOR=0;LSEQ=CAAAGATATCTTTTTTCCTG;RSEQ=TTTTTGTCAATATTATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:2,0:160,10:0.0116:2,0:41.5:1:32:0:1:0:60:4:0.0119:0:1 0/0:118:0:0,0:109,9:0:2,0:23.2:1:31.9:1:1:0:60:58:1:0:0.1 -2 227660049 . CGCT C 92 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.57899;SOR=0.62524;LSEQ=GCTGTGGCGTTTCACATCCT;RSEQ=GCTGCTGCTGCTACCGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:609:8:6,2:234,364:0.0131:2,2:26.1:1:30.8:1:0.06347:4.66:60:16:0.0134:0.0049:0.3 0/0:606:5:1,4:278,323:0.0083:2,2:25:1:32.5:1:0.3808:3.43658:60:10:0.0084:0.0017:0.2 -2 227660306 . G A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0469;SOR=Inf;LSEQ=AGTGGGCAGCCAGCTCTGCT;RSEQ=CCCCTTGAGGCCCAGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:145,237:0:2,0:23.6:1:31.8:1:1:0:60:62.667:1:0:0.2 0/1:334:4:3,1:128,202:0.012:2,2:18.3:1:24.5:1:0.30383:4.71:60:8:0.0122:0:1 -2 227660544 . C T 151 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=42.26773;LSEQ=CCTGCAAATGCTAGCAGCCC;RSEQ=GGGAGGTGCAGGGCCCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:0,1:215,148:0.0027:2,0:1:0:27:0:0.40934:0:60:2:0.0028:0:1 0/1:335:35:19,16:162,138:0.1045:2,2:22.2:1:29.5:1:1:1.01:60:16.5:0.1:0:1.1 -2 227660807 . GGCT G 133 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.34813;SOR=0.66556;LSEQ=GCTCTGGAGGGTGCAGCAAG;RSEQ=GCTGCTGCTGCTGCTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:607:18:9,9:306,283:0.0297:2,2:29.7:1:32.1:1:1:1.08111:60:36:0.0303:0.0049:0.1 0/1:552:11:4,7:268,272:0.0199:2,2:29.9:1:31.8:1:0.54505:1.72259:60:22:0.0204:0.0018:0.1 -2 227661395 . TTGC T 155 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.27174;SOR=1.31751;LSEQ=TGGTCCCGGAAGGGACGGCG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:851:33:22,11:373,442:0.0388:2,2:26.2:1:30.6:1:0.02064:2.37:60:66:0.0394:0.0071:0.1 0/1:733:37:15,22:302,389:0.0505:2,2:27.5:1:29.9:1:0.73693:1.13843:59.3:74:0.051:0.0068:0.4 -2 227661663 . G GC 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05026;SOR=0.36871;LSEQ=GGAGCTGTCTGGGCGGTGGT;RSEQ=CCCCCCCCGACGCTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:16:8,8:278,279:0.0278:2,2:15.4:1:30.8:1:1:1.00:60:32:0.0284:0.0069:0.1 0/1:576:6:3,3:265,303:0.0104:2,2:27:1:29.8:1:1:1.14:60:12:0.0106:0.0017:0 -2 227662753 . C T 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCACCTGCATCCAGAACTC;RSEQ=CCGGGCCCCGTCACGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:852:0:0,0:375,477:0:2,0:25.8:1:30.6:1:1:0:60:29.429:1:0:0.2 0/1:928:63:27,36:388,474:0.0679:2,2:24.9:1:29.6:1:0.79376:1.09128:60:62:0.0682:0:1.1 -2 227663428 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4995;SOR=0;LSEQ=ACCTTGCGCACGTCCGAGAA;RSEQ=CCATCGCTCTCCGGAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:61,113:0.0113:2,2:42:1:30:1:1:1.85:60:4:0.0116:0:1 0/0:162:0:0,0:68,94:0:2,0:24.2:1:31.7:1:1:0:60:80:1:0:0.2 -2 227663433 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22068;SOR=Inf;LSEQ=GCGCACGTCCGAGAAGCCAT;RSEQ=GCTCTCCGGAGGGCTCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:57,114:0:2,0:22.7:1:29.8:1:1:0:60:56:1:0:0.2 0/1:152:2:1,1:61,89:0.0132:2,2:27:1:28.5:1:1:1.46:60:4:0.0133:0:1 -2 227663446 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49821;SOR=0;LSEQ=AAGCCATCGCTCTCCGGAGG;RSEQ=CTCGCCATGCTGCCACCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:46,91:0.0144:2,2:35:1:30:1:1:1.97:60:4:0.0146:0:1 0/0:137:0:0,0:56,81:0:2,0:25.7:1:31.4:1:1:0:60:44.667:1:0:0.2 -2 227664109 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4898;SOR=Inf;LSEQ=GCTGCTGCTGCTGCTGCTGC;RSEQ=GCCGCCCGCGGGCGCGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:27.2:1:27:1:1:0:60:5.25:1:0:0.2 0/1:25:2:1,1:8,15:0.08:2,2:29.5:1:31:1:1:1.83:60:4:0.08:0:1.5 -2 227665416 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18708;SOR=Inf;LSEQ=CTGTTAGGGACCTTCAGAGG;RSEQ=TTCATAAGGCCAAAACCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:215,31:0:2,0:22.6:1:31.5:1:1:0:60:122:1:0:0.1 0/1:188:2:1,1:161,25:0.0106:2,2:20.5:1:27.5:1:0.25811:6.33453:60:4:0.0108:0:1 -2 227665694 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21603;SOR=Inf;LSEQ=CCCAGAGTTTTTTTATTTTT;RSEQ=AAGCCGACCTATAAACAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:11,160:0:2,0:20.4:1:28.3:1:1:0:60:56:1:0:0.1 0/1:149:2:1,1:10,137:0.0134:2,2:10.5:1:27:1:0.14266:13.11:60:4:0.0134:0:1 -2 227665698 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50476;SOR=0;LSEQ=GAGTTTTTTTATTTTTTAAG;RSEQ=CGACCTATAAACAAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:7,147:0.0128:1,2:9:1:26:1:0.10025:19.71:60:4:0.0131:0:1 0/0:124:0:0,0:5,119:0:1,0:23.8:1:31.7:1:1:0:60:248:1:0:0.1 -2 230579184 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50026;SOR=Inf;LSEQ=CGGAGCCAGGACGCAGTGAC;RSEQ=GCGGCGGCGGTGGCAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:26:1:29.8:1:1:0:60:26:1:0:0.3 0/1:35:2:1,1:19,14:0.0571:2,2:40.5:1:28:1:1:1.34517:60:4:0.0588:0:1 -2 232422661 . T C 78 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0.20187;LSEQ=GGCAGGCCCAAGAACACGCA;RSEQ=GCCTAGGAAGTCTCCAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:20.8:1:30.3:1:1:0:60:5:0.7143:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:37:0:28:0:1:0:60:2:0.3333:0:1 -2 232422782 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=TGGGTTCCTGTCCCAAGTCT;RSEQ=CCCCCTGATGGTAAGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:9,19:0:2,0:21:1:31.8:1:1:0:60:56:1:0:0.1 0/1:28:3:2,1:12,13:0.1071:2,2:25:1:27.3:1:1:2.11:60:6:0.1111:0:1.3 -2 232422824 . A AATCAGTGGAGAGGTAATAC 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.78393;LSEQ=CTTCTTCAGCCAAATTTCAT;RSEQ=ATTTACCTCCTGGGGTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:2,7:2,6:0.5294:2,2:24.1:1:31.4:1:1:1.15611:60:18:0.5294:0.2353:0.2 0/1:15:7:2,5:3,5:0.4667:2,2:13.7:1:29.2:1:1:1.46001:60:14:0.4667:0.4667:0.4 -2 232424786 . T C 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25295;SOR=Inf;LSEQ=ATGCCCCACAAGTGTCACCA;RSEQ=GGCAAAACTGGAAGAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:114,106:0:2,0:28.3:1:30.5:1:1:0:59.7:54:1:0:0.1 0/1:257:3:2,1:137,117:0.0117:2,2:36.7:1:22.3:1:1:1.70:60:2:0.0079:0:1.3 -2 232424847 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=TTGGCATTGTAAACAAACAA;RSEQ=TTCAGGGCAACATTCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:44,89:0:2,0:19.7:1:31.5:1:1:0:60:132:0.9925:0:0.1 0/1:147:2:1,1:53,91:0.0136:2,2:19:1:28:1:1:1.71:60:4:0.0138:0:1 -2 233708806 . A G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.00102;SOR=0.18989;LSEQ=GCTCTTCAGCAGCAGCAGCA;RSEQ=CAGCAACAGCAGAAACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:24:14,10:7,8:0.6154:2,2:26.3:1:30.8:1:0.52538:1.58:60:11:0.5946:0:1.2 0/1:35:8:4,4:15,12:0.2286:2,2:27.6:1:31.8:1:1:1.242:60:16:0.2353:0:1.1 -2 233708909 . AAGC A 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.51475;SOR=Inf;LSEQ=AAGAGGCCAGGCAAATGCAA;RSEQ=AGCAGCAGCAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:29.9:1:31.2:1:1:0:60:48:1:0:0.1 0/1:37:2:1,1:14,21:0.0541:2,2:22.5:1:30:1:1:1.48:60:4:0.0541:0:0.5 -2 233790649 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24242;SOR=Inf;LSEQ=AACAAAATTCCGGAGTCAGC;RSEQ=CGGCTTAACAGCATGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:29.8:1:31.7:1:1:0:60:40:1:0:0.1 0/1:25:3:2,1:11,11:0.12:2,2:11.7:1:30:1:1:1.95:60:6:0.12:0:1.3 -2 233791390 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGGCTTCCAGGTCTTCC;RSEQ=TGATGGGGGATAGTGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 237242082 . T C 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01283;SOR=0.10489;LSEQ=CCACATCTTCACTTGAGATC;RSEQ=GGTGTGTCTTCCGTCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:6,1:2,1:0.6364:2,2:15.9:1:29:1:1:2.65:60:14:0.6364:0:2.1 0/1:21:3:2,1:9,4:0.1429:2,2:39.3:1:30.7:1:1:1.11662:60:6:0.15:0:2 -2 237242097 . C T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04074;SOR=0.19619;LSEQ=AGATCTGGTGTGTCTTCCGT;RSEQ=CAAATTTATAACATCTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:7,3:2,1:0.7692:2,2:22:1:30.5:1:1:1.15:60:20:0.7692:0:1.8 0/1:26:10:7,3:10,6:0.3846:2,2:28:1:29.6:1:1:1.38:60:20:0.3846:0:1.9 -2 237242244 . T C 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GGGTTTCATGCTTGCGGACT;RSEQ=GGTTCTGGGCACGCATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:21.7:1:29.2:1:1:0:60:12:1:0:1 0/0:2:0:0,0:0,2:0:0,0:38:1:31.5:1:1:0:60:4:1:0:0 -2 237971395 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49485;SOR=0;LSEQ=TTGAAGGAATCTCAGGATTT;RSEQ=CAACCTGCTGGAAGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:39,8:0.0408:2,2:21.5:1:28:1:0.33673:4.65478:60:4:0.0408:0:1 0/0:48:0:0,0:37,11:0:2,0:23.4:1:31.6:1:1:0:60:47:1:0:0.1 -2 237971465 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50951;SOR=Inf;LSEQ=CCACGCAATGACAGCATGGC;RSEQ=CACGCTGACCCCGGCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:59,63:0:2,0:26:1:29.9:1:1:0:60:39.667:1:0:0.2 0/1:165:2:1,1:84,79:0.0121:2,2:27:1:32.5:1:1:1.06293:60:4:0.0123:0:1 -2 238791396 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCAAGTAACTAGTGGAGG;RSEQ=GAAGAGGGCCCTGGAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1.5 -2 238792003 . A G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32518;LSEQ=AGGCGGCCGGCCAGCCTTTT;RSEQ=TGGGATACACACACAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:86:48,38:43,49:0.4831:2,2:25.8:1:31.9:1:0.23451:1.44:60:172:0.4831:0:1.1 0/1:215:50:25,25:80,84:0.2326:2,2:27.5:1:31.6:1:1:1.05:60:49:0.229:0:1.3 -2 238792133 . A G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05771;SOR=0.38042;LSEQ=CCGTGATCCCTGCTTTACTC;RSEQ=GGACGTTGAATAGAAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:20:3,17:2,13:0.5714:2,2:20.7:1:30.9:1:1:1.14:60:40:0.5882:0:1 0/1:36:12:2,10:6,18:0.3333:2,2:19.1:1:30.9:1:0.69099:1.64434:60:24:0.3333:0:1.3 -2 239542321 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=0;LSEQ=CCTTGTCAGTCAGTTCAGCG;RSEQ=GTCGCCTTCCTTGTCAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:0.3:2,0:16.3:1:31.3:1:1:0:60:6:0.3333:0:1 0/0:4:0:0,0:0,4:0:0,0:16:1:30:1:1:0:57.8:8:1:0:0 -2 239999464 . T C 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49053;SOR=1.83912;LSEQ=AAACAGCAGACATCAGGCGC;RSEQ=GCGACTCCTAAAACACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:3,3:5,4:0.4:2,2:24.8:1:30.2:1:1:1.23147:60:12:0.4:0:1 1/0:18:10:5,5:4,3:0.5556:2,2:29:1:29.2:1:1:1.31092:60:20:0.5882:0:1 -2 240678139 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.49913;SOR=Inf;LSEQ=CTGAGCATGGCTCTGTTAGC;RSEQ=TCCTTCGCAGGAGACACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:97,47:0:2,0:24.8:1:31.5:1:1:0:60:288:1:0:1 0/1:156:2:1,1:95,59:0.0128:2,2:36:0:31:1:1:1.60502:60:4:0.0132:0:1.5 -2 240678158 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.98644;LSEQ=CCTCCTTCGCAGGAGACACA;RSEQ=GGCCGTGGGAAGGAAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:119,76:0.0051:2,0:3:0:14:0:0.39286:0:60:0:0:0:3 0/1:198:2:1,1:116,80:0.0101:2,2:13.5:1:29:1:1:1.44719:60:4:0.0103:0:1.5 -2 240678163 . G T 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61014;SOR=1.12561;LSEQ=TTCGCAGGAGACACACGGCC;RSEQ=TGGGAAGGAAGCTGCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:211:135:78,57:50,25:0.6398:2,2:25.7:1:30.8:1:0.23865:1.45891:60:134:0.6381:0:1.9 1/0:213:142:82,60:43,28:0.6667:2,2:26.9:1:29.8:1:0.76835:1.12308:60:27.4:0.6618:0:1.8 -2 240678202 . T G 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4284;SOR=1.15098;LSEQ=GTGTTCACTCGCATCAATGT;RSEQ=CATTGTTCTTCACGGCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:279:181:93,88:49,48:0.6487:2,2:25.3:1:32:1:0.90052:1.04:60:180:0.6569:0:1.7 1/0:297:202:106,96:51,42:0.6801:2,2:24.5:1:31.4:1:0.80179:1.09938:60:100:0.6826:0:1.6 -2 240712124 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12581;SOR=0;LSEQ=GCACCGAGCACTCTTCCTCC;RSEQ=GGGCATGGAGCCCTCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:25:1:29.5:1:1:1.13389:60:4:0.1176:0:1 0/0:30:0:0,0:16,14:0:2,0:27.8:1:30.2:1:1:0:60:60:1:0:0.3 -2 240712125 . G A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33632;SOR=0.34187;LSEQ=CACCGAGCACTCTTCCTCCC;RSEQ=GGCATGGAGCCCTCCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:7,7:0.1765:2,2:42:1:31.7:1:1:1.92:60:6:0.1765:0:1.3 0/1:30:2:1,1:15,13:0.0667:2,2:6:0:32.5:1:1:1.14834:60:4:0.0714:0:1.5 -2 241362873 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.21257;LSEQ=CAAGGCTCGCTCAGGGTTCA;RSEQ=TTAGAAAAACAATGCCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:100,25:0.0157:2,0:26.5:1:24.5:1:1:0:60:1:0.008:0:1 0/1:105:2:1,1:82,21:0.019:2,2:6.5:1:27.5:1:0.37674:3.83818:60:4:0.019:0:1.5 -2 241362975 . T A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10675;SOR=0;LSEQ=GCGCCCACAGTGGCTCACCC;RSEQ=GATCACTCTGGGTGAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:113,172:0.0104:2,2:19.7:1:29:1:0.56574:3.03:60:6:0.0105:0:1 0/0:318:0:0,0:140,178:0:2,0:26.5:1:30:1:1:0:60:78.5:1:0:0.5 -2 241362987 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24935;SOR=Inf;LSEQ=GCTCACCCTGATCACTCTGG;RSEQ=TGAGGGTGTGAATGGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:96,170:0:2,0:25.1:1:31.7:1:1:0:60:265:1:0:0.2 0/1:283:3:2,1:112,167:0.0106:2,2:27:1:23.3:1:0.56755:2.97:60:2:0.0072:0:1 -2 241363000 . T C 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCTGGGTGAGGGTGTGAA;RSEQ=GGGAACCCTCTTTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:76,151:0:2,0:23.4:1:30.3:1:1:0:60:112.5:1:0:0.2 0/1:235:93:31,62:53,88:0.3957:2,2:23.3:1:29.8:1:0.578:1.20359:60:30:0.3879:0:1.2 -2 241363006 . C A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62391;SOR=2.8313;LSEQ=GGTGAGGGTGTGAATGGGAA;RSEQ=CCTCTTTTTTCTTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:1,0:60,133:0.0052:2,0:1:0:27:0:0.31443:0:60:2:0.0052:0:1 0/1:207:3:2,1:71,133:0.0145:2,2:16.3:1:29:1:0.2844:3.72:60:6:0.0148:0:1.3 -2 242440221 . G A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.6044;SOR=0.52327;LSEQ=AGCTTGGTGCTCTGGGACCG;RSEQ=AGACAAACCCATCAGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:9:0:31.5:1:1:2.44949:60:4:0.3333:0:1.5 0/1:10:2:1,1:5,3:0.2:2,2:16.5:1:27.5:1:1:1.58108:60:4:0.2:0:1 -2 242440325 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20168;SOR=0;LSEQ=GCCCCACCGGTCCCATCCCT;RSEQ=CCAAGAACCCTGAACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:0.125:2,2:45.5:1:29.5:1:1:1.30929:60:4:0.125:0:1.5 0/0:19:0:0,0:8,11:0:2,0:25.4:1:30.8:1:1:0:60:18:1:0:0.3 -2 242440327 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50202;SOR=Inf;LSEQ=CCCACCGGTCCCATCCCTGC;RSEQ=AAGAACCCTGAACAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:29:1:31.7:1:1:0:60:26:1:0:0.4 0/1:19:2:1,1:7,10:0.1053:2,2:35.5:1:29:1:1:1.40:60:4:0.1053:0:1 -2 242793115 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16531;SOR=Inf;LSEQ=CTCAGCCCCTGGACGGCCTG;RSEQ=AATGGCCTGCACCCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:119,16:0:2,0:21.9:1:32.2:1:1:0:60:134:1:0:0.1 0/1:93:2:1,1:83,8:0.0215:2,2:24.5:1:32.5:1:0.18513:9.84041:60:4:0.022:0:1 -2 242793122 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31761;SOR=4.03373;LSEQ=CCTGGACGGCCTGCAATGGC;RSEQ=TGCACCCTGCCTGCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:1,0:129,21:0.0066:2,0:16:0:31:0:1:0:60:2:0.0068:0:1 0/1:114:3:1,2:94,17:0.0263:2,2:10.7:1:27.7:1:0.07159:10.68996:60:6:0.0265:0:1 -2 242793273 . A G 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.4467;LSEQ=TGGGCACTCCGAGGGCCGTC;RSEQ=GCTGAGCCCCTGCGGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:646:525:273,252:68,53:0.8127:2,2:25:1:30.1:1:0.42057:1.18401:60:64.625:0.8155:0:1.1 1/0:605:399:217,182:106,98:0.6595:2,2:23.7:1:29.4:1:0.60494:1.10:60:48.875:0.6582:0:1.2 -2 242793503 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19352;SOR=Inf;LSEQ=CGGCCCACCGCAGGAAGGAG;RSEQ=CCCGCGGCTCCACAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:46,207:0:2,0:24.4:1:31.5:1:1:0:60:30.625:1:0:0.2 0/1:200:2:1,1:42,155:0.01:2,2:17:1:27:1:0.38633:3.66:60:4:0.0103:0:1 -2 242793519 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18837;SOR=Inf;LSEQ=GGAGGCCCGCGGCTCCACAG;RSEQ=CTGGCTGCAGTACCGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:20,158:0:2,0:24:1:31.6:1:1:0:60:58.333:1:0:0.3 0/1:137:2:1,1:19,116:0.0146:2,2:28.5:1:30:1:0.27158:5.98:60:4:0.0149:0:1.5 -2 242793559 . T C 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05845;SOR=0.43741;LSEQ=CGAACCTGGGCCCCCCACTA;RSEQ=GAGCTGCTTACCCTGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:65:6,59:1,15:0.8025:1,2:23.9:1:30.4:1:1:1.52:60:130:0.8125:0:1.1 1/0:47:30:2,28:2,15:0.6383:2,2:24.1:1:30.1:1:0.61304:1.8407:60:60:0.6383:0:1 -2 242793977 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20491;SOR=Inf;LSEQ=TGCTGCCTGGGGGCTGGGGA;RSEQ=GTGGGGTCCTGGCTATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:150,9:0:2,0:23.8:1:32:1:1:0:60:38.75:1:0:0.1 0/1:132:2:1,1:119,11:0.0152:2,2:25:1:28.5:1:0.17418:10.40114:60:4:0.0155:0:1 -2 242793992 . A T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24983;SOR=0;LSEQ=GGGGAGGTGGGGTCCTGGCT;RSEQ=TAATAGAATGTGAGTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:181,24:0.0144:2,2:7.3:1:22.3:1:0.04177:14.71021:60:2:0.0099:0:1 0/0:189:0:0,0:157,32:0:2,0:21.1:1:28.2:1:1:0:60:46.25:1:0:0.1 -2 242794190 . T TG 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGAGCCGTGCTCCTAGG;RSEQ=GGGGGGTCTTAGTCCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:170,237:0:2,0:24.4:1:28.8:1:1:0:60:15.958:1:0:0.2 0/1:384:22:8,14:129,229:0.0573:2,2:28.7:1:30.9:1:1:1.01:60:44:0.0599:0:0.1 -2 242794234 . CG C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16298;SOR=Inf;LSEQ=TCATCAGGGACTTAGCCTGG;RSEQ=GGGAGATGGGGGGAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:113,95:0:2,0:20.4:1:30.4:1:1:0:59.7:103:0.9952:0:0.8 0/1:142:2:1,1:64,75:0.0141:2,2:21:1:29:1:1:1.17:60:4:0.0143:0.007:0.5 -2 242794289 . G T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18646;SOR=4.71699;LSEQ=AGGGTGGAGGAAGGGGAGGC;RSEQ=GGAGTGAGGGCCGCCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:1:0,1:239,125:0.0027:2,0:37:0:17:0:0.34521:0:60:0:0:0:8 0/1:312:4:1,3:205,103:0.0128:2,2:11.3:1:27.3:1:0.11544:5.93515:60:8:0.0129:0:1.5 -2 242794530 . T G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09568;SOR=Inf;LSEQ=AAGGGCACAAAGGTCAGGGG;RSEQ=TAGGACGGGGTCAGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:81,250:0:2,0:25.3:1:29.6:1:1:0:60:35.778:1:0:0.2 0/1:280:3:1,2:74,203:0.0107:2,2:13.3:1:30.3:1:1:1.37:60:6:0.0108:0:1.3 -2 242796574 . G A 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCTGCATAGGCGTGTGC;RSEQ=GCGTGGGCCCGGGGAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:12:1:29:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 242796660 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGACTCTCAGGGCCAGC;RSEQ=GGCAGCCAGGCCAGGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:13:1:33:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -2 242800561 . C T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10294;SOR=Inf;LSEQ=CCCGTCATTCTACAGAAACA;RSEQ=GCAGCCCCAAGGACCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:24:1:31.6:1:1:0:60:14:1:0:0 0/1:10:4:2,2:3,3:0.4:2,2:16.5:1:28.3:1:1:1:60:8:0.4:0:1.5 -2 242800740 . AC A 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0.94039;LSEQ=AAGGCTGGGCCTGCCACAGC;RSEQ=CCCCCGACCTGCCAGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:87,7:0.0208:2,2:16.5:1:32:1:0.16053:11.6927:60:4:0.0208:0:0 0/1:51:1:1,0:46,4:0.0196:2,0:19:0:33:0:1:0:60:2:0.02:0:0 -2 242800832 . AC A 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.25012;SOR=3.23337;LSEQ=AGGGCCAGGCCCGCCTCAGC;RSEQ=CCCCCGACCTGCCAGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:476:2:2,0:360,113:0.0042:2,0:24:1:34:0:1:0:60:4:0.0043:0:0 0/1:371:5:4,1:261,105:0.0135:2,2:26:1:32.6:1:1:1.61:60:10:0.0136:0:0.2 -2 242802389 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACACCCACCCTTGTGCC;RSEQ=CAGGGGCTGGGGCTCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:0:32:0:1:0:60:4:1:0:1.5 -2 242982298 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50489;SOR=Inf;LSEQ=GATGTAGCAAAACTTGAAAC;RSEQ=CCACTGTTGAGTTTTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:68,41:0:2,0:27:1:30.5:1:1:0:60:108:1:0:0.1 0/1:138:2:1,1:70,66:0.0145:2,2:28.5:1:29:0:1:1.06018:60:4:0.0145:0:1.5 -2 242982321 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22825;SOR=0;LSEQ=ACTGTTGAGTTTTCTTCCCG;RSEQ=GGAGGATGGACCCAAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:66,56:0.0161:2,2:17.5:1:28.5:1:1:1.177:60:4:0.0163:0:1 0/0:135:0:0,0:63,72:0:2,0:29.3:1:30.3:1:1:0:60:66.5:1:0:0.2 -2 243062168 . A G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.49505;SOR=1.75394;LSEQ=CTCGTGTAGCTGCGGGGGGG;RSEQ=GGGGGGGTCAGGAAGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:11,2:0.2632:2,0:8:0:30:1:0.00245:0:55.6:10:0.2941:0:1 0/1:18:7:0,7:9,2:0.3889:2,0:8:0:28.6:1:0.00226:0:57.1:14:0.4667:0:1 -2 243062377 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGGCTTGGGCCCAGAGAAGG;RSEQ=GAGGTTGGAGAGGAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:44.5:1:32:1:1:0:52:4:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:37:1:28:1:1:0:60:4:0.6667:0:1 -20 61053 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATCAACAGACCACTTGCAG;RSEQ=TATACTTCACAGCCCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:20.5:1:29:1:1:1.11803:60:4:0.1111:0:1.5 0/0:9:0:0,0:5,3:0:2,0:26:1:29.9:1:1:0:60:16:0.8889:0:0.4 -20 61098 . C T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06342;SOR=0;LSEQ=CTGCCAAGCACAGACAACCA;RSEQ=TGGGCCCCAGGGGAGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:2,4:5,6:0.3529:2,2:20.7:1:31.7:1:1:1.6177:60:12:0.3529:0:1.3 0/0:9:0:0,0:5,4:0:2,0:25.3:1:31.3:1:1:0:60:18:1:0:0.2 -20 61138 . C CT 31 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.18333;SOR=8.44314;LSEQ=AGGTCTCCTGGTCACCTAAT;RSEQ=TTTTTTTTTTTTATACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:2,4:0.1429:2,0:48:0:30:0:0.42857:0:60:2:0.1667:0:2 1/0:3:2:0,2:0,0:0.6667:0,0:23.5:1:31.5:1:1:0:60:4:0.6667:0:0 -20 306766 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=GACCAGTGGCCCGACATGCA;RSEQ=AACGCCGAGATCTCCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:0:2,0:20:1:32.6:1:1:0:60:20:1:0:0.1 1/0:4:2:1,1:1,1:0.5:2,2:20:0:33.5:1:1:1:60:4:0.5:0:1.5 -20 308878 . C T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCCTGTCCCTGTTGCTGTGG;RSEQ=CCCTCTCACGCCGCCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:18.3:1:32.7:1:1:0:60:6:1:0:1.7 1/1:2:2:1,1:0,0:1:0,2:22:0:30.5:1:1:0:60:4:1:0:2.5 -20 308884 . T C 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=CCCTGTTGCTGTGGCCCCTC;RSEQ=CACGCCGCCATCTCTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:15:0:33:1:1:0:60:4:0.6667:0:2.5 0/0:2:0:0,0:1,1:0:2,0:28:0:32:1:1:0:60:4:1:0:2.5 -20 345775 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=0;LSEQ=TCAGCAAGCCTTGCAGGTCT;RSEQ=TTCTGGTTTCAGAACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:99,82:0.0109:2,2:17:1:28:1:1:1.20606:60:4:0.0112:0:1 0/0:167:0:0,0:100,66:0:2,0:23.5:1:30.9:1:1:0:60:54.333:1:0:0.2 -20 345816 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10405;SOR=Inf;LSEQ=CATTTTGTCCTTCACTCCAG;RSEQ=CTGCCTCAGAGACATGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:115,135:0:2,0:26.8:1:31.4:1:1:0:60:40.667:1:0:0.4 0/1:223:3:2,1:112,108:0.0135:2,2:16.7:1:27.3:1:1:1.92:60:6:0.014:0:1.7 -20 345864 . C T 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.041;SOR=1.63135;LSEQ=TACACAACAATGTGTGCACG;RSEQ=TGGCACACATGCACATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:67:21,46:35,62:0.4085:2,2:24.9:1:29.8:1:0.61597:1.23496:60:134:0.4085:0:1.1 1/0:149:79:28,51:26,43:0.5302:2,2:23.9:1:29.5:1:0.86443:1.10061:60:158:0.5374:0:1.1 -20 345885 . GCA G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.49945;SOR=0;LSEQ=TGGCACACATGCACATGCAT;RSEQ=CACACACACTCTGCATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:32,84:0.0169:2,0:21.5:1:34:0:1:0:60:4:0.0171:0:0.5 0/0:105:0:0,0:32,73:0:2,0:22.6:1:31:1:1:0:60:51.5:1:0:0.6 -20 1420200 . CT C 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGGTATAAGATGGAAC;RSEQ=TAAGTTCAAAGCCTGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:47:0:32.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 1421627 . GC G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAACACAGGAGCCCAAC;RSEQ=CCATTTAAAGAAGGAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:17.3:1:31:1:1:0:60:6:0.75:0.25:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 1421836 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16256;SOR=Inf;LSEQ=ATGGGTATGAAAAGGGCCGC;RSEQ=GCCCCTCTGGAAGACACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:94,37:0:2,0:21.7:1:30.2:1:1:0:60:42.667:1:0:0.2 0/1:89:2:1,1:64,23:0.0225:2,2:35:1:30.5:1:0.46885:2.74522:60:4:0.0227:0:1.5 -20 1421932 . C T 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10962;SOR=1.342;LSEQ=CCTTCTACTGAGGAAGCAGC;RSEQ=GGATCTGTGCAAGACTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:139:69,70:80,86:0.4542:2,2:22.6:1:30.3:1:0.81891:1.06:60:278:0.4572:0:1.3 1/0:216:114:53,61:49,53:0.5278:2,2:27.9:1:30:1:0.89158:1.06376:60:37:0.5236:0:1.2 -20 1421958 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17881;SOR=Inf;LSEQ=TGTGCAAGACTCTACCTACA;RSEQ=GGTTGCTGGGCATGATTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:110,150:0:2,0:26.4:1:31:1:1:0:60:64:1:0:0.6 0/1:191:2:1,1:81,108:0.0105:2,2:19:0:32:0:1:1.33:60:4:0.0111:0:1 -20 1421974 . T C 168 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACAGGGTTGCTGGGCATGA;RSEQ=TGTTAACAAGATCAAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:37:14,23:63,124:0.1652:2,2:26.5:1:32.4:1:0.70539:1.20:60:74:0.1682:0:1.9 0/0:152:0:0,0:57,95:0:2,0:23.6:1:29:1:1:0:60:29.4:1:0:0.7 -20 1422057 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5443;SOR=0;LSEQ=AAGGGCATCATGACAATTAC;RSEQ=TTGCCTATTTTTCATTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:0,50:0.0385:1,2:18.5:1:29.5:1:0.03846:0:60:4:0.04:0:1 0/0:27:0:0,0:2,25:0:2,0:22.3:1:29.8:1:1:0:60:26:1:0:0.1 -20 1624766 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15967;SOR=0.19579;LSEQ=GGAGTGAGTGTGCTTCAGTG;RSEQ=GGAAAAACCCACTTATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:1,3:0.5556:2,2:25.8:1:30.6:1:1:1.85:60:10:0.5556:0:1 0/1:11:2:1,1:2,7:0.1818:2,2:10.5:1:28.5:1:0.49091:3.06:60:4:0.1818:0:1 -20 1626068 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGTAAACATTTTTGTCA;RSEQ=AGTTTCCCAGGTGATTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 2135803 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17976;SOR=Inf;LSEQ=TTCCTGAGCCTCTGCTATGT;RSEQ=CAAAACTCCATGCACCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:183,50:0:2,0:23.9:1:32.1:1:1:0:60:76.667:1:0:0.1 0/1:172:2:1,1:123,47:0.0116:2,2:8.5:1:27:1:0.48144:2.60013:60:4:0.0119:0:1 -20 2135905 . A G 191 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=120.10928;LSEQ=ACCTTGAGAACTTTTGTTCC;RSEQ=GGCAAGAGGGATCTAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:1:1,0:348,330:0.0015:2,0:23:0:29:0:1:0:60:2:0.0015:0:1 0/1:591:89:49,40:256,245:0.1506:2,2:25.1:1:29.5:1:0.56515:1.17:60:178:0.1527:0:1.2 -20 4040556 . TG T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50094;SOR=Inf;LSEQ=GAACAATGCCAACGGCATGC;RSEQ=GGGAACATTGCAGACTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:38,23:0:2,0:25.8:1:31.6:1:1:0:60:29.5:1:0:0.1 0/1:74:2:1,1:38,34:0.027:2,2:30:1:31.5:1:1:1.11596:60:4:0.027:0:1 -20 4040736 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49321;SOR=0;LSEQ=GAACATATATCGGGTGCCTC;RSEQ=CCTCTTTTCCTCTGTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:9,17:0.0714:2,2:30:1:31:1:1:1.84:60:4:0.0714:0:1.5 0/0:24:0:0,0:8,16:0:2,0:20.1:1:29.4:1:1:0:54:48:1:0:0.3 -20 4040763 . T C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02357;SOR=0.13895;LSEQ=TTCCTCTGTGTTCATCATCT;RSEQ=GGCGAATTACTGGAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:4,9:2,3:0.7222:2,2:26.7:1:29.8:1:1:1.46553:60:26:0.7222:0:1.1 0/1:12:3:0,3:2,7:0.25:2,0:28.3:1:25.7:1:1:0:60:6:0.25:0:1 -20 4040828 . T C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=GTGTTTATTATTTGATCAAA;RSEQ=ATATCAAATCAAATAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:7.5:1:33:0:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:0,2:0:0,0:13.5:1:29:1:1:0:60:4:1:0:0 -20 4040961 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTGCCTGCCAGCAGAAC;RSEQ=TGAGACAAAGGCTTGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:20.5:1:33.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 4610341 . A C 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61637;LSEQ=TACACAGGTTACCAGTGTCG;RSEQ=ACCTGATGAAGTCAGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:9,0:0.25:0,2:23.3:1:33.3:1:0.25:0:60:6:0.2727:0:1 0/1:6:1:1,0:5,0:0.1667:0,0:1:0:30:0:1:0:60:2:0.1667:0:1 -20 4610408 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11416;SOR=Inf;LSEQ=GGTGTCATTCACCTTGATGA;RSEQ=GGGATCAGGGTAGCAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:30,18:0:2,0:25.6:1:31.7:1:1:0:60:96:1:0:0.1 0/1:25:2:1,1:11,12:0.08:2,2:17.5:1:32:0:1:1.09:60:4:0.08:0:2 -20 4610410 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.53722;SOR=0;LSEQ=TGTCATTCACCTTGATGAGG;RSEQ=GATCAGGGTAGCAGATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:27,17:0.0435:2,2:11.5:1:28.5:1:1:1.57176:60:4:0.0435:0:1 0/0:25:0:0,0:12,13:0:2,0:25.4:1:30.5:1:1:0:59.4:24:1:0:0.4 -20 5529295 . T C 26 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAATAAAACAAAGATTC;RSEQ=TTTCAATAAAATCCGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:9,1:0.1667:2,0:17:0:26.5:1:1:0:60:4:0.1667:0:2 0/0:4:0:0,0:4,0:0:0,0:28.3:1:32.3:1:1:0:60:8:1:0:0.3 -20 5529310 . G A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36146;SOR=0.2838;LSEQ=GATTCTTTTCAATAAAATCC;RSEQ=TAAGTAAGAGAAAAACCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:8,1:6,0:0.6:0,2:29.3:1:31.3:1:1:0:60:18:0.6:0:1.3 0/1:7:2:2,0:5,0:0.2857:0,0:20.5:1:31:1:1:0:60:4:0.2857:0:1 -20 5529992 . A T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08696;SOR=Inf;LSEQ=ACTACTGAATGTGAAAACAG;RSEQ=GAAGCTGTTACACATATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:58,117:0:2,0:25.3:1:30.1:1:1:0:59.9:28.167:1:0:0.1 0/1:141:3:1,2:40,98:0.0213:2,2:16.7:1:27.3:1:1:1.22:60:6:0.0219:0:1 -20 5530075 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13543;SOR=Inf;LSEQ=GATTGGTTATCAGTCCCATG;RSEQ=AGACACAGCTACTAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:13,72:0:2,0:26.3:1:32.3:1:1:0:60:170:1:0:0.1 0/1:50:2:1,1:19,29:0.04:2,2:25.5:1:28.5:1:1:1.51:60:4:0.04:0:1.5 -20 5530428 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAATCCTTAATGA;RSEQ=TTCAGGGAAATAGCATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:18.5:1:28:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 6201402 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTGCTCAAGTAGCATGTG;RSEQ=CAAACTTGTGGGGTTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15.8:1:31:1:1:0:60:8:1:0:0 0/1:9:2:1,1:2,5:0.2222:2,2:37:1:30:1:1:2.24:60:4:0.2222:0:1 -20 6952343 . A C 109 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00879;SOR=0;LSEQ=CCATGAAAAGGCAGACTGAT;RSEQ=AAATTTAAGACGATATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:31:1:31.6:1:1:0:60:22:1:0:1 0/1:4:1:1,0:3,0:0.25:0,0:36:0:28:0:1:0:60:2:0.25:0:1 -20 6952495 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19575;SOR=Inf;LSEQ=AATTTAGACTTAATTGAAAG;RSEQ=CATTTTAAGTCTAATTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:140,61:0:2,0:25.3:1:31.7:1:1:0:60:200:1:0:0.2 0/1:160:2:1,1:101,57:0.0125:2,2:8.5:1:27:1:1:1.76517:60:4:0.0127:0:2 -20 6952571 . C A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.63302;LSEQ=AGCAATTACCACCATAATAG;RSEQ=CAGAAATAAATTGATTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:106:49,57:100,130:0.3155:2,2:25.9:1:29.2:1:0.63881:1.12:60:105:0.3144:0:1.1 1/0:226:124:55,69:42,60:0.5487:2,2:25.6:1:29.1:1:0.68607:1.14:60:40.333:0.5426:0:1.2 -20 6952618 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.16606;SOR=Inf;LSEQ=ATGTTTTGAACCAAATGCAT;RSEQ=CATAATTTTTGCCTAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:71,158:0:2,0:24.1:1:32:1:1:0:60:37.167:1:0:0.3 0/1:158:2:1,1:57,99:0.0127:2,2:10:0:31.5:1:1:1.73:60:4:0.0127:0:2.5 -20 6952790 . C T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTCCATATTTCCTCTCTCA;RSEQ=TCTAGGAGCTTAAGGATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:24.1:1:30.9:1:1:0:60:20:1:0:1.4 1/1:2:2:0,2:0,0:1:0,0:24.5:1:29.5:1:1:0:60:4:1:0:1.5 -20 6952829 . T G 78 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATATTGAGTATGGGCCAG;RSEQ=TAGCTTGCCGCCAAAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:17.4:1:33.8:1:1:0:60:10:1:0:1.8 1/1:1:1:0,1:0,0:1:0,0:26:0:33:0:1:0:60:2:1:0:2 -20 7600865 . AT A 90 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.25701;SOR=0.22815;LSEQ=TTGCTCTGCTGTCTTTGAGC;RSEQ=TTTTTTTTTCCTGGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:7:7,0:73,3:0.0843:1,0:20.3:1:32.1:1:1:0:60:14:0.0843:0.0241:0 0/1:49:1:1,0:46,2:0.0204:1,0:37:0:31:0:1:0:60:2:0.0208:0:0 -20 7601013 . A T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.63201;LSEQ=TGTAAATGAATCTGAATGTT;RSEQ=TCAACAGACAGAACAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:154:63,91:107,144:0.3793:2,2:24.8:1:29.9:1:0.75649:1.07309:60:153:0.3806:0:1.1 1/0:342:211:95,116:59,71:0.617:2,2:26.1:1:29.8:1:1:1.01464:60:104.5:0.6183:0:1.1 -20 7601180 . A AATG 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00432;SOR=6.98701;LSEQ=CCTCCCAAAGAAATACTGAA;RSEQ=ATATTATAAATGATGTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:0,9:1,23:0.2727:1,0:33.2:1:30.6:1:1:0:60:18:0.2813:0.0303:0 1/0:15:11:0,11:1,3:0.7333:2,0:24:1:29.7:1:0.26667:0:60:22:0.7857:0.2667:0 -20 7602473 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGTCTGTTTCAACAAGGT;RSEQ=CTGATTGGTGCGTTTACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29.5:1:1:0:60:4:1:0:1.5 -20 8678446 . G A 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TCAAGGTAGAGTATATGAAT;RSEQ=TTACTAAGAGAGGCAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24:1:30.3:1:1:0:60:6:1:0:1 0/0:1:0:0,0:0,1:0:0,0:2:0:30:0:1:0:60:2:1:0:0 -20 8679696 . A T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31712;SOR=4.0635;LSEQ=CTGGGGTCCTAGGTACTTGG;RSEQ=GAGTGACTGGAGAAAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:0,1:137,70:0.0048:2,0:1:0:27:0:0.34135:0:60:2:0.005:0:1 0/1:156:3:1,2:100,53:0.0192:2,2:20.7:1:27:1:0.28394:3.73987:60:6:0.0194:0:1 -20 8679723 . C T 47 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13748;SOR=0;LSEQ=CTGGAGAAAGAAGTTGTGGG;RSEQ=TTCAGGGAACATGTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:4:1,3:191,151:0.0115:2,2:12.3:1:23.5:1:0.32718:3.78098:60:3:0.0087:0:1.8 0/0:266:0:0,0:153,113:0:2,0:25.3:1:31.7:1:1:0:60:43.333:1:0:0.2 -20 8679854 . G T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01872;SOR=Inf;LSEQ=CCTGTTGCCTGGGATACCTG;RSEQ=GTCTCAGGGAAGTGTCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:2,84:0:1,0:26.9:1:31.1:1:1:0:60:85:1:0:0 0/1:52:4:0,4:1,47:0.0769:1,0:39.5:1:30.3:1:1:0:60:8:0.0769:0:1 -20 9520133 . G A 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGATGCCTGTATTGTCTCAT;RSEQ=AGGGGGACGATGCAAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1082:0:0,0:613,466:0:2,0:24.7:1:31.5:1:1:0:60:82:0.9972:0:0.4 0/1:654:33:16,17:346,273:0.0505:2,2:24.3:1:29.5:1:0.47313:1.34598:60:66:0.051:0:1.1 -20 9520142 . G A 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42889;LSEQ=TATTGTCTCATGAGGGGGAC;RSEQ=ATGCAAGACGGTGGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1128:271:158,113:462,394:0.2402:2,2:25.3:1:30:1:0.23369:1.19:60:66.75:0.2399:0:1.1 0/1:712:85:47,38:340,286:0.1194:2,2:26:1:29.7:1:0.9079:1.04:60:170:0.1206:0:1.2 -20 9523379 . A G 215 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGTCCACCTGTTAGGCAC;RSEQ=CCCTACTGGTTATCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:912:0:0,0:337,574:0:2,0:24:1:29.8:1:1:0:60:81.818:0.9989:0:0.1 0/1:625:137:57,80:175,313:0.2192:2,2:25.5:1:30.4:1:0.23065:1.27:60:67.5:0.2188:0:1.1 -20 9523663 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGTAGTTAACTGTCTAT;RSEQ=AGGGCAGATGAGAAAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:17:1:29.5:1:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:0:0,0:26:0:32:0:1:0:60:2:1:0:0 -20 9525091 . C T 167 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=30.93546;LSEQ=CCAACCAATGATTTCCTCTT;RSEQ=GGCACCTCTTTGGAAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1394:2:1,1:669,723:0.0014:2,2:10:1:19:1:1:1.08:50.5:1:7e-04:0:2 0/1:1127:48:21,27:536,541:0.0426:2,2:27.8:1:30:1:0.46219:1.27356:60:96:0.043:0:1.1 -20 9543622 . C T 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=1.54828;LSEQ=CATCGCCGACAAGGTAGCTG;RSEQ=TGTACATGTCAACCACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1143:282:127,155:377,482:0.2467:2,2:25.6:1:30.1:1:0.78227:1.05:60:140:0.2487:0:1.1 0/1:939:316:138,178:304,318:0.3365:2,2:23.9:1:29.6:1:0.14617:1.23279:60:104.333:0.338:0:1.5 -20 9543681 . C T 201 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=201.46577;LSEQ=ATGATCACGACCTGGGGAAA;RSEQ=GGGAAATATACTTTTGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:696:1:1,0:224,469:0.0014:2,0:43:0:31:0:0.32421:0:60:2:0.0015:0:6 0/1:475:107:35,72:118,229:0.2253:2,2:23.7:1:29.9:1:0.90693:1.05989:60:214:0.2286:0:2.6 -20 9543688 . T G 206 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=186.82144;LSEQ=CGACCTGGGGAAACGGGAAA;RSEQ=ATACTTTTGACTTGTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:624:1:1,0:199,424:0.0016:2,0:50:0:32:0:0.32051:0:60:2:0.0016:0:6 0/1:415:96:33,63:100,218:0.2313:2,2:22.7:1:31.4:1:0.61874:1.14:60:192:0.2336:0:2.7 -20 9543833 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02023;SOR=Inf;LSEQ=AAAAGCATCAAGGGTAGCTA;RSEQ=TAGAAATAAAAGGAATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:0:1,0:22.9:1:31.3:1:1:0:60:47:1:0:0.1 0/1:19:3:0,3:1,15:0.1579:1,0:22.3:1:32:0:1:0:60:6:0.1579:0:1 -20 9546554 . G A 131 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=36.78039;LSEQ=CTTTACCTCATTGAAAAGCA;RSEQ=TTCTCGTCTCTGTTGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:980:1:1,0:615,364:0.001:2,0:1:0:26:0:1:0:60:2:0.001:0:1 0/1:745:27:19,8:441,274:0.0362:2,2:27.4:1:27.7:1:0.42344:1.47:60:12.5:0.0342:0:1.4 -20 9547018 . C G 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.076;SOR=0.67392;LSEQ=GGCTGAGGACCATCTGTGCT;RSEQ=GATCGTAATCCACCTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:80:15,65:57,206:0.2326:2,2:24.6:1:31.1:1:0.64021:1.19845:60:79:0.2351:0:1.1 0/1:236:40:9,31:53,143:0.1695:2,2:24.2:1:30.6:1:0.69399:1.2753:60:80:0.1709:0:1.1 -20 9547028 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15268;SOR=Inf;LSEQ=CATCTGTGCTCGATCGTAAT;RSEQ=CACCTGGGAAGACAGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:55,228:0:2,0:24.1:1:31.1:1:1:0:60:34.375:1:0:0.4 0/1:182:2:1,1:41,139:0.011:2,2:16:1:25.5:1:0.40926:3.36:60:4:0.011:0:1 -20 9547288 . T G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCTATTTTCTTGTTCAG;RSEQ=AATGAAAAACCCCATCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:40:1:30.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 9560633 . C T 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74304;SOR=0.69454;LSEQ=GCCTTATCCTAAACCTCTGC;RSEQ=CTGGGGCCTCACAAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:15:15,0:38,0:0.283:1,1:21.7:1:32:1:1:0:60:30:0.2941:0:1.4 0/1:14:3:3,0:11,0:0.2143:0,0:17.7:1:30:1:1:0:60:6:0.2143:0:2 -20 9560712 . A G 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30093;SOR=0.75667;LSEQ=AAACAAGTACTTTACAATCC;RSEQ=ATCGTATAAAAAGGTCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:59:54,5:94,7:0.3688:2,2:25.1:1:29.4:1:0.76112:1.24164:60:58:0.3694:0:1.3 0/1:111:34:33,1:67,10:0.3063:2,1:23.1:1:29.6:1:0.16762:4.87:60:33:0.3:0:1.1 -20 9561601 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16124;SOR=4.84552;LSEQ=GGAATAATAGAGGGAATATT;RSEQ=TTTAAAGAAAATATTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:1,0:50,210:0.0038:2,0:1:0:24:0:0.1954:0:60:2:0.0039:0:1 0/1:164:3:2,1:42,119:0.0183:2,2:25:1:28.3:1:0.17563:5.59:60:6:0.0186:0:1 -20 9624587 . C T 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.00168;SOR=0;LSEQ=ACATCTAAAGCCAAAGTTCC;RSEQ=TTTCATGGGCTGCAATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:33,0:0,0:1:0,1:26.1:1:31.1:1:1:0:60:32:1:0:1.2 0/0:2:0:0,0:2,0:0:0,0:18:1:31:1:1:0:60:4:1:0:0 -20 9625003 . G A 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0184;SOR=0;LSEQ=AAAACCTGGGAAATATAAAT;RSEQ=GAAAAGAGGCAGCCATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:301:301:39,262:0,0:1:0,2:22:1:30.7:1:1:0:60:36.625:1:0:1.1 1/1:248:243:36,207:1,4:0.9798:2,2:23.5:1:30.4:1:0.55737:1.43513:60:33.714:0.9793:0:1.2 -20 9625011 . G A 39 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10062;SOR=Inf;LSEQ=GGAAATATAAATGGAAAAGA;RSEQ=GCAGCCATTTATATCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:24,229:0:2,0:21.4:1:31.1:1:1:0:60:49.6:1:0:1 0/1:221:3:1,2:26,191:0.0136:2,2:14:1:24.7:1:0.32614:3.64:60:2:0.0093:0:4 -20 9625015 . G T 50 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25178;SOR=0;LSEQ=ATATAAATGGAAAAGAGGCA;RSEQ=CCATTTATATCTTGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:3:1,2:19,203:0.0133:2,2:7:0:31.7:1:0.24466:5.27:60:6:0.0134:0:2.3 0/0:196:0:0,0:20,176:0:2,0:20.8:1:31.9:1:1:0:60:38.2:1:0:1.1 -20 10488852 . G A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11778;SOR=0.32357;LSEQ=AGCCAGTGTGTGTGCCCACA;RSEQ=CCCTGCCCTTGGAGCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:4,5:10,10:0.3103:2,2:31.9:1:28.1:1:1:1.24042:60:8:0.2857:0:1.1 0/1:32:4:2,2:14,14:0.125:2,2:30:1:25:1:1:1:60:3:0.0968:0:1.3 -20 10869335 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11661;SOR=Inf;LSEQ=ACTTTAATGACTAAAGTCCC;RSEQ=GTAGCAGCACTGGGTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:195,182:0:2,0:25.1:1:30.5:1:1:0:60:187.5:1:0:0.1 0/1:196:2:1,1:90,104:0.0102:2,2:32:1:27:0:1:1.15:60:4:0.0104:0:1.5 -20 10869731 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12363;SOR=Inf;LSEQ=TTTTCTGCAATTACAGTCAC;RSEQ=TGAACCTCTTTTTTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:65,266:0:2,0:21.4:1:30.6:1:1:0:60:32.1:1:0:0.2 0/1:180:2:1,1:47,131:0.0111:2,2:7:0:32.5:1:0.46331:2.77:60:4:0.0114:0:1.5 -20 10869747 . AT A 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.78834;SOR=1.19349;LSEQ=TCACATGAACCTCTTTTTTT;RSEQ=TTTTTTTTTTGACGGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:10:1,9:28,174:0.0465:2,2:31.9:1:31:1:1:1.44604:60:20:0.0476:0.0047:1.5 0/1:109:6:0,6:21,82:0.055:2,0:31.5:1:31.3:1:0.59374:0:60:12:0.055:0:0.3 -20 10869778 . G A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20842;SOR=0.55303;LSEQ=TGACGGAGTTTTGCTCTGTC;RSEQ=CCCAGGCTGGAGTGTCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:38:2,36:2,44:0.4524:1,2:22.9:1:29.9:1:1:1.22:59.2:37:0.4512:0:1.3 0/1:32:10:1,9:1,21:0.3125:1,2:27.6:1:31.2:1:0.53427:2.27:60:20:0.3333:0:1 -20 11361032 . G A 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCAAATCAGATTAATAG;RSEQ=GCCTGAACTGAACCCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:0.8333:0,2:24.6:1:24.4:1:1:0:60:1.5:0.75:0:2.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 11361090 . TG T 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.06014;SOR=0.09974;LSEQ=CAGAAGAGGGAACTGACCAC;RSEQ=GGGGGAAAAAAAAAAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:3,0:0.6667:0,2:34.3:1:27.5:1:1:0:60:2:0.8:0:1.5 0/1:7:1:1,0:6,0:0.1429:0,0:37:0:31:0:1:0:60:2:0.1667:0:2 -20 11361096 . G A 28 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=AGGGAACTGACCACTGGGGG;RSEQ=AAAAAAAAAAACAGAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,1:0.2:2,0:30:1:28.5:1:1:0:60:4:0.25:0:4 0/0:8:0:0,0:5,0:0:0,0:29.2:1:17.2:1:1:0:60:0.25:0.3333:0:2 -20 12158670 . G C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.26953;LSEQ=ATTTTAAAGTTTAATATCTT;RSEQ=TTGTTAGGTTTGTATTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:6,1:8,1:0.4375:2,2:19.9:1:31.4:1:1:1.30929:60:14:0.4375:0:1.1 1/0:4:2:2,0:2,0:0.5:0,0:19:1:29.5:1:1:0:60:4:0.5:0:1.5 -20 12158734 . C T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01218;LSEQ=GCACTGAAAAACACAGCTGC;RSEQ=GGAGTCAGATGGGTGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:2,1:22,19:0.0682:2,2:30:1:28.3:1:1:1.71:60:6:0.0682:0:1.3 0/1:29:2:1,1:15,12:0.069:2,2:37:1:30:1:1:1.24034:60:4:0.069:0:1.5 -20 12335467 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17622;SOR=Inf;LSEQ=AAAAACATTAGAGCACTTTG;RSEQ=AGTCTAAGGAAGTTTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:25,13:0:2,0:21.4:1:31.3:1:1:0:60:37:1:0:0.2 0/1:28:2:1,1:14,12:0.0714:2,2:32:1:27.5:1:1:1.16024:60:4:0.0714:0:1 -20 12335510 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51787;SOR=0;LSEQ=GCCATTCAGTGTTCTTGAGC;RSEQ=AAAGTCTGTCATCAGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:20,19:0.0488:2,2:36.5:1:32.5:1:1:1.05134:60:4:0.0488:0:1 0/0:26:0:0,0:10,16:0:2,0:34.4:1:29.6:1:1:0:60:52:1:0:0.1 -20 15770383 . A G 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.4179;LSEQ=ACACTACATAAAGAAGGAAG;RSEQ=AAACACAAGTGCATAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:136:57,79:78,85:0.4548:2,2:28.2:1:31:1:0.35071:1.27079:60:135:0.453:0:1.2 0/1:333:86:44,42:118,129:0.2583:2,2:25.8:1:30.7:1:0.61773:1.14:60:85:0.256:0:1.5 -20 15770394 . G A 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05266;SOR=0;LSEQ=AGAAGGAAGAAAACACAAGT;RSEQ=CATAAAATTTAAAATGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:4:2,2:123,166:0.0137:2,2:16.5:1:30:1:1:1.35:60:8:0.0138:0:1 0/0:317:0:0,0:144,173:0:2,0:25.7:1:31.6:1:1:0:60:104.667:1:0:0.4 -20 15770428 . G A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03696;LSEQ=ATGGCATAAAGGAAATGAGA;RSEQ=TTATATTAGAAATTAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:27:7,20:54,127:0.1292:2,2:27.8:1:30.2:1:0.82194:1.21378:60:54:0.1337:0:1.8 0/1:210:28:13,15:60,121:0.1333:2,2:28.3:1:29.8:1:0.20234:1.74:60:56:0.1346:0:2 -20 16141991 . G T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAACCTGAATCACCCAAA;RSEQ=TTCTCCCTGGGACCTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:28.7:1:30.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 16142184 . C T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4196;SOR=0.71374;LSEQ=GGTACATAGGTTGCACCACC;RSEQ=TTATTAAGAAGAATCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:41:41,0:25,0:0.6212:1,1:22.8:1:31:1:1:0:60:19.5:0.6094:0:1 1/0:39:21:21,0:18,0:0.5385:1,1:24.9:1:31.8:1:1:0:60:42:0.5385:0:1 -20 16142254 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17338;SOR=Inf;LSEQ=ACAAATCTATGGATTGTCTG;RSEQ=ATGCCTAGAAGGCATTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:178,81:0:2,0:24.3:1:31.1:1:1:0:60:128.5:1:0:0.4 0/1:186:2:1,1:126,58:0.0108:2,2:12:1:25:1:0.53496:2.1625:60:4:0.0108:0:1 -20 16142258 . C T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56969;SOR=2.91961;LSEQ=ATCTATGGATTGTCTGGATG;RSEQ=CTAGAAGGCATTCGATAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:0,1:188,89:0.0036:2,0:1:0:27:0:0.32374:0:60:2:0.0037:0:1 0/1:192:2:0,2:128,62:0.0104:2,0:6.5:1:24:0:0.10995:0:60:4:0.0105:0:1 -20 16142333 . A C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08435;LSEQ=ATTTTCCTACAGACGACAAC;RSEQ=TCTGAGCAACAGAATAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:465:279:139,140:94,92:0.6:2,2:25.7:1:31.2:1:0.92465:1.02904:60:54.8:0.5996:0:1.1 0/1:366:41:17,24:160,165:0.112:2,2:22.4:1:30.2:1:0.40816:1.36781:60:82:0.1142:0:1.2 -20 16142702 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTAGCCAACCTCCCTG;RSEQ=CCCAAACAATAAATTACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:27:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 16911203 . T C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCTGACAGCCACACAGGG;RSEQ=CGTGGAGCCCACATCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:36.7:1:31.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 16911205 . G A 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGACAGCCACACAGGGTC;RSEQ=TGGAGCCCACATCCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:34.7:1:30.3:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 16912013 . T G 67 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCAGGAGCGATCCTACTG;RSEQ=CATCGGGTTGGTGCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:22.8:1:33.5:1:1:0:60:8:1:0:1.3 1/1:3:3:1,2:0,0:1:0,2:28:1:30.7:1:1:0:60:6:1:0:1 -20 16912245 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GCATCAACAACAAAAAAAGT;RSEQ=CCCACAAAACCCCATCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:19.5:1:29.5:1:1:2.44949:60:4:0.3333:0:1 0/0:4:0:0,0:3,1:0:2,0:34.8:1:32.5:1:1:0:60:8:1:0:0.3 -20 16912401 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=ATGTCTCTCCAGGAAGGATG;RSEQ=AGACCTGGATAGAGGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:41.5:1:30.5:1:1:1.83:60:4:0.25:0:1 0/0:5:0:0,0:2,3:0:2,0:28.6:1:32.6:1:1:0:60:10:1:0:0 -20 16985836 . C T 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.77001;LSEQ=TGCTTCCCTCCAGACTCTAT;RSEQ=TTTATGGAATAGAAACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:15.5:1:29.5:1:1:0:60:8:0.5714:0:1.3 1/0:4:2:0,2:0,2:0.5:0,0:36.5:1:28.5:1:1:0:60:4:0.5:0:1 -20 16985920 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAACCAATTTATTAATAA;RSEQ=TTATATGTCTTTAACTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 18465583 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGCGGCTTTTTAGAATT;RSEQ=CAGCTTCATATTTTCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19.5:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 18465644 . T A 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTATCCAAGCCAAAAACA;RSEQ=GGGACCCATGGAAAGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:24.6:1:28.8:1:1:0:60:10:0.7143:0:1.4 1/1:2:2:2,0:0,0:1:0,0:25:1:29.5:1:1:0:60:4:1:0:1 -20 18465840 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06447;SOR=Inf;LSEQ=CAAAAATTATTTCAAGTATT;RSEQ=AATATACATACATATATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:179,66:0:2,0:22.1:1:31.6:1:1:0:60:60.25:1:0:0.1 0/1:165:3:1,2:115,47:0.0182:2,2:14:1:26.7:1:0.21063:4.83989:60:6:0.0186:0:1 -20 18465846 . A T 52 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.01335;SOR=Inf;LSEQ=TTATTTCAAGTATTGAATAT;RSEQ=CATACATATATAAGATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:190,91:0:2,0:22.3:1:28.5:1:1:0:60:562:1:0:0.1 0/1:207:5:1,4:134,68:0.0242:2,2:10.2:1:22.8:1:0.05068:7.80339:60:4:0.0195:0:1 -20 18465943 . G A 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05823;SOR=Inf;LSEQ=CGGAAAGAGGAGAGGCACCC;RSEQ=ATATATGTTCTCTAGGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:128,175:0:2,0:22.4:1:30:1:1:0:60:49.5:0.9933:0:0.2 0/1:296:4:3,1:119,173:0.0135:2,2:14.3:1:28:1:0.30964:4.34:60:8:0.0137:0:1 -20 18466145 . A G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.60972;SOR=2.17304;LSEQ=GGCATTGTTGTAAATAAACA;RSEQ=GGGCAATATTCTTGCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:1,0:69,139:0.0048:2,0:29:0:29:0:0.33493:0:60:2:0.0048:0:1 0/1:194:2:1,1:68,124:0.0103:2,2:24:1:30.5:1:1:1.82:60:4:0.0103:0:1 -20 18466346 . G A 58 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=GGCTCAGGCGGGCAGATCAC;RSEQ=AGGTGAAGAGATCGAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:27.8:1:29:1:1:0:60:8:0.5714:0:1 1/0:2:1:0,1:0,1:0.5:0,0:39:0:32:0:1:0:60:2:0.5:0:1 -20 18466743 . A AAT 24 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTAAAAAATTATATATATA;RSEQ=ATATATATAAATATAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:24:1:1:0:59:4:1:0.5:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 19414754 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08425;SOR=Inf;LSEQ=AGGAAATGAAAGACGTGATT;RSEQ=ATACACATCACTGAGCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:55,0:0:1,0:22.6:1:28.6:1:1:0:60:110:1:0:0.1 0/1:23:2:1,1:21,0:0.087:1,2:21.5:1:28:1:0.08696:0:60:4:0.087:0:1 -20 19414947 . G A 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCCCCTTTTGATCACTCC;RSEQ=CAGCGAGGGCTTGGGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:146,240:0:2,0:26.1:1:30.8:1:1:0:60:47.25:1:0:0.2 0/1:267:109:45,64:74,84:0.4082:2,2:24:1:28.9:1:0.38337:1.25185:60:108:0.4091:0:1.1 -20 19414986 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.17974;SOR=Inf;LSEQ=GCTCTCTAGAGAGAAGCAGG;RSEQ=AGCTGAACAAGGTGCGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:57,157:0:2,0:23.1:1:32:1:1:0:60:41.8:1:0:0.1 0/1:158:2:1,1:48,108:0.0127:2,2:10.5:1:26:1:0.52544:2.24:60:4:0.0131:0:1 -20 19506525 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACAGGCGCGGCTGTGC;RSEQ=GTGAGGATTCACATGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:2,0:27,1:0.0667:1,0:16.5:1:29.5:1:1:0:60:4:0.0667:0:1 0/0:8:0:0,0:8,0:0:0,0:25.3:1:31.3:1:1:0:60:16:1:0:0.1 -20 19506547 . G A 95 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14993;SOR=0.20446;LSEQ=TGAGGATTCACATGCCTCAC;RSEQ=AGGGTCCTCTGGGAGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:10,0:29,1:0.25:1,0:25.2:1:28.7:1:1:0:60:9:0.2308:0:1.4 0/1:16:1:1,0:15,0:0.0625:1,0:33:0:31:0:1:0:60:2:0.0625:0:1 -20 19506609 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54482;SOR=0;LSEQ=ATTCTCCTGGAGTTTCTCCA;RSEQ=TTCTGAACGAACTCGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:81,23:0.0189:2,2:22:1:32.5:1:0.40323:3.46866:60:4:0.019:0:1 0/0:56:0:0,0:48,8:0:2,0:22.4:1:31.4:1:1:0:60:112:1:0:0.1 -20 19506623 . C T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27605;SOR=3.81968;LSEQ=TCTCCAGTTCTGAACGAACT;RSEQ=GGAGGTAGGGGAGTGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:1,0:110,38:0.0067:2,0:6:0:32:0:1:0:60:2:0.0068:0:1 0/1:79:2:1,1:58,19:0.0253:2,2:7:1:24.5:1:0.44466:3.00087:60:4:0.0253:0:1 -20 19506644 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14159;SOR=Inf;LSEQ=GGAGGTAGGGGAGTGGGAGA;RSEQ=GATGCCCTGCCTCTCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:149,64:0:2,0:25.2:1:31.4:1:1:0:60:29.429:1:0:0.3 0/1:129:2:1,1:88,39:0.0155:2,2:28:0:32:0:0.52568:2.24068:60:4:0.0155:0:1.5 -20 19506665 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1626;SOR=Inf;LSEQ=GATGCCCTGCCTCTCATCCA;RSEQ=CTACCCAGCTTTGACACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:174,101:0:2,0:26.4:1:31.9:1:1:0:60:136.5:1:0:0.4 0/1:187:2:1,1:120,65:0.0107:2,2:16.5:1:25.5:1:1:1.8398:60:4:0.0108:0:1 -20 19506666 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16086;SOR=Inf;LSEQ=ATGCCCTGCCTCTCATCCAG;RSEQ=TACCCAGCTTTGACACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:177,103:0:2,0:26.3:1:31.8:1:1:0:60:55:1:0:0.4 0/1:188:2:1,1:121,65:0.0106:2,2:31:0:31.5:1:1:1.85507:60:4:0.0107:0:1.5 -20 19506707 . C T 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.36204;SOR=1.28075;LSEQ=CCTGGAATGGTCACACCCTC;RSEQ=GCGGGTGTGCTGTGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:33:14,19:172,156:0.0914:2,2:22:1:30.3:1:0.28043:1.49466:60:66:0.0922:0:1.8 0/1:289:33:18,15:138,118:0.1142:2,2:22.3:1:29.7:1:1:1.03:60:32:0.1115:0:1.8 -20 19506729 . A G 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63764;SOR=1.07784;LSEQ=CGGGTGTGCTGTGTCACCCC;RSEQ=CTGCCAGTCTCCCCGATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:155:71,84:99,114:0.4212:2,2:25:1:30.6:1:0.916:1.02736:60:76.5:0.4227:0:1.3 0/1:298:131:69,62:78,88:0.4396:2,2:27.3:1:30.2:1:0.35132:1.25:60:42.667:0.4414:0:1.3 -20 19506958 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05714;SOR=Inf;LSEQ=TGCAAGCCCTGGCTATGCCA;RSEQ=GTACTGCCTATGTGACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:0:0,0:27.2:1:28.3:1:1:0:60:10:1:0:0.2 1/0:4:2:0,2:0,2:0.5:0,0:39.5:1:32:0:1:0:60:4:0.5:0:1 -20 19601874 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10644;SOR=Inf;LSEQ=CTCTTTGTGCAGCAGTCATG;RSEQ=AGGATGCTTGAGTGGATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:125,2:0:1,0:25.8:1:32:1:1:0:60:62.5:1:0:0 0/1:62:2:2,0:60,0:0.0323:1,0:32.5:1:32:0:1:0:60:4:0.0328:0:1 -20 19602042 . G A 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.47947;LSEQ=TCAGAAGTAGATTTGTAGAA;RSEQ=GGTTGTTGGTTGGTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1229:145:68,77:546,535:0.118:2,2:23.8:1:30.6:1:0.42718:1.1555:60:144:0.118:0:1.1 0/1:875:218:114,104:327,330:0.2491:2,2:24.4:1:29.9:1:0.53252:1.11:60:35.333:0.2448:0:1.3 -20 19602477 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCTCCACCATTTCTCCT;RSEQ=AGAAATGCTCCTCTTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:17.5:1:28:0:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 20566463 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTAAAAAGACACAGCTG;RSEQ=CAGTGGGCCTTGAACCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:23,3:0.0714:2,0:27:1:31:1:1:0:60:4:0.0714:0:1 0/0:11:0:0,0:10,1:0:2,0:22.1:1:31.8:1:1:0:60:22:1:0:0.1 -20 20566526 . A T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08084;SOR=Inf;LSEQ=AGAGTTAAAAGAAAAAAAAG;RSEQ=ATGCCCCACAAATGTTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:34,29:0:2,0:26.3:1:30:1:1:0:60:126:1:0:0.1 0/1:49:3:2,1:23,21:0.0612:2,2:31.7:1:27:1:1:1.80:60:6:0.0612:0:1 -20 21115991 . G A 43 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATGTTAGGTTCTACCTCT;RSEQ=TTACAGTTACTTGCGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:35.7:1:27.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 21116216 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.509;SOR=0;LSEQ=TTGCAAATCTTTGTTTTGAG;RSEQ=GTGAATATTTTTGTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:2,0:103,9:0.0175:2,0:42.5:1:29.5:1:1:0:60:4:0.0175:0:1 0/0:84:0:0,0:68,16:0:2,0:22.9:1:30.7:1:1:0:60:168:1:0:0.3 -20 21116302 . A G 273 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42371;SOR=0.85814;LSEQ=GCCAACAATTGAAATGCTGT;RSEQ=TAACAGGGAAGAAGAGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:449:374:205,169:32,42:0.833:2,2:28.3:1:32:1:0.07507:1.59:60:92.5:0.8315:0:1.1 1/1:417:338:191,147:46,33:0.8106:2,2:26.7:1:31.1:1:0.80213:1.07267:60:66.6:0.8182:0:1.1 -20 21117899 . CT C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTCTCTGGTTCTGGCAC;RSEQ=TTTTCCCCTTGAAGTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:32.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 21177898 . G A 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.40061;LSEQ=AGACTCTTATCACTTACTCA;RSEQ=TAGACTGGATATAGATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:61:27,34:157,220:0.1393:2,2:22.7:1:30:1:0.78001:1.11:60:122:0.1422:0:1 0/1:325:91:38,53:112,122:0.28:2,2:25.5:1:29.8:1:0.38581:1.27944:60:182:0.2844:0:1.1 -20 21377044 . C T 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56425;SOR=3.0829;LSEQ=GAGAAGAGCACGCGGCGCTT;RSEQ=CTTCGCGGAGCGGCTGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:0,1:10,151:0.0062:2,0:39:0:28:0:1:0:60:2:0.0064:0:1 0/1:106:2:1,1:8,95:0.0189:2,2:14:0:31.5:1:0.16484:11.25:60:4:0.019:0:2 -20 21377119 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GCGTCCGCGATGCCGGTCAG;RSEQ=GACCCCATGCCGGCCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:22.4:1:31.2:1:1:0:60:10:1:0:0.4 1/0:4:2:0,2:1,1:0.5:2,0:18.5:1:29:1:1:0:60:4:0.5:0:1 -20 21377205 . G A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGGGGAAGGCGAGTGA;RSEQ=CTCCAGGCCCGCCGGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:14:0:32:0:1:1:60:4:0.5:0:1 -20 21377636 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52569;SOR=0;LSEQ=GGGTTGGCGCCGTACCAGCC;RSEQ=GTGGCCGCGCCGCCCCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:34.5:1:30.5:1:1:1.55:60:4:0.1429:0:1.5 0/0:8:0:0,0:4,4:0:2,0:19.3:1:25.9:1:1:0:60:7:1:0:0.3 -20 21492794 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13205;SOR=Inf;LSEQ=CACCCGGCGCGGCGAGGGCA;RSEQ=GGGCGTCACCTCCATACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:252,91:0:2,0:21.7:1:31.2:1:1:0:60:37.111:0.9911:0:0.2 0/1:198:2:1,1:137,59:0.0101:2,2:24.5:1:30:1:0.51531:2.31102:60:4:0.0103:0:1.5 -20 21493012 . TC T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.52758;SOR=1.80625;LSEQ=GCTTTCGCTTCTTGCCGGCG;RSEQ=CCCCCCGCCGCCCGGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:2,78:0.0244:1,0:45.5:1:30.5:1:1:0:60:4:0.0253:0:0.5 0/1:23:1:0,1:0,22:0.0435:1,0:35:0:32:0:1:0:60:2:0.0476:0:1 -20 21494676 . T G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCGGCCGCTCGGCGCGCGG;RSEQ=GGCGGCTGGTGGCGAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:24.3:1:26:1:1:0:60:6:1:0:2 0/1:10:2:1,1:4,4:0.2:2,2:10:0:32:1:1:1:60:4:0.2222:0:1.5 -20 22562674 . T C 290 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=2.00063;LSEQ=TTGAGGTCCATTTTGTGGGG;RSEQ=TGGTGGTGGTGGTGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:769:603:371,232:89,69:0.7841:2,2:23.9:1:31.4:1:0.23638:1.24:60:36.688:0.7922:0:1.1 1/1:488:429:255,174:27,21:0.8791:2,2:24.9:1:30.8:1:0.75718:1.14:60:27.6:0.9059:0:1.2 -20 22562823 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGGGCCCAGCAGGTGGG;RSEQ=CGCGGCCTGCTGCTGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:3,171:0.0114:1,2:5.5:1:29.5:1:0.04506:49.50:60:4:0.0119:0:1.5 0/0:85:0:0,0:4,81:0:1,0:22.2:1:31.2:1:1:0:60:27.333:1:0:0.1 -20 22563356 . G T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03064;SOR=0;LSEQ=GGCTCTGCTGGATGGCCATG;RSEQ=TGATGAGCGAGATGTACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:9:3,6:251,470:0.0123:2,2:12.9:1:25.8:1:1:1.06799:60:3.5:0.0098:0:2.1 0/0:425:0:0,0:187,238:0:2,0:26.5:1:31:1:1:0:60:211.5:1:0:0.2 -20 22563439 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53475;SOR=0;LSEQ=GGGTCGCGGGCGCGGCTCAG;RSEQ=CCCGCCTGCCCGTACATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:38,158:0.0101:2,2:5:1:29:1:0.35595:4.12:60:4:0.0103:0:1 0/0:114:0:0,0:28,86:0:2,0:20.7:1:31:1:1:0:60:37:1:0:0.1 -20 22964590 . C T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09516;SOR=3.18595;LSEQ=ATCAGCTTCAAAGCTACTTT;RSEQ=CCTTTTCCACATTCTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:12:12,0:28,0:0.3:1,0:19.3:1:29.8:1:1:0:60:24:0.3077:0:1.2 1/0:12:7:7,0:5,0:0.5833:0,0:36.9:1:30.9:1:1:0:60:14:0.5833:0:1 -20 22964619 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCTGCTCTGTGGAAGT;RSEQ=CATAAGAGCCGCCCCCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:2,0:58,0:0.0333:1,0:22:1:26:1:1:0:60:4:0.0333:0:1.5 0/0:19:0:0,0:19,0:0:1,0:22.9:1:32:1:1:0:60:38:1:0:0.4 -20 22964757 . C G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.41684;LSEQ=AGATGCGTAGATACTTCTCT;RSEQ=TATGTTTGTGAAAACACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:258:154,104:175,104:0.4787:2,2:25.4:1:31.2:1:0.4795:1.13609:60:22.455:0.4687:0:1.8 0/1:376:104:62,42:154,118:0.2766:2,2:24.6:1:30.9:1:0.64176:1.13:60:33.667:0.2737:0:1.8 -20 22964799 . T G 269 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.54782;LSEQ=TCAATTAAAGACAAAAGCCA;RSEQ=CTTGTCCTCTGCTCCCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:719:359:179,180:183,177:0.4993:2,2:26:1:31.8:1:0.82308:1.03964:60:50.286:0.5014:0:1.6 0/1:487:172:88,84:151,163:0.3532:2,2:23.9:1:31.6:1:0.5693:1.13:60:33.4:0.3523:0:1.7 -20 22964817 . C A 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=30.70434;LSEQ=CATCTTGTCCTCTGCTCCCC;RSEQ=CTACATCCTTCCTCCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:691:1:1,0:325,364:0.0014:2,0:1:0:25:0:0.47246:0:60:2:0.0015:0:3 0/1:492:21:10,11:223,248:0.0427:2,2:23.4:1:27.9:1:1:1.01:60:20:0.0411:0:2 -20 22964937 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.08452;SOR=Inf;LSEQ=ATGTTAGGCAGTCTCTTGGG;RSEQ=GGTCGAAAGGGCCAAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:4,107:0:1,0:24.6:1:31.3:1:1:0:60:110:1:0:0.4 0/1:46:2:1,1:3,41:0.0435:2,2:15.5:1:28.5:1:0.16812:11.98:60:4:0.0435:0:1 -20 22964954 . T C 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55437;SOR=1.26737;LSEQ=GGGGGGTCGAAAGGGCCAAA;RSEQ=GTGTACTTAGATGTGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:33:0,33:1,54:0.375:1,1:22.5:1:30.5:1:1:0:60:66:0.375:0:1.5 0/1:37:16:2,14:0,21:0.4324:1,2:21.3:1:28.4:1:0.18018:0:60:15:0.4167:0:1.6 -20 22964982 . T C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4303;SOR=1.54515;LSEQ=TAGATGTGGATTTCACAGAG;RSEQ=GATTAGGTATGTGGATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:20:0,20:0,28:0.4167:1,1:26.4:1:30.5:1:1:0:60:40:0.4167:0:1.8 1/0:19:10:0,10:0,9:0.5263:0,0:28.4:1:27.2:1:1:0:60:4:0.4706:0:2.2 -20 23946690 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49826;SOR=0;LSEQ=GGACCCACAAAGGACACTCA;RSEQ=TTGCACGCACATGTGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:0.0833:2,2:8.5:1:29:1:1:1:60:4:0.0909:0:2.5 0/0:18:0:0,0:12,6:0:2,0:25.9:1:31.5:1:1:0:60:36:1:0:1.1 -20 23946710 . C T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCACGCACATGTGCACA;RSEQ=GCACACACGCAATTAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:9,12:0,0:1:0,2:32.6:1:30.5:1:1:0:60:42:1:0:1.2 1/1:19:19:11,8:0,0:1:0,2:32.1:1:30.3:1:1:0:60:38:1:0:1.2 -20 25079606 . A G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGCGGAGCTTGCAGTGAGC;RSEQ=GAGATCGCGCCACTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:25,0:0,0:1:0,1:21:1:27.1:1:1:0:47.7:7.333:1:0:2.1 1/1:11:11:11,0:0,0:1:0,0:26.2:1:28.6:1:1:0:46.5:22:1:0:1.4 -20 25079639 . C T 39 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07291;SOR=Inf;LSEQ=CTGCACTCCAGCCTGGGAGA;RSEQ=AGAGTGAGACTCTGTCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:37,0:0:1,0:25.8:1:31.6:1:1:0:50.7:17.5:1:0:2.5 0/1:29:3:3,0:26,0:0.1034:1,0:13.3:1:24.7:1:1:0:60:2:0.0769:0:5.7 -20 25079657 . CA C 135 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.0784;SOR=0.42304;LSEQ=GACAGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:20:20,0:31,0:0.2941:1,1:20.8:1:31.3:1:1:0:57.1:40:0.2941:0.1029:1.6 0/1:47:7:7,0:24,0:0.1489:1,0:17.7:1:30.3:1:1:0:52.9:14:0.1489:0.0638:2.4 -20 25080206 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.05129;SOR=Inf;LSEQ=TAGACTATAATGCCAACTCA;RSEQ=AGACCTTGCGATGTGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:175,280:0:2,0:23:1:31.4:1:1:0:60:40.364:1:0:0.1 0/1:270:3:2,1:100,167:0.0111:2,2:33.3:1:24:1:0.55894:3.32:60:2:0.0075:0:1 -20 25519823 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.48846;SOR=0;LSEQ=TGGGACAGCAAAGATAAGGA;RSEQ=TCAGCGAACAGCCATGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:37.5:1:30:1:1:1.11:60:4:0.0952:0:1.5 0/0:19:0:0,0:10,9:0:2,0:21.9:1:31.3:1:1:0:60:38:1:0:0.2 -20 25560101 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12919;SOR=Inf;LSEQ=AGCCACAACCAGTGCACAAG;RSEQ=CATGCACGGGGACTGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:27,22:0:2,0:28.3:1:29.2:1:1:0:60:98:1:0:0.2 0/1:28:2:1,1:14,12:0.0714:2,2:8:0:33:0:1:1.16024:60:4:0.0714:0:1.5 -20 25560148 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16553;SOR=Inf;LSEQ=CACGCTACCTTATGGTGAGG;RSEQ=TCACACAGCCCCCACGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:16,26:0:2,0:27.6:1:32:1:1:0:60:41:1:0:0.3 0/1:30:2:1,1:14,14:0.0667:2,2:17:0:31:1:1:1:60:4:0.069:0:1 -20 25733062 . T G 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31676;SOR=0;LSEQ=CTTTAACCATACCCAAAGTC;RSEQ=ATTTTTATTTCTTGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:6,0:32,1:0.1538:1,0:13.8:1:26.2:1:1:0:60:5:0.1316:0:1 0/0:11:0:0,0:10,1:0:2,0:30.2:1:31.5:1:1:0:60:22:1:0:0 -20 25733129 . T G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2173;SOR=0.3389;LSEQ=GCTGTGGTTTAAAACTGACT;RSEQ=TTTCATTTAAGGCAATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:10:10,0:101,12:0.0813:2,0:32.7:1:33.5:1:0.59581:0:26.8:20:0.0833:0:2.4 0/1:69:2:2,0:58,9:0.029:2,0:31.5:1:34:0:1:0:25:4:0.029:0:2 -20 25733169 . C A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13501;SOR=0.29218;LSEQ=GACTCTATTAGTGAGAAATG;RSEQ=ATTGTTTTTCTTGGTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:10:10,0:187,52:0.0402:2,0:26.7:1:28.9:1:0.12729:0:26.8:20:0.0407:0:2.4 0/1:166:2:2,0:116,48:0.012:2,0:29.5:1:27.5:1:1:0:25:4:0.0121:0:2 -20 25733244 . CT TC 88 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00084;SOR=Inf;LSEQ=AAGCTCCATCCTCTCCAATT;RSEQ=GGGGCAACCGTGTGGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:329,224:0:2,0:26:1:31.6:1:1:0:52.3:275.5:1:0:0.1 0/1:393:8:8,0:213,172:0.0204:2,0:10.1:1:29.6:1:0.01068:0:29.3:16:0.0205:0.0153:5.1 -20 25733278 . C T 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=1.83377;LSEQ=TGGAGATGATCAAAATGCTT;RSEQ=ACCTTCAAAACTTTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:96:78,18:332,290:0.1337:2,2:16.2:1:30.5:1:0:3.78:41.8:95:0.1332:0:5.3 0/1:503:111:91,20:197,193:0.2207:2,2:16.4:1:30.2:1:0:4.45:40.8:222:0.2229:0:5.1 -20 25733297 . G C 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.87896;LSEQ=TCACCTTCAAAACTTTCAAA;RSEQ=GAAGAGTTAATACAGAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:765:162:115,47:287,315:0.2118:2,2:24.3:1:31.4:1:0:2.68:42.3:80:0.2111:0:4.8 0/1:599:201:148,53:186,211:0.3356:2,2:22.9:1:30.7:1:0:3.16:41.6:402:0.3401:0:4.7 -20 25733312 . G A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.79056;LSEQ=TCAAAGGAAGAGTTAATACA;RSEQ=AGTATGGATCGTGTAGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:855:248:159,89:266,341:0.2901:2,2:25.5:1:30:1:0:2.29:44.7:81.667:0.2889:0:4.2 0/1:691:292:195,97:180,218:0.4226:2,2:25:1:29.5:1:0:2.43:43.7:72:0.4217:0:4.2 -20 25733331 . C T 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.75884;LSEQ=AGAGTATGGATCGTGTAGAT;RSEQ=GAGAAATTGCAAAAGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:877:314:185,129:232,330:0.358:2,2:27.9:1:30:1:0:2.04:45.2:77.5:0.3563:0:3.9 0/1:741:367:222,145:171,202:0.4953:2,2:27.9:1:29.4:1:7e-05:1.81:45.3:182.5:0.4946:0:3.8 -20 25733334 . G A 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.75405;LSEQ=GTATGGATCGTGTAGATCGA;RSEQ=AAATTGCAAAAGTAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:888:324:190,134:231,331:0.3649:2,2:28:1:30.1:1:0:2.03:45:648:0.3665:0:3.8 1/0:755:379:228,151:171,202:0.502:2,2:28.1:1:29.5:1:0.00011:1.78:45.4:93.75:0.502:0:3.8 -20 25733412 . A G 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=6.64951;LSEQ=TTGCCTAATATATTCTAAGA;RSEQ=TGTATTTTTTTCTCCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:5:1,4:94,308:0.0123:2,2:16.2:1:32.2:1:1:1.22021:45.6:10:0.0124:0:3.6 0/1:392:30:4,26:109,252:0.0765:2,2:21.8:1:32.2:1:0.05879:2.80555:44.8:60:0.0769:0:3.7 -20 25733418 . T G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00063;SOR=1.7098;LSEQ=AATATATTCTAAGAATGTAT;RSEQ=TTTTTCTCCCTACCGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:120:20,100:52,188:0.3333:2,2:22.8:1:32.6:1:0.32791:1.38177:39.7:240:0.3352:0:3.1 0/1:334:154:23,131:62,117:0.4611:2,2:21.2:1:31.6:1:5e-05:3.00833:41.5:153:0.4595:0:3 -20 25733432 . C A 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03939;SOR=1.51876;LSEQ=ATGTATTTTTTTCTCCCTAC;RSEQ=GAAGATATTTTTGAGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:76:3,73:24,142:0.314:2,1:21:1:31.6:1:0.0153:4.09426:36.3:37:0.3083:0:3.4 0/1:212:87:3,84:36,89:0.4104:2,1:22.9:1:32:1:0:11.22563:36.5:174:0.4104:0:3.3 -20 25733440 . T A 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0092;SOR=1.77429;LSEQ=TTTTCTCCCTACCGAAGATA;RSEQ=TTTTGAGTTTTCCATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:55:1,54:18,122:0.2821:2,1:19.5:1:31.8:1:0.01634:7.91533:35.5:110:0.285:0:3.7 0/1:180:74:0,74:25,81:0.4111:2,1:18.3:1:31.2:1:0:0:35.9:148:0.4134:0:3.5 -20 25733459 . T C 138 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00457;SOR=0.18329;LSEQ=ATTTTTGAGTTTTCCATATT;RSEQ=TGAAACATTACATAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:18:0,18:4,102:0.1452:1,1:9.9:1:33.3:1:1:0:34.7:36:0.15:0:4.7 0/1:100:3:0,3:10,87:0.03:2,0:20.7:1:33.3:1:1:0:24.7:6:0.0303:0:5 -20 25733466 . A T 128 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34897;SOR=1.47225;LSEQ=AGTTTTCCATATTTTGAAAC;RSEQ=TTACATAAAAGGAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:18:0,18:3,87:0.1667:1,1:8:1:31.1:1:1:0:32.3:36:0.1667:0:4.7 0/1:79:18:0,18:7,54:0.2278:2,1:10.9:1:30.8:1:0.34121:0:29.6:36:0.2338:0:4.6 -20 25733688 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATGGCATGTGCCCAGGA;RSEQ=TGGCAGTGCTTGGCCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,1:0.4:2,0:17:1:31:0:0.4:0:32.5:4:0.4:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 25733832 . AT A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGCCTTTACTTGATATC;RSEQ=TTTTTTCAGTTGAATATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:29:1:1:0:25:4:1:0:4 -20 25733846 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATCATTTTTTTCAGTTG;RSEQ=ATATGAAATAGTCTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:30.5:1:1:0:25:4:1:0:4 -20 25733862 . C G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTTGAATATGAAATAGTCTT;RSEQ=TGTGGTTTGGAAGAAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:32.5:1:1:0:25:4:1:0:4 -20 25733876 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTTCTGTGGTTTGGAAG;RSEQ=AGGCTGAGCTTATTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:1:30:1:1:0:25:4:1:0:4 -20 26083884 . T TCA 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.54545;SOR=2.97405;LSEQ=ACCATCGTTTGTATGGATTA;RSEQ=AAAAAAAATCAAAAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:4,1:0.375:2,0:13:1:31.5:1:1:0:41:6:0.375:0.25:2 1/0:3:2:2,0:1,0:0.6667:0,0:17:1:29.6:1:1:0:40.5:4:0.6667:0.3333:2 -20 26083909 . C A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11339;SOR=4.79313;LSEQ=AAAATCAAAAATAGAATGGA;RSEQ=AAACAAATTTCACTCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:8,1:11,2:0.4091:2,2:18.2:1:30.8:1:1:1.43:38.7:18:0.4091:0:2.7 1/0:9:7:6,1:2,0:0.7778:0,2:15:1:30.3:1:1:0:41.6:14:0.7778:0:2.6 -20 26083928 . A G 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01272;SOR=6.02549;LSEQ=ACAAACAAATTTCACTCTCT;RSEQ=CAATCATATAATCAGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:11:10,1:14,2:0.4074:2,2:29:1:32.7:1:1:1.41:38.9:22:0.4074:0:2.5 1/1:16:13:10,3:3,0:0.8125:0,2:21.8:1:31.4:1:1:0:43.5:12:0.8:0:2.3 -20 26083987 . G A 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13931;SOR=2.12977;LSEQ=GAATGTAAGAAAACCACAAT;RSEQ=GTAGCAAAAAACAGCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:15:12,3:41,2:0.2586:1,2:23.1:1:27.5:1:0.10313:4.94588:33.3:14:0.2456:0:3.8 0/1:28:12:9,3:16,0:0.4286:1,2:21.6:1:28.8:1:0.06716:0:41.5:24:0.4286:0:2.9 -20 26084014 . TA CG 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0093;SOR=2.68775;LSEQ=AAAAACAGCAAGTCAGAATA;RSEQ=TAAGGAATGATTCCTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:20:17,3:63,2:0.2353:1,2:20.9:1:31:1:0.08236:5.41334:33:40:0.2353:0.0235:3.9 0/1:55:25:22,3:28,2:0.4545:2,2:12.8:1:30.6:1:0.64988:1.88662:34.9:50:0.4545:0.1636:3.2 -20 26084017 . A G 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.79371;LSEQ=AACAGCAAGTCAGAATATAT;RSEQ=AGGAATGATTCCTTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:4:4,0:79,5:0.0455:2,0:27.5:1:32.5:1:1:0:30.3:8:0.046:0:4 0/1:55:2:2,0:50,3:0.0364:2,0:16.5:1:34:0:1:0:40:4:0.0364:0:4 -20 26084021 . A C 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04419;SOR=2.11845;LSEQ=GCAAGTCAGAATATATAAGG;RSEQ=ATGATTCCTTTTATGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:21:18,3:68,2:0.2308:1,2:21.6:1:31.4:1:0.07851:5.52523:32.9:20:0.2222:0:4 0/1:59:23:22,1:34,2:0.3898:2,1:18.4:1:33.1:1:1:1.29:34.1:46:0.3966:0:3.3 -20 26084047 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10715;SOR=0.4744;LSEQ=TCCTTTTATGTAAAGTTTCA;RSEQ=AATATGGAAAACTCAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:21:15,6:98,10:0.1628:2,2:24.1:1:32.3:1:0.02474:3.86386:34.3:42:0.1628:0:4 0/1:95:8:7,1:77,10:0.0842:2,2:29.1:1:30.6:1:1:1.09889:38.9:16:0.0851:0:4.1 -20 26084066 . A T 173 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00349;SOR=1.99322;LSEQ=AAAATATGGAAAACTCAAAA;RSEQ=TATCTTCTGTAGGGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:50:27,23:111,19:0.2778:2,2:24.2:1:30.2:1:2e-05:4.92239:32.7:49:0.2737:0:3.5 0/1:145:63:40,23:68,14:0.4345:2,2:24.7:1:29:1:0.01194:2.77223:37.2:126:0.4345:0:3.3 -20 26084094 . T C 133 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=6.17614;LSEQ=TGTAGGGAGAAAAACATACA;RSEQ=TCTTAGAATATATTAGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:4:2,2:192,90:0.014:2,2:28.8:1:31.3:1:0.59618:2.12719:33.5:8:0.0142:0:4.3 0/1:260:21:10,11:147,92:0.0808:2,2:22.4:1:30.5:1:0.24757:1.7536:37:42:0.0808:0:4.2 -20 26084111 . A G 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.3519;LSEQ=ACATTCTTAGAATATATTAG;RSEQ=CGAAGACTTTTACTTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:50:21,29:196,93:0.1466:2,2:35:1:30.8:1:7e-04:2.90043:32:15.667:0.1407:0:3.3 0/1:302:87:33,54:143,72:0.2881:2,2:32.7:1:31.2:1:1e-05:3.23644:36.2:86:0.2857:0:3.6 -20 26084113 . G A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=2.19355;LSEQ=ATTCTTAGAATATATTAGAC;RSEQ=AAGACTTTTACTTGTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:50:21,29:203,98:0.1425:2,2:35.5:1:30.2:1:0.00077:2.85126:32.6:100:0.1433:0:3.3 0/1:318:85:31,54:154,79:0.2673:2,2:34.1:1:29.6:1:0:3.38171:36.2:84:0.2675:0:3.6 -20 26084172 . C T 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=4.23545;LSEQ=CTGTTCTACTTTTGCAATTT;RSEQ=TCGATCTACACGATCCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:11:7,4:256,207:0.0232:2,2:20.8:1:27.5:1:0.76159:1.41:33.7:4.5:0.0192:0:4.8 0/1:426:39:10,29:223,164:0.0915:2,2:11.9:1:30:1:0.00015:3.93093:30.4:38:0.0898:0:4.2 -20 26084175 . G A 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.79245;LSEQ=TTCTACTTTTGCAATTTCTC;RSEQ=ATCTACACGATCCATACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:7:5,2:250,206:0.015:2,2:26:1:31.1:1:0.46654:2.06:29.1:14:0.0152:0:5.7 0/1:419:34:8,26:222,163:0.0811:2,2:10.3:1:29.9:1:0.00022:4.41131:30.6:33:0.0803:0:4.3 -20 26084193 . AC TT 70 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22952;SOR=0.23982;LSEQ=TCGATCTACACGATCCATAC;RSEQ=TCTATTAACTCTTCCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:478:5:4,1:253,220:0.0105:2,2:34.4:1:30.4:1:0.3795:3.47:25.4:10:0.0106:0.0021:4.8 0/0:396:1:1,0:216,178:0.0025:2,0:20:0:32.5:0:1:0:31:2:0.0026:0:6 -20 26084228 . G A 91 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09276;SOR=2.82421;LSEQ=CCTTTGAAAGTTTTGAAGGT;RSEQ=AAGCATTTTGATCATCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:4:4,0:230,240:0.0084:2,0:11:1:30.3:1:0.05862:0:30:8:0.0085:0:5.8 0/1:383:9:6,3:180,194:0.0235:2,2:16.3:1:29:1:0.3258:2.15:25.7:18:0.0237:0:4.6 -20 26084251 . C T 121 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00274;SOR=4.708;LSEQ=GCATTTTGATCATCTCCACA;RSEQ=GGTTGCCCCAGAATTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:4:3,1:200,253:0.0087:2,2:5.3:1:30.5:1:0.32725:3.78:38:8:0.0087:0:2.3 0/1:402:16:13,3:169,217:0.0398:2,2:25.3:1:30.3:1:0.0039:5.54:27.8:32:0.0399:0:3.9 -20 26084261 . AG GA 142 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00407;SOR=2.61256;LSEQ=CATCTCCACACGGTTGCCCC;RSEQ=AATTGGAGAGGATGGAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:13:13,0:187,255:0.0286:2,1:8.5:1:30.4:1:2e-05:0:38.9:26:0.0288:0.0154:2.1 0/1:406:29:25,4:157,220:0.0714:2,2:20:1:29.4:1:0:8.72:36.3:58:0.072:0.0222:1.9 -20 26084295 . CA TG 155 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00018;SOR=0.21145;LSEQ=TGGAGCTTCATGTTTGCCTC;RSEQ=AATGCTGGATCCTTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:29:23,6:157,245:0.0673:2,2:21.1:1:32.1:1:5e-05:5.96:35.7:58:0.0678:0.0093:1.4 0/1:400:6:5,1:173,221:0.015:2,2:23.3:1:31.8:1:0.09277:6.36:40.5:12:0.0151:0.0025:1 -20 26084296 . A G 151 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00365;SOR=2.55475;LSEQ=GGAGCTTCATGTTTGCCTCC;RSEQ=AATGCTGGATCCTTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:14:13,1:143,246:0.0327:2,1:25.7:1:31.4:1:3e-05:22.23:36.3:28:0.0349:0:1.4 0/1:402:32:29,3:147,218:0.0796:2,2:21:1:30.3:1:0:14.26:34.3:31:0.0791:0:1.6 -20 26084377 . A C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00134;SOR=2.0764;LSEQ=CCAGATTGCCTTAAATGAAA;RSEQ=AGTCAGTTTTAAACCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:83:17,66:11,84:0.4663:2,2:23.1:1:31.7:1:0.1478:1.96:39.7:82:0.4659:0:2.2 1/0:155:100:25,75:8,47:0.6452:2,2:22.5:1:31.3:1:0.15373:1.95:41.1:200:0.6452:0:2.2 -20 26084383 . GT G 127 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.03154;SOR=0.29732;LSEQ=TGCCTTAAATGAAAAAGTCA;RSEQ=TTTAAACCACAGCAGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:15:2,13:14,135:0.0909:2,2:27.2:1:32.7:1:0.6433:1.48:49.8:30:0.0926:0.0061:0.1 0/1:139:4:1,3:16,119:0.0288:2,2:12:1:28.5:1:0.41018:2.46:48:8:0.0288:0.0144:0.8 -20 26084411 . C A 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09398;SOR=1.62905;LSEQ=CCACAGCAGAGCCATGTGTA;RSEQ=TATGTGTCTAATGAAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:75:4,71:0,53:0.5859:1,2:27.9:1:30.7:1:0.14138:0:43.8:36.5:0.584:0:2.6 1/0:96:67:5,62:0,29:0.6979:1,2:29:1:30:1:0.31815:0:44.1:134:0.6979:0:2.7 -20 26084427 . AC A 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1616;SOR=3.07088;LSEQ=TGTACTATGTGTCTAATGAA;RSEQ=CTTTAGTAGTAACTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:3:0,3:3,99:0.0286:1,0:37:1:32.3:1:1:0:51.7:6:0.0286:0:3 0/1:72:6:0,6:3,63:0.0833:1,0:22.7:1:32.1:1:1:0:39.5:12:0.0845:0.0139:2.8 -20 26084429 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02603;SOR=Inf;LSEQ=TACTATGTGTCTAATGAAAC;RSEQ=TTTAGTAGTAACTTTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:3,102:0:1,0:27.8:1:32.8:1:1:0:50:210:1:0:1.7 0/1:72:4:0,4:3,65:0.0556:1,0:32.5:1:30:1:1:0:45.3:8:0.0563:0:3.8 -20 26084434 . GT TC 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.15055;SOR=Inf;LSEQ=TGTGTCTAATGAAACCTTTA;RSEQ=AGTAACTTTCATATTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:2,95:0:1,0:28.2:1:32.5:1:1:0:50.2:96:1:0:1.7 0/1:62:2:0,2:2,57:0.0323:1,0:19.5:1:30.8:1:1:0:42:4:0.0328:0:4 -20 26084435 . T C 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0538;SOR=2.1314;LSEQ=GTGTCTAATGAAACCTTTAG;RSEQ=AGTAACTTTCATATTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:58:2,56:0,37:0.6105:1,1:30.2:1:32.8:1:0.51937:0:43.5:116:0.6105:0:2.8 1/0:61:47:3,44:0,12:0.7705:0,2:27.4:1:32.1:1:1:0:46.4:46:0.7931:0:2.9 -20 26084497 . C A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21025;SOR=4.92745;LSEQ=TTTTATAGTTTAGATATACC;RSEQ=TGTACTATTTTGAAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:15:2,13:0,11:0.5769:0,2:14.6:1:30.9:1:0.49231:0:42.1:30:0.5769:0:2.9 1/1:8:7:1,6:0,1:0.875:0,2:16.4:1:31.7:1:1:0:50.4:14:0.875:0:2.9 -20 26084507 . T C 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18809;SOR=3.52582;LSEQ=TAGATATACCCTGTACTATT;RSEQ=TGAAGAGCCTAAAAGCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:0,14:0.2632:1,2:25.2:1:30.8:1:0.05848:0:42.2:10:0.2632:0:3 1/0:7:4:0,4:1,2:0.5714:2,0:12:1:33:1:0.42857:0:51.5:8:0.5714:0:3.3 -20 26084548 . T C 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.9219;LSEQ=CAAAGTCAGGTGAGTTAGTG;RSEQ=TGATCAGCCTCTAGTGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:1,6:1,6:0.5:2,2:27.9:1:31:1:1:1:40.7:14:0.5:0:1.7 1/0:3:2:0,2:1,0:0.6667:0,0:36:1:34:0:0.33333:0:51.5:4:0.6667:0:2.5 -20 26084615 . CAAAG C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTAAATAATGCAATCATGA;RSEQ=GAAGATACCAACTTCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:1,8:0.25:2,0:27.7:1:31.6:1:1:0:45:6:0.2727:0.0833:1 0/0:2:0:0,0:0,1:0:0,0:47:0:29:0:1:0:27:2:0.5:0:0 -20 26084906 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTAGCCAAAAACATCCCA;RSEQ=TGCACCTCCAAATCAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:18:0:28:0:1:0:30:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:47:0:32:1:1:0:49:4:1:0:1.5 -20 26093110 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGGAGGAGGACTGACA;RSEQ=GGGTGGGTGTCAAGGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:30.5:1:1:0:40:4:1:0:4 -20 26093120 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGACTGACATGGGTGGGTG;RSEQ=CAAGGAGAATGGGGTGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:31:1:1:0:40:4:1:0:4 -20 26093128 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGGTGGGTGTCAAGGAG;RSEQ=ATGGGGTGCCAAGGAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:30:1:1:0:40:4:1:0:4 -20 26093145 . T C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAATGGGGTGCCAAGGAA;RSEQ=GTGCTGGAGTGTTAGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:29:1:1:0:40:4:1:0:4 -20 26094192 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGACATGCCAAGTTATCT;RSEQ=GCCAGCTTAAAACTCAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:15.5:1:29.5:1:1:0:35.5:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 26094383 . CA TG 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7622;LSEQ=ATTCCCAACCTTTGGTTCCT;RSEQ=TCTTTGTAAATAGCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:3:3,0:84,5:0.0326:2,0:13.3:1:31.3:1:1:0:30:6:0.0326:0.0217:3 0/1:40:1:1,0:35,4:0.025:2,0:7:0:23:0:1:0:31:2:0.025:0:7 -20 26094400 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54748;SOR=0;LSEQ=CCTCATCTTTGTAAATAGCT;RSEQ=TTGCCATTTAAAAAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:116,7:0.016:2,2:7.5:1:27.5:1:0.12439:15.56459:60:4:0.0163:0:1.5 0/0:65:0:0,0:59,6:0:2,0:20.7:1:31.1:1:1:0:55.5:31.5:1:0:0.6 -20 26094407 . TTT CTTA 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.3467;SOR=1.99287;LSEQ=TTTGTAAATAGCTCTTGCCA;RSEQ=AAAAAAAAGGTAAATTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:6:6,0:120,10:0.0441:2,0:17:1:31.6:1:1:0:25.5:12:0.0458:0:2.3 0/1:71:6:5,1:58,7:0.0845:2,2:18.7:1:31.8:1:0.52558:1.64336:28:12:0.087:0:2.2 -20 26094420 . T C 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00124;SOR=2.29379;LSEQ=CTTGCCATTTAAAAAAAAGG;RSEQ=AAATTTGGTGGTTTCTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:41:41,0:156,19:0.1889:2,1:15.7:1:32.2:1:0.02796:0:34.5:19.5:0.184:0:2 0/1:129:45:43,2:75,9:0.3488:2,1:15.5:1:32.1:1:0.32711:2.56:35.2:21.5:0.3413:0:2 -20 26094476 . CAAAAAACAT AAAAAAC 273 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05125;SOR=1.21973;LSEQ=AGGAAAAGTAAAGAAAAACA;RSEQ=GTGCAATTTGCATAGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:489:409,80:377,115:0.4949:2,2:21.3:1:30.6:1:0.00649:1.56:48.8:162:0.4959:0.1619:0.9 1/0:674:367:301,66:222,84:0.5445:2,2:26.9:1:30.7:1:0.00388:1.72:51:734:0.5486:0.0089:0.8 -20 26094485 . T C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51246;SOR=0.85851;LSEQ=AAAGAAAAACACAAAAAACA;RSEQ=GTGCAATTTGCATAGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:52:51,1:356,133:0.0594:2,1:33.4:1:32:1:1e-05:19.00:27.9:51:0.096:0:1.8 0/1:720:37:34,3:216,103:0.0514:2,2:32.6:1:31.2:1:0.00192:5.39:30:74:0.1063:0:2 -20 26094501 . T C 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.11368;LSEQ=AACATGTGCAATTTGCATAG;RSEQ=ATTTGTTCCTTACCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1372:30:23,7:996,346:0.0219:2,2:25.2:1:32.1:1:1:1.14:54.6:29:0.0214:0:2.1 0/1:1180:235:171,64:657,288:0.1992:2,2:24.4:1:31.6:1:0.34047:1.17:53.9:46:0.1969:0:2.2 -20 26094525 . T C 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21215;SOR=1.18596;LSEQ=TGTTCCTTACCTGCTGGTGG;RSEQ=GGGTGCTGGGAAACGTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1988:124:99,25:1173,688:0.0624:2,2:17.2:1:31:1:1e-04:2.32:31.3:40.333:0.0624:0:2.1 0/1:1723:126:94,32:954,637:0.0731:2,2:17.5:1:30.8:1:0.00118:1.96:32:41:0.073:0:2.2 -20 26094564 . T G 316 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-04;SOR=1.2533;LSEQ=ACTTTACAGAGTGAGGAGGA;RSEQ=AATGACTTTGTTCTGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2205:1141:573,568:530,534:0.5175:2,2:29.6:1:31.2:1:0.86468:1.02:50:70.313:0.5168:0:3.3 1/0:1962:1125:531,594:429,407:0.5734:2,2:29.2:1:31:1:0.07493:1.17901:51.9:65.176:0.572:0:3.4 -20 26094567 . T C 312 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.5065;LSEQ=TTACAGAGTGAGGAGGATAA;RSEQ=GACTTTGTTCTGTGCTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2196:1345:662,683:417,434:0.6125:2,2:29.7:1:30.4:1:0.93022:1.01:47.5:69.789:0.6108:0:3.1 1/0:1951:1374:651,723:280,295:0.7043:2,2:29.3:1:30:1:0.61913:1.05407:48.7:97.143:0.7032:0:3.1 -20 26094605 . G A 288 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15344;SOR=1.10811;LSEQ=AATGCTCCTTGGTTGGGAGG;RSEQ=TAACCTGAACTTGACATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1724:711:210,501:387,625:0.4124:2,2:23.9:1:30.5:1:0.00021:1.47689:46.2:87.875:0.414:0:4.6 0/1:1504:658:192,466:351,491:0.4375:2,2:24.3:1:29.6:1:0:1.73437:47:218.333:0.439:0:4.5 -20 26094609 . C A 276 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09102;SOR=1.13468;LSEQ=CTCCTTGGTTGGGAGGGTAA;RSEQ=CTGAACTTGACATTATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1624:654:180,474:358,610:0.4027:2,2:23.6:1:29.6:1:7e-05:1.54504:45.3:71.667:0.4046:0:4.7 0/1:1435:622:165,457:334,478:0.4334:2,2:23.4:1:29.5:1:0:1.93444:46.2:61.2:0.434:0:4.7 -20 26094638 . C T 256 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55553;SOR=1.06041;LSEQ=GACATTATCAGTAAAGAAGT;RSEQ=CTCACCAGACTGTGAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:987:375:37,338:174,438:0.3799:2,2:20.7:1:30:1:0:3.62476:39.3:92.75:0.3797:0:5.2 0/1:782:308:45,263:158,314:0.3939:2,2:21.2:1:29.2:1:0:2.93698:41.1:101.667:0.3966:0:5.3 -20 26094648 . CTG C 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00067;SOR=1.73897;LSEQ=GTAAAGAAGTCCTCACCAGA;RSEQ=TGAGATCAATGCCAATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:804:80:16,64:122,601:0.0995:2,2:18.4:1:31.8:1:0.53153:1.23:32:160:0.1011:0.0274:1.3 0/1:614:99:18,81:105,409:0.1612:2,2:19:1:31.9:1:0.68214:1.15499:31.4:198:0.1634:0.0407:1.5 -20 26094651 . T C 245 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.95429;SOR=1.01133;LSEQ=AAGAAGTCCTCACCAGACTG;RSEQ=GAGATCAATGCCAATAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:289:16,273:100,356:0.3813:2,2:21.8:1:30:1:0:4.78404:39.1:143.5:0.3873:0:5.2 0/1:560:215:20,195:82,253:0.3839:2,2:20.1:1:29.8:1:1e-05:3.15418:40:52.75:0.3872:0:5.3 -20 26094660 . T C 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02492;SOR=1.32672;LSEQ=TCACCAGACTGTGAGATCAA;RSEQ=GCCAATAAACAATCATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:611:285:14,271:55,271:0.4664:2,1:23.1:1:30.1:1:0:3.92062:37.2:141.5:0.4678:0:4.2 1/0:445:239:22,217:51,154:0.5371:2,2:20.8:1:30.1:1:1e-05:3.25776:36.1:78.667:0.5388:0:3.9 -20 26094689 . A C 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.37232;SOR=1.18293;LSEQ=ACAATCATGTTTCTAGGAAA;RSEQ=CATCTAAACAGGATGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:147:2,145:12,190:0.4212:2,1:26.4:1:31.7:1:0.04946:4.56311:37.9:72.5:0.4191:0:3.9 0/1:201:93:6,87:11,97:0.4627:2,2:25.4:1:31.2:1:0.44811:1.64036:35.9:92:0.4646:0:3.8 -20 26094706 . G GA 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05244;SOR=0;LSEQ=AAAACATCTAAACAGGATGG;RSEQ=AAAAAAATAGAATTAATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:7:0,7:9,260:0.0254:1,0:20.6:1:31.3:1:1:0:40.4:14:0.0256:0.0036:3 0/0:156:0:0,0:13,142:0:2,0:22.7:1:30.9:1:1:0:46.7:76.5:0.9935:0:1.7 -20 26094769 . C A 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32636;SOR=1.44508;LSEQ=CTAATAAATTATAACTATAG;RSEQ=TACATAAATAAAACCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:46:2,44:9,60:0.4:2,1:26.5:1:31.8:1:0.19528:3.27058:39.8:92:0.4:0:2.2 0/1:57:28:1,27:3,26:0.4912:2,1:23.2:1:30.8:1:0.61148:3.05839:35.4:56:0.4912:0:2.1 -20 26094796 . T G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.65655;SOR=1.3251;LSEQ=AATAAAACCACAATTACCAG;RSEQ=AAAAGCTTCCTCTCAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:25:1,24:6,40:0.3521:2,1:20:1:31.6:1:0.40856:3.54787:40:24:0.3429:0:2.6 0/1:31:13:1,12:3,15:0.4194:2,1:16:1:31.5:1:0.62072:2.33811:36.2:26:0.4194:0:2.4 -20 26094812 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78405;LSEQ=CCAGTAAAAGCTTCCTCTCA;RSEQ=GTATTTACTTAATAAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:13:0,13:5,28:0.2826:2,1:16.8:1:30.5:1:0.30146:0:38.8:12:0.2667:0:3.1 0/1:17:4:0,4:2,11:0.2353:2,0:24.8:1:30.8:1:1:0:37:8:0.2353:0:3.3 -20 30253628 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53997;SOR=0;LSEQ=GGACCAGATCTGGGCCCAAC;RSEQ=CTGTGATGGGCAGGTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:124,5:0.0153:1,2:23:1:28:1:0.08984:22.73079:60:4:0.0156:0:1 0/0:72:0:0,0:69,3:0:1,0:22.4:1:30.5:1:1:0:60:71:1:0:0.1 -20 30253937 . T G 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16423;SOR=Inf;LSEQ=TTTTAGTCCTCAGAGAGTGA;RSEQ=GTAGGTGGGTGGGGAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:45,170:0:2,0:23:1:29.7:1:1:0:60:29.714:1:0:0.2 0/1:147:2:1,1:25,120:0.0136:2,2:5:0:28.5:1:0.32346:4.73:60:4:0.0137:0:0.5 -20 30254264 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATGATGGTGCAGGGGTG;RSEQ=GCAAGAGCCAGACCATACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:35:1:31.5:1:1:1.73:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 30254773 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGACGCTTAGAACATAAC;RSEQ=TTTATGAGTAAGCGTAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29:1:1:0:60:4:1:0:1.5 -20 30263317 . G T 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04404;SOR=0.5109;LSEQ=CGGAGACTCGGAAGAAGTGA;RSEQ=GTTTGTGGTTGGAATCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:60:59,1:64,0:0.4839:1,1:23.4:1:31.6:1:0.48387:0:60:120:0.4878:0:1.1 0/1:65:21:21,0:44,0:0.3231:1,1:21.3:1:31:1:1:0:60:42:0.3231:0:1.1 -20 30263418 . T C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33483;LSEQ=TCCTCTCCCCCACGGAAACA;RSEQ=AGGCCTGGAGGTGGGCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:313:232,81:268,86:0.4679:2,2:22:1:31.6:1:0.65507:1.08787:60:312:0.472:0:1.1 0/1:550:125:87,38:305,117:0.2273:2,2:23.2:1:31.2:1:0.57314:1.13834:60:124:0.2279:0:1.1 -20 30263528 . G A 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=24.85096;LSEQ=GTCCAGCCGGCCCAGGTATG;RSEQ=GTGGGTGCCACAGCAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1576:2:1,1:726,846:0.0013:2,2:6.5:1:21.5:1:1:1.17:60:1:6e-04:0:2.5 0/1:1404:43:21,22:645,712:0.0306:2,2:26.6:1:29.5:1:0.87806:1.05:60:86:0.031:0:1.2 -20 30281755 . T TA 63 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.87218;LSEQ=GTATTTATGATAAATTTCTT;RSEQ=AAAAAAAAAAAGTGTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:12,1:0.2778:1,0:22.6:1:27.2:1:1:0:60:10:0.2778:0:0 0/1:4:1:1,0:3,0:0.25:0,0:15:0:26:0:1:0:60:2:0.25:0:1 -20 30281959 . A AG 73 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.08894;SOR=6.81886;LSEQ=GCCCAGGAACTGGCACCTGT;RSEQ=GGGGGGGCTTCTGGACAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:1:1,0:384,167:0.0018:2,0:42:0:33:0:1:0:60:2:0.0018:0:1 0/1:409:5:3,2:261,141:0.0122:2,2:20.8:1:31.6:1:1:1.23337:60:10:0.0123:0.0073:0.2 -20 30282223 . T C 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00402;SOR=0.39501;LSEQ=TGAGAATGAGATTAGGTTTC;RSEQ=TGGGAAGGGCTCATCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:65:0,65:3,68:0.4779:1,1:24.1:1:32:1:0.24592:0:60:31.5:0.4701:0:1.1 0/1:68:18:1,17:1,49:0.2647:1,1:19.7:1:30.7:1:0.46225:2.83:60:36:0.2687:0:1.3 -20 30282238 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTTTCTTGGGAAGGGCTCAT;RSEQ=TATCTAATGCTCCCCGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:1,101:0.0192:1,2:28.5:1:30.5:1:0.03827:71.89:60:4:0.0196:0:1 0/0:43:0:0,0:0,43:0:1,0:20.8:1:31.5:1:1:0:60:42:1:0:0.3 -20 30282922 . A T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCAGTTGGTCCAACCTTC;RSEQ=AATTGTATTGAAGCTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:27.5:1:1:0:60:4:1:0:1 -20 30296095 . A C 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGCACACACAAGGGAAG;RSEQ=AGCAGCAGCCTTACTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:42.5:1:31.5:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 30296396 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15091;SOR=Inf;LSEQ=CCCACCCTCCCTGAAATCTG;RSEQ=ACCTGCTCCCAAACTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:198,9:0:1,0:24.1:1:32.3:1:1:0:60:68:1:0:0.7 0/1:132:2:2,0:118,12:0.0152:2,0:23.5:1:29:1:1:0:60:4:0.0153:0:1.5 -20 30296422 . C T 211 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCCAAACTGACCCCTCCC;RSEQ=CCAGCTGAGCCCAGCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:118:97,21:188,32:0.3471:2,2:23.9:1:30.7:1:0.43676:1.27095:60:117:0.3514:0:1.1 0/0:248:0:0,0:200,48:0:2,0:22.7:1:30.3:1:1:0:60:247:1:0:0.1 -20 30296428 . T C 189 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACTGACCCCTCCCCCCAGC;RSEQ=GAGCCCAGCTGTCAACGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:78:63,15:251,57:0.2021:2,2:22.8:1:30.2:1:0.87164:1.04833:60:25:0.1979:0:1.2 0/0:267:0:0,0:210,57:0:2,0:23.5:1:30.3:1:1:0:60:52.4:1:0:0.1 -20 30296664 . G C 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05439;SOR=0;LSEQ=CTGGCATTGTCACTGCAGGT;RSEQ=GCAGGAGACAGGTGATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:8:1,7:16,199:0.0359:2,2:22.6:1:29.3:1:0.47532:1.77:60:16:0.0369:0:1 0/0:121:0:0,0:9,112:0:2,0:22.2:1:30.6:1:1:0:60:242:1:0:0.1 -20 30309261 . TG T 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22121;SOR=0.5062;LSEQ=TGACCAGGGTGAAAGATGCC;RSEQ=ATCTCTGAAGCACAGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:35:35,0:41,3:0.443:2,1:23.8:1:30.9:1:0.25024:0:60:34:0.4416:0.0506:0.2 0/1:21:6:6,0:14,1:0.2857:1,0:24.2:1:31.5:1:1:0:60:12:0.3158:0.0952:0 -20 30309960 . C G 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAACTGACTCCAGCTGTAT;RSEQ=CTTTCTGGGAAAGCTTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:29:7,22:232,409:0.0433:2,2:26.9:1:32.7:1:0.23537:1.78134:60:58:0.0438:0:1.1 0/0:574:0:0,0:238,336:0:2,0:24.9:1:30.6:1:1:0:60:70.75:1:0:0.1 -20 30310051 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14793;SOR=Inf;LSEQ=AGGGATGGGCTCAACCAGTC;RSEQ=ATTGTCCAAAACACCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:24,139:0:2,0:23.9:1:31.5:1:1:0:60:26.167:1:0:0.1 0/1:103:2:1,1:23,78:0.0194:2,2:36:1:28.5:1:0.41348:3.34:60:4:0.0196:0:1.5 -20 30310158 . G GA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAGAGAAAGAGCTTCAG;RSEQ=AAAAAAAAATAATTAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:1,38:0.0488:1,0:40:1:30:1:1:0:60:4:0.0488:0:0 0/0:14:0:0,0:0,14:0:1,0:18.9:1:31.1:1:1:0:60:28:1:0:0.1 -20 30433033 . C T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0348;SOR=Inf;LSEQ=GCGGCGGCGTAGGAAGCTGC;RSEQ=GTGCTCAAACATGTCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:82,17:0:2,0:21.5:1:30.7:1:1:0:60:98:1:0:0.1 0/1:49:3:3,0:40,6:0.0612:2,0:14.7:1:30.3:1:1:0:60:6:0.0612:0:1 -20 30433139 . G A 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCACTCGTTGAGTGACAG;RSEQ=TTGTGGCGGATGCTGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:114,134:0:2,0:28.3:1:31.4:1:1:0:60:81.667:1:0:0.2 0/1:168:14:5,9:69,84:0.0833:2,2:26.4:1:29.1:1:0.58222:1.4752:60:28:0.0843:0:1 -20 30433175 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18407;SOR=Inf;LSEQ=TTCTGCCAGCCGGGCCGGTT;RSEQ=TGGCGGTAGAAGGCGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:58,117:0:2,0:24.1:1:31.6:1:1:0:60:57.333:1:0:0.2 0/1:132:2:1,1:44,86:0.0152:2,2:36:1:28.5:1:1:1.94:60:4:0.0152:0:1.5 -20 30433352 . C T 61 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGCTGCTGCTGCATGCTGGC;RSEQ=GGGCTGCCAGGCTGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:0,2:0.6667:0,2:29.8:1:30.5:1:1:0:60:8:0.6667:0:1 0/0:1:0:0,0:0,1:0:0,0:23:0:10:0:1:0:60:0:0:0:0 -20 30434084 . GAC G 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACACACACAGAAACACAGA;RSEQ=ACAGACACAGACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:30:1:1:0:60:4:1:0:0 -20 30672279 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18542;SOR=Inf;LSEQ=TGGGAGAAAGATGCCTGGGA;RSEQ=ATCCCTCGGGAATCCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:27,12:0:2,0:20.2:1:31.8:1:1:0:60:78:1:0:0.2 0/1:30:2:1,1:20,8:0.0667:2,2:5:1:29:1:0.51724:2.41524:60:4:0.0667:0:1 -20 30672319 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15745;SOR=Inf;LSEQ=AGCTGGAGAAGAAACTTGGA;RSEQ=CTGGGCAGTTTGGGGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:28,29:0:2,0:32.5:1:31.8:1:1:0:60:56:1:0:0.2 0/1:38:2:1,1:20,16:0.0526:2,2:20:1:26:1:1:1.24262:60:4:0.0541:0:1 -20 30946526 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.06257;SOR=Inf;LSEQ=GCCCCGCGCCACCGCCCCAG;RSEQ=CCGCCCAGCCCGGAGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:121,43:0:2,0:14.8:1:31.5:1:1:0:60:26.333:1:0:0.2 0/1:183:5:1,4:126,52:0.0273:2,2:9.2:1:25:1:0.03118:9.5626:60:10:0.0276:0:1.2 -20 30946542 . G T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12461;SOR=Inf;LSEQ=CCAGCCCGCCCAGCCCGGAG;RSEQ=TCCCGCGTGGAGCTGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:224,107:0:2,0:19:1:31.5:1:1:0:60:65.2:1:0:0.2 0/1:352:4:1,3:226,122:0.0114:2,2:5.8:1:26.3:1:0.13012:5.52968:60:8:0.0115:0:1 -20 30946563 . G A 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.03228;SOR=Inf;LSEQ=TCCCGCGTGGAGCTGCCGCC;RSEQ=CCGCCGGGGAGAAGGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:506:0:0,0:300,204:0:2,0:26.3:1:30.7:1:1:0:60:62:1:0:0.2 0/1:566:6:3,3:334,224:0.0106:2,2:30:1:28.5:1:0.6889:1.48995:60:12:0.0108:0:1 -20 30946591 . CAGA C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.22402;SOR=1.62823;LSEQ=GGAGAAGGATGAAGGACAAA;RSEQ=AGAAGAAGAAGGAGCGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:784:12:7,5:409,361:0.0153:2,2:31.9:1:31.8:1:0.77825:1.24:60:24:0.0157:0:0.2 0/1:891:22:11,11:456,412:0.0247:2,2:16.8:1:31:1:0.83232:1.10667:60:44:0.0253:0.0112:0.4 -20 30946676 . TG T 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49937;SOR=0;LSEQ=GGGCTCCGTGGGGCCCGGGG;RSEQ=GGGGGGGCTCGCCGCGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:49,131:0.0109:2,2:25:0:33.5:1:0.47508:2.66:60:4:0.0109:0:0.5 0/0:170:0:0,0:44,126:0:2,0:16.1:1:30.3:1:1:0:60:84:1:0:0.4 -20 30946683 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.42489;SOR=2.28355;LSEQ=GTGGGGCCCGGGGTGGGGGG;RSEQ=GCTCGCCGCGCACCCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:2,0:35,106:0.0139:2,0:1:0:25.5:1:0.0656:0:60:4:0.0142:0:1 0/1:128:4:3,1:26,98:0.0313:2,2:21.5:1:27.3:1:0.03614:11.03:60:8:0.0323:0:1 -20 30946705 . T TG 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.632;LSEQ=CTCGCCGCGCACCCCCCCAC;RSEQ=GGGGGGGGAGGGGCAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:0,2:8,36:0.0435:2,0:8:1:30.8:1:1:0:60:4:0.0465:0.0217:0.5 0/1:36:1:0,1:8,27:0.0278:2,0:18:0:27:0:1:0:60:2:0.0278:0:5 -20 30946712 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.18995;SOR=Inf;LSEQ=CGCACCCCCCCACTGGGGGG;RSEQ=GAGGGGCAAGGCCCTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:5,28:0:2,0:18.5:1:31.5:1:1:0:60:66:1:0:0.8 0/1:26:2:1,1:3,21:0.0769:2,2:21:1:28.5:1:0.28923:6.21:60:4:0.0769:0:1.5 -20 30946846 . G GC 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTCCGCTCGCCCTCGC;RSEQ=CCCCCCCCGCCCCGCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43:0:32.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 30954295 . A G 234 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTGTTCTTGTTGCTTAAC;RSEQ=TGAGGGTTTCATAGGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:674:0:0,0:238,436:0:2,0:25.3:1:30.6:1:1:0:60:133.8:1:0:0.1 0/1:600:204:74,130:145,251:0.34:2,2:26.2:1:30.6:1:1:1.01484:60:408:0.3429:0:1.1 -20 30955332 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTTTAGGGTCAAAAGGC;RSEQ=TTCACTTTCCAGTTGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:39,1:0.0476:1,0:20.5:1:32:0:1:0:60:4:0.0476:0:1 0/0:12:0:0,0:12,0:0:0,0:29.4:1:30.8:1:1:0:60:24:1:0:0 -20 30956937 . T C 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACGCTCAAGGTAAGTGATA;RSEQ=GAACTCTCTTTTGGTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:906:0:0,0:365,541:0:2,0:25.8:1:30.2:1:1:0:60:44.3:1:0:0.1 0/1:802:31:13,18:317,451:0.0387:2,2:22.7:1:30.5:1:1:1.03:60:62:0.0389:0:1.2 -20 30956978 . G A 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03068;SOR=Inf;LSEQ=GATTCTTGGACTTTTAATGT;RSEQ=CATAAAAATCACCTGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:130,407:0:2,0:22.9:1:31.5:1:1:0:60:47.818:1:0:0.1 0/1:388:4:2,2:92,292:0.0103:2,2:17.5:1:25.5:1:0.24815:3.16:60:8:0.0104:0:1.8 -20 30959704 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07656;SOR=9.1772;LSEQ=GCAACCATACCTGGCCCTCT;RSEQ=TTATCTCATATATAGCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:0.2222:1,0:13.3:1:32:1:1:0:60:8:0.2222:0:1 1/0:4:3:3,0:1,0:0.75:0,0:25.3:1:34:0:1:0:60:6:0.75:0:1 -20 30959782 . A G 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00351;SOR=Inf;LSEQ=TTAATACATATATGTTTATT;RSEQ=CAAATATGCCTGTTAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:108,1:0:1,0:24:1:28.3:1:1:0:60:26.25:1:0:0.1 0/1:54:5:5,0:49,0:0.0926:1,0:14:1:33.8:1:1:0:60:10:0.0926:0:1 -20 31015838 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29918;SOR=3.56625;LSEQ=CTTGTCAGTATTCTAAATCC;RSEQ=TCTTTTTCAAAAGCATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:0,1:85,5:0.011:2,0:2:0:28:0:0.06593:0:60:2:0.0111:0:1 0/1:52:2:2,0:47,3:0.0385:2,0:6.5:1:31:1:1:0:60:4:0.0392:0:1 -20 31016119 . C T 232 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=0.01056;LSEQ=GGACTAACCTTTATTTTCCT;RSEQ=TCTTCCAGTATCTCTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1683:206:109,97:720,757:0.1224:2,2:24.4:1:30.2:1:0.26565:1.18:60:205:0.1228:0:1.1 0/0:1361:2:1,1:708,651:0.0015:2,2:3.5:1:27:1:1:1.08748:60:4:0.0015:0:1 -20 31016287 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51799;SOR=0;LSEQ=ACAGGTATAAGGCAAGATCC;RSEQ=TCCTTCTCCTGTAGTGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:7,182:0.0105:1,2:37.5:1:31.5:1:0.08223:24.39:60:4:0.0106:0:2 0/0:128:0:0,0:9,119:0:2,0:23.1:1:31.6:1:1:0:60:63:1:0:0.3 -20 31016291 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52033;SOR=0;LSEQ=GTATAAGGCAAGATCCCTCC;RSEQ=TCTCCTGTAGTGAGCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:6,165:0.0116:1,2:33.5:1:32.5:1:0.07951:25.54:60:4:0.0118:0:2 0/0:113:0:0,0:8,105:0:2,0:23.9:1:29:1:1:0:60:15.143:1:0:0.3 -20 31016314 . A G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTGTAGTGAGCTGTGAAC;RSEQ=TGTTCAGAGAGTGAAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:0,109:0:1,0:22.2:1:31.3:1:1:0:60:108:1:0:0.1 0/1:63:25:0,25:1,37:0.3968:1,1:24.2:1:31.4:1:1:0:60:50:0.3968:0:1.1 -20 31017119 . T C 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGTTGACTTGGGCTCTCT;RSEQ=TTGTTCTCTCTTGGAACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:691:0:0,0:451,240:0:2,0:24.6:1:29.9:1:1:0:60:85.375:1:0:0.1 0/1:572:19:13,6:335,218:0.0332:2,2:32.8:1:31.5:1:0.63449:1.41:60:38:0.0335:0:1.1 -20 31017650 . A T 44 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16577;SOR=5.72837;LSEQ=GAGAAATGAGCTTGTCTGAG;RSEQ=GCCATGGGCGCGGCTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:1:0,1:285,157:0.0023:2,0:1:0:27:0:0.35666:0:60:2:0.0023:0:2 0/1:312:4:0,4:191,117:0.0128:2,0:6.8:1:22:1:0.02194:0:60:3:0.0097:0:1 -20 31017651 . G T 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24123;SOR=2.8164;LSEQ=AGAAATGAGCTTGTCTGAGA;RSEQ=CCATGGGCGCGGCTTGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:2:1,1:288,159:0.0045:2,2:18.5:1:27.5:1:1:1.80868:60:4:0.0046:0:1 0/1:321:4:1,3:196,121:0.0125:2,2:11.8:1:25.8:1:0.3025:4.83589:60:8:0.0126:0:1 -20 31019024 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGATTGTGTGCAGATAACT;RSEQ=CTGGGTAGCTTGGGTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:54:53,1:135,3:0.2813:1,1:26.1:1:30.4:1:1:1.18:60:53:0.2789:0:1.1 1/1:86:86:86,0:0,0:1:0,1:24.4:1:30:1:1:0:60:85:1:0:1.2 -20 31019299 . C T 183 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03243;LSEQ=GACAGACAGGTGCACATGGG;RSEQ=AGCCTCCCCTTTGCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:900:82:29,53:332,486:0.0911:2,2:27.8:1:28.9:1:0.40859:1.24817:60:164:0.0927:0:1.1 0/0:618:2:1,1:253,362:0.0032:2,2:37:1:28:1:1:1.43:60:4:0.0033:0:1 -20 31019509 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08354;SOR=Inf;LSEQ=AGACTTGGTCATCTCGGACG;RSEQ=CTTGCGACGCACCTGTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:62,237:0:2,0:22.7:1:31.7:1:1:0:60:41.714:0.9966:0:0.1 0/1:234:3:2,1:63,168:0.0128:2,2:28:1:25.7:1:0.18746:5.29:60:6:0.0132:0:1 -20 31020649 . A T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07704;SOR=Inf;LSEQ=GACAGACATTAATATCCCGA;RSEQ=TGCACTTACTAGAAGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:281,93:0:2,0:23.9:1:30.2:1:1:0:60:186:1:0:0.1 0/1:278:3:1,2:190,85:0.0108:2,2:12.7:1:21.7:1:0.23164:4.4438:60:2:0.0074:0:1 -20 31021743 . G A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01073;LSEQ=AGGAGACTGTTTGATTCCTG;RSEQ=CTGCCCTGGAGCCAGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:2,1:62,173:0.0126:2,2:16.7:1:28:1:0.17689:5.53:60:6:0.0132:0:1 0/1:157:2:2,0:45,110:0.0127:2,0:1:0:23.5:1:0.08827:0:60:4:0.0128:0:1 -20 31021769 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13891;SOR=Inf;LSEQ=CTGGAGCCAGGTTTTCTTTG;RSEQ=GGGTCATGAGATTATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:29,125:0:2,0:24.4:1:30.2:1:1:0:60:18.25:1:0:0.1 0/1:92:2:1,1:14,76:0.0217:2,2:29:1:30:1:0.301:5.28:60:4:0.022:0:1 -20 31022186 . G T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.018;SOR=Inf;LSEQ=TTTTGCTTTACAGTCCCTAG;RSEQ=TCAGATCACCCAGTCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:576:0:0,0:423,152:0:2,0:25.9:1:31.3:1:1:0:60:62.889:1:0:0.1 0/1:469:5:1,4:332,132:0.0107:2,2:8:1:27.2:1:0.02647:10.00621:60:10:0.0109:0:1.2 -20 31022441 . AG A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05413;SOR=2.29662;LSEQ=GCGGCCACCACTGCCATCGG;RSEQ=GGGGGGGTGGCCCGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:10:5,5:234,216:0.0217:2,2:29.9:1:32.4:1:1:1.08313:60:20:0.0222:0.0022:0 0/1:288:14:7,7:131,141:0.0486:2,2:29.9:1:31.8:1:1:1.08:60:28:0.0493:0.0035:0.3 -20 31022495 . C T 41 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04955;SOR=Inf;LSEQ=GCCACCGATGAGGGAGGTGG;RSEQ=AGAGGCAGCAGCAGTGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:0:0,0:338,165:0:2,0:23.9:1:31.9:1:1:0:60:44.727:1:0:0.1 0/1:293:3:2,1:196,94:0.0102:2,2:8:1:26:1:1:1.0424:60:6:0.0103:0:1 -20 31022766 . G A 136 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=39.10582;LSEQ=GAGATGCCTCCCAACTCCCC;RSEQ=TTGCTCCCACTGGGGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:703:1:1,0:341,358:0.0014:2,0:1:0:26:0:0.48857:0:60:2:0.0014:0:1 0/1:416:22:12,10:197,196:0.0529:2,2:26.1:1:30.6:1:0.82728:1.19:60:44:0.0541:0:1.2 -20 31022959 . T C 305 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00374;SOR=0.08267;LSEQ=TGCAGACAATGGTCCCATTC;RSEQ=GTCTCTAGTGGGAGATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1094:1093:605,488:0,1:0.9991:0,2:24.6:1:30.3:1:0.44698:0:60:67.313:1:0:1.1 1/1:730:722:384,338:1,3:0.989:2,2:23.4:1:29.7:1:0.34641:3.40:60:119.333:0.9931:0:1.1 -20 31024274 . T C 250 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=534.70235;LSEQ=CGTGCTATGTCACAGGACAG;RSEQ=AATTCAAATGCTGCTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:928:1:1,0:501,422:0.0011:2,0:10:0:33:0:1:0:60:2:0.0011:0:1 0/1:660:240:120,120:221,198:0.3636:2,2:23.2:1:31.7:1:0.51754:1.11597:60:47:0.361:0:1.1 -20 31024488 . C T 164 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=75.3403;LSEQ=GGCCTGCGGACCCGATGCCT;RSEQ=TTCCTGCTGAGATCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1061:1:0,1:532,527:9e-04:2,0:1:0:26:0:0.49811:0:60:2:0.001:0:1 0/1:752:50:25,25:338,363:0.0665:2,2:21:1:29.2:1:0.88384:1.07:60:49:0.0661:0:1.2 -20 31025163 . A G 199 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=92.40472;LSEQ=AAATTATGGCCATGGGAAAC;RSEQ=TTGTATATTTAGTGTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:2:1,1:117,275:0.0051:2,2:24.5:1:28:1:0.50982:2.34:60:4:0.0051:0:1.5 0/1:295:95:26,69:66,134:0.322:2,2:24:1:30.3:1:0.34955:1.30595:60:46.5:0.3185:0:1.2 -20 31025208 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11929;SOR=Inf;LSEQ=GATAATGATTGATCTTAAAT;RSEQ=TGTATACAGAATATCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:12,169:0:2,0:22.8:1:32:1:1:0:60:59.333:1:0:0 0/1:96:2:1,1:9,85:0.0208:2,2:17.5:1:30.5:1:0.19846:9.01:60:4:0.0208:0:2.5 -20 31025231 . T C 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATACAGAATATCATTGATA;RSEQ=AATACTCTTTAGGCAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:1,118:0:1,0:24.4:1:28.5:1:1:0:60:118:1:0:0.1 0/1:55:13:0,13:0,42:0.2364:1,1:26.2:1:32.5:1:1:0:60:26:0.2364:0:1.8 -20 31367948 . C T 152 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=51.93581;LSEQ=CCAAGTCCTGAGCCTCCAAG;RSEQ=TTGGTGAGGGGGAGGCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:768:1:1,0:330,434:0.0013:2,0:47:0:25:0:0.43268:0:60:2:0.0013:0:1 0/1:645:41:17,24:266,338:0.0636:2,2:27.2:1:28.4:1:0.87107:1.11082:60:40:0.0629:0:1.1 -20 31368060 . G T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03166;SOR=Inf;LSEQ=AACACAGAGCCCATGGCGGG;RSEQ=GAACACTGTCCCTCTCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:320,181:0:2,0:23.7:1:30.6:1:1:0:60:26.833:1:0:0.1 0/1:367:4:0,4:233,130:0.0109:2,0:11.5:1:24.3:1:0.01727:0:60:3:0.0084:0:1.3 -20 31368254 . G A 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08152;SOR=4.00374;LSEQ=CCCAATCCTGGAGGCTATCC;RSEQ=CACCCCGGAGATCAGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:2:2,0:235,393:0.0032:2,0:1:0:27.5:1:0.14115:0:60:4:0.0032:0:1 0/1:476:6:4,2:180,290:0.0126:2,2:16.8:1:29.3:1:0.2119:3.21:60:12:0.0129:0:1.2 -20 31368350 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11008;SOR=Inf;LSEQ=CAGACAACTGGAGGCTTTGG;RSEQ=GAGAGTCTCTGACAACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:11,133:0:2,0:23.2:1:31.2:1:1:0:60:71:1:0:0.2 0/1:72:2:1,1:3,67:0.0278:1,2:28:1:31:1:0.10876:19.49:60:4:0.0278:0:1 -20 31368423 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07684;SOR=Inf;LSEQ=GCAAGGAGGGATGCAGGGTC;RSEQ=AGCCCTTCACACCTGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,43:0:1,0:23.2:1:30.8:1:1:0:60:20.5:1:0:0 0/1:17:2:1,1:1,14:0.1176:1,2:39:1:30.5:1:0.22794:10.25:60:4:0.1176:0:1 -20 31368560 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTCTCAGCATGGGCCCT;RSEQ=GGAGAGCCCTTCTGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:13:1:31.5:1:1:0:60:4:0.25:0:1 0/0:1:0:0,0:0,1:0:0,0:2:0:32:0:1:0:60:2:1:0:0 -20 31368957 . T C 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03168;SOR=Inf;LSEQ=TTTGGGTCCTGTCACGTGCC;RSEQ=GGCCCAGGGCTCTGTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:41,0:0:1,0:21.2:1:31.8:1:1:0:60:82:1:0:0.4 0/1:20:3:3,0:17,0:0.15:1,0:12:1:31:1:1:0:60:6:0.15:0:1 -20 31368960 . C A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16263;SOR=2.31538;LSEQ=GGGTCCTGTCACGTGCCTGG;RSEQ=CCAGGGCTCTGTTGTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:11:11,0:31,0:0.2619:1,0:19.2:1:27.5:1:1:0:60:4.5:0.2368:0:1.1 0/1:22:10:10,0:12,0:0.4545:0,0:20.4:1:29.7:1:1:0:60:20:0.4545:0:1 -20 31369067 . C T 43 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41293;SOR=2.55299;LSEQ=AGTGTAGGGGAGATCCCAGG;RSEQ=CACGCCACGGAGAAAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:2:0,2:232,57:0.0069:2,0:1:0:25:0:0.04055:0:60:4:0.007:0:1 0/1:230:4:1,3:171,55:0.0174:2,2:5.8:1:21.5:1:0.05046:9.21517:60:3:0.0133:0:1 -20 31369126 . C G 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCCAGACTGGTGCCTGCCCC;RSEQ=ACAAAACAGACTCCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:436,290:0:2,0:25.8:1:31.3:1:1:0:60:89.75:0.9972:0:0.2 0/1:689:31:17,14:397,260:0.045:2,2:28.4:1:31.1:1:0.57567:1.25703:60:62:0.0454:0:1.2 -20 31369136 . AC A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.10458;LSEQ=TGCCTGCCCCCACAAAACAG;RSEQ=TCCTGGCTGTTTCCTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:799:202:118,84:332,265:0.2528:2,2:25.3:1:30.7:1:0.51208:1.12:59.9:404:0.2554:0.0451:0.2 1/0:759:389:228,161:212,158:0.5125:2,2:26:1:29.9:1:0.7686:1.06:60:388:0.5146:0.0711:0.3 -20 31369479 . G A 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55731;SOR=2.66173;LSEQ=CTTGCAGTCAACTGCCGTCT;RSEQ=AAAGTATTAAATGGAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:33:1:31.8:1:1:0:60:10:0.2778:0:1 1/0:4:2:0,2:0,2:0.5:0,0:19.5:1:32:0:1:0:60:4:0.5:0:1 -20 31372736 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17623;SOR=Inf;LSEQ=GCATACATAGCATGCTACAT;RSEQ=CATAGCATAGCTCCTTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:20,188:0:2,0:20.6:1:29.7:1:1:0:60:68.333:1:0:0.1 0/1:151:2:1,1:15,134:0.0132:2,2:12.5:1:27.5:1:0.20132:8.68:60:4:0.0132:0:1 -20 31372748 . T A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56872;SOR=2.93134;LSEQ=TGCTACATACATAGCATAGC;RSEQ=CCTTAGGGGAGCTTTTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:0,1:6,149:0.0064:1,0:37:0:31:0:1:0:60:2:0.0066:0:1 0/1:108:2:1,1:7,99:0.0185:2,2:24.5:1:29:0:0.1433:13.30:60:4:0.0189:0:1 -20 31372847 . C CT 38 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.31935;SOR=3.13885;LSEQ=GTTGGAGGGTTTTCTTTTTT;RSEQ=TTTTTTTTTTTCTGAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:0,3:1,23:0.1034:1,0:21.7:1:29.7:1:1:0:60:6:0.1034:0:0 0/1:11:3:0,3:0,8:0.2727:0,0:19.7:1:24:1:1:0:60:2:0.2:0.0909:0.3 -20 31374259 . C T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.47079;LSEQ=CTTCTGGCCCCGCCAGACCC;RSEQ=AGGCCTCCAGTCACCTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:650:154:105,49:341,155:0.2369:2,2:24.7:1:30.1:1:0.92093:1.02665:60:153:0.2391:0:1.1 1/0:474:246:157,89:144,84:0.519:2,2:25.4:1:29.2:1:0.92401:1.03:60:40:0.5161:0:1.1 -20 31374520 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.91035;LSEQ=CACTACTGGTTGTGGCTGGT;RSEQ=GATAATCTGTGTCCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:87:9,78:18,207:0.2788:2,2:24.2:1:30.8:1:0.50613:1.33:60:42.5:0.2778:0:1 1/0:234:141:15,126:10,83:0.6026:2,2:24:1:30.3:1:1:1.012:60:140:0.6087:0:1 -20 31374848 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06388;SOR=Inf;LSEQ=TCATCTTTCTGTCTCTGGGA;RSEQ=AGTTACAATGACTTTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:28,3:0:2,0:21.6:1:31.2:1:1:0:60:14.5:1:0:0.5 0/1:11:2:2,0:9,0:0.1818:0,0:25.5:1:30:1:1:0:60:4:0.1818:0:1 -20 31374959 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18887;SOR=Inf;LSEQ=TCTTTCTTTTTGCCTAGGAG;RSEQ=CATATGGGGGTGCCGTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:180,20:0:2,0:23.2:1:31.6:1:1:0:60:32.333:0.9949:0:0.3 0/1:155:2:2,0:135,18:0.0129:2,0:20.5:1:27:1:1:0:60:4:0.0136:0:1.5 -20 31374991 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.72219;LSEQ=GCCGTTGGTCTCTGGTCACC;RSEQ=ACATCCTTTGCTCTGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:114:88,26:202,57:0.3056:2,2:25:1:29.7:1:0.89284:1.04692:60:56:0.3019:0:1 1/0:319:174:126,48:112,33:0.5455:2,2:23.4:1:29.6:1:0.36657:1.29189:60:173:0.5475:0:1.1 -20 31375287 . T C 133 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=32.08866;LSEQ=AGAGGGGCTCCTGCCCAGGG;RSEQ=GACTGAGGACCCTGAACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:1:0,1:117,319:0.0023:2,0:16:0:8:0:1:0:60:0:0:0:4 0/1:320:22:8,14:77,219:0.0688:2,2:20.3:1:30:1:0.31964:1.62:60:21:0.0675:0:1 -20 31375311 . A G 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00257;SOR=1.80822;LSEQ=TGAGGACCCTGAACACGGGG;RSEQ=AAAACCAGTTACCTGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:95:16,79:35,158:0.3287:2,2:24.5:1:31.1:1:0.87028:1.09343:60:94:0.3298:0:1.1 0/1:183:86:12,74:14,83:0.4699:2,2:22.2:1:31.1:1:1:1.03995:60:172:0.4778:0:1 -20 31375386 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13483;SOR=Inf;LSEQ=TCGTAATTGTAATAATTGAC;RSEQ=TGTTTGAATTCTAAGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:0,56:0:1,0:23.2:1:30.6:1:1:0:60:17.667:1:0:0.4 0/1:33:2:1,1:0,31:0.0606:1,2:27.5:1:32:0:0.06061:0:60:4:0.0606:0:1 -20 31376490 . T C 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04588;SOR=3.34351;LSEQ=CTGGCCTCAAGCGATCCCCC;RSEQ=GCCTCGGTCTCCCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:11:11,0:24,0:0.3143:1,0:21.1:1:30.6:1:1:0:60:22:0.3143:0:1.2 1/0:18:11:10,1:6,1:0.6111:2,2:24:1:30.5:1:1:1.62:60:22:0.6471:0:1 -20 31379184 . C A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93553;LSEQ=TCCACAGTGGAAGTGTCGTA;RSEQ=CTAACAAGGTTCTGGATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:10,0:14,0:0.4167:1,0:24.3:1:29.8:1:1:0:60:20:0.4167:0:1 0/1:5:2:2,0:3,0:0.4:0,0:9.5:1:31:1:1:0:60:4:0.4:0:2 -20 31379310 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13481;SOR=Inf;LSEQ=AATGGTCTCTTGGTTAAAGT;RSEQ=TGTGAAAATCTTCTGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:171,16:0:2,0:24.5:1:31.9:1:1:0:60:61.333:1:0:0.1 0/1:109:2:1,1:100,7:0.0183:2,2:5:1:28.5:1:0.14203:13.42973:60:4:0.0185:0:1.5 -20 31379323 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.56087;SOR=3.24831;LSEQ=TTAAAGTGTGTGAAAATCTT;RSEQ=TGCATCTGATGGACAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:1:1,0:203,30:0.0043:2,0:25:0:11:0:1:0:60:0:0:0:5 0/1:145:2:1,1:125,18:0.0138:2,2:13.5:1:28:1:0.24569:6.7853:60:4:0.014:0:1.5 -20 31379665 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24005;SOR=2.1769;LSEQ=CAACATAACATGATGGCCAC;RSEQ=GGATTGGGCCTCCCAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:11:0,11:1,26:0.2895:1,0:21.5:1:31.3:1:1:0:60:22:0.2973:0:1 0/1:19:9:0,9:0,10:0.4737:0,0:29.1:1:28.9:1:1:0:60:18:0.5:0:1 -20 31380201 . A T 67 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31579;SOR=Inf;LSEQ=ACATTCCCTAGGGGGAAGAG;RSEQ=TCCTATTTGGTGCCTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:12,1:0.2778:1,0:24.6:1:29:1:1:0:60:10:0.3125:0:1 1/1:1:1:1,0:0,0:1:0,0:8:0:30:0:1:0:60:2:1:0:1 -20 31380309 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=4.1263;LSEQ=TACCACAGCCCAGGACAGCT;RSEQ=TCTGGCTATGAAAGGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:34:34,0:72,1:0.3178:1,1:23:1:27.9:1:1:0:60:68:0.3238:0:1.2 1/0:50:33:32,1:17,0:0.66:1,1:21.3:1:28.1:1:1:0:60:66:0.66:0:1.1 -20 31380332 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.54353;SOR=0;LSEQ=TGGCTATGAAAGGGCCCAGT;RSEQ=TGAAGGGGAATGTAGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:151,9:0.0123:2,0:8.5:1:29:1:1:0:60:4:0.0123:0:1.5 0/0:87:0:0,0:82,5:0:2,0:23.4:1:31.1:1:1:0:60:42.5:1:0:0.7 -20 31380340 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13343;SOR=Inf;LSEQ=AAAGGGCCCAGTGTGAAGGG;RSEQ=AATGTAGGCCCTGGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:166,26:0:2,0:21.8:1:31:1:1:0:60:37.4:1:0:0.3 0/1:111:2:1,1:100,9:0.018:2,2:23.5:1:29.5:1:0.17281:10.59364:60:4:0.0187:0:1.5 -20 31380350 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14127;SOR=Inf;LSEQ=GTGTGAAGGGGAATGTAGGC;RSEQ=CTGGCTGGGGGAATCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:179,44:0:2,0:23.3:1:30.8:1:1:0:60:54.75:0.9955:0:0.3 0/1:136:2:1,1:114,19:0.0147:2,2:16:1:28:1:0.27529:5.8737:60:4:0.0149:0:1 -20 31380364 . TC T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15563;SOR=Inf;LSEQ=GTAGGCCCTGGCTGGGGGAA;RSEQ=CCTGGGTGTGGCCTGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:229,68:0:2,0:24.5:1:31.1:1:1:0:60:41.429:1:0:0.2 0/1:194:2:1,1:154,38:0.0103:2,2:13:1:27.5:1:0.36248:4.01331:60:4:0.0105:0.0052:0.5 -20 31380398 . AC A 89 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.0042;SOR=11.83707;LSEQ=CTGGCGAGCACCTCCTCCCC;RSEQ=CCCCCCATTCATCACAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:1:1,0:389,171:0.0018:2,0:22:0:34:0:1:0:60:2:0.0018:0:0 0/1:387:8:5,3:263,116:0.0207:2,2:14.4:1:29.8:1:0.70565:1.35924:59.4:16:0.0211:0.0129:0.3 -20 31380639 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1806;SOR=Inf;LSEQ=TGGGACCACTTCTTGGGAGA;RSEQ=TCAGCCACCCCTGCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:20,208:0:2,0:23.6:1:32.1:1:1:0:60:113:1:0:0.1 0/1:169:2:1,1:22,145:0.0118:2,2:24:1:31:1:0.25437:6.47:60:4:0.012:0:1 -20 31380643 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18434;SOR=Inf;LSEQ=ACCACTTCTTGGGAGAGTCA;RSEQ=CCACCCCTGCTGCCCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:18,190:0:2,0:23.9:1:32.2:1:1:0:60:103:1:0:0.2 0/1:157:2:1,1:17,138:0.0127:2,2:15:1:25.5:1:0.21681:7.92:60:4:0.013:0:1 -20 31381229 . G A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13894;SOR=2.69082;LSEQ=GGTTGCAGTGCGCCGAGATC;RSEQ=CACCACTGCATTCAAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:8,0:19,1:0.2857:1,0:21.9:1:31.4:1:1:0:60:16:0.2857:0:1 1/0:21:11:11,0:10,0:0.5238:0,0:24.5:1:30.5:1:1:0:60:22:0.5238:0:1.5 -20 31381507 . T G 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00761;SOR=Inf;LSEQ=GAATCAAATTTCTTGAAAAG;RSEQ=CAATCTGAACTCCCTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:8,111:0:2,0:23.8:1:30.1:1:1:0:60:58.5:1:0:0 0/1:74:5:0,5:7,62:0.0676:2,0:23.8:1:32.2:1:1:0:60:10:0.0676:0:1 -20 31381690 . A T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.7321;LSEQ=TTGTCACTAAAGGGTCCTTA;RSEQ=GATTTTTAATGGCTGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:49:0:30:0:1:0:60:2:0.5:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:27.5:1:31.5:1:1:0:60:4:0.6667:0:1 -20 31383353 . T G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.80092;LSEQ=GAGCCGAGGTGATTGTTGGG;RSEQ=ACCTGGGATCATGGGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:878:227:92,135:268,381:0.2585:2,2:24.6:1:31:1:0.87558:1.03215:60:55.75:0.259:0:1.1 0/1:698:345:137,208:136,215:0.4943:2,2:25.2:1:30.8:1:0.81608:1.04:60:48.286:0.4927:0:1.2 -20 31383530 . C T 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.01349;LSEQ=TCTCCCTCCCAGTCATCCCC;RSEQ=TCACACCCTGGCTAGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:958:251:113,138:315,389:0.262:2,2:26.5:1:30.3:1:0.94123:1.01:60:61.75:0.2614:0:1.1 1/0:880:455:198,257:190,232:0.517:2,2:26:1:29.8:1:0.68325:1.06291:60:64:0.5155:0:1.2 -20 31383726 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05314;SOR=Inf;LSEQ=AAGGGTATGGTGAGGAACAA;RSEQ=GGAAGCTGGGCCATTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:0,35:0:1,0:23.3:1:31.6:1:1:0:60:70:1:0:0.4 0/1:11:2:1,1:1,8:0.1818:2,2:26:1:30:0:0.34545:6.00:60:4:0.1818:0:1 -20 31384136 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCAGGGATGCAACTCC;RSEQ=TGCTGACCTGGTGATATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:12.5:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 31384488 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1373;SOR=Inf;LSEQ=TGAGGTGCAAAGAGTCCTTG;RSEQ=CAAGCTGCTGGCCTGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:186,17:0:2,0:24.9:1:31.1:1:1:0:60:28:1:0:0.1 0/1:120:2:1,1:109,9:0.0167:2,2:49:1:28:1:0.16036:11.54243:60:4:0.0167:0:1.5 -20 31384764 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15153;SOR=Inf;LSEQ=CAGCACCTGTGTGGAGACTC;RSEQ=GTGAAGCCCACTCATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:36,277:0:2,0:22.6:1:30.9:1:1:0:60:61.6:1:0:0.1 0/1:200:2:1,1:26,172:0.01:2,2:16.5:1:30.5:1:0.25236:6.51:60:4:0.0102:0:1 -20 31385234 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.1111;SOR=Inf;LSEQ=GGAGCTAATTTGCCCTGGAA;RSEQ=CAGCACACAGGGTTTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:4,119:0:1,0:22.7:1:32:1:1:0:60:29.75:1:0:0.2 0/1:62:2:1,1:2,58:0.0323:1,2:18:0:31.5:1:0.09519:23.88:60:4:0.0328:0:2 -20 31385269 . G T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01271;SOR=3.19437;LSEQ=TATATTTTGTGGTGGCTGTG;RSEQ=TTGTAGCATAATTGGAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:21:1,20:0,44:0.3231:1,1:30.8:1:30.4:1:0.32308:0:60:42:0.3281:0:1 1/0:28:17:2,15:0,11:0.6071:0,2:24.2:1:30.2:1:0.50529:0:60:34:0.6071:0:1.1 -20 31385452 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTATAGGCACATGCCA;RSEQ=CACACCCAGCTAGTTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:10:1:33:0:0.4:0:58.5:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 31386332 . G A 168 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=33.82545;LSEQ=GCGGCCGAGGCCAAGCTTCA;RSEQ=GAGCCCTGGAGCTGTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:888:2:2,0:434,452:0.0023:2,0:1:0:26:1:0.24079:0:60:4:0.0023:0:1 0/1:718:51:25,26:332,334:0.071:2,2:23.2:1:29.7:1:1:1.03373:60:50:0.0701:0:1.9 -20 31386347 . T C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.57044;LSEQ=CTTCAGGAGCCCTGGAGCTG;RSEQ=TACATGTGTCTCCCGCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:904:249:122,127:309,345:0.2754:2,2:24:1:32:1:0.65515:1.07:60:82:0.2739:0:1.2 1/0:684:394:190,204:150,138:0.576:2,2:22.8:1:31.5:1:0.35225:1.16678:60:48.25:0.5719:0:1.3 -20 31386449 . T C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.83429;LSEQ=AGTGACACGGGGCTTGAATA;RSEQ=GTAAGCCACAGGCTCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:206:88,118:248,344:0.2575:2,2:27.1:1:30.7:1:0.86995:1.03:60:102:0.2615:0:1.1 1/0:704:402:165,237:131,167:0.571:2,2:25.7:1:29.3:1:0.48627:1.12653:60:32.5:0.5702:0:1.2 -20 31387737 . CTAGT C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13785;SOR=5.5289;LSEQ=TAAGTATAATTGGAGATAAA;RSEQ=TAACAACTACTGCTACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:0.1176:1,0:35:1:34:0:1:0:60:4:0.1176:0:0 0/1:9:4:4,0:5,0:0.4444:0,0:38.3:1:31:1:1:0:60:8:0.4444:0:0 -20 31387951 . C G 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTTCTGTGTCTCTCTGGC;RSEQ=CCCACAGGCTACCTAGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:729:0:0,0:457,271:0:2,0:24.3:1:30.7:1:1:0:60:51:0.9986:0:0.4 0/1:610:36:22,14:337,212:0.059:2,2:26.9:1:30.2:1:1:1.01156:60:72:0.0604:0:1.2 -20 31387954 . C G 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.08864;LSEQ=TTCTGTGTCTCTCTGGCCCC;RSEQ=ACAGGCTACCTAGTCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:771:199:120,79:350,222:0.2581:2,2:24.1:1:30:1:0.8661:1.03789:60:48.75:0.2573:0:1.1 0/1:639:269:175,94:209,161:0.421:2,2:26.4:1:29.8:1:0.03336:1.43:60:66.25:0.4226:0:1.2 -20 31388080 . C T 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AATATCAAATACGTGAACGA;RSEQ=GTGAGGAACATCACAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:750:0:0,0:287,462:0:2,0:25.2:1:30.4:1:1:0:60:67.091:0.9986:0:0.1 0/1:669:36:13,23:262,369:0.0538:2,2:23.9:1:29.7:1:0.6032:1.25578:60:35:0.0532:0:1.1 -20 31388461 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03018;SOR=3.8493;LSEQ=TTCTAGTAGAGTTGGGGTTT;RSEQ=TCCATGTTGGCCAAGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:12:11,1:40,2:0.2222:1,2:20.5:1:29.2:1:0.53717:1.79524:60:11:0.2115:0:1.2 1/0:17:9:9,0:8,0:0.5294:0,0:19.6:1:28.8:1:1:0:60:8:0.5:0:1 -20 31388496 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01895;SOR=Inf;LSEQ=GCTGGTCTCGAACTCCTGAC;RSEQ=TCAGGTAATCCACCCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:97,2:0:1,0:27:1:30.3:1:1:0:60:18.8:1:0:0.2 0/1:37:3:3,0:34,0:0.0811:1,0:21.7:1:29.7:1:1:0:60:6:0.0833:0:1 -20 31388636 . T C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=3.41557;LSEQ=TCCTGACTCTGTCTCTCTCT;RSEQ=TCAGATTGAAGAATGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:899:238:129,109:378,281:0.2647:2,2:27.9:1:31.3:1:0.4026:1.13647:60:118:0.2673:0:1.2 1/0:812:448:253,195:197,164:0.5517:2,2:24.8:1:31.1:1:0.61847:1.08:60:111:0.5543:0:1.1 -20 31388737 . C T 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAGGCCTGTATGGTGAG;RSEQ=ATCCTTCTCTCTGGCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:643:0:0,0:236,406:0:2,0:24.4:1:31.9:1:1:0:60:70.333:1:0:0.1 0/1:533:21:9,12:192,318:0.0394:2,2:25:1:27.8:1:0.65088:1.24:60:42:0.0396:0:1 -20 31388805 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52461;SOR=0;LSEQ=GGCCCAGGTGCAGCAGCCTG;RSEQ=GAAGGAGCCACTTGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:0,2:18,178:0.0101:2,0:17:1:30.5:1:1:0:60:4:0.0104:0:1 0/0:125:0:0,0:17,108:0:2,0:24.5:1:30.3:1:1:0:60:40.667:1:0:0.2 -20 31389009 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.36341;LSEQ=AGGAGGCCATTGGGAACCTG;RSEQ=TGGTCTCAGGGAATAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:61:51,10:144,29:0.2607:2,2:21.4:1:30:1:1:1.03:60:29.5:0.2588:0:1.1 1/0:174:114:93,21:45,15:0.6552:2,2:21.8:1:29.8:1:0.32937:1.47:60:228:0.659:0:1.1 -20 31389036 . G T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.411;SOR=2.64899;LSEQ=CAGGGAATAAGGTGGGTTGG;RSEQ=CTGGAGGTTTCAAATGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:2:1,1:262,120:0.0052:2,2:2.5:1:28:0:0.53148:2.17848:60:4:0.0054:0:1 0/1:292:4:2,2:198,90:0.0137:2,2:27.8:1:27.5:1:0.59278:2.19349:60:8:0.0139:0:1.3 -20 31389279 . A G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19558;SOR=Inf;LSEQ=CACAGACAGCCAGGGCAGGG;RSEQ=AAGCGCTGCTGGCAGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:32,207:0:2,0:22.8:1:30.4:1:1:0:60:118.5:1:0:0.1 0/1:190:2:1,1:32,156:0.0105:2,2:22.5:1:26.5:1:0.31796:4.82:60:4:0.0106:0:1 -20 31389284 . G A 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.82772;LSEQ=ACAGCCAGGGCAGGGAAAGC;RSEQ=CTGCTGGCAGTGATGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:3:1,2:25,180:0.0144:2,2:11.7:1:31.3:1:0.33147:3.57:60:6:0.0145:0:1 0/1:168:2:2,0:23,143:0.0119:2,0:1:0:24:0:0.02139:0:60:4:0.012:0:1 -20 31389349 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0465;SOR=Inf;LSEQ=ACTTTCCCGTTCTTGGTCTG;RSEQ=CTAGATCCAATAGTGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:1,72:0:1,0:28.7:1:32.1:1:1:0:60:72:1:0:0.1 0/1:42:3:0,3:0,39:0.0714:1,0:30.7:1:29.7:1:1:0:60:6:0.0714:0:1 -20 31389518 . A G 52 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTACCTCAGCCTCCCAA;RSEQ=TGGCTGGGACTACAGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:26.3:1:33.3:1:1:0:60:6:0.3333:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 31390128 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.3032;LSEQ=ATAGCCCTGTCACCTGCAAA;RSEQ=GTCTGGTTGACACTGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:2:1,1:177,46:0.0089:2,2:2.5:1:28.5:1:0.37488:3.81741:60:4:0.009:0:1 0/1:173:2:1,1:131,40:0.0116:2,2:5:1:28:1:0.41887:3.24712:60:4:0.0116:0:1 -20 31390138 . A G 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00113;SOR=Inf;LSEQ=CACCTGCAAAGGTCTGGTTG;RSEQ=CACTGAAACTCTAATAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:209,68:0:2,0:23.6:1:29.5:1:1:0:60:54.4:1:0:0.1 0/1:211:8:7,1:147,56:0.0379:2,2:27.6:1:31.8:1:0.68552:2.66:60:16:0.0381:0:1 -20 31390533 . T C 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AAGTCCCACGTGGCTGGGTG;RSEQ=GGTGGCTCACGCCTGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:9:1:31:0:1:0:60:6:0.3333:0:1 1/1:1:1:0,1:0,0:1:0,0:44:0:27:0:1:0:60:2:1:0:1 -20 31393065 . T G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00119;SOR=Inf;LSEQ=CAGGGCACATCTCTGCAACA;RSEQ=AGACCCTCACTCCCACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:256,63:0:2,0:23.5:1:30.4:1:1:0:60:62.8:1:0:0.1 0/1:245:8:6,2:181,56:0.0327:2,2:19.1:1:32.3:1:1:1.07706:60:16:0.0332:0:1.3 -20 31393256 . C A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04029;SOR=Inf;LSEQ=GGAAAAATGCACTTGGTGAC;RSEQ=TCCAAGTGGGGACTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:149,305:0:2,0:24.8:1:31.6:1:1:0:60:74.667:1:0:0.1 0/1:370:4:3,1:121,245:0.0108:2,2:21.5:1:29.5:1:0.11151:6.04:60:8:0.0108:0:1 -20 31393352 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=4.0676;LSEQ=TGGGCTTCCCTCTCCCACAT;RSEQ=ATTGTTCTGTCCCATCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:18:0,18:0,71:0.2022:1,1:26.9:1:29:1:1:0:60:17:0.1932:0:1.1 1/0:47:24:0,24:2,21:0.5106:2,1:23.6:1:30.9:1:0.23404:0:60:48:0.5106:0:1 -20 31393803 . T C 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17391;SOR=Inf;LSEQ=AAGCACAAAATGTTCTTGTC;RSEQ=CTCCAACTCTGCTTTTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:3,0:18,1:0.1364:1,0:26.7:1:31.3:1:1:0:60:6:0.1364:0:1 1/1:1:1:1,0:0,0:1:0,0:12:0:31:0:1:0:60:2:1:0:1 -20 31393918 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53008;SOR=0;LSEQ=TGCCACTCTTCTGCCGCACC;RSEQ=GCGCTCTCCCCTCCATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:2,0:142,7:0.0132:1,0:38.5:1:31.5:1:1:0:60:4:0.0133:0:1 0/0:90:0:0,0:82,8:0:2,0:23.4:1:30.6:1:1:0:60:89:1:0:0.1 -20 31394185 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50652;SOR=0;LSEQ=GTGTAGATCAAAACACAAAT;RSEQ=GGCAGACATGGGCAGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:31,154:0.0107:2,2:21.5:1:29:1:0.31373:4.91:60:4:0.0109:0:1 0/0:145:0:0,0:21,124:0:2,0:23:1:30:1:1:0:60:47.333:1:0:0.1 -20 31395475 . G T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.96025;LSEQ=ACTGATGGGACTGAGGGATG;RSEQ=CGAGGGCAGAAAGAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:0,1:142,22:0.0061:2,0:1:0:28:0:0.13939:0:60:2:0.0063:0:1 0/1:169:2:1,1:144,23:0.0118:2,2:7.5:1:24:1:0.26458:6.15031:60:4:0.0122:0:1 -20 31999353 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15441;SOR=Inf;LSEQ=GACTGCAGCACCTCCCCACT;RSEQ=CCATCCTGCACTCTCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:23.6:1:30:1:1:0:60:20:1:0:0.3 0/1:7:2:1,1:2,3:0.2857:2,2:27:1:29.5:1:1:1.41:60:4:0.2857:0:1 -20 32452555 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0991;SOR=Inf;LSEQ=CGGAGGCCATGCAGTCACTG;RSEQ=CTCTGCAGAACCTGGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:9,16:0:2,0:29.7:1:32.1:1:1:0:60:50:1:0:0 0/1:12:2:1,1:5,5:0.1667:2,2:6.5:1:27.5:1:1:1:60:4:0.1667:0:1 -20 33345691 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49776;SOR=Inf;LSEQ=GTTGCTGTGGGGGTCTTGCC;RSEQ=GCAACTGTTGTTGCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:49,60:0:2,0:28.9:1:30:1:1:0:60:35.333:1:0:0.1 0/1:111:2:1,1:61,48:0.018:2,2:22.5:1:30:1:1:1.26806:60:4:0.0182:0:2.5 -20 33345746 . G A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51359;SOR=Inf;LSEQ=CTGCTGCTGCTGCTGCTGCT;RSEQ=TTGTTGTTGTTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:28,42:0:2,0:26.5:1:32:1:1:0:60:69:1:0:0.1 0/1:101:2:1,1:41,58:0.0198:2,2:22:0:29.5:1:1:1.41:27:4:0.02:0:5 -20 33345753 . T C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51553;SOR=Inf;LSEQ=TGCTGCTGCTGCTGTTGTTG;RSEQ=TGTTGCTGCTGCTGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:26,39:0:2,0:25.7:1:30.2:1:1:0:58:130:1:0:0.4 0/1:96:2:1,1:39,55:0.0208:2,2:15:0:32:1:1:1.41:27:4:0.0211:0:5 -20 33345756 . T A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51377;SOR=Inf;LSEQ=TGCTGCTGCTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:25,37:0:2,0:24.7:1:30.4:1:1:0:57.9:61:1:0:0.4 0/1:90:2:1,1:37,51:0.0222:2,2:12:0:29:1:1:1.37:27:4:0.0225:0:5 -20 33345762 . C A 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.21011;SOR=0.3085;LSEQ=TGCTGTTGTTGTTGTTGCTG;RSEQ=TGCTGCTGCAGCTGGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:4:2,2:20,32:0.0714:2,2:10:0:30.8:1:0.64157:1.59:27.5:8:0.0714:0:3.8 0/1:87:2:1,1:35,50:0.023:2,2:10:0:29:1:1:1.42:22:4:0.0233:0:4 -20 33345787 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54036;SOR=Inf;LSEQ=GCTGCAGCTGGGGAAAATTA;RSEQ=CTGGGTTCATTTGTCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:9,21:0:2,0:15.6:1:31.3:1:1:0:60:29:1:0:0.1 0/1:56:2:1,1:15,39:0.0357:2,2:25.5:1:28.5:1:0.49351:2.55:60:4:0.0364:0:2 -20 33578899 . T C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97877;LSEQ=GCCAAGGGTTCCCCAACAGG;RSEQ=TGCTCTACACCGACTTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:31:20,11:10,3:0.7045:2,2:26.3:1:32.3:1:0.49843:1.80934:60:30:0.6977:0:1.2 1/0:30:21:14,7:6,3:0.7:2,2:15.4:1:30.9:1:1:1:60:20:0.6897:0:1.3 -20 33579073 . T C 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=CCAGGTATCCCAGCAAGACA;RSEQ=GGGGGTGGCTCAGACCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:28.3:1:28.7:1:1:0:60:6:0.375:0:1 1/1:4:4:0,4:0,0:1:0,0:25.8:1:31.5:1:1:0:60:8:1:0:1 -20 34962410 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50226;SOR=0;LSEQ=GGGTGACCAGGTATCTGGGG;RSEQ=GTGGCGACTCTGTGGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:0.0667:2,2:17:1:29:1:1:1:60:4:0.0667:0:1 0/0:22:0:0,0:12,10:0:2,0:27.1:1:30.4:1:1:0:60:44:1:0:0.3 -20 35477852 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTTTTACTTATTTTATT;RSEQ=TTTAAGACAGGGTCCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:43:1:31.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 35478058 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50467;SOR=0;LSEQ=TTAGTGATTTACCAGCCTGG;RSEQ=CTGGTAAATCACACTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:85,30:0.0169:2,2:34:1:30:1:0.46139:2.80361:60:4:0.0183:0:1 0/0:93:0:0,0:72,20:0:2,0:22.1:1:31:1:1:0:60:184:0.9892:0:0.2 -20 35478072 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22542;SOR=Inf;LSEQ=GCCTGGGCTGGTAAATCACA;RSEQ=TTTAAGTGTTCTAAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:105,46:0:2,0:27.8:1:31.1:1:1:0:60:24.167:1:0:0.3 0/1:137:2:1,1:103,32:0.0146:2,2:23.5:1:27.5:1:0.42508:3.18495:60:4:0.0147:0:1.5 -20 35478142 . C A 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=0.48873;LSEQ=TAAAATGATTTACGTTTGTA;RSEQ=ACTGAGGACAGCGGGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:110:58,52:99,94:0.363:2,2:26.3:1:30.1:1:0.90488:1.06:60:109:0.3633:0:1.2 0/1:317:69:38,31:133,114:0.2177:2,2:25.9:1:28.9:1:0.89193:1.05:60:138:0.2219:0:1.1 -20 35478151 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37494;SOR=3.72818;LSEQ=TTACGTTTGTACACTGAGGA;RSEQ=AGCGGGGGGAAGTTTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:1:0,1:158,152:0.0032:2,0:1:0:24:0:0.49196:0:60:2:0.0033:0:1 0/1:336:4:1,3:176,156:0.0119:2,2:9.3:1:25.3:1:0.34797:3.37328:60:8:0.0122:0:1 -20 35478182 . T C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1139;SOR=Inf;LSEQ=AGTTTAGATTTGGGGCCCAC;RSEQ=GGAACCTTTGCACGTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:131,173:0:2,0:24.9:1:30.3:1:1:0:60:100.333:1:0:0.4 0/1:287:3:1,2:117,166:0.0105:2,2:36:1:30:1:1:1.40801:60:6:0.0106:0:1.7 -20 35478214 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49919;SOR=0;LSEQ=ACGTGGCTCCAGATGCATGG;RSEQ=TATGACGGAATTGGCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:2,0:67,130:0.0101:2,0:13:1:27.5:1:0.11908:0:60:4:0.0102:0:2 0/0:187:0:0,0:65,122:0:2,0:25.2:1:31.3:1:1:0:60:45.75:1:0:0.3 -20 35478228 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50324;SOR=0;LSEQ=GCATGGCTATGACGGAATTG;RSEQ=CCTGCAGCAGCTGGTGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:49,115:0.012:2,0:5:1:28.5:1:0.0931:0:60:4:0.0121:0:1.5 0/0:137:0:0,0:42,94:0:2,0:26.2:1:31.4:1:1:0:60:135:0.9926:0:0.2 -20 35478352 . G A 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.23147;LSEQ=GCTCCCAGCTGGGAGGACAC;RSEQ=GAGAGAACCAAGGGGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:19.3:1:29.3:1:1:0:60:8:0.4444:0:1 1/0:6:3:0,3:0,3:0.5:0,0:22:1:30.3:1:1:0:60:6:0.5:0:1 -20 36012348 . C A 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30042;SOR=0.36998;LSEQ=CGGGTTTCCGCGTGTTGGCC;RSEQ=GGCAGGTCTCAAACTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:11,0:26,0:0.2973:1,0:22.5:1:29.9:1:1:0:60:10:0.2778:0:1.3 0/1:15:2:2,0:13,0:0.1333:1,0:6.5:1:28.5:1:1:0:60:4:0.1333:0:1.5 -20 36012386 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.07705;SOR=7.59195;LSEQ=TGATCTCAAGTGATCCGCCC;RSEQ=CTTCGGCCTCCCAAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:74,1:0.0132:1,0:1:0:31:0:1:0:60:2:0.0139:0:1 0/1:32:3:3,0:29,0:0.0938:1,0:33:1:29:1:1:0:60:6:0.0968:0:1 -20 36012434 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCGTGAGCCACCGCGCC;RSEQ=GGCCCTGCTGCCTCTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:2,0:172,3:0.0112:1,0:9:1:32.5:1:1:0:60:4:0.0116:0:1.5 0/0:72:0:0,0:70,2:0:1,0:23.8:1:30.5:1:1:0:60:71:1:0:0.1 -20 36012494 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01941;SOR=Inf;LSEQ=GTGGAATGGGTGGGAGGGAG;RSEQ=CCGGCCAAGGGGCCCCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:0:0,0:371,145:0:2,0:21.8:1:30.8:1:1:0:60:38.692:0.996:0:0.1 0/1:310:4:2,2:220,85:0.0129:2,2:13.5:1:27.5:1:0.31549:2.57906:60:8:0.0132:0:1 -20 36012701 . G A 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37509;SOR=0.26793;LSEQ=CCTCGGCCGACGGCCACCGC;RSEQ=GCCCCAGCGCGGCCTTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:4:3,1:211,171:0.0104:2,2:14.8:1:29.3:1:0.63196:2.43:60:8:0.0108:0:1.3 0/0:358:1:1,0:192,163:0.0028:2,0:1:0:28:0:1:0:60:2:0.0029:0:1 -20 36012785 . C A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30049;SOR=2.21954;LSEQ=CGGACACCGTCACCTCCCCG;RSEQ=AGAGGGCGGGCCCGCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:3:3,0:299,350:0.0046:2,0:1:0:28:1:0.09884:0:60:6:0.0047:0:1.3 0/1:492:5:4,1:224,263:0.0102:2,2:7.6:1:26.2:1:0.18756:4.68:60:10:0.0102:0:1.4 -20 36012799 . G A 77 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02411;SOR=9.41692;LSEQ=TCCCCGCAGAGGGCGGGCCC;RSEQ=CTGGCCGGTCAGTGCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:1:1,0:226,292:0.0019:2,0:1:0:28:0:0.43738:0:60:2:0.002:0:1 0/1:392:7:5,2:171,214:0.0179:2,2:11.4:1:27.7:1:0.25074:3.12:60:14:0.018:0:1.1 -20 36012837 . C A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25565;SOR=0;LSEQ=GGGCGGCGCGGGGTCCTCGC;RSEQ=CACCTGGGGCCACGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:3:2,1:43,112:0.019:2,2:10.7:1:30:1:0.19546:5.15:60:6:0.019:0:1 0/0:128:0:0,0:41,87:0:2,0:13.6:1:30.8:1:1:0:60:63:1:0:0.3 -20 36013017 . A G 59 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGCTTTGGGGTGGAGCA;RSEQ=GCGCAAAAGACACGGGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:10.3:1:29.8:1:1:0:60:8:1:0:2 1/1:1:1:1,0:0,0:1:0,0:22:0:34:0:1:0:34:2:1:0:4 -20 36014324 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGGATGCAGTGGACACGT;RSEQ=CACAGGCCCATCTTCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:2,0:109,0:0.018:1,0:27:1:30:0:1:0:60:4:0.0187:0:1 0/0:42:0:0,0:42,0:0:1,0:22:1:32:1:1:0:60:41:1:0:0.1 -20 36014631 . C T 101 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=3e-04;SOR=17.75275;LSEQ=TGGGTGGTGGGACTTCAAAG;RSEQ=GGGCAGGGGCTCATGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:1:0,1:97,343:0.0023:2,0:11:0:25:0:1:0:60:2:0.0023:0:1 0/1:257:10:1,9:59,188:0.0389:2,2:24.1:1:30.5:1:0.46082:2.81609:60:20:0.0395:0:1 -20 36014794 . C A 31 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02381;SOR=Inf;LSEQ=GAACTCCTCCCAATCCCTGG;RSEQ=TCTCGCTTGCTCCCTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:2,28:0:2,0:25.4:1:32.6:1:1:0:60:60:1:0:0.1 0/1:6:2:1,1:0,4:0.3333:0,2:12:0:31.5:1:0.33333:0:60:4:0.3333:0:1.5 -20 36022097 . A G 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01333;SOR=Inf;LSEQ=ATCTGATCCAGCTTTGGCAA;RSEQ=AAGGCGTCTGCGCCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:65,0:0:1,0:21.1:1:30.9:1:1:0:60:130:1:0:0 0/1:9:2:1,1:7,0:0.2222:0,2:24.5:1:31:1:0.22222:0:60:4:0.2222:0:1.5 -20 36022169 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGTGGGGACTCACGCTG;RSEQ=CCCCACCACCTCCCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:2,0:191,1:0.0103:1,0:6.5:1:31.5:1:1:0:60:4:0.0109:0:1 0/0:61:0:0,0:59,2:0:1,0:20.4:1:31.1:1:1:0:60:29.5:1:0:0.1 -20 36022539 . T C 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ACTGTGAGTGGGCAGAAGCC;RSEQ=GGACAGTCAGCACCATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:662:0:0,0:381,281:0:2,0:23.4:1:30.7:1:1:0:60:81.75:1:0:0.1 0/1:395:11:5,6:230,154:0.0278:2,2:23.2:1:29.5:1:0.36402:1.78943:60:22:0.0281:0:1.2 -20 36022763 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13457;SOR=Inf;LSEQ=TGTGGAATGAGCAGGAGTTT;RSEQ=GTTTGTGGAGTAGGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:22,293:0:2,0:23.4:1:31:1:1:0:60:34:1:0:0.1 0/1:183:2:1,1:17,164:0.0109:2,2:9.5:1:27.5:1:0.18753:9.40:60:4:0.011:0:1 -20 36024493 . G T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55521;SOR=0;LSEQ=TCCAATGTCAGGCAGGCACA;RSEQ=AACGGTGTCCAGAGCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:258,31:0.0103:2,2:24.3:1:22.7:1:0.29495:4.1286:60:2:0.0071:0:2.3 0/0:159:0:0,0:138,21:0:2,0:23.9:1:31.7:1:1:0:60:78.5:1:0:0.1 -20 36024741 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01575;SOR=Inf;LSEQ=CAGCCTCGGAGGGCGGAGGG;RSEQ=GGGCGGGCAAAGCCTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:566:0:0,0:119,446:0:2,0:22.5:1:29.8:1:1:0:60:50.364:1:0:0.1 0/1:312:4:2,2:79,229:0.0128:2,2:16.5:1:23.8:1:0.27743:2.89:60:3:0.0096:0:2.5 -20 36024820 . T C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.00627;SOR=Inf;LSEQ=GGGACTTCTGTTATCCTGCT;RSEQ=CTCTCCCCACTTCCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:1,156:0:1,0:24.1:1:29.8:1:1:0:60:30.4:1:0:0.2 0/1:63:4:0,4:3,56:0.0635:2,0:21.3:1:32:1:1:0:60:8:0.0656:0:1 -20 36025230 . A G 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACCCACCTGGGCATCCG;RSEQ=AGCTGACTGCAGTGTCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:29:1:33:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 36025965 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05793;SOR=Inf;LSEQ=GGCTGTGTGCACACAGATGT;RSEQ=GATGCCTGGCTTTGAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:152,1:0:1,0:24.4:1:28.2:1:1:0:60:75.5:1:0:0.1 0/1:49:2:2,0:47,0:0.0408:1,0:20.5:1:27.5:1:1:0:60:4:0.0408:0:1 -20 36026026 . G T 53 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.0184;LSEQ=CTGTGTGCATCTGGCATGTA;RSEQ=GGCGACACACACTGAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:2,2:338,49:0.0102:2,2:14.3:1:26.5:1:0.08426:6.83893:60:3:0.0079:0:2 0/1:192:2:1,1:160,30:0.0104:2,2:19.5:1:27.5:1:0.29756:5.26309:60:4:0.0106:0:1 -20 36026071 . C T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1087;SOR=4.27797;LSEQ=AGGCCCCAGGGCAGAAGACC;RSEQ=GCCTAACTGCTCCTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:838:2:0,2:544,292:0.0024:2,0:1:0:28:1:0.12281:0:60:4:0.0024:0:1 0/1:493:5:1,4:315,173:0.0101:2,2:11.2:1:27.4:1:0.05827:7.25447:60:10:0.0103:0:1 -20 36028831 . T C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04806;SOR=Inf;LSEQ=GAGCCAAATTCTCTGTTGCC;RSEQ=GGGCCGGAGTGTGGTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:0,77:0:1,0:21.7:1:30.2:1:1:0:60:76:1:0:0 0/1:45:3:0,3:4,38:0.0667:2,0:13.7:1:30.3:1:1:0:60:6:0.0667:0:1 -20 36029758 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTCCTGTTGTTGCTGAG;RSEQ=GGGACTCCGCTGTCTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:29,0:0.0645:1,0:18:1:31.5:1:1:0:60:4:0.0645:0:1 0/0:2:0:0,0:2,0:0:0,0:10.5:1:33:1:1:0:60:4:1:0:0 -20 36029901 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13792;SOR=Inf;LSEQ=TTTACGTAAAATCTGCTGTG;RSEQ=TGGTTAAAGCAAGGCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:287,27:0:2,0:23.3:1:32:1:1:0:60:43.857:1:0:0.1 0/1:186:2:1,1:157,27:0.0108:2,2:27:1:25.5:1:0.2791:5.72824:60:4:0.0109:0:1 -20 36030405 . CTT C 27 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGGCAGTGGTCAACAAGC;RSEQ=TTTTTTTTTCATTTAATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:17.5:1:27.5:1:1:2.24:60:4:0.2222:0:0 0/0:2:0:0,0:1,1:0:2,0:25:1:30:1:1:0:60:4:1:0:0 -20 36030658 . C T 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28003;SOR=0;LSEQ=GTGCCCTGTGCTCCCTACTC;RSEQ=CGCAGAGCACTGCTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:5,4:14,2:0.36:2,2:26.2:1:29.4:1:0.14245:5.16859:60:8:0.381:0:1.3 0/0:4:0:0,0:3,1:0:2,0:32:1:30.3:1:1:0:60:8:1:0:0 -20 36030939 . G C 296 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6867;SOR=0.65622;LSEQ=AACCTGGTGTGCAAAGTGGC;RSEQ=GACTTTGGGCTGGCTCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:942:939:463,476:0,1:0.9968:0,2:26.6:1:30:1:1:0:60:51.167:0.9989:0:1.2 1/1:619:616:299,317:0,0:0.9952:0,2:26:1:29.3:1:1:0:60:43:0.995:0:1.2 -20 36030995 . G A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02537;SOR=Inf;LSEQ=GTACACGGCGCGGCAAGGTG;RSEQ=GCAGGGGCTGTGTGGTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:591:0:0,0:245,346:0:2,0:24.9:1:30.9:1:1:0:60:58.1:1:0:0.6 0/1:394:4:3,1:153,237:0.0102:2,2:9.8:1:28.8:1:0.30519:4.63:60:8:0.0102:0:1.8 -20 36031055 . C T 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=GTCACGTCCCGCTCTGAGCC;RSEQ=CAGTTTTTTCCTCAGCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:217,170:0:2,0:23:1:30.9:1:1:0:60:31.25:1:0:0.7 0/1:201:8:4,4:88,105:0.0398:2,2:24.4:1:28.9:1:1:1.19:60:7:0.0357:0:2.1 -20 36031097 . A G 289 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCTCATGGTGCTTATCTA;RSEQ=CAGAGCGGTCATGACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:532:531:361,170:0,0:0.9981:0,2:24.6:1:32:1:1:0:60:47.273:0.9981:0:1.1 1/1:255:255:167,88:0,0:1:0,2:21.3:1:31.6:1:1:0:60:62.75:1:0:1.2 -20 36031843 . G A 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTGGGTGGCCCCTGTCTC;RSEQ=GGGCTTGCCCCACTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:46,291:0:2,0:22.5:1:30.4:1:1:0:60:32.7:0.997:0:0.1 0/1:176:18:3,15:25,132:0.1023:2,2:26.8:1:31.1:1:1:1.06:60:36:0.1065:0:1.2 -20 36031871 . G C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00347;SOR=Inf;LSEQ=CCCCACTCTGCCTGCCTGCT;RSEQ=TTGGTCCTCTCTCTGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:11,191:0:2,0:26:1:32.2:1:1:0:60:66.333:1:0:0.1 0/1:98:5:1,4:5,88:0.051:2,2:26.6:1:32.6:1:0.27586:4.28:60:10:0.0532:0:1.2 -20 36970823 . C A 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.22078;SOR=0;LSEQ=CAAGATCCCTGGGGGACTTG;RSEQ=CTGCACGTCTTTGTTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:15.6:1:31.4:1:1:0:60:10:0.5:0:1 0/0:4:0:0,0:3,1:0:2,0:26:1:32.5:1:1:0:60:8:1:0:0 -20 36970964 . AC A 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56514;SOR=1.28477;LSEQ=GGCCTTGACAAAAAACCTGT;RSEQ=AGACTTTGGAAAAGGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:23:21,2:73,1:0.2371:1,2:28.3:1:30:1:0.13899:6.77386:60:46:0.2371:0.0309:0.1 0/1:56:16:16,0:40,0:0.2857:1,1:26.3:1:30.5:1:1:0:60:32:0.2857:0.0179:0.1 -20 36971052 . G A 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04162;SOR=0;LSEQ=CAGAAGAAATGCTCAGTGTT;RSEQ=CTAATTGTGTCCAACAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:6:3,3:337,174:0.0116:2,2:25:1:28.5:1:0.41667:1.93419:60:12:0.0118:0:1 0/0:382:0:0,0:228,153:0:2,0:25.1:1:31.6:1:1:0:60:75.2:0.9973:0:0.3 -20 36971119 . T A 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.31688;SOR=1.16439;LSEQ=CATTGGTTCTTGGGATTTGA;RSEQ=TAAAGTGGCTATTTCTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:667:124:49,75:246,297:0.1859:2,2:27.2:1:30.6:1:0.27063:1.26733:60:123:0.1872:0:1.1 0/1:576:121:56,65:211,244:0.2101:2,2:24.5:1:29.6:1:1:1.00373:60:242:0.2115:0:1.1 -20 37606489 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17378;SOR=Inf;LSEQ=TCTTTTCCATTCTGATTTGA;RSEQ=TTTTGTGCATTTTTTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:67,47:0:2,0:28.2:1:32.5:1:1:0:59.9:228:1:0:0.2 0/1:82:2:1,1:46,34:0.0244:2,2:16:0:32:0:1:1.34787:60:4:0.0244:0:1.5 -20 37606544 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51678;SOR=0;LSEQ=GCTTTCTTTACTGGGGCTTT;RSEQ=TCTTCAGTTTCCTCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:47,41:0.0222:2,2:21:1:28:1:1:1.1446:60:4:0.0222:0:1 0/0:60:0:0,0:29,31:0:2,0:21.6:1:29.8:1:1:0:60:120:1:0:0.2 -20 37606562 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52519;SOR=0;LSEQ=TTTTCTTCAGTTTCCTCATC;RSEQ=TCAAAATCATCATCATTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:41,37:0.025:2,2:27:1:29:1:1:1.10668:60:4:0.026:0:1 0/0:49:0:0,0:24,25:0:2,0:22.9:1:28.7:1:1:0:60:15.333:1:0:0.1 -20 37606668 . A T 22 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23914;SOR=Inf;LSEQ=CAGATATACTTAAGAATTTC;RSEQ=CATCTTCTTCCTCTTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:84,44:0:2,0:24.1:1:30.3:1:1:0:60:127:1:0:0.1 0/1:123:2:1,1:80,41:0.0163:2,2:18:1:22:1:1:1.93993:60:4:0.0164:0:1 -20 37606675 . C A 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10752;SOR=Inf;LSEQ=ACTTAAGAATTTCACATCTT;RSEQ=TTCCTCTTCATCTTCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:94,56:0:2,0:22.7:1:31.9:1:1:0:59.6:149:1:0:0.1 0/1:137:3:2,1:87,46:0.0219:2,2:37:1:23.7:1:1:1.06:60:2:0.0149:0:1 -20 37606744 . G A 33 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.62488;SOR=0.36355;LSEQ=CTGTCCACTAATATGCACTG;RSEQ=CCCTGAGCCACACTTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:3:3,0:110,112:0.0133:2,0:11.7:1:21:1:0.24667:0:60:2:0.009:0:2.3 0/0:205:1:1,0:92,111:0.0049:2,0:1:0:25:0:0.45588:0:60:2:0.005:0:1 -20 37606789 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22473;SOR=Inf;LSEQ=GACCACCGGTGGTATTATTT;RSEQ=AAAGCCCCTAAGGGAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:64,83:0:2,0:23.4:1:31.6:1:1:0:60:146:1:0:0.1 0/1:133:2:1,1:58,73:0.015:2,2:9:0:33.5:1:1:1.26:60:4:0.0153:0:2 -20 37606836 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50151;SOR=0;LSEQ=GTACAGACATTTTCAAAGTT;RSEQ=CCAGTGTTACTTTAATTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:73,61:0.0147:2,2:26:1:27:1:1:1.19513:60:4:0.0149:0:1 0/0:115:0:0,0:60,55:0:2,0:25.3:1:31.7:1:1:0:56.5:37.333:1:0:0.2 -20 37606909 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20191;SOR=Inf;LSEQ=AATGTGCAATTCATCCTTTG;RSEQ=ACCAGCCCCTGAGCTGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:123,107:0:2,0:26.2:1:31.9:1:1:0:56.1:56.5:1:0:0.1 0/1:189:2:1,1:93,94:0.0106:2,2:44:0:29:1:1:1.01:60:4:0.0107:0:1 -20 37606914 . G T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25646;SOR=0;LSEQ=GCAATTCATCCTTTGCACCA;RSEQ=CCCCTGAGCTGACCGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:1,2:120,109:0.0129:2,2:21.7:1:29.3:1:0.60773:2.1946:60:6:0.0132:0:1 0/0:188:0:0,0:90,98:0:2,0:28.3:1:31.4:1:1:0:57.6:36.6:1:0:0.1 -20 37607141 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=TGCTCCAGAGAACAGCTGTG;RSEQ=AGGGCGGAATCACACCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:49,107:0:2,0:21.9:1:31.6:1:1:0:60:30.2:1:0:0.6 0/1:159:2:1,1:59,98:0.0126:2,2:37:1:28:1:1:1.66:60:4:0.0127:0:1 -20 37607146 . C T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21491;LSEQ=CAGAGAACAGCTGTGCAGGG;RSEQ=GGAATCACACCCTTTTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:136:75:23,52:15,46:0.5515:2,2:22.3:1:29.7:1:0.44993:1.35:60:150:0.5515:0:1.1 0/1:149:31:9,22:44,73:0.2081:2,2:22:1:28.6:1:0.40837:1.46963:60:30:0.2083:0:1.1 -20 37607201 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24139;SOR=Inf;LSEQ=TTTTAGTTTTTTGCTATTGA;RSEQ=TTGTTTGAGCACCTTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:0:1,0:23.4:1:30.8:1:1:0:60:19.5:1:0:0.4 0/1:43:3:0,3:0,40:0.0698:1,0:32.3:1:30.7:1:1:0:60:6:0.0714:0:1.7 -20 38290465 . C A 72 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTAGAAGTAAGATCAATA;RSEQ=AGGAGACTAGAACCCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:23.8:1:31.4:1:1:0:60:10:1:0:1.8 1/1:1:1:0,1:0,0:1:0,0:3:0:28:0:1:0:60:2:1:0:1 -20 38290480 . C T 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATACAGGAGACTAGAACC;RSEQ=GTTGGTCTCTCTTCTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:20.5:1:31.8:1:1:0:60:8:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 38820366 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50198;SOR=0;LSEQ=ATATTTCAAACTCCAAGTGC;RSEQ=GGGCTCTCTTCATTGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:9,3:0.1429:2,2:20:1:31:1:0.50549:2.73861:60:4:0.1429:0:1 0/0:9:0:0,0:7,2:0:2,0:13.6:1:31.3:1:1:0:60:18:1:0:0.2 -20 39657098 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGGACGCCGGATACCAGC;RSEQ=CTGCCCAAGATTGCTGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:29.5:1:1:0:60:4:1:0:1 -20 39657625 . C A 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCGAGCCTCCGGAGTCCC;RSEQ=GTCCGCCCGCACAGGCCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:0:0,0:390,209:0:2,0:23.7:1:30.1:1:1:0:60:65.556:0.9983:0:0.1 0/1:441:36:23,13:261,142:0.0816:2,2:21.4:1:29:1:1:1.03877:60:35:0.0799:0:1.1 -20 39657783 . G A 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02619;SOR=Inf;LSEQ=CGGCCCCGGACCCCGGCCTG;RSEQ=CCGTCCCGCGACCCCCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:93,250:0:2,0:18.2:1:32.1:1:1:0:60:84.75:1:0:0.3 0/1:322:5:4,1:111,206:0.0155:2,2:5:1:28:1:0.05667:7.38:60:10:0.0159:0:1 -20 39657894 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53694;SOR=0;LSEQ=GAGTAGATCGGCTCGCTAGG;RSEQ=CGCGAGCGAGGGCCGCGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:154,0:0.0128:1,2:21.5:1:29:1:0.01282:0:60:4:0.013:0:1 0/0:88:0:0,0:87,1:0:1,0:25.2:1:32.5:1:1:0:60:176:1:0:0.1 -20 39658170 . G A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48232;SOR=1.94833;LSEQ=CCGCGCCCTGCCGGTGCCGG;RSEQ=CAGAGGACAGACATGGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:3:3,0:133,439:0.0052:2,0:1:0:26.7:1:0.01301:0:60:6:0.0053:0:1 0/1:494:5:4,1:125,363:0.0101:2,2:5:1:25.4:1:0.01801:11.55:60:10:0.0102:0:1.2 -20 39658311 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50376;SOR=0;LSEQ=CCCTCCCAAGAGGGGACAAC;RSEQ=GAGACCCCGTGTCGTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:0,2:0,31:0.0606:1,0:18:1:32.5:1:1:0:60:4:0.0606:0:1 0/0:24:0:0,0:2,22:0:2,0:21.8:1:30.6:1:1:0:60:48:1:0:0 -20 39690342 . T C 91 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03186;SOR=18.53432;LSEQ=GATGTATAAAGCAAGTATGT;RSEQ=TAATTTTCTTTTAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:0.2:0,0:49:0:34:0:1:0:60:2:0.2:0:1 1/1:8:7:1,6:0,1:0.875:0,2:20.3:1:32.6:1:1:0:60:14:0.875:0:1 -20 39704995 . G A 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTTTTGTTTACCTTTGAAA;RSEQ=CAGATATCTTAATTGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:29:3,26:26,130:0.1568:2,2:22.3:1:29.9:1:0.57872:1.7289:60:58:0.1593:0:1 0/0:161:0:0,0:28,133:0:2,0:22.4:1:31.8:1:1:0:60:79.5:1:0:0.1 -20 39706300 . G A 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12384;SOR=6.02433;LSEQ=AAGACTTTGCTGCTGCGTGG;RSEQ=CTTCCCTTTCTCTGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:1:1,0:207,356:0.0018:2,0:1:0:26:0:0.36879:0:60:2:0.0018:0:1 0/1:566:6:4,2:218,342:0.0106:2,2:15.2:1:25.7:1:0.21693:3.13:60:12:0.0108:0:1 -20 39706331 . G A 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12523;SOR=0;LSEQ=TCTGGGTGGACAGCAGGCCA;RSEQ=CTGCCTGTGTTGTAGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:4:2,2:98,279:0.0105:2,2:11:1:28.3:1:0.28244:2.84:60:8:0.0107:0:1 0/0:351:0:0,0:111,239:0:2,0:23.8:1:31.6:1:1:0:60:49:1:0:0.1 -20 39708708 . AT A 96 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01892;SOR=4.41756;LSEQ=TTCTAGCACTCTGACCAGCA;RSEQ=TTTTTTTCTCTTTAGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:612:3:3,0:365,244:0.0049:2,0:17:1:32:1:0.27961:0:60:6:0.0049:0.0016:0 0/1:422:9:5,4:261,152:0.0213:2,2:28.7:1:30.3:1:0.73123:1.37258:60:18:0.0214:0:0.1 -20 39708889 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19547;SOR=Inf;LSEQ=TTAAAGAATAAATGTGATGT;RSEQ=TTTCTTTATAATACATATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:10,137:0:2,0:23.7:1:32.3:1:1:0:60:294:1:0:0 0/1:117:2:1,1:14,101:0.0171:2,2:6:1:26.5:1:0.24094:7.00:60:4:0.0171:0:1 -20 39712830 . TAA T 29 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCAAACTCCTTTGAGGT;RSEQ=AAAAAAAAAAGTTTCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:27:1:29.5:1:1:0:60:4:0.25:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 39713352 . A C 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=TAGAGTAACTTTCTGAAGTA;RSEQ=GTTTTCCAACTTCTAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:0,27:0:1,0:25.2:1:31.2:1:1:0:60:26:1:0:0 1/0:11:6:1,5:0,5:0.5455:0,2:20.7:1:30.5:1:1:0:60:12:0.5455:0:1 -20 39721040 . G T 41 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04075;SOR=Inf;LSEQ=GTTGAGCGGATAATTATTTG;RSEQ=CATTTAATCAGTGATGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:282,42:0:2,0:23.5:1:31.2:1:1:0:60:53:1:0:0 0/1:171:3:1,2:138,30:0.0175:2,2:14.7:1:26:1:0.09026:9.02315:60:6:0.018:0:1 -20 39721346 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTATTTCATTTTGTTTT;RSEQ=TTGCCATGCAATTTTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:1,92:0.0211:1,2:37:1:30.5:1:0.04188:65.40:60:4:0.0213:0:1 0/0:46:0:0,0:0,46:0:1,0:22:1:30.5:1:1:0:60:92:1:0:0.1 -20 39721373 . A G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57003;SOR=0.6488;LSEQ=TGCAATTTTGAGGAAGGGGC;RSEQ=TCAGGTGTTAACTCTTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:15:1,14:1,45:0.2459:1,1:28.8:1:33:1:0.43443:3.14:60:30:0.2542:0:1 0/1:23:4:0,4:0,19:0.1739:1,0:26:1:32.8:1:1:0:60:8:0.1739:0:1 -20 39725802 . A G 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAATTCGCTAGCCCTGGGT;RSEQ=TTTATGCTTAGAACATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:273,81:0:2,0:21.7:1:28.8:1:1:0:60:708:1:0:0.1 0/1:215:16:13,3:145,53:0.0744:2,2:22:1:31.2:1:0.57033:1.58:60:32:0.0755:0:1.1 -20 39725993 . C A 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02988;SOR=Inf;LSEQ=TGGAGAAAGGTACTGTAGCC;RSEQ=ATGTGTTAATATCCTAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:145,318:0:2,0:24.7:1:31.3:1:1:0:60:37.583:1:0:0.1 0/1:331:4:2,2:104,223:0.0121:2,2:6.3:1:27:1:0.59571:2.14:60:8:0.0122:0:1 -20 39726776 . T C 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.19299;LSEQ=CTGAAAAAATGGTGCTTGGG;RSEQ=GTATTTGCAAAGAAACCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:40:36,4:105,14:0.2516:2,2:20.8:1:30.8:1:1:1.20:60:39:0.2516:0:1 0/1:99:6:5,1:85,7:0.0606:2,2:22.3:1:31.8:1:0.40851:2.39852:60:12:0.0612:0:1.2 -20 39728677 . C T 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03756;SOR=Inf;LSEQ=ATCTGAATCTATTTTGAGTA;RSEQ=TTTCTTGCTGTCTTCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:276,129:0:2,0:23:1:31.9:1:1:0:60:100.25:1:0:0.1 0/1:320:4:1,3:212,104:0.0125:2,2:18:1:25.3:1:0.11064:6.07896:60:3:0.0096:0:1.5 -20 39729777 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15602;SOR=Inf;LSEQ=TTATGCTCAGCAGATAGGTC;RSEQ=ACTTGGGGTCATGAAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:234,43:0:2,0:23.4:1:31:1:1:0:60:45.167:1:0:0.1 0/1:182:2:1,1:144,36:0.011:2,2:27.5:1:29:1:0.36616:3.95925:60:4:0.0111:0:1.5 -20 39730165 . AT A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCTTCCTACAGTGCCTCC;RSEQ=TTTTTTGGTCACATTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:0,48:0.04:1,0:23.5:1:31:0:1:0:60:4:0.0417:0:0 0/0:17:0:0,0:0,17:0:1,0:20.8:1:29.3:1:1:0:60:34:1:0:0.1 -20 39741340 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53482;SOR=0;LSEQ=AGCTGGGATTATAGGCTTGC;RSEQ=CCACCTTGCCTGGCTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:2,0:131,5:0.0145:1,0:17:1:29.5:1:1:0:60:4:0.0148:0:1 0/0:79:0:0,0:74,5:0:2,0:22.6:1:29.6:1:1:0:60:38.5:1:0:0.1 -20 39741348 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.534;SOR=0;LSEQ=TTATAGGCTTGCGCCACCTT;RSEQ=CCTGGCTATATTCAAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:150,9:0.0124:2,0:14.5:1:30.5:1:1:0:60:4:0.0126:0:1 0/0:93:0:0,0:83,10:0:2,0:22.9:1:31.7:1:1:0:60:92:1:0:0.1 -20 39741622 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53599;SOR=0;LSEQ=AGCTTAACAAAGGGAGTTTC;RSEQ=GCTCTGCCCCAGGCCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:25,166:0.0104:2,2:8:1:29:1:0.25189:6.53:60:4:0.0105:0:1 0/0:110:0:0,0:12,98:0:2,0:24.9:1:30.1:1:1:0:60:109:1:0:0.1 -20 39742944 . T C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01792;SOR=3.39053;LSEQ=CATGCCTGTAGACCCAGCTA;RSEQ=TCAGAAGGCTGAGACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:36:0,36:0,54:0.4:1,1:26.3:1:32.3:1:1:0:60:35:0.3977:0:1.3 1/0:23:16:0,16:0,7:0.6957:0,1:20.6:1:31.4:1:1:0:60:15:0.6818:0:1 -20 39743905 . G A 139 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00012;SOR=0;LSEQ=TCTCGGTGACGGATGTATGC;RSEQ=TGTTCCTTGTGCCTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:24:22,2:153,8:0.1297:1,2:22.3:1:30.4:1:0.62107:1.73244:60:48:0.1311:0:1.2 0/0:82:0:0,0:78,4:0:1,0:25.1:1:29.9:1:1:0:60:81:1:0:0.4 -20 39743916 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11848;SOR=Inf;LSEQ=GATGTATGCGTGTTCCTTGT;RSEQ=CCTTTTTCTTTGCAAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:184,17:0:2,0:25.8:1:32.4:1:1:0:60:200:1:0:0.3 0/1:106:2:1,1:94,9:0.0189:2,2:7.5:1:25.5:1:0.18223:9.96106:60:4:0.0196:0:1 -20 39743921 . T G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGCGTGTTCCTTGTGCCTT;RSEQ=TTCTTTGCAAGTTTCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:193,21:0:2,0:25.8:1:30.7:1:1:0:60:428:1:0:0.2 0/1:126:27:21,6:89,10:0.2143:2,2:20.7:1:31.2:1:0.10842:2.52036:60:54:0.2195:0:1.1 -20 39744650 . A G 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4697;SOR=Inf;LSEQ=TGAGCCCGGGAGGTGGAGGC;RSEQ=GCAGTGAACCGAGATTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:16.6:1:31:1:1:0:60:10:0.5:0:1.4 1/1:2:2:2,0:0,0:1:0,0:44.5:1:28.5:1:1:0:60:4:1:0:1 -20 39744789 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTCTTTTCCTCTTTCC;RSEQ=TAACTTCCCACTTGTAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:2,0:121,0:0.0163:1,0:35.5:1:30:1:1:0:60:4:0.0163:0:2.5 0/0:56:0:0,0:56,0:0:1,0:18:0:16:0:1:0:60:0:0:0:4 -20 39744810 . C A 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31985;SOR=0;LSEQ=TAACTTCCCACTTGTAGGGC;RSEQ=ATAAACTTGACAAGATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:185:185:182,3:0,0:1:0,1:23:1:30.4:1:1:0:60:184:1:0:1.1 1/1:87:86:84,2:0,0:0.9885:0,1:25.5:1:30.1:1:1:0:60:172:1:0:1.1 -20 39745104 . C G 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00512;SOR=Inf;LSEQ=TGACCTTGCTTATCTAAGGC;RSEQ=TAGAGTCAGTTCTACTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:24,295:0:2,0:23.7:1:32.2:1:1:0:60:78.75:0.9968:0:0.1 0/1:173:5:0,5:20,148:0.0289:2,0:30.4:1:32:1:1:0:60:10:0.0292:0:1.2 -20 39746588 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05645;SOR=Inf;LSEQ=GAGTTCCTCTTGTGATAGGA;RSEQ=TTTACCCAGGCCAAGCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:0:1,0:26.5:1:30.6:1:1:0:60:48:1:0:0 0/1:8:2:1,1:5,1:0.25:2,2:24:1:27.5:1:0.46429:3.87298:60:4:0.25:0:1 -20 39750210 . G GT 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.23927;SOR=4.37272;LSEQ=GCCTTCATGAAGCCACCCTT;RSEQ=TTTTTTTTTATCTGACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:1:1,0:79,3:0.012:1,0:41:0:28:0:1:0:60:2:0.0122:0:0 0/1:39:2:2,0:37,0:0.0513:1,0:13.5:1:30.1:1:1:0:60:4:0.0513:0.0256:0 -20 39750978 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGTCTGTAAATGCATTG;RSEQ=AACATTCTGGTTGCTCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:0,39:0.0488:1,2:24:1:27.5:1:0.04878:0:60:4:0.0488:0:1 0/0:8:0:0,0:0,8:0:0,0:25.9:1:34:0:1:0:60:16:1:0:0 -20 39751809 . C T 172 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0.02777;LSEQ=TTGCTGAGTCACCCTAATCC;RSEQ=CCCCTTATTTCTCCTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:971:52:32,20:546,373:0.0536:2,2:25.6:1:30.3:1:0.8847:1.09:60:104:0.054:0:1.1 0/0:638:1:0,1:386,251:0.0016:2,0:1:0:23:0:0.39498:0:60:2:0.0016:0:1 -20 39763263 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCAGCCCCCGTCTGCC;RSEQ=TCCTGGTCTCATCACTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:1,13:0.125:1,2:29:1:31.5:1:0.24167:9.54:60:4:0.125:0:1 0/0:6:0:0,0:0,6:0:0,0:28.8:1:30:1:1:0:60:12:1:0:0.2 -20 39792593 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16663;SOR=Inf;LSEQ=GGACCAGTTCTCCAGTGAGT;RSEQ=CTCCTTGGAAGCCTATGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:86,51:0:2,0:26.6:1:30.4:1:1:0:60:26.4:1:0:0.2 0/1:95:2:1,1:55,38:0.0211:2,2:5:1:27:1:1:1.44159:60:4:0.0215:0:1 -20 39792604 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17834;SOR=Inf;LSEQ=CCAGTGAGTCCTCCTTGGAA;RSEQ=CCTATGCTCGCTGCCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:96,62:0:2,0:27.8:1:31.9:1:1:0:60:51.667:1:0:0.1 0/1:116:2:1,1:66,48:0.0172:2,2:7.5:1:27.5:1:1:1.37115:60:4:0.0174:0:1.5 -20 39792622 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16834;SOR=Inf;LSEQ=AAGCCTATGCTCGCTGCCTG;RSEQ=GGATGGGCTGTCGCTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:110,79:0:2,0:27.2:1:31.4:1:1:0:60:378:1:0:0.2 0/1:132:2:1,1:72,58:0.0152:2,2:25.5:1:31:0:1:1.23933:60:4:0.0157:0:1 -20 39792643 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15343;SOR=Inf;LSEQ=GGATGGGCTGTCGCTGCATT;RSEQ=AGTGTGCGTGGGGTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:100,98:0:2,0:25.6:1:31.4:1:1:0:60:32:1:0:0.2 0/1:128:2:1,1:61,65:0.0156:2,2:42.5:1:30:1:1:1.07:60:4:0.0157:0:1 -20 39792671 . A G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29259;SOR=0;LSEQ=GTGGGGTCCAGGGCTGGGGG;RSEQ=GGGAAGATGGGAGGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:1,2:73,81:0.0191:2,2:27.3:1:31:1:1:1.79599:60:6:0.0199:0:1 0/0:95:0:0,0:42,53:0:2,0:22.7:1:28.8:1:1:0:60:22.75:1:0:0.1 -20 39794101 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTTCCAGGAATGGTATCC;RSEQ=CACTACTTTGTTCTGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:13:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 39924558 . C T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01896;SOR=Inf;LSEQ=AGTGTAAGAATTTGTACATT;RSEQ=GCAAGAAATGAAATAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:0:0,0:304,190:0:2,0:27.7:1:30.3:1:1:0:59.9:40.167:0.9979:0:0.2 0/1:411:5:1,4:238,168:0.0122:2,2:8.2:1:25:1:0.16596:5.64501:60:4:0.0099:0:1.4 -20 39924613 . T G 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTTTGATCTTCTCGTTCAGT;RSEQ=GGTTGTCCTTTATAATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:0:0,0:275,346:0:2,0:25.3:1:30:1:1:0:60:50.75:1:0:0.1 0/1:558:15:6,9:258,285:0.0269:2,2:31.5:1:30.8:1:0.61037:1.35716:60:30:0.027:0:1.9 -20 39924630 . G T 217 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=276.85206;LSEQ=AGTTGGTTGTCCTTTATAAT;RSEQ=CTATTTAAGTTCATAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:534:1:1,0:235,298:0.0019:2,0:34:0:13:0:0.44195:0:60:0:0:0:4 0/1:505:173:76,97:151,180:0.3426:2,2:25.2:1:29.3:1:0.77738:1.07052:60:85.5:0.3413:0:1.2 -20 39925035 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATACTACCTGTCACCAC;RSEQ=GGGATCACCAGGACTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40709305 . G A 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57299;SOR=0;LSEQ=TGGCTGGTTAGGTTGAAAAG;RSEQ=AAGCCTGGGCCTTTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:5,0:40,0:0.1111:1,0:22.4:1:29.2:1:1:0:60:10:0.1163:0:1 0/0:12:0:0,0:12,0:0:0,0:23.9:1:31.3:1:1:0:60:24:1:0:0.1 -20 40709990 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACGTTAATATGGCCTCA;RSEQ=TTTGACTAAGACCACTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:45:1:30.5:1:0.33333:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40710055 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCTCCTCGTGCATGGTGC;RSEQ=GTGGTCCACCATGGTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:21.3:1:31.3:1:1:1.73:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40710486 . C T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1631;SOR=0;LSEQ=AGGTCAAGGGAACTAGTCAG;RSEQ=CCTGGCTGTTGGAGAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:5:2,3:335,146:0.0103:2,2:11.6:1:24.6:1:0.17081:3.43182:60:4:0.0084:0:1 0/0:293:0:0,0:192,101:0:2,0:25.2:1:31.1:1:1:0:60:57.6:1:0:0.1 -20 40710711 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1321;SOR=Inf;LSEQ=TAGGTCCCTTCCAGGCACCT;RSEQ=ATGATTCTAAAGCTACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:14,148:0:2,0:20.9:1:30.9:1:1:0:60:39.5:1:0:0.1 0/1:93:2:1,1:12,79:0.0215:2,2:26:1:27.5:1:0.26134:6.36:60:4:0.0215:0:1 -20 40713251 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33946;SOR=3.03613;LSEQ=CCTAGGACTGGGGTATGTGG;RSEQ=CAGCAGCATCTGCAAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:2:0,2:413,107:0.0038:2,0:4:1:28.5:1:0.04329:0:60:4:0.0039:0:1 0/1:260:3:1,2:189,68:0.0115:2,2:19.7:1:27:1:0.17737:5.51497:60:6:0.0116:0:1 -20 40713469 . C T 131 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=16.88394;LSEQ=ACTGGAGGTGCTGGACTATA;RSEQ=GATAACCATCCTGTGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:936:2:0,2:360,573:0.0021:2,0:17:1:22.5:1:0.52593:0:50:1:0.0011:0:4 0/1:601:21:8,13:249,330:0.0349:2,2:30:1:30:1:0.8231:1.22573:60:20:0.0341:0:1.1 -20 40713532 . G A 129 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.55048;LSEQ=GTTCTGCTGGGGATGCTTGC;RSEQ=TACATGCACCTTGCAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:2:2,0:107,329:0.0046:2,0:1:0:26:1:0.0615:0:60:4:0.0046:0:1 0/1:281:21:8,13:81,177:0.0747:2,2:19.3:1:29.4:1:0.62685:1.34:60:42:0.0769:0:1.2 -20 40713538 . G A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30465;SOR=4.73638;LSEQ=CTGGGGATGCTTGCGTACAT;RSEQ=CACCTTGCAGATACCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:1:0,1:83,300:0.0026:2,0:47:0:12:0:1:0:60:0:0:0:8 0/1:245:3:1,2:76,166:0.0122:2,2:25.7:1:30:1:1:1.09:60:6:0.0123:0:1.3 -20 40713997 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCCTCATGGAAGTAAGTA;RSEQ=TCACTTTTCATCTAGGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:37:1:31.5:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40714006 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGTAAGTAATCACTTTT;RSEQ=ATCTAGGTGTTGGCAGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:28:1:29:1:1:0:60:4:0.3333:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40714097 . G C 71 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAGACACAGTGGGGAA;RSEQ=AGCTAATGTCTAAGAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:6,0:0.4545:0,2:23:1:30.6:1:0.45455:0:60:10:0.4545:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40714218 . G A 79 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18296;SOR=0;LSEQ=TCATTGCTGAGTCTGGAGCC;RSEQ=GAATCAGCACAGGCATCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:6:6,0:73,1:0.075:1,0:31.2:1:30.7:1:1:0:60:12:0.0779:0:1 0/0:31:0:0,0:30,1:0:1,0:19.8:1:29.4:1:1:0:60:30:1:0:0.1 -20 40714305 . T C 189 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGGCTCAGCGGGATCCTCTC;RSEQ=CGGCAGCCTCCATCTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:66:56,10:254,62:0.1728:2,2:25:1:31.4:1:0.48988:1.37:60:132:0.1769:0:2.1 0/0:205:0:0,0:149,56:0:2,0:23.6:1:30:1:1:0:60:40:1:0:0.1 -20 40714307 . G A 208 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCAGCGGGATCCTCTCTC;RSEQ=GCAGCCTCCATCTGTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:121:97,24:220,64:0.298:2,2:25.3:1:30.2:1:0.59987:1.18:60:59.5:0.3013:0:1.7 0/0:224:0:0,0:159,65:0:2,0:22.6:1:29.5:1:1:0:60:55:1:0:0.1 -20 40714479 . G A 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=1.55124;LSEQ=CCGGAGGTCTTCTCAGGCCA;RSEQ=TACTGCATACAGAACTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:782:230:86,144:223,329:0.2941:2,2:24.8:1:30:1:0.47022:1.13476:60:37.333:0.2898:0:1.8 0/1:438:172:65,107:108,158:0.3927:2,2:26.1:1:29.6:1:0.61693:1.12492:60:85:0.3917:0:1.6 -20 40714524 . C G 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1187;SOR=0.77322;LSEQ=GAAAGAGGTCACAGAAGGAG;RSEQ=TCAAAGGCAGGGGGCGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:442:267:44,223:31,142:0.6041:2,2:26.3:1:31.7:1:0.69891:1.10618:60:88:0.6097:0:2.1 1/0:231:125:29,96:29,76:0.5411:2,2:23.4:1:30:1:0.45063:1.26186:60:30.25:0.545:0:2.2 -20 40714539 . C T 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07937;SOR=1.43231;LSEQ=AGGAGCTCAAAGGCAGGGGG;RSEQ=GGGTATCAAAGTCTCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:94:8,86:27,229:0.2655:2,2:26.3:1:30.3:1:0.68954:1.26661:60:93:0.2711:0:2.7 0/1:167:57:9,48:17,93:0.3413:2,2:25.4:1:28.9:1:1:1.03:60:27.5:0.3416:0:2.8 -20 40714540 . G C 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00032;SOR=0.43536;LSEQ=GGAGCTCAAAGGCAGGGGGC;RSEQ=GGTATCAAAGTCTCATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:116:10,106:26,207:0.3324:2,2:26.3:1:29.8:1:0.57608:1.33034:60:115:0.3343:0:2 0/1:163:29:4,25:20,114:0.1779:2,2:25.1:1:29.1:1:1:1.09588:60:28:0.1761:0:2 -20 40714592 . CT C 94 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.73408;SOR=1.37377;LSEQ=TCTTTTCTTTTTTTCTTTTT;RSEQ=TTTTTTTTTTTGAGATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:7:0,7:1,105:0.0619:1,0:24.4:1:33.6:1:1:0:60:14:0.0654:0:1 0/1:48:4:0,4:2,42:0.0833:1,0:32.3:1:32.8:1:1:0:60:8:0.0909:0:1.5 -20 40726827 . C T 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06118;SOR=Inf;LSEQ=CAACAGAGTCTGGTCCCGGG;RSEQ=GGGGAGTTGGACAAAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:15,0:13,1:0.5172:1,1:18.7:1:27.4:1:0.48276:0:60:6.5:0.4815:0:1.5 1/1:6:6:6,0:0,0:1:0,0:34:1:27.2:1:1:0:60:5:1:0:1 -20 40727000 . C T 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGGCTGTCAAGGGATCTC;RSEQ=CTCCAGGTTTAGAGCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:409,119:0:2,0:24.3:1:30.5:1:1:0:60:36.714:1:0:0.1 0/1:227:28:22,6:148,51:0.1233:2,2:21.9:1:30.7:1:0.81652:1.26:60:56:0.1239:0:1.1 -20 40727005 . A T 32 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03065;SOR=Inf;LSEQ=CTGTCAAGGGATCTCCCTCC;RSEQ=GGTTTAGAGCATGGCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:562:0:0,0:423,139:0:2,0:24.8:1:29.9:1:1:0:60:42.231:1:0:0.1 0/1:257:3:0,3:188,66:0.0117:2,0:5.7:1:20.7:1:0.01874:0:60:2:0.0079:0:1 -20 40727345 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATCTCTCCACGCCCTGGC;RSEQ=GCAAAGGGGACCTTCTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:0,2:0,52:0.037:1,0:26:1:31.5:1:1:0:60:4:0.037:0:1 0/0:12:0:0,0:1,11:0:2,0:21.3:1:30.8:1:1:0:60:24:1:0:0 -20 40730515 . C T 77 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGACTTGCCATGGTGACA;RSEQ=GGGAGCCACCTTACGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:0.5455:0,0:28.8:1:30:1:1:0:60:12:0.5455:0:1 0/0:1:0:0,0:1,0:0:0,0:2:0:30:0:1:0:60:2:1:0:1 -20 40730976 . T A 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=AATAGATAGGCCCTGCTCAT;RSEQ=TGGCTGCCCCTGAGCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:47,228:0:2,0:25.1:1:29.9:1:1:0:60:38.286:1:0:0.1 0/1:145:8:3,5:28,109:0.0552:2,2:12.6:1:28.1:1:0.3682:2.32:60:16:0.0567:0:1 -20 40731628 . T C 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCTCTACTTCAGATCAATAA;RSEQ=GGCTATTTGTTTTAGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:37:0:14:0:1:0:60:0:0:0:1 1/1:2:2:1,1:0,0:1:0,2:16.5:1:28.5:1:1:0:60:4:1:0:1 -20 40732807 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGAACGGGATTAGTGCTC;RSEQ=TATAAGAAGAAACATGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:30.5:1:31:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40733082 . C T 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2737;SOR=0.66572;LSEQ=GATTTACTGGAAGCTTGATG;RSEQ=TGGGCTTCTCAGCCTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:119:78:76,2:41,0:0.6555:1,1:26.7:1:30.4:1:0.54451:0:60:156:0.661:0:1.1 1/0:43:24:24,0:19,0:0.5581:1,1:28.1:1:30.2:1:1:0:60:23:0.575:0:1 -20 40733136 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10553;SOR=Inf;LSEQ=AGTGTCTGTCATTTAAACCA;RSEQ=CCAATCTATGGAAATTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:294,104:0:2,0:21.5:1:31.6:1:1:0:60:98.5:1:0:0.2 0/1:192:2:1,1:145,45:0.0104:2,2:40:1:30.5:1:0.42272:3.19797:60:4:0.0105:0:1 -20 40733340 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06864;SOR=6.72323;LSEQ=CGCTTCCAGGATGGCATCGT;RSEQ=CACAAACACATATTGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:1:0,1:207,331:0.0019:2,0:20:0:26:0:1:0:60:2:0.0019:0:1 0/1:324:4:2,2:129,190:0.0123:2,2:9:1:28.5:1:1:1.47:60:8:0.0125:0:1 -20 40733361 . G A 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04909;SOR=Inf;LSEQ=CACAAACACATATTGCTCCT;RSEQ=CAAAGTCAGAAGAGAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:147,310:0:2,0:26.1:1:31.7:1:1:0:60:44.7:1:0:0.1 0/1:265:3:2,1:104,158:0.0113:2,2:13.7:1:26.7:1:0.56581:3.03:60:6:0.0114:0:1 -20 40733362 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14183;SOR=5.22892;LSEQ=ACAAACACATATTGCTCCTG;RSEQ=AAAGTCAGAAGAGAGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:1:1,0:142,307:0.0022:2,0:1:0:27:0:0.31778:0:60:2:0.0023:0:1 0/1:260:3:2,1:100,155:0.0115:2,2:11.3:1:27:1:0.5641:3.09:60:6:0.0117:0:1 -20 40733421 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13043;SOR=Inf;LSEQ=AGTGGCCTGGGAATTAGCTG;RSEQ=CCACATTTAGTGTTGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:23,153:0:2,0:23.9:1:29.6:1:1:0:60:34.2:1:0:0 0/1:100:2:1,1:20,78:0.02:2,2:24.5:1:28.5:1:0.37758:3.83:60:4:0.0208:0:1.5 -20 40733646 . G T 28 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTTGGTGTCCAGCCCAT;RSEQ=TCCCCTCAGCTTTCACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:30.5:1:28:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40738925 . C T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12783;SOR=5.56395;LSEQ=TGGTCTCGAACTCCTGACCT;RSEQ=GTGATCTGCCCGCCTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:1:1,0:328,96:0.0024:2,0:20:0:14:0:1:0:60:0:0:0:1 0/1:231:3:2,1:172,56:0.013:2,2:20.7:1:29.3:1:0.57445:1.53258:60:6:0.013:0:1.3 -20 40738926 . G A 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTCTCGAACTCCTGACCTC;RSEQ=TGATCTGCCCGCCTCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:53:41,12:297,90:0.1199:2,2:23.3:1:29.9:1:1:1.04:60:52:0.1201:0:1.1 0/0:241:0:0,0:179,61:0:2,0:23.6:1:29.8:1:1:0:60:119:0.9958:0:0.1 -20 40739158 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30509;SOR=4.70012;LSEQ=AACGGGCCTCTGTTCTTCCA;RSEQ=CTGCTGCCCTCGCATACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:1:1,0:108,294:0.0025:2,0:1:0:28:0:0.27047:0:60:2:0.0025:0:1 0/1:259:3:2,1:79,177:0.0116:2,2:5.7:1:27:1:0.2313:4.45:60:6:0.0119:0:1.3 -20 40739205 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAACACGTGGAGCCATAGCT;RSEQ=CTGCACTGAGGAACCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:18,164:0.0109:2,2:25.5:1:26:1:0.19636:8.90:60:4:0.0111:0:1 0/0:85:0:0,0:13,72:0:2,0:22.3:1:31.8:1:1:0:60:41.5:1:0:0.2 -20 40739243 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06708;SOR=Inf;LSEQ=CCGCAGGGACAGGGCCCTCA;RSEQ=AGTGTTTGTTAATAGGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:1,112:0:1,0:23.5:1:32:1:1:0:60:36.667:1:0:0.1 0/1:40:2:1,1:0,38:0.05:1,2:39.5:1:29.5:1:0.05:0:60:4:0.0513:0:1 -20 40739367 . T C 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TCTCAGAGTCTTGAGTGTGC;RSEQ=CATACACACTCTGAATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:13:1:29.5:1:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:0,1:0:0,0:50:0:28:0:1:0:60:2:0.5:0:0 -20 40739420 . T TTTTG 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCACCCTAGGAGACCTTC;RSEQ=TTTGTTTGCCTAGGGGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:38:0:31.9:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40743756 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11384;SOR=Inf;LSEQ=GGGGCTGGACGTAGAGCAGA;RSEQ=CCTCAGTTACCACATGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:197,20:0:2,0:22.6:1:31.7:1:1:0:60:42.4:1:0:0.3 0/1:111:2:2,0:104,5:0.018:1,0:23:1:32:0:1:0:60:4:0.0187:0:2 -20 40743829 . A G 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00072;SOR=1.47949;LSEQ=CCGGCTGCCCACAGCCTCCA;RSEQ=GAAGCTTACCTTCTGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:735:394:256,138:206,135:0.5361:2,2:24.5:1:31.6:1:0.22082:1.22:60:130.333:0.5364:0:1.1 1/0:542:342:223,119:118,81:0.631:2,2:23.5:1:30.9:1:0.19599:1.29:60:56:0.6316:0:1.2 -20 40744209 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGCAAAGCTCCTTGTAA;RSEQ=TTTCCAATGCATTATCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:7.5:1:28.5:1:1:0:60:4:0.2222:0:1 0/0:2:0:0,0:0,2:0:0,0:19:1:32.5:1:1:0:60:4:1:0:1 -20 40746918 . C T 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00068;SOR=0;LSEQ=AATAGGAGTGATGACACCTC;RSEQ=CTTGTAGGTTGCCGTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:25:25,0:93,2:0.2066:1,1:27.1:1:30.6:1:1:0:60:11.5:0.2035:0:1.2 0/0:41:0:0,0:41,0:0:1,0:20.8:1:30.2:1:1:0:60:40:1:0:0 -20 40747209 . C T 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGCTGAGAAGGTTTGTCCC;RSEQ=CCGGTTGGTCAAGTCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:43,244:0:2,0:23.9:1:30.7:1:1:0:60:34.875:1:0:0.1 0/1:173:12:1,11:36,125:0.0694:2,2:23.8:1:29.3:1:0.4652:3.15284:60:24:0.0714:0:1 -20 40747211 . C T 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GCTGAGAAGGTTTGTCCCCC;RSEQ=GGTTGGTCAAGTCTCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:41,232:0:2,0:24.1:1:29.7:1:1:0:60:67.25:1:0:0.1 0/1:168:11:3,8:32,125:0.0655:2,2:16.6:1:30:1:0.6999:1.46:60:22:0.0671:0:1 -20 40748532 . C A 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGCCCTTTCCCCTGGGACC;RSEQ=CTGAAGCCTCTCTGAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:27:20,7:368,185:0.0465:2,2:19:1:29.6:1:0.53145:1.44:60:54:0.0469:0:1.1 0/0:369:0:0,0:240,129:0:2,0:23.6:1:30:1:1:0:60:91.25:1:0:0.1 -20 40748802 . C A 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31714;SOR=0;LSEQ=GTGTAGTAAGTCACTAAATG;RSEQ=TAGCTATTTTTATAGTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:5:0,5:0,57:0.0806:1,0:25.6:1:31.8:1:1:0:60:10:0.0806:0:1 0/0:23:0:0,0:0,23:0:1,0:22:1:32:1:1:0:60:22:1:0:0.1 -20 40750184 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTCCGGAACTCAGCTGC;RSEQ=TGGGTTTGAACGCTGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:16:0:32.5:1:1:1:60:4:0.5:0:1.5 -20 40756792 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTGCTATTCTCTCTAAC;RSEQ=AGAGGCCCCTCTCCCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:5:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40757307 . C T 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=39.10074;LSEQ=CCAGACTGCTCTGGAAGGGC;RSEQ=ACCTTCTGGAGGAGAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:907:1:0,1:612,293:0.0011:2,0:1:0:24:0:0.3245:0:60:2:0.0011:0:1 0/1:555:23:17,6:354,177:0.0414:2,2:22.6:1:30.3:1:0.65117:1.42:60:46:0.0423:0:1.2 -20 40770705 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09473;SOR=Inf;LSEQ=AGCTTTATGGAAGTGGAGAT;RSEQ=AACCAACAGGGCAAAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:55,252:0:2,0:23.9:1:31.3:1:1:0:60:60.4:1:0:0.1 0/1:137:2:1,1:26,109:0.0146:2,2:19.5:1:29:1:0.35648:4.13:60:4:0.0149:0:1 -20 40790143 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02813;SOR=Inf;LSEQ=GGTAGGGATGAGTCTGGATC;RSEQ=TGAGGGTGGGCTGGGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:0:0,0:175,375:0:2,0:26.2:1:31.2:1:1:0:60:182.333:1:0:0.1 0/1:383:4:1,3:137,241:0.0104:2,2:20.5:1:25.3:1:1:1.70322:60:3:0.008:0:1 -20 40790182 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14181;SOR=Inf;LSEQ=GCTCCCCGCGGCTGCCATCT;RSEQ=CTTCGAAAAGAAGGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:61,261:0:2,0:23:1:32.2:1:1:0:60:106.333:1:0:0.1 0/1:195:2:1,1:47,146:0.0103:2,2:21:1:27:1:0.43267:3.08:60:4:0.0105:0:1 -20 40790219 . T C 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54097;SOR=0;LSEQ=GCAGAACAGATCATCACCTA;RSEQ=AGAAGCTTTGCCCTTTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:23,134:0.0126:2,2:33:0:31.5:1:0.27991:5.72:60:4:0.0129:0:1 0/0:87:0:0,0:16,71:0:2,0:20.8:1:28:1:1:0:60:42.5:1:0:0.1 -20 40790248 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCTTTGTCCTCCCTGTC;RSEQ=CCCCCAGCTTGGCCTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:11,86:0.0202:2,2:19.5:1:29:1:0.22882:7.53:60:4:0.0208:0:1.5 0/0:36:0:0,0:3,33:0:2,0:22.9:1:28.7:1:1:0:60:35:1:0:0.1 -20 40827713 . A T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00925;SOR=0.24584;LSEQ=TTCCTTTTCATCTTAGGATG;RSEQ=ACTGCCCCAAGTCTTTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:36:36,0:68,0:0.3462:1,1:20:1:30.8:1:1:0:60:72:0.3529:0:1.2 0/1:35:4:4,0:30,1:0.1143:1,0:24.8:1:31:1:1:0:60:8:0.1143:0:1 -20 40827934 . C T 179 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=90.33201;LSEQ=GCCTTCATCATTGCGGCTGG;RSEQ=GCTGAGCTTGGTGGTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1312:1:0,1:644,667:8e-04:2,0:1:0:31:0:1:0:60:2:8e-04:0:1 0/1:1007:65:27,38:447,495:0.0645:2,2:24.7:1:29.8:1:0.37144:1.27063:60:130:0.0658:0:1.2 -20 40828272 . A G 51 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCTAAAATGGGAAATC;RSEQ=ATGAGACTTGTACAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:0.2308:0,0:28.7:1:32.7:1:1:0:60:6:0.2308:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40843031 . C G 77 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08462;SOR=5.24148;LSEQ=ATGAGCATCCTGTCTGCTCA;RSEQ=TGCCTCTGTTGGGTACCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:2,0:22,0:0.0833:1,0:36:1:30:0:1:0:60:4:0.0833:0:1 0/1:15:5:5,0:10,0:0.3333:0,0:16.6:1:33.2:1:1:0:60:10:0.3333:0:1 -20 40843115 . TC T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.16991;SOR=Inf;LSEQ=CCTCATCTAGGGCTTGTGAA;RSEQ=CCCCAGCATGGCAAAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:93,66:0:2,0:26.8:1:31.1:1:1:0:60:158:1:0:0.2 0/1:112:2:1,1:64,46:0.0179:2,2:30:0:30.5:1:1:1.38711:60:4:0.0183:0:0 -20 40843148 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.5128;SOR=0;LSEQ=CAAAGTTACAGAAGCAACAG;RSEQ=AGCAGCAACAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:99,100:0.01:2,2:37.5:1:29.5:1:1:1.01:60:4:0.0101:0:1 0/0:143:0:0,0:72,71:0:2,0:28.3:1:32:1:1:0:60:142:1:0:0.1 -20 40863924 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTATTATTATTTTGAGA;RSEQ=GGAGTTTTGCTCTTGTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40877252 . CA C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54478;SOR=0;LSEQ=CTGGACAATGATCAACAGAG;RSEQ=AAAACCTGGCCACACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:163,17:0.011:2,2:16.5:1:31:1:0.18851:9.34663:60:4:0.011:0:0 0/0:97:0:0,0:82,15:0:2,0:26.4:1:30.6:1:1:0:60:194:1:0:0.1 -20 40877288 . C T 113 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=30.67567;LSEQ=CAGCAGTGTTGAGGTCACCT;RSEQ=GGGTCAGCAGAGTCTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:0,1:255,72:0.003:2,0:1:0:26:0:0.22256:0:60:2:0.0031:0:1 0/1:174:15:11,4:120,39:0.0862:2,2:22.3:1:29.1:1:1:1.11813:60:30:0.0862:0:1.1 -20 40877300 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11414;SOR=Inf;LSEQ=GGTCACCTCGGGTCAGCAGA;RSEQ=TCTTGCAGGCAGCAGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:391:0:0,0:289,102:0:2,0:25.2:1:31.8:1:1:0:60:47.875:1:0:0.1 0/1:200:2:1,1:143,55:0.01:2,2:23:0:31.5:1:0.48261:2.58568:60:4:0.0101:0:1.5 -20 40877528 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15612;SOR=Inf;LSEQ=ATGCGACTAGACAATCATCA;RSEQ=AATGACAACAGCTTCCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:31,155:0:2,0:22.8:1:28.4:1:1:0:60:185:1:0:0.1 0/1:122:2:1,1:22,97:0.0164:2,2:20:1:30:1:0.34532:4.33:60:4:0.0167:0:1 -20 40898921 . T G 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=1;SOR=0.97945;LSEQ=TGGGTGAATGGGTGGGGGGG;RSEQ=GGGTGGGTGGGTGGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:27:1,26:468,0:0.0537:1,1:9.3:1:23.9:1:0:0:60:4.4:0.0476:0:4.2 0/1:266:14:1,13:248,2:0.0526:1,1:10.1:1:20.1:1:0:1197.75516:58.9:1.8:0.0363:0:4.1 -20 40898925 . T G 110 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=4;SSF=0.2275;SOR=1.38687;LSEQ=TGAATGGGTGGGGGGGTGGG;RSEQ=GGGTGGGTGGGGTGGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:537:38:1,37:495,1:0.0708:1,1:10:1:21.1:1:0:10696.02929:60:2.455:0.0537:0:3.9 0/1:293:28:1,27:258,6:0.0956:1,1:7.9:1:18.7:1:0:1029.97409:56.1:1.545:0.0627:0:3.6 -20 40898929 . T G 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=4;SSF=0.52995;SOR=1.1965;LSEQ=TGGGTGGGGGGGTGGGTGGG;RSEQ=GGGTGGGGTGGAAAGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:45:4,41:506,7:0.0801:1,2:12.9:1:22.7:1:0:666.8098:60:2.462:0.0624:0:3.4 0/1:318:30:0,30:273,13:0.0943:1,1:10.1:1:21.7:1:0:0:56.7:2.75:0.0748:0:3.3 -20 40898933 . T G 143 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=1.01102;LSEQ=TGGGGGGGTGGGTGGGTGGG;RSEQ=GGGGTGGAAAGACTGCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:618:68:7,61:531,16:0.11:1,2:12.6:1:23.6:1:0:276.15038:59.9:3.533:0.0925:0:2.8 0/1:360:40:2,38:290,21:0.1111:2,2:12.3:1:19.7:1:0:252.24295:59:1.857:0.08:0:2.7 -20 40900992 . T C 46 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGAAAATATTTACTATC;RSEQ=GTCCTTTTACAGAGGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:31.3:1:29.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:47:0:32:0:1:0:60:2:1:0:1 -20 40910575 . C T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCCAGGCAATTCAATTA;RSEQ=AATTAGGAAAACAAAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:17:1:30.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40910951 . G A 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAACTTTTACTCTATTTTAC;RSEQ=CACTGTGCTACTAATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:127,1:0:1,0:21.4:1:30.3:1:1:0:60:256:0.9922:0:0.1 0/1:44:8:8,0:36,0:0.1818:1,0:11.5:1:30.1:1:1:0:60:16:0.1818:0:1 -20 40944032 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGAGAGGTCATGTAATTT;RSEQ=CTCAAGTAAAGCACCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:37.5:1:32:0:1:0:60:4:0.2222:0:1 0/0:1:0:0,0:1,0:0:0,0:22:0:28:0:1:0:60:2:1:0:2 -20 40944069 . A G 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=0;LSEQ=TCTCTTTACTTTAATACAGG;RSEQ=GTGTGCAAAGGTTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:0.7:0,0:34:1:32.4:1:1:0:60:14:0.7:0:1.4 0/0:2:0:0,0:2,0:0:0,0:24:1:22.5:1:1:0:60:1:1:0:1 -20 40944812 . C T 78 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTTGTAGAACTTTACCTC;RSEQ=ACTTAGCTGTCTCAGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:0.4118:0,0:25.7:1:28.1:1:1:0:60:14:0.4118:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40979160 . T C 219 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.05792;LSEQ=CTTCCTCCGAGGAAGCTTTG;RSEQ=TCCTGGCCAGTCTTGCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:121:119:119,0:2,0:0.9835:0,1:23.6:1:31.8:1:1:0:60:28.75:0.9829:0:1.1 1/0:57:44:44,0:13,0:0.7719:1,1:25.1:1:33:1:1:0:60:88:0.7719:0:1 -20 40979188 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52625;SOR=0;LSEQ=CAGTCTTGCCCATGGGCATT;RSEQ=CCAGTCACATGATTCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:165,19:0.0108:2,2:20.5:1:27.5:1:0.20401:8.48825:60:4:0.011:0:1.5 0/0:115:0:0,0:106,9:0:2,0:22.8:1:32.2:1:1:0:60:230:1:0:0.5 -20 40979190 . C T 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30074;SOR=0;LSEQ=GTCTTGCCCATGGGCATTGC;RSEQ=AGTCACATGATTCAACTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:4:4,0:170,24:0.0202:2,0:24:1:32.8:1:1:0:60:8:0.0204:0:1 0/0:117:0:0,0:108,9:0:2,0:23.4:1:30.6:1:1:0:60:116:1:0:0.4 -20 40979203 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16669;SOR=Inf;LSEQ=GCATTGCCAGTCACATGATT;RSEQ=AACTGGAGGCCCATGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:207,43:0:2,0:23.3:1:31.3:1:1:0:60:82.333:1:0:0.4 0/1:173:2:1,1:138,33:0.0116:2,2:14.5:1:30:1:0.35536:4.13476:60:4:0.0116:0:1.5 -20 40979430 . C T 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00932;SOR=0.53047;LSEQ=ATTCCCAACTGGCTCCCCAC;RSEQ=GCCCCTTGCTGCCATCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:186:95:5,90:4,87:0.5108:1,2:22.9:1:30.5:1:1:1.21:60:94:0.5137:0:1 0/1:118:42:2,40:2,74:0.3559:1,1:25.9:1:30.5:1:0.61524:1.84:60:41:0.3534:0:1.1 -20 40979469 . A T 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=0;LSEQ=TAAAGACACAGCATGGATAG;RSEQ=GGGAGGACGTTTAGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:0,20:2,81:0.1942:1,1:23.4:1:30.6:1:1:0:60:40:0.198:0:1.5 0/0:57:0:0,0:1,56:0:1,0:22.2:1:31.2:1:1:0:60:56:1:0:0.3 -20 40980486 . G C 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTGTACTATTTAATGCAA;RSEQ=CCTGTGGGAAAATTATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:0.6364:0,0:38.3:1:32.6:1:1:0:60:14:0.6364:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40980495 . A C 102 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTAATGCAAGCCTGTGGG;RSEQ=AAATTATTTAGTGGCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:10,0:4,0:0.7143:0,0:25.4:1:30.9:1:1:0:60:9:0.6923:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 40980684 . G T 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15647;SOR=0.21725;LSEQ=GAAAATCAGGAAGTGGGGGT;RSEQ=AAACAACCTTTTTTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:7:1,6:278,65:0.02:2,2:8.9:1:25.3:1:0.00034:25.32967:60:14:0.0201:0:1 0/0:227:1:0,1:176,50:0.0044:2,0:1:0:21:0:0.22467:0:60:2:0.0044:0:1 -20 40980773 . T C 158 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=51.6456;LSEQ=ACAGGGGGCCCAAAGCCCTT;RSEQ=GCTGTGCTGGCCTTGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1064:1:1,0:601,462:9e-04:2,0:28:0:15:0:1:0:60:0:0:0:1 0/1:840:39:24,15:423,378:0.0464:2,2:24.9:1:29.9:1:0.32616:1.43:60:38:0.0456:0:1.2 -20 40980987 . G A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09729;LSEQ=CACTCAGGAAGCTGGATGGA;RSEQ=CTCCTTTAGAGGAACCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:181:98:3,95:7,75:0.5414:2,1:25.3:1:29.5:1:0.18932:2.93825:60:18.6:0.5345:0:1.1 0/1:88:9:0,9:7,72:0.1023:2,0:19.8:1:29.4:1:1:0:60:18:0.1023:0:1 -20 40981002 . C A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03227;SOR=Inf;LSEQ=ATGGAGCTCCTTTAGAGGAA;RSEQ=CTTAGGGAGGCGGGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:4,133:0:1,0:22.8:1:30.8:1:1:0:60:26.4:1:0:0.7 0/1:65:3:0,3:3,59:0.0462:1,0:18.7:1:29.7:1:1:0:60:6:0.0476:0:1 -20 40981098 . C A 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.16186;LSEQ=TTTCCAGATGATCCCAGCCT;RSEQ=CAAATACCCCATTGCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:18:0,18:0,14:0.5625:1,1:25.3:1:30.7:1:1:0:60:36:0.5625:0:1.1 1/0:5:3:0,3:0,2:0.6:0,0:10.7:1:28.7:1:1:0:60:6:0.6:0:1 -20 41076539 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCCCAGACGAACTTTCA;RSEQ=TACTGTTTGCCAGGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:36:1:30.5:1:1:0:60:4:0.1667:0:1 0/0:3:0:0,0:2,1:0:2,0:30:1:31.3:1:1:0:60:6:1:0:0.3 -20 41076751 . T A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=3.55389;LSEQ=CAGAAACCTTTTGGTATGTC;RSEQ=CATCTTACTCACCTTTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:27:27,0:183,3:0.1268:1,1:27.2:1:29.6:1:1:0:60:26:0.1244:0:1.2 0/1:82:28:26,2:53,1:0.3415:1,2:20.2:1:30.2:1:0.26748:4.00182:60:27:0.3375:0:1.2 -20 41077028 . G A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00295;SOR=Inf;LSEQ=CACATCATTTCTCCAGCCCC;RSEQ=CTGACCTAGAACAGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:44,303:0:2,0:23.5:1:31.6:1:1:0:60:56.833:1:0:0.1 0/1:214:6:1,5:26,181:0.028:2,2:18.3:1:28.2:1:0.56119:1.39:60:12:0.0284:0:1 -20 41077037 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14767;SOR=Inf;LSEQ=TCTCCAGCCCCGCTGACCTA;RSEQ=AACAGGGGTTGACAAAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:23,263:0:2,0:25.2:1:31.2:1:1:0:60:39.857:1:0:0 0/1:179:2:1,1:15,162:0.0112:2,2:15.5:1:30.5:1:0.17124:10.49:60:4:0.0114:0:1 -20 41100774 . G A 110 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02843;SOR=2.91681;LSEQ=TACATAGTCCTTCATTGAAG;RSEQ=CCTAAGAAAAGAAAGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:12:12,0:68,0:0.15:1,0:25.8:1:30:1:1:0:60:24:0.1538:0:1.2 0/1:38:13:13,0:25,0:0.3421:1,1:20.9:1:29.9:1:1:0:60:26:0.3421:0:1 -20 41100875 . A T 57 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0152;SOR=9.64594;LSEQ=TGAATAGATTCAATATCCCC;RSEQ=TTCCCATGTAAGCTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:774:1:0,1:509,264:0.0013:2,0:1:0:25:0:0.34238:0:60:2:0.0013:0:1 0/1:486:6:1,5:299,180:0.0123:2,2:7.2:1:22.3:1:0.0322:8.27411:60:2:0.0084:0:1 -20 41100922 . C T 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=24.29574;LSEQ=TCACCGTCTTCCTCAGTCTG;RSEQ=ACCACCAGCTCCTCGCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1038:2:0,2:546,490:0.0019:2,0:16:1:27.5:1:0.22442:0:60:4:0.002:0:1 0/1:758:34:17,17:386,338:0.0449:2,2:26.7:1:27.9:1:0.72812:1.14181:60:68:0.0452:0:1.1 -20 41101051 . G A 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.68131;LSEQ=TGGATGACCTCCTCGGCCTC;RSEQ=TACTGCTGCTGGTTGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1070:1:1,0:508,561:9e-04:2,0:1:0:26:0:0.4757:0:60:2:9e-04:0:1 0/1:681:25:14,11:321,335:0.0367:2,2:19.2:1:29.7:1:0.54458:1.33:60:24:0.0355:0:1.2 -20 41101067 . A T 186 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTCGTACTGCTGCTGGTTG;RSEQ=ACACATACTGGTACTGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1064:90:43,47:456,517:0.0846:2,2:24.3:1:28.7:1:0.91228:1.04:60:89:0.0848:0:1.1 0/0:685:0:0,0:327,358:0:2,0:25.9:1:29.4:1:1:0:60:61.273:1:0:0.2 -20 41101161 . T G 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGTCAGCTGCCGGGCTC;RSEQ=GATGTCTACGATTTCCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:189,378:0:2,0:24.9:1:30.2:1:1:0:60:69.875:1:0:0.2 0/1:334:18:6,12:111,205:0.0539:2,2:24.8:1:28.4:1:1:1.08268:60:17:0.0517:0:2.2 -20 41101180 . G A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGATGTCTACGATTTCCAC;RSEQ=TTCTGTGGGCCATGTACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:126,325:0:2,0:25.6:1:31.1:1:1:0:60:44.1:1:0:0.2 0/1:248:13:3,10:69,165:0.0524:2,2:21.2:1:29.5:1:0.76132:1.39222:60:12:0.0494:0:2.7 -20 41101195 . T C 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCCACGTTCTGTGGGCCATG;RSEQ=ACCGGATCTGCAAAACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:91,294:0:2,0:24.7:1:28.4:1:1:0:60:41.778:1:0:0.2 0/1:192:10:1,9:50,132:0.0521:2,2:18.7:1:32.2:1:0.29511:3.3928:60:20:0.0524:0:3 -20 41101274 . C A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07567;SOR=3.22455;LSEQ=CTGGGGTACATGTTCTGCTA;RSEQ=AACAGGGAACACAGCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:9:0,9:9,84:0.0882:2,0:22.6:1:30.8:1:1:0:60:18:0.0891:0:1 0/1:25:6:0,6:4,15:0.24:2,0:21.7:1:30.2:1:0.5404:0:60:12:0.24:0:1 -20 41306435 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54641;SOR=0;LSEQ=GAATTATCTGTCACAGGAAG;RSEQ=CAAGAGGAAAGCCAGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:2,0:179,4:0.0108:1,0:18:1:31.5:1:1:0:60:4:0.0112:0:1 0/0:98:0:0,0:93,5:0:2,0:23.1:1:30.9:1:1:0:60:97:1:0:0.3 -20 41306488 . G GAA 206 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=0;SOR=2.3479;LSEQ=CCTCTCATAATGGAGCCTGG;RSEQ=AAAAAAAAAAATCTTACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:124:94,30:156,38:0.3116:2,2:28:1:29.8:1:0.33056:1.30903:59.9:40.333:0.3143:0:0.4 1/0:258:133:91,42:33,8:0.5155:2,2:28.7:1:29.2:1:0.16839:1.89733:59.9:266:0.5278:0.0194:0.4 -20 41306600 . A G 216 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCGGATCTCATACTCAAC;RSEQ=TCGGGGTCCAGATGCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1165:0:0,0:591,574:0:2,0:24.9:1:30.1:1:1:0:60:36.581:1:0:0.1 0/1:888:153:74,79:377,356:0.1723:2,2:24.9:1:29.8:1:0.53393:1.13038:60:152:0.1745:0:1.1 -20 41306899 . CA C 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.7057;LSEQ=CAGAATTCTTGATGTAGCCA;RSEQ=AAAAAAATAGTCAGAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:3:0,3:1,75:0.038:1,0:28.7:1:33.3:1:1:0:60:6:0.038:0:0 0/1:37:1:0,1:1,35:0.027:1,0:29:0:34:0:1:0:60:2:0.027:0:0 -20 41384481 . G A 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAACTCATTGGATGAGATA;RSEQ=CATACGATCACTAAGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:32:0:1:0:60:4:1:0:2.5 -20 41384942 . C T 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06;SOR=Inf;LSEQ=GATTTTACCATAGTTTCTCC;RSEQ=GTTTGGGGAGTTTGTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:92,2:0:1,0:25.6:1:31.3:1:1:0:60:46:1:0:0.2 0/1:31:2:2,0:25,4:0.0645:2,0:32:1:33:0:1:0:60:4:0.0645:0:1.5 -20 41385323 . G A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15736;SOR=4.90469;LSEQ=GGAGGAATCATAGCATCATA;RSEQ=GCTTCTAGGTGACTCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:1:1,0:125,355:0.0021:2,0:1:0:30:0:0.26195:0:60:2:0.0021:0:1 0/1:296:3:2,1:75,218:0.0101:2,2:8.7:1:21.3:1:0.16686:5.77:60:2:0.0068:0:1.7 -20 41385368 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08906;SOR=Inf;LSEQ=ATATCCACCCATCCTCACAC;RSEQ=CCTGGGGCTCAAGACTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:9,192:0:1,0:22:1:31.3:1:1:0:60:66:1:0:0.1 0/1:86:2:1,1:4,80:0.0233:1,2:16:1:30:1:0.11354:18.00:60:4:0.0233:0:1 -20 41386028 . C G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTGGTGCCCTGCTACCCCA;RSEQ=CCCACAGGCTCTGAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:21:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:32:0:1:0:60:4:1:0:1.5 -20 41399995 . C T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55569;SOR=0;LSEQ=TGTTCAATACACTTGTGTTG;RSEQ=CATAGAGCTGCTTCCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:2,1:251,13:0.0112:1,2:9:1:23.3:1:0.14973:9.44524:60:2:0.0077:0:1.3 0/0:119:0:0,0:97,22:0:2,0:22:1:31.6:1:1:0:60:118:1:0:0.1 -20 41400114 . A T 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGAGACCACTTCCCACC;RSEQ=GCAATGCACTGAAATGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1018:0:0,0:493,525:0:2,0:25.5:1:30.1:1:1:0:60:32.933:1:0:0.1 0/1:692:27:16,11:337,328:0.039:2,2:20.9:1:29.4:1:0.43553:1.41:60:54:0.0398:0:1 -20 41400229 . G A 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80362;SOR=1.0561;LSEQ=AACACAAGAGAATGAGATTC;RSEQ=ACAGCCTGCACCACTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:172:51,121:51,155:0.455:2,2:21.8:1:30:1:0.2971:1.28:60:85:0.4533:0:1.1 0/1:239:112:36,76:37,90:0.4686:2,2:21.2:1:29.7:1:0.67355:1.15:60:111:0.4684:0:1.1 -20 41408489 . GT G 63 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGTTTTGGTGGTGGTGT;RSEQ=TTTTTTTTTTTTAAGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:5,0:0.4444:0,2:41:1:31.5:1:0.44444:0:60:8:0.4444:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 41408784 . G T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0595;SOR=7.16253;LSEQ=GTTTGTAAGCTGAATGAATG;RSEQ=AAGGGATTGCAGGCTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:1:1,0:440,102:0.0018:2,0:49:0:32:0:1:0:60:2:0.0019:0:1 0/1:306:4:1,3:241,60:0.0131:2,2:5.3:1:25.3:1:0.02887:11.91935:60:8:0.0135:0:1 -20 41408808 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00401;SOR=Inf;LSEQ=GGATTGCAGGCTCTATGCTA;RSEQ=CCAGTCTGGCATGGATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:0:0,0:551,230:0:2,0:25.6:1:31.5:1:1:0:60:85.778:1:0:0.1 0/1:520:6:1,5:342,172:0.0115:2,2:6.2:1:25.8:1:0.01905:9.90029:60:12:0.0116:0:1 -20 41408964 . A G 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACACACAGGGCGGGAGTCA;RSEQ=TTTCACAGAAACAGTTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:741:0:0,0:248,492:0:2,0:25.2:1:30.3:1:1:0:60:81.222:1:0:0.1 0/1:526:22:7,15:186,318:0.0418:2,2:20.3:1:30.7:1:0.82174:1.25282:60:44:0.0427:0:1.2 -20 41419718 . A G 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33366;SOR=0.65722;LSEQ=GCTTGGCTAGGAGGAGAAGC;RSEQ=CAGTAAACACGAGTGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:49:49,0:71,2:0.4016:1,1:26.1:1:29.9:1:0.51538:0:60:48:0.3967:0:1.1 0/1:36:11:10,1:25,0:0.3056:1,2:21.5:1:30:1:0.30556:0:60:22:0.3056:0:1.2 -20 41420095 . T C 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCCCAGAGCTGTTCACCA;RSEQ=CATGAAAGATCCTGGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:0:0,0:176,512:0:2,0:25.5:1:29.8:1:1:0:60:48.143:1:0:0.1 0/1:408:25:3,22:107,276:0.0613:2,2:25.1:1:31.4:1:0.1033:2.83732:60:50:0.0627:0:1 -20 41446905 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=AAGTGAACCCCCAGCAAACT;RSEQ=CAGAAGCCCTAATGAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:0.0952:2,2:35:1:29:1:1:1.35399:60:4:0.1:0:1 0/0:20:0:0,0:11,9:0:2,0:23.1:1:30.7:1:1:0:60:19:1:0:0.2 -20 41446916 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23171;SOR=Inf;LSEQ=CAGCAAACTGCAGAAGCCCT;RSEQ=ATGAAGAGGGACCTGACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:27.2:1:29:1:1:0:60:20:1:0:0.2 0/1:20:2:0,2:12,6:0.1:2,0:7:1:29:1:0.14737:0:60:4:0.1:0:1.5 -20 41447003 . C CA 69 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05276;SOR=Inf;LSEQ=ACAACAACAACAAAAAGACC;RSEQ=AAAAAAAAAACCCATTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:21.4:1:29.8:1:1:0:60:7.333:1:0:0.3 0/1:28:5:2,3:12,11:0.1786:2,2:33.6:1:30:1:1:1.60791:60:10:0.1786:0:0.2 -20 41447118 . T C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAAAGGCCAGAGTGCCT;RSEQ=TCCTCCTCCAAACGACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:1:0,2:24:1:31.9:1:1:0:60:16:1:0:1 1/1:3:3:0,3:0,0:1:0,0:19.7:1:34:0:1:0:60:6:1:0:1 -20 41514162 . G A 94 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCCCTGACACGCCACT;RSEQ=TCATCAGGCTCCCAAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:16.5:1:27.2:1:1:0:60:10:1:0:1.9 1/1:1:1:1,0:0,0:1:0,0:21:0:29:0:1:0:60:2:1:0:2 -20 41514406 . A G 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGATTCACGGTAAAAACT;RSEQ=GCCATCCCCATTACAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:0:0,0:429,202:0:2,0:25.7:1:29:1:1:0:60:51.583:1:0:0.1 0/1:487:17:12,5:312,158:0.0349:2,2:23.5:1:30.6:1:0.79982:1.21:60:16:0.0333:0:1.4 -20 41514541 . G A 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGCCACACTATAACCACA;RSEQ=TTGCTGTAGTGCTCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1011:0:0,0:416,594:0:2,0:25.5:1:32:1:1:0:60:90.818:1:0:0.1 0/1:713:38:14,24:279,396:0.0533:2,2:20.5:1:29.8:1:0.61591:1.20748:60:76:0.0542:0:1.2 -20 41514613 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12938;SOR=Inf;LSEQ=GGTAAATACATTCCCGTGTC;RSEQ=GAGGCTTGGTTCGTTACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:55,277:0:2,0:23.6:1:30.2:1:1:0:60:65.4:1:0:0.1 0/1:187:2:1,1:37,148:0.0107:2,2:7.5:1:28:1:0.36599:3.96:60:4:0.0108:0:1 -20 41514622 . G C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=Inf;LSEQ=ATTCCCGTGTCTGAGGCTTG;RSEQ=TTCGTTACCTCTGTCTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:35,238:0:2,0:23.7:1:31.7:1:1:0:60:67.25:1:0:0.1 0/1:150:7:3,4:22,121:0.0467:2,2:26.1:1:33.3:1:0.09093:4.07:60:14:0.0476:0:1.4 -20 41514690 . C CAT 112 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=11.000;MSILEN=2;SSF=0.58027;SOR=0.66168;LSEQ=AAACTCTGGAGAAGATTTTC;RSEQ=ATATATATATATATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:16:0,16:1,52:0.2162:1,1:31.4:1:28.1:1:1:0:60:32:0.2286:0.027:0.1 0/1:26:4:0,4:0,18:0.1538:1,0:24:1:27.4:1:1:0:60:8:0.16:0.0385:0.3 -20 41514712 . A T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.11853;SOR=5.96949;LSEQ=TATATATATATATATATATA;RSEQ=AAGATGAGCAAATTGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:0,2:0,50:0.0385:1,0:19:1:29:0:1:0:57.5:4:0.0385:0:1 0/1:10:2:0,2:0,8:0.2:0,0:36:1:29.5:1:1:0:60:4:0.2:0:1 -20 41759356 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGTTCGTCATGCTGAAAA;RSEQ=GAGGCCAAGGGCTCTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:17,1:0.1:1,2:31:0:33:1:0.19474:12.36938:60:4:0.1:0:1.5 0/0:7:0:0,0:7,0:0:0,0:17.1:1:30.6:1:1:0:60:14:1:0:0.3 -20 41759470 . G A 56 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77066;SOR=0.74406;LSEQ=TTTTCAAAAAAAAAAAAAAA;RSEQ=GAAAAAGTATGTATGGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:9:9,0:94,18:0.0744:2,0:8.4:1:17.8:1:0.35281:0:56.8:0.5:0.0316:0:1.4 0/1:71:4:4,0:56,11:0.0563:2,0:7:0:24.8:1:1:0:55.3:3:0.0508:0:1.3 -20 41759523 . C T 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTAAAAAATCAATGAAA;RSEQ=GGAATAAAGCTCAGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:256,160:0:2,0:27.2:1:30.5:1:1:0:59.9:25:1:0:0.4 0/1:327:21:11,10:178,126:0.0642:2,2:27.6:1:27.9:1:0.64989:1.28325:60:20:0.0643:0:1.1 -20 41759541 . C G 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00024;SOR=1.90736;LSEQ=AACGGAATAAAGCTCAGAAA;RSEQ=AAGCCAAAGTATAACAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:70:37,33:240,180:0.1414:2,2:27.2:1:31:1:0.51733:1.18876:59.6:22.333:0.1408:0:1.5 0/1:393:94:52,42:164,133:0.2392:2,2:27.6:1:31.4:1:1:1.00:60:46:0.2427:0:1.4 -20 41759593 . G A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06856;SOR=0;LSEQ=CAACTGGTGCAGAGACAGCT;RSEQ=GCTAAGCATCTAAATACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:5:4,1:133,228:0.0137:2,2:5:1:27:1:0.06741:6.82:60:10:0.0137:0:1.2 0/0:296:0:0,0:115,181:0:2,0:24.1:1:30.3:1:1:0:59.9:97.667:1:0:0.8 -20 41759619 . C T 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00024;SOR=0;LSEQ=GCATCTAAATACAAATGAAG;RSEQ=CAGGATCTCCACCTGACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:243:243:58,185:0,0:1:0,2:23.2:1:29.8:1:1:0:60:120.5:1:0:1.2 1/1:191:181:50,131:4,6:0.9476:2,2:23:1:28.3:1:0.47251:1.74102:59.8:59.333:0.9468:0:1.2 -20 41818162 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=CAAGCTGAGACCCGGGTTCC;RSEQ=GCCATGGGGACCCGCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:10,0:0:0,0:26.6:1:30.8:1:1:0:60:20:1:0:0.1 0/1:10:2:2,0:8,0:0.2:0,0:22.5:1:28.5:1:1:0:60:4:0.2:0:1.5 -20 41818236 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.5363;SOR=0;LSEQ=CCGCGGCTGGGGGCCCGCGC;RSEQ=CATCCAGGAGGGAGCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:66,49:0.0171:2,2:25:1:29.5:1:1:1.34345:60:4:0.0171:0:1.5 0/0:66:0:0,0:34,32:0:2,0:22.5:1:29.9:1:1:0:60:65:1:0:0.5 -20 41818242 . A G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53297;SOR=0;LSEQ=CTGGGGGCCCGCGCGCATCC;RSEQ=GGAGGGAGCGGGGAGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:74,60:0.0147:2,2:11:0:31.5:1:1:1.23141:60:4:0.015:0:2 0/0:79:0:0,0:42,37:0:2,0:21.2:1:29.7:1:1:0:60:38.5:1:0:0.5 -20 41818251 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.14938;SOR=Inf;LSEQ=CGCGCGCATCCAGGAGGGAG;RSEQ=GGGGAGCCCAGGGGAGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:81,68:0:2,0:25.7:1:30.6:1:1:0:60:28.8:1:0:1.1 0/1:95:2:1,1:48,45:0.0211:2,2:33.5:1:30:1:1:1.06598:60:4:0.0215:0:1 -20 41818258 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28184;SOR=0;LSEQ=ATCCAGGAGGGAGCGGGGAG;RSEQ=CCAGGGGAGCCGGGCGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:1,2:88,82:0.0173:2,2:16:1:28.7:1:0.61212:2.13718:60:6:0.0175:0:2.3 0/0:112:0:0,0:56,56:0:2,0:22.5:1:31.3:1:1:0:60:55:1:0:0.6 -20 41818274 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15661;SOR=Inf;LSEQ=GGAGCCCAGGGGAGCCGGGC;RSEQ=GGCGCACTCACCTGCGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:106,107:0:2,0:26.5:1:30.3:1:1:0:60:70:1:0:1.2 0/1:140:2:1,1:65,73:0.0143:2,2:28:0:31:1:1:1.12:60:4:0.0145:0:1.5 -20 41818289 . C G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09432;LSEQ=CGGGCGGGCGCACTCACCTG;RSEQ=GGCGCTCTGAGCCCGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:229:206:99,107:11,11:0.8996:2,2:25.4:1:30.8:1:1:1.08043:60:50.5:0.8978:0:1.3 0/1:136:62:28,34:35,39:0.4559:2,2:26.5:1:30.2:1:0.86367:1.08905:60:61:0.4519:0:1.2 -20 41818371 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23251;SOR=Inf;LSEQ=GCGAGCGCGGCGAGGCTCGC;RSEQ=ATCCGGGCGGCGGCGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:36,44:0:2,0:20.9:1:32.1:1:1:0:60:160:1:0:0.6 0/1:75:2:1,1:34,39:0.0267:2,2:43.5:1:29.5:1:1:1.14:60:4:0.0282:0:1 -20 41818376 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49767;SOR=Inf;LSEQ=CGCGGCGAGGCTCGCCATCC;RSEQ=GGCGGCGGCGGGCAGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:29,38:0:2,0:20.5:1:31.4:1:1:0:60:134:1:0:0.6 0/1:74:2:1,1:34,38:0.027:2,2:14:0:30.5:1:1:1.12:60:4:0.0286:0:1.5 -20 41818391 . G A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05546;SOR=0;LSEQ=CATCCGGGCGGCGGCGGGCA;RSEQ=CTCAGCCCCTTCCCGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:2,1:15,18:0.0789:2,2:13:1:30.3:1:0.59286:2.34:60:6:0.0789:0:1.3 0/0:60:0:0,0:30,29:0:2,0:17.6:1:30.6:1:1:0:60:28.5:1:0:0.5 -20 41955344 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CAGCACACACGCATGTGCGC;RSEQ=CGCACATACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1 -20 41956519 . A G 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACATCCTGACTTTTTA;RSEQ=TGATCACCATTCTAACTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:23.5:1:32.5:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 41956785 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91866;LSEQ=TTTCTCCCATCCTATAGGTT;RSEQ=CCTGTTTACTCTGATGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:93,8:0.0194:2,2:8.5:1:28.5:1:0.1679:11.01924:60:4:0.0196:0:1 0/1:56:1:0,1:47,8:0.0179:2,0:1:0:25:0:0.16071:0:60:2:0.0185:0:1 -20 41956808 . A G 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27957;SOR=0;LSEQ=TGTTTACTCTGATGATAAAG;RSEQ=GCTTCTGCACAGCAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:2,1:120,28:0.0199:2,2:23:1:23.7:1:0.47511:2.1297:60:2:0.0133:0:1.3 0/0:99:0:0,0:70,29:0:2,0:21.9:1:28.6:1:1:0:60:32:1:0:0.1 -20 41956839 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1519;SOR=Inf;LSEQ=AGCAAAAGAGTCACCTATTT;RSEQ=TTAGAGCAACACTGACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:172,84:0:2,0:24.1:1:29.6:1:1:0:60:41.667:1:0:0.5 0/1:164:2:1,1:106,56:0.0122:2,2:19.5:1:30.5:1:1:1.88508:60:4:0.0124:0:1.5 -20 41956920 . A G 267 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGATAGGACCAAGAGCTC;RSEQ=CCTGCCAGTGGGTGGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:396:396:169,227:0,0:1:0,2:26:1:31:1:1:0:60:78.2:1:0:1.3 1/0:260:167:75,92:42,51:0.6423:2,2:23.9:1:30.2:1:1:1.01016:60:54.667:0.6381:0:1.4 -20 41956960 . A G 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=0.45162;LSEQ=ATTCTCAAAATATAAAGTAT;RSEQ=TAATTCTTTATACTGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:117:40,77:39,88:0.4795:2,2:21.9:1:32.2:1:0.58599:1.17:60:234:0.4795:0:1.8 0/1:167:49:16,33:40,78:0.2934:2,2:23.7:1:31.1:1:1:1.05735:60:98:0.2952:0:1.8 -20 42630762 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15024;SOR=Inf;LSEQ=ATCACCCCAGAAAGTAGAGT;RSEQ=CCACTGCCAGCTTTCCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:108,65:0:2,0:25:1:31.1:1:1:0:60:56.667:1:0:0.2 0/1:110:2:1,1:58,50:0.0182:2,2:25:1:28:1:1:1.15843:60:4:0.0183:0:1 -20 42630772 . G T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28491;SOR=0;LSEQ=AAAGTAGAGTCCCACTGCCA;RSEQ=CTTTCCAGTTCAGAGTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:1,2:114,78:0.0154:2,2:28.7:1:29.3:1:0.56906:2.90694:60:6:0.0159:0:1 0/0:124:0:0,0:68,56:0:2,0:27.7:1:32.1:1:1:0:60:123:1:0:0.3 -20 42630773 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.56429;SOR=3.09145;LSEQ=AAGTAGAGTCCCACTGCCAG;RSEQ=TTTCCAGTTCAGAGTCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:0,1:117,80:0.0051:2,0:1:0:29:0:0.40909:0:60:2:0.0051:0:1 0/1:129:2:1,1:70,57:0.0155:2,2:34:1:28:1:1:1.2261:60:4:0.0156:0:1 -20 42630821 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.16134;SOR=Inf;LSEQ=GAAGCCTTCCCAACCCCTCT;RSEQ=CCCATTCTAAGGCAAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:77,101:0:2,0:26.3:1:31.7:1:1:0:60:43.5:1:0:0.2 0/1:120:2:1,1:56,62:0.0167:2,2:9:0:29.5:1:1:1.11:60:4:0.0167:0:1.5 -20 45867566 . TTGC T 69 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.2274;SOR=3.47386;LSEQ=TGAGGCTGCTGCTGCTGGTT;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:16,18:0.0556:2,2:48.5:1:30:0:1:1.12:60:4:0.0588:0:0 0/1:29:5:3,2:10,12:0.1724:2,2:31.6:1:30:1:0.64831:1.76:60:10:0.1724:0:0.2 -20 46250585 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTATTTTTAGTAGAGA;RSEQ=GGGGTTTCACCATGTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:30:1:28:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 46251242 . G GT 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.06329;LSEQ=ATCTTTTTGATGTAATAGAA;RSEQ=TTTTTTTTTTATTGCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:12:0,12:1,114:0.093:1,0:28.2:1:31.3:1:1:0:60:24:0.096:0:0.1 0/1:61:6:0,6:1,54:0.0984:1,0:43.3:1:27.5:1:1:0:60:5:0.0862:0:0 -20 46252535 . A AG 77 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.42785;SOR=0.3046;LSEQ=AGAGCGAAAACTCTGTCTCG;RSEQ=GGAAAAAAAAAAAAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:6:6,0:183,0:0.0316:1,0:20:1:29.9:1:1:0:60:5:0.0275:0.0105:1 0/0:102:1:1,0:100,1:0.0098:1,0:17:0:34:0:1:0:60:2:0.0103:0:0 -20 46252605 . G GAT 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.0014;SOR=Inf;LSEQ=TCTGCTAACAGCTCTTTTGT;RSEQ=ATATATATATTATGTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:822:0:0,0:605,215:0:2,0:25.3:1:31:1:1:0:60:19.5:1:0:0.2 0/1:531:7:3,4:355,169:0.0132:2,2:24.7:1:26.9:1:0.22256:2.7948:60:14:0.0138:0.0019:0.4 -20 46252975 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00539;SOR=2.97086;LSEQ=CACATTACGTTTGTGGTGCA;RSEQ=TTTATTTCTATTATGGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:32:0,32:0,91:0.2602:1,1:28.2:1:32.6:1:1:0:60:64:0.2623:0:1 1/0:39:20:0,20:0,19:0.5128:1,1:25.4:1:33.1:1:1:0:60:40:0.5128:0:1 -20 46255238 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CTCCCCCACCCCCAATTATT;RSEQ=TTCTTTTTTTTTCCCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:22.9:1:24.1:1:1:0:60:1.333:1:0:0.6 1/0:4:2:1,1:1,1:0.5:2,2:17.5:1:29.5:1:1:1:60:4:0.5:0:1 -20 46255251 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=AATTATTCTTCTTTTTTTTT;RSEQ=CCCCCAGTAAGGCCTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:33.2:1:29.2:1:1:0:60:4:1:0:0.4 1/0:3:2:1,1:0,1:0.6667:0,2:26:1:27:1:1:0:60:4:0.6667:0:1 -20 46256424 . C T 266 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00225;LSEQ=TAAACGCCAGTCCTGAAATG;RSEQ=GCCAGAGATATGAAACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1971:476:212,264:659,833:0.2415:2,2:24.4:1:30:1:0.91561:1.02:60:157.667:0.2429:0:1.1 0/0:1402:1:0,1:664,734:7e-04:2,0:1:0:25:0:1:0:60:2:7e-04:0:1 -20 46256785 . GTC G 207 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.04968;SOR=0.69429;LSEQ=CAGGTAAAAACTCTTTTTTT;RSEQ=TCTCTCTCTCTCTGTGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1347:89:27,62:436,814:0.0661:2,2:27.1:1:32:1:0.42081:1.22973:60:178:0.0668:0.0134:0.3 0/1:1004:47:19,28:354,598:0.0468:2,2:36.7:1:31.6:1:0.64643:1.15:60:94:0.0474:0:0.1 -20 46262180 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13868;SOR=Inf;LSEQ=CAGTGCTAAGCCATGTGTAG;RSEQ=CAGCCAGTAAATACTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:300,16:0:2,0:24.3:1:31.4:1:1:0:60:51.667:1:0:0 0/1:188:2:1,1:171,15:0.0106:2,2:25:1:28.5:1:0.16339:11.07055:60:4:0.0112:0:1 -20 46262701 . T G 187 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCTTGGATTTTTAGAAA;RSEQ=GTACTTGAAGTATATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:729:0:0,0:594,135:0:2,0:22.5:1:30.6:1:1:0:60:71.9:1:0:0.1 0/1:358:66:58,8:229,62:0.1844:2,2:20.9:1:31:1:0.12101:1.96:60:32:0.1818:0:1.3 -20 46262994 . G A 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCAGCAGTGTTCTCAAAAT;RSEQ=CTTTATTATTAAAGTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:608:0:0,0:95,511:0:2,0:21.6:1:32.1:1:1:0:60:100:0.9967:0:0.1 0/1:345:56:12,44:60,229:0.1623:2,2:19.3:1:29.2:1:0.85958:1.04:60:112:0.1642:0:1.1 -20 46263720 . A T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGATCTGTCACCCAGGC;RSEQ=GGTGTGCAGTAGTGCCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:5,0:0.375:0,2:26:1:31.3:1:0.375:0:60:6:0.4286:0:1.3 0/0:1:0:0,0:1,0:0:0,0:8:0:31:0:1:0:60:2:1:0:0 -20 46264508 . C G 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCTTTTTAAGTAATTATT;RSEQ=TTTCCATACTACTATAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1085:0:0,0:375,708:0:2,0:22:1:31.7:1:1:0:60:62.706:0.9991:0:0.1 0/1:789:37:15,22:243,505:0.0469:2,2:25.6:1:30.5:1:0.3698:1.42:60:36:0.0465:0:1.1 -20 46267576 . CG C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTGGCTGGCAGGGGGG;RSEQ=GGGGGTGGCGGTGGTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:2,0:132,4:0.0145:1,0:26:1:31.5:1:1:0:60:4:0.015:0:1 0/0:34:0:0,0:34,0:0:1,0:24.3:1:29.5:1:1:0:60:33:1:0:0.1 -20 46267950 . C T 321 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01654;LSEQ=TTATGGCTCAAGTATGGGTA;RSEQ=GTTATTTCTAATTAGTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1568:1566:573,993:0,0:0.9987:0,2:25.2:1:30.3:1:1:0:60:81.421:0.9987:0:1.1 1/1:1086:1008:387,621:30,46:0.9282:2,2:25.4:1:29.9:1:0.90283:1.04644:60:90.636:0.9274:0:1.2 -20 46268008 . A G 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=105.40204;LSEQ=AGCATATTTAAAATACTTAA;RSEQ=GCCATCTAAATAATTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:1:0,1:70,478:0.0018:2,0:22:0:27:0:1:0:60:2:0.0018:0:1 0/1:290:47:4,43:34,209:0.1621:2,2:22.3:1:30.6:1:0.47737:1.74599:60:46:0.1597:0:1.8 -20 46268493 . A G 236 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGGTGGCTCTATTCCCAC;RSEQ=TTGCCTCTTCGGTCTAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2121:0:0,0:1051,1068:0:2,0:24:1:30.3:1:1:0:60:83.76:0.999:0:0.1 0/1:1455:227:110,117:612,615:0.156:2,2:23.7:1:30.2:1:0.71819:1.05844:60:74.667:0.1554:0:1.1 -20 46270624 . T C 110 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTACCTCCTTCACTGTTTT;RSEQ=GTGAGGAGTATCTTCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:24.8:1:31.8:1:1:0:60:22:1:0:1 1/1:1:1:1,0:0,0:1:0,0:5:0:32:0:1:0:60:2:1:0:1 -20 46270865 . G T 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13525;SOR=5.37983;LSEQ=TTTGTAGCATTTGAGTTACT;RSEQ=TTCATTAAAAATACTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:1:1,0:432,21:0.0022:1,0:1:0:31:0:1:0:60:2:0.0022:0:2 0/1:255:3:1,2:232,20:0.0118:2,2:6.7:1:24.3:1:0.02027:22.48466:60:2:0.008:0:3.3 -20 46270911 . GA G 221 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.54788;SOR=0.90432;LSEQ=GCTGTGATCTATTACTCTTA;RSEQ=AAAAAAAAAAGCACCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1133:127:93,34:709,285:0.1121:2,2:25.3:1:31.7:1:0.75411:1.10:60:126:0.1126:0.0168:0.2 0/1:771:79:49,30:446,240:0.1025:2,2:21.7:1:30.2:1:0.61997:1.13755:59.8:38.5:0.1014:0.0272:0.1 -20 46271008 . G A 239 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02359;LSEQ=GTTGGGCCACCTTCCAACCT;RSEQ=GAAGGCCAGAGTGACGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2367:286:145,141:1063,1015:0.1208:2,2:25.2:1:29.3:1:0.89972:1.0184:60:56.2:0.1209:0:1.1 0/0:1548:5:4,1:790,751:0.0032:2,2:11.8:1:25:1:0.37511:3.80:60:10:0.0033:0:1 -20 46275917 . A C 215 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGACAGACATACCCAGCAC;RSEQ=GGGGCCTCCAATGCAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2348:145:71,74:1092,1108:0.0618:2,2:24.3:1:30:1:0.93171:1.0272:60:28:0.0602:0:1.2 0/0:1521:0:0,0:777,743:0:2,0:24:1:30.4:1:1:0:60:107.571:0.9993:0:0.1 -20 46277834 . A T 209 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01107;LSEQ=GGTGATGAGGCCTATGATGC;RSEQ=GCCCCAGGTGAGCTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1671:114:50,64:744,811:0.0682:2,2:27.4:1:30.6:1:0.43787:1.17414:60:113:0.0685:0:1.2 0/0:1236:1:0,1:576,658:8e-04:2,0:1:0:28:0:1:0:60:2:8e-04:0:1 -20 46279531 . T C 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.12797;SOR=3.68735;LSEQ=GCAGAAGACTCACTTGAACC;RSEQ=GGGAGACGAAGGTTGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:11:11,0:21,0:0.3438:1,0:18.1:1:28.9:1:1:0:60:10:0.3226:0:1.3 1/0:9:6:6,0:3,0:0.6667:0,0:17.2:1:30.8:1:1:0:60:12:0.6667:0:1.3 -20 46279604 . T TA 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.15068;SOR=2.65704;LSEQ=GCGACAGAGTGAGACCCTGT;RSEQ=AAAAAAAAGAAGGCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:5:5,0:120,3:0.0391:1,0:27.2:1:28.8:1:1:0:57.6:10:0.0397:0.0078:2.4 0/1:51:5:5,0:43,2:0.098:1,0:26.6:1:29:1:1:0:60:10:0.098:0:1.4 -20 46279612 . AG A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0.75706;LSEQ=GTGAGACCCTGTTAAAAAAA;RSEQ=AAGGCCCTGGGTGTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:9:9,0:118,4:0.0559:1,0:19.1:1:30.6:1:1:0:60:18:0.057:0.0062:0.3 0/1:70:3:2,1:26,0:0.0429:1,2:27.3:1:30.7:1:0.10345:0:60:6:0.0429:0:0.7 -20 46279613 . G A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.37147;LSEQ=TGAGACCCTGTTAAAAAAAA;RSEQ=AAGGCCCTGGGTGTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:29:28,1:118,4:0.1801:1,1:21.1:1:29.8:1:1:1.05321:59.6:28:0.1772:0:1.3 1/0:70:41:40,1:26,0:0.5857:1,1:21.8:1:30.2:1:1:0:60:82:0.5857:0:1.5 -20 46279814 . TGCAGCAGCA T 211 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=3;SSF=0;SOR=0.20021;LSEQ=ACAGAGGGTGGCTATGATGA;RSEQ=GCAGCAGCAGCAACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1076:118:65,53:500,430:0.1097:2,2:22.2:1:30.8:1:0.84472:1.05:59.9:117:0.1108:0.0539:0.7 0/1:790:19:13,6:418,341:0.0241:2,2:18.9:1:31.5:1:0.35054:1.77:59.7:38:0.0245:0.0089:0.1 -20 46279827 . G A 210 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ATGATGATGCAGCAGCAGCA;RSEQ=CAGCAGCAACAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1013:0:0,0:517,440:0:2,0:23.2:1:31.8:1:1:0:59.9:44.571:1:0:0.1 0/1:774:144:76,68:344,282:0.186:2,2:21.1:1:29.3:1:0.64377:1.09133:60:35:0.1842:0:1.7 -20 46279836 . ACAG A 246 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=9.000;MSILEN=3;SSF=0;SOR=1.71812;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1004:239:130,109:397,353:0.238:2,2:25.3:1:31.7:1:0.71021:1.06:60:238:0.2402:0.0518:0.2 0/1:770:269:148,121:261,226:0.3494:2,2:24.6:1:30.5:1:0.76049:1.06:59.8:268:0.3526:0.0857:0.2 -20 46279866 . A G 211 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=6;SSF=0;SOR=32.67762;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAACAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1285:5:3,2:711,567:0.0039:2,2:26.8:1:29:1:1:1.20:54.8:4:0.0032:0:2 0/1:962:109:56,53:440,384:0.1133:2,2:24.5:1:31.2:1:0.75945:1.08435:60:35.333:0.1153:0:1.7 -20 46281061 . T TA 148 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.26791;SOR=0.67922;LSEQ=CCCTCCACCCCCACCTCCTT;RSEQ=AAAAAAAAAACAAAATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:33:33,0:322,9:0.0894:1,1:22.7:1:29.4:1:1:0:59.1:66:0.0892:0.0244:0.4 0/1:208:13:11,2:182,7:0.0625:1,2:30.9:1:29.1:1:0.1066:4.66204:60:26:0.0631:0:0.7 -20 46281422 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09899;SOR=Inf;LSEQ=CCTTTTTGGATGGAGAGGTT;RSEQ=AAAGGACTGGGTTCATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:19,213:0:2,0:24.4:1:31.3:1:1:0:60:57:1:0:0.1 0/1:107:2:1,1:5,100:0.0187:1,2:22:0:30.5:1:0.1095:18.34:60:4:0.0187:0:1.5 -20 46281500 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07544;SOR=Inf;LSEQ=CAAGCACGCACATATCTATT;RSEQ=GGGTGTCTAGTACAGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:82,54:0:2,0:22.3:1:29.9:1:1:0:60:135:1:0:0 0/1:52:2:1,1:33,17:0.0385:2,2:7.5:1:31.5:1:1:1.91492:60:4:0.04:0:1 -20 46282222 . T C 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGACACTGCACTAGGATTA;RSEQ=TGGGAAGGAATCATTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:0:0,0:337,388:0:2,0:24.3:1:29.9:1:1:0:60:35.25:1:0:0.2 0/1:498:26:13,13:213,259:0.0522:2,2:26.5:1:31.4:1:0.68809:1.22:60:52:0.0532:0:1.2 -20 47416665 . T A 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=TACACTCATTTAAACTTCAC;RSEQ=ACAACCCTTAAGGTAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:1,3:1,4:0.4:2,2:21:1:30:1:1:1.29:60:8:0.5:0:1 0/0:5:0:0,0:2,3:0:2,0:29:1:24.6:1:1:0:60:4:1:0:0.2 -20 47418179 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACACCCACGTCTCTCCCC;RSEQ=GGGCTGTTGCAGTCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:28.5:1:1:0:60:4:1:0:1 -20 48191784 . G A 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=1.20595;LSEQ=TGGGAGGATTGCTTGAACCC;RSEQ=GGAGGTAGAGGTTGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:6,0:16,0:0.2727:1,0:21.5:1:31.7:1:1:0:58.2:12:0.2857:0:1 0/1:16:5:5,0:10,1:0.3125:2,0:19.2:1:27.6:1:1:0:60:10:0.3125:0:1 -20 48191854 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55169;SOR=0;LSEQ=GGGCGACGGAGTGAGACCCT;RSEQ=TCTTAGCAACAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:0,2:70,42:0.0174:2,0:22:1:29.5:1:0.14687:0:60:4:0.0174:0:1 0/0:58:0:0,0:32,26:0:2,0:24.5:1:31.6:1:1:0:60:116:1:0:0.1 -20 48191860 . GCAA G 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0.9921;LSEQ=CGGAGTGAGACCCTGTCTTA;RSEQ=CAACAACAACACAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:77,47:0.0157:2,2:14:0:33.5:1:1:1.63157:60:4:0.0157:0:0.5 0/1:64:1:1,0:34,28:0.0156:2,0:39:0:34:0:1:0:60:2:0.0159:0:0 -20 48191871 . AACACAG A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.1258;SOR=Inf;LSEQ=CCTGTCTTAGCAACAACAAC;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:83,58:0:2,0:25.9:1:30.2:1:1:0:60:69.5:1:0:0.2 0/1:78:2:1,1:40,36:0.0256:2,2:39.5:1:31:1:1:1.10961:60:4:0.026:0:0 -20 48191877 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.54447;SOR=0;LSEQ=TTAGCAACAACAACAACACA;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:85,64:0.0132:2,2:28.5:1:28.5:1:1:1.32559:60:4:0.0135:0:1 0/0:81:0:0,0:41,38:0:2,0:24.1:1:32.1:1:1:0:60:78:1:0:0.2 -20 48191955 . C G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15349;SOR=Inf;LSEQ=ATTACCAAGTATTTATTTGC;RSEQ=AACACTGTGCAGGCCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:13,39:0:2,0:24.3:1:31.9:1:1:0:60:104:1:0:0.1 0/1:34:2:1,1:10,22:0.0588:2,2:13:1:27:1:1:2.14:60:4:0.0625:0:2 -20 48450753 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATATATATATATATATATA;RSEQ=ACACACACACTATGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:0,12:3,0:0.8:0,0:8:1:27.2:1:0.0022:0:59.9:24:0.8:0:1.1 1/1:2:2:0,2:0,0:1:0,0:7:0:27:1:1:0:60:4:1:0:1 -20 48450851 . G GTA 29 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.10784;SOR=10.41485;LSEQ=ACACACTATATATACAGTGT;RSEQ=TATATATATATATACTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:9,3:0.1333:2,2:32:1:31.3:1:0.50549:2.73861:57.5:4:0.1429:0:2 1/0:3:2:0,2:0,1:0.6667:0,0:18.5:1:29:1:1:0:60:4:0.6667:0.3333:0 -20 48450866 . C CTG 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGTGTATATATATATATA;RSEQ=TGTGTATATATATATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:4,3:0.3846:2,0:30:1:32.7:1:0.20455:0:52.8:10:0.4167:0.0769:0 0/0:1:0:0,0:0,1:0:0,0:17:0:34:0:1:0:60:2:1:0:0 -20 48450870 . GTA G 33 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTATATATATATATACTGT;RSEQ=TATATATATATACTGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:9,2:0.1538:2,2:45:1:33:1:0.42308:3.87298:42:4:0.1538:0:4.5 0/0:1:0:0,0:0,1:0:0,0:12:0:30:0:1:0:60:2:1:0:0 -20 48450887 . GTA G 44 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTATATATATATATACT;RSEQ=TATATATATATACTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,0:0.3:0,0:29.3:1:28:1:1:0:53:6:0.3:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 48450891 . ATATATATATACTGTG A 48 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATATATATATACTGTAT;RSEQ=TATATATATATATACTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,1:0.3:2,0:37:1:30.3:1:1:0:60:6:0.3333:0:0 0/0:1:0:0,0:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:1 -20 48450900 . T C 33 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATACTGTATATATATATA;RSEQ=ACTGTGTATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,0:0.2:0,2:18:1:33.5:1:0.33333:0:42:4:0.3333:0:4.5 0/0:1:0:0,0:1,0:0:0,0:9:0:32:0:1:0:60:2:1:0:1 -20 48450903 . T A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACTGTATATATATATATAC;RSEQ=GTGTATATATATATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,0:0.2:0,2:15:1:32.5:1:0.33333:0:42:4:0.4:0:4.5 0/0:1:0:0,0:1,0:0:0,0:12:0:33:0:1:0:60:2:1:0:1 -20 48450906 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTATATATATATATACTGT;RSEQ=TATATATATATATACTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,0:0.2222:0,2:12:1:30:1:0.4:0:42:4:0.5:0:4.5 0/0:1:0:0,0:1,0:0:0,0:15:0:34:0:1:0:60:2:1:0:1 -20 48450925 . G A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=2;SSF=0.10714;SOR=Inf;LSEQ=TGTATATATATATATACTGT;RSEQ=TATATATATATACTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:5,0:0.1667:0,0:16:0:29:0:1:0:39:2:0.1667:0:1 1/1:2:2:2,0:0,0:1:0,0:21:1:29:0:1:0:60:4:1:0:1 -20 48450944 . ATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG A 43 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=8.000;MSILEN=2;SSF=0.2;SOR=0;LSEQ=TGTATATATATATACTGTGT;RSEQ=TATATATATATATACTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:3,0:0.5:0,2:5.3:1:27.3:1:1:0:60:6:0.5:0.3333:0.7 0/0:4:0:0,0:4,0:0:0,0:23.3:1:30.8:1:1:0:60:8:1:0:0.8 -20 48450957 . G GTA 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1;LSEQ=ACTGTGTATATATATATACT;RSEQ=TATATATATACTGTATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,0:0.2857:0,0:23:1:30.3:1:1:0:45.5:4:0.3333:0.1429:1.5 0/1:7:2:2,0:5,0:0.2857:0,0:6:1:30.1:1:1:0:60:4:0.2821:0.2857:2 -20 48450987 . C TACTG 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.04482;SOR=0;LSEQ=ACTGTATATATATATATATA;RSEQ=TGTATATATATATACTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:10:9,1:25,0:0.2778:1,2:11.5:1:29.8:1:0.28571:0:58:20:0.2857:0.1944:1 0/0:13:0:0,0:13,0:0:1,0:26.3:1:27.1:1:1:0:59.8:12:1:0:0.8 -20 48451006 . G GTA 116 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.13054;SOR=0.29298;LSEQ=ACTGTATATATATATACTGT;RSEQ=TATATATATATATACTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:15:13,2:28,1:0.2778:1,2:24.5:1:29.8:1:0.26427:4.15305:60:30:0.3061:0.0185:0.3 0/1:20:2:2,0:16,1:0.1:1,0:32:1:27:1:1:0:60:4:0.1111:0:1 -20 48451012 . A ACAGTGTGTGTATATACATAGTGTGTGTG 79 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=2;SSF=0.00065;SOR=Inf;LSEQ=TATATATATACTGTGTATAT;RSEQ=TATATATACTGTATATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:51,7:0:2,0:25.9:1:29:1:1:0:59.7:116:0.9508:0:0.5 0/1:28:6:6,0:19,2:0.2143:2,0:17.7:1:30.9:1:1:0:60:12:0.2222:0.2143:1 -20 48451022 . T A 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0.19815;SOR=1.63046;LSEQ=CTGTGTATATATATATATAC;RSEQ=GTATATATACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:28:25,3:62,9:0.2828:2,2:8.4:1:30.6:1:1:1.21:59.4:56:0.2857:0:1.1 0/1:51:20:15,5:28,3:0.3922:2,2:10.2:1:29.8:1:0.2367:3.03828:60:40:0.4082:0:1.2 -20 48451030 . TAC T 57 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.68467;SOR=1.57109;LSEQ=ATATATATATACTGTATATA;RSEQ=ACACACACACTATATATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:4:3,1:109,16:0.0308:2,2:34.5:1:28.5:1:0.43586:2.25203:60:8:0.0313:0.0077:0.3 0/1:63:3:1,2:53,9:0.0476:2,2:10:1:25.7:1:0.07177:11.07065:60:8:0.0441:0.0381:2 -20 48451129 . A T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0629;LSEQ=TAGATTGATTTGACCTAACT;RSEQ=TGAGCCTCAATCTCAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:481:426:209,217:26,29:0.8857:2,2:27:1:30:1:0.88626:1.07:60:70:0.8879:0:1.1 0/1:346:113:58,55:126,107:0.3266:2,2:26.9:1:29.9:1:0.64736:1.1163:60:112:0.3246:0:1.1 -20 48451219 . T C 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01927;SOR=0.52106;LSEQ=ATAATAACAATAATATCACA;RSEQ=TGTATTTTACAGCGCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:64:15,49:20,81:0.3879:2,2:26.7:1:31.6:1:0.6963:1.24:60:31:0.3875:0:1.3 0/1:113:28:6,22:15,70:0.2478:2,2:20.4:1:31.7:1:0.77975:1.27:60:56:0.2523:0:1.4 -20 48631241 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTCATCTGGGTAAGCTGGT;RSEQ=TGTCTTTGTGTGTTGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:29.7:1:29.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 48631321 . A G 80 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=ATCTAGGAAGGGTGTCAGGC;RSEQ=GTGTGAGTCAGCGTGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:20.8:1:30.4:1:1:0:60:10:1:0:1.4 1/0:8:6:3,3:1,1:0.75:2,2:19.3:1:31:1:1:1:60:12:0.75:0:1.8 -20 48631365 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=0;LSEQ=GGCTGTGTGTGTGAGCAGGG;RSEQ=TCCGTTCTGAGAGTGCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:18.5:1:30.5:1:1:1.41:60:4:0.2857:0:1.5 0/0:10:0:0,0:5,5:0:2,0:24.7:1:31.2:1:1:0:60:20:1:0:1.3 -20 48631385 . G C 78 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03571;SOR=Inf;LSEQ=GTCCGTTCTGAGAGTGCGTT;RSEQ=TGTACGTGTGTGTCAGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:0:32:1:1:0:60:4:1:0:1.5 1/1:6:6:3,3:0,0:1:0,2:12.8:1:30.5:1:1:0:60:12:1:0:1.8 -20 48631777 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.17505;SOR=Inf;LSEQ=AGCCCCCTGCCTGCCGGCCC;RSEQ=CCCATCGGGGTGGGAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:31,10:0:2,0:24.9:1:29.9:1:1:0:60:40:1:0:0 0/1:30:2:1,1:19,9:0.0667:2,2:13.5:1:28.5:1:1:2.05485:60:4:0.0667:0:1 -20 48631827 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59381;SOR=2.38856;LSEQ=AGTAACAAATGTCCTGTAGC;RSEQ=AGCGTGGAGTCAGCGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:0,1:47,49:0.0103:2,0:1:0:23:0:1:0:60:2:0.0105:0:1 0/1:82:2:1,1:38,42:0.0244:2,2:49:1:30:0:1:1.10:60:4:0.0247:0:2 -20 48631860 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21777;SOR=Inf;LSEQ=GCGTGGAGCCGGCATGGAGG;RSEQ=AGCCCCCGCCCCACAGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:38,54:0:2,0:28.6:1:32.4:1:1:0:60:184:1:0:0.1 0/1:81:2:1,1:35,44:0.0247:2,2:30:0:31:1:1:1.25:60:4:0.025:0:1.5 -20 48631873 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20769;SOR=Inf;LSEQ=ATGGAGGCAGCCCCCGCCCC;RSEQ=CAGCGGGGGGTAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:31,52:0:2,0:25.1:1:29.7:1:1:0:60:166:1:0:0.1 0/1:70:2:1,1:30,38:0.0286:2,2:30:0:32.5:1:1:1.26:60:4:0.029:0:1.5 -20 48631877 . CG C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.23106;SOR=Inf;LSEQ=AGGCAGCCCCCGCCCCACAG;RSEQ=GGGGGTAGAGAGAGAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:26,48:0:2,0:24.7:1:30.2:1:1:0:60:73:1:0:0.1 0/1:69:2:1,1:29,37:0.029:2,2:25:0:33:1:1:1.27:60:4:0.0294:0:0.5 -20 48631884 . TAG T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.6717;SOR=1.63208;LSEQ=CCCCGCCCCACAGCGGGGGG;RSEQ=AGAGAGAGAGTATAAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:19,40:0.0328:2,2:17:1:30:1:1:2.08:60:4:0.0328:0.0164:0 0/1:57:3:1,2:24,30:0.0526:2,2:23:1:31.3:1:1:1.58736:60:6:0.0545:0:0.3 -20 48807628 . G T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCCTGCCGCCGCCGCCGCCT;RSEQ=CCTTTAAATCCATGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:29.5:1:31:1:1:0:60:8:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:38.5:1:29:1:1:1:60:4:0.4:0:1 -20 48808321 . G A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.30246;SOR=0;LSEQ=CCCCGACCGCCTGCTACGCG;RSEQ=GGGCCGCGCCGGCGCCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:255,16:0.0109:2,2:25.7:1:24.3:1:0.17542:7.82897:60:2:0.0075:0:2.7 0/0:158:0:0,0:145,13:0:2,0:20.2:1:31.2:1:1:0:60:51.667:1:0:0.1 -20 51363052 . A C 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGCAGCAGCATTAGATT;RSEQ=TCATAGGAGTGCGAACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:2,6:0,0:1:0,2:19.6:1:32.6:1:1:0:60:16:1:0:1 1/1:2:2:0,2:0,0:1:0,0:49:1:34:0:1:0:60:4:1:0:1 -20 51970878 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10914;SOR=Inf;LSEQ=GTGTTGATTTGAAAACTTCT;RSEQ=ATATTCTTTCTTTTAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:163,63:0:2,0:23.1:1:27.9:1:1:0:60:21.6:1:0:0.3 0/1:112:2:1,1:74,36:0.0179:2,2:21.5:1:29.5:1:1:2.0413:60:4:0.0182:0:2 -20 51970913 . G C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1134;SOR=Inf;LSEQ=AGGAGATCTTCTTGATAGTT;RSEQ=CAGAAATTCTGACTGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:227,161:0:2,0:25.1:1:31.7:1:1:0:60:63.667:0.9974:0:0.4 0/1:198:2:1,1:108,87:0.0101:2,2:9:0:33:0:1:1.24:60:4:0.0103:0:1 -20 51970961 . T A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.51885;LSEQ=GTCTTGCTATTTGGCTTGTA;RSEQ=AGTAGCAGCATAAAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:184:91,93:126,147:0.4026:2,2:25.9:1:29.7:1:0.50489:1.14:60:45:0.3991:0:1.1 1/0:243:153:81,72:41,48:0.6296:2,2:25.6:1:29.7:1:0.35104:1.32:60:50:0.6303:0:1.1 -20 51971037 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54681;SOR=0;LSEQ=ACAAGAAGATGACTCAAACT;RSEQ=AGCCACTGCAAAGCAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:33,144:0.0112:2,2:29.5:1:28:1:0.34467:4.31:60:4:0.0114:0:1 0/0:94:0:0,0:24,70:0:2,0:25:1:30.8:1:1:0:60:22.5:1:0:0.3 -20 51971152 . T C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14383;SOR=Inf;LSEQ=AAACATGATTTAATTATATA;RSEQ=GTCTTGCCTGATTTTTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:0,6:0.6471:0,0:15.5:1:30.5:1:1:0:60:22:0.6471:0:1.1 1/1:6:6:0,6:0,0:1:0,0:25.8:1:29.8:1:1:0:60:12:1:0:1 -20 52240073 . CCCT C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.53629;SOR=0;LSEQ=TTAAAGTCCCCTTGGCTCTG;RSEQ=CCTCCTCCTCCTCGTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:1,2:13,7:0.1304:2,2:24.7:1:31:1:0.53755:3.49692:60:6:0.1364:0:0 0/0:10:0:0,0:7,3:0:2,0:26.9:1:30.4:1:1:0:60:20:1:0:0.1 -20 52776739 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24359;LSEQ=TAAGAAATTCAAACATTGAG;RSEQ=TGAGTACTCCAGCTACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:90:81,9:92,39:0.4072:2,2:25.1:1:30.1:1:0.00043:3.79:60:180:0.4128:0:1.9 0/1:91:13:9,4:53,25:0.1429:2,2:19.2:1:27.7:1:1:1.06:60:12:0.1348:0:2.1 -20 52776755 . C T 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0214;SOR=Inf;LSEQ=TGAGCTGAGTACTCCAGCTA;RSEQ=AGTTTCTGACAAAGGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:205,89:0:2,0:24.5:1:31.8:1:1:0:60:72.5:1:0:0.9 0/1:114:3:1,2:69,42:0.0263:2,2:14.3:1:26.7:1:0.5581:3.25059:60:6:0.0273:0:1 -20 52776769 . G T 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05484;SOR=0.66966;LSEQ=CAGCTACAGTTTCTGACAAA;RSEQ=GCCCACACCCTTTTAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:147:106,41:124,79:0.42:2,2:24.2:1:30.5:1:0.03983:1.64:60:294:0.4249:0:2 0/1:144:47:28,19:56,41:0.3264:2,2:25.6:1:29.1:1:0.85889:1.08:60:14.667:0.3165:0:1.7 -20 52776805 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08958;SOR=Inf;LSEQ=AGTGGCATCTTTTATTTCCT;RSEQ=TGCACAGGCAATGACTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:0:0,0:244,209:0:2,0:25.9:1:31.5:1:1:0:60:89.6:1:0:0.8 0/1:194:2:1,1:99,93:0.0103:2,2:34:1:30.5:1:1:1.06421:60:4:0.0104:0:1 -20 52776841 . A G 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=0.46214;LSEQ=TAGAGAAAAAATATTGGTGG;RSEQ=AACAGCCAATGTAGCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:203:90,113:114,123:0.4603:2,2:26.2:1:31.3:1:0.4443:1.16328:60:406:0.4645:0:1.5 0/1:177:50:20,30:61,66:0.2825:2,2:24.4:1:30.5:1:0.40276:1.38381:60:49:0.2784:0:1.6 -20 52776892 . T A 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=21.34236;LSEQ=ATTCACCACTAGTAGTCATA;RSEQ=GTATTTATTTTTTAGGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:0,1:96,212:0.0032:2,0:3:0:28:0:1:0:60:2:0.0033:0:1 0/1:123:8:2,6:40,75:0.065:2,2:14.4:1:31:1:0.7144:1.59434:60:16:0.0656:0:1.1 -20 52776917 . T C 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98071;LSEQ=TTATTTTTTAGGCCGTACTT;RSEQ=GCTAATTTAAGCCAAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:93:25,68:31,83:0.4493:2,2:24.6:1:29.7:1:1:1.01583:60:30:0.4455:0:1.4 0/1:72:32:8,24:9,31:0.4444:2,2:29:1:31.1:1:1:1.15:60:64:0.4444:0:1.5 -20 52777119 . G A 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCAGAGGACTGGCAGCCTC;RSEQ=GCTGCAAATAAACTGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:23:1:32:1:1:0:60:10:0.5556:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 52779052 . G A 63 d7;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=ATGGAGGCACCGTGGCGTCT;RSEQ=GTATGAGGCCGTGCGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:19:0:31.5:1:1:0:60:8:1:0:2.3 0/0:1:0:0,0:0,1:0:0,0:49:0:29:0:1:0:60:2:1:0:0 -20 52779082 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGCGCTGAGGCACCGTGG;RSEQ=ATAGATGCTGTGCGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:39:1:29.5:1:1:0:60:4:0.6667:0:3 0/0:1:0:0,0:0,1:0:0,0:22:0:34:0:1:0:60:2:1:0:0 -20 52908407 . ACAG A 30 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.21344;SOR=4.96199;LSEQ=CAGGCTCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:1:0,1:17,19:0.027:2,0:45:0:31:0:1:0:60:2:0.027:0:0 0/1:16:2:2,0:6,8:0.125:2,0:35.5:1:30.5:1:0.46667:0:60:4:0.125:0:3 -20 54944939 . C A 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACCATGCCTAGCACAGG;RSEQ=TGACGGGGCGGCTGCAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:3,1:8,0:0.3333:0,2:22.3:1:29:1:0.33333:0:60:8:0.3636:0:1 0/0:2:0:0,0:2,0:0:0,0:14.5:1:30.5:1:1:0:55.5:4:1:0:0 -20 54945145 . C T 208 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCAGTCAATGGTAAAATAAA;RSEQ=TTCAGTAGCATGTTCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:110:88,22:320,69:0.22:2,2:24.4:1:30.7:1:0.57824:1.15904:60:54:0.2204:0:1.1 0/0:257:0:0,0:204,53:0:2,0:21.4:1:31.4:1:1:0:60:127.5:1:0:0.1 -20 54945783 . A G 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96605;LSEQ=CACAACAGCTGCTAACAATC;RSEQ=TTAAAGAGTCCACTAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:57:1,56:3,141:0.2836:1,1:23.2:1:32:1:1:1.19048:60:56:0.2963:0:1.1 0/1:94:26:0,26:4,64:0.2766:2,1:24.4:1:30.3:1:0.57271:0:60:25:0.2717:0:1 -20 54956064 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAAACTATCCTAGCCAGG;RSEQ=ACAATGGTGTGCACCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:36.5:1:32:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 54956422 . G T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11524;SOR=5.90113;LSEQ=CCCACTCTACTATGATGAAA;RSEQ=GTACATTGCTATGGAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:1:1,0:424,128:0.0018:2,0:7:0:32:0:1:0:60:2:0.0018:0:1 0/1:283:3:0,3:210,70:0.0106:2,0:12:1:21.7:1:0.01664:0:60:2:0.0072:0:1 -20 54956707 . A G 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76674;SOR=0.88278;LSEQ=AAATGTCAAACAAACTCTTC;RSEQ=TGTAAAACCAGTGGTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:51:2,49:6,129:0.2742:1,1:21.3:1:32.5:1:1:1.13875:60:102:0.2757:0:1.1 0/1:84:21:1,20:2,61:0.25:1,1:20.4:1:30.4:1:1:1.52:60:42:0.25:0:1 -20 54957969 . G T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34419;SOR=2.9154;LSEQ=AAGGGACCTGGGCAGTGGGA;RSEQ=GCTGACATTACAGGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:2:1,1:340,135:0.0042:2,2:21.5:1:20:1:0.48937:2.51294:60:1:0.0022:0:3 0/1:247:3:1,2:173,70:0.0121:2,2:17.3:1:27:1:0.20579:4.90601:60:6:0.0123:0:1 -20 54959296 . G C 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11209;SOR=0.79876;LSEQ=TAATATATTCTAGTAGAACA;RSEQ=TACAGAACTTTGTAAATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:744:192:113,79:337,215:0.2581:2,2:23.5:1:31.8:1:0.60777:1.09569:60:384:0.2588:0:1.1 0/1:460:100:62,38:221,135:0.2174:2,2:25.5:1:31.5:1:1:1.00334:60:99:0.2162:0:1.1 -20 54959467 . C A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55489;SOR=0;LSEQ=AGGTGAATCAAAGAATTGGT;RSEQ=ACCAAAATATTAATGGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:3:1,2:7,203:0.014:1,2:17.3:1:21.3:1:0.10899:13.92:60:2:0.0102:0:3.7 0/0:97:0:0,0:7,90:0:2,0:27.3:1:30.8:1:1:0:60:9.778:1:0:0.1 -20 54959505 . GT G 52 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.55106;SOR=0;LSEQ=ATGTCAAGAATGATAAATCT;RSEQ=TTTTTTTTTTTAAAGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:3:0,3:0,96:0.0303:1,0:31.7:1:33:1:1:0:60:6:0.0316:0:0 0/0:48:0:0,0:0,48:0:1,0:20.1:1:30.1:1:1:0:59.6:47:1:0:0.1 -20 54959518 . A T 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.73716;LSEQ=TAAATCTGTTTTTTTTTTTT;RSEQ=AAGTTTTCCTTATAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:0,3:0,75:0.0385:1,0:10.7:1:27:1:1:0:60:6:0.0385:0:1.3 0/1:35:1:0,1:0,34:0.0286:1,0:34:0:30:0:1:0:60:2:0.0286:0:1 -20 54961073 . A G 106 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCAAAAGGACACCAATTT;RSEQ=TGCTGTGTCCTCCCTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:29.1:1:29.6:1:1:0:60:5:1:0:1 1/1:1:1:1,0:0,0:1:0,0:8:0:32:0:1:0:60:2:1:0:1 -20 54961214 . A C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55011;SOR=0;LSEQ=CCCATCCTCAACAGATATAA;RSEQ=AGCTAAGGCTCCAAACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:173,12:0.0107:2,2:15.5:1:34:0:0.13455:13.89107:60:4:0.0108:0:1 0/0:96:0:0,0:87,9:0:2,0:23.2:1:30.1:1:1:0:60:47:1:0:0.1 -20 54961236 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28033;SOR=3.74828;LSEQ=GCTAAGGCTCCAAACAATAA;RSEQ=TGCAAGTATATACACTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:1:0,1:249,63:0.0032:2,0:1:0:27:0:0.20447:0:60:2:0.0032:0:1 0/1:168:2:1,1:135,31:0.0119:2,2:16:1:30:1:0.34559:4.3021:60:4:0.0121:0:1 -20 54961463 . T C 294 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0737;LSEQ=CTTTTGTGCTTGCAAAGGAA;RSEQ=GCGCTGGGAAGAATTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:803:798:373,425:0,4:0.9938:0,2:24.8:1:30.5:1:0.12772:0:59.1:56:0.9962:0:1.1 1/1:548:505:237,268:23,18:0.9215:2,2:25.2:1:30.1:1:0.32941:1.44392:59.2:71.143:0.9222:0:1.2 -20 54961541 . A T 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.43343;SOR=1.11117;LSEQ=TAATGGATTCTGACAAGGAA;RSEQ=TTGCTGAGTCACGAGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:745:190:75,115:223,332:0.255:2,2:24.8:1:30:1:0.93166:1.02988:59.9:62.333:0.2548:0:1.4 0/1:508:140:55,85:156,212:0.2756:2,2:27.3:1:30.2:1:0.54678:1.13693:59.9:139:0.2774:0:1.4 -20 54961545 . C T 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00973;SOR=10.20223;LSEQ=GGATTCTGACAAGGAAATTG;RSEQ=TGAGTCACGAGAACACGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:1:0,1:292,434:0.0014:2,0:1:0:29:0:1:0:60:2:0.0014:0:1 0/1:505:7:2,5:206,292:0.0139:2,2:7.1:1:28.6:1:0.70536:1.76185:60:14:0.014:0:1.6 -20 54961651 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.11214;SOR=Inf;LSEQ=GCAAAAGATGAATATATTGA;RSEQ=AATTTCACAAAGTTTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:14,130:0:2,0:22.3:1:31.1:1:1:0:60:35:1:0:0.1 0/1:73:2:1,1:6,65:0.0274:2,2:11.5:1:28.5:1:0.18379:10.11:60:4:0.0278:0:1 -20 54963149 . C CGACAAGACCAACCTCCATGTGGGTTTATAAATGTGAATGAGATTACAGATTATTCAATTTA 305 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29977;SOR=0.89754;LSEQ=GTAAAGGCGGAAAGAATTCC;RSEQ=GACAAGACCAACCTCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1469:1145:650,495:252,66:0.7794:2,2:28.1:1:30.1:1:0:2.90573:59.6:380.667:0.7811:0.6501:0.1 1/0:826:628:357,271:138,57:0.7603:2,2:27.8:1:29.4:1:0.00058:1.8365:59.7:627:0.7609:0.6453:0 -20 54963303 . C T 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATTTGAACAAAGCCACCTG;RSEQ=TTAAAGTGCTGTTGCTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:665:0:0,0:190,474:0:2,0:25:1:32.3:1:1:0:60:220.333:0.9985:0:0.1 0/1:416:20:8,12:135,260:0.0481:2,2:27:1:29.3:1:0.63277:1.28:60:40:0.0488:0:1.1 -20 54963331 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12771;SOR=5.56761;LSEQ=GCTGTTGCTCGATAGGCAGC;RSEQ=TTACAGTTCCCCAATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:416:1:1,0:86,329:0.0024:2,0:1:0:25:0:0.20913:0:60:2:0.0024:0:1 0/1:226:3:2,1:55,168:0.0133:2,2:19:1:28:1:0.15749:6.05:60:6:0.0136:0:1 -20 54963739 . T G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGCTGAGCGTGGTGGCAG;RSEQ=CACCTGTAATCCCAGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:17.7:1:31:1:1:0:48:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 55177781 . C T 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCAGGAGAATCACTTGAACT;RSEQ=GGGAAGTGGAGGTTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:35.7:1:30.3:1:1:0:60:6:0.75:0:1.3 0/0:2:0:0,0:2,0:0:0,0:13:1:31:1:1:0:60:4:1:0:0 -20 55177856 . CA C 61 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.26769;SOR=0;LSEQ=GACAGAGCGAGACTCTACCT;RSEQ=AAAAAAAAAAAGCTGCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:0.2222:1,0:17:1:30.7:1:1:0:60:8:0.2222:0.0556:0.5 0/0:9:0:0,0:8,0:0:0,0:17.9:1:29.1:1:1:0:60:16:0.8889:0:0 -20 55178081 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18134;LSEQ=TGGACATTTATGTGTTCCAT;RSEQ=GCAATACACGTATACATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:437:233:113,120:92,111:0.5332:2,2:26.4:1:29.6:1:0.56395:1.14:60:115.5:0.5347:0:1.1 0/1:327:56:25,31:132,139:0.1713:2,2:23.3:1:28.8:1:0.65991:1.17697:60:55:0.1708:0:1.1 -20 55178144 . A AT 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.16749;SOR=Inf;LSEQ=ATGTACGTATGCCTTCCTGG;RSEQ=TTTTAAAAATACATTAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:70,166:0:2,0:23.3:1:30.5:1:1:0:60:77.667:1:0:0.4 0/1:164:2:1,1:51,111:0.0122:2,2:31:1:29.5:1:0.53494:2.17:60:4:0.0122:0:0 -20 55178239 . C G 149 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=4e-05;SOR=0.06653;LSEQ=ACCCACCACTCACCTGCCTT;RSEQ=CCCACTTCCAGGCAGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:26:0,26:0,20:0.5652:1,1:29.3:1:31.8:1:1:0:60:52:0.5778:0:1.2 0/1:26:2:0,2:0,24:0.0769:1,0:10.5:1:24:1:1:0:60:1:0.0417:0:3 -20 57414681 . C A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGGCCCACTAGGGTCTGCGC;RSEQ=ACAGGCTCGGCGCCACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:35:1:31:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 57415082 . G T 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2211;SOR=4.59687;LSEQ=CATAGGGTGTACCTTTCCCG;RSEQ=CTCCAGCAGCCAATGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:0,1:389,41:0.0023:2,0:15:0:25:0:0.09745:0:60:2:0.0024:0:2 0/1:189:2:1,1:157,30:0.0106:2,2:14.5:1:25:1:0.30187:5.16473:60:4:0.0106:0:1.5 -20 57415110 . A G 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01451;SOR=1.41298;LSEQ=AGCCAATGTGCTTCGGAGCC;RSEQ=CTCTCTGCAGAGCCAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:675:426:330,96:183,66:0.6311:2,2:24.1:1:30.3:1:0.26275:1.24:60:105.5:0.6317:0:1.1 1/0:376:266:184,82:79,31:0.7074:2,2:23.1:1:29.8:1:0.71084:1.13529:60:87.667:0.707:0:1.1 -20 57415294 . C A 74 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01855;SOR=6.12562;LSEQ=CCATCGCGCTCCTCCGCGCC;RSEQ=TTGCCACCTCCAACGCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1208:2:1,1:604,602:0.0017:2,2:25.5:1:22:1:1:1.00332:60:1:8e-04:0:1.5 0/1:596:6:3,3:295,295:0.0101:2,2:20.5:1:29:1:1:1:60:12:0.0102:0:1 -20 57415455 . C T 220 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=58.60221;LSEQ=GACCTTGAGCTGTCCCTCCC;RSEQ=GAGTGCCTAGAGTACGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1890:5:1,4:935,949:0.0026:2,2:7.6:1:26.8:1:0.37444:3.93825:60:10:0.0027:0:1 0/1:1122:151:79,72:503,462:0.1346:2,2:23.5:1:30.4:1:1:1.01:60:302:0.1354:0:1.1 -20 57415876 . C A 187 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=153.50466;LSEQ=AGTCCCCTTCCAAAAAGGGA;RSEQ=CCATCCCCATCCGGCGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1716:1:1,0:768,946:6e-04:2,0:1:0:25:0:0.4484:0:60:2:6e-04:0:1 0/1:1009:83:39,44:430,494:0.0823:2,2:24.3:1:29.4:1:1:1.02:60:40.5:0.0814:0:1.4 -20 57415962 . C T 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTAGTTGCCCACCGCTAAA;RSEQ=TGGGGAGCCTGAGGGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:702:0:0,0:197,504:0:2,0:26.4:1:32.1:1:1:0:60:86.625:0.9986:0:0.4 0/1:412:98:29,69:95,217:0.2379:2,2:23:1:29.6:1:0.90041:1.04154:60:48:0.2376:0:1.8 -20 57415967 . G A 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGCCCACCGCTAAACTGGG;RSEQ=AGCCTGAGGGCGGTGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:0:0,0:174,477:0:2,0:26:1:31.2:1:1:0:60:129.2:1:0:0.5 0/1:374:23:5,18:99,252:0.0615:2,2:20.7:1:29.6:1:0.63415:1.4131:60:46:0.062:0:2.4 -20 57415995 . A G 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06764;SOR=1.41905;LSEQ=GGGCGGTGTGGGAGCAGCGC;RSEQ=GGTGGAAAGGAGGTGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:392:263:43,220:22,107:0.6709:2,2:23.2:1:31.1:1:0.88553:1.05181:60:262:0.6718:0:1.1 1/0:222:165:26,139:11,45:0.7432:2,2:21.5:1:29.9:1:0.53611:1.30521:60:81.5:0.7443:0:1.4 -20 57416009 . T A 35 v4;q23;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55497;SOR=0;LSEQ=CAGCGCAGGTGGAAAGGAGG;RSEQ=GAGAAGGAAAGGCAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:3,0:33,251:0.0105:2,0:5.3:1:22.3:1:0.00183:0:60:2:0.0071:0:2.3 0/0:155:0:0,0:17,138:0:2,0:22.8:1:29.8:1:1:0:60:154:1:0:0.9 -20 57428215 . T G 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00328;SOR=Inf;LSEQ=AGGCCGGTGAACTTTCCAGC;RSEQ=GGTACTTTGATTTTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:197,2:0:1,0:20.7:1:31.3:1:1:0:60:65.333:1:0:0.1 0/1:95:5:5,0:90,0:0.0526:1,0:28.8:1:25.8:1:1:0:60:4:0.0426:0:1.2 -20 57428287 . C G 195 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGTGCTCCATCTTACGGAG;RSEQ=CCCAAACTTATTTTGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1037:78:58,20:701,258:0.0752:2,2:27.7:1:31.1:1:0.89458:1.07:60:25:0.0737:0:1.1 0/0:572:0:0,0:358,212:0:2,0:25.5:1:31.2:1:1:0:60:80.429:0.9982:0:0.2 -20 57429447 . C T 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=80.07843;LSEQ=GGGAGGAAAAGTACCCTCTC;RSEQ=GGGGTACGGATCCCCTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:886:1:0,1:375,510:0.0011:2,0:1:0:26:0:1:0:60:2:0.0011:0:1 0/1:420:35:18,17:158,226:0.0833:2,2:22.4:1:31.3:1:0.28374:1.51:60:70:0.0847:0:1.1 -20 57429607 . C T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00544;SOR=Inf;LSEQ=GGGGCATTCGCAGCCGATCC;RSEQ=GACTCCGGGGCAGCCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:733:0:0,0:263,468:0:2,0:25.4:1:29.6:1:1:0:59.9:33.81:0.9986:0:0.2 0/1:401:5:3,2:159,236:0.0125:2,2:24.4:1:29.4:1:0.39858:2.22:60:10:0.0126:0:1.2 -20 57429626 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12963;SOR=3.26278;LSEQ=CCGACTCCGGGGCAGCCCCT;RSEQ=CCGCCCCAGCCGATCCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:644:3:2,1:199,441:0.0047:2,2:25:1:26.7:1:0.23168:4.42:60:6:0.0048:0:1 0/1:332:5:3,2:122,205:0.0151:2,2:14.2:1:26:1:0.36896:2.51:60:10:0.0154:0:1.4 -20 57429627 . C A 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGACTCCGGGGCAGCCCCTG;RSEQ=CGCCCCAGCCGATCCCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:640:0:0,0:195,445:0:2,0:25.4:1:31.1:1:1:0:59.9:36.647:1:0:0.2 0/1:327:31:14,17:109,187:0.0948:2,2:27.3:1:27.9:1:0.43617:1.41:56.2:30:0.0943:0:1.3 -20 57429687 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59643;SOR=2.13139;LSEQ=CCCAGCCGATCCCGACTCCG;RSEQ=GGCGGCCCCTGACGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:2:2,0:81,235:0.0063:2,0:1:0:27.5:1:0.06752:0:60:4:0.0064:0:1 0/1:150:2:2,0:45,102:0.0133:2,0:9:1:28:1:0.09804:0:60:4:0.0133:0:1 -20 57429696 . C G 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01222;SOR=Inf;LSEQ=TCCCGACTCCGGGGCGGCCC;RSEQ=TGACGCCCCAGCCGATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:77,194:0:2,0:24.6:1:32:1:1:0:59.6:53.2:1:0:0.1 0/1:137:4:2,2:44,89:0.0292:2,2:19:1:29:1:0.60208:2.01:60:8:0.0296:0:1.5 -20 57429716 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55364;SOR=0;LSEQ=CTGACGCCCCAGCCGATCCA;RSEQ=ATGCCGGGGCGGCCCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:73,140:0.0139:2,2:27:1:28:1:0.27699:3.81:60:6:0.0141:0:1 0/0:111:0:0,0:48,63:0:2,0:21.7:1:31.1:1:1:0:59.3:36:1:0:0.4 -20 57429741 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12723;SOR=Inf;LSEQ=CGGGGCGGCCCCTGAGGCTC;RSEQ=CGCCGCCCCTGCGGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:85,71:0:2,0:21.9:1:30.6:1:1:0:60:30.2:1:0:0.2 0/1:87:2:1,1:42,43:0.023:2,2:22:1:31.5:1:1:1.02:60:4:0.023:0:1 -20 57429743 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.952;LSEQ=GGGCGGCCCCTGAGGCTCCC;RSEQ=CCGCCCCTGCGGCTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:93,65:0.0125:2,2:25:1:28.5:1:1:1.42748:60:4:0.0127:0:1 0/1:84:1:1,0:44,39:0.0119:2,0:1:0:25:0:1:0:60:2:0.0119:0:1 -20 57429767 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21927;SOR=4.64769;LSEQ=CCCCTGCGGCTGCTGAGACC;RSEQ=GGGCAGCCCATGTCGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:0,1:156,59:0.0046:2,0:1:0:26:0:0.27778:0:60:2:0.0047:0:1 0/1:94:2:1,1:61,31:0.0213:2,2:21:1:29:1:1:1.95263:60:4:0.0215:0:1 -20 57429782 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0945;SOR=Inf;LSEQ=AGACCCGGGCAGCCCATGTC;RSEQ=CCCCAGCTGCGCCAGACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:215,60:0:2,0:23.3:1:30.5:1:1:0:60:54:0.9963:0:0.2 0/1:123:2:1,1:87,34:0.0163:2,2:26:1:28:1:0.4898:2.53646:60:4:0.0165:0:1 -20 57429940 . G A 81 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00986;SOR=6.73451;LSEQ=GAGATCCAGGCTGCCGATCC;RSEQ=CCTACTCCGCGGCCTACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1304:2:1,1:648,654:0.0015:2,2:16:1:29:1:1:1.01:60:4:0.0016:0:1 0/1:683:7:4,3:326,350:0.0102:2,2:32.6:1:29.1:1:0.71699:1.43:60:14:0.0105:0:1 -20 57430051 . C T 82 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00256;SOR=8.54707;LSEQ=AGCAGCGACGATGACTCCAG;RSEQ=GGAGACGAGTCCGACGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:933:2:0,2:532,398:0.0021:2,0:1:0:25.5:1:0.18394:0:60:4:0.0022:0:1 0/1:443:8:5,3:250,184:0.0181:2,2:23.5:1:27.4:1:1:1.23:60:7:0.0162:0:1 -20 57430477 . C G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=3.28323;LSEQ=CCTGGTGGGGCTAGGGGCTC;RSEQ=GCAGTGGGAGGAGGGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:48:0,48:1,186:0.2034:1,1:26.5:1:31.3:1:1:0:60:96:0.2069:0:1.3 0/1:70:32:1,31:1,37:0.4571:1,1:29.7:1:29.5:1:1:1.19:60:31:0.4493:0:1.1 -20 57430493 . G A 25 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCGCAGTGGGAGGAGGG;RSEQ=GTCCAGCCAAAGGCGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:0,2:1,189:0.0104:1,0:35.5:1:25.5:1:1:0:60:4:0.0106:0:4.5 0/0:54:0:0,0:1,53:0:1,0:22.6:1:29.7:1:1:0:60:17:1:0:0.6 -20 57466761 . CCCG C 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.09768;SOR=3.51281;LSEQ=CCGCCGCAGCCCGGCCGCGC;RSEQ=CCGCCGCCGCCGCCGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:3:3,0:171,35:0.0141:2,0:8.7:1:31.1:1:1:0:60:6:0.0142:0.0094:0 0/1:146:7:5,2:100,38:0.0479:2,2:8.4:1:31.6:1:1:1.05226:59.3:14:0.0479:0.0205:0.3 -20 57466764 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.16967;SOR=Inf;LSEQ=CCGCAGCCCGGCCGCGCCCC;RSEQ=CCGCCGCCGCCGCCGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:189,40:0:2,0:11.4:1:30.1:1:1:0:60:44.8:1:0:0.2 0/1:163:2:1,1:111,44:0.0123:2,2:21:0:32:0:0.49241:2.50576:60:4:0.0127:0:1.5 -20 57466776 . G A 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.01254;SOR=Inf;LSEQ=CGCGCCCCGCCGCCGCCGCC;RSEQ=CCGCCATGGGCTGCCTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:305,103:0:2,0:15.9:1:30.3:1:1:0:60:50:0.9975:0:0.2 0/1:294:5:3,2:197,91:0.017:2,2:25.2:1:28.8:1:0.65404:1.44134:60:10:0.0174:0:1 -20 57466901 . G A 99 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09669;SOR=2.35948;LSEQ=AAGCAGGTCTACCGGGCCAC;RSEQ=CACCGCCTGCTGCTGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:929:6:4,2:333,590:0.0065:2,2:23.2:1:29.2:1:0.19738:3.54:60:12:0.0066:0:1.5 0/1:794:12:10,2:304,477:0.0151:2,2:9.6:1:27.8:1:0.0024:7.83:60:24:0.0153:0:1.2 -20 57466907 . CCTG C 88 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.36324;SOR=2.07778;LSEQ=GTCTACCGGGCCACGCACCG;RSEQ=CTGCTGCTGGGTAAGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:807:4:1,3:264,538:0.005:2,2:29.3:1:31.5:1:1:1.47146:60:8:0.005:0.0012:0.3 0/1:683:7:3,4:252,423:0.0102:2,2:24.1:1:31.4:1:0.71657:1.26:60:14:0.0104:0.0029:0.6 -20 57467859 . CT C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTCATTTTACAGTGTGAC;RSEQ=TTTTTTCCCCTTCCAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:31.5:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 57470517 . G A 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.11015;LSEQ=GATTTCCTTTTCTCTGCGTC;RSEQ=AAATGTCAAGGAAAGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:9:9,0:80,0:0.1011:1,0:28.4:1:29.8:1:1:0:60:18:0.1011:0:1.1 0/1:36:4:4,0:32,0:0.1111:1,0:19.3:1:29.8:1:1:0:60:8:0.1176:0:1 -20 57473892 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20299;SOR=Inf;LSEQ=CTGGCGCGCGAATTGTTGCT;RSEQ=TTGCTCTTGGCTGATGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:110,15:0:2,0:23:1:30.3:1:1:0:60:30.25:1:0:0.1 0/1:103:2:1,1:83,18:0.0194:2,2:13:0:31:1:0.33638:4.5151:60:4:0.0194:0:1 -20 57473904 . T C 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0815;SOR=Inf;LSEQ=TTGTTGCTTTTGCTCTTGGC;RSEQ=GATGGTTGAGGAATGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:132,30:0:2,0:24:1:30.5:1:1:0:60:26:1:0:0.1 0/1:125:3:2,1:94,28:0.024:2,2:17:1:22:1:0.55034:1.67075:60:2:0.0164:0:1 -20 57473962 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08824;SOR=Inf;LSEQ=TGTGACACTGCGGTGCCTTG;RSEQ=AGATTAGGTGAGCTTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:201,123:0:2,0:25.1:1:31.4:1:1:0:60:28.455:1:0:0.1 0/1:261:3:2,1:157,100:0.0115:2,2:16.7:1:26.7:1:1:1.27:60:6:0.0116:0:1 -20 57473997 . G T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14292;SOR=0;LSEQ=TTCAATCTCTCTTTAAAAGG;RSEQ=GCGGCGAAGAGGACCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:4:1,3:209,177:0.0103:2,2:37.5:1:29.8:1:0.339:3.53171:60:8:0.0106:0:1.3 0/0:283:0:0,0:151,129:0:2,0:24.4:1:30:1:1:0:60:69:0.9928:0:0.1 -20 57478448 . A T 107 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00884;SOR=3.96066;LSEQ=ATGTTTATTCAGCTACCTCC;RSEQ=ATCTTTGCACAGATCCGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:6:6,0:83,5:0.0638:2,0:29.3:1:31.8:1:1:0:60:12:0.0645:0:1.2 0/1:56:12:10,2:39,5:0.2143:2,2:20.4:1:30.1:1:0.63475:1.54647:60:11:0.2:0:1.1 -20 57478807 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.36332;LSEQ=CAGTTCAGAGTGGACTACAT;RSEQ=CTGAGTGTGATGAACGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:961:111:48,63:400,447:0.1155:2,2:25.1:1:29.6:1:0.47913:1.1743:60:26.75:0.1133:0:1.1 0/1:757:312:147,165:211,232:0.4122:2,2:25:1:28.6:1:0.94101:1.02083:60:25:0.4076:0:1.2 -20 57478939 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05372;LSEQ=GACAGCCCTGCACATGGGCA;RSEQ=GAGCATCCAAACCACACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:195:183:4,179:0,12:0.9385:0,1:24.8:1:31.5:1:1:0:60:366:0.9385:0:1.1 0/1:94:42:4,38:2,50:0.4468:1,2:23:1:31.3:1:0.40212:2.60:60:84:0.4516:0:1.1 -20 57480545 . C T 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=Inf;LSEQ=TGTGCCCAGTAGTAAGTAAC;RSEQ=GCCACCCAACCCATCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:183,305:0:2,0:25.2:1:29.8:1:1:0:60:43.364:1:0:0.1 0/1:394:10:5,5:151,233:0.0254:2,2:14:1:27.9:1:0.52594:1.54:60:9:0.0233:0:1.2 -20 57483948 . G A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=3.83897;LSEQ=TGTTTGTGTGGCCCCACTGC;RSEQ=TCGAGGCCACAGGCTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:35.6:1:30.2:1:1:0:60:10:0.625:0:1.6 1/1:8:7:6,1:1,0:0.875:0,2:18:1:31:1:1:0:60:14:0.875:0:1 -20 57484085 . T C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06362;SOR=2.68708;LSEQ=AACCAACACACAAGCAAATG;RSEQ=GCCATTGACTTAGTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:8:8,0:101,5:0.0702:1,0:30.8:1:32.4:1:1:0:60:16:0.0714:0:1 0/1:59:10:10,0:47,2:0.1695:1,0:20.2:1:32.1:1:1:0:60:9:0.1552:0:1.1 -20 57484241 . C T 136 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.53372;LSEQ=CTGGACAAGATCGACGTGAT;RSEQ=AAGCAGGCTGACTATGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:4:1,3:397,313:0.0056:2,2:14.8:1:22.5:1:0.32694:3.79843:60:3:0.0042:0:1.3 0/1:499:28:15,13:248,223:0.0561:2,2:24.3:1:28.4:1:1:1.04:60:56:0.0567:0:1.3 -20 57484661 . G A 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=26.32704;LSEQ=TGCTGTGGGCTTGGCTGTTC;RSEQ=TAAAGAACGCTTTGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:1:1,0:299,249:0.0018:2,0:1:0:25:0:1:0:60:2:0.0018:0:1 0/1:458:21:13,8:231,205:0.0459:2,2:26.5:1:29.7:1:0.50506:1.44:60:20:0.0442:0:1.1 -20 57484934 . C T 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06391;SOR=0.73045;LSEQ=CTGTTTATAGAGAAGAACCC;RSEQ=GTGCAAGCATTCCAGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:147:66,81:176,196:0.2832:2,2:21.7:1:30.1:1:0.62693:1.10183:60:28.4:0.2779:0:1.2 0/1:326:73:33,40:127,125:0.2239:2,2:21.7:1:30.4:1:0.50651:1.23072:60:35.5:0.2205:0:1.1 -20 57485201 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55912;SOR=3.35274;LSEQ=CTTTTTCAAACGGTCAGGCT;RSEQ=AAAACCCCCATCCCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:46,221:0.0037:2,0:1:0:30:0:1:0:60:2:0.0038:0:1 0/1:162:2:1,1:28,132:0.0123:2,2:8.5:1:27:1:0.32689:4.65:60:4:0.0129:0:1.5 -20 57485324 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14589;SOR=Inf;LSEQ=AAGACTTCAGGAGCTACAGA;RSEQ=ATGCTAGCACCCCAGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:172,78:0:2,0:25.9:1:31.8:1:1:0:60:82.333:1:0:0.1 0/1:155:2:1,1:111,42:0.0129:2,2:24:1:27.5:1:0.47918:2.62369:60:4:0.013:0:1 -20 57485489 . G A 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TGTCTTTAGTTTCCTCTCTT;RSEQ=TTCCTCCTCTTTTTCTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:627:0:0,0:248,378:0:2,0:25.1:1:31.8:1:1:0:60:68.556:1:0:0.1 0/1:523:15:5,10:198,310:0.0287:2,2:24.8:1:28.6:1:0.7913:1.27683:60:30:0.0291:0:1.1 -20 57485538 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16113;SOR=Inf;LSEQ=TTTACTTAATTCCAAATTCA;RSEQ=GGGTTCAGCTACCCAGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:73,222:0:2,0:22.1:1:31.2:1:1:0:60:146.5:0.9966:0:0.3 0/1:199:2:1,1:43,153:0.0101:2,2:24:1:28:1:0.39594:3.53:60:4:0.0103:0:1 -20 57485611 . T C 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.009;SOR=0.36639;LSEQ=TTGAGCTCTTTGCGCCCCTC;RSEQ=TTTTGCTTTTGTTTTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:185:107,78:9,5:0.9296:2,2:24.3:1:31.7:1:0.78145:1.3104:60:60.667:0.9286:0:1.1 1/1:99:82:50,32:11,6:0.8283:2,2:23.3:1:30.7:1:1:1.17146:60:40:0.8333:0:1.2 -20 57485941 . G T 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAATTAATTAAAAGTGAAAC;RSEQ=TAATTGTACAAGCAGTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:37,244:0:2,0:23.2:1:31.4:1:1:0:60:39.143:1:0:0.1 0/1:202:14:2,12:30,157:0.0693:2,2:22:1:29.6:1:1:1.14575:60:28:0.0697:0:1.2 -20 58054448 . G A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0.53881;LSEQ=TAGTCACAAACCTTAAGTGT;RSEQ=TTTTACGGGAATGCAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:508:294:146,148:106,106:0.5787:2,2:26.6:1:29.3:1:1:1.01367:60:146:0.5817:0:1.1 0/1:381:162:79,83:105,112:0.4252:2,2:25.4:1:28.5:1:1:1.02:60:161:0.4248:0:1.1 -20 58054459 . A G 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTTAAGTGTGTTTTACGGGA;RSEQ=TGCAAGCACTTCAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:237,251:0:2,0:27.8:1:30.5:1:1:0:60:487:1:0:0.6 0/1:381:14:6,8:172,195:0.0367:2,2:28.1:1:31.8:1:0.79313:1.17557:60:28:0.0371:0:1.1 -20 58054528 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16991;SOR=Inf;LSEQ=TCTTCTAGTGTTTTAAAGAG;RSEQ=TGGTTAGCACAGCCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:58,178:0:2,0:21.8:1:31.8:1:1:0:60:77.667:1:0:0.3 0/1:166:2:1,1:41,123:0.012:2,2:27.5:1:30.5:1:0.44315:2.98:60:4:0.0122:0:1 -20 58054565 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12363;SOR=Inf;LSEQ=ACACCACATGGGGAAGTTCT;RSEQ=GCTGATGGCGGACCATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:9,121:0:2,0:25.9:1:31.3:1:1:0:60:129:1:0:0.1 0/1:71:2:1,1:3,66:0.0282:1,2:13.5:1:28:1:0.11026:19.20:60:4:0.0286:0:1.5 -20 58054767 . A G 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTACCATGCAGCCCAGGTGT;RSEQ=TAGTAGGCTGTACCATCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:7.5:1:32.5:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:1:0,0:41:0:33:0:1:0:60:2:1:0:1 -20 58055043 . A G 34 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTCCTAATTAGTTAACT;RSEQ=CATTTTACAGTGATCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:41:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:14:1:34:0:1:0:60:4:1:0:2 -20 58196318 . AC A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.10074;SOR=Inf;LSEQ=TAGGTTATTTGTAGGTGAGC;RSEQ=CCCAGTGCACATAGACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:79,21:0:2,0:25.7:1:31.3:1:1:0:60:19:1:0:0.2 0/1:47:2:1,1:35,10:0.0426:2,2:36:1:31:1:0.41721:3.38437:60:4:0.0426:0:0.5 -20 58196400 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15429;SOR=Inf;LSEQ=TTGCCCAGACTCCTGCTCTT;RSEQ=CCCTGTGGAAGGACCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:114,97:0:2,0:25.4:1:31.9:1:1:0:60:51.75:1:0:0.3 0/1:137:2:1,1:73,62:0.0146:2,2:5.5:1:24:0:1:1.17601:60:4:0.0147:0:1.5 -20 58196423 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27739;SOR=0;LSEQ=CTGTGGAAGGACCTATGAGT;RSEQ=GGACCCCACACAGGGATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:1,2:109,108:0.0136:2,2:12:1:30.7:1:1:2.01231:60:6:0.0139:0:1 0/0:148:0:0,0:72,74:0:2,0:25:1:30.5:1:1:0:60:292:0.9865:0:0.6 -20 58196424 . G A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.56484;LSEQ=TGTGGAAGGACCTATGAGTC;RSEQ=GACCCCACACAGGGATTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:40:21,19:89,91:0.1818:2,2:24.3:1:30.2:1:0.86143:1.13:60:80:0.1843:0:1.1 0/1:149:66:31,35:43,40:0.443:2,2:26.1:1:29.9:1:0.62185:1.21212:60:65:0.4483:0:1.2 -20 58196450 . C T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29849;SOR=0;LSEQ=CACACAGGGATTAGGTGGGG;RSEQ=CATGCTGGGCAGCCCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:1,2:96,112:0.0142:2,2:19.3:1:22:1:1:1.71009:60:2:0.0101:0:1 0/0:124:0:0,0:56,67:0:2,0:26.6:1:30.8:1:1:0:60:40:0.9917:0:0.5 -20 58196490 . A T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29275;SOR=0;LSEQ=CAGCCTGGCACATCTTGGGG;RSEQ=CTGTCCACAGTGTCAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:1,2:51,95:0.0201:2,2:29:1:29:1:1:1.07318:60:6:0.021:0:1 0/0:90:0:0,0:33,57:0:2,0:20.8:1:28.5:1:1:0:60:44:1:0:0.3 -20 58197161 . GTT G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=ATGTGCATGTACAAGTATGT;RSEQ=TGTGTGTGCAGGTGTGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26.5:1:28.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:32:1:1:0:60:4:1:0:0.5 -20 58198325 . G A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATCAGGCTTGGTCCAGCCC;RSEQ=TGTTATGACCTTCCAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 59632034 . C T 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02876;SOR=0;LSEQ=TCAGGATTTGAAGTTTCACG;RSEQ=CCAGCAGCAGCCCAGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:7,3:8,4:0.4545:2,2:26.7:1:30.2:1:1:1.16:60:20:0.4545:0:1.1 0/0:8:0:0,0:5,3:0:2,0:24.6:1:33.5:1:1:0:60:16:1:0:0.3 -20 59926780 . CT C 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTTTTATTTTTATTTAT;RSEQ=TTTTTTTTTTTGAGACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 59927881 . T A 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29022;SOR=0.58698;LSEQ=TTTTCTGCTCTTCGGAGTTC;RSEQ=TCATCCGGCAGTGCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:22:19,3:63,11:0.2292:2,2:23.3:1:30.6:1:1:1.10:60:44:0.234:0:1.1 0/1:54:8:7,1:39,7:0.1481:2,2:14.8:1:29.4:1:1:1.25:60:16:0.1481:0:1 -20 59927925 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14251;SOR=Inf;LSEQ=CCCATCACCCCGTGCACCTG;RSEQ=GAGACGCTGCGGACAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:129,73:0:2,0:24.4:1:29.9:1:1:0:60:404:1:0:0.4 0/1:123:2:1,1:73,48:0.0163:2,2:27:1:28.5:1:1:1.51547:60:4:0.0163:0:1 -20 59927968 . G A 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.82501;LSEQ=TGTCAATGTCCCATCCTTGC;RSEQ=GCGCACAGGAGGTTCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:11:7,4:137,123:0.0406:2,2:23.5:1:30.5:1:0.54953:1.57:60:22:0.041:0:2.4 0/1:200:34:16,18:83,82:0.17:2,2:28.6:1:30.3:1:0.85094:1.13798:60:33:0.1692:0:2.1 -20 59927999 . C T 35 v4;q23;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07435;SOR=Inf;LSEQ=GGTTCCAGGACCCAGGAAGC;RSEQ=TCAACATTCTCTCTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:129,148:0:2,0:25.1:1:31.2:1:1:0:60:45.167:1:0:1.1 0/1:202:3:1,2:89,109:0.0149:2,2:33.7:1:22.7:1:1:1.62921:60:2:0.0101:0:4.3 -20 59928005 . A G 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43949;SOR=0.85747;LSEQ=AGGACCCAGGAAGCCTCAAC;RSEQ=TTCTCTCTGCCTGTGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:274:171:72,99:48,55:0.6241:2,2:25:1:31:1:0.52991:1.19919:60:342:0.6264:0:1.9 1/0:189:111:48,63:34,44:0.5873:2,2:25.5:1:30.4:1:1:1.01413:60:222:0.5936:0:2.1 -20 59928030 . G A 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49529;SOR=0.85424;LSEQ=CTCTGCCTGTGTGGCATGCC;RSEQ=GACCAAGGGGCCCCTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:214:140:52,88:31,43:0.6542:2,2:23.8:1:30.6:1:0.5559:1.21888:60:139:0.6557:0:2.2 1/0:136:84:33,51:22,30:0.6176:2,2:25.2:1:30.2:1:0.85745:1.13228:60:168:0.6222:0:2.3 -20 59928076 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09393;SOR=Inf;LSEQ=TCAGGCTCTGGGGACCCCAC;RSEQ=GGCCCCATCTCCTCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:20,92:0:2,0:21.7:1:30.5:1:1:0:60:55:1:0:1.3 0/1:50:2:1,1:11,36:0.04:2,2:9:1:24.5:1:0.43367:3.18:60:4:0.0408:0:3 -20 59928077 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09631;SOR=Inf;LSEQ=CAGGCTCTGGGGACCCCACG;RSEQ=GCCCCATCTCCTCCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:19,91:0:2,0:21.5:1:30.6:1:1:0:60:35.667:1:0:1.3 0/1:50:2:1,1:11,37:0.04:2,2:19.5:1:28.5:1:0.42612:3.26:60:4:0.0417:0:1 -20 59928091 . C T 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=1.09208;LSEQ=CCCACGGGCCCCATCTCCTC;RSEQ=CCTCCCCTCTCTTAGCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:79:48:3,45:4,26:0.6076:2,2:24.2:1:28.8:1:0.41904:2.28184:60:15:0.6:0:2.1 1/0:35:22:4,18:2,11:0.6286:2,2:15.3:1:26.1:1:1:1.22:60:4.5:0.5806:0:2.2 -20 59928237 . T C 91 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.41667;SOR=0;LSEQ=GTTTCCACCTGTGGAAAGCA;RSEQ=ATACATGATGAATGTGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:1,6:0,4:0.6364:0,2:16.6:1:32.6:1:1:0:60:14:0.6364:0:1.3 0/0:1:0:0,0:0,1:0:0,0:19:0:30:0:1:0:60:2:1:0:0 -20 59931355 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAACCTGCTCTGTGTCATC;RSEQ=CAGCACCACATCCTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 60424439 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCACTGTGTAACGAATCAG;RSEQ=ACAAACTTAGTGGCTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:28:1:1:0:60:4:1:0:1 -20 60425089 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCAGCCTGAGTACGCTGAC;RSEQ=ACTGTGACACGTGTCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7:0:29:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:19:1:28:0:1:0:60:4:1:0:1 -20 60426113 . T C 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04556;SOR=0.62287;LSEQ=GCGTGTGGGAAACACATCCA;RSEQ=AGCAGGACGGAGCTGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:217:151:68,83:24,42:0.6959:2,2:27.9:1:32.1:1:0.29598:1.43:60:302:0.6959:0:1.2 1/0:126:74:35,39:24,28:0.5873:2,2:24.4:1:31.3:1:1:1.05:60:73:0.5887:0:1.3 -20 60426146 . G T 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04258;SOR=Inf;LSEQ=CTGCAGATGGGTCGGGGATG;RSEQ=GGGAGTCTGCCCGCGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:52,112:0:2,0:23:1:31.2:1:1:0:60:328:1:0:0.8 0/1:89:3:1,2:35,51:0.0337:2,2:33.7:1:29.3:1:1:1.36784:60:6:0.0341:0:2 -20 60426150 . A G 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55339;SOR=0;LSEQ=AGATGGGTCGGGGATGGGGG;RSEQ=GTCTGCCCGCGACGGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:3:2,1:48,105:0.0192:2,2:10.3:1:25.3:1:0.24081:4.33:60:2:0.013:0:3 0/0:83:0:0,0:32,51:0:2,0:26.3:1:28.9:1:1:0:60:15.6:1:0:0.9 -20 60426165 . G C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=GGGGGAGTCTGCCCGCGACG;RSEQ=GGCGGGGACAGCCGGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:25,84:0:2,0:24.4:1:31.1:1:1:0:60:108:1:0:0.6 0/1:67:9:4,5:20,38:0.1343:2,2:26.1:1:29.4:1:0.71142:1.51:60:18:0.1364:0:2.2 -20 60427195 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCACGGATCCCCCCAC;RSEQ=CCACCACCCATATTCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 60561917 . A C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTCCAATTAATAAATGT;RSEQ=AACAGAAAGACAGAAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:30:1:1:0:60:4:1:0:1.5 -20 60562181 . C A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01329;SOR=0.1462;LSEQ=GACACCACCTGCCTCCCAAT;RSEQ=CAGTGCTCTGAGGACACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:11,18:2,2:0.8788:2,2:27.4:1:28.2:1:1:1.61126:60:28:0.875:0:1.2 1/0:12:6:3,3:3,3:0.5:2,2:29.2:1:28.7:1:1:1:60:12:0.5:0:1 -20 60562394 . G A 50 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGAGCCGAGGAGCCGC;RSEQ=AGGGTCCCGGGGCAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:1:0,0:33:1:32:0:1:0:60:6:1:0:1 -20 60577258 . G A 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=CTTCTCACTGAAGTATCAGC;RSEQ=TCACGCTGGGCCCAGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:30.3:1:30.3:1:1:0:60:6:0.75:0:1.7 1/0:2:1:0,1:0,1:0.5:0,0:48:0:29:0:1:0:60:2:0.5:0:1 -20 61041333 . C T 132 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00042;SOR=0.02774;LSEQ=CCCGGGGGTGGTGCCGCAGT;RSEQ=GGCCGGCCGGGACATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:19,0:3,0:0.8636:0,1:25.1:1:31.2:1:1:0:60:38:0.8636:0:1.1 0/1:8:1:1,0:7,0:0.125:0,0:33:0:31:0:1:0:60:2:0.125:0:1 -20 61041423 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17678;SOR=5.58319;LSEQ=CTTGGTCTGAGAGTGCGGAC;RSEQ=GCGCTCGCTAGGAGGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:1,0:99,3:0.0097:1,0:36:0:14:0:1:0:60:0:0:0:1 0/1:38:2:2,0:33,3:0.0526:2,0:16:1:29:1:1:0:60:4:0.0541:0:1 -20 61041456 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10284;SOR=Inf;LSEQ=AGGCTGGACAGAGGCCTCCC;RSEQ=GCCCTGCCCCGGGGACCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:157,57:0:2,0:21.7:1:30.1:1:1:0:60:41.8:0.9952:0:0.1 0/1:102:2:1,1:71,29:0.0196:2,2:39:1:25.5:1:0.50379:2.42403:60:4:0.0198:0:1 -20 61041467 . G C 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.55394;SOR=0;LSEQ=AGGCCTCCCCGCCCTGCCCC;RSEQ=GGGACCACACTCACCCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:1,2:187,73:0.0113:2,2:20:1:29.3:1:0.19658:5.08631:60:6:0.0115:0:1 0/0:135:0:0,0:91,43:0:2,0:23.9:1:29.6:1:1:0:60:133:0.9925:0:0.2 -20 61041544 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11947;SOR=Inf;LSEQ=CTCCCCCTCCGAGTTCCGCC;RSEQ=CCACAGCGTGGTGTTGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:171,201:0:2,0:29.1:1:30.5:1:1:0:60:73.4:1:0:0.1 0/1:197:2:1,1:87,107:0.0102:2,2:31:1:30:1:1:1.23:60:4:0.0104:0:2 -20 61041653 . G C 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.76621;SOR=0.75258;LSEQ=GAGCCCCGGGCCGGGTGCGC;RSEQ=GCTGGAGCAGGGGGACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:48:0,48:0,24:0.6667:1,1:23.4:1:29.9:1:1:0:60:23:0.6571:0:1.1 1/0:15:9:0,9:1,5:0.6:2,0:27.8:1:29.9:1:0.4:0:60:18:0.6:0:1.3 -20 61041687 . C T 49 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02417;SOR=11.00425;LSEQ=GACGGAAGCGAGACTCAGGT;RSEQ=GGCCTTGCGGCCACGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:0,2:1,39:0.0476:1,0:11:1:32:1:1:0:60:4:0.0476:0:2.5 0/1:8:3:0,3:0,5:0.375:0,0:12.7:1:31:1:1:0:60:6:0.375:0:2 -20 61048479 . C T 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03112;SOR=Inf;LSEQ=CAGGCGCTTCTGAGGCCGAA;RSEQ=GAGCGGCCGGTTGACGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:295,167:0:2,0:25.7:1:30.5:1:1:0:60:50.333:1:0:0.5 0/1:213:3:1,2:131,79:0.0141:2,2:12.7:1:26.7:1:0.55898:3.29724:60:6:0.0144:0:1 -20 61048549 . G A 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.47216;LSEQ=CACAGGTAGTGGCCGGTGCC;RSEQ=TCTCGGCGCCACAGCGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:571:450:175,275:47,74:0.7881:2,2:25.4:1:30.3:1:1:1.00:60:63.286:0.7869:0:1.1 1/0:314:200:83,117:52,62:0.6369:2,2:26:1:29.5:1:0.48012:1.18164:60:65.667:0.6355:0:1.2 -20 61048601 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55328;SOR=0;LSEQ=CGCAGTTGACACACTCACGA;RSEQ=CCTCACCCGGGAACTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:0,2:15,178:0.0103:2,0:19.5:1:28.5:1:1:0:60:4:0.0106:0:2 0/0:98:0:0,0:12,86:0:2,0:19.6:1:30.3:1:1:0:60:48:1:0:0.6 -20 61048931 . G A 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTCCCGGCTCCGGGACC;RSEQ=GGGGCCAGCACTGGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:10:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 61283771 . G A 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09306;LSEQ=TGCTTTCTGTTTCGGCGGCC;RSEQ=GCGGCCGGTGGAGCCCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:6,1:19,4:0.2333:2,2:21.7:1:28.9:1:1:1.25:60:14:0.2414:0:1.1 0/1:16:4:3,1:10,2:0.25:2,2:15.3:1:29.3:1:1:1.60994:60:8:0.2667:0:1 -20 61283797 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53329;SOR=0;LSEQ=CGGTGGAGCCCTTGCGCCTC;RSEQ=TCGTCAGTCCCGCCCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:38,20:0.0333:2,2:13.5:1:29.5:1:1:1.87852:60:4:0.0339:0:1.5 0/0:34:0:0,0:21,13:0:2,0:24.2:1:29.4:1:1:0:60:16:1:0:0.4 -20 61283840 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14454;SOR=Inf;LSEQ=CTTGCTCCTCCGGCTTTTCC;RSEQ=CTGACTCCTGGCATTCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:49,48:0:2,0:29.8:1:30.7:1:1:0:60:31.333:1:0:0.2 0/1:60:2:1,1:31,27:0.0333:2,2:22:0:30:1:1:1.1455:60:4:0.0357:0:1.5 -20 61283891 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15099;SOR=Inf;LSEQ=CACATGCTCCTGGGACGTCA;RSEQ=CCTTGTGACAGCTCGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:20,39:0:2,0:19.5:1:29.1:1:1:0:60:18.667:1:0:0.1 0/1:38:2:1,1:12,24:0.0526:2,2:28.5:1:31:1:1:1.96:60:4:0.0526:0:1 -20 61284092 . C G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTGGCATTGTAAATAAAC;RSEQ=CCCGGGTGTGGCCGCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:22:1:32.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 61285758 . G C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GCACCGGTCCGCCCACCCCA;RSEQ=CCCCAGCGCAGGCCCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:25.3:1:31.8:1:1:0:60:20:1:0:0.1 0/1:15:2:1,1:6,7:0.1333:2,2:50:0:31.5:1:1:1.15:60:4:0.1333:0:1 -20 62173029 . A G 71 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAACGGCCGGTGAGGCC;RSEQ=GCGTCCACCCACGTCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:1,1:0.7143:2,0:28.6:1:30.8:1:0.28571:0:60:10:0.7143:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 62173796 . A G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGATCTCGGGGCCTCACCTG;RSEQ=CTTGATGACCTTGATCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:4.3:1:28:1:1:0:60:6:1:0:0 1/0:4:2:1,1:2,0:0.5:0,2:25.5:1:30:1:1:0:60:4:0.5:0:1 -20 62174970 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCCTGAGATGGTCAGAGCT;RSEQ=TGTGGAGGAGGGAGTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:29.5:1:1:0:60:4:1:0:1.5 -20 62678476 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGACAGGTCACCCGGGTG;RSEQ=GGGGAGCGCTGTGGGTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -20 62680235 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1162;SOR=Inf;LSEQ=CTTGTAGTTGGGGTGGTCGC;RSEQ=CAAGTGCTGCACGCGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:179,141:0:2,0:26.1:1:30.4:1:1:0:60:34.556:1:0:0.2 0/1:166:2:1,1:99,65:0.012:2,2:16:0:32:0:1:1.51907:60:4:0.0122:0:1 -20 62680270 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13267;SOR=Inf;LSEQ=GCAGCCGTTCGGCTTCCTCC;RSEQ=CGAAGGGCCGCTTCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:154,181:0:2,0:26.7:1:29.3:1:1:0:60:40.875:1:0:0.2 0/1:193:2:1,1:89,102:0.0104:2,2:18:1:28:1:1:1.15:60:4:0.0105:0:1 -20 62680296 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14248;SOR=Inf;LSEQ=GGCCGCTTCTCCGCCGCGTT;RSEQ=AGCTCCTTCCACGCTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:98,170:0:2,0:23.6:1:31.4:1:1:0:60:52.6:1:0:0.2 0/1:163:2:1,1:60,101:0.0123:2,2:24.5:1:28:1:1:1.68:60:4:0.0124:0:1 -20 62680311 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16126;SOR=Inf;LSEQ=GCGTTCAGCTCCTTCCACGC;RSEQ=TTGCCTGCGGGCCGTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:56,134:0:2,0:24.9:1:29.8:1:1:0:60:26.143:1:0:0.2 0/1:128:2:1,1:40,86:0.0156:2,2:17:1:32:0:0.53974:2.14:60:4:0.0161:0:1 -20 62680322 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.56016;SOR=3.25529;LSEQ=CTTCCACGCTTTGCCTGCGG;RSEQ=CCGTGGGCGCCAGTGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:1,0:41,116:0.0063:2,0:1:0:26:0:0.26582:0:60:2:0.0065:0:1 0/1:98:2:0,2:21,74:0.0204:2,0:10:1:30.5:1:1:0:60:4:0.0211:0:1 -20 62680331 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14592;SOR=Inf;LSEQ=TTTGCCTGCGGGCCGTGGGC;RSEQ=CCAGTGAGTGGAACGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:30,97:0:2,0:25:1:31.3:1:1:0:60:41.333:1:0:0.2 0/1:79:2:1,1:15,62:0.0253:2,2:6.5:1:27.5:1:0.36611:4.03:60:4:0.026:0:1.5 -20 62680504 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCTCTGCCGCCCTCCCG;RSEQ=CGCTCACCCAGCATCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:74,26:0.0194:2,2:40:1:29.5:1:0.46127:2.81176:60:4:0.0196:0:1.5 0/0:50:0:0,0:32,18:0:2,0:20:1:31.3:1:1:0:60:100:1:0:0.4 -20 62680539 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13233;SOR=Inf;LSEQ=CTTGCTGAGCACCGCGTTGT;RSEQ=CAGGTCCGGGTTCTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:127,82:0:2,0:27.8:1:32.3:1:1:0:60:208:1:0:0.2 0/1:120:2:1,1:67,51:0.0167:2,2:15:1:27.5:1:1:1.31069:60:4:0.0171:0:1 -20 62680559 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13023;SOR=Inf;LSEQ=GCAGGTCCGGGTTCTGCTGA;RSEQ=CCAGCCGCTTGCGCTCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:141,122:0:2,0:26.2:1:31.9:1:1:0:60:130.5:1:0:0.2 0/1:149:2:1,1:77,70:0.0134:2,2:16.5:1:27:1:1:1.0993:60:4:0.0139:0:1 -20 62680560 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30161;SOR=0;LSEQ=CAGGTCCGGGTTCTGCTGAG;RSEQ=CAGCCGCTTGCGCTCGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:4:1,3:141,123:0.0149:2,2:23.5:1:30:1:0.3448:3.42437:60:8:0.0151:0:1 0/0:150:0:0,0:79,71:0:2,0:27.4:1:30.9:1:1:0:60:49:1:0:0.3 -20 62680610 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12843;SOR=Inf;LSEQ=CCATGAAGGCGTTCATGGGC;RSEQ=GCCGGATGCGCGACTCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:64,140:0:2,0:25.9:1:29.5:1:1:0:60:50:0.995:0:0.1 0/1:115:2:1,1:41,72:0.0174:2,2:34.5:1:30.5:1:1:1.75:60:4:0.0177:0:1 -20 62680817 . CGGCG C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGGCCCATGCACAGTCG;RSEQ=GGCGGGCGGGTCGTCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31.5:1:1:0:60:4:1:0:0.5 -20 62921841 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49981;SOR=0;LSEQ=TCCAGCCTCTGGGAACCATG;RSEQ=AGCAGCTCCCAGCGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:22,33:0.0351:2,2:35:1:29:1:1:1.49:23:4:0.0351:0:1 0/0:47:0:0,0:22,25:0:2,0:29.7:1:31.2:1:1:0:30.3:94:1:0:0 -20 62922184 . G A 27 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCATAGTGGGCCTGGAGGGC;RSEQ=GCTGTGGCCTAGTGGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34:1:27.5:1:1:0:21:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:1:0:31:0:1:0:25:2:1:0:0 -20 62922372 . TG T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.04871;SOR=0;LSEQ=CGCATCACACATGGCACACT;RSEQ=GGGGTGTTGGGCTTTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:3,1:13,12:0.1379:2,2:37.3:1:30.3:1:0.60591:2.68:42.3:8:0.1379:0:0.5 0/0:31:0:0,0:18,13:0:2,0:24.7:1:31.3:1:1:0:45.6:62:1:0:0.1 -20 62922607 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17143;SOR=Inf;LSEQ=GAGCCTGGTAGCTCCAGGTC;RSEQ=CCCACACTTTCAGGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:26,3:0:2,0:18.8:1:29.9:1:1:0:22.7:28:1:0:0.3 0/1:21:2:2,0:18,1:0.0952:1,0:24:1:31:0:1:0:20:4:0.1053:0:1.5 -20 62922621 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49648;SOR=0;LSEQ=CAGGTCGCCCACACTTTCAG;RSEQ=TCTCTTGCACCAGAAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:30,8:0.05:2,2:14:1:31.5:1:0.40385:3.5936:27:4:0.05:0:1 0/0:34:0:0,0:27,7:0:2,0:22.3:1:29.8:1:1:0:27.7:16:1:0:0.2 -20 62922665 . G A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GATCCATTGGGAGGAAACAG;RSEQ=CCACCTTGGAAGGTGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:36,27:0.0308:2,2:19:1:29:1:1:1.32735:20:4:0.0328:0:2 0/1:65:2:1,1:40,23:0.0308:2,2:43.5:1:30.5:1:1:1.72358:26:4:0.0323:0:2 -20 62922689 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49781;SOR=0;LSEQ=CCTTGGAAGGTGTCCCTGGG;RSEQ=CCCCATCCCCAGGGGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:38,43:0.0241:2,2:19.5:1:28.5:1:1:1.13:27:4:0.0244:0:1 0/0:76:0:0,0:40,36:0:2,0:25.3:1:30.4:1:1:0:32.4:37:1:0:0.3 -20 62922708 . A G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20681;SOR=0.49535;LSEQ=GCCCCCATCCCCAGGGGTTG;RSEQ=GGCCGTAGGGGGCCCGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:11:0,11:27,39:0.1429:2,0:42.1:1:31.5:1:0.00651:0:20:22:0.1429:0:1.3 0/1:79:6:1,5:36,37:0.0759:2,2:22.3:1:31.3:1:0.20633:4.78237:22:12:0.0759:0:1.5 -20 62922740 . C G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24312;SOR=Inf;LSEQ=GCCCGCTCTGCTGCGTTGAC;RSEQ=AGACTCCTGGGCTTTGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:17,38:0:2,0:25.9:1:32.6:1:1:0:32.1:110:1:0:0.3 0/1:55:3:0,3:19,33:0.0545:2,0:32.3:1:32:1:0.54374:0:29.7:6:0.0545:0:1 -20 62922763 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49556;SOR=Inf;LSEQ=ACTCCTGGGCTTTGAAGGCT;RSEQ=CTGGGCCCAGTAAGAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:10,26:0:2,0:17.5:1:30.9:1:1:0:33.5:35:1:0:0.2 0/1:41:2:1,1:12,27:0.0488:2,2:32:1:28.5:1:0.53902:2.20:20:4:0.0488:0:1 -20 62922991 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22;SOR=0;LSEQ=CCTCTGGCTCCTCCCCAGAG;RSEQ=TGTCCCCACTCTCAGTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:10,0:0.2308:0,0:15:1:31.3:1:1:0:25.7:6:0.25:0:2 0/0:13:0:0,0:12,1:0:1,0:26.7:1:32:1:1:0:28.8:26:1:0:0 -20 62923006 . G C 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21476;SOR=0.28968;LSEQ=CAGAGCTGTCCCCACTCTCA;RSEQ=TCGGTCACCCACTCCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:0.3571:0,0:20.8:1:33:1:1:0:23.4:10:0.4167:0:1.6 0/1:15:2:2,0:12,1:0.1333:1,0:14.5:1:32.5:1:1:0:30.5:4:0.1333:0:1 -20 62923305 . A G 80 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33824;SOR=0.27028;LSEQ=GTCAGTTCCCGTAGTGCCTG;RSEQ=CGGTCTATTTCCCTGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:0.5:0,0:24.8:1:31.3:1:1:0:38.5:12:0.5:0:1 0/1:5:1:0,1:0,4:0.2:0,0:4:0:31:0:1:0:31:2:0.2:0:1 -20 62923514 . G A 61 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.54771;LSEQ=GCCCGTCTCTGATATGCTCC;RSEQ=CTCCCACGAGCCCTTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:21.5:1:30.8:1:1:0:24.3:8:0.8:0:1 1/0:3:2:2,0:1,0:0.6667:0,0:10:1:31:0:1:0:25:4:0.6667:0:1 -20 62923745 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2953;SOR=3.60517;LSEQ=GCCCCGCCAGGGCCTGGTGC;RSEQ=GCTTGCTGAAGATCATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:1:0,1:54,46:0.0099:2,0:1:0:16:0:0.46535:0:20:0:0:0:3 0/1:57:2:1,1:25,30:0.0351:2,2:30:1:30:1:1:1.20:37:4:0.0351:0:1 -20 62923766 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5181;SOR=0;LSEQ=GCTTGCTGAAGATCATGAGC;RSEQ=CCACTCATGGGCCACCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:35,38:0.0267:2,2:45.5:1:30.5:1:1:1.08:47:4:0.027:0:2 0/0:49:0:0,0:19,30:0:2,0:23.9:1:30.1:1:1:0:34.8:48:1:0:0.1 -20 62953546 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17534;SOR=0;LSEQ=CTTGGAAACCCTGCCAGATG;RSEQ=CCTCACCTCCGAGAGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:0.08:2,2:39.5:1:31.5:1:1:1.0871:49:4:0.0833:0:1 0/0:34:0:0,0:19,14:0:2,0:29.2:1:30.5:1:1:0:49.8:15.5:1:0:0.2 -20 62953632 . C A 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.73582;SOR=1.4556;LSEQ=TACTAAGCTGCCGGCCTCAC;RSEQ=TCTGAGAGTCTGCTGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:2,3:11,11:0.1852:2,2:28:1:30.4:1:1:1.47778:52:10:0.1852:0:2 0/1:24:6:3,3:10,8:0.25:2,2:29.8:1:30:1:1:1.23836:59:12:0.25:0:2 -20 62953650 . T C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48388;SOR=0.54072;LSEQ=ACCTCTGAGAGTCTGCTGGG;RSEQ=GCAGTGAGAGTGTCCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:8,12:2,2:0.8333:2,2:24.6:1:30.1:1:1:1.47432:53:40:0.8333:0:1.3 1/0:22:16:7,9:3,2:0.7273:2,2:28.3:1:29.5:1:0.63512:1.86862:57.1:32:0.7619:0:1.4 -21 9825838 . T TGCG 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.38454;SOR=2.57068;LSEQ=TCCGGGGGACCGGCCGCGAC;RSEQ=GCGGCGGCGGTGGTGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:29.5:1:32.2:1:1:1:47.5:4:0.1538:0:0.5 0/1:13:4:2,2:2,2:0.3077:2,2:32.5:1:31.7:1:1:1:39:8:0.3333:0:1 -21 9825852 . T TG 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.2092;SOR=0;LSEQ=CGCGACTGCGGCGGCGGTGG;RSEQ=GGGGGGAGCCGCGGGGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:19:0:33.5:1:1:1:47:4:0.1538:0:1.5 0/0:16:0:0,0:8,8:0:2,0:20:1:28.4:1:1:0:48.1:15:1:0:1 -21 9825932 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.49673;SOR=Inf;LSEQ=GCCGGCGGCGGTGAGGCCCC;RSEQ=CGCGTGTGTCCCGGCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:3.6:1:30.9:1:1:0:48.1:14:1:0:1 0/1:11:2:1,1:5,4:0.1818:2,2:17:1:30:1:1:1.22474:47:4:0.1818:0:1 -21 9825966 . A C 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.54335;SOR=0.29492;LSEQ=GCTGCGGTCGGCCGCGCTCG;RSEQ=GGGGTCCCCGTGGCGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:0.1818:2,2:13.5:1:31:1:1:1.87089:60:4:0.1818:0:1.5 0/1:17:1:1,0:8,8:0.0588:2,0:24:0:34:0:1:0:25:2:0.0588:0:1 -21 9825981 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=GCTCGAGGGGTCCCCGTGGC;RSEQ=TCCCCTTCCCCGCCGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:35.8:1:31.3:1:1:0:37.8:20:1:0:0.4 0/1:16:2:1,1:7,7:0.125:2,2:23.5:1:28.5:1:1:1:25:4:0.125:0:1 -21 9826003 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=CCCCTTCCCCGCCGGCCGCC;RSEQ=TTCTCGCGCCTTCCCCGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:9.5:1:30:1:1:1.22474:48:4:0.1818:0:1.5 0/0:11:0:0,0:5,6:0:2,0:22.5:1:30.2:1:1:0:42:22:1:0:0.5 -21 9826229 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50054;SOR=Inf;LSEQ=TGCGCCCGAGCGCGGCCCGG;RSEQ=GGTCCCTCCCGGACAGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:0:2,0:19:1:29.5:1:1:0:44.6:66:1:0:0.8 0/1:42:2:1,1:22,18:0.0476:2,2:19.5:1:30:1:1:1.21636:49:4:0.0488:0:1.5 -21 9826288 . G A 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11742;SOR=0;LSEQ=GGGTCGACCTCCGCCTTGCC;RSEQ=GTCGCTCGCCCTTTCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:8,13:0.16:2,2:38.3:1:27.5:1:1:1.59:25:3:0.125:0:2 0/0:20:0:0,0:9,11:0:2,0:23:1:28:1:1:0:40.2:19:1:0:1 -21 9826301 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGCCGGTCGCTCGCCCT;RSEQ=TCCCCGGGTCGGGGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:10,15:0,0:1:0,2:20:1:32.2:1:1:0:38.9:50:1:0:1.4 1/1:15:15:6,9:0,0:1:0,2:17.1:1:30.5:1:1:0:37.3:14:1:0:1.3 -21 9826870 . TCCCGTCCG T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=2.000;MSILEN=8;SSF=0.49206;SOR=Inf;LSEQ=CCCCGCGCCCGCTCGCTCCC;RSEQ=CCCGTCCGCGGCCCGTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:26.3:1:29.3:1:1:0:60:5:1:0:0.7 0/1:16:2:1,1:8,6:0.125:2,2:36:0:32:0:1:1.30929:60:4:0.125:0:0.5 -21 9826890 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17235;SOR=0;LSEQ=TCCCGTCCGCCCGTCCGCGG;RSEQ=CCGTCCGTCCGTCCGTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:34.5:1:29.5:1:1:1:60:4:0.1667:0:1 0/0:19:0:0,0:9,8:0:2,0:25.2:1:32.6:1:1:0:54.5:34:0.8947:0:0.4 -21 9827073 . C CG 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1836;SOR=0;LSEQ=CATGCATGTCTAAGTACGCA;RSEQ=GGCCGGTACAGTGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:14,7:0.087:2,2:22.5:1:29.5:1:1:1.93655:25:4:0.0909:0.0435:0.5 0/0:30:0:0,0:17,13:0:2,0:25.8:1:30.6:1:1:0:45.4:60:1:0:0.1 -21 9827521 . CG AA 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGACCCGGGGAGGTAGTGA;RSEQ=AAAAATAACAATACAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:31.5:1:1:0:51:4:1:0:2 -21 9827538 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACGAAAAATAACAATACA;RSEQ=GACTCTTTCGAGGCCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:44:1:31:1:1:0:51:4:1:0:2 -21 9829008 . C G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTTAAGTTGTGGGTGACT;RSEQ=ATGGAAAGGAGGAGTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:33.5:1:1:0:60:4:1:0:2.5 -21 9829054 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTTTCCACTGCTAGGCTGC;RSEQ=CGCGATGCTATTTAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29.5:1:1:0:60:4:1:0:2.5 -21 10818258 . G C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CAATGGAATGGAATGGAATG;RSEQ=AATGGAACGGACTCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:33.5:1:1:0:50:4:1:0:2 -21 10818266 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGACTCAAATGGAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:31.5:1:1:0:50:4:1:0:2 -21 10818867 . G T 29 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAAAGGGTTGGAATAGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:29:1:1:0:28:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 10819321 . GACTCGACTGGAATGAAATGGAATGGACCAGAAATG C 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGCTTAGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:1:29.3:1:1:0:44.5:4:1:1:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 10819364 . T A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=TGGACCAGAAATGAATGGAA;RSEQ=GGAATGGAATGCAATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:29.5:1:1:0:44.5:4:1:0:7 0/0:2:0:0,0:1,1:0:2,0:4:0:29.5:1:1:0:25:4:1:0:2 -21 10819375 . G A 24 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGAATGGAATGGAATGGAAT;RSEQ=CAATGAAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19:0:31.5:1:1:0:44.5:4:1:0:7 1/1:2:2:1,1:0,0:1:0,2:15:0:24:0:1:0:25:4:1:0:2 -21 10819401 . G C 33 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=AAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:0:33:1:1:0:44.5:4:1:0:7 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 10819420 . GG TC 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=AATGCAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:32.5:0:1:0:44.5:4:1:0:6 0/0:1:0:0,0:0,1:0:0,0:6:0:31:0:1:0:25:2:1:0:3 -21 10819423 . A G 34 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=TGCAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:34:0:1:0:44.5:4:1:0:6 0/0:1:0:0,0:0,1:0:0,0:3:0:31:0:1:0:25:2:1:0:3 -21 10819426 . C A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:32:0:1:0:44.5:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 10819440 . G A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGCAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7:1:30.5:1:1:0:44.5:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 10819525 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGCAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:11:0:30.5:1:1:0:30.5:4:0.5:0:8 -21 10819535 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGCAAT;RSEQ=GAATGGAATGGAATGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:21:0:30.5:1:1:0:30.5:4:0.5:0:8 -21 10819550 . G A 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAATGGAATGGAATGGAAT;RSEQ=CAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:15:0:34:0:1:0:29:2:1:0:3 0/1:10:2:1,1:5,2:0.2:2,2:36:0:27.5:1:1:2.23609:30.5:4:0.2222:0:8 -21 10819553 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATGGAATGGAATGCA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:18:0:32:0:1:0:29:2:1:0:3 0/1:11:2:1,1:5,4:0.1818:2,2:39:0:33:1:1:1.22474:30.5:4:0.1818:0:8 -21 10819555 . G GGAACAACCCGAATGGAATGGAATGTAATGGAGAGTAAGGGAGTTGAATAGAATCAATCC 114 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGAATGGAATGGAATGCAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:20:0:34:0:1:0:29:2:1:0:3 1/0:24:15:9,6:3,4:0.625:2,2:39.4:1:29.2:1:0.6517:1.94:33.1:30:0.625:0.625:2 -21 10819558 . A G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.52767;SOR=Inf;LSEQ=ATGGAATGGAATGCAATGGA;RSEQ=TGGAATGGAATGGAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:11,3:0:2,0:4.3:1:31.1:1:1:0:30.6:28:1:0:2.6 0/1:25:2:1,1:12,11:0.08:2,2:44:0:32:1:1:1.0871:30.5:4:0.08:0:8 -21 10819561 . G T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.01481;SOR=0.09455;LSEQ=GAATGGAATGCAATGGAATG;RSEQ=AATGGAATGGAATGCAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:10,3:1,0:0.9286:0,2:5.8:1:30.7:1:1:0:30.8:26:0.9286:0:2.6 1/0:26:14:8,6:6,5:0.5385:2,2:5.9:1:28.1:1:1:1.11:32.4:28:0.5385:0:1.8 -21 10819569 . T G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGCAATGGAATGGAATGGAA;RSEQ=GGAATGCAACGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,3:0:2,0:13.8:1:31.7:1:1:0:30.8:26:0.9286:0:2.6 0/1:37:2:1,1:15,17:0.0541:2,2:5:0:32:1:1:1.13:57.5:4:0.0556:0:0 -21 10819576 . C T 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AACGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:11,3:0:2,0:22.1:1:32.9:1:1:0:30.6:28:1:0:2.6 0/1:38:2:1,1:16,16:0.0526:2,2:28:0:27.5:1:1:1:30.5:4:0.0541:0:8 -21 10819578 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATGGAATGGAATGCA;RSEQ=CGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:11,4:0:2,0:22:1:30.5:1:1:0:30.5:30:1:0:2.5 0/1:39:2:1,1:17,19:0.0513:2,2:14:1:29.5:1:1:1.11:32:4:0.0526:0:2.5 -21 10819616 . G A 28 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.50909;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGCAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:4,8:0:2,0:14.7:1:30.2:1:1:0:29.4:24:0.7059:0:3.8 0/1:27:2:1,1:10,14:0.0741:2,2:9:1:28:1:1:1.38:34:4:0.0769:0:2.5 -21 10819619 . T A 31 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.51052;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGCAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,8:0:2,0:18.8:1:29.4:1:1:0:29.2:26:0.8125:0.0588:3.4 0/1:26:2:1,1:7,13:0.0769:2,2:34.5:1:31:1:1:1.80:39:4:0.08:0:5 -21 10819620 . G T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.16585;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGCAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:4,7:0.1176:2,2:18.5:1:32:0:1:1.67:23.5:4:0.1429:0:5.5 0/0:24:0:0,0:8,14:0:2,0:18.8:1:31:1:1:0:41.3:44:0.9565:0:2.5 -21 10819626 . C G 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.32104;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:1,2:5,4:0.2:2,2:5.3:1:30.7:1:1:2.31595:41:6:0.2308:0.0667:1.7 0/1:16:4:1,3:3,6:0.25:2,2:20.3:1:31.8:1:1:1.45539:35.5:8:0.2667:0:4.5 -21 10819629 . T A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60153;SOR=2.89897;LSEQ=TGGAATGGAATGGAATGCAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:6,5:0.0714:2,0:27:0:28:0:1:0:22:2:0.0769:0:8 0/1:16:3:1,2:4,9:0.1875:2,2:11:0:31:1:1:1.12:45.7:6:0.1875:0:1.7 -21 10819636 . G GAATCAACCCGAGTAC 77 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.01686;SOR=Inf;LSEQ=GAATGGAATGCAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:0:2,0:23.3:1:29.7:1:1:0:26.5:26:0.9286:0:4.6 0/1:15:6:2,4:3,6:0.4:2,2:11:1:30:1:1:1:49.5:12:0.4:0.4:1.3 -21 10819653 . A G 33 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.48571;SOR=0;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:33.5:1:33:1:1:2.24:23:4:0.2222:0:6.5 0/0:6:0:0,0:1,5:0:2,0:9.3:1:30.5:1:1:0:29.2:12:1:0.1667:3 -21 10819670 . G CAACCCGAGTA 29 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=CAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:23:1:29.8:1:1:2.24:26:4:0.2222:0.1111:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 10820044 . T C 33 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:2,0:1,3:0.3333:2,0:29.5:1:33:0:0.4:0:27.5:4:0.3333:0:4.5 -21 10820525 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGATT;RSEQ=GAATGGAATGGAGTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:30:1:1:0:60:4:1:0:1 -21 10821003 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GCATTCGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:32:1:1:0:36:4:1:0:5 -21 10821005 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=ATTCGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:33:0:1:0:36:4:1:0:5 -21 10821012 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGGAATGCATTCGA;RSEQ=TGGAATGGAATGGAATTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:33.5:1:1:0:36:4:1:0:5 -21 10821029 . T G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATGGAATGGAATGGAAT;RSEQ=GACTCGAATGGAATAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:32:0:1:0:36:4:1:0:5 -21 10994373 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGGGGTTTCACTATGTTG;RSEQ=CCAGGCTGGGCTCGAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 10995994 . A AG 276 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0;SOR=0.07766;LSEQ=CCAAGGGGTTACATAAAAAA;RSEQ=AAAAAATTTTAAGTCAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:412:410:357,53:0,0:0.9951:0,2:21.4:1:31.9:1:1:0:59.8:101.5:0.9975:0.2864:0.9 1/1:422:397:330,67:20,4:0.9408:2,2:21.4:1:31.8:1:1:1.01512:59.8:131.333:0.9403:0.2583:1 -21 10996025 . C T 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTCAGTACTATACCATCA;RSEQ=CTCTGCAAGGTAACTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:820:820:614,206:0,0:1:0,2:23.2:1:30.7:1:1:0:54:81:1:0:1.1 1/1:841:816:585,231:17,5:0.9703:2,2:23.6:1:29.5:1:0.6404:1.34208:54.4:67:0.9722:0:1.1 -21 10996028 . C A 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00048;SOR=Inf;LSEQ=TCAGTACTATACCATCACCT;RSEQ=TGCAAGGTAACTGCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:866:0:0,0:626,240:0:2,0:23.7:1:31.5:1:1:0:54.2:122.714:1:0:1 0/1:903:12:9,3:627,264:0.0133:2,2:27.4:1:27.2:1:1:1.26:57.1:24:0.0134:0:1 -21 10996341 . A G 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39516;SOR=0.26458;LSEQ=AAGGCAAAGCCACTGTTACC;RSEQ=CTTATCAAACAGAATACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:24:1,23:0,1:0.96:0,1:19.9:1:32.2:1:1:0:53.8:48:0.96:0:2 1/1:7:6:0,6:0,1:0.8571:0,0:20.5:1:31.2:1:1:0:55.2:12:0.8571:0:2.7 -21 10998086 . T A 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.18238;SOR=0.20658;LSEQ=TCTTTAATTTATGTGCACAT;RSEQ=TTTTTGTTTAGACAGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:198:197,1:0,0:0.995:0,1:24.5:1:28.6:1:1:0:38.5:65:0.9949:0:1.4 1/1:167:163:154,9:3,1:0.976:2,2:23.7:1:28.7:1:0.22066:5.58:37.1:326:0.976:0:1.4 -21 10998165 . C A 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTATTTTTCTTTAATTAAC;RSEQ=AAGTGTTGATGATATTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:567:567:440,127:0,0:1:0,2:24.7:1:29.8:1:1:0:34.8:69.875:1:0:1.2 1/1:508:475:349,126:25,8:0.935:2,2:23.1:1:29.4:1:1:1.12796:34.4:117.75:0.9345:0:1.2 -21 10998257 . A G 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACACCATCTGTTCCTTCC;RSEQ=CTCCCTTAGTTTCATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1581:0:0,0:783,798:0:2,0:27.2:1:29.6:1:1:0:42.2:82.211:1:0:0.1 0/1:1867:53:26,27:926,880:0.0284:2,2:28.8:1:29.8:1:0.78168:1.09268:44:25.5:0.028:0:1.7 -21 10998319 . A T 155 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=37.32096;LSEQ=GATTCTGATTTTCCATCACA;RSEQ=TCCATAAGTTCTCCTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1017:1:0,1:334,680:0.001:2,0:29:0:13:0:1:0:50:0:0:0:1 0/1:1128:40:14,26:389,698:0.0355:2,2:22.7:1:29.2:1:1:1.03497:43:19:0.0345:0:1.9 -21 11011818 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08462;SOR=11.3341;LSEQ=ATGATACCCAATAAAAACTA;RSEQ=GAACAATAGGTCAAACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:0,1:3,17:0.0476:2,0:47:0:30:0:1:0:25:2:0.0476:0:1 0/1:5:2:0,2:1,2:0.4:2,0:33:1:29.5:1:1:0:24:4:0.4:0:1 -21 11012809 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=TTACCAACATTATGGAATTT;RSEQ=GATAGAACACCCATATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:14,1:0.1176:1,0:30:1:31:1:1:0:39:4:0.125:0:1 0/0:16:0:0,0:16,0:0:1,0:15.4:1:31.9:1:1:0:35.3:32:1:0:0.4 -21 11012843 . G C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.21157;LSEQ=TATGATTGAAGCAGATTTTA;RSEQ=AAGTGGTAAGCCAATTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:4:4,0:33,1:0.1053:1,0:33.8:1:33.3:1:1:0:30:8:0.1081:0:1.3 0/1:48:6:6,0:42,0:0.125:1,0:37:1:32.5:1:1:0:33:12:0.125:0:1.2 -21 11013029 . TAA T 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00264;SOR=0;LSEQ=GTAATTCTTTTCAGAAAAGG;RSEQ=AGTGTATTTACATACTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:7:0,7:21,121:0.047:2,0:27.9:1:32.9:1:0.59379:0:43:14:0.0483:0:0 0/0:195:0:0,0:27,167:0:2,0:21.7:1:29.8:1:1:0:44.1:26.714:1:0:0.6 -21 11013031 . A G 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62458;SOR=0.85073;LSEQ=AATTCTTTTCAGAAAAGGTA;RSEQ=AGTGTATTTACATACTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:20:6,14:11,104:0.1408:2,2:15.8:1:30.3:1:0.02127:3.99:47.6:9:0.1364:0:1.8 0/1:188:23:3,20:21,144:0.1223:2,2:20.1:1:30.8:1:1:1.03:46.2:22:0.1196:0:1.8 -21 11013050 . T C 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.30991;SOR=1.93342;LSEQ=AAAGTGTATTTACATACTTA;RSEQ=ATATGATTAAAATTTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:6:1,5:7,84:0.0619:2,2:16.5:1:32.8:1:0.41194:2.37:37.7:12:0.0619:0:2.3 0/1:97:11:0,11:3,82:0.1134:1,0:16.1:1:33.4:1:1:0:41.1:22:0.1146:0:1.9 -21 11013077 . G C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1024;SOR=Inf;LSEQ=TTAAAATTTCTGTTTCTATA;RSEQ=TCATTTTATTAAAATAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:4,54:0:2,0:27.9:1:31.7:1:1:0:38.7:28:1:0:0.2 0/1:52:3:0,3:5,44:0.0577:2,0:5.7:1:32:1:1:0:29.7:6:0.0588:0:1.7 -21 11013622 . A AT 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08527;SOR=0;LSEQ=TAAAAAGACCATATTTGTAC;RSEQ=TTTTTTTTTAAAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:6:1,5:45,186:0.0253:2,2:32.7:1:27.3:1:1:1.20876:25.5:5:0.0216:0:0.3 0/0:158:0:0,0:36,122:0:2,0:26.1:1:29.7:1:1:0:26.3:51.667:1:0:0.1 -21 11014896 . C T 46 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48669;SOR=1.86048;LSEQ=TTTTTTTTTTTGCTACATTT;RSEQ=AAAGAGAAAAGCTTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:3:2,1:222,86:0.0095:2,2:10.7:1:16.7:1:1:1.28961:46.7:0.5:0.0039:0:3 0/1:286:5:1,4:188,92:0.0175:2,2:7:1:20.2:1:0.04555:8.11266:52.6:4:0.0163:0:2.2 -21 11020280 . A G 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCACACGATACCACTTAAA;RSEQ=GGTTCCCCAGAAAGCCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:19:1:30:0:1:0:24:4:0.6667:0:1 1/1:1:1:1,0:0,0:1:0,0:9:0:34:0:1:0:25:2:1:0:1 -21 11020653 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATAGAGGAGCAAATTTCTT;RSEQ=AGATAGGAAACCCTTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:11,2:0.1333:2,0:21.5:1:32.5:1:1:0:32.5:4:0.1429:0:1.5 0/0:3:0:0,0:1,2:0:2,0:34.7:1:31:1:1:0:24.7:6:1:0:0 -21 11020706 . C T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTAAATACTGTCACATA;RSEQ=GTTTAATAATCATAATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:26,0:0,0:1:0,1:28.8:1:30:1:1:0:34.2:12:1:0:1.2 1/1:12:12:12,0:0,0:1:0,0:20.7:1:30.6:1:1:0:29.8:24:1:0:1.2 -21 11020738 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01932;SOR=Inf;LSEQ=ATAATACTTAATTGTGAGAA;RSEQ=TGGGAGCTCATGTTACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:57,1:0:1,0:23.4:1:32.1:1:1:0:35.8:57:1:0:0.5 0/1:36:4:4,0:31,1:0.1111:1,0:18.8:1:30:1:1:0:36:8:0.1111:0:1.3 -21 11020779 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22058;SOR=Inf;LSEQ=AAAACCAAATAAAAATTCAG;RSEQ=ACATATTTGTTAACTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:107,11:0:2,0:22.5:1:30:1:1:0:41.6:236:1:0:0.1 0/1:105:2:2,0:92,11:0.019:2,0:28:1:32:1:1:0:46:4:0.0194:0:1 -21 11020826 . C A 110 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00929;SOR=0.20521;LSEQ=TGTTTACCTTAATACTGACA;RSEQ=AGTATGGATGGTAACACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:13:11,2:180,85:0.0464:2,2:15.9:1:29.8:1:0.35732:2.59:25.2:26:0.0466:0:3 0/0:304:3:3,0:206,94:0.0099:2,0:13.7:1:31:1:0.55492:0:24.7:6:0.01:0:3 -21 11020827 . A T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3749;SOR=3.72272;LSEQ=GTTTACCTTAATACTGACAC;RSEQ=GTATGGATGGTAACACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:1:0,1:195,95:0.0034:2,0:1:0:26:0:0.3299:0:50:2:0.0035:0:1 0/1:315:4:2,2:212,99:0.0127:2,2:28.3:1:29.3:1:0.59582:2.13579:48.5:8:0.0129:0:1 -21 11020831 . T C 119 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00258;SOR=0.17658;LSEQ=ACCTTAATACTGACACAGTA;RSEQ=GGATGGTAACACTGACCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:14:12,2:190,100:0.0459:2,2:18.9:1:31.3:1:0.15233:3.15:25.4:28:0.0462:0:3 0/0:357:3:3,0:234,120:0.0084:2,0:15.3:1:32.7:1:0.55371:0:24.7:6:0.0085:0:3 -21 11020869 . G A 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.1358;LSEQ=ACACTGAGAACAGGCAAGTA;RSEQ=TCTTCCTTCTGCTCCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:40:36,4:232,207:0.0833:2,2:24.8:1:30.2:1:0:8.00:25.9:39:0.0826:0:2.2 0/1:575:7:7,0:309,259:0.0122:2,0:21.4:1:30.6:1:0.01829:0:26.6:14:0.0123:0:2.1 -21 11021014 . T C 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=8e-05;SOR=Inf;LSEQ=TCTTAACTAATATAGCTCTA;RSEQ=AGCTAAATATTGGATCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:831:0:0,0:722,108:0:2,0:23.1:1:30.5:1:1:0:39.6:47.824:0.9988:0:0.4 0/1:705:12:10,2:594,99:0.017:2,2:24.3:1:31.5:1:0.68541:1.19965:40.9:24:0.0173:0:1 -21 11021018 . TAA T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.18097;LSEQ=AACTAATATAGCTCTATAGC;RSEQ=ATATTGGATCACTTCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:928:106:89,17:711,111:0.1142:2,2:23.3:1:30.9:1:0.45648:1.22322:39.8:212:0.1156:0.0269:1.1 0/1:790:18:15,3:649,122:0.0228:2,2:20.7:1:30.6:1:1:1.06386:46.3:36:0.0231:0.0089:1 -21 11021038 . T A 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.25552;LSEQ=TAAATATTGGATCACTTCTG;RSEQ=GTAGATGAGATAAAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1268:138:107,31:906,224:0.1088:2,2:23.5:1:30:1:0.49949:1.1717:40.7:137:0.1099:0:1.3 0/1:1124:34:28,6:813,277:0.0302:2,2:20:1:29.4:1:0.42184:1.59:45.5:33:0.0299:0:1.1 -21 11021095 . T C 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07117;SOR=1.29216;LSEQ=TCAATGAGGAAGACAGTAAA;RSEQ=TGTCAAGTTCAAACCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2482:93:62,31:1485,903:0.0375:2,2:23.7:1:31.9:1:0.44528:1.22:47:92:0.0375:0:1 0/1:2589:124:70,54:1451,1014:0.0479:2,2:23.7:1:31.3:1:0.6404:1.10384:50.8:123:0.0478:0:1.1 -21 11021097 . G T 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.55543;LSEQ=AATGAGGAAGACAGTAAATT;RSEQ=TCAAGTTCAAACCTGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2523:161:109,52:1444,915:0.0638:2,2:23.9:1:29.9:1:0.11152:1.33:49.6:322:0.0645:0:3 0/1:2632:96:59,37:1469,1067:0.0365:2,2:22.4:1:29:1:0.52829:1.16:49.5:47:0.036:0:2.8 -21 11021106 . A G 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09896;SOR=0.72017;LSEQ=GACAGTAAATTGTCAAGTTC;RSEQ=AACCTGATTCAAAGTGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2770:62:24,38:1594,1111:0.0224:2,2:23.6:1:30.5:1:0.00166:2.27101:37.5:124:0.0226:0:1.1 0/1:2836:46:15,31:1564,1221:0.0162:2,2:23:1:30.7:1:0.00157:2.64634:38.9:92:0.0163:0:1.1 -21 11021107 . A T 223 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.0051;LSEQ=ACAGTAAATTGTCAAGTTCA;RSEQ=ACCTGATTCAAAGTGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2805:179:106,73:1527,1099:0.0638:2,2:25.8:1:29.9:1:0.81449:1.05:50.5:358:0.0647:0:1.2 0/0:2864:1:0,1:1592,1270:3e-04:2,0:1:0:26:0:0.44394:0:60:2:4e-04:0:1 -21 11021125 . C T 298 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.67235;LSEQ=CAAACCTGATTCAAAGTGAA;RSEQ=TTGTCACTGCTAGAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3166:719:412,307:1263,1183:0.2271:2,2:26.9:1:30.5:1:0.00745:1.26:53.4:358.5:0.2278:0:1.7 0/1:3308:1090:610,480:1116,1097:0.3295:2,2:27.3:1:29.6:1:0.00303:1.25:55:89.833:0.3294:0:1.3 -21 11021134 . G A 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.62002;LSEQ=TTCAAAGTGAACTTGTCACT;RSEQ=CTAGAAAACAACACAACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3295:266:144,122:1527,1496:0.0807:2,2:25.6:1:28.8:1:0.27694:1.16:55.2:265:0.0813:0:2.4 0/1:3428:177:95,82:1671,1578:0.0516:2,2:28:1:28.4:1:0.58921:1.09:55.9:58:0.0513:0:2.4 -21 11021163 . T TA 288 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18385;SOR=0.93177;LSEQ=CAACACAACCGTAGTGTGCA;RSEQ=AGAGTTTTCTTCATCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3534:969:438,531:1153,1409:0.2742:2,2:26.5:1:29.1:1:0.93958:1.01:56.2:56:0.2724:0.0376:0.2 0/1:3695:962:435,527:1293,1437:0.2604:2,2:26.4:1:28.9:1:0.25977:1.09006:57.5:95.2:0.2603:0.0284:0.1 -21 11021189 . G A 187 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=0.05512;LSEQ=TTTCTTCATCATCCTTATTT;RSEQ=ATGAAATATCTGCAGTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2772:88:33,55:1013,1671:0.0317:2,2:24.8:1:29:1:1:1.01037:56.4:28.333:0.031:0:1.2 0/0:2772:5:5,0:1131,1634:0.0018:2,0:1:0:20.6:1:0.01154:0:60:4:0.0015:0:1.6 -21 11021215 . T TA 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=2.30435;LSEQ=ATATCTGCAGTAGACACCTA;RSEQ=AAAAAGCAAAATACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1935:293:82,211:447,1192:0.1514:2,2:25.4:1:29.4:1:0.83106:1.04:50:40.857:0.1504:0.0155:0.1 0/1:1877:547:190,357:424,906:0.2914:2,2:24.6:1:29:1:0.23408:1.14:52.1:135.75:0.2919:0.0368:0.2 -21 11021242 . G A 119 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01689;SOR=3.67091;LSEQ=CAAAATACACAAAATACGAA;RSEQ=TTATATTTTTCACTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1068:4:1,3:165,899:0.0037:2,2:17.8:1:31:1:0.49173:1.81:33.8:8:0.0038:0:1 0/1:1028:14:4,10:208,806:0.0136:2,2:16.6:1:31.4:1:0.50372:1.55:32:28:0.0138:0:1.6 -21 11021330 . CA TG 93 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08436;SOR=0.16443;LSEQ=TTTGCTAAGGTCTAGAATAA;RSEQ=ATTCCAAATATTAATGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:8:0,8:13,177:0.0404:2,0:18.8:1:31.3:1:1:0:36.3:16:0.041:0.0101:1.1 0/0:146:1:0,1:9,136:0.0068:2,0:25:0:32.5:0:1:0:40:2:0.0069:0:1 -21 11021356 . G C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30018;SOR=0.60777;LSEQ=CAAATATTAATGCTAAGATA;RSEQ=TACTATAAAATGGAGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:19:0,19:12,109:0.1357:2,1:24.3:1:33.3:1:0.37029:0:30:38:0.1367:0:4.1 0/1:92:8:0,8:6,78:0.087:2,0:17.1:1:33.8:1:1:0:29.3:16:0.087:0:3.8 -21 11021360 . TA AG 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68551;SOR=0.78703;LSEQ=TATTAATGCTAAGATAGTAC;RSEQ=TAAAATGGAGTCATGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:19:0,19:12,109:0.1357:2,1:19.3:1:32.8:1:0.37029:0:30:38:0.1357:0:3.1 0/1:91:10:1,9:6,75:0.1099:2,2:11.7:1:31.4:1:0.5704:1.38:37.3:20:0.1099:0.033:2.2 -21 11021436 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54204;SOR=0;LSEQ=ATTCCTATAGACCAATAAGT;RSEQ=ATGAGAAAATATAATAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:0,2:3,28:0.0606:2,0:32:1:27:1:1:0:42.5:4:0.0625:0:1 0/0:17:0:0,0:4,13:0:2,0:21.6:1:28.6:1:1:0:57.1:16:1:0:0.1 -21 11021499 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52696;SOR=0;LSEQ=GCAGAATTCTAATCAAGAAA;RSEQ=TATAAATGATAATATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:2,12:0.1765:2,0:41.3:1:29:1:1:0:35.7:6:0.1875:0:2.7 0/0:8:0:0,0:2,6:0:2,0:24.4:1:31.4:1:1:0:55.9:16:1:0:0.1 -21 11021519 . T G 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.11371;SOR=0;LSEQ=CTATAAATGATAATATTATA;RSEQ=GTATGTACACACACAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:2,6:0.3846:2,0:34:1:31.6:1:0.48718:0:37.4:10:0.4167:0:2 0/0:7:0:0,0:2,5:0:2,0:23:1:29:1:1:0:53.1:14:1:0:0.1 -21 11021767 . G A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGGCTGGAGTGTAATAGC;RSEQ=TGATCTCAGCTCATTGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:34.5:1:31:1:1:0:60:4:0.6667:0:2 1/1:1:1:1,0:0,0:1:0,0:8:0:31:0:1:0:49:2:1:0:2 -21 11021780 . A G 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAATAGCGTGATCTCAGCTC;RSEQ=TTGCAACCTCTGCCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:47:1:31:1:1:0:60:4:0.6667:0:2 1/1:1:1:1,0:0,0:1:0,0:21:0:31:0:1:0:49:2:1:0:2 -21 11022466 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCTTGAGCTCAGGAGTT;RSEQ=GAGACCAGCCTGGGCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29:1:1:0:54.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11025762 . C G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCACTGCACTCCAGCCA;RSEQ=GAATTAGAACGAGAACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:28.5:1:1:0:50:4:1:0:2 -21 11025880 . G C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAGAAAAGGGAGTACAC;RSEQ=GTTAACAAATACAACAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:32:0:1:0:60:4:1:0:1 -21 11026351 . A G 68 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGATTTTAATAAAATAGC;RSEQ=AAGTTATTACATAAAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:22.4:1:29.4:1:1:0:42.4:10:1:0:1 1/1:2:2:2,0:0,0:1:0,0:7:1:31.5:1:1:0:53:4:1:0:1 -21 11026430 . T TAGTA 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.26024;SOR=2.75268;LSEQ=AATAAAGCTTCATAACATGA;RSEQ=AGCAAATATCTATCAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:9,0:10,1:0.45:2,0:19.8:1:30.7:1:1:0:31.1:18:0.5:0.2:0.7 1/0:10:7:5,2:3,0:0.7:0,2:23.7:1:26.8:1:1:0:43.9:14:0.7:0.1:0.6 -21 11026454 . AT A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.30258;SOR=0;LSEQ=AAATATCTATCAATCTTAAA;RSEQ=TTTTTAAATAAAAGAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:3,1:20,3:0.1481:2,2:23.8:1:30.5:1:0.49544:2.14404:25.8:8:0.1481:0:1 0/0:11:0:0,0:9,2:0:2,0:25.4:1:29.8:1:1:0:46.5:22:1:0:0.3 -21 11026473 . A T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7236;LSEQ=AATTTTTTAAATAAAAGAGC;RSEQ=ACTATATTACATAATGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:5,1:20,3:0.2069:2,2:30:1:30.2:1:1:1.31934:30.3:12:0.2143:0:1 0/1:19:3:2,1:14,2:0.1579:2,2:32:1:29.7:1:0.42208:3.20798:48:6:0.1579:0:1 -21 11026527 . C CAAAGAGGAAGGTAAGA 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=4.000;MSILEN=1;SSF=6e-05;SOR=0.11456;LSEQ=GGCATAGAAAGATAAGGAGT;RSEQ=AAAGAGGAAGGTAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:28:24,4:48,9:0.3294:2,2:19.5:1:30.5:1:1:1.12:41.4:27:0.3253:0.1882:1.3 0/1:57:3:3,0:45,9:0.0526:2,0:11.3:1:30.3:1:1:0:32.3:6:0.0536:0.0526:1.3 -21 11026547 . G A 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.01536;SOR=0.38614;LSEQ=CAAAGAGGAAGGTAAGAAAA;RSEQ=AGAAAGGATGAGAAAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:34:27,7:88,14:0.25:2,2:23.4:1:30.7:1:0.41109:1.62328:46.4:68:0.25:0:2 0/1:88:10:9,1:65,13:0.1136:2,2:22.6:1:29.8:1:1:1.79:48.1:20:0.1136:0:2 -21 11026550 . A G 146 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00043;SOR=0.15065;LSEQ=AGAGGAAGGTAAGAAAAGAG;RSEQ=AAGGATGAGAAAGTAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:26:21,5:105,17:0.1757:2,2:22.1:1:31.2:1:0.54416:1.46642:36.7:52:0.1793:0:1.8 0/1:97:3:3,0:77,17:0.0309:2,0:15.3:1:31.3:1:1:0:36.7:6:0.0316:0:2 -21 11026554 . G A 128 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00622;SOR=2.77201;LSEQ=GAAGGTAAGAAAAGAGAAAG;RSEQ=ATGAGAAAGTAAATATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:14:12,2:122,22:0.0886:2,2:16.6:1:31.1:1:1:1.08:52.5:28:0.0897:0:1.2 0/1:108:23:20,3:70,15:0.213:2,2:19.1:1:28.4:1:0.7584:1.42:52:46:0.215:0:1.3 -21 11026555 . A G 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.89078;SOR=1.05633;LSEQ=AAGGTAAGAAAAGAGAAAGG;RSEQ=TGAGAAAGTAAATATACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:43:36,7:99,16:0.2722:2,2:23.8:1:31.5:1:0.8004:1.20164:46.8:42:0.271:0:1.8 0/1:113:32:24,8:71,10:0.2832:2,2:20.8:1:30.7:1:0.15091:2.34646:47.3:64:0.2857:0:1.4 -21 11026589 . A T 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.23966;LSEQ=ATACAAGAAAATGTAACCAG;RSEQ=GGCTCAAAAAAAAGTAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:45:34,11:154,18:0.2074:2,2:31.6:1:29.9:1:0.02427:2.75211:36.2:90:0.2083:0:1.6 0/1:187:11:11,0:146,30:0.0588:2,0:34.2:1:29.5:1:0.21684:0:31.7:22:0.0595:0:1.4 -21 11026598 . A AAAAAG 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.18679;SOR=1.40589;LSEQ=AATGTAACCAGAGGCTCAAA;RSEQ=AAAAGTAGGACAGTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:40:35,5:139,22:0.1905:2,2:36.7:1:30.9:1:1:1.11:46.4:80:0.1914:0.0143:1.3 0/1:197:49:40,9:120,20:0.2487:2,2:34.6:1:30.1:1:0.49582:1.34776:45:98:0.2539:0.0102:0.7 -21 11026600 . A AAAAGCG 145 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=8.000;MSILEN=1;SSF=0.00596;SOR=0.35607;LSEQ=TGTAACCAGAGGCTCAAAAA;RSEQ=AAGTAGGACAGTAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:28:20,8:167,17:0.1315:2,2:36.8:1:30.3:1:0.00774:3.89382:32.5:56:0.1321:0:1.6 0/1:196:10:10,0:155,31:0.051:2,0:38.6:1:30:1:0.36821:0:31.6:20:0.0513:0:1.4 -21 11026644 . C CATAAG 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05477;SOR=1.46028;LSEQ=TTTGACCTATTTATATGACT;RSEQ=ATCAAAATAACTTGCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:62:50,12:204,30:0.2081:2,2:15.7:1:29.9:1:0.21896:1.62902:35.2:124:0.2102:0.1174:0.6 0/1:292:81:68,13:153,41:0.2774:2,2:13.9:1:28.4:1:0.40597:1.40:39.9:80:0.2778:0.1815:0.5 -21 11026645 . A ATAAGG 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00329;SOR=Inf;LSEQ=TTGACCTATTTATATGACTC;RSEQ=TCAAAATAACTTGCTATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:253,44:0:2,0:21.4:1:30.2:1:1:0:51.8:296:0.9933:0:0.2 0/1:290:8:6,2:225,55:0.0276:2,2:32.6:1:29.1:1:0.65971:1.36204:48.1:16:0.0283:0.0034:0.1 -21 11026647 . C A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06148;SOR=0;LSEQ=GACCTATTTATATGACTCAT;RSEQ=AAAATAACTTGCTATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:5:5,0:233,46:0.0176:2,0:10:1:26.4:1:1:0:49.4:10:0.0177:0:1.6 0/0:277:0:0,0:213,57:0:2,0:20.3:1:30.6:1:1:0:49.7:53:1:0:0.2 -21 11026651 . A T 128 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0201;SOR=0.33929;LSEQ=TATTTATATGACTCATCAAA;RSEQ=TAACTTGCTATGAGATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:17:12,5:227,59:0.0561:2,2:10.6:1:31.4:1:0.36895:1.60031:29.3:34:0.0563:0:2.1 0/1:304:6:6,0:220,78:0.0197:2,0:6.7:1:30.8:1:0.34396:0:30.7:12:0.02:0:2.2 -21 11026667 . T C 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00078;SOR=0.30941;LSEQ=CAAAATAACTTGCTATGAGA;RSEQ=TTTCATCATTAACTGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:32:24,8:241,108:0.084:2,2:18.8:1:31.8:1:0.55234:1.34:28.7:31:0.0836:0:1.8 0/1:363:10:10,0:227,125:0.0275:2,0:17.8:1:32.5:1:0.01744:0:28.2:20:0.0279:0:1.7 -21 11026697 . G T 130 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00574;SOR=0.37889;LSEQ=TAACTGACATTTAGATTAGA;RSEQ=AAAATATACATGAAGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:547:29:5,24:344,173:0.053:2,2:22.8:1:26.9:1:0:9.50516:28:28:0.0524:0:2 0/1:530:11:0,11:350,169:0.0208:2,0:32.9:1:26.5:1:1e-05:0:31.7:22:0.0209:0:1.4 -21 11026722 . C A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TATACATGAAGCAAGCCTCA;RSEQ=CCCAGGCAATACAACAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:0:0,0:449,230:0:2,0:26.6:1:31.6:1:1:0:32.8:51.231:1:0:0.7 0/1:696:17:9,8:492,187:0.0244:2,2:27.5:1:28.2:1:0.09872:2.33544:39.9:16:0.0233:0:1.1 -21 11026734 . C A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AAGCCTCACCCCAGGCAATA;RSEQ=AACAGCTCCGATTCCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:775:0:0,0:492,283:0:2,0:24.9:1:32.1:1:1:0:32.1:76.5:1:0:0.8 0/1:825:14:11,3:545,266:0.017:2,2:23.4:1:31.1:1:0.56634:1.79:31.1:28:0.0171:0:2.4 -21 11026737 . C G 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=1.83754;LSEQ=CCTCACCCCAGGCAATACAA;RSEQ=AGCTCCGATTCCACTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:796:193:141,52:353,249:0.2425:2,2:25.4:1:31.5:1:0.00033:1.91:30.2:31.167:0.2404:0:1.8 0/1:872:323:250,73:316,232:0.3704:2,2:23.3:1:31.8:1:0:2.51:30.3:63.6:0.3676:0:1.6 -21 11026744 . G A 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04415;SOR=1.39779;LSEQ=CCAGGCAATACAACAGCTCC;RSEQ=ATTCCACTTTTCAGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:859:68:48,20:470,321:0.0792:2,2:24.3:1:30:1:0.07221:1.64:27.8:67:0.0788:0:1.8 0/1:960:103:63,40:538,319:0.1073:2,2:24.3:1:30:1:0.74759:1.07073:29:206:0.1079:0:1.8 -21 11026766 . C T 153 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13335;LSEQ=TTCCACTTTTCAGCTTTGAC;RSEQ=TGCCTCGGCCACCTCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1019:31:7,24:575,413:0.0304:2,2:23.2:1:30.9:1:0.00013:4.76652:28.7:62:0.0306:0:2.4 0/0:1201:5:1,4:705,489:0.0042:2,2:15.8:1:30.6:1:0.16581:5.75947:28.2:10:0.0042:0:2 -21 11026767 . T C 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=68.4825;LSEQ=TCCACTTTTCAGCTTTGACC;RSEQ=GCCTCGGCCACCTCGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1021:1:1,0:579,441:0.001:2,0:35:0:17:0:1:0:25:0:0:0:4 0/1:1207:76:48,28:662,467:0.063:2,2:28.9:1:29.1:1:0.47159:1.21:32:75:0.0628:0:1.8 -21 11026782 . G A 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00242;SOR=1.49638;LSEQ=TGACCTGCCTCGGCCACCTC;RSEQ=CCCCGACAGTCCTGCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1133:97:59,38:541,494:0.0856:2,2:21.9:1:29.4:1:0.11157:1.42:30.5:194:0.0875:0:2.1 0/1:1432:176:101,75:668,585:0.1229:2,2:21.1:1:28.7:1:0.33299:1.18:31.9:34.2:0.1215:0:2.1 -21 11026786 . C T 132 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=0.16531;LSEQ=CTGCCTCGGCCACCTCGCCC;RSEQ=GACAGTCCTGCACCTCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1174:19:7,12:602,553:0.0162:2,2:16.5:1:31.2:1:0.24748:1.86519:28.6:38:0.0165:0:2.6 0/0:1476:4:2,2:778,694:0.0027:2,2:12.3:1:27:1:1:1.12095:40.3:3:0.0021:0:2.8 -21 11026803 . G A 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.66241;LSEQ=CCCCGACAGTCCTGCACCTC;RSEQ=AGGTCTCCGCTTTCTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1243:237:115,122:476,529:0.1907:2,2:27.2:1:29.6:1:0.77265:1.05:36.9:58.25:0.1905:0:1.3 0/1:1630:220:106,114:684,725:0.135:2,2:26.6:1:29.2:1:0.94226:1.01464:36.5:54:0.1347:0:1.6 -21 11026806 . G A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42317;LSEQ=CGACAGTCCTGCACCTCGAG;RSEQ=TCTCCGCTTTCTTGGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1256:327:151,176:434,495:0.2604:2,2:29.2:1:30.4:1:0.89749:1.02191:37.6:108:0.2621:0:2.6 0/1:1628:211:97,114:675,739:0.1296:2,2:28.5:1:29.2:1:0.65785:1.0734:38.8:69.333:0.1297:0:2.5 -21 11026812 . G A 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.65373;LSEQ=TCCTGCACCTCGAGGTCTCC;RSEQ=CTTTCTTGGAAATCCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1278:383:167,216:403,491:0.2997:2,2:27:1:29.9:1:0.66726:1.06158:37.6:94.75:0.3006:0:2.5 0/1:1660:688:302,386:457,512:0.4145:2,2:27.2:1:29.4:1:0.1936:1.14075:38.6:85:0.4156:0:1.9 -21 11026835 . T C 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=1.61641;LSEQ=TTCTTGGAAATCCAGACCCA;RSEQ=GGCCCTATGTAACAGATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1143:137:59,78:367,639:0.1199:2,2:31.1:1:30.7:1:0.15753:1.32:34.5:136:0.1211:0:1.6 0/1:1452:262:129,133:453,735:0.1804:2,2:29.5:1:30.1:1:0.00105:1.57:35.9:86.333:0.1815:0:1.7 -21 11026874 . G T 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00386;SOR=1.39751;LSEQ=AGGAAAAGTCAACATTCTGT;RSEQ=ACAGCCCAAAATAATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:189:50,139:105,269:0.2825:2,2:22.7:1:28.7:1:0.76447:1.085:35.2:93.5:0.2825:0:2.3 0/1:769:273:66,207:142,254:0.355:2,2:21.5:1:28.6:1:0.00163:1.75193:35.6:135.5:0.3556:0:2 -21 11026875 . A T 90 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01475;SOR=0.10725;LSEQ=GGAAAAGTCAACATTCTGTG;RSEQ=CAGCCCAAAATAATTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:8:6,2:175,472:0.0122:2,2:28.6:1:30:1:0.00695:8.06:33.4:16:0.0123:0:1.5 0/0:756:1:1,0:229,526:0.0013:2,0:28:0:32:0:0.30423:0:40:2:0.0013:0:1 -21 11026921 . T C 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.0321;SOR=Inf;LSEQ=AATGCCACTGAGATAAAACA;RSEQ=TTTATTAAATGTTATACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:22,224:0:2,0:23.4:1:30.3:1:1:0:33.8:492:1:0:0.4 0/1:278:6:1,5:32,240:0.0216:2,2:30:1:29.8:1:0.53492:1.50:41.8:5:0.0182:0:1.3 -21 11026960 . T G 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07355;SOR=0.28349;LSEQ=AACACTTCTTTAGATAAGTA;RSEQ=TAAAAGACCTGGCTTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:9:2,7:9,124:0.0634:2,2:33.1:1:32.8:1:0.14563:3.88:45.7:18:0.0638:0:1.4 0/1:160:3:0,3:26,131:0.0188:2,0:22.3:1:32:1:1:0:39.7:6:0.019:0:1.7 -21 11026964 . A G 92 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00811;SOR=0.09717;LSEQ=CTTCTTTAGATAAGTATTAA;RSEQ=AGACCTGGCTTATTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:9:0,9:10,123:0.0634:2,0:20.6:1:29.3:1:1:0:25.2:18:0.0647:0:4.3 0/0:154:1:0,1:26,127:0.0065:2,0:35:0:33:0:1:0:24:2:0.0066:0:3 -21 11026966 . G A 84 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00791;SOR=0.09635;LSEQ=TCTTTAGATAAGTATTAAAA;RSEQ=ACCTGGCTTATTATTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:9:0,9:10,121:0.0643:2,0:22.6:1:26.8:1:1:0:25.2:8:0.058:0:4.3 0/0:153:1:0,1:26,126:0.0065:2,0:37:0:32:0:1:0:24:2:0.0066:0:3 -21 11027038 . C A 110 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00268;SOR=0.07929;LSEQ=TAAATATAAAATGCTTACAA;RSEQ=CTTAGAATCATACTTTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:12:0,12:3,39:0.2222:2,0:23.1:1:30.8:1:1:0:30.7:24:0.2222:0:3.8 0/1:46:1:0,1:9,36:0.0217:2,0:29:0:32:0:1:0:40:2:0.0217:0:3 -21 11027052 . T C 104 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01463;SOR=0.09156;LSEQ=TTACAACCTTAGAATCATAC;RSEQ=TTAGGCCTGTCACTGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:9:0,9:3,30:0.2143:2,0:15.9:1:33:1:1:0:34.3:18:0.2143:0:3.7 0/1:42:1:0,1:7,34:0.0238:2,0:43:0:34:0:1:0:40:2:0.0238:0:3 -21 11027065 . C A 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69202;SOR=1.6923;LSEQ=ATCATACTTTAGGCCTGTCA;RSEQ=TGTGAACGCTATCAGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:0,3:3,29:0.0857:2,0:29.3:1:32.7:1:1:0:56.3:6:0.0857:0:1.7 0/1:29:4:1,3:4,21:0.1379:2,2:28:1:30.3:1:0.55261:1.71:58.3:8:0.1379:0:2 -21 11027085 . A C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05468;SOR=3.85961;LSEQ=CTGTGAACGCTATCAGCAAG;RSEQ=CTTTGCATGATTTTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:0,9:2,8:0.4737:2,0:23.2:1:31.2:1:0.47368:0:47.8:18:0.4737:0:2.1 1/0:23:18:3,15:0,5:0.7826:0,2:18.1:1:31.2:1:1:0:54.2:17:0.7727:0:1.6 -21 11027129 . C T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63956;SOR=1.89552;LSEQ=CACTCCTACATTCTCGGTGA;RSEQ=GACAACAACTGTAGCCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:1,4:2,11:0.2778:2,2:28:1:29.8:1:1:1.35:52.8:10:0.2778:0:2 0/1:7:3:1,2:1,3:0.4286:2,2:14:1:31.3:1:1:1.41:60:6:0.4286:0:2 -21 11027175 . T C 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.12136;LSEQ=TATTTCGAAGTGCAACAAAT;RSEQ=GTATTCAATATAGAGTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:1,3:1,8:0.3077:2,2:25.3:1:29.3:1:1:2.45:51:8:0.3077:0:2 1/0:2:1:0,1:1,0:0.5:0,0:22:0:25:0:1:0:40:2:0.5:0:4 -21 11027188 . G C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAAATTGTATTCAATATA;RSEQ=AGTAAGGATAAGGAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:1,7:0.2727:2,0:28.3:1:32:1:1:0:33:6:0.2727:0:1 0/0:2:0:0,0:1,1:0:2,0:36.5:1:31:1:1:0:50:4:1:0:2 -21 11027227 . A G 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.23609;LSEQ=CTCTCTCATTAACTGGTCTC;RSEQ=CGGTGATTACAGTAATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:23:1:31.5:1:1:0:35.5:4:0.2857:0:1.5 1/0:2:1:0,1:0,1:0.5:0,0:27:0:34:0:1:0:40:2:0.5:0:4 -21 11028179 . AT A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGTTTCCAAGTCAAAA;RSEQ=TTATGGTGATACTGTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:1:31.5:1:1:0:27:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11028504 . GC G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTTCAAACAATTCTCCT;RSEQ=CTCAGCTTCCCTAGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35:0:33:1:1:0:60:4:1:0:0.5 -21 11029336 . A C 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.2807;SOR=0;LSEQ=ATGAAAAGATCCTTAATTAC;RSEQ=TTTTGGTCTACATGTCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:4,0:11,0:0.2667:0,0:20.5:1:31.8:1:1:0:39:8:0.2667:0:1.5 0/0:6:0:0,0:4,1:0:2,0:21:1:30.8:1:1:0:55.4:10:0.8333:0:0 -21 11029406 . TA T 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.86153;LSEQ=ACAACAAAAGGAATTAACCA;RSEQ=AAAAGAGGTATTAAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:9,0:29,0:0.2368:1,0:27.9:1:31.7:1:1:0:35.7:18:0.25:0.0263:0.3 0/1:19:4:4,0:12,3:0.2105:2,0:22.3:1:29.7:1:1:0:33:8:0.2105:0.0526:0.5 -21 11029490 . T C 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79551;SOR=1.08487;LSEQ=AAATTTTTAGATTTAAAAAG;RSEQ=GTTTCTGGAAGCTCAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:45:43,2:124,12:0.2473:2,1:22.9:1:32:1:0.52262:2.07:39.1:44:0.2444:0:3 0/1:137:36:35,1:89,12:0.2628:2,1:20.1:1:32.4:1:0.18332:4.68:38.4:72:0.2628:0:3.6 -21 11029497 . G A 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00047;SOR=Inf;LSEQ=TAGATTTAAAAAGTGTTTCT;RSEQ=GAAGCTCAATCTAGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:186,15:0:2,0:24.5:1:32.1:1:1:0:44.5:66:1:0:1.1 0/1:154:9:8,1:131,14:0.0584:2,2:25:1:28.1:1:1:1.16837:52.1:18:0.0584:0:1.9 -21 11029501 . G A 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46996;SOR=1.16999;LSEQ=TTTAAAAAGTGTTTCTGGAA;RSEQ=CTCAATCTAGAAAAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:85:80,5:113,11:0.4048:2,2:25.8:1:29.8:1:0.59775:1.55:38.9:41.5:0.4029:0:2.4 0/1:176:78:72,6:84,14:0.4432:2,2:21.7:1:30.4:1:0.23272:1.99:40.4:156:0.4457:0:3 -21 11029520 . G T 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.01234;SOR=Inf;LSEQ=AGCTCAATCTAGAAAAGAAA;RSEQ=ATTTAATTCTTAACATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:237,26:0:2,0:25.7:1:32.4:1:1:0:48.5:262:1:0:1.1 0/1:246:6:4,2:213,27:0.0244:2,2:21.8:1:29.3:1:0.14925:3.90966:57:12:0.0248:0:1 -21 11029522 . T C 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAATCTAGAAAAGAAAGA;RSEQ=TTAATTCTTAACATCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:244,27:0:2,0:25.6:1:31.2:1:1:0:48.8:89.333:1:0:1.1 0/1:255:34:31,3:193,27:0.1333:2,2:23.4:1:31.3:1:0.77676:1.44:43.8:68:0.136:0:3.9 -21 11029526 . A G 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00192;SOR=0;LSEQ=ATCTAGAAAAGAAAGATTTA;RSEQ=TTCTTAACATCCAGTAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:10:8,2:250,30:0.0345:2,2:14.6:1:32.5:1:0.30406:2.07653:57.4:20:0.0351:0:1 0/0:269:0:0,0:230,37:0:2,0:24.5:1:29.8:1:1:0:50.1:52.4:0.9924:0:1.6 -21 11029529 . C G 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGAAAAGAAAGATTTAATT;RSEQ=TTAACATCCAGTAGGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:268,36:0:2,0:24.7:1:31.3:1:1:0:49.4:49.667:1:0:1.2 0/1:283:20:16,4:223,38:0.0707:2,2:28.1:1:31.4:1:0.51501:1.46487:56.8:19:0.0683:0:1.4 -21 11029536 . T C 81 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12351;SOR=0.17042;LSEQ=GAAAGATTTAATTCTTAACA;RSEQ=CCAGTAGGGCAAAACAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:6:6,0:298,52:0.0169:2,0:27.8:1:31.7:1:0.59834:0:36:12:0.0171:0:2.2 0/0:344:1:1,0:282,61:0.0029:2,0:43:0:33:0:1:0:25:2:0.0029:0:2 -21 11029561 . A C 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00033;SOR=1.60648;LSEQ=TAGGGCAAAACAAATCAGAC;RSEQ=GAAGTGATATATGAATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:141:107,34:276,96:0.2743:2,2:23.6:1:30.7:1:0.73407:1.09:44.1:69.5:0.2731:0:3.7 0/1:553:209:161,48:238,106:0.3779:2,2:25:1:29.6:1:0.05052:1.49:43.5:51.25:0.3741:0:3.8 -21 11029565 . G A 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=1.0867;LSEQ=GCAAAACAAATCAGACAGAA;RSEQ=TGATATATGAATGTAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:279:209,70:202,85:0.4921:2,2:22.3:1:29.9:1:0.25801:1.26:44.8:33.875:0.4883:0:3 1/0:583:299:221,78:194,88:0.5129:2,2:25.2:1:29.7:1:0.19831:1.28:44.2:148.5:0.5121:0:3.3 -21 11029594 . G T 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.86233;SOR=0.93795;LSEQ=GAATGTAAATGTAATTTTAT;RSEQ=TACCACTTTGATGCTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:859:16:14,2:526,316:0.0186:2,2:7:1:30.3:1:0.06354:4.20:45.8:32:0.0188:0:3.3 0/1:972:17:15,2:591,363:0.0175:2,2:8.4:1:30.6:1:0.03973:4.60:42.4:34:0.0177:0:3.5 -21 11029596 . AC A 185 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTAAATGTAATTTTATGT;RSEQ=CACTTTGATGCTCCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:900:0:0,0:564,334:0:2,0:24.5:1:31.5:1:1:0:53.8:80.636:0.9989:0:1.5 0/1:1014:62:32,30:592,358:0.0611:2,2:26.5:1:31.1:1:0.1058:1.54952:60:124:0.0619:0.0069:0.2 -21 11029604 . GA TG 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65264;SOR=0.89489;LSEQ=GTAATTTTATGTACCACTTT;RSEQ=TGCTCCAAATGGCACTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:977:41:30,11:579,357:0.042:2,2:10.7:1:31.2:1:0.18719:1.68:48.9:82:0.0426:0.0143:1.3 0/1:1087:41:27,14:619,425:0.0377:2,2:11.2:1:31.1:1:0.42319:1.32:46.1:82:0.0381:0.012:1.4 -21 11029616 . G T 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00107;SOR=1.32336;LSEQ=ACCACTTTGATGCTCCAAAT;RSEQ=GCACTGCCAGGAAGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1049:445:278,167:360,244:0.4242:2,2:27.4:1:30:1:0.37045:1.13:45.5:88:0.4264:0:3.1 0/1:1191:588:333,255:335,266:0.4937:2,2:27.9:1:29.6:1:0.77028:1.04:45.1:146:0.4966:0:3.1 -21 11029624 . C T 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.91169;LSEQ=GATGCTCCAAATGGCACTGC;RSEQ=AGGAAGCTGCCTGGGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1118:249:154,95:499,370:0.2227:2,2:25.9:1:29.8:1:0.21608:1.20:44.2:123.5:0.225:0:3.2 0/1:1260:446:254,192:428,385:0.354:2,2:28.6:1:29.3:1:0.15585:1.19:44.6:73.333:0.3548:0:3.1 -21 11029630 . GC G 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.99753;LSEQ=CCAAATGGCACTGCCAGGAA;RSEQ=TGCCTGGGTTTAAAAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1137:228:139,89:505,404:0.2005:2,2:28.1:1:32.1:1:0.15565:1.25:43.9:456:0.2025:0.0211:3.1 0/1:1285:429:243,186:440,415:0.3339:2,2:29.4:1:31.3:1:0.08558:1.23:44.4:858:0.3375:0.0233:3 -21 11029653 . C T 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.55429;LSEQ=GCCTGGGTTTAAAAATTTCC;RSEQ=GACCTCCTGAAATGTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1287:218:104,114:532,535:0.1694:2,2:24.1:1:30.5:1:0.60296:1.08993:43.7:217:0.1705:0:3.1 0/1:1369:139:61,78:608,618:0.1015:2,2:25.3:1:29.7:1:0.21105:1.25778:42:68.5:0.101:0:3 -21 11029659 . CC AA 131 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTAAAAATTTCCCGACCT;RSEQ=TGAAATGTCTGGGGACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1294:0:0,0:629,665:0:2,0:25.4:1:31:1:1:0:52.3:79.875:1:0:1.1 0/1:1373:22:6,16:655,693:0.016:2,2:23.5:1:29.5:1:0.05374:2.51868:49.6:44:0.0162:7e-04:4 -21 11029675 . A C 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08487;LSEQ=ACCTCCTGAAATGTCTGGGG;RSEQ=CCACGAGGGTGGGCTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1248:133:58,75:527,586:0.1066:2,2:26.9:1:31.3:1:0.46228:1.16277:40.8:43.333:0.1054:0:3.3 0/1:1398:14:7,7:625,756:0.01:2,2:28.6:1:31:1:0.79102:1.21:39.5:28:0.0102:0:3.1 -21 11029677 . C A 125 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTCCTGAAATGTCTGGGGAC;RSEQ=ACGAGGGTGGGCTCACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1245:0:0,0:575,665:0:2,0:26:1:31.2:1:1:0:51.4:52.913:0.9967:0:1 0/1:1399:19:7,12:621,755:0.0136:2,2:18.2:1:29.6:1:0.49801:1.40969:46.4:18:0.013:0:4 -21 11029679 . C G 282 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02448;SOR=1.19506;LSEQ=CCTGAAATGTCTGGGGACCA;RSEQ=GAGGGTGGGCTCACTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1250:493:234,259:340,412:0.3944:2,2:26.1:1:31.2:1:0.45013:1.09:41.6:60.625:0.3937:0:2.2 0/1:1396:611:273,338:351,432:0.4377:2,2:23.5:1:30.5:1:1:1.00595:41.4:75.375:0.4366:0:2 -21 11029721 . A G 166 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01409;SOR=0.46975;LSEQ=TGGGTACTCCAAGCCTCCTA;RSEQ=GATATGGCAGTTGAGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:981:33:29,4:316,632:0.0336:2,2:19.8:1:33:1:0:14.47:31.9:66:0.0343:0:1 0/1:1057:17:17,0:400,639:0.0161:2,1:21.5:1:33.2:1:0:0:32.2:34:0.0164:0:1.1 -21 11029842 . G T 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00432;SOR=0;LSEQ=ATGGAAATTTAGGACAAATT;RSEQ=CTTCAAGGAAGGCAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:12:1,11:33,182:0.0529:2,2:26.8:1:30.1:1:1:1.98964:54.5:24:0.0533:0:1 0/0:142:0:0,0:29,113:0:2,0:23.5:1:31.9:1:1:0:51.3:70:1:0:0.3 -21 11029855 . C T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3925;SOR=0.76065;LSEQ=ACAAATTGCTTCAAGGAAGG;RSEQ=AAAATAAGCTAATCACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:47:4,43:21,117:0.2541:2,2:21.9:1:28.7:1:0.32628:1.92347:54.6:94:0.2568:0:1 0/1:107:22:3,19:13,70:0.2056:2,2:20.1:1:27.4:1:1:1.17443:54.5:21:0.2:0:1.1 -21 11029894 . C G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48481;SOR=0.49436;LSEQ=ACAGTGATTTAAACATTTAA;RSEQ=TATAACAAATAACTTAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:7:0,7:3,52:0.1129:2,0:17.3:1:29.6:1:1:0:29.4:6:0.0984:0:1 0/1:34:2:0,2:2,30:0.0588:2,0:34.5:1:33:0:1:0:32:4:0.0588:0:1.5 -21 11029900 . CAAATAACTT C 46 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53479;LSEQ=ATTTAAACATTTAACTATAA;RSEQ=AAATGTTTGCTGCTACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:0,3:3,48:0.0556:2,0:35:1:29.2:1:1:0:25:6:0.0577:0.0185:1 0/1:33:1:0,1:3,29:0.0303:2,0:43:0:34:0:1:0:24:2:0.0303:0:1 -21 11029936 . C T 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0241;SOR=4.79388;LSEQ=TTGCTGCTACAGAGACATCA;RSEQ=TACAATGAAACATTAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:2,18:0.2:2,0:18:1:30:1:1:0:42.2:10:0.2:0:2 1/0:18:10:1,9:0,8:0.5556:0,2:27.7:1:29.9:1:1:0:43.7:20:0.5556:0:2.2 -21 11029967 . G A 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02881;SOR=12.68572;LSEQ=CATTAAAAATTAAGGTTTAT;RSEQ=TGACATCAACATTGACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:1,7:0.3846:2,0:36.2:1:30.8:1:1:0:27.4:10:0.3846:0:2 1/1:10:9:1,8:0,1:0.9:0,2:18.3:1:29.9:1:1:0:39.9:18:0.9:0:2.3 -21 11029978 . A T 69 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01806;SOR=15.15841;LSEQ=AAGGTTTATGTGACATCAAC;RSEQ=TTGACTCATGAACTGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:1,10:0.2143:2,0:24.3:1:30.7:1:1:0:30:6:0.2143:0:3 1/1:6:5:1,4:0,1:0.8333:0,2:23.6:1:30:1:1:0:40.6:10:0.8333:0:3.2 -21 11030021 . A C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=TGCACCAAAAAGTAAATAAA;RSEQ=GTCAATCACACTTTAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:2,6:0.2:2,0:28.5:1:31.5:1:1:0:25:4:0.2:0:3 1/1:2:2:0,2:0,0:1:0,0:12:1:29.5:1:1:0:39:4:1:0:3.5 -21 11038164 . A G 67 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTATCTTTACTTACTGAAA;RSEQ=TCAATAGTACAATTCTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:24.8:1:33.8:1:1:0:40.3:8:0.8:0:1 1/1:1:1:1,0:0,0:1:0,0:33:0:33:0:1:0:60:2:1:0:1 -21 11038338 . A G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAGTTAAAAATATATACAAT;RSEQ=AATAATATCAATAAATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:30.5:1:28:1:1:0:49.5:4:1:0:0 1/1:2:2:0,2:0,0:1:0,0:25:1:32.5:1:1:0:44.5:4:1:0:1.5 -21 11038464 . C T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.54972;SOR=0;LSEQ=AAGAATTTTTAAAGTTCTTT;RSEQ=TATTAGAAACTATTATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:4,0:19,1:0.1667:1,0:15:1:31:1:1:0:38.5:8:0.1739:0:2 0/0:8:0:0,0:7,1:0:2,0:25.4:1:31.8:1:1:0:55.5:16:1:0:0.4 -21 11038477 . T G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27881;SOR=3.13122;LSEQ=GTTCTTTCTATTAGAAACTA;RSEQ=TATCCATAGTTTGCATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:25,1:0.0714:1,0:8.5:1:32.5:1:1:0:58.5:4:0.0714:0:2 0/1:10:2:2,0:6,2:0.2:2,0:26.5:1:33:1:1:0:42:4:0.2:0:2 -21 11038487 . T G 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02297;SOR=0.1745;LSEQ=TTAGAAACTATTATCCATAG;RSEQ=TTGCATCTTTATGGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:30:29,1:7,0:0.8108:0,1:23.6:1:31.5:1:1:0:50.4:29:0.8056:0:1.5 0/1:12:5:5,0:5,2:0.4167:2,0:18:1:32:1:0.4697:0:42.6:10:0.4545:0:1.4 -21 11038501 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06335;SOR=Inf;LSEQ=CCATAGTTTGCATCTTTATG;RSEQ=CCCAGCTGAGTTGAAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:46,6:0:2,0:24.4:1:31.8:1:1:0:51.4:51:1:0:1 0/1:18:2:2,0:14,2:0.1111:2,0:5.5:1:31:0:1:0:40.5:4:0.1111:0:1.5 -21 11038549 . T C 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.879;LSEQ=ATCCCTTCAAATTTAATAAA;RSEQ=GGCATTCTTCATTAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:60,12:0.027:2,0:33:1:33:0:1:0:24:4:0.027:0:3 0/1:42:1:1,0:36,5:0.0238:2,0:29:0:32:0:1:0:27:2:0.0238:0:3 -21 11038551 . G A 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00218;SOR=0;LSEQ=CCCTTCAAATTTAATAAATG;RSEQ=CATTCTTCATTAACAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:14:11,3:55,9:0.1795:2,2:34.6:1:29.5:1:0.44292:1.65453:51.7:28:0.1842:0:1.3 0/0:41:0:0,0:36,5:0:2,0:33.9:1:31:1:1:0:38.8:19.5:1:0:0.5 -21 11038560 . A T 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87591;LSEQ=TTTAATAAATGGCATTCTTC;RSEQ=TTAACAGCATTTAAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:2,0:65,12:0.0253:2,0:33:1:33.5:1:1:0:24:4:0.0253:0:3 0/1:45:1:1,0:36,8:0.0222:2,0:40:0:31:0:1:0:27:2:0.0222:0:3 -21 11038593 . C T 92 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02006;SOR=4.17528;LSEQ=AAAAAATAATGGCTGAAACA;RSEQ=ATAATCAACATTACACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:4:4,0:70,11:0.0471:2,0:31.3:1:31.3:1:1:0:27:8:0.0471:0:1 0/1:58:10:9,1:42,6:0.1724:2,2:21.4:1:27.7:1:1:1.28:27.9:20:0.1724:0:1.1 -21 11038602 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6711;LSEQ=TGGCTGAAACACATAATCAA;RSEQ=ATTACACTGAAGTTCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:2,0:74,9:0.0235:2,0:11.5:1:30.5:1:1:0:27:4:0.0235:0:2.5 0/1:63:1:1,0:55,7:0.0159:2,0:19:0:25:0:1:0:27:2:0.0161:0:3 -21 11038649 . C A 143 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53715;SOR=1.25495;LSEQ=AGAAAAAGTTGCCATCCACA;RSEQ=CAAAGCTACACATATACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:27:23,4:124,13:0.1646:2,2:27.1:1:30.2:1:0.48655:1.65304:37.3:54:0.1646:0:1.6 0/1:126:25:25,0:86,14:0.1984:2,1:26.6:1:30.5:1:0.07045:0:38.7:50:0.2016:0:1.4 -21 11038700 . T A 136 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5609;SOR=0.82527;LSEQ=AGAATTGTTCCAATATCTTT;RSEQ=CTGTCAATATCATTAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:31:24,7:351,48:0.0721:2,2:20.1:1:27.5:1:0.09681:2.1281:34.1:30:0.0704:0:1.8 0/1:332:20:19,1:265,47:0.0602:2,1:23.9:1:28.1:1:0.32952:3.36:40.3:40:0.061:0:1.9 -21 11038722 . C A 263 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68539;SOR=1.05472;LSEQ=TGTCAATATCATTAAAATCA;RSEQ=CCTACCTGTTTGGACCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:709:448:334,114:200,61:0.6319:2,2:22:1:29.9:1:0.58814:1.11888:45.9:88.6:0.6302:0:1.4 1/0:593:382:269,113:151,59:0.6442:2,2:20.6:1:29.4:1:0.77661:1.075:46.4:94.5:0.6429:0:1.5 -21 11038748 . C T 96 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83034;SOR=1.18329;LSEQ=CTGTTTGGACCGAGGTCTAC;RSEQ=AGGAGAAAATTTTCTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1108:11:9,2:717,380:0.0099:2,2:19.5:1:27.7:1:0.34795:2.38:30:22:0.01:0:1.3 0/1:938:11:3,8:580,346:0.0117:2,2:17.6:1:27.9:1:0.02488:4.46289:42.5:22:0.0119:0:1.3 -21 11038796 . T C 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=0.48506;LSEQ=TGGTTTACCCATGCCAGTTT;RSEQ=TTGGAGTGACTGAGATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1507:359:172,187:606,540:0.2382:2,2:27.7:1:31.4:1:0.10262:1.21992:49.6:58.833:0.2387:0:1.9 0/1:1291:170:78,92:574,547:0.1317:2,2:26.6:1:31.4:1:0.21699:1.2375:51.1:55.667:0.1317:0:1.9 -21 11038802 . G A 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.74084;LSEQ=ACCCATGCCAGTTTTTTGGA;RSEQ=TGACTGAGATGTAAGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1447:133:65,68:673,640:0.0919:2,2:25.8:1:29.9:1:0.64925:1.10002:55.4:25.6:0.0896:0:2.1 0/1:1252:344:168,176:461,447:0.2748:2,2:27.4:1:29.5:1:0.56894:1.08036:55.7:85:0.2749:0:1.9 -21 11038843 . G C 277 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52697;SOR=0.94398;LSEQ=GGCATGATGTTTCCAGCAGA;RSEQ=GAACTAAGAGCTGAAGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1045:537:215,322:253,252:0.5139:2,2:23.2:1:30.6:1:0.00119:1.50299:50.4:106.4:0.517:0:1.9 0/1:919:459:169,290:228,231:0.4995:2,2:21.8:1:29.9:1:0.00011:1.69274:51.9:113.75:0.4989:0:1.9 -21 11038868 . C T 265 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12889;SOR=0.86319;LSEQ=TAAGAGCTGAAGGGTAATTA;RSEQ=GCAGCATGTCATGCGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:996:408:214,194:294,294:0.4096:2,2:15.1:1:30.6:1:0.47844:1.10:38.8:80.6:0.4108:0:2.1 0/1:873:327:177,150:256,290:0.3746:2,2:15.2:1:29.9:1:0.04256:1.34:37.4:64.4:0.3731:0:2.1 -21 11038882 . C T 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00093;SOR=1.66011;LSEQ=TAATTACGCAGCATGTCATG;RSEQ=GAAGGCAAGTCTGAAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1150:81:66,15:554,515:0.0704:2,2:14.6:1:30.3:1:0:4.09:36.9:162:0.0715:0:2.4 0/1:1029:115:89,26:458,456:0.1118:2,2:13.6:1:29.8:1:0:3.40:38.1:56.5:0.1111:0:2.4 -21 11038909 . G T 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=1.56702;LSEQ=AAGTCTGAAGAAGGTGTTGG;RSEQ=GAGGAAGACACATCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1481:230:165,65:664,586:0.1553:2,2:25.4:1:30.1:1:0:2.24:40.2:229:0.1562:0:1.9 0/1:1435:321:214,107:571,539:0.2237:2,2:24.3:1:29.8:1:0:1.89:42.5:52.5:0.2234:0:1.8 -21 11038957 . T C 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=1.80133;LSEQ=TCTGCTGATAATGAAAATGA;RSEQ=GACTCTGTCTCAGATGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1888:126:83,43:975,787:0.0667:2,2:27.8:1:31.1:1:0.02544:1.56:43.6:252:0.0672:0:1.2 0/1:1840:210:122,88:894,734:0.1141:2,2:26.7:1:30.3:1:0.41743:1.14:42.1:209:0.1141:0:1.3 -21 11038967 . T C 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=0.51539;LSEQ=ATGAAAATGATGACTCTGTC;RSEQ=CAGATGATAACTTTATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1842:119:71,48:955,767:0.0646:2,2:25.4:1:30.8:1:0.39166:1.19:41.7:38.667:0.064:0:2.1 0/1:1775:61:33,28:933,776:0.0344:2,2:22.1:1:29.6:1:1:1.02014:41.9:60:0.0343:0:1.8 -21 11038970 . G A 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=9.85701;LSEQ=AAAATGATGACTCTGTCTCA;RSEQ=ATGATAACTTTATAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1774:2:2,0:986,785:0.0011:2,0:1:0:20:1:0.50628:0:50:1:6e-04:0:1.5 0/1:1726:19:9,10:926,779:0.011:2,2:23.4:1:30.7:1:0.64535:1.32056:38.2:38:0.0111:0:1.9 -21 11038994 . C T 189 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAACTTTATAGATTTGCCT;RSEQ=CTTGGTATGAAACATCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1727:76:50,26:916,732:0.044:2,2:22.2:1:30.4:1:0.09746:1.54:43.8:152:0.0447:0:2.4 0/0:1629:0:0,0:886,740:0:2,0:22.8:1:30.6:1:1:0:41.8:57.071:0.9981:0:0.4 -21 11038998 . G A 203 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=49.74082;LSEQ=CTTTATAGATTTGCCTCCTT;RSEQ=GTATGAAACATCTTTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1699:3:3,0:951,745:0.0018:2,0:1:0:25:1:0.26091:0:51.7:6:0.0018:0:1 0/1:1593:129:67,62:791,668:0.081:2,2:23.1:1:29:1:0.64551:1.0957:40.5:63.5:0.0809:0:1.5 -21 11039033 . G A 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07612;SOR=0.7084;LSEQ=TCACACAACCCTCAATTGTA;RSEQ=GAGTCATTTCAGAGTCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1805:71:41,30:977,757:0.0393:2,2:26.7:1:30.2:1:0.90296:1.06:42.4:70:0.0394:0:1.1 0/1:1703:48:25,23:916,737:0.0282:2,2:27.9:1:30.2:1:0.66125:1.14335:41.6:96:0.0286:0:1.1 -21 11039055 . A G 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.57259;LSEQ=AGTCATTTCAGAGTCCATCA;RSEQ=TCCAGTAGAAAGTTCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2004:151:94,57:997,854:0.0753:2,2:26.2:1:32:1:0.05059:1.41:45.6:74.5:0.0753:0:2.1 0/1:2064:92:57,35:1046,924:0.0446:2,2:24.7:1:31.8:1:0.10866:1.44:47.4:184:0.0452:0:1.6 -21 11039072 . G T 217 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=106.62601;LSEQ=TCAATCCAGTAGAAAGTTCA;RSEQ=AATCTTCTTTCTGTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2208:2:0,2:1153,1052:9e-04:2,0:1:0:24:0:0.22796:0:52.5:4:9e-04:0:1 0/1:2313:204:107,97:1095,1013:0.0882:2,2:24.9:1:28.4:1:0.94153:1.02:51.2:39.8:0.0873:0:1.3 -21 11039079 . C A 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.53857;LSEQ=AGTAGAAAGTTCAGAATCTT;RSEQ=TTTCTGTTCCTTTTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2267:499:263,236:800,760:0.2201:2,2:26.1:1:29.4:1:0.60691:1.06:51.5:61.375:0.2205:0:1.1 0/1:2433:321:165,156:1011,975:0.1319:2,2:23.7:1:28.6:1:0.90425:1.02:50.8:79.25:0.1318:0:1.1 -21 11039091 . T A 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.36972;LSEQ=AGAATCTTCTTTCTGTTCCT;RSEQ=TTCTCCTTGTAGCCTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2421:186:107,79:1156,1078:0.0768:2,2:24.3:1:29.1:1:0.14653:1.26:52.9:92:0.077:0:1.7 0/1:2513:75:49,26:1238,1200:0.0298:2,2:23.9:1:27.9:1:0.0137:1.83:54.5:36.5:0.0293:0:1.8 -21 11039142 . T A 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.59786;LSEQ=TTCCTCAGGACATAATGAAG;RSEQ=GCTTTCCTCATGTGGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2538:178:92,86:1162,1198:0.0701:2,2:26.1:1:29.9:1:0.5351:1.10:58.8:24.429:0.0683:0:2 0/1:2631:283:154,129:1158,1189:0.1076:2,2:24.2:1:29.1:1:0.11565:1.23:59.3:27.3:0.1052:0:2.1 -21 11039152 . A C 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.65869;LSEQ=CATAATGAAGTGCTTTCCTC;RSEQ=TGTGGGGACACTAAGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2531:178:92,86:1163,1187:0.0703:2,2:24.9:1:31.2:1:0.58701:1.09:59.2:88:0.0709:0:2 0/1:2583:288:149,139:1121,1169:0.1115:2,2:23.8:1:30.4:1:0.3819:1.12:59.8:71:0.1124:0:2.1 -21 11039298 . C T 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.47543;LSEQ=AGTGATCTGGTGTGTAACGA;RSEQ=TTCAATGTTTTCTGTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1868:285:121,164:677,906:0.1526:2,2:25.9:1:30.4:1:0.94819:1.01278:52:94:0.1527:0:1.6 0/1:2093:165:71,94:922,1005:0.0788:2,2:26.3:1:30.2:1:0.25568:1.21449:54.1:330:0.0798:0:1.5 -21 11039302 . A G 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.44229;LSEQ=ATCTGGTGTGTAACGACTTC;RSEQ=ATGTTTTCTGTCACTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1849:159:62,97:718,971:0.086:2,2:24.6:1:30.5:1:0.40234:1.15677:53.3:78.5:0.086:0:1.6 0/1:2078:83:38,45:937,1057:0.0399:2,2:27.2:1:30.3:1:0.91073:1.04976:51.1:166:0.0402:0:1.6 -21 11039344 . G A 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.60826;LSEQ=TTATCTTCAATTTGATCTTC;RSEQ=CCACAAATATGCTTCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1530:829:334,495:273,424:0.5418:2,2:25.3:1:29.6:1:0.67462:1.05:52.5:50.813:0.5427:0:1.4 0/1:1690:707:305,402:435,545:0.4183:2,2:24.2:1:29:1:0.61932:1.05201:52.2:57.917:0.4184:0:1.3 -21 11039393 . G A 126 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=18.1099;LSEQ=TTTTCATTTCTTCACTATCA;RSEQ=CCTCATTAGAAATCTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1168:1:1,0:396,771:9e-04:2,0:1:0:25:0:0.3399:0:60:2:9e-04:0:1 0/1:1308:20:7,13:480,807:0.0153:2,2:28.8:1:29.3:1:1:1.10455:59.8:40:0.0155:0:1.9 -21 11039394 . C T 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.91152;LSEQ=TTTCATTTCTTCACTATCAG;RSEQ=CTCATTAGAAATCTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1163:215:65,150:331,617:0.1849:2,2:25.1:1:30:1:0.20275:1.23778:59.9:106.5:0.1864:0:1.4 0/1:1296:392:154,238:326,577:0.3025:2,2:26.8:1:28.9:1:0.28736:1.15:59.9:97:0.3031:0:1.3 -21 11039406 . T C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.44898;LSEQ=ACTATCAGCCTCATTAGAAA;RSEQ=CTGTTTTTCCAATTCGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1020:103:28,75:298,619:0.101:2,2:23.7:1:31:1:0.31614:1.28918:59.9:102:0.1017:0:2 0/1:1146:55:14,41:394,697:0.048:2,2:25.6:1:31.3:1:0.11435:1.65479:60:110:0.0484:0:2 -21 11039441 . G C 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12156;SOR=0.78211;LSEQ=CGGTATTCACTGTATGTTGG;RSEQ=ATGATATTACAAAATTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:662:106:22,84:136,420:0.1601:2,2:24.9:1:32.4:1:0.45724:1.23595:59.6:212:0.1626:0:1.8 0/1:686:89:22,67:173,424:0.1297:2,2:23.7:1:31.9:1:0.45129:1.24226:60:88:0.1298:0:1.9 -21 11039450 . A G 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00511;SOR=0.70683;LSEQ=CTGTATGTTGGGATGATATT;RSEQ=CAAAATTCAGAACATTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:241:48,193:68,252:0.4288:2,2:26:1:31.7:1:0.75241:1.0848:59:29.125:0.4213:0:1.3 0/1:577:200:57,143:93,284:0.3466:2,2:26.3:1:31.7:1:0.32051:1.22:59.5:65.667:0.3444:0:1.2 -21 11039487 . A C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46862;SOR=1.25293;LSEQ=TGTTATGGTAATGTACAAAC;RSEQ=AATTTTAAATTTTCTAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:24:1,23:29,230:0.0845:2,1:16.8:1:32.3:1:0.48826:2.8924:57:48:0.0851:0:1.1 0/1:270:28:3,25:49,193:0.1037:2,2:29.4:1:32.3:1:0.31325:2.11096:57.1:56:0.1045:0:1 -21 11039527 . G A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31829;SOR=0.51132;LSEQ=ATAGATATATAAAACATTTG;RSEQ=CTACACTAGAACTTAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:13:0,13:5,109:0.1024:1,1:21.4:1:29.7:1:1:0:54.2:12:0.0968:0:1 0/1:91:5:0,5:6,80:0.0549:2,0:16.6:1:30.2:1:1:0:51.2:10:0.0556:0:1 -21 11039570 . A G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1831;LSEQ=AGGTATTCATCAAAGCAGAC;RSEQ=ATTATTAAGTGAATGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:6:0,6:3,61:0.0857:1,0:28.2:1:32.3:1:1:0:40.7:12:0.087:0:1 0/1:30:3:0,3:3,24:0.1:2,0:31.7:1:33:0:1:0:40:6:0.1:0:1.3 -21 11039583 . A G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62834;SOR=1.64163;LSEQ=AGCAGACAATTATTAAGTGA;RSEQ=TGAAAGCCAAAGTACACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:0,3:3,54:0.05:2,0:23.3:1:32.3:1:1:0:40:6:0.0517:0:2 0/1:25:2:0,2:4,19:0.08:2,0:10.5:1:30.5:1:1:0:50:4:0.08:0:2.5 -21 11039600 . C T 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17084;SOR=0;LSEQ=TGAATGAAAGCCAAAGTACA;RSEQ=AAGGATTTATGGATTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:6:1,5:4,39:0.1224:2,2:14:1:29:1:0.4952:1.92:41.2:12:0.125:0:1.2 0/0:20:0:0,0:4,16:0:2,0:23.4:1:31.8:1:1:0:46:40:1:0:0.8 -21 11039609 . A T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.25983;LSEQ=GCCAAAGTACACAAGGATTT;RSEQ=TGGATTAGAATCAGCCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:0,2:5,38:0.0444:2,0:18:1:28.5:1:1:0:50:4:0.0465:0:3 0/1:18:1:0,1:4,13:0.0556:2,0:28:0:26:0:1:0:60:2:0.0556:0:4 -21 11039627 . T C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52694;SOR=0.64671;LSEQ=TTATGGATTAGAATCAGCCA;RSEQ=ACACCAGAAAACCTAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:26:3,23:0,10:0.7222:0,2:25.2:1:31.2:1:0.54482:0:50:25:0.7143:0:1.5 1/0:16:10:2,8:3,3:0.625:2,2:27.1:1:31.2:1:0.29945:3.63046:51.2:20:0.625:0:1.6 -21 11039703 . T C 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.11896;LSEQ=TGAAAATTACACAGGAAAAG;RSEQ=TCTCATACTCATTTTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:0,6:0,9:0.4:0,0:29.5:1:31.8:1:1:0:53.2:12:0.4:0:1.3 0/1:7:3:1,2:1,3:0.4286:2,2:33:1:32.3:1:1:1.41:60:6:0.4286:0:1.3 -21 11040374 . TCTGATACCAAA T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=3.000;MSILEN=1;SSF=0.01818;SOR=Inf;LSEQ=TTGCCCAGGCCTATACATGT;RSEQ=CTGATACCAAACTGAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:25.4:1:29.9:1:1:0:60:7:1:0:0.4 1/0:4:3:2,1:1,0:0.75:0,2:18:1:30.9:1:1:0:55:6:0.75:0.5:0 -21 11040446 . TA T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=TGAAAGACTACAGGTAAGGA;RSEQ=AAAGAAAACTACCAAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:15,1:0.1111:1,0:28.5:1:33:0:1:0:60:4:0.1111:0:0.5 0/0:12:0:0,0:11,1:0:2,0:19:1:28.7:1:1:0:56.4:24:1:0:1.3 -21 11040477 . A G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26857;SOR=1.93354;LSEQ=TACCAAATAACAGATCTGAT;RSEQ=GTACAAAATATTTTTAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:7:5,2:25,1:0.2121:1,2:24.4:1:32:1:0.10649:9.02549:55.3:14:0.2121:0:3.4 0/1:29:10:9,1:17,2:0.3448:2,2:24.7:1:31.6:1:1:1.06:55.1:20:0.3448:0:3 -21 11040478 . G A 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59032;SOR=2.41063;LSEQ=ACCAAATAACAGATCTGATA;RSEQ=TACAAAATATTTTTAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:1,0:29,4:0.0294:2,0:18:0:32:0:1:0:60:2:0.0294:0:2 0/1:29:2:2,0:24,3:0.069:2,0:23:1:32:0:1:0:60:4:0.0714:0:2 -21 11040501 . CATCCCCCCTCC TATGCCCCTCCAAAA 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.24176;SOR=0;LSEQ=CAAAATATTTTTAATCATGA;RSEQ=AAAAAAAAAGCCTTTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:3,0:37,3:0.0652:2,0:20:1:30.6:1:1:0:60:6:0.0682:0.0217:3.3 0/0:45:0:0,0:27,4:0:2,0:25:1:30.2:1:1:0:60.3:9.333:0.6829:0:1.5 -21 11040502 . A C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20626;SOR=0.57168;LSEQ=AAAATATTTTTAATCATGAC;RSEQ=TCCCCCCTCCAAAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:33:31,2:9,2:0.6875:2,2:23.4:1:31.1:1:0.25646:3.33:59.4:66:0.75:0:1.5 1/0:45:25:23,2:7,1:0.5556:2,2:26.5:1:30.4:1:1:1.62:60:24:0.75:0:1.8 -21 11040512 . C CAA 124 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=11.000;MSILEN=1;SSF=0.1204;SOR=2.08901;LSEQ=TAATCATGACATCCCCCCTC;RSEQ=AAAAAAAAAGCCTTTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:13:11,2:18,1:0.2708:1,2:27.8:1:31.3:1:0.55181:3.1502:59.8:26:0.2889:0:2.1 0/1:41:18:15,3:11,2:0.439:2,2:26.9:1:29.8:1:1:1.09661:59.9:17:0.4359:0:1.8 -21 11040523 . C G 120 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02076;SOR=2.7928;LSEQ=TCCCCCCTCCAAAAAAAAAG;RSEQ=CTTTCAAGAGAAACTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:9:8,1:56,2:0.1304:1,2:14.4:1:25.3:1:0.35589:3.40584:53.2:2:0.0938:0:3.9 0/1:64:19:18,1:40,5:0.2969:2,1:16.7:1:28.4:1:0.66018:2.23:56.4:5.333:0.2807:0:3.4 -21 11040527 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49693;SOR=0;LSEQ=CCCTCCAAAAAAAAAGCCTT;RSEQ=CAAGAGAAACTAACCTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:2,0:69,4:0.0267:2,0:21.5:1:27:1:1:0:60:4:0.0278:0:3.5 0/0:71:0:0,0:64,7:0:2,0:21.1:1:29.6:1:1:0:58.8:70:1:0:2 -21 11040535 . A C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.27359;SOR=1.74895;LSEQ=AAAAAAAGCCTTTCAAGAGA;RSEQ=ACTAACCTACTTTAGATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:9:8,1:75,5:0.1011:2,2:20.8:1:31.8:1:0.48288:1.85878:59.7:18:0.1047:0:2.4 0/1:91:15:13,2:71,5:0.1648:2,2:23.9:1:28.7:1:0.32475:2.16166:59.9:6.5:0.1461:0:3 -21 11040542 . C A 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00601;SOR=2.54556;LSEQ=GCCTTTCAAGAGAAACTAAC;RSEQ=TACTTTAGATCCATTGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:16:12,4:80,3:0.1616:1,2:17.6:1:28.8:1:0.01228:8.57206:55.2:15:0.1596:0:2.9 0/1:106:35:32,3:64,6:0.3302:2,2:20.2:1:29.5:1:1:1:58:34:0.3434:0:2.8 -21 11040581 . T C 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01615;SOR=2.3091;LSEQ=AATTCTTTTCCAGAATCTCT;RSEQ=AACTAAAAGATTTAGTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:14:14,0:159,3:0.0795:1,1:22:1:30.4:1:1:0:56.7:13:0.076:0:4.3 0/1:186:31:30,1:148,7:0.1667:1,1:27.7:1:30.4:1:1:1.42:58.8:30:0.1648:0:3.7 -21 11040593 . T G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.23873;LSEQ=GAATCTCTTAACTAAAAGAT;RSEQ=TAGTTACTGTAATGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:34:32,2:171,1:0.165:1,2:22.9:1:32.2:1:0.07137:10.49152:54.1:33:0.1634:0:2.2 0/1:243:95:90,5:143,5:0.3909:1,2:22.2:1:31.1:1:0.51873:1.58571:55.2:18:0.3814:0:2.4 -21 11040610 . T G 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01999;SOR=1.75753;LSEQ=GATTTAGTTACTGTAATGTA;RSEQ=ATACATACAGCAATTGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:30:23,7:249,35:0.0955:2,2:20.3:1:31.1:1:0.09673:2.15861:49.1:29:0.0942:0:4.7 0/1:351:55:44,11:256,40:0.1567:2,2:21.6:1:30.1:1:0.21426:1.59761:50.5:12.75:0.1474:0:4.4 -21 11040635 . T C 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00696;SOR=1.66784;LSEQ=ATACAGCAATTGCAAAAATG;RSEQ=CTTTGGGATAAAGACATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:506:49:36,13:334,122:0.0968:2,2:23.6:1:31.3:1:1:1.01:47.6:48:0.0958:0:4.5 0/1:626:95:61,34:372,159:0.1518:2,2:23.2:1:30.7:1:0.27803:1.30353:48.1:30.667:0.1496:0:4.4 -21 11040641 . G A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00012;SOR=0.63814;LSEQ=CAATTGCAAAAATGTCTTTG;RSEQ=GATAAAGACATTATCTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:262:177,85:239,80:0.4509:2,2:23.9:1:30:1:0.05271:1.43374:60:86.333:0.4536:0:2.1 0/1:701:241:156,85:306,154:0.3438:2,2:21.1:1:29.1:1:0.67505:1.08254:59.6:59.25:0.344:0:2.4 -21 11040652 . T C 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00476;SOR=1.60295;LSEQ=ATGTCTTTGGGATAAAGACA;RSEQ=TATCTTATAACTCAGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:716:63:46,17:447,206:0.088:2,2:25.8:1:31.8:1:0.5689:1.25:50.3:62:0.0878:0:4.2 0/1:836:112:69,43:460,264:0.134:2,2:28.3:1:30.9:1:0.75214:1.08575:49.9:55:0.1327:0:4.2 -21 11040653 . T A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTCTTTGGGATAAAGACAT;RSEQ=ATCTTATAACTCAGTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:729:0:0,0:502,227:0:2,0:24.6:1:29.3:1:1:0:56.5:90.125:1:0:1.9 0/1:850:37:29,8:505,308:0.0435:2,2:26.5:1:28.2:1:0.05485:2.21:51.8:74:0.0438:0:2.8 -21 11040667 . G A 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.67552;LSEQ=AGACATTATCTTATAACTCA;RSEQ=TCAAATCAGACAATATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:867:347:232,115:313,206:0.4002:2,2:25.3:1:30:1:0.05284:1.33:52.7:68.4:0.3986:0:2.6 1/0:1038:548:323,225:288,199:0.5279:2,2:26.3:1:29.4:1:1:1.00813:52.7:44.667:0.5255:0:2.7 -21 11040674 . C T 285 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00044;SOR=1.56043;LSEQ=ATCTTATAACTCAGTCAAAT;RSEQ=AGACAATATGAACATACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:923:757:455,302:101,63:0.8202:2,2:26.6:1:29.2:1:0.79175:1.06403:56.4:83.111:0.822:0:2.3 1/1:1104:968:552,416:81,55:0.8768:2,2:27.2:1:28.8:1:0.64357:1.10975:55.7:87:0.8772:0:2.5 -21 11040693 . G A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=TCAGACAATATGAACATACT;RSEQ=CTTACCAGCAATGAGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1005:0:0,0:520,485:0:2,0:28.2:1:31.9:1:1:0:57.6:76.308:1:0:1.7 0/1:1200:14:7,7:590,595:0.0117:2,2:27.7:1:28.6:1:1:1.01:60:13:0.011:0:2.9 -21 11040713 . C T 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00137;SOR=1.44356;LSEQ=GCTTACCAGCAATGAGAAGA;RSEQ=TATCTGTGTCCTCTATACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:934:152:63,89:353,427:0.1627:2,2:26.7:1:30:1:0.42252:1.16768:59.9:49.667:0.1613:0:2.2 0/1:1118:245:111,134:376,495:0.2191:2,2:27.1:1:29.7:1:0.56037:1.09:60:490:0.2211:0:2.2 -21 11040737 . G A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58629;SOR=0.83992;LSEQ=CTGTGTCCTCTATACCCTCA;RSEQ=TGTAGGGAAAGGCTTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:738:29:11,18:257,452:0.0393:2,2:23.6:1:29.6:1:0.84605:1.07:60:28:0.0384:0:2 0/1:813:27:10,17:285,501:0.0332:2,2:18.1:1:29.2:1:1:1.03:60:26:0.0324:0:2.1 -21 11040748 . G A 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=1.5603;LSEQ=ATACCCTCAGTGTAGGGAAA;RSEQ=GCTTTCTGAATATGACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:596:131:39,92:122,343:0.2198:2,2:22.1:1:30.9:1:0.43646:1.19:59.6:130:0.2211:0:1.9 0/1:645:197:55,142:140,308:0.3054:2,2:22.6:1:30.5:1:0.45657:1.17327:59.8:394:0.3088:0:2 -21 11040773 . CC AT 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31741;SOR=0.78912;LSEQ=TCTGAATATGACTCAAAAAT;RSEQ=AGAAGCAAAAGAAGATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:50:2,48:30,293:0.1337:2,1:22.8:1:29.7:1:0.28411:2.45292:59.9:100:0.137:0.0187:1 0/1:387:42:7,35:39,306:0.1085:2,2:20.9:1:29.2:1:0.3133:1.57:59.5:84:0.1099:0.0078:1 -21 11040785 . G A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49291;SOR=1.25454;LSEQ=TCAAAAATCCAGAAGCAAAA;RSEQ=AAGATTAATAAATCTAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:26:1,25:8,257:0.0893:1,1:22.6:1:31.3:1:0.5746:1.28:58.1:52:0.0906:0:1.5 0/1:301:33:2,31:15,253:0.1096:2,2:23.6:1:30.8:1:1:1.09:58.9:66:0.1107:0:1.4 -21 11040822 . T G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36576;SOR=1.91281;LSEQ=ACTCCACAAAAAGAAACTTT;RSEQ=GCATGGCAAAAAAATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:4:0,4:6,155:0.0242:1,0:20.3:1:29.5:1:1:0:60:8:0.0248:0:2 0/1:154:7:0,7:9,138:0.0455:2,0:13.6:1:30.9:1:1:0:60:14:0.0455:0:1.7 -21 11040829 . C CA 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.3257;SOR=1.68514;LSEQ=AAAAAGAAACTTTTGCATGG;RSEQ=AAAAAAATAATAATAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:7:1,6:5,138:0.0467:1,2:28.1:1:30.7:1:0.25306:4.51:55.7:14:0.047:0:2 0/1:131:10:0,10:8,112:0.0763:2,0:29.2:1:30.3:1:1:0:54.8:20:0.0775:0:1.6 -21 11040835 . AAT A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=1.05628;LSEQ=AAACTTTTGCATGGCAAAAA;RSEQ=AATAATAAAAACAAAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:19:1,18:4,107:0.1462:1,1:28.4:1:30.8:1:0.55225:1.48:58.9:38:0.1462:0:1.4 0/1:111:17:3,14:4,90:0.1532:1,2:24.4:1:30.4:1:0.07128:4.72:57.1:34:0.1532:0:1.5 -21 11040836 . AT A 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=9.000;MSILEN=1;SSF=0.77765;SOR=1.08799;LSEQ=AACTTTTGCATGGCAAAAAA;RSEQ=AATAATAAAAACAAAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:39:3,36:0,30:0.3305:1,2:28.7:1:31.1:1:0.25192:0:58.7:78:0.4021:0:0.6 0/1:103:36:2,34:0,16:0.3495:1,2:26.1:1:31:1:1:0:59.6:72:0.4186:0:0.6 -21 11040837 . T A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.23636;SOR=1.44296;LSEQ=ACTTTTGCATGGCAAAAAAA;RSEQ=AATAATAAAAACAAAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:30:1,29:0,30:0.2542:1,1:22.3:1:30.9:1:1:0:55.1:60:0.3093:0:1.7 0/1:103:34:2,32:0,16:0.3301:1,2:23.8:1:30.6:1:1:0:54.9:68:0.3953:0:1.6 -21 11040864 . C T 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07462;SOR=0;LSEQ=AAAAACAAAGTCAAAAGACA;RSEQ=ATAATACAGCCTGGATAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:5:1,4:0,65:0.0714:1,2:21:1:26.4:1:0.07143:0:53:10:0.0725:0:3.2 0/0:50:0:0,0:3,47:0:2,0:22.8:1:32.4:1:1:0:57.4:100:1:0:0.9 -21 11040872 . A C 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71483;LSEQ=AGTCAAAAGACACATAATAC;RSEQ=GCCTGGATAACATGGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:0,2:1,56:0.0339:1,0:16.5:1:31.5:1:1:0:60:4:0.0345:0:1.5 0/1:41:1:0,1:1,39:0.0244:1,0:25:0:32:0:1:0:60:2:0.0244:0:2 -21 11040880 . T C 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.11269;LSEQ=GACACATAATACAGCCTGGA;RSEQ=AACATGGTGAGACCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:0,5:1,38:0.1136:1,0:18.6:1:32.8:1:1:0:56:10:0.1163:0:1.2 0/1:32:4:0,4:1,27:0.125:1,0:12:1:31.5:1:1:0:47.8:8:0.125:0:2.3 -21 11040889 . G A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.7847;SOR=1.22305;LSEQ=TACAGCCTGGATAACATGGT;RSEQ=AGACCCTGTCTCTACAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:11:0,11:1,23:0.3143:1,0:19.1:1:30.7:1:1:0:54.6:22:0.3235:0:2.2 0/1:25:9:1,8:0,16:0.36:1,2:15.7:1:29.2:1:0.36:0:56.9:18:0.36:0:1.9 -21 11040897 . G A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06501;SOR=0.25637;LSEQ=GGATAACATGGTGAGACCCT;RSEQ=TCTCTACAAAAGTAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:1,11:0,19:0.3871:1,2:27.7:1:30.3:1:0.3871:0:53.3:24:0.3871:0:2.8 0/1:22:3:0,3:1,18:0.1364:1,0:23.7:1:31.3:1:1:0:53:6:0.1429:0:2.3 -21 11040920 . G T 41 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59475;LSEQ=TCTACAAAAGTAAAAAATTA;RSEQ=CTGGGCTTTGTGGTACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:0,14:0.1765:1,0:24.7:1:26:1:1:0:46.7:2:0.125:0:4 0/1:9:1:0,1:0,8:0.1111:0,0:15:0:29:0:1:0:52:2:0.1111:0:4 -21 11040929 . T C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35;SOR=0;LSEQ=GTAAAAAATTAGCTGGGCTT;RSEQ=GTGGTACATATAACTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1:0,1:23.5:1:28.8:1:1:0:48.1:12:1:0:3.5 1/1:7:6:0,6:0,0:0.8571:0,0:31.8:1:29.8:1:1:0:44.2:12:0.8571:0:3.7 -21 11040938 . T C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.52222;LSEQ=TAGCTGGGCTTTGTGGTACA;RSEQ=ATAACTCCTAGCTAACTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:0.9091:0,0:20.5:1:31.5:1:1:0:44.6:20:0.9091:0:3.9 1/1:6:5:0,5:0,1:0.8333:0,0:31.6:1:32:1:1:0:42.6:10:0.8333:0:3.6 -21 11040956 . T C 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATATAACTCCTAGCTAACT;RSEQ=GGGAGGCTGAGGCAGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:21.2:1:28.2:1:1:0:40:5:0.8333:0:4.3 1/1:4:4:0,4:0,0:1:0,0:22:1:29.5:1:1:0:39.8:8:1:0:4 -21 11041440 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGGTGGCAATGCAAAGT;RSEQ=CCATAAGCCCCAAAAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:31:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11042951 . C G 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AATGTGGTGGGAGTGCTAGA;RSEQ=CTGGAAATGCATCATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:28.7:1:31:1:1:0:50.7:6:1:0:1 1/0:2:1:1,0:0,0:0.5:0,0:21:0:34:0:1:0:60:2:0.5:0:1 -21 11045280 . T C 45 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGATCACAACCAAGACTC;RSEQ=GAAAGGTTGAGGGTAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:38:1:28.7:1:1:0:56:6:1:0:2.7 -21 11045286 . G A 43 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAACCAAGACTCTGAAAG;RSEQ=TTGAGGGTAAAGTTGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:40.3:1:27.7:1:1:0:56:6:1:0:2.7 -21 11045344 . G A 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAAGAAAATTGTGACA;RSEQ=GGTTTACAATCTAGGTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:32.5:1:33:0:1:0:54:4:1:0:2.5 -21 11046346 . T A 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGAGAAGGAATCTGAAC;RSEQ=ACCTGAGGAAGCAGGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:0:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11046605 . A G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTACAGAATCTCTCTGC;RSEQ=TCTGCTCCCACCTCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:27:1:31.3:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11046622 . G C 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATCTGCTCCCACCTCCT;RSEQ=CCCACACCAGGGACCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:0.8:0,2:35:1:32.3:1:1:0:60:8:0.8:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11046628 . A G 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCCCACCTCCTGCCCAC;RSEQ=CCAGGGACCTGGGGTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:0.8:0,2:32:1:31.3:1:1:0:60:8:0.8:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11047018 . A G 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATAATAGCTCAAAATTTT;RSEQ=AAGGACCCAAATGTTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:25:1:31:1:1:3.1622:36.5:4:0.2857:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11047125 . C A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60268;SOR=1.92451;LSEQ=TCTGTGCAGCAATAGGGATG;RSEQ=ATTTCAAAATAATTACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:9.5:1:24.5:1:1:0:35:1:0.0909:0:2.5 0/1:7:2:2,0:4,1:0.2857:2,0:33.5:1:31:0:1:0:33.5:4:0.2857:0:3 -21 11047128 . T A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.60268;SOR=1.92451;LSEQ=GTGCAGCAATAGGGATGCAT;RSEQ=TCAAAATAATTACACTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:9.5:1:28.5:1:1:0:35:4:0.1667:0:2.5 0/1:7:2:2,0:4,1:0.2857:2,0:36.5:1:29:1:1:0:33.5:4:0.2857:0:3 -21 11047145 . G T 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63956;SOR=1.89552;LSEQ=CATTTCAAAATAATTACACT;RSEQ=AGTTAAAGAAGCCAGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:13,0:0.2353:1,0:17.8:1:29.3:1:1:0:45.5:8:0.25:0:1.8 0/1:8:3:2,1:5,0:0.375:0,2:34.7:1:30:1:0.375:0:54.7:6:0.375:0:2 -21 11047158 . C G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=TTACACTGAGTTAAAGAAGC;RSEQ=AGACCAAAAACGAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:0.1053:1,0:31:1:28:1:1:0:58.5:4:0.1053:0:1 0/0:11:0:0,0:10,1:0:2,0:27.5:1:30.6:1:1:0:45.3:22:1:0:1.4 -21 11047169 . C T 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1214;LSEQ=TAAAGAAGCCAGACCAAAAA;RSEQ=GAGTATATACTATATGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:4,0:18,0:0.1818:1,0:24:1:29.8:1:1:0:50.3:8:0.1818:0:1.8 0/1:15:3:2,1:12,0:0.2:0,2:39:1:28.7:1:0.2:0:54.7:6:0.2:0:2 -21 11047179 . C G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19789;SOR=2.48333;LSEQ=AGACCAAAAACGAGTATATA;RSEQ=TATATGAAGCTTTTATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:7,0:20,0:0.2593:1,0:30.1:1:33.4:1:1:0:33:14:0.2593:0:1.3 0/1:17:8:8,0:8,1:0.4706:2,0:21.1:1:33.3:1:1:0:39.9:16:0.4706:0:1.6 -21 11047253 . A T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.07628;LSEQ=AAAGCAGACTAGGAAGACAG;RSEQ=GGGTTTGGGTTTGAACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:2,0:81,3:0.0233:1,0:21.5:1:31.5:1:1:0:60:4:0.0235:0:1 0/1:40:1:1,0:31,8:0.025:2,0:40:0:25:0:1:0:57:2:0.025:0:1 -21 11047289 . A T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01457;SOR=Inf;LSEQ=CAGCCACAAAGCAAGCCAAG;RSEQ=GGCACCAGGAAACTTTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:113,10:0:2,0:24.1:1:30:1:1:0:57.8:60.5:1:0:0.5 0/1:67:4:2,2:51,12:0.0597:2,2:26:1:30.3:1:0.19008:4.12891:51.8:8:0.0597:0:1.8 -21 11047308 . C T 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58154;SOR=1.19634;LSEQ=GAGGCACCAGGAAACTTTGA;RSEQ=GGTGATGACTATGTTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:49:44,5:80,8:0.3577:2,2:23.2:1:31.2:1:1:1.13528:57.7:98:0.3657:0:1.3 0/1:95:38:30,8:47,10:0.4:2,2:25.1:1:30:1:0.79047:1.2503:59.4:76:0.4043:0:1.2 -21 11047322 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16779;SOR=Inf;LSEQ=CTTTGACGGTGATGACTATG;RSEQ=TCATTATCTTGAAGAGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:162,16:0:2,0:22.1:1:30:1:1:0:59.2:58.333:1:0:0.5 0/1:124:2:1,1:104,18:0.0161:2,2:14.5:1:27.5:1:0.28403:5.65071:60:4:0.0163:0:1 -21 11047334 . A G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05926;SOR=0.34668;LSEQ=TGACTATGTTCATTATCTTG;RSEQ=AGAGTGTACAGTTTACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:15:14,1:183,16:0.0694:2,1:17.9:1:30.8:1:1:1.22:57.7:30:0.0708:0:1.2 0/1:159:4:2,2:131,23:0.0252:2,2:33.8:1:29.5:1:0.11812:5.5994:60:8:0.0258:0:1 -21 11047339 . T C 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03352;SOR=Inf;LSEQ=ATGTTCATTATCTTGAAGAG;RSEQ=GTACAGTTTACTGTATGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:225,19:0:2,0:21.6:1:30.1:1:1:0:59.6:47.8:1:0:0.5 0/1:184:4:4,0:150,30:0.0217:2,0:31.8:1:31.8:1:1:0:60:8:0.0222:0:1 -21 11047371 . A G 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.3985;LSEQ=TGTATGTCAGTTATATGTCA;RSEQ=TAAAGCTGTTTTTAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:81:77,4:351,24:0.1776:2,1:24.1:1:32.8:1:0.8003:1.32:60:162:0.1792:0:1.7 0/1:341:27:24,3:279,35:0.0792:2,2:25.5:1:32.1:1:1:1.00:59.9:26:0.0767:0:1.8 -21 11047421 . T C 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=19.31987;LSEQ=TGTATAGATTTGAATAGATA;RSEQ=CCGATTTGTCTGTTCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1132:1:0,1:1011,120:9e-04:2,0:17:0:11:0:0.10689:0:60:0:0:0:4 0/1:952:16:12,4:796,140:0.0168:2,2:23.4:1:30.6:1:0.28404:1.89359:60:32:0.0169:0:2.4 -21 11047441 . T C 299 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00277;SOR=0.79605;LSEQ=TCCGATTTGTCTGTTCTCCA;RSEQ=ATAAAACATACAGAGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1510:656:530,126:706,148:0.4344:2,2:25:1:32:1:0.38126:1.13397:60:163:0.435:0:1.7 0/1:1381:524:419,105:663,194:0.3794:2,2:24.1:1:31.1:1:0.28142:1.17:60:173.667:0.38:0:1.8 -21 11047496 . G A 348 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.68623;LSEQ=CTTACTTTGCATTTCCAGCC;RSEQ=TTGGTTGGTACAGATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3489:3234:1927,1307:149,102:0.9269:2,2:24.9:1:30.2:1:0.94686:1.01:59.8:70.867:0.927:0:1.3 1/1:3784:3394:1958,1436:219,162:0.8969:2,2:25.4:1:29.7:1:0.95642:1.01:59.9:93.278:0.8979:0:1.3 -21 11047515 . A G 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.36572;LSEQ=CGTTGGTTGGTACAGATTTC;RSEQ=TAATTCGTTGAAGACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3885:143:68,75:2023,1713:0.0368:2,2:24.6:1:31:1:0.12456:1.30244:59.7:142:0.0369:0:1.9 0/1:4209:349:192,157:2042,1812:0.0829:2,2:27:1:30.2:1:0.50154:1.09:59.8:348:0.0836:0:1.9 -21 11047582 . C T 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.72136;LSEQ=ACACACTAGCATCTTGCTAT;RSEQ=TTCTCCCGATTGTCTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3138:448:161,287:992,1694:0.1428:2,2:26:1:30.1:1:0.71123:1.04388:58.8:73.667:0.1421:0:1.3 0/1:3105:333:126,207:1099,1669:0.1072:2,2:25.9:1:29.7:1:0.55306:1.08178:58.6:82.25:0.1065:0:1.3 -21 11047599 . A T 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.21633;LSEQ=TATCTTCTCCCGATTGTCTA;RSEQ=AAAGTAAGATAGCATTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2480:173:55,118:703,1603:0.0698:2,2:26.6:1:28.9:1:0.73245:1.06:58.5:172:0.0703:0:1.1 0/1:2444:39:15,24:827,1577:0.016:2,2:24.3:1:28.5:1:0.61253:1.19:58.2:78:0.0162:0:1.1 -21 11047650 . C T 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00115;SOR=0;LSEQ=TTTAAACTTATGTTTTGCAA;RSEQ=ATAAGTAATCATGAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1001:11:2,9:89,901:0.011:2,2:26.3:1:28.2:1:0.26377:2.25:60:22:0.0111:0:1 0/0:885:0:0,0:106,778:0:2,0:23:1:31.7:1:1:0:59.7:109.5:0.9989:0:0.2 -21 11047685 . C T 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04159;SOR=0.64227;LSEQ=AAATCATCAGTCCTGGGAAC;RSEQ=GCACAGTTCATAAATACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:542:71:0,71:15,456:0.131:1,1:23.2:1:30.7:1:0.23826:0:54.5:70:0.1301:0:1.1 0/1:442:39:0,39:18,385:0.0882:1,1:29.1:1:30.4:1:0.38874:0:52.3:78:0.0894:0:1.2 -21 11047759 . TC GA 91 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03158;SOR=3.56907;LSEQ=GGTAACCCTACCATAAGGAT;RSEQ=CCTCCTAAATGGTGATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:5:0,5:1,136:0.0352:1,0:33.4:1:31.2:1:1:0:43:10:0.036:0:1 0/1:69:8:1,7:4,57:0.1159:2,2:24.6:1:30.4:1:0.47065:2.01:39.5:16:0.1159:0.0145:0.9 -21 11047760 . C A 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00672;SOR=0.33922;LSEQ=GTAACCCTACCATAAGGATT;RSEQ=CCTCCTAAATGGTGATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:138:123:0,123:1,9:0.8913:2,1:23.3:1:30.5:1:0.07519:0:43.8:246:0.9248:0:1.1 1/0:64:47:2,45:2,8:0.7344:2,1:18:1:30.1:1:0.13796:5.37831:45.5:94:0.8246:0:1.2 -21 11047824 . A T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.81888;LSEQ=CTTGCTCTAGCCATTTTAGG;RSEQ=TTCCTGCAAAGGAGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:7:0,7:1,38:0.1489:1,0:26.6:1:31.3:1:1:0:41.1:14:0.1522:0:3.1 0/1:16:2:0,2:2,12:0.125:2,0:9:1:29.5:1:1:0:50:4:0.125:0:2.5 -21 11047835 . G T 66 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6614;SOR=0.41632;LSEQ=CATTTTAGGATTCCTGCAAA;RSEQ=GAGGAAGGGTTAAGGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:6:0,6:1,36:0.1395:1,0:22.7:1:25.7:1:1:0:41.3:2:0.1026:0:3.3 0/1:16:1:0,1:3,12:0.0625:2,0:6:0:31:0:1:0:40:2:0.0625:0:3 -21 11047866 . C T 72 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.86984;LSEQ=TAAGGCAAGATGAATAGCCT;RSEQ=TGATCTTTACTTTTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:0,5:1,25:0.1613:1,0:12.6:1:31.4:1:1:0:45.8:10:0.1724:0:1.2 0/1:7:1:0,1:1,5:0.1429:2,0:49:0:27:0:1:0:25:2:0.1429:0:1 -21 11047909 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44737;SOR=0.30861;LSEQ=ATTTTTGAGAGGAAGGCGCT;RSEQ=TAACTGCTATGTGCTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:2,12:0,1:0.9333:0,2:32.9:1:31.8:1:1:0:58.4:28:0.9333:0:1.4 1/1:5:4:1,3:0,1:0.8:0,2:24:1:30.8:1:1:0:60:8:0.8:0:1.5 -21 11047958 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAAATCTTGGCACAGCAA;RSEQ=TTGAAAAGACTGTCATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:46.5:1:32:1:1:0:60:4:0.2857:0:3 0/0:2:0:0,0:1,1:0:2,0:15:1:31.5:1:1:0:60:4:1:0:2 -21 11047979 . CA TG 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=TTGAAAAGACTGTCATATAA;RSEQ=TAAAGAGGATCAAATTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:0.7143:0,2:24.8:1:31.7:1:1:0:60:10:0.7143:0.1429:1.8 0/0:1:0:0,0:1,0:0:0,0:42:0:33:0:1:0:60:2:1:0:3 -21 11047980 . A G 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGAAAAGACTGTCATATAAC;RSEQ=TAAAGAGGATCAAATTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,0:0.3333:0,0:14.5:1:33:0:1:0:60:4:1:0:2 1/1:1:1:1,0:0,0:1:0,0:43:0:32:0:1:0:60:2:1:0:3 -21 11047999 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CATAAAGAGGATCAAATTTG;RSEQ=CATCAGATCTCTATTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:18.3:1:32.5:1:1:0:60:8:1:0:2 1/1:2:2:1,1:0,0:1:0,2:26:1:27.5:1:1:0:54.5:4:1:0:2.5 -21 11048020 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCAGATCTCTATTTGTAT;RSEQ=CAGGCTGCTGTTTTCTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17.5:1:33:0:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:26:1:30.5:1:1:0:54.5:4:1:0:2.5 -21 11048194 . T C 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TAATTATTTCAAAAGACGAA;RSEQ=CTTGTCATAATTATTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:48.5:1:32:1:1:0:29:4:0.6667:0:1.5 0/0:2:0:0,0:1,1:0:2,0:46.5:1:30:1:1:0:60:4:1:0:0 -21 11049125 . G A 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCTATCACATCCCCTCCCC;RSEQ=GTGCCCCTGAAGACAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:24:1:31.5:1:1:0:60:4:0.2857:0:2 1/1:1:1:0,1:0,0:1:0,0:37:0:33:0:1:0:60:2:1:0:2 -21 11049143 . C T 48 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCGGTGCCCCTGAAGACAAG;RSEQ=TACTTTATTCTTCTCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:28:1:30.7:1:1:0:60:6:0.4286:0:2 1/1:1:1:0,1:0,0:1:0,0:19:0:29:0:1:0:60:2:1:0:2 -21 11049225 . A G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.30312;SOR=2.85648;LSEQ=TAAATTTAAATTAGCTCTTT;RSEQ=GAAGATCAGAGCAATTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:31.3:1:33.3:1:1:0:42:6:0.1579:0:4 0/1:6:2:2,0:4,0:0.3333:0,0:33.5:1:32.5:1:1:0:52:4:0.3333:0:4.5 -21 11049227 . AA GC 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57372;SOR=2.31555;LSEQ=AATTTAAATTAGCTCTTTAG;RSEQ=GATCAGAGCAATTTAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:15,0:0.1429:1,0:32.7:1:33.2:1:1:0:42:6:0.15:0:3 0/1:7:2:2,0:4,0:0.2857:0,0:36.5:1:32:1:1:0:52:4:0.2857:0:3.5 -21 11049228 . A C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31922;LSEQ=ATTTAAATTAGCTCTTTAGA;RSEQ=GATCAGAGCAATTTAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:10,0:4,0:0.5:0,0:25:1:32.2:1:1:0:46.2:20:0.7692:0:2.2 1/0:7:4:4,0:0,0:0.5714:0,0:20.8:1:31.3:1:1:0:52.3:8:1:0:3 -21 11049231 . T C 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06813;SOR=Inf;LSEQ=TAAATTAGCTCTTTAGAAGA;RSEQ=CAGAGCAATTTAAATGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:12,0:8,0:0.6:0,0:25.4:1:32.8:1:1:0:47.4:24:0.6667:0:2.4 1/1:7:7:7,0:0,0:1:0,0:27.7:1:32.4:1:1:0:53.3:14:1:0:3 -21 11049236 . G A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.62202;SOR=1.68152;LSEQ=TAGCTCTTTAGAAGATCAGA;RSEQ=CAATTTAAATGATTAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:18.7:1:32:0:1:0:60:6:0.1429:0:2.3 0/1:9:2:2,0:7,0:0.2222:0,0:30.5:1:31.5:1:1:0:52:4:0.2222:0:3 -21 11049251 . A G 53 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.63894;SOR=0.39525;LSEQ=TCAGAGCAATTTAAATGATT;RSEQ=AAATCAGTTTTGTTTAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:4,0:28,0:0.125:1,0:31.5:1:26.5:1:1:0:42:3:0.1:0:2 0/1:19:1:1,0:17,1:0.0526:1,0:15:0:34:0:1:0:60:2:0.0526:0:2 -21 11049300 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20138;SOR=Inf;LSEQ=AATAATATAAACGTTAATAT;RSEQ=CAGTAATTTTTTTAAGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:77,1:0:1,0:23.8:1:30.8:1:1:0:59.5:18.5:1:0:0.7 0/1:64:2:2,0:54,8:0.0313:2,0:23:1:32:0:1:0:60:4:0.0313:0:2 -21 11049306 . A AT 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0953;SOR=Inf;LSEQ=ATAAACGTTAATATCCAGTA;RSEQ=TTTTTTTAAGTATGATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:87,1:0:1,0:23.7:1:29.9:1:1:0:59.6:43:1:0:0.9 0/1:75:3:2,1:64,8:0.04:2,2:9.7:1:30.1:1:0.32233:3.88636:57:6:0.04:0.0267:0.3 -21 11049343 . C T 117 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11553;SOR=2.20486;LSEQ=GAAGTCACTCTGAATGAATA;RSEQ=AGCCAAAATATGAACAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:7:7,0:185,5:0.0355:1,0:10.7:1:31.1:1:1:0:50.6:14:0.0361:0:2.9 0/1:186:14:14,0:153,19:0.0753:2,1:21:1:30.8:1:0.36764:0:54.9:28:0.0753:0:2.1 -21 11049346 . C T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08767;SOR=0.3008;LSEQ=GTCACTCTGAATGAATACAG;RSEQ=CAAAATATGAACAACCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:10:10,0:187,6:0.0493:1,0:30.7:1:30.6:1:1:0:60:20:0.05:0:1.9 0/1:196:3:3,0:173,20:0.0153:2,0:17.3:1:30.7:1:1:0:49:6:0.0154:0:2 -21 11049360 . A T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.30754;SOR=1.60142;LSEQ=ATACAGCCAAAATATGAACA;RSEQ=CCTCTATTATATTACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:10:8,2:243,22:0.0364:2,2:32.5:1:30.5:1:0.21354:2.74652:53.4:20:0.0366:0:4.1 0/1:263:15:12,3:212,36:0.057:2,2:31.7:1:30:1:0.47264:1.46979:52.7:14:0.0538:0:3.8 -21 11049364 . C T 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.0088;LSEQ=AGCCAAAATATGAACAACCT;RSEQ=TATTATATTACACAAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:60:55,5:207,22:0.2076:2,2:27.8:1:30.2:1:1:1.17:56.5:59:0.2085:0:1.9 0/1:287:60:49,11:195,30:0.2091:2,2:20.5:1:30.3:1:0.30937:1.4571:55.4:120:0.2091:0:1.9 -21 11049384 . T C 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00259;SOR=0.3772;LSEQ=CTATTATATTACACAAACTT;RSEQ=TAGCGCCTAGTAATAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:34:27,7:299,67:0.085:2,2:20.5:1:30.8:1:0.81705:1.15659:51:33:0.0838:0:1.9 0/1:414:14:11,3:316,84:0.0338:2,2:22.4:1:30:1:1:1.02591:48.9:13:0.0319:0:1.8 -21 11049389 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17937;SOR=1.77312;LSEQ=ATATTACACAAACTTTTAGC;RSEQ=CCTAGTAATAGGGTCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:10:8,2:329,85:0.0236:2,2:22:1:28.7:1:1:1.03:53.4:20:0.0239:0:4.1 0/1:438:18:11,7:319,101:0.0411:2,2:26.7:1:27.8:1:0.16576:2.00629:48.4:17:0.039:0:3.8 -21 11049395 . T C 268 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.79264;SOR=1.06331;LSEQ=CACAAACTTTTAGCGCCTAG;RSEQ=AATAGGGTCCCTCTTAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:448:367:272,95:60,20:0.8192:2,2:26:1:31.7:1:1:1.04769:50.9:51.429:0.8182:0:2 1/1:448:371:265,106:58,19:0.8281:2,2:26.3:1:31.5:1:0.57692:1.22048:50.9:91.75:0.8266:0:2.1 -21 11049404 . C G 258 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.89163;SOR=0.97255;LSEQ=TTAGCGCCTAGTAATAGGGT;RSEQ=CCTCTTAAACCCAATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:463:294:206,88:118,51:0.635:2,2:28.3:1:31.5:1:1:1.01:48.5:31.667:0.6319:0:2.1 1/0:463:291:187,104:117,54:0.6285:2,2:27.5:1:31.3:1:0.41658:1.20451:50.4:144.5:0.6338:0:2.1 -21 11049461 . G T 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06632;SOR=0.62336;LSEQ=AAAACTTACTTGCAGTTCTG;RSEQ=CACACTTTGCACTCAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:46:19,27:138,211:0.1165:2,2:24.1:1:29.4:1:0.8731:1.08:39.4:92:0.1195:0:2.3 0/1:369:28:9,19:122,218:0.0759:2,2:22.8:1:29.1:1:0.83795:1.18088:36.7:56:0.0776:0:2.3 -21 11049495 . C A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14447;SOR=0.63909;LSEQ=CAGGACATTGCCAACCTGCA;RSEQ=GTTTTAATGGAGTAACCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:33:8,25:60,174:0.1236:2,2:25.3:1:31.5:1:1:1.07729:34.1:66:0.1255:0:2.5 0/1:230:19:3,16:36,174:0.0826:2,2:31.9:1:31.1:1:1:1.10299:32.5:38:0.083:0:2.7 -21 11049503 . T A 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19745;SOR=0.7612;LSEQ=TGCCAACCTGCACGTTTTAA;RSEQ=GGAGTAACCGCTGTATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:93:21,72:42,107:0.3843:2,2:21.7:1:30.9:1:0.36867:1.34417:33.6:92:0.3849:0:1.8 0/1:205:66:13,53:32,107:0.322:2,2:24.2:1:31.1:1:0.71842:1.21811:33.6:65:0.3186:0:1.8 -21 11049516 . G A 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84966;LSEQ=GTTTTAATGGAGTAACCGCT;RSEQ=TATCCAGGCACATTCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:221:219:67,152:1,1:0.991:2,2:23.6:1:30.4:1:0.52168:2.25934:32.2:72:0.9908:0:1.6 1/1:188:186:53,133:0,0:0.9894:0,2:23.4:1:29.9:1:1:0:32.2:372:0.9894:0:1.5 -21 11049584 . C T 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12006;SOR=0.65292;LSEQ=AACTGATCTAAGAGGTCTCC;RSEQ=GGGCTGTCGCACACTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:38:21,17:174,175:0.0982:2,2:26.9:1:30.2:1:0.60927:1.24:39.9:76:0.099:0:2.2 0/1:407:27:16,11:227,153:0.0663:2,2:30.5:1:29.9:1:1:1.01997:38.2:54:0.0672:0:2.1 -21 11049592 . C T 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10515;SOR=0.65601;LSEQ=TAAGAGGTCTCCCGGGCTGT;RSEQ=GCACACTGCACAGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:41:22,19:182,199:0.0972:2,2:26.6:1:29.9:1:0.51323:1.27:40.6:82:0.0976:0:2.1 0/1:440:29:16,13:234,176:0.0659:2,2:30.3:1:29.7:1:0.84852:1.08006:39.2:58:0.0665:0:2 -21 11049596 . C T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.45446;SOR=0.77576;LSEQ=AGGTCTCCCGGGCTGTCGCA;RSEQ=ACTGCACAGTTTGCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:26:13,13:195,214:0.0596:2,2:22.3:1:29:1:0.84216:1.10:37.5:52:0.0598:0:2.7 0/1:448:21:12,9:236,191:0.0469:2,2:31.1:1:28.6:1:1:1.08:38.5:42:0.0474:0:2.9 -21 11049617 . C G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGCACAGTTTGCATCTTC;RSEQ=TTCGCTATAATTAACAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:0:0,0:191,278:0:2,0:26.5:1:31.4:1:1:0:43.3:155.333:1:0:0.5 0/1:480:36:16,20:216,227:0.075:2,2:25.9:1:28.8:1:0.72932:1.189:42.9:17:0.0725:0:1.3 -21 11049621 . G A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30451;SOR=0.71542;LSEQ=CACAGTTTGCATCTTCCTTC;RSEQ=CTATAATTAACAGTAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:28:7,21:171,259:0.061:2,2:28:1:29:1:0.16085:1.97798:38.8:56:0.0619:0:2.8 0/1:473:21:10,11:212,240:0.0444:2,2:29:1:29.6:1:1:1.03:40:42:0.0454:0:2.9 -21 11049623 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23527;SOR=0.67331;LSEQ=CAGTTTGCATCTTCCTTCGC;RSEQ=ATAATTAACAGTAAAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:452:28:7,21:166,258:0.0619:2,2:28:1:31:1:0.16212:1.92765:38.8:56:0.0625:0:2.8 0/1:470:20:9,11:209,241:0.0426:2,2:29:1:31.2:1:1:1.05982:40.7:40:0.0433:0:3 -21 11049650 . G T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05897;SOR=0;LSEQ=AACAGTAAAACAATGAAATT;RSEQ=TTGTATAAGAATTTAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:4:1,3:104,252:0.0111:2,2:38.5:1:31.3:1:1:1.23738:49.8:8:0.0111:0:1 0/0:369:0:0,0:115,253:0:2,0:24.2:1:30.7:1:1:0:47.6:72.6:0.9973:0:0.3 -21 11049651 . T C 149 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09753;LSEQ=ACAGTAAAACAATGAAATTG;RSEQ=TGTATAAGAATTTAAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:28:13,15:89,236:0.0791:2,2:26.4:1:31:1:0.04835:2.29:48.4:27:0.0778:0:1.3 0/0:362:3:1,2:108,251:0.0083:2,2:24.7:1:31:1:1:1.16:56.3:6:0.0083:0:1 -21 11049664 . T A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.73473;LSEQ=GAAATTGTTGTATAAGAATT;RSEQ=AAATTTTTTCTGACTACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:1,2:73,220:0.0101:2,2:32:1:28.7:1:1:1.50:34.3:6:0.0103:0:1.7 0/0:268:2:1,1:69,197:0.0075:2,2:21:1:25.5:1:0.45489:2.84:54:4:0.0075:0:1 -21 11049730 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24419;SOR=Inf;LSEQ=TCATGAACCTTTCAGACATT;RSEQ=GAAGTTATTCACATTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:7,58:0:2,0:20.9:1:30.1:1:1:0:44.8:64:1:0:0.2 0/1:64:2:1,1:5,57:0.0313:2,2:21.5:1:29:1:0.18006:10.50:49:4:0.0317:0:1 -21 11049763 . G A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.80776;SOR=1.15134;LSEQ=ATTGAATTGTCATCTAATCA;RSEQ=AAAGAGGTATCAATAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:1,12:1,18:0.4063:1,1:29.2:1:30.3:1:1:1.48:35.5:26:0.4194:0:1 0/1:34:15:2,13:1,18:0.4412:1,2:18.3:1:30:1:0.57136:2.69:44.5:30:0.4412:0:1.1 -21 11049792 . G T 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55014;SOR=3.2739;LSEQ=ATCAATAAAAACACTGTAGG;RSEQ=TATTTAATCTAAATGTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:3,19:0.0435:2,0:7:0:25:0:1:0:27:2:0.0455:0:2 0/1:15:2:0,2:0,13:0.1333:1,0:16:1:32:0:1:0:49:4:0.1333:0:1 -21 11049870 . A G 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GGCTATATCTACTTAAGACC;RSEQ=TAAGCAGGTCTTCTTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:2,5:0.4167:2,2:23.4:1:30.6:1:1:1.53983:40.6:10:0.4167:0:1.2 0/0:2:0:0,0:1,1:0:2,0:29:0:31.5:1:1:0:50:4:1:0:0 -21 11050241 . A G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AATATACTAATTCTATATTC;RSEQ=TCTATATTAATTTCTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:12:0:32:0:1:0:26:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:30:1:1:0:27:4:1:0:1 -21 11050676 . T TTTG 25 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTCCTTTTTTTTTTT;RSEQ=AGACAGTTTCACTCTGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:25:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11055963 . T C 30 d7;v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TAAAAATACAAAAAATTAGC;RSEQ=GGGTGTTATGGTGTGCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:0:30.5:1:1:0:60:4:1:0:2.5 0/1:3:1:1,0:1,1:0.3333:2,0:4:0:32:0:1:0:60:2:0.3333:0:3 -21 11055966 . G A 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=0;LSEQ=AAATACAAAAAATTAGCTGG;RSEQ=TGTTATGGTGTGCGCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:31:1:1:0:60:4:1:0:2.5 0/0:4:0:0,0:2,2:0:2,0:8:1:30.8:1:1:0:60:8:1:0:1.3 -21 11056023 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTGAGGCAGGAGAAATC;RSEQ=CCTGAACCCGGAAAGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:40:1:30.5:1:1:0:60:4:1:0:2.5 -21 11056032 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGAAATCACCTGAACC;RSEQ=GGAAAGCGGAGTTTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:29:1:1:0:60:4:1:0:2.5 -21 11057198 . T A 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTAATGGAAAATGAAAT;RSEQ=AGGTTACTCAACAAAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:28.5:1:1:0:50:4:1:0:2.5 -21 11057202 . T G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGGAAAATGAAATTAGG;RSEQ=TACTCAACAAAGATAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:31:1:1:0:50:4:1:0:2.5 -21 11057448 . T G 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATAGACTAGGAGAAAAAA;RSEQ=ATCCCAAAATATACATGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18:1:34:0:1:0:37.3:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11057451 . C G 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACTAGGAGAAAAAATAT;RSEQ=CCAAAATATACATGCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:19:1:34:0:1:0:37.3:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11057521 . C T 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATCTCTATTTAATGATACAA;RSEQ=AGTAGAGTTATAATTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:12:1:26.5:1:1:0:39:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11057546 . A T 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAGTTATAATTTCCTGTATA;RSEQ=TGTAAATTTCAAGCATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:8:0:27:0:1:0:41:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:13:0:32:0:1:0:53:4:1:0:1.5 -21 11057674 . AT A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAAAAGGTGCTAGCAGAG;RSEQ=TTCTATCACACCTATCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:48:1:30.5:1:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11057701 . C A 70 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACACCTATCAGGGATACA;RSEQ=AATTTCCAAGAATTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:2,1:0.5556:2,2:9.4:1:30.2:1:1:1.83:53:10:0.5556:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11057855 . A T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12917;SOR=Inf;LSEQ=TTTAATAATTTTATAGTATA;RSEQ=GTCAGAAATACTGCACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:11,0:4,2:0.6471:2,0:21.4:1:31.4:1:0.11029:0:43.5:22:0.6471:0:3.2 1/1:8:8:8,0:0,0:1:0,0:17.9:1:31.4:1:1:0:54.1:16:1:0:2.8 -21 11057866 . C T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39986;SOR=2.33149;LSEQ=TATAGTATAAGTCAGAAATA;RSEQ=TGCACAGTCCCTATTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:6,0:16,2:0.25:2,0:18.8:1:31.5:1:1:0:43:12:0.2727:0:3.7 0/1:9:4:4,0:5,0:0.4444:0,0:25.8:1:30.8:1:1:0:51:8:0.4444:0:3.3 -21 11057888 . T A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.35448;SOR=1.9136;LSEQ=GCACAGTCCCTATTTACATC;RSEQ=TTCTACAGTGGTTTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:12,0:12,2:0.4615:2,0:29.3:1:29.3:1:0.48308:0:40.2:11:0.44:0:2.7 1/0:16:10:10,0:5,1:0.625:2,0:29.8:1:30.1:1:0.375:0:52:20:0.6667:0:2.2 -21 11057905 . A T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14303;SOR=5.48788;LSEQ=ATCTTTCTACAGTGGTTTTT;RSEQ=AAATGTTTTAAGAATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:1,0:32,2:0.0286:2,0:39:0:28:0:1:0:34:2:0.0286:0:3 0/1:21:3:2,1:16,2:0.1429:2,2:18.7:1:28.7:1:0.38647:3.64884:51.7:6:0.1429:0:3 -21 11057929 . T C 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39354;SOR=0.54302;LSEQ=TGTTTTAAGAATAAAAAACA;RSEQ=GCAAACTTTATTTGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:11:11,0:41,2:0.193:1,0:11.4:1:29.6:1:1:0:47.5:10:0.1852:0:3.1 0/1:35:4:3,1:27,4:0.1143:2,2:20.3:1:31:1:0.4766:2.18628:50.3:8:0.1143:0:3 -21 11057931 . C A 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08989;LSEQ=TTTTAAGAATAAAAAACATG;RSEQ=AAACTTTATTTGATTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:11:11,0:46,2:0.1864:1,0:22.4:1:30:1:1:0:45.3:22:0.1897:0:2.7 0/1:35:7:7,0:23,5:0.2:2,0:21.9:1:27.7:1:0.5585:0:52.9:14:0.2121:0:2.6 -21 11057949 . T C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78577;SOR=0.7283;LSEQ=TGCAAACTTTATTTGATTTT;RSEQ=CTGAGGAAATAACTTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:12:12,0:64,4:0.15:2,0:20.2:1:30.8:1:1:0:48.5:11:0.1447:0:3.8 0/1:44:5:3,2:32,7:0.1136:2,2:21.8:1:29.8:1:0.26716:2.95185:49.4:10:0.1163:0:3.8 -21 11057983 . G A 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02288;SOR=0;LSEQ=TTTTTGGATTTAATTTCAAT;RSEQ=AAACCGTTGATAACATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:8:8,0:108,9:0.064:2,0:30.9:1:28.1:1:1:0:39.4:16:0.0645:0:3 0/0:83:0:0,0:62,20:0:2,0:21.2:1:31.2:1:1:0:53.4:40:0.9877:0:2.4 -21 11057984 . A C 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68232;SOR=1.55218;LSEQ=TTTTGGATTTAATTTCAATG;RSEQ=AACCGTTGATAACATTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:3:2,1:118,8:0.0233:2,2:30.7:1:31.7:1:0.19646:7.13385:59:6:0.0242:0:4 0/1:84:3:2,1:62,19:0.0357:2,2:41.7:1:33.3:1:0.56274:1.62101:50.7:6:0.0361:0:4.3 -21 11057988 . C T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7741;LSEQ=GGATTTAATTTCAATGAAAC;RSEQ=GTTGATAACATTTCCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:6:5,1:124,9:0.0432:2,2:23.8:1:30.3:1:0.36655:2.72597:54.2:12:0.0432:0:3.5 0/1:89:3:3,0:67,19:0.0337:2,0:19.3:1:31.7:1:1:0:53:6:0.0341:0:4 -21 11058008 . G C 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTGATAACATTTCCCTCC;RSEQ=CAACAATCTCTGGCAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:157:141,16:0,0:1:0,2:26.1:1:31:1:1:0:48.8:51.333:1:0:2.9 1/1:97:97:76,21:0,0:1:0,2:27.3:1:30.3:1:1:0:51.6:47.5:1:0:2.7 -21 11058025 . T C 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00296;SOR=0.39205;LSEQ=TCCGCAACAATCTCTGGCAA;RSEQ=GATCCCTCAGATTTTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:150:127:108,19:22,1:0.8467:1,2:30.8:1:31.6:1:0.31371:3.84665:47.2:126:0.8456:0:3.2 1/0:101:69:53,16:25,6:0.6832:2,2:30.8:1:31.1:1:0.79669:1.25505:47.7:138:0.6832:0:3.1 -21 11058042 . AA GT 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19442;SOR=0.31884;LSEQ=CAATGATCCCTCAGATTTTA;RSEQ=GATTATGTATTATTACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:8:7,1:108,19:0.0593:2,2:26:1:30.4:1:1:1.23:42:16:0.0611:0.0074:3.9 0/1:102:2:2,0:76,24:0.0196:2,0:34.5:1:30:1:1:0:44:4:0.02:0:4 -21 11058043 . A T 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.78067;SOR=0.92136;LSEQ=AATGATCCCTCAGATTTTAA;RSEQ=GATTATGTATTATTACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:92:75,17:34,2:0.6815:2,2:29.2:1:29.8:1:0.09523:3.8219:45.2:91:0.7222:0:3.3 1/0:101:67:49,18:27,5:0.6634:2,2:28.8:1:29.6:1:0.30955:1.9709:48.6:134:0.6768:0:3.1 -21 11058058 . A C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25322;SOR=0.56624;LSEQ=TTTAAAGATTATGTATTATT;RSEQ=CCTTTTAATACAAGTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:13:10,3:90,17:0.1083:2,2:25.5:1:29.7:1:0.45291:1.58137:46.8:26:0.1083:0:4.5 0/1:109:7:4,3:80,22:0.0642:2,2:17.6:1:27.1:1:0.19612:2.69657:39.4:6:0.0561:0:4.1 -21 11058059 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23639;SOR=Inf;LSEQ=TTAAAGATTATGTATTATTA;RSEQ=CTTTTAATACAAGTAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:101,19:0:2,0:25:1:30.9:1:1:0:45.9:119:1:0:2.6 0/1:115:2:1,1:88,25:0.0174:2,2:24.5:1:24:1:0.40259:3.47105:48.5:4:0.0174:0:3.5 -21 11058066 . A T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87567;LSEQ=TTATGTATTATTACCTTTTA;RSEQ=TACAAGTAGAATAACACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:5:4,1:106,22:0.0376:2,2:19:1:30:1:1:1.20273:47:10:0.0376:0:4.2 0/1:121:4:3,1:92,25:0.0331:2,2:14.5:1:28.5:1:1:1.22448:34.3:8:0.0342:0:3.8 -21 11058076 . A C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19458;SOR=0.47436;LSEQ=TTACCTTTTAATACAAGTAG;RSEQ=ATAACACTCAGGGAATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:10:6,4:99,24:0.0752:2,2:19.2:1:30.2:1:0.21732:2.72415:41.3:20:0.0752:0:4.7 0/1:135:5:1,4:103,27:0.037:2,2:19.2:1:29.6:1:0.00993:14.85862:40.8:10:0.037:0:4.2 -21 11058081 . C A 81 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03227;SOR=0.13;LSEQ=TTTTAATACAAGTAGAATAA;RSEQ=ACTCAGGGAATTTACAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:7:3,4:98,25:0.0538:2,2:15:1:29.1:1:0.04361:5.13853:30.7:14:0.0556:0:3.9 0/0:137:1:1,0:99,37:0.0073:2,0:4:0:27:0:1:0:24:2:0.0074:0:4 -21 11058085 . C A 103 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00763;SOR=6.11655;LSEQ=AATACAAGTAGAATAACACT;RSEQ=AGGGAATTTACAACATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:2,0:89,34:0.016:2,0:17:1:27.5:1:1:0:33:4:0.016:0:3 0/1:143:13:10,3:93,37:0.0909:2,2:16.7:1:28.1:1:1:1.32:34.7:26:0.0915:0:2.9 -21 11058119 . C T 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01037;SOR=0.57544;LSEQ=CATTTGTTATTTTCAGTAAA;RSEQ=ACATTGGTTGAAGTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:195:145:91,54:37,12:0.7436:2,2:24.4:1:29.8:1:0.11844:1.82424:30.4:71.5:0.7487:0:1.4 1/0:248:155:106,49:61,31:0.625:2,2:24.8:1:29.1:1:0.77919:1.10:30.5:76.5:0.6245:0:1.3 -21 11058146 . G C 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=0.41329;LSEQ=GTTGAAGTTTAAAAGTCTAT;RSEQ=CGTAGTAAACTTACATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:42:0,42:211,126:0.1108:2,1:27.7:1:30.3:1:0:0:30.8:20:0.107:0:2.4 0/1:470:23:2,21:264,182:0.0489:2,2:24.3:1:31.5:1:0:15.16109:29:46:0.0497:0:2.3 -21 11058147 . C T 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00085;SOR=Inf;LSEQ=TTGAAGTTTAAAAGTCTATG;RSEQ=GTAGTAAACTTACATCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:213,169:0:2,0:24.3:1:31:1:1:0:41.9:62.667:1:0:0.9 0/1:475:12:8,4:261,201:0.0253:2,2:22.5:1:29.9:1:0.56581:1.54:33.4:24:0.0256:0:1.8 -21 11058148 . G A 95 Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07028;SOR=0.29633;LSEQ=TGAAGTTTAAAAGTCTATGC;RSEQ=TAGTAAACTTACATCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:8:0,8:214,164:0.0207:2,0:23.3:1:31.8:1:0.00142:0:32.5:16:0.0209:0:3.3 0/0:482:3:0,3:274,205:0.0062:2,0:26:1:32:0:0.0797:0:29:6:0.0063:0:3.7 -21 11058226 . G C 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02874;SOR=0.74221;LSEQ=TGTGACTGAAATCCTGAAAG;RSEQ=TGTCGGCTCCTGCAGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:208:88,120:110,118:0.4771:2,2:24:1:31.9:1:0.24788:1.27047:49.4:68.333:0.4745:0:1.2 0/1:493:199:92,107:166,127:0.4037:2,2:26.3:1:31.9:1:0.02724:1.51885:47.1:98.5:0.4037:0:1.1 -21 11058227 . T A 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0873;SOR=0.76593;LSEQ=GTGACTGAAATCCTGAAAGG;RSEQ=GTCGGCTCCTGCAGCACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:413:113:63,50:128,172:0.2736:2,2:16.6:1:31.1:1:0.0201:1.69:32.8:112:0.2745:0:2.2 0/1:478:107:75,32:176,195:0.2238:2,2:13.5:1:30.2:1:4e-05:2.59:34.3:214:0.2262:0:1.9 -21 11058229 . T C 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01307;SOR=0.66188;LSEQ=GACTGAAATCCTGAAAGGTG;RSEQ=CGGCTCCTGCAGCACAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:101:59,42:125,171:0.2488:2,2:17.6:1:32.4:1:0.00554:1.92:32.1:202:0.2531:0:2.2 0/1:473:85:63,22:180,204:0.1797:2,2:13.9:1:32.4:1:0:3.24:31.7:84:0.1803:0:2.1 -21 11058248 . G A 145 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12745;LSEQ=GTCGGCTCCTGCAGCACAAG;RSEQ=ATAATGATACATCTGGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:30:13,17:222,245:0.0602:2,2:17.4:1:29.6:1:0.70883:1.18453:35.4:29:0.0591:0:1.9 0/0:618:5:3,2:315,297:0.0081:2,2:6.6:1:29.2:1:1:1.41:40.4:10:0.0082:0:2 -21 11058261 . C CT 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00651;SOR=Inf;LSEQ=GCACAAGGATAATGATACAT;RSEQ=TGGGTACATTTCTCTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:262,290:0:2,0:24.8:1:31.6:1:1:0:45.1:109.4:0.9982:0:0.7 0/1:720:10:5,5:368,342:0.0139:2,2:26.6:1:30.2:1:1:1.07589:51.6:20:0.014:0:1.1 -21 11058316 . G T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02405;SOR=Inf;LSEQ=CTCCAAAGTGCTTACAAAAT;RSEQ=CACATCGCTGAAAGGGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:531:0:0,0:208,320:0:2,0:25.6:1:31.9:1:1:0:44.8:57.667:0.9943:0:0.4 0/1:736:8:3,5:304,423:0.0109:2,2:19:1:29.5:1:1:1.19749:50:16:0.011:0:1.4 -21 11058322 . C T 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=AGTGCTTACAAAATGCACAT;RSEQ=GCTGAAAGGGGTAAAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:180,299:0:2,0:24.8:1:30.3:1:1:0:44.8:118.75:1:0:0.3 0/1:680:18:8,10:261,399:0.0265:2,2:26.6:1:30.1:1:0.80786:1.22:43.7:36:0.0268:0:1.2 -21 11058323 . G A 73 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.56257;SOR=0.6851;LSEQ=GTGCTTACAAAATGCACATC;RSEQ=CTGAAAGGGGTAAAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:6:5,1:167,285:0.0131:2,2:6.8:1:27.3:1:0.02993:8.50:46.8:12:0.0132:0:1.7 0/0:666:6:4,2:260,400:0.009:2,2:21.5:1:28.5:1:0.22086:3.07:51.3:12:0.0091:0:1.3 -21 11058330 . G A 104 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02714;SOR=0.27475;LSEQ=CAAAATGCACATCGCTGAAA;RSEQ=GGGTAAAGGAGAGAAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:10:3,7:143,259:0.0243:2,2:28:1:31.6:1:1:1.28754:42:20:0.0243:0:1.4 0/0:590:4:1,3:217,369:0.0068:2,2:16.8:1:30:1:1:1.76268:38:8:0.0068:0:2 -21 11058340 . A C 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32104;SOR=1.44331;LSEQ=ATCGCTGAAAGGGGTAAAGG;RSEQ=GAGAAATCTCTTTATAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:13:3,10:94,228:0.0388:2,2:22.8:1:30.1:1:0.76356:1.3731:44.4:26:0.0392:0:1.2 0/1:472:26:10,16:146,300:0.0551:2,2:21.2:1:30.3:1:0.52815:1.28:47.3:52:0.0557:0:1.3 -21 11058349 . T G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20193;SOR=1.41392;LSEQ=AGGGGTAAAGGAGAGAAATC;RSEQ=CTTTATAAAACCTTGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:24:5,19:59,170:0.0949:2,2:21.9:1:31:1:0.8055:1.31742:46.3:23:0.092:0:1.1 0/1:364:47:10,37:102,214:0.1291:2,2:23.5:1:31.5:1:0.17488:1.76103:48.7:94:0.1313:0:1 -21 11058353 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23643;SOR=1.75726;LSEQ=GTAAAGGAGAGAAATCTCTT;RSEQ=ATAAAACCTTGAAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:8:0,8:55,161:0.0357:2,0:21.5:1:32.1:1:0.20449:0:32:16:0.0362:0:1.1 0/1:327:20:5,15:88,219:0.0612:2,2:22.3:1:31.9:1:1:1.2048:43.9:40:0.0625:0:1.1 -21 11058377 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25521;SOR=Inf;LSEQ=AAACCTTGAAAAGGAATATT;RSEQ=AAATATAAGCTGGGAAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:22,100:0:2,0:17.4:1:32:1:1:0:44.4:60:1:0:0.3 0/1:150:3:0,3:27,120:0.02:2,0:10.7:1:29.7:1:1:0:49:6:0.02:0:2 -21 11058383 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19279;SOR=0;LSEQ=TGAAAAGGAATATTCAAATA;RSEQ=AAGCTGGGAAGGTATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:10,84:0.0208:2,2:29:1:30.5:1:0.21711:8.06:27:4:0.0211:0:1.5 0/0:122:0:0,0:20,102:0:2,0:16.3:1:28.3:1:1:0:45.3:39.667:1:0:0.4 -21 11058404 . A ACT 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.21678;SOR=0.56705;LSEQ=AAGCTGGGAAGGTATAAAAA;RSEQ=CTCTGTACATCACAAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:38:2,36:0,14:0.717:1,2:27.5:1:31.3:1:1:0:42.5:76:0.7451:0.1132:0.3 1/0:51:30:7,23:4,17:0.5882:2,2:29.9:1:30.5:1:1:1.29:45.1:60:0.5882:0.0784:0.2 -21 11058430 . G T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.39243;SOR=0.51871;LSEQ=TACATCACAAGTAAACAAAT;RSEQ=GAACCTGCAAAATATTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:10:1,9:2,33:0.2222:2,2:13.8:1:29.4:1:0.53876:1.81:35.4:20:0.2222:0:3.5 0/1:39:5:2,3:7,27:0.1282:2,2:16.6:1:29.8:1:0.57162:2.50:35.2:10:0.1316:0:3.2 -21 11058443 . T C 47 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6178;SOR=0.37175;LSEQ=AACAAATGGAACCTGCAAAA;RSEQ=ATTAAACAAAGGATTCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:0,3:2,31:0.0833:2,0:36.7:1:30:1:1:0:38.3:6:0.0833:0:5 0/1:31:1:0,1:6,24:0.0323:2,0:33:0:29:0:1:0:45:2:0.0333:0:6 -21 11058446 . TAAAC T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22356;SOR=Inf;LSEQ=AAATGGAACCTGCAAAATAT;RSEQ=AAAGGATTCGTTAGAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:2,32:0:2,0:26.9:1:30.9:1:1:0:49.1:68:1:0:0.9 0/1:31:2:1,1:5,24:0.0645:2,2:42.5:1:29.5:1:0.35484:4.47:35.5:4:0.0645:0:4 -21 11058460 . G A 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48949;SOR=0.49206;LSEQ=AAATATTAAACAAAGGATTC;RSEQ=TTAGAAATAATAAAATCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:8:1,7:1,21:0.2667:1,2:38.1:1:30.6:1:0.46897:2.87:38.3:16:0.2667:0:4.3 0/1:20:3:1,2:3,14:0.15:2,2:47.3:1:29.3:1:0.50877:2.22:38.7:6:0.1579:0:4.7 -21 11058464 . G A 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.7365;SOR=0.63104;LSEQ=ATTAAACAAAGGATTCGTTA;RSEQ=AAATAATAAAATCTACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:1,7:1,19:0.2857:1,2:37.8:1:30.1:1:0.49735:2.60:38.3:16:0.2857:0:4.3 0/1:20:4:2,2:2,14:0.2:2,2:34:1:29.8:1:0.16202:6.10:35.8:8:0.2:0:3.8 -21 11058493 . A T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49505;SOR=0.58011;LSEQ=AAATCTACATTACTCAATTT;RSEQ=GTGCTTCGTGTGCTACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:1,6:0,13:0.35:1,2:25:1:31.3:1:0.35:0:38.1:14:0.35:0:3 0/1:17:4:2,2:1,12:0.2353:1,2:15.3:1:29.3:1:0.12059:9.64:42.3:8:0.25:0:2.5 -21 11058500 . C T 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50969;LSEQ=CATTACTCAATTTAGTGCTT;RSEQ=GTGTGCTACCAACTCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:1,15:0.1111:1,0:11.5:1:31:0:1:0:44:4:0.1111:0:5 0/1:17:1:0,1:3,13:0.0588:2,0:11:0:32:0:1:0:45:2:0.0588:0:6 -21 11058545 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=TTCAAATTAGAAAGTTAGAA;RSEQ=TTCATTCCTTATATTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:1,7:0.2:2,0:29.5:1:33.5:1:1:0:35:4:0.2:0:1 0/0:11:0:0,0:3,8:0:2,0:35.2:1:28.8:1:1:0:45.7:22:1:0:1.2 -21 11058580 . G C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30245;SOR=4.19343;LSEQ=TTTCAAAAATAAATTGTGAA;RSEQ=CATTTTTGAAACAAAACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:1,6:0.2222:2,0:12:0:26.5:1:1:0:20:4:0.2222:0:4 1/0:7:4:1,3:0,3:0.5714:0,2:23.8:1:31.3:1:1:0:46:8:0.5714:0:1.8 -21 11058587 . TG AT 30 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76645;LSEQ=AATAAATTGTGAAGCATTTT;RSEQ=AAACAAAACCTAAAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,3:0.25:2,0:24:1:30.8:1:1:0:34.5:4:0.25:0:2 0/1:5:1:0,1:0,0:0.2:0,0:9:0:30:0:1:0:49:2:0.2:0:1 -21 11058610 . T G 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAAAACCTAAAGATTTTT;RSEQ=TTTAAAGCAAATAGTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,4:0.3333:0,2:13:0:33.5:1:0.33333:0:50:4:0.3333:0:1.5 0/0:1:0:0,0:0,1:0:0,0:14:0:32:0:1:0:48:2:1:0:2 -21 11058613 . T TA 29 d7;v4;MAF0.05;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AAAACCTAAAGATTTTTTTT;RSEQ=AAAGCAAATAGTAATATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,2:0.3333:2,0:46:0:29:0:1:0:20:4:0.3333:0:4 1/1:1:1:0,1:0,0:1:0,0:10:0:32:0:1:0:48:2:1:0:2 -21 11058623 . AG GC 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTTTTTTTAAAGCAAAT;RSEQ=TAATATGGTTAAAGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:44:0:32:0:1:0:20:4:0.4:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11058683 . C T 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATTATAAAGTTTTTAAATCC;RSEQ=ACCAAAACTAGTAATAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:25.5:1:26:1:1:0:28:4:0.4:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 11059849 . G T 25 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAAATTAGCCGGACGTG;RSEQ=TGGCAGGCACCTGTAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:9:0:25:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 15373007 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTCCCTTGTTTGGGAAG;RSEQ=ACTGTTTTTGATATACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:31:0:1:0:41:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 15373078 . G A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTTTTTTAATTTGAGAA;RSEQ=CATTTAAATGATGACCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1:0,1:29.5:1:31.5:1:1:0:40.7:26:1:0:1.1 1/1:5:5:5,0:0,0:1:0,0:16.2:1:31:1:1:0:38.2:10:1:0:1 -21 15373208 . A T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50614;LSEQ=GTAAATCTGGAATAGAAGAA;RSEQ=CTTCATATATTATCTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:93,16:0.018:2,2:30:1:29:1:0.28403:5.66924:60:4:0.0185:0:1 0/0:109:1:0,1:84,24:0.0092:2,0:1:0:23:0:0.22936:0:60:2:0.0092:0:1 -21 15373420 . C A 288 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45145;SOR=0;LSEQ=GTCCATGGTGGTTGATCTTA;RSEQ=GGTAACATGCTTATTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:661:661:252,409:0,0:1:0,2:26.1:1:30.8:1:1:0:42.4:219.333:1:0:1.1 1/1:544:543:222,321:0,0:0.9982:0,2:26.1:1:30:1:1:0:42.3:59.333:0.9981:0:1.1 -21 15373568 . G A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98305;LSEQ=CTTGCTTTTGTTGTTACTGC;RSEQ=TTCATCAGTCTAAATGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:29:1,28:0,6:0.8286:0,1:21.3:1:31.3:1:1:0:34.8:28:0.8235:0:1 1/1:23:19:2,17:0,4:0.8261:0,2:25.6:1:30.8:1:1:0:31:38:0.8261:0:1.1 -21 15373954 . G C 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGCCTTGTTTCTTGCCTTC;RSEQ=TGTAAGCCCTCACAACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:0:0,0:165,315:0:2,0:27.2:1:31.3:1:1:0:55.7:239:0.9938:0:0.1 0/1:464:22:7,15:164,278:0.0474:2,2:30.1:1:31.2:1:0.82135:1.26349:57.2:21:0.0458:0:1.2 -21 15374017 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50717;SOR=0;LSEQ=TTTTTATCTAACTATGTTTA;RSEQ=TGATGCCGTTATCCTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:30,146:0.0111:2,2:19.5:1:29.5:1:0.3188:4.80:52:4:0.0112:0:1 0/0:138:0:0,0:16,122:0:2,0:22.6:1:32:1:1:0:57.8:137:1:0:0.1 -21 15374041 . G A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03218;SOR=Inf;LSEQ=TGCCGTTATCCTTTATAAAC;RSEQ=GAAAGACTAGAGGGATAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:19,96:0:2,0:23.9:1:30.7:1:1:0:53.8:56.5:1:0:0.1 0/1:86:4:0,4:6,76:0.0465:2,0:36.5:1:32:1:1:0:57.3:8:0.0465:0:1 -21 15374210 . C CT 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0159;SOR=Inf;LSEQ=TTTCTCATAGAAATAATCTG;RSEQ=TTTTTTTTCTTTTTCTATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:217,46:0:2,0:22.7:1:31.9:1:1:0:46.2:51.6:1:0:0.1 0/1:206:5:3,2:159,42:0.0243:2,2:25:1:29.6:1:0.29001:2.50983:51.2:10:0.0244:0.0049:0.4 -21 15374268 . A T 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCACATTCTACATTTCACT;RSEQ=TGTGCTGGTAAATTCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:278,239:0:2,0:30.3:1:29.1:1:1:0:43.1:56.444:0.9961:0:0.1 0/1:444:19:12,7:227,198:0.0428:2,2:22.9:1:30.5:1:0.48461:1.49:43.6:38:0.0439:0:1.2 -21 15374334 . TA T 207 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.2779;LSEQ=AATAGGCATTGCTAAACTAC;RSEQ=AAAAAAAAAATTTCATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:116:28,88:50,139:0.3754:2,2:30.6:1:30.3:1:0.68688:1.13007:38.1:232:0.388:0.0065:0.1 0/1:266:38:10,28:78,150:0.1429:2,2:30.1:1:30.3:1:0.45649:1.45404:37.9:76:0.1473:0:0.2 -21 15374345 . A T 53 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12951;SOR=0;LSEQ=CTAAACTACTAAAAAAAAAA;RSEQ=TTTCATTATTTTCTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:4:2,2:58,219:0.0142:2,2:26.5:1:26.5:1:0.20088:3.75:42.8:3:0.0109:0:1.3 0/0:235:0:0,0:69,166:0:2,0:23.4:1:29.4:1:1:0:49.7:46:1:0:0.2 -21 15374346 . T A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0938;SOR=Inf;LSEQ=TAAACTACTAAAAAAAAAAA;RSEQ=TTCATTATTTTCTTTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:58,222:0:2,0:24.4:1:29.9:1:1:0:45.9:55:0.9964:0:0.2 0/1:235:3:2,1:66,166:0.0128:2,2:23.3:1:23.3:1:0.20162:4.99:49.3:2:0.0087:0:1.7 -21 15374385 . G A 85 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03462;SOR=5.29355;LSEQ=TATTTCTTTTTACGAAACGC;RSEQ=CTCTTGGTTTTCAAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:4,126:0.015:1,2:10:1:30:1:0.0746:28.30:33:4:0.0152:0:1 0/1:93:7:1,6:2,84:0.0753:1,2:32:1:30.4:1:0.21135:6.71:39.3:14:0.0753:0:1.4 -21 15377537 . G A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TCAGGCTCTGCTGGTTCTTC;RSEQ=TCAGTTAGATAGCATTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:0:0,0:342,269:0:2,0:26.8:1:30.4:1:1:0:48.8:121.2:1:0:0.1 0/1:446:12:7,5:242,192:0.0269:2,2:29.1:1:29.4:1:1:1.11:47.7:24:0.0273:0:1 -21 15377657 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17091;SOR=Inf;LSEQ=ATTTTATTTTGTATTTTTTG;RSEQ=CTTGAAATATTAACTCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:26,161:0:2,0:22.2:1:29.9:1:1:0:44.8:45.75:1:0:0.1 0/1:133:2:1,1:15,115:0.015:2,2:28.5:1:30:1:0.22854:7.46:49:4:0.0155:0:1 -21 15377688 . T C 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0069;SOR=0;LSEQ=TAACTCTATAGTATTTAGTA;RSEQ=ATTGTAAAACTTATACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:10:0,10:0,90:0.1:1,0:30.3:1:32.6:1:1:0:40.2:20:0.1:0:1.1 0/0:64:0:0,0:0,64:0:1,0:22.2:1:28.1:1:1:0:45.3:63:1:0:0.1 -21 15377728 . AT A 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.05289;SOR=0.25821;LSEQ=CAAAGGTTTTATGATTTTGT;RSEQ=TTTTTTGACTTCAAATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:18:0,18:1,31:0.36:1,1:29.2:1:32.7:1:1:0:40.6:36:0.36:0:0.1 0/1:24:3:0,3:0,21:0.125:1,0:48.3:1:30.7:1:1:0:41:6:0.125:0:0 -21 17798796 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05271;SOR=Inf;LSEQ=ATGACACTATGAAAGTTATT;RSEQ=AGCTATAGGTGAAAGAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:78,2:0:1,0:28:1:31.3:1:1:0:60:39:1:0:0.1 0/1:49:3:3,0:45,1:0.0612:1,0:36.7:1:31.3:1:1:0:60:6:0.0625:0:1 -21 17798845 . TG T 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.69301;LSEQ=TGTTCATAAAATGGTATGTG;RSEQ=GGGGGGAGGTGTGGGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:4:3,1:157,41:0.0198:2,2:32.3:1:33:1:1:1.27478:60:8:0.0201:0:0 0/1:145:2:1,1:116,27:0.0138:2,2:32.5:1:29:1:0.35:4.23703:60:4:0.0139:0:0 -21 17798860 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59085;SOR=2.44866;LSEQ=ATGTGTGGGGGGGAGGTGTG;RSEQ=GTGTGTATGTGTGAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:1:0,1:173,65:0.0042:2,0:18:0:16:0:0.27615:0:60:0:0:0:2 0/1:196:2:1,1:140,54:0.0102:2,2:12:1:29:1:0.48352:2.57808:60:4:0.0103:0:1 -21 17798960 . A G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.34652;LSEQ=TGTTTGAAATATGCAAGTCT;RSEQ=TTAAATTGTTTTTACATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:392:314:127,187:26,51:0.801:2,2:25.2:1:31.9:1:0.29998:1.33:60:103.667:0.8015:0:1.1 1/0:335:195:82,113:53,86:0.5821:2,2:25.4:1:31.3:1:0.49866:1.18:60:390:0.5838:0:1.1 -21 18677386 . T A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATCCTATTACCACGCACTC;RSEQ=CAAAGGATTTCTCTGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:21.5:1:29:1:1:1:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 18677639 . T C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.28225;SOR=0.5162;LSEQ=CAGACAACACCTTTCAAACT;RSEQ=TTATACCAACCTCTGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:9,6:5,5:0.6:2,2:28.7:1:30.9:1:0.69683:1.48:49.7:30:0.6:0:1.1 0/1:30:13:8,5:10,7:0.4333:2,2:20.5:1:30.1:1:1:1.12:54.8:26:0.4333:0:1 -21 18677740 . TTTTTA T 62 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=0.56488;SOR=3.5981;LSEQ=TCAGGCCCTGTATTTTTATT;RSEQ=TTTTTTTTTTTTAATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:1,3:0.2:2,0:34:0:32:0:1:0:60:2:0.2:0:5 1/0:8:4:0,4:0,4:0.5:0,0:20.3:1:31:1:1:0:55:8:0.5:0.125:1.8 -21 18677759 . ATT A 32 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=TTTTTTATTTTTTTTTTTTA;RSEQ=TTTTTTTTTTATTATACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:0.2:0,0:20:0:33:0:1:0:60:2:0.2:0:5 0/1:5:2:0,2:0,3:0.4:0,0:47:1:32:0:1:0:50:4:0.4:0:1 -21 19048959 . T A 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGACACAAGACAAAACGAT;RSEQ=AAGAGAAAAGAGCTGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:25.1:1:27.7:1:1:0:60:14:1:0:1.3 1/1:3:3:3,0:0,0:1:0,0:23:1:30:0:1:0:60:6:1:0:1 -21 19048976 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTAAGAGAAAAGAGCTGG;RSEQ=CCCGGGGACCACTACCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:37.5:1:32:0:1:0:60:4:0.2857:0:2 0/0:2:0:0,0:2,0:0:0,0:26:1:31:0:1:0:60:4:1:0:1 -21 19049131 . C T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22506;SOR=0;LSEQ=CAAGTCACATGATCACAGGA;RSEQ=AGGTGGCCCTTCCTTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:11,20:0.0606:2,2:17:1:25.5:1:1:1.78:60:4:0.0606:0:2.5 0/0:36:0:0,0:18,18:0:2,0:27.9:1:31.3:1:1:0:59.6:17:1:0:0.3 -21 19049137 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.74298;LSEQ=ACATGATCACAGGACAGGTG;RSEQ=CCCTTCCTTCTTAGGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:0,1:10,19:0.0333:2,0:46:0:32:0:1:0:60:2:0.0345:0:1 0/1:35:2:0,2:18,15:0.0571:2,0:23.5:1:28.5:1:0.22857:0:60:4:0.0571:0:1 -21 20195100 . T A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02411;SOR=Inf;LSEQ=ACAGATAGAGAAATGTAGAA;RSEQ=AACATGTACATAAATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:108,45:0:2,0:22.5:1:29.8:1:1:0:60:306:1:0:0.3 0/1:101:4:3,1:74,23:0.0396:2,2:22.3:1:30:1:1:1.07172:60:8:0.0396:0:2 -21 20195110 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51677;SOR=0;LSEQ=AAATGTAGAATAACATGTAC;RSEQ=TAAATATACATATATCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:126,62:0.0105:2,2:31:1:32.5:1:1:2.02411:60:4:0.0106:0:1 0/0:129:0:0,0:88,39:0:2,0:24.7:1:29.8:1:1:0:60:126:0.9921:0:0.5 -21 20195182 . C T 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=0.52403;LSEQ=GGAATAGTAACAAATAGTTA;RSEQ=TTGAATATGCAAACAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:318:212:105,107:56,49:0.6667:2,2:27.1:1:30.5:1:0.55202:1.16406:60:105:0.6646:0:1.9 1/0:262:134:70,64:67,61:0.5115:2,2:26.9:1:29.6:1:1:1.0042:60:66:0.5116:0:1.9 -21 20195191 . G A 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1853;SOR=4.75263;LSEQ=ACAAATAGTTACTTGAATAT;RSEQ=CAAACAGTTAACACTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:1:1,0:151,161:0.0032:2,0:1:0:23:0:0.48562:0:60:2:0.0032:0:1 0/1:266:4:3,1:130,132:0.015:2,2:20:1:24.5:1:0.62215:3.03:60:3:0.0116:0:1.5 -21 20195198 . G A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33721;SOR=3.56954;LSEQ=GTTACTTGAATATGCAAACA;RSEQ=TTAACACTAAATTTATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:1:1,0:145,165:0.0032:2,0:1:0:26:0:0.46945:0:60:2:0.0033:0:2 0/1:263:3:2,1:126,134:0.0114:2,2:23.7:1:30:1:0.61375:2.12:60:6:0.0116:0:3 -21 20195202 . A G 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00021;SOR=0.52186;LSEQ=CTTGAATATGCAAACAGTTA;RSEQ=CACTAAATTTATGTTTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:304:205:93,112:44,55:0.6743:2,2:24.8:1:31.8:1:0.90263:1.04:60:67.333:0.6733:0:2 1/0:262:136:66,70:57,69:0.5191:2,2:24.6:1:31.7:1:0.62161:1.14:60:135:0.5172:0:1.9 -21 20195250 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50239;SOR=0;LSEQ=TTGTATTTATTTTTCATATA;RSEQ=AGGGATCATAAAAATTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:59,125:0.0108:2,2:25:1:28.5:1:0.54228:2.11:60:4:0.011:0:2 0/0:156:0:0,0:50,106:0:2,0:26.6:1:31.1:1:1:0:60:77:1:0:0.7 -21 20195258 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21716;SOR=Inf;LSEQ=ATTTTTCATATACAGGGATC;RSEQ=TAAAAATTGTTACTCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:50,111:0:2,0:26.1:1:30.2:1:1:0:60:31.2:1:0:0.7 0/1:141:2:1,1:41,98:0.0142:2,2:34:1:28.5:1:0.50851:2.37:60:4:0.0142:0:1.5 -21 20195300 . C T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03116;SOR=Inf;LSEQ=ATTTTGGTTTATTTCTTAAA;RSEQ=GTTAAATATTTCTTAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:15,74:0:2,0:24:1:30.3:1:1:0:60:178:1:0:0.1 0/1:66:4:0,4:10,52:0.0606:2,0:19.3:1:27.3:1:1:0:60:3:0.0462:0:1.8 -21 20195328 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.28063;SOR=0;LSEQ=ATTTCTTAAATGTATGTGAT;RSEQ=CAACAAAACATTAAGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:0,3:5,43:0.0588:2,0:34.3:1:29:1:1:0:60:6:0.0588:0:1 0/0:32:0:0,0:2,30:0:2,0:20.8:1:31.7:1:1:0:60:31:1:0:0.2 -21 20195560 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATTTTTTTACTGTCATGGT;RSEQ=TAACAAAAAAGATGATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:20:1:31:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 21055586 . A G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTTGACATGAGACAAGA;RSEQ=CCCTGGTGGTCCTCCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 21055851 . G GT 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12969;SOR=0;LSEQ=TTTCTCATCTTCATGAGTTT;RSEQ=CTGGTTTTGATCGCTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:11,14:0,0:1:0,2:26.6:1:29.3:1:1:0:60:24:1:0.16:0.1 1/1:34:30:15,15:2,2:0.8824:2,2:30.4:1:28.6:1:1:1:60:29:0.8788:0.0588:0.3 -21 21056158 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01752;SOR=0.20322;LSEQ=CTTCTGTATATGGTGTCTGG;RSEQ=GACCTCTGTTGGGGTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:10,5:2,2:0.7895:2,2:18.8:1:30.7:1:0.60268:1.92:60:30:0.7895:0:1.4 0/1:26:11:7,4:9,6:0.4231:2,2:21.3:1:28.2:1:1:1.16:60:22:0.4231:0:1 -21 21056234 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01658;SOR=0.11888;LSEQ=AACGAAGCACTTTGGCTGTC;RSEQ=TTTGGTGGCGGGGCTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:3,6:0.4375:2,2:23.9:1:31.1:1:1:1.46:60:14:0.4375:0:1.6 0/1:25:2:1,1:9,14:0.08:2,2:5.5:1:30:1:1:1.53:60:4:0.08:0:1.5 -21 21057031 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTATCAGATGGGCTGAGG;RSEQ=ACCACCCTGCTCTTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 27340014 . C T 66 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.48822;LSEQ=TTCTGTCTATGAAGGATAAG;RSEQ=AGAACGCTGAGAGTTACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:33.4:1:28.8:1:1:0:60:10:0.4167:0:1.4 0/1:4:1:1,0:2,1:0.25:2,0:31:0:32:0:1:0:60:2:0.25:0:2 -21 27340020 . G C 28 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.45761;LSEQ=CTATGAAGGATAAGCAGAAC;RSEQ=CTGAGAGTTACAAGGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:31:1:28:1:1:0:60:4:0.1818:0:2 0/1:4:1:1,0:2,1:0.25:2,0:37:0:32:0:1:0:60:2:0.25:0:2 -21 27340191 . C T 67 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12012;SOR=0.19381;LSEQ=GTATTTAATCTGGTAGCTTG;RSEQ=AGGCCTCCAAAGGTGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:5:3,2:133,32:0.0292:2,2:19.2:1:29:1:0.26147:2.74974:60:10:0.0298:0:1 0/0:173:1:1,0:136,36:0.0058:2,0:15:0:32:0:1:0:60:2:0.0058:0:1 -21 27340215 . TA T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25029;SOR=Inf;LSEQ=CCTCCAAAGGTGGTAGAAGT;RSEQ=ACCTCCTGTGCTGCAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:179,69:0:2,0:24.3:1:28.6:1:1:0:60:123:1:0:0.1 0/1:273:3:1,2:194,76:0.011:2,2:25.3:1:26.7:1:0.19728:5.06987:60:6:0.0112:0.0037:2 -21 27340301 . A T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=5.35891;LSEQ=TGATTTTCCAAAGAAAGTCT;RSEQ=AGGAAAGTAAAAAGGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:69:37,32:304,269:0.1075:2,2:23.1:1:28.3:1:1:1.02:60:22:0.1039:0:1.1 0/1:721:283:145,138:213,225:0.3925:2,2:25.6:1:28.6:1:0.5418:1.11:60:69.75:0.3919:0:1.1 -21 27340400 . C CT 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10415;SOR=5.71573;LSEQ=AAAGACACAGCTCTGCTCAA;RSEQ=TTTTTTTTCCCATGGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:1:0,1:39,195:0.0043:2,0:32:0:32:0:1:0:60:2:0.0044:0:0 0/1:209:5:1,4:44,159:0.0239:2,2:31.8:1:29.8:1:1:1.10639:60:10:0.024:0:0 -21 28398955 . T A 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41631;LSEQ=CAGTTGAATTGGTAGACTAA;RSEQ=TAGAGTAGATGGCCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:13,0:0.1875:1,0:24.3:1:31.7:1:1:0:60:6:0.1875:0:1 0/1:4:1:1,0:3,0:0.25:0,0:1:0:29:0:1:0:60:2:0.25:0:1 -21 28399182 . T C 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=1.84034;LSEQ=GACTCAGTCTAGATCCACAA;RSEQ=ATTTGCTCTCTTAGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:127:65,62:82,108:0.4006:2,2:26.8:1:32:1:0.16947:1.38:60:126:0.4:0:1.1 1/0:328:181:92,89:74,73:0.5518:2,2:25.8:1:30.8:1:1:1.02:60:59.333:0.5477:0:1.1 -21 28399257 . T A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4985;SOR=0;LSEQ=TTCATAAGATTATAAGCCAA;RSEQ=TCCTTCTGGTGACTATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:37,122:0.0124:2,2:22.5:1:32:0:0.41747:3.27:60:4:0.0125:0:1 0/0:157:0:0,0:44,113:0:2,0:23.1:1:29.2:1:1:0:60:51.333:1:0:0.4 -21 28423608 . T A 56 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TCTGACAGTTCATCCATCTG;RSEQ=TCTTCCATTCAGGCACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:20.3:1:30:1:1:0:60:6:0.6:0:1.7 1/1:5:5:3,2:0,0:1:0,2:27.2:1:24.4:1:1:0:60:4:1:0:2.4 -21 28423657 . T G 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25824;SOR=Inf;LSEQ=GATGTTGTGATCATTTGGAG;RSEQ=AGAAGAGGTCCTCTGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:3,3:3,2:0.5455:2,2:21.7:1:30.7:1:1:1.44544:60:12:0.5455:0:1.5 1/1:3:3:1,2:0,0:1:0,2:22:1:32.3:1:1:0:60:6:1:0:3 -21 28424677 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACATATACACACATATATAC;RSEQ=TATACATATATACACACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:30:1:1:0:60:4:1:0:2 -21 28424718 . C T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCATATACATATATACACA;RSEQ=ATATACATATACATATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:19.5:1:31:1:1:0:60:4:0.6667:0:2 -21 28424933 . T TATATATATATA 47 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAACATATATATATATAA;RSEQ=ATATATATATATAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:17:1:29.9:1:1:0:60:6:0.6:0.4:0 0/0:1:0:0,0:0,1:0:0,0:13:0:30:0:1:0:60:2:1:0:0 -21 28425056 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12896;SOR=0;LSEQ=CAGCAGCCTCAAAGACCAAA;RSEQ=CTGGACAAACTCACAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:5,12:0.1053:2,2:10.5:1:30:1:1:2.28:60:4:0.1111:0:2.5 0/0:33:0:0,0:17,16:0:2,0:19:1:28.3:1:1:0:60:66:1:0:0.4 -21 28425059 . G A 23 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63592;SOR=0.61361;LSEQ=CAGCCTCAAAGACCAAAACT;RSEQ=GACAAACTCACAAAGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:5,12:0.1053:2,2:7.5:1:27.5:1:1:2.28:60:4:0.1111:0:2.5 0/1:30:2:2,0:14,14:0.0667:2,0:1:0:23.5:1:0.48506:0:60:4:0.0714:0:1 -21 28425164 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18803;SOR=Inf;LSEQ=CGCAACATCTCTCCATCAAG;RSEQ=GTGCAGAACTGAATGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:31:1:31.4:1:1:0:60:30:1:0:0.1 0/1:12:2:1,1:6,4:0.1667:2,2:14:1:25.5:1:1:1.4491:60:4:0.1667:0:1 -21 28978057 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATATGTCACTCGAGGAG;RSEQ=CTGGAGAACAGCAAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:23:1:29.5:1:1:1.41:60:4:0.2857:0:1.5 0/0:2:0:0,0:1,1:0:2,0:19:1:23:1:1:0:60:1:1:0:0 -21 28978108 . A C 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63287;SOR=1.91506;LSEQ=CTTCCTCTGGGATCTCTAAA;RSEQ=TCAAGGCGTATCAACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:3,2:2,2:0.5556:2,2:16.6:1:32.2:1:1:1.43:60:10:0.5556:0:1.2 1/0:7:5:4,1:1,1:0.7143:2,2:24:1:31.4:1:1:3.16:60:10:0.7143:0:1 -21 28978250 . G A 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03036;SOR=0;LSEQ=GAGCTGTCCCTTTTTGGAGG;RSEQ=GGTGTGCTACGTTGGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:6,8:0.3636:2,2:27.3:1:31.6:1:1:1.23744:60:16:0.3636:0:1 0/0:12:0:0,0:4,8:0:2,0:25:1:30.4:1:1:0:60:24:1:0:0 -21 28978809 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGAGAATCTGTGCATCTC;RSEQ=GTGGTTGGGACCCTAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:32:0:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:36:1:29:1:1:0:60:4:1:0:1 -21 28978981 . G T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCAGTGTGGCTCTCAGGTG;RSEQ=GCGGCCTCAACACACTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:4:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:31.5:1:1:0:60:4:1:0:2 -21 28979005 . T C 49 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCAACACACTGCTCTTC;RSEQ=TTCCTCTCTGTGGGTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:33:1:31:1:1:0:60:6:1:0:1.7 -21 30728127 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49317;SOR=Inf;LSEQ=GAAAGGGGAGAAGCCATGTT;RSEQ=CCCAACTCCAGAGGTTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:21,13:0:2,0:29.8:1:32.6:1:1:0:59.1:68:1:0:0.1 0/1:36:2:1,1:18,16:0.0556:2,2:14.5:1:30:0:1:1.12132:60:4:0.0556:0:1.5 -21 31252048 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.083;SOR=Inf;LSEQ=TTTAGGAAAAACGGTAGCTC;RSEQ=TTAAGGAGCTAGTTTATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:0:1,0:23.6:1:31.6:1:1:0:60:32:1:0:0 0/1:7:2:2,0:5,0:0.2857:0,0:7.5:1:30.5:1:1:0:60:4:0.2857:0:1 -21 31252105 . C G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00672;SOR=Inf;LSEQ=AAGGCCAAGCAATTTTGCAA;RSEQ=TGTCTTCTGCTTATTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:0:1,0:24.1:1:32.8:1:1:0:60:122:1:0:0 0/1:26:4:4,0:22,0:0.1538:1,0:23.3:1:31.5:1:1:0:60:8:0.1538:0:1 -21 31252172 . A AT 61 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.40261;SOR=0.34131;LSEQ=CACACAGCCCCAGTTCTTTG;RSEQ=TTTTTTTTTTAACAAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:4:4,0:122,14:0.0286:2,0:20.3:1:30.6:1:1:0:60:8:0.0299:0.0071:0 0/0:101:1:1,0:90,10:0.0099:2,0:50:0:28:0:1:0:60:2:0.01:0:0 -21 31252298 . T C 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=19.5353;LSEQ=AAAGAGTTTACATATGCAAT;RSEQ=GTTACAGTAATAGTTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:1:1,0:206,263:0.0021:2,0:30:0:15:0:0.44043:0:60:0:0:0:1 0/1:375:15:7,8:154,205:0.04:2,2:28:1:31.1:1:0.7954:1.16:60:30:0.04:0:1 -21 31252311 . G A 183 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=116.7612;LSEQ=ATGCAATTGTTACAGTAATA;RSEQ=TTCCCTGAAGCCCCTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:1:1,0:172,258:0.0023:2,0:1:0:27:0:0.40139:0:60:2:0.0024:0:1 0/1:336:72:28,44:113,150:0.2143:2,2:23.3:1:29.8:1:0.59095:1.18322:60:144:0.2162:0:1.1 -21 31252384 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15188;SOR=Inf;LSEQ=GAATACGATTTGTATAATAA;RSEQ=CCTAATCAGAAAAATAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:41,143:0:2,0:22.8:1:31.5:1:1:0:60:183:1:0:0.1 0/1:118:2:1,1:33,83:0.0169:2,2:32.5:1:29.5:1:0.495:2.49:60:4:0.0171:0:1 -21 31384240 . C T 133 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00166;SOR=0.16797;LSEQ=GCCTTTTGACCCAAAAAGAC;RSEQ=GCATAGCCTCCAATTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:19:8,11:187,141:0.0548:2,2:32.2:1:31.5:1:0.23816:1.82035:60:38:0.0556:0:1.5 0/0:312:3:1,2:170,139:0.0096:2,2:29:1:28.7:1:0.5912:2.43919:60:6:0.0098:0:1.3 -21 31384297 . A G 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25222;LSEQ=ATTTCATCTGCATTCTACCT;RSEQ=TTTCAGTACATAATCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:433:400:165,235:15,17:0.9238:2,2:26.4:1:31.6:1:0.57862:1.256:60:43.444:0.9243:0:1.1 1/0:389:293:134,159:43,53:0.7532:2,2:26.5:1:31:1:0.90636:1.04:60:145.5:0.7519:0:1.1 -21 31384366 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=TGTTAATAAGGTCTTATGTA;RSEQ=ATATTTATATTTTCTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:37,127:0.012:2,2:20.5:1:30.5:1:0.4065:3.40:60:4:0.0124:0:1 0/0:159:0:0,0:45,114:0:2,0:25.7:1:29.7:1:1:0:60:38.75:1:0:0.5 -21 31384543 . T C 74 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.52273;SOR=0.28305;LSEQ=TGAATCATGGCAAATATGTA;RSEQ=ACTTCTATAGTCAGAAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:0.6667:0,0:38.3:1:29:1:1:0:60:5:0.625:0:1.2 0/1:3:1:0,1:0,2:0.3333:0,0:45:0:34:0:1:0:60:2:0.3333:0:2 -21 32273182 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50274;SOR=Inf;LSEQ=GGTTTTTGCTAAGCTGACTT;RSEQ=GCGGAGTTCTTGGCTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:17,14:0:2,0:27.3:1:29.3:1:1:0:60:30:1:0:0.9 0/1:41:2:1,1:24,15:0.0488:2,2:15.5:1:29.5:1:1:1.58108:60:4:0.05:0:1 -21 32273185 . G A 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7664;SOR=0.78956;LSEQ=TTTTGCTAAGCTGACTTAGC;RSEQ=GAGTTCTTGGCTAAAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:27:15,12:2,3:0.8438:2,2:28.3:1:31.1:1:0.64544:1.84:60:54:0.8438:0:1 1/1:42:34:20,14:5,3:0.8095:2,2:23.6:1:30.4:1:1:1.16243:60:68:0.8095:0:1.1 -21 32273325 . G A 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41667;SOR=0;LSEQ=ATATTCCTGTACTTCCAAGC;RSEQ=ATTCAACTATCTTGAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:14.3:1:27.4:1:1:0:60:6:1:0:1.1 1/1:5:4:0,4:0,1:0.8:0,0:16.8:1:31:1:1:0:60:8:0.8:0:1 -21 32380890 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16075;SOR=Inf;LSEQ=CAAGGAATGCCCAAACTTGC;RSEQ=AGCAAACCACCAAAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:30,32:0:2,0:25.6:1:31.5:1:1:0:60:124:1:0:0.2 0/1:42:2:1,1:19,21:0.0476:2,2:35:1:28.5:1:1:1.10:60:4:0.0476:0:1 -21 33044256 . GGCT G 63 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=1;SOR=0.75459;LSEQ=GAGGCTGTTGTGATGGTGGT;RSEQ=GCTGCTGCTGCTGCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:2,2:12,8:0.1667:2,2:31.8:1:31.8:1:1:1.47432:60:8:0.1667:0:0 0/1:23:3:1,2:10,10:0.1304:2,2:28.3:1:31.7:1:1:1.94223:60:6:0.1304:0:0 -21 36164388 . G C 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00713;SOR=0;LSEQ=AGGCCCGCGCGCCCGGAGGC;RSEQ=AAGGCGGCGGCCCGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:9,0:23,0:0.2727:1,0:7:1:31.8:1:1:0:60:18:0.3:0:1 0/0:24:0:0,0:21,3:0:2,0:9.5:1:27.9:1:1:0:60:11:1:0:1 -21 36164405 . G T 150 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=47.59961;LSEQ=GGCGAAGGCGGCGGCCCGCG;RSEQ=GGCCCAGCCGGGCCAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:2,0:81,8:0.022:2,0:16.5:1:30.5:1:1:0:60:4:0.0222:0:1 1/0:63:33:30,3:27,3:0.5238:2,2:14.8:1:29.9:1:1:1.11:60:66:0.5323:0:1.1 -21 36164413 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51551;SOR=0;LSEQ=CGGCGGCCCGCGGGGCCCAG;RSEQ=CGGGCCAGGCCTGGCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:104,20:0.0159:2,2:7:1:28.5:1:0.30667:5.09915:60:4:0.0159:0:1 0/0:86:0:0,0:72,14:0:2,0:17.8:1:32.2:1:1:0:60:85:1:0:0.6 -21 36164469 . G T 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.09585;SOR=6.16228;LSEQ=CGGCCTCCTCCAGGCGCGCG;RSEQ=AGGGCGCCATGTTGGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:1:0,1:324,143:0.0021:2,0:1:0:23:0:0.30769:0:60:2:0.0022:0:1 0/1:384:5:2,3:247,132:0.013:2,2:13.2:1:27.6:1:0.3494:2.79874:60:10:0.0134:0:1 -21 36164889 . G A 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.098;SOR=6.03032;LSEQ=ACTGGCGCGGGTCGCTGAAC;RSEQ=CTGTCAGGTCGGGTGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:1:1,0:223,358:0.0017:2,0:24:0:12:0:0.38488:0:60:0:0:0:3 0/1:486:5:3,2:193,288:0.0103:2,2:20.2:1:27.8:1:0.39704:2.23:60:10:0.0104:0:1.2 -21 36164953 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.51673;SOR=0;LSEQ=CGGAAGTGAGTAGGAGGTTG;RSEQ=GGAGGCCACAGCTCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:19,153:0.0115:2,2:10:0:31.5:1:0.21726:7.87:60:4:0.0117:0:1.5 0/0:118:0:0,0:14,104:0:2,0:22.3:1:28.7:1:1:0:60:15.857:1:0:0.3 -21 36165041 . T C 90 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=28.99651;LSEQ=GCCACCCAGGATGCTACTGC;RSEQ=GGGGAGGACGGGGACCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:0,3:0,39:0.0714:1,0:15:1:29.3:1:1:0:60:6:0.075:0:1.3 1/0:14:10:0,10:0,4:0.7143:0,0:21.1:1:27.1:1:1:0:60:9:0.6923:0:1 -21 36192484 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAGGGCTGGGGTGCCGG;RSEQ=TGGGGCTGCGGAGGGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 36193871 . T C 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0214;LSEQ=AACGTGCATTCTGAGGGCTG;RSEQ=CATCTTTCTTCTGAGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:378:376:309,67:0,1:0.9947:0,2:24.8:1:32:1:0.18037:0:60:93:0.9973:0:1.1 1/1:190:152:118,34:27,11:0.8:2,2:23.7:1:31.5:1:0.39916:1.41:60:37:0.7957:0:1.1 -21 36194056 . G A 104 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00026;SOR=16.57636;LSEQ=GGACAATTCTTTATAGAGCC;RSEQ=CGAATGCATTCCCCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:1:1,0:199,438:0.0016:2,0:1:0:28:0:0.31348:0:60:2:0.0016:0:1 0/1:473:12:5,7:157,304:0.0254:2,2:20.5:1:29.2:1:0.55501:1.38:60:24:0.0258:0:1 -21 36206932 . G A 249 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGAGGGGAGGGGATGGG;RSEQ=GGAGGGAAGGAGGGAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:311:311:91,220:0,0:1:0,2:24.4:1:30.1:1:1:0:60:22.923:1:0:1.2 1/1:248:248:83,165:0,0:1:0,2:22.9:1:29.6:1:1:0:60:30:1:0:1.1 -21 36229637 . G A 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06923;LSEQ=ACAGCCAGACCGTTACAATC;RSEQ=CATAGACATCTTTTTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:121:115:63,52:4,2:0.9504:2,2:22.8:1:29.3:1:0.69083:1.64423:60:56.5:0.9496:0:1.1 1/1:86:82:47,35:2,2:0.9535:2,2:24.9:1:29.1:1:1:1.34:60:81:0.9643:0:1.1 -21 36229647 . C CT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50992;SOR=0;LSEQ=CGTTACAATCGCATAGACAT;RSEQ=TTTTTTCCCCTCTGACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:69,59:0.0154:2,2:41.5:1:31:1:1:1.16808:60:4:0.0155:0:1.5 0/0:95:0:0,0:54,41:0:2,0:27.3:1:30.8:1:1:0:60:46.5:1:0:1 -21 36229695 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50393;SOR=0;LSEQ=AAAAGTCAGAGTCGCCACCA;RSEQ=TTGTTTTCTGAAGCTCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:90,106:0.0101:2,2:23.5:1:31:1:1:1.18:60:4:0.0104:0:1 0/0:161:0:0,0:76,85:0:2,0:26.3:1:29.9:1:1:0:60:79.5:1:0:0.5 -21 36229712 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5003;SOR=0;LSEQ=CCATTTGTTTTCTGAAGCTC;RSEQ=ATAACTTTGTTATTTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:72,88:0.0123:2,2:34:0:32:0:1:1.22:60:4:0.0123:0:1 0/0:143:0:0,0:61,82:0:2,0:24.8:1:29.4:1:1:0:60:46.667:1:0:0.4 -21 36229760 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50129;SOR=0;LSEQ=CAGGAAATGCTGGCAGTGAG;RSEQ=CAAAACCCAGCCTTCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:20,40:0.0323:2,2:31:1:28:1:1:1.98:60:4:0.0345:0:1 0/0:50:0:0,0:13,36:0:2,0:22.6:1:30.8:1:1:0:60:23.5:0.9792:0:0.1 -21 36229941 . C T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATTTCTCTAAGTTTAGT;RSEQ=ACCCTCAAAGTCGATTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:31:0:29:0:1:0:60:2:1:0:1 1/1:3:3:2,1:0,0:1:0,2:30.7:1:29.7:1:1:0:60:6:1:0:1.3 -21 36229995 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTCCCTCCCAGCCAGGC;RSEQ=CCTTGCCATAATTCAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:28:1:29:1:1:0:60:4:0.6667:0:1.5 -21 36231556 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10917;SOR=Inf;LSEQ=GTCAGCCTAATTTCCTTTTG;RSEQ=CCTCTAAAAGGATGCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:147,6:0:1,0:25.2:1:32:1:1:0:60:50:1:0:0.1 0/1:76:2:1,1:68,6:0.0263:2,2:22:1:29:1:0.17684:10.56963:60:4:0.0263:0:1 -21 36231564 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTCCTTTTGCCCTCTAA;RSEQ=AGGATGCTTCAAAAAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:174,11:0.0107:2,2:7.5:1:29.5:1:0.12455:15.18781:60:4:0.0108:0:1.5 0/0:93:0:0,0:85,8:0:2,0:24.5:1:30.2:1:1:0:60:186:1:0:0.1 -21 36232156 . C A 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTTAAGTCAGGATTTC;RSEQ=GGAAACCATAGAGTCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:1,6:0.2222:2,0:25.5:1:31.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 36233905 . C G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTAATTTCTCACTCACCCC;RSEQ=TCTCCTCCGCATACCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:30:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 36252595 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTAGTAAAAATCTCAGGC;RSEQ=TTTCTTTGAAATTCACAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:5,0:0.2857:0,2:34.5:1:32.5:1:0.28571:0:60:4:0.2857:0:2.5 0/0:2:0:0,0:2,0:0:0,0:26.5:1:31:1:1:0:60:4:1:0:0 -21 36252622 . T C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATTCACAATTCCTACG;RSEQ=TGCATGTTCCAAATCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:10,0:0.1667:0,2:39.5:1:34.5:1:0.16667:0:60:4:0.1667:0:2.5 0/0:3:0:0,0:3,0:0:0,0:24.3:1:28.7:1:1:0:60:6:1:0:0 -21 36252870 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTACCTCTTCCACTTCGACC;RSEQ=ACAAACCTGAGGTCATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:711:0:0,0:402,309:0:2,0:25.2:1:30.3:1:1:0:60:100.571:1:0:0.1 0/1:715:21:13,8:394,299:0.0294:2,2:18.1:1:30.2:1:0.82363:1.23:60:42:0.0295:0:1.1 -21 36253146 . ATAACT A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.03517;SOR=0.1967;LSEQ=GTTGCAGAGGAATAGCAATG;RSEQ=TAAGCAAAACAACAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:15:0,15:0,23:0.3947:1,1:24.5:1:31.6:1:1:0:60:30:0.3947:0.0526:0.1 0/1:18:2:0,2:0,16:0.1111:1,0:14.5:1:31.4:1:1:0:60:4:0.1176:0.0556:0 -21 36258839 . T C 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52857;SOR=0;LSEQ=GGGTTATAACTTTTCCTACT;RSEQ=TGTATCAAAGCTAAGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:3,1:9,0:0.3077:0,2:18.3:1:31.3:1:0.30769:0:60:8:0.3077:0:1 0/0:3:0:0,0:2,1:0:2,0:28.3:1:30:1:1:0:60:6:1:0:0 -21 36259498 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18877;SOR=Inf;LSEQ=TCAGCAAGCAGCTCCCGGGA;RSEQ=ACCAACATACACGTTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:10,113:0:2,0:21.6:1:31.8:1:1:0:60:60.5:1:0:0.2 0/1:95:2:1,1:15,77:0.0211:2,2:8:1:28:1:0.31297:5.00:60:4:0.0213:0:1 -21 36259539 . T G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=1.14498;LSEQ=GCCTTTATTACTGCGGGGGG;RSEQ=GGGGGGGGGCGGGGGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:34:0,34:3,10:0.7234:2,1:6.8:1:28.5:1:0.01764:0:48.9:10.333:0.7561:0:2.5 1/0:28:21:0,21:2,5:0.75:2,1:7:0:28.3:1:0.05556:0:49.7:20:0.7692:0:1.9 -21 36259549 . C G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.29928;SOR=0.42472;LSEQ=CTGCGGGGGGTGGGGGGGGG;RSEQ=GGGGGTGGTTAGGGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:35:0,35:4,0:0.8974:0,1:16.5:1:23.4:1:1e-05:0:48.9:2.5:0.8929:0:2.5 1/0:28:22:1,21:1,4:0.7857:2,1:14.6:1:22.3:1:0.34188:4.80632:52:2.667:0.8889:0:1.9 -21 36260693 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGACCACAGAGCACTTTC;RSEQ=CCCCCTGTTGTAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:21:0:32.5:1:1:1.7321:60:4:0.4:0:1.5 -21 36265299 . G A 36 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.0946;LSEQ=GGAAAATAAAAGTAATGCAA;RSEQ=TTTAAAAATTAACTTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:4:0,4:84,221:0.0128:2,0:27.3:1:18:1:0.57762:0:60:0.333:0.0036:0:5.3 0/1:214:3:2,1:65,142:0.014:2,2:7:1:21:1:0.23929:4.34:60:2:0.0102:0:1.7 -21 36265319 . C A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.27968;SOR=0;LSEQ=GTTTAAAAATTAACTTTCCC;RSEQ=CGACTTTTTTTTTTTTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:2,1:30,175:0.0144:2,2:7.7:1:22.7:1:0.06241:11.44:60:2:0.0105:0:1.3 0/0:137:0:0,0:33,104:0:2,0:25.9:1:29:1:1:0:59.8:10.417:1:0:0.3 -21 36265323 . CT C 139 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.73323;SOR=1.17688;LSEQ=AAAAATTAACTTTCCCCCGA;RSEQ=TTTTTTTTTTTGCTAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:23:3,20:20,141:0.123:2,2:30.3:1:30.9:1:1:1.06:59.1:10.5:0.1257:0.0053:0.3 0/1:127:18:3,15:20,83:0.1417:2,2:29.1:1:31.2:1:1:1.20303:60:36:0.1513:0.0157:0.3 -21 36421036 . T C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18444;SOR=0.65357;LSEQ=TCACAAACAAGACAGGGAAC;RSEQ=GGCAGGCACCGAGGCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:53:52,1:51,3:0.4953:2,1:25.5:1:30.2:1:0.61789:3.03:60:16.667:0.4808:0:1.1 0/1:82:32:31,1:48,2:0.3902:1,1:26.8:1:29.9:1:1:1.29:60:31:0.3827:0:1.3 -21 36421059 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50373;SOR=0;LSEQ=CAGGCACCGAGGCATCTCTG;RSEQ=ACCGAGGTGAAACAAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:144,25:0.0117:2,2:8:1:29.5:1:0.28173:5.66778:60:4:0.0119:0:1 0/0:139:0:0,0:117,22:0:2,0:22.3:1:31.9:1:1:0:60:68.5:1:0:0.3 -21 36421116 . T C 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00528;SOR=Inf;LSEQ=AAGCTGAGCAAAAGTAGATA;RSEQ=TACAAGACCAGCATGTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:265,162:0:2,0:27:1:30.6:1:1:0:60:105.75:1:0:0.1 0/1:386:7:6,1:233,146:0.0181:2,2:28.7:1:32:1:0.25964:3.75:60:14:0.0184:0:1.1 -21 36421263 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09616;SOR=0;LSEQ=TGATTTCTTTTACCTTCGGA;RSEQ=CGAAAACCAAGACAGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:3:2,1:53,153:0.0144:2,2:25.7:1:24.7:1:0.16997:5.71:60:2:0.0098:0:1 0/0:246:0:0,0:61,185:0:2,0:24.8:1:32:1:1:0:60:492:1:0:0.1 -21 36421280 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50297;SOR=Inf;LSEQ=GGAGCGAAAACCAAGACAGG;RSEQ=CACTGTTTCAGCCTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:22,126:0:2,0:22.6:1:30:1:1:0:60:147:1:0:0.1 0/1:179:2:1,1:32,145:0.0112:2,2:24:1:33:1:0.33557:4.48:60:4:0.0114:0:1 -21 36421331 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87023;LSEQ=CATCTCTCTTTCTTCTCCCC;RSEQ=CTGCTGGATACCTCTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:11:0,11:0,56:0.1642:1,0:24.2:1:31.5:1:1:0:60:22:0.1774:0:1.2 0/1:48:7:0,7:0,41:0.1458:1,0:31.9:1:31.6:1:1:0:60:14:0.1522:0:1.1 -21 36421412 . TA T 58 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=1.3537;LSEQ=ATATTCAAATTGTTAAAGAT;RSEQ=AAAAAAAAAAAAAAGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:0,9:0.2667:0,0:23.3:1:29.3:1:1:0:60:8:0.2857:0.0667:1 0/1:6:2:0,2:1,3:0.3333:2,0:33:1:30:1:1:0:60:4:0.3333:0:0.5 -21 36971791 . G A 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAGGCAAGTTCAATCTGATT;RSEQ=GATCCTGGATCCCATCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:8,0:8,0:0.5:0,0:33.5:1:28:1:1:0:60:16:0.5:0:1.1 1/0:2:1:1,0:1,0:0.5:0,0:6:0:30:0:1:0:60:2:0.5:0:2 -21 36971853 . G A 119 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04101;SOR=0.12689;LSEQ=CCCTGATCCTCGGTCAGAGC;RSEQ=AGCGCTTAGGTTCCCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:15,0:24,0:0.3846:1,1:20.2:1:30.7:1:1:0:60:30:0.3846:0:1.1 0/1:14:1:1,0:13,0:0.0714:1,0:33:0:27:0:1:0:60:2:0.0714:0:2 -21 36971941 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.15969;SOR=Inf;LSEQ=CCTGGGAGTCCACGACAACT;RSEQ=AAAAAACTCAAAACTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:151,6:0:1,0:22.3:1:32.2:1:1:0:60:51.333:1:0:0.1 0/1:105:2:1,1:99,4:0.019:1,2:13:1:27.5:1:0.09341:22.24888:60:4:0.0194:0:2 -21 36972001 . A AGAG 233 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0;SOR=0.42708;LSEQ=AGCTGAGGCAGCTGTTTCAG;RSEQ=GAGGAGGAGGAGGAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:181:105,76:225,120:0.3428:2,2:27:1:31.1:1:0.1077:1.35631:59.8:180:0.3509:0.0625:0.1 0/1:390:71:44,27:182,134:0.1821:2,2:28.1:1:30:1:0.59429:1.20:59.9:70:0.1823:0.0205:0.2 -21 36972392 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00092;SOR=0.27135;LSEQ=GTTTGAAATTCTGAATTTGC;RSEQ=AAGTACTATAAGAATAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:38:0,38:1,33:0.5278:1,1:24.5:1:31.8:1:0.47222:0:59.1:76:0.5352:0:1.1 0/1:52:12:0,12:1,39:0.2308:1,0:14.9:1:31.1:1:1:0:60:24:0.2308:0:1 -21 36972552 . A AG 53 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAAATTGAAAAAAAAA;RSEQ=TTGAGTCTGATGGGTCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:0,4:0.4286:0,2:33:1:34:0:0.42857:0:60:6:0.4286:0:0.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 36972695 . A C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTGCAGAAGTGTATCTG;RSEQ=TTAACTCTTGACAACTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:28:1:33.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 37555326 . C G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCACTGTAGGATGTTTT;RSEQ=TTTTGTTTAAGAGGCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:0:33.5:1:1:0:60:4:1:0:1.5 -21 37557225 . A T 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06462;SOR=Inf;LSEQ=AGGAGTTAACATCTCATTTC;RSEQ=TTAGAGCATGCCAGTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:0:1,0:29.4:1:31.1:1:1:0:60:38:1:0:0 0/1:7:2:2,0:5,0:0.2857:0,0:17:1:33:0:1:0:60:4:0.2857:0:1 -21 37557351 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50403;SOR=0;LSEQ=GTCCCGAAGGCGTTCTTCCT;RSEQ=TTCTTCTGTCTCTGACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:130,64:0.0102:2,2:25:1:27.5:1:1:2.02336:60:4:0.0103:0:1 0/0:159:0:0,0:118,41:0:2,0:22:1:29.8:1:1:0:60:52:1:0:0.1 -21 37557420 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35184;SOR=3.31414;LSEQ=GTTTGTTAAACAGATCATTT;RSEQ=TATGTGCAATAAAATATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:1:1,0:138,173:0.0032:2,0:1:0:27:0:0.44551:0:60:2:0.0033:0:1 0/1:284:3:2,1:132,149:0.0106:2,2:18.3:1:26.7:1:0.60359:2.25:60:6:0.0106:0:1 -21 37557425 . T A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25012;SOR=0;LSEQ=TTAAACAGATCATTTGTATG;RSEQ=GCAATAAAATATGTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:128,166:0.0101:2,2:17.3:1:24.7:1:0.58311:2.59:60:2:0.0069:0:1 0/0:273:0:0,0:122,151:0:2,0:25.6:1:29.4:1:1:0:60:67.25:1:0:0.3 -21 37557447 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22844;SOR=Inf;LSEQ=CAATAAAATATGTTTAAAAA;RSEQ=TAGAAAAATAACATCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:86,133:0:2,0:25:1:30:1:1:0:59.9:53.75:1:0:0.4 0/1:201:2:1,1:70,129:0.01:2,2:40.5:1:28.5:1:1:1.84:57.5:4:0.0101:0:3 -21 37557474 . T C 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=0.32466;LSEQ=AATAACATCTCCCGATACTA;RSEQ=GTTATTTTATATTTTTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:49:20,29:30,71:0.2882:2,2:21.2:1:30.2:1:0.19862:1.63:60:48:0.2892:0:1 0/1:164:19:4,15:45,62:0.1159:2,2:13.2:1:29.4:1:0.12444:2.70216:60:38:0.1159:0:1.1 -21 37557492 . A T 165 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=2.91209;LSEQ=TATGTTATTTTATATTTTTA;RSEQ=TGGTATGATTACTTTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:20:6,14:40,83:0.1399:2,2:21.9:1:30.8:1:1:1.12361:59.8:40:0.1408:0:2.2 0/1:149:48:16,32:40,61:0.3221:2,2:18.1:1:29.7:1:0.47641:1.30911:59.9:96:0.3265:0:1.9 -21 37558998 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGGCTTTGCAGGGCGCTGG;RSEQ=GGACCTGAAATACTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7:0:33:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:33:1:30.5:1:1:0:60:4:1:0:1 -21 37954473 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18502;SOR=4.36956;LSEQ=GGAAAGGATGGAGAACAGAT;RSEQ=TCAAAGGCTGACATAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:12,1:0.35:1,0:17.6:1:33:1:1:0:60:14:0.35:0:1 1/0:7:5:5,0:2,0:0.7143:0,0:34.8:1:31.4:1:1:0:60:10:0.7143:0:1 -21 37954502 . G GA 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.02761;SOR=4.84794;LSEQ=TGACATAGATTTTCTGAGCA;RSEQ=AAAAAATAAGGTAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:16:16,0:23,1:0.4:1,1:25.2:1:31:1:1:0:60:32:0.4:0.1:0.4 1/0:13:10:10,0:3,0:0.7692:0,0:19.4:1:28.6:1:1:0:60:20:0.7692:0.1538:0.6 -21 37954611 . G A 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=TGGCCCCTGCACAAGGACTC;RSEQ=TTCCATGAGGCAGCGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:180,54:0:2,0:21.8:1:29.8:1:1:0:60:116:1:0:0.9 0/1:159:9:7,2:111,39:0.0566:2,2:32.9:1:27.3:1:1:1.23:60:8:0.0506:0:2 -21 37954652 . C T 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=0.05635;LSEQ=GCCCACATGTGTACAGTTGA;RSEQ=TTCCACCGATTGTTCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:416:415:248,167:1,0:0.9976:0,2:26:1:30.2:1:1:0:60:68.167:1:0:1.3 1/1:365:350:213,137:8,6:0.9589:2,2:25.6:1:29.8:1:0.78629:1.17:60:86.5:0.9584:0:1.4 -21 37954722 . A T 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.11979;LSEQ=TGACACAAGTTCTATCTCCA;RSEQ=CAAACCAGCTGTCAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:202:80,122:145,178:0.384:2,2:25.5:1:29.9:1:0.24015:1.24176:60:66.333:0.3872:0:1.5 1/0:504:287:139,148:95,122:0.5694:2,2:26.9:1:28.8:1:0.32166:1.21:60:56.4:0.5663:0:1.5 -21 37954734 . T A 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06193;SOR=0;LSEQ=TATCTCCAACAAACCAGCTG;RSEQ=CAGGAAATGGTCTCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:5:3,2:188,274:0.0107:2,2:32.4:1:27.6:1:0.40344:2.18:60:10:0.011:0:1.6 0/0:455:0:0,0:209,246:0:2,0:26.5:1:28.8:1:1:0:60:64:1:0:0.9 -21 37954773 . C A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25144;SOR=0;LSEQ=CTCCAAGAACAGAAACTTCT;RSEQ=TTGACAGTGCATTCTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:85,208:0.0101:2,2:13:1:21:1:0.20751:4.86:60:2:0.0069:0:2 0/0:262:0:0,0:86,176:0:2,0:21.8:1:31.5:1:1:0:60:130:1:0:0.5 -21 37954982 . T C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52797;SOR=0;LSEQ=ATCATAAAAAACCTGCCCCA;RSEQ=TCCCCCACAACCCTTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:27:1:31.3:1:1:0:60:6:0.3:0:1.7 0/0:3:0:0,0:1,2:0:2,0:18.7:1:31.3:1:1:0:60:6:1:0:0.3 -21 37954987 . C A 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52273;SOR=0.28305;LSEQ=AAAAAACCTGCCCCATTCCC;RSEQ=CACAACCCTTTCCCAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:0.6667:0,0:35.7:1:27.8:1:1:0:60:5:0.625:0:1.3 0/1:3:1:0,1:1,1:0.3333:2,0:5:0:28:0:1:0:60:2:0.3333:0:1 -21 37955122 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTGGAGACAGAGTGGC;RSEQ=TCCTGGGCCCCGAATAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:45.5:1:33:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 37955134 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGGCTTCCTGGGCCCC;RSEQ=AATAACCTTTGGGGGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:30:1:29.7:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 37955163 . C T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGGGGCCTGCCTGATGAC;RSEQ=CTCCACAGCAACCATGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20.3:1:30.3:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 37955178 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGACCCTCCACAGCAACCA;RSEQ=GTGGATTCTGGTACTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24:1:30.5:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 39625613 . A AT 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.56855;SOR=0;LSEQ=AGGATTGGAAACATTATAGC;RSEQ=TTTTTTTTTCTTTTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:4:4,0:61,0:0.0615:1,0:35:1:31:1:1:0:60:8:0.0635:0:1.5 0/0:20:0:0,0:20,0:0:1,0:19.6:1:29.5:1:1:0:60:40:1:0:0.2 -21 39625779 . C A 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.60773;LSEQ=GACACAACTAAGAGTCTTTC;RSEQ=GTTAACTGTGGAGGTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:705:514:268,246:90,98:0.7291:2,2:26.7:1:30.2:1:0.34849:1.19:60:56.111:0.7298:0:1.2 1/0:606:376:195,181:125,105:0.6205:2,2:25:1:29.7:1:0.55848:1.10482:60:33.182:0.6166:0:1.1 -21 39625891 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19529;SOR=Inf;LSEQ=GGTCAGTAAAATTAACCATG;RSEQ=TCAATTATGAAATGATTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:21,187:0:2,0:23.8:1:30:1:1:0:60:68.333:0.9951:0:0.1 0/1:166:2:1,1:21,143:0.012:2,2:26:1:31:1:0.24819:6.68:60:4:0.0122:0:1 -21 39627712 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGCACTTGGGGTGAATTGC;RSEQ=GAGCCCAGTACTCTGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:31:1:1:0:60:4:1:0:1 -21 39739136 . A G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGCGATGTACTAGGTTAG;RSEQ=CAGAAGTCACAGGCCGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18:1:30.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 39739478 . A G 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00332;SOR=0.56192;LSEQ=GAATAAGTGATGCAAAGAGA;RSEQ=GGCCACGCTGCCTTCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:122:94,28:154,34:0.3935:2,2:25.8:1:31.8:1:0.31157:1.34783:60:121:0.3916:0:1 0/1:206:55:40,15:104,47:0.267:2,2:22.8:1:31:1:0.73154:1.20:60:54:0.2634:0:1 -21 39739665 . T A 239 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08345;LSEQ=AGACAGAATTCTGCACAGAC;RSEQ=TTCATCAACAATAACTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:240:233:45,188:1,6:0.9708:2,2:23.1:1:30.5:1:1:1.43:60:45.6:0.9702:0:1.1 1/0:173:127:29,98:9,37:0.7341:2,2:19.9:1:29.4:1:0.83553:1.22:60:126:0.7368:0:1.1 -21 39740158 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCCCTTGCTTTTCCTC;RSEQ=TTTTTTTGTTTGTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:26.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 39755227 . T C 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2786;SOR=0;LSEQ=CAGCCCCAGTAAAGCTTTTT;RSEQ=CATTCCTCTTGAGGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:2,1:231,23:0.0117:2,2:17.7:1:26.3:1:0.25571:4.96549:60:2:0.0079:0:1 0/0:171:0:0,0:151,20:0:2,0:21.2:1:30.1:1:1:0:60:170:1:0:0.1 -21 39755976 . T A 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13002;SOR=0;LSEQ=TCACCAGGCCTGTCCGTCCA;RSEQ=CCCTCAGCTGCAGGGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:0,7:0,11:0.3889:0,0:33.1:1:29.4:1:1:0:60:14:0.4118:0:1 0/0:6:0:0,0:1,5:0:2,0:33.8:1:28.2:1:1:0:60:5:1:0:0 -21 39762883 . T C 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.33797;LSEQ=TAACCACTGCCAAAAAGTAA;RSEQ=TTTGTAAGAAGAAAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:121:87,34:282,149:0.2192:2,2:25.6:1:32.2:1:0.19146:1.35:60:242:0.2208:0:1.1 0/1:462:40:22,18:262,160:0.0866:2,2:25.3:1:30.9:1:0.39858:1.33887:60:80:0.0879:0:1.1 -21 39763354 . C A 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14682;SOR=0.32767;LSEQ=AAAGAAGCAGCCTGTGTGCA;RSEQ=GTAGAATTTTTTTCCCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:21:20,1:8,0:0.7241:0,1:20.1:1:30.6:1:1:0:60:42:0.7241:0:1.1 0/1:11:5:4,1:6,0:0.4545:0,2:19.6:1:31.6:1:0.45455:0:60:10:0.5:0:1 -21 39764016 . A T 82 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATGGCCAAGATTCAGGAAA;RSEQ=CACCGATTATTTAATGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:3,4:6,1:0.5:2,2:30:1:29.3:1:0.26573:6.78852:60:14:0.5385:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 39764211 . T A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00028;SOR=0.44378;LSEQ=ACATGTTGCAAAATCACAGA;RSEQ=TAACCACAGAAATTATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:194:119:108,11:65,10:0.6134:2,2:24.5:1:30.2:1:0.47723:1.51:60:38.667:0.6073:0:1.1 0/1:143:59:52,7:74,10:0.4126:2,2:23.3:1:30.2:1:1:1.00:60:118:0.4126:0:1.1 -21 39764222 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17934;SOR=Inf;LSEQ=AATCACAGATTAACCACAGA;RSEQ=ATTATTATATACTCCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:198,45:0:2,0:23.6:1:30:1:1:0:60:80:1:0:0.5 0/1:179:2:1,1:137,40:0.0112:2,2:19:1:27.5:1:0.40663:3.39522:60:4:0.0113:0:1.5 -21 39764366 . T A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05989;SOR=Inf;LSEQ=TGGGGGGCTCATATGGTAAA;RSEQ=CTGTAAAGACAAATAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:129,276:0:2,0:24.6:1:30.3:1:1:0:60:404:1:0:0.2 0/1:398:4:3,1:145,249:0.0101:2,2:7.3:1:23.8:1:0.14715:5.13:60:3:0.0077:0:1 -21 39764401 . C G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=3e-04;SOR=Inf;LSEQ=AAATTGACTAAAAGATCAAT;RSEQ=ATGTAATTTTTATAAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:53,183:0:2,0:23.2:1:31.8:1:1:0:60:117:0.9957:0:0.3 0/1:223:11:4,7:54,158:0.0493:2,2:23.7:1:31.5:1:0.48232:1.67:60:22:0.0505:0:1.5 -21 39764437 . T C 187 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01631;SOR=0.48678;LSEQ=GAGATGCTTTGGTTTTTTAT;RSEQ=TGATTTTGTATTTATTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:55:6,49:9,42:0.5189:2,2:21.8:1:32.4:1:0.40667:1.74076:60:110:0.5189:0:1.1 0/1:99:34:1,33:8,57:0.3434:2,1:26.6:1:31:1:0.15872:4.57777:60:16:0.3299:0:1.2 -21 39764588 . G A 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=TTGTCTGAAAACTTCCATTG;RSEQ=CAGATTCTCCCAGAGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:12.8:1:27.4:1:1:0:60:10:0.7143:0:1.2 0/0:1:0:0,0:0,1:0:0,0:20:0:34:0:1:0:60:2:1:0:0 -21 39772561 . G A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09035;SOR=6.642;LSEQ=TATTTGGGAAAATAAAAGCT;RSEQ=CACCCCCTGCAGACAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:1:1,0:193,439:0.0016:2,0:1:0:24:0:0.30648:0:60:2:0.0016:0:1 0/1:480:5:4,1:183,292:0.0104:2,2:7.4:1:25.6:1:0.07819:6.36:60:10:0.0105:0:1 -21 39774197 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGAAGACTGTAATCCGG;RSEQ=AAATGTGAGCTAAGTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:16,0:0.1111:1,2:32.5:1:31:0:0.11111:0:60:4:0.1111:0:1 0/0:3:0:0,0:3,0:0:0,0:14.7:1:31.7:1:1:0:60:6:1:0:0 -21 39774348 . C G 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76118;SOR=1.12269;LSEQ=GTGGTACATTCCTAAGTATC;RSEQ=GAAAGTATTCTGAATCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:40:39,1:65,1:0.3774:1,1:22:1:30.3:1:1:1.65824:60:80:0.3774:0:1.2 0/1:79:32:31,1:46,0:0.4051:1,1:22.1:1:30.2:1:0.41026:0:60:64:0.4103:0:1.3 -21 39774592 . G GA 144 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.10294;SOR=1.6846;LSEQ=ACAAAAAGCGACATCAAAAT;RSEQ=AAAAAAAAAAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:19:3,16:86,253:0.0519:2,2:28.8:1:31:1:0.42584:1.81034:59.7:38:0.0581:0:0.7 0/1:355:30:9,21:92,223:0.0845:2,2:33.4:1:29.5:1:1:1.04:59:60:0.0938:0:0.5 -21 39774601 . AAG A 69 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.06173;SOR=Inf;LSEQ=GACATCAAAATGAAAAAAAA;RSEQ=AGAGAGAGAGAAAGAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:51,252:0:2,0:20.6:1:30.7:1:1:0:59.3:29.3:1:0:0.7 0/1:317:5:1,4:68,244:0.0158:2,2:21.6:1:29.9:1:1:1.11438:54:10:0.016:0.0032:1.2 -21 39774632 . T TA 66 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29952;SOR=0.39474;LSEQ=AGAAAGAGAATTACCTTTCT;RSEQ=ACAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:6:0,6:6,118:0.0438:1,0:31.3:1:25.7:1:1:0:50.2:5:0.045:0.0073:2.3 0/1:113:2:0,2:5,104:0.0177:1,0:36:1:17.5:1:1:0:60:1:0.0125:0:1.5 -21 39774634 . C AAA 45 q23;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.3816;SOR=0.29813;LSEQ=GAAAGAGAATTACCTTTCTT;RSEQ=AAAAAAAAAAAAAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:4:0,4:6,118:0.0292:1,0:31.3:1:22.8:1:1:0:56:8:0.036:0:4.3 0/0:113:1:0,1:5,104:0.0088:1,0:33:0:21.5:0:1:0:56:2:0.0125:0:7 -21 39774658 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08677;SOR=Inf;LSEQ=AAAAAAAAAAAAAAAAGAAA;RSEQ=AAAAAGAAAGAAAGAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:1,72:0:1,0:21.8:1:30.9:1:1:0:54.6:146:1:0:1.9 0/1:59:3:1,2:0,56:0.0508:1,2:12.3:1:24:1:0.05085:0:48.3:2:0.0351:0:3.3 -21 39774660 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20405;SOR=Inf;LSEQ=AAAAAAAAAAAAAAGAAAGA;RSEQ=AAAGAAAGAAAGAAAACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:1,70:0:1,0:21.9:1:30.2:1:1:0:54.6:142:1:0:1.8 0/1:59:2:0,2:1,56:0.0339:1,0:7.5:1:33:0:1:0:42.5:4:0.0339:0:3.5 -21 39775373 . A G 232 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTTGAACCCTCTGAAGCTC;RSEQ=GGTCATAAGAACCATAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:232:232:200,32:0,0:1:0,2:21.5:1:29.6:1:1:0:60:37.667:1:0:1.1 1/0:145:106:92,14:33,6:0.731:2,2:22.1:1:30.1:1:0.78754:1.19:60:212:0.731:0:1.1 -21 39775417 . G T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09392;SOR=6.30141;LSEQ=CCATCTATCCTTGGAGGAAG;RSEQ=GGGAGCTTACTCTCTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:1:1,0:367,133:0.002:2,0:13:0:31:0:1:0:60:2:0.002:0:1 0/1:401:5:1,4:267,129:0.0125:2,2:9.4:1:26.2:1:0.04343:8.2345:60:10:0.0127:0:1.2 -21 39775468 . G A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGAGAGAAGGATGTCGGC;RSEQ=TTGTAGCTGGGGGTGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:885:0:0,0:513,371:0:2,0:24.2:1:30.2:1:1:0:60:39.182:1:0:0.2 0/1:882:34:20,14:460,388:0.0385:2,2:26.6:1:30:1:0.72601:1.20:60:68:0.0389:0:1.3 -21 39775626 . T A 57 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00878;SOR=Inf;LSEQ=ATGGTCTGTACTCCATAGCG;RSEQ=AGGATCTGAAAGGGGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:146,310:0:2,0:24.2:1:28.7:1:1:0:60:227:1:0:0.1 0/1:382:6:5,1:130,246:0.0157:2,2:10:1:22.2:1:0.02245:9.41:60:2:0.0106:0:1.7 -21 39794880 . T G 69 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACAATAATCTCCAAGAAG;RSEQ=GGCAATTCCTCCCTAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:24:1:29.8:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 39795170 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06198;SOR=Inf;LSEQ=TGCTGTCGATCCGTGAACAT;RSEQ=TCCTCATGCATAGACCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:92,0:0:1,0:26.1:1:32.7:1:1:0:60:91:1:0:0.5 0/1:31:2:2,0:28,1:0.0645:1,0:22.5:1:31.5:1:1:0:60:4:0.069:0:1 -21 39795202 . T G 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45097;SOR=0.78102;LSEQ=AGACCTCTGCCAGCTCCCAT;RSEQ=TACAAGCCCTGCTCTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:57:55,2:87,0:0.3958:1,1:23.9:1:32.4:1:0.15501:0:60:114:0.3986:0:1.1 0/1:68:23:22,1:44,1:0.3382:1,1:29:1:32:1:1:1.9782:60:22:0.3284:0:1.2 -21 39795217 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATTTACAAGCCCTGCTC;RSEQ=GGACAAAGGAGATGTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:164,3:0.0118:1,2:27:1:30:1:0.04691:47.48808:60:4:0.012:0:2 0/0:84:0:0,0:82,2:0:1,0:25.1:1:31.2:1:1:0:60:41:1:0:0.4 -21 39795279 . A T 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCTCCCTGAGGCTCAGCCT;RSEQ=GCCTTGGGGAAGTTGCGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:35:27,8:361,93:0.0716:2,2:21.6:1:30.9:1:0.67112:1.14977:60:70:0.0725:0:1.1 0/0:359:0:0,0:275,84:0:2,0:22.5:1:28.5:1:1:0:60:118.667:1:0:0.1 -21 39817064 . TTT C 48 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=17;MSI=19.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TTTCTTTCTTTCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTGTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,0:0.6:0,0:18:1:30.3:1:1:0:60:6:0.75:0.4:0.7 0/0:2:0:0,0:1,0:0:0,0:39:0:33:0:1:0:60:2:0.5:0:2 -21 39817598 . T A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10671;SOR=Inf;LSEQ=CTCCAACAGACAGTCATGTT;RSEQ=CAAAAAGTTGTTGATTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:56,251:0:2,0:23.7:1:29.7:1:1:0:60:42.857:1:0:0.1 0/1:278:3:2,1:66,209:0.0108:2,2:12.3:1:25.7:1:0.1492:6.28:60:6:0.0109:0:1 -21 39818701 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CCAGTCCAAACTTGTCATCT;RSEQ=CAAATGAGAAATCTGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:18:1:31:1:1:0:60:8:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:24:1:28:1:1:0:60:4:1:0:1 -21 39870310 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=4.82778;LSEQ=AATAGTGCTGGCCATAATGC;RSEQ=ATCAAGTTTATTGATCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:734:527:213,314:83,122:0.718:2,2:23.8:1:30.1:1:1:1.00292:60:57.556:0.7225:0:1.1 1/1:612:566:244,322:21,25:0.9248:2,2:24:1:29.5:1:0.75878:1.10834:60:55.6:0.9236:0:1.1 -21 39947487 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17105;SOR=Inf;LSEQ=TTTCTTAGCTCCTGGGCTGT;RSEQ=TTGACTGACCCCTAATTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:221,25:0:2,0:23.8:1:32.2:1:1:0:60:60.5:1:0:0.1 0/1:174:2:1,1:143,29:0.0115:2,2:7:1:26:1:0.31593:4.86516:60:4:0.0118:0:2.5 -21 39947697 . A G 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=AGACAAAAGGAACAACATAC;RSEQ=TAATAATAAACAACTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:77,295:0:2,0:22.2:1:30.7:1:1:0:60:123:1:0:0.1 0/1:250:25:7,18:64,161:0.1:2,2:23.3:1:30.1:1:1:1.02209:60:50:0.102:0:1 -21 39947747 . C A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.94012;LSEQ=TATGTTCTAGCAGGACAGGA;RSEQ=ACAATTCACCAATGGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:7:1,6:2,123:0.053:1,2:30.7:1:29.7:1:0.1519:9.80:60:6:0.0462:0:1 0/1:80:4:0,4:3,73:0.05:1,0:33.5:1:27.3:1:1:0:60:3:0.038:0:1 -21 41326462 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49893;SOR=Inf;LSEQ=CACGTAACCTTCACAAAGAC;RSEQ=AGCTGATTGACTAATGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:149,43:0:2,0:22.8:1:31.1:1:1:0:60:63:1:0:0.1 0/1:200:2:1,1:144,54:0.01:2,2:22.5:1:26.5:1:0.47538:2.65147:60:4:0.0101:0:1 -21 41326577 . G A 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.24729;LSEQ=AAGACTATCTACGGTAGGTC;RSEQ=TTAAGCAGCCAATGATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:569:484:235,249:37,48:0.8506:2,2:24.7:1:30.5:1:0.41189:1.22:60:241:0.8531:0:1.3 1/0:539:315:150,165:102,122:0.5844:2,2:25.4:1:29.8:1:0.66186:1.09:60:630:0.5877:0:1.2 -21 41326640 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11648;SOR=Inf;LSEQ=ATGTGCCACTTTGTTTTGCA;RSEQ=GATGCAGCAGGCCGACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:98,208:0:2,0:23.5:1:31.4:1:1:0:60:152:0.9967:0:1.1 0/1:295:3:1,2:103,189:0.0102:2,2:30:1:31:1:1:1.08964:60:6:0.0103:0:1.3 -21 41326645 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.10827;SOR=Inf;LSEQ=CCACTTTGTTTTGCAGGATG;RSEQ=AGCAGGCCGACAGTCATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:88,203:0:2,0:22.4:1:32:1:1:0:60:71.75:1:0:1.2 0/1:266:3:1,2:87,174:0.0113:2,2:7.3:1:27.3:1:1:1:60:6:0.0113:0:2 -21 41326658 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05111;LSEQ=CAGGATGCAGCAGGCCGACA;RSEQ=TCATAGGCGGCCTGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:216:186:47,139:5,25:0.8611:2,2:23.2:1:30.1:1:0.36506:1.69:60:30:0.8612:0:1.4 0/1:201:48:12,36:41,112:0.2388:2,2:21.9:1:30:1:0.85342:1.09773:60:96:0.24:0:1.4 -21 41326917 . T A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGAGGAAGGGCCAGAAAC;RSEQ=CATGGAAAGCTCTAGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21:1:31:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:43:0:30:0:1:0:60:2:1:0:1 -21 41918860 . G T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22745;SOR=Inf;LSEQ=GCTGGGGTGGGAGCCTGGAG;RSEQ=ATCCTTTCTAAAGGCTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:129,24:0:2,0:24.7:1:31.1:1:1:0:60:152:1:0:0.1 0/1:140:2:1,1:102,36:0.0143:2,2:14:0:27:1:0.46012:2.80845:60:4:0.0146:0:1.5 -21 41918958 . A G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15536;LSEQ=AACCCCATCCAAATCCCCTC;RSEQ=TAACATCAAGCAGAGCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:466:256:135,121:103,107:0.5494:2,2:26.2:1:30.8:1:0.45679:1.16:60:255:0.5519:0:1.1 0/1:453:72:32,40:197,184:0.1589:2,2:26.4:1:29.8:1:0.30405:1.33745:60:35:0.1563:0:1.3 -21 41919040 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08015;SOR=Inf;LSEQ=CCTCACCGTCCTCTCTGTCC;RSEQ=CAACCCTGTCTATCCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:54,165:0:2,0:23.7:1:30.9:1:1:0:60:53.75:1:0:0.3 0/1:167:3:2,1:46,118:0.018:2,2:25:1:26.7:1:0.19876:5.07:60:6:0.0185:0:1 -21 41936517 . C G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGCCTGGATCCTGCCAAC;RSEQ=CTGCCTCCTACAAAAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:16,19:0,0:1:0,2:27.5:1:31.2:1:1:0:60:70:1:0:1.1 1/1:7:7:4,3:0,0:1:0,2:18.1:1:29.7:1:1:0:60:14:1:0:1 -21 41936617 . T C 61 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTAAATGGAATGAGCACG;RSEQ=GAAACGGGAACCTGCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:22.8:1:30.8:1:1:0:60:8:1:0:1 1/1:2:2:0,2:0,0:1:0,0:17:1:30.5:1:1:0:60:4:1:0:1 -21 42461865 . A AG 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACTCCAGTGTCAGATGCT;RSEQ=TTCAGTGCCCTGATAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:30.3:1:33.7:1:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42462100 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32988;LSEQ=CATTTGTGACCTGGAGGGTC;RSEQ=CTTAATGCTTTTGGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:195:127,68:31,21:0.7895:2,2:26.3:1:30.5:1:0.51638:1.26:60:390:0.7992:0:1.2 1/0:248:137:87,50:70,40:0.5524:2,2:24.9:1:29.8:1:1:1.00572:60:136:0.5528:0:1.3 -21 42462148 . G T 52 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06169;SOR=Inf;LSEQ=CCAATGTTTGGAAAACCCTT;RSEQ=TTCTTTCATCATCATGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:164,172:0:2,0:26.3:1:31.6:1:1:0:60:83:0.997:0:1 0/1:346:5:1,4:164,177:0.0145:2,2:29.2:1:22.4:1:0.37406:3.69391:60:1.5:0.0088:0:2.2 -21 42462188 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29794;LSEQ=TGTCACAACTAGTCATGGAC;RSEQ=TGTGTCTACCCCATCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:305:234:87,147:26,45:0.7672:2,2:25.9:1:31.1:1:1:1.02:60:233:0.769:0:1.8 0/1:295:146:55,91:70,78:0.4949:2,2:22.5:1:30.3:1:0.10013:1.48281:60:145:0.4966:0:1.9 -21 42462244 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.22733;LSEQ=ACAGCCTCAGTGTGGAGTTC;RSEQ=CAGAGAGCTCTCCCTATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:122:30,92:9,24:0.7871:2,2:24.4:1:30.3:1:0.82177:1.14893:60:121:0.7857:0:2.6 0/1:134:61:17,44:22,51:0.4552:2,2:22.5:1:29.7:1:0.8495:1.11558:60:29.5:0.4538:0:2.6 -21 42462249 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50345;SOR=0;LSEQ=CTCAGTGTGGAGTTCCCAGA;RSEQ=AGCTCTCCCTATAAGACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:30,112:0.0139:2,2:19:1:28:1:0.38539:3.69:60:4:0.0139:0:4 0/0:117:0:0,0:32,85:0:2,0:23.2:1:31:1:1:0:60:57.5:1:0:1.4 -21 42462253 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.2167;LSEQ=GTGTGGAGTTCCCAGAGAGC;RSEQ=CTCCCTATAAGACTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:133:106:18,88:7,20:0.797:2,2:24.1:1:31:1:0.28284:1.70345:60:52:0.7939:0:2.6 0/1:107:49:13,36:14,43:0.4579:2,2:20.8:1:31:1:0.82705:1.11:60:98:0.4667:0:2.8 -21 42462562 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTCAAACCTGACTTCGTA;RSEQ=CCATTAAGTATCTCAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42837800 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATCTCAATGGGGCAGCC;RSEQ=CCACCCCTCTCCTCCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:0.1053:1,0:13.5:1:30.5:1:1:0:60:4:0.1053:0:1.5 0/0:3:0:0,0:3,0:0:0,0:19.3:1:31.7:1:1:0:60:6:1:0:0.7 -21 42837848 . C T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=CAGTGCCCACAACCAGCCGG;RSEQ=CATCACCCCTTGCGGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:41,0:0:1,0:22.7:1:31.1:1:1:0:60:12.667:1:0:0.1 0/1:28:8:8,0:19,1:0.2857:1,0:27.9:1:30.3:1:1:0:60:16:0.2857:0:1 -21 42838093 . G GA 152 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.15925;SOR=1.45441;LSEQ=CCGTCTGCCTGTTCAAATAG;RSEQ=AAAAAAAAAAGTGTGTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:27:11,16:196,419:0.0417:2,2:28.5:1:29.9:1:0.40005:1.47:59.3:54:0.0432:0.0046:0.3 0/1:621:37:15,22:210,371:0.0596:2,2:28.1:1:29.2:1:0.60037:1.20:59.5:36:0.0597:0.0064:0.5 -21 42838138 . A T 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAGACAAACAAAGGTGGAA;RSEQ=ATAATTTTTTCCTCTAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:26,227:0:2,0:21.6:1:30.1:1:1:0:60:125.5:1:0:0.1 0/1:253:31:8,23:37,185:0.1225:2,2:19.5:1:27.8:1:0.21523:1.73:60:14.5:0.1169:0:1.4 -21 42838198 . G A 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=CCAAATAAGCAAGCTTAATA;RSEQ=CACAAAGGGATCATTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:1,74:0:1,0:21.8:1:32.4:1:1:0:60:74:1:0:0 0/1:52:9:0,9:1,42:0.1731:1,0:26:1:29.9:1:1:0:60:18:0.18:0:1.8 -21 42839299 . C G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCACTCCAGCCTGGGCGACA;RSEQ=AGTGAGACTCCATCTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:16.7:1:32:1:1:0:43.3:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42839603 . G T 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.03904;SOR=Inf;LSEQ=CAGAACCACGCCTAACAGAT;RSEQ=TCTGGCTTTGGCTCGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:335,137:0:2,0:23.3:1:31.6:1:1:0:60:66.429:1:0:0.1 0/1:380:4:2,2:239,137:0.0105:2,2:10.8:1:26.3:1:0.62551:1.74175:60:8:0.0106:0:1 -21 42839859 . T A 43 v4;q23;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07404;SOR=6.52401;LSEQ=AGCAGAAAATCAAGTCACAA;RSEQ=CTGCCGCACACCACTGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:1,0:49,231:0.0036:2,0:1:0:25:0:0.17794:0:60:2:0.0036:0:1 0/1:175:4:4,0:28,143:0.0229:2,0:11:1:21.8:1:0.00095:0:60:3:0.0176:0:1.3 -21 42840580 . T C 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02128;SOR=0;LSEQ=CAGATGGTCACAGCCCTATT;RSEQ=TCCAGCCCTGCCCCGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:73:0,73:0,0:1:0,1:21.5:1:33:1:1:0:60:146:1:0:1.8 1/1:29:26:1,25:1,2:0.8966:2,1:23.8:1:32.2:1:0.19951:10.40842:60:52:0.8966:0:1.8 -21 42840595 . G C 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27632;SOR=0;LSEQ=CTATTTTCCAGCCCTGCCCC;RSEQ=GTCAGCTCATCCCAGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:55:0,55:0,0:1:0,1:18.4:1:30.1:1:1:0:60:110:1:0:2 1/1:21:20:1,19:0,1:0.9524:0,1:21.8:1:30.5:1:1:0:60:40:0.9524:0:2.1 -21 42842203 . T C 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCACCATGGGTCCAGGA;RSEQ=GCCCGTCCTCACCAAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:20:1:33.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42842591 . C T 150 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.06703;LSEQ=TCACCTTTCTCCTCGGTGGC;RSEQ=CCCCACCCGGAAATCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:990:33:19,14:530,424:0.0333:2,2:25.9:1:29.9:1:0.86033:1.09:60:32:0.0331:0:1.2 0/0:868:2:1,1:475,391:0.0023:2,2:22:1:28:1:1:1.21456:60:4:0.0023:0:1 -21 42842713 . C CCTAAGGCCTCGGG 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07166;LSEQ=AGTGAGCCAGGCGGGTATCA;RSEQ=CTATGTCTCCACCTGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:694:645:216,429:20,26:0.9294:2,2:22.6:1:30.4:1:0.19768:1.52684:59.8:214:0.9277:0.4568:0.1 0/1:495:240:58,182:110,141:0.4848:2,2:32.1:1:30:1:0:2.44349:60:239:0.4908:0.0444:0.1 -21 42842771 . C G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=0.29942;LSEQ=GGGCCTGGCACCCTGGCCAC;RSEQ=CTGCCCAGAGGACCCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:74:1,73:3,97:0.4253:1,1:25.8:1:31.4:1:0.63757:2.24818:59.9:17.5:0.4167:0:1.5 0/1:83:15:0,15:0,68:0.1807:1,1:24.3:1:33.1:1:1:0:60:30:0.1899:0:1.2 -21 42842834 . T C 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14851;SOR=0;LSEQ=CTTTCTCCCCCTGCCAGACC;RSEQ=CTCCTTCTGGCAGGCAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:86:86:0,86:0,0:1:0,1:25.6:1:30.8:1:1:0:60:27.667:1:0:1.9 1/1:15:14:0,14:0,1:0.9333:0,1:16.4:1:31.9:1:1:0:60:28:0.9333:0:1.5 -21 42842854 . C A 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07463;SOR=0;LSEQ=TCTCCTTCTGGCAGGCAAGA;RSEQ=GTTATGCTACTTATAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:62:1,61:0,0:1:0,1:27:1:31.5:1:1:0:60:61:1:0:2 1/1:5:4:0,4:0,1:0.8:0,0:13.5:1:32.5:1:1:0:60:8:0.8:0:2 -21 42842949 . T C 85 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTACATATCTCCAGGTGA;RSEQ=CAAGACGGGAAAGACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:1:0,2:23.1:1:28.6:1:1:0:60:7:1:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42842988 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=CAGGAGGCAACAGCCAAAAA;RSEQ=CCGATGGAGTCAATGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:1,4:0.1667:2,0:37:0:25:0:1:0:60:2:0.1667:0:1 1/1:2:2:1,1:0,0:1:0,2:18:1:31.5:1:1:0:60:4:1:0:1 -21 42843565 . G A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.27765;LSEQ=TGCTGCCTCCCCCAAAATGC;RSEQ=GCAGGTGCTCTTAGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:14:14,0:15,0:0.4828:1,1:25.7:1:30.9:1:1:0:60:28:0.4828:0:1.1 1/0:11:6:5,1:5,0:0.5455:0,2:16.2:1:29.8:1:1:0:60:12:0.5455:0:1.3 -21 42843960 . A G 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=GCCATAAACACAGAGCTCTC;RSEQ=GTGGATGAACTTCCAACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:188:188:19,169:0,0:1:0,2:23:1:31:1:1:0:60:61.667:1:0:1.5 1/1:164:153:23,130:3,7:0.9329:2,2:23.3:1:29.9:1:0.20009:2.40564:60:75.5:0.9321:0:1.7 -21 42843962 . T A 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=2.2311;LSEQ=CATAAACACAGAGCTCTCAG;RSEQ=GGATGAACTTCCAACGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:74:4,70:12,88:0.4253:2,2:25.6:1:31.5:1:0.1862:2.37533:60:73:0.4269:0:2.2 1/0:154:96:13,83:9,49:0.6234:2,2:25.2:1:30.6:1:0.81341:1.17145:60:95:0.6209:0:2 -21 42844052 . T G 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0678;SOR=0;LSEQ=CAGGGAGATAGTGGAAGAGG;RSEQ=GCTCGGTCTCCCCTTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:1,43:0,0:1:0,1:24.4:1:31.2:1:1:0:60:43:1:0:1.8 1/1:16:14:0,14:0,2:0.875:0,1:22.3:1:29.7:1:1:0:60:13:0.8667:0:1.5 -21 42844057 . G A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18029;SOR=0.27258;LSEQ=AGATAGTGGAAGAGGTGCTC;RSEQ=GTCTCCCCTTCTCCCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:1,14:1,23:0.3846:1,1:32.9:1:32.1:1:1:1.62:60:30:0.3947:0:2.1 0/1:14:2:0,2:0,12:0.1429:0,0:23:1:31.5:1:1:0:60:4:0.1429:0:2 -21 42844510 . A G 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGGGAGCACCCTTGGGTAAC;RSEQ=GCCCTTGCTTCCTTGACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:28.5:1:1:0:60:4:1:0:1 -21 42845167 . G C 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00271;SOR=Inf;LSEQ=AACACAAGGATGCCGGGGCT;RSEQ=CAAGGGTTGAGACCTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:113,7:0:2,0:22.4:1:31.7:1:1:0:60:19:1:0:0.1 0/1:74:6:6,0:65,3:0.0811:1,0:30.2:1:30.2:1:1:0:60:12:0.0811:0:1 -21 42845216 . T C 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13905;SOR=0;LSEQ=GGGTGGCTGTAGGCCAGCCC;RSEQ=GAGCCCCCACCCGGCCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:4:2,2:214,56:0.0146:2,2:8:1:30.8:1:0.19793:3.79687:60:8:0.0148:0:1 0/0:205:0:0,0:157,48:0:2,0:26:0:12:0:1:0:60:0:0:0:3 -21 42845232 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08646;SOR=Inf;LSEQ=GCCCTGAGCCCCCACCCGGC;RSEQ=CGCGCCGCCCCTGGCATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:251,106:0:2,0:23.7:1:30.6:1:1:0:60:50:1:0:0.1 0/1:284:3:2,1:197,84:0.0106:2,2:18.3:1:29.3:1:1:1.17192:60:6:0.0107:0:1 -21 42845241 . C T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17527;SOR=5.12764;LSEQ=CCCCACCCGGCCCGCGCCGC;RSEQ=CCTGGCATACTTTTCCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:1:0,1:309,143:0.0022:2,0:1:0:29:0:0.31788:0:60:2:0.0023:0:1 0/1:356:4:1,3:233,119:0.0112:2,2:16.5:1:28:1:0.11834:5.84357:60:8:0.0114:0:1.3 -21 42845374 . G A 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.83248;LSEQ=GCCCCCGGGAGCGCGCTCTC;RSEQ=CCGCCCACAATCCTGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:24:9,15:280,337:0.0374:2,2:26.8:1:28.8:1:0.53306:1.38408:60:48:0.038:0:1.1 0/1:550:87:40,47:212,250:0.1582:2,2:23.5:1:29.6:1:1:1.00:60:174:0.1629:0:1.3 -21 42845377 . G A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05048;SOR=7.37115;LSEQ=CCCGGGAGCGCGCTCTCGCC;RSEQ=CCCACAATCCTGCTCTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:1:1,0:291,350:0.0016:2,0:1:0:26:0:0.45483:0:60:2:0.0016:0:1 0/1:527:6:4,2:241,280:0.0114:2,2:12.7:1:25.3:1:0.42374:2.32:60:12:0.0116:0:1.3 -21 42845383 . A G 256 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21096;SOR=1.16699;LSEQ=AGCGCGCTCTCGCCGCCCAC;RSEQ=ATCCTGCTCTGGCGGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:631:349:155,194:128,154:0.5531:2,2:24.9:1:30.4:1:0.80973:1.04026:60:115.333:0.5563:0:1.1 1/0:528:312:146,166:102,114:0.5909:2,2:25.6:1:30.1:1:0.92957:1.01727:60:77:0.5912:0:1.2 -21 42845473 . C A 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14755;SOR=0;LSEQ=GTGAGACCAGCAGAAGCCGC;RSEQ=CAGCCACCCAGCGCCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:4:3,1:74,219:0.0135:2,2:6.3:1:27.3:1:0.05492:8.80:60:8:0.014:0:1.3 0/0:207:0:0,0:60,147:0:2,0:23.1:1:29.7:1:1:0:60:22:1:0:0.3 -21 42845638 . C T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.60281;LSEQ=GGAAGCACCACTTCCCTGAA;RSEQ=ACTCCTGTGATCCCATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:0,11:0,9:0.55:0,0:25.5:1:28.5:1:1:0:60:22:0.5789:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:11.5:1:30:0:1:0:60:4:0.6667:0:1 -21 42845800 . G T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.1;SOR=Inf;LSEQ=GGGCAGGGCTGGAAGTGAGT;RSEQ=AGGGGGTGAGGAGACGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:28:1:30:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:39:0:30.5:1:1:0:60:4:1:0:1.5 -21 42846888 . AGGGGTGGGTGAGGTGGTGAGTGAGGGGGTGAGGGGTGAGTGAGGGGGGTGAGGGGTAAGGAGGTGAGGGGGTGGGTGAGGGGTGGGTGAGGTGGTGGGTGAGGGGGTGAAGGGGTGAGTGAG A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAGTGAGGGGGTGGGTG;RSEQ=GGGGTGAGTGAGGGGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:25:1:29.8:1:1:0:60:6:1:1:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42847017 . A G 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0.14286;SOR=0;LSEQ=AAGGGGTGAGTGAGGGGGTG;RSEQ=GTGAGGGGATGAGGGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:7.3:1:32.5:1:1:0:60:8:0.8:0:2.3 0/0:2:0:0,0:1,1:0:2,0:19:0:27.5:1:1:0:60:4:1:0:0.5 -21 42847036 . A G 75 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGAGGGGATGAGGGAGT;RSEQ=ATTCAGAGGGTGAAGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:26:1:32.4:1:1:0:60:10:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42847077 . AT A 25 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAGGGAGTGAAGGCATG;RSEQ=TGAGGGGGTGAAGGGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:10.5:1:25:1:1:1.7321:60:4:0.4:0.2:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42847266 . GT G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGAGTGAGGAGGTGAAG;RSEQ=GTGAGTGAGGGCGTGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:31.5:1:1:0:60:4:1:0:0 -21 42847358 . AAGGGGTGAGTGAGGGGGTGC A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGTGGGTGAGTGGATG;RSEQ=AGGGGTGAGTGAGGGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:27.5:1:1:0:60:4:1:0:0 -21 42847606 . G C 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGGGAGTGAGGGGGTGA;RSEQ=TGAGGGGGCGAGGGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:7.3:1:33:1:1:0:36.7:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42848115 . G C 38 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCACCTGGTGGCCACAC;RSEQ=GTGGTGCTGGACCACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:24:1:24:1:1:0:60:2:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42848187 . C T 85 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGGGCTCACTAACGCCA;RSEQ=CCCCCTTTGCTTTCTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1:0,2:22.3:1:30.4:1:1:0:60:14:1:0:1.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42848494 . A C 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATCAAAAGGGGGACTCCAG;RSEQ=TGAACTTACCTATACAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1059:0:0,0:548,511:0:2,0:26.4:1:30.3:1:1:0:60:74.643:1:0:0.1 0/1:927:35:22,13:456,435:0.0378:2,2:22.6:1:31.5:1:0.2272:1.61:60:70:0.0381:0:1.2 -21 42848560 . CAG C 290 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01218;LSEQ=AGGCATCACTGCAAAAAGAA;RSEQ=GGGAAATTCTGGTCACGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:630:629:215,414:0,0:0.9984:0,2:27.9:1:31.3:1:1:0:60:156.25:1:0.0381:0.1 1/1:657:581:229,352:31,43:0.8843:2,2:25:1:29.9:1:0.7061:1.10798:60:95.833:0.886:0.1553:0.2 -21 42848684 . C T 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGTCTGCTAGTTACAACT;RSEQ=CAATAAGGTAAGTAAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:0,87:0:1,0:22.1:1:31.5:1:1:0:60:42.5:1:0:0.2 0/1:53:14:0,14:1,38:0.2642:1,1:30.1:1:29.2:1:1:0:60:28:0.2692:0:1.1 -21 42848747 . C T 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56914;SOR=0;LSEQ=AGACACTGAGCCAAGGTACG;RSEQ=GGCTCACATCCCCACAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:5:0,5:2,28:0.1429:2,0:36.8:1:29.2:1:1:0:60:10:0.1471:0:1.2 0/0:7:0:0,0:0,7:0:0,0:15.3:1:30:1:1:0:60:14:1:0:0.7 -21 42848835 . T C 95 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGACGGTTGTGAGGGTAAG;RSEQ=ATACAATAATGCTAGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:1:0,2:15.3:1:31.9:1:1:0:60:16:1:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42849097 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGCTATGCTGAGAAGG;RSEQ=AAGACGCGGCCCCTGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:33.3:1:30:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42849134 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCAGAGCTGGCCCGCCC;RSEQ=GATAGCTGGGCCGTGTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:23.7:1:30.3:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42849137 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGCTGGCCCGCCCTGA;RSEQ=AGCTGGGCCGTGTGCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:20.7:1:30.7:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42850911 . C T 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02206;SOR=0;LSEQ=TAGCAGAGAAACCTCAGCCA;RSEQ=TTCCTATGAATAAACCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:14,0:1,0:0.9333:0,1:21.4:1:31.9:1:1:0:60:28:0.9333:0:2.1 0/0:2:0:0,0:2,0:0:0,0:21.5:1:33:0:1:0:60:4:1:0:0.5 -21 42850977 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05906;LSEQ=CAGACTCTAATCTCCTCCCA;RSEQ=TGCAAAACCCATCCAGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:59:58,1:18,0:0.7662:1,1:23.7:1:32.9:1:1:0:60:118:0.7763:0:2.2 0/1:38:6:6,0:32,0:0.1579:1,0:20.5:1:31.2:1:1:0:60:5:0.1351:0:2 -21 42851006 . A G 197 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09433;LSEQ=CCATCCAGACCGAGTATTGC;RSEQ=GCTCAGAGAAATCAGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:99:93,6:29,1:0.7557:1,2:24.5:1:29.8:1:1:1.86335:60:48.5:0.7638:0:1.6 0/1:85:19:18,1:61,5:0.2235:2,1:24.2:1:29.8:1:1:1.47:60:18:0.2169:0:1.3 -21 42851038 . C T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.25685;SOR=0;LSEQ=TCAGACTCAGGACAACGATT;RSEQ=CCCATGGTGTCTCCTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:1,2:190,28:0.0136:2,2:5.7:1:21.3:1:0.04911:13.28415:60:2:0.0092:0:3 0/0:178:0:0,0:151,27:0:2,0:23.9:1:30.8:1:1:0:60:177:1:0:0.2 -21 42851262 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52298;SOR=0;LSEQ=TAAGGCATAAGCAAACACAA;RSEQ=TCCTATACTATGTCATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:19,157:0.0112:2,2:20.5:1:28.5:1:0.21266:8.08:60:4:0.0112:0:1 0/0:114:0:0,0:24,90:0:2,0:20.4:1:29.6:1:1:0:60:56:1:0:0.1 -21 42851565 . TGG T 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGGTTCCTGGACTGTGA;RSEQ=GGGGGCTTTGCTGTGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33:1:33:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42852311 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01119;SOR=Inf;LSEQ=CAATTGTCCCCAGCACTCAT;RSEQ=TGCCGGTGCTTTCACAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:111,4:0:1,0:24.5:1:32.6:1:1:0:60:230:1:0:0.3 0/1:81:5:5,0:72,4:0.0617:2,0:19.6:1:29.4:1:1:0:60:10:0.0625:0:1 -21 42852320 . C A 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=3.71167;LSEQ=CCAGCACTCATGTGCCGGTG;RSEQ=TTTCACAGGGAGGCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:27:27,0:102,4:0.2015:1,1:21.3:1:30.2:1:0.58187:0:60:54:0.2015:0:1.1 0/1:101:49:45,4:48,4:0.4851:2,2:21.4:1:29.9:1:1:1.06595:60:98:0.4851:0:1.1 -21 42852334 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58099;SOR=2.63064;LSEQ=CCGGTGCTTTCACAGGGAGG;RSEQ=AGAGAGAGGGTCTTCTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:0,1:166,19:0.0053:2,0:1:0:27:0:0.10753:0:60:2:0.0054:0:1 0/1:143:2:1,1:125,16:0.014:2,2:21.5:1:27:1:0.22437:7.60942:60:4:0.014:0:1.5 -21 42852497 . C T 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCTCTGAGATGAGTACA;RSEQ=CTGAAGGATGAAGTTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1072:0:0,0:472,600:0:2,0:25.6:1:31:1:1:0:60:41.88:1:0:0.1 0/1:1037:137:60,77:441,457:0.1321:2,2:22.8:1:29:1:0.27105:1.23814:60:274:0.1348:0:1.2 -21 42852565 . C CT 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.36902;SOR=0.74436;LSEQ=GATTATCCATGAGTTTCTTT;RSEQ=TTTTTTTTTCTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:652:27:8,19:181,439:0.0414:2,2:29:1:30.7:1:1:1.02:60:54:0.0421:0:0 0/1:610:19:7,12:219,371:0.0311:2,2:27.7:1:30.2:1:1:1.01192:60:38:0.0318:0.0016:0.2 -21 42852575 . C CT 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0057;SOR=Inf;LSEQ=GAGTTTCTTTCTTTTTTTTT;RSEQ=TTTTTTTTGAGACGGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:0:0,0:142,413:0:2,0:20.8:1:31.8:1:1:0:60:54.5:0.9963:0:0.1 0/1:514:7:3,4:166,335:0.0136:2,2:19.7:1:29.5:1:0.69059:1.51:60:14:0.014:0.0019:0.4 -21 42860136 . G T 95 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14911;SOR=0.20277;LSEQ=CTGTCATCTCCCACCTGCTG;RSEQ=GTGAGGTTGGGCCGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:9:9,0:34,0:0.2093:1,0:26.7:1:30.1:1:1:0:60:18:0.2093:0:1 0/1:20:1:1,0:19,0:0.05:1,0:7:0:32:0:1:0:60:2:0.05:0:1 -21 42860258 . G T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02311;SOR=Inf;LSEQ=CCAGTCACCCAAAGGCCCCT;RSEQ=GACCCGGCTGCTGTCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:0:0,0:370,144:0:2,0:23.3:1:31.4:1:1:0:60:50.4:1:0:0.9 0/1:330:4:1,3:230,96:0.0121:2,2:13.3:1:28.5:1:0.08243:7.13966:60:8:0.0124:0:2 -21 42860307 . C T 290 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGGAGTCCCTTCCCAAGGT;RSEQ=AAGGCTGACTCACCACACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:961:961:552,409:0,0:1:0,2:25.9:1:29.3:1:1:0:60:119.125:1:0:1.1 1/0:772:598:329,269:95,78:0.7746:2,2:24.7:1:28.5:1:1:1.00:60:53.364:0.7744:0:1.2 -21 42860485 . G C 254 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCCCTTCAGGCTGAGAAAC;RSEQ=CAATGAGCCTCATGGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:299:299:56,243:0,0:1:0,2:24.1:1:31:1:1:0:60:48.833:1:0:1.1 1/0:239:183:40,143:11,43:0.7657:2,2:22.7:1:30.8:1:1:1.09:60:182:0.7679:0:1.1 -21 42860494 . C G 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTGAGAAACGCAATGAGC;RSEQ=TCATGGAGTGAGGAACACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:40,221:0:2,0:24.2:1:31.6:1:1:0:60:42.5:1:0:1 0/1:207:20:4,16:35,152:0.0966:2,2:20:1:30.5:1:1:1.09:60:40:0.0985:0:1 -21 42860522 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14859;SOR=Inf;LSEQ=GTGAGGAACACCGTGGCATT;RSEQ=CTGTAGCTCGCTGCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:11,154:0:2,0:25.2:1:30:1:1:0:60:164:1:0:0.9 0/1:104:2:1,1:7,95:0.0192:2,2:17:1:30.5:1:0.14862:12.76:60:4:0.0194:0:2 -21 42860532 . G A 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05303;SOR=0;LSEQ=CCGTGGCATTACTGTAGCTC;RSEQ=CTGCAGCCTCCAACTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:8:0,8:4,124:0.0588:1,0:23.5:1:30.3:1:1:0:60:16:0.0593:0:1.8 0/0:77:0:0,0:6,70:0:2,0:25.8:1:31.9:1:1:0:60:75:0.9868:0:0.9 -21 42860593 . C T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00124;SOR=Inf;LSEQ=TTTTGTTTTTGAGATGAAGT;RSEQ=TCATTCTGTCACCCAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:1,41:0:1,0:26.4:1:32.9:1:1:0:60:84:1:0:0.2 0/1:17:5:0,5:0,12:0.2941:0,0:18.4:1:30.2:1:1:0:60:10:0.3125:0:1 -21 42861332 . C T 221 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08809;LSEQ=TATGTAAGAGAGGAACCTCA;RSEQ=GGAGGGCCTCCAGAGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:198:151:143,8:40,7:0.7626:2,2:25.1:1:30.6:1:0.05197:3.11:60:36.75:0.7577:0:1.1 0/1:96:21:20,1:69,6:0.2188:2,1:20.2:1:30.4:1:1:1.73:60:42:0.2211:0:1.1 -21 42861616 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51782;SOR=0;LSEQ=TTTATAGTACACCACATTAA;RSEQ=AAATAATTATTTCATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:5,191:0.0101:1,2:8.5:1:28.5:1:0.05984:34.97:60:4:0.0103:0:1 0/0:133:0:0,0:9,124:0:2,0:21.4:1:31.2:1:1:0:60:266:1:0:0 -21 42865324 . G A 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=3.51553;LSEQ=GGGGTAGAAACGCAGGAGCG;RSEQ=CAGCACTTGTCCTGAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:24.7:1:32:0:1:0:60:6:0.5:0:1.3 1/1:5:4:4,0:1,0:0.8:0,0:31.5:1:29.3:1:1:0:60:8:0.8:0:1 -21 42865906 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGGACTGTATGACAAA;RSEQ=GTAAGATAGTTGATTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 42866107 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.6361;SOR=2.20879;LSEQ=TAGGCCTGGCAGCGACAGCT;RSEQ=TGACCCAGCAGGAAGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:24,0:0.0769:1,0:33:1:33:0:1:0:60:4:0.0769:0:1 0/1:19:3:3,0:16,0:0.1579:1,0:34:1:31:1:1:0:60:6:0.1579:0:1 -21 42866296 . TG CA 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0;LSEQ=ATCCTACTTGAGGTGCACAC;RSEQ=TCCCGGATGGGGATTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:16:13,3:331,192:0.0296:2,2:23.3:1:30.8:1:0.18884:2.51:60:32:0.0303:0.0074:0.9 0/0:453:0:0,0:230,172:0:2,0:25.4:1:30.4:1:1:0:60:200:0.8909:0:0.2 -21 42866730 . G A 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28997;SOR=0.35915;LSEQ=CTACAAGGCTGGGTGCGGTG;RSEQ=CTCATGCCTGTAATCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:6:4,2:128,282:0.0144:2,2:16.3:1:27.8:1:0.08354:4.39:60:12:0.0147:0:1 0/0:383:2:2,0:138,243:0.0052:2,0:1:0:24.5:1:0.13301:0:60:4:0.0053:0:1 -21 42866736 . G A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43277;SOR=2.19881;LSEQ=GGCTGGGTGCGGTGGCTCAT;RSEQ=CCTGTAATCCCAGCACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:2:2,0:106,255:0.0055:2,0:1:0:24:1:0.08794:0:60:4:0.0057:0:1 0/1:332:4:3,1:116,212:0.012:2,2:12.8:1:25:1:0.1333:5.45:58.3:8:0.0121:0:1.8 -21 42866756 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08034;SOR=Inf;LSEQ=GCCTGTAATCCCAGCACTTT;RSEQ=GGAGGCCGAGGCGGGCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:53,225:0:2,0:23.2:1:30.9:1:1:0:59.4:68.5:1:0:0.1 0/1:212:3:2,1:47,162:0.0142:2,2:15.3:1:28.3:1:0.1342:6.81:60:6:0.0145:0:3.3 -21 42866763 . C T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07705;SOR=Inf;LSEQ=ATCCCAGCACTTTGGGAGGC;RSEQ=GAGGCGGGCGGATCATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:38,205:0:2,0:24.2:1:29.9:1:1:0:59.4:80:1:0:0.1 0/1:181:3:1,2:30,147:0.0166:2,2:11.7:1:31.7:1:0.43478:2.43:60:6:0.0169:0:3 -21 42866768 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06426;SOR=Inf;LSEQ=AGCACTTTGGGAGGCCGAGG;RSEQ=GGGCGGATCATGAGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:30,193:0:2,0:25:1:29.9:1:1:0:59.3:36.167:1:0:0.1 0/1:150:3:1,2:23,121:0.02:2,2:13.7:1:30.3:1:0.41654:2.61:59.3:6:0.0207:0:1 -21 42866772 . C A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15743;SOR=Inf;LSEQ=CTTTGGGAGGCCGAGGCGGG;RSEQ=GGATCATGAGGTCAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:23,182:0:2,0:25.7:1:30.1:1:1:0:59.2:204:1:0:0.1 0/1:136:2:1,1:16,117:0.0147:2,2:6.5:1:31.5:1:0.23682:7.12:60:4:0.0149:0:4 -21 42866801 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53906;SOR=0;LSEQ=AGGTCAGGAGATCGAGACCA;RSEQ=CGTGGCCAACATGGTGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:0,2:10,127:0.0144:2,0:16:1:32.5:1:1:0:40:4:0.0147:0:2.5 0/0:77:0:0,0:1,76:0:1,0:22:1:28.8:1:1:0:59.9:37.5:1:0:0.2 -21 42866803 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54325;SOR=0;LSEQ=GTCAGGAGATCGAGACCATC;RSEQ=TGGCCAACATGGTGGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:0,2:11,123:0.0147:2,0:14:1:33.5:1:1:0:40:4:0.0152:0:2.5 0/0:73:0:0,0:2,71:0:1,0:22.2:1:30.8:1:1:0:59.9:72:1:0:0.2 -21 42866994 . CAA C 235 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0;SOR=0.15279;LSEQ=GACAGAGCAAGACTATGTCT;RSEQ=AAAAAAAAAAAAAAGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:393:201:155,46:58,8:0.5115:2,2:19.1:1:30.8:1:0.07646:2.14617:59.5:66:0.5143:0.1552:1 0/1:269:37:29,8:104,26:0.1375:2,2:27.5:1:31.6:1:0.81969:1.10278:59.4:74:0.1396:0:0.9 -21 42867003 . A T 216 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=1;SSF=0;SOR=0.00544;LSEQ=AGACTATGTCTCAAAAAAAA;RSEQ=AAAAAAAGTAATAGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:142:109,33:238,79:0.3094:2,2:18.7:1:30.3:1:0.72586:1.10:59.9:141:0.3092:0:1 0/0:413:1:0,1:293,119:0.0024:2,0:1:0:22:0:0.29056:0:60:2:0.0024:0:1 -21 42867220 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02002;SOR=Inf;LSEQ=TTAATACAATATTTATTCAC;RSEQ=ATTACAGTTGAGAAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:573:0:0,0:234,339:0:2,0:25:1:30.5:1:1:0:60:80.857:1:0:0.1 0/1:485:5:3,2:177,303:0.0103:2,2:31.4:1:25.2:1:0.36514:2.56:60:4:0.0084:0:2.4 -21 42867277 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14898;SOR=Inf;LSEQ=AAATACAGATTTGGCTGGGC;RSEQ=CAGTGGGTCACTCCTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:62,179:0:2,0:24.6:1:31:1:1:0:60:59.25:1:0:0.1 0/1:152:2:1,1:37,113:0.0132:2,2:18:1:26:1:0.43874:3.03:60:4:0.0132:0:2.5 -21 42867289 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13031;SOR=Inf;LSEQ=GGCTGGGCGCAGTGGGTCAC;RSEQ=CCTGTAATCCCAGCACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:40,168:0:2,0:22.7:1:30:1:1:0:59.9:103:1:0:0.1 0/1:118:2:1,1:20,96:0.0169:2,2:12:1:29.5:1:0.32551:4.71:60:4:0.0171:0:2.5 -21 42867515 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11898;SOR=Inf;LSEQ=TGAATGGAGATCACGTCACT;RSEQ=CACTCCAGCCTGGGCGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:82,11:0:2,0:24.1:1:28.4:1:1:0:58.6:92:1:0:1.1 0/1:50:2:1,1:42,6:0.04:2,2:5.5:1:30:1:0.26286:6.55744:42:4:0.0426:0:1 -21 42867553 . CA C 190 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.5732;SOR=0.87322;LSEQ=CAAGAGCGAAACTCCCGTCT;RSEQ=AAAAAAAAAAAAAAACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:73:61,12:99,12:0.3411:2,2:16.9:1:30.8:1:0.27356:1.61849:58.8:35.5:0.3381:0.1449:1.7 0/1:151:47:41,6:56,15:0.3113:2,2:16.6:1:30.6:1:0.32736:1.82:59.1:94:0.3133:0.106:1.8 -21 42868206 . T C 216 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCCTAAAGGAGCATAGTCTC;RSEQ=GTGTTATCCTGCAAATACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:800:0:0,0:441,359:0:2,0:25.9:1:30.6:1:1:0:60:56.143:1:0:0.1 0/1:660:165:83,82:247,245:0.25:2,2:26.2:1:29.4:1:1:1.00:60:40.25:0.2469:0:1.2 -21 42868876 . G A 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11679;SOR=3.40749;LSEQ=CTCCCAGGTTCAAGTGATTC;RSEQ=TCTGCCTCAGCCGCCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:4:1,3:19,31:0.0741:2,2:19.5:1:23:1:1:1.81977:57.3:1:0.0476:0:1.3 0/1:23:5:2,3:1,17:0.2174:1,2:15.6:1:27.2:1:0.10728:9.66:58.4:4:0.25:0:1.8 -21 42868888 . C T 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.17792;SOR=0.46808;LSEQ=AGTGATTCGTCTGCCTCAGC;RSEQ=GCCCGAGTAGCTGGGATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:35:15,20:10,8:0.6604:2,2:22.5:1:29.3:1:0.40222:1.65044:58.5:16.5:0.66:0:1.5 0/1:19:9:1,8:2,8:0.4737:2,2:17.1:1:29.4:1:1:1.9301:59.8:18:0.6:0:1.9 -21 42868997 . A C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08152;LSEQ=AGGCTGGTCTCGAACTCCCA;RSEQ=CCTCAGGTGATCTGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:151:95:91,4:53,3:0.6291:2,1:26.5:1:32.3:1:0.71068:1.29:60:94:0.6351:0:1.5 0/1:108:13:13,0:95,0:0.1204:1,1:22.1:1:31.5:1:1:0:60:26:0.1238:0:1.5 -21 42869063 . A G 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.53468;LSEQ=AGGCATGAGCCACCACGCCC;RSEQ=GCCTGCCCCTTGTCTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:466:334:220,114:79,50:0.7167:2,2:22.9:1:29.7:1:0.38621:1.22:60:82.5:0.7205:0:1.3 1/0:421:242:155,87:108,69:0.5748:2,2:23.3:1:29.3:1:0.54067:1.14:60:47.4:0.5766:0:1.2 -21 42869606 . A G 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTAGCCACATTTGTCTCCA;RSEQ=AGGGAGTGGGCTCCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:0:0,0:319,307:0:2,0:26.7:1:30.1:1:1:0:60:155.5:1:0:0.1 0/1:475:55:28,27:218,201:0.1158:2,2:25.1:1:30.8:1:0.88691:1.04576:60:17.333:0.1116:0:1.2 -21 42869735 . G A 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69022;SOR=1.06205;LSEQ=TGGAACATACCCCTGTTATC;RSEQ=CCATCCTGCCTCATCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:769:164:81,83:289,316:0.2133:2,2:23.5:1:30:1:0.72526:1.07:60:328:0.2175:0:1.1 0/1:586:131:66,65:220,232:0.2235:2,2:26.7:1:29.1:1:0.76629:1.07:60:42.667:0.2215:0:1.2 -21 42870262 . A G 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACCTTTGGCCTGCATCTTC;RSEQ=CCACTGCTTCCCCACATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1063:0:0,0:501,561:0:2,0:25.1:1:29.9:1:1:0:60:87.5:1:0:0.1 0/1:810:82:45,37:340,386:0.1012:2,2:24.6:1:30.2:1:0.19933:1.38:60:26.333:0.0988:0:1.1 -21 42870522 . C T 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=57.5507;LSEQ=GTGCCACTAAGCCCAGGCAT;RSEQ=CTGCTGGACTTAACCCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:727:1:0,1:368,357:0.0014:2,0:2:0:31:0:0.49311:0:60:2:0.0014:0:1 0/1:584:43:21,22:280,261:0.0736:2,2:24.8:1:30:1:0.75284:1.12366:60:86:0.0747:0:1.1 -21 42871220 . C T 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0011;SOR=1.37988;LSEQ=AGCTAGAGATGCCGTCAACA;RSEQ=GAAATGCTGTATAGTAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1177:263:132,131:437,475:0.2234:2,2:24.2:1:30.4:1:0.52909:1.10:60:86.667:0.2222:0:1.1 0/1:1066:303:136,167:365,396:0.2842:2,2:25.9:1:29.9:1:0.3769:1.13168:60:302:0.2849:0:1.1 -21 42871273 . T C 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49332;SOR=1.10048;LSEQ=TCACTCTCCATGGACAAAGA;RSEQ=TCTTCGCTTGATCAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1170:116:58,58:492,562:0.0991:2,2:27:1:31.8:1:0.55669:1.14:60:37.667:0.098:0:1.1 0/1:1120:121:50,71:465,533:0.108:2,2:22.9:1:31.6:1:0.28907:1.2386:60:242:0.1091:0:1.2 -21 42871545 . A AT 301 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=0.11619;LSEQ=CTTGATGTTTTCTCTTTGTG;RSEQ=TTTTTCCACCCACCAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1535:963:513,450:312,256:0.6274:2,2:26.9:1:30.4:1:0.55944:1.06901:60:49.684:0.6268:0.0821:0.1 0/1:1352:221:122,99:611,519:0.1635:2,2:25.1:1:29.7:1:0.7683:1.05:60:220:0.1653:0.02:0.2 -21 42871730 . A AT 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.19955;SOR=0.7512;LSEQ=TTAACAAGTCTCATTGGACG;RSEQ=TTTTTTTTTCTTTAACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1182:54:22,32:471,653:0.0457:2,2:24.9:1:29.7:1:0.88884:1.04911:60:53:0.0458:0.0076:0.2 0/1:1066:37:16,21:458,570:0.0347:2,2:29.7:1:29.4:1:1:1.05457:59.9:36:0.0341:0.0019:0.3 -21 42871941 . G C 290 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21108;LSEQ=TGTCCACTGTCTGTGACATG;RSEQ=CCACAGAAGAATATTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:595:574:266,308:10,11:0.9647:2,2:24.6:1:31.7:1:1:1.05257:60:113.8:0.9677:0:1.1 1/1:453:386:169,217:30,34:0.8521:2,2:23.9:1:31:1:0.68454:1.13264:60:47.25:0.8552:0:1.1 -21 42872398 . C T 200 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01191;LSEQ=TTCAGTACACCATCGCTTTC;RSEQ=TGTGTCCTAAGCAGAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1052:93:45,48:452,507:0.0884:2,2:22.7:1:30.6:1:0.82859:1.05:60:186:0.089:0:1.1 0/0:868:1:0,1:410,456:0.0012:2,0:1:0:24:0:1:0:60:2:0.0012:0:1 -21 42872751 . T C 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.76868;SOR=0.96516;LSEQ=CCTTGCCTATGTCTGCTTTG;RSEQ=GAAGAGAGAGGATCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:955:224:105,119:358,373:0.2346:2,2:25.8:1:30.6:1:0.59354:1.08766:60:43.8:0.2332:0:1.1 0/1:701:160:87,73:254,286:0.2282:2,2:25.7:1:31.1:1:0.106:1.34:60:159:0.2288:0:1.1 -21 42872897 . G C 334 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22456;LSEQ=ATGCCTCTGGTTTCTCGGCT;RSEQ=TCCTATCTCCCCAGTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1568:1501:775,726:34,33:0.9573:2,2:25.6:1:31.7:1:0.90122:1.04:60:82.389:0.9568:0:1.1 1/1:1284:1071:560,511:107,104:0.8341:2,2:25.5:1:31.2:1:0.70645:1.07:60:65.938:0.8333:0:1.1 -21 42873283 . T C 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.094;SOR=Inf;LSEQ=CGGCGGCTCCTGCCTATAAT;RSEQ=CCAGCACTTTGGGAGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:68,287:0:2,0:22.2:1:29.6:1:1:0:59.8:38.444:1:0:0.1 0/1:297:3:1,2:64,227:0.0101:2,2:18:1:32.7:1:0.52881:1.77:49:6:0.0106:0:5 -21 42873348 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTCAAGACCAGCCTGGC;RSEQ=AACATAGTGAAACCCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:0,2:8,145:0.0129:2,0:9:1:27:1:1:0:60:4:0.0135:0:2.5 0/0:69:0:0,0:1,68:0:1,0:24.3:1:31.4:1:1:0:59.4:33.5:1:0:0.3 -21 42873558 . A G 203 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=28.000;MSILEN=1;SSF=0;SOR=0.16889;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAAGAAACAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:119:81,38:202,72:0.296:2,2:17.3:1:29.5:1:0.27194:1.3152:59.6:8.154:0.2896:0:1.3 0/1:272:18:14,4:156,88:0.0662:2,2:18.2:1:28.7:1:0.30989:1.97:60:5:0.0598:0:1.4 -21 42873605 . G A 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.02058;SOR=1.54231;LSEQ=AATTGAAAATAAAACAAGGG;RSEQ=GGGAATGTCCCGCTCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:58:36,22:553,305:0.0632:2,2:27.9:1:30.5:1:0.77728:1.10789:60:57:0.0633:0:1.1 0/1:742:70:40,30:391,279:0.0943:2,2:29.8:1:29.1:1:0.89884:1.05098:59.6:34:0.0942:0:1.3 -21 42875004 . C T 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24044;SOR=1.27857;LSEQ=TTTTATATACCAACAACAGA;RSEQ=GATCGGAAATGTAAATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:56:18,38:250,435:0.0754:2,2:26.9:1:31:1:0.56511:1.21294:60:112:0.0764:0:1 0/1:625:59:28,31:229,335:0.0944:2,2:24:1:29.9:1:0.33218:1.32:60:118:0.0956:0:1.1 -21 42875652 . G T 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=60.28026;LSEQ=CCTAAAAATGTATGTTTCAA;RSEQ=ACTGGAGGATCATTTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1133:2:0,2:535,596:0.0018:2,0:10.5:1:17:1:0.50111:0:60:1:9e-04:0:1 0/1:839:81:34,47:371,385:0.0965:2,2:26.2:1:28.5:1:0.24324:1.33163:60:39.5:0.095:0:1.1 -21 42876400 . C T 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35197;LSEQ=TGCCAGAAAACCAGCCTCGA;RSEQ=TCCCAACCAGCGCATTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1406:858:366,492:252,295:0.6102:2,2:26.5:1:30.4:1:0.22532:1.1482:60:60.286:0.6085:0:1.1 0/1:1236:439:197,242:365,430:0.3552:2,2:25:1:29.7:1:0.76535:1.04272:60:53.875:0.3536:0:1.2 -21 42876598 . T C 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.94925;SOR=1.01196;LSEQ=CTTTTGCTCCTCCTTGGGTG;RSEQ=CCACAGGCTCGGTGGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:786:177:82,95:292,317:0.2252:2,2:24.8:1:31.3:1:0.73276:1.06705:60:43.25:0.2238:0:1.1 0/1:638:145:74,71:240,252:0.2273:2,2:28.2:1:31.5:1:0.63799:1.09:60:290:0.2305:0:1.1 -21 42877161 . AAAAT A 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.40475;SOR=0.70936;LSEQ=AATTTTCAAGAGGGCTTAGA;RSEQ=AAATAAATAAATAAGATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:919:23:9,14:367,529:0.025:2,2:22.9:1:30.7:1:1:1.07911:60:46:0.0253:0.0054:0.1 0/1:783:14:4,10:325,444:0.0179:2,2:26.4:1:29.4:1:0.41556:1.82863:60:28:0.018:0.0026:0.1 -21 42877382 . T C 178 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=89.58606;LSEQ=ATCGTGGTGGTGGTGGTTAC;RSEQ=GGCATAAGGTACTGCACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1353:1:1,0:584,766:7e-04:2,0:8:0:15:0:0.43301:0:60:0:0:0:4 0/1:1109:69:28,41:474,566:0.0622:2,2:24.7:1:29.3:1:0.45517:1.22605:60:33.5:0.0614:0:1.1 -21 42877542 . C A 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00525;SOR=0.63382;LSEQ=TACTGCTAGAGGGAGCAGCA;RSEQ=GGAGCCCAGGTAGGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:633:544:291,253:54,35:0.8594:2,2:23.7:1:30.5:1:0.25083:1.34076:60:107.8:0.8596:0:1.1 1/0:458:364:201,163:50,44:0.7948:2,2:22.3:1:30.1:1:0.72892:1.08:60:51:0.7916:0:1.1 -21 42877555 . G T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01241;SOR=Inf;LSEQ=AGCAGCACGGAGCCCAGGTA;RSEQ=GGCTGTGGGCAGGGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:0:0,0:376,310:0:2,0:23.3:1:31.6:1:1:0:60:97:1:0:0.8 0/1:490:5:2,3:269,216:0.0102:2,2:9.4:1:28.2:1:0.66046:1.86564:60:10:0.0104:0:1.2 -21 42878126 . A C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07524;LSEQ=CCTGAGGCTCCAGCAACAGC;RSEQ=CAAGCTTGTTGTTAGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:804:491:251,240:167,146:0.6107:2,2:25.5:1:30.6:1:0.56278:1.09358:60:39.917:0.6102:0:1.1 0/1:655:69:44,25:304,280:0.1053:2,2:24.9:1:29.8:1:0.07416:1.62:60:33.5:0.1039:0:1.1 -21 42878611 . C T 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03055;SOR=1.27929;LSEQ=ACTCCCAACCCCCATCCTTC;RSEQ=TTCAGGGGAGGCTGGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:213:107,106:381,404:0.213:2,2:25.5:1:30.5:1:0.69935:1.07:60:70:0.2132:0:1.2 0/1:762:196:95,101:282,284:0.2572:2,2:22.5:1:30.4:1:0.80368:1.05563:60:97:0.2556:0:1.1 -21 42878761 . C T 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCATGATTCGGGAGGTT;RSEQ=TCGCGGCTGGGAGCTCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:785:0:0,0:323,460:0:2,0:25.3:1:31.6:1:1:0:60:64.25:0.9974:0:0.2 0/1:652:16:5,11:281,354:0.0245:2,2:22.6:1:30.3:1:0.44528:1.74491:60:32:0.0247:0:1 -21 42878780 . T G 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCGCGGCTGGGAGCTCCG;RSEQ=GAGGTCAGGCATTGCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:661:52:19,33:237,370:0.0787:2,2:26.6:1:31.5:1:0.76862:1.11237:60:104:0.0801:0:1.2 0/0:528:0:0,0:219,309:0:2,0:23.8:1:29.2:1:1:0:60:51.8:1:0:0.2 -21 42878913 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08988;SOR=Inf;LSEQ=CTGCCCACAGGGCTCACCTC;RSEQ=GGCCGCCGTGCTATCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:182,168:0:2,0:24.4:1:30.1:1:1:0:60:86.5:1:0:0.1 0/1:285:3:1,2:149,133:0.0105:2,2:5.7:1:26:1:0.60483:2.23446:60:6:0.0106:0:2 -21 42879057 . G T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04484;SOR=Inf;LSEQ=AAGGCCCTCCTCTGCCACAA;RSEQ=CGCTCAGGGCTCTCGGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:223,221:0:2,0:25.8:1:31.9:1:1:0:60:43.4:1:0:0.1 0/1:380:4:1,3:184,192:0.0105:2,2:12.3:1:28.5:1:0.62354:2.86798:60:8:0.0108:0:1 -21 42879101 . T A 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01533;SOR=Inf;LSEQ=ACTTTCTGGACATGGGGCAG;RSEQ=TTTTCAGCTGGACCCGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:499:0:0,0:252,246:0:2,0:24.7:1:29.5:1:1:0:60:48.8:1:0:0.1 0/1:384:5:3,2:187,192:0.013:2,2:25:1:28.2:1:0.68262:1.54:60:10:0.0131:0:1.4 -21 42879231 . TC T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.07721;SOR=Inf;LSEQ=AGCGCCCAGGTGCCCCGCCT;RSEQ=CCCCCAACCCGGCACGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:124,205:0:2,0:25.8:1:30.9:1:1:0:60:46:1:0:0.2 0/1:245:3:2,1:98,143:0.0122:2,2:25.3:1:28.3:1:0.56947:2.91:60:6:0.0125:0.0041:0.7 -21 42879262 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15139;SOR=Inf;LSEQ=CGGCACGGAGCGCAAGCGGA;RSEQ=GAGCCAGACCGGCTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:88,164:0:2,0:23.6:1:31.1:1:1:0:60:83:1:0:0.1 0/1:161:2:1,1:60,99:0.0124:2,2:17:1:29.5:1:1:1.64:60:4:0.0127:0:1 -21 42879308 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16742;SOR=Inf;LSEQ=GGTTCCTGCCGGTGCCGGGT;RSEQ=TCCAGGAGGCCCCGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:68,106:0:2,0:24:1:32:1:1:0:60:42.5:1:0:0.2 0/1:121:2:1,1:53,66:0.0165:2,2:7:1:28.5:1:1:1.24:60:4:0.0168:0:1 -21 42879403 . A T 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGACTGACTGGCCGTTCGC;RSEQ=CCTCGCCCGGGGGCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:237,96:0:2,0:25.2:1:30:1:1:0:60:82.25:1:0:0.2 0/1:230:75:52,23:104,49:0.3261:2,2:23.1:1:30.3:1:0.88034:1.06:60:74:0.3274:0:1.2 -21 42879604 . C A 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02864;SOR=1.45772;LSEQ=ACAGCACTCCCAGTCCTCCT;RSEQ=CCCAAAGAGAAAAGGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:904:71:32,39:400,433:0.0785:2,2:25.6:1:29.1:1:0.71075:1.12572:60:34.5:0.0773:0:1.2 0/1:778:86:45,41:323,369:0.1105:2,2:23.9:1:28.1:1:0.36005:1.25:60:85:0.1102:0:1.2 -21 42879724 . G A 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06724;SOR=0.76932;LSEQ=AACTGGCTAGGGACTCGCAG;RSEQ=ACCACCTGCCCCAACCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:664:173:79,94:199,292:0.2605:2,2:26.6:1:30.1:1:0.24527:1.23:60:85.5:0.2615:0:1.1 0/1:469:100:44,56:167,201:0.2132:2,2:22.1:1:29.2:1:0.82167:1.05734:60:24:0.2105:0:1.2 -21 42879797 . C T 56 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00528;SOR=Inf;LSEQ=CGGCCGTGCGCAAGGGGTCC;RSEQ=AGGCGCCCAGCACTCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:548:0:0,0:232,316:0:2,0:23.1:1:31.3:1:1:0:60:48.818:1:0:0.2 0/1:395:6:1,5:177,212:0.0152:2,2:7.3:1:21.8:1:0.22894:4.16209:60:2:0.0104:0:1.2 -21 42879909 . C A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42457;LSEQ=GCTCCTCACACCCGCTTTCA;RSEQ=CTCCGGGCGGGGCAGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:669:431:183,248:110,127:0.6442:2,2:25:1:29.8:1:0.32942:1.1735:60:142.667:0.6475:0:1.3 0/1:603:262:125,137:160,181:0.4345:2,2:25.5:1:28.9:1:0.8695:1.03:60:86.333:0.4346:0:1.4 -21 42879936 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02763;SOR=Inf;LSEQ=GCGGGGCAGGGGGCATCGGC;RSEQ=GGTCCCAGGCGCCCAGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:210,295:0:2,0:23.8:1:30.2:1:1:0:60:49.5:1:0:0.8 0/1:483:5:4,1:216,262:0.0104:2,2:6.2:1:29.4:1:0.18257:4.84:60:10:0.0105:0:1.6 -21 42879982 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49867;SOR=0;LSEQ=CCCAGCCCGGACCCCGAGCC;RSEQ=GGACCCTGGTACCGGCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:49,128:0.011:2,2:12:0:32:1:0.48177:2.60:60:4:0.0114:0:1.5 0/0:178:0:0,0:58,117:0:2,0:21.5:1:28.2:1:1:0:60:11.5:0.9938:0:0.5 -21 42880506 . G GA 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCTGGGCAAGGACCCAG;RSEQ=GTAGGCCTTGGGGACTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29:1:1:0:60:4:1:0:0.5 -21 43124132 . T C 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=GGGAGTGGGGGGAGCCAAGG;RSEQ=CCGGGAGACGGAGGCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:22:18,4:35,16:0.3014:2,2:28.6:1:31.5:1:0.39124:2.04:60:44:0.3099:0:2.5 0/0:45:0:0,0:26,19:0:2,0:19.6:1:29.2:1:1:0:60:90:1:0:1.7 -21 43124139 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12536;SOR=Inf;LSEQ=GGGGGAGCCAAGGTCCGGGA;RSEQ=ACGGAGGCTCACTCCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:57,26:0:2,0:24.5:1:31.6:1:1:0:60:40.5:1:0:1.9 0/1:46:2:1,1:25,19:0.0435:2,2:38.5:1:29:1:1:1.30786:60:4:0.0435:0:3 -21 43124156 . G A 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.16901;SOR=0.63571;LSEQ=GGAGACGGAGGCTCACTCCC;RSEQ=CCCCAGATGACAGACCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:60:37,23:35,24:0.5:2,2:21.8:1:28.3:1:0.8523:1.10:60:14:0.487:0:2.4 0/1:67:26:12,14:24,17:0.3881:2,2:31.7:1:29.4:1:0.45113:1.63463:60:52:0.3939:0:2.1 -21 43124186 . A G 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.02155;SOR=1.84277;LSEQ=ACAGACCCCTCGCATCACAC;RSEQ=CCAGGCTGACTCCTCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:71:38,33:43,43:0.4522:2,2:28.5:1:30.2:1:0.74866:1.15:60:22.667:0.4444:0:2.3 1/0:101:61:30,31:20,20:0.604:2,2:27.4:1:30.9:1:1:1.03301:60:60:0.6:0:2.3 -21 43124190 . G C 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39147;SOR=0;LSEQ=ACCCCTCGCATCACACACCA;RSEQ=GCTGACTCCTCCACACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:157:79,78:0,0:1:0,2:28.6:1:30.5:1:1:0:60:38.25:1:0:2.1 1/1:101:100:50,50:0,0:0.9901:0,2:26:1:30.5:1:1:0:60:99:0.99:0:2.2 -21 43124240 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGAGGGGAAACACCCT;RSEQ=CCAGCGAGAGACCCGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:39,70:0.018:2,2:40:1:30:1:1:1.78:60:4:0.0192:0:3 0/0:42:0:0,0:16,24:0:2,0:23:1:30.8:1:1:0:60:80:0.9524:0:1.5 -21 43124280 . CAT TGC 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02756;SOR=0;LSEQ=CCCAACTCCCCCCACCCCAC;RSEQ=GCCCCCGCCCAGCCTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:11:0,11:2,31:0.2292:2,0:17.2:1:32:1:1:0:60:22:0.2391:0.0625:1.4 0/0:18:0:0,0:2,16:0:2,0:22.1:1:31.3:1:1:0:60:36:1:0:0.7 -21 43124322 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54023;SOR=0;LSEQ=CTGCAGCTGTAGTCCTAAGC;RSEQ=GGGCCACTCTGCCCGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:0,18:0.1:1,0:11:1:28.5:1:1:0:60:4:0.1:0:2 0/0:10:0:0,0:0,10:0:0,0:25.5:1:31.2:1:1:0:60:20:1:0:0 -21 43124367 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=CAGTGCCTTGGCCTCGAGGA;RSEQ=GCCCCACGTGTTGGGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:45:1:32:1:1:0:60:4:0.25:0:2 0/0:5:0:0,0:0,5:0:0,0:26.6:1:32.2:1:1:0:60:10:1:0:0.2 -21 43124416 . A C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCTGCAACCTGCAAA;RSEQ=CTCCCAGCTTCTCGCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:3:0:23.5:1:1:0:60:1:1:0:1 1/1:2:2:0,2:0,0:1:0,0:24:0:33:0:1:0:60:4:1:0:1 -21 43174165 . A T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=0.42987;LSEQ=TTGTATACTATTTACATTTA;RSEQ=CTGCTTCATGAAGTAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:0.8333:0,0:17.2:1:31.1:1:1:0:60:20:0.8333:0:1.1 1/0:3:2:2,0:1,0:0.6667:0,0:16:1:32:0:1:0:60:4:0.6667:0:1 -21 43174284 . G T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17903;SOR=2.17926;LSEQ=TGGCAACTTAGGATCTAATT;RSEQ=CAGGATTCTGGATTACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:8:8,0:43,1:0.1538:1,0:26.3:1:28.8:1:1:0:60:7:0.1373:0:1 0/1:35:10:8,2:24,1:0.2857:1,2:17.1:1:29.4:1:0.19022:5.63898:60:20:0.2941:0:1 -21 43174332 . G C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.26226;LSEQ=ATTGAATAACTGTCTACTGA;RSEQ=GACTGCCCAGAAGCCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:13:10,3:117,29:0.0813:2,2:28.1:1:31.2:1:0.72606:1.20883:60:26:0.0833:0:1 0/1:116:37:28,9:60,19:0.319:2,2:24.8:1:30.9:1:1:1.01491:60:74:0.3246:0:1.1 -21 43174337 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18848;SOR=Inf;LSEQ=ATAACTGTCTACTGAGGACT;RSEQ=CCCAGAAGCCCAGTGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:138,36:0:2,0:22.5:1:31.6:1:1:0:60:28:1:0:0.2 0/1:134:2:1,1:99,33:0.0149:2,2:39:1:29.5:1:0.44451:2.97043:60:4:0.0154:0:2 -21 43174348 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17988;SOR=Inf;LSEQ=CTGAGGACTGCCCAGAAGCC;RSEQ=AGTGGTCAGTCCATGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:165,57:0:2,0:22.7:1:30.9:1:1:0:60:36:1:0:0.2 0/1:164:2:1,1:117,45:0.0122:2,2:17:1:27.5:1:0.48354:2.58256:60:4:0.0123:0:1 -21 43174396 . G A 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30953;SOR=4.40021;LSEQ=ACTTCGTCTTCAGGAACAAA;RSEQ=GCGCTGACTCTCAGAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:1,0:212,179:0.0026:2,0:1:0:25:0:1:0:60:2:0.0026:0:1 0/1:269:3:3,0:155,110:0.0112:2,0:15:1:20.7:1:0.27134:0:60:2:0.0077:0:3 -21 43174436 . A C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.78078;LSEQ=CGACACACACTCCCTGCTGC;RSEQ=CTCTACGCACACCAGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:115:54,61:132,156:0.2854:2,2:27.7:1:31:1:0.91195:1.05:60:114:0.285:0:1.4 1/0:294:177:85,92:57,60:0.602:2,2:26.8:1:29.9:1:1:1.02815:60:58:0.6021:0:1.3 -21 43174491 . T C 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20099;SOR=1.37415;LSEQ=ATAAGTATGTCACGTAAAGG;RSEQ=ATTTTTCGGTTTGTTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:45:13,32:73,141:0.1737:2,2:23:1:30.7:1:0.60221:1.27325:60:44:0.1719:0:1.7 0/1:214:48:15,33:59,107:0.2243:2,2:25.2:1:31.8:1:0.61037:1.21201:60:96:0.2286:0:1.8 -21 43791944 . A T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGTAATGGAGCCCCTGG;RSEQ=ATTCAGTGGATGATTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:30.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 43792665 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCAACAGAGCGAGACTCCA;RSEQ=CTCAAAAAAACAAAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:32:0:1:0:60:4:1:0:1 -21 43795470 . GC G 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=CCGCACTGTCTCAGCCCCCC;RSEQ=CCCCTCCCACTTTCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:31:1:1:0:60:4:1:0:0 0/0:5:0:0,0:3,2:0:2,0:30.2:1:30:1:1:0:60:10:1:0:1 -21 43995829 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19501;SOR=Inf;LSEQ=AAATGAGTTGAGAATTTCAG;RSEQ=AATATCAACTCACTCAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:191,60:0:2,0:22.1:1:30.2:1:1:0:60:124.5:1:0:0.2 0/1:199:2:1,1:151,46:0.0101:2,2:40:1:32:1:0.41749:3.25822:60:4:0.0102:0:1 -21 43995923 . G A 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=1.599;LSEQ=CACATACAAAATCAAATACC;RSEQ=ACTCTCAACCTATGAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:310:157,153:179,165:0.474:2,2:25.7:1:29.9:1:0.75419:1.0571:60:37.75:0.4697:0:1.7 1/0:564:333:157,176:115,114:0.5904:2,2:26.6:1:29:1:0.49273:1.1306:60:26.75:0.5868:0:1.8 -21 43995954 . A G 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.87639;LSEQ=TATGAACTTACTAGGTTTAA;RSEQ=TGGCTGTTCTTTGGATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:238:100,138:136,156:0.4482:2,2:25.5:1:31.8:1:0.33384:1.20265:60:78.333:0.4502:0:1.8 1/0:452:273:111,162:81,98:0.604:2,2:23.2:1:30.9:1:0.38131:1.20578:60:67.25:0.6072:0:1.9 -21 43995980 . G T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0346;SOR=Inf;LSEQ=GTTCTTTGGATCATCTGTGG;RSEQ=TTCTTTTAATGCCTGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:122,265:0:2,0:24.7:1:31.5:1:1:0:60:76.4:1:0:0.8 0/1:295:4:2,2:104,187:0.0136:2,2:12:1:29:1:0.62033:1.79:60:8:0.0138:0:1.8 -21 44513091 . C G 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01365;SOR=Inf;LSEQ=TTATCACTACAAATTTTATT;RSEQ=AGAAACCCATCTTTGTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:99,3:0:1,0:27.1:1:31.4:1:1:0:60:101:1:0:0.2 0/1:77:5:3,2:69,3:0.0649:1,2:25:1:31.6:1:0.0315:14.03092:59:10:0.0658:0:1 -21 44513110 . GT G 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.82933;SOR=0.87396;LSEQ=TCAGAAACCCATCTTTGTAT;RSEQ=TTTTTTTTTTGTTGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:13:11,2:128,6:0.0884:1,2:22.3:1:32.2:1:0.14928:3.82244:60:26:0.0884:0.0204:0.1 0/1:128:10:9,1:103,14:0.0781:2,2:19.8:1:32:1:1:1.22:60:20:0.0787:0.0234:0.1 -21 44513131 . T TA 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.29619;SOR=0.38345;LSEQ=TTTTTTTTTTTGTTGTTTTT;RSEQ=AAAAAAAATTCCCCTTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:6:4,2:197,28:0.026:2,2:16:1:29.8:1:0.17557:3.48929:47:12:0.0267:0.013:0.5 0/1:198:2:2,0:151,45:0.0101:2,0:13.5:1:27:1:1:0:60:4:0.0103:0.0051:1.5 -21 44513287 . G A 101 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.18716;SOR=1.99171;LSEQ=CCGCCGCCACCTCCACCACC;RSEQ=CCACCGCCACCGCCACGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1048:7:5,2:481,556:0.0067:2,2:14.6:1:24.7:1:0.26084:2.89:60:6:0.0059:0:1.9 0/1:1059:14:9,5:491,548:0.0132:2,2:19.1:1:26.7:1:0.28219:2.01:60:13:0.013:0:1.4 -21 44513411 . G A 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57948;SOR=2.66785;LSEQ=CATCCAAACCACGGCACGCA;RSEQ=CACAGAACCACACCCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:1,0:54,203:0.0039:2,0:1:0:29:0:0.21318:0:60:2:0.004:0:1 0/1:195:2:1,1:45,147:0.0103:2,2:23:1:26:1:0.41894:3.24:60:4:0.0104:0:1 -21 44513420 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.15653;SOR=Inf;LSEQ=CACGGCACGCAGCACAGAAC;RSEQ=ACACCCACTCTCTCAACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:40,196:0:2,0:23.3:1:31.7:1:1:0:59.9:117:1:0:0.2 0/1:155:2:1,1:29,124:0.0129:2,2:23:1:27.5:1:0.35065:4.22:60:4:0.0131:0:1 -21 44513429 . T C 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.55877;SOR=3.34865;LSEQ=CAGCACAGAACCACACCCAC;RSEQ=CTCTCAACACGCGCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:18,176:0.0051:2,0:32:0:11:0:1:0:45:0:0:0:4 0/1:118:2:1,1:14,101:0.0169:2,2:28:1:31:1:0.24094:7.00:60:4:0.0183:0:1 -21 44513479 . ACTG A 101 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.04506;SOR=3.07112;LSEQ=CGGCACTGATAAGGAAAAAC;RSEQ=CTGAAGAGACTGCACGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:7:0,7:2,80:0.0787:1,0:22.3:1:27.9:1:1:0:57.9:6:0.0674:0.0337:1.6 0/1:43:9:0,9:1,33:0.2093:1,0:28.1:1:32.1:1:1:0:60:18:0.2093:0:0.8 -21 44513500 . C T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20102;SOR=2.57907;LSEQ=CTGCTGAAGAGACTGCACGC;RSEQ=GTGACTGAGACACACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:0,5:2,52:0.0847:1,0:19:1:26.8:1:1:0:57:4:0.0714:0:2.2 0/1:36:7:0,7:1,28:0.1944:1,0:25.4:1:30.3:1:1:0:60:14:0.1944:0:1 -21 44514488 . G A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36743;SOR=1.32102;LSEQ=GCCTTTTAAAAAACAGAAAC;RSEQ=ACACCTATGCCAAAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:33:29,4:106,12:0.2185:2,2:22:1:29.7:1:0.75234:1.21675:60:15.5:0.2095:0:1.1 0/1:100:27:24,3:67,5:0.27:2,2:26.9:1:29:1:0.67968:1.66549:60:26:0.2653:0:1.1 -21 44514503 . AT A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1776;SOR=0.49516;LSEQ=GAAACGACACCTATGCCAAA;RSEQ=TTTTTTTTTGGAAGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:15:12,3:162,32:0.0718:2,2:26.4:1:31:1:0.72102:1.2641:60:30:0.0721:0.0096:0.3 0/1:163:6:4,2:122,34:0.0368:2,2:16:1:31.7:1:0.6154:1.7867:59.2:12:0.0373:0.0123:0.8 -21 44514514 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07653;SOR=Inf;LSEQ=TATGCCAAAATTTTTTTTTT;RSEQ=GAAGGGGGAGGGTTGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:208,58:0:2,0:22.7:1:31.4:1:1:0:60:87.667:1:0:0.3 0/1:198:3:1,2:142,53:0.0152:2,2:15:1:23.3:1:0.18725:5.30498:60:2:0.0102:0:2 -21 44514969 . A ATG 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00048;SOR=2.52103;LSEQ=TCTCAATTACCAATCCAAGT;RSEQ=TATCAGAGAGAGATATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:40:3,37:6,80:0.315:2,2:24.4:1:30.3:1:1:1.08:59.9:80:0.3252:0.0866:0.1 1/0:119:64:5,59:3,52:0.5378:2,2:21.2:1:30.5:1:0.72369:1.46:59.9:63:0.5385:0.1681:0.1 -21 44515346 . T C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6457;SOR=1.83303;LSEQ=ACCGCCACATATGACGCAGC;RSEQ=GGTAGGCGCCGAGCCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:7,1:14,1:0.3478:1,2:24.9:1:28.9:1:1:1.93655:60:7:0.3182:0:1.1 1/0:6:3:2,1:3,0:0.5:0,2:22.7:1:31.7:1:1:0:60:6:0.5:0:1.3 -21 44515504 . T C 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=1.84311;LSEQ=TCGCCTGTTGGCCTTGGCCC;RSEQ=GGCACACTAAGCGGCCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:111:83,28:191,66:0.3008:2,2:25.3:1:30.3:1:1:1.02:60:222:0.3016:0:1.1 0/1:339:150:111,39:139,50:0.4425:2,2:24.3:1:29.5:1:1:1.02:60:74:0.4431:0:1.1 -21 44515685 . T C 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.26063;LSEQ=GGTTTAAGACTCGTTATACA;RSEQ=TACAAAGTGTCATTAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:607:159:62,97:210,236:0.2619:2,2:24.6:1:32.3:1:0.09452:1.39139:60:158:0.2651:0:1.1 0/1:631:281:130,151:151,196:0.4453:2,2:25:1:31.4:1:0.51886:1.12:60:92.667:0.4462:0:1.1 -21 44520474 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22103;SOR=Inf;LSEQ=CTCTAGTGAAACGCGGTCCT;RSEQ=GACACTAGCACGGCAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:159,14:0:2,0:21.7:1:30:1:1:0:60:85.5:1:0:0 0/1:154:2:2,0:131,21:0.013:2,0:7:1:29.5:1:1:0:60:4:0.0132:0:1 -21 44521550 . GA G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.76109;SOR=1.26397;LSEQ=GAATCAAGATGGTCTGCGGG;RSEQ=AAAAAAAATAAAAAGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:4:2,2:67,179:0.0159:2,2:17.5:1:27.4:1:0.30566:2.66:60:8:0.0163:0.004:0.5 0/1:299:6:0,6:90,202:0.0201:2,0:19.2:1:32.2:1:0.18316:0:60:12:0.0205:0:0.2 -21 44524006 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CAATCACGCTAACTTGGAAG;RSEQ=TGGCTCCATCACCTCTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:29:1:30.7:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1 -21 44524290 . A C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-04;SOR=0.08199;LSEQ=GCCTCACTATTATTTAAATA;RSEQ=AAGAACACACTTATGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:22,0:37,1:0.3667:1,1:22.2:1:31.9:1:1:0:60:44:0.3667:0:1.1 0/1:45:2:2,0:42,1:0.0444:1,0:10:1:29:1:1:0:60:4:0.0444:0:1 -21 44527249 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGAGGCGGCTTCCGGGAG;RSEQ=CGGCGACTCGGAGGCCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:16:0:32:0:1:0:60:2:1:0:0 1/0:4:2:1,1:0,2:0.5:0,2:10:1:31:1:1:0:60:4:0.6667:0:2 -21 44527289 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTCGGGCGATCAGCCAGT;RSEQ=CGGACCCCAAGGCCGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:42.5:1:29.5:1:1:0:60:4:0.5:0:2 -21 44527361 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCATTCTGCCCGCTCCA;RSEQ=TTTTCCGCCGCGCGGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:1:28:1:1:0:60:4:1:0:1.5 -21 44527669 . T G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.83258;LSEQ=CGCCGACCCTGCCGACGCCC;RSEQ=CGGGAGACGTCACCCGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:135:33,102:105,271:0.2642:2,2:24.6:1:31.2:1:0.49804:1.19716:60:32.75:0.2636:0:1.1 1/0:444:224:55,169:63,156:0.5045:2,2:25.5:1:30.9:1:0.33461:1.2403:60:43.8:0.5093:0:1.2 -21 44529540 . A T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGACACGGTCTGGGAAC;RSEQ=AAGACTGCTGGAGAGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:24.5:1:28.5:1:1:0:60:4:0.6667:0:1 -21 44588757 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGTGTCTAACGGGGGTGTG;RSEQ=GCTCTCCCTCCTCTGGCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:29:1:1:0:60:4:1:0:2 -21 44589215 . C T 84 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67277;SOR=1.63263;LSEQ=GTACCAAAGCTGAACATGGA;RSEQ=GTGACCATCCAGCACCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:1,7:3,7:0.4444:2,2:20.5:1:28:1:0.58824:2.83009:60:7:0.4118:0:1 1/0:7:4:2,2:1,2:0.5714:2,2:3.5:1:29.8:1:1:1.81:60:8:0.5714:0:1 -21 44985111 . G A 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=TCGTCTCAGGCTCGTAGTTC;RSEQ=CCTTCAACATGCCGGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:48,7:0:2,0:23.4:1:30:1:1:0:48.1:26.5:0.9815:0:0.1 0/1:39:9:9,0:26,4:0.2308:2,0:11.8:1:29.3:1:0.55575:0:50.9:18:0.2308:0:1.3 -21 44985199 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49816;SOR=0;LSEQ=TAAGGCGCAGAAGAAGGACG;RSEQ=CAGGAAGCGCAAGCGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:52,54:0.0185:2,2:27:1:28.5:1:1:1.04:49:4:0.0189:0:1 0/0:101:0:0,0:53,48:0:2,0:24.6:1:30.9:1:1:0:45.8:100:1:0:0.4 -21 44985202 . G A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15985;SOR=0.5971;LSEQ=GGCGCAGAAGAAGGACGGCA;RSEQ=GAAGCGCAAGCGCAGCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:24:8,16:41,40:0.2286:2,2:25.1:1:30.4:1:0.16575:2.03622:34:23:0.2233:0:1.2 0/1:100:15:4,11:48,37:0.15:2,2:22.2:1:29.7:1:0.04861:3.52331:34.7:14:0.1443:0:1.6 -21 44985211 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49777;SOR=0;LSEQ=GAAGGACGGCAGGAAGCGCA;RSEQ=GCGCAGCCGCAAGGAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:42,57:0.0198:2,2:43.5:1:31:1:1:1.35:49.5:4:0.02:0:1.5 0/0:96:0:0,0:48,48:0:2,0:28.3:1:30.2:1:1:0:44.6:95:1:0:0.4 -21 44985219 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24607;SOR=Inf;LSEQ=GCAGGAAGCGCAAGCGCAGC;RSEQ=GCAAGGAGAGCTACTCCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:42,54:0:2,0:27.7:1:30.7:1:1:0:41.9:95:1:0:0.5 0/1:95:2:1,1:44,49:0.0211:2,2:41.5:1:30:1:1:1.11:49:4:0.0213:0:1 -21 44985235 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4985;SOR=0;LSEQ=CAGCCGCAAGGAGAGCTACT;RSEQ=CGTATACGTGTACAAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:48,54:0.0192:2,2:33:1:30:1:1:1.12:27:4:0.0194:0:1 0/0:95:0:0,0:48,47:0:2,0:27.9:1:30.6:1:1:0:41.6:94:1:0:0.3 -21 44985272 . C T 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11953;SOR=0.58953;LSEQ=GTGCTGAAGCAGGTCCACCC;RSEQ=GACACCGGCATCTCCTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:35:18,17:27,41:0.3398:2,2:27.5:1:30.5:1:0.29763:1.60:36:70:0.3431:0:1.2 0/1:99:23:13,10:32,44:0.2323:2,2:21.7:1:30.1:1:0.24208:1.78:33.7:46:0.2323:0:1.4 -21 44985333 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50554;SOR=Inf;LSEQ=CCTTCGTCAACGACATCTTC;RSEQ=AACGCATCGCAGGTGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:32,54:0:2,0:26:1:30.5:1:1:0:47:172:1:0:0.3 0/1:111:2:1,1:43,66:0.018:2,2:16:1:28:1:1:1.53:27:4:0.018:0:1 -21 44985473 . C T 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43297;SOR=0.76875;LSEQ=GTGTCCGAGGGCACCAAGGC;RSEQ=GTCACCAAGTACACCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:30:20,10:29,23:0.3659:2,2:26.7:1:30.4:1:0.36023:1.58:52:60:0.3659:0:1 0/1:101:31:16,15:40,30:0.3069:2,2:27.4:1:30.1:1:0.66713:1.24721:53.6:30:0.303:0:1.2 -21 45648880 . C T 226 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=325.31583;LSEQ=CCTCTCACGGTGGCGTCTCA;RSEQ=GGAAGCCCTGTCCACGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:844:1:0,1:513,330:0.0012:2,0:1:0:15:0:0.39218:0:60:0:0:0:1 0/1:756:210:121,89:328,218:0.2778:2,2:21.1:1:29.4:1:0.56316:1.10653:60:34:0.2738:0:1.2 -21 45648992 . T C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21377;LSEQ=TTCCCTTCTGCAGGCAGACG;RSEQ=CGGTTTTCTCAGGACTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:844:712:269,443:56,75:0.8436:2,2:25.9:1:31:1:0.28451:1.22932:60:43.5:0.8447:0:1.1 1/0:751:402:174,228:135,210:0.5353:2,2:26:1:30.8:1:0.26416:1.19:60:29.923:0.5351:0:1.2 -21 45649209 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22727;SOR=0;LSEQ=TCCACAGGTGACACCACAGC;RSEQ=TGGTGGCTGCGCACACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:4,13:0,0:1:0,2:20.8:1:29.8:1:1:0:60:16:1:0:1.2 1/1:5:4:0,4:0,1:0.8:0,0:26.3:1:32.5:1:1:0:60:8:0.8:0:1 -21 45649428 . A T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51167;SOR=0;LSEQ=CACATCTATGTTGCTCCTGG;RSEQ=ACTGAGGGGCAAACGAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:110,59:0.0117:2,2:12:0:30.5:1:1:1.85726:60:4:0.0119:0:1 0/0:123:0:0,0:81,42:0:2,0:26.3:1:29:1:1:0:60:60.5:1:0:0.6 -21 45649437 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19561;SOR=Inf;LSEQ=GTTGCTCCTGGAACTGAGGG;RSEQ=CAAACGAGAGCTGCAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:120,66:0:2,0:29.2:1:31.4:1:1:0:60:61:1:0:0.8 0/1:148:2:1,1:91,55:0.0135:2,2:24.5:1:28:1:1:1.64862:60:4:0.0137:0:1.5 -21 45649481 . G T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07872;SOR=Inf;LSEQ=TGCCACAGAGAGAAGCTGGC;RSEQ=GTGCCCGGACCCACTCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:141,137:0:2,0:24:1:29.6:1:1:0:59.6:38.714:1:0:1.5 0/1:211:3:0,3:119,89:0.0142:2,0:7.7:1:21.7:1:0.08136:0:60:2:0.0096:0:3 -21 45649487 . C T 111 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44139;SOR=1.41205;LSEQ=AGAGAGAAGCTGGCGGTGCC;RSEQ=GGACCCACTCCGGACACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:14:8,6:136,137:0.0488:2,2:6.4:1:30.6:1:0.78525:1.34:48.9:28:0.0504:0:3.4 0/1:222:15:8,7:114,93:0.0676:2,2:4.6:1:28.5:1:1:1.07223:54.7:14:0.0633:0:3.2 -21 45649494 . A G 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02576;SOR=0.55124;LSEQ=AGCTGGCGGTGCCCGGACCC;RSEQ=CTCCGGACACCCCACAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:294:266:130,136:15,12:0.9048:2,2:26.8:1:30.1:1:0.54936:1.30649:60:37:0.9056:0:1.7 1/1:243:204:109,95:21,16:0.8395:2,2:24.8:1:30.3:1:0.72434:1.14329:59.7:67:0.841:0:1.6 -21 45649499 . G A 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=0.47907;LSEQ=GCGGTGCCCGGACCCACTCC;RSEQ=GACACCCCACAGGGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:101:51,50:101,113:0.3196:2,2:28.1:1:30.1:1:0.62961:1.14:60:32.667:0.3192:0:2.1 0/1:267:49:27,22:115,103:0.1835:2,2:24.9:1:29.9:1:0.87431:1.10:60:48:0.1832:0:2.1 -21 45649509 . CA TG 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.89796;SOR=1.03266;LSEQ=GACCCACTCCGGACACCCCA;RSEQ=GGGGCTGGGCGCCGGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:36:18,18:155,169:0.0997:2,2:20.2:1:30.6:1:0.86138:1.09:45.8:35:0.0997:0.0083:3.1 0/1:302:31:16,15:143,127:0.1026:2,2:18.6:1:30:1:1:1.05545:52.3:62:0.1033:0.0166:2.6 -21 45649510 . A G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10753;SOR=0.68207;LSEQ=ACCCACTCCGGACACCCCAC;RSEQ=GGGGCTGGGCGCCGGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:55:34,21:128,153:0.1491:2,2:8.7:1:30.2:1:0.03818:1.93:58:54:0.1636:0:1.4 0/1:300:32:18,14:129,113:0.1067:2,2:8.5:1:27.2:1:0.8511:1.13:54.9:15:0.1107:0:1.2 -21 45649543 . G C 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01091;SOR=0.65796;LSEQ=CGGTGCCTGGACCCGCCCTG;RSEQ=ACACCCCACGGGGGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:145:59,86:241,175:0.2585:2,2:22.5:1:31.4:1:0.00048:2.00485:60:23.167:0.255:0:1.7 0/1:370:69:28,41:171,130:0.1865:2,2:25.3:1:31.6:1:0.0162:1.92268:59.6:138:0.1938:0:1.8 -21 45649580 . A G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23814;SOR=0.70932;LSEQ=GGGCGCCGGTGCCTGGACCC;RSEQ=CTCCGGACACCCCATGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:663:43:26,17:385,235:0.0649:2,2:24.7:1:28:1:0.87152:1.07108:43.6:7.6:0.0586:0:4.1 0/1:448:21:13,8:257,169:0.0469:2,2:25.5:1:29.6:1:1:1.07:42.5:20:0.0455:0:4.1 -21 45649582 . T C 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50577;SOR=0.82643;LSEQ=GCGCCGGTGCCTGGACCCAC;RSEQ=CCGGACACCCCATGGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:663:39:23,16:386,238:0.0588:2,2:24.6:1:29.4:1:0.73625:1.12803:42.6:18.5:0.0579:0:4.3 0/1:448:22:12,10:256,170:0.0491:2,2:24.8:1:28.9:1:0.65844:1.25424:42.9:10:0.0456:0:4.2 -21 45649584 . C T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34068;SOR=0.73781;LSEQ=GCCGGTGCCTGGACCCACTC;RSEQ=GGACACCCCATGGGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:39:23,16:389,241:0.0583:2,2:22.6:1:29.1:1:0.73688:1.12266:42.6:12:0.055:0:4.3 0/1:458:20:11,9:262,175:0.0437:2,2:22.9:1:29.5:1:0.6496:1.22437:41.6:19:0.042:0:4.1 -21 45649595 . T C 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.44262;SOR=0.75951;LSEQ=GACCCACTCCGGACACCCCA;RSEQ=GGGGGCTGGGCGCCGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:691:29:18,11:416,246:0.042:2,2:15.3:1:29.3:1:1:1.0334:42.6:28:0.042:0:4.4 0/1:497:16:10,6:287,193:0.0322:2,2:15.4:1:29.3:1:1:1.12:42.9:32:0.0327:0:4.3 -21 45649640 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=4.60008;LSEQ=CCCGCCCTGGACACCCTGGT;RSEQ=GGGGCTGGGCACTGGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:104:60,44:408,286:0.13:2,2:23.7:1:29.7:1:0.83176:1.04606:60:33.667:0.1283:0:1.2 0/1:709:289:170,119:252,167:0.4076:2,2:22.1:1:29.7:1:0.75548:1.05619:60:95.333:0.4086:0:1.2 -21 45649666 . G A 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1e-05;SOR=0.66375;LSEQ=TGGGCACTGGGGAGCGCGGG;RSEQ=GTCTAGCACTCGTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:962:496:272,224:261,203:0.5156:2,2:27.2:1:30.4:1:0.69667:1.05874:60:69.857:0.5186:0:1.2 0/1:947:392:219,173:301,251:0.4139:2,2:25.1:1:29.7:1:0.69089:1.06:60:97:0.4163:0:1.2 -21 45649748 . C T 195 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGCACACCAGGATGCCATC;RSEQ=CATGCCAAGGGGAGGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:88:43,45:334,377:0.11:2,2:24.4:1:30.2:1:0.82104:1.08:60:43:0.1101:0:1.9 0/0:770:0:0,0:363,407:0:2,0:23.1:1:30.1:1:1:0:60:50.333:1:0:0.5 -21 45649778 . A G 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13215;LSEQ=GGGAGGCTGCAGGAAATGCC;RSEQ=TGCGCACCATCGAGGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:749:635:273,362:51,62:0.8478:2,2:24.2:1:30.8:1:0.68143:1.09062:60:62.5:0.8503:0:1.5 0/1:654:277:115,162:172,204:0.4235:2,2:23.7:1:30.5:1:0.30016:1.18741:60:554:0.4288:0:1.4 -21 45649848 . T C 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.16216;LSEQ=AGGCAAGGGACTTTTGCCTT;RSEQ=TGAAAGTTTTTTGAAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:892:756:400,356:71,62:0.8475:2,2:24.5:1:31.6:1:0.9253:1.01917:60:93.5:0.8519:0:1.3 0/1:705:334:177,157:184,186:0.4738:2,2:22.5:1:31.2:1:0.40666:1.14:60:110.333:0.4749:0:1.3 -21 45650007 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13782;SOR=Inf;LSEQ=AAAATGGTCAGGGCAGCAGC;RSEQ=ATGGGGGGTGTCCCTAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:30,252:0:2,0:22.5:1:30.6:1:1:0:60:30.333:1:0:1.1 0/1:167:2:1,1:21,144:0.012:2,2:17:1:27.5:1:0.24681:6.72:60:4:0.0122:0:1 -21 45650009 . T C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=0.31434;LSEQ=AATGGTCAGGGCAGCAGCGA;RSEQ=GGGGGGTGTCCCTAAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:275:174:19,155:2,36:0.6327:2,2:19.9:1:29.8:1:0.38101:2.20:60:86:0.823:0:1.2 0/1:154:54:10,44:7,72:0.3506:2,2:21.7:1:29.3:1:0.11805:2.32:60:17:0.3864:0:1.2 -21 45650085 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00205;SOR=0.1932;LSEQ=CCCTACTTGGAAGTCTCCCC;RSEQ=AGGCTCCCAGCTCCAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:53:0,53:0,12:0.8154:0,1:21.5:1:31.6:1:1:0:60:52:0.8387:0:1.5 0/1:22:10:1,9:1,11:0.4545:2,2:16.7:1:30.4:1:1:1.21:60:20:0.4545:0:1.8 -21 45650800 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTGCTCTGTCGCCCAGG;RSEQ=TGGAGTGTAGTGGCGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:28.5:1:32:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 45651003 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00828;SOR=Inf;LSEQ=ATCTCGTGATCCACTCGCCT;RSEQ=GGCCTCCCAAAGTGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:52,0:0:1,0:28:1:31.3:1:1:0:57:104:1:0:0.1 0/1:24:4:4,0:20,0:0.1667:1,0:27:1:31.3:1:1:0:60:8:0.1667:0:1 -21 45651275 . G A 212 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02521;LSEQ=CACGTGGCCGCGTTTTTCTC;RSEQ=CCGGTACTGACTGGATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1141:151:71,80:455,532:0.1323:2,2:25.1:1:29.3:1:0.86108:1.04:60:36.75:0.1311:0:1.2 0/0:1044:4:3,1:523,516:0.0038:2,2:8.8:1:27.3:1:0.62434:2.96:60:8:0.0039:0:1 -21 45651380 . C CT 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.65576;SOR=2.02191;LSEQ=GGATCTTAGAGGAAAAGGGT;RSEQ=TTTTTTTTCATCCTTGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:2:0,2:81,313:0.0051:2,0:27.5:1:28.5:1:1:0:60:4:0.0051:0:0 0/1:295:3:1,2:62,230:0.0102:2,2:34.3:1:30:1:0.51495:1.85:60:6:0.0103:0:0.7 -21 45651413 . A G 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CTTGAGTAGAAAGTGTTGCA;RSEQ=GGAAGTATTTATTCCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:180:180:8,172:0,0:1:0,1:24.5:1:30.9:1:1:0:60:35:1:0:1.2 1/1:118:106:4,102:1,11:0.8983:2,1:23.9:1:30:1:0.42079:2.29604:60:52:0.8966:0:1.2 -21 45651497 . A G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=0.05995;LSEQ=TGAGATGAGGGTTTTCTCTT;RSEQ=CAGAGGGGCTTCATTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:32:0,32:0,2:0.9412:0,1:20.8:1:32.6:1:1:0:60:31:0.9394:0:1.3 0/1:17:8:0,8:0,9:0.4706:0,0:26.3:1:32:1:1:0:60:16:0.4706:0:1.5 -21 45655124 . A T 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.004;SOR=1.84919;LSEQ=CCCTGGCCCCACTGTCGGGC;RSEQ=CAGCTCAGCACGCAGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:96:64,32:88,25:0.4593:2,2:27:1:30.2:1:0.0865:1.75521:60:95:0.4612:0:1.1 1/0:175:107:75,32:53,15:0.6114:2,2:28.4:1:29.7:1:0.29591:1.50408:60:106:0.6092:0:1 -21 45655163 . C T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34056;SOR=3.50579;LSEQ=CCGGGACCTTACCTGTCTGG;RSEQ=TGCCGACAGTCAGGTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:1:0,1:202,127:0.003:2,0:1:0:29:0:0.38788:0:60:2:0.0031:0:1 0/1:284:3:1,2:174,107:0.0106:2,2:24.7:1:28.7:1:0.56068:3.23848:60:6:0.0106:0:1 -21 45655658 . G A 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=AGTCCCAGTAGCCAGGGACC;RSEQ=CTGAGCCTGTCGGGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:20.5:1:31.5:1:1:0:60:4:0.2857:0:1 1/1:1:1:0,1:0,0:1:0,0:46:0:32:0:1:0:60:2:1:0:1 -21 45656668 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51337;SOR=0;LSEQ=ACTGGAAGAAACAGTGAATG;RSEQ=GCCAGGGAGGGGGTTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:116,12:0.0154:2,2:16.5:1:30:1:0.1907:9.32738:60:4:0.0154:0:1 0/0:91:0:0,0:79,12:0:2,0:24.7:1:29:1:1:0:60:90:1:0:0.1 -21 45656698 . C T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2604;SOR=0;LSEQ=GGGGTTTCATGAACACTTGT;RSEQ=CACGATGTGAGGCTGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:3:1,2:162,60:0.0133:2,2:7:1:21.3:1:0.18474:5.35215:60:2:0.009:0:2.3 0/0:174:0:0,0:131,43:0:2,0:24.7:1:30.8:1:1:0:60:86:1:0:0.3 -21 45656774 . C T 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01887;SOR=1.35327;LSEQ=CACATGCAGTGTAACCTCAA;RSEQ=GCTCAAAACCTCCTGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:223:136,87:183,131:0.4145:2,2:26.8:1:30.7:1:0.53411:1.12:60:222:0.4189:0:1.1 0/1:470:230:125,105:135,105:0.4894:2,2:27:1:29.5:1:0.71087:1.07982:60:31.857:0.4848:0:1.2 -21 45657140 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=GCAAAATCTGTTTTCGGAGG;RSEQ=TGATGCCCAGGCCATGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:15,132:0:2,0:24.8:1:32:1:1:0:60:72.5:1:0:0.1 0/1:123:2:0,2:19,102:0.0163:2,0:7.5:1:30.5:1:1:0:60:4:0.0164:0:1 -21 45657142 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19847;SOR=Inf;LSEQ=AAAATCTGTTTTCGGAGGCT;RSEQ=ATGCCCAGGCCATGAAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:13,132:0:2,0:24.6:1:30.8:1:1:0:60:28:1:0:0.1 0/1:117:2:1,1:17,98:0.0171:2,2:9.5:1:27:1:0.28515:5.63:60:4:0.0172:0:1.5 -21 45657848 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCTTGGCCTCCCAAAGT;RSEQ=CTGGGATTACAGGAGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:16:1:33.5:1:1:0:48.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -21 45657970 . T C 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAGGTTTGTGCTGCGGTGC;RSEQ=TCGTCCTTATTCCTGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:10.7:1:30:1:1:0:60:6:0.75:0:1 1/1:2:2:1,1:0,0:1:0,2:31.5:1:32.5:1:1:0:60:4:1:0:1 -21 45658256 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02145;SOR=Inf;LSEQ=AGGCTGCTCCCAGTGCCCTG;RSEQ=GGCCAGCAGTCCACACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:300,151:0:2,0:26:1:31.3:1:1:0:60:89.2:1:0:0.1 0/1:392:5:1,4:252,135:0.0128:2,2:6:1:27:1:0.05546:7.42883:60:10:0.013:0:1.2 -21 45658443 . C T 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTATCTTCCAAACAGGAA;RSEQ=AGGCTGGTTCCCATGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:506:0:0,0:155,351:0:2,0:24.5:1:31.7:1:1:0:60:83.333:1:0:0.3 0/1:408:22:7,15:120,265:0.0539:2,2:22.4:1:28.1:1:1:1.03:60:44:0.0549:0:1 -21 45658474 . A G 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02479;SOR=1.53925;LSEQ=CCATGAGCAGGAGGTAGTTA;RSEQ=GCCCATCACAGAAATGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:115:12,103:23,131:0.4275:2,2:24.7:1:31.3:1:0.36006:1.50476:60:114:0.4318:0:1.2 1/0:200:107:12,95:12,81:0.535:2,2:23.8:1:30.1:1:0.82807:1.1719:60:52.5:0.5385:0:1.1 -21 45658538 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12288;SOR=Inf;LSEQ=CTCTGTTCTCCATGGGAATT;RSEQ=GGGGTCCGGGGCCAGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:1,86:0:1,0:22.7:1:29.6:1:1:0:60:86:1:0:0.3 0/1:48:2:0,2:0,46:0.0417:1,0:26.5:1:30.5:1:1:0:60:4:0.0426:0:1.5 -21 45660599 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=GCACCTCCAGGCGAGCCCCG;RSEQ=AGGCCCCGCGTCCGAGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:26.5:1:27.5:1:1:2.64575:60:4:0.2:0:1 0/0:7:0:0,0:4,3:0:2,0:7.3:1:29.4:1:1:0:60:6:1:0:0.1 -21 45660631 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49503;SOR=Inf;LSEQ=CCGAGCCGAGCTGGGGACGC;RSEQ=CGGGCCGAGCCACCCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:25,14:0:2,0:17.5:1:30.5:1:1:0:60:38:1:0:0.2 0/1:43:2:1,1:28,13:0.0465:2,2:7.5:1:29.5:1:1:2.11228:60:4:0.05:0:1 -21 45660676 . C T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.04803;SOR=Inf;LSEQ=CCGCGGCGCCTCCGCTCCTT;RSEQ=CCCGGCTCACCTGCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:198,90:0:2,0:22.2:1:31.3:1:1:0:60:56.6:1:0:0.2 0/1:255:4:2,2:168,83:0.0157:2,2:16:1:25.5:1:0.6026:2.0181:60:3:0.0119:0:2 -21 45660682 . C T 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3766;SOR=0.27624;LSEQ=CGCCTCCGCTCCTTCCCCGG;RSEQ=TCACCTGCCCAGCCGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:4:1,3:229,102:0.0119:2,2:18.3:1:27.8:1:0.09293:6.69358:60:8:0.0121:0:1 0/0:302:1:0,1:190,111:0.0033:2,0:1:0:24:0:0.37086:0:60:2:0.0034:0:1 -21 45660698 . C T 51 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10733;SOR=5.57928;LSEQ=CCGGCTCACCTGCCCAGCCG;RSEQ=ATGGTGCGGGCGGAGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:1:0,1:315,179:0.002:2,0:1:0:24:0:0.36364:0:60:2:0.0021:0:1 0/1:447:5:1,4:264,178:0.0112:2,2:9.4:1:22.2:1:0.16352:5.91079:60:4:0.0091:0:1 -21 45660835 . C A 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0713;SOR=0.56185;LSEQ=GGCTCTAACTGCGCTCCCGC;RSEQ=GCGCCCGAGGCTCTGAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:68:3,65:6,58:0.5152:2,1:25.4:1:31.8:1:0.31445:2.22805:60:136:0.5231:0:1.1 0/1:67:25:2,23:4,38:0.3731:2,2:22.2:1:30.7:1:1:1.20713:60:50:0.3788:0:1.1 -21 46552894 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49025;SOR=Inf;LSEQ=AAAGCCACAGTCAGCGTTTC;RSEQ=CTGCCAGCTCCTCCAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:15,8:0:2,0:30.6:1:30.3:1:1:0:60:46:1:0:0 0/1:25:2:1,1:14,9:0.08:2,2:34:0:31.5:1:1:1.52748:60:4:0.08:0:1 -21 46552998 . T C 93 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GCGCAAAGCCCTGGTGAGCC;RSEQ=GGCTCGTTTCCCTGGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:29.9:1:31.1:1:1:0:60:16:1:0:1.9 1/0:7:5:0,5:0,2:0.7143:0,0:27:1:30.6:1:1:0:60:10:0.7143:0:1 -21 47061267 . A G 113 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33088;SOR=0.18157;LSEQ=CAGGAACTGCAAATAATAGA;RSEQ=AGTCTTTAGGGTCTAACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:4,9:0,2:0.8667:0,2:24.2:1:30.8:1:1:0:60:26:0.8667:0:1 1/0:2:1:0,1:0,1:0.5:0,0:47:0:30:0:1:0:60:2:0.5:0:1 -21 47061914 . TTTC T 28 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=17.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CCAGGCTTTTTTTTTTTTTT;RSEQ=TTCTATTTTAAGGTTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23:1:20.5:1:1:0:60:1:1:0:1.5 1/0:3:2:1,1:1,1:0.6667:2,2:21:1:28:1:1:1:60:4:0.6667:0.3333:1 -22 16345954 . A C 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00055;SOR=2.03479;LSEQ=AGTAACAAGCCTTAAATTTA;RSEQ=AGAAAAACCTACAGGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:41:26,15:307,184:0.0771:2,2:25.8:1:32.2:1:1:1.04:42.8:82:0.0785:0:1.1 0/1:523:76:51,25:264,183:0.1453:2,2:23.4:1:30.8:1:0.20605:1.41:43.4:152:0.147:0:1.1 -22 16346007 . A G 129 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=11.04012;LSEQ=GTAAGTATCTTCTCTTGTCC;RSEQ=TGGTGAAACTAATTCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:715:2:1,1:352,361:0.0028:2,2:18.5:1:29.5:1:1:1.03:53.5:4:0.0028:0:1 0/1:665:20:12,8:298,347:0.0301:2,2:29.8:1:30:1:0.25925:1.75:49.9:40:0.0305:0:1.1 -22 16346045 . T C 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.4692;LSEQ=GCAGATCCAGAGCTCTTGCT;RSEQ=TGTGTAAGTGTTTTTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:167:64,103:140,234:0.3087:2,2:24.8:1:31.9:1:0.84826:1.04:50.4:334:0.3145:0:1.1 0/1:491:85:25,60:145,261:0.1731:2,2:25.4:1:31.9:1:0.31611:1.33257:50.6:84:0.175:0:1 -22 16346071 . C T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00478;SOR=Inf;LSEQ=AAGTGTTTTTTTATGAAATA;RSEQ=GTCAAAATTACCACACTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:105,265:0:2,0:23.5:1:30.2:1:1:0:56.8:60.667:0.9973:0:0.4 0/1:327:7:1,6:101,219:0.0214:2,2:26.7:1:31:1:0.44162:2.7603:25.9:14:0.0214:0:1.1 -22 16346096 . T C 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06445;SOR=1.82598;LSEQ=AAATTACCACACTAAGTTCA;RSEQ=TTGGTTTAACTGAAACGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:21:2,19:32,170:0.0938:2,2:28.9:1:32.2:1:0.74877:1.78427:55.5:42:0.095:0:1 0/1:176:28:3,25:28,120:0.1591:2,2:22.6:1:32.2:1:0.41954:1.93818:57.9:56:0.1618:0:1 -22 16346113 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50397;SOR=0;LSEQ=TCATTTGGTTTAACTGAAAC;RSEQ=CCAAGACCTTGAGGGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:2,0:7,146:0.0129:1,0:6:1:30.5:1:0.00302:0:40:4:0.0131:0:2.5 0/0:125:0:0,0:14,111:0:2,0:21.5:1:31.5:1:1:0:55.2:40.667:1:0:0.3 -22 16346169 . G A 47 v4;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55248;SOR=0;LSEQ=CTTACTGATCCTTTCTGATC;RSEQ=TAACTGAAAACTAAGACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:3:3,0:9,68:0.0375:2,0:29.3:1:30:1:0.00268:0:40:6:0.038:0:2 0/0:45:0:0,0:3,42:0:2,0:27.2:1:31.2:1:1:0:46.1:44:1:0:0.2 -22 16346245 . G T 68 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.73106;LSEQ=ATTAGATCAGATTCTTAATT;RSEQ=CCCTTACCATTTCTTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:3,2:25,15:0.1111:2,2:18.8:1:29.4:1:1:1.10848:42.2:10:0.1111:0:1.2 0/1:12:1:1,0:6,4:0.0833:2,0:19:0:31:0:1:0:40:2:0.0833:0:1 -22 16346327 . T C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7688;LSEQ=TTAACATAACTAAGCTTCTC;RSEQ=AAGCTGGTATTCATTATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:8:8,0:107,22:0.0584:2,0:24.1:1:31.8:1:0.35427:0:55.4:16:0.0597:0:2 0/1:66:3:3,0:58,5:0.0455:2,0:21.3:1:30:1:1:0:48.3:6:0.0455:0:1.7 -22 16346383 . A T 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00392;SOR=0.35713;LSEQ=TGTCTGGTTATATCTGCATT;RSEQ=GGTTATTGTTGATGCTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:42:36,6:244,51:0.1246:2,2:23.4:1:30.5:1:0.82598:1.25:58.5:84:0.1265:0:2 0/1:207:10:8,2:158,39:0.0483:2,2:17.9:1:28.4:1:1:1.01276:59.5:9:0.0441:0:1.9 -22 16346391 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.39603;LSEQ=TATATCTGCATTAGGTTATT;RSEQ=TTGATGCTAGTGACAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:371:214:176,38:123,33:0.5768:2,2:23.6:1:28.9:1:0.42525:1.24:55.5:428:0.5784:0:1.3 0/1:237:83:64,19:127,26:0.3502:2,2:20.4:1:28.3:1:0.29968:1.44782:57.8:166:0.3532:0:1.3 -22 16346398 . C G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3602;SOR=1.53948;LSEQ=GCATTAGGTTATTGTTGATG;RSEQ=TAGTGACAATAAATTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:10:6,4:318,80:0.0244:2,2:29.8:1:30.5:1:0.12884:2.64205:32.7:20:0.025:0:1 0/1:269:10:6,4:205,54:0.0372:2,2:22.9:1:30.7:1:0.23009:2.52015:34.4:20:0.038:0:1.4 -22 16346480 . A G 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.22997;LSEQ=TAACTAGTCATTAAATGCTT;RSEQ=GTAGCACAGAAATTCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:191:92,99:252,285:0.2624:2,2:26.1:1:31:1:0.80038:1.05:47.8:62.667:0.2597:0:1.1 0/1:556:42:23,19:257,257:0.0755:2,2:21.9:1:30.4:1:0.63107:1.21:49.2:84:0.0765:0:1.2 -22 16346521 . C G 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25406;SOR=0.82981;LSEQ=TGGTTGCAGGAAATTTTGAT;RSEQ=TGCAGGAATAAATTTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:658:130:40,90:184,344:0.1976:2,2:24.1:1:32.1:1:0.40955:1.20315:37.2:260:0.1982:0:1.6 0/1:507:86:28,58:175,246:0.1696:2,2:28.4:1:31.4:1:0.14705:1.47248:35.2:85:0.1697:0:1.7 -22 16346553 . A G 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17303;SOR=0.77619;LSEQ=ATTTTTTTCTTAAAAATAAG;RSEQ=TAAACGAAATGACATCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:90:18,72:88,244:0.2133:2,2:27.6:1:32.1:1:0.22079:1.44144:33.5:180:0.2148:0:1.9 0/1:351:61:14,47:89,200:0.1738:2,2:26.3:1:31.1:1:0.27918:1.49231:35:60:0.1734:0:2 -22 16346747 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTATTCTGAAGCTTTGGC;RSEQ=GTAAAACCACACTGTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:1,18:0.0909:1,0:22:1:32:0:1:0:60:4:0.0909:0:1 0/0:3:0:0,0:1,2:0:2,0:21.7:1:30.3:1:1:0:60:6:1:0:0 -22 16347954 . A G 80 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53327;LSEQ=AATTTCCTTCAAGGTGGGGC;RSEQ=TAGAGATTGAGAGGAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:6:5,1:126,8:0.0429:2,2:21.5:1:31:1:0.33385:3.10978:31.7:12:0.0429:0:1 0/1:43:1:1,0:36,6:0.0233:2,0:33:0:32:0:1:0:25:2:0.0233:0:1 -22 16347994 . C A 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42832;SOR=0.75138;LSEQ=TTTTCTAGGAGAGTCTCAAA;RSEQ=AGGAAGACAACCGATATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:46:43,3:176,9:0.1991:1,2:24.8:1:30.7:1:0.70987:1.36235:45.5:92:0.2:0:1.1 0/1:89:14:12,2:70,5:0.1573:2,2:23.5:1:30.1:1:0.3028:2.30558:47.4:28:0.1573:0:1.1 -22 16348018 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10902;SOR=Inf;LSEQ=AAGACAACCGATATAAGTGT;RSEQ=TATTCCTCTTGGTTGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:307,47:0:2,0:22.2:1:30.6:1:1:0:42.7:117:1:0:0.2 0/1:175:2:1,1:149,24:0.0114:2,2:23:1:29.5:1:0.26601:6.10329:47:4:0.0118:0:1 -22 16348231 . T A 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50761;SOR=0.88932;LSEQ=AAGGGAACTCCTCTATGGTC;RSEQ=GCTTCTTTTGTAATTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:124:23,101:161,311:0.2077:2,2:23.9:1:31.6:1:0.00069:2.27044:27.6:248:0.2127:0:1.1 0/1:365:69:5,64:103,193:0.189:2,2:22.3:1:32.1:1:0:6.80491:26.1:138:0.1906:0:1.1 -22 16348253 . T C 81 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07348;SOR=3.74169;LSEQ=CTTCTTTTGTAATTTTCCTG;RSEQ=ATCATCTCGTGTGCTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:3:0,3:110,337:0.0067:2,0:14:1:33:0:1:0:30:6:0.0067:0:2 0/1:245:6:1,5:60,177:0.0245:2,2:20.8:1:31.7:1:1:1.69179:32.2:12:0.0248:0:2 -22 16348310 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10007;SOR=Inf;LSEQ=TTTGGTAAATTTCATCCAGG;RSEQ=AATATAGAGTAATAGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:6,155:0:1,0:26.6:1:28.5:1:1:0:35.3:160:1:0:0.2 0/1:75:2:1,1:3,70:0.0267:1,2:26:1:29:1:0.1045:20.35:42.5:4:0.027:0:1 -22 16348351 . T C 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02445;SOR=0.20609;LSEQ=AACTGCTTAGACTCTAGTTC;RSEQ=ATCACTGCTCTTTATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:27:2,25:5,75:0.2523:2,2:25.9:1:32.5:1:1:1.20:36:54:0.2547:0:1 0/1:31:2:0,2:3,26:0.0645:2,0:40:1:31.5:1:1:0:25:4:0.0645:0:1 -22 16349168 . T C 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.54228;SOR=0.73454;LSEQ=GAAATTGGACAGATAGTAGC;RSEQ=TTATGTTGGTCCAGATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:58:53,5:38,2:0.5918:2,2:25.6:1:30:1:0.697:1.78245:51.4:10.6:0.5699:0:1.2 1/0:33:17:14,3:13,2:0.5152:2,2:23.4:1:29.5:1:1:1.37864:51.3:16:0.5161:0:1.1 -22 16349306 . C T 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGACACACACACACACACA;RSEQ=GCAGTTTATTGCATTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:648:0:0,0:548,100:0:2,0:25.7:1:31.3:1:1:0:51.3:42.2:1:0:0.2 0/1:451:26:20,6:348,77:0.0576:2,2:25.2:1:29.2:1:0.60049:1.35485:52.8:52:0.0584:0:1.3 -22 16349345 . C A 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=GGGTTTTATACATAAAATTA;RSEQ=CCAAGTTGCAAATATATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:943:19:16,3:702,221:0.0201:2,2:19.8:1:29.9:1:0.58768:1.68:45.5:18:0.0196:0:1.3 0/0:699:0:0,0:522,176:0:2,0:23.9:1:30.6:1:1:0:44.9:76.556:1:0:0.2 -22 16349359 . A G 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=3e-05;SOR=20.31872;LSEQ=AAATTACCCAAGTTGCAAAT;RSEQ=TATGTCTACCACCCTTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1243:1:1,0:879,362:8e-04:2,0:16:0:15:0:1:0:60:0:0:0:1 0/1:931:15:11,4:624,290:0.0161:2,2:19.8:1:31.3:1:0.78603:1.28:50.3:30:0.0163:0:1.4 -22 16349415 . C G 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGATGCAGCGGAACCCCC;RSEQ=TGACTTGCTGACAAGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2450:0:0,0:1249,1200:0:2,0:29.2:1:31.4:1:1:0:54.8:110.318:1:0:0.2 0/1:1986:45:20,25:977,962:0.0227:2,2:29:1:30:1:0.45425:1.26934:54.1:90:0.0229:0:1.2 -22 16349432 . G A 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=3.73854;LSEQ=CCCCTGACTTGCTGACAAGC;RSEQ=CAGACCAGTCTAGAAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2476:80:37,43:1143,1249:0.0323:2,2:28.2:1:30.1:1:0.82067:1.06353:57.4:160:0.0328:0:1.1 0/1:2036:226:106,120:866,941:0.111:2,2:27:1:29.5:1:0.77808:1.04184:56.5:74.333:0.1111:0:1.2 -22 16349562 . T C 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGTGGGGTGGACGAAGTG;RSEQ=CGGTGCGTAACCTCTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1310:0:0,0:568,741:0:2,0:26.2:1:29.7:1:1:0:53.7:67.895:1:0:0.2 0/1:1032:27:12,15:466,539:0.0262:2,2:31.4:1:29.9:1:1:1.08065:52.7:12.5:0.0246:0:2 -22 16349564 . G A 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.70291;LSEQ=TGTGGGGTGGACGAAGTGTC;RSEQ=GTGCGTAACCTCTTGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1326:42:20,22:559,723:0.0317:2,2:28:1:30.4:1:0.63747:1.18:50.6:84:0.0324:0:1.1 0/1:1042:139:62,77:420,481:0.1334:2,2:29.5:1:30.4:1:0.71491:1.08432:54.2:138:0.1357:0:1.4 -22 16349587 . CT C 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02254;SOR=0.7565;LSEQ=GCGTAACCTCTTGCCCAACT;RSEQ=TAACACATTCATGGAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1174:202:64,138:417,554:0.1721:2,2:29:1:31.5:1:0.00355:1.62237:36.1:100:0.1735:0.0179:0.2 0/1:957:130:45,85:359,467:0.1358:2,2:29.1:1:31.2:1:0.06927:1.4515:36.5:129:0.1375:0.0167:0.2 -22 16349713 . A T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29853;SOR=1.71329;LSEQ=GAGAATGTATTTAAGATTAC;RSEQ=CTTCTGTAAGTTTACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:10:0,10:0,116:0.0794:1,0:29.5:1:28.2:1:1:0:38.2:9:0.0726:0:1 0/1:62:8:0,8:1,53:0.129:1,0:20.4:1:29.5:1:1:0:40:16:0.129:0:1.1 -22 16349916 . T C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=GTTTGTATGACTATGTAATT;RSEQ=ATGTTATCCATATACATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:7,4:0.2143:2,0:36.3:1:32:1:0.50549:0:35:6:0.2143:0:1 0/0:5:0:0,0:1,4:0:2,0:15:1:30.2:1:1:0:37.2:10:1:0:0 -22 16350007 . C T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.29657;SOR=2.807;LSEQ=TGGATAGTGAAGTTTACACA;RSEQ=ATTGGCATTTGTTTTGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:52,5:0.0339:2,2:15:1:31.5:1:0.19462:9.58472:41.5:4:0.0339:0:1 0/1:22:2:2,0:17,3:0.0909:2,0:34.5:1:30.5:1:1:0:47:4:0.0909:0:1 -22 16350056 . C T 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39986;SOR=0.62063;LSEQ=GTGGGAATAGCTATTTTATG;RSEQ=TGTGGACATTGTAGAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:26:26,0:106,9:0.1844:2,1:26.4:1:29.4:1:0.21042:0:37.5:25:0.1838:0:2.1 0/1:57:7:7,0:45,5:0.1228:2,0:17.6:1:28.6:1:1:0:33.1:6:0.1091:0:2 -22 16350086 . C T 125 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00104;SOR=0;LSEQ=TGTAGAGTCTAAGATAAGTA;RSEQ=CTTTCCTGTGAGGTTAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:17:16,1:192,8:0.0783:1,1:25.1:1:30.8:1:0.52703:1.49672:35.8:16:0.0755:0:1.1 0/0:109:0:0,0:102,7:0:2,0:22.1:1:31.2:1:1:0:42:35.333:1:0:0.2 -22 16350109 . G A 174 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00811;SOR=0.45876;LSEQ=TTCCTGTGAGGTTAGTGAAC;RSEQ=GAAGTTTTTGGCTTTATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:56:52,4:266,12:0.1672:1,2:25.1:1:30:1:0.32102:1.70196:46.7:55:0.1657:0:1.5 0/1:190:16:16,0:160,13:0.0842:2,1:18.5:1:29.1:1:0.60695:0:48.7:15:0.0806:0:1.4 -22 16350245 . C A 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.55117;LSEQ=TGCTGTTGTAGTTGCTTAGG;RSEQ=ACAGCAGCACTTCCGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1626:336:170,166:653,634:0.2066:2,2:25.2:1:30:1:1:1.00573:48.9:111:0.2073:0:1.6 0/1:1211:152:82,70:542,517:0.1255:2,2:27.4:1:28.7:1:0.54433:1.12:49.2:18:0.1208:0:1.6 -22 16350293 . C T 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.54786;LSEQ=CACTGCTGAGGCGCACTGAG;RSEQ=ATCCCACTGCAGGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1654:139:67,72:685,828:0.084:2,2:28.1:1:28.4:1:0.53384:1.12:51.5:45.333:0.0838:0:2.9 0/1:1233:59:28,31:552,621:0.0479:2,2:26.5:1:27.9:1:1:1.02:52.3:18.667:0.0459:0:3 -22 16350323 . T C 302 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.59935;LSEQ=CAGGAAACACTGAGGTGTGC;RSEQ=CTAAGCAACAAAAACACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1348:972:411,561:147,228:0.7211:2,2:27.6:1:30.5:1:0.32363:1.14:57.5:27.588:0.7182:0:1.4 1/0:961:584:249,335:149,226:0.6077:2,2:27.5:1:29.9:1:0.38332:1.13:58.1:31.444:0.6008:0:1.3 -22 16350338 . C T 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00649;SOR=0.60435;LSEQ=TGTGCTCTAAGCAACAAAAA;RSEQ=ACCTCTCCCAGGCACCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1240:102:34,68:437,700:0.0823:2,2:21.8:1:28.7:1:0.33887:1.24835:58.3:33:0.0809:0:3 0/1:837:43:16,27:317,475:0.0514:2,2:22.5:1:28.5:1:0.75182:1.12606:58.4:86:0.052:0:3.1 -22 16350349 . G C 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.16838;LSEQ=CAACAAAAACACCTCTCCCA;RSEQ=GCACCCACGCTCGATTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1080:39:14,25:379,661:0.0361:2,2:23.8:1:29.5:1:1:1.02386:60:18.5:0.035:0:1.1 0/1:697:74:25,49:238,383:0.1062:2,2:24.1:1:29.6:1:0.52637:1.21762:60:73:0.1072:0:1.1 -22 16350350 . G A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61993;SOR=1.20329;LSEQ=AACAAAAACACCTCTCCCAG;RSEQ=CACCCACGCTCGATTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1067:22:7,15:379,665:0.0206:2,2:21.3:1:29.8:1:0.82358:1.221:60:44:0.0212:0:2 0/1:688:17:8,9:250,421:0.0247:2,2:23.4:1:27.4:1:0.4515:1.50:60:34:0.0253:0:2.1 -22 16350425 . C T 249 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06518;SOR=0.73342;LSEQ=TTTGAAGTAAATCCAAGATA;RSEQ=GTGCATATTACAAGTATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:456:287:87,200:79,90:0.6294:2,2:26.5:1:30.5:1:0.00059:2.01466:52.9:94.667:0.6325:0:1.2 1/0:220:122:26,96:42,56:0.5545:2,2:25.7:1:30.3:1:0.00072:2.75584:55.6:121:0.5525:0:1.1 -22 16350628 . G A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91806;LSEQ=CAAAAGCCCAAATGGAAGAT;RSEQ=GCCAGGTAAGTCTGTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:11:6,5:143,67:0.0498:2,2:26.7:1:29.1:1:0.34339:1.77372:30.2:22:0.0502:0:1.1 0/1:109:5:5,0:79,25:0.0459:2,0:16.2:1:22.4:1:0.58711:0:25:4:0.0377:0:1.4 -22 16350688 . T A 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72788;SOR=1.40674;LSEQ=GATCTGCTAAATATATGTCC;RSEQ=TCTCTTTGGTAATCTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:5:0,5:37,125:0.0299:2,0:15.6:1:30.2:1:0.58754:0:25:10:0.0301:0:1 0/1:96:4:0,4:21,71:0.0417:2,0:26:1:26:1:0.57314:0:25:3:0.0319:0:1 -22 16350691 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12687;SOR=Inf;LSEQ=CTGCTAAATATATGTCCTTC;RSEQ=CTTTGGTAATCTTTCACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:34,135:0:2,0:22.5:1:29:1:1:0:28.9:32.8:1:0:0.1 0/1:94:2:1,1:17,75:0.0213:2,2:30:1:28.5:1:0.34798:4.32:47:4:0.0215:0:1 -22 16351206 . A T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATATGGACAGTTCCTTC;RSEQ=ACTATTACTATTGACTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:39:0:30:0:1:0:24:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 16351223 . A G 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCAACTATTACTATTGACT;RSEQ=TATTATCCATTACTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:22:0:34:0:1:0:24:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 16351604 . G C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCATCAATTGAGAAAAAAA;RSEQ=CCGGTATCCTTTAGCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:22.3:1:31:1:1:0:49.7:6:0.6:0:1 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29.5:1:1:0:60:4:1:0:2 -22 16351866 . T C 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14239;SOR=6.6052;LSEQ=TACTTTGGCAATTATATTAG;RSEQ=GTATGACAAAAATAAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:1,0:85,6:0.0109:2,0:8:0:33:0:1:0:60:2:0.011:0:1 0/1:29:2:2,0:23,4:0.069:2,0:8:1:33.5:1:1:0:48.5:4:0.069:0:1 -22 16351935 . AT A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.61955;SOR=1.80436;LSEQ=TAGGGGGTTGATTTTAATGT;RSEQ=TTTTTTACATTTTTTTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:2:2,0:227,17:0.0081:2,0:29:1:31:1:1:0:23.5:4:0.0083:0:1 0/1:137:2:2,0:123,12:0.0146:2,0:16:1:30.3:1:1:0:24:4:0.0146:0.0073:1 -22 16351957 . G T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18758;SOR=2.16972;LSEQ=TTTTTTACATTTTTTTGTAC;RSEQ=TTTGTCACGGAAGAAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:7:6,1:262,22:0.0241:2,2:16:1:31.7:1:0.44158:1.97874:23.7:14:0.0243:0:1.3 0/1:177:9:9,0:145,18:0.0508:2,0:20.8:1:32.3:1:0.59998:0:26.4:18:0.0514:0:1 -22 16352062 . G T 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01958;SOR=0;LSEQ=TTGTGTTTAGGCTGTTGAAA;RSEQ=CTTCACAAGACCATTGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:10:5,5:245,218:0.0211:2,2:29.7:1:31.3:1:1:1.12357:26.3:20:0.0213:0:2 0/0:239:0:0,0:112,127:0:2,0:27.6:1:32.1:1:1:0:26.3:118.5:1:0:0.4 -22 16352076 . T C 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00027;SOR=1.77248;LSEQ=TTGAAAGCTTCACAAGACCA;RSEQ=TGTTAAGAGGCGAATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:154:67,87:197,168:0.2967:2,2:24.2:1:31.7:1:0.0344:1.52138:26.6:50.333:0.2984:0:1.1 0/1:271:116:45,71:81,74:0.428:2,2:22.5:1:31.5:1:0.03623:1.72355:27.1:115:0.4291:0:1 -22 16352504 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGACAGGTAAAGTGTGCT;RSEQ=TTTTTTATTTTTCACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:4,81:0.023:1,2:16.5:1:31:1:0.11227:18.22:42:4:0.0241:0:2.5 0/0:37:0:0,0:5,32:0:2,0:23.5:1:32.1:1:1:0:55.2:36:1:0:0.1 -22 16353275 . C T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.13784;SOR=0.52312;LSEQ=CTTGTGTCTGTATCTGATAA;RSEQ=TTTTTTATTGTCTCTATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:31:31,0:94,20:0.2123:2,1:25:1:32.1:1:0.00755:0:26.2:62:0.2123:0:1.9 0/1:73:9:9,0:43,21:0.1233:2,0:27.8:1:30.8:1:0.05195:0:25.3:18:0.1268:0:1.7 -22 16353291 . A G 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7609;LSEQ=ATAACTTTTTTATTGTCTCT;RSEQ=TGTCTGTATAGGTACGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:6:6,0:163,24:0.0311:2,0:40.8:1:33.3:1:1:0:25.5:12:0.0317:0:4 0/1:84:2:2,0:54,28:0.0238:2,0:48.5:1:30:1:0.5502:0:25:4:0.0244:0:4 -22 16353306 . C T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.66744;LSEQ=TCTCTATGTCTGTATAGGTA;RSEQ=GTTTGTGTGCTTGGGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:6:6,0:180,32:0.0275:2,0:32:1:31.7:1:0.59568:0:25.5:12:0.0278:0:4 0/1:108:2:2,0:74,31:0.0185:2,0:35:1:27:0:1:0:25:4:0.0189:0:4 -22 16353310 . T C 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0.95146;LSEQ=TATGTCTGTATAGGTACGTT;RSEQ=GTGTGCTTGGGAATATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:6:6,0:182,33:0.0271:2,0:28:1:31.7:1:0.59492:0:25.5:12:0.0275:0:4 0/1:116:3:3,0:79,34:0.0259:2,0:24.3:1:23.7:1:0.55451:0:25.7:2:0.0177:0:5.3 -22 16353399 . C G 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42559;SOR=0.85373;LSEQ=ATGGCAAGGAGAGATGACCT;RSEQ=TCATTTTGCCGAGAGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:118:82,36:186,126:0.2738:2,2:23.2:1:31.4:1:0.0741:1.54:26.2:117:0.2766:0:1.5 0/1:267:65:48,17:134,68:0.2434:2,2:21.8:1:31:1:0.28678:1.43:25.8:64:0.2433:0:1.3 -22 16353415 . A G 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00047;SOR=0.34004;LSEQ=ACCTCTCATTTTGCCGAGAG;RSEQ=TGAAATTTAGGTGAGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:53:29,24:197,226:0.1113:2,2:23.2:1:29.1:1:0.30757:1.39:26.4:12.25:0.1045:0:1.1 0/1:294:12:7,5:139,143:0.0408:2,2:20.1:1:29.7:1:0.57097:1.44:26:24:0.0418:0:1 -22 16353422 . T G 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00011;SOR=0.38474;LSEQ=ATTTTGCCGAGAGATGAAAT;RSEQ=TAGGTGAGTTCTCAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:80:40,40:167,240:0.1643:2,2:23.3:1:31.1:1:0.14024:1.44:26.1:39:0.1632:0:2 0/1:299:21:9,12:124,154:0.0702:2,2:15.9:1:30:1:1:1.07336:26:42:0.0717:0:2.1 -22 16353470 . T A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=Inf;LSEQ=GGGTCTTGTAAATCTTAATT;RSEQ=GTTGAATGAAGTACAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:0:0,0:33,441:0:2,0:28.5:1:30.1:1:1:0:27.7:66.714:1:0:0.8 0/1:267:11:2,9:23,233:0.0412:2,2:27.2:1:30.5:1:0.27496:2.24:30.6:22:0.0418:0:1.1 -22 16353491 . A G 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.39444;SOR=0.83897;LSEQ=GTTGAATGAAGTACAGAAAT;RSEQ=GAGTAGATATCTGGTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:109:4,105:14,257:0.2868:2,1:27.8:1:31.3:1:0.78975:1.42875:26.2:53.5:0.2846:0:1.9 0/1:222:56:2,54:13,153:0.2523:2,1:26.9:1:30.4:1:0.36623:2.28711:26:55:0.25:0:1.9 -22 16353509 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12903;SOR=0.35458;LSEQ=ATAGAGTAGATATCTGGTTA;RSEQ=TGGTAGGAAGAAAGACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:15:0,15:13,240:0.056:2,1:29.3:1:31.7:1:1:0:24.9:14:0.0532:0:4 0/1:146:3:0,3:10,133:0.0205:2,0:24:1:25.7:1:1:0:24.7:2:0.0138:0:4.3 -22 16353520 . A G 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07772;SOR=0.62624;LSEQ=ATCTGGTTATTGGTAGGAAG;RSEQ=AAGACATAAAAAGAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:75:1,74:8,126:0.3589:2,1:20.7:1:31.8:1:0.16156:4.67292:25.5:74:0.3558:0:2.4 0/1:108:28:0,28:8,72:0.2593:2,1:18:1:31.8:1:0.10894:0:25.5:56:0.2593:0:2.3 -22 16353651 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAGCTAAGAATTTGAT;RSEQ=CTGTTTCCAATCTGATAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:3,3:0.25:2,0:47:1:30.5:1:0.46429:0:26:4:0.25:0:1 0/0:3:0:0,0:1,2:0:2,0:41:1:31.3:1:1:0:26.3:6:1:0:0 -22 16353834 . T TG 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.55931;SOR=3.28116;LSEQ=CATCACTGAAGGTGTGTGTG;RSEQ=GGGGGGGTATGACTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:1:0,1:93,39:0.0075:2,0:17:0:33:0:0.30075:0:25:2:0.0077:0:0 0/1:82:2:2,0:54,26:0.0244:2,0:26:1:31:1:1:0:25:4:0.025:0.0122:0.5 -22 17052949 . G A 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTAGAGACAATGAATTAA;RSEQ=GGAAAATGACAAAGAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:199,153:0:2,0:27:1:31.6:1:1:0:41.6:116.333:0.9971:0:0.1 0/1:359:22:11,11:195,141:0.0613:2,2:30.1:1:28.6:1:0.5083:1.38169:37:21:0.0597:0:1.2 -22 17053093 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23066;SOR=Inf;LSEQ=TTTTCTTTATTACAGAAAAA;RSEQ=TAACTGACTTTGGCTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:15,97:0:2,0:23.3:1:31.1:1:1:0:58.5:224:1:0:0.1 0/1:104:2:1,1:11,91:0.0192:2,2:12:1:28.5:1:0.21845:7.96:60:4:0.0194:0:1.5 -22 17053107 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57043;LSEQ=GAAAAAATAACTGACTTTGG;RSEQ=TGATCTCAGCATGTTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:9,74:0.0235:2,2:27:1:31:1:0.22269:7.85:54.5:4:0.0235:0:1.5 0/1:74:1:0,1:7,66:0.0135:2,0:32:0:26:0:1:0:60:2:0.0139:0:1 -22 17053109 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5011;SOR=0;LSEQ=AAAAATAACTGACTTTGGCT;RSEQ=ATCTCAGCATGTTTTTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:7,72:0.0247:2,2:12.5:1:27.5:1:0.18889:9.69:60:4:0.0247:0:1.5 0/0:67:0:0,0:7,60:0:2,0:23.4:1:30.6:1:1:0:58.3:32.5:1:0:0.2 -22 17053497 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCAGTTGCAGTGCATTT;RSEQ=TGCAGAAAGTCCATTAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:21,0:0,0:1:0,1:26:1:31.9:1:1:0:40.3:42:1:0:1 1/1:16:16:16,0:0,0:1:0,1:21.1:1:30.8:1:1:0:40:15:1:0:1.1 -22 17053602 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23615;SOR=Inf;LSEQ=AGGTGAAAAATATGAGCTAT;RSEQ=TTCTGTCTGTTAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:70,49:0:2,0:26.2:1:29.4:1:1:0:58.5:238:1:0:0.1 0/1:113:2:1,1:63,47:0.0177:2,2:33.5:1:29:1:1:1.33686:60:4:0.0179:0:1 -22 17053658 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49818;SOR=0;LSEQ=GCCCAGGTAAATGTATGTTT;RSEQ=AGATTACTAGATAACTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:55,63:0.0167:2,2:11:1:30.5:1:1:1.14:60:4:0.0167:0:1 0/0:114:0:0,0:45,69:0:2,0:23.5:1:31:1:1:0:50.5:56:1:0:0.1 -22 17053738 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18712;SOR=Inf;LSEQ=AGTCCACATAAATAAATGAA;RSEQ=TAGACTAATAATAGTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:11,29:0:2,0:26.9:1:31.6:1:1:0:55.4:80:1:0:0.1 0/1:31:2:0,2:6,23:0.0645:2,0:40:1:30.5:1:1:0:60:4:0.0645:0:1 -22 17053961 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09957;SOR=Inf;LSEQ=GTATTGCTTGGTAAAAGATT;RSEQ=GCCTCCAATCAAACCTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:219,97:0:2,0:24:1:31.4:1:1:0:45.3:38.5:1:0:0.1 0/1:274:3:2,1:183,88:0.0109:2,2:23.7:1:23.7:1:1:1.03961:46.7:2:0.0074:0:1 -22 17054103 . G A 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96686;LSEQ=TATTTAATTCAGCTAGTACA;RSEQ=GTAAAATAATGTAAAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:35:12,23:113,171:0.1097:2,2:29.6:1:31.3:1:0.58571:1.26565:56.1:70:0.1111:0:1.2 0/1:263:28:10,18:82,153:0.1065:2,2:25.7:1:30:1:1:1.04:56.9:56:0.1077:0:1.3 -22 17054155 . T C 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTACAATAATAATTTATT;RSEQ=TAGATCCATACAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:135:135:54,81:0,0:1:0,2:21.4:1:31.8:1:1:0:41.1:134:1:0:1.1 1/1:105:105:37,68:0,0:1:0,2:19.4:1:32:1:1:0:40.9:104:1:0:1.1 -22 17054210 . TA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50618;SOR=0;LSEQ=GCACTAACTAGTTTTATGCT;RSEQ=AAAAAAATTATTACCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:2,0:124,50:0.0114:2,0:35:1:31.5:1:1:0:39:4:0.0114:0:0.5 0/0:137:0:0,0:118,19:0:2,0:26.1:1:28.4:1:1:0:54.2:44.667:1:0:0.3 -22 17054291 . T C 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15919;SOR=0.75612;LSEQ=CATGCAGAAACTGAACCTGA;RSEQ=TTGTTTTTTTTGAATCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:76:53,23:371,176:0.1218:2,2:24.9:1:32.5:1:0.79387:1.09:56.7:152:0.1226:0:1.9 0/1:548:52:31,21:319,177:0.0949:2,2:23.1:1:31:1:0.5448:1.22042:55.9:51:0.0944:0:1.9 -22 17054294 . G GT 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.95712;LSEQ=GCAGAAACTGAACCTGATTT;RSEQ=TTTTTTTTGAATCACCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:639:7:4,3:423,208:0.011:2,2:16.9:1:30.6:1:0.69008:1.52421:56.6:14:0.011:0.0031:0.3 0/1:572:6:5,1:350,215:0.0105:2,2:33.5:1:29.5:1:0.41657:3.07:59:12:0.0106:0:0.2 -22 17054332 . T C 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08144;SOR=0.72723;LSEQ=AGGTCCTAAAATATGAACAA;RSEQ=ATTTGGATAACTTGCTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:680:90:47,43:288,301:0.1324:2,2:28.5:1:31.3:1:0.57319:1.14:48.2:89:0.1324:0:1.7 0/1:601:60:27,33:244,297:0.0998:2,2:30.4:1:31.4:1:1:1.00411:51:120:0.1014:0:1.9 -22 17054720 . T C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=GCTGTAGGTTTCACTGTGTG;RSEQ=ATGGATTAAAATATCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:24.3:1:31:1:1:0:57.7:6:0.75:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:22:1:33:0:1:0:55.5:4:0.6667:0:1 -22 17055074 . T A 36 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GATTATTTTTGTGCTCAATT;RSEQ=CCTTTTTTCATGCTTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:15.7:1:23:1:1:0:33.7:2:1:0:1.7 1/0:2:1:1,0:1,0:0.5:0,0:7:0:26:0:1:0:49:2:0.5:0:1 -22 17055316 . CTA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.21171;SOR=Inf;LSEQ=ATTTGTATACTGATTTAAGA;RSEQ=TATATATATTTTTCTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:192,28:0:2,0:22.2:1:30.6:1:1:0:58:109:1:0:0.1 0/1:188:2:1,1:158,28:0.0106:2,2:23:1:30.5:1:0.28541:5.5623:60:4:0.0107:0:0 -22 17055458 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24398;LSEQ=AGCACCTGAATAGGCAAGTC;RSEQ=AGGCAATGGAAAAGCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:260:110,150:143,209:0.4248:2,2:24.4:1:29.9:1:0.679:1.07:47.6:64:0.4267:0:1.1 0/1:590:90:39,51:212,288:0.1525:2,2:24.5:1:29.4:1:0.90801:1.04:47.9:180:0.1528:0:1.1 -22 17055569 . T G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.52721;LSEQ=TGAGACTCTTTTCACTGCAG;RSEQ=GGGGCAGAGTTGTTTAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:57:9,48:12,95:0.3476:2,2:27:1:30.8:1:0.46413:1.48:53.6:114:0.354:0:1.2 1/0:137:97:20,77:5,35:0.708:2,2:23.1:1:29.8:1:0.33491:1.81:57.1:31.333:0.7015:0:1.1 -22 17055619 . G A 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00143;SOR=0;LSEQ=TATACAGATCATGGTCCTTG;RSEQ=AATCAAGCAGATTAGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:13:1,12:0,50:0.2063:1,1:20.6:1:30.8:1:0.20635:0:48.8:26:0.2063:0:1.2 0/0:40:0:0,0:2,38:0:2,0:28.8:1:31.4:1:1:0:46.5:80:1:0:0.4 -22 17055768 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATTGTGAGAATTAAATT;RSEQ=CATGAGATATGCAAAGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:22.5:1:31:1:1:0:53.5:4:0.25:0:1 0/0:1:0:0,0:0,1:0:0,0:12:0:32:0:1:0:60:2:1:0:0 -22 17055818 . C T 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGGAACACAGAAGGTGC;RSEQ=CAATAAATGTTAGATCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:25:1:29.8:1:1:0:33.3:8:0.6667:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 17055841 . C T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAATGTTAGATCCCTTTA;RSEQ=TTTCCCTTCCTTTCTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:38.7:1:31:1:1:0:24.3:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 17082878 . AGCG A 34 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.58335;SOR=2.58104;LSEQ=CGGGGAGGAGGAACCCGAGC;RSEQ=GCGGCGGCGGCCGCGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:1:1,0:146,20:0.006:2,0:10:0:34:0:1:0:58:2:0.0061:0:0 0/1:131:2:2,0:103,25:0.0153:2,0:22:1:34:0:1:0:60:4:0.0157:0:0 -22 17082880 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.50448;SOR=0;LSEQ=GGGAGGAGGAACCCGAGCAG;RSEQ=GGCGGCGGCGGCCGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:148,20:0.0117:2,2:19:1:26.5:1:0.23244:7.24494:60:4:0.0118:0:1 0/0:137:0:0,0:107,28:0:2,0:21.5:1:30.8:1:1:0:59.7:32.75:1:0:0.1 -22 17082886 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.50649;SOR=0;LSEQ=AGGAACCCGAGCAGCGGCGG;RSEQ=GGCGGCCGCGGCGGCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:167,28:0.0102:2,2:25.5:1:28:1:0.27339:5.87811:56:4:0.0104:0:1 0/0:153:0:0,0:117,36:0:2,0:22.5:1:30.6:1:1:0:59.8:29.6:1:0:0.2 -22 17083152 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=6.62379;LSEQ=CGGGAGCCAGCGGCGGCGCC;RSEQ=GGCCGGAGCTGCCACCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:104:23,81:33,115:0.4127:2,2:18.4:1:31.7:1:1:1.01054:54.6:208:0.4143:0:1.1 1/1:244:201:58,143:13,30:0.8238:2,2:19.4:1:30.9:1:0.85477:1.0681:53.9:402:0.8272:0:1.2 -22 17083172 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24615;SOR=Inf;LSEQ=GGGCCGGAGCTGCCACCGGG;RSEQ=GCCCGCCCCGCGGCCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:12,85:0:2,0:8.2:1:29.9:1:1:0:50:31.333:0.9895:0:0.5 0/1:97:2:1,1:26,69:0.0206:2,2:10:0:32.5:1:0.48131:2.62:50:4:0.0211:0:2.5 -22 17519358 . GT G 52 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATGTAGTCCCATATGTT;RSEQ=TTTTTTTTTTTTGCGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:30.7:1:33.3:1:1:0:60:6:0.3:0:0.3 0/0:2:0:0,0:2,0:0:0,0:17:1:30.5:1:1:0:60:4:1:0:0.5 -22 17519531 . A G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04654;SOR=Inf;LSEQ=TACCAGAGCAGTTGTATTAT;RSEQ=TTTCAAAATGTAAGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:84,63:0:2,0:28:1:29.1:1:1:0:59.9:72.5:1:0:0.3 0/1:129:4:2,2:78,47:0.031:2,2:27.3:1:31.8:1:0.63433:1.65273:60:8:0.0315:0:1.5 -22 17519556 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50099;SOR=0;LSEQ=AAAATGTAAGATGATTTTTA;RSEQ=AAGCCTGAGTACCTAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:91,80:0.0116:2,2:6:1:31.5:1:1:1.13665:60:4:0.012:0:1 0/0:150:0:0,0:79,71:0:2,0:28.6:1:29.6:1:1:0:59.9:149:1:0:0.2 -22 17519565 . G A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60226;SOR=2.27078;LSEQ=GATGATTTTTAAAAGCCTGA;RSEQ=TACCTAAGATGCAATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:1:1,0:92,81:0.0057:2,0:1:0:24:0:1:0:60:2:0.0058:0:1 0/1:154:2:1,1:79,73:0.013:2,2:43.5:1:31:1:1:1.08162:60:4:0.0132:0:1 -22 17519579 . A G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05947;LSEQ=GCCTGAGTACCTAAGATGCA;RSEQ=TTATATGAACTCTACTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:54:25,29:63,59:0.3068:2,2:24.6:1:32.6:1:0.62412:1.23713:60:108:0.3086:0:1 0/1:157:4:2,2:75,78:0.0255:2,2:19.5:1:31.3:1:1:1.04:60:8:0.0256:0:1.3 -22 18501506 . ATATCTATC A 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=7.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GAAAAAAATAAAAATAAAAA;RSEQ=TATCTATCTATCTATCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16.5:1:32.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 18501543 . C T 29 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATCTATCTATCTACACACA;RSEQ=ACACACATACACACATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:37.5:1:29:1:1:0:60:4:0.6667:0:1 1/1:1:1:1,0:0,0:1:0,0:29:0:30:0:1:0:60:2:1:0:1 -22 18501960 . CA C 64 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.52128;LSEQ=GACAGAGGGAGACCCTGTCT;RSEQ=AAAAAAAAAGGACCCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:4,0:33,0:0.1081:1,0:32.8:1:32:1:1:0:60:8:0.1081:0:0.3 0/1:17:1:1,0:15,0:0.0588:1,0:14:0:33:0:1:0:60:2:0.0588:0:0 -22 18502110 . T G 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07045;SOR=0.59195;LSEQ=TGGCAAATCATTGGATATGG;RSEQ=GGGGAAAGTGGAAATATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:38:15,23:83,116:0.1603:2,2:26.6:1:30.2:1:0.85863:1.09666:60:18:0.1558:0:1.1 0/1:207:21:11,10:80,106:0.1014:2,2:29.4:1:30.1:1:0.48904:1.45:60:42:0.1019:0:1.2 -22 18502135 . G C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19277;SOR=Inf;LSEQ=AAAGTGGAAATATCTATTAT;RSEQ=TCGGTTGGAAATAAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:71,120:0:2,0:23.5:1:31.6:1:1:0:60:62.667:1:0:0.3 0/1:150:2:1,1:63,85:0.0133:2,2:27:1:27.5:1:1:1.35:60:4:0.0135:0:1.5 -22 18502211 . G A 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18954;SOR=2.21409;LSEQ=TGTCTCACGCCGGTAATCCC;RSEQ=GCACTTTGGGAGGCCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:25:4,21:3,13:0.6098:2,2:22.4:1:31.1:1:1:1.20579:54.2:50:0.6098:0:1.6 1/0:27:21:3,18:1,5:0.7778:2,2:20.8:1:31.3:1:1:1.19167:58:42:0.8077:0:1.4 -22 18502256 . G T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40652;SOR=2.41155;LSEQ=AGATCACCTGAGGTCAGGAG;RSEQ=TCGAGACCAGCCTGGCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:0,9:0,9:0.5:0,0:31.6:1:28.8:1:1:0:40.7:8:0.4706:0:2.4 1/0:7:5:0,5:0,2:0.7143:0,0:27.6:1:29.8:1:1:0:43.8:10:0.7143:0:2.4 -22 18502277 . G A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0515;SOR=Inf;LSEQ=TCGAGACCAGCCTGGCCAAC;RSEQ=TGGCGAAACCCTGTCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:0,7:0,7:0.5:0,0:27.3:1:29.3:1:1:0:39:6:0.4615:0:2.6 1/1:6:6:0,6:0,0:1:0,0:29.7:1:29.7:1:1:0:44.3:12:1:0:2.2 -22 18502467 . T TA 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.10397;LSEQ=CAAGACTCTGTCTCAAAAAT;RSEQ=AAAAAAAAAGAAAAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:12,4:6,3:0.6154:2,2:30.8:1:29.1:1:0.67288:1.48:60:32:0.64:0:0 1/0:36:23:13,10:8,5:0.6389:2,2:20.4:1:27.6:1:1:1.22371:60:22:0.6286:0.1944:0.1 -22 18502789 . C CAGGAT 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CGGGGTTTCACTGTGTCAGC;RSEQ=AGGATGGTCTCGATCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:7,0:0.2222:0,2:28.5:1:24.4:1:0.22222:0:60:4:0.2222:0.1111:0 0/0:3:0:0,0:3,0:0:0,0:24.7:1:29.3:1:1:0:60:6:1:0:0 -22 18503211 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GGTATTTCTTAATATTATGA;RSEQ=CAAGAGTTTTATCGGCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:39:1:32:0:1:0:60:4:0.5:0:1 0/0:2:0:0,0:1,1:0:2,0:4:0:32:0:1:0:60:4:1:0:0 -22 19053282 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.116;SOR=Inf;LSEQ=AGCTCACCTTAGGTAACACC;RSEQ=GTGACCTCTTTTATAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:99,22:0:2,0:21.7:1:30.2:1:1:0:60:59.5:1:0:0.2 0/1:63:2:1,1:55,6:0.0317:2,2:5.5:1:30:1:0.21147:8.56132:60:4:0.0317:0:1 -22 19053290 . C G 124 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00107;SOR=5.31352;LSEQ=TTAGGTAACACCAGTGACCT;RSEQ=TTTTATAGAATCTTTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:5:4,1:107,25:0.0365:2,2:27.2:1:32.8:1:1:1.06947:60:10:0.0368:0:1.4 0/1:83:14:12,2:58,11:0.1687:2,2:22.6:1:32.7:1:1:1.14:60:28:0.1707:0:1 -22 19053325 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30903;SOR=4.40766;LSEQ=TAACCTTCAAATGTTGGGTA;RSEQ=CTCATATTAGTACACTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:0,1:181,99:0.0036:2,0:1:0:27:0:0.35587:0:60:2:0.0036:0:1 0/1:193:3:2,1:134,56:0.0155:2,2:30.7:1:29.7:1:1:1.19525:60:6:0.0158:0:1 -22 19053390 . C T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12731;SOR=0;LSEQ=CAGTTGTAAAATTAAAAATG;RSEQ=CATTTTTAAAGTGCAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:4:2,2:186,191:0.0104:2,2:21:1:28.3:1:1:1.03:60:8:0.0107:0:1 0/0:335:0:0,0:165,170:0:2,0:25.7:1:30.8:1:1:0:60:54.833:1:0:0.3 -22 19053406 . G T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=11.32647;LSEQ=AATGCCATTTTTAAAGTGCA;RSEQ=CTATGTCTTGTGGCACTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:11:2,9:174,196:0.0287:2,2:29.6:1:30.5:1:0.07:3.98246:60:22:0.0293:0:1.5 0/1:330:83:36,47:113,134:0.2515:2,2:21:1:28.3:1:0.79889:1.10063:60:19.75:0.2438:0:1.2 -22 19053443 . T A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10573;SOR=Inf;LSEQ=TAGTAAAACTTCTAGACACG;RSEQ=ATCCCCATGTATTTATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:96,176:0:2,0:26.3:1:28.7:1:1:0:60:544:1:0:0.2 0/1:245:3:2,1:81,161:0.0122:2,2:12.7:1:25.7:1:0.26565:3.95:60:6:0.0125:0:1.7 -22 19053454 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2126;SOR=Inf;LSEQ=CTAGACACGTATCCCCATGT;RSEQ=TTTATTATGTAAGCATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:77,155:0:2,0:26.5:1:29.7:1:1:0:60:76.333:1:0:0.2 0/1:199:2:1,1:66,131:0.0101:2,2:43:1:31.5:1:1:1.98:60:4:0.0102:0:1 -22 19053467 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50393;SOR=0;LSEQ=CCCATGTATTTATTATGTAA;RSEQ=CATGTGTGTGTGTGACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:57,139:0.0101:2,2:15:1:29.5:1:0.5011:2.43:60:4:0.0102:0:1 0/0:161:0:0,0:51,110:0:2,0:23.6:1:32:1:1:0:60:79.5:1:0:0.3 -22 19053469 . A ATG 125 v4;MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=5e-05;SOR=11.53005;LSEQ=CATGTATTTATTATGTAAGC;RSEQ=TGTGTGTGTGTGACTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:0,2:57,134:0.0104:2,0:37.5:1:31.5:1:1:0:60:4:0.0105:0:0.5 0/1:157:17:2,15:46,94:0.1083:2,2:31.6:1:30.8:1:0.09599:3.64661:60:34:0.1097:0:0.5 -22 19053471 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.50586;SOR=0;LSEQ=TGTATTTATTATGTAAGCAT;RSEQ=TGTGTGTGTGACTTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:53,133:0.0105:2,2:17.5:1:28:1:0.49306:2.50:60:4:0.0108:0:1 0/0:149:0:0,0:45,103:0:2,0:22.6:1:31.5:1:1:0:60:296:1:0:0.3 -22 19053472 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.50634;SOR=0;LSEQ=GTATTTATTATGTAAGCATG;RSEQ=GTGTGTGTGACTTCTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:53,133:0.0106:2,2:5.5:1:29.5:1:0.49306:2.50:60:4:0.0106:0:1 0/0:147:0:0,0:43,104:0:2,0:22.4:1:29.7:1:1:0:60:146:1:0:0.3 -22 19053477 . G T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.00118;SOR=Inf;LSEQ=TATTATGTAAGCATGTGTGT;RSEQ=TGTGACTTCTTCATAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:45,133:0:2,0:22.6:1:32:1:1:0:60:177:1:0:0.1 0/1:138:8:3,5:37,93:0.058:2,2:18.6:1:30.3:1:0.69053:1.50:60:16:0.0588:0:1.9 -22 19466757 . A AG 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.33484;SOR=0.24961;LSEQ=GTGCCGGACCCGAGACCCGG;RSEQ=GGGGGGGTGCCCGGGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:1,4:1,3:0.5556:2,2:34.2:1:29.7:1:1:1.29098:60:10:0.625:0.1111:0 0/1:9:2:1,1:1,6:0.2222:2,2:31.5:1:29.5:1:0.41667:4.58:60:4:0.2222:0:0 -22 19466758 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=TGCCGGACCCGAGACCCGGA;RSEQ=GGGGGGTGCCCGGGACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:31.7:1:31.7:1:1:0:60:18:1:0:0 0/1:9:2:1,1:1,6:0.2222:2,2:18.5:1:28.5:1:0.41667:4.58:60:4:0.2222:0:1.5 -22 19868218 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCCGGCCATGATCGCT;RSEQ=TGGGTGTCAGCTCAGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:45:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 20918816 . ACAG A 32 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=1;SOR=0.71413;LSEQ=CAGCAGCAGCAGGCGGCGCT;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:12,13:0.069:2,2:38.5:1:33.5:1:1:1.08:60:4:0.069:0:0 0/1:40:2:1,1:19,19:0.05:2,2:28.5:1:32:1:1:1:60:4:0.0513:0:0 -22 20918896 . TGCA T 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.13428;SOR=0;LSEQ=GCAGCAGTTCCAAGCAGTAG;RSEQ=GCAGCAGCAGCAGCTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:6,15:0.16:2,2:33.8:1:32.3:1:0.56996:2.40:60:8:0.16:0:0.3 0/0:17:0:0,0:7,10:0:2,0:17.1:1:29.8:1:1:0:60:7.5:1:0:0.2 -22 20920760 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.18995;SOR=Inf;LSEQ=TGTTCTGTCTCTAGATACAG;RSEQ=AGCAGCAACAGCAGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:0:2,0:19.1:1:32.7:1:1:0:60:66:1:0:0.2 0/1:26:2:1,1:14,10:0.0769:2,2:24:1:27.5:1:1:1.38168:60:4:0.0769:0:1 -22 20920781 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50554;SOR=0;LSEQ=AGCAGCAACAGCAGCTGCAG;RSEQ=GAATAGCACAGCTGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:18,20:0.05:2,2:28.5:1:29:1:1:1.11:60:4:0.05:0:1 0/0:29:0:0,0:17,12:0:2,0:28.6:1:31.3:1:1:0:60:58:1:0:0.2 -22 20920799 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15449;SOR=Inf;LSEQ=AGCGAATAGCACAGCTGCAG;RSEQ=TCCAACAACAGCAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:20,23:0:2,0:33.3:1:32:1:1:0:60:86:0.9773:0:0.1 0/1:29:2:1,1:14,13:0.069:2,2:33:1:31:0:1:1.07415:60:4:0.069:0:1 -22 20920898 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCACCGATGCAGCAGCCA;RSEQ=AGCCTCCGCCCTCCCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:11:1:28.5:1:1:1.40151:60:4:0.1053:0:1 0/0:8:0:0,0:1,6:0:2,0:21.3:1:31.9:1:1:0:60:14:0.875:0:0 -22 21135656 . G T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10106;SOR=0;LSEQ=ACACACAACCACTTCTCTTT;RSEQ=CCACCAAGGACTACCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:2,1:129,46:0.0169:2,2:18:1:31:1:1:1.39932:60:6:0.0173:0:1 0/0:203:0:0,0:144,59:0:2,0:23.8:1:30.9:1:1:0:60:32.833:1:0:0.1 -22 21135659 . A T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10991;SOR=0;LSEQ=CACAACCACTTCTCTTTGCC;RSEQ=CCAAGGACTACCAGGTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:2,1:138,54:0.0154:2,2:25.3:1:31.3:1:1:1.27612:60:6:0.0159:0:1.3 0/0:211:0:0,0:147,64:0:2,0:24.3:1:29.2:1:1:0:60:104.5:1:0:0.1 -22 21135741 . G A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11222;SOR=0.18531;LSEQ=GCTCCCGTGGTTTTATAGCA;RSEQ=CCCAGGCGAAGGAAGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:5:4,1:222,208:0.0114:2,2:6.2:1:26.8:1:0.37404:3.74:60:10:0.0117:0:1 0/0:468:1:1,0:211,256:0.0021:2,0:1:0:25:0:0.45299:0:60:2:0.0022:0:1 -22 21135763 . C A 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.661;SOR=1.07506;LSEQ=CCAGGCGAAGGAAGGAGACC;RSEQ=CCCCCAGCTCCTGGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:147:65,82:125,137:0.3594:2,2:26.4:1:29.6:1:0.53584:1.15064:60:72.5:0.358:0:1.1 0/1:396:149:54,95:109,138:0.3763:2,2:23.8:1:29.2:1:0.14022:1.3884:60:73.5:0.3769:0:1.1 -22 21135811 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16943;SOR=Inf;LSEQ=AAAGGGGGCCAGAGCCCCTC;RSEQ=TGATCTGTCCACACACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:71,177:0:2,0:23:1:31.6:1:1:0:60:61:1:0:0.4 0/1:174:2:1,1:45,127:0.0115:2,2:22:1:29:1:0.45997:2.80:60:4:0.0115:0:1.5 -22 21272141 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51332;SOR=0;LSEQ=GAGGCCCTTCCTCGGCCCCA;RSEQ=AGCCGTCTGCCGGGCTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:145,33:0.0111:2,2:27:1:31:1:0.34295:4.34375:60:4:0.0113:0:1 0/0:127:0:0,0:99,28:0:2,0:22.2:1:29.7:1:1:0:60:254:1:0:0.1 -22 21272175 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6691;SOR=1.70976;LSEQ=GCTAAGGCGTGCAGAGCAGG;RSEQ=GAGGACAGCCGCCGCCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:2:0,2:222,102:0.0061:2,0:1:0:26.5:1:0.1011:0:60:4:0.0062:0:1 0/1:287:3:1,2:175,109:0.0105:2,2:5:1:27.3:1:0.56157:3.19766:60:6:0.0107:0:1 -22 21272198 . G A 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13296;SOR=0.1959;LSEQ=GGACAGCCGCCGCCCCTACC;RSEQ=CCGCAGAGTCCCCGGTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:6:4,2:289,164:0.0131:2,2:33.3:1:28.8:1:1:1.13:60:12:0.0132:0:1.3 0/0:387:1:1,0:228,158:0.0026:2,0:3:0:30:0:1:0:60:2:0.0026:0:1 -22 21272718 . GT G 110 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.49175;SOR=0.5074;LSEQ=GTCACTGGATAAGAGGATGC;RSEQ=TTTTTTTTTTTCCCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:12:0,12:1,15:0.375:1,0:22.8:1:30.8:1:1:0:60:11:0.3793:0.0625:0.3 0/1:13:3:0,3:1,7:0.2308:2,0:37:1:31.7:1:1:0:60:6:0.2308:0:0.3 -22 21272752 . C T 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26632;SOR=0;LSEQ=CCTCTCACGAGGCTGTTTCT;RSEQ=AATGTGAAGAGGATGCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:0.3333:0,0:25.2:1:28.6:1:1:0:60:10:0.3333:0:2.2 0/0:5:0:0,0:1,4:0:2,0:16.8:1:31.4:1:1:0:60:10:1:0:0.4 -22 21280419 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17353;SOR=Inf;LSEQ=GGTGGTAGAAGAGATGGTGG;RSEQ=AGTGCTTGCTGGTAAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:241,9:0:1,0:25.8:1:32.2:1:1:0:60:61.5:1:0:0.9 0/1:179:2:2,0:155,21:0.0112:2,0:42.5:1:31.5:1:1:0:60:4:0.0114:0:1.5 -22 21280463 . G C 278 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01725;LSEQ=TTATAATTAATGTAGATGAT;RSEQ=GGCAGGAACCTAGGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:575:571:386,185:0,0:0.993:0,2:23.2:1:30.4:1:1:0:60:113.2:0.993:0:1.1 1/0:463:329:226,103:88,45:0.7106:2,2:23.7:1:30.4:1:0.65972:1.12:60:328:0.713:0:1.1 -22 21287911 . A G 106 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01423;SOR=0;LSEQ=GTTTGCAGTGAGCTAAGATC;RSEQ=CGCTATTGCACTCCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:23.9:1:27.9:1:1:0:57.6:13:1:0:1.3 1/0:9:5:5,0:4,0:0.5556:0,0:16:1:30.6:1:1:0:60:10:0.5556:0:1.2 -22 21288518 . G A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06543;SOR=0;LSEQ=CCTGTGCTTATGACAAGACT;RSEQ=CCTTGGCATTAGAGGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:5:4,1:122,260:0.0129:2,2:6.8:1:25.6:1:0.04053:8.48:60:10:0.0131:0:1 0/0:331:0:0,0:124,207:0:2,0:42:0:13:0:1:0:60:0:0:0:6 -22 21288558 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17941;SOR=Inf;LSEQ=ATCTGTTCAGATTAGCTTTT;RSEQ=GGTCCTTTGACATTTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:59,188:0:2,0:21.3:1:31.4:1:1:0:60:122.5:1:0:0.1 0/1:182:2:1,1:52,128:0.011:2,2:16:1:29.5:1:0.49876:2.45:60:4:0.011:0:2 -22 21294854 . CTTTTTTT C 193 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=20.000;MSILEN=1;SSF=0.12682;SOR=0.64292;LSEQ=TTTCCTCATCTTTGGTGCTC;RSEQ=TTTTTTTTTTTTTGGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:72:68,4:18,1:0.4832:1,2:21.2:1:31.4:1:1:1.05814:59.4:35:0.4861:0.1342:0.3 0/1:80:30:28,2:21,0:0.375:1,2:23.3:1:30.6:1:0.50588:0:58.7:60:0.3797:0.1125:1.5 -22 21294878 . AT A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.29245;SOR=0;LSEQ=TTTTTTTTTTTTTTTTTGGC;RSEQ=TTTTTTTCTTAGTGATACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:2,1:158,4:0.0182:1,2:18.7:1:32:1:0.08871:18.4469:60:6:0.0184:0:1.3 0/0:100:0:0,0:96,3:0:1,0:21.7:1:29:1:1:0:58.5:98:1:0:1.1 -22 21294918 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06957;SOR=Inf;LSEQ=TCAGCGTTCTTTGAGGTCAC;RSEQ=AGCATCCTCAACATTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:347,80:0:2,0:23.9:1:30.8:1:1:0:59.8:37.818:1:0:0.1 0/1:300:3:1,2:236,61:0.01:2,2:14.7:1:27.3:1:0.11281:7.66552:60:6:0.0104:0:1 -22 21303711 . G A 53 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACTGCATTCCAGCCTGG;RSEQ=CGACAGACCCCGTCTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:9.5:1:26.8:1:1:0:60:3:1:0:1.8 1/1:1:1:1,0:0,0:1:0,0:18:0:31:0:1:0:60:2:1:0:1 -22 21303797 . G A 29 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45254;SOR=2.50894;LSEQ=CTATTCAAGAGGTGGAGGTG;RSEQ=AAGGATCACTTGAGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:26,0:0.0714:1,0:18:1:29.5:1:1:0:60:4:0.0769:0:2 0/1:6:1:1,0:5,0:0.1667:0,0:24:0:31:0:1:0:60:2:0.1667:0:1 -22 21303818 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66321;SOR=1.69925;LSEQ=AAGGATCACTTGAGCCCAGG;RSEQ=GTTAGAGGTTACATTGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:8:8,0:23,0:0.2581:1,0:25.1:1:29.8:1:1:0:60:16:0.2581:0:1 0/1:8:3:3,0:5,0:0.375:0,0:17.7:1:28:1:1:0:60:6:0.375:0:1 -22 21304408 . A G 109 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGTGGAGAGAAGTTGAC;RSEQ=TGGAAAGGGTCTTCCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:19.9:1:31.7:1:1:0:60:22:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 21304463 . T C 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTACATGGGACTGATTCTGT;RSEQ=GTGTTCACCAGAGAAAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:31:0:1:0:60:4:1:0:2 1/1:1:1:0,1:0,0:1:0,0:35:0:30:0:1:0:60:2:1:0:1 -22 22123189 . A C 63 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGGACAGGCAGCAAGGAA;RSEQ=GGATGAGAACCCAAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:21.5:1:31.5:1:1:0:60:8:0.8:0:1.5 1/1:1:1:1,0:0,0:1:0,0:8:0:25:0:1:0:60:2:1:0:1 -22 22127080 . G C 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=ATGGCAGCAGGTATATCTCA;RSEQ=GAAAATCTAAGCAAGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:204,25:0:2,0:21.4:1:32.1:1:1:0:60:228:1:0:0.1 0/1:158:10:8,2:130,18:0.0633:2,2:26.9:1:30.7:1:0.61636:1.79741:60:20:0.0645:0:1 -22 22127095 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08742;SOR=Inf;LSEQ=TCTCAGGAAAATCTAAGCAA;RSEQ=ATATGGTTGGTCCACTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:249,48:0:2,0:23.1:1:32.1:1:1:0:60:147.5:1:0:0.1 0/1:238:3:1,2:186,48:0.0126:2,2:27.7:1:26.7:1:0.11352:7.65858:60:6:0.0128:0:1 -22 22127490 . C T 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28989;SOR=0;LSEQ=ACCGCAAACAAAAACACTGG;RSEQ=ACTACTTAATGAAGCGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:0,5:1,11:0.2941:2,0:30:1:28.4:1:1:0:60:10:0.3125:0:1.2 0/0:5:0:0,0:0,5:0:0,0:26.2:1:33.6:1:1:0:60:10:1:0:0.2 -22 22141229 . G T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGGGTGGGGGGTCATTA;RSEQ=TCGGCCTATCATGGTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:27.5:1:1:0:60:4:1:0:1 -22 22142388 . CA C 140 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.11256;SOR=1.94623;LSEQ=TACTGCACTGCCACTGTTTC;RSEQ=AAAAAAAAAAGGGGGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:21:21,0:39,0:0.3281:1,1:27.8:1:31.6:1:1:0:60:42:0.3281:0.0625:0.2 0/1:45:22:21,1:20,1:0.4889:1,1:23.7:1:31.4:1:1:1.05:60:44:0.5:0.0889:0 -22 22142450 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50734;SOR=0;LSEQ=AAAGAAAGCATTATCCAATA;RSEQ=CCATAGGCTCATTTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:173,8:0.0109:1,2:31.5:1:29.5:1:0.0962:20.44712:60:4:0.0116:0:1 0/0:140:0:0,0:125,15:0:2,0:23:1:31.6:1:1:0:59.9:45.667:1:0:0.1 -22 22142732 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.222;SOR=Inf;LSEQ=GACCAAGGTAAATGACTACA;RSEQ=ACCATCAACTCTGAGTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:25,108:0:2,0:24.3:1:32.2:1:1:0:60:132:1:0:0.1 0/1:119:2:0,2:29,88:0.0168:2,0:50:0:28:1:1:0:60:4:0.0174:0:1.5 -22 22143392 . A T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAGGCCGAGGCGGGCGG;RSEQ=TCACTTGAGGCCAGGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:34.5:1:27.5:1:1:0:30.5:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 22144873 . CCTGAGTAGCTGGCACTA C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTCACCTCAGCCAGGT;RSEQ=CTGAGTAGCTGGCACACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:30.4:1:1:0:39:4:1:1:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 22153006 . C CA 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAAATTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:15:1:31.5:1:1:0:42:4:0.5:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 22153194 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51278;SOR=0;LSEQ=AGACAGCACCTTGTCTCTGG;RSEQ=CAGACAGGCAAACTCTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:2,0:105,0:0.0187:1,0:40.5:1:31.5:1:1:0:60:4:0.0187:0:1 0/0:75:0:0,0:74,1:0:1,0:22.1:1:32.4:1:1:0:60:150:1:0:0.1 -22 22153236 . A T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37135;SOR=0.32846;LSEQ=CAGAGGGAGACTTACGGCTT;RSEQ=CTGCAATGCATTCAGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:199,37:0.0126:2,2:28:1:27.7:1:0.07003:10.58498:60:6:0.0126:0:1.3 0/0:241:1:0,1:187,53:0.0041:2,0:1:0:23:0:0.22407:0:60:2:0.0042:0:1 -22 22153239 . G A 133 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02729;SOR=0.43595;LSEQ=AGGGAGACTTACGGCTTACT;RSEQ=CAATGCATTCAGAAAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:26:20,6:186,46:0.1008:2,2:17.5:1:28.3:1:0.79628:1.21211:60:52:0.1012:0:1.1 0/1:258:12:7,5:190,55:0.0465:2,2:18.2:1:28.4:1:0.15813:2.45715:60:24:0.0472:0:1 -22 22153426 . G GA 68 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.26236;SOR=0.35054;LSEQ=AAAGTCACAGATCTAAGAGA;RSEQ=AAAAAAAACAGGATAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:5:3,2:109,270:0.013:2,2:31.8:1:29.6:1:0.15083:3.70:60:10:0.0133:0:0 0/0:435:2:2,0:148,285:0.0046:2,0:25.5:1:26.5:1:0.11839:0:60:4:0.0047:0.0023:0.5 -22 22153494 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=Inf;LSEQ=ACATCACAAAAATAAAAAAG;RSEQ=CAATAGGAATAATAATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:4,101:0:1,0:25.4:1:32.5:1:1:0:60:104:1:0:0.1 0/1:106:2:1,1:8,96:0.0189:2,2:17:1:28.5:1:0.16334:11.37:60:4:0.0189:0:1.5 -22 22160384 . T C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97351;LSEQ=TGGTCACATTTAGCAAAGCA;RSEQ=TGAAAACAAAAATGCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:15:3,12:40,197:0.0595:2,2:22.3:1:31.9:1:0.72589:1.23:60:30:0.06:0:1.1 0/1:224:13:6,7:52,159:0.058:2,2:22:1:29.8:1:0.10429:2.61:60:26:0.0588:0:1.1 -22 22162126 . A G 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGAACTTTGTTGACATTATC;RSEQ=TAAGCAGAGCTTAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:107,307:0:2,0:23.6:1:30.4:1:1:0:59.9:58.143:1:0:0.1 0/1:382:52:14,38:116,214:0.1361:2,2:24.8:1:30.6:1:0.27335:1.46988:60:104:0.1376:0:1.1 -22 22162143 . AAG A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.39468;SOR=0.56282;LSEQ=ATCATAAGCAGAGCTTAAAA;RSEQ=AGAGAGAGAGATGGCATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:8:3,5:57,232:0.0269:2,2:23.5:1:29.4:1:0.20531:2.43:60:16:0.0271:0.0034:0 0/1:261:4:2,2:58,199:0.0153:2,2:29.3:1:31:1:0.22728:3.41:60:8:0.0154:0:1 -22 22162257 . G C 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00866;SOR=Inf;LSEQ=GTTTCATACCCGTGAAGGCA;RSEQ=CATGTATATTATCCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:0:1,0:19.1:1:32.3:1:1:0:60:29:1:0:0.1 0/1:21:5:1,4:0,16:0.2381:1,2:25.2:1:31.4:1:0.2381:0:60:10:0.2381:0:1 -22 22162374 . A T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCCCTGTTAACTGGGTGAA;RSEQ=GTCTTGCCTTTATAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:15:0:30.5:1:1:0:60:4:0.6667:0:1 1/1:2:2:0,2:0,0:1:0,0:16.5:1:27.5:1:1:0:60:4:1:0:1.5 -22 22221552 . T A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49637;SOR=Inf;LSEQ=GGCGCGGGCGAGGCCGAGGC;RSEQ=GCGTCCGCTGCGGCCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:50,13:0:2,0:8.5:1:30.9:1:1:0:60:126:1:0:0.3 0/1:66:2:1,1:50,14:0.0303:2,2:9:0:28:1:0.40559:3.48449:60:4:0.0308:0:2 -22 22221563 . C T 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19028;SOR=0.21715;LSEQ=GGCCGAGGCTGCGTCCGCTG;RSEQ=GGCCCCGGGCGGTGGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:4:2,2:91,30:0.032:2,2:10.3:1:28.8:1:0.27025:3.00103:60:8:0.0336:0:1.3 0/0:141:1:0,1:91,49:0.0071:2,0:1:0:25:0:0.35461:0:60:2:0.0071:0:1 -22 22221575 . G T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37891;SOR=3.49185;LSEQ=GTCCGCTGCGGCCCCGGGCG;RSEQ=TGGGGGGGCCGGGCGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:1,0:148,69:0.0046:2,0:9:0:14:0:1:0:60:0:0:0:2 0/1:252:4:1,3:154,94:0.0159:2,2:13.3:1:27.3:1:0.16042:4.88418:60:8:0.0162:0:1.3 -22 22221576 . TG T 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.09315;SOR=0;LSEQ=TCCGCTGCGGCCCCGGGCGG;RSEQ=GGGGGGCCGGGCGTGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:2,1:157,74:0.0128:2,2:21.7:1:33.7:1:1:1.06054:60:6:0.0133:0:0 0/0:281:0:0,0:176,105:0:2,0:16.8:1:30.3:1:1:0:60:39.143:1:0:0.3 -22 22221584 . C T 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7387;SOR=0.67032;LSEQ=GGCCCCGGGCGGTGGGGGGG;RSEQ=CGGGCGTGGCCGGTCGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:5:1,4:184,94:0.0177:2,2:7.8:1:27:1:0.05043:7.77271:60:10:0.0184:0:1 0/1:336:4:1,3:203,129:0.0119:2,2:4.8:1:22:1:0.30399:4.69956:60:3:0.0091:0:1.3 -22 22221589 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38264;SOR=3.38195;LSEQ=CGGGCGGTGGGGGGGCCGGG;RSEQ=GTGGCCGGTCGCGGACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:1:1,0:212,114:0.0031:2,0:16:0:32:0:1:0:60:2:0.0032:0:1 0/1:389:4:1,3:233,152:0.0103:2,2:11:1:28.5:1:0.30583:4.58111:60:8:0.0104:0:1.3 -22 22221680 . C T 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCGGCCCCACGTCGAACAC;RSEQ=TGCCCGCGGACCATCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:0:0,0:219,305:0:2,0:25.1:1:31.7:1:1:0:60:64.5:0.9981:0:0.2 0/1:614:64:28,36:240,309:0.1042:2,2:25.4:1:30.1:1:1:1.00:60:31:0.1028:0:1.4 -22 22221708 . CCCG C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=1.0052;LSEQ=GGACCATCTCCGGGCCCGCG;RSEQ=CCGCCGCCGCCGCCGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:7:4,3:72,169:0.0282:2,2:19.6:1:30:1:0.20565:3.11:60:14:0.0288:0.0121:0.6 0/1:282:8:2,6:96,178:0.0284:2,2:24.4:1:31.9:1:0.71799:1.61544:60:16:0.0293:0.0035:0.3 -22 22221725 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.50043;SOR=Inf;LSEQ=GCGCCCGCCGCCGCCGCCGC;RSEQ=GCCATGTTGGCTGCCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:40,95:0:2,0:12.8:1:30:1:1:0:60:44:1:0:0.2 0/1:154:2:1,1:48,104:0.013:2,2:6.5:1:29:1:0.53654:2.15:60:4:0.0132:0:1 -22 22221954 . C T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACGGGCGGGCCGGCGGG;RSEQ=GGGCGGAGGGAGGGGCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:26.5:1:1:0:60:4:1:0:1 -22 22534324 . C A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACTTGTGGGTACCTGCC;RSEQ=CTTCAATTGTGAAATCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31:1:1:0:60:4:1:0:1 -22 22534988 . T A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04919;SOR=4.4735;LSEQ=GAGCCTTTGTTGAAGATATC;RSEQ=CTGAATACCTCTCATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:0.2222:1,0:23.3:1:30:1:1:0:60:8:0.2222:0:1 1/0:21:12:11,1:9,0:0.5714:0,2:22.4:1:30.3:1:1:0:60:24:0.5714:0:1.1 -22 22535064 . CT C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49697;SOR=Inf;LSEQ=TTTGTGCTTATTTTTCTAAC;RSEQ=TTATGACTGATTATCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:52,20:0:2,0:21.7:1:30.7:1:1:0:60:35:1:0:0.1 0/1:76:2:1,1:45,29:0.0263:2,2:33:1:32:0:1:1.54245:60:4:0.0263:0:0.5 -22 22535082 . T C 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02982;SOR=Inf;LSEQ=ACCTTTATGACTGATTATCA;RSEQ=TTAAGCTTAATATGAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:55,32:0:2,0:23.5:1:30.4:1:1:0:60:86:1:0:0.1 0/1:96:6:4,2:49,41:0.0625:2,2:25.2:1:30.8:1:0.68815:1.66:60:12:0.0625:0:1 -22 22535137 . A G 120 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01401;SOR=3.12668;LSEQ=GATATATAAATATGTCATCA;RSEQ=TGGTCAATATTATTAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:7:4,3:81,66:0.0452:2,2:26.1:1:32.7:1:1:1.09:60:14:0.0464:0:1.9 0/1:116:15:7,8:47,54:0.1293:2,2:28.5:1:30.8:1:1:1.01:60:30:0.1316:0:2.1 -22 22535144 . A G 118 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01639;SOR=2.97847;LSEQ=AAATATGTCATCAATGGTCA;RSEQ=TATTATTAAAGTTATAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:8:4,4:80,74:0.0494:2,2:23.8:1:32.5:1:1:1.08054:60:16:0.0497:0:1.8 0/1:119:16:8,8:46,57:0.1345:2,2:26.3:1:29.5:1:0.78958:1.24:60:15:0.1271:0:2 -22 22535184 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17315;SOR=Inf;LSEQ=AGTAATGCAAAATTGTAGCT;RSEQ=TATATCATTTCACTTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:59,75:0:2,0:26.7:1:30.2:1:1:0:60:133:1:0:0.1 0/1:96:2:1,1:36,58:0.0208:2,2:19.5:1:28.5:1:1:1.60:60:4:0.0211:0.0104:0.5 -22 22535223 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16838;SOR=Inf;LSEQ=TCACTAACATTAATATGTGA;RSEQ=GTGAGAAGATCACTTTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:21,53:0:2,0:22.4:1:30.7:1:1:0:60:148:1:0:0 0/1:52:2:1,1:15,35:0.0385:2,2:30:1:32.5:1:0.52489:2.29:60:4:0.0392:0:1 -22 22820648 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19346;SOR=Inf;LSEQ=GGGGTGGAGGCTATGAAAGG;RSEQ=ACCGGAGCTCAGCGTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:18.1:1:30.3:1:1:0:60:20:1:0:0.1 0/1:17:2:1,1:9,6:0.1176:2,2:7:1:30.5:1:1:1.46382:60:4:0.125:0:1 -22 23655620 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCTAGAGTGGGTGCTGGTG;RSEQ=GTGCAGTACCTGTGGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:33:1:1:0:49:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 23656843 . C A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.243;SOR=0;LSEQ=GAAGGAGAGCAAGCTCCCTG;RSEQ=CAACCCCAGCCAGCCTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:3:2,1:25,25:0.0566:2,2:15:1:28.3:1:1:1.97:56.7:6:0.0566:0:1 0/0:51:0:0,0:24,27:0:2,0:18.8:1:30.6:1:1:0:53.5:50:1:0:0.3 -22 24129240 . C T 131 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02647;SOR=0.32775;LSEQ=GCTGAGGCGCCAGTACCCGG;RSEQ=CCGGTCCGCATTTCGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:20:20,0:52,0:0.2778:1,1:20.7:1:30.5:1:1:0:60:40:0.2778:0:1.1 0/1:54:6:6,0:48,0:0.1111:1,0:21.5:1:29.5:1:1:0:60:12:0.1176:0:1 -22 24129493 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10421;SOR=Inf;LSEQ=CTCCCCGGGCTCGGCCCCGC;RSEQ=GGAGCCCCGGGGCGGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:54,242:0:2,0:23.6:1:31:1:1:0:60:73:0.9966:0:0.2 0/1:265:3:2,1:66,196:0.0113:2,2:20:1:27.7:1:0.16268:5.89:60:6:0.0114:0:1 -22 24134302 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22857;SOR=0;LSEQ=TCCAGCAGGGCCATTGGGTA;RSEQ=GTGAGCGGGCCGGGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:1,26:0,0:1:0,1:21.7:1:29.5:1:1:0:60:26:1:0:1.1 1/1:8:7:1,6:0,1:0.875:0,2:32:1:30:1:1:0:60:14:0.875:0:1.3 -22 24134394 . T C 79 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCGATGCTCTGCCATCTG;RSEQ=CGTGGGTGTGTCGCCATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:23.8:1:30.8:1:1:0:60:12:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 24135672 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15214;SOR=Inf;LSEQ=GCATGCGAGGACCTTGATGT;RSEQ=CTGCATCCACTTGGCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:172,18:0:2,0:22.7:1:32.3:1:1:0:60:62.333:1:0:0.1 0/1:122:2:2,0:113,7:0.0164:2,0:19:1:29.5:1:1:0:60:4:0.0168:0:1 -22 24135703 . A T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03053;SOR=Inf;LSEQ=TTGGCTGGCTGCTGTGTGCC;RSEQ=CCGCCACCAGCAGAGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:264,75:0:2,0:24.9:1:30.1:1:1:0:60:678:1:0:0.1 0/1:245:4:4,0:186,55:0.0163:2,0:20.5:1:32.3:1:0.57751:0:60:8:0.0165:0:1 -22 24135716 . G T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41087;SOR=2.66738;LSEQ=GTGTGCCACCGCCACCAGCA;RSEQ=AGTGACCCAGTGATGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:2:1,1:322,112:0.0046:2,2:12:1:29:1:0.45162:2.86669:60:4:0.0046:0:1 0/1:329:4:1,3:229,96:0.0122:2,2:15.5:1:27.8:1:0.08312:7.10865:60:8:0.0123:0:1.3 -22 24135968 . C CT 133 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.20997;SOR=1.50429;LSEQ=GTTGAAGTTAAATTGAAACA;RSEQ=TTTTTTTTTTTTTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:27:0,27:2,83:0.2015:1,1:31.7:1:30.5:1:1:0:58.7:54:0.2269:0:1.3 0/1:98:27:0,27:6,50:0.2755:2,1:30.6:1:28.1:1:0.17039:0:57.2:12.5:0.3289:0.0102:2.3 -22 24135986 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50389;SOR=0;LSEQ=CACTTTTTTTTTTTTTTTTT;RSEQ=AGATGGAATCTTGTTCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:0,2:0,82:0.0238:1,0:24:1:30.5:1:1:0:60:4:0.0241:0:3.5 0/0:66:0:0,0:1,62:0:1,0:20.8:1:30.9:1:1:0:58.3:20:1:0:1.9 -22 24136007 . C T 53 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04261;SOR=Inf;LSEQ=AGATGGAATCTTGTTCTTGT;RSEQ=GCCCAGGCTGGAGTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:0:1,0:23.9:1:27.8:1:1:0:58.8:12:1:0:1.1 0/1:34:4:0,4:0,30:0.1176:1,0:12:1:26.5:1:1:0:51.5:3:0.1034:0:4 -22 24142977 . GC CT 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07312;SOR=2.54206;LSEQ=ATCTGATGACAGCCTGGGGA;RSEQ=AGGCTCCTGCAAAGTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:41:40,1:31,0:0.5616:1,1:24:1:31.7:1:1:0:60:82:0.5775:0.0685:1 1/0:30:23:21,2:7,0:0.7667:0,2:22.3:1:30.3:1:1:0:60:46:0.7667:0.1667:1 -22 24143502 . C G 291 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.02804;LSEQ=TCCTCCTCACCTCTCTGGCC;RSEQ=CTCAAGTGGAGTTACTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:662:658:242,416:0,0:0.994:0,2:25.9:1:31.1:1:1:0:60:72.111:0.9939:0:1.1 1/1:622:511:202,309:47,63:0.8215:2,2:26:1:30.8:1:0.59199:1.14096:60:45.455:0.821:0:1.2 -22 24143573 . C A 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=44.4388;LSEQ=AGTTTCACATGAGTGGGCCA;RSEQ=AGCCAGTCTGATGGTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:1:1,0:93,250:0.0029:2,0:1:0:26:0:0.27326:0:60:2:0.0029:0:2 0/1:330:38:12,26:100,192:0.1152:2,2:22.6:1:29.8:1:0.85615:1.12809:60:76:0.1162:0:1.6 -22 24143607 . A T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25399;SOR=0;LSEQ=GTGCAGATGCCATCCACGTG;RSEQ=CTCCCACTGTGCCACCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:43,162:0.0144:2,2:12.7:1:23.3:1:0.51175:1.88:60:2:0.0099:0:1.3 0/0:174:0:0,0:45,129:0:2,0:22.8:1:28.9:1:1:0:60:57:1:0:0.2 -22 24143628 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19084;SOR=Inf;LSEQ=CTCCCACTGTGCCACCATTT;RSEQ=CCAGAGCCTGCTGGAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:14,122:0:2,0:25.6:1:31.4:1:1:0:60:135:1:0:0.1 0/1:106:2:1,1:14,90:0.0189:2,2:33.5:1:28.5:1:0.26415:6.24:60:4:0.0196:0:1 -22 24144125 . A C 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCATCTCGGCGCGTGG;RSEQ=GATCCAGCCCTCTCCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:31.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:12.5:1:28.5:1:1:0:60:4:1:0:1 -22 24145395 . A G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03602;SOR=0;LSEQ=TCCCCAGATGGGTTTGCAGA;RSEQ=GCCTGCTGTGCAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:146:146:140,6:0,0:1:0,1:25.2:1:32.5:1:1:0:60:145:1:0:1.1 1/1:73:70:63,7:1,2:0.9589:2,2:23.5:1:32:1:0.03839:16.61:60:69:0.9583:0:1.1 -22 24145622 . C T 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00225;SOR=Inf;LSEQ=CATGAATGGTACAAGGCAGT;RSEQ=GGGCTTGGCTGGGCCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:150,313:0:2,0:23.6:1:30.2:1:1:0:60:76.167:0.9978:0:0.4 0/1:337:7:2,5:114,216:0.0208:2,2:21.6:1:27.3:1:1:1.31842:60:6:0.0182:0:1 -22 24145635 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07102;SOR=Inf;LSEQ=AGGCAGTCGGGCTTGGCTGG;RSEQ=CCTGGCCCCAACCCCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:104,261:0:2,0:24.2:1:31.7:1:1:0:60:72:1:0:0.5 0/1:259:3:2,1:79,177:0.0116:2,2:7.3:1:26.3:1:0.2313:4.45:60:6:0.012:0:1 -22 24145675 . G C 242 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12799;SOR=0;LSEQ=TGTTACGTGGGAACAGTCCC;RSEQ=TTTCCTGCCAGCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:184:184:26,158:0,0:1:0,2:23.8:1:32.2:1:1:0:60:91:1:0:1.3 1/1:103:101:16,85:0,2:0.9806:0,2:20:1:31.4:1:1:0:60:202:0.9806:0:1.3 -22 24145727 . C T 182 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGACCTGACACGCAGGACAT;RSEQ=GGGGCATAGTTTTGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:70:1,69:0,0:1:0,1:24.9:1:29.8:1:1:0:60:22.333:1:0:1.8 1/0:29:19:0,19:0,10:0.6552:0,1:31.4:1:30.3:1:1:0:60:38:0.6552:0:1.8 -22 24158709 . A G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTATGAGTGGAATGAGGG;RSEQ=AGTGTTTATGGCCATGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:24.5:1:31.9:1:1:0:60:16:1:0:1.1 1/1:2:2:2,0:0,0:1:0,0:26.5:1:32.5:1:1:0:60:4:1:0:2 -22 24158755 . T G 27 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03529;SOR=Inf;LSEQ=AGGGCATGGAGCAGGAGGTC;RSEQ=GTGCAGGATGAGGGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:26,2:0:2,0:23.2:1:31.9:1:1:0:60:56:1:0:0.3 0/1:7:2:2,0:5,0:0.2857:0,0:29:1:27:1:1:0:60:4:0.2857:0:1.5 -22 24158826 . AC A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00056;SOR=Inf;LSEQ=TCCCAGTTTCCAGGAAGGCC;RSEQ=CCCCAGTGCCCTGGTTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:74,2:0:1,0:25:1:32.3:1:1:0:60:152:1:0:0.3 0/1:24:5:5,0:19,0:0.2083:1,0:23.6:1:32:1:1:0:60:10:0.2174:0:0.8 -22 24158895 . A G 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=21.81791;LSEQ=CAAAGAAGAAGGGGTGAGGG;RSEQ=GGCCGGTCCATGCCCAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:2:2,0:186,47:0.0085:2,0:27:1:33:0:1:0:60:4:0.0087:0:1 0/1:190:30:26,4:121,39:0.1579:2,2:20.8:1:30.4:1:0.23785:2.09:60:29:0.1551:0:1.1 -22 24158899 . C A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32075;LSEQ=GAAGAAGGGGTGAGGGAGGC;RSEQ=GGTCCATGCCCAAGCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:261:134:102,32:100,27:0.5134:2,2:23.8:1:30.5:1:0.65843:1.16128:60:133:0.5155:0:1.1 0/1:210:53:39,14:121,35:0.2524:2,2:25.1:1:30.1:1:0.57612:1.23967:60:106:0.2536:0:1.1 -22 24159175 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23585;SOR=Inf;LSEQ=TCCTGGCCCTCAGGGTGGGT;RSEQ=TCATCATGGAGCACTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:47,159:0:2,0:21.5:1:31.8:1:1:0:60:50.5:1:0:0.1 0/1:195:2:1,1:48,145:0.0103:2,2:27.5:1:30.5:1:0.44039:3.00:60:4:0.0105:0:1 -22 24159176 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2367;SOR=Inf;LSEQ=CCTGGCCCTCAGGGTGGGTG;RSEQ=CATCATGGAGCACTGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:42,158:0:2,0:21.7:1:29.9:1:1:0:60:65.667:1:0:0 0/1:190:2:1,1:47,141:0.0105:2,2:7:1:29:1:0.44244:2.98:60:4:0.0108:0:1.5 -22 24159244 . G A 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00294;SOR=Inf;LSEQ=TTTGGGTTCCATATCATCTG;RSEQ=AAAGTCATAACACCTGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:0,75:0:1,0:27.2:1:30.6:1:1:0:60:17.75:1:0:0.3 0/1:36:5:0,5:1,30:0.1389:1,0:26.2:1:31.6:1:1:0:60:10:0.1389:0:2.2 -22 24159307 . A T 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCATAGGCTGAGTTCTC;RSEQ=TAGTAAAGTGTTATATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:0,24:0,0:1:0,1:24.1:1:30.1:1:1:0:60:23:1:0:1.3 1/1:7:7:0,7:0,0:1:0,0:22:1:29.6:1:1:0:60:14:1:0:1.1 -22 24159437 . G T 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCTGAGTGCTCCAGGG;RSEQ=GGCCTAGTAACCCAATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:28.1:1:30.5:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 24167098 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=GCAGGAGCGAAGGGCAGAAA;RSEQ=GAAGGTCCCCACCAGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:19.3:1:32:1:1:0:60:12:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:23:1:29.5:1:1:0:60:4:0.6667:0:1 -22 24167329 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17594;SOR=Inf;LSEQ=ACCCTGGTGGGCAGGGCCCA;RSEQ=CCCAGGCCTGGCAGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:159,23:0:2,0:22.9:1:31.6:1:1:0:60:90:1:0:0.1 0/1:132:2:1,1:99,31:0.0152:2,2:7:1:25.5:1:0.42748:3.15908:60:4:0.0153:0:1 -22 24167513 . G A 192 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCCCTGAAGCTGTGCTC;RSEQ=GAGCTGGGGTTGGGCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:0:0,0:293,395:0:2,0:24.1:1:30.5:1:1:0:60:136.6:1:0:0.1 0/1:649:85:37,48:275,289:0.131:2,2:26.7:1:30.1:1:0.41543:1.23405:60:170:0.1316:0:1.1 -22 24167657 . G GAA 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=TCCCTGCAAAACTGTTTTGA;RSEQ=AAAGACTTCTCTGTGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:9,108:0:2,0:22.8:1:31.4:1:1:0:60:234:1:0:0.1 0/1:83:8:3,5:13,62:0.0964:2,2:20.9:1:28.6:1:0.17826:2.82:60:16:0.0964:0.0361:0.1 -22 24167744 . GTCC G 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.00718;SOR=Inf;LSEQ=GGGGTCTGTGTGTTTGCTCC;RSEQ=TCCTCCTGCCCTATGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:0,18:0:1,0:25.4:1:28.1:1:1:0:60:5:1:0:0.4 0/1:9:4:1,3:0,5:0.4444:0,2:31.3:1:32.5:1:0.44444:0:60:8:0.4444:0:0.3 -22 24175440 . G T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGCATCAGCATGGTCCA;RSEQ=CCCGTGCTGTCCTGTCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:35.3:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 24175583 . A C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03254;SOR=Inf;LSEQ=TCATGGCGACAACACTTGTT;RSEQ=TGGAAAGGCCCTGGCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:49,0:0:1,0:26.2:1:28.4:1:1:0:60:98:1:0:0.1 0/1:24:3:3,0:20,1:0.125:1,0:32.3:1:30.3:1:1:0:60:6:0.1364:0:1.3 -22 24175620 . G A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03103;SOR=Inf;LSEQ=CCTCCAGCAGCTCCCTTGAG;RSEQ=TTCAGGTGACTGGAGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:95,0:0:1,0:24.7:1:31.6:1:1:0:60:190:0.9896:0:0 0/1:45:3:3,0:42,0:0.0667:1,0:22.7:1:28.3:1:1:0:60:6:0.0698:0:1.3 -22 24175650 . C T 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=Inf;LSEQ=CTGGAGCATCCACTGGGTGC;RSEQ=AGCAGTGCTGCTGGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:132,2:0:1,0:24.6:1:31.4:1:1:0:60:268:1:0:0 0/1:74:7:6,1:66,1:0.0946:1,2:21:1:30.9:1:0.18141:10.26095:60:14:0.0946:0:1 -22 24175923 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.3145;SOR=4.17994;LSEQ=CTGTGGTCCTGGGCTCTGCC;RSEQ=ACAGGCACCTGGCTTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:1:1,0:106,310:0.0024:2,0:1:0:28:0:0.25659:0:60:2:0.0025:0:1 0/1:301:3:2,1:99,199:0.01:2,2:11.3:1:27:1:0.26148:4.00:60:6:0.0102:0:1.3 -22 24175943 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16324;SOR=Inf;LSEQ=CACAGGCACCTGGCTTTCCA;RSEQ=GCAGAGGCAGGGCCATTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:50,231:0:2,0:22.4:1:30.7:1:1:0:60:30.222:1:0:0.1 0/1:191:2:1,1:45,144:0.0105:2,2:8.5:1:30:1:0.42463:3.18:60:4:0.0105:0:1 -22 24176053 . G T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00356;SOR=Inf;LSEQ=TGATAAGGCCCCATCCAAAC;RSEQ=CCAGGGTATGTTTCCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:15,39:0:2,0:22.5:1:32.2:1:1:0:60:108:1:0:0.1 0/1:19:4:1,3:3,12:0.2105:2,2:35:1:29.8:1:1:1.31:60:8:0.25:0:1 -22 24176164 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0103;SOR=Inf;LSEQ=TGATGAGCAGGGCCTGAGTG;RSEQ=CAGACAGGCGAGGCTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:83,10:0:2,0:25.3:1:30.9:1:1:0:60:22.25:1:0:0.1 0/1:45:4:4,0:38,3:0.0889:2,0:18.5:1:28:1:1:0:60:8:0.0909:0:1 -22 24176232 . C T 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCACATCCTGCCTCTGTTCC;RSEQ=ACCCCTACACTTGGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:25:19,6:265,46:0.0744:2,2:19.7:1:30.8:1:0.2471:1.81534:60:50:0.0753:0:1 0/0:226:0:0,0:181,45:0:2,0:22:1:30.3:1:1:0:60:112:1:0:0.2 -22 24176275 . C T 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09493;SOR=6.23044;LSEQ=TAGAGCCTTGGGAAGGGCAG;RSEQ=GCCCAGGCTGGGAGCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:1:0,1:397,217:0.0016:2,0:1:0:26:0:0.35447:0:60:2:0.0016:0:1 0/1:497:5:1,4:309,182:0.0101:2,2:16.2:1:29:1:0.06821:6.766:60:10:0.0102:0:1 -22 24176287 . G A 192 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=144.0479;LSEQ=AAGGGCAGCGCCCAGGCTGG;RSEQ=AGCTGGCCCCGACTCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:744:1:0,1:446,295:0.0013:2,0:47:0:30:0:0.39892:0:60:2:0.0014:0:1 0/1:627:102:59,43:312,211:0.1627:2,2:25.1:1:28.8:1:0.74202:1.07755:60:204:0.1648:0:1.2 -22 24176460 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16017;SOR=Inf;LSEQ=GGACAGAGGCGAGGGGACAG;RSEQ=CCAGCGCCATCCTGAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:80,204:0:2,0:23.3:1:31.3:1:1:0:60:46.333:1:0:0.2 0/1:190:2:1,1:46,142:0.0105:2,2:14.5:1:27.5:1:0.43453:3.06:60:4:0.0108:0:1 -22 24176480 . C CG 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAGCGCCATCCTGAGGAT;RSEQ=GGGTGGGGGTGGAGTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:71,138:0:2,0:23.4:1:30.5:1:1:0:60:103.5:1:0:0.1 0/1:140:16:5,11:30,94:0.1143:2,2:23.3:1:29.6:1:0.54689:1.42:60:15:0.1087:0.0071:0.1 -22 24176527 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16804;SOR=Inf;LSEQ=GGTGGCCCTTCCCGGCACAC;RSEQ=TTCCATTTGTTGAGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:143,65:0:2,0:24:1:30.5:1:1:0:60:68.333:1:0:0.6 0/1:145:2:1,1:94,49:0.0138:2,2:22:1:30.5:1:1:1.90923:60:4:0.014:0:1 -22 24176544 . C T 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57283;SOR=2.82956;LSEQ=CACATTCCATTTGTTGAGCC;RSEQ=CAGTCCTGCCCCCCACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:1:0,1:185,83:0.0037:2,0:1:0:27:0:0.31227:0:60:2:0.0038:0:1 0/1:191:2:1,1:134,55:0.0105:2,2:8.5:1:32:1:0.50152:2.42352:60:4:0.0106:0:1 -22 24176677 . GCAACAGGTCATGTTCAATTTCTT G 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14596;LSEQ=TAACAGTTTTTAAATAAAAG;RSEQ=CAACAGGTCATGTTCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:140:55,85:205,255:0.2329:2,2:32.1:1:32:1:0.28514:1.24198:59.9:280:0.2365:0.0266:0.1 0/1:637:27:14,13:276,333:0.0424:2,2:28.9:1:31.2:1:0.55669:1.30:60:54:0.0431:0.0126:0.1 -22 24176763 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50365;SOR=0;LSEQ=TAATGAGAGCCAGGAGTGGG;RSEQ=CCGGGGCCTGGGGGGACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:0,2:25,139:0.012:2,0:12.5:1:31:1:1:0:60:4:0.0121:0:1 0/0:135:0:0,0:23,112:0:2,0:21.6:1:31.9:1:1:0:60:270:1:0:0.1 -22 24176959 . CA C 77 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAGCTGTGAGGCTCAGGG;RSEQ=AGAGGCTCTCTGCCTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:1,0:0.8333:0,0:16:1:33.3:1:0.16667:0:60:10:0.8333:0.1667:2.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 24656027 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGAGAGTGGCTCAGAGC;RSEQ=GGGCTCACAGCTGCTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:1:30.5:1:1:0:31:4:1:0:1 -22 24656692 . A G 90 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22164;SOR=0.21568;LSEQ=TGGGGTTGCATGGGCTGGAG;RSEQ=CTGTCTTCCCATACCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:7,0:17,2:0.2692:2,0:23.1:1:32.3:1:1:0:34:14:0.2692:0:2 0/1:14:1:1,0:10,3:0.0714:2,0:16:0:33:0:1:0:34:2:0.0769:0:2 -22 24656710 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56222;SOR=0.60748;LSEQ=AGACTGTCTTCCCATACCTG;RSEQ=GACATGACCTCCAAGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:14:14,0:24,3:0.3415:2,1:25.6:1:31.3:1:0.53902:0:37:13:0.3333:0:1.5 0/1:21:5:5,0:13,3:0.2381:2,0:12.4:1:30.6:1:0.54887:0:39.4:10:0.2381:0:1.2 -22 24656730 . T A 49 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.23265;LSEQ=AGACATGACCTCCAAGGACC;RSEQ=GCTGTCAGTCATGGTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:3,0:50,13:0.0455:2,0:6.7:1:31.3:1:1:0:42.3:6:0.0484:0:2.3 0/1:36:2:1,1:24,10:0.0556:2,2:9.5:1:25.5:1:0.52381:2.33552:35:1:0.0286:0:1 -22 24656818 . A T 111 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01789;SOR=0.12076;LSEQ=AGCAGCGTGGGGCCAAAGAC;RSEQ=GTGGCGAGGTTGTGCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:12:7,5:45,73:0.0923:2,2:30.4:1:31:1:0.22021:2.26:31.2:24:0.0923:0:3.2 0/1:83:1:1,0:34,47:0.012:2,0:17:0:33:0:0.42683:0:23:2:0.0128:0:2 -22 24656822 . G C 114 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01737;SOR=0.11857;LSEQ=GCGTGGGGCCAAAGACAGTG;RSEQ=CGAGGTTGTGCAGGGACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:12:7,5:42,71:0.096:2,2:29.8:1:31.8:1:0.21401:2.35:31.2:24:0.0976:0:3.2 0/1:81:1:1,0:32,48:0.0123:2,0:13:0:34:0:0.40741:0:23:2:0.0127:0:2 -22 24656851 . T C 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74387;SOR=0.65361;LSEQ=TGCAGGGACATCTTATTGAC;RSEQ=GCTTCCTTCTCTGCCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:8:1,7:24,42:0.1081:2,2:25:1:30.1:1:0.25281:3.94157:36.8:16:0.1081:0:1.6 0/1:41:3:1,2:14,23:0.0732:2,2:17.3:1:20.7:1:1:1.21153:30:2:0.05:0:1.7 -22 24656854 . T C 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66892;SOR=0.77354;LSEQ=AGGGACATCTTATTGACTGC;RSEQ=TCCTTCTCTGCCACCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:35:13,22:7,20:0.5645:2,2:25.4:1:32.3:1:0.41816:1.67:38.5:70:0.5645:0:1.7 1/0:34:17:4,13:7,10:0.5:2,2:23.4:1:29.4:1:0.46464:2.21979:42.9:16:0.5161:0:1.2 -22 24656881 . G T 83 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25317;SOR=0.26023;LSEQ=TCTGCCACCCTGTAGAGGAC;RSEQ=GAAGCAGAGGGTGCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:7:1,6:6,28:0.1707:2,2:9.6:1:29.6:1:1:1.27827:25.6:14:0.1707:0:3.7 0/1:20:1:0,1:3,16:0.05:2,0:47:0:29:0:1:0:23:2:0.0526:0:3 -22 24656904 . C T 45 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61853;LSEQ=AGCAGAGGGTGCTGTTTCAA;RSEQ=GCCACCACCAGGAGAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:0,3:2,20:0.12:2,0:34.3:1:29:1:1:0:24.7:6:0.12:0:3 0/1:13:1:0,1:2,10:0.0769:2,0:24:0:32:0:1:0:23:2:0.0833:0:3 -22 24656936 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54644;SOR=0;LSEQ=GAGAGAGGCAGAGGGGCTGT;RSEQ=CCGTGCTAGAGTCCTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:0,3:1,14:0.1667:1,0:34.7:1:29.3:1:1:0:24.7:6:0.1667:0:3 0/0:6:0:0,0:2,4:0:2,0:29.3:1:33.3:1:1:0:34.2:12:1:0:0.8 -22 24656967 . C G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=3.98567;LSEQ=GTCCTCAGGGAGGGAGTGAC;RSEQ=TCGACCCTGGCTGTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:1,8:0.1818:2,0:9.5:1:32.5:1:1:0:36:4:0.1818:0:1 1/0:4:2:1,1:1,1:0.5:2,2:14:1:32.5:1:1:1:23:4:0.5:0:1.5 -22 24657936 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCTCTGTGCATGGGCCC;RSEQ=GGAGGCAGACCTGCCCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31.5:1:1:0:48:4:1:0:1.5 -22 25045815 . G C 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18528;SOR=0.20944;LSEQ=GAAACAGCACCCTCTGCTTC;RSEQ=GTCCTCTACAGGGTGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:12,5:0.1905:2,0:22:1:32.3:1:0.53216:0:35.3:8:0.2105:0:1.5 0/1:22:1:1,0:17,3:0.0455:2,0:24:0:32:0:1:0:27:2:0.0455:0:2 -22 25045851 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50771;SOR=0;LSEQ=GCAGAGAAGGAGGCGGTCAA;RSEQ=AAGGTGTCCCTGCACAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:32,20:0.037:2,2:15:1:30.5:1:1:1.58559:40:4:0.037:0:2 0/0:39:0:0,0:24,15:0:2,0:21.4:1:26.9:1:1:0:52.3:18.5:1:0:0.7 -22 25045855 . G A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.9787;LSEQ=AGAAGGAGGCGGTCAATAAG;RSEQ=TGTCCCTGCACAACCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:18:13,5:23,16:0.3158:2,2:19.8:1:30.2:1:0.38933:1.79:43:36:0.3158:0:1.2 0/1:45:14:9,5:17,14:0.3111:2,2:30.2:1:28.9:1:0.74599:1.47:44.1:28:0.3256:0:1.4 -22 25045910 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22031;SOR=Inf;LSEQ=CACGCTGCTCCGGCCCTCCG;RSEQ=GAAGGAGAGCAAGCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:30,35:0:2,0:26.8:1:29.9:1:1:0:54.2:31.5:1:0:0.4 0/1:58:2:1,1:22,34:0.0345:2,2:22.5:1:28.5:1:1:1.53:54.5:4:0.0351:0:1.5 -22 25045947 . TG CA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23973;SOR=0;LSEQ=CCTGCCAACCCCAGCCAGCC;RSEQ=TCACCATGACTGACAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:13,21:0.0556:2,0:24:1:31.5:1:0.5254:0:36:4:0.0556:0.0278:0.5 0/0:37:0:0,0:13,24:0:2,0:20.7:1:29.3:1:1:0:58.2:17.5:1:0:0.2 -22 25046040 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CCCCAGCCTGACAGAGGTGG;RSEQ=CTCTGCCTGCCCCACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:1,7:0.2:2,0:36:0:30:1:1:0:33.5:4:0.2:0:1 0/0:6:0:0,0:2,4:0:2,0:27.5:1:30.5:1:1:0:39.3:12:1:0:0 -22 25159950 . G A 42 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCTCCGCGGGGTCAGAGGC;RSEQ=CAAAGCCCCTTTTCCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:0.6:2,2:12:1:27:1:1:1.73:60:6:0.6:0:1.3 -22 25160592 . CGTGTGT C 49 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=38;MSI=22.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCATTCTTTTTGACCTTGC;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:7,0:0.2308:0,0:22.7:1:31.1:1:1:0:53.3:6:0.2308:0.0769:0.7 0/0:1:0:0,0:1,0:0:0,0:33:0:31:0:1:0:60:2:1:0:0 -22 25160668 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02734;SOR=Inf;LSEQ=CTCTCTCTTTTGCCCAGGCT;RSEQ=GAGTGCAACAATGCAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:23,1:0:1,0:23.3:1:30.6:1:1:0:60:11:1:0:0.3 0/1:18:4:4,0:14,0:0.2222:1,0:21.8:1:29.3:1:1:0:60:8:0.2222:0:1 -22 25160783 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20637;SOR=Inf;LSEQ=AACAAAACCCAGCGGGAAAA;RSEQ=TTTGCCTGCCATTGGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:97,91:0:2,0:25.8:1:32.1:1:1:0:60:93:1:0:0.2 0/1:157:2:1,1:79,76:0.0127:2,2:48:0:29:1:1:1.03923:60:4:0.0127:0:1 -22 25160785 . T C 144 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=6.54893;LSEQ=CAAAACCCAGCGGGAAAAGT;RSEQ=TGCCTGCCATTGGCATGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:5:2,3:93,88:0.0269:2,2:23.4:1:33:1:0.67745:1.58133:60:10:0.0273:0:1 0/1:156:24:13,11:66,66:0.1538:2,2:27.6:1:31.6:1:0.82523:1.18:60:48:0.1538:0:1 -22 25160792 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50151;SOR=0;LSEQ=CAGCGGGAAAAGTTTGCCTG;RSEQ=CATTGGCATGGCTGATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:89,90:0.011:2,2:22:1:29.5:1:1:1.01:60:4:0.0116:0:1 0/0:155:0:0,0:77,78:0:2,0:29.6:1:31.2:1:1:0:60:37.75:1:0:0.3 -22 25494553 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15061;SOR=Inf;LSEQ=AGAAGCATCAAGGCTGCGTA;RSEQ=GATCTGCAGGCAGCTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:26,0:0:1,0:23.2:1:33:1:1:0:60:52:1:0:0.1 0/1:17:2:2,0:14,1:0.1176:1,0:13:1:31:1:1:0:60:4:0.125:0:1.5 -22 25494592 . A G 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.10574;SOR=Inf;LSEQ=GGTTGGAAACAACTGGGTGG;RSEQ=GGGGGCGGGGGGGGGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:38,1:0:1,0:24:1:29.6:1:1:0:60:38:1:0:0.1 0/1:36:3:1,2:33,0:0.0833:1,2:11.3:1:22.3:1:0.00476:0:60:2:0.0606:0:2.7 -22 25494598 . CG C 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.59206;SOR=2.39706;LSEQ=AAACAACTGGGTGGAGGGGG;RSEQ=GGGGGGGGTTTGCTCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:1,0:44,2:0.0213:1,0:48:0:30:0:1:0:60:2:0.0213:0:2 0/1:40:2:1,1:34,4:0.05:2,2:25:1:28.8:1:0.23718:7.71345:60:4:0.0513:0.025:0 -22 25494629 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17339;SOR=Inf;LSEQ=TTGCTCTGATTGCCCTGATG;RSEQ=CAGGGGCTCTGGAAGAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:75,21:0:2,0:21.1:1:31.2:1:1:0:60:47:1:0:0.1 0/1:69:2:1,1:50,17:0.029:2,2:27.5:1:25:1:0.45652:2.88688:60:4:0.0317:0:1.5 -22 25494682 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20342;SOR=Inf;LSEQ=GCCCAAGGTCTAGGACTCTG;RSEQ=GGCTGTGGAATGTGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:137,89:0:2,0:25.8:1:30.1:1:1:0:60:44.2:1:0:0.1 0/1:187:2:1,1:102,83:0.0107:2,2:14.5:1:32.5:1:1:1.22755:60:4:0.011:0:1 -22 25494744 . C T 186 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=119.8108;LSEQ=GGGGACCTGTGGAGTGACAC;RSEQ=CCTTTGTCAAGATGCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:120,149:0.0037:2,0:46:0:14:0:1:0:60:0:0:0:3 0/1:252:78:37,41:78,96:0.3095:2,2:25.5:1:29.6:1:0.78458:1.11:60:156:0.3171:0:1.2 -22 25494775 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.20426;SOR=Inf;LSEQ=GATGCCAGGGCTGCCTGGCT;RSEQ=CCCCATTCCCTGCCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:86,143:0:2,0:24.1:1:32:1:1:0:60:75.333:0.9956:0:0.1 0/1:191:2:1,1:71,117:0.0105:2,2:24.5:1:28:1:1:1.64:60:4:0.0106:0:2 -22 25495049 . T C 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTTGCCTTGCCCAGAGAG;RSEQ=GGAAGCTGTTGAGCACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:20.7:1:30.7:1:1:0:60:6:0.75:0:1 1/1:1:1:0,1:0,0:1:0,0:22:0:32:0:1:0:60:2:1:0:1 -22 25495827 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAATGGTGGGATTCCAAT;RSEQ=GGGCAGTCCCCATTGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:45.5:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 25593452 . A G 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08908;SOR=5.00307;LSEQ=GTGAATGAATAGAGTCTCCC;RSEQ=TGCATGCAGGCCCTGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:14,9:0.08:2,0:24.5:1:29.5:1:0.52:0:60:4:0.0833:0:1 0/1:16:5:3,2:6,4:0.3125:2,2:17:1:30.6:1:1:1:60:10:0.3125:0:1.2 -22 25593459 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.52367;SOR=0;LSEQ=AATAGAGTCTCCCATGCATG;RSEQ=AGGCCCTGACTGGGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:16,11:0.069:2,2:19:1:28:1:1:1.43545:60:4:0.069:0:1 0/0:17:0:0,0:10,7:0:2,0:28.1:1:32.2:1:1:0:60:34:1:0:0.8 -22 25594000 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGTGCAGTAGGTCTGCAAG;RSEQ=TCCTCAAAGATGTGATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 25770400 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAACGCCAGCCTCAAGTG;RSEQ=CATCAGGGACCTCCCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:18:1:28.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 25770473 . T C 81 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACATTGGGCCCTCAGCC;RSEQ=GGCCAGACGGTCTGCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1:0,2:22.1:1:28.9:1:1:0:55:6:1:0:1.1 1/1:1:1:1,0:0,0:1:0,0:3:0:30:0:1:0:60:2:1:0:1 -22 25770706 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13257;SOR=Inf;LSEQ=TGCCTGCATGGTAGTGATGG;RSEQ=AACCCCAGAGACAGTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:124,62:0:2,0:27.6:1:32.4:1:1:0:60:61:1:0:0.2 0/1:107:2:1,1:66,39:0.0187:2,2:36.5:1:30.5:1:1:1.68356:60:4:0.0189:0:1 -22 25770725 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15761;SOR=Inf;LSEQ=GCAACCCCAGAGACAGTGGG;RSEQ=TCCTGGGCAAAAGGCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:131,89:0:2,0:26.1:1:32.2:1:1:0:60:109:1:0:0.4 0/1:146:2:1,1:90,54:0.0137:2,2:40.5:1:29:1:1:1.66052:60:4:0.0138:0:1 -22 25770790 . T A 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1316;SOR=0.76273;LSEQ=CACTGTCCCTCTTGCCAGGA;RSEQ=GGCCAAGCTTGTCACTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:307:170:85,85:67,70:0.5537:2,2:26.9:1:30.7:1:0.90869:1.04:60:340:0.5574:0:1.1 0/1:216:105:57,48:56,55:0.4861:2,2:24:1:30:1:0.58835:1.17:60:104:0.486:0:1.1 -22 25770879 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13538;SOR=Inf;LSEQ=CCAGCACCTCATTCTAACCA;RSEQ=GGGAAAGCTGGGGTGTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:36,104:0:2,0:26.1:1:31:1:1:0:59.9:139:1:0:0.2 0/1:82:2:1,1:21,59:0.0244:2,2:19.5:1:28:1:0.46703:2.77:60:4:0.0244:0:1.5 -22 25770897 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1124;SOR=Inf;LSEQ=CAGGGGAAAGCTGGGGTGTA;RSEQ=CAGCCCCAAAATACGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:19,95:0:2,0:24.1:1:31.9:1:1:0:59.9:113:1:0:0.1 0/1:58:2:1,1:8,48:0.0345:2,2:15.5:1:30.5:1:0.28857:5.72:60:4:0.0345:0:1 -22 26043158 . C T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00244;SOR=Inf;LSEQ=CGGGCCTCACCTCCACCCAC;RSEQ=GCCCCCTCCCACCACCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:28,2:0:2,0:11.4:1:25.5:1:1:0:59.8:4:1:0:2.3 0/1:20:6:6,0:14,0:0.3:1,0:28:1:29.8:1:1:0:60:12:0.3158:0:1 -22 26043803 . T C 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=0.29958;LSEQ=GAGAGAGTGAAATGGCTGGG;RSEQ=GCAGTGGCTCATGCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:34:3,31:28,108:0.2:2,2:25.1:1:30.3:1:0.13949:2.66643:59.5:68:0.2012:0:1 0/1:144:10:1,9:26,106:0.0694:2,2:25.2:1:29.9:1:0.68744:2.19764:60:20:0.0709:0:1.1 -22 26043805 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58658;SOR=2.51934;LSEQ=GAGAGTGAAATGGCTGGGTG;RSEQ=AGTGGCTCATGCCTGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:1:1,0:30,133:0.0061:2,0:1:0:25:0:0.18902:0:60:2:0.0061:0:1 0/1:131:2:2,0:24,104:0.0153:2,0:8.5:1:27:1:0.03876:0:60:4:0.0156:0:2 -22 26043815 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18419;SOR=Inf;LSEQ=TGGCTGGGTGCAGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:16,119:0:2,0:22.1:1:30.1:1:1:0:59.3:66.5:1:0:0.3 0/1:102:2:1,1:10,90:0.0196:2,2:23.5:1:32:0:0.20501:8.63:60:4:0.0202:0:2.5 -22 26044080 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00648;SOR=Inf;LSEQ=GCGACAAGAGCAAAAACTCC;RSEQ=TCTAAAAAACAAATAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:114,6:0:2,0:22.4:1:30.4:1:1:0:60:240:1:0:0 0/1:71:5:3,2:63,3:0.0704:1,2:22.8:1:29.6:1:0.03682:12.81827:60:10:0.0704:0:1.2 -22 26044112 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18219;SOR=Inf;LSEQ=AATAAGCAAACAGAACAAAA;RSEQ=AAAACAAAAACGAGAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:201,36:0:2,0:23.2:1:31.9:1:1:0:60:78:1:0:0.1 0/1:177:2:1,1:148,27:0.0113:2,2:27:1:26.5:1:0.29212:5.40096:60:4:0.0114:0:1 -22 26388019 . G T 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02006;SOR=0;LSEQ=AGATGGGCTGAGTATCCACT;RSEQ=TGCGTGGTGGTGCAGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:7,1:52,6:0.1212:2,2:25.8:1:30.8:1:1:1.23383:60:16:0.1231:0:1.1 0/0:46:0:0,0:39,7:0:2,0:20.1:1:31.6:1:1:0:60:92:1:0:0 -22 26388087 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19955;SOR=Inf;LSEQ=GGGAGCAGCACCCCCTGCAC;RSEQ=GGTGAGCAAGCTCTGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:138,92:0:2,0:24.2:1:30.3:1:1:0:60:114:0.9956:0:0.4 0/1:187:2:1,1:111,73:0.0107:2,2:30:1:29:1:1:1.51698:60:4:0.0108:0:1.5 -22 26388111 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08271;SOR=Inf;LSEQ=GAGCAAGCTCTGTGTGCCAT;RSEQ=CCCTGGAGTATCTATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:160,133:0:2,0:25.9:1:32.1:1:1:0:60:47.833:0.9965:0:0.5 0/1:228:3:1,2:120,105:0.0132:2,2:24.7:1:27.3:1:0.60152:2.27768:60:6:0.0133:0:2.3 -22 26388119 . G A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1674;SOR=1.4734;LSEQ=TCTGTGTGCCATGCCCTGGA;RSEQ=TATCTATTCCCTCCTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:28:16,12:152,133:0.0895:2,2:26.5:1:30.5:1:0.84301:1.17:60:27:0.0865:0:1.9 0/1:245:31:17,14:106,107:0.1265:2,2:24.1:1:29.3:1:0.70151:1.22:60:62:0.1286:0:2 -22 26388144 . T A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.75913;LSEQ=TATTCCCTCCTCTATGAAAC;RSEQ=TGGAACACCTGGTTGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:104:53,51:113,108:0.32:2,2:27.2:1:30.3:1:1:1.00679:60:103:0.3209:0:1.3 1/0:269:172:83,89:50,47:0.6394:2,2:23.4:1:29.6:1:0.614:1.14017:60:85:0.6439:0:1.3 -22 26388180 . G A 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96054;LSEQ=AGGATCCCATAAATCTGTCC;RSEQ=CAGAGAGAGCCTCTCACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:2,1:112,143:0.0116:2,2:12.3:1:29.7:1:0.58511:2.54:60:6:0.0119:0:1.7 0/1:179:2:2,0:76,101:0.0112:2,0:1:0:24:1:0.1885:0:60:4:0.0112:0:2 -22 26388192 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15773;SOR=Inf;LSEQ=ATCTGTCCGCAGAGAGAGCC;RSEQ=CTCACGGAGAACTTACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:91,141:0:2,0:23.3:1:29.8:1:1:0:60:45.4:0.9956:0:0.4 0/1:154:2:1,1:60,92:0.013:2,2:26:0:32.5:1:1:1.53:60:4:0.0132:0:1 -22 26790704 . G T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64239;SOR=1.94933;LSEQ=TGTGAGATGGAGGTCACAGT;RSEQ=AGCCGACACCATACCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:3,1:16,0:0.2:1,2:32.8:1:30:1:0.2:0:60:8:0.2105:0:1 0/1:9:3:3,0:6,0:0.3333:0,0:33.3:1:31.7:1:1:0:60:6:0.3333:0:1.3 -22 26790759 . CAA C 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=1;SOR=0.89749;LSEQ=GAGACAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAATTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:14:13,1:8,2:0.3784:2,1:24.9:1:31.5:1:0.5504:3.09:60:28:0.3784:0.1351:0.1 0/1:34:12:7,5:10,0:0.3529:0,2:19.1:1:30.8:1:0.03964:0:60:24:0.3636:0.0588:0.3 -22 26790778 . AAAAG A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18651;SOR=0.5779;LSEQ=TCAAAAAAAAAAAAAAATTG;RSEQ=AAAGAAAGGAAAAAGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:28:23,5:28,5:0.4516:2,2:17:1:30.4:1:1:1.21345:60:56:0.4667:0.129:0.1 0/1:56:18:11,7:27,11:0.3214:2,2:25.7:1:29.6:1:0.54478:1.54925:60:36:0.3214:0.0714:0.2 -22 26790885 . G C 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0673;SOR=0.62553;LSEQ=GGCAGGGCCAGAGCTCAGCT;RSEQ=ATCATTCATGGGCTTGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:63:27,36:74,72:0.3014:2,2:26.1:1:31.5:1:0.36565:1.36829:60:126:0.3043:0:1 0/1:146:31:14,17:58,57:0.2123:2,2:24.9:1:31.3:1:0.68722:1.2338:60:62:0.2168:0:1.2 -22 26790901 . G GTCAC 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50469;SOR=0.86015;LSEQ=AGCTGATCATTCATGGGCTT;RSEQ=TCAGTCAGTAAAAGAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:118:51,67:42,41:0.5813:2,2:28.1:1:30.9:1:0.31777:1.34375:60:117:0.5879:0.1034:0.7 1/0:136:74:34,40:28,34:0.5441:2,2:26.1:1:30.2:1:1:1.03:59.9:148:0.5481:0.1029:0.5 -22 26790928 . G T 29 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77385;LSEQ=AGTAAAAGAATGGGGATTCC;RSEQ=AGGAAGGACAAACAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:61,106:0.0118:2,2:18:0:29.5:1:1:1.73:60:4:0.012:0:1.5 0/0:109:1:0,1:43,65:0.0092:2,0:1:0:22:0:1:0:60:2:0.0095:0:2 -22 26790999 . G T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94474;LSEQ=CCAGATGCCTCAGAAACCCA;RSEQ=ATCCTGTTTCCCAGGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:14:1,13:2,36:0.2692:2,1:30.1:1:28.5:1:1:1.38:60:28:0.2692:0:1.1 0/1:31:8:1,7:1,22:0.2581:1,2:23:1:28.6:1:0.45591:3.01:60:16:0.2581:0:1.1 -22 27561447 . A T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03184;SOR=Inf;LSEQ=CAGGTAGAGTTGGAGGAGGG;RSEQ=TAAGAGATAAATTATGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:266,149:0:2,0:25.3:1:29.8:1:1:0:60:36.727:1:0:0.6 0/1:305:4:1,3:174,127:0.0131:2,2:17.5:1:28.5:1:0.31602:4.09211:60:8:0.0133:0:1.3 -22 27561500 . G A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.48523;LSEQ=TACCAAGCCAGTCCATCCAT;RSEQ=GGCAACACTACAAAGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:503:375:184,191:59,65:0.7455:2,2:25.1:1:29.6:1:0.83593:1.06:60:374:0.751:0:1.1 1/0:334:196:93,103:62,76:0.5868:2,2:25.9:1:29:1:0.65764:1.11:60:97:0.5915:0:1.1 -22 27561618 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52506;SOR=0;LSEQ=TAATGATTATTTTTTCCTTT;RSEQ=TACCCTACTTTCTTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:8,92:0.0196:2,2:5.5:1:27.5:1:0.16948:10.90:60:4:0.0198:0:1 0/0:63:0:0,0:5,58:0:2,0:19.7:1:31.8:1:1:0:59.7:30.5:1:0:0.1 -22 27661288 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49757;SOR=Inf;LSEQ=TCTGTAGGTGATGGCTTTTG;RSEQ=TGTTGCTGCTGTTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:20,16:0:2,0:26.4:1:31.6:1:1:0:60:35:1:0:0.1 0/1:43:2:1,1:21,20:0.0465:2,2:30:0:31.5:1:1:1.04883:60:4:0.0476:0:1.5 -22 27661307 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49562;SOR=Inf;LSEQ=GCTGTTGCTGCTGTTGCTGT;RSEQ=GTTGTTTTGTTGTTGTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:15,22:0:2,0:25.8:1:29.3:1:1:0:60:36:1:0:0.1 0/1:42:2:1,1:18,21:0.0476:2,2:26.5:1:29:1:1:1.16:60:4:0.0488:0:1 -22 28194872 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0687;SOR=Inf;LSEQ=CTGCTTAATCATGAGGGCCG;RSEQ=GTTTTGGCGCTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:59,52:0:2,0:30.2:1:30.3:1:1:0:60:21.2:1:0:0.1 0/1:78:3:1,2:45,30:0.0385:2,2:16:1:29:1:0.56465:2.95754:60:6:0.0385:0:1.3 -22 28194880 . CGCT C 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.13867;SOR=3.4907;LSEQ=TCATGAGGGCCGCGTTTTGG;RSEQ=GCTGCTGCTGCTGCTGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:0,2:58,53:0.0177:2,0:39.5:1:33.5:1:0.23467:0:60:4:0.0182:0:0 0/1:84:5:4,1:45,34:0.0595:2,2:33.2:1:32:1:0.3956:2.99:60:10:0.0602:0:0 -22 28194912 . TTGC T 96 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.01175;SOR=6.20952;LSEQ=TGCTGCTGTTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:59,73:0.0149:2,2:39:0:29:1:1:1.24:60:4:0.015:0:0 0/1:104:9:5,4:47,44:0.0865:2,2:34:1:30.3:1:1:1.17:58.3:18:0.0874:0:0.6 -22 28194923 . G GCTGTTGTTACCACTATTGCTACTGCAACTGCTGTTGTTACTA 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.08996;SOR=Inf;LSEQ=CTGTTGCTGTTGCTGCTGCT;RSEQ=CTGCTGCTGTTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:46,54:0:2,0:25.3:1:31.5:1:1:0:60:24:0.9897:0:0.2 0/1:83:3:2,1:42,38:0.0361:2,2:35.3:1:29.4:1:1:1.80:50.7:6:0.0366:0.0361:2 -22 28194930 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.19905;SOR=Inf;LSEQ=TGTTGCTGCTGCTGCTGCTG;RSEQ=TGTTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:40,49:0:2,0:27.1:1:31.6:1:1:0:60:28.667:1:0:0.2 0/1:73:2:1,1:35,34:0.0274:2,2:7:1:31.5:1:1:1.029:46:4:0.0286:0.0274:1 -22 28195624 . GGCT G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.19212;SOR=Inf;LSEQ=GCTGCTGCTGCTGCTGCTGG;RSEQ=GCTGCTGCTGCTGGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:21.6:1:31.1:1:1:0:60:15:1:0:0.3 0/1:13:2:1,1:6,5:0.1538:2,2:25:0:33.5:1:1:1.18321:60:4:0.1538:0:0.5 -22 29083769 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23838;SOR=Inf;LSEQ=TTAATTGTACATCAGTGACT;RSEQ=TGAAAAAGCAATTATTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:84,14:0:2,0:25.6:1:31.9:1:1:0:54:48:1:0:0.1 0/1:94:2:1,1:84,8:0.0213:2,2:6.5:1:26.5:1:0.18325:9.95828:48.5:4:0.0213:0:1 -22 29083808 . TA T 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.18879;SOR=0.21522;LSEQ=CATAATTAAAATACAAACTA;RSEQ=AAAAAACAGACTCAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:4:2,2:138,43:0.0216:2,2:21.8:1:30:1:0.24912:3.18446:31.3:8:0.0222:0.0054:1.3 0/0:212:1:0,1:162,49:0.0047:2,0:10:0:31:0:0.23585:0:28:2:0.0047:0:0 -22 29085257 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34646;SOR=0.58797;LSEQ=CTGAAGGATAATAAACTCCT;RSEQ=GAATGACAGGGCTAGCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:13:0,13:33,154:0.065:2,1:21.6:1:32.4:1:0.13192:0:29.9:26:0.0653:0:2.2 0/1:153:6:0,6:25,122:0.0392:2,0:20:1:31:1:0.59003:0:31.5:12:0.0395:0:2 -22 29085269 . C G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52207;SOR=0.54499;LSEQ=AAACTCCTAGAATGACAGGG;RSEQ=TAGCATGCCCCTGTGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:7:0,7:19,146:0.0407:2,0:22.3:1:33.4:1:1:0:30:14:0.0432:0:2.1 0/1:133:3:0,3:22,107:0.0226:2,0:21:1:33:0:1:0:34.7:6:0.0233:0:2 -22 29085384 . T A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09059;SOR=Inf;LSEQ=CCTCTACCTTCCCAGAGGAG;RSEQ=CTAATTAGCAGTCAATGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:4,25:0:2,0:24.8:1:29.8:1:1:0:56.3:28:1:0:0.4 0/1:13:2:1,1:2,9:0.1538:2,2:13.5:1:25.5:1:0.42308:3.87:50:4:0.1538:0:1 -22 29085434 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTGACTCACATCCACAT;RSEQ=CCTAAAAGCTCTCAGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:1,10:0.1538:2,2:20.5:1:30:1:0.29487:7.42:60:4:0.1538:0:1 0/0:5:0:0,0:1,4:0:2,0:30.2:1:28.8:1:1:0:53.2:4:1:0:0.6 -22 29089846 . C CA 95 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.2143;SOR=0.38015;LSEQ=GACAGAACAAGAACCTGTCT;RSEQ=AAAAAAAAAAATAAAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:10,0:27,3:0.25:2,0:24.3:1:28.7:1:0.55972:0:58.4:9:0.2308:0.075:0.8 0/1:27:3:2,1:19,2:0.1111:2,2:20.7:1:29:1:0.34289:4.30947:56.7:6:0.12:0.037:0.7 -22 29089858 . T A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0323;SOR=Inf;LSEQ=ACCTGTCTCAAAAAAAAAAA;RSEQ=AAAACAGGTTGTAACCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:52,3:0:2,0:20.3:1:30.3:1:1:0:59.7:17.333:1:0:0.2 0/1:42:4:3,1:33,5:0.0952:2,2:23.5:1:30:1:0.47373:2.14919:57.5:8:0.1026:0:2 -22 29090089 . C A 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00139;SOR=Inf;LSEQ=GGATCCACTACCAACAACTT;RSEQ=TTGACAAGGTCCAGAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:687:0:0,0:291,396:0:2,0:26.2:1:31.5:1:1:0:54.8:97.143:1:0:0.1 0/1:823:11:6,5:360,452:0.0134:2,2:13.9:1:28.9:1:0.55177:1.51:45.2:22:0.0135:0:1.5 -22 29090363 . G A 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGCCTGTTCCCTCTCTT;RSEQ=TTGCTAGACTCAAGGTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:16.8:1:30.4:1:1:0:52.6:10:0.5556:0:1 0/0:1:0:0,0:0,1:0:0,0:10:0:32:0:1:0:60:2:1:0:0 -22 29090768 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTAAAAAGTTACAAGTGC;RSEQ=TTTATTTTGCTCACTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:35.5:1:31:1:1:0:42.5:4:0.2222:0:1 0/0:1:0:0,0:1,0:0:0,0:28:0:30:0:1:0:60:2:1:0:0 -22 29090890 . G A 27 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04983;SOR=Inf;LSEQ=AGAAAGAAATTGGAGATGGA;RSEQ=GTTAAATAACTTGCCTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:0:1,0:24.3:1:32.2:1:1:0:50.5:66:1:0:0.1 0/1:10:2:1,1:8,0:0.2:0,2:29.5:1:27.5:1:0.2:0:54.5:4:0.2:0:3.5 -22 29091017 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19595;SOR=Inf;LSEQ=ATAGAAAATAAGAACAGAAT;RSEQ=GACAGGAGAAAACACCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:208,18:0:2,0:22.3:1:30.2:1:1:0:58.2:36.667:1:0:0.7 0/1:180:2:1,1:156,22:0.0111:2,2:39:0:30:1:0.23985:6.95722:60:4:0.0114:0:2 -22 29091037 . G C 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16744;SOR=0.79746;LSEQ=TGACAGGAGAAAACACCATG;RSEQ=AATTTGGGAAGAAACTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:346:227:187,40:97,22:0.6561:2,2:22.7:1:32:1:0.88303:1.06:59:36.833:0.6577:0:1.1 1/0:305:184:150,34:96,24:0.6033:2,2:22.8:1:32.2:1:0.76652:1.10:59.5:368:0.6033:0:1.1 -22 29091840 . TG CA 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGGTCTCTCCCAAAATCT;RSEQ=GAGTGCCCAAAATCAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:0:0,0:252,469:0:2,0:26.9:1:30.1:1:1:0:54.8:102:1:0:0.1 0/1:709:35:18,17:263,407:0.0494:2,2:29.5:1:31.2:1:0.1601:1.64:45.5:70:0.0498:0.0056:1.3 -22 29092639 . A G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAGGTGTGAGCCACCAT;RSEQ=CCCAGCCCACTCGTCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:21.4:1:30.4:1:1:0:57.5:13:1:0:1.5 1/1:3:3:3,0:0,0:1:0,0:19.3:1:30.3:1:1:0:60:6:1:0:1.3 -22 29092720 . C T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51304;SOR=0.54575;LSEQ=ACAACAGAGCTCAATAAATG;RSEQ=TCATTCGAATCTGGATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:8:8,0:38,1:0.1702:1,0:30.3:1:31.1:1:1:0:60:16:0.1778:0:1.1 0/1:30:3:3,0:26,1:0.1:1,0:15.7:1:30.7:1:1:0:60:6:0.1:0:1 -22 29092998 . C A 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19724;SOR=4.43131;LSEQ=ACACAGAAAGGCAGGCATGA;RSEQ=CCTCAGATTCATGCAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:1:1,0:141,294:0.0023:2,0:1:0:25:0:0.32569:0:60:2:0.0023:0:1 0/1:396:4:1,3:118,273:0.0101:2,2:12.5:1:26:1:1:1.29586:60:3:0.0077:0:2.5 -22 29093029 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17421;SOR=Inf;LSEQ=ATGCAGTAGATACTTAAGTA;RSEQ=AATCAAAGTTACCAACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:38,199:0:2,0:23.6:1:30.9:1:1:0:60:46.4:0.9957:0:0.1 0/1:171:2:1,1:29,140:0.0117:2,2:10.5:1:28.5:1:0.32095:4.76:60:4:0.0117:0:1.5 -22 29093239 . A G 87 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TAATAAACAACTCTTCACAC;RSEQ=GCAGAAATGTAAGGTGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:19:1:31.3:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 29095634 . AC A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04194;SOR=Inf;LSEQ=TGCTGGGATTATGGGCATGA;RSEQ=CACCGCGCCTCGCCAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:0:1,0:23.8:1:31.3:1:1:0:60:14:1:0:0.1 0/1:17:3:3,0:14,0:0.1765:1,0:24.3:1:27.8:1:1:0:60:6:0.1765:0.0588:0.7 -22 29095725 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19416;SOR=Inf;LSEQ=ACAGCAAACACACAGATTCT;RSEQ=TTCTGAGTTTTAATCCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:136,3:0:1,0:24.1:1:31.3:1:1:0:60:45.333:1:0:0.1 0/1:110:2:1,1:103,5:0.0182:1,2:13.5:1:27.5:1:0.10659:18.88648:60:4:0.0185:0:1 -22 29099459 . G T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6862;SOR=1.92251;LSEQ=GCTTTATAAAGCATTTGAAT;RSEQ=GAAACAGAAATTTTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:2:0,2:177,79:0.0078:2,0:1:0:26.5:1:0.09773:0:60:4:0.0078:0:1 0/1:270:4:1,3:190,76:0.0148:2,2:11.8:1:27:1:0.07669:7.43676:60:8:0.0149:0:1 -22 29099754 . T C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07523;SOR=0.16771;LSEQ=GTGAGAACATGCAAGAAATT;RSEQ=TCCACCCCACCATGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:0,13:0,5:0.7222:0,1:25.1:1:32.3:1:1:0:60:26:0.7222:0:1.3 0/1:7:2:0,2:0,5:0.2857:0,0:32:1:33:1:1:0:60:4:0.2857:0:1 -22 29106174 . A G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00179;SOR=Inf;LSEQ=CCAGCTCTACTTATACAAAG;RSEQ=AATCAAAGCCCAGGTCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:0,38:0:1,0:27.2:1:30.9:1:1:0:60:76:1:0:0.1 0/1:29:7:0,7:0,22:0.2414:1,0:33.6:1:30.7:1:1:0:60:14:0.2414:0:1.1 -22 29107646 . G GA 31 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGACTTTGAACTTGGAAGAA;RSEQ=AAAAAAAAAAACTTCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:7.5:1:31.1:1:1:0:60:4:0.2:0.1:0 0/0:1:0:0,0:1,0:0:0,0:35:0:28:0:1:0:60:2:1:0:0 -22 29107806 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20051;SOR=Inf;LSEQ=CCATCTAAGCAGGGGGTTAT;RSEQ=CCTGAGTTTAAAAATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:185,8:0:1,0:24.7:1:30.4:1:1:0:60:192:1:0:0.1 0/1:157:2:1,1:148,7:0.0127:1,2:18.5:1:27.5:1:0.09962:19.84568:60:4:0.0128:0:1 -22 29108082 . G GTATTAGAATTTACAGACATTCCA 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=1.130;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=CACTCCTGGGTCCACTTCAA;RSEQ=TATTAGAATTTACAGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:7,169:0:1,0:25.6:1:32.2:1:1:0:59.9:87:1:0:0.1 0/1:141:10:0,10:5,126:0.0709:1,0:27.5:1:31.2:1:1:0:59.5:20:0.0709:0.0213:0.6 -22 29108112 . A C 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00571;SOR=Inf;LSEQ=TTACAGACATTCCATATAAC;RSEQ=GCCTTTCCATTGTCCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:2,112:0:1,0:23.7:1:31.6:1:1:0:59.8:56:1:0:0.2 0/1:65:5:0,5:0,60:0.0769:1,0:25.6:1:32:0:1:0:60:10:0.0781:0:1 -22 29108229 . A G 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.74089;LSEQ=ATTCCATTTCTGAGCCCAGC;RSEQ=ATACAAACATGGGTCTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:0.7333:0,0:26.7:1:29.5:1:1:0:60:10:0.7143:0:1.1 1/0:3:2:0,2:0,1:0.6667:0,0:22.5:1:32:0:1:0:60:4:0.6667:0:1 -22 29115552 . A G 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=Inf;LSEQ=GATTCTAAAATTTATTCATC;RSEQ=TATGGAATATAAGAACTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:3,99:0:1,0:24.1:1:31.4:1:1:0:60:101:1:0:0 0/1:55:9:0,9:0,46:0.1636:1,0:18.3:1:32:1:1:0:60:18:0.1636:0:1 -22 29120797 . A G 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62739;SOR=1.61978;LSEQ=CTCCTGACCTCAGGTGATCC;RSEQ=TCCGCCTCAGCCTCCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:4,0:36,0:0.1:1,0:29.8:1:30.3:1:1:0:58.5:8:0.1:0:1 0/1:13:2:2,0:11,0:0.1538:0,0:19:1:32:0:1:0:60:4:0.1538:0:1 -22 29120913 . T A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24863;SOR=0;LSEQ=GACAGGACAAATTTTCCTCC;RSEQ=ATGAGAGAGTGGAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:1,2:205,60:0.0112:2,2:28.3:1:24.3:1:0.13472:6.76984:60:2:0.0076:0:3 0/0:264:0:0,0:186,78:0:2,0:21.7:1:29.2:1:1:0:59.9:36.714:1:0:0.2 -22 29120915 . T A 152 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGGACAAATTTTCCTCCTA;RSEQ=GAGAGAGTGGAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:34:28,6:185,62:0.121:2,2:23.4:1:30:1:0.39982:1.56:59.6:68:0.1241:0:1.1 0/0:271:0:0,0:193,78:0:2,0:5:0:17:0:1:0:35:0:0:0:5 -22 29120925 . G GA 137 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.29473;SOR=1.4101;LSEQ=TTTCCTCCTATGAGAGAGTG;RSEQ=AAAAAAAAAATTCCAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:21:15,6:232,93:0.0603:2,2:25.1:1:30.7:1:1:1.00:60:42:0.0614:0.0144:0.3 0/1:325:27:19,8:203,93:0.0831:2,2:23.4:1:28.9:1:1:1.09:59.1:54:0.0857:0.0185:0.6 -22 29121457 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52979;SOR=0;LSEQ=AGGAAAATAGCCTAAGAAGG;RSEQ=AATCAGAATTATCAATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:0,2:0,119:0.0165:1,0:32.5:1:29.5:1:1:0:60:4:0.0165:0:1 0/0:72:0:0,0:3,69:0:1,0:24.2:1:31.9:1:1:0:60:71:1:0:0.1 -22 29130012 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTCATTTGCATAAGGCG;RSEQ=CAATCCACACCAGTCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:20:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 29130300 . C T 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01745;SOR=0.47366;LSEQ=CAACGTGCCAAAAACCTGGA;RSEQ=AACTCCAATCAGAACCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:48:47,1:60,5:0.4248:2,1:22.5:1:30.8:1:0.23852:3.88:60:47:0.4273:0:1 0/1:89:23:21,2:60,6:0.2584:2,2:24.8:1:29:1:1:1.05:60:46:0.2584:0:1 -22 29130320 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59798;SOR=2.33176;LSEQ=CAACTCCAATCAGAACCTTC;RSEQ=ACCTGGTAATACAACTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:1:0,1:142,17:0.0063:2,0:1:0:23:0:0.1125:0:60:2:0.0063:0:1 0/1:138:2:1,1:115,21:0.0145:2,2:25:1:30.5:1:0.2944:5.37359:60:4:0.0149:0:1.5 -22 29130332 . C T 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.11509;SOR=Inf;LSEQ=GAACCTTCCACCTGGTAATA;RSEQ=AACTTTCTGTAAGTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:180,47:0:2,0:21.9:1:31.8:1:1:0:59.9:74.667:1:0:0.3 0/1:216:3:1,2:164,49:0.0139:2,2:8:1:20:1:0.13958:6.61833:60:2:0.0093:0:2.3 -22 29130347 . G GT 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAATACAACTTTCTGTAAGT;RSEQ=TTTTTCTGAACAAAACGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:223,74:0:2,0:23.5:1:32.1:1:1:0:59.9:98:1:0:0.2 0/1:288:27:20,7:184,77:0.0938:2,2:20.8:1:28.9:1:0.82564:1.19:59.8:54:0.0934:0.0278:0.2 -22 29130748 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17631;SOR=Inf;LSEQ=GTGTCCAACAACAAAGGTGA;RSEQ=TTTCAAGGCACAAGACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:23,149:0:2,0:25.2:1:31.3:1:1:0:60:18.111:1:0:0.3 0/1:125:2:1,1:20,103:0.016:2,2:23.5:1:28.5:1:0.3089:5.05:60:4:0.016:0:1 -22 29413305 . G A 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGCCCCCATCAGGCAGGT;RSEQ=TACACTGTCCAGTCTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:24:1:28.3:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 29413785 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.31101;SOR=0.4698;LSEQ=GCTTATATCCGTCAACCAGG;RSEQ=TGAGTGCAGAAAAGACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:14:14,0:8,1:0.6087:2,1:18.5:1:31.4:1:0.3913:0:60:28:0.6087:0:1.1 0/1:12:5:5,0:7,0:0.4167:0,0:14.4:1:32.2:1:1:0:60:10:0.4167:0:1 -22 29413894 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51273;SOR=0;LSEQ=GAGAAAGGAGGCTTTTAGAT;RSEQ=TGTCCTTAAGCATTGAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:109,36:0.0136:2,2:6.5:1:28.5:1:0.44134:3.00025:60:4:0.0137:0:1 0/0:104:0:0,0:85,19:0:2,0:21.9:1:31.6:1:1:0:60:208:1:0:0.1 -22 29413919 . G T 41 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.88917;LSEQ=CTTAAGCATTGAAGCGCTTT;RSEQ=AGAGGTAATCAAGGGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:1,2:160,72:0.0128:2,2:11.7:1:26:1:0.234:4.41315:60:6:0.0128:0:1 0/1:176:2:0,2:117,57:0.0114:2,0:1:0:21.5:1:0.1111:0:60:4:0.0116:0:1.5 -22 29414001 . A G 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.86103;LSEQ=GAAGATGTGCGTATGCCTTA;RSEQ=CTTTTCAGAAATGGGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:160:81,79:153,135:0.3571:2,2:25.6:1:31.9:1:0.62294:1.1051:60:39:0.3537:0:1.1 1/0:411:209:102,107:101,101:0.5085:2,2:26:1:31.8:1:0.84381:1.04887:60:103.5:0.5124:0:1.2 -22 29414085 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18453;SOR=Inf;LSEQ=GAGGGGAGGGCGGACGGGCA;RSEQ=ACCGGATCCAAACTGGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:61,184:0:2,0:22.6:1:31.4:1:1:0:60:80.667:1:0:0.2 0/1:185:2:1,1:59,124:0.0108:2,2:27:1:30:1:0.54465:2.09:60:4:0.0109:0:1.5 -22 29414090 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.184;SOR=Inf;LSEQ=GAGGGCGGACGGGCAGACCG;RSEQ=ATCCAAACTGGATCCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:54,160:0:2,0:23.1:1:31.2:1:1:0:60:70.333:0.9953:0:0.2 0/1:162:2:1,1:48,112:0.0123:2,2:34:1:27:1:0.51476:2.32:60:4:0.0124:0:1 -22 29682881 . CT C 75 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.56028;SOR=0;LSEQ=CAAGCCTCTTTCTAAAAAAG;RSEQ=TTTTTTTTTTTCTCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,0:0.2:1,0:24.2:1:32.4:1:1:0:60:10:0.2:0.04:0 0/0:7:0:0,0:6,1:0:2,0:31.4:1:30.6:1:1:0:60:14:1:0:1.3 -22 29683377 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53518;SOR=0;LSEQ=CAGCTATTTTTTGTATTTTT;RSEQ=GTAGAGACGGGGTTTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:2,0:105,40:0.0136:2,0:21.5:1:31.5:1:1:0:50:4:0.0139:0:1 0/0:84:0:0,0:66,18:0:2,0:23.7:1:30.6:1:1:0:59.9:41:1:0:0.2 -22 29683875 . GA G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14242;SOR=Inf;LSEQ=TTGTTTATATCCATTAAGGG;RSEQ=AAAATGGCCAGGCATGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:91,154:0:2,0:24.7:1:30.2:1:1:0:60:244:1:0:0.1 0/1:149:2:0,2:53,94:0.0134:2,0:17.5:1:32:1:0.53855:0:60:4:0.0136:0:0 -22 29683916 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCACACCTGTAATCCCAG;RSEQ=ACTTTGGGGGAGGCCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:76,100:0.0112:2,2:30:1:26.5:1:1:1.31:60:4:0.0113:0:1 0/0:87:0:0,0:36,51:0:2,0:22.9:1:31.2:1:1:0:60:42.5:1:0:0.1 -22 29683924 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTAATCCCAGCACTTTGG;RSEQ=GGAGGCCAAGGCAGGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:77,86:0.0121:2,2:28.5:1:31:1:1:1.12:60:4:0.0121:0:1 0/0:78:0:0,0:32,46:0:2,0:24.5:1:30.7:1:1:0:60:156:1:0:0.1 -22 29684236 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07409;SOR=Inf;LSEQ=CCCTAGCAGTGTGCTAAAGC;RSEQ=CTAAGAAACCTGGCTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:170,235:0:2,0:25.2:1:30.9:1:1:0:60:44:1:0:0.1 0/1:295:3:2,1:131,161:0.0102:2,2:22:1:27.7:1:0.59048:2.45:60:6:0.0103:0:1 -22 29685163 . A G 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=25.69565;LSEQ=TGTCTTGAAATACCTGGTGT;RSEQ=TATACTGCAGAAAAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:1:1,0:295,337:0.0016:2,0:41:0:17:0:0.46761:0:60:0:0:0:2 0/1:511:20:11,9:238,253:0.0391:2,2:24.2:1:31.8:1:0.65103:1.30:60:40:0.0394:0:1.1 -22 29685604 . T A 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.42918;SOR=2.24727;LSEQ=TTCTGTGTGTGTTCTGTCCC;RSEQ=ATATAAACTGGTAAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:2:1,1:146,295:0.0045:2,2:24:1:19.5:1:0.55405:2.02:60:1:0.0023:0:1 0/1:397:4:3,1:157,236:0.0101:2,2:12.8:1:23:1:0.30724:4.49:60:3:0.0078:0:2 -22 29685620 . G GA 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.28862;SOR=1.38927;LSEQ=TCCCTATATAAACTGGTAAA;RSEQ=AAAAAAAAAAGTTATGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:23:7,16:117,234:0.0612:2,2:30.8:1:28.6:1:1:1.14248:60:22:0.063:0.0053:0.1 0/1:289:24:8,16:106,159:0.083:2,2:28.4:1:29:1:0.6638:1.33204:59.8:48:0.0873:0.0104:0.2 -22 29685711 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.76059;LSEQ=AAATAGCATTTTTTAAAAAA;RSEQ=AGAATGAACTTCAAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:55:26,29:122,111:0.191:2,2:20.5:1:30.4:1:0.54979:1.22505:60:110:0.1916:0:1.1 1/0:186:137:67,70:22,27:0.7366:2,2:24.7:1:28.8:1:0.73925:1.17:60:136:0.7351:0:1.3 -22 29685752 . A G 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTTGATTTTTAACTTCCAT;RSEQ=TTAGCAAATACTCTTCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:158,121:0:2,0:26.7:1:29.5:1:1:0:60:278:1:0:0.2 0/1:198:32:18,14:91,75:0.1616:2,2:23.9:1:31.3:1:1:1.06:60:64:0.1641:0:1.6 -22 29685754 . T A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=TTGATTTTTAACTTCCATAT;RSEQ=AGCAAATACTCTTCACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:161,122:0:2,0:26.4:1:29.4:1:1:0:60:282:1:0:0.2 0/1:199:9:4,5:107,83:0.0452:2,2:18.8:1:30.1:1:0.51242:1.60752:60:18:0.0459:0:1.9 -22 29685775 . G T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26727;SOR=0;LSEQ=AGCAAATACTCTTCACTACT;RSEQ=AAAGACAGTACTATTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:175,119:0.0101:2,2:31.3:1:30.3:1:1:1.36:60:6:0.0102:0:1 0/0:216:0:0,0:122,94:0:2,0:24.4:1:31.2:1:1:0:60:107:1:0:0.5 -22 29686200 . C T 46 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.38977;SOR=0.31339;LSEQ=CAGACTGTGAAGCAGTCTGT;RSEQ=GGATCCTGTGGGGATAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:4:1,3:224,149:0.0106:2,2:12:1:23.3:1:0.30716:4.49259:60:3:0.0081:0:1 0/0:299:1:0,1:185,113:0.0033:2,0:1:0:24:0:0.38127:0:60:2:0.0033:0:1 -22 29686918 . T C 144 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.64649;LSEQ=AGTCATTATTCTAACTGATA;RSEQ=GTCTATAAAGTTGCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:958:2:1,1:518,438:0.0021:2,2:8.5:1:11.5:1:1:1.18244:60:0:0:0:1.5 0/1:842:30:17,13:450,362:0.0356:2,2:26:1:29.5:1:1:1.05:60:60:0.0359:0:1.1 -22 29687464 . C T 49 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0618;SOR=Inf;LSEQ=GGAGATGTGTTTAGCCAGTG;RSEQ=CCTTCTTCCCCACGAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:228,219:0:2,0:26.9:1:31.6:1:1:0:60:62.857:1:0:0.1 0/1:447:5:2,3:233,209:0.0112:2,2:13.8:1:21.4:1:0.67155:1.67032:60:1.5:0.0069:0:1.4 -22 29687621 . T TA 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.88694;LSEQ=GTATTACCATAGATAGTGTT;RSEQ=AAAAAAAAATGCAGTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:7:5,2:116,136:0.027:2,2:18:1:29.5:1:0.25705:2.92:60:14:0.0275:0.0077:0.1 0/1:208:5:3,2:93,110:0.024:2,2:25:1:28.2:1:0.66376:1.77:60:10:0.0242:0.0096:0.2 -22 29688184 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1509;SOR=Inf;LSEQ=TTTGAATTCTAGTTGTGCTT;RSEQ=ATATCGTGCTTTGTAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:153,128:0:2,0:24.7:1:31.8:1:1:0:60:92.667:1:0:0.1 0/1:179:2:1,1:92,85:0.0112:2,2:11:1:29:1:1:1.08186:60:4:0.0113:0:1 -22 29688632 . T G 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.2215;SOR=1.17447;LSEQ=CCAGGTCATCTGGCAGAACT;RSEQ=TAAACCACAGAGCATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:777:146:86,60:341,289:0.1879:2,2:26.2:1:32.3:1:0.31091:1.21:60:292:0.1891:0:1.1 0/1:730:156:90,66:317,257:0.2137:2,2:24.3:1:31.2:1:0.64958:1.11:60:312:0.2161:0:1.1 -22 29688849 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04018;SOR=Inf;LSEQ=ACTGCAACCTCTGTTCAAGC;RSEQ=AATCTCCTGCCTCAGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:11,60:0:2,0:28.3:1:30.3:1:1:0:60:16.75:1:0:0.1 0/1:38:3:0,3:1,34:0.0789:1,0:15.7:1:29:1:1:0:60:6:0.0789:0:1 -22 29688980 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21674;SOR=Inf;LSEQ=AACTCCTGACCTCAGGTGAT;RSEQ=TGCCCACCTTGGCGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:108,20:0:2,0:25.9:1:31.4:1:1:0:60:41.667:1:0:0.1 0/1:112:2:1,1:81,29:0.0179:2,2:18.5:1:26.5:1:0.46573:2.76306:60:4:0.0179:0:1 -22 29688993 . C T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50042;SOR=0;LSEQ=AGGTGATCTGCCCACCTTGG;RSEQ=GCCTCCCAAAGTGCTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:115,51:0.0119:2,2:13:0:28:1:0.52452:2.24284:60:4:0.012:0:1 0/0:148:0:0,0:94,54:0:2,0:24.1:1:30.5:1:1:0:60:48.333:1:0:0.2 -22 29689130 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52864;SOR=0;LSEQ=CCACAGCCTCTTGAGGTAGC;RSEQ=GGACTTATAGGCACATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:61,108:0.0116:2,2:20:1:30:1:1:1.76:60:4:0.0118:0:1 0/0:104:0:0,0:29,75:0:2,0:22.7:1:30.6:1:1:0:60:208:1:0:0.1 -22 29689145 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.54807;SOR=0;LSEQ=GTAGCTGGACTTATAGGCAC;RSEQ=TGCCACCACACCCAACTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:58,94:0.013:2,2:27.5:1:29.5:1:1:1.62:60:4:0.013:0:1 0/0:80:0:0,0:22,58:0:2,0:23.9:1:30.1:1:1:0:60:79:1:0:0 -22 29689509 . CT C 163 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=13.87602;LSEQ=TTTTTATGATACTGAGTGAT;RSEQ=TTTTTTCCCCATGAAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:831:3:2,1:373,452:0.0036:2,2:40.3:1:32.3:1:0.59274:2.42:60:6:0.0036:0:0 0/1:751:36:18,18:331,382:0.0479:2,2:28.8:1:31.6:1:0.7334:1.15:60:72:0.0482:0.0067:0.2 -22 29689613 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52746;SOR=0;LSEQ=CACCAGGCTGGAGTGCAGTG;RSEQ=CACGATCTCGGCTCACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:0,2:0,136:0.0145:1,0:28:0:31.5:1:1:0:60:4:0.0148:0:2.5 0/0:84:0:0,0:3,81:0:1,0:24.2:1:32.2:1:1:0:60:168:1:0:0.1 -22 29689837 . A G 84 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTTTTGTGATTGCAGAC;RSEQ=TGAGCCACTGTGCCTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:5,2:0,0:1:0,2:23.1:1:30:1:1:0:60:14:1:0:1.9 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 29689868 . G A 87 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGGCCTGTCTCTATTT;RSEQ=TTATTTTATTTTACTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:1:0,2:17.9:1:29.1:1:1:0:60:16:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 29690104 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18178;SOR=Inf;LSEQ=CTCACGTGATCCACCCACCT;RSEQ=GGCCTCCCAAAGTGCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:236,22:0:2,0:23.4:1:28.4:1:1:0:60:128:0.9961:0:0.1 0/1:193:2:2,0:177,14:0.0104:2,0:26.5:1:31.5:1:1:0:50:4:0.0105:0:4.5 -22 29690246 . G A 211 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGTTTATTTTCAAGTTGCT;RSEQ=TGGTTAAGGGTCTTCGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1728:0:0,0:925,800:0:2,0:25.2:1:32.1:1:1:0:60:142.75:0.9983:0:0.1 0/1:1646:168:87,81:768,710:0.1021:2,2:26.5:1:28.6:1:1:1.00709:60:55:0.1009:0:1.1 -22 29690345 . T C 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=13.58209;LSEQ=GTAGCTCACGCCTGTAATCC;RSEQ=AGCACTTTGGGAGGCCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:748:134:36,98:167,445:0.1791:2,2:24.3:1:31.4:1:1:1.02157:54.2:43.667:0.179:0:1.1 1/0:699:523:172,351:56,118:0.7482:2,2:23.3:1:30.5:1:0.92575:1.03:56.1:64.375:0.7475:0:1.1 -22 29690370 . T A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04515;SOR=Inf;LSEQ=CTTTGGGAGGCCGAGGCGGG;RSEQ=GGATCACGAGGTCAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:0:0,0:46,419:0:2,0:23.5:1:30.1:1:1:0:56:115.25:0.9978:0:0.3 0/1:400:4:3,1:51,344:0.01:2,2:5.8:1:26.5:1:0.00853:19.96:60:8:0.0102:0:2 -22 29690423 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52173;SOR=0;LSEQ=GGCTAACACGATGAAACCCC;RSEQ=TCTCTACTATAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:0,2:0,181:0.0109:1,0:29:1:31:1:1:0:53:4:0.011:0:1 0/0:118:0:0,0:0,118:0:1,0:20.7:1:31.8:1:1:0:48.3:236:1:0:0.5 -22 29690886 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24866;SOR=Inf;LSEQ=CACTCCAGCCTGGCGACAGA;RSEQ=CAAGACTCCATCTCAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:126,60:0:2,0:20.4:1:30.6:1:1:0:59.8:13.308:1:0:0.3 0/1:197:3:1,2:138,56:0.0152:2,2:9.7:1:29:1:0.20769:4.88288:60:6:0.0162:0:1 -22 29690900 . C CA 144 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.96585;LSEQ=GACAGAGCAAGACTCCATCT;RSEQ=AAAAAAAAAAAGGAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:28:18,10:138,81:0.1124:2,2:28:1:29.9:1:1:1.06:58.9:56:0.1176:0:0.4 0/1:266:29:20,9:147,84:0.109:2,2:30.2:1:29.8:1:0.68286:1.27:60:58:0.1124:0:0.3 -22 29690905 . A C 65 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.12515;SOR=Inf;LSEQ=AGCAAGACTCCATCTCAAAA;RSEQ=AAAAAAGGAAATACAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:182,106:0:2,0:21.7:1:29.9:1:1:0:59.7:143:0.9965:0:0.3 0/1:315:4:2,2:189,122:0.0127:2,2:29:1:32.8:1:0.6478:1.54691:60:8:0.0131:0:2.3 -22 29691109 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21857;SOR=Inf;LSEQ=CTGTTGCCCAGACTGGAGTG;RSEQ=AGTGGCACAATTTCAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:76,132:0:2,0:23.3:1:32:1:1:0:60:103:1:0:0.1 0/1:184:2:1,1:64,118:0.0109:2,2:23.5:1:27.5:1:1:1.84:60:4:0.0111:0:1 -22 29691382 . A T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.47157;LSEQ=CTTTGGGAGGCCAAGGCAGG;RSEQ=GGATCCCAAGGATTGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:31:9,22:81,118:0.1348:2,2:23.9:1:29.7:1:0.24096:1.67437:60:14.5:0.1283:0:1.1 1/0:159:124:44,80:10,25:0.7799:2,2:22.6:1:29.5:1:0.54586:1.37:60:123:0.7785:0:1.1 -22 29691450 . C T 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.15965;LSEQ=AACAGAGTGAGACTCTGTCT;RSEQ=ACAAAAAAGAAAAAAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:141,120:0.0114:2,2:15.3:1:21.7:1:0.59716:2.3426:60:2:0.0078:0:1 0/1:228:3:0,3:128,97:0.0132:2,0:1:0:22.7:1:0.08295:0:60:6:0.0132:0:1 -22 29691521 . AG A 282 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4231;SOR=1.71509;LSEQ=ATATTTTCTTTTCAGTTTTT;RSEQ=GGTATCACGTTCCTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:502:493:257,236:6,3:0.9821:2,2:28.4:1:31.6:1:0.50842:1.83443:60:163.333:0.982:0.1155:0.1 1/1:475:470:244,226:2,3:0.9895:2,2:27.5:1:31.2:1:0.67569:1.62:60:155.667:0.9873:0.1053:0.2 -22 29691556 . C A 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1705;SOR=5.37214;LSEQ=TTTTTTTAAGTCAGAGGTAT;RSEQ=AATATATATATCCTGTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:1:1,0:223,217:0.0023:2,0:1:0:14:0:1:0:60:0:0:0:1 0/1:331:4:3,1:159,167:0.0121:2,2:20:1:26.3:1:0.3638:3.14:60:8:0.0122:0:1 -22 29691695 . ATACAAGGTAGCTCC A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=GTACACGTGAAGATATTCTT;RSEQ=TGAATTCAAGTCAACCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:0:0,0:279,243:0:2,0:25.2:1:29.6:1:1:0:60:103.4:0.9981:0:0.1 0/1:386:9:5,4:203,174:0.0233:2,2:26:1:30.1:1:1:1.07:60:18:0.0233:0.0026:0.1 -22 29691910 . C T 182 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAAAGTCTGACTACCCCTA;RSEQ=GAGGTGGCTGTGCTCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:60:36,24:194,160:0.1446:2,2:30:1:30.9:1:0.48495:1.24:60:120:0.1456:0:1.1 0/0:364:0:0,0:193,169:0:2,0:24.2:1:30:1:1:0:60:71.4:0.9944:0:0.2 -22 29691920 . G A 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTACCCCTACGAGGTGGCT;RSEQ=TGCTCAGTGGATACCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:0:0,0:241,171:0:2,0:25.4:1:31.9:1:1:0:60:44.778:1:0:0.3 0/1:366:36:23,13:173,156:0.0984:2,2:16.4:1:28.6:1:0.22085:1.59:60:72:0.0994:0:1.2 -22 29691922 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19148;SOR=4.57569;LSEQ=TACCCCTACGAGGTGGCTGT;RSEQ=CTCAGTGGATACCTGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:1,0:242,165:0.0024:2,0:1:0:24:0:1:0:60:2:0.0025:0:1 0/1:360:4:2,2:192,163:0.0111:2,2:37:1:30:1:1:1.17737:60:8:0.0113:0:1.3 -22 29692275 . A G 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0416;SOR=Inf;LSEQ=GATCCACATCTACCTGGACA;RSEQ=GGAAACAGGAAAGCCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:234,227:0:2,0:26:1:30.6:1:1:0:60:91.2:0.9978:0:0.1 0/1:382:4:2,2:199,179:0.0105:2,2:35:1:30.5:1:1:1.11142:60:8:0.0107:0:1.3 -22 29692331 . G A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09625;SOR=6.13758;LSEQ=CCTATGAAGACCCACCCACT;RSEQ=CCAAGGCTGCCGTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:1:1,0:245,269:0.0019:2,0:1:0:23:0:0.47767:0:60:2:0.002:0:1 0/1:423:5:4,1:200,218:0.0118:2,2:13.2:1:25.8:1:0.20102:4.35:60:10:0.012:0:1 -22 29692488 . G T 254 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTAGATGGCCGGTCTCCCT;RSEQ=CAGTAGTAGTAGCACCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:361:361:198,163:0,0:1:0,2:26.7:1:30:1:1:0:60:39.111:1:0:2 1/0:273:182:94,88:44,47:0.6667:2,2:26.7:1:28.3:1:0.61059:1.14:60:25:0.6654:0:2.1 -22 29692497 . G T 260 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CCGGTCTCCCTGCAGTAGTA;RSEQ=TAGCACCCAGCCATTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:372:372:208,164:0,0:1:0,2:26.5:1:30.5:1:1:0:60:52.143:1:0:2 1/0:278:184:96,88:44,50:0.6619:2,2:27:1:29.4:1:0.4473:1.24:60:60.333:0.6606:0:2.1 -22 29692867 . CA C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.55321;SOR=0;LSEQ=ATGGCAAAACCCTGTCTCTA;RSEQ=AAAAAAATACAAAAATTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:3:1,2:47,72:0.0246:2,2:24.7:1:32.3:1:1:1.30279:60:6:0.025:0:0 0/0:55:0:0,0:11,44:0:2,0:24.8:1:30.5:1:1:0:60:54:1:0:0.1 -22 29693540 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0446;SOR=Inf;LSEQ=AACAATTTTGTAAAATTAGT;RSEQ=GGGCATGGTGATGCGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:38,2:0:2,0:24.9:1:31.8:1:1:0:60:80:1:0:0.1 0/1:23:3:3,0:20,0:0.1304:1,0:19.7:1:31:1:1:0:60:6:0.1304:0:1 -22 29693640 . G A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGCCACTGCACTCCAGCCC;RSEQ=GGCAACAGAGTGAGACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:166,25:0:2,0:21.6:1:29.6:1:1:0:60:46.75:1:0:0.1 0/1:152:17:13,4:108,26:0.1118:2,2:24:1:29.1:1:0.74747:1.27591:60:16:0.1096:0:1.2 -22 29693885 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06811;SOR=Inf;LSEQ=AGCCTCCAATGAACAGTATG;RSEQ=GGGGTGGTCTGCCACCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:119,148:0:2,0:24.2:1:30.9:1:1:0:60:88:0.9962:0:0.1 0/1:186:3:1,2:77,106:0.0161:2,2:18.7:1:29:1:1:1.45003:60:6:0.0164:0:1 -22 29693900 . C T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03197;SOR=Inf;LSEQ=GTATGCGGGGTGGTCTGCCA;RSEQ=CCCGTGAGGGCAGAGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:124,136:0:2,0:24.5:1:31.4:1:1:0:60:51:1:0:0.1 0/1:192:4:3,1:87,101:0.0208:2,2:14.3:1:28.3:1:0.3424:3.46:60:8:0.0209:0:1 -22 29693990 . A G 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11738;SOR=1.41087;LSEQ=AAAGGTTTTCAGTACACTTC;RSEQ=TACCCTTGAGAAACTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:54:30,24:183,109:0.1561:2,2:23.9:1:29.7:1:0.36184:1.34192:59.8:17:0.15:0:1.2 0/1:285:59:36,23:145,81:0.207:2,2:22.7:1:30.1:1:0.65203:1.14314:60:118:0.2085:0:1 -22 29694312 . G A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=32.20571;LSEQ=TTAAGACCAGCCTGGCCAAC;RSEQ=TGGTGAAACTCCCTCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:8:0,8:4,44:0.1429:2,0:23.3:1:28.1:1:1:0:52.9:3:0.1111:0:1.1 1/1:27:23:1,22:1,3:0.8519:2,1:23.2:1:30.6:1:0.2792:6.49359:52.3:46:0.8519:0:1.1 -22 29694479 . A G 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5519;SOR=0;LSEQ=TGCACTCCAGCCTGGGCAAC;RSEQ=GTGTGAGACTCCGTCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:3:1,2:110,7:0.025:2,2:14.7:1:22.3:1:0.01453:28.91892:60:2:0.0177:0:1.7 0/0:58:0:0,0:51,7:0:2,0:23.9:1:29.4:1:1:0:55.8:57:1:0:2.4 -22 29694483 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=11.92154;LSEQ=CTCCAGCCTGGGCAACAGTG;RSEQ=GAGACTCCGTCTCCAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:21:19,2:102,8:0.1603:2,2:22.6:1:31.3:1:0.66191:1.33883:50.4:20:0.16:0:1.8 1/0:63:44:38,6:15,4:0.6984:2,2:23.9:1:29.3:1:0.47233:1.67:54.9:7.8:0.7222:0:2.5 -22 29694558 . T C 49 q23;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04904;SOR=0.3572;LSEQ=GAGCACGTGGAACACGCTCC;RSEQ=CACAGGGAAGGGGGCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:17:17,0:334,195:0.0311:2,1:17.9:1:12.1:1:0.00056:0:60:0:0:0:4.5 0/1:441:5:5,0:275,158:0.0113:2,0:20.6:1:20.6:1:0.16455:0:60:1.5:0.0074:0:5.4 -22 29999236 . G C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTCTAAGTGGTTTCCC;RSEQ=GGTAAGGTCAGCAGAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33:1:31.5:1:1:0:60:4:1:0:1 -22 29999784 . C A 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCCCTGCAGCCGTCAGGG;RSEQ=CCGTCCCCCAACTCCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:28.5:1:30.7:1:1:0:60:12:0.75:0:1.2 1/1:2:2:2,0:0,0:1:0,0:21.5:1:29.5:1:1:0:60:4:1:0:1 -22 29999878 . G C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.79262;SOR=0.79763;LSEQ=CCAGACCGTTCCCGGGCCGG;RSEQ=CAGCCGGCCACCATGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:44:42,2:14,0:0.7586:1,1:23.1:1:32.3:1:1:0:60:43:0.7544:0:1.1 1/0:28:20:20,0:8,0:0.7143:0,1:24.4:1:33.4:1:1:0:60:40:0.7143:0:1.1 -22 29999965 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09872;SOR=Inf;LSEQ=GCAGGCCGTGGGGCGCGAGG;RSEQ=TCCCGGGCCTGAGCCCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:274,53:0:2,0:23.6:1:31.1:1:1:0:60:64.4:1:0:0.1 0/1:282:3:1,2:231,48:0.0106:2,2:21.7:1:27.3:1:0.08215:9.50774:60:6:0.0107:0:1.3 -22 30000039 . C T 88 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09116;SOR=0.29788;LSEQ=TCAGCTCTCTCAAGAGGAAG;RSEQ=AACCCAAGACGTTCACCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:928:10:2,8:519,399:0.0108:2,2:14.9:1:26.6:1:0.02546:5.19519:60:20:0.011:0:1 0/0:928:3:0,3:518,407:0.0032:2,0:1:0:23.7:1:0.08589:0:60:6:0.0033:0:1 -22 30032654 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50912;SOR=0;LSEQ=TAGTGTCATCCCCACGTTTT;RSEQ=GAACCTGAGAGTGGAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:151,19:0.0116:2,2:18.5:1:28:1:0.21964:7.77158:60:4:0.0118:0:1 0/0:128:0:0,0:108,20:0:2,0:22.9:1:31.6:1:1:0:60:127:1:0:0.1 -22 30032665 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=CCACGTTTTGGAACCTGAGA;RSEQ=TGGAGAGTGCAGAGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:182,27:0:2,0:25.1:1:32.1:1:1:0:60:103.5:1:0:0.1 0/1:154:2:1,1:120,32:0.013:2,2:13:1:30:1:0.38375:3.70832:60:4:0.0133:0:1 -22 30032931 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18193;SOR=Inf;LSEQ=CCAGTTTTTCCCTGAGCAGG;RSEQ=GCCTAGCTCATCACTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:18,182:0:2,0:23.6:1:29.8:1:1:0:60:39:0.9949:0:0.1 0/1:150:2:1,1:25,123:0.0133:2,2:23:1:28.5:1:0.31758:4.84:60:4:0.0137:0:1 -22 30033036 . T A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28327;SOR=4.19245;LSEQ=AGAGATGCTACCAGTTTCCT;RSEQ=CTCCTCACAGGCTCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:0,5:0,15:0.25:1,0:20.6:1:30.8:1:1:0:60:10:0.25:0:1 1/0:5:3:0,3:0,2:0.6:0,0:28:1:31:1:1:0:60:6:0.6:0:1 -22 30034994 . G T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22113;LSEQ=TAGTGGGAAAAAAATTTAAT;RSEQ=CACGCCTTGCAAAGGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:188:118:107,11:64,5:0.6277:2,2:21.4:1:30.1:1:0.78845:1.31402:60:58:0.627:0:1 0/1:122:33:29,4:79,9:0.2705:2,2:16.7:1:29.8:1:0.74904:1.20871:60:66:0.275:0:1.1 -22 30035021 . G A 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=22.8225;LSEQ=TTGCAAAGGCTTCTTTGAGG;RSEQ=TAGCACAGGAGGAAGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:1:1,0:270,64:0.003:2,0:23:0:27:0:1:0:60:2:0.003:0:1 0/1:218:14:12,2:154,50:0.0642:2,2:27.2:1:28.9:1:0.52689:1.94:60:13:0.061:0:1.3 -22 30038041 . T TA 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.76926;LSEQ=TCTCCACCTGTCTGCATCAG;RSEQ=AAAAAAAAAATTGTACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:9:9,0:133,0:0.0621:1,0:22.4:1:27.9:1:1:0:60:18:0.0634:0.0138:0 0/1:62:3:3,0:59,0:0.0484:1,0:34.3:1:28.3:1:1:0:60:6:0.0484:0:0 -22 30038052 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0923;SOR=Inf;LSEQ=CTGCATCAGTAAAAAAAAAA;RSEQ=TGTACCCTTTGTCAGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:172,1:0:1,0:23.6:1:31.1:1:1:0:60:172:1:0:0.1 0/1:76:2:2,0:74,0:0.0263:1,0:23:1:27.5:1:1:0:60:4:0.0263:0:1 -22 30038152 . A C 228 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCCTACACACCTCACTTCC;RSEQ=CTCACAGAGTATCATGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:735:0:0,0:450,283:0:2,0:26.4:1:29.6:1:1:0:60:90.625:0.9986:0:0.1 0/1:561:178:106,72:227,154:0.3173:2,2:27.8:1:30.5:1:1:1.00122:60:356:0.319:0:1.1 -22 30038463 . ATG A 72 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.65036;SOR=0.44836;LSEQ=TTGTATAATCTTGTGTGTGT;RSEQ=TGTGTGTGTGTGTATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:0,5:2,20:0.1852:2,0:31.6:1:31.2:1:1:0:60:10:0.1852:0:0 0/1:11:1:0,1:0,10:0.0909:0,0:49:0:29:0:1:0:60:2:0.0909:0:0 -22 30051433 . C T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32547;SOR=1.75092;LSEQ=AGAATGGTGCCTTATTTACA;RSEQ=GCCCTCTCTCTGTGTGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:10:10,0:56,0:0.1515:1,0:25:1:31.9:1:1:0:60:20:0.1538:0:1 0/1:46:11:11,0:35,0:0.2391:1,0:26.4:1:29.5:1:1:0:60:10:0.2222:0:1 -22 30051704 . GC G 75 q23;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47765;SOR=1.47024;LSEQ=TGGTTTACATTCCTTTATGG;RSEQ=TTTTTTTTTTTTTTTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:8:0,8:92,224:0.0203:2,0:26.3:1:24.6:1:0.11103:0:56.9:3:0.0244:0:2.1 0/1:338:10:0,10:113,170:0.0296:2,0:27.6:1:22.8:1:0.00797:0:55.5:2.333:0.0343:0:3.5 -22 30053939 . C A 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54941;SOR=0;LSEQ=GAAACTAAGGCCAAGAAACT;RSEQ=CGTGATGAGTCTGTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:5,0:15,1:0.2381:1,0:14:1:28.4:1:1:0:60:10:0.2381:0:1.6 0/0:4:0:0,0:4,0:0:0,0:24.8:1:31.5:1:1:0:60:8:1:0:0 -22 30054024 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00858;SOR=3.53495;LSEQ=GTTTAATAGACTCAGGGCCG;RSEQ=GCAGAGCTTTGCTGGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:11:11,0:49,1:0.1803:1,0:22.2:1:30.3:1:1:0:60:22:0.1803:0:1.3 0/1:34:15:15,0:19,0:0.4412:1,1:32.9:1:29.1:1:1:0:60:14:0.4242:0:1.3 -22 30056718 . AT A 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTGCCACCATGCCCGGCTA;RSEQ=TTTTTTGTGTGTATTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21.5:1:30:1:1:0:46.5:4:0.6667:0:0.5 1/1:1:1:1,0:0,0:1:0,0:46:0:30:0:1:0:60:2:1:0:0 -22 30056945 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTCTTCCTTTAGCCATC;RSEQ=AGCCAGTGACAGAAGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:37.7:1:31:1:1:0:60:6:0.1429:0:1.3 0/0:1:0:0,0:1,0:0:0,0:20:0:25:0:1:0:60:2:1:0:0 -22 30057124 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16315;SOR=Inf;LSEQ=GTGACAGTGTGTGCCAGATT;RSEQ=TTTGGAAGGTTGAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:195,33:0:2,0:23.6:1:31.2:1:1:0:60:56:1:0:0.1 0/1:155:2:1,1:130,23:0.0129:2,2:24.5:1:28:1:0.28655:5.55448:60:4:0.0132:0:1 -22 30057574 . A G 45 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCCAAAGAATAGTGAAC;RSEQ=AAAACAGTAACATTTTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:0.1875:1,0:38:1:29:1:1:0:60:6:0.2:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 30061225 . GT G 111 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.03565;SOR=3.44845;LSEQ=CTAAATTATATCATGAAGAA;RSEQ=TTTTTTTTTTGTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:11:0,11:1,42:0.2037:1,0:24.4:1:32.2:1:1:0:60:22:0.2037:0:0.1 0/1:19:9:0,9:0,8:0.4737:0,0:30:1:32.7:1:1:0:60:18:0.4737:0:0 -22 30061237 . GT G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.56351;SOR=0;LSEQ=ATGAAGAAGTTTTTTTTTTT;RSEQ=TTTTTTTTTGAGACAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:0,3:0,41:0.0682:1,0:12:1:31.3:1:1:0:60:6:0.0698:0.0227:0 0/0:15:0:0,0:0,15:0:1,0:16.9:1:31:1:1:0:60:30:1:0:0.1 -22 30064073 . A AGT 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0.58042;SOR=2.18727;LSEQ=GCACCCAGAAGACATGGTGA;RSEQ=GTGTCCTCCAGTCCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:38.3:1:31.5:1:1:0:60:6:0.3:0:0.7 1/0:4:2:2,0:2,0:0.5:0,0:11.5:1:31.8:1:1:0:60:4:0.5:0.25:1 -22 30064117 . C T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46506;SOR=1.9087;LSEQ=TTATGATTTTTACCTCCTGG;RSEQ=ATATCTGAGGCGCCTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:12,1:0.2778:1,0:14.2:1:30.2:1:1:0:60:10:0.2778:0:1 0/1:14:6:6,0:8,0:0.4286:0,0:26.5:1:30.3:1:1:0:60:12:0.4286:0:1 -22 30064232 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51538;SOR=0;LSEQ=CACGTTTACTGCTACCTGCA;RSEQ=GAGCTCAAACTGCTATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:175,13:0.0105:2,2:26:1:30:1:0.1423:13.00892:60:4:0.0108:0:1 0/0:131:0:0,0:116,15:0:2,0:22:1:29.8:1:1:0:60:130:1:0:0.1 -22 30064512 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17306;SOR=Inf;LSEQ=GAGGCGAGGAGTGGTCATGG;RSEQ=CTGGCAGGAGTCTTTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:19,167:0:2,0:22.6:1:31.9:1:1:0:60:36.2:1:0:0.1 0/1:133:2:1,1:19,112:0.015:2,2:17:1:27:1:0.27911:5.77:60:4:0.0155:0:1 -22 30064731 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAAGAGTGCATGCATCT;RSEQ=TCCGTCCGGCTAGCTAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:23:1:33.5:1:1:0:60:4:0.2222:0:1 0/0:1:0:0,0:0,1:0:0,0:3:0:27:0:1:0:60:2:1:0:0 -22 30068066 . A T 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTAATTTCAGCTTTGAAAA;RSEQ=ATCAGTGCCTTTTCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:0,105:0:1,0:22.3:1:30.4:1:1:0:60:51.5:1:0:0.1 0/1:53:18:0,18:0,35:0.3396:1,1:28.1:1:27.7:1:1:0:60:17:0.3269:0:1.1 -22 30068851 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCTGACCTCAGGTGATC;RSEQ=GCCCGCCTCAGCCTCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:25.7:1:30.3:1:1:0:47.3:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 30069207 . C T 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00787;SOR=0.51227;LSEQ=GTGTTCAAGGCAGATCTGGG;RSEQ=GGGAGAACAGCACATGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:58:44,14:140,37:0.2458:2,2:25.3:1:29.2:1:0.58725:1.20292:60:57:0.2489:0:1.1 0/1:196:28:21,7:113,54:0.1429:2,2:19:1:29.4:1:0.51414:1.43:60:56:0.1458:0:1.2 -22 30070223 . T A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAGGCCCCTTACTGTAT;RSEQ=CGGGGGTCACTCCCTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:33:1:28.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 30070699 . CT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54429;SOR=0;LSEQ=AATATCCCTGTCTCACTGTC;RSEQ=TTTTCACCTCTTTGGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:2,0:109,2:0.0177:1,0:22.5:1:33:0:1:0:60:4:0.018:0:0 0/0:60:0:0,0:59,1:0:1,0:21.5:1:31.5:1:1:0:60:120:1:0:0.2 -22 30070755 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20907;SOR=Inf;LSEQ=CCCAGGTCCCTCCTCTGCAG;RSEQ=GGTGGGGTGGTGTCTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:204,34:0:2,0:25.3:1:31.2:1:1:0:60:78.333:1:0:0.1 0/1:201:2:2,0:165,34:0.01:2,0:17.5:1:30:1:1:0:60:4:0.0102:0:1 -22 30070763 . T G 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25467;SOR=0;LSEQ=CCTCCTCTGCAGGGGTGGGG;RSEQ=GGTGTCTTTTCCTGCTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:3,0:234,47:0.0106:2,0:18.7:1:23:1:1:0:60:2:0.0072:0:3 0/0:237:0:0,0:191,46:0:2,0:23.7:1:28.5:1:1:0:60:18.75:1:0:0.1 -22 30070770 . T C 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10199;SOR=Inf;LSEQ=TGCAGGGGTGGGGTGGTGTC;RSEQ=TTTCCTGCTACCTGCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:255,69:0:2,0:23.4:1:31:1:1:0:60:648:0.9969:0:0.1 0/1:286:3:1,2:216,67:0.0105:2,2:14.3:1:25:1:0.14553:6.39456:60:2:0.0071:0:1 -22 30071358 . C T 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTACTGCCGTGCAAGAA;RSEQ=GAGCAGCCACTCTCAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:29.7:1:32.3:1:1:0:60:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 30073959 . T TTGAGGGA 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05378;SOR=5.0336;LSEQ=CATGAAGAACGGTTAGAGAT;RSEQ=TGAGGGATGATTTTCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:5,0:33,0:0.1316:1,0:24.6:1:32.1:1:1:0:60:10:0.1316:0.0263:0 0/1:9:4:4,0:5,0:0.4444:0,0:20.8:1:31.3:1:1:0:60:8:0.5:0.1111:0.3 -22 30077361 . G A 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41667;SOR=0;LSEQ=CACCAAGCAGCTTGTGGGCC;RSEQ=CAGAGCACCTGAGCCGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:119:119:109,10:0,0:1:0,2:26.1:1:29.9:1:1:0:60:28.75:1:0:1.1 1/1:85:84:73,11:0,0:0.9882:0,2:21.8:1:29.8:1:1:0:60:83:0.9881:0:1.1 -22 30077658 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17723;SOR=Inf;LSEQ=ATGAAATGTGCGGTTGGCAT;RSEQ=TGGTTTCCTCAGTAGCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:28,190:0:2,0:24.8:1:32.3:1:1:0:60:71.667:1:0:0.1 0/1:159:2:1,1:24,133:0.0126:2,2:25.5:1:30:1:0.29058:5.45:60:4:0.0128:0:1 -22 30077659 . T A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26719;SOR=0;LSEQ=TGAAATGTGCGGTTGGCATC;RSEQ=GGTTTCCTCAGTAGCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:2,1:26,185:0.014:2,2:6.7:1:22.3:1:0.04569:13.91:60:2:0.0095:0:1.3 0/0:155:0:0,0:23,132:0:2,0:23.3:1:30.3:1:1:0:60:310:1:0:0.1 -22 30078935 . C T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33411;SOR=3.6305;LSEQ=AGGCCTATCCAAGCATTTTG;RSEQ=AGATGGCACTTATGGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:1,0:239,17:0.0039:2,0:47:0:32:0:1:0:60:2:0.004:0:1 0/1:214:3:2,1:193,17:0.014:2,2:23.7:1:28.7:1:0.23371:5.58848:60:6:0.0142:0:1 -22 30078942 . C T 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77201;LSEQ=TCCAAGCATTTTGCAGATGG;RSEQ=ACTTATGGCATTGTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:266,28:0.0101:2,2:16.7:1:26.7:1:0.02781:18.58834:60:6:0.0104:0:1 0/0:256:2:1,1:221,32:0.0078:2,2:13:1:27.5:1:0.24252:6.81543:60:4:0.0079:0:1 -22 30078965 . C T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12147;SOR=5.10527;LSEQ=TTATGGCATTGTTGATATCA;RSEQ=AGGGTATGTTTTTGTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:1:0,1:388,111:0.002:2,0:1:0:23:0:0.224:0:60:2:0.002:0:1 0/1:494:5:2,3:360,129:0.0101:2,2:9:1:27:1:0.1214:4.17137:60:10:0.0102:0:1.2 -22 30079164 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28393;SOR=0;LSEQ=GCCACACTGAGCCCTTACGA;RSEQ=GGCAGGTGGTGCCTGGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:3:0,3:11,262:0.0108:1,0:27.7:1:24:1:1:0:60:2:0.0074:0:1 0/0:178:0:0,0:21,157:0:2,0:22.1:1:30.4:1:1:0:60:58.333:1:0:0.2 -22 30079213 . T C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=3.83073;LSEQ=GCATGCTTTGAGTCTAAAAG;RSEQ=AGGCACCCACCCTGTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:19:0,19:1,103:0.1545:1,1:30.5:1:32.2:1:1:0:60:38:0.1583:0:1.1 0/1:58:24:0,24:0,34:0.4138:1,1:23:1:31.3:1:1:0:60:48:0.4138:0:1 -22 30090900 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13283;SOR=Inf;LSEQ=AGCTGGCTGGGGGTTTCCGT;RSEQ=GGAGCTCCAGAACTTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:15,230:0:2,0:24.8:1:31.2:1:1:0:60:80.667:1:0:0.1 0/1:141:2:1,1:8,131:0.0142:2,2:14.5:1:26:1:0.12401:15.49:60:4:0.0145:0:1 -22 30091145 . T C 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCCAGCCTGGGAAGTCA;RSEQ=TGTAGGGAGTGAGACACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:2,2:0.3333:2,0:38.5:1:32.5:1:0.46667:0:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:0:0,0:26:0:32:0:1:0:60:2:1:0:0 -22 30936374 . T C 32 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=23.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTTTTTTTTTTTTTTT;RSEQ=TTTGAGTATTGTATTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:32.5:1:1:0:60:4:1:0:1 -22 30937190 . T TTTG 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=11.02856;LSEQ=ACACAACTTTTAAAAAAATT;RSEQ=TTATTTATTTTTTAATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:39:35,4:75,8:0.3197:2,2:24.3:1:30.5:1:1:1.07082:60:78:0.3305:0.0738:0 1/1:100:84:71,13:12,3:0.84:2,2:23.3:1:30.1:1:0.70523:1.36:59.9:41:0.8454:0.21:0.1 -22 30937307 . A G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.76872;LSEQ=CATACTCCCCTCCCAGCTTT;RSEQ=TTAAGGTATGAATGGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:131:53,78:137,178:0.2924:2,2:23.6:1:31.8:1:0.59965:1.1324:60:64.5:0.2919:0:1.2 1/0:384:234:102,132:71,79:0.6094:2,2:24.6:1:30.8:1:0.52837:1.1626:60:57.5:0.6085:0:1.2 -22 30937512 . G A 51 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04096;SOR=18.0326;LSEQ=AAAGATTAGCCAGGTATGGT;RSEQ=GCACACGCCTGTGATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,9:0.1:0,0:11:0:32:0:1:0:60:2:0.1:0:1 1/0:4:3:0,3:0,1:0.75:0,0:21.3:1:32.7:1:1:0:60:6:0.75:0:1.3 -22 31327019 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49503;SOR=0;LSEQ=GCCTACAATCCATGATCAGT;RSEQ=TCCTGACGACCTCTGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:22,19:0.0465:2,2:20:0:31.5:1:1:1.15394:60:4:0.0476:0:1.5 0/0:39:0:0,0:25,14:0:2,0:25.8:1:31.4:1:1:0:60:78:1:0:0.1 -22 33131355 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGGGAAGTACTTGGCAC;RSEQ=TAGTAAATTCTCAATCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 33131486 . T C 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGCTGGAACATCATTCC;RSEQ=GTATTTGTTTGTTTGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:21.7:1:30.7:1:1:0:60:6:0.5:0:1 0/0:1:0:0,0:1,0:0:0,0:33:0:32:0:1:0:60:2:1:0:0 -22 33131697 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21531;SOR=0;LSEQ=GACTCCTGAAACACGGTCAG;RSEQ=AGCCCCTAGCAGCCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:0.0556:2,2:25:1:29:1:1:1.26:60:4:0.0556:0:1.5 0/0:41:0:0,0:19,22:0:2,0:29.9:1:31.5:1:1:0:60:82:1:0:0.5 -22 33131729 . T C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57718;SOR=1.49549;LSEQ=GCCAGAGAGGTCATTGGGTC;RSEQ=CCCAGCCCACAGGGAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:3,7:4,10:0.4167:2,2:17.3:1:29:1:1:1.07:60:9:0.3913:0:1 1/0:27:14:7,7:5,8:0.5185:2,2:23.2:1:30.1:1:0.70357:1.57:60:28:0.5185:0:1.1 -22 33828581 . T G 34 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=8.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCATTCATTCATTCATTCAT;RSEQ=CATGCATGCATGCATGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:27.5:1:34:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 33828911 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19737;SOR=Inf;LSEQ=CAAGAGTGTTGTCTAGATAA;RSEQ=AACTGCTCCTCTGTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:147,30:0:2,0:23.2:1:31.9:1:1:0:60:176:1:0:0.2 0/1:142:2:1,1:108,32:0.0141:2,2:22.5:1:25.5:1:0.41205:3.33877:60:4:0.0143:0:1 -22 33828944 . T A 198 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCCCAGAGCTGGCGTTGA;RSEQ=GTTGGCCTCAGTCTCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:207,84:0:2,0:25.5:1:30.5:1:1:0:60:96:1:0:0.3 0/1:244:93:56,37:91,60:0.3811:2,2:25.5:1:30.3:1:1:1.00207:60:186:0.3859:0:1.8 -22 33828996 . G A 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07348;SOR=1.29715;LSEQ=CTTAGGCAAGTTAGCCTTGT;RSEQ=GTCAATCTCTTAGGGCGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:170:94,76:148,140:0.3704:2,2:24.3:1:29:1:0.43932:1.17:60:55.667:0.3711:0:1.2 0/1:365:158:78,80:103,104:0.4329:2,2:24.6:1:29:1:1:1.01574:60:38.5:0.4302:0:1.6 -22 33829087 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29944;LSEQ=ATCATGCAGAAGGCCTTCTC;RSEQ=TGCAATTATTACCAATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:79:25,54:41,113:0.3376:2,2:23.3:1:31.1:1:0.44489:1.27:60:78:0.3391:0:1.3 0/1:159:21:9,12:45,93:0.1321:2,2:22.4:1:31.8:1:0.45844:1.55:60:42:0.1355:0:1.2 -22 33829090 . C A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05922;SOR=Inf;LSEQ=ATGCAGAAGGCCTTCTCTTG;RSEQ=AATTATTACCAATACCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:63,164:0:2,0:22:1:31.6:1:1:0:60:36.833:1:0:0.5 0/1:146:3:3,0:45,98:0.0205:2,0:5:1:20.7:1:0.03404:0:60:2:0.0139:0:1 -22 34729259 . T TACCAGC 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=33;MSI=6.000;MSILEN=6;SSF=0.10177;SOR=1.61234;LSEQ=TCACAATCTGCACCGGTGTC;RSEQ=ACCAGCACCAGCACCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:28:14,14:39,30:0.2887:2,2:25.5:1:31.2:1:0.65419:1.29645:59.8:56:0.2887:0.0619:0.1 0/1:149:59:26,33:54,36:0.396:2,2:25.9:1:30.4:1:0.0658:1.89549:59.7:118:0.396:0.1477:0.2 -22 34729300 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51878;SOR=Inf;LSEQ=CAGCACCAGCACCTGATGTA;RSEQ=GTTGGTGGGGAACCAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:29,48:0:2,0:25.3:1:30.4:1:1:0:59.9:76:1:0:0.1 0/1:117:2:1,1:48,67:0.0171:2,2:31.5:1:31.5:1:1:1.39:60:4:0.0171:0:1 -22 34729364 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48936;SOR=Inf;LSEQ=CAGTTGTCCGGTGTTCCCCC;RSEQ=AAGCCAGGCACCTCGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:1,22:0:1,0:26:1:31.6:1:1:0:60:46:1:0:0.3 0/1:24:2:0,2:0,22:0.0833:1,0:47.5:1:29.5:1:1:0:60:4:0.0833:0:1 -22 35397186 . GT G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22433;SOR=Inf;LSEQ=GTAGTTGCTACAGAGACCAT;RSEQ=GGCCTGCAAAACCTAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:12,23:0:2,0:26.2:1:29.5:1:1:0:60:34:1:0:0.1 0/1:32:2:1,1:9,21:0.0625:2,2:21:0:33:1:0.53427:2.27:60:4:0.0625:0:0 -22 35397293 . C T 70 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55944;SOR=0.29522;LSEQ=GAAACAGAATGCAGGCAGAG;RSEQ=GTCAGGAAGAATGTGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:25.6:1:30.2:1:1:0:60:10:0.5556:0:1.2 0/1:4:1:0,1:1,2:0.25:2,0:12:0:32:0:1:0:60:2:0.25:0:1 -22 36521857 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49269;SOR=0;LSEQ=GGCTATGCACTAAATCTGAC;RSEQ=AGCCATTGTGTGTAAGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:0.0645:2,2:8.5:1:28.5:1:1:1.22249:60:4:0.0667:0:1.5 0/0:28:0:0,0:18,10:0:2,0:27.1:1:30.6:1:1:0:60:56:1:0:0.2 -22 36521859 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23004;SOR=Inf;LSEQ=CTATGCACTAAATCTGACCA;RSEQ=CCATTGTGTGTAAGGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:0:2,0:27.3:1:31.8:1:1:0:60:31:1:0:0.3 0/1:30:2:1,1:18,10:0.0667:2,2:40:1:29.5:1:1:1.76317:60:4:0.069:0:1 -22 37627234 . T C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14901;SOR=2.48028;LSEQ=GGCCAAGTCAGGGCCTCCCC;RSEQ=GCAGCCAGATCGCCCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:11,0:15,0:0.4231:1,0:22.7:1:31.5:1:1:0:60:22:0.4231:0:2 1/0:20:13:13,0:7,0:0.65:0,1:24.8:1:29.8:1:1:0:60:26:0.65:0:2.2 -22 37627246 . G C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.80133;SOR=1.24563;LSEQ=GCCTCCCCTGCAGCCAGATC;RSEQ=CCCCTCTGAGCCCGAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:16:14,2:18,2:0.4444:2,2:21.9:1:31:1:1:1.27668:60:32:0.4444:0:1.7 1/0:28:14:12,2:12,2:0.5:2,2:26:1:29.7:1:1:1:60:28:0.5:0:2.1 -22 37627845 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCTGCCAGCCCTGGTTG;RSEQ=CACTGGGGACCCTCTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30:1:1:0:60:4:1:0:1 -22 37640107 . A T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65298;SOR=2.12879;LSEQ=CACCAGGGCGGAAGGATCTC;RSEQ=GGGCATCCCAGTTGGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:2:0,2:150,69:0.009:2,0:2:1:26:0:0.10222:0:60:4:0.0093:0:1 0/1:157:3:1,2:104,49:0.0191:2,2:11:1:22:1:0.24927:4.20188:60:2:0.0132:0:1.3 -22 37640188 . T A 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06219;SOR=Inf;LSEQ=CACACACTTGATGGCCTGCA;RSEQ=CGTGTCCGGAGCCTGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:176,226:0:2,0:25.8:1:30.2:1:1:0:60:49.25:1:0:0.2 0/1:424:5:3,2:193,226:0.0118:2,2:16.2:1:29.4:1:0.66595:1.75:60:10:0.012:0:1 -22 37640232 . C T 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00697;SOR=Inf;LSEQ=CGGTGGTGACAGCTCAGGGC;RSEQ=AGGCGCGTTTCTGCGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:76,141:0:2,0:20.5:1:30.6:1:1:0:60:42.4:1:0:0.1 0/1:171:6:2,4:51,114:0.0351:2,2:18.7:1:28.7:1:1:1.12:60:12:0.0355:0:1.3 -22 37640246 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19624;SOR=Inf;LSEQ=CAGGGCCAGGCGCGTTTCTG;RSEQ=GGGCGCAAGGGGTGTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:39,110:0:2,0:22.2:1:29.7:1:1:0:60:73.5:1:0:0.1 0/1:119:2:1,1:25,92:0.0168:2,2:28:1:27:1:0.39069:3.63:60:4:0.0171:0:1 -22 37641410 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCCACTGGTCACCCACCC;RSEQ=GGACTCGTCACTCGGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 37903975 . G A 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=GCAGGTACTGAGGGTGGCAC;RSEQ=GGGCGGGGTCAGACCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:0.4545:2,2:10.2:1:30.6:1:1:1.30:60:10:0.4545:0:1 0/0:4:0:0,0:1,3:0:2,0:20.5:1:30:1:1:0:60:8:1:0:0.3 -22 37912009 . C T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64649;SOR=2.12446;LSEQ=CAGGTCACGGCTGCGAAGTA;RSEQ=AGCCGAGTTCTTCTCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:30,20:0.0385:2,2:44.5:1:29.5:1:1:1.48801:60:4:0.0392:0:1 0/1:38:3:1,2:20,15:0.0789:2,2:27:1:28.3:1:0.57681:2.59906:60:6:0.0789:0:1 -22 37912060 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52027;SOR=0;LSEQ=CAGGCGCATGGCGATCATGT;RSEQ=GTTCTCATCCTTGAGCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:23,38:0.0317:2,2:26:0:33.5:1:1:1.64:60:4:0.0323:0:1.5 0/0:40:0:0,0:16,24:0:2,0:27.2:1:30.1:1:1:0:60:80:1:0:0.2 -22 37912078 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52344;SOR=0;LSEQ=GTAGTTCTCATCCTTGAGCC;RSEQ=CAGCAGCTCCAGGCTGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:15,26:0.0465:2,2:25.5:1:30:1:1:1.71:60:4:0.0488:0:1 0/0:26:0:0,0:9,17:0:2,0:26.7:1:31.1:1:1:0:60:52:1:0:0.1 -22 38012918 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22178;SOR=Inf;LSEQ=ACTCTGGCTCTGTGTTGTTC;RSEQ=TCCCACCCAGGCCTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:20,21:0:2,0:30.9:1:31.1:1:1:0:60:40:1:0:0.2 0/1:37:2:1,1:17,18:0.0541:2,2:14:0:28:0:1:1.06:60:4:0.0541:0:1.5 -22 38012937 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10734;SOR=Inf;LSEQ=CCTCCCACCCAGGCCTCCAC;RSEQ=CGCCACCCGGCTGCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:18,22:0:2,0:21:1:29:1:1:0:60:9:1:0:0.2 0/1:20:2:1,1:9,9:0.1:2,2:35:1:30:1:1:1:60:4:0.1111:0:1 -22 38369976 . A G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34438;SOR=0.50101;LSEQ=GCTGCTGAGTAGCTGCTCAC;RSEQ=TGGCCTGGGTGCCCATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:5,7:3,2:0.7059:2,2:25.9:1:32:1:0.61991:2.00863:60:24:0.7059:0:1.1 1/0:24:13:8,5:5,6:0.5417:2,2:17.5:1:29.4:1:0.68239:1.87:60:26:0.5417:0:1.2 -22 38374009 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52081;SOR=0;LSEQ=CTCCCCACCGGGGCACTCCG;RSEQ=CTCGCCCTGGGCGGCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:64,17:0.0241:2,2:17.5:1:28.5:1:0.38877:3.68736:60:4:0.0253:0:1 0/0:53:0:0,0:38,14:0:2,0:18.5:1:31.1:1:1:0:60:51:0.9808:0:0.1 -22 38374064 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49905;SOR=0;LSEQ=CTGGGCTGGTACTTGTAGTC;RSEQ=GGGTGGTCTTTCTTGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:95,76:0.0115:2,2:39:1:30.5:1:1:1.24837:60:4:0.0118:0:1 0/0:163:0:0,0:94,69:0:2,0:30:0:16:0:1:0:60:0:0:0:1 -22 38374085 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22072;SOR=Inf;LSEQ=GGGTGGTCTTTCTTGTGCTG;RSEQ=ATACGGAGCCGCTCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:83,97:0:2,0:27.9:1:32.2:1:1:0:60:360:1:0:0.1 0/1:160:2:1,1:82,76:0.0125:2,2:37:0:31:0:1:1.07841:60:4:0.0125:0:1 -22 38379411 . C A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0839;SOR=Inf;LSEQ=AGCTCAGCGTTGTGCAGGTG;RSEQ=GGGTACTGGTCCGCGAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:211,155:0:2,0:26.4:1:30.8:1:1:0:60:35.6:1:0:0.2 0/1:286:3:2,1:159,123:0.0105:2,2:32.3:1:29.3:1:1:1.54:60:6:0.0105:0:1 -22 38379645 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.14728;SOR=Inf;LSEQ=TTCTTGACCTTGCCCAGCTC;RSEQ=CCTGGCCCCGGGCTGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:35,188:0:2,0:24.4:1:31.6:1:1:0:60:43.6:0.9954:0:0.1 0/1:140:2:1,1:27,111:0.0143:2,2:35.5:1:29:1:0.36115:4.06:60:4:0.0143:0:1 -22 39240008 . G A 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.54034;LSEQ=GAGCCGGAGCTGGAGCTGTC;RSEQ=CCGCGGCCGCTGCTGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:24:0:32:0:1:1.11803:60:4:0.1111:0:1 0/1:17:1:1,0:8,8:0.0588:2,0:1:0:27:0:1:0:60:2:0.0588:0:1 -22 39407399 . T C 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCAGCGATAGGTAAGCTTC;RSEQ=GTGCAGGAACGGGCGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:20.7:1:30:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39407410 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAGCTTCTGTGCAGGAAC;RSEQ=GGCGCTGCTGCACCCCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24.3:1:31:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39408841 . G A 47 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.69379;LSEQ=ACAAGACAAAGAGATAAAGC;RSEQ=AAAACAGCTGGGCCCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:41:1:29.7:1:1:0:60:6:0.4286:0:1.3 0/1:3:1:1,0:2,0:0.3333:0,0:39:0:31:0:1:0:60:2:0.3333:0:1 -22 39408940 . G A 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ATTTATTGCATACAAGACAA;RSEQ=GGGGGCAGGGTAAGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:36,24:0:2,0:19.5:1:31.2:1:1:0:57.8:59:1:0:0.2 0/1:41:11:6,5:18,12:0.2683:2,2:20.5:1:29.8:1:1:1.24314:59.3:22:0.2683:0:1.2 -22 39408956 . A G 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57401;SOR=2.7564;LSEQ=ACAAGGGGGGCAGGGTAAGG;RSEQ=GGGTGAGTCGTCCAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:41,34:0.0132:2,0:1:0:12:0:1:0:60:0:0:0:2 0/1:56:2:1,1:28,26:0.0357:2,2:28:1:32:0:1:1.07547:60:4:0.037:0:2 -22 39408959 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50484;SOR=0;LSEQ=AGGGGGGCAGGGTAAGGAGG;RSEQ=TGAGTCGTCCAAGTGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:38,33:0.0274:2,2:22:0:32:0:1:1.14928:52:4:0.0286:0:1.5 0/0:56:0:0,0:28,28:0:2,0:25.1:1:30.1:1:1:0:58.1:55:1:0:0.3 -22 39639257 . GTCTCTC G 44 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCCGTCTCTCTCTCC;RSEQ=TCTCTCTCTCTCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:32.3:1:28.3:1:1:0:60:6:1:0.3333:0.7 -22 39640006 . G T 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGCGGGGCCCCGGACGC;RSEQ=TAGATCGAGCGCGCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:0:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39640933 . G T 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GGGAGGCAGCGGGGGAGGCT;RSEQ=CGGGTGCGCAGGGAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:24.8:1:31.3:1:1:0:60:8:1:0:0 0/1:5:2:1,1:2,1:0.4:2,2:22:0:29.5:1:1:1.7321:60:4:0.4:0:2 -22 39640950 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.5;SOR=Inf;LSEQ=GCTGCGGGTGCGCAGGGAGG;RSEQ=AGGCAGGCCGCTCCCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:22.3:1:33.7:1:1:0:60:6:1:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:36:1:28.5:1:1:2.44949:60:4:0.3333:0:1 -22 39641035 . G T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.88734;LSEQ=AAGGAGAAGGGAGAGTGCGA;RSEQ=AGGTGGGTGGAGACAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:0.08:2,2:14.5:1:27.5:1:1:1.0871:60:4:0.08:0:1 0/1:14:1:0,1:8,5:0.0714:2,0:1:0:22:0:0.42857:0:60:2:0.0714:0:1 -22 39641067 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51711;SOR=0;LSEQ=GACAGCCTTTCCTCTTCTGG;RSEQ=CCGGAGTCAGCGCCAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:23:0:30.5:1:1:1.07415:60:4:0.0714:0:1.5 0/0:18:0:0,0:9,9:0:2,0:31.9:1:31.3:1:1:0:60:17:1:0:0.5 -22 39641096 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4958;SOR=0;LSEQ=AGCGCCAGGAGGGGGGGGAC;RSEQ=CGGGAGCTGGGGGAGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:6,12:0.1:2,2:22.5:1:30:1:1:1.93:60:4:0.1:0:1.5 0/0:15:0:0,0:7,8:0:2,0:18.2:1:29.8:1:1:0:60:30:1:0:0.9 -22 39641913 . G T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCCTCGGGACACGCAG;RSEQ=CTCCTGCATCACCCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:30.5:1:30:1:1:1:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39642740 . A T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGAAGCAAGCGCCTGGA;RSEQ=CCTTCCATGCAGCCTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39756743 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17823;SOR=Inf;LSEQ=AAATATGGAGGTGAGCACAG;RSEQ=CCCCTAGAGAGGGACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:0:2,0:21:1:28.8:1:1:0:60:38:1:0:0.2 0/1:29:2:1,1:18,9:0.069:2,2:21:0:33.5:1:1:1.94942:60:4:0.069:0:1 -22 39756854 . G C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.82263;LSEQ=AGCGAGGGCAAATGCTGAAA;RSEQ=GCCTGGCAGAGCAGAGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:1,7:0,6:0.5714:0,2:23.3:1:30.6:1:1:0:60:16:0.5714:0:1 1/0:23:12:2,10:3,8:0.5217:2,2:12.4:1:29.8:1:0.64041:1.82405:60:24:0.5455:0:1.2 -22 39756896 . G A 50 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18182;SOR=Inf;LSEQ=GCTGTCGCCCCTGCTGGGGT;RSEQ=TACGCTTGGAGGGCGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:16.2:1:27.7:1:1:0:60:5:1:0:1 1/0:6:3:0,3:0,3:0.5:0,0:21.3:1:32:0:1:0:60:6:0.5:0:1 -22 39756985 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCCAACTATGGATGGA;RSEQ=GTGGCGGGAACTGCACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:31:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39758830 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGATTCTCCTTTCTACCC;RSEQ=CCGTGCTGCCTGGCCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:31:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39758844 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACCCCCCGTGCTGCCTGG;RSEQ=CCTCTCTGACTATCAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38.5:1:32.5:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39758881 . A G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGCTGTCTACTCCCCTC;RSEQ=AAGCCTTTCCTGACCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:32:0:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39866646 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGAGGAGGCAGAGAGAG;RSEQ=TCCATCCTGGGAGCATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:48.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 39866891 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.69461;LSEQ=AGGGCAGGATTTGAATCCAG;RSEQ=CCCTTTTGAGTCTAGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:102,52:0.0128:2,2:20.5:1:29.5:1:1:1.95251:60:4:0.013:0:1.5 0/0:112:1:0,1:72,39:0.0089:2,0:1:0:25:0:0.35714:0:60:2:0.0091:0:2 -22 39866923 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.58639;SOR=2.52814;LSEQ=CTAGACTCCAGAGAGCTATG;RSEQ=CCCCAAAGCAGCCCTCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:1,0:140,107:0.004:2,0:37:0:12:0:1:0:60:0:0:0:3 0/1:197:2:0,2:109,86:0.0102:2,0:17.5:1:27.5:1:0.19828:0:60:4:0.0105:0:1 -22 39866938 . T C 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=2.61334;LSEQ=CTATGGCCCCAAAGCAGCCC;RSEQ=CGCCCCACGCTGACTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:29:12,17:135,122:0.1014:2,2:25.9:1:30:1:0.32754:1.56515:60:28:0.1011:0:1.4 0/1:228:52:26,26:90,86:0.2281:2,2:25.5:1:31:1:1:1.04633:60:104:0.2311:0:1.2 -22 39867018 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51464;SOR=0;LSEQ=GAGAGCCCTCTCACAGAGGC;RSEQ=GAAGCACTCAGCCCAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:21,82:0.019:2,2:7.5:1:29:1:0.37674:3.84:60:4:0.019:0:1 0/0:72:0:0,0:19,53:0:2,0:20.5:1:30.2:1:1:0:60:17:1:0:0.3 -22 40982888 . AGTGCTGCTG A 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=24;MSI=2.667;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCATCTGATTTGGCCTCT;RSEQ=GTGCTGCTGGTGCTGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:0:2,0:29.5:1:31.4:1:1:0:60:34:1:0:0.3 0/1:57:28:14,14:16,13:0.4912:2,2:29:1:30.9:1:0.79304:1.22628:59.8:56:0.4912:0.0175:0 -22 40982928 . GTGC G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.2578;SOR=Inf;LSEQ=TGCTGCTGGTGCTGGTGCTG;RSEQ=TGCTGCTGCTGCTGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:23,23:0:2,0:25.9:1:29.8:1:1:0:60:45:1:0:0.3 0/1:61:3:1,2:26,32:0.0492:2,2:22.3:1:31.3:1:1:1.61261:60:6:0.0492:0.0164:0 -22 40982971 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19989;SOR=0;LSEQ=GCCGCCGCTGCCTTATCCAC;RSEQ=TGGAGTTTGTGGTTGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:10,16:0.0714:2,2:43:1:30:1:1:1.57:60:4:0.0741:0:1 0/0:34:0:0,0:10,24:0:2,0:23.2:1:31.5:1:1:0:59.9:68:1:0:0.1 -22 41461514 . C CA 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAAAGCGAGGCCCTGTCT;RSEQ=AAAAAAAAAAAACAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,0:0.5:0,0:10.5:1:28.8:1:1:0:60:4:0.5:0.25:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41461721 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49859;SOR=0;LSEQ=CTCTTCCTGCACCCCTTTTC;RSEQ=TGTTTAATGGTAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:130,28:0.0125:2,2:14.5:1:29.5:1:0.33058:4.57964:60:4:0.0125:0:1.5 0/0:154:0:0,0:118,36:0:2,0:22.6:1:30.6:1:1:0:60:153:1:0:0.1 -22 41461836 . A G 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36905;LSEQ=ATTTCTCCTCTCTATCCCCA;RSEQ=TGACAGGTTGCCACACGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:483:344:175,169:68,68:0.7122:2,2:25:1:31.8:1:0.91938:1.04:60:67.8:0.7122:0:1.2 0/1:524:250:125,125:135,139:0.4771:2,2:24.2:1:30.9:1:0.93032:1.03:60:30.25:0.4717:0:1.6 -22 41461865 . T G 239 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09971;SOR=1.24713;LSEQ=TGCCACACGCTATCTTACAA;RSEQ=TTCACAATGACCCTCCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:186:78,108:120,158:0.4009:2,2:27.2:1:32.3:1:0.8482:1.05152:60:92:0.3991:0:1.3 0/1:477:217:98,119:114,146:0.4549:2,2:25.4:1:30.9:1:0.78209:1.05:60:42.4:0.4511:0:1.6 -22 41461964 . G A 33 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21596;SOR=3.1478;LSEQ=AAAGGGATATGAGTGGACAT;RSEQ=AATTTTGTCCCTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:0,2:13,87:0.019:2,0:18:1:29.5:1:1:0:50:4:0.0244:0:3 0/1:69:4:0,4:7,57:0.058:2,0:26.8:1:16.5:1:1:0:45:0.333:0.0204:0:4.5 -22 41488906 . GC G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.22686;SOR=Inf;LSEQ=CCCCCTCGGGTGCCGTCGGA;RSEQ=CCCCCAGCCCACCCCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:112,4:0:1,0:24.2:1:31.8:1:1:0:60:28:1:0:0.1 0/1:106:2:2,0:101,3:0.0189:1,0:14.5:1:34:0:1:0:60:4:0.0192:0:0 -22 41489173 . A AT 94 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.58716;SOR=0.65733;LSEQ=CGGTGCGCCTTTATTCTTCC;RSEQ=TTTTTTTTTTCTTCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:9:2,7:22,157:0.0471:2,2:21.7:1:29.9:1:0.32234:2.03:60:18:0.0492:0.0052:0.6 0/1:159:5:0,5:17,135:0.0314:2,0:30.2:1:28.8:1:1:0:60:10:0.0331:0:0 -22 41489487 . T C 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATTTCGAATCCTTTCTC;RSEQ=TTACTGTACTTACTGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:19:1:33:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41513094 . G T 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2997;SOR=0.68535;LSEQ=GAAAAACATGGAGTGAGGTT;RSEQ=GGAAATGACATTTAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:99:64:64,0:33,2:0.6465:2,1:20.4:1:30.4:1:0.12266:0:60:63:0.6563:0:1.1 1/0:54:30:29,1:24,0:0.5556:1,1:20.4:1:29.6:1:1:0:60:29:0.5472:0:1.1 -22 41513121 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51225;SOR=0;LSEQ=GACATTTAATGCTTATTGAG;RSEQ=ACAATATAGAGCAGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:152,10:0.0122:2,2:10:0:32.5:1:0.13003:14.53793:60:4:0.0125:0:1.5 0/0:117:0:0,0:103,14:0:2,0:22:1:28.9:1:1:0:60:57.5:1:0:0.3 -22 41513857 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12363;SOR=Inf;LSEQ=TTTGGTTTGTGTGCACAATC;RSEQ=GCATGCATGTGAGTATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:72,201:0:2,0:23.4:1:30.5:1:1:0:60:90:1:0:0.1 0/1:274:4:2,2:87,183:0.0146:2,2:23.3:1:29.3:1:0.5978:2.10:60:8:0.015:0:1.3 -22 41514155 . G A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GAGATGGCTGGCATTACACT;RSEQ=TCTTCAGATGGATACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:23.5:1:31.5:1:1:0:60:4:0.4:0:1 1/1:2:2:1,1:0,0:1:0,2:40.5:1:29:1:1:0:60:4:1:0:1 -22 41521557 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGATTACAGGTATGAGTC;RSEQ=CCAGGCCCGGCCACTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:21.3:1:31.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41521717 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1628;LSEQ=TTAGTAGAGATGGGGTTTTG;RSEQ=CACGTTGCCCAAGCTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:21:21,0:14,0:0.6:1,1:26.3:1:31.2:1:1:0:60:20:0.5882:0:1 1/0:11:7:7,0:4,0:0.6364:0,0:41:1:30:1:1:0:60:6:0.6:0:1.7 -22 41523809 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2068;SOR=Inf;LSEQ=TTTACAGCCAGGGAGAAGAA;RSEQ=GAAAATGTGATCAAGTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:23,215:0:2,0:24.2:1:31.2:1:1:0:60:237:1:0:0.2 0/1:199:2:1,1:21,176:0.0101:2,2:16:1:25:1:0.20938:8.21:60:4:0.0101:0:1 -22 41523937 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0764;SOR=0.1724;LSEQ=TGTGGTGTCTCACACTTACA;RSEQ=TCCCAGCACTTTGGTAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:15:0,15:0,6:0.7143:0,1:28:1:31.1:1:1:0:60:14:0.7:0:1 0/1:7:2:0,2:0,5:0.2857:0,0:16.5:1:32.5:1:1:0:60:4:0.3333:0:1 -22 41525892 . A G 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATATGTTTTCTTCTCTTT;RSEQ=GTGGCACACTGTGCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:510:28:17,11:314,168:0.0549:2,2:23.9:1:31.9:1:0.68519:1.20891:60:56:0.0559:0:1.1 0/0:484:0:0,0:298,184:0:2,0:24.6:1:28.6:1:1:0:60:42.818:0.9958:0:0.1 -22 41526364 . C G 32 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=CCCAGGAGTTCAAGACCAGC;RSEQ=TAGGCAACTTAGCAAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:33:1:30:1:1:0:60:5:1:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:32.5:1:1:0:60:4:1:0:1 -22 41527338 . C CT 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.50973;SOR=0.55096;LSEQ=TTTTTATTAGACATGTTAGT;RSEQ=TTTTTTTTCTCACCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:6:6,0:240,44:0.0207:2,0:28.2:1:32.1:1:0.59567:0:60:12:0.021:0.0034:0 0/1:261:3:2,1:199,59:0.0115:2,2:20:1:29.6:1:0.54484:1.68262:60:6:0.0116:0.0077:0 -22 41531569 . C CT 50 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCGCCTGGTCACATTTG;RSEQ=TTTTTTTTTTTAAGTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:21,0:0.125:1,0:12.7:1:31.8:1:1:0:60:6:0.125:0.0833:0 0/0:1:0:0,0:1,0:0:0,0:34:0:34:0:1:0:60:2:1:0:1 -22 41532025 . A G 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.03433;SOR=Inf;LSEQ=GAGGATGTCTTTGAATACAG;RSEQ=TAGATGTTTGAGTCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:0,84:0:1,0:23.5:1:30.8:1:1:0:60:27:1:0:0 0/1:65:4:0,4:1,60:0.0615:1,0:27.5:1:32.5:1:1:0:60:8:0.0625:0:1 -22 41533590 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16758;SOR=Inf;LSEQ=CATTACAATAATCAGTGTCA;RSEQ=CTTGAATTAAATGAGGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:221,25:0:2,0:26:1:32.5:1:1:0:60:245:1:0:0 0/1:171:2:1,1:138,31:0.0117:2,2:30.5:1:26.5:1:0.34014:4.39736:60:4:0.012:0:1 -22 41536305 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09946;SOR=Inf;LSEQ=TAATAGCCAAGATTGAACCT;RSEQ=TTGTGGTTATTTTATTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:68,232:0:2,0:23.7:1:31.7:1:1:0:60:41.857:1:0:0.1 0/1:260:3:2,1:72,185:0.0115:2,2:23.7:1:27.3:1:0.19589:5.10:60:6:0.0116:0:1 -22 41537234 . G T 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00024;SOR=0.06129;LSEQ=GGAATGACTTCTAGTAAGTG;RSEQ=TTTTTGTTATATTTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:372:371:104,267:0,0:0.9973:0,2:24.6:1:30.1:1:1:0:60:122.667:1:0:1.1 1/1:379:363:119,244:6,10:0.9578:2,2:25.2:1:29.3:1:0.78686:1.22953:60:59.5:0.9571:0:1.1 -22 41542753 . A G 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTACTCTAGATGGCCCTCT;RSEQ=CCTGACCCAAGTATGATCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:890:0:0,0:426,464:0:2,0:24.7:1:28.8:1:1:0:60:97.889:1:0:0.1 0/1:1035:29:15,14:481,523:0.028:2,2:27.1:1:30.8:1:0.71005:1.16:60:13.5:0.0264:0:1.2 -22 41542838 . T A 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGTAAATAGTGAAAAAAA;RSEQ=TTTTTTATTTTAAAAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:30:5,25:53,229:0.0955:2,2:20.5:1:30.1:1:1:1.15668:60:29:0.0932:0:1.2 0/0:351:0:0,0:94,256:0:2,0:22.8:1:29.9:1:1:0:60:115.667:0.9971:0:0.1 -22 41544167 . C T 52 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7099;LSEQ=AGTGTTTAGTGGCCTGCATG;RSEQ=GTTTTCACGGTCACTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:1,3:0,14:0.2222:1,2:19.3:1:26:1:0.22222:0:60:3:0.1765:0:1.5 0/1:6:1:0,1:0,5:0.1667:0,0:13:0:25:0:1:0:60:2:0.1667:0:1 -22 41545330 . TGAA T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00265;SOR=0.21368;LSEQ=GACTTAGGGTATTCTGAACA;RSEQ=GAGATTATTCTGTGACATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:26:1,25:1,20:0.5532:1,1:27.2:1:30.9:1:1:1.24403:59.4:25:0.5556:0.0851:0.2 0/1:34:7:0,7:0,27:0.2059:1,0:21.3:1:31.6:1:1:0:60:14:0.2121:0:0.3 -22 41545452 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAATCTTAGAATTAAACA;RSEQ=AATGTAGAAGGAAATCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:15,11:0.0714:2,2:16:0:32:0:1:1.34838:60:4:0.0714:0:1.5 0/0:2:0:0,0:0,2:0:0,0:16.5:1:34:0:1:0:60:4:1:0:0 -22 41545611 . G C 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.43269;SOR=0;LSEQ=GGTGCTGTCCAAAGATACAT;RSEQ=CCCAGTAATAGGGTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:59:59:56,3:0,0:1:0,2:25.1:1:31.3:1:1:0:60:58:1:0:1 1/1:45:44:44,0:0,0:0.9778:0,1:25.2:1:31.5:1:1:0:60:43:0.9773:0:1.1 -22 41545623 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02246;SOR=Inf;LSEQ=AGATACATGCCCAGTAATAG;RSEQ=GTATTTTACACATTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:89,2:0:1,0:22.2:1:31.5:1:1:0:60:182:1:0:0.6 0/1:59:4:4,0:54,1:0.0678:1,0:24.8:1:30.3:1:1:0:60:8:0.069:0:2 -22 41545666 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16326;SOR=Inf;LSEQ=GACACATTGCTACTCTTTGT;RSEQ=TAATCAGTTTGTGTCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:184,7:0:1,0:25.9:1:30.4:1:1:0:60:190:1:0:0.3 0/1:130:2:1,1:118,10:0.0154:2,2:17.5:1:29.5:1:0.16267:11.29871:60:4:0.0156:0:1.5 -22 41546187 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20579;SOR=Inf;LSEQ=ACAGCACCGCTGCTTCCTCC;RSEQ=CAGCCTGCAACTCCAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:49,172:0:2,0:26.5:1:31.2:1:1:0:60:30.571:1:0:0.1 0/1:184:2:1,1:54,128:0.0109:2,2:24:1:29.5:1:0.50962:2.36:60:4:0.011:0:1 -22 41547677 . A AG 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16113;SOR=Inf;LSEQ=CCTGTTCTTAAGCATAATTA;RSEQ=GGGAGGTGAAATGGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:41,0:0:1,0:21:1:30.2:1:1:0:60:40:1:0:0.1 0/1:28:2:2,0:25,1:0.0714:1,0:11.5:1:31.7:1:1:0:60:4:0.0714:0.0357:0 -22 41547766 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19271;SOR=Inf;LSEQ=TTCTGCTATCCTGTTGCTTA;RSEQ=CTTACATTCTGATTGTATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:193,29:0:2,0:23.5:1:31.7:1:1:0:60:43.4:1:0:0.1 0/1:175:2:1,1:147,26:0.0114:2,2:13:1:28.5:1:0.28552:5.56707:60:4:0.0114:0:1 -22 41547819 . C T 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGTGTGTCTCACCTACTTC;RSEQ=CTTTTTTTTCTGCCCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:526:0:0,0:344,182:0:2,0:24:1:30.8:1:1:0:60:51.6:1:0:0.2 0/1:505:25:13,12:292,188:0.0495:2,2:26.4:1:28.4:1:0.40613:1.43263:60:24:0.0477:0:1.1 -22 41547820 . C CT 96 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.42175;SOR=0.57126;LSEQ=CGTGTGTCTCACCTACTTCC;RSEQ=TTTTTTTTCTGCCCAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:9:7,2:335,183:0.017:2,2:25.6:1:30.6:1:0.5046:1.91:60:8:0.0154:0:0.4 0/0:510:5:2,3:305,200:0.0098:2,2:27.8:1:30.4:1:0.39138:2.2837:60:10:0.0098:0.002:0.2 -22 41548008 . A G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.16713;LSEQ=CAGATACTCAGCCGGAGGAT;RSEQ=TTTCAGAGGTGAGAGTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:576:338:128,210:93,143:0.5868:2,2:26.1:1:32:1:0.72786:1.06686:60:111.667:0.5877:0:1.2 0/1:616:118:46,72:214,284:0.1916:2,2:26.6:1:31.2:1:0.46872:1.17911:60:117:0.1902:0:1.1 -22 41548369 . C A 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4534;SOR=2.33601;LSEQ=AAAAGAGTGAGTCTCTGAAG;RSEQ=CATTCGTTCTGGAGGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:2:1,1:147,258:0.0049:2,2:17.5:1:27:0:1:1.75:60:4:0.005:0:1 0/1:438:5:4,1:163,270:0.0114:2,2:6.4:1:27.6:1:0.07228:6.60:60:10:0.0116:0:1 -22 41548421 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50646;SOR=0;LSEQ=AGACCCAGGGCAGAATTGCG;RSEQ=TCATGCCTCTTGGGCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:32,139:0.0116:2,2:21.5:1:28.5:1:0.34601:4.29:60:4:0.0116:0:1 0/0:134:0:0,0:26,108:0:2,0:21.6:1:30.9:1:1:0:60:133:1:0:0.1 -22 41548519 . CT C 61 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.24477;SOR=3.23423;LSEQ=GTTACTAATAATTTTTCTTT;RSEQ=TTTTTTTTTTTTTAATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:0,4:0,24:0.129:1,0:23:1:30.8:1:1:0:60:8:0.1429:0.0323:0.5 0/1:6:2:0,2:0,4:0.3333:0,0:27:1:27.5:1:1:0:60:4:0.3333:0:0 -22 41550954 . C T 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2641;SOR=0.80861;LSEQ=AATGATTTTTTAAAGTTCTT;RSEQ=TGCTTAATTGGTAACTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:261:154:139,15:100,6:0.59:2,2:23.7:1:29.7:1:0.25798:1.79474:60:37.5:0.5929:0:1.4 1/0:212:114:102,12:88,9:0.5377:2,2:22.8:1:30:1:0.82075:1.14957:59.9:113:0.5433:0:1.6 -22 41550956 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25456;SOR=0;LSEQ=TGATTTTTTAAAGTTCTTCT;RSEQ=CTTAATTGGTAACTAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:3,0:245,25:0.011:2,0:8.7:1:22:1:1:0:60:2:0.0075:0:2.3 0/0:228:0:0,0:199,27:0:2,0:22.3:1:31.7:1:1:0:60:74.333:1:0:0.9 -22 41550984 . C CT 174 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.06496;SOR=1.50501;LSEQ=GGTAACTAATTTCAAATGCA;RSEQ=TTTTTTTTTTTAAGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:39:35,4:332,84:0.0839:2,2:28.4:1:30.8:1:0.20076:2.21:60:18.5:0.0817:0:0.9 0/1:454:55:45,10:293,95:0.1211:2,2:27:1:30.2:1:0.39679:1.46:59.3:26.5:0.1213:0:1.1 -22 41551018 . A G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTTCAAACCAGAAGAACT;RSEQ=CGACAGGCACTGATGCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:848:0:0,0:568,278:0:2,0:24.7:1:28.4:1:1:0:60:37.455:0.9988:0:0.8 0/1:942:27:19,8:581,332:0.0287:2,2:20:1:31.3:1:0.54657:1.36:60:54:0.0294:0:1 -22 41551039 . T A 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.69257;LSEQ=CGACAGGCACTGATGCCAAC;RSEQ=TTGGAGGCACTTTACCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1088:656:390,266:251,181:0.6029:2,2:26.6:1:29.7:1:0.65994:1.06:60:23.296:0.5973:0:1.2 1/0:1235:633:360,273:336,263:0.5126:2,2:25.7:1:29.1:1:0.81815:1.03:60:41.2:0.5116:0:1.2 -22 41551231 . AT A 140 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.3645;SOR=0.67932;LSEQ=TTCAAATTTGTAATTCAGTG;RSEQ=TTTTTTTTTTTCCCCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:23:0,23:0,114:0.1679:1,1:30.7:1:31.1:1:1:0:59.8:46:0.1742:0:0.1 0/1:108:13:0,13:2,91:0.1204:1,1:23.8:1:30.8:1:1:0:60:26:0.1238:0.0093:0.8 -22 41551244 . C T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.65722;SOR=1.89963;LSEQ=TTCAGTGATTTTTTTTTTTT;RSEQ=CCCCTGAGACAGGGTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:0,2:0,107:0.0182:1,0:13:1:31.5:1:1:0:60:4:0.0189:0:1 0/1:88:3:1,2:0,85:0.0341:1,2:9.7:1:31:0:0.03409:0:60:6:0.0345:0:1 -22 41552926 . T G 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAGAACCTGAAGTTGC;RSEQ=TCAGTAGAATATCAGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:11,0:0.1538:0,0:40:1:31.5:1:1:0:60:4:0.1667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41553123 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1169;SOR=Inf;LSEQ=ATGGATGATACTCCATCTCC;RSEQ=GTAAAAATAGTGAGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:230,71:0:2,0:22.6:1:30.7:1:1:0:60:149.5:1:0:0.1 0/1:289:3:1,2:218,67:0.0104:2,2:12.7:1:26.7:1:0.1437:6.45368:60:6:0.0107:0:1 -22 41553469 . A G 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61216;SOR=2.14261;LSEQ=TGGGATACCTAGAATAATAT;RSEQ=GTGGTGACTGGGATAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:1:0,1:29,173:0.0049:2,0:40:0:8:0:1:0:60:0:0:0:7 0/1:193:2:1,1:43,148:0.0104:2,2:32.5:1:28:1:0.4049:3.41:60:4:0.011:0:1 -22 41554278 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13406;SOR=Inf;LSEQ=GTAAACTGAGAATGATTTTC;RSEQ=GGAACTGAATTAGCCCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:101,2:0:1,0:24.2:1:30.3:1:1:0:60:206:1:0:0.1 0/1:60:2:2,0:56,2:0.0333:1,0:35:1:31:1:1:0:60:4:0.0333:0:1 -22 41554559 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25624;SOR=0;LSEQ=GTCCACATGTCCAGGGAGTG;RSEQ=ATGCGGATGGGCCAGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:1,2:47,214:0.0113:2,2:23.7:1:28:1:0.45368:2.27:60:6:0.0114:0:1 0/0:216:0:0,0:35,181:0:2,0:21.1:1:31.4:1:1:0:60:26:1:0:0.1 -22 41556423 . C CA 46 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.50893;SOR=0;LSEQ=TCTGCACTTGGCTTTGATTG;RSEQ=AAAAAAAAAAACAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:7,0:0.2727:0,0:9.3:1:29.2:1:1:0:60:6:0.2727:0.0909:0 0/0:5:0:0,0:4,0:0:0,0:7:1:30.5:1:1:0:52:8:0.8:0:2.5 -22 41556435 . C CA 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.07;SOR=Inf;LSEQ=TTTGATTGCAAAAAAAAAAA;RSEQ=AAAAAAAAACAAAAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:16,2:0:2,0:17.7:1:28.2:1:1:0:60:5:1:0:0.1 0/1:7:2:2,0:4,0:0.2857:0,0:19.5:1:31:1:1:0:50:4:0.4:0:1.5 -22 41556520 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20229;SOR=Inf;LSEQ=CATTGAATGTCCTTGTCGCC;RSEQ=TTGATGACCTGCTCTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:61,2:0:1,0:25.2:1:29.7:1:1:0:60:62:1:0:0.3 0/1:52:2:1,1:50,0:0.0385:1,2:33:1:31:1:0.03846:0:60:4:0.0392:0:1 -22 41556812 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18857;SOR=Inf;LSEQ=TTTCTAAATGAACTTAAGCT;RSEQ=TGCTGTTGAATATGGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:1,70:0:1,0:27:1:31:1:1:0:60:70:1:0:0.1 0/1:55:2:1,1:2,51:0.0364:1,2:28:1:32.5:1:0.10707:21.02:60:4:0.0364:0:1 -22 41558232 . A G 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTCTAGGCCATAACTAGT;RSEQ=TAAGAAACGGTTTTCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:13:1:34:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41559963 . C T 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAGTTCTTTGGTCATGAC;RSEQ=TTGGCTGTCTTTGTCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:349,47:0:2,0:25.2:1:31.1:1:1:0:60:55.571:1:0:0.1 0/1:323:23:17,6:254,46:0.0712:2,2:17.1:1:29.9:1:0.2326:1.94409:60:46:0.0723:0:1.4 -22 41560212 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08971;SOR=Inf;LSEQ=GTTTTTTATTCTATGCAATT;RSEQ=ACTGTATTATATCTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:33,215:0:2,0:23.1:1:31.3:1:1:0:60:123:1:0:0 0/1:202:3:2,1:30,169:0.0149:2,2:14:1:25.7:1:0.06597:11.05:60:6:0.015:0:1 -22 41562177 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTTATTTACTTGGTTG;RSEQ=TGAACAAGTTTATACAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41562785 . A G 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=0;LSEQ=TAATAGAGTAAAAATAAAAT;RSEQ=ATTCTATAATCTCCTTATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:10:0,10:1,31:0.2381:1,0:26:1:32.5:1:1:0:60:20:0.2381:0:1.2 0/0:47:0:0,0:0,47:0:1,0:23.9:1:29.6:1:1:0:60:22.5:1:0:0.1 -22 41564287 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=0.1758;LSEQ=GCATGTTCCCTGCACTCATA;RSEQ=GACATGTAAATCTGCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:34:34,0:19,0:0.6415:1,1:25.7:1:32.1:1:1:0:60:33:0.6346:0:1 0/1:34:8:8,0:26,0:0.2353:1,0:16.8:1:32.9:1:1:0:60:16:0.2353:0:1.1 -22 41564708 . C A 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.54332;LSEQ=GTTATGTTGTGGTTCCCCCA;RSEQ=CATCTCAATTGTATAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:741:184:104,80:289,268:0.2483:2,2:27.3:1:30.3:1:0.30672:1.21:60:183:0.249:0:1 0/1:710:108:56,52:322,280:0.1521:2,2:25.8:1:29.5:1:0.75471:1.06774:60:53:0.1504:0:1.1 -22 41565051 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07563;SOR=Inf;LSEQ=AAACCCCCAAACAAAATAAC;RSEQ=GCTCAATACTGCTCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:3,22:0:2,0:19.5:1:28.2:1:1:0:60:24:1:0:0.3 0/1:10:2:0,2:0,8:0.2:0,0:7:1:32:0:1:0:60:4:0.2:0:1 -22 41565439 . A C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50062;SOR=0;LSEQ=GAGAGGGTGTTATTAGGCAC;RSEQ=TGGAGTAAAGAACTCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:163,16:0.011:2,2:26:1:30.5:1:0.1795:9.91362:60:4:0.0112:0:1 0/0:159:0:0,0:134,24:0:2,0:21.2:1:30:1:1:0:60:157:0.9937:0:0.1 -22 41565469 . CT C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.21312;SOR=0.49292;LSEQ=GAACTCATTATGTGACCTGA;RSEQ=TTTTTTTTCCTCTTCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:11:8,3:262,76:0.0315:2,2:22.5:1:32.5:1:0.71693:1.29175:59.1:22:0.0317:0.0029:0.3 0/1:317:5:3,2:215,96:0.0158:2,2:26:1:31.2:1:0.64732:1.49105:60:10:0.0158:0:0 -22 41565827 . A G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20156;SOR=0.22573;LSEQ=GCCCTAGTTTCACCCATCCA;RSEQ=CATTAGTTTTGTTTGTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:0.6111:0,0:21.5:1:31.2:1:1:0:60:10:0.5882:0:1 0/1:8:2:0,2:1,5:0.25:2,0:12:1:32.5:1:1:0:60:4:0.25:0:1 -22 41566595 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20288;LSEQ=GGTCAGTTGGGACATAGGGG;RSEQ=CAGGTGCTGACAATAGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:539:294:83,211:75,168:0.5455:2,2:28.5:1:28.9:1:0.50732:1.13463:60:17.375:0.5462:0:1.3 0/1:491:96:33,63:136,258:0.1955:2,2:24.3:1:28.3:1:1:1.00633:60:31:0.1979:0:1.2 -22 41566728 . C T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30003;SOR=3.02178;LSEQ=CAGGCTGGAGTGCAGTGACA;RSEQ=GATTTTGGCTCACTTCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:0,19:0.0952:1,0:21.5:1:31:1:1:0:60:4:0.1429:0:2.5 0/1:8:2:0,2:0,6:0.25:0,0:22:1:30:1:1:0:56.5:4:0.2857:0:1 -22 41566823 . A G 39 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACAGGCTCCTGCCATCAC;RSEQ=CCCGGCTAAATTTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:25.3:1:25:1:1:0:59.7:2:0.5:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41566868 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTAGAGACGGGGTTTCAC;RSEQ=GTGTTAGCCAGGATGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:31.5:1:1:0:42:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41567975 . TAC T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATAGGTTGTCTCATGA;RSEQ=AGACTTGTCTTCCTCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:30.5:1:32.5:1:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41568480 . T C 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00507;SOR=0.65492;LSEQ=AAAGAACATAGAAATTCCTA;RSEQ=ATGTACATGCATGTTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:358:222:164,58:97,39:0.6201:2,2:24.3:1:32:1:0.62518:1.14:60:110:0.6197:0:1.1 1/0:393:203:147,56:120,70:0.5165:2,2:23:1:30.9:1:0.05232:1.53:60:202:0.5193:0:1 -22 41568714 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20367;SOR=Inf;LSEQ=CTTCTATCATGATTCTAATA;RSEQ=TTAATCCAGAAGTGCACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:34,166:0:2,0:22.1:1:30.3:1:1:0:60:65.667:1:0:0.1 0/1:165:2:1,1:30,133:0.0121:2,2:17:1:29.5:1:0.34139:4.38:60:4:0.0125:0:1 -22 41568720 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50535;SOR=0;LSEQ=TCATGATTCTAATATTTAAT;RSEQ=CAGAAGTGCACTTAAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:0,2:25,154:0.011:2,0:14:1:31.5:1:1:0:60:4:0.0112:0:1 0/0:143:0:0,0:24,119:0:2,0:21:1:30.7:1:1:0:60:142:1:0:0.1 -22 41568804 . TAGAG T 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.00063;SOR=0;LSEQ=TTGGACAAGAAATATTGGCT;RSEQ=AGGTTATTAGGGTTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:18:0,18:0,29:0.383:1,1:24.5:1:31.8:1:1:0:60:36:0.3913:0.0851:0.1 0/0:21:0:0,0:0,21:0:1,0:19.1:1:32:1:1:0:60:42:1:0:0 -22 41569043 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACACTCTTTTTAAATGT;RSEQ=AAAAACCATTCTTAGCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:13.5:1:29.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41569609 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=8.69314;LSEQ=AAACCTTATTTTCTTGTCTC;RSEQ=TTTGTGCTACTCTGCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:16:13,3:254,70:0.0471:2,2:17.3:1:31.1:1:1:1.19:60:32:0.0479:0:1.1 0/1:279:84:64,20:144,51:0.3011:2,2:24.9:1:31.1:1:0.76508:1.13:60:83:0.3007:0:1.1 -22 41569887 . G A 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00817;SOR=11.47643;LSEQ=GCACTTTGGGAGGCCAAGGC;RSEQ=GGTGGATCACCTGAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:1:0,1:0,57:0.0172:1,0:31:0:28:0:1:0:60:2:0.0179:0:1 0/1:41:7:0,7:0,34:0.1707:1,0:21.9:1:31.6:1:1:0:55.4:14:0.1707:0:2 -22 41570071 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAGTGAGCCGAGGTCAC;RSEQ=CCATTGCACTCCAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:14:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 41572193 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24292;SOR=Inf;LSEQ=AAGATCACGCCACTGCATTC;RSEQ=AGCCTGGATGACAGAGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:137,23:0:2,0:20.8:1:31.5:1:1:0:60:159:1:0:0.1 0/1:156:2:1,1:130,24:0.0128:2,2:23:1:25.5:1:0.2957:5.3277:60:4:0.0132:0:1.5 -22 41572223 . CA C 87 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20585;SOR=0.38501;LSEQ=GACAGAGCGAGGCCCTGTCT;RSEQ=AAAAAAAGAGACTGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:7:5,2:225,88:0.0218:2,2:22.3:1:31:1:1:1.02266:60:14:0.022:0:0.4 0/0:353:3:2,1:240,110:0.0085:2,2:19:1:30.7:1:1:1.09063:60:6:0.0086:0:0 -22 41572541 . C T 103 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00215;SOR=12.4884;LSEQ=ACTGTCTGTGAGGTAGGCAC;RSEQ=GGGTTGTGGGAAGGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:1:1,0:163,248:0.0024:2,0:40:0:16:0:0.39806:0:60:0:0:0:1 0/1:373:11:3,8:128,232:0.0295:2,2:20.5:1:30:1:0.75309:1.46983:60:22:0.0304:0:1 -22 41572578 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.4011;LSEQ=GAGGTGAGCTCCGCAGGGTT;RSEQ=TTCTGAGGGGCCATGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:2:2,0:75,176:0.0079:2,0:1:0:23.5:1:0.09179:0:60:4:0.0081:0:1 0/1:181:2:1,1:54,125:0.011:2,2:9.5:1:28.5:1:0.51657:2.30:60:4:0.0114:0:1 -22 41572582 . T C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06619;SOR=Inf;LSEQ=TGAGCTCCGCAGGGTTGTTC;RSEQ=GAGGGGCCATGCAGCCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:71,165:0:2,0:23.5:1:30.3:1:1:0:60:46.2:0.9957:0:0.1 0/1:162:3:1,2:46,112:0.0185:2,2:36.7:1:32:0:1:1.22:60:6:0.0188:0:1 -22 41572671 . GT G 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=1.91483;LSEQ=GGGCAGAGCTGAAGAGGCTA;RSEQ=TTTTGTTCTACGAAAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:141,46:0.0053:2,0:10:0:33:0:0.25:0:60:2:0.0055:0:0 0/1:197:2:2,0:164,31:0.0102:2,0:29:1:33:1:1:0:60:4:0.0103:0:0 -22 41574383 . A C 202 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0;SOR=0;LSEQ=AGTTGGCTACCCACCACAGC;RSEQ=GCAGCAGCGGATGCAGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:96:46,50:403,487:0.0974:2,2:24.1:1:30.7:1:0.66658:1.11:60:192:0.0986:0:1.1 0/0:1042:0:0,0:470,571:0:2,0:25.7:1:30.3:1:1:0:60:68.4:0.999:0:0.2 -22 41574969 . TGTA T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0;SOR=0.16476;LSEQ=GACATACACTAGAGACACCT;RSEQ=GTATTTTGGGAGCAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:529:255:83,172:95,177:0.482:2,2:25.5:1:31.7:1:0.58129:1.11202:59.9:84:0.4837:0.0718:0.1 0/1:565:75:27,48:184,304:0.1327:2,2:26:1:30.5:1:0.7994:1.0759:60:74:0.1319:0.0195:0.1 -22 42683520 . C T 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11888;SOR=9.76063;LSEQ=AGCACAGATCCATCCCATCA;RSEQ=GTATGCATGCATTCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:29.3:1:26.7:1:1:0:60:2:0.2222:0:1.3 1/1:6:5:4,1:1,0:0.8333:0,2:17.8:1:27.4:1:1:0:60:10:0.8333:0:1 -22 42684161 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTAATCCCAGCATTCTGG;RSEQ=AGGCCAACGTGGGTGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 42927816 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24501;SOR=Inf;LSEQ=CGCCGACGTATGCTGCCTTC;RSEQ=CTCTCTGCTTCAGCTACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:23,3:0:2,0:24.4:1:29.9:1:1:0:60:12:1:0:0.2 0/1:32:3:2,1:22,7:0.0938:2,2:23:1:30:1:1:1.54738:60:6:0.0938:0:1 -22 42927873 . TGCTC T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52964;SOR=Inf;LSEQ=TGTCCTATGATCACGTGACT;RSEQ=GACCTTATCAATCACTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:45,35:0:2,0:29.2:1:31.8:1:1:0:59.2:79:1:0:0.3 0/1:134:2:1,1:73,59:0.0149:2,2:31.5:1:30:1:1:1.2353:60:4:0.0154:0:0 -22 42927912 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14085;SOR=0;LSEQ=CTTGGACGACTCACCCTCCT;RSEQ=ACCCTGCTCCCCTTGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:32,44:0.0256:2,2:35.5:1:31:1:1:1.37:60:4:0.0263:0:1 0/0:129:0:0,0:61,67:0:2,0:24.7:1:28:1:1:0:57.5:41.667:0.9921:0:0.2 -22 42927983 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19861;SOR=0;LSEQ=TTGGGGTCACTACCGGTCTC;RSEQ=GTGTCTTGGTGGTAGTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:1,16:0.1053:1,2:42.5:1:31:0:0.20468:11.66:60:4:0.1053:0:1.5 0/0:23:0:0,0:1,22:0:1,0:21.9:1:29.8:1:1:0:60:46:1:0:0.1 -22 43170994 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCCTGAAGGCTGAAGGC;RSEQ=GGGCTGCCAGATCCACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:32:0:1:0:60:4:1:0:2 -22 43171045 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTGTGGTACCTCTTCTGG;RSEQ=TGCCCATGCACCAACTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:28:1:1:0:60:4:1:0:2 -22 43172308 . T C 33 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=Inf;LSEQ=GCAAGCTTGTTTCTCATAAA;RSEQ=GATGTGACTTCAAGTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:24:1:33:0:1:0:51:4:0.3333:0:1 1/1:1:1:1,0:0,0:1:0,0:4:0:32:0:1:0:45:2:1:0:1 -22 43172357 . G T 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTTTTTTTTTTGCTG;RSEQ=CCCTAAGTTTATTGTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:5,2:0,0:1:0,2:23.3:1:27.9:1:1:0:51.7:14:1:0:1.1 1/1:7:7:6,1:0,0:1:0,2:10.4:1:29.3:1:1:0:60:14:1:0:1.1 -22 43172444 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49917;SOR=Inf;LSEQ=CCGCTCCTGAGCTCTGAGGA;RSEQ=GCTTGCCTTCTTTTGAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:34,24:0:2,0:24.9:1:30.3:1:1:0:54.9:18.333:1:0:0.8 0/1:68:2:1,1:39,27:0.0294:2,2:48.5:1:31:1:1:1.43646:60:4:0.0299:0:2 -22 43172489 . G A 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63083;SOR=0.73951;LSEQ=ATCCTTCTTCTGAGCAAGGG;RSEQ=CATTTTGGGAAGGTTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:53:28,25:3,7:0.8413:2,2:27.8:1:28.9:1:0.30202:2.57:57.2:25.5:0.8361:0:1.1 1/0:54:43:19,24:4,7:0.7963:2,2:28.1:1:27.7:1:0.74118:1.38:55.9:20.5:0.7885:0:1.2 -22 43172646 . G A 56 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=3.38757;LSEQ=TATTGAGAGAACTGTTTCTT;RSEQ=TAAGCATCGTCATCTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:25:0:33:0:1:0:60:2:0.3333:0:1 1/0:6:4:2,2:1,1:0.6667:2,2:20.3:1:28:1:1:1:55.8:8:0.6667:0:1.3 -22 43523991 . C A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCAGCTCCTGGCACTCG;RSEQ=CCCCTGCCACCTGTCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:27.5:1:1:0:60:4:1:0:2 -22 43524000 . A T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGCACTCGCCCCCTGCC;RSEQ=CCTGTCCCTGGCATTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:27.5:1:1:0:60:4:1:0:2 -22 43525176 . C T 89 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCGTCTGGCCCCATTGC;RSEQ=GGGGCCTGCCCCGAGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:24.4:1:31.8:1:1:0:60:10:1:0:1 1/1:8:8:4,4:0,0:1:0,2:11.3:1:29.9:1:1:0:60:16:1:0:1.1 -22 43525244 . CGCT C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.16585;SOR=Inf;LSEQ=CTGCGAACAGGTGCTGCTGG;RSEQ=GCTGCTGCTGCTGGCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:25.9:1:30:1:1:0:60:23:1:0:0.1 0/1:17:2:1,1:6,9:0.1176:2,2:38:1:31:1:1:1.46:60:4:0.125:0:1 -22 43525278 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11092;SOR=Inf;LSEQ=CTGGCGCTGCTGCTGCCGCT;RSEQ=CTCAGCGGGGGCCTGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:0:2,0:30.4:1:32.6:1:1:0:60:46:1:0:0 0/1:12:2:1,1:4,6:0.1667:2,2:23.5:1:24:1:1:1.45:60:4:0.1667:0:1 -22 43623353 . G A 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCAGGTGCAGGGGAGG;RSEQ=GCCAGCAGCACAGGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:22.3:1:30.3:1:1:0:60:6:0.75:0:2 -22 43623395 . C G 45 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACCCACGCAATCCTTCC;RSEQ=GTTCCAGTGGAGCCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:0.6:2,2:32.3:1:29:1:1:1.73:60:6:0.6:0:2 -22 43623612 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=TCTCCTGACCCCACCGAGTC;RSEQ=GACAGCATCACGGGATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:26.5:1:29.2:1:1:0:60:42:1:0:0.1 0/1:14:2:1,1:9,3:0.1429:2,2:39.5:1:28.5:1:0.50549:2.73861:60:4:0.1429:0:1 -22 43623759 . G C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=GCAGCTGCACCCCAGGCTAG;RSEQ=GGGCAGAGGAGGTAGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:28:1:31:1:1:0:60:6:0.5:0:2 1/0:3:2:1,1:0,1:0.6667:0,2:33.5:1:30.5:1:1:0:60:4:0.6667:0:2 -22 43623770 . G C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=CCAGGCTAGGGGGCAGAGGA;RSEQ=GTAGCACACGATTAAAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:26:1:32:0:1:0:60:4:0.4:0:2.5 1/0:3:2:1,1:0,1:0.6667:0,2:23:1:30:1:1:0:60:4:0.6667:0:2 -22 43788785 . GGAGA G 123 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=12.000;MSILEN=2;SSF=0.61314;SOR=0.71963;LSEQ=AATGAGTAAAGTCTGTAAAA;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:12,3:7,1:0.4688:2,2:22.7:1:31.6:1:1:1.71054:60:30:0.4688:0.0938:1.2 0/1:31:12:8,4:12,1:0.3871:1,2:22.2:1:31.7:1:0.16025:5.59171:60:24:0.4:0:1.1 -22 43788811 . CGA C 77 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=1.12917;LSEQ=AGAGAGAGAGAGAGAGAGAA;RSEQ=GAGAGAGAGAGAACAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:6:2,4:34,18:0.1034:2,2:21.5:1:29.8:1:0.18725:3.68669:60:12:0.1091:0:0.5 0/1:52:6:3,3:28,18:0.1154:2,2:43.5:1:30:1:0.67544:1.54199:60:12:0.1154:0:0.3 -22 43788830 . C G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.86648;SOR=0.93794;LSEQ=ACGAGAGAGAGAGAGAACAA;RSEQ=AGCACACGTATGTGTGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:39:25,14:22,17:0.5:2,2:28.2:1:31.4:1:0.64391:1.37:60:18.5:0.4933:0:1.4 0/1:62:30:16,14:18,14:0.4839:2,2:30.3:1:31.1:1:1:1.12286:60:60:0.5:0:1.2 -22 43788833 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58116;SOR=2.60563;LSEQ=AGAGAGAGAGAGAACAACAG;RSEQ=ACACGTATGTGTGTGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:0,1:48,32:0.0123:2,0:1:0:27:0:0.40741:0:60:2:0.0127:0:1 0/1:63:2:1,1:34,27:0.0317:2,2:35:1:27.5:1:1:1.25461:60:4:0.0317:0:1 -22 43788936 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17534;SOR=Inf;LSEQ=GATCTACTAGAGACCCCAAG;RSEQ=CAGTCCCAGGTGGAAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:6,28:0:2,0:18.7:1:29.7:1:1:0:60:68:1:0:0.1 0/1:25:2:0,2:6,17:0.08:2,0:26:1:33.5:1:1:0:60:4:0.08:0:1 -22 44445578 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08156;SOR=Inf;LSEQ=CATGTTGCAAGGAACCCTAG;RSEQ=GGCTGCCATAGCCCTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:139,83:0:2,0:24.6:1:30.2:1:1:0:60:30.714:1:0:0.2 0/1:171:3:1,2:110,58:0.0175:2,2:6:1:27.3:1:0.28174:3.76213:60:6:0.0178:0:1 -22 44445659 . C T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=4.64093;LSEQ=ATTAAAGCAGGAGACCTCTG;RSEQ=CCGGGAACGGGCCATTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:55:25,30:106,141:0.1821:2,2:21.8:1:29.7:1:0.76477:1.11:60:110:0.1864:0:1.1 1/0:222:113:54,59:48,61:0.509:2,2:24:1:28.9:1:0.5925:1.16:60:226:0.509:0:1.2 -22 44445727 . C A 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00114;SOR=Inf;LSEQ=GTAGGTTTTATTGCCAAAGC;RSEQ=GTCCCGGCCTTGGCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:49,116:0:2,0:24.2:1:30:1:1:0:60:81.5:1:0:0.2 0/1:104:7:2,5:31,66:0.0673:2,2:21.9:1:29.4:1:1:1.17246:60:14:0.068:0:1.1 -22 44773398 . C T 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.01026;SOR=0.09886;LSEQ=TAAATATCCATTTCAAGAGG;RSEQ=AAAAAGAAACCCCCCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:9,8:2,1:0.85:2,2:21.5:1:28.2:1:1:1.72884:60:16:0.8421:0:1.2 0/1:9:3:3,0:2,4:0.3333:2,0:20.7:1:29:1:0.16667:0:60:6:0.3333:0:1.7 -22 44773410 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.09073;SOR=Inf;LSEQ=TCAAGAGGCAAAAAGAAACC;RSEQ=CCCAAAACCCCCAAAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,11:0:2,0:27.4:1:30.6:1:1:0:60:42:1:0:0.8 0/1:10:2:1,1:3,4:0.2:2,2:31:0:32.5:1:1:1.29:60:4:0.2:0:1.5 -22 44773420 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12381;SOR=Inf;LSEQ=AAAAGAAACCCCCCAAAACC;RSEQ=CCAAAACAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:30:1:30.7:1:1:0:60:46:1:0:0.9 0/1:13:2:1,1:5,6:0.1538:2,2:19.5:1:27:0:1:1.18:60:4:0.1538:0:2 -22 44773543 . C G 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAATCAACAAGGTTTAA;RSEQ=GTTTATTTTTCAAATGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:25:1:30.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 45133340 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTTTCAGGCATCTGAGTC;RSEQ=GCGTTTACCCAGGGGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 45133657 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCGCAGGTTTCCAGGGTCTG;RSEQ=GTGGAGGGGGCAGACCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 45134006 . C T 43 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02757;SOR=Inf;LSEQ=CTCCCCTGCAGCCTCACTAT;RSEQ=CCCAGACAGGCTTTCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:21,2:0:2,0:28.7:1:31.2:1:1:0:60:46:1:0:0.5 0/1:11:3:3,0:8,0:0.2727:0,0:27.7:1:27.7:1:1:0:60:2:0.2:0:2 -22 45134049 . G C 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94839;LSEQ=CCTCAGGTGGGCAGGATACC;RSEQ=CATCAGCCGTAGCAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:19:17,2:16,2:0.5135:2,2:22.2:1:31.1:1:1:1.06:60:38:0.5135:0:1.1 1/0:12:6:5,1:6,0:0.5:0,2:26.2:1:31:1:1:0:60:12:0.5:0:2 -22 45134193 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13867;SOR=Inf;LSEQ=CAGCCTTCCCTAGCCACCCC;RSEQ=GCCGTTTTAAAGCATCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:116,109:0:2,0:24:1:29.8:1:1:0:60:44:1:0:0.5 0/1:134:2:1,1:74,58:0.0149:2,2:33.5:1:30:1:1:1.27351:60:4:0.0153:0:2 -22 45134197 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=2.65312;LSEQ=CTTCCCTAGCCACCCCCGCC;RSEQ=TTTTAAAGCATCGGGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:68:37,31:78,80:0.3009:2,2:24.6:1:30:1:0.56212:1.22:60:33:0.2973:0:1.3 1/0:133:71:37,34:35,27:0.5338:2,2:23.9:1:30:1:0.72744:1.18962:60:142:0.5338:0:1.2 -22 45134257 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06052;SOR=Inf;LSEQ=GTGGAGGGGTCTCTAACGGC;RSEQ=GGCACCTTTCCACACCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:68,113:0:2,0:27.4:1:30.3:1:1:0:60:89.5:1:0:0.3 0/1:118:3:2,1:46,69:0.0254:2,2:9.3:1:27.3:1:0.56571:2.97:60:6:0.0265:0:1.7 -22 45134339 . A G 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21013;SOR=0.47239;LSEQ=GCCTCTCATGGCGTTTTCTC;RSEQ=AGGTGGGAAAGGAGTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:20:2,18:1,13:0.5882:1,2:27.9:1:32.2:1:1:1.43:60:40:0.6061:0:1.1 0/1:30:12:1,11:1,17:0.4:1,2:16.7:1:31.8:1:1:1.52:60:24:0.4444:0:1.3 -22 45565915 . T G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=AAAGTCTTTGATCTTTCTGA;RSEQ=AAGTGCATAGAAGAAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:23.9:1:31.4:1:1:0:60:14:1:0:0.6 0/1:11:2:2,0:7,2:0.1818:2,0:27:1:33.5:1:1:0:60:4:0.1818:0:1 -22 45565937 . G A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44948;SOR=2.32381;LSEQ=AGTGCATAGAAGAAAATGCT;RSEQ=ACGTACGCCGCCTTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:7,2:0.3571:2,0:14:1:30:1:0.50549:0:60:10:0.3571:0:2 1/0:14:8:6,2:5,1:0.5714:2,2:29.4:1:29.4:1:1:1.60839:57.3:16:0.5714:0:2.1 -22 45565946 . C T 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96351;LSEQ=AAGAAAATGCTGACGTACGC;RSEQ=GCCTTCCTTCTCTGCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:10,0:6,1:0.5882:2,0:14.7:1:32.5:1:0.41176:0:60:20:0.5882:0:1.6 1/0:19:11:8,3:6,2:0.5789:2,2:24.3:1:31.1:1:1:1.11808:58:22:0.5789:0:1.8 -22 45714398 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTTCTAGGACCTGGTGC;RSEQ=GAGTGCTTTTGAGATCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:0:31.5:1:1:0:60:4:1:0:1.5 -22 45714489 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTATTGTGAGATTTGACTC;RSEQ=GATGTTTAGGCTGCTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 45714765 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52886;SOR=0;LSEQ=GGAGCCAGCACCAGACCTGC;RSEQ=GTTCAGGCTGAGAAAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:103,2:0.0187:1,2:26:1:31.5:1:0.05555:42.2832:60:4:0.019:0:1 0/0:64:0:0,0:63,1:0:1,0:22.3:1:30.9:1:1:0:60:128:1:0:0 -22 45714782 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51861;SOR=0;LSEQ=TGCAGTTCAGGCTGAGAAAG;RSEQ=GGTTTTGAGCACTTAAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:130,7:0.0144:2,2:19.5:1:28:1:0.11219:17.43693:60:4:0.0145:0:1 0/0:92:0:0,0:87,4:0:1,0:22.7:1:29.2:1:1:0:60:44.5:1:0:0 -22 45714801 . G T 22 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50717;SOR=0;LSEQ=GAGGTTTTGAGCACTTAAGC;RSEQ=AGCCACAGACCACCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:0,2:164,28:0.0103:2,0:10.5:1:22.5:1:0.02324:0:60:4:0.0104:0:1 0/0:149:0:0,0:130,19:0:2,0:22.3:1:29.9:1:1:0:60:48.667:1:0:0 -22 45714937 . T C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14695;LSEQ=GCCTGCAAAAGTTTAATTTG;RSEQ=TCATACTGTTTTTGAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:531:390:168,222:60,79:0.7345:2,2:25.8:1:31.6:1:1:1.00361:60:42.333:0.7299:0:1.1 0/1:596:172:78,94:192,231:0.2886:2,2:24.4:1:31.9:1:1:1.00166:60:56.333:0.2864:0:1.2 -22 47217677 . C T 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGAATTTACATGTTGGC;RSEQ=CGTCTTGCTAGGTTGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:20:1:30.8:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 47218466 . A C 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTGATTCACTCCCATGCCT;RSEQ=GAGATGTCACTCATGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:14:0:25:0:1:0:60:2:1:0:1 1/1:3:3:1,2:0,0:1:0,2:29.3:1:27.7:1:1:0:60:6:1:0:1 -22 47218730 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53202;SOR=Inf;LSEQ=GCTAAGGGTTGGTGGGGGCT;RSEQ=AGGTCACCAAATGAAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:22.6:1:31.5:1:1:0:60:20:1:0:0 0/1:19:2:1,1:7,10:0.1053:2,2:16.5:1:27:1:1:1.40:60:4:0.1053:0:1.5 -22 47788223 . C CCA 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAATCACACACATCATACA;RSEQ=CACACACAGGATACACAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 -22 47788380 . A C 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CACAAACACATCATACACCC;RSEQ=CACACACACACACACGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:41:0:28:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:32:1:1:0:60:4:1:0:3.5 -22 47788382 . A C 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CAAACACATCATACACCCAC;RSEQ=CACACACACACACGCGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:39:0:28:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:33:0:32:1:1:0:60:4:1:0:3.5 -22 47788396 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCCACACACACACACACAC;RSEQ=CGATACACAGGTATCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:25:0:26:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:44.5:1:28.5:1:1:0:60:4:1:0:3.5 -22 47788564 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49269;SOR=0;LSEQ=GAAACTGTCCACTGGGAGTC;RSEQ=GCGTCAGGTCAGGATGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:14,15:0.0645:2,2:36:1:30:1:1:1.07:60:4:0.0645:0:1 0/0:28:0:0,0:15,13:0:2,0:24.4:1:30.3:1:1:0:60:56:1:0:0.2 -22 47788629 . C T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.59956;SOR=3.33655;LSEQ=TGGAGCCCGTGACCGGGCAG;RSEQ=CCCCAGCCTCCTCTGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:2,13:0.0625:2,0:48:0:30:0:1:0:60:2:0.0667:0:1 0/1:16:3:1,2:5,8:0.1875:2,2:28.7:1:30.3:1:1:1.23302:60:6:0.1875:0:1 -22 48775198 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21235;SOR=3.23164;LSEQ=GGGTTGAGGTCTGAAGCCCT;RSEQ=TGATGGCCATCAGACCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:2,0:30,3:0.0571:2,0:20:1:32.5:1:1:0:60:4:0.0571:0:1 0/1:24:4:3,1:15,5:0.1667:2,2:10.5:1:31:1:1:1:60:8:0.1667:0:1 -22 48775249 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49902;SOR=0;LSEQ=TGCAGCCACGAAGAGCCTGG;RSEQ=CAGTGACCCTCAGTGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:43,28:0.0274:2,2:13:1:26:1:1:1.52641:60:4:0.0278:0:1 0/0:63:0:0,0:36,27:0:2,0:28.8:1:31.9:1:1:0:60:62:1:0:0.2 -22 48775261 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49754;SOR=0;LSEQ=GAGCCTGGGCAGTGACCCTC;RSEQ=GTGCCGGAGGAAGCGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:51,37:0.0222:2,2:38.5:1:30.5:1:1:1.37337:60:4:0.023:0:2 0/0:85:0:0,0:45,40:0:2,0:24:1:30.3:1:1:0:60:84:1:0:0.3 -22 48775266 . CG C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4973;SOR=0;LSEQ=TGGGCAGTGACCCTCAGTGC;RSEQ=GAGGAAGCGTGCAGATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:49,39:0.0222:2,2:11:1:29.5:1:1:1.25319:60:4:0.0227:0:0 0/0:87:0:0,0:44,43:0:2,0:24.6:1:30.3:1:1:0:60:174:1:0:0.3 -22 48775300 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=AGATAAATGGCTCCCACTGG;RSEQ=CTGAGTCCAGGGTGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:34,51:0.023:2,2:15:1:29.5:1:1:1.49:60:4:0.0235:0:2 0/0:64:0:0,0:31,33:0:2,0:28.2:1:31.5:1:1:0:60:128:1:0:0.2 -22 48775314 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03225;SOR=Inf;LSEQ=CACTGGCCTGAGTCCAGGGT;RSEQ=CCCACAGTAATGCTGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:24,46:0:2,0:27.6:1:31.1:1:1:0:60:22.333:1:0:0.1 0/1:53:4:2,2:24,25:0.0755:2,2:20.3:1:29:1:1:1.04:60:8:0.0769:0:1 -22 49025257 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGGATGCCCCACAGTCC;RSEQ=CAGCTCCCTGGGCCCCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 49026230 . T C 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64241;SOR=1.74629;LSEQ=AGGCTTGCTCCACTGCTGCC;RSEQ=CGGCCCTGGCTTTGGGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:8,1:0.3571:2,0:24.4:1:31.8:1:1:0:60:10:0.3846:0:1 1/0:6:3:3,0:3,0:0.5:0,0:28.7:1:29:1:1:0:60:6:0.5:0:1.3 -22 49026292 . G A 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55355;SOR=0.58557;LSEQ=TTTGTTGAGTCGTCAGCGGC;RSEQ=TGTGATGACCAGGTGTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:11:11,0:40,0:0.2157:1,0:26.4:1:31.2:1:1:0:60:22:0.2245:0:1 0/1:29:4:4,0:25,0:0.1379:1,0:25:1:29.8:1:1:0:60:8:0.1379:0:1.3 -22 49026358 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18075;SOR=Inf;LSEQ=CGCTCGGGCCCAGGGCAGGT;RSEQ=GCCACGCCTTCTTACTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:111,33:0:2,0:21.4:1:31.7:1:1:0:60:143:1:0:0.2 0/1:107:2:1,1:77,28:0.0187:2,2:28.5:1:28:1:0.47046:2.71966:60:4:0.0196:0:1 -22 49026397 . G T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6362;SOR=0.43131;LSEQ=ACAGGTTCACGGGATAATTG;RSEQ=TGGGGCCAGGTGGACCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:1,2:151,119:0.011:2,2:17:1:29:1:0.58598:2.52931:60:6:0.0112:0:1.7 0/0:210:1:0,1:118,91:0.0048:2,0:1:0:26:0:0.4381:0:60:2:0.005:0:1 -22 49026453 . C G 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.44068;LSEQ=GAAGTCTGTGCAGTGAGTGC;RSEQ=GCTTCCAGAACAATGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:85:40,45:122,138:0.2457:2,2:26:1:30.1:1:1:1.01:60:27.333:0.2426:0:1.2 0/1:273:121:56,65:71,81:0.4432:2,2:24.6:1:29.5:1:1:1.01736:60:59.5:0.4407:0:1.2 -22 49026497 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18868;SOR=Inf;LSEQ=CACGTCTTCACCGCCCTCCA;RSEQ=CAGGGGCCGCCTAGAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:85,124:0:2,0:23.8:1:29.8:1:1:0:60:33.833:1:0:0.3 0/1:161:2:1,1:56,101:0.0124:2,2:31:0:30:1:1:1.80:60:4:0.0132:0:1 -22 49026541 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.53526;SOR=0;LSEQ=AGGCTGCAGGGCTGGCTACC;RSEQ=GGGCCCTGAATCACGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:21,81:0.0192:2,2:12.5:1:29.5:1:0.37995:3.79:60:4:0.0194:0:1.5 0/0:59:0:0,0:10,49:0:2,0:23.6:1:29.9:1:1:0:60:118:1:0:0.3 -22 49026549 . G A 91 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00207;SOR=9.06658;LSEQ=GGGCTGGCTACCGGGGCCCT;RSEQ=AATCACGGGGGCGATGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:0,2:13,71:0.0233:2,0:18:1:32:0:1:0:60:4:0.0241:0:1 0/1:50:9:2,7:6,35:0.18:2,2:24.8:1:28.9:1:0.62312:1.65:60:18:0.1837:0:1 -22 49026616 . G GCTT 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.50551;LSEQ=GCTGGGCACTCGGCTGTGGG;RSEQ=CTTTTGTTTCTACCTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:23:0,23:0,7:0.7667:0,1:26.3:1:31.4:1:1:0:60:46:0.7931:0.0667:0.2 1/1:6:5:0,5:0,1:0.8333:0,0:22.2:1:31.7:1:1:0:60:10:0.8333:0.1667:0.2 -22 49026883 . T C 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGTGGCTCCCCGCCCTG;RSEQ=CCTTTCTAAGGACGGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:17.8:1:30.3:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 49370602 . G C 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.81119;LSEQ=TGAGGCCCCTGCCCAGGGCT;RSEQ=CGCTCCTCCCAACAGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:26.2:1:30.8:1:1:0:60:10:0.7143:0:1 1/0:9:6:6,0:2,1:0.6667:2,0:28.7:1:31.5:1:0.33333:0:60:12:0.6667:0:1 -22 49370678 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14119;SOR=Inf;LSEQ=TATACACAGGGCCAGGGCCT;RSEQ=TTTTTGTCTTTTTGCATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:0:1,0:24.9:1:31.8:1:1:0:60:98:1:0:0.2 0/1:30:2:1,1:26,2:0.0667:2,2:39:1:28:1:0.1931:10.81688:60:4:0.069:0:1 -22 49370710 . G T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15988;SOR=4.9145;LSEQ=TTGCATAATTCCTCCTGCAG;RSEQ=GGCCCCACCCCAGCAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:0,1:100,14:0.0087:2,0:1:0:25:0:0.13043:0:60:2:0.0088:0:2 0/1:72:3:1,2:57,12:0.0417:2,2:11.7:1:21.3:1:0.0946:9.06976:60:2:0.0294:0:1.7 -22 49370723 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51561;SOR=0;LSEQ=CCTGCAGGGGCCCCACCCCA;RSEQ=CAGGGCCTCAGCCCAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:112,25:0.0144:2,2:19:1:28.5:1:0.34021:4.41258:60:4:0.0148:0:1 0/0:95:0:0,0:72,23:0:2,0:24.7:1:30.9:1:1:0:60:18:1:0:0.5 -22 49370754 . A G 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=2.32878;LSEQ=GCCCAAGGCTCCAGTGGCTG;RSEQ=GCGGCCCCCTTCCAGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:42:29,13:130,63:0.1787:2,2:27.1:1:30.9:1:1:1.08:60:41:0.183:0:1.4 0/1:193:65:42,23:79,49:0.3368:2,2:25.3:1:28.6:1:0.75397:1.13:60:9.833:0.3189:0:1.5 -22 49370758 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26264;SOR=0;LSEQ=AAGGCTCCAGTGGCTGAGCG;RSEQ=CCCCCTTCCAGCTTCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:167,89:0.0115:2,2:22.3:1:28.3:1:0.2828:3.7327:60:6:0.012:0:1 0/0:197:0:0,0:122,75:0:2,0:26:1:30.9:1:1:0:60:48.25:1:0:0.7 -22 49370764 . T C 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08114;SOR=Inf;LSEQ=CCAGTGGCTGAGCGGCCCCC;RSEQ=TCCAGCTTCCCTGGTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:178,101:0:2,0:25.8:1:30.3:1:1:0:60:45.5:1:0:0.4 0/1:214:3:1,2:130,81:0.014:2,2:25:1:24.7:1:0.56118:3.192:60:2:0.0095:0:3.3 -22 49370800 . G A 125 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=23.8885;LSEQ=CAGGAAACACCCCCTCTTGC;RSEQ=GCTGCCCAGAGACAAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:1:1,0:180,149:0.003:2,0:1:0:26:0:1:0:60:2:0.0031:0:1 0/1:265:18:11,7:129,118:0.0679:2,2:28.2:1:30.2:1:0.62601:1.44:60:36:0.0698:0:1.9 -22 49370817 . G A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=23.77757;LSEQ=TGCGGCTGCCCAGAGACAAA;RSEQ=GGTCCCCTGGGTGTGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:1,0:160,159:0.0031:2,0:1:0:27:0:1:0:60:2:0.0032:0:1 0/1:273:19:9,10:123,131:0.0696:2,2:23.5:1:28.6:1:1:1.04311:60:18:0.0672:0:1.8 -22 49370834 . C G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.97447;LSEQ=AAAGGGTCCCCTGGGTGTGG;RSEQ=ACTTGCTGTCAGGCATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:54:23,31:119,135:0.1742:2,2:23.6:1:31.4:1:0.65256:1.18742:60:108:0.1759:0:1.3 0/1:254:116:54,62:61,76:0.4567:2,2:26.6:1:30.2:1:0.80034:1.08:60:37.667:0.4538:0:1.4 -22 49370864 . G A 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=Inf;LSEQ=CAGGCATATTCTAAGCCCCA;RSEQ=GCAAGCATCCTGAATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:103,168:0:2,0:25.8:1:31.3:1:1:0:60:89.333:1:0:0.2 0/1:220:10:4,6:83,127:0.0455:2,2:28.5:1:30.8:1:1:1.02:60:20:0.0457:0:1.9 -22 49370962 . T C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.09313;LSEQ=CCCAGGCCACCTGCAGCCCA;RSEQ=GAGGGGCCTACCAAGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:41:3,38:3,14:0.7069:2,2:24.8:1:29.4:1:0.34497:2.66139:60:40:0.7018:0:1.1 0/1:28:5:0,5:3,20:0.1786:2,0:21.6:1:29.4:1:1:0:60:10:0.1852:0:1 -22 49371163 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATCTGGGTCCCACCCCCT;RSEQ=GCCACGTGTCCCCCCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:28:1:28:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 49371286 . A G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAACACTGCCCCTCCTGGA;RSEQ=TGCACCCCCGGCCATGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 49371352 . C CG 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCATCTTCAAGTGAGAAA;RSEQ=TCTTCCTCTGCCCCACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17:1:32.3:1:1:0:60:4:1:0.5:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 50353917 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAGGCCGCGGGACAAGCG;RSEQ=AGGTCGCCTCCCGCACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:32.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 50353919 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCCGCGGGACAAGCGCA;RSEQ=GTCGCCTCCCGCACTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:32.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 50354819 . C A 119 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05155;SOR=5.46737;LSEQ=AAGGCGTACCAGGTGGGCGC;RSEQ=GTGCTGGGTAGCGGCGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:5,2:0.3:2,2:26.7:1:30.7:1:0.5:4.17095:60:6:0.3:0:1.3 1/0:21:15:7,8:3,3:0.7143:2,2:30.8:1:30.5:1:1:1.1356:60:30:0.7143:0:1.3 -22 50354820 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGCGTACCAGGTGGGCGCC;RSEQ=TGCTGGGTAGCGGCGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:30.8:1:31.6:1:1:0:60:18:1:0:0.6 0/1:21:2:1,1:9,10:0.0952:2,2:20.5:1:30:1:1:1.11:60:4:0.0952:0:1.5 -22 50354942 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCTTGCGCCTCGCTTGGCCC;RSEQ=GCCTGACCCCCGCGTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:24.3:1:30.3:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:32.5:1:1:0:60:4:1:0:1.5 -22 50355381 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17096;SOR=Inf;LSEQ=ACGAAAATCTGCTTGTGGAC;RSEQ=TGCGCTCCGGAGAGCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:0:2,0:25.3:1:30.4:1:1:0:60:12:1:0:0.2 0/1:28:2:1,1:15,11:0.0714:2,2:13.5:1:29:1:1:1.34838:60:4:0.0714:0:1 -22 50356274 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=AGGGAGTTAACCAGCAGGGA;RSEQ=CTCGCCGTCTGTTGAGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:7:1:28.5:1:1:0:60:4:0.3333:0:1.5 1/0:4:2:2,0:2,0:0.5:0,0:33.5:1:28.5:1:1:0:60:4:0.5:0:1.5 -22 50356302 . C T 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.30579;LSEQ=TCTGTTGAGCGGCTCTGCCT;RSEQ=TGTGGTGGGCGTGCTAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:4,2:0.3333:2,2:18:1:31.7:1:1:1:60:6:0.3333:0:1.3 0/1:5:2:2,0:3,0:0.4:0,0:20.5:1:28.5:1:1:0:60:4:0.4:0:1.5 -22 50356350 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTAGGCACCCGAGTGTA;RSEQ=AGCCCCCCGGAGTGGATCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:12,10:0.0833:2,2:44.5:1:28:1:1:1.19087:60:4:0.0833:0:2 0/0:11:0:0,0:6,5:0:2,0:27.5:1:31:1:1:0:60:22:1:0:0.4 -22 50357125 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CCAAGCCCACCTCCCGCCCT;RSEQ=AGTCCTGCGGTGTGCGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:27:1:30.3:1:1:0:60:6:1:0:1 0/0:2:0:0,0:1,1:0:2,0:15.5:1:30:1:1:0:60:4:1:0:0 -22 50358008 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGGCCCTGAGGATGCA;RSEQ=CAACCCACACTAGTCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:43:1:30.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 50358197 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGGGTTTTGAAGGACA;RSEQ=GGAGGAGTTTGCCAGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -22 50704661 . T C 25 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGCACCAACTCACGTGTTC;RSEQ=GAGGAGATTTTTGCCAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:29:1:29.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:25:1:1:0:60:4:1:0:1.5 -22 50705059 . A G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63325;SOR=2.38223;LSEQ=CACTGTGCGAGGGCGAGGGG;RSEQ=CCTCCATCAGTGTGCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:3,3:3,3:0.5:2,2:19.5:1:32.3:1:1:1:60:12:0.5455:0:1.7 1/0:7:5:2,3:0,2:0.7143:0,2:20.2:1:30.6:1:1:0:60:10:0.7143:0:1 -22 50705304 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00364;SOR=Inf;LSEQ=CTAAGACCTGGCATGCAGAG;RSEQ=CAGTCGAGGGCCAGACGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:57,1:0:1,0:26.1:1:32.4:1:1:0:60:57:1:0:0.1 0/1:30:5:5,0:25,0:0.1667:1,0:21.6:1:29.8:1:1:0:60:10:0.1667:0:1 -22 50705449 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1637;SOR=Inf;LSEQ=AGCCGGTCATCTCCTCGTCC;RSEQ=CCTGGCGCGCCAGCCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:88,132:0:2,0:23.8:1:30.3:1:1:0:60:35.667:1:0:0.8 0/1:150:2:1,1:57,91:0.0133:2,2:15.5:1:24:1:1:1.59:60:4:0.0142:0:2 -22 50705455 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17433;SOR=Inf;LSEQ=TCATCTCCTCGTCCGCCTGG;RSEQ=GCGCCAGCCCAAAATCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:71,125:0:2,0:23.2:1:30:1:1:0:60:48:1:0:0.9 0/1:141:2:1,1:54,85:0.0142:2,2:30.5:1:30:1:1:1.57:60:4:0.0148:0:2 -22 50705461 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50742;SOR=0;LSEQ=CCTCGTCCGCCTGGCGCGCC;RSEQ=GCCCAAAATCCAGGATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:57,114:0.0116:2,2:26:1:28.5:1:1:1.99:60:4:0.0118:0:1.5 0/0:132:0:0,0:47,85:0:2,0:19.6:1:29.1:1:1:0:60:32:1:0:0.9 -22 50705466 . A G 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57175;SOR=0.3518;LSEQ=TCCGCCTGGCGCGCCAGCCC;RSEQ=AAATCCAGGATCTGGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:147:42,105:1,0:0.9932:0,2:23.8:1:30.5:1:0.29054:0:60:72.5:0.9932:0:1.1 1/1:105:103:29,74:2,0:0.981:0,2:21.2:1:30.3:1:0.08516:0:60:206:0.981:0:1.1 -22 51081332 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTGGGACTACGGGAGCCCGC;RSEQ=ACCACGCCTCGCTAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:23:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:30.5:1:1:0:60:4:1:0:1 -22 51081636 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24085;SOR=Inf;LSEQ=GCCCATCTGTGCACTTCCTT;RSEQ=TAAAATCCAGTTTTAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:37,32:0:2,0:27.8:1:31.8:1:1:0:60:138:1:0:0.1 0/1:67:2:1,1:28,37:0.0299:2,2:25.5:1:28.5:1:1:1.32:60:4:0.0303:0:1.5 -22 51081657 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49806;SOR=0;LSEQ=TAAAATCCAGTTTTAGTAAG;RSEQ=ACCTGATCACCCTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:28,31:0.0328:2,2:39.5:1:29.5:1:1:1.11:60:4:0.0333:0:1 0/0:53:0:0,0:18,35:0:2,0:23:1:30.5:1:1:0:60:52:1:0:0.2 -22 51082180 . G T 22 d7;v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCTGCACTGATCTTACTTAG;RSEQ=AGCAGTTTAGGGAGGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:28:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:36:1:22.5:1:1:0:60:4:1:0:3.5 -3 1449822 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50237;SOR=Inf;LSEQ=AAAATCCTGACTTTTTTAAT;RSEQ=TCTTAAAATATGGAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:72,52:0:2,0:25.4:1:29:1:1:0:60:123:1:0:0.6 0/1:149:2:1,1:85,62:0.0134:2,2:21.5:1:29.5:1:1:1.368:60:4:0.0138:0:1 -3 1449841 . A G 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01111;SOR=3.07854;LSEQ=TATCTTAAAATATGGAAATT;RSEQ=TTTGCTTTCCACTTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:7:3,4:65,61:0.0526:2,2:26.7:1:31:1:0.71404:1.41702:60:14:0.0526:0:1.9 0/1:157:23:12,11:66,68:0.1465:2,2:29.7:1:31.6:1:0.82503:1.12:60:46:0.1465:0:1.8 -3 1449872 . A C 212 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11907;LSEQ=ACTTTTCTATGTTAAAAATT;RSEQ=TTTCATGAAATTAAATATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:113:108:47,61:1,4:0.9558:2,2:27.4:1:31.5:1:0.39268:3.06:60:35:0.9545:0:1.1 1/0:135:97:43,54:14,24:0.7185:2,2:27.8:1:31.1:1:0.44653:1.36:60:96:0.7164:0:1.2 -3 1449979 . C A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01294;SOR=0.22572;LSEQ=ATAATTTTTATTGAAAGATA;RSEQ=ATTTATTTCTTCAGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:1,15:0,10:0.6154:0,1:18.1:1:31.1:1:1:0:60:32:0.6154:0:1 0/1:27:7:0,7:3,17:0.2593:2,0:27.9:1:30.7:1:0.5453:0:60:14:0.2593:0:1 -3 1808553 . C T 39 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04762;SOR=Inf;LSEQ=CCTTACCATATAATAATAAT;RSEQ=TCTAAGGGCTTTCTTTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:21.2:1:28:1:1:0:60:4:1:0:1.2 1/0:4:3:3,0:1,0:0.75:0,0:26:1:24.7:1:1:0:60:2:0.6667:0:1 -3 1808586 . A AAT 81 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.10865;SOR=0.21713;LSEQ=CTTTAGATCAGTGGTCAGCA;RSEQ=TTTTTTTTTTTATAAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:3,3:6,2:0.4286:2,2:20.5:1:31.6:1:0.58042:2.76:60:12:0.5:0:0.2 0/1:15:2:1,1:4,1:0.1333:2,2:33.5:1:29.3:1:1:3.1622:60:4:0.1429:0:0.5 -3 1947364 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1551;SOR=Inf;LSEQ=ACAAAGGGAAAGAGGAGAGG;RSEQ=ACCCGATATATGTTCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:26,4:0:2,0:25.6:1:30.4:1:1:0:56.6:60:1:0:0 0/1:20:2:1,1:14,4:0.1:2,2:5.5:1:29:1:0.44737:3.24034:33:4:0.1053:0:1.5 -3 1947477 . T C 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00315;SOR=Inf;LSEQ=CATCAAGGGAATGGGCACTG;RSEQ=TCAAAAAGGAACGCCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:113,68:0:2,0:22.6:1:29.9:1:1:0:59.8:362:1:0:0.1 0/1:241:11:6,5:131,99:0.0456:2,2:26:1:31.6:1:1:1.10224:60:22:0.046:0:1.2 -3 1947557 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23421;SOR=0;LSEQ=CCCAGCATGCTGTTGGCATT;RSEQ=TTGTAAACAAACAAGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:75,112:0.0106:2,2:17:1:28.5:1:1:1.49:60:4:0.0106:0:1 0/0:201:0:0,0:86,114:0:2,0:23:1:30.8:1:1:0:59.7:99:0.995:0:0.2 -3 1947774 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=GAACCAATGGGAAAGAGCCC;RSEQ=AGCTGCTGGAACCTATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:13:0:32:0:1:0:42:2:0.3333:0:1 1/0:4:2:1,1:1,1:0.5:2,2:17:0:31.5:1:1:1:52:4:0.5:0:1 -3 2001631 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04858;SOR=Inf;LSEQ=AAAATAAAGGATGTGAAAAA;RSEQ=GCTACCAATAGCTTTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:40,0:0:1,0:24.4:1:32.2:1:1:0:60:39:1:0:0.1 0/1:24:3:3,0:21,0:0.125:1,0:32.7:1:29:1:1:0:60:6:0.1304:0:1.3 -3 2001689 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20482;SOR=Inf;LSEQ=TCAGTAGCACCTGTCATTTT;RSEQ=CCTTCTGTAGTCACTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:73,28:0:2,0:21.4:1:28.2:1:1:0:60:100:1:0:0.1 0/1:84:2:1,1:60,22:0.0238:2,2:10.5:1:32.5:1:0.47504:2.68946:60:4:0.0238:0:1 -3 2001802 . G T 197 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGAAGAAAGATTCCATGC;RSEQ=TCTATTGTAGCCCCAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:137,138:0:2,0:25.9:1:30.7:1:1:0:60:54:1:0:0.1 0/1:278:102:47,55:89,86:0.3669:2,2:24.1:1:29.6:1:0.4573:1.21019:60:33:0.3613:0:1.1 -3 2001855 . G T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11723;SOR=0;LSEQ=CAGCACATAAATGGGAAATT;RSEQ=AACTTTCATTGAAGACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:1,2:58,125:0.0161:2,2:22:1:22.7:1:1:1.08:60:2:0.0111:0:1.7 0/0:193:0:0,0:71,121:0:2,0:27.4:1:30.7:1:1:0:60:31:0.9947:0:0.4 -3 2001883 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24322;SOR=0;LSEQ=ATTGAAGACTCTTGAGTAAA;RSEQ=ACAGGGAAGAATGTTAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:30,95:0.0157:2,2:29.5:1:28.5:1:0.43007:3.13:60:4:0.0163:0:1 0/0:130:0:0,0:35,95:0:2,0:22:1:30.9:1:1:0:60:64:1:0:0.3 -3 2001904 . T C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.0787;SOR=Inf;LSEQ=ACAGGGAAGAATGTTAACCC;RSEQ=GTTGCCCATACCATGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:11,81:0:2,0:24.1:1:30.2:1:1:0:60:45:1:0:0.1 0/1:70:3:0,3:10,57:0.0429:2,0:18.7:1:29.7:1:1:0:60:6:0.0429:0:1.3 -3 2569037 . G A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00667;SOR=Inf;LSEQ=CTGTCACCTTAGAAGTGGTC;RSEQ=TTAAAAGCTGCCATTTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:12,5:0:2,0:17.4:1:29.2:1:1:0:48.7:16:1:0:0.4 0/1:12:5:4,1:6,1:0.4167:2,2:14:1:27.8:1:1:1.4491:56:10:0.4167:0:1.2 -3 2569091 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5338;SOR=Inf;LSEQ=ACACCAAATGAGGGAACAAT;RSEQ=TATGCTGCTGCTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:17,11:0:2,0:33.7:1:31:1:1:0:54.6:13:1:0:0.5 0/1:50:2:1,1:26,22:0.04:2,2:10:0:30:0:1:1.17786:60:4:0.0408:0:2 -3 2569093 . A ATGCTGC 105 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=10.000;MSILEN=3;SSF=0.20036;SOR=0.49049;LSEQ=ACCAAATGAGGGAACAATGT;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:6,5:11,6:0.3235:2,2:23.6:1:30.6:1:0.70114:1.50442:46.1:22:0.3333:0.1765:0.5 0/1:53:10:4,6:24,17:0.1887:2,2:32.6:1:30.5:1:0.316:2.08614:60:20:0.1961:0:0.2 -3 2569120 . T C 74 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17402;SOR=Inf;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTATTGTTGCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:14,12:0:2,0:25.8:1:30.7:1:1:0:52.9:52:1:0:0.2 0/1:80:5:3,2:39,36:0.0625:2,2:31.6:1:32:1:1:1.38:49.6:10:0.0625:0:1.2 -3 2569139 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTGCTGTTATTGTTGCTGC;RSEQ=GTTGTTGTGGTTGTGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,15:0:2,0:28.1:1:30.3:1:1:0:48.9:58:1:0:0.5 0/1:76:2:1,1:34,40:0.0263:2,2:32.5:1:27.5:1:1:1.17:32.5:4:0.0274:0:1.5 -3 2569205 . C T 50 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30609;SOR=0.24398;LSEQ=TCAAGATTTAGCATCTGAAA;RSEQ=GAGAAGTGTGTTGAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:0.25:0,0:34:1:32:0:1:0:33.7:6:0.25:0:1.3 0/1:14:1:0,1:1,12:0.0714:1,0:46:0:28:0:1:0:21:2:0.0714:0:1 -3 2569215 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.07792;SOR=Inf;LSEQ=GCATCTGAAACGAGAAGTGT;RSEQ=TTGAGGAGATGGGATTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:0:0,0:30.7:1:32.8:1:1:0:44.3:24:1:0:0.3 0/1:10:3:0,3:0,7:0.3:0,0:17:1:32:0:1:0:40:6:0.3:0:1.3 -3 2576521 . T C 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTATGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTATTGTTGCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:7,11:2,2:0.7826:2,2:31.9:1:32.8:1:1:1.53863:52.6:36:0.8182:0:1.1 0/0:21:0:0,0:10,11:0:2,0:26.3:1:29.5:1:1:0:53.7:42:1:0:0.5 -3 2576606 . C T 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TCAAGATTTAGCATCTGAAA;RSEQ=GAGAAGTGTGTTGAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:17:1:29.5:1:1:0:50:4:0.6667:0:1.5 0/0:5:0:0,0:0,5:0:0,0:25.4:1:29.4:1:1:0:36.2:10:1:0:0 -3 2576692 . C G 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.41418;LSEQ=GTCAAAGCCTTGCTTCAGCT;RSEQ=TAAAGGACCTTCTTTACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:26.5:1:33.5:1:1:0:60:4:0.4:0:1.5 1/0:2:1:0,1:0,1:0.5:0,0:18:0:33:0:1:0:51:2:0.5:0:2 -3 6422783 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23357;SOR=0;LSEQ=CCCCAGCCACTGGATGGATG;RSEQ=CTGACCTTGGTTATTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:77,29:0.0183:2,0:37:1:31:1:1:0:60:4:0.0187:0:1.5 0/0:116:0:0,0:88,28:0:2,0:21.9:1:31.1:1:1:0:60:115:1:0:0.8 -3 6422814 . C A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.95154;LSEQ=TTATTTGGCCTTTGATCCTG;RSEQ=ATATGTCTCTTTTGTCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:68:45,23:66,46:0.3778:2,2:23.6:1:30.1:1:0.34779:1.36:60:67:0.3807:0:1.5 1/0:207:133:89,44:44,30:0.6425:2,2:25:1:29:1:0.29353:1.38:60:132:0.6408:0:1.4 -3 6422825 . T C 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=TTGATCCTGCATATGTCTCT;RSEQ=TTGTCAACCAGAACAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:121,83:0:2,0:25.1:1:29.9:1:1:0:60:39.8:1:0:0.9 0/1:248:16:7,9:141,91:0.0645:2,2:30:1:31.4:1:0.19647:1.98647:60:32:0.0653:0:1.3 -3 6422885 . G C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.23781;LSEQ=TTTTCAGCCTTTTTCTACAT;RSEQ=TTTGTGTTCTCACATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:180:79,101:24,14:0.8257:2,2:26:1:31.2:1:0.03334:2.18377:60:35:0.8216:0:1.3 1/0:310:164:78,86:69,77:0.529:2,2:27.9:1:31.2:1:1:1.01:60:40:0.5246:0:1.4 -3 6422914 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17634;SOR=0;LSEQ=CTCACATAAAAACGAATTTT;RSEQ=AATTGGTTCTCTATATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:75,111:0.0106:2,2:6:0:31:1:1:1.48:60:4:0.011:0:1.5 0/0:259:0:0,0:110,149:0:2,0:24.2:1:31.1:1:1:0:60:258:1:0:0.7 -3 6422931 . A G 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00155;SOR=Inf;LSEQ=TTTGAATTGGTTCTCTATAT;RSEQ=ATTTTCACCACTTACTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:60,103:0:2,0:25:1:29.2:1:1:0:60:80.5:1:0:0.6 0/1:205:12:6,6:75,118:0.0585:2,2:25.8:1:31.8:1:0.54603:1.57:60:24:0.0588:0:2 -3 6610068 . T C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=8.52595;LSEQ=AATTTCAGGGCAACAATGTG;RSEQ=TATATTTAGTCATGACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:12:6,6:123,118:0.0474:2,2:25.1:1:31.4:1:1:1.04222:60:24:0.0478:0:1.6 0/1:365:109:48,61:116,140:0.2986:2,2:26.6:1:31.4:1:0.90852:1.05285:60:108:0.2975:0:1.3 -3 6610126 . G A 148 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00049;SOR=3.61108;LSEQ=GATGAGTTGCAAAATCCTGT;RSEQ=AATTCTAATATCCTTAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:9:1,8:46,118:0.052:2,2:31.2:1:29.4:1:0.4472:3.10301:60:18:0.0523:0:2.2 0/1:199:33:8,25:47,119:0.1658:2,2:26.9:1:29.5:1:0.83142:1.23303:60:32:0.1641:0:2.1 -3 6610132 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50022;SOR=Inf;LSEQ=TTGCAAAATCCTGTGAATTC;RSEQ=AATATCCTTAAATCTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:42,122:0:2,0:25.2:1:28.8:1:1:0:60:163:1:0:0.2 0/1:184:2:1,1:49,133:0.0109:2,2:5:1:28:1:0.47072:2.70:60:4:0.011:0:1 -3 6610161 . T C 118 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04945;SOR=2.90905;LSEQ=TAAATCTCAAGAGAGAAAAA;RSEQ=ATTATTCCCTTCCTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:5:0,5:11,79:0.0526:2,0:20.6:1:33.8:1:1:0:60:10:0.0538:0:2.2 0/1:93:13:3,10:14,66:0.1398:2,2:20.2:1:32.1:1:0.69992:1.41:60:26:0.1413:0:2.1 -3 9005826 . T C 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11507;SOR=Inf;LSEQ=AAAAACCCTGCTAAATCAAG;RSEQ=TACCAAGAATCCCCACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:10,28:0:2,0:27.1:1:29.5:1:1:0:60:37:1:0:0.6 0/1:38:4:1,3:13,21:0.1053:2,2:29.8:1:32:1:1:1.82944:60:8:0.1053:0:1.5 -3 9005863 . T G 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41304;SOR=0;LSEQ=CTTTGATATGTGATCACTCT;RSEQ=GATATCTGATGTGTTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:3,24:0,0:1:0,2:23.1:1:31.1:1:1:0:60:26:1:0:1.1 1/1:19:18:4,14:0,1:0.9474:0,2:25.5:1:30.7:1:1:0:60:36:0.9474:0:1.2 -3 9039103 . C T 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCCGCTTCTCCCCACAG;RSEQ=AGCCTAGAGGGTCCTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 9040714 . A G 93 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=TCTTTGCATCTGTACAGTGT;RSEQ=AATTGACTATATAGATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:26.6:1:33.3:1:1:0:60:14:1:0:1 1/0:2:1:1,0:1,0:0.5:0,0:5:0:31:0:1:0:60:2:0.5:0:1 -3 9040851 . C G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22586;SOR=1.90067;LSEQ=ACAGCCCAGCCCCTGAGCTA;RSEQ=AGGAGAGGTTGAGACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:18:16,2:18,2:0.4737:2,2:17.4:1:32.2:1:1:1.12151:60:36:0.4865:0:1.9 1/0:30:19:16,3:9,2:0.6333:2,2:19.5:1:30.2:1:1:1.18:60:18:0.6207:0:1.7 -3 9040889 . G C 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05263;SOR=2.05122;LSEQ=TCTCAGTAGGGGCCTGGCTG;RSEQ=AGTCACATTTTAGGAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:36:28,8:33,12:0.4444:2,2:26.1:1:32.3:1:0.79644:1.27:60:72:0.4444:0:2.5 1/0:53:33:25,8:15,5:0.6226:2,2:20.6:1:31.8:1:1:1.04:60:66:0.6226:0:2.6 -3 9040951 . G A 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07367;SOR=1.50039;LSEQ=AGTGGAGGGATTGGAGGGGA;RSEQ=AGGCTGGAGGCAGCAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:88:47,41:45,32:0.5301:2,2:28.8:1:29.8:1:0.53375:1.2252:60:87:0.537:0:2.9 1/0:159:100:62,38:31,28:0.6289:2,2:27.5:1:29.2:1:0.24943:1.47:60:99:0.6266:0:3 -3 9040955 . C A 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04571;SOR=1.59316;LSEQ=GAGGGATTGGAGGGGAGAGG;RSEQ=TGGAGGCAGCAGTGGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:169:88:45,43:46,35:0.5207:2,2:29.3:1:30.4:1:0.53715:1.25417:60:176:0.5269:0:2.9 1/0:164:104:64,40:31,29:0.6341:2,2:27.3:1:28.5:1:0.25168:1.49:60:51:0.6296:0:3 -3 9040994 . G A 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01806;SOR=1.69429;LSEQ=AGAGACGGCTACACTGGTGC;RSEQ=GCCTCTGAACTAGCATGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:173:99:40,59:33,40:0.5723:2,2:24.8:1:30.6:1:0.53703:1.21547:60:98:0.5731:0:2.3 1/0:206:143:72,71:28,35:0.6942:2,2:24.3:1:30.1:1:0.45323:1.27:60:70.5:0.6912:0:2.1 -3 9040999 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50171;SOR=Inf;LSEQ=CGGCTACACTGGTGCGGCCT;RSEQ=TGAACTAGCATGGGCTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:72,99:0:2,0:25:1:31.5:1:1:0:60:56:1:0:1.3 0/1:200:2:1,1:96,102:0.01:2,2:6:0:31:1:1:1.06:60:4:0.0103:0:2.5 -3 9041094 . G C 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09102;SOR=2.17573;LSEQ=TCTGAAGGTTGGACATTTAT;RSEQ=CTTCTCTACCCATCAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:27:7,20:5,17:0.551:2,2:22.7:1:30.1:1:1:1.19:60:26:0.5417:0:1.1 1/0:48:35:5,30:2,10:0.7292:2,2:23.5:1:31.5:1:1:1.19517:60:70:0.7292:0:1.1 -3 9065474 . T A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTCCTGGGGCTCCCTGG;RSEQ=TCTAAGCACCCGAGATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:29:1:1:0:60:4:1:0:1 -3 9066519 . T C 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18903;LSEQ=TAGCATCATTTACAGATTCA;RSEQ=ATGAATATTCCAGAGCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:26.2:1:29.6:1:1:0:60:10:0.3846:0:1 0/1:7:3:3,0:4,0:0.4286:0,0:27.7:1:31.3:1:1:0:60:6:0.4286:0:1.7 -3 9066587 . C G 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCAGTCCCCTGGAGAAA;RSEQ=CACCCAAAAGCAGTAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:50:39,11:0,0:1:0,2:25:1:31:1:1:0:60:24:1:0:1.2 1/1:63:62:49,13:0,0:0.9841:0,2:24.1:1:31.8:1:1:0:60:124:0.9841:0:1.1 -3 9066645 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.18871;SOR=0;LSEQ=TCATAGTAGTAGTAACAGTG;RSEQ=TGGTGGTGCTGGTGCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:69,57:0.0156:2,2:24.5:1:31:1:1:1.20871:60:4:0.016:0:1.5 0/0:166:0:0,0:92,74:0:2,0:26.1:1:30.7:1:1:0:60:332:1:0:0.4 -3 9066678 . G T 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01717;SOR=Inf;LSEQ=TGCTGGTGCTGGTGCTGGTG;RSEQ=TAGGTAAATGTTGAACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:57,79:0:2,0:25.3:1:31.5:1:1:0:59.9:272:1:0:0.3 0/1:163:7:2,5:67,89:0.0429:2,2:29:1:27:1:0.69985:1.8752:60:6:0.038:0:1.3 -3 9066679 . TAGGT AGGA 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50309;SOR=Inf;LSEQ=GCTGGTGCTGGTGCTGGTGG;RSEQ=AAATGTTGAACAGTTAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:56,78:0:2,0:25.4:1:28.3:1:1:0:59.9:43.667:1:0:0.2 0/1:163:2:1,1:68,93:0.0123:2,2:9.5:1:28.1:1:1:1.36:60:4:0.0125:0.0061:0 -3 9066709 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19359;SOR=0;LSEQ=TTGAACAGTTAACTCTTTGG;RSEQ=AGGTAACAATTAGAACTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:31,50:0.0241:2,2:17.5:1:27:1:1:1.60:60:4:0.0244:0:1.5 0/0:105:0:0,0:36,69:0:2,0:24.8:1:31.1:1:1:0:60:34:1:0:0.1 -3 10183241 . C CAA 62 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAAAAAACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:1,0:0.5714:0,0:13:1:31.3:1:1:0:60:8:0.5714:0.4286:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 10183274 . C T 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACACCAAACCTTAGAGGGG;RSEQ=GAAAAAAAATTTTATAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:13,0:0,0:0.9286:0,1:21.5:1:29:1:1:0:60:12:1:0:2.3 1/1:2:2:2,0:0,0:1:0,0:9:1:29.5:1:1:0:60:4:1:0:2 -3 10183337 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75685;LSEQ=AGCCTCGCCTCCGTTACAAC;RSEQ=GCCTACGGTGCTGGAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:20:20,0:5,0:0.8:0,1:21.8:1:28.8:1:1:0:60:19:0.7917:0:1.7 1/0:8:6:6,0:2,0:0.75:0,0:30.3:1:30.7:1:1:0:60:12:0.75:0:1.3 -3 10183832 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2579;SOR=Inf;LSEQ=AGCCGCAGCCCTACCCAACG;RSEQ=TGCCGCCTGGCACGGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:88,143:0:2,0:25.6:1:31.7:1:1:0:60:37.5:1:0:0.1 0/1:289:3:2,1:125,161:0.0104:2,2:27.7:1:28.3:1:0.584:2.57:60:6:0.0107:0:1.3 -3 10183851 . G A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13238;SOR=Inf;LSEQ=GCTGCCGCCTGGCACGGGCC;RSEQ=CCGCATCCACAGCTACCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:62,123:0:2,0:27.1:1:31.3:1:1:0:60:91.5:1:0:0.1 0/1:231:4:2,2:86,141:0.0173:2,2:17:1:28.8:1:0.63669:1.64:60:8:0.0177:0:1.3 -3 10183867 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50312;SOR=Inf;LSEQ=GGCCGCCGCATCCACAGCTA;RSEQ=CGAGGTACGGGCCCGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:48,114:0:2,0:24.9:1:31.4:1:1:0:60:161:1:0:0.1 0/1:196:2:1,1:67,126:0.0102:2,2:18:0:31.5:1:1:1.87:60:4:0.0103:0:1.5 -3 10183876 . G C 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03011;SOR=Inf;LSEQ=ATCCACAGCTACCGAGGTAC;RSEQ=GGCCCGGCGCTTAGGCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:36,108:0:2,0:23.4:1:30.6:1:1:0:60:47:1:0:0.1 0/1:153:6:2,4:45,102:0.0392:2,2:21.2:1:26.8:1:1:1.13:60:5:0.0331:0:2.7 -3 10185535 . G T 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34919;SOR=3.35581;LSEQ=GGAGGGGAAAGACTGCTGTC;RSEQ=AGGAAGCAGTTAGGTAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:1,0:226,51:0.0036:2,0:2:0:30:0:1:0:60:2:0.0036:0:1 0/1:251:3:1,2:198,50:0.012:2,2:23.3:1:22.7:1:0.10982:7.82993:60:2:0.0081:0:2 -3 10185803 . A C 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1238;SOR=Inf;LSEQ=GCTCCTATTTTATATAGGAA;RSEQ=TTGTATGAATTTTGTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:0,106:0:1,0:21.9:1:31.6:1:1:0:60:212:1:0:0.1 0/1:118:4:0,4:1,113:0.0339:1,0:29.5:1:32.8:1:1:0:60:8:0.0339:0:1 -3 10187634 . G T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCAGAAAGGGCATGGGATT;RSEQ=AGAGCTTTAAGTACGCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:44:0:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 10188010 . AC A 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.09677;SOR=0;LSEQ=TGGGACTACAGGCGCTCGCC;RSEQ=CACACCTGGCTAATTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:21,0:0,0:1:0,1:22.5:1:32.3:1:1:0:59.7:42:1:0.3333:0.1 1/1:10:8:8,0:2,0:0.8:0,0:19.8:1:31.8:1:1:0:57:16:0.8:0.2:0.1 -3 10188106 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20284;SOR=Inf;LSEQ=CTGACCTCATGATCCGCCTG;RSEQ=CTCGGCCTCCCAAAGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:104,4:0:1,0:20.8:1:31.9:1:1:0:59.7:107:1:0:0 0/1:89:2:1,1:81,6:0.0225:2,2:16:1:28:1:0.15194:12.57557:60:4:0.023:0:1 -3 10188360 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25087;SOR=Inf;LSEQ=TAAAAAGATAAGGTTGTTGT;RSEQ=GTAAGTACAGGATAGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:52,195:0:2,0:22:1:30.7:1:1:0:60:48.4:1:0:0.3 0/1:276:3:1,2:65,208:0.0109:2,2:27.3:1:25.3:1:0.56103:1.60:60:2:0.0074:0:1.7 -3 10188428 . T G 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00101;SOR=0;LSEQ=TTTGCCTGATGTCAGGCACG;RSEQ=TATCCAATCTTTTTGTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:69:1,68:0,0:1:0,1:22.7:1:31.9:1:1:0:60:33.5:1:0:1.1 1/1:64:55:2,53:0,9:0.8594:0,1:25.7:1:30.9:1:1:0:60:54:0.8571:0:1.3 -3 10191219 . C G 95 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTGCCAGTGTCGCTTCATC;RSEQ=ACATTCAGTTAGTTAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:9,0:2,0:0.8182:0,0:18.8:1:30:1:1:0:60:18:0.8182:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 10191380 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50092;SOR=0;LSEQ=ACCTAAAGTGAGATCCATCA;RSEQ=TAGTACAGGTAGTTGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:92,9:0.0194:2,2:5.5:1:30:1:0.18561:9.75023:60:4:0.0198:0:1.5 0/0:87:0:0,0:76,11:0:2,0:23.2:1:31.9:1:1:0:60:86:1:0:0.1 -3 10191397 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49913;SOR=Inf;LSEQ=TCAGTAGTACAGGTAGTTGT;RSEQ=GGCAAAGCCTCTTGTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:114,21:0:2,0:24.5:1:29.9:1:1:0:60:44:1:0:0.1 0/1:147:2:1,1:116,29:0.0136:2,2:27:1:31.5:1:0.36763:3.94968:60:4:0.0136:0:1 -3 10191678 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49883;SOR=Inf;LSEQ=GTTGAAACTTACACTGTTTC;RSEQ=TCTCAGCTTTTGATGGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:44,139:0:2,0:23.3:1:30.7:1:1:0:60:366:1:0:0.1 0/1:190:2:1,1:42,146:0.0105:2,2:25.5:1:29:1:0.40234:3.45:60:4:0.0106:0:1 -3 10192672 . G A 49 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=ACTGCAACCTCTGCCTCCTG;RSEQ=GTTCACGTAATCCTCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:22.3:1:31.3:1:1:0:60:6:0.4286:0:2.7 1/0:4:2:1,1:2,0:0.5:0,2:18:1:23:1:1:0:60:1:0.3333:0:1.5 -3 10192709 . C T 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23537;LSEQ=TGAGTAGCTGGGATTACAGG;RSEQ=GCCTGCCACCACGCTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:24.4:1:30.8:1:1:0:60:10:0.5:0:2.4 1/0:9:5:4,1:4,0:0.5556:0,2:21:1:28:1:1:0:60:10:0.5556:0:2 -3 10192762 . T C 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45283;SOR=0;LSEQ=TTAGTAGAGACAGTGTTTCG;RSEQ=CATGTTGGCCAGGCTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:29,0:0,0:1:0,1:19.6:1:31.7:1:1:0:58.9:28:1:0:1.2 1/1:24:23:23,0:1,0:0.9583:0,1:25.1:1:32.8:1:1:0:59.1:46:0.9583:0:1.3 -3 10192866 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25667;SOR=Inf;LSEQ=GTGGGCCACCGTGCCTGGCT;RSEQ=ATTCAGCATTTTTTATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:184,44:0:2,0:23.3:1:31.8:1:1:0:60:56:1:0:0.1 0/1:281:3:1,2:216,62:0.0107:2,2:8:1:25.3:1:0.13096:6.90484:60:6:0.0107:0:1.3 -3 10193056 . A AT 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.85135;SOR=0.93396;LSEQ=CAGTTTTTTGTAACTAATAG;RSEQ=TTTTTTTTTCCACTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:13:2,11:98,247:0.0362:2,2:24.9:1:30.9:1:0.52868:2.17824:60:26:0.0368:0.0028:0.2 0/1:472:16:5,11:135,321:0.0339:2,2:28.1:1:29.4:1:1:1.08:60:32:0.0343:0.0042:0.2 -3 12027806 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17845;SOR=Inf;LSEQ=TTGGCTTGAGGACTTCCCAG;RSEQ=AACATTGTCAGGCCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:51,2:0:1,0:23.7:1:32.1:1:1:0:60:52:1:0:0.1 0/1:40:2:2,0:38,0:0.05:1,0:25.5:1:30:1:1:0:60:4:0.05:0:1.5 -3 12027851 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22344;SOR=0;LSEQ=CACATGGTAGTTCAGGATGC;RSEQ=CCTTCTCACTCCCTTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:102,22:0.0159:2,2:25.5:1:29:1:0.33295:4.55665:60:4:0.0161:0:1 0/0:140:0:0,0:110,30:0:2,0:20:1:29.9:1:1:0:60:34:1:0:0.2 -3 12027856 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50169;SOR=Inf;LSEQ=GGTAGTTCAGGATGCTCCTT;RSEQ=TCACTCCCTTTCAGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:110,31:0:2,0:22.5:1:31.1:1:1:0:60:46:1:0:0.2 0/1:166:2:1,1:119,45:0.012:2,2:28:1:29.5:1:0.47864:2.62651:60:4:0.012:0:1.5 -3 12028100 . A T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55045;SOR=0;LSEQ=AATAGCATTTTGCTGAGGAC;RSEQ=CATTTCCCTCACACTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:0,4:0,18:0.1818:1,0:23:1:30:1:1:0:60:8:0.1818:0:1 0/0:8:0:0,0:0,8:0:0,0:30.1:1:28.8:1:1:0:60:7:1:0:0 -3 12030034 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGTTCAGACCAGAGAGA;RSEQ=AGGATCGATTGGGGTAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 12625968 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50592;SOR=Inf;LSEQ=CAGAAAAGTGGTGCCTGCTG;RSEQ=CTTCTCCTCCTCCCCTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:113,23:0:2,0:23.7:1:31:1:1:0:60:26.2:1:0:0.1 0/1:174:2:1,1:126,46:0.0115:2,2:19:1:26.5:1:0.46841:2.72057:60:4:0.012:0:1 -3 12626194 . C A 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62343;SOR=2.95412;LSEQ=AATGCTCTCATTAGCTGTGT;RSEQ=TCAAAGACACAGGATGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:1:1,0:105,119:0.0044:2,0:1:0:25:0:0.47111:0:60:2:0.0045:0:1 0/1:230:3:3,0:101,126:0.013:2,0:7.7:1:26:1:0.09099:0:60:6:0.0132:0:1 -3 12626516 . G A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.75657;LSEQ=CAGCTGAGCTAATGGGGGGT;RSEQ=AATGAACAACAGATAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:27:16,11:194,150:0.0728:2,2:21.7:1:29.2:1:0.84205:1.12:60:54:0.0732:0:1 0/1:385:120:60,60:131,134:0.3117:2,2:25.4:1:28.9:1:1:1.02:60:240:0.3133:0:1.1 -3 12627100 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24389;SOR=Inf;LSEQ=TCGGGGAAATGTACAGAAAC;RSEQ=CTTTAAGTTTGCACATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:92,11:0:2,0:22.8:1:29.5:1:1:0:60:102:1:0:0 0/1:101:2:1,1:89,10:0.0198:2,2:6.5:1:26.5:1:0.20693:8.53143:60:4:0.02:0:1.5 -3 12629181 . G A 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=AAAATAAGTTTGAGGGGCAT;RSEQ=AGTAGAAAGCAGTTTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:62,131:0:2,0:23.1:1:31.3:1:1:0:60:63.333:1:0:0.1 0/1:349:16:6,10:127,206:0.0458:2,2:23.1:1:29.3:1:1:1.02743:60:32:0.0461:0:1.1 -3 12629207 . C A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29836;SOR=Inf;LSEQ=AAAGCAGTTTTAAACTACAG;RSEQ=TAAGAAGTAAAGCCACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:29,82:0:2,0:21.7:1:31.7:1:1:0:60:110:1:0:0.1 0/1:189:3:1,2:56,130:0.0159:2,2:15:1:31.3:1:1:1.16:60:6:0.0163:0:1.3 -3 12631981 . A G 24 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATAGGCATGTGCCACCAG;RSEQ=CTTGGTTCATTCTTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28:1:33:0:1:0:60:4:1:0:2 1/1:2:2:2,0:0,0:1:0,0:26:1:24.5:1:1:0:60:1:1:0:3 -3 12631983 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGGCATGTGCCACCAGAC;RSEQ=TGGTTCATTCTTGTATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30:1:32:1:1:0:60:4:1:0:2 1/1:2:2:2,0:0,0:1:0,0:28:1:31:1:1:0:60:4:1:0:3 -3 12632239 . C T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24921;SOR=0;LSEQ=GCTTTTCCTGATCCTGGTTC;RSEQ=AATTTAGGGACAAATTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:168,17:0.0159:2,2:12.7:1:22:1:0.02741:19.07513:60:2:0.011:0:1.3 0/0:174:0:0,0:141,32:0:2,0:24.1:1:30.2:1:1:0:59.8:172:1:0:0.1 -3 12632652 . G C 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01204;SOR=Inf;LSEQ=CGGGTGGCATTCTGAGCAAA;RSEQ=AGAAGCCCACCATTAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:1,18:0:1,0:26.2:1:30.7:1:1:0:60:38:1:0:0 0/1:11:4:0,4:1,6:0.3636:2,0:15.5:1:34:0:1:0:60:8:0.3636:0:1 -3 12633083 . A G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=GGAGGAGCATCCAACCACAG;RSEQ=AACTCCACAGTGAGTCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:80,0:0:1,0:23.2:1:30.3:1:1:0:60:160:1:0:0.1 0/1:79:12:12,0:64,3:0.1519:1,0:22.3:1:30.2:1:1:0:60:11:0.141:0:1 -3 12633168 . A G 155 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=8;SSF=0;SOR=32.06024;LSEQ=GTCCTTGTACTCCCCACTCC;RSEQ=GCACTCCAGAGGGACTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:0,1:249,113:0.0027:2,0:16:0:15:0:0.31405:0:60:0:0:0:3 0/1:455:37:26,11:283,133:0.0813:2,2:23.6:1:29.8:1:0.85546:1.11:60:74:0.0833:0:1.2 -3 12633378 . A G 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50043;SOR=Inf;LSEQ=TGAGGAAGATACAGTGAATC;RSEQ=TTTATCCAAAGAATCACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:11,123:0:2,0:27.4:1:30.2:1:1:0:60:12.4:1:0:0.3 0/1:154:2:1,1:12,140:0.013:2,2:6:0:27.5:1:0.16221:11.25:60:4:0.0133:0:1 -3 12641347 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25861;SOR=Inf;LSEQ=TTATTATACTCCATGCAATG;RSEQ=TAATAATCTTTTGATAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:33,187:0:2,0:21.9:1:31.6:1:1:0:60:54:0.9954:0:0.1 0/1:279:3:1,2:58,217:0.0108:2,2:11.3:1:28:1:0.51255:1.87:60:6:0.0108:0:1 -3 12641518 . A G 161 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=38.30328;LSEQ=AGTGTGCCAAAAATGACAGT;RSEQ=ACATTTATAATCTCCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:3,0:45,15:0.0476:2,0:42.3:1:32.7:1:1:0:60:6:0.0484:0:1 1/0:51:34:32,2:17,0:0.6667:1,2:27.7:1:31.8:1:0.54667:0:60:16:0.6667:0:1.1 -3 12641996 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22686;SOR=Inf;LSEQ=AAAAAAGAGGAGGAGGATGT;RSEQ=CAAGAACAAAATAGATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:7,109:0:2,0:24:1:32.4:1:1:0:60:115:1:0:0.1 0/1:106:2:1,1:18,86:0.0189:2,2:6:0:31.5:1:0.32776:4.68:60:4:0.0189:0:1.5 -3 12645626 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25653;SOR=Inf;LSEQ=ACATTACCACCCCCAAGGTG;RSEQ=CCTATTACCTCAATCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:186,59:0:2,0:23.8:1:31.7:1:1:0:60:48:1:0:0.1 0/1:301:3:1,2:214,84:0.01:2,2:26.7:1:27.3:1:0.19737:5.06325:60:6:0.01:0:1 -3 12645868 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50422;SOR=Inf;LSEQ=TCAAGTACATATTTGACTAA;RSEQ=TAAGATGCTTAAGGGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:1,106:0:1,0:22.1:1:32.3:1:1:0:60:106:1:0:0.1 0/1:134:2:1,1:14,118:0.0149:2,2:8:0:28:1:0.2121:8.18:60:4:0.015:0:1 -3 12647547 . T TG 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=99.86797;LSEQ=AAACAGAAATTTCTACCTTT;RSEQ=CTGTACCACCAGTATCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:1:1,0:41,0:0.0238:1,0:12:0:29:0:1:0:60:2:0.025:0:0 1/0:33:24:24,0:8,1:0.7273:2,1:19.5:1:31.8:1:0.27273:0:60:48:0.7273:0.1818:0.1 -3 12650482 . T A 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGATGACAAAAGACAAC;RSEQ=TCATTTCTTGGCCTCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:95:17,78:0,0:1:0,2:22.7:1:30.3:1:1:0:60:30.667:1:0:1.1 1/1:100:100:17,83:0,0:1:0,2:20.5:1:30.2:1:1:0:60:99:1:0:1.1 -3 12650635 . CTA C 108 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.90561;LSEQ=AAGAACTTTAAACAATCCAA;RSEQ=TATATATATATACATACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:10:6,4:79,9:0.101:2,2:24.6:1:32.6:1:0.0256:5.68708:60:20:0.102:0:0 0/1:65:6:6,0:54,5:0.0923:2,0:23.5:1:32.1:1:1:0:60:12:0.0938:0.0154:0 -3 12650677 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62218;SOR=2.02698;LSEQ=ATATTACCTGAGAAATCTCT;RSEQ=TTATGCCTGGCAAAGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:0,1:163,37:0.005:2,0:1:0:25:0:0.18905:0:60:2:0.0051:0:1 0/1:199:2:2,0:155,42:0.0101:2,0:24.5:1:28.5:1:1:0:60:4:0.0102:0:1 -3 12650688 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21822;SOR=4.669;LSEQ=GAAATCTCTGTTATGCCTGG;RSEQ=AAAGCCCTCAACATGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:1:0,1:180,55:0.0042:2,0:1:0:26:0:0.23729:0:60:2:0.0043:0:1 0/1:256:5:1,4:182,69:0.0195:2,2:17:1:23.8:1:0.02431:10.44236:60:4:0.016:0:1 -3 12653204 . G GA 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGACTCCACCTCAAAAA;RSEQ=AAAAAAAAATTACAGGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:25.5:1:31:0:1:0:60:4:0.5:0:0.5 0/0:1:0:0,0:1,0:0:0,0:29:0:26:0:1:0:60:2:1:0:1 -3 12653370 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50049;SOR=Inf;LSEQ=ATTCTATAGGAAGCTAGTAC;RSEQ=ATTTAATACAAACATAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:121,11:0:2,0:22.9:1:30.5:1:1:0:60:131:1:0:0.1 0/1:151:2:1,1:135,14:0.0132:2,2:16.5:1:28.5:1:0.1894:9.35033:60:4:0.0132:0:1 -3 12653652 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49855;SOR=Inf;LSEQ=AAATGCACCAGTCTGTATTG;RSEQ=TTGTGATGGCCCACGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:13,137:0:2,0:22.4:1:32.5:1:1:0:60:300:1:0:0 0/1:156:2:1,1:7,147:0.0128:1,2:29.5:1:28.5:1:0.10025:19.71:60:4:0.0129:0:1 -3 12659494 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGAAAAAATAAACTAC;RSEQ=CAGAACTAAGTGGCTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 12659889 . GA G 85 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.73358;SOR=0.66851;LSEQ=AAAAAATAAATCTGCAGTTA;RSEQ=AAAAAAAAAATAAAGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:6,0:75,0:0.0732:1,0:25.2:1:33.1:1:1:0:60:12:0.0741:0.0122:0.2 0/1:60:3:3,0:56,1:0.05:1,0:36:1:33.7:1:1:0:60:6:0.05:0:0 -3 12660291 . C T 190 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACTCTAGAACAAAAGTATT;RSEQ=AACCCAAGAACACAATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:110:110:9,101:0,0:1:0,2:23.9:1:28.1:1:1:0:60:109:1:0:1.1 1/0:115:86:9,77:3,26:0.7478:2,2:24.1:1:27.8:1:1:1.01:60:42:0.7434:0:1.1 -3 12955982 . G A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.98679;LSEQ=GAAAATGTGGCCCAGCCTGG;RSEQ=GTGCTTAGGTTGCAAAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:207:104,103:114,117:0.4726:2,2:28.7:1:30.4:1:0.92377:1.04:60:50.75:0.4743:0:1.1 1/0:460:335:162,173:67,58:0.7283:2,2:26.9:1:29.7:1:0.3461:1.23304:60:82.75:0.7275:0:1.2 -3 13333548 . G A 31 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGAAAGTTTTTAATTGACA;RSEQ=GGAAATTTAGTTATTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:35:1:31:1:1:0:60:4:0.6667:0:1 1/1:1:1:1,0:0,0:1:0,0:26:0:13:0:1:0:60:0:0:0:1 -3 13333690 . C A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.66927;SOR=0.51536;LSEQ=ATTAACAACATATCCACACA;RSEQ=ATATAACTTACAAACAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:7,0:7,0:0.5:0,0:31.3:1:30.6:1:1:0:60:14:0.5:0:1 0/1:9:3:3,0:6,0:0.3333:0,0:30.7:1:26.3:1:1:0:60:6:0.3333:0:1 -3 13333844 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52609;SOR=Inf;LSEQ=ATCATTTATCATTTGACAAT;RSEQ=CCTCCCATACAATTTACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:38,42:0:2,0:28.3:1:31.8:1:1:0:60:79:1:0:0.1 0/1:130:2:1,1:59,69:0.0154:2,2:28:1:27.5:1:1:1.17:60:4:0.0157:0:1 -3 13333861 . C T 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=AATGCCTCCCATACAATTTA;RSEQ=CAAACAATTTAAATCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:29,41:0:2,0:25.2:1:31.3:1:1:0:60:69:0.9857:0:0.1 0/1:118:19:8,11:41,58:0.161:2,2:22.7:1:28.4:1:1:1.03:60:38:0.161:0:1.2 -3 13333862 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13886;SOR=0;LSEQ=ATGCCTCCCATACAATTTAC;RSEQ=AAACAATTTAAATCATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:28,40:0.0286:2,2:7:0:31.5:1:1:1.42:60:4:0.0286:0:1 0/0:117:0:0,0:48,69:0:2,0:23.6:1:30.7:1:1:0:60:234:1:0:0.3 -3 13334021 . A G 72 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63248;LSEQ=CACTTGCCAGTGTAAGCTCC;RSEQ=TGTGTGTTATACACAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:30.8:1:31.2:1:1:0:60:10:0.625:0:1 1/0:2:1:0,1:0,1:0.5:0,0:12:0:32:0:1:0:60:2:0.5:0:1 -3 14386870 . GA G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50181;SOR=0;LSEQ=GAAACCCTCCGAGGAGCTCT;RSEQ=AAGAGCAGCGGGTGCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:105,6:0.0177:2,2:21:1:29.5:1:0.12058:16.27862:60:4:0.0177:0:1.5 0/0:94:0:0,0:82,12:0:2,0:22.7:1:29:1:1:0:60:93:1:0:0.1 -3 14387023 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11306;SOR=Inf;LSEQ=TTCCACGAACTCAGACTCAG;RSEQ=TGGCTCTGGGTTGGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:37,167:0:2,0:25.6:1:32.2:1:1:0:60:203:1:0:0.1 0/1:192:3:1,2:41,148:0.0156:2,2:18.7:1:31:1:0.52527:1.80:60:6:0.0159:0:1 -3 14387154 . T C 139 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07407;SOR=0;LSEQ=CATTTCTGTTGTTGGGACTT;RSEQ=TCCTGATGCCCTTTAGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:1:0,1:25.6:1:32.3:1:1:0:60:40:1:0:1.2 1/0:8:6:1,5:0,2:0.75:0,2:14.8:1:32.5:1:1:0:60:12:0.75:0:1.2 -3 14387169 . A AG 114 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=7e-04;SOR=0;LSEQ=GACTTTTCCTGATGCCCTTT;RSEQ=GTAGCCGAGCTGGCTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:1:0,0:27.1:1:31.8:1:1:0:60:24:1:0.0833:1.3 0/1:6:1:0,1:1,4:0.1667:2,0:36:0:32:0:1:0:60:2:0.1667:0:0 -3 14387203 . T C 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAAGCCAAGAACCTGAC;RSEQ=GTATTCAGCCTCCAACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:11:1:29.5:1:1:0:60:4:0.6667:0:2 0/0:1:0:0,0:0,1:0:0,0:2:0:30:0:1:0:60:2:1:0:0 -3 16403766 . C T 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00684;SOR=0.70425;LSEQ=CACTCCAACTTCTTGTTTCC;RSEQ=ATCCTGAGAGTCTGTTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:453:259:117,142:91,102:0.5717:2,2:27:1:29.4:1:0.70331:1.0826:60:518:0.573:0:1.1 0/1:516:250:107,143:134,131:0.4845:2,2:26.8:1:29.1:1:0.09312:1.3662:60:500:0.4883:0:1.1 -3 16403839 . TTCCTCCCAAGTGCTTATTCCATGGCCTCCTAAGAGACATGTTTCATAGGTTATCAGGGAAAAACA GAGAACTATCTTATGTTGGGATAATATCAGGATAAG 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25629;SOR=Inf;LSEQ=TCATCTGCTTTGCTGAAATG;RSEQ=GCTGCTCTGCAGCTAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:29,131:0:2,0:25.4:1:30.4:1:1:0:60:79:0.9937:0:0.4 0/1:199:3:0,3:49,147:0.0151:2,0:22:1:30.8:1:1:0:60:6:0.0152:0.0151:0.3 -3 16403843 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.2071;SOR=0;LSEQ=CTGCTTTGCTGAAATGTTCC;RSEQ=CCCAAGTGCTTATTCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:24,128:0.0129:2,2:20:1:30.5:1:0.29921:5.25:60:4:0.0132:0:1 0/0:185:0:0,0:42,143:0:2,0:22.5:1:29.1:1:1:0:60:184:1:0:0.3 -3 16770096 . C T 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.15695;LSEQ=TTAGTTAGTGCAGGAGCCCA;RSEQ=ACTGGCACCCAGGGACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:181:87,94:115,109:0.4447:2,2:26.5:1:29.1:1:0.54918:1.13956:60:59.333:0.4417:0:1.1 1/0:393:249:122,127:72,71:0.6336:2,2:23.9:1:28.7:1:0.83408:1.05547:60:248:0.6343:0:1.1 -3 16770289 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00402;SOR=Inf;LSEQ=GTTCCAAGATTCTTTTTGCT;RSEQ=ATTTTATCATGGTGCCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:1,27:0:1,0:25.5:1:32.7:1:1:0:60:56:1:0:0 0/1:16:5:0,5:1,10:0.3125:2,0:32.6:1:28.6:1:1:0:60:10:0.3125:0:1 -3 16770360 . CG C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGGGTATACAGATCTAA;RSEQ=TTGTGTCTCAGGGGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:1,9:0.2308:2,2:24:1:32.7:1:0.42308:3.87:60:6:0.2308:0:1 0/0:2:0:0,0:1,1:0:2,0:15.5:1:32.5:1:1:0:60:4:1:0:1 -3 16770398 . C A 29 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACCTTGTTACTCTTGA;RSEQ=ATTTGGACCAGATATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:1,7:0.2:2,2:43:1:29.5:1:0.37778:5.29:60:4:0.2:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 16771147 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.43328;LSEQ=GATAATCAGATATTGAAGAC;RSEQ=GAGCGTTCTGGCTAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:36.5:1:31.5:1:1:0:60:4:0.4:0:2 1/0:4:2:2,0:1,1:0.5:2,0:35.5:1:30:1:1:0:60:4:0.5:0:2 -3 16771177 . T G 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.30792;LSEQ=GGCTAAACTTACTAAGCAGG;RSEQ=CCCTTTGCTAAAGCTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:3,1:3,1:0.5:2,2:20:1:32.3:1:1:1:60:8:0.5:0:2 1/0:7:4:2,2:2,1:0.5714:2,2:26.8:1:30:1:1:1.81007:60:8:0.5714:0:1.5 -3 16771252 . G C 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=GGTCCAGAATCCTGAGTAAA;RSEQ=TTTGGCCAAGAGAAGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,2:0.5714:2,2:20.5:1:32.3:1:1:1.41418:60:8:0.5714:0:1.8 0/0:6:0:0,0:2,4:0:2,0:23.3:1:31.7:1:1:0:60:12:1:0:0.3 -3 17744103 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49731;SOR=Inf;LSEQ=TCCCCATCAAATGAAATTGA;RSEQ=AGGACAATCATTAGGCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:54,22:0:2,0:23.8:1:29.2:1:1:0:60:37:1:0:0 0/1:81:2:1,1:60,19:0.0247:2,2:25.5:1:31.5:1:0.43519:3.10369:60:4:0.0247:0:1 -3 17744147 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51061;SOR=Inf;LSEQ=GTAGATAAACTAAACGAAAT;RSEQ=ATGCATTAACTTATTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:66,49:0:2,0:26.4:1:31.7:1:1:0:60:56.5:1:0:0.4 0/1:158:2:1,1:93,63:0.0127:2,2:23:0:28:1:1:1.47243:60:4:0.0127:0:1.5 -3 17744159 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50565;SOR=Inf;LSEQ=AACGAAATGATGCATTAACT;RSEQ=ATTTGATTCATTGTCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:72,63:0:2,0:23.8:1:29:1:1:0:60:66.5:1:0:0.5 0/1:172:2:1,1:98,71:0.0116:2,2:34:1:33:0:1:1.37762:60:4:0.0118:0:1 -3 17744180 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51618;SOR=Inf;LSEQ=ATTTGATTCATTGTCATCAA;RSEQ=ATGAACGAGATTGATGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:64,70:0:2,0:25.1:1:29.4:1:1:0:60:268:1:0:0.7 0/1:196:2:1,1:98,96:0.0102:2,2:22.5:1:30.5:1:1:1.02073:60:4:0.0103:0:2 -3 17744193 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.51164;SOR=Inf;LSEQ=TCATCAATATGAACGAGATT;RSEQ=ATGAACAAAATTTAGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:62,75:0:2,0:24.1:1:31.7:1:1:0:60:274:1:0:0.8 0/1:190:2:1,1:91,96:0.0105:2,2:34.5:1:30:0:1:1.05:60:4:0.0106:0:1 -3 17744199 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.26518;SOR=Inf;LSEQ=ATATGAACGAGATTGATGAA;RSEQ=AAAATTTAGCAAGATTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:60,70:0:2,0:25.3:1:32:1:1:0:60:129:1:0:0.9 0/1:177:3:1,2:80,94:0.0169:2,2:6.3:1:28.7:1:1:1.69723:60:6:0.017:0:2 -3 17744210 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.29739;LSEQ=ATTGATGAACAAAATTTAGC;RSEQ=AGATTACTTTTTAAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:107:50,57:10,10:0.8425:2,2:25.1:1:30.5:1:0.81183:1.13882:60:106:0.8413:0:1.1 1/0:168:103:46,57:28,37:0.6131:2,2:28.4:1:30.5:1:0.87425:1.07:60:206:0.6205:0:1.1 -3 17744212 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51136;SOR=Inf;LSEQ=TGATGAACAAAATTTAGCAA;RSEQ=ATTACTTTTTAAATTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:57,65:0:2,0:26.1:1:31.7:1:1:0:60:121:1:0:1 0/1:169:2:1,1:73,94:0.0118:2,2:37:1:28.5:1:1:1.29:60:4:0.0119:0:2 -3 17822644 . A G 85 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GAGACCTAGACCTCCTCACT;RSEQ=CTGAGAAAGGAGGACTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:33.8:1:33:1:1:0:54.5:12:0.8571:0:1 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 17822824 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50351;SOR=Inf;LSEQ=CATGACTTCTCCCCTTTCTA;RSEQ=GTCCCGTGACAGCCATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:10,19:0:2,0:24.7:1:30.9:1:1:0:56.6:58:1:0:0.1 0/1:39:2:1,1:17,20:0.0513:2,2:18:0:28.5:1:1:1.17:60:4:0.0513:0:1 -3 18391132 . CCTG C 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.52032;SOR=0.74843;LSEQ=TGGCTGTGGAGGCGGCGGTG;RSEQ=CTGCTGCTGCTGCTGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:12:9,3:71,44:0.0945:2,2:25:1:31:1:0.53291:1.85:60:24:0.0952:0.0315:0.3 0/1:152:11:6,5:87,54:0.0724:2,2:22.9:1:31.6:1:0.75087:1.3399:60:22:0.0738:0.0263:0.1 -3 18391145 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=1.56698;LSEQ=GGCGGTGCCTGCTGCTGCTG;RSEQ=TGCTGCTGTTGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:1:0,1:83,59:0.007:2,0:1:0:26:0:0.41958:0:60:2:0.0072:0:1 0/1:183:2:1,1:102,79:0.0109:2,2:18.5:1:29:0:1:1.28931:44:4:0.0112:0:2 -3 18391148 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.50561;SOR=Inf;LSEQ=GGTGCCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:86,62:0:2,0:23.1:1:31.5:1:1:0:60:23.667:1:0:0.2 0/1:188:2:1,1:104,82:0.0106:2,2:13.5:1:28:1:1:1.26667:60:4:0.0108:0:1.5 -3 18391151 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.50618;SOR=Inf;LSEQ=GCCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGCTGTTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:84,65:0:2,0:23.5:1:31.7:1:1:0:60:28.8:1:0:0.2 0/1:191:2:1,1:104,85:0.0105:2,2:21:1:28.5:1:1:1.22222:60:4:0.0106:0:1 -3 18391154 . T C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.59579;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:1,0:82,69:0.0066:2,0:45:0:15:0:1:0:60:0:0:0:8 0/1:191:2:1,1:104,85:0.0105:2,2:27.5:1:32.5:1:1:1.22222:60:4:0.0107:0:1.5 -3 18391165 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.19969;SOR=0;LSEQ=CTGCTGCTGTTGCTGTTGCT;RSEQ=CTGCTGTTGCTGCAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:76,75:0.013:2,2:22:1:30:1:1:1.01325:60:4:0.0132:0:1 0/0:190:0:0,0:97,93:0:2,0:29.4:1:31.8:1:1:0:59.8:94:1:0:0.2 -3 18391213 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62348;SOR=2.73787;LSEQ=ACAATCAGAGCTCTGCTATC;RSEQ=TGGAGTTCCACACAAAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:1,0:39,60:0.01:2,0:1:0:25:0:0.4:0:60:2:0.0101:0:3 0/1:111:3:2,1:34,74:0.027:2,2:11:1:27:1:0.2452:4.29:60:6:0.027:0:1 -3 18391218 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50074;SOR=Inf;LSEQ=CAGAGCTCTGCTATCGTGGA;RSEQ=TTCCACACAAAGCCGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:35,56:0:2,0:22.4:1:31.6:1:1:0:60:90:1:0:0.2 0/1:107:2:1,1:32,73:0.0187:2,2:11.5:1:28.5:1:0.52372:2.26:60:4:0.019:0:1 -3 18391303 . A T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11434;SOR=0.24322;LSEQ=ATAGGGATGAAGATTTAGAA;RSEQ=GAAAAGGTAGGCCGGCGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:0,18:0,5:0.7826:0,1:20.3:1:30.6:1:1:0:60:36:0.7826:0:1.2 0/1:11:5:0,5:0,6:0.4545:0,0:14.8:1:27.6:1:1:0:60:4:0.4:0:1 -3 18392827 . G T 26 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGAGCAGCACCGAGCCAT;RSEQ=GTGCAGGGGTCGGCAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12:0:26.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 22112060 . T A 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00113;SOR=0.55904;LSEQ=GGACACACTGTGATGAAAGA;RSEQ=TATAAAAGGATGAAACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:122:62,60:69,59:0.488:2,2:26.5:1:30.3:1:0.70406:1.1312:60:60:0.4858:0:1.1 0/1:285:99:52,47:98,88:0.3474:2,2:29:1:29.5:1:1:1.00653:60:48.5:0.3477:0:1.1 -3 23146580 . TA AT 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5044;SOR=Inf;LSEQ=CTTAGGCTATCACTTCAATT;RSEQ=TTCCCACATGTCAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:97,27:0:2,0:24.8:1:29.8:1:1:0:60:248:1:0:0.1 0/1:155:2:1,1:115,38:0.0129:2,2:25:1:29.5:1:0.44114:3.00022:60:4:0.013:0:1 -3 23146591 . G T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62855;SOR=2.53716;LSEQ=ACTTCAATTTATTCCCACAT;RSEQ=TCAAATAAATAACCATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:1,0:111,45:0.0064:2,0:43:0:32:0:1:0:60:2:0.0065:0:1 0/1:187:3:1,2:129,55:0.016:2,2:13:1:27.7:1:0.22075:4.64723:60:6:0.016:0:1 -3 23146682 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.3968;LSEQ=CAATATAGACCCTGTTACTA;RSEQ=TTTTCAACCAGGAAATATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:146:66,80:70,85:0.485:2,2:27.9:1:30.5:1:1:1.00:60:145:0.4849:0:1.1 0/1:390:106:49,57:131,153:0.2718:2,2:28.4:1:29.8:1:1:1.00:60:212:0.2739:0:1.1 -3 23146730 . T A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04024;SOR=0;LSEQ=TTAGCCATTGCTTTTTCACC;RSEQ=TGTGAAAACAATGGCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:4:2,2:38,125:0.024:2,2:10.5:1:24.3:1:0.24273:3.26:60:3:0.0183:0:1.3 0/0:204:0:0,0:73,131:0:2,0:23.4:1:29.8:1:1:0:60:203:1:0:0.4 -3 23146734 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50513;SOR=Inf;LSEQ=CCATTGCTTTTTCACCTTGT;RSEQ=AAAACAATGGCAAATTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:31,115:0:2,0:26.8:1:31.4:1:1:0:60:292:1:0:0.5 0/1:184:2:1,1:62,120:0.0109:2,2:12:1:28.5:1:1:1.93:60:4:0.011:0:1 -3 23146772 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00148;SOR=0.33135;LSEQ=CACAGGATTTGCCCTTGGAG;RSEQ=CAGGAAGTTGGGAGTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:34:2,32:2,44:0.425:1,2:27.6:1:30.3:1:1:1.37:60:33:0.4177:0:1.1 0/1:92:18:2,16:9,65:0.1957:2,2:23.3:1:29.8:1:1:1.10649:60:17:0.1868:0:1.3 -3 23317493 . A G 37 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09779;SOR=0;LSEQ=GGCTTTAACTGAATGATACC;RSEQ=GGGGCTTTGCAGATTGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:130,126:0.0116:2,2:13:0:23.7:1:1:1.93:60:2:0.0079:0:1.3 0/0:302:0:0,0:156,145:0:2,0:26.5:1:30.1:1:1:0:60:149.5:1:0:0.3 -3 23317542 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04719;LSEQ=GTGGGGAAGAAAAGTAGAGA;RSEQ=AAGCCTATTTAAAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:180:73,107:4,11:0.9184:2,2:24:1:29.2:1:0.41168:1.87:60:179:0.9179:0:1.1 0/1:258:89:40,49:72,97:0.345:2,2:24.1:1:28.4:1:0.79178:1.10:60:88:0.3438:0:1.1 -3 23317552 . TA T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.07583;SOR=0;LSEQ=AAAGTAGAGACAAGCCTATT;RSEQ=AAAAAAATTTCTATGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:3:1,2:65,104:0.0174:2,2:13:1:30.3:1:1:1.2484:60:6:0.0174:0.0058:1 0/0:233:0:0,0:96,137:0:2,0:23.5:1:29:1:1:0:60:466:1:0:0.4 -3 23317674 . C T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65289;SOR=0.52623;LSEQ=TTTCCATTATTCATTTCCTT;RSEQ=AGACAGCTCCTTTAGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:27:2,25:0,3:0.9:0,2:18:1:28:1:1:0:60:54:0.9:0:1.5 1/1:17:14:0,14:0,3:0.8235:0,1:24.4:1:28.9:1:1:0:60:28:0.8235:0:1.4 -3 23317706 . T C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03931;SOR=0.1351;LSEQ=TTAGTAACTTAGGTACATCC;RSEQ=ACCTTCCCCCACCAAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:0.7333:0,0:25.5:1:32.8:1:1:0:60:22:0.7857:0:2.2 0/1:8:2:0,2:0,6:0.25:0,0:19:1:33.5:1:1:0:60:4:0.25:0:2 -3 24138093 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGACTTAATTTTGCAGTATT;RSEQ=CCCAGGACTGTTCAATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:28.1:1:31.6:1:1:0:60:20:1:0:0.1 0/1:24:2:1,1:12,10:0.0833:2,2:13.5:1:27:1:1:1.19087:60:4:0.087:0:1.5 -3 24138327 . A G 66 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05311;SOR=Inf;LSEQ=TCACTGGAGCTTTTTCTTCA;RSEQ=TTTCTTCATCATCAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:0:2,0:29.1:1:30.3:1:1:0:60:66:1:0:0.1 0/1:33:5:3,2:14,14:0.1515:2,2:21.6:1:28.6:1:1:1.48:60:4:0.129:0:1.2 -3 24138352 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50034;SOR=Inf;LSEQ=TTCATCATCAAAATTATCAT;RSEQ=ATCATCATCTTCATCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:0:2,0:25.7:1:30.9:1:1:0:60:33:1:0:0.1 0/1:43:2:1,1:18,23:0.0465:2,2:20:0:31:1:1:1.27:60:4:0.0476:0:1.5 -3 24138381 . AC A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28847;SOR=Inf;LSEQ=CTTCATCAGCAGCAAGTTTT;RSEQ=TTTTTTTTCTGTGGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:0:2,0:19.4:1:32.3:1:1:0:60:46:1:0:0 0/1:39:3:1,2:14,22:0.0769:2,2:13.7:1:28.7:1:1:1.26509:60:6:0.0789:0.0256:1.3 -3 24138576 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20756;SOR=0;LSEQ=GTAATCCCACGGCTGATGTT;RSEQ=TTTCAAAGCCCCCAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:21,16:0.0513:2,2:31.5:1:32:1:1:1.30327:60:4:0.0513:0:1.5 0/0:46:0:0,0:25,21:0:2,0:27.8:1:28.5:1:1:0:60:45:1:0:0.2 -3 24138663 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49315;SOR=Inf;LSEQ=TAGGACTGCCTTCATAATTC;RSEQ=TTGCCTCTGCTTCAACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:0:2,0:22.9:1:29.3:1:1:0:60:17:1:0:0.2 0/1:37:2:1,1:19,16:0.0541:2,2:23:1:29.5:1:1:1.18197:60:4:0.0541:0:1 -3 24138699 . A T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29402;SOR=4.9693;LSEQ=CAATGTGCAATTCATCTTTT;RSEQ=CACAGCCCCTAACCTGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:0,1:22,27:0.02:2,0:1:0:26:0:1:0:60:2:0.0204:0:1 0/1:32:3:2,1:16,13:0.0938:2,2:22.3:1:27:1:1:1.60:60:6:0.0968:0:1.3 -3 24138715 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52266;SOR=0;LSEQ=TTTTACACAGCCCCTAACCT;RSEQ=ACCGTGCTTAAAGATAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:24,26:0.0385:2,2:29:1:28.5:1:1:1.08:60:4:0.04:0:1 0/0:32:0:0,0:16,16:0:2,0:25.8:1:30.7:1:1:0:60:31:1:0:0.2 -3 24138787 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21076;SOR=Inf;LSEQ=CGATCATCTTCATCGGCCTT;RSEQ=AGTTCACAACCAAAAGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,23:0:2,0:23.6:1:29.1:1:1:0:60:86:1:0:0.3 0/1:37:2:1,1:15,20:0.0541:2,2:46:0:32.5:1:1:1.32:60:4:0.0556:0:1.5 -3 24205123 . A C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16903;SOR=Inf;LSEQ=ATACTATTAAATGAAATAGC;RSEQ=CATGTTCAATGTACCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:89,21:0:2,0:23:1:29.8:1:1:0:60:54:0.9908:0:0 0/1:78:2:1,1:57,19:0.0256:2,2:34.5:1:28.5:1:0.44955:2.94953:60:4:0.0256:0:1 -3 24205147 . T C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10463;SOR=Inf;LSEQ=GTTCAATGTACCTCAAATGT;RSEQ=TCCATTAGGGGACTTACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:99,48:0:2,0:26.7:1:30:1:1:0:60:294:1:0:0.1 0/1:132:3:1,2:87,42:0.0227:2,2:19.7:1:25.3:1:0.25755:4.0944:60:2:0.0154:0:1 -3 24205250 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10876;SOR=Inf;LSEQ=ATAAATAAAAATCAAGATGA;RSEQ=AAACTCTAAATATATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:88,108:0:2,0:26.3:1:31.5:1:1:0:60:97:1:0:0.1 0/1:180:3:1,2:76,101:0.0167:2,2:17.3:1:26.3:1:1:1.50167:60:6:0.0168:0:1.3 -3 24205251 . A C 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATAAAAATCAAGATGAG;RSEQ=AACTCTAAATATATTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:88,108:0:2,0:26.4:1:29.9:1:1:0:60:48:1:0:0.1 0/1:182:53:22,31:57,72:0.2912:2,2:24.9:1:31.9:1:0.86938:1.11486:60:106:0.2944:0:1.1 -3 24205268 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50131;SOR=0;LSEQ=GAGAAACTCTAAATATATTT;RSEQ=ATGCTGTAATCCCCTTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:78,109:0.0106:2,2:28.5:1:29:1:1:1.39:60:4:0.0107:0:1 0/0:163:0:0,0:66,97:0:2,0:24.9:1:31.4:1:1:0:60:162:1:0:0.4 -3 24205281 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19079;SOR=Inf;LSEQ=TATATTTCATGCTGTAATCC;RSEQ=CTTAATATTTCATGATTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:68,108:0:2,0:25.6:1:30.5:1:1:0:60:28.333:1:0:0.1 0/1:137:2:1,1:51,84:0.0146:2,2:34:1:30:1:1:1.64:60:4:0.015:0:1 -3 25408318 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58502;SOR=2.53213;LSEQ=TAAATATTATCCTTGCATTT;RSEQ=GAATTGTTCATGGGCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:1:0,1:68,11:0.0125:2,0:1:0:25:0:0.15:0:60:2:0.0127:0:1 0/1:64:2:0,2:56,6:0.0313:2,0:13.5:1:27:1:0.01389:0:60:4:0.0317:0:1 -3 25408324 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02043;SOR=Inf;LSEQ=TTATCCTTGCATTTGGAATT;RSEQ=TTCATGGGCCTCATTTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:75,18:0:2,0:21.3:1:32:1:1:0:60:92:1:0:0.1 0/1:81:5:2,3:64,12:0.0617:2,2:13:1:29.4:1:0.04173:7.69371:60:10:0.0617:0:1.4 -3 25408332 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21838;SOR=Inf;LSEQ=GCATTTGGAATTGTTCATGG;RSEQ=CCTCATTTTACCTCATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:80,29:0:2,0:22:1:30.7:1:1:0:60:35.333:1:0:0.1 0/1:97:2:1,1:74,21:0.0206:2,2:23:1:31.5:1:0.40399:3.46583:60:4:0.0208:0:1 -3 25408368 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22659;SOR=0;LSEQ=TGAGGTAAAGAGATTACTTG;RSEQ=AGAGTGGTGAACATATTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:123,69:0.0103:2,2:42:1:29:1:1:1.77692:60:4:0.0107:0:1 0/0:213:0:0,0:137,76:0:2,0:25.1:1:31.7:1:1:0:60:212:1:0:0.3 -3 25408383 . A T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09999;SOR=0;LSEQ=ACTTGCAGAGTGGTGAACAT;RSEQ=TTGTTAGGCCCAAATTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:0,3:142,89:0.0128:2,0:5.3:1:22.3:1:0.05957:0:60:2:0.0088:0:1.7 0/0:269:0:0,0:164,105:0:2,0:24.9:1:28.2:1:1:0:60:32.625:1:0:0.4 -3 25408405 . A AT 117 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.04063;SOR=0.44284;LSEQ=TGTTAGGCCCAAATTTAACC;RSEQ=TTTTTTTTTCTTGTGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:20:11,9:149,122:0.0687:2,2:27.4:1:27.3:1:1:1.00:60:5.667:0.0596:0.0103:0.8 0/1:348:11:6,5:183,154:0.0316:2,2:22.1:1:28.9:1:1:1.01:60:22:0.0326:0.0057:0.2 -3 25408451 . G A 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.87279;SOR=0.96811;LSEQ=CAGGATTGTAGCAACAGGCA;RSEQ=AATGTCGTAAAGAAATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:137:65,72:74,75:0.479:2,2:25.9:1:30.1:1:0.72377:1.09258:60:274:0.4893:0:1.1 0/1:344:162:76,86:88,94:0.4709:2,2:26:1:29.6:1:0.82911:1.05915:60:53:0.4746:0:1.2 -3 25408509 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10908;SOR=0;LSEQ=AAAGGATGACCCTTAAACAG;RSEQ=CAGCCTGTCTCATACCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:2,1:59,122:0.0163:2,2:20.3:1:29.3:1:0.25561:4.10:60:6:0.0164:0:1.7 0/0:200:0:0,0:80,120:0:2,0:24.3:1:31.1:1:1:0:60:65.667:1:0:0.4 -3 25408621 . T C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38681;SOR=0.5566;LSEQ=AAAAAAGATTCTCTCCAGTA;RSEQ=TTCCTCAGGTTGGAATAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:0,14:0,10:0.5833:0,1:22.3:1:32.7:1:1:0:60:28:0.5833:0:1 0/1:23:10:0,10:0,13:0.4348:1,0:24.2:1:32.8:1:1:0:60:20:0.4348:0:1.1 -3 25408748 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAATTCCAGGCTATGGTA;RSEQ=CATTTGAGCAATCTCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:24:1:31:1:1:0:60:4:0.4:0:1.5 0/0:1:0:0,0:0,1:0:0,0:12:0:27:0:1:0:60:2:1:0:0 -3 25482508 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.175;SOR=Inf;LSEQ=TGCAATCATATACCTAGGTA;RSEQ=CTTTTGACTGCATTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:20.8:1:32.1:1:1:0:60:18:1:0:0.3 0/1:7:2:1,1:5,0:0.2857:0,2:9.5:1:28.5:1:0.28571:0:60:4:0.3333:0:1.5 -3 25482570 . AT A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.2377;SOR=Inf;LSEQ=ACCAATAACAGGAAGAAGAA;RSEQ=TTTTTTTCGGGGGGGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:27,3:0:2,0:23.9:1:29.5:1:1:0:58.7:14:1:0:0.8 0/1:31:3:2,1:24,4:0.0968:2,2:8.3:1:27.1:1:0.42158:2.86274:60:6:0.1071:0.0645:1.3 -3 25482579 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00016;SOR=0.07069;LSEQ=AGGAAGAAGAAATTTTTTTT;RSEQ=GGGGGGGTGGGTGGGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:16:15,1:11,0:0.5333:0,1:30.6:1:28.1:1:1:0:58.8:7:0.5385:0:1.1 0/1:28:2:1,1:23,1:0.0714:1,2:23:1:28:1:0.15077:16.61257:60:4:0.08:0:2.5 -3 25482587 . T G 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.17722;LSEQ=GAAATTTTTTTTCGGGGGGG;RSEQ=GGGTGGGAATGAAATGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:7:0,7:32,0:0.1795:1,0:12.9:1:19.9:1:0:0:54.3:1.333:0.1176:0:2.4 0/1:39:8:0,8:27,4:0.2051:2,0:10.5:1:22.5:1:1e-05:0:57.5:3:0.1765:0:2.5 -3 25482591 . T G 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.41483;SOR=1.65639;LSEQ=TTTTTTTTCGGGGGGGTGGG;RSEQ=GGGAATGAAATGTTTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:0,6:31,2:0.1538:2,0:17.7:1:24.7:1:1e-05:0:53.3:5:0.1351:0:2.5 0/1:43:10:0,10:30,2:0.2326:2,0:14.2:1:20.8:1:0:0:58:2.333:0.1842:0:2.5 -3 25482594 . G GGA 56 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01319;LSEQ=TTTTTCGGGGGGGTGGGTGG;RSEQ=AATGAAATGTTTCCCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:5:0,5:32,5:0.1163:2,0:21.6:1:22.6:1:3e-04:0:52:10:0.1316:0.0465:1.8 0/1:51:6:0,6:31,10:0.1176:2,0:14.2:1:21.7:1:0.00075:0:60:2:0.1081:0.098:0.5 -3 25482630 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4963;SOR=0;LSEQ=ATCATAGTGGACTCCTAAGC;RSEQ=CGTTCTCTACGTATGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:34,32:0.0294:2,2:37:1:31:1:1:1.06158:60:4:0.0299:0:1 0/0:68:0:0,0:37,31:0:2,0:28.1:1:29.3:1:1:0:60:136:1:0:0.6 -3 25482633 . T A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24453;SOR=0;LSEQ=ATAGTGGACTCCTAAGCACG;RSEQ=TCTCTACGTATGCAGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:33,33:0.0294:2,2:25:0:32.5:1:1:1:60:4:0.0299:0:1 0/0:69:0:0,0:37,32:0:2,0:28.5:1:29:1:1:0:60:68:1:0:0.6 -3 25482663 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22476;SOR=Inf;LSEQ=ATGCAGTGTGCTGATGTCTT;RSEQ=TGGCATAATTGTTAAACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:26,40:0:2,0:29:1:31.2:1:1:0:60:32:1:0:0.3 0/1:60:2:1,1:26,32:0.0333:2,2:44.5:1:30:1:1:1.23:60:4:0.0345:0:1 -3 25502791 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51538;SOR=0;LSEQ=TCGTCTGCCAGGACAAATCA;RSEQ=CAGGGTACCACTATGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:42,39:0.0241:2,2:38:0:33:0:1:1.07594:60:4:0.0247:0:1.5 0/0:56:0:0,0:30,26:0:2,0:29.9:1:28.6:1:1:0:60:55:1:0:0.2 -3 25502851 . G A 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07228;SOR=0;LSEQ=AGGTGAGTATTCACACTTCT;RSEQ=TGCCTGATGAACTCTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:2,3:15,29:0.102:2,2:20:1:27.6:1:1:1.28:60:10:0.102:0:1 0/0:35:0:0,0:13,22:0:2,0:26.4:1:31.3:1:1:0:60:70:1:0:0.2 -3 25502869 . T G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05915;SOR=Inf;LSEQ=CTGTGCCTGATGAACTCTCA;RSEQ=TCTCCATGTACTTTATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:10,26:0:2,0:20.8:1:29.5:1:1:0:60:35:1:0:0.4 0/1:24:3:1,2:7,14:0.125:2,2:24:1:31:1:1:1:60:6:0.125:0:1.3 -3 25542781 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1249;SOR=Inf;LSEQ=GATGCCAATACTGTCGACTC;RSEQ=AGAAGTGCTTTGAAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:18,14:0:2,0:30:1:31.7:1:1:0:60:64:1:0:0.1 0/1:18:2:1,1:9,7:0.1111:2,2:26.5:1:28:1:1:1.26772:60:4:0.1111:0:1 -3 25569355 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23774;SOR=3.41534;LSEQ=AACCTCCAAAGAAAAGCCCT;RSEQ=CCCTTCGCCCCCCACAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:0.3077:0,0:23.5:1:29.8:1:1:0:60:8:0.3077:0:1 1/0:13:8:7,1:5,0:0.6154:0,2:20.5:1:29.1:1:1:0:60:16:0.6154:0:1.1 -3 25569463 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49786;SOR=Inf;LSEQ=AGCAACAAGGCCCTGCACAA;RSEQ=GCCAGGCGGGAGGCCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:76,16:0:2,0:21.8:1:30.1:1:1:0:60:184:1:0:0.1 0/1:98:2:1,1:68,28:0.0204:2,2:5.5:1:28:1:0.50642:2.40383:60:4:0.0206:0:2.5 -3 25569471 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49787;SOR=Inf;LSEQ=GGCCCTGCACAAAGCCAGGC;RSEQ=GGAGGCCTGTGGATGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:90,25:0:2,0:19.6:1:29.7:1:1:0:60:114:1:0:0.1 0/1:117:2:1,1:78,37:0.0171:2,2:13.5:1:32:0:0.54598:2.09353:60:4:0.0172:0:2.5 -3 25569473 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49794;SOR=Inf;LSEQ=CCCTGCACAAAGCCAGGCGG;RSEQ=AGGCCTGTGGATGAGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:94,25:0:2,0:19.6:1:30.9:1:1:0:60:238:1:0:0.2 0/1:121:2:1,1:80,39:0.0165:2,2:24:1:28:1:1:2.03815:60:4:0.0168:0:1 -3 25569486 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49847;SOR=Inf;LSEQ=CAGGCGGGAGGCCTGTGGAT;RSEQ=AGGTGCTCTGCAAGCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:104,44:0:2,0:21.1:1:31.7:1:1:0:60:296:1:0:0.3 0/1:153:2:1,1:100,51:0.0131:2,2:23.5:1:26:1:1:1.95159:60:4:0.0132:0:1 -3 25569491 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10997;SOR=0;LSEQ=GGGAGGCCTGTGGATGAGGT;RSEQ=CTCTGCAAGCTGAGCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:3:1,2:101,46:0.02:2,2:11:1:27.3:1:0.24007:4.34348:60:6:0.0201:0:1.3 0/0:162:0:0,0:106,56:0:2,0:25.2:1:31.9:1:1:0:60:324:1:0:0.3 -3 25569503 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22896;SOR=0;LSEQ=GATGAGGTGCTCTGCAAGCT;RSEQ=AGCCAGAAGCCTTAGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:111,59:0.0116:2,2:23.5:1:30.5:1:1:1.87407:60:4:0.0116:0:1 0/0:188:0:0,0:113,75:0:2,0:26:1:31.4:1:1:0:60:187:1:0:0.3 -3 25569565 . C T 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0.51876;LSEQ=TGACTAATTGGTAATGTCTG;RSEQ=GGAGTTGGCACCAGGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:129:60,69:89,88:0.4216:2,2:23.8:1:29.4:1:0.56302:1.16249:60:63.5:0.4205:0:1.4 0/1:321:88:41,47:128,105:0.2741:2,2:26.5:1:29.5:1:0.21047:1.39596:60:176:0.2767:0:1.2 -3 25569630 . G T 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0;SOR=0;LSEQ=TTGAGGAAGGAAGACAGACA;RSEQ=ACTTGAAGCCAAGCCTCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:56:18,38:32,60:0.3784:2,2:24.4:1:29.5:1:0.85806:1.12503:60:112:0.3784:0:1.7 0/0:233:0:0,0:95,138:0:2,0:23.3:1:31.1:1:1:0:60:76.667:1:0:0.3 -3 25569639 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51805;SOR=Inf;LSEQ=GAAGACAGACAGACTTGAAG;RSEQ=CAAGCCTCGAGTGTTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:43,89:0:2,0:22.8:1:31.2:1:1:0:60:43:1:0:0.6 0/1:197:2:1,1:75,120:0.0102:2,2:23.5:1:28:1:1:1.60:60:4:0.0105:0:1 -3 25569761 . A C 115 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18424;SOR=0.16114;LSEQ=GCCCAGATGGCCAGCATTTG;RSEQ=TTTAGCTGTTCAGGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:0,11:0,10:0.5238:0,0:24.9:1:33.4:1:1:0:60:22:0.5238:0:1.1 0/1:7:1:0,1:0,6:0.1429:0,0:26:0:34:0:1:0:60:2:0.1429:0:1 -3 25622130 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48413;SOR=0;LSEQ=GCATTATTAAGATCGTGGAG;RSEQ=TTGCTAAACGTCTGCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:20:1:30.5:1:1:1.15:60:4:0.1333:0:1 0/0:13:0:0,0:5,8:0:2,0:23.4:1:28:1:1:0:60:26:1:0:0.1 -3 25622158 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=ACGTCTGCCTGGTTTCACTG;RSEQ=CTTGACCATCGCAGACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:16:1:28.5:1:1:1.29:60:4:0.2222:0:1 0/0:8:0:0,0:2,6:0:2,0:29.5:1:32:1:1:0:60:16:1:0:0.1 -3 26805180 . G T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGGAAGGAAGGAAGGA;RSEQ=GGAAGGAAGGAAAGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:30:1:1:0:23:4:1:0:2 -3 26805252 . A C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGGAAGGGAGGAAGAA;RSEQ=GGAAGGAAGTGAGGAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:0:31:0:1:0:60:4:1:0:1.5 -3 26805488 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGGAAGGGAAGGGAAGG;RSEQ=AAGGAGGAAAAGAAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:19:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 26806016 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=GAGTGCCATTGCCCTTCGGC;RSEQ=CATGGAGGAAGGAGTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:99,52:0:2,0:24.7:1:30.4:1:1:0:60:36.75:1:0:0.1 0/1:160:2:1,1:106,52:0.0125:2,2:18.5:1:28.5:1:1:2.0287:60:4:0.0127:0:1 -3 26806092 . G T 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32602;SOR=0.2617;LSEQ=TTCACTCCACTTGATTTCAA;RSEQ=TGTCTTTATCCTCTACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:0,3:153,144:0.01:2,0:16:1:22:1:0.11642:0:60:2:0.0068:0:2 0/0:380:1:0,1:195,184:0.0026:2,0:1:0:26:0:0.48684:0:60:2:0.0026:0:2 -3 26806108 . C G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.22142;LSEQ=TCAAGTGTCTTTATCCTCTA;RSEQ=CTGCCCTCATGGCACCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:47:22,25:123,123:0.1604:2,2:28.6:1:32.4:1:0.75119:1.13587:60:94:0.1604:0:1.1 1/0:404:202:98,104:97,105:0.5:2,2:26.3:1:31.7:1:1:1.02:60:404:0.5037:0:1.1 -3 26806208 . T TC 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04857;SOR=1.84203;LSEQ=TCTCACATCACTTGGCCAGT;RSEQ=ACTGGAATGTCTGAATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:50:6,44:4,32:0.5814:2,2:19.2:1:31.9:1:1:1.09:60:100:0.5814:0.2093:0 1/0:107:77:20,57:5,24:0.7196:2,2:20.2:1:31:1:0.44543:1.68:59.9:76:0.7379:0.243:0.1 -3 28650238 . C T 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=0.5559;LSEQ=TTCTGAGAAAGAGGATTACA;RSEQ=GTGATAAAATGATGCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:117:48,69:106,141:0.3197:2,2:27.3:1:29.9:1:0.82036:1.08042:60:38:0.3184:0:1.1 0/1:401:83:36,47:139,178:0.207:2,2:26.3:1:30.1:1:1:1.01946:60:166:0.2075:0:1.1 -3 28650262 . T A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=Inf;LSEQ=ATAAAATGATGCCTTGTGTC;RSEQ=TAAATATTTAAAAAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:94,184:0:2,0:24.3:1:30.3:1:1:0:60:68.5:1:0:0.4 0/1:287:3:2,1:103,181:0.0105:2,2:14.7:1:27.7:1:0.55642:3.50:60:6:0.0106:0:1 -3 28744027 . C T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCGCTGGGATTACAGGTG;RSEQ=CTGCCACGACACCCGACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:26.5:1:1:0:60:4:1:0:1 -3 28745955 . T A 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00341;SOR=0;LSEQ=CATCTCTCATTGTCCAATGA;RSEQ=TAAAGACTTAAAGTGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:137:137:100,37:0,0:1:0,2:20.7:1:30.1:1:1:0:60:136:1:0:1.4 1/1:137:128:90,38:8,1:0.9343:2,2:23.2:1:30:1:0.4453:3.35516:60:127:0.9407:0:1.3 -3 28746022 . G T 44 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12877;SOR=Inf;LSEQ=GCCACCTCTGAACATTTGAT;RSEQ=TTGAATCCCCTCAATTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:151,135:0:2,0:26.2:1:32:1:1:0:60:285:0.9965:0:0.9 0/1:339:4:0,4:184,151:0.0118:2,0:10:1:22.3:1:0.04279:0:60:3:0.009:0:2.8 -3 28746030 . C T 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.87059;SOR=1.03302;LSEQ=TGAACATTTGATGTTGAATC;RSEQ=CCTCAATTTTGTGATGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:296:176:93,83:57,62:0.5946:2,2:27.6:1:30.4:1:0.40926:1.22:60:57.667:0.5966:0:1.3 1/0:332:200:108,92:70,62:0.6024:2,2:24.4:1:29.5:1:0.91062:1.04:60:65.667:0.6043:0:1.3 -3 28746143 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50413;SOR=Inf;LSEQ=GGCCTAGTATACTCTCACAA;RSEQ=AGAGGACACTTCTGTAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:13,61:0:2,0:22.7:1:32.4:1:1:0:60:73:1:0:0.1 0/1:94:2:1,1:19,73:0.0213:2,2:39:1:28.5:1:0.38206:3.77:60:4:0.0213:0:1 -3 29047500 . A G 66 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.30341;SOR=0.18229;LSEQ=ATCTCAGTATTTTAGAATGA;RSEQ=AATATATCCCTTAGTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:30.8:1:33.3:1:1:0:60:8:0.4444:0:1.5 0/1:10:1:1,0:8,1:0.1:2,0:5:0:33:0:1:0:60:2:0.1:0:1 -3 29047673 . A G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.40449;LSEQ=AGTAAATAAGCCTAAGGAGC;RSEQ=ACACTCACAGCATAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:92:44,48:32,30:0.5935:2,2:25.3:1:30.5:1:0.74269:1.16249:60:45:0.5882:0:1.3 0/1:205:76:37,39:65,64:0.3707:2,2:28.5:1:30.1:1:0.88525:1.07016:60:152:0.3707:0:1.1 -3 29047705 . C A 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=0;LSEQ=ATAAGAAAATATTTAAGACT;RSEQ=TAAGAAACAAGATTAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:12:4,8:57,74:0.0839:2,2:29.8:1:31.3:1:0.55719:1.53605:60:24:0.0857:0:2.3 0/0:203:0:0,0:87,116:0:2,0:25.9:1:31.5:1:1:0:60:66.667:1:0:0.4 -3 29047750 . T A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.8016;SOR=1.20512;LSEQ=ATATTGGTACATATTTTATA;RSEQ=CCTCTATTTTCACTAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:7:2,5:20,56:0.0843:2,2:18.1:1:28:1:1:1.12:60:6:0.0741:0:2.6 0/1:100:10:3,7:29,61:0.1:2,2:17:1:29.6:1:1:1.10817:60:20:0.101:0:1.5 -3 29049048 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATGTGTATATATATATA;RSEQ=ACACATATATATATGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:27.5:1:1:0:60:4:1:0:1.5 -3 29049074 . T TATA 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATATATGTGTATATATA;RSEQ=GGCACATATACACCATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:29.7:1:1:0:60:4:1:0:1.5 -3 29250643 . AT A 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.56797;LSEQ=CCTGGAGTTCTTTTTCTTTG;RSEQ=GGTTAGAGAATAGGTATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:39:22,17:198,133:0.1054:2,2:28.4:1:31.1:1:0.73145:1.14993:60:78:0.106:0.0162:0.7 0/1:400:93:58,35:166,141:0.2325:2,2:25.4:1:30.7:1:0.18962:1.41:60:45.5:0.2316:0.04:0.7 -3 29250696 . C T 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50783;SOR=1.09834;LSEQ=AATCACACTTAACGGAAAAC;RSEQ=ATTTGTATGCCTTTAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:440:212:99,113:102,126:0.4818:2,2:25.4:1:29.2:1:0.70233:1.08:60:52:0.4804:0:1.1 1/0:473:239:105,134:110,124:0.5053:2,2:25.7:1:28.9:1:0.51898:1.13181:60:78.667:0.5054:0:1.1 -3 29476247 . C G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24545;SOR=Inf;LSEQ=TTTCCAGCAGTCCTATGCAC;RSEQ=AGCTCCCCACCCCATGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:56,27:0:2,0:23.4:1:31.1:1:1:0:60:82:1:0:0.1 0/1:82:2:1,1:57,23:0.0244:2,2:40.5:1:27.5:1:0.50226:2.44728:60:4:0.0244:0:1 -3 29476286 . ACAG A 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.50426;SOR=Inf;LSEQ=TCCTCCCAGCCCCAGCACAA;RSEQ=CAGCAGCAACAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:79,71:0:2,0:28.3:1:31.9:1:1:0:60:149:1:0:0.2 0/1:186:2:1,1:98,86:0.0108:2,2:30:0:33.5:1:1:1.13873:60:4:0.0109:0:0.5 -3 29476292 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.20166;SOR=0;LSEQ=CAGCCCCAGCACAAACAGCA;RSEQ=CAGCAACAACAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:78,77:0.0127:2,2:26:1:29:1:1:1.01291:60:4:0.0131:0:1 0/0:192:0:0,0:100,92:0:2,0:28.7:1:32:1:1:0:60:95:1:0:0.2 -3 29476357 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50687;SOR=Inf;LSEQ=AAACCAACCTGTACATTCGA;RSEQ=GCCTCCCACCAGGCACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:22,52:0:2,0:20.3:1:30.7:1:1:0:60:73:1:0:0.1 0/1:98:2:1,1:35,61:0.0204:2,2:39.5:1:29:1:1:1.73:60:4:0.0206:0:1 -3 29476358 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50563;SOR=Inf;LSEQ=AACCAACCTGTACATTCGAG;RSEQ=CCTCCCACCAGGCACCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:21,52:0:2,0:19.9:1:31.5:1:1:0:60:146:1:0:0.2 0/1:95:2:1,1:34,59:0.0211:2,2:8:1:27:1:1:1.72:60:4:0.0213:0:1.5 -3 29476407 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5148;SOR=Inf;LSEQ=CTAATCAAGCTGTGCCAACC;RSEQ=TAAGTGTCCTTCTGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:1,16:0:1,0:30.7:1:31.1:1:1:0:60:16:1:0:0.4 0/1:27:2:1,1:0,25:0.0741:1,2:38:1:29:1:0.07407:0:60:4:0.0741:0:2 -3 29476428 . G A 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.43375;SOR=2.16695;LSEQ=TAAGTGTCCTTCTGCTGCCC;RSEQ=TGCTGTTTCTCACTCCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:1,6:0.4167:2,0:28.2:1:31.8:1:1:0:60:10:0.4167:0:1.2 1/0:13:8:1,7:0,5:0.6154:0,2:28.9:1:30.1:1:1:0:60:16:0.6154:0:1.5 -3 30648304 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49817;SOR=0;LSEQ=AGAGGGCGCGGCGCGGAGGC;RSEQ=CAGCCAGGGGTCCGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:101,16:0.0168:2,2:19:1:29:1:0.26634:6.15428:60:4:0.0171:0:1 0/0:113:0:0,0:89,24:0:2,0:18.2:1:30.3:1:1:0:60:112:1:0:0.2 -3 30686181 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49978;SOR=Inf;LSEQ=GCATAACATCTTCAGGAATT;RSEQ=ATTGGCAGGCTGCCTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:147,14:0:2,0:22.2:1:31.2:1:1:0:60:39.25:1:0:0 0/1:178:2:1,1:150,26:0.0112:2,2:21.5:1:27:1:0.28109:5.68028:60:4:0.0113:0:1 -3 30686414 . A G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.08071;LSEQ=TGTGTGGCTGTATGGTAAGC;RSEQ=AGCCTTTTAAGAAGTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:31:9,22:32,152:0.1442:2,2:18.7:1:31.1:1:0.1405:1.94:60:62:0.1476:0:1.1 0/1:245:100:23,77:33,112:0.4082:2,2:24.2:1:30.8:1:1:1.01:60:99:0.4074:0:1.1 -3 30686447 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20998;SOR=0;LSEQ=AGTTATTCTTTCTTTTCCCC;RSEQ=TTTTACATAATGTATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:10,90:0.0196:2,2:29:1:33:0:0.20501:8.63:60:4:0.0202:0:1 0/0:120:0:0,0:18,102:0:2,0:24.1:1:30:1:1:0:60:39:1:0:0.5 -3 30691473 . G A 62 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGACTTAAATATGTAAA;RSEQ=TTCTCCACCAGGACTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:18.8:1:31:1:1:0:60:8:0.5714:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 30691871 . GA G 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.77163;SOR=0.91832;LSEQ=CTCCAAAGTGCATTATGAAG;RSEQ=AAAAAAAAAGCCTGGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:23:7,16:224,291:0.0428:2,2:28.3:1:32:1:0.28267:1.7577:60:46:0.044:0.0019:0.1 0/1:660:26:12,14:281,351:0.0394:2,2:28.2:1:30.9:1:1:1.07:60:52:0.0399:0.003:0.2 -3 30691998 . AT A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.58524;SOR=0.39246;LSEQ=GGGACCTGAGATCTGTGCCA;RSEQ=TTTTTGTATCCTTGGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:33,133:0.0119:2,2:14.5:1:30:1:0.36477:3.99:60:4:0.0122:0:0.5 0/0:213:1:0,1:50,162:0.0047:2,0:27:0:26:0:1:0:60:2:0.0048:0:0 -3 30692033 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50107;SOR=Inf;LSEQ=GGTCTGCAGTGTCATAGAGC;RSEQ=CATTCCTCCTGTGGTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:3,81:0:1,0:24.3:1:29.4:1:1:0:60:41:1:0:0.1 0/1:100:2:1,1:13,85:0.02:2,2:5.5:1:28:1:0.26162:6.34:60:4:0.02:0:1 -3 30692219 . T C 72 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTCTCAAAGTGCGGCC;RSEQ=CTTGAGCAGCCAGCATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:14.2:1:31.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 30713126 . T A 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCTTGTTTTGTTTCCCCA;RSEQ=CAGAATATAACACCAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:149,115:0:2,0:27.2:1:30.3:1:1:0:60:65:1:0:0.1 0/1:353:42:25,17:180,131:0.119:2,2:30.1:1:28.9:1:0.86935:1.07:60:41:0.1192:0:1 -3 30713794 . G A 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATGTGGGAGGCCCAAGAT;RSEQ=CCCATCGTGCACAGGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:0:0,0:319,292:0:2,0:26.3:1:32.1:1:1:0:60:86.286:1:0:0.1 0/1:699:25:13,12:372,301:0.0358:2,2:22.8:1:28.4:1:0.83858:1.14059:60:50:0.0363:0:1 -3 30713834 . G A 156 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02023;LSEQ=TCAAGAGCTCCAATATCCTC;RSEQ=TGAAGAACGACCTAACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:727:37:23,14:363,327:0.0509:2,2:22.5:1:30.1:1:0.3111:1.48:60:36:0.0504:0:1.1 0/0:925:1:1,0:494,429:0.0011:2,0:1:0:28:0:1:0:60:2:0.0011:0:1 -3 30715977 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATAAACCTTTGTATAATTA;RSEQ=TCTTCTCTTGACACATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:0.3:2,0:18.7:1:31:1:1:0:60:6:0.3:0:1 0/0:1:0:0,0:0,1:0:0,0:2:0:33:0:1:0:60:2:1:0:0 -3 30729836 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49841;SOR=Inf;LSEQ=ATTTCCTTTGGCTGCACATG;RSEQ=CATTCTCAGTGACCCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:123,32:0:2,0:24:1:31.9:1:1:0:60:76.5:1:0:0.1 0/1:157:2:1,1:119,36:0.0127:2,2:30.5:1:30:1:0.41695:3.27423:60:4:0.0129:0:1 -3 30730074 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49754;SOR=Inf;LSEQ=TTAGGTGGCAGAGAATTCTG;RSEQ=AATATTGAGCTTAAATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:3,82:0:1,0:26.2:1:31.2:1:1:0:60:170:1:0:0.1 0/1:90:2:1,1:5,83:0.0222:2,2:35.5:1:29.5:1:0.12959:15.24:60:4:0.0225:0:1 -3 30733025 . G T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01001;SOR=Inf;LSEQ=GAGCTGGAGCATCTGGACAG;RSEQ=CTCTCGGGGAGGAGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:0:0,0:286,296:0:2,0:24.9:1:31.5:1:1:0:60:63.667:1:0:0.2 0/1:716:8:3,5:329,378:0.0112:2,2:12.8:1:23.6:1:0.73062:1.44988:60:3:0.0086:0:1.1 -3 30733187 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.2006;SOR=Inf;LSEQ=CCCTGAACTGATGCTTCCTG;RSEQ=AAAACCAAGGGGGTCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:1,96:0:1,0:25.2:1:31.7:1:1:0:60:194:0.9898:0:0.1 0/1:80:2:0,2:2,76:0.025:1,0:18:1:29:1:1:0:60:4:0.025:0:1.5 -3 31310597 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14773;SOR=Inf;LSEQ=ACAATGGTGTGCCCTCTACT;RSEQ=AGGAGTGAAGAAACCTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:0:2,0:23.1:1:30.7:1:1:0:60:19:1:0:0.1 0/1:13:2:1,1:6,5:0.1538:2,2:8.5:1:27:1:1:1.18321:60:4:0.1667:0:1 -3 31310976 . GGA G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=ATGGCGTGAACCCGGGAGGC;RSEQ=GCTTGCTGTGAGCCAAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,4:0.3333:0,2:16.5:1:30:1:0.33333:0:60:4:0.3333:0:0 0/0:6:0:0,0:0,6:0:0,0:28.7:1:30.7:1:1:0:52.5:12:1:0:0.3 -3 32071654 . G A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06221;SOR=0;LSEQ=AAATTTTACTGCTTCCTTTC;RSEQ=GCCAGAACCGCCATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:164,128:0.0102:2,2:13:1:24.3:1:0.58471:2.55446:60:2:0.0069:0:2.7 0/0:448:0:0,0:259,188:0:2,0:26:1:29:1:1:0:59.9:48.667:1:0:0.1 -3 32071729 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18083;SOR=0;LSEQ=AGGAGAGACACGTGATACAT;RSEQ=TTCTCCAGGCCTTTTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:71,128:0.01:2,2:32.5:1:29:1:1:1.80:60:4:0.0103:0:1 0/0:271:0:0,0:97,174:0:2,0:22.4:1:30.8:1:1:0:60:53.2:1:0:0.1 -3 32072055 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=Inf;LSEQ=GAAAGAAGCCAAAGACAAAC;RSEQ=TACCTGGGTTCAACTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:18:1:30:1:1:0:60:6:1:0:0 0/1:13:2:1,1:2,9:0.1538:2,2:16.5:1:28.5:1:0.42308:3.87:60:4:0.1538:0:1 -3 32670121 . T C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CAGGCGCCCACCACCACACC;RSEQ=GGCCATGGTTTTCTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:28.5:1:31.5:1:1:0:60:4:0.5:0:2.5 0/0:4:0:0,0:4,0:0:0,0:16.5:1:30.8:1:1:0:60:8:1:0:0.8 -3 32670172 . G A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84715;LSEQ=TTGTTATAGGGGCCTCAGCC;RSEQ=TGGACCTTTTAATGGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:14,0:10,0:0.5833:0,1:26.6:1:30.7:1:1:0:60:28:0.6087:0:2.8 1/0:24:13:13,0:11,0:0.5417:0,1:20.7:1:30.7:1:1:0:60:26:0.5417:0:1.5 -3 32670183 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01047;SOR=0.23899;LSEQ=GCCTCAGCCGTGGACCTTTT;RSEQ=ATGGGTAAGATATTATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:18:18,0:15,0:0.5455:1,1:26.1:1:33:1:1:0:60:36:0.5455:0:2.8 0/1:32:7:7,0:25,0:0.2188:1,0:13.1:1:32.9:1:1:0:60:14:0.2258:0:2.6 -3 32670232 . G A 166 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1699;LSEQ=CCACAATATACTCACTAAAC;RSEQ=TCCAGCAGTGGAAATGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:41:40,1:40,1:0.5:1,1:25.8:1:31:1:1:1:60:82:0.5:0:2.3 0/1:125:18:17,1:99,7:0.144:2,1:30.6:1:30.4:1:1:1.20:60:36:0.1452:0:2.2 -3 32670281 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17449;LSEQ=TTTGTGATTTTGATGAAATA;RSEQ=TATTGCATTAAATTTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:99:73,26:79,25:0.4877:2,2:22.7:1:32.5:1:0.74805:1.12482:60:198:0.4877:0:1.7 0/1:324:46:30,16:205,73:0.142:2,2:22:1:30.8:1:0.28402:1.49573:60:92:0.1438:0:1.7 -3 32670357 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1697;LSEQ=AATGAATGTCATGGGATAAT;RSEQ=CTTGATTTGGTAAAAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:209:103,106:121,117:0.4655:2,2:27:1:28.8:1:0.77643:1.06415:60:103.5:0.4631:0:1.3 0/1:669:86:42,44:283,299:0.1286:2,2:26.5:1:28.6:1:1:1.01:60:172:0.1295:0:1.3 -3 32670533 . G C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=0.06423;LSEQ=AGGCCAAGGCAGGTGGATTG;RSEQ=TTGAGTCCAGGCGTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:0,16:0,9:0.64:0,1:26.2:1:33.4:1:1:0:60:32:0.64:0:1.4 0/1:31:3:0,3:1,27:0.0968:1,0:19.3:1:33.3:1:1:0:60:6:0.1:0:1 -3 32670602 . C A 67 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58042;SOR=0.27349;LSEQ=TCTTTATAAGAAATACAAAA;RSEQ=AACTGGGGCCGGACGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:17.8:1:29.2:1:1:0:60:10:0.5:0:2 0/1:5:1:0,1:0,4:0.2:0,0:39:0:32:0:1:0:60:2:0.2:0:1 -3 33432091 . G A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10319;SOR=0.20732;LSEQ=CTGGCCCACTATCAACGCCC;RSEQ=CATTCCAACACTGTCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:12,0:7,0:0.6316:0,0:19:1:29.3:1:1:0:60:11:0.6111:0:1.7 0/1:8:2:2,0:6,0:0.25:0,0:29.5:1:32:0:1:0:60:4:0.25:0:1 -3 33432214 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25833;SOR=Inf;LSEQ=GTGAAATATACTGTGTCAGG;RSEQ=CAGAGGACCTGAGGGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:113,40:0:2,0:23.6:1:31:1:1:0:60:50:1:0:0.2 0/1:194:3:1,2:142,49:0.0155:2,2:19.3:1:27.3:1:0.16955:5.73232:60:6:0.0158:0:1 -3 33432307 . C A 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.46287;LSEQ=AGATTTCAAACATTTTAAAA;RSEQ=TGTATCATTCCTTTTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:294:163:77,86:61,70:0.5544:2,2:23.7:1:30.1:1:1:1.03:60:39.75:0.5483:0:1.1 0/1:408:149:75,74:117,142:0.3652:2,2:24.8:1:29.5:1:0.35407:1.23:60:73.5:0.363:0:1.1 -3 33432368 . TA T 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.58421;SOR=0.38965;LSEQ=AGAAGCAATATAGGCATTCA;RSEQ=AAAAAATGATTTTTCTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:0,2:45,105:0.0132:2,0:26.5:1:32:0:1:0:60:4:0.0132:0:0 0/0:194:1:0,1:60,132:0.0052:2,0:18:0:32:0:1:0:60:2:0.0053:0:1 -3 33432401 . TA T 80 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.75526;SOR=1.28878;LSEQ=TTTCTCATGACGACAAAGTT;RSEQ=AAAAAAAAAACAAAACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:4:0,4:8,66:0.0513:2,0:29.8:1:31.5:1:1:0:60:8:0.0513:0:0 0/1:92:6:1,5:14,72:0.0652:2,2:19.5:1:31:1:1:1.03:60:12:0.0652:0.0109:0.3 -3 33494445 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18857;SOR=0;LSEQ=CAACATGGTTTCTCCCCTTT;RSEQ=TAGGTCCCGTGGCAGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:7,13:0.0909:2,2:19.5:1:27.5:1:1:1.80:57:4:0.0909:0:1 0/0:28:0:0,0:12,16:0:2,0:23.3:1:30.8:1:1:0:57.9:56:1:0:0.3 -3 34786345 . C T 38 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62343;SOR=0.33261;LSEQ=GAACCTCAAAAGCCCCTATC;RSEQ=TTGTTTCTCCAGCAATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:185,52:0.0125:2,2:10.3:1:24:1:0.12788:7.0388:60:2:0.0084:0:1.3 0/0:239:1:0,1:182,56:0.0042:2,0:1:0:29:0:0.23849:0:60:2:0.0042:0:1 -3 34786456 . T C 234 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATCTCCTCATTCTGACAA;RSEQ=TGCTCATTTCAGAAACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:226,304:0:2,0:25.6:1:30.2:1:1:0:60:65.25:1:0:0.1 0/1:614:185:83,102:194,235:0.3013:2,2:25.1:1:31.1:1:1:1.01449:60:60.667:0.3028:0:1.1 -3 35897771 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18526;SOR=0;LSEQ=ATGACCCTACCCACAAGTAG;RSEQ=TGGTTATGGAACAGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:23,8:0.0606:2,2:25.5:1:29:1:0.47727:2.76887:60:4:0.0625:0:1 0/0:43:0:0,0:26,17:0:2,0:25.9:1:31.2:1:1:0:60:86:1:0:0.2 -3 35897772 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49883;SOR=Inf;LSEQ=TGACCCTACCCACAAGTAGC;RSEQ=GGTTATGGAACAGGGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:25,10:0:2,0:25.6:1:30.7:1:1:0:60:34:1:0:0.1 0/1:43:2:1,1:25,16:0.0465:2,2:34.5:1:28:1:1:1.54582:60:4:0.0476:0:1 -3 35897806 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4972;SOR=Inf;LSEQ=GGGTTGGATAGTTGCACTGT;RSEQ=ATTTTGCTGCTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:37,25:0:2,0:23.7:1:31.5:1:1:0:60:124:1:0:0.1 0/1:68:2:1,1:38,28:0.0294:2,2:33.5:1:29.5:1:1:1.35095:60:4:0.0308:0:1 -3 35897810 . TTGC T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.49761;SOR=Inf;LSEQ=TGGATAGTTGCACTGTGATT;RSEQ=TGCTGCTGCTGCTCTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:36,27:0:2,0:24.9:1:30.3:1:1:0:60:126:1:0:0.1 0/1:70:2:1,1:39,29:0.0286:2,2:11:1:32:0:1:1.33905:60:4:0.029:0:0.5 -3 35897819 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.49966;SOR=Inf;LSEQ=GCACTGTGATTTTGCTGCTG;RSEQ=TGCTGCTCTTGTTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:0:2,0:26.9:1:31.9:1:1:0:60:60:1:0:0.1 0/1:72:2:1,1:37,33:0.0278:2,2:30:0:32:0:1:1.11943:60:4:0.0278:0:1.5 -3 36107937 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCACATAGAGAGAATGTCAT;RSEQ=TGAAGATGAAGAGAGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:27:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:1.5 -3 36109775 . T C 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.33587;LSEQ=GGAAAATTAGTATTTTCCAA;RSEQ=AGTACCCTTAGCCAGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:175:80,95:14,10:0.8794:2,2:26.6:1:31.8:1:0.28027:1.65822:60:350:0.8794:0:1.1 1/0:210:149:65,84:27,34:0.7095:2,2:23.6:1:31.1:1:1:1.02613:60:298:0.7095:0:1.1 -3 36109777 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23605;SOR=0;LSEQ=AAAATTAGTATTTTCCAATA;RSEQ=TACCCTTAGCCAGCAGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:91,105:0.0101:2,2:22.5:1:32:0:1:1.15:60:4:0.0102:0:2 0/0:209:0:0,0:89,120:0:2,0:23.6:1:31.2:1:1:0:60:51.25:1:0:0.8 -3 36515636 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.49882;SOR=Inf;LSEQ=ATCTATTATGGGTACCCACA;RSEQ=CCCTACAGCAGCTGGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:126,63:0:2,0:25.2:1:30.2:1:1:0:60:36.8:1:0:0.3 0/1:195:2:1,1:118,75:0.0103:2,2:11.5:1:28.5:1:1:1.5695:60:4:0.0105:0:3.5 -3 36515638 . C T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03008;SOR=Inf;LSEQ=CTATTATGGGTACCCACATC;RSEQ=CTACAGCAGCTGGCCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:131,66:0:2,0:24.8:1:30.6:1:1:0:60:38.4:1:0:0.4 0/1:199:6:3,3:118,75:0.0302:2,2:19.3:1:30.5:1:0.68085:1.56958:60:12:0.0306:0:1 -3 36515716 . G A 236 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATATGTAACCCATCACAAAT;RSEQ=TGATGAGAATCACATTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:258:258:120,138:0,0:1:0,2:24.8:1:29.5:1:1:0:60:257:1:0:1.1 1/0:221:167:75,92:30,24:0.7557:2,2:25.6:1:28.9:1:0.21015:1.53032:60:166:0.758:0:1.1 -3 36515853 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10653;SOR=Inf;LSEQ=CTTGCTACTTCTCTCTCAAC;RSEQ=TCATCCTCATTGACCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:7,58:0:2,0:26.9:1:30.1:1:1:0:60:31.5:1:0:0.2 0/1:32:2:0,2:1,29:0.0625:1,0:9:1:31.5:1:1:0:60:4:0.0625:0:2 -3 37034946 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03755;LSEQ=GGATGGCGTAAGCTACAGCT;RSEQ=AAGGAAGAACGTGAGCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:55:54,1:44,4:0.534:2,1:23.3:1:27.1:1:0.18155:4.84:60:17.333:0.5253:0:1.1 0/1:123:5:5,0:110,8:0.0407:2,0:19.4:1:27.4:1:1:0:60:10:0.041:0:1.4 -3 37038235 . C T 69 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06663;SOR=Inf;LSEQ=AAAGTAGCAGGATGTTTGTG;RSEQ=GCTTCATGGAAGAGTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:124,275:0:2,0:25:1:30.3:1:1:0:60:65.5:1:0:0.1 0/1:476:5:2,3:184,287:0.0105:2,2:33.8:1:29.8:1:1:1.04:60:10:0.0105:0:1 -3 37040501 . C A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTAATGCTATCCCTCCCC;RSEQ=CTCCCCCACCCCACAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:27.5:1:1:0:21:4:1:0:3 -3 37040513 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCTCCCCCCTCCCCCACCC;RSEQ=ACAACAGTCCCCAGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29:1:1:0:21:4:1:0:3 -3 37040515 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCCCTCCCCCACCCCA;RSEQ=AACAGTCCCCAGTGTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:29.5:1:1:0:21:4:1:0:3 -3 37042325 . GA G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.51951;SOR=0;LSEQ=AAAAACAAAAACCAAGAAAA;RSEQ=AAAAAAAACTCTTCTAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:2,0:80,0:0.0244:1,0:8:1:32.3:1:1:0:60:4:0.0256:0.0122:0 0/0:53:0:0,0:52,1:0:1,0:20.6:1:27.5:1:1:0:59.6:7.833:1:0:0.5 -3 37042348 . A AT 40 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.77753;LSEQ=AAAAAAACTCTTCTAAGAGG;RSEQ=TTTTTTTTTCCTGGATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:3:3,0:111,2:0.0259:1,0:28:1:25.7:1:1:0:60:2:0.0196:0:1 0/1:99:2:2,0:92,5:0.0202:2,0:24:1:30.8:1:1:0:60:4:0.0206:0.0101:0 -3 37042373 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49873;SOR=0;LSEQ=TTTTTCCTGGATTAAATCAA;RSEQ=AAAATGGGAATTCAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:160,25:0.0105:2,2:37.5:1:30.5:1:0.25939:6.2953:60:4:0.0118:0:1 0/0:187:0:0,0:161,25:0:2,0:32:0:13:0:1:0:60:0:0:0:4 -3 37042757 . T C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51703;SOR=0;LSEQ=ACCTGCAGAGACCTCTGATA;RSEQ=ATGTTTCTTGATGGAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:0.2308:0,0:40.7:1:34:1:1:0:60:6:0.2308:0:1 0/0:6:0:0,0:0,6:0:0,0:18.8:1:26.7:1:1:0:60:5:1:0:0 -3 37046012 . AT A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.37424;SOR=3.79796;LSEQ=ATATATTCATTCTGAAATGT;RSEQ=TTTTTGCCTAGGTCTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:1:0,1:91,240:0.003:2,0:48:0:30:0:1:0:60:2:0.003:0:0 0/1:352:4:3,1:115,233:0.0114:2,2:10.5:1:28.3:1:0.11153:6.05:60:8:0.0115:0.0057:0.8 -3 37048292 . C CA 58 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.14245;SOR=5.16859;LSEQ=ACAAGAGCAAAACTCCGTCT;RSEQ=AAAAAAAAAAAAAATCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:13,1:0.125:1,0:29:1:28.5:1:1:0:60:4:0.125:0:1.5 0/1:9:4:3,1:3,1:0.4444:2,2:12:1:29.3:1:1:1:60:8:0.4444:0.2222:0 -3 37048417 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=TATTGTTGATATGATTTTCT;RSEQ=TTTTCCCCTTGGGATTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:137,23:0:2,0:22.8:1:31.6:1:1:0:60:79:1:0:0.1 0/1:179:2:1,1:145,32:0.0112:2,2:27:1:30.5:1:0.33557:4.47744:60:4:0.0114:0:1 -3 37048633 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.71837;LSEQ=TAAAAAATAAAATTGCTTCT;RSEQ=AGTTTTCAGGGTAATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:16:3,13:9,88:0.1416:2,2:25.1:1:31.7:1:0.37255:2.24:60:32:0.1416:0:1 1/0:153:86:13,73:13,54:0.5621:2,2:25.6:1:31.4:1:0.52049:1.34914:60:85:0.5592:0:1.1 -3 37050240 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24196;SOR=Inf;LSEQ=TAAGACCTCGCTTTTGCCAG;RSEQ=ACATCTTGGGTTTTATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:127,14:0:2,0:24.9:1:31.7:1:1:0:60:282:1:0:0.5 0/1:137:2:1,1:119,16:0.0146:2,2:17:1:31:1:0.23358:7.24458:60:4:0.0148:0:1 -3 37050254 . T C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.049;LSEQ=TGCCAGGACATCTTGGGTTT;RSEQ=ATTTTCAAGTACTTCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:67:59,8:98,22:0.3583:2,2:23:1:31.4:1:0.30266:1.65:60:66:0.3568:0:1.1 0/1:189:5:5,0:144,40:0.0265:2,0:23.2:1:30.8:1:0.586:0:60:10:0.0266:0:1 -3 37053568 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.20213;LSEQ=CCGTGGACAATATTCGCTCC;RSEQ=TCTTTGGAAATGCTGTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:94:43,51:272,413:0.1207:2,2:27.9:1:31.3:1:0.26494:1.28:60:188:0.1222:0:1.1 0/1:943:393:173,220:258,291:0.4168:2,2:28:1:30.3:1:0.3888:1.12732:60:195.5:0.4186:0:1.1 -3 37055703 . G A 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=4;SSF=0.05;SOR=Inf;LSEQ=GTGGGTGGGTGGGTGGGTGG;RSEQ=TGGATGGATGGATGGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:18.8:1:32:1:1:0:60:24:1:0:0.1 1/0:4:2:2,0:2,0:0.5:0,0:16.5:1:29.5:1:1:0:55:4:0.5:0:3 -3 37055711 . AT GA 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.00585;SOR=Inf;LSEQ=GTGGGTGGGTGGGTGGATGG;RSEQ=GGATGGGAGGATGGGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:0:1,0:21.9:1:29.4:1:1:0:60:13:1:0:0.1 1/0:7:4:4,0:3,0:0.5714:0,0:14.8:1:31:1:1:0:57.5:8:0.5714:0.1429:1.5 -3 37055712 . T TGGGA 27 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.53333;SOR=0;LSEQ=TGGGTGGGTGGGTGGATGGA;RSEQ=GGATGGGAGGATGGGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:0.1429:0,0:39:0:27.9:1:1:0:60:4:0.1538:0:0 0/0:7:0:0,0:3,0:0:0,0:16:1:31.3:1:1:0:60:6:1:0:0 -3 37056078 . C A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25226;SOR=Inf;LSEQ=GGAAATCCACTCACAGGAAA;RSEQ=ACCCACAGGGAATTTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:44,184:0:2,0:22.7:1:31.8:1:1:0:60:113:0.9956:0:0.2 0/1:264:3:3,0:60,201:0.0114:2,0:8.3:1:21.3:1:0.0131:0:60:2:0.0076:0:3 -3 37056209 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTCCTAAGTCTGTGCTC;RSEQ=GCCCTCCCACATGTGCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:0,17:0.1053:1,2:21.5:1:29:1:0.10526:0:60:4:0.1111:0:1 0/0:9:0:0,0:0,9:0:0,0:23.8:1:31.9:1:1:0:60:18:1:0:0 -3 37061720 . G C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11316;LSEQ=CATCTGGCCTCAAATCTTCT;RSEQ=GCCACCACATACACCATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:56:45,11:99,12:0.3353:2,2:22.7:1:30.5:1:0.15316:2.00761:60:55:0.3333:0:1.1 0/1:149:8:6,2:119,22:0.0537:2,2:28.5:1:30.4:1:0.61546:1.79459:60:16:0.0552:0:1 -3 37062040 . T C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.44994;LSEQ=GCCCAGATTTTTGCCTGTTA;RSEQ=TTAGGAACTTTCTTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:15:1,14:9,106:0.1154:2,1:28.7:1:32.9:1:1:1.18719:60:30:0.1154:0:1.1 1/0:128:77:8,69:5,46:0.6016:2,2:22.6:1:32:1:1:1.07:60:154:0.6063:0:1.1 -3 37067050 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.50776;LSEQ=ATTTGGGGACCTGTATATCT;RSEQ=TACTTCTTATTCTGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:6,0:45,0:0.1176:1,0:32:1:33.5:1:1:0:60:12:0.1176:0:1.3 1/0:54:29:29,0:25,0:0.537:1,1:21.4:1:32.3:1:1:0:59.5:58:0.537:0:2 -3 37067099 . A T 146 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=21.000;MSILEN=1;SSF=0;SOR=0.14202;LSEQ=ATATATATATATATATATAT;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:31:29,2:25,1:0.4079:1,2:20.2:1:29.6:1:1:1.70837:55.9:62:0.5167:0:2.7 0/1:136:12:9,3:61,9:0.0882:2,2:18.5:1:25.2:1:0.37055:2.23219:55:5:0.1282:0:1.8 -3 37067120 . T A 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00335;SOR=10.86633;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=AATACAGACTTTGCTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:1:1,0:135,37:0.0057:2,0:32:0:28:0:1:0:40:2:0.0063:0:7 0/1:253:15:13,2:175,63:0.0593:2,2:11.5:1:23.9:1:0.36695:2.33:56.5:2:0.0448:0:2.4 -3 37067565 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50161;SOR=0;LSEQ=TAAAACTGCCTTCTAACTTT;RSEQ=GCTTTTCATGAATCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:19,104:0.016:2,2:26.5:1:28:1:0.29548:5.36:60:4:0.0164:0:1 0/0:105:0:0,0:19,86:0:2,0:20.9:1:30.3:1:1:0:60:210:1:0:0 -3 37070106 . C T 102 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.013;SOR=7.07658;LSEQ=TTGTCAGATAAGCAGTCTAC;RSEQ=AGAGAACAGACTGATCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:3,0:20,0:0.1304:1,0:30.3:1:30.3:1:1:0:60:6:0.1304:0:1.3 1/0:17:9:9,0:8,0:0.5294:0,0:17:1:32.2:1:1:0:60:18:0.5294:0:1.1 -3 37070208 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20369;SOR=0;LSEQ=TTGCTCCTCCAAAATGCAAC;RSEQ=CACAAAATTTGGCTAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:114,12:0.0156:2,0:11.5:1:30.5:1:1:0:60:4:0.0156:0:1 0/0:155:0:0,0:138,17:0:2,0:23:1:30.1:1:1:0:60:37.75:1:0:0.1 -3 37070437 . G A 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGAGGGTACGTAAACGCT;RSEQ=TGGCCTGCCTGGGATGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:85,240:0:2,0:23.5:1:31.9:1:1:0:60:80.25:1:0:0.1 0/1:385:23:8,15:111,250:0.0597:2,2:20.4:1:28.7:1:0.64987:1.20:60:22:0.0588:0:1.2 -3 37070441 . C A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3838;SOR=3.34312;LSEQ=AGGGTACGTAAACGCTGTGG;RSEQ=CTGCCTGGGATGCATAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:1,0:70,223:0.0034:2,0:1:0:26:0:0.2415:0:60:2:0.0035:0:1 0/1:354:4:2,2:102,248:0.0113:2,2:17.5:1:23.8:1:0.58404:2.42:60:3:0.0087:0:2.3 -3 37070444 . G A 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13113;SOR=Inf;LSEQ=GTACGTAAACGCTGTGGCCT;RSEQ=CCTGGGATGCATAGGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:65,208:0:2,0:24.1:1:32:1:1:0:60:53.6:1:0:0.1 0/1:333:4:2,2:96,231:0.012:2,2:14.3:1:27.5:1:0.58473:2.40:60:8:0.0122:0:1 -3 37081627 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50707;SOR=Inf;LSEQ=TGGTCAATGAAGTGGGGTTG;RSEQ=TAGGATTCTATTACTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:128,11:0:2,0:21.9:1:31.5:1:1:0:60:278:1:0:0.1 0/1:181:2:1,1:149,30:0.011:2,2:15:1:29:1:0.314:4.90237:60:4:0.011:0:1 -3 37083740 . A G 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.0084;LSEQ=TTCAGCTTTTCCTTAAAGTC;RSEQ=CTTCATTTTTATTTTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:591:71:48,23:304,216:0.1201:2,2:24.2:1:30.5:1:0.15712:1.48:60:142:0.1224:0:1.1 0/1:844:413:247,166:258,170:0.4893:2,2:24.4:1:30.3:1:0.94387:1.01994:60:205.5:0.4905:0:1.1 -3 37085559 . T C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTCTTTTTTTAAGACGGAGT;RSEQ=TTGCTCTTGTCACCCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:30.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:42:1:28.5:1:1:0:60:4:1:0:0 -3 37089174 . G A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14046;SOR=Inf;LSEQ=TTCTCTTTGGAAATTGATGA;RSEQ=GTGTGACAGCCATTCTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:80,207:0:2,0:26:1:31.4:1:1:0:60:94.667:1:0:0.1 0/1:387:4:3,1:130,253:0.0103:2,2:11:1:25.8:1:0.11934:5.81:60:8:0.0104:0:1 -3 37089840 . CT C 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0.95876;LSEQ=GTTTGTCAGGATGAAAAACT;RSEQ=TTTTTAAGTGTTTAGGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:32:32,0:23,0:0.5818:1,1:19.7:1:31.6:1:1:0:60:31:0.5741:0.1455:0.2 1/0:35:20:20,0:15,0:0.5714:1,1:23.1:1:31.7:1:1:0:60:40:0.5714:0.1143:0.1 -3 37090274 . C T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.97659;LSEQ=ATATTCAGCAGTCCCATTTA;RSEQ=AGTTTTAACGCCTAAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:14:12,2:68,28:0.1273:2,2:20.9:1:30.6:1:0.34295:2.45:60:28:0.1308:0:1 0/1:79:37:32,5:32,10:0.4684:2,2:22.9:1:30.3:1:0.26814:1.98:60:36:0.4615:0:1 -3 37090552 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22405;SOR=Inf;LSEQ=ACCCCAGGACTAGGACAGGA;RSEQ=CTCATACAATCTTTAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:28,135:0:2,0:25.3:1:31:1:1:0:60:31.6:1:0:0.1 0/1:147:2:1,1:29,116:0.0136:2,2:8.5:1:24.5:1:0.36763:3.95:60:4:0.0138:0:3 -3 37091917 . G T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36289;SOR=3.15363;LSEQ=GTGCACATCCCATCAGCCAG;RSEQ=ACACCAGTGTATGTTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:1:1,0:202,34:0.0042:2,0:43:0:12:0:1:0:60:0:0:0:1 0/1:227:3:1,2:173,51:0.0132:2,2:15.3:1:22:1:0.13681:6.7105:60:2:0.009:0:3 -3 37092173 . GTTC G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0;SOR=0.11637;LSEQ=ATTTATGCACTGTGGGATGT;RSEQ=TTCTTTCTCTGTATTCCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:149:47,102:97,194:0.3379:2,2:25:1:32:1:0.74797:1.08487:59.9:298:0.3394:0.0363:0.1 0/1:447:25:8,17:145,277:0.0559:2,2:24.2:1:31.5:1:1:1.11212:60:50:0.0566:0.0045:0.1 -3 37107012 . C G 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGGTATACTAGACTATCT;RSEQ=TTTGCAGAACAGTTTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:246,107:0:2,0:23.9:1:31.2:1:1:0:60:69.6:1:0:0.2 0/1:362:55:41,14:222,85:0.1519:2,2:24.4:1:31.6:1:0.86969:1.12:60:110:0.1541:0:1 -3 37107022 . C A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.35856;LSEQ=TAGACTATCTCTTTGCAGAA;RSEQ=AGTTTGTAGTTAAGTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:33:22,11:253,123:0.0807:2,2:25.8:1:29.3:1:1:1.02841:60:32:0.0794:0:1.1 1/0:434:217:148,69:150,66:0.5:2,2:24.2:1:29.7:1:0.83576:1.05941:60:107.5:0.4988:0:1.1 -3 37789382 . G C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26573;SOR=6.78852;LSEQ=GTTACACACCACCACGCCTA;RSEQ=CTAATTTTTTTTGTGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:25:1:31.3:1:1:0:60:6:0.3333:0:1 1/1:5:4:4,0:1,0:0.8:0,0:20.5:1:31.3:1:1:0:60:8:0.8:0:1.3 -3 37789529 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22094;SOR=0;LSEQ=CTTGTTGTTGCAAAATTTTG;RSEQ=AACATTTCAATCACCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:121,54:0.0113:2,2:12.5:1:31:1:0.52613:2.22947:60:4:0.0117:0:1 0/0:199:0:0,0:145,54:0:2,0:21.5:1:30.5:1:1:0:60:48.75:1:0:0.1 -3 37789630 . G C 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=3.68518;LSEQ=CACAAAGGGAAAGAGGAAAG;RSEQ=CACCTGATATATGTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:9:1,8:101,150:0.0345:2,2:21.8:1:32.3:1:0.09384:5.36114:60:18:0.035:0:1 0/1:309:36:15,21:108,164:0.1165:2,2:20.4:1:31.5:1:0.85737:1.08:60:72:0.1184:0:1.1 -3 37789655 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50415;SOR=Inf;LSEQ=TGATATATGTTCTCTAGGCT;RSEQ=TTTAGAAAACATGGAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:46,106:0:2,0:21.8:1:30.1:1:1:0:60:75:1:0:0.1 0/1:188:2:1,1:54,132:0.0106:2,2:34.5:1:29.5:1:0.50063:2.43:60:4:0.0108:0:1 -3 37789755 . AG GT 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49626;SOR=Inf;LSEQ=TGGGTACTGTTCAAAAAGGA;RSEQ=GCCCCGCAAGTATTACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:22,39:0:2,0:22.4:1:31:1:1:0:60:60:1:0:0.1 0/1:64:2:1,1:29,32:0.0313:2,2:8.5:1:28.4:1:1:1.10:60:4:0.0313:0.0156:0.5 -3 37791729 . G A 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGAAAGAGAATATGGTA;RSEQ=TTTCAAAGTTTGAGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:0:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 38178224 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCACTCCCCCATGCCCA;RSEQ=CCCAGGGAGACAAAGCGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:35.5:1:30:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 38179665 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCCGTTTCCCACTCCCA;RSEQ=CTCGGGGAGCACAGCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:27.5:1:1:0:60:4:1:0:1 -3 38180103 . C CGGCGG 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=4.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=GCTTCTCGGAAAGCGAAAGC;RSEQ=GGCGGGGCGGGGCGGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:162,25:0:2,0:24.8:1:30.8:1:1:0:60:45.75:1:0:0.2 0/1:131:8:6,2:96,27:0.0611:2,2:20.9:1:29.9:1:1:1.18362:60:16:0.0615:0.0153:0.1 -3 38180548 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.23599;SOR=Inf;LSEQ=GTCCCCTTCCTGGCCTCGTA;RSEQ=CTGGGGGGTGAGGAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:46,144:0:2,0:26.5:1:31.2:1:1:0:60:62.333:1:0:0.1 0/1:180:2:1,1:57,121:0.0111:2,2:16.5:1:28.5:1:0.54184:2.11:60:4:0.0112:0:1.5 -3 38181293 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1841;SOR=Inf;LSEQ=TGGGACAGCGGCTGGATCCT;RSEQ=ACTGTGGGTAAAGAGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:127,36:0:2,0:22.1:1:31.3:1:1:0:60:26.167:1:0:0.1 0/1:123:2:1,1:97,24:0.0163:2,2:16:1:26.5:1:0.36652:3.98037:60:4:0.0169:0:1 -3 38181876 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45531;SOR=2.27607;LSEQ=CCACCCTTGTGCTCTGCACC;RSEQ=AGGGCATATGCCTGAGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:2:0,2:233,187:0.0047:2,0:23.5:1:24:0:0.2:0:60:4:0.0048:0:2 0/1:467:5:2,3:273,189:0.0107:2,2:26.8:1:25.2:1:0.40593:2.16303:60:4:0.0087:0:1.2 -3 38182112 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24878;SOR=Inf;LSEQ=ATGCATGAAGCCCTGCCCTG;RSEQ=GGTCCAGATACTGGGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:118,174:0:2,0:22.9:1:30.6:1:1:0:60:35.5:1:0:0.1 0/1:297:3:2,1:118,176:0.0101:2,2:8.3:1:26.7:1:0.56757:2.97:60:6:0.0102:0:2 -3 38182407 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10492;SOR=Inf;LSEQ=GGGCCTCTGGATTGTCAGCC;RSEQ=TCCCTCCCCAAGGACTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:43,189:0:2,0:24.3:1:30.3:1:1:0:60:115:0.9957:0:0.1 0/1:209:3:2,1:40,165:0.0144:2,2:6.7:1:28:1:0.10445:8.13:60:6:0.0149:0:1.3 -3 38182530 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50982;SOR=0;LSEQ=TGCCAGGGGTACTTAGATGG;RSEQ=GGATGGCTGTTGTTAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:137,28:0.012:2,0:19:1:28.5:1:1:0:60:4:0.0122:0:1 0/0:123:0:0,0:99,24:0:2,0:21.4:1:30.8:1:1:0:60:29.75:1:0:0.1 -3 38182539 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51388;SOR=0;LSEQ=TACTTAGATGGGGGATGGCT;RSEQ=TTGTTAACCCTGGGGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:169,27:0.0101:2,2:16.5:1:29:1:0.26345:6.16464:60:4:0.0102:0:1 0/0:139:0:0,0:114,25:0:2,0:23.1:1:31.9:1:1:0:60:68.5:1:0:0.1 -3 38183201 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAGACCAGGCTTGGCTG;RSEQ=GGGAGAGCTGGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:24.5:1:30.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 38545856 . C CA 28 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGCAAGACCCTATCT;RSEQ=AAAAAAAAAAGTTCCTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:28.5:1:1:0:60:4:1:0:0.5 -3 38548021 . T C 232 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATCATCTTGTTGGAATGA;RSEQ=ACATAATTCTTGAAAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:131,151:0:2,0:26.8:1:29.3:1:1:0:60:140:1:0:0.1 0/1:347:171:89,82:87,88:0.4928:2,2:26.4:1:31.3:1:0.66881:1.10:60:170:0.4942:0:1.1 -3 38548104 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50104;SOR=Inf;LSEQ=TGAATTCCAGAATGTACTCT;RSEQ=AGCGCACATAAAGAAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:26,94:0:2,0:23.4:1:31.1:1:1:0:60:59:1:0:0.1 0/1:140:2:1,1:38,100:0.0143:2,2:6.5:1:28.5:1:0.48099:2.61:60:4:0.0145:0:2 -3 38548248 . G C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=TGTTTAATTTCTCAAATGCA;RSEQ=TTTTTCTTGGTATCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:20:1:31:1:1:0:60:4:0.3333:0:1 0/0:5:0:0,0:0,5:0:0,0:15.8:1:30.4:1:1:0:60:10:1:0:0 -3 38949363 . A C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAACTGAATAAATGAATT;RSEQ=TTTCAATTTGATTGGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:33.5:1:1:0:60:4:1:0:1.5 -3 38951372 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49922;SOR=Inf;LSEQ=CGTGCCTGGCCAATTTTCTT;RSEQ=AAGTTTCTAACAGAATTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:15,17:0:2,0:25:1:31.8:1:1:0:60:31:1:0:0.1 0/1:40:2:1,1:20,18:0.05:2,2:22.5:1:29:1:1:1.10818:60:4:0.0513:0:1 -3 39452917 . AT A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=TGCATAAGAATTGCCCAGAT;RSEQ=TTTTTTTAAATGCCAGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:72,4:0:2,0:23.2:1:31.2:1:1:0:60:152:1:0:0.1 0/1:77:2:2,0:67,8:0.026:2,0:28.5:1:32:0:1:0:60:4:0.026:0:0 -3 39452934 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24699;SOR=Inf;LSEQ=GATATTTTTTTTAAATGCCA;RSEQ=TGTCCAGGCATTTTTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:103,16:0:2,0:21.2:1:32:1:1:0:60:58.5:1:0:0.1 0/1:122:3:1,2:95,24:0.0246:2,2:12:1:25.7:1:0.11448:7.73378:60:6:0.0248:0:1 -3 39452940 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49833;SOR=Inf;LSEQ=TTTTTTAAATGCCAGTGTCC;RSEQ=GGCATTTTTTTTTCAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:114,20:0:2,0:21.7:1:30.1:1:1:0:60:43.667:1:0:0.1 0/1:139:2:1,1:107,30:0.0144:2,2:5.5:1:29.5:1:0.39756:3.52481:60:4:0.0146:0:1.5 -3 39452944 . A AT 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.20461;SOR=0.23405;LSEQ=TTAAATGCCAGTGTCCAGGC;RSEQ=TTTTTTTTTCAATCCCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:4:3,1:111,26:0.0284:2,2:32:1:31:1:0.57706:1.41915:60:8:0.0296:0:0 0/0:148:1:1,0:111,36:0.0068:2,0:38:0:32:0:1:0:60:2:0.0069:0:0 -3 39453057 . C T 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.57568;LSEQ=GATGTCTGTACTTTTGGTAC;RSEQ=TAGATGATGTAAGAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:402:251:113,138:69,82:0.6244:2,2:25.7:1:30.5:1:0.91784:1.02757:60:124.5:0.6256:0:1.1 0/1:493:241:126,115:122,130:0.4888:2,2:26.8:1:30:1:0.41786:1.17:60:39.167:0.4845:0:1.1 -3 39453135 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17911;SOR=0;LSEQ=TTTAATAATCTGCCACTCTT;RSEQ=GCAGGGAGCTCACTCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:51,117:0.0118:2,2:20.5:1:30:1:0.51946:2.28:60:4:0.0119:0:1.5 0/0:231:0:0,0:70,159:0:2,0:23.2:1:30.4:1:1:0:59.9:228:0.9913:0:0.3 -3 39453155 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5023;SOR=Inf;LSEQ=GGCAGGGAGCTCACTCAGTG;RSEQ=GTTTGATGTGGTGGATGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:29,89:0:2,0:24.2:1:31:1:1:0:58.8:38.333:0.9914:0:0.2 0/1:143:2:1,1:29,111:0.014:2,2:9.5:1:27.5:1:0.37908:3.78:50:4:0.0142:0:1 -3 39453160 . G A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGCTCACTCAGTGGGTTT;RSEQ=ATGTGGTGGATGCTGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:22,86:0:2,0:23.6:1:31.2:1:1:0:58.3:35:1:0:0.2 0/1:129:20:5,15:19,90:0.155:2,2:25:1:28.9:1:0.53079:1.57:58:40:0.155:0:1 -3 39453165 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20855;SOR=0;LSEQ=TCACTCAGTGGGTTTGATGT;RSEQ=GTGGATGCTGGCTCGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:17,79:0.0204:2,2:16.5:1:26:0:0.33516:4.54:50:4:0.0208:0:1 0/0:116:0:0,0:19,97:0:2,0:24.3:1:30.7:1:1:0:57.8:232:1:0:0.2 -3 41265450 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21418;SOR=Inf;LSEQ=CATTTAACAGGTATCCCAGT;RSEQ=ACTTAGGAGTATTAATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:136,12:0:2,0:25.3:1:32.4:1:1:0:60:147:1:0:0 0/1:128:2:1,1:105,20:0.0156:2,2:16.5:1:27:1:0.30446:5.14794:60:4:0.0159:0:1.5 -3 41265953 . CT C 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.34773;SOR=0.4821;LSEQ=AATGGGTCATATCACAGATT;RSEQ=TTTTTTTTAAATTAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:7:5,2:145,20:0.0407:2,2:22.1:1:31.8:1:0.22053:2.87497:60:14:0.0412:0.0116:0 0/1:150:3:3,0:125,21:0.02:2,0:40:1:31.7:1:1:0:60:6:0.0201:0:0 -3 41265962 . TA T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.50029;SOR=0;LSEQ=TATCACAGATTCTTTTTTTT;RSEQ=AATTAAAGTAACATTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:2,0:158,33:0.0104:2,0:25:1:28.5:1:1:0:60:4:0.0106:0.0052:4.5 0/0:172:0:0,0:143,28:0:2,0:23.1:1:28.2:1:1:0:60:84.5:0.9941:0:0.2 -3 41266226 . A G 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGGATTTTCTCAGTCCTTC;RSEQ=CTCAAGAACAAGTAGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:34:14,20:221,319:0.0591:2,2:25.7:1:30.8:1:1:1.01:60:68:0.0598:0:1.1 0/0:639:0:0,0:294,344:0:2,0:26.7:1:29.4:1:1:0:60:158.5:1:0:0.2 -3 41266750 . G A 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTTGAAGTAAATGCTCAA;RSEQ=GGGAGTAGTTTCAGAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:168,148:0:2,0:22.5:1:31.8:1:1:0:60:157:1:0:0.1 0/1:254:19:11,8:129,106:0.0748:2,2:19.5:1:29.1:1:1:1.13:60:18:0.072:0:1.1 -3 41267385 . G T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10881;SOR=0;LSEQ=TTCTTTATGTGGTTTTCATG;RSEQ=AGCATTGGACACCTCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:2,1:53,187:0.0123:2,2:38.7:1:29.3:1:0.1293:6.98:60:6:0.0124:0:1 0/0:266:0:0,0:75,191:0:2,0:23.3:1:30.6:1:1:0:60:43.333:1:0:0.1 -3 41267525 . A G 87 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=57.77024;LSEQ=ATGACACCATTCCACCTCAG;RSEQ=TAATCAGGCATTAGATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:0,22:0.0435:1,0:1:0:31:0:1:0:60:2:0.0455:0:1 1/0:9:7:0,7:0,2:0.7778:0,0:23.7:1:31.1:1:1:0:60:14:0.7778:0:1 -3 41268676 . GAT G 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.29711;SOR=1.5937;LSEQ=CAAGATTCCTTGACTAACAA;RSEQ=ATATATATATATCTTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:9:7,2:229,96:0.0269:2,2:25.6:1:32.2:1:1:1.47:60:18:0.0271:0:0 0/1:331:14:10,4:221,95:0.0423:2,2:23.6:1:31.3:1:1:1.07:60:28:0.0428:0.0091:0.1 -3 41274764 . C A 231 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACCTCCTAAGGCTAGAA;RSEQ=AGATATTTAGGATTGATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:218:197,21:0,0:1:0,2:22.9:1:30:1:1:0:60:53.5:1:0:1.1 1/1:221:220:184,36:0,0:0.9955:0,2:22.2:1:29.7:1:1:0:60:54:0.9954:0:1.1 -3 41274905 . C A 152 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.56998;LSEQ=CAGAACTGTCTTTGGACTCT;RSEQ=AGGAATCTTTCAGATGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:672:1:0,1:315,356:0.0015:2,0:38:0:28:0:1:0:60:2:0.0015:0:1 0/1:773:40:20,20:346,387:0.0517:2,2:20.2:1:28.7:1:0.74766:1.12:60:80:0.0522:0:1.1 -3 41275350 . C T 223 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ACCCACCATCCCACTGGCCT;RSEQ=TGATAAAGGTAAATTGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:168:56,112:74,130:0.4492:2,2:26.2:1:30.3:1:0.58579:1.13806:60:167:0.4514:0:1.1 0/0:425:0:0,0:178,246:0:2,0:24.7:1:30.9:1:1:0:60:37.545:0.9976:0:0.1 -3 41275402 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23941;SOR=0;LSEQ=CCTTTGTTGCAGAATTGAAA;RSEQ=TGAAGCATCTCTAGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:46,124:0.0116:2,2:26.5:1:32:1:0.473:2.68:60:4:0.0117:0:1 0/0:179:0:0,0:42,137:0:2,0:23.3:1:30:1:1:0:60:178:1:0:0.1 -3 41277040 . C T 83 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00109;SOR=22.39046;LSEQ=GCTGCTTTGAATTAGTGCTG;RSEQ=CAGGAGGCCTCTTTTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:1,0:28,0:0.0345:1,0:27:0:32:0:1:0:60:2:0.0345:0:1 0/1:15:7:7,0:8,0:0.4667:0,0:25.3:1:29.7:1:1:0:60:14:0.4667:0:1 -3 41278759 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATTGTTAGGTTTACAAC;RSEQ=ATGCAGCTCTTGAGACCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 41279324 . GA G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.50046;SOR=0;LSEQ=TTTAATGTGAGGTGCAAAGA;RSEQ=AAAAAAAATGTATCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:25,0:0.0741:1,0:41.5:1:30:1:1:0:60:4:0.0769:0:0 0/0:20:0:0,0:20,0:0:1,0:14.2:1:29.3:1:1:0:60:40:1:0:0.2 -3 41279408 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24405;SOR=Inf;LSEQ=AATGTTGGAGTTACTTGTTC;RSEQ=TTTTGTAATCTGAAAGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:138,10:0:2,0:23.8:1:31.5:1:1:0:60:48.333:1:0:0.4 0/1:145:2:1,1:135,8:0.0138:2,2:33.5:1:29.5:1:0.12069:15.97515:60:4:0.0139:0:1 -3 41279440 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22362;LSEQ=GAAAGTATGCTTTAAAAAAA;RSEQ=TTAGTGTACTTTTGAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:122:104,18:129,23:0.4453:2,2:22.9:1:31.7:1:1:1.03:60:39.667:0.4474:0:1.1 0/1:303:46:35,11:205,52:0.1518:2,2:19.5:1:31.1:1:0.5581:1.23811:60:45:0.1495:0:1.1 -3 41279651 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24068;SOR=Inf;LSEQ=AGAGCCGGTTTGCTCATCTG;RSEQ=GAAACCAGTGTTGGCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:33,170:0:2,0:25.3:1:30.4:1:1:0:60:24.375:1:0:0 0/1:196:2:1,1:30,164:0.0102:2,2:14:1:32:1:0.29199:5.39:60:4:0.0103:0:1 -3 41279657 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24653;SOR=Inf;LSEQ=GGTTTGCTCATCTGGGAAAC;RSEQ=AGTGTTGGCAGAAAAGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:17,164:0:2,0:26:1:32.1:1:1:0:60:59.333:1:0:0 0/1:179:2:1,1:23,154:0.0112:2,2:30:0:32:0:0.25083:6.58:60:4:0.0112:0:1 -3 41280525 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21311;SOR=Inf;LSEQ=TGACAAGTTTGCTGCTGAAC;RSEQ=TTGGATGCCCTAACCTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:191,9:0:1,0:23.8:1:30.9:1:1:0:60:32.333:1:0:0.1 0/1:172:2:1,1:164,6:0.0116:1,2:8.5:1:30.5:1:0.07997:25.38307:60:4:0.0117:0:1 -3 41443220 . C A 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCCACTCAATACTTCCACC;RSEQ=CAATTTCTCAATTTCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:20:10,10:168,174:0.0552:2,2:19.9:1:30:1:1:1.04:60:40:0.056:0:1.2 0/0:451:0:0,0:234,217:0:2,0:25.7:1:30.4:1:1:0:60:149.333:1:0:0.3 -3 41443267 . C T 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCAGTTATACAAGGGATA;RSEQ=ATTTGGCATACAGACTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:137,178:0:2,0:24.6:1:32.2:1:1:0:60:314:0.9968:0:0.2 0/1:376:97:43,54:125,152:0.258:2,2:24.2:1:28.8:1:0.90618:1.03266:60:96:0.2588:0:1.1 -3 41443310 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21536;SOR=0;LSEQ=CATTGACTGCACTAAGTCCA;RSEQ=TTTGGCTTTAATGGAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:63,126:0.0105:2,2:11:1:27.5:1:1:1.99:60:4:0.0105:0:1 0/0:220:0:0,0:78,142:0:2,0:25.2:1:31.1:1:1:0:60:219:1:0:0.3 -3 43176797 . T G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1516;SOR=0.26682;LSEQ=CTTTCTTTTCTCCTTCTATT;RSEQ=TCTCATCGTGTGTGTATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:13,0:10,0:0.5652:0,1:24.3:1:33.2:1:1:0:60:26:0.5652:0:1.8 0/1:12:3:3,0:9,0:0.25:0,0:8.7:1:31.7:1:1:0:60:6:0.25:0:2 -3 43176831 . T C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00224;SOR=0.15294;LSEQ=GTATCCATTGTAGCTCAGGC;RSEQ=CATTAAAAGACTGATGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:22:22,0:11,0:0.6667:0,1:24.3:1:30.9:1:1:0:60:44:0.6667:0:1.5 0/1:22:5:3,2:17,0:0.2273:1,2:25:1:31.2:1:0.04329:0:60:10:0.2381:0:1.4 -3 43177020 . A T 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.61791;SOR=1.09664;LSEQ=TAATCCCACTGAATATTAGA;RSEQ=ACATACAAGACTATCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:263:138:57,81:51,74:0.5247:2,2:21.1:1:28.9:1:1:1.02:60:137:0.5269:0:1.1 1/0:325:178:78,100:65,82:0.5477:2,2:26.8:1:28.5:1:1:1.01621:60:88:0.55:0:1.1 -3 43177084 . TA T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23242;SOR=Inf;LSEQ=TCAAGGAAAGTCAAAATAAC;RSEQ=ATTAGAGCAGTGCTTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:20,103:0:2,0:22.4:1:29.4:1:1:0:60:40:1:0:0.5 0/1:115:2:1,1:15,98:0.0174:2,2:22:1:28.5:1:0.25995:6.36:60:4:0.0175:0:2 -3 43177107 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22967;SOR=Inf;LSEQ=TTAGAGCAGTGCTTATGTTT;RSEQ=CTTTTTCAATTTTCATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:4,65:0:2,0:24.6:1:31.5:1:1:0:60:138:1:0:0.3 0/1:64:2:1,1:4,58:0.0313:2,2:19.5:1:31:1:0.15129:13.08:60:4:0.0313:0:1.5 -3 43359194 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49492;SOR=Inf;LSEQ=AGCCCGGTCCTACCTCAGGG;RSEQ=CATCCATCTCCCTCCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,16:0:2,0:29.4:1:30.4:1:1:0:60:23:1:0:0 0/1:29:2:1,1:12,15:0.069:2,2:22:1:28.5:1:1:1.24:60:4:0.069:0:1 -3 43360244 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAAAGAATCGAGTCCGGC;RSEQ=TGGTGGCTCATGCCTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:31.5:1:1:0:60:4:1:0:1 -3 44585886 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.37239;LSEQ=CTAGAAAGGGGAGAAGCCAT;RSEQ=TCACCCAACTCCAGAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:14,17:0.0313:2,0:1:0:28:0:1:0:49:2:0.0313:0:1 0/1:47:2:1,1:24,21:0.0426:2,2:43.5:1:29.5:1:1:1.1396:60:4:0.0426:0:1 -3 45924953 . T C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATTTCTTGGACATAATTC;RSEQ=TCTCAAACCTTTTCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1:0,0:29.3:1:30.4:1:1:0:60:14:1:0:1 1/1:2:2:1,1:0,0:1:0,2:13.5:1:26.5:1:1:0:60:4:1:0:2.5 -3 45925443 . G A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12533;SOR=Inf;LSEQ=GCCTTGGAACCAGAAAGGTG;RSEQ=CTCAGTGACAAATGAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:130,200:0:2,0:24.7:1:31.4:1:1:0:60:35.667:1:0:0.1 0/1:360:4:3,1:159,196:0.0111:2,2:21.5:1:27.3:1:0.33137:3.69:60:8:0.0113:0:1 -3 45925498 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25259;SOR=Inf;LSEQ=ATTCTGGGGTAGGTTGGGTC;RSEQ=TGAAGAAATCCTGAGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:90,150:0:2,0:27.2:1:31.5:1:1:0:60:59:1:0:0.1 0/1:278:3:2,1:114,161:0.0108:2,2:20.3:1:26:1:0.57294:2.81:60:6:0.0109:0:1 -3 45925574 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49917;SOR=0;LSEQ=CTCAGCCTCCTTGGGCACCA;RSEQ=AGAGGGCACTCAGCCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:12,75:0.0225:2,2:8:1:28:1:0.27222:6.04:60:4:0.0227:0:1 0/0:78:0:0,0:12,66:0:2,0:30.1:1:31.2:1:1:0:60:38:1:0:0.1 -3 46183820 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23788;SOR=Inf;LSEQ=GGGGGTATAAATACACATGT;RSEQ=CTTCTAGAAATAAGGCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:59,35:0:2,0:25.2:1:31.6:1:1:0:58.7:46:1:0:0.1 0/1:90:2:1,1:58,30:0.0222:2,2:14.5:1:29.5:1:1:1.91829:60:4:0.0227:0:2.5 -3 46183846 . A C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49897;SOR=Inf;LSEQ=AGAAATAAGGCTTCGTGTCA;RSEQ=ACTCTAGACGGGTGGAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:64,42:0:2,0:28.1:1:29.8:1:1:0:58.9:52:1:0:0.1 0/1:117:2:1,1:70,45:0.0171:2,2:22:0:33.5:1:1:1.54946:60:4:0.0179:0:2.5 -3 46183922 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52293;SOR=Inf;LSEQ=AGGGGCGGGGAGCAGCACGC;RSEQ=GTCTTCCTTTCCAGCTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:75,52:0:2,0:25.9:1:30.2:1:1:0:60:62.5:1:0:0.1 0/1:199:2:1,1:115,82:0.0101:2,2:29:1:31:1:1:1.39999:60:4:0.0102:0:1.5 -3 46183970 . T A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26686;SOR=Inf;LSEQ=TAGGTGAACCTGCCCTTGCC;RSEQ=TTGCTGATGTGCCCACTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:118,67:0:2,0:25.6:1:30.8:1:1:0:60:370:1:0:0.1 0/1:254:3:2,1:139,112:0.0118:2,2:20:1:27.7:1:1:1.61:60:6:0.0119:0:1 -3 46184057 . CAA C 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTACTTTTGCTAGTTAGTCT;RSEQ=GTCAATCTTGAGCGAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:183,126:0:2,0:24.9:1:29.9:1:1:0:60:43.143:0.9967:0:0.2 0/1:404:35:22,13:214,155:0.0866:2,2:25.2:1:30.3:1:0.72015:1.23:59.4:70:0.0875:0.0149:0.3 -3 46184620 . C G 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATTTCCCACAGCAATACTC;RSEQ=CTAAGACCGCACATCGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:183,235:0:2,0:24:1:30.7:1:1:0:60:37:1:0:0.1 0/1:463:45:21,24:184,233:0.0972:2,2:30.2:1:30.6:1:0.75457:1.11:60:90:0.0991:0:2.2 -3 46184629 . G A 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGCAATACTCCCTAAGACC;RSEQ=CACATCGCTGTTGGTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:189,218:0:2,0:25.2:1:30.8:1:1:0:60:57.143:1:0:0.1 0/1:469:18:6,12:208,242:0.0384:2,2:26:1:29.2:1:0.3397:1.71709:60:36:0.039:0:1.1 -3 46184639 . G C 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTAAGACCGCACATCGCT;RSEQ=TTGGTGCTGTAGATTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:207,210:0:2,0:25.1:1:31.6:1:1:0:60:40.7:1:0:0.1 0/1:444:61:31,30:184,198:0.1374:2,2:27:1:31.1:1:0.78292:1.11:59.8:122:0.1386:0:2.4 -3 46184680 . C T 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGATAGATTCAAGAGCCA;RSEQ=CCATTTCAGAGGAAGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:215,185:0:2,0:24.6:1:31.7:1:1:0:60:132.333:1:0:0.1 0/1:412:57:30,27:187,166:0.1383:2,2:21.1:1:29.3:1:1:1.01382:59.8:114:0.1404:0:2.4 -3 46184689 . G A 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TTCAAGAGCCACCCATTTCA;RSEQ=AGGAAGTCAAGTACCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:226,192:0:2,0:23.4:1:31.5:1:1:0:60:138.333:1:0:0.1 0/1:428:16:6,10:220,191:0.0374:2,2:19:1:30.4:1:0.30732:1.9168:60:32:0.0378:0:1.4 -3 46184725 . C G 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTTTCTCACATAATCGG;RSEQ=GTTCTTGTAAATATCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:482:0:0,0:245,237:0:2,0:25.4:1:30.5:1:1:0:60:47.2:1:0:0.1 0/1:529:77:42,35:245,203:0.1456:2,2:24:1:29.5:1:1:1.00574:59.8:18.25:0.1404:0:1.5 -3 46185176 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50239;SOR=Inf;LSEQ=ACCATCAGAGGCCCTTTGTT;RSEQ=GCTGATCTGACCCCAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:57,99:0:2,0:23.8:1:29.8:1:1:0:60:38:1:0:0.1 0/1:186:2:1,1:65,119:0.0108:2,2:18:0:32.5:1:1:1.82:60:4:0.011:0:1.5 -3 46185332 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2;SOR=Inf;LSEQ=AACCCCTTATCTTCTTTTTT;RSEQ=TGTTTTATTCTACACATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:25.6:1:32.6:1:1:0:60:16:1:0:0 0/1:7:2:0,2:1,4:0.2857:2,0:5.5:1:27:0:1:0:60:4:0.2857:0:1.5 -3 47058057 . A G 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACAAGGCAGCCTGCTTT;RSEQ=GAATATTTACATGATAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:30.3:1:33.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 47058479 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22894;SOR=Inf;LSEQ=TCCCCAGGGTGATGTATCAT;RSEQ=AGTAGCACAGTGCTGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:99,3:0:1,0:25.6:1:31.9:1:1:0:60:101:1:0:0 0/1:95:2:1,1:90,3:0.0211:1,2:25:1:29.5:1:0.08287:26.12488:60:4:0.0211:0:1 -3 47058777 . A G 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08601;SOR=0;LSEQ=CAGGAAGAGAGACCACAGCC;RSEQ=CCAATCAGAGCAGAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:1,2:79,194:0.0109:2,2:32.7:1:25.7:1:1:1.23:60:2:0.0074:0:1 0/0:348:0:0,0:99,249:0:2,0:23.1:1:29.4:1:1:0:60:68.6:1:0:0.2 -3 47058807 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=GCAGAAATTATATGAGGGGG;RSEQ=GGACAGGGGTGGTAATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:29,141:0.0116:2,2:17.5:1:30:1:0.31926:4.80:60:4:0.0118:0:1 0/0:159:0:0,0:31,128:0:2,0:22.1:1:30.3:1:1:0:60:52:1:0:0.1 -3 47059029 . G GA 120 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30055;SOR=1.65723;LSEQ=CCAGCTCTGACATCTGACAA;RSEQ=AAAAAAAAAAATACTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:9:9,0:100,6:0.0763:2,0:20.9:1:30.8:1:1:0:60:18:0.0783:0.0424:0 0/1:141:17:17,0:113,11:0.1206:2,1:22.1:1:29.6:1:0.36031:0:60:34:0.125:0.0426:0.1 -3 47059069 . G T 43 q23 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03183;SOR=0;LSEQ=ATGATGAAAAGGGCTTCTTA;RSEQ=AAGGTACACAGTTTGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:4:2,2:257,63:0.0123:2,2:11.8:1:21.5:1:0.18079:4.05547:60:3:0.0095:0:2.8 0/0:441:0:0,0:311,130:0:2,0:23:1:31.1:1:1:0:60:43.1:1:0:0.1 -3 47059268 . C A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2485;SOR=Inf;LSEQ=GAACACGTTGCTCAACAGTC;RSEQ=AGAGAGGGCAAGGAGTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:20,176:0:2,0:25:1:31.9:1:1:0:60:64.333:1:0:0.2 0/1:205:3:2,1:29,173:0.0146:2,2:24:1:30.3:1:0.06036:11.69:60:6:0.0149:0:1 -3 47059269 . A G 20 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49898;SOR=Inf;LSEQ=AACACGTTGCTCAACAGTCC;RSEQ=GAGAGGGCAAGGAGTTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:18,172:0:2,0:25.3:1:30.9:1:1:0:60:37:1:0:0.2 0/1:199:2:1,1:28,169:0.0101:2,2:5:1:20.5:1:0.27085:5.95:60:4:0.0101:0:1 -3 47059323 . C T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09977;SOR=1.95036;LSEQ=AGAAAAGGTAGTGAGTAAAG;RSEQ=CAGCCAATCCTTCTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:26:0,26:0,36:0.4194:1,1:24.2:1:30.1:1:1:0:60:25:0.4098:0:1.1 1/0:58:34:1,33:0,24:0.5862:1,1:21.1:1:28.6:1:1:0:60:33:0.6:0:1.1 -3 47059325 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23494;SOR=Inf;LSEQ=AAAAGGTAGTGAGTAAAGCC;RSEQ=GCCAATCCTTCTCCTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:0,59:0:1,0:23.1:1:31.9:1:1:0:60:118:1:0:0.5 0/1:56:2:0,2:1,52:0.0357:1,0:19.5:1:29.5:1:1:0:60:4:0.037:0:3.5 -3 47061135 . C T 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23592;SOR=0;LSEQ=GACATACACACAAGGAACAC;RSEQ=TTGTGTTCCTGCCTATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:2,0:173,4:0.0112:1,0:13.5:1:24:1:1:0:60:4:0.0114:0:1.5 0/0:189:0:0,0:182,7:0:1,0:22.5:1:30.7:1:1:0:60:378:1:0:0.2 -3 47061183 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33176;LSEQ=GGAGATATTCGACATACTTA;RSEQ=GACAAGAAATGAAAGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:171:120,51:214,82:0.3662:2,2:23.9:1:30:1:0.67059:1.1089:60:33.2:0.364:0:1.1 0/1:529:85:59,26:292,152:0.1607:2,2:22.8:1:29.8:1:0.53428:1.18:60:41.5:0.159:0:1.1 -3 47061433 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49746;SOR=0;LSEQ=TTTCCCCTAGCAGGGATACC;RSEQ=GATTCTTGGTATTAGAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:2,95:0.0202:1,0:17.5:1:30:1:1:0:60:4:0.0206:0:1.5 0/0:99:0:0,0:7,92:0:2,0:23.7:1:29.7:1:1:0:60:23.75:1:0:0.2 -3 47061453 . C T 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGATTCTTGGTATTAGAATC;RSEQ=GTTTAGAGGCCCTGACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:31:0,31:0,37:0.4559:1,1:23.4:1:29.5:1:1:0:60:30:0.4688:0:1.1 0/0:65:0:0,0:1,64:0:1,0:20.6:1:28.9:1:1:0:60:15.25:1:0:0.3 -3 47061700 . T C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCCACCTCTGACACTC;RSEQ=AGGATTCCAGGACAGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:15.5:1:34:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 47079112 . G A 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0207;SOR=1.32296;LSEQ=CATGCGGGATGGTCTTGGAC;RSEQ=GACTCCCAAATGATCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:565:276:184,92:193,96:0.4885:2,2:25.4:1:30.7:1:1:1.0052:60:275:0.4893:0:1.1 1/0:575:321:209,112:165,89:0.5583:2,2:24.9:1:29.9:1:1:1.01:60:79.25:0.5581:0:1.1 -3 47083995 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2442;SOR=Inf;LSEQ=TAAAACTCCCCTTATAGTGG;RSEQ=AACTTCTTTGATTAAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:162,33:0:2,0:23.4:1:32.2:1:1:0:60:96.5:1:0:0.1 0/1:191:2:1,1:137,52:0.0105:2,2:12.5:1:28.5:1:0.47903:2.61915:60:4:0.0106:0:1 -3 47087837 . T A 120 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.001;SOR=9.57168;LSEQ=ACTCTGTCTCAAAAAAAAAA;RSEQ=AAAATAAAATAAAATAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:2,0:51,1:0.037:1,0:19:1:31.5:1:1:0:60:4:0.0377:0:3 0/1:55:15:15,0:34,2:0.2727:2,1:17.7:1:30.8:1:1:0:58.7:30:0.3:0:2.1 -3 47087869 . G GA 56 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.86665;LSEQ=AAATAAAACAAAGAACACGT;RSEQ=AAAAAAAAACCCAAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:4:4,0:95,2:0.0396:1,0:42.5:1:31.3:1:1:0:60:8:0.0404:0:0 0/1:116:4:3,1:107,3:0.0345:1,2:26.5:1:28.3:1:0.13483:11.17954:60:8:0.0374:0.0086:0.3 -3 47087939 . G T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0724;SOR=0;LSEQ=AACCTTCCAAAGACAAAGTA;RSEQ=ACAGCCAATGAGTTTTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:199,82:0.0106:2,2:7:1:27:1:0.20979:4.82284:60:6:0.0109:0:1 0/0:396:0:0,0:257,138:0:2,0:24.4:1:30.8:1:1:0:60:38.5:1:0:0.1 -3 47097985 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCTTGGGAGAAATGGAG;RSEQ=CCTGCTAACAACAATGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:27:1:29.7:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 47098264 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22924;SOR=Inf;LSEQ=ACCAGATTTAACTAACATCC;RSEQ=ATGAACAGACCATAAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:176,39:0:2,0:25.9:1:31:1:1:0:60:70.667:1:0:0.3 0/1:198:2:1,1:144,52:0.0101:2,2:11.5:1:29:1:0.4647:2.75249:60:4:0.0102:0:1 -3 47098278 . A G 196 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACATCCCATGAACAGACCAT;RSEQ=AAGCAGAAAAGAAAAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:70:53,17:166,49:0.2456:2,2:23.4:1:32.1:1:0.87054:1.08631:60:140:0.2491:0:1.1 0/0:308:0:0,0:203,103:0:2,0:13:0:16:0:1:0:60:0:0:0:2 -3 47098997 . G A 42 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13515;SOR=Inf;LSEQ=ATATCTAGAAAGAAAATAAG;RSEQ=ACCACAAAAAGTTGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:69,168:0:2,0:26.3:1:30.8:1:1:0:60:58.25:1:0:0.1 0/1:304:4:3,1:96,204:0.0132:2,2:11:1:21:1:0.10295:6.33:60:3:0.01:0:1 -3 47103376 . C T 58 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCCCACCAACCCCCATTG;RSEQ=GCTCGAAAGAACAAATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:16.5:1:29.3:1:1:0:60:8:0.8:0:1.8 1/1:1:1:1,0:0,0:1:0,0:24:0:30:0:1:0:60:2:1:0:1 -3 47103861 . GTT G 215 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=14.000;MSILEN=1;SSF=0.94056;SOR=0.98304;LSEQ=GGGAAAAGGGTGGTTTGTTT;RSEQ=TTTTTTTTTTTTAAGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:113:22,91:70,157:0.2783:2,2:27.4:1:31.6:1:0.02794:1.84106:60:55.5:0.2846:0.0099:0.6 0/1:502:138:47,91:93,175:0.2749:2,2:28.4:1:30.3:1:0.91272:1.02887:60:68:0.2776:0.0179:0.6 -3 47103876 . A T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12988;SOR=Inf;LSEQ=TGTTTGTTTTTTTTTTTTTT;RSEQ=AGTTTATTTGGTGGACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:68,247:0:2,0:21.9:1:29.5:1:1:0:59.6:27.636:0.9967:0:0.8 0/1:379:4:2,2:109,266:0.0106:2,2:6:1:23.3:1:0.58385:2.43:57.5:3:0.0082:0:1 -3 47108330 . C T 61 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63801;SOR=0.51956;LSEQ=AGAAAAAAAGCTAGTAAAGA;RSEQ=TGAGTTCAAGGAAAGCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:26.3:1:30.5:1:1:0:60:8:0.4:0:1 0/1:8:2:2,0:6,0:0.25:0,0:25.5:1:23:1:1:0:60:1:0.1429:0:3 -3 47108361 . G A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06732;SOR=0.2937;LSEQ=GAAAGCGACAACAAAACAGT;RSEQ=TAAGAGACATTTCCTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:12,1:6,0:0.6842:0,1:23.6:1:28.5:1:1:0:60:26:0.6842:0:1 0/1:21:8:8,0:13,0:0.381:1,0:21.4:1:28.4:1:1:0:60:16:0.381:0:1 -3 47108704 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50074;SOR=Inf;LSEQ=CATGACAATAAAGAAATGGA;RSEQ=AGTAACAAGCTGGTACTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:17,114:0:2,0:21.8:1:30.2:1:1:0:60:64.5:1:0:0.2 0/1:151:2:1,1:21,128:0.0132:2,2:21.5:1:30.5:1:0.27099:5.98:60:4:0.0134:0:1 -3 47125124 . TA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.24352;SOR=0;LSEQ=TTTTCAGAAATATGCATGGC;RSEQ=AAAAAAGTAGTTAATTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:2,0:124,7:0.015:2,0:41:1:31:1:1:0:60:4:0.0155:0:0 0/0:136:0:0,0:128,8:0:2,0:22.3:1:28.4:1:1:0:60:135:1:0:0.1 -3 47125385 . G A 280 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.46942;LSEQ=TTGTGCCGTTGCTCTCTTTG;RSEQ=GCTCTATTTCAGCGTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1025:423:217,206:322,279:0.4127:2,2:27:1:30.5:1:0.48492:1.09552:60:51.875:0.4125:0:1.1 1/0:1368:695:355,340:329,338:0.508:2,2:26.6:1:29.7:1:0.55102:1.07:60:76.222:0.5078:0:1.1 -3 47125884 . TA T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.21888;SOR=0;LSEQ=CTTTATAATCTGATTAAACA;RSEQ=AAAAAAAATTACATCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:21,83:0.0189:2,2:23.5:1:32:1:0.37358:3.88:60:4:0.0194:0:0 0/0:120:0:0,0:29,90:0:2,0:24.3:1:28.7:1:1:0:59.5:38.667:1:0:0.7 -3 47125899 . T A 35 v4;q23;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24916;SOR=Inf;LSEQ=AAACATAAAAAAAAATTACA;RSEQ=CACTTTGTACAGTTGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:12,72:0:2,0:19.8:1:27.1:1:1:0:59.6:4.25:1:0:0.7 0/1:96:3:1,2:16,77:0.0313:2,2:20.3:1:22.7:1:0.44654:2.38:52:2:0.0274:0:4.3 -3 47127855 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21345;SOR=Inf;LSEQ=AGCATTGGGAGGCAATATCA;RSEQ=AATATTACAAAGAGCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:17,114:0:2,0:22.3:1:31.4:1:1:0:60:130:1:0:0.1 0/1:113:2:1,1:19,92:0.0177:2,2:5:1:25.5:1:0.32396:4.75:60:4:0.0179:0:1 -3 47129364 . C CAGG 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.46001;LSEQ=AGCTACTCAGGACGCTGAGG;RSEQ=AGAATTGCTTGCACCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:42.8:1:32.5:1:1:0:60:10:0.5:0:0 1/0:5:3:3,0:2,0:0.6:0,0:27.7:1:31.9:1:1:0:60:6:0.6:0:0 -3 47129454 . TAAAC T 129 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=7.000;MSILEN=4;SSF=0.09551;SOR=2.38735;LSEQ=TGACAGAACAAGACCCCATC;RSEQ=AAACAAACAAACAAACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:12:12,0:29,0:0.2927:1,0:24.1:1:32.4:1:1:0:57.5:24:0.2927:0.0976:0.8 1/0:34:17:17,0:17,0:0.5:1,1:21.5:1:31.7:1:1:0:59.7:34:0.5:0.1176:0.5 -3 47129486 . T C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=4;SSF=0.59877;SOR=2.31084;LSEQ=CAAACAAACAAACAAACAAA;RSEQ=AAATAAATAAATAAAATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:1:1,0:79,0:0.0125:1,0:26:0:34:0:1:0:60:2:0.0127:0:1 0/1:70:2:2,0:67,1:0.0286:1,0:26.5:1:32.5:1:1:0:57.5:4:0.0286:0:1 -3 47129781 . CA C 115 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.07668;LSEQ=TTTTTATAAAACAACAACAA;RSEQ=AAAAAAAAAACCAAAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:13:0,13:23,147:0.071:2,1:26.1:1:32:1:0.37678:0:60:26:0.073:0.0055:0.1 0/1:184:14:3,11:31,138:0.0761:2,2:26.3:1:30.3:1:0.72653:1.21:60:28:0.0773:0.0109:0.4 -3 47129903 . C T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49735;SOR=0.38389;LSEQ=GTTAAGAAGGCTGATAATAA;RSEQ=AAGTCTACTGTTGATGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:0,19:0,1:0.95:0,1:21.9:1:29.4:1:1:0:60:38:0.95:0:1 1/1:8:7:0,7:0,1:0.875:0,0:29:1:29.3:1:1:0:60:14:0.875:0:1 -3 47142907 . TCC T 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.02604;SOR=1.43027;LSEQ=TTATATCTGAACAGCCTATT;RSEQ=CCATCAGAAGCAGCAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:136:107,29:135,36:0.4416:2,2:29.4:1:31.7:1:1:1.01631:60:272:0.4459:0.0065:0.1 1/0:324:172:131,41:111,41:0.5309:2,2:25.8:1:31.2:1:0.52507:1.18:60:171:0.5344:0.0185:0.1 -3 47143125 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23763;SOR=0;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GCATATATAAAGATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:2,115:0.0157:1,2:32:1:29.5:1:0.04999:47.15:60:4:0.0168:0:1 0/0:133:0:0,0:7,124:0:2,0:22:1:28.8:1:1:0:59.5:20.833:1:0:0.6 -3 47144731 . A G 21 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94985;LSEQ=AATAAAGTAGAATAGGAAAA;RSEQ=GGGACTAAAAAATTCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:166,23:0.0105:2,2:23.5:1:31.5:1:0.2361:7.08652:60:4:0.0105:0:1 0/1:201:2:2,0:173,26:0.01:2,0:24:1:21.5:1:1:0:60:1:0.005:0:3.5 -3 47146932 . C T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.46214;SOR=2.00565;LSEQ=AAAAAAGGCACTCTGGGGGT;RSEQ=ATCAATAATTTCTAAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:0.4667:0,0:20.9:1:25.6:1:1:0:60:2.5:0.4167:0:2.6 1/0:14:9:9,0:5,0:0.6429:0,0:23.4:1:30.4:1:1:0:60:18:0.6429:0:1.6 -3 47147001 . C T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12005;SOR=Inf;LSEQ=TACATATATATATGTAAATT;RSEQ=CTCTCTCTTCCATGTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:55,10:0:2,0:24.2:1:30.2:1:1:0:60:12:1:0:0.3 0/1:69:4:3,1:57,8:0.058:2,2:12.3:1:31:1:0.43593:2.33631:60:8:0.0606:0:1.5 -3 47147076 . G A 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04635;SOR=Inf;LSEQ=CTTTTTGAAAACAAATAGAC;RSEQ=CTATTTATACTGCTCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:79,80:0:2,0:27.4:1:30.6:1:1:0:60:52:1:0:0.1 0/1:251:7:4,3:122,122:0.0279:2,2:33.3:1:30.9:1:1:1.33:60:14:0.028:0:1 -3 47147087 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.143;SOR=0;LSEQ=CAAATAGACGCTATTTATAC;RSEQ=GCTCTGCCCCTCATTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:73,83:0.0127:2,2:21.5:1:30:1:1:1.14:60:4:0.0127:0:1 0/0:259:0:0,0:126,133:0:2,0:26.5:1:30.4:1:1:0:60:258:1:0:0.2 -3 47147131 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50642;SOR=Inf;LSEQ=TTAATATATTTTAGAAATCA;RSEQ=TCGGCAGGACACGGTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:41,73:0:2,0:25.1:1:31.9:1:1:0:60:228:0.9913:0:0.1 0/1:149:2:1,1:58,89:0.0134:2,2:31.5:1:29.5:1:1:1.53:60:4:0.0136:0:1.5 -3 47147150 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50092;SOR=Inf;LSEQ=AGTCGGCAGGACACGGTGGC;RSEQ=CATGCCTGTAATCTCAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:25,62:0:2,0:25.7:1:30.2:1:1:0:60:86:1:0:0.1 0/1:103:2:1,1:37,64:0.0194:2,2:7.5:1:28:1:1:1.72:60:4:0.0196:0:1.5 -3 47155261 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.51871;SOR=Inf;LSEQ=ATTGCTTGAATCCGGGAGGT;RSEQ=GAGGTTCCAGTGAGCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:73,0:0:1,0:22.7:1:28.3:1:1:0:60:72:1:0:0 0/1:111:2:2,0:106,3:0.018:1,0:10.5:1:32:1:1:0:50:4:0.019:0:3.5 -3 47155283 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52287;SOR=Inf;LSEQ=AGGTTCCAGTGAGCCAAGAT;RSEQ=GTGCCACTGCACTCCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:109,9:0:2,0:22.4:1:31.3:1:1:0:60:236:1:0:0.1 0/1:185:2:2,0:154,28:0.0108:2,0:21.5:1:30:0:1:0:50:4:0.011:0:3.5 -3 47155293 . C T 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64822;SOR=2.07851;LSEQ=GAGCCAAGATCGTGCCACTG;RSEQ=ACTCCAGTCTGGGTGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:1:0,1:131,21:0.0065:2,0:1:0:24:0:0.14379:0:60:2:0.0066:0:1 0/1:222:3:1,2:176,43:0.0135:2,2:17:1:24.7:1:0.1053:8.0777:53.3:6:0.0136:0:2.7 -3 47155304 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15247;SOR=0;LSEQ=GTGCCACTGCACTCCAGTCT;RSEQ=GGTGAAAGAGTGAGACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:145,38:0.0108:2,2:19.5:1:28.5:1:0.37808:3.77952:60:4:0.011:0:1 0/0:288:0:0,0:211,77:0:2,0:23:1:30.9:1:1:0:59.9:95:1:0:0.1 -3 47162661 . A G 277 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42176;SOR=1.07935;LSEQ=TGAGAAAGTTCAGGCAGGCG;RSEQ=TTATCTATTTGTTTTCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:329:146,183:217,201:0.4393:2,2:25.3:1:31.5:1:0.04647:1.35263:60:53.833:0.4407:0:1.1 0/1:1135:520:264,256:317,290:0.4581:2,2:25.9:1:30.8:1:0.63292:1.05991:60:73.286:0.4597:0:1.1 -3 47164928 . G A 56 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82521;LSEQ=GTGAGATCTGCTCCGCCGTC;RSEQ=CTCTCTTTCTGATCTACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:149,133:0.0105:2,2:13.7:1:26.3:1:1:1.78:60:6:0.0108:0:1 0/0:463:4:3,1:232,227:0.0086:2,2:21.5:1:28.3:1:0.62354:2.93:60:8:0.0087:0:1.3 -3 47164945 . C T 46 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16288;SOR=Inf;LSEQ=GTCGCTCTCTTTCTGATCTA;RSEQ=ATCGGGAAGATACATACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:162,148:0:2,0:22.4:1:32.1:1:1:0:60:102.333:1:0:0.1 0/1:477:5:2,3:236,236:0.0105:2,2:20.4:1:20.2:1:1:1.49873:60:1.5:0.0063:0:1 -3 47168219 . T C 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13366;SOR=Inf;LSEQ=TCATAAATACTTAAAAACGA;RSEQ=TGAAATAATAGTTATTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:34,145:0:2,0:21.2:1:30.3:1:1:0:60:58.667:1:0:0.1 0/1:227:4:1,3:44,179:0.0176:2,2:14.8:1:32:1:1:1.35:60:8:0.0178:0:1 -3 47204939 . G T 59 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACCGGCGCCCTCTTGCC;RSEQ=GGCCCGGCACCGGCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:33.8:1:29.5:1:1:0:60:8:1:0:1 -3 47205254 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58744;SOR=0.39869;LSEQ=GGGCCTGTTACTCCTCGCGC;RSEQ=GGCCCGCGCCGCCACCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:157,26:0.0108:2,2:24:1:28.5:1:0.27127:5.94445:60:4:0.011:0:1 0/0:231:1:0,1:189,41:0.0043:2,0:1:0:25:0:0.18182:0:60:2:0.0043:0:1 -3 48285282 . CA C 89 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.25873;SOR=0.34112;LSEQ=CCAAGAGTGAAAGTCTGTCT;RSEQ=AAAAAAAAAAAAAAGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:7,0:8,1:0.4118:2,0:22.4:1:31.9:1:1:0:57.9:14:0.4118:0.1176:0.6 0/1:16:3:3,0:12,1:0.1875:1,0:17.3:1:31.2:1:1:0:59.7:6:0.1875:0.0625:3 -3 48285318 . C A 24 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51186;SOR=Inf;LSEQ=GGCAGTAACACTAAGTTGAA;RSEQ=TTTAGAAGGATAATAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:16,8:0:2,0:21:1:29.3:1:1:0:60:7:1:0:1 0/1:36:2:2,0:22,12:0.0556:2,0:24:1:24.5:1:0.54286:0:59.5:4:0.0714:0:6 -3 48456008 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATCAGGACCCGGGCCACCA;RSEQ=CCAAGCAGTCCAGCTCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:29.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:23:0:28:0:1:0:60:2:1:0:0 -3 48514994 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23436;SOR=0;LSEQ=CAGCACTCTCTCCAATCTGT;RSEQ=TCCCCATGTTCTCCCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:90,38:0.0154:2,2:9.5:1:30.5:1:0.51163:2.35083:60:4:0.0155:0:1 0/0:138:0:0,0:94,44:0:2,0:25.6:1:30.8:1:1:0:60:45:1:0:0.2 -3 48515064 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25871;SOR=Inf;LSEQ=CATGTCACCACCTGCTCAAA;RSEQ=GCCAGCTATGGCTCCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:91,108:0:2,0:25:1:30.5:1:1:0:60:198:1:0:0.5 0/1:252:3:1,2:124,125:0.0119:2,2:21.7:1:28.7:1:1:1.97881:60:6:0.0121:0:2.7 -3 48515065 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58531;SOR=0.39237;LSEQ=ATGTCACCACCTGCTCAAAC;RSEQ=CCAGCTATGGCTCCTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:2,0:89,106:0.0102:2,0:24:1:29:1:0.21211:0:60:4:0.0102:0:1.5 0/0:250:1:1,0:126,122:0.004:2,0:1:0:25:0:1:0:60:2:0.0041:0:1 -3 48515079 . C T 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45084;SOR=0.85654;LSEQ=TCAAACGCCAGCTATGGCTC;RSEQ=TGTAGCTCTTGCGATTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:97:42,55:43,61:0.4826:2,2:25.3:1:29.7:1:0.88645:1.08:60:31.333:0.4796:0:1.1 0/1:259:115:57,58:61,83:0.444:2,2:21.7:1:30.4:1:0.26072:1.34:60:230:0.4475:0:1.2 -3 48515221 . G A 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=GGCTCACACCTGCAATCCCA;RSEQ=CACTTTGGGAGGCCGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:0,9:1,8:0.5:2,0:33.2:1:30.8:1:1:0:60:18:0.5:0:1 0/0:29:0:0,0:1,28:0:1,0:18.8:1:32.2:1:1:0:60:58:1:0:0 -3 48541446 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2757;SOR=Inf;LSEQ=ACGGGCCGCCCCCACCCCCG;RSEQ=CTCACCACCCGGAGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:38,52:0:2,0:27.6:1:31.2:1:1:0:60:89:1:0:0.1 0/1:134:3:1,2:62,69:0.0224:2,2:5:1:30:1:1:1.78957:60:6:0.0227:0:1.3 -3 48541449 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51542;SOR=Inf;LSEQ=GGCCGCCCCCACCCCCGGCT;RSEQ=ACCACCCGGAGGCGGCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:41,57:0:2,0:26.7:1:31.3:1:1:0:60:97:1:0:0.2 0/1:143:2:1,1:66,75:0.014:2,2:19:1:29:1:1:1.14:60:4:0.0141:0:1 -3 48541480 . CA C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.52389;SOR=Inf;LSEQ=GGCGGCGTTAGCAGCAGCAG;RSEQ=ACAGCAACGGCAACAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:30,67:0:2,0:30.1:1:30.5:1:1:0:60:96:1:0:0.2 0/1:154:2:1,1:60,92:0.013:2,2:28.5:1:31:1:1:1.53:60:4:0.0132:0:0 -3 48541513 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26973;SOR=Inf;LSEQ=AACAGGATCCGCGGCGCGGG;RSEQ=ACCGGCGCAGTCATGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:16,45:0:2,0:23:1:30.7:1:1:0:60:29.5:1:0:0.2 0/1:88:3:2,1:25,60:0.0341:2,2:14:1:27.3:1:0.22177:4.70:60:6:0.0345:0:1.3 -3 49259335 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52425;SOR=0;LSEQ=GAAAGGCACTGTCTGATTTC;RSEQ=GAAGCCTTTTCCTATAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:13,22:0.0541:2,2:13:0:32:0:1:1.67:60:4:0.0541:0:1.5 0/0:22:0:0,0:8,14:0:2,0:18.1:1:30.6:1:1:0:60:44:1:0:0 -3 49259423 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=ACTCTTACCCTAAGAAGGTG;RSEQ=AGAGTCCTCCTTTCTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:11.3:1:30.5:1:1:0:60:5:1:0:0 0/1:5:2:1,1:1,2:0.4:2,2:28:1:29:0:1:1.73:60:4:0.4:0:1 -3 49396360 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGCCTCCTCAGGCTGCA;RSEQ=TCACCCTACCCCCAAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30:1:1:0:60:4:1:0:1 -3 49397284 . T A 38 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTACCTTGCAGCTGACAGA;RSEQ=AATAGGCAGGACATGTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:28.3:1:24:1:1:0:60:2:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 49397824 . G GA 146 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.0407;SOR=2.22783;LSEQ=TTTCACCGGCTCCTAGCAAA;RSEQ=AAAAAAAAATAGTCCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:9:1,8:107,342:0.0196:2,2:28.7:1:30.2:1:0.69244:2.49919:60:18:0.02:0.0022:0.1 0/1:656:28:4,24:195,430:0.0427:2,2:28.2:1:30.4:1:0.06064:2.71758:59.3:56:0.0439:0:0.4 -3 49397900 . A AT 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.66116;SOR=1.81738;LSEQ=TATTCAAATTCATCTAAAAG;RSEQ=TTTTTTTTTCTTTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:0,2:0,113:0.0174:1,0:27.5:1:31.5:1:1:0:60:4:0.0179:0:0 0/1:96:3:0,3:1,91:0.0313:1,0:28:1:32:0:1:0:60:6:0.0319:0:0 -3 49400143 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1884;SOR=Inf;LSEQ=CCTCAGTGAAATTGCAGAGA;RSEQ=ACTTTCTTTGTGGCTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:2,116:0:1,0:27.7:1:31.8:1:1:0:60:22.6:1:0:0.1 0/1:91:2:1,1:1,88:0.022:1,2:44.5:1:31:1:0.04371:62.58:60:4:0.022:0:2 -3 49406080 . T C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=20.80481;LSEQ=TACATTGAAATGGCAGACCA;RSEQ=TGAAATGGCAGACGGTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:9:0,9:1,123:0.0677:1,0:27:1:32.8:1:1:0:60:18:0.0703:0:1.2 1/0:114:69:1,68:1,44:0.6053:1,1:27:1:31.1:1:1:1.53934:60:16.25:0.5909:0:1.1 -3 49406095 . G A 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00791;SOR=Inf;LSEQ=GACCATTGAAATGGCAGACG;RSEQ=TCTAAAACAGTAAAACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:1,105:0:1,0:26.2:1:30.8:1:1:0:60:12.25:1:0:0.3 0/1:88:6:0,6:1,81:0.0682:1,0:27.5:1:30.3:1:1:0:60:12:0.0698:0:1.5 -3 49406126 . A AT 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.1559;SOR=Inf;LSEQ=TAAAACACAGGAGTATTTAC;RSEQ=TTTTTTCTTTTTTCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:0,58:0:1,0:20.7:1:30.1:1:1:0:59:10.6:1:0:0.6 0/1:39:2:0,2:0,37:0.0513:1,0:43:1:28.5:1:1:0:58.5:4:0.0571:0:5 -3 49406140 . C T 69 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=1;SSF=0.10907;SOR=3.13797;LSEQ=ATTTACATTTTTTCTTTTTT;RSEQ=TTTTTTTTTTTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:0,5:0,26:0.1282:1,0:18:1:26:1:1:0:50.8:4:0.1538:0:2.4 0/1:25:8:0,8:0,16:0.32:1,0:22.3:1:23.3:1:1:0:47.1:1.667:0.2941:0:3.5 -3 49433133 . G A 42 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTAGCCTGGGCAACAGAGC;RSEQ=AGACTCTGTCTCCAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:21.3:1:27:1:1:0:60:2:0.6667:0:1 -3 49433201 . G GT 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00191;SOR=0.03302;LSEQ=AGGGCACGAAAAGTGATTGA;RSEQ=TGGTTAACTGGATAGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:10,0:1,0:0.9091:0,0:25.5:1:30.4:1:1:0:60:20:0.9091:0.0909:0.5 0/1:10:2:2,0:8,0:0.2:0,0:18:1:30:1:1:0:60:4:0.25:0.1:0 -3 49433401 . C T 272 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.2661;LSEQ=GTAAAAACAGCATAGTCTTC;RSEQ=AGTGTATGGAATGGAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:474:473:275,198:0,0:0.9979:0,2:24.8:1:29.6:1:1:0:60:58.125:1:0:1.2 1/1:600:599:344,255:0,1:0.9983:0,2:24.2:1:29.5:1:0.42667:0:60:148.75:0.9983:0:1.2 -3 49721532 . G A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.80692;LSEQ=CGTGAAGACAGCTGGCCAGC;RSEQ=GGACCTTGCGCATACTCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1716:146:74,72:792,774:0.0851:2,2:23.1:1:30.7:1:1:1.00:59.6:292:0.0864:0:1.1 0/1:1814:261:133,128:765,784:0.1439:2,2:23:1:30.1:1:0.64028:1.06:59.8:64.25:0.1428:0:1.2 -3 49721561 . A C 152 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00777;SOR=2.45925;LSEQ=CGCATACTCGGTTGGGGATT;RSEQ=TAATTCCTTCCAGGACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1721:12:8,4:875,830:0.007:2,2:15.3:1:30.2:1:0.38837:1.90:36.1:11:0.0064:0:2.9 0/1:1767:30:23,7:857,877:0.017:2,2:14:1:31:1:0.00302:3.36:30.9:60:0.0172:0:2 -3 49721622 . C T 165 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00124;SOR=0.40723;LSEQ=AAGTGGGCCCCCGTAGTCAC;RSEQ=CTGGCAGGTAGGAGAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1197:46:25,21:481,666:0.0384:2,2:31:1:30:1:0.12726:1.65:32.9:92:0.0393:0:2 0/1:1062:17:8,9:415,629:0.016:2,2:29.5:1:28.4:1:0.62008:1.35:31.2:16:0.0154:0:3.1 -3 49721653 . G A 143 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=18.18047;LSEQ=GGAGAACTGATGAGGGCCCC;RSEQ=GGCCACAGCAATGACTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:764:2:2,0:262,500:0.0026:2,0:1:0:26.5:1:0.11911:0:48:4:0.0026:0:2 0/1:570:26:9,17:172,370:0.0456:2,2:19.6:1:30.5:1:0.82988:1.14:29.2:25:0.0444:0:1.2 -3 49721663 . A C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.04634;LSEQ=TGAGGGCCCCGGGCCACAGC;RSEQ=ATGACTAGCCTGCTTCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:668:19:4,15:226,423:0.0284:2,2:17.6:1:31.4:1:0.32673:2.00171:26.6:38:0.0288:0:2.1 0/1:471:14:3,11:124,333:0.0297:2,2:12.6:1:30.6:1:0.76793:1.36449:27.1:28:0.03:0:1.8 -3 49721798 . C A 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.77111;LSEQ=TCAGTGCACATCTCACTCTC;RSEQ=CGCACACGTCCTCGGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1469:144:71,73:621,702:0.098:2,2:24.2:1:29.3:1:0.599:1.10:56.3:71:0.098:0:1.1 0/1:1499:242:119,123:670,585:0.1614:2,2:23.4:1:29.3:1:0.23284:1.18366:56.5:47.4:0.1596:0:1.2 -3 49722356 . G A 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.89624;LSEQ=TAGGTCATTTGTGACTCTCA;RSEQ=TCCATTGCCCCAAGGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1453:84:41,43:708,660:0.0578:2,2:26.1:1:31.1:1:0.65324:1.12496:51.7:168:0.0584:0:1.1 0/1:1295:135:68,67:579,581:0.1042:2,2:26.6:1:30.1:1:0.92782:1.02:51.4:270:0.1056:0:1.2 -3 49722503 . C CCG 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCTTCACTAGAGACCCCC;RSEQ=GCAGAAATGCTGGCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1110:0:0,0:549,561:0:2,0:25.8:1:30.3:1:1:0:39.8:91.5:1:0:0.1 0/1:955:78:35,43:416,458:0.0817:2,2:24.1:1:30:1:0.72283:1.11578:36:156:0.0825:0.0188:0.2 -3 49722761 . C A 228 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=232.75416;LSEQ=CAACCACGCGCAGCTTGGAA;RSEQ=GCCGCTGATCCAGCCGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1403:1:1,0:721,681:7e-04:2,0:1:0:14:0:1:0:50:0:0:0:2 0/1:1432:203:100,103:618,609:0.1418:2,2:25.2:1:29.8:1:0.82024:1.04521:55.7:39.6:0.1409:0:1.2 -3 49722905 . T TGGG 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=9.000;MSILEN=1;SSF=0.01825;SOR=0.51372;LSEQ=AACTGGCCCAACTCCTAACC;RSEQ=GGGGGGTCCAGGATTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1625:40:20,20:818,761:0.0246:2,2:27.8:1:31.2:1:0.87347:1.07483:30.4:80:0.0251:0:0.2 0/1:1563:20:10,10:756,755:0.0128:2,2:25.1:1:31.5:1:1:1.00132:31:40:0.0131:0:0.2 -3 49722981 . G GGT 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.74175;SOR=0.92021;LSEQ=GGTTAAGGGAGCCAGCCTTT;RSEQ=GGTGGGGGCTGAGGCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1509:46:22,24:770,690:0.0305:2,2:23.4:1:30.8:1:0.55056:1.21723:41:92:0.0307:0.004:0.4 0/1:1387:39:17,22:658,676:0.0281:2,2:22.3:1:30.2:1:0.51871:1.25945:47.1:78:0.0286:0.0065:0.4 -3 49723144 . C T 136 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20464;SOR=0.64988;LSEQ=TTCTCCTCCAGTTGTGCATG;RSEQ=GGTTCGGAGGTAAACGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1719:24:20,4:758,935:0.014:2,2:13.9:1:29.8:1:0.00023:6.16:35.2:23:0.0136:0:2.7 0/0:1755:16:12,4:816,921:0.0091:2,2:16.2:1:29.4:1:0.04085:3.38:40.3:15:0.0087:0:2.4 -3 49723147 . T C 244 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCCAGTTGTGCATGCGG;RSEQ=TCGGAGGTAAACGTGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1718:0:0,0:774,940:0:2,0:24.1:1:29.8:1:1:0:59.2:73.522:0.9988:0:0.2 0/1:1751:211:104,107:720,817:0.1205:2,2:24.2:1:31.7:1:0.50906:1.10:60:104.5:0.1212:0:1.2 -3 49723274 . G A 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.51566;LSEQ=GTTAGGGCCCTGGCGGGGCC;RSEQ=GGAGCACCAGGGACTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2383:486:278,208:966,922:0.2039:2,2:24:1:30.5:1:0.01911:1.28:39.7:80:0.2049:0:1.5 0/1:2263:633:352,281:820,803:0.2797:2,2:22.5:1:30.2:1:0.03103:1.23:41.7:104.5:0.2799:0:1.5 -3 49723296 . G A 149 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31957;SOR=1.33968;LSEQ=GAGCACCAGGGACTCACTGC;RSEQ=GCTTGTGCGGCGTCTCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2732:21:0,21:1310,1398:0.0077:2,1:22.7:1:32.4:1:0:0:27.2:42:0.0078:0:1.3 0/1:2726:28:4,24:1332,1365:0.0103:2,2:18.1:1:31:1:0.00018:5.85178:29:56:0.0104:0:1 -3 49723321 . AGCGCTG A 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00509;SOR=1.37172;LSEQ=GTGCGGCGTCTCAGCGGACC;RSEQ=GCACTGGACACCCTTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2554:148:69,79:1123,1275:0.0579:2,2:27.9:1:31.4:1:1:1.00843:39.9:48.333:0.0576:0.0098:1.2 0/1:2493:194:91,103:1081,1211:0.0778:2,2:25.9:1:31.1:1:1:1.01036:40.4:193:0.0785:0.0176:1.2 -3 49723379 . T C 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20507;SOR=0.84736;LSEQ=GTGCCGCGGTACTGCTCCCC;RSEQ=GCGCCGTGGTAGCAGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1551:157:7,150:681,708:0.1012:2,1:8:1:29.7:1:0:20.58955:33.1:51.333:0.1011:0:1.2 0/1:1366:119:10,109:608,636:0.0871:2,2:7.6:1:30:1:0:10.40687:32.7:118:0.0877:0:1.2 -3 49723687 . T C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52511;SOR=0.82012;LSEQ=GCCTTGAGCCCGTGACTACC;RSEQ=TCCTCCCGTCTCACCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:39:22,17:474,435:0.0411:2,2:12.7:1:25.6:1:0.62719:1.19:39.1:2:0.0306:0:4 0/1:765:26:22,4:399,338:0.034:2,2:8.3:1:30:1:0.00209:4.65:34.9:25:0.0359:0:3.3 -3 49723735 . C G 207 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=12.000;MSILEN=1;SSF=0.52021;SOR=1.08111;LSEQ=TCCCAACGCCCGCCCCCCCC;RSEQ=CCCACCTCACTTGCACGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1110:196:101,95:426,487:0.1766:2,2:27.2:1:27.3:1:0.23713:1.22:38.7:5.533:0.1631:0:1.7 0/1:882:166:80,86:372,338:0.1882:2,2:27.9:1:27.9:1:0.34356:1.18291:41:7.737:0.1849:0:1.7 -3 49723750 . A G 136 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=16.02712;LSEQ=CCCCCCCCCACCTCACTTGC;RSEQ=CGCGTATTTTTCTGGCGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:892:2:0,2:262,610:0.0022:2,0:21:1:12:0:1:0:43.5:0:0:0:6 0/1:718:25:6,19:236,442:0.0348:2,2:18.6:1:29.3:1:0.29343:1.68965:48.7:11.5:0.0361:0:1.8 -3 49723784 . C A 295 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.6301;LSEQ=GGCGTAAATCGGTGCTGATG;RSEQ=GGGATTTGCGCGTCCCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1159:785:367,418:203,163:0.6773:2,2:24.4:1:30.7:1:0.00648:1.41801:49.1:30.4:0.6941:0:1.4 1/0:1045:595:291,304:221,226:0.5694:2,2:24.2:1:29.8:1:0.90039:1.02155:48.8:32.056:0.5828:0:1.4 -3 49723823 . A G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00372;SOR=0.71879;LSEQ=CGCTGGCAAGGTACGCCCGC;RSEQ=GTGGTGGTATTGGCTGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1468:216:148,68:694,555:0.1471:2,2:27.6:1:30.1:1:0.00034:1.74:33.2:42.2:0.1469:0:1.2 0/1:1396:154:94,60:671,566:0.1103:2,2:25.9:1:30.4:1:0.12213:1.32:34.9:308:0.1121:0:1.2 -3 49723881 . G C 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.42432;LSEQ=TCCCGCGGAAGCAGCTGACA;RSEQ=TTGTGGCCTCTTGGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1697:88:64,24:824,781:0.0519:2,2:24.6:1:31.9:1:1e-04:2.53:28.6:28.333:0.0508:0:1.9 0/1:1764:40:35,5:892,827:0.0227:2,2:13:1:32.1:1:0:6.48:27.8:80:0.0229:0:1.4 -3 49723916 . T G 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26715;LSEQ=CGGGGCTGTGCCTCGGACCC;RSEQ=TAGATGGACCGAGATAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1637:190:104,86:657,784:0.1161:2,2:25.7:1:30.2:1:0.02016:1.44:31.9:30.667:0.1148:0:1.6 0/1:1653:56:35,21:730,862:0.0339:2,2:23.6:1:30:1:0.01971:1.97:34.9:55:0.0339:0:1.4 -3 49724011 . G T 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20801;SOR=0.73247;LSEQ=CCAGGTGTACGGTACTCCAC;RSEQ=GGGTATGCTCTCAGGTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:54:12,42:206,292:0.0975:2,2:19.4:1:30.8:1:0.00782:2.46549:28.4:108:0.0987:0:2 0/1:423:31:10,21:150,241:0.0733:2,2:21.5:1:29.8:1:0.56774:1.30625:28.2:62:0.0743:0:2 -3 49724014 . G A 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12539;SOR=1.25482;LSEQ=GGTGTACGGTACTCCACGGG;RSEQ=TATGCTCTCAGGTCACGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:527:141:38,103:176,210:0.2676:2,2:21.9:1:30.9:1:0.00013:2.26826:29.6:69.5:0.2658:0:1.4 0/1:404:127:33,94:126,151:0.3144:2,2:23:1:29.7:1:0.00019:2.37192:30.2:62.5:0.3125:0:1.3 -3 49724048 . TC T 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5869;SOR=1.0721;LSEQ=CACGCCCAGCCCCTCTTACC;RSEQ=CCCGGCCAAGCCACGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:243:154,89:250,186:0.3579:2,2:24:1:31.7:1:0.14214:1.29:29.1:120.5:0.3592:0.0265:0.4 0/1:524:196:118,78:204,124:0.374:2,2:23.7:1:31.6:1:0.71071:1.0873:29.7:392:0.3798:0.0172:0.4 -3 49724172 . C T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=0.39466;LSEQ=TGCGGATCCGTAGTGTAGCA;RSEQ=CATGGCCGCTCGGAGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:70:25,45:341,297:0.0989:2,2:22.8:1:29.9:1:0.00544:2.06459:30.9:34:0.0976:0:2.8 0/1:434:18:2,16:225,191:0.0415:2,2:24.3:1:28:1:0.00038:9.38544:25.8:8:0.0375:0:2.2 -3 49724183 . C G 237 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.39938;LSEQ=AGTGTAGCACCATGGCCGCT;RSEQ=GGAGCCGTCAGGATTCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:197:57,140:345,226:0.2565:2,2:23:1:31.1:1:0:3.74257:31.4:97.5:0.2579:0:2.7 0/1:504:61:1,60:272,171:0.121:2,1:23.2:1:30.7:1:0:94.79132:25.1:122:0.124:0:2 -3 49724197 . T C 237 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27818;LSEQ=GCCGCTCGGAGCCGTCAGGA;RSEQ=TCCGGCAATAGTTGTCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:834:172:52,120:385,277:0.2062:2,2:26.6:1:32:1:0:3.20291:31.5:171:0.208:0:2.9 0/1:579:39:0,39:310,230:0.0674:2,1:23.6:1:32.2:1:0:0:25:38:0.067:0:2.5 -3 49724236 . C A 130 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CCAGACCTTGGTCGAGGAAC;RSEQ=TGGGGGCGGTAATGGGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:20:5,15:434,435:0.0225:2,2:27.1:1:30.3:1:0.03946:2.98985:30.1:19:0.0217:0:3.8 0/0:684:0:0,0:334,349:0:2,0:29.3:1:30.4:1:1:0:46.6:39.176:1:0:0.2 -3 49724260 . C G 194 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGCGGTAATGGGGCGTGAA;RSEQ=AAGACCCTGGGACTCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:834:69:12,57:344,421:0.0827:2,2:12.3:1:31.8:1:1e-05:3.87562:32.3:68:0.083:0:3.5 0/0:662:0:0,0:285,376:0:2,0:24.1:1:31.2:1:1:0:50.8:93.429:0.9985:0:0.2 -3 49724808 . T C 322 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.09854;LSEQ=TTGTCTCACTTGTGATCATT;RSEQ=GGGAACTTGTGGCTCCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1588:1582:781,801:0,1:0.9962:0,2:25:1:30.5:1:1:0:50.4:104.467:0.9968:0:1.1 1/1:1645:1584:801,783:29,32:0.9629:2,2:24.4:1:30.3:1:0.69624:1.13:50.1:120.846:0.9626:0:1.2 -3 49724986 . T C 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27831;SOR=1.1661;LSEQ=TGCCCCTCTCCACCCCCACT;RSEQ=GCCTTTCTTCTGGAAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1386:114:64,50:659,612:0.0823:2,2:37.4:1:30:1:0.4338:1.19:48.6:37:0.0817:0:3.2 0/1:1321:125:79,46:605,590:0.0946:2,2:32.8:1:30:1:0.0083:1.67:56.2:61.5:0.0954:0:3.5 -3 49725021 . C T 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01049;SOR=1.34312;LSEQ=AGAGGTCACAGCGCCCAGAA;RSEQ=GCCGCAGCCTCGTGTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1486:156:75,81:693,635:0.105:2,2:21.9:1:30:1:0.35204:1.17851:45.6:38:0.1048:0:3.6 0/1:1440:196:104,92:612,631:0.1361:2,2:23.1:1:29.1:1:0.35642:1.17:52.3:48:0.1357:0:3.7 -3 49725034 . T A 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00229;SOR=1.42951;LSEQ=CCCAGAACGCCGCAGCCTCG;RSEQ=GTGGGGCGAGTGTTGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1543:148:64,84:734,658:0.0959:2,2:20.4:1:30.1:1:0.03052:1.46372:43.8:48.333:0.0965:0:3.8 0/1:1473:194:85,109:635,642:0.1317:2,2:23.3:1:28.8:1:0.14295:1.26816:49.2:15.167:0.127:0:4 -3 49725038 . G C 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00019;SOR=1.57747;LSEQ=GAACGCCGCAGCCTCGTGTG;RSEQ=GGCGAGTGTTGAGTCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1534:127:48,79:746,661:0.0828:2,2:22.9:1:30.4:1:0.00113:1.85671:42.7:126:0.0837:0:3.9 0/1:1460:182:75,107:639,636:0.1247:2,2:24:1:30:1:0.02645:1.43303:48.5:44.5:0.1241:0:4 -3 49725041 . C T 153 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=46.88169;LSEQ=CGCCGCAGCCTCGTGTGGGG;RSEQ=GAGTGTTGAGTCCATGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1537:1:0,1:784,749:7e-04:2,0:1:0:28:0:0.48892:0:60:2:7e-04:0:1 0/1:1450:43:19,24:690,716:0.0297:2,2:25.3:1:28.2:1:0.54037:1.21712:52:42:0.0294:0:4.8 -3 49725086 . G A 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10879;SOR=1.34596;LSEQ=TGGCAACCATGGCTGCTCAC;RSEQ=TTGTAGTGGAAGGCCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1478:57:23,34:684,737:0.0386:2,2:21.6:1:30.5:1:0.28036:1.37166:36.3:56:0.0383:0:3.5 0/1:1464:75:22,53:670,718:0.0512:2,2:23.3:1:30.2:1:0.0013:2.24687:43.5:150:0.052:0:4 -3 49725284 . CT C 195 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATGTAGCAGGTGCTGTAG;RSEQ=CTGTGCCCCGGAGCACTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1060:70:26,44:476,510:0.066:2,2:28.8:1:31.9:1:0.08278:1.57881:54.1:140:0.0669:0.0038:0.2 0/0:1084:0:0,0:523,560:0:2,0:24.9:1:29.7:1:1:0:54.9:62.706:1:0:0.1 -3 49725432 . AG A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00162;SOR=0.39062;LSEQ=TTCAGGGGATCAAAGCTACA;RSEQ=GCTTCTGGGATGGACCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:207:183:11,172:5,19:0.8841:2,2:24.9:1:32.1:1:0.02489:4.07255:44.6:182:0.8792:0.1836:0.1 1/0:131:98:9,89:5,28:0.7481:2,2:23.8:1:31.5:1:0.3409:1.75734:45.3:97:0.7462:0.1756:0.2 -3 49725468 . G A 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00063;SOR=Inf;LSEQ=CCCTGTATGCACTTTCAAGG;RSEQ=CCAGTCTAGCCCCCTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:9,118:0:2,0:24:1:31.8:1:1:0:51:30.75:1:0:0.1 0/1:71:7:1,6:5,59:0.0986:2,2:27.1:1:29.3:1:0.47651:1.94:53.3:14:0.1:0:1 -3 49725685 . G A 87 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATCACATTACCCAGCCA;RSEQ=GGGCCCTGGCTAGGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:7,0:5,1:0.5385:2,0:28:1:31.3:1:0.46154:0:40.9:14:0.5385:0:1 0/0:1:0:0,0:0,1:0:0,0:15:0:24:0:1:0:50:2:1:0:0 -3 49725728 . C T 76 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAAATCTGGGCTCTCAC;RSEQ=TGCACAAAGGCATATGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:17,3:0.2:2,0:35.8:1:33:1:1:0:33.4:10:0.2:0:4 0/0:3:0:0,0:2,1:0:2,0:23.3:1:30.7:1:1:0:56.7:6:1:0:0 -3 49725734 . A G 73 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGGCTCTCACCTGCAC;RSEQ=AAGGCATATGCTAGGTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:5,0:18,4:0.1852:2,0:39.2:1:31.8:1:0.56125:0:33.4:10:0.1852:0:4 0/0:3:0:0,0:2,1:0:2,0:25.3:1:31.3:1:1:0:56.7:6:1:0:0 -3 49725737 . G A 73 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCTCTCACCTGCACAAA;RSEQ=GCATATGCTAGGTTAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:5,0:18,5:0.1786:2,0:39.8:1:31.8:1:0.5495:0:33.4:10:0.1786:0:4 0/0:3:0:0,0:2,1:0:2,0:26.3:1:32.7:1:1:0:56.7:6:1:0:0 -3 49725743 . T C 86 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACCTGCACAAAGGCATA;RSEQ=GCTAGGTTAGAGGGGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:5,1:20,4:0.2:2,2:39.7:1:33.3:1:1:1:32:12:0.2:0:3.7 0/0:4:0:0,0:3,1:0:2,0:22.3:1:31.5:1:1:0:57.5:8:1:0:0 -3 49725815 . G A 26 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46701;SOR=2.23875;LSEQ=GCGTGCATCTGTGTGGTCCT;RSEQ=ACACTGCTTCAGTGCTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:2,0:54,5:0.0328:2,0:43.5:1:26.5:1:1:0:21:4:0.0333:0:1 0/1:14:1:1,0:11,2:0.0714:2,0:29:0:24:0:1:0:27:2:0.0714:0:1 -3 49725854 . C T 44 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08997;SOR=6.89062;LSEQ=AGCAGACGTGCTAATAGAGG;RSEQ=CTAAGTGGGCAATGTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:1,0:110,4:0.0087:1,0:50:0:25:0:1:0:27:2:0.0091:0:3 0/1:52:3:2,1:46,3:0.0577:2,2:18.3:1:28.3:1:0.21738:7.08391:50:6:0.0577:0:5 -3 49725865 . A C 58 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03799;SOR=8.80393;LSEQ=TAATAGAGGCCTAAGTGGGC;RSEQ=ATGTCTATGTGTTCCTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:1,0:133,5:0.0072:1,0:39:0:14:0:1:0:27:0:0:0:3 0/1:66:4:3,1:60,2:0.0606:1,2:24:1:29:1:0.17351:9.21209:51.3:8:0.0615:0:5 -3 49725904 . G A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40035;SOR=1.44384;LSEQ=GGCTTCCCAGCTGTGCTCAA;RSEQ=AGGGCAAGGTCACTGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:12:12,0:240,10:0.0458:1,0:10.8:1:31.3:1:1:0:34:24:0.0467:0:4.1 0/1:185:12:10,2:161,12:0.0649:2,2:25.4:1:30.6:1:0.22663:2.663:40:24:0.0656:0:4.3 -3 49725908 . G C 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1481;SOR=1.48295;LSEQ=TCCCAGCTGTGCTCAAGAGG;RSEQ=CAAGGTCACTGCCCCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:35:35,0:225,11:0.1292:1,1:14.8:1:33.3:1:0.36898:0:32.9:70:0.1311:0:3.4 0/1:194:35:31,4:146,13:0.1804:2,2:21.3:1:32:1:0.51589:1.44609:36:34:0.1799:0:3.5 -3 49725910 . A G 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21267;SOR=1.32758;LSEQ=CCAGCTGTGCTCAAGAGGGC;RSEQ=AGGTCACTGCCCCATGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:53:53,0:238,13:0.1743:2,1:11.5:1:30.6:1:0.13478:0:34.4:106:0.1749:0:2.9 0/1:210:46:39,7:151,13:0.219:2,2:17.7:1:30.2:1:0.15647:2.07637:37.3:92:0.219:0:3.2 -3 49725948 . C T 259 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58547;SOR=1.06334;LSEQ=CCACTGAGCCTCTGGCTCCC;RSEQ=GACTTTTTTCTCATCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:773:319:259,60:370,83:0.4127:2,2:23.1:1:31.2:1:0.92508:1.03268:42.6:105.333:0.4125:0:1.9 0/1:622:266:214,52:272,82:0.4277:2,2:21.3:1:31.4:1:0.32429:1.24:43.8:532:0.4283:0:1.9 -3 49726028 . T C 297 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31384;SOR=0.93445;LSEQ=GGATCAGGGTTGGGGGCACT;RSEQ=ACCAGGGACCCCTAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2110:718:353,365:733,658:0.3403:2,2:29.6:1:31.4:1:0.12933:1.15177:39.9:78.778:0.3389:0:1.7 0/1:1891:615:306,309:671,600:0.3252:2,2:28.4:1:30.7:1:0.2195:1.12922:40.7:75.875:0.3237:0:1.7 -3 49726070 . G A 263 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51626;SOR=0.9418;LSEQ=AGTCAGAAGCAGCAGGAGTG;RSEQ=GAGCCACCCCATCCTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1591:391:82,309:551,647:0.2458:2,2:19.7:1:30.6:1:0:3.20695:32.9:96.75:0.2489:0:1.8 0/1:1350:317:62,255:505,526:0.2348:2,2:19.6:1:30.3:1:0:3.94491:33.8:104.667:0.2372:0:1.8 -3 49726178 . G A 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02757;SOR=8.29986;LSEQ=GGGTGGCTCTGGCTCCACAC;RSEQ=TCAGCTCAGGGCCTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:526:1:1,0:129,396:0.0019:2,0:1:0:25:0:0.24715:0:45:2:0.0019:0:1 0/1:449:7:1,6:112,330:0.0156:2,2:12:1:30.3:1:0.68529:2.0338:40.7:14:0.0158:0:1 -3 49726318 . T C 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01857;SOR=Inf;LSEQ=GGAAGGTTTGGTGGGGACAC;RSEQ=TGAGGTGCCCTGGGGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:1,35:0:1,0:25.8:1:30:1:1:0:56.3:72:1:0:0 0/1:14:3:1,2:0,11:0.2143:0,2:28.7:1:33:1:0.21429:0:54:6:0.2143:0:1.3 -3 49924940 . T C 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.61824;LSEQ=CACCTCCCCCACTAGTACTC;RSEQ=GAAGGTGGGTCGCACTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1116:64:30,34:456,594:0.0573:2,2:24.6:1:29.6:1:0.60553:1.15:60:20.333:0.0559:0:1.2 0/1:1047:455:189,266:265,327:0.4346:2,2:24.4:1:29.7:1:0.31437:1.14041:60:112.75:0.4357:0:1.2 -3 49926904 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCTCAGCACCGAACCCACC;RSEQ=CGTAGGCACTGAGGACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:31:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29.5:1:1:0:60:4:1:0:1 -3 49927503 . G T 214 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAATGACCACTGTGGAAA;RSEQ=GGGGAGGTGAGGGGACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1089:0:0,0:443,643:0:2,0:25:1:31.2:1:1:0:60:97.727:0.9972:0:0.2 0/1:1023:151:59,92:375,496:0.1476:2,2:23.7:1:29.7:1:0.3739:1.17873:60:150:0.1473:0:1.1 -3 49927593 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15077;SOR=Inf;LSEQ=AGAGTCCTTCAGCTGGAAAT;RSEQ=GAAGACCCTACCCTCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:14,242:0:2,0:26:1:31.3:1:1:0:60:84.333:1:0:0.1 0/1:163:2:0,2:6,155:0.0123:1,0:10:1:31.5:1:1:0:60:4:0.0123:0:1 -3 49927722 . A C 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00379;SOR=Inf;LSEQ=TGGATTATCTGTGAGGAGCC;RSEQ=GTGAGTTCCCAGCCTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:43,19:0:2,0:22:1:30.7:1:1:0:60:124:1:0:0 0/1:22:4:3,1:12,6:0.1818:2,2:31:1:29.3:1:1:1.47:60:8:0.1818:0:1 -3 49928160 . GA G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20603;SOR=Inf;LSEQ=ACCTGTTCTAGGCCCTTACA;RSEQ=ATTTTTTTTTTTTTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:12,220:0:2,0:23.7:1:30.3:1:1:0:59.8:28:0.9956:0:0.4 0/1:195:2:0,2:14,179:0.0103:2,0:17.5:1:26.5:1:1:0:60:4:0.0106:0.0051:1.5 -3 49928614 . T A 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTTTGCTTCACCCCAGC;RSEQ=ACTCTGGACTCTCACATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:682:0:0,0:451,231:0:2,0:24.4:1:29.8:1:1:0:60:67.2:1:0:0.4 0/1:702:41:30,11:428,233:0.0584:2,2:26.2:1:30.6:1:0.31341:1.48:60:82:0.0591:0:1.6 -3 49928691 . T C 310 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.65445;SOR=0.74639;LSEQ=CTCTGCCAGGTACTCCATGC;RSEQ=GCGGGCTACCTGCAGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1272:1264:653,611:1,3:0.9937:2,2:25.1:1:30.4:1:0.35936:3.20:60:69.222:0.996:0:1.1 1/1:1427:1415:701,714:0,6:0.9916:0,2:25.5:1:29.7:1:0.031:0:60:82.235:0.9929:0:1.2 -3 49929025 . C A 204 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGATGCCTGCAGAGCAG;RSEQ=GCAAGTCAGGCACAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:756:0:0,0:304,451:0:2,0:25.4:1:30.5:1:1:0:60:57.077:0.9987:0:0.1 0/1:707:119:45,74:232,353:0.1683:2,2:25.8:1:29.7:1:0.75788:1.08067:60:58.5:0.1671:0:1.2 -3 49929047 . G T 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=Inf;LSEQ=CAAGTCAGGCACAGGGCAGG;RSEQ=CGTCCCTTTATAAGGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:674:0:0,0:281,393:0:2,0:23.9:1:31.4:1:1:0:60:43.933:1:0:0.1 0/1:571:30:14,16:212,329:0.0525:2,2:26.6:1:29.5:1:0.44626:1.36:60:60:0.053:0:1.1 -3 49929321 . G A 64 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02692;SOR=8.43454;LSEQ=GAGGGGATCCAGGGCCCAAG;RSEQ=CTCACACCACACATTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:796:1:1,0:244,551:0.0013:2,0:1:0:27:0:0.30779:0:60:2:0.0013:0:1 0/1:666:7:5,2:225,434:0.0105:2,2:9.6:1:22.9:1:0.05164:4.81:60:6:0.0092:0:1.3 -3 49932459 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10185;SOR=Inf;LSEQ=TTTCACTGTGTTAGCCAGGA;RSEQ=GGTCTCGATCTCCTGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:112,0:0:1,0:25.4:1:32.4:1:1:0:56:111:1:0:0 0/1:53:2:2,0:51,0:0.0377:1,0:14.5:1:29:1:1:0:50:4:0.0385:0:1.5 -3 49934446 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57;SOR=2.89701;LSEQ=CCCACCTGCCCCACTCCATG;RSEQ=TCTGTCTGAAAATAAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:1:1,0:11,162:0.0057:2,0:28:0:14:0:0.06897:0:60:0:0:0:6 0/1:121:2:1,1:1,118:0.0165:1,2:20.5:1:28.5:1:0.03292:83.68:60:4:0.0171:0:1.5 -3 49934678 . C T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00702;SOR=0;LSEQ=GGTCCCCACCTGGATAGAAC;RSEQ=CTGCGGCCTCCCATGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:7:1,6:352,167:0.0133:2,2:11.6:1:27.3:1:0.00605:12.59002:60:14:0.0136:0:1 0/0:539:0:0,0:366,172:0:2,0:23.3:1:30:1:1:0:60:88.667:0.9981:0:0.2 -3 49935385 . TC T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00545;SOR=Inf;LSEQ=AACCACTGCAGCTTCCCCCA;RSEQ=CCCCCTTGCCTCTGATAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:711:0:0,0:463,247:0:2,0:24.6:1:30.8:1:1:0:60:63.545:0.9986:0:0.1 0/1:646:7:3,4:422,217:0.0108:2,2:13:1:27.9:1:0.2383:2.5888:60:14:0.0111:0.0062:0.6 -3 49935526 . T G 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGTGGCCGGCAGGGACTT;RSEQ=GGCCCACAGTGACCTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1498:0:0,0:750,745:0:2,0:24.4:1:30.1:1:1:0:60:64:0.998:0:0.1 0/1:1574:34:15,19:748,789:0.0216:2,2:22.3:1:31:1:0.60878:1.2007:60:68:0.0218:0:1.3 -3 49936102 . T C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.41442;LSEQ=AGTGGCGGCAGCCAGGGCCT;RSEQ=GGATAGGTACCTGGAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1339:74:35,39:584,679:0.0553:2,2:24.7:1:30.1:1:0.90477:1.04:60:36:0.0549:0:1.1 0/1:1309:551:244,307:348,406:0.4209:2,2:23.6:1:30:1:0.53583:1.07839:60:41.385:0.419:0:1.2 -3 49936278 . G A 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCCACAACCCTGGCCCCAG;RSEQ=CCCTGCCCCTGCCCACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:0:0,0:478,303:0:2,0:24.7:1:31.2:1:1:0:60:36.19:1:0:0.1 0/1:740:41:25,16:446,252:0.0554:2,2:19.7:1:28:1:0.73935:1.1325:60:82:0.0566:0:1.1 -3 49936626 . G A 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=41.99761;LSEQ=CATTGAATAGGTCCACACGT;RSEQ=AGAAGCTGCTACTGACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1292:2:2,0:618,672:0.0015:2,0:1:0:26.5:1:0.23009:0:60:4:0.0016:0:1 0/1:1504:92:49,43:693,718:0.0612:2,2:23:1:28.4:1:0.45323:1.18:60:45:0.0605:0:1.2 -3 49936715 . G A 214 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=155.15548;LSEQ=GGCTGGGAAAGGTCAGGGAA;RSEQ=GGAAGGAGTCAGGGTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:1:1,0:234,478:0.0014:2,0:1:0:26:0:0.32959:0:60:2:0.0014:0:1 0/1:728:130:43,87:214,384:0.1786:2,2:22.7:1:30.6:1:0.61306:1.12732:60:129:0.1784:0:1.2 -3 49936910 . T A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00923;SOR=Inf;LSEQ=GCCCAGGCTGGAAGGTCCAC;RSEQ=CCTCATTCTCCCTGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:0:1,0:24.8:1:28.9:1:1:0:60:22:1:0:0.1 1/0:3:2:0,2:0,1:0.6667:0,0:7.5:1:31:0:1:0:60:4:0.6667:0:1 -3 49939587 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05303;SOR=Inf;LSEQ=GCAGGTAGGGGAAAGAGCAA;RSEQ=ATGAGGCAGCCACAAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:0:1,0:25.9:1:32.6:1:1:0:60:50:1:0:0.4 0/1:8:2:2,0:6,0:0.25:0,0:9:1:30:0:1:0:60:4:0.25:0:1 -3 49939704 . G A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26877;SOR=0;LSEQ=GAGAGAGAATGCTTCTTTCC;RSEQ=CCTGCCCCCCCACCGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:2,1:254,7:0.0113:1,2:25.7:1:23.3:1:0.08851:17.41132:60:2:0.0078:0:2 0/0:190:0:0,0:185,5:0:1,0:24.1:1:29.8:1:1:0:60:37:1:0:0.2 -3 49940812 . G T 157 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=19.24759;LSEQ=TCAGGCCCAAGCACATGCAG;RSEQ=CGATTGCGTATGGCTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1359:2:0,2:662,693:0.0015:2,0:25.5:1:19.5:1:0.49993:0:60:1:8e-04:0:4.5 0/1:1558:43:20,23:738,775:0.0276:2,2:25.9:1:29:1:0.87731:1.09501:60:42:0.0274:0:1.1 -3 50138144 . TA T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CCAAAGGAGTGACTTTTTTT;RSEQ=AAAAAAAAGCTTTGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:29.6:1:30.9:1:1:0:60:14:1:0:0 0/1:6:2:0,2:0,4:0.3333:0,0:13.5:1:31.8:1:1:0:60:4:0.3333:0.1667:0 -3 50153003 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53529;SOR=Inf;LSEQ=CCAGTTCCCGAACAAAGATG;RSEQ=CCTAGTCAGGCACCAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:33.8:1:30.9:1:1:0:60:18:1:0:0.4 0/1:35:2:1,1:13,20:0.0571:2,2:43.5:1:29.5:1:1:1.52:60:4:0.0588:0:2 -3 50154728 . T A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16304;SOR=0;LSEQ=GGCATTGACCACAGTAACAT;RSEQ=GGCAACAAGATGCTGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:33:0:30.5:1:1:1:60:4:0.2:0:1 0/0:14:0:0,0:7,7:0:2,0:30.1:1:29.7:1:1:0:60:28:1:0:0.2 -3 50231540 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4902;SOR=0;LSEQ=CGCAGGATGTTCGATGTGGG;RSEQ=GGGCAGCGCTCGGAGCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:0.0769:2,2:40:0:32:1:1:1:60:4:0.0769:0:1 0/0:25:0:0,0:12,13:0:2,0:28.6:1:30.6:1:1:0:60:50:1:0:0.2 -3 52167577 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50113;SOR=Inf;LSEQ=ACACCAGCACACAGGTCCAG;RSEQ=CCAGGAGACCCAGGGCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:50,94:0:2,0:24.1:1:31.3:1:1:0:60:143:1:0:0.1 0/1:167:2:1,1:63,102:0.012:2,2:19.5:1:27.5:1:1:1.61:60:4:0.0123:0:1.5 -3 52436262 . C T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0422;SOR=Inf;LSEQ=GGGAAGGACCCTGGTGAGGG;RSEQ=CACACGGCAAGAGTGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:0:0,0:336,123:0:2,0:25.5:1:31.5:1:1:0:60:56.375:1:0:0.1 0/1:382:4:1,3:265,113:0.0105:2,2:9:1:28:1:0.08539:6.99565:60:8:0.0105:0:1 -3 52436441 . C A 231 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGGTTGGCCAGCATGCCTG;RSEQ=GAAGAGGTAGAGACCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:188:73,115:87,163:0.4282:2,2:24.8:1:30.6:1:0.42287:1.19:60:61.667:0.4263:0:1.1 0/0:333:0:0,0:116,217:0:2,0:21.9:1:30.2:1:1:0:60:110:1:0:0.1 -3 52436456 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06808;SOR=Inf;LSEQ=GCCTGCGAAGAGGTAGAGAC;RSEQ=CTTGAGCAGGTGCTGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:122,231:0:2,0:24.5:1:31.1:1:1:0:60:49.429:1:0:0.5 0/1:246:3:2,1:75,168:0.0122:2,2:5.7:1:28:1:0.2316:4.45:60:6:0.0124:0:1 -3 52436473 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13489;SOR=Inf;LSEQ=GACCCTTGAGCAGGTGCTGG;RSEQ=TGCCTCAGGCCAGGAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:119,173:0:2,0:23.5:1:31.9:1:1:0:60:31.444:1:0:0.4 0/1:170:2:1,1:55,112:0.0118:2,2:33.5:1:28:1:1:2.03:60:4:0.012:0:1 -3 52436545 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08374;SOR=Inf;LSEQ=CTGCTCAAGCCTCAGGAGAG;RSEQ=CCAGGGGAGGGGAGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:187,109:0:2,0:23.7:1:31.3:1:1:0:60:48.333:0.9966:0:0.1 0/1:232:3:0,3:151,77:0.0129:2,0:6.7:1:26.7:1:0.04052:0:60:6:0.0132:0:1 -3 52436946 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17879;SOR=Inf;LSEQ=CCAGCAACAAAGCCCCACGA;RSEQ=CAATAGGCAGCTAGAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:37,193:0:2,0:22.2:1:31.5:1:1:0:60:22:1:0:0.2 0/1:169:2:1,1:17,150:0.0118:2,2:29.5:1:28:1:0.20224:8.60:60:4:0.012:0:1 -3 52438183 . A T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAAGCTGCCTCCCCACC;RSEQ=CCCACATCTCCTCCATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:10,39:0.0392:2,2:5:0:31.5:1:0.38824:3.77:60:4:0.0408:0:0 0/0:18:0:0,0:3,15:0:2,0:27.7:1:27.4:1:1:0:60:8:1:0:0.1 -3 52438386 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0902;SOR=Inf;LSEQ=GCTCAACATTATCTGCTGCA;RSEQ=GGCATTCTCAGACACAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:168,14:0:2,0:22.8:1:32.1:1:1:0:60:90:1:0:0 0/1:149:3:2,1:128,18:0.0201:2,2:18.7:1:28.3:1:0.33782:3.51008:60:6:0.0203:0:1 -3 52438651 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5027;SOR=0;LSEQ=CAAGTGCTGCTCGGCCCAGG;RSEQ=TGAGCCTAGACACTCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:29,133:0.0122:2,2:26.5:1:29:1:0.33331:4.53:60:4:0.0123:0:1 0/0:136:0:0,0:23,113:0:2,0:27:1:32.1:1:1:0:60:67:1:0:0.1 -3 52439375 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19911;SOR=Inf;LSEQ=CAAGAAAAGCTCACAGTCTC;RSEQ=CCGGCCCTGTGAACCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:21,100:0:2,0:22.3:1:31.3:1:1:0:60:59.5:1:0:0.1 0/1:98:2:1,1:14,82:0.0204:2,2:32.5:1:28.5:1:0.28403:5.69:60:4:0.0215:0:1 -3 52440173 . GT G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.19536;SOR=Inf;LSEQ=AAGCCCAGATCTACAAGAGA;RSEQ=ATGTTCACGAATCAGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:168,22:0:2,0:23.5:1:29.3:1:1:0:60:30.667:1:0:0.1 0/1:151:2:1,1:129,20:0.0132:2,2:33:1:31.5:1:0.2596:6.31891:60:4:0.0133:0:0 -3 52440188 . A G 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07993;SOR=Inf;LSEQ=AGAGAGTATGTTCACGAATC;RSEQ=GAGACAAATGCTGTGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:210,49:0:2,0:23.2:1:30.1:1:1:0:60:31.375:1:0:0.1 0/1:197:3:2,1:158,36:0.0152:2,2:14.3:1:28.7:1:0.46615:2.18367:60:6:0.0155:0:1 -3 52440195 . A T 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26296;SOR=0;LSEQ=ATGTTCACGAATCAGAGACA;RSEQ=ATGCTGTGGGGGAAGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:0,3:229,64:0.0101:2,0:9.3:1:20.7:1:0.0112:0:60:2:0.0069:0:1.3 0/0:224:0:0,0:176,48:0:2,0:22.7:1:29.1:1:1:0:60:27:1:0:0.2 -3 52440742 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.20959;SOR=Inf;LSEQ=AAGCCTGATCTTGCCAGATT;RSEQ=ACCATATGGCCTTGCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:174,22:0:2,0:23.6:1:31.4:1:1:0:60:48:1:0:0.1 0/1:166:2:1,1:145,19:0.012:2,2:9.5:1:28.5:1:0.22709:7.46392:60:4:0.0121:0:1 -3 52441559 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2224;SOR=Inf;LSEQ=AGGCAAAGCTTCAGAGAGCA;RSEQ=CCTGGAGGCATTCCAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:34,166:0:2,0:23.8:1:32:1:1:0:60:49:1:0:0.1 0/1:179:2:1,1:31,146:0.0112:2,2:26.5:1:31:1:0.32641:4.65:60:4:0.0112:0:1 -3 52441564 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21907;SOR=Inf;LSEQ=AAGCTTCAGAGAGCAGCCTG;RSEQ=AGGCATTCCAGGAATCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:24,154:0:2,0:24.3:1:31.4:1:1:0:60:88:0.9944:0:0.1 0/1:158:2:1,1:21,135:0.0127:2,2:19:1:31:1:0.25986:6.30:60:4:0.0127:0:1 -3 52441565 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22137;SOR=Inf;LSEQ=AGCTTCAGAGAGCAGCCTGG;RSEQ=GGCATTCCAGGAATCGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:23,152:0:2,0:24.2:1:31.2:1:1:0:60:57.333:1:0:0 0/1:156:2:1,1:20,134:0.0128:2,2:30:1:29.5:1:0.25186:6.56:60:4:0.0131:0:1 -3 52441589 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21382;SOR=Inf;LSEQ=ATTCCAGGAATCGGAAGGAA;RSEQ=ACAGACGAACTTTCTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:8,110:0:2,0:23.3:1:32.3:1:1:0:60:58:1:0:0.1 0/1:102:2:1,1:4,96:0.0196:1,2:27.5:1:26.5:1:0.0961:21.58:60:4:0.0198:0:1 -3 52441606 . A T 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02849;SOR=Inf;LSEQ=GAACACAGACGAACTTTCTT;RSEQ=AAAGGCTGGTGGGGGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:5,76:0:2,0:25.5:1:30:1:1:0:60:39.5:1:0:0.1 0/1:58:4:0,4:2,52:0.069:1,0:23.5:1:25:1:1:0:60:8:0.069:0:1 -3 52442055 . G A 78 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09143;SOR=0.24906;LSEQ=CTGCTGCAGTTCAGGAGCAC;RSEQ=CTCAGCAAGGCATGAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:594:7:5,2:253,334:0.0118:2,2:15.3:1:28.1:1:0.24866:3.29:60:14:0.0119:0:1 0/0:676:2:2,0:320,354:0.003:2,0:1:0:24.5:1:0.22652:0:60:4:0.003:0:1 -3 52442131 . C A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24904;SOR=Inf;LSEQ=GTCACCCATACACAGCACCC;RSEQ=TCACTGCAAGCCCCAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:73,189:0:2,0:25.1:1:31.5:1:1:0:60:51.4:1:0:0.1 0/1:275:3:1,2:73,199:0.0109:2,2:14.3:1:25.7:1:1:1.36:60:2:0.0074:0:2 -3 52442132 . T C 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11587;SOR=0;LSEQ=TCACCCATACACAGCACCCC;RSEQ=CACTGCAAGCCCCAAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:1,2:71,181:0.0118:2,2:22:1:23.7:1:1:1.27:60:2:0.0081:0:3 0/0:267:0:0,0:70,196:0:2,0:23.9:1:28.7:1:1:0:60:21.167:0.9961:0:0.2 -3 52442142 . C A 43 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05619;SOR=Inf;LSEQ=ACAGCACCCCTCACTGCAAG;RSEQ=CCCAAGCCCATATACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:56,169:0:2,0:25.4:1:31.1:1:1:0:60:44:1:0:0.2 0/1:215:4:3,1:44,167:0.0186:2,2:5.8:1:21.8:1:0.03353:11.21:60:3:0.0143:0:1.8 -3 52442625 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.232;SOR=Inf;LSEQ=ATAAATCCATATACAGGGCT;RSEQ=GGGGAAGTAAGGGGCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:54,151:0:2,0:23.6:1:30.8:1:1:0:60:50.25:1:0:0.1 0/1:191:2:1,1:47,141:0.0105:2,2:9:0:32:0:0.44244:2.98:60:4:0.0105:0:2.5 -3 52443494 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05861;SOR=Inf;LSEQ=GGGTTCCTGGCACTGTCTTC;RSEQ=CTAAGGGGCCCTGTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:205,65:0:2,0:22.4:1:30.4:1:1:0:60:37.571:1:0:0.1 0/1:264:4:1,3:194,66:0.0152:2,2:12.5:1:23.3:1:0.05601:8.73023:60:3:0.0115:0:1.3 -3 52444117 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACAGCAGATGCGGGCATG;RSEQ=GCTCGAAGGCGAACGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:27:1:30.5:1:1:0:60:4:0.2222:0:1 0/0:1:0:0,0:0,1:0:0,0:32:0:31:0:1:0:60:2:1:0:0 -3 52526796 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1787;SOR=Inf;LSEQ=CACGTGACACTGTGGGTCTG;RSEQ=CTTTCTCTTCTACACGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:73,26:0:2,0:22.6:1:29.5:1:1:0:59.9:98:1:0:0.2 0/1:73:2:1,1:51,20:0.0274:2,2:28:1:30:1:0.49543:2.51283:57.5:4:0.0282:0:1 -3 52526815 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10079;SOR=Inf;LSEQ=GACTTTCTCTTCTACACGTC;RSEQ=TTTCCTGAAGTGTCGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:90,49:0:2,0:24.9:1:30.7:1:1:0:60:45.333:1:0:0.2 0/1:122:3:1,2:72,47:0.0246:2,2:10.3:1:23.3:1:0.56384:3.0354:60:2:0.0171:0:1 -3 52526820 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22902;SOR=Inf;LSEQ=TCTCTTCTACACGTCCTTTC;RSEQ=TGAAGTGTCGAGTCCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:96,56:0:2,0:25:1:30.7:1:1:0:60:49.667:1:0:0.2 0/1:140:2:1,1:82,54:0.0143:2,2:20:1:28:1:1:1.51376:60:4:0.0146:0:1 -3 52526835 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22733;SOR=Inf;LSEQ=CTTTCCTGAAGTGTCGAGTC;RSEQ=AGTCCTTTGTTGCTGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:107,79:0:2,0:26.2:1:31.3:1:1:0:60:61:1:0:0.2 0/1:170:2:1,1:100,68:0.0118:2,2:21:0:32:0:1:1.46714:60:4:0.0122:0:1 -3 52526842 . TTGTTGC T 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=6.000;MSILEN=6;SSF=0.81417;SOR=0.93971;LSEQ=GAAGTGTCGAGTCCAGTCCT;RSEQ=TGTTGCTGTTGCTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:153:74,79:35,8:0.7688:2,2:25.1:1:30.5:1:0.00011:4.63627:60:306:0.7727:0.201:0.1 1/0:198:150:81,69:29,11:0.7576:2,2:25.6:1:29.6:1:0.04681:2.23664:59.7:49:0.7538:0.1768:0.2 -3 52581999 . TC T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.61731;SOR=0.48077;LSEQ=AATTATCCTCCTTTGTTCCT;RSEQ=CCCCCACCCCCAGTAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:135,6:0.014:1,2:23.5:1:29.5:1:0.09583:20.90802:60:4:0.0143:0.007:0.5 0/0:148:1:1,0:131,16:0.0068:2,0:28:0:27:0:1:0:60:2:0.007:0:0 -3 52582031 . G T 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32904;SOR=0.26704;LSEQ=CAGTAACTAAAATGGCTACT;RSEQ=ATCCACAACTCTTTATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:2,1:192,55:0.012:2,2:19.3:1:24.7:1:0.53434:1.74101:60:2:0.0083:0:1.7 0/0:310:1:0,1:238,71:0.0032:2,0:1:0:24:0:0.23226:0:60:2:0.0033:0:1 -3 52584415 . G T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12436;SOR=Inf;LSEQ=GAAGCATGTATTTCACAAAG;RSEQ=CTTATTTAGAAGGAATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:266,119:0:2,0:25.2:1:31.2:1:1:0:59.9:63.167:1:0:0.1 0/1:401:4:1,3:264,133:0.01:2,2:23.8:1:25.3:1:0.11523:5.9272:60:3:0.0076:0:2.3 -3 52584431 . T TCTC 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.74331;SOR=0.95438;LSEQ=AAAGGCTTATTTAGAAGGAA;RSEQ=CTTACCTGCCAGTGTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:209:146,63:177,96:0.4336:2,2:24.6:1:30.7:1:0.28232:1.26:59.9:68.667:0.4319:0.1266:0.2 0/1:469:198:124,74:179,92:0.4222:2,2:29.8:1:30.8:1:0.49389:1.16074:60:197:0.4246:0.0192:0.2 -3 52584477 . C T 85 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01454;SOR=0.10646;LSEQ=TTGCTAATGCTGTTGGACTC;RSEQ=GCACTGAGTCCTTCAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:703:8:2,6:399,296:0.0114:2,2:7.5:1:28.6:1:0.08048:4.03628:60:16:0.0115:0:1 0/0:818:1:0,1:457,359:0.0012:2,0:1:0:25:0:0.44064:0:60:2:0.0012:0:2 -3 52584715 . A G 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02658;SOR=0.78917;LSEQ=CTGCACATGTTCTGAGAAGG;RSEQ=TAACTCGAATTCTGTCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:722:293:174,119:242,187:0.4058:2,2:25.1:1:31.2:1:0.44379:1.13:60:25.636:0.3994:0:1.4 0/1:811:284:154,130:272,255:0.3502:2,2:25.1:1:30.7:1:0.5073:1.11:60:39.571:0.3471:0:1.5 -3 52584787 . T C 259 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00752;SOR=0.77274;LSEQ=TGTCCATATGGACTTCCACC;RSEQ=GGTGCTGGAGTCCCTACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:913:383:190,193:247,282:0.4195:2,2:25.6:1:30.2:1:0.42037:1.12:60:75.6:0.4205:0:1.4 0/1:935:335:158,177:283,317:0.3583:2,2:24.3:1:29.6:1:1:1.00012:60:82.75:0.3575:0:1.5 -3 52588655 . G A 115 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04678;SOR=0.38313;LSEQ=GCCTGGCCACAATGGGCCAC;RSEQ=GGTGCCTCCTGGAACAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:15:13,2:101,15:0.1145:2,2:19.7:1:29.5:1:1:1.03562:60:14:0.1077:0:1 0/1:170:8:7,1:128,34:0.0471:2,2:20.6:1:30.3:1:1:1.85:60:16:0.0473:0:1 -3 52592204 . G GA 170 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.75793;SOR=0.9214;LSEQ=GTGGCCTACTCCTTATTGGA;RSEQ=AAAAAAAAAATGAAGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:48:32,16:297,117:0.1021:2,2:25.1:1:29.1:1:0.50124:1.26859:60:23:0.1015:0.0255:0.3 0/1:622:59:36,23:386,171:0.0949:2,2:23.6:1:28.9:1:0.2378:1.4413:60:118:0.0975:0.0048:0.2 -3 52592427 . G A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13454;SOR=Inf;LSEQ=CTCAGCAACTTTAGCTGCCC;RSEQ=CTCTGTAAAGGCATTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:77,219:0:2,0:22.3:1:31.7:1:1:0:60:97.667:1:0:0.1 0/1:376:4:3,1:123,249:0.0106:2,2:15.8:1:28.8:1:0.1115:6.04:60:8:0.0107:0:1 -3 52592471 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25662;SOR=Inf;LSEQ=TCAATTCTGTTTTTAACCCA;RSEQ=GAATTCAAAATACCATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:32,106:0:2,0:26.5:1:31:1:1:0:60:33.5:1:0:0.1 0/1:172:3:2,1:48,121:0.0174:2,2:7:1:22.3:1:0.20286:4.99:53.3:2:0.0118:0:2.3 -3 52595715 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.08769;SOR=0;LSEQ=TAAGAACAAGAGTAAAACCT;RSEQ=TCTGTGCGCGTGCATTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:224,57:0.0106:2,2:23:1:25:1:0.49744:1.95946:60:2:0.0072:0:1 0/0:354:0:0,0:252,102:0:2,0:22.6:1:31.3:1:1:0:60:87.5:1:0:0.1 -3 52596058 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23683;SOR=Inf;LSEQ=CTCAAAATTTCAGAAGCCAG;RSEQ=CGGGCGCGGTGGCTCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:4,121:0:1,0:23.4:1:31.1:1:1:0:60:40.667:1:0:0 0/1:119:2:1,1:1,116:0.0168:1,2:17:1:31:1:0.03347:82.30:60:4:0.0168:0:1 -3 52596173 . TA T 50 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.50909;SOR=0;LSEQ=CAGTGAAACCCCGTTTCTAC;RSEQ=AAAAAAAAAATACAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:23.3:1:31.7:1:1:0:59.7:6:0.3333:0:0 0/0:3:0:0,0:0,3:0:0,0:11.3:1:27.3:1:1:0:60:2:1:0:0 -3 52596398 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGTGATTCACTAGTTAC;RSEQ=GCTTTATTGACACGTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:41.3:1:30.3:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 52597664 . G A 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00055;SOR=0;LSEQ=GAGTTTAAATGTGTATTTAT;RSEQ=AAATTACTTGTACTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:3,13:1,8:0.64:2,2:22.6:1:29.7:1:1:1.80:60:32:0.64:0:1 0/0:10:0:0,0:0,10:0:0,0:16.7:1:31.8:1:1:0:60:20:1:0:0 -3 52598289 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49873;SOR=Inf;LSEQ=AGAAATTAAAGGAGTAAACT;RSEQ=TGGTCATAGTTACTAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:28,165:0:2,0:22.1:1:32:1:1:0:60:63.333:0.9948:0:0.1 0/1:196:2:1,1:33,161:0.0102:2,2:11:1:30.5:1:0.31758:4.82:60:4:0.0102:0:1 -3 52598290 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24805;SOR=Inf;LSEQ=GAAATTAAAGGAGTAAACTG;RSEQ=GGTCATAGTTACTAACTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:28,165:0:2,0:21.8:1:30:1:1:0:60:37.6:1:0:0.1 0/1:192:2:1,1:32,158:0.0104:2,2:8.5:1:29:1:0.31495:4.88:60:4:0.0105:0:1 -3 52598540 . G A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATGTTGTGGTGCATGCCTGT;RSEQ=GTCCCAGCTACTCGGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:39:0:27:0:1:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:1:0,2:19:1:28:1:1:0:60:4:1:0:1.5 -3 52610415 . T C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22159;SOR=0.5812;LSEQ=TTTATCGACTGACTCCCCAA;RSEQ=CTCTGCCCCAACATAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:31:31,0:31,1:0.4921:1,1:24.9:1:33:1:1:0:60:62:0.5:0:1.1 0/1:39:14:14,0:24,1:0.359:1,1:23.2:1:31.7:1:1:0:60:28:0.359:0:1 -3 52610651 . T A 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.54396;LSEQ=GGCTCATGCTCTGTTTCTTC;RSEQ=GGGTGAATGAAGATGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:310:137,173:167,209:0.4506:2,2:25.8:1:30.4:1:1:1.009:60:61:0.4532:0:1.1 0/1:762:235:114,121:254,273:0.3084:2,2:26.6:1:30:1:0.93763:1.01:59.9:57.75:0.3068:0:1.2 -3 52613278 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23987;SOR=0;LSEQ=AAGGAATAGAGAAGGTAAGA;RSEQ=ACGAAAGCAGACTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:7,147:0.0128:1,2:17.5:1:30:1:0.10025:19.71:60:4:0.0128:0:1 0/0:162:0:0,0:12,150:0:2,0:24.3:1:30.4:1:1:0:60:324:1:0:0.1 -3 52620360 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17476;SOR=0;LSEQ=GTTGTTGCTCTTTTTCTAAG;RSEQ=TTGAATACTTTATTCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:134,29:0.0121:2,2:23.5:1:30.5:1:0.33149:4.55997:60:4:0.0123:0:1 0/0:229:0:0,0:172,57:0:2,0:24:1:29.4:1:1:0:60:228:1:0:0 -3 52620628 . GT G 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00518;SOR=0;LSEQ=TAATTTTCTTAAAAGATTTG;RSEQ=TTTGGCAGAATACCGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:516:6:2,4:195,310:0.0116:2,2:24.2:1:31.7:1:1:1.25749:60:12:0.0121:0:0.2 0/0:721:0:0,0:308,410:0:2,0:25.7:1:29:1:1:0:60:28.917:1:0:0.2 -3 52620713 . TG T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.19808;SOR=0;LSEQ=CTTAAAGTATTCCTGGGGGG;RSEQ=GGGAGGGCATAAGAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:62,136:0.01:2,2:27.5:1:33:1:0.53186:2.18:60:4:0.0103:0:0 0/0:250:0:0,0:68,182:0:2,0:23.4:1:30:1:1:0:60:49:1:0:0.4 -3 52621607 . A T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67553;SOR=0.62581;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=AAGAGACTGGGTCTCACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:0,3:1,71:0.0395:1,0:9.7:1:28.7:1:1:0:53.3:6:0.04:0:1.7 0/1:80:2:0,2:1,76:0.025:1,0:19:1:26.5:1:1:0:60:4:0.0256:0:2.5 -3 52621627 . C T 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.37173;SOR=1.60661;LSEQ=AAAGAGACTGGGTCTCACTA;RSEQ=GTTGCCCAGGCTGGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:0,17:0,28:0.3696:1,1:23.3:1:28.9:1:1:0:55.9:16:0.381:0:1.5 0/1:37:18:0,18:0,19:0.4865:1,1:22.6:1:29.7:1:1:0:58:36:0.4865:0:2.3 -3 52623304 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50055;SOR=0;LSEQ=AATAAATAAATAAAGGAAAA;RSEQ=GGTACTCACCAAAGGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:16,130:0.0135:2,2:35:1:30:1:0.21723:7.91:60:4:0.0137:0:1.5 0/0:129:0:0,0:15,114:0:2,0:22.5:1:30.5:1:1:0:60:128:1:0:0.1 -3 52637486 . C G 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00063;SOR=1.78309;LSEQ=CACAGCTAATTATGAGAACA;RSEQ=CTAGAAGACAGTGCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:137:99,38:113,40:0.4724:2,2:22.6:1:31.5:1:0.79173:1.08404:60:67.5:0.4704:0:1 1/0:291:179:135,44:80,32:0.6151:2,2:20.9:1:31.7:1:0.49373:1.23:60:178:0.6159:0:1.1 -3 52643258 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49843;SOR=Inf;LSEQ=AGTGGAAATAGTACATCAAA;RSEQ=CAATATTCTTTCATCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:118,18:0:2,0:24.1:1:31.9:1:1:0:60:44.333:1:0:0.4 0/1:142:2:1,1:113,27:0.0141:2,2:17:1:27.5:1:0.35661:4.12792:60:4:0.0143:0:1 -3 52643307 . A G 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00141;SOR=0.60698;LSEQ=ATAGCACATATCCTCAAAAT;RSEQ=AAAATGGCTTTGAAAACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:139:106,33:138,41:0.4357:2,2:25.4:1:31.5:1:0.89402:1.04774:60:45.333:0.4317:0:1 0/1:395:126:88,38:186,83:0.319:2,2:23.7:1:31.3:1:0.90739:1.03:60:125:0.3189:0:1.1 -3 52643685 . T C 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.56091;LSEQ=AAAGACTCCGGCTCATTGTA;RSEQ=GTACAGGCATTATTAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:197:97,100:110,90:0.4937:2,2:23.9:1:30.7:1:0.26982:1.25928:60:97.5:0.4924:0:1.1 0/1:464:164:79,85:167,133:0.3534:2,2:23.2:1:30.2:1:0.14437:1.3501:60:328:0.3565:0:1.1 -3 52649349 . A T 64 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03098;SOR=Inf;LSEQ=TAGACTAAACTAAATAATGA;RSEQ=GTGTGAGGCTGCCTTACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:304,121:0:2,0:25.7:1:30.2:1:1:0:60:84:1:0:0.1 0/1:446:6:0,6:281,159:0.0135:2,0:7:1:24.8:1:0.00242:0:60:5:0.0114:0:1 -3 52649748 . A G 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCACTGCAGGTTTTAACA;RSEQ=AAGTCCTGAAACACATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:19:1:30.3:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 52651966 . A C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCCTCACTTCCAAGTACA;RSEQ=AAACAAAACAAAATAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 52659079 . T C 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00159;SOR=Inf;LSEQ=GTCCAAAGTACCAAAGACAA;RSEQ=ATTTGAAACATTTCAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:0,55:0:1,0:22.9:1:28.3:1:1:0:60:54:1:0:0.2 0/1:48:8:0,8:1,39:0.1667:1,0:18.1:1:32.4:1:1:0:60:16:0.1702:0:1.1 -3 52659124 . T C 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20003;SOR=0.3943;LSEQ=ACAGATGTTGGCAGAAAGAA;RSEQ=GCACCCCCAGAATGAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:15:0,15:0,13:0.5357:1,1:25.3:1:30.2:1:1:0:60:30:0.5357:0:1 0/1:13:4:0,4:0,9:0.3077:0,0:21.5:1:31:1:1:0:60:8:0.3077:0:1 -3 52661018 . G GA 51 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAAAATGCCACATTAAAA;RSEQ=AAAAAAAAAAACCCAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:18.3:1:25.8:1:1:0:60:3:0.375:0:2.3 0/0:1:0:0,0:1,0:0:0,0:44:0:34:0:1:0:60:2:1:0:0 -3 52661194 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50055;SOR=Inf;LSEQ=TACCATTTATTTAAAGCTTA;RSEQ=AACTTGATAGCTTAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:135,17:0:2,0:24:1:31.9:1:1:0:60:75:1:0:0.1 0/1:173:2:1,1:147,24:0.0116:2,2:13:1:24:1:0.26885:6.02165:60:4:0.0117:0:1 -3 52661422 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50169;SOR=Inf;LSEQ=TCTCAGGAGTTGAGCTCATG;RSEQ=GCCAAACACTCCTCTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:38,134:0:2,0:21.9:1:30:1:1:0:60:344:1:0:0.1 0/1:201:2:1,1:42,157:0.01:2,2:13:1:28:1:0.38294:3.71:60:4:0.01:0:1 -3 52661640 . G C 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCATTTATGACTATAATG;RSEQ=GTGCTAACTGGTTAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:8.7:1:30.7:1:1:0:60:6:0.4286:0:1 0/0:1:0:0,0:0,1:0:0,0:35:0:32:0:1:0:60:2:1:0:0 -3 52662722 . T A 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8237;LSEQ=GGTCTTGAACTCCTGAGCTC;RSEQ=AGTGATTCTCTCACCTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:11,0:9,0:0.55:0,0:24.6:1:31:1:1:0:60:22:0.55:0:1.5 1/0:10:5:5,0:5,0:0.5:0,0:26.8:1:31.8:1:1:0:60:10:0.5:0:1 -3 52662814 . TG T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.17342;SOR=0;LSEQ=TGTAATATTACTGCTGAGGG;RSEQ=GGGGGGATCACACATCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:2,0:73,3:0.0253:1,0:30:1:33.5:1:1:0:60:4:0.026:0:0 0/0:110:0:0,0:100,9:0:2,0:21.8:1:31.4:1:1:0:60:218:0.9909:0:0.1 -3 52663039 . C A 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30612;SOR=0.21625;LSEQ=AAAGTTTCATATTCTTGATT;RSEQ=TTCAGTTTTGTTCTGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:91,201:0.0102:2,2:8:1:24.7:1:0.23467:4.39:60:6:0.0105:0:1 0/0:452:1:0,1:170,281:0.0022:2,0:27:0:29:0:1:0:60:2:0.0023:0:1 -3 52663084 . T A 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGAAATTGCTAGAATTTTC;RSEQ=GTCATGAAAATTATGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:15:2,13:24,118:0.0955:2,2:22.4:1:31.4:1:1:1.31985:60:30:0.0962:0:1.3 0/0:215:0:0,0:51,164:0:2,0:22.2:1:30.2:1:1:0:60:430:1:0:0.1 -3 52663113 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.97158;LSEQ=AATTATGAAACATTCTTCCT;RSEQ=AAAGTCCAATGCAAAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:1:0,1:7,85:0.0108:2,0:47:0:16:0:1:0:60:0:0:0:4 0/1:95:2:0,2:10,83:0.0211:2,0:24:1:28.5:1:1:0:60:4:0.0211:0:1 -3 52668499 . T TA 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22118;SOR=Inf;LSEQ=GAACAGTTAAAATTTGAGGT;RSEQ=AAAAAAAAACACCATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:55,2:0:1,0:24.5:1:28.6:1:1:0:60:7.143:0.9804:0:0.7 0/1:52:2:2,0:49,0:0.0385:1,0:23:1:28.2:1:1:0:60:4:0.0417:0.0192:2 -3 52668863 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22022;SOR=0;LSEQ=AAAAAAGTATTTATAAAGGG;RSEQ=CGAATGAGATGAAGAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:34,143:0.0111:2,2:18.5:1:30.5:1:0.35371:4.16:60:4:0.0114:0:1 0/0:203:0:0,0:43,160:0:2,0:21.1:1:28.6:1:1:0:60:49.75:1:0:0.1 -3 52676065 . C T 169 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0.12378;SOR=0.76952;LSEQ=GTACTGCTCTTTTATTACTA;RSEQ=AAAAAAAAAAAAAGCAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:113:35,78:65,121:0.3038:2,2:21.6:1:24.9:1:0.52826:1.19645:59.8:3.913:0.3136:0:1.5 0/1:390:98:44,54:91,156:0.2513:2,2:21.1:1:25.9:1:0.1797:1.40:60:7.167:0.2688:0:1.4 -3 52676079 . G A 51 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06168;SOR=0;LSEQ=TTACTACAAAAAAAAAAAAA;RSEQ=CAATTAGACAGGGAAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:5:3,2:64,237:0.0162:2,2:13.8:1:22.2:1:0.07189:5.51:60:1.5:0.0117:0:2 0/0:298:0:0,0:68,229:0:2,0:7:0:11:0:1:0:60:0:0:0:2 -3 52676190 . A C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43029;SOR=0.5979;LSEQ=TTCTATTCAATTGCCTCCTT;RSEQ=GTTTATCTCTGTACTTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:0,15:0,16:0.4839:1,1:27.9:1:30.5:1:1:0:60:30:0.4839:0:1 0/1:28:10:0,10:0,17:0.3571:1,0:27:1:30.1:1:1:0:60:20:0.3571:0:1 -3 52677387 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00403;SOR=Inf;LSEQ=GAGATAAGATAAAAAGCTTA;RSEQ=AAACTTGGTAGCTGAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:24,197:0:2,0:24.5:1:31.2:1:1:0:60:72.667:1:0:0.1 0/1:247:9:2,7:36,201:0.0364:2,2:30.2:1:29.6:1:0.63252:1.59:60:18:0.0373:0:1 -3 52678370 . C T 63 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTTCACTACCTAGAAAA;RSEQ=TCAGCAAATATAAAGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:33.8:1:31.5:1:1:0:60:8:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 52678494 . G A 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.387;SOR=0.33035;LSEQ=CACTGTAACCTCTGCCTCCC;RSEQ=GGTTCAAGCAATTCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:0.5455:0,0:22.5:1:30.8:1:1:0:58.2:12:0.5455:0:1 0/1:11:3:3,0:8,0:0.2727:0,0:18.7:1:31:1:1:0:60:6:0.2727:0:1 -3 52678621 . G A 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTTGGCCAGGATGGTCTC;RSEQ=ATCTCTTGACCTCGTGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:140,0:0:1,0:23.8:1:30.1:1:1:0:57.2:280:1:0:0.1 0/1:151:41:40,1:109,0:0.2715:1,1:18.7:1:30.4:1:0.27333:0:54.8:82:0.2715:0:1.1 -3 52678627 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=GCCAGGATGGTCTCGATCTC;RSEQ=TGACCTCGTGATCCGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:150,3:0:1,0:23:1:31.3:1:1:0:57.4:152:1:0:0.1 0/1:166:2:2,0:162,2:0.012:1,0:13.5:1:31.5:1:1:0:40:4:0.012:0:3 -3 52678642 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2006;SOR=0;LSEQ=ATCTCTTGACCTCGTGATCC;RSEQ=CCCACCTCAGCCTCCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:2,0:181,13:0.0102:2,0:18.5:1:31:1:1:0:41.5:4:0.0105:0:4 0/0:241:0:0,0:218,23:0:2,0:22.7:1:29.9:1:1:0:58:119.5:1:0:0.3 -3 52678668 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.75042;SOR=0.73125;LSEQ=CTCAGCCTCCCAAAGTGCTG;RSEQ=GATTACAGGCATGAGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:5:2,3:226,100:0.0151:2,2:12.4:1:30.6:1:0.17659:3.37573:52.6:10:0.0153:0:2.8 0/1:451:5:2,3:305,140:0.0111:2,2:19.6:1:27.8:1:0.33248:3.25827:53.4:10:0.0114:0:2.2 -3 52682205 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01704;SOR=0.1446;LSEQ=AGTGCCGGGATTACAGGCGT;RSEQ=AGCCACTGCGCCCAGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:16,0:8,0:0.6667:0,1:22:1:28.1:1:1:0:58.2:32:0.6957:0:1.1 0/1:14:3:3,0:11,0:0.2143:0,0:24:1:26:1:1:0:60:6:0.2143:0:1 -3 52682329 . AAAC A 128 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.72071;SOR=1.19289;LSEQ=TTATCTACTATTACCAAGGA;RSEQ=AACAACAACAACAACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:13:10,3:231,78:0.0401:2,2:23.5:1:30.4:1:1:1.13:60:26:0.041:0.0154:0.2 0/1:421:20:11,9:285,116:0.0475:2,2:21.1:1:29.8:1:0.13646:2.00656:60:40:0.0478:0.0143:0.1 -3 52682516 . T A 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.71096;LSEQ=GAGAGTTCATCAGTACAACC;RSEQ=TTAAAAAAAGAACCCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:21,131:0.013:2,2:7.5:1:23.5:1:0.26611:6.12:60:4:0.0131:0:1.5 0/0:216:2:2,0:26,188:0.0093:2,0:1:0:26:0:0.01628:0:60:4:0.0094:0:1 -3 52684128 . A T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCACACCTATAATCTCT;RSEQ=TGCACTTTGGGAGGCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:27:1:1:0:60:4:1:0:1 -3 52685397 . A G 75 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAACAACAGGTTACCCC;RSEQ=TCTACCCTGATGTGATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:28:1:29.3:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 52686087 . A C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTATTATGCAACTAGCATA;RSEQ=AATTTAATGTTTTAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:25.3:1:31.8:1:1:0:60:18:1:0:1 1/1:2:2:0,2:0,0:1:0,0:23.5:1:33:1:1:0:60:4:1:0:1 -3 52692124 . G A 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13759;SOR=0.68809;LSEQ=CGGCCCAACATCTTCCTTTT;RSEQ=AACTTACTTTATTTATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:57:52,5:59,6:0.4634:2,2:19.1:1:28.8:1:1:1.06:60:114:0.4672:0:1 0/1:145:54:47,7:84,7:0.3724:2,2:20.7:1:28.3:1:0.38459:1.77981:60:53:0.3759:0:1.1 -3 52692359 . C G 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=0.50075;LSEQ=TGTGGAGAAAAAAGTACTTT;RSEQ=TAAGAGAAATAATAAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:122:18,104:23,102:0.4919:2,2:24:1:31.8:1:0.49587:1.30143:60:39.667:0.5021:0:1.1 0/1:282:92:28,64:49,140:0.3262:2,2:20.9:1:30.6:1:0.4766:1.25:60:45:0.3285:0:1.1 -3 52692379 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49849;SOR=Inf;LSEQ=CTAAGAGAAATAATAAAATG;RSEQ=TGAATATTACATAGCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:20,145:0:2,0:26.9:1:31.8:1:1:0:60:26.5:1:0:0.7 0/1:166:2:1,1:34,129:0.012:2,2:15:1:27.5:1:0.38027:3.75:60:4:0.0129:0:2 -3 52692721 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGCCAAAGAAAGCAACT;RSEQ=CTAAGCAGTACTTATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:45:0:33:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 52695835 . T C 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02098;SOR=0;LSEQ=CAACACTGCCTTTCCTTACA;RSEQ=GATGTCTCAATGTAGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:22.3:1:31.6:1:1:0:60:14:0.7778:0:1 0/0:4:0:0,0:3,1:0:2,0:5:1:28.8:1:1:0:60:8:1:0:0 -3 52696310 . G GA 134 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.04111;LSEQ=TGGCTGTATGTTAGCAAAGA;RSEQ=AAAAAAAAAAACACTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:20:2,18:48,180:0.0781:2,2:33.3:1:31.1:1:0.3824:2.3935:60:40:0.0858:0:0 0/1:296:24:3,21:77,184:0.0811:2,2:25.8:1:29.4:1:0.0965:2.92061:60:23:0.0858:0.0034:0.2 -3 52702452 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21613;SOR=0;LSEQ=GCCAGGTTTATAAATATTAA;RSEQ=AAGCCAATTATCAAATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:106,15:0.0163:2,2:7.5:1:28:1:0.24417:6.87422:60:4:0.0164:0:1 0/0:141:0:0,0:122,19:0:2,0:24:1:31.8:1:1:0:60:69.5:1:0:0.1 -3 52703254 . GA G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACAACCAAACTCTTCG;RSEQ=AAAAAAAAACCATGGGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:1:30.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 52712629 . G A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.38048;SOR=3.455;LSEQ=GCAATCTACACATTAGCAAA;RSEQ=GAGAAAAAAATCACTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:1,0:73,254:0.003:2,0:1:0:25:0:0.22561:0:60:2:0.0031:0:1 0/1:382:4:2,2:109,268:0.0105:2,2:9.3:1:25:1:0.58333:2.45:60:3:0.008:0:2.3 -3 52713306 . T TC 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGAAAAATGGGCTTGTT;RSEQ=CCACATGGCTATATCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:35.5:1:32:0:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 55235124 . C G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAGAGCCCCTTCCCCACCC;RSEQ=ACAGGTGCATTAGTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:26:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 55235377 . G A 87 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00024;SOR=60.61251;LSEQ=CCTCCTTTCTGGGAGCTCCT;RSEQ=AAAAGACAAGCCCTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:12,0:0.0769:0,0:11:0:29:0:1:0:60:2:0.0769:0:1 1/1:9:8:8,0:1,0:0.8889:0,0:20.1:1:29.3:1:1:0:60:16:0.8889:0:1 -3 55235436 . A AT 48 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.14414;SOR=5.41961;LSEQ=CCCAGGGGTTTATGCATTGA;RSEQ=TTTTTTTTTTAATACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:1:1,0:38,1:0.025:1,0:13:0:32:0:1:0:60:2:0.027:0:0 0/1:24:3:3,0:21,0:0.125:1,0:26:1:30.9:1:1:0:60:6:0.1304:0.0417:0 -3 55235552 . A T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12109;SOR=0;LSEQ=GAGATGATCTGAGGGGATGC;RSEQ=GTATTTATGAACTATGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:0,3:176,104:0.0106:2,0:5:1:27.7:1:0.05311:0:60:6:0.0107:0:1 0/0:288:0:0,0:171,117:0:2,0:23.8:1:29.9:1:1:0:60:143:1:0:0.4 -3 55235608 . T G 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=24.97286;LSEQ=GGCATTTATATGAACTAGGG;RSEQ=TTTTAATAAGGTAACCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:1:1,0:192,199:0.0025:2,0:35:0:11:0:0.49235:0:60:0:0:0:1 0/1:451:27:11,16:210,213:0.0599:2,2:26.9:1:30.9:1:0.42985:1.43291:60:54:0.0608:0:1.4 -3 55235625 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.00353;LSEQ=GGGTTTTTAATAAGGTAACC;RSEQ=CTCTGAGTTTGGCATTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:66:33,33:153,175:0.1675:2,2:25.9:1:30.8:1:0.68565:1.14:60:65:0.1688:0:1.2 1/0:451:247:119,128:96,107:0.5477:2,2:26.4:1:30:1:0.92447:1.04:60:29.875:0.5457:0:1.2 -3 55235665 . G A 54 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19356;SOR=0.22118;LSEQ=ATAGAAAACATGCGTATTGT;RSEQ=CTTTCCTTGCATGTGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:4:2,2:113,173:0.0138:2,2:12.3:1:27:1:0.6502:1.53:60:8:0.014:0:1 0/0:325:1:0,1:134,190:0.0031:2,0:1:0:29:0:1:0:60:2:0.0031:0:2 -3 55235685 . A T 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=GCTTTCCTTGCATGTGAGGA;RSEQ=TCTCGTTGAAAGTACCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:75,144:0:2,0:24.5:1:30.6:1:1:0:60:218:1:0:0.2 0/1:232:13:4,9:76,143:0.056:2,2:20.7:1:29.6:1:1:1.19494:60:26:0.0563:0:1.5 -3 55235741 . A G 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01624;SOR=Inf;LSEQ=TTGTAAACAGTGATGATTTT;RSEQ=GTCTATGGTGAATCCTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:7,80:0:2,0:24.2:1:31.1:1:1:0:60:174:1:0:0.1 0/1:70:5:0,5:5,59:0.0714:2,0:22.8:1:30.6:1:1:0:60:10:0.0735:0:2 -3 55235828 . TTA G 96 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00042;SOR=22.74585;LSEQ=GTTTATTTTCGTTCAAGGAG;RSEQ=ATAAATGGGAATGTCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:0.1304:1,0:18:1:29.7:1:1:0:60:6:0.1304:0.0435:1.3 1/1:10:8:0,8:0,2:0.8:0,0:23.5:1:32.1:1:1:0:60:16:0.8:0.1:0.5 -3 55235867 . G A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TCTTTGTATCACATCACCCC;RSEQ=AAGGACTTTGCTGTGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:37:1:30:1:1:0:60:6:0.375:0:2 1/1:2:2:0,2:0,0:1:0,0:9.5:1:29:1:1:0:60:4:1:0:2 -3 55487201 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23807;SOR=0;LSEQ=TCCCAATTGCTTAACAAATG;RSEQ=CAATGGTCTCTTGCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:119,30:0.0132:2,2:15:1:30:1:0.36954:3.91853:60:4:0.0133:0:1 0/0:159:0:0,0:126,33:0:2,0:21.2:1:29.5:1:1:0:60:158:1:0:0.1 -3 55487222 . A T 98 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0041;SOR=0.08718;LSEQ=CAATGGTCTCTTGCTCTTGC;RSEQ=GCCCCAGGTCAGAAATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:10:6,4:156,62:0.0439:2,2:29.5:1:29.6:1:0.48052:1.67328:60:20:0.0441:0:1 0/0:252:1:0,1:170,81:0.004:2,0:1:0:23:0:0.3254:0:60:2:0.004:0:1 -3 55487289 . C T 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCGTCTTTGATTTTCCTT;RSEQ=ATCCCCAAGCTTTACTATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:0:0,0:238,221:0:2,0:26.8:1:31.5:1:1:0:60:458:1:0:0.8 0/1:547:34:19,15:271,240:0.0622:2,2:23.6:1:28.6:1:0.85956:1.12:60:33:0.061:0:1.1 -3 55487317 . T A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09298;LSEQ=AGCTTTACTATAGGAAGTCA;RSEQ=GAGTCAGACTTAGATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:428:378:163,215:22,28:0.8832:2,2:25.2:1:30.5:1:1:1.0363:60:188:0.8847:0:1.1 0/1:500:206:88,118:148,146:0.412:2,2:24.8:1:30.4:1:0.10171:1.35842:60:205:0.4141:0:1.1 -3 55487428 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05787;LSEQ=TACACAGGAAAAATTTCTTG;RSEQ=TAGTTCCCAGTCTGACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:53:2,51:1,7:0.8689:2,1:21:1:31.1:1:0.3491:3.53024:60:52:0.8667:0:1.2 0/1:70:19:2,17:2,49:0.2714:1,2:28.1:1:30.1:1:0.29591:2.83:60:38:0.2754:0:1 -3 55487515 . C T 131 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.00818;LSEQ=GTGCTATGATTCCAAACTGC;RSEQ=AAACTGCTGAGCAATCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:28:0,28:0,1:0.9655:0,1:24.5:1:27.3:1:1:0:60:27:0.9643:0:1.3 0/1:8:1:0,1:0,7:0.125:0,0:39:0:29:0:1:0:60:2:0.125:0:1 -3 55524478 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48;SOR=0;LSEQ=TCCCTGCCCTGCCACTTTCC;RSEQ=GCTGTCACACCTTGTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:0.1538:2,2:35.5:1:29.5:1:1:2.4495:60:4:0.1538:0:1 0/0:13:0:0,0:10,3:0:2,0:22.4:1:29.3:1:1:0:60:26:1:0:0.1 -3 57775195 . C T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02288;SOR=Inf;LSEQ=GCCAGGGTGTTCAGACATCA;RSEQ=CTGAGGGATGGTAGATAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:0:2,0:23.2:1:32:1:1:0:60:20:1:0:0 1/0:8:4:2,2:3,1:0.5:2,2:21.5:1:27.3:1:1:2.60168:60:8:0.5:0:1 -3 59788677 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCTTGAACTGTAGTGATACG;RSEQ=GTATACATCTTACCTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:45:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:32:1:1:0:60:4:1:0:1.5 -3 59789058 . C T 172 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGAGGACCTTACAGGCGAG;RSEQ=ACGGGGCCAGCGAAGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:49,7:0,0:1:0,2:26.4:1:29.7:1:1:0:60:112:1:0:1.8 1/0:52:34:30,4:14,4:0.6538:2,2:19.3:1:29.9:1:0.42484:2.11:60:68:0.6538:0:1.8 -3 59789101 . G A 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00736;SOR=0;LSEQ=TTTTAAGATCATCTCCTGGT;RSEQ=CTCATTAGTGCTGTTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:107:73,34:0,0:1:0,2:25:1:28.7:1:1:0:60:214:1:0:1.8 1/1:118:110:76,34:5,3:0.9322:2,2:24.7:1:28.3:1:0.70453:1.34:60:109:0.9316:0:1.6 -3 59789139 . CT TG 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13362;SOR=Inf;LSEQ=TCTTCACCTGGGTGAGCGGG;RSEQ=TGCTTCCATGGAGAAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:79,59:0:2,0:25.5:1:31.7:1:1:0:60:68:1:0:1.5 0/1:176:4:2,2:95,74:0.0227:2,2:9:1:30.5:1:1:1.2819:60:8:0.0227:0.0114:0.8 -3 59789176 . C T 210 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGACCTCCGCCAGCTCCTG;RSEQ=TGCATTAACGGTCTCCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:138:138:61,77:0,0:1:0,2:24.7:1:29.6:1:1:0:60:68:1:0:1.3 1/0:173:135:64,71:19,19:0.7803:2,2:26:1:29.2:1:0.85484:1.10871:60:134:0.7791:0:1.4 -3 59789419 . A G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTGACCCAACAAAGCAAA;RSEQ=TGGCTTTGTTCCCCAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20.7:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 59789614 . G T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACATCCGGGGCATGTAGAT;RSEQ=CTCGGTAGCAATGAATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 59967386 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=TGCCCGCACATTAACGCAGA;RSEQ=AGATGCCCTTGATAATTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:19.3:1:28.8:1:1:0:60:3:1:0:1 1/1:2:2:2,0:0,0:1:0,0:11.5:1:31.5:1:1:0:60:4:1:0:1 -3 59967565 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24586;SOR=0;LSEQ=TTAATCATTTTCTGGAATTC;RSEQ=AGAAAAAGTCTGATGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:71,17:0.0222:2,2:28.5:1:29:1:0.3618:4.08728:60:4:0.0225:0:1.5 0/0:91:0:0,0:66,25:0:2,0:23:1:29.8:1:1:0:60:182:1:0:0.9 -3 59967597 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=80.30722;LSEQ=GATGTGGTTAATTTAAAATT;RSEQ=TATTTTATGATAGAGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:100:50,50:46,38:0.5435:2,2:21.3:1:29.1:1:0.55546:1.20926:60:200:0.5495:0:1.1 1/1:195:193:113,80:0,0:0.9897:0,2:25.2:1:28.5:1:1:0:60:192:0.9948:0:1.3 -3 59967673 . G A 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTGCCACTCCTTTTTGCT;RSEQ=CCAGGGTCAGCAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:51,109:0:2,0:21.7:1:31.5:1:1:0:60:31:1:0:0.4 0/1:181:81:28,53:43,57:0.4475:2,2:23.9:1:28.5:1:0.28511:1.42512:59.9:80:0.4469:0:1.6 -3 59967683 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24895;SOR=Inf;LSEQ=CCTTTTTGCTGCCAGGGTCA;RSEQ=CAAAAAGAAAAAAAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:33,96:0:2,0:19.2:1:31.5:1:1:0:60:24.8:1:0:0.3 0/1:142:3:2,1:48,91:0.0211:2,2:9.7:1:22.7:1:0.28319:3.75:60:2:0.0152:0:1.3 -3 59967690 . G GA 163 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=5.62669;LSEQ=GCTGCCAGGGTCAGCAAAAA;RSEQ=AAAAAAAAAATTATTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:9:2,7:19,62:0.1:2,2:21.7:1:29.6:1:1:1.07176:60:18:0.1059:0.0111:0 0/1:119:46:16,30:23,44:0.3866:2,2:25.3:1:29.6:1:1:1.02:59.6:92:0.3898:0.0252:0.3 -3 60170982 . GA G 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATAGTTTCATGGTGTGGG;RSEQ=AAAAAAAAAATCGCATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:30.1:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 60458418 . C G 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTGTTTTAAAAGCAGCGCT;RSEQ=GTCTTTGCTGCCTTTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:34:1:30.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:31:1:1:0:60:4:1:0:1 -3 60458976 . C T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66685;SOR=0.54001;LSEQ=CCATATCCACAGATAGCTGG;RSEQ=TTCTTCGATAAAATTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:26:1:30:1:1:0:60:10:0.4167:0:1 0/1:11:3:3,0:8,0:0.2727:0,0:18.7:1:31.7:1:1:0:60:6:0.2727:0:1 -3 60459187 . G C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0;SOR=0.218;LSEQ=TGTGAGAGACATTATCAAGA;RSEQ=AGAATAAATACAATGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:360:190:97,93:91,76:0.5278:2,2:25.7:1:31.6:1:0.52582:1.14755:60:62.333:0.5268:0:1.9 0/1:455:89:49,40:175,189:0.1956:2,2:25.2:1:31:1:0.28715:1.32:60:43.5:0.1942:0:1.9 -3 60459201 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.29994;LSEQ=TCAAGAGAGAATAAATACAA;RSEQ=GTGAAGAGACAACCTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:364:184:85,99:91,89:0.5055:2,2:27.1:1:30.8:1:0.46286:1.1903:60:183:0.5097:0:2 0/1:448:105:55,50:154,188:0.2344:2,2:24.6:1:30.5:1:0.21872:1.34:60:104:0.2348:0:1.9 -3 60459291 . A G 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01824;SOR=0.56;LSEQ=ATTAACCAATAGGGCTAACT;RSEQ=CAAAGGTGGTGCTTTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:73:21,52:13,46:0.553:2,2:19.8:1:31.5:1:0.42744:1.43:60:23.333:0.5469:0:1.3 0/1:159:65:16,49:26,68:0.4088:2,2:19.8:1:31.6:1:0.71721:1.1698:60:130:0.4114:0:1.2 -3 60459656 . CA C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGCGAGACTCCATTTC;RSEQ=AAAAAAAAAGAAAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:30:1:1:0:60:4:1:0:0.5 -3 61186878 . G A 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=CTTCCTGTATGTAGACTGCA;RSEQ=CCTTCTCTCGGAAGAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:30.7:1:33.3:1:1:0:60:12:1:0:0.2 1/0:3:2:1,1:1,0:0.6667:0,2:20.5:1:26.5:1:1:0:60:4:0.6667:0:2 -3 61187046 . A T 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08159;SOR=0.55601;LSEQ=CAACAGTAATAACTTACAGT;RSEQ=TCGTGAAGCTGGTTCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:44:44,0:52,1:0.4536:1,1:22.9:1:30.1:1:1:0:60:88:0.4632:0:1 0/1:73:23:22,1:48,2:0.3151:1,1:21.8:1:30.3:1:1:1.08959:60:46:0.3151:0:1 -3 61187197 . C T 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.49974;LSEQ=GATAGACAGCTACACCACAG;RSEQ=TTTTCCATGGTTCTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:171:68,103:117,162:0.38:2,2:25.1:1:29.3:1:0.69335:1.09374:60:41.75:0.3813:0:1.2 0/1:495:116:48,68:170,208:0.2343:2,2:26.4:1:29.1:1:0.52251:1.15751:60:57:0.2365:0:1.2 -3 61187210 . C CT 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.81372;SOR=1.18613;LSEQ=ACCACAGCTTTTCCATGGTT;RSEQ=TTTTTTTTTCCTTCAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:8:3,5:145,228:0.021:2,2:25.5:1:29.9:1:1:1.05979:60:16:0.0216:0.0026:0.4 0/1:403:10:3,7:160,233:0.0248:2,2:39.9:1:27.6:1:0.74613:1.60052:60:9:0.0226:0:0.4 -3 61187274 . T A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=21.29835;LSEQ=CTGGGCTGTTTCCCTCCACA;RSEQ=CCCTCTATTCCATCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:1:1,0:11,106:0.0085:2,0:1:0:14:0:0.10169:0:60:0:0:0:1 0/1:129:20:4,16:18,91:0.155:2,2:22.8:1:28:1:0.7476:1.26:60:19:0.1496:0:1.6 -3 61187278 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23615;SOR=0;LSEQ=GCTGTTTCCCTCCACATCCC;RSEQ=CTATTCCATCAAAGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:10,101:0.0177:2,2:38:0:32:1:0.186:9.68:60:4:0.0182:0:1.5 0/0:119:0:0,0:17,102:0:2,0:22.2:1:29.2:1:1:0:60:58.5:1:0:0.3 -3 61187340 . C T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04534;SOR=0.31343;LSEQ=CAAAGAACAGGTCAGACTTA;RSEQ=GGGCTAAGATGTAAATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:18:0,18:0,25:0.4186:1,1:26.2:1:30.4:1:1:0:60:36:0.4186:0:1.1 0/1:33:6:0,6:1,26:0.1818:1,0:20.7:1:30.5:1:1:0:60:12:0.1818:0:1.5 -3 61187422 . C T 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22797;SOR=0;LSEQ=TCAGAAATTTCTCCTTCCCC;RSEQ=TGAGCTACACCGTTTACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:24.8:1:31.5:1:1:0:60:8:0.4444:0:1.3 0/0:4:0:0,0:0,4:0:0,0:21.5:1:33:1:1:0:60:8:1:0:0.3 -3 62110040 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49714;SOR=0;LSEQ=AGGCTGACAATAGTGGGATG;RSEQ=AAGTCCAGGGTGATCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:41,23:0.0303:2,2:13:1:26:1:1:1.76614:60:4:0.0303:0:1 0/0:60:0:0,0:34,26:0:2,0:23.4:1:31.1:1:1:0:59.6:120:1:0:0.3 -3 63597115 . A C 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.23316;LSEQ=GGACATTAATGAACCAAAAC;RSEQ=CAATATTTTTATTACAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:9.5:1:32.5:1:1:0:60:4:0.1667:0:1 0/1:5:1:1,0:3,0:0.2:0,0:3:0:30:0:1:0:60:2:0.2:0:1 -3 63597263 . A C 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0147;SOR=Inf;LSEQ=AGGCTGCCAGGAAGCTGGAC;RSEQ=GTTCTCATCCTCCATCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:121,43:0:2,0:21.8:1:30:1:1:0:60:163:1:0:0 0/1:168:7:6,1:110,50:0.0417:2,2:23.9:1:28:1:0.67683:2.71:60:6:0.0364:0:1 -3 63597293 . T C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.25066;SOR=Inf;LSEQ=CTCCATCTCTCATCTCTCTT;RSEQ=CTTTCTGTGTCCCTGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:151,116:0:2,0:25.3:1:29.9:1:1:0:60:88:1:0:0.1 0/1:296:3:2,1:172,121:0.0101:2,2:38.3:1:25.3:1:1:1.41:60:2:0.0069:0:1 -3 63597363 . C CT 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09929;SOR=0;LSEQ=TTTCAGGTGAAACTTTATTT;RSEQ=TTTTTTTTCATCCACACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:112,143:0.0116:2,2:30.7:1:31.7:1:1:1.56382:60:6:0.0118:0:0.3 0/0:298:0:0,0:130,167:0:2,0:23.7:1:31.3:1:1:0:60:147.5:0.9966:0:0.5 -3 63597382 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=21.37938;LSEQ=TCTTTTTTTTCATCCACACA;RSEQ=CAGAAGATAGCCACTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:14:7,7:93,106:0.0657:2,2:22.2:1:29:1:1:1.14:60:28:0.0664:0:1.2 1/0:244:147:62,85:46,49:0.6025:2,2:24.4:1:28.9:1:0.35658:1.28567:60:35.75:0.6059:0:1.1 -3 63597468 . C G 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00327;SOR=Inf;LSEQ=TGAATGAAAATCACTCAGGT;RSEQ=CAGTTGCAAATTTCTGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:25,81:0:2,0:22.1:1:30.5:1:1:0:60:20.2:1:0:0.1 0/1:106:9:3,6:30,67:0.0849:2,2:22.3:1:31.6:1:1:1.12:60:18:0.0857:0:1.2 -3 65425560 . T TCTG 117 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=11.000;MSILEN=3;SSF=0.16716;SOR=0.5133;LSEQ=GGAAAGAGGCCAACCTTCTG;RSEQ=CTGCTGCTGCTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:15:8,7:15,10:0.375:2,2:25.1:1:30.1:1:0.74858:1.30352:59.3:6.5:0.3514:0.075:0.1 0/1:47:11:7,4:26,9:0.234:2,2:25.4:1:31.1:1:0.70235:1.63177:59.5:22:0.2444:0:0.2 -3 66687512 . GT CC 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50769;SOR=Inf;LSEQ=CTGGGTGACAGAGTGAGACT;RSEQ=GTCTCAAAAAAAAAGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:62,29:0:2,0:21.5:1:32:1:1:0:60:182:1:0:0 0/1:121:2:1,1:82,37:0.0165:2,2:21:1:28.8:1:0.53127:2.20019:58:4:0.0167:0.0083:3.5 -3 66687518 . CA C 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.1625;SOR=0.17003;LSEQ=GACAGAGTGAGACTGTGTCT;RSEQ=AAAAAAAAGCCTTCCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:4:2,2:66,34:0.0385:2,2:25.5:1:32.3:1:0.60763:1.92803:60:8:0.0385:0:0.3 0/0:149:1:1,0:95,52:0.0067:2,0:12:0:32:0:1:0:60:2:0.0068:0:0 -3 66687528 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50736;SOR=Inf;LSEQ=GACTGTGTCTCAAAAAAAAA;RSEQ=CCTTCCTTTTGGCTGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:81,47:0:2,0:24:1:31.6:1:1:0:60:41.667:1:0:0.1 0/1:169:2:1,1:102,65:0.0118:2,2:37:0:31:0:1:1.56486:60:4:0.012:0:1.5 -3 66687586 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50961;SOR=Inf;LSEQ=CGCCAAAATGATGAACACAA;RSEQ=GAGAAAGAGAAGAGGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:67,76:0:2,0:24.8:1:30.3:1:1:0:60:46.667:1:0:0.1 0/1:193:2:1,1:86,104:0.0104:2,2:5:0:32.5:1:1:1.21:60:4:0.0106:0:1.5 -3 66687723 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51307;SOR=Inf;LSEQ=AATGGGTACTGTTCAAAAAG;RSEQ=AATGCCCCATAAGTGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:47,40:0:2,0:23.4:1:31.3:1:1:0:60:86:1:0:0.1 0/1:124:2:1,1:69,52:0.0161:2,2:5.5:1:29:1:1:1.32382:60:4:0.0164:0:1.5 -3 66687728 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17283;SOR=0;LSEQ=GTACTGTTCAAAAAGGAATG;RSEQ=CCCATAAGTGTTACCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:50,41:0.0215:2,2:21.5:1:29:1:1:1.21689:60:4:0.0215:0:1 0/0:130:0:0,0:74,56:0:2,0:20.6:1:31.1:1:1:0:60:260:1:0:0.2 -3 69591582 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17293;SOR=Inf;LSEQ=AGCCCGACTCCCGGGCTCTC;RSEQ=GGGCAGCCAGCGCCTGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:25,8:0:2,0:24.7:1:31.4:1:1:0:60:66:1:0:0.3 0/1:24:2:1,1:13,9:0.0833:2,2:26:0:31.5:1:1:1.42202:60:4:0.0833:0:1 -3 69788682 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=Inf;LSEQ=CTCGGGGGACCCAGGCCCAG;RSEQ=TACCTTCCCTCCGCCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:118,7:0:2,0:24.5:1:32.3:1:1:0:60:61.5:1:0:0.1 0/1:136:2:1,1:126,8:0.0147:2,2:22.5:1:29:1:0.12843:14.90803:60:4:0.015:0:1 -3 69788686 . CT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22611;SOR=0;LSEQ=GGGGACCCAGGCCCAGCTAC;RSEQ=TCCCTCCGCCCCCGGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:138,11:0.0132:2,2:18.5:1:30.4:1:0.15311:12.05496:60:4:0.0134:0.0066:1 0/0:166:0:0,0:147,18:0:2,0:20.8:1:31:1:1:0:60:81.5:0.9939:0:0.1 -3 69788697 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20066;SOR=0;LSEQ=CCCAGCTACCTTCCCTCCGC;RSEQ=CCCGGGCTCTGTTCTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:169,21:0.0104:2,2:17:1:29.5:1:0.21657:7.88555:60:4:0.0107:0:1 0/0:236:0:0,0:196,40:0:2,0:19.8:1:30.1:1:1:0:60:58:1:0:0.2 -3 69788752 . C T 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06682;SOR=0.22272;LSEQ=GACGGGAAGCGGGAGCCATG;RSEQ=AGTCCGAATCGGGGATCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:6:3,3:355,199:0.0107:2,2:24.8:1:28.8:1:0.67235:1.78188:60:12:0.0108:0:1 0/0:832:2:1,1:499,331:0.0024:2,2:20:1:28.5:1:1:1.50675:60:4:0.0024:0:1 -3 69915345 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50077;SOR=0;LSEQ=GGATTGGAGTTTCCAGGGCC;RSEQ=TATCAGGAGCCACCCCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:127,21:0.0133:2,2:16:1:29:1:0.27266:5.93182:60:4:0.0135:0:1 0/0:130:0:0,0:108,22:0:2,0:24.2:1:30.4:1:1:0:60:42.333:1:0:0.1 -3 69915355 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22423;SOR=Inf;LSEQ=TTCCAGGGCCTTATCAGGAG;RSEQ=CACCCCTAGTGACACAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:148,36:0:2,0:22.2:1:31.3:1:1:0:60:45:1:0:0.2 0/1:166:2:1,1:132,32:0.012:2,2:15.5:1:28:1:0.35904:4.07738:60:4:0.0123:0:1 -3 69928212 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21718;SOR=Inf;LSEQ=TTATAGTTTGGTGCAATTTA;RSEQ=GATACCCCCAAAGTGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:181,43:0:2,0:22.3:1:31.8:1:1:0:60:73.667:1:0:0.1 0/1:196:2:1,1:152,42:0.0102:2,2:17.5:1:28.5:1:0.39152:3.58815:60:4:0.0104:0:1 -3 69986144 . A G 88 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2125;SOR=0;LSEQ=TGTGTGGCTAAACTATCTTC;RSEQ=TCAGCTCCTGTTCATTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:0.5385:0,0:20.6:1:31.7:1:1:0:60:14:0.5833:0:1.7 0/0:3:0:0,0:0,3:0:0,0:14.7:1:28.7:1:1:0:60:6:1:0:2.7 -3 69986516 . GGT G 30 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=38;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACAGTTGGTTCTTAAGGA;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,2:0.25:2,2:42.5:1:30:1:1:1.41418:60:4:0.25:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 69986691 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CCTAAGATAATTTCAAACTT;RSEQ=TAATTATTAGATATGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:18.1:1:31.7:1:1:0:60:14:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:22:1:30:1:1:0:60:4:0.6667:0:1 -3 69986916 . C T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62368;SOR=0.33635;LSEQ=TTTGTGCCTGAAGGAAGAGC;RSEQ=GTCTGAAACTCACAAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:228,48:0.0108:2,2:16.3:1:23:1:0.08382:9.38414:60:2:0.0073:0:1.3 0/0:275:1:0,1:213,60:0.0036:2,0:1:0:26:0:0.22263:0:60:2:0.0037:0:1 -3 69987248 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23709;SOR=Inf;LSEQ=TTTTCTTATGCTAAATAACT;RSEQ=GTCTGTTGAATATGATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:53,153:0:2,0:22.9:1:30.1:1:1:0:60:67.667:1:0:0.1 0/1:196:2:1,1:59,134:0.0102:2,2:20.5:1:31:1:0.52181:2.26:60:4:0.0103:0:1.5 -3 69987435 . C T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68747;SOR=1.84635;LSEQ=CTCCAAGTGAAATGTGGAGG;RSEQ=GAGGACACTTTTGCCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:2:0,2:172,83:0.0078:2,0:1:0:27:1:0.10852:0:60:4:0.0079:0:1 0/1:281:4:1,3:182,94:0.0142:2,2:19.8:1:28.3:1:0.12147:5.77072:60:8:0.0145:0:1.3 -3 69987707 . C T 114 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00977;SOR=0.12171;LSEQ=TATAGCACATGAGACTTTAA;RSEQ=GGAAACGCAAAGGTTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:1,13:0,13:0.5185:1,1:21.9:1:30.2:1:1:0:60:28:0.5385:0:1 0/1:18:2:0,2:0,16:0.1111:1,0:18.5:1:22.5:1:1:0:60:1:0.0588:0:1 -3 69988183 . G T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36231;SOR=3.16163;LSEQ=CTGTGCCATCAGCTTTGTGT;RSEQ=AACAGGTCATTAAAAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:0,1:182,82:0.0038:2,0:1:0:23:0:0.31321:0:60:2:0.0038:0:1 0/1:253:3:1,2:167,83:0.0119:2,2:23.7:1:25.3:1:0.2619:4.00019:60:6:0.0121:0:1.3 -3 69988421 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.18275;SOR=Inf;LSEQ=ACCTTCCTGAAAACTTAAGC;RSEQ=TTTTTTCCCCCATTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:3,74:0:1,0:21.2:1:29.6:1:1:0:60:24.667:1:0:1 0/1:58:2:0,2:4,51:0.0345:2,0:18.5:1:28.5:1:1:0:60:4:0.0364:0:0 -3 69988434 . A AT 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.24524;SOR=0;LSEQ=CTTAAGCATTTTTTTCCCCC;RSEQ=TTGTTTTTTTTTTTTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:3:0,3:1,43:0.0545:1,0:32:1:23.3:1:1:0:60:2:0.0645:0:3.7 0/0:49:0:0,0:2,44:0:1,0:20.9:1:25.3:1:1:0:60:2.538:1:0:0.6 -3 69990522 . T A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24898;SOR=Inf;LSEQ=AAGTAGAAAATCTTGAGGTG;RSEQ=TTCCAGGGTTCTTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:56,230:0:2,0:22.7:1:30:1:1:0:60:56.2:1:0:0.1 0/1:298:3:2,1:83,212:0.0101:2,2:5.3:1:20.3:1:0.19678:5.08:60:2:0.0068:0:1.3 -3 69998349 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24974;SOR=Inf;LSEQ=TAGTAAATGTGCCTCTTACT;RSEQ=CAGATTTCTGTCCATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:61,200:0:2,0:23.5:1:31.6:1:1:0:60:42.5:1:0:0.1 0/1:282:3:1,2:74,204:0.0106:2,2:17.7:1:28.7:1:1:1.38:60:6:0.0109:0:1 -3 70000954 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.036;SOR=Inf;LSEQ=ACTTCTAATGACTTCATTCA;RSEQ=GTGCACAGCGTGTATTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:251,164:0:2,0:24.7:1:31.1:1:1:0:60:206.5:1:0:0.1 0/1:513:6:3,3:321,186:0.0117:2,2:17.5:1:24.5:1:0.67427:1.7238:60:5:0.0099:0:1.5 -3 70005281 . A G 72 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAATTTGGGCTTTCACCAG;RSEQ=TATTGTTGGATGTCCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:27.2:1:31.4:1:1:0:60:10:0.8333:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 70005509 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49981;SOR=0;LSEQ=TTCAGGTTTCCGTTGTCATG;RSEQ=CCTGGAGAAGTTAATATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:2,0:137,13:0.0132:2,0:31.5:1:31.5:1:1:0:60:4:0.0133:0:1 0/0:136:0:0,0:114,22:0:2,0:24.3:1:29:1:1:0:60:44.333:1:0:0.1 -3 70005712 . T C 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TCGCGTGTTAATCTGCATCA;RSEQ=ATATTTTTCGTACCTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:24:8,16:136,275:0.055:2,2:24.7:1:31.5:1:1:1.01:60:23:0.0536:0:1.4 0/0:449:0:0,0:162,287:0:2,0:6:0:15:0:1:0:60:0:0:0:5 -3 70007486 . C T 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGTGGGTATCTCAGGACATT;RSEQ=CCCTGGGTTGCCATCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:28:1:1:0:60:4:1:0:1 -3 70008316 . T TA 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50183;SOR=0;LSEQ=TTCCCCCAAAACTATTGAAA;RSEQ=AAAAAAAAATTTTAAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:2,0:42,0:0.0455:1,0:32.5:1:26.5:1:1:0:60:4:0.0465:0:0 0/0:34:0:0,0:34,0:0:1,0:17.8:1:30.9:1:1:0:60:68:1:0:0.1 -3 70008602 . G A 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13847;SOR=Inf;LSEQ=TGAGTTGTGTAAAGTTTACT;RSEQ=CTTTTTACCGACTTCAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:26,116:0:2,0:22:1:31.6:1:1:0:60:34.5:1:0:0.1 0/1:190:4:2,2:46,140:0.0211:2,2:18.3:1:29.5:1:0.26507:3.02:60:8:0.0213:0:1.3 -3 70008612 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50797;SOR=Inf;LSEQ=AAAGTTTACTGCTTTTTACC;RSEQ=ACTTCAAGACAGTAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:17,93:0:2,0:23.2:1:30.9:1:1:0:60:220:1:0:0.1 0/1:146:2:1,1:27,116:0.0137:2,2:17.5:1:30.5:1:0.35:4.24:60:4:0.014:0:1 -3 70013474 . GTGAGAGACCATCTCTATTTTTCATACATAATCAAATCTATAAAACACCTAAAAATTTATTTCACATACTGCCAGTGGTACTTCTCCTATACTTTAGAACATACAGAGCTCATTAATTTAAAAGAACAAAAAACTTTTATTTTGAGGATTTATTGTTTTCCAAGTATCTGATTTTTAAAAATAGACTTTATTTTTCAGGACAGTTTTTGGTTCACAGTAAAATTGAAATGAAGCTGCAGATATTTCCCATACACCTCATTCCCCCAAGCACGCACAGCCTTCCCCATTATCAACATTCCCTACCAGAGTGGCACATTTATTAGAATCAATGAACCCGCAGTGACATTTCATTATCCTCCAAAGTCTATACTTTACATTCCCTCTGGTATTGTACATTTTGTGGGTTTGGCCAAA G 162 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0303;SOR=Inf;LSEQ=CAGTGTGAACATTAATATCT;RSEQ=TGTCTAATGACGCGCATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:48:0:30:0:1:0:60:2:1:0:0 1/1:32:32:31,1:0,0:1:0,1:26.2:1:32.4:1:1:0:59.7:64:1:0.0625:0.1 -3 70014447 . T C 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01916;LSEQ=AAACTGCTTCCTTTCTTGAT;RSEQ=CGTAGATTTAATAACTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1159:992:376,616:63,101:0.8559:2,2:25.1:1:31:1:0.93086:1.0219:60:75.308:0.8565:0:1.1 0/1:1374:140:61,79:511,723:0.1019:2,2:25.3:1:30.7:1:0.65143:1.09:60:280:0.1025:0:1.1 -3 70014804 . G GA 31 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGTAAAGCAACCAAAAA;RSEQ=AAAAAAAAAAAGAAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,7:0.2:0,0:25:1:31.5:1:1:0:60:4:0.2222:0:0 0/0:1:0:0,0:1,0:0:0,0:15:0:34:0:1:0:60:2:1:0:0 -3 70348641 . A C 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01136;SOR=0;LSEQ=CCCCTAGAGACATATTAAAA;RSEQ=TTCCCATTGAATCCAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,1:0.7:2,0:22.6:1:32.1:1:0.3:0:60:14:0.7778:0:1.3 0/0:6:0:0,0:6,0:0:0,0:36.5:1:29.7:1:1:0:60:12:1:0:0.2 -3 70348685 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=TGTAATCTCTGACAACTCCT;RSEQ=TCTCTCTGATCCCTTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:0.0952:2,2:28.5:1:28.5:1:1:1.10554:60:4:0.0952:0:1.5 0/0:21:0:0,0:13,8:0:2,0:23.4:1:31.5:1:1:0:60:42:1:0:0.2 -3 70348776 . A G 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24252;SOR=Inf;LSEQ=CCTTTGTTTTCATTGCCCTG;RSEQ=AAACCAATATCTCAAATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:25.7:1:30.6:1:1:0:60:38:1:0:0.2 0/1:24:3:1,2:8,13:0.125:2,2:28.7:1:33:0:1:1.22038:60:6:0.1304:0:2 -3 70348796 . G A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23361;SOR=Inf;LSEQ=AAAACCAATATCTCAAATTC;RSEQ=GAATTCATGCCTTCTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,8:0:2,0:14:1:29.9:1:1:0:60:30:0.9375:0:0.1 0/1:19:3:1,2:5,11:0.1579:2,2:21.7:1:32.3:1:1:1.09:60:6:0.1667:0:2 -3 71007140 . GT G 29 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.13725;SOR=Inf;LSEQ=GCAGCTGCTCGGGGAAGCCG;RSEQ=TTTTTTTTTTGGCCATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:10,1:0:2,0:21.7:1:27.4:1:1:0:60:10:1:0:0.8 0/1:7:2:1,1:5,0:0.2857:0,2:31.5:1:29.5:1:0.28571:0:60:4:0.3333:0:0 -3 71007308 . G T 21 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71748;LSEQ=AGTGCTGCCTATGTTTCCTT;RSEQ=TGCTGGTAGAATGTGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:3,0:212,2:0.0138:1,0:19.3:1:13.3:1:1:0:60:0:0:0:4.3 0/1:201:2:1,1:191,7:0.01:1,2:11.5:1:25.5:1:0.07859:25.59044:60:4:0.0126:0:2 -3 71007361 . G T 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10806;SOR=1.17227;LSEQ=TTGCTGCAAAAAAAAAAAAA;RSEQ=AAAAGAAAAGAAAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:812:292:177,115:291,169:0.3596:2,2:20.1:1:26.1:1:0.48772:1.11857:60:4.615:0.3922:0:1.4 0/1:995:395:229,166:338,217:0.397:2,2:20.3:1:25.4:1:0.3833:1.12895:60:4.896:0.4189:0:1.4 -3 71007462 . C CT 203 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.62309;SOR=1.08065;LSEQ=TGTTCCTAGAGTTTGTCTCT;RSEQ=TTTTTTTTTTCTGTCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1156:99:38,61:472,572:0.0856:2,2:28.3:1:29.2:1:0.20535:1.3243:60:15.5:0.0842:0.0035:0.4 0/1:1360:125:51,74:526,690:0.0919:2,2:29.9:1:29.2:1:0.63588:1.106:60:16.857:0.0908:0:0.5 -3 71008251 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5015;SOR=Inf;LSEQ=GGTTCTTGATGGCACTAAGA;RSEQ=TTAACACATTTCAGAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:91,1:0:1,0:23.7:1:32.4:1:1:0:60:45:1:0:0.1 0/1:110:2:2,0:107,1:0.0182:1,0:26:1:32:0:1:0:60:4:0.0182:0:1 -3 71015021 . G T 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.40453;LSEQ=GGGTCAGATAGCAAAGACCT;RSEQ=TTGGGTGGACAATACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:404:361:254,107:31,11:0.8936:2,2:23.1:1:30:1:0.72247:1.18667:60:50.571:0.8939:0:1.1 1/0:492:380:252,128:77,34:0.7724:2,2:25.4:1:29.6:1:0.56843:1.14998:60:37:0.7692:0:1.2 -3 71015640 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATCAGATTATCCTGGCC;RSEQ=CACCGCTCAAACTTATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:34:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 71019750 . T C 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08459;SOR=0.50023;LSEQ=GTGTTTGCCTCCAGGGAGTA;RSEQ=GATGCTTTGTGCACTTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:27:27,0:30,0:0.4737:1,1:21.2:1:31.6:1:1:0:60:54:0.4821:0:1.9 0/1:55:17:16,1:38,0:0.3091:1,1:23.8:1:31.7:1:0.30909:0:60:34:0.3148:0:1.2 -3 71019797 . A T 179 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00899;LSEQ=TTTAACGGAATTAAAATTTA;RSEQ=TATCTAATTAGAGCAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:56:50,6:89,13:0.3544:2,2:23.7:1:30.9:1:0.80225:1.22:60:112:0.3544:0:1.5 0/0:206:1:0,1:175,30:0.0049:2,0:1:0:26:0:0.15049:0:60:2:0.0049:0:1 -3 71019871 . C T 67 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08288;SOR=0.25199;LSEQ=CCTCTGCTGCATATTCGGGA;RSEQ=GGCCGTTAATCTTACCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:6:3,3:312,234:0.0109:2,2:18.5:1:26.2:1:1:1.33262:60:5:0.0093:0:1 0/0:725:2:0,2:400,323:0.0028:2,0:1:0:24.5:1:0.20061:0:60:4:0.0028:0:1 -3 71019931 . G A 76 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31322;SOR=2.74151;LSEQ=GCAGTAGGCGTGGCTGCTCT;RSEQ=CATGTTTTTAATAAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:2:2,0:220,324:0.0037:2,0:1:0:25:0:0.16488:0:60:4:0.0037:0:1 0/1:701:7:4,3:303,388:0.01:2,2:14.6:1:27.4:1:0.70531:1.71:60:14:0.0102:0:1.1 -3 71021128 . G GA 167 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.72406;SOR=1.1105;LSEQ=GCAAAGCCAAAGCAACAGCA;RSEQ=AAAAAAAAAACAAAAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:33:26,7:176,53:0.1183:2,2:24.8:1:30.2:1:1:1.12:60:66:0.1213:0.0143:0.6 0/1:401:52:43,9:239,91:0.1297:2,2:32.3:1:29.3:1:0.12939:1.82:60:104:0.1361:0:0.5 -3 71021355 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18203;SOR=Inf;LSEQ=GGATAGGAGCAGCAGCAAAG;RSEQ=AGATGGAGTGGCAACAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:52,204:0:2,0:26.3:1:30.9:1:1:0:60:31:1:0:0.1 0/1:191:2:1,1:34,154:0.0105:2,2:33:1:27:1:0.33528:4.48:60:4:0.0106:0:1 -3 71025935 . C T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22;SOR=0.52141;LSEQ=GAGCATTTCAACCACAATGG;RSEQ=ACTATTTTCCCAATCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:23:23,0:10,0:0.697:0,1:28.6:1:30.3:1:1:0:60:46:0.697:0:1.1 1/0:35:19:19,0:16,0:0.5429:1,1:25.9:1:29.7:1:1:0:60:38:0.5429:0:1 -3 71026053 . C T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09298;SOR=0;LSEQ=ACAACAAACTGTTCTATGAA;RSEQ=GTCAAGATCCAAGAATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:203,94:0.01:2,2:23.7:1:29.3:1:0.24087:4.2959:60:6:0.0102:0:1 0/0:361:0:0,0:233,128:0:2,0:26.2:1:30.1:1:1:0:60:71.2:1:0:0.1 -3 71026265 . A G 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60912;SOR=2.17887;LSEQ=GTCATTCCACAGTTTCTCGA;RSEQ=AATATAAAATCACTGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:0,1:14,140:0.0065:2,0:17:0:15:0:1:0:60:0:0:0:4 0/1:143:2:1,1:14,127:0.014:2,2:26.5:1:33:1:0.19945:8.80:60:4:0.0141:0:1.5 -3 71036994 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02255;LSEQ=TATGACCTTCATCATAAAGG;RSEQ=TAACCAGAAACAGTCGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:65:63,2:6,0:0.9155:0,1:22.7:1:31.4:1:1:0:60:64:0.9143:0:1.1 0/1:48:9:9,0:38,1:0.1875:1,0:27.2:1:31.6:1:1:0:60:18:0.1875:0:1.2 -3 71037061 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2554;SOR=Inf;LSEQ=TCCACCAAAGTAGGCTGGTC;RSEQ=TCCTTCCTCCATTTGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:177,28:0:2,0:23.5:1:30.9:1:1:0:60:67.333:1:0:0.3 0/1:249:3:1,2:194,52:0.012:2,2:16.7:1:28.7:1:0.11953:7.38061:60:6:0.0123:0:1.3 -3 71049945 . A AAAAATAAAAT 125 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=53;MSI=12.000;MSILEN=5;SSF=5e-05;SOR=0;LSEQ=TGAACCTGCCCAAAGAGGTA;RSEQ=AAAATAAAATAAAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:16:16,0:2,0:0.6957:0,1:12.1:1:31.3:1:1:0:57.9:32:0.6957:0.4348:0 0/0:13:0:0,0:5,0:0:0,0:22.4:1:30.4:1:1:0:60:10:0.3846:0:0 -3 71050054 . A C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49919;SOR=Inf;LSEQ=TGAGTACACAGGAACTCATT;RSEQ=CAGAACACTACAGAAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:158,31:0:2,0:26.2:1:28.2:1:1:0:60:46.25:1:0:0 0/1:201:2:1,1:157,40:0.01:2,2:15.5:1:26.5:1:0.37044:3.88917:60:4:0.01:0:1 -3 71064654 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49902;SOR=Inf;LSEQ=GCAAAGCATGAACGGTGGGA;RSEQ=GTGTTGGCTATGTAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:127,27:0:2,0:22.1:1:32:1:1:0:60:76:1:0:0.1 0/1:165:2:2,0:125,38:0.0121:2,0:26.5:1:32:0:1:0:60:4:0.0123:0:1 -3 71064664 . A T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12449;SOR=Inf;LSEQ=AACGGTGGGAGGTGTTGGCT;RSEQ=TGTAAAAGAAGAAAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:147,41:0:2,0:22.8:1:28.7:1:1:0:60:93:1:0:0.1 0/1:205:4:1,3:143,58:0.0195:2,2:18.5:1:26:1:0.07983:7.31562:60:8:0.0196:0:1 -3 71096086 . C T 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09442;SOR=0.15965;LSEQ=TATGCCTTCTGTAAAATCAA;RSEQ=GCATACCTTGAGCAAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:5:2,3:240,151:0.0126:2,2:28.8:1:25.8:1:0.38132:2.3787:60:1.5:0.0077:0:1.2 0/0:493:1:0,1:276,216:0.002:2,0:1:0:28:0:0.44016:0:60:2:0.002:0:1 -3 71096576 . A C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTATGCACACTAGAGAGA;RSEQ=GACTGCATCACTCTAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:16:1:28:1:1:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 71097955 . T TG 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTGAAAGCAGACTATAA;RSEQ=GGGGGGGGTACAGCTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21:1:33.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 71101321 . GA G 30 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCCAAGCTCTGTGAGCTGGG;RSEQ=AAAAAAAAAAAAATTAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:21.5:1:30:1:1:0:60:4:0.5:0:0 0/0:2:0:0,0:1,1:0:2,0:39.5:1:30:1:1:0:60:4:1:0:1 -3 71101450 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=CTGAAGACTCTGTCAACGAT;RSEQ=CCTCTCCTGCTCCTCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:17,0:0.1053:1,2:40:1:29:1:0.10526:0:60:4:0.1111:0:1 0/0:11:0:0,0:11,0:0:0,0:21.2:1:32.2:1:1:0:60:22:1:0:0.2 -3 71101580 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23422;SOR=Inf;LSEQ=TCTGAAAGCTGAGAACCGAT;RSEQ=GAGTCAGCTCAGTTGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:179,6:0:1,0:23.6:1:28.5:1:1:0:60:184:1:0:0 0/1:174:2:2,0:162,10:0.0115:2,0:25.5:1:31:1:1:0:60:4:0.0115:0:1 -3 71102157 . G A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCAGTGTGTGCATGGACA;RSEQ=CCTGGGAGCTTCCGCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:32:0:1:0:60:4:1:0:1 -3 71102941 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13105;SOR=Inf;LSEQ=GAACCTAGAATGTTAATGAA;RSEQ=GATAAATAGGAAGCCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:98,197:0:2,0:25.6:1:31.1:1:1:0:60:58:1:0:0.1 0/1:359:4:2,2:129,225:0.0111:2,2:8.8:1:24.8:1:0.62553:1.74:60:3:0.0085:0:1.8 -3 71103136 . T C 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02424;SOR=0;LSEQ=GTAAAATCTTGCAGTACTGA;RSEQ=GGGGGTTCCAGGCAGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:14.7:1:30.1:1:1:0:60:14:0.875:0:1 0/0:3:0:0,0:0,3:0:0,0:14.3:1:31.7:1:1:0:60:6:1:0:0 -3 71153524 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49583;SOR=Inf;LSEQ=AAGACCTCATTGTGGGATCA;RSEQ=AGCCTATCCAAGAAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:29,20:0:2,0:29.8:1:32:1:1:0:60:48:1:0:0.2 0/1:53:2:1,1:32,18:0.0377:2,2:24:1:29:1:1:1.7571:60:4:0.0385:0:1 -3 71153542 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51398;SOR=Inf;LSEQ=CACAGCCTATCCAAGAAGAA;RSEQ=CCGCCCTTCTGCTGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:30,29:0:2,0:29.1:1:32.2:1:1:0:60:118:1:0:0.2 0/1:86:2:1,1:49,35:0.0233:2,2:18.5:1:30.5:1:1:1.39441:60:4:0.0233:0:1.5 -3 71153709 . T G 92 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAATTCTTTCACATCCTC;RSEQ=AACTGTCATCAACATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:18.3:1:31.5:1:1:0:60:8:1:0:1.5 1/1:8:8:0,8:0,0:1:0,0:19.5:1:30.8:1:1:0:60:16:1:0:1 -3 71161817 . C T 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01532;SOR=Inf;LSEQ=AAAAACAAGAAAATCCTTTG;RSEQ=GTTACTACACAGGTTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:74,233:0:2,0:24.3:1:30.1:1:1:0:60:60.4:1:0:0.1 0/1:323:7:2,5:88,226:0.0217:2,2:14.6:1:29.4:1:1:1.03:60:14:0.0221:0:1.1 -3 71161847 . TA T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.22696;SOR=Inf;LSEQ=CAGGTTCAGGGGACTCTTCA;RSEQ=AAAAAGGATTCCAGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:21,151:0:2,0:23.7:1:30:1:1:0:60:42:1:0:0.1 0/1:157:2:0,2:29,125:0.0127:2,0:19:1:31:1:1:0:60:4:0.0132:0.0064:0.5 -3 71162001 . G A 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCGGCCAGTTTCATCCAC;RSEQ=GTTCCACAGGCATCTAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:0.625:0,2:29.4:1:30.8:1:1:0:60:10:0.7143:0:1.2 1/1:1:1:0,1:0,0:1:0,0:40:0:31:0:1:0:60:2:1:0:1 -3 71179582 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50639;SOR=Inf;LSEQ=CCTTCAGAGAATGTCTGCAC;RSEQ=AGAACGGATCCCTAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:80,12:0:2,0:25.3:1:30.3:1:1:0:60:184:1:0:0.1 0/1:120:2:1,1:102,16:0.0167:2,2:23.5:1:27:1:0.26429:6.21491:60:4:0.0168:0:1 -3 71179882 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50057;SOR=Inf;LSEQ=TTTGCCTCCACAGTAGCTGG;RSEQ=TGGGCTCTCACTAAATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:3,62:0:1,0:22.7:1:31.9:1:1:0:60:31.5:1:0:0.1 0/1:79:2:1,1:12,65:0.0253:2,2:25.5:1:27.5:1:0.3038:5.24:60:4:0.0256:0:1 -3 71179921 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21647;SOR=Inf;LSEQ=CAAAGAAACCACAAGAATTC;RSEQ=TCAAGTAATTCTTCACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:1,26:0:1,0:22.5:1:32.4:1:1:0:60:54:1:0:0 0/1:24:2:1,1:0,22:0.0833:1,2:36.5:1:30:1:0.08333:0:60:4:0.0833:0:1.5 -3 71246918 . C T 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATGTATTTATTTCAACTCT;RSEQ=CTTACTCATCTACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:15,1:16,0:0.5:1,1:26.1:1:30.6:1:1:0:60:32:0.5:0:1.1 0/0:35:0:0,0:34,1:0:1,0:20.1:1:29.9:1:1:0:60:16.5:1:0:0.3 -3 71247014 . A T 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00056;SOR=0;LSEQ=CGTTTAATTTTTATTTTTGC;RSEQ=TGAAAGCAGTGGGAACCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:9:7,2:178,35:0.0405:2,2:24.2:1:31.7:1:0.64735:1.45033:60:18:0.0411:0:1 0/0:283:0:0,0:199,84:0:2,0:22.5:1:29.3:1:1:0:60:39.429:1:0:0.1 -3 71247304 . A G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.1111;LSEQ=TAAGTGTAAAATTCAGCAGT;RSEQ=AAATTCGCACCCACCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:118:81,37:131,64:0.3758:2,2:22.8:1:31.8:1:0.80437:1.07:60:38.333:0.3746:0:1.1 0/1:384:24:14,10:243,117:0.0625:2,2:26:1:31.2:1:0.37478:1.48195:60:48:0.0628:0:1.1 -3 71247356 . TTGC T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.58175;SOR=1.29417;LSEQ=ACTCCAAAGCCCAGTACCTG;RSEQ=TGCTGCTGCTGGGCGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:11:6,5:315,204:0.0208:2,2:28.5:1:30:1:0.75911:1.28612:60:22:0.021:0.0019:0.5 0/1:749:20:11,9:436,293:0.0267:2,2:23.1:1:28.9:1:0.65272:1.21717:60:40:0.027:0.008:0.2 -3 71247572 . A T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07771;LSEQ=AGGATTTCCAAGATGGGGGG;RSEQ=GGGAGGGGGGGAGAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:132:72,60:11,11:0.528:2,2:14.7:1:27.1:1:0.81808:1.20:59.8:8.429:0.5673:0:1.3 0/1:314:25:15,10:124,61:0.0796:2,2:13.5:1:26.1:1:0.50462:1.35311:60:7.333:0.0833:0:1.2 -3 71247576 . A T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=15.53591;LSEQ=TTTCCAAGATGGGGGGAGGG;RSEQ=GGGGGGGAGAAAAAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:16:7,9:65,37:0.0737:2,2:13.8:1:24.8:1:0.16903:2.24237:58.8:3:0.0784:0:2.1 1/0:276:153:106,47:14,10:0.5543:2,2:17.5:1:25.5:1:0.34788:1.61:59.5:5.955:0.6422:0:1.4 -3 71247585 . G GA 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.11265;SOR=0.45534;LSEQ=TGGGGGGAGGGAGGGGGGGA;RSEQ=AAAAAAAAAGCAGCTGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:13:5,8:45,130:0.0681:2,2:18:1:28.2:1:0.33604:1.80:57.4:26:0.0751:0.0157:1.7 0/1:249:8:3,5:86,150:0.0321:2,2:24.9:1:30.6:1:1:1.05:55.1:16:0.0362:0:1.8 -3 71247595 . G A 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00312;SOR=Inf;LSEQ=GAGGGGGGGAGAAAAAAAAA;RSEQ=CAGCTGTTAAAGCAGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:30,149:0:2,0:19:1:31.8:1:1:0:57:43.75:1:0:1.5 0/1:235:11:2,9:60,164:0.0468:2,2:21.7:1:29.6:1:0.73218:1.64326:56.5:22:0.0485:0:2.6 -3 71247604 . A T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50409;SOR=Inf;LSEQ=AGAAAAAAAAAGCAGCTGTT;RSEQ=AAGCAGTTGTTGTGCATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:22,136:0:2,0:21.1:1:29.7:1:1:0:58.9:78:1:0:1.4 0/1:195:2:1,1:42,151:0.0103:2,2:10:0:27:0:0.39329:3.56:50:4:0.0106:0:2.5 -3 72211513 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51153;SOR=Inf;LSEQ=AGCCCCACCCTGCTTCTCTG;RSEQ=ACCGCTGACTCCTCTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:0:2,0:30.7:1:32.1:1:1:0:60:26:1:0:0.2 0/1:40:2:1,1:21,17:0.05:2,2:20.5:1:29:1:1:1.22874:60:4:0.05:0:1.5 -3 72213025 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGACAGACCAGGTTCCA;RSEQ=GTAATTGTGGCCAAGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:31.5:1:31.5:1:1:1.73:60:4:0.4:0:1 -3 72322897 . C T 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.15267;LSEQ=GGAATTGTTGGTATTCAAGC;RSEQ=GGCTCTCTGGAGGCCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,1:0.3:2,0:33.3:1:31.3:1:1:0:60:6:0.3:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:39:0:28:0:1:0:60:2:0.3333:0:1 -3 72323024 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25195;SOR=Inf;LSEQ=AGCCCCCAACAGCCAACAGA;RSEQ=CTGAGCACTGCCCTGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:77,3:0:1,0:22.4:1:31.9:1:1:0:60:79:1:0:0.1 0/1:96:3:1,2:82,11:0.0313:2,2:19.3:1:29:1:0.04731:14.14585:60:6:0.033:0:1 -3 72323061 . A G 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57592;SOR=0.36454;LSEQ=TGGCTCCACACACAGCTCTC;RSEQ=GGAACTCCAGAACTTCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:96,37:0.0148:2,2:32.5:1:30:1:0.48524:2.57353:60:4:0.0149:0:1 0/0:184:1:1,0:133,50:0.0054:2,0:4:0:27:0:1:0:60:2:0.0056:0:1 -3 72323080 . G A 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGGAACTCCAGAACTTCCC;RSEQ=AGCACCTTGTCTGGTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:21:15,6:117,40:0.118:2,2:22.9:1:29.7:1:0.79248:1.16891:60:20:0.113:0:1.4 0/0:242:0:0,0:177,65:0:2,0:26.3:1:29.3:1:1:0:60:25.889:1:0:0.1 -3 72323171 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20143;LSEQ=TTACGTTTAAAACCACAAAA;RSEQ=AGAAGGGAGGTTTGTAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:568:325:175,150:137,105:0.5722:2,2:25.2:1:29.3:1:0.55047:1.11815:60:53.167:0.5686:0:1.2 0/1:849:180:96,84:347,322:0.212:2,2:24.7:1:28.5:1:0.73747:1.06:60:89:0.2129:0:1.1 -3 72323287 . A G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08131;LSEQ=ACTTCGGGTTTCCCCAAGAC;RSEQ=CTCAGGGTTCCCCAGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:68:9,59:11,85:0.4146:2,2:25:1:31.4:1:0.81032:1.18:60:33:0.4074:0:1.1 0/1:148:8:0,8:15,125:0.0541:2,0:34.3:1:32.8:1:1:0:60:16:0.0541:0:1 -3 72323384 . T A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03722;SOR=0.24248;LSEQ=AAAGTAAGAATGTGACTCTT;RSEQ=CACAAATAGTAAATGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:0,14:0,14:0.5:1,1:29.4:1:30.5:1:1:0:60:28:0.5:0:1.1 0/1:21:4:0,4:2,15:0.1905:2,0:34.3:1:30.3:1:1:0:60:8:0.2:0:1.8 -3 72323412 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20308;SOR=Inf;LSEQ=AGTAAATGAGCACATGTCAA;RSEQ=GATCTCTTTAACCTATGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:0:1,0:22.3:1:31.1:1:1:0:60:28:1:0:0.8 0/1:12:2:1,1:0,10:0.1667:0,2:7.5:1:27.5:1:0.16667:0:60:4:0.1667:0:2 -3 72427252 . A AT 48 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAATTGTGCACAGCAG;RSEQ=TTTTTTTTTTTTTATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:33.3:1:30.7:1:1:0:60:6:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 72427853 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50057;SOR=Inf;LSEQ=GATCAAAAACAGCTTCTGGC;RSEQ=GAATATCATCAATACGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:5,52:0:2,0:23.8:1:31.4:1:1:0:60:114:1:0:0.1 0/1:69:2:1,1:8,59:0.029:2,2:35.5:1:28.5:1:0.24552:7.01:60:4:0.029:0:1 -3 72428110 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21536;SOR=0;LSEQ=TCTTAGCCTACAAACCCAAG;RSEQ=CACAAAACCACCCTGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:165,24:0.0105:2,2:27.5:1:27:1:0.24525:6.75521:60:4:0.0108:0:1 0/0:220:0:0,0:183,36:0:2,0:23.9:1:31.1:1:1:0:60:53.75:0.9954:0:0.1 -3 72428323 . C CA 73 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.27603;SOR=2.64377;LSEQ=ATACAAAACAAACAAACAAA;RSEQ=AAAAAAAACAGGCATTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:2:1,1:262,206:0.0042:2,2:12.5:1:31.2:1:1:1.27118:60:4:0.0043:0.0021:0 0/1:449:5:2,3:254,186:0.0111:2,2:17.2:1:31.6:1:0.65468:2.04507:60:10:0.0113:0:0.2 -3 72455797 . A C 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00207;SOR=0;LSEQ=AACAAAGGTATTTTAAATAG;RSEQ=TCCCCCGAGGAGATTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:11,0:10,0:0.5238:0,0:24.3:1:32.8:1:1:0:60:22:0.5238:0:1 0/0:12:0:0,0:12,0:0:0,0:14.7:1:28.4:1:1:0:60:11:1:0:0.1 -3 72456179 . G GA 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.67267;SOR=1.65527;LSEQ=GTAAAATCCATAAAGTGCCA;RSEQ=AAAAAAAATGAGATGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:2:1,1:23,207:0.0085:2,2:21:1:26.5:1:0.1966:8.83:60:4:0.0088:0.0043:0.5 0/1:213:3:1,2:27,183:0.0141:2,2:28:1:28.3:1:0.3462:3.36:60:6:0.0143:0.0047:0.3 -3 72456199 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23549;SOR=Inf;LSEQ=GAAAAAAAATGAGATGAGTG;RSEQ=TTTCTGTCCAACAAAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:3,162:0:1,0:24.7:1:30.6:1:1:0:60:19.625:1:0:0.3 0/1:157:2:1,1:7,148:0.0127:1,2:10:1:29:1:0.09962:19.85:60:4:0.0131:0:1 -3 72495593 . T TA 174 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.56099;SOR=1.15227;LSEQ=AGGCTCACTACCCTCTCACT;RSEQ=AAAAAAAAAAAAAAAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:41:31,10:59,9:0.3154:2,2:29.3:1:28:1:0.19207:2.09943:58.3:19.5:0.312:0.0462:2 0/1:222:77:54,23:86,30:0.3468:2,2:25.9:1:27.9:1:0.62172:1.2197:58.5:76:0.3636:0.0405:2.2 -3 72495777 . C G 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03399;LSEQ=CGCTTGTCTTTTTGGCCTTC;RSEQ=GAGGAGTGGAGAGTGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:511:509:194,315:0,0:0.9961:0,2:26.1:1:30.1:1:1:0:60:49.9:0.996:0:1.2 1/1:800:717:286,431:37,43:0.8963:2,2:27.2:1:29.7:1:0.28176:1.29627:60:88.625:0.8975:0:1.2 -3 72495945 . A G 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTCCGGGGACTGGAAGAG;RSEQ=GAGCGAGGAAGGGAACCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1:0,1:24:1:30.9:1:1:0:60:26:1:0:1.1 1/1:15:14:0,14:0,1:0.9333:0,1:21:1:30.1:1:1:0:60:28:0.9333:0:1.1 -3 72799703 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.46232;LSEQ=GAAAGGGACCTTGCAAAGAA;RSEQ=TGACTGTCTCAGATGGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:36:16,20:288,263:0.0612:2,2:23.8:1:30.6:1:0.39299:1.36808:60:72:0.0616:0:1.2 0/1:677:241:119,122:207,228:0.356:2,2:21.7:1:29.8:1:0.68808:1.07:60:119.5:0.3562:0:1.2 -3 72800061 . C CA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20184;SOR=0;LSEQ=ATAACAGGTTATACAGCTTC;RSEQ=AAAAAAATAAAGTTGAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:0,2:0,76:0.0256:1,0:19.5:1:30.5:1:1:0:60:4:0.0256:0.0128:0.5 0/0:95:0:0,0:10,85:0:2,0:23.8:1:31.7:1:1:0:60:94:1:0:0.1 -3 72861740 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4987;SOR=Inf;LSEQ=TATTTATATACAGTAAAAAA;RSEQ=CAAAAATCATTATTATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:122,8:0:2,0:22.9:1:32.2:1:1:0:60:129:1:0:0.1 0/1:139:2:1,1:116,21:0.0144:2,2:7:1:26.5:1:0.29246:5.42011:60:4:0.0146:0:1.5 -3 72862375 . T C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTCATGCCTGTAAAGCACT;RSEQ=TGGGACTCCAGGCGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:28.5:1:27:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:33:0:32:1:1:0:60:4:1:0:1 -3 72866303 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50011;SOR=Inf;LSEQ=TCACCACCAGTTCTACTCTA;RSEQ=ACAAGAAAGACTGATGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:119,9:0:2,0:22.8:1:32.2:1:1:0:60:127:1:0:0.2 0/1:145:2:1,1:119,24:0.0138:2,2:5.5:1:25:1:0.31609:4.87862:60:4:0.0142:0:1.5 -3 72873492 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4993;SOR=Inf;LSEQ=ATAAGGCAATTACAACTATA;RSEQ=GCTTAATAATATGGAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:117,13:0:2,0:24:1:31.7:1:1:0:60:64:1:0:0 0/1:143:2:1,1:129,12:0.014:2,2:25:1:25.5:1:0.17414:10.3683:60:4:0.0142:0:1 -3 72873527 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09158;SOR=0;LSEQ=AAGGCAGTAAACGTGGTACA;RSEQ=CATGAGATTTTAAAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:1,2:196,72:0.0111:2,2:23.3:1:28:1:0.18196:5.40403:60:6:0.0112:0:1 0/0:329:0:0,0:243,86:0:2,0:23.6:1:30.6:1:1:0:60:108.667:1:0:0.1 -3 72873748 . CT C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.19134;SOR=0;LSEQ=ACTATACAGGATTTCACTGG;RSEQ=TTTACTTTTTAACATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:0,2:43,153:0.0101:2,0:25.5:1:31:1:1:0:60:4:0.0102:0.0051:1 0/0:254:0:0,0:66,188:0:2,0:20.7:1:30:1:1:0:60:62.5:1:0:0.1 -3 72873809 . A G 126 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0014;SOR=7.17156;LSEQ=AGAAATACAGATTTTAATTC;RSEQ=AAGTACATTTCAAGGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:0,3:1,53:0.0526:1,0:13.7:1:32.7:1:1:0:60:6:0.0536:0:1 0/1:52:15:0,15:0,37:0.2885:1,1:21.9:1:32.5:1:1:0:60:30:0.2885:0:1 -3 72881716 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50657;SOR=Inf;LSEQ=TTTTATACAAAATGCCAAAG;RSEQ=ACAGGAAGAACCTAACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:4,83:0:1,0:24.5:1:32.3:1:1:0:60:174:1:0:0 0/1:114:2:1,1:9,103:0.0175:2,2:27.5:1:28.5:1:0.16845:10.91:60:4:0.0179:0:1 -3 72889294 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCTGTAATCCCAGCTAC;RSEQ=TGGGAGGCTGAGGCAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:30.5:1:1:0:48:4:1:0:5.5 -3 72889308 . C G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTACTTGGGAGGCTGAGG;RSEQ=AGGACAATCACTTGGACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:32:1:1:0:48:4:1:0:5.5 -3 72889329 . G T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGACAATCACTTGGACCCG;RSEQ=GAGGCAGAGGTTGCAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:32:0:1:0:48:4:1:0:5.5 -3 72889338 . G T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGGACCCGGGAGGCAGA;RSEQ=GTTGCAGTGAGCCAAGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:32:0:1:0:48:4:1:0:5.5 -3 72890370 . A AT 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.13469;SOR=Inf;LSEQ=CCTGAATGTGTTAAATTTTA;RSEQ=TTTTTTTTAAGTATTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:58,216:0:2,0:23.5:1:30.3:1:1:0:59.9:29.444:1:0:0.2 0/1:349:4:1,3:96,249:0.0115:2,2:22.5:1:30.2:1:1:1.15616:60:8:0.0116:0.0029:0 -3 72890421 . GA G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49939;SOR=0;LSEQ=TAGGGGAAGAAAAAGTATAG;RSEQ=AAAAATGCCCACAAAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:0,97:0.0202:1,0:26.5:1:29.5:1:1:0:60:4:0.0206:0:2 0/0:87:0:0,0:7,80:0:2,0:24.1:1:29.7:1:1:0:60:42.5:1:0:0.1 -3 72890430 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20292;SOR=Inf;LSEQ=AAAAAGTATAGGAAAAAATG;RSEQ=CCACAAAGATGTACCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:0,86:0:1,0:23.9:1:30.8:1:1:0:60:27.667:1:0:0.3 0/1:71:2:1,1:1,68:0.0282:1,2:18.5:1:24:0:0.05594:48.43:60:4:0.0282:0:1 -3 72891500 . G A 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAGCAGTTAACATGTTCA;RSEQ=CCCCTCAAAATGCTGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:570:0:0,0:262,307:0:2,0:27.3:1:31.9:1:1:0:60:70.125:1:0:0.1 0/1:860:43:21,22:385,431:0.05:2,2:24.9:1:29.7:1:0.87623:1.07:60:86:0.0506:0:1.2 -3 72897298 . G T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.65404;SOR=2.49123;LSEQ=CCTTGCATTCTCCCTCTAAA;RSEQ=CAGCTATCTAACGAATGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:0,1:178,49:0.0044:2,0:1:0:28:0:0.2193:0:60:2:0.0045:0:2 0/1:368:4:1,3:272,92:0.0109:2,2:11.5:1:26.3:1:0.0545:8.80535:60:8:0.011:0:1 -3 72897516 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1429;SOR=Inf;LSEQ=GCACCGGACGCAAGGGCCGG;RSEQ=GCCGCTCGCTCTCACTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:50,151:0:2,0:25.7:1:30.1:1:1:0:60:99.5:1:0:0.1 0/1:278:4:2,2:77,196:0.0144:2,2:10.8:1:29.3:1:0.32183:2.54:60:8:0.0144:0:2 -3 73129574 . G A 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00559;SOR=Inf;LSEQ=TGGGAGGGCCAGCTGTCTGC;RSEQ=CTTTCTGTCAAGACCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:29.4:1:30.2:1:1:0:60:36:1:0:0.2 0/1:23:8:3,5:5,10:0.3478:2,2:26.3:1:28.9:1:1:1.19:60:16:0.3478:0:1 -3 74788556 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.15584;SOR=Inf;LSEQ=TTGCTATCCACTGACCTCCA;RSEQ=ACTGCTTCATGGCTATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:23.5:1:32.2:1:1:0:60:26:1:0:0 0/1:9:2:1,1:3,4:0.2222:2,2:20:1:28:1:1:1.29:60:4:0.2222:0:1 -3 75010988 . T A 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=2.29617;LSEQ=GGATGGTAGCAGGATAGAAT;RSEQ=TTTATCTTTGCAATTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:178:85,93:75,73:0.546:2,2:25.8:1:29.2:1:0.65651:1.12369:60:43.5:0.5421:0:1.1 1/0:448:329:173,156:62,57:0.7344:2,2:25.5:1:28.6:1:1:1.02:60:108.667:0.7359:0:1.2 -3 75011086 . G T 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.97992;LSEQ=ATAGTAATGCAAAATTATGT;RSEQ=ATTGTTTTAAAATGATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:1:0,1:25,106:0.0076:2,0:13:0:11:0:1:0:60:0:0:0:2 0/1:134:2:1,1:20,112:0.0149:2,2:9:0:31:1:0.28987:5.49:60:4:0.0155:0:1 -3 75139687 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35096;LSEQ=GTGCTTTGAAGCAGTGGGAA;RSEQ=GCCAAATCTGAAACCATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:129:75,54:84,69:0.4574:2,2:29.3:1:30.6:1:0.63041:1.14:60:42:0.4532:0:1.1 0/1:307:70:36,34:123,111:0.228:2,2:29:1:30.3:1:0.89216:1.04641:60:140:0.2303:0:1.1 -3 75139814 . G C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07521;SOR=0.46283;LSEQ=ATCAACCTCAATGAGAATGT;RSEQ=ACAAATCAATGCTGTAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:33:3,30:2,32:0.4853:2,2:22.7:1:32.4:1:0.67284:1.59:60:66:0.4853:0:1.1 0/1:43:13:1,12:1,29:0.3023:1,1:28.9:1:31.2:1:0.51827:2.36:60:26:0.3023:0:1 -3 75164778 . C T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.251;SOR=Inf;LSEQ=TGGAATAGGGCATTAGTTCT;RSEQ=ATTATTCATTCAATTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:67,36:0:2,0:26.1:1:31.8:1:1:0:60:206:1:0:0.2 0/1:120:3:1,2:79,38:0.025:2,2:8.3:1:20.3:1:0.25737:4.10424:60:2:0.0168:0:1 -3 75164797 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58922;SOR=0.40465;LSEQ=TCATTATTCATTCAATTTTT;RSEQ=CTCAAAGACATTTAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:80,41:0.0163:2,2:34.5:1:30.5:1:1:1.93993:60:4:0.0164:0:1 0/0:151:1:1,0:99,50:0.0066:2,0:1:0:24:0:1:0:60:2:0.0066:0:1 -3 75164800 . C CA 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=3e-05;SOR=0.34045;LSEQ=TTATTCATTCAATTTTTGCT;RSEQ=AAAGACATTTAAAATCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:61:40,21:53,26:0.4357:2,2:24.3:1:30.1:1:0.85882:1.06967:60:29.5:0.4307:0.0857:0.6 0/1:159:33:20,13:81,45:0.2075:2,2:27.7:1:30.3:1:0.6901:1.16882:60:66:0.2089:0.0314:0.6 -3 75164849 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19501;SOR=0;LSEQ=AGCAATATCTATGTCCTGAG;RSEQ=ATTCTGAAAGTTATACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:108,89:0.0101:2,2:11:1:28:1:1:1.21229:60:4:0.0103:0:1 0/0:251:0:0,0:134,116:0:2,0:25:1:30.8:1:1:0:60:249:0.996:0:0.3 -3 75164859 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32576;LSEQ=ATGTCCTGAGGATTCTGAAA;RSEQ=TTATACACCTCAGCTCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:81:41,40:60,50:0.4241:2,2:28.9:1:30.3:1:0.66046:1.16976:60:80:0.4301:0:1.1 0/1:259:50:26,24:103,106:0.1931:2,2:26.6:1:30.1:1:0.755:1.11:60:100:0.1953:0:1 -3 75164938 . A T 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATGCCCCATAATTTGAATA;RSEQ=ATAATCAAGAAAATGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:44:8,36:16,35:0.4632:2,2:24:1:28.3:1:0.16173:2.04174:60:43:0.4574:0:1.1 0/0:137:0:0,0:41,96:0:2,0:22.1:1:29.8:1:1:0:60:274:1:0:0.1 -3 75164989 . G GA 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50366;SOR=Inf;LSEQ=AAATTTCAAAAAATTAAAAG;RSEQ=AAAAAATGCAGTCACATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:1,36:0:1,0:25.5:1:31.2:1:1:0:60:74:0.9737:0:0.3 0/1:50:2:0,2:6,42:0.04:2,0:27.5:1:32:0:1:0:60:4:0.04:0:0 -3 76716532 . T G 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76283;LSEQ=GTTATTGTAAAAGCAGCTAT;RSEQ=GAAAGCTAAATGCAAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:29.4:1:31.2:1:1:0:60:10:0.5:0:1 0/1:7:3:3,0:4,0:0.4286:0,0:14:1:31:1:1:0:60:6:0.4286:0:1 -3 76716724 . G GA 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.1585;SOR=1.31276;LSEQ=GCAGGTTAATGATCAAATCA;RSEQ=AAAAAACAACATTAATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:87:52,35:72,44:0.4265:2,2:26.4:1:30.4:1:0.77234:1.10087:60:174:0.4286:0.0686:0.6 0/1:255:126:79,47:78,49:0.4941:2,2:25.5:1:29.4:1:0.89708:1.06:60:125:0.4941:0.0784:0.6 -3 76716794 . G A 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01704;SOR=1.43346;LSEQ=GTATTTTAGAGTAATCAGGC;RSEQ=TACTGTTTTTGGTAAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:156:78,78:83,87:0.4785:2,2:27:1:30.5:1:0.91174:1.05:60:312:0.4785:0:1.1 1/0:403:229:106,123:82,92:0.5682:2,2:23.8:1:29.7:1:0.91978:1.03418:60:75.333:0.5693:0:1.1 -3 76716827 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24945;SOR=Inf;LSEQ=TAAATATAATTGTTCTTATT;RSEQ=TTTAGGGCTATTTTTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:103,153:0:2,0:25.5:1:31.8:1:1:0:60:127:1:0:0.5 0/1:274:3:1,2:108,162:0.0109:2,2:15.3:1:27:1:1:1.33198:60:6:0.0109:0:1.3 -3 76716837 . ATTTTTAGCAGTGATCAGACTTTTTGGCTCA CTAAACAATTGTTAGGGCTCTAAACATTG 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTCTTATTGTTTAGGGCT;RSEQ=TAAGTGCTCTAAACAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:87,141:0:2,0:25.3:1:29.6:1:1:0:60:113:1:0:0.4 0/1:244:51:18,33:78,114:0.209:2,2:26.5:1:29.5:1:0.52301:1.25323:59.6:102:0.2099:0.1393:1 -3 76716955 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.08905;LSEQ=TATCTAATAAAAGATAGAAA;RSEQ=TGTTCAATATTTCATAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:0,11:0,12:0.4783:0,0:21.2:1:33.1:1:1:0:60:22:0.4783:0:1 1/0:28:14:0,14:0,14:0.5:1,1:24.9:1:31.4:1:1:0:60:28:0.5:0:1.4 -3 76716986 . C T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10446;SOR=Inf;LSEQ=TTCATAAGATTACATAAAAA;RSEQ=GACTGTAGTTATAACAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:0:0,0:23.6:1:30.4:1:1:0:60:20:1:0:0.5 0/1:13:4:0,4:0,9:0.3077:0,0:22.8:1:30.3:1:1:0:60:8:0.3333:0:1.5 -3 76717014 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=GTTATAACAAATATTCTACA;RSEQ=CATGATTTAATAAAAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:26:1:32.5:1:1:0:60:16:1:0:0.3 0/1:5:2:0,2:0,3:0.4:0,0:35.5:1:31.5:1:1:0:60:4:0.4:0:2 -3 76717350 . T C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTCGACCTCCTAGACTC;RSEQ=GGTGATCCTCCCACCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33:0:31.5:1:1:0:60:4:1:0:1.5 -3 78330200 . G A 125 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AGAAGCAGCAAGGTTCAGAG;RSEQ=CTCCCATCAGAAAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:8,13:0,0:1:0,2:22.4:1:28.6:1:1:0:60:20:1:0:1.2 0/1:24:10:3,7:6,8:0.4167:2,2:33:1:29.5:1:0.67846:1.70978:60:20:0.4167:0:1.3 -3 78330515 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TAGCATCCCAACTCCAGAAC;RSEQ=GGCAGAGCCTTACAGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:24:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:29:1:1:0:60:4:1:0:1 -3 78331073 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20434;SOR=0;LSEQ=AAACACACCCTCTCCAACAA;RSEQ=GGACAAAGTGCTTAATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:17,31:0.04:2,2:20:0:32:1:1:1.80:60:4:0.04:0:1.5 0/0:60:0:0,0:27,33:0:2,0:21.1:1:30.5:1:1:0:60:59:1:0:0.3 -3 78331074 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24615;SOR=Inf;LSEQ=AACACACCCTCTCCAACAAG;RSEQ=GACAAAGTGCTTAATTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:17,32:0:2,0:23.9:1:30.2:1:1:0:60:15.333:1:0:0.2 0/1:56:3:3,0:24,29:0.0536:2,0:15.3:1:29:1:0.10552:0:60:6:0.0556:0:1 -3 78331221 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52941;SOR=Inf;LSEQ=CAAGGTCAGAGGTCCCAGAA;RSEQ=AAGGAGCAGGCACCCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:29.3:1:31.3:1:1:0:60:12:1:0:0.3 0/1:12:2:0,2:6,4:0.1667:2,0:23:1:30:0:0.45455:0:60:4:0.1818:0:1 -3 78331246 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.5;SOR=Inf;LSEQ=AGCAGGCACCCATCTTTGCT;RSEQ=CTCTCCAGGCTCTTTGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:20.2:1:29.6:1:1:0:60:4:1:0:0.2 0/1:15:2:1,1:7,6:0.1333:2,2:18:1:31:1:1:1.1547:60:4:0.1333:0:1 -3 78331555 . C A 69 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1009;SOR=Inf;LSEQ=GCAGAGTGCCTCTTCTCCTC;RSEQ=AAATGATTGCAATGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:31:1:32.4:1:1:0:60:10:1:0:0.2 1/0:10:5:2,3:1,4:0.5:2,2:17.6:1:29.8:1:1:2.41:60:10:0.5:0:1.2 -3 78521896 . A C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTAGAAGCAGCTCATGTG;RSEQ=CTCACTTTTACGGAGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:25.3:1:31.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 78616968 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGCAAAGAACCCTATTAAG;RSEQ=TGGTTTAGTGAGAAACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:7,16:0:2,0:29.3:1:33:1:1:0:60:46:1:0:1.3 0/1:49:2:1,1:18,29:0.0408:2,2:29.5:1:28.5:1:1:1.59:60:4:0.0417:0:2 -3 78616977 . T C 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTATTAAGCTGGTTTAG;RSEQ=GAGAAACCCCCGTCGTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:7,15:0,0:1:0,2:24.8:1:28.7:1:1:0:60:10:1:0:1.4 1/1:44:44:17,27:0,0:1:0,2:21.6:1:30.6:1:1:0:60:88:1:0:1.2 -3 87347911 . G C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15696;SOR=0.32521;LSEQ=TTTCAATTTTCAAGAAAAAT;RSEQ=TAACAACTATTTATTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:0.6154:0,0:19.5:1:31.3:1:1:0:60:16:0.6154:0:1 0/1:18:6:6,0:12,0:0.3333:0,0:24.2:1:29.8:1:1:0:60:5:0.2941:0:1 -3 87347973 . G T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08098;SOR=0;LSEQ=GAAACCATCAATACATGAAC;RSEQ=ATTATAATATTTTTAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:3,0:41,2:0.0652:1,0:19:1:31.7:1:1:0:60:6:0.0652:0:1.3 0/0:59:0:0,0:56,3:0:2,0:25.1:1:29.9:1:1:0:60:118:1:0:0.2 -3 87347995 . AG A 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02125;SOR=0.48399;LSEQ=TTATAATATTTTTAAAACAA;RSEQ=TTATGCTGTACTGCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:41:35,6:30,5:0.5395:2,2:22.8:1:31.3:1:1:1.0282:60:82:0.5395:0.0789:0.7 0/1:97:35:27,8:52,10:0.3608:2,2:21.8:1:29.5:1:0.42711:1.5337:60:70:0.3608:0.1031:0.7 -3 87348021 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.58361;SOR=0.3884;LSEQ=GCTGTACTGCAAAGTATTTT;RSEQ=AAAATTTGCAGTACCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:92,28:0.0164:2,2:33.5:1:30:1:0.4204:3.24605:60:4:0.0164:0:1.5 0/0:156:1:0,1:110,45:0.0064:2,0:1:0:23:0:0.29487:0:60:2:0.0065:0:1 -3 87348032 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17223;SOR=0;LSEQ=AAGTATTTTCAAAATTTGCA;RSEQ=TACCAAAGATCACATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:98,36:0.0147:2,2:29:1:32:1:0.47157:2.69885:60:4:0.0149:0:2 0/0:191:0:0,0:117,73:0:2,0:23.7:1:31.3:1:1:0:60:380:0.9948:0:0.4 -3 87348062 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14211;SOR=0;LSEQ=TCACATTATATATGTTTGCT;RSEQ=GCATAAGTTTTGCTGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:105,72:0.0112:2,2:43.5:1:32:1:1:1.45516:60:4:0.0112:0:2.5 0/0:295:0:0,0:157,138:0:2,0:24.7:1:28.9:1:1:0:60:72.75:1:0:0.5 -3 87348066 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04437;LSEQ=ATTATATATGTTTGCTAGCA;RSEQ=AAGTTTTGCTGAATATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:187:172:97,75:9,6:0.9198:2,2:25.5:1:31.7:1:1:1.15888:60:344:0.9198:0:1.1 0/1:298:100:54,46:105,93:0.3356:2,2:26.9:1:30.7:1:0.90258:1.04:60:24:0.3288:0:1.1 -3 87348159 . A C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19258;SOR=0;LSEQ=ATAAACTTGTATCTCTACGT;RSEQ=CAATTGAAATAAGATATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:14,76:0.0217:2,2:25:1:30:1:0.301:5.28:60:4:0.022:0:1 0/0:117:0:0,0:30,87:0:2,0:21.9:1:29.2:1:1:0:60:234:1:0:0.2 -3 87348221 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.76882;SOR=0.7998;LSEQ=ACCAACACCCTAGAACAACA;RSEQ=ACTAGGAAAACTCTTTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:0,8:0,11:0.4211:0,0:27.1:1:28.8:1:1:0:60:16:0.4444:0:1 0/1:30:11:0,11:1,18:0.3667:1,0:16.9:1:26.4:1:1:0:60:10:0.3448:0:1 -3 87348307 . A ATTTG 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.00466;SOR=0;LSEQ=GAACGTAGCTATGTATGTTC;RSEQ=TTTGTGTATTGTCTATGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:33.7:1:31.8:1:1:0:60:14:0.875:0:0.1 0/0:5:0:0,0:0,5:0:0,0:10.4:1:30.2:1:1:0:60:10:1:0:0.6 -3 87348364 . T G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGTTGAACAACTGTGTTA;RSEQ=AGATGGGCTGGCCCACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:26:1:30:0:1:0:60:4:0.5:0:1 0/0:1:0:0,0:0,1:0:0,0:42:0:30:0:1:0:60:2:1:0:0 -3 88892593 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1535;SOR=0;LSEQ=GCATTTTCAGTGAAATTTTA;RSEQ=TGACCACGCCAGCTGGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:93,82:0.0113:2,2:11.5:1:26:1:1:1.13334:60:4:0.0114:0:2 0/0:274:0:0,0:148,126:0:2,0:25.1:1:31:1:1:0:60:44.667:1:0:0.5 -3 88892634 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15626;SOR=0;LSEQ=AATCTTTCTCCAAATGCAAG;RSEQ=TTTCTGCAGCATGACAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:76,98:0.0113:2,2:36.5:1:29.5:1:1:1.29:60:4:0.0116:0:1 0/0:270:0:0,0:129,141:0:2,0:25.6:1:30.6:1:1:0:60:32.75:1:0:0.8 -3 88892638 . C A 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.34783;LSEQ=TTTCTCCAAATGCAAGGTTT;RSEQ=TGCAGCATGACAAAATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:175:149:68,81:9,17:0.8514:2,2:25.2:1:29.5:1:0.3925:1.58:60:48.667:0.8538:0:1.1 1/0:266:177:83,94:39,50:0.6654:2,2:24.2:1:28.8:1:0.69615:1.13:60:87.5:0.6629:0:1.1 -3 89156692 . A G 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.00736;SOR=0;LSEQ=ATCCCGCTCTGCTTCAGCGC;RSEQ=CGCTGAAGACGGCACTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:9,1:17,0:0.3704:1,2:33.2:1:31:1:0.37037:0:60:20:0.3704:0:1.3 0/0:15:0:0,0:15,0:0:1,0:27.2:1:30.4:1:1:0:60:30:1:0:0.1 -3 89156791 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50157;SOR=Inf;LSEQ=AGTGTCAAACTTGACATCAG;RSEQ=CTGCGAGCGGAGCATGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:143,9:0:2,0:25:1:31.8:1:1:0:60:37:1:0:0.1 0/1:179:2:1,1:164,13:0.0112:2,2:24:1:26.5:1:0.15071:12.19364:60:4:0.0114:0:1 -3 89156795 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50193;SOR=Inf;LSEQ=TCAAACTTGACATCAGCCTG;RSEQ=GAGCGGAGCATGGTAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:151,12:0:2,0:24.5:1:31.8:1:1:0:60:53.333:1:0:0.1 0/1:192:2:1,1:170,20:0.0104:2,2:8:1:28.5:1:0.2073:8.31843:60:4:0.0107:0:1 -3 89157126 . C CT 125 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00377;SOR=0.17762;LSEQ=AGAGTGAAGGAAAGATGTGC;RSEQ=TTTTTTTTTTCCAACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:20:0,20:0,41:0.3226:1,1:27.9:1:29:1:1:0:59:19:0.3167:0.0323:0.6 0/1:39:3:0,3:2,32:0.0769:2,0:25.3:1:30.7:1:1:0:60:6:0.0789:0:0.3 -3 89259656 . GT G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50384;SOR=0;LSEQ=TGCTGGCTATGAAGAAAGAG;RSEQ=TTTATGTGCCAAGGTAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:34,126:0.0123:2,2:47.5:1:32:1:0.38647:3.67:60:4:0.0123:0:0 0/0:132:0:0,0:40,92:0:2,0:26.4:1:29.4:1:1:0:60:65:1:0:0.1 -3 89259713 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50361;SOR=0;LSEQ=TTTGAGCAATATTTCTCACC;RSEQ=ATGAGTTTATCATAGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:5,49:0.0357:2,2:37:1:31.5:1:0.20455:9.04:60:4:0.0357:0:1 0/0:43:0:0,0:10,33:0:2,0:27.9:1:28.6:1:1:0:60:42:1:0:0 -3 89390014 . A T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.25312;SOR=Inf;LSEQ=TACTTAAATCTGTTTTACAT;RSEQ=TTTTCAAAAAAATTATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:174,55:0:2,0:25.1:1:28.6:1:1:0:59.9:56.25:1:0:0.1 0/1:268:3:0,3:200,65:0.0112:2,0:8.7:1:20.3:1:0.0158:0:60:2:0.0075:0:1.7 -3 89390828 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50001;SOR=Inf;LSEQ=GTTATTTACCTCATTCAGTT;RSEQ=CATTGTAAATTATCTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:125,10:0:2,0:24.7:1:31.5:1:1:0:60:134:1:0:0 0/1:152:2:1,1:132,18:0.0132:2,2:28.5:1:30:0:0.2351:7.16421:60:4:0.0133:0:1 -3 89390849 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25146;SOR=Inf;LSEQ=CATTGTAAATTATCTATTTC;RSEQ=CTTGTAGTAGAAAACAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:167,43:0:2,0:23.5:1:30.5:1:1:0:60:41:1:0:0 0/1:239:3:1,2:183,53:0.0126:2,2:11.3:1:25.3:1:0.13329:6.83308:60:6:0.0128:0:1.3 -3 89391192 . TC T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.07165;SOR=0;LSEQ=ATGGGGTGTCAGAGCTGAGC;RSEQ=CCCACCAAGACAGTTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:85,200:0.0104:2,2:16:1:30.3:1:1:1.18:60:6:0.0106:0.0035:1.7 0/0:404:0:0,0:138,266:0:2,0:24:1:30.5:1:1:0:60:66.333:1:0:0.1 -3 89391236 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27481;SOR=Inf;LSEQ=GTCAGCATCACAACTAATCA;RSEQ=GCTGGTGAGTACATACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:36,130:0:2,0:26.1:1:31.5:1:1:0:60:82:1:0:0.1 0/1:243:3:2,1:63,177:0.0123:2,2:22.3:1:27.7:1:0.17524:5.57:60:6:0.0124:0:1.3 -3 89444754 . C T 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=AGCAGCAGAGAATCTCAGCA;RSEQ=ATTTTCCCTAGGCCTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:27.3:1:32.3:1:1:0:60:8:0.5:0:1 0/0:2:0:0,0:2,0:0:0,0:29:1:32.5:1:1:0:60:4:1:0:0 -3 89444882 . T C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01857;SOR=Inf;LSEQ=CCAAAAAACTGGAACAATGA;RSEQ=AGACTCCATTTGCATGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:128,1:0:1,0:24.3:1:31.7:1:1:0:60:258:1:0:0.1 0/1:77:4:4,0:70,2:0.0519:1,0:13.8:1:32.3:1:1:0:60:8:0.0533:0:1.3 -3 89444909 . C T 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00655;SOR=Inf;LSEQ=CATTTGCATGTTCCCTTCTC;RSEQ=CTCTGTTCTTATTCGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:188,33:0:2,0:24.2:1:31:1:1:0:60:43.2:1:0:0 0/1:171:6:5,1:139,25:0.0351:2,2:16:1:29:1:1:1.11131:60:5:0.0298:0:2.8 -3 89444923 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25416;SOR=0;LSEQ=CTTCTCCCTCTGTTCTTATT;RSEQ=GCCACCCTTTCTAACCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:1,2:213,60:0.0109:2,2:10.3:1:27.3:1:0.12766:7.03359:60:6:0.0109:0:1 0/0:232:0:0,0:188,44:0:2,0:23.1:1:30.8:1:1:0:60:464:1:0:0.2 -3 89444939 . C A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=TATTCGCCACCCTTTCTAAC;RSEQ=CATTAATTTGCTTCCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:259,89:0:2,0:25.3:1:30.8:1:1:0:60:68.6:1:0:0.1 0/1:342:13:11,2:242,87:0.038:2,2:22.8:1:29.5:1:0.52675:1.97:60:12:0.0356:0:2.5 -3 89444953 . C G 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTAACCCATTAATTTGCTT;RSEQ=CTTCCACCTTCCCCTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:288,133:0:2,0:25:1:30.9:1:1:0:60:69.167:0.9952:0:0.1 0/1:429:18:13,5:286,123:0.042:2,2:23.1:1:31.7:1:1:1.12:60:36:0.0422:0:1.8 -3 89445155 . C T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=TGGGCTGTGTAGGCAAGAAG;RSEQ=TGTTTCCTCATGAGCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:60,195:0:2,0:24.4:1:32.1:1:1:0:60:84:1:0:0.1 0/1:305:14:5,9:96,194:0.0459:2,2:26.7:1:30:1:1:1.12:60:28:0.0461:0:1.1 -3 89448277 . TA T 48 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.11455;SOR=5.80153;LSEQ=TGACAAAGCAAGACTTTGTC;RSEQ=AAAAAAAAAAAAATGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:11,1:0.1875:2,0:27.7:1:31.6:1:1:0:60:6:0.1875:0.0625:0 1/0:5:3:3,0:2,0:0.6:0,0:5.7:1:30.8:1:1:0:60:6:0.6:0.4:0.3 -3 89448404 . T C 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00203;SOR=Inf;LSEQ=CAGGTTTGAGTGGTTCACTG;RSEQ=TTATCATTTTATAGCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:136,7:0:1,0:23.6:1:30.2:1:1:0:60:142:1:0:0.1 0/1:163:10:7,3:128,25:0.0613:2,2:21.3:1:30.1:1:0.37801:2.18129:60:9:0.0556:0:1.5 -3 89448446 . A AT 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.38129;SOR=0.65924;LSEQ=AAGATTTGATTTTAACATGA;RSEQ=TTTTTTTTTCTGACCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:12:10,2:237,81:0.0364:2,2:24.1:1:31.7:1:0.73712:1.71:60:24:0.037:0.0061:0.2 0/1:371:9:7,2:242,119:0.0243:2,2:23.6:1:29.9:1:0.72369:1.72:60:18:0.0247:0.0027:0.4 -3 89448887 . TT ATTTG 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AATGCTTCTGTTTTTTTTTT;RSEQ=AGCCATAAATTGCTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:18:1:31.2:1:1:0:60:4:0.3333:0.1667:1 0/0:1:0:0,0:0,1:0:0,0:28:0:32:0:1:0:60:2:1:0:0 -3 89456534 . T C 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTGGGAGGTGAGTTCACAG;RSEQ=CTGTTTCACTATTCACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:725:0:0,0:273,451:0:2,0:26.4:1:29.8:1:1:0:60:79.444:0.9986:0:0.5 0/1:879:59:23,36:358,461:0.0671:2,2:26.4:1:31:1:0.49994:1.21524:60:58:0.0671:0:1 -3 89456555 . T A 254 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.52216;LSEQ=CTGTTTCACTATTCACTTTC;RSEQ=TTGTTGCTTTGTTTGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:560:316:105,211:82,162:0.5643:2,2:25.3:1:30.6:1:0.92827:1.01714:60:157:0.5668:0:1.1 0/1:667:269:99,170:142,256:0.4033:2,2:24.8:1:29.4:1:0.80543:1.05:60:43.833:0.3997:0:1.2 -3 89462238 . ATTGT A 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.00265;SOR=Inf;LSEQ=GCCATAAAATTTGATCTATA;RSEQ=TTGTACAAATCTAGCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:123,10:0:2,0:23.4:1:31:1:1:0:60:65.5:1:0:0 0/1:165:10:10,0:137,18:0.0606:2,0:29:1:31.2:1:0.60317:0:60:20:0.0606:0:0 -3 89462245 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.50209;SOR=Inf;LSEQ=AATTTGATCTATAATTGTTT;RSEQ=TACAAATCTAGCTACAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:133,18:0:2,0:23.4:1:32.1:1:1:0:60:36.75:1:0:0 0/1:179:2:1,1:152,24:0.0112:2,2:25:1:29:0:0.26185:6.22576:60:4:0.0112:0:1 -3 89462266 . C T 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00266;SOR=Inf;LSEQ=TACAAATCTAGCTACAATTG;RSEQ=GCCTTTCTTTCTTTCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:180,54:0:2,0:23.1:1:31.3:1:1:0:60:57.5:1:0:0.1 0/1:286:10:6,4:194,82:0.035:2,2:22.7:1:28.5:1:0.49439:1.57453:60:20:0.0355:0:1.1 -3 89462464 . G A 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=TAGTACTGTATGTGAATCAC;RSEQ=ATTGCTCAGTCTCTGAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:33,157:0:2,0:23.5:1:30.8:1:1:0:60:94:1:0:0.1 0/1:198:13:3,10:41,144:0.0657:2,2:28.1:1:27.5:1:1:1.05:60:12:0.0615:0:1 -3 89462469 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=Inf;LSEQ=CTGTATGTGAATCACGATTG;RSEQ=TCAGTCTCTGAAACCTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:28,156:0:2,0:22.6:1:32.1:1:1:0:60:183:0.9946:0:0.1 0/1:186:2:1,1:36,148:0.0108:2,2:9:1:29.5:1:0.35914:4.07:60:4:0.0108:0:1 -3 89468268 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2362;SOR=Inf;LSEQ=GGCACAAATATTTTAAATGG;RSEQ=AATTTTGAAATAAAACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:45,1:0:1,0:20.3:1:30.1:1:1:0:60:45:1:0:0.2 0/1:44:2:1,1:39,3:0.0455:2,2:7:1:30.5:1:0.17548:11.40199:60:4:0.0455:0:1 -3 89468314 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21129;SOR=Inf;LSEQ=CTACTGATGAATTTTTATTA;RSEQ=AGAATTCCTTACATTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:115,29:0:2,0:25.8:1:30.2:1:1:0:60:47:1:0:0.1 0/1:123:2:1,1:90,31:0.0163:2,2:39.5:1:32.5:1:0.45422:2.87333:60:4:0.0164:0:1 -3 89468653 . C A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09029;SOR=Inf;LSEQ=TCATAAGTATCTCAGTTTTA;RSEQ=CAAAAAGAAAAGTTTAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,42:0:1,0:25:1:30.4:1:1:0:60:20:1:0:0.1 0/1:36:3:0,3:0,33:0.0833:1,0:14.7:1:31.7:1:1:0:60:6:0.0833:0:1.3 -3 89478212 . C T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1242;SOR=Inf;LSEQ=TATATGTTCATTGTATAATA;RSEQ=TTGAACTGTACTGATTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:227,96:0:2,0:23.4:1:31.8:1:1:0:60:106.667:1:0:0.1 0/1:337:4:1,3:235,98:0.0119:2,2:11:1:27.5:1:0.08224:7.14694:60:8:0.012:0:1.3 -3 89480226 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49981;SOR=Inf;LSEQ=GTTACAAAATTCAATATGTG;RSEQ=GATTTTAACCAATAAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:133,23:0:2,0:23.1:1:30.1:1:1:0:60:77:1:0:0.2 0/1:173:2:1,1:142,29:0.0116:2,2:17:1:32.5:1:0.31758:4.83125:60:4:0.0116:0:1 -3 89480265 . A G 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0022;SOR=1.74014;LSEQ=TATATCTTTAAGAAATAGGA;RSEQ=CGTATCTTAATTGTACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:54:37,17:206,80:0.1584:2,2:19.9:1:32.2:1:0.62354:1.18249:60:108:0.1593:0:1.1 0/1:466:115:76,39:226,124:0.2468:2,2:23.7:1:31.4:1:0.82214:1.07:60:37.333:0.244:0:1.1 -3 89480630 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50397;SOR=0;LSEQ=TTATGCTTTCCACAATAGAA;RSEQ=ACATATCTTAAAATTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:0,47:0.0408:1,2:27.5:1:30.5:1:0.04082:0:60:4:0.0408:0:1 0/0:37:0:0,0:0,37:0:1,0:19.5:1:29.5:1:1:0:60:11.333:1:0:0.2 -3 89498301 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50014;SOR=0;LSEQ=ACTATGAGAAATTCTGTCCG;RSEQ=TTTCAGATTATGTTATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:116,10:0.0156:2,2:13:1:29:1:0.16511:11.10804:60:4:0.0163:0:1 0/0:112:0:0,0:96,16:0:2,0:35:0:13:0:1:0:60:0:0:0:1 -3 89498305 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22095;SOR=Inf;LSEQ=TGAGAAATTCTGTCCGGTTT;RSEQ=AGATTATGTTATGTATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:131,15:0:2,0:22.2:1:30.7:1:1:0:60:17.25:1:0:0.2 0/1:130:2:1,1:106,22:0.0154:2,2:13.5:1:28:0:0.32367:4.7345:60:4:0.0156:0:1 -3 89498619 . A G 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.00583;SOR=0;LSEQ=AACTGGGTGGCTCCTGGTTT;RSEQ=TAACACTGAAATAAAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:97:97:2,95:0,0:1:0,1:23.3:1:32:1:1:0:60:47.5:1:0:1.1 1/1:74:68:2,66:0,6:0.9189:0,1:25.9:1:31.4:1:1:0:60:67:0.9178:0:1.1 -3 89499250 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25052;SOR=Inf;LSEQ=AAAATAAGCATATTTGTGAG;RSEQ=CCCGCCCATGAAAACGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:169,40:0:2,0:22.8:1:31.6:1:1:0:60:68.667:1:0:0.1 0/1:233:3:2,1:168,62:0.0129:2,2:31.3:1:31:1:1:1.35296:60:6:0.0131:0:1 -3 89499253 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25065;SOR=Inf;LSEQ=ATAAGCATATTTGTGAGCCC;RSEQ=GCCCATGAAAACGTAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:177,49:0:2,0:22.5:1:30.4:1:1:0:60:55.5:1:0:0.1 0/1:252:3:2,1:178,71:0.0119:2,2:10:1:30.3:1:1:1.25239:60:6:0.0121:0:1.3 -3 89521509 . C A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08563;SOR=2.00945;LSEQ=TTCCACAAATGAAAGGAACA;RSEQ=CATATGAAGTCTGGAAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:14:14,0:74,0:0.1591:1,1:25.9:1:31.1:1:1:0:60:28:0.1609:0:1.1 0/1:76:21:21,0:55,0:0.2763:1,1:21.2:1:30.3:1:1:0:60:42:0.2763:0:1.2 -3 89521598 . G GT 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.70583;SOR=0.59198;LSEQ=CTGATCTGTCTCCCTTTGGT;RSEQ=TTTTTTTTCTTGCAGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:4:3,1:250,130:0.0104:2,2:20.8:1:31:1:1:1.56:60:8:0.0105:0:0.3 0/0:486:3:2,1:295,187:0.0062:2,2:29:1:30:1:1:1.27:60:6:0.0063:0:0.3 -3 89521602 . T TC 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=8.000;MSILEN=1;SSF=0.00268;SOR=1.65874;LSEQ=TCTGTCTCCCTTTGGTGTTT;RSEQ=TTTTCTTGCAGGCCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:69:43,26:222,126:0.1651:2,2:26:1:31:1:0.8912:1.06517:60:68:0.1635:0.0383:0.3 0/1:510:126:74,52:233,151:0.2471:2,2:25.1:1:30.6:1:0.75319:1.08413:60:125:0.248:0.0569:0.3 -3 89521664 . G A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=8.28596;LSEQ=TGTGGATATCACTACCTTCC;RSEQ=CACAACAGGTGACTGGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:3:2,1:325,300:0.0047:2,2:14:1:28.3:1:1:1.84:60:6:0.0048:0:1 0/1:762:29:16,13:383,347:0.0381:2,2:24.6:1:29.2:1:0.85077:1.11:60:58:0.0392:0:1.6 -3 89521693 . T C 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.17924;LSEQ=GTGACTGGCTTAATGGTGTC;RSEQ=GGACAGCACACTGCAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:665:80:39,41:277,307:0.1203:2,2:25.1:1:30.2:1:0.90508:1.05:60:160:0.1216:0:1.9 0/1:752:228:122,106:254,270:0.3032:2,2:26.6:1:29.5:1:0.23399:1.22:60:44.6:0.3005:0:1.9 -3 89521725 . T C 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.93598;LSEQ=TGCAAGGAAATCTTCACGGG;RSEQ=GTGGAGTACAGTTCTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:65:24,41:193,292:0.118:2,2:21.4:1:30.1:1:0.68742:1.12886:60:31.5:0.1162:0:2 0/1:677:191:87,104:208,277:0.2821:2,2:26.1:1:30.3:1:0.54728:1.11:60:37.2:0.2797:0:2 -3 89521774 . G GA 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58959;SOR=0.65062;LSEQ=CCAAGATTTCCACAGAGTAA;RSEQ=AAAAAAAAATTCATTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:8:1,7:73,207:0.0278:2,2:14.5:1:28:1:0.68454:2.46236:60:7:0.0248:0.0139:1.4 0/1:329:6:2,4:85,238:0.0182:2,2:28:1:27.7:1:0.6569:1.40:60:12:0.0186:0.0061:0.7 -3 89521821 . TGGCTTGACATGAAAGATTTG GCTGAATAT 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00275;SOR=2.68302;LSEQ=AGGATTCTTTTGAACTTTCT;RSEQ=TAACATCTTGGCTTGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:17:0,17:3,103:0.1382:1,1:28.1:1:31.4:1:1:0:60:34:0.1393:0.0244:0.4 0/1:116:35:2,33:6,75:0.3017:2,2:23.5:1:30.6:1:1:1.31704:59.9:70:0.307:0.1034:0.7 -3 89521900 . G T 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4727;SOR=1.8073;LSEQ=GATCTGAGGTACTGACTACC;RSEQ=CCTGGAACTGCTAATCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:0,5:1,21:0.1852:1,0:33.8:1:31.8:1:1:0:60:10:0.1923:0:2 0/1:17:5:0,5:0,12:0.2941:0,0:20.8:1:26.4:1:1:0:60:4:0.25:0:3.6 -3 89528461 . A T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06533;SOR=2.57853;LSEQ=GTCCACAGTACTAGAATATA;RSEQ=CATCGTGCAAATTGTGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:8:8,0:50,2:0.1333:1,0:26.6:1:29.4:1:1:0:60:7:0.1207:0:1.9 0/1:56:16:15,1:40,0:0.2857:1,1:17:1:30.7:1:0.28571:0:60:32:0.2857:0:2.1 -3 89528477 . G A 115 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12833;SOR=2.11817;LSEQ=TATAACATCGTGCAAATTGT;RSEQ=CTAATTGAAAATCTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:9:8,1:60,2:0.1268:1,2:27.3:1:28.3:1:0.33829:3.6465:60:18:0.1268:0:1.8 0/1:72:17:16,1:52,3:0.2361:2,1:28.1:1:28.3:1:1:1.08212:60:16:0.2254:0:2 -3 89528502 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5017;SOR=Inf;LSEQ=TTGAAAATCTCCTGCTTATA;RSEQ=ACTATCGAGGAAACCGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:100,18:0:2,0:23.2:1:32.1:1:1:0:60:236:1:0:0.2 0/1:140:2:1,1:119,19:0.0143:2,2:11.5:1:27:1:0.26619:6.13018:60:4:0.0143:0:1 -3 89905902 . C G 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTATAGGTGAGGTGAAAAT;RSEQ=CAGTGGTTGAGATTCTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:36:0,36:0,63:0.3636:1,1:29:1:31.8:1:1:0:60:17:0.3542:0:1.2 0/0:86:0:0,0:3,83:0:1,0:23.2:1:31.7:1:1:0:60:172:1:0:0.2 -3 89905924 . C A 112 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=23.7807;LSEQ=AGTGGTTGAGATTCTAACAG;RSEQ=GTATGTTTTATGTAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:1:0,1:0,77:0.0128:1,0:38:0:16:0:1:0:60:0:0:0:6 0/1:50:12:0,12:2,36:0.24:2,0:19.6:1:31.3:1:1:0:60:24:0.24:0:1 -3 94370332 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22102;SOR=Inf;LSEQ=CAAAAAACAGCTCCCAGATG;RSEQ=ATTGATTTTTTGGAGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:60,42:0:2,0:24.7:1:31.9:1:1:0:60:50:1:0:0.2 0/1:91:2:1,1:50,39:0.022:2,2:32:0:31:1:1:1.27851:60:4:0.0222:0:1.5 -3 94370362 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49772;SOR=Inf;LSEQ=TTGGAGGGCTTTTTGTATCT;RSEQ=TGTCTCCTTCAATTCTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:51,53:0:2,0:32.3:1:31.1:1:1:0:60:25:1:0:0.2 0/1:107:2:1,1:54,51:0.0187:2,2:26:1:27.5:1:1:1.05828:60:4:0.0189:0:1 -3 94370381 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49773;SOR=Inf;LSEQ=TCTGTCTCCTTCAATTCTAC;RSEQ=CTGATTTTACATTAATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:44,56:0:2,0:24.7:1:29.7:1:1:0:60:32.333:1:0:0.2 0/1:104:2:1,1:49,53:0.0192:2,2:20:0:32.5:1:1:1.08:60:4:0.0192:0:1 -3 94370412 . GGC CAA 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49895;SOR=Inf;LSEQ=ATTAATCCCCAAGACAATGG;RSEQ=AAATGTCCCCAGGGCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:10,37:0:2,0:21.7:1:29.6:1:1:0:60:14.667:1:0:0.1 0/1:56:2:1,1:22,32:0.0357:2,2:22:1:31.5:1:1:1.44:60:4:0.0357:0:2 -3 94370422 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50078;SOR=Inf;LSEQ=AAGACAATGGGGCAAATGTC;RSEQ=CCAGGGCATGTCAGAGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:4,35:0:2,0:20.8:1:29.8:1:1:0:60:8.75:1:0:0.2 0/1:49:2:1,1:17,30:0.0408:2,2:14:1:31.5:1:1:1.74:60:4:0.0426:0:2 -3 94370571 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCAGCCATTCCAGCCCT;RSEQ=TCTGAAAGGGGCCAAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:12:1:28:1:1:0:60:4:1:0:1 -3 94429115 . A G 187 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0;LSEQ=ATTCTTAGTGGGGAACAACA;RSEQ=CCACGGAAATTAGAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:54:33,21:387,267:0.0763:2,2:27.7:1:32.5:1:0.8856:1.08:60:108:0.077:0:1.1 0/0:662:0:0,0:376,285:0:2,0:26.2:1:29.3:1:1:0:60:164.25:1:0:0.5 -3 94429172 . G C 289 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=1.69305;LSEQ=GCTACAACAAATTAAGTGTG;RSEQ=TGTCAAATATGTCACAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:811:535:241,294:123,153:0.6597:2,2:26.3:1:31.9:1:0.94063:1.02:60:88.167:0.6604:0:1.1 1/0:681:522:229,293:77,81:0.7665:2,2:23.1:1:31.7:1:0.3155:1.21593:60:260:0.7681:0:1.1 -3 94942937 . G T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0046;LSEQ=TCTTATTCTTTATTAATCTA;RSEQ=CTAGTGGTCTATCTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:36:27,9:36,13:0.4235:2,2:17.9:1:29.7:1:1:1.08:60:35:0.4167:0:1.1 0/1:73:31:21,10:31,11:0.4247:2,2:20.2:1:29.1:1:0.6089:1.33651:60:62:0.4306:0:1.1 -3 94943018 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19985;SOR=Inf;LSEQ=TTTGGAGGGTTTTTGTGTCT;RSEQ=TATCTCCTTCAGTTATACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:122,126:0:2,0:26.9:1:31.6:1:1:0:60:81.667:1:0:0.3 0/1:201:2:1,1:86,113:0.01:2,2:29:1:28:1:1:1.31:60:4:0.0101:0:1 -3 94943031 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19875;SOR=Inf;LSEQ=TGTGTCTCTATCTCCTTCAG;RSEQ=TATACTCTCATCTTGGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:91,109:0:2,0:25.2:1:29.7:1:1:0:60:65.667:0.9899:0:0.3 0/1:163:2:1,1:64,96:0.0123:2,2:6.5:1:28.5:1:1:1.50:60:4:0.0123:0:1.5 -3 94943046 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5063;SOR=0;LSEQ=TTCAGTTATACTCTCATCTT;RSEQ=GTTATTTCTTGTCTTTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:64,88:0.0129:2,2:27.5:1:29.5:1:1:1.37:60:4:0.0133:0:2 0/0:120:0:0,0:49,71:0:2,0:22.8:1:30.3:1:1:0:60:119:1:0:0.1 -3 94944898 . T G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTTCTTTTCTAAACTG;RSEQ=TTATTCTGGTTAGCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33:1:31:1:1:0:60:4:1:0:1 -3 95307592 . A G 50 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGCTGGCAGTACTGGG;RSEQ=AACTGGGCGCACCCTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:20:1:31.7:1:1:0:60:6:1:0:1.7 -3 95307625 . G A 45 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCGCAGCTGCTGGCCCC;RSEQ=GTGCTAAGCCCCTCACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:27.3:1:29:1:1:0:60:6:0.75:0:1.7 -3 95308235 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49367;SOR=Inf;LSEQ=GGGCCCAAAGGTGAGTAACA;RSEQ=CAAGATGGCTGCCACGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:29,10:0:2,0:22.4:1:32.2:1:1:0:48.7:38:1:0:0.1 0/1:40:2:1,1:23,15:0.05:2,2:13.5:1:27:1:1:1.51653:46:4:0.0513:0:3 -3 95308266 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49758;SOR=0;LSEQ=GCCACGGGACCTAGAAAGGG;RSEQ=AGAAGCCATGTTGCCCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:38,28:0.0294:2,2:30:0:31.5:1:1:1.35095:45:4:0.0303:0:1.5 0/0:61:0:0,0:28,32:0:2,0:26.9:1:29.9:1:1:0:52.3:29:1:0:0.3 -3 95454362 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=AAATAAGCATGTTCCAACGT;RSEQ=TGTCATGAATAAAACTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:96,28:0:2,0:23.3:1:28.6:1:1:0:60:123:1:0:0.1 0/1:133:2:1,1:96,35:0.015:2,2:32.5:1:28:1:0.46958:2.71854:60:4:0.0153:0:1 -3 95454378 . T C 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00219;SOR=Inf;LSEQ=ACGTATGTCATGAATAAAAC;RSEQ=TGCCATTAGCAAAGCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:103,45:0:2,0:24.8:1:30.6:1:1:0:60:73:1:0:0.1 0/1:173:10:5,5:115,48:0.0578:2,2:20.9:1:31.7:1:0.17761:2.38234:60:20:0.0581:0:1.3 -3 95454468 . T G 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.9288;SOR=0.97993;LSEQ=ATTCGCCTCCATGATAAAAT;RSEQ=GTAAGGCTGTGACTGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:88:33,55:75,90:0.3478:2,2:27.1:1:31.6:1:0.23298:1.38708:60:176:0.3492:0:1 0/1:303:104:52,52:84,114:0.3432:2,2:24.8:1:30.1:1:0.22496:1.36:60:25:0.3344:0:1.1 -3 95454475 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25384;SOR=Inf;LSEQ=TCCATGATAAAATTGTAAGG;RSEQ=TGTGACTGGTCACAGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:105,142:0:2,0:26.6:1:32.1:1:1:0:60:60.75:1:0:0.4 0/1:292:3:2,1:128,161:0.0103:2,2:13.7:1:28.3:1:0.58721:2.51:60:6:0.0105:0:1.7 -3 95454510 . A G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00153;SOR=Inf;LSEQ=GACCCTCAAAAGACCTTTCC;RSEQ=TTCTTTTAATTAGCTGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:57,118:0:2,0:24.2:1:30.9:1:1:0:60:350:1:0:0.3 0/1:170:9:3,6:51,110:0.0529:2,2:18.8:1:30.6:1:1:1.08:60:18:0.0536:0:1 -3 96727142 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08772;SOR=Inf;LSEQ=TGTTTTTTGGAGGCTTTGTT;RSEQ=ATTATTTTTCATTCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:21.3:1:29.4:1:1:0:60:12:1:0:0.3 0/1:6:2:1,1:2,2:0.3333:2,2:11.5:1:27.5:1:1:1:60:4:0.3333:0:1 -3 96727580 . A T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50034;SOR=Inf;LSEQ=TTTTTCATTGATTCTCATCT;RSEQ=TGTGAATTTGTGTAGTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:0:2,0:20.4:1:29.5:1:1:0:60:68:1:0:0.1 0/1:43:2:1,1:22,19:0.0465:2,2:7:0:27.5:1:1:1.15394:60:4:0.0465:0:1 -3 96727778 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=TTTACTTCATGCCTTATTCA;RSEQ=CTGATTCGCCCCCCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:0,6:0.25:0,2:32:1:32.5:1:0.25:0:60:4:0.25:0:1 0/0:4:0:0,0:2,2:0:2,0:28.8:1:30.5:1:1:0:60:8:1:0:0 -3 96728036 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2092;SOR=Inf;LSEQ=AGTCTGGGCTGCCTGGATTC;RSEQ=TCAGAACTACCAAGAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:0:2,0:25.7:1:32.2:1:1:0:60:32:1:0:0.3 0/1:14:2:1,1:5,7:0.1429:2,2:30:1:31.5:1:1:1.37:60:4:0.1429:0:1 -3 97251336 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50077;SOR=Inf;LSEQ=TAAGAGAAGCTAGTATCATG;RSEQ=GCCAGTTTGACCATCCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:38,34:0:2,0:26.9:1:30.9:1:1:0:60:71:1:0:0.1 0/1:86:2:0,2:45,39:0.0233:2,0:25:1:27:1:0.22435:0:60:4:0.0238:0:1 -3 97439141 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53842;SOR=0;LSEQ=TAAGGTGGACAGCCCCAGAA;RSEQ=CCATCGCCTACAGAAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:56,22:0.025:2,2:29:1:27:1:0.49494:2.51164:60:4:0.0253:0:1 0/0:44:0:0,0:29,15:0:2,0:24.8:1:31.8:1:1:0:60:88:1:0:0.2 -3 97439159 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1111;SOR=Inf;LSEQ=AAGCCATCGCCTACAGAAAA;RSEQ=TCTCCTCAGCAAGCGATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:56,33:0:2,0:23.2:1:30.5:1:1:0:60:178:1:0:0.1 0/1:45:2:1,1:27,16:0.0444:2,2:25.5:1:30.5:1:1:1.66708:60:4:0.0444:0:1 -3 97439220 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.54348;SOR=0;LSEQ=GTGGGAGGTCATGTCCTATG;RSEQ=AGAGAGACCTTATTGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:43,60:0.019:2,2:25:0:30.5:1:1:1.39:60:4:0.019:0:1.5 0/0:56:0:0,0:25,31:0:2,0:29.6:1:30.6:1:1:0:60:55:1:0:0.2 -3 97439237 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11422;SOR=Inf;LSEQ=ATGGAGAGAGACCTTATTGG;RSEQ=AAATGTCTAACCAAGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:35,60:0:2,0:25.6:1:31.5:1:1:0:60:190:1:0:0.1 0/1:49:2:1,1:19,28:0.0408:2,2:6.5:1:28:1:1:1.46:60:4:0.0417:0:1.5 -3 98267289 . C T 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.97618;LSEQ=TGCAACCCTGCCCTCTGGGA;RSEQ=GATCAACTGATTTGGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:112:53,59:130,139:0.2932:2,2:26.2:1:30:1:0.91053:1.04104:60:36.333:0.2899:0:1.1 0/1:355:160:80,80:91,104:0.4507:2,2:25.9:1:29.2:1:0.59365:1.14:60:159:0.4543:0:1.1 -3 98267536 . C G 52 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAGGGCATTTGAACCTGT;RSEQ=GGGGTGGGGAAGTGGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:32.3:1:33:0:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:15:0:34:0:1:0:60:2:1:0:1 -3 100629641 . C A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=AACATACTTTACAAATTAAA;RSEQ=ATGCTAAGACTTATCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:27.5:1:28.5:1:0.4:0:60:4:0.4:0:1 0/0:3:0:0,0:1,2:0:2,0:4:1:29:1:1:0:60:6:1:0:0 -3 100629651 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=ACAAATTAAACATGCTAAGA;RSEQ=TTATCTGTGGATTACTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:14:1:32:1:1:0:60:4:0.3333:0:1 0/0:3:0:0,0:1,2:0:2,0:14:1:31:1:1:0:60:6:1:0:0 -3 100629803 . TA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.52925;SOR=0;LSEQ=AAAAAAATCTCCTTTTAGGT;RSEQ=AAAGGATCAAGATGTAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:60,6:0.0294:2,2:29.5:1:30:1:0.19666:9.33504:60:4:0.0303:0:1 0/0:40:0:0,0:28,12:0:2,0:30.6:1:28:1:1:0:60:39:1:0:0.1 -3 100630141 . C T 132 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00209;SOR=2.66201;LSEQ=ATGTCTGTTTTTTAAAGACA;RSEQ=AACACACGAATGAAGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:18:4,14:57,224:0.0602:2,2:19.2:1:28.9:1:0.76896:1.12:60:36:0.0604:0:1.1 0/1:185:27:7,20:33,125:0.1459:2,2:16.5:1:27.9:1:0.61362:1.32:58.5:26:0.1453:0:1.3 -3 100630148 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15231;SOR=Inf;LSEQ=TTTTTTAAAGACACAACACA;RSEQ=GAATGAAGAAATTCAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:50,207:0:2,0:22.4:1:30.3:1:1:0:60:256:1:0:0.1 0/1:165:2:1,1:34,128:0.0121:2,2:12.5:1:30:1:0.38231:3.73:60:4:0.0123:0:1.5 -3 100630177 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13502;SOR=Inf;LSEQ=AAATTCAGAATCTGGATAAA;RSEQ=GGTCCATAATGCTTGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:37,136:0:2,0:22.7:1:31.1:1:1:0:60:172:1:0:0.1 0/1:101:2:1,1:28,71:0.0198:2,2:28.5:1:29:1:0.49386:2.51:60:4:0.0198:0:1 -3 100630266 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.16317;SOR=Inf;LSEQ=CCTGAATCTATGCTCATCTC;RSEQ=TTTTTTCCAATTTCTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:87,79:0:2,0:26:1:31.4:1:1:0:60:82:1:0:0.2 0/1:113:2:1,1:65,46:0.0177:2,2:28:0:32.5:1:1:1.40862:60:4:0.0179:0:1.5 -3 100630340 . CT C 54 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.28378;SOR=0;LSEQ=TGCTTGTTCATTGTTTTTCA;RSEQ=TTTTTTTGCATATACTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:0,3:126,60:0.0159:2,0:24:1:34.3:1:0.03586:0:60:6:0.0161:0:0 0/0:121:0:0,0:72,49:0:2,0:23.4:1:30.2:1:1:0:59.8:242:1:0:0.2 -3 100630604 . T C 283 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57802;SOR=0.3694;LSEQ=GTTTCAGTCGATGAGTAGCG;RSEQ=AGCTTTCTGTTATTATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:455:454:208,246:0,1:0.9978:0,2:25.1:1:32.1:1:1:0:60:74.667:1:0:1.1 1/1:337:335:175,160:0,1:0.9941:0,2:24:1:31.6:1:0.47917:0:59.9:110.667:0.994:0:1.1 -3 100631031 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02648;SOR=0.3306;LSEQ=TTACCCTTCGTGCTGCCGTC;RSEQ=GCTCAGGCTTCAGGAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:33:1,32:1,30:0.5156:1,1:19.5:1:30.8:1:1:1.06563:60:32:0.5079:0:1.1 0/1:31:8:0,8:1,22:0.2581:1,0:21.3:1:31.8:1:1:0:60:16:0.2667:0:1.3 -3 104282289 . G A 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.34522;LSEQ=TTCACTTACTGTACATTGAG;RSEQ=TCTTTGGGAAAAGGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:0.2857:0,0:27.8:1:31:1:1:0:60:8:0.2857:0:1.8 1/0:2:1:1,0:1,0:0.5:0,0:7:0:30:0:1:0:60:2:0.5:0:2 -3 104282306 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTCTTTGGGAAAAGGGA;RSEQ=GAGACTTTTCAACCCATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:1:0,1:26.5:1:30.4:1:1:0:60:34:1:0:1.3 1/1:5:5:5,0:0,0:1:0,0:20:1:32:0:1:0:60:10:1:0:1.2 -3 104282451 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21068;SOR=Inf;LSEQ=GCTTAAAGCTCTGCTTACAA;RSEQ=TCCAATGAATTTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:175,45:0:2,0:24.3:1:31.9:1:1:0:60:72.333:1:0:0.2 0/1:188:2:1,1:126,60:0.0106:2,2:28.5:1:28.5:1:0.54483:2.09102:60:4:0.0107:0:1 -3 104282534 . C T 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15635;SOR=1.22417;LSEQ=AGGAACTTATTTTATAATTT;RSEQ=GAAGAGTAGACTACCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:139:74,65:175,183:0.2797:2,2:26.5:1:30.2:1:0.42424:1.19:60:138:0.2794:0:1.6 0/1:450:145:74,71:161,144:0.3222:2,2:26.6:1:29.9:1:0.76236:1.07256:60:144:0.3214:0:1.6 -3 104282582 . T C 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48364;SOR=1.11922;LSEQ=TTGAGATAACAGGTACTTTT;RSEQ=CTTGGCCTGAAAATTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:432:116:46,70:118,195:0.2685:2,2:25.8:1:31:1:0.73786:1.09:60:57:0.2701:0:1.7 0/1:388:113:45,68:127,148:0.2912:2,2:26:1:30.6:1:0.26282:1.29583:60:55.5:0.2898:0:1.8 -3 105495432 . G T 91 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATAAGAAATAAACACCTA;RSEQ=ATGCATGCAAATTTTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:29.5:1:29.2:1:1:0:60:12:1:0:1.2 1/1:10:10:2,8:0,0:1:0,2:28.3:1:27.5:1:1:0:60:20:1:0:1.1 -3 105822703 . G A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGGTTCACTTCAGGCCC;RSEQ=ATTCATGATTCACTCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:5,8:0,0:1:0,2:32.8:1:30.7:1:1:0:60:26:1:0:1.3 1/1:8:8:3,5:0,0:1:0,2:19:1:28.5:1:1:0:60:16:1:0:1.1 -3 105822731 . A G 63 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.36022;SOR=0.29661;LSEQ=ATTCACTCCCTTGCCTGGAT;RSEQ=TGTCACTCAAGGAGGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:4,5:0.3077:2,2:31:1:31.8:1:1:1.23:60:8:0.3077:0:2 0/1:9:1:0,1:5,3:0.1111:2,0:28:0:33:0:0.44444:0:60:2:0.1111:0:2 -3 105823159 . G C 46 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22857;SOR=Inf;LSEQ=AGGATGGGTCAGGGTTGGGC;RSEQ=TGAAGAGGCCCTCTGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:33.2:1:27.2:1:1:0:60:5:1:0:0.3 0/1:9:3:2,1:4,2:0.3333:2,2:34:1:29.3:1:1:1:60:6:0.3333:0:2.7 -3 105823185 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AGGCCCTCTGGCCGCAGACT;RSEQ=CCACAGCCGGTGTGTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:24.2:1:29:1:1:0:60:5:1:0:0.3 0/1:10:2:1,1:5,3:0.2:2,2:40.5:1:29:1:1:1.58108:60:4:0.2:0:3 -3 105823194 . G A 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GGCCGCAGACTGCCACAGCC;RSEQ=GTGTGTTTGGCTGTGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:18.2:1:30.5:1:1:0:60:12:1:0:0.3 0/1:10:3:2,1:4,3:0.3:2,2:31.7:1:29:1:1:1.44:60:6:0.3:0:2.7 -3 105823884 . A T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGCACTGAGATTTTTTTTA;RSEQ=TATCATATTTTACATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:28:1:1:0:60:4:1:0:1.5 -3 106127714 . C A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.19622;LSEQ=TTACACCTAAAGTAGTGAAA;RSEQ=AAAAATCCCCCATTTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:562:413:194,219:58,73:0.7349:2,2:24.7:1:29.9:1:0.61605:1.11:60:205.5:0.7555:0:1.4 0/1:574:202:100,102:170,190:0.3519:2,2:23.9:1:29.8:1:0.66008:1.10:60:100:0.3578:0:1.5 -3 106127786 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20624;LSEQ=TCTCTTTGATCATACTCAGG;RSEQ=GAGGTTTGCTGCTTAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:277:216:62,154:19,42:0.7798:2,2:22.4:1:30.1:1:0.75066:1.12317:60:42.2:0.7757:0:1.6 0/1:254:107:42,65:44,103:0.4213:2,2:21.6:1:30.3:1:0.14015:1.51:60:214:0.4246:0:1.6 -3 106128036 . A G 54 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTTGTGATAGTGAGTTC;RSEQ=TTCTCAGGAGATCTGACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:23.3:1:27:1:1:0:60:3:0.75:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 106128083 . T G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCCTTCCCCCTTCGCTC;RSEQ=GCATTAATTCTCTCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33:1:32.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 106567549 . G A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAAAACAGGAAGTATGC;RSEQ=ACCATGAAGTGAATGCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:24:0:32:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 106567717 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14228;SOR=Inf;LSEQ=ACACAGCTGGGCCCACCTTA;RSEQ=CACATCCTGTTTGACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:47,5:0:2,0:24.4:1:31.4:1:1:0:60:51:1:0:0.1 0/1:32:2:2,0:26,4:0.0625:2,0:27:1:32:0:1:0:60:4:0.0625:0:1 -3 106567782 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51446;SOR=0;LSEQ=CAAACTGGACTTAGTGTAGT;RSEQ=AATGATGGACTGTCTGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:88,66:0.0127:2,2:22.5:1:26.5:1:1:1.33083:60:4:0.0129:0:1 0/0:109:0:0,0:64,45:0:2,0:25.4:1:30.6:1:1:0:60:53.5:1:0:0.2 -3 106567794 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.5115;SOR=0;LSEQ=AGTGTAGTCAATGATGGACT;RSEQ=TCTGTATGCCAAGTGTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:92,78:0.0116:2,2:20:0:31.5:1:1:1.17835:60:4:0.0118:0:1 0/0:124:0:0,0:67,57:0:2,0:26.5:1:31.2:1:1:0:60:248:1:0:0.2 -3 106567825 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50659;SOR=0;LSEQ=AAGTGTATCCCTTGTATAAC;RSEQ=GATTGTGTAATGGCTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:69,91:0.0123:2,2:17.5:1:28:1:1:1.32:60:4:0.0126:0:1 0/0:125:0:0,0:60,65:0:2,0:28.5:1:30.2:1:1:0:60:61.5:1:0:0.2 -3 106567840 . TG CA 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00714;SOR=Inf;LSEQ=ATAACTGATTGTGTAATGGC;RSEQ=AAATTGGGAAATTAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:58,82:0:2,0:24.6:1:29.7:1:1:0:59.5:69:1:0:0.1 0/1:112:6:3,3:46,60:0.0536:2,2:18.2:1:29.2:1:1:1.30:60:12:0.0541:0.0179:0.8 -3 106567854 . T C 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21319;SOR=Inf;LSEQ=AATGGCTGAAATTGGGAAAT;RSEQ=AGGGCAGAAGTATGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:40,69:0:2,0:23:1:28.1:1:1:0:59.8:35.333:1:0:0.1 0/1:94:2:1,1:37,55:0.0213:2,2:22:0:27.5:1:1:1.48:60:4:0.0213:0:1 -3 106567870 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22201;SOR=Inf;LSEQ=AAATTAGGGCAGAAGTATGG;RSEQ=GCAGCTGTAAGGATTGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:21,57:0:2,0:22.9:1:30.3:1:1:0:59.9:38:1:0:0.2 0/1:70:2:1,1:22,46:0.0286:2,2:33:1:29:1:1:2.07:60:4:0.0286:0:1 -3 106582908 . T C 148 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03125;SOR=2.1422;LSEQ=AACAAGAACAAATGGGGATT;RSEQ=ACAGTCAAAGATCATCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:15:10,5:76,25:0.1293:2,2:20:1:30.7:1:0.53094:1.51412:60:30:0.1339:0:1.8 0/1:124:30:19,11:65,29:0.2419:2,2:18:1:30.2:1:0.6544:1.29481:60:60:0.2479:0:1.9 -3 106582948 . T A 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07301;SOR=0.69243;LSEQ=CGGGTATGTGGATAAAAAAT;RSEQ=ACAAAGAGAAAACATCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:143:86,57:32,27:0.7044:2,2:26:1:28.8:1:0.53027:1.27:60:70.5:0.705:0:1.2 1/0:249:155:89,66:55,39:0.6225:2,2:26.7:1:28.5:1:0.89527:1.04564:60:76.5:0.6194:0:1.3 -3 106583010 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19499;SOR=0;LSEQ=CCAGCTCACCAGGATTCTTT;RSEQ=AGAAGACAAGACAAGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:51,93:0.0137:2,2:23.5:1:28:1:1:1.82:60:4:0.0139:0:2 0/0:184:0:0,0:65,116:0:2,0:25.7:1:30.6:1:1:0:60:29.167:0.9887:0:0.5 -3 106583012 . GA G 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01035;SOR=Inf;LSEQ=AGCTCACCAGGATTCTTTCA;RSEQ=AGACAAGACAAGGTGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:49,92:0:2,0:23.7:1:29.6:1:1:0:60:140:1:0:0.5 0/1:180:8:3,5:59,113:0.0444:2,2:20.8:1:31.8:1:1:1.15:60:16:0.0447:0:0.1 -3 106583022 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51315;SOR=Inf;LSEQ=GATTCTTTCAGAAGACAAGA;RSEQ=AAGGTGATCAGATATTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:32,83:0:2,0:24.4:1:31.7:1:1:0:60:114:1:0:0.4 0/1:163:2:1,1:52,109:0.0123:2,2:12:1:28.5:1:0.54594:2.09:60:4:0.0126:0:1 -3 106583166 . A G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=CTCACAGCTGTAATCCCAGC;RSEQ=CTTTGCGGGGCCAAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:36:0:34:0:1:0:60:2:0.25:0:1 1/0:4:2:1,1:0,2:0.5:0,2:38.5:1:28:1:1:0:60:4:0.6667:0:1.5 -3 106584051 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCTGCAGGGCTCTGAAT;RSEQ=CTGGCAACTGTGTGAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:27.5:1:1:0:60:4:1:0:1 -3 106823388 . GA G 33 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGTTAAGGTTATAAAAA;RSEQ=AAAAAAAAAAACAACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:26:1:33.5:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:0:0,0:28:0:32:0:1:0:60:2:1:0:4 -3 106823432 . T C 61 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAACTAGAATTTGAATCC;RSEQ=CATAATCTGCAAAATATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:30:1:30.8:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:1:0,0:30:0:27:0:1:0:60:2:1:0:4 -3 106824274 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05966;LSEQ=GGCACTCCGTGGTACAGCCA;RSEQ=GTCCACAAGTGGTATTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:92:52,40:78,67:0.3882:2,2:23.9:1:30.7:1:0.69034:1.12:60:184:0.3898:0:1.8 0/1:248:9:5,4:127,112:0.0363:2,2:24:1:30.3:1:1:1.10:60:18:0.0364:0:1.7 -3 106824304 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0924;LSEQ=TGGTATTGCCAGACCATTCT;RSEQ=TCCATATTCCCTTGTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:106:62,44:80,83:0.3941:2,2:23.1:1:30.2:1:0.13607:1.46:60:212:0.3985:0:1.7 0/1:248:14:10,4:121,111:0.0565:2,2:20.2:1:28.9:1:0.18018:2.29:60:13:0.0533:0:1.6 -3 106824338 . A G 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32525;SOR=3.83969;LSEQ=GTCCAATCTTTGAAAGTTTA;RSEQ=GTTTTCTTAGCTTATAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:1:1,0:195,149:0.0029:2,0:14:0:15:0:1:0:60:0:0:0:1 0/1:272:3:1,2:156,113:0.011:2,2:42:1:24.7:1:0.57544:2.75081:60:2:0.0075:0:1.3 -3 106824379 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04174;SOR=Inf;LSEQ=TGAGTGGTGCTTTCTTTGAC;RSEQ=TTCCTAACATGCACGATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:0:0,0:273,197:0:2,0:26.7:1:30.4:1:1:0:60:35.154:1:0:0.2 0/1:390:4:2,2:222,164:0.0103:2,2:32.3:1:25:1:1:1.35258:60:3:0.0078:0:1.3 -3 106824513 . G A 129 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=25.3788;LSEQ=GTTTTCTTGGAACACTATCC;RSEQ=CCAAAAGTCATTCACAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:618:1:1,0:309,308:0.0016:2,0:1:0:26:0:1:0:60:2:0.0016:0:1 0/1:556:22:8,14:264,270:0.0396:2,2:32.8:1:29.1:1:0.27907:1.70949:60:44:0.04:0:1.1 -3 106824707 . ATC A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.85079;LSEQ=GCAGGATGTTTTGTTTTTAT;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:14,87:0.0192:2,0:24.5:1:31:1:1:0:60:4:0.029:0.0096:1.5 0/1:61:1:0,1:11,46:0.0164:2,0:29:0:26:0:1:0:60:2:0.0222:0:6 -3 106824935 . C G 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00893;SOR=Inf;LSEQ=GGCCAGGGTGGTCTCGATCT;RSEQ=CTGACCTTGTGATCTGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:57,1:0:1,0:25.2:1:31.3:1:1:0:59:116:1:0:1.1 0/1:39:5:5,0:33,1:0.1282:1,0:18.8:1:32.6:1:1:0:60:10:0.1351:0:2 -3 106824950 . T C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.54264;LSEQ=GATCTCCTGACCTTGTGATC;RSEQ=GCCCGCCTTGGCCTCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:62:61,1:0,0:0.9688:0,1:27.5:1:30.6:1:1:0:59.1:30:0.9836:0:1.3 1/1:49:48:47,1:0,0:0.9796:0,1:26:1:30.5:1:1:0:60:47:0.9792:0:1.3 -3 106825018 . A AT 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.06153;SOR=0;LSEQ=CGCGCCCGGCCTTTATATCT;RSEQ=TTTTTGGTTTTGTTTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:5:1,4:233,73:0.0161:2,2:12.8:1:28.2:1:0.01433:12.64045:60:10:0.0164:0.0096:0.6 0/0:306:0:0,0:221,85:0:2,0:21.2:1:28.4:1:1:0:60:152:1:0:0.3 -3 106825024 . G C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08663;LSEQ=CGGCCTTTATATCTATTTTT;RSEQ=GTTTTGTTTTCTTGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:177:131,46:124,42:0.513:2,2:21.6:1:30.8:1:0.90213:1.03662:59.9:87.5:0.5147:0:1.3 0/1:336:28:20,8:218,90:0.0833:2,2:25.7:1:30.8:1:1:1.03:60:56:0.0843:0:1.3 -3 106825180 . A T 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=ACTCTGCTTTCTATTTCAGC;RSEQ=GCATTTGTACAAGTCGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:38:21,17:373,347:0.0501:2,2:21:1:31:1:0.74047:1.15:59.4:76:0.0505:0:1.2 0/0:724:0:0,0:329,395:0:2,0:25.8:1:30.4:1:1:0:59.6:102.429:1:0:0.2 -3 106825268 . A AC 310 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08691;SOR=0.41317;LSEQ=GATTCTTCTTCTAATGTTCC;RSEQ=AAGATCTGTCAAAGCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:858:852:406,446:2,4:0.993:2,2:26:1:31.9:1:0.68866:1.82:58.6:93.667:0.9929:0.162:0.1 1/1:656:645:336,309:3,1:0.9832:2,2:26.5:1:31.2:1:0.62535:2.75484:58.2:106.5:0.9907:0.1524:0.2 -3 106825838 . A G 299 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89824;LSEQ=ATTTGGGTGAAACCATTTCC;RSEQ=TGATGTCATGTTCCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:827:825:322,503:1,0:0.9976:0,2:23.7:1:30.9:1:0.39104:0:59.5:81.5:0.9976:0:1.1 1/1:743:741:308,433:2,0:0.9973:0,2:23.7:1:30.1:1:0.17375:0:59.6:81.333:0.9973:0:1.2 -3 106825888 . G A 50 v4;q23;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0199;SOR=Inf;LSEQ=CCGCGATGGACCTGCTTCTT;RSEQ=CTCAGGGTCTGCTGGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:0:0,0:145,327:0:2,0:25.8:1:32.2:1:1:0:60:235:1:0:0.8 0/1:399:5:5,0:129,265:0.0125:2,0:6.4:1:21.8:1:0.00406:0:60:4:0.0101:0:2 -3 106825950 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14547;SOR=Inf;LSEQ=GGAGGCCTGCTCAGGACTGG;RSEQ=CGTGGGGCAGAGCCAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:5,158:0:1,0:23.3:1:31.4:1:1:0:60:162:1:0:0.1 0/1:101:2:1,1:8,91:0.0198:2,2:20:0:28:1:0.17109:10.78:60:4:0.0204:0:1 -3 106827174 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCTTTTCACCTTCCACC;RSEQ=TGATTGTGAAGCCTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:28.5:1:1:0:60:4:1:0:1.5 -3 109128451 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23928;SOR=Inf;LSEQ=TCCCAAAGTGCTGGGATTAC;RSEQ=GGCGTGAGCCACCGCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:57,2:0:1,0:22.8:1:30.6:1:1:0:57.7:118:1:0:0.1 0/1:57:2:1,1:53,2:0.0351:1,2:35.5:1:29.5:1:0.10338:21.8405:60:4:0.0357:0:1 -3 109128547 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34355;SOR=0.28973;LSEQ=AAGCACGTTTTCCTTGTATG;RSEQ=GGCGTGCTAGCTGGATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:1,2:149,126:0.0108:2,2:14:1:28:1:0.59619:2.35795:60:6:0.0109:0:1 0/0:318:1:0,1:169,148:0.0031:2,0:1:0:31:0:0.46855:0:60:2:0.0032:0:1 -3 109128553 . G T 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTTTTCCTTGTATGCGGCGT;RSEQ=CTAGCTGGATTTCTTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:147,137:0:2,0:27.8:1:31.8:1:1:0:60:46.333:1:0:0.1 0/1:316:18:11,7:152,146:0.057:2,2:24.3:1:29.7:1:0.47183:1.51:60:36:0.0581:0:1.1 -3 109128577 . ATAGT A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GCTGGATTTCTTTTGGCATA;RSEQ=TAGCCGTTTGGCATGGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:107,143:0:2,0:25.6:1:28.8:1:1:0:60:61.5:1:0:0.1 0/1:296:17:9,8:125,154:0.0574:2,2:22.9:1:29:1:0.61804:1.38:60:34:0.058:0.0135:0.9 -3 109128618 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50202;SOR=Inf;LSEQ=ATAGCACACAGGTTGCTGTC;RSEQ=TCAAAAAGGCCAACCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:33,106:0:2,0:25.5:1:30.2:1:1:0:60:68.5:1:0:0.2 0/1:165:2:1,1:54,109:0.0121:2,2:20.5:1:29.5:1:1:2.01:60:4:0.0123:0:1 -3 109128643 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49974;SOR=Inf;LSEQ=AAAGGCCAACCAGGTAGGCC;RSEQ=CACTTGCCTCCTGCAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:24,80:0:2,0:22.2:1:30.4:1:1:0:59.5:103:1:0:0.4 0/1:118:2:1,1:34,82:0.0169:2,2:9.5:1:31.5:1:0.50703:2.39:60:4:0.0171:0:2 -3 109128653 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20703;SOR=0;LSEQ=CAGGTAGGCCTCACTTGCCT;RSEQ=CTGCAAAGCTCCAATAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:21,66:0.0225:2,2:11.5:1:31:0:0.43539:3.09:33:4:0.023:0:1.5 0/0:106:0:0,0:28,78:0:2,0:24:1:30.4:1:1:0:60:20.2:1:0:0.4 -3 109128692 . C T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60104;SOR=0.80555;LSEQ=TGCACTCTGGAAGCGTAGAT;RSEQ=TGTTTTCAAGTCCTGAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:35:15,20:12,17:0.5469:2,2:25.3:1:30.1:1:1:1.06:60:34:0.5484:0:1.1 0/1:67:33:12,21:10,24:0.4925:2,2:27.8:1:29.3:1:0.60875:1.36:60:15.5:0.4844:0:1.4 -3 109128982 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5082;SOR=0;LSEQ=ATCCTTCAGCTGGAGCTCTG;RSEQ=GAGCCAGAGGCAGCGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:10,24:0.0556:2,2:28.5:1:31.5:1:0.52381:2.34:60:4:0.0556:0:1.5 0/0:25:0:0,0:5,20:0:2,0:25.5:1:29.6:1:1:0:60:50:1:0:0 -3 109129029 . TGCG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.5148;SOR=0;LSEQ=GAGTGATGGCGGCATGGCGG;RSEQ=GCGGCGGCTGCGAACACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:4,21:0.0741:2,2:35:1:31.5:1:0.34188:4.81:60:4:0.0741:0:0 0/0:17:0:0,0:3,14:0:2,0:26.4:1:32.3:1:1:0:60:34:1:0:0.1 -3 112352947 . C G 51 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=AGGGAAGACACTTTAAGTCT;RSEQ=AGATTATTCAAAATACTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:32.3:1:32.7:1:1:0:60:6:1:0:1.3 0/0:1:0:0,0:1,0:0:0,0:30:0:33:0:1:0:60:2:1:0:0 -3 112352986 . A AT 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=CGTTAGGCTCAAAATGCTAG;RSEQ=TTTTTTTTTACAGGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:30.3:1:32.3:1:1:0:60:6:0.75:0:0.3 1/0:4:2:2,0:1,0:0.5:0,0:8:1:31.1:1:1:0:60:4:0.5:0.25:0 -3 112353099 . T C 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATAAGTAGATGGTTGTCC;RSEQ=AATACACAGATGTCTGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:62:57,5:0,0:0.9841:0,2:24.1:1:31.2:1:1:0:60:61:1:0:1 1/1:54:54:48,6:0,0:1:0,2:19.7:1:30.7:1:1:0:60:108:1:0:1 -3 112353238 . C A 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTTGTTAATTGACAAGTGA;RSEQ=TAGATCTCAGAGCGCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:320:320:152,168:0,0:1:0,2:25.5:1:30.3:1:1:0:60:63:1:0:1.1 1/1:261:220:108,112:18,22:0.8429:2,2:26.5:1:29.5:1:0.73149:1.18:60:54:0.8438:0:1.1 -3 112353331 . A C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.01364;LSEQ=CCTATAGTCTCACTATCGTC;RSEQ=ACCTCAAACTGACACCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:29:9,20:23,66:0.2458:2,2:21.7:1:31.6:1:0.63343:1.29:60:58:0.2522:0:1.7 1/0:95:54:10,44:12,29:0.5684:2,2:22.6:1:31.5:1:0.23156:1.809:60:108:0.5684:0:1.6 -3 112353355 . C T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17223;SOR=0;LSEQ=TCAAACTGACACCAAGCAGA;RSEQ=TGAAGAATTAGGTTAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:74:7,67:0,0:1:0,2:21.2:1:30.3:1:1:0:60:36:1:0:1.2 1/1:53:51:6,45:0,0:0.9623:0,2:23.8:1:30.5:1:1:0:60:102:0.9623:0:1.6 -3 112547386 . T C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59703;SOR=1.96324;LSEQ=AAATTGGTGACATTGTCAAA;RSEQ=ATAGCCTTTGGATATTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:6,0:30,0:0.1667:1,0:13.5:1:32.5:1:1:0:60:12:0.1667:0:1 0/1:7:2:2,0:4,1:0.2857:2,0:40:1:28:1:1:0:60:4:0.2857:0:1.5 -3 112547496 . C A 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86701;LSEQ=TCTGTATATTCAATCCAATT;RSEQ=TCAGGTGTAAATGTAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:195:160,35:0,0:0.9949:0,2:24.5:1:28.6:1:1:0:60:96.5:0.9948:0:1.1 1/1:170:169:140,29:0,0:0.9941:0,2:22.6:1:28.3:1:1:0:60:83.5:1:0:1.1 -3 112547601 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.33774;LSEQ=CATAGATTCTCATGCATCTC;RSEQ=TAAGCCAACACAATGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:208:103,105:209,205:0.3344:2,2:25.8:1:30.6:1:0.86511:1.03926:60:207:0.3355:0:1.1 1/0:496:268:128,140:104,122:0.5403:2,2:25.3:1:29.8:1:0.71805:1.07:60:133:0.5429:0:1.1 -3 112547684 . G A 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58244;SOR=2.60493;LSEQ=GTATCTGTCACTACTCACCT;RSEQ=TAACAAAGGTGAGTGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:1:1,0:56,191:0.004:2,0:1:0:23:0:0.22984:0:60:2:0.004:0:2 0/1:192:2:1,1:53,137:0.0104:2,2:10:1:26.5:1:0.48446:2.57:60:4:0.0104:0:2 -3 112547771 . GT G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTATGTGGATGAAGTTT;RSEQ=TTTTGCTACACCCTGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:0,2:0,55:0.0351:1,0:19:1:30.5:1:1:0:60:4:0.0357:0.0175:0.5 0/0:23:0:0,0:0,23:0:1,0:23.3:1:29.7:1:1:0:60:46:1:0:0 -3 112649289 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.48837;SOR=Inf;LSEQ=TCCAATTATCAACACTAAAG;RSEQ=CGTAAGTTGATCCCTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:16,6:0:2,0:25.6:1:31.3:1:1:0:60:44:1:0:0 0/1:22:2:1,1:16,4:0.0909:2,2:15.5:1:27:1:0.41126:3.6879:60:4:0.0952:0:1 -3 112649386 . C T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02874;LSEQ=ACCTCATGCATCCCATAAAT;RSEQ=GACACAATGTGTCAGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:9:3,6:8,14:0.2903:2,2:12.8:1:29.9:1:1:1.13798:60:18:0.2903:0:1.7 0/1:27:8:2,6:6,13:0.2963:2,2:24.5:1:29.6:1:1:1.36848:60:16:0.2963:0:1.6 -3 112649401 . G T 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72335;SOR=1.41685;LSEQ=TAAATCGACACAATGTGTCA;RSEQ=TGACTTGGTAAGGGTTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:6,14:0.2:2,0:26:1:30.4:1:0.28871:0:60:10:0.2:0:2 0/1:19:5:0,5:4,10:0.2632:2,0:28.2:1:31:1:0.53044:0:60:10:0.2632:0:2 -3 112649613 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGTGTCACCTGTCTCTTA;RSEQ=ATGGTTTGTACTCTAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 112760178 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14806;SOR=Inf;LSEQ=TCATGGTCAACTGGAGAACG;RSEQ=TCCAGAAATCCTTGAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:245,34:0:2,0:22.7:1:31.2:1:1:0:60:92:1:0:0.1 0/1:175:2:1,1:147,26:0.0114:2,2:28.5:1:27:1:0.28552:5.56707:60:4:0.0116:0:1 -3 113012189 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.19075;SOR=Inf;LSEQ=TGGAGTCAGCGTTGGAGGCA;RSEQ=ACAGACCTGAATTTCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:56,62:0:2,0:26.8:1:31.8:1:1:0:60:236:1:0:0.1 0/1:92:2:1,1:44,46:0.0217:2,2:20:0:32:0:1:1.04:60:4:0.0217:0:1.5 -3 113012193 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.19825;SOR=Inf;LSEQ=GTCAGCGTTGGAGGCAGACA;RSEQ=ACCTGAATTTCAAAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:52,61:0:2,0:26.8:1:31.5:1:1:0:60:55.5:1:0:0.1 0/1:92:2:1,1:43,47:0.0217:2,2:23:1:27:1:1:1.09:60:4:0.0217:0:1 -3 113012261 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15152;SOR=Inf;LSEQ=CAGCAAGTTACTCAGCTCCT;RSEQ=TGAGCTTTAGAAAGTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:7,33:0:2,0:20.8:1:31.6:1:1:0:60:39:1:0:0.1 0/1:26:2:1,1:7,17:0.0769:2,2:24:1:28.5:1:0.52923:2.34:60:4:0.0769:0:1 -3 113012330 . C G 74 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18321;LSEQ=GAAGAGGCCATACATGTAAA;RSEQ=ATATACTGTGTAAAGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:0.4545:0,0:33.2:1:32:1:1:0:60:10:0.4545:0:1 1/0:2:1:0,1:0,1:0.5:0,0:38:0:33:0:1:0:60:2:0.5:0:1 -3 113012343 . A C 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=ATGTAAACATATACTGTGTA;RSEQ=AGAGACAGATAACTAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:8:1:32.5:1:1:0:60:4:0.3333:0:1 1/0:2:1:0,1:0,1:0.5:0,0:43:0:34:0:1:0:60:2:0.5:0:1 -3 113068563 . T C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGGGCTCCCGGGGCAAG;RSEQ=GCCAGCTCATGTCATCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:33:1:1:0:60:4:1:0:2.5 -3 113069023 . AAG A 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AGAAAGACCAGCAGAGAGGA;RSEQ=AGAGAGAGAGAGAGGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:32:0:24:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:35:1:31:1:1:0:60:4:1:0:0 -3 113070399 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CAGTGACTCTCCAAAACCGC;RSEQ=AAGACCTAGATCTCCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:26.7:1:31.6:1:1:0:60:14:1:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:42:0:30:1:1:2.44949:60:4:0.3333:0:1.5 -3 113070440 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14229;SOR=Inf;LSEQ=GCTGAGAAAGGAGGACTCTG;RSEQ=ACCTTCTTAGGGGAAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:13,1:0:1,0:27.1:1:30.5:1:1:0:58:28:1:0:0.2 0/1:9:2:1,1:4,3:0.2222:2,2:7.5:1:32.5:1:1:1.29098:53.5:4:0.2222:0:1 -3 113070498 . G A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74407;SOR=0.75453;LSEQ=AGTCAGGGATAGTACGAGAT;RSEQ=CCAACCGGCATTTACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:6,2:15,6:0.2759:2,2:17.5:1:29.3:1:1:1.19:56.5:16:0.2857:0:1 0/1:18:4:4,0:11,3:0.2222:2,0:33.3:1:27.5:1:1:0:60:8:0.2222:0:1.3 -3 113070516 . GA G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50274;SOR=Inf;LSEQ=ATGCCAACCGGCATTTACAG;RSEQ=AAAGGCTTCTGAAATCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:19,12:0:2,0:27.8:1:29.4:1:1:0:59.4:30:1:0:0.3 0/1:41:2:1,1:27,12:0.0488:2,2:11:1:30.7:1:0.53902:2.20143:60:4:0.0513:0.0244:0 -3 113070575 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50734;SOR=Inf;LSEQ=CATACCAACCTCTGGAGTTG;RSEQ=GCGACATGGCTTCTCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:29,32:0:2,0:24.6:1:30.3:1:1:0:58.1:14.25:1:0:0.3 0/1:82:2:1,1:42,38:0.0244:2,2:38.5:1:27.5:1:1:1.10391:60:4:0.025:0:1 -3 113070598 . T TA 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0926;SOR=1.9381;LSEQ=GACATGGCTTCTCCCCTTTC;RSEQ=GGTCCCGTGACAGCCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:15:6,9:15,23:0.283:2,2:27.2:1:28.3:1:1:1.02:53.8:6.5:0.2549:0.0755:0.2 0/1:69:30:12,18:19,20:0.4348:2,2:24.2:1:29.3:1:0.62583:1.41766:49.2:60:0.4839:0.1159:0.1 -3 113070611 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22483;SOR=0;LSEQ=CCCTTTCTGGTCCCGTGACA;RSEQ=CCATCTTGCTATTACTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:18,31:0.0392:2,2:17.5:1:29:1:1:1.70:60:4:0.0392:0:1.5 0/0:56:0:0,0:23,33:0:2,0:23.1:1:30.9:1:1:0:55.5:17.667:1:0:0.2 -3 113376050 . A T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54581;SOR=Inf;LSEQ=CTCTCTGCATGAGGTACATG;RSEQ=TGCTGCATTTGATATAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:0:2,0:20.7:1:29.7:1:1:0:60:46:1:0:0 0/1:44:3:0,3:25,15:0.0682:2,0:8:1:21:1:0.06612:0:60:2:0.0488:0:1.3 -3 113376110 . TTGC T 118 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=34;MSI=12.000;MSILEN=3;SSF=0.00073;SOR=0.23468;LSEQ=CCTGCTTGTTGTTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:17:8,9:7,9:0.4474:2,2:28.8:1:29.1:1:1:1.14:60:34:0.4474:0.0263:0.2 0/1:95:15:6,9:25,28:0.1579:2,2:24.1:1:29.7:1:0.77116:1.33358:60:30:0.1579:0.0316:0.3 -3 113802083 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17143;SOR=Inf;LSEQ=AATATCCCTTCTTCAGAATG;RSEQ=TTGGAACCAGAAGTGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:17.6:1:31.1:1:1:0:60:24:1:0:0 0/1:9:2:1,1:3,4:0.2222:2,2:31:1:28:1:1:1.29:60:4:0.2222:0:1 -3 113802161 . CTGTTGT C 129 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=12.000;MSILEN=3;SSF=0.0999;SOR=2.41239;LSEQ=TGTTGTTGCTGTTGCTGCTG;RSEQ=TGTTGTTGTTGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:10:5,5:13,13:0.2326:2,2:27.4:1:31.8:1:1:1:60:20:0.2326:0.0233:0.1 0/1:40:17:9,8:10,12:0.425:2,2:29.9:1:31.7:1:0.75119:1.34:60:34:0.4474:0.025:0.2 -3 113820868 . G A 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTTTTTTTGCAAGACT;RSEQ=TTTCATAGGTGATGATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45:0:29:1:1:0:60:4:1:0:1 -3 113822125 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19192;SOR=Inf;LSEQ=GCTGGTATACTTGGTGATGG;RSEQ=CTTGGTGCCCTCGGACACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:22.5:1:31.2:1:1:0:60:24:1:0:0.1 0/1:20:2:1,1:8,10:0.1:2,2:27:0:31.5:1:1:1.24:60:4:0.1:0:1.5 -3 113822276 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51966;SOR=Inf;LSEQ=ACGTGCTCAAAGATGTCGTT;RSEQ=ACGAAGGAGTTCATGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:50,31:0:2,0:24.8:1:31.5:1:1:0:60:162:1:0:0.1 0/1:124:2:1,1:63,59:0.0161:2,2:9:1:28.5:1:1:1.0672:60:4:0.0163:0:1 -3 113822288 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13998;SOR=0;LSEQ=ATGTCGTTGACGAAGGAGTT;RSEQ=ATGATCCCCATGGCCTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:46,35:0.0241:2,2:39.5:1:28.5:1:1:1.3099:60:4:0.0241:0:1 0/0:138:0:0,0:68,70:0:2,0:27:1:31.2:1:1:0:60:137:1:0:0.2 -3 113822432 . G GA 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10777;SOR=Inf;LSEQ=CCGTAGTCACCCACCTCTTG;RSEQ=AGCCCTAATTGGGATCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:2,20:0:2,0:23.5:1:31.2:1:1:0:60:44:1:0:0 0/1:21:3:0,3:7,11:0.1429:2,0:16.3:1:31.5:1:0.52105:0:60:6:0.15:0.0476:0 -3 113824222 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGCCCTAAACAGGTGTA;RSEQ=CATTTTAAAAGGTACAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29:1:1:0:60:4:1:0:1 -3 114328765 . A T 66 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=ATCTCTGCTAGCCACAAGAA;RSEQ=ATTAGCAGTCAACATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:28.8:1:30.8:1:1:0:60:10:1:0:0.2 1/1:6:5:5,0:1,0:0.8333:0,0:11.8:1:28.6:1:1:0:60:10:0.8333:0:1.2 -3 114328901 . ACAG A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.24352;SOR=Inf;LSEQ=ATGATAAAGCCATGGCAATC;RSEQ=CAGCAGCAGCAGCAGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:32,20:0:2,0:25.3:1:31.7:1:1:0:60:51:1:0:0 0/1:55:3:2,1:29,23:0.0545:2,2:31.3:1:31.3:1:1:1.57:60:6:0.0556:0:0 -3 114328937 . GC AT 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.15999;SOR=2.42965;LSEQ=CAGCAAAAGCAGCAACAGCA;RSEQ=AGCTGAAGCAGCAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:4:2,2:37,39:0.05:2,2:18:0:30:1:1:1.05:28:8:0.0513:0:2 0/1:79:9:5,4:35,35:0.1139:2,2:18:0:31:1:1:1.25:26.9:18:0.1169:0:2 -3 114328942 . T A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15675;SOR=2.47091;LSEQ=AAAGCAGCAACAGCAGCAGC;RSEQ=GAAGCAGCAACAGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:4:2,2:35,39:0.0513:2,2:22:0:31.3:1:1:1.11:28:8:0.0533:0:2 0/1:76:9:5,4:33,34:0.1184:2,2:22:0:32:1:1:1.28:26.9:18:0.1216:0:2 -3 115560700 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21315;SOR=0;LSEQ=TGGCATACTTACTGAAAAGG;RSEQ=CTAGGCTGGCATTGGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:78,38:0.0169:2,2:18:1:27.5:1:1:2.03915:60:4:0.0171:0:1 0/0:137:0:0,0:82,55:0:2,0:20.6:1:28.2:1:1:0:60:44.667:1:0:0.1 -3 115560748 . TA T 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50016;SOR=Inf;LSEQ=TGTTGGCAGCCACACAGGTG;RSEQ=GTTGCCGTAGTGCTCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:75,94:0:2,0:28.3:1:29.3:1:1:0:60:41.25:1:0:0.1 0/1:189:2:1,1:86,101:0.0106:2,2:18.5:1:33.5:1:1:1.17:60:4:0.0106:0:0 -3 115560763 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50066;SOR=Inf;LSEQ=AGGTGTAGTTGCCGTAGTGC;RSEQ=CCTCAGTGACGTTGGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:61,96:0:2,0:27.8:1:30.1:1:1:0:60:51.333:1:0:0.1 0/1:179:2:1,1:77,100:0.0112:2,2:19:1:29.5:1:1:1.30:60:4:0.0114:0:1 -3 116164290 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=CGGGCGGGCGGGCGAGGGAG;RSEQ=CGGCACCAAGCCTGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:12,4:0.1111:2,2:20.5:1:29.5:1:0.4902:2.79285:60:4:0.1111:0:1 0/0:11:0:0,0:10,1:0:2,0:29.1:1:31.6:1:1:0:60:22:1:0:0.1 -3 116506147 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCTTTTGTTCACATCTTTT;RSEQ=GTCCATGTGTACTGAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:17.5:1:28.5:1:1:0:60:4:0.6667:0:2.5 1/1:2:2:1,1:0,0:1:0,2:31:0:31.5:1:1:0:60:4:1:0:1.5 -3 116506453 . C T 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGGATGTCTGTGGTGGGA;RSEQ=CTGTGGAACAGCCTCGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:0:0,0:247,273:0:2,0:25.8:1:31.2:1:1:0:60:73.286:1:0:0.3 0/1:451:26:11,15:202,223:0.0576:2,2:24.7:1:28.7:1:0.68789:1.23465:60:25:0.0562:0:1.8 -3 116506471 . G A 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=2.14123;LSEQ=GACCTGTGGAACAGCCTCGA;RSEQ=GTCACTGTTAGGTACAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:107:49,58:182,220:0.2102:2,2:27.5:1:30.5:1:1:1.02:60:214:0.2127:0:1.2 0/1:435:158:75,83:129,148:0.3632:2,2:23.6:1:30.2:1:0.92047:1.04:60:51.667:0.3664:0:1.2 -3 116506560 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22885;SOR=Inf;LSEQ=TTACTTATGTACTGTTTCAA;RSEQ=GATGGTTCTATCCTCCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:45,142:0:2,0:25.2:1:31.3:1:1:0:60:92.5:1:0:0.1 0/1:172:2:1,1:49,121:0.0116:2,2:19.5:1:28:1:0.4981:2.45:60:4:0.0116:0:1.5 -3 117078179 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49195;SOR=Inf;LSEQ=GGGCAGCCCAGATGAGTGAA;RSEQ=TTCTCCCCAGCAAAGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:0:2,0:24.5:1:31.6:1:1:0:60:26:1:0:0.2 0/1:17:2:1,1:9,6:0.1176:2,2:19:1:28:1:1:1.46382:60:4:0.1176:0:1.5 -3 117078225 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19843;SOR=Inf;LSEQ=CTTCATTAAATGGGTCCTTC;RSEQ=CCCCGGGCCACCCAACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:18,10:0:2,0:31.3:1:29.3:1:1:0:60:13:1:0:0.2 0/1:23:2:1,1:10,11:0.087:2,2:48.5:1:30.5:1:1:1.10:60:4:0.087:0:1.5 -3 117078556 . C G 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00027;SOR=0;LSEQ=AAAAAGGCCTCCACAAAAAA;RSEQ=CCATCCAAGGGTCAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:9:5,4:19,17:0.2:2,2:22.6:1:32.1:1:1:1.12:60:18:0.2045:0:1.1 0/0:61:0:0,0:31,30:0:2,0:26.4:1:31:1:1:0:60:60:1:0:0.3 -3 117078557 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5052;SOR=Inf;LSEQ=AAAAGGCCTCCACAAAAAAC;RSEQ=CATCCAAGGGTCAGCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:24,22:0:2,0:27.3:1:30.6:1:1:0:60:22:1:0:0.9 0/1:61:2:1,1:30,29:0.0328:2,2:23:1:30.5:1:1:1.03392:60:4:0.0333:0:1 -3 117078561 . C T 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCTCCACAAAAAACCCAT;RSEQ=CAAGGGTCAGCAGCCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:21:10,11:13,10:0.4565:2,2:26.3:1:29.5:1:0.76304:1.41833:60:20:0.4651:0:1.2 0/0:61:0:0,0:30,31:0:2,0:25.3:1:30.7:1:1:0:60:29.5:1:0:0.3 -3 117079025 . GA G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GATATGCAGAAAAGCATAGA;RSEQ=AAAAAAAAATAATGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,1:0.5:2,0:22:1:33.3:1:1:0:60:6:0.5:0:0 0/0:10:0:0,0:8,2:0:2,0:17.7:1:29.6:1:1:0:60:20:1:0:0.1 -3 117862801 . A G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTCTTTTTATGAGGTCTC;RSEQ=TATTTCTTGGAGGCTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:30.5:1:33:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:0,1:0:0,0:6:0:31:0:1:0:60:2:1:0:0 -3 117863210 . G T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0625;SOR=0.16987;LSEQ=TTGTGGAGGCAATTTCTGCT;RSEQ=GTTTGTTTTTCTTTCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:3,5:5,6:0.4211:2,2:31.5:1:30:1:1:1.36508:60:16:0.4211:0:2 0/1:19:2:0,2:7,10:0.1053:2,0:19.5:1:32:0:0.50877:0:60:4:0.1053:0:1.5 -3 117863221 . C A 85 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03518;SOR=0.08879;LSEQ=ATTTCTGCTGGTTTGTTTTT;RSEQ=TTTCAATAGTCAGGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:3,5:0.4667:2,2:29.6:1:30.3:1:1:1.46001:60:14:0.4667:0:2.1 0/1:15:1:0,1:6,8:0.0667:2,0:19:0:32:0:1:0:60:2:0.0667:0:2 -3 117863755 . T C 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAGTTAGGCCTGAAAAGG;RSEQ=GCTCTGGCTGCAGATTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:25.5:1:31:1:1:0:60:4:0.5:0:1 1/1:1:1:1,0:0,0:1:0,0:38:0:34:0:1:0:60:2:1:0:2 -3 117863938 . CG TC 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCTAGTTTCAGTGCTGG;RSEQ=GCTGCCCCTCCCCCAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:47.5:1:30.8:1:1:1.73:60:4:0.4:0:1 0/0:1:0:0,0:0,1:0:0,0:46:0:30:0:1:0:60:2:1:0:0 -3 118605433 . C T 57 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03082;SOR=Inf;LSEQ=AGAAATGGCTGAGTTTTGAG;RSEQ=AGAATATACTGTGATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:0:0,0:261,220:0:2,0:26.7:1:32:1:1:0:60:59.125:1:0:0.3 0/1:491:6:1,5:259,226:0.0122:2,2:7.7:1:22.2:1:0.10422:5.7124:60:5:0.0103:0:1.5 -3 118605469 . T C 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.00856;LSEQ=TTTTTACGTGTGTTTTTCAA;RSEQ=GGCCCTATACTTGGATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:166:86,80:186,187:0.3074:2,2:24.4:1:31:1:0.7094:1.08:60:165:0.3096:0:1.1 0/1:526:248:120,128:123,155:0.4715:2,2:23.3:1:30:1:0.38108:1.18:60:247:0.4759:0:1.1 -3 118605684 . T C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00182;SOR=Inf;LSEQ=TGCATTTCTTGCCTGAATTA;RSEQ=TGAAATAATCACCCAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:1,24:0:1,0:24.4:1:30.2:1:1:0:60:50:1:0:0.1 0/1:12:5:1,4:0,7:0.4167:0,2:12.8:1:32.6:1:0.41667:0:60:10:0.4167:0:1 -3 118844792 . A G 58 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATGCCACCGGGGCCTAGC;RSEQ=TCCCAGTCCTGGAATGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:22.3:1:29.3:1:1:0:60:8:1:0:1 1/1:2:2:1,1:0,0:1:0,2:37:0:30.5:1:1:0:60:4:1:0:2 -3 118845129 . T C 32 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03158;SOR=Inf;LSEQ=CCAGAGTGCCTCTTCAGGTC;RSEQ=AACCCTGACCCATCCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:0:2,0:30.4:1:29.2:1:1:0:58.6:15:1:0:0.3 1/0:4:2:1,1:0,2:0.5:0,2:16:0:32.5:1:1:0:60:4:0.5:0:2 -3 118845271 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48308;SOR=0;LSEQ=GCTGCAGTCTCTGCAGACCA;RSEQ=CAAACTTAGCTGATCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:0.1429:2,2:14.5:1:31.5:1:1:1.37:60:4:0.1429:0:2 0/0:12:0:0,0:8,4:0:2,0:23.2:1:31.3:1:1:0:60:24:1:0:0.3 -3 118845275 . A G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01718;SOR=0.11454;LSEQ=CAGTCTCTGCAGACCAGCAA;RSEQ=CTTAGCTGATCCTCCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:5,6:1,2:0.7857:2,2:19.8:1:32:1:1:1.61:60:22:0.7857:0:1.2 0/1:11:3:2,1:5,3:0.2727:2,2:12:1:33.7:1:1:1.18:60:6:0.2727:0:1.3 -3 118845411 . G T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTCCCTGTACCACCCAACT;RSEQ=GGTGAGGCACTCCAACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:19:1:31.3:1:1:0:60:6:1:0:0 0/1:13:2:1,1:3,8:0.1538:2,2:30.5:1:31.5:1:1:2.45:60:4:0.1667:0:1.5 -3 118845663 . T C 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02424;SOR=0;LSEQ=AAAGAAAAACAAGCAGAAAG;RSEQ=GACAACAACAGCATCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:2,5:1,0:0.875:0,2:24.4:1:31.4:1:0.375:0:60:14:0.875:0:1 0/0:3:0:0,0:1,2:0:2,0:11:1:31:1:1:0:60:6:1:0:0.3 -3 118845677 . TCAA T 46 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.30769;SOR=Inf;LSEQ=AGAAAGTGACAACAACAGCA;RSEQ=CAACAACAACAACAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:4,5:0.25:2,2:22.3:1:29.6:1:1:2.32:60:6:0.25:0.1667:0 1/1:1:1:0,1:0,0:1:0,0:20:0:33:0:1:0:60:2:1:0:0 -3 119545503 . T TA 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.21963;SOR=Inf;LSEQ=AATAAGAACAACAATAATAA;RSEQ=AAAAAAATTGAACACTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:88,1:0:1,0:25.7:1:31.1:1:1:0:60:178:1:0:0 0/1:79:2:1,1:76,1:0.0253:1,2:31.5:1:28.5:1:0.05031:54.10049:60:4:0.0253:0:0.5 -3 119545532 . A AT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50181;SOR=Inf;LSEQ=TGAACACTAAAATGAACAGG;RSEQ=TTTTTTTCTCTTTTTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:136,9:0:2,0:25.2:1:29.4:1:1:0:60:28:1:0:0.1 0/1:171:2:2,0:149,20:0.0117:2,0:8:1:31:1:1:0:60:4:0.0119:0.0058:0.5 -3 119545705 . G A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11521;SOR=5.29504;LSEQ=GGTCTCCAGTATTAGCATCT;RSEQ=CAAGTCAAAAAGTCCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:1:1,0:184,306:0.002:2,0:1:0:25:0:0.37678:0:60:2:0.0021:0:1 0/1:467:5:4,1:172,290:0.0107:2,2:6.8:1:25.4:1:0.06939:6.72:60:10:0.0108:0:1 -3 119561962 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50747;SOR=0;LSEQ=AGTAGAGACAAGGTTTCACC;RSEQ=TGTTGGTCAGGCTGGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:57,0:0.0339:1,0:5:1:30.5:1:1:0:44:4:0.0339:0:2 0/0:43:0:0,0:43,0:0:1,0:22.8:1:30.9:1:1:0:58.2:42:1:0:0.1 -3 119562007 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24167;SOR=Inf;LSEQ=CCTGACCTCAGGTGATCCAC;RSEQ=CACCTCGGCCTCCCAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:104,2:0:1,0:26:1:30.8:1:1:0:58.6:52:1:0:0.1 0/1:103:2:1,1:94,7:0.0194:2,2:16.5:1:32:1:0.15001:12.628:60:4:0.0196:0:2 -3 119562009 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.23957;SOR=Inf;LSEQ=TGACCTCAGGTGATCCACCC;RSEQ=CCTCGGCCTCCCAAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:107,2:0:1,0:25.7:1:30.3:1:1:0:58.7:218:1:0:0.1 0/1:105:2:1,1:95,8:0.019:2,2:18.5:1:33:1:0.16484:11.25491:60:4:0.0194:0:2 -3 119562316 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18571;SOR=Inf;LSEQ=ACTACCAGTTTATGCCGGGC;RSEQ=CAGTGGCTCACGCCTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:0,68:0:1,0:22.3:1:31.6:1:1:0:59.9:21.667:1:0:0.2 0/1:52:2:1,1:0,50:0.0385:1,2:46:1:30:1:0.03846:0:59.5:4:0.0385:0:4.5 -3 119562328 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17105;SOR=Inf;LSEQ=TGCCGGGCGCAGTGGCTCAC;RSEQ=CCTGTAATCCTAGCACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:0,56:0:1,0:22.8:1:31.4:1:1:0:59.9:17.667:1:0:0.3 0/1:40:2:1,1:0,38:0.05:1,2:42.5:1:30.5:1:0.05:0:59.5:4:0.05:0:4.5 -3 119562339 . T C 32 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55386;SOR=3.37343;LSEQ=GTGGCTCACGCCTGTAATCC;RSEQ=AGCACTTTGGGAGGCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:0,1:0,48:0.0204:1,0:2:0:32:0:1:0:60:2:0.0208:0:1 0/1:30:2:1,1:0,28:0.0667:1,2:31.5:1:32.5:1:0.06667:0:59.5:4:0.0667:0:4.5 -3 119562352 . G C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10383;SOR=Inf;LSEQ=GTAATCCTAGCACTTTGGGA;RSEQ=GCCAAGGTGGGTGAATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:0:1,0:26.7:1:30.4:1:1:0:59.8:40:1:0:0 0/1:20:2:1,1:1,17:0.1:1,2:18.5:1:32.5:1:0.19474:12.37:59.5:4:0.1:0:4.5 -3 119582218 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21276;SOR=Inf;LSEQ=GAATGTCATTTCACACCCAG;RSEQ=GTGTAGCTTTCCTAGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:172,53:0:2,0:21.1:1:30.9:1:1:0:60:111.5:1:0:0.1 0/1:194:2:1,1:143,48:0.0103:2,2:32.5:1:28.5:1:0.4443:2.95885:60:4:0.0106:0:1 -3 119585372 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1002;SOR=Inf;LSEQ=TAATTATTTAGCCTCTCAAA;RSEQ=AAGATTTCCCCCAAGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:233,90:0:2,0:23.3:1:31.5:1:1:0:60:52.833:1:0:0.1 0/1:282:3:2,1:193,86:0.0106:2,2:34.3:1:29.7:1:1:1.12162:60:6:0.0108:0:1.3 -3 119585415 . G GA 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.67911;SOR=0.82576;LSEQ=GACCTGCCCTGAAATTTTGG;RSEQ=AAAAAAAAATTAAGTACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:13:8,5:288,210:0.0254:2,2:27:1:30.1:1:1:1.17:60:26:0.0259:0.0039:0.2 0/1:474:10:6,4:272,188:0.0211:2,2:25.7:1:29.3:1:1:1.04:60:20:0.0217:0.0042:0 -3 119585581 . T TG 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.80575;LSEQ=GTTATAAGAAATCCATGGTG;RSEQ=GGGGGGGGACATAGAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:3:0,3:7,121:0.0229:2,0:22.7:1:31.3:1:1:0:60:6:0.0236:0.0076:0 0/1:108:2:0,2:11,95:0.0185:2,0:19:1:30.3:1:1:0:60:4:0.0189:0.0093:0 -3 119585681 . G A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04991;SOR=Inf;LSEQ=ATTATTTCACCACAGTGTAT;RSEQ=CAAAAAAATTTTTTTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:0:1,0:29.2:1:30.6:1:1:0:60:7.667:1:0:0.3 0/1:8:2:1,1:0,6:0.25:0,2:37:1:28.5:1:0.25:0:60:4:0.25:0:1 -3 119585690 . T A 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0.52426;LSEQ=CCACAGTGTATGCAAAAAAA;RSEQ=TTTTTTTGATTGTGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:0,5:0,18:0.2174:1,0:26.2:1:31:1:1:0:60:10:0.2273:0:1 0/1:8:1:0,1:1,6:0.125:2,0:9:0:31:0:1:0:60:2:0.125:0:1 -3 119586123 . TCTGCTAAAAGATGTTTCTTTGCTGACATTCTCATTATCTTAGGACTCATCAGGAAATT CCCTGTTTGGATTATTTCACTGCATTATCATCTTTAGGATTCGTCAGGAACAG 46 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CTCCATTTTGGATTGACTTC;RSEQ=GACATATCACCTCAGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:17.5:1:32.5:1:1:0:60:4:1:0:0 0/1:7:3:1,2:2,2:0.4286:2,2:33.7:1:29.2:1:1:1.81007:60:6:0.4286:0.4286:0.3 -3 119586168 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATTCTCATTATCTTAGGA;RSEQ=TCATCAGGAAATTGACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:38.5:1:31.5:1:1:0:60:4:1:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:41:0:30.5:1:1:2.45:21:4:0.3333:0:6 -3 119586171 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTCTCATTATCTTAGGACTC;RSEQ=TCAGGAAATTGACATATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:19.3:1:30:1:1:0:60:8:1:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:38:0:31:1:1:2.45:21:4:0.3333:0:6 -3 119586179 . ATT CAG 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ATCTTAGGACTCATCAGGAA;RSEQ=GACATATCACCTCAGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:19.3:1:30.3:1:1:0:60:8:1:0:0 0/1:6:2:1,1:1,3:0.3333:2,2:28:0:32.5:1:1:2.45:21:4:0.3333:0:4 -3 119586187 . A T 49 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23636;SOR=Inf;LSEQ=ACTCATCAGGAAATTGACAT;RSEQ=TCACCTCAGGAGTGCGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:19.3:1:27.8:1:1:0:60:8:1:0:0 0/1:7:3:1,2:1,3:0.4286:2,2:16.7:1:31.3:1:1:1.41:34:6:0.4286:0:3 -3 119595240 . T TA 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.64663;SOR=1.2861;LSEQ=TAACTACTGATTAATATACT;RSEQ=AAAAAAAAATCTAACTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:9:5,4:376,164:0.0163:2,2:20.4:1:28.1:1:0.46628:1.83183:60:8:0.0148:0.0036:0.2 0/1:479:10:7,3:309,158:0.0209:2,2:20.8:1:27.7:1:1:1.19:60:20:0.0213:0.0063:0 -3 119595503 . A G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAGCAGTGCCATGATTTGA;RSEQ=TATGTCCCCCAAAGCTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:0,37:0,0:1:0,1:27:1:31.8:1:1:0:60:36:1:0:1 1/1:16:16:0,16:0,0:1:0,1:20.1:1:31.7:1:1:0:60:32:1:0:1 -3 119631350 . TA T 69 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.63336;SOR=2.17754;LSEQ=GACACAAACCTTTGAGAGGT;RSEQ=AAAAAAAAAAAGCAGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:5,0:15,0:0.25:1,0:23.2:1:29.8:1:1:0:60:10:0.25:0.05:0.4 0/1:7:3:2,1:4,0:0.4286:0,2:15.7:1:30:1:0.42857:0:60:6:0.4286:0.1429:0 -3 119631814 . A G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00976;SOR=7.0675;LSEQ=TGTAAACTGTAACTATCTCT;RSEQ=ATAAAAGAAATTTACAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:0,5:0,28:0.1515:1,0:26.8:1:31:1:1:0:60:10:0.1563:0:1 1/0:14:8:0,8:0,6:0.5714:0,0:28.1:1:31.5:1:1:0:60:16:0.5714:0:1 -3 119632125 . C A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTGACTCACGGCGAATATTT;RSEQ=AAGGCTTATAGACTCAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:12:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:27.5:1:1:0:60:4:1:0:1 -3 119642101 . A G 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01289;SOR=Inf;LSEQ=ACAAAGTTCCAACAATACCT;RSEQ=CTTTACAGTTTTTCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:59,2:0:1,0:20:1:28.1:1:1:0:60:19.333:1:0:0.1 0/1:46:5:5,0:40,1:0.1087:1,0:29.4:1:31.6:1:1:0:60:10:0.1111:0:1 -3 119666019 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.49932;SOR=0;LSEQ=GTTTCGGAATTTTTCCATTC;RSEQ=ATTAGCAAAACTGTCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:97,5:0.0192:1,2:20.5:1:31:1:0.11258:17.79785:60:4:0.0194:0:1 0/0:92:0:0,0:86,6:0:2,0:22.8:1:30.2:1:1:0:60:184:1:0:0.1 -3 119721104 . A AT 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.85074;SOR=1.14813;LSEQ=CTCCTAAAGGAAGAAAGGAA;RSEQ=TTTTTTTTTCACGAGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:14:5,9:128,350:0.0285:2,2:29.4:1:28.6:1:0.54134:1.52:60:13:0.0271:0.002:0.4 0/1:461:15:2,13:155,290:0.0325:2,2:23.2:1:31.1:1:0.10081:3.46687:60:30:0.0333:0:0.2 -3 119721117 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02647;SOR=Inf;LSEQ=AAAGGAAATTTTTTTTTCAC;RSEQ=AGAACTGTAAGGAATTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:0:0,0:88,307:0:2,0:25.6:1:30.4:1:1:0:60:78:1:0:0.2 0/1:372:5:4,1:103,264:0.0134:2,2:13.2:1:24.2:1:0.02551:10.18:60:4:0.0109:0:1 -3 119721171 . T C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.96214;LSEQ=AAAATATACAAGGTAAACTA;RSEQ=ATTCTTTATTTTTTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:30:0,30:0,122:0.1974:1,1:19.2:1:31.8:1:1:0:59.8:14:0.1905:0:1.1 0/1:115:22:0,22:3,90:0.1913:1,1:25.4:1:32.5:1:1:0:60:44:0.1947:0:1 -3 119721191 . A AT 96 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.29367;SOR=1.81447;LSEQ=TATTCTTTATTTTTTATTTT;RSEQ=TTTTTTTTTTTGAGATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:7:0,7:0,85:0.0761:1,0:39.1:1:29.7:1:1:0:60:14:0.0778:0:0.4 0/1:69:9:0,9:0,60:0.1304:1,0:21.8:1:30.3:1:1:0:57.8:18:0.1304:0:0.1 -3 119813282 . A G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCGCATTCGCCCGGGTCAGG;RSEQ=GCTGCTCTGTGTGAGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:31:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:6:0:32:0:1:0:60:2:1:0:0 -3 120222544 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49512;SOR=Inf;LSEQ=CATAGACACAAGCATCAAAA;RSEQ=CTGACTCCGGCTGATTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:21,19:0:2,0:27.3:1:31.8:1:1:0:60:19:1:0:0.2 0/1:44:2:1,1:20,22:0.0455:2,2:35:1:28:1:1:1.10:60:4:0.0455:0:1 -3 123714862 . CT C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.13177;LSEQ=GTTTACTGAATTAAATTCTC;RSEQ=TTTTTTTCTCTCCTTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:80:61,19:77,12:0.4734:2,2:22.3:1:31.2:1:0.11117:1.99043:60:160:0.4734:0.0828:0.1 0/1:133:14:10,4:92,27:0.1053:2,2:24.2:1:31.5:1:0.73833:1.35959:60:28:0.1061:0:0.6 -3 123714982 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36371;LSEQ=CTTAGGGACTAAAGTTCTAT;RSEQ=TGGCCAAGTAACCATAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:223:100,123:128,161:0.4355:2,2:26.8:1:30.1:1:0.92866:1.02:60:446:0.439:0:1.1 0/1:443:97:46,51:156,190:0.219:2,2:25.6:1:29.4:1:0.72975:1.10:60:96:0.2182:0:1.1 -3 125683874 . A C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.35607;SOR=2.08007;LSEQ=GAAGTGAGCCACAGTATAAG;RSEQ=CACACAGGATAGGGAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:13:12,1:15,0:0.4643:1,1:24.9:1:32.3:1:0.46429:0:59.2:26:0.4643:0:1.1 1/0:17:11:10,1:6,0:0.6471:0,2:19.4:1:32.5:1:1:0:60:22:0.6471:0:1.5 -3 125683918 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15421;SOR=Inf;LSEQ=TTTCTGAGCTCATAGCTAGT;RSEQ=TGAGACAGTTGATACTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:57,18:0:2,0:22:1:28.5:1:1:0:60:36.5:1:0:0.3 0/1:49:2:1,1:34,13:0.0408:2,2:38.5:1:31:1:0.49405:2.55705:60:4:0.0408:0:1.5 -3 125683989 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21;SOR=Inf;LSEQ=GGATTCCCACTCTCTGGTGC;RSEQ=AGACCGGTCGTCACCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:94,64:0:2,0:26.2:1:31.2:1:1:0:60:157:1:0:0.2 0/1:135:2:1,1:77,56:0.0148:2,2:14.5:1:29.5:1:1:1.37169:60:4:0.015:0:1 -3 125684001 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50054;SOR=0;LSEQ=TCTGGTGCCAGACCGGTCGT;RSEQ=ACCTGGCCAAATAGAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:93,66:0.0124:2,2:43:1:28.5:1:1:1.40601:60:4:0.0125:0:1 0/0:141:0:0,0:80,61:0:2,0:26.4:1:31.3:1:1:0:60:282:1:0:0.1 -3 125684052 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15459;SOR=Inf;LSEQ=ATACTGAACATGCAAATCTC;RSEQ=ATGGACACTGAAGTATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:64,105:0:2,0:25.3:1:29.7:1:1:0:60:55.333:1:0:0.1 0/1:110:2:1,1:45,63:0.0182:2,2:20.5:1:30:1:1:1.40:60:4:0.0182:0:1 -3 126249824 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGACAGTGGGCTTCAG;RSEQ=TACACGCAGCAGGGTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29.5:1:1:0:60:4:1:0:1 -3 127838589 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22956;SOR=0;LSEQ=GATGACATTTAATTTGATAT;RSEQ=TGAACCTCTGGGAGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:65,54:0.0165:2,2:47:1:30.5:1:1:1.20185:60:4:0.0167:0:1 0/0:131:0:0,0:78,53:0:2,0:26:1:31.1:1:1:0:60:64.5:1:0:0.2 -3 127838630 . G C 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=GAGTCAGCGTTCCAGGCAAA;RSEQ=AAAACAGCGAATTCAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:56,76:0:2,0:26.2:1:31.7:1:1:0:60:65:1:0:0.1 0/1:152:14:7,7:62,76:0.0921:2,2:23.4:1:30.6:1:0.78254:1.22:60:13:0.0872:0:1.4 -3 127838657 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50227;SOR=Inf;LSEQ=GCGAATTCAGAAAATCCAAA;RSEQ=CAGAAACAAGCTTGGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:35,52:0:2,0:24.2:1:32:1:1:0:59.8:42.5:1:0:0.2 0/1:106:2:1,1:41,63:0.0189:2,2:12:1:26.5:1:1:1.53:60:4:0.019:0:1 -3 128199662 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01129;SOR=Inf;LSEQ=GGAAACCCCACCTGGGCAGC;RSEQ=GTCAGGTGCGGAGGCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:23,1:0:1,0:23.4:1:30.1:1:1:0:60:48:1:0:0.1 0/1:8:3:3,0:4,1:0.375:2,0:27.3:1:31.7:1:1:0:60:6:0.375:0:1 -3 128199913 . G T 229 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00484;LSEQ=TGGGGGTGGCCGAAGGAGAG;RSEQ=CTGGAGGAGGGGTGGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:895:223:129,94:374,296:0.2492:2,2:24.5:1:29.4:1:0.64019:1.09:60:43.6:0.2489:0:1.2 0/0:622:1:0,1:327,294:0.0016:2,0:1:0:23:0:0.47428:0:60:2:0.0016:0:1 -3 128200072 . C T 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=45.9162;LSEQ=GACAGCTCCTCGAAGCACTC;RSEQ=GCCCCTTTCTTGCTCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1324:1:1,0:616,706:8e-04:2,0:30:0:16:0:0.46636:0:60:0:0:0:1 0/1:1131:38:19,19:536,557:0.0336:2,2:23.4:1:30.3:1:1:1.04:60:76:0.0342:0:1.1 -3 128200152 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16901;SOR=5.47066;LSEQ=TTCCTTCTTCATGGTCAGTG;RSEQ=CCTGTTAACCTAGAGGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:1:1,0:131,354:0.0021:2,0:1:0:25:0:0.2716:0:60:2:0.0021:0:1 0/1:358:4:2,2:90,263:0.0112:2,2:17.8:1:27:1:0.27423:2.91:60:8:0.0113:0:1.3 -3 128200459 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55309;SOR=Inf;LSEQ=CAGAGAAACCACTTCCCTAG;RSEQ=CCGAGACCCTGTCCTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:23:21,2:8,1:0.7188:2,2:22.2:1:32.8:1:1:1.30:60:46:0.7188:0:1.6 1/1:4:4:3,1:0,0:1:0,2:9.5:1:32.8:1:1:0:60:8:1:0:1.8 -3 128200534 . G A 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.43113;SOR=0.7294;LSEQ=TTACGGGAAGCCCTTCTGGC;RSEQ=CTCACTCAGGGCAGCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:71:70,1:29,2:0.6961:2,1:23.2:1:29.9:1:0.21846:4.74:60:34.5:0.69:0:1.3 1/0:40:25:24,1:15,0:0.625:1,1:21.6:1:30.1:1:1:0:60:24:0.6154:0:1.2 -3 128200806 . G A 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=142.81647;LSEQ=GACTGGGAGGGCAAGGCAGC;RSEQ=TCAGCAGGCTGGACTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:1:1,0:151,341:0.002:2,0:1:0:25:0:0.30832:0:60:2:0.002:0:1 0/1:350:79:32,47:96,175:0.2257:2,2:23.5:1:29:1:0.42765:1.24:60:38.5:0.2219:0:1.1 -3 128201013 . A C 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03623;SOR=Inf;LSEQ=CTCAGAAGCCTGATGTTAGA;RSEQ=TCAACGGGATTGCAAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:0,19:0:1,0:24.8:1:31.2:1:1:0:60:38:1:0:0.4 0/1:5:2:0,2:0,3:0.4:0,0:7:1:32:1:1:0:60:4:0.4:0:1 -3 128203006 . G T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.72596;SOR=0.70614;LSEQ=GCCTGGGCAGGAAGAGGGAC;RSEQ=AGAGGGTCTCCCACATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:20:0,20:0,10:0.6667:0,1:27.3:1:28.7:1:1:0:60:40:0.6667:0:1.6 1/0:12:7:0,7:0,5:0.5833:0,0:21.9:1:26.9:1:1:0:60:14:0.6364:0:1.4 -3 128203035 . A G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34419;SOR=0.37389;LSEQ=TCCCACATGGGAGGGGGCAC;RSEQ=GGTCCAGAGTCGTTTAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:0,14:0,5:0.7368:0,1:22.2:1:30.9:1:1:0:60:28:0.7368:0:1.8 1/0:6:3:0,3:0,3:0.5:0,0:38:1:31:1:1:0:60:6:0.5:0:2 -3 128204488 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14346;SOR=Inf;LSEQ=GATCTGGGAAACCAACACTG;RSEQ=CACCTCTCCCAAGTCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:192,45:0:2,0:23.4:1:32:1:1:0:60:117.5:1:0:0.1 0/1:145:2:1,1:116,27:0.0138:2,2:34:1:29:1:0.35:4.23703:60:4:0.0142:0:1.5 -3 128204877 . C G 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGCTGGAGACGCAGCCCC;RSEQ=GTGGTGCTAGGGTCAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1287:0:0,0:607,679:0:2,0:23.1:1:30:1:1:0:60:57.455:0.9992:0:0.1 0/1:791:34:15,19:333,420:0.043:2,2:23.6:1:27.9:1:1:1.00428:60:33:0.0424:0:1.1 -3 128204951 . C T 193 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=97.07715;LSEQ=AAGGTGGGAGCCAGAGTGGG;RSEQ=TGCTGTAGGGGTGAGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1231:2:1,1:558,671:0.0016:2,2:31.5:1:29:1:1:1.20:60:4:0.0017:0:1 0/1:768:105:51,54:298,365:0.1367:2,2:23.5:1:28.8:1:0.5273:1.16:60:34:0.1349:0:1.2 -3 128204960 . G C 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAGAGTGGGCTGCTGTAG;RSEQ=GGTGAGGGAGGCCACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1163:0:0,0:526,635:0:2,0:24.2:1:31.2:1:1:0:60:115.1:0.9983:0:0.2 0/1:704:16:7,9:315,371:0.0227:2,2:21.3:1:30.4:1:1:1.09154:60:32:0.0231:0:1.2 -3 128205133 . G A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12448;SOR=3.7457;LSEQ=CCGCAGCGGCAGAGAGGGCT;RSEQ=CTTTGCCCCCGTCCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:2:2,0:299,384:0.0029:2,0:1:0:26:1:0.19273:0:60:4:0.003:0:1 0/1:461:5:4,1:216,240:0.0108:2,2:7:1:23.8:1:0.19725:4.43:60:10:0.0109:0:1.2 -3 128205221 . AAG A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.07157;SOR=Inf;LSEQ=GGTCAGGCGGGCTGCGGGCA;RSEQ=AGAGAGAGGATCAGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:122,240:0:2,0:25.2:1:30.9:1:1:0:60:180:1:0:0.2 0/1:258:3:1,2:90,166:0.0116:2,2:16:1:28.7:1:1:1.08401:60:6:0.0119:0.0039:0.3 -3 128205519 . G A 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00047;SOR=Inf;LSEQ=CCGCTGCTCCCACCTCTCCC;RSEQ=CCCCAATTTTTCAGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:84,4:0:1,0:22.3:1:29.7:1:1:0:60:43:1:0:0.1 0/1:37:6:6,0:28,3:0.1622:2,0:20.2:1:31.2:1:1:0:60:12:0.1622:0:1 -3 128205545 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTCAGCAGCTCGATTC;RSEQ=TGCGGATCCTACATCCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:134,4:0.0143:1,2:20.5:1:29.5:1:0.0704:30.0704:60:4:0.0147:0:1 0/0:58:0:0,0:53,5:0:2,0:23.5:1:30.4:1:1:0:60:116:1:0:0.1 -3 128205831 . G A 71 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01572;SOR=9.54551;LSEQ=GGTGCTGCGCATTCAGCACG;RSEQ=CCGGGTGCGCCATCCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:828:1:1,0:250,576:0.0012:2,0:1:0:28:0:0.30351:0:60:2:0.0012:0:1 0/1:525:6:3,3:184,335:0.0114:2,2:21.3:1:27.5:1:0.67124:1.82:60:12:0.0117:0:1 -3 128205856 . G A 43 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07891;SOR=6.30835;LSEQ=GTGCGCCATCCAGCGCGGCT;RSEQ=CTCGGGCGCCACCTCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:1:1,0:132,410:0.0018:2,0:16:0:12:0:0.24494:0:60:0:0:0:2 0/1:347:4:3,1:95,248:0.0115:2,2:11:1:21.8:1:0.06987:7.78:60:3:0.0087:0:2 -3 128205860 . G C 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00223;SOR=1.58482;LSEQ=GCCATCCAGCGCGGCTGCTC;RSEQ=GGCGCCACCTCCATGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:511:292:69,223:51,168:0.5714:2,2:23.3:1:29.7:1:1:1.02:60:35.5:0.5714:0:1.1 1/0:327:222:59,163:27,78:0.6789:2,2:22.8:1:29.6:1:0.89389:1.05:60:110:0.6769:0:1.1 -3 128205890 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16097;SOR=Inf;LSEQ=TCCATGGCCGGCGGCGGCGG;RSEQ=TCAGGGTCTGGGTGCAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:39,207:0:2,0:22.7:1:32:1:1:0:60:40:1:0:0.7 0/1:166:2:1,1:33,131:0.012:2,2:9:0:30:1:0.36867:3.93:60:4:0.0121:0:2 -3 128205930 . A T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.16863;SOR=Inf;LSEQ=GGCAACGGCCCTGCGCGAGG;RSEQ=AGGGGGAGTGAGGCGTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:10,84:0:2,0:23.6:1:30.3:1:1:0:60:93:1:0:0.5 0/1:66:2:1,1:10,54:0.0303:2,2:26.5:1:26:1:0.30769:5.20:60:4:0.0303:0:1.5 -3 128814031 . T C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1257;SOR=Inf;LSEQ=AGCTAAAGAAATAAGGTTCC;RSEQ=CAGTGAACCCAGTGGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:75,146:0:2,0:21.6:1:29.9:1:1:0:60:54.25:0.9954:0:0.1 0/1:248:4:2,2:93,149:0.0161:2,2:27.3:1:26.3:1:0.64113:1.60:60:3:0.0124:0:1 -3 134069661 . G A 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80286;SOR=1.03942;LSEQ=CCCCTGTGAGTTGTTCTTGG;RSEQ=ACCCAAACACTACAAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:608:367:183,184:122,119:0.6036:2,2:26:1:30:1:0.8686:1.03077:60:121.333:0.6057:0:1.2 1/0:483:296:162,134:93,93:0.6128:2,2:25.6:1:28.8:1:0.34872:1.21:60:41.286:0.6123:0:1.1 -3 134069962 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=GCTCACACACCTACCTCCAC;RSEQ=TCCACCTGCTCATTCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:1,11:0.2:2,0:23:1:28.7:1:1:0:60:6:0.2:0:1 0/0:2:0:0,0:0,2:0:0,0:23.5:1:33:1:1:0:60:4:1:0:0 -3 134512680 . A C 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGTAGGAGGGAGGGGAGGGG;RSEQ=GGAGGAAGGCAGCCTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:0:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134513356 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGTGGAAGTTCACAATG;RSEQ=ACTGGGAAGTGAACACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134514248 . AAC A 31 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACACACCCACCTCTCCCATA;RSEQ=ACACACACACACATGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:1:0:27:0:1:0:60:2:1:0:0 0/1:5:2:1,1:3,0:0.4:0,2:18:0:31:1:0.4:0:60:4:0.4:0:0 -3 134514579 . T C 311 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.40562;SOR=0.46201;LSEQ=GCTGCTGGTGCCGGCCGCCT;RSEQ=GGGACTGCTGTGCTCCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1317:1315:569,746:0,0:0.9985:0,2:26:1:30.1:1:1:0:60:92.929:0.9985:0:1.2 1/1:914:911:387,524:0,0:0.9967:0,2:25.5:1:30.1:1:1:0:60:129.143:0.9967:0:1.2 -3 134516015 . T G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCCCTCAGTCTCCTGCT;RSEQ=CCCTCAGGGACTGCTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134644121 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGAGTTGATGGGAAGT;RSEQ=ACCCAAGGGTGTCAATATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25.5:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134644433 . G A 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63723;SOR=1.5253;LSEQ=CACTGGACTTAGCATCAGAC;RSEQ=TGAAGTCTGTATCCAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:5,0:26,1:0.1563:1,0:20.8:1:31.4:1:1:0:60:10:0.1563:0:1.4 0/1:9:2:2,0:7,0:0.2222:0,0:7.5:1:31.5:1:1:0:60:4:0.2222:0:2 -3 134644517 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.98704;LSEQ=GCCTTGGGCTTCACAGAGAG;RSEQ=CCTGGGCTTGAAGATGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:33:32,1:67,2:0.3235:1,1:25.8:1:31.9:1:1:1.0464:60:66:0.3235:0:1.2 1/0:58:41:39,2:16,0:0.7069:1,1:25:1:31.4:1:1:0:60:40:0.7143:0:1.1 -3 134644553 . C T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26095;SOR=0;LSEQ=GCACAAACCTCCTTGTAGTA;RSEQ=TGTCATTTACTATCACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:3:2,1:144,41:0.016:2,2:35.3:1:24.3:1:0.5338:1.75008:60:2:0.0108:0:2 0/0:144:0:0,0:111,33:0:2,0:21.4:1:30.8:1:1:0:60:71:1:0:0.6 -3 134644635 . C T 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCATTGTTTTTGTTTATT;RSEQ=GTTTTTTCTTTTTAATCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:0:0,0:296,250:0:2,0:24.2:1:30.8:1:1:0:60:90:1:0:0.5 0/1:475:21:11,10:264,190:0.0442:2,2:27.6:1:30.1:1:0.65453:1.26252:60:42:0.0445:0:1 -3 134644636 . G T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.54833;LSEQ=CTCATTGTTTTTGTTTATTC;RSEQ=TTTTTTCTTTTTAATCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:545:197:109,88:184,163:0.3615:2,2:22.5:1:30.6:1:0.65473:1.10:60:196:0.363:0:1.1 1/0:476:343:200,143:74,59:0.7206:2,2:24.3:1:30.3:1:0.60676:1.11:60:113.333:0.7203:0:1.1 -3 134644975 . C G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ACCTAGACAACTAGGGCCAT;RSEQ=GCTGTGTGGGGATGGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:17:1:32:1:1:0:60:8:0.5:0:1 1/1:2:2:0,2:0,0:1:0,0:28.5:1:31.5:1:1:0:60:4:1:0:1 -3 134669965 . G A 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22857;SOR=Inf;LSEQ=ATGAGCATTATGGGTTAGGC;RSEQ=AGGGACAGCTTTCTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:6,0:0.5:0,0:27.5:1:30.7:1:1:0:60:12:0.5:0:1.3 1/1:3:3:3,0:0,0:1:0,0:21:1:31:1:1:0:60:6:1:0:1 -3 134670080 . A C 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00097;SOR=0;LSEQ=CTTAGATGTGTTCATTTCTC;RSEQ=AGTCAATCTGCTGGACTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:20:19,1:88,1:0.1835:1,1:25.1:1:31:1:0.33469:4.5399:60:19:0.1776:0:1.1 0/0:45:0:0,0:44,0:0:1,0:20.9:1:30.2:1:1:0:60:43:0.9773:0:0.1 -3 134670524 . C T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.49699;LSEQ=ACCATTGCTGCAGATGAGAG;RSEQ=TTCTCCCAGGTGGACTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1087:391:225,166:384,312:0.3597:2,2:24.9:1:29.8:1:0.48378:1.10:60:77.2:0.3587:0:1.1 1/0:834:487:292,195:200,146:0.5839:2,2:23.8:1:29.4:1:0.56744:1.09:60:80.167:0.5852:0:1.1 -3 134670787 . A G 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0374;SOR=Inf;LSEQ=CCCCAACGCAGAGGAAGTGG;RSEQ=CGTGCCCATCAAACTCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:190,310:0:2,0:24.6:1:29.8:1:1:0:60:82.333:1:0:0.1 0/1:394:4:2,2:143,247:0.0102:2,2:21.8:1:31:1:0.62724:1.72:60:8:0.0104:0:1 -3 134670806 . C T 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03548;SOR=Inf;LSEQ=GACGTGCCCATCAAACTCTA;RSEQ=TGCAACGGGGATGGGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:164,267:0:2,0:23.6:1:32.2:1:1:0:60:214.5:1:0:0.1 0/1:332:4:1,3:118,209:0.012:2,2:9.8:1:26.8:1:1:1.69132:60:8:0.0123:0:1 -3 134670913 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08526;SOR=Inf;LSEQ=GGGTAAGCTTTGGAGCCTCT;RSEQ=CTTCCTGCCCATCTATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:51,122:0:2,0:22.6:1:31.4:1:1:0:60:23.714:1:0:0.1 0/1:137:3:2,1:42,92:0.0219:2,2:22.7:1:26.3:1:0.24145:4.33:60:6:0.0224:0:1.3 -3 134670929 . T A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09628;SOR=Inf;LSEQ=CTCTGCTTCCTGCCCATCTA;RSEQ=GGCAGGGCCAGATCTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:30,100:0:2,0:23.2:1:30.2:1:1:0:60:42.333:1:0:0.1 0/1:111:3:2,1:29,79:0.027:2,2:15.3:1:31.3:1:0.18797:5.35:60:6:0.0278:0:1 -3 134825097 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGTCATTGGTACCAAGAAG;RSEQ=TATATTTCACAAAGGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:0.1053:1,0:24:1:31.5:1:1:0:60:4:0.1053:0:1 0/0:5:0:0,0:5,0:0:0,0:29:1:29:1:1:0:60:10:1:0:0 -3 134825512 . G C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04146;SOR=0.6797;LSEQ=TGGTGCAAGTGGTGGGTCTG;RSEQ=GGCAAGGAAGAGAAGACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:120:22,98:29,133:0.424:2,2:21.8:1:30.1:1:1:1.03:60:59:0.4214:0:1.1 0/1:216:72:17,55:30,114:0.3333:2,2:22.5:1:29.8:1:0.72679:1.17:60:71:0.3349:0:1.1 -3 134851419 . A T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00707;SOR=Inf;LSEQ=CTTTTAAAATGAATTGAAGC;RSEQ=TAGCCATTTGGGGTTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:100,4:0:1,0:24.3:1:30.3:1:1:0:60:51:1:0:0.1 0/1:44:4:4,0:39,1:0.0909:1,0:25.5:1:31:1:1:0:60:8:0.0909:0:1.3 -3 134851577 . A T 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGTCCCATCAGGTCCCCGCA;RSEQ=TGTTATCTCCATCGTCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:841:95:56,39:412,334:0.113:2,2:25.4:1:30.3:1:0.51246:1.16:60:46.5:0.1122:0:1.2 0/0:707:0:0,0:388,319:0:2,0:24.7:1:29.7:1:1:0:60:87.375:1:0:0.2 -3 134852051 . C A 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTTGTGATCACATAGAG;RSEQ=AGGCAGGTGTAGTGTTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:0,42:0,0:1:0,1:22:1:30.6:1:1:0:60:84:1:0:1 1/1:17:17:0,17:0,0:1:0,1:19.9:1:30:1:1:0:60:34:1:0:1 -3 134872920 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1799;SOR=Inf;LSEQ=AATGCCATTTTTCTCCCTAC;RSEQ=TACCTCTGGAAGATGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:226,34:0:2,0:22.2:1:29.9:1:1:0:59.9:51:1:0:0.1 0/1:192:2:1,1:164,26:0.0104:2,2:19:1:29:1:0.26211:6.20863:60:4:0.0106:0:1 -3 134873388 . A AT 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGGAAGGACCAGTCCC;RSEQ=TTTTTCCAGTCACATGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:0,10:0.1667:0,0:21:1:29:1:1:0:60:4:0.1667:0:0 0/0:4:0:0,0:1,3:0:2,0:25.3:1:29:1:1:0:60:8:1:0:0 -3 134880488 . A C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGATGTTGCCTAGTTTG;RSEQ=GTCTGCTGAGGTCAGAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134880745 . G T 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90061;SOR=0.9465;LSEQ=GCCTGGAGCTGATGACAACT;RSEQ=CTAGCAGATATGCAGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:85:85,0:86,1:0.4942:1,1:22.9:1:30.7:1:1:0:60:170:0.4971:0:1 0/1:102:49:46,3:51,2:0.4804:1,2:21.4:1:30.3:1:0.66925:1.65481:60:98:0.4804:0:1 -3 134881023 . G A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16706;SOR=5.61929;LSEQ=CTTCCAGACTCTGACTGACG;RSEQ=TAAGGGTCGGGGAGGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:1:1,0:177,324:0.002:2,0:1:0:15:0:0.35458:0:60:0:0:0:1 0/1:360:4:3,1:133,222:0.0111:2,2:12:1:26.8:1:0.15439:4.99:60:8:0.0113:0:1 -3 134884473 . C T 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTAGATAAGTCCCCTT;RSEQ=ATTGGAATGTCCTTAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:5,1:0.25:2,0:36:1:31.5:1:1:0:60:4:0.25:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134884541 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGAGGGAATGTAGATTGG;RSEQ=AATCATCTCTGCTCCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:22.1:1:30.6:1:1:0:60:16:1:0:1.1 1/1:4:4:4,0:0,0:1:0,0:18.8:1:32.3:1:1:0:60:8:1:0:1.5 -3 134884601 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13462;SOR=Inf;LSEQ=CAGATTCTGTCACGGCTGTT;RSEQ=TGTTTTCATTGTCCTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:24,1:0:1,0:20.4:1:29.8:1:1:0:60:24:1:0:0.5 0/1:15:2:1,1:11,2:0.1333:2,2:38:1:31:1:0.37143:4.69047:60:4:0.1333:0:2.5 -3 134884652 . A C 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18607;SOR=0.51866;LSEQ=TTTGTTTATTTATAACTTAA;RSEQ=AATTGCTGTTTGTTTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:33:33,0:32,2:0.4925:2,1:26.1:1:32.3:1:0.49254:0:60:66:0.4925:0:1.2 0/1:30:10:10,0:17,3:0.3333:2,0:25:1:31.5:1:0.53202:0:60:20:0.3448:0:1 -3 134884695 . G C 149 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=ACTTACAACTCTGACACATA;RSEQ=AAACTATCCTCTACATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:25:24,1:93,3:0.2066:1,1:22.4:1:32.1:1:1:1.28874:60:50:0.2083:0:1.1 0/0:67:0:0,0:65,2:0:1,0:23.1:1:31.8:1:1:0:60:32.5:1:0:0.2 -3 134885042 . A C 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACAATCATCACTCCATCTC;RSEQ=ATCCAAGAGCAGCCTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:40:0,40:0,91:0.3053:1,1:22.4:1:32.3:1:1:0:60:80:0.315:0:1.1 0/0:58:0:0,0:1,57:0:1,0:21.2:1:30.7:1:1:0:60:57:1:0:0.1 -3 134885561 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05319;SOR=Inf;LSEQ=CACAGTCCCGCCAGGCTTCT;RSEQ=CAAGACCTTGGCTGGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:0:1,0:24.5:1:32.3:1:1:0:60:44:1:0:0.1 0/1:14:2:2,0:12,0:0.1429:0,0:25:1:31.5:1:1:0:60:4:0.1429:0:1.5 -3 134885704 . C A 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGGTGAGCCCCTATCTGG;RSEQ=CTGGGGCCTAGATGGAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:0:0,0:297,136:0:2,0:25:1:31.2:1:1:0:60:35.083:1:0:0.1 0/1:274:31:22,9:169,74:0.1131:2,2:19.8:1:27.6:1:1:1.07:60:62:0.1152:0:1.1 -3 134885719 . G T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07358;SOR=4.23356;LSEQ=TCTGGCCTGGGGCCTAGATG;RSEQ=AGGTACCTGGAACAGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:2:0,2:334,195:0.0038:2,0:1:0:23.5:1:0.1372:0:60:4:0.0039:0:1 0/1:381:6:2,4:245,130:0.0157:2,2:11.8:1:24.7:1:0.19014:3.75567:60:12:0.0161:0:1 -3 134885886 . A G 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ACCCGGTGTCTGACCCCCAC;RSEQ=GGCCACTGAGTCAAGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:70,226:0:2,0:24.3:1:30.4:1:1:0:60:36:0.9965:0:0.1 0/1:232:13:5,8:61,158:0.056:2,2:25.6:1:29.9:1:0.52671:1.62:60:26:0.0568:0:1.3 -3 134898742 . C T 275 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0219;SOR=1.21446;LSEQ=TACATTGACCCCTTCACTTA;RSEQ=GAGGATCCCAACGAAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1253:556:260,296:350,345:0.4437:2,2:25.1:1:30.2:1:0.21095:1.15482:60:41.769:0.44:0:1.1 0/1:1075:529:279,250:294,249:0.4921:2,2:25.4:1:29.5:1:0.66833:1.05792:60:74.571:0.4901:0:1.2 -3 134898960 . G A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TCTTTCTCCTCAGAAGATGA;RSEQ=TCTGAACTATCTACATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:1,82:0:1,0:22.4:1:32.5:1:1:0:60:82:1:0:0.1 0/1:42:9:0,9:1,32:0.2143:1,0:18.2:1:30.1:1:1:0:60:18:0.2143:0:1.2 -3 134911143 . A AAAAACAAACTCACATATATTCTGAAATTCCACTT 109 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAAATTAAGTGTGGGG;RSEQ=AAAACAAACTCACATATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:12,0:2,0:0.8571:0,0:18.8:1:30.6:1:1:0:57.5:24:0.8571:0.6429:0.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134911712 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20144;SOR=Inf;LSEQ=TGCACTTGGATGCAGGTGAA;RSEQ=GATGGCTGGGGAGAGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:63,181:0:2,0:23.8:1:29.9:1:1:0:60:39.667:1:0:0.2 0/1:200:2:1,1:56,141:0.01:2,2:28.5:1:30:1:0.49185:2.50:60:4:0.0101:0:1 -3 134911917 . A G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAAATGAATAGAGAGGG;RSEQ=CAAAGAATGGCCATTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:30:1:33:1:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:0:0,0:34:0:31:0:1:0:60:2:1:0:0 -3 134912008 . G A 62 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TGTGATTCATGCAGACATCC;RSEQ=CGGCCATCTCTGCCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:33.3:1:31.3:1:1:0:60:8:0.8:0:2 0/0:2:0:0,0:1,1:0:2,0:39.5:1:32.5:1:1:0:60:4:1:0:0 -3 134912028 . T C 66 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GCGGCCATCTCTGCCTTTCA;RSEQ=CAGCACAGCCACCCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:23.5:1:33:0:1:0:60:8:0.8:0:2 0/0:2:0:0,0:1,1:0:2,0:37.5:1:27.5:1:1:0:60:4:1:0:0 -3 134920243 . G T 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41123;SOR=0.30461;LSEQ=AGAAGCTGACAAGCAGCAGG;RSEQ=CCACAACATCTCTCCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:5:3,2:282,85:0.0134:2,2:16.8:1:27.6:1:0.33301:2.2062:60:4:0.0109:0:1 0/0:243:1:1,0:188,53:0.0041:2,0:23:0:24:0:1:0:60:2:0.0042:0:1 -3 134920546 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02039;SOR=Inf;LSEQ=TCCTTGGTGAGTCCTTCTTG;RSEQ=CATTCTCAAGTAGAAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:0:0,0:169,418:0:2,0:24.8:1:31.8:1:1:0:60:82.857:0.9983:0:0.1 0/1:501:5:3,2:174,322:0.01:2,2:12.4:1:26:1:0.35126:2.77:60:10:0.01:0:1.2 -3 134920603 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50886;SOR=0;LSEQ=ACTCTACATGGCTGGGAACT;RSEQ=TGACAGGGCACACTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:16,173:0.0105:2,0:16:0:31.5:1:1:0:60:4:0.0106:0:1 0/0:143:0:0,0:15,128:0:2,0:22.2:1:31.4:1:1:0:60:286:1:0:0.1 -3 134959888 . T C 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3515;SOR=0.37827;LSEQ=CTGTCATAATTCACAAGATA;RSEQ=GGGAGTGAGAGTTTGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:11:11,0:111,5:0.0866:1,0:24.2:1:33.4:1:1:0:60:22:0.0866:0:1 0/1:58:2:2,0:51,5:0.0345:2,0:26:1:30:0:1:0:60:4:0.0351:0:1.5 -3 134960304 . T A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09898;SOR=Inf;LSEQ=AGCATGGATGTTGGAACTAA;RSEQ=CAAAGAGCCCAGCATGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:2,47:0:1,0:22.1:1:29.7:1:1:0:60:23.5:1:0:0.1 0/1:23:2:1,1:1,20:0.087:1,2:33:0:28.5:1:0.16996:14.49:60:4:0.087:0:1 -3 134960472 . T C 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTACCCTGCTTCTAAGTG;RSEQ=TCAGGTTCTGTGTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:15:1:32.2:1:1:0:60:10:0.625:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134966964 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACTACAATGTGGCCCCTG;RSEQ=TTTCTAGGAGCCCAATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:18,0:0.1:1,0:7.5:1:31:0:1:0:60:4:0.1053:0:1 0/0:4:0:0,0:4,0:0:0,0:33.8:1:33:1:1:0:60:8:1:0:0 -3 134967265 . G A 151 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.0907;LSEQ=CAGAAGGACCGGAACAGCCG;RSEQ=CCCCGGTTTGCGGAGATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:918:33:19,14:463,421:0.0359:2,2:25.7:1:30:1:0.59805:1.23:60:66:0.037:0:1.1 0/0:891:3:2,1:456,432:0.0034:2,2:23:1:29:1:1:1.89:60:6:0.0034:0:1 -3 134967350 . G A 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGTGGCAACCATCACCGCC;RSEQ=TGTGAGTCTAGTGAAACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:0:0,0:248,381:0:2,0:24:1:31:1:1:0:60:208.667:1:0:0.2 0/1:543:32:12,20:197,314:0.0589:2,2:23.3:1:30.7:1:1:1.04557:60:64:0.0593:0:1.8 -3 134967368 . G A 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.52854;LSEQ=CCGTGTGAGTCTAGTGAAAC;RSEQ=GTGATCCCTAAATATGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:34:13,21:144,297:0.0716:2,2:24.7:1:30.5:1:0.57086:1.28:60:68:0.072:0:1 0/1:397:85:29,56:108,204:0.2141:2,2:23.2:1:30.7:1:1:1.02226:60:170:0.2168:0:1.4 -3 134967413 . G A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.27263;SOR=0;LSEQ=CATGGTCAGGGGCATAGCCA;RSEQ=CAGCCTCTGACCATGATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:2,1:28,201:0.0129:2,2:11:1:30:1:0.04475:14.05:60:6:0.013:0:1 0/0:161:0:0,0:33,128:0:2,0:21.9:1:31.6:1:1:0:60:160:1:0:0.2 -3 134967507 . A C 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15331;LSEQ=AGCAACATGCATGAAGAAAG;RSEQ=CAGGAGAACATTGCAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:5:0,5:0,52:0.0877:1,0:22.4:1:29.8:1:1:0:60:4:0.0714:0:1 0/1:20:2:0,2:0,18:0.1:1,0:14:1:32.5:1:1:0:60:4:0.1:0:1 -3 134967823 . A G 47 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATATCTGGGGAGGTTGTG;RSEQ=TAAAATATGCATATTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:4,1:0.375:2,0:15.7:1:29.7:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 134968032 . A G 138 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0461;SOR=2.18141;LSEQ=GCTGATTTAGGATTCCATGA;RSEQ=GAAGAAAGGTTCAGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:21:20,1:84,0:0.2:1,1:24.4:1:31.6:1:0.2:0:60:20:0.2:0:1 0/1:48:17:17,0:29,1:0.3542:1,1:23.5:1:33.3:1:1:0:60:34:0.3617:0:1 -3 134968079 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15084;SOR=Inf;LSEQ=CTATAATCCTCATTCCATCA;RSEQ=GGATGCTGCCTTCCATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:228,9:0:1,0:25.6:1:32:1:1:0:60:58.25:1:0:0.2 0/1:151:2:2,0:135,14:0.0132:2,0:13:1:31.5:1:1:0:60:4:0.0132:0:1.5 -3 134968084 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15231;SOR=Inf;LSEQ=ATCCTCATTCCATCAGGGAT;RSEQ=CTGCCTTCCATGAAGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:239,17:0:2,0:25.3:1:31.8:1:1:0:60:35.571:1:0:0.1 0/1:165:2:1,1:146,16:0.0121:2,2:9:1:24:1:0.19714:8.88358:60:4:0.0123:0:1 -3 134968089 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15914;SOR=Inf;LSEQ=CATTCCATCAGGGATGCTGC;RSEQ=TTCCATGAAGTCAGCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:251,27:0:2,0:25:1:30.7:1:1:0:60:38.714:1:0:0.1 0/1:185:2:1,1:159,24:0.0108:2,2:25.5:1:29.5:1:0.25264:6.51153:60:4:0.011:0:1 -3 134968440 . C CGTCT 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0.82296;SOR=1.10866;LSEQ=TGGCCTCATCCCTGGAGCTC;RSEQ=GTCTCTGTATAGACCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:19:0,19:1,87:0.1759:1,1:28.9:1:30.9:1:1:0:60:38:0.1827:0.0278:0.8 0/1:47:9:0,9:0,38:0.1915:1,0:22.7:1:31.6:1:1:0:60:18:0.1957:0.0426:0.6 -3 134968465 . T C 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTATAGACCAGGCCTGGA;RSEQ=GGGGAGCACCTTGGAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:73:0,73:0,0:1:0,1:24.9:1:29.4:1:1:0:60:35.5:1:0:1 1/1:25:25:0,25:0,0:1:0,1:19.2:1:30.1:1:1:0:60:50:1:0:1 -3 134968574 . T A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=AGTTATAGCCATATGTCATT;RSEQ=GCCTAATCACCCAGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:15.8:1:28.2:1:1:0:60:4:0.4444:0:1.6 1/1:2:2:0,2:0,0:1:0,0:47:1:31:1:1:0:60:4:1:0:1 -3 134968601 . A G 57 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCACCCAGAGTCTCTTCCCC;RSEQ=TTTAAGTTTTTAAACTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:34.8:1:28.5:1:1:0:60:3:0.6:0:1.5 0/0:2:0:0,0:0,2:0:0,0:25.5:1:32:0:1:0:60:4:1:0:1 -3 134977790 . GT G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16342;SOR=Inf;LSEQ=GAACATGGCTTTAGTGATGA;RSEQ=TTTGATCTGCGAAAAGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:220,45:0:2,0:23.7:1:29.6:1:1:0:60:43.167:1:0:0.1 0/1:181:2:1,1:140,38:0.011:2,2:15.5:1:33.5:1:0.38734:3.65:60:4:0.0114:0:0 -3 134978060 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51543;SOR=0;LSEQ=TGTACTGGAGAGACTGGCTT;RSEQ=TCAGCTGAGGAATGCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:2,159:0.0123:1,2:13.5:1:28.5:1:0.03658:65.10:60:4:0.0125:0:1 0/0:112:0:0,0:3,109:0:1,0:21.8:1:31.9:1:1:0:60:36.333:1:0:0.1 -3 134978236 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGACAAAACAATATGCATC;RSEQ=GGAGAACAAGAGTAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:20.5:1:32:0:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:0:0,0:28:0:33:0:1:0:60:2:1:0:1 -3 134978264 . T C 50 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGTAAACCCAGCTCCCA;RSEQ=TCTCAGTGGGCTGCAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:24:1:32:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:1:0,0:45:0:34:0:1:0:60:2:1:0:1 -3 135644725 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=GCTCAAGTGATTCTCCCACC;RSEQ=CAGCCTCCTCTCTGTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:116,50:0.0118:2,2:21.5:1:28.5:1:0.51625:2.30705:60:4:0.0119:0:1 0/0:156:0:0,0:104,51:0:2,0:21.8:1:29.3:1:1:0:60:30:1:0:0.2 -3 135644807 . C G 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00123;SOR=1.90065;LSEQ=AATATCTGGGGCCTGCAGTT;RSEQ=TTATACAGGCCTATCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:58:36,22:148,123:0.1763:2,2:22.3:1:32.6:1:0.31212:1.36:60:116:0.1785:0:1.1 0/1:273:79:48,31:103,91:0.2894:2,2:23:1:31.4:1:0.28364:1.37:60:158:0.2937:0:1.2 -3 135644964 . C T 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAATCCAGGGAAGGCTACTG;RSEQ=GGAAATCAAGAAAATGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:32:8,24:52,121:0.1561:2,2:23:1:30.2:1:0.67456:1.28769:60:31:0.1535:0:1.2 0/0:193:0:0,0:60,133:0:2,0:23:1:30.2:1:1:0:60:95.5:1:0:0.1 -3 135644998 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50325;SOR=0;LSEQ=ATGTTGGTAACCTATAAGGA;RSEQ=AAGAAAGTTTCAGCTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:44,101:0.0136:2,2:26.5:1:31:1:0.51999:2.28:60:4:0.0138:0:2.5 0/0:120:0:0,0:34,86:0:2,0:26.4:1:31:1:1:0:60:240:1:0:0.1 -3 135645021 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50777;SOR=0;LSEQ=GAAAGTTTCAGCTTAATTGT;RSEQ=CCCATGCTAAACATGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:43,89:0.0149:2,2:46:1:30.5:1:0.55056:2.06:60:4:0.015:0:1 0/0:101:0:0,0:33,67:0:2,0:27.5:1:28.8:1:1:0:60:32.333:0.9898:0:0.1 -3 135645058 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13573;SOR=Inf;LSEQ=CTTGTAACCAGTTCAGAGCT;RSEQ=AACATAATTTAGATCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:28,74:0:2,0:24.7:1:30.7:1:1:0:60:33:1:0:0.1 0/1:60:2:1,1:15,43:0.0333:2,2:23.5:1:27.5:1:0.46554:2.81:60:4:0.0333:0:1 -3 136076644 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=0;LSEQ=CAGATTAGGAGGTGGATACT;RSEQ=TTGTCCTTTCTGATTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:0.1538:2,2:25:1:27.5:1:1:2.45:60:4:0.1667:0:1 0/0:11:0:0,0:3,8:0:2,0:27.1:1:32:1:1:0:60:22:1:0:0.1 -3 136081447 . C CA 29 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGTGAAACATCATCTCTG;RSEQ=AAAAAAAAAAAAAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:1:29.5:1:1:0:50:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 136082119 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50758;SOR=Inf;LSEQ=TATAAAATGACCTAGTTTAA;RSEQ=TGAGATGAGATACCTAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:0:1,0:29.3:1:30:1:1:0:60:26:1:0:0.2 0/1:20:2:2,0:18,0:0.1:1,0:47:1:30.5:1:1:0:60:4:0.1:0:1 -3 136082291 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50736;SOR=Inf;LSEQ=CAGTGTTTCCTTAATAATAT;RSEQ=ACCATAGTCATTGTAATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:11,57:0:2,0:21.7:1:31:1:1:0:60:21.667:1:0:0.2 0/1:91:2:1,1:21,68:0.022:2,2:7:1:26.5:1:0.42711:3.19:60:4:0.0222:0:1 -3 136196071 . C T 85 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41667;SOR=Inf;LSEQ=ACTACTGTCATTTTGATTCC;RSEQ=AGCATTTTAGTACTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:30.5:1:31.5:1:1:0:60:8:0.8:0:1.3 1/1:7:7:7,0:0,0:1:0,0:25.6:1:30.4:1:1:0:60:14:1:0:1.1 -3 136196178 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52341;SOR=Inf;LSEQ=TTTTAGGTAACTGTCATTTA;RSEQ=GAAGGCATCACTATACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:18,17:0:2,0:30.9:1:31:1:1:0:60:34:1:0:0.1 0/1:57:2:1,1:30,25:0.0351:2,2:33:0:29.5:1:1:1.19614:60:4:0.0357:0:1 -3 137443260 . G A 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01149;SOR=0;LSEQ=GCTGATGAAGATGATGATAT;RSEQ=ATGATGCAGATGATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:2,3:18,22:0.1111:2,2:29.6:1:27.6:1:1:1.22176:60:4:0.093:0:1 0/0:62:0:0,0:29,33:0:2,0:25:1:31:1:1:0:60:19.667:1:0:0.3 -3 137483362 . G T 66 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGGTCCCAGCCCCTGGT;RSEQ=CCTGAAGCCCCCCGGCCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:18:1:28.8:1:1:0:60:10:1:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 137483689 . C T 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23339;SOR=0.24661;LSEQ=TTCATGGTATGGTCCCGGGG;RSEQ=CAGCGGCGCAAGATGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:5:3,2:256,207:0.0107:2,2:28.4:1:28.4:1:1:1.21:60:10:0.0109:0:1.4 0/0:377:1:0,1:218,158:0.0027:2,0:1:0:22:0:0.42175:0:60:2:0.0027:0:1 -3 138374293 . C T 167 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01849;LSEQ=CACTTTAGTAGTCCAGCTTT;RSEQ=CCTGAGCGCCTCATCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:891:50:20,30:406,433:0.0561:2,2:24.2:1:29.7:1:0.30782:1.40593:60:100:0.0573:0:1 0/0:912:1:0,1:424,486:0.0011:2,0:1:0:30:0:1:0:60:2:0.0011:0:1 -3 138374926 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11008;SOR=Inf;LSEQ=CCACTTGAATAAAACAGGCA;RSEQ=CTAAAACTGAGCTCAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:168,58:0:2,0:24.8:1:31.7:1:1:0:60:36.667:1:0:0.1 0/1:209:3:1,2:148,58:0.0144:2,2:15:1:27.7:1:0.19866:5.05733:60:6:0.0145:0:1 -3 138376323 . T C 156 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01204;SOR=0.07558;LSEQ=ATTGGAATAAAATATAATAA;RSEQ=TATTTTAAATTTCTAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:31:31,0:11,0:0.7381:0,1:21:1:31.5:1:1:0:60:14.5:0.725:0:1.2 0/1:6:1:1,0:5,0:0.1667:0,0:3:0:29:0:1:0:60:2:0.1667:0:1 -3 138376717 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=TAATTTCCTTCATTTTTCTG;RSEQ=TGGGTTCCAAATATAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:21,139:0.0123:2,2:13:1:29:1:0.25389:6.49:60:4:0.0123:0:1 0/0:161:0:0,0:24,137:0:2,0:24.2:1:31:1:1:0:60:79.5:1:0:0.1 -3 138383144 . A C 94 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGGCTGTGAGTAGACT;RSEQ=ATGTTCACAGTACTTAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:1,2:0.7:2,0:23.3:1:33.6:1:0.3:0:60:14:0.7:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 138383201 . C A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGATCATGCTAGGGGTTGGG;RSEQ=ACATTTTAGTTAGTTTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:23.5:1:31.5:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 138383765 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49802;SOR=0;LSEQ=TCTAACAAGAAATGAAGCAA;RSEQ=AGATAAAAAACACTAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:95,0:0.0206:1,2:24:1:28.5:1:0.02062:0:60:4:0.0208:0:1 0/0:90:0:0,0:88,2:0:1,0:23.3:1:30.4:1:1:0:60:180:1:0:0 -3 138401270 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51678;SOR=Inf;LSEQ=TTCACTGCGCAAAGCACAGT;RSEQ=ACTTACTAGAGGTCCGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:29,31:0:2,0:28.2:1:31.4:1:1:0:59.8:59:1:0:0.8 0/1:90:2:1,1:43,45:0.0222:2,2:37.5:1:30:1:1:1.05:60:4:0.0225:0:1.5 -3 138401299 . A C 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00081;SOR=0.30705;LSEQ=GAGGTCCGAGAGGATAACAC;RSEQ=TGGGTTCAGGGGTACTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:40:14,26:9,13:0.6452:2,2:28.1:1:31.4:1:0.78446:1.28043:60:80:0.6452:0:1.3 0/1:87:31:12,19:24,32:0.3563:2,2:30.5:1:30.5:1:0.82117:1.18516:60:14.5:0.3452:0:1.1 -3 138402193 . CA C 32 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:21.5:1:32.2:1:1:0:53.5:4:0.5:0.25:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 138402350 . GA G 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54682;SOR=0;LSEQ=AAATCATTTTATAAGAGGGG;RSEQ=AAAAAAAAGCATTTAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:3,0:48,0:0.0577:1,0:30.3:1:28:1:1:0:60:2:0.0408:0.0192:0 0/0:26:0:0,0:26,0:0:1,0:26.7:1:28.5:1:1:0:60:52:1:0:0 -3 138403390 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.22489;LSEQ=TTCCTGAGGCTGACAGCTGG;RSEQ=CCTACTACTCCCATAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:190:143:138,5:47,0:0.7526:1,1:25.9:1:30.7:1:0.33523:0:59.3:286:0.7526:0:1 0/1:121:49:46,3:69,3:0.405:1,2:25:1:30.4:1:0.68521:1.49482:59.5:98:0.4118:0:1.1 -3 138403728 . T A 22 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22559;SOR=Inf;LSEQ=TCATATCAATCAATAACACC;RSEQ=GCTCCCAACATATACACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:16,157:0:2,0:22.1:1:30:1:1:0:60:85.5:1:0:0.1 0/1:157:2:1,1:11,144:0.0127:2,2:10:1:22.5:1:0.14748:12.58:60:4:0.0129:0:1 -3 138412084 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCTGGGACCACAGGTGCG;RSEQ=ACCTCCACGCCCAGCTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:1:29:1:1:0:60:4:1:0:1 -3 138413373 . C T 28 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTGTAAGTGACTATGTG;RSEQ=TGAGTTCTGAGTCCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:10,0:0.1667:0,2:22.5:1:28:1:0.16667:0:60:4:0.1818:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 138413557 . A T 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49961;SOR=0;LSEQ=TTTCTTTCTTATGAGACATC;RSEQ=AGGAGACACCCTCATCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:0,2:126,25:0.0131:2,0:15:1:24.5:1:0.03019:0:60:4:0.0132:0:1 0/0:138:0:0,0:112,26:0:2,0:22.2:1:29.7:1:1:0:60:45:1:0:0.1 -3 138417989 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15809;LSEQ=AATTGTGCAAACACCACAGC;RSEQ=AACTTTCAGTAAATTTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:123:99:7,92:4,20:0.8049:2,2:22:1:30.2:1:0.22252:2.60302:60:48.5:0.8083:0:1.2 0/1:107:42:4,38:7,58:0.3925:2,2:25.1:1:30.1:1:1:1.14508:60:41:0.3981:0:1.2 -3 138418082 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10847;SOR=0.24333;LSEQ=CCATAAAAAAAAAAAAAAGG;RSEQ=AGATCCTTTAATAATTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:0,14:0,4:0.7778:0,1:25.9:1:32.4:1:1:0:58.6:28:0.7778:0:1.8 0/1:9:4:0,4:0,5:0.4444:0,0:29:1:32.5:1:1:0:60:8:0.4444:0:1.5 -3 138419027 . G T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCATGATCGTGTCACT;RSEQ=CACTCCAGTCTGGGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:30:1:1:0:50:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 138423164 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20865;SOR=Inf;LSEQ=CATGTGCATACTTACCCACA;RSEQ=TCACAGACTGTTCTTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:143,11:0:2,0:23.1:1:32.3:1:1:0:60:153:1:0:0.1 0/1:130:2:1,1:115,13:0.0154:2,2:14:1:27:1:0.20453:8.55932:60:4:0.0156:0:1 -3 138423181 . CAT C 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ACACTCACAGACTGTTCTTG;RSEQ=ATGAGTTACGGTCTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:34:28,6:159,30:0.1525:2,2:24.8:1:31.7:1:0.80141:1.13502:59.4:33:0.1493:0.0269:0.3 0/0:204:0:0,0:153,51:0:2,0:22.7:1:30:1:1:0:60:101:1:0:0.1 -3 138426428 . T C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTAATTGGAACTGCTCTC;RSEQ=CTCCATCAAAATTAGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:16.3:1:32.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 138433543 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12425;SOR=Inf;LSEQ=GAGCTCAGTACCATGAAAAA;RSEQ=ACCAGCCCTGACATGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:138,250:0:2,0:26.1:1:31.5:1:1:0:60:128.333:1:0:0.6 0/1:401:4:2,2:149,248:0.01:2,2:27.3:1:23.8:1:0.63393:1.66:60:3:0.0076:0:3 -3 138433568 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16783;LSEQ=GCCCTGACATGAACCTGTAA;RSEQ=GAAGCAGACAAAAACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:295:217:58,159:22,56:0.7356:2,2:24.5:1:30.5:1:0.88204:1.0767:60:107.5:0.7338:0:1.1 0/1:274:87:30,57:53,133:0.3175:2,2:26.5:1:30:1:0.32607:1.32:60:86:0.3197:0:1.1 -3 138433625 . TTTTG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16578;SOR=Inf;LSEQ=GTACCACGAAAAACATCTCT;RSEQ=TTTGTTTGTTTGTTTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:3,88:0:1,0:24.4:1:30.1:1:1:0:60:29.333:1:0:0.6 0/1:63:2:0,2:8,53:0.0317:2,0:34.5:1:29.5:1:1:0:60:4:0.0323:0:0 -3 138452310 . T A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11875;SOR=Inf;LSEQ=AATAAAATAAATACAAATTA;RSEQ=TTTAATGAAAGAAATGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:56,244:0:2,0:22.9:1:30.2:1:1:0:60:74:1:0:0.1 0/1:291:3:2,1:75,212:0.0103:2,2:12.3:1:26:1:0.17311:5.61:60:2:0.007:0:1.3 -3 138453794 . A T 116 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=1;SSF=0.11222;SOR=0.2325;LSEQ=CAAGAAATTAAAAAAAAAAA;RSEQ=TTTTTTTTTTTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:18:0,18:0,6:0.6429:0,1:16.2:1:27.9:1:1:0:60:5:0.7143:0:1.3 0/1:7:2:0,2:0,4:0.2857:0,0:6:0:31.5:1:1:0:60:4:0.2857:0:2.5 -3 138456476 . T A 21 v4;q23;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50221;SOR=0;LSEQ=GTGGGAACACATTTTTAAAG;RSEQ=CAGAAATAAAATATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:0,2:157,9:0.0119:2,0:7:1:21:1:0.00392:0:40:4:0.012:0:3.5 0/0:141:0:0,0:125,16:0:2,0:22.6:1:29.1:1:1:0:59.6:22.5:1:0:0.1 -3 138456483 . TAA T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.25313;SOR=0;LSEQ=CACATTTTTAAAGTCAGAAA;RSEQ=AATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:3,0:177,15:0.0154:2,0:25.3:1:30:1:1:0:58.3:6:0.0155:0.0103:0.7 0/0:165:0:0,0:137,28:0:2,0:23.3:1:28.5:1:1:0:59.6:164:1:0:0.1 -3 138456780 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23375;SOR=0;LSEQ=GTAAATGTTATATTTATGCT;RSEQ=AAAAATCACATTACAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:19,177:0.0101:2,2:35:1:30:0:0.19228:9.11:60:4:0.0102:0:1 0/0:211:0:0,0:41,170:0:2,0:23.9:1:31.1:1:1:0:60:104.5:1:0:0.1 -3 138461345 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21871;SOR=Inf;LSEQ=TCTAAAAATGCAGTTGTATT;RSEQ=GGGTAAAAATGAGAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:156,21:0:2,0:23.5:1:30.7:1:1:0:60:43.25:1:0:0.1 0/1:156:2:1,1:124,30:0.0128:2,2:25:1:28:1:0.35897:4.08248:60:4:0.013:0:1 -3 138461381 . TA T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.04979;SOR=0;LSEQ=ATTTATTACAAAATATTTCT;RSEQ=AAAAAATATAATCCTACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:4:2,2:244,74:0.0124:2,2:26:1:28.8:1:0.23761:3.28205:60:8:0.0125:0.0031:0.3 0/0:358:0:0,0:253,105:0:2,0:23.5:1:28.5:1:1:0:60:357:1:0:0.1 -3 138474572 . C CT 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.72802;SOR=0.66593;LSEQ=AGATATATTAAGAATTTGTA;RSEQ=TTTTTTTTTATTTTTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:5:3,2:249,65:0.0156:2,2:17.4:1:27.8:1:0.28285:2.54452:60:4:0.0126:0:0.4 0/1:287:3:2,1:219,63:0.0105:2,2:29.7:1:24.7:1:0.53515:1.73424:60:2:0.0071:0:1.7 -3 138474986 . T C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3446;SOR=0.38458;LSEQ=AATTATAGAATATTACAGAA;RSEQ=GGTGAAAATAATAGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:0,18:0,5:0.7826:0,1:23.7:1:29.9:1:1:0:60:36:0.7826:0:1.1 1/0:7:4:0,4:0,3:0.5714:0,0:28.3:1:28.3:1:1:0:60:8:0.5714:0:1 -3 138478246 . AT A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.24788;SOR=Inf;LSEQ=GCAAAACAACCATCAGCCAA;RSEQ=TTTATACCAAGATATGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:14,131:0:2,0:23.5:1:29.8:1:1:0:60:47.333:1:0:0.1 0/1:152:3:2,1:28,121:0.0197:2,2:6:1:27.3:1:0.09956:8.47:60:6:0.0197:0.0132:0.7 -3 138661770 . CACAA C 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.29151;SOR=0;LSEQ=AATTTTCACGCTAGACAAAG;RSEQ=ACAGACATGCACACAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:4,1:18,2:0.2:2,2:17.4:1:30.4:1:0.50435:2.16466:60:10:0.2:0.04:0.2 0/0:10:0:0,0:10,0:0:0,0:13:1:29.8:1:1:0:60:9:1:0:0 -3 138661895 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13879;SOR=Inf;LSEQ=AGCCTCTAGGGCTTCCTGCT;RSEQ=CAGCTGAGCCTCCCTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:193,14:0:2,0:24.1:1:31.2:1:1:0:60:33.5:1:0:0.1 0/1:124:2:1,1:113,9:0.0161:2,2:22.5:1:27.5:1:0.15539:11.96401:60:4:0.0164:0:2 -3 138661896 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14296;SOR=Inf;LSEQ=GCCTCTAGGGCTTCCTGCTC;RSEQ=AGCTGAGCCTCCCTCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:198,15:0:2,0:23.9:1:31.1:1:1:0:60:52.25:1:0:0.1 0/1:130:2:1,1:115,13:0.0154:2,2:23:1:28:1:0.20453:8.55932:60:4:0.0159:0:1 -3 138661897 . A ATCCT 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00837;SOR=Inf;LSEQ=CCTCTAGGGCTTCCTGCTCC;RSEQ=GCTGAGCCTCCCTCTCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:202,16:0:2,0:23.8:1:30.5:1:1:0:60:71.667:1:0:0.1 0/1:138:5:4,1:117,16:0.0362:2,2:18.2:1:31:1:0.48713:1.81832:60:10:0.0373:0.0145:0 -3 138661907 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16591;SOR=Inf;LSEQ=TTCCTGCTCCAGCTGAGCCT;RSEQ=CCTCTCCATCCTGCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:231,36:0:2,0:22.8:1:31.2:1:1:0:60:65.75:1:0:0.2 0/1:184:2:1,1:149,33:0.0109:2,2:7:0:31.5:1:0.33624:4.46317:60:4:0.011:0:1.5 -3 138661990 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19845;LSEQ=CCTGAGAATCCCCGTGGCTT;RSEQ=GTCTCCTGCCTTGTAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:864:235:134,101:364,264:0.272:2,2:26.3:1:28.8:1:0.8167:1.03921:60:46:0.2725:0:1.2 0/1:841:58:31,27:449,332:0.069:2,2:23.2:1:28.9:1:0.5835:1.17767:60:28:0.0679:0:1.3 -3 138662193 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.19103;SOR=Inf;LSEQ=CCACCAGCCGGCCTGGACCT;RSEQ=CCGCCACATTGCTGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:18,190:0:2,0:20.3:1:30.7:1:1:0:59.9:15:1:0:0.4 0/1:162:2:0,2:15,145:0.0123:2,0:22.5:1:27:1:1:0:60:4:0.0125:0:2 -3 138662226 . C CG 100 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.20795;SOR=0.34069;LSEQ=TGGCCAGGCCCCGAGATAGA;RSEQ=GGGGGGGGGGCAGTGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:9:0,9:1,91:0.0882:1,0:32.3:1:31.6:1:1:0:60:18:0.1023:0:0.7 0/1:63:2:0,2:0,59:0.0317:1,0:45:1:30:1:1:0:60:4:0.0345:0:2 -3 138662227 . G GGGGGGGGGGGGT 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.0092;SOR=0;LSEQ=GGCCAGGCCCCGAGATAGAC;RSEQ=GGGGGGGGGCAGTGAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:11:0,11:1,101:0.094:1,0:42:1:25:1:1:0:59.3:22:0.1019:0.0855:0.1 0/0:62:0:0,0:0,60:0:1,0:19.5:1:29.7:1:1:0:59.9:59:0.9672:0:0.5 -3 138662229 . G C 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=CCAGGCCCCGAGATAGACGG;RSEQ=GGGGGGGCAGTGAGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:1,116:0:1,0:22:1:30.9:1:1:0:59.6:57.5:1:0:0.4 0/1:56:8:0,8:0,48:0.1429:1,0:22.4:1:29.5:1:1:0:60:16:0.1429:0:1 -3 138663113 . AC A 85 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.00722;SOR=Inf;LSEQ=GGGAATCGACAAGGCAAAAA;RSEQ=AAAAACAAAACAAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:263,53:0:2,0:21.7:1:32.3:1:1:0:60:632:1:0:0.3 0/1:312:7:6,1:236,69:0.0224:2,2:21.1:1:30.6:1:1:1.75:59.9:14:0.0225:0.0096:1.1 -3 138663179 . A G 254 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=TAGAAAATTTGGTCCCCCAA;RSEQ=CAACAAGCTACAGTACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:791:243:149,94:314,232:0.3072:2,2:28.4:1:32.1:1:0.34749:1.17:60:120.5:0.3082:0:1.1 0/0:789:0:0,0:427,361:0:2,0:26.5:1:29.4:1:1:0:60:97.5:1:0:0.2 -3 138663401 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22304;SOR=Inf;LSEQ=GGACTTGCATCGAAAGATCC;RSEQ=GGGACATTTGTTTTTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:14,124:0:2,0:23.8:1:31.1:1:1:0:60:137:1:0:0.1 0/1:124:2:1,1:13,109:0.0161:2,2:7.5:1:28:1:0.21387:8.12:60:4:0.0164:0:1.5 -3 138664405 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21613;SOR=Inf;LSEQ=GCGCGTCCCTGCATCCTCGC;RSEQ=TCCGTCTGCACCGGCATGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:151,51:0:2,0:23.9:1:29.5:1:1:0:60:27.857:1:0:0.2 0/1:176:2:1,1:118,56:0.0114:2,2:18.5:1:28.5:1:0.54409:2.09746:60:4:0.012:0:1.5 -3 138664517 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.052;SOR=Inf;LSEQ=CATCATGGCGAGCTCGGGCT;RSEQ=CCGGGCACAAGCGAACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:109,234:0:2,0:27.6:1:32.2:1:1:0:60:67.6:1:0:0.2 0/1:315:4:3,1:115,196:0.0127:2,2:14:1:23.8:1:0.14972:5.09:60:8:0.0128:0:1.5 -3 138664596 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48663;SOR=0;LSEQ=GCGGTGGCTGGGCTGGCAGG;RSEQ=CTGAGCTGGCCCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:5,11:0.1111:2,2:27.5:1:31.5:1:1:2.10:60:4:0.125:0:1.5 0/0:16:0:0,0:6,10:0:2,0:11.4:1:31.9:1:1:0:60:32:1:0:0.3 -3 138664682 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.24891;SOR=0;LSEQ=CGCGTGCAGATGGTGTGCGT;RSEQ=CGGATGCGGGTGGGGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:0,3:91,60:0.0195:2,0:7:1:23:1:0.06653:0:60:2:0.0133:0:1 0/0:141:0:0,0:78,62:0:2,0:21.9:1:31.4:1:1:0:60:27:0.9926:0:0.4 -3 138664683 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24964;SOR=0;LSEQ=GCGTGCAGATGGTGTGCGTG;RSEQ=GGATGCGGGTGGGGGTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:1,2:92,62:0.0191:2,2:9.7:1:29.7:1:0.56727:2.94706:60:6:0.0192:0:1.3 0/0:141:0:0,0:79,62:0:2,0:1:0:17:0:1:0:60:0:0:0:2 -3 138664689 . C T 40 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.09647;LSEQ=AGATGGTGTGCGTGCGGATG;RSEQ=GGGTGGGGGTGCGGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:1,2:101,69:0.0173:2,2:8.7:1:28.7:1:0.56875:2.90929:60:6:0.0182:0:1.3 0/1:158:3:0,3:88,67:0.019:2,0:1:0:25.7:1:0.08487:0:60:6:0.0211:0:1.3 -3 138664697 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50072;SOR=0;LSEQ=TGCGTGCGGATGCGGGTGGG;RSEQ=GTGCGGCGGAGGCGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:117,80:0.0101:2,2:15.5:1:26.5:1:1:1.45961:60:4:0.0105:0:1 0/0:175:0:0,0:101,74:0:2,0:22.9:1:30:1:1:0:60:57.333:1:0:0.4 -3 138664700 . G A 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25012;SOR=0;LSEQ=GTGCGGATGCGGGTGGGGGT;RSEQ=CGGCGGAGGCGGGGGTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:3:3,0:116,80:0.0151:2,0:14.7:1:20.3:1:0.27516:0:60:2:0.0104:0:2.7 0/0:179:0:0,0:104,74:0:2,0:23.5:1:30.9:1:1:0:60:24.429:0.9942:0:0.4 -3 138664707 . A C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0025;SOR=Inf;LSEQ=TGCGGGTGGGGGTGCGGCGG;RSEQ=GGCGGGGGTGCGGCCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:131,86:0:2,0:25:1:30.4:1:1:0:60:42.4:0.9953:0:0.3 0/1:199:8:6,2:110,79:0.0402:2,2:19.4:1:31.1:1:0.47458:2.15:60:16:0.0426:0:1.4 -3 138664718 . C T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62357;SOR=0.3412;LSEQ=GTGCGGCGGAGGCGGGGGTG;RSEQ=GGCCGGCGGGCCTCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:139,98:0.0125:2,2:22.7:1:29:1:0.57236:2.82442:60:6:0.013:0:1 0/0:233:1:0,1:131,100:0.0043:2,0:1:0:23:0:0.43534:0:60:2:0.0045:0:1 -3 138664725 . C T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.67803;LSEQ=GGAGGCGGGGGTGCGGCCGG;RSEQ=GGGCCTCCCAGGCCATTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:1,2:142,108:0.0119:2,2:15:1:31:1:0.58126:2.61971:60:6:0.0123:0:1 0/0:248:2:0,2:138,108:0.0081:2,0:16.5:1:20.5:1:0.19574:0:60:1:0.0042:0:1 -3 138664770 . C T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3725;SOR=3.95603;LSEQ=TTCACTACGCCGGGGGGCAG;RSEQ=GCCATGCTCTGCACGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:1:0,1:105,130:0.0042:2,0:1:0:26:0:1:0:60:2:0.0044:0:1 0/1:241:4:2,2:113,122:0.0166:2,2:16.5:1:30.3:1:1:1.08:60:8:0.0175:0:1.3 -3 138664804 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11631;SOR=Inf;LSEQ=CGCGTGTGTACGGCCCGTAC;RSEQ=AGGCGGCCGGGCCCGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:54,97:0:2,0:23.5:1:30.7:1:1:0:60:150:1:0:0.3 0/1:145:3:2,1:56,86:0.0207:2,2:16.7:1:22.7:1:0.56399:3.05:60:2:0.0144:0:1.3 -3 138664810 . G A 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47396;LSEQ=TGTACGGCCCGTACGAGGCG;RSEQ=CCGGGCCCGCCAGCCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:43,81:0.0159:2,2:8:1:29:1:1:1.87:60:4:0.0161:0:1 0/1:129:3:2,1:48,78:0.0233:2,2:17.7:1:27:1:0.55923:3.22:60:6:0.0234:0:1 -3 138664812 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4982;SOR=Inf;LSEQ=TACGGCCCGTACGAGGCGGC;RSEQ=GGGCCCGCCAGCCCCTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:36,79:0:2,0:26.3:1:30.3:1:1:0:60:230:1:0:0.3 0/1:121:2:1,1:43,76:0.0165:2,2:29.5:1:29:0:1:1.76:60:4:0.0169:0:1 -3 138664851 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21611;SOR=Inf;LSEQ=ACCACAGCGGCCGCGCCAGG;RSEQ=CTACCGGGGCCCGCGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:46,34:0:2,0:16.7:1:31.8:1:1:0:60:39:1:0:0.2 0/1:70:2:1,1:36,32:0.0286:2,2:7:0:31.5:1:1:1.1231:60:4:0.0294:0:2 -3 138664885 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21251;SOR=Inf;LSEQ=CGGCTGCAGCCGCAGCTGCT;RSEQ=CAGCCGCTGCGGCTGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:91,23:0:2,0:25:1:32.3:1:1:0:60:113:1:0:0.1 0/1:98:2:1,1:74,21:0.0204:2,2:8:1:27.5:1:0.40399:3.46583:60:4:0.0211:0:1 -3 138664903 . G T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35615;SOR=3.24722;LSEQ=CTGCAGCCGCTGCGGCTGCC;RSEQ=CCATCTGGCAGGAGGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:0,1:112,52:0.0061:2,0:1:0:24:0:0.32121:0:60:2:0.0063:0:1 0/1:154:3:1,2:102,49:0.0195:2,2:27:1:27.7:1:0.2549:4.12133:60:6:0.02:0:1.7 -3 138665029 . G C 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00501;SOR=Inf;LSEQ=AGCCGTCGGCCCCGGCGCCC;RSEQ=CCACGCCGCACCCGCCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:24,53:0:2,0:17.5:1:30.7:1:1:0:59.7:24.667:0.9867:0:0.2 0/1:72:7:3,4:21,44:0.0972:2,2:11.6:1:30.6:1:0.67918:1.56:60:14:0.0972:0:1.1 -3 138665051 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.15269;SOR=Inf;LSEQ=CACGCCGCACCCGCCTGCGG;RSEQ=GCCTCCGGCCCCGAAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:69,30:0:2,0:11.5:1:31.4:1:1:0:60:32:1:0:0.2 0/1:64:2:1,1:36,26:0.0313:2,2:22:0:32:0:1:1.37745:60:4:0.0317:0:1.5 -3 138665064 . G A 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00137;SOR=Inf;LSEQ=CCTGCGGCGCCTCCGGCCCC;RSEQ=AAGAGCCCCTTGCCGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:115,22:0:2,0:16.4:1:30.8:1:1:0:60:274:0.9928:0:0.1 0/1:72:6:4,2:55,11:0.0833:2,2:21.8:1:30.8:1:0.29505:2.46054:60:12:0.087:0:1.2 -3 138665100 . C T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30815;SOR=4.46875;LSEQ=GGCTGGAAGTGCGCGGGCGG;RSEQ=GGCCGGAAGGGCCTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:1:0,1:267,72:0.0029:2,0:1:0:25:0:0.21471:0:60:2:0.003:0:1 0/1:230:3:1,2:161,66:0.013:2,2:23.7:1:29:1:0.20942:4.84038:60:6:0.0134:0:1.3 -3 138665439 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.02388;SOR=Inf;LSEQ=GGCTTCTCCGGGGCTGTCCC;RSEQ=CCGCCACCCCCACCGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:0:0,0:163,355:0:2,0:24.5:1:30.7:1:1:0:60:33.533:1:0:0.1 0/1:337:4:1,3:116,217:0.0119:2,2:31:1:25:1:1:1.60162:60:3:0.0091:0:1.3 -3 138665454 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06107;SOR=Inf;LSEQ=GTCCCGCCGCCACCCCCACC;RSEQ=CCCTTGCCTGGGCTCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:122,309:0:2,0:24.4:1:31:1:1:0:60:32.154:1:0:0.1 0/1:281:3:1,2:94,183:0.0107:2,2:21.7:1:25.3:1:1:1.02722:60:2:0.0073:0:2.3 -3 138665528 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05914;SOR=Inf;LSEQ=CTCTGGGGCCAGCAGGGCCC;RSEQ=CGCCGCGTCCTCGGGCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:34,107:0:2,0:23.5:1:30.4:1:1:0:60:19.143:1:0:0.2 0/1:91:3:2,1:22,66:0.033:2,2:22:1:27:1:0.16888:5.86:60:6:0.0341:0:1.3 -3 138665616 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50909;SOR=0;LSEQ=TCTGCTCTCCGCTCCAGGCG;RSEQ=TGGCGCGGCAAAGAGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:8,17:0.0741:2,2:36:0:30.5:1:1:2.06:60:4:0.08:0:1 0/0:18:0:0,0:7,11:0:2,0:24.6:1:31.6:1:1:0:60:36:1:0:0.1 -3 138666413 . G T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02457;SOR=Inf;LSEQ=CGAGGGGGCTGGACGGGGTA;RSEQ=GGTGGGGAGAGCTGCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:396,90:0:2,0:22.5:1:31.6:1:1:0:60:53:1:0:0.1 0/1:320:4:1,3:261,55:0.0125:2,2:5.3:1:27:1:0.01984:14.06352:60:8:0.0128:0:1 -3 138666707 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14993;SOR=Inf;LSEQ=TAGATGCCCCTCAGCTATTG;RSEQ=ACTAACACAGGCGGGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:5,268:0:1,0:26.2:1:32.2:1:1:0:60:33.125:1:0:0.1 0/1:173:2:0,2:6,165:0.0116:1,0:32.5:1:24.5:1:1:0:60:4:0.0118:0:1 -3 138667669 . G T 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGGGCTCTTTGGAATTCA;RSEQ=CATCTTGAAGATGACACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:123,316:0:2,0:23.9:1:31.9:1:1:0:60:145.333:0.9977:0:0.1 0/1:335:17:6,11:97,221:0.0507:2,2:23.2:1:30.2:1:0.78783:1.24:60:34:0.0515:0:1.2 -3 138667689 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14502;SOR=Inf;LSEQ=GCATCTTGAAGATGACACCA;RSEQ=AGAGGTCAGCAGGGCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:63,263:0:2,0:21:1:31.1:1:1:0:60:107.667:1:0:0.1 0/1:201:2:1,1:43,156:0.01:2,2:6.5:1:27:1:0.39075:3.60:60:4:0.0101:0:1.5 -3 138667699 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14606;SOR=Inf;LSEQ=GATGACACCAGAGAGGTCAG;RSEQ=AGGGCAGCCCTTGCCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:34,219:0:2,0:22.9:1:32.1:1:1:0:60:83.333:1:0:0.1 0/1:157:2:1,1:26,129:0.0127:2,2:23:1:30.5:1:0.31529:4.89:60:4:0.0131:0:1 -3 140596681 . G T 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCTTTGGCAGCAGTGAC;RSEQ=CTCCAAAACTGCCAAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:24:1:31.3:1:1:1.7321:60:6:0.6:0:1.7 0/0:1:0:0,0:0,1:0:0,0:20:0:34:0:1:0:60:2:1:0:1 -3 140596755 . T G 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31561;SOR=4.58929;LSEQ=GCGCCTTCTTAGGGGAAAAG;RSEQ=GTTTTTACACTAACTAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:4,2:5,0:0.5455:0,2:15.2:1:31.3:1:0.45455:0:60:12:0.5455:0:1.3 1/1:7:6:4,2:1,0:0.8571:0,2:25.5:1:30.7:1:1:0:60:12:0.8571:0:1.2 -3 142167976 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTAAAAGGAAATCAAT;RSEQ=GAAGTTGTAAAATGAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:16.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 142168331 . C T 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00699;SOR=1.49214;LSEQ=AAGTTTTCATCAGTAGCTTC;RSEQ=TGTATAAGGTAATGCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:707:571:335,236:75,58:0.8076:2,2:26:1:30.4:1:0.62721:1.10:60:70.375:0.8101:0:1.1 1/1:654:564:311,253:48,41:0.8624:2,2:26.1:1:30.1:1:0.90881:1.05:60:93:0.8611:0:1.1 -3 142171883 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56263;SOR=3.17693;LSEQ=TATTTCCAAGCAGTTCTCAT;RSEQ=CATAGAGATGAGAACTATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:1,0:270,23:0.0034:2,0:6:0:32:0:1:0:60:2:0.0034:0:1 0/1:186:2:1,1:167,17:0.0108:2,2:25:1:30.5:1:0.18466:9.5753:60:4:0.0108:0:1 -3 142177776 . G T 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37545;SOR=0.27059;LSEQ=ATTGAGAGAAAACACAATTA;RSEQ=TAAGAGTAACTCATATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:353:4:1,3:259,90:0.0113:2,2:10:1:29.3:1:0.05764:8.56986:60:8:0.0115:0:1.3 0/0:324:1:1,0:223,100:0.0031:2,0:3:0:28:0:1:0:60:2:0.0031:0:1 -3 142178144 . C T 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=61.2379;LSEQ=GCCTGGGCAGGAGAAATTCT;RSEQ=GGAATACTTTGAGTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:1:0,1:257,289:0.0018:2,0:1:0:25:0:1:0:60:2:0.0019:0:1 0/1:564:57:28,29:250,257:0.1011:2,2:24.8:1:28.6:1:1:1.00749:60:18:0.0973:0:1.1 -3 142178267 . GA G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.51973;SOR=0;LSEQ=ATTAATCACATCAGCCAAAT;RSEQ=AAAAAGGGGCAAAGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:18,146:0.012:2,2:12:0:33:1:0.21643:7.92:60:4:0.0123:0:0.5 0/0:109:0:0,0:10,99:0:2,0:19.3:1:30.1:1:1:0:60:108:1:0:0.1 -3 142183869 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=TGAAATAAAAGCAATCTGGT;RSEQ=TTATAATAGTCAAAAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:156,11:0:2,0:23.8:1:30.1:1:1:0:60:40.75:1:0:0 0/1:174:2:1,1:148,24:0.0115:2,2:8:1:31:1:0.26742:6.06247:60:4:0.0118:0:1 -3 142184161 . T A 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.49946;LSEQ=ATATTATAAACCTTGAGTTA;RSEQ=GTAAAAAAAAAAAAAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:3:2,1:5,113:0.0248:1,2:6.3:1:23.3:1:0.00843:40.36:60:2:0.0174:0:1.7 0/1:80:1:1,0:1,78:0.0125:1,0:1:0:25:0:0.025:0:60:2:0.0133:0:1 -3 142185078 . T C 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCACAAATAAGATTCACG;RSEQ=AGATTTTGTGAAATACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:112,3:0:1,0:25.2:1:29.9:1:1:0:60:114:1:0:0.1 0/1:104:16:15,1:84,4:0.1538:1,1:25.6:1:31.4:1:0.574:1.39498:60:15:0.1471:0:1.1 -3 142185091 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24287;SOR=Inf;LSEQ=ATTCACGTAGATTTTGTGAA;RSEQ=TACACTTTTTATCTTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:148,11:0:2,0:22.7:1:30.1:1:1:0:60:52:1:0:0.1 0/1:155:2:1,1:134,19:0.0129:2,2:9:1:29.5:1:0.24214:6.8995:60:4:0.0131:0:1.5 -3 142185393 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49913;SOR=0;LSEQ=AACCTGAAAAAATAAATAGT;RSEQ=CATTTTAATTTGTTTTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:27,123:0.0132:2,2:33.5:1:29:1:0.33548:4.49:60:4:0.0134:0:1 0/0:140:0:0,0:34,106:0:2,0:22.7:1:31.8:1:1:0:60:45.667:1:0:0.1 -3 142185415 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20338;SOR=Inf;LSEQ=ATTTTAATTTGTTTTTACCT;RSEQ=AAATTCCACTATAACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:15,83:0:2,0:23.1:1:28.6:1:1:0:60:97:1:0:0.1 0/1:81:2:1,1:15,64:0.0247:2,2:23.5:1:29:1:0.35802:4.16:60:4:0.0247:0:1.5 -3 142186894 . C T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04452;SOR=Inf;LSEQ=TTTCCTTGCATCTGTTCACA;RSEQ=GCATGGGATAAGATGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:0:0,0:129,299:0:2,0:24.1:1:30.3:1:1:0:60:84.6:0.9976:0:0.1 0/1:366:4:2,2:134,228:0.0109:2,2:30.8:1:30.5:1:0.6299:1.70:60:8:0.0111:0:1.3 -3 142188088 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=AATACAGGAGAGACGCCCTG;RSEQ=AACTTGTATCTACATATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:2,1:74,1:0.0385:1,2:16:1:30:1:0.07592:30.41285:60:6:0.039:0:1 0/0:66:0:0,0:62,4:0:2,0:21.2:1:31.4:1:1:0:60:65:1:0:0 -3 142188172 . C A 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATATAAAAAGGTAAAAGACC;RSEQ=TTTTACCTTTGACACAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:47:29,18:214,101:0.1298:2,2:22:1:29.9:1:0.40842:1.31405:60:46:0.1281:0:1.2 0/0:353:0:0,0:219,133:0:2,0:25:1:30.6:1:1:0:60:175:0.9972:0:0.1 -3 142188373 . C A 52 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06186;SOR=0;LSEQ=GATAACCTTGTTTATTTTAC;RSEQ=CAAATCATTCCTCATTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:5:3,2:187,284:0.0105:2,2:20:1:22.4:1:0.39246:2.27:60:1.5:0.0065:0:2 0/0:470:0:0,0:188,282:0:2,0:26.9:1:30.3:1:1:0:60:66.143:1:0:0.1 -3 142188413 . T A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12306;SOR=0;LSEQ=ACACGATCGGAGCGGCCAGC;RSEQ=GGGGGAAGAAATAAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:85,200:0.0104:2,2:11.3:1:23.3:1:0.21775:4.68:60:2:0.0072:0:2.3 0/0:290:0:0,0:81,208:0:2,0:21.8:1:29.9:1:1:0:60:47.167:1:0:0.1 -3 142204149 . T C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.08651;SOR=Inf;LSEQ=AAAAAAGAACATAGGATACC;RSEQ=ACCTAAGGAAATCCCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:72,241:0:2,0:24.9:1:28.9:1:1:0:60:77.25:0.9968:0:0.1 0/1:250:3:1,2:64,183:0.012:2,2:27:1:31.3:1:1:1.43:60:6:0.0121:0:1 -3 142210992 . T C 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTACTGCCCTTCTAGTA;RSEQ=GGATATAGAGTAGTTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:26:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 142211868 . CA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.14909;SOR=Inf;LSEQ=TTATATACTCACTGAAAAGT;RSEQ=AAAAAATTTCCTGGTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:90,3:0:1,0:21.8:1:30.8:1:1:0:60:186:1:0:0.1 0/1:59:2:2,0:57,0:0.0339:1,0:14.5:1:30:1:1:0:60:4:0.0339:0.0169:0.5 -3 142211899 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51666;SOR=0;LSEQ=CCTGGTTATTTTTATACATG;RSEQ=GCTTTGCCATATAGACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:156,26:0.0109:2,2:25:1:31:1:0.27263:5.90671:60:4:0.0109:0:1 0/0:125:0:0,0:111,14:0:2,0:24:1:29.8:1:1:0:60:250:1:0:0.1 -3 142212225 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50545;SOR=0;LSEQ=TTTTCTGCAAAAGTATTAGT;RSEQ=CATTATGTTTTTGTACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:0,2:5,136:0.014:1,0:17.5:1:31.5:1:1:0:60:4:0.0143:0:1 0/0:112:0:0,0:4,108:0:1,0:23.6:1:29.2:1:1:0:60:111:1:0:0 -3 142215120 . C CAT 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50693;SOR=1.33874;LSEQ=AGGAAGTACATAATTCCCGA;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:14:14,0:128,6:0.0927:1,1:32.1:1:31.7:1:1:0:53.3:28:0.0959:0:1 0/1:83:10:10,0:65,3:0.1205:1,0:29.6:1:30.9:1:1:0:54.6:20:0.1235:0:1.2 -3 142215121 . TA AT 161 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=29.000;MSILEN=2;SSF=0.00059;SOR=0.26088;LSEQ=GGAAGTACATAATTCCCGAC;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:44:44,0:38,1:0.2304:1,1:29:1:29.6:1:0.46988:0:60:88:0.2353:0:2 0/1:97:7:6,1:58,0:0.0722:1,2:31.3:1:28.9:1:0.10769:0:60:14:0.0737:0:1.6 -3 142215149 . T C 175 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=29.000;MSILEN=2;SSF=0;SOR=0.09743;LSEQ=TATATATATATATATATATA;RSEQ=ATATATATATATATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:46:35,11:128,30:0.2244:2,2:23.4:1:31.7:1:0.53082:1.33893:56.8:45:0.225:0:2.5 0/1:110:3:3,0:80,23:0.0273:2,0:19.3:1:32.7:1:1:0:53.3:6:0.0283:0:4 -3 142215178 . A C 238 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0;SOR=0.37822;LSEQ=ATATATATATATATATATAT;RSEQ=TGATGACATTTCCCTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:317:235:151,84:52,27:0.7413:2,2:22.5:1:30.3:1:0.89195:1.07116:59.1:17.077:0.7525:0:1.8 1/0:279:145:90,55:83,47:0.5197:2,2:14.7:1:30.4:1:0.80313:1.07889:59.1:28:0.5243:0:1.7 -3 142215223 . C T 79 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03979;SOR=7.45873;LSEQ=CTTGGACCAGAGCCACTTTG;RSEQ=CCTTTCCACGTACAGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:742:1:0,1:421,320:0.0013:2,0:1:0:31:0:0.43261:0:60:2:0.0014:0:1 0/1:802:8:1,7:466,328:0.01:2,2:12:1:26.5:1:0.01093:9.92094:60:16:0.0102:0:1.4 -3 142217537 . A G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05481;SOR=1.62226;LSEQ=CTCACTAGTTTCAGTGAGTC;RSEQ=TAAAAAGCTGTGATATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:26:12,14:323,379:0.0357:2,2:30.1:1:29.3:1:1:1.01:60:7.667:0.032:0:1.2 0/1:829:47:27,20:389,391:0.0567:2,2:24.6:1:29.3:1:0.3681:1.36:60:46:0.0559:0:1.1 -3 142217650 . G A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=16.72768;LSEQ=GAAGAGTCAAGAAATGTCAC;RSEQ=GTAGCTGGGTCCAAGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:1,0:54,203:0.0039:2,0:2:0:28:0:0.21318:0:60:2:0.0039:0:1 0/1:261:16:3,13:50,194:0.0613:2,2:21.8:1:30.3:1:1:1.11638:60:32:0.062:0:1.1 -3 142218348 . G T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02285;LSEQ=GGGTTTCACTGTGTTAGCCA;RSEQ=GATGGTCTCGATCTCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:9:9,0:89,0:0.0918:1,0:27:1:31.3:1:1:0:51.4:18:0.0938:0:1 0/1:64:6:6,0:58,0:0.0938:1,0:29.3:1:30.2:1:1:0:51:12:0.0984:0:1.2 -3 142218624 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=GGTGACATTCAGAGATTTTT;RSEQ=ATTGGTTTACATACTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:16,162:0:2,0:25.5:1:32.2:1:1:0:60:58.333:1:0:0.1 0/1:191:2:1,1:13,175:0.0105:2,2:19:1:29.5:1:0.1423:13.01:60:4:0.0106:0:1 -3 142218675 . T A 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01047;SOR=0;LSEQ=ATTGAATTTGCATTATATTG;RSEQ=ATTTTGTTCTTAGATATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:8:0,8:1,72:0.0988:1,0:11.3:1:29.5:1:1:0:60:7:0.0921:0:1.3 0/0:61:0:0,0:3,58:0:1,0:24.3:1:28.5:1:1:0:60:122:1:0:0.1 -3 142220845 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATGATACACCCGCCTTGGCC;RSEQ=CCCAGAGTGCTGCAATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:45:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30:1:1:0:60:4:1:0:1 -3 142221956 . A G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGAGCCTCACCAATAGCC;RSEQ=GTGGGTTCTAGAAGTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:4.3:1:30.3:1:1:0:60:6:0.75:0:1 1/1:2:2:1,1:0,0:1:0,2:12.5:1:28.5:1:1:0:60:4:1:0:1 -3 142222056 . G GA 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54965;SOR=3.59652;LSEQ=CTGACTATGAAAAACTTGAG;RSEQ=AAAAAAAAATGTTGGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:1:1,0:44,0:0.0222:1,0:17:0:32:0:1:0:60:2:0.0227:0:0 0/1:26:2:2,0:24,0:0.0769:1,0:44:1:29:1:1:0:60:4:0.0769:0:0 -3 142222074 . C T 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.15746;LSEQ=AGGAAAAAAAAATGTTGGTG;RSEQ=TTATCTCCAATACCATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:40:40,0:18,0:0.6897:1,1:22.8:1:30.1:1:1:0:60:80:0.6897:0:1.1 0/1:47:12:12,0:35,0:0.2553:1,0:23.1:1:29.1:1:1:0:60:24:0.2609:0:1 -3 142222090 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=GGTGCTTATCTCCAATACCA;RSEQ=GAAAACACATAAAACATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:73,0:0.0267:1,2:10:1:31:1:0.02667:0:60:4:0.0274:0:1.5 0/0:65:0:0,0:64,1:0:1,0:22.6:1:30:1:1:0:60:130:1:0:0.2 -3 142222124 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49981;SOR=0;LSEQ=ACATTTATTACTCTACTAAA;RSEQ=ATTAAATTACCCAATTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:133,17:0.0132:2,2:9.5:1:29.5:1:0.22351:7.63155:60:4:0.0132:0:1 0/0:136:0:0,0:120,16:0:2,0:23.6:1:30.9:1:1:0:59.9:135:1:0:0.1 -3 142222148 . TA T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.24894;SOR=Inf;LSEQ=AAATTACCCAATTCACTAAC;RSEQ=AAAATTCTCCATTCAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:162,49:0:2,0:26.4:1:28.6:1:1:0:60:422:1:0:0.1 0/1:224:3:1,2:173,48:0.0134:2,2:23.3:1:28.7:1:0.12593:7.12427:60:6:0.0134:0.0045:0.3 -3 142222284 . A G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16395;LSEQ=ATGGACTTTACTACACCATG;RSEQ=TAATGAATGATCTAGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:429:264:96,168:72,93:0.6154:2,2:23.7:1:31.5:1:0.15466:1.35384:60:51.8:0.6123:0:1.1 0/1:458:95:30,65:141,222:0.2074:2,2:25.6:1:31.2:1:0.23343:1.37519:60:94:0.2084:0:1 -3 142223906 . CA C 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.63019;SOR=0.40231;LSEQ=AAAAACAAAACAAAACAAAA;RSEQ=AAAAAAACTAAGGTTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:192,26:0.0136:2,2:20:1:31.9:1:0.32485:3.65894:60:6:0.0138:0.0045:0 0/0:182:1:1,0:160,21:0.0055:2,0:15:0:33:0:1:0:60:2:0.0056:0:0 -3 142226705 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50691;SOR=0;LSEQ=ATAAAACATTCAATAAAATG;RSEQ=ACAACATAAACATAAAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:115,9:0.0159:2,2:26:1:29:1:0.15302:12.1748:60:4:0.016:0:1 0/0:96:0:0,0:80,16:0:2,0:23.7:1:28.9:1:1:0:60:95:1:0:0.1 -3 142226734 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20965;SOR=Inf;LSEQ=AACATAAAAGACTGGCCACA;RSEQ=TAATTTTCATTATTAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:175,47:0:2,0:23.5:1:30.3:1:1:0:60:73:1:0:0.2 0/1:188:2:1,1:138,48:0.0106:2,2:31.5:1:30.5:1:0.45437:2.8558:60:4:0.0106:0:1 -3 142227152 . T C 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTATAACTTACCTTTCTT;RSEQ=GGACAGTCATTTAATTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:0,11:0.2667:0,0:28.8:1:31.3:1:1:0:60:8:0.2667:0:1 0/0:2:0:0,0:0,2:0:0,0:30:1:32:0:1:0:60:4:1:0:0 -3 142230846 . A G 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGCACCTGTAATCCCA;RSEQ=CTACTTGGGAGGCTGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:16.3:1:32:1:1:0:49.3:6:0.5:0:1 0/0:1:0:0,0:1,0:0:0,0:30:0:31:0:1:0:60:2:1:0:0 -3 142232243 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52431;SOR=0;LSEQ=AACATACATAGCCATACATA;RSEQ=GTCTACATTTCCTACTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:110,4:0.0171:1,2:18:1:30:1:0.08471:24.70868:60:4:0.0174:0:1 0/0:73:0:0,0:71,2:0:1,0:23.4:1:31.7:1:1:0:60:72:1:0:0 -3 142233990 . T C 60 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TACAATATAAAAGGAATAAA;RSEQ=GTAATTTTACACACACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:21.5:1:30.3:1:1:0:60:8:1:0:1 1/0:2:1:1,0:1,0:0.5:0,0:22:0:33:0:1:0:60:2:0.5:0:1 -3 142234534 . G A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01068;SOR=Inf;LSEQ=GTCATTCTTGGACACCTAAA;RSEQ=TACTTCTAAGGATTTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:0,20:0:1,0:25.5:1:32.1:1:1:0:60:40:1:0:0.5 0/1:7:3:0,3:0,4:0.4286:0,0:16.7:1:31.3:1:1:0:60:6:0.4286:0:1.3 -3 142234589 . C A 92 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=CCTCAGATCCTTCCAACTCT;RSEQ=TTCTTATATAAGAAAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:0.7273:0,0:25.3:1:30.9:1:1:0:60:16:0.7273:0:1.9 0/0:1:0:0,0:0,1:0:0,0:1:0:30:0:1:0:60:2:1:0:0 -3 142237274 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACTGAGGCAGGAGAATC;RSEQ=CTTGAACCCAGGAGGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:29.5:1:1:0:60:4:1:0:1.5 -3 142238145 . AT A 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATATCAAAAATCACATTA;RSEQ=TTTTTTTTTTTTTTCCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19.5:1:32.5:1:1:0:55:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 142238441 . CA C 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.55639;LSEQ=CGTGAGCCACTGCACCCGGC;RSEQ=AAAAAATCGCATTATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:112,8:0.0163:2,2:23:1:27.5:1:0.14266:13.25815:60:4:0.0164:0.0081:0.5 0/0:110:1:1,0:94,15:0.0091:2,0:17:0:32:0:1:0:60:2:0.0091:0:0 -3 142238771 . GT G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53846;SOR=0;LSEQ=ATTTATGCTTCATGGATGCT;RSEQ=TTTTTTTGTCTGTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:0,2:0,32:0.0588:1,0:21:1:33.5:1:1:0:60:4:0.0606:0:0.5 0/0:18:0:0,0:1,17:0:1,0:23.6:1:31.4:1:1:0:60:36:1:0:0.1 -3 142239107 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTCATATTTCCAAAGAC;RSEQ=TAAGAATATTGAAATTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:43:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 142241690 . C CA 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03087;SOR=0;LSEQ=TCTTCTACTCCAGTCTCAAT;RSEQ=AGAAAAAAAAAAAAGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:6:1,5:170,360:0.0112:2,2:26.8:1:25.8:1:0.66982:2.35799:60:5:0.01:0.0056:1.7 0/0:526:0:0,0:185,340:0:2,0:22.6:1:29.8:1:1:0:60:17.75:0.998:0:0.3 -3 142241692 . GA G 162 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.44144;SOR=0.79868;LSEQ=TTCTACTCCAGTCTCAATCA;RSEQ=AAAAAAAAAAAGAAAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:36:10,26:142,304:0.0738:2,2:26.7:1:31.4:1:0.71115:1.21397:60:72:0.0747:0.002:0.3 0/1:485:29:11,18:154,296:0.0598:2,2:29.4:1:30.3:1:0.69023:1.17:60:58:0.0608:0.0021:0.1 -3 142241705 . G A 69 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.81244;SOR=0.80871;LSEQ=TCAATCAGAAAAAAAAAAAA;RSEQ=AAAATTCCAGGATAACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:10:9,1:89,292:0.0256:2,2:9.7:1:20.8:1:2e-05:29.25:60:1.5:0.0172:0:1.1 0/1:385:8:8,0:107,269:0.0208:2,0:11.3:1:16.4:1:5e-05:0:60:0.6:0.009:0:1.6 -3 142242788 . C T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11054;SOR=Inf;LSEQ=TAAATGAAATATATAAACCT;RSEQ=AATAGGACAGAGAACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:237,61:0:2,0:21.9:1:31.2:1:1:0:60:58.6:1:0:0.1 0/1:276:3:1,2:206,67:0.0109:2,2:7.3:1:25:1:0.15522:6.09897:60:6:0.011:0:1 -3 142243092 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21578;SOR=Inf;LSEQ=GTAATTTCTACAAACTAGTA;RSEQ=GTTTTCCTGAGCTAGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:9,108:0:2,0:22:1:30:1:1:0:60:38:1:0:0.1 0/1:102:2:2,0:10,90:0.0196:2,0:10:1:28.5:1:0.01281:0:60:4:0.0202:0:1 -3 142255076 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49892;SOR=Inf;LSEQ=TGGAATAAAAAGAATTATTT;RSEQ=CCAAGAATATGAATACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:27,126:0:2,0:23.1:1:32.1:1:1:0:60:75.5:1:0:0.1 0/1:163:2:1,1:34,127:0.0123:2,2:41:1:30.5:1:0.38438:3.70:60:4:0.0123:0:2 -3 142255080 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=ATAAAAAGAATTATTTGCCA;RSEQ=GAATATGAATACTAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:24,118:0:2,0:23.3:1:31.1:1:1:0:60:141:1:0:0.1 0/1:150:2:1,1:28,120:0.0133:2,2:19:1:29:1:0.35034:4.23:60:4:0.0136:0:1 -3 142255090 . T C 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATTTGCCAAGAATATGAA;RSEQ=ACTAAAAAAATGTAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:17,103:0:2,0:22.9:1:28.8:1:1:0:60:119:1:0:0.1 0/1:124:28:6,22:17,79:0.2258:2,2:25.6:1:31.5:1:0.78251:1.26:60:56:0.2276:0:1.3 -3 142257269 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49905;SOR=0;LSEQ=TACCATCAGTAATTTTGAGA;RSEQ=ATAAAAATACAGTTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:152,21:0.0114:2,2:20.5:1:26:1:0.23626:7.09472:60:4:0.0116:0:1 0/0:164:0:0,0:142,22:0:2,0:22.2:1:31:1:1:0:60:53.667:1:0:0.1 -3 142259898 . C G 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TATAGAGTTAAGTAGTGCTT;RSEQ=AGAGTAAAGCTTATAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:51,225:0:2,0:22.3:1:31.5:1:1:0:60:38.429:1:0:0.1 0/1:266:13:3,10:61,192:0.0489:2,2:22.1:1:30.2:1:1:1.05879:60:26:0.0494:0:1.1 -3 142259937 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22002;SOR=Inf;LSEQ=ATGCTGCCAGAAGCAGATGA;RSEQ=CCCTAAGGACAAGTGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:8,125:0:2,0:27:1:32.2:1:1:0:60:65.5:1:0:0.1 0/1:118:2:1,1:12,104:0.0169:2,2:22:1:24:0:0.20904:8.37:60:4:0.0171:0:3 -3 142261339 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57624;SOR=2.45727;LSEQ=CTAAACTAAAGAAATGAAAC;RSEQ=AATACAATTCCAATTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:39,1:0.0476:1,0:9.5:1:32:1:1:0:60:4:0.0476:0:1 0/1:18:2:2,0:16,0:0.1111:1,0:8.5:1:31:0:1:0:60:4:0.1111:0:1 -3 142261548 . G A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00884;SOR=Inf;LSEQ=AACACTAGAGCTCAGTAACT;RSEQ=CATGTTAAAAAAAGCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:658:0:0,0:303,355:0:2,0:26.9:1:32:1:1:0:60:72.111:1:0:0.1 0/1:762:8:6,2:365,386:0.0105:2,2:13.3:1:24.3:1:0.1686:3.17:60:7:0.0093:0:1.3 -3 142266439 . C T 148 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCTTTTCAAAATAAAAATA;RSEQ=CAACTTAAAATTTAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:30:30,0:23,0:0.566:1,1:25.9:1:30.2:1:1:0:60:9:0.54:0:1 0/0:29:0:0,0:28,1:0:1,0:18.8:1:31.3:1:1:0:60:58:1:0:0.2 -3 142268498 . T A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0838;SOR=Inf;LSEQ=TTGGCAGCAAGATCAGGTAG;RSEQ=AGAACTTGTAATGTCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:114,224:0:2,0:24.7:1:28.5:1:1:0:60:66.6:1:0:0.1 0/1:264:3:2,1:104,157:0.0114:2,2:7.3:1:29.7:1:0.56637:3.01:60:6:0.0114:0:1.7 -3 142268553 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51487;SOR=0;LSEQ=AATTACCAAAAAGTACATTT;RSEQ=TCTGGGTGAAAAAAATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:35,141:0.0112:2,2:39.5:1:31:1:0.3645:3.99:60:4:0.0112:0:1 0/0:124:0:0,0:38,85:0:2,0:23.6:1:31.2:1:1:0:60:122:0.9919:0:0.1 -3 142271797 . A C 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACACACACTGGGGCCTGT;RSEQ=AGGGGGGTGGGGGAAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:40:1:29.3:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 142272275 . A AAC 201 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=13.000;MSILEN=2;SSF=0;SOR=0.29546;LSEQ=AACATACATATGAATACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:101:28,73:103,148:0.273:2,2:31.7:1:30.3:1:0.02078:1.81143:59.5:49.5:0.2829:0.0135:0.8 0/1:341:34:7,27:105,191:0.0997:2,2:30.1:1:27.8:1:0.0886:2.11611:59.4:68:0.1076:0.0117:0.8 -3 142272314 . G A 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00117;SOR=0.52259;LSEQ=ACACACATACACACACATAT;RSEQ=TATCTCCAATATCCCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:237:130:49,81:40,67:0.5485:2,2:23.4:1:29.9:1:1:1.01:59.8:42.333:0.5546:0:1.2 0/1:183:71:23,48:30,82:0.388:2,2:22.8:1:29.6:1:0.50378:1.31:59.6:70:0.3846:0:1.1 -3 142273032 . T C 126 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00695;SOR=0.06042;LSEQ=TAGGAAATTAAAATGGATAC;RSEQ=TATAAATTAAAATTACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:0,16:0,2:0.8889:0,1:27.9:1:31.6:1:1:0:60:15:0.8824:0:1.3 0/1:7:2:0,2:0,5:0.2857:0,0:3.5:1:31:0:1:0:60:4:0.2857:0:1 -3 142273069 . CT C 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTATATTTAATAAATGTCA;RSEQ=TTTTTTTTTTGATATAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:0.2:0,0:16:1:32.5:1:1:0:60:4:0.2222:0.1:1 0/0:1:0:0,0:0,1:0:0,0:25:0:32:0:1:0:60:2:1:0:0 -3 142274003 . AG GT 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGAATCGTCTGAACCC;RSEQ=GAGGCAGAGGTTGCAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:31.3:1:1:0:27:4:1:0:4 -3 142274013 . G T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGAACCCAGGAGGCAGA;RSEQ=GTTGCAGTGAGCCAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:27:4:1:0:4 -3 142274026 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAGAGGTTGCAGTGAGC;RSEQ=AAGATGGCGCCATTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:32:0:1:0:27:4:1:0:4 -3 142274049 . G C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGCGCCATTGTACTTCA;RSEQ=CCTGGGCAACAAGAGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:31:1:1:0:27:4:1:0:4 -3 142274534 . C T 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43315;SOR=0.42867;LSEQ=AAAATCCCAAAATCACCTCT;RSEQ=CTACCAGTTTTGTGATGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:12,0:10,0:0.5455:0,0:26.8:1:30.6:1:1:0:60:24:0.5455:0:1.1 0/1:9:3:3,0:6,0:0.3333:0,0:12.7:1:29.3:1:1:0:60:6:0.3333:0:1.3 -3 142274660 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.26157;SOR=0;LSEQ=TTCAGTCTAATTCTTTTACT;RSEQ=ATTTGAAAAGCAGAGCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:3:1,2:168,49:0.0136:2,2:16:1:28.3:1:0.13499:6.77942:60:6:0.0137:0:1 0/0:168:0:0,0:114,54:0:2,0:23.4:1:31.1:1:1:0:60:167:1:0:0 -3 142274739 . A AT 166 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.55886;SOR=0.86747;LSEQ=CAAGTTTTACTGGACTAGGT;RSEQ=TTTTTTTTTTCAGTAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:47:29,18:304,156:0.0923:2,2:24.4:1:29.9:1:0.62874:1.20907:60:94:0.0944:0.0177:0.3 0/1:407:33:17,16:241,132:0.0811:2,2:19.5:1:28.1:1:0.13672:1.71604:59.8:15.5:0.0779:0.0344:0.6 -3 142277365 . AAAAT A 179 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=9.000;MSILEN=4;SSF=0.00038;SOR=0.3337;LSEQ=CAGAGTAAGACTCCGTCTCA;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:52:50,2:50,1:0.5049:1,1:19.2:1:31.5:1:1:1.98706:60:104:0.5098:0.233:0.3 0/1:91:23:23,0:62,2:0.2527:1,1:14.8:1:30.9:1:1:0:60:46:0.2556:0.0989:0.2 -3 142277423 . GATAA G 74 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=4;SSF=0.06239;SOR=Inf;LSEQ=GATAGATAGATAGATAGATA;RSEQ=ATAAAACAAACCACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:257,87:0:2,0:23.3:1:30.2:1:1:0:60:171:1:0:0.1 0/1:370:5:4,1:251,113:0.0135:2,2:36.8:1:32:1:1:1.80:60:10:0.0137:0:0 -3 142277536 . A G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.21925;LSEQ=GTGGTCAACTTTAAACAGCC;RSEQ=TCATCAGAATGGGAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:640:382:168,214:117,140:0.5969:2,2:24.7:1:30.8:1:0.74555:1.06443:60:62.667:0.5949:0:1.6 0/1:678:166:79,87:237,275:0.2448:2,2:25.3:1:30.2:1:0.78873:1.05:60:165:0.2452:0:1.6 -3 142277575 . A T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38792;LSEQ=ATCCATGGAAGTGAGAGCAT;RSEQ=CCACATAAATCTTCCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:574:334:128,206:100,140:0.5819:2,2:27:1:30:1:0.43717:1.14927:60:54.667:0.5785:0:1.8 0/1:605:212:90,122:170,223:0.3504:2,2:23.8:1:29.2:1:0.8637:1.03334:60:211:0.3517:0:1.5 -3 142277643 . T A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13424;SOR=Inf;LSEQ=AGAAGCACAAAATAAGTCAT;RSEQ=AATTATAACTTTTCCTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:44,185:0:2,0:24.5:1:28.3:1:1:0:59.9:75.333:1:0:0.4 0/1:291:4:3,1:93,194:0.0137:2,2:7.3:1:23.3:1:0.10655:6.22:60:8:0.0137:0:1.8 -3 142278013 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20831;SOR=Inf;LSEQ=TATTCCAAACACGCACTTAG;RSEQ=CTTCAGGCAAAAAAGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:140,19:0:2,0:22:1:31.5:1:1:0:60:78.5:1:0:0.1 0/1:134:2:1,1:120,12:0.0149:2,2:5:1:28:1:0.18528:9.64765:60:4:0.015:0:1 -3 142278101 . T C 235 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTTGTACTCACCTTGCATA;RSEQ=AAATCAAAGCATCATAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:164:100,64:271,211:0.2539:2,2:26.7:1:32:1:0.31497:1.22:60:53.667:0.2543:0:1.1 0/0:656:0:0,0:375,281:0:2,0:25.6:1:28.8:1:1:0:60:130.2:1:0:0.1 -3 142278201 . T C 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTACAGCTCTTAAGCACTT;RSEQ=TGTGTAAAAATCCAATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:581:0:0,0:250,331:0:2,0:23.3:1:29.9:1:1:0:60:47.417:1:0:0.1 0/1:521:50:21,29:193,278:0.096:2,2:23.1:1:31.9:1:0.88115:1.04:60:100:0.0971:0:1 -3 142278357 . T C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09904;SOR=Inf;LSEQ=AGTCAAACATAAAATTGTAG;RSEQ=AAAGCCAAAAGAAATTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:13,95:0:2,0:25.2:1:28.9:1:1:0:60:216:1:0:0.1 0/1:94:3:0,3:8,83:0.0319:2,0:12.3:1:33:1:1:0:60:6:0.0326:0:1 -3 142279406 . AT A 70 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.73855;SOR=1.41148;LSEQ=AATATCAACTATTCAAAAAA;RSEQ=TTTTTTTTTTTGTGAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:5:0,5:1,50:0.0893:1,0:20.6:1:32:1:1:0:60:10:0.0962:0:0 0/1:41:5:0,5:0,36:0.122:1,0:19.2:1:30.4:1:1:0:60:10:0.125:0.0244:0.2 -3 142280321 . T G 125 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00782;SOR=0.20828;LSEQ=AGAAAATATATTTATATTAT;RSEQ=CATAGGCAGCAAGAATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:16:2,14:6,90:0.1429:2,2:22.4:1:31.4:1:0.32005:2.12:60:32:0.1429:0:1 0/1:90:3:0,3:8,79:0.0333:2,0:18.3:1:29.7:1:1:0:60:6:0.0333:0:1 -3 142280359 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19501;SOR=Inf;LSEQ=TATTAGATGTTAGGTGTTTT;RSEQ=TAGTGAAACTACTTTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:0,55:0:1,0:21:1:32.1:1:1:0:60:26.5:1:0:0.3 0/1:44:2:1,1:1,41:0.0455:1,2:6:0:33:0:0.08985:29.33:60:4:0.0455:0:1.5 -3 142280924 . AG TAGT 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12483;SOR=Inf;LSEQ=AGTAAAAGTCCATAATAGTG;RSEQ=CCAGACTACACTATGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:42,1:0:1,0:25.1:1:30.6:1:1:0:60:86:1:0:0 0/1:24:2:2,0:22,0:0.0833:1,0:24.5:1:32.4:0:1:0:60:4:0.0833:0:0 -3 142281018 . A T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63002;SOR=0.40041;LSEQ=TACATTTTGCACATATGTAT;RSEQ=CAATTAAATGATGAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:194,53:0.012:2,2:5:1:27.7:1:0.12274:7.24306:60:6:0.012:0:1 0/0:207:1:0,1:163,43:0.0048:2,0:1:0:24:0:0.21256:0:60:2:0.0049:0:1 -3 142281612 . A G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42093;LSEQ=CAATAATACGAGTAAGAACC;RSEQ=TTAATAAAGTGACTTCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:524:330:151,179:83,111:0.6298:2,2:22.8:1:31:1:0.5252:1.13:60:109:0.6313:0:1.1 0/1:458:191:90,101:136,129:0.417:2,2:24.1:1:30.2:1:0.39395:1.18268:60:94.5:0.4172:0:1.1 -3 142284987 . G A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAACTGCCTTTGGCCTCAT;RSEQ=GCTTCCACTCACATTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:868:0:0,0:470,398:0:2,0:25.4:1:31.5:1:1:0:60:143.667:1:0:0.1 0/1:872:32:18,14:452,388:0.0367:2,2:23.6:1:29.2:1:0.8577:1.10:60:64:0.0369:0:1.1 -3 142285138 . C A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.62394;SOR=2.9146;LSEQ=TTCATTTTAAAGAGTCATGA;RSEQ=AAATTAAACAATGGTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:1,0:54,235:0.0034:2,0:1:0:28:0:0.18966:0:60:2:0.0034:0:1 0/1:300:3:2,1:74,223:0.01:2,2:10.3:1:29.7:1:0.15908:5.98:60:6:0.0102:0:1 -3 142285165 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24425;SOR=Inf;LSEQ=AACAATGGTCCTTTTGTTAA;RSEQ=AAACCAGACTGTGGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:14,139:0:2,0:24.1:1:31.3:1:1:0:60:152:1:0:0 0/1:150:2:1,1:13,135:0.0133:2,2:5:1:28:1:0.17852:10.04:60:4:0.0137:0:1 -3 142286851 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22823;SOR=Inf;LSEQ=TGCTACTATAATTTATACAT;RSEQ=GAAAAGAAAAGTCTAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:178,39:0:2,0:22.8:1:31.6:1:1:0:60:42.4:1:0:0.1 0/1:199:2:1,1:153,44:0.0101:2,2:40:1:29.5:1:0.40201:3.44952:60:4:0.0104:0:1 -3 142287047 . T A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18268;SOR=1.58856;LSEQ=TAAAGTGACTCAGTTTCATT;RSEQ=GCAAAAAAAATTTCTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:18:2,16:37,179:0.0769:2,2:21.7:1:30.9:1:0.74484:1.65054:60:36:0.0776:0:1.2 0/1:188:22:6,16:35,131:0.117:2,2:20.7:1:29.6:1:0.58255:1.40:60:44:0.1189:0:1 -3 142287049 . CA C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20725;SOR=Inf;LSEQ=AAGTGACTCAGTTTCATTTG;RSEQ=AAAAAAATTTCTCTAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:34,176:0:2,0:24.4:1:30:1:1:0:60:69:1:0:0.2 0/1:176:2:0,2:37,137:0.0114:2,0:18:1:33:1:1:0:60:4:0.0118:0:0 -3 142297576 . G A 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06932;SOR=0.16506;LSEQ=GCGAGGCACTAGTCAACCAC;RSEQ=CCAACGCGGGTTCCCGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:6:4,2:187,355:0.0109:2,2:14.5:1:28.8:1:0.18992:3.79:60:12:0.0112:0:1 0/0:549:1:1,0:222,326:0.0018:2,0:1:0:25:0:0.40619:0:60:2:0.0018:0:1 -3 143592482 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11294;SOR=0;LSEQ=GACATGGAGACTGGTAGTGG;RSEQ=CCCGAATGTCTGGGTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:12,1:0.2353:1,0:29:1:29.3:1:1:0:60:8:0.2353:0:1 0/0:13:0:0,0:11,2:0:2,0:23.9:1:31.4:1:1:0:60:12:1:0:0.1 -3 143592641 . A G 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13736;SOR=Inf;LSEQ=CCGAAGCAGAGAGAGAAGGC;RSEQ=GCATATGTCAGCATATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:7,21:0:2,0:23.7:1:30.3:1:1:0:60:56:1:0:0.1 0/1:40:4:2,2:9,27:0.1:2,2:25:1:30.8:1:0.30031:2.90:60:8:0.1026:0:1.3 -3 143592698 . CT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16304;SOR=0;LSEQ=TAAAGACTTTAAGACTTTCA;RSEQ=TTTTTTTTTACCATTATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,5:0.2:2,2:28:1:30.5:1:1:2.24:60:4:0.2222:0:0 0/0:14:0:0,0:2,12:0:2,0:19.7:1:30.1:1:1:0:60:28:1:0:0.4 -3 143779996 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14773;SOR=Inf;LSEQ=ATAGTTTCTTCTTTATTAGG;RSEQ=CAATAATACACAGTCATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:22.6:1:29.6:1:1:0:60:19:1:0:0 0/1:13:2:1,1:4,7:0.1538:2,2:25:1:27.5:1:1:1.67:60:4:0.1538:0:1 -3 144050136 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CATAGTTCACCTGAAGAACG;RSEQ=ATCTCTATAATGGAAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:1,7:0.2:2,2:7:1:25.5:1:0.37778:5.29:60:4:0.2:0:1 0/0:6:0:0,0:1,5:0:2,0:23.8:1:31.7:1:1:0:60:12:1:0:0.2 -3 144623447 . G C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24548;SOR=Inf;LSEQ=TTGGTATAAGAGTTTGAAAG;RSEQ=TGTTGTCTGATTTCAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:0:2,0:19.8:1:31.7:1:1:0:58.9:46:1:0:0.2 0/1:29:3:1,2:11,15:0.1034:2,2:22.7:1:31.7:1:1:1.44805:60:6:0.1034:0:1 -3 144623474 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16256;SOR=Inf;LSEQ=CTGATTTCAGAAGCCTTTTC;RSEQ=TGTAAATGCCGGGCAGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:21.1:1:31.3:1:1:0:54.1:34:1:0:0.2 0/1:12:2:1,1:1,9:0.1667:2,2:20:1:29:1:0.31818:6.71:41.5:4:0.1667:0:7.5 -3 144623487 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=Inf;LSEQ=CCTTTTCCTGTAAATGCCGG;RSEQ=CAGCATCTCATACTATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:28.6:1:31.9:1:1:0:53.5:28:1:0:0.3 0/1:13:2:1,1:1,10:0.1538:2,2:33:1:28.5:1:0.29487:7.42:41.5:4:0.1538:0:7.5 -3 144623490 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48276;SOR=Inf;LSEQ=TTTCCTGTAAATGCCGGGCA;RSEQ=CATCTCATACTATCCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:29.2:1:31.9:1:1:0:53.5:28:1:0:0.3 0/1:15:2:1,1:3,10:0.1333:2,2:36:1:28.5:1:0.47619:3.03:41.5:4:0.1333:0:7.5 -3 144623492 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48276;SOR=Inf;LSEQ=TCCTGTAAATGCCGGGCAGC;RSEQ=TCTCATACTATCCCTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:29.5:1:29.7:1:1:0:53.5:13:1:0:0.3 0/1:15:2:1,1:3,10:0.1333:2,2:38:1:29.5:1:0.47619:3.03:41.5:4:0.1333:0:7.5 -3 144623509 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19928;SOR=Inf;LSEQ=AGCATCTCATACTATCCCTG;RSEQ=CTGGTTAGTGTAAAAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:28.5:1:28.6:1:1:0:53:12:1:0:0.3 0/1:11:2:1,1:3,6:0.1818:2,2:40.5:1:32:1:1:1.87:41.5:4:0.1818:0:7.5 -3 144623523 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18947;SOR=Inf;LSEQ=TCCCTGACTGGTTAGTGTAA;RSEQ=AACAACACTCTTCCCCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:23.8:1:30.1:1:1:0:51.7:22:1:0:0.2 0/1:9:2:1,1:3,4:0.2222:2,2:29:1:33:1:1:1.29:41.5:4:0.2222:0:7.5 -3 144623530 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47619;SOR=Inf;LSEQ=CTGGTTAGTGTAAAAACAAC;RSEQ=CTCTTCCCCTAAGAAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:20:1:29.9:1:1:0:50.9:20:1:0:0.2 0/1:11:2:1,1:3,6:0.1818:2,2:22:1:31.5:1:1:1.87:41.5:4:0.1818:0:7.5 -3 144624183 . TCTGA T 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTTCCTCTCTCTCTCTCTC;RSEQ=CTTTCTGTCTCTTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:45.5:1:31:0:1:0:60:4:0.6667:0:0 -3 145542203 . GC AT 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06218;SOR=2.52015;LSEQ=TTCTGATCATTTTCCTTCAT;RSEQ=ATTTCAGGAAGCTATCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:22:21,1:31,2:0.4:2,1:22.1:1:29.5:1:1:1.35:45.3:44:0.4074:0.0727:0.9 1/0:27:17:15,2:10,0:0.6296:0,2:26.3:1:28.2:1:0.51567:0:47.2:16:0.6154:0.037:1.1 -3 145542355 . G T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.00037;SOR=0;LSEQ=GACTCTTCCAGTTTTGCCAT;RSEQ=GTAACACTTGTGGGGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:17:8,9:57,74:0.1149:2,2:25.7:1:30.3:1:0.8004:1.15:37:34:0.1172:0:1 0/0:87:0:0,0:42,45:0:2,0:25.4:1:31.7:1:1:0:35.3:174:1:0:0.1 -3 145542411 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19052;SOR=Inf;LSEQ=CCATTCCCTTGATGTCTACA;RSEQ=TATCACCTTTCTTATAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:38,84:0:2,0:27.9:1:30.4:1:1:0:47.2:244:1:0:0.1 0/1:95:2:1,1:45,48:0.0211:2,2:21.5:1:30:1:1:1.07:45.5:4:0.0211:0:1 -3 145542420 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18422;SOR=Inf;LSEQ=TGATGTCTACAATATCACCT;RSEQ=TCTTATAGATTCGCATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:39,88:0:2,0:25.8:1:29.8:1:1:0:49.6:62.5:1:0:0.1 0/1:96:2:1,1:43,51:0.0208:2,2:27:1:30:0:1:1.18:27:4:0.0208:0:1 -3 145542498 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21239;SOR=Inf;LSEQ=TAGAGAACATATATCGGGTG;RSEQ=CTCTCCTCTTTCCCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:38,55:0:2,0:22.1:1:31.8:1:1:0:59.5:92:1:0:0.1 0/1:80:2:1,1:31,47:0.025:2,2:8:1:31.5:1:1:1.51:60:4:0.0253:0:1 -3 145542558 . T G 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00947;SOR=Inf;LSEQ=ACTGGAAGATGGCGGTTCCG;RSEQ=CCAAAAGCTCCTTTTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:35,45:0:2,0:28.2:1:30.1:1:1:0:59.9:160:1:0:0.1 0/1:54:5:2,3:18,31:0.0926:2,2:15.8:1:32.2:1:1:1.15:50.6:10:0.0943:0:1.2 -3 145542567 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13135;SOR=Inf;LSEQ=TGGCGGTTCCGTCCAAAAGC;RSEQ=CCTTTTTGGTTCTGTATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:32,41:0:2,0:25.4:1:30.2:1:1:0:60:72:1:0:0.1 0/1:42:2:1,1:13,27:0.0476:2,2:25:1:28.5:1:1:2.04:60:4:0.0476:0:1 -3 145542604 . T A 56 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06112;LSEQ=TGATGTAATTTGGCTCTGTG;RSEQ=CACCACCCAAATCTCATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:4:0,4:11,23:0.1053:2,0:25.3:1:28:1:0.30258:0:60:8:0.1053:0:1 0/1:9:1:0,1:0,8:0.1111:0,0:34:0:32:0:1:0:60:2:0.1111:0:1 -3 146192553 . C G 76 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CATTCTCCCTGTCTCCTCCT;RSEQ=GTACTCCAATCAATCTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:9:0:32:0:1:0:60:2:1:0:0 1/0:8:6:3,3:1,1:0.75:2,2:23.2:1:29.7:1:1:1:60:12:0.75:0:1.2 -3 146194118 . TG T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCAGCCAAGGGAGGCGC;RSEQ=AGTGTTCATGCTACCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:32.5:1:1:0:60:4:1:0:0 -3 146994528 . C T 27 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58441;SOR=2.56268;LSEQ=ATACAGCCTTTTGGCTGGAA;RSEQ=CGTCATCTTCCAGTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:1:0,1:108,86:0.0051:2,0:1:0:25:0:0.44615:0:60:2:0.0052:0:1 0/1:153:2:1,1:81,70:0.0131:2,2:8:0:27:1:1:1.15603:60:4:0.0132:0:1.5 -3 146994550 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18147;SOR=Inf;LSEQ=GTCATCTTCCAGTAATTTTG;RSEQ=CAAAATGACGAACACAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:117,106:0:2,0:28.5:1:31.3:1:1:0:60:30.857:1:0:0.1 0/1:166:2:1,1:84,80:0.012:2,2:35:0:32:0:1:1.04971:60:4:0.0123:0:1.5 -3 146994559 . C T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07524;SOR=Inf;LSEQ=CAGTAATTTTGCCAAAATGA;RSEQ=GAACACAAAGGGAAAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:110,109:0:2,0:28.6:1:30.8:1:1:0:60:72:1:0:0.1 0/1:161:3:2,1:75,83:0.0186:2,2:31:1:23.7:1:0.60679:2.20:60:2:0.0127:0:1 -3 146994601 . GT G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13507;SOR=Inf;LSEQ=AGGCACCCGATATATGTTCT;RSEQ=AGGCCTTTTAGAAAGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:113,72:0:2,0:22.3:1:29.4:1:1:0:60:184:1:0:0.1 0/1:108:2:1,1:59,47:0.0185:2,2:5.5:1:28:1:1:1.25265:60:4:0.0187:0.0093:0.5 -3 146994746 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08183;SOR=Inf;LSEQ=TGTTACCCAGCATGCTTTTG;RSEQ=CATTGTTGTAAACAAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:99,176:0:2,0:24:1:31.2:1:1:0:59.9:44.833:1:0:0.1 0/1:212:3:2,1:77,132:0.0142:2,2:16.3:1:30:1:0.55707:3.41:54:6:0.0142:0:1 -3 146994754 . G A 31 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.32929;SOR=3.73492;LSEQ=AGCATGCTTTTGGCATTGTT;RSEQ=TAAACAAACAGCAGCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:1,0:79,152:0.0043:2,0:1:0:24:0:0.34483:0:60:2:0.0045:0:1 0/1:188:3:2,1:65,120:0.016:2,2:15:1:20:1:0.28943:3.67:60:2:0.0108:0:1.3 -3 147090929 . T TA 49 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.52381;SOR=3.76419;LSEQ=ATATTGTAGGACAAAGGAGC;RSEQ=AAAAAAAAAAAAAACCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:39:0:32:0:1:0:60:2:0.3333:0:1 1/0:5:3:0,3:0,2:0.6:0,0:23.7:1:31:0:1:0:60:6:0.6:0:2 -3 147308948 . G T 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTAGACGTAAGTCCTTTG;RSEQ=GCGTTTTAGGAGTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:41:0:31:0:0.4:0:60:4:0.5:0:3 0/0:1:0:0,0:0,1:0:0,0:38:0:30:0:1:0:60:2:1:0:8 -3 147309195 . G T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47913;SOR=0.67487;LSEQ=TCTTGCTACCACCTCCAGGG;RSEQ=CAGATTGCCTTCCAGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:20:7,13:6,9:0.5714:2,2:27.7:1:30.2:1:1:1.23051:60:40:0.5714:0:1.2 0/1:36:17:10,7:10,9:0.4722:2,2:29.8:1:29.8:1:0.74857:1.28:60:34:0.4722:0:1.1 -3 147309475 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=ATTCATCCTTTGCACGAGCC;RSEQ=CTAAACTCACCATTCTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:22:1:30.8:1:1:0:60:46:1:0:0 0/1:23:2:1,1:10,11:0.087:2,2:35.5:1:29.5:1:1:1.10:60:4:0.0909:0:1 -3 147309587 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52034;SOR=0;LSEQ=GAAAAGATAGTTTAGGGTCT;RSEQ=AAGGGGCTCATGTCTATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:41,14:0.0351:2,2:7.5:1:27.5:1:0.46053:2.86356:60:4:0.0351:0:1.5 0/0:36:0:0,0:27,8:0:2,0:22.5:1:31.2:1:1:0:60:16.5:1:0:0.1 -3 148294839 . G A 78 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAAATAGACTCTTTGGCA;RSEQ=CAGTGACTCTCCAAAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:19.2:1:30.2:1:1:0:48.7:12:1:0:1 1/1:3:3:3,0:0,0:1:0,0:30.3:1:28.7:1:1:0:46.7:6:1:0:1 -3 148294962 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1124;SOR=Inf;LSEQ=CAGGGATAGTAAGAGATGCT;RSEQ=CCCAGCATTTACGGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:21,9:0:2,0:20.5:1:31.4:1:1:0:59.1:29:1:0:0.2 0/1:29:3:2,1:16,10:0.1034:2,2:16.3:1:25:1:1:1.24:60:2:0.0714:0:1 -3 148295063 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTCTCCCCTTTCTAGG;RSEQ=CCTGTGACAGCCATCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:28,42:0.0278:2,2:13:1:27:1:1:1.49:51.5:4:0.0282:0:1 0/0:26:0:0,0:10,16:0:2,0:26.9:1:28.2:1:1:0:43.2:52:1:0:0 -3 148295212 . G A 94 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21053;SOR=0;LSEQ=CTCAACTAACAACTTCTACC;RSEQ=AGGACCACTGGACCGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:2,7:0,0:1:0,2:20.2:1:29.8:1:1:0:47.4:18:1:0:2.1 1/0:10:7:2,5:1,2:0.7:2,2:27.3:1:30:1:1:1.22183:44.4:14:0.7:0:2.1 -3 148295219 . A C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAACTTCTACCGAGGACC;RSEQ=CTGGACCGACGGGCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:23.7:1:31.1:1:1:0:50.3:14:1:0:2.4 1/1:10:10:3,7:0,0:1:0,2:23.3:1:31.1:1:1:0:49.1:20:1:0:2 -3 148295275 . C T 70 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTCCCCTCTGGAGGACA;RSEQ=TACAACTGCAGGGCCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:29.8:1:30.4:1:1:0:54.8:10:1:0:2.2 1/1:3:3:0,3:0,0:1:0,0:16.3:1:29:1:1:0:60:6:1:0:2 -3 149114614 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTTGTTGGCCTCGTTCA;RSEQ=TTTTCATTCAATTAATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:24:1:33.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 149140381 . A AT 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACTTTGGTGACGGAGTATA;RSEQ=TTTTTTTTTTTTAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:47:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:32:0:1:0:60:4:1:0:0 -3 149140532 . C G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTACAGGCGTGAGCCACCAT;RSEQ=TCTGGCTAATTTTTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:32.5:1:1:0:60:4:1:0:1 -3 149657050 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50084;SOR=Inf;LSEQ=TTCCTCACTGGTGCTTTTTA;RSEQ=CCAGTTTCCTCATCATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:46,52:0:2,0:22.6:1:30.7:1:1:0:60:196:1:0:0.1 0/1:115:2:1,1:55,58:0.0174:2,2:42.5:1:29.5:1:1:1.05:60:4:0.0179:0:1 -3 149657159 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49727;SOR=Inf;LSEQ=CTTTTCTGCCACCTCCGGGG;RSEQ=CAGATCGCTTTCCAGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:51,38:0:2,0:24:1:31.5:1:1:0:60:178:1:0:0 0/1:91:2:1,1:55,34:0.022:2,2:17.5:1:28:1:1:1.60874:60:4:0.022:0:1 -3 149657220 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21189;SOR=0;LSEQ=CTTCTTCATCTTCTGACTCT;RSEQ=CATCTTCCTCCACAGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:80,78:0.0125:2,2:26:0:32:0:1:1.02548:60:4:0.0125:0:1.5 0/0:187:0:0,0:96,91:0:2,0:27:1:31.7:1:1:0:59.5:92.5:1:0:0.2 -3 149657235 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50337;SOR=Inf;LSEQ=ACTCTGCATCTTCCTCCACA;RSEQ=CTACTAAGTGCTGTCCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:80,82:0:2,0:28.4:1:31.9:1:1:0:60:53:1:0:0.1 0/1:197:2:1,1:95,100:0.0102:2,2:43:1:29:1:1:1.05:60:4:0.0103:0:1 -3 149657237 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20043;SOR=0;LSEQ=TCTGCATCTTCCTCCACAGC;RSEQ=ACTAAGTGCTGTCCACTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:77,82:0.0124:2,2:44.5:1:32.5:1:1:1.06:60:4:0.0126:0:1 0/0:198:0:0,0:97,101:0:2,0:25.7:1:29:1:1:0:59.5:48.5:1:0:0.2 -3 149657240 . TA T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50317;SOR=Inf;LSEQ=GCATCTTCCTCCACAGCTAC;RSEQ=AGTGCTGTCCACTAATATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:77,84:0:2,0:28.5:1:29:1:1:0:60:160:1:0:0.1 0/1:195:2:1,1:91,102:0.0103:2,2:25.5:1:29:1:1:1.12:60:4:0.0104:0:1 -3 149657287 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49774;SOR=Inf;LSEQ=CTCTGAAGCACACTTCAACC;RSEQ=TAAGATCACCAGTGGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:45,63:0:2,0:22.2:1:30.7:1:1:0:60:53:1:0:0.1 0/1:110:2:1,1:45,62:0.0182:2,2:8:1:28:1:1:1.37:60:4:0.0185:0:1 -3 149657498 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49827;SOR=Inf;LSEQ=TCATTATTCACCTTAAAGTG;RSEQ=TAATCTTTGTCGGCCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:82,63:0:2,0:25:1:30.2:1:1:0:59.8:47.333:1:0:0.1 0/1:145:2:1,1:68,75:0.0138:2,2:37.5:1:30:1:1:1.10:60:4:0.0138:0:1 -3 149657503 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.91123;LSEQ=ATTCACCTTAAAGTGATAAT;RSEQ=TTTGTCGGCCTTTTGTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:1,0:77,59:0.0073:2,0:1:0:24:0:1:0:60:2:0.0074:0:1 0/1:144:2:1,1:69,73:0.0139:2,2:23.5:1:27:1:1:1.06:60:4:0.0139:0:1 -3 149657555 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24283;SOR=Inf;LSEQ=TAGTTCTGGGGCCTCAGAGG;RSEQ=CTCATGTCCATGTCCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:68,55:0:2,0:20.8:1:31.4:1:1:0:60:122:1:0:0.1 0/1:120:2:1,1:64,54:0.0167:2,2:23:1:29.5:1:1:1.1835:60:4:0.0168:0:1 -3 149657610 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50315;SOR=0;LSEQ=GGTGACACGCACTTAGGTGG;RSEQ=AGAGAAGGTGGACAGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:89,91:0.011:2,2:19.5:1:28.5:1:1:1.02:60:4:0.011:0:1.5 0/0:150:0:0,0:75,75:0:2,0:26.8:1:30.8:1:1:0:60:300:1:0:0.1 -3 149657626 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.5061;SOR=0;LSEQ=GTGGGAGAGAAGGTGGACAG;RSEQ=GATAAACGACTGCTGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:81,98:0.011:2,2:22:1:32.5:1:1:1.21:60:4:0.0113:0:1 0/0:142:0:0,0:64,78:0:2,0:28.4:1:29.5:1:1:0:60:46.333:1:0:0.1 -3 149657634 . G T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50849;SOR=0;LSEQ=GAAGGTGGACAGAGATAAAC;RSEQ=ACTGCTGCTCCAGAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:78,97:0.0113:2,2:23:0:28:1:1:1.24:60:4:0.0117:0:1 0/0:133:0:0,0:58,75:0:2,0:28.7:1:30.2:1:1:0:60:43.333:1:0:0.1 -3 150742609 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24917;SOR=Inf;LSEQ=AGTCCAGATTCAAGAGGAGG;RSEQ=CAAATAAGTTCCACCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:183,54:0:2,0:24:1:31.2:1:1:0:60:58.25:0.9957:0:0.2 0/1:253:3:2,1:176,74:0.0119:2,2:23.3:1:26.3:1:1:1.18832:60:6:0.0121:0:1 -3 150742677 . A G 254 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=2.23215;LSEQ=GAGGGGAGAAACTGATGGGA;RSEQ=CCATATTTGAGGACTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:154:82,72:190,167:0.3014:2,2:30.3:1:32.1:1:1:1.00:60:76:0.301:0:1.1 0/1:540:265:141,124:135,139:0.4907:2,2:26.7:1:31.6:1:0.38907:1.17:60:87.333:0.4925:0:1.1 -3 153741490 . C G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68017;SOR=0.51492;LSEQ=ATGTCATCCTTTTATACCAT;RSEQ=AGATCTCAGAGAGAGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:6,0:0.5714:0,0:26.4:1:31.9:1:1:0:60:16:0.5714:0:1 0/1:10:4:4,0:6,0:0.4:0,0:20.3:1:31.8:1:1:0:60:8:0.4:0:1 -3 153741556 . A C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10231;SOR=Inf;LSEQ=CAACAATATAAAAATTAATA;RSEQ=CTGCAGAATCAAAGCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:48,18:0:2,0:22.6:1:30.3:1:1:0:60:132:1:0:1 0/1:59:3:2,1:41,15:0.0508:2,2:13:1:30.3:1:1:1.359:60:6:0.0508:0:1.7 -3 153741592 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49803;SOR=Inf;LSEQ=TACAAAAATAGCTCTTTCAG;RSEQ=CAGAACCACCATCTTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:74,47:0:2,0:26.9:1:31.3:1:1:0:60:59.5:1:0:1.5 0/1:124:2:1,1:69,53:0.0161:2,2:21.5:1:28:1:1:1.29908:60:4:0.0164:0:1.5 -3 153741599 . CA TG 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4982;SOR=Inf;LSEQ=ATAGCTCTTTCAGCCAGAAC;RSEQ=CCATCTTCCAGTAATTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:74,49:0:2,0:28.2:1:31.1:1:1:0:60:40:1:0:1.5 0/1:128:2:1,1:70,56:0.0156:2,2:25:1:29.5:1:1:1.2478:60:4:0.0156:0.0078:1.5 -3 153741618 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23537;SOR=0;LSEQ=CCACCATCTTCCAGTAATTC;RSEQ=CCAAAATGACGAACACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:64,56:0.0163:2,2:30:1:31:0:1:1.1416:60:4:0.0169:0:2 0/0:130:0:0,0:65,65:0:2,0:30:1:29.4:1:1:0:59.5:129:1:0:1.6 -3 153741628 . C T 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00657;SOR=3.09261;LSEQ=CCAGTAATTCACCAAAATGA;RSEQ=GAACACAAAGGGAAACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:118:96:49,47:9,13:0.8136:2,2:26.9:1:30.6:1:0.48061:1.50:60:192:0.8205:0:2.3 1/1:131:122:56,66:4,5:0.9313:2,2:27.3:1:29.7:1:1:1.06:59.4:121:0.9308:0:1.8 -3 153741637 . A C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19302;LSEQ=CACCAAAATGACGAACACAA;RSEQ=GGGAAACAGGAGAGTCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:117:87:43,44:12,18:0.7436:2,2:21.8:1:30.8:1:0.40348:1.46:60:174:0.75:0:2.4 0/1:126:45:20,25:34,47:0.3571:2,2:25:1:29.9:1:0.85186:1.10:58.4:44:0.3577:0:2.4 -3 153741644 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24428;SOR=0;LSEQ=ATGACGAACACAAAGGGAAA;RSEQ=AGGAGAGTCACCTGATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:51,55:0.0185:2,2:10.5:1:31.5:1:1:1.08:60:4:0.0187:0:3 0/0:110:0:0,0:45,64:0:2,0:23.8:1:31.4:1:1:0:60:218:0.9909:0:1.8 -3 153741680 . C T 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01875;SOR=5.60962;LSEQ=TAATTGTTCTCTTGGCCTTT;RSEQ=AGAAAACATAGAATTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:66:33,33:2,9:0.8571:2,2:25.3:1:29.6:1:0.05837:4.42:60:132:0.8571:0:1.9 1/1:70:68:29,39:0,2:0.9714:0,2:19.2:1:29.1:1:0.50766:0:60:67:0.971:0:1.9 -3 153741705 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18007;SOR=Inf;LSEQ=AACATAGAATTGTTCCTTTG;RSEQ=CCACATACATGGGAATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:43,35:0:2,0:25.7:1:31.9:1:1:0:60:77:1:0:1.1 0/1:58:2:1,1:31,25:0.0345:2,2:23:0:31:1:1:1.23537:60:4:0.0351:0:1 -3 153741735 . G A 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGAATCCACAAGAAAGGC;RSEQ=ATATTGTAGACATCAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:53,29:0:2,0:24.1:1:30.4:1:1:0:60:26.333:1:0:0.5 0/1:78:20:13,7:43,15:0.2564:2,2:21.7:1:31:1:0.56514:1.53464:60:40:0.2632:0:1.4 -3 153741861 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24295;SOR=Inf;LSEQ=GCATTGTTCTAAACAAACAA;RSEQ=GGCAGGATTCTTGCCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:41,84:0:2,0:17.7:1:30.9:1:1:0:60:124:1:0:0.1 0/1:122:2:1,1:33,87:0.0164:2,2:34.5:1:29.5:1:0.48137:2.61:60:4:0.0164:0:1.5 -3 153741874 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21963;SOR=0;LSEQ=CAAACAAGGGCAGGATTCTT;RSEQ=CCAAGAGAATTAATGTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:17,60:0.0253:2,2:9.5:1:27:1:0.40604:3.46:60:4:0.0256:0:1 0/0:89:0:0,0:16,73:0:2,0:23.1:1:32:1:1:0:60:178:1:0:0 -3 153742413 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGTTCCCCTCTCTGTGTC;RSEQ=ATGTTTTCTCATTGTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:28.5:1:1:0:60:4:1:0:3 -3 153742415 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTCCCCTCTCTGTGTCCA;RSEQ=GTTTTCTCATTGTTCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29.5:1:1:0:60:4:1:0:3 -3 153742440 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCATTGTTCAGCTCCCAC;RSEQ=TAGACTGAGAACATGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:31.5:1:1:0:60:4:1:0:3 -3 154880370 . C T 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10467;SOR=1.2781;LSEQ=AACCTCTTTTCATATGCTTG;RSEQ=CTGGTTCTTGAACAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:124:71,53:183,165:0.2622:2,2:27.6:1:29.6:1:0.40206:1.21:60:61:0.2607:0:1.1 0/1:429:134:72,62:162,133:0.3124:2,2:24.3:1:28.7:1:0.83488:1.04879:60:43.667:0.3104:0:1.1 -3 155180003 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16338;SOR=0;LSEQ=TGTTGCTACCACAATGGGGG;RSEQ=AGAGAGGAGTACATCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:17,10:0.069:2,2:25.5:1:28.5:1:1:1.66781:60:4:0.069:0:1 0/0:42:0:0,0:25,17:0:2,0:26.2:1:31.5:1:1:0:60:84:1:0:0.1 -3 155180082 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49463;SOR=Inf;LSEQ=CCAGTGAAACTTGTAAATGG;RSEQ=CACCTGCAGCAACTATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:11,24:0:2,0:21.9:1:31.4:1:1:0:60:34:1:0:0.1 0/1:39:2:1,1:13,24:0.0513:2,2:28:1:30.5:1:1:1.82:60:4:0.0513:0:1 -3 155180174 . G A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=ACTACTGACTGAAGATGTGG;RSEQ=AAATAAGAATAGGTGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:19:1:31.5:1:1:0:60:4:0.5:0:1 0/1:4:1:0,1:0,3:0.25:0,0:14:0:31:0:1:0:60:2:0.25:0:1 -3 155829057 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05303;SOR=Inf;LSEQ=TATTTAAACAAAGCTCTTAA;RSEQ=ATAACAACGTGGTTAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:0:1,0:22.3:1:31.3:1:1:0:60:50:1:0:0.1 0/1:8:2:2,0:5,1:0.25:2,0:8:1:31.5:1:1:0:60:4:0.2857:0:2 -3 155829059 . T A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04234;SOR=Inf;LSEQ=TTTAAACAAAGCTCTTAAAA;RSEQ=AACAACGTGGTTAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:0:1,0:23.6:1:32.2:1:1:0:60:50:1:0:0.1 0/1:7:2:2,0:5,0:0.2857:0,0:10:1:31:0:1:0:60:4:0.2857:0:2 -3 155829377 . T C 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00074;SOR=1.53575;LSEQ=TTGATGTGTCTGTGAAGTGG;RSEQ=AGGAAAAATGTCTTCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:269:112,157:125,170:0.477:2,2:24.9:1:32:1:0.86483:1.03068:60:66.25:0.4741:0:1.1 1/0:473:276:116,160:88,105:0.5835:2,2:23.7:1:32.1:1:0.4506:1.15563:60:552:0.5872:0:1.1 -3 155829458 . G A 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17703;SOR=5.04797;LSEQ=AGTGACATTTTGGGAAGGCT;RSEQ=CTGTCTTGTAGATTTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:0,1:165,203:0.0027:2,0:36:0:32:0:1:0:60:2:0.0028:0:1 0/1:295:4:3,1:125,166:0.0136:2,2:10.8:1:24.3:1:0.31999:3.97:60:8:0.0137:0:1 -3 155829701 . C G 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGTTCTGCTAAATCTATA;RSEQ=TCATAAGGTCATCAGCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:0:0,0:265,368:0:2,0:24.2:1:31.8:1:1:0:59.8:62.3:1:0:0.1 0/1:581:26:14,12:242,312:0.0448:2,2:25.8:1:31.8:1:0.31986:1.50:60:52:0.0454:0:1.2 -3 155829782 . T C 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCCCTGTTAATAGCCTCA;RSEQ=GGACGTCATCATCTTCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:49,190:0:2,0:23.1:1:30.3:1:1:0:60:46.8:1:0:0.2 0/1:156:16:6,10:35,105:0.1026:2,2:19.6:1:29.5:1:0.36719:1.79:60:32:0.1039:0:1.4 -3 155829829 . T A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTGTCTGTTTTCTCTGAA;RSEQ=CGACATACTTCCTCATTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:36,102:0:2,0:22:1:30:1:1:0:60:45:1:0:0.6 0/1:91:13:6,7:21,57:0.1429:2,2:21.2:1:29.5:1:0.19432:2.30:60:26:0.1494:0:1.7 -3 155829855 . C T 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09982;SOR=1.59785;LSEQ=TACTTCCTCATTGATTTTAT;RSEQ=TTCTAGGGCATCAATATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:48:10,38:21,47:0.4138:2,2:22.7:1:30.4:1:0.28847:1.69027:60:96:0.4486:0:1.8 1/0:98:52:16,36:20,26:0.5306:2,2:25.4:1:29.4:1:0.21376:1.721:60:25:0.5747:0:2 -3 155829895 . T TG 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22212;SOR=0.4058;LSEQ=CGTTCTTAAAGAAAATGCTG;RSEQ=GTTTTTTTTTTTTGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:8:2,6:23,60:0.087:2,2:35.9:1:28.6:1:1:1.14827:60:7:0.0833:0:2.8 0/1:81:3:1,2:26,51:0.037:2,2:26.3:1:30:1:1:1.01936:60:6:0.04:0:1 -3 155829896 . GT G 74 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.21757;SOR=0.22244;LSEQ=GTTCTTAAAGAAAATGCTGT;RSEQ=TTTTTTTTTTTGTTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:5:1,4:16,46:0.0556:2,2:27.4:1:32.3:1:1:1.3849:60:10:0.0568:0.0222:1.6 0/1:78:1:0,1:16,31:0.0128:2,0:48:0:32:0:1:0:60:2:0.013:0:0 -3 155829897 . T G 150 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.17881;SOR=1.62646;LSEQ=TTCTTAAAGAAAATGCTGTG;RSEQ=TTTTTTTTTTTGTTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:23:6,17:16,46:0.2556:2,2:25.9:1:30.6:1:1:1.01:57.7:10.5:0.2386:0:2.7 0/1:78:28:7,21:16,31:0.359:2,2:29:1:31.4:1:0.45016:1.53955:60:56:0.3636:0:3 -3 155829917 . G T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.09179;SOR=Inf;LSEQ=TTTTTTTTTTTTGTTTTTTT;RSEQ=TTTTTTTTTGTGTTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:19,53:0:2,0:16.9:1:29.7:1:1:0:59.1:7:0.9844:0:1.6 0/1:61:3:3,0:15,42:0.0492:2,0:10.3:1:20.3:1:0.02385:0:60:2:0.0377:0:2.3 -3 155829925 . T G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.68094;SOR=1.21971;LSEQ=TTTTGTTTTTTTGTTTTTTT;RSEQ=TGTGTTTTTTTGAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:19:2,17:9,23:0.3654:2,2:19.9:1:29.6:1:0.1761:3.25626:57.5:5.333:0.3404:0:3.3 0/1:46:19:5,14:8,19:0.413:2,2:13:1:29.6:1:1:1.17476:59.6:8.5:0.3864:0:3.4 -3 155829938 . A C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57542;SOR=0.68344;LSEQ=TTTTTTTTTGTGTTTTTTTG;RSEQ=GACAGAGTCTCTCTCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:2,12:5,14:0.4242:2,2:17.2:1:24.9:1:0.66975:2.09577:58:3.667:0.3929:0:3.3 0/1:21:7:1,6:3,11:0.3333:2,2:10.3:1:29.6:1:1:1.60054:59:14:0.3684:0:3.7 -3 155829952 . T A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.02311;SOR=Inf;LSEQ=TTTTTGAGACAGAGTCTCTC;RSEQ=CTGTCACCCAGGCTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:7,18:0:2,0:25.1:1:29.4:1:1:0:57.1:11.5:1:0:1.3 0/1:11:3:0,3:1,7:0.2727:2,0:11.3:1:29.3:1:1:0:60:6:0.3:0:2.7 -3 155830077 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=TACAGGCGCCTGCCACCATG;RSEQ=CCAGCTAATTTTTTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:19,2:0:2,0:26:1:30:1:1:0:59.8:42:1:0:0.1 0/1:12:2:2,0:10,0:0.1667:0,0:20:1:33:0:1:0:60:4:0.1667:0:1 -3 155830096 . AT A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.15;SOR=Inf;LSEQ=GTCCAGCTAATTTTTTTTCT;RSEQ=TTTTTAGTAGAGATGGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:31,3:0:2,0:23:1:31.3:1:1:0:59.4:68:1:0:0.1 0/1:22:2:2,0:20,0:0.0909:1,0:39.5:1:30.5:1:1:0:60:4:0.0909:0:1 -3 155830167 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02429;SOR=Inf;LSEQ=TCCTGACCTTGTGATCCACC;RSEQ=GCCTCGGCCTCCCAAAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:124,4:0:1,0:25.6:1:31.1:1:1:0:59.4:256:1:0:0.1 0/1:85:4:4,0:80,1:0.0471:1,0:13:1:31.8:1:1:0:53.5:8:0.0471:0:1 -3 155830211 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=GATTAGAGATGTGAGCCTCC;RSEQ=CGCCCAGACGAAATTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:214,45:0:2,0:21.3:1:29.9:1:1:0:60:85.333:1:0:0.3 0/1:239:16:12,4:176,47:0.0669:2,2:16.2:1:28.7:1:0.7527:1.24701:60:15:0.0633:0:1.1 -3 155830283 . T C 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.76942;LSEQ=CAATGGCATCTTTCTCCTCC;RSEQ=TGTCCACAAATTCTTGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:322:181,141:239,206:0.4193:2,2:28.1:1:31.2:1:0.50884:1.11:59.4:52.667:0.4191:0:1.1 1/0:713:400:212,188:166,147:0.561:2,2:26.8:1:30.8:1:1:1.00141:59.6:132.333:0.5631:0:1.2 -3 155830631 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.58725;LSEQ=AAGAATTACCTAGATGTTCC;RSEQ=ATTTAGCATTTTCAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:95:34,61:52,81:0.4148:2,2:23:1:29.4:1:0.67814:1.15107:60:46.5:0.4152:0:1.1 1/0:176:114:54,60:26,36:0.6477:2,2:23.6:1:29.3:1:0.52862:1.24:60:113:0.6532:0:1.1 -3 155830919 . G GT 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.33386;SOR=3.62994;LSEQ=GTTGTTCATTTTTGTTTTTT;RSEQ=TTTTTTTTAGATGGAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:0,1:58,106:0.0061:2,0:25:0:32:0:1:0:60:2:0.0063:0:0 0/1:138:3:2,1:42,93:0.0217:2,2:26:1:29.7:1:0.23841:4.38:60:6:0.0217:0.0072:0.3 -3 155831114 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09956;SOR=Inf;LSEQ=AGACGGGGTTTTACCATGTT;RSEQ=GTCAGGCTGGTCTCGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:73,4:0:2,0:23.6:1:32.3:1:1:0:59.5:76:1:0:0.1 0/1:36:2:2,0:34,0:0.0556:1,0:10.5:1:30.5:1:1:0:60:4:0.0556:0:1 -3 155831270 . C T 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=24.31654;LSEQ=ATGGCCCCAGATAACAAGAT;RSEQ=AATGAAGTCATCCAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:1:0,1:311,262:0.0017:2,0:27:0:11:0:0.45819:0:60:0:0:0:5 0/1:515:21:11,10:262,232:0.0408:2,2:19.6:1:29:1:1:1.0266:58.8:42:0.041:0:1.1 -3 155831386 . T C 143 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=15.42641;LSEQ=GTTCTCATCTTCTTTTGATC;RSEQ=CAACATTGTTATTTCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:2:1,1:262,278:0.0037:2,2:24:0:33:0:1:1.06:60:4:0.0038:0:1.5 0/1:480:26:11,15:220,234:0.0542:2,2:27.7:1:30.6:1:0.68727:1.28139:60:52:0.0546:0:1.3 -3 155831479 . T C 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00091;SOR=Inf;LSEQ=GCAATGTTTGTGCTTCCTTT;RSEQ=TGAAGCAAAACCAGACTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:182,169:0:2,0:23.3:1:30.3:1:1:0:59.9:116:0.9971:0:0.1 0/1:303:9:5,4:139,155:0.0297:2,2:26.2:1:32.3:1:0.74053:1.39:60:18:0.0298:0:1.1 -3 155831899 . A G 172 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=57.79779;LSEQ=ATGTATCATTTCCTCTGACT;RSEQ=CATCTTTCTCCATAAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:0,1:111,184:0.0034:2,0:24:0:11:0:1:0:60:0:0:0:8 0/1:249:41:19,22:87,121:0.1647:2,2:25.1:1:32.2:1:0.60811:1.20:59.3:82:0.166:0:1.2 -3 155831926 . A G 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00014;SOR=Inf;LSEQ=TCTCCATAAATCCAAGATCA;RSEQ=TATCTGTTGCAACTAAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:97,153:0:2,0:26.5:1:30.5:1:1:0:60:34.714:1:0:0.1 0/1:207:11:7,4:86,110:0.0531:2,2:19.9:1:32.7:1:0.22669:2.23:60:22:0.0531:0:1.1 -3 155832010 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.22181;SOR=Inf;LSEQ=TTATGGTCAGTCAAGCTCCT;RSEQ=TGGGACCAAGTTCTTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:87,118:0:2,0:29.9:1:31.9:1:1:0:59.6:50.25:1:0:0.1 0/1:183:2:1,1:78,102:0.0109:2,2:37:1:31:1:1:1.31:60:4:0.0111:0:1 -3 155848828 . G C 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00083;SOR=Inf;LSEQ=ATTTCAGAATTTGAGTTTAA;RSEQ=TCAGGCTTTGGCCATCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:97,2:0:1,0:23.5:1:32.5:1:1:0:60:98:1:0:0.4 0/1:73:8:7,1:55,10:0.1096:2,2:23.6:1:30.9:1:1:1.27:60:16:0.1111:0:1.9 -3 155848833 . G T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00317;SOR=2.50648;LSEQ=AGAATTTGAGTTTAAGTCAG;RSEQ=CTTTGGCCATCTCCTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:47:44,3:62,3:0.4196:1,2:23.9:1:30.3:1:0.69408:1.40468:60:94:0.4196:0:1.1 1/0:79:51:40,11:23,4:0.6456:2,2:19.1:1:29.5:1:0.55766:1.57241:60:102:0.6538:0:1.2 -3 155848952 . T C 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.09135;LSEQ=TGCTAATGTCCTGCCAGGGA;RSEQ=TTTTACCATTGTATTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:208:108,100:129,143:0.4324:2,2:27:1:31.9:1:0.3573:1.20:60:68.333:0.4334:0:1.1 1/0:397:244:128,116:78,75:0.6146:2,2:27:1:31:1:0.83656:1.06:60:243:0.6215:0:1.1 -3 155849093 . G A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59975;SOR=1.2143;LSEQ=CCCCAGGTATGTGAAATGTC;RSEQ=TCAGATGTCAGTTTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:50:2,48:1,37:0.5682:1,1:21.8:1:31.2:1:1:1.53:60:100:0.5747:0:1.2 1/0:52:32:4,28:1,19:0.6154:1,2:21.2:1:30.2:1:0.63739:2.67:60:64:0.6275:0:1 -3 155849212 . T C 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.32867;SOR=0.31293;LSEQ=AAGAAACTTGCCAAATATTT;RSEQ=TTCAGTCTCCAAAAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:0.7:0,0:22:1:29.4:1:1:0:60:6:0.6667:0:1.3 0/1:5:2:0,2:0,3:0.4:0,0:24.5:1:34:0:1:0:60:4:0.4:0:1 -3 156800360 . A G 239 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24222;SOR=1.23742;LSEQ=CCAGTCACCGCTTTGTTCAG;RSEQ=TGACTCAGGTAAATAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:302:213:116,97:50,39:0.7053:2,2:25.1:1:31.5:1:0.80105:1.07179:60:105.5:0.7057:0:2 1/0:317:237:125,112:43,37:0.7476:2,2:24.9:1:30.4:1:0.89758:1.04118:60:46.4:0.7484:0:2 -3 156800384 . C T 240 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27052;SOR=1.21377;LSEQ=CTCAGGTAAATAAATGAGGC;RSEQ=GCACAGGCTGTCCTGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:337:236:119,117:49,51:0.7003:2,2:25.3:1:30.6:1:0.90506:1.06:60:235:0.7036:0:1.9 1/0:353:261:128,133:42,50:0.7394:2,2:27.2:1:30:1:0.628:1.15:60:42.5:0.737:0:1.9 -3 156800426 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1105;SOR=0;LSEQ=CACACCTCTAGAATACCCTG;RSEQ=CTGTGCTGGGAGCTATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:120,164:0.0105:2,2:29.7:1:28.3:1:0.57663:2.72:60:6:0.0108:0:1.7 0/0:310:0:0,0:134,176:0:2,0:24.7:1:31.5:1:1:0:60:102.333:1:0:1 -3 156800472 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=CTGAGTATTTTCATCCCTGT;RSEQ=CAAGTCACAATGATCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:42,98:0:2,0:22.8:1:30.7:1:1:0:60:69:1:0:0.2 0/1:148:2:1,1:41,104:0.0135:2,2:27:0:32.5:1:0.49119:2.52:60:4:0.0135:0:1.5 -3 156800489 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23577;SOR=Inf;LSEQ=TGTCCAAGTCACAATGATCT;RSEQ=ACTGTACCAGCCTGTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:20,78:0:2,0:23.8:1:30.9:1:1:0:60:23.5:1:0:0.1 0/1:93:2:1,1:19,72:0.0215:2,2:23.5:1:26.5:1:0.38569:3.72:60:4:0.0217:0:1 -3 156800696 . GA G 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATATGCAAGACTCAGGCAG;RSEQ=AAAAAAAAAGGTAATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:30:1:30.7:1:1:0:60:6:0.5:0.1667:0.3 1/1:1:1:0,1:0,0:1:0,0:39:0:31:0:1:0:60:2:1:0:0 -3 156952051 . C CT 70 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22977;SOR=0.24463;LSEQ=GTCATTGCAATCTGAATCAG;RSEQ=TTTTTTTTTCCTGAGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:5:4,1:78,7:0.0556:2,2:16.4:1:30.4:1:0.37916:2.7405:60:10:0.0562:0.0222:0 0/1:71:1:1,0:67,2:0.0141:1,0:49:0:30:0:1:0:60:2:0.0145:0:0 -3 156952194 . A T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=0.53412;LSEQ=AATAAATCTAATCTTTAGGA;RSEQ=TGTCCATGGCTTTGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:117:52,65:81,85:0.4134:2,2:25.3:1:30.4:1:0.54551:1.19044:60:57.5:0.4137:0:1.2 0/1:322:88:37,51:107,127:0.2733:2,2:25.3:1:29.4:1:0.61542:1.16077:60:87:0.2719:0:1.1 -3 158104613 . AC A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49718;SOR=Inf;LSEQ=ATGTGAGTCGTATTCACTAG;RSEQ=CAAAAAAAAAAAAAAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:74,15:0:2,0:24.5:1:31.4:1:1:0:59.6:43.5:1:0:0.5 0/1:89:2:1,1:66,21:0.0225:2,2:6:1:31.5:1:0.43539:3.09405:60:4:0.0238:0.0112:1 -3 158104706 . A G 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=2.10825;LSEQ=TGGTAGTACATGGAAATAAA;RSEQ=TGAATATTTTGAGCAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:69:27,42:97,108:0.2518:2,2:27.4:1:31.2:1:0.26482:1.39542:60:22:0.2435:0:1.2 0/1:207:86:36,50:56,65:0.4155:2,2:25.9:1:30.7:1:0.57165:1.19554:60:42:0.4118:0:1.1 -3 159246336 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15;SOR=Inf;LSEQ=CACTCCTGGCTTAATTGTGT;RSEQ=GCTTCCTGCACCTTCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:10,24:0:2,0:21.9:1:29.6:1:1:0:60:68:1:0:0.1 0/1:22:2:1,1:5,15:0.0909:2,2:28.5:1:31.5:1:0.48052:2.83:60:4:0.0909:0:1 -3 159601639 . C CT 116 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.64225;SOR=0.75791;LSEQ=GACTACTAAATCTCCCCCAA;RSEQ=TTTTTTTTTTCTTTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:15:11,4:161,28:0.0714:2,2:25.1:1:29.7:1:0.26215:2.08169:60:14:0.0683:0.0095:0.9 0/1:109:6:6,0:92,10:0.055:2,0:32.5:1:31.7:1:1:0:60:12:0.0566:0:0 -3 159601763 . G A 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0029;SOR=1.41388;LSEQ=GATCAGACTTTCTTCTGAGT;RSEQ=AAAATACATATATCTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:656:296:138,158:176,184:0.4512:2,2:24.5:1:29.4:1:0.58301:1.095:60:592:0.4526:0:1.1 1/0:571:307:152,155:122,142:0.5377:2,2:25.4:1:28.9:1:0.45031:1.14:60:306:0.5406:0:1.1 -3 160603511 . C T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACTCTGTCAGCCACGGAT;RSEQ=GGAAGATCCCACTCACCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9.5:1:31.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:25.5:1:27:1:1:0:60:4:1:0:1 -3 160603613 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAATCTGCTTAAGCCTG;RSEQ=GGAGCTCCCCTGGGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:28.5:1:32:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 160604387 . G A 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=AAGTGAATCCCCAGCAAACC;RSEQ=CAGCAGCCCTACAGAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:0.6:0,2:15:1:31.3:1:1:0:60:6:0.6:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:34:0:32:0:1:0:60:2:0.3333:0:1 -3 160604864 . A G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGCATAGATAAGTATCA;RSEQ=TAGCTGAATCAATCAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:13.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 160605052 . A G 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAGGAGACGGGGAGAAT;RSEQ=AAAACAAGGTGGAAAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:17.8:1:32.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 162297000 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGTTTACAGGAAAAGG;RSEQ=TTCTGAAATCAGACAGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:24,16:0.0465:2,2:31:1:30:1:1:1.48518:60:4:0.0476:0:1 0/0:12:0:0,0:10,2:0:2,0:19.8:1:31.5:1:1:0:60:11:1:0:0.1 -3 162297038 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52954;SOR=0;LSEQ=GCCTTTCAAACTCTTATACC;RSEQ=ACCTCTGGAGTTGGGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:26,27:0.0364:2,2:32.5:1:28.5:1:1:1.04:60:4:0.0364:0:1.5 0/0:32:0:0,0:21,11:0:2,0:30.5:1:29.6:1:1:0:60:31:1:0:0.2 -3 162297058 . A G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01838;SOR=Inf;LSEQ=AACCTCTGGAGTTGGGTGAC;RSEQ=TGGTTTCTCCCCTTTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:24,30:0:2,0:27:1:31:1:1:0:59.7:108:1:0:0.3 0/1:33:4:2,2:18,11:0.1212:2,2:40.8:1:30.3:1:1:1.61126:60:8:0.129:0:1 -3 162297104 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.17857;SOR=0;LSEQ=TGACAGCCATCTTACTACTA;RSEQ=TCGCCTTCAGGCCCTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:5,14:0.0952:2,2:29.5:1:31:1:0.5:2.65:60:4:0.0952:0:1 0/0:28:0:0,0:12,16:0:2,0:16.9:1:31.3:1:1:0:60:56:1:0:0.2 -3 162769145 . T C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.61462;SOR=2.79379;LSEQ=TGAGTATACTGTAAATTGCT;RSEQ=ATTATTGTTAAATAAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:11,0:8,0:0.5789:0,0:18.2:1:32.3:1:1:0:60:22:0.5789:0:1.1 1/1:5:4:4,0:1,0:0.8:0,0:36.8:1:31.3:1:1:0:60:8:0.8:0:1 -3 162769266 . T C 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0241;SOR=2.07313;LSEQ=AACAATTATTTGTCACCTGG;RSEQ=CATGAATGATTTATTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:118:71:54,17:32,15:0.6017:2,2:22.2:1:31.5:1:0.39961:1.48:60:142:0.6121:0:1 1/0:87:66:50,16:15,5:0.7586:2,2:22.5:1:31.6:1:1:1.04:60:65:0.7558:0:1.1 -3 162769378 . A T 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04476;SOR=1.49127;LSEQ=AAAATGTGGTCAAATGTGCT;RSEQ=AAATTATACATATTTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:95:45,50:77,91:0.3612:2,2:25.5:1:29.4:1:0.89765:1.06:60:94:0.3602:0:1.1 0/1:201:92:40,52:44,65:0.4577:2,2:26.4:1:28.3:1:0.6694:1.14:60:45:0.4523:0:1.2 -3 162769431 . G C 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09542;SOR=1.6999;LSEQ=TGAGAGGGTATTGGTATAGA;RSEQ=GAAATTTCTGTATTCTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:34:13,21:37,74:0.2329:2,2:23.4:1:30.4:1:0.68094:1.24:60:68:0.2329:0:1.3 0/1:88:30:9,21:15,43:0.3409:2,2:27:1:29.7:1:0.80136:1.23:60:29:0.3372:0:1.1 -3 162769497 . A G 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.3732;SOR=2.0662;LSEQ=GTGCAAATATGACAGATTTC;RSEQ=CACAACAAAATTGACTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:28:0,28:2,16:0.6087:2,1:26.2:1:31.7:1:0.14783:0:60:27:0.6:0:1.2 1/0:17:13:1,12:0,4:0.7647:0,1:28.5:1:33:1:1:0:60:26:0.7647:0:1.1 -3 164564437 . CTAGT C 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CCTCGAATTATCCAGCTGAC;RSEQ=TTATTTATAAGTTTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:35,0:0:1,0:23.1:1:31.8:1:1:0:60:70:1:0:0.1 0/1:36:14:13,1:20,2:0.3889:2,1:27.6:1:31.9:1:1:1.29:60:28:0.3889:0.0278:0 -3 164564465 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19923;SOR=Inf;LSEQ=TTTATAAGTTTTTCATTGTT;RSEQ=TAAAAACTGCATTTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:70,10:0:2,0:21.2:1:28.4:1:1:0:60:39:1:0:0.2 0/1:65:2:1,1:51,12:0.0308:2,2:25.5:1:30:1:0.3625:4.12311:60:4:0.0313:0:1 -3 164564512 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20549;SOR=Inf;LSEQ=ACAACAAACCTTTCTACTTG;RSEQ=TATGTACTTTTATAACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:129,72:0:2,0:25.9:1:29.7:1:1:0:60:99.5:1:0:0.2 0/1:168:2:1,1:101,65:0.0119:2,2:34.5:1:33:1:1:1.5496:60:4:0.012:0:1 -3 164564572 . A G 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25158;SOR=0;LSEQ=GCCAATTTAGAAGGGCATGC;RSEQ=CTACATGAAATCTGTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:1,2:119,144:0.0113:2,2:28.7:1:25.3:1:1:1.64979:60:2:0.0077:0:2 0/0:234:0:0,0:110,124:0:2,0:26:1:29.5:1:1:0:60:77:1:0:0.6 -3 164564579 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=2.96842;LSEQ=TAGAAGGGCATGCACTACAT;RSEQ=AAATCTGTACTGACTATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:58:24,34:90,109:0.2257:2,2:26.7:1:28.7:1:0.65388:1.16901:60:28:0.2222:0:1.1 0/1:239:111:51,60:58,70:0.4644:2,2:24.9:1:28.6:1:1:1.03:60:36:0.4596:0:1.2 -3 164564612 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19767;SOR=Inf;LSEQ=ACTATTGAACTATATATTAT;RSEQ=TCCATAATTACTACAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:69,124:0:2,0:24.2:1:30:1:1:0:60:95.5:1:0:0.3 0/1:155:2:1,1:56,97:0.0129:2,2:21.5:1:27.5:1:1:1.73:60:4:0.013:0:1.5 -3 166228705 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=CTGCTGCAGGATCTCCAATA;RSEQ=CTCCAGAGGTTCAGGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:18:1:28.5:1:1:1.58:60:4:0.2:0:1 0/0:8:0:0,0:4,4:0:2,0:25.4:1:31.3:1:1:0:60:16:1:0:0.1 -3 166229033 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=AGGTCCCATAAGAAGGAGGA;RSEQ=GCACTCATTTTTGCTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:29.7:1:32:1:1:1.73:60:6:0.6:0:1 1/0:3:2:0,2:1,0:0.6667:0,0:30:1:29:1:0.33333:0:60:4:0.6667:0:1 -3 166229202 . TCAA T 107 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=8.000;MSILEN=3;SSF=0.48127;SOR=0.522;LSEQ=AGAAAGTGACAACAGCGTCA;RSEQ=CAACAACAACAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:6,5:3,6:0.55:2,2:27.5:1:31:1:0.40586:2.29:59.5:22:0.5789:0.1:0.4 0/1:13:5:2,3:6,2:0.3846:2,2:26.2:1:28.4:1:0.29293:3.95135:60:10:0.3846:0.0769:0.6 -3 166229205 . A T 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=7.000;MSILEN=3;SSF=0.51337;SOR=0;LSEQ=AAGTGACAACAGCGTCATCA;RSEQ=CAACAACAACAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:3,7:0.0952:2,2:18:1:29.5:1:1:2.16:60:4:0.1667:0:2 0/0:13:0:0,0:6,3:0:2,0:17.6:1:29.1:1:1:0:60:18:1:0:0 -3 166229248 . C T 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00226;SOR=0;LSEQ=AAAGGCCCCCACAAAAGCCC;RSEQ=ATCCAAGGGTCAGCAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:6,6:10,12:0.3529:2,2:29.5:1:29.5:1:1:1.19:60:24:0.3529:0:1.3 0/0:19:0:0,0:9,10:0:2,0:25.3:1:30.5:1:1:0:59.2:38:1:0:0.2 -3 168576555 . A C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=ACTTCTCTTGAACCCAGGTG;RSEQ=CTTTCTCTTTGGCTTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:20.5:1:27.5:1:1:0:60:5:1:0:0.3 0/1:11:2:1,1:6,3:0.1818:2,2:9.5:1:31:1:1:1.87089:43:4:0.2:0:1.5 -3 168576567 . G GCTT 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=CCCAGGTGACTTTCTCTTTG;RSEQ=CTTTCTTCTTTTCTGATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:24.2:1:32:1:1:0:60:12:1:0:0.2 0/1:11:2:1,1:6,3:0.1818:2,2:22.5:1:31.7:1:1:1.87089:43:4:0.1818:0:1.5 -3 168576672 . C T 23 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52063;SOR=Inf;LSEQ=AATAATTCTCCTGACAAGAA;RSEQ=CTTGCCCATAACTTGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:17,9:0:2,0:20.7:1:31.1:1:1:0:60:25:1:0:0.5 0/1:42:2:0,2:26,14:0.0476:2,0:6:0:23.5:1:0.13937:0:43:4:0.0488:0:4 -3 168576680 . A T 24 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54386;SOR=Inf;LSEQ=TCCTGACAAGAACCTTGCCC;RSEQ=TAACTTGTTTGCTTACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:18,8:0:2,0:25.3:1:29.7:1:1:0:60:25:1:0:0.5 0/1:50:2:0,2:30,18:0.04:2,0:14:0:24:1:0.1551:0:43:4:0.0408:0:4 -3 168576724 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=18.74672;LSEQ=CCAACAGCATGCTGTGTAAC;RSEQ=TTGTAGACCCTCCCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:10:5,5:17,19:0.2174:2,2:27.4:1:30.8:1:1:1.11:60:20:0.2222:0:1.9 1/1:83:70:36,34:7,6:0.8434:2,2:28.6:1:30:1:1:1.10056:59.5:69:0.8415:0:2.2 -3 168576736 . C T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=22.46049;LSEQ=TGTGTAACATTGTAGACCCT;RSEQ=CCAGTTTTGCCTTCGTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:3,5:14,19:0.1951:2,2:30.1:1:29.4:1:1:1.222:60:16:0.2051:0:2.1 1/1:80:68:34,34:6,6:0.85:2,2:29.4:1:29.4:1:1:1:59.5:136:0.85:0:2.2 -3 168576801 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50321;SOR=Inf;LSEQ=AGTATTCATTCCCTGGATGT;RSEQ=TACAATATCACCTTTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:0:2,0:22:1:31.1:1:1:0:60:24:1:0:0.7 0/1:34:2:1,1:6,26:0.0588:2,2:15:1:28:1:0.37433:4.09:60:4:0.0588:0:1 -3 168576884 . T C 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03165;SOR=0;LSEQ=TAAAAGGCCTAGAGAACACG;RSEQ=ATCAAGTGCCTCTCCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:4,5:6,8:0.3913:2,2:21.4:1:32.3:1:1:1.06:60:18:0.3913:0:1.2 0/0:10:0:0,0:1,9:0:2,0:18.7:1:28.7:1:1:0:60:20:1:0:0.1 -3 169490890 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50099;SOR=0;LSEQ=CCGCGGTGCTGTGCTGCCGG;RSEQ=CCTCGGCGCAGAGCCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:36,18:0.0357:2,2:30:1:27.5:1:1:1.97357:60:4:0.0364:0:1 0/0:45:0:0,0:26,19:0:2,0:29.9:1:31:1:1:0:60:90:1:0:0.2 -3 169491012 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4873;SOR=Inf;LSEQ=AGCTCTCGTATCCATGACGC;RSEQ=TGCTGCTTCGGGGGACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:0:1,0:23.6:1:32.2:1:1:0:60:34:1:0:0 0/1:19:2:1,1:3,14:0.1053:2,2:23:1:28.5:1:0.38596:4.18:60:4:0.1053:0:1 -3 173189273 . T C 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.7746;LSEQ=TCTATCTGTGTATGTAGCTC;RSEQ=GTGTCAAAATTTCCTGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:29.8:1:27.8:1:1:0:60:8:0.6667:0:1 1/0:2:1:0,1:0,1:0.5:0,0:4:0:27:0:1:0:60:2:0.5:0:2 -3 177193106 . T G 67 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33824;SOR=0.27028;LSEQ=TTTCCTCATCTATAATGATA;RSEQ=CTGCCTCACAGAACTCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:26.8:1:33.8:1:1:0:60:8:0.4:0:1 0/1:7:1:1,0:6,0:0.1429:0,0:50:0:31:0:1:0:60:2:0.1429:0:1 -3 177193276 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=CGCTGACTCCGGGGAGCAGG;RSEQ=AGAGGAACAGAGGGGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:57,58:0:2,0:27.6:1:32.1:1:1:0:60:56.5:1:0:0.1 0/1:129:2:1,1:61,66:0.0155:2,2:8:0:30.5:1:1:1.08:60:4:0.0156:0:1.5 -3 177418073 . A G 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1453;SOR=7.245;LSEQ=GGCAGTGGTGCCCACCTTGA;RSEQ=CATGCTGAGGTAGAAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:19,1:0.0476:1,0:21:0:14:0:1:0:60:0:0:0:6 0/1:7:2:2,0:5,0:0.2857:0,0:17:1:33.5:1:1:0:60:4:0.2857:0:3 -3 177418088 . A G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02291;SOR=4.91322;LSEQ=CTTGAACATGCTGAGGTAGA;RSEQ=GCTGCTGGGGCCTGCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:6,1:18,1:0.2593:1,2:26.1:1:29.4:1:0.47385:2.85369:60:6:0.25:0:1 1/0:14:9:9,0:4,1:0.6429:2,0:24.8:1:32.7:1:0.35714:0:60:18:0.6429:0:1.7 -3 177418132 . G A 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTCACCTCCAGGTGCTAC;RSEQ=TTACCGTACATCTTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:38,27:0:2,0:21.8:1:30.7:1:1:0:60:130:0.9848:0:0.3 0/1:52:15:10,5:23,14:0.2885:2,2:18:1:28.7:1:1:1.21:60:14:0.28:0:1.9 -3 177418225 . G C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.01664;SOR=0.21516;LSEQ=GCAGAATAGACCCATGAGAA;RSEQ=ATGTTCTGGGAGTGCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:15:7,8:14,22:0.2941:2,2:15.7:1:31.5:1:0.75652:1.37:60:30:0.3:0:1.1 0/1:37:3:1,2:10,24:0.0811:2,2:23.3:1:27.7:1:1:1.19:60:2:0.0588:0:1 -3 177418320 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5098;SOR=0;LSEQ=TGGATGCTACTGAACTTGTG;RSEQ=AGGTGTAGTGGCTGCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:26,22:0.04:2,2:15.5:1:28.5:1:1:1.17786:60:4:0.04:0:1.5 0/0:35:0:0,0:21,14:0:2,0:22.2:1:31.9:1:1:0:60:70:1:0:0.1 -3 177418753 . A C 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00996;SOR=Inf;LSEQ=GACACCAGCTTTGCGTCATC;RSEQ=TTTTCCCAAAGAGTGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:0:1,0:32.7:1:30.3:1:1:0:60:32:1:0:0.1 0/1:9:4:4,0:5,0:0.4444:0,0:25:1:28:1:1:0:60:8:0.5:0:1.8 -3 177418774 . C T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00625;SOR=Inf;LSEQ=TTTTCCCAAAGAGTGAGTCC;RSEQ=AGGGAACCACCTCTAGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:21,7:0:2,0:22.4:1:30.9:1:1:0:60:56:1:0:0.2 0/1:18:5:4,1:12,1:0.2778:1,2:21.4:1:27.6:1:0.4902:2.79285:60:10:0.2778:0:1.6 -3 177418792 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1996;SOR=Inf;LSEQ=CCCAGGGAACCACCTCTAGG;RSEQ=TAGTGGTAGCTCAGCTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:27,12:0:2,0:20.9:1:31.1:1:1:0:60:18.5:1:0:0.2 0/1:32:2:1,1:23,7:0.0625:2,2:11.5:1:27:1:0.44355:3.1396:60:4:0.0625:0:1.5 -3 177418817 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22911;SOR=0;LSEQ=GGTAGCTCAGCTATGTGGTG;RSEQ=CTCTGCTGCCAAAGACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:30,19:0.0392:2,2:22.5:1:32:1:1:1.56436:60:4:0.0392:0:1.5 0/0:55:0:0,0:35,20:0:2,0:26.9:1:29.1:1:1:0:60:54:1:0:0.3 -3 177418818 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22949;SOR=0;LSEQ=GTAGCTCAGCTATGTGGTGT;RSEQ=TCTGCTGCCAAAGACCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:30,20:0.0385:2,2:26.5:1:30.5:1:1:1.48801:60:4:0.0385:0:1 0/0:56:0:0,0:36,20:0:2,0:27:1:31.5:1:1:0:60:112:1:0:0.3 -3 177418846 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49677;SOR=Inf;LSEQ=CCAAAGACCAACTGCTCCTG;RSEQ=TGGCTGGGCTTGGGCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:29,31:0:2,0:28.7:1:32.2:1:1:0:60:59:1:0:0.2 0/1:65:2:1,1:34,29:0.0308:2,2:42:0:30.5:1:1:1.16953:60:4:0.0308:0:1.5 -3 177577349 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20139;SOR=Inf;LSEQ=ATGGATTCTTTTTCATCTTC;RSEQ=TGAGTTTGTCTAGTTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:25.7:1:31:1:1:0:57.5:70:1:0:0.1 0/1:29:2:1,1:15,12:0.069:2,2:20.5:1:28.5:1:1:1.24034:60:4:0.0714:0:1.5 -3 177577357 . G C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18173;SOR=Inf;LSEQ=TTTTTCATCTTCGTGAGTTT;RSEQ=TCTAGTTTTGGTCTTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:19,18:0:2,0:26.3:1:32.1:1:1:0:57.7:36:1:0:0.1 0/1:28:2:1,1:13,13:0.0714:2,2:5:0:33.5:1:1:1:60:4:0.0714:0:0.5 -3 177577766 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49209;SOR=Inf;LSEQ=AGCACTTTGTCCCTTGGTGG;RSEQ=GAGGGTGTGTTTTGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:0:2,0:26:1:30.4:1:1:0:59.4:58:1:0:0.1 0/1:31:2:1,1:14,15:0.0645:2,2:24:1:28.5:1:1:1.07:60:4:0.0667:0:1 -3 177577798 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4949;SOR=Inf;LSEQ=TTGCTGGAGGGAAACCCACT;RSEQ=GTTGGGCCACCTGGATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:0:2,0:23.7:1:30:1:1:0:60:22:1:0:0.1 0/1:28:2:1,1:11,15:0.0714:2,2:18:1:28.5:1:1:1.35:60:4:0.0741:0:1 -3 177577866 . T C 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=CAGCTGGTCTGCAGAGACTT;RSEQ=GGCCACCCCTCCCCCTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:29.5:1:31.2:1:1:0:60:12:1:0:0 1/0:4:2:0,2:0,2:0.5:0,0:23:1:28.5:1:1:0:60:4:0.5:0:1.5 -3 177577935 . G C 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTGAGCCTCTGGCTGGA;RSEQ=TTATTGGAGTTCCTGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:32:1:1:0:60:4:1:0:1 1/0:2:1:1,0:0,1:0.5:0,0:8:0:32:0:1:0:60:2:0.5:0:1 -3 177578395 . G A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62848;SOR=2.53692;LSEQ=TGAGTTGCACAGTTCCATGG;RSEQ=AAAAGCAGTTTCCCTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:2,2:0.6:2,2:28.5:1:30:1:1:1.86:60:12:0.6:0:1 1/1:10:8:4,4:1,1:0.8:2,2:32.8:1:29.8:1:1:1:60:16:0.8:0:1.5 -3 177578423 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13725;SOR=Inf;LSEQ=GTTTCCCTGGCTGGGTAGTG;RSEQ=ACTAACTCACCACCCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:17.6:1:32.1:1:1:0:60:22:1:0:0.4 0/1:7:2:1,1:3,2:0.2857:2,2:8:0:31:0:1:1.41418:60:4:0.2857:0:2.5 -3 177899353 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23199;LSEQ=AGAAATTGTGTAGGACCAAA;RSEQ=AGTCTTCTTGGAATGATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:415:309:142,167:53,53:0.7446:2,2:25.4:1:29.1:1:0.49971:1.17559:60:102:0.7445:0:1.1 0/1:402:162:77,85:113,127:0.403:2,2:25.2:1:28.6:1:1:1.02:60:80:0.401:0:1.2 -3 177899380 . G A 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00089;SOR=Inf;LSEQ=CTTGGAATGATGCCATAGAA;RSEQ=TATGTCAATGTTTTTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:0:0,0:156,208:0:2,0:26:1:31.9:1:1:0:60:71.8:1:0:0.7 0/1:362:10:4,6:153,199:0.0276:2,2:32:1:30:1:1:1.1528:60:20:0.0277:0:1.9 -3 177899444 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50136;SOR=0;LSEQ=ATGCATTTTCAAATAAAATA;RSEQ=TAAAATTTTCTTAGTTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:28,110:0.0143:2,2:46.5:1:31:1:0.37256:3.88:60:4:0.0144:0:1 0/0:119:0:0,0:34,84:0:2,0:22.2:1:29.4:1:1:0:60:58:0.9915:0:0.3 -3 177899517 . A G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44047;SOR=0.63417;LSEQ=TAAAAATAGATCTATGAGAA;RSEQ=TACTTTGAGGTATTGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:22:2,20:0,12:0.6471:0,2:22.7:1:31.5:1:0.52941:0:60:21:0.6364:0:1 1/0:28:15:0,15:0,13:0.5357:1,1:17.7:1:28.6:1:1:0:60:4:0.48:0:1.1 -3 177899939 . C T 26 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAGGAAAATGAGATCATTGC;RSEQ=AAATTTAACTGATAGATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:39.5:1:26:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:39:0:33:0:1:0:60:2:1:0:0 -3 178511054 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACACTTTCAGCTATGGAA;RSEQ=TGCAGACAGTTGATGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:18.5:1:33.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 178511254 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49533;SOR=0;LSEQ=GCTGGACTACAGTGATGGAG;RSEQ=GAAGGAATTGAGAGAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:39,11:0.0377:2,2:25.5:1:29:1:0.41176:3.43763:60:4:0.04:0:1 0/0:51:0:0,0:34,17:0:2,0:22.7:1:29.5:1:1:0:60:24.5:1:0:0.3 -3 178511285 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16207;SOR=Inf;LSEQ=AGAGAGCAAGCCACCAAGCG;RSEQ=AAGCTGCTCTTCACCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:52,17:0:2,0:24.9:1:30.8:1:1:0:60:68:1:0:0.1 0/1:47:2:1,1:30,15:0.0426:2,2:22:1:30.5:1:1:1.96856:60:4:0.0426:0:1.5 -3 178511302 . TG T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.27725;SOR=0;LSEQ=GCGGAAGCTGCTCTTCACCC;RSEQ=GGGGGGTGGGCAATGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:2,1:59,16:0.0385:2,2:8.7:1:30.7:1:0.52692:1.82707:60:6:0.0385:0.0128:0.3 0/0:51:0:0,0:32,19:0:2,0:24.7:1:30.8:1:1:0:60:102:1:0:0.4 -3 178511310 . T G 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00245;SOR=Inf;LSEQ=TGCTCTTCACCCTGGGGGGG;RSEQ=GGGCAATGGACAGCAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:67,20:0:2,0:26.1:1:29.4:1:1:0:60:42.5:1:0:0.1 0/1:53:6:3,3:31,16:0.1132:2,2:26.5:1:26.8:1:0.65457:1.91207:60:5:0.098:0:2.3 -3 178511403 . AC A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50348;SOR=0;LSEQ=GTTGATACACTCCCTGAAGC;RSEQ=CACGGCATGAAATGGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:125,74:0.01:2,2:38.5:1:32:1:1:1.68451:60:4:0.0102:0:0 0/0:165:0:0,0:103,62:0:2,0:25.6:1:31.2:1:1:0:60:330:1:0:0.1 -3 178511531 . C A 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=GGCATGGGGCTATCAGGGAT;RSEQ=CAAGCCAGCTACCTCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:17:7,10:155,153:0.0523:2,2:23.4:1:29.1:1:0.61962:1.44561:60:16:0.0502:0:1.1 0/0:283:0:0,0:144,139:0:2,0:24.2:1:30.9:1:1:0:60:140.5:1:0:0.1 -3 178511579 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=CAGCAGGTGACTCTTCCCAT;RSEQ=CAGATGACAGCCAAGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:154,147:0:2,0:23.1:1:32:1:1:0:60:99.333:1:0:0.1 0/1:254:3:1,2:133,118:0.0118:2,2:26:1:27.7:1:0.60381:2.24725:60:6:0.012:0:1 -3 178511689 . A C 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAACTCTGCCTCAAAAAACA;RSEQ=AGATAAAGGGAACAAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:89,210:0:2,0:22.7:1:30:1:1:0:59.9:98.667:1:0:0.1 0/1:245:32:11,21:71,142:0.1306:2,2:22.5:1:31.3:1:1:1.05:60:31:0.1281:0:1.2 -3 178511724 . A C 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAAACAAACAAGCAGAG;RSEQ=CCTTTCTGCACTGAGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:4,123:0:1,0:25.7:1:29.8:1:1:0:59.8:62.5:1:0:0.1 0/1:101:28:3,25:8,65:0.2772:2,2:25.6:1:31.1:1:1:1.02539:60:56:0.28:0:1 -3 178917005 . A G 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=7.79891;LSEQ=TCTAAAATGCAAATAACCAT;RSEQ=AAGCTTAACTGTTGTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:17:6,11:179,540:0.0231:2,2:26.4:1:29.9:1:0.39432:1.64:60:16:0.0219:0:1.3 0/1:571:89:24,65:127,354:0.1559:2,2:23.8:1:30.8:1:0.89661:1.03:60:28.667:0.1528:0:1.2 -3 178917088 . C CATT 109 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=10.88476;LSEQ=ATAGCTTTCTAAATAAAAAT;RSEQ=ATAAATCTAAAGTATGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:0,2:1,146:0.0134:1,0:18.5:1:30.8:1:1:0:60:4:0.0135:0:0.5 0/1:100:13:0,13:1,86:0.13:1,1:24.2:1:29.6:1:1:0:60:26:0.1313:0.04:0.4 -3 178917412 . C CA 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.85338;LSEQ=TCTACAGAGTTCCCTGTTTG;RSEQ=AAAAAAAACATGTTCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:3:2,1:98,12:0.0265:2,2:32.3:1:29.7:1:0.30938:4.00369:60:6:0.0273:0:0 0/1:88:2:2,0:77,9:0.0227:2,0:31.5:1:27:1:1:0:60:4:0.0227:0:0 -3 178917436 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=0.19297;SOR=Inf;LSEQ=AAAAACATGTTCATGCTGTG;RSEQ=ATGTAATAGAATGTTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:159,28:0:2,0:23.1:1:29.9:1:1:0:60:92.5:1:0:0.1 0/1:147:2:1,1:115,30:0.0136:2,2:28:1:28:1:0.37844:3.78736:60:4:0.0137:0:1 -3 178917697 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20492;SOR=Inf;LSEQ=ATTAGATAAAGGTAAGAAAA;RSEQ=GACTAATCTACTCTAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:55,185:0:2,0:24.9:1:29.5:1:1:0:60:20.818:1:0:0.1 0/1:199:2:1,1:51,146:0.0101:2,2:39.5:1:27.5:1:0.45531:2.84:60:4:0.0103:0:1 -3 178921028 . G A 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GTGAGCCACCACGCCCGGCC;RSEQ=TGATCCTTGTTTTTAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23.5:1:29:1:1:0:60:4:1:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:33:0:32:0:1:0:60:2:0.3333:0:1 -3 178921048 . CT C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=GTGATCCTTGTTTTTAATTC;RSEQ=TTTTTTGCCTCCAGTTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:19.3:1:28.8:1:1:0:60:5:1:0:0.5 1/0:3:2:1,1:1,0:0.6667:0,2:26:0:33.5:1:1:0:60:4:0.6667:0:0.5 -3 178921158 . G A 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17022;SOR=0;LSEQ=GATTGATCTTGTGCTTCAAC;RSEQ=TAAATCCTAAATGTTAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:6,0:33,0:0.1538:1,0:15:1:29.7:1:1:0:60:12:0.1579:0:1.2 0/0:15:0:0,0:12,3:0:2,0:21.6:1:30.3:1:1:0:60:30:1:0:0 -3 178921253 . G GTAAA 122 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00079;SOR=3.69714;LSEQ=TCACCTTTGCAGATTAATAT;RSEQ=TAGTCATAATACTCTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:11:11,0:176,3:0.0579:1,0:30:1:28.8:1:1:0:60:22:0.0579:0.0105:0.2 0/1:113:21:19,2:84,8:0.1858:2,2:23:1:28:1:1:1.10428:60:42:0.1858:0.0442:0 -3 178921628 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.15643;SOR=Inf;LSEQ=ATAGAAATTATTTTAGATAA;RSEQ=CTTTTTCTTGCACTATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:26,149:0:2,0:20.8:1:31.6:1:1:0:60:350:1:0:0.6 0/1:115:2:1,1:20,93:0.0174:2,2:24.5:1:29:1:0.33318:4.56:60:4:0.0179:0:1.5 -3 178921639 . C A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=0.36391;LSEQ=TTTAGATAACCTTTTTCTTG;RSEQ=ACTATACAGTAATCTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:129:97:10,87:3,28:0.7519:2,2:22.2:1:30.3:1:1:1.07:60:96:0.7619:0:1 1/0:86:45:4,41:8,33:0.5233:2,2:17.7:1:30:1:0.21566:2.45885:60:90:0.5294:0:1.1 -3 178922222 . G T 125 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00209;SOR=4.33049;LSEQ=TTCCGTGGTTTTATATTTGA;RSEQ=TCTATCGAGTGTGTGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:6:6,0:171,16:0.0311:2,0:25.8:1:31.2:1:1:0:60:12:0.0313:0:1.8 0/1:147:18:15,3:119,10:0.1224:2,2:15.8:1:30.2:1:0.20008:2.36193:60:36:0.1233:0:1.9 -3 178922231 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.18513;SOR=Inf;LSEQ=TTTATATTTGAGTCTATCGA;RSEQ=TGTGTGCATATGTGTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:212,27:0:2,0:23.9:1:32.2:1:1:0:60:118.5:1:0:0.7 0/1:181:2:2,0:155,24:0.011:2,0:35:1:32:0:1:0:60:4:0.0111:0:1.5 -3 178922274 . C A 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00031;SOR=0.59734;LSEQ=GTGTATACATTAGTATATAC;RSEQ=TACTTTTTTCTTTTAGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:463:313:240,73:103,47:0.676:2,2:25.2:1:29.9:1:0.07052:1.50:60:38.125:0.6703:0:1.1 1/0:393:218:162,56:120,54:0.5547:2,2:24.5:1:29.7:1:0.25906:1.30:60:217:0.5564:0:1.2 -3 178922430 . A G 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27725;SOR=0.82045;LSEQ=TTATATTAGTGTTTAGCAGT;RSEQ=TGATCCATAAAAGTAGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:319:231:40,191:15,72:0.7241:2,2:23:1:32:1:1:1.01:60:114.5:0.7224:0:1.1 1/0:268:183:39,144:13,72:0.6828:2,2:24.2:1:31:1:0.31932:1.50:60:60:0.6818:0:1 -3 178922682 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCGGGCGTGGTGGCGGGC;RSEQ=CCTGTAATCCCAGCTACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:47.5:1:32.5:1:1:0:39.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 178927259 . CCAAT C 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.01338;SOR=Inf;LSEQ=GACCTTATAAAGTGCCTTTT;RSEQ=CAATCTCTTTCCTGTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:95,1:0:1,0:25.3:1:30.6:1:1:0:60:23:1:0:0.1 0/1:51:4:3,1:46,1:0.0784:1,2:30:1:27.8:1:0.15216:13.42263:60:3:0.0612:0:0.5 -3 178927345 . T C 119 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00597;SOR=0.09725;LSEQ=ATATACTTTGATGAAGACTT;RSEQ=TCTTGATGTATTATTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:14:11,3:273,87:0.0374:2,2:22:1:31.4:1:1:1.17:60:28:0.0376:0:1 0/0:266:1:1,0:196,69:0.0038:2,0:16:0:25:0:1:0:60:2:0.0038:0:1 -3 178927410 . A G 204 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAATGGCTGAATTATGATAT;RSEQ=TACATTCCTGATCTTCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:0:0,0:418,374:0:2,0:26.3:1:29.2:1:1:0:60:98:0.9975:0:0.1 0/1:716:91:49,42:333,292:0.1271:2,2:25:1:31.5:1:1:1.02:60:90:0.1275:0:1.2 -3 178927645 . C T 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00032;SOR=0.08317;LSEQ=AATGTATCATGGAAGAATAC;RSEQ=TTGGGAGAGCTTCAGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:25:4,21:4,14:0.5814:2,2:24.8:1:30:1:0.70102:1.4856:60:24:0.5714:0:1 0/1:20:2:0,2:1,17:0.1:1,0:15.5:1:31:1:1:0:60:4:0.1:0:1 -3 178927848 . AT A 70 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.89653;LSEQ=GCTTAAACCTTGAAAAATCA;RSEQ=TTTTTTTTTTTAGATATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:5,0:47,0:0.0962:1,0:21.6:1:30.3:1:1:0:60:10:0.0962:0.0192:0.4 0/1:23:2:2,0:18,2:0.087:2,0:22:1:26.5:1:1:0:60:4:0.087:0.0435:0.5 -3 178927948 . G T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6283;SOR=0.3902;LSEQ=GTGTTTTATAATTTAGACTA;RSEQ=TGAATATTTTTCTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:185,51:0.0126:2,2:12.7:1:28.7:1:0.1245:7.17507:60:6:0.0127:0:1 0/0:203:1:0,1:166,36:0.0049:2,0:1:0:25:0:0.18227:0:60:2:0.0049:0:1 -3 178935943 . C T 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01721;SOR=Inf;LSEQ=CTGTAAATCATCTGTGAATC;RSEQ=AGAGGGGAAAAATATGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:169,19:0:2,0:28.4:1:30.9:1:1:0:46:46:1:0:0.1 0/1:152:5:4,1:124,23:0.0329:2,2:25.2:1:30.6:1:0.58183:1.34492:38.8:10:0.0338:0:1 -3 178935950 . GA G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21216;SOR=Inf;LSEQ=TCATCTGTGAATCCAGAGGG;RSEQ=AAAATATGACAAAGAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:175,27:0:2,0:28.3:1:29.9:1:1:0:45:100:1:0:0.1 0/1:173:2:2,0:133,38:0.0116:2,0:19:1:32.5:1:1:0:27:4:0.0118:0:0 -3 178935976 . A G 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25401;SOR=0;LSEQ=TATGACAAAGAAAGCTATAT;RSEQ=AGATATTATTTTATTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:2,1:213,64:0.0107:2,2:23.7:1:30.3:1:0.54874:1.66065:38:6:0.0108:0:2 0/0:236:0:0,0:171,65:0:2,0:24.6:1:28.2:1:1:0:38.7:117:1:0:0.1 -3 178936158 . CT C 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.09433;SOR=Inf;LSEQ=GAGATTCTCTGTTTCTTTTT;RSEQ=TTATTACAGAAAAAATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:66,226:0:2,0:22.3:1:30.5:1:1:0:58.9:291:1:0:0.1 0/1:245:3:2,1:61,181:0.0122:2,2:20.3:1:26.7:1:0.16321:5.88:60:6:0.0123:0.0041:1 -3 178936213 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05243;SOR=Inf;LSEQ=CTCAGCATGTTTTTACCATA;RSEQ=CTATTGGAATAAATAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:4,108:0:1,0:25.1:1:31.7:1:1:0:57.5:224:1:0:0.1 0/1:68:3:0,3:5,60:0.0441:2,0:11.7:1:30.3:1:1:0:51:6:0.0455:0:1 -3 178936227 . T G 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17281;SOR=0;LSEQ=ACCATACCTATTGGAATAAA;RSEQ=AAAGCAGAATTTACATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:5:0,5:2,82:0.0562:1,0:36.8:1:31.4:1:1:0:60:10:0.0562:0:1 0/0:43:0:0,0:2,41:0:1,0:23.5:1:28.5:1:1:0:60:86:1:0:0.1 -3 178937126 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15376;SOR=Inf;LSEQ=ATTGGTATGTCACTTAAATT;RSEQ=TTTTCTCTCAGAAAGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:26,167:0:2,0:24.4:1:31.9:1:1:0:47.9:63.333:1:0:0.1 0/1:125:2:0,2:11,112:0.016:2,0:22.5:1:30.5:1:1:0:50:4:0.016:0:3.5 -3 178937593 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1767;SOR=Inf;LSEQ=TTCTAGATCCATACAACTTC;RSEQ=TTTTAAAAAACCTACTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:112,130:0:2,0:23.8:1:31.9:1:1:0:57.9:47.4:1:0:0.1 0/1:176:2:1,1:74,100:0.0114:2,2:14:1:30.5:1:1:1.35:60:4:0.0116:0:1 -3 178937630 . TA T 142 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.10444;SOR=0.50798;LSEQ=GCACTAACTAGTTTTATGCT;RSEQ=AAAAAAAAAATTATTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:24:15,9:160,64:0.0968:2,2:23.7:1:31.1:1:0.35549:1.49739:48.6:48:0.0976:0.0081:0.4 0/1:194:10:8,2:126,54:0.0515:2,2:30.5:1:30.3:1:0.726:1.71:45.9:20:0.0521:0:0 -3 178937682 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10813;SOR=5.54774;LSEQ=TTTCTTTCTGAAAAAATTTT;RSEQ=TTTAGATCGGCCATGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:1:0,1:343,136:0.0021:2,0:16:0:32:0:0.28542:0:60:2:0.0021:0:1 0/1:436:5:3,2:299,132:0.0115:2,2:19.6:1:24:1:0.64518:1.50858:41.2:1.5:0.007:0:3 -3 178937877 . A G 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08908;SOR=0;LSEQ=TCCCATTAAATTCTTAAGGT;RSEQ=CATATTACTTGCTTTCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:6:3,3:30,136:0.0349:2,2:20.8:1:29.3:1:0.08553:4.48:30.2:12:0.0349:0:1 0/0:99:0:0,0:23,76:0:2,0:21.1:1:29.4:1:1:0:34.6:198:1:0:0 -3 178937950 . G T 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04168;SOR=Inf;LSEQ=TTGTTTATGTTTGGCTGGAA;RSEQ=AGTTTTCCATACTAAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:0,81:0:1,0:29.9:1:31.8:1:1:0:34:162:1:0:0.1 0/1:44:3:0,3:1,40:0.0682:1,0:26:1:23:1:1:0:29:2:0.0465:0:3.3 -3 178938023 . A C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11917;SOR=0.31736;LSEQ=CTCTTTGAAATTTAAAAAGC;RSEQ=GTAAATTCAAAACTAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:21:2,19:0,13:0.6176:1,2:23.1:1:29.1:1:0.51337:0:52.1:20:0.6061:0:1 0/1:15:5:1,4:1,9:0.3333:2,2:37.4:1:31.2:1:1:2.12:54.6:10:0.3333:0:1 -3 178938735 . CTA C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=1.02152;LSEQ=ATTTGTATACTGATTTAAGA;RSEQ=TATATATATATTTTTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:8:6,2:263,53:0.0247:2,2:20.6:1:31.3:1:0.62761:1.6511:50.5:16:0.0249:0.0093:0 0/1:238:6:5,1:182,50:0.0252:2,2:29.5:1:30.9:1:1:1.37:56.3:12:0.0254:0.0042:0.2 -3 178938747 . A T 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0;SOR=4.42594;LSEQ=ATTTAAGACTATATATATAT;RSEQ=TTTTTAATTTTGCACGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:16:13,3:274,85:0.0427:2,2:21.9:1:30.3:1:0.77209:1.34:55.1:32:0.0428:0:1.1 0/1:309:51:35,16:191,67:0.165:2,2:21.5:1:29.8:1:0.48929:1.30207:55.5:102:0.1672:0:1.1 -3 178938749 . T A 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.70879;SOR=1.57511;LSEQ=TTAAGACTATATATATATAT;RSEQ=TTTAATTTTGCACGATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:3:3,0:293,90:0.0078:2,0:32.3:1:27.3:1:1:0:60:6:0.0079:0:1 0/1:328:4:3,1:232,92:0.0122:2,2:18:1:26.3:1:1:1.19:55.5:8:0.0123:0:1 -3 178939018 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=0.13989;LSEQ=TTGTTTAGAAGCCCAGTGTA;RSEQ=ATACAGATCATGGTCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:74:4,70:4,97:0.4229:1,2:21.2:1:32.4:1:0.72316:1.38:52.4:73:0.4244:0:1 0/1:119:11:1,10:7,101:0.0924:2,2:22.3:1:32.4:1:0.55113:1.44:54.4:22:0.0932:0:1.1 -3 178941853 . C CT 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.68925;SOR=0.82954;LSEQ=AGTTTCTTACTGTGACTATC;RSEQ=TTTTTTTTTAATCAGGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:14:8,6:307,147:0.0298:2,2:26:1:30.3:1:0.40051:1.56476:59.6:28:0.0304:0.0064:0.1 0/1:443:11:10,1:270,158:0.0248:2,2:29.8:1:31.7:1:0.06371:5.83:60:22:0.025:0:0 -3 178942431 . C G 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00642;SOR=0.49053;LSEQ=TTATATTTTAAAATAAATTT;RSEQ=AGGGTAAAATAATAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:169:141:111,30:24,3:0.8343:2,2:22.8:1:32.1:1:0.29543:2.15383:60:282:0.8343:0:1.1 1/0:201:143:105,38:41,17:0.7114:2,2:21.5:1:31.2:1:0.72837:1.14:60:142:0.71:0:1.1 -3 178943123 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGCATGTTGCAAAGGAA;RSEQ=AGTGTAGTCTGCTCAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:28.7:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 178943714 . G A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCCCAAATTTGCATCTGT;RSEQ=GCATTAAATGGTGATACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:275,127:0:2,0:26.5:1:31.7:1:1:0:60:66:1:0:0.1 0/1:367:19:14,5:221,127:0.0518:2,2:28.3:1:27.2:1:0.46581:1.61:60:18:0.0495:0:1.1 -3 178943972 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08688;SOR=Inf;LSEQ=TGATTACACTATAGTACTTT;RSEQ=ACATATCCTCCTCTTACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:0,61:0:1,0:26.9:1:32.3:1:1:0:60:122:1:0:0 0/1:26:2:0,2:0,24:0.0769:1,0:33.5:1:27.5:1:1:0:60:4:0.0769:0:1 -3 178943987 . T TACTTG 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.38916;LSEQ=ACTTTGACATATCCTCCTCT;RSEQ=ACTTAGAATAGCTAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:43:0,43:0,6:0.8776:0,1:23.3:1:31.5:1:1:0:60:86:0.8776:0.2449:0 1/1:22:20:0,20:0,2:0.9091:0,1:32.9:1:31.1:1:1:0:60:40:0.9091:0.0455:0.2 -3 178947289 . C T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=Inf;LSEQ=TTTTTGTTAGATGAGTCTGT;RSEQ=GGTGTTTGTGTATTCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:13,133:0:2,0:25.2:1:29.9:1:1:0:60:72:1:0:0.1 0/1:138:11:4,7:20,106:0.0797:2,2:22.1:1:30.2:1:0.10183:3.00:60:22:0.0797:0:1 -3 178947344 . GA G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.23557;SOR=Inf;LSEQ=AAACAATTGTACTTTCTATG;RSEQ=AAAAAATATGCTCAACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:0:1,0:21.2:1:30.6:1:1:0:60:88:1:0:0 0/1:42:2:0,2:0,40:0.0476:1,0:10.5:1:32.5:1:1:0:60:4:0.0488:0:0 -3 178948196 . A G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01502;SOR=Inf;LSEQ=CAATTAAAAACACAAAATAA;RSEQ=GAGTTCTGGCTGCTCTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:36,210:0:2,0:23.5:1:31.1:1:1:0:60:245:1:0:0 0/1:252:7:3,4:58,187:0.0278:2,2:39.3:1:29.6:1:0.36487:2.41:60:14:0.028:0:1 -3 178951818 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33763;SOR=3.55966;LSEQ=CTAATTTTGTGACATTTGAG;RSEQ=AAAGACCTGAAGGTATTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:1:0,1:210,41:0.004:2,0:1:0:23:0:0.16667:0:60:2:0.004:0:2 0/1:214:3:1,2:147,63:0.014:2,2:7:1:27.7:1:0.22136:4.62867:60:6:0.0142:0:1 -3 178952020 . C T 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTGCATACATTCGAAAGAC;RSEQ=CTAGCCTTAGATAAAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:0:0,0:360,372:0:2,0:24.9:1:30.7:1:1:0:60:44.75:1:0:0.1 0/1:713:47:25,22:311,354:0.0659:2,2:21.6:1:29.7:1:0.45058:1.29:60:94:0.0671:0:1 -3 178952201 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15519;SOR=Inf;LSEQ=TCTGGATTCCACACTGCACT;RSEQ=TTAATAACTCTCAGCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:36,174:0:2,0:22:1:31.7:1:1:0:59.9:51.5:1:0:0.2 0/1:137:2:1,1:28,107:0.0146:2,2:29.5:1:27.5:1:0.37978:3.77:60:4:0.0148:0:1 -3 179366819 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=GTACGTTTTGACCCCATGGG;RSEQ=AAAAAAAAATAGATAACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:3:0:30:0:1:0:60:2:0.5:0:1 1/0:5:3:2,1:1,1:0.6:2,2:25:1:21.3:1:1:1.73:60:2:0.5:0:4 -3 179367238 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24412;SOR=0;LSEQ=GCGTGAGCCACCGTGCCCAG;RSEQ=ATAGTGGATTCTTAAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:75,28:0.019:2,2:13.5:1:26:0:0.47802:2.64948:60:4:0.019:0:1 0/0:107:0:0,0:74,33:0:2,0:20:1:31:1:1:0:60:52.5:1:0:0.1 -3 179367265 . A C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2297;SOR=0;LSEQ=GATTCTTAAGCACATTCTTC;RSEQ=GGTATGTGGTGTGTTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:87,56:0.0138:2,2:19:1:32:0:1:1.54866:60:4:0.014:0:1 0/0:157:0:0,0:89,67:0:2,0:26.8:1:29.9:1:1:0:60:77:0.9935:0:0.1 -3 179367383 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23705;SOR=Inf;LSEQ=AGGCCTCACTTGCCTCCTGC;RSEQ=AAGCACCAACAGCTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:26,62:0:2,0:25:1:30.4:1:1:0:60:87:1:0:0.1 0/1:84:2:1,1:26,56:0.0238:2,2:26.5:1:31:1:0.54217:2.13:60:4:0.0241:0:1.5 -3 179367608 . G GTT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GTAGCTAGTTGCTTCCTGGA;RSEQ=TTTTTTTTGTTTGTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:1,14:0:1,0:23.9:1:32.5:1:1:0:60:30:1:0:0.4 0/1:21:2:1,1:5,12:0.0952:2,2:25:1:31.5:1:1:2.28:60:4:0.1:0:0 -3 179367638 . GT G 49 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.26573;SOR=0.19359;LSEQ=TTTGTTTTTTTTTGCTTTTT;RSEQ=TTTTTTTTTTTTTTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:28.7:1:31.3:1:1:0:60:6:0.5:0:2 0/1:7:1:0,1:2,4:0.1429:2,0:14:0:31:0:1:0:60:2:0.1429:0:0 -3 179367651 . T G 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCTTTTTGTTTTTTTTTTTT;RSEQ=TTTGTTTGAGACGGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:25.5:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:3:0:0,0:0,2:0:0,0:17.5:1:29:1:1:0:60:4:1:0:2.5 -3 179367923 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.51377;SOR=Inf;LSEQ=CCTCGGCCTCCCAAAGTGCT;RSEQ=GGATTGCTTCCTGGGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:41,21:0:2,0:19.7:1:31.5:1:1:0:60:124:1:0:0.4 0/1:90:2:1,1:66,22:0.0222:2,2:16.5:1:27.5:1:0.44794:2.95616:60:4:0.0227:0:1 -3 179367994 . T A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=4.27568;LSEQ=TTGTACCAGCCATGGTATAG;RSEQ=GACCTCCTTACTTAGACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:85:57:23,34:9,19:0.6706:2,2:28.4:1:30.2:1:0.4873:1.42:60:27.5:0.6627:0:1.1 1/1:127:114:48,66:5,8:0.8976:2,2:28.1:1:29.4:1:1:1.16:60:113:0.8968:0:1.1 -3 179368001 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.32056;LSEQ=AGCCATGGTATAGTGACCTC;RSEQ=TTACTTAGACCCGTTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:1,0:28,52:0.0123:2,0:28:0:32:0:0.35802:0:60:2:0.0123:0:2 0/1:123:2:1,1:47,74:0.0163:2,2:10.5:1:28:1:1:1.57:60:4:0.0164:0:2.5 -3 179368044 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51418;SOR=Inf;LSEQ=TGGAGCGTGGCGAGTGACAG;RSEQ=CGGCGCTGGTGTTGGAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:6,33:0:2,0:23.3:1:32.1:1:1:0:60:38:1:0:0.5 0/1:58:2:1,1:9,47:0.0345:2,2:12.5:1:25:1:0.3176:5.01:60:4:0.037:0:2 -3 180017244 . T G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05714;SOR=3.40792;LSEQ=TGACTAGAGGAGCCAAACTG;RSEQ=ATGATAAGTCTGATGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:6:6,0:33,0:0.15:1,0:11.2:1:32.3:1:1:0:60:12:0.15:0:1 0/1:21:8:7,1:13,0:0.381:1,2:20.1:1:32.5:1:0.38095:0:60:16:0.381:0:1.1 -3 180017320 . AT A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19566;SOR=Inf;LSEQ=TAACACCATGTTTCAAAACA;RSEQ=GGACTGGTTTTCCAGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:123,39:0:2,0:23.4:1:30.9:1:1:0:60:324:1:0:0.1 0/1:129:2:1,1:95,32:0.0155:2,2:33:1:29.5:1:0.44767:2.93865:60:4:0.0155:0:0 -3 180017359 . G T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62353;SOR=0.34144;LSEQ=TCAATTAAATCCACATAGTT;RSEQ=AGTGTTCCTGCATTCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:1,2:144,86:0.0129:2,2:22.7:1:27.3:1:0.55855:3.33092:60:6:0.013:0:1 0/0:226:1:0,1:132,93:0.0044:2,0:1:0:23:0:0.41593:0:60:2:0.0045:0:1 -3 180017424 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.59279;LSEQ=ATTGCTGTCAAAAGCCATAT;RSEQ=ATCTCAAGTTAATTTTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:49:22,27:119,142:0.1581:2,2:25.3:1:31.3:1:1:1.0284:60:48:0.1574:0:1.1 0/1:300:121:58,63:81,98:0.4033:2,2:24.2:1:31.1:1:0.72342:1.11:60:120:0.4027:0:1.2 -3 181428123 . G GT 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.21502;SOR=0.69728;LSEQ=TAAAAAAGAAATGGCATCAG;RSEQ=TTTTTTTTTCTTTATTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:673:35:9,26:186,446:0.052:2,2:25.9:1:29.4:1:0.70676:1.20444:60:34:0.0514:0:0.4 0/1:543:20:6,14:172,347:0.0368:2,2:24.8:1:29.1:1:1:1.15626:60:19:0.0353:0.0018:0.4 -3 181428167 . G A 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0622;SOR=Inf;LSEQ=ACCCCACCCTTTGTAGTCAA;RSEQ=TGCATTTTAGCCACAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:39,217:0:2,0:23.5:1:31:1:1:0:60:18.692:1:0:0.2 0/1:169:3:2,1:26,140:0.0178:2,2:7.3:1:23.7:1:0.07159:10.53:60:2:0.0123:0:1.7 -3 181430117 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1908;SOR=Inf;LSEQ=CGGGCCGAGGGTCGGCGGCC;RSEQ=CCGGCGGGCCGGGCCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:22,7:0:2,0:16.3:1:30.3:1:1:0:60:58:1:0:0.3 0/1:23:2:1,1:14,7:0.087:2,2:11:0:31:1:1:1.93655:60:4:0.1:0:1 -3 181430130 . G T 49 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29658;SOR=0;LSEQ=GGCGGCCGCCGGCGGGCCGG;RSEQ=CCCGCGCACAGCGCCCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:4:1,3:68,17:0.0449:2,2:14.8:1:24.8:1:0.0342:11.55446:60:3:0.0345:0:1.5 0/0:52:0:0,0:38,14:0:2,0:14.8:1:30.8:1:1:0:60:25:1:0:0.4 -3 181430136 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1647;SOR=Inf;LSEQ=CGCCGGCGGGCCGGGCCCGC;RSEQ=CACAGCGCCCGCATGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:88,23:0:2,0:16:1:29.8:1:1:0:60:17.5:0.9906:0:0.3 0/1:77:2:1,1:52,22:0.026:2,2:29.5:1:28.5:1:0.51649:2.33383:60:4:0.0267:0:1 -3 181430168 . C T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12666;SOR=0;LSEQ=CATGTACAACATGATGGAGA;RSEQ=GGAGCTGAAGCCGCCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:4:1,3:213,55:0.0147:2,2:19.8:1:28.8:1:0.0315:11.47325:60:8:0.0149:0:1.3 0/0:239:0:0,0:175,64:0:2,0:20.8:1:30.8:1:1:0:60:78.667:1:0:0.2 -3 181430601 . G A 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=51.34362;LSEQ=GTGGGCGCCGGCCTGGGCGC;RSEQ=GGCGTGAACCAGCGCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:662:1:1,0:327,333:0.0015:2,0:48:0:14:0:0.49622:0:60:0:0:0:3 0/1:484:35:17,18:202,247:0.0723:2,2:29.8:1:31:1:0.72631:1.15:60:70:0.0737:0:1.1 -3 181431115 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12749;SOR=Inf;LSEQ=ACATGTGAGGGCCGGACAGC;RSEQ=AACTGGAGGGGGGAGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:38,232:0:2,0:21:1:30.7:1:1:0:60:44:1:0:0.1 0/1:151:2:1,1:28,121:0.0132:2,2:14.5:1:27.5:1:0.34826:4.26:60:4:0.0136:0:1 -3 181431127 . G T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.03809;SOR=Inf;LSEQ=CGGACAGCGAACTGGAGGGG;RSEQ=GAGAAATTTTCAAAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:21,190:0:2,0:21.3:1:30.5:1:1:0:60:34.167:1:0:0.1 0/1:108:3:1,2:13,91:0.0278:2,2:25.3:1:29.7:1:0.34622:3.44:60:6:0.0291:0:1 -3 181431226 . GA G 31 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACGCTCAAAAAGAAAAAG;RSEQ=AAAAAAAAAATCCCATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:0,2:2,41:0.0435:1,0:35.5:1:31:1:1:0:60:4:0.0444:0:0.5 0/0:7:0:0,0:0,7:0:0,0:26:1:28.3:1:1:0:60:14:1:0:0.1 -3 181434168 . TA T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02438;SOR=Inf;LSEQ=TGCACTCACCTCTCATTTTT;RSEQ=AAAAAAAGCCCACAGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:139,3:0:1,0:26.8:1:28.4:1:1:0:60:46.333:1:0:0.1 0/1:59:3:3,0:53,1:0.0508:1,0:41:1:31.3:1:1:0:60:6:0.0526:0:0 -3 181434222 . A T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56102;SOR=3.25648;LSEQ=CAAAATGGTCAGGTTCAAAT;RSEQ=TTTAGCAAAAGGAAAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:1:0,1:279,36:0.0032:2,0:1:0:25:0:0.11709:0:60:2:0.0032:0:1 0/1:195:2:1,1:160,33:0.0103:2,2:35.5:1:29:1:0.31906:4.79162:60:4:0.0103:0:1 -3 182178216 . A G 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01557;SOR=Inf;LSEQ=GGTGTCTACTTAAACAACAA;RSEQ=CCTATTTTCAGTGGTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:49,2:0:1,0:21.4:1:29.3:1:1:0:59.5:16:1:0:0 0/1:18:3:3,0:13,2:0.1667:2,0:26.3:1:31:1:1:0:60:6:0.1667:0:1 -3 182178323 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14642;SOR=Inf;LSEQ=TTTTCTTGTATACCCTCCCC;RSEQ=TATGTGTAACAGCTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:165,52:0:2,0:23.9:1:30.3:1:1:0:59.4:216:1:0:0.1 0/1:135:2:1,1:90,43:0.0148:2,2:17.5:1:28.5:1:0.54726:2.08062:60:4:0.0149:0:1 -3 182178480 . C T 194 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=203.26914;LSEQ=TGTCTCTAGCCAAAAGCAAT;RSEQ=GAGGTCACTTCATCTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1002:1:0,1:497,502:0.001:2,0:1:0:25:0:1:0:60:2:0.001:0:1 0/1:615:104:55,49:262,248:0.1691:2,2:25.1:1:29.1:1:0.82979:1.06:60:33.667:0.1681:0:1.1 -3 182178717 . A G 196 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTGCTTTTACCATTTTT;RSEQ=AAAAACCAGAGGGCCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:678:0:0,0:264,412:0:2,0:26.6:1:29.3:1:1:0:60:83.5:1:0:0.1 0/1:542:79:34,45:189,274:0.1458:2,2:25.3:1:31.1:1:0.71242:1.10:60:158:0.1468:0:1.1 -3 182178853 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16882;SOR=Inf;LSEQ=GGGTGGTTTCCTGTTCGACA;RSEQ=TCGCCATTTTTGATGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:35,122:0:2,0:20.5:1:31.6:1:1:0:60:156:1:0:0.2 0/1:110:2:1,1:25,83:0.0182:2,2:22:1:30:1:0.41852:3.28:60:4:0.0187:0:1 -3 182664547 . G A 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGCTGAGTAGGAATTGAA;RSEQ=GAAACAGAAGAATATGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:22:1:28.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 182664889 . C CA 81 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03345;SOR=5.39324;LSEQ=AACAGAATGAGACTCTATCT;RSEQ=AAAAAAAACAAAAACAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:2,0:172,0:0.0115:1,0:39:1:32:0:1:0:60:4:0.0116:0:0 0/1:118:7:6,1:104,5:0.0593:1,2:25.1:1:29.2:1:0.31753:3.40715:60:14:0.0593:0.0085:0 -3 182664992 . T TA 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28362;SOR=1.48993;LSEQ=TATGGGATAAAAAGGCACAT;RSEQ=AAAAAAAAGTGGTGTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:944:13:6,7:577,353:0.0138:2,2:25:1:28.7:1:0.26071:1.90567:60:12:0.0129:0.0042:0.5 0/1:883:18:11,7:504,361:0.0204:2,2:26.7:1:27.8:1:1:1.13:60:17:0.0196:0.0023:0.3 -3 182678979 . C T 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65744;SOR=1.94879;LSEQ=GTCAATGTATTTGAATATAT;RSEQ=TGAAACACCAAATATAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:2:0,2:245,49:0.0068:2,0:1:0:27.5:1:0.0292:0:60:4:0.0068:0:1 0/1:229:3:2,1:187,39:0.0131:2,2:10.7:1:23:1:0.43938:2.38575:60:2:0.0088:0:2.3 -3 182681606 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50176;SOR=0;LSEQ=CTTTAAATTTACACTAAAAA;RSEQ=TTCATGACATAATTCAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:2,0:153,26:0.011:2,0:29:1:29.5:1:1:0:60:4:0.0112:0:1 0/0:154:0:0,0:127,27:0:2,0:22.8:1:31.6:1:1:0:60:76:1:0:0.1 -3 182681740 . C T 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.60373;LSEQ=GTTGCTGCTCTGAACTTCCA;RSEQ=GCAATAATCAACACACTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:942:337:183,154:317,288:0.3577:2,2:24.8:1:30.4:1:0.58642:1.08:59.8:83.25:0.3569:0:1.2 1/0:929:550:277,273:194,180:0.592:2,2:24.6:1:29.6:1:0.68761:1.06212:59.9:77.571:0.5909:0:1.1 -3 182681853 . T C 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.06932;LSEQ=AGGGTCTTTAAAAATAACAA;RSEQ=GCAATATTAAAGTAGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:440:172:42,130:73,195:0.3909:2,2:24.5:1:30:1:0.57846:1.15834:60:85:0.3917:0:1.1 1/0:382:218:65,153:46,118:0.5707:2,2:23.6:1:29.8:1:0.73375:1.09:60:108:0.5745:0:1.1 -3 182682264 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTATCAGAAAAACTGTGA;RSEQ=CTAAACTATGCAATTCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:37.5:1:29.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 182683592 . T A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50038;SOR=Inf;LSEQ=TATGTAAAATCACATAAGAC;RSEQ=AAATATTTCTATATGGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:27,124:0:2,0:22.7:1:28.7:1:1:0:60:49.333:1:0:0.2 0/1:171:2:1,1:32,137:0.0117:2,2:7.5:1:25:1:0.34964:4.23:60:4:0.0118:0:2 -3 182698083 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGCTCTCGCGTAGCGGCTG;RSEQ=GCCCGGGCGGGAAGGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:39:0:10:0:1:0:60:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:23.5:1:29:1:1:1:60:4:0.5:0:2 -3 182698221 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5311;SOR=0;LSEQ=GGCGGCCGGGGCGGGGGTGC;RSEQ=CGGCAGCGCCGGCCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:34,13:0.0408:2,2:5.5:1:29.5:1:0.49405:2.55705:60:4:0.0426:0:1 0/0:28:0:0,0:21,7:0:2,0:7:1:28.5:1:1:0:60:13:1:0:0.2 -3 182698233 . G GC 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.21888;SOR=Inf;LSEQ=GGGGGTGCGCGGCAGCGCCG;RSEQ=CCCCCAGCCGGCAGGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:83,37:0:2,0:11.5:1:31.4:1:1:0:60:119:1:0:0.3 0/1:106:2:1,1:66,38:0.0189:2,2:20.5:1:31:1:1:1.72729:60:4:0.0192:0:0.5 -3 182698254 . C T 73 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50474;SOR=0.51447;LSEQ=CCCCCAGCCGGCAGGGCGGG;RSEQ=GGGCGGCCGCAGTGCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:6:1,5:159,101:0.0226:2,2:14.7:1:28.5:1:0.03855:7.81752:60:12:0.0229:0:1 0/1:256:3:0,3:153,100:0.0117:2,0:1:0:28.7:1:0.06399:0:60:6:0.012:0:1 -3 182698263 . G T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02612;SOR=Inf;LSEQ=GGCAGGGCGGGCGGGCGGCC;RSEQ=CAGTGCCTCACCATGTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:209,144:0:2,0:22.6:1:30.4:1:1:0:60:31.091:1:0:0.3 0/1:331:5:3,2:189,137:0.0151:2,2:20.6:1:30.4:1:1:1.09:59:10:0.0153:0:1.2 -3 182698328 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03235;SOR=Inf;LSEQ=CTCCGGCTCCGCAGCGAATG;RSEQ=ACGGCGGCGGCGGCGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:188,216:0:2,0:26.1:1:30.9:1:1:0:60:49.5:1:0:0.2 0/1:455:6:6,0:212,235:0.0132:2,0:7:1:24.5:1:0.01198:0:60:5:0.0114:0:1 -3 182698329 . ACGG A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.17062;SOR=1.83443;LSEQ=TCCGGCTCCGCAGCGAATGG;RSEQ=CGGCGGCGGCGGCGGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:9:4,5:174,204:0.0231:2,2:31.8:1:29.9:1:1:1.06602:60:18:0.0234:0.0026:0.1 0/1:432:18:7,11:194,217:0.0417:2,2:29.9:1:29.7:1:0.63096:1.40377:59.7:36:0.0424:0.0046:0.4 -3 182698341 . G A 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.42721;SOR=0.44019;LSEQ=GCGAATGGACGGCGGCGGCG;RSEQ=CGGCGGCTCCTCTCACGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:4:3,1:128,178:0.0129:2,2:9.8:1:29.8:1:0.31429:4.15:60:8:0.0131:0:1 0/0:350:2:2,0:154,194:0.0057:2,0:1:0:24.5:1:0.19795:0:60:4:0.0058:0:1 -3 182698361 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37693;SOR=3.56446;LSEQ=GCGGCGGCTCCTCTCACGGG;RSEQ=TTGCCCGGCTCCCGCTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:0,1:64,129:0.0052:2,0:2:0:32:0:1:0:60:2:0.0053:0:1 0/1:220:4:2,2:78,138:0.0182:2,2:25.8:1:28.8:1:0.62296:1.76:60:8:0.0187:0:1 -3 182698375 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25044;SOR=Inf;LSEQ=CACGGGCTTGCCCGGCTCCC;RSEQ=CTCATGCGCAGTGCGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:20,85:0:2,0:16.4:1:31.7:1:1:0:60:34:1:0:0.1 0/1:121:3:2,1:31,87:0.0248:2,2:8.3:1:27.3:1:0.18029:5.52:60:6:0.0256:0:1 -3 182698686 . C G 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACGCAGGCTGGAAGCGGG;RSEQ=ACGAGCGGCGGCGGATAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:36:0:33:0:1:0:60:2:1:0:2 1/1:5:5:2,3:0,0:1:0,2:31.6:1:31:1:1:0:60:10:1:0:1 -3 183169595 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0.14783;SOR=0;LSEQ=CAAATCCATGAGATTTACTA;RSEQ=AAATTAAATACAAGTACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:7.5:1:27.5:1:1:1.62:60:4:0.1176:0:1 0/0:28:0:0,0:10,18:0:2,0:19.9:1:31.6:1:1:0:60:27:1:0:0.2 -3 184296627 . T A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAGGAGGTGGACTTGAGC;RSEQ=GAGCCAGGCGGGATGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 184298292 . CT C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19357;SOR=Inf;LSEQ=TGAACTATGTGCACCGCGAC;RSEQ=GGCTGCTCGCAACATCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:19,30:0:2,0:26.5:1:30.6:1:1:0:60:48:1:0:0.1 0/1:39:2:1,1:14,23:0.0513:2,2:16.5:1:29:1:1:1.62:60:4:0.0526:0.0256:0.5 -3 184298448 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=AGACTGGGGGCGGGGCCTAT;RSEQ=AGCCAGGGGCTCGGGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:24.6:1:31.6:1:1:0:60:10:1:0:0 0/1:5:2:1,1:0,3:0.4:0,2:6.5:1:29.5:1:0.4:0:60:4:0.4:0:1.5 -3 184298663 . G A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14055;SOR=0;LSEQ=TACTGGGACATGAGCAACCA;RSEQ=GATGTGAGTGAGGCTACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:6,9:0.2857:2,2:21.3:1:29.7:1:0.36146:2.84:60:12:0.2857:0:1 0/0:9:0:0,0:5,4:0:2,0:27.1:1:30.4:1:1:0:60:18:1:0:0.1 -3 184489727 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCTTGTGTGACTCTCC;RSEQ=GCTGGCGTGGCTGCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:27.5:1:1:0:60:4:1:0:1.5 -3 184492221 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCTTGAACCCAGGAGGC;RSEQ=GAGGTTGCTGTGAGGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:30.5:1:1:0:53.5:4:1:0:1.5 -3 184630256 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12;SOR=Inf;LSEQ=CCAAAGGTAGCCAGGATTTT;RSEQ=GTTTGTTTGTTTTTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:3,13:0:2,0:20.4:1:28.3:1:1:0:60:15:1:0:0.3 0/1:9:2:1,1:1,6:0.2222:2,2:15:0:32:0:0.41667:4.58:60:4:0.2222:0:1.5 -3 184630294 . A G 76 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TTTGTTTTTTACATGACTCA;RSEQ=TTCCGAAGCTTAACTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:31:1:32.8:1:1:0:60:10:1:0:1 0/1:3:1:0,1:0,2:0.3333:0,0:18:0:33:0:1:0:60:2:0.3333:0:1 -3 184673185 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16159;SOR=0;LSEQ=CATATGCTGCCTTCTCTATC;RSEQ=CTGCGGTGGCTACCTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:41,18:0.0328:2,2:29.5:1:30:1:0.52951:2.24393:60:4:0.0333:0:1 0/0:90:0:0,0:54,36:0:2,0:26.6:1:29:1:1:0:60:17:1:0:0.2 -3 184673209 . A T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19052;SOR=0;LSEQ=CGGTGGCTACCTAAAAGGGA;RSEQ=GGGCCCCCTGTCCCATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:57,36:0.0211:2,2:40:0:31.5:1:1:1.57538:60:4:0.0215:0:1.5 0/0:122:0:0,0:68,54:0:2,0:28.9:1:29.4:1:1:0:59.9:23.4:1:0:0.2 -3 184673217 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50469;SOR=Inf;LSEQ=ACCTAAAAGGGAAGGGCCCC;RSEQ=TGTCCCATGATCATGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:60,42:0:2,0:27.5:1:30.9:1:1:0:59.8:50:1:0:0.2 0/1:129:2:1,1:72,53:0.0155:2,2:36:1:30.5:1:1:1.35515:60:4:0.0163:0:1 -3 184673222 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50261;SOR=Inf;LSEQ=AAAGGGAAGGGCCCCCTGTC;RSEQ=CATGATCATGTGACTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:62,45:0:2,0:27.9:1:30.7:1:1:0:59.8:34.667:1:0:0.2 0/1:130:2:1,1:73,55:0.0154:2,2:35:1:28.5:1:1:1.32433:60:4:0.0161:0:1 -3 184673261 . A G 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10608;SOR=0;LSEQ=TTCACCTTATCACTTAGAAG;RSEQ=TTCATCCTCCTTACCCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:2,1:39,48:0.0333:2,2:21.7:1:25:1:0.58958:2.44:60:2:0.0235:0:1.7 0/0:99:0:0,0:41,58:0:2,0:21.5:1:28.4:1:1:0:59.9:32:1:0:0.3 -3 184673338 . T C 124 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02442;SOR=0;LSEQ=CAGTCGTTTGAGGCCACTGC;RSEQ=GGTCTCCGCGTCTTGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:1,18:0,0:1:0,1:27.6:1:29.2:1:1:0:60:18:1:0:1.7 1/0:23:17:1,16:1,5:0.7391:2,1:29.6:1:29.6:1:0.46245:3.01096:60:34:0.7391:0:1.8 -3 184673365 . T C 120 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10122;SOR=0;LSEQ=CGCGTCTTGGTGGTAGTGGT;RSEQ=CCCCGGGCCCAGCTATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:1,15:0,0:1:0,1:20.2:1:30.1:1:1:0:60:15:1:0:1.9 1/0:16:12:1,11:2,2:0.75:2,2:32.1:1:30.8:1:0.13571:8.85639:60:11:0.7333:0:2.1 -3 185003285 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19706;SOR=Inf;LSEQ=GTACCTTAGGTCTGTACATT;RSEQ=ACATTCTTGAGGTTTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:159,17:0:2,0:23.1:1:31.9:1:1:0:60:43:1:0:0 0/1:141:2:1,1:122,17:0.0142:2,2:5.5:1:26.5:1:0.23982:7.00279:60:4:0.0142:0:1 -3 185046766 . T A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.49134;SOR=1.92252;LSEQ=TTGGTGTAAGTAGTTTTTTT;RSEQ=AAAAAAAACTATTATGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:20:20,0:9,0:0.6897:0,1:18.9:1:28.9:1:1:0:60:40:0.6897:0:1 1/1:16:13:13,0:3,0:0.8125:0,1:22:1:29:1:1:0:60:26:0.8125:0:1.1 -3 185046909 . AT A 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=4e-05;SOR=1.98681;LSEQ=CAGCACTCAGCAGTAGTTTT;RSEQ=TTTTTTTTAATGGAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:381:224:167,57:112,42:0.5879:2,2:23.4:1:30.8:1:0.72175:1.10:60:223:0.5868:0.0761:0.8 1/0:307:227:160,67:58,22:0.7394:2,2:28.1:1:29.9:1:0.77603:1.10365:60:112.5:0.7377:0.0293:0.7 -3 185046975 . T C 303 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.51461;LSEQ=TGCTGCTAAAACAGGTCCCG;RSEQ=GTGCACGAAATGATTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:936:935:508,427:0,1:0.9989:0,2:26.8:1:30.7:1:0.45726:0:60:61.333:0.9989:0:1.1 1/1:964:962:496,466:0,1:0.9979:0,2:26.4:1:30.6:1:0.48494:0:60:52.444:0.9989:0:1.2 -3 185047301 . A G 95 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAATGTATTTTCAAAGAGG;RSEQ=AGAACTTTGTAAAACAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,0:0.9:0,0:20.2:1:30.2:1:1:0:60:18:0.9:0:1 1/1:1:1:0,1:0,0:1:0,0:24:0:33:0:1:0:60:2:1:0:1 -3 185146373 . G A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04038;SOR=Inf;LSEQ=GTTATACTCATGGCACGATG;RSEQ=CCAACTTTCAGGAGCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:193,118:0:2,0:24.5:1:31.3:1:1:0:60:61.2:0.9967:0:0.1 0/1:255:4:2,2:150,101:0.0157:2,2:10.5:1:28.5:1:1:1.48275:60:8:0.016:0:1.3 -3 185146499 . G A 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.16307;LSEQ=ACCCTTCTCCCAAGCTGCTC;RSEQ=AGGACCAGCAGGAAAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:1:1,0:311,275:0.0017:2,0:1:0:25:0:1:0:60:2:0.0017:0:1 0/1:544:30:18,12:280,233:0.0551:2,2:26.2:1:30.4:1:0.70643:1.25:60:60:0.0561:0:1.1 -3 185146702 . C T 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGACGGAGAGAGCACAAG;RSEQ=GGAACTGAAGACATAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:318,248:0:2,0:24.6:1:30.7:1:1:0:60:50.455:1:0:0.1 0/1:573:104:61,43:239,230:0.1815:2,2:24.5:1:29.2:1:0.16018:1.36:60:51:0.1821:0:1.1 -3 185146868 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17661;SOR=Inf;LSEQ=AGCTAGAATATGGACTTGGA;RSEQ=GATATTTCTTGTGTAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:38,211:0:2,0:23.2:1:31.3:1:1:0:60:248:1:0:0.1 0/1:181:2:1,1:39,140:0.011:2,2:16.5:1:31:0:0.39411:3.56:60:4:0.0111:0:1 -3 185155224 . T C 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTTCAAGCTTATTTCTTGCT;RSEQ=GTGTGCCTAGATACTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:304,171:0:2,0:24.3:1:30:1:1:0:60:78.167:1:0:0.1 0/1:467:24:17,7:282,161:0.0514:2,2:23:1:31:1:0.52174:1.39:60:48:0.0523:0:1 -3 185155430 . C CT 240 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00307;SOR=0.69505;LSEQ=CGCATTCAAGTAGGTCAAGG;RSEQ=TTTTTTTTTTTAAGAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:517:262:80,182:68,123:0.5068:2,2:28.2:1:29.9:1:0.26596:1.25707:59.9:20.833:0.5081:0.0193:0.4 0/1:593:247:79,168:106,130:0.4165:2,2:31.2:1:29.2:1:0.00374:1.73202:59.9:26.444:0.4161:0:0.5 -3 185155442 . A T 73 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00191;SOR=Inf;LSEQ=GGTCAAGGCTTTTTTTTTTT;RSEQ=AGAAGTAGACCTATTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:123,314:0:2,0:21.9:1:29.1:1:1:0:59.9:30.214:0.9976:0:0.5 0/1:471:10:9,1:140,321:0.0212:2,2:8.2:1:22.2:1:0.00019:20.51:60:2.333:0.0153:0:1.7 -3 185155807 . G A 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAAAACAAAGTTGGCCGGGC;RSEQ=CAGTGGCTCATGTCTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:22:1:30.6:1:1:0:59:10:1:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 185159826 . C CA 29 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACAGAGCGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19:0:29:1:1:0:50:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 185161145 . A G 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12789;SOR=Inf;LSEQ=TTTTAAAATAATTCGGGTAT;RSEQ=GAATTGGTTTTTATTAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:221,17:0:2,0:22.3:1:28.6:1:1:0:60:118:1:0:0.1 0/1:133:2:1,1:114,16:0.015:2,2:18:0:28:1:0.24185:6.94249:60:4:0.0153:0:1 -3 185165534 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=TTAGAATCATGGTTTTCGTT;RSEQ=GTACTAATGATCCAGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:180,19:0:2,0:24.1:1:28.7:1:1:0:60:398:1:0:0.1 0/1:199:2:1,1:154,43:0.0101:2,2:24.5:1:28:0:0.39419:3.55169:60:4:0.0101:0:1 -3 185167159 . TA T 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=23.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACAGAGCAAGATGCTGTC;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,1:0.5:0,0:23:1:32.5:1:0.33333:0:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 185167519 . AT A 159 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.67643;SOR=0.77469;LSEQ=GTGTTGATTACCCCACATAG;RSEQ=TTTTTTTTTTTTTTCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:33:31,2:21,0:0.4925:1,2:30.6:1:31.6:1:0.51572:0:60:66:0.5:0.0746:0.7 0/1:35:15:12,3:11,0:0.4286:0,2:29.1:1:30.2:1:0.23846:0:60:30:0.4286:0.0286:0.1 -3 185167910 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50937;SOR=0;LSEQ=TATTTGGAGTAAATATCCTG;RSEQ=TGGTGGAAAGAATAGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:17,146:0.012:2,2:25:1:28.5:1:0.20687:8.37:60:4:0.0122:0:1 0/0:123:0:0,0:20,103:0:2,0:19.8:1:31:1:1:0:60:122:1:0:0 -3 185168877 . CA C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.18995;SOR=Inf;LSEQ=GACAGAGCGAGACTCCGTCT;RSEQ=AAAAAAAGAAAAAAAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:0:1,0:18.8:1:30.9:1:1:0:59.8:66:1:0:0.1 0/1:26:2:2,0:23,1:0.0769:1,0:16.5:1:31.5:1:1:0:60:4:0.0769:0:0 -3 185170285 . A T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCCTGCCTCGGCCTCCC;RSEQ=AACTGCTGGGATTACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:29:1:1:0:60:4:1:0:1 -3 185180812 . T C 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCAACTCCAAATTCCCGTA;RSEQ=AGCTTCTTATATTTCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:29.5:1:32.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 185181248 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52064;SOR=0;LSEQ=GGCTCTTCAGTAGAAGCATG;RSEQ=AGGGAAAAAAAATCTTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:2,0:161,5:0.0118:1,0:30.5:1:31.5:1:1:0:60:4:0.0121:0:1 0/0:110:0:0,0:106,4:0:1,0:24.4:1:32.3:1:1:0:60:109:1:0:0.1 -3 185181543 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57784;SOR=2.69831;LSEQ=ACCATTTCACTTTCCACACA;RSEQ=CTTTCACCTCTGCTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:0,1:10,170:0.0055:2,0:15:0:14:0:1:0:60:0:0:0:6 0/1:135:2:1,1:9,124:0.0148:2,2:6.5:1:27:1:0.14317:13.12:60:4:0.015:0:1 -3 185183418 . G C 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGACAAGGGAGGCTTAAA;RSEQ=TAAGAGGGCCTTGGGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:96:96:96,0:0,0:1:0,1:25.4:1:32.1:1:1:0:60:47:1:0:1.2 1/1:55:55:53,2:0,0:1:0,1:21.4:1:31:1:1:0:60:110:1:0:1.1 -3 185183491 . C T 211 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01122;LSEQ=CATCAAGCGGACTTTTTTCT;RSEQ=CCGAAGTTGGTTGGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:129:85,44:192,99:0.3071:2,2:26.8:1:30.1:1:1:1.00391:60:128:0.3107:0:1.2 0/0:406:2:0,2:254,150:0.0049:2,0:1:0:25.5:1:0.13959:0:60:4:0.0051:0:1 -3 185183656 . G A 217 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00406;LSEQ=AGAAGGAGCTCATTAAGTAT;RSEQ=TATCCAGACTAGTGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:162:55,107:133,199:0.3279:2,2:25.9:1:29.6:1:0.20056:1.29954:60:39.5:0.3251:0:1.1 0/0:508:1:1,0:198,309:0.002:2,0:1:0:23:0:0.39173:0:60:2:0.002:0:1 -3 185183717 . C A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32098;SOR=3.9419;LSEQ=AATCAGCAGAAACATACTAC;RSEQ=CTTCCATGTTGCTGCTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:0,1:18,168:0.0053:2,0:27:0:12:0:1:0:60:0:0:0:6 0/1:144:3:2,1:11,130:0.0208:2,2:16.7:1:27.3:1:0.02155:22.38:60:6:0.0211:0:1 -3 185191198 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05093;SOR=Inf;LSEQ=GCTCAGAGACAGCTGCCCGG;RSEQ=TCGAGCCCTGACCTCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:185,220:0:2,0:23.4:1:31.8:1:1:0:60:49.625:1:0:0.1 0/1:368:4:2,2:153,211:0.0109:2,2:28:1:24.8:1:1:1.38:60:3:0.0084:0:1.5 -3 185195227 . G GA 160 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=9.85676;LSEQ=ATTGCTTTTAGTGGAATGGG;RSEQ=AAAAAAAATCCTAAGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:5:3,2:184,405:0.0084:2,2:29.6:1:29:1:0.18235:3.29:60:10:0.0085:0.0017:0.2 0/1:582:45:11,34:188,344:0.0773:2,2:23:1:29.3:1:0.19059:1.6878:60:44:0.0763:0.0069:0.1 -3 185197965 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19479;SOR=Inf;LSEQ=TACTATGAGTGACAGATAAG;RSEQ=AAAGAAAAGCAGTTGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:185,46:0:2,0:22.8:1:31:1:1:0:60:24.667:1:0:0.1 0/1:183:2:1,1:134,47:0.0109:2,2:23:1:31:1:0.45685:2.83172:60:4:0.0113:0:1 -3 185199743 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTATCCGGGCATGGTGGCAC;RSEQ=CGCCTGTAGTCCCAGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:37.5:1:29.5:1:1:0:58:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 185200783 . A C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACATTTTAGAACACAAAG;RSEQ=ACAGCAAAAGAAAAGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:10:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 185200873 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTACGGAAATGACCTA;RSEQ=AAAAGTCTGGTGACCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 186073482 . T C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00499;LSEQ=CTACCATCATTACCCCATTA;RSEQ=CACCATCACCAGCACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:17:11,6:14,9:0.425:2,2:29.5:1:32.2:1:1:1.17:60:34:0.4595:0:1.3 0/1:61:26:14,12:17,18:0.4262:2,2:25.6:1:30.5:1:0.7972:1.23:60:25:0.431:0:1.2 -3 186490322 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53613;SOR=0;LSEQ=CGGCGGGCAGAGCTGGCCTG;RSEQ=GGGCCGGGTCCCGTGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:20,1:0.087:1,2:20.5:1:31.5:1:0.16996:14.49116:60:4:0.0909:0:1 0/0:12:0:0,0:12,0:0:0,0:19.7:1:28.8:1:1:0:60:5:1:0:0.4 -3 186490810 . G T 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56342;SOR=3.11046;LSEQ=CGGAAGTCCGTGGGCTCAGC;RSEQ=GCGGCTTTTGCAGGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:0,1:89,61:0.0066:2,0:1:0:25:0:0.4106:0:60:2:0.0067:0:1 0/1:98:2:1,1:57,39:0.0204:2,2:37:0:32:0:1:1.45573:60:4:0.0204:0:1.5 -3 186490832 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51443;SOR=0;LSEQ=CGGCTTTTGCAGGGACCCCA;RSEQ=AGCAGGCAGCCTGGGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:88,74:0.0122:2,2:18.5:1:29.5:1:1:1.18792:60:4:0.0123:0:1.5 0/0:114:0:0,0:63,51:0:2,0:26.5:1:31.1:1:1:0:60:56:1:0:0.2 -3 186490848 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17547;SOR=Inf;LSEQ=CCCAGAGCAGGCAGCCTGGG;RSEQ=GGTGCCGCTGGGACTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:85,77:0:2,0:29.8:1:30.8:1:1:0:60:53:0.9938:0:0.1 0/1:118:2:1,1:57,59:0.0169:2,2:19.5:1:30:1:1:1.03:60:4:0.0172:0:1.5 -3 186491092 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22691;SOR=Inf;LSEQ=AGGTTTCCCTGGTCCATCCT;RSEQ=CCTGACCCCCATGCATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:58,14:0:2,0:23:1:31.4:1:1:0:60:71:1:0:1 0/1:66:2:1,1:52,12:0.0303:2,2:40.5:1:30:1:0.35758:4.20318:60:4:0.0303:0:2 -3 186491101 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49729;SOR=0;LSEQ=TGGTCCATCCTCCCTGACCC;RSEQ=CATGCATGCCCAGGTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:65,19:0.0233:2,2:17.5:1:32.5:1:0.41313:3.35992:60:4:0.0233:0:2 0/0:82:0:0,0:64,18:0:2,0:25.9:1:30.2:1:1:0:60:26.333:1:0:1.1 -3 186491116 . T C 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03482;SOR=8.46071;LSEQ=GACCCCCATGCATGCCCAGG;RSEQ=TCTGCATCCAGGCCCTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:90:70,20:5,2:0.9184:2,2:26.2:1:32:1:0.65516:1.39:60:89:0.9271:0:1.2 1/1:97:96:73,23:1,0:0.9897:0,2:27.8:1:31.9:1:1:0:60:95:0.9896:0:1.2 -3 186491156 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2195;SOR=0;LSEQ=CTCCTTGCCTAATCCCAGCT;RSEQ=CCCGCGAAGATGCAGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:106,45:0.0131:2,2:36.5:1:29.5:1:0.5123:2.3408:60:4:0.0132:0:2 0/0:173:0:0,0:114,59:0:2,0:20.4:1:30.4:1:1:0:60:85.5:1:0:0.6 -3 186491189 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.35971;SOR=3.19751;LSEQ=CAGCCAGCAGGAACGTCTAG;RSEQ=TTTTGCAGCTACCAACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:1,0:158,109:0.0037:2,0:1:0:25:0:1:0:60:2:0.0038:0:1 0/1:253:3:2,1:142,108:0.0119:2,2:15.3:1:25.7:1:1:1.52:60:6:0.012:0:2 -3 186491192 . T C 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24911;SOR=0;LSEQ=CCAGCAGGAACGTCTAGGTT;RSEQ=TGCAGCTACCAACCAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:1,2:156,112:0.0111:2,2:27.3:1:25:1:0.57444:2.77523:60:2:0.0075:0:2.7 0/0:257:0:0,0:142,114:0:2,0:25.2:1:29:1:1:0:60:35.571:1:0:0.3 -3 186491195 . C T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36277;SOR=3.15544;LSEQ=GCAGGAACGTCTAGGTTTTG;RSEQ=AGCTACCAACCAACCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:1:0,1:157,117:0.0036:2,0:1:0:26:0:0.42909:0:60:2:0.0037:0:1 0/1:263:3:1,2:142,118:0.0114:2,2:17.3:1:28.3:1:0.59353:2.39894:60:6:0.0115:0:1 -3 186491296 . CCA C 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.21159;SOR=0.19927;LSEQ=GCTTCAATTTCGTCCTGCCC;RSEQ=CACACACACCATGGGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:5:1,4:12,80:0.0521:2,2:16.2:1:32:1:0.52096:1.66:60:10:0.0526:0.0313:0.6 0/1:93:1:0,1:16,76:0.0108:2,0:26:0:28:0:1:0:60:2:0.0109:0:1 -3 186501502 . C A 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.43906;LSEQ=GGAGATGATAGTGGATGGCA;RSEQ=GGAGGCAAAAACTCTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1187:535:188,347:224,428:0.4507:2,2:24.6:1:30.8:1:0.80646:1.04:60:534:0.4545:0:1.1 1/0:1441:961:356,605:186,292:0.6669:2,2:24.9:1:30.3:1:0.52525:1.08246:60:191.2:0.6709:0:1.1 -3 186501648 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCTAAAGGGCGTTTTTCCTC;RSEQ=CTAAGACATTACGAAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:26:1,25:3,60:0.2921:1,1:19.3:1:30.3:1:1:1.24698:60:12:0.2824:0:1.5 1/1:43:43:0,43:0,0:1:0,1:20.6:1:30.3:1:1:0:60:20.5:1:0:1.2 -3 186501900 . C T 51 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55379;SOR=0;LSEQ=CGGTGAACCGTTGGCATCGC;RSEQ=CTCGCCAGGCCGCTCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:10,4:0.2222:2,0:36.5:1:25.8:1:0.52418:0:60:3:0.1875:0:1 0/0:4:0:0,0:4,0:0:0,0:34.5:1:30.5:1:1:0:60:8:1:0:0 -3 186502017 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07671;SOR=Inf;LSEQ=AAACGGGATCGCCATGCGCT;RSEQ=GGGCCTGGGGGGCTGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:44,2:0:1,0:23.9:1:30.9:1:1:0:60:45:1:0:0.2 0/1:35:3:3,0:31,1:0.0857:1,0:34.3:1:29.7:1:1:0:60:6:0.0882:0:1 -3 186502034 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23997;SOR=Inf;LSEQ=GCTCGGGCCTGGGGGGCTGC;RSEQ=TTCCGGGCATCCGCAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:60,3:0:1,0:23.6:1:30.9:1:1:0:60:20:1:0:0.2 0/1:61:2:1,1:59,0:0.0328:1,2:34:1:30:1:0.03279:0:60:4:0.0333:0:0 -3 186502665 . C T 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGATCACTTGATTATTTGGG;RSEQ=ATAATGTTCCAAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:264,53:0:2,0:24:1:32:1:1:0:60:34.222:1:0:0.1 0/1:250:36:32,4:191,23:0.144:2,2:23.1:1:29.3:1:1:1.03789:60:72:0.144:0:1.1 -3 186503435 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=TGTAGGAAACGTTATTCTTG;RSEQ=ATTGTCTAGCTGATGCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:13:11,2:22,0:0.3714:1,2:24.9:1:30.8:1:0.13109:0:60:26:0.3714:0:1.1 1/1:8:8:8,0:0,0:1:0,0:32.4:1:28.1:1:1:0:60:7:1:0:1 -3 186503571 . TA T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.17813;SOR=Inf;LSEQ=AGTTTTGTGCTGTGCATGCA;RSEQ=AAAGCTGTTGGCAGACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:225,3:0:1,0:24.9:1:28.3:1:1:0:60:56:1:0:0.1 0/1:167:2:1,1:158,7:0.012:1,2:19.5:1:27:1:0.09379:21.18043:60:4:0.012:0.006:0.5 -3 186504148 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=3.8735;LSEQ=AATACAACTGATGTGTTTTG;RSEQ=TGTCGTTCCCCCTGCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:72:10,62:48,225:0.2087:2,2:22.6:1:32.3:1:0.5951:1.32171:60:144:0.213:0:1.1 1/0:251:127:24,103:22,101:0.506:2,2:24.1:1:31.6:1:0.87143:1.07:60:41.333:0.5082:0:1.1 -3 186504212 . CAG C 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.02542;SOR=Inf;LSEQ=ACCTTCATTCCGTAGTAAGA;RSEQ=AGACGCTTGGCTTCAGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:147,105:0:2,0:24.8:1:31:1:1:0:60:83:1:0:0.1 0/1:169:4:2,2:103,62:0.0237:2,2:33:1:32.8:1:0.63417:1.65603:60:8:0.0238:0:0 -3 186504406 . A C 211 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTGACCCTTGAAGGAATCA;RSEQ=ACAGTTTTATATTAATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1326:91:44,47:546,687:0.0686:2,2:28.3:1:32.5:1:0.51223:1.18:59.8:90:0.0686:0:1.1 0/0:1489:0:0,0:691,795:0:2,0:25.3:1:29.9:1:1:0:59.8:122.833:0.9986:0:0.2 -3 186504901 . T C 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGACTGTTAACTTTAAC;RSEQ=TCTAAACATTACAGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1007:0:0,0:600,407:0:2,0:25.7:1:30.6:1:1:0:60:142.857:1:0:0.1 0/1:1168:33:21,12:668,467:0.0283:2,2:17.8:1:31.1:1:0.72012:1.22:60:66:0.0287:0:1.1 -3 186505706 . A C 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTTGGCTGTATTGAAAAAA;RSEQ=TTCATACGTTTTTCTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:578:0:0,0:156,422:0:2,0:24.2:1:30.7:1:1:0:60:114.6:1:0:0.1 0/1:573:20:7,13:174,379:0.0349:2,2:25:1:31.7:1:0.80739:1.17:60:40:0.0353:0:1.2 -3 186505900 . T G 64 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.63282;SOR=0.42811;LSEQ=TTTTTCCACAATTGTTGGTC;RSEQ=TACCTTATGCTTGAGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:0,4:0,15:0.2105:1,0:23.8:1:32:1:1:0:60:8:0.2105:0:1 0/1:10:1:0,1:2,7:0.1:2,0:10:0:32:0:1:0:60:2:0.1111:0:1 -3 187303758 . G A 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TTGTATATTTCCTACAAGGG;RSEQ=GGAATTTAGTTTGCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:5,0:0.3333:0,0:37.3:1:31.3:1:1:0:60:6:0.375:0:1 1/1:1:1:1,0:0,0:1:0,0:5:0:28:0:1:0:60:2:1:0:2 -3 187304069 . G A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.23386;LSEQ=AAAGGGGCAAAAAAGCAAAA;RSEQ=GAAGAAATCACCCTTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:218:119,99:182,154:0.3935:2,2:24.8:1:30.2:1:0.93067:1.02:60:71.667:0.3981:0:1.1 1/0:446:264:141,123:80,86:0.5919:2,2:26.3:1:30:1:0.32203:1.23:60:263:0.5923:0:1.1 -3 187440092 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGGCTCCCAGTCCCCCAG;RSEQ=CCCCGACCCCCACCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:2,0:44,0:0.0435:1,0:20:1:29:1:1:0:60:4:0.0455:0:1 0/0:20:0:0,0:18,2:0:2,0:28.9:1:29.1:1:1:0:60:9:1:0:1.8 -3 187440126 . G C 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08579;SOR=0;LSEQ=CACCCCCAACCCCCAGCTAT;RSEQ=ATTTGCACTAGTGGATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:6:6,0:62,0:0.0882:1,0:18.8:1:26.2:1:1:0:60:2:0.0784:0:1.3 0/0:38:0:0,0:36,2:0:2,0:20.5:1:27.9:1:1:0:60:3.222:1:0:1 -3 187440458 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19582;SOR=Inf;LSEQ=GATGTCATTGCTCAAAGACC;RSEQ=AGAGAGGAAGATTCTCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:25,151:0:2,0:23.9:1:32:1:1:0:60:87:1:0:0.4 0/1:141:2:1,1:22,117:0.0142:2,2:14.5:1:26.5:1:0.30061:5.22:60:4:0.0144:0:1.5 -3 187440506 . C A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=0.18528;LSEQ=CTGGGGCAGCTCTTGCCTCT;RSEQ=CAAGGCCAGGTGAAGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:75:1,74:0,10:0.8824:0,1:26.7:1:30.4:1:1:0:60:150:0.8929:0:1.1 1/0:45:26:0,26:1,18:0.5778:1,1:25.1:1:30.1:1:0.42222:0:60:52:0.5778:0:1.2 -3 187442168 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGACCCCGCCCTAGAACA;RSEQ=TCCAATCCCAGTGAACCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 187442527 . C A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56804;SOR=0.41784;LSEQ=TGAGTCCCCTAATGCTTGGG;RSEQ=CAAGGTCAAGCAGGGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:15:15,0:3,0:0.8333:0,1:20.2:1:29.7:1:1:0:60:14:0.8235:0:1.1 1/0:6:4:4,0:2,0:0.6667:0,0:30.3:1:29.3:1:1:0:60:8:0.6667:0:1 -3 187442662 . G C 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00182;SOR=Inf;LSEQ=TGCTCCACCTCCTTCCCTGC;RSEQ=CTCCACCTCCTTCCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:182,30:0:2,0:23.9:1:29.8:1:1:0:60:52:1:0:0.1 0/1:148:7:7,0:117,24:0.0473:2,0:12.4:1:31.1:1:0.59893:0:60:14:0.0473:0:1.1 -3 187442666 . C T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.01227;SOR=Inf;LSEQ=CCACCTCCTTCCCTGCGCTC;RSEQ=ACCTCCTTCCCTGCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:197,33:0:2,0:23.5:1:31.1:1:1:0:60:114:1:0:0.1 0/1:165:5:2,3:131,29:0.0303:2,2:12.4:1:27.6:1:0.05061:6.66257:60:10:0.0303:0:1 -3 187443213 . T C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41584;SOR=1.34992;LSEQ=TGCCTGCCCACTCCTCCGCT;RSEQ=GCCTGCCCACTCCTCCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:25:22,3:102,16:0.1736:2,2:25:1:31:1:1:1.15:60:50:0.1953:0:1.8 0/1:104:23:18,5:69,12:0.2212:2,2:26:1:30:1:0.52298:1.58941:60:46:0.2255:0:2 -3 187443225 . CCTCCGCTCGCCTGCCCG C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73723;SOR=1.13067;LSEQ=CCTCCGCTTGCCTGCCCACT;RSEQ=CTCCGCTCGCCTGCCCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:22:19,3:125,23:0.1294:2,2:26.1:1:31.8:1:1:1.16:59.1:44:0.1366:0.0176:2 0/1:132:19:13,6:95,17:0.1439:2,2:22.8:1:30.9:1:0.10286:2.55639:60:38:0.1473:0.0379:1.9 -3 187443238 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.32887;SOR=3.74186;LSEQ=GCCCACTCCTCCGCTCGCCT;RSEQ=CCCGCTCCGCTCGCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:1:1,0:148,32:0.005:2,0:6:0:29:0:1:0:60:2:0.0058:0:2 0/1:162:3:2,1:116,28:0.0185:2,2:17:1:28.7:1:0.48538:2.05912:60:6:0.021:0:1.3 -3 187443241 . C T 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=CACTCCTCCGCTCGCCTGCC;RSEQ=GCTCCGCTCGCCTGCCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:150,35:0:2,0:22:1:29.9:1:1:0:60:29.833:0.9944:0:0.2 0/1:167:11:6,5:115,27:0.0659:2,2:15.8:1:27.6:1:0.05287:3.5114:60:10:0.0662:0:1.1 -3 187443250 . C T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41755;SOR=2.42744;LSEQ=GCTCGCCTGCCCGCTCCGCT;RSEQ=GCCTGCCCGCTCCGCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:2:2,0:189,53:0.0082:2,0:8.5:1:31.5:1:1:0:60:4:0.0086:0:2.5 0/1:203:4:4,0:147,52:0.0197:2,0:6.8:1:27:1:0.57416:0:60:8:0.02:0:2.5 -3 187443267 . C T 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3429;SOR=0.78833;LSEQ=GCTCGCCTGCCCGCTCCGCT;RSEQ=GCCTGCCCACTCTGCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:50:31,19:208,69:0.1529:2,2:21.8:1:29:1:0.0589:1.84386:59.6:11.5:0.1447:0:1.6 0/1:265:33:21,12:162,70:0.1245:2,2:24.2:1:29.8:1:0.5464:1.32105:60:32:0.1226:0:1.5 -3 187443268 . G A 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33016;SOR=3.71957;LSEQ=CTCGCCTGCCCGCTCCGCTC;RSEQ=CCTGCCCACTCTGCTCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:1:0,1:241,87:0.003:2,0:17:0:12:0:0.26748:0:60:0:0:0:2 0/1:267:3:2,1:182,82:0.0112:2,2:6.3:1:26:1:1:1.10931:60:6:0.0115:0:2 -3 187443274 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33476;SOR=3.62;LSEQ=TGCCCGCTCCGCTCGCCTGC;RSEQ=CACTCTGCTCACCTGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:1:1,0:252,101:0.0028:2,0:2:0:32:0:1:0:60:2:0.003:0:1 0/1:295:3:2,1:199,93:0.0102:2,2:20:1:30:1:1:1.06964:60:6:0.0104:0:1 -3 187443314 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCTGGCTCCGCAGGTTTC;RSEQ=CATTTGTAGGGCTTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:645:0:0,0:409,236:0:2,0:24.9:1:30.4:1:1:0:60:106.5:1:0:0.2 0/1:597:21:13,8:339,233:0.0352:2,2:23.1:1:30.1:1:1:1.12:60:42:0.0358:0:1.1 -3 187444210 . T C 65 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCTGGCTTTACAAAAAT;RSEQ=GAATCTATTTGTCTTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:34:1:32.8:1:1:0:60:8:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:28:0:33:0:1:0:60:2:1:0:1 -3 187445197 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACACAAAGCATTCCAGG;RSEQ=ATGTAAGATATAGGTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:29.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 187445892 . A G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAGCTACTTTTGCTGGC;RSEQ=TGAAGCTAAAATGACTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:1:0,1:26:1:28.8:1:1:0:60:16:1:0:1.3 1/1:5:5:4,1:0,0:1:0,2:37:1:29.6:1:1:0:60:10:1:0:1.6 -3 187445909 . G A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00706;SOR=Inf;LSEQ=GGCATGAAGCTAAAATGACT;RSEQ=TATGGTAAGTCTTGATTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:0:1,0:19.9:1:31:1:1:0:60:24:1:0:0.6 0/1:7:3:2,1:4,0:0.4286:0,2:33.3:1:28:1:0.42857:0:60:6:0.4286:0:2 -3 187446035 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41335;SOR=1.58688;LSEQ=GGAGTGCCAGTGGACTTCCA;RSEQ=TTGAGGACTGCTCCAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:8:8,0:145,4:0.051:1,0:21.5:1:32.6:1:1:0:60:16:0.0519:0:1 0/1:89:7:7,0:82,0:0.0787:1,0:17.6:1:27.4:1:1:0:60:2.5:0.0581:0:2.1 -3 187446059 . C T 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0039;SOR=Inf;LSEQ=AGGACTGCTCCAATCAGAGA;RSEQ=AACAGCATAAGTAAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:225,16:0:2,0:23.7:1:31.7:1:1:0:60:33.429:1:0:0.1 0/1:161:6:5,1:146,9:0.0373:2,2:17.8:1:29.5:1:0.32366:3.20668:60:12:0.038:0:1 -3 187446082 . A T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07227;SOR=Inf;LSEQ=CAGCATAAGTAAAATGGAGC;RSEQ=CAAAACCTATGGAGCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:325,49:0:2,0:22.2:1:30.1:1:1:0:60:73.8:1:0:0.1 0/1:268:3:1,2:218,47:0.0112:2,2:10.3:1:27:1:0.08699:9.16072:60:6:0.0113:0:1 -3 187446211 . C T 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAGGGAACGTGGGGCCAG;RSEQ=GGTGTGGAGGCACATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1167:0:0,0:534,632:0:2,0:25.1:1:30.3:1:1:0:60:43.846:0.9991:0:0.1 0/1:1057:56:26,30:472,529:0.053:2,2:26.1:1:28.6:1:1:1.0295:60:55:0.0529:0:1.2 -3 187446493 . A G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTCCAAACAGTATCTGC;RSEQ=GAAAGATCACTGACCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:7,29:0,0:1:0,2:25.6:1:30.9:1:1:0:60:35:1:0:1.4 1/1:7:7:0,7:0,0:1:0,0:22.7:1:31:1:1:0:60:14:1:0:1.1 -3 187446731 . T C 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01769;SOR=Inf;LSEQ=ACTCAATCTATAGGCACTGA;RSEQ=TCCACACCTCTAATAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:130,5:0:1,0:26.2:1:31.1:1:1:0:60:44:1:0:0.1 0/1:79:4:3,1:72,3:0.0506:1,2:17.5:1:32.5:1:0.19105:7.54641:60:8:0.0506:0:1 -3 187447032 . G A 306 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3932;LSEQ=CCCTCTGGTTTGGCATTCTG;RSEQ=TTGAGGCTGTTGAGCACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1411:1179:571,608:104,127:0.8356:2,2:25.7:1:30:1:0.35007:1.15:60:30.026:0.8335:0:1.1 1/0:1181:787:375,412:190,200:0.6664:2,2:24.9:1:29:1:0.75676:1.04372:60:36.476:0.6626:0:1.2 -3 187447581 . G T 87 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05631;SOR=4.3496;LSEQ=TCATCGGAGAAGAGGAGGCT;RSEQ=CTGACAGGGAGGTGGCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:653:2:0,2:331,320:0.0031:2,0:1:0:28:1:0.24277:0:60:4:0.0031:0:1 0/1:606:8:3,5:310,286:0.0132:2,2:22.3:1:29:1:0.4912:1.80477:60:16:0.0133:0:1.4 -3 187447926 . C T 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10103;SOR=0.25375;LSEQ=AATTAGCTAGACATAGGTGA;RSEQ=GTGGCTCTGGAGCAGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:39:0,39:0,6:0.8667:0,1:25.8:1:30.6:1:1:0:60:78:0.8667:0:1.1 1/0:13:8:0,8:0,5:0.6154:0,0:23.8:1:29.5:1:1:0:60:16:0.6154:0:1.3 -3 187448009 . T G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAATTGGGAAGACTGAG;RSEQ=CCCAGAGAAGGGAAGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:29.7:1:32.7:1:1:0:60:20:1:0:1.1 1/1:4:4:0,4:0,0:1:0,0:14.3:1:28.3:1:1:0:60:3:1:0:1.5 -3 187449922 . G C 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCGTTTGCTCCTTACAAC;RSEQ=CTGCAAGGTAGGTACTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:1,14:0,0:1:0,1:23.5:1:32:1:1:0:60:30:1:0:1.1 1/1:4:4:0,4:0,0:1:0,0:31.8:1:27.5:1:1:0:60:3:1:0:1.3 -3 187451113 . G A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTCTATGCCCACAGAAC;RSEQ=TGGCTCTTTCTTTTCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:31,0:0,0:1:0,1:20.2:1:29.5:1:1:0:60:14.5:1:0:1 1/1:7:7:7,0:0,0:1:0,0:14.9:1:30:1:1:0:60:14:1:0:1 -3 187451349 . C A 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CATGAGGACCGTTTTATGGG;RSEQ=TCTAAACTGCTCACGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:962:29:14,15:461,470:0.0301:2,2:25.1:1:30.3:1:1:1.05088:60:28:0.0297:0:1.1 0/0:857:0:0,0:445,412:0:2,0:25.3:1:31.6:1:1:0:60:49.412:1:0:0.2 -3 187451469 . C T 77 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73875;SOR=0.62977;LSEQ=GAACTGGATACAGCTGTCAG;RSEQ=CGGCGAGGCCATTTTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:6:3,3:190,403:0.01:2,2:15.2:1:30:1:0.39299:2.12:60:12:0.0103:0:1.5 0/0:474:3:2,1:175,293:0.0063:2,2:26.3:1:18.3:1:0.55943:3.34:60:0.5:0.0022:0:2.7 -3 187451609 . A G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCAACTCAGGTCCCTTGT;RSEQ=TTTGATCTTTGAACAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:2,42:0,0:1:0,1:23.1:1:31.4:1:1:0:60:21:1:0:1.1 1/1:32:32:3,29:0,0:1:0,2:24.1:1:31.8:1:1:0:60:64:1:0:1 -3 187451701 . T C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58533;SOR=0.47979;LSEQ=TTTTATCCAACAAGTTGGGA;RSEQ=AGAAAGCCCTTTAGGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:0,13:0,3:0.8125:0,1:22.4:1:32.6:1:1:0:60:26:0.8125:0:2.1 1/0:6:4:0,4:0,2:0.6667:0,0:20.5:1:32.3:1:1:0:60:8:0.6667:0:2 -3 187451709 . C T 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57562;SOR=0.44667;LSEQ=AACAAGTTGGGATAGAAAGC;RSEQ=CTTTAGGGGAAAAGCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:14:0,14:0,3:0.8235:0,1:21.4:1:29.8:1:1:0:60:28:0.8235:0:1.9 1/0:6:4:0,4:0,2:0.6667:0,0:20.5:1:29.5:1:1:0:60:8:0.6667:0:2 -3 187451910 . G GC 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATCTCAGCTCACTGCAA;RSEQ=TCCGCCTTCCCAGGTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24:1:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 188183768 . A C 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.89036;LSEQ=TTGAACTATCCATTAAGTCA;RSEQ=AGGGGATAGGCTATTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:15:15,0:29,1:0.3333:1,1:27.3:1:32.1:1:1:0:60:30:0.3409:0:1.2 0/1:26:8:8,0:16,2:0.3077:2,0:19.1:1:31.9:1:1:0:60:16:0.3333:0:1.1 -3 188183865 . C T 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.36523;SOR=0.82069;LSEQ=TCAGAATCCTAGGTACTCTC;RSEQ=TTTAGACTGCCTGGTGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:82:58,24:117,49:0.3306:2,2:25.6:1:30.1:1:1:1.01:60:40:0.3292:0:1.1 0/1:215:62:41,21:98,55:0.2884:2,2:22.4:1:30.6:1:0.87511:1.10:60:124:0.2925:0:1.3 -3 188183879 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09944;SOR=Inf;LSEQ=ACTCTCCTTTAGACTGCCTG;RSEQ=TGACTACTCATTTGTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:196,111:0:2,0:24.4:1:30.9:1:1:0:60:37.375:1:0:0.4 0/1:266:3:1,2:158,105:0.0113:2,2:17.7:1:27:1:0.56666:2.99694:60:6:0.0115:0:1.7 -3 188183932 . T A 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAATAGTTCAGTAGAATA;RSEQ=AACTTTGTGGAAATTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:180,196:0:2,0:27.4:1:29.5:1:1:0:60:375:1:0:0.2 0/1:345:82:46,36:133,130:0.2377:2,2:26.6:1:29.8:1:0.44776:1.25:60:81:0.2362:0:1.1 -3 188184000 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21242;SOR=Inf;LSEQ=CAGTGAGATGGGAGAGTCAG;RSEQ=GTCATTCATTGGTATTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:64,159:0:2,0:26.8:1:30.7:1:1:0:60:30.857:1:0:0.1 0/1:192:2:1,1:64,125:0.0104:2,2:26.5:1:29:1:1:1.95:60:4:0.0106:0:1 -3 188184054 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20546;SOR=Inf;LSEQ=CTTTTTGTCTGATCTTGCCT;RSEQ=GAGAATTATTTTTAAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:4,75:0:2,0:22.5:1:31:1:1:0:60:25.333:1:0:0.1 0/1:66:2:1,1:4,60:0.0303:2,2:15.5:1:32:0:0.14685:13.53:60:4:0.0323:0:1 -3 189348968 . GCTCCA G 67 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTCAGAGATGCCTCCA;RSEQ=AATTGCCAACAACAAGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:36.3:1:33.5:1:1:0:60:8:0.8:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 189349077 . T C 34 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04329;SOR=Inf;LSEQ=CCCAGCTGGTAAGAATCGAG;RSEQ=GTTTATGAAGTTTTAGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:0:1,0:19.6:1:30.5:1:1:0:60:34:1:0:0.3 0/1:5:2:2,0:3,0:0.4:0,0:36:1:34:0:1:0:60:4:0.4:0:1 -3 189349247 . A T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.19638;LSEQ=ATCTATATATACACAGGTAT;RSEQ=TGTGTATATTTTATATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:335:306:241,65:21,7:0.9134:2,2:24.2:1:29.6:1:0.63424:1.24:60:24.5:0.9102:0:1.1 1/0:233:157:118,39:56,20:0.6738:2,2:22.4:1:29.4:1:0.87261:1.08:60:38.25:0.6711:0:1.1 -3 189349251 . G T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16615;SOR=5.67217;LSEQ=ATATATACACAGGTATATGT;RSEQ=TATATTTTATATAATTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:1:1,0:273,81:0.0028:2,0:1:0:31:0:1:0:60:2:0.0028:0:1 0/1:253:4:1,3:186,63:0.0158:2,2:12.5:1:27.5:1:0.05566:8.76466:60:8:0.016:0:1 -3 189349456 . C A 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57415;SOR=2.7932;LSEQ=GCTGTGTACAAAGAACAATT;RSEQ=CTCCTTGTTTAGTCAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:1,0:27,218:0.0041:2,0:1:0:23:0:0.11382:0:60:2:0.0042:0:1 0/1:177:2:1,1:22,153:0.0113:2,2:16:1:24:1:0.24364:6.82:60:4:0.0114:0:1 -3 189349472 . G A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78893;LSEQ=AATTCCTCCTTGTTTAGTCA;RSEQ=CACAGTGATATTATTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:0,2:6,169:0.0113:1,0:30.5:1:31.5:1:1:0:60:4:0.0116:0:2 0/0:112:1:1,0:8,103:0.0089:2,0:1:0:28:0:0.08036:0:60:2:0.0089:0:1 -3 189349501 . G A 180 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01506;LSEQ=TATTATTTTGGACTTTCTGT;RSEQ=GACTTAAAGTGGTCTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:54:0,54:0,56:0.4909:1,1:26:1:31.3:1:1:0:60:108:0.5094:0:1 0/1:71:1:0,1:0,70:0.0141:1,0:2:0:31:0:1:0:60:2:0.0143:0:1 -3 189455380 . A G 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96049;LSEQ=CACTACCTGAAGAAATGCCA;RSEQ=TTGTGCAACTTGTAACATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:4:4,0:48,0:0.0769:1,0:26:1:33.8:1:1:0:60:8:0.0769:0:1 0/1:27:2:1,1:25,0:0.0741:1,2:40:1:32:1:0.07407:0:60:4:0.0741:0:1 -3 189455688 . C A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27127;SOR=0;LSEQ=AACAAGCAAGAAATGTTTTG;RSEQ=TTGAGCTAAATAGGTAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:2,1:49,231:0.0106:2,2:13.3:1:28.3:1:0.08471:9.32:60:6:0.0108:0:1 0/0:199:0:0,0:43,156:0:2,0:19.9:1:32.1:1:1:0:60:98.5:1:0:0.1 -3 189456354 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17439;SOR=Inf;LSEQ=TGACTTTGAAGCAGAAAATG;RSEQ=TTGTTGTTAACAACAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:198,36:0:2,0:23:1:31.8:1:1:0:60:116:1:0:0.1 0/1:169:2:1,1:134,32:0.0118:2,2:23:1:28.5:1:0.35522:4.13892:60:4:0.0119:0:1 -3 189456639 . T C 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00118;SOR=Inf;LSEQ=TAAACCTGTCTTTTCAGTCA;RSEQ=GTGTGAAAAGGCAGGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:6,160:0:1,0:24.6:1:30.4:1:1:0:60:165:1:0:0.1 0/1:129:8:2,6:4,117:0.062:1,2:20:1:29.5:1:0.04474:9.36:60:16:0.0625:0:1 -3 189456729 . C G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1635;LSEQ=AAGATTTGGTGTGGATTATG;RSEQ=ATTCTGGGTCTGCCGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:0,18:0,24:0.4286:1,1:22:1:31.4:1:1:0:60:36:0.4286:0:1.1 0/1:15:7:0,7:0,8:0.4667:0,0:25.4:1:31:1:1:0:60:14:0.5:0:1 -3 189456903 . T G 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGAATCAGAAATTTATT;RSEQ=TATTTATATATTTATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:20:1:31.5:1:1:0:60:4:0.2857:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 189485909 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGTGTATGAATAACTAACCA;RSEQ=CTCTAGGTTTTAGGGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:0.1053:2,2:17:1:30:1:1:1.77272:60:4:0.1176:0:1 0/0:6:0:0,0:4,2:0:2,0:13.2:1:28.3:1:1:0:60:5:1:0:0.3 -3 189485975 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11067;SOR=Inf;LSEQ=TTTTGCAAAACGGGATTAAT;RSEQ=TGACTATGGTGAAAACTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:31.3:1:29.6:1:1:0:60:30:1:0:0.4 0/1:8:2:1,1:3,3:0.25:2,2:12:1:31.5:1:1:1:60:4:0.25:0:1 -3 189486023 . A G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAATATAAAGAGCTTACC;RSEQ=CAATAGCATTGGTTCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:31:1:34:0:1:0:60:4:0.2857:0:1 0/0:2:0:0,0:0,2:0:0,0:45.5:1:30.5:1:1:0:60:4:1:0:0.5 -3 189507490 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=GACTTGAGTTCTGTTATCTT;RSEQ=TTAAGTAGATTCATATTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:186,18:0:2,0:23.6:1:31:1:1:0:59.9:28.143:1:0:0.1 0/1:138:9:8,1:112,17:0.0652:2,2:22.8:1:28:1:1:1.21:60:8:0.0606:0:1.1 -3 189507518 . C CAGAG 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.02685;LSEQ=GATTCATATTGTAAGGGTCT;RSEQ=GGGGTGGGGGGGTTGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:333:258,75:15,3:0.9:2,2:23.7:1:30.4:1:0.77288:1.45205:59.7:165.5:0.9093:0.2324:0.1 0/1:228:44:37,7:129,48:0.193:2,2:26:1:30.6:1:0.17179:1.96:59.5:88:0.1973:0.0088:0.2 -3 189507519 . GGGGTG AGAGGGGGT 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=7.000;MSILEN=1;SSF=0.82652;SOR=0.84921;LSEQ=ATTCATATTGTAAGGGTCTC;RSEQ=GGGGGGTTGGCAAAATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:14:13,1:279,84:0.037:2,1:12.9:1:28.3:1:0.20658:3.90:58.2:28:0.038:0.0291:0.5 0/1:253:8:7,1:181,64:0.0316:2,2:13.5:1:28.9:1:0.68393:2.47:60:16:0.032:0.0158:0.4 -3 189507689 . T TA 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.17623;SOR=Inf;LSEQ=CTTTTTAATTTTTATTTTTG;RSEQ=AAAAAAACTTACGTATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:51,204:0:2,0:22.9:1:28.4:1:1:0:60:126.5:1:0:0.1 0/1:185:2:1,1:47,136:0.0108:2,2:32.5:1:29:1:0.45264:2.87:60:4:0.011:0:0 -3 189507711 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18896;SOR=Inf;LSEQ=AAAAAACTTACGTATTTGCG;RSEQ=TTCTCGGTCACCCAATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:11,134:0:2,0:24.6:1:31.9:1:1:0:60:35.25:1:0:0.1 0/1:112:2:0,2:16,94:0.0179:2,0:8:0:31:0:1:0:60:4:0.0183:0:1 -3 189525713 . G A 80 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAACCTCAAAATGGAATA;RSEQ=CAGGCAGTATTTATTTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:24:1:31:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 189526135 . C T 183 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTCCTCGTCCACCAGTCC;RSEQ=TATAACACAGACCACGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1251:0:0,0:664,585:0:2,0:24.7:1:31.6:1:1:0:60:82.267:0.9984:0:0.1 0/1:1029:64:36,28:521,443:0.0622:2,2:24.3:1:30.5:1:0.79609:1.09:60:128:0.0634:0:1.2 -3 189581535 . TA T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAACAGATATTCCATCT;RSEQ=AAAAAAATCCCATGAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:17:1:32:0:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 189582241 . T G 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATCTCTAACTGTTCAACC;RSEQ=CCTTGAAGGTCAAGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:77,260:0:2,0:20.9:1:29.5:1:1:0:60:27.083:1:0:0.1 0/1:311:23:3,20:70,217:0.074:2,2:20.4:1:30.6:1:0.30815:2.14615:60:22:0.0728:0:1 -3 189582249 . G A 161 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=48.73601;LSEQ=AACTGTTCAACCTCCTTGAA;RSEQ=GTCAAGATTCTGTGGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:1:0,1:58,226:0.0035:2,0:10:0:17:0:1:0:60:0:0:0:6 0/1:265:39:9,30:48,178:0.1472:2,2:24.6:1:30.6:1:0.83337:1.11:60:78:0.15:0:1.2 -3 189584420 . C T 153 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03103;LSEQ=ATGCAATTTCATTTTATTTT;RSEQ=TTTATTTTTAAGGTAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:34:29,5:180,29:0.1399:2,2:23.1:1:30.2:1:1:1.06986:60:68:0.1405:0:1.1 0/0:200:1:0,1:158,41:0.005:2,0:1:0:23:0:0.21:0:60:2:0.005:0:1 -3 189584890 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTTTTATCCAACTGGCA;RSEQ=TTGGACGGGTAGTGGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:26:1:32.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 189585208 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=AAGATGTTATTAATGGAAGT;RSEQ=TATATTCAAATCTATATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:7.5:1:33:0:0.33333:0:60:4:0.3333:0:1 1/1:2:2:1,1:0,0:1:0,2:20:0:33.5:1:1:0:60:4:1:0:1.5 -3 189585542 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17561;SOR=Inf;LSEQ=TTCATCAGAAGTGGAATTCC;RSEQ=TAAATAGAGGGAAGAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:206,47:0:2,0:22.5:1:30.7:1:1:0:60:41.167:1:0:0.1 0/1:183:2:1,1:142,39:0.0109:2,2:27:0:33:1:0.39032:3.60751:60:4:0.0109:0:1.5 -3 189585563 . G T 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3989;SOR=0.33229;LSEQ=TAAATAGAGGGAAGAACTGA;RSEQ=AAGGAACAACGTCAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:4:1,3:262,95:0.0111:2,2:11.3:1:27.8:1:0.06267:8.21647:60:8:0.0111:0:1 0/0:270:1:0,1:187,82:0.0037:2,0:1:0:23:0:0.30741:0:60:2:0.0037:0:2 -3 189585692 . G A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00821;SOR=0;LSEQ=TTGTGTTGGAGGGATGAACC;RSEQ=CCGTCCAATTTTAATCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:8:6,2:331,450:0.0101:2,2:7:1:27.3:1:0.07908:4.07:60:7:0.009:0:1.3 0/0:714:0:0,0:323,390:0:2,0:25.3:1:30.3:1:1:0:60:49.929:1:0:0.1 -3 189585852 . C T 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03479;SOR=Inf;LSEQ=GAGAGCTTGTCCTTTGTGCT;RSEQ=TAAATCCTTGCTACAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:1,65:0:1,0:25.3:1:32.5:1:1:0:60:132:1:0:0.1 0/1:33:3:0,3:2,28:0.0909:2,0:25.3:1:31.7:1:1:0:60:6:0.0968:0:1 -3 189586182 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05645;SOR=Inf;LSEQ=ATGGAATGTTATTTACTAAT;RSEQ=TTACTTGTGGCATGTTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:20,4:0:2,0:28.7:1:29.2:1:1:0:60:48:1:0:0.1 0/1:8:2:2,0:6,0:0.25:0,0:29.5:1:31:1:1:0:60:4:0.25:0:1 -3 189586310 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51353;SOR=0;LSEQ=AGTGGAAGTGGTAGATCTTC;RSEQ=GGGGACTTTCAAAATGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:98,40:0.0143:2,2:13.5:1:28:1:0.50144:2.43227:60:4:0.0145:0:1 0/0:98:0:0,0:65,33:0:2,0:24.1:1:29.8:1:1:0:60:97:1:0:0.1 -3 189586466 . G A 136 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAGCATCAGAAAGCAGCAA;RSEQ=TTTCGGACAGTACAAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:25:13,12:238,263:0.0475:2,2:22.9:1:29.4:1:0.68653:1.20:60:24:0.0462:0:1.1 0/0:493:0:0,0:253,239:0:2,0:25.1:1:31.3:1:1:0:60:97.4:0.998:0:0.2 -3 189586470 . C T 215 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATCAGAAAGCAGCAAGTTT;RSEQ=GGACAGTACAAAGAACGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:150:69,81:179,191:0.2885:2,2:27:1:29.8:1:0.62954:1.09996:60:49:0.2899:0:1.1 0/0:485:0:0,0:245,239:0:2,0:25.8:1:30.2:1:1:0:60:59.5:0.9979:0:0.2 -3 189586532 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11083;SOR=Inf;LSEQ=AGATGTAGTGGCCAAATGGG;RSEQ=TAGGGTTGAATCTTCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:92,212:0:2,0:24.6:1:31.7:1:1:0:60:151:1:0:0.3 0/1:282:3:2,1:95,184:0.0106:2,2:11:1:29:1:0.2728:3.85:60:6:0.0106:0:1.7 -3 189586535 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25026;SOR=0;LSEQ=TGTAGTGGCCAAATGGGGTA;RSEQ=GGTTGAATCTTCTCCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:0,3:88,204:0.0102:2,0:29.7:1:28.7:1:0.557:0:60:6:0.0103:0:1 0/0:269:0:0,0:88,180:0:2,0:23.3:1:30.4:1:1:0:60:88.333:0.9962:0:0.1 -3 189586553 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20534;SOR=Inf;LSEQ=TAGGGTTGAATCTTCTCCAG;RSEQ=TGTTGGAGAATGGGGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:42,171:0:2,0:21.7:1:30.2:1:1:0:60:25.625:1:0:0.2 0/1:177:2:1,1:34,141:0.0113:2,2:26:1:29.5:1:0.35728:4.10:60:4:0.0116:0:1 -3 189586572 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21163;SOR=Inf;LSEQ=GATGTTGGAGAATGGGGTGA;RSEQ=ATTGGAGAAGCTGCATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:16,136:0:2,0:22.6:1:28.2:1:1:0:60:75:1:0:0.1 0/1:130:2:1,1:16,111:0.0154:2,2:32.5:1:30:1:0.24709:6.76:60:4:0.0155:0:1 -3 189586630 . C G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9182;LSEQ=CAGCAAGTGGGACGTCAGCC;RSEQ=TCAGAGCCAGTGAGAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:13:0,13:2,44:0.2203:1,1:24.4:1:32.2:1:1:0:60:26:0.2203:0:1 0/1:34:7:2,5:1,26:0.2059:1,2:24.7:1:31:1:0.1006:9.38:60:14:0.2121:0:1.1 -3 189586876 . T C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49275;SOR=Inf;LSEQ=TTCTTTTATGTATTCTTCCC;RSEQ=ACCATCCTTCCACCTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:11,1:10,0:0.5455:0,2:19:1:31.3:1:1:0:60:24:0.5455:0:1 1/1:2:2:2,0:0,0:1:0,0:9.5:1:31.5:1:1:0:60:4:1:0:1 -3 189587091 . A G 217 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAGTGTTCCCAGGATGAA;RSEQ=CTTGCATTTTTCCTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:0:0,0:461,256:0:2,0:26.4:1:29.9:1:1:0:60:70.7:1:0:0.1 0/1:507:111:68,43:243,151:0.2189:2,2:26.2:1:32:1:1:1.0176:60:110:0.2187:0:1.1 -3 189587235 . C T 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATGGTTGCTTCATTTTAA;RSEQ=CTTCTTTGAATGGGCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:146,345:0:2,0:26.3:1:31.4:1:1:0:60:60.375:0.9979:0:0.2 0/1:382:26:8,18:134,222:0.0681:2,2:24.2:1:29.2:1:0.53548:1.35706:60:52:0.069:0:1 -3 189587274 . A G 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00578;SOR=1.73454;LSEQ=TACAGTATGATCATCATCTC;RSEQ=TTATCTGTGACAATGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:88:20,68:20,158:0.3308:2,2:21.9:1:31.5:1:0.01764:2.32:60:87:0.3308:0:1 0/1:184:85:19,66:21,78:0.462:2,2:21.5:1:30.6:1:0.85978:1.07:60:84:0.459:0:1.1 -3 189590559 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54015;SOR=0;LSEQ=AAATAAACAAATTGCAATTA;RSEQ=GGAATCCTCAAATAATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:165,0:0.012:1,2:27.5:1:31:1:0.01198:0:60:4:0.0121:0:1 0/0:92:0:0,0:90,2:0:1,0:23.5:1:31.4:1:1:0:60:91:1:0:0.1 -3 189590824 . G C 201 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTAGGAGGCATGAGTGA;RSEQ=GGTGACTTTATTTGGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:508:0:0,0:136,372:0:2,0:23.7:1:31.3:1:1:0:60:100.6:1:0:0.2 0/1:391:109:34,75:63,141:0.2788:2,2:23:1:29.7:1:1:1.01:60:108:0.2784:0:1.1 -3 189590871 . G A 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGATTGATGAGCAATGTG;RSEQ=AACATAATGGGAGATAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:57:6,51:8,145:0.2714:2,2:20.7:1:30.4:1:0.21256:2.12:60:114:0.2754:0:1.1 0/0:134:0:0,0:14,119:0:2,0:23.2:1:31.1:1:1:0:60:43.333:1:0:0.5 -3 189591053 . G T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=3.51553;LSEQ=AACTCACACTAACAGTTCTC;RSEQ=TCTCTATATGCCTGGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:15.7:1:29.7:1:1:0:60:6:0.4286:0:1 1/0:4:3:0,3:0,1:0.75:0,0:36.3:1:30.3:1:1:0:60:6:0.75:0:1 -3 189597951 . G A 241 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00871;LSEQ=ACATTCCAAGCCCCCAAACC;RSEQ=ATCAGTGTACCCATAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1067:267:111,156:332,464:0.2502:2,2:26.7:1:29.9:1:1:1.00559:60:32.375:0.2486:0:1.2 0/0:1037:3:3,0:441,593:0.0029:2,0:1:0:25.3:1:0.07819:0:60:6:0.003:0:1 -3 189598021 . AGT A 123 MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.09526;SOR=0.36223;LSEQ=TATTTCCATGTGTATATGTG;RSEQ=GTGTGTGTGTGTATGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:15:1,14:39,277:0.0453:2,1:22.5:1:31.5:1:1:1.96793:60:14:0.0435:0.0151:0.3 0/1:237:4:0,4:31,202:0.0169:2,0:25.3:1:32.3:1:1:0:60:8:0.0171:0:0.3 -3 189598045 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13827;SOR=Inf;LSEQ=TGTGTGTGTGTATGTGTGTG;RSEQ=GTGTGTATCTAGCCCTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:6,206:0:1,0:23.9:1:29.4:1:1:0:60:25.5:1:0:0.2 0/1:126:2:1,1:3,121:0.0159:1,2:6.5:1:32:0:0.06273:35.08:60:4:0.0159:0:2 -3 189598095 . G A 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01133;SOR=0;LSEQ=TGAAGACACTTTGGCTCAGA;RSEQ=ACCCAACTGCTCAAAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:14:1,13:2,85:0.1386:1,1:24:1:29.7:1:0.36397:3.21:60:13:0.1383:0:1.5 0/0:38:0:0,0:1,37:0:1,0:23.6:1:31.1:1:1:0:60:37:1:0:0.1 -3 189604149 . T G 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.66451;LSEQ=TCCCCACTCTTCAGTGTCCC;RSEQ=TGCTCACCATTATTTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:845:433:295,138:269,142:0.5124:2,2:24.9:1:30.2:1:0.42177:1.13:60:71.167:0.512:0:2.1 1/0:616:392:244,148:138,86:0.6364:2,2:24.1:1:29.9:1:0.93126:1.03:60:64.333:0.637:0:2.1 -3 189604160 . T C 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.76826;LSEQ=CAGTGTCCCTTGCTCACCAT;RSEQ=ATTTCCATGTTTGTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:941:476:311,165:286,179:0.5058:2,2:26.1:1:31.3:1:0.22401:1.18:60:94.2:0.5054:0:2 1/0:683:440:270,170:142,101:0.6442:2,2:26.2:1:31.3:1:0.4632:1.13:60:439:0.6484:0:2 -3 189607032 . A T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.15282;SOR=Inf;LSEQ=AAAAGGAAGGCTGGTAGTTT;RSEQ=GGCCCTTGATAAAATTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:237,38:0:2,0:23.7:1:28.4:1:1:0:60:90.667:1:0:0.1 0/1:177:2:1,1:146,29:0.0113:2,2:16.5:1:25:1:0.31106:4.96692:60:4:0.0114:0:1.5 -3 189607037 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15656;SOR=Inf;LSEQ=GAAGGCTGGTAGTTTAGGCC;RSEQ=TTGATAAAATTTAACCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:247,47:0:2,0:24.3:1:30.7:1:1:0:60:31.667:1:0:0.1 0/1:193:2:1,1:154,37:0.0104:2,2:5.5:1:27:1:0.35584:4.12035:60:4:0.0108:0:1.5 -3 189607076 . G T 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02753;SOR=Inf;LSEQ=ACAAGATGGACCACTGGGAT;RSEQ=CTGGTACATGATGATGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:0:0,0:395,179:0:2,0:24.7:1:31.9:1:1:0:60:62.778:1:0:0.1 0/1:396:4:1,3:260,132:0.0101:2,2:7.5:1:26.8:1:0.11682:5.88146:60:8:0.0102:0:1.3 -3 189607319 . G A 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=11.22876;LSEQ=GGGCCTGCCCTAAGCATCCC;RSEQ=GGATGGTGGAGGGCGGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:507:2:2,0:102,401:0.0039:2,0:1:0:26:0:0.04209:0:60:4:0.004:0:1 0/1:328:14:3,11:79,235:0.0427:2,2:20.9:1:29.1:1:1:1.23187:60:13:0.0404:0:1.1 -3 189608731 . A T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05595;SOR=Inf;LSEQ=ATTTCTTTCCTCTGATGACA;RSEQ=CCGCCTTGTAGTTCAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:38,272:0:2,0:23.3:1:29.8:1:1:0:60:76.5:1:0:0.1 0/1:193:3:1,2:27,163:0.0155:2,2:16.3:1:23.7:1:0.37681:2.99:60:2:0.0106:0:1 -3 189608961 . C A 89 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTATTCCCGCAATCAAAA;RSEQ=ATTCATAATTTCTAAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:0,7:0,2:0.7778:0,0:30.7:1:32:1:1:0:60:14:0.7778:0:1.9 1/1:1:1:0,1:0,0:1:0,0:35:0:13:0:1:0:60:0:0:0:2 -3 189612328 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18054;SOR=Inf;LSEQ=TCTTCCTATCCCTCTCCTAA;RSEQ=TGCCAGCCCCCTAAAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:28,196:0:2,0:23.8:1:32.4:1:1:0:60:111:1:0:0.1 0/1:166:2:1,1:30,134:0.012:2,2:31:1:28.5:1:0.33954:4.41:60:4:0.0122:0:1 -3 189612336 . C T 79 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00369;SOR=12.4134;LSEQ=TCCCTCTCCTAACTGCCAGC;RSEQ=CCCTAAAAGCACTCCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:24,165:0.0053:2,0:44:0:14:0:1:0:60:0:0:0:6 0/1:129:8:3,5:21,100:0.062:2,2:24.5:1:26.6:1:0.16728:2.83:60:7:0.0565:0:1 -3 190212442 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86551;LSEQ=TCCAGCACCCAGAACATTAC;RSEQ=TGGCATAACAGAGTTATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:0.6364:0,0:21.6:1:32:1:1:0:60:14:0.6364:0:1 1/0:5:3:3,0:2,0:0.6:0,0:28.3:1:30.3:1:1:0:60:6:0.6:0:1 -3 190212706 . C T 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01448;SOR=1.48283;LSEQ=GAAAACTCACAATTTGTTTA;RSEQ=TTTAAAATTATAAGCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:405:232:109,123:76,97:0.5728:2,2:25.1:1:30.4:1:0.54714:1.13:60:115:0.5736:0:1.1 1/0:290:193:89,104:46,50:0.6655:2,2:25.2:1:30:1:0.80309:1.07479:60:386:0.6678:0:1.1 -3 190212795 . A AT 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10766;SOR=1.52781;LSEQ=CATTCCCTACTTAAATATGT;RSEQ=TTTTTTTTATCCTTAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:79:18,61:17,66:0.4817:2,2:25.4:1:30.1:1:0.84882:1.14:60:78:0.4815:0.0183:0.2 1/0:109:64:12,52:13,32:0.5872:2,2:28:1:29.1:1:0.25134:1.75109:60:128:0.5872:0.0642:0.1 -3 192873634 . T C 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGTGAGAGTCACAGGTGT;RSEQ=GTAGCAGCCGTGGAGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:17:0:33:0:1:0:60:2:1:0:1 1/1:8:8:8,0:0,0:1:0,0:24.5:1:30.4:1:1:0:60:7:1:0:1.6 -3 192873745 . ATGT A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.50515;SOR=Inf;LSEQ=TTCCCTGGCCAGCTTGTCAC;RSEQ=TGTTGTTGCTGTTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:22,20:0:2,0:26:1:30.4:1:1:0:60:84:1:0:0.3 0/1:56:2:1,1:28,26:0.0357:2,2:42:1:29.5:1:1:1.07547:60:4:0.0364:0:0 -3 192873757 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19358;SOR=0;LSEQ=CTTGTCACATGTTGTTGTTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:23,25:0.04:2,2:46:0:31:0:1:1.09:60:4:0.04:0:1 0/0:63:0:0,0:31,32:0:2,0:24:1:30.7:1:1:0:59.3:20:1:0:0.8 -3 192873763 . T C 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACATGTTGTTGTTGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:23,27:0:2,0:26.5:1:30:1:1:0:60:100:1:0:0.3 1/0:62:31:16,15:14,17:0.5:2,2:22.7:1:31.1:1:0.79967:1.29:58.6:30:0.4918:0:1.3 -3 192873766 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=3;SSF=0.19358;SOR=0;LSEQ=TGTTGTTGTTGCTGTTGTTG;RSEQ=TGCTGCTGCTGCTTTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:21,27:0.04:2,2:13:0:32:0:1:1.28:60:4:0.04:0:1.5 0/0:63:0:0,0:30,33:0:2,0:25.1:1:31.2:1:1:0:59.3:30.5:1:0:0.8 -3 193971987 . C T 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39091;SOR=0;LSEQ=CCTGCACTGGCACCTCAGAG;RSEQ=CGCCACCCCTGCCATTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:67:36,31:0,0:1:0,2:21.1:1:29.6:1:1:0:60:66:1:0:2.5 1/1:43:42:22,20:1,0:0.9767:0,2:23.6:1:28.4:1:1:0:60:41:0.9762:0:2.7 -3 193972016 . A G 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18513;SOR=0;LSEQ=CTGCCATTCACTATGGCACA;RSEQ=GGCACAGCGTCAGGGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:19,28:0,0:1:0,2:31.2:1:30.7:1:1:0:60:22.5:1:0:3.4 1/1:36:34:16,18:1,1:0.9444:2,2:30:1:29.2:1:1:1.12132:60:7.5:0.9677:0:3.2 -3 193972034 . C G 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16553;SOR=0;LSEQ=CAAGGCACAGCGTCAGGGCT;RSEQ=CTCCTTCAATCCCAGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:18,25:0,0:1:0,2:31.1:1:32:1:1:0:60:86:1:0:3.6 1/1:30:28:13,15:1,1:0.9333:2,2:24.4:1:30.8:1:1:1.14834:60:27:0.931:0:3.4 -3 193972070 . G T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.60176;LSEQ=GGCCATCCTTACCCAGCAAG;RSEQ=CTCAGCTCGGCTGGTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:27:7,20:0,1:0.931:0,2:19.5:1:29.7:1:1:0:60:54:0.931:0:3.6 1/1:9:8:3,5:0,1:0.8889:0,2:21.1:1:28:1:1:0:60:16:1:0:3.5 -3 193972099 . C T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGTCTTCTAAGGCTGG;RSEQ=AACGAGGTAACTGAGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:22.6:1:29.2:1:1:0:60:22:1:0:3 1/1:5:5:0,5:0,0:1:0,0:15.4:1:26.4:1:1:0:60:10:1:0:2.6 -3 194238312 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24426;SOR=Inf;LSEQ=CATCAGAAGCTGAAAAAAAC;RSEQ=GTGCTGAGAAACGTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:127,70:0:2,0:25.1:1:30.3:1:1:0:60:196:1:0:0.8 0/1:193:2:1,1:115,76:0.0104:2,2:10:1:29:1:1:1.50978:60:4:0.0104:0:1 -3 194238335 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30413;LSEQ=GCTGAGAAACGTGGCCTGCC;RSEQ=TCTTTCCAGCTAAGGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:262:149:93,56:67,46:0.5687:2,2:26:1:30.6:1:0.61166:1.14:60:298:0.5687:0:1.6 0/1:231:66:38,28:96,69:0.2857:2,2:29.5:1:29.8:1:1:1.02507:60:132:0.2882:0:1.5 -3 194238390 . C T 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.42733;SOR=0.86152;LSEQ=TGGGTTGTCCTCTGCAAACG;RSEQ=GCTGCTGCAGGTTGCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:289:169:84,85:60,58:0.5848:2,2:25.7:1:29.8:1:0.90466:1.04666:60:83.5:0.5901:0:1.5 1/0:239:131:62,69:48,60:0.5481:2,2:25.5:1:29.5:1:0.69664:1.12:60:130:0.5508:0:1.4 -3 194238468 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56175;SOR=3.181;LSEQ=GAACTGACTGAAATTGGATG;RSEQ=TAATAAGTTGCTAGGTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:1:1,0:32,123:0.0064:2,0:1:0:25:0:0.21154:0:60:2:0.0065:0:2 0/1:99:2:1,1:22,75:0.0202:2,2:8.5:1:28.5:1:0.41249:3.36:60:4:0.0206:0:1.5 -3 194238483 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53041;SOR=0;LSEQ=GGATGGTAATAAGTTGCTAG;RSEQ=TTATTTTCCACTTTTTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:20,93:0.0174:2,2:19.5:1:29.5:1:0.33318:4.56:60:4:0.0175:0:1 0/0:68:0:0,0:14,54:0:2,0:24.9:1:30.3:1:1:0:60:33:1:0:0.2 -3 195384760 . G C 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06061;SOR=Inf;LSEQ=CCCGCCCTATCTCGGTCGGG;RSEQ=AGCGCGGGACCTCCGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:0.4:2,0:20:1:33:1:0.4:0:42.5:4:0.4:0:1.5 1/1:6:6:3,3:0,0:1:0,2:25.2:1:33.2:1:1:0:49.3:12:1:0:1.2 -3 195384844 . T G 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01358;SOR=0.16302;LSEQ=GTCCCCGCCCATTAGACCCC;RSEQ=GCCCGGGCGTGTCGTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:38:33,5:2,1:0.9268:2,2:18.2:1:28.9:1:0.38602:3.17:54.7:18:0.9231:0:1.8 1/0:24:16:13,3:6,2:0.6667:2,2:14.1:1:29.3:1:1:1.42:53.3:15:0.6522:0:1.5 -3 195384849 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCATTAGACCCCTGCCC;RSEQ=GGCGTGTCGTGGTGCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:2,0:44,8:0.0357:2,0:22:1:31.5:1:1:0:58.5:4:0.0377:0:1.5 0/0:25:0:0,0:19,6:0:2,0:20.3:1:30.4:1:1:0:55.7:50:1:0:1 -3 195384898 . T C 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3432;SOR=0.70489;LSEQ=CCCCCACTAGCGCCCCGCCT;RSEQ=GACCCGGCCGTGGTGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:54:36,18:61,27:0.3803:2,2:27.3:1:29.8:1:0.85282:1.12865:42.4:17:0.3696:0:1.6 0/1:63:19:11,8:29,15:0.3016:2,2:29.4:1:29.6:1:0.57849:1.39827:50.5:38:0.3276:0:1.3 -3 195384920 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56054;SOR=0;LSEQ=ACCCGGCCGTGGTGCGCAGG;RSEQ=GCAGTCTGCGCAGGGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:3:1,2:137,66:0.0146:2,2:11:1:29:1:0.25385:4.12028:40.7:6:0.0152:0:1.7 0/0:82:0:0,0:57,25:0:2,0:24.6:1:29.2:1:1:0:39.9:10.714:1:0:1 -3 195384951 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.55417;SOR=0;LSEQ=CAGGGACTGGCGGGACTGCG;RSEQ=GGCGGCGACTACAGACGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:1,2:152,137:0.0102:2,2:22.7:1:28.3:1:0.60645:2.21312:35.3:6:0.0109:0:1 0/0:151:0:0,0:81,69:0:2,0:23.7:1:29.4:1:1:0:40.2:15.667:1:0:0.7 -3 195384954 . C A 95 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1e-05;SOR=Inf;LSEQ=GGACTGGCGGGACTGCGCGG;RSEQ=GGCGACTACAGACGTGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:153,142:0:2,0:25.5:1:29.8:1:1:0:38.9:18.667:0.9929:0:0.4 0/1:155:11:7,4:75,68:0.071:2,2:24.8:1:27.6:1:0.54376:1.58:38.8:10:0.0699:0:5 -3 195384959 . A T 98 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCGGGACTGCGCGGCGGCG;RSEQ=CTACAGACGTGTCGGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:154,155:0:2,0:26.1:1:28.4:1:1:0:39.4:15.263:1:0:0.4 0/1:169:12:7,5:80,77:0.071:2,2:23.4:1:27.4:1:0.76728:1.35:38.8:24:0.0745:0:4.9 -3 195384968 . G T 100 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCGCGGCGGCGACTACAGAC;RSEQ=TGTCGGGGGTCCGGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:155,187:0:2,0:26.7:1:30.1:1:1:0:40.3:41.75:1:0:0.3 0/1:188:13:7,6:87,88:0.0691:2,2:22.8:1:27.2:1:1:1.18:39.5:12:0.0659:0:4.8 -3 195384977 . G T 95 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGACTACAGACGTGTCGGGG;RSEQ=TCCGGGGCCTGTCGCGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:152,199:0:2,0:27.9:1:31.1:1:1:0:40.7:34.1:1:0:0.3 0/1:200:14:7,7:86,100:0.07:2,2:23.6:1:25.1:1:0.78941:1.16:37.6:3.667:0.057:0:4.5 -3 195384986 . C T 106 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGTGTCGGGGGTCCGGGGC;RSEQ=TGTCGCGGTTGCCAAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:144,197:0:2,0:29.5:1:31:1:1:0:41.2:41.625:1:0:0.3 0/1:202:15:6,9:86,100:0.0743:2,2:25.5:1:27.2:1:0.78948:1.28838:36.9:4:0.0615:0:4.1 -3 195385044 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.05297;SOR=Inf;LSEQ=GCTGGCCAAGGCGGTGAGTC;RSEQ=CTGCCGCGGACCGGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:35,103:0:2,0:18.6:1:30.9:1:1:0:45.8:26.6:1:0:0.2 0/1:84:3:2,1:24,57:0.0357:2,2:13.3:1:27.7:1:0.22512:4.65:49.7:6:0.037:0:1 -3 195385064 . G A 21 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19604;SOR=Inf;LSEQ=CCTGCCGCGGACCGGGGCAG;RSEQ=GCAGGCGGGGGGCGAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:10,46:0:2,0:15.6:1:31.2:1:1:0:44.7:112:1:0:0.1 0/1:45:2:1,1:10,33:0.0444:2,2:15:1:21.5:1:0.43333:3.19:50:4:0.0465:0:1 -3 195385177 . G T 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGGGAAGGGGCTGGGAGA;RSEQ=CCCTGGGCCGGTGCGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:5:0:29:1:1:0:48:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195388540 . T G 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5457;SOR=0.27439;LSEQ=CATAAGAAGGTGAACAGTTT;RSEQ=CAAGGGGAAGTTTGAATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:12,4:0.1111:2,0:19.5:1:31:1:0.09804:0:25:4:0.1111:0:1 0/1:31:1:0,1:28,2:0.0323:2,0:27:0:34:0:0.09677:0:25:2:0.0323:0:1 -3 195388608 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.21849;SOR=0;LSEQ=GACACTAACCCTCTGGATCT;RSEQ=TGTCTTCTGTGTCTCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:2,0:12,26:0.05:2,0:41.5:1:33:0:0.11667:0:24.5:4:0.05:0:1 0/0:45:0:0,0:16,29:0:2,0:26.3:1:29.7:1:1:0:26.7:90:1:0:0.1 -3 195388714 . T TA 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00435;SOR=3.59483;LSEQ=TGCTAAAGTTTCAGATTCCG;RSEQ=AAGTTCATGCTTTTTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:16:16,0:64,15:0.1684:2,1:30.8:1:28:1:0.06685:0:24.8:15:0.1596:0.0105:0.5 0/1:33:14:14,0:9,10:0.4242:2,1:31.2:1:29.1:1:0.00142:0:24.9:28:0.4242:0.0606:0 -3 195388761 . G C 111 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.06212;SOR=0;LSEQ=AATGATTTTTTTGGCTTGGG;RSEQ=GTAAGGATCTATACCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:11:11,0:61,6:0.141:2,0:18.5:1:32.1:1:0.5864:0:24.8:22:0.1486:0:1.1 0/0:27:0:0,0:24,3:0:2,0:24.6:1:29.7:1:1:0:25:26:1:0:0.1 -3 195389397 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACAAGAGTCTTCATGTTT;RSEQ=GCATAGTGGAACCTGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:9,2:0:2,0:28.5:1:28.6:1:1:0:29.2:4.5:1:0:0.6 0/1:103:2:1,1:77,24:0.0194:2,2:11:1:28:1:0.42833:3.16385:37:4:0.02:0:1 -3 195389706 . C G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16613;SOR=Inf;LSEQ=CCTCCTCCCTGTGCTCCAGC;RSEQ=ACTTGGCCTCTTGCTGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:12,105:0:2,0:23.9:1:32.2:1:1:0:35.7:57.5:1:0:0.1 0/1:81:2:1,1:3,76:0.0247:1,2:24.5:1:28.5:1:0.09691:22.08:49:4:0.025:0:1.5 -3 195390147 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGTTAATAAAATTATG;RSEQ=GGAGAGATTCATGGAGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:29.5:1:1:0:43.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195390357 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00458;LSEQ=TGTCAGGCCTGGCTGCTCCT;RSEQ=TGCTGAGGTCAGCCCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:36:33,3:1,0:0.973:0,2:26.7:1:30.9:1:1:0:29.3:35:0.9722:0:1.1 0/1:33:4:4,0:27,2:0.1212:2,0:20.8:1:31.5:1:1:0:32.5:8:0.1212:0:1 -3 195390398 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19195;SOR=0;LSEQ=GGGAGTCACCATGTGAGTAG;RSEQ=TGGCTTTCTCTGAATCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:58,6:0.0303:2,0:6:1:29.5:1:1:0:31:4:0.0308:0:1 0/0:84:0:0,0:74,10:0:2,0:25.6:1:31.6:1:1:0:31.9:20:1:0:0.2 -3 195390454 . G A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=20.47306;LSEQ=GCCTGGAAGACAAAGCTGGG;RSEQ=CTCCTGTTTGTGGCTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:1,0:50,35:0.0116:2,0:13:0:25:0:1:0:27:2:0.0119:0:1 0/1:97:19:9,10:47,31:0.1959:2,2:23.9:1:28.5:1:0.31614:1.67528:29.5:38:0.1979:0:1 -3 195390554 . T C 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02334;SOR=Inf;LSEQ=AACTGGAGGTGGCATTTCTA;RSEQ=GACACCGTGAAGGGCTCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:62,22:0:2,0:27.9:1:31:1:1:0:27.7:83:1:0:0.1 0/1:77:5:1,4:46,26:0.0649:2,2:21.6:1:29.4:1:0.0724:6.90188:26.2:10:0.0649:0:1.4 -3 195390609 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15962;SOR=0;LSEQ=AGGATGCCATCCACTACGTG;RSEQ=CGGAGCAGGCCCCCACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:65,18:0.0235:2,2:13:1:27.5:1:0.39916:3.54148:47.5:4:0.0241:0:1 0/0:127:0:0,0:76,51:0:2,0:26:1:28.1:1:1:0:39.9:30.75:1:0:0.3 -3 195390637 . A C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07118;LSEQ=GGCCCCCACTGCCATGGTCG;RSEQ=GGTGATGGGCGGGAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:56:42,14:6,16:0.7179:2,2:27.6:1:31:1:0.00019:7.75:31.1:55:0.7237:0:1 0/1:152:23:18,5:59,70:0.1513:2,2:27.2:1:30.6:1:0.00578:4.23:28.7:22:0.1549:0:1.3 -3 195390664 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52182;SOR=Inf;LSEQ=GGGCGGGAGGCTCTGGGTGC;RSEQ=CTGGTGGTCTGTTTCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:40,55:0:2,0:23.2:1:29.1:1:1:0:36.2:18:1:0:0.6 0/1:148:2:1,1:49,95:0.0135:2,2:23.5:1:31.5:1:1:1.93:52:4:0.014:0:1.5 -3 195390680 . C T 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.732;SOR=1.38923;LSEQ=GTGCTCTGGTGGTCTGTTTC;RSEQ=AGTACAAGAGTCCTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:3:3,0:32,69:0.0288:2,0:6.7:1:31.7:1:0.03594:0:32:6:0.03:0:1.3 0/1:126:5:2,3:35,86:0.0397:2,2:23.2:1:29:1:0.63009:1.63:25:10:0.0403:0:1.4 -3 195390776 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.36939;SOR=0.42713;LSEQ=CACAAGAGAAGTCTTTGTCC;RSEQ=TCATGAACTATGTATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:18:16,2:40,71:0.1395:2,2:26.1:1:28.6:1:4e-05:13.93:29.8:17:0.1328:0:1.3 0/1:31:2:2,0:7,22:0.0645:2,0:12:1:28.5:1:0.07742:0:27:4:0.0645:0:1 -3 195390794 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATCATGAACTATGTATTA;RSEQ=ATGTAATAAGAAAAACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:70,45:0.0171:2,2:17.5:1:30.5:1:1:1.54946:49.5:4:0.0179:0:1 0/0:33:0:0,0:18,15:0:2,0:18.2:1:31.6:1:1:0:37.3:66:1:0:0.1 -3 195390857 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11539;SOR=Inf;LSEQ=TCATAAAATAGGTTAATTTG;RSEQ=GTTTGCAGATTTGTATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:219,23:0:2,0:22.1:1:31.5:1:1:0:36.4:79.667:1:0:0.1 0/1:125:2:1,1:114,9:0.016:2,2:32.5:1:30:1:0.15419:12.0694:27:4:0.0163:0:1 -3 195390918 . TA T 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGAATATCTTGACTCCTT;RSEQ=GGGTAATAAGGCTTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:757:0:0,0:556,199:0:2,0:23:1:28.6:1:1:0:40.3:67.636:0.9987:0:0.1 0/1:453:16:9,7:318,119:0.0353:2,2:21:1:30.3:1:0.16042:2.0747:33.6:32:0.036:0.011:0.3 -3 195390937 . T G 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=TTAGGGTAATAAGGCTTTTG;RSEQ=TTGTTTTTATCTTTCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:911:0:0,0:607,304:0:2,0:25.5:1:29.6:1:1:0:38.9:90.1:1:0:0.1 0/1:541:7:4,3:337,197:0.0129:2,2:25.9:1:27.1:1:0.71317:1.28236:39.6:6:0.0112:0:1.3 -3 195391050 . A G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62238;SOR=1.08508;LSEQ=GCCTCAAGTTTGGAAAGGGC;RSEQ=GGCAGGCCCATCGGTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1150:117:17,100:452,580:0.1017:2,2:29.3:1:30.9:1:0:4.57899:26.7:116:0.102:0:1.4 0/1:603:66:16,50:242,295:0.1095:2,2:31.5:1:29.8:1:0.00141:2.55969:27.2:132:0.1106:0:1.4 -3 195391111 . T C 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00012;SOR=0.47463;LSEQ=CCACTCAATATTGCACACCT;RSEQ=ATATGGGAGGGTAAGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:128:6,122:122,308:0.229:2,1:21.1:1:32.8:1:0:8.03215:33.8:127:0.2305:0:2.2 0/1:324:40:3,37:92,190:0.1235:2,2:20.8:1:31.8:1:0.00067:5.94829:29.2:39:0.1223:0:2.3 -3 195391129 . T C 179 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00197;SOR=0.38343;LSEQ=CTTATATGGGAGGGTAAGGC;RSEQ=GCCCCCCGTCCACCTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:57:0,57:76,248:0.1496:2,1:22.8:1:30.8:1:0:0:28.8:56:0.1501:0:3.1 0/1:206:13:2,11:57,136:0.0631:2,2:30.4:1:28.6:1:0.35632:2.29738:26.5:12:0.0591:0:2.8 -3 195391130 . GC G 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.01535;SOR=Inf;LSEQ=TTATATGGGAGGGTAAGGCT;RSEQ=CCCCCGTCCACCTGAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:73,298:0:2,0:24.4:1:31.4:1:1:0:54.8:73.2:1:0:0.5 0/1:203:4:2,2:54,145:0.0197:2,2:19.3:1:32.3:1:0.30528:2.67:60:8:0.02:0:0.3 -3 195391133 . C A 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00178;SOR=Inf;LSEQ=TATGGGAGGGTAAGGCTGCC;RSEQ=CCCGTCCACCTGAGACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:69,297:0:2,0:23.8:1:31:1:1:0:54.5:39.667:1:0:0.5 0/1:198:6:2,4:53,139:0.0303:2,2:35.2:1:28.5:1:0.6706:1.31:28.2:12:0.0314:0:3.7 -3 195391145 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1046;SOR=Inf;LSEQ=AGGCTGCCCCCCGTCCACCT;RSEQ=AGACAGGACACATAGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:51,245:0:2,0:23.1:1:31.4:1:1:0:54:73:1:0:0.5 0/1:142:2:1,1:33,107:0.0141:2,2:9:0:30:1:0.42283:3.21:60:4:0.0141:0:1.5 -3 195391182 . C T 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01075;SOR=Inf;LSEQ=GCTGGGGCTTGTGGTGACAG;RSEQ=GGGGAATGGGTTAGCGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:15,125:0:2,0:24.1:1:30.1:1:1:0:53.4:45.667:1:0:0.2 0/1:68:4:1,3:7,57:0.0588:2,2:24:1:26.8:1:0.40122:2.66:54.5:8:0.0606:0:1.3 -3 195391183 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1022;SOR=Inf;LSEQ=CTGGGGCTTGTGGTGACAGC;RSEQ=GGGAATGGGTTAGCGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:14,119:0:2,0:25:1:31.1:1:1:0:53.1:132:1:0:0.2 0/1:63:2:0,2:7,54:0.0317:2,0:6:1:31:1:1:0:26:4:0.0323:0:4.5 -3 195391247 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAGCAACAGAGAACAGC;RSEQ=GTGTGGGGCACATGCAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:1,33:0.0556:1,0:34.5:1:32:1:1:0:25:4:0.0556:0:2 0/0:13:0:0,0:0,13:0:1,0:16.5:1:29:1:1:0:51.5:26:1:0:0.2 -3 195392403 . G A 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAACGGCAGGTCCAGGC;RSEQ=GGCAGCGCTGTCCGGCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:29:1:30.8:1:1:0:46.8:8:0.8:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195392644 . A G 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=CAGACTCCGAGTGGAGCTGC;RSEQ=TGCGGCCACCGGACAGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:3,2:0.4444:2,2:12.3:1:29.5:1:1:1.85:29.8:8:0.4444:0:1.5 0/0:3:0:0,0:2,1:0:2,0:22:1:31:1:1:0:49:6:1:0:0.3 -3 195392753 . T C 107 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19847;SOR=0;LSEQ=CTCTAGCACACCTGCCTTGT;RSEQ=GGTACTGCTGGGCGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:11:10,1:59,2:0.1528:1,2:15.3:1:31.2:1:0.39655:2.89012:27:22:0.1528:0:2.1 0/0:14:0:0,0:13,1:0:1,0:20.4:1:31.1:1:1:0:29:28:1:0:0.6 -3 195392763 . G C 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10291;SOR=0.38126;LSEQ=CCTGCCTTGTTGGTACTGCT;RSEQ=GGCGTGGAATGCCTCTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:69:66,3:11,0:0.8519:0,1:26.4:1:32:1:1:0:27.7:138:0.8519:0:1.2 1/0:19:13:12,1:6,0:0.6842:0,1:23.8:1:31.5:1:1:0:28.9:26:0.6842:0:1.2 -3 195392835 . C T 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04055;SOR=Inf;LSEQ=CTCCTTGGATTTACCTGGTC;RSEQ=ATTTGGATCAAGTTCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:224,11:0:1,0:26:1:30.8:1:1:0:30.4:57.75:1:0:0.5 0/1:124:3:3,0:118,3:0.0242:1,0:29.3:1:26.7:1:1:0:30.7:2:0.0165:0:1 -3 195392842 . A G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=GATTTACCTGGTCCATTTGG;RSEQ=TCAAGTTCTTTCACCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:246,12:0:1,0:24.9:1:29.8:1:1:0:30.1:42:1:0:0.4 0/1:143:9:9,0:131,3:0.0629:1,0:23.4:1:31.1:1:1:0:27.6:18:0.0643:0:1.1 -3 195392856 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05638;SOR=Inf;LSEQ=ATTTGGATCAAGTTCTTTCA;RSEQ=CTATTCACATGAGCAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:312,16:0:1,0:22.7:1:31.7:1:1:0:29.7:53.667:1:0:0.4 0/1:205:3:3,0:194,8:0.0146:1,0:26:1:31.3:1:1:0:31.3:6:0.0149:0:1 -3 195392868 . A T 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=37.13661;LSEQ=TTCTTTCACCTATTCACATG;RSEQ=GCAGATATCACCTTAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:1:0,1:379,26:0.0025:2,0:1:0:25:0:0.0665:0:48:2:0.0025:0:1 0/1:261:22:21,1:229,9:0.0843:1,1:22.5:1:29.3:1:0.59364:1.21068:28.8:44:0.0859:0:1.1 -3 195392916 . C CT 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.70785;SOR=1.18782;LSEQ=TTGGCTTAACACTTCTTGCC;RSEQ=TTTTTTTTTCTTTCTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:16:12,4:304,119:0.0363:2,2:35.2:1:31.3:1:1:1.17:27.5:32:0.037:0:0.6 0/1:327:14:7,7:226,87:0.0428:2,2:31.6:1:25.3:1:0.12594:2.58902:26.9:6:0.0373:0:0.7 -3 195392991 . A T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTGCCTTGGATCTCCTG;RSEQ=TGGAGAATGGGGAGTGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:0:0,0:137,341:0:2,0:27.5:1:30.2:1:1:0:31.5:30.867:1:0:0.3 0/1:302:19:8,11:61,222:0.0629:2,2:26:1:29.2:1:0.04917:2.64:32.4:18:0.0604:0:1.1 -3 195393024 . C T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04823;SOR=Inf;LSEQ=AGTGCCGTGGTGTCTTCGCA;RSEQ=TGTGCATACAGGACGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:172,291:0:2,0:26.1:1:32.2:1:1:0:32:114.75:1:0:0.3 0/1:266:3:0,3:101,162:0.0113:2,0:27.3:1:30.3:1:0.29075:0:27:6:0.0115:0:2 -3 195393030 . A G 221 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.657;SOR=0.90881;LSEQ=GTGGTGTCTTCGCACTGTGC;RSEQ=TACAGGACGGGTCCATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:121:2,119:173,162:0.2654:2,1:27.3:1:32:1:0:63.25578:28.7:39.333:0.2622:0:1.1 0/1:259:64:0,64:105,90:0.2471:2,1:28.1:1:31.7:1:0:0:27.9:128:0.25:0:1.1 -3 195393134 . T C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06611;SOR=0.36164;LSEQ=TTTGTAAAAATGAATAAATT;RSEQ=CATTTAGAGTCTCTTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:16:0,16:30,240:0.0559:2,1:27:1:31.2:1:0.3898:0:26.7:32:0.0573:0:1 0/1:191:4:1,3:29,158:0.0209:2,2:14.8:1:31.5:1:0.49813:1.81:32:8:0.0213:0:1 -3 195393212 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.40315;LSEQ=CACAGGCCTTGATATAACCA;RSEQ=GTGAGGGTGATGGCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:0,2:1,61:0.0313:1,0:41:1:29:1:1:0:27:4:0.0323:0:1.5 0/1:23:1:0,1:0,22:0.0435:1,0:30:0:32:0:1:0:44:2:0.0435:0:1 -3 195393238 . A G 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01056;SOR=Inf;LSEQ=GGTGATGGCCTTTCCCAGCC;RSEQ=TGGTTCCTCACCTGTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:0:1,0:26:1:31.7:1:1:0:56.3:38:1:0:0.1 0/1:12:3:0,3:0,9:0.25:0,0:27.3:1:31.3:1:1:0:52:6:0.25:0:1 -3 195394580 . T C 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAAGAGAGTAGACCTTAGG;RSEQ=GTCTGTATCTCCAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5:1:28.5:1:1:0:44.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195394600 . A C 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGTATCTCCAAAAAAA;RSEQ=GGATAATTGTATGAGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:32:1:1:0:44.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195394620 . T G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATAATTGTATGAGGTGA;RSEQ=AGATGTGTATTAAGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:1:32.5:1:1:0:44.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195395107 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCGTACTCCAGCCTGGGC;RSEQ=ACAAGAGTTAGACCCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:22:1:30.5:1:1:0:41:4:0.1667:0:4 0/0:3:0:0,0:2,1:0:2,0:38.7:1:31:1:1:0:54.7:6:1:0:0 -3 195395124 . A G 34 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGACAAGAGTTAGACCCT;RSEQ=TCTCAAAATAAATAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:18,1:0.0952:1,0:37.5:1:34:0:1:0:41:4:0.1:0:4 0/0:4:0:0,0:3,1:0:2,0:33:1:27:1:1:0:56:8:1:0:0 -3 195395129 . AAAAT A 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=5.000;MSILEN=4;SSF=0.29014;SOR=0;LSEQ=CAAGAGTTAGACCCTATCTC;RSEQ=AAATAAATAAATAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:5,1:14,1:0.2609:1,2:18.2:1:30.2:1:0.5:2.64575:36.2:12:0.2609:0.087:0.2 0/0:7:0:0,0:6,1:0:2,0:21:1:29.4:1:1:0:57.7:14:1:0:0.7 -3 195395142 . AAAT A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.26528;LSEQ=CTATCTCAAAATAAATAAAT;RSEQ=AAATAAAATATAAATGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:11:11,0:19,2:0.3438:2,0:14.5:1:29.5:1:0.53427:0:42.3:10:0.3226:0.2188:1.6 0/1:10:4:3,1:5,1:0.4:2,2:24:1:28.8:1:1:1.58108:56:8:0.4:0:1.3 -3 195395145 . T TA 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=4;SSF=1;SOR=0.87478;LSEQ=TCTCAAAATAAATAAATAAA;RSEQ=AAATAAAATATAAATGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:13:12,1:10,1:0.4333:2,1:26.8:1:28.4:1:1:1.19:58.8:26:0.5417:0:0.1 0/1:10:4:3,1:2,0:0.4:0,2:13:1:28.3:1:1:0:55.8:8:0.6667:0:3 -3 195395156 . T C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20669;SOR=2.29728;LSEQ=ATAAATAAATAAATAAAATA;RSEQ=AAATGGAAGTCTCTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:12:12,0:30,2:0.2727:2,0:15.2:1:31.8:1:1:0:34.7:11:0.2558:0:2.5 0/1:15:7:6,1:7,1:0.4667:2,2:16:1:31.7:1:1:1.1547:52.4:14:0.4667:0:4 -3 195395168 . T C 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00192;SOR=6.12915;LSEQ=ATAAAATATAAATGGAAGTC;RSEQ=CTTCTCTGATCCCAGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:10:10,0:61,2:0.137:1,0:14.5:1:31.9:1:1:0:45.4:20:0.1389:0:3.7 1/0:18:9:8,1:8,1:0.5:2,2:23.2:1:31.1:1:1:1:53.1:18:0.5294:0:3.8 -3 195395200 . C G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.1827;LSEQ=CCAGGCTTCTATCCTACCTG;RSEQ=GCAGGGTAGCAGCACCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:12:12,0:102,4:0.1017:1,0:31.1:1:31.8:1:1:0:50.8:24:0.1026:0:3.4 1/0:33:17:16,1:15,1:0.5152:1,1:31.9:1:31.6:1:1:1.06:55.5:34:0.5152:0:3.1 -3 195395203 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.85608;LSEQ=GGCTTCTATCCTACCTGCGC;RSEQ=GGGTAGCAGCACCACTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:14:14,0:108,4:0.1111:1,1:28.1:1:30.4:1:1:0:49.5:28:0.1129:0:3.4 1/0:36:18:17,1:17,1:0.5:1,1:31.1:1:29.9:1:1:1:55.8:36:0.5:0:2.9 -3 195395223 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30729;SOR=2.65243;LSEQ=AGGGTAGCAGCACCACTGGC;RSEQ=TGGCCCCCAGTGATGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:2,0:146,6:0.013:1,0:18.5:1:32.5:1:1:0:40:4:0.0135:0:2.5 0/1:59:2:2,0:52,5:0.0339:2,0:7:1:31:1:1:0:40:4:0.0339:0:1 -3 195395272 . C T 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.05465;SOR=1.69794;LSEQ=CGTGAGTAGGGGGTTGTGTG;RSEQ=ACACAGCACTGAGAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:39:34,5:219,11:0.145:1,2:29.5:1:29.7:1:0.06407:2.91197:39.7:78:0.1477:0:1.8 0/1:143:32:30,2:103,8:0.2238:2,2:27.3:1:30.3:1:1:1.16:41.2:64:0.2286:0:1.8 -3 195395289 . A T 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01443;SOR=0.56255;LSEQ=GTGCACACAGCACTGAGAAG;RSEQ=TGGTGCCCGGGGGCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:78:74,4:215,29:0.2422:2,2:29.2:1:29.5:1:0.13087:2.49:42.1:38:0.2436:0:4.5 0/1:197:30:25,5:155,12:0.1523:2,2:24.7:1:28.9:1:0.14711:2.56727:42.9:29:0.1495:0:5.2 -3 195395314 . G A 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00442;SOR=0.6096;LSEQ=GCCCGGGGGCTGCCCTGTCC;RSEQ=TTCTGTGATCTCATTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:127:111,16:311,67:0.2515:2,2:22.1:1:29.9:1:0.21312:1.49:42.7:126:0.253:0:5.5 0/1:359:61:47,14:246,51:0.1699:2,2:22.5:1:29.3:1:0.27906:1.43523:44.1:60:0.17:0:5.8 -3 195395328 . T C 269 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.46196;LSEQ=CTGTCCGTTCTGTGATCTCA;RSEQ=TAGACAGGAGGTCCGGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:606:368:283,85:195,42:0.6073:2,2:22.3:1:31.6:1:0.12536:1.39374:38.7:39.889:0.6064:0:3.5 0/1:461:192:144,48:209,60:0.4165:2,2:22.8:1:30.6:1:0.50555:1.16073:45.2:26.429:0.4084:0:3.5 -3 195395334 . A T 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00137;SOR=0.64778;LSEQ=GTTCTGTGATCTCATTAGAC;RSEQ=GGAGGTCCGGACGTGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:666:192:151,41:365,108:0.2883:2,2:21:1:30.6:1:0.7583:1.09:49.1:63:0.289:0:5.3 0/1:539:112:78,34:320,107:0.2078:2,2:20.4:1:29.7:1:0.27741:1.30299:49.9:55:0.2068:0:5.3 -3 195395347 . G A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=0.64413;LSEQ=ATTAGACAGGAGGTCCGGAC;RSEQ=TGGGCCACTGTGTGCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:828:245:177,68:415,167:0.2959:2,2:23:1:30.4:1:0.80069:1.05:52.6:48:0.2956:0:4.8 0/1:709:151:104,47:396,160:0.213:2,2:22.7:1:29.7:1:0.61427:1.11832:52.7:74.5:0.2119:0:4.8 -3 195395354 . A G 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00085;SOR=0.68711;LSEQ=AGGAGGTCCGGACGTGGGCC;RSEQ=CTGTGTGCAGTCACTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:916:261:179,82:449,203:0.2849:2,2:25.2:1:30.5:1:0.93714:1.01323:53.8:51.2:0.2838:0:4.5 0/1:805:173:110,63:433,199:0.2149:2,2:23.8:1:30.1:1:0.23428:1.24581:54.1:56.667:0.2136:0:4.4 -3 195395379 . T G 272 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08647;SOR=0.85417;LSEQ=GTGCAGTCACTGCTCTCTGT;RSEQ=GTTTCCATAGGCTACGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1249:390:250,140:551,308:0.3122:2,2:26.6:1:31.7:1:1:1.00182:56.3:77:0.3128:0:3.2 0/1:1113:311:195,116:492,310:0.2794:2,2:26.6:1:31.1:1:0.73119:1.06:56.3:310:0.2823:0:2.7 -3 195395399 . G A 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.12799;LSEQ=TGTTTCCATAGGCTACGGGC;RSEQ=CACCTACTTGAGCTGCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1467:317:211,106:692,453:0.2161:2,2:27.9:1:30:1:0.05014:1.30:27.7:78.25:0.2178:0:2.2 0/1:1439:49:38,11:795,594:0.0341:2,2:25.4:1:28.9:1:0.00478:2.58:27.8:15.333:0.0327:0:2.2 -3 195395402 . C A 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12973;LSEQ=TTCCATAGGCTACGGGCGCA;RSEQ=CTACTTGAGCTGCACGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1489:309:205,104:704,475:0.2075:2,2:28.9:1:30.2:1:0.03593:1.33:27.7:102:0.2092:0:2.2 0/1:1462:48:38,10:794,619:0.0328:2,2:25.2:1:28.9:1:0.0016:2.96:27.2:15:0.0313:0:2.2 -3 195395515 . A C 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAGTTCCACCCCACAGGT;RSEQ=GGGCAGGACGCCTTGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2415:0:0,0:962,1450:0:2,0:28.7:1:29.5:1:1:0:39.4:79.4:0.9987:0:0.4 0/1:1583:26:10,16:632,925:0.0164:2,2:26.2:1:29.5:1:1:1.09315:35.2:52:0.0166:0:1.1 -3 195395524 . C T 143 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=23.20762;LSEQ=ACCCCACAGGTAGGGCAGGA;RSEQ=GCCTTGCCCGGAAGGCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2369:2:1,1:855,1511:8e-04:2,2:33:1:22.5:1:1:1.77:48:1:4e-04:0:1 0/1:1507:29:13,16:554,923:0.0192:2,2:27.7:1:29.6:1:0.44262:1.35:42.4:58:0.0196:0:1.2 -3 195395533 . C T 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.58715;LSEQ=GTAGGGCAGGACGCCTTGCC;RSEQ=GGAAGGCGTTCGGCTCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2281:407:130,277:623,1250:0.1784:2,2:25.2:1:30.3:1:0.64193:1.06196:43.2:134.667:0.1795:0:1.2 0/1:1412:362:124,238:362,688:0.2564:2,2:25.3:1:29.9:1:0.94896:1.00989:42.8:180:0.2584:0:1.3 -3 195395549 . C CAT 307 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00943;SOR=0.81026;LSEQ=TGCCCGGAAGGCGTTCGGCT;RSEQ=GTGTGTCTTGTAAGCGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1710:1147:253,894:171,388:0.6708:2,2:25.3:1:30.3:1:0.00017:1.55696:40.5:113.7:0.6724:0.1275:0.6 1/0:1100:685:168,517:120,283:0.6227:2,2:23.3:1:29.6:1:0.06429:1.30454:42.4:136:0.6227:0.1555:0.8 -3 195395564 . C T 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47174;SOR=0.89194;LSEQ=CGGCTCGTGTGTCTTGTAAG;RSEQ=GTGTGGTGCCTACTCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1183:151:24,127:160,868:0.1276:2,2:26:1:30.2:1:0.90463:1.03:37.6:150:0.1279:0:1.1 0/1:719:83:13,70:106,529:0.1154:2,2:25.4:1:30:1:1:1.07885:37.1:82:0.1152:0:1.1 -3 195395565 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=Inf;LSEQ=GGCTCGTGTGTCTTGTAAGC;RSEQ=TGTGGTGCCTACTCATTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1138:0:0,0:170,968:0:2,0:25.5:1:31.9:1:1:0:40.6:102.455:1:0:0.4 0/1:703:10:2,8:113,580:0.0142:2,2:16:1:28:1:0.67134:1.28:35:9:0.013:0:1.6 -3 195395624 . A G 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43756;SOR=0.67533;LSEQ=ATAACATGGTTTTGAAGATC;RSEQ=GCTTCCATAGCTCTCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:23:0,23:4,177:0.1127:1,1:16.8:1:30.5:1:1:0:33.9:22:0.1095:0:2.2 0/1:114:9:1,8:4,101:0.0789:1,2:17.3:1:29.1:1:0.34224:3.11:37.9:18:0.0796:0:2 -3 195395631 . A T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52211;SOR=0.78013;LSEQ=GGTTTTGAAGATCAGCTTCC;RSEQ=TAGCTCTCAGGTCCTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:39:0,39:3,115:0.2484:1,1:14.1:1:29.3:1:0.5745:0:32.2:38:0.2452:0:1.8 0/1:83:17:0,17:2,64:0.2048:1,1:14.7:1:29.4:1:1:0:32.5:34:0.2048:0:1.6 -3 195395637 . C G 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00569;SOR=13.11489;LSEQ=GAAGATCAGCTTCCATAGCT;RSEQ=TCAGGTCCTAACTTCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:0,1:3,132:0.0074:1,0:15:0:32:0:1:0:49:2:0.0076:0:1 0/1:67:6:0,6:2,59:0.0896:1,0:20.7:1:31.2:1:1:0:47:12:0.0896:0:1 -3 195395663 . C T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18715;SOR=0.37656;LSEQ=TCCTAACTTCAATGTCATTT;RSEQ=CTTAAGGAGACTTTTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:17:0,17:2,85:0.1635:1,1:32.1:1:29.3:1:1:0:34.3:16:0.1616:0:2.9 0/1:44:3:0,3:2,39:0.0682:1,0:27.7:1:30:1:1:0:25:6:0.0682:0:3 -3 195395726 . T A 92 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.6719;LSEQ=TTGGGCCACCATCTTATGCA;RSEQ=TTCTCAAGAGCCCTAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:8:0,8:1,31:0.2:1,0:21.3:1:30.9:1:1:0:44.6:16:0.2:0:2.1 0/1:7:1:0,1:0,6:0.1429:0,0:34:0:29:0:1:0:44:2:0.1429:0:2 -3 195395779 . A G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTATGCCAGCAGTAAAGC;RSEQ=GGGATTGAGGCCGGGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:0.4286:0,0:11.7:1:31.7:1:1:0:34.3:6:0.4286:0:1 0/0:1:0:0,0:0,1:0:0,0:14:0:30:0:1:0:44:2:1:0:2 -3 195396935 . AT A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTAGAGACAGGGTGTCACC;RSEQ=TTTAAGCCCAGGCTGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:28.5:1:1:0:27:4:1:0:0 -3 195397842 . T C 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.25816;LSEQ=GTGCTTTTTGTTATCCAGAC;RSEQ=TTCTACTGTATCTTAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:5,0:18,1:0.2083:1,0:19:1:31.4:1:1:0:27:10:0.2083:0:1.6 0/1:12:3:3,0:9,0:0.25:0,0:14.7:1:30.3:1:1:0:27:6:0.25:0:1.3 -3 195397908 . T A 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28391;SOR=0.76504;LSEQ=TGCCTTCTGCATATCTTTTT;RSEQ=GTCTCTCCCCCAAAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:91:87,4:108,2:0.4527:1,1:22:1:29:1:0.41303:2.47174:33.2:182:0.455:0:1.1 0/1:111:43:40,3:65,2:0.3874:1,2:24.4:1:28.4:1:0.37727:2.41705:35.1:86:0.3909:0:1.1 -3 195397926 . T A 220 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25418;LSEQ=TTTGTCTCTCCCCCAAAAAA;RSEQ=ATCTTGTAAAAAAAAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:151:145,6:156,13:0.4704:2,1:23.5:1:30.5:1:0.23566:2.01:34.6:74.5:0.4745:0:1.1 0/1:185:34:33,1:136,14:0.1838:2,1:25.6:1:29.7:1:0.31135:3.38:30.9:33:0.1813:0:1.1 -3 195397933 . T TA 79 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05157;SOR=0;LSEQ=CTCCCCCAAAAAATATCTTG;RSEQ=AAAAAAAAGTAATGCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:7:6,1:335,43:0.0182:2,2:20.3:1:28.3:1:0.57542:1.29748:30:14:0.0182:0.0052:0.7 0/0:222:0:0,0:182,24:0:2,0:24.4:1:29.6:1:1:0:35.2:205:0.9276:0:0.5 -3 195398105 . T C 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.02867;SOR=0.62436;LSEQ=TATGGAGCGATACGCCCCCA;RSEQ=CGCGAAGGACCTGGCGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:128:20,108:48,96:0.4706:2,2:24.6:1:31.5:1:0.00077:2.69024:27.3:127:0.4739:0:1.1 0/1:143:51:8,43:22,70:0.3566:2,2:24.6:1:31.3:1:0.28894:1.68338:28.2:102:0.3592:0:1.1 -3 195398195 . C T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00799;SOR=Inf;LSEQ=CGTGTGGTTTACCACCAGCA;RSEQ=TGTCTGAGCGGGCACACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:21,88:0:2,0:23.7:1:31:1:1:0:30.3:35.333:1:0:0.4 0/1:48:4:1,3:9,35:0.0833:2,2:16.3:1:28.5:1:1:1.29:32:8:0.0833:0:1.3 -3 195398250 . C A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.84016;SOR=0.87796;LSEQ=GTGAGTTTCAGCACCGCTCG;RSEQ=CCTCACCTTCGTGTGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:29:1,28:4,70:0.2816:2,1:22.4:1:29.6:1:1:1.59343:35:28:0.2828:0:1.7 0/1:43:11:1,10:3,29:0.2558:2,2:22.2:1:30.8:1:1:1.0337:28.8:22:0.2558:0:1.4 -3 195398271 . A G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09021;SOR=0.35497;LSEQ=CCTCACCTTCGTGTGCAGGC;RSEQ=CATGTGCACAGCCACCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:22:0,22:3,59:0.2619:1,1:24.4:1:32:1:0.56339:0:36.5:21:0.253:0:1.9 0/1:36:4:1,3:4,27:0.1111:2,2:21.8:1:26.3:1:0.4766:2.19:36.5:3:0.0857:0:3 -3 195398365 . T G 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.10229;SOR=0;LSEQ=TTTGAAAATTTTAGCCAGTT;RSEQ=CTTTCTCAAATCTGTGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:1,5:0,6:0.5:0,2:17.8:1:29.2:1:1:0:37.7:5:0.4545:0:1 0/0:5:0:0,0:1,4:0:2,0:22.2:1:26.2:1:1:0:31:4:1:0:0.4 -3 195399268 . A C 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36956;SOR=2.5055;LSEQ=CTCAGTATCAAAACATGTTG;RSEQ=AACTCACACGCTTCCAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:2,0:168,18:0.0106:2,0:6.5:1:33:0:1:0:27:4:0.0108:0:1 0/1:114:3:2,1:92,19:0.0263:2,2:5.7:1:27.7:1:0.44256:2.39721:31:6:0.0265:0:1 -3 195399318 . A G 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01551;SOR=0;LSEQ=TCAGGTCTGCTGCCGTTGCC;RSEQ=TTCTCTGCCTTATGTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:10:9,1:115,93:0.0459:2,2:25.7:1:29.2:1:0.0459:7.23:37.4:9:0.0421:0:1 0/0:132:0:0,0:70,62:0:2,0:26.8:1:28.4:1:1:0:33.3:65:1:0:0.1 -3 195399395 . C G 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01931;SOR=Inf;LSEQ=ATCACGTCTACCTGCAGCTG;RSEQ=ACCACCTACCTCCAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:86,93:0:2,0:24.7:1:32.3:1:1:0:34.4:58.667:0.9944:0:0.1 0/1:67:3:2,1:13,51:0.0448:2,2:16:1:32:1:0.12347:7.53:40:6:0.0455:0:1 -3 195399422 . A G 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01332;SOR=Inf;LSEQ=TACCTCCAGAGCAGCTGGCC;RSEQ=TGCCCTTGCCCGGCATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:139,67:0:2,0:22.9:1:30.5:1:1:0:35.1:50.5:1:0:0.2 0/1:65:3:2,1:24,38:0.0462:2,2:43:1:31:1:0.55893:3.11:40:6:0.0462:0:1 -3 195399475 . C G 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01678;SOR=Inf;LSEQ=ATCTTCGCTGGTGTGGACGT;RSEQ=ACGAAGGAGCCGATCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:250,29:0:2,0:25.7:1:31.1:1:1:0:37.2:33.875:1:0:0.4 0/1:97:3:3,0:81,13:0.0309:2,0:20:1:32.3:1:1:0:31.3:6:0.0316:0:1 -3 195399487 . G A 117 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1698;SOR=1.80734;LSEQ=GTGGACGTCACGAAGGAGCC;RSEQ=ATCCCTGTCCTCCCCACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:16:16,0:282,25:0.0495:2,1:26.9:1:29.4:1:0.62287:0:35.9:32:0.0503:0:1.9 0/1:116:10:10,0:97,9:0.0862:2,0:30.4:1:29.8:1:1:0:38.5:20:0.0862:0:2 -3 195399505 . C T 212 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.34019;LSEQ=CCGATCCCTGTCCTCCCCAC;RSEQ=GTGCATTATAACATGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:130:125,5:185,32:0.3746:2,1:25.3:1:30.3:1:0.00108:4.31:37:20.667:0.3669:0:1.2 0/1:142:24:23,1:106,12:0.169:2,1:27.3:1:30:1:0.6965:2.59:35.1:23:0.1631:0:1.5 -3 195399599 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.44823;SOR=1.24324;LSEQ=TGGAAAGAAGGCTGGGACAA;RSEQ=GGGGCCCATCTCGCAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:37:14,23:57,362:0.0811:2,2:20:1:28.7:1:0.00046:3.85:39.2:36:0.0811:0:2.3 0/1:192:19:6,13:43,130:0.099:2,2:25.9:1:27.2:1:0.58062:1.39:36.2:18:0.0947:0:2.4 -3 195399602 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.08672;SOR=Inf;LSEQ=AAAGAAGGCTGGGACAATGG;RSEQ=GCCCATCTCGCAGTTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:65,389:0:2,0:25:1:30.4:1:1:0:52.4:25.706:1:0:0.6 0/1:190:2:1,1:42,146:0.0105:2,2:18.5:1:28:1:0.40234:3.45:52:4:0.0108:0:1 -3 195399620 . C G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.20585;LSEQ=GGGGCCCATCTCGCAGTTGT;RSEQ=TCTTTAGATCTTAGAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:172:21,151:20,178:0.4636:2,2:24.9:1:31.7:1:0.61888:1.24:54.4:85:0.4645:0:1.7 0/1:146:22:3,19:14,110:0.1507:2,2:30.5:1:29.2:1:0.72252:1.24:41.9:21:0.1458:0:2.4 -3 195399678 . G T 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11999;SOR=0.59742;LSEQ=CAGAAAGTACTGTATTGTTT;RSEQ=CTAAATTGCACTTGAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:150:77:4,73:4,69:0.5133:2,2:24.1:1:30.3:1:1:1.0576:51.4:37.5:0.5102:0:2.1 0/1:57:22:1,21:3,32:0.386:2,1:29:1:28.3:1:1:1.94747:51.5:21:0.3818:0:2.1 -3 195399747 . A G 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50117;SOR=1.69382;LSEQ=ATAATTTATTCCTCCTTAGT;RSEQ=AACTGTCATAGATACATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:10:1,9:5,36:0.1961:2,2:24.8:1:32:1:1:1.24482:46.3:20:0.1961:0:1.3 0/1:17:5:1,4:1,11:0.2941:2,2:23.2:1:31.6:1:0.51471:2.57:59.4:10:0.2941:0:1.6 -3 195400355 . T C 47 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCGCGATCTCGGCTCAC;RSEQ=GCAACCTCCGCCTCCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:10,2:0.2:2,0:17:1:30:1:1:0:43:6:0.2143:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195400451 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCATGCCTGGCTAATTTTT;RSEQ=TATTTTTAGTTGAGACGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:39,0:0.0488:1,0:43:1:33:0:1:0:27:4:0.0513:0:1 0/0:14:0:0,0:13,1:0:1,0:23.4:1:28.8:1:1:0:56.7:28:1:0:1.3 -3 195400488 . A T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79661;SOR=1.2575;LSEQ=GGGGTTTCACCATGTTAGCC;RSEQ=GACAGGTCTCGAACCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:22:21,1:52,0:0.2973:1,1:30:1:30.5:1:0.2973:0:40.4:21:0.3:0:2.3 0/1:23:8:8,0:14,1:0.3478:1,0:34.6:1:29.8:1:1:0:43.4:7:0.3333:0:2.9 -3 195400498 . C T 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32688;SOR=1.66769;LSEQ=CATGTTAGCCAGACAGGTCT;RSEQ=GAACCCCTGAACTCAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:22:21,1:59,0:0.2716:1,1:31.4:1:30.4:1:0.2716:0:39.9:44:0.2821:0:2.3 0/1:26:10:10,0:15,1:0.3846:1,0:29.9:1:30.1:1:1:0:40.1:20:0.3846:0:2.9 -3 195400556 . A G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79255;SOR=1.13911;LSEQ=CCCAAAGTGCTGGGATTACA;RSEQ=GCGTGAGCCACTGCATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:17:13,4:83,1:0.1683:1,2:17.2:1:29.9:1:0.0026:24.16779:29.2:16:0.1616:0:2.4 0/1:32:6:4,2:25,1:0.1875:1,2:22.2:1:28.2:1:0.08266:11.00554:31.3:12:0.1935:0:2.7 -3 195400578 . A G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78371;SOR=0.70096;LSEQ=CGTGAGCCACTGCATGCCCG;RSEQ=CCTACTTCCCTCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:14:9,5:115,3:0.1045:1,2:20:1:30.9:1:3e-04:20.17665:35.2:13:0.1032:0:2.4 0/1:53:4:2,2:45,4:0.0755:2,2:27.5:1:27.8:1:0.05864:10.282:33.5:8:0.0769:0:2.5 -3 195400638 . TGTG T 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01036;SOR=0.37519;LSEQ=CCTGTTGAGGGAGGTGGGCT;RSEQ=GAGGAATGGGCATCTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:41:20,21:281,55:0.1088:2,2:28.1:1:30.7:1:0:5.33145:37.1:82:0.1111:0.008:1.5 0/1:183:8:0,8:142,33:0.0437:2,0:31.6:1:29.8:1:0:0:31.9:16:0.0442:0:1.1 -3 195400642 . G T 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03741;SOR=Inf;LSEQ=TTGAGGGAGGTGGGCTTGTG;RSEQ=AGGAATGGGCATCTTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:317,85:0:2,0:22.8:1:30.8:1:1:0:33.5:39.2:1:0:0.2 0/1:203:3:2,1:149,50:0.0148:2,2:14:1:29:1:1:1.48679:41.7:6:0.015:0:1.3 -3 195400654 . T C 165 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00331;SOR=0.33558;LSEQ=GGCTTGTGGAGGAATGGGCA;RSEQ=CTTGACATTTCACCTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:42:21,21:350,141:0.0788:2,2:30.3:1:30.6:1:0.00785:2.47752:37.1:84:0.0808:0:1.5 0/1:287:8:0,8:203,76:0.0279:2,0:38.3:1:28.6:1:4e-05:0:31.9:7:0.0251:0:1.1 -3 195400728 . A G 168 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17316;LSEQ=GCCAGGATCAGATTGTGCCC;RSEQ=GCCTGTACGCCTGTGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1182:50:35,15:585,547:0.0423:2,2:20.5:1:29.9:1:0.01332:2.18:39.6:100:0.043:0:2.6 0/0:791:6:5,1:401,383:0.0076:2,2:23.8:1:30.5:1:0.21806:4.77:33.3:12:0.0077:0:2.5 -3 195400795 . C T 195 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37095;LSEQ=CAACCGCCTCGGGGCAAACT;RSEQ=GCTGTTGGACCTGGTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:938:87:72,15:403,448:0.0928:2,2:27.3:1:30.4:1:0:5.33:40.2:86:0.0934:0:3.9 0/1:712:26:26,0:326,359:0.0365:2,1:28.2:1:30:1:0:0:35.3:52:0.037:0:4.5 -3 195400799 . G A 183 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.37593;LSEQ=CGCCTCGGGGCAAACTCGCT;RSEQ=TTGGACCTGGTTGTCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:926:88:75,13:391,447:0.095:2,2:26.9:1:28.4:1:0:6.58:40.1:43:0.0942:0:4 0/1:685:26:26,0:314,345:0.038:2,1:28.7:1:27.7:1:0:0:35.3:25:0.037:0:4.5 -3 195400807 . T C 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAAACTCGCTGTTGGACC;RSEQ=GGTTGTCTGGTCAGGCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:889:0:0,0:428,460:0:2,0:26.4:1:30.3:1:1:0:45.6:34.52:1:0:0.5 0/1:661:18:8,10:312,330:0.0272:2,2:24.1:1:29.4:1:0.81354:1.18152:44.1:17:0.0264:0:1.2 -3 195400814 . C CTT 156 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.80097;SOR=1.06939;LSEQ=TCGCTGTTGGACCTGGTTGT;RSEQ=TGGTCAGGCATGTGCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:38:33,5:317,448:0.0434:2,2:22.2:1:29.9:1:0:9.30:41:37:0.0434:0.0148:3.9 0/1:627:29:29,0:270,324:0.0463:2,1:26.6:1:31.1:1:0:0:34.1:58:0.0477:0.008:4.2 -3 195400816 . GGTCAGG TTGGTCGGA 186 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=GCTGTTGGACCTGGTTGTCT;RSEQ=CATGTGCCCTGAGCATCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:70:59,11:317,448:0.0799:2,2:22.3:1:30.5:1:0:7.56:40.6:140:0.0821:0.0251:3.4 0/0:627:0:0,0:270,324:0:2,0:26.6:1:31:1:1:0:46:36.125:0.9507:0:0.2 -3 195400822 . G A 159 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.90468;SOR=1.02467;LSEQ=GGACCTGGTTGTCTGGTCAG;RSEQ=CATGTGCCCTGAGCATCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:841:44:39,5:297,451:0.0523:2,2:17.9:1:29.2:1:0:11.81:40.8:21:0.0541:0:3.7 0/1:579:31:31,0:245,302:0.0535:2,1:24:1:29.2:1:0:0:35.7:62:0.0542:0:4.2 -3 195400825 . T A 83 v4;NM4;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03512;SOR=5.24421;LSEQ=CCTGGTTGTCTGGTCAGGCA;RSEQ=GTGCCCTGAGCATCGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:854:2:2,0:385,467:0.0023:2,0:14.5:1:31:0:0.20506:0:38:4:0.0024:0:3.5 0/1:575:7:7,0:266,301:0.0122:2,0:20.6:1:29.7:1:0.00528:0:37:14:0.0123:0:4.4 -3 195400841 . C A 160 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11544;SOR=1.45881;LSEQ=GGCATGTGCCCTGAGCATCG;RSEQ=AGAGTCGTGCAGGCCTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:781:40:38,2:299,442:0.0512:2,2:20.3:1:30.2:1:0:28.00:40.5:80:0.0523:0:3.5 0/1:493:36:36,0:177,280:0.073:2,1:23.4:1:29.4:1:0:0:35.4:35:0.0717:0:3.8 -3 195400848 . G A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48914;SOR=1.17948;LSEQ=GCCCTGAGCATCGCAGAGTC;RSEQ=TGCAGGCCTGGTAAGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:733:49:41,8:267,415:0.0668:2,2:18.8:1:29.7:1:0:7.95:40.8:48:0.0673:0:2.9 0/1:462:36:34,2:162,263:0.0779:2,2:24.3:1:30.4:1:0:27.45:35.9:72:0.0789:0:3.4 -3 195400889 . T G 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01139;SOR=6.5356;LSEQ=TCTTCAGGACCCAGACTATT;RSEQ=GAGAAGGCGCAGGAGGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:2:0,2:115,395:0.0039:2,0:10:1:15.5:1:1:0:60:0:0:0:2.5 0/1:280:7:2,5:73,200:0.025:2,2:27.6:1:28.7:1:1:1.10:56.6:14:0.0253:0:1.4 -3 195400918 . C CT 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00292;SOR=0.55689;LSEQ=GCAGGAGGTTAGTCTTTTTT;RSEQ=TTTTTTTTTGAGACAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:138:22,116:42,188:0.367:2,2:34.3:1:29.4:1:0.67029:1.17743:53.1:18.714:0.3649:0.0027:0.3 0/1:205:50:9,41:34,115:0.2439:2,2:32.6:1:28.7:1:0.55469:1.34492:49.8:100:0.2525:0.0098:0.3 -3 195401163 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTCTTCTGCCTCAGCTT;RSEQ=CCAAAGTATTGGGATTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:23.5:1:33:0:1:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195401426 . T C 50 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAGTCATTATTTTCTG;RSEQ=TTAGAAAAAGCACTATTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20:1:32:1:1:0:55.7:6:1:0:1.3 1/1:1:1:0,1:0,0:1:0,0:38:0:33:0:1:0:60:2:1:0:2 -3 195404474 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=GCAGTGTGTTAGCTCAGGAG;RSEQ=CTTACACCGTTTCCAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:0:2,0:23.4:1:31.5:1:1:0:43.2:20:1:0:0.9 0/1:16:2:2,0:14,0:0.125:1,0:20:1:32.5:1:1:0:58.5:4:0.125:0:1 -3 195404482 . C A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05915;SOR=0.22171;LSEQ=TTAGCTCAGGAGACTTACAC;RSEQ=GTTTCCAGGCTCCTTGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:5,1:6,0:0.5:0,2:24.5:1:31.8:1:1:0:27:12:0.5:0:1.7 0/1:23:4:4,0:19,0:0.1739:1,0:14.5:1:30.8:1:1:0:27:8:0.1818:0:1.3 -3 195404506 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.08883;LSEQ=TCCAGGCTCCTTGAGCGGCT;RSEQ=TGCTACATTTTTGTGTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:17:14,3:27,0:0.3864:1,2:13.2:1:32.5:1:0.05134:0:29.2:34:0.3864:0:1.3 0/1:58:3:3,0:55,0:0.0517:1,0:13.7:1:32:1:1:0:27:6:0.0517:0:1.3 -3 195404521 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.23448;SOR=0;LSEQ=CGGCTATGCTACATTTTTGT;RSEQ=TGTAGTACTAAATCCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:69,14:0.0235:2,2:30.5:1:27.5:1:0.32353:4.7959:27:4:0.0235:0:2.5 0/0:90:0:0,0:76,14:0:2,0:22.3:1:31.9:1:1:0:41.7:180:1:0:0.1 -3 195404649 . A G 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06971;LSEQ=TGGGGAAGAATCTGTCACGA;RSEQ=TCTTGACAAATTGAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:559:520:286,234:18,21:0.9302:2,2:27.9:1:31.8:1:0.31919:1.42:38.7:73.286:0.9293:0:1.1 0/1:636:306:157,149:167,162:0.4811:2,2:26.8:1:31.3:1:0.93671:1.02:42:152:0.4833:0:1.2 -3 195404701 . G T 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.47249;LSEQ=AGCATAAGAACATCGGAACT;RSEQ=CGACTCAGCATGCAGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:2:1,1:96,214:0.0064:2,2:34:1:29.5:1:0.52583:2.22:27:4:0.0065:0:2 0/1:310:33:9,24:95,182:0.1065:2,2:21.8:1:28.9:1:0.55884:1.39052:36.4:66:0.1071:0:2.1 -3 195404754 . T G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11582;LSEQ=TCGCTCTGGAGTGAGCAGGC;RSEQ=GGCTGCATACCTGGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:99:0,99:8,15:0.8115:2,1:25.1:1:31.4:1:0:0:26.9:198:0.8182:0:1 0/1:103:34:0,34:4,65:0.3301:2,1:23.4:1:30.4:1:0.29941:0:26.8:33:0.3235:0:1.4 -3 195407853 . T C 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.16025;SOR=5.59171;LSEQ=GTGTGTGGGTCTAAGATATG;RSEQ=ATATAATAGAAACATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:6,2:9,3:0.4:2,2:27.9:1:30.6:1:1:1:32.4:16:0.4:0:1.5 1/1:5:4:3,1:1,0:0.8:0,2:19:1:32.5:1:1:0:46.5:8:0.8:0:1.3 -3 195407868 . T G 79 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=ATATGTATATAATAGAAACA;RSEQ=TTATTCAGAAGCTTTAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:6,4:0.375:2,0:18.7:1:30.8:1:0.23352:0:27:12:0.375:0:1.3 0/0:2:0:0,0:2,0:0:0,0:31:1:30:1:1:0:27:4:1:0:1 -3 195407890 . G A 54 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TATTCAGAAGCTTTAGTCAA;RSEQ=ACTTCATTTTTAAGTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:3,1:1,3:0.5:2,2:11.3:1:27.3:1:0.48571:6.41:27:8:0.5:0:2 1/0:2:1:1,0:1,0:0.5:0,0:10:0:32:0:1:0:27:2:1:0:2 -3 195408130 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGTTGTGGGAAAATCAGC;RSEQ=AGCTCTATGGAGACCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:0,10:0.1667:0,0:21.5:1:28.5:1:1:0:33.5:4:0.1667:0:1 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:27:2:1:0:1 -3 195408146 . T G 43 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAAGCTCTATGGAGACC;RSEQ=GAAGCATCTGAAGACGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:13:1:27.7:1:1:0:40:6:0.3:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195408171 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCTGAAGACGTTTGACCG;RSEQ=GGTGAGCAGACAGTGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:29.5:1:32:1:1:0:27:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195408621 . AT A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=CACCCCTGCATTTTCTCTGC;RSEQ=TTTATGTCGTTTCCCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:0.8333:0,0:27.6:1:31.6:1:1:0:31.6:20:0.8333:0.0833:1.5 1/1:7:7:7,0:0,0:1:0,0:34.7:1:30:1:1:0:30.6:14:1:0:2.3 -3 195408646 . T A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.91287;LSEQ=ATGTCGTTTCCCCAAAAGTA;RSEQ=ATCCAAAAAATGCCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:11,0:1,0:0.9167:0,0:22.2:1:29.2:1:1:0:32.4:10:0.9091:0:2 1/1:11:10:10,0:1,0:0.9091:0,0:28.5:1:28.5:1:1:0:30.8:20:0.9091:0:2.2 -3 195408669 . T C 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90414;LSEQ=CCAAAAAATGCCTTTTTCCC;RSEQ=CTGGTAACTTTGATCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:0.8333:0,0:24.1:1:31:1:1:0:30.6:20:0.8333:0:2.1 1/1:11:9:9,0:2,0:0.8182:0,0:25.4:1:27.9:1:1:0:31.2:18:0.8182:0:2.3 -3 195408850 . T G 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0122;SOR=Inf;LSEQ=AGGAAATAAATGCCAGTTTA;RSEQ=TAAATAACGAGTAAGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:4,23:0:2,0:30:1:29.4:1:1:0:30.1:54:1:0:0 0/1:15:4:0,4:2,9:0.2667:2,0:24.5:1:30.8:1:1:0:31.8:8:0.2857:0:1 -3 195409076 . T C 65 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.67325;LSEQ=CTGTGGAGGAAATGCCAGTT;RSEQ=ATTAAATAACAAGTAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:4,3:0.3636:2,2:11.5:1:32.8:1:1:1.29868:36.5:8:0.3636:0:1.5 1/0:2:1:1,0:1,0:0.5:0,0:44:0:30:0:1:0:27:2:0.5:0:1 -3 195409087 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCAGTTTATTAAATAAC;RSEQ=AGTAAGTCACCGTTTCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:0.1538:2,2:16.5:1:29.5:1:1:1.18:36:4:0.1667:0:1.5 0/0:2:0:0,0:2,0:0:0,0:34.5:1:30:1:1:0:38.5:4:1:0:0.5 -3 195409858 . A G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACCATGTTGGCCAGGCT;RSEQ=GTCTCGAACTCCCGACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:31.5:1:1:0:43:4:1:0:2 -3 195409863 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGTTGGCCAGGCTAGTCT;RSEQ=GAACTCCCGACCTCAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:30:1:1:0:43:4:1:0:2 -3 195410304 . T C 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0321;SOR=5.88026;LSEQ=TGTTTTTAATAAAAACAGGC;RSEQ=GAAAGAAAAGATGGAGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:25,0:0.1667:1,0:26.4:1:31.8:1:1:0:42:10:0.1786:0:1.2 1/0:9:5:4,1:2,0:0.5556:0,2:28.6:1:31.6:1:1:0:60:10:0.5556:0:1 -3 195410426 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.42664;SOR=0.69033;LSEQ=ATGGATTACTCTGGACTCAC;RSEQ=GCTGGCTGCACATCGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:26:26,0:75,2:0.2524:1,1:28.3:1:31.8:1:1:0:42.8:52:0.2524:0:1.7 0/1:53:10:10,0:37,6:0.1887:2,0:22.1:1:31.1:1:0.5807:0:46.6:20:0.1923:0:2 -3 195410440 . C T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30451;SOR=0;LSEQ=ACTCACTGCTGGCTGCACAT;RSEQ=GCTGGCCAGCCATGTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:4:4,0:130,2:0.0294:1,0:26.8:1:29.8:1:1:0:27:8:0.0301:0:2 0/0:67:0:0,0:58,9:0:2,0:24.2:1:30.9:1:1:0:54.1:134:1:0:0.7 -3 195410466 . G T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55587;SOR=0;LSEQ=CCAGCCATGTGGCCTCTGTG;RSEQ=GTTCTGAACGTGTTGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:3,0:205,9:0.0137:1,0:35.3:1:30.3:1:1:0:27:6:0.0142:0:2.3 0/0:96:0:0,0:83,13:0:2,0:24.6:1:30.7:1:1:0:53.6:95:1:0:0.9 -3 195410491 . A G 186 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01227;LSEQ=TGAACGTGTTGATGGTGCCA;RSEQ=CCTCCTGGGCTGAAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:61:55,6:231,16:0.1981:2,2:24.2:1:31.5:1:0.40367:1.5724:43:60:0.1987:0:2.1 0/1:135:27:26,1:86,22:0.2:2,1:26.4:1:31.9:1:0.04491:6.59:41.8:54:0.2:0:2.3 -3 195410520 . G A 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.06999;LSEQ=GCTGAAGTGGAAATGGAATG;RSEQ=GTTCTAGGGCATCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:428:422:387,35:6,0:0.986:0,2:24.7:1:30:1:1:0:48.5:27.133:0.9855:0:1.2 1/1:248:206:173,33:37,5:0.8306:2,2:21.9:1:29.4:1:0.64069:1.40971:47.4:67.667:0.8286:0:1.2 -3 195410627 . A G 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30457;LSEQ=GTGTTTCTGGCCTCAGGTGC;RSEQ=GATTGATGAGTATGATCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2115:240:173,67:1015,856:0.1135:2,2:22.6:1:30.6:1:0:2.18:34.2:239:0.1146:0:1.9 0/1:1706:64:18,46:907,733:0.0375:2,2:17.6:1:29.8:1:2e-05:3.16014:38.6:63:0.0375:0:1.7 -3 195410640 . T C 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18165;LSEQ=CAGGTGCAGATTGATGAGTA;RSEQ=GATCACTCCAAGCCCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2220:258:184,74:1022,938:0.1162:2,2:21.4:1:31.4:1:0:2.28:35.7:85:0.1161:0:1.9 0/1:1801:42:7,35:935,821:0.0233:2,2:12.7:1:29.7:1:0:5.6891:33:84:0.0236:0:2.2 -3 195410687 . T A 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37524;SOR=0.85353;LSEQ=ACAGAAGAAGCCCTTTGAGG;RSEQ=GCACTGGAGGAAGCACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2527:101:67,34:1176,1249:0.04:2,2:27.6:1:30.7:1:5e-04:2.09:31:100:0.0399:0:2.2 0/1:1836:63:51,12:835,937:0.0343:2,2:23.7:1:29.1:1:0:4.76:31:62:0.034:0:2.1 -3 195410689 . C T 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30806;SOR=0.83979;LSEQ=AGAAGAAGCCCTTTGAGGTG;RSEQ=ACTGGAGGAAGCACACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2510:108:69,39:1161,1241:0.043:2,2:27.9:1:29.3:1:0.0016:1.89:31.7:107:0.0431:0:2.1 0/1:1814:66:47,19:814,931:0.0364:2,2:24.7:1:29.7:1:8e-05:2.83:31.2:132:0.0368:0:2 -3 195410751 . C T 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.81885;LSEQ=GGGAAGGTCAGTGTGGAGCT;RSEQ=GTTCTCACCACAGCCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1594:390:140,250:433,770:0.2447:2,2:24.2:1:29.8:1:1:1.00417:53.8:77:0.2449:0:1.1 0/1:1068:396:142,254:256,416:0.3708:2,2:23.8:1:29.7:1:0.47195:1.10066:54.2:395:0.3723:0:1.1 -3 195410794 . T C 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39418;SOR=1.14518;LSEQ=CACACGGCCCCGCCCAGGTC;RSEQ=GCGGGCTGGCCTTGCTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:839:130:26,104:110,598:0.1549:2,2:23.6:1:29.6:1:0.19841:1.36:43.1:64:0.1557:0:1.9 0/1:484:84:22,62:78,322:0.1736:2,2:23.6:1:29.2:1:0.18271:1.46:42.6:41:0.1705:0:1.5 -3 195410820 . C T 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0889;SOR=0.68788;LSEQ=CTGGCCTTGCTGATGGTGAA;RSEQ=GCGGAGGAGCAGGCCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:609:96:9,87:41,472:0.1576:2,2:26.8:1:29.9:1:0.68483:1.19:46.2:31:0.1558:0:2.4 0/1:307:35:5,30:37,235:0.114:2,2:24.9:1:29.9:1:1:1.06:44.2:34:0.1118:0:2 -3 195410875 . A T 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGATTTGAGGCACCGCTG;RSEQ=AAAAGGCACTCTGACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:53:1,52:8,160:0.2387:1,1:23:1:28.7:1:0.69034:2.59152:54.8:52:0.2364:0:1.1 0/0:80:0:0,0:8,72:0:2,0:20.3:1:30.1:1:1:0:57.1:79:1:0:0.4 -3 195410876 . A C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.48641;SOR=0.73674;LSEQ=CAGATTTGAGGCACCGCTGA;RSEQ=AAAGGCACTCTGACAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:40:1,39:8,174:0.1802:1,1:20.2:1:32.5:1:1:1.78914:47.4:39:0.1773:0:2.4 0/1:79:11:0,11:8,60:0.1392:2,0:20.4:1:33.5:1:0.59125:0:52.4:22:0.1392:0:1.8 -3 195410916 . A G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGGCTTCGGGCTGGAAAC;RSEQ=GAATCCAGTGCCTGCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:4,81:0.023:1,2:21:0:31.5:1:0.11227:18.22:50:4:0.0233:0:1 0/0:30:0:0,0:4,26:0:2,0:28.1:1:31.2:1:1:0:54.7:29:1:0:0.2 -3 195410967 . T C 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04661;SOR=0;LSEQ=GCCTTAAGGAAGGGTTGCTC;RSEQ=GTGGTGTGGGCCAGATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:12:0,12:1,22:0.3429:1,0:17.3:1:29.5:1:1:0:40.4:24:0.3429:0:2 0/0:9:0:0,0:1,8:0:2,0:22.4:1:30.1:1:1:0:51.9:18:1:0:0.1 -3 195410987 . A C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGTGTGGGCCAGATGGA;RSEQ=GTCACTGGGCAGGAGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:0,3:1,23:0.1111:1,0:32.3:1:31.3:1:1:0:27.7:6:0.1111:0:2.3 0/0:6:0:0,0:1,5:0:2,0:21.8:1:31.8:1:1:0:52.8:12:1:0:0.2 -3 195411037 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.56923;SOR=2.61246;LSEQ=CTGGTGGCAGGGGAGGAGAT;RSEQ=ATGATTGTGGACCTAGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:1,6:0.4167:2,0:23.8:1:31:1:1:0:57.8:10:0.4167:0:1.4 1/0:3:2:1,1:0,1:0.6667:0,2:17.5:1:28:1:1:0:60:4:0.6667:0:1.5 -3 195412489 . T C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.21891;SOR=0.20694;LSEQ=TTTTCGTTGCTCTGTTCCAC;RSEQ=CTACCGATCTGCCGTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:0.8462:0,0:14.6:1:31.7:1:1:0:34.7:22:0.8462:0:1.1 1/0:4:2:2,0:2,0:0.5:0,0:36:1:30.5:1:1:0:40:4:0.5:0:1 -3 195412514 . T TC 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.17606;SOR=3.73572;LSEQ=CGATCTGCCGTCATTTACAG;RSEQ=CCCCTGTTGCGCATGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:3,0:24,5:0.0938:2,0:11.7:1:32.1:1:1:0:27:6:0.0938:0.0313:0.7 0/1:14:4:3,1:9,1:0.2857:2,2:13:1:28.7:1:0.50549:2.73861:27:8:0.3077:0.1429:0.3 -3 195412525 . G A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59375;SOR=2.11233;LSEQ=CATTTACAGTCCCCTGTTGC;RSEQ=CATGTAGATCATTTTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:2,0:41,6:0.0408:2,0:17.5:1:32:0:1:0:27:4:0.0408:0:1 0/1:24:2:2,0:19,3:0.0833:2,0:6:1:30.5:1:1:0:27:4:0.0833:0:1.5 -3 195412596 . A G 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02006;SOR=Inf;LSEQ=TTAAAGTTCACATGCCGTAA;RSEQ=TCTACTTTTATAGTTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:182,20:0:2,0:26.7:1:30.2:1:1:0:36.3:100:1:0:0.4 0/1:124:4:3,1:106,14:0.0323:2,2:34:1:32:1:0.40698:2.49808:36.5:8:0.0325:0:1 -3 195412616 . T A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22952;SOR=1.5404;LSEQ=ATCTACTTTTATAGTTAAAA;RSEQ=TTTTCAAAAGGAACACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:21:16,5:178,47:0.0854:2,2:26.1:1:30.3:1:0.78081:1.1827:28.1:42:0.0864:0:3.1 0/1:151:19:15,4:102,30:0.1258:2,2:28:1:27.8:1:1:1.10:30.6:18:0.12:0:2.6 -3 195412620 . TC T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.07246;LSEQ=ACTTTTATAGTTAAAATTTT;RSEQ=AAAAGGAACACAAGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:3:0,3:167,44:0.0118:2,0:7.3:1:29.4:1:0.01007:0:22.3:6:0.012:0.0079:3.7 0/1:158:2:0,2:95,30:0.0127:2,0:8.5:1:28.9:1:0.06199:0:27:4:0.0129:0.0063:2 -3 195412621 . C T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.34824;SOR=1.30502;LSEQ=CTTTTATAGTTAAAATTTTT;RSEQ=AAAAGGAACACAAGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:40:32,8:167,44:0.1575:2,2:29.4:1:28.8:1:1:1.05:29.5:39:0.1554:0:2.2 0/1:158:31:24,7:95,30:0.1962:2,2:26.7:1:28:1:1:1.08:28.8:62:0.2:0:2 -3 195412634 . A T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57112;SOR=0.73495;LSEQ=AATTTTTCAAAAGGAACACA;RSEQ=GAGATGGCTTTTTGTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:22:13,9:198,67:0.0767:2,2:25.9:1:30:1:0.13149:2.04021:26.4:44:0.0783:0:3.4 0/1:174:10:7,3:121,43:0.0575:2,2:23.6:1:28.3:1:0.72529:1.20459:32.4:20:0.0581:0:3.2 -3 195412710 . A G 128 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00528;SOR=2.87152;LSEQ=TCACTGTGGAATATAGACCC;RSEQ=TAATTGACAAAACTTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:11:0,11:253,250:0.0214:2,0:23.5:1:33.1:1:0.00089:0:24.6:22:0.0219:0:3.5 0/1:355:21:1,20:162,172:0.0592:2,1:30.1:1:29.3:1:5e-05:18.74267:28.7:6:0.0519:0:3.3 -3 195412715 . T C 177 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03938;SOR=0.58489;LSEQ=GTGGAATATAGACCCATAAT;RSEQ=GACAAAACTTTGAACGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:54:10,44:252,216:0.1034:2,2:31.1:1:30.8:1:0:5.11879:27.8:53:0.1052:0:2 0/1:364:23:1,22:170,171:0.0632:2,1:32.3:1:30.3:1:1e-05:21.75925:26.8:46:0.0641:0:2.9 -3 195412748 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83647;SOR=0.85088;LSEQ=AACGAGGCTGACTGTGCCAC;RSEQ=GTCCCCCCAGCCATTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:506:16:5,11:224,266:0.0316:2,2:19.3:1:30.9:1:0.31258:1.85048:30.8:32:0.0323:0:2.8 0/1:333:9:1,8:141,183:0.027:2,2:18.1:1:30.8:1:0.08394:6.13919:27.7:18:0.0274:0:3.9 -3 195412765 . A G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01387;LSEQ=CACTGTCCCCCCAGCCATTC;RSEQ=CTCCTACTGATGAGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:6:2,4:181,257:0.0135:2,2:18:1:32.3:1:1:1.40751:30.8:12:0.0138:0:3.2 0/1:292:4:0,4:118,170:0.0137:2,0:8.5:1:32.5:1:0.15018:0:25.8:8:0.0139:0:4 -3 195412788 . T C 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00569;SOR=0;LSEQ=CCTACTGATGAGACAAGATG;RSEQ=GGTGATGACAGAATCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:13:8,5:133,234:0.0342:2,2:28.8:1:30.5:1:0.08057:2.81:30.9:12:0.0319:0:1.6 0/0:212:0:0,0:74,136:0:2,0:24.2:1:29.3:1:1:0:54.8:29:0.9951:0:0.2 -3 195412839 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTATAATAGCTCATGCATGT;RSEQ=TCAATGTCATAACTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:30,129:0.0124:2,2:21:1:29:1:0.34899:4.25:49:4:0.0127:0:1 0/0:69:0:0,0:13,56:0:2,0:23.2:1:31.2:1:1:0:42.4:33.5:1:0:0.3 -3 195412842 . A C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55553;SOR=0;LSEQ=TAATAGCTCATGCATGTGTC;RSEQ=ATGTCATAACTGTCTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:3:1,2:24,126:0.0196:2,2:15.7:1:31:1:0.41673:2.60:31.3:6:0.0199:0:3.7 0/0:66:0:0,0:12,54:0:2,0:22.8:1:30.2:1:1:0:42.1:65:1:0:0.3 -3 195412859 . T C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.76483;SOR=0.73374;LSEQ=GTCAATGTCATAACTGTCTT;RSEQ=ATACGCTTCTGCACTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:12:1,11:13,113:0.087:2,2:12.9:1:29.4:1:1:1.26349:40.6:11:0.0803:0:2.4 0/1:46:3:0,3:6,37:0.0652:2,0:7.7:1:28:1:1:0:42.3:6:0.0667:0:2 -3 195412863 . C T 92 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06498;SOR=0;LSEQ=ATGTCATAACTGTCTTTATA;RSEQ=GCTTCTGCACTCTGGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:10:4,6:9,106:0.08:2,2:21.3:1:27.9:1:0.01068:7.62:46.4:20:0.0826:0:2.1 0/0:44:0:0,0:6,38:0:2,0:21.6:1:30.2:1:1:0:40.3:88:1:0:0.7 -3 195412864 . G A 88 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2915;SOR=0.29003;LSEQ=TGTCATAACTGTCTTTATAC;RSEQ=CTTCTGCACTCTGGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:9:0,9:13,96:0.0763:2,0:17.2:1:27.8:1:0.5946:0:43.3:18:0.0776:0:2.3 0/1:43:1:1,0:5,37:0.0233:2,0:2:0:30:0:0.13953:0:60:2:0.0233:0:1 -3 195412876 . T C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00161;SOR=0.2631;LSEQ=CTTTATACGCTTCTGCACTC;RSEQ=GGGGAAGAAGGAGTACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:107:78:7,71:4,25:0.729:2,2:21.9:1:29.5:1:0.48454:1.61491:44:77:0.7333:0:1.5 0/1:34:14:2,12:2,18:0.4118:2,2:22.7:1:30.6:1:1:1.48:41.9:28:0.4118:0:1.6 -3 195412879 . GGAA G 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TATACGCTTCTGCACTCTGG;RSEQ=GAAGGAGTACATTGAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:10,89:0:2,0:24.2:1:30.8:1:1:0:44.1:98:1:0:1.5 0/1:31:7:0,7:4,20:0.2258:2,0:30.7:1:31.8:1:0.54972:0:30.4:14:0.2258:0.0323:0 -3 195412920 . C T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53945;SOR=1.45278;LSEQ=GGGGATTGGCACCCAGTGGC;RSEQ=GGGGAGCGTGGCACTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:15:3,12:5,65:0.1765:2,2:33.9:1:26.9:1:0.14411:3.19:49.4:6.5:0.1605:0:1.6 0/1:21:5:1,4:3,13:0.2381:2,2:34.2:1:30.8:1:1:1.08:43.6:10:0.25:0:2.2 -3 195412928 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16714;SOR=0.39099;LSEQ=GCACCCAGTGGCCGGGGAGC;RSEQ=TGGCACTTACCTTTGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:37:3,34:5,38:0.4625:2,2:23.4:1:30.7:1:0.71882:1.48393:53.8:74:0.4744:0:1.8 0/1:16:4:1,3:3,9:0.25:2,2:18.3:1:30.5:1:1:1:52.3:8:0.25:0:1.8 -3 195412948 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCACTTACCTTTGTCCC;RSEQ=TGCTTCATTCTTGTGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:4,57:0.0317:2,2:25.5:1:30.5:1:0.15361:12.86:60:4:0.0333:0:2.5 0/0:12:0:0,0:3,9:0:2,0:26.3:1:29.6:1:1:0:53.9:24:1:0:1.4 -3 195412951 . C G 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTTACCTTTGTCCCTTG;RSEQ=TTCATTCTTGTGACAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:4:0,4:5,48:0.0702:2,0:34:1:31.3:1:1:0:60:8:0.0714:0:2.3 0/0:12:0:0,0:3,9:0:2,0:25:1:30.9:1:1:0:53.5:24:1:0:1.4 -3 195412960 . T C 99 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18928;SOR=0;LSEQ=TTTGTCCCTTGCTTCATTCT;RSEQ=GTGACAAGATAAAACTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:10:0,10:3,34:0.2128:2,0:27.4:1:30.1:1:1:0:46.3:20:0.2128:0:2.2 0/0:9:0:0,0:3,6:0:2,0:27.3:1:28.2:1:1:0:56.2:18:1:0:1.2 -3 195412985 . C G 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11453;SOR=8.83467;LSEQ=CAAGATAAAACTGGGCACAG;RSEQ=TGTTAAATAAAATATAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:0,1:1,19:0.0476:1,0:7:0:33:0:1:0:60:2:0.0476:0:3 0/1:6:2:0,2:0,4:0.3333:0,0:17.5:1:32.5:1:1:0:45.5:4:0.3333:0:3.5 -3 195412987 . G C 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGATAAAACTGGGCACAGCT;RSEQ=TTAAATAAAATATAAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:1,13:0.3333:1,0:23:1:32.9:1:1:0:40.9:14:0.3333:0:2.1 0/1:6:2:0,2:0,4:0.3333:0,0:15.5:1:33:1:1:0:45.5:4:0.4:0:3.5 -3 195412992 . A G 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=AAACTGGGCACAGCTGTTAA;RSEQ=TAAAATATAAATGAACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:1,18:0:1,0:23.5:1:31.7:1:1:0:48.6:38:1:0:1.3 0/1:6:2:0,2:0,4:0.3333:0,0:10.5:1:30.5:1:1:0:45.5:4:0.3333:0:3.5 -3 195413035 . T G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTATTTCCAAATCCAT;RSEQ=TAAAATATTTTCCTGTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:42.5:1:31:0:1:0:42:4:0.4:0:3 0/0:1:0:0,0:0,1:0:0,0:14:0:27:0:1:0:55:2:1:0:0 -3 195413037 . A C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATTTCCAAATCCATTT;RSEQ=AAATATTTTCCTGTTATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:44.5:1:31:0:1:0:42:4:0.4:0:3 0/0:1:0:0,0:0,1:0:0,0:12:0:32:0:1:0:55:2:1:0:0 -3 195413047 . C A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCCATTTAAAATATTTT;RSEQ=CTGTTATGACTTGTCATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:46.5:1:30:0:1:0:42:4:0.6667:0:3 0/0:1:0:0,0:0,1:0:0,0:2:0:32:0:1:0:55:2:1:0:0 -3 195413351 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCTCAAACTGCTGGGCT;RSEQ=AAGTGATCGTTCCTCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:30:1:1:0:48:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195413378 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTTCCTCCTTGGCCTCCC;RSEQ=AAGTGCTGGAATTATAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36.5:1:28.5:1:1:0:48:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195494232 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGATGCTGCCACTGCTGC;RSEQ=ACCACCACCACCACCATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:35.7:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195494501 . T C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGCCACCACCATCACCACCA;RSEQ=CACCACCACCATCGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:3:0:27:0:1:0:44:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:33:0:1:0:60:4:1:0:1.5 -3 195494558 . GCCACCCCCCAAAAAA CCACCCCCAACAC 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACCATCACCACCATCACT;RSEQ=TACCACCATCGGCCACCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:0:32.2:1:1:0:22:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:45:1:30.6:1:1:0:60:4:1:0:1.5 -3 195494583 . CG C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCAAAAAATACCACCAT;RSEQ=GCCACCACCACCATCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:31.5:1:1:0:22:4:1:0:2 1/1:2:2:1,1:0,0:1:0,2:32:1:33:0:1:0:60:4:1:0:3.5 -3 195494610 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=CACCACCATCACCACCACCA;RSEQ=CACCATCGCCACCACCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:1:30:1:1:0:60:4:1:0:3.5 -3 195495721 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GACAAATGGGTGATCTTGTC;RSEQ=TGGGAAGCAGCCAGATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:13,6:0:2,0:24.5:1:31.1:1:1:0:60:38:1:0:0.2 0/1:13:2:1,1:6,5:0.1538:2,2:11.5:1:30.5:1:1:1.18321:60:4:0.1538:0:1.5 -3 195688543 . TCA T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGATCACAGGGGGCGGAGC;RSEQ=CACAGTAATGCTCTGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:31.8:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195689449 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGATCTGTGGCCTGGGGA;RSEQ=TGGGGACCCTGATTTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195689824 . CAA C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTGCACTGATCCTGTCT;RSEQ=AAAAAAAAAAAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19:1:32.6:1:1:0:54:4:1:0.5:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195690110 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00496;SOR=Inf;LSEQ=TACTCCTTCTTCCCCAGAGT;RSEQ=CAGAAGCGTATAAAGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:94,7:0:2,0:20.5:1:32.6:1:1:0:41.1:202:1:0:0.7 0/1:38:4:3,1:28,5:0.1053:2,2:16:1:28:1:0.52358:1.82997:44:8:0.1081:0:1.3 -3 195690117 . C T 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76644;SOR=1.26492;LSEQ=TCTTCCCCAGAGTGCAGAAG;RSEQ=GTATAAAGACAGTTATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:10:10,0:107,7:0.0806:2,0:14.7:1:30.3:1:1:0:26.5:20:0.0806:0:4.9 0/1:50:5:4,1:37,7:0.1:2,2:15.8:1:27.6:1:1:1.31336:24.4:10:0.1:0:5 -3 195690122 . A G 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5668;SOR=1.50788;LSEQ=CCCAGAGTGCAGAAGCGTAT;RSEQ=AAGACAGTTATGACATTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:10:10,0:125,11:0.0685:2,0:18.7:1:33.3:1:1:0:26.5:20:0.0694:0:4.9 0/1:60:6:5,1:45,9:0.1:2,2:14.2:1:28.7:1:1:1:24.5:5:0.0847:0:5 -3 195690139 . T G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1795;SOR=1.82076;LSEQ=TATAAAGACAGTTATGACAT;RSEQ=GACACATGCATGAGCTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:16:16,0:175,32:0.0717:2,1:23.1:1:32.9:1:0.13662:0:26.3:32:0.0731:0:4.7 0/1:89:11:10,1:63,15:0.1236:2,2:15.9:1:30.8:1:0.681:2.36:26.4:10:0.1149:0:4.6 -3 195690148 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09338;SOR=Inf;LSEQ=AGTTATGACATTGACACATG;RSEQ=ATGAGCTATTATACATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:219,48:0:2,0:23.6:1:32.2:1:1:0:41.9:43.5:1:0:0.6 0/1:118:2:1,1:93,22:0.0169:2,2:38.5:1:27:1:0.35588:4.15652:49:4:0.0171:0:1 -3 195690168 . T C 52 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03212;SOR=Inf;LSEQ=CATGAGCTATTATACATAAT;RSEQ=ACAAAAGCTGATTCTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:304,93:0:2,0:26.2:1:29.7:1:1:0:45.1:65.167:1:0:0.5 0/1:186:3:3,0:136,47:0.0161:2,0:20.7:1:33:0:0.57282:0:23.3:6:0.0163:0:4.3 -3 195690192 . C T 106 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=28.79453;LSEQ=AAAGCTGATTCTGTCATCAC;RSEQ=GCATCTTGTCTCATCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:627:1:0,1:438,186:0.0016:2,0:1:0:25:0:0.2992:0:60:2:0.0016:0:1 0/1:272:12:10,2:179,81:0.0441:2,2:28:1:29.8:1:0.35583:2.26:47.9:11:0.0409:0:2.8 -3 195690216 . T C 165 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01002;SOR=1.94007;LSEQ=TCTTGTCTCATCAGTAGGAG;RSEQ=GAATGGCTGGGGGGACAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:39:32,7:456,284:0.0501:2,2:23.3:1:31.4:1:0.0103:2.84:26.4:38:0.0496:0:3.6 0/1:334:31:27,4:177,126:0.0928:2,2:24.8:1:29.8:1:0.00161:4.79:26.5:30:0.0901:0:3.7 -3 195690233 . A G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16694;SOR=1.39784;LSEQ=GAGTGAATGGCTGGGGGGAC;RSEQ=GTGGCACAGTCAGCCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:831:48:32,16:450,333:0.0578:2,2:21.5:1:29.7:1:0.23079:1.48:26.7:47:0.0573:0:3 0/1:380:30:19,11:186,161:0.0789:2,2:19.7:1:27.8:1:0.34363:1.49:26.1:60:0.0804:0:3.2 -3 195690244 . C G 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGGGACAGTGGCACAGT;RSEQ=AGCCTCATTCAAAGTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:846:0:0,0:468,376:0:2,0:26.2:1:31.3:1:1:0:51.6:59.286:0.9976:0:0.4 0/1:384:14:9,5:191,179:0.0365:2,2:26.4:1:28.9:1:0.42111:1.68:59.2:13:0.0343:0:1.9 -3 195690251 . A G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0.4892;LSEQ=ACAGTGGCACAGTCAGCCTC;RSEQ=TTCAAAGTTTTGTCGATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:159:71,88:396,318:0.1821:2,2:25:1:31:1:0.01399:1.54265:31.1:158:0.1835:0:1.4 0/1:387:38:18,20:174,173:0.0982:2,2:20.9:1:28.9:1:0.86459:1.11721:27:76:0.0997:0:2.6 -3 195690271 . T C 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.86102;LSEQ=ATTCAAAGTTTTGTCGATTA;RSEQ=GGGTCTATATTCCACAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:879:10:7,3:395,474:0.0114:2,2:16:1:32:1:0.19984:2.80:28:20:0.0117:0:2.8 0/1:382:28:13,15:154,200:0.0733:2,2:20.6:1:28.6:1:0.84393:1.13:27.4:13:0.0691:0:2.8 -3 195690286 . C G 125 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0012;SOR=3.66825;LSEQ=GATTATGGGTCTATATTCCA;RSEQ=AGTGACCTTGAAAAGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:774:11:7,4:299,462:0.0142:2,2:28.3:1:32.7:1:0.12438:2.70:27.7:22:0.0144:0:2.9 0/1:338:17:7,10:120,201:0.0503:2,2:29.3:1:30.6:1:0.79983:1.17:28.2:16:0.0479:0:3.2 -3 195690308 . G A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41694;SOR=1.66801;LSEQ=GTGACCTTGAAAAGAAGTCA;RSEQ=TGGTAAGTTAAGCACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:9:3,6:179,439:0.0144:2,2:30.3:1:30.6:1:0.72355:1.23:54.4:18:0.0146:0:1.3 0/1:295:7:2,5:97,191:0.0237:2,2:13.9:1:30.3:1:1:1.26869:58.1:14:0.0241:0:1.1 -3 195690347 . T A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18177;SOR=2.03176;LSEQ=AATGTACAAAAAGCCATCTC;RSEQ=TGTGTTCCTTTTGAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:10:7,3:36,282:0.0305:2,2:12.7:1:30:1:4e-05:17.97:30.1:20:0.0308:0:3 0/1:133:8:3,5:21,104:0.0602:2,2:15:1:29.6:1:0.15584:2.94:28.6:16:0.0615:0:3.4 -3 195690360 . G A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13429;SOR=1.84106;LSEQ=CCATCTCTTGTGTTCCTTTT;RSEQ=AAAAATTTTAACTATAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:19:2,17:7,180:0.0922:1,2:18.7:1:30.8:1:0.19639:3.00:25.4:38:0.0941:0:1.4 0/1:76:12:1,11:2,62:0.1579:1,2:16.8:1:30.3:1:0.40734:2.77:27.3:24:0.1579:0:1.9 -3 195690365 . A T 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12499;SOR=4.14292;LSEQ=TCTTGTGTTCCTTTTGAAAA;RSEQ=TTTTAACTATAAAAGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:0,2:3,175:0.0111:1,0:25.5:1:31:0:1:0:26:4:0.0112:0:3.5 0/1:67:3:0,3:2,62:0.0448:1,0:18.3:1:32:0:1:0:25:6:0.0448:0:3.3 -3 195690385 . T C 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0178;SOR=Inf;LSEQ=ATTTTAACTATAAAAGTAGA;RSEQ=TTACGGCATGTAAACTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:1,115:0:1,0:20.6:1:30.2:1:1:0:32.9:28:1:0:0.8 0/1:42:3:0,3:2,37:0.0714:2,0:18:1:33.3:1:1:0:35.3:6:0.0714:0:1.7 -3 195690397 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03106;SOR=0.31058;LSEQ=AAAGTAGATTTACGGCATGT;RSEQ=AACTTTAAGGTATTTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:57:0,57:0,13:0.7808:1,1:25.7:1:31.5:1:1:0:29.8:114:0.8143:0:1.1 1/0:23:12:0,12:1,10:0.5217:2,0:23.3:1:32.3:1:0.47826:0:30.2:24:0.5217:0:1.2 -3 195690462 . A AG 29 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.48846;SOR=2.28102;LSEQ=AAATGATCTACATGCGCAAC;RSEQ=GGGGACTGTAAATGACGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:0,19:0.0952:1,0:15.5:1:29:1:1:0:27:4:0.1053:0.0476:3 0/1:5:1:0,1:0,4:0.2:0,0:30:0:32:0:1:0:21:2:0.2:0:3 -3 195690487 . G C 28 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.9145;LSEQ=ACTGTAAATGACGGCAGATC;RSEQ=GTAGAGTGGAACAGAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:0,12:0.1429:0,0:36:1:28.5:1:1:0:27:4:0.1538:0:3 0/1:4:1:0,1:0,3:0.25:0,0:46:0:32:0:1:0:21:2:0.3333:0:3 -3 195690495 . G C 29 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.76214;LSEQ=TGACGGCAGATCGGTAGAGT;RSEQ=GAACAGAGCAACGAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:0,11:0.1538:0,0:36:1:29:1:1:0:27:4:0.1538:0:3 0/1:4:1:0,1:0,3:0.25:0,0:38:0:32:0:1:0:21:2:0.25:0:3 -3 195691976 . T C 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04615;SOR=Inf;LSEQ=TGTCCCCACTACACAGATGC;RSEQ=TTCTCGCTAGGTCCATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:19,1:0:1,0:24.8:1:31.4:1:1:0:58.1:40:1:0:0.2 0/1:6:2:1,1:2,2:0.3333:2,2:46.5:1:31.5:1:1:1:60:4:0.3333:0:1 -3 195691993 . AATC A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.00779;SOR=Inf;LSEQ=TGCTTTCTCGCTAGGTCCAT;RSEQ=ATCATCTCTTCCCCTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:22,2:0:2,0:23.8:1:29:1:1:0:53.6:23:1:0:0.3 0/1:7:3:2,1:2,2:0.4286:2,2:25:1:29.7:1:1:1.81:60:6:0.4286:0.1429:1.3 -3 195692069 . A G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56973;SOR=Inf;LSEQ=GTCCATCTGGCCCACACCAC;RSEQ=GAGCAACCCTTCCTTAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:33:27,6:6,0:0.8462:0,2:21.1:1:29.8:1:0.56354:0:46.3:66:0.8462:0:1.2 1/1:7:7:7,0:0,0:1:0,0:17.6:1:30.3:1:1:0:50.1:14:1:0:1.1 -3 195692156 . CT C 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.23732;SOR=4.36579;LSEQ=CCCAACTGCTGTCAGAGTGC;RSEQ=TTTTCAGCGGTGCCTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:1:1,0:137,5:0.0069:1,0:28:0:28:0:1:0:49:2:0.007:0:0 0/1:67:2:1,1:63,2:0.0299:1,2:31.5:1:31.5:1:0.0882:25.92315:60:4:0.0313:0:0.5 -3 195692167 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09532;SOR=Inf;LSEQ=TCAGAGTGCCTTTTTCAGCG;RSEQ=TGCCTCAAATCTGTCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:170,8:0:1,0:23.4:1:31.3:1:1:0:58.6:43.5:1:0:0.2 0/1:80:2:1,1:75,3:0.025:1,2:9:1:30.5:1:0.0981:21.79466:60:4:0.0253:0:1 -3 195692213 . T C 119 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60964;SOR=0.63246;LSEQ=TTAAATCTGGCCTGCTCCTC;RSEQ=GCGTTCACCATCAGCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:15:14,1:401,28:0.0338:2,1:15.8:1:30.5:1:1:1.02291:28.2:14:0.0321:0:2.8 0/1:185:4:4,0:159,22:0.0216:2,0:18.3:1:31.5:1:1:0:32.3:8:0.0219:0:3.3 -3 195692216 . G A 121 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45876;SOR=0.59131;LSEQ=AATCTGGCCTGCTCCTCTGC;RSEQ=TTCACCATCAGCAAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:16:16,0:430,37:0.0331:2,1:14.4:1:30.3:1:0.62426:0:27.8:15:0.0316:0:3.3 0/1:202:4:4,0:174,24:0.0198:2,0:21.3:1:31.5:1:1:0:32.3:8:0.02:0:3.3 -3 195692242 . A G 144 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27603;SOR=0.62406;LSEQ=CATCAGCAAGGCCAGCCCGC;RSEQ=GACCTGGGCGGGGCCGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:28:28,0:576,102:0.0396:2,1:28.3:1:30:1:0.02383:0:29.5:27:0.0388:0:2.6 0/1:319:8:8,0:245,66:0.0251:2,0:32.3:1:30.6:1:0.21335:0:30.1:16:0.0253:0:2.6 -3 195692311 . T C 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82895;SOR=0.96287;LSEQ=CACACTGACCTTCCCAGTGC;RSEQ=GACGTCCACATAGGACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1867:138:118,20:1033,694:0.0739:2,2:19.8:1:30.6:1:0:3.96:31.1:68:0.0736:0:2 0/1:1149:82:68,14:599,468:0.0714:2,2:20:1:29.8:1:0:3.79:31.5:40:0.0702:0:2 -3 195692347 . G A 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01971;SOR=1.24286;LSEQ=CAGGGTGTGCTTCCTCCAGT;RSEQ=CTCCTCAAAGGGCTTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2798:330:218,112:1381,1083:0.1179:2,2:26.3:1:28.6:1:0.00058:1.53:37:109:0.1186:0:1.8 0/1:1649:235:157,78:753,657:0.1425:2,2:23.8:1:28.3:1:0.00013:1.76:38.8:234:0.1442:0:1.9 -3 195692349 . T A 229 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00938;LSEQ=GGGTGTGCTTCCTCCAGTGC;RSEQ=CCTCAAAGGGCTTCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2864:171:154,17:1471,1222:0.0597:2,2:23:1:30.9:1:0:7.52:35.1:56:0.06:0:1.7 0/0:1677:1:1,0:915,758:6e-04:2,0:1:0:27:0:1:0:51:2:6e-04:0:1 -3 195692419 . C G 308 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.55907;LSEQ=CTCATCAATCCGCACCTGAG;RSEQ=CCAGAAACACCATCACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3128:897:419,478:923,1295:0.2868:2,2:29.1:1:31.4:1:0.00944:1.23:41.4:68:0.2881:0:1.4 0/1:1613:296:121,175:597,715:0.1835:2,2:28.8:1:31.4:1:0.15482:1.20745:43.2:58.2:0.1829:0:1.6 -3 195692482 . G A 188 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.91022;SOR=1.02386;LSEQ=ACAGAAAAAACACAGCAAAC;RSEQ=TTAAAATGATCTAAGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1197:69:5,64:244,884:0.0576:2,2:13.4:1:30.8:1:0.00324:3.53056:33.4:68:0.0576:0:2.1 0/1:509:30:0,30:128,351:0.0589:2,1:13.1:1:30.4:1:0.00027:0:36.1:60:0.0596:0:2 -3 195692516 . C T 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.10109;LSEQ=AGAGACAGATGCCCTAGAAC;RSEQ=CATTCCATTTCCACTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:116:9,107:29,367:0.2266:2,2:22.9:1:29.8:1:0.84206:1.06:41.4:28:0.2222:0:1.6 0/1:209:6:0,6:16,187:0.0287:2,0:14.2:1:29.2:1:1:0:30.2:12:0.0294:0:2.2 -3 195692545 . T C 105 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30506;SOR=0.25013;LSEQ=TTCCACTTCAGCCCAGGAGG;RSEQ=TGGCACCATCAACACGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:10:0,10:27,275:0.0321:2,0:19.5:1:31.9:1:1:0:26.2:20:0.0325:0:3.3 0/0:122:1:0,1:7,114:0.0082:2,0:50:0:31:0:1:0:30:2:0.0084:0:3 -3 195692570 . G A 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCATCAACACGTTCAGAAC;RSEQ=CACAGAGGCCACATGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:51:5,46:18,151:0.2257:2,2:24.9:1:30.2:1:1:1.09624:44:102:0.2318:0:1.6 0/0:72:0:0,0:4,66:0:2,0:23.7:1:32.4:1:1:0:55.5:69:0.9718:0:0.1 -3 195692586 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GAACGCACAGAGGCCACATG;RSEQ=CTGGCCAGCAATGTGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:14,164:0.0111:2,2:18.5:1:29:1:0.16015:11.35:55:4:0.0114:0:1 0/0:52:0:0,0:3,49:0:2,0:20.8:1:32.8:1:1:0:55:104:1:0:0.1 -3 195692596 . A G 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCACATGGCTGGCCAGC;RSEQ=ATGTGCAGCCAGCAGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:0,3:12,150:0.0182:2,0:22.7:1:32.7:1:1:0:29.3:6:0.0184:0:3.3 0/0:35:0:0,0:1,34:0:1,0:23.5:1:29.7:1:1:0:57.9:16.5:1:0:0.1 -3 195692610 . A G 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCCAGCAATGTGCAGCCAGC;RSEQ=GTGAGTCCAGAGTAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:3:0,3:8,123:0.0224:2,0:18:1:32.7:1:1:0:29.3:6:0.0226:0:3.3 0/0:26:0:0,0:1,25:0:1,0:23.8:1:31.7:1:1:0:57.8:52:1:0:0 -3 195693977 . A G 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAACTGGCATTTCCTCC;RSEQ=CAGGGCAGGCTTGAAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:3,0:30,5:0.0789:2,0:19:1:30:1:1:0:39.7:6:0.0789:0:1.3 0/0:10:0:0,0:7,3:0:2,0:22.1:1:30.4:1:1:0:49.8:20:1:0:0.2 -3 195693994 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACAGGGCAGGCTTGAAA;RSEQ=GGTGGCTTACTCGTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:2,0:39,5:0.0435:2,0:44.5:1:30.5:1:1:0:32.5:4:0.0476:0:2 0/0:9:0:0,0:6,3:0:2,0:28.3:1:28.8:1:1:0:49.4:8:1:0:0.2 -3 195694007 . G A 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02656;SOR=Inf;LSEQ=CTTGAAATGGTGGCTTACTC;RSEQ=TTATTTAATAAACTGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:52,7:0:2,0:24.4:1:30.2:1:1:0:39.3:118:1:0:0.2 0/1:12:2:0,2:9,1:0.1667:2,0:31.5:1:32:0:0.04545:0:52.5:4:0.1667:0:1 -3 195694127 . C T 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07297;SOR=0;LSEQ=GGCTGCACTTCTAACCTTGG;RSEQ=CTTCTAACAGCAAAGCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:3,10:14,5:0.4063:2,2:16.5:1:26.8:1:0.01045:8.57696:29.6:12:0.3871:0:1 0/0:7:0:0,0:2,5:0:2,0:20.7:1:30.9:1:1:0:29.7:14:1:0:0.1 -3 195694147 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCTAACAGCAAAGCACA;RSEQ=TGGCTTGGAGATGCCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:0,22:0.0833:1,0:19:1:29:1:1:0:27:4:0.0833:0:2 0/0:7:0:0,0:0,7:0:0,0:27.9:1:29.7:1:1:0:32.1:14:1:0:0.3 -3 195694159 . T C 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCACATTGGCTTGGAGA;RSEQ=GCCACTGCTGGCATCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:0,3:0,32:0.0857:1,0:23.3:1:27.3:1:1:0:27:6:0.0882:0:1.7 0/0:7:0:0,0:0,7:0:0,0:31:1:30.1:1:1:0:32.1:14:1:0:0.3 -3 195694184 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11974;SOR=5.86449;LSEQ=CTGCTGGCATCAGTGGATGC;RSEQ=GACCCAAAGCAAGGAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:0,2:0,55:0.0351:1,0:17:1:28.5:1:1:0:24:4:0.037:0:2 0/1:11:2:0,2:0,9:0.1818:0,0:23.5:1:31:1:1:0:26:4:0.1818:0:1 -3 195694253 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63907;SOR=1.52276;LSEQ=CCAGGGATCAAAGTTACCAG;RSEQ=GGGAAAAAGGCATTTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:15:0,15:0,45:0.2459:1,1:30.4:1:31.1:1:1:0:28.1:30:0.2632:0:2.3 0/1:6:2:0,2:0,4:0.3333:0,0:21.5:1:31.5:1:1:0:27:4:0.3333:0:1.5 -3 195694256 . G GA 80 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATCAAAGTTACCAGAGG;RSEQ=AAAAAGGCATTTTTTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:6:0,6:0,55:0.0984:1,0:31:1:31.3:1:1:0:28.2:12:0.0984:0.0164:2.7 0/0:6:0:0,0:0,6:0:0,0:21.2:1:32.3:1:1:0:29.2:12:1:0:0.7 -3 195694276 . A T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.80034;LSEQ=GAAAAAGGCATTTTTTGGAT;RSEQ=TACTTTTGGGGAAACGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:32:0,32:0,17:0.6531:1,1:24.2:1:30.6:1:1:0:31.2:64:0.6531:0:1.6 1/0:5:3:0,3:0,2:0.6:0,0:17.3:1:29.3:1:1:0:25:6:0.6:0:1.3 -3 195694296 . TA T 75 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.35556;SOR=4.39698;LSEQ=ATACTTTTGGGGAAACGACA;RSEQ=AAATGCAGAGAAAATGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:0,6:0,28:0.1765:1,0:17.5:1:29.1:1:1:0:29.2:12:0.1818:0.0882:2.2 1/0:2:1:0,1:0,1:0.5:0,0:41:0:28:0:1:0:21:2:0.5:0:1 -3 195694321 . G A 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGAGAAAATGCAGGGGT;RSEQ=GGGCTGAGTCCCACCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:0,4:0,16:0.2:1,0:40:1:32.3:1:1:0:29.3:8:0.2:0:2 0/0:2:0:0,0:0,2:0:0,0:43.5:1:31.5:1:1:0:24:4:1:0:1 -3 195694325 . C A 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAAAATGCAGGGGTGGGG;RSEQ=TGAGTCCCACCAGGCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:0,4:0,14:0.2222:1,0:36:1:32.3:1:1:0:29.3:8:0.2222:0:2 0/0:2:0:0,0:0,2:0:0,0:40:1:33.5:1:1:0:24:4:1:0:1 -3 195695655 . T A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATTTCATCTGATTTTCC;RSEQ=TAGACTCATACATAATCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:32:1:1:0:54.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195697427 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGCTGGGGACGGAGCTTCTC;RSEQ=GGTGGTCCTGCGGCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:30:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:0:2,0:47:0:30:1:1:0:48:4:1:0:1 -3 195697430 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGGGACGGAGCTTCTCCGG;RSEQ=GGTCCTGCGGCTCCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:9.5:1:29:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:45.5:1:31:1:1:0:48:4:1:0:1 -3 195697824 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAAAAAGAATGCAATCA;RSEQ=GTCTTCCGCAGCCAGACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:10,1:0.1538:2,0:22:1:33:0:1:0:56:4:0.1538:0:1 0/0:1:0:0,0:1,0:0:0,0:28:0:32:0:1:0:60:2:1:0:0 -3 195697848 . A C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCGCAGCCAGACGGATGG;RSEQ=ACGGGAGGTCACTATCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:11,0:0.1538:0,0:30.5:1:33.5:1:1:0:47:4:0.1538:0:1.5 0/0:2:0:0,0:1,1:0:2,0:28.5:1:27.5:1:1:0:60:4:1:0:0 -3 195697927 . A G 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=CTTGGAAGTGGGAGCTGAAC;RSEQ=GTGAGTACACATGGACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:12,1:1,0:0.9286:0,1:24.9:1:28.2:1:1:0:49.2:26:1:0:1.2 0/0:1:0:0,0:0,1:0:0,0:14:0:33:0:1:0:60:2:1:0:0 -3 195698026 . C T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.01764;LSEQ=TACCTGCTGAGTACAACACA;RSEQ=ACGACTTGGGTGACGGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:7:6,1:52,5:0.1094:2,2:18:1:29:1:0.51599:1.71574:47.4:14:0.1111:0:1.1 0/1:18:2:2,0:13,3:0.1111:2,0:18:1:31.5:1:1:0:38:4:0.1111:0:1 -3 195698159 . A C 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0938;SOR=0.45012;LSEQ=GCAGGGCCAGGTATGCAGCC;RSEQ=GCCTGCTCACTCCAGAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:33:21,12:339,22:0.0838:2,2:23:1:29.8:1:0:8.71173:29.4:32:0.0829:0:1.1 0/1:152:6:5,1:142,4:0.0395:1,2:17:1:30.7:1:0.18464:6.89267:29.2:12:0.04:0:1 -3 195698267 . G A 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=51.31612;LSEQ=ATCTCAATTTGTCAACATTC;RSEQ=TGACAGATTCTTCCCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1767:1:1,0:954,812:6e-04:2,0:1:0:25:0:1:0:50:2:6e-04:0:2 0/1:849:24:10,14:436,389:0.0283:2,2:28:1:30:1:0.30566:1.56831:42.4:48:0.0285:0:1.3 -3 195698371 . A C 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.70923;LSEQ=TTGAAAACCGTTTTAAAAAA;RSEQ=CAAATGGATTTAGTACGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:74:27,47:169,556:0.0925:2,2:26.2:1:30.9:1:0.01564:1.89:38.7:148:0.0931:0:1.1 0/1:411:89:32,57:93,229:0.2165:2,2:26.3:1:30.9:1:0.24115:1.38:38.2:178:0.2176:0:1 -3 195698388 . G T 123 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36662;SOR=0.68051;LSEQ=AAAACAAATGGATTTAGTAC;RSEQ=ACACACAAAAATGTAGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:26:1,25:118,503:0.0402:2,1:28.1:1:26.2:1:0.06615:5.85564:27.2:25:0.0396:0:1.3 0/1:325:9:0,9:67,249:0.0277:2,0:31.2:1:26:1:0.21264:0:25.7:18:0.0282:0:1.7 -3 195698407 . T C 113 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60621;SOR=0.62923;LSEQ=CGACACACAAAAATGTAGCA;RSEQ=AGCCGCTCAAGGAGCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:14:1,13:35,425:0.0295:2,1:25.3:1:29.9:1:1:1.07044:34.2:28:0.0299:0:1.6 0/1:213:4:0,4:17,192:0.0188:2,0:40.8:1:30.8:1:1:0:25.5:8:0.019:0:2 -3 195698582 . G C 76 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=2.09766;LSEQ=ATCTTAGAGTGAATAAACTA;RSEQ=AAATCATCTCTAAAATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,11:0.3125:0,0:14.8:1:33:1:1:0:35.6:10:0.3571:0:1 1/0:2:1:0,1:0,1:0.5:0,0:19:0:32:0:1:0:21:2:0.5:0:2 -3 195700978 . A C 84 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CTGTTCTATAAAAACAGCAG;RSEQ=AATGATGCTAAACAGTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:6,0:4,0:0.6:0,0:21.8:1:32.7:1:1:0:47.5:12:0.6:0:1 0/0:2:0:0,0:2,0:0:0,0:32:1:31:0:1:0:45:4:1:0:0 -3 195701115 . A G 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00398;SOR=0.17785;LSEQ=AGCACACGAGGCTGCATAAC;RSEQ=ACCGTGAGGATCTCTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:32:31,1:43,0:0.4267:1,1:24.2:1:30.3:1:0.42667:0:56:64:0.4324:0:1 0/1:26:3:3,0:18,4:0.1154:2,0:23:1:28.7:1:1:0:60:6:0.12:0:1 -3 195701198 . C CA 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00028;SOR=0.25862;LSEQ=AGGGCACTAAGACCCTGTCT;RSEQ=AAAAAAAAAGAAAAAAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:60:59,1:336,37:0.1382:2,1:9.3:1:30.8:1:0.045:6.48:32.2:59:0.1382:0.0991:1 0/1:176:7:7,0:150,15:0.0398:2,0:20.1:1:30.4:1:1:0:44.4:14:0.0407:0:1.3 -3 195701237 . A C 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06004;SOR=5.00867;LSEQ=CTAACCTCCTGCGCCTTCTC;RSEQ=AATAGTCTGGGTCCTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:970:2:1,1:841,127:0.0021:2,2:26:1:14:0:0.24662:6.60005:42.5:0:0:0:2 0/1:390:4:4,0:325,61:0.0103:2,0:34.3:1:31.3:1:1:0:33.5:8:0.0104:0:3.3 -3 195701278 . C T 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.15171;LSEQ=AAACACTTACCAGGCCTGCA;RSEQ=GACTCTGCGATGCTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1742:132:117,15:1080,528:0.0758:2,2:23.3:1:30.8:1:0:3.81:33.5:65:0.0757:0:3.5 0/1:780:117:102,15:410,253:0.15:2,2:22.8:1:30:1:0:4.19:33.5:234:0.1521:0:3.7 -3 195701285 . G T 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.05582;LSEQ=TACCAGGCCTGCACGACTCT;RSEQ=CGATGCTCAGGGCACATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1898:157:138,19:1140,599:0.0827:2,2:20.7:1:29.9:1:0:3.81:35.2:51.333:0.0824:0:3.5 0/1:863:135:117,18:428,299:0.1564:2,2:21.3:1:29.7:1:0:4.53:34.1:134:0.158:0:3.7 -3 195701301 . A T 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0;SOR=3.49496;LSEQ=CTCTGCGATGCTCAGGGCAC;RSEQ=TGCCTGACCAGACAACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2177:26:19,7:1354,797:0.0119:2,2:20.2:1:30.6:1:0.31564:1.60:37.4:52:0.0121:0:4.1 0/1:1085:44:33,11:608,433:0.0406:2,2:19.4:1:30.6:1:0.02885:2.14:38.7:43:0.0403:0:3.8 -3 195701304 . C T 270 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.63543;LSEQ=TGCGATGCTCAGGGCACATG;RSEQ=CTGACCAGACAACCAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2150:534:374,160:951,664:0.2484:2,2:25.7:1:29.8:1:0:1.63:37.6:132.5:0.25:0:3 0/1:1095:190:141,49:499,406:0.1735:2,2:21.7:1:29.4:1:0:2.34:38.4:189:0.1752:0:3.4 -3 195701306 . T C 253 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06717;LSEQ=CGATGCTCAGGGCACATGCC;RSEQ=GACCAGACAACCAGGTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2178:328:215,113:1120,730:0.1506:2,2:29.4:1:30.3:1:0.09669:1.24:36.9:64.6:0.1497:0:2.9 0/1:1105:13:12,1:629,463:0.0118:2,1:24.5:1:30.2:1:0.01048:8.82:37.9:12:0.011:0:4 -3 195701310 . C CAA 279 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.5207;LSEQ=GCTCAGGGCACATGCCTGAC;RSEQ=AGACAACCAGGTCCAATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2353:646:420,226:994,712:0.2745:2,2:24.4:1:29.9:1:0.00295:1.33:41:214.333:0.2757:0.065:2.7 0/1:1124:185:134,51:512,427:0.1646:2,2:25.7:1:29.9:1:1e-05:2.19:39.2:60.667:0.164:0.0125:3.4 -3 195701331 . G A 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.75409;LSEQ=AGACAACCAGGTCCAATAGC;RSEQ=AGTTTGCCCCGAGGCGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2710:808:475,333:1018,881:0.2982:2,2:24.8:1:29.9:1:0.0143:1.23:45.3:56.714:0.2983:0:2.2 0/1:1455:353:228,125:559,542:0.2426:2,2:24.1:1:29.6:1:1e-05:1.77:46.1:57.833:0.2427:0:2.3 -3 195701338 . C T 156 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=12.3905;LSEQ=CAGGTCCAATAGCGAGTTTG;RSEQ=CCCGAGGCGGTTGACACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2801:7:3,4:1492,1301:0.0025:2,2:19.6:1:28:1:0.71168:1.52883:43.4:6:0.0022:0:2.3 0/1:1494:45:22,23:769,677:0.0301:2,2:25.1:1:28.5:1:0.64974:1.18739:46:44:0.0298:0:2.9 -3 195701388 . GC AA 299 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31918;LSEQ=CACAGGCGGCCTCCCCACAG;RSEQ=GTACAGGCCGGGCACAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3345:925:457,468:1169,1226:0.2765:2,2:26.7:1:30.4:1:0.78637:1.02:46.1:1850:0.2812:0.0117:1.1 0/1:1950:212:104,108:873,853:0.1087:2,2:27.5:1:30.1:1:0.71606:1.06281:47.6:424:0.11:0.0031:1.1 -3 195701472 . A G 279 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.66443;SOR=1.04667;LSEQ=ATTTCAGGTGAAATGTCAAG;RSEQ=TGCCCATTCCTCCACAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1446:488:108,380:238,717:0.3375:2,2:20.9:1:31.3:1:0.26791:1.1678:32.7:80.333:0.3394:0:1.3 0/1:716:249:53,196:134,333:0.3478:2,2:21.3:1:30.4:1:0.03237:1.48732:31.8:30.125:0.3428:0:1.3 -3 195701483 . TCCA T 268 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49389;SOR=0.92058;LSEQ=AATGTCAAGATGCCCATTCC;RSEQ=CAAGCCCACCTCCCTCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1079:371:52,319:112,596:0.3438:2,2:22:1:31.5:1:0.47548:1.15263:32:122.667:0.3433:0.0982:1.4 0/1:504:164:19,145:68,271:0.3254:2,2:25.9:1:31.4:1:0.02311:1.91264:30.4:81:0.3266:0.0536:1.3 -3 195701515 . G GT 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.35263;LSEQ=CCTCCCTCAACAGGGTGTCT;RSEQ=TGCTGCAGGTCAGAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:618:114:4,110:8,496:0.1845:1,1:22.6:1:30.7:1:0.24838:2.25:28.6:113:0.1849:0.0421:0.1 0/1:271:20:1,19:3,248:0.0738:1,1:20.3:1:31:1:0.26541:4.31:28.4:40:0.0741:0.0111:0.2 -3 195701548 . T C 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98542;LSEQ=GAGAAAGAGAGGGAAGTAGG;RSEQ=CGGGCATGCAGTGGCTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:127:0,127:1,220:0.3649:1,1:23.1:1:31:1:1:0:28.3:30.75:0.3618:0:2.2 0/1:130:47:0,47:0,83:0.3615:1,1:18.6:1:31.2:1:1:0:29:94:0.3643:0:2.3 -3 195701570 . T C 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3178;SOR=0.73101;LSEQ=GGGCATGCAGTGGCTCACGC;RSEQ=TGTAATCCCAGCACTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:66:0,66:0,147:0.3099:1,1:26.8:1:32.8:1:1:0:28.7:65:0.311:0:2.3 0/1:81:20:0,20:0,61:0.2469:1,1:23.8:1:31.4:1:1:0:29.2:19:0.2405:0:2.5 -3 195701628 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14742;SOR=4.88512;LSEQ=TCACCTGAGTTCAGGGGTTC;RSEQ=AGAACTGTCTGGCTAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:0,80:0.0244:1,0:1.5:1:31:0:1:0:27:4:0.025:0:3 0/1:18:2:0,2:0,16:0.1111:1,0:5.5:1:29:1:1:0:39:4:0.1111:0:3.5 -3 195701699 . G A 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAGCCAGGCATGATGGC;RSEQ=GGTGCCTGTAATCCCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:0,2:0,29:0.0645:1,0:38.5:1:31:1:1:0:27:4:0.0645:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195701777 . G C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCGGAGGTTGCAGTGAG;RSEQ=CGAGATCGCGCCATTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:20:1:32.3:1:1:0:35.7:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195702270 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACAAGATCATTAGAAATA;RSEQ=CAATTATAAAGATCCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:36.3:1:30.5:1:1:0:46.8:8:0.3636:0:1 0/0:1:0:0,0:1,0:0:0,0:7:0:33:0:1:0:27:2:1:0:0 -3 195702421 . C G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40471;SOR=0.53569;LSEQ=AAGCCTCCTTCCATCCTCCA;RSEQ=TGATAGAAATTTCAAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:18:18,0:77,3:0.1837:1,1:23.8:1:31.8:1:1:0:56.4:17:0.1771:0:1 0/1:28:3:3,0:24,1:0.1071:1,0:39:1:33.7:1:1:0:55.3:6:0.1071:0:1 -3 195702506 . G C 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00272;SOR=9.1861;LSEQ=CTTCCTCTAAGATCTAAAGA;RSEQ=ACAACTGCAAGATGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:2:2,0:431,38:0.0042:2,0:16.5:1:33.5:1:1:0:27:4:0.0043:0:2 0/1:185:7:7,0:154,24:0.0378:2,0:25.4:1:31.7:1:0.59727:0:27:14:0.0383:0:2.1 -3 195702515 . A G 106 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02172;SOR=3.03356;LSEQ=AGATCTAAAGAGACAACTGC;RSEQ=AGATGGGCCCCGTTGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:9:9,0:482,55:0.0165:2,0:7.3:1:30.6:1:0.60879:0:27.7:18:0.0167:0:1.3 0/1:227:11:10,1:177,39:0.0485:2,2:22.9:1:30.9:1:0.69397:2.20:24.8:22:0.0487:0:1.8 -3 195702621 . G A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63966;SOR=0.82206;LSEQ=CCGTCCATGTTATAATGCAC;RSEQ=GTGGGGAGGACAGGGATCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:45:37,8:91,404:0.0833:2,2:26:1:29.7:1:0:20.37:29.9:21.5:0.0813:0:1.7 0/1:187:13:6,7:22,152:0.0695:2,2:21.1:1:29.8:1:0.00544:5.83:28:12:0.0659:0:1.8 -3 195702639 . C T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24784;SOR=1.49753;LSEQ=ACGGTGGGGAGGACAGGGAT;RSEQ=GGCTCCTTCGTGACGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:27:20,7:115,384:0.0513:2,2:25.1:1:30.8:1:0:9.49:27.7:54:0.0521:0:2.1 0/1:160:12:5,7:19,129:0.075:2,2:24.9:1:30.2:1:0.01921:4.78:27.6:24:0.0755:0:1.8 -3 195702692 . C T 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0166;SOR=Inf;LSEQ=CATGGCTGTCTCTGAAATGC;RSEQ=GGGCAAGGGCATGGCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:232,170:0:2,0:24.8:1:30.4:1:1:0:33.8:43.667:1:0:0.3 0/1:139:3:2,1:81,55:0.0216:2,2:45.3:1:27:1:1:1.36:27:2:0.0145:0:1.7 -3 195702704 . T C 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00512;SOR=0.33782;LSEQ=TGAAATGCCGGGCAAGGGCA;RSEQ=GGCCAGCTGCTCTGGAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:53:28,25:252,126:0.123:2,2:23.1:1:30.9:1:0.06416:1.78324:35.1:106:0.1253:0:1.1 0/1:155:7:5,2:100,48:0.0452:2,2:23.7:1:31.4:1:1:1.20:32.6:14:0.0458:0:1 -3 195702731 . G C 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCTCTGGAGGTAGGTGGT;RSEQ=CAGCTGCAGGTAGACGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:382,104:0:2,0:24.4:1:32:1:1:0:32.9:33.714:1:0:0.2 0/1:195:12:11,1:155,28:0.0615:2,2:22.3:1:31.8:1:1:1.98:29.2:24:0.0625:0:1.3 -3 195702738 . C T 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGTAGGTGGTGCAGCTG;RSEQ=AGGTAGACGTGATCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:508:0:0,0:411,97:0:2,0:24.9:1:32.3:1:1:0:32.8:71.571:1:0:0.2 0/1:198:16:13,3:162,20:0.0808:2,2:34.1:1:29.6:1:0.40647:1.86216:31.9:32:0.0816:0:1.1 -3 195702808 . T C 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00112;SOR=0.57125;LSEQ=CCATCACATAAGGCAGAGAA;RSEQ=GGCAACGGCAGCAGACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:827:177:87,90:271,379:0.214:2,2:25.8:1:29.9:1:0.08693:1.35:32.8:176:0.216:0:1.4 0/1:379:51:27,24:151,177:0.1346:2,2:25.1:1:28.5:1:0.36981:1.32:32.6:50:0.133:0:1.1 -3 195702877 . A G 211 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCAACATGTTTTGATACTG;RSEQ=GGAAAATTTCCCCTCATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:119:6,113:21,404:0.2188:1,2:26.2:1:30.7:1:1:1.02:43.2:22.8:0.2163:0:1.6 0/0:234:0:0,0:17,217:0:2,0:23.7:1:31.3:1:1:0:41.4:233:1:0:0.2 -3 195702938 . G A 132 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00295;SOR=3.40212;LSEQ=CTTTTCTAAGCATCTACTGT;RSEQ=TGCCAGGGACAATCCTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:18:0,18:4,144:0.1084:1,1:25.5:1:31.7:1:1:0:31.7:36:0.1098:0:1.1 0/1:51:15:0,15:6,30:0.2941:2,1:18.9:1:29.9:1:0.16218:0:34.7:30:0.2941:0:1.3 -3 195702973 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00974;SOR=Inf;LSEQ=CTAGGTGCTGGGACACAGCT;RSEQ=AGAACCAGAACAAATACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:0,92:0:1,0:22:1:31.2:1:1:0:53.6:45:1:0:0.2 0/1:26:3:0,3:5,18:0.1154:2,0:24:1:31.7:1:1:0:52:6:0.1154:0:1.3 -3 195703038 . C T 72 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9361;LSEQ=TCAGGGATCACAGCCTGCAG;RSEQ=GGCTGTCCTTGGTAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:12.8:1:31.4:1:1:0:41.4:10:0.2632:0:1 0/1:4:1:0,1:0,3:0.25:0,0:48:0:32:0:1:0:44:2:0.25:0:1 -3 195703260 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTGTACAGCAACTCCAG;RSEQ=ATTACTCATAGTACCTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:43:1:30.5:1:1:0:54:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195703817 . T C 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AAATATCGCAGACTAACAGA;RSEQ=GCCTGCCGGCAGCTGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:12,0:0.2:0,0:14.3:1:33:1:1:0:25:6:0.2:0:1 1/1:1:1:1,0:0,0:1:0,0:1:0:31:0:1:0:21:2:1:0:1 -3 195703854 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08227;SOR=Inf;LSEQ=GAGAGGTGGCTGTGCACATG;RSEQ=GCCTGCACACGAAGGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:39,2:0:1,0:24.6:1:30:1:1:0:36.2:40:1:0:0.1 0/1:17:2:2,0:15,0:0.1176:1,0:13:1:33.5:1:1:0:26:4:0.1176:0:1 -3 195704005 . G A 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGACACCACATCTCTAGAC;RSEQ=CCAGGTCCTTCGCGATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:120,37:0:2,0:26.5:1:30:1:1:0:27.2:77.5:1:0:0.1 0/1:68:11:7,4:31,26:0.1618:2,2:28.4:1:29.3:1:0.74338:1.46:27:22:0.1618:0:1.2 -3 195704020 . A G 106 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01856;SOR=3.255;LSEQ=TAGACGCCAGGTCCTTCGCG;RSEQ=TGGGGGCGTATCGCTCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:9:0,9:157,33:0.0452:2,0:22.1:1:32.1:1:0:0:26.3:18:0.0471:0:1.2 0/1:82:11:0,11:53,18:0.1341:2,0:33.1:1:30.8:1:0:0:25.7:22:0.1341:0:1 -3 195704071 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24344;SOR=4.24186;LSEQ=CTTGACTGTTAATGAGAATG;RSEQ=CTCCCTCTCCACGACATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:0,1:273,95:0.0027:2,0:1:0:25:0:0.26016:0:50:2:0.0028:0:1 0/1:175:2:1,1:130,43:0.0114:2,2:26:1:30:0:0.44072:3.00017:27:4:0.0116:0:1 -3 195704183 . C CT 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.38475;SOR=2.19665;LSEQ=TCTCTATTTCAAATGCATTA;RSEQ=TTTTTTTTACAAGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:3:1,2:69,314:0.0077:2,2:24.3:1:32:0:0.45229:2.27:43:6:0.0079:0:0.3 0/1:178:3:1,2:41,134:0.0169:2,2:30:1:28.7:1:0.55632:1.63:46:6:0.0169:0.0056:0.3 -3 195704198 . TA T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0.30615;LSEQ=CATTACTTTTTTTTACAAGA;RSEQ=TTTTTTGGGGGAGAGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:227:120:10,110:9,98:0.5286:2,2:23.1:1:30.9:1:1:1.01016:34.3:240:0.5333:0.1189:0.3 0/1:102:26:3,23:6,70:0.2549:2,2:23.2:1:30.4:1:0.68979:1.51:36.8:52:0.2549:0.049:0.3 -3 195704217 . A T 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=ATATTTTTTGGGGGAGAGAC;RSEQ=AAAAAGATATGCAGAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:27:1,26:5,102:0.2015:1,1:21.3:1:28.7:1:1:1.27235:32.7:54:0.203:0:1.1 0/0:62:0:0,0:0,62:0:1,0:18.3:1:30.4:1:1:0:36.5:124:1:0:0 -3 195704533 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTACCCAAACAGTGGCAAG;RSEQ=ACAGTAATAATGATTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:35.5:1:31.5:1:1:0:27:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195704832 . A C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAACAAAGGAGATCAAAA;RSEQ=CCCTAAACTAAATGTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:30:1:1:0:49:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195706290 . T G 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCTCAGGTGATCCACCTGCC;RSEQ=TGGCCTCCCAAAGTGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:35.8:1:30.5:1:1:0:39.5:8:0.5714:0:1.8 0/0:2:0:0,0:1,1:0:2,0:19.5:1:30.5:1:1:0:27:4:1:0:0.5 -3 195706348 . T C 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATGCCCGGCCTCAATCCC;RSEQ=GCTTTACTGCTGGCATAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:0.2222:1,0:19.3:1:27.8:1:1:0:35:8:0.2222:0:1.8 0/0:1:0:0,0:0,1:0:0,0:42:0:30:0:1:0:27:2:1:0:0 -3 195706464 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54858;SOR=1.40546;LSEQ=GTGGGAAAAGTCTCCTTAAG;RSEQ=AAATGACATTGAAGTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:10:10,0:87,6:0.0971:2,0:10.1:1:30.9:1:1:0:29.2:20:0.0971:0:2.1 0/1:38:5:5,0:33,0:0.1316:1,0:18.2:1:29.6:1:1:0:28.2:10:0.1351:0:2 -3 195706503 . T C 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50602;SOR=0.6663;LSEQ=GACCTGAGAGCTAAGGAAGC;RSEQ=GATCTTCAAAACCATGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:21:19,2:159,11:0.1099:2,2:33.1:1:31.7:1:0.63948:1.51769:31.1:42:0.1099:0:1.6 0/1:79:6:5,1:66,7:0.0759:2,2:34:1:29.8:1:0.48475:1.8672:30:12:0.0769:0:2 -3 195706563 . G A 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83235;SOR=1.16461;LSEQ=GCAATGAGTAGGCACCACAC;RSEQ=CTTACAAGACACACGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:17:16,1:194,12:0.0762:2,1:12.9:1:27.5:1:1:1.01037:31:34:0.0762:0:1.1 0/1:114:10:8,2:92,12:0.0877:2,2:14:1:29:1:0.35436:1.90347:33.7:20:0.0893:0:1.1 -3 195706577 . C CAT 145 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03316;SOR=0.46291;LSEQ=CCACACGCTTACAAGACACA;RSEQ=GAGCCGAACGCTTTCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:33:29,4:167,9:0.1579:2,2:6.8:1:28.9:1:0.12966:2.54451:31.1:66:0.161:0.1244:0.7 0/1:138:11:7,4:108,18:0.0797:2,2:5.9:1:28.3:1:0.07694:3.38667:34.2:22:0.0809:0.0652:1 -3 195706589 . T C 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00771;LSEQ=AAGACACACGAGCCGAACGC;RSEQ=TTCCGGGCAAGGCGTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:242:241:232,9:0,0:0.9959:0,1:23.1:1:31:1:1:0:27.8:39.167:0.9958:0:1.1 1/0:156:101:93,8:36,19:0.6474:2,2:23.4:1:30.2:1:9e-05:6.05:28.1:32.667:0.6447:0:1.1 -3 195706603 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=GAACGCTTTCCGGGCAAGGC;RSEQ=TCCTGCCCTACCTGTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:287,54:0:2,0:21.3:1:29.9:1:1:0:30:33.1:1:0:0.8 0/1:194:10:7,3:150,34:0.0515:2,2:18.3:1:28.2:1:0.40591:1.88336:31.5:9:0.0474:0:1.7 -3 195706728 . C T 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0184;SOR=0.51829;LSEQ=ACGTGCAGCTCAAGTAGTTG;RSEQ=GCCAGTAGCCTATGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1401:56:8,48:526,811:0.04:2,2:17.9:1:30:1:0.00011:3.88847:30.5:55:0.0401:0:1.9 0/1:805:17:5,12:318,469:0.0211:2,2:7.5:1:29.2:1:0.45744:1.62636:31.9:16:0.0201:0:1.4 -3 195706732 . A C 159 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00084;SOR=0.26655;LSEQ=GCAGCTCAAGTAGTTGCGCC;RSEQ=GTAGCCTATGGAAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1369:39:3,36:509,821:0.0285:2,2:19.6:1:30.1:1:3e-05:7.43368:27.4:78:0.0287:0:2.2 0/0:774:6:1,5:302,466:0.0078:2,2:14.8:1:30.2:1:0.4125:3.23634:29:12:0.0078:0:2 -3 195706799 . A G 75 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78641;LSEQ=ACGTCCGGACCTCCTGTCTA;RSEQ=TGAGATCACAGAACGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:5:1,4:70,327:0.0124:2,2:13.8:1:32.4:1:1:1.17:29.6:10:0.0126:0:2.4 0/0:204:2:0,2:47,155:0.0098:2,0:29.5:1:25.5:1:1:0:43.5:4:0.01:0:1 -3 195706806 . C A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03947;SOR=Inf;LSEQ=GACCTCCTGTCTAATGAGAT;RSEQ=ACAGAACGGACAGGGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:50,289:0:2,0:20.2:1:31.8:1:1:0:46.3:47.429:1:0:0.1 0/1:176:3:1,2:31,142:0.017:2,2:15.7:1:29.7:1:0.45438:2.28:52.3:6:0.0174:0:1 -3 195706826 . C T 118 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=38.71798;LSEQ=CACAGAACGGACAGGGCAGC;RSEQ=CCCGGGCACCATCTTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:0,1:20,182:0.0049:2,0:14:0:15:0:1:0:40:0:0:0:7 0/1:111:18:2,16:11,82:0.1622:2,2:20.7:1:28.4:1:1:1.07249:41.2:8:0.1509:0:1 -3 195706971 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAGAAGAGACTTCCATTT;RSEQ=TATTTTATTTATTTATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:0,2:0,32:0.0588:1,0:41:1:32.5:1:1:0:42.5:4:0.0588:0:1 0/0:10:0:0,0:1,9:0:2,0:21.3:1:30.2:1:1:0:50.2:20:1:0:0.4 -3 195708525 . AT A 57 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGATATATGGTTTGGAAAAT;RSEQ=TTTTTTCCCAACCTGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:50:0:30:0:1:0:27:2:0.5:0:0 1/1:4:4:2,2:0,0:1:0,2:29:1:28.8:1:1:0:35:8:1:0:0 -3 195708741 . C T 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAACCCCATGTGACTCTT;RSEQ=GGGCCACAGTTTCCTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:9,1:0.2308:2,0:6:1:31:1:1:0:33:6:0.2308:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195708767 . C T 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTTTCCTCATCTAAAAT;RSEQ=GGGAGAGGTACGCTGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:5,0:21,1:0.1852:1,0:23.6:1:31.8:1:1:0:43.8:10:0.1852:0:2.6 0/0:1:0:0,0:1,0:0:0,0:3:0:29:0:1:0:38:2:1:0:0 -3 195708778 . C A 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34476;SOR=4.65478;LSEQ=ATCTAAAATCGGGAGAGGTA;RSEQ=GCTGTGAACCTGACGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:24,1:0.1667:1,0:34.6:1:31:1:1:0:43.8:10:0.1667:0:2.6 1/0:2:1:1,0:1,0:0.5:0,0:2:0:32:0:1:0:45:2:0.5:0:1 -3 195708849 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50309;SOR=1.95954;LSEQ=CACCCCCTGAGGCAGGTGCT;RSEQ=CTGTCCTCACCCTTTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:2,0:79,0:0.0247:1,0:14.5:1:29:1:1:0:46.5:4:0.025:0:2 0/1:21:1:1,0:19,1:0.0476:1,0:27:0:28:0:1:0:60:2:0.05:0:1 -3 195708880 . C T 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58551;SOR=0.77042;LSEQ=CCTTTACAGGTGAGGAACCA;RSEQ=GGCTGGGAAAGGCCATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:115:58:56,2:55,2:0.5043:1,1:27.8:1:30.9:1:1:1.02:41.2:57:0.5:0:1.3 0/1:41:18:16,2:21,2:0.439:2,2:28.2:1:30.3:1:1:1.30372:44.2:36:0.439:0:1.3 -3 195708907 . C T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69637;SOR=1.45478;LSEQ=GAAAGGCCATCACCCTCACA;RSEQ=GGTTATATCAAGGCCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:5:5,0:161,9:0.0286:2,0:17.8:1:31.2:1:1:0:42:10:0.0292:0:1.4 0/1:73:3:3,0:63,7:0.0411:2,0:19.3:1:30.3:1:1:0:43.3:6:0.0417:0:1.3 -3 195708912 . A G 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00013;SOR=Inf;LSEQ=GCCATCACCCTCACACGGTT;RSEQ=TATCAAGGCCTGTGTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:178,13:0:2,0:23.4:1:28.1:1:1:0:48.1:62.667:1:0:0.6 0/1:77:7:7,0:63,7:0.0909:2,0:26.1:1:32.6:1:1:0:50.3:14:0.0909:0:1.7 -3 195708973 . C G 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74768;SOR=0.92289;LSEQ=TATTTTCCTTAAAATAAAGA;RSEQ=ACTCTAAATGGAATTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:87:73,14:264,21:0.2339:2,2:22.5:1:30.5:1:0.02048:2.40423:36.1:16.4:0.2247:0:1.1 0/1:182:40:33,7:129,13:0.2198:2,2:18.5:1:30.2:1:0.15466:2.09495:37.4:39:0.2155:0:1.2 -3 195709088 . T C 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=2.08839;LSEQ=ATGGATGGACCCGTCCTGTA;RSEQ=GCACAGTGCGAAGACACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:105:0,105:133,238:0.2201:2,1:24.2:1:30:1:0:0:34.4:210:0.2215:0:1 0/1:194:72:0,72:44,77:0.3711:2,1:27.3:1:29.8:1:0:0:34.9:144:0.375:0:1.1 -3 195709094 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02238;SOR=Inf;LSEQ=GGACCCGTCCTGTATGCACA;RSEQ=TGCGAAGACACCACGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:0:0,0:138,336:0:2,0:24.7:1:32:1:1:0:33:117.5:1:0:0.3 0/1:187:3:0,3:48,136:0.016:2,0:40.7:1:29.7:1:0.57073:0:27:6:0.0164:0:2 -3 195709109 . G A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00159;SOR=Inf;LSEQ=GCACAGTGCGAAGACACCAC;RSEQ=GCACTCCCCATTCTCCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:165,279:0:2,0:26.8:1:30.6:1:1:0:32.1:87.8:1:0:0.2 0/1:171:5:4,1:49,117:0.0292:2,2:31.2:1:31.2:1:0.03258:9.42:27:10:0.0294:0:1 -3 195709172 . A G 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00081;SOR=Inf;LSEQ=CACAAAACAGCTGGTATCAT;RSEQ=TCGCAGAGACTAAAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:130,266:0:2,0:20.9:1:29:1:1:0:30.9:35:1:0:0.2 0/1:128:5:2,3:40,83:0.0391:2,2:24.4:1:30.4:1:0.66288:1.38:27:10:0.04:0:1 -3 195709192 . G GA 103 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.20522;SOR=0.25787;LSEQ=ATCGCAGAGACTAAAAGAAA;RSEQ=AAAAAAAAAGGGCAAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:12:1,11:91,255:0.0332:2,2:24.6:1:29:1:0.31011:3.91535:31.9:24:0.0351:0.0083:0.7 0/0:114:1:0,1:30,83:0.0088:2,0:38:0:32:0:1:0:27:2:0.009:0:1 -3 195709242 . G A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.36421;SOR=2.43925;LSEQ=ACCTTTAAGGTTTTAAGGTG;RSEQ=TATCTGCTCATGTGAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:4:0,4:16,257:0.0144:2,0:24:1:32.8:1:1:0:24.5:8:0.0146:0:1 0/1:87:3:0,3:7,77:0.0345:2,0:22:1:31.7:1:1:0:25:6:0.0353:0:1 -3 195709312 . G C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57562;SOR=2.23879;LSEQ=AAATCCAAGGAGATCAGCAA;RSEQ=AGTGTCAATGACACTGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:0,14:0.1765:1,0:8.7:1:32.3:1:1:0:29:6:0.1875:0:1.3 0/1:6:2:1,1:0,4:0.3333:0,2:26.5:1:33:1:0.33333:0:25.5:4:0.3333:0:1.5 -3 195709355 . C G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CCCGAGAGGCATTCCACGCC;RSEQ=AGCAGTACCAACAAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:27.3:1:33.1:1:1:0:31.9:14:1:0:0 1/0:4:2:2,0:0,2:0.5:0,0:18:1:28.5:1:0.33333:0:33.5:4:0.5:0:1.5 -3 195710815 . C T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.14665;SOR=3.13105;LSEQ=GCAGCTTCTCAAGGCACACG;RSEQ=CTGCTCCTGTCACATCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:7:7,0:29,1:0.1892:1,0:20.4:1:29.7:1:1:0:28.6:14:0.1892:0:1.7 0/1:14:6:6,0:8,0:0.4286:0,0:13.3:1:30.3:1:1:0:35:12:0.4286:0:2 -3 195710829 . A C 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.77959;SOR=0.76695;LSEQ=CACACGCCTGCTCCTGTCAC;RSEQ=TCCACAGTCGCTGCATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:20:18,2:22,2:0.4545:2,2:24.5:1:30.6:1:1:1.21662:38.5:40:0.4545:0:1.3 0/1:18:7:7,0:10,1:0.3889:2,0:20.7:1:31.3:1:1:0:39.9:14:0.3889:0:1.7 -3 195710926 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08074;SOR=Inf;LSEQ=CGCTAACCCATTCCCCGCTG;RSEQ=CACCACAAGCCCCAGCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:312,47:0:2,0:25.1:1:29.8:1:1:0:48:70.8:1:0:0.6 0/1:143:2:1,1:122,19:0.014:2,2:23.5:1:28.5:1:0.26101:6.28407:54.5:4:0.0141:0:1 -3 195710940 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08426;SOR=Inf;LSEQ=CCGCTGTCACCACAAGCCCC;RSEQ=GCACTACGTGTCCTGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:0:0,0:372,62:0:2,0:24.5:1:30.1:1:1:0:48.7:42.4:1:0:0.6 0/1:178:2:2,0:149,26:0.0112:2,0:13:1:28:1:1:0:37:4:0.0114:0:2 -3 195710971 . G T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.09515;SOR=1.39178;LSEQ=TCCTGTCTCAGGTGGACGGG;RSEQ=GGCGGCCTTACCCTCCCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:610:81:69,12:405,124:0.1328:2,2:23.6:1:29.8:1:0.08685:1.76:40.6:39.5:0.1321:0:2.7 0/1:313:55:46,9:204,54:0.1757:2,2:23.1:1:29.4:1:0.57855:1.35:40.1:54:0.1759:0:2.8 -3 195710975 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0134;SOR=Inf;LSEQ=GTCTCAGGTGGACGGGGGGC;RSEQ=GCCTTACCCTCCCGTATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:635:0:0,0:493,142:0:2,0:24.5:1:29.8:1:1:0:52:69.556:1:0:0.8 0/1:329:4:4,0:258,66:0.0122:2,0:28:1:29:1:0.58696:0:26:8:0.0123:0:3.8 -3 195710978 . C G 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00038;SOR=0;LSEQ=TCAGGTGGACGGGGGGCGGC;RSEQ=TTACCCTCCCGTATAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:19:13,6:490,150:0.0288:2,2:21:1:27.7:1:0.41505:1.50666:35.1:18:0.0277:0:2.3 0/0:346:0:0,0:273,71:0:2,0:24:1:30:1:1:0:51.4:56.333:0.9941:0:1.1 -3 195710989 . G A 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=1.7428;LSEQ=GGGGGCGGCCTTACCCTCCC;RSEQ=TATAAGGTGTGCAATATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:705:158:123,35:397,149:0.2241:2,2:26.9:1:30.1:1:0.21781:1.32:35.5:78:0.2241:0:2.5 0/1:412:138:116,22:200,74:0.335:2,2:24.6:1:29.4:1:0.01339:1.95:38.9:276:0.3391:0:2.4 -3 195710993 . A G 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=1.82555;LSEQ=GCGGCCTTACCCTCCCGTAT;RSEQ=AGGTGTGCAATATTGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:760:158:120,38:428,174:0.2079:2,2:24.2:1:31.3:1:0.2338:1.28:36.8:30.6:0.2037:0:2.5 0/1:466:151:126,25:226,87:0.324:2,2:23.4:1:30.9:1:0.00783:1.94:40.8:74.5:0.3232:0:2.3 -3 195710995 . G C 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCTTACCCTCCCGTATAA;RSEQ=GTGTGCAATATTGAGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:0:0,0:561,220:0:2,0:24.6:1:31.5:1:1:0:52.6:51.067:0.9987:0:0.7 0/1:503:30:23,7:353,119:0.0596:2,2:24:1:30.3:1:1:1.11:57.9:14:0.057:0:1.3 -3 195711016 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGTGCAATATTGAGTGGCC;RSEQ=GTCCGATCAGCCACACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1016:0:0,0:640,376:0:2,0:24.1:1:29.8:1:1:0:52.4:62.5:1:0:0.6 0/1:726:21:13,8:466,238:0.0289:2,2:27.6:1:30.2:1:0.64872:1.20458:58.1:42:0.0293:0:1.4 -3 195711042 . C G 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.54812;LSEQ=ATCAGCCACACAGCAGCACC;RSEQ=ATGGGCCTGCCCGCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1242:203:82,121:599,439:0.1634:2,2:23.8:1:30.1:1:1e-05:2.01229:37.8:66.667:0.1625:0:1.2 0/1:1003:97:47,50:539,364:0.0967:2,2:24.3:1:29.4:1:0.039:1.57451:36.3:31.333:0.0945:0:1.1 -3 195711167 . A C 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.0081;SOR=Inf;LSEQ=CCTGTGAAAGATAAAAACAA;RSEQ=CAAAAGCCTTATTAACCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:18,259:0:2,0:22.2:1:30:1:1:0:34.9:68.25:1:0:0.6 0/1:173:5:0,5:16,152:0.0289:2,0:21.4:1:28.4:1:1:0:37.4:4:0.0235:0:2 -3 195711182 . A C 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6075;SOR=0.85237;LSEQ=AACAAACAAAAGCCTTATTA;RSEQ=CCTAAAGGAGTCAAGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:187:129:0,129:12,46:0.6898:2,1:24.6:1:31.3:1:0:0:31.7:42:0.6961:0:1.1 1/0:110:72:0,72:9,29:0.6545:2,1:22.3:1:31.6:1:4e-05:0:31:144:0.6606:0:1.1 -3 195711423 . A G 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13328;SOR=1.42497;LSEQ=TTTTCCAGGACTCTTGTACT;RSEQ=GAAACAGACCACCAGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:820:51:50,1:647,121:0.0622:2,1:21.9:1:32.6:1:0.00374:9.34:30.1:50:0.062:0:1.1 0/1:440:38:35,3:319,83:0.0864:2,2:18.1:1:31.7:1:0.08375:3.03:30.3:37:0.0853:0:1.1 -3 195711497 . C G 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.48851;LSEQ=AGTGGGGGCCTGCTCCGTCA;RSEQ=GTAGTGGATGGCATCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1663:34:19,15:935,693:0.0204:2,2:28.7:1:32:1:0.86262:1.06511:41.3:68:0.0206:0:1.4 0/1:972:66:34,32:471,434:0.0679:2,2:25.8:1:30.6:1:1:1.0214:44.2:65:0.0678:0:1.4 -3 195711539 . T TCA 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=CCCCAGCCAGTCGGAGCCCT;RSEQ=CACGGTGTCATAGAAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1387:0:0,0:578,805:0:2,0:22.1:1:29.4:1:1:0:33.5:35.395:0.997:0:0.3 0/1:676:9:4,5:231,436:0.0133:2,2:27.8:1:29.1:1:0.50714:1.51:35.2:18:0.0136:0.003:0.3 -3 195711550 . T C 258 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15447;SOR=1.18268;LSEQ=CGGAGCCCTTCACGGTGTCA;RSEQ=AGAAATGCCACCTCCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1283:298:110,188:407,575:0.2323:2,2:23.6:1:31.5:1:0.17773:1.20956:33.1:41.571:0.231:0:1.2 0/1:554:146:42,104:138,270:0.2635:2,2:24.1:1:31:1:0.30329:1.26508:32.8:35.5:0.261:0:1.3 -3 195711560 . A C 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00112;SOR=16.94267;LSEQ=CACGGTGTCATAGAAATGCC;RSEQ=CCTCCAGTTGTCCTCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1138:1:0,1:439,696:9e-04:2,0:30:0:12:0:1:0:25:0:0:0:3 0/1:476:7:1,6:153,314:0.0147:2,2:31.7:1:31.4:1:0.43622:2.91836:37.4:14:0.0149:0:2.3 -3 195711648 . A G 270 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=4e-05;SOR=0.51352;LSEQ=CTTACAAGCCACAAACAGGA;RSEQ=CCCCAGCTTTGTCTTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:576:440:223,217:41,94:0.7639:2,2:20.4:1:30.8:1:3e-05:2.35:28.8:47.889:0.7642:0:1.1 1/0:266:166:91,75:42,57:0.6241:2,2:20.6:1:30.4:1:0.05734:1.64:29:54.333:0.6221:0:1.1 -3 195711735 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06517;SOR=Inf;LSEQ=CGGTGACTCCCAGTGAGGGC;RSEQ=GACCTCAGCAGAGGAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:0:0,0:34,548:0:2,0:27.8:1:30.7:1:1:0:41.5:96:1:0:0.3 0/1:200:2:1,1:16,181:0.01:2,2:35.5:1:28.5:1:0.16395:11.01:60:4:0.0101:0:1 -3 195711742 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06136;SOR=Inf;LSEQ=TCCCAGTGAGGGCTGACCTC;RSEQ=GCAGAGGAGCAGCCAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:0:0,0:26,507:0:1,0:26.4:1:31.8:1:1:0:42.2:132.25:1:0:0.2 0/1:176:2:1,1:13,161:0.0114:2,2:29.5:1:30.5:1:0.15318:11.97:47.5:4:0.0116:0:1 -3 195711746 . G A 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00392;SOR=Inf;LSEQ=AGTGAGGGCTGACCTCAGCA;RSEQ=AGGAGCAGCCAGGCCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:25,480:0:1,0:25.3:1:32:1:1:0:42.7:504:1:0:0.2 0/1:170:4:1,3:13,153:0.0235:2,2:32.3:1:31:1:0.29318:3.87:52.5:8:0.024:0:1 -3 195711785 . C T 125 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01444;SOR=0;LSEQ=CAGATTCCAGATCACAACCC;RSEQ=TCCCAGACTCACCCAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:17:0,17:3,136:0.1083:1,1:15:1:30.6:1:1:0:35.4:34:0.109:0:1.2 0/0:50:0:0,0:6,44:0:2,0:15.7:1:31.1:1:1:0:40.5:24:1:0:0.3 -3 195711867 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGGGAACTCCAGGAAGG;RSEQ=CTGACTGGAGCAGTGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:0.2:0,0:26.5:1:31.5:1:1:0:32.5:4:0.2:0:1.5 0/0:4:0:0,0:0,4:0:0,0:12.3:1:28:1:1:0:32.5:3:1:0:0.3 -3 195712477 . A G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=CCTGCACGGAGTGGGAGCAC;RSEQ=GTGGGGCACCTTTCTCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:0:0,0:289,181:0:2,0:24.1:1:30.2:1:1:0:25.7:46:1:0:0.2 0/1:305:9:2,7:187,109:0.0295:2,2:28.9:1:27.7:1:0.02962:5.9698:25:18:0.0299:0:1 -3 195712478 . G A 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75161;SOR=1.09959;LSEQ=CTGCACGGAGTGGGAGCACA;RSEQ=TGGGGCACCTTTCTCTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:25:3,22:285,161:0.0531:2,2:25.6:1:29.8:1:0:12.91913:24.6:50:0.054:0:1.8 0/1:310:18:3,15:189,103:0.0581:2,2:18.3:1:27.1:1:7e-05:9.11135:24.8:36:0.0584:0:1.9 -3 195712579 . T C 163 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.56438;LSEQ=TCTGCCTCGGAAAGGCCAAA;RSEQ=GCAGCTCGCAAAGCCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1566:7:0,7:833,725:0.0045:2,0:11.4:1:29.9:1:0.00482:0:25:14:0.0046:0:1.1 0/1:1092:45:22,23:571,476:0.0412:2,2:24.9:1:29.8:1:0.5415:1.25384:41.9:44:0.041:0:1.3 -3 195712586 . C T 205 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=74.72883;LSEQ=CGGAAAGGCCAAATGCAGCT;RSEQ=GCAAAGCCGGCCCCTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1666:3:0,3:856,807:0.0018:2,0:1:0:26.3:1:0.11471:0:49:6:0.0018:0:1 0/1:1168:139:69,70:540,489:0.119:2,2:24.3:1:28.9:1:0.58746:1.12019:38.6:68.5:0.1186:0:1.2 -3 195712663 . G T 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=42.06962;LSEQ=TGGATACTGAGCAGAAATCT;RSEQ=GAAAAGAAAAATTCACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:860:1:0,1:274,581:0.0012:2,0:23:0:28:0:1:0:47:2:0.0012:0:1 0/1:556:26:9,17:151,378:0.0468:2,2:18.8:1:29.2:1:0.51004:1.32:34.8:52:0.0471:0:1.4 -3 195712679 . C A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02834;SOR=Inf;LSEQ=ATCTGGAAAAGAAAAATTCA;RSEQ=CTGTCAATCACAGGTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:544:0:0,0:94,450:0:2,0:21.4:1:31.1:1:1:0:29.7:59.444:1:0:0.1 0/1:380:4:2,2:63,313:0.0105:2,2:14:1:30:1:0.13717:4.94:30:8:0.0106:0:1 -3 195712728 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1051;SOR=Inf;LSEQ=ACATGAAGACTCTTGTGCCA;RSEQ=TGAAAGAGCTTGACAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:0,222:0:1,0:24.5:1:32.2:1:1:0:25:54.5:1:0:0.1 0/1:107:2:0,2:0,104:0.0187:1,0:26.5:1:28:1:1:0:25:4:0.0187:0:1 -3 195712729 . T C 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGAAGACTCTTGTGCCAG;RSEQ=GAAAGAGCTTGACAAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:0,217:0:1,0:24.6:1:30.6:1:1:0:25:71.333:1:0:0.1 0/1:102:16:0,16:0,86:0.1569:1,1:25:1:30.4:1:1:0:25:32:0.1584:0:1.1 -3 195712899 . A C 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=GGTCTATTCCATGGGATCAG;RSEQ=CTGAGGACCACAACTCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:32:1:32:1:1:0:25:10:0.7143:0:1 0/0:1:0:0,0:0,1:0:0,0:33:0:31:0:1:0:25:2:1:0:0 -3 195713302 . C TTTCA 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.04722;SOR=Inf;LSEQ=GAGAAATTTTTCCCTTATGT;RSEQ=TATGACTCATATGAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:56,7:0:2,0:23.1:1:29.7:1:1:0:26.5:62:1:0:0.4 0/1:18:2:1,1:14,2:0.1111:2,2:12.5:1:32.1:1:0.31373:5.91609:25.5:4:0.1111:0.0556:1.5 -3 195713316 . A G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.02396;SOR=3.77848;LSEQ=TTATGTCTATGACTCATATG;RSEQ=AAACAAACTGGTATAGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:15:9,6:67,5:0.1724:2,2:31.1:1:31.7:1:0.00275:8.58148:25.8:30:0.1744:0:1.1 0/1:18:8:4,4:8,2:0.4444:2,2:11.9:1:29.3:1:0.32127:3.68059:26.3:16:0.4706:0:1 -3 195713360 . T C 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=CCCCCAAGCCAAAAAAATCA;RSEQ=TTATAATGGAACAAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:171,16:0:2,0:23.9:1:31.1:1:1:0:26.9:92.5:1:0:0.2 0/1:52:6:5,1:38,8:0.1154:2,2:19.2:1:29.8:1:1:1.05:25:12:0.1176:0:2 -3 195713385 . C CT 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.27672;SOR=1.33411;LSEQ=AATGGAACAAAAAGCATGAA;RSEQ=TTACGGAATCTGAAACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:59:59,0:195,16:0.2185:2,1:24.5:1:31.6:1:0.02686:0:25.9:118:0.221:0.0556:0.1 0/1:103:28:28,0:64,11:0.2718:2,1:23:1:31.2:1:0.03293:0:26:27:0.2673:0.0291:0.3 -3 195713404 . T C 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=ACTTACGGAATCTGAAACTT;RSEQ=AGCAGATGCCCTCTCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:309,12:0:1,0:26.3:1:30.5:1:1:0:25.8:320:1:0:0.1 0/1:137:8:7,1:120,9:0.0584:2,2:28.8:1:30.9:1:0.46371:1.89345:24.8:16:0.0593:0:1.9 -3 195713476 . C A 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00445;SOR=Inf;LSEQ=GTTTGCAACACTGTTGGCCA;RSEQ=TGGAGACACAGAAGACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:580:0:0,0:439,139:0:2,0:22.3:1:31.4:1:1:0:26.3:71.25:1:0:0.3 0/1:299:5:4,1:208,86:0.0167:2,2:20:1:28.4:1:1:1.65:25:10:0.0169:0:1 -3 195713477 . T C 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCAACACTGTTGGCCAC;RSEQ=GGAGACACAGAAGACACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:597:0:0,0:438,159:0:2,0:22:1:30.1:1:1:0:26.3:48.75:1:0:0.3 0/1:306:14:10,4:201,91:0.0458:2,2:21.6:1:28.2:1:1:1.13:27:6:0.0404:0:1.3 -3 195713494 . C G 202 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CACTGGAGACACAGAAGACA;RSEQ=AGATCCAGAGGGTTAGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:755:102:51,51:325,324:0.1351:2,2:21.5:1:30.4:1:1:1.00308:25.7:101:0.1348:0:1.1 0/0:394:0:0,0:199,195:0:2,0:22.5:1:30.1:1:1:0:27:130.333:1:0:0.3 -3 195713516 . T C 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18911;SOR=1.25225;LSEQ=GATCCAGAGGGTTAGTGTCC;RSEQ=GAAGGAACAAATGCTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:816:105:37,68:257,454:0.1287:2,2:29.6:1:29.4:1:0.91349:1.04032:28:210:0.13:0:1.1 0/1:410:64:21,43:135,211:0.1561:2,2:30.7:1:29.1:1:0.40135:1.30924:28.6:128:0.1572:0:1.1 -3 195713585 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07205;SOR=Inf;LSEQ=ACTGTTCACCTTCTTATGTA;RSEQ=CCAGGTGCTCCTGTGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:26,406:0:2,0:21.1:1:31.8:1:1:0:27.8:215:1:0:0.2 0/1:159:2:1,1:9,148:0.0126:2,2:24.5:1:28:1:0.1222:15.65:47:4:0.0127:0:1 -3 195713774 . AC GT 51 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGATACGAGATGAAAAAG;RSEQ=GCACTTCCTCTGGGAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,2:0.4286:0,0:10.7:1:32.2:1:1:0:25.7:6:0.4286:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -3 195717037 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50276;SOR=0;LSEQ=CTCGCCCCCCGCCTGCCCTG;RSEQ=CCCGGTCCGCGGCAGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:75,22:0.02:2,2:6:1:29:1:0.41249:3.35625:39:4:0.02:0:2.5 0/0:81:0:0,0:63,18:0:2,0:13.4:1:32.1:1:1:0:46.7:162:1:0:0.2 -3 195717061 . C A 153 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00031;SOR=3.07335;LSEQ=GGTCCGCGGCAGGGACTCAC;RSEQ=GCCTTGGCCAGCGCCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:15:12,3:179,84:0.0538:2,2:22.6:1:31.1:1:0.40433:1.87:42.7:30:0.0543:0:1.1 0/1:235:35:23,12:124,75:0.1489:2,2:16.3:1:30:1:0.84988:1.16:44.9:70:0.1528:0:1.5 -3 195717077 . A AGCGCCAG 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=2.000;MSILEN=1;SSF=0;SOR=0.31301;LSEQ=TCACCGCCTTGGCCAGCGCC;RSEQ=GCGCCAGGCGCCGAGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:113:75,38:208,131:0.2457:2,2:21.1:1:31.3:1:0.37024:1.24:43.4:226:0.2534:0.0957:0.3 0/1:368:34:19,15:205,127:0.0924:2,2:18:1:30.1:1:0.58011:1.27347:45.6:68:0.0944:0.0353:0.2 -3 195717080 . G T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.03787;SOR=Inf;LSEQ=CCGCCTTGGCCAGCGCCAGC;RSEQ=CCAGGCGCCGAGCGCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:496:0:0,0:309,186:0:2,0:23.6:1:30.4:1:1:0:45.4:48.5:1:0:0.3 0/1:393:4:1,3:232,154:0.0102:2,2:11:1:25.5:1:0.30705:4.50252:47.5:3:0.008:0:1.3 -3 195717157 . C A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30812;SOR=4.48598;LSEQ=GTCGCCGCCGCGCAGTCCCG;RSEQ=CAGTCCCTGCGCAGACTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:1:1,0:190,248:0.0023:2,0:1:0:25:0:0.43508:0:50:2:0.0024:0:1 0/1:296:3:2,1:125,168:0.0101:2,2:12:1:21.3:1:0.57863:2.68:43:2:0.0069:0:1.7 -3 195717187 . C A 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=3.06934;LSEQ=CGCAGACTGCGCCTGCGCAC;RSEQ=ACGGCCGGGTCAAGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:21:6,15:73,164:0.0814:2,2:27.6:1:29.8:1:1:1.11236:33.9:42:0.0833:0:2.6 0/1:168:36:9,27:41,90:0.2143:2,2:29.1:1:29.2:1:0.54142:1.3642:30.4:72:0.2143:0:2.6 -3 195717191 . G C 153 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=3.25333;LSEQ=GACTGCGCCTGCGCACCACG;RSEQ=CCGGGTCAAGGCGGGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:17:4,13:67,148:0.0733:2,2:33.7:1:31.2:1:0.59586:1.469:34.4:34:0.0756:0:2.8 0/1:156:32:8,24:40,83:0.2051:2,2:30:1:30.6:1:0.52128:1.44249:30.4:64:0.2105:0:2.6 -3 195717197 . T C 100 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00166;SOR=13.90905;LSEQ=GCCTGCGCACCACGGCCGGG;RSEQ=CAAGGCGGGGCGCTAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:1:1,0:64,149:0.0047:2,0:19:0:12:0:0.30374:0:40:0:0:0:1 0/1:146:9:2,7:40,96:0.0616:2,2:30.6:1:31.8:1:1:1.45483:36:18:0.0625:0:1 -3 195717242 . G C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14557;SOR=2.06719;LSEQ=ATTGCGCCTGCGCACCACGC;RSEQ=ACGCCCGGGCCGGGGTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:10:0,10:12,73:0.1053:2,0:14.7:1:32.5:1:0.35204:0:35.4:20:0.1075:0:3.3 0/1:56:11:0,11:12,33:0.1964:2,0:11.4:1:32.3:1:0.09656:0:35.4:22:0.2:0:3.5 -3 195717246 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52156;SOR=0;LSEQ=CGCCTGCGCACCACGCGACG;RSEQ=CCGGGCCGGGGTCTAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:10,67:0.0253:2,2:25.5:1:27.5:1:0.26063:6.44:60:4:0.026:0:2 0/0:50:0:0,0:12,38:0:2,0:22.8:1:31.5:1:1:0:52.9:49:1:0:0.8 -3 195717252 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51698;SOR=0;LSEQ=CGCACCACGCGACGCCCGGG;RSEQ=CGGGGTCTAATGGGCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:7,55:0.0313:2,2:25.5:1:29.5:1:0.23611:7.42:60:4:0.0317:0:2 0/0:42:0:0,0:11,31:0:2,0:21.8:1:31.2:1:1:0:55.1:20:1:0:0.5 -3 195717263 . T G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.74462;LSEQ=ACGCCCGGGCCGGGGTCTAA;RSEQ=GGGCGGGGACGCCGCGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:0,2:8,38:0.0417:2,0:19.5:1:32:0:1:0:32.5:4:0.0426:0:4 0/1:32:1:0,1:8,23:0.0313:2,0:11:0:32:0:1:0:39:2:0.0323:0:5 -3 195717267 . C A 33 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.81008;LSEQ=CCGGGCCGGGGTCTAATGGG;RSEQ=GGGGACGCCGCGCCTGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:0,2:8,34:0.0455:2,0:15.5:1:33:0:1:0:32.5:4:0.0465:0:4 0/1:27:1:0,1:8,18:0.037:2,0:7:0:33:0:1:0:39:2:0.037:0:5 -3 196248206 . T C 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28205;SOR=6.15667;LSEQ=CCGGGTTCCTCTTTGAAGTT;RSEQ=GTAGCAGATAGTGGTAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:30:1:31.5:1:1:0:60:8:0.3636:0:1 1/1:5:4:3,1:1,0:0.8:0,2:41:1:31:1:1:0:60:8:0.8:0:1 -3 196248332 . GC G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.53362;SOR=0;LSEQ=CGGCTACCTAAAAGGGAAGG;RSEQ=CCCCTGTCCCATGATCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:68,48:0.0169:2,2:28.5:1:30.5:1:1:1.41238:60:4:0.0175:0:0 0/0:68:0:0,0:36,32:0:2,0:24.7:1:30.7:1:1:0:59.5:67:1:0:0.1 -3 196248368 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50087;SOR=0;LSEQ=TCACGTGACTTGCTTGACCT;RSEQ=ATCAATCACTTGGACGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:64,80:0.0137:2,2:38:1:32.5:1:1:1.25:60:4:0.014:0:1 0/0:126:0:0,0:64,62:0:2,0:27.9:1:28.8:1:1:0:58.7:62:1:0:0.2 -3 196248390 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.2321;SOR=Inf;LSEQ=TCAATCACTTGGACGACTCA;RSEQ=CCTCCTTACCCTGCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:51,84:0:2,0:29.2:1:31.5:1:1:0:59.6:270:1:0:0.2 0/1:126:2:1,1:59,65:0.0159:2,2:29:0:31.5:1:1:1.10:60:4:0.0163:0:1.5 -3 196248551 . G A 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24242;SOR=6.43915;LSEQ=TTTATTTCTTACTATCTTTC;RSEQ=TCTCCGTACATGGGGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:0.2:0,0:10:0:33:0:1:0:60:2:0.2:0:1 1/0:6:4:0,4:0,2:0.6667:0,0:27.8:1:31:1:1:0:60:8:0.6667:0:2.3 -3 196366964 . G A 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAAATACCTCCCTCCAG;RSEQ=AGCACTTAGAGCTGAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:0,1:0.6667:0,0:22:1:32:0:1:0:60:4:0.6667:0:1 -3 196547222 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15758;SOR=Inf;LSEQ=TCCATGGAAGCCATTAACTC;RSEQ=GTTTTGTTTTGTTTTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:113,26:0:2,0:24.8:1:30.6:1:1:0:60:45.333:1:0:0 0/1:92:2:1,1:69,21:0.0217:2,2:20:1:29:1:0.42308:3.23333:60:4:0.0222:0:1 -3 196547446 . G C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3428;SOR=2.11345;LSEQ=AAATCCCTTGAGGGTAAGAT;RSEQ=AGTTAAACACCAGCCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:21:4,17:2,18:0.5122:2,2:22:1:30.3:1:0.6628:2.08:60:9.5:0.4872:0:1.3 1/0:13:9:2,7:2,2:0.6923:2,2:26.8:1:32.2:1:0.53007:3.13792:60:18:0.6923:0:1 -3 196547538 . G A 51 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53981;LSEQ=TCCAAGAATTTAAAGTAGAA;RSEQ=GTTGATAAAACCTAATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:16.7:1:32.3:1:1:0:60:6:0.6:0:1.3 0/1:3:1:0,1:0,2:0.3333:0,0:20:0:33:0:1:0:60:2:0.3333:0:1 -3 196625640 . C T 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17582;SOR=0.13707;LSEQ=TAGTTCCATTCGATTCTATG;RSEQ=GATGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:20.5:1:31:0:1:0:26.5:4:0.5:0:6.5 0/1:10:1:1,0:9,0:0.1:0,0:18:0:32:0:1:0:40:2:0.1:0:5 -3 196625655 . A T 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.55084;LSEQ=CTATGCGATGATTCCATTCC;RSEQ=TTCCATTGGAAGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:4,0:0.2:0,0:43:0:31:0:1:0:28:2:0.2:0:5 0/1:17:2:2,0:14,1:0.1176:1,0:28.5:1:33:0:1:0:22:4:0.1176:0:2 -3 196625663 . G T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80884;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=GAAGATGATTCCATTCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:6,1:1,1:0.7:2,2:20.9:1:31.4:1:0.41667:4.58:35.6:14:0.7:0:2.7 1/0:23:15:14,1:0,0:0.6522:0,1:20.9:1:29.3:1:1:0:31.7:14:0.6364:0:2.9 -3 196625671 . A G 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10862;SOR=0.1204;LSEQ=TTCCATTCCATTGGAAGATG;RSEQ=TTCCATTCGAGACCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:0.1538:2,2:23.5:1:31:1:1:2.4495:25:4:0.1538:0:6 0/1:49:1:1,0:30,18:0.0204:2,0:39:0:32:0:1:0:25:2:0.0213:0:5 -3 196625676 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTGGAAGATGATTCC;RSEQ=TTCGAGACCATTCGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:21.6:1:30.5:1:1:0:34.5:30:1:0:2.5 0/1:65:2:1,1:36,27:0.0308:2,2:28:1:28.5:1:1:1.32735:43:4:0.0313:0:2.5 -3 196625679 . C G 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57396;SOR=Inf;LSEQ=CATTGGAAGATGATTCCATT;RSEQ=GAGACCATTCGATGATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:18.1:1:30.1:1:1:0:35.1:40:1:0:2.5 0/1:73:4:2,2:37,32:0.0548:2,2:9:1:28:1:1:1.15394:41.5:3:0.0417:0:2.5 -3 196625682 . G A 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03997;SOR=0;LSEQ=TGGAAGATGATTCCATTCGA;RSEQ=ACCATTCGATGATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:25:1:31.5:1:1:1:24:4:0.1:0:2.5 0/0:78:0:0,0:39,39:0:2,0:18.3:1:30.4:1:1:0:35.4:25:1:0:2.2 -3 196625685 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGATGATTCCATTCGAGAC;RSEQ=ATTCGATGATTGCATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:21.7:1:31.8:1:1:0:35.1:40:1:0:2.5 0/1:78:2:1,1:37,37:0.0256:2,2:14:0:31.5:1:1:1:40:4:0.026:0:2.5 -3 196625690 . GA AT 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCGAGACCATTC;RSEQ=TGATTGCATTCAATTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,12:0:2,0:20.8:1:30.8:1:1:0:36.6:48:0.96:0:2.5 0/1:79:2:1,1:37,38:0.0253:2,2:20:0:32:0:1:1.03:49:4:0.0263:0:1 -3 196625691 . A T 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.72582;SOR=1.731;LSEQ=ATTCCATTCGAGACCATTCG;RSEQ=TGATTGCATTCAATTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:0.0769:2,2:30:1:29:1:1:1:25:4:0.0769:0:6 0/1:79:10:5,5:33,34:0.1266:2,2:20.9:1:30.1:1:1:1.03:36.6:20:0.1299:0:2.2 -3 196625695 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCGAGACCATTCGATGA;RSEQ=TGCATTCAATTCATTCGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:21.9:1:30.5:1:1:0:36.1:52:1:0:2.5 0/1:82:2:1,1:39,41:0.0244:2,2:31.5:1:29:1:1:1.05:25:4:0.0247:0:3.5 -3 196625697 . G C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05855;SOR=0;LSEQ=TTCGAGACCATTCGATGATT;RSEQ=CATTCAATTCATTCGATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:12,12:0.0741:2,2:30:1:30.5:1:1:1:25:4:0.0741:0:6 0/0:83:0:0,0:40,40:0:2,0:28:1:31.2:1:1:0:35.6:39:0.963:0:2.1 -3 196625700 . T G 97 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0611;SOR=Inf;LSEQ=GAGACCATTCGATGATTGCA;RSEQ=TCAATTCATTCGATGACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:0:2,0:21.3:1:30.2:1:1:0:36.4:60:1:0:2.5 0/1:85:10:5,5:37,38:0.1176:2,2:30:1:29.4:1:1:1.03:30.4:9:0.1084:0:2.6 -3 196625701 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06636;SOR=0;LSEQ=AGACCATTCGATGATTGCAT;RSEQ=CAATTCATTCGATGACGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:0.0667:2,2:24.5:1:28:1:1:1:37:4:0.0667:0:3 0/0:85:0:0,0:42,43:0:2,0:30:1:28.7:1:1:0:35.9:41.5:1:0:2.2 -3 196625702 . C A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACCATTCGATGATTGCATT;RSEQ=AATTCATTCGATGACGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:0:2,0:22.4:1:31.3:1:1:0:36.4:60:1:0:2.5 0/1:85:2:1,1:41,42:0.0235:2,2:32.5:1:27.5:1:1:1.02:23:4:0.0238:0:7 -3 196625715 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGCATTCAATTCATTCGAT;RSEQ=ACGATTCCATTCAATTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,15:0:2,0:29.2:1:31.8:1:1:0:36.7:58:1:0:2.4 0/1:85:2:1,1:40,41:0.0235:2,2:36:1:31:1:1:1.02:43:4:0.0241:0:3 -3 196625718 . G C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14751;SOR=0.29456;LSEQ=CATTCAATTCATTCGATGAC;RSEQ=ATTCCATTCAATTCCGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:1,2:12,13:0.1071:2,2:34:1:32.7:1:1:1.80746:32:6:0.1071:0:5 0/1:89:3:1,2:43,43:0.0337:2,2:41.7:1:32.3:1:1:1.98502:36.3:6:0.0341:0:4.3 -3 196625721 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0557;SOR=0;LSEQ=TCAATTCATTCGATGACGAT;RSEQ=CCATTCAATTCCGTTCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:12,14:0.0714:2,2:31.5:1:31.5:1:1:1.16:30:4:0.0714:0:3.5 0/0:89:0:0,0:44,45:0:2,0:33.7:1:28.9:1:1:0:36.5:88:1:0:2.1 -3 196625725 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCATTCGATGACGATTCCA;RSEQ=TCAATTCCGTTCAATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:11,14:0:2,0:36.2:1:30:1:1:0:36:24:1:0:2.7 0/1:88:2:1,1:41,45:0.0227:2,2:30.5:1:31.5:1:1:1.10:43:4:0.0233:0:3 -3 196625727 . CA TC 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCGATGACGATTCCATT;RSEQ=ATTCCGTTCAATGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:11,14:0:2,0:36.2:1:31.9:1:1:0:36:50:1:0:2.7 0/1:88:2:1,1:41,45:0.0227:2,2:37:0:32:1:1:1.10:47:4:0.023:0:1 -3 196625733 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00416;SOR=0.22343;LSEQ=ATGACGATTCCATTCAATTC;RSEQ=GTTCAATGATTCCATTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:5,6:5,8:0.4583:2,2:39.5:1:30.1:1:1:1.32:38.1:10:0.4348:0:2.2 0/1:83:13:5,8:31,37:0.1566:2,2:37.8:1:30.5:1:0.76453:1.33576:35.6:26:0.1605:0:2 -3 196625745 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAATTCCGTTCAATGATT;RSEQ=CATTAGATTCCATTTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:0:2,0:26.8:1:30.4:1:1:0:37:10.5:1:0:2.5 0/1:78:2:1,1:30,44:0.0256:2,2:22.5:1:31:1:1:1.46:43:4:0.026:0:3.5 -3 196625747 . A G 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAATTCCGTTCAATGATTCC;RSEQ=TTAGATTCCATTTGATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:0:2,0:24.8:1:31.3:1:1:0:37:46:1:0:2.5 0/1:75:3:1,2:29,43:0.04:2,2:19:1:26.7:1:1:1.34364:36.3:6:0.0405:0:4.3 -3 196625749 . T C 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08761;SOR=0.27605;LSEQ=ATTCCGTTCAATGATTCCAT;RSEQ=AGATTCCATTTGATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:2,2:7,12:0.1739:2,2:28.8:1:32.3:1:1:1.67:37:8:0.1818:0:3 0/1:74:4:2,2:27,43:0.0541:2,2:24.3:1:30.3:1:0.64236:1.58:37.3:8:0.0541:0:2.5 -3 196625750 . A T 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6412;SOR=1.26074;LSEQ=TTCCGTTCAATGATTCCATT;RSEQ=GATTCCATTTGATGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:4,6:5,7:0.4348:2,2:20.2:1:30.4:1:1:1.06805:36:20:0.4348:0:2.6 0/1:71:35:12,23:14,22:0.493:2,2:15.3:1:30.5:1:0.80649:1.21628:35.9:70:0.493:0:2.3 -3 196625752 . A T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05914;SOR=0;LSEQ=CCGTTCAATGATTCCATTAG;RSEQ=TTCCATTTGATGATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:8,13:0.087:2,2:21:0:31.5:1:1:1.59:44.5:4:0.0909:0:2.5 0/0:70:0:0,0:25,45:0:2,0:16.4:1:29.3:1:1:0:37.4:34:1:0:2 -3 196625765 . A T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.77773;SOR=0.79013;LSEQ=CCATTAGATTCCATTTGATG;RSEQ=TGATTCCATTCGTCTCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:2,6:4,6:0.4444:2,2:10.3:1:31.1:1:0.63801:1.9247:35.8:16:0.4444:0:2.6 0/1:44:17:3,14:8,19:0.3864:2,2:7.1:1:29.4:1:0.48559:1.9361:35.2:34:0.3864:0:2.7 -3 196625767 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ATTAGATTCCATTTGATGAT;RSEQ=ATTCCATTCGTCTCTACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:0:2,0:8.1:1:32.3:1:1:0:37.1:36:1:0:2.6 0/1:38:2:1,1:8,27:0.0526:2,2:9:0:29.5:1:0.43243:3.24:22:4:0.0541:0:1.5 -3 197346485 . T C 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00856;SOR=Inf;LSEQ=GAAAGGCCATCACCCTCACA;RSEQ=GGTTATATCAAGGCCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:60,2:0:1,0:21.1:1:30.8:1:1:0:56:61:1:0:0.1 0/1:41:5:5,0:32,4:0.122:2,0:28.2:1:30.2:1:1:0:43:10:0.122:0:1.4 -3 197346530 . C G 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=0;LSEQ=ACTGCTATTCTACAATGCCT;RSEQ=TATTTTCCTTAAAATAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:20:20,0:122,4:0.137:1,1:20.3:1:32.8:1:1:0:58.9:40:0.1379:0:1.2 0/0:91:0:0,0:83,7:0:2,0:22.2:1:31.5:1:1:0:58.2:180:0.989:0:0.3 -3 197346558 . A C 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTAAAATAAAGACACTCTA;RSEQ=AAGAAATTTATTCATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:234,35:0:2,0:24:1:30.2:1:1:0:59.3:43.833:1:0:0.1 0/1:205:18:13,5:149,38:0.0878:2,2:26.2:1:31.3:1:0.54313:1.50478:59.3:36:0.0887:0:2.1 -3 197346566 . T G 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGACACTCTAAAAGAAAT;RSEQ=TATTCATTTTTACAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:266,59:0:2,0:22.9:1:30.1:1:1:0:59.4:64:1:0:0.1 0/1:257:30:19,11:173,54:0.1167:2,2:25.5:1:31.8:1:0.17776:1.84991:59.6:60:0.1186:0:1.7 -3 197346770 . G GA 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00359;SOR=2.65693;LSEQ=ATCTCAGAGACTAAAAGAAA;RSEQ=AAAAAAAAAGGGCAAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:13:2,11:72,282:0.0351:2,2:29.8:1:29.8:1:1:1.40306:51.2:26:0.037:0.0054:0.2 0/1:317:28:6,22:72,216:0.0883:2,2:21.6:1:29.6:1:0.82005:1.22146:50.5:56:0.0924:0.0252:0.3 -3 197346781 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09228;SOR=Inf;LSEQ=TAAAAGAAAGAAAAAAAAAG;RSEQ=GCAAGAAGTGTTAAGCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:52,267:0:2,0:24.1:1:30.8:1:1:0:50.1:38.875:1:0:0.2 0/1:264:3:1,2:55,206:0.0114:2,2:6.7:1:27:1:0.51243:1.87:60:6:0.0115:0:1.3 -3 197348431 . A G 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63771;SOR=0.3685;LSEQ=CTCCTGTCACCTCCACAGTC;RSEQ=CTGCATGTGCCCCACACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:4,0:28,1:0.1212:1,0:39:1:29.5:1:1:0:35.8:8:0.1212:0:1.5 0/1:21:1:1,0:18,2:0.0476:2,0:40:0:23:0:1:0:27:2:0.05:0:1 -3 197348473 . T C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52757;SOR=0;LSEQ=GTTCTCTGTTGCTTTTTACG;RSEQ=AATCTCTGGCTGACTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:54,3:0.0339:2,0:14.5:1:34:0:1:0:33.5:4:0.0339:0:2 0/0:35:0:0,0:30,5:0:2,0:23.7:1:29.2:1:1:0:56.4:70:1:0:0.2 -3 197348560 . G A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00222;SOR=Inf;LSEQ=GTGTCCTGTCTCAGGTGGAC;RSEQ=GAGGGCGGCCTTACCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:282,82:0:2,0:22.8:1:30.1:1:1:0:54.3:120.333:1:0:0.7 0/1:265:7:6,1:184,74:0.0264:2,2:18.4:1:30.6:1:0.67699:2.41:60:14:0.0269:0:2.1 -3 197348562 . A G 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00128;SOR=0.54232;LSEQ=GTCCTGTCTCAGGTGGACGG;RSEQ=GGGCGGCCTTACCCTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:107:63,44:220,39:0.2869:2,2:24:1:30.6:1:0:3.92241:42.3:52.5:0.2885:0:2.1 0/1:285:51:29,22:158,49:0.1789:2,2:20.3:1:29.2:1:0.00818:2.43664:43.8:24.5:0.175:0:1.8 -3 197348570 . C G 187 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGGTGGACGGAGGGCGGC;RSEQ=TTACCCTCCCATATGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:77:42,35:288,90:0.1692:2,2:24.9:1:29.9:1:0.00023:2.66029:43.1:37.5:0.1678:0:2.3 0/0:334:0:0,0:227,104:0:2,0:23.7:1:30.5:1:1:0:55.2:109.333:0.9909:0:0.6 -3 197348587 . G A 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCTTACCCTCCCATATGA;RSEQ=GTGTGCAATATTGAGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:560:0:0,0:382,178:0:2,0:25.6:1:31.5:1:1:0:54:61.222:1:0:0.6 0/1:473:17:14,3:297,157:0.0359:2,2:24.4:1:29.7:1:0.19506:2.46:58.4:16:0.0343:0:1.6 -3 197348638 . G A 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCACACAGCAGCACCGATG;RSEQ=GCCTGCCTGCCCTTTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:796:0:0,0:452,343:0:2,0:25.9:1:30.8:1:1:0:53:65.25:0.9987:0:0.3 0/1:765:65:41,24:384,315:0.085:2,2:25:1:29.8:1:0.24052:1.40:50.8:130:0.0874:0:1.2 -3 197348646 . T C 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.00037;SOR=2.42172;LSEQ=GCAGCACCGATGGGCCTGCC;RSEQ=GCCCTTTCCAAACTTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:799:23:5,18:434,341:0.0288:2,2:16.7:1:29.3:1:0.00122:4.57377:41.5:10.5:0.0269:0:1.9 0/1:791:53:18,35:414,324:0.067:2,2:16.6:1:30.5:1:0.00243:2.48174:43.8:106:0.0679:0:1.9 -3 197348668 . C G 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=0.4376;LSEQ=CCCTTTCCAAACTTGAGGCT;RSEQ=TGTCCACCAAATGCACGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:771:87:37,50:351,333:0.1128:2,2:20.3:1:32:1:0.13907:1.42373:38.7:174:0.114:0:1.2 0/1:778:41:16,25:377,360:0.0527:2,2:19.3:1:31.4:1:0.14963:1.63525:36.1:82:0.0532:0:1.7 -3 197348739 . G C 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=5e-04;SOR=Inf;LSEQ=CGGCATGCCATAATTTTCTA;RSEQ=CTGTGAAAGATAAAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:144,318:0:2,0:27.3:1:31.7:1:1:0:49.6:45.2:1:0:0.1 0/1:410:10:3,7:131,268:0.0244:2,2:21:1:29.9:1:1:1.14018:39.2:20:0.0253:0:1.6 -3 197348786 . C A 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTTATTACCTTAAAGGAGT;RSEQ=AAGATATTCACAGCTAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:45,197:0:2,0:23.5:1:32.1:1:1:0:59.5:120:1:0:0 0/1:166:28:5,23:19,119:0.1687:2,2:23.7:1:29.9:1:0.56163:1.36:60:56:0.1697:0:1.1 -3 197349029 . G C 77 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00533;SOR=Inf;LSEQ=TTGTACTAGAAACAGACCAC;RSEQ=AGAGCACCCAGAGCCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:240,95:0:2,0:25.5:1:29.9:1:1:0:49.3:36.222:1:0:0.1 0/1:243:6:0,6:159,78:0.0247:2,0:19.7:1:30:1:0.00151:0:31.7:12:0.0252:0:1 -3 197349042 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACCACGAGAGCACCCAGA;RSEQ=CCTCCCGCCCATCACCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:230,122:0:2,0:27.8:1:31.8:1:1:0:48:43:1:0:0.2 0/1:255:16:9,7:144,95:0.0627:2,2:30.1:1:28.7:1:0.79558:1.17817:51.3:32:0.0637:0:1.9 -3 197349090 . C G 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30801;SOR=4.47456;LSEQ=AGTGGGGGCCTGCTCCGTCA;RSEQ=GTAGTGGATGGCATCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:1:0,1:148,181:0.003:2,0:13:0:26:0:1:0:25:2:0.003:0:2 0/1:223:3:1,2:97,122:0.0135:2,2:16.7:1:29.3:1:1:1.58698:25:6:0.0136:0:2.3 -3 197349091 . G A 133 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=37.50391;LSEQ=GTGGGGGCCTGCTCCGTCAC;RSEQ=TAGTGGATGGCATCCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:1:1,0:145,181:0.0031:2,0:34:0:31:0:0.44648:0:25:2:0.0031:0:1 0/1:222:23:10,13:88,111:0.1036:2,2:23.3:1:29.5:1:1:1.0305:42:46:0.1045:0:1.7 -3 197349104 . T A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06236;SOR=Inf;LSEQ=CCGTCACGTAGTGGATGGCA;RSEQ=CCTGGTCCCCCAGCCAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:127,188:0:2,0:22.6:1:29.6:1:1:0:34.9:27.636:1:0:0.3 0/1:208:3:2,1:84,121:0.0144:2,2:20.3:1:24:1:0.5706:2.87:38:2:0.0098:0:2.7 -3 197349123 . C T 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCCTGGTCCCCCAGCCAGT;RSEQ=GGAGCCCTTCACGGTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:55:13,42:72,154:0.1957:2,2:25.8:1:30.5:1:0.25621:1.50838:33.5:110:0.1971:0:1.1 0/0:161:0:0,0:49,112:0:2,0:24.8:1:29.5:1:1:0:31.9:31.2:1:0:0.3 -3 197349142 . A G 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04752;SOR=Inf;LSEQ=TCGGAGCCCTTCACGGTGTC;RSEQ=TAGAAATGCCACCTCCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:112,175:0:2,0:26.3:1:30.7:1:1:0:29.2:286:1:0:0.3 0/1:164:3:2,1:65,96:0.0183:2,2:31:1:31:1:0.56779:2.93:25.7:6:0.0186:0:1 -3 197349143 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47675;SOR=0.71377;LSEQ=CGGAGCCCTTCACGGTGTCA;RSEQ=AGAAATGCCACCTCCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:26:11,15:103,160:0.09:2,2:26.5:1:32.2:1:0.83421:1.14:25:52:0.0906:0:1.2 0/1:167:11:9,2:60,96:0.0659:2,2:20.8:1:32.4:1:0.00826:7.12:25:22:0.0671:0:1.5 -3 197349298 . A G 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30194;SOR=0;LSEQ=GGGGGATTCAGAGAAAGCCA;RSEQ=CTACTCACATGGTGACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:4:0,4:21,284:0.0129:2,0:35.8:1:34:0:1:0:27:8:0.013:0:1.8 0/0:173:0:0,0:12,161:0:2,0:18.5:1:30.2:1:1:0:28.8:346:1:0:0.5 -3 197349308 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=0;LSEQ=GAGAAAGCCAACTACTCACA;RSEQ=GGTGACTCCCAGTGAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:8,108:0.0169:2,0:35:1:28:1:1:0:25:4:0.0174:0:3.5 0/0:98:0:0,0:6,92:0:2,0:21.7:1:29.6:1:1:0:30.2:48:1:0:0.7 -3 197349309 . G A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=36.86486;LSEQ=AGAAAGCCAACTACTCACAT;RSEQ=GTGACTCCCAGTGAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:1:0,1:7,105:0.0088:2,0:45:0:33:0:1:0:25:2:0.0092:0:1 0/1:96:24:2,22:4,68:0.25:2,2:20.1:1:30.8:1:0.63778:1.54:29.9:48:0.25:0:1.5 -3 197349339 . G A 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.77042;SOR=0.82807;LSEQ=AGTGAGGGCTGACCTCAGCA;RSEQ=AGGAGCAGCCAGGCCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:48:2,46:0,7:0.8727:0,1:22.9:1:31.2:1:1:0:29.9:96:0.8889:0:1.1 1/1:40:34:0,34:0,6:0.85:0,1:23.5:1:30.6:1:1:0:29.6:68:0.85:0:1.4 -3 197350071 . G A 57 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.55454;LSEQ=CTGCACGGAGTGGGAGCACA;RSEQ=TGGGGCACCTTTCTCTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:13,0:0.2353:1,0:20:1:28.8:1:1:0:25:8:0.2353:0:1 0/1:7:1:1,0:6,0:0.1429:0,0:23:0:25:0:1:0:25:2:0.1429:0:1 -3 197350172 . T C 230 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38734;SOR=1.16197;LSEQ=TCTGCCTCGGAAAGGCCAAA;RSEQ=GCAGCTCGCAAAGCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:140:134,6:355,10:0.2772:1,1:28.6:1:32.3:1:0.39839:1.58796:25:45.667:0.2729:0:1.2 0/1:240:74:73,1:161,5:0.3083:1,1:28.1:1:31.7:1:0.66936:2.26:25:148:0.3122:0:1.3 -3 197350256 . G T 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.32529;LSEQ=TGGATACTGAGCAGAAATCT;RSEQ=GAAAAGAAAAATTCACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:716:86:31,55:218,410:0.1201:2,2:26.8:1:29.5:1:0.81022:1.06:24.9:42:0.1197:0:1.4 0/1:365:88:28,60:88,188:0.2411:2,2:26.9:1:28.9:1:1:1.00303:24.8:43:0.2382:0:1.2 -3 197350322 . T C 64 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02252;SOR=10.68404;LSEQ=CATGAAGACTCTTGTGCCAG;RSEQ=GAAAGAGCTTGACAAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:0,1:0,252:0.0039:1,0:48:0:8:0:1:0:25:0:0:0:3 0/1:98:4:0,4:0,93:0.0408:1,0:19.8:1:32:0:1:0:25:8:0.0408:0:1 -3 197350815 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13289;SOR=Inf;LSEQ=TTAACATCTATGTTTATATT;RSEQ=GTACTTGCAATTAAGTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:26,1:0:1,0:25.4:1:32.4:1:1:0:36.7:26:1:0:0.1 0/1:16:2:2,0:14,0:0.125:1,0:42.5:1:32:0:1:0:25:4:0.1333:0:1 -3 197351126 . C T 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00033;SOR=Inf;LSEQ=TCCTGAAGGAACAAATGCTG;RSEQ=GGGGGATAGTAATTCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:78,263:0:2,0:24.9:1:30.4:1:1:0:38.3:169.5:1:0:0.1 0/1:242:9:0,9:56,177:0.0372:2,0:18.6:1:30.8:1:0.12242:0:26.2:18:0.0373:0:1.2 -3 197354616 . CG A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49527;SOR=Inf;LSEQ=CCTACCGCCGCCTCGTCCCC;RSEQ=CCTGCCCTGCCCCGGTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:40,6:0:2,0:18.2:1:31.9:1:1:0:59.8:92:0.9787:0:0.2 0/1:50:2:1,1:41,7:0.04:2,2:17:1:32.6:1:0.29714:5.54533:60:4:0.0408:0:0 -3 197354659 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49997;SOR=0;LSEQ=GCAGGGACTCACAGCCTTGG;RSEQ=CAGCGCCAGCGCCAGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:126,64:0.0103:2,2:23:1:29.5:1:1:1.96135:60:4:0.0104:0:1 0/0:175:0:0,0:106,69:0:2,0:23:1:31.2:1:1:0:60:174:1:0:0.2 -3 197354663 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=1.08128;LSEQ=GGACTCACAGCCTTGGCCAG;RSEQ=GCCAGCGCCAGGCGCCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:131,68:0.01:2,2:8.5:1:29.5:1:1:1.91981:60:4:0.0102:0:1 0/1:186:2:1,1:111,73:0.0108:2,2:33:1:28:1:1:1.51698:60:4:0.0108:0:1 -3 197354669 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.21575;SOR=Inf;LSEQ=ACAGCCTTGGCCAGCGCCAG;RSEQ=GCCAGGCGCCGAGCGCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:144,85:0:2,0:26.5:1:30.8:1:1:0:59.9:44.8:1:0:0.2 0/1:200:2:1,1:114,84:0.01:2,2:20:1:28:1:1:1.35502:60:4:0.0101:0:1 -3 197354729 . C A 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33056;SOR=3.70722;LSEQ=ACCCCCGATACGTCTGCAGT;RSEQ=GCCTCCGCGCAGTCCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:1,0:112,142:0.0039:2,0:1:0:28:0:0.44314:0:60:2:0.004:0:1 0/1:208:3:2,1:90,115:0.0144:2,2:10.7:1:26:1:0.58489:2.54:60:6:0.0149:0:1.3 -3 197354758 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51842;SOR=0;LSEQ=GCAGTCCCGCCAGTCCCTGC;RSEQ=CAGACTGCGCCTGCGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:62,119:0.0109:2,2:21.5:1:29:1:1:1.91:52:4:0.0111:0:2 0/0:122:0:0,0:43,78:0:2,0:24.3:1:29.9:1:1:0:58:23.2:0.9915:0:0.2 -3 197354759 . C A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78511;LSEQ=CAGTCCCGCCAGTCCCTGCG;RSEQ=AGACTGCGCCTGCGCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:62,120:0.0109:2,2:18:1:28:1:1:1.93:54.5:4:0.011:0:1 0/0:117:1:1,0:41,75:0.0085:2,0:1:0:23:0:0.35897:0:60:2:0.0087:0:1 -3 197354771 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50792;SOR=0;LSEQ=TCCCTGCGCAGACTGCGCCT;RSEQ=CGCACCACGGCCGGGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:36,95:0.015:2,2:21.5:1:31:1:0.48052:2.62:52:4:0.015:0:2 0/0:100:0:0,0:33,67:0:2,0:22.9:1:31.2:1:1:0:57.6:99:1:0:0.2 -3 197354777 . C A 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.65786;SOR=1.88609;LSEQ=CGCAGACTGCGCCTGCGCAC;RSEQ=ACGGCCGGGTCAAGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:24,87:0.0177:2,2:12.5:1:31.5:1:0.39507:3.57:60:4:0.018:0:2.5 0/1:91:3:1,2:24,64:0.033:2,2:13:1:27.7:1:1:1.33:49.3:6:0.0333:0:3 -3 197354781 . G C 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66051;SOR=1.82334;LSEQ=GACTGCGCCTGCGCACCACG;RSEQ=CCGGGTCAAGGCGGGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:20,80:0.0196:2,2:6.5:1:31.5:1:0.371:3.93:42:4:0.02:0:3 0/1:85:3:1,2:23,59:0.0353:2,2:17:1:28.3:1:1:1.28:49.3:6:0.0361:0:3 -3 197354792 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50816;SOR=0;LSEQ=CGCACCACGGCCGGGTCAAG;RSEQ=CGGGGCGCTAGTGGGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:14,63:0.0253:2,2:12:1:29.5:1:0.34567:4.38:60:4:0.0253:0:3 0/0:58:0:0,0:10,48:0:2,0:25.3:1:30.7:1:1:0:55.2:18.333:1:0:0.3 -3 197354857 . C A 91 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04718;SOR=6.18053;LSEQ=CCGGGCCGGGGTCTAAGGGG;RSEQ=GGGGACGCCGCGCCTGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:2,7:0.25:2,2:24:1:32.3:1:1:1.66:48:6:0.25:0:2.7 1/0:13:9:4,5:0,4:0.6923:0,2:25.2:1:28.9:1:0.22797:0:54.2:18:0.6923:0:2.1 -3 197354909 . C A 51 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=CGGACGGTGGCGCTGGGTGG;RSEQ=CACGGAGGTCCCGCGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:17.3:1:31.3:1:1:0:60:6:1:0:0 1/1:4:4:2,2:0,0:1:0,2:21:1:25.8:1:1:0:55:3:1:0:2 -4 897403 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCGTGGGATGAGCAGGA;RSEQ=TGCGGGGCCTGAACTGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 899168 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACGGTTAACATCATCAC;RSEQ=GTGGAGCAATCAGTGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:26:1:32:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 899265 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=1.41488;LSEQ=CTCCGCCACGCCCCATGCCA;RSEQ=GCTACGGACTCCGCCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:21:11,10:1,2:0.875:2,2:29.5:1:31.2:1:1:2.13:57.2:42:0.875:0:1.2 1/1:11:10:7,3:1,0:0.9091:0,2:23:1:29.7:1:1:0:60:20:0.9091:0:1.4 -4 899352 . T C 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66685;SOR=0.48195;LSEQ=CTCCGCCACGCCCCAGGCCA;RSEQ=GCTACGGACTTCGCCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:2,5:0.4167:2,2:11.4:1:31.6:1:1:1.53983:55.4:10:0.4167:0:1.6 0/1:12:3:1,2:4,4:0.25:2,2:9.3:1:32:1:1:1.87936:60:6:0.25:0:1.7 -4 1402372 . A G 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GCACACCAGACACTTTCCAG;RSEQ=TTGCTGCGCCCCCTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:17.3:1:27.8:1:1:0:60:3:0.5:0:1.3 0/0:2:0:0,0:2,0:0:0,0:12.5:1:30.5:1:1:0:60:4:1:0:0 -4 1402580 . T C 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.85985;LSEQ=CCACCCTGCCGGGTCCCAGA;RSEQ=AGTTGGAACACCTGCGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:38:25,13:131,58:0.1674:2,2:22:1:31.9:1:0.70307:1.17362:60:76:0.1704:0:1.1 0/1:175:64:40,24:75,36:0.3657:2,2:25.1:1:31:1:0.51239:1.24837:60:128:0.3699:0:1.1 -4 1402650 . A T 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=0.45677;LSEQ=CTCTTAGTACAACTTTCAAA;RSEQ=CGAACACAATCACATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:69:36,33:182,159:0.1679:2,2:26.2:1:29.3:1:0.89517:1.04917:60:12.8:0.16:0:1.1 0/1:344:29:13,16:155,160:0.0843:2,2:23.6:1:29.2:1:0.70102:1.1917:60:58:0.085:0:1.1 -4 1781058 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGTCCCCGGGCTGGCGG;RSEQ=TGACATGAGGCACAAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:28.5:1:1:0:60:4:1:0:1 -4 1795557 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTGCCTTCCTCCTCCTG;RSEQ=AGTCTCCCGAGCGGCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 1795701 . G T 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.077;SOR=0;LSEQ=CCCTCGCGCTCTGCGTGGCC;RSEQ=TGGCCATCGTGGCCGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:5:2,3:257,111:0.0134:2,2:21.8:1:28.2:1:0.16919:3.45983:60:10:0.0139:0:1 0/0:272:0:0,0:180,92:0:2,0:23.8:1:29.9:1:1:0:60:53.4:1:0:0.2 -4 1795719 . G A 78 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.04255;SOR=0;LSEQ=CCGTGGCCATCGTGGCCGGC;RSEQ=CCTCCTCGGAGTCCTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:6:3,3:336,157:0.012:2,2:20.5:1:30.2:1:0.39093:2.13659:60:12:0.0124:0:1.2 0/0:364:0:0,0:231,131:0:2,0:27.7:1:29.9:1:1:0:60:50.714:0.9972:0:0.2 -4 1795762 . G A 175 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01973;LSEQ=GGAGCAGCGCGTCGTGGGGC;RSEQ=AGCGGCAGGTAAGAAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:65:37,28:394,281:0.0878:2,2:27:1:29.1:1:0.89537:1.06098:60:20.667:0.0854:0:1.2 0/0:528:1:1,0:277,250:0.0019:2,0:1:0:27:0:1:0:60:2:0.002:0:1 -4 1795924 . G A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55417;SOR=0;LSEQ=CCTCCTTGCCGGAGAGCGCG;RSEQ=CCAGAGCTAGCGCGGCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:1,2:4,53:0.05:2,2:38.3:1:30.3:1:0.23334:6.24:60:6:0.05:0:1 0/0:24:0:0,0:1,23:0:1,0:28.6:1:32.8:1:1:0:60:48:1:0:0.1 -4 1801148 . C T 87 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00526;SOR=11.2032;LSEQ=GTGTCCTGGTGGGGCCCCAG;RSEQ=GGCTGCAGGTGCTGAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:862:1:0,1:398,463:0.0012:2,0:1:0:26:0:1:0:60:2:0.0012:0:1 0/1:622:8:3,5:288,326:0.0129:2,2:12.8:1:29.1:1:0.72936:1.47149:60:16:0.0131:0:1.1 -4 1801259 . T C 39 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04396;SOR=Inf;LSEQ=TGCGGGTGACAGGTGAGCTC;RSEQ=GGGGCCACGCCAGCTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:161,312:0:2,0:25.2:1:30.4:1:1:0:60:58.125:1:0:0.1 0/1:259:3:2,1:90,165:0.0116:2,2:14.3:1:25:1:0.29001:3.65:60:2:0.0079:0:3.3 -4 1801278 . G A 34 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04145;SOR=Inf;LSEQ=CTGGGGCCACGCCAGCTACA;RSEQ=AAAGGAGCCGAGTGCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:121,255:0:2,0:25.6:1:31.6:1:1:0:60:124.333:1:0:0.1 0/1:200:3:3,0:69,128:0.015:2,0:14.7:1:22:1:0.04541:0:60:2:0.0103:0:2 -4 1801286 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01029;SOR=Inf;LSEQ=ACGCCAGCTACAGAAAGGAG;RSEQ=CGAGTGCCGGGCTCCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:119,233:0:2,0:24.4:1:31.1:1:1:0:60:34.2:1:0:0.1 0/1:166:4:2,2:56,105:0.0241:2,2:33.8:1:23.8:1:0.61333:1.87:60:3:0.0184:0:3 -4 1801295 . G A 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2332;SOR=4.40389;LSEQ=ACAGAAAGGAGCCGAGTGCC;RSEQ=GGCTCCCTGAGTCCCTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:1:1,0:117,186:0.0033:2,0:1:0:27:0:0.38816:0:60:2:0.0033:0:1 0/1:140:2:1,1:45,93:0.0143:2,2:17:0:32.5:1:0.55077:2.06:60:4:0.0145:0:1.5 -4 1801363 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08481;SOR=Inf;LSEQ=GGTCATTGGTGGAGAGGAGG;RSEQ=CACCCCCAGGAAGTGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:158,71:0:2,0:25.6:1:31.1:1:1:0:60:24.444:0.9955:0:0.1 0/1:95:2:1,1:70,23:0.0211:2,2:26.5:1:27.5:1:0.44345:3.0006:60:4:0.0215:0:1 -4 1801408 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09649;SOR=Inf;LSEQ=TGGGGGACCCTGCCCCATCT;RSEQ=GGAGGGGCACCTGGGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:295,130:0:2,0:22:1:31.5:1:1:0:60:59.714:1:0:0.1 0/1:192:2:1,1:142,48:0.0104:2,2:26:1:30:1:0.44628:2.93815:60:4:0.0106:0:2 -4 1801511 . C T 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=39.60693;LSEQ=GATGACGAAGACGGGGAGGA;RSEQ=GAGGCTGAGGACACAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1199:1:0,1:610,588:8e-04:2,0:1:0:29:0:0.49124:0:60:2:8e-04:0:1 0/1:749:24:14,10:368,356:0.032:2,2:30.3:1:29.6:1:0.53689:1.35:60:48:0.0328:0:1.2 -4 1803000 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1296;SOR=Inf;LSEQ=CAGGACGGGAAACTGAGGCT;RSEQ=GGGATGGGCAGGGGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:171,29:0:2,0:21.9:1:31.7:1:1:0:60:65.667:1:0:0.2 0/1:113:2:1,1:89,22:0.0177:2,2:26:1:29:1:0.3671:3.9787:60:4:0.0179:0:2 -4 1803013 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14123;SOR=Inf;LSEQ=TGAGGCTGGGGATGGGCAGG;RSEQ=GCAGCTCTGGGAAGGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:193,47:0:2,0:22.4:1:30.6:1:1:0:60:25.667:1:0:0.2 0/1:145:2:1,1:106,37:0.0138:2,2:6.5:1:29:1:0.4568:2.84022:60:4:0.0144:0:1 -4 1803024 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1454;SOR=Inf;LSEQ=ATGGGCAGGGGCAGCTCTGG;RSEQ=AAGGGGGTTGTTCAGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:219,68:0:2,0:22.9:1:30.8:1:1:0:60:40:0.9964:0:0.2 0/1:178:2:1,1:121,54:0.0112:2,2:26:1:27:1:0.52613:2.22947:60:4:0.0114:0:1 -4 1803044 . G A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00145;SOR=Inf;LSEQ=GAAGGGGGTTGTTCAGAGGG;RSEQ=CCTCTGCTCCCACTCGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:273,139:0:2,0:23.8:1:30.9:1:1:0:60:33.333:0.9975:0:0.2 0/1:271:7:4,3:165,98:0.0258:2,2:23.9:1:26.6:1:1:1.26162:60:14:0.0263:0:1.4 -4 1803051 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4419;SOR=2.07852;LSEQ=GTTGTTCAGAGGGGCCTCTG;RSEQ=TCCCACTCGGGTCATGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:3:2,1:302,162:0.0064:2,2:11:1:30.3:1:1:1.07:60:6:0.0066:0:1 0/1:302:4:2,2:185,113:0.0132:2,2:23.5:1:28.5:1:0.63699:1.63433:60:8:0.0135:0:1 -4 1803307 . T C 183 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCTGGCAGGCGCGGTGGT;RSEQ=GCTGCCTCCGCTCACTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:0:0,0:389,332:0:2,0:23.4:1:29.9:1:1:0:60:89.125:1:0:0.1 0/1:424:72:43,29:190,162:0.1698:2,2:24.1:1:29.7:1:0.43573:1.26:60:71:0.169:0:1.2 -4 1803457 . G A 68 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13582;SOR=2.54683;LSEQ=AGCATCCGGCAGACGTACAC;RSEQ=CTGGACGTGCTGGGTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1000:4:3,1:452,543:0.004:2,2:19:1:27.3:1:0.33588:3.60:60:8:0.0041:0:1.3 0/1:691:7:4,3:312,372:0.0101:2,2:25.6:1:24.4:1:0.70823:1.59:60:2.5:0.0073:0:1.4 -4 1803704 . T C 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAAGCACGTGGAGGTGAA;RSEQ=GGCAGCAAGGTGGGCCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1453:0:0,0:665,787:0:2,0:25.1:1:30.5:1:1:0:60:131:0.9993:0:0.2 0/1:1003:70:34,36:435,496:0.0698:2,2:27.4:1:30.4:1:0.80447:1.08:60:140:0.0705:0:1.3 -4 1803763 . G A 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0534;SOR=3.70299;LSEQ=CGTGCTCAAGGTGGGCCACC;RSEQ=TGTGCACGTGGGTGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:664:3:3,0:196,464:0.0045:2,0:1:0:26:1:0.02676:0:60:6:0.0046:0:1 0/1:423:7:6,1:141,275:0.0165:2,2:14.9:1:27:1:0.00818:11.64:60:14:0.0166:0:1.1 -4 1803801 . G A 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25794;SOR=4.03602;LSEQ=CCGCTGGGGCTCCTGGGCTG;RSEQ=CCCCAAGGGTGCCCCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:1:0,1:32,304:0.003:2,0:10:0:31:0:1:0:60:2:0.003:0:1 0/1:168:2:1,1:24,142:0.0119:2,2:15:1:25:1:0.27623:5.82:60:4:0.012:0:1 -4 1803810 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.10856;SOR=Inf;LSEQ=CTCCTGGGCTGGCCCCAAGG;RSEQ=TGCCCCTTGGCTGCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:20,270:0:2,0:24.5:1:32.2:1:1:0:60:289:1:0:0.1 0/1:143:2:1,1:14,127:0.014:2,2:11:1:26.5:1:0.19945:8.80:60:4:0.014:0:1 -4 1803824 . C G 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0032;SOR=Inf;LSEQ=CCAAGGGTGCCCCTTGGCTG;RSEQ=GGGTTGCGTGAGGATTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:7,217:0:1,0:25.2:1:29.5:1:1:0:60:27:1:0:0.1 0/1:106:5:0,5:1,100:0.0472:1,0:11.8:1:30:1:1:0:60:10:0.0476:0:1.2 -4 1804377 . G A 102 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CCTCGGGCCCTGTCCAGGGT;RSEQ=CAGGTTCTGCAAGAGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:10,2:0,0:1:0,2:24.3:1:28.7:1:1:0:60:24:1:0:1 1/0:2:1:1,0:1,0:0.5:0,0:4:0:30:0:1:0:60:2:0.5:0:2 -4 1804846 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.29988;SOR=3.52186;LSEQ=GCTCCAGCTCCAAGGCCCTG;RSEQ=CCGCGCGCCCTGCACGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:1,0:43,266:0.0032:2,0:1:0:24:0:0.14194:0:60:2:0.0033:0:1 0/1:177:2:1,1:37,138:0.0113:2,2:13:1:28:1:0.38424:3.69:60:4:0.0114:0:1 -4 1804862 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25999;SOR=4.02019;LSEQ=CCTGGCCGCGCGCCCTGCAC;RSEQ=CCCCGCACGCCCAGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:1,0:16,183:0.005:2,0:1:0:26:0:0.085:0:60:2:0.005:0:1 0/1:101:2:1,1:13,86:0.0198:2,2:12.5:1:30:1:0.25921:6.41:60:4:0.02:0:1 -4 1805279 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10924;SOR=Inf;LSEQ=GAGGGCCCTCAGCCGCGTGG;RSEQ=GGTGACCAAGTTGGCGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:79,1:0:1,0:22:1:32.5:1:1:0:60:160:1:0:1.1 0/1:40:2:1,1:35,2:0.05:2,2:26:0:32:0:0.1498:14.49018:60:4:0.0526:0:2.5 -4 1805296 . G A 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01265;SOR=0;LSEQ=TGGCGGTGACCAAGTTGGCG;RSEQ=TGGCTGAGGAGTTGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:104:104:103,1:0,0:1:0,1:25.2:1:29.1:1:1:0:60:12:1:0:1.1 1/1:54:50:47,3:3,0:0.9259:0,2:22.4:1:28.7:1:1:0:60:11.5:0.9388:0:1.3 -4 1805573 . TCTG T 97 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.05268;SOR=3.13066;LSEQ=GGTGCTGCCAGGTACCGGCT;RSEQ=CTGCTGCTGCTGCTCCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:4:1,3:209,446:0.0061:2,2:21:1:30.9:1:1:1.40518:60:8:0.0061:0.0015:0 0/1:480:9:1,8:172,299:0.0188:2,2:29.8:1:30.9:1:0.16627:4.59132:60:18:0.019:0.0021:0 -4 1806012 . T TG 190 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.90868;SOR=0.94504;LSEQ=GGGCATCCATGGGAGCCCCG;RSEQ=GGGGGGGGGGGCCAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:67:60,7:388,74:0.122:2,2:25.8:1:31.4:1:0.27942:1.63:60:21.333:0.1311:0.0219:1.1 0/1:267:31:26,5:174,52:0.1161:2,2:27.9:1:29.9:1:0.49277:1.55:58.6:62:0.1314:0.0375:0.8 -4 1806024 . C G 70 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27762;SOR=0.27594;LSEQ=GAGCCCCGTGGGGGGGGGGG;RSEQ=CAGGCCAGGCCTCAACGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:694:7:5,2:518,168:0.0101:2,2:15.7:1:25:1:0.68222:1.23296:60:2.5:0.0077:0:1.9 0/0:357:1:1,0:249,106:0.0028:2,0:12:0:28:0:1:0:60:2:0.0029:0:3 -4 1806028 . G T 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19197;SOR=3.72601;LSEQ=CCCGTGGGGGGGGGGGCCAG;RSEQ=CCAGGCCTCAACGCCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:722:2:2,0:522,194:0.0028:2,0:29:1:12:0:1:0:60:0:0:0:3 0/1:390:4:1,3:263,123:0.0103:2,2:21.8:1:26.5:1:0.10108:6.38191:60:8:0.0111:0:1.3 -4 1806478 . G A 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02554;SOR=Inf;LSEQ=ACGCCCCCCCTTCTGGCCCA;RSEQ=CACTGACCCCCGGCTGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:285,36:0:2,0:25.8:1:31.7:1:1:0:60:21.929:1:0:0.3 0/1:135:3:2,1:114,18:0.0222:2,2:7:1:23.3:1:0.36792:3.12836:60:2:0.0153:0:1 -4 1806519 . C T 182 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00059;SOR=0.41597;LSEQ=TCCACGCCCTGTCGCCCACG;RSEQ=GGCGCCAACCTGCCCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:73:48,25:375,127:0.1267:2,2:24.2:1:29.5:1:0.11827:1.53666:60:35.5:0.1259:0:1.1 0/1:334:19:13,6:213,101:0.0569:2,2:26.3:1:28.9:1:1:1.03:60:18:0.0557:0:1.2 -4 1806725 . T A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28279;SOR=2.43484;LSEQ=TGCTGAGGGCCAGCGTTGGC;RSEQ=GTAGGGGGCTTGGTGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:696:3:3,0:222,470:0.0043:2,0:3.3:1:22.7:1:0.03362:0:60:2:0.003:0:1 0/1:479:5:4,1:159,314:0.0104:2,2:10:1:24.8:1:0.04827:7.86:60:4:0.0087:0:1.2 -4 1806834 . G C 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGGCTGGGGTTCTGTGGA;RSEQ=ATGCTCCTGGGACGGGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:11,95:0,0:1:0,2:24.9:1:32.6:1:1:0:60:105:1:0:1.1 1/1:48:48:7,41:0,0:1:0,2:21.6:1:32.5:1:1:0:60:96:1:0:1.1 -4 1806937 . C T 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00113;SOR=0;LSEQ=GGTGACACTCTTCGTCCTTA;RSEQ=GAGCAGGCTGTAGGGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:22:19,3:77,9:0.2018:2,2:23:1:31.1:1:0.70669:1.34686:60:21:0.2:0:1.4 0/0:37:0:0,0:30,7:0:2,0:19.3:1:31:1:1:0:60:17.5:1:0:0.3 -4 1806989 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10897;SOR=Inf;LSEQ=CCTGGAGGTGGTGGCTCTGG;RSEQ=CCTCAAGGGCTGGGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:184,24:0:2,0:25:1:31:1:1:0:60:40.6:1:0:0.2 0/1:103:2:1,1:80,21:0.0194:2,2:8:1:27.5:1:0.38321:3.74522:60:4:0.0198:0:1 -4 1807008 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10591;SOR=Inf;LSEQ=GGCCTCAAGGGCTGGGCCAG;RSEQ=CTGGGGTGGGGACCGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:229,56:0:2,0:23.5:1:31.1:1:1:0:60:56:1:0:0.2 0/1:138:2:1,1:104,32:0.0145:2,2:18:0:28:1:0.42241:3.21572:60:4:0.0148:0:1.5 -4 1807244 . GCGC G 100 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09954;SOR=0.17836;LSEQ=GGTGCAGAGCAGGGCTGGGG;RSEQ=CGCCGCCGCCTGACACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:745:9:4,5:377,358:0.0121:2,2:23.1:1:31.8:1:0.74712:1.31585:60:18:0.0123:0.0027:0.1 0/0:460:1:1,0:249,208:0.0022:2,0:14:0:34:0:1:0:60:2:0.0022:0:0 -4 1807347 . C T 145 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=9.38243;LSEQ=ATGGAGATGATGAAGATGAT;RSEQ=GGGAAACACAAAAACATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1162:4:0,4:556,601:0.0034:2,0:1:0:26.5:1:0.12569:0:60:8:0.0035:0:1 0/1:923:29:14,15:427,466:0.0314:2,2:21.2:1:30:1:1:1.02:60:58:0.0318:0:1.2 -4 1807478 . G T 120 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=30.10155;LSEQ=GAGGAGCCCGTGTCCCCAGG;RSEQ=CCCCTGTACGTGCTGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1042:1:0,1:546,495:0.001:2,0:1:0:26:0:0.47601:0:60:2:0.001:0:1 0/1:604:17:8,9:308,279:0.0281:2,2:20.1:1:29.5:1:0.80651:1.24149:60:34:0.029:0:1.3 -4 1807894 . G A 296 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGACTACTACAAGAAGAC;RSEQ=ACCAACGTGAGCCCGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:976:975:461,514:0,0:0.999:0,2:24.5:1:29.9:1:1:0:60:64:0.999:0:1.1 1/1:629:629:282,347:0,0:1:0,2:23.7:1:29.7:1:1:0:60:103.833:1:0:1.2 -4 1807995 . C T 82 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04067;SOR=4.84814;LSEQ=CCCTCCCAGGGCCGGCTGCC;RSEQ=GTGAAGTGGATGGCGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:924:2:0,2:444,478:0.0022:2,0:1:0:27.5:1:0.50022:0:60:4:0.0022:0:1 0/1:672:7:2,5:327,336:0.0104:2,2:17.6:1:29.3:1:0.45119:2.43018:60:14:0.0105:0:1.1 -4 1808427 . G A 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24956;SOR=2.47141;LSEQ=ACCTGTGAGTGGCATCCCTG;RSEQ=CCCTCCACTGGGTCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:3:2,1:281,411:0.0043:2,2:12.3:1:27.7:1:0.5699:2.92:60:6:0.0044:0:1 0/1:377:4:3,1:143,229:0.0106:2,2:9.3:1:25.8:1:0.30333:4.78:60:8:0.0108:0:1 -4 1808438 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03451;SOR=Inf;LSEQ=GCATCCCTGGCCCTCCACTG;RSEQ=GTCCTCAGGGGTGGGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:248,361:0:2,0:24.1:1:30.9:1:1:0:60:59.9:1:0:0.1 0/1:295:3:2,1:110,182:0.0102:2,2:10:1:29:1:0.55962:3.30:60:6:0.0104:0:1 -4 1809127 . CGTGT C 122 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=9.000;MSILEN=2;SSF=0.00708;SOR=0;LSEQ=GGTCTGTGTGTGTGTGTGTG;RSEQ=GTGTGTGTGTGTGTGCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:14:1,13:1,20:0.2857:1,1:32.4:1:32.1:1:1:1.52:60:28:0.2917:0.0612:0 0/0:19:0:0,0:0,12:0:0,0:12.4:1:30.6:1:1:0:60:11:0.6111:0:1.3 -4 1809787 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAGCAGAGGACCAGGGC;RSEQ=TTTTCTGGCACCGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 1999836 . C CAAT 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.02601;SOR=Inf;LSEQ=AACAGCATCAACAACAACAA;RSEQ=AACAACCACAACAAAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:22.5:1:32.1:1:1:0:60:22:1:0:0.1 0/1:9:4:2,2:4,1:0.4444:2,2:12:1:28.1:1:0.52381:3.38757:60:8:0.4444:0.3333:0.8 -4 3715974 . C CTG 33 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=1.42272;LSEQ=TGTGGGGTGTATGTGTGTGT;RSEQ=TGTGTGTGTGTGCATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:21,29:0.0385:2,2:46.5:1:31.3:1:1:1.37:60:4:0.0385:0:0 0/1:37:2:1,1:18,16:0.0541:2,2:11:0:33:1:1:1.12132:60:4:0.0541:0:0.5 -4 3716031 . T A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.54386;SOR=Inf;LSEQ=CTGTGGAGGGTATGTGTGTG;RSEQ=GCATATGTGCGATGTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:0:2,0:17:1:31.2:1:1:0:60:26:1:0:0.1 0/1:26:2:1,1:9,15:0.0769:2,2:5:0:29:1:1:1.63:60:4:0.0769:0:0 -4 3716037 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52941;SOR=Inf;LSEQ=AGGGTATGTGTGTGTGCATA;RSEQ=GTGCGATGTGTGGATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:0:2,0:13:1:30.7:1:1:0:60:24:1:0:0.1 0/1:22:2:1,1:8,12:0.0909:2,2:26.5:1:32:1:1:1.47:60:4:0.0909:0:1.5 -4 3753097 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CAAACATGAGCCCAGAGCCC;RSEQ=GGCCCCTGCTGCCACGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:29.3:1:29.3:1:1:0:60:8:1:0:0.3 1/0:4:2:0,2:0,2:0.5:0,0:20:1:28.5:1:1:0:60:4:0.5:0:1.5 -4 4763704 . G A 46 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20635;SOR=0.11969;LSEQ=TGCCAGCGAGGAGCCTTAGA;RSEQ=CAAGTGACTTAACCTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:36.3:1:29.3:1:1:0:60:6:0.75:0:1 0/1:5:1:0,1:0,4:0.2:0,0:36:0:31:0:1:0:60:2:0.2:0:1 -4 4763850 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTTACCTTAGCGTAAACA;RSEQ=ATAAGAGAGCGAAAAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:28.3:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 4807909 . T A 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12898;SOR=Inf;LSEQ=CAGTCAGCGTTCCAGTGGAG;RSEQ=GTGGTTCCTGCAGGTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:31.8:1:30.8:1:1:0:60:52:1:0:0.1 0/1:35:4:2,2:14,16:0.1143:2,2:9.5:1:29.5:1:1:1.14:60:8:0.125:0:1.5 -4 4808990 . G A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGGGGGTCCATGTGGCC;RSEQ=GTGCTGCTGCCCAGGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 4809712 . G A 30 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGACAGCTCATGCAAACCCA;RSEQ=GCTAACCAGGCCTACAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:0:30:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:8.5:1:30.5:1:1:0:60:4:1:0:0 -4 4998256 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCCAGTTTTGTCCTAAT;RSEQ=CTCTCCCTCCCCTTGCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:0.1667:2,2:15:0:30.5:1:1:2.16:60:4:0.1818:0:1 0/0:4:0:0,0:2,2:0:2,0:24.3:1:31:1:1:0:60:8:1:0:0 -4 5812778 . G A 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTAGTTTAAGACCAGTC;RSEQ=GTGGGACAAGACCTGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:21.3:1:31.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 6113431 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15293;SOR=Inf;LSEQ=GCTCCTCCCCTCTGTGACAG;RSEQ=CCGTGCTTTAATTAGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:94,21:0:2,0:24.5:1:31.5:1:1:0:60:37.333:0.9912:0:0.2 0/1:75:2:1,1:54,19:0.0267:2,2:18:1:31.5:1:0.46486:2.79567:60:4:0.027:0:1 -4 6113451 . C G 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=CCCGTGCTTTAATTAGACTG;RSEQ=CAGCACCCAACCAGGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:18:14,4:111,43:0.1047:2,2:22.2:1:31.2:1:0.78233:1.35:60:36:0.1078:0:1 0/0:128:0:0,0:85,42:0:2,0:24.3:1:31.6:1:1:0:60:254:1:0:0.1 -4 6113559 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26764;LSEQ=GCTCTGTTCCAAGCTCTTTA;RSEQ=CTAGCAGAGCCCTGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:317:177:78,99:69,71:0.5584:2,2:25.5:1:29.8:1:0.36647:1.23265:60:43.25:0.5599:0:1.2 0/1:313:79:40,39:116,118:0.2524:2,2:25.2:1:29.1:1:0.89701:1.04:60:78:0.2541:0:1.1 -4 6113563 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02613;SOR=Inf;LSEQ=TGTTCCAAGCTCTTTACCTA;RSEQ=CAGAGCCCTGAGTCCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:145,179:0:2,0:25.1:1:31.8:1:1:0:60:80:1:0:0.7 0/1:304:5:2,3:145,154:0.0164:2,2:13.4:1:29.4:1:1:1.41075:60:10:0.0168:0:1.2 -4 6113578 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11106;SOR=Inf;LSEQ=ACCTAGCAGAGCCCTGAGTC;RSEQ=AGACCACAGCCCCATCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:134,174:0:2,0:26.7:1:31.2:1:1:0:60:43:0.9967:0:0.6 0/1:287:3:1,2:125,159:0.0105:2,2:16:1:29.3:1:1:1.56995:60:6:0.0105:0:1 -4 6113869 . T C 57 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCATGCATGAGTTCCTATA;RSEQ=GATGAACTGCAACCTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:16.3:1:28.8:1:1:0:60:8:1:0:1 1/1:1:1:0,1:0,0:1:0,0:20:0:32:0:1:0:60:2:1:0:1 -4 6141497 . TATAAA T 83 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=6.000;MSILEN=5;SSF=0.18333;SOR=0.11844;LSEQ=AGTGAGACTCCATCTCAAAA;RSEQ=ATAAAATAAAATAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:29:1:32.2:1:1:0:60:12:0.8571:0.2857:0.3 0/1:3:1:1,0:2,0:0.3333:0,0:45:0:32:0:1:0:60:2:0.3333:0:0 -4 6141538 . G T 78 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0068;SOR=17.95587;LSEQ=ATAAAATAAAATAAGGAAAT;RSEQ=GGAGCACAGAGACACAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:14,0:0.0667:1,0:35:0:31:0:1:0:60:2:0.0667:0:1 1/0:10:6:6,0:4,0:0.6:0,0:23:1:30.5:1:1:0:60:12:0.6:0:1 -4 6141611 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50241;SOR=0;LSEQ=AGGTCACGGGGCAGATTCCA;RSEQ=GAGCCAAGGAATACCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:18,22:0.0476:2,2:9.5:1:29.5:1:1:1.22:60:4:0.0488:0:1.5 0/0:32:0:0,0:16,16:0:2,0:29.8:1:30.3:1:1:0:60:64:1:0:0.3 -4 6141635 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19096;SOR=Inf;LSEQ=CCAAGGAATACCAAGGACTG;RSEQ=CACCAAAGCACAGGAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:14,24:0:2,0:27.8:1:31.2:1:1:0:60:37:1:0:0.2 0/1:30:2:1,1:11,17:0.0667:2,2:22.5:1:31.5:1:1:1.52:60:4:0.0667:0:1 -4 6141665 . C A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14634;SOR=5.52365;LSEQ=ACAGGAAGCCAGGGGAGAGG;RSEQ=CTGGGGCAGAGTCCCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:1,0:8,17:0.0385:2,0:1:0:25:0:0.34615:0:60:2:0.0385:0:1 0/1:16:3:0,3:5,8:0.1875:2,0:13:1:27.7:1:0.50893:0:60:6:0.1875:0:1 -4 6142049 . C G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACATCTTCCCACATAAAT;RSEQ=ATAATGCACACCTGATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:0:33:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 6926997 . A C 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GAATGAGACTCCATCTCAAA;RSEQ=AAACAAACAAACAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:8,0:16,0:0.3333:1,0:28.8:1:33:1:1:0:60:16:0.3333:0:1 0/1:21:7:7,0:14,0:0.3333:1,0:23.1:1:32.1:1:1:0:60:14:0.3333:0:1 -4 6927011 . A G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.2795;SOR=0.33483;LSEQ=CTCAAAAAAACAAACAAACA;RSEQ=AAAAAGAATCGTGATCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:7:7,0:30,0:0.1892:1,0:17.4:1:33.3:1:1:0:60:14:0.1944:0:1.7 0/1:28:2:2,0:26,0:0.0714:1,0:34.5:1:30.5:1:1:0:60:4:0.0714:0:1 -4 6927079 . G T 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36722;SOR=0.5835;LSEQ=GGCCGGGGCTTGGCAGGTGG;RSEQ=AACATTTCTGCAGTTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:18:18,0:130,1:0.1208:1,1:26.9:1:30.1:1:1:0:60:36:0.125:0:1.3 0/1:81:6:6,0:72,3:0.0741:1,0:17:1:31.2:1:1:0:60:12:0.075:0:1 -4 6927471 . T G 72 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCTTGTCACTATCCCTTC;RSEQ=GAGGCTGTAGCCATATCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:29:1:31.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 6927667 . G C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGATGGGTTTTCAGAAAT;RSEQ=TGGGAAACCTTGCTTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23.5:1:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 6959929 . G A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.76179;SOR=0.72369;LSEQ=TGTCCAGATGACTGCTCCAG;RSEQ=TGGCCAGCCCACAGTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:5,2:11,6:0.2917:2,2:30.6:1:29.4:1:1:1.35:60:14:0.3182:0:1.3 0/1:35:8:4,4:17,10:0.2286:2,2:21.6:1:28.4:1:0.68529:1.67357:60:16:0.2286:0:1.1 -4 6959951 . C T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4955;SOR=Inf;LSEQ=GGCCAGCCCACAGTTAGAGC;RSEQ=GGAGTCTGCAGTTGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:23,12:0:2,0:24.2:1:30.2:1:1:0:60:34:1:0:0.4 0/1:40:2:1,1:22,16:0.05:2,2:12.5:1:23:0:1:1.36391:60:4:0.05:0:1.5 -4 6960001 . T TC 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2179;SOR=0.5096;LSEQ=TTCCAACAGCCTCACCTGCT;RSEQ=CATACTGGGGGTCGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:19:8,11:6,7:0.5938:2,2:21.9:1:29.7:1:1:1.17251:59.4:18:0.5806:0.125:0.4 0/1:33:14:3,11:6,13:0.4242:2,2:24.6:1:31.7:1:0.6982:1.66595:60:28:0.4242:0.0909:0.5 -4 6960010 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=CCTCACCTGCTTCATACTGG;RSEQ=GGTCGAGGGGGTTATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:0:2,0:22.9:1:30.5:1:1:0:60:56:1:0:0.2 0/1:27:2:1,1:7,18:0.0741:2,2:19:1:32:1:0.51282:2.47:60:4:0.0741:0:1.5 -4 6960015 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49061;SOR=Inf;LSEQ=CCTGCTTCATACTGGGGGTC;RSEQ=AGGGGGTTATGTCCCTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:23.8:1:30.2:1:1:0:60:48:1:0:0.2 0/1:26:2:1,1:7,17:0.0769:2,2:40:1:29.5:1:0.52923:2.34:60:4:0.08:0:1 -4 7647801 . C T 69 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24242;SOR=0.16477;LSEQ=CCTTGCGCACCCGGCAGCCA;RSEQ=GGATTCCGGGCTACCGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:26.8:1:29.8:1:1:0:60:10:0.7143:0:1.2 0/1:4:1:0,1:0,3:0.25:0,0:21:0:32:0:1:0:60:2:0.25:0:1 -4 8042066 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCAGGGTGGCCAGGCGC;RSEQ=GTGGCTCACACCTGTACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:29.5:1:1:0:60:4:1:0:1.5 -4 8043638 . G GA 120 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.36541;SOR=0.64112;LSEQ=GAGACTCCACTTCAAAAAAA;RSEQ=AAAAAAAAAAGAGCTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:16:13,3:11,2:0.4706:2,2:16.2:1:30.6:1:1:1.25893:59.7:32:0.4706:0.2353:2.1 0/1:47:17:13,4:23,6:0.3617:2,2:19.1:1:29.4:1:1:1.1752:60:34:0.3696:0.1702:1.6 -4 8043682 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00045;SOR=3.32014;LSEQ=ATGAGCAGTTACTATGTGCC;RSEQ=TGCAGGTTCCAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:15:11,4:34,19:0.2174:2,2:27.5:1:30.1:1:0.75803:1.53:60:30:0.2174:0:1.2 0/1:108:52:30,22:32,24:0.4815:2,2:32.1:1:29.6:1:1:1.02:60:104:0.486:0:3 -4 8043700 . A G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=6.00701;LSEQ=CCGTGCAGGTTCCAACAACA;RSEQ=CAGCAGCAACAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:85:48:26,22:25,12:0.5647:2,2:27.2:1:32.2:1:0.2662:1.75109:60:96:0.5647:0:2.3 1/1:133:118:67,51:7,7:0.8872:2,2:27.5:1:31.6:1:0.77722:1.31:60:117:0.8931:0:2.6 -4 8043703 . G A 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=TGCAGGTTCCAACAACAACA;RSEQ=CAGCAACAACAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:48:25,23:25,12:0.5581:2,2:27.3:1:29.5:1:0.18513:1.90197:60:47:0.5663:0:2.2 0/0:135:0:0,0:7,7:0:2,0:28.4:1:32.1:1:1:0:60:28:1:0:0.1 -4 8043737 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51278;SOR=Inf;LSEQ=AACAGCAACAGCTACCACGA;RSEQ=TGAGCGCTTAGCAGGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:33,42:0:2,0:26.9:1:30.5:1:1:0:59.7:150:1:0:1.2 0/1:107:2:1,1:44,61:0.0187:2,2:37.5:1:30:1:1:1.38:60:4:0.019:0:2 -4 8508579 . C G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGAAATGCTGCTTGGTGAG;RSEQ=TGGGCTGGCTGGGCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:24:1:34.5:1:1:0:60:4:1:0:0 0/1:6:2:1,1:4,0:0.3333:0,2:25:0:33:0:0.33333:0:60:4:0.3333:0:1.5 -4 8508614 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=TGCTGGCCCTCGGTCAGCCG;RSEQ=CTGCAACAGGCAGGGCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:22:1:31.1:1:1:0:60:14:1:0:0.1 0/1:12:2:1,1:6,4:0.1667:2,2:8:1:27.5:1:1:1.4491:60:4:0.1667:0:1 -4 8508678 . T C 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08669;SOR=Inf;LSEQ=TGGAGGCAGCGTGGGTGGAA;RSEQ=TGTGGAATTGTCATCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:22.6:1:30.4:1:1:0:60:20:1:0:0.1 0/1:10:4:2,2:1,5:0.4:2,2:24:1:32.8:1:0.5:4.17:60:8:0.4444:0:1 -4 8509451 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGGCTGTCGCTCCATG;RSEQ=ACAGACAGGAGTCCAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:22:1:31:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 10256323 . AT A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGTGGGAACTGTCTGGA;RSEQ=ACACCTTACTGTGTCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18:1:30.8:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 10256455 . C G 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCAGTCAGAACAGCAAG;RSEQ=CTTTCTGGGCTGAGGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:1:0,1:22.9:1:31:1:1:0:60:32:1:0:1.3 1/1:5:5:5,0:0,0:1:0,0:17.6:1:28.8:1:1:0:60:4:1:0:1.2 -4 10256518 . G T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18655;SOR=Inf;LSEQ=CAATGCAGTTGGCTCCTCAG;RSEQ=AAAAACTGGTGTTTTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:32,16:0:2,0:22.4:1:29.6:1:1:0:60:11:1:0:0.5 0/1:37:2:1,1:24,11:0.0541:2,2:22.5:1:23.5:1:1:2.13205:60:4:0.0541:0:1.5 -4 10256577 . C T 117 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01373;SOR=3.14754;LSEQ=ACCAGCCTCTTCATTGCTTT;RSEQ=GGGCAGTTCTTGTGTATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:8:3,5:35,38:0.0988:2,2:30.8:1:30.4:1:0.71678:1.52712:60:16:0.0988:0:1.1 0/1:62:16:8,8:23,23:0.2581:2,2:35:1:29.3:1:1:1:60:32:0.2623:0:1.2 -4 10256768 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.29475;SOR=0;LSEQ=TTTTACCCTTCGTTCAGATC;RSEQ=CCTCTGGGGCCATTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:15,1:0.2:1,2:34.8:1:30.8:1:0.08772:11.97303:60:8:0.2:0:2 0/0:8:0:0,0:7,1:0:2,0:20.8:1:29.4:1:1:0:60:16:1:0:0.6 -4 10256784 . C A 140 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00106;SOR=0;LSEQ=GATCGCCTCTGGGGCCATTG;RSEQ=CTGTGGGTTTCCTTAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:22,4:0,0:1:0,2:24.8:1:29.8:1:1:0:60:25:1:0:1.2 1/0:11:6:4,2:5,0:0.5455:0,2:29.2:1:27.7:1:0.45455:0:60:12:0.5455:0:1.3 -4 10256936 . C T 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03045;LSEQ=TTCTCTGCATGCCAACTAGT;RSEQ=CCTTCCCTGAGCTGTCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:212:211:152,59:0,0:0.9953:0,2:24.6:1:29.9:1:1:0:60:104.5:0.9952:0:1.1 1/1:155:134:90,44:16,5:0.8645:2,2:23.3:1:28.9:1:0.4616:1.56022:60:66:0.8627:0:1.1 -4 10257087 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1591;SOR=Inf;LSEQ=TGAACCCCAACAAGAGCAGA;RSEQ=TGTCCACATGTCCTACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:100,166:0:2,0:23.4:1:30:1:1:0:60:37:1:0:0.2 0/1:177:2:1,1:70,105:0.0113:2,2:22:1:27:1:1:1.50:60:4:0.0114:0:1 -4 10257145 . G A 28 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55656;SOR=3.48356;LSEQ=ATCTCTGAAGGCCTGGAACT;RSEQ=CTCTGGGGGTCAGGTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:1:0,1:50,125:0.0057:2,0:34:0:30:0:1:0:60:2:0.0057:0:1 0/1:102:2:1,1:37,63:0.0196:2,2:39:0:28:1:1:1.69:60:4:0.0198:0:1 -4 10257734 . G A 134 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04685;SOR=0;LSEQ=TCCAGCCCACGTGCCTAGTG;RSEQ=GTACTTTAGTGCTATAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:16,7:0,0:1:0,2:25.3:1:29.7:1:1:0:60:46:1:0:1 1/0:14:11:8,3:2,1:0.7857:2,2:30.7:1:28.8:1:1:1.31:60:22:0.7857:0:1 -4 10257897 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51395;SOR=0;LSEQ=CTCAGGAAATCTACCTGAAG;RSEQ=TCTTCCCCCATCAGGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:47,51:0.02:2,2:41.5:1:30.5:1:1:1.08:60:4:0.0202:0:1 0/0:69:0:0,0:29,40:0:2,0:28.6:1:31.3:1:1:0:60:22:1:0:0.1 -4 10257932 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11899;SOR=Inf;LSEQ=GCAGCATCAGTATTCCAATA;RSEQ=AAATGCCTTTTTACCCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:27,48:0:2,0:22.3:1:28.3:1:1:0:60:24:1:0:0.1 0/1:40:2:1,1:14,24:0.05:2,2:26:1:33.5:1:1:1.69:60:4:0.05:0:1 -4 10258057 . C G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14716;SOR=0.20091;LSEQ=TTTGCACACTGACCACTGTT;RSEQ=TTTGCTTATTGGCAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:3,13:0,1:0.8889:0,2:25.4:1:32.3:1:1:0:60:32:0.9412:0:1.1 1/0:10:6:1,5:1,3:0.6:2,2:18.5:1:29.7:1:1:1.58108:60:12:0.6:0:1 -4 12321563 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=AGTGTAAGAGCAGTGGAAGG;RSEQ=AGCCAACGAAAAGCTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:110,50:0.0123:2,2:25:1:27.5:1:0.53186:2.18824:60:4:0.0125:0:1 0/0:161:0:0,0:118,43:0:2,0:23.6:1:30.6:1:1:0:60:160:1:0:0.2 -4 12321669 . C G 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16996;SOR=0.7966;LSEQ=GATTGAAGACTTCATCACCA;RSEQ=TCTTTTCTGTTTTATGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:300:157:75,82:59,83:0.5233:2,2:26.6:1:32:1:0.29638:1.29:60:156:0.5253:0:1.1 0/1:313:146:60,86:74,92:0.4665:2,2:23:1:30.6:1:0.56761:1.15237:60:28.2:0.4593:0:1.1 -4 12322014 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAGTAATTACATGGGCA;RSEQ=TTATCTGTTAACATTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 13633615 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=TGTGTTTCAGGAAGCTATCT;RSEQ=GGCTCTTAGTGAGCTTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:19,4:0:2,0:23.4:1:30.8:1:1:0:60:22:1:0:0 0/1:23:2:1,1:14,7:0.087:2,2:39.5:1:31:1:1:1.93655:60:4:0.087:0:1 -4 13633735 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18367;SOR=Inf;LSEQ=ACATTGTAGACTCTTCTAGT;RSEQ=GTGCCATGGTAACACTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:49,53:0:2,0:30.6:1:30.1:1:1:0:60:101:1:0:0.2 0/1:77:2:1,1:38,37:0.026:2,2:40.5:1:27:1:1:1.02668:60:4:0.026:0:1 -4 13634228 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53946;SOR=Inf;LSEQ=CTTTGTGTTCGTCATTTTGG;RSEQ=GAATTACTGGAAGACAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:0:2,0:25.5:1:31.1:1:1:0:60:32:1:0:0.1 0/1:61:2:1,1:30,29:0.0328:2,2:36:1:29.5:1:1:1.03392:60:4:0.0328:0:1 -4 15499251 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.05819;LSEQ=AATTTATATTCCTACCAGCA;RSEQ=AGAAGTTTTAATTTATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:117:56,61:211,213:0.2163:2,2:25.6:1:31.8:1:0.75449:1.07889:60:116:0.2168:0:1.1 0/1:452:207:105,102:128,117:0.458:2,2:27:1:31.2:1:0.77728:1.0626:59.9:50.75:0.4572:0:1.2 -4 15499343 . T C 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGTGAAGTGGTACCTAA;RSEQ=TGTGGTTTTGGTTTCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:54,160:0:2,0:23.7:1:29.8:1:1:0:60:52.5:1:0:0.1 0/1:153:34:10,24:28,91:0.2222:2,2:19.7:1:30.3:1:0.50409:1.35:60:33:0.22:0:1.3 -4 15499481 . A AT 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00155;SOR=Inf;LSEQ=AAAAGCAGGATCTTTGTGGT;RSEQ=TATGGCTTATATGTCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:0:0,0:29.7:1:31.1:1:1:0:60:24:1:0:0.1 1/0:9:6:0,6:0,3:0.6667:0,0:19.7:1:30.9:1:1:0:60:12:0.6667:0.2222:0 -4 16611214 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50588;SOR=Inf;LSEQ=ATCGGCTGTGGCAGTCTGCG;RSEQ=CCAGAGTGCCTCTTCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:31.1:1:31.6:1:1:0:60:42:1:0:0.4 0/1:30:2:1,1:11,17:0.0667:2,2:27.5:1:27:1:1:1.52:60:4:0.069:0:1 -4 16611273 . C A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.08684;LSEQ=CCTCAGGCAGTGCTTCCCTG;RSEQ=AGGATCTCCAATAACTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:4,7:1,3:0.7333:2,2:20.5:1:28.5:1:1:1.66:60:10:0.7143:0:1 1/0:8:6:3,3:0,2:0.75:0,2:14:1:29:1:0.46429:0:60:12:0.75:0:1 -4 16611787 . T C 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCAGAAAGTGGCAACAA;RSEQ=AGCATCAACAACAAAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:13,18:0,0:1:0,2:23.7:1:31.5:1:1:0:60:30:1:0:1 1/1:24:24:11,13:0,0:1:0,2:23.3:1:31.6:1:1:0:60:48:1:0:1.2 -4 16611905 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54023;SOR=0;LSEQ=AGTGAAAAAATGCTGAAAAC;RSEQ=CAAAAGGCCAGAGTGCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:0.1:2,2:28:1:30.5:1:1:1.54:60:4:0.1053:0:1 0/0:10:0:0,0:5,5:0:2,0:16.1:1:30.1:1:1:0:60:20:1:0:0.1 -4 18537350 . T C 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00135;SOR=Inf;LSEQ=ATCACCCTGGCATGGTGTAC;RSEQ=CATGGTGTACAGAGTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:0:2,0:24:1:30.2:1:1:0:60:26:1:0:0 1/0:7:5:3,2:1,1:0.7143:2,2:23.2:1:30.6:1:1:1.41:60:10:0.7143:0:1 -4 20891259 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52005;SOR=0;LSEQ=AAATAGGAACTATTGGCCTG;RSEQ=TTGGCCCTAAATGGAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:33,115:0.0133:2,2:27:1:30.5:1:0.40313:3.45:60:4:0.0137:0:1 0/0:98:0:0,0:23,75:0:2,0:21.3:1:32.1:1:1:0:60:196:1:0:0.1 -4 20891275 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15188;SOR=Inf;LSEQ=CCTGCTTGGCCCTAAATGGA;RSEQ=GGGCTGATATTTTAAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:9,92:0:2,0:23.5:1:30.9:1:1:0:59.9:49.5:1:0:0.2 0/1:65:2:1,1:5,58:0.0308:2,2:6.5:1:27.5:1:0.1774:10.68:60:4:0.0313:0:1 -4 20891283 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14157;SOR=Inf;LSEQ=GCCCTAAATGGAAGGGCTGA;RSEQ=ATTTTAAGTTGATTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:6,86:0:2,0:22.7:1:27.9:1:1:0:59.9:45:1:0:0.2 0/1:56:2:0,2:2,52:0.0357:1,0:8:1:31.5:1:1:0:60:4:0.037:0:1 -4 20891334 . A T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.54536;SOR=0;LSEQ=ATCCAACCTAATTCTTTTTA;RSEQ=TTTGGTTGAATGTTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:0,3:1,38:0.0714:1,0:9.7:1:31.7:1:1:0:60:6:0.0732:0:1 0/0:22:0:0,0:1,21:0:1,0:25:1:30.9:1:1:0:60:44:1:0:0.1 -4 21650176 . C T 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55547;SOR=0;LSEQ=ACTACCAGACACACCTTCCA;RSEQ=AGTCTCAAGCTCTAAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:32,1:0.0833:1,0:21.7:1:32.7:1:1:0:60:6:0.0833:0:1 0/0:13:0:0,0:13,0:0:1,0:20.8:1:32.1:1:1:0:60:26:1:0:0 -4 21650368 . G A 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42234;LSEQ=AGCATTGGCCTAACTCTGAA;RSEQ=TGGCAAAGTAGGGTTGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:513:114:49,65:194,205:0.2222:2,2:25.1:1:30.4:1:0.33853:1.25479:60:113:0.2216:0:1.8 0/1:474:51:19,32:198,225:0.1076:2,2:27.4:1:29.6:1:0.23435:1.48089:60:102:0.1078:0:2.1 -4 21650403 . T A 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39495;SOR=0.84026;LSEQ=TGTTTAGAAAGGAAAAATTC;RSEQ=GTCAAATTTAGCATATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:73:21,52:121,177:0.1968:2,2:24.1:1:30.6:1:0.08023:1.69045:60:35.5:0.1929:0:2.3 0/1:375:64:22,42:129,182:0.1707:2,2:23.7:1:30.4:1:0.32869:1.35208:60:63:0.1703:0:2.1 -4 21650441 . T A 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5781;SOR=1.21117;LSEQ=TATTTTCTGTTTACATAATC;RSEQ=AGTAGAGGCCCCGCACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:30:3,27:45,122:0.1523:2,2:25.3:1:31:1:0.06272:3.30391:60:60:0.1546:0:2.3 0/1:179:32:11,21:46,101:0.1788:2,2:24.7:1:29.7:1:0.83446:1.15:60:64:0.1788:0:2.3 -4 21776672 . A AT 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.55547;SOR=0;LSEQ=TGTCCTTTTGGGTTTTCAGC;RSEQ=TTTTTTTCATTGATTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:1,2:17,16:0.0833:2,2:5.3:1:28.8:1:1:2.08218:60:6:0.0833:0.0556:0.7 0/0:13:0:0,0:8,5:0:2,0:24.5:1:28.6:1:1:0:60:26:1:0:0.2 -4 21776779 . G T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.52559;SOR=1.74948;LSEQ=AGGCCTTTTTTTGGTTGGTG;RSEQ=TGTTGATGCTGCTGTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:19:7,12:3,5:0.7037:2,2:22.9:1:29.4:1:1:1.02751:60:38:0.7037:0:1.1 1/1:26:21:8,13:2,2:0.8077:2,2:22.7:1:29.6:1:1:1.59276:60:42:0.84:0:1.2 -4 21777782 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48667;SOR=0;LSEQ=CTGGGTAGCATGCTCACTCA;RSEQ=CACCTCCCTTGGCTGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:8.5:1:27:1:1:1:60:4:0.1429:0:1 0/0:11:0:0,0:2,9:0:2,0:19.7:1:31.8:1:1:0:60:22:1:0:0 -4 24030690 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.21778;SOR=Inf;LSEQ=TAACCTCAACCAATGTTAGT;RSEQ=ATTTATATAATTATTTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:107,65:0:2,0:22.5:1:29.4:1:1:0:60:171:1:0:0.1 0/1:151:2:1,1:90,59:0.0132:2,2:20:0:33.5:1:1:1.521:60:4:0.0134:0:1 -4 24030761 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.81966;LSEQ=CAAAAATTCAAGCAGCATCA;RSEQ=GATGATAAATTCAAGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:25:12,13:143,136:0.0822:2,2:23.5:1:31.3:1:0.83589:1.1386:60:24:0.0803:0:1.2 0/1:231:114:54,60:58,59:0.4935:2,2:25.1:1:30.5:1:0.79273:1.09186:60:113:0.5022:0:1.2 -4 25133364 . C T 107 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=ACTTAGTTTGTCCCCCAGTT;RSEQ=TTAGCTCACAAATTCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:25.6:1:30.1:1:1:0:60:24:1:0:1.2 1/0:4:3:3,0:1,0:0.75:0,0:28.7:1:31.3:1:1:0:60:6:0.75:0:1 -4 25133430 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTCTTATCCAATTCAGCAG;RSEQ=TATTTGCAACAATAAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:0.1176:1,0:13:1:32:1:1:0:60:4:0.1176:0:1.5 0/0:5:0:0,0:5,0:0:0,0:21.4:1:26.6:1:1:0:60:10:1:0:0.4 -4 25133516 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22395;SOR=Inf;LSEQ=TAAACAGAATAATGATCTTC;RSEQ=CCAGAAGCAAAACAGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:62,2:0:1,0:24.5:1:31:1:1:0:60:63:1:0:0.1 0/1:58:2:1,1:53,2:0.0345:1,2:16.5:1:29:1:0.10338:21.8405:60:4:0.0351:0:1 -4 25133641 . T C 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGTTAAATTCATGGTTA;RSEQ=TTCTCCCCTCAATGAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:281,220:0:2,0:25.3:1:30.3:1:1:0:60:82.5:1:0:0.8 0/1:431:24:12,12:209,198:0.0557:2,2:31.7:1:31.5:1:1:1.05545:60:48:0.0559:0:2 -4 25133669 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15445;LSEQ=CTCAATGAAGCAAATGTGTT;RSEQ=ATCAGGAAGGGGATAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:530:486:242,244:20,23:0.917:2,2:26.8:1:28.9:1:0.75121:1.14:60:68.429:0.9176:0:1.1 1/0:427:269:125,144:73,83:0.63:2,2:23.7:1:28.6:1:1:1.01318:60:88.667:0.6274:0:1.2 -4 25134045 . A G 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAACCAATAAACTATCAC;RSEQ=ATTAAATTTTCACAGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:9.3:1:29:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 25241780 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53026;SOR=0;LSEQ=TTGCCCAACTCCAGAGGTTG;RSEQ=TATAAGAGTTTGAAAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:22,28:0.0385:2,2:17:1:29.5:1:1:1.27:60:4:0.0385:0:1 0/0:30:0:0,0:12,18:0:2,0:28.8:1:30.9:1:1:0:51.6:60:1:0:0.3 -4 27498143 . A G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=4.9538;LSEQ=TTAAGATTGGGAAACAAAGA;RSEQ=AGTCTGAAAGAGCCAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:15:1:31:1:1:0:60:4:0.25:0:1 1/0:3:2:1,1:1,0:0.6667:0,2:20.5:1:30.5:1:1:0:60:4:0.6667:0:1 -4 27498290 . G C 86 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20623;SOR=0.19007;LSEQ=GAGCAAATCAGAGGAATAGG;RSEQ=CCTGAAGTGAACCCCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:4,3:5,9:0.3333:2,2:26:1:30.9:1:0.39721:2.30:60:14:0.3333:0:1 0/1:12:1:0,1:6,5:0.0833:2,0:25:0:33:0:1:0:60:2:0.0909:0:1 -4 28143780 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50664;SOR=0;LSEQ=GGGGGAAGTCCCTGAAAACA;RSEQ=ACCTGGTGGTTCTAAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:131,67:0.01:2,2:25:1:30.5:1:1:1.94825:60:4:0.0101:0:1 0/0:155:0:0,0:97,58:0:2,0:23.8:1:30:1:1:0:60:76.5:1:0:0.2 -4 28143801 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19649;SOR=Inf;LSEQ=ACCTGGTGGTTCTAAATGAA;RSEQ=TTTTCTTTGCCAGTACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:150,88:0:2,0:27.5:1:32.3:1:1:0:60:237:1:0:0.2 0/1:190:2:1,1:114,74:0.0105:2,2:44.5:1:30.5:1:1:1.53689:60:4:0.0106:0:1 -4 28143847 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09705;SOR=Inf;LSEQ=CCTTTTGAATAGGCACAGAT;RSEQ=TGTCCCTCAGTATCTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:191,142:0:2,0:24.4:1:31.4:1:1:0:60:110:0.997:0:0.3 0/1:285:3:2,1:157,125:0.0105:2,2:12.7:1:28.3:1:1:1.59:60:6:0.0106:0:1.7 -4 28143857 . G A 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00318;SOR=1.79598;LSEQ=AGGCACAGATCTGTCCCTCA;RSEQ=TATCTCATTAGAACTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:57:35,22:158,148:0.157:2,2:21.6:1:29.2:1:0.1948:1.49:60:27.5:0.1536:0:1.1 0/1:295:74:39,35:120,100:0.2508:2,2:22.6:1:29.5:1:0.78913:1.07665:60:73:0.25:0:1.2 -4 28143921 . AT A 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.21626;SOR=4.96885;LSEQ=CTTAGAATTCCAGTTCCCGG;RSEQ=TTTTTTTACTTCACTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:0,1:95,172:0.0037:2,0:38:0:32:0:1:0:60:2:0.0038:0:0 0/1:273:5:3,2:114,154:0.0183:2,2:19.2:1:28.6:1:0.65422:2.02:60:10:0.0185:0.0037:0.2 -4 28143957 . A G 99 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.008;SOR=10.34119;LSEQ=TCACTTTTCATTGATTGAGG;RSEQ=TTGATTGATTTTTAATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:1,0:31,117:0.0067:2,0:23:0:14:0:0.21477:0:60:0:0:0:7 0/1:137:9:2,7:40,88:0.0657:2,2:18.9:1:31.3:1:0.72148:1.58598:60:18:0.0672:0:1.2 -4 28204105 . G A 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=2.48136;LSEQ=AATCTAAAAAATTTTTCAGG;RSEQ=CAATGTAACATCTAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:35:17,18:117,147:0.1171:2,2:24.1:1:30.1:1:0.71838:1.19:60:70:0.1186:0:1.3 0/1:234:58:29,29:82,94:0.2479:2,2:22.6:1:29.4:1:0.76192:1.15:60:116:0.2479:0:1.1 -4 28204197 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53038;SOR=0;LSEQ=ATTTTAAGTGAGTTTATGAA;RSEQ=GGTTCTGATATGCATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:20,88:0.0182:2,2:16.5:1:29:1:0.34679:4.32:60:4:0.0183:0:1 0/0:65:0:0,0:11,54:0:2,0:23.3:1:30.6:1:1:0:60:130:1:0:0.1 -4 28310225 . G A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGACAGAAAGAGAAGGAA;RSEQ=GAGAGAGATGGAAGTAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:0:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 28400060 . A G 71 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AATACATGCTTCTGTTTCTC;RSEQ=AGTGTGAAAAATCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:13.6:1:30.8:1:1:0:60:10:1:0:2.4 0/0:1:0:0,0:1,0:0:0,0:40:0:27:0:1:0:60:2:1:0:0 -4 28400087 . C A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATCTGTTTCTGGTTAT;RSEQ=CCATGTCTAGTATTTATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:26.8:1:29.8:1:1:0:60:8:0.5:0:2.5 0/0:1:0:0,0:1,0:0:0,0:13:0:25:0:1:0:60:2:1:0:0 -4 28400119 . C T 102 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09341;SOR=0.07274;LSEQ=ATTTATGATTGTTTGCTATA;RSEQ=TGTAAGATGTTTGGATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:10,0:1,0:0.9091:0,0:31.6:1:31:1:1:0:60:20:0.9091:0:1.9 0/1:3:1:1,0:2,0:0.3333:0,0:18:0:32:0:1:0:60:2:0.3333:0:1 -4 28400261 . G T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59718;LSEQ=TAATTTTTTGCCTAGTTATA;RSEQ=TCTGTAACTCCTACTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:130,25:0.0127:2,2:21:1:30:1:0.30467:5.11873:60:4:0.0129:0:1 0/0:131:1:0,1:111,19:0.0076:2,0:1:0:24:0:0.15267:0:60:2:0.008:0:1 -4 28400383 . T C 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0.59738;LSEQ=TACTGAAATATTTCCCAGAA;RSEQ=TGAGCAACCTCTGAAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:484:244:108,136:112,127:0.5041:2,2:27.4:1:32.2:1:0.5844:1.11029:60:243:0.5052:0:1.1 0/1:458:173:76,97:126,159:0.3777:2,2:25.3:1:31.1:1:1:1.0114:60:56.667:0.3803:0:1.1 -4 28400454 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18551;SOR=Inf;LSEQ=CAGGCCTTAAAGTCTCACCT;RSEQ=GAGCATGCATAGCCTTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:55,173:0:2,0:23.3:1:30.2:1:1:0:60:113:1:0:0.5 0/1:173:2:1,1:46,124:0.0116:2,2:32:1:31.5:1:0.473:2.68:60:4:0.0116:0:1.5 -4 28400468 . C T 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCACCTTGAGCATGCATAGC;RSEQ=TTGTCCTCATCATCCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:33:7,26:20,123:0.1875:2,2:22.8:1:31.1:1:0.2934:1.65:60:66:0.1886:0:1.1 0/0:139:0:0,0:30,109:0:2,0:21.7:1:31.7:1:1:0:60:278:1:0:0.2 -4 28401647 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGATCGAGACCATCCTG;RSEQ=CTAACATAGTGAAGCCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:28:1:1:0:60:4:1:0:1 -4 28745882 . A G 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10008;SOR=0.30822;LSEQ=TGTTCCCACAAGAAAAACGG;RSEQ=TATGGCATAGGTTTGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:25:24,1:6,0:0.8065:0,1:19.6:1:31.4:1:1:0:60:50:0.8333:0:1 1/0:18:10:10,0:7,1:0.5556:2,0:21.9:1:29.8:1:0.44444:0:60:9:0.5294:0:1.1 -4 28745978 . AT A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16741;SOR=Inf;LSEQ=CGTTTGAGGTTTTGCATATC;RSEQ=TTTCTGTCCTTTCTGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:144,43:0:2,0:24.2:1:30.6:1:1:0:60:45.75:1:0:0.1 0/1:130:2:1,1:104,24:0.0154:2,2:13:0:32:0:0.34884:4.26615:60:4:0.0155:0:0.5 -4 28746092 . C A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.41059;LSEQ=TTTCCATCCTGCTTAGCTAC;RSEQ=ACCAAAGTAAACCTGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:477:360:159,201:55,62:0.7547:2,2:26.7:1:29.9:1:0.59465:1.12115:60:119:0.7596:0:1.1 1/0:466:260:130,130:102,104:0.5579:2,2:26:1:29.4:1:0.92595:1.02:60:129:0.5584:0:1.1 -4 28746179 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23643;SOR=0;LSEQ=TATATATTTATCCTATATCT;RSEQ=TATCTCTGGTTAGTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:46,138:0.0108:2,2:28.5:1:28:1:0.44255:2.98:60:4:0.0109:0:1 0/0:196:0:0,0:48,148:0:2,0:24.5:1:31.1:1:1:0:60:64.333:1:0:0.7 -4 28746194 . GT G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.22344;SOR=0;LSEQ=TATCTGTATCTCTGGTTAGT;RSEQ=TTTTTTGTGTACTGTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:0,2:25,99:0.0159:2,0:47.5:1:31.5:1:1:0:60:4:0.0167:0:1 0/0:140:0:0,0:31,109:0:2,0:21.7:1:30:1:1:0:60:280:1:0:0.9 -4 28746210 . T C 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.07305;SOR=1.84612;LSEQ=TAGTGTTTTTTTGTGTACTG;RSEQ=TTATGTGTGGCTTTTAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:72:13,59:5,27:0.6923:2,2:21.2:1:32.2:1:1:1.19:60:144:0.6923:0:2 1/1:93:75:9,66:4,14:0.8065:2,2:20.2:1:32.5:1:0.26951:2.0759:60:150:0.8152:0:1.7 -4 28746238 . T G 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03565;LSEQ=TGGCTTTTAATCGCCCTTTA;RSEQ=AATTAGGTCTTCTTGTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:37:1,36:0,20:0.6491:1,1:20.1:1:31.5:1:1:0:60:74:0.6491:0:3 1/0:35:23:0,23:0,12:0.6571:0,1:20.7:1:31.9:1:1:0:60:46:0.6571:0:3 -4 28746246 . T A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31489;SOR=1.84721;LSEQ=AATCGCCCTTTATAATTAGG;RSEQ=CTTCTTGTCTAGGCAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:30:0,30:0,17:0.6383:1,1:21.1:1:29.8:1:1:0:60:60:0.6522:0:3.2 1/0:30:23:0,23:0,7:0.7667:0,1:20.8:1:29.7:1:1:0:60:46:0.7667:0:3.1 -4 28746281 . T A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50544;SOR=0.57988;LSEQ=AGAATACTCTCAGTTGGGCC;RSEQ=AATCCAGTTCTTTAGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:0,16:0,8:0.6667:0,1:27.9:1:30.4:1:1:0:60:15:0.6522:0:3.2 1/0:15:8:0,8:0,7:0.5333:0,0:25.4:1:30.5:1:1:0:60:16:0.5333:0:3.6 -4 28746368 . A T 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTTAAGTTCTGGGATAC;RSEQ=TGTGCAGAACATGCAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:24.3:1:31.7:1:1:0:49.3:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 28747068 . C T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAGACTTTTAGGAAGAG;RSEQ=TTGTAGATAACAAGAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:32:0:1:0:60:4:1:0:1.5 -4 29722826 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14687;SOR=Inf;LSEQ=GAGTTTGTAATATCTTACAA;RSEQ=GTGATTTCTTTCTGTACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:70,0:0:1,0:25.7:1:32.1:1:1:0:60:140:1:0:0.1 0/1:44:2:2,0:41,1:0.0455:1,0:23:1:31:0:1:0:60:4:0.0455:0:1 -4 29722943 . G T 165 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=27.32536;LSEQ=AGCATATGGGAAAGTGAAGA;RSEQ=TTCCCAGGGTCCCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:2:1,1:197,181:0.0053:2,2:20.5:1:30:1:1:1.08814:60:4:0.0053:0:2.5 0/1:387:49:30,19:188,150:0.1266:2,2:27.7:1:29.5:1:0.53834:1.26:60:48:0.1253:0:1.6 -4 29722997 . G C 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71194;SOR=1.05678;LSEQ=CTCCATATTTATTTAAGTTT;RSEQ=TATAAATCAATAAGCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:165:66,99:74,104:0.481:2,2:25:1:31.4:1:0.82612:1.06709:60:81.5:0.4808:0:1.1 0/1:390:193:91,102:93,100:0.4949:2,2:24.1:1:31.4:1:0.91885:1.04233:60:192:0.4936:0:1.2 -4 29723320 . C T 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATAGATTTCTATGCAAC;RSEQ=ATAGTAACAGAGAAACTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14:1:26.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 34486801 . TTG T 28 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTGTGGTGTGTGTGTGTG;RSEQ=TGTGTGTGTGTGTGTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:28.5:1:1:0:22:4:1:0:0.5 -4 34488836 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15103;SOR=0;LSEQ=TGCTGCTGCTGCTTCTTCTG;RSEQ=TGTTGCTGACTCTGGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:17,26:0.0444:2,2:18.5:1:30:1:1:1.51:60:4:0.0455:0:1 0/0:70:0:0,0:32,38:0:2,0:30.2:1:31.5:1:1:0:60:22.333:1:0:0.2 -4 34488861 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13455;SOR=0;LSEQ=GCTGACTCTGGTGGCCATGG;RSEQ=TGTGCCTCAAGAGGAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:12,23:0.0541:2,2:32:1:30.5:1:1:1.88:60:4:0.0541:0:1 0/0:63:0:0,0:26,37:0:2,0:23.5:1:28.7:1:1:0:60:62:1:0:0.2 -4 35860893 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCTGATTGGTGCGGTTT;RSEQ=TAGAGCACTGATTGGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:1 -4 35861430 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51763;SOR=Inf;LSEQ=GGAGAAGCCATGTCACCCAA;RSEQ=TCTAGAGGTTGGTATAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:22,17:0:2,0:33.3:1:32.3:1:1:0:59:78:1:0:0.5 0/1:60:2:1,1:31,27:0.0333:2,2:43:1:28:1:1:1.1455:60:4:0.0345:0:1 -4 35861432 . C T 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=0;LSEQ=AGAAGCCATGTCACCCAACT;RSEQ=TAGAGGTTGGTATAAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:10:6,4:16,13:0.2564:2,2:33.4:1:30.3:1:1:1.21:58.2:20:0.2703:0:1.2 0/0:60:0:0,0:32,28:0:2,0:31.5:1:31:1:1:0:60:59:1:0:0.2 -4 35861468 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54834;SOR=Inf;LSEQ=GAGTTTGAAAGGCATTGTCT;RSEQ=ATTTCAGAAGCCTTTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:12,17:0:2,0:18:1:31.4:1:1:0:60:58:1:0:0.4 0/1:54:3:2,1:22,29:0.0556:2,2:15:1:24.3:1:0.5791:2.59:60:6:0.0556:0:1.3 -4 35861516 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.53297;SOR=Inf;LSEQ=CGGGTGGCATCTCATACTAT;RSEQ=CCTGACTGGTTAGGAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:2,8:0:2,0:24.9:1:31.6:1:1:0:60:20:1:0:0.1 0/1:18:3:0,3:3,12:0.1667:2,0:17:1:30.7:1:1:0:60:6:0.1667:0:1.3 -4 37310266 . GT G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCCTGGGCAGCAGGGTA;RSEQ=TCTTAGGCCCCTTGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:28.9:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 37822911 . TA T 57 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.71059;SOR=0.6208;LSEQ=AAACACCCAAGAATGATCAA;RSEQ=AAAAAAAAAAGAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:3,1:34,13:0.0784:2,2:6.8:1:26.5:1:1:1.14:60:3:0.0698:0.0392:0.5 0/1:80:4:3,1:54,22:0.05:2,2:18:1:28.8:1:1:1.22:50:8:0.0506:0:0.3 -4 37822922 . AG GA 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15246;SOR=0;LSEQ=AATGATCAATAAAAAAAAAA;RSEQ=AAAAAAAAAAAAGATTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:2,0:42,16:0.0323:2,0:29.5:1:32.8:1:1:0:60:4:0.0333:0:1 0/0:96:0:0,0:60,35:0:2,0:19.4:1:28.8:1:1:0:56.5:30.667:0.9892:0:0.9 -4 37822923 . G A 64 q23;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=12.000;MSILEN=1;SSF=0.00047;SOR=0;LSEQ=ATGATCAATAAAAAAAAAAA;RSEQ=AAAAAAAAAAAAGATTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:8:2,6:36,9:0.125:2,2:13.3:1:21.4:1:0.00425:11.2728:57.5:1.667:0.119:0:1.3 0/0:97:0:0,0:51,31:0:2,0:12:0:10:0:1:0:60:0:0:0:1 -4 37822944 . C T 35 v4;q23;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.59283;LSEQ=AAAAAAAAAAAAGATTTAGC;RSEQ=TTTCTGCCAGAACCGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:1:0,1:58,34:0.0108:2,0:1:0:25:0:0.37634:0:60:2:0.0111:0:1 0/1:176:3:3,0:97,76:0.017:2,0:35.7:1:22.3:1:0.25974:0:53.3:2:0.0126:0:5 -4 37822969 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12829;SOR=0;LSEQ=TGCCAGAACCGCCATCTTCC;RSEQ=GTAATTCACCAAAATGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:60,49:0.018:2,2:31.5:1:31:1:1:1.22224:60:4:0.0185:0:1 0/0:198:0:0,0:99,99:0:2,0:31:1:29.6:1:1:0:59.6:18.8:1:0:0.6 -4 37823011 . G T 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0079;SOR=Inf;LSEQ=CACAAAGGGAAAGAGGAGAG;RSEQ=CACCCGATATATGTTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:49,53:0:2,0:23.5:1:31.4:1:1:0:57.7:204:1:0:0.1 0/1:161:11:4,7:69,81:0.0683:2,2:19.5:1:28.6:1:0.75544:1.48713:58.4:22:0.0705:0:1.1 -4 37823017 . G T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=GGGAAAGAGGAGAGGCACCC;RSEQ=ATATATGTTCTCCAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:44,51:0:2,0:23.4:1:30.4:1:1:0:57.4:190:1:0:0.1 0/1:142:17:8,9:57,68:0.1197:2,2:28.7:1:29.2:1:1:1.06:56.6:34:0.1223:0:1.1 -4 37823041 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16954;SOR=0;LSEQ=TATGTTCTCCAGGCCTTTTA;RSEQ=AAAACATGGAGTTGTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:24,41:0.0299:2,2:28.5:1:29.5:1:1:1.69:42.5:4:0.0303:0:1.5 0/0:95:0:0,0:38,55:0:2,0:23.2:1:30.6:1:1:0:55.1:30:0.9783:0:0.2 -4 37823185 . C T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01369;SOR=Inf;LSEQ=TGGAGGAGTCTACAGTGTTA;RSEQ=CCAGCATGCTGTTGGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:79,97:0:2,0:29.2:1:31.3:1:1:0:59.6:43:1:0:0.1 0/1:272:9:3,6:124,139:0.0331:2,2:31.9:1:28.3:1:0.50931:1.78052:60:8:0.0301:0:1.1 -4 37823221 . G A 79 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08453;SOR=Inf;LSEQ=CATTGTTGTAAACAAACAAG;RSEQ=ACAAGATTCTTGCCAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:42,72:0:2,0:21.2:1:30.8:1:1:0:60:56:1:0:0.1 0/1:165:6:3,3:60,99:0.0364:2,2:25.3:1:30.8:1:0.67536:1.64:60:12:0.0366:0:1.3 -4 38912621 . G A 55 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTTAACAGGACCACTCT;RSEQ=GTTCCTGGGTAGAAAATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:27.3:1:27.5:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 38912816 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17994;SOR=0.43995;LSEQ=GAACCATTAGACCAGGATGC;RSEQ=GGTCCCACCCCAGTGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:3,8:10,16:0.2973:2,2:28.7:1:30:1:0.71057:1.64446:60:22:0.2973:0:1.4 0/1:45:7:3,4:17,21:0.1556:2,2:17.6:1:30.9:1:1:1.07757:60:14:0.1628:0:1.4 -4 38912824 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50786;SOR=Inf;LSEQ=AGACCAGGATGCCGGTCCCA;RSEQ=CCCAGTGAAGAGAAGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:11,20:0:2,0:23.4:1:31:1:1:0:60:30:0.9677:0:0.6 0/1:45:2:1,1:19,24:0.0444:2,2:28:1:25.5:1:1:1.26:60:4:0.0455:0:1 -4 38912884 . A C 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTCCCAGACTGCAGTGCGGC;RSEQ=TGGGAAAGGCTGGGCGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:0.2727:0,0:18:1:32.7:1:1:0:60:6:0.2727:0:1.7 0/1:11:3:1,2:0,8:0.2727:0,2:18:1:28:1:0.27273:0:60:6:0.2727:0:1.3 -4 38928641 . A G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.59985;SOR=1.36115;LSEQ=TCTCTGCCTCCTCCCTGCGC;RSEQ=CACCTGCCTCACTCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:5,4:9,4:0.4091:2,2:26.4:1:31.2:1:0.66192:1.75137:60:18:0.4091:0:1.4 0/1:37:18:10,8:9,10:0.4865:2,2:25.7:1:30.6:1:0.74585:1.38:60:36:0.4865:0:1.2 -4 39351868 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAACAAGGCTCAATGATC;RSEQ=GTGAGACAATATCAAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:21.5:1:32:1:1:0:60:4:0.4:0:1 0/0:1:0:0,0:1,0:0:0,0:42:0:27:0:1:0:60:2:1:0:0 -4 39352061 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53688;SOR=Inf;LSEQ=AGAAAACCACACTCAGGTAA;RSEQ=CCATAGTCAAACTGCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:39,33:0:2,0:30.1:1:32:1:1:0:60:144:1:0:0.2 0/1:128:2:1,1:68,58:0.0156:2,2:16.5:1:33:0:1:1.17095:60:4:0.0159:0:1 -4 39352073 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54687;SOR=Inf;LSEQ=TCAGGTAAGCCATAGTCAAA;RSEQ=TGCTGAAAACCAAAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:33,36:0:2,0:27.9:1:31.7:1:1:0:60:68:1:0:0.2 0/1:132:2:1,1:61,69:0.0152:2,2:18:0:32:0:1:1.13:60:4:0.0152:0:1 -4 39352099 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54819;SOR=Inf;LSEQ=AAAACCAAAAATTAAAAAAT;RSEQ=CTTTAATGAACCATGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:20,31:0:2,0:22.2:1:30:1:1:0:60:102:1:0:0.2 0/1:99:2:1,1:36,61:0.0202:2,2:16:0:33:0:1:1.68:60:4:0.0206:0:1 -4 39933884 . G A 31 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55247;LSEQ=GGCCTGATAAGCATTTGTAC;RSEQ=TTGAGATTGCAATGCCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:20:1:31:0:1:0:60:4:0.5:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:4:0:30:0:1:0:60:2:0.3333:0:1 -4 39934071 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.51782;SOR=Inf;LSEQ=CAAAGTAGAGCTTCATAAAT;RSEQ=CACACAACCAAGGGGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:82,51:0:2,0:25.3:1:28.2:1:1:0:60:43.333:1:0:0.1 0/1:198:2:1,1:114,82:0.0101:2,2:31:1:32:1:1:1.38787:60:4:0.0103:0:1 -4 39934080 . C G 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTCATAAATACACACAAC;RSEQ=AAGGGGAGAAAACCTGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:91,68:0:2,0:25:1:30.9:1:1:0:60:38.75:0.9936:0:0.1 0/1:224:27:15,12:107,90:0.1205:2,2:21.3:1:29.8:1:1:1.05:60:54:0.125:0:1.1 -4 39934103 . C T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15677;SOR=0;LSEQ=GGGGAGAAAACCTGTGGTGG;RSEQ=TGTGAAGGTCCTGATGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:89,95:0.0108:2,2:24:0:30.5:1:1:1.07:60:4:0.0109:0:2 0/0:283:0:0,0:134,148:0:2,0:28.5:1:31.8:1:1:0:60:46:1:0:0.3 -4 41332071 . CT C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCCTTGATTACCCACCC;RSEQ=TTTTTTTTTAGCTGAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:1:30:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 41333410 . C T 170 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03371;SOR=0.59167;LSEQ=GGCAACTAAAGTTCTGCAGA;RSEQ=TTGTAAATAAATTATATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:50:33,17:105,67:0.2252:2,2:24.4:1:30.2:1:0.61989:1.24:60:24:0.2192:0:2.7 0/1:266:39:23,16:140,87:0.1466:2,2:23.2:1:29.1:1:0.85898:1.11896:60:38:0.1456:0:2.6 -4 41333429 . T G 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=0.48748;LSEQ=ACTTGTAAATAAATTATATC;RSEQ=AACTGTACATAACCTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:67:45,22:102,84:0.2648:2,2:24.6:1:29.5:1:0.08505:1.68:60:21.333:0.2602:0:2.6 0/1:315:47:25,22:150,118:0.1492:2,2:25.6:1:29.6:1:0.75206:1.11824:60:46:0.1465:0:2.6 -4 41333444 . T C 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATCTAACTGTACATAACC;RSEQ=GGGTTACATTCTTGAGCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:155,131:0:2,0:26.2:1:30.5:1:1:0:60:46.667:1:0:0.9 0/1:363:40:23,17:169,154:0.1102:2,2:22.3:1:29.9:1:0.61555:1.23:60:80:0.1127:0:1.9 -4 41333461 . C T 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.39667;SOR=0.87125;LSEQ=ACCTGGGTTACATTCTTGAG;RSEQ=GAATCATATCAACATTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:301:153:76,77:75,73:0.5083:2,2:26.9:1:29.9:1:0.90838:1.0408:60:152:0.5067:0:1.7 0/1:382:181:87,94:97,103:0.4738:2,2:26.4:1:29.4:1:1:1.01748:60:180:0.4737:0:1.6 -4 41333541 . CT C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49884;SOR=Inf;LSEQ=GTTAAACAGTTTATTCTTCC;RSEQ=TCATACCAAGTTCCTTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:28,106:0:2,0:23.7:1:30:1:1:0:60:133:1:0:0.2 0/1:144:2:1,1:43,99:0.0139:2,2:10.5:1:29.5:1:0.51923:2.29:60:4:0.0144:0:0.5 -4 41333562 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49727;SOR=0;LSEQ=TTCATACCAAGTTCCTTAGG;RSEQ=ATTTGGATTCACCCTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:11,78:0.022:2,2:22:0:32:0:0.24762:6.83:60:4:0.0227:0:1.5 0/0:89:0:0,0:20,69:0:2,0:20.6:1:31.4:1:1:0:60:88:1:0:0.1 -4 41333674 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=AGAACTTGCTATAAAAGCAT;RSEQ=TTAATCTTTTGTTAACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:0.2:0,0:30:1:32:1:1:0:60:4:0.2:0:1 0/0:8:0:0,0:0,8:0:0,0:23.6:1:33.6:1:1:0:60:16:1:0:0 -4 41746460 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGTAGAGGAGACAGTCTG;RSEQ=ACTGATATTAACACGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 41746862 . GA G 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.57655;SOR=2.72824;LSEQ=GGGTAGGCGGGAGCGAGGGG;RSEQ=AAAAAAGAGTTGCGAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:1:1,0:173,9:0.0055:1,0:23:0:33:0:1:0:60:2:0.0057:0:0 0/1:135:2:2,0:126,6:0.0148:1,0:36:1:31.5:1:1:0:60:4:0.0149:0:0 -4 41747149 . T TA 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54594;SOR=0.88073;LSEQ=GGGGGCTGGAACGGCGTCCC;RSEQ=ACTCTTCCCTGAAGAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:54:21,33:158,321:0.1013:2,2:27.9:1:29.7:1:0.44736:1.29:60:53:0.1002:0.0113:0.1 0/1:609:55:20,35:194,355:0.0903:2,2:21.8:1:28.7:1:0.88325:1.05:60:26.5:0.0888:0.0296:0.2 -4 41747225 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53493;SOR=0;LSEQ=TTAGGGGTTCACAAGATCGA;RSEQ=CCTTCAGCTCCAGCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:0,2:2,141:0.0138:1,0:39.5:1:32:0:1:0:60:4:0.0143:0:1 0/0:83:0:0,0:3,80:0:1,0:25.5:1:31.8:1:1:0:60:40.5:1:0:0.1 -4 41747663 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGAAATGAGGGCGACGC;RSEQ=GTTTTCCCTTTATTCTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:6,3:0.1818:2,0:12:0:32:0:1:0:60:4:0.1818:0:1 0/0:4:0:0,0:4,0:0:0,0:31:1:23:1:1:0:60:3:1:0:0 -4 41747691 . C G 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06291;SOR=0;LSEQ=CTTTATTCTTAGCGCGATTA;RSEQ=TTTAGGCCCTCAATGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:13,2:0.25:2,2:8.2:1:31.8:1:1:1.58265:60:10:0.25:0:1.2 0/0:14:0:0,0:13,1:0:1,0:19.7:1:29.6:1:1:0:60:13:1:0:0 -4 41747763 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21453;SOR=Inf;LSEQ=GCCTACCCGCTCGCCCACTC;RSEQ=CCCGCCCGGGCCCTGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:97,15:0:2,0:19.1:1:30:1:1:0:60:111:1:0:0.2 0/1:98:2:1,1:82,14:0.0204:2,2:34:1:30:1:0.28403:5.69299:60:4:0.0208:0:1 -4 41747779 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49859;SOR=0;LSEQ=ACTCGCCCGCCCGGGCCCTG;RSEQ=CTCGCCCGCTGTCGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:145,25:0.0116:2,2:26.5:1:29.5:1:0.28023:5.707:60:4:0.0119:0:1 0/0:168:0:0,0:135,32:0:2,0:18.7:1:31.2:1:1:0:60:82.5:0.994:0:0.2 -4 41747783 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23761;SOR=0;LSEQ=GCCCGCCCGGGCCCTGGCTC;RSEQ=CCCGCTGTCGCCGCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:156,27:0.0108:2,2:34:1:30.5:1:0.28049:5.69188:60:4:0.011:0:1.5 0/0:194:0:0,0:155,39:0:2,0:19.3:1:29.8:1:1:0:60:37.8:1:0:0.2 -4 41747786 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21497;SOR=0;LSEQ=CGCCCGGGCCCTGGCTCGCC;RSEQ=GCTGTCGCCGCCGCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:2,0:163,30:0.0103:2,0:12:1:29:1:1:0:60:4:0.0105:0:1.5 0/0:225:0:0,0:168,56:0:2,0:19.1:1:30.1:1:1:0:60:73.667:0.9955:0:0.3 -4 41747791 . TCGC T 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.14908;SOR=0.56684;LSEQ=GGGCCCTGGCTCGCCCGCTG;RSEQ=CGCCGCCGCCGCCGCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:20:12,8:173,49:0.0823:2,2:19.2:1:30.7:1:0.09562:2.34395:60:40:0.0844:0.0247:0.1 0/1:269:13:7,6:183,68:0.0483:2,2:19.2:1:30.5:1:0.20083:2.29843:59.6:26:0.0492:0.0149:0.3 -4 41747797 . C T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=3;SSF=0.67597;SOR=0.61861;LSEQ=TGGCTCGCCCGCTGTCGCCG;RSEQ=CGCCGCCGCCGCCGCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:2,1:209,71:0.0106:2,2:16:1:29.3:1:1:1.46964:60:6:0.0107:0:1 0/0:304:2:0,2:214,85:0.0066:2,0:1:1:26.5:1:0.08286:0:60:6:0.0057:0:1 -4 41748117 . G A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=3.000;MSILEN=1;SSF=0.67105;SOR=0.59522;LSEQ=CGGAGCTCCAGCCGGGCTGG;RSEQ=CCCGCCGCCGCCGCCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:207,48:0.0116:2,2:17.3:1:28.7:1:0.46986:2.14839:60:6:0.0117:0:1 0/0:289:2:1,1:214,72:0.0069:2,2:10:0:31.5:1:0.44336:2.95862:60:4:0.0072:0:1.5 -4 41748118 . CCCG C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.78086;SOR=0.77091;LSEQ=GGAGCTCCAGCCGGGCTGGG;RSEQ=CCGCCGCCGCCTCCATTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:7:4,3:215,52:0.0255:2,2:29.3:1:31.7:1:0.14673:3.08421:60:14:0.0257:0.0036:0.1 0/1:303:6:5,1:219,78:0.0198:2,2:28.2:1:31.6:1:1:1.78:59.2:12:0.0202:0.0033:0.7 -4 41748217 . G A 196 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03018;LSEQ=TCAGTGCTCTTGGCCTCTTT;RSEQ=CTCTCGTCGTCCCTGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1221:118:60,58:606,497:0.0966:2,2:25.4:1:28.6:1:0.43672:1.17851:60:38.333:0.0961:0:1.1 0/0:1555:5:5,0:844,704:0.0032:2,0:1:0:24.6:1:0.06756:0:60:10:0.0033:0:1 -4 41748511 . T G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09684;SOR=0.19567;LSEQ=CCAAGTCTACCGCTTCTTAT;RSEQ=GCTGTGCATTTTCGGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:0,6:0.6471:0,0:22.5:1:32.1:1:1:0:60:22:0.6471:0:1.3 0/1:8:2:0,2:0,6:0.25:0,0:8.5:1:30.5:1:1:0:60:4:0.25:0:1 -4 41749265 . T C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.61971;SOR=0.71005;LSEQ=CATGGGGCCCTAGGTCCTTC;RSEQ=CACTCGAGGCTCCAGGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:12:11,1:27,1:0.3:1,2:28.8:1:31.9:1:0.51538:2.39319:60:24:0.3077:0:1 0/1:43:10:9,1:31,2:0.2326:2,2:11.5:1:30.7:1:0.5579:1.69793:60:20:0.2326:0:1.1 -4 41749354 . A T 38 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35361;SOR=0.30424;LSEQ=GCGGAGCGGGGTCGGTTTCC;RSEQ=GGCGCGCGTACCTGGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:1,2:174,92:0.0112:2,2:5.3:1:24:1:0.28022:3.76309:53.3:2:0.0077:0:2.7 0/0:293:1:0,1:181,110:0.0034:2,0:1:0:28:0:0.38014:0:60:2:0.0034:0:1 -4 41749576 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20868;SOR=0;LSEQ=AGAGTATGACAGAGGAGACA;RSEQ=AAAGTGAGCAAATCAGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:48,133:0.0109:2,2:25:1:29.5:1:0.4649:2.75:60:4:0.011:0:2 0/0:217:0:0,0:64,152:0:2,0:23.8:1:30.9:1:1:0:60:71:0.9953:0:0.2 -4 41749584 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=ACAGAGGAGACAGAAAGTGA;RSEQ=CAAATCAGCCGGCAGCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:40,127:0:2,0:22.2:1:32.2:1:1:0:60:334:1:0:0.1 0/1:175:2:1,1:48,124:0.0114:2,2:29:0:28.5:1:0.48508:2.57:60:4:0.0116:0:1 -4 41749668 . C T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.76104;SOR=1.2444;LSEQ=CGGCAGCCGCTACCTACACC;RSEQ=GCGCGAGAGAGTTGCCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:16:2,14:0,20:0.4444:1,2:22.6:1:31.1:1:0.19048:0:60:32:0.4444:0:1 1/0:14:7:0,7:0,7:0.5:0,0:28.9:1:28.4:1:1:0:60:6:0.4615:0:1 -4 41750650 . G A 78 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03458;SOR=7.40967;LSEQ=AAAAGGTTCTGGATGGCTCA;RSEQ=CCAAGTGGAAAAATGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:1:1,0:129,219:0.0029:2,0:32:0:15:0:0.37249:0:60:0:0:0:3 0/1:335:7:5,2:120,208:0.0209:2,2:25.7:1:28.1:1:0.10705:4.31:60:14:0.0211:0:1 -4 41753130 . A C 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCTCTGCTGTAGGGTTTA;RSEQ=GCGCGTTTCCCTGCAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:0:0,0:198,406:0:2,0:24.5:1:30.5:1:1:0:60:59.4:1:0:0.1 0/1:813:63:26,37:292,456:0.0775:2,2:24.4:1:30.1:1:0.78844:1.10:60:62:0.0772:0:1.1 -4 46047034 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACGTATGAAAGTAAAAT;RSEQ=CGATGGTTGCAAACTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34.5:1:30:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 46047311 . T G 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00632;SOR=Inf;LSEQ=TCATAAAGTTATTGTAAATT;RSEQ=TTAATAAGCTAAAAGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:85,28:0:2,0:24.5:1:29.9:1:1:0:60:36.667:1:0:0.1 0/1:163:10:7,3:105,48:0.0613:2,2:14.7:1:31.6:1:1:1.07:60:20:0.0625:0:1 -4 46047406 . T C 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.59183;SOR=0.90796;LSEQ=TAAAAGGAAAATCTGGAATA;RSEQ=ATGCTGAACCTAAGAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:113:48,65:47,63:0.5045:2,2:26.7:1:32.1:1:1:1.01021:60:112:0.5045:0:1.1 0/1:279:134:67,67:62,83:0.4803:2,2:27:1:31.4:1:0.23221:1.34:60:133:0.4801:0:1.1 -4 46047625 . GA G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.37796;LSEQ=TGGAAAGTTTCTTAAGAAAA;RSEQ=AAAAAAGTTTTATCTGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:15.8:1:32.3:1:1:0:60:12:0.8571:0:0.3 1/0:3:2:0,2:0,1:0.6667:0,0:32.5:1:33:0:1:0:60:4:0.6667:0:0 -4 46477824 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19026;SOR=0;LSEQ=CACCAACCCCCTACCCTGAT;RSEQ=CTTGGCTACAAATCCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:35,37:0.027:2,2:14:1:27.5:1:1:1.06:60:4:0.0282:0:1 0/0:95:0:0,0:50,45:0:2,0:28.6:1:30.9:1:1:0:60:190:1:0:0.2 -4 46725771 . TG T 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00184;SOR=Inf;LSEQ=GGCTCCACCGTTTTTTTTCT;RSEQ=GTTTTTTTTTTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:44,1:0:1,0:22.4:1:31.3:1:1:0:56.4:21.5:0.9773:0:1.4 0/1:42:8:7,1:32,1:0.1905:1,2:19.6:1:30.5:1:0.3561:4.34249:52.5:16:0.2051:0.0952:2.5 -4 46725949 . C T 129 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=23.46253;LSEQ=TTGATGCCTCGCTGTGTGAG;RSEQ=GCCGAGCGCTCCAGGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:1:1,0:206,165:0.0027:2,0:20:0:31:0:1:0:60:2:0.0028:0:1 0/1:369:22:14,8:191,155:0.0596:2,2:22.5:1:29.1:1:0.51119:1.42:58.6:44:0.0606:0:1.1 -4 46726006 . C T 87 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04055;SOR=7.28567;LSEQ=TTAGCCATGGCTAGACCCTG;RSEQ=GGATAGGTGATGGGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:1:0,1:260,217:0.0021:2,0:1:0:25:0:0.45607:0:50:2:0.0021:0:1 0/1:531:8:2,6:296,225:0.0151:2,2:28:1:29.3:1:0.08474:3.93697:56.1:16:0.0152:0:1.3 -4 46726267 . C T 195 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03019;LSEQ=CCAGCTGTATCCCATAAGCC;RSEQ=AGATTCACCGGTTTTCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:639:99:47,52:255,285:0.1549:2,2:27.4:1:29.5:1:1:1.01:53.3:98:0.1551:0:1.1 0/0:728:4:2,2:357,366:0.0055:2,2:5:1:24.3:1:1:1.03:52.3:3:0.0042:0:1.3 -4 46726433 . G A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37766;SOR=3.57073;LSEQ=TGATGGCCTGCATCAGGGCC;RSEQ=CTCGCTGGGCCGCGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:1:1,0:76,245:0.0031:2,0:1:0:26:0:0.23913:0:60:2:0.0031:0:1 0/1:363:4:2,2:115,244:0.011:2,2:28.3:1:23.5:1:0.59699:2.12:57.3:3:0.0084:0:1 -4 46726444 . CGCG C 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.1851;SOR=2.25655;LSEQ=ATCAGGGCCGCTCGCTGGGC;RSEQ=GCGGCGGCGGCAGGGCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:4:1,3:53,201:0.0155:2,2:24.5:1:31.3:1:1:1.26:60:8:0.0159:0.0039:0.3 0/1:291:10:5,5:80,199:0.0344:2,2:22.6:1:30:1:0.16515:2.48:56.4:20:0.0352:0.0103:0.3 -4 46726491 . G T 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00487;SOR=0;LSEQ=TAGGAAGCGGCGGGCTCGGG;RSEQ=CGCGGCGGACGGGCGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:10:1,9:5,38:0.1887:2,2:10.8:1:28.7:1:1:1.18059:47.5:9:0.1765:0:1 0/0:36:0:0,0:3,33:0:2,0:7.5:1:32.1:1:1:0:49.5:72:1:0:0.3 -4 46726505 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCGGGGCGCGGCGGACGGG;RSEQ=GCGCGGCTTCCGGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:0,13:0.1333:1,2:31.5:1:30.5:1:0.13333:0:51:4:0.1429:0:1.5 0/0:2:0:0,0:0,2:0:0,0:14:1:29:1:1:0:46:4:1:0:0 -4 47493210 . C G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00116;SOR=0.22596;LSEQ=TGCTTAATGTGCTCAATATG;RSEQ=ACATTAATTCTCTTGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:21:19,2:28,3:0.4038:2,2:29.9:1:30.5:1:1:1.02:60:9.5:0.3958:0:1 0/1:61:8:7,1:50,3:0.1311:2,2:22.6:1:31.4:1:0.43888:2.33716:60:16:0.1333:0:1.1 -4 47493308 . G GTAACAC 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=2.000;MSILEN=2;SSF=0;SOR=0.27211;LSEQ=ACTCTTCCAGTTTTGCCATG;RSEQ=TAACACTGGTGGGGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:53:25,28:54,60:0.3174:2,2:28.7:1:30.7:1:1:1.00795:59.9:52:0.321:0.0419:0.1 0/1:259:29:15,14:107,123:0.112:2,2:27.2:1:29.3:1:0.69403:1.23:58.6:58:0.1146:0.0232:0.1 -4 47493401 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50122;SOR=Inf;LSEQ=ATTCACAGGTATGTGGCCAA;RSEQ=GGAACAACTCCATGTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:82,24:0:2,0:22.8:1:30.9:1:1:0:59.9:105:1:0:0.2 0/1:125:2:1,1:86,37:0.016:2,2:9:1:29:1:0.51729:2.30686:60:4:0.0164:0:1 -4 47493437 . C T 41 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.39271;LSEQ=TTTCTAAAAGGCCTAGAGAA;RSEQ=ATGTATGGGGTGCCGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:2:0,2:147,69:0.0092:2,0:1:0:22.5:1:0.10506:0:60:4:0.0094:0:1 0/1:314:4:1,3:202,108:0.0127:2,2:8.3:1:20.5:1:0.12839:5.57951:60:3:0.0098:0:1.5 -4 48087855 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCTCCCCATGCATCCC;RSEQ=CTGAGAGCCATCTCCATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 48088069 . C T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAACACCTCTAGACACTGT;RSEQ=GTGGGGCCAGAGCCCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 48088419 . C T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59207;SOR=0.32855;LSEQ=AGGTGTGGCTGCCTCCAAAG;RSEQ=TCATGTTGTTTCCATGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:21:1:30.2:1:1:0:60:10:0.7143:0:2 0/1:7:3:3,0:4,0:0.4286:0,0:21.7:1:31.3:1:1:0:60:6:0.4286:0:1.7 -4 48088446 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13846;SOR=0;LSEQ=TGTTTCCATGACACCAGGGC;RSEQ=TGGTATGATATTTATCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:12,4:0,0:1:0,2:17.4:1:30.3:1:1:0:60:32:1:0:1.4 1/1:10:8:7,1:1,1:0.8:2,2:32.8:1:30.1:1:0.37778:5.29:60:16:0.8:0:1.3 -4 48355959 . C T 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGAGAGAAAACAGTCGA;RSEQ=ATTGGCTCAAAAATTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:28.3:1:30.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 48356063 . C T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=TTAGAGCTCTGTGACTGACA;RSEQ=CAAGGAGAAAGATTAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:3,0:0.25:0,0:3:0:29:0:1:0:60:2:0.25:0:1 1/0:4:2:2,0:2,0:0.5:0,0:28:1:32:0:1:0:60:4:0.5:0:1.5 -4 48356096 . T G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.47619;SOR=0;LSEQ=TTAGAACTATCAGAAAATTA;RSEQ=GTATGTCCAAAAACCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:6.5:1:33:0:1:0:60:4:0.1818:0:1 0/0:10:0:0,0:10,0:0:0,0:26.7:1:31.5:1:1:0:60:20:1:0:0.3 -4 48356153 . T TA 47 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.26454;LSEQ=AGCAACAAAAACTTTCAAAT;RSEQ=AAAAAAAAAAGTTATCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:33,0:0.0833:1,0:32:1:30:0:1:0:60:6:0.0833:0:0.3 0/1:29:3:3,0:25,1:0.1034:1,0:34.3:1:30:0:1:0:60:6:0.1034:0:0 -4 48356244 . C T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26308;SOR=Inf;LSEQ=TGATAGAATAACAAAAAGAT;RSEQ=CTGGGCTATATAAAGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:147,66:0:2,0:24:1:30.9:1:1:0:60:70:1:0:0.2 0/1:282:3:1,2:193,85:0.0106:2,2:17.3:1:20.3:1:0.22734:4.51385:60:2:0.0072:0:1.7 -4 48356333 . G A 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0074;SOR=0.68677;LSEQ=TCATCACTTCTAGCTTGGGT;RSEQ=ATTAAACTGTTGTAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:352:225:107,118:61,65:0.6392:2,2:24.9:1:28.7:1:0.91155:1.03485:60:55.25:0.6351:0:1.1 1/0:574:315:152,163:123,135:0.5488:2,2:24.2:1:28.6:1:0.93307:1.02:60:77.75:0.5495:0:1.1 -4 48356375 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05213;SOR=0;LSEQ=TAGAAAAAACTGATGGGAAA;RSEQ=GGAAAAAGTTAAGGGATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:102,187:0.0103:2,2:23.7:1:25.3:1:1:1.0906:60:2:0.0069:0:2 0/0:488:0:0,0:189,299:0:2,0:25.3:1:30.5:1:1:0:60:96.6:1:0:0.5 -4 48356478 . C T 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45452;SOR=1.49597;LSEQ=GAGATCCTCGTTAATTGTTA;RSEQ=GGATATTTTTTTTTTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:24:0,24:0,13:0.6486:1,1:19.5:1:30.5:1:1:0:60:23:0.6765:0:1.3 1/0:34:25:0,25:0,9:0.7353:0,1:16.4:1:31:1:1:0:60:50:0.7353:0:1.2 -4 48356483 . AT A 115 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.79101;SOR=1.16822;LSEQ=CCTCGTTAATTGTTACGGAT;RSEQ=TTTTTTTTTTCCCCCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:0,13:0,17:0.4194:1,1:21.7:1:31.1:1:1:0:60:26:0.4483:0.0968:1.2 0/1:24:11:0,11:0,13:0.4583:1,0:18.2:1:30.8:1:1:0:60:22:0.4583:0.2083:1.5 -4 49093275 . G C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTCCGTTTCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:32.5:1:1:0:29:4:1:0:3.5 -4 49093282 . A T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTTTCATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCTACACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:31:1:1:0:29:4:1:0:3.5 -4 49093302 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCTACACG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:28.5:1:1:0:29:4:1:0:3.5 -4 49093349 . A T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCAGTCGTGTTGAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:30:1:1:0:60:4:1:0:2.5 -4 49093386 . A T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATGCCATTCCATTC;RSEQ=ATTCAATTCCATTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:37:0:32:0:1:0:44:2:1:0:6 1/1:2:2:2,0:0,0:1:0,0:14.5:1:30.5:1:1:0:37:4:1:0:5.5 -4 49093390 . C CGCGTT 55 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATGCCATTCCATTCAATT;RSEQ=AATTCCATTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:27.3:1:1:0:52:4:1:0.5:5.5 1/1:4:4:3,1:0,0:1:0,2:14:1:27.8:1:1:0:39.5:8:1:0.75:6.3 -4 49093414 . TA GC 33 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TCCATTCCACTCCATTCCAT;RSEQ=CATTCCATTCCACTCGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:17:0:33.8:1:1:1:45:4:0.5:0:3.5 0/0:6:0:0,0:3,3:0:2,0:27.8:1:27.8:1:1:0:39.8:12:1:0:6 -4 49093425 . C G 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=CCATTCCATTACATTCCATT;RSEQ=CACTCGAGTTGATTCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:1:31.5:1:1:1:52:4:0.5:0:5.5 1/1:6:6:3,3:0,0:1:0,2:33.7:1:31.2:1:1:0:39.8:12:1:0:6 -4 49093428 . C A 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=TTCCATTACATTCCATTCCA;RSEQ=TCGAGTTGATTCTATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:1:29.5:1:1:1:52:4:0.5:0:5.5 1/1:6:6:3,3:0,0:1:0,2:34.7:1:26.8:1:1:0:39.8:5:1:0:6 -4 49093429 . T A 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TCCATTACATTCCATTCCAC;RSEQ=CGAGTTGATTCTATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:31:0:31:0:1:1:45:4:0.5:0:3.5 0/0:6:0:0,0:3,3:0:2,0:35:1:26:1:1:0:39.8:5:1:0:6 -4 49093432 . A G 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=ATTACATTCCATTCCACTCG;RSEQ=GTTGATTCTATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:34:0:32.5:1:1:1:45:4:0.5:0:3.5 0/0:6:0:0,0:3,3:0:2,0:36:1:26.7:1:1:0:39.8:5:1:0:6 -4 49093433 . G C 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=TTACATTCCATTCCACTCGA;RSEQ=TTGATTCTATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:1:31:1:1:1:52:4:0.5:0:5.5 1/0:6:4:2,2:1,1:0.6667:2,2:38:1:31.5:1:1:1:43.3:8:0.6667:0:6.8 -4 49093441 . T C 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=CATTCCACTCGAGTTGATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:26.5:1:30.5:1:1:1:52:4:0.5:0:5.5 1/0:6:4:2,2:1,1:0.6667:2,2:35:1:31:1:1:1:43.3:8:1:0:6.8 -4 49093466 . C A 50 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.19643;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:11:1:31.3:1:1:0:50:6:1:0:4 1/0:5:3:1,2:1,1:0.6:2,2:15.3:1:32:0:1:1.7321:44:6:0.6:0:7 -4 49093468 . T G 33 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.46429;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:9:1:30.7:1:1:0:50:6:1:0:4 0/1:5:2:1,1:1,1:0.4:2,2:10:0:33.5:1:1:1:42:4:0.5:0:7 -4 49093472 . A T 51 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.4;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:18:0:33:0:1:0:60:2:1:0:5 1/0:4:3:1,2:0,1:0.75:0,2:9.3:1:32.3:1:1:0:44:6:1:0:7 -4 49093869 . CA TGTTTTATTCAG 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=TTCCATTACATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:27.5:1:29.5:1:1:1:40.5:4:0.5:0.25:4.5 0/0:1:0:0,0:1,0:0:0,0:15:0:32:0:1:0:22:2:1:0:5 -4 49093891 . CG TT 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCCATTACATTCCATTCCA;RSEQ=CGAATTGATTCTATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:18.5:1:28.8:1:1:1:24:4:0.5:0:4 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49093893 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCATTACATTCCATTCCACG;RSEQ=GAATTGATTCTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22:1:30:1:1:1:40.5:4:0.6667:0:4.5 0/0:1:0:0,0:1,0:0:0,0:39:0:33:0:1:0:22:2:1:0:4 -4 49093896 . A T 59 d7;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=TTACATTCCATTCCACGCGA;RSEQ=TTGATTCTATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:16.8:1:29.5:1:1:0:32.3:8:1:0:4.3 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49093904 . T C 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCACGCGAATTGATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:11:1:32:1:1:1:40.5:4:0.5:0:4.5 1/1:1:1:1,0:0,0:1:0,0:35:0:32:0:1:0:22:2:1:0:4 -4 49093914 . C TATTACGTTTCTTTCCATTCCACGCCATATG 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=1;LSEQ=GAATTGATTCTATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:22:1:30.3:1:1:0:40.5:4:0.6667:0.6667:4.5 1/0:3:2:1,1:1,0:0.6667:0,2:4:1:30.5:1:1:0:60:4:0.6667:0.6667:7.5 -4 49093918 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.4;SOR=Inf;LSEQ=TGATTCTATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:32.5:1:1:0:40.5:4:1:0.5:3.5 1/0:3:2:1,1:1,0:0.6667:0,2:8:0:29.5:1:1:0:60:4:0.6667:0:7.5 -4 49093921 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=0.4;SOR=Inf;LSEQ=TTCTATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:31.5:1:1:0:40.5:4:1:0.5:3.5 1/0:3:2:1,1:1,0:0.6667:0,2:11:0:33:1:1:0:60:4:0.6667:0:7.5 -4 49093928 . C G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCGGGTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:32:0:1:0:40:2:1:0:4 1/0:3:2:1,1:1,0:0.6667:0,2:18:0:32:0:1:0:60:4:0.6667:0:7.5 -4 49093952 . G T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCGGGTTCATTCCAT;RSEQ=CCATTCAATTCCATTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:38:0:30:0:1:0:40:2:1:0:4 0/1:5:2:1,1:2,1:0.4:2,2:9:0:31:1:1:1.7321:26:4:0.4:0:3.5 -4 49093955 . A AATCCGTTCCATTCTACTCTGGTTGATTCAATTCT 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCGGGTTCATTCCATGCC;RSEQ=TTCAATTCCATTCTGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:28:0:1:0:40:2:1:0:4 0/1:6:2:1,1:2,2:0.3333:2,2:37.5:1:28.5:1:1:1:45:4:0.3333:0.3333:3.5 -4 49093963 . CC AA 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATTCCATGCCATTCAATT;RSEQ=ATTCTGTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:27:0:28:0:1:0:40:2:1:0:4 0/1:7:2:1,1:3,2:0.2857:2,2:21:0:31.5:1:1:1.41418:26:4:0.2857:0:2.5 -4 49093964 . C A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATGCCATTCAATTC;RSEQ=ATTCTGTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:26:0:28:0:1:0:40:2:1:0:4 0/1:7:2:1,1:2,1:0.2857:2,2:35.5:1:29:1:1:1.7321:60:4:0.4:0:7.5 -4 49093969 . T C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCATTCAATTCCATTC;RSEQ=GTTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:3,2:0.2857:2,2:30.5:1:29.5:1:1:1.41418:60:4:0.2857:0:7.5 -4 49093983 . C G 33 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCTGTTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:8:1:29.5:1:1:0:42:4:1:0:2 0/1:8:2:1,1:4,2:0.25:2,2:28:0:33:1:1:1.8258:45:4:0.25:0:3.5 -4 49093984 . C CATTCCACTCAACCCGGATTT 29 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCTGTTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:8:1:29.5:1:1:0:42:4:1:0:2 0/1:9:2:1,1:4,3:0.2222:2,2:17:1:29.4:1:1:1.29098:45.5:4:0.2222:0.2222:3 -4 49093985 . A T 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCTGTTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:8:1:28.5:1:1:0:42:4:1:0:2 0/1:9:2:1,1:3,3:0.2222:2,2:28:1:31.5:1:1:1:45:4:0.2222:0:3.5 -4 49093994 . C T 25 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:8:1:31.5:1:1:0:42:4:1:0:2 0/1:9:2:1,1:4,3:0.2222:2,2:5.5:1:25:0:1:1.29098:60:4:0.2222:0:7.5 -4 49094019 . C G 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTGCCTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:33:0:1:0:44:2:1:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:28:1:30:1:1:0:45.5:4:0.6667:0:3 -4 49094040 . AC GATCCAA 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.14286;SOR=Inf;LSEQ=ATTCCATTGCCTTCCATTCC;RSEQ=TCCATTGCCTTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:7.5:1:30.3:1:1:0:34.8:8:1:0:2.8 1/0:3:2:1,1:1,0:0.6667:0,2:29.5:1:28.8:1:1:0:45.5:4:0.6667:0.3333:3 -4 49094046 . TTG CCC 30 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TTGCCTTCCATTCCACTCCA;RSEQ=CCTTCCATTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:18:0:30.2:1:1:0:34:4:0.5:0:2.5 0/0:2:0:0,0:1,1:0:2,0:24:1:32:0:1:0:36.5:4:1:0:4 -4 49094061 . C A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CTCCATTGCCTTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:24.7:1:31:1:1:0:31.7:6:0.75:0:2.3 0/1:7:2:0,2:4,1:0.2857:2,0:14:1:32:0:0.14286:0:35:4:0.2857:0:6 -4 49094073 . CC TA 27 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=15.000;MSILEN=5;SSF=0.09524;SOR=0;LSEQ=CCATTCCACTCCATTCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:15.5:1:27.8:1:0.4:0:34:4:0.4:0.2:3 0/0:10:0:0,0:5,5:0:2,0:13.7:1:32.2:1:1:0:34.8:20:1:0.1:4.9 -4 49094083 . C T 29 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=15.000;MSILEN=5;SSF=0.17582;SOR=0.13707;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,1:0.5:0,0:24:1:29:1:0.33333:0:25.5:4:0.5:0:3.5 0/1:10:1:1,0:4,5:0.1:2,0:21:0:32:0:1:0:23:2:0.1:0:3 -4 49094096 . T C 31 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=5;SSF=0.12281;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:19.5:1:31:1:1:1.41418:51.5:4:0.2857:0:4.5 0/0:12:0:0,0:6,6:0:2,0:25.3:1:30.1:1:1:0:35.2:24:1:0:4.3 -4 49094106 . T C 34 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.18947;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:14.5:1:34:0:1:1.29:58.5:4:0.2222:0:2.5 0/0:11:0:0,0:5,6:0:2,0:28.2:1:29.7:1:1:0:36.3:22:1:0:4.3 -4 49094111 . T C 48 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.21842;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:19.7:1:30.4:1:1:0:45.9:18:1:0:3 0/1:11:3:1,2:4,4:0.2727:2,2:21.7:1:30.3:1:1:1.87936:36:6:0.3:0:4 -4 49094125 . A T 61 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.11497;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:28.4:1:30.4:1:1:0:45.9:18:1:0:3 0/1:13:4:1,3:5,4:0.3077:2,2:34:1:30.5:1:0.55944:3.3873:39:8:0.3333:0:4 -4 49094138 . C G 34 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.47895;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:33.7:1:31.2:1:1:0:45.9:18:1:0:3 0/1:11:2:1,1:4,3:0.1818:2,2:22:1:34:0:1:1.29098:31:4:0.2:0:4.5 -4 49094141 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:36.3:1:32.5:1:1:0:48.6:16:1:0:2.8 0/1:8:2:1,1:1,5:0.25:2,2:32.5:1:30.5:1:0.46429:3.87:51:4:0.2857:0:4 -4 49094143 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGTTGATTCCATACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:26.5:1:30:1:1:1.83:51.5:4:0.25:0:4.5 0/0:7:0:0,0:2,5:0:2,0:21.6:1:28.3:1:1:0:36.4:6:1:0:4.6 -4 49094145 . G A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCATACCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:2,2:0.375:2,2:41:1:32:1:1:1.81007:54.3:6:0.375:0:1.3 0/0:7:0:0,0:2,4:0:2,0:21.5:1:28.3:1:1:0:38.8:5:0.8333:0:4.7 -4 49094149 . GATTCC G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATACCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:31.8:1:30.9:1:1:0:48.6:16:1:0:2.8 0/1:7:2:1,1:1,4:0.2857:2,2:23.5:1:30.5:1:1:3.16:51:4:0.3333:0:4 -4 49094162 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGGTTGATTCCATACCTT;RSEQ=CCATTCCATTCCATTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:18.5:1:30.5:1:1:2.24:48.5:4:0.2222:0:3.5 0/0:4:0:0,0:2,2:0:2,0:20.3:1:25.3:1:1:0:40.5:3:1:0:4.3 -4 49094243 . G C 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTGCTTTCCATTC;RSEQ=ATTCCATTGCATGCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:32.5:1:1:0:50:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49094369 . A G 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TACCATTCCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:14.5:1:30.5:1:1:0:45.5:8:1:0:4.5 1/1:2:2:1,1:0,0:1:0,2:21:0:30:1:1:0:42:4:1:0:5 -4 49094371 . A T 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTGCATTCCAT;RSEQ=CCATTCCATTCCACTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:16.5:1:30:1:1:0:45.5:8:1:0:4.5 1/1:2:2:1,1:0,0:1:0,2:23:0:29:1:1:0:42:4:1:0:5 -4 49094376 . T G 34 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCCATTGCATTCCATACCAT;RSEQ=CCATTCCACTCGGGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:20:0:34:0:1:1:51:4:0.5:0:3.5 0/0:3:0:0,0:1,2:0:2,0:19.3:1:27.3:1:1:0:35.7:6:1:0:4.7 -4 49094377 . C A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CCATTGCATTCCATACCATT;RSEQ=CATTCCACTCGGGATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22.5:1:31.8:1:1:0:45.5:8:1:0:4.5 1/0:3:2:1,1:0,1:0.6667:0,2:29:0:29:1:1:0:42:4:0.6667:0:5 -4 49094382 . C CCCCTG 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GCATTCCATACCATTCCATT;RSEQ=CACTCGGGATGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:25:1:33:0:1:0:47.3:6:0.75:0:3.7 1/0:3:2:1,1:0,1:0.6667:0,2:35:0:31.4:1:1:0:42:4:0.6667:0:5 -4 49094389 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=ATACCATTCCATTCCACTCG;RSEQ=GATGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:32:1:32.3:1:1:0:47.3:6:0.75:0:3.7 1/0:3:2:1,1:0,1:0.6667:0,2:39.5:1:32:1:1:0:42:4:0.6667:0:5 -4 49094404 . A T 31 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=ACTCGGGATGATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28.5:1:31.5:1:1:1:51:4:0.5:0:3.5 0/0:3:0:0,0:1,2:0:2,0:26.3:1:31.3:1:1:0:35.7:6:1:0:4.7 -4 49094423 . C A 48 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.14286;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,2:0:2,0:6:1:32.2:1:1:0:47.3:6:0.75:0:4.7 1/0:4:3:2,1:0,1:0.75:0,2:10:1:30.3:1:1:0:43.3:6:0.75:0:4.7 -4 49094516 . T A 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCCACTCCATTCCATTTCAC;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:31:1:1:0:49:4:1:0:3 0/0:2:0:0,0:1,1:0:2,0:18:0:32:1:1:0:22:4:1:0:3 -4 49094522 . C T 31 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=CCATTCCATTTCACTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:32:0:32.5:1:1:0:49:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:20:0:31.5:1:1:0:22:4:1:0:3 -4 49094525 . T C 33 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTTCACTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:0:33.5:1:1:0:49:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:17:0:33.5:1:1:0:22:4:1:0:3 -4 49094535 . T G 33 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=CTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24:0:32.5:1:1:0:49:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:7:0:33.5:1:1:0:22:4:1:0:3 -4 49094545 . T C 34 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:0:34.5:1:1:0:49:4:1:0:3 0/0:1:0:0,0:1,0:0:0,0:3:0:28:0:1:0:60:2:1:0:0 -4 49094772 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATTACGTTTCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:8.1:1:31.4:1:1:0:34:20:1:0:3.4 0/1:32:2:1,1:15,14:0.0625:2,2:7:1:31.5:1:1:1.06901:25.5:4:0.0625:0:5.5 -4 49094774 . A C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55294;SOR=0.58585;LSEQ=ATTACGTTTCATTCCATTGC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:6,5:0.0833:2,0:10:0:32:0:1:0:40:2:0.0833:0:5 0/1:40:2:1,1:22,16:0.05:2,2:7:1:30.5:1:1:1.36391:25:4:0.05:0:1.5 -4 49094775 . T A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTACGTTTCATTCCATTGCA;RSEQ=TCCATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:9.7:1:30.4:1:1:0:32.1:24:1:0:3.5 0/1:41:2:1,1:22,17:0.0488:2,2:10:0:28.5:1:1:1.28591:44:4:0.0488:0:5 -4 49094779 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.56351;SOR=0.61043;LSEQ=GTTTCATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:7,6:0.0714:2,0:17:0:29:0:1:0:34:2:0.0714:0:3 0/1:45:2:2,0:23,19:0.0444:2,0:15.5:1:32:0:0.49789:0:33.5:4:0.0444:0:5 -4 49094780 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.58855;SOR=0.46035;LSEQ=TTTCATTCCATTGCATTCCA;RSEQ=TCCATTCCATTCCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:0.1333:2,2:5:1:31:1:1:1.1547:21:4:0.1333:0:3 0/1:46:3:3,0:24,19:0.0652:2,0:5:1:31:1:0.25652:0:35:6:0.0652:0:3.7 -4 49094782 . C A 68 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=5;SSF=0.31624;SOR=Inf;LSEQ=TCATTCCATTGCATTCCATT;RSEQ=CATTCCATTCCACTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:12.2:1:30.5:1:1:0:30.7:36:1:0:4 0/1:51:5:4,1:27,19:0.098:2,2:11.4:1:29.6:1:0.63643:2.77:37.8:10:0.098:0:5 -4 49094784 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTGCATTCCATTCC;RSEQ=TTCCATTCCACTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,7:0:2,0:14.6:1:30.1:1:1:0:31.2:34:0.9444:0:4.1 0/1:51:2:1,1:30,18:0.0392:2,2:17.5:1:27.5:1:1:1.64896:42:4:0.0408:0:3.5 -4 49094786 . T G 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.4352;SOR=2.79808;LSEQ=TCCATTGCATTCCATTCCAT;RSEQ=CCATTCCACTCGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:11,8:0.05:2,0:6:0:33:0:0.45:0:22:2:0.05:0:6 0/1:54:7:4,3:28,17:0.1296:2,2:15.3:1:32.7:1:1:1.23018:41.9:14:0.1321:0:5.3 -4 49094787 . C A 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=0.74381;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTCCACTCGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:0,1:11,9:0.0476:2,0:25:0:28:0:0.47619:0:34:2:0.05:0:3 0/1:56:2:2,0:31,22:0.0357:2,0:23.5:1:29.5:1:0.51111:0:33.5:4:0.0364:0:5 -4 49094789 . AT CC 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.56957;SOR=Inf;LSEQ=ATTGCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,10:0:2,0:16.4:1:30.1:1:1:0:33.1:42:1:0:3.7 0/1:60:4:2,2:34,21:0.0667:2,2:23.8:1:30.6:1:0.63918:1.60536:33.3:8:0.0678:0:6 -4 49094792 . C G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.13652;SOR=0.45175;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:12:5,7:0,0:0.48:0,2:10.1:1:30:1:1:0:34.8:11:0.4783:0:4.1 0/1:65:19:11,8:12,5:0.2923:2,2:15.9:1:30.8:1:0.50179:1.71849:38.3:8.5:0.2931:0:4.4 -4 49094794 . A C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=CTCGGGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:11,13:0:2,0:18.9:1:29.7:1:1:0:32.9:48:1:0:4.3 0/1:68:2:1,1:35,25:0.0294:2,2:12.5:1:27.5:1:1:1.39226:22:4:0.0323:0:3 -4 49094795 . C A 32 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74871;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:11,11:0.0385:2,0:23:0:31:0:1:0:25:2:0.0417:0:5 0/1:69:2:1,1:34,26:0.029:2,2:32:1:32:0:1:1.30197:26.5:4:0.0317:0:4.5 -4 49094796 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAC;RSEQ=CGGGTTGATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,14:0:2,0:20.8:1:29.6:1:1:0:33.4:25:1:0:4.1 0/1:72:2:1,1:39,30:0.0278:2,2:15:1:31:1:1:1.29514:29:4:0.029:0:5.5 -4 49094797 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:13,15:0:2,0:20.4:1:30.2:1:1:0:33.8:56:1:0:4.1 0/1:73:2:1,1:40,30:0.0274:2,2:33:0:31.5:1:1:1.32793:42:4:0.0278:0:4.5 -4 49094799 . G C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01085;SOR=0.2849;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:5,7:9,8:0.3871:2,2:24.1:1:28.5:1:0.71038:1.55033:35.6:11:0.3929:0:5.3 0/1:73:11:4,7:32,21:0.1507:2,2:30.6:1:30.6:1:0.18839:2.62498:37.8:22:0.1594:0:4.1 -4 49094803 . G C 51 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.27122;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:14,16:0.0313:2,0:42:0:34:0:1:0:28:2:0.0313:0:5 0/1:76:3:1,2:40,30:0.0395:2,2:10:1:32.7:1:0.57811:2.63133:20.7:6:0.0405:0:6 -4 49094834 . AT A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=0.07124;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:15,16:0.0588:2,2:32:1:29.5:1:1:1.06:42:4:0.0606:0:5.5 0/0:92:0:0,0:44,44:0:2,0:29.7:1:29:1:1:0:34:21:0.9767:0:3.8 -4 49094853 . C CGGATG 84 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.04105;SOR=0.27313;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:3,4:9,10:0.25:2,2:29.9:1:31.5:1:1:1.19164:34:14:0.2692:0:2.4 0/1:85:7:3,4:35,34:0.0824:2,2:28.6:1:30.2:1:1:1.36686:37.9:14:0.0864:0:1.9 -4 49094857 . C G 47 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.05412;SOR=0.10963;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:2,1:9,15:0.1071:2,2:18.7:1:30:1:0.54872:3.18:34.3:6:0.1071:0:3.3 0/1:79:1:1,0:36,40:0.0127:2,0:7:0:33:0:0.48052:0:26:2:0.0128:0:4 -4 49094859 . A G 43 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.60966;SOR=0.53949;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTGCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:0,2:12,13:0.0741:2,0:29.5:1:34:0:0.48718:0:40:4:0.0741:0:5 0/1:73:3:2,1:32,36:0.0411:2,2:19.7:1:27.3:1:0.60381:2.23:38:6:0.0469:0:6 -4 49094862 . C G 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.56912;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTGCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:0:2,0:17.7:1:31.4:1:1:0:33.7:48:1:0:4 0/1:71:4:4,0:27,36:0.0563:2,0:19.5:1:29:1:0.04105:0:41.3:8:0.058:0:3 -4 49094864 . A G 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0.86217;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTGCATTCCATTCCATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:9,11:0.087:2,0:19:1:30:0:0.47619:0:27:4:0.087:0:2 0/1:66:5:2,3:28,30:0.0758:2,2:23.8:1:26.4:1:1:1.39263:42.8:4:0.0656:0:5.4 -4 49094867 . G C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29454;SOR=0.54085;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:4,6:5,4:0.4762:2,2:18.3:1:30.9:1:0.65628:1.81296:37.4:20:0.5263:0:5.1 0/1:61:20:12,8:15,20:0.3279:2,2:15.7:1:29.2:1:0.26947:1.97:37.7:40:0.3448:0:4.3 -4 49094868 . C A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28058;SOR=0.33887;LSEQ=CATTCCATTCCATTCCATTG;RSEQ=ATTCCATTCCATTCCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:13:0:31:0:1:1.11:60:4:0.0952:0:2 0/1:59:2:1,1:27,28:0.0339:2,2:8:0:29.5:1:1:1.04:40:4:0.037:0:1 -4 49094874 . A G 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70215;SOR=0.74586;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TTCCATTCCGTTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:7,7:0.1765:2,2:8.7:1:32.3:1:1:1.9219:25.3:6:0.1765:0:2.3 0/1:51:7:3,4:20,23:0.1373:2,2:12:1:24.1:1:1:1.15601:39.9:2.5:0.1087:0:2.9 -4 49094884 . G A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGCATTCCATTCCATTCC;RSEQ=TTCCTTTCCATTCGTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,4:0:2,0:10.6:1:31.4:1:1:0:37.8:10:0.8333:0:6.8 0/1:21:3:0,3:5,11:0.1429:2,0:29.3:1:29.7:1:0.53044:0:30.7:6:0.1579:0:5.7 -4 49094889 . T G 64 d7;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02763;SOR=0.06446;LSEQ=ATTCCATTCCATTCCGTTCC;RSEQ=TTCCATTCGTGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:1,0:0.6667:0,0:6.5:1:32:1:0.2:0:41:8:0.6667:0:6.8 0/1:11:1:0,1:2,1:0.0909:2,0:7:0:32:0:1:0:39:2:0.1111:0:6 -4 49094892 . C G 43 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51648;SOR=Inf;LSEQ=CCATTCCATTCCGTTCCTTT;RSEQ=CATTCGTGTTGATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:10.5:1:32.8:1:1:0:41.5:8:1:0:5.8 0/1:11:3:0,3:3,4:0.2727:2,0:32.7:1:27.3:1:0.475:0:32.7:2:0.2222:0:6.3 -4 49094895 . T C 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCGTTCCTTTCCA;RSEQ=TCGTGTTGATTCCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:12.3:1:31:1:1:0:42:6:1:0:5.7 0/1:11:3:0,3:4,3:0.2727:2,0:31.7:1:32.3:1:0.2:0:32.7:6:0.3:0:6.3 -4 49094899 . T C 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCGTTCCTTTCCATTCG;RSEQ=GTTGATTCCACTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:32:0:1:0:42:2:1:0:3 0/1:8:3:0,3:3,1:0.375:2,0:28.3:1:30:1:0.14286:0:32.7:6:0.4286:0:6.3 -4 49094910 . C T 63 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=TTCCATTCGTGTTGATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:1:31:1:1:0:51:4:1:0:2 0/1:11:5:1,4:3,3:0.4545:2,2:9.6:1:27.4:1:0.54545:3.51553:46.8:4:0.4:0:3.6 -4 49094938 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=TTTCCAATCCATGACATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:1:28:1:1:0:51:4:1:0:2 0/1:7:2:1,1:2,3:0.2857:2,2:40:1:30.5:1:1:1.41:59.5:4:0.2857:0:3.5 -4 49094962 . A AG 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAATCCATGACATTCAACT;RSEQ=GGTTGAATCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:44:0:31:0:1:0:60:2:1:0:1 1/0:7:5:2,3:0,0:0.7143:0,2:21.4:1:31.4:1:1:0:52.8:10:1:0:2.2 -4 49094976 . G T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAACTAGGTTGAATCCATT;RSEQ=CATTCCATTCCAATCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:30:0:33:0:1:0:60:2:1:0:1 0/1:6:2:1,1:1,3:0.3333:2,2:17.5:1:27.5:1:1:2.45:59.5:4:0.3333:0:3.5 -4 49095011 . A C 49 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCTCTCCATTCAATT;RSEQ=CTCTCTGATTCAATCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:22.3:1:31.3:1:1:0:60:6:1:0:2 -4 49095673 . GG T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCATTTCCATTACACTCG;RSEQ=GTTGATTCCATAGCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:26.2:1:1:0:21:4:1:0.5:1.5 -4 49096627 . A T 30 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:31.5:1:31.5:1:1:0:40:4:1:0:3 0/1:7:2:1,1:1,3:0.2857:2,2:12:0:30:0:1:2.45:30:4:0.3333:0:8 -4 49096631 . CA TC 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=TTCCATTCCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27.5:1:33.5:1:1:0:40:4:1:0:3 0/1:7:2:1,1:2,3:0.2857:2,2:17:0:32.3:1:1:1.41:30:4:0.2857:0:7 -4 49096647 . T G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.44721;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:15:0:32:0:1:0:40:2:0.5:0:3 0/1:7:2:1,1:2,3:0.2857:2,2:32:0:31.5:1:1:1.41:30:4:0.2857:0:7 -4 49096651 . CA AG 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCTTTC;RSEQ=TTCCATTCCGTTCTGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7.5:1:34:1:1:0:40:4:1:0:3 0/1:6:2:1,1:1,3:0.3333:2,2:37:0:32:1:1:2.45:30:4:0.3333:0:6 -4 49096662 . G A 27 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCTGTTCCATTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:39:0:27.5:1:1:0:30:4:0.6667:0:6 -4 49096694 . A T 56 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTTCCATTGCATTCCAT;RSEQ=CCATTCCATTCCACTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:12.3:1:28:1:1:0:34.5:8:1:0:6.3 -4 49109721 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCCATTCCGTTCCTTTC;RSEQ=ATTGCATTCCATTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:29.5:1:1:0:27:4:1:0:3 -4 49109729 . T TCCCCTGCACTCGGGTTGATC 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTTCCTTTCGATTGCAT;RSEQ=CCATTCCATTGCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:28:1:32.2:1:1:1:37:4:0.5:0.5:0 -4 49109730 . CCATTCCATTG C 43 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=31;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCGTTCCTTTCGATTGCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:0,1:0.75:0,2:10.3:1:27.7:1:1:0:31.3:6:0.75:0.5:3.7 -4 49109750 . C G 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.14286;SOR=0;LSEQ=CCATTCCATTGCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:30:1:1:0:58:4:1:0:3.5 0/1:5:1:1,0:2,2:0.2:2,0:16:0:32:0:1:0:40:2:0.2:0:5 -4 49109796 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCGTGTTGATGC;RSEQ=ATTCCAATCCATACCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:41:0:33:0:1:0:58:4:1:0:3.5 0/1:6:2:1,1:2,2:0.3333:2,2:40:1:28:1:1:1:41:4:0.3333:0:3 -4 49109797 . A T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCGTGTTGATGCC;RSEQ=TTCCAATCCATACCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:40:0:30.5:1:1:0:58:4:1:0:3.5 0/1:6:2:1,1:2,2:0.3333:2,2:40:0:31.5:1:1:1:37:4:0.3333:0:2.5 -4 49109813 . T G 34 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.06593;SOR=0;LSEQ=TGCCATTCCAATCCATACCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:24:0:34:1:1:1:58:4:0.5:0:3.5 0/0:10:0:0,0:5,4:0:2,0:15.2:1:30.6:1:1:0:36.6:18:1:0:3.1 -4 49109824 . T C 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.12821;SOR=0;LSEQ=TCCATACCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:12:0:32:0:1:1.7321:30:4:0.4:0:5.5 0/0:8:0:0,0:5,3:0:2,0:13.6:1:29.5:1:1:0:37.8:16:1:0:3.3 -4 49109825 . C T 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.12821;SOR=0;LSEQ=CCATACCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:12:0:31.5:1:1:1.7321:58:4:0.4:0:3.5 0/0:8:0:0,0:5,3:0:2,0:13.4:1:28.9:1:1:0:37.8:7:1:0:3.3 -4 49109829 . T C 33 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.12821;SOR=0;LSEQ=ACCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCGTTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:17:0:33:0:1:1.7321:30:4:0.4:0:5.5 0/0:8:0:0,0:5,3:0:2,0:12.4:1:24.9:1:1:0:37.8:1.667:1:0:3.3 -4 49109831 . C A 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.12821;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCGTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:19:0:32:1:1:1.7321:30:4:0.4:0:5.5 0/0:8:0:0,0:5,3:0:2,0:11.9:1:28.9:1:1:0:37.8:7:1:0:3.3 -4 49109845 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=CCATTCCATTCCATTCCGTT;RSEQ=CATTCCTTTCGTGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,0:0.4:0,2:33:0:29.5:1:1:0:30:4:0.6667:0:5.5 0/0:4:0:0,0:2,2:0:2,0:30.5:1:26.8:1:1:0:32.5:3:1:0:4.8 -4 49109857 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=ATTCCGTTCCATTCCTTTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,1:0:2,0:38.3:1:30:1:1:0:28.3:6:1:0:4.7 0/1:6:2:1,1:2,1:0.3333:2,2:30.5:1:30:1:1:1.7321:20:4:0.4:0:4 -4 49109866 . C CTTTCA 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.45455;SOR=Inf;LSEQ=CATTCCTTTCGTGTTGATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:21.8:1:31.4:1:1:0:38.4:10:1:0:3.4 0/1:6:2:1,1:2,2:0.3333:2,2:30.5:1:29.6:1:1:1:20:4:0.3333:0.1667:4 -4 49109872 . A C 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.18182;SOR=0;LSEQ=TTTCGTGTTGATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:11:0:33:1:1:1.7321:53.5:4:0.4:0:1.5 0/0:6:0:0,0:3,3:0:2,0:29:1:29.5:1:1:0:34:12:1:0:4.7 -4 49109893 . C A 27 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCAATCCATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:9:1:27:1:1:0:27.5:4:0.5:0:4.5 0/0:5:0:0,0:1,2:0:2,0:31.7:1:31.3:1:1:0:41.3:6:0.6:0:5 -4 49109896 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=ATTCCAATCCATTACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:28:1:30.3:1:1:0:44:6:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:45:1:30.5:1:1:1.73:37:4:0.4:0:5.5 -4 49109929 . T C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TACATTCCACTCGGGTTGAA;RSEQ=CCATTCCTTTCCATTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:5:1:29:1:1:0:53.5:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:23:1:29.5:1:1:0:37:4:1:0:5.5 -4 49109932 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCACTCGGGTTGAATCC;RSEQ=TTCCTTTCCATTCCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:4:0:32:0:1:0:53:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:37:4:1:0:5.5 -4 49109937 . T A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGGGTTGAATCCATTCC;RSEQ=TTCCATTCCAATCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:1:27.5:1:1:0:37:4:1:0:5.5 -4 49110289 . C CGGAAG 50 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:10:0:33:0:1:0:41:2:1:0:2 0/1:14:3:2,1:5,4:0.2143:2,2:14:1:31.7:1:1:1.54:37.3:6:0.2143:0.1429:5 -4 49110296 . T C 33 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCAATCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:4.4:1:31.4:1:1:0:38.6:10:1:0:3.6 0/1:15:2:1,1:6,5:0.1333:2,2:18:1:33.5:1:1:1.18321:38:4:0.1333:0:8 -4 49110298 . C G 78 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.26045;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCAATCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:5.6:1:32.4:1:1:0:38.6:10:1:0:3.6 0/1:15:6:2,4:6,3:0.4:2,2:12.8:1:30.5:1:0.31469:3.61926:48:12:0.4:0:7.5 -4 49110299 . C T 28 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCAATCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:7.8:1:32.5:1:1:0:38:8:1:0:4 0/1:15:2:1,1:7,6:0.1333:2,2:35:1:28:1:1:1.1547:47.5:4:0.1333:0:3.5 -4 49110303 . C G 50 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CAATCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:11.8:1:32.3:1:1:0:38:8:1:0:4 0/1:15:3:2,1:6,6:0.2:2,2:26:1:32:1:1:1.91:37.3:6:0.2:0:5 -4 49110304 . C T 31 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.02857;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=AATCCATTCCATTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:13:0:31:1:1:1:28:4:0.5:0:5 0/0:17:0:0,0:9,8:0:2,0:22.9:1:30.6:1:1:0:42.6:34:1:0:6.3 -4 49110306 . A C 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:14.5:1:32:1:1:1:48:4:0.5:0:3 0/0:17:0:0,0:5,2:0:2,0:32.1:1:29.3:1:1:0:40.4:14:0.4118:0:4.4 -4 49110310 . A T 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCAATCC;RSEQ=TTCCATTCCACTCCACTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.8:1:31.8:1:1:0:38:8:1:0:4 0/1:18:3:1,2:8,7:0.1667:2,2:21.7:1:30:1:1:2.18465:35.3:6:0.1875:0:7.3 -4 49110320 . A T 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.02372;SOR=0;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=CTCCACTCCGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28.5:1:32:1:1:1:48:4:0.5:0:3 0/0:19:0:0,0:4,2:0:2,0:34.3:1:28.5:1:1:0:41.2:12:0.3158:0:5.3 -4 49110321 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCAATCCATTCCATTCCA;RSEQ=TCCACTCCGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:29.8:1:33:1:1:0:38:8:1:0:4 0/1:19:2:1,1:7,7:0.1053:2,2:43:1:30.5:1:1:1:38:4:0.125:0:8 -4 49110323 . C G 107 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10446;SOR=Inf;LSEQ=CCAATCCATTCCATTCCACT;RSEQ=CACTCCGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:31.8:1:32.3:1:1:0:38:8:1:0:4 1/0:19:10:4,6:4,2:0.5263:2,2:29.4:1:32.3:1:0.60839:2.79346:42.6:20:0.6667:0:7.1 -4 49110326 . C T 31 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.02372;SOR=0;LSEQ=ATCCATTCCATTCCACTCCA;RSEQ=TCCGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:35:0:31.5:1:1:1:28:4:0.5:0:5 0/0:19:0:0,0:8,8:0:2,0:32.1:1:32:1:1:0:42.1:32:1:0:6.4 -4 49110327 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCACTCCAC;RSEQ=CCGGTTGATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:32:1:31.3:1:1:0:38:8:1:0:4 0/1:19:2:1,1:7,7:0.1053:2,2:44.5:1:29.5:1:1:1:57:4:0.1333:0:8 -4 49110329 . CG GC 103 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10446;SOR=Inf;LSEQ=CATTCCATTCCACTCCACTC;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:30:1:31.5:1:1:0:38:8:1:0:4 1/0:19:10:4,6:2,1:0.5263:2,2:35.8:1:31.2:1:0.55944:2.75172:42.6:20:0.625:0:6.1 -4 49110331 . G T 30 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02372;SOR=0;LSEQ=TTCCATTCCACTCCACTCCG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:30:0:30.5:1:1:1:28:4:0.5:0:5 0/0:19:0:0,0:10,9:0:2,0:33.7:1:30.4:1:1:0:41.3:38:1:0:5.7 -4 49110333 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCACTCCACTCCGGT;RSEQ=GATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:26:1:30.8:1:1:0:38:8:1:0:4 0/1:18:2:1,1:8,8:0.1111:2,2:30:0:31.5:1:1:1:39:4:0.1176:0:6.5 -4 49110334 . G A 29 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07273;SOR=0.07389;LSEQ=CATTCCACTCCACTCCGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:27:0:29.5:1:1:1:28:4:0.5:0:5 0/1:18:1:0,1:9,8:0.0556:2,0:28:0:32:0:1:0:22:2:0.0556:0:7 -4 49110336 . T A 30 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03333;SOR=0;LSEQ=TTCCACTCCACTCCGGTTGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:25:0:30.5:1:1:1.7321:28:4:0.4:0:5 0/0:20:0:0,0:11,9:0:2,0:31.1:1:29.7:1:1:0:40.2:40:1:0:5.6 -4 49110342 . T A 30 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.03077;SOR=0;LSEQ=TCCACTCCGGTTGATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:15:0:30.5:1:1:1.7321:48:4:0.4:0:3 0/0:21:0:0,0:12,9:0:2,0:28:1:29.5:1:1:0:39.6:42:1:0:5.5 -4 49110344 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CACTCCGGTTGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:13.8:1:32.2:1:1:0:38.4:10:1:0:3.2 0/1:21:2:1,1:11,8:0.0952:2,2:35:1:28.5:1:1:1.35399:38:4:0.1:0:8 -4 49110350 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGTTGATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCGTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:10.2:1:31.2:1:1:0:38.4:10:1:0:3.2 0/1:22:2:1,1:12,8:0.0909:2,2:29:1:29.5:1:1:1.47192:38:4:0.0952:0:8 -4 49110354 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCGTTCCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:7.8:1:30.8:1:1:0:38.4:10:1:0:3.2 0/1:22:2:1,1:11,8:0.0909:2,2:25:1:28:1:1:1.35399:38:4:0.0952:0:8 -4 49110365 . G A 26 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCGTTCCGTTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:13:1:29.7:1:1:0:52.7:6:1:0:4 0/1:22:2:2,0:13,7:0.0909:2,0:17.5:1:26:1:1:0:31.5:4:0.0909:0:4 -4 49110370 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCGTTCC;RSEQ=TTCCGTTCCGTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:17:1:29.3:1:1:0:52.7:6:1:0:4 0/1:22:2:1,1:13,7:0.0909:2,2:20.5:1:29.5:1:1:1.80284:39.5:4:0.0909:0:4.5 -4 49110374 . C G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCGTTCCGTTC;RSEQ=GTTCCGTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:18.3:1:30:1:1:0:52.7:6:1:0:4 0/1:21:2:1,1:12,7:0.0952:2,2:6:0:32:0:1:1.66897:30:4:0.0952:0:4.5 -4 49110380 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCGTTCCGTTCCGTTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:20.3:1:30.7:1:1:0:52.7:6:0.75:0:4 0/1:16:2:2,0:9,5:0.125:2,0:45.5:1:30.5:1:1:0:33.5:4:0.125:0:4.5 -4 49110391 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.51087;SOR=Inf;LSEQ=TTCCGTTCCGTTCCATTCCA;RSEQ=TCCATTCCATACCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:13.2:1:29.9:1:1:0:50.3:18:1:0:4 0/1:15:2:2,0:9,2:0.1333:2,0:28:1:29.5:1:1:0:27.5:4:0.1538:0:3.5 -4 49110395 . A G 29 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.13043;SOR=0;LSEQ=GTTCCGTTCCATTCCATTCC;RSEQ=TTCCATACCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:9.5:1:29:1:1:1.29098:48:4:0.2222:0:5 0/0:15:0:0,0:12,3:0:2,0:22:1:29.7:1:1:0:41.7:30:1:0:4.2 -4 49110397 . T G 32 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.12;SOR=0;LSEQ=TCCGTTCCATTCCATTCCAT;RSEQ=CCATACCATTCCACTCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:15.5:1:32.5:1:1:1.29098:44:4:0.2222:0:6 0/0:16:0:0,0:12,4:0:2,0:20.6:1:28.9:1:1:0:40.6:32:1:0:4.3 -4 49110399 . CATACCATTCCAC TAT 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.52;SOR=Inf;LSEQ=CGTTCCATTCCATTCCATTC;RSEQ=TCGGGTTGATTCCATACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,3:0:2,0:14:1:31.6:1:1:0:47.9:14:1:0:3.4 0/1:16:2:1,1:6,3:0.125:2,2:19.5:1:29.2:1:1:1.87089:39.5:4:0.2:0.0625:6 -4 49110408 . C T 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54416;SOR=0.30916;LSEQ=CCATTCCATTCCATACCATT;RSEQ=CACTCGGGTTGATTCCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:26.5:1:31.5:1:1:1.29098:44:4:0.2222:0:6 0/1:13:1:1,0:5,4:0.0769:2,0:18:0:32:0:1:0:40:2:0.1:0:6 -4 49110409 . C T 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54416;SOR=0.30916;LSEQ=CATTCCATTCCATACCATTC;RSEQ=ACTCGGGTTGATTCCATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:43.5:1:29:1:1:1.29098:59:4:0.2222:0:6 0/1:13:1:1,0:5,4:0.0769:2,0:30:0:28:0:1:0:42:2:0.1:0:6 -4 49110410 . A C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15584;SOR=0;LSEQ=ATTCCATTCCATACCATTCC;RSEQ=CTCGGGTTGATTCCATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,3:0.2222:2,2:28.5:1:32.5:1:1:1:44:4:0.2222:0:6 0/0:13:0:0,0:5,3:0:2,0:24.4:1:27.4:1:1:0:42.1:16:0.8:0:4.1 -4 49110411 . C T 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55338;SOR=0.33645;LSEQ=TTCCATTCCATACCATTCCA;RSEQ=TCGGGTTGATTCCATACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:45.5:1:28:1:1:1.29098:59:4:0.2222:0:6 0/1:12:1:1,0:4,4:0.0833:2,0:28:0:27:0:1:0:42:2:0.1:0:6 -4 49110412 . T A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=TCCATTCCATACCATTCCAC;RSEQ=CGGGTTGATTCCATACCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:30.5:1:31:1:1:1:44:4:0.2:0:6 0/0:17:0:0,0:9,6:0:2,0:24.1:1:28.5:1:1:0:42.1:30:1:0:4.5 -4 49110416 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=TTCCATACCATTCCACTCGG;RSEQ=TTGATTCCATACCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:30.5:1:30:1:1:1:48:4:0.2:0:5 0/0:17:0:0,0:9,6:0:2,0:24.9:1:29.6:1:1:0:42.1:30:1:0:4.5 -4 49110419 . G T 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11905;SOR=0;LSEQ=CATACCATTCCACTCGGGTT;RSEQ=ATTCCATACCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,3:0.2:2,2:44:0:30:1:1:1.29098:59:4:0.2:0:6 0/0:18:0:0,0:5,5:0:2,0:26.8:1:30.5:1:1:0:44.2:20:0.625:0:3.8 -4 49110426 . TA AT 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16774;SOR=0;LSEQ=TTCCACTCGGGTTGATTCCA;RSEQ=CCATTCCATTCCATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:0.1538:2,2:36:0:30.8:1:1:1.67325:59:4:0.1538:0:5 0/0:18:0:0,0:8,7:0:2,0:24:1:27.8:1:1:0:41.3:30:1:0:4.4 -4 49110427 . A T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71783;SOR=1.41541;LSEQ=TCCACTCGGGTTGATTCCAT;RSEQ=CCATTCCATTCCATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:3,1:4,3:0.3077:2,2:8.3:1:29.3:1:1:2.09:32.5:8:0.3636:0.0769:4.5 0/1:18:7:5,2:3,5:0.3889:2,2:15.6:1:27.4:1:0.31469:3.76:36.7:14:0.5:0:5.3 -4 49110433 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.18717;SOR=0;LSEQ=CGGGTTGATTCCATACCATT;RSEQ=CATTCCATTCCACTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,4:0.1333:2,2:12:0:33.5:1:1:1.89743:44:4:0.1333:0:6 0/0:19:0:0,0:9,10:0:2,0:20.8:1:28.6:1:1:0:41.6:18:1:0:4.5 -4 49110443 . C G 75 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.07552;SOR=0.13317;LSEQ=CCATACCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:3,2:6,4:0.3333:2,2:21.4:1:32.6:1:1:1:47.6:10:0.3333:0:4.4 0/1:17:1:0,1:5,8:0.0588:2,0:32:0:32:0:1:0:30:2:0.0625:0:7 -4 49110446 . C A 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34188;SOR=3.81579;LSEQ=TACCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:7,3:0.0833:2,0:35:0:29:0:0.36364:0:40:2:0.0833:0:6 0/1:15:4:1,3:2,7:0.2667:2,2:22.8:1:25.8:1:1:1.15:37.5:3:0.2308:0:5 -4 49110449 . G A 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1746;SOR=0;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:0.1667:2,2:30:0:32:0:1:1.4491:48:4:0.1667:0:5 0/0:16:0:0,0:4,12:0:2,0:27.3:1:27.6:1:1:0:41.8:7:1:0:4.4 -4 49110450 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1746;SOR=0;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,3:0.1667:2,2:32.5:1:29:1:1:1.87089:40:4:0.1667:0:4.5 0/0:16:0:0,0:4,10:0:2,0:27.1:1:28.5:1:1:0:42.1:13:0.8667:0:4.5 -4 49110454 . G GATTCT 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.19212;SOR=0;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,5:0.1538:2,2:23:1:29.5:1:1:1:46:4:0.1667:0.0769:1.5 0/0:16:0:0,0:4,11:0:2,0:29.7:1:30.4:1:1:0:41.9:30:0.9375:0:4.2 -4 49110459 . CA TT 48 v4;MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.6254;SOR=0.42903;LSEQ=CATTCCACTCGGGTTGATTC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:5,5:0.2308:2,2:26:1:30.8:1:1:1.90:43.7:6:0.2308:0:3.7 0/1:18:2:0,2:3,11:0.1111:2,0:25.5:1:29.8:1:1:0:39.5:4:0.1176:0:3.5 -4 49110498 . C G 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.51703;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCGTGTTGATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:11.3:1:31:1:1:0:37.8:12:1:0:3.3 0/1:13:3:0,3:2,8:0.2308:2,0:42.7:1:32.7:1:1:0:33.3:6:0.2308:0:6 -4 49110501 . T A 61 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.51648;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGTGTTGATTCCATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:12.8:1:30.5:1:1:0:43:8:1:0:3 0/1:12:4:1,3:1,6:0.3333:2,2:36.5:1:30.5:1:1:1.87:30.3:8:0.3333:0:5.5 -4 49110505 . T A 72 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCG;RSEQ=GTTGATTCCATTGCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:18.5:1:30.5:1:1:0:46:4:1:0:1.5 1/0:9:5:1,4:1,0:0.5556:0,2:35.4:1:31.4:1:0.33333:0:30:10:0.625:0:5.2 -4 49110511 . T A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCGTGTTGA;RSEQ=TCCATTGCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:12.5:1:31.5:1:1:0:46:4:1:0:1.5 0/1:9:2:0,2:2,4:0.2222:2,0:31.5:1:31.5:1:1:0:35.5:4:0.2857:0:7 -4 49110518 . G C 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CCATTCGTGTTGATTCCATT;RSEQ=CATTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:5.5:1:31.5:1:1:0:46:4:1:0:1.5 0/1:9:4:1,3:1,3:0.4444:2,2:19:1:32:1:1:1:34:8:0.5:0:4.3 -4 49110536 . C T 61 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TTGCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:6:0:33:0:1:0:30:2:1:0:2 1/0:6:4:1,3:0,1:0.6667:0,2:17.3:1:30.5:1:1:0:31:8:0.8:0:5.5 -4 49110595 . T A 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:29:1:1:0:50:4:1:0:1 -4 49110610 . A T 29 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=0.46667;SOR=0;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCATTCTACTCGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:0.5:0,2:15:0:29.5:1:1:0:23:4:0.6667:0:2 0/0:2:0:0,0:1,1:0:2,0:9:0:29:1:1:0:50:4:1:0:1 -4 49110613 . C A 28 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.46667;SOR=0;LSEQ=CCTTTCCATTCCATTCCATT;RSEQ=CATTCTACTCGGTTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:18:0:28:1:1:0:23:4:0.5:0:2 0/0:2:0:0,0:1,1:0:2,0:6:0:30:1:1:0:50:4:1:0:1 -4 49110614 . CATTCTACTCGGTTTG C 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTTTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:3,2:0.2857:2,0:13:1:28.5:1:0.42857:0:30:4:0.2857:0.2857:7 0/0:2:0:0,0:1,1:0:2,0:4:0:28:1:1:0:50:4:1:0:1 -4 49110625 . G A 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCTACTCG;RSEQ=TTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,1:0.2857:2,2:20.5:1:31.5:1:1:1.7321:43.5:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49110634 . C CTGTCA 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCTACTCGGTTTGATTC;RSEQ=ATTCCATTCCATTTCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:14:1:30.2:1:1:1.41:23:4:0.2857:0.1429:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49110635 . A C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCTACTCGGTTTGATTCC;RSEQ=TTCCATTCCATTTCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:2,2:0.3333:2,0:6:0:31:1:0.46667:0:30:4:0.3333:0:7 0/0:1:0:0,0:1,0:0:0,0:1:0:28:0:1:0:60:2:1:0:1 -4 49110656 . TT AC 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTTCATTCCA;RSEQ=CGATTTCATTCCACTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:28:0:30.8:1:1:0:30:4:0.4:0:6 0/0:1:0:0,0:1,0:0:0,0:22:0:31:0:1:0:60:2:1:0:1 -4 49110659 . G C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTTCATTCCATTC;RSEQ=ATTTCATTCCACTGGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,0:0.6667:0,0:30:0:32.5:1:1:0:30:4:0.6667:0:6 0/0:1:0:0,0:1,0:0:0,0:25:0:29:0:1:0:60:2:1:0:1 -4 49110670 . A C 31 d7;v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCGATTTCATTCC;RSEQ=CTGGTGTTTATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:41:0:32:1:1:0:30:4:1:0:6 1/0:3:2:1,1:1,0:0.6667:0,2:5:0:31.5:1:1:0:55:4:0.6667:0:2 -4 49110697 . T TGCGTC 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTTATTCCATTCCACTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:17.7:1:32:0:1:0:36.3:6:1:0:5 0/1:8:2:1,1:3,3:0.25:2,2:33:0:32.2:1:1:1:55:4:0.25:0:2 -4 49110706 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0.69289;LSEQ=TTCCACTCCATTCCATTCCA;RSEQ=TCCATTCCATTCGGGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:10:0:33:0:1:0:40:2:0.3333:0:6 0/1:8:2:1,1:3,3:0.25:2,2:40:0:32.5:1:1:1:55:4:0.25:0:2 -4 49110714 . C T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCGGGTTTATTCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:18.5:1:33:1:1:0:44.5:4:1:0:4 0/1:8:2:1,1:3,3:0.25:2,2:23:0:30.5:1:1:1:39:4:0.2857:0:3 -4 49110718 . CGGGTT C 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=TATTCCATTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:40:0:33:0:1:0:49:2:1:0:2 0/1:8:2:1,1:3,3:0.25:2,2:27:0:31.5:1:1:1:55:4:0.25:0:2 -4 49110724 . T A 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCGGGTT;RSEQ=ATTCCATTTCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:43:0:30:0:1:0:49:2:1:0:2 0/1:8:2:1,1:3,3:0.25:2,2:33:0:29:1:1:1:39:4:0.25:0:3 -4 49110754 . C T 27 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTGCATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:13:0:33:0:1:0:49:2:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:14:0:27.5:1:1:1.73:39:4:0.4:0:3 -4 49110756 . T C 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TGCATTCCATTCCTTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:11:0:31:0:1:0:49:2:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:30.5:1:33:0:1:1.73:60:4:0.4:0:3.5 -4 49110763 . CCATTCCTTTCCATTCTATTCCATTCCATTCCATTCCATTTGTGTTGATTCCATTCCATTCCATTCCACTGCATTCCAACCCATTA C 85 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=CCATTCCATTCCATTGCATT;RSEQ=CATTGCACTCGGGTTGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:3:0:30:0:1:0:49:2:1:0:2 1/1:7:7:3,4:0,0:1:0,2:39.3:1:30.6:1:1:0:45.1:14:1:1:3.6 -4 49110768 . C G 34 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTGCATTCCATT;RSEQ=CTTTCCATTCTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:0,1:0.4:0,2:18.5:1:34:0:1:0:60:4:0.6667:0:3.5 -4 49110779 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCTTTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:0,0:0.4:0,2:7.5:1:32.5:1:1:0:60:4:1:0:3.5 -4 49111523 . C G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=AATTCCATTGCATTCCATTC;RSEQ=ATTCCATTCCACTCGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:21.3:1:32.3:1:1:0:29.3:6:1:0:4 0/1:17:2:1,1:7,8:0.1176:2,2:30.5:1:29.5:1:1:1.13:37:4:0.1176:0:2.5 -4 49111527 . C A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTCCACTCGGGTGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:25:1:31.7:1:1:0:29.3:6:1:0:4 0/1:17:2:1,1:7,8:0.1176:2,2:34.5:1:28.5:1:1:1.13:37:4:0.1176:0:2.5 -4 49111532 . C CCCCTG 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CACTCGGGTGGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:17.5:1:33:0:1:0:32:4:0.6667:0:4.5 0/1:17:3:2,1:5,4:0.1765:2,2:26:1:29.9:1:1:1.54:30.3:6:0.1875:0:2.7 -4 49111542 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCACTCGGGT;RSEQ=GATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,0:0:0,0:30.5:1:32:1:1:0:32:4:0.6667:0:4.5 0/1:16:2:2,0:5,9:0.125:2,0:38.5:1:28:1:0.175:0:30:4:0.125:0:5 -4 49111545 . T C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCACTCGGGTGGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:31:1:30.7:1:1:0:29.3:6:1:0:4 0/1:20:2:1,1:9,8:0.1:2,2:27:0:33:0:1:1.11803:45:4:0.1053:0:3 -4 49111664 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCAATCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:15:1:30:1:1:0:30:4:0.6667:0:6 -4 49111685 . C T 61 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCAATCCATTCCATTCCA;RSEQ=TCCACTCCGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:3,1:0,0:1:0,2:31.3:1:30.8:1:1:0:27.8:8:1:0:6 -4 49111703 . C A 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.125;SOR=0;LSEQ=CACTCCACTCCGGTTGATTC;RSEQ=ATTCCATTCTATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,1:0.3333:2,2:13.5:1:28.5:1:1:1.7321:42.5:4:0.4:0:5.5 0/0:10:0:0,0:4,5:0:2,0:16.8:1:30.7:1:1:0:30.9:18:1:0:4.4 -4 49111707 . C T 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11053;SOR=0;LSEQ=CCACTCCGGTTGATTCCATT;RSEQ=CATTCTATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,1:0.2857:2,2:17.5:1:28.5:1:1:2.44949:42.5:4:0.3333:0:5.5 0/0:13:0:0,0:7,6:0:2,0:15.8:1:30.2:1:1:0:32.2:26:1:0:5 -4 49111713 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53333;SOR=Inf;LSEQ=CGGTTGATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,2:0:2,0:17.8:1:29.8:1:1:0:35:12:1:0:3.5 0/1:14:2:2,0:6,4:0.1429:2,0:10.5:1:32:0:0.51515:0:32:4:0.1538:0:7 -4 49111723 . C TCTTCGGGTTA 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0.8225;LSEQ=CATTCCATTCTATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:7.5:1:28.4:1:1:1:42:6:0.1415:0.1405:3.5 0/1:25:3:1,2:13,8:0.12:2,2:12:1:26.9:1:0.5504:3.08979:45.3:6:0.125:0.12:3.7 -4 49111754 . A T 78 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.18245;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCACTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:28.2:1:30.5:1:1:0:36.5:38:1:0:3.6 0/1:52:6:3,3:21,24:0.1154:2,2:23.8:1:30.5:1:1:1.14:38.3:12:0.12:0:5.8 -4 49111756 . T G 32 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCACTCGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:28:1:30.3:1:1:0:38.2:34:1:0:3.6 0/1:52:2:2,0:22,28:0.0385:2,0:37.5:1:32.5:1:0.20814:0:27:4:0.04:0:5.5 -4 49111757 . C A 65 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.31346;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:29.3:1:31.5:1:1:0:36.5:38:1:0:3.6 0/1:51:5:3,2:19,22:0.098:2,2:26:1:28.2:1:0.65891:1.72:38:10:0.1:0.0196:3.4 -4 49111758 . C G 27 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.73814;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCACTCGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:8,10:0.0526:2,0:44:0:30:0:0.47368:0:30:2:0.0526:0:7 0/1:51:2:1,1:22,27:0.0392:2,2:19:1:27.5:1:1:1.22:21.5:4:0.0408:0:5 -4 49111762 . C G 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.71424;SOR=1.74296;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:6,9:0.1111:2,0:42.5:1:31.5:1:0.20588:0:35:4:0.1111:0:5.5 0/1:50:9:4,5:17,19:0.18:2,2:30.7:1:31:1:1:1.11565:29.8:18:0.1837:0:4.4 -4 49111763 . C T 66 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=0.31465;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,9:0:2,0:32.4:1:31.9:1:1:0:37.3:34:1:0:3.7 0/1:50:5:5,0:17,24:0.1:2,0:37.8:1:28.6:1:0.01921:0:31:4:0.087:0:7 -4 49111765 . C A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92417;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:4,5:3,4:0.5:2,2:36:1:30.7:1:1:1.06:39:18:0.5294:0:4.1 0/1:50:24:8,16:9,9:0.48:2,2:34.1:1:27:1:0.34828:1.9664:42.2:5:0.4348:0:3.3 -4 49111768 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:33.2:1:30.5:1:1:0:37.3:34:1:0:3.7 0/1:50:2:1,1:21,25:0.04:2,2:27:0:31.5:1:1:1.19:35:4:0.0417:0:7 -4 49111769 . G A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.92417;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:4,5:3,3:0.5:2,2:38.7:1:31.1:1:1:1.23147:39:18:0.5294:0:4.1 0/1:50:24:9,15:12,11:0.48:2,2:35.5:1:28.3:1:0.38516:1.79488:41.3:11:0.4783:0:3.4 -4 49111770 . G T 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCACTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,9:0:2,0:31:1:31.9:1:1:0:37.3:34:1:0:3.5 0/1:50:2:1,1:22,25:0.04:2,2:29:0:32:0:1:1.13:35:4:0.0444:0:7 -4 49111773 . G A 53 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56733;SOR=Inf;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:32.1:1:31.7:1:1:0:36.3:36:1:0:3.5 0/1:49:4:4,0:18,27:0.0816:2,0:32:1:26.5:1:0.03452:0:32.8:8:0.0816:0:7 -4 49111778 . C A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.10702;LSEQ=CATTCCACTCGGGTTGATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:7,10:0.0556:2,0:17:0:32:0:1:0:45:2:0.0556:0:5 0/1:49:3:0,3:21,22:0.0612:2,0:32.7:1:31.7:1:0.23913:0:36.7:6:0.0625:0:5 -4 49111780 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCACTCGGGTTGATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:28.1:1:30.6:1:1:0:36.3:36:1:0:3.5 0/1:49:2:1,1:21,26:0.0408:2,2:39:0:31.5:1:1:1.23:35:4:0.0417:0:7 -4 49111783 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CACTCGGGTTGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,10:0:2,0:26.7:1:31.6:1:1:0:35.8:34:0.9444:0:3.4 0/1:47:2:1,1:19,25:0.0426:2,2:24.5:1:30.5:1:1:1.31:35.5:4:0.0435:0:4 -4 49111784 . A T 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.66572;SOR=0.74775;LSEQ=ACTCGGGTTGATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:13:1:29:1:1:1.62:22:4:0.1111:0:3.5 0/1:47:4:2,2:18,24:0.0851:2,2:40.5:1:29.3:1:1:1.32:36.3:8:0.0851:0:2.8 -4 49111787 . C G 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.18331;SOR=0.17965;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:7,9:0.1111:2,0:16.5:1:33.5:1:0.49673:0:30:4:0.1111:0:3.5 0/1:47:1:0,1:22,23:0.0213:2,0:13:0:33:0:1:0:49:2:0.0213:0:5 -4 49111795 . T TTCGGGTTGAA 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCACTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:0:2,0:17.5:1:30.6:1:1:0:35.4:32:1:0:3.6 0/1:47:2:1,1:21,24:0.0426:2,2:34:1:26.4:1:1:1.14:42.5:4:0.0426:0:1 -4 49111805 . C T 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55349;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,7:0:2,0:13.5:1:32.2:1:1:0:38.4:22:1:0:3.6 0/1:33:3:2,1:10,20:0.0909:2,2:13.3:1:27.7:1:0.53812:3.82:32.3:6:0.0909:0:6 -4 49111815 . TTCCATTCCTTTCAAC G 70 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00192;SOR=0;LSEQ=TTCCATTCCACTCCATTCCA;RSEQ=TCCTTTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:0,2:0.5556:0,2:10.8:1:30.5:1:1:0:47.8:10:0.625:0.5556:4.4 0/0:17:0:0,0:5,7:0:2,0:7.8:1:28.5:1:1:0:36.7:24:1:0:4.3 -4 49111816 . T G 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.52105;SOR=Inf;LSEQ=TCCATTCCACTCCATTCCAT;RSEQ=CCATTCCTTTCAACTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,4:0:2,0:6.2:1:30.6:1:1:0:43.8:10:1:0:3.6 0/1:14:3:1,2:3,8:0.2143:2,2:5.7:1:32.3:1:1:1.31:40:6:0.2308:0:4.3 -4 49111818 . C G 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.52941;SOR=Inf;LSEQ=CATTCCACTCCATTCCATTC;RSEQ=ATTCCTTTCAACTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,4:0:0,0:5.5:1:33:1:1:0:39.8:8:1:0:3.5 0/1:12:2:1,1:2,8:0.1667:2,2:9:1:27.5:1:0.45455:3.46:35:4:0.1818:0:7 -4 49111824 . T A 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCATTCCATTCCATTCC;RSEQ=TTCAACTCCTTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:0,3:0,0:0.75:0,0:5.7:1:30:1:1:0:35:6:1:0:6.3 -4 49111851 . T G 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCTTTCCATTCCATTCCAT;RSEQ=CCATTCCACTTGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:16:0:31:1:1:0:31:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49111871 . T TC 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCACTTGGGTTGAT;RSEQ=CCTTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:37:0:31.5:1:1:0:31:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49111878 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CACTTGGGTTGATTCCTTCC;RSEQ=TTCCATTCCACTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:44:0:31:1:1:0:31:4:1:0:4 0/0:2:0:0,0:0,1:0:0,0:7:0:32:0:1:0:27:2:1:0:7 -4 49111889 . CTCCAC T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=7;MSI=2.000;MSILEN=5;SSF=0.4;SOR=0;LSEQ=ATTCCTTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:44.5:1:31.5:1:1:0:31:4:1:0:3 0/0:2:0:0,0:0,1:0:0,0:14:0:31:0:1:0:27:2:1:0:7 -4 49111904 . T A 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TTCCACTCCACTCGGGTTGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:30.5:1:31.5:1:1:1.7321:31:4:0.4:0:4 0/0:5:0:0,0:2,3:0:2,0:12.2:1:32:0:1:0:26.6:10:1:0:3.6 -4 49111910 . T A 26 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.44444;SOR=0;LSEQ=TCCACTCGGGTTGATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:8:0:26.5:1:1:1.7321:40:4:0.4:0:3 0/0:5:0:0,0:2,3:0:2,0:18.2:1:31.2:1:1:0:26.6:10:1:0:3.6 -4 49111938 . A T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.45455;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTGCGTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:21.6:1:30.6:1:1:0:35:10:1:0:4 0/1:6:2:2,0:1,2:0.3333:2,0:30:1:32:1:0.4:0:32.5:4:0.3333:0:6.5 -4 49111941 . G C 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=4.91839;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CGTTCCATTCCATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,1:0.25:2,0:19:0:33:0:1:0:40:2:0.25:0:5 1/0:6:4:2,2:1,1:0.6667:2,2:35.3:1:32.5:1:1:1:30.3:8:0.6667:0:5.8 -4 49111942 . CGTTCC A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTG;RSEQ=ATTCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:28.5:1:21:1:1:0:36:1:1:0:4 0/1:7:2:1,1:2,3:0.2857:2,2:23.5:1:28.9:1:1:1.41:29:4:0.2857:0.1429:1.5 -4 49111943 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.09375;LSEQ=ATTCCATTCCATTCCATTGC;RSEQ=TTCCATTCCATTCCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:21:0:31:0:1:0:40:2:0.3333:0:5 0/1:7:3:2,1:1,2:0.4286:2,2:23:1:30.3:1:1:3.11:32.7:6:0.5:0:4 -4 49111953 . A G 27 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.10989;SOR=0;LSEQ=ATTCCATTGCGTTCCATTCC;RSEQ=TTCCATTGCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,0:0.4:0,2:29:0:27.5:1:1:0:40:4:0.5:0:3 0/0:9:0:0,0:4,5:0:2,0:22.1:1:27.8:1:1:0:28.9:8:1:0:3.6 -4 49111968 . A T 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.09524;SOR=0;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCACTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:27.5:1:28:1:1:1:36.5:4:0.5:0:4.5 0/0:10:0:0,0:5,5:0:2,0:19.7:1:27.9:1:1:0:32:9:1:0:3.5 -4 49111977 . C T 29 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.09524;SOR=0;LSEQ=CATTGCATTCCATTCCATTC;RSEQ=ATTCCACTCGTGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:5:0:29:1:1:1:40:4:0.5:0:3 0/0:10:0:0,0:5,4:0:2,0:17:1:29.8:1:1:0:32.6:18:0.9:0:2.9 -4 49111981 . C CCCCTG 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=0.50549;SOR=Inf;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CACTCGTGTTGATTCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:16:1:30.3:1:1:0:38.3:8:1:0:3.8 0/1:10:3:1,2:5,2:0.3:2,2:38:1:29.9:1:0.5:4.17095:29:6:0.3:0:2.7 -4 49111987 . G C 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=TGTTGATTCCCTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:31:1:27.5:1:1:0:36.5:4:1:0:4.5 0/1:7:2:1,1:2,2:0.2857:2,2:16:1:27.5:1:1:1:50:4:0.3333:0:5.5 -4 49111988 . T C 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCCTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:31:1:26.5:1:1:0:36.5:4:1:0:4.5 0/1:7:2:1,1:3,2:0.2857:2,2:37:0:31:1:1:1.41418:29:4:0.2857:0:2.5 -4 49112041 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CCACTTGGGTTGATTCCATT;RSEQ=CGTTCCTTTCCATTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,1:0.5:0,0:14.5:1:31:1:1:0:28.5:4:0.6667:0:4.5 0/0:5:0:0,0:2,3:0:2,0:34.6:1:31.4:1:1:0:52:10:1:0:4 -4 49112043 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=ACTTGGGTTGATTCCATTCC;RSEQ=TTCCTTTCCATTTCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,2:0:0,0:30:1:33.5:1:1:0:42:4:0.6667:0:5.5 0/1:5:2:1,1:1,2:0.4:2,2:29.5:1:30:1:1:1.73:60:4:0.4:0:3.5 -4 49112051 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=TGATTCCATTCCGTTCCTTT;RSEQ=CATTTCATTCCATACCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:24.7:1:32.7:1:1:0:39:6:1:0:5 0/1:5:2:1,1:1,2:0.4:2,2:26:1:28.5:1:1:1.73:60:4:0.4:0:3.5 -4 49112056 . T G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCATTCCGTTCCTTTCCATT;RSEQ=CATTCCATACCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:23:1:30.3:1:1:0:39:6:1:0:5 1/0:4:2:1,1:0,2:0.5:0,2:28.5:1:33:1:1:0:40:4:0.5:0:4 -4 49112062 . C A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CGTTCCTTTCCATTTCATTC;RSEQ=ATACCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:32.5:1:33.5:1:1:0:42:4:1:0:5.5 1/0:4:2:1,1:0,1:0.5:0,2:22.5:1:31:0:1:0:40:4:0.5:0:4 -4 49112065 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCCTTTCCATTTCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:31:0:31:0:1:0:60:2:0.5:0:6 1/0:4:2:1,1:0,2:0.5:0,2:19.5:1:29.5:1:1:0:40:4:0.5:0:4 -4 49112338 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCACTCGGGATGATT;RSEQ=CATTCAATTCCATTATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:32.5:1:1:0:60:4:1:0:3.5 -4 49112344 . A T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCGGGATGATTTCATTC;RSEQ=ATTCCATTATATTCCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:31.5:1:1:0:60:4:1:0:3.5 -4 49112349 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATGATTTCATTCAATTC;RSEQ=ATTATATTCCATTCAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:31.5:1:1:0:60:4:1:0:3.5 -4 49112409 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCACTCGGGTTGATTC;RSEQ=ATTCCGTTCCTTTCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:6:0:31.5:1:1:1:60:4:0.5:0:5.5 -4 49112415 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGGGTTGATTCCATTCC;RSEQ=TTCCTTTCCATTTCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:12:0:32:0:1:1:60:4:0.5:0:5.5 -4 49112416 . T A 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGGGTTGATTCCATTCCG;RSEQ=TCCTTTCCATTTCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:13:0:28:1:1:1:37:4:0.5:0:3.5 -4 49112420 . T A 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGATTCCATTCCGTTCC;RSEQ=TTCCATTTCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:17:0:28.5:1:1:1:37:4:0.5:0:3.5 -4 49112452 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCGT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:33.5:1:29.5:1:1:1:60:4:0.3333:0:5.5 -4 49112462 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCATTCCGTTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:23.5:1:31:1:1:1:60:4:0.3333:0:5.5 -4 49112469 . C A 30 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CGTTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:6.5:1:30.5:1:1:1:42:4:0.3333:0:1 -4 49112471 . T A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:18.5:1:30:1:1:1:37:4:0.3333:0:3.5 -4 49112573 . CCATTTTATTC T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATGAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18:1:31.9:1:1:0:30.5:4:1:0.5:4.5 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49112624 . A G 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CATTCCATTCCACTCCACTC;RSEQ=GGTTGATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:28:1:31.7:1:1:0:27.3:6:1:0:5.3 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49112638 . C T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCACTCAGGTTGATTCCTTT;RSEQ=CATTCCATTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:26.7:1:31.7:1:1:0:27.3:6:1:0:5.3 1/1:2:2:1,1:0,0:1:0,2:32:1:28.5:1:1:0:44:4:1:0:3.5 -4 49112648 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCCTTTCCATTCCATT;RSEQ=CATTCCATTCCTTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:29:1:1:0:44:4:1:0:3.5 -4 49112681 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCACTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:34:0:27:0:1:0:51:2:0.5:0:3 1/1:2:2:2,0:0,0:1:0,0:8.5:1:30.5:1:1:0:34:4:1:0:4 -4 49112691 . C T 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=TTCCATTCCACTCCACTCCA;RSEQ=TCCATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:30:1:32.5:1:1:0:36:4:1:0:4.5 1/0:8:4:3,1:3,1:0.5:2,2:7.8:1:30.3:1:1:1:28.5:8:0.5:0:5.3 -4 49112705 . A T 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ACTCCACTCCATTCCATTCC;RSEQ=TTCCACTCGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:22.5:1:30.5:1:1:0:36:4:1:0:4.5 0/1:16:4:4,0:7,5:0.25:2,0:20.8:1:32:1:0.24451:0:31.8:8:0.25:0:4.3 -4 49112710 . A C 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCCATTCCATTCCATTCC;RSEQ=CTCGGGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:13.3:1:28.7:1:1:0:36.3:6:1:0:3 0/1:17:4:3,1:7,4:0.2353:2,2:23.3:1:31.3:1:1:1.66:45:8:0.25:0:4.3 -4 49112714 . G T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:14.7:1:32:1:1:0:36.3:6:1:0:3 0/1:18:2:2,0:11,4:0.1111:2,0:26:1:32:1:1:0:29:4:0.1111:0:4 -4 49112715 . G C 51 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:15:1:32.3:1:1:0:36.3:6:1:0:3 0/1:18:3:2,1:11,2:0.1667:2,2:22:1:32.3:1:0.48929:2.54679:53.3:6:0.1765:0:3.7 -4 49112724 . C A 25 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCACTCGGGTTGATTC;RSEQ=ATTCCATTCCATTCCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:18:1:33.7:1:1:0:36.3:6:1:0:3 0/1:24:2:1,1:15,6:0.0833:2,2:34:1:25:0:0.52569:2.39047:20:4:0.087:0:6.5 -4 49112728 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCACTCGGGTTGATTCCATT;RSEQ=CATTCCATTCCAATCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15.5:1:32.8:1:1:0:35.8:8:1:0:3.5 0/1:26:2:1,1:17,5:0.0769:2,2:37.5:1:28.5:1:0.44565:3.19373:21:4:0.087:0:5 -4 49112734 . C T 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGGTTGATTCCATTCCATTC;RSEQ=ATTCCAATCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,3:0:2,0:16.3:1:33:1:1:0:35.8:8:0.8:0:4.3 0/1:28:3:2,1:16,6:0.1071:2,2:32.3:1:29:1:1:1.31736:21.3:6:0.1111:0:6.3 -4 49112741 . A T 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77523;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:11:0:32:0:1:0:34:2:0.2:0:8 0/1:31:5:3,2:16,7:0.1613:2,2:33:1:30:1:1:1.49999:26.4:10:0.1724:0:5.8 -4 49112743 . C T 42 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45552;SOR=0.42653;LSEQ=CCATTCCATTCCATTCCAAT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:5:0:32:0:1:0:51:2:0.2:0:3 0/1:32:3:2,1:19,10:0.0938:2,2:32.7:1:27:1:1:1.05:36.7:6:0.0938:0.0313:2.3 -4 49112755 . A G 96 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.56608;SOR=Inf;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:15.8:1:31.8:1:1:0:29.5:8:1:0:5.3 0/1:39:9:4,5:14,11:0.2308:2,2:29:1:30.3:1:0.7027:1.5691:44.6:18:0.2308:0:5.2 -4 49112760 . A G 94 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.5664;SOR=Inf;LSEQ=AATCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:22.8:1:31.6:1:1:0:30.2:10:1:0.2:5.2 0/1:38:9:5,4:12,12:0.2368:2,2:34.1:1:29.9:1:1:1.24:45.8:18:0.2571:0:5.4 -4 49112763 . C G 32 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.06131;SOR=0.07727;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:20:1:32:1:1:1.41:29.5:4:0.2857:0.1429:3 0/1:37:1:1,0:17,17:0.027:2,0:25:0:28:0:1:0:40:2:0.0286:0:7 -4 49112765 . A G 99 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=1.97048;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:3,2:0.1667:2,0:5:0:34:0:1:0:40:2:0.1667:0:2 0/1:35:10:5,5:10,11:0.2857:2,2:35.9:1:29.9:1:1:1.10:45.4:20:0.303:0:5.1 -4 49112788 . C A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCGGGTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,2:0:2,0:30.4:1:31.8:1:1:0:33.2:10:0.8333:0:5.4 0/1:28:2:1,1:10,14:0.0714:2,2:33:1:27.5:1:1:1.38:50:4:0.0741:0:3.5 -4 49112789 . C T 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.38004;SOR=3.75652;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCGGGTTCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:3,3:0.1429:2,0:29:0:30:0:1:0:40:2:0.1429:0:2 0/1:28:11:5,6:6,9:0.3929:2,2:31.1:1:28.5:1:1:1.24:42.7:10:0.4:0:5.3 -4 49112791 . T C 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.03743;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:3,1:0.2857:2,0:21.5:1:31.5:1:0.4:0:37:4:0.2857:0:8 0/0:27:0:0,0:8,14:0:2,0:29.5:1:29.1:1:1:0:37.5:44:0.88:0:4.9 -4 49112794 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=GGTTCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,2:0:2,0:30:1:29.3:1:1:0:35.7:6:0.6:0:3.7 0/1:26:2:1,1:8,15:0.0769:2,2:47:1:31.5:1:1:1.83:30.5:4:0.08:0:6.5 -4 49112796 . GT TA 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCGG;RSEQ=TCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:28:1:30.5:1:1:0:34.3:12:1:0:5.3 0/1:25:2:1,1:7,13:0.08:2,2:46:1:30.3:1:1:1.80:30.5:4:0.0952:0:5.5 -4 49112799 . C G 58 d7 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01574;SOR=0.0819;LSEQ=CATTCCATTCCATTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:0,0:0.6667:0,2:29:1:29.3:1:1:0:33:8:0.6667:0:6.3 0/1:24:3:1,2:2,6:0.125:2,2:27:1:28.7:1:1:1.44:41:6:0.1364:0:6.7 -4 49112826 . T A 29 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.74089;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCACTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:1,3:0.2:2,0:38:0:28:0:1:0:40:2:0.2:0:8 0/1:13:2:1,1:2,9:0.1538:2,2:22:0:29:1:0.42308:3.87:31:4:0.1667:0:2 -4 49112832 . T G 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCACTCGTGTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,2:0:2,0:18:1:29.3:1:1:0:32.7:6:0.75:0:6 0/1:11:2:1,1:2,7:0.1818:2,2:27:0:32:1:0.49091:3.06:31:4:0.1818:0:2 -4 49112845 . TG GT 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=TTGTTTCCATTCCATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:33:0:30:0:1:0:40:2:1:0:8 0/1:5:2:1,1:1,2:0.4:2,2:34.5:1:29.3:1:1:1.73:41.5:4:0.4:0:5.5 -4 49112853 . CC AA 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCACTCGTGTTGTTT;RSEQ=ATTCCATTCCTTTCAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:25:0:32:0:1:0:40:2:1:0:8 1/0:4:2:1,1:1,1:0.5:2,2:26.5:1:30:0:1:1:41.5:4:0.5:0:4.5 -4 49112858 . C CTTTCCATTCCATTCAAGTTGAATG 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCACTCGTGTTGTTTCCATT;RSEQ=CATTCCTTTCAATTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:20:0:32:0:1:0:40:2:1:0:8 1/0:4:2:1,1:1,1:0.5:2,2:32:1:31.7:1:1:1:31:4:0.5:0.5:2 -4 49112937 . A T 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACTCGGGTTGATTCCAT;RSEQ=CCATTCTATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:27.5:1:1:0:37:4:1:0:6.5 -4 49112943 . CT GC 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGTTGATTCCATACCATT;RSEQ=ATTCCATTCCATTCCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:29.8:1:1:0:37:4:1:0:5.5 -4 49112981 . T C 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCAATTCCGTTCCATTCCA;RSEQ=TCCATTCCATTCCATTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:30.5:1:1:0:37:4:1:0:5.5 -4 49113068 . AG GC 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=TTTCTAATCGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28.8:1:1:0:42.5:4:1:0.5:5.5 -4 49113104 . T C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATTCCAATCCATTCCATTA;RSEQ=ATTCAAGTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:28.5:1:1:0:42.5:4:1:0:5.5 -4 49113464 . A C 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=ATTCCATACCATTCCACCAA;RSEQ=GTTGATTGCATGCTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:32.5:1:1:0:44:4:1:0:1.5 0/0:4:0:0,0:1,2:0:2,0:20:1:29.7:1:1:0:45.3:6:0.75:0:1.3 -4 49113473 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CATTCCACCAAAGTTGATTG;RSEQ=ATGCTATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:12:0:33.5:1:1:0:44:4:1:0:1.5 1/0:4:2:1,1:1,1:0.5:2,2:20.5:1:27.5:1:1:1:38:4:0.5:0:2 -4 49113503 . C A 30 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:33:0:30.5:1:1:1:38:4:0.3333:0:2 -4 49113535 . C A 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TTGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:0.6:2,2:28.7:1:29:1:1:1.7321:47:6:0.6:0:4 -4 49113540 . G A 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCACTTGG;RSEQ=TTGATTCCATTCCATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:18:0:28.5:1:1:0:52:4:0.6667:0:3 -4 49113545 . T A 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCACTTGGGTTGA;RSEQ=TCCATTCCATTCAATTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:13:0:28:1:1:0:52:4:0.6667:0:3 -4 49113761 . T G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTCTGTTCCATTCCAT;RSEQ=CCCTTTTATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:1:30.5:1:1:0:27:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49118963 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=ATTCCATTCCATTCCATTTC;RSEQ=TTCCATTGCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:41.5:1:32:1:1:1:59:4:0.5:0:7 0/0:4:0:0,0:2,2:0:2,0:21:1:30:1:1:0:53.3:8:1:0:2.5 -4 49118971 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCATTCCATTTCATTCCATT;RSEQ=CATTCCACTCGGTTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:49:1:31.5:1:1:1:59:4:0.5:0:7 0/0:4:0:0,0:2,2:0:2,0:29:1:31.3:1:1:0:53.3:8:1:0:2.5 -4 49118972 . CATTCC T 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CATTCCATTTCATTCCATTG;RSEQ=ACTCGGTTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:21.5:1:28.3:1:1:1:24:4:0.5:0.25:2.5 0/0:4:0:0,0:2,2:0:2,0:30:1:31.8:1:1:0:53.3:8:1:0:2.5 -4 49118977 . C T 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=CATTTCATTCCATTGCATTC;RSEQ=ACTCGGTTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45.5:1:30:0:1:0:59:4:1:0:7 0/0:4:0:0,0:2,2:0:2,0:35:1:30.3:1:1:0:53.3:8:1:0:2.5 -4 49118979 . C T 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TTTCATTCCATTGCATTCCA;RSEQ=TCGGTTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:43.5:1:31:1:1:0:59:4:0.6667:0:7 0/0:4:0:0,0:2,2:0:2,0:37:1:31:1:1:0:53.3:8:1:0:2.5 -4 49118982 . G C 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CATTCCATTGCATTCCACTC;RSEQ=GTTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:40.5:1:30.5:1:1:0:59:4:0.6667:0:7 0/0:4:0:0,0:1,1:0:2,0:43.5:1:29.5:1:1:0:60:4:0.5:0:0 -4 49118984 . T G 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=TTCCATTGCATTCCACTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:34:0:33:0:1:0:24:2:0.3333:0:3 1/0:4:2:1,1:1,1:0.5:2,2:34:1:27.5:1:1:1:46.5:4:0.5:0:5 -4 49118985 . T A 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TCCATTGCATTCCACTCGGT;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:29:1:1:0:59:4:0.6667:0:7 0/0:4:0:0,0:2,2:0:2,0:37.8:1:28.8:1:1:0:53.3:8:1:0:2.5 -4 49118991 . C G 31 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.14286;SOR=0;LSEQ=GCATTCCACTCGGTTTGATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:31.5:1:31.5:1:1:0:59:4:0.6667:0:7 0/0:4:0:0,0:2,2:0:2,0:36.5:1:30.5:1:1:0:53.3:8:1:0:2.5 -4 49119011 . C G 29 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATACACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:10:1:30.3:1:1:0:47.3:6:1:0:5.7 1/0:4:2:1,1:1,1:0.5:2,2:38.5:1:29:1:1:1:46.5:4:0.5:0:5 -4 49119027 . A C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATAC;RSEQ=CTTCGGGTTGATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:31.5:1:1:0:46.5:4:1:0:5 -4 49119282 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TATTCAATTCCGTTCTGTTC;RSEQ=GTTCCGTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:31:0:1:0:51:4:1:0:5 -4 49119293 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTTCTGTTCTGTTCCGTTCC;RSEQ=TTCCATTCCATTCCATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31:1:1:0:51:4:1:0:5 -4 49119313 . A T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTTC;RSEQ=TTCCATTGCATTGCACTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42:1:29.5:1:1:0:51:4:1:0:5 -4 49119343 . A G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCACTCGAGTTGATTCC;RSEQ=TTCCTTTCCATTCTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29:1:1:0:51:4:1:0:5 -4 49119531 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCGTTCCATTCCATT;RSEQ=CGTTCCATTCCATACCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:0:31.5:1:1:0:23:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49119685 . A T 63 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TCCACTAGGGTTGATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:8:0:28.5:1:1:0:49:4:1:0:3 1/0:7:4:3,1:2,1:0.5714:2,2:11.8:1:31.5:1:1:1.41:33.5:8:0.5714:0:4.3 -4 49119702 . C G 30 d7;v4;MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.17828;SOR=0.17611;LSEQ=CATACCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:25:0:31:1:1:1:49:4:0.5:0:3 0/1:15:2:1,1:7,6:0.1333:2,2:20.5:1:30.5:1:1:1.1547:29:4:0.1333:0:4.5 -4 49119706 . C G 31 d7;v4;MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.17828;SOR=0.17611;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:29:0:32.5:1:1:1:49:4:0.5:0:3 0/1:15:2:1,1:7,6:0.1333:2,2:24.5:1:31.5:1:1:1.1547:29:4:0.1333:0:4.5 -4 49119728 . A C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGTGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:30.8:1:31.8:1:1:0:40.5:8:1:0:3 0/1:15:2:1,1:6,6:0.1333:2,2:31.5:1:29.5:1:1:1:50:4:0.1429:0:6.5 -4 49119738 . T G 44 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:17.3:1:30.7:1:1:0:43.3:6:1:0:2.7 0/1:15:3:2,1:6,6:0.2:2,2:22.7:1:28.3:1:1:1.91:42.3:6:0.2:0:5.7 -4 49119745 . T A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCCACTCGTGTTGAT;RSEQ=CCATTCCATTCCATTCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:16.3:1:30.8:1:1:0:40.5:8:1:0:2.8 0/1:15:2:1,1:7,6:0.1333:2,2:20:1:27.5:1:1:1.1547:50:4:0.1333:0:6.5 -4 49119753 . A T 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.51648;SOR=3.98567;LSEQ=ACTCGTGTTGATTCCATTCC;RSEQ=TTCCATTCCAATGCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:4:0:32.5:1:1:1:49:4:0.5:0:3 1/1:11:9:4,5:1,1:0.8182:2,2:8:1:30.4:1:1:1.22474:39.4:18:0.8182:0:2.3 -4 49119764 . A T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TGCATTCCATTCCAGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:15:0:32:0:1:0:32:2:1:0:3 1/1:3:3:1,2:0,0:1:0,2:5.7:1:30.7:1:1:0:43:6:1:0:3 -4 49119979 . C A 25 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTCCATACCATTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:25.5:1:1:0:60:4:1:0:3.5 -4 49119988 . A T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCACCAAAGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:27.5:1:1:0:60:4:1:0:3.5 -4 49120011 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCACCAAAGTTGATTGC;RSEQ=TGCTATTCCATTCCATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:11:0:32.5:1:1:1:60:4:0.5:0:2.5 -4 49120045 . A C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCGTTCCATTCCATTC;RSEQ=ATTCCATTCCTTTCCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:17.5:1:28.5:1:1:1.73:53.5:4:0.4:0:5 -4 49120056 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCAATTCCATTCC;RSEQ=TTCCACTTGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:8.5:1:30.5:1:1:1.73:60:4:0.4:0:2.5 -4 49120068 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCTTTCCACTTGGG;RSEQ=TGATTCCATTCCATTCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:31:1:1:0:53.5:4:1:0:5 -4 49120096 . G A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCAATTCCGTTCC;RSEQ=TTCTGTCCCGTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29.5:1:1:0:53.5:4:1:0:5 -4 49120200 . CC TA 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=TTCGGGTTAATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29.3:1:1:0:57:4:1:0:1 -4 49120230 . C GATTGCAATCGAGTTG 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AATTCCTTTCCATTCCATTC;RSEQ=ATTCCATACCATTCCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:31.6:1:1:0:57:4:1:1:2 -4 49120231 . A T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCATACCATTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:1:32:1:1:0:57:4:1:1:2 -4 49120233 . T C 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCTTTCCATTCCATTCCAT;RSEQ=CCATACCATTCCGTTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:1:33:1:1:0:57:4:1:1:2 -4 49120235 . C A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTTTCCATTCCATTCCATTC;RSEQ=ATACCATTCCGTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:1:30:1:1:0:57:4:1:1:2 -4 49120236 . A T 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTTCCATTCCATTCCATTCC;RSEQ=TACCATTCCGTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:1:32:1:1:0:57:4:1:1:2 -4 49120238 . A C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCGTTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:1:32.5:1:1:0:57:4:1:1:2 -4 49120405 . TT CC 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:31.8:1:1:0:60:4:1:0:3 -4 49120408 . C G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CACTCGGGTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:32:0:1:0:60:4:1:0:3 -4 49120503 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTGCATTCCACTCGGGA;RSEQ=GATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29.5:1:1:0:20:4:1:0:3.5 -4 49120543 . C G 33 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:0.5:2,0:31:0:33:0:1:0:21.5:4:0.5:0:5 -4 49120549 . C T 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:0.5:2,0:37:0:31.5:1:1:0:21.5:4:0.5:0:5 -4 49120555 . AT A 45 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCATTCCCTTCGAGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:0.6:2,2:31.7:1:28.6:1:1:1.73:22:6:0.6:0.2:5.3 -4 49120565 . C A 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCGAGTTGATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:32.3:1:28.7:1:1:0:22:6:1:0:5.3 -4 49120569 . G A 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCCTTC;RSEQ=AGTTGATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:31:1:28.7:1:1:0:22:6:1:0:5.3 -4 49120572 . T A 44 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCCTTCGAG;RSEQ=TGATTCCTTTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:30:1:28:1:1:0:22:6:1:0:5.3 -4 49120586 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCGAGTTGATTCCTTTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:4:0:33:0:1:0:36:2:0.5:0:8 0/1:8:2:1,1:3,3:0.25:2,2:11:0:33.5:1:1:1:24:4:0.25:0:5 -4 49120592 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTGATTCCTTTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14.5:1:29:1:1:0:36.5:4:1:0:8 0/1:8:2:1,1:3,3:0.25:2,2:17:0:33:0:1:1:24:4:0.25:0:5 -4 49120601 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCACTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26:1:31:0:1:0:36.5:4:1:0:8 0/1:8:2:1,1:3,3:0.25:2,2:26:0:33.5:1:1:1:24:4:0.25:0:5 -4 49120606 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:21.3:1:31.3:1:1:0:31.3:6:1:0:6.3 0/1:10:2:1,1:4,4:0.2:2,2:31:0:33:1:1:1:24:4:0.2:0:5 -4 49120616 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=1;LSEQ=TTCCATTCCATTCCACTCCA;RSEQ=TCCATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,2:0.25:2,0:39:0:31:0:1:0:36:2:0.25:0:8 0/1:8:2:1,1:1,4:0.25:2,2:14:0:31.5:1:1:3.16:34:4:0.2857:0:3 -4 49120623 . CCATTCC AT 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.51515;SOR=Inf;LSEQ=CCATTCCACTCCATTCCATT;RSEQ=ATTCCACTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:32.7:1:32:1:1:0:31.3:6:0.75:0:6.3 0/1:8:2:1,1:2,4:0.25:2,2:48.5:1:27.2:1:1:1.83:50:4:0.25:0:5.5 -4 49120628 . C T 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.51515;SOR=Inf;LSEQ=CCACTCCATTCCATTCCATT;RSEQ=CATTCCACTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:31:1:31.7:1:1:0:31.3:6:0.75:0:6.3 0/1:8:2:1,1:1,3:0.25:2,2:26:0:29.5:1:1:2.45:34:4:0.3333:0:3 -4 49120645 . A T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.49091;SOR=Inf;LSEQ=ATTCCATTCCACTCCATTCC;RSEQ=TTCCATTCCATTCCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,2:0:2,0:30.7:1:31.3:1:1:0:26.3:6:0.75:0:5.7 0/1:7:2:1,1:1,2:0.2857:2,2:31.5:1:31:0:1:1.73:50:4:0.2857:0:5.5 -4 49120648 . C A 57 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.22797;SOR=Inf;LSEQ=CCATTCCACTCCATTCCATT;RSEQ=CATTCCATTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:25.8:1:31:1:1:0:28.8:8:1:0:6.3 0/1:9:4:2,2:2,3:0.4444:2,2:15.8:1:28.8:1:1:1.43:55:8:0.4444:0:3.3 -4 49120653 . C A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=1.1321;LSEQ=CCACTCCATTCCATTCCATT;RSEQ=CATTCCACTCCATTCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:3,1:0.2:2,0:41:0:31:0:0.4:0:21:2:0.2:0:6 0/1:9:2:1,1:3,4:0.2222:2,2:23.5:1:27.5:1:1:1.29:50:4:0.2222:0:5.5 -4 49120746 . GTCCAT G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCAATTCCATTGGG;RSEQ=TCCATTCCATTCCATTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:22.7:1:31:1:1:0:60:6:1:0.3333:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49120794 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTCCGTTCCATTCCATTC;RSEQ=ATTCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:0.4:2,0:8:1:32.5:1:0.4:0:24:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49120867 . G T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:34:0:31:0:1:0:31:2:1:0:6 1/0:5:3:2,1:1,1:0.6:2,2:17:1:30.7:1:1:1.73:34.7:6:0.6:0:6 -4 49120883 . TG GT 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATGCCATTCCATTCCATT;RSEQ=ACTCAGGTTGATTCCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:48:0:30:0:1:0:31:2:1:0:6 0/1:6:2:1,1:1,1:0.3333:2,2:39.5:1:30:1:1:1:40:4:0.3333:0:5 -4 49120889 . A G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTTGACTC;RSEQ=GGTTGATTCCGTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:42:0:29:0:1:0:31:2:1:0:6 0/1:6:2:1,1:3,1:0.3333:2,2:39.5:1:29:1:1:2.44949:40:4:0.3333:0:5 -4 49120895 . A T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTTGACTCAGGTTG;RSEQ=TTCCGTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:36:0:28:0:1:0:31:2:1:0:6 0/1:10:2:1,1:7,1:0.2:2,2:27:0:30.5:1:0.37778:5.29155:60:4:0.2:0:2 -4 49120900 . G T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGACTCAGGTTGATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,0:0:0,0:16:1:30.5:1:1:0:30:4:0.6667:0:6.5 0/1:10:2:1,1:4,1:0.2:2,2:39.5:1:29.5:1:1:3.1622:40:4:0.2857:0:5 -4 49120920 . A T 81 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.02613;SOR=0.18767;LSEQ=GTTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:2,5:3,2:0.5833:2,2:5:1:29.1:1:0.55808:3.3264:23.9:14:0.5833:0:4.4 0/1:30:6:4,2:16,6:0.2:2,2:6.8:1:30:1:1:1.31925:29.7:12:0.2:0:4.8 -4 49120940 . A T 29 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.11515;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCAGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:26.5:1:29:1:1:1.12:30.5:4:0.1111:0:6 0/0:36:0:0,0:20,13:0:2,0:29:1:29.3:1:1:0:36.5:32:0.9412:0:4.7 -4 49120943 . C G 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.08607;SOR=0.33025;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCAGTTGATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:5,8:4,2:0.6842:2,2:25.5:1:31.5:1:0.34985:3.00217:23.8:12:0.7059:0:4.9 0/1:34:14:7,7:12,7:0.4118:2,2:31.9:1:29.4:1:0.49694:1.68608:34.8:13:0.4063:0:4.9 -4 49120946 . T A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.04535;SOR=0.27976;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCAGTTGATTCCATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:5,8:3,1:0.6842:2,2:28.4:1:31.1:1:0.29412:4.3679:23.8:26:0.6842:0:4.9 0/1:35:13:6,7:13,7:0.3714:2,2:34.4:1:28.5:1:0.472:2.11481:33.9:12:0.3871:0:4.9 -4 49120948 . C G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.53529;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CAGTTGATTCCATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,10:0:2,0:28.9:1:31.3:1:1:0:25.1:36:0.9474:0:4.9 0/1:35:2:1,1:19,13:0.0571:2,2:24.5:1:31:1:1:1.44493:35:4:0.0606:0:5 -4 49120949 . C G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.26352;SOR=0.4978;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=AGTTGATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:5,7:4,3:0.6316:2,2:30.7:1:31.5:1:0.64992:1.80535:23.9:24:0.6316:0:5.2 0/1:35:16:8,8:12,6:0.4571:2,2:34.9:1:29.9:1:0.48671:1.95878:34.8:32:0.4706:0:5 -4 49120951 . G CTGGCA 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.53939;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TTGATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,10:0:2,0:30.8:1:30.9:1:1:0:25.4:34:0.8947:0:5 0/1:36:2:1,1:16,13:0.0556:2,2:27.5:1:30.8:1:1:1.22249:35:4:0.0588:0:5 -4 49120956 . T A 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68;SOR=0.6534;LSEQ=TTCCATTCCATTCCAGTTGA;RSEQ=TCCATTGCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:8,10:0.1429:2,2:30:1:30.7:1:0.58647:2.39:25.3:6:0.1429:0:6.3 0/1:41:4:3,1:20,13:0.0976:2,2:32:1:28.5:1:1:1.92:46.8:8:0.1026:0:5.8 -4 49120959 . CATTGCATTC AATTG 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11458;SOR=0;LSEQ=CATTCCATTCCAGTTGATTC;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:2,0:9,10:0.0909:2,0:16.5:1:31.6:1:0.47619:0:30.5:4:0.1:0.0455:1.5 0/0:42:0:0,0:24,16:0:2,0:27.7:1:30.6:1:1:0:36.3:39:0.975:0:4.4 -4 49120960 . A ATTGCT 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.04602;SOR=0.24267;LSEQ=ATTCCATTCCAGTTGATTCC;RSEQ=TTGCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:6,5:0.3636:2,2:40.8:1:31.9:1:0.64992:1.92733:22.8:16:0.381:0:4 0/1:42:5:3,2:20,10:0.119:2,2:35.8:1:30:1:1:1.32203:27.2:10:0.125:0.0238:5.2 -4 49120961 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54167;SOR=Inf;LSEQ=TTCCATTCCAGTTGATTCCA;RSEQ=TGCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,11:0:2,0:32.5:1:30.9:1:1:0:26.4:42:1:0:5 0/1:42:2:1,1:24,15:0.0476:2,2:23:1:32.5:1:1:1.58108:50:4:0.05:0:3 -4 49120963 . G C 83 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05468;LSEQ=CCATTCCAGTTGATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:2,1:8,10:0.1364:2,2:23:1:30:1:0.58647:2.39:25.7:6:0.1429:0:5.7 0/1:42:6:4,2:21,14:0.1429:2,2:31.8:1:32.2:1:1:1.32:29.8:12:0.15:0:5.3 -4 49120964 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53324;SOR=Inf;LSEQ=CATTCCAGTTGATTCCATTG;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,12:0:2,0:31.7:1:32.7:1:1:0:25.9:46:1:0:4.9 0/1:43:2:1,1:23,16:0.0465:2,2:23:1:30.5:1:1:1.42455:34:4:0.0488:0:5 -4 49120970 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.5338;SOR=Inf;LSEQ=AGTTGATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:28:1:30.3:1:1:0:26.1:27:1:0:4.6 0/1:50:2:2,0:25,21:0.04:2,0:9.5:1:29:1:0.49734:0:32.5:4:0.0408:0:7 -4 49120973 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.11667;SOR=0;LSEQ=TGATTCCATTGCATTCCATT;RSEQ=CATTCCATTCCATTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:13,13:0.0714:2,2:7:0:31:0:1:1:25:4:0.0714:0:1 0/0:53:0:0,0:28,24:0:2,0:20.4:1:30.3:1:1:0:36.6:25:1:0.0189:4.7 -4 49120974 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.53719;SOR=Inf;LSEQ=GATTCCATTGCATTCCATTC;RSEQ=ATTCCATTCCATTCCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,14:0:2,0:26.6:1:31.7:1:1:0:26.4:56:0.9655:0:4.4 0/1:53:2:1,1:25,22:0.0377:2,2:29.5:1:29:1:1:1.13339:40:4:0.0385:0:6.5 -4 49120975 . A T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.53026;SOR=Inf;LSEQ=ATTCCATTGCATTCCATTCC;RSEQ=TTCCATTCCATTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:0:2,0:26.2:1:29.7:1:1:0:26.2:14:1:0:4.5 0/1:52:2:1,1:26,22:0.0385:2,2:5.5:1:27.5:1:1:1.17786:42:4:0.0417:0:7 -4 49120976 . T C 52 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.04584;SOR=0;LSEQ=TTCCATTGCATTCCATTCCA;RSEQ=TCCATTCCATTCCGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:2,1:13,14:0.1:2,2:29.3:1:33.3:1:1:2.10:42:6:0.1:0:4 0/0:52:0:0,0:27,22:0:2,0:19.6:1:29.3:1:1:0:36.7:48:0.9796:0.0192:4.7 -4 49120978 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.13426;SOR=0;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTCCATTCCGTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:0.0667:2,2:27.5:1:31.5:1:1:1:20:4:0.0667:0:5 0/0:51:0:0,0:24,23:0:2,0:20.8:1:30.7:1:1:0:36.4:94:0.9592:0:4.8 -4 49120984 . CA GG 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.13766;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=TTCCGTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:0.0667:2,2:35:0:32.5:1:1:1:43:4:0.0667:0:4 0/0:50:0:0,0:23,20:0:2,0:19.9:1:30.3:1:1:0:35.7:86:0.9149:0:4.7 -4 49120988 . C T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.26694;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CGTTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:0:2,0:23.3:1:31.6:1:1:0:26.2:60:1:0:4.5 0/1:44:3:2,1:19,20:0.0682:2,2:39.7:1:29.7:1:1:2.07:26:6:0.0714:0:5.7 -4 49120990 . G GGATGA 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76626;SOR=0.74081;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:3,4:6,7:0.2593:2,2:20.3:1:30.7:1:1:1.13526:22.9:14:0.2593:0.037:4.3 0/1:39:8:3,5:7,7:0.2051:2,2:15.6:1:28.7:1:0.67492:1.62835:30.9:7:0.2059:0.0769:4.5 -4 49120992 . T A 36 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27273;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCGT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,13:0:2,0:24:1:30.6:1:1:0:26.2:50:0.9615:0:4.3 0/1:40:3:1,2:17,18:0.075:2,2:22.3:1:23.3:1:1:1.8586:40.3:2:0.0556:0:7.3 -4 49120993 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51662;SOR=Inf;LSEQ=CCATTCCATTCCATTCCGTT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:11,14:0:2,0:22.8:1:29.8:1:1:0:27.2:11.5:0.9583:0:4.3 0/1:42:2:1,1:17,21:0.0476:2,2:12.5:1:28:0:1:1.23:44:4:0.0526:0:7 -4 49120994 . C CGGAAG 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2829;SOR=Inf;LSEQ=CATTCCATTCCATTCCGTTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,14:0:2,0:22.5:1:31.3:1:1:0:27.1:25:1:0:4.4 0/1:44:3:1,2:18,21:0.0682:2,2:34:1:30:1:1:1.69323:37.3:6:0.0714:0:6 -4 49120995 . A T 29 v4;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.23445;LSEQ=ATTCCATTCCATTCCGTTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:12,13:0.037:2,0:3:0:22:0:1:0:51:2:0.04:0:7 0/1:44:2:1,1:18,21:0.0455:2,2:26.5:1:29:1:1:1.16:40:4:0.05:0:6.5 -4 49121000 . A G 50 v4;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.6429;SOR=2.60399;LSEQ=ATTCCATTCCGTTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:13,14:0.0357:2,0:37:0:30:0:1:0:22:2:0.037:0:4 0/1:45:4:2,2:14,23:0.0889:2,2:24.3:1:25.3:1:0.63661:1.62:38:3:0.0769:0:5.8 -4 49121003 . C G 79 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.15794;SOR=0.33879;LSEQ=CCATTCCGTTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:2,4:9,10:0.2222:2,2:10.7:1:30.8:1:0.66087:1.75892:21.5:12:0.2308:0:5.2 0/1:46:4:0,4:19,21:0.087:2,0:8:1:32.8:1:0.12174:0:29.3:8:0.093:0:4.5 -4 49121004 . C T 44 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.88781;LSEQ=CATTCCGTTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:12,14:0.0714:2,2:20:0:30:0:1:1.16:43:4:0.0741:0:4 0/1:47:3:3,0:16,27:0.0638:2,0:21:1:28.3:1:0.06383:0:26.7:6:0.0682:0:5.7 -4 49121008 . C G 62 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.2954;LSEQ=CCGTTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:12,12:0.0714:2,2:16:0:32:1:1:1:43:4:0.0714:0:4 0/1:44:4:1,3:17,20:0.0909:2,2:35:1:31:1:0.61776:2.49691:33.8:8:0.093:0:5.8 -4 49121010 . A T 89 v4;NM4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.01002;SOR=Inf;LSEQ=GTTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:16:1:29.1:1:1:0:30.2:27:1:0:4.2 0/1:44:9:5,4:12,19:0.2045:2,2:18.3:1:28.3:1:0.45608:1.94:33.7:8:0.2:0:4.9 -4 49121011 . T C 51 v4;NM4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.29307;SOR=0.203;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:2,1:11,11:0.1071:2,2:20.7:1:32.3:1:1:1.95:25.3:6:0.1154:0:4.3 0/1:43:1:0,1:17,22:0.0233:2,0:18:0:27:0:1:0:49:2:0.0238:0:7 -4 49121012 . T A 26 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.51549;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:15.6:1:28.6:1:1:0:30.2:27:1:0:4.2 0/1:43:2:2,0:16,24:0.0465:2,0:18:0:26.5:1:0.1777:0:22:4:0.0488:0:6 -4 49121013 . C G 46 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.05583;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:12,11:0.1111:2,2:6.7:1:29.3:1:1:2.11883:39.7:6:0.1111:0:4.3 0/0:42:0:0,0:18,23:0:2,0:22.7:1:30:1:1:0:36.3:19.5:1:0:5 -4 49121014 . C T 28 v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.52063;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:16.9:1:30.1:1:1:0:30.9:25:1:0.0769:4.1 0/1:42:2:1,1:17,22:0.0476:2,2:5:0:28.5:1:1:1.29:40:4:0.0526:0:0 -4 49121015 . ATTCCATTCCATTCCT A 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=5;SSF=0.00326;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:3,3:10,11:0.2222:2,2:27.5:1:30.2:1:1:1.10:34.2:12:0.2308:0.1852:3.8 0/0:39:0:0,0:15,23:0:2,0:24.4:1:29.3:1:1:0:36.2:18:1:0:4.9 -4 49121019 . C T 57 NM4;MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.04972;SOR=0.11906;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCTTTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:8,6:0.2:2,2:14.5:1:28.8:1:1:1.31198:43:8:0.2222:0:4 0/1:36:1:0,1:14,20:0.0278:2,0:49:0:30:0:1:0:36:2:0.0313:0:4 -4 49121021 . T C 32 v4;pSTD;NM4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.28788;SOR=0.26391;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCTTTCCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,8:0.1:2,2:26:0:32:1:1:1.11803:43:4:0.1053:0:4 0/1:36:1:1,0:13,21:0.0278:2,0:15:0:33:0:0.4:0:34:2:0.0303:0:6 -4 49121028 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CTTTCCACTCGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,7:0:2,0:29.1:1:31.2:1:1:0:32.7:26:1:0:4.7 0/1:38:2:1,1:13,21:0.0526:2,2:29:1:31.5:1:1:1.59:60:4:0.0556:0:4 -4 49121030 . TT CC 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.75452;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:2,3:0.1429:2,2:25.5:1:31.3:1:1:1.41:43:4:0.25:0:4 0/1:36:4:1,3:7,13:0.1111:2,2:26.5:1:31:1:1:1.58529:33.8:8:0.1538:0:4.8 -4 49121033 . C G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05655;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:5,5:0.2857:2,2:32.8:1:32.3:1:1:1:43:8:0.2857:0:4 0/1:37:11:5,6:7,15:0.2973:2,2:24.5:1:32.4:1:0.47128:1.75:35.9:22:0.3143:0:3.9 -4 49121035 . A G 51 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06125;SOR=0.11071;LSEQ=ATTCCATTCCATTCCTTTCC;RSEQ=CTCGGGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:5,5:0.2143:2,2:28.7:1:32.3:1:1:1.90:25.3:6:0.2143:0:4.3 0/1:36:1:0,1:14,18:0.0278:2,0:42:0:30:0:1:0:49:2:0.0294:0:7 -4 49121036 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCTTTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:0:2,0:29.4:1:32:1:1:0:34.2:26:0.9286:0:4.2 0/1:35:2:1,1:12,19:0.0571:2,2:37:1:33:0:1:1.56:60:4:0.0606:0:4 -4 49121037 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCTTTCCAC;RSEQ=CGGGTTGATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:28.9:1:30.5:1:1:0:33.2:28:1:0:4.4 0/1:36:2:1,1:14,20:0.0556:2,2:13:1:27.5:1:1:1.41:23:4:0.0625:0.0278:3 -4 49121039 . G C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCTTTCCACTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,6:0:2,0:29.1:1:30.3:1:1:0:35.1:24:0.8571:0:3.9 0/1:36:2:1,1:14,20:0.0556:2,2:19:0:31:1:1:1.41:42:4:0.0588:0:5.5 -4 49121040 . G A 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25144;SOR=3.91451;LSEQ=ATTCCATTCCTTTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:7,6:0.0667:2,0:19:0:33:0:1:0:22:2:0.0667:0:4 0/1:36:8:4,4:10,14:0.2222:2,2:33.9:1:28.6:1:0.70349:1.39:39.9:16:0.2286:0:5.8 -4 49121044 . G A 23 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCTTTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:24.5:1:31.9:1:1:0:35:30:1:0:4.2 0/1:35:2:2,0:12,21:0.0571:2,0:32:1:23:0:0.15294:0:31:4:0.0588:0:5.5 -4 49121054 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.86944;LSEQ=CACTCGGGTTGATTCCATTC;RSEQ=ATTCCATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:5,8:0.0714:2,0:11:0:26:0:0.42857:0:25:2:0.0714:0:6 0/1:32:2:1,1:11,18:0.0625:2,2:43.5:1:29.5:1:1:1.61:37:4:0.0645:0:8 -4 49121057 . T G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCGGGTTGATTCCATTCCAT;RSEQ=CCATTCCTTTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:18.5:1:30.7:1:1:0:35.3:26:1:0:4.4 0/1:30:2:1,1:11,17:0.0667:2,2:24:0:30:1:1:1.52:46:4:0.069:0:5.5 -4 49121063 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0.80603;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CTTTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:4,4:0.1111:2,0:19:0:31:0:1:0:51:2:0.1111:0:7 0/1:22:2:1,1:8,12:0.0909:2,2:23:0:31.5:1:1:1.47:45:4:0.0909:0:1.5 -4 49121065 . T A 94 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1872;SOR=5.67647;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:2,4:0.1429:2,0:17:0:32:0:1:0:51:2:0.1429:0:7 1/0:22:11:5,6:3,5:0.5:2,2:22.8:1:27.2:1:1:1.37:36.9:10:0.5:0:6.1 -4 49121068 . C G 86 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14137;SOR=Inf;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CATTCCATTCCATTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:21.3:1:33.1:1:1:0:45.1:14:1:0:4 0/1:21:7:3,4:6,8:0.3333:2,2:24:1:30.9:1:1:1:39.9:14:0.3333:0:6.3 -4 49121080 . A G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCGTTCCACTCGGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:12.7:1:31:1:1:0:45.1:14:1:0:4 0/1:18:2:1,1:6,10:0.1111:2,2:45:0:30.5:1:1:1.62:39:4:0.1111:0:6 -4 49121082 . T G 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.54067;SOR=Inf;LSEQ=TCCTTTCCATTCCATTCCAT;RSEQ=CCGTTCCACTCGGCTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:13.2:1:31.2:1:1:0:44.2:12:1:0:3.5 0/1:16:4:1,3:5,7:0.25:2,2:16:1:30.3:1:1:2.04824:38.3:8:0.25:0:7 -4 49121085 . G A 59 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23739;SOR=Inf;LSEQ=TTTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGGCTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:11.2:1:31.8:1:1:0:44.2:12:1:0:3.5 0/1:11:4:2,2:3,4:0.3636:2,2:14.8:1:29.5:1:1:1.30:37:8:0.3636:0:7.3 -4 49121094 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCGTTCCACTC;RSEQ=GCTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:46:0:33:0:1:0:60:2:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:31:0:31.5:1:1:1.73:39:4:0.4:0:6 -4 49121096 . C G 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCCATTCCGTTCCACTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:44:0:34:0:1:0:60:2:1:0:2 1/1:5:4:2,2:0,1:0.8:0,2:20.5:1:31:1:1:0:38:8:0.8:0:7 -4 49121105 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GTTCCACTCGGCTTGATTCC;RSEQ=TTCCATTCCATTCCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:35:0:33:0:1:0:60:2:1:0:2 1/0:4:2:1,1:0,2:0.5:0,2:20:0:32.5:1:1:0:39:4:0.5:0:6 -4 49121118 . C A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.4;SOR=Inf;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTTTTTCCAATCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14:1:33:0:1:0:60:4:1:0:4 1/0:3:2:1,1:0,1:0.6667:0,2:7:0:29.5:1:1:0:39:4:0.6667:0:6 -4 49121130 . A C 34 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATTCCATTCCATTTTTTCCA;RSEQ=TCCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:34:0:1:0:60:4:1:0:4 0/0:1:0:0,0:0,1:0:0,0:21:0:25:0:1:0:21:2:1:0:6 -4 49121139 . G T 60 d7;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CATTTTTTCCAATCCACTCG;RSEQ=GTTGATTCCATTCTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:13.5:1:30:1:1:0:33.5:8:1:0:4.8 0/1:5:2:0,2:1,2:0.4:2,0:9:0:32:0:1:0:41:4:0.4:0:5 -4 49121153 . TA T 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CACTCGGGTTGATTCCATTC;RSEQ=TTCCATTCCATTCCAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:1,1:0.6:2,0:24:0:29.7:1:0.4:0:24.7:6:0.6:0:4.3 1/0:5:3:1,2:0,1:0.6:0,2:24:0:32.3:1:1:0:35:6:0.75:0:4.3 -4 49121168 . C A 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.52381;SOR=3.76419;LSEQ=CATTCTATTCCATTCCATTC;RSEQ=AGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,1:0.4:2,0:37:0:30:1:1:0:22.5:4:0.5:0:3.5 1/0:4:3:1,2:0,0:0.75:0,2:36:1:32:0:1:0:35:6:0.75:0:4.3 -4 49121175 . T A 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=TTCCATTCCATTCCAGTTGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,1:0.4:2,0:38:0:31.5:1:1:0:25.5:4:0.5:0:5 1/1:4:4:1,3:0,0:1:0,2:34.5:1:29.5:1:1:0:31.5:8:1:0:4.3 -4 49121187 . C G 53 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.52381;SOR=4.91839;LSEQ=CCAGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:2,2:0.3333:2,0:26:0:33:1:0.46667:0:25.5:4:0.3333:0:5 1/0:4:3:1,2:0,1:0.75:0,2:22.3:1:33.7:1:1:0:35:6:0.75:0:4.3 -4 49121203 . C G 33 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.52381;SOR=3.38757;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:2,2:0.3333:2,0:10:0:33:0:0.46667:0:25.5:4:0.3333:0:5 1/0:3:2:0,2:0,1:0.6667:0,0:10:0:33:0:1:0:41:4:0.6667:0:5 -4 49121247 . C G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGATTCAGTTCCTTTCCATT;RSEQ=CATTCCATTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:12:0:33:0:1:0:60:2:0.3333:0:4 1/1:2:2:2,0:0,0:1:0,0:22.5:1:33.5:1:1:0:46.5:4:1:0:3.5 -4 49121257 . T G 39 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCCATTCCATTCCATT;RSEQ=CATTCCATTCCAGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:16.3:1:25:1:1:0:53.3:2:1:0:3.7 1/1:2:2:2,0:0,0:1:0,0:32.5:1:32:1:1:0:46.5:4:1:0:3.5 -4 49121284 . G A 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCAGTTGATTCCATTGC;RSEQ=TTCCATTCCATTCAAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:40:0:32:0:1:0:40:2:1:0:3 1/1:3:3:2,1:0,0:1:0,2:31:1:29.3:1:1:0:51:6:1:0:3 -4 49121312 . C G 30 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCAAATGCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:7:1:30.5:1:1:3.16:44.5:4:0.2857:0:6 0/0:3:0:0,0:2,1:0:2,0:30.3:1:30.7:1:1:0:42.7:6:1:0:2.7 -4 49121326 . T C 29 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.12821;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:16.8:1:30.1:1:1:0:36.8:16:1:0:4.8 0/1:5:2:1,1:1,2:0.4:2,2:25.5:1:29.5:1:1:1.73:46.5:4:0.4:0:3 -4 49121336 . T A 29 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.175;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:31:1:29:1:1:1.41:44.5:4:0.2857:0:6 0/0:9:0:0,0:6,3:0:2,0:15.9:1:29.2:1:1:0:38.2:18:1:0.2222:3.2 -4 49121338 . C CTTTCCACTCGTGTGG 29 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.475;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:30:1:29.4:1:1:0:36.3:6:1:0:5 0/1:9:2:2,0:4,3:0.2222:2,0:25:1:29.9:1:0.5:0:30:4:0.2222:0.2222:1 -4 49121347 . CC TA 29 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.15441;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:43:1:29.8:1:1:1.41:44.5:4:0.2857:0:5 0/0:10:0:0,0:6,3:0:2,0:20.2:1:31.1:1:1:0:37.4:18:0.9:0:2.9 -4 49121360 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.49673;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:36.3:1:31.2:1:1:0:38.7:12:0.8571:0:4.7 0/1:11:2:1,1:6,2:0.1818:2,2:37:1:30.5:1:1:2.64575:40.5:4:0.2:0:5 -4 49121365 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCGG;RSEQ=TTGATTCCATTCCATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:32.4:1:29.9:1:1:0:36.3:6:1:0:4.6 0/1:10:2:2,0:5,3:0.2:2,0:27:0:30:1:1:0:30:4:0.2:0:1 -4 49121368 . G GAAGGC 25 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=CATTCCATTCCATTCGGGTT;RSEQ=ATTCCATTCCATTCAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:29.3:1:32.8:1:1:0:35.7:12:0.8571:0:4.7 0/1:10:2:2,0:3,3:0.2:2,0:31:0:25.7:1:0.46429:0:30:4:0.2:0:1 -4 49121369 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=ATTCCATTCCATTCGGGTTG;RSEQ=TTCCATTCCATTCAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:28.4:1:29.1:1:1:0:36.3:6:1:0:4.6 0/1:10:2:1,1:6,2:0.2:2,2:23.5:1:29.5:1:1:2.64575:46:4:0.2:0:3.5 -4 49121373 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.15441;SOR=0;LSEQ=CATTCCATTCGGGTTGATTC;RSEQ=ATTCCATTCAATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:27.5:1:30:1:1:1.41:39:4:0.2857:0:4.5 0/0:10:0:0,0:7,3:0:2,0:30.4:1:30.8:1:1:0:36.9:20:1:0:3 -4 49121377 . C G 33 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13725;SOR=0;LSEQ=CCATTCGGGTTGATTCCATT;RSEQ=CATTCAATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:21:0:33.5:1:1:1.41:44.5:4:0.3333:0:5 0/0:11:0:0,0:7,4:0:2,0:26.2:1:31.2:1:1:0:37.5:22:1:0:2.8 -4 49121383 . A G 31 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11029;SOR=0;LSEQ=GGGTTGATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,2:0.3333:0,2:15:0:31:1:1:0:44.5:4:0.3333:0:5 0/0:11:0:0,0:4,4:0:2,0:23:1:29.8:1:1:0:37.8:16:0.7273:0:2.3 -4 49121386 . T A 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=TTGATTCCATTCCATTCAAT;RSEQ=CCATTCCATTCCACTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:14.5:1:28:1:1:2.45:39:4:0.3333:0:4.5 0/0:10:0:0,0:7,3:0:2,0:22.5:1:28.3:1:1:0:39.1:9:1:0:2.7 -4 49121396 . T G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=TCCATTCAATTCCATTCCAT;RSEQ=CCACTCCATTCCATTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:3.8:1:30.5:1:1:0:38.2:12:1:0:4.5 0/1:9:2:1,1:5,2:0.2222:2,2:11:0:33.5:1:1:2.23609:46:4:0.2222:0:3.5 -4 49121400 . C T 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53451;LSEQ=TTCAATTCCATTCCATTCCA;RSEQ=TCCATTCCATTACATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:1:0:31:0:1:0:39:2:0.5:0:5 0/1:9:3:2,1:4,2:0.3333:2,2:8:1:31.7:1:1:1:48.7:6:0.3333:0:3.7 -4 49121403 . C CATTACAATCGTGTTG 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTCCATTCCATTCCACTC;RSEQ=ATTCCATTACATTTCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:22:2:1:0:4 0/1:10:2:1,1:4,3:0.2:2,2:25:1:32:1:1:1.29098:46:4:0.2222:0.2:3.5 -4 49121412 . A C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCACTCCATTCCATT;RSEQ=CATTTCATTGCACTCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:5:1:32.5:1:1:1:46:4:0.3333:0.3333:3.5 -4 49121417 . T C 62 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTCCATTCCATTACATT;RSEQ=CATTGCACTCTGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:22:1:31.3:1:1:0:31.5:8:1:0:3.8 -4 49121462 . G C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCAATCCATT;RSEQ=CATTCCGTTCCATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:31:1:1:0:28.5:4:1:0:6.5 -4 49121469 . G A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCAATCCATTGCATTCC;RSEQ=TTCCATTGCATTCGGGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:29.5:1:1:0:28.5:4:1:0:6.5 -4 49121477 . G C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTGCATTCCGTTCCATT;RSEQ=CATTCGGGTTCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:30:1:1:0:28.5:4:1:0:6.5 -4 49121524 . A T 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=GTTCCGTTCCATTCCATTCC;RSEQ=TTCCATTCCAATCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:10.5:1:32.5:1:1:0:33.5:4:1:0:5 0/0:2:0:0,0:1,1:0:2,0:17:1:31.5:1:1:0:24.5:4:1:0:6 -4 49121535 . A T 64 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:13.3:1:32.3:1:1:0:46.8:8:1:0:4.3 1/0:3:2:2,0:0,1:0.6667:0,0:15:1:32:0:0.33333:0:27:4:0.6667:0:4.5 -4 49121555 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=ATCCATTCCATTGCATTCCA;RSEQ=TCGTGTTGATTCCATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:33.3:1:32.5:1:1:0:46.8:8:1:0:4.3 0/1:5:2:1,1:2,1:0.4:2,2:45.5:1:30.5:1:1:1.7321:24.5:4:0.4:0:5.5 -4 49121559 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=ATTCCATTGCATTCCATTCG;RSEQ=GTTGATTCCATTGCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:36.5:1:31.3:1:1:0:46.8:8:1:0:4.3 0/1:5:2:1,1:2,1:0.4:2,2:45.5:1:30.5:1:1:1.7321:24.5:4:0.4:0:5.5 -4 49121572 . G T 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=CCATTCGTGTTGATTCCATT;RSEQ=CATTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:30.5:1:31:1:1:0:60:4:0.5:0:3.5 0/0:6:0:0,0:3,2:0:2,0:32:1:32.6:1:1:0:34:10:0.8333:0:3 -4 49121590 . C T 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55944;SOR=0.36341;LSEQ=TTGCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:12.5:1:30:1:1:1:60:4:0.3333:0:3.5 0/1:7:1:0,1:4,2:0.1429:2,0:13:0:31:0:0.42857:0:22:2:0.1667:0:7 -4 49121608 . C T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06993;SOR=Inf;LSEQ=CACTCCATTCCATTCCATTT;RSEQ=ATTCCATTCCAGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:15.4:1:29.6:1:1:0:39.1:14:1:0:4.3 1/0:7:4:2,2:2,1:0.5714:2,2:22.5:1:27.3:1:1:1.81007:35.8:8:0.6667:0:3.3 -4 49121614 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=ATTCCATTCCATTTCATTCC;RSEQ=TTCCAGTTGATTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:19.7:1:29:1:1:0:39.1:14:1:0:4.3 0/1:6:2:1,1:2,2:0.3333:2,2:26.5:1:29.5:1:1:1:44.5:4:0.3333:0:2 -4 49121620 . G T 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19231;SOR=0;LSEQ=TTCCATTTCATTCCATTCCA;RSEQ=TTGATTCCATTCCTTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:15.3:1:29.7:1:1:1.81007:38:6:0.4286:0:5.7 0/0:6:0:0,0:2,4:0:2,0:25:1:29.8:1:1:0:40:12:1:0:3 -4 49121663 . T C 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=GTTACATTCTACTCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:1,1:0.6667:2,2:30.3:1:31.3:1:1:2.44949:37.5:8:0.6667:0:4 1/1:3:3:1,2:0,0:1:0,2:34.7:1:29.3:1:1:0:41.3:6:1:0:3.7 -4 49121667 . A C 82 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCTGTT;RSEQ=CATTCTACTCGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:26.3:1:32:1:1:0:41.2:12:1:0:3.8 1/1:3:3:1,2:0,0:1:0,2:30.7:1:30.7:1:1:0:41.3:6:1:0:3.7 -4 49121689 . A G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.46429;SOR=5.78427;LSEQ=ATTCTACTCGGGTTGATTCC;RSEQ=TTCCATTCCATTTCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:18:0:34:0:1:0:27:2:0.2:0:6 1/0:3:2:1,1:0,0:0.6667:0,2:12:1:29.5:1:1:0:48.5:4:0.6667:0:3 -4 49121744 . A T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGTGTTTATTCCATTCC;RSEQ=CTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:7:0:30:0:1:0:40:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49121756 . T G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCATTCCACTCCATTCCAT;RSEQ=CCATTCCATTCGGGTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:19:0:33:1:1:0:40:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49121765 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTTATTCCATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:26.5:1:31.5:1:1:0:40:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49121995 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACTTGGGTTGATTCCA;RSEQ=TCCATTCCTTTCCATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:31.5:1:29:1:1:1.7321:53:4:0.4:0:5.5 0/0:2:0:0,0:1,1:0:2,0:16:0:32:0:1:0:60:4:1:0:0.5 -4 49121997 . CC GT 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCACTTGGGTTGATTCCATT;RSEQ=ATTCCTTTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:34.5:1:32:1:1:1.7321:53:4:0.4:0:4.5 0/0:2:0:0,0:1,1:0:2,0:14:0:31.5:1:1:0:60:4:1:0:0.5 -4 49122012 . G C 64 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCTTTCCATT;RSEQ=CATTCCATTCCATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:15.5:1:32.3:1:1:0:39:8:0.8:0:4.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49122027 . G C 29 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:6:1:29.5:1:1:1:24:4:0.6667:0:3 1/1:1:1:0,1:0,0:1:0,0:23:0:26:0:1:0:23:2:1:0:5 -4 49122066 . T C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TCCATTTCATTCCATTCTAT;RSEQ=CCATTCCGTTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:21:1:30.8:1:1:0:43.3:8:1:0:1.8 1/0:4:2:1,1:1,1:0.5:2,2:22:0:32:1:1:1:29:4:0.5:0:2 -4 49122068 . C A 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CATTTCATTCCATTCTATTC;RSEQ=ATTCCGTTCCATTCCATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,2:0:2,0:20:1:33.3:1:1:0:48:6:0.75:0:1 1/0:4:2:1,1:1,1:0.5:2,2:20:0:29.5:1:1:1:29:4:0.5:0:2 -4 49122127 . C T 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.10714;SOR=0;LSEQ=CCATACCATTCCATTCCATT;RSEQ=CATTCCGTTCCGTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31:1:32:0:1:0:31:4:1:0:3.5 0/1:6:1:1,0:2,1:0.1667:2,0:33:0:27:0:1:0:36:2:0.1667:0:3 -4 49122129 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATACCATTCCATTCCATTCC;RSEQ=TTCCGTTCCGTTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:33:1:32:0:1:0:31:4:1:0:3.5 0/1:6:2:1,1:3,1:0.3333:2,2:27.5:1:32:1:1:2.44949:35:4:0.3333:0:4.5 -4 49122133 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=GTTCCGTTCCATTCCTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:37:1:32.5:1:1:0:31:4:1:0:3.5 0/1:6:2:1,1:3,1:0.3333:2,2:39:0:32:1:1:2.44949:60:4:0.3333:0:5.5 -4 49122134 . G A 47 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCGTTCCATTCCTTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:38:1:31:0:1:0:31:4:1:0:3.5 1/0:6:3:2,1:2,1:0.5:2,2:30.3:1:29.7:1:1:1:35.3:6:0.5:0:4 -4 49122147 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCGTTCCGTTCCATT;RSEQ=CTTTCGTGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:43.5:1:32:1:1:0:31:4:1:0:3.5 0/1:8:2:1,1:5,1:0.25:2,2:25:0:31:1:0.46429:3.87298:60:4:0.25:0:5.5 -4 49122149 . T A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCGTTCCGTTCCATTCC;RSEQ=TTCGTGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:43.5:1:32:1:1:0:31:4:1:0:3.5 0/1:8:2:1,1:5,1:0.25:2,2:47:1:30.5:1:0.46429:3.87298:35:4:0.25:0:4.5 -4 49122150 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCGTTCCGTTCCATTCCT;RSEQ=TCGTGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:43.5:1:31:1:1:0:31:4:1:0:3.5 0/1:8:2:1,1:5,1:0.25:2,2:22:0:31:1:0.46429:3.87298:60:4:0.25:0:5.5 -4 49122166 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCTTTCGTGTTGATTCCAT;RSEQ=CCATTCCATTCCACTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:31:1:29:1:1:0:31:4:1:0:3 0/1:10:2:1,1:5,3:0.2:2,2:6:0:31:1:1:1.58108:60:4:0.2:0:5.5 -4 49122199 . A T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCCATTCCAATCCATTAC;RSEQ=TTCCACTCGGGTTGAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:5.3:1:28:1:1:0:35.7:6:1:0:4 0/1:11:2:1,1:5,4:0.1818:2,2:45.5:1:31:1:1:1.22474:45:4:0.1818:0:5 -4 49122203 . CA C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCAATCCATTACATTC;RSEQ=CTCGGGTTGAATCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:28.5:1:1:0:38:4:1:0:4.5 0/1:11:2:1,1:5,4:0.1818:2,2:24:1:29.5:1:1:1.22474:36:4:0.1818:0:2 -4 49122207 . C T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.40825;LSEQ=CCAATCCATTACATTCCACT;RSEQ=GGGTTGAATCCATTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:17:0:25:0:1:0:31:2:0.5:0:4 0/1:11:3:1,2:5,3:0.2727:2,2:34:1:29.7:1:0.54545:2.97405:28.7:6:0.2727:0:3 -4 49122209 . G T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.40825;LSEQ=AATCCATTACATTCCACTCG;RSEQ=GTTGAATCCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:19:0:26:0:1:0:31:2:0.5:0:4 0/1:11:3:1,2:5,3:0.2727:2,2:45:1:30.3:1:0.54545:2.97405:42:6:0.2727:0:4.3 -4 49122220 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCACTCGGGTTGAATCCA;RSEQ=TCCTTTCCATTCCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26.5:1:29.5:1:1:0:38:4:1:0:4.5 0/1:14:2:1,1:6,6:0.1429:2,2:32:1:30.5:1:1:1:45:4:0.1429:0:5 -4 49122227 . C A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGTTGAATCCATTCCTTT;RSEQ=CATTCCAATCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:33.5:1:30.5:1:1:0:38:4:1:0:4.5 0/1:14:2:1,1:6,6:0.1429:2,2:30:1:27.5:1:1:1:25:4:0.1429:0:4 -4 49122239 . A G 57 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCTTTCCATTCCAATCC;RSEQ=TTCCATTCCTTTCCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:45.5:1:30:0:1:0:38:4:1:0:4.5 0/1:14:4:2,2:4,6:0.2857:2,2:15.5:1:28.5:1:1:1.46:35:8:0.2857:0:4 -4 49122242 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTTCCATTCCAATCCATT;RSEQ=CATTCCTTTCCAATCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:47:1:31:0:1:0:38:4:1:0:4.5 0/1:14:2:1,1:5,7:0.1429:2,2:10:1:28:1:1:1.37:45:4:0.1429:0:5 -4 49122255 . A T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCCATTCCATTCCTTTCCA;RSEQ=TCCATTCCATTCCATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:24.3:1:29.8:1:1:0:37.3:8:1:0:5 0/1:14:2:1,1:4,8:0.1429:2,2:38.5:1:30:1:1:1.90:25:4:0.1429:0:4 -4 49122259 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCTTTCCAATCC;RSEQ=TTCCATTCCATTCAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:24.3:1:29.8:1:1:0:37.3:8:1:0:5 0/1:12:2:1,1:4,6:0.1667:2,2:26.5:1:29.5:1:1:1.45:25:4:0.1667:0:4 -4 49122281 . C A 79 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18545;LSEQ=TCCATTCCATTCAATTCCAC;RSEQ=TGGATTCAATCTATTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,0:0.5:0,0:22:1:32.5:1:1:0:31:4:0.5:0:6 1/0:11:6:1,5:0,0:0.5455:0,2:16.8:1:30.7:1:1:0:29.3:12:0.5455:0:3.5 -4 49122286 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58042;SOR=0.45719;LSEQ=TCCATTCAATTCCACCTGGA;RSEQ=TCAATCTATTCTTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:22:1:33.5:1:1:0:31:4:0.4:0:6 0/1:9:2:0,2:2,5:0.2222:2,0:6.5:1:33.5:1:1:0:38:4:0.2222:0:3 -4 49122292 . C G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CAATTCCACCTGGATTCAAT;RSEQ=TATTCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:27.3:1:31.8:1:1:0:39.5:8:1:0:5 0/1:7:2:0,2:1,4:0.2857:2,0:18.5:1:29.5:1:1:0:36.5:4:0.2857:0:4.5 -4 49122295 . T G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTCCACCTGGATTCAATCTA;RSEQ=TCTTTCCATTCCATTCCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:28.8:1:29.8:1:1:0:39.5:8:1:0:5 0/1:6:2:1,1:0,4:0.3333:0,2:19:0:33.5:1:0.33333:0:48:4:0.3333:0:3 -4 49122298 . T A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=CACCTGGATTCAATCTATTC;RSEQ=TTCCATTCCATTCCGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,2:0:0,0:33.5:1:31:1:1:0:35.5:4:0.6667:0:6 0/1:5:2:1,1:0,3:0.4:0,2:16:0:32:0:0.4:0:48:4:0.4:0:3 -4 49122313 . G A 33 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TATTCTTTCCATTCCATTCC;RSEQ=TTCTGTTCCATTGCAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:33.5:1:33:0:1:0:35.5:4:0.6667:0:6 0/0:5:0:0,0:1,4:0:2,0:14.4:1:31.4:1:1:0:38.8:10:1:0:4 -4 49122326 . G C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCGTTCTGTTCCATT;RSEQ=CAGTCCATTGCATTAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:29.3:1:32.7:1:1:0:37.7:6:1:0:5 1/1:2:2:0,2:0,0:1:0,0:28.5:1:31:1:1:0:36.5:4:1:0:5.5 -4 49122329 . G T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCGTTCTGTTCCATTGCA;RSEQ=TCCATTGCATTAGATACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:33:1:31:1:1:0:41:4:0.6667:0:3.5 1/1:2:2:0,2:0,0:1:0,0:25.5:1:30:1:1:0:36.5:4:1:0:5.5 -4 49122422 . C A 27 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCACTCAGGTGGATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:27.5:1:1:0:31:4:1:0:6 -4 49122432 . CA TG 30 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AGGTGGATTCCATTCCATTC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:30:1:1:0:31:4:1:0:5 -4 49122442 . C T 29 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:29:1:1:0:31:4:1:0:5 -4 49122482 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCACTCGGTTT;RSEQ=ATTCCATTCCGTTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:33:1:1:0:31:4:1:0:5 -4 49122493 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGGTTTGATTCCATTCC;RSEQ=TTCCTTTCCATTTCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:31.5:1:1:0:31:4:1:0:5 -4 49122639 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTCCATTCCATCCCATTCGG;RSEQ=TTGATTCCATTCTATTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29.5:1:1:0:28:4:1:0:3 0/0:2:0:0,0:1,1:0:2,0:6.5:1:29.5:1:1:0:26:4:1:0:2 -4 49122694 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TTCCATTCCGTTCCATTCCA;RSEQ=TCGGGTTGATTCTATACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:8:1:28.5:1:1:0:29:4:1:0:6 1/0:4:2:1,1:1,1:0.5:2,2:36:0:31:1:1:1:53.5:4:0.5:0:6 -4 49122696 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCATTCCGTTCCATTCCATT;RSEQ=GGGTTGATTCTATACCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:8:1:31:1:1:0:29:4:1:0:6 1/0:4:2:1,1:1,1:0.5:2,2:36:1:29.5:1:1:1:53.5:4:0.5:0:6 -4 49122703 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTTCCATTCCATTCGGGTTG;RSEQ=TTCTATACCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,0:0.5:0,0:20:0:29:0:1:0:30:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:20:0:29.5:1:1:1:36:4:0.5:0:3.5 -4 49122706 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCATTCCATTCGGGTTGATT;RSEQ=TATACCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:23:0:31:0:1:0:30:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:29:1:1:1:53.5:4:0.5:0:6 -4 49122707 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=CATTCCATTCGGGTTGATTC;RSEQ=ATACCATTCCATTCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,0:0.5:0,0:24:0:29:0:1:0:30:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:24:0:30.5:1:1:1:36:4:0.5:0:3.5 -4 49122710 . A T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TCCATTCGGGTTGATTCTAT;RSEQ=CCATTCCATTCCATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:27:0:26:0:1:0:30:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:30.5:1:27.5:1:1:1:53.5:4:0.5:0:6 -4 49122727 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TATACCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22.5:1:28.5:1:1:0:30:4:1:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:30:1:1:1:53.5:4:0.5:0:6 -4 49122736 . C T 29 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCTATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:22:0:26:0:1:0:30:2:0.5:0:7 1/1:2:2:0,2:0,0:1:0,0:24.5:1:29.5:1:1:0:47.5:4:1:0:6 -4 49122887 . C T 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.1;SOR=0;LSEQ=TGTTCCATTCCATTCCATTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:1:28.5:1:1:0:60:4:1:0:6 0/0:3:0:0,0:2,1:0:2,0:15.7:1:32.3:1:1:0:43:6:1:0:2.3 -4 49122907 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CACTCGGGTTGATTCCATTC;RSEQ=GTTCCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,1:0:2,0:19.3:1:31:1:1:0:59.8:8:1:0:6.3 0/1:6:2:1,1:3,1:0.3333:2,2:31.5:1:31.5:1:1:2.44949:46:4:0.3333:0:2 -4 49122918 . A T 30 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53846;SOR=0.31377;LSEQ=ATTCCATTCCGTTCCTTTCC;RSEQ=TTCCATTCCTTTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,0:0.3333:0,2:42:1:30.5:1:0.4:0:60:4:0.4:0:6 0/1:8:1:1,0:5,2:0.125:2,0:25:0:33:0:1:0:60:2:0.125:0:3 -4 49122919 . T A 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=TTCCATTCCGTTCCTTTCCA;RSEQ=TCCATTCCTTTCCGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:2,1:0.3333:2,0:19.5:1:31.5:1:1:0:59.5:4:0.4:0:6.5 0/0:10:0:0,0:7,3:0:2,0:13.8:1:31.2:1:1:0:52.7:20:1:0:3.2 -4 49122923 . A C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16374;SOR=0;LSEQ=ATTCCGTTCCTTTCCATTCC;RSEQ=TTCCTTTCCGTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:3,2:0.25:2,0:23.5:1:33:0:1:0:59.5:4:0.2857:0:6.5 0/0:11:0:0,0:7,4:0:2,0:14.1:1:30.5:1:1:0:53.4:22:1:0:3.2 -4 49122925 . T G 34 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=TCCGTTCCTTTCCATTCCAT;RSEQ=CCTTTCCGTTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:3,2:0.2222:2,0:25.5:1:34:0:1:0:59.5:4:0.2857:0:6.5 0/0:11:0:0,0:7,4:0:2,0:15:1:30.5:1:1:0:53.4:22:1:0:3.2 -4 49122928 . T A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.26953;LSEQ=GTTCCTTTCCATTCCATTCC;RSEQ=TTCCGTTCCATTCCATTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:5,2:0,0:0.7778:0,2:24.6:1:31.4:1:1:0:58:14:1:0:6.6 1/1:11:9:6,3:1,1:0.8182:2,2:15.4:1:30.7:1:1:1.87:51.9:18:0.8182:0:3.2 -4 49122930 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=TCCTTTCCATTCCATTCCTT;RSEQ=CCGTTCCATTCCATTCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,2:0.1818:2,2:43.5:1:31.5:1:1:2.23609:60:4:0.2222:0:6 0/0:11:0:0,0:7,4:0:2,0:17.3:1:29.9:1:1:0:53.4:22:1:0:3.2 -4 49122932 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=CTTTCCATTCCATTCCTTTC;RSEQ=GTTCCATTCCATTCGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,3:0:2,0:21.5:1:31.3:1:1:0:58.4:16:0.8889:0:5.8 0/1:11:2:1,1:6,3:0.1818:2,2:14:0:32.5:1:1:1.87089:60:4:0.1818:0:3.5 -4 49122942 . C T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.62992;SOR=2.00028;LSEQ=CATTCCTTTCCGTTCCATTC;RSEQ=ATTCGTGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:7,2:0.1538:2,0:23.5:1:33:0:1:0:60:4:0.1818:0:7 0/1:11:3:2,1:5,3:0.2727:2,2:40.3:1:30.3:1:1:1.18:59.3:6:0.2727:0:4 -4 49122947 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20635;SOR=Inf;LSEQ=CTTTCCGTTCCATTCCATTC;RSEQ=TGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,4:0:2,0:22.1:1:31.8:1:1:0:58.6:28:1:0:4.4 0/1:13:2:1,1:7,4:0.1538:2,2:36:1:30:1:1:1.67325:60:4:0.1538:0:3 -4 49122949 . G T 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.476;LSEQ=TTCCGTTCCATTCCATTCGT;RSEQ=TTGATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:8,4:0.1333:2,0:30.5:1:31:0:1:0:60:4:0.1429:0:7 0/1:15:1:1,0:8,6:0.0667:2,0:42:0:30:0:1:0:58:2:0.0667:0:6 -4 49122951 . T A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22581;SOR=0;LSEQ=CCGTTCCATTCCATTCGTGT;RSEQ=GATTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:9,3:0.1333:2,2:24:1:31:1:0.50549:2.73861:60:4:0.1429:0:6 0/0:16:0:0,0:9,7:0:2,0:24.1:1:29.6:1:1:0:55.1:32:1:0:2.9 -4 49122970 . T A 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43814;SOR=0.46842;LSEQ=TTGATTCCATTCCATTCCAC;RSEQ=CCAATCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:9,4:0.2778:2,2:32:1:29.4:1:0.32598:3.13525:57.4:10:0.2778:0:7 0/1:20:3:2,1:7,9:0.15:2,2:32.7:1:28.7:1:0.58204:2.45:59.3:6:0.1579:0:4 -4 49122971 . C T 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32819;SOR=0.27215;LSEQ=TGATTCCATTCCATTCCACT;RSEQ=CAATCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:2,1:8,5:0.1667:2,2:34:1:31.3:1:1:1.23:59.7:6:0.1667:0:5.3 0/1:20:1:0,1:7,7:0.05:2,0:15:0:24:0:1:0:23:2:0.0526:0:5 -4 49122977 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=CATTCCATTCCACTCCAATC;RSEQ=ATTCCATTCCATTCCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:29:1:30:0:1:1.40151:60:4:0.1053:0:7 0/0:20:0:0,0:9,11:0:2,0:29.7:1:30.5:1:1:0:52.2:40:1:0:2.9 -4 49122978 . A G 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.23077;SOR=0;LSEQ=ATTCCATTCCACTCCAATCC;RSEQ=TTCCATTCCATTCCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:25:1:29:0:1:1.40151:60:4:0.1053:0:4 0/0:20:0:0,0:9,11:0:2,0:29.9:1:28.7:1:1:0:52.2:19:1:0:2.9 -4 49122979 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.23077;SOR=0;LSEQ=TTCCATTCCACTCCAATCCA;RSEQ=TCCATTCCATTCCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:19.5:1:33:1:1:1.40151:43:4:0.1053:0:2.5 0/0:20:0:0,0:9,11:0:2,0:30.1:1:29.2:1:1:0:52.2:40:1:0:2.9 -4 49122982 . C G 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.59459;SOR=0.43056;LSEQ=CATTCCACTCCAATCCATTC;RSEQ=ATTCCATTCCAATCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,5:0.1111:2,2:29:1:30.5:1:1:1.73197:60:4:0.1111:0:7 0/1:20:1:1,0:8,11:0.05:2,0:26:0:26:0:0.45:0:58:2:0.05:0:6 -4 49122983 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.21764;SOR=0;LSEQ=ATTCCACTCCAATCCATTCC;RSEQ=TTCCATTCCAATCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,5:0.1111:2,2:23.5:1:31.5:1:1:1.73197:43:4:0.125:0:2.5 0/0:20:0:0,0:9,11:0:2,0:30.9:1:28.7:1:1:0:52.2:19:1:0:2.9 -4 49122989 . TTCCAATC AAT 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23269;SOR=Inf;LSEQ=CTCCAATCCATTCCATTCCA;RSEQ=CATTCCATTCCATTCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:0:2,0:29:1:31.2:1:1:0:55.3:38:1:0:4.1 0/1:21:3:1,2:9,9:0.1429:2,2:33.3:1:30.8:1:1:1.93674:47.7:6:0.1429:0:1.7 -4 49122996 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48897;SOR=Inf;LSEQ=CCATTCCATTCCATTCCAAT;RSEQ=CATTCCATTCCATTCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:25.5:1:31.3:1:1:0:55.5:40:1:0:4.3 0/1:22:2:1,1:8,9:0.0909:2,2:48.5:1:32.5:1:1:1.12:52:4:0.1053:0:3 -4 49122998 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.4878;SOR=Inf;LSEQ=ATTCCATTCCATTCCAATCC;RSEQ=TTCCATTCCATTCAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:23.8:1:30.3:1:1:0:55.7:42:1:0:4.2 0/1:21:2:1,1:8,11:0.0952:2,2:33:1:31:1:1:1.35:50:4:0.1:0:2 -4 49123003 . A G 59 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.34647;SOR=0.2443;LSEQ=ATTCCATTCCAATCCATTCC;RSEQ=TTCCATTCAATTCCACTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:2,2:11,7:0.1818:2,2:12.5:1:29.8:1:1:1.53863:58.3:8:0.1818:0:4.3 0/1:20:1:1,0:8,11:0.05:2,0:19:0:32:0:0.45:0:60:2:0.05:0:4 -4 49123008 . A T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.06695;SOR=0.18818;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=TTCAATTCCACTCGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:6,2:5,6:0.381:2,2:26:1:30.5:1:0.35207:3.36:55.5:16:0.381:0:5.6 0/1:20:2:0,2:7,9:0.1:2,0:14:1:29.5:1:0.49673:0:48.5:4:0.1:0:3 -4 49123011 . C G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05419;LSEQ=CCAATCCATTCCATTCCATT;RSEQ=AATTCCACTCGCATTCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:0.0952:2,2:24.5:1:31:1:1:1.35399:60:4:0.0952:0:4 0/1:20:2:1,1:6,11:0.1:2,2:30:1:30:1:1:1.77:49.5:4:0.1:0:4 -4 49123012 . A C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48897;SOR=0;LSEQ=CAATCCATTCCATTCCATTC;RSEQ=ATTCCACTCGCATTCAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:25:1:30.5:1:1:1.21106:60:4:0.0952:0:4 0/0:20:0:0,0:8,12:0:2,0:26.2:1:29.7:1:1:0:52.3:19:1:0:2.9 -4 49123013 . A T 40 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65604;SOR=1.74099;LSEQ=AATCCATTCCATTCCATTCA;RSEQ=TTCCACTCGCATTCAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:12,8:0.0909:2,0:12.5:1:28.5:1:0.19481:0:60:4:0.0909:0:3.5 0/1:20:3:2,1:6,11:0.15:2,2:28.3:1:25.3:1:0.53684:3.42:53:2:0.1053:0:4 -4 49123019 . C G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48649;SOR=Inf;LSEQ=TTCCATTCCATTCAATTCCA;RSEQ=TCGCATTCAATCTATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:20.1:1:31.4:1:1:0:57.1:38:1:0:4.1 0/1:19:2:1,1:5,10:0.1053:2,2:25.5:1:33.5:1:1:1.91:60:4:0.1053:0:2.5 -4 49123021 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21587;SOR=0;LSEQ=CCATTCCATTCAATTCCACT;RSEQ=GCATTCAATCTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:24.5:1:28.5:1:1:1.13389:60:4:0.1176:0:4 0/0:19:0:0,0:7,11:0:2,0:23.6:1:30.6:1:1:0:54.6:36:0.9474:0:2.8 -4 49123023 . C T 76 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04075;SOR=0.11459;LSEQ=ATTCCATTCAATTCCACTCG;RSEQ=ATTCAATCTATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:3,3:6,5:0.3529:2,2:25.7:1:29.5:1:1:1.18716:60:12:0.3529:0:6 0/1:18:1:0,1:6,10:0.0556:2,0:18:0:30:0:1:0:60:2:0.0588:0:4 -4 49123025 . T A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8418;LSEQ=TCCATTCAATTCCACTCGCA;RSEQ=TCAATCTATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:8,7:0.0625:2,0:50:0:32:0:1:0:60:2:0.0625:0:4 0/1:18:2:1,1:5,10:0.1111:2,2:16:1:27.5:1:1:1.91:49.5:4:0.1176:0:4 -4 49123028 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=Inf;LSEQ=ATTCAATTCCACTCGCATTC;RSEQ=ATCTATTCCATTCCATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:23.5:1:29.9:1:1:0:55.6:32:1:0:4.1 0/1:17:2:1,1:5,10:0.1176:2,2:16.5:1:32.5:1:1:1.91:60:4:0.1176:0:2.5 -4 49123029 . AT GC 52 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09173;SOR=0;LSEQ=TTCAATTCCACTCGCATTCA;RSEQ=CTATTCCATTCCATTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:1,2:5,4:0.2:2,2:31:1:33.3:1:1:2.31595:60:6:0.2:0:5.7 0/0:17:0:0,0:6,10:0:2,0:21.8:1:30.1:1:1:0:51.7:32:0.9412:0:2.9 -4 49123031 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21169;SOR=0;LSEQ=CAATTCCACTCGCATTCAAT;RSEQ=TATTCCATTCCATTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:0.1333:2,2:15.5:1:29:1:1:1.1547:60:4:0.1333:0:6 0/0:17:0:0,0:6,11:0:2,0:20.8:1:31.7:1:1:0:52.2:34:1:0:2.9 -4 49123039 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21169;SOR=0;LSEQ=CTCGCATTCAATCTATTCCA;RSEQ=TCCATTTCATTCCGTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:5,8:0.1333:2,0:31:1:30.5:1:0.2:0:42:4:0.1333:0:3 0/0:17:0:0,0:6,11:0:2,0:17.2:1:30.1:1:1:0:53.8:34:1:0:2.9 -4 49123041 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48589;SOR=Inf;LSEQ=CGCATTCAATCTATTCCATT;RSEQ=CATTTCATTCCGTTCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,8:0:2,0:28.6:1:31.8:1:1:0:54.9:28:0.9333:0:4.2 0/1:17:2:1,1:5,10:0.1176:2,2:7.5:1:26:1:1:1.91:52:4:0.1176:0:3 -4 49123044 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48148;SOR=Inf;LSEQ=ATTCAATCTATTCCATTCCA;RSEQ=TTCATTCCGTTCTGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:0:2,0:29.9:1:31.1:1:1:0:53.8:28:1:0:4.4 0/1:14:2:1,1:4,8:0.1429:2,2:7:1:30:1:1:1.90:41.5:4:0.1429:0:4 -4 49123054 . T C 51 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25296;SOR=0;LSEQ=TTCCATTCCATTTCATTCCG;RSEQ=TCTGTTCCATTCCATTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:5,6:0.2143:2,2:31.3:1:32.3:1:1:1.60839:60:6:0.2143:0:5.7 0/0:9:0:0,0:3,6:0:2,0:22.9:1:30.7:1:1:0:50.8:18:1:0:3.3 -4 49123056 . CTG TT 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49351;SOR=0;LSEQ=CCATTCCATTTCATTCCGTT;RSEQ=TTCCATTCCATTCTATTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:5,6:0.1538:2,0:15.5:1:31.8:1:0.48718:0:60:4:0.1538:0.0769:4 0/0:9:0:0,0:3,6:0:2,0:22.1:1:32.1:1:1:0:50.8:18:1:0:3.3 -4 49123061 . CC TA 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15584;SOR=Inf;LSEQ=CCATTTCATTCCGTTCTGTT;RSEQ=ATTCCATTCTATTGCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:29.7:1:31.2:1:1:0:55.5:26:1:0:4.1 0/1:9:2:1,1:3,4:0.2222:2,2:21.5:1:30.8:1:1:1.29:55:4:0.2222:0:1.5 -4 49123062 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.13333;SOR=Inf;LSEQ=CATTTCATTCCGTTCTGTTC;RSEQ=ATTCCATTCTATTGCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:29.5:1:31.6:1:1:0:55.5:26:1:0:4.1 0/1:8:2:1,1:2,2:0.25:2,2:23:0:31.5:1:1:1:60:4:0.3333:0:4.5 -4 49123071 . C T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57143;SOR=2.62608;LSEQ=CCGTTCTGTTCCATTCCATT;RSEQ=TATTGCTTTCCATACCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:5,6:0.0833:2,0:23:0:32:0:1:0:60:2:0.0833:0:6 0/1:10:2:1,1:4,4:0.2:2,2:14:0:32:0:1:1:60:4:0.2:0:4.5 -4 49123077 . CT GA 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58647;SOR=2.39416;LSEQ=TGTTCCATTCCATTCTATTG;RSEQ=TTCCATACCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:4,6:0.0909:2,0:46:0:33:0:0.45455:0:25:2:0.0909:0:2 0/1:10:2:1,1:4,4:0.2:2,2:14.5:1:28.5:1:1:1:60:4:0.2:0:2 -4 49123078 . T A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58647;SOR=0.41768;LSEQ=GTTCCATTCCATTCTATTGC;RSEQ=TTCCATACCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:4,6:0,0:0.9091:0,2:26.7:1:30.1:1:1:0:57.6:20:1:0:4 1/1:10:8:4,4:0,0:0.8:0,2:10.9:1:30:1:1:0:56.3:16:1:0:3.4 -4 49123087 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=0;LSEQ=CATTCTATTGCTTTCCATAC;RSEQ=ATTCCATTCCACTCGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:15.5:1:28.5:1:1:1.58:60:4:0.2:0:5.5 0/0:5:0:0,0:2,3:0:2,0:22.2:1:32:1:1:0:56:10:1:0:2.8 -4 49123124 . T C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=GATGATTCCATTCCATTCCA;RSEQ=TATATTCCGTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:19.5:1:28.8:1:1:0:36.8:8:1:0:2.8 1/0:4:2:1,1:1,1:0.5:2,2:22:0:33:0:1:1:60:4:0.5:0:2 -4 49123133 . G GTTCCATTCCA 61 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=5.000;MSILEN=5;SSF=0.06061;SOR=0;LSEQ=ATTCCATTCCATTATATTCC;RSEQ=TTCCATTCCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:1,1:0.6667:2,2:15.5:1:30.7:1:1:2.44949:42.8:8:0.6667:0.5:4 0/0:6:0:0,0:3,3:0:2,0:10.3:1:31.2:1:1:0:50:12:1:0:3.3 -4 49123138 . A T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=ATTCCATTATATTCCGTTCC;RSEQ=TTCCATTCCACTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:15.3:1:30.3:1:1:0:35.9:14:1:0:3.7 0/1:7:2:1,1:3,2:0.2857:2,2:10:1:27.5:1:1:1.41418:40:4:0.2857:0:5 -4 49123147 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.4697;SOR=0;LSEQ=TATTCCGTTCCATTCCATTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:17.5:1:31.5:1:1:3.16:49:4:0.2857:0:6 0/0:5:0:0,0:2,2:0:2,0:13.5:1:31.3:1:1:0:42.8:8:0.8:0:3.8 -4 49123149 . C T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=TTCCGTTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,4:0:2,0:21.7:1:31.5:1:1:0:33.2:12:1:0:4.2 1/0:4:2:1,1:1,1:0.5:2,2:21:1:27.5:1:1:1:40:4:0.5:0:5 -4 49123157 . GATTCC G 28 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=46;MSI=10.000;MSILEN=5;SSF=0.10909;SOR=Inf;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:21.3:1:30.3:1:1:0:34.1:14:1:0:4 1/0:4:2:1,1:1,1:0.5:2,2:22.5:1:28:1:1:1:45.5:4:0.5:0:4 -4 49123159 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=TTCCATTCCACTCGGGTTGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,4:0:2,0:22:1:29.8:1:1:0:36.3:12:0.8571:0:4.2 1/0:4:2:1,1:0,0:0.5:0,2:31:1:28:1:1:0:40:4:1:0:5 -4 49123163 . A T 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.49091;SOR=0;LSEQ=ATTCCACTCGGGTTGATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:23.5:1:29:1:1:3.16:30:4:0.2857:0:3 0/0:4:0:0,0:2,2:0:2,0:28.8:1:24.8:1:1:0:42.8:3:1:0:4.5 -4 49123179 . T C 32 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=0.44444;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:48:1:32:1:0.4:0:49:4:0.4:0:6 0/0:4:0:0,0:2,2:0:2,0:40:1:28.3:1:1:0:42.8:8:1:0:4.5 -4 49123201 . C G 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.44444;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGTTTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:29.5:1:31.5:1:0.4:0:49:4:0.4:0:6 0/0:4:0:0,0:2,2:0:2,0:29.5:1:30.8:1:1:0:42.8:8:1:0:4.5 -4 49123211 . C T 26 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGTTTGTTTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,3:0:2,0:25:1:30.8:1:1:0:39.5:8:1:0:4.8 1/0:4:2:1,1:1,1:0.5:2,2:10:1:26:1:1:1:40:4:0.6667:0:5 -4 49123214 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=TTCCATTCCATTCCACTCGG;RSEQ=TTGTTTCCATTCCATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,0:0.4:0,2:16.5:1:30:1:1:0:49:4:0.6667:0:6 1/0:3:2:0,2:1,0:0.6667:0,0:23:1:32.5:1:0.33333:0:40:4:0.6667:0:6 -4 49123217 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=CATTCCATTCCACTCGGTTT;RSEQ=TTTCCATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,2:0.4:0,2:13.5:1:28:1:1:0:49:4:0.5:0:6 0/0:3:0:0,0:1,2:0:2,0:19.7:1:27.7:1:1:0:43.7:2:1:0:4.7 -4 49123218 . T A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=ATTCCATTCCACTCGGTTTG;RSEQ=TTCCATTCCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,3:0:2,0:18:1:30.3:1:1:0:39.5:8:1:0:4.3 1/0:4:2:0,2:1,1:0.5:2,0:19:1:32:0:1:0:40:4:0.5:0:6 -4 49123919 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTAGTTTCCATTCCATTC;RSEQ=ATTCCTTTCGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:29:1:1:0:23:4:1:0:5 -4 49123948 . C G 33 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:0:33.5:1:1:0:23:4:1:0:5 -4 49123955 . A T 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:32:1:1:0:23:4:1:0:5 -4 49123974 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCTTTCCACTCAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:31.5:1:1:0:23:4:1:0:5 -4 49123980 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCAGGGTGATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:31.5:1:1:0:23:4:1:0:5 -4 49147328 . C T 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:30:0:32:0:1:0:33:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:21.5:1:30:0:1:1:43:4:0.5:0:7 -4 49147334 . A G 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:36:0:25:0:1:0:33:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:15.5:1:31:1:1:1:43:4:0.5:0:7 -4 49147336 . T A 28 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:38:0:29:0:1:0:33:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:28.5:1:1:1:43:4:0.5:0:7 -4 49147350 . TTCCAC T 27 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGTTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.1:1:24.1:1:1:0:33:4:1:1:6 1/1:2:2:1,1:0,0:1:0,2:12.5:1:27.5:1:1:0:46:4:1:0.5:2 -4 49147358 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GGTTGTTTCCATTCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:29.5:1:1:0:33:4:1:0:6 0/0:1:0:0,0:0,1:0:0,0:20:0:31:0:1:0:40:2:1:0:3 -4 49147420 . T A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCCATTCCATTTTATTCCA;RSEQ=TCCATTTCATTCCATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:17:0:32:0:1:0:33:2:1:0:5 1/1:2:2:1,1:0,0:1:0,2:14:0:31.5:1:1:0:22:4:1:0:1 -4 49147607 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CGTTCCGTTCCGTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:13:0:33:0:1:1:28:4:0.3333:0:4 -4 49147609 . G A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTAC;RSEQ=TTCCGTTCCGTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:28:0:32:0:1:1:48:4:0.4:0:3 -4 49147616 . T A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCATTCCATTACGTTCCGT;RSEQ=CCGTTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:22:0:30:0:1:1:28:4:0.3333:0:4 -4 49147619 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTACGTTCCGTTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:19:0:31.5:1:1:1:48:4:0.3333:0:3 -4 49147643 . C T 27 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:23:0:32:0:1:0:37:2:1:0:3 0/1:6:2:1,1:2,2:0.3333:2,2:5:0:27.5:1:1:1:60:4:0.3333:0:0 -4 49147654 . A G 30 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:30:0:1:0:37:2:1:0:3 1/0:4:2:1,1:1,1:0.5:2,2:18:0:30.5:1:1:1:28:4:0.5:0:4 -4 49147658 . C CAGTTG 30 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.06667;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTAAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:30.5:1:1:0:37:4:1:0.5:4.5 0/0:4:0:0,0:2,2:0:2,0:22.8:1:31:1:1:0:29:8:1:0:4 -4 49147659 . A G 29 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTAAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22.5:1:30.5:1:1:0:37:4:1:0:4.5 1/0:4:2:1,1:1,1:0.5:2,2:13:0:29:1:1:1:28:4:0.5:0:4 -4 49147672 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=AATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:31:1:1:0:37:4:1:0:4.5 0/0:2:0:0,0:1,1:0:2,0:33.5:1:29.5:1:1:0:30:4:1:0:4 -4 49147681 . T A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=TCCATTCCATTAAATTCCAT;RSEQ=CCATTCCATTCCATTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:29.5:1:1:0:37:4:1:0:4.5 1/0:4:2:1,1:1,0:0.5:0,2:8:0:28:1:1:0:53:4:0.6667:0:5 -4 49147684 . A GTTCCT 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.46667;SOR=Inf;LSEQ=ATTCCATTAAATTCCATTCC;RSEQ=TTCCATTCCATTCCTCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:29.5:1:1:0:37:4:1:0:4.5 1/0:4:2:1,1:1,1:0.5:2,2:31.5:1:29.7:1:1:1:30:4:0.5:0.25:4 -4 49147692 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=AAATTCCATTCCATTCCATT;RSEQ=CATTCCTCTCGGGTCGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:30.5:1:1:0:37:4:1:0:4.5 1/0:4:2:1,1:1,1:0.5:2,2:19:0:30:1:1:1:53:4:0.5:0:5 -4 49147699 . T A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=CTCGGGTCGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:29.5:1:1:0:37:4:1:0:4.5 1/1:3:3:1,2:0,0:1:0,2:27:1:30:1:1:0:45.3:6:1:0:5.3 -4 49147705 . GT AA 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCTCTCGG;RSEQ=CGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:43:0:34:0:1:0:37:2:1:0:6 1/0:3:2:1,1:0,1:0.6667:0,2:33:0:31.3:1:1:0:53:4:0.6667:0:4 -4 49148117 . CATGCCCTTTT C 69 d7;v4;NM4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=12.000;MSILEN=5;SSF=0.04762;SOR=Inf;LSEQ=GGGTTGATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27.5:1:30:1:1:0:42.5:4:1:0:1 1/1:5:5:2,3:0,0:1:0,2:6:1:30:1:1:0:42.6:10:1:1:4.6 -4 49148123 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATGCC;RSEQ=TTTTATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30.5:1:1:0:42.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49148142 . C T 63 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.51515;SOR=Inf;LSEQ=CCTTTTATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27.5:1:31:1:1:0:42.5:4:1:0:1 0/1:10:4:2,2:3,3:0.4:2,2:12.5:1:31.5:1:1:1:45:8:0.4:0:4 -4 49148151 . C T 79 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.45455;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19.5:1:30.5:1:1:0:42.5:4:1:0:1 1/0:10:6:3,3:2,2:0.6:2,2:23:1:30.8:1:1:1:44.3:12:0.6:0:5 -4 49148153 . A G 53 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.51515;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:17.5:1:24.5:1:1:0:42.5:1:1:0:1 0/1:10:4:2,2:3,3:0.4:2,2:26.5:1:26.8:1:1:1:48:3:0.3333:0:5 -4 49148167 . C T 77 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.45455;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATACCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:18:0:34:0:1:0:45:2:1:0:1 1/0:10:6:3,3:2,2:0.6:2,2:35.5:1:30:1:1:1:44.3:12:0.6:0:5 -4 49148173 . A G 50 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TACCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:12:0:32:0:1:0:45:2:1:0:1 0/1:10:4:2,2:3,3:0.4:2,2:29.3:1:25.3:1:1:1:48:3:0.3333:0:5 -4 49148190 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCATACCATTCCATTCCAT;RSEQ=CCATTCCATTCCATACCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:4,4:0.2:2,2:16:1:30:1:1:1:37:4:0.2:0:5 -4 49148205 . A T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCACCAAGTTGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:7:1:30:1:1:0:29:4:0.6667:0:5 -4 49148621 . T TTCTAC 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCTATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:30.2:1:1:0:43.5:4:1:0.5:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49148633 . CC TG 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:32.3:1:1:0:43.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49148658 . C T 30 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:0:30:1:1:0:43.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49149291 . T TTCCATTCCATTGCATTCCATTCCCTCGTGTTGATTCCATTCTTTCCATTCCATTCAAGTTGAA 68 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=23;MSI=2.000;MSILEN=1;SSF=0.002;SOR=0;LSEQ=CTAGGGTTGATCCCATACCA;RSEQ=TCCATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:2,0:0.8333:0,2:17.6:1:29.7:1:1:0:28.2:10:0.8333:0.8333:4.2 0/0:9:0:0,0:7,2:0:2,0:2.6:1:31.8:1:1:0:32.7:18:1:0:5.3 -4 49149298 . C G 34 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATCCCATACCATTCCATT;RSEQ=CATTGCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:8.3:1:31.9:1:1:0:31.6:14:1:0:5.3 0/1:19:2:1,1:11,6:0.1053:2,2:11:0:34:0:1:1.77272:32:4:0.1053:0:4 -4 49149313 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.55034;SOR=Inf;LSEQ=CCATTCCATTGCATTCCATT;RSEQ=CATTCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:21.5:1:30.4:1:1:0:32.3:16:1:0:5.1 0/1:25:4:2,2:13,8:0.16:2,2:18:1:29.3:1:1:1.59276:33:8:0.16:0:3.3 -4 49149317 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCATTGCATTCCATTCCAT;RSEQ=CCATTCCATTCCACTCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:20.8:1:28.7:1:1:0:33.5:20:1:0:5.3 0/1:28:2:1,1:16,10:0.0714:2,2:30:0:32.5:1:1:1.57244:32:4:0.0714:0:4 -4 49149319 . C G 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTGCATTCCATTCCATTC;RSEQ=ATTCCATTCCACTCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:22.8:1:30.7:1:1:0:33.5:20:1:0:5.3 0/1:28:2:0,2:17,8:0.0714:2,0:28:0:31.5:1:0.12821:0:37:4:0.0714:0:4 -4 49149325 . AT CC 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.71101;SOR=0.61909;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:1,3:0.5:2,2:36:1:29.9:1:0.20635:8.35:28.2:10:0.5:0:4.8 0/1:29:11:8,3:6,8:0.3793:2,2:33.5:1:31.3:1:0.22716:3.37:32.3:22:0.3929:0:5 -4 49149326 . T C 32 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.06073;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:0,3:0.2:0,2:37:0:32.5:1:0.4:0:40:4:0.4:0:4 0/0:29:0:0,0:8,9:0:2,0:25.5:1:30.1:1:1:0:35.3:34:1:0:4.2 -4 49149328 . CC GT 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.44592;SOR=0.45991;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:0,3:0.5:0,2:39.8:1:30.6:1:0.14286:0:30.8:10:0.5:0:3.2 0/1:29:9:6,3:8,6:0.3103:2,2:36.3:1:30.6:1:1:1.47:33.8:18:0.3103:0:3.6 -4 49149329 . C CCCTGT 78 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.30721;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,4:0:2,0:25.4:1:29.2:1:1:0:36.2:10:1:0:5.4 0/1:31:6:2,4:6,3:0.1935:2,2:25.5:1:30.3:1:0.31469:3.61926:35.3:12:0.3158:0.0645:1.2 -4 49149331 . C T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06969;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:4,5:0.0909:2,0:15:0:25:0:1:0:39:2:0.0909:0:6 0/1:31:3:2,1:13,10:0.0968:2,2:28:1:28.3:1:1:1.51:36.7:6:0.1111:0:5.3 -4 49149333 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:31.7:1:28.8:1:1:0:33.5:22:1:0:4 0/1:31:2:2,0:14,10:0.0645:2,0:35.5:1:30:1:0.50769:0:29:4:0.0741:0:6 -4 49149339 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,5:0:2,0:27.5:1:30.9:1:1:0:33.2:22:0.9167:0:4.1 0/1:34:2:1,1:17,14:0.0588:2,2:29:1:28.5:1:1:1.20712:38:4:0.0588:0:5.5 -4 49149341 . TTCCATTCCATTCCATTCCAA T 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=2.000;MSILEN=1;SSF=0.56115;SOR=Inf;LSEQ=TTCCATTCCACTCGGGTTGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:27:1:28.8:1:1:0:34.2:26:1:0:4.5 0/1:38:3:1,2:19,16:0.0789:2,2:17.7:1:27.9:1:0.59459:2.32256:24:6:0.0789:0.0526:4 -4 49149346 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCACTCGGGTTGATTCCA;RSEQ=TCCATTCCATTCCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:26.8:1:29.5:1:1:0:34.2:26:1:0:4.5 0/1:36:2:1,1:18,15:0.0556:2,2:31:1:31.5:1:1:1.19373:29.5:4:0.0571:0:6.5 -4 49149351 . T C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.55827;SOR=Inf;LSEQ=CTCGGGTTGATTCCATTCCA;RSEQ=TCCATTCCAATCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:26.1:1:29.4:1:1:0:34.2:26:1:0:4.5 0/1:37:3:1,2:18,15:0.0811:2,2:11:1:31:1:0.59286:2.34335:35.3:6:0.0833:0:4.7 -4 49149353 . C G 34 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=CATTCCAATCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:25.5:1:30.1:1:1:0:34.2:26:1:0:4.5 0/1:36:2:0,2:19,14:0.0556:2,0:15.5:1:34:0:0.20168:0:37:4:0.0571:0:4 -4 49149361 . A T 92 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70214;SOR=1.90291;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,5:0.1333:2,2:24.5:1:28:1:1:1.18321:33:4:0.1429:0:5 0/1:35:8:5,3:13,9:0.2286:2,2:24.5:1:30.8:1:1:1.15:36.5:16:0.2424:0:5.6 -4 49149365 . A T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0.94542;LSEQ=ATTCCATTCCATTCCAATCC;RSEQ=TTCCATTCCATTCCATTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:10,6:0.0556:2,0:26:0:33:0:1:0:40:2:0.0588:0:6 0/1:38:2:1,1:17,15:0.0526:2,2:22.5:1:29:1:1:1.12916:34:4:0.0588:0:6 -4 49149367 . T G 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=1.12789;LSEQ=TCCATTCCATTCCAATCCAT;RSEQ=CCATTCCATTCCATTCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:4,2:7,5:0.3333:2,2:7.5:1:30.2:1:1:1.40:31.2:12:0.3333:0:2.8 0/1:36:13:7,6:12,11:0.3611:2,2:8.5:1:30.8:1:1:1.07:32.9:26:0.3611:0:3 -4 49149370 . A T 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=1.03164;LSEQ=ATTCCATTCCAATCCATTCC;RSEQ=TTCCATTCCATTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:7,7:0.1111:2,0:7:1:32.5:1:0.475:0:32:4:0.1111:0:3.5 0/1:35:4:3,1:12,12:0.1143:2,2:30.3:1:30:1:0.6:2.89:32:8:0.1176:0:6 -4 49149378 . C A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.53902;SOR=Inf;LSEQ=CCAATCCATTCCATTCCATT;RSEQ=CATTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,5:0:2,0:20.8:1:31.8:1:1:0:37:26:0.9286:0:5.4 0/1:27:2:1,1:13,12:0.0741:2,2:20:1:28.5:1:1:1.0801:36:4:0.0741:0.037:5.5 -4 49149380 . ATTCGGGTTG GGTTC 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53333;SOR=Inf;LSEQ=AATCCATTCCATTCCATTCC;RSEQ=ATTCCATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:23:1:30.6:1:1:0:37.1:28:1:0:5.4 0/1:26:2:1,1:12,12:0.0769:2,2:17.5:1:28.5:1:1:1:32.5:4:0.08:0.0385:4 -4 49149381 . T C 34 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.60171;SOR=0.50933;LSEQ=ATCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:42.5:1:33.5:1:1:1.36624:38:4:0.1429:0:7 0/1:26:2:0,2:11,7:0.0769:2,0:44.5:1:34:0:0.18947:0:37.5:4:0.0833:0:6.5 -4 49149383 . CG AC 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53333;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:24:1:31.5:1:1:0:37.1:28:1:0:5.4 0/1:26:2:2,0:10,11:0.0769:2,0:41:0:28.5:0:0.47826:0:40:4:0.0833:0:6 -4 49149385 . G A 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13629;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCG;RSEQ=GTTGATTCCATTCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,5:0:2,0:26.5:1:31.5:1:1:0:37.1:24:0.9231:0:5.7 0/1:23:5:1,4:7,8:0.2174:2,2:17.2:1:30.6:1:0.60268:3.30211:34.4:10:0.2381:0.087:3.2 -4 49149386 . G A 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54414;SOR=0.28302;LSEQ=TTCCATTCCATTCCATTCGG;RSEQ=TTGATTCCATTCCATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:8,4:0.1429:2,2:31:1:30:1:1:1.89743:48.5:4:0.1429:0:6.5 0/1:23:1:0,1:11,11:0.0435:2,0:7:1:30:1:1:0:28:2:0.0455:0.0435:1 -4 49149387 . T A 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50925;SOR=Inf;LSEQ=TCCATTCCATTCCATTCGGG;RSEQ=TGATTCCATTCCATTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:23.4:1:30.7:1:1:0:37.8:30:1:0:5.1 0/1:23:2:2,0:9,12:0.087:2,0:38:0:27:1:0.21739:0:40:4:0.087:0:6 -4 49149389 . G C 92 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11205;SOR=6.63125;LSEQ=CATTCCATTCCATTCGGGTT;RSEQ=ATTCCATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:9,4:0.0714:2,0:31:0:34:0:0.35714:0:38:2:0.0714:0:6 0/1:23:8:3,5:7,6:0.3478:2,2:27.6:1:30.9:1:0.65944:1.88324:35.1:16:0.3636:0.0435:4.1 -4 49149391 . T A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65396;SOR=0.55417;LSEQ=TTCCATTCCATTCGGGTTGA;RSEQ=TCCATTCCATTCCTTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:6,6:0.2:2,0:25.7:1:30.7:1:0.22857:0:28:6:0.2:0:4.3 0/1:25:3:1,2:9,12:0.12:2,2:20.3:1:28.3:1:1:1.47566:25.3:6:0.12:0.04:3.7 -4 49149399 . C T 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.547;SOR=0.29235;LSEQ=CATTCGGGTTGATTCCATTC;RSEQ=ATTCCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:0.1333:2,2:27.5:1:29:1:1:1.54914:40:4:0.1333:0:5.5 0/1:24:1:0,1:11,12:0.0417:2,0:29:0:30:0:1:0:42:2:0.0417:0:6 -4 49149403 . C G 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.65089;SOR=0.53054;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=CTTTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:6,4:0.2:2,2:36.7:1:31.7:1:1:1.30:40.3:6:0.2:0:6 0/1:26:3:2,1:11,12:0.1154:2,2:28.7:1:29:1:1:2.12:34.7:6:0.1154:0:4.7 -4 49149405 . T A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10021;SOR=0.31583;LSEQ=GGTTGATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:7,1:2,5:0.5333:2,2:33.1:1:30.8:1:0.04056:13.59:37.1:16:0.5333:0:4.5 0/1:27:7:7,0:7,13:0.2593:2,0:14.9:1:29.4:1:0.0058:0:35.7:14:0.2593:0:5.7 -4 49149407 . TC AT 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12195;SOR=0;LSEQ=TTGATTCCATTCCATTCCTT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:0.1333:2,2:35:1:31:1:1:1.54914:48.5:4:0.1429:0:5.5 0/0:27:0:0,0:13,14:0:2,0:22.2:1:29.1:1:1:0:35.7:54:1:0:4.6 -4 49149415 . A G 75 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.23404;SOR=4.06749;LSEQ=ATTCCATTCCTTTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:9,7:0.0588:2,0:5:0:31:0:0.47059:0:38:2:0.0588:0:6 0/1:29:6:2,4:10,11:0.2069:2,2:27:1:29.3:1:0.66184:1.77914:36.2:12:0.2069:0:4.3 -4 49149449 . C G 31 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.53202;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCGAGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,5:0:2,0:21.8:1:32.1:1:1:0:42.6:18:0.9:0:3.8 0/1:19:2:1,1:6,11:0.1053:2,2:35:1:31:1:1:1.77:49.5:4:0.1053:0:5.5 -4 49149453 . C A 29 v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.21538;SOR=0.19096;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCGAGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,4:0.25:2,0:21:1:29.5:1:1:0:40:4:0.25:0.125:4 0/1:18:1:1,0:4,8:0.0556:2,0:35:0:30:0:0.38462:0:31:2:0.0556:0:3 -4 49149456 . T A 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.60542;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGAGTTGATTCCATTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:2,1:0.25:2,0:31.5:1:31:1:0.4:0:33.5:4:0.2857:0:3.5 0/1:17:6:3,3:2,5:0.3529:2,2:36:1:30.2:1:0.59207:2.32:37.3:12:0.3529:0:5.2 -4 49149466 . TT AC 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCGAGTTGA;RSEQ=CCATTCTATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:14.3:1:30.7:1:1:0:41.4:14:1:0:3 0/1:15:2:1,1:5,7:0.1333:2,2:29.5:1:32:1:1:1.37:26:4:0.1429:0:3.5 -4 49149474 . T C 88 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46843;LSEQ=CATTCGAGTTGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,2:0.4:0,0:13.5:1:33:0:1:0:33.5:4:0.4:0:3.5 1/0:14:7:3,4:2,2:0.5:2,2:15.9:1:31.7:1:1:1.29868:33.3:14:0.5385:0:3.3 -4 49149483 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCTATTCCATT;RSEQ=CATTCCATTCCATTGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,4:0:0,0:10.5:1:31:1:1:0:30.5:8:0.8:0:4.3 0/1:15:2:1,1:6,7:0.1333:2,2:19:0:29.5:1:1:1.15:41:4:0.1333:0:4 -4 49149488 . C A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCTATTCCATTCCATT;RSEQ=CATTCCATTGGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:12:1:30.8:1:1:0:31:8:1:0:3.5 0/1:12:2:1,1:4,6:0.1667:2,2:24:0:30:1:1:1.45:41:4:0.1667:0:4 -4 49149494 . CATTGGGGTTG C 46 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=34;MSI=13.000;MSILEN=5;SSF=0.52797;SOR=Inf;LSEQ=TATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:17.3:1:30.3:1:1:0:28:6:1:0:3.7 0/1:10:3:2,1:3,3:0.3:2,2:12:1:29.6:1:1:1.85:43.3:6:0.375:0.2:6.3 -4 49149498 . G T 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=GGGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:30.5:1:31.5:1:1:0:26.5:4:1:0:1.5 0/1:7:3:1,2:1,0:0.4286:0,2:30.7:1:29.7:1:1:0:35.3:6:0.75:0:4.3 -4 49149565 . A ATTCCG 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCGACTCGGGTTG;RSEQ=TTCCAATCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:0.6:2,2:23.3:1:29:1:1:1.73:34.7:6:0.6:0.2:4.3 -4 49149571 . A TTCTATTAGTT 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TTCGACTCGGGTTGATTCCA;RSEQ=TCCATTCCATTCCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:0,2:3,1:0.3333:2,0:14.5:1:30.5:1:0.4:0:40:4:0.3333:0.3333:0 -4 49149586 . A T 45 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCAATCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:3:1,2:2,2:0.4286:2,2:13:1:29:1:1:1.81007:27:6:0.6:0.1429:3.7 -4 49149595 . A T 58 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCAATCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:4:2,2:1,2:0.5714:2,2:29.3:1:29:1:1:1.81:36:8:0.5714:0:3.8 -4 49149600 . A G 56 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:4:2,2:1,2:0.5714:2,2:28.8:1:28.3:1:1:1.81:36:8:0.5714:0:3.8 -4 49149625 . A G 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCTGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:0,2:0.4:0,2:8:0:31.5:1:1:0:32:4:0.4:0:4 -4 49149778 . C A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTGCTTTCCATTCCATT;RSEQ=CATTCCTTTCCACTCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:30:1:1:0:60:4:1:0:3 -4 49149781 . T A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGCTTTCCATTCCATTCCA;RSEQ=TCCTTTCCACTCAGGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:31.5:1:1:0:60:4:1:0:3 -4 49149790 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCTTTCC;RSEQ=CTCAGGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:33:1:1:0:60:4:1:0:3 -4 49149959 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCTCTTGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:32:1:1:0:51:4:1:0:3 -4 49149969 . T C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=CTTGGGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:31:1:1:0:51:4:1:0:3 -4 49149977 . T A 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCATTCCATTCCTCTTGGGT;RSEQ=GATTCCATTCCAATCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:1:29.5:1:1:0:27:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:13:0:29.5:1:1:0:51:4:1:0:3 -4 49149990 . A T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGGTTGATTCCATTCCA;RSEQ=TCCATGCCCCTTTATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:29:1:1:0:27:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49149996 . G T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTCCATTCCAATCCAT;RSEQ=CCCCTTTATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:29:1:1:0:27:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49150065 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCATTCCACCAAAGTTGA;RSEQ=TGCATGCTATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:1:30.5:1:1:0:27:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49150117 . C G 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:31:1:1:0:24:4:1:0:6 -4 49150139 . TT CC 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTGATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:30.8:1:1:0:24:4:1:0:5 -4 49150142 . C G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CACTCGGGTTGATTACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:31.5:1:1:0:24:4:1:0:5 -4 49150548 . T G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCGTTCCGTTCCGTTCG;RSEQ=TTCCATTCCATTCCATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:33:0:1:0:60:4:1:0:1 -4 49150702 . C T 26 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCACTCCATTCCGCTC;RSEQ=ATTCCATTCGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:25:1:26.5:1:1:1.7321:35.5:4:0.4:0:5.5 -4 49150714 . G T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCGCTCCATTCCATTCGG;RSEQ=TTGATTCCGTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:25:1:28:1:1:1:35.5:4:0.5:0:5.5 -4 49150902 . GTTTCCATTCCATTCAATTCCGTTCCATTCCATTCCGTTCCATTCCATTCCATTCCGTTTCATTCCATTGCATTCCACTCGGGTTGATTTCATTCC G 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCTTTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:31.6:1:1:0:30:4:1:1:2.5 -4 49151023 . A G 30 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCCTTCGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:30.5:1:1:0:39:4:1:0:5.5 -4 49151033 . C T 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCGGTTTGATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:30:1:1:0:39:4:1:0:5.5 -4 49151037 . G A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCCTTC;RSEQ=GTTTGATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:29.5:1:1:0:39:4:1:0:5.5 -4 49151172 . C CATTCCATTCCATTCCATTCCGGAAG 164 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTAGGGTTGATTCCATGC;RSEQ=ATTCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:45:45:26,19:0,0:1:0,2:12.2:1:29.9:1:1:0:41.1:90:1:1:1.9 -4 49151178 . A T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTGATTCCATGCCATTCC;RSEQ=TTCCATTGCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:5.9:1:28.9:1:1:0:42.6:13:1:0:1.7 0/1:60:2:1,1:31,27:0.0333:2,2:6:0:29:1:1:1.1455:43:4:0.0345:0:1 -4 49151181 . C A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15984;SOR=0.21321;LSEQ=TGATTCCATGCCATTCCATT;RSEQ=CATTGCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:9:0:27.5:1:1:1.36624:50:4:0.1538:0:3.5 0/1:60:2:1,1:31,27:0.0333:2,2:9:0:30:1:1:1.1455:31:4:0.0339:0:2 -4 49151182 . C G 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GATTCCATGCCATTCCATTC;RSEQ=ATTGCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:9.9:1:30.9:1:1:0:42.6:28:1:0:1.7 0/1:60:2:1,1:31,27:0.0333:2,2:10:0:28.5:1:1:1.1455:42:4:0.0333:0:2 -4 49151183 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATGCCATTCCATTCC;RSEQ=TTGCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:10.9:1:28.9:1:1:0:42.6:13:1:0:1.7 0/1:60:2:1,1:31,27:0.0333:2,2:9.5:1:28:1:1:1.1455:44:4:0.0339:0:5 -4 49151186 . G T 62 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56764;SOR=Inf;LSEQ=CCATGCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:10.7:1:31.3:1:1:0:41.9:18:1:0:1.9 0/1:61:4:3,1:27,26:0.0656:2,2:14:0:31.3:1:0.61347:2.84:45.5:8:0.0667:0:2.5 -4 49151193 . A G 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=1;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCACTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,8:0.0952:2,2:21:0:32:0:1:1.11803:50:4:0.1:0:2 0/1:63:6:3,3:30,26:0.0952:2,2:15.3:1:31:1:1:1.15118:33:12:0.0984:0:3.5 -4 49151201 . C A 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.25891;SOR=0.45231;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTCCACTCGCGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:2,2:9,7:0.1905:2,2:23.3:1:29.8:1:1:1.26953:54.5:8:0.2:0:2 0/1:63:6:3,3:30,26:0.0952:2,2:23.3:1:28.8:1:1:1.15118:33:12:0.0984:0:3.5 -4 49151202 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTGCATTCCATTCCATTC;RSEQ=ATTCCACTCGCGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:25.5:1:31.3:1:1:0:40.4:20:1:0.0476:2 0/1:63:2:1,1:32,27:0.0317:2,2:30:0:31:1:1:1.18187:37:4:0.0317:0:2 -4 49151203 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTGCATTCCATTCCATTCC;RSEQ=TTCCACTCGCGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:26.4:1:29.4:1:1:0:40.4:9.5:1:0.0476:2 0/1:63:2:1,1:31,27:0.0317:2,2:31:0:32:0:1:1.1455:29:4:0.0323:0:3.5 -4 49151205 . T TCCCCA 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGCATTCCATTCCATTCCAT;RSEQ=CCACTCGCGTTGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:27.8:1:29.3:1:1:0:40.4:9.5:1:0.0476:2 0/1:63:2:1,1:33,27:0.0317:2,2:34:0:31:1:1:1.21824:49.5:4:0.0333:0:0.5 -4 49151206 . C CCCCTG 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.33627;SOR=0.38707;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CACTCGCGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:10,9:0,0:0.9048:0,2:28.8:1:31.6:1:1:0:41.2:38:0.9048:0:1.8 1/0:65:51:26,25:8,3:0.7846:2,2:32.1:1:30.9:1:0.31699:2.5271:39.6:102:0.7969:0.0308:2 -4 49151208 . ACTCGC CCTGTACTCGG 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:28.6:1:32.4:1:1:0:40.4:20:1:0:2 0/1:65:2:2,0:30,28:0.0308:2,0:36:0:31.4:0:0.49379:0:31.5:4:0.0313:0:3.5 -4 49151214 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCACTCGC;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:27.4:1:32:1:1:0:40.4:42:1:0:2 0/1:66:2:1,1:34,30:0.0303:2,2:47:0:31:1:1:1.13118:45:4:0.0308:0:4 -4 49151227 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.05613;SOR=0;LSEQ=CACTCGCGTTGATTCCATTC;RSEQ=ATTCCATTCCAATCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:0.0952:2,2:28:1:31.5:1:1:1.10554:50:4:0.1:0:3.5 0/0:66:0:0,0:34,30:0:2,0:18.1:1:30.4:1:1:0:38.2:63:0.9692:0:2 -4 49151229 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.05025;SOR=0;LSEQ=CTCGCGTTGATTCCATTCCA;RSEQ=TCCATTCCAATCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:36.5:1:31.5:1:1:1.11803:21:4:0.1053:0:3 0/0:64:0:0,0:34,30:0:2,0:17:1:29.5:1:1:0:38.2:63:1:0:2.1 -4 49151233 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CGTTGATTCCATTCCATTCC;RSEQ=TTCCAATCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:15.1:1:31.1:1:1:0:40.8:32:1:0:2.4 0/1:61:2:1,1:32,27:0.0328:2,2:17:0:32.5:1:1:1.18187:57:4:0.0333:0:2 -4 49151234 . T A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.09712;SOR=0.11222;LSEQ=GTTGATTCCATTCCATTCCA;RSEQ=TCCAATCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:12.5:1:30.5:1:1:1.36624:30:4:0.1429:0:2.5 0/1:57:1:1,0:28,26:0.0175:2,0:17:0:30:0:1:0:27:2:0.0179:0:6 -4 49151236 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CAATCCATTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,5:0:2,0:15.5:1:31.6:1:1:0:41.9:22:0.7857:0:2.4 0/1:51:2:1,1:23,23:0.0392:2,2:12:1:32.5:1:1:1:30:4:0.04:0:4.5 -4 49151237 . C T 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=AATCCATTCCATTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:13.1:1:31.5:1:1:0:39.5:28:1:0:2.5 0/1:48:2:1,1:22,22:0.0417:2,2:16:0:30.5:1:1:1:44:4:0.0435:0:5 -4 49151239 . A T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28993;SOR=0.32006;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCACTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:5,4:0,0:0.8182:0,2:15.8:1:30.3:1:1:0:36.8:18:0.8182:0:3 1/0:41:24:10,14:9,7:0.5854:2,2:11.8:1:30.8:1:0.51965:1.77336:39.7:48:0.6154:0:2.8 -4 49151241 . C T 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55881;SOR=Inf;LSEQ=CCATTCCATTCCATTCCAAT;RSEQ=CATTCCATTCCACTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:12.4:1:31.5:1:1:0:40.8:22:1:0:2.8 0/1:35:4:2,2:14,15:0.1143:2,2:10.8:1:31.5:1:1:1.07:43:8:0.1143:0:2.3 -4 49151242 . C T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5579;SOR=Inf;LSEQ=CATTCCATTCCATTCCAATC;RSEQ=ATTCCATTCCACTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:12.5:1:31.9:1:1:0:40:20:1:0:3 0/1:33:4:1,3:13,14:0.1212:2,2:15.3:1:28.3:1:0.60667:2.70153:39.8:8:0.1212:0:2.5 -4 49151245 . T G 98 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08431;SOR=Inf;LSEQ=TCCATTCCATTCCAATCCAT;RSEQ=CCATTCCACTCCTTTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:9.5:1:30.7:1:1:0:40:20:1:0:3 0/1:33:10:5,5:10,13:0.303:2,2:9.3:1:29.7:1:1:1.29:32.5:9:0.2813:0:2.7 -4 49151253 . AC GT 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=TCCTTTCCATTCCTTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,2:0:2,0:8:1:30.6:1:1:0:40.2:10:1:0:3.8 0/1:16:2:1,1:5,9:0.125:2,2:11.5:1:32.3:1:1:1.73:45:4:0.125:0:3 -4 49151254 . CTCCTTTCCATTCCTTTCC TTCT 48 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01471;SOR=0;LSEQ=TTCCAATCCATTCCATTCCA;RSEQ=ATTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:0,0:0.6:0,2:11.7:1:30.9:1:1:0:37.3:6:1:0.4:4 0/0:12:0:0,0:4,4:0:2,0:3.9:1:33.2:1:1:0:34.6:14:0.7:0:2.9 -4 49151258 . T G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=AATCCATTCCATTCCACTCC;RSEQ=TTCCATTCCTTTCCATTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:0,0:0.25:0,0:2:0:28:0:1:0:40:2:1:0:5 0/1:5:2:1,1:0,1:0.4:0,2:7.5:1:31.5:1:1:0:45:4:0.6667:0:3 -4 49151320 . ACCATTCCACTAGGGTTGATACCATGCCATTCCATTCCATTCCATTCCATTCCATTCCACTCGGGTTGATTACATTCCATTCCATTCCAAT A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:10.5:1:29.9:1:1:0:43.5:4:1:1:2.5 -4 49151379 . CTCGGGTTGATTACAT C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:13.3:1:30.7:1:1:0:38.7:6:1:0:5.3 0/1:12:2:1,1:4,4:0.1667:2,2:5.5:1:30.7:1:1:1:38:4:0.2:0.1667:4 -4 49151381 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGTTGATTACATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:16.5:1:30:1:1:0:28:4:0.6667:0:6 0/1:12:2:2,0:2,4:0.1667:2,0:24.5:1:28.5:1:0.42857:0:27.5:4:0.25:0:6 -4 49151387 . GATTAC G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.59752;SOR=0.51822;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:1,1:0.3333:2,0:13.5:1:32.5:1:1:0:50:6:0.3833:0.2762:4.5 0/1:15:3:0,3:5,3:0.2:2,0:22.7:1:33:1:0.18182:0:39:6:0.3:0.1333:3.7 -4 49151391 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCACTCGGGTTGATT;RSEQ=CATTCCATTCCATTCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:1,1:0:2,0:26.5:1:27:1:1:0:28:4:0.6667:0:6 0/1:17:2:2,0:3,4:0.1176:2,0:31.5:1:29.5:1:0.44444:0:27.5:4:0.2222:0:6 -4 49151393 . A C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.64299;LSEQ=ATTCCACTCGGGTTGATTAC;RSEQ=TTCCATTCCATTCCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:0.1429:2,0:22:0:32:0:1:0:60:2:0.1429:0:4 0/1:21:2:2,0:4,11:0.0952:2,0:31.5:1:29.5:1:0.11029:0:27.5:4:0.1176:0:6 -4 49151396 . C G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=1.10164;LSEQ=CCACTCGGGTTGATTACATT;RSEQ=CATTCCATTCCAATCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:6,1:0.125:2,0:14:1:27:1:0.25:0:40:2:0.125:0.125:1 0/1:22:3:1,2:6,10:0.1364:2,2:24.7:1:32:1:1:1.18873:35.7:6:0.15:0:4.3 -4 49151398 . A T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59412;SOR=0.48718;LSEQ=ACTCGGGTTGATTACATTCC;RSEQ=TTCCATTCCAATCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,3:0.1667:2,2:31.5:1:30:1:1:2.16028:35:4:0.1667:0.0833:3.5 0/1:23:2:0,2:9,10:0.087:2,0:22:1:31:1:0.48571:0:38.5:4:0.1:0:3.5 -4 49151403 . A T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54472;SOR=Inf;LSEQ=GGTTGATTACATTCCATTCC;RSEQ=TTCCAATCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,5:0:2,0:14.6:1:29.7:1:1:0:39.8:26:0.9286:0.1429:3.9 0/1:28:2:1,1:11,12:0.0714:2,2:44:1:32.5:1:1:1.09:49.5:4:0.0769:0:4.5 -4 49151407 . C G 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=1.1502;LSEQ=GATTACATTCCATTCCATTC;RSEQ=AATCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:9,4:0.0625:2,0:7:0:31:0:1:0:39:2:0.0625:0:2 0/1:28:2:2,0:10,12:0.0714:2,0:31.5:1:28:1:0.47826:0:27.5:4:0.08:0:6 -4 49151408 . A G 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12121;SOR=0;LSEQ=ATTACATTCCATTCCATTCC;RSEQ=ATCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:10,3:0.125:2,2:11:0:28.5:1:0.47619:3.02781:53.5:4:0.125:0:2.5 0/0:29:0:0,0:10,13:0:2,0:18.8:1:29.4:1:1:0:34:22:0.9167:0:4.5 -4 49151409 . A T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.75264;SOR=0.78982;LSEQ=TTACATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:5,1:7,3:0.3529:2,2:11.8:1:30.7:1:1:2.05:33.3:12:0.4:0.0588:5.7 0/1:30:9:3,6:5,10:0.3:2,2:12:1:30.8:1:1:1:39.1:18:0.3333:0:4.6 -4 49151426 . CC TCATTCTATTCGGGTTA 95 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.03212;SOR=Inf;LSEQ=CCAATCCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:35,21:0:2,0:15.3:1:29.7:1:1:0:35.6:55:1:0.0172:4.5 0/1:126:10:3,7:65,50:0.0794:2,2:10.9:1:28.7:1:0.18361:3.00699:32.4:20:0.0806:0.0794:5.7 -4 49151468 . A G 59 NM4;MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.04767;SOR=0.12618;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCACTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:4:2,2:63,60:0.0305:2,2:23:1:29.8:1:1:1.04962:35.5:8:0.0313:0:5.3 0/0:254:1:0,1:135,112:0.0039:2,0:15:0:33:0:0.45565:0:24:2:0.0041:0:3 -4 49151469 . T C 84 v4;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.43029;SOR=3.15049;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCACTCGGGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:1:0,1:66,63:0.0076:2,0:37:0:34:0:0.49231:0:24:2:0.0078:0:8 0/1:253:6:3,3:135,109:0.0237:2,2:34:1:32.7:1:1:1.23746:32.3:12:0.0242:0:6 -4 49151470 . T G 135 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.10041;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCACTCGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:9:6,3:61,61:0.0687:2,2:25:1:33.1:1:0.49324:1.99:33.1:18:0.0709:0:4.4 0/1:253:19:11,8:127,105:0.0751:2,2:32.2:1:32:1:0.81603:1.14:31.6:38:0.076:0:4.9 -4 49151471 . C T 29 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.1164;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:65,62:0.0153:2,2:32:1:29.5:1:1:1.04802:40:4:0.0155:0:4.5 0/0:252:0:0,0:133,110:0:2,0:32.2:1:31:1:1:0:31.9:59.75:0.9637:0:5 -4 49151472 . C G 100 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.03756;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCACTCGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:5:2,3:64,58:0.0388:2,2:25.6:1:30.8:1:0.67061:1.64865:25.2:10:0.0397:0:5.4 0/1:249:10:8,2:128,106:0.0402:2,2:30.7:1:30.3:1:0.19225:3.30:27.9:20:0.0413:0:5.2 -4 49151473 . AT CC 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.249;SOR=1.57919;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:12:5,7:57,53:0.0938:2,2:36.5:1:31:1:0.55597:1.50062:36.1:24:0.0952:0:4.9 0/1:249:35:21,14:104,94:0.1406:2,2:35.5:1:30.6:1:0.46513:1.35:30.8:70:0.1429:0:5.1 -4 49151476 . C G 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.28045;SOR=1.33426;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:32:16,16:39,38:0.25:2,2:33.5:1:30.6:1:1:1.02608:33.6:15:0.2439:0:5 0/1:250:77:51,26:59,72:0.308:2,2:33.5:1:31.7:1:0.00394:2.38:31.2:154:0.3156:0:5 -4 49151477 . C T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=0.53596;SOR=0.76676;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:11:5,6:52,49:0.0859:2,2:33.7:1:26.6:1:0.75945:1.27072:34.7:4.5:0.0811:0:5.8 0/1:253:17:9,8:115,94:0.0672:2,2:35.4:1:29.6:1:1:1.08707:30.2:34:0.0746:0:5.6 -4 49151478 . A G 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60444;SOR=0.50097;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=CTCGGGTTGATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:62,60:0.0157:2,0:25.5:1:31.5:1:0.49646:0:30.5:4:0.0164:0:4.5 0/0:252:2:1,1:134,110:0.0079:2,2:24:1:31.5:1:1:1.21719:33.5:4:0.0082:0:5.5 -4 49151479 . C T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24016;SOR=0.62169;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:14:6,8:52,49:0.1102:2,2:33:1:30.7:1:0.58127:1.4107:30.6:28:0.112:0:5.5 0/1:252:18:10,8:101,94:0.0714:2,2:36.1:1:28.7:1:0.80952:1.16:32.6:17:0.0697:0:5.7 -4 49151480 . T A 51 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23067;SOR=0.37306;LSEQ=TCCATTCCATTCCATTCCAC;RSEQ=CGGGTTGATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:4:1,3:65,58:0.0313:2,2:34.5:1:25.8:1:0.35008:3.33245:24.5:3:0.025:0:6.3 0/1:253:3:2,1:138,111:0.0119:2,2:36.3:1:27.7:1:1:1.61:32.3:6:0.0121:0:4.3 -4 49151481 . C A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12478;SOR=0.29624;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:5:4,1:59,60:0.0391:2,2:30.8:1:28.4:1:0.36505:4.03:34.8:10:0.0403:0:5.2 0/1:253:3:3,0:135,110:0.0119:2,0:38.7:1:27.3:1:0.25656:0:34.7:6:0.012:0:6 -4 49151482 . G C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41121;SOR=0.50693;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:3:1,2:64,59:0.0231:2,2:40:1:29:1:0.6102:2.15662:28:6:0.024:0:6 0/1:254:3:2,1:132,106:0.0118:2,2:38.3:1:30.3:1:1:1.60:29:6:0.012:0:5 -4 49151483 . G A 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08134;LSEQ=ATTCCATTCCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:10:6,4:53,54:0.0769:2,2:33.1:1:30.9:1:0.74282:1.52:33.7:20:0.0794:0:5.4 0/1:254:21:17,4:109,102:0.0827:2,2:37:1:29:1:0.01115:3.96:35.2:42:0.0857:0:4.9 -4 49151484 . G T 54 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49445;SOR=0.63331;LSEQ=TTCCATTCCATTCCACTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:4:1,3:63,57:0.0308:2,2:31.8:1:29:1:0.35316:3.28626:38.3:8:0.0325:0:6.3 0/1:254:5:4,1:134,110:0.0197:2,2:33:1:23.6:1:0.38478:3.27:28.2:1.5:0.0125:0:6.8 -4 49151485 . T A 62 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66833;SOR=2.58509;LSEQ=TCCATTCCATTCCACTCGGG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:0,1:66,61:0.0077:2,0:44:0:31:0:0.48438:0:54:2:0.0078:0:2 0/1:254:5:3,2:138,111:0.0197:2,2:26:1:27:1:1:1.21:34.4:4:0.0159:0:4.2 -4 49151486 . T G 35 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76857;LSEQ=CCATTCCATTCCACTCGGGT;RSEQ=GATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:0,2:67,60:0.0154:2,0:19:1:33:0:0.22905:0:38.5:4:0.0155:0:4 0/1:253:3:3,0:136,111:0.0119:2,0:19:1:22.7:1:0.25643:0:36.7:2:0.0081:0:5 -4 49151487 . G A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26358;SOR=0.65882;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:15:9,6:58,51:0.1154:2,2:29.3:1:30:1:0.78383:1.32:31.5:30:0.1181:0:5.3 0/1:253:20:11,9:125,100:0.0791:2,2:32.5:1:27.7:1:1:1.02264:33.1:19:0.0766:0:5.4 -4 49151488 . A T 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.53441;LSEQ=ATTCCATTCCACTCGGGTTG;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:1:0,1:67,60:0.0078:2,0:50:0:32:0:0.47656:0:40:2:0.0081:0:7 0/1:253:3:3,0:137,111:0.0119:2,0:39.7:1:29.7:1:0.25705:0:29:6:0.0122:0:5.7 -4 49151489 . TT CA 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11462;SOR=0;LSEQ=TTCCATTCCACTCGGGTTGA;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:65,61:0.0154:2,2:19:0:32.8:1:1:1.06508:30:4:0.0159:0:2 0/0:253:0:0,0:139,110:0:2,0:29.4:1:29.6:1:1:0:31.8:123.5:0.9841:0:4.6 -4 49151490 . T A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11462;SOR=0;LSEQ=TCCATTCCACTCGGGTTGAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:65,60:0.0154:2,2:41:1:28.5:1:1:1.08263:33:4:0.016:0:7 0/0:253:0:0,0:141,112:0:2,0:29:1:29:1:1:0:31.8:83.333:1:0:4.7 -4 49151538 . A G 51 v4;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.57163;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCACTCCATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:12,17:0.0323:2,0:10:0:33:0:1:0:30:2:0.0345:0:4 0/1:60:3:1,2:26,30:0.05:2,2:11.7:1:32.3:1:1:1.71787:28:6:0.0517:0:4 -4 49151541 . C G 50 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.54876;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCCATTCCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:7,18:0:2,0:8.2:1:31.3:1:1:0:32.9:24:0.8571:0:4.3 0/1:53:3:1,2:20,28:0.0566:2,2:10:1:31.7:1:1:1.41896:26:6:0.0566:0:5 -4 49151543 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.53964;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCCATTCCGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:6,17:0:2,0:11:1:31:1:1:0:35.1:46:0.9583:0:3.7 0/1:45:2:0,2:16,26:0.0444:2,0:8.5:1:32:1:0.52643:0:35:4:0.0455:0:5 -4 49151544 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.12216;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCATTCCGTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:4,16:0.0909:2,2:13:1:30.5:1:0.41126:3.69:33:4:0.0909:0:2 0/0:40:0:0,0:16,24:0:2,0:5.3:1:29.4:1:1:0:31.4:80:1:0.05:3.9 -4 49151549 . C T 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCGTTACATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:3,5:0:2,0:14.5:1:31.9:1:1:0:37.6:16:1:0:3 1/0:10:7:2,5:1,2:0.7:2,2:6.6:1:28.9:1:1:1.22183:29.9:14:0.7:0:3.4 -4 49151558 . G T 29 v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCACTCCATTCC;RSEQ=TTACATTCCATTCTACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,2:0.2857:2,2:19:0:29.5:1:1:1:48:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49151572 . T CATTAC 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=CATTCCGTTACATTCCATTC;RSEQ=ACTCTGTTTAATTCCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22:1:30.4:1:1:1:27:4:0.5:0.25:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49151644 . TTGGGG T 58 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=15.000;MSILEN=5;SSF=0.49091;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,1:0:0,0:40:0:31:0:1:0:20:2:1:0:7 0/1:9:4:2,2:0,4:0.4444:0,2:33.8:1:29.1:1:0.42857:0:35.5:8:0.5:0.2222:2.5 -4 49151646 . G C 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=GGGTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:0,2:0,1:0.2222:0,0:32:1:27.5:1:1:0:22:4:0.5:0:5 -4 49151649 . G T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTGGG;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:2:0,2:0,2:0.25:0,0:34.5:1:29.5:1:1:0:32:4:0.6667:0:5.5 -4 49151653 . A G 31 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.68606;LSEQ=ATTCCATTCCATTGGGGTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,1:0.25:2,0:48:0:33:0:1:0:20:2:0.3333:0:4 0/1:11:2:0,2:3,5:0.1818:2,0:38.5:1:31:1:1:0:32:4:0.2222:0:5.5 -4 49151674 . T A 26 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.02857;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCGTTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23.5:1:26.5:1:1:1:20:4:0.5:0:4 0/0:17:0:0,0:6,11:0:2,0:26.9:1:29.2:1:1:0:31.9:16:1:0:2.9 -4 49151681 . C A 28 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCGTTCCGTTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:25.8:1:25.5:1:1:0:20:3:1:0:4 0/1:16:2:1,1:5,9:0.125:2,2:21.5:1:28:1:1:1.73:44:4:0.125:0:1 -4 49151698 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCGTTCCGTTCC;RSEQ=TTCCATTCCATTCAAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,1:0:0,0:8:0:30:0:1:0:20:2:0.5:0:4 0/1:16:2:1,1:5,8:0.125:2,2:17:1:28:1:1:1.55:32:4:0.1333:0:3.5 -4 49151702 . C G 27 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.00794;SOR=0;LSEQ=CATTCCGTTCCGTTCCGTTC;RSEQ=ATTCCATTCAAATCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:12:0:27.5:1:1:0:20:4:0.6667:0:3.5 0/0:25:0:0,0:5,7:0:2,0:12.3:1:31.7:1:1:0:30.9:24:1:0:3.8 -4 49151703 . A G 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29792;SOR=0.19267;LSEQ=ATTCCGTTCCGTTCCGTTCC;RSEQ=TTCCATTCAAATCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:3:0:28:0:1:0:20:2:0.3333:0:4 0/1:25:2:1,1:4,6:0.08:2,2:7:1:27.5:1:1:1.45:36:4:0.2:0:4.5 -4 49151712 . A C 43 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTTCCGTTCCATTCCATTC;RSEQ=AATCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:2:0:15:1:1:0:20:0:0:0:3.5 0/1:15:3:2,1:0,0:0.2:0,2:7.3:1:27.7:1:1:0:31.7:6:0.75:0:4.3 -4 49151714 . A T 66 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCGTTCCATTCCATTCAA;RSEQ=TCCATTCCATTGCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:16:5:3,2:0,0:0.3125:0,2:10.6:1:28.6:1:1:0:30.4:10:1:0:5.2 -4 49151723 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCAAATCCATTCC;RSEQ=TTGCATTCCATACCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7.5:1:28.5:1:1:0:21:4:1:0.5:5.5 0/1:16:2:2,0:1,3:0.125:2,0:7.5:1:31:0:0.4:0:38.5:4:0.3333:0:6 -4 49151726 . G C 73 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12281;SOR=0;LSEQ=CCATTCAAATCCATTCCATT;RSEQ=CATTCCATACCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29:1:1:0:21:4:1:0.5:5.5 0/1:17:5:3,2:0,2:0.2941:0,2:11.8:1:31.8:1:0.42857:0:35.2:10:0.7143:0:6.4 -4 49151735 . A T 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTGCATTCCAT;RSEQ=CCATTCCATTCCATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:9.3:1:29.9:1:1:0:30.6:14:1:0:4.6 1/1:31:29:12,17:0,1:0.9355:0,2:8.9:1:28.7:1:1:0:36.5:58:0.9667:0.0968:4.7 -4 49151747 . C T 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=1.86056;LSEQ=CATTCCATACCATTCCATTC;RSEQ=ATTCTATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:7,8:0.0625:2,0:11:0:25:0:1:0:40:2:0.0667:0:5 0/1:54:6:3,3:22,22:0.1111:2,2:16.5:1:28.5:1:1:1:40:12:0.1132:0:5.8 -4 49151751 . CT GC 67 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56644;SOR=Inf;LSEQ=CCATACCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:18.3:1:31.1:1:1:0:34.9:32:1:0:4.1 0/1:53:4:2,2:24,20:0.0755:2,2:14.8:1:33.8:1:1:1.19542:38.3:8:0.0784:0:6.3 -4 49151752 . T TATTCGGGTTA 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.0018;SOR=0.18037;LSEQ=CATACCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:5,7:1,1:0.5217:2,2:18.7:1:28.2:1:1:1.36624:39.4:24:0.5217:0.2609:4.2 0/1:56:9:4,5:4,2:0.1607:2,2:21.9:1:29.6:1:0.60839:2.34872:39.3:18:0.1915:0:3.9 -4 49151759 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCTATTCCA;RSEQ=TCCATTCCATTCCATTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:0:2,0:22.3:1:29.8:1:1:0:37.2:48:1:0:4.4 0/1:93:2:1,1:42,48:0.0215:2,2:41:0:30:1:1:1.14:41.5:4:0.022:0:5.5 -4 49151764 . TTCCA T 31 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03866;SOR=0;LSEQ=TTCCATTCTATTCCATTCCA;RSEQ=TTCCATTGCACTCGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:8,14:0.0833:2,2:28:0:31.5:1:1:1.71:48:4:0.0833:0:2 0/0:96:0:0,0:45,50:0:2,0:24.5:1:29.4:1:1:0:39.5:94:1:0:4.3 -4 49151766 . C A 70 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=1.24783;LSEQ=CCATTCTATTCCATTCCATT;RSEQ=CATTCCATTGCACTCGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:8,13:0.0417:2,0:24:0:29:0:1:0:40:2:0.0455:0:3 0/1:97:5:3,2:42,49:0.0515:2,2:24:0:30.2:1:0.66271:1.74:34.8:10:0.0532:0:4.4 -4 49151767 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCTATTCCATTCCATTC;RSEQ=ATTCCATTGCACTCGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,14:0:2,0:29.5:1:31.6:1:1:0:36.2:44:1:0:4.6 0/1:97:2:1,1:44,50:0.0206:2,2:46.5:1:30.5:1:1:1.13:41.5:4:0.0215:0:5.5 -4 49151768 . A G 70 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.58177;SOR=Inf;LSEQ=ATTCTATTCCATTCCATTCC;RSEQ=TTCCATTGCACTCGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,14:0:2,0:30.1:1:30.6:1:1:0:36.2:44:1:0:4.6 0/1:98:5:3,2:42,49:0.051:2,2:24.6:1:30.4:1:0.66271:1.74:39.8:10:0.0538:0:5.4 -4 49151770 . T C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCTATTCCATTCCATTCCAT;RSEQ=CCATTGCACTCGAGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:0:2,0:30.9:1:30:1:1:0:37.2:48:1:0:4.4 0/1:98:2:1,1:44,51:0.0204:2,2:34:0:32.5:1:1:1.16:49:4:0.0211:0:4.5 -4 49151772 . C G 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.65066;SOR=0.78342;LSEQ=TATTCCATTCCATTCCATTC;RSEQ=ATTGCACTCGAGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:5,7:4,8:0.5:2,2:30.9:1:30.3:1:1:1.41:39.4:24:0.5:0:4.2 0/1:98:43:18,25:25,26:0.4388:2,2:28.9:1:30.1:1:0.53719:1.33134:38.8:42:0.4375:0:4.3 -4 49151773 . AT CC 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0.97796;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TGCACTCGAGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:8,14:0.0833:2,2:20.5:1:33:0:1:1.71:50:4:0.087:0:5.5 0/1:98:8:4,4:40,47:0.0816:2,2:27.6:1:30.3:1:1:1.17:42.3:16:0.0851:0:5.4 -4 49151776 . G A 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04062;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCGAGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:10,14:0.0769:2,0:33:1:30.5:1:0.50769:0:22.5:4:0.0769:0:3.5 0/0:101:0:0,0:43,53:0:2,0:28.9:1:31.7:1:1:0:40.1:47:0.9792:0:4.3 -4 49151777 . C A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05784;SOR=0.15812;LSEQ=CATTCCATTCCATTCCATTG;RSEQ=ACTCGAGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:2,1:8,15:0.1154:2,2:37.3:1:30.3:1:0.53846:3.55:38.7:6:0.1154:0:4 0/1:101:2:1,1:41,51:0.0198:2,2:36:1:29:1:1:1.24:42.5:4:0.0206:0:3.5 -4 49151778 . ACT CAA 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTGC;RSEQ=CGAGTTGATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:10,16:0:2,0:30.4:1:30:1:1:0:37.8:25:1:0:4.5 0/1:101:2:1,1:41,52:0.0198:2,2:28:0:29.8:1:1:1.27:40:4:0.0208:0:5 -4 49151779 . C A 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45914;SOR=0.62292;LSEQ=TTCCATTCCATTCCATTGCA;RSEQ=TCGAGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:21:7,14:3,2:0.8077:2,2:33:1:30.8:1:0.34022:2.86687:36.4:42:0.84:0:4 1/0:101:73:33,40:8,9:0.7228:2,2:30.7:1:29.8:1:1:1.07655:39.4:35.5:0.7802:0:4.1 -4 49151781 . C G 33 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49704;SOR=0.50322;LSEQ=CCATTCCATTCCATTGCACT;RSEQ=GAGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:10,15:0.0385:2,0:34:0:26:0:1:0:40:2:0.04:0:5 0/1:102:2:2,0:43,54:0.0196:2,0:33.5:1:33:1:0.20408:0:38:4:0.0202:0:6.5 -4 49151782 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTGCACTC;RSEQ=AGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:28.9:1:30.4:1:1:0:37.3:26:1:0:4.6 0/1:101:2:1,1:45,54:0.0198:2,2:30:0:31:0:1:1.20:40:4:0.0206:0:3 -4 49151783 . A C 73 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03422;SOR=0.23272;LSEQ=ATTCCATTCCATTGCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:3,2:7,15:0.1852:2,2:23.4:1:31:1:0.32615:3.07:43.4:10:0.2:0:6.8 0/1:101:5:4,1:39,47:0.0495:2,2:32.6:1:31.6:1:0.1849:4.75:44.8:10:0.0526:0:5.6 -4 49151793 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTGCACTCGAGTTGATTCC;RSEQ=TTCCATTCCATTCCATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:12,18:0:2,0:24.5:1:30.9:1:1:0:36.6:60:1:0:4.5 0/1:112:2:1,1:50,60:0.0179:2,2:29.5:1:29.5:1:1:1.20:40:4:0.0182:0:5.5 -4 49151796 . C G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GCACTCGAGTTGATTCCATT;RSEQ=CATTCCATTCCATTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:12,18:0:2,0:23.3:1:31.9:1:1:0:36.6:60:1:0:4.5 0/1:117:2:1,1:53,62:0.0171:2,2:32.5:1:31.5:1:1:1.17:45.5:4:0.0171:0:4.5 -4 49151798 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ACTCGAGTTGATTCCATTCC;RSEQ=TTCCATTCCATTCCGTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:13,18:0:2,0:20.7:1:30.8:1:1:0:35.4:62:1:0:4.4 0/1:118:2:1,1:53,62:0.0169:2,2:30.5:1:29:1:1:1.17:45.5:4:0.0172:0:4.5 -4 49151801 . C G 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.57676;SOR=Inf;LSEQ=CGAGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCGTTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,19:0:2,0:19.5:1:30.8:1:1:0:35.9:32:1:0:4.3 0/1:118:4:2,2:51,61:0.0339:2,2:36.5:1:30.8:1:1:1.19:39.5:8:0.0345:0:5.5 -4 49151802 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GAGTTGATTCCATTCCATTC;RSEQ=ATTCCATTCCGTTCCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,19:0:2,0:19.1:1:31.7:1:1:0:35.9:66:1:0:4.3 0/1:116:2:1,1:52,62:0.0172:2,2:21.5:1:32:0:1:1.19:34:4:0.0172:0:2.5 -4 49151803 . A G 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=AGTTGATTCCATTCCATTCC;RSEQ=TTCCATTCCGTTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:13,19:0:2,0:19.3:1:29.8:1:1:0:35.8:31:1:0:4.4 0/1:116:3:2,1:51,62:0.0259:2,2:19.7:1:28.3:1:0.59162:2.41:34.7:6:0.0268:0:5 -4 49151808 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCGTTCCGTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:12,17:0:2,0:19:1:30.7:1:1:0:36.7:58:1:0:4.6 0/1:107:2:1,1:47,58:0.0187:2,2:44:1:30.5:1:1:1.23:59:4:0.0194:0:5.5 -4 49151811 . C A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CGTTCCGTTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:12,17:0:2,0:17.9:1:31.5:1:1:0:36.7:58:1:0:4.6 0/1:96:2:1,1:41,51:0.0208:2,2:20.5:1:26.5:1:1:1.24:30:4:0.0211:0:5 -4 49151813 . G A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26736;SOR=0.56321;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCGTTCCATTCCATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:17:5,12:5,3:0.6296:2,2:12.4:1:30.3:1:0.19355:3.76229:37.1:34:0.6296:0:4.5 0/1:82:40:13,27:19,17:0.4878:2,2:17.1:1:29.4:1:0.10367:2.2949:35.5:39:0.4937:0:4.8 -4 49151816 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06061;SOR=0;LSEQ=CCATTCCATTCCATTCCGTT;RSEQ=CGTTCCATTCCATTCCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:10,12:0.08:2,2:43:0:33:1:1:1.19:45:4:0.08:0:7.5 0/0:75:0:0,0:30,42:0:2,0:20.4:1:31:1:1:0:36.3:71:0.9861:0:4.4 -4 49151818 . G A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28606;SOR=0.52172;LSEQ=ATTCCATTCCATTCCGTTCC;RSEQ=TTCCATTCCATTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:4,5:5,3:0.4091:2,2:13:1:26.2:1:0.63719:1.99353:36.8:3.5:0.3684:0:4.8 0/1:72:19:4,15:20,21:0.2639:2,2:13.4:1:29.6:1:0.05126:3.49848:35.1:38:0.2754:0:4.9 -4 49151823 . A T 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56814;SOR=Inf;LSEQ=ATTCCATTCCGTTCCGTTCC;RSEQ=TTCCATTCCGTTCCATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:7,12:0:2,0:22.5:1:30.9:1:1:0:36.5:38:0.95:0:4.6 0/1:64:4:1,3:24,34:0.0625:2,2:14.3:1:31.8:1:0.64184:2.09441:37.3:8:0.0635:0:5.8 -4 49151825 . T G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCCGTTCCGTTCCAT;RSEQ=CCATTCCGTTCCATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:23.5:1:29.8:1:1:0:36.6:38:1:0:4.7 0/1:62:2:1,1:25,33:0.0323:2,2:32:0:33.5:1:1:1.31:28:4:0.0333:0:3 -4 49151828 . A T 51 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCGTTCCGTTCCATTCC;RSEQ=TTCCGTTCCATTCTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,9:0:2,0:25.9:1:30.8:1:1:0:35.9:32:0.9412:0:4.8 0/1:58:3:1,2:24,28:0.0517:2,2:13:0:32.3:1:1:1.69821:38.7:6:0.0556:0:5.3 -4 49151831 . C T 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCGTTCCGTTCCATTCCATT;RSEQ=CGTTCCATTCTATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:0:2,0:29:1:30.9:1:1:0:35.5:26:0.9286:0:4.8 0/1:48:3:2,1:21,22:0.0625:2,2:17:1:27:1:1:2.06:28:6:0.0638:0:6 -4 49151833 . G A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75983;SOR=0.68928;LSEQ=GTTCCGTTCCATTCCATTCC;RSEQ=TTCCATTCTATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:4,4:3,2:0.5714:2,2:30.6:1:29.1:1:1:1.45385:36:7:0.5385:0:4.6 0/1:44:21:13,8:5,8:0.4773:2,2:23.3:1:29.8:1:0.29055:2.53:34.3:42:0.4773:0:3.9 -4 49151835 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCGTTCCATTCCATTCCGT;RSEQ=CCATTCTATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:28.2:1:29.4:1:1:0:34.8:28:1:0:4.9 0/1:42:2:0,2:21,19:0.0476:2,0:35:1:30.5:1:0.4878:0:30.5:4:0.0488:0:5.5 -4 49151838 . A G 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13577;SOR=0.1408;LSEQ=GTTCCATTCCATTCCGTTCC;RSEQ=TTCTATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:0.1538:2,2:42:1:30.5:1:1:1.18321:31:4:0.1538:0:4.5 0/1:42:1:0,1:21,20:0.0238:2,0:33:0:33:0:1:0:21:2:0.0244:0:6 -4 49151842 . T C 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50245;SOR=0.63289;LSEQ=CATTCCATTCCGTTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:3,2:4,3:0.3846:2,2:18.8:1:29.6:1:1:1.11:37:10:0.4167:0:6.6 0/1:32:9:3,6:9,9:0.2813:2,2:13.3:1:29.3:1:0.68284:1.94945:43.3:8:0.2581:0:5.1 -4 49151847 . C GGGTTA 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.7294;SOR=1.48507;LSEQ=CATTCCGTTCCATTCTATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:3,1:3,4:0.3333:2,2:25:0:31.4:1:0.54545:3.52:28.5:8:0.3333:0:2.5 0/1:28:12:7,5:3,9:0.4286:2,2:23.2:1:29.6:1:0.21376:3.94:31.9:24:0.4444:0.1071:3 -4 49151848 . A G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=1.55309;LSEQ=ATTCCGTTCCATTCTATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:6,5:0.0833:2,0:40:0:33:0:1:0:24:2:0.0833:0:6 0/1:24:3:1,2:7,14:0.125:2,2:27:1:30.3:1:1:1:36:6:0.125:0:4 -4 49151849 . T C 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.09244;SOR=0;LSEQ=TTCCGTTCCATTCTATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:0.1818:2,2:25.5:1:30.5:1:1:1.22:40:4:0.1818:0:3.5 0/0:24:0:0,0:8,16:0:2,0:18:1:29.9:1:1:0:35.6:48:1:0:3.4 -4 49151853 . A G 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.08523;SOR=0;LSEQ=GTTCCATTCTATTCCATTCC;RSEQ=TTCCATTCCATTCCATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:17.5:1:30:1:1:1:45:4:0.2:0:7.5 0/0:23:0:0,0:8,15:0:2,0:15:1:29.8:1:1:0:35.3:46:1:0:3.3 -4 49151854 . T C 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.09073;SOR=0;LSEQ=TTCCATTCTATTCCATTCCA;RSEQ=TCCATTCCATTCCATTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:25.5:1:31.5:1:1:1:40:4:0.2:0:3.5 0/0:22:0:0,0:7,14:0:2,0:15.2:1:30:1:1:0:32.9:42:0.9545:0:3.4 -4 49151858 . A G 29 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.09677;SOR=0;LSEQ=ATTCTATTCCATTCCATTCC;RSEQ=TTCCATTCCATTAAATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:12.5:1:29:1:1:1:45:4:0.2:0:7.5 0/0:21:0:0,0:7,14:0:2,0:11.2:1:29.3:1:1:0:32.9:42:1:0:3.4 -4 49152030 . C G 29 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:1:29.5:1:1:0:40.5:4:1:0:6.5 -4 49152035 . C T 28 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:1:28:1:1:0:40.5:4:1:0:6.5 -4 49152070 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTCCATTCCACTCGGGT;RSEQ=GTTTCCATTCCATTTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:46:0:30.5:1:1:0:40.5:4:1:0:6.5 -4 49152076 . C A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCACTCGGGTCGTTTC;RSEQ=ATTCCATTTCATTAGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:0:30.5:1:1:0:40.5:4:1:0:6.5 -4 49152085 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGTCGTTTCCATTCCATT;RSEQ=CATTAGTTTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:32.5:1:1:0:40.5:4:1:0:6.5 -4 49152105 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCATTAGTTTCCATTCCATT;RSEQ=CATTCCATTCCATTTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:33.5:1:1:0:40.5:4:1:0:6.5 -4 49152442 . T A 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGATTCCATTCCATTCC;RSEQ=TTCCATTCTGTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:29.5:1:1:0:40:4:1:0:2 -4 49152475 . C G 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCGTTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13.5:1:30:1:1:0:31:4:1:0:6.5 0/1:5:2:1,1:2,1:0.4:2,2:16:0:32.5:1:1:1.7321:40:4:0.4:0:2 -4 49152506 . C A 38 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.52206;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTGCATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,1:0:2,0:25:1:32.8:1:1:0:26.3:8:0.8:0:6.5 0/1:13:3:2,1:6,4:0.2308:2,2:18.3:1:24.3:1:1:1.30:52.7:2:0.1667:0:4.3 -4 49152510 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0.74089;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTGCATTCCACTCGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:3,1:0.2:2,0:44:0:29:0:0.4:0:20:2:0.2:0:8 0/1:13:2:1,1:7,4:0.1538:2,2:12.5:1:28.5:1:1:1.67325:35:4:0.1538:0:3.5 -4 49152512 . A C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTGCATTCCACTCGGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:32.3:1:25.3:1:1:0:26.3:3:0.75:0:6.5 0/1:13:2:1,1:7,4:0.1538:2,2:14.5:1:30:1:1:1.67325:35:4:0.1538:0:3.5 -4 49152515 . G C 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58275;SOR=0.47231;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGGGTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:39.5:1:33:1:1:1.7321:20:4:0.4:0:8 0/1:13:3:2,1:4,2:0.2308:2,2:27.7:1:29:1:1:1:37.3:6:0.2308:0:4.7 -4 49152523 . C T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.91372;LSEQ=TTCCATTCCATTGCATTCCA;RSEQ=TCGGGGTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:3,0:0.1667:0,0:31:0:31:0:0.25:0:20:2:0.1667:0:8 0/1:13:2:1,1:7,4:0.1538:2,2:27:0:32:0:1:1.67325:60:4:0.1667:0:2.5 -4 49152529 . G T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61715;LSEQ=TCCATTGCATTCCACTCGGG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,2:0.3333:2,2:20.5:1:28.5:1:1:1.73:41:4:0.4:0:4.5 0/1:13:3:1,2:6,4:0.2308:2,2:32.7:1:30.3:1:0.55944:2.75172:36.7:6:0.2308:0:5.3 -4 49152545 . C G 46 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.22222;SOR=Inf;LSEQ=CGGGGTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:0:2,0:18.2:1:31.3:1:1:0:30:26:0.9286:0:3.8 0/1:14:3:1,2:5,6:0.2143:2,2:27.7:1:29.3:1:1:1.60839:36.7:6:0.2143:0:5.3 -4 49152586 . C G 32 v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.11029;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTTCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:21.8:1:30.5:1:1:0:29.8:22:1:0:3.5 0/1:6:2:1,1:1,3:0.3333:2,2:30:0:32:1:1:2.45:42:4:0.3333:0:2 -4 49152592 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.50549;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTTCATTCCATTCCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:28:0:32.5:1:1:1.29:52.5:4:0.2222:0:6 0/0:5:0:0,0:1,4:0:2,0:18.2:1:30.8:1:1:0:37.6:10:1:0:2.4 -4 49152597 . A G 78 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26573;SOR=0.14731;LSEQ=ATTCCATTCCATTCCATTTC;RSEQ=TTCCATTCCATTGCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,2:0.6667:2,2:12.8:1:30.2:1:1:1.85:23.3:12:0.6667:0:1.5 0/1:5:1:0,1:1,2:0.2:2,0:13:0:31:0:1:0:28:2:0.2:0:1 -4 49152843 . ATG TTCAAATC 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=ATCCATTCCATTCCATTCCA;RSEQ=CATTCCATTTTTTTCAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36:0:28:1:1:0:60:4:1:0:5 -4 49152936 . C T 29 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCTATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:29.5:1:1:0:54.5:4:1:0:3.5 -4 49152947 . A T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCTATTGCATTTCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:54.5:4:1:0:3.5 -4 49152970 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTATTGCATTTCATTCCATT;RSEQ=CATTCTACTCAGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:31.5:1:1:0:33:4:1:0:7.5 0/0:2:0:0,0:1,1:0:2,0:7:1:24:1:1:0:54.5:1:1:0:3.5 -4 49152978 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCATTCCATTCCATTCTA;RSEQ=TCAGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:32.5:1:1:0:33:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49152981 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCTACTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19:0:32.5:1:1:0:33:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49152986 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCTACTCAGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:0:30.5:1:1:0:33:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49153008 . T C 33 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42.5:1:33:1:1:0:33:4:1:0:7.5 0/0:1:0:0,0:0,1:0:0,0:22:0:27:0:1:0:25:2:1:0:3 -4 49153018 . T G 32 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:32:1:1:0:33:4:1:0:7.5 0/0:1:0:0,0:0,1:0:0,0:32:0:26:0:1:0:25:2:1:0:3 -4 49153022 . A T 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:30.5:1:1:0:33:4:1:0:7.5 0/0:1:0:0,0:0,1:0:0,0:35:0:29:0:1:0:25:2:1:0:3 -4 49153137 . A C 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCAATGCATTCCATTCC;RSEQ=GTTGATACCATTGCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:0,0:0.6:0,2:41.7:1:30.3:1:1:0:33.3:6:0.6:0:2.7 -4 49153145 . C G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTCCATTCCAGTTGATA;RSEQ=CATTGCATTGCATTGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:31.5:1:30.5:1:1:1:37:4:0.3333:0:6.5 -4 49153167 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTGCATTGCATTGTTTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:13:1:29.5:1:1:1:30:4:0.3333:0:2.5 -4 49153172 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTGCATTGTTTCCATTCCA;RSEQ=TCCATTCCATTCCATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:28:1:29:1:1:1:40:4:0.3333:0:4.5 -4 49153175 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GCATTGTTTCCATTCCATTC;RSEQ=ATTCCATTCCATTCAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:31.5:1:29.5:1:1:1:37:4:0.3333:0:6.5 -4 49153190 . A C 59 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCTACTCGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:24:1:29.5:1:1:0:38.5:8:1:0:5.5 -4 49154393 . CC AG 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCGTT;RSEQ=TTTCCACTTGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:27.5:1:1:0:31:4:1:0:4 -4 49154404 . G C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCGTTCCTTTCCACTT;RSEQ=GGTTGATTCCATTCTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:28.5:1:1:0:31:4:1:0:4 -4 49154624 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCTGTTCCATTCCATTC;RSEQ=GGTTGATTCTGTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29.5:1:1:0:22:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49154893 . T TTTCCA 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATACCCTTCGGGTTGATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:29.4:1:1:0:27:4:1:0.5:1 -4 49155092 . C G 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:8:1:32.5:1:1:0:26:4:1:1:2 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:31:1:1:1:45:4:0.5:0:5.5 -4 49155093 . A C 33 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.06667;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCAATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:1:33:1:1:0:26:4:1:1:2 0/0:4:0:0,0:2,2:0:2,0:10.3:1:31:1:1:0:50.5:8:1:0:2.8 -4 49155096 . C G 32 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCAATTCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:12:1:32.5:1:1:0:26:4:1:1:2 1/0:4:2:1,1:1,1:0.5:2,2:17.5:1:32.5:1:1:1:45:4:0.5:0:5.5 -4 49155107 . A T 29 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCAATTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:29.5:1:1:0:26:4:1:0:2 0/0:4:0:0,0:2,2:0:2,0:24.3:1:31.8:1:1:0:50.5:8:1:0:2.8 -4 49155108 . A T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCA;RSEQ=TTCAATTCCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:11:0:29.5:1:1:0:26:4:1:0:2 1/0:4:2:1,1:1,1:0.5:2,2:29.5:1:31.5:1:1:1:45:4:0.5:0:5.5 -4 49155111 . C CTCTTA 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CCATTCCATTCCATTCAATT;RSEQ=AATTCCATTCCTTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14:0:30:1:1:0:26:4:1:0:2 1/0:4:3:1,2:1,0:0.75:0,2:17:1:29:1:1:0:55:6:0.75:0.25:0.3 -4 49155112 . A G 30 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=CATTCCATTCCATTCAATTC;RSEQ=ATTCCATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:30:1:1:0:26:4:1:0:2 0/0:5:0:0,0:2,2:0:2,0:26:1:31.8:1:1:0:50.5:8:1:0:2.8 -4 49155136 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCATTCCTTTCCATTCCATT;RSEQ=CTTTCCACTCGGGTTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:8:0:29:1:1:0:26:4:1:0:2 1/0:4:2:1,1:1,1:0.5:2,2:7:0:31:1:1:1:45:4:0.6667:0:5.5 -4 49155138 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCACTCGGGTTGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:6:0:29.5:1:1:0:26:4:1:0:2 1/0:4:2:1,1:1,1:0.5:2,2:5:0:31:1:1:1:45:4:0.6667:0:5.5 -4 49155206 . CCATT C 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.02646;SOR=0;LSEQ=CCGTTCCGTTCCATTCCATT;RSEQ=CATTCCATTGCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:28.5:1:32:1:0.4:0:44:4:0.4:0:4 0/0:23:0:0,0:12,8:0:2,0:12:1:31.4:1:1:0:43.3:40:0.8696:0.0435:5.5 -4 49155208 . A T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GTTCCGTTCCATTCCATTCC;RSEQ=TTCATTCCATTGCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,0:0:0,0:13:1:31.3:1:1:0:38.3:6:1:0:5 0/1:23:2:1,1:14,7:0.087:2,2:13:1:28.5:1:1:1.93655:60:4:0.087:0:5 -4 49155211 . C CG 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=1.07463;LSEQ=CCGTTCCATTCCATTCCATT;RSEQ=ATTCCATTGCATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:3,1:2,1:0.5:2,2:6.3:1:30.2:1:1:1.41:35:8:0.5714:0.375:4.8 1/0:27:14:8,6:8,5:0.5185:2,2:14.5:1:29.9:1:1:1.19191:50.3:28:0.5185:0.0741:5.4 -4 49155212 . A C 102 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38749;SOR=3.98018;LSEQ=CGTTCCATTCCATTCCATTC;RSEQ=TTCCATTGCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:4,2:0.125:2,0:13:0:32:0:1:0:56:2:0.1429:0:5 0/1:27:10:7,3:9,8:0.3704:2,2:18.1:1:30.9:1:0.44755:2.02:36.3:20:0.3704:0:5.7 -4 49155213 . T TA 47 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01126;SOR=0;LSEQ=GTTCCATTCCATTCCATTCA;RSEQ=TCCATTGCATTCCACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:4,2:0.3:2,2:10.3:1:30:1:1:1:47.3:6:0.3333:0.2:5 0/0:31:0:0,0:9,8:0:2,0:12.6:1:29.1:1:1:0:45.1:34:0.5484:0:5.1 -4 49155220 . G C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72987;SOR=1.5835;LSEQ=TCCATTCCATTCATTCCATT;RSEQ=CATTCCACTCGGGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:3,2:0,0:0.4545:0,2:14:1:32.6:1:1:0:40.4:10:0.4545:0:5 1/0:35:20:12,8:1,1:0.5714:2,2:19:1:30.1:1:1:1.47:37.3:19:0.5588:0:5.3 -4 49155225 . C G 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.64976;LSEQ=TCCATTCATTCCATTGCATT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:6,4:1,1:0.8333:2,2:16.9:1:32.7:1:1:1.45:38.2:20:0.8333:0:4.6 1/0:38:29:16,13:1,1:0.7632:2,2:21.6:1:31.4:1:1:1.22:42.4:58:0.7632:0:4.9 -4 49155226 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06964;SOR=0;LSEQ=CCATTCATTCCATTGCATTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:37:0:31:1:1:1.13:44:4:0.1176:0:4 0/0:46:0:0,0:20,20:0:2,0:18.6:1:30.8:1:1:0:42.8:39:1:0:4.3 -4 49155228 . C T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06847;SOR=0;LSEQ=ATTCATTCCATTGCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:35:0:32:1:1:1:44:4:0.1:0:4 0/0:55:0:0,0:28,27:0:2,0:18.1:1:31.1:1:1:0:39.4:110:1:0:3.9 -4 49155231 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTGCATTCCACTC;RSEQ=GGTTGATTCCATTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:16.9:1:30.7:1:1:0:35.9:40:1:0:3.9 0/1:58:2:1,1:27,29:0.0345:2,2:25:1:28.5:1:1:1.07:43:4:0.0351:0:5.5 -4 49155232 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTGCATTCCACTCG;RSEQ=GTTGATTCCATTCCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:17.7:1:31.3:1:1:0:35.9:40:1:0:3.9 0/1:58:2:1,1:27,28:0.0345:2,2:38:1:29:1:1:1.04:50:4:0.0345:0:4 -4 49155236 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06327;SOR=0;LSEQ=CATTGCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTGCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:27:0:31:1:1:1:44:4:0.1:0:4 0/0:58:0:0,0:28,30:0:2,0:24.4:1:31.1:1:1:0:39.2:116:1:0:3.9 -4 49155239 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCATTCCACTCGGGTTGAT;RSEQ=CCATTCCATTGCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:22.4:1:30.4:1:1:0:35.9:40:1:0:3.9 0/1:58:2:1,1:27,29:0.0345:2,2:45:1:30.5:1:1:1.07:60:4:0.0345:0:5 -4 49155245 . C G 51 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01682;SOR=0;LSEQ=CCACTCGGGTTGATTCCATT;RSEQ=CATTGCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:9,9:0.1429:2,2:23.3:1:32.3:1:1:1.94:33.3:6:0.1429:0.0476:3.7 0/0:58:0:0,0:28,29:0:2,0:30.8:1:30.8:1:1:0:39.1:114:1:0:3.9 -4 49155250 . G C 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06816;SOR=0;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:0.0952:2,2:39:0:32:1:1:1.10554:36:4:0.0952:0:5 0/0:58:0:0,0:28,30:0:2,0:32.8:1:31.1:1:1:0:39.2:28:1:0:3.9 -4 49155252 . A ATTCCG 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTGATTCCATTCCATTGC;RSEQ=TTCCATTCCATTCCATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:28.7:1:30.9:1:1:0:35.5:42:1:0.0476:3.8 0/1:58:2:1,1:27,29:0.0345:2,2:28:0:30.7:1:1:1.07:48:4:0.0357:0:2 -4 49155255 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCCATTGCATT;RSEQ=CATTCCATTCCATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:29.7:1:31.6:1:1:0:35.5:42:1:0.0476:3.8 0/1:58:2:1,1:27,29:0.0345:2,2:39.5:1:29:1:1:1.07:45:4:0.0351:0:7 -4 49155260 . C A 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.06646;SOR=0;LSEQ=CCATTCCATTGCATTCCATT;RSEQ=CATTCCATTGCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:0.0952:2,2:32:0:29.5:1:1:1.10554:36:4:0.0952:0:5 0/0:59:0:0,0:29,30:0:2,0:32.6:1:30.9:1:1:0:38.9:58:1:0:3.8 -4 49155263 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTGCATTCCATTCCA;RSEQ=TCCATTGCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:32:1:31:1:1:0:34.6:38:1:0:3.7 0/1:59:2:1,1:28,29:0.0339:2,2:31.5:1:29.5:1:1:1.04:48.5:4:0.0339:0:5 -4 49155264 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCATTGCATTCCATTCCAT;RSEQ=CCATTGCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:31.7:1:29.6:1:1:0:34.6:18:1:0:3.7 0/1:59:2:1,1:28,29:0.0339:2,2:36:0:32:1:1:1.04:33:4:0.0339:0:7.5 -4 49155265 . C G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTGCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:31.2:1:31.6:1:1:0:34.6:38:1:0:3.7 0/1:59:2:1,1:27,28:0.0339:2,2:34:1:31:1:1:1.04:47.5:4:0.0345:0:4.5 -4 49155267 . A G 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.56698;SOR=Inf;LSEQ=ATTGCATTCCATTCCATTCC;RSEQ=TTGCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:29.4:1:30.8:1:1:0:34.6:38:1:0:3.7 0/1:59:4:2,2:27,28:0.0678:2,2:35:1:31:1:1:1.04:32:8:0.069:0:6 -4 49155269 . TGC GCA 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCATTCCATTCCATTCCAT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:27.6:1:30.3:1:1:0:34.6:38:1:0:3.7 0/1:59:2:1,1:28,29:0.0339:2,2:19:1:28.7:1:1:1.04:40.5:4:0.0339:0.0169:3.5 -4 49155270 . G C 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:5,4:2,2:0.4737:2,2:27.4:1:31:1:1:1.23:38.2:18:0.4737:0:3.3 0/0:58:0:0,0:5,6:0:2,0:22:1:32.8:1:1:0:47.8:22:0.3667:0:3.1 -4 49155272 . A C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTGC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:24.9:1:30.7:1:1:0:34.6:38:1:0:3.4 0/1:57:2:1,1:25,28:0.0351:2,2:29:0:31:1:1:1.12:43.5:4:0.0357:0:5 -4 49155277 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:21.7:1:29.8:1:1:0:34.9:17:1:0:3.4 0/1:55:2:1,1:23,28:0.0364:2,2:24:0:32.5:1:1:1.21:48:4:0.0364:0:2 -4 49155282 . A G 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0.86342;LSEQ=ATTCCATTGCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:2,3:6,6:0.2941:2,2:19.2:1:31.4:1:1:1.46472:30.8:10:0.2941:0:3.6 0/1:53:14:6,8:18,21:0.2642:2,2:16.7:1:29.1:1:1:1.13999:40.2:13:0.2549:0:4.6 -4 49155283 . T A 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.05631;SOR=0;LSEQ=TTCCATTGCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:22:0:32:0:1:1.13:43:4:0.1176:0:4 0/0:53:0:0,0:24,29:0:2,0:14.6:1:30.1:1:1:0:39.7:106:1:0:3.6 -4 49155285 . C A 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.0597;SOR=0;LSEQ=CCATTGCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:17:0:28:1:1:1.13:39:4:0.1176:0:3 0/0:51:0:0,0:23,28:0:2,0:13.1:1:31:1:1:0:40.4:50:1:0:3.6 -4 49155287 . A G 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.35971;LSEQ=ATTGCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,8:0.125:2,2:14.5:1:29.5:1:1:1.31:49.5:4:0.125:0:4.5 0/1:49:8:4,4:18,23:0.1633:2,2:14.1:1:30.3:1:1:1.27:36.9:16:0.1633:0:3.5 -4 49155290 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATACCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:10.6:1:30.8:1:1:0:35.9:32:1:0:3.5 0/1:44:2:1,1:18,24:0.0455:2,2:13.5:1:31.5:1:1:1.32:43:4:0.0455:0:5.5 -4 49155292 . A G 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.67595;SOR=0.61697;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATACCCTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:5,6:0.2143:2,2:12.7:1:33:1:1:1.60839:38:6:0.2143:0:3 0/1:42:6:3,3:15,21:0.1429:2,2:7.3:1:29.3:1:1:1.39:42.8:12:0.1429:0:3.5 -4 49155295 . C A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATACCCTTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:7.4:1:31.2:1:1:0:36.5:26:1:0:3.5 0/1:36:2:1,1:13,21:0.0556:2,2:6:0:29.5:1:1:1.59:43.5:4:0.0556:0:5 -4 49155297 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATACCCTTCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:5.4:1:30.5:1:1:0:36.5:26:1:0:3.5 0/1:32:2:0,2:12,18:0.0625:2,0:8:1:33:0:0.51613:0:41:4:0.0645:0:3 -4 49155474 . T G 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.03251;SOR=0;LSEQ=TCCATTGCATTCCATTCCAT;RSEQ=CCATTCCACTCGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:3,2:0.4444:2,2:26.5:1:33.5:1:1:1.43328:37:8:0.4444:0:2.8 0/0:10:0:0,0:4,6:0:2,0:23.8:1:29:1:1:0:32.2:20:1:0:1.5 -4 49155476 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0.88119;LSEQ=CATTGCATTCCATTCCATTC;RSEQ=ATTCCACTCGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:30:0:30.5:1:1:1.29098:37:4:0.2222:0:1.5 0/1:10:2:1,1:3,5:0.2:2,2:26.5:1:29:1:1:1.58:25:4:0.2222:0:1.5 -4 49155480 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.47368;SOR=Inf;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:31.4:1:32.3:1:1:0:37.3:18:1:0:1.9 0/1:10:2:0,2:3,4:0.2:2,0:26.5:1:29.5:1:0.5:0:31:4:0.2222:0:3 -4 49155481 . C CCCTGT 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.62848;SOR=1.92739;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,1:0.6667:2,2:33.2:1:32.2:1:1:1:36.7:12:0.6667:0:1.2 1/1:10:8:3,5:1,1:0.8:2,2:34.4:1:29.6:1:1:1.58108:28.5:16:0.8:0:1 -4 49155491 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=CATTCCATTCCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:42:1:30:0:1:1.29098:43:4:0.2222:0:4 0/0:11:0:0,0:5,6:0:2,0:25.3:1:30.5:1:1:0:32.9:10:1:0:1.6 -4 49155508 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.51087;SOR=Inf;LSEQ=GTTGATTCCATTCCATTCCA;RSEQ=TCCAATCCGTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:15.4:1:31:1:1:0:37.3:18:1:0:1.9 0/1:15:2:1,1:7,6:0.1333:2,2:32:0:31.5:1:1:1.1547:47:4:0.1429:0:3 -4 49155520 . C T 29 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=CCATTCCATTCCAATCCGTT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21:0:29.5:1:1:0:43:4:0.6667:0:4 0/0:7:0:0,0:4,1:0:2,0:21.4:1:29.8:1:1:0:36.4:4:0.6667:0:3.2 -4 49155535 . C A 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.49091;SOR=Inf;LSEQ=CCGTTCCATTCCATTCCATT;RSEQ=CATTCCTTTCCATTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,1:0:2,0:6:0:30:1:1:0:43:4:1:0:4 0/1:7:2:1,1:4,1:0.2857:2,2:6:0:28.5:1:1:3.1622:40:4:0.3333:0:2 -4 49155605 . CC AA 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.4;SOR=0;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=TTTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:13.5:1:28.3:1:1:0:37:4:0.6667:0:5 0/0:3:0:0,0:1,2:0:2,0:28:1:32:1:1:0:26.3:6:1:0:3.3 -4 49155622 . A T 29 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.16484;SOR=0;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:12:1:29:1:1:1:46.5:4:0.3333:0:3 0/0:8:0:0,0:4,4:0:2,0:13.6:1:29.1:1:1:0:28.6:16:1:0.125:4.1 -4 49155632 . A G 48 d7;v4;MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.26213;SOR=0.20269;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:2,1:0.5:2,2:20.7:1:30.7:1:1:3.10575:41:6:0.5:0:4.7 0/1:13:2:1,1:6,5:0.1538:2,2:10:0:29.5:1:1:1.18321:29:4:0.1538:0:3.5 -4 49155650 . C G 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.52206;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCCAATTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:38.2:1:31.8:1:1:0:38.8:10:1:0:4 0/1:13:3:1,2:6,4:0.2308:2,2:34.7:1:30:1:0.55944:2.75172:33:6:0.2308:0:4.3 -4 49155653 . C T 57 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68235;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCAATTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:42.5:1:29.5:1:1:1.7321:46.5:4:0.4:0:3 0/1:13:4:3,1:3,4:0.3077:2,2:29.5:1:28.8:1:0.54545:3.52:28.8:8:0.3077:0:4 -4 49155656 . CA TT 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07353;SOR=0;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=ATTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:28:1:31.3:1:1:1:37:4:0.4:0:4 0/0:12:0:0,0:6,3:0:2,0:27:1:29.9:1:1:0:31:18:0.75:0:2.7 -4 49155658 . A AAATG 61 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.2451;SOR=Inf;LSEQ=TTCCATTCCATTCCACTCCA;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:29.3:1:30.2:1:1:0:35.8:12:1:0:3.8 0/1:12:4:2,2:4,3:0.3333:2,2:27:1:30.8:1:1:1.29868:35.5:8:0.3636:0:1.3 -4 49155670 . C A 30 v4;NM4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.27018;SOR=0.22752;LSEQ=CCACTCCAATTGATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,1:0.2857:2,2:15:1:30.5:1:1:2.44949:37:4:0.3333:0:4 0/1:13:1:1,0:7,5:0.0769:2,0:3:0:24:0:1:0:31:2:0.0769:0:7 -4 49155680 . C G 52 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.51703;SOR=Inf;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,2:0:2,0:18.6:1:32.8:1:1:0:35.6:10:1:0:4.2 0/1:13:3:1,2:7,3:0.2308:2,2:12.7:1:33.3:1:0.51049:4.09114:38.3:6:0.2308:0:2.7 -4 49155690 . C G 51 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.2125;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,2:0:2,0:11.8:1:32.5:1:1:0:35.8:12:1:0:4 0/1:9:3:2,1:3,3:0.3333:2,2:10.7:1:32.3:1:1:1.85:28.3:6:0.3333:0:3.3 -4 49155704 . T TC 31 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.10714;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CATTCCATTCCAGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:33.5:1:31.5:1:1:0:29:4:1:0:4.5 0/0:5:0:0,0:2,2:0:2,0:9:1:30:1:1:0:30.8:8:1:0:5.5 -4 49155712 . T C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=ATTCCATTCCATTCATTCCA;RSEQ=TCCAGTTGATTCCATTCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,0:0:0,0:33.5:1:29:1:1:0:29:4:1:0:4.5 1/0:4:2:1,1:0,1:0.5:0,2:26:1:29.5:1:1:0:31:4:0.6667:0:5 -4 49155715 . C G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=CCATTCCATTCATTCCATTC;RSEQ=AGTTGATTCCATTCGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,0:0:0,0:33.5:1:28:1:1:0:29:4:1:0:4.5 1/0:4:2:1,1:0,1:0.5:0,2:29:1:29.5:1:1:0:31:4:0.6667:0:5 -4 49155761 . A C 33 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:19:1:23.3:1:1:0:28.8:1:1:0:4.5 0/1:9:2:1,1:3,3:0.2222:2,2:30:0:33:1:1:1:60:4:0.25:0:3.5 -4 49155777 . T G 33 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:27.7:1:30.7:1:1:0:26:6:1:0:5 0/1:8:2:1,1:3,3:0.25:2,2:28.5:1:33:0:1:1:42:4:0.25:0:2.5 -4 49155781 . A T 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCGACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:29:1:20.7:1:1:0:26:0.5:1:0:5 0/1:8:2:1,1:3,3:0.25:2,2:24.5:1:31.5:1:1:1:42:4:0.25:0:2.5 -4 49155788 . T G 32 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCGACTCGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:28.3:1:25.7:1:1:0:26:2:1:0:5 0/1:7:2:1,1:3,2:0.2857:2,2:32.5:1:32.5:1:1:1.41418:60:4:0.2857:0:4.5 -4 49155795 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ACTCGGGTTGATTCCAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,2:0:0,0:19:1:31:1:1:0:28.5:4:1:0:4.5 0/1:7:2:1,1:3,2:0.2857:2,2:25.5:1:32.5:1:1:1.41418:60:4:0.2857:0:4.5 -4 49155812 . A C 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=TTCGACTCGGGTTGATTCCA;RSEQ=TCCATTCCATTCCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23:1:29.5:1:1:0:20.5:4:1:0:5 0/0:5:0:0,0:1,0:0:0,0:50:0:25:0:1:0:50:2:0.2:0:0 -4 49156242 . CC GT 49 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCACTCCATTCCGTT;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:40.7:1:31.3:1:1:0:48:6:1:0:3.7 -4 49156247 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTCCATTCCGTTCCACT;RSEQ=GGGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:37:0:30.5:1:1:0:49:4:0.6667:0:3 -4 49156249 . G T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCATTCCGTTCCACTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:35:0:31:1:1:0:49:4:0.6667:0:3 -4 49156408 . T C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCCATAACATTCCATTC;RSEQ=ATTCCATTGCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:23:1:28.5:1:1:1:50:4:0.5:0:7 -4 49156418 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=CATTCCATTCTATTCCATTG;RSEQ=ATTCCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:6.8:1:31.6:1:1:0:33.6:10:1:0.2:4.8 0/1:7:2:1,1:3,2:0.2857:2,2:33:1:27.5:1:1:1.41418:50:4:0.2857:0:7 -4 49156424 . T A 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.86551;LSEQ=ATTCTATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:8:1:28.5:1:1:1.7321:30:4:0.4:0.2:4.5 0/1:11:4:3,1:3,4:0.3636:2,2:10:1:31:1:0.54545:3.52:46.5:8:0.3636:0:5 -4 49156426 . T TCCATC 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.52941;SOR=Inf;LSEQ=TCTATTCCATTGCATTCCTT;RSEQ=CCATTCCATTCCACTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:12.7:1:29.3:1:1:0:37.5:12:1:0.1667:4.7 0/1:12:2:1,1:6,4:0.1667:2,2:18.5:1:29.6:1:1:1.4491:45.5:4:0.1667:0.0833:4 -4 49156428 . C T 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.51471;SOR=Inf;LSEQ=TATTCCATTGCATTCCTTTC;RSEQ=ATTCCATTCCACTTGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:14.7:1:30.8:1:1:0:37.5:12:1:0.1667:4.7 0/1:12:3:2,1:5,4:0.25:2,2:30.3:1:30:1:1:1.54:48:6:0.25:0:6 -4 49156429 . A ACTCCATTACATTTCT 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12281;SOR=0;LSEQ=ATTCCATTGCATTCCTTTCC;RSEQ=TTCCATTCCACTTGTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:19.5:1:29.4:1:1:1.41418:26:4:0.2857:0.2857:2 0/0:12:0:0,0:7,5:0:2,0:17.7:1:29.3:1:1:0:46.5:24:1:0:4.8 -4 49156432 . C A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52105;SOR=Inf;LSEQ=CCATTGCATTCCTTTCCATT;RSEQ=CATTCCACTTGTGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:14.4:1:29.9:1:1:0:35.9:14:1:0:4.3 0/1:13:2:1,1:5,4:0.1538:2,2:35.5:1:27:1:1:1.22474:50:4:0.1538:0:7 -4 49156437 . C G 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.75091;LSEQ=GCATTCCTTTCCATTCCATT;RSEQ=CACTTGTGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:4,2:0.1429:2,0:20:0:28:0:0.42857:0:34:2:0.1429:0:7 0/1:13:3:3,0:4,5:0.2308:2,0:25.7:1:33.7:1:0.20455:0:42:6:0.2308:0:5.3 -4 49156440 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCTTTCCATTCCATTCCA;RSEQ=TTGTGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,2:0:2,0:20.4:1:31.8:1:1:0:39:10:0.8333:0:3.2 0/1:16:2:1,1:5,6:0.125:2,2:6:1:30.5:1:1:1.18:31:4:0.1429:0:5.5 -4 49156442 . T C 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12648;SOR=0.19441;LSEQ=CCTTTCCATTCCATTCCACT;RSEQ=GTGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,1:0.4286:2,2:31:1:28.7:1:1:3.10575:40:6:0.5:0:5 0/1:17:2:0,2:6,4:0.1176:2,0:21.5:1:30.5:1:0.45455:0:48:4:0.1333:0:7 -4 49156443 . G T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTTTCCATTCCATTCCACTT;RSEQ=TGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:23.8:1:30.8:1:1:0:38.2:12:1:0:3.8 0/1:20:2:1,1:7,9:0.1:2,2:35.5:1:30:1:1:1.27:50:4:0.1111:0:7 -4 49156444 . T G 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5453;SOR=Inf;LSEQ=TTTCCATTCCATTCCACTTG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:24.8:1:29.3:1:1:0:38.2:12:1:0:3.8 0/1:20:3:1,2:7,7:0.15:2,2:33:1:30:1:1:1.9219:46.7:6:0.1667:0:6.7 -4 49156508 . C G 48 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.56179;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCGGGTTGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,13:0:2,0:23:1:31.9:1:1:0:36:54:0.9643:0:3.9 0/1:76:3:2,1:33,39:0.0395:2,2:20:0:30.7:1:0.59571:2.34:49:6:0.0405:0:4.3 -4 49156509 . A T 58 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.56989;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:24.1:1:29.9:1:1:0:36.2:25:1:0:3.9 0/1:76:4:2,2:33,37:0.0526:2,2:26:1:29.3:1:1:1.12:40:8:0.0563:0:6 -4 49156511 . T C 60 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.56989;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCGGGTTGATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,12:0:2,0:23.6:1:30.2:1:1:0:36.8:50:0.9615:0:3.8 0/1:76:4:3,1:32,38:0.0526:2,2:39.8:1:30:1:0.33883:3.51:49.5:8:0.0526:0:5.5 -4 49156512 . C G 81 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.33214;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:25:1:30.3:1:1:0:36.1:11.5:1:0:4 0/1:75:6:2,4:31,32:0.08:2,2:30:1:31.5:1:0.67504:1.91959:38:12:0.0811:0:4.8 -4 49156513 . C T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.5807;SOR=0.68454;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCGGGTTGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:3,4:8,7:0.2917:2,2:31.6:1:30.1:1:1:1.49477:32.7:14:0.2917:0:4.7 0/1:73:16:6,10:28,27:0.2192:2,2:31.3:1:29.9:1:0.40335:1.71518:40.8:32:0.2319:0:4.8 -4 49156515 . T A 86 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.44522;SOR=2.76982;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCGGGTTGATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:11,10:0.0435:2,0:47:0:30:0:1:0:57:2:0.0435:0:5 0/1:71:8:3,5:29,29:0.1127:2,2:32.3:1:28.8:1:0.70964:1.65399:46:16:0.1143:0:4.6 -4 49156517 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.64106;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=GGGTTGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:12,9:0.0435:2,0:49:0:29:0:0.45455:0:57:2:0.0435:0:5 0/1:71:2:1,1:32,36:0.0282:2,2:39:1:29:1:1:1.12:59.5:4:0.0286:0:3.5 -4 49156518 . G C 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=GGTTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:9,10:0:2,0:29.9:1:30.8:1:1:0:36.5:38:0.9048:0.0476:3.5 0/1:67:3:1,2:28,34:0.0448:2,2:19.7:1:28.3:1:1:1.63495:29:6:0.0469:0:5.3 -4 49156519 . G A 81 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67347;SOR=2.35378;LSEQ=ATTCCATTCCATTCCATTCG;RSEQ=GTTGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:0,1:9,9:0.0476:2,0:50:0:31:0:1:0:57:2:0.05:0:5 0/1:66:7:3,4:22,31:0.1061:2,2:35:1:29:1:1:1.06:49.3:14:0.1061:0:4.3 -4 49156520 . G A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,10:0:2,0:29.5:1:31.7:1:1:0:35.8:40:1:0.0476:3.7 0/1:66:2:1,1:27,37:0.0303:2,2:13:0:28.5:1:1:1.36:40:4:0.0313:0:6 -4 49156521 . T A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24449;SOR=0.30207;LSEQ=TCCATTCCATTCCATTCGGG;RSEQ=TGATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,9:0.0952:2,2:26:1:29.5:1:1:1:22:4:0.1:0:2.5 0/1:66:2:0,2:28,36:0.0303:2,0:25.5:1:31.5:1:0.50396:0:31:4:0.0303:0:4.5 -4 49156523 . G A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57164;SOR=0.738;LSEQ=CATTCCATTCCATTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:3,3:7,7:0.2857:2,2:24.2:1:29.3:1:1:1:34.3:12:0.3:0.0476:4 0/1:66:15:6,9:22,28:0.2273:2,2:24.6:1:30:1:1:1.17561:40.6:30:0.2273:0:4.9 -4 49156525 . T A 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56558;SOR=Inf;LSEQ=TTCCATTCCATTCGGGTTGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,11:0:2,0:24:1:30.6:1:1:0:34.4:44:1:0.0435:3.8 0/1:66:3:1,2:26,36:0.0455:2,2:16.3:1:30.7:1:1:1.43659:36.3:6:0.0462:0:4 -4 49156527 . CC TT 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.06461;SOR=0;LSEQ=CCATTCCATTCGGGTTGATT;RSEQ=ATTCCATTCCATTCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:0.087:2,2:16:0:31:0:1:1.09544:41.5:4:0.087:0:1 0/0:66:0:0,0:25,36:0:2,0:23.6:1:30.9:1:1:0:40:122:0.9385:0:4.6 -4 49156528 . C T 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.56404;SOR=Inf;LSEQ=CATTCCATTCGGGTTGATTC;RSEQ=ATTCCATTCCATTCCATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,10:0:2,0:22.2:1:30:1:1:0:33.7:9.5:1:0.0435:4.1 0/1:65:3:2,1:22,35:0.0462:2,2:12.7:1:27.7:1:0.55815:3.12:34.3:6:0.05:0:6.3 -4 49156530 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.06609;SOR=0;LSEQ=TTCCATTCGGGTTGATTCCA;RSEQ=TCCATTCCATTCCATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:0.087:2,2:19:1:31.5:1:1:1.09544:41.5:4:0.087:0:4.5 0/0:65:0:0,0:26,38:0:2,0:21.3:1:29.3:1:1:0:40.4:128:1:0:4.5 -4 49156537 . CC GT 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=ATTCCATTTCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:16.9:1:31.7:1:1:0:34.8:40:1:0:4 0/1:61:2:1,1:22,34:0.0328:2,2:27.5:1:28.3:1:1:1.53:51.5:4:0.0339:0:5.5 -4 49156538 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGGTTGATTCCATTCCATTC;RSEQ=ATTCCATTTCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:16.1:1:31.2:1:1:0:34.8:19:1:0:4 0/1:59:2:1,1:22,33:0.0339:2,2:20:1:29.5:1:1:1.49:23:4:0.0357:0:4.5 -4 49156541 . T A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTGATTCCATTCCATTCCAT;RSEQ=CCATTTCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:14.5:1:30.4:1:1:0:35.5:38:1:0:4.2 0/1:56:2:1,1:22,32:0.0357:2,2:17:1:26.5:1:1:1.44:23:4:0.0377:0:4.5 -4 49156542 . C A 23 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0.6831;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTTCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:8,8:0.0526:2,0:26:0:32:0:1:0:22:2:0.0556:0:4 0/1:55:2:2,0:21,32:0.0364:2,0:7.5:1:23.5:1:0.17037:0:33:4:0.037:0:5 -4 49156543 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=ATTTCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:15.3:1:31.6:1:1:0:35.5:32:1:0:4.6 0/1:45:2:0,2:19,24:0.0444:2,0:16.5:1:32:0:0.50101:0:25:4:0.0444:0:4.5 -4 49156547 . T C 71 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00034;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:1,2:0.4545:2,2:17.2:1:30.6:1:1:1.29:36:10:0.4545:0:4 0/0:35:0:0,0:7,11:0:2,0:17.2:1:26.9:1:1:0:47.2:8:0.8:0:4.3 -4 49156558 . C G 31 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.0873;SOR=0;LSEQ=CATTCCATTTCATTCCATTC;RSEQ=ATTCCATTCCATTACACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:0.1818:2,2:35:0:31.5:1:1:1.87:21:4:0.2:0:5.5 0/0:25:0:0,0:8,16:0:2,0:9.4:1:29.4:1:1:0:39.2:11:0.9565:0:4.7 -4 49156562 . C G 38 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=1.41488;LSEQ=CCATTTCATTCCATTCCATT;RSEQ=CATTCCATTACACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:4,6:0.0909:2,0:3:0:29:0:1:0:43:2:0.0909:0:6 0/1:24:3:1,2:7,12:0.125:2,2:6:1:24.3:1:1:1.15862:36:2:0.087:0:5.7 -4 49156565 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.51087;SOR=Inf;LSEQ=TTTCATTCCATTCCATTCCA;RSEQ=TCCATTACACTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,4:0:2,0:16.7:1:30.4:1:1:0:31.7:14:0.7778:0:4.9 0/1:15:2:1,1:4,9:0.1333:2,2:14.5:1:30:1:1:2.12:43:4:0.1429:0:4 -4 49156572 . A C 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.7746;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,0:0.8:0,2:26.5:1:31.8:1:1:0:28.5:8:1:0:5.5 1/0:4:3:1,2:0,1:0.75:0,2:18.3:1:31.7:1:1:0:42:6:1:0:6 -4 49156577 . CC AA 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCATTCCATTCCATTACACT;RSEQ=ATTCCATTCCATTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:24.5:1:29:1:1:1:21:4:0.5:0:4.5 0/0:4:0:0,0:0,3:0:0,0:29.3:1:30.3:1:1:0:42:6:0.75:0:5.7 -4 49156587 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.18182;SOR=0;LSEQ=CCATTACACTCCATTCCATT;RSEQ=CATTCCACTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:15.5:1:28:1:1:1.7321:21:4:0.4:0:4.5 0/0:6:0:0,0:2,4:0:2,0:21:1:28.2:1:1:0:37.7:5:1:0:5.3 -4 49156593 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.18182;SOR=0;LSEQ=CACTCCATTCCATTCCATTC;RSEQ=ACTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:43.5:1:30.5:1:1:1.7321:36:4:0.4:0:5.5 0/0:6:0:0,0:2,4:0:2,0:24.3:1:29.8:1:1:0:37.7:12:1:0.1667:5.3 -4 49156595 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=CTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:45.5:1:30.5:1:1:1.7321:36:4:0.4:0:5.5 0/0:6:0:0,0:2,3:0:2,0:29.8:1:30.8:1:1:0:36:10:0.8333:0:6 -4 49156606 . T TGCACA 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.46429;SOR=Inf;LSEQ=TCCATTCCACTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:34.7:1:26.3:1:1:0:41:2:1:0:5 0/1:5:2:1,1:1,2:0.4:2,2:29.5:1:30.3:1:1:1.73:30:4:0.4:0:3.5 -4 49156617 . C G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.5;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:31:1:31:1:1:0:41:6:1:0:5 0/1:6:2:1,1:1,3:0.3333:2,2:34:0:33:1:1:2.45:30:4:0.3333:0:3.5 -4 49156620 . T G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.5;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:30:1:30:1:1:0:41:6:1:0:5 0/1:6:2:1,1:1,3:0.3333:2,2:31:0:32.5:1:1:2.45:30:4:0.3333:0:3.5 -4 49156635 . T C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.44444;SOR=Inf;LSEQ=TTCCATTCCACTCCATTCCA;RSEQ=TCCATTCCATTCCACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:20.8:1:29.5:1:1:0:40.8:8:1:0:5 0/1:5:2:1,1:0,2:0.4:0,2:16:0:33:0:1:0:30:4:0.4:0:3.5 -4 49156639 . A G 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.16667;SOR=0;LSEQ=ATTCCACTCCATTCCATTCC;RSEQ=TTCCATTCCACCCAGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:9:1:28:1:1:1:36:4:0.5:0:5.5 0/0:5:0:0,0:2,3:0:2,0:11.4:1:30:1:1:0:36:10:1:0:4.6 -4 49156669 . A T 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCAGATTGATTCCATTCT;RSEQ=TTCCATTCCATTCCGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:29:1:1:0:45.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49156677 . C G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGATTCCATTCTATTCCATT;RSEQ=CATTCCGTTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:31:1:1:0:45.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49156684 . G A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29.5:1:1:0:45.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49156764 . GG TT 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCCACTCCATTCCACTCG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27.5:1:30:1:1:0:52.5:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:26:0:29.3:1:1:0:57:4:1:0:4.5 -4 49156794 . G TTTCCA 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.33333;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGGGTTGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:28.2:1:1:0:52.5:4:1:0.5:1.5 0/0:2:0:0,0:1,1:0:2,0:43.5:1:30:1:1:0:57:4:1:0:4.5 -4 49156816 . T C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCACTCGGGTTGATTCCAT;RSEQ=CCATTCCTTTCCATTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:21:0:29:0:1:0:45:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:16.5:1:29:1:1:0:57:4:1:0:4.5 -4 49156824 . T A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGTTGATTCCATTCCATTCC;RSEQ=TTCCATTGCATTTCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:13:0:31:0:1:0:45:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:8.5:1:27:1:1:0:57:4:1:0:4.5 -4 49156938 . C G 64 d7;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=AATTCCATTCCATTCCATTC;RSEQ=ATTGCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:7:0:32.3:1:1:0:29:8:1:0:1 1/0:3:2:1,1:1,0:0.6667:0,2:7:0:31.5:1:1:0:24:4:0.6667:0:1 -4 49157009 . G C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCG;RSEQ=GTTGATCCCTTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:1:23:1:1:0:60:1:1:0:2 1/1:2:2:1,1:0,0:1:0,2:22:1:29:1:1:0:51.5:4:1:0:1 -4 49157093 . CATTCCATTCCATTGAATTCCTTTCCGTACCACTCCATTCT C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTACATTCCATTCCACTC;RSEQ=ATTCCATTCTATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:12.5:1:30.1:1:1:0:27:4:0.6667:0.6667:4 -4 49157141 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACTCCATTCTATTCCAT;RSEQ=CTATTCCACTCGGGTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:8:0:33.5:1:1:1:27:4:0.5:0:4 -4 49157149 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTATTCCATTCTATTCC;RSEQ=CTCGGGTTTATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:16:0:31.5:1:1:1:27:4:0.5:0:4 -4 49157169 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGGGTTTATTCCATTCC;RSEQ=TTCCAATCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:7:0:32.5:1:1:0:27:4:0.6667:0:4 -4 49157175 . A ATCCAT 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTTTATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:16.7:1:30.7:1:1:0:38:6:1:0.6667:3.3 -4 49157313 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTCCGTTCCATTCCATTC;RSEQ=ATTCATTTCCATTCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:31:1:1:0:24:4:1:0:3.5 -4 49157329 . T A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTATTCATTTCCATTCC;RSEQ=TTCCATTGCACTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:31:1:1:0:24:4:1:0:3.5 -4 49157454 . C A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:31.5:1:1:0:22.5:4:1:0:4 1/1:2:2:1,1:0,0:1:0,2:16:0:32:0:1:0:50:4:1:0:1 -4 49157480 . T TGAAAA 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCCTTCCA;RSEQ=TCCATTCCATTCAATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:27:1:31:1:1:1:25:4:0.5:0.2:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49157488 . CATTCA C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCCTTCCATTCCATTC;RSEQ=ATTCCATTCCGTTGCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:27:0:33.5:1:1:1:44:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49157493 . A C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCGTTGCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,0:0.4:0,2:29:1:31.5:1:1:0:25:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49157502 . C G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCAATTCCATT;RSEQ=CGTTGCATTGGAATCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:29:1:32:1:1:1:25:4:0.5:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49157504 . G T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCAATTCCATTCC;RSEQ=TTGCATTGGAATCGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:37:0:32:0:1:0:44:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49157512 . G T 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATTCCATTCCGTTGCATT;RSEQ=GAATCGGGTTGATTCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:29:1:29.5:1:1:1:25:4:0.5:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49157609 . G A 25 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACGTTGAATTGCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38.5:1:25.5:1:1:0:60:4:1:0:1.5 -4 49158020 . T A 28 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:18:0:28:1:1:0:38:4:0.6667:0:1 -4 49158140 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CATTCCATTGCATTCCACTC;RSEQ=GGTTGACTCCATTCCATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:28:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30:1:1:0:36.5:4:1:0:3.5 -4 49158159 . A C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGGGTTGACTCCATTCCATG;RSEQ=CATTGCATTCCATTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:9:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29.5:1:1:0:36.5:4:1:0:3.5 -4 49158256 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTATTCCATTCCGTACA;RSEQ=TTCCATTCCATTCCATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:33:0:1:0:27:4:1:0:2 -4 49158259 . C G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTATTCCATTCCGTACAATT;RSEQ=CATTCCATTCCATTTCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:33:1:1:0:27:4:1:0:2 -4 49158441 . AT TG 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAACTCCATTCCATTCCA;RSEQ=CCATTCCTCTCGGGTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:33:0:1:0:32:4:1:0:5 -4 49158448 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCAATCCATT;RSEQ=CTCTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:33:1:1:0:32:4:1:0:5 -4 49158469 . C A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=CTCTCGGGTTGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:13:1:32:1:1:0:34.8:8:1:0:5.8 1/0:4:2:1,1:2,0:0.5:0,2:22.5:1:31:1:1:0:32:4:0.5:0:5 -4 49158476 . T A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.44444;SOR=Inf;LSEQ=GTTGATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:20:1:31:1:1:0:34.8:8:1:0:5.8 0/1:5:2:1,1:2,1:0.4:2,2:9.5:1:28:1:1:1.7321:40.5:4:0.4:0:4 -4 49158484 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.16667;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCAATCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:31.5:1:30.5:1:1:1:47.5:4:0.5:0:5.5 0/0:5:0:0,0:3,2:0:2,0:16.8:1:30:1:1:0:33:10:1:0:4.2 -4 49158485 . A G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.44444;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCAATCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:29:1:31:1:1:0:34.8:8:1:0:5.8 0/1:5:2:1,1:2,1:0.4:2,2:6.5:1:30:1:1:1.7321:32:4:0.4:0:5 -4 49158486 . T G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.16667;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCAATCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:33.5:1:32:1:1:1:47.5:4:0.5:0:5.5 0/0:5:0:0,0:3,2:0:2,0:17.2:1:29.2:1:1:0:33:10:1:0:4.2 -4 49158489 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.16667;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=AATCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:36.5:1:31:1:1:1:47.5:4:0.5:0:5.5 0/0:5:0:0,0:3,2:0:2,0:17.8:1:29.6:1:1:0:33:10:1:0:4.2 -4 49158492 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCCATTCCATTCCATTCCAA;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:39.5:1:32:1:1:1:47.5:4:0.5:0:5.5 0/0:3:0:0,0:2,1:0:2,0:29.7:1:29.3:1:1:0:33.7:6:1:0:3.3 -4 49158494 . C G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CATTCCATTCCATTCCAATC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:32:1:1:1:22:4:0.5:0:6 0/0:4:0:0,0:2,2:0:2,0:23.3:1:29.8:1:1:0:30.5:8:1:0:2.5 -4 49158498 . CC TG 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=CCATTCCATTCCAATCCATT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:39.5:1:31.8:1:1:1:22:4:0.5:0:5 0/0:4:0:0,0:2,2:0:2,0:25.3:1:31.3:1:1:0:30.5:8:1:0:2.5 -4 49158500 . A T 29 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=ATTCCATTCCAATCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:39.3:1:31.3:1:1:0:34.8:8:1:0:5.3 1/0:4:2:1,1:1,1:0.5:2,2:33.5:1:29.5:1:1:1:40.5:4:0.5:0:4 -4 49158505 . A G 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:39.3:1:31.3:1:1:0:34.8:8:1:0:5.3 1/0:4:2:1,1:1,1:0.5:2,2:38.5:1:30:1:1:1:40.5:4:0.5:0:4 -4 49158526 . T C 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.16667;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:27:0:31.5:1:1:1:22:4:0.5:0:5 0/0:5:0:0,0:2,3:0:2,0:17.8:1:29:1:1:0:28.4:10:1:0:2 -4 49158531 . T A 32 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCGTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:7:0:32:0:1:1:47.5:4:0.5:0:5.5 0/0:4:0:0,0:1,3:0:2,0:18.8:1:30:1:1:0:30.5:8:1:0:2 -4 49158536 . T G 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.42857;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCGTTCCATTCCATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:17:0:31:1:1:1:22:4:0.5:0:5 0/0:4:0:0,0:1,3:0:2,0:15:1:29.5:1:1:0:30.5:8:1:0:2 -4 49158540 . G T 29 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTTCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:29:1:1:0:22:4:1:0:5 0/0:4:0:0,0:1,3:0:2,0:11:1:31:1:1:0:30.5:8:1:0:2 -4 49635393 . A T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAATGGAATGGAAAGGA;RSEQ=TCAACCCGAAGGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:30:1:1:0:60:4:1:0:3.5 -4 49635404 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAGGAATCAACCCGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45.5:1:30.5:1:1:0:60:4:1:0:3.5 -4 49635439 . T G 29 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:19:0:33:0:1:0:22:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:10.5:1:29:1:1:1:60:4:0.5:0:3.5 -4 49635461 . A T 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAATGGAATGGAATGGAATC;RSEQ=ACCCGAGTGGAATGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:28:1:1:0:22:4:1:0:6.5 0/0:2:0:0,0:1,1:0:2,0:45.5:1:29.5:1:1:0:45:4:1:0:1 -4 49635481 . G A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AACCCGAGTGGAATGCAATG;RSEQ=AATGAAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:0:29.5:1:1:0:22:4:1:0:6.5 0/0:2:0:0,0:1,1:0:2,0:35.5:1:32.5:1:1:0:45:4:1:0:1 -4 49635485 . GA CC 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CGAGTGGAATGCAATGGAAT;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:0:31:1:1:0:22:4:1:0:5.5 0/0:2:0:0,0:1,1:0:2,0:31.5:1:33:1:1:0:45:4:1:0:1 -4 49635493 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=ATGCAATGGAATGAAATGGA;RSEQ=TGGAATGGAATGGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:32.5:1:1:0:22:4:1:0:5.5 0/0:2:0:0,0:1,1:0:2,0:23.5:1:32:0:1:0:45:4:1:0:1 -4 49635500 . G C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=GGAATGAAATGGAATGGAAT;RSEQ=GAATGGAACGGAACAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:0:31:1:1:0:22:4:1:0:5.5 0/0:2:0:0,0:1,1:0:2,0:16.5:1:33:1:1:0:45:4:1:0:1 -4 49635713 . T C 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAACGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:9.5:1:31:1:1:0:22:4:1:0:3 1/1:2:2:1,1:0,0:1:0,2:24:0:31:1:1:0:26:4:1:0:1 -4 49636347 . T G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTGAATGGAATGGAAT;RSEQ=GAATGGAATGGAACGGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:29:1:1:0:44:4:1:0:5.5 -4 49636383 . G T 27 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=GAACGGAACGGAATGGAATG;RSEQ=AATGGAGTGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:21:0:32.5:1:1:0:52:4:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:19:0:27.5:1:1:1:54:4:0.5:0:1.5 -4 49636385 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=ACGGAACGGAATGGAATGGA;RSEQ=TGGAGTGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:0:32.5:1:1:0:52:4:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:32:0:31.5:1:1:1:44:4:0.5:0:5.5 -4 49636390 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ACGGAATGGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:17:0:34:0:1:0:52:4:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:27:0:31:1:1:1:44:4:0.5:0:5.5 -4 49636396 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=TGGAATGGAATGGAGTGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:11:0:32:0:1:0:52:4:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:21:0:31.5:1:1:1:44:4:0.5:0:5.5 -4 49636472 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGAATGCAGTGGAATGGAAT;RSEQ=GAACGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:9.5:1:32.5:1:1:0:20:4:1:0:1.5 1/0:3:2:1,1:1,0:0.6667:0,2:9.5:1:31.5:1:1:0:46:4:0.6667:0:6 -4 49636501 . C G 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TGGAATGGAATGGAATCAAC;RSEQ=CGAGTGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7:0:32.5:1:1:0:20:4:1:0:1.5 0/0:3:0:0,0:2,1:0:2,0:37:1:31.3:1:1:0:45.3:6:1:0:6.7 -4 49636507 . GG TC 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGAATGGAATCAACCCGAGT;RSEQ=AATGGAATGGAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:1:0:34:0:1:0:20:4:1:0:1.5 1/0:3:2:1,1:1,0:0.6667:0,2:36:0:30.5:1:1:0:46:4:0.6667:0:5 -4 49636520 . A G 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCCGAGTGGAATGGAATGGA;RSEQ=TGGAATGCAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:24:0:30.5:1:1:0:46:4:0.6667:0:5 -4 49636528 . C G 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:18:1:30.7:1:1:0:45.3:6:1:0:5.7 -4 49636531 . T G 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGCAA;RSEQ=GGAATGGAATGGTATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:13:0:29.5:1:1:0:46:4:0.6667:0:5 -4 49636544 . T AACAACCCGAATGGA 58 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AATGCAATGGAATGGAATGG;RSEQ=ATGGAATCAACCCTAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:1,0:0.8:0,2:10.5:1:29.3:1:1:0:45.8:8:0.8:0.8:6.3 -4 49636810 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGAATGGAATCAACCCGAG;RSEQ=GGAAAGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:36:0:29.5:1:1:0:43:4:1:0:3 0/1:5:2:1,1:2,1:0.4:2,2:30:0:32:0:1:1.7321:45:4:0.4:0:5.5 -4 49636811 . G T 30 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=GGAATGGAATCAACCCGAGT;RSEQ=GAAAGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:0:30:1:1:0:43:4:1:0:3 0/0:5:0:0,0:3,2:0:2,0:24.6:1:30:1:1:0:43.6:10:1:0:4.2 -4 49636812 . G C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATCAACCCGAGTG;RSEQ=AAAGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:38:0:31.5:1:1:0:43:4:1:0:3 0/1:5:2:1,1:2,1:0.4:2,2:28:1:31:1:1:1.7321:34:4:0.4:0:3.5 -4 49636815 . A T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATCAACCCGAGTGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:41:0:30.5:1:1:0:43:4:1:0:3 0/1:5:2:1,1:2,1:0.4:2,2:31:1:30:1:1:1.7321:34:4:0.4:0:3.5 -4 49636816 . G T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATCAACCCGAGTGGAAA;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:42:0:31.5:1:1:0:43:4:1:0:3 0/1:5:2:1,1:2,1:0.4:2,2:36:0:30.5:1:1:1.7321:45:4:0.4:0:5.5 -4 49636819 . A G 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=ATCAACCCGAGTGGAAAGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:45:0:30.5:1:1:0:43:4:1:0:3 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:31:1:1:1:34:4:0.5:0:3.5 -4 49636834 . A G 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=AAGGAATGGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35:0:31.5:1:1:0:43:4:1:0:3 0/1:5:2:1,1:1,2:0.4:2,2:31.5:1:31:1:1:1.73:45:4:0.4:0:5.5 -4 49636835 . T A 32 d7;v4;MAF0.05;pSTD;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.14286;SOR=0;LSEQ=AGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:0:32:0:1:0:43:4:1:0:3 0/1:5:1:0,1:2,2:0.2:2,0:8:0:32:0:1:0:40:2:0.2:0:2 -4 49636847 . G T 27 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:0:32.5:1:1:0:43:4:1:0:3 0/1:5:2:1,1:1,2:0.4:2,2:18.5:1:27.5:1:1:1.73:45:4:0.4:0:5.5 -4 49636850 . T C 29 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19:0:32.5:1:1:0:43:4:1:0:3 0/1:5:2:1,1:1,2:0.4:2,2:15.5:1:29:1:1:1.73:45:4:0.4:0:5.5 -4 49637125 . T G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACACGAGTGGAATGCAA;RSEQ=GGAATGAAATGGAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:22.5:1:30:1:1:0:22:4:0.6667:0:4.5 -4 49637127 . G C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACGAGTGGAATGCAATG;RSEQ=AATGAAATGGAATGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:24.5:1:30.5:1:1:0:22:4:0.5:0:4.5 -4 49637132 . A G 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGGAATGCAATGGAATG;RSEQ=AATGGAATGGAAAGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:17.3:1:30.3:1:1:0:22.3:6:0.75:0.25:5.7 -4 49637140 . T A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAATGGAATGAAATGGAA;RSEQ=GGAAAGGAATGGAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:15:0:30.5:1:1:0:22:4:0.5:0:4.5 -4 49637155 . C TAGTATCAACTCGATTGCAATGGAAA 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TGGAATGGAAAGGAATGGAA;RSEQ=GGAATTGAATGGAATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:41:1:32:1:1:0:22:4:0.5:0.5:4.5 -4 49637157 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAAAGGAATGGAACG;RSEQ=AATTGAATGGAATGAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:2:0:27:0:1:0:46:2:1:0:7 1/0:4:2:1,1:2,0:0.5:0,2:13:1:31.5:1:1:0:22:4:0.5:0.5:4.5 -4 49637159 . A T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAAAGGAATGGAACGGA;RSEQ=TTGAATGGAATGAAATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:4:0:26:0:1:0:46:2:1:0:7 1/0:4:2:1,1:2,0:0.5:0,2:11:1:32:1:1:0:22:4:0.5:0.5:4.5 -4 49637160 . T G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAAGGAATGGAACGGAA;RSEQ=TGAATGGAATGAAATCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:5:0:25:0:1:0:46:2:1:0:7 1/0:4:2:1,1:2,0:0.5:0,2:10:1:33:1:1:0:22:4:0.5:0.5:4.5 -4 49637161 . T G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAAGGAATGGAACGGAAT;RSEQ=GAATGGAATGAAATCAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:6:0:25:0:1:0:46:2:1:0:7 1/0:4:2:1,1:1,0:0.5:0,2:9:1:33:1:1:0:22:4:0.5:0.5:4.5 -4 49637162 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAAGGAATGGAACGGAATT;RSEQ=AATGGAATGAAATCAACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:7:0:26:0:1:0:46:2:1:0:7 0/1:6:2:1,1:2,0:0.3333:0,2:8:1:31:1:1:0:22:4:0.4:0.3333:4.5 -4 49637164 . A T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGAATGGAACGGAATTGA;RSEQ=TGGAATGAAATCAACCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:5.5:1:26.5:1:1:0:35:4:1:0:6 0/1:6:2:1,1:3,0:0.3333:0,2:6:1:32:1:0.4:0:22:4:0.4:0.3333:4.5 -4 49637165 . T G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGAATGGAACGGAATTGAA;RSEQ=GGAATGAAATCAACCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:6.5:1:26:1:1:0:35:4:1:0:6 0/1:6:2:1,1:3,0:0.3333:0,2:5:1:33:1:0.4:0:22:4:0.4:0.3333:4.5 -4 49637172 . A G 29 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GAACGGAATTGAATGGAATG;RSEQ=AATCAACCCGAGTGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:13.5:1:26.5:1:1:0:35:4:1:0:6 1/0:4:2:1,1:1,0:0.5:0,2:21:1:29.5:1:1:0:23:4:0.6667:0:7 -4 49637182 . G A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=GAATGGAATGAAATCAACCC;RSEQ=AGTGGAAAGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:6:0:30:1:1:0:37.5:4:0.5:0:5.5 0/1:5:2:1,1:1,1:0.4:2,2:21.5:1:27:1:1:1:23:4:0.5:0:7 -4 49637225 . T G 31 v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATCAACCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,10:0:2,0:29.3:1:31.3:1:1:0:30.6:36:0.9474:0:3.9 0/1:41:2:1,1:19,19:0.0488:2,2:35:0:31:1:1:1:30:4:0.0526:0:3 -4 49637226 . G T 31 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.09344;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATCAACCCGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:34:0:31.5:1:1:1.12:33:4:0.1053:0:3 0/0:42:0:0,0:21,21:0:2,0:30.5:1:30.5:1:1:0:31.6:41:1:0:3.2 -4 49637227 . G T 29 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATCAACCCGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,10:0:2,0:30.2:1:32:1:1:0:30.4:36:0.9474:0:3.9 0/1:42:2:1,1:20,20:0.0476:2,2:40:0:29.5:1:1:1:40:4:0.0488:0:5 -4 49637232 . G C 51 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.02692;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATCAACCCGAGTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:8,8:0.1579:2,2:26.3:1:32.3:1:1:1.9301:38.3:6:0.1579:0:5.3 0/0:42:0:0,0:19,18:0:2,0:31.9:1:31:1:1:0:31.4:74:0.881:0:3 -4 49637234 . A G 50 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.02692;SOR=0;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=TCAACCCGAGTGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:8,8:0.1579:2,2:24.3:1:32:1:1:1.9301:38.3:6:0.1579:0:5.3 0/0:42:0:0,0:21,20:0:2,0:33.7:1:29.9:1:1:0:31.8:40:0.9756:0:3.1 -4 49637236 . C G 82 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16336;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=AACCCGAGTGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:31.9:1:32.4:1:1:0:30.2:38:1:0:3.9 0/1:41:6:3,3:17,18:0.1463:2,2:43.5:1:31.8:1:1:1.06:31.5:12:0.1463:0:4.3 -4 49637238 . A C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09661;SOR=0;LSEQ=AATGGAATGGAATGGAATCA;RSEQ=CCCGAGTGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,8:0.1053:2,2:38.5:1:32.5:1:1:1:20:4:0.1053:0:3.5 0/0:41:0:0,0:20,21:0:2,0:35.1:1:30.1:1:1:0:31.6:82:1:0:3.2 -4 49637239 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATGGAATGGAATCAA;RSEQ=CCGAGTGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:31.9:1:32.3:1:1:0:30.2:38:1:0:3.9 0/1:40:2:1,1:18,20:0.05:2,2:44:0:31:1:1:1.11:41:4:0.05:0:4.5 -4 49637240 . C G 104 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34238;SOR=2.25625;LSEQ=TGGAATGGAATGGAATCAAC;RSEQ=CGAGTGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:2,1:6,8:0.1579:2,2:29.3:1:32:1:0.57647:2.52:25.3:6:0.1579:0:3.3 0/1:40:12:6,6:11,10:0.3:2,2:42.8:1:29.2:1:1:1.09682:31.3:11:0.2895:0:2.9 -4 49637243 . AGT TGTGCAGG 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=AATGGAATGGAATCAACCCG;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,10:0:2,0:31.9:1:30.6:1:1:0:30.4:17:0.9444:0:3.8 0/1:40:2:1,1:18,19:0.05:2,2:43:0:31.1:1:1:1.05:23:4:0.05:0:5 -4 49637244 . G T 86 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08456;SOR=Inf;LSEQ=ATGGAATGGAATCAACCCGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,9:0:2,0:29.1:1:32.9:1:1:0:30.3:36:0.9474:0:3.7 0/1:40:7:2,5:16,14:0.175:2,2:23:0:30.7:1:0.40479:2.77898:32.4:14:0.1944:0:4.1 -4 49637245 . T TGCAGG 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16854;SOR=0.44276;LSEQ=TGGAATGGAATCAACCCGAG;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:5,6:4,4:0.5789:2,2:29.3:1:32:1:1:1.18851:28.5:22:0.5789:0.1579:3.6 0/1:40:15:8,7:4,9:0.375:2,2:38:1:30.8:1:0.27606:2.48:34.9:30:0.4054:0:3.7 -4 49637246 . GG TC 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATGGAATCAACCCGAGT;RSEQ=AATGGAATGGAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:25.8:1:32.3:1:1:0:30.2:38:1:0:4.1 0/1:40:2:1,1:18,20:0.05:2,2:20:0:29.5:1:1:1.11:40:4:0.0513:0:4 -4 49637247 . G C 85 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16409;SOR=Inf;LSEQ=GAATGGAATCAACCCGAGTG;RSEQ=AATGGAATGGAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,8:0:2,0:29.4:1:31.9:1:1:0:29.3:32:1:0:3.9 0/1:40:6:1,5:17,15:0.15:2,2:17:1:33:1:0.18392:5.43925:31.2:12:0.1622:0:3.5 -4 49637251 . G C 50 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.54652;SOR=Inf;LSEQ=GGAATCAACCCGAGTGGAAT;RSEQ=GAATGGAATGGAATGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:25.4:1:31.8:1:1:0:29.3:32:1:0:3.9 0/1:38:3:0,3:19,16:0.0789:2,0:16:0:31.7:1:0.22973:0:30.3:6:0.0789:0:4.3 -4 49637252 . G T 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.41048;SOR=0.51681;LSEQ=GAATCAACCCGAGTGGAATG;RSEQ=AATGGAATGGAATGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:7,6:0.1875:2,2:29:0:30.3:1:1:2.21433:33.3:6:0.1875:0:4.3 0/1:38:4:2,2:17,17:0.1053:2,2:29:0:29:1:1:1:30:8:0.1081:0:4.8 -4 49637253 . A T 27 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.08386;SOR=0;LSEQ=AATCAACCCGAGTGGAATGG;RSEQ=ATGGAATGGAATGCAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,7:0.125:2,2:8:0:27.5:1:1:1.15:40:4:0.125:0:5.5 0/0:38:0:0,0:18,18:0:2,0:23.9:1:29.4:1:1:0:31.4:35:0.9459:0:3.4 -4 49637255 . T A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.0762;SOR=0;LSEQ=TCAACCCGAGTGGAATGGAA;RSEQ=GGAATGGAATGCAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:26:0:30.5:1:1:1.15:20:4:0.1333:0:3.5 0/0:38:0:0,0:19,19:0:2,0:22.4:1:30.1:1:1:0:31.9:37:1:0:3.5 -4 49637257 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=AACCCGAGTGGAATGGAATG;RSEQ=AATGGAATGCAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:21.5:1:31.8:1:1:0:29.4:30:1:0.0667:3.9 0/1:38:2:1,1:18,18:0.0526:2,2:14.5:1:27.5:1:1:1:45:4:0.0541:0:3.5 -4 49637260 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.38944;SOR=0.47811;LSEQ=CCGAGTGGAATGGAATGGAA;RSEQ=GGAATGCAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:1,2:6,6:0.2:2,2:21:0:32.3:1:1:1.91151:33.3:6:0.2:0:4.3 0/1:38:4:2,2:17,17:0.1053:2,2:21:0:31:1:1:1:30:8:0.1081:0:4.8 -4 49637265 . T C 30 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.05612;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GCAATGGAATGGAATGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:28:0:30.5:1:1:1:33:4:0.1667:0:3 0/0:37:0:0,0:18,18:0:2,0:13.7:1:29.4:1:1:0:32.2:17:0.9714:0:3.4 -4 49637270 . T TGGAATGGAATCATCC 85 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=TGGAATGGAATGGAATGCAA;RSEQ=GGAATGGAATGGTATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:2,5:4,0:0.5833:0,2:10.6:1:30.3:1:0.06061:0:26.9:14:0.5833:0.5833:4.1 0/0:30:0:0,0:17,13:0:2,0:11.5:1:29.7:1:1:0:32:60:1:0:3.3 -4 49637274 . A T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0.77466;LSEQ=ATGGAATGGAATGCAATGGA;RSEQ=TGGAATGGTATGGAATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:4,6:0.0909:2,0:18:0:33:0:0.45455:0:24:2:0.0909:0:5 0/1:28:2:1,1:15,11:0.0714:2,2:31:0:31.5:1:1:1.34838:41:4:0.0741:0:5.5 -4 49637277 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATGGAATGCAATGGAATG;RSEQ=AATGGTATGGAATCAACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:7.5:1:31.5:1:1:0:27.8:20:1:0:4 0/1:28:2:1,1:15,11:0.0714:2,2:28:0:31.5:1:1:1.34838:41:4:0.0714:0:5.5 -4 49637283 . T A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGCAATGGAATGGAATGG;RSEQ=ATGGAATCAACCCGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:6:1:31:1:1:1.7321:21.3:6:0.6:0.4:3.3 1/1:2:2:1,1:0,0:1:0,2:22:0:31.5:1:1:0:41:4:1:0:5.5 -4 49637295 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGTATGGAATCAAC;RSEQ=CGAGTGGAATTGTATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:32:1:1:0:41:4:1:0:5.5 -4 49637522 . G C 34 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=GAACGGAATTGAATGGAATG;RSEQ=AATCAACACGAGTGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:6.8:1:30.3:1:1:0:30.8:8:1:0:4.8 0/1:7:2:1,1:2,2:0.2857:2,2:6:0:34:0:1:1:22:4:0.3333:0:3 -4 49637540 . A T 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52941;SOR=Inf;LSEQ=TGGAATCAACACGAGTGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,2:0:2,0:19.5:1:31:1:1:0:35.8:8:1:0:3.8 0/1:12:2:1,1:6,4:0.1667:2,2:6:0:28:1:1:1.4491:40:4:0.1667:0:5 -4 49637541 . G A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=GGAATCAACACGAGTGGAAA;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,4:0:2,0:13.9:1:30.8:1:1:0:33.4:16:1:0:4.1 0/1:14:2:1,1:6,5:0.1429:2,2:25:0:29.5:1:1:1.18321:47:4:0.1429:0:6 -4 49637543 . A C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48148;SOR=Inf;LSEQ=AATCAACACGAGTGGAAAGG;RSEQ=ATGGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,6:0:2,0:11:1:28.8:1:1:0:35.8:11:1:0:3.8 0/1:14:2:1,1:7,5:0.1429:2,2:27:0:33.5:1:1:1.36624:22:4:0.1429:0:3 -4 49637561 . G A 67 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.24044;SOR=3.04461;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:21:0:29:1:1:1.21106:22:4:0.0909:0:4 0/1:21:5:2,3:9,7:0.2381:2,2:24.4:1:29:1:0.63512:1.86862:43.6:10:0.2381:0:4.4 -4 49637575 . TGG CGAATTGT 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.40518;SOR=2.39786;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=AATGGAATGGAATTGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:0.0833:2,2:35:0:31.2:1:1:1:22:4:0.0909:0:4 0/1:22:4:2,2:9,9:0.1818:2,2:40.5:1:30.1:1:1:1:44.5:8:0.1818:0:4.8 -4 49637584 . AT CA 33 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.23256;SOR=Inf;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=GGAATTGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:31.5:1:31.1:1:1:0:37.1:44:1:0:3.7 0/1:21:2:1,1:9,10:0.0952:2,2:20:0:33:1:1:1.11:47:4:0.0952:0:5 -4 49637586 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.48837;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATTGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:0.0909:2,2:35:1:31:1:1:1.21:50:4:0.0909:0:2 0/0:21:0:0,0:10,10:0:2,0:29.2:1:31.5:1:1:0:39.8:40:0.9524:0:2.9 -4 49637589 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.4878;SOR=0;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=TTGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:35:1:30:1:1:1.11:50:4:0.0952:0:2 0/0:21:0:0,0:10,11:0:2,0:27.4:1:30.7:1:1:0:39:42:1:0:2.8 -4 49637591 . T G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40989;SOR=0.34549;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:2,3:7,7:0.2381:2,2:32.8:1:32.2:1:1:1.46843:39.2:10:0.2381:0:4.6 0/1:21:2:1,1:8,9:0.0952:2,2:14:0:33:1:1:1.12:47:4:0.0952:0:5 -4 49637592 . GAATGGAAT AACCCGAATAGAAA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.4878;SOR=0;LSEQ=GAATGGAATGGAATGGAATT;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:7,7:0.0952:2,2:41.5:1:31.5:1:1:1:34:4:0.0952:0:3.5 0/0:21:0:0,0:8,9:0:2,0:27.5:1:30.4:1:1:0:37.5:34:0.8095:0:2.6 -4 49637593 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=AATGGAATGGAATGGAATTG;RSEQ=ATGGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:7,10:0.0952:2,0:40:1:29.5:1:0.21053:0:35.5:4:0.1053:0:5.5 0/0:21:0:0,0:8,9:0:2,0:24.8:1:30.5:1:1:0:37.9:34:0.85:0:2.9 -4 49637636 . T G 45 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:0,1:0.6:0,2:11.3:1:29:1:1:0:37:6:0.6:0.2:3.7 0/0:3:0:0,0:1,2:0:2,0:12.7:1:30:1:1:0:44.3:6:1:0:2.3 -4 49638289 . G C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATCAACTAGAATGGAAT;RSEQ=GAATGGAATGGAATGGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:1:28:1:1:0:45.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49638308 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATCAACCTGAGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:29.5:1:1:0:45.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49639102 . AGCAAT A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCGAGTGAAATGGAATGGAA;RSEQ=GGAATGGAATGAACCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:19:0:34:0:1:0:34:2:1:0:2 1/0:4:2:1,1:1,1:0.5:2,2:14:0:31.5:1:1:1:30:4:0.5:0:1 -4 49639104 . CAATGG C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTGAAATGGAATGGAAAG;RSEQ=AATGGAATGAACCCGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:21:0:32:0:1:0:34:2:1:0:2 1/0:4:2:1,1:0,0:0.5:0,2:17:0:33:0:1:0:50:4:1:0:3 -4 49639118 . G C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAAGCAATGGAATGGAAT;RSEQ=AACCCGAGTGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:34:0:1:0:34:2:1:0:2 0/1:5:2:1,1:2,1:0.4:2,2:25:0:32.5:1:1:1.7321:50:4:0.4:0:3 -4 49639135 . A C 65 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.06061;SOR=Inf;LSEQ=AATGAACCCGAGTGGAATGG;RSEQ=ATGGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:11.8:1:27.2:1:1:0:38.6:4:1:0:5.2 1/0:6:4:2,2:1,1:0.6667:2,2:34:1:32.5:1:1:1:40:8:0.6667:0:2 -4 49639154 . G A 28 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=1.22862;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:25.5:1:31.5:1:1:1.41418:40:4:0.3333:0:8 0/1:6:2:1,1:2,2:0.3333:2,2:19:0:28.5:1:1:1:50:4:0.3333:0:3 -4 49639158 . G A 48 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.19231;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATCAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:2,2:0.4286:2,2:22.7:1:30.7:1:1:1.81:38:6:0.5:0:6 0/0:6:0:0,0:3,3:0:2,0:16.8:1:31.2:1:1:0:40.2:12:1:0:2.5 -4 49639159 . G C 31 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.46154;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATCAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:13.5:1:31:1:1:1.41418:55.5:4:0.2857:0:7.5 0/0:6:0:0,0:3,3:0:2,0:15.8:1:31.2:1:1:0:40.2:12:1:0:2.5 -4 49639164 . G C 31 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.46154;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATCAACCAGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:18.5:1:31.5:1:1:1.41418:55.5:4:0.2857:0:7.5 0/0:6:0:0,0:3,3:0:2,0:10.8:1:30.5:1:1:0:40.2:12:1:0:2.5 -4 49639168 . G T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.46667;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATCAACCAGAGTGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:39.5:1:31:1:1:1:40:4:0.3333:0:8 0/0:4:0:0,0:2,2:0:2,0:11.8:1:30.3:1:1:0:45.3:8:1:0:3.3 -4 49639172 . T A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=CAACCAGAGTGGAATGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:43.5:1:30.5:1:1:1:40:4:0.4:0:8 0/0:4:0:0,0:2,2:0:2,0:7.8:1:28.8:1:1:0:45.3:8:1:0:3.3 -4 49639177 . CAGAGTGGAATGGAG AGGAGGGAAAGGAT 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATCAAC;RSEQ=TGGAATGGAATGCAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:40.5:1:30.6:1:1:1:40:4:0.4:0:5 0/0:1:0:0,0:1,0:0:0,0:19:0:32:0:1:0:45:2:1:0:5 -4 49639188 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCAACCAGAGTGGAAT;RSEQ=GAGTGGAATGGAATGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:0.3333:2,2:39:0:31:1:1:1:55.5:4:0.5:0:7.5 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49639194 . G T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCAGAGTGGAATGGAGTG;RSEQ=AATGGAATGCAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:33:0:30:1:1:1:55.5:4:0.3333:0:7.5 0/0:1:0:0,0:1,0:0:0,0:2:0:27:0:1:0:45:2:1:0:5 -4 49639197 . T A 27 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTGGAATGGAGTGGAA;RSEQ=GGAATGCAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:6:0:27.5:1:1:1:39.5:4:0.3333:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49639201 . AT TC 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTGGAATGGAGTGGAATGGA;RSEQ=GCAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:25:0:32:1:1:1:55.5:4:0.3333:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49639204 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAGTGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23:0:31.5:1:1:1:55.5:4:0.5:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49639323 . G GGAATCAAATGGAATTTAATTGAATGGAAGTGAAAGTAGTA 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.14286;SOR=Inf;LSEQ=GGAATGGAATGGAGTGGAAT;RSEQ=GAATGGAATGGAGTGTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15.8:1:30.8:1:1:0:36.8:8:1:0.5:1.8 1/0:3:2:1,1:1,0:0.6667:0,2:46:1:28.5:1:1:0:25:4:0.6667:0.6667:0 -4 49639333 . G GGAAACTACAAGAATGGAATGGAATGTAATGGAGTGTAAAGGAATTGAAAAGAATCAATCA 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.46429;SOR=0;LSEQ=GGAGTGGAATGGAATGGAAT;RSEQ=GAGTGTAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:50:1:29.1:1:1:1.73:42:4:0.4:0.4:1 0/0:3:0:0,0:2,1:0:2,0:12:1:31.7:1:1:0:25:6:1:0:1 -4 49639345 . A AATAAT 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.10714;SOR=Inf;LSEQ=AATGGAATGGAGTGTAATGG;RSEQ=ATGGAATGGAGTGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:17:1:29.8:1:1:0:38.2:10:1:0:1.6 1/0:3:2:1,1:1,0:0.6667:0,2:23:0:30.9:1:1:0:25:4:0.6667:0:0 -4 49639357 . T C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAATGGAATGGAATGGAG;RSEQ=GGAATGGAATGGAATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:14:1:30:0:1:1.73:42:4:0.4:0:1 0/0:2:0:0,0:1,1:0:2,0:11.5:1:30.5:1:1:0:25:4:1:0:0 -4 49639539 . GAAAGGAATGGAATGGAAAGGAATAAAATGGATTGG C 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=8;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAGTGGAATGGAATGGAATG;RSEQ=AATGGAATGGCATCAACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:27.5:1:1:0:33:4:1:1:3 -4 49639585 . C G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGATTGGAATGGAATGG;RSEQ=ATCAACCCGAGTGAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:28:0:32:0:1:0:40:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:11:0:30.5:1:1:0:33:4:1:0:3 -4 49639613 . G C 31 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CGAGTGAAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:27:0:30:0:1:0:40:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:20:0:31:1:1:0:33:4:1:0:3 -4 49639617 . T A 32 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGAAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:28:0:1:0:40:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:16:0:32:1:1:0:33:4:1:0:3 -4 49642625 . C T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=ATGGAATGGAATGGAATCAA;RSEQ=CTGAGTGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:27.3:1:30:1:1:0:41.7:6:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:26:0:31.5:1:1:1:25:4:0.3333:0:3.5 -4 49642630 . GT CTGCAGG 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.5;SOR=Inf;LSEQ=ATGGAATGGAATCAACCTGA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:30.3:1:30.3:1:1:0:41.7:6:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:26:0:32.4:1:1:1:42:4:0.3333:0:2 -4 49642631 . T TGCAGG 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=TGGAATGGAATCAACCTGAG;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:31:0:31.4:1:1:0:42.5:4:0.6667:0:1 0/0:6:0:0,0:1,1:0:2,0:32:1:31:1:1:0:25:4:0.5:0:3.5 -4 49642632 . G GCAGGT 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GGAATGGAATCAACCTGAGT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:37:1:30.3:1:1:0:41.7:6:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:34:0:32:1:1:1:25:4:0.3333:0:3.5 -4 49642650 . A C 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.5;SOR=Inf;LSEQ=GTGGAATGGAATGGAATGGA;RSEQ=TGCAATGGAATGGAATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:25.3:1:31.3:1:1:0:41.7:6:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:17:0:31.5:1:1:1:42:4:0.3333:0:2 -4 49642658 . G C 33 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=GAATGGAATGGAATGCAATG;RSEQ=AATGGAATGGTATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:9:0:33.5:1:1:0:42.5:4:0.6667:0:1 0/0:6:0:0,0:3,3:0:2,0:7:1:30.2:1:1:0:33:12:1:0:2.3 -4 49642870 . A T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAACGGAATCAACCCGA;RSEQ=TGGAATGGAACGGAATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:12:0:30.5:1:1:0:37:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49642974 . AATGGAATCAACATGAGTGGAATGCAATGGAATGAAATGGAATGGAATGGAACGGAATGGAACGGAACGGAATTGA C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AATGGAATGCAATGGAATGG;RSEQ=ATGGAATGAAATCAACCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35:1:30.7:1:1:0:31.5:4:1:1:4.5 -4 49643026 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATGGAATGGAATGGAA;RSEQ=GGAATGGAACGGAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:17.5:1:27:0:1:0:46.5:4:1:0:3.5 -4 49643041 . CGGAATTGAATGGAATGAAATCAACCCGAGT C 43 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=5;SSF=0.46429;SOR=Inf;LSEQ=TGGAACGGAATGGAACGGAA;RSEQ=GGAAAGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:1.5:1:29:1:1:0:41.5:4:1:0:7 1/0:6:3:2,1:1,1:0.5:2,2:7.3:1:27.3:1:1:1.73:35:6:0.6:0.5:3.3 -4 49643058 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=GAACGGAATTGAATGGAATG;RSEQ=AATCAACCCGAGTGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:17.5:1:30.5:1:1:0:41.5:4:0.6667:0:7 0/1:6:2:1,1:0,1:0.3333:0,2:14.5:1:33:0:1:0:23.5:4:0.6667:0:5 -4 49643066 . C T 45 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22222;SOR=0.13854;LSEQ=TTGAATGGAATGAAATCAAC;RSEQ=CGAGTGGAAAGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:2,0:0.6:0,2:18.3:1:28.7:1:0.4:0:41:6:0.6:0:6.3 0/1:7:1:0,1:1,2:0.1429:2,0:17:0:31:0:1:0:23:2:0.25:0:6 -4 49643081 . T G 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.5;SOR=Inf;LSEQ=TCAACCCGAGTGGAAAGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:28.8:1:29.3:1:1:0:40.2:12:1:0:4.7 0/1:10:2:1,1:4,3:0.2:2,2:10:0:29:1:1:1.29098:40.5:4:0.2:0:3 -4 49643091 . TG ATTAATA 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.48529;SOR=Inf;LSEQ=TGGAAAGGAATGGAATGGAA;RSEQ=GAATGGAATGGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:31.1:1:31.4:1:1:0:39.9:14:1:0:4.3 0/1:10:2:1,1:4,4:0.2:2,2:26.5:1:28.7:1:1:1:24:4:0.2:0:4.5 -4 49643096 . T A 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.26154;SOR=0.18798;LSEQ=AGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:3,1:0.4286:2,2:39:1:31.3:1:0.48571:4.4496:41:6:0.4286:0:6.3 0/1:9:1:0,1:5,3:0.1111:2,0:27:0:33:0:0.44444:0:23:2:0.1111:0:6 -4 49643097 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.475;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATCAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:34.4:1:31.9:1:1:0:39.9:14:1:0:4.3 0/1:9:2:1,1:4,3:0.2222:2,2:26:0:29:1:1:1.29098:40.5:4:0.25:0:3 -4 49643108 . G A 48 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.26154;SOR=0.18798;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATCAACCCGAGTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:3,1:0.4286:2,2:31:1:30.3:1:0.48571:4.4496:41:6:0.4286:0:6.3 0/1:9:1:0,1:5,3:0.1111:2,0:15:0:32:0:0.44444:0:23:2:0.1111:0:6 -4 49643116 . C T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76457;LSEQ=TGGAATGGAATGGAATCAAC;RSEQ=CGAGTGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:3,0:0.5714:0,2:24:1:29.3:1:0.14286:0:40.3:8:0.5714:0:5.8 1/0:8:4:2,2:1,1:0.5:2,2:25.3:1:30.3:1:1:1:41.8:8:0.5:0:4.5 -4 49643120 . G T 40 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=3.3097;LSEQ=ATGGAATGGAATCAACCCGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:4,2:0.1429:2,0:23:0:31:0:0.42857:0:38:2:0.1429:0:4 0/1:8:3:2,1:2,3:0.375:2,2:27.3:1:25.3:1:1:2.60:48:2:0.2857:0:4 -4 49643121 . T TGCAGG 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TGGAATGGAATCAACCCGAG;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:22.3:1:29.2:1:1:0:40.2:12:0.8571:0:4.7 0/1:8:2:1,1:3,2:0.25:2,2:39.5:1:32.4:1:1:1.41418:40.5:4:0.25:0:3 -4 49643123 . G C 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55944;SOR=4.03195;LSEQ=GAATGGAATCAACCCGAGTG;RSEQ=AATGGAATGGAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:4,2:0.1429:2,0:20:0:33:0:0.42857:0:38:2:0.1429:0:4 0/1:7:3:2,1:1,2:0.4286:2,2:24.3:1:27:1:1:3.11:48:2:0.3333:0:4 -4 49643127 . G C 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.55944;SOR=4.03195;LSEQ=GGAATCAACCCGAGTGGAAT;RSEQ=GAATGGAATGGAATGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:4,2:0.1429:2,0:16:0:31:0:0.42857:0:38:2:0.1429:0:4 0/1:7:3:2,1:2,2:0.4286:2,2:20.3:1:29.3:1:1:1.81:48:6:0.4286:0:4 -4 49643128 . G A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.46154;SOR=0;LSEQ=GAATCAACCCGAGTGGAATG;RSEQ=AATGGAATGGAATGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:13.5:1:28.5:1:1:1.41418:41.5:4:0.2857:0:6.5 0/0:7:0:0,0:4,3:0:2,0:26.9:1:30.7:1:1:0:38.9:14:1:0:4.1 -4 49643849 . A C 31 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0.32198;LSEQ=AATCAACCCGAGTGGAATGG;RSEQ=ATGGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:26:1:31:1:1:0:55:4:0.6667:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:17:0:33:0:1:0:31:2:0.3333:0:1 -4 49643852 . G T 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.4;SOR=Inf;LSEQ=CAACCCGAGTGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:30.7:1:30:1:1:0:45:6:1:0:2 1/0:3:2:1,1:1,0:0.6667:0,2:17:0:32:0:1:0:26:4:0.6667:0:2.5 -4 49644115 . C T 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGGAATGGAATAAA;RSEQ=CCGAGTGGAATGCAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:37:1:31:0:1:1.73:26:4:0.4:0:8 -4 49644119 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGAATGGAATAAACCCG;RSEQ=GTGGAATGCAATGGAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:40.5:1:31.5:1:1:1.73:26:4:0.4:0:8 -4 49644125 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATAAACCCGAGTGGA;RSEQ=TGCAATGGAATGAAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:36:0:32:1:1:1.73:26:4:0.5:0:8 -4 49644128 . C G 62 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATAAACCCGAGTGGAATG;RSEQ=AATGGAATGAAATGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:0,0:0.8:0,2:24.8:1:31:1:1:0:24:8:0.8:0:5 -4 49644138 . A T 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGGAATGCAATGGAATG;RSEQ=AATGGAATTGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:23:0:28.5:1:1:1:26:4:0.5:0:8 -4 49644143 . G T 27 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGCAATGGAATGAAATG;RSEQ=AATTGAATGGAATGGAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:18:0:27.5:1:1:1:26:4:0.5:0:8 -4 49644145 . A G 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCAATGGAATGAAATGGA;RSEQ=TTGAATGGAATGGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:30.5:1:1:0:26:4:1:0:8 -4 49644147 . T G 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATGGAATGAAATGGAAT;RSEQ=GAATGGAATGGAACGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:29.5:1:1:0:26:4:1:0:8 -4 49644633 . G A 50 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=GAGGAATGGAATGGAATGGA;RSEQ=TGGAATGGAATAGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:11:1:31.7:1:1:0:21.7:6:1:0:4.7 0/1:5:2:0,2:2,1:0.4:2,0:8.5:1:26.5:1:0.4:0:31:4:0.4:0:5.5 -4 49644635 . GG CGAATCAACTAGAGAGC 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.52857;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAGT;RSEQ=AATGGAATAGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:9.3:1:29.8:1:1:0:21.5:8:1:0:4.5 0/1:12:3:2,1:3,6:0.25:2,2:18.3:1:30:1:0.52273:3.53:28.3:6:0.3:0.25:3.3 -4 49644642 . A T 26 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATGGAGTGGAATGG;RSEQ=ATAGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:11:1:30:1:1:0:28.4:16:1:0.125:5.1 0/1:19:2:1,1:7,10:0.1053:2,2:6:0:26.5:1:1:1.40:32:4:0.1176:0:5 -4 49644645 . A G 33 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08615;SOR=0;LSEQ=GGAATGGAGTGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:2,4:0.25:2,0:14.5:1:33:1:0.42857:0:26.5:4:0.25:0.125:4 0/0:18:0:0,0:8,9:0:2,0:20:0:14:0:1:0:32:0:0:0:7 -4 49644649 . T C 32 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.1417;SOR=0;LSEQ=TGGAGTGGAATGGAATAGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:7,6:0.1333:2,0:16.5:1:32:0:0.48571:0:33:4:0.1333:0:4.5 0/0:24:0:0,0:12,12:0:2,0:13.2:1:26.8:1:1:0:35:11:1:0:4.2 -4 49644651 . G T 28 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.15385;SOR=0;LSEQ=GAGTGGAATGGAATAGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,6:0.125:2,2:6:0:28.5:1:1:1.1547:42.5:4:0.125:0:2.5 0/0:24:0:0,0:12,12:0:2,0:15.2:1:29.4:1:1:0:35:11:1:0:4.2 -4 49644661 . G T 45 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.06209;SOR=0;LSEQ=GAATAGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:1,2:11,8:0.1364:2,2:14:1:29:1:0.57143:2.62608:42:6:0.1364:0:3.3 0/0:32:0:0,0:16,16:0:2,0:20.5:1:29.8:1:1:0:33.9:15:1:0:3.7 -4 49644662 . A G 31 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.16143;SOR=0;LSEQ=AATAGAATGGAATGGAATGG;RSEQ=ATGGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,8:0.0909:2,2:15:1:31:1:1:1.23603:44:4:0.0909:0:3.5 0/0:32:0:0,0:16,16:0:2,0:21.3:1:28.7:1:1:0:33.9:31:1:0:3.7 -4 49644667 . A C 33 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.51111;SOR=Inf;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=ATGGAATGGAATGGAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:23.6:1:30.7:1:1:0:33.5:44:1:0:4.5 0/1:33:2:1,1:15,16:0.0606:2,2:36:0:33:1:1:1.06:27:4:0.0667:0:5 -4 49644669 . T C 72 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.24384;SOR=0.3471;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:2,3:10,7:0.2273:2,2:25:1:31.2:1:0.62406:2.06844:39.8:10:0.2273:0:3.8 0/1:33:3:2,1:13,16:0.0909:2,2:27.3:1:25:1:0.58871:2.39:43.3:2:0.0645:0:4.7 -4 49644670 . G C 32 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.51111;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:26:1:32:1:1:0:33.5:44:1:0:4.5 0/1:33:2:1,1:15,16:0.0606:2,2:33:0:32:1:1:1.06:27:4:0.0625:0:5 -4 49644674 . T C 48 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.26667;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATAGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:29.3:1:31:1:1:0:33.5:44:1:0:4.5 0/1:33:3:1,2:15,15:0.0909:2,2:31.7:1:30.3:1:1:1.9597:30.7:6:0.1034:0:3.7 -4 49644675 . GG TA 30 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=7.000;MSILEN=5;SSF=1;SOR=0.65049;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=AATGGAATAGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:42:0:30.3:1:1:1.21106:44:4:0.0909:0:6 0/1:33:2:1,1:15,16:0.0606:2,2:35:0:30.5:1:1:1.06:26:4:0.0645:0:4 -4 49644676 . G T 29 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.15556;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATAGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,8:0.0909:2,2:43.5:1:29.5:1:1:1.23603:21:4:0.1:0:4.5 0/0:33:0:0,0:14,14:0:2,0:28.9:1:31.1:1:1:0:35:56:0.9333:0:3.5 -4 49644677 . A T 83 NM4;MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.00488;SOR=0.07038;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=ATGGAATAGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:4,3:8,7:0.3182:2,2:28.3:1:29.7:1:1:1.16:33.1:14:0.3182:0:4.3 0/1:33:1:0,1:16,16:0.0303:2,0:30:0:28:0:1:0:60:2:0.0323:0:5 -4 49644678 . ATG CCC 32 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.15556;SOR=0;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=GAATAGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:46:0:32:1:1:1.21106:44:4:0.0909:0:4 0/0:33:0:0,0:15,16:0:2,0:30.8:1:29.6:1:1:0:34.3:30:0.9375:0:3.6 -4 49644679 . T C 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.04656;SOR=0.17245;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATAGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:3,3:6,4:0.2727:2,2:31.5:1:32.5:1:1:1.46198:31.3:12:0.3:0:4.8 0/1:34:2:1,1:10,12:0.0588:2,2:40.5:1:27.5:1:1:1.19:50:4:0.0588:0:5.5 -4 49644680 . G TAACCC 54 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=1.32669;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATAGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:6,4:0.0909:2,2:47.5:1:31:1:1:1.4491:21:4:0.1:0:4.5 0/1:34:4:2,2:10,12:0.1176:2,2:31.3:1:27.4:1:1:1.19:49.3:8:0.1176:0.0294:3.5 -4 49644683 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=5;SSF=0.51429;SOR=Inf;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=TAGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:35.4:1:30.9:1:1:0:33.5:44:1:0:4.2 0/1:34:2:1,1:15,17:0.0588:2,2:20:0:33.5:1:1:1.13:27:4:0.0667:0:5 -4 49644685 . A G 51 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.00888;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:12,9:0.0455:2,0:45:0:33:0:0.45455:0:22:2:0.0455:0:6 0/1:34:3:2,1:14,16:0.0882:2,2:27:1:32.7:1:0.60117:2.23:28.3:6:0.0968:0:5.3 -4 49644686 . G T 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51003;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATA;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:0:2,0:34.1:1:32.1:1:1:0:33:46:1:0:4.1 0/1:34:2:1,1:15,17:0.0588:2,2:32:0:29.5:1:1:1.13:32:4:0.0588:0:5 -4 49644709 . T C 101 v4;MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.02771;SOR=5.61173;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:10.5:1:32:1:1:1.21106:32:4:0.0909:0:3.5 0/1:30:11:6,5:8,11:0.3667:2,2:20.4:1:29.4:1:0.70652:1.62:35.5:22:0.3793:0:3.4 -4 49644727 . A T 25 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.51933;SOR=Inf;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=ATGGAATAGAATGAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:0:2,0:11.2:1:29.2:1:1:0:32.1:26:1:0:4.5 0/1:22:2:1,1:10,10:0.0909:2,2:30.5:1:25:1:1:1:40.5:4:0.1:0:5 -4 49644729 . T A 25 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.50202;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATAGAATGAAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,5:0:2,0:9.3:1:29.8:1:1:0:31.9:24:0.9231:0:4.3 0/1:19:2:1,1:9,8:0.1053:2,2:28.5:1:25:1:1:1.11803:40.5:4:0.1111:0:5 -4 49644735 . A G 27 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52689;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGAAATGGAAAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,1:0.2857:2,0:9:1:27:0:1:0:28:4:0.2857:0:5.5 0/1:6:1:1,0:1,4:0.1667:2,0:2:0:28:0:0.33333:0:27:2:0.1667:0:4 -4 49644741 . A G 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GAATGGAATGGAATAGAATG;RSEQ=AATGGAAAGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:17.7:1:27.3:1:1:0:24.7:6:1:0:3.3 1/0:4:3:1,2:0,1:0.75:0,2:17:1:29.3:1:1:0:39.3:6:0.75:0:4.7 -4 49644751 . G A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAATAGAATGAAATGGAAAG;RSEQ=AATGGAATGGAAACAACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28:1:28:1:1:0:35:4:1:0:2.5 1/0:3:2:1,1:0,1:0.6667:0,2:6.5:1:27:1:1:0:40.5:4:0.6667:0:5 -4 49645029 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGAATGGAATCCACCTGAT;RSEQ=GGAATGAAGTGGAATGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:2:0:30:0:1:0:48:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29.5:1:1:0:40:4:1:0:5.5 -4 49645038 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATCCACCTGATAGGAATGAA;RSEQ=TGGAATGTAATCCAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:11:0:33:0:1:0:48:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:31:1:29:1:1:0:40:4:1:0:5.5 -4 49645050 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAATGAAGTGGAATGTAAT;RSEQ=CAATGGAACGGAGTGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:23:0:33:0:1:0:48:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:31:1:30:1:1:0:40:4:1:0:5.5 -4 49645059 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGAATGTAATCCAATGGAA;RSEQ=GGAGTGGAATCAACTCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:32:0:33:0:1:0:48:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:25.5:1:28:1:1:0:40:4:1:0:5.5 -4 49645088 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=ATCAACTCGAGTGGAATGGA;RSEQ=TGGAAAGGAACGGAATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:32:1:1:0:54:4:1:0:3 0/0:1:0:0,0:0,1:0:0,0:11:0:31:0:1:0:40:2:1:0:6 -4 49645094 . A T 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAGTGGAATGGAATGGAA;RSEQ=GGAACGGAATCGAATCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:30:1:1:0:54:4:1:0:3 1/1:1:1:0,1:0,0:1:0,0:5:0:31:0:1:0:40:2:1:0:6 -4 49645121 . A T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATCCAATGGATTC;RSEQ=ACTGGAAAGCAATGCAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:28:1:1:0:54:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49645161 . G C 77 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.16667;SOR=Inf;LSEQ=AATTTAAATGGAATGGAATG;RSEQ=AATGGAATGGAATCATCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:5:0:33:0:1:0:60:2:1:0:3 1/1:5:5:3,2:0,0:1:0,2:6.2:1:33.4:1:1:0:28.2:10:1:0:2 -4 49645179 . CGAGT C 61 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATCATC;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:0,0:0.8:0,2:22.3:1:30.8:1:1:0:29.5:8:0.8:0:1.5 -4 49645551 . C A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCGAATGAAATTAAC;RSEQ=CTAGTGGAATAGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30:1:1:0:50:4:1:0:1.5 -4 49645676 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCAACCCGAGTGGAA;RSEQ=GCAATGGAAGGTAATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23:1:29:1:1:1:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49645707 . G T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTAATTGAATGGAATGGAAT;RSEQ=GAATGGAATCAACCCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49646684 . AG GA 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=CCCGAGTGCAATGGAATGGA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:0:32.8:1:1:0:45:4:1:0:4.5 0/0:4:0:0,0:1,1:0:2,0:26:0:31.5:1:1:0:46:4:0.5:0:6.5 -4 49646685 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGAGTGCAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:27:0:32.5:1:1:0:46:4:1:0:6.5 -4 49646689 . A C 33 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=GTGCAATGGAATGGAAGGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35:0:32:1:1:0:45:4:1:0:4.5 1/0:4:2:1,1:1,1:0.5:2,2:31:0:33:1:1:1:46:4:0.5:0:6.5 -4 49646698 . AA CG 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=AATGGAAGGGAATGGAATGG;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:42.5:1:31:1:1:0:45:4:1:0:4.5 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:31.3:1:1:1:46:4:0.5:0:5.5 -4 49646706 . G C 31 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.06667;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:31:1:1:0:45:4:1:0:4.5 0/0:4:0:0,0:2,2:0:2,0:34.5:1:31:1:1:0:33.5:8:1:0:4 -4 49646711 . G C 31 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.06667;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31:1:1:0:45:4:1:0:4.5 0/0:4:0:0,0:1,1:0:2,0:21.5:1:30.5:1:1:0:46:4:0.5:0:3.5 -4 49646718 . A G 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=ATGGAATGGAATGGAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22.5:1:30:1:1:0:45:4:1:0:4.5 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:30.5:1:1:1:46:4:0.5:0:5.5 -4 49646725 . T A 29 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATCAACCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:15.5:1:29.5:1:1:0:45:4:1:0:4.5 1/0:4:2:1,1:1,1:0.5:2,2:14.5:1:29.5:1:1:1:21:4:0.5:0:4.5 -4 49657894 . G A 45 d7;v4;NM4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAAAGGAACGAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:33.3:1:29:1:1:0:41.3:6:1:0:5.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49657897 . T A 47 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAAAGGAACGAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:36.3:1:30:1:1:0:41.3:6:1:0:5.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49657908 . G A 48 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAAAGGAAC;RSEQ=AAATGGAATCAACCCGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:38.7:1:30.3:1:1:0:41.3:6:1:0:5.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49657922 . C A 48 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAACGAAATGGAATCAAC;RSEQ=CGAGTGGAATGGAATGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24.7:1:30.7:1:1:0:41.3:6:1:0:5.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49658277 . A C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCGAATGGAAAGGAATGAAC;RSEQ=CGAAGGTTATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:29:1:1:0:60:4:1:0:1 -4 49658676 . T G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTGAGTGGAAAGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:33:1:1:0:33:4:1:0:2 -4 49659131 . G T 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=CGAGTGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:31.5:1:1:0:51.5:4:1:0:6 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 49659136 . G A 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:31:1:1:0:51.5:4:1:0:6 0/0:2:0:0,0:1,1:0:2,0:18.5:1:28:1:1:0:56.5:4:1:0:2.5 -4 49659149 . A G 22 d7;v4;MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.81007;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=TGGAATCAACCCCAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:34:0:32.5:1:1:1:51.5:4:0.6667:0:6 1/0:3:2:1,1:1,0:0.6667:0,2:31.5:1:22:1:1:0:56.5:1:0.5:0:2.5 -4 49659158 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AATGGAATGGAATGGAATCA;RSEQ=CCCCAGTGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:20:0:31:1:1:1:52.5:4:0.5:0:5.5 0/0:3:0:0,0:2,1:0:2,0:28.3:1:27.3:1:1:0:50.7:6:1:0:3.3 -4 49659179 . AT CC 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.13333;SOR=0;LSEQ=CCCCAGTGGAATGGAATGGA;RSEQ=GGAATGGAACGGAACATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:15.5:1:30:1:1:1:51.5:4:0.5:0:5 0/0:6:0:0,0:3,3:0:2,0:16.5:1:28.7:1:1:0:51.8:12:1:0:3.7 -4 49659185 . T A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAACGGAACATAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23.5:1:29.5:1:1:0:52:8:1:0:5 0/1:6:2:1,1:2,1:0.3333:2,2:33:1:31:1:1:1.7321:39:4:0.3333:0:6.5 -4 49659188 . A C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=ACGGAACATAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:20.5:1:21.3:1:1:0:52:1:1:0:5 0/1:6:2:1,1:2,2:0.3333:2,2:36:1:32:1:1:1:39:4:0.3333:0:6.5 -4 49659190 . C A 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAACATAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:5.5:1:29:1:1:1:51.5:4:0.5:0:5 0/1:5:1:1,0:2,2:0.2:2,0:1:0:23:0:1:0:53:2:0.2:0:3 -4 49659195 . C T 44 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TGGAATGGAATGGAACGGAA;RSEQ=ATAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:18:1:28.3:1:1:0:52:6:1:0:5.3 1/0:4:2:1,1:0,0:0.5:0,2:36.5:1:28.5:1:1:0:39:4:0.5:0:6.5 -4 49659221 . A C 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATCATCC;RSEQ=GAGTGGAATGGAATGGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:30:0:1:0:45:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:32:1:28.5:1:1:1:39:4:0.5:0:6.5 -4 49659227 . G A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATCATCCAGAGTG;RSEQ=AATGGAATGGTATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:26:1:27:1:1:1:39:4:0.5:0:6.5 -4 49659235 . T A 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCCAGAGTGGAATGGAA;RSEQ=GGTATGGAATGCAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:29:1:32:0:1:1:60:4:0.5:0:2 -4 49659464 . A T 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTGGAACGGAATGGAATGGA;RSEQ=TGCACCCAACTGGAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:1:31.5:1:1:0:40:4:1:0:4.5 -4 49659467 . C A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAACGGAATGGAATGGAATG;RSEQ=ACCCAACTGGAATGAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:1:31:0:1:0:40:4:1:0:4.5 -4 49659487 . C G 51 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCAACTGGAATGAAATG;RSEQ=AATGAAATGCAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:14.3:1:32.7:1:1:0:36.3:6:1:0:5 -4 49659492 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGGAATGAAATGCAATG;RSEQ=AATGCAATGGAATGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:10:0:32.5:1:1:0:40:4:0.6667:0:4.5 -4 49659504 . ATGCAGTGGAATCAACTCGAG A 83 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATGCAATGAAATGCAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:8:7:6,1:1,0:0.875:0,2:7:1:29.9:1:1:0:38.1:14:0.875:0.875:5.3 -4 49659537 . G A 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=1.4677;LSEQ=AACTCGAGTGGAATGGAATG;RSEQ=AATGGAATGGAACCGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:11.5:1:32:0:1:0:40:4:0.5:0:4.5 1/0:15:9:9,0:4,1:0.6:2,0:11.9:1:30.6:1:0.35714:0:35.4:18:0.6429:0:6.4 -4 49659544 . A T 81 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.2807;SOR=Inf;LSEQ=GTGGAATGGAATGGAATGGA;RSEQ=TGGAACCGAATCGAATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:19.3:1:31.8:1:1:0:45:8:1:0:3.8 0/1:17:6:6,0:8,2:0.3529:2,0:18.7:1:31.5:1:0.5:0:33.2:12:0.375:0:6.3 -4 49659549 . A T 114 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29187;SOR=3.2706;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=CCGAATCGAATCCAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:23.5:1:33:0:1:0:40:4:0.5:0:4.5 1/0:18:14:12,2:2,1:0.7778:2,2:19.9:1:30:1:0.46471:2.77:37.4:28:0.8235:0:6.2 -4 49659551 . C A 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54386;SOR=0.32848;LSEQ=GGAATGGAATGGAATGGAAC;RSEQ=GAATCGAATCCAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:0.5:0,2:27:0:32.5:1:1:0:50:4:0.5:0:3 0/1:17:4:4,0:1,0:0.2353:0,0:27:0:31.5:1:1:0:44.8:8:0.25:0:6 -4 49659556 . C G 127 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1929;SOR=3.38494;LSEQ=GGAATGGAATGGAACCGAAT;RSEQ=GAATCCAATGGAATCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:1,2:0.4286:2,0:21:1:33.3:1:0.4:0:46.7:6:0.4286:0:4 1/0:22:16:13,3:1,2:0.7273:2,2:22.7:1:31.8:1:0.1548:7.43:37.7:32:0.8:0:5.4 -4 49659564 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAACCGAATCGAATCCA;RSEQ=TGGAATCAACTGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,3:0:2,0:21.2:1:30.5:1:1:0:51.2:20:0.9091:0:3.9 0/1:28:2:1,1:17,8:0.0714:2,2:18:1:28:1:1:2.0616:41.5:4:0.0741:0:6.5 -4 49659600 . T A 97 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.00439;SOR=0.17608;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:5,4:7,8:0.3462:2,2:29.2:1:30.9:1:1:1.41:57.1:18:0.3462:0:4.4 0/1:60:5:3,2:28,24:0.0833:2,2:20.8:1:29.6:1:1:1.28:54:10:0.0877:0:5.4 -4 49659615 . T C 61 v4;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.62079;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGAATCCGGGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:10,12:0.0435:2,0:44:0:30:0:0.47826:0:34:2:0.0455:0:4 0/1:58:4:2,2:26,26:0.069:2,2:38:1:30.5:1:1:1:43.8:8:0.0702:0:5.8 -4 49659621 . G A 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43173;SOR=0.29521;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=AATCCGGGTGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:21:10,11:0,0:0.9545:0,2:34.8:1:29.4:1:1:0:52.9:42:0.9545:0:4 1/1:57:49:22,27:3,2:0.8596:2,2:29.7:1:29:1:0.65338:1.82015:49.9:98:0.8909:0:4.5 -4 49659624 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATGGAATGGAATGAA;RSEQ=CCGGGTGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:33.6:1:28.9:1:1:0:53:10:1:0:4.2 0/1:54:2:1,1:22,28:0.037:2,2:35:0:31:1:1:1.27:60:4:0.0408:0:3 -4 49659629 . G T 68 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31321;SOR=Inf;LSEQ=ATGGAATGGAATGAATCCGG;RSEQ=TGGAATGGAATGGAATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:29.3:1:31:1:1:0:53:21:1:0:4.2 0/1:53:5:3,2:20,27:0.0943:2,2:37.6:1:29.4:1:0.6443:2.00:47:10:0.098:0:5.4 -4 49659634 . A G 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.03333;SOR=6.08254;LSEQ=ATGGAATGAATCCGGGTGGA;RSEQ=TGGAATGGAATGTAATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:20:9,11:2,3:0.8:2,2:22.4:1:31.7:1:1:1.22:52.5:19:0.7917:0:4 1/1:52:50:22,28:1,1:0.9615:2,2:28:1:31.3:1:1:1.26678:50.6:24:0.96:0:4.4 -4 49659637 . G C 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54716;SOR=Inf;LSEQ=GAATGAATCCGGGTGGAATG;RSEQ=AATGGAATGTAATGGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:11,14:0:2,0:19.5:1:30.3:1:1:0:51.4:11.5:1:0:4 0/1:53:3:2,1:21,29:0.0566:2,2:23.7:1:30.3:1:0.57291:2.71:49.7:6:0.0566:0:5.7 -4 49659647 . T G 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.77205;LSEQ=GGGTGGAATGGAATGGAATG;RSEQ=AATGGAGTGGAATGGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:0,1:8,12:0.0476:2,0:17:0:33:0:1:0:55:2:0.05:0:8 0/1:54:2:0,2:24,28:0.037:2,0:15:1:29.5:1:0.49686:0:50:4:0.037:0:4.5 -4 49659651 . G A 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31287;SOR=Inf;LSEQ=GGAATGGAATGGAATGTAAT;RSEQ=GAGTGGAATGGATTGGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:8,13:0:2,0:10.1:1:31.5:1:1:0:50.8:42:1:0:4.2 0/1:53:5:3,2:20,28:0.0943:2,2:15.6:1:31.2:1:0.64206:2.07:47:10:0.098:0:5.4 -4 49659659 . A ATGTAATGGAATTTAG 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=ATGGAATGTAATGGAGTGGA;RSEQ=TGGATTGGATTGGAGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:3,4:2,5:0.5:2,2:11.9:1:29.1:1:1:1.79:58.7:14:0.5385:0.5:3.4 0/0:49:0:0,0:21,28:0:2,0:13.7:1:30.2:1:1:0:50:98:1:0.0204:4.4 -4 49659662 . G T 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65256;SOR=0.70684;LSEQ=GAATGTAATGGAGTGGAATG;RSEQ=ATTGGATTGGAGTGGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:0,5:0.2857:0,2:16.5:1:27.5:1:0.28571:0:34:4:0.2857:0:6 0/1:32:7:2,5:11,13:0.2188:2,2:38.6:1:29:1:0.66719:2.06667:46:14:0.2188:0:6.1 -4 49659664 . T A 135 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55309;SOR=0;LSEQ=ATGTAATGGAGTGGAATGGA;RSEQ=TGGATTGGAGTGGAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:14:1:32.3:1:1:0:46.3:8:1:0.25:6 1/0:31:22:10,12:1,0:0.7097:0,2:14.1:1:30.3:1:0.47826:0:49:44:0.7097:0.0323:5 -4 49659669 . T A 81 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=ATGGAGTGGAATGGATTGGA;RSEQ=TGGAGTGGAGTGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:32.5:1:1:0:42.5:4:1:0.5:6.5 0/1:15:7:2,5:1,2:0.4667:2,2:31.7:1:29.1:1:1:1.22183:43:14:0.7:0:6.6 -4 49659670 . T G 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAGTGGAATGGATTGGAT;RSEQ=GGAGTGGAGTGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:21.5:1:32:1:1:0:42.5:4:1:0.5:6.5 0/1:15:2:1,1:1,5:0.1333:2,2:30:0:30:1:0.46429:3.87:40.5:4:0.2:0:5.5 -4 49659671 . GG TT 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42647;SOR=0.27733;LSEQ=GGAGTGGAATGGATTGGATT;RSEQ=AGTGGAGTGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:35:0:30.5:0:1:0:34:2:0.5:0:7 0/1:15:3:0,3:2,2:0.2:2,0:33:1:29.3:1:0.42857:0:52.7:6:0.375:0:6.7 -4 49659674 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GTGGAATGGATTGGATTGGA;RSEQ=TGGAGTGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:17.5:1:33:1:1:0:42.5:4:1:0.5:6 0/1:15:2:1,1:1,5:0.1333:2,2:32:1:29.5:1:0.46429:3.87:40.5:4:0.25:0:5.5 -4 49659679 . G A 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.3125;SOR=0;LSEQ=ATGGATTGGATTGGAGTGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:28:0:33:0:1:0:34:2:1:0:7 0/1:15:4:0,4:2,6:0.2667:2,0:34.3:1:30.3:1:0.51515:0:49.5:8:0.3333:0:6.5 -4 49659682 . G A 44 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTGGATTGGAGTGGAGTG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:25:0:34:0:1:0:34:2:1:0:7 0/1:15:3:1,2:2,10:0.2:2,2:33:1:28.3:1:0.51648:2.33:40.3:6:0.2:0:5.7 -4 49659702 . G GAGTGTAATGC 28 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:5:0:33:0:1:0:34:2:1:0:7 0/1:13:2:1,1:2,9:0.1538:2,2:15.5:1:28.7:1:0.42308:3.87:40.5:4:0.1538:0.1538:5.5 -4 49659707 . G C 31 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATCAACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:12:2:1,1:1,8:0.1667:2,2:21:0:31:1:0.34545:6.00:47:4:0.1818:0:1 -4 49659727 . G GAGTTC 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATCAACCC;RSEQ=AATGGAATGGAGAGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:0,4:0.3333:0,2:28:0:31.5:1:0.33333:0:47:4:0.3333:0:1 -4 49659739 . G A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCAACCCGAATGGAATGGA;RSEQ=AGGAATGGAATGGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:0,2:1,1:0.4:2,0:20:1:30.5:1:1:0:33:4:0.4:0:7 -4 49659815 . GGGAAG T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACACGAATGGGATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:29.5:1:28.9:1:1:0:59:4:0.6667:0:4.5 -4 49659820 . G A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAATGGGATGGAAGGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:5:0:33:0:1:0:20:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29:1:1:0:50:4:1:0:4 -4 49659830 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGGAAGGGAAGGGAATGGAA;RSEQ=GGAATGGAATGGAATGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:15:0:32:0:1:0:20:2:1:0:3 0/1:5:2:1,1:1,2:0.4:2,2:43.5:1:29.5:1:1:1.73:59:4:0.4:0:5.5 -4 49659859 . A C 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGCTATGGAATCAA;RSEQ=CGGAGTGTAATGTAAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:34:0:32:0:1:0:20:2:1:0:3 1/0:5:3:0,3:0,0:0.6:0,0:28.7:1:28.7:1:1:0:51.3:6:0.6:0:2.7 -4 49659866 . G T 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCTATGGAATCAAACGGAGT;RSEQ=TAATGTAAATGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:27:0:32:0:1:0:20:2:1:0:3 0/1:5:2:0,2:1,2:0.4:2,0:33:0:28.5:1:1:0:47:4:0.4:0:2.5 -4 49659887 . C G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGTAAATGAATGGAATG;RSEQ=AATGGAATGGAATGCTACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:6:0:28:0:1:0:20:2:1:0:3 1/0:4:2:0,2:0,2:0.5:0,0:6:0:32.5:1:1:0:59:4:0.5:0:4 -4 54243905 . T C 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97851;LSEQ=GAGCTTTCTTCGTTCGTTCG;RSEQ=CGGCGGGTTCGCGCCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:32:29,3:29,4:0.4923:2,2:23.6:1:32.1:1:1:1.33:60:64:0.4923:0:1.2 0/1:76:37:33,4:31,8:0.4868:2,2:23.8:1:30.5:1:0.3483:2.11:60:17.5:0.4795:0:1.1 -4 54244003 . G A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14388;SOR=Inf;LSEQ=TTTAAGTTGCGCTCGGGGCG;RSEQ=CCATGTCGGCCGGCGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:169,103:0:2,0:25.6:1:31.5:1:1:0:60:135:1:0:0.2 0/1:378:4:3,1:222,151:0.0106:2,2:14:1:28.5:1:0.65088:2.04:60:8:0.0109:0:1.3 -4 54244130 . G A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30962;SOR=0.22745;LSEQ=TGTCTCTCGGGTTCTCTCAG;RSEQ=CCTCCCCTCTTGGCCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:101,170:0.0109:2,2:5:1:28.7:1:0.55851:3.35:60:6:0.0112:0:1 0/0:399:1:1,0:166,232:0.0025:2,0:1:0:23:0:0.41855:0:60:2:0.0025:0:1 -4 54244141 . T A 38 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.65647;SOR=0.50373;LSEQ=TTCTCTCAGGCCTCCCCTCT;RSEQ=GGCCCTCAAACGGCCGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:1,2:83,160:0.0122:2,2:19.7:1:24:1:1:1.03735:60:2:0.0082:0:1.7 0/0:324:2:2,0:127,195:0.0062:2,0:1:0:22:0:0.15778:0:60:4:0.0063:0:1 -4 54244144 . C A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13455;SOR=Inf;LSEQ=TCTCAGGCCTCCCCTCTTGG;RSEQ=CCTCAAACGGCCGGCGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:79,154:0:2,0:22.8:1:30.9:1:1:0:60:37.833:1:0:0.1 0/1:297:4:3,1:111,182:0.0135:2,2:14.8:1:27:1:0.15952:4.89:60:8:0.0138:0:1.8 -4 54244179 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50287;SOR=Inf;LSEQ=CGTCCCTGGCCTCTCGCGCC;RSEQ=CCGCTTCGGGCCTCTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:8,95:0:2,0:22.7:1:31.7:1:1:0:60:206:1:0:0.1 0/1:126:2:1,1:4,120:0.0159:1,2:19.5:1:28:1:0.0781:26.95:60:4:0.0163:0:1 -4 54244321 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTGGCGGCCGGGCCGGG;RSEQ=TGGGGGGCTGTGACCGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:29:1:1:0:60:4:1:0:1.5 -4 54245138 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24453;SOR=Inf;LSEQ=AATCTTCATTACCTCTTAAA;RSEQ=TTAAGCTTATTTTTATAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:64,5:0:2,0:21.2:1:30.8:1:1:0:60:138:1:0:0 0/1:68:2:1,1:63,3:0.0294:1,2:23:1:30:1:0.11501:18.32472:60:4:0.0294:0:1 -4 54245169 . A AT 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.30674;SOR=2.90641;LSEQ=TTTTATAGCAGTAAAGTCTG;RSEQ=TTTTTTTTTCCATAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:100,20:0.0164:2,0:16.5:1:32:0:1:0:60:4:0.0164:0:0 0/1:151:7:6,1:108,35:0.0464:2,2:35.6:1:30.6:1:1:1.94:60:14:0.0473:0:0.3 -4 54245372 . T A 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0147;SOR=0;LSEQ=TTGTTTGCTTATTTATTTAT;RSEQ=TGTTTATTTTACTTGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:5:2,3:202,222:0.0117:2,2:23:1:31.2:1:1:1.36389:60:10:0.0118:0:1 0/0:566:0:0,0:285,280:0:2,0:23.1:1:29.7:1:1:0:60:79.714:0.9982:0:0.1 -4 54245476 . A T 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTACACAGGTTGTGTGA;RSEQ=ACAATGGTTCTGTCAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:298:298:104,194:0,0:1:0,2:23.7:1:28.9:1:1:0:60:98.333:1:0:1.1 1/1:324:324:100,224:0,0:1:0,2:23.1:1:28.5:1:1:0:60:107:1:0:1.2 -4 54245499 . A G 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AATGGTTCTGTCAGTTGTCA;RSEQ=AATTATTTTCTTACAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:46,142:0:2,0:22.1:1:29.9:1:1:0:60:93:1:0:1 0/1:183:16:4,12:24,143:0.0874:2,2:20.8:1:30:1:0.27512:1.98:60:32:0.0909:0:1.9 -4 54245749 . T G 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGCTACTGATAAAAATA;RSEQ=TTTAACTTAATTGAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:22.3:1:34:0:1:0:60:6:0.5:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 54245775 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAATTGAAAATGTTTTTA;RSEQ=GTAAATCAGGAACACTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:28.5:1:32.5:1:1:0:60:4:0.3333:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 54248276 . C A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09943;SOR=3.76069;LSEQ=CAATGTTGAGTACTTGTCTT;RSEQ=TGCAAGTTACTAGAAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:10,0:12,0:0.4545:0,0:17.9:1:28.9:1:1:0:60:20:0.4545:0:1 1/0:17:13:13,0:4,0:0.7647:0,1:21.8:1:28.5:1:1:0:60:26:0.7647:0:1.1 -4 54248418 . A G 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCGAAAAGTAATGCCTGAC;RSEQ=TGTATACTTACTTTTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:200,108:0:2,0:24.9:1:30.3:1:1:0:60:101.667:1:0:0.1 0/1:409:79:50,29:198,132:0.1932:2,2:25.8:1:30.1:1:0.61079:1.15:60:78:0.1926:0:1.1 -4 54248698 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67919;SOR=0.6129;LSEQ=GAGGAAAAGAAATAGTAGAA;RSEQ=GACTGCAGAGGAAAATAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:1,7:0,8:0.5:0,2:12.4:1:30.9:1:1:0:60:16:0.5:0:1.1 0/1:8:3:0,3:0,5:0.375:0,0:12.3:1:31.3:1:1:0:60:6:0.375:0:1 -4 54249842 . G GA 108 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.25461;SOR=1.7143;LSEQ=CTGTCTCAAGACAGAAGAAA;RSEQ=AAAAAAAAAAACAGGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:10:10,0:52,0:0.1587:1,0:30.1:1:30:1:1:0:60:20:0.1695:0.0159:0.5 0/1:53:13:13,0:40,0:0.2453:1,1:22.2:1:29.3:1:1:0:60:26:0.2453:0.0566:0.1 -4 54249881 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22814;SOR=0;LSEQ=GTTACTTTTTTTAGTTATTA;RSEQ=TATTAGATGTTGAAATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:115,17:0.0149:2,2:11.5:1:28.5:1:0.25149:6.60263:60:4:0.0171:0:1 0/0:146:0:0,0:129,17:0:2,0:21:0:15:0:1:0:60:0:0:0:3 -4 54250092 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50827;SOR=Inf;LSEQ=GTGTAAATGCTATATAGTAA;RSEQ=GAGAGTGTGCCTATATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:19,126:0:2,0:22.9:1:31.2:1:1:0:60:290:1:0:0.1 0/1:192:2:1,1:33,156:0.0104:2,2:9:0:32:0:0.3251:4.67:60:4:0.0104:0:1 -4 54250189 . T G 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.02865;SOR=4.74712;LSEQ=TGTTAAAGTTTCATCATGAA;RSEQ=ATACTTCTTTGCTAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:0,7:0,16:0.3043:1,0:17.6:1:30.9:1:1:0:60:14:0.3043:0:1 1/0:19:13:1,12:0,6:0.6842:0,1:27.5:1:31.5:1:1:0:60:26:0.6842:0:1.1 -4 54250332 . T C 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCTGTAATCCCAGGACT;RSEQ=TGGGAGGCCGAGGCGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:30.5:1:32:1:1:2.45:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:0:0,0:14:0:32:0:1:0:60:2:1:0:0 -4 54255950 . G GT 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.09181;LSEQ=AGCTTTTCAGGATAATTTCT;RSEQ=TTTTTTTTTGTTTGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:11:8,3:167,53:0.0476:2,2:18.4:1:28.8:1:0.73041:1.18068:60:22:0.0482:0:0.5 0/1:367:19:15,4:250,93:0.0518:2,2:22.6:1:29.2:1:0.79065:1.39:60:18:0.0501:0.0109:0.1 -4 54256108 . CT C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.84967;SOR=0.88912;LSEQ=TCTTAAATAGGTCTTAATAG;RSEQ=TTTTTTTTTAGTCGGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:14:3,11:38,150:0.069:2,2:33.7:1:31.4:1:1:1.08:60:28:0.0711:0.0049:0.5 0/1:259:16:3,13:55,185:0.0618:2,2:30.1:1:31.1:1:1:1.28708:60:15:0.06:0:0.4 -4 54256167 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00036;SOR=0.18539;LSEQ=TCAGGCTGGAGTACAGTGGC;RSEQ=CAATCTTAGTTCACTGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:27:0,27:2,35:0.4219:2,1:20.4:1:30.2:1:0.50446:0:60:54:0.4219:0:1.2 0/1:51:6:0,6:1,44:0.1176:1,0:28.7:1:31.7:1:1:0:60:12:0.1176:0:1.2 -4 54256478 . C A 84 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02301;SOR=11.64655;LSEQ=GACTGGTAAAGTTTTTCTGG;RSEQ=AAGAGTCCAGTAGCACGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:6,1:0.2222:2,2:25.5:1:32.5:1:0.41667:4.58262:60:4:0.2222:0:1 1/1:10:8:8,0:2,0:0.8:0,0:17.3:1:28.3:1:1:0:60:16:0.8:0:1.3 -4 54256824 . C A 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22473;SOR=4.33966;LSEQ=ATTGTGGATTATATTAATTT;RSEQ=AATATTTTCAGTGTGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:1:1,0:98,248:0.0029:2,0:1:0:24:0:0.2853:0:60:2:0.0029:0:1 0/1:403:5:4,1:122,276:0.0124:2,2:10.6:1:26.8:1:0.03492:9.00:60:10:0.0125:0:1 -4 54256853 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.21837;SOR=Inf;LSEQ=CAGTGTGAAGTCATCAGAAA;RSEQ=TTTTTTGAACATCAATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:31,193:0:2,0:23.2:1:30.5:1:1:0:60:111:1:0:0 0/1:197:2:1,1:26,169:0.0102:2,2:23:1:28:1:0.25593:6.40:60:4:0.0103:0.0051:0.5 -4 54257034 . A T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAATAATTTGATCAAAAATG;RSEQ=TATAGTCTTTTTGCCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:25,6:0,0:1:0,2:23.2:1:30.5:1:1:0:60:62:1:0:1 1/1:19:19:17,2:0,0:1:0,2:26.8:1:30.1:1:1:0:60:38:1:0:1 -4 54257131 . A T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24846;LSEQ=ATTTTTGATGCTGCATAAAA;RSEQ=TAGAGCTGAAATATTTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:143:81:73,8:54,8:0.5664:2,2:26.4:1:30.9:1:0.60133:1.35:60:26:0.5612:0:1.1 0/1:172:42:34,8:106,24:0.2442:2,2:24.5:1:29.8:1:1:1.03898:60:84:0.2471:0:1 -4 54257507 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50298;SOR=0;LSEQ=TGATGTTCTTACTTTCAAAT;RSEQ=ACAGACTAGCCACAGCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:115,21:0.0145:2,2:12:1:27.5:1:0.2944:5.37359:60:4:0.0146:0:1 0/0:113:0:0,0:97,16:0:2,0:33:0:12:0:1:0:60:0:0:0:1 -4 54257719 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=Inf;LSEQ=ATTTTTTGTTCTTGAGTCTG;RSEQ=TCCCATGCCACTACTCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:25,157:0:2,0:25.7:1:32.4:1:1:0:60:181:1:0:0 0/1:187:3:2,1:36,147:0.016:2,2:19.3:1:27.7:1:0.10659:8.04:60:6:0.0163:0:1 -4 54265667 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=AGTTTATTCGGCTTCTAAGT;RSEQ=TTATTAATGTGAACTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:31.3:1:29:1:1:0:60:6:0.375:0:1 0/0:5:0:0,0:5,0:0:0,0:16.4:1:32.4:1:1:0:60:10:1:0:0 -4 54265883 . CT C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.55166;SOR=1.16553;LSEQ=AAATTCAACAAGCTAATAAC;RSEQ=TTTTTTTTTAAGGTACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:34:19,15:350,167:0.0612:2,2:23.4:1:30.9:1:0.18721:1.65301:60:68:0.0623:0.0126:0.3 0/1:581:41:26,15:334,206:0.0706:2,2:23:1:31.5:1:1:1.07:60:82:0.0723:0.0155:0.3 -4 54265894 . A T 83 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03529;SOR=3.81892;LSEQ=GCTAATAACCTTTTTTTTTT;RSEQ=AGGTACAGCAGGGAAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:649:3:0,3:418,227:0.0046:2,0:24.3:1:21.7:1:0.04434:0:60:2:0.0032:0:1.3 0/1:688:12:4,8:398,278:0.0174:2,2:10.5:1:23.2:1:0.08436:2.85892:60:11:0.0164:0:1.4 -4 54280705 . GA G 161 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.77223;SOR=1.13199;LSEQ=CTTTAGAAAAAGCATGTCAA;RSEQ=AAAAAAAAAAAACAGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:30:29,1:74,3:0.2632:1,1:24.8:1:32.2:1:1:1.17:60:60:0.2679:0.0351:0.7 0/1:125:36:30,6:77,9:0.288:2,2:25.6:1:31.3:1:0.37182:1.70294:60:72:0.2927:0.04:0.8 -4 54281075 . C T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.27101;LSEQ=CCCAGCACTTGTCTTGCTAC;RSEQ=CATCTTTCTGGCTGTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:0,7:1,8:0.4375:2,0:32.1:1:29.9:1:1:0:60:14:0.4375:0:1.1 1/0:6:3:0,3:0,3:0.5:0,0:16:1:30.3:1:1:0:60:6:0.5:0:1 -4 54281140 . A AT 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTAATGGATGCTCAGTA;RSEQ=TTTTTTTTTTCGTTCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:35:1:30.5:1:1:0:60:4:0.2857:0:0.5 0/0:1:0:0,0:0,1:0:0,0:50:0:29:0:1:0:60:2:1:0:0 -4 54292133 . G GTTAATCTCCTGTAACATAAAAATTGAATCAATTCAGT 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12988;SOR=Inf;LSEQ=ATGAGAACAGCAACATACAG;RSEQ=TTTAGTATTTTAAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:92,174:0:2,0:25:1:31.1:1:1:0:60:43.333:1:0:0.1 0/1:319:4:1,3:117,197:0.0125:2,2:16.3:1:27.2:1:1:1.77878:60:8:0.0127:0.0125:0.8 -4 54292164 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23687;SOR=0;LSEQ=TAAAATAAATAATTTTCTTT;RSEQ=ACTGAAGGATGATATCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:39,115:0.0128:2,2:38:1:30.5:1:0.4483:2.92:60:4:0.0132:0:1 0/0:164:0:0,0:41,123:0:2,0:21.5:1:28.9:1:1:0:59.9:53.667:1:0:0.1 -4 55124831 . A C 88 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06837;SOR=6.95138;LSEQ=TTGACTAAAATGATGCTGTT;RSEQ=ATATTTTCTGTTGTGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:1,0:228,21:0.004:2,0:26:0:15:0:1:0:60:0:0:0:2 0/1:258:7:6,1:220,29:0.0271:2,2:24.1:1:31.6:1:0.5867:1.26311:60:14:0.0276:0:1 -4 55125058 . A T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00124;SOR=1.97366;LSEQ=GCTTTGTGCTGCATGGGTTT;RSEQ=TTACCAGTACTCTGCATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:42:7,35:53,308:0.1042:2,2:22.5:1:30.4:1:0.65397:1.16:60:41:0.1038:0:1.1 0/1:396:74:14,60:76,245:0.1869:2,2:23.3:1:29.6:1:0.44356:1.32855:60:73:0.1862:0:1.1 -4 55129831 . C T 238 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CTTCATTCTTTTTTAAACCA;RSEQ=AGACCCAGATGTAGCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:258:172,86:240,130:0.4102:2,2:24.3:1:29.8:1:0.6699:1.08:60:257:0.4105:0:1.1 0/0:686:0:0,0:412,274:0:2,0:24.8:1:31.2:1:1:0:60:227.667:1:0:0.1 -4 55130078 . T C 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.95051;LSEQ=TTCCAGACCATCCCATTTAA;RSEQ=GTTTATGCTTTAAAAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:584:65:26,39:188,331:0.1113:2,2:22.6:1:30.3:1:0.58586:1.17:60:130:0.1138:0:1.3 0/1:663:179:75,104:202,280:0.27:2,2:25.5:1:30.3:1:1:1.00039:60:178:0.2726:0:1.3 -4 55130125 . T A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12108;SOR=0;LSEQ=CATCTCCTTCCTTCTTTAAA;RSEQ=AAGAGTAACAGGCAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:66,213:0.0106:2,2:16.3:1:22:1:0.14538:6.40:60:2:0.0078:0:2 0/0:287:0:0,0:81,206:0:2,0:24.2:1:27.4:1:1:0:60:22.917:1:0:0.5 -4 55130147 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21811;SOR=Inf;LSEQ=AGAGTAACAGGCAAAATCAT;RSEQ=AGGTGCGTGTAGGATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:23,175:0:2,0:20.1:1:29.3:1:1:0:59.8:13.143:1:0:0.6 0/1:174:2:1,1:22,150:0.0115:2,2:18:0:33.5:1:0.24756:6.69:60:4:0.0117:0:1 -4 55130154 . G A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05422;SOR=1.79652;LSEQ=CAGGCAAAATCATAAGGTGC;RSEQ=TGTAGGATTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:22:1,21:14,123:0.1375:2,1:16.7:1:31.2:1:0.69589:2.3803:60:44:0.1538:0:1.7 0/1:148:33:3,30:11,103:0.223:2,2:20.3:1:28.4:1:1:1.06749:60:7.25:0.2148:0:1.6 -4 55130177 . A T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.78153;LSEQ=TAGGATTTTTTTTTTTTTTT;RSEQ=AATCATCATCACTGGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:3:0,3:4,92:0.0303:1,0:7:1:27.7:1:1:0:60:6:0.0309:0:1.7 0/1:84:2:1,1:4,78:0.0238:1,2:2:1:19:1:0.11618:17.55:60:1:0.0127:0:1.5 -4 55131118 . C T 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGATCTAGAAATGGAAGCT;RSEQ=TTAAAACCGTGTATAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:723:0:0,0:400,323:0:2,0:25.4:1:31.6:1:1:0:60:119.5:1:0:0.1 0/1:942:49:25,24:496,397:0.052:2,2:21.3:1:29.2:1:0.55759:1.19916:60:48:0.0518:0:1.1 -4 55133252 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10086;SOR=4.74956;LSEQ=GTTTTAGGTTTACAGCAAAA;RSEQ=TGAGAGGTACAGAGATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:3,0:30,0:0.0909:1,0:39.3:1:34:0:1:0:60:6:0.0938:0:1.3 0/1:9:3:3,0:6,0:0.3333:0,0:25.7:1:31.7:1:1:0:60:6:0.3333:0:1 -4 55133383 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24796;SOR=Inf;LSEQ=ACATCCATATCATCCAGAGT;RSEQ=CATAGTTTATCTTAGAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:159,25:0:2,0:23.3:1:30.9:1:1:0:60:35.8:1:0:0 0/1:183:2:1,1:151,30:0.0109:2,2:12.5:1:28:1:0.31087:4.96799:60:4:0.011:0:1 -4 55133400 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24901;SOR=Inf;LSEQ=AGTCCATAGTTTATCTTAGA;RSEQ=TTCACTCCTAGGAGCGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:193,54:0:2,0:24.4:1:32:1:1:0:60:60.75:1:0:0.1 0/1:260:3:1,2:193,64:0.0115:2,2:12.3:1:26.7:1:0.15951:5.97987:60:6:0.0117:0:1 -4 55133726 . T G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.26232;LSEQ=CTTCCCTGTACAGAGAAAGG;RSEQ=TTCATTGAAATCAAACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:784:93:52,41:372,317:0.1186:2,2:26.2:1:31.2:1:0.74086:1.08:60:92:0.1195:0:1.1 0/1:788:184:99,85:321,281:0.2335:2,2:26.2:1:31.1:1:0.93284:1.02:60:91:0.2342:0:1.2 -4 55133936 . C T 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=3.4929;LSEQ=AACTCTCTGCCCAAGTATGC;RSEQ=TTTTTTTAGTGTGCATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:31:11,20:111,187:0.0942:2,2:24.2:1:30.2:1:1:1.07901:60:62:0.0954:0:1.6 0/1:401:107:38,69:106,187:0.2668:2,2:24.4:1:30.1:1:1:1.0292:60:52.5:0.2665:0:1.6 -4 55133959 . C T 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.53917;LSEQ=TTTTTAGTGTGCATCAGAGG;RSEQ=GGACTGAGGTTTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:22:6,16:67,148:0.0924:2,2:27.8:1:28:1:0.81183:1.20631:60:10:0.087:0:1.9 0/1:226:60:18,42:49,117:0.2655:2,2:20.7:1:29.6:1:1:1.02:60:120:0.2667:0:2 -4 55133980 . CT C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50753;SOR=0;LSEQ=GGACTGAGGTTTGTGTGTGT;RSEQ=TACAACCCAGACCCAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:35,135:0.0116:2,2:12.5:1:27.5:1:0.37576:3.82:60:4:0.0116:0:1 0/0:131:0:0,0:24,107:0:2,0:19.9:1:29.7:1:1:0:60:130:1:0:0.5 -4 55134183 . G T 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03846;SOR=Inf;LSEQ=TCAGCTAGGGTGGAAGAAAG;RSEQ=AAGTAAAATTGGACTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:0:0,0:30.3:1:29.8:1:1:0:60:9:1:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:27.5:1:29.5:1:1:0:60:4:1:0:1 -4 55134231 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGATTGAATATATTCCCT;RSEQ=ATGTTCATCATCCATATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:15:1:33.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55138521 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37446;SOR=3.77758;LSEQ=TAGTCTCATATGTTCTGGGA;RSEQ=ACGAGCTATTCCATTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:1:0,1:230,103:0.003:2,0:1:0:24:0:0.31138:0:60:2:0.003:0:1 0/1:356:4:2,2:242,110:0.0112:2,2:19:1:23.5:1:0.59296:2.19466:60:3:0.0085:0:2.8 -4 55138785 . G C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10413;SOR=0;LSEQ=TACTTATTGACTATAAGATA;RSEQ=GGTTTTGGGTGTGATAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:0,3:1,29:0.0909:1,0:20.3:1:32:0:1:0:60:6:0.0909:0:1 0/0:36:0:0,0:2,33:0:2,0:21.1:1:30.2:1:1:0:60:70:0.9722:0:0.1 -4 55139624 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50148;SOR=0;LSEQ=AAGGTCCCAACTCCTTGCCA;RSEQ=CTTAGAGTGTTCCCGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:123,3:0.0156:1,2:21.5:1:27.5:1:0.06176:35.64812:60:4:0.0159:0:1 0/0:108:0:0,0:104,4:0:1,0:23.5:1:30:1:1:0:60:216:1:0:0.1 -4 55139691 . T C 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00939;SOR=Inf;LSEQ=TTGGCCCTATACTTAGGCCC;RSEQ=TTTTCTCTCTAGATGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:279,135:0:2,0:24.4:1:30.8:1:1:0:60:206:0.9976:0:0.1 0/1:498:8:4,4:308,182:0.0161:2,2:16.4:1:27.8:1:0.47924:1.69036:60:7:0.0142:0:1 -4 55139771 . T C 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.68572;LSEQ=ACATCATCACGGAGATCCAC;RSEQ=CCCGAGACAGGAGTACCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:732:78:40,38:326,328:0.1066:2,2:25.2:1:31:1:0.90473:1.06:60:25:0.1056:0:1.2 0/1:851:260:135,125:291,300:0.3055:2,2:22.5:1:30:1:0.50315:1.11:60:51:0.3047:0:1.2 -4 55139944 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2379;SOR=0;LSEQ=TCATCAGCTGAGCCGCATCT;RSEQ=CCCCAGGCGGAACTTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:14,94:0.0182:2,2:35:1:28.5:1:0.25521:6.52:60:4:0.0187:0:1.5 0/0:115:0:0,0:19,96:0:2,0:21.5:1:32.2:1:1:0:60:114:1:0:0.5 -4 55139978 . T C 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGAATCCCAGATAGGGGT;RSEQ=ATATAGAAATGAAGGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:3,53:0,0:1:0,2:23.9:1:32.5:1:1:0:60:55:1:0:2.1 1/1:44:44:1,43:0,0:1:0,1:22.8:1:32.3:1:1:0:60:88:1:0:1.5 -4 55140016 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15104;SOR=0.32935;LSEQ=CCAAGGCAGAAATTCAGTTA;RSEQ=GAATGCTCTTAAAGTCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:2,27:0,4:0.8788:0,2:30.6:1:30.6:1:1:0:60:58:0.9063:0:2.7 1/0:20:14:0,14:0,6:0.7:0,1:25.5:1:30.1:1:1:0:60:28:0.7:0:2.4 -4 55140031 . T G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTATGAATGCTCTTAAAG;RSEQ=CATGTGGGACTTTGTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:1,25:0,0:1:0,1:26.7:1:30.8:1:1:0:60:7.667:1:0:2.8 1/1:14:14:0,14:0,0:1:0,1:26.4:1:32.6:1:1:0:60:28:1:0:2.4 -4 55140912 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17761;SOR=Inf;LSEQ=CATGTGGAGTGAACGTTGTT;RSEQ=GACTCTACTGTGTCCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:135,62:0:2,0:22.9:1:31.4:1:1:0:60:31.833:1:0:0.1 0/1:144:2:2,0:92,50:0.0139:2,0:22.5:1:32:0:0.54351:0:60:4:0.014:0:1 -4 55141055 . A G 281 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36424;SOR=2.02498;LSEQ=GTCATTGAATCAATCAGCCC;RSEQ=GATGGACATGAATATATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:641:634:317,317:1,0:0.9891:0,2:24.3:1:30.4:1:1:0:60:104.667:0.9921:0:1.1 1/1:738:734:371,363:3,1:0.9946:2,2:24.6:1:29.6:1:0.62412:2.93163:60:65.727:0.9945:0:1.2 -4 55141293 . G A 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39651;SOR=2.60624;LSEQ=AATACATTTCTGTCTTGACA;RSEQ=TAAGTTAATTGGATCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:0,3:0,26:0.1034:1,0:38:1:27:1:1:0:60:2:0.0769:0:2.7 0/1:17:4:0,4:0,13:0.2353:1,0:29.5:1:30.8:1:1:0:60:8:0.2353:0:1 -4 55143286 . G A 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCACGGAGCTGGTAGACAGC;RSEQ=CGCTCACACCAGGGAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:19.7:1:31.7:1:1:0:60:6:0.75:0:1 1/1:3:3:3,0:0,0:1:0,0:28:1:31.7:1:1:0:60:6:1:0:1 -4 55143321 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=AGGGCTGCACCCTCCTTTCT;RSEQ=CCGTCTGTGTTTTCTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:8.5:1:31:0:1:0:60:4:0.1818:0:1 0/0:6:0:0,0:6,0:0:0,0:20.2:1:31.8:1:1:0:60:12:1:0:0.3 -4 55143577 . G A 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.82682;LSEQ=CGGGTCTTGGGGTCTGGAGC;RSEQ=TTTGGGAAGGTGGTTGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:750:84:44,40:337,328:0.112:2,2:25.8:1:30.2:1:0.81723:1.07:60:41:0.1104:0:1.1 0/1:966:254:123,131:361,351:0.2629:2,2:25.5:1:29.6:1:0.55904:1.09528:60:126:0.2639:0:1.2 -4 55143693 . G A 97 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02153;SOR=8.41955;LSEQ=CCTGGGGATTTTTTGAGCAC;RSEQ=GGGATTTTTTGAGCATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:0,1:35,165:0.005:2,0:34:0:29:0:1:0:60:2:0.0051:0:4 0/1:222:9:3,6:45,168:0.0405:2,2:24:1:30.9:1:0.41028:1.86:60:18:0.0413:0:1 -4 55143986 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21642;SOR=Inf;LSEQ=ATATCCAATCACAGGATTAG;RSEQ=CATATTCTTGGTTTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:170,26:0:2,0:21.8:1:29.8:1:1:0:60:195:1:0:0 0/1:171:2:1,1:144,25:0.0117:2,2:8.5:1:29.5:1:0.28173:5.66778:60:4:0.0119:0:1 -4 55144420 . A G 184 LongAT STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00511;SOR=0.30861;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=CTTTTTTGGTATCTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:61:57,4:9,0:0.8472:0,2:15.9:1:31.1:1:1:0:59.3:11.2:0.8615:0:2.7 1/0:62:39:36,3:20,0:0.629:1,2:17.1:1:30.5:1:0.54413:0:59.1:12:0.6923:0:2.8 -4 55144429 . G T 25 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22752;SOR=Inf;LSEQ=AAAAAAAAAAAACTTTTTTG;RSEQ=TATCTTATTTTTTTCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:104,4:0:1,0:17.2:1:30.8:1:1:0:59.6:20.6:1:0:2 0/1:99:2:1,1:90,6:0.0202:2,2:14.5:1:25:0:0.13844:13.96517:50:4:0.023:0:4 -4 55144447 . T C 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45102;SOR=2.35467;LSEQ=TGGTATCTTATTTTTTTCTG;RSEQ=GCCATATGGTCTGCAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:201:196:177,19:1,1:0.9751:2,2:22:1:30.9:1:0.19228:9.11:59.9:13:0.9785:0:1.5 1/1:187:185:147,38:0,0:0.9893:0,2:19.7:1:30.8:1:1:0:59.7:15.818:0.9886:0:1.5 -4 55144448 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23839;SOR=Inf;LSEQ=GGTATCTTATTTTTTTCTGT;RSEQ=CCATATGGTCTGCAGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:181,22:0:2,0:21.9:1:27.9:1:1:0:59.9:7.458:1:0:1.5 0/1:198:2:1,1:153,41:0.0101:2,2:23:1:26.5:1:0.38352:3.6993:60:4:0.011:0:2 -4 55146072 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTTTTATAGCTGAGTTA;RSEQ=ATATATATATATATATATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:7:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55146389 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00391;SOR=3.98279;LSEQ=CCAGTTAGCTCCCATGCCTA;RSEQ=CTCAGTACCTGGCACATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:9:9,0:63,0:0.125:1,0:18.3:1:31.7:1:1:0:59.4:18:0.125:0:1.1 0/1:41:15:15,0:26,0:0.3659:1,1:22:1:31.2:1:1:0:60:30:0.3659:0:1.1 -4 55146406 . T TTGTAGGTCCCCCAG 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.3158;LSEQ=CTACCTCAGTACCTGGCACA;RSEQ=AATCATCATCTACTGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:128:126:112,14:1,0:0.9844:0,2:21.6:1:31.1:1:1:0:59.8:252:0.9844:0.4844:0.2 1/1:84:83:76,7:1,0:0.9881:0,2:21.6:1:30.5:1:1:0:59.6:166:0.9881:0.4405:0.3 -4 55146754 . C A 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=3.15981;LSEQ=GGGATGGTAAGTGAACCTGG;RSEQ=AGCCCACGTGGTCTCTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:16:3,13:18,152:0.086:2,2:26.4:1:31.1:1:0.3982:1.94:60:32:0.0879:0:1 0/1:161:37:7,30:19,105:0.2298:2,2:22.5:1:28.8:1:0.61476:1.29:60:17.5:0.2229:0:1.1 -4 55146921 . ATT A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=GGTGTGTTCCTGCAGTAAAC;RSEQ=TTTTAAAAAAAATAATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:5.3:1:31.2:1:1:0:60:6:0.375:0.25:0.3 0/0:4:0:0,0:0,4:0:0,0:10.5:1:30.8:1:1:0:60:8:1:0:0.5 -4 55146926 . TT AA 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=GTTCCTGCAGTAAACATTTT;RSEQ=AAAAAAAATAATTATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,1:0.6:0,0:42:1:31:1:1:0:60:6:0.75:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:14.5:1:30.3:1:1:0:60:4:0.6667:0.3333:0.5 -4 55151711 . C A 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12263;SOR=Inf;LSEQ=TTCAGTGAGTGGAGTGTGGA;RSEQ=GGAGATGCTAGGAGATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:313:310:51,259:0,0:0.9904:0,2:24.4:1:31:1:1:0:60:50.667:0.9935:0:1.1 1/1:316:316:66,250:0,0:1:0,2:22.5:1:30.7:1:1:0:60:62.2:1:0:1.1 -4 55151934 . G T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63484;SOR=0.42673;LSEQ=CCAAGTGCCACCATGGATCA;RSEQ=CCAGTCTTGCAGGGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:2,1:162,36:0.0149:2,2:17.7:1:29:1:0.45866:2.23871:60:6:0.0151:0:1 0/0:156:1:0,1:127,28:0.0064:2,0:1:0:23:0:0.1859:0:60:2:0.0065:0:1 -4 55151958 . T TA 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23198;LSEQ=GTCTTGCAGGGGTGATGCTA;RSEQ=TCAGCTACAGATGGCTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:265:191,74:24,8:0.8923:2,2:24.7:1:28.7:1:0.83594:1.16172:60:52:0.8966:0.1751:0.1 1/0:242:159:116,43:58,22:0.657:2,2:26.4:1:28.3:1:1:1.02:60:52:0.661:0.0496:0.2 -4 55152040 . C T 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.87735;LSEQ=GATCTGGCTGCTCGCAACGT;RSEQ=CTCCTGGCACAAGGAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:712:88:46,42:335,289:0.1236:2,2:27:1:29.5:1:0.82021:1.05826:60:28.333:0.1216:0:1.2 0/1:741:214:106,108:284,241:0.2888:2,2:23.4:1:28.9:1:0.29099:1.20035:60:34.667:0.2869:0:1.2 -4 55152199 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20633;SOR=Inf;LSEQ=ATCTCTAAAGTCAGGTGTTG;RSEQ=TTCTAGAGATTCGGTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:14,150:0:2,0:22.9:1:32:1:1:0:59.9:53.667:1:0:0.1 0/1:137:2:1,1:18,117:0.0146:2,2:25.5:1:28:1:0.25902:6.35:60:4:0.0146:0:1 -4 55152284 . T G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05158;SOR=0;LSEQ=TGGCAGCAGATTGCCCAGGT;RSEQ=TGAGTGCCAGCTCCACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:0,32:0,0:1:0,1:24.2:1:32.5:1:1:0:60:31:1:0:1.3 1/1:20:17:0,17:0,3:0.85:0,1:23.8:1:31.5:1:1:0:60:34:0.85:0:1.6 -4 55153837 . A G 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCCAGTATGCTGCAGCC;RSEQ=CCTCAAACCACATGTTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:66:0,66:0,0:1:0,1:25.3:1:32.4:1:1:0:60:132:1:0:1.1 1/1:52:52:2,50:0,0:1:0,1:24.7:1:31.3:1:1:0:60:25:1:0:1.3 -4 55153921 . T C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTTGGGGGTTGCGTCT;RSEQ=ACTCCTGGCCTCTGCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:1:0,1:20.7:1:31.5:1:1:0:60:38:1:0:1.5 1/1:4:4:0,4:0,0:1:0,0:12:1:33:1:1:0:60:8:1:0:1.8 -4 55154527 . C G 58 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCACAATGGATCATCCCC;RSEQ=AGTGGCTTAATGGAGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:0.8:0,2:36:1:29.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55154891 . T C 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.1276;LSEQ=TCTGAAAGGTTTTCTAACAG;RSEQ=GTTCTATCATGCCAAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:63:46,17:318,126:0.1238:2,2:23.4:1:31.8:1:0.88195:1.07:60:126:0.126:0:1.1 0/1:519:120:73,47:285,114:0.2312:2,2:21.6:1:31.1:1:0.03246:1.60808:60:240:0.2348:0:1.1 -4 55155498 . A G 85 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCTTTCATCTTATATGT;RSEQ=CAGTACCTGTAAGCACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:22.3:1:33:1:1:0:60:12:1:0:1 1/1:3:3:0,3:0,0:1:0,0:23.7:1:32.7:1:1:0:60:6:1:0:1.7 -4 55155693 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTGGTTTTTTGTGGAAT;RSEQ=GGAAGCATTGTTCAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:11:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55156091 . T G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCTTTTCACATCCAATGT;RSEQ=AGACCTCTCCAATGTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55156300 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTCTTTACCATTGGTGGCCC;RSEQ=TTCTTCATGTTCTATGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:24:1:30:1:1:0:60:6:0.1429:0:1.7 0/1:14:2:2,0:12,0:0.1429:0,0:20.5:1:32.5:1:1:0:60:4:0.1429:0:1.5 -4 55156380 . G A 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATCTTCCAGGTAGTTTGGA;RSEQ=ATATGTACAGTTAAATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:76,6:0,0:1:0,2:17.3:1:29.7:1:1:0:60:26.333:1:0:2 1/1:70:70:63,7:0,0:1:0,2:21.7:1:29.7:1:1:0:60:69:1:0:1.8 -4 55156400 . A G 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.14033;LSEQ=GATATGTACAGTTAAATAAT;RSEQ=GTAAGTTCTGAGTGTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:123:119:103,16:3,1:0.9675:2,2:21.7:1:32.2:1:0.45282:2.13:60:238:0.9675:0:1.7 1/1:108:87:76,11:16,5:0.8056:2,2:22.6:1:31.4:1:0.30091:2.14:60:86:0.8037:0:1.6 -4 55156699 . C G 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTCCCTGAGGAGGAGGAC;RSEQ=TGGGCAAGAGGAACAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:112,235:0:2,0:24.3:1:31.3:1:1:0:59.9:48.571:1:0:0.1 0/1:338:21:5,16:115,202:0.0621:2,2:23.3:1:30.2:1:0.34698:1.81884:60:20:0.0612:0:1.2 -4 55156715 . G C 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24989;SOR=0;LSEQ=GGACCTGGGCAAGAGGAACA;RSEQ=ACACAGGTAGCTGTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:1,2:87,211:0.01:2,2:21:1:24.3:1:1:1.21:60:2:0.0068:0:2.3 0/0:278:0:0,0:97,181:0:2,0:25.5:1:31.1:1:1:0:60:38.714:1:0:0.3 -4 55161254 . C T 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00168;SOR=0.39258;LSEQ=AGTCTAGGTCTAGTTCTGTG;RSEQ=AGGAGTTGTAATATTTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:199:157,42:16,3:0.9128:2,2:23.7:1:29.4:1:0.77026:1.42459:60:98.5:0.9163:0:1.1 1/1:199:160:118,42:28,11:0.804:2,2:21.1:1:28.9:1:0.84081:1.10:60:159:0.803:0:1.1 -4 55161391 . T C 292 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.47139;SOR=0.49661;LSEQ=GAAGACATCGACATGATGGA;RSEQ=GACATCGGCATAGACTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:666:664:329,335:0,2:0.997:0,2:24.7:1:30.5:1:0.49932:0:60:59.364:0.9969:0:1.1 1/1:829:824:434,390:0,2:0.994:0,2:23.9:1:30.2:1:0.22492:0:60:136.333:0.9939:0:1.2 -4 55161516 . CA TG 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03112;SOR=0;LSEQ=AAAACCACTTTATTGCAATG;RSEQ=GAGGTTGAGAGGAGGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:6:2,4:31,174:0.0284:2,2:18.7:1:28.3:1:0.23736:2.79:60:12:0.0288:0.0047:0.8 0/0:192:0:0,0:32,160:0:2,0:21.2:1:30:1:1:0:60:95:1:0:1.1 -4 55161517 . A G 231 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06239;SOR=Inf;LSEQ=AAACCACTTTATTGCAATGC;RSEQ=GAGGTTGAGAGGAGGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:203:198:28,170:0,0:0.9754:0,2:24.1:1:30.4:1:1:0:60:38.6:1:0:1.1 1/1:184:184:30,154:0,0:1:0,2:21.6:1:29.8:1:1:0:60:35.8:1:0:1.1 -4 55523938 . G A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTCCTCCTCCCGGCGGGCAC;RSEQ=GCCCCCCGGCATTAACACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:3:0:30:0:1:0:60:2:0.3333:0:1 1/1:3:3:2,1:0,0:1:0,2:42.3:1:31.3:1:1:0:60:6:1:0:1.3 -4 55524252 . G A 139 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=26.03687;LSEQ=GCTTCGCGTCCAGACAGGTG;RSEQ=GACACCGCGGCTGGCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:809:1:1,0:387,419:0.0012:2,0:1:0:25:0:0.48079:0:60:2:0.0013:0:1 0/1:864:27:12,15:376,458:0.0313:2,2:26:1:29.4:1:1:1.02617:60:54:0.0317:0:1.2 -4 55524304 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=28.49818;LSEQ=TACTCGGCGAAGCCTGTGCC;RSEQ=GGGAGGGTGGTACCCGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:40:14,26:106,279:0.0941:2,2:23:1:29.9:1:0.35648:1.42:60:39:0.0938:0:1.1 1/0:378:283:78,205:29,65:0.7487:2,2:22.5:1:29.6:1:0.59761:1.17206:60:282:0.752:0:1.1 -4 55524328 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17196;SOR=Inf;LSEQ=AGGGTGGTACCCGCCAGGGT;RSEQ=CATCCGGAGAGAGGACTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:52,231:0:2,0:23.6:1:31.7:1:1:0:60:39.429:1:0:0.2 0/1:201:2:1,1:30,169:0.01:2,2:14.5:1:29:1:0.28532:5.56:60:4:0.0101:0:2 -4 55524399 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAGACTCCAGGTGGCCC;RSEQ=CGGACTCTCCGGCGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:1,74:0.026:1,0:7.5:1:31:1:1:0:60:4:0.027:0:1 0/0:32:0:0,0:2,30:0:2,0:19.3:1:28.3:1:1:0:60:9.667:1:0:0.4 -4 55525153 . A G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTGCGTTCCCTGACTCC;RSEQ=ACCGCCTAGCACGCCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:31.5:1:1:0:60:4:1:0:1 -4 55561637 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10403;SOR=Inf;LSEQ=AAGTGCTTTATTTCGCCAAG;RSEQ=AAGAAGATCATACTCAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:176,56:0:2,0:25:1:31.1:1:1:0:60:45.4:1:0:0.1 0/1:207:3:1,2:143,61:0.0145:2,2:15.3:1:27.7:1:0.22029:4.64908:60:6:0.0147:0:1 -4 55561966 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25038;SOR=Inf;LSEQ=AGGTAAATGCTTGGCTTTCT;RSEQ=CAGTGCTGTGCTTTCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:63,188:0:2,0:24:1:32:1:1:0:60:82.667:0.992:0:0.1 0/1:279:3:1,2:77,199:0.0108:2,2:31.3:1:29.7:1:1:1.29:60:6:0.0108:0:1 -4 55562002 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21944;SOR=Inf;LSEQ=AAGAATTTAATATCCTGCTC;RSEQ=TAATTTTGGATGACATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:21,118:0:2,0:24.3:1:30.5:1:1:0:60:138:1:0:0 0/1:123:2:1,1:20,101:0.0163:2,2:28.5:1:32:0:0.31347:4.95:60:4:0.0165:0:1 -4 55564184 . A G 67 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTATGAAATGGCAATAAT;RSEQ=ATAGTACTGATCATGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:28:1:33.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55566075 . A G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01033;SOR=Inf;LSEQ=GGAGAGTGTTGGGATTGCAT;RSEQ=TTTCCCCCTTTCATACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:0:1,0:23.4:1:31:1:1:0:60:96:1:0:0.1 0/1:24:4:0,4:0,20:0.1667:1,0:23.5:1:31.8:1:1:0:60:8:0.1739:0:1 -4 55569859 . A AT 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.96159;LSEQ=TAAATTATATGGTAATCTTC;RSEQ=TTTTTTTTTCTCCTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:10:9,1:148,24:0.0549:2,2:24:1:31.9:1:1:1.46:60:20:0.0556:0.0165:0.7 0/1:170:9:7,2:131,30:0.0529:2,2:21.8:1:29.3:1:0.67777:1.2459:60:8:0.0479:0.0176:0.1 -4 55569877 . C T 33 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62354;SOR=0.33812;LSEQ=TCATTTTTTTTTCTCCTTTT;RSEQ=TGAAACCAGCAGACTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:3:1,2:194,51:0.0121:2,2:6.7:1:21.3:1:0.11632:7.52349:60:2:0.0083:0:3 0/0:243:1:0,1:183,59:0.0041:2,0:1:0:22:0:0.24691:0:60:2:0.0042:0:1 -4 55569887 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2489;SOR=Inf;LSEQ=TTCTCCTTTTCTGAAACCAG;RSEQ=AGACTAAACTACAGGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:215,75:0:2,0:25.2:1:31.7:1:1:0:60:40.429:1:0:0.1 0/1:299:3:1,2:214,80:0.01:2,2:15.3:1:26:1:0.18568:5.31434:60:6:0.0102:0:1 -4 55572872 . C T 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTATTAAACATTAGGGCTC;RSEQ=CTTGTTTTCCCTTAATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:31.8:1:30.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55572970 . T A 46 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAATTCTTTTAACCTAA;RSEQ=AAACATCAAGACTAGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:15.3:1:29.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:31:0:26:0:1:0:60:2:1:0:1 -4 55573177 . G T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0.57538;LSEQ=ATACTGGAAATCAACCAATT;RSEQ=TTTTTGTAATTCCAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:118,6:0.0159:1,2:21:1:28.5:1:0.10844:18.27967:60:4:0.016:0:1 0/0:109:1:0,1:99,9:0.0092:2,0:1:0:29:0:0.09174:0:60:2:0.0094:0:1 -4 55573495 . CT C 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51271;SOR=0;LSEQ=GGGGGATTACACATTACCCC;RSEQ=TTTCCAGTGGGCTTATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:13,143:0.0127:2,2:14.5:1:26:1:0.16988:10.64:60:4:0.013:0.0063:0 0/0:112:0:0,0:11,101:0:2,0:22.8:1:30:1:1:0:60:55:1:0:0.1 -4 55575274 . C G 86 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGGGAGGAAGTGGTATG;RSEQ=GGACAGCCCAGGGTGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:1:0,2:23.8:1:28.9:1:1:0:60:7:1:0:1.9 1/1:2:2:1,1:0,0:1:0,2:4.5:1:27:1:1:0:60:4:1:0:0.5 -4 55575506 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50288;SOR=0;LSEQ=ATTTTTCCTCAAACAGGCAT;RSEQ=GATTTCCAGGTAGAAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:175,18:0.0103:2,2:29:1:28.5:1:0.18583:9.48992:60:4:0.0103:0:1 0/0:162:0:0,0:145,17:0:2,0:22:1:29:1:1:0:60:324:1:0:0.1 -4 55589945 . A AT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.50144;SOR=0;LSEQ=AATTTCAAATATGTTTTCTG;RSEQ=TTTTTTTTAAAAAAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:0,2:8,137:0.0136:2,0:32:1:31:1:1:0:60:4:0.014:0:0 0/0:125:0:0,0:7,118:0:2,0:25.1:1:29.8:1:1:0:60:24:1:0:0.2 -4 55589953 . TA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.50149;SOR=0;LSEQ=ATATGTTTTCTGATTTTTTT;RSEQ=AAAAAGCTTTGTTTTGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:0,2:1,116:0.0168:1,0:22.5:1:30.5:1:1:0:60:4:0.0172:0.0084:0.5 0/0:100:0:0,0:3,97:0:1,0:25.8:1:30.4:1:1:0:60:99:1:0:0.1 -4 55589977 . G GT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.18724;SOR=Inf;LSEQ=AAAGCTTTGTTTTGATTATT;RSEQ=TTTTTTTTCTAGCCATGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:0,78:0:1,0:22.9:1:32.1:1:1:0:60:77:1:0:0.2 0/1:60:2:0,2:0,58:0.0333:1,0:9.5:1:31.5:1:1:0:60:4:0.0351:0.0167:0 -4 55592325 . T C 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01785;SOR=Inf;LSEQ=ATGTCATTTCTGGTAATACA;RSEQ=GCATCACACCATACTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:2,70:0:1,0:24.1:1:30.5:1:1:0:60:71:1:0:0.3 0/1:43:4:0,4:2,37:0.093:2,0:17.5:1:28:1:1:0:60:8:0.093:0:1 -4 55593464 . A C 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GCATGATGTGCATTATTGTG;RSEQ=TGATTCTGACCTACAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:993:0:0,0:457,536:0:2,0:24.5:1:30.2:1:1:0:60:61.063:1:0:0.1 0/1:1012:52:26,26:443,517:0.0514:2,2:24.8:1:31.6:1:0.66887:1.17:60:104:0.0521:0:1.2 -4 55593481 . A G 184 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=61.85533;LSEQ=GTGATGATTCTGACCTACAA;RSEQ=TATTTACAGGTAACCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:885:1:1,0:383,501:0.0011:2,0:36:0:13:0:0.4339:0:60:0:0:0:1 0/1:855:56:25,31:359,440:0.0655:2,2:24.6:1:31.7:1:1:1.01171:60:55:0.0651:0:1.2 -4 55593865 . G A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00171;SOR=Inf;LSEQ=GGTTTGCCATAGAGAACATC;RSEQ=TAGGAAAATGTCTCTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:77,21:0:2,0:25.1:1:30.3:1:1:0:60:48:1:0:0.2 0/1:69:7:5,2:53,9:0.1014:2,2:20.3:1:31.4:1:0.30864:2.31958:60:14:0.1029:0:1 -4 55593909 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23657;SOR=Inf;LSEQ=TTGTTTTTAATTCCTTTATT;RSEQ=ATTTTGAAACTGCACAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:170,28:0:2,0:23.4:1:31.9:1:1:0:60:48.5:1:0:0.1 0/1:188:2:1,1:150,36:0.0106:2,2:15.5:1:28:1:0.35573:4.12365:60:4:0.0109:0:1 -4 55593921 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1183;SOR=Inf;LSEQ=CCTTTATTGATTTTGAAACT;RSEQ=CACAAATGGTCCTTCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:200,51:0:2,0:23.2:1:31.7:1:1:0:60:40.833:0.9959:0:0.1 0/1:244:3:1,2:187,54:0.0123:2,2:17.3:1:27.7:1:0.13266:6.85441:60:6:0.0126:0:1 -4 55594325 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12371;SOR=Inf;LSEQ=CTGCCTTTTATTGTCTGTCA;RSEQ=GTTATCAAAACATGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:61,230:0:2,0:22.9:1:30.9:1:1:0:60:47.5:1:0:0.1 0/1:290:3:2,1:87,199:0.0103:2,2:13.3:1:28:1:0.22525:4.55:60:6:0.0104:0:1 -4 55595418 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18255;SOR=Inf;LSEQ=AGCTGAATATTAATGGCCAT;RSEQ=ACCACCCTTGGGTATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:172,15:0:2,0:23.3:1:32.2:1:1:0:60:92.5:1:0:0.1 0/1:140:2:1,1:124,14:0.0143:2,2:24:1:29:1:0.20349:8.58908:60:4:0.0144:0:1 -4 55595429 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57099;SOR=2.87928;LSEQ=AATGGCCATGACCACCCTTG;RSEQ=GTATTTTTATGGGAGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:0,1:212,42:0.0039:2,0:1:0:25:0:0.16863:0:60:2:0.004:0:1 0/1:178:2:1,1:147,29:0.0112:2,2:5.5:1:27:1:0.30946:5.00084:60:4:0.0114:0:1 -4 55595681 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=ATTTACATAAATAGTTAGCT;RSEQ=TTGACAGGCAGTTCATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:27,146:0.0114:2,2:28.5:1:28:1:0.29517:5.33:60:4:0.0117:0:1 0/0:144:0:0,0:27,117:0:2,0:24.9:1:30.9:1:1:0:60:47:1:0:0.1 -4 55597645 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05845;SOR=Inf;LSEQ=AGAGAGTATGTATATCATGC;RSEQ=AATGTGGAATATAACATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:56,242:0:2,0:21:1:28.8:1:1:0:60:73.5:1:0:0.1 0/1:190:3:2,1:38,149:0.0158:2,2:11:1:21:1:0.11276:7.73:60:2:0.0106:0:1.7 -4 55597969 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24928;SOR=0;LSEQ=CCAGCCTTTGGTATGTCATT;RSEQ=CCACTGTCTTTTCCTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:3:2,1:215,18:0.0127:2,2:16.7:1:25.7:1:0.22347:5.88395:60:6:0.0129:0:1 0/0:220:0:0,0:196,24:0:2,0:20.7:1:31.5:1:1:0:60:54:1:0:0.1 -4 55598449 . G T 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60467;SOR=2.23905;LSEQ=GAAATTCTTTTAAAACTTTT;RSEQ=GCTTTTAGGATATAGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:0,1:9,202:0.0047:1,0:26:0:14:0:1:0:60:0:0:0:1 0/1:191:2:0,2:7,182:0.0105:1,0:22:0:32:0:1:0:60:4:0.0107:0:1 -4 55599129 . T A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0819;SOR=Inf;LSEQ=ATACTTTAAAACAAAAGTAT;RSEQ=GGATTTTTTATAATATAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:56,0:0:1,0:26.1:1:30.5:1:1:0:60:112:1:0:0 0/1:44:3:3,0:41,0:0.0682:1,0:33.7:1:27.7:1:1:0:60:6:0.0714:0:2 -4 55599159 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50924;SOR=0;LSEQ=ATAATATAAGCAACACTATA;RSEQ=TATTAAAAAGTTAGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:111,3:0.0171:1,2:30.5:1:32:0:0.06807:32.17955:60:4:0.0172:0:1 0/0:86:0:0,0:50,6:0:2,0:26.8:1:31.3:1:1:0:59.8:27:0.6429:0:0.1 -4 55599268 . C T 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GACTTGGCAGCCAGAAATAT;RSEQ=CTCCTTACTCATGGTCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:0:0,0:329,258:0:2,0:26.6:1:31:1:1:0:60:82.857:1:0:0.1 0/1:586:17:10,7:315,254:0.029:2,2:23:1:26.9:1:0.81043:1.15:60:7.5:0.0262:0:1.3 -4 55599431 . T C 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.63352;LSEQ=TTTCGATAAAAATTGTTTCC;RSEQ=GTGATTTTCATAATGTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:14,133:0.0133:2,2:22.5:1:29.5:1:0.19182:9.21:60:4:0.0135:0:2 0/0:118:1:0,1:16,101:0.0085:2,0:44:0:30:0:1:0:60:2:0.0085:0:1 -4 55599436 . T C 227 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAAAAATTGTTTCCTGTGA;RSEQ=TTTCATAATGTAAATCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:127:11,116:0,0:1:0,2:24.1:1:32.5:1:1:0:60:254:1:0:1.1 0/1:97:47:7,40:4,46:0.4845:2,2:22.9:1:32.1:1:0.34711:2.00:60:94:0.4845:0:1 -4 55602765 . G C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26633;LSEQ=GGGATTTTTCTTTGGGAGCT;RSEQ=TTCTCTTTAGGTAAAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:208:84,124:184,235:0.3307:2,2:25.6:1:31.9:1:0.44051:1.15556:60:68.333:0.328:0:1.1 0/1:680:79:39,40:270,331:0.1162:2,2:23.6:1:30.6:1:0.47279:1.19:60:25.333:0.1126:0:1.1 -4 55603022 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23881;SOR=0;LSEQ=TTTTTCCTTTAGGTCACGTT;RSEQ=TCCCTTTTATTTTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:35,147:0.0109:2,2:10.5:1:28.5:1:0.35388:4.16:60:4:0.011:0:1 0/0:192:0:0,0:32,160:0:2,0:20.9:1:30.2:1:1:0:60:191:1:0:0.1 -4 55603271 . TG T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66865;SOR=1.71332;LSEQ=GGAATTATTACTGAAGTTGC;RSEQ=GATGCCCATACATTTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:2:1,1:212,43:0.0078:2,2:22:1:30:1:0.31366:4.88546:60:4:0.0078:0:0 0/1:226:3:1,2:171,50:0.0133:2,2:18:1:31.8:1:0.13536:6.76402:60:6:0.0134:0.0044:0.3 -4 55603365 . G A 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0019;SOR=Inf;LSEQ=GACATAATGAAGACTTGCTG;RSEQ=GATGCAGATCCCCTAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:855:0:0,0:453,401:0:2,0:25.1:1:30.9:1:1:0:60:121:0.9988:0:0.1 0/1:863:10:5,5:445,407:0.0116:2,2:19.2:1:27:1:1:1.09325:60:9:0.0106:0:1.1 -4 55603649 . T C 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55309;SOR=0;LSEQ=TGTTCTGAGCCAAAGAAGGA;RSEQ=GTGAGATTGAGGGGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:0,4:0,22:0.1538:1,0:23:1:30.3:1:1:0:60:8:0.16:0:1 0/0:9:0:0,0:0,9:0:0,0:21.8:1:31.4:1:1:0:60:18:1:0:0 -4 55604872 . C T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01916;SOR=Inf;LSEQ=TCTGAGCACACTTTAGTGGC;RSEQ=GATGATTTTTGTCATCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:0:1,0:25.7:1:29.4:1:1:0:60:29:1:0:0.2 0/1:12:3:0,3:0,9:0.25:0,0:19:1:30.3:1:1:0:60:6:0.25:0:1 -4 55943950 . G A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGGATGGGTGTGTGGG;RSEQ=GGTGGGTGTGTGTGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:12:1:27.5:1:1:0:60:4:1:0:1 -4 55946081 . A G 273 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21022;SOR=2.53043;LSEQ=GCACCTCTCATGTGATGTCC;RSEQ=GGAGTTGGGGGTGTGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:558:551:370,181:0,0:0.9875:0,2:25.4:1:30:1:1:0:60:109.2:0.9909:0:1.1 1/1:601:598:388,210:0,0:0.995:0,2:25.1:1:29.6:1:1:0:60:98.667:0.9966:0:1.2 -4 55946354 . G T 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGAAGAAATGGCAAACAAA;RSEQ=GAGTTGGCAGAGAGAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:49,161:0:2,0:22:1:30.8:1:1:0:60:51.5:1:0:0.1 0/1:185:15:4,11:42,128:0.0811:2,2:18.6:1:28.3:1:1:1.11:60:30:0.0815:0:1.1 -4 55946366 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.58304;SOR=2.5874;LSEQ=CAAACAAAGGAGTTGGCAGA;RSEQ=AGAAGACAATTCTTTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:0,1:30,140:0.0058:2,0:34:0:11:0:1:0:60:0:0:0:4 0/1:133:2:1,1:22,109:0.015:2,2:22:1:30:1:0.31704:4.87:60:4:0.0152:0:1 -4 55948108 . A G 295 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGAAATTTGTCTTTTTAAT;RSEQ=TGGCTGAGTCTTACCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:609:609:381,228:0,0:1:0,2:24.3:1:31.9:1:1:0:60:86:1:0:1.1 1/1:577:577:346,231:0,0:1:0,2:24.8:1:31.2:1:1:0:60:95.167:1:0:1.1 -4 55948850 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5057;SOR=0;LSEQ=AGTGGTGGTATATTTGACTG;RSEQ=AGATCGGCTACCTAAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:18,136:0.0128:2,2:14.5:1:28:1:0.22945:7.38:60:4:0.0128:0:1 0/0:122:0:0,0:12,110:0:2,0:20.6:1:31.1:1:1:0:60:39.667:1:0:0.1 -4 55953330 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTAATTCCGGACACAGA;RSEQ=CCATGGCTTTCTGTATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55953380 . A G 35 d7;v4;q23;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAAGCATGTTCTCATGC;RSEQ=AGCACAGAACTCTTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:35.3:1:22.7:1:1:0:60:2:0.6667:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55953737 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0989;SOR=5.97669;LSEQ=TCCCGAGATGGCCTTGAAGT;RSEQ=ACCCTCCCCCGGGGGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:1:0,1:340,139:0.0021:2,0:1:0:23:0:0.29167:0:60:2:0.0021:0:1 0/1:405:5:2,3:271,128:0.0123:2,2:14.6:1:25.2:1:0.33457:3.16574:60:10:0.0126:0:1.2 -4 55953969 . T C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1961;SOR=Inf;LSEQ=TGTTGTTATGGCTTCAGTTC;RSEQ=TCAAGTGCCTTTTCATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:36,175:0:2,0:23:1:30.5:1:1:0:60:210:0.9953:0:0.1 0/1:169:2:1,1:22,145:0.0118:2,2:11:0:29:1:0.25437:6.47:60:4:0.012:0:1 -4 55954971 . C A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08754;SOR=Inf;LSEQ=TAGCCATGAGACAGTTCAGG;RSEQ=AGTAGGAAAGTCCTTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:238,50:0:2,0:24.1:1:31.7:1:1:0:60:35:1:0:0.1 0/1:231:3:2,1:181,47:0.013:2,2:29.3:1:23.3:1:0.50452:1.91899:60:2:0.0088:0:1 -4 55955232 . T C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6376;SOR=0.83473;LSEQ=AGTACACATTTGTAAAGAGC;RSEQ=GACGAGGTGAGATGCTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:85:10,75:1,28:0.7456:1,2:24.3:1:29.5:1:0.28474:3.70:60:27.333:0.7387:0:1.2 1/0:93:66:2,64:0,27:0.7097:1,1:20.5:1:29.7:1:1:0:60:132:0.7097:0:1 -4 55955737 . A AT 211 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.09951;LSEQ=TCCTCATCACCTATGTATCT;RSEQ=TTTTTTTTTTCAAAGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:223:118:54,64:33,65:0.5291:2,2:27.5:1:30.8:1:0.09427:1.66:60:117:0.5318:0.0628:0.2 0/1:120:12:4,8:45,60:0.1:2,2:25.6:1:30:1:0.7588:1.49497:60:24:0.1008:0:0.8 -4 55955760 . G T 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25864;SOR=4.03351;LSEQ=TTTTTTTTCAAAGCTTCCGA;RSEQ=AAGTTTTGCCTGATAGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:1:0,1:143,96:0.0041:2,0:19:0:11:0:0.40417:0:60:0:0:0:4 0/1:121:2:2,0:75,43:0.0165:2,0:23:0:30.5:1:0.53627:0:60:4:0.0174:0:1 -4 55956225 . C T 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATAAGAGGATATTTCGTGC;RSEQ=GCCAGGTCCCTGTGGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:0:0,0:323,407:0:2,0:24.8:1:30.2:1:1:0:60:90.25:0.9972:0:0.1 0/1:724:24:7,17:291,409:0.0331:2,2:26.5:1:29.7:1:0.29262:1.72668:60:48:0.0334:0:1.2 -4 55956320 . CA C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.77293;SOR=0.74453;LSEQ=TCTGTTGTGACCTCATGCAT;RSEQ=AAAAAAAATCCCACATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:9:0,9:8,156:0.052:1,0:33.9:1:33.7:1:1:0:60:18:0.0526:0:0.1 0/1:102:4:0,4:4,94:0.0392:1,0:21:1:32.3:1:1:0:55:8:0.0396:0.0098:1 -4 55961159 . T C 233 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACAAACAAACTCCTTGAA;RSEQ=ACAAAATGAGTCTTTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:79,287:0:2,0:22.9:1:28.6:1:1:0:60:51.286:1:0:0.1 0/1:376:180:51,129:54,142:0.4787:2,2:24.6:1:31.2:1:0.9086:1.04:60:44:0.4757:0:1.1 -4 55961665 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19764;SOR=Inf;LSEQ=AAGTTCTTCACAAAATTTCA;RSEQ=CTAAAAAACTAACCTGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:220,23:0:2,0:24.2:1:30.2:1:1:0:60:120.5:1:0:0.1 0/1:195:2:1,1:168,25:0.0103:2,2:21:1:27.5:1:0.24948:6.60909:60:4:0.0103:0:2 -4 55961890 . G A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=ACTCATATTCCTCACTAAGC;RSEQ=TTTAATATAGTGATGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:25,199:0:2,0:25.3:1:32:1:1:0:60:448:1:0:0 0/1:183:11:2,9:27,145:0.0601:2,2:25.7:1:30.9:1:0.68701:1.19:60:22:0.0601:0:1.1 -4 55961944 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15071;SOR=Inf;LSEQ=AAGAAGGCTACAACCTTTCA;RSEQ=TGGGACAGGAGTGTAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:1,77:0:1,0:24.2:1:30.5:1:1:0:60:156:1:0:0.1 0/1:50:2:0,2:0,48:0.04:1,0:25:1:31.5:1:1:0:60:4:0.04:0:1 -4 55962165 . AC TT 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05878;SOR=0;LSEQ=CTTCTCTGGACATCTGTTAC;RSEQ=AAGTAACAAACTGTATCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:10,2:10,2:0.5:2,2:18.8:1:29.2:1:1:1:60:24:0.5:0.0417:1.1 0/0:5:0:0,0:5,0:0:0,0:22.4:1:30.6:1:1:0:60:10:1:0:0.2 -4 55962358 . T C 117 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00059;SOR=14.5344;LSEQ=AACACTATCAGAGAGGCATG;RSEQ=TAAAATTGGGTGACCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:1:1,0:383,197:0.0017:2,0:9:0:34:0:1:0:60:2:0.0017:0:1 0/1:532:13:8,5:326,193:0.0244:2,2:20.2:1:31.8:1:1:1.05559:60:26:0.0246:0:1.2 -4 55962545 . T TG 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGAGGGAAATCATAGGTA;RSEQ=GGACATTTCCTTCAATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:66,238:0:2,0:23.7:1:30.2:1:1:0:60:100.333:1:0:0.1 0/1:237:75:17,58:40,122:0.3165:2,2:25.6:1:30.5:1:0.87033:1.11812:60:36.5:0.3133:0.0338:0.1 -4 55962556 . T A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27321;SOR=0;LSEQ=TCATAGGTATGGACATTTCC;RSEQ=TCAATAATTGGGGTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:2,1:46,204:0.0119:2,2:10.7:1:26.7:1:0.09318:8.76:60:6:0.012:0:1 0/0:175:0:0,0:28,147:0:2,0:20.9:1:30.1:1:1:0:60:174:1:0:0.1 -4 55962570 . TC T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53381;SOR=0;LSEQ=ATTTCCTTCAATAATTGGGG;RSEQ=CCTCCCTCCCTGCATGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:22,164:0.0106:2,2:20:1:30.6:1:0.23029:7.31:60:4:0.0109:0.0053:0 0/0:109:0:0,0:10,98:0:2,0:21.1:1:30.9:1:1:0:60:53:1:0:0.1 -4 55962574 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53805;SOR=0;LSEQ=CCTTCAATAATTGGGGTCCC;RSEQ=CCCTCCCTGCATGCCACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:19,161:0.011:2,2:25:1:27.5:1:0.20824:8.28:60:4:0.0112:0:1 0/0:102:0:0,0:7,95:0:2,0:20.8:1:29:1:1:0:60:24.5:1:0:0.1 -4 55964101 . T C 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTAATAACTCCCCCTTCAC;RSEQ=CTCCAAATGTCCTGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:19,29:0:2,0:23.4:1:29.9:1:1:0:60:15:1:0:0.1 1/0:22:11:8,3:6,5:0.5:2,2:20.8:1:29.5:1:0.65944:2.14:60:22:0.5:0:1.1 -4 55964158 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18789;SOR=Inf;LSEQ=CCTACCTCTAAGTGGCTATA;RSEQ=GAATGATTATACAAATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:56,10:0:2,0:22.8:1:31.3:1:1:0:60:132:1:0:0 0/1:51:2:1,1:46,3:0.0392:2,2:21:1:32:1:0.15216:13.42263:60:4:0.0392:0:1 -4 55964219 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17087;SOR=Inf;LSEQ=AAACCAGAATCCAACATCTG;RSEQ=ATACACCACATTTGTCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:223,36:0:2,0:23.6:1:30.3:1:1:0:60:258:1:0:0 0/1:183:2:1,1:161,20:0.0109:2,2:27:1:27.5:1:0.2169:7.88009:60:4:0.0112:0:1 -4 55964502 . T A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=TGGCTGTTGTTTTGTGTGCT;RSEQ=GTTATTGCTGTTTATTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:42,220:0:2,0:22.7:1:30:1:1:0:60:86.333:1:0:0.1 0/1:271:3:2,1:54,214:0.0111:2,2:7:1:25.7:1:0.10938:7.84:60:6:0.0112:0:1.3 -4 55964504 . T A 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11907;SOR=0;LSEQ=GCTGTTGTTTTGTGTGCTTG;RSEQ=TATTGCTGTTTATTGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:36,207:0.0122:2,2:7.7:1:26.3:1:0.0631:11.31:60:6:0.0123:0:1 0/0:253:0:0,0:46,207:0:2,0:22.3:1:29.8:1:1:0:60:506:1:0:0.2 -4 55964565 . A G 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AATAAAACTCATGGAGTTTG;RSEQ=GAGTGGTCCTATTATAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:12,94:0:2,0:23.4:1:31.7:1:1:0:60:212:1:0:0.2 0/1:60:24:1,23:1,35:0.4:1,1:18.3:1:31.4:1:1:1.51:60:48:0.4:0:1.1 -4 55964605 . C T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=CTGCTTCTAGTTTCCCTTGT;RSEQ=CCCCAAAGGAGCTCAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:16,46:0:2,0:25.8:1:30.5:1:1:0:60:30:1:0:0.2 0/1:16:5:2,3:1,10:0.3125:2,2:11:1:29.6:1:0.21429:5.76:60:10:0.3125:0:1.4 -4 55964776 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=GCCCATTGAGCCAATAACAA;RSEQ=GGAAGAAACAACTCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:157,25:0:2,0:23.5:1:32.1:1:1:0:60:90:0.9945:0:0.1 0/1:160:2:1,1:129,28:0.0125:2,2:33.5:1:29.5:1:0.33246:4.54454:60:4:0.0128:0:0 -4 55964835 . C T 115 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00124;SOR=7.86353;LSEQ=TAATCATGAAAACCAATGTG;RSEQ=ATGGGCAGAAGGGAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:2:0,2:289,159:0.0044:2,0:7.5:1:17.5:1:0.12749:0:60:1:0.0023:0:1 0/1:471:16:11,5:275,180:0.034:2,2:27:1:28.8:1:0.60816:1.44:60:32:0.0345:0:1.1 -4 55965031 . AT A 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00017;SOR=0;LSEQ=TTATACTTTTTGTTTGTAAG;RSEQ=GACAAATTTTAGCACTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:13:2,11:5,94:0.1161:2,2:24:1:31.8:1:0.18698:3.36:60:26:0.1161:0.0268:0.2 0/0:110:0:0,0:9,101:0:2,0:23.8:1:30.1:1:1:0:60:220:1:0:0.2 -4 55967806 . A G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TGCATTAGCTATTTTTCCTG;RSEQ=TGCTCTCCTTCTCCCCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:13:1:31.3:1:1:0:60:6:1:0:1 0/0:2:0:0,0:2,0:0:0,0:23:1:31:0:1:0:60:4:1:0:0 -4 55968008 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1909;SOR=Inf;LSEQ=CATGATCAGATTCCTTTTTA;RSEQ=GGCTGCATAGCATTCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:149,5:0:1,0:23.1:1:31.9:1:1:0:60:50.333:1:0:0.5 0/1:120:2:2,0:103,15:0.0167:2,0:7.5:1:32:0:1:0:60:4:0.0168:0:3.5 -4 55968019 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10288;SOR=Inf;LSEQ=TCCTTTTTACGGCTGCATAG;RSEQ=ATTCCATGGTGTATATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:170,16:0:2,0:22.8:1:31.9:1:1:0:60:92:1:0:0.6 0/1:165:3:2,1:130,32:0.0182:2,2:14.7:1:31.3:1:0.49035:2.02087:60:6:0.0185:0:3.3 -4 55968038 . A G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2488;SOR=Inf;LSEQ=GCATTCCATGGTGTATATGT;RSEQ=CCACATTTTTTTTTATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:234,56:0:2,0:22.6:1:28.2:1:1:0:60:40.429:1:0:0.7 0/1:296:3:2,1:214,79:0.0101:2,2:33.7:1:32.7:1:1:1.35295:60:6:0.0102:0:3.3 -4 55968043 . A AT 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.96017;LSEQ=CCATGGTGTATATGTACCAC;RSEQ=TTTTTTTTTATCCCACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:6:6,0:246,66:0.0188:2,0:18.3:1:31.7:1:0.35097:0:60:12:0.0194:0.0094:0.8 0/1:332:6:5,1:232,91:0.0181:2,2:27:1:29.8:1:1:1.96:60:12:0.0185:0:0.2 -4 55968053 . A C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13042;LSEQ=TATGTACCACATTTTTTTTT;RSEQ=TCCCACTGACCTTCTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:366:218:168,50:112,36:0.5956:2,2:24.2:1:31.2:1:0.80207:1.08:60:26.25:0.5932:0:1.1 0/1:392:63:42,21:219,108:0.1607:2,2:23.3:1:31.3:1:1:1.01386:60:126:0.1628:0:1.1 -4 55968745 . C G 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=ATGGTTCTGGTATCAGCAAA;RSEQ=TTTTAAACAGTTTAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:6,142:0:1,0:23.5:1:32.7:1:1:0:60:147:1:0:0.1 0/1:144:10:0,10:12,122:0.0694:2,0:25.7:1:31.7:1:1:0:60:20:0.0694:0:1 -4 55970668 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5046;SOR=0;LSEQ=ATTATTAGCTTCTTTCTTCC;RSEQ=CAAGGACTTTCGGTGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:148,7:0.0127:1,2:21.5:1:30:1:0.09962:19.84568:60:4:0.0129:0:1 0/0:126:0:0,0:109,17:0:2,0:23.8:1:30.6:1:1:0:60:62:1:0:0.2 -4 55970680 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09659;LSEQ=TTTCTTCCTCAAGGACTTTC;RSEQ=GTGAAGAAGTGTGCACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:198:121:111,10:65,12:0.6111:2,2:23.7:1:30.5:1:0.1626:2.04:60:120:0.6218:0:1.1 0/1:168:22:18,4:117,29:0.131:2,2:20.1:1:29.9:1:1:1.11:60:44:0.1325:0:1 -4 55970782 . G A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.64323;LSEQ=AAGGCATTCCAACTGCCTCT;RSEQ=CACAATGATCCAGAATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:3:2,1:399,300:0.0043:2,2:23.7:1:27:1:1:1.50:60:6:0.0043:0:1.7 0/1:611:29:14,15:322,257:0.0475:2,2:22.5:1:29.1:1:0.45072:1.34174:60:28:0.0464:0:1 -4 55971846 . G T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.18769;LSEQ=CAGGAGATACCTGAGAAGTT;RSEQ=TAATTTATGAATGAAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:44:42,2:25,1:0.6286:1,1:25.8:1:30.2:1:1:1.18754:60:21:0.6176:0:1.1 0/1:42:10:10,0:32,0:0.2381:1,0:30:1:31:1:1:0:60:20:0.2381:0:1 -4 55971919 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18989;SOR=Inf;LSEQ=CCATGCCACTCACATGAATG;RSEQ=CAAAAACAACAGGGAATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:183,30:0:2,0:24.2:1:31.2:1:1:0:60:34.5:1:0:0.2 0/1:165:2:2,0:124,39:0.0121:2,0:35.5:1:30:1:1:0:60:4:0.0126:0:1 -4 55972782 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15457;SOR=Inf;LSEQ=TGATTATTAATCTCCAATAT;RSEQ=CCTCACATATTATTGTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:213,43:0:2,0:20.3:1:32.3:1:1:0:60:127:1:0:0.1 0/1:167:2:1,1:140,25:0.012:2,2:22:1:27:1:0.28793:5.51091:60:4:0.0121:0:1 -4 55972814 . AAG A 68 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.46197;SOR=0.46832;LSEQ=ATTGTACCATCCTTCCATTA;RSEQ=AGAGAGAGATTTTCAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:446:5:2,3:296,144:0.0112:2,2:33.6:1:29.4:1:0.33751:3.07477:60:10:0.0113:0.0022:0.2 0/0:379:2:2,0:253,124:0.0053:2,0:18:1:30.8:1:1:0:60:4:0.0054:0.0026:0 -4 55972946 . A G 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=12.82111;LSEQ=CACACTTCTCCATTCTTCAC;RSEQ=AGGGTATGGGTTTGTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:736:3:1,2:311,422:0.0041:2,2:38.3:1:25.7:1:1:1.47319:60:2:0.0028:0:2 0/1:661:33:11,22:270,358:0.0499:2,2:22.5:1:30.5:1:0.36661:1.50747:60:32:0.0494:0:1.6 -4 55972974 . T A 221 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=162.8982;LSEQ=GGGTTTGTCACTGAGACAGC;RSEQ=TGGCTATAAGAAAGAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:597:2:0,2:203,392:0.0034:2,0:30.5:1:31.5:1:0.55043:0:60:4:0.0034:0:1 0/1:482:171:63,108:118,193:0.3548:2,2:24.7:1:29.8:1:0.84449:1.04803:60:342:0.357:0:1.2 -4 55973007 . T A 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3209;SOR=3.95932;LSEQ=AGAGATAACAGCGCATATTA;RSEQ=GATTTAATTTTTCTTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:1:1,0:74,258:0.003:2,0:1:0:28:0:0.22523:0:60:2:0.0031:0:1 0/1:254:3:3,0:70,181:0.0118:2,0:6:1:21.7:1:0.02304:0:60:2:0.0081:0:2 -4 55974095 . T C 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=AACAACTTTTGAATTGTCAG;RSEQ=CAGCTTTGAAGAATGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:20,153:0:2,0:23.9:1:29.6:1:1:0:60:33.6:1:0:0.1 0/1:139:11:3,8:15,113:0.0791:2,2:27:1:32.3:1:0.15437:2.80:60:22:0.0821:0:1.2 -4 55974106 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50855;SOR=0;LSEQ=AATTGTCAGTCAGCTTTGAA;RSEQ=AATGGGAAATAGAGGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:8,131:0.0141:2,2:24.5:1:28:1:0.12401:15.49:60:4:0.0143:0:1 0/0:106:0:0,0:10,96:0:2,0:25.3:1:31.2:1:1:0:60:212:1:0:0.2 -4 55974290 . C G 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAATCTCAGTATTTTGGGA;RSEQ=GCCAAGGTAGGTGGATCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:22.8:1:32.8:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55976168 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCTGATACATCAACTACAA;RSEQ=ATCAAACTAGAAGCTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:12:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55976451 . G A 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08009;LSEQ=ACGCCAGATGACTTTTGTAC;RSEQ=CAGGCCCAGCCATGATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:63:63,0:31,0:0.6702:1,1:24.3:1:30.4:1:1:0:60:62:0.6667:0:1 0/1:87:12:12,0:73,2:0.1379:1,0:24.9:1:29.6:1:1:0:60:24:0.1379:0:1.2 -4 55976462 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49787;SOR=Inf;LSEQ=CTTTTGTACGCAGGCCCAGC;RSEQ=ATGATATGAGTGAAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:117,0:0:1,0:23.2:1:30.9:1:1:0:60:38:1:0:0.6 0/1:118:2:2,0:115,1:0.0169:1,0:27:1:32:0:1:0:60:4:0.0171:0:1 -4 55976709 . C G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTTAATTGTGTGATTGGA;RSEQ=TCAAGGGGTATTCCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:880:0:0,0:392,487:0:2,0:25.5:1:31.9:1:1:0:60:42.95:0.9988:0:0.1 0/1:849:24:12,12:369,453:0.0283:2,2:32.1:1:31.7:1:0.67988:1.23:60:48:0.0284:0:1.2 -4 55976739 . A G 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCCATTTTTATACCTATG;RSEQ=AAAAAAATTCTCAGGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:706:0:0,0:336,367:0:2,0:24.7:1:30.1:1:1:0:60:86.875:0.9971:0:0.1 0/1:634:60:30,30:270,300:0.0946:2,2:24:1:30.8:1:0.78606:1.11:60:120:0.0954:0:1.1 -4 55976939 . G GA 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.93576;LSEQ=AGCAACAAAAGGTTTTTCTG;RSEQ=AAGAAAATAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:5:0,5:133,339:0.0103:2,0:31:1:31.4:1:0.32858:0:58.6:10:0.011:0:3.6 0/0:518:5:0,5:187,317:0.0097:2,0:33.2:1:23.9:1:0.16353:0:60:4:0.0081:0.0019:4.6 -4 55976992 . A G 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50195;SOR=0;LSEQ=TGTAAATGGTCATTTGATTT;RSEQ=GTTTTTCATTTCAAGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:10,155:0.012:2,2:21.5:1:26.5:1:0.12777:14.83:60:4:0.0122:0:1 0/0:141:0:0,0:9,132:0:2,0:23.4:1:30.8:1:1:0:60:34.25:1:0:0.6 -4 55979558 . C T 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTGGTCACTCCGGGTTA;RSEQ=ACCATCTATAGTTAAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:935:0:0,0:456,479:0:2,0:24.4:1:31.9:1:1:0:60:115.875:1:0:0.1 0/1:995:101:48,53:448,444:0.1015:2,2:25.3:1:28.5:1:0.67472:1.11399:60:100:0.1018:0:1.2 -4 55979609 . G A 173 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02748;LSEQ=CTTCATCTCACTCCCAGACT;RSEQ=GGTTTTTAGGTCTCGGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:780:57:26,31:298,425:0.0731:2,2:24.9:1:29.7:1:0.57708:1.20:60:114:0.0736:0:1.1 0/0:926:2:2,0:400,524:0.0022:2,0:1:0:24.5:1:0.1882:0:60:4:0.0022:0:1 -4 55980239 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.96578;LSEQ=TATCTCTCAAGCAAACTTCA;RSEQ=TGGGGCTTATTATCTAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:119:91,28:162,53:0.3563:2,2:25.2:1:30.3:1:0.8942:1.06:60:58.5:0.3545:0:1.1 1/0:304:209:152,57:73,22:0.6875:2,2:22.7:1:29.2:1:0.48328:1.24344:60:28.857:0.6801:0:1 -4 55980456 . C T 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCAAGTAAATTGAAAAAA;RSEQ=AGAACATGAGAGAGCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:97,310:0:2,0:24.5:1:32.1:1:1:0:60:100.75:0.9975:0:0.1 0/1:298:68:22,46:57,173:0.2282:2,2:24:1:28.7:1:0.2152:1.45:60:136:0.2305:0:1.1 -4 55980998 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1971;SOR=Inf;LSEQ=TATCTCCAAGATCTTAATAC;RSEQ=AGGATATGTTATTAATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:146,45:0:2,0:23.7:1:30.2:1:1:0:60:94.5:1:0:0.1 0/1:153:2:1,1:111,40:0.0131:2,2:26:1:27:1:0.46543:2.75327:60:4:0.0133:0:1 -4 55981634 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18501;SOR=Inf;LSEQ=GTATTTACTAGAAAAGTTGG;RSEQ=CATTTTTCAGGTTCCTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:7,97:0:2,0:22.9:1:30.3:1:1:0:60:208:1:0:0.1 0/1:79:2:1,1:10,67:0.0253:2,2:14.5:1:28.5:1:0.26063:6.44:60:4:0.0253:0:1 -4 55981683 . G T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.46001;SOR=1.77541;LSEQ=GACAAGTGAATGACTGGAAG;RSEQ=GACACCTCACACAACCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:6:0,6:0,43:0.1224:1,0:18:1:31.5:1:1:0:60:12:0.1277:0:1 0/1:20:4:0,4:1,15:0.2:1,0:21.8:1:29.8:1:1:0:60:8:0.2105:0:1 -4 55985009 . G T 47 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0569;SOR=0;LSEQ=GGTATTAATATGAAGTGCCA;RSEQ=ACTGTGAGGCTATTTCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:4:1,3:48,234:0.014:2,2:12.3:1:23.5:1:0.53051:1.62:60:3:0.0106:0:2 0/0:298:0:0,0:58,240:0:2,0:24.6:1:30.9:1:1:0:60:58.6:1:0:0.1 -4 55985017 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24918;SOR=Inf;LSEQ=TATGAAGTGCCAGACTGTGA;RSEQ=GCTATTTCTAAGAAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:33,214:0:2,0:22.7:1:31.3:1:1:0:60:81.333:1:0:0.1 0/1:262:3:1,2:44,215:0.0115:2,2:6.3:1:30.3:1:0.43319:2.43:60:6:0.0115:0:1.3 -4 55985142 . A G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01811;SOR=9.16888;LSEQ=TCCCAGCACTTTGGGAGGCC;RSEQ=AGGCGGATGGATCACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:0,6:0,15:0.2857:1,0:21.2:1:30.7:1:1:0:54:12:0.2857:0:1.8 1/1:10:8:0,8:0,2:0.8:0,0:12.4:1:31.4:1:1:0:60:16:0.8:0:1.4 -4 55985149 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.32783;SOR=2.86325;LSEQ=ACTTTGGGAGGCCAAGGCGG;RSEQ=TGGATCACCTGAGGCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:0,4:0,16:0.2:1,0:24.8:1:32.3:1:1:0:51:8:0.2:0:2.5 0/1:7:3:0,3:0,4:0.4286:0,0:11.3:1:30.3:1:1:0:60:6:0.4286:0:2 -4 55985209 . C G 84 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46154;SOR=0;LSEQ=AACATGGTAAAACCCTGTCT;RSEQ=TACTAAAAATACAAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:0,6:0,5:0.5455:0,0:32.8:1:32.7:1:1:0:60:12:0.5455:0:1.8 0/0:2:0:0,0:0,2:0:0,0:16.5:1:33.5:1:1:0:60:4:1:0:1 -4 55987002 . G T 49 d7;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GTTATTGGAATGTGGGTGTG;RSEQ=GTGTGTATTTGTGTGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:31:1:24.5:1:1:0:60:3:1:0:1.3 1/0:4:2:1,1:1,1:0.5:2,2:9:0:16:1:1:1:60:0:0:0:1.5 -4 55987018 . C CGT 69 d7;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=11.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTGGGTGTGTATTTGTGTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:0,1:0.8333:0,0:21:1:29.8:1:0.16667:0:60:10:0.8333:0.3333:0.4 1/1:2:2:1,1:0,0:1:0,2:22.5:1:28.3:1:1:0:60:4:1:0:0.5 -4 55991042 . G T 56 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CAGACAACTTTTCACCGCCT;RSEQ=TTCTCGCCTGCGGAGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:23.8:1:28.3:1:1:0:60:3:1:0:1.3 0/0:1:0:0,0:1,0:0:0,0:50:0:29:0:1:0:60:2:1:0:0 -4 55991138 . T C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTCGGCATCTCAGGACA;RSEQ=GCTCCAGCCGAGGTCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:21,0:0,0:1:0,1:24.5:1:32.3:1:1:0:60:42:1:0:1.1 1/1:7:7:5,2:0,0:1:0,2:17.9:1:31.1:1:1:0:60:14:1:0:1.1 -4 55991422 . G T 173 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=73.63081;LSEQ=GCGGCCCGGGTCTCCACGCA;RSEQ=AGCCACAGGGCGACGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:911:1:0,1:413,495:0.0011:2,0:14:0:30:0:1:0:60:2:0.0011:0:2 0/1:974:73:35,38:406,493:0.0749:2,2:25.6:1:28:1:0.71415:1.12:60:72:0.0748:0:1.1 -4 55991731 . T C 89 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=GGAAACGCAGCGACCACACA;RSEQ=TGACCGCTCTCCCGGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:1,6:0,0:0.875:0,2:25.3:1:32:1:1:0:60:14:1:0:1.6 0/0:1:0:0,0:0,1:0:0,0:5:0:31:0:1:0:60:2:1:0:0 -4 55991779 . T A 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGCAGGGTGGGAGCTGG;RSEQ=GCCGAAACTCTAGAGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:7.8:1:32:1:1:0:60:8:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 55991885 . C G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCACCCGGGTACCCGGCGG;RSEQ=GATCTCCAGCTCCCCAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:15.7:1:33:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 56218221 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51811;SOR=Inf;LSEQ=TTGGTGATCCTTAGAGCCAC;RSEQ=CCATACTTCTGCTCCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:21,9:0:2,0:30.7:1:30.9:1:1:0:60:60:1:0:0.2 0/1:47:2:1,1:30,15:0.0426:2,2:19.5:1:28.5:1:1:1.96856:60:4:0.0426:0:1 -4 56974810 . A G 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.25882;SOR=Inf;LSEQ=GCTGATATTTATTGCATACA;RSEQ=GACAAGGGGGGCAGGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:16.4:1:29.6:1:1:0:60:28:1:0:0.2 0/1:21:3:2,1:10,8:0.1429:2,2:22:1:28.3:1:1:1.57:60:6:0.15:0:1 -4 59330811 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22868;SOR=0;LSEQ=TAGGTCCCATGGCAGCCATC;RSEQ=TGCTCTTACTCGCCTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:6,20:0.0714:2,2:25.5:1:30:1:0.44444:3.16:54.5:4:0.0714:0:1 0/0:30:0:0,0:13,17:0:2,0:15.2:1:30.1:1:1:0:51.6:60:1:0:0.2 -4 60522652 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12805;SOR=Inf;LSEQ=AAACCCCATCTTAGGGTCAG;RSEQ=AACCTCAAAGACCAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:22.9:1:30.9:1:1:0:60:25:1:0:0.2 0/1:15:2:1,1:6,7:0.1333:2,2:34:1:29.5:1:1:1.15:60:4:0.1333:0:1 -4 60522704 . G GA 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.52569;SOR=0;LSEQ=AAAGATGAGAAAGAATCAAT;RSEQ=AAAAAAATGTTGAAAACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:4,9:0.1333:2,2:18:0:30.5:1:1:2.12:60:4:0.1333:0:0 0/0:8:0:0,0:4,4:0:2,0:24:1:31:1:1:0:60:16:1:0:0.9 -4 60522757 . G A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACTTCTCCTCCAAATGA;RSEQ=CACAATGTCTCTCCATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:32.7:1:30.4:1:1:0:60:14:1:0:1 1/1:5:5:2,3:0,0:1:0,2:24:1:28.4:1:1:0:60:10:1:0:1.2 -4 62068481 . CGT C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.24582;SOR=0;LSEQ=TGGGTGTGTGTGTGTCTGTG;RSEQ=GTGTGTGTGGTGTGTAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:3:2,1:51,33:0.0345:2,2:11.7:1:31.8:1:1:1.29:60:6:0.0345:0.023:2 0/0:84:0:0,0:58,26:0:2,0:23.5:1:29.4:1:1:0:60:41:1:0:0.1 -4 62068536 . C T 25 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6885;LSEQ=CCTCTACCAGCCTTACTTGG;RSEQ=GGCGGAGTCAGCGTTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:0,2:78,74:0.013:2,0:21:1:27:1:0.24191:0:60:4:0.0135:0:1 0/0:223:2:0,2:111,110:0.009:2,0:1:0:25:0:0.49776:0:60:4:0.0091:0:1 -4 62068561 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17446;SOR=0;LSEQ=GAGTCAGCGTTTGAGTGTGT;RSEQ=CGCATTTTTGCGCCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:63,89:0.013:2,2:25:1:29:1:1:1.41:60:4:0.0133:0:1 0/0:214:0:0,0:91,121:0:2,0:25.6:1:31.9:1:1:0:60:105:0.9953:0:0.2 -4 62068571 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16923;SOR=0;LSEQ=TTGAGTGTGTGCGCATTTTT;RSEQ=CGCCCCAGGGACGGCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:53,71:0.0157:2,2:30.5:1:32:0:1:1.34:60:4:0.016:0:1.5 0/0:181:0:0,0:73,106:0:2,0:25:1:31.8:1:1:0:60:88.5:0.9888:0:0.2 -4 62707476 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13078;SOR=Inf;LSEQ=GCTGAATGCCCATAAGAATA;RSEQ=TAAATCGTCTGTACTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:0:1,0:20.4:1:32.6:1:1:0:60:90:1:0:0 0/1:26:2:2,0:23,1:0.0769:1,0:15.5:1:31.5:1:1:0:60:4:0.0769:0:2 -4 62707491 . T C 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02364;SOR=Inf;LSEQ=GAATACTAAATCGTCTGTAC;RSEQ=TGGCTGGAGTTTTCTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:54,1:0:1,0:25.1:1:31.8:1:1:0:60:54:1:0:0 0/1:37:4:4,0:32,1:0.1081:1,0:16.8:1:30.8:1:1:0:60:8:0.1081:0:1.5 -4 62707653 . C T 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACCGAAATTTGGCTTTAG;RSEQ=TGTCCTTAGTAAGAGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:0:0,0:182,213:0:2,0:24.9:1:31.8:1:1:0:60:38.5:1:0:0.2 0/1:489:122:58,64:177,190:0.2495:2,2:24.8:1:29.7:1:0.917:1.0279:60:244:0.2542:0:1.1 -4 62707719 . G T 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00269;SOR=0.40886;LSEQ=AATCATTTGTTTAATTAGCT;RSEQ=AATCTCCTAAGGGAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:39:7,32:31,97:0.2335:2,2:24.9:1:28.3:1:0.51538:1.45784:60:18.5:0.2327:0:1.3 0/1:190:21:8,13:42,127:0.1105:2,2:17.1:1:28.8:1:0.19807:1.85:60:42:0.1123:0:1 -4 65603107 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTTCTTACAGCATGTGG;RSEQ=CTCCTTATAAAAGAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 65604616 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.17645;LSEQ=TTCATTTACAAGAACCTTTA;RSEQ=TATCAATACAATAATGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:33:15,18:65,76:0.1897:2,2:26.7:1:31.8:1:1:1.02617:60:66:0.1976:0:1.1 1/0:173:95:42,53:36,42:0.5491:2,2:23.3:1:31.8:1:0.87819:1.08114:60:190:0.5523:0:1.1 -4 65604620 . C T 167 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01192;LSEQ=TTTACAAGAACCTTTAATAT;RSEQ=AATACAATAATGCCATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:59:27,32:51,66:0.3352:2,2:25:1:28.5:1:0.87252:1.09:59.9:118:0.343:0:2.7 0/0:169:1:0,1:79,89:0.0059:2,0:1:0:24:0:1:0:60:2:0.006:0:1 -4 65604632 . G GA 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12123;SOR=0.16637;LSEQ=TTTAATATCAATACAATAAT;RSEQ=CCATGAGCTAGACTTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:6:4,2:14,21:0.0357:2,2:26:1:24.7:1:0.37729:2.92:60:2:0.0241:0.006:2.8 0/0:164:1:1,0:49,54:0.0061:2,0:10:0:29:0:0.48077:0:60:2:0.0061:0:2 -4 65604633 . CC AGT 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.14669;LSEQ=TTAATATCAATACAATAATG;RSEQ=ATGAGCTAGACTTCTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:127:46,81:14,21:0.756:2,2:26.7:1:30.1:1:0.6964:1.17273:59.9:254:0.7651:0.1488:2.3 0/1:164:51:22,29:49,54:0.311:2,2:26:1:29.4:1:0.61185:1.19474:60:102:0.3129:0.061:2 -4 65604634 . C CT 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=7.34482;LSEQ=TAATATCAATACAATAATGC;RSEQ=ATGAGCTAGACTTCTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:32:12,20:1,0:0.227:0,2:28.9:1:29.3:1:0.39394:0:60:64:0.8205:0.0284:1 1/0:146:100:46,54:1,0:0.6849:0,2:28.6:1:29.5:1:0.46535:0:60:200:0.9709:0.0616:0.9 -4 65604674 . G T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.49876;SOR=Inf;LSEQ=TCTTTCTTGATATCCTTGAA;RSEQ=TAAGTTTTTCTAATTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:31,76:0:2,0:25:1:32.3:1:1:0:59.9:214:1:0:1.6 0/1:117:2:1,1:38,77:0.0171:2,2:22:0:26.5:1:1:2.01:60:4:0.0174:0:3.5 -4 65604715 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21572;SOR=Inf;LSEQ=GTTTTAATTTGATGAGGTAT;RSEQ=CTGATATCTTTATAGTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:9,40:0:2,0:20.9:1:31.5:1:1:0:59.9:98:1:0:0.6 0/1:43:2:1,1:7,34:0.0465:2,2:36:1:30:0:0.34109:4.61:60:4:0.0476:0:1 -4 65763540 . C A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.24859;SOR=Inf;LSEQ=GAATTCTTTTATAATTATCT;RSEQ=TCTCACCATGCTGTTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:142,82:0:2,0:24.8:1:31.8:1:1:0:60:448:0.9912:0:0.5 0/1:234:3:1,2:134,97:0.0128:2,2:25:1:23:1:0.57525:2.75095:60:2:0.0088:0:2.3 -4 65763592 . A G 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15016;SOR=0.79276;LSEQ=TTACAACCATTTTCATGCCT;RSEQ=TAATGCAGAAATGATCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:189:105,84:63,60:0.6058:2,2:25.8:1:32:1:0.48659:1.19:60:93.5:0.6032:0:1.1 1/0:326:179:84,95:70,76:0.5491:2,2:25.6:1:31.3:1:0.91118:1.04156:60:178:0.5494:0:1.1 -4 66189675 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52325;SOR=0;LSEQ=ACTAAGAACTGGATACTTCA;RSEQ=TAAAACCATGATTACAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:70,2:0.027:1,0:15.5:1:29.5:1:1:0:60:4:0.027:0:1 0/0:46:0:0,0:46,0:0:1,0:21.4:1:32.5:1:1:0:60:92:1:0:0 -4 66189753 . C CT 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.14857;LSEQ=CACTGTTTTCCCTTTTCCCC;RSEQ=TTTTTTTGTTAAAATAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:64:57,7:185,38:0.2078:2,2:28.5:1:31.6:1:0.32898:1.67:60:128:0.2254:0:0.1 0/1:294:11:11,0:225,55:0.0374:2,0:25.6:1:30.8:1:0.13281:0:60:22:0.0375:0.0068:0.5 -4 66189835 . C T 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=76.18984;LSEQ=GCGACATTTACATGAAGTTA;RSEQ=AATGGCACCATTCCGTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:922:1:0,1:510,410:0.0011:2,0:1:0:24:0:0.44625:0:60:2:0.0011:0:1 0/1:1033:79:44,35:519,435:0.0765:2,2:27:1:28.7:1:0.90653:1.05:60:78:0.0761:0:1.2 -4 66190274 . C CTGCAGATT 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATTGAAAAGTTTTGAAA;RSEQ=TGCAGATTTACAATATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:13:1:30.6:1:1:0:60:4:0.5:0.5:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66197804 . C T 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.25399;LSEQ=TCACCTACTGATCTGTAGGC;RSEQ=CCAGATCCTAGTGGGCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:774:572:239,333:83,117:0.739:2,2:27.7:1:30.2:1:1:1.01:60:46.667:0.7388:0:1.1 0/1:763:319:140,179:201,241:0.4181:2,2:25:1:29.5:1:0.71193:1.06625:60:318:0.4212:0:1.1 -4 66198059 . G A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTATCCATAATTAATGA;RSEQ=GACTTAACATGAAGACTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:26.2:1:31.9:1:1:0:60:22:1:0:1 1/1:5:5:0,5:0,0:1:0,0:25.2:1:31.4:1:1:0:60:10:1:0:1.4 -4 66201374 . AT A 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATGAAAATACACACATTTA;RSEQ=TTTTTTTTATGCTACCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:29.2:1:32.7:1:1:0:60:12:0.8571:0:0 1/1:3:3:3,0:0,0:1:0,0:34.3:1:29.8:1:1:0:60:6:1:0.3333:0 -4 66213336 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTTAATTTAAAGAAAC;RSEQ=TAGACTATTCCTTTTTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:19:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66214043 . G A 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.38687;SOR=0.65351;LSEQ=AAGTGAATCTGTTTGACAGC;RSEQ=CGCAGTGTCTTTTCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:53:0,53:0,21:0.7162:1,1:20:1:30:1:1:0:60:106:0.7162:0:1.1 1/0:37:23:0,23:0,14:0.6216:1,1:22:1:28.9:1:1:0:60:22:0.6286:0:1 -4 66214395 . TATATATATATATATATATATAA T 45 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=9.000;MSILEN=2;SSF=0.25;SOR=0;LSEQ=GAGATATATATATATATATA;RSEQ=AATATATATGTGTGTGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:22:1:28.8:1:1:0:60:6:1:1:0.3 0/0:1:0:0,0:0,1:0:0,0:7:0:31:0:1:0:60:2:1:0:2 -4 66216523 . C T 69 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATTTTCCATAGTGTAGA;RSEQ=GTAACAGTTTTTAAATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:21.8:1:30:1:1:0:60:10:1:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66216588 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTTTTGAAGGAATAGCT;RSEQ=TTTTTTCCCTACAATGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:11.5:1:28.5:1:0.4:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66216749 . CTA C 50 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATACACAGACACATACATA;RSEQ=TATATATATATATATAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:34:1:32:1:1:0:60:6:0.75:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66216856 . A AT 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATCCATTCTGAAGTAAG;RSEQ=TTTTTTATTTTTAGTATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:44:1:29.5:1:1:0:60:4:0.2:0:0.5 0/0:4:0:0,0:4,0:0:0,0:21:1:29.8:1:1:0:60:8:1:0:0 -4 66218334 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCACTTATAGGCTCTAAC;RSEQ=TGACACCTTTATTAATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:42:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66218505 . A AT 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.66569;SOR=1.83446;LSEQ=ATTCCCTTCTACTTCTCTGC;RSEQ=TTTTTTTTTTCAAATTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:15,0:11,0:0.5172:0,1:30.2:1:30.6:1:1:0:59.6:30:0.5357:0.0345:0.6 1/0:6:4:4,0:1,0:0.6667:0,0:24:1:31.5:1:1:0:60:8:0.6667:0:0 -4 66218527 . A T 105 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17194;SOR=0;LSEQ=TTTTTTTTTCAAATTAAGAC;RSEQ=TACTTAAATAAAACTTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:10:10,0:28,0:0.2632:1,0:29.6:1:31.8:1:1:0:60:20:0.2632:0:1.1 0/0:9:0:0,0:9,0:0:0,0:25.4:1:29.8:1:1:0:60:18:1:0:0 -4 66218677 . C T 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTGGCCCAAATTCAACTT;RSEQ=AACATCACAGCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:28:21,7:306,93:0.0656:2,2:23:1:29.4:1:0.81929:1.09654:60:56:0.0671:0:1.9 0/0:364:0:0,0:273,91:0:2,0:24.7:1:30.8:1:1:0:59.9:59.667:1:0:0.6 -4 66218696 . T A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=3e-05;SOR=Inf;LSEQ=TCAACATCACAGCATCATCA;RSEQ=CACAGCACAACATCACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:361,177:0:2,0:26.8:1:30.3:1:1:0:60:58.778:1:0:1 0/1:482:14:12,2:303,165:0.029:2,2:16.1:1:28.7:1:0.15334:3.26:60:28:0.0294:0:1.8 -4 66218728 . C T 289 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00509;LSEQ=ATCACAATATATAAATAACA;RSEQ=CTTGAATAACTAAATTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:792:790:468,322:0,1:0.9975:0,2:24.8:1:30.1:1:0.40834:0:60:64.833:0.9987:0:1.1 1/0:697:465:265,200:134,98:0.6671:2,2:24.7:1:29:1:0.87114:1.03192:60:65.429:0.6676:0:1.1 -4 66218756 . C T 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTAAATTATTCCCCAATC;RSEQ=TACCTTCAAAAATGTATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:987:0:0,0:514,472:0:2,0:25.1:1:31.5:1:1:0:60:97.6:0.999:0:0.8 0/1:877:38:18,20:438,398:0.0433:2,2:23.1:1:30.8:1:0.61945:1.2225:60:37:0.0425:0:1.1 -4 66218980 . G GAAAT 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.32034;SOR=0.29281;LSEQ=AAAAATAAAATTTATTAAAT;RSEQ=AAAGATATTTAAATATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:51:0,51:0,1:0.9623:0,1:25.4:1:30:1:1:0:59.8:102:0.9808:0.2264:0.1 1/1:25:22:0,22:0,3:0.88:0,1:24:1:29.6:1:1:0:60:44:0.88:0.2:0.1 -4 66230452 . TA T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTAAAAGAGCCAATAGT;RSEQ=AAAAAAAAGTTGATATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:23.5:1:31:1:1:0:60:4:0.4:0.2:0 0/0:2:0:0,0:2,0:0:0,0:19:1:29.5:1:1:0:60:4:1:0:0 -4 66232950 . CT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGTAACAAATAGAACA;RSEQ=TTTAAAAAAAAAAAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:2,0:61,0:0.0317:1,0:20.5:1:33:0:1:0:60:4:0.0323:0:1 0/0:29:0:0,0:28,1:0:1,0:17.7:1:30.6:1:1:0:60:58:1:0:1.1 -4 66232954 . T AA 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.54962;SOR=0;LSEQ=TGTAACAAATAGAACACTTT;RSEQ=AAAAAAAAAAAAAACAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:3,0:63,0:0.0455:1,0:29.3:1:30.2:1:1:0:60:6:0.0462:0:2.7 0/0:30:0:0,0:29,1:0:1,0:17.5:1:30:1:1:0:60:60:1:0:1.2 -4 66233029 . A G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01852;SOR=1.49523;LSEQ=AGAAACTTAAATAACAATAA;RSEQ=GTGTCCCCTATTTTATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:298:151:122,29:123,23:0.5067:2,2:24.6:1:31.3:1:0.44949:1.27017:60:20.571:0.5088:0:1.2 1/0:274:166:136,30:85,23:0.6058:2,2:21.5:1:31.1:1:0.53378:1.23:60:54.333:0.6105:0:1.1 -4 66241504 . TACAC T 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=24;MSI=14.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCACAGAAACACACACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:31:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66242656 . C T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12397;SOR=Inf;LSEQ=ATGGAGAAAGAAAAGGAATG;RSEQ=CGACGGTAATACATATAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:242,124:0:2,0:21.9:1:31.7:1:1:0:60:182:1:0:0.1 0/1:366:4:1,3:230,132:0.0109:2,2:18.3:1:27.3:1:0.14394:5.20352:60:8:0.011:0:1 -4 66270051 . G T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12716;SOR=Inf;LSEQ=TCAGATCAAGGTGAGGAAGA;RSEQ=ATCAGCTGCAGAACTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:240,78:0:2,0:23.6:1:31.9:1:1:0:60:105:1:0:0.1 0/1:364:4:2,2:264,96:0.011:2,2:5.5:1:26.5:1:0.29409:2.74103:60:8:0.0111:0:1 -4 66270241 . A G 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTTGTGGTTAAAGTGATC;RSEQ=CATGCATTCAAAATAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:55,226:0:2,0:23.2:1:30:1:1:0:60:92.667:1:0:0.1 0/1:248:83:17,66:36,129:0.3347:2,2:19.2:1:31.3:1:0.87061:1.08312:60:166:0.3374:0:1.1 -4 66270271 . G A 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00773;SOR=Inf;LSEQ=AAAATAAAAGTTGCTTAATA;RSEQ=ACAGTAATCAATTCATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:13,135:0:2,0:23.4:1:31.1:1:1:0:60:48.333:1:0:0.1 0/1:121:6:1,5:12,103:0.0496:2,2:21.3:1:29.8:1:0.50211:1.71:60:12:0.0496:0:1 -4 66270345 . G A 88 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17595;SOR=0;LSEQ=CCTAATATCCTTTCTTAAAA;RSEQ=TGTGTAATTGAAAAGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:7:0,7:0,36:0.1628:1,0:24.9:1:31.4:1:1:0:60:14:0.1667:0:1 0/0:14:0:0,0:0,14:0:1,0:19.1:1:32.6:1:1:0:60:28:1:0:0.1 -4 66277927 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCACTCCAGTCTGGGCCA;RSEQ=AGAGTGAGACTCTCTCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:47.5:1:32:1:1:0:60:4:1:0:1.5 -4 66279935 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=AGAGTGCCCAGGGAGGGTAT;RSEQ=GATCCACTGACTCTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:160,20:0:2,0:24.1:1:30.3:1:1:0:60:89:1:0:0.1 0/1:187:2:1,1:156,29:0.0107:2,2:15:1:27:0:0.29584:5.30593:60:4:0.0108:0:1 -4 66280107 . C G 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGAAGCTGGTTTCAAGCCCT;RSEQ=TGCAGTAATAGTTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:0:0,0:231,387:0:2,0:23.9:1:31.5:1:1:0:60:76.25:1:0:0.2 0/1:716:24:9,15:292,400:0.0335:2,2:22.5:1:29.9:1:0.6809:1.21634:60:23:0.0328:0:1 -4 66280171 . C T 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13122;SOR=1.48541;LSEQ=GTCTCTTGGTCCTTGGGATG;RSEQ=GCATGCATATACAATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:28:6,22:52,219:0.0936:2,2:21.1:1:29.7:1:0.80221:1.15:60:56:0.0962:0:1.3 0/1:323:43:14,29:76,204:0.1331:2,2:22.3:1:28.9:1:0.46833:1.29:60:86:0.1348:0:1.1 -4 66285765 . T C 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTGTCTCATCTTTTTTC;RSEQ=TATCTCCTTAACAGTATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:16:1:29.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66286088 . G A 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAACATACTCTTCTGCAA;RSEQ=TTGGATAATTGTAGTTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:237:237:207,30:0,0:1:0,2:23.4:1:30.1:1:1:0:59.9:46.4:1:0:2.2 1/1:176:176:149,27:0,0:1:0,2:21.7:1:30:1:1:0:60:352:1:0:2 -4 66286100 . T C 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00729;SOR=0;LSEQ=TTCTGCAAGTTGGATAATTG;RSEQ=AGTTGCTAAAATGAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:293:293:242,51:0,0:1:0,2:24.4:1:31.8:1:1:0:59.9:28.3:1:0:2 1/1:233:227:171,56:4,2:0.9742:2,2:21.9:1:31.6:1:0.64043:1.52:60:55.75:0.9738:0:1.8 -4 66286113 . G GA 212 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.1484;LSEQ=ATAATTGTAGTTGCTAAAAT;RSEQ=AAAAAAAAAAGAAAGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:140:112,28:146,40:0.3989:2,2:28.3:1:29.8:1:0.78408:1.10:60:45.667:0.4018:0:1.6 0/1:302:27:17,10:197,77:0.0894:2,2:24.5:1:27.3:1:0.37419:1.50279:60:12.5:0.0842:0.0099:1.5 -4 66286376 . G A 95 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05177;SOR=0.15512;LSEQ=TATATTGGCATTTTGAGAAC;RSEQ=TAGCAATATAAAAAAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:9:0,9:1,89:0.0909:1,0:21.8:1:30.1:1:1:0:60:18:0.0928:0:1.7 0/1:66:1:0,1:1,64:0.0152:1,0:23:0:32:0:1:0:60:2:0.0154:0:1 -4 66286385 . TA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.51589;SOR=0;LSEQ=ATTTTGAGAACGTAGCAATA;RSEQ=AAAAAAATCCCAATTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:1,79:0.0244:1,0:32:1:31.5:1:1:0:60:4:0.0247:0:1 0/0:55:0:0,0:1,54:0:1,0:24.5:1:30.8:1:1:0:60:110:1:0:0.5 -4 66286414 . T C 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAATTAAATTTTAGTTT;RSEQ=TCTATATAAGGTTTAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:46:0,46:0,0:1:0,1:22.7:1:32.4:1:1:0:60:45:1:0:1.2 1/1:26:26:0,26:0,0:1:0,1:19.2:1:32.8:1:1:0:60:52:1:0:1 -4 66286633 . C T 67 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAGCTCTATATGACATAT;RSEQ=CCATTATGCTAATAGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:21.8:1:29.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66355888 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.0326;SOR=0.19386;LSEQ=AAATGTTTTGTTTTGTTTTG;RSEQ=TTTCCTGTAAATGGGATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:19:19,0:7,0:0.7308:0,1:26.6:1:32.5:1:1:0:60:38:0.7308:0:1.4 0/1:12:4:4,0:8,0:0.3333:0,0:24:1:33.8:1:1:0:60:8:0.3333:0:1 -4 66355901 . G T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=TGTTTTGTTTTCCTGTAAAT;RSEQ=GGATTGCTAACAAAGCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:0:1,0:25:1:31.5:1:1:0:60:29:1:0:0.9 0/1:17:7:7,0:10,0:0.4118:0,0:20.6:1:30:1:1:0:60:14:0.4118:0:1 -4 66360718 . GAAGAAGA G 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGAGGAAGAAGAGGAAG;RSEQ=AAGAAGAAAGAAGAAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:24.3:1:31.5:1:1:0:58.8:8:0.8:0.2:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66361319 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.24997;SOR=Inf;LSEQ=ACAGATGCAGTGTTTGTTTT;RSEQ=TGAATAATGTCATTATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:4,102:0:1,0:23.8:1:32.3:1:1:0:60:34.333:1:0:0.1 0/1:121:3:2,1:13,105:0.0248:2,2:12.7:1:27:1:0.04023:15.44:60:6:0.025:0:1 -4 66468046 . TA T 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04488;SOR=0.57797;LSEQ=TACAATATAAAATAGAAAGA;RSEQ=AAAAAAATTCAAAAAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:188:17,171:5,26:0.8584:2,2:27.1:1:30.5:1:0.21047:1.92747:60:187:0.8618:0.0685:0.2 1/0:171:133:15,118:12,24:0.7778:2,2:27.4:1:30.2:1:0.0035:3.89282:60:266:0.7824:0.0526:0.1 -4 66468381 . T C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCAAAGAAAGAAAAATA;RSEQ=GTATATTTTGAATAAAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:18.3:1:32:0:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 66508839 . C T 115 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03158;SOR=0;LSEQ=TGCTGAAGGAAACTTCACAT;RSEQ=TCTTTGTGGAACAATACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:1:0,1:23.7:1:28.9:1:1:0:60:15:1:0:1.4 1/0:4:2:2,0:2,0:0.5:0,0:29:1:31.5:1:1:0:60:4:0.5:0:1 -4 66508962 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.19671;SOR=Inf;LSEQ=CCCTCACCCCATCCAACACA;RSEQ=ACATAGCACCTCCTGTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:96,5:0:1,0:26.7:1:32.5:1:1:0:60:202:1:0:0.1 0/1:81:2:1,1:72,7:0.0247:2,2:25:0:33.5:1:0.18889:9.688:60:4:0.0253:0:1.5 -4 66509085 . T G 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTCATAAAACTTACCCCA;RSEQ=TTTTTGGAAAAGCAATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:0:0,0:311,282:0:2,0:26.3:1:30.3:1:1:0:60:97.833:0.9966:0:0.1 0/1:579:81:42,39:269,229:0.1399:2,2:25.4:1:31.5:1:0.72039:1.0906:60:162:0.1424:0:1.1 -4 66509194 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.64988;LSEQ=GAAATGTATATTATCATGAA;RSEQ=ATTGTATCTCTATTTTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:78:18,60:22,105:0.3805:2,2:22.6:1:32:1:0.36503:1.43:60:77:0.3812:0:1.1 1/0:200:124:32,92:16,60:0.62:2,2:22.5:1:31.1:1:0.49777:1.30:60:61:0.6162:0:1.1 -4 66535209 . G T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08684;SOR=Inf;LSEQ=AGCAGCGTCCAGCGCGCTGA;RSEQ=ACCTGAACTCCCAGGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:294,52:0:2,0:22.5:1:31.5:1:1:0:60:48.429:1:0:0.2 0/1:276:3:1,2:227,46:0.0109:2,2:7.7:1:20.3:1:0.07919:9.74424:60:2:0.0074:0:1.7 -4 66535284 . G A 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19839;LSEQ=ACCCCCATCTCCCTACCTTC;RSEQ=TTGCTGGGGCTGGCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:218:115,103:432,356:0.2163:2,2:25.3:1:29.5:1:0.59168:1.08677:60:26.25:0.2141:0:1.1 0/1:964:50:26,24:490,421:0.0519:2,2:25.9:1:29.6:1:0.88444:1.07427:60:100:0.053:0:1.2 -4 66535498 . G A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1209;SOR=0;LSEQ=CGGTGCCGCTGTCCCGAGCG;RSEQ=CTCAGTCCACCGCTTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:3:2,1:70,107:0.0167:2,2:23.3:1:28.7:1:0.56477:3.04:60:6:0.0169:0:1 0/0:183:0:0,0:75,108:0:2,0:12:0:14:0:1:0:60:0:0:0:3 -4 66535529 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=CGCTTCGGCCTCGCAGAGCG;RSEQ=CGAAGGGAGACTCGGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:27,69:0:2,0:21.4:1:31.8:1:1:0:60:192:1:0:0.1 0/1:106:2:1,1:30,74:0.0189:2,2:19.5:1:28:1:0.50135:2.44:60:4:0.0194:0:1 -4 67137334 . C G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTACATTGCCAACAAACA;RSEQ=ATGAATAAAGCTCAACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:31:1:1:0:60:4:1:0:1 -4 67138143 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18162;LSEQ=CCAGATGGGAGAAACAACCC;RSEQ=AGGTAACAGAACAATTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:459:251:132,119:107,101:0.5468:2,2:25.6:1:29.4:1:0.85124:1.05:60:124.5:0.5473:0:1.1 0/1:546:98:54,44:248,200:0.1795:2,2:27.3:1:29.2:1:1:1.01035:60:97:0.18:0:1.1 -4 67138228 . A C 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACACTCAATTCCAATCCC;RSEQ=ATTGTAGTAGTATATTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:64,178:0:2,0:24.4:1:30.1:1:1:0:60:79.667:1:0:0.2 0/1:282:35:10,25:75,172:0.1241:2,2:22.6:1:31:1:1:1.0898:60:34:0.1241:0:1.1 -4 67138251 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5008;SOR=Inf;LSEQ=TGTAGTAGTATATTCACATT;RSEQ=TTGTGATACTTTTTAAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:25,124:0:2,0:21.4:1:30.5:1:1:0:60:73.5:1:0:0.1 0/1:171:2:1,1:30,139:0.0117:2,2:8:1:27:1:0.33058:4.57:60:4:0.012:0:1.5 -4 67138309 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.00131;SOR=0.20609;LSEQ=AATCAAAAATAAGAGTCTTC;RSEQ=TAATTACAGTATTGGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:21:0,21:0,18:0.5385:1,1:30.5:1:31.9:1:1:0:60:42:0.5385:0:1 0/1:42:8:0,8:0,34:0.1905:1,0:19.8:1:30.5:1:1:0:60:16:0.1905:0:1.3 -4 67138353 . TAA T 96 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.48959;SOR=0.56593;LSEQ=TAATACTCATTTGACAAAAA;RSEQ=AAAAAAAAAATGATGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:0,9:0,9:0.5:0,0:23.3:1:30.3:1:1:0:60:18:0.5:0:0.6 0/1:14:5:0,5:0,7:0.3571:0,0:30.8:1:30.2:1:1:0:60:10:0.3571:0:1 -4 67191468 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50619;SOR=Inf;LSEQ=GAATGAAACCTTCATCTCAA;RSEQ=AAGTTTGGGAAAAAAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:100,33:0:2,0:23.7:1:31.6:1:1:0:60:266:1:0:0.3 0/1:171:2:1,1:123,46:0.0117:2,2:24:0:30.5:1:0.47534:2.65605:60:4:0.0117:0:1.5 -4 67191491 . A C 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.38285;SOR=3.35942;LSEQ=GTTTGGGAAAAAAATAGAAA;RSEQ=ATAGAAGGAAGGAATAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:1:1,0:129,88:0.0046:2,0:47:0:13:0:1:0:60:0:0:0:4 0/1:263:4:2,2:153,106:0.0152:2,2:38.3:1:32.3:1:1:1.44131:60:8:0.0154:0:1.8 -4 67191539 . A T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20555;LSEQ=TAGCAGGGAAAATGACTACC;RSEQ=TAGGAAAATACCAGTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:286:149:75,74:70,67:0.521:2,2:27.9:1:30.2:1:0.90634:1.03075:60:23.833:0.5162:0:1.2 0/1:362:66:32,34:138,158:0.1823:2,2:25.6:1:30.2:1:0.78696:1.08:60:65:0.1836:0:1.4 -4 67191541 . A G 137 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=16.62405;LSEQ=GCAGGGAAAATGACTACCAT;RSEQ=GGAAAATACCAGTAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:1,0:139,141:0.0036:2,0:3:0:30:0:0.49822:0:60:2:0.0036:0:1 0/1:356:20:9,11:154,182:0.0562:2,2:30.2:1:31.8:1:1:1.0341:60:40:0.057:0:2.1 -4 67191574 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21099;SOR=0;LSEQ=TAAAAATACTATATATTGGA;RSEQ=TTGTATATTTTCTTTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:74,124:0.01:2,2:24:1:31:1:1:1.67:60:4:0.0102:0:2 0/0:236:0:0,0:85,151:0:2,0:24.7:1:29.3:1:1:0:60:32.714:1:0:0.3 -4 67191597 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50581;SOR=Inf;LSEQ=GTATATTTTCTTTAAGAATT;RSEQ=AGGGTAAAGCACCCAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:36,89:0:2,0:27.3:1:27.7:1:1:0:60:24:1:0:0.4 0/1:160:2:1,1:46,112:0.0125:2,2:41:1:32:1:0.50252:2.42:60:4:0.0127:0:1 -4 67840231 . A G 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.01556;SOR=Inf;LSEQ=CACTTGAAGATATTTCTAAA;RSEQ=TAAAATTGTCAAAACTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:80,29:0:2,0:25.6:1:30.1:1:1:0:60:108:1:0:0.2 0/1:124:7:3,4:84,33:0.0565:2,2:29.4:1:32.1:1:0.19511:3.35535:60:14:0.0565:0:1.3 -4 67840237 . T C 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24845;SOR=Inf;LSEQ=AAGATATTTCTAAAATAAAA;RSEQ=TGTCAAAACTAAAGCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:86,34:0:2,0:25.7:1:30.4:1:1:0:60:59:1:0:0.2 0/1:131:3:1,2:89,39:0.0229:2,2:33.7:1:24.7:1:0.23067:4.50517:60:2:0.0154:0:1 -4 67840314 . G T 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.64873;SOR=0.91557;LSEQ=AAACAACTTTCCAATTAGTT;RSEQ=TAGAGGTATTCAGGAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:95:49,46:76,65:0.4025:2,2:24:1:29.2:1:0.79059:1.09721:60:30.667:0.3966:0:1.1 0/1:270:103:53,50:82,85:0.3815:2,2:25.4:1:29.1:1:0.80222:1.10:60:50.5:0.3769:0:1.3 -4 67840369 . A C 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGTTTCATGAATAATTCA;RSEQ=ATTCCAGTGTCAGTCGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:80,120:0:2,0:26.7:1:30.3:1:1:0:60:199:1:0:0.4 0/1:230:20:9,11:86,124:0.087:2,2:25.3:1:30.2:1:0.81348:1.18:60:19:0.0837:0:1.8 -4 67840426 . G T 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02008;SOR=2.24601;LSEQ=AACTATTTCTGAATTATCTG;RSEQ=TTTGAAGCTACCTGTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:25:2,23:6,42:0.3425:2,2:23.6:1:30:1:0.70702:1.63247:60:50:0.3425:0:1 1/0:74:40:11,29:7,27:0.5405:2,2:20.7:1:29.5:1:0.59084:1.46:60:39:0.5493:0:1.3 -4 68141830 . A G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70293;SOR=1.33847;LSEQ=GTAACAGCAAGATGGCTGCC;RSEQ=TGGGACCTAGAAAGGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:4:2,2:41,27:0.0556:2,2:10.3:1:31.8:1:1:1.50946:52:8:0.0571:0:3.8 0/1:41:3:2,1:24,14:0.0732:2,2:17:1:30:1:1:1.16:28.3:6:0.075:0:5.3 -4 68141861 . C T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48434;SOR=1.63947;LSEQ=AAAGGGAGAAGCCATGTTGC;RSEQ=CAACTCCAGAGGTTGGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:4:2,2:36,43:0.0482:2,2:33:1:31.3:1:1:1.19:52:8:0.0488:0:3.8 0/1:52:4:2,2:25,23:0.0769:2,2:40.3:1:30.3:1:1:1.0852:27:8:0.0816:0:5.3 -4 68141897 . G T 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.40211;SOR=2.6982;LSEQ=GTATAAGAGTTTGAAAGGCA;RSEQ=TGTCTGATTTCAGAAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:21,47:0.0286:2,2:22:1:29.5:1:0.53292:2.21:44:4:0.0286:0:5 0/1:54:4:2,2:23,27:0.0741:2,2:19.3:1:30.3:1:1:1.17:27:8:0.0741:0:5.3 -4 68141903 . G T 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40452;SOR=2.58665;LSEQ=GAGTTTGAAAGGCAGTGTCT;RSEQ=ATTTCAGAAACCTTTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:16,44:0.0323:2,2:16:1:27.5:1:0.47647:2.70:44:4:0.0323:0:5 0/1:50:4:2,2:22,23:0.08:2,2:13.3:1:28:1:1:1.04:27:8:0.0816:0:5.3 -4 68141904 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50051;SOR=0;LSEQ=AGTTTGAAAGGCAGTGTCTG;RSEQ=TTTCAGAAACCTTTTCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:16,42:0.0333:2,2:9.5:1:29.5:1:0.48983:2.58:60:4:0.0333:0:1.5 0/0:49:0:0,0:24,25:0:2,0:23:1:28.5:1:1:0:56.8:98:1:0:0.5 -4 68141913 . AC GA 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66221;SOR=1.74562;LSEQ=GGCAGTGTCTGATTTCAGAA;RSEQ=CTTTTCCTGTAAATGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:14,34:0.04:2,2:7.5:1:30.4:1:0.51429:2.38:44:4:0.0408:0.02:4.5 0/1:44:3:1,2:18,23:0.0682:2,2:6.7:1:29.5:1:1:1.54994:25.7:6:0.0682:0.0227:4.3 -4 68263831 . T G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGGCTAGGCTCAGCTGG;RSEQ=TGATTCTTCTGATCTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 68264241 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGTTTCACATCTGCTC;RSEQ=GTCTAAAGGTTGGTTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:1:29.5:1:1:0:53.5:4:1:0:2 -4 68264361 . A C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAGGCCTCAAAGAGGT;RSEQ=TAAATATCCACTTGCAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,1:0.4:2,2:37.5:1:31.5:1:1:1:46:4:0.4:0:3.5 -4 68264384 . ACAAAGAGAGTT GCAAAGAGTG 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATCCACTTGCAGACTTT;RSEQ=TTTCCAAACTGCTCTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:23:0:32.5:1:1:0:46:4:0.6667:0:2.5 -4 68264417 . A G 33 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTCCAAACTGCTCTATGAAA;RSEQ=GAAAGGTTAAACTCGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19:1:33.5:1:1:0:60:4:1:0:2 1/0:2:1:1,0:1,0:0.5:0,0:4:0:33:0:1:0:60:2:0.5:0:2 -4 68264432 . G T 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAAAGAAAGGTTAAACTC;RSEQ=GCGAGTTGAACGCACACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:1:31.5:1:1:0:60:4:1:0:2 1/1:1:1:1,0:0,0:1:0,0:19:0:33:0:1:0:60:2:1:0:2 -4 68264531 . T A 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCATTGGCCTCAAAGCGA;RSEQ=TGAAATCTGCACCTGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:1,2:1,2:0.5:2,2:24.3:1:30.3:1:1:1:34:6:0.5:0:6 -4 68264543 . C A 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCGATTGAAATCTGCA;RSEQ=CTGGAAATTCCACAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:1,2:1,2:0.5:2,2:21.3:1:30.7:1:1:1:60:6:0.5:0:1.3 -4 68264552 . T A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATCTGCACCTGGAAAT;RSEQ=CCACAAAAAGAGTGTATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:42:0:30:0:1:1.73:21:4:0.4:0:8 -4 68264554 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATCTGCACCTGGAAATTC;RSEQ=ACAAAAAGAGTGTATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:40:0:30.5:1:1:1.73:21:4:0.4:0:8 -4 68264562 . GA CG 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTGGAAATTCCACAAAAA;RSEQ=GTGTATCAAATCTGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:31:0:31.8:1:1:1.73:21:4:0.4:0:7 -4 68264568 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTCCACAAAAAGAGTGT;RSEQ=TCAAATCTGCTCTGTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:26:0:32:0:1:1.73:21:4:0.4:0:7 -4 68264574 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAAAAGAGTGTATCAAA;RSEQ=CTGCTCTGTCAAAAGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:20:0:31.5:1:1:1.73:21:4:0.4:0:7 -4 68264579 . TCTGTCAAAAGGAAGTTTC T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGTGTATCAAATCTGC;RSEQ=AATTCTGCTAGTTGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:27:1:31.8:1:1:1.73:60:4:0.4:0.4:1 -4 68264582 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTATCAAATCTGCTCT;RSEQ=TCAAAAGGAAGTTTCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:0,1:0.4:0,2:12:0:30.5:1:1:0:21:4:0.6667:0:7 -4 68264641 . A T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACAAATAAGTTTCTGAG;RSEQ=ATTCTTCTGTCTAACATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:6:0:29.5:1:1:1:40.5:4:0.5:0:6 -4 68264652 . C G 65 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCTGAGAATTCTTCTGT;RSEQ=TAACATTATATGAAGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:17.3:1:32.5:1:1:0:42.8:8:1:0:4.5 -4 68264666 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTCTAACATTATATGA;RSEQ=GAAATCCCGTTTCCAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:31:0:31.5:1:1:1:40.5:4:0.5:0:6 -4 68264676 . T C 34 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTATATGAAGAAATCCCG;RSEQ=TTCCAACGAAGGCCTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:20:0:34:0:1:1:45:4:0.5:0:3 -4 68264684 . G T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGAAATCCCGTTTCCAAC;RSEQ=AAGGCCTCAAAGGTGTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:12:0:31.5:1:1:1:45:4:0.5:0:3 -4 68264697 . G C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCCAACGAAGGCCTCAAAG;RSEQ=TGTCCAAATATCCACTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30.5:1:1:0:40.5:4:1:0:6 -4 68264699 . G A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAACGAAGGCCTCAAAGGT;RSEQ=TCCAAATATCCACTGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:12.5:1:27:1:1:0:40.5:4:0.6667:0:6 -4 68264702 . C A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAAGGCCTCAAAGGTGTC;RSEQ=AAATATCCACTGGCAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:9.5:1:28:1:1:0:40.5:4:0.6667:0:6 -4 68264714 . G T 50 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AAGGTGTCCAAATATCCACT;RSEQ=GCAAACTTTACAAAGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:6:0:31.7:1:1:0:49.7:6:1:0:5.3 0/0:2:0:0,0:1,1:0:2,0:9.5:1:31:1:1:0:46.5:4:1:0:3.5 -4 68264718 . A G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48571;SOR=4.4496;LSEQ=TGTCCAAATATCCACTGGCA;RSEQ=ACTTTACAAAGAGAGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:10:0:33:0:1:0:29:2:0.3333:0:7 1/0:4:3:2,1:1,0:0.75:0,2:8:1:31.3:1:1:0:45:6:0.75:0:6.7 -4 68264729 . G C 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2;SOR=Inf;LSEQ=CCACTGGCAAACTTTACAAA;RSEQ=AGAGTGTTTCCAAACTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.5:1:33:0:1:0:52.3:8:1:0:5.8 1/0:6:3:2,1:2,1:0.5:2,2:14.3:1:31:1:1:1:53:6:0.5:0:4.7 -4 68264731 . G C 67 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07619;SOR=0;LSEQ=ACTGGCAAACTTTACAAAGA;RSEQ=AGTGTTTCCAAACTGCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:20.5:1:33.8:1:1:0:52.3:8:1:0:5.8 0/1:6:2:2,0:2,2:0.3333:2,0:13.5:1:33:0:0.46667:0:56.5:4:0.3333:0:7.5 -4 68264737 . T C 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55808;SOR=3.3264;LSEQ=AAACTTTACAAAGAGAGTGT;RSEQ=TCCAAACTGCTCAATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:24:1:33:1:1:1.73:44.5:4:0.4:0:7 1/0:7:5:3,2:1,1:0.7143:2,2:17.2:1:30.8:1:1:1.41:50.4:10:0.7143:0:7 -4 68264744 . C T 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=ACAAAGAGAGTGTTTCCAAA;RSEQ=TGCTCAATCAAAAGAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:36:0:32:0:1:1.73:60:4:0.4:0:4.5 0/0:8:0:0,0:4,4:0:2,0:25.9:1:31.8:1:1:0:48.1:16:1:0:5.9 -4 68264746 . G C 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29293;SOR=3.95135;LSEQ=AAAGAGAGTGTTTCCAAACT;RSEQ=CTCAATCAAAAGAAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:33:1:32.5:1:1:1.73:44.5:4:0.4:0:7 1/0:8:6:3,3:1,1:0.75:2,2:23.3:1:31:1:1:1:48.7:12:0.75:0:6.7 -4 68264750 . A C 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30579;LSEQ=AGAGTGTTTCCAAACTGCTC;RSEQ=ATCAAAAGAAAGGTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:30:1:31.3:1:1:1.7321:41:6:0.6:0:7.3 1/0:9:6:3,3:1,2:0.6667:2,2:27.3:1:31:1:1:1.85:48.7:12:0.6667:0:6.7 -4 68264767 . A T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76283;LSEQ=CTCAATCAAAAGAAAGGTTA;RSEQ=ACTCTGTGAATTGAATGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:1,2:0.625:2,2:25.4:1:31.4:1:0.46429:5.78:45.2:10:0.625:0:4.8 1/0:9:5:3,2:1,2:0.5556:2,2:45:1:30:1:1:2.60:50.4:10:0.7143:0:6.4 -4 68264774 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18301;SOR=0;LSEQ=AAAAGAAAGGTTAAACTCTG;RSEQ=GAATTGAATGCACACATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:9.5:1:30.5:1:1:1.8258:60:4:0.25:0:4.5 0/0:10:0:0,0:4,6:0:2,0:33.9:1:29.3:1:1:0:48.5:20:1:0:5.2 -4 68264783 . T C 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.34996;SOR=2.89722;LSEQ=GTTAAACTCTGTGAATTGAA;RSEQ=GCACACATCACAAAGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:0,1:0.4286:0,0:28:1:33.7:1:0.25:0:45.7:6:0.4286:0:3.3 1/0:10:7:3,4:1,1:0.7:2,2:28.6:1:29.3:1:1:1.29098:49.4:14:0.7778:0:4.7 -4 68264797 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=ATTGAATGCACACATCACAA;RSEQ=GTAGTTTCTGAGAATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:24.2:1:30.2:1:1:0:44.6:18:1:0:4.8 0/1:12:2:1,1:5,5:0.1667:2,2:24:1:29:1:1:1:46.5:4:0.1667:0:6.5 -4 68264798 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.48571;SOR=Inf;LSEQ=TTGAATGCACACATCACAAA;RSEQ=TAGTTTCTGAGAATGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:24.6:1:32:1:1:0:44.6:18:1:0:4.8 0/1:12:2:1,1:5,5:0.1667:2,2:24.5:1:29:1:1:1:60:4:0.1667:0:5.5 -4 68264824 . C G 85 MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.10256;SOR=0.10559;LSEQ=TCTGAGAATGATTCTGTCTA;RSEQ=TTTTTATACGAAGATATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:1,1:0.75:2,2:25.5:1:33:1:1:1:37.7:12:0.75:0:4.5 0/1:5:1:0,1:2,2:0.2:2,0:25:0:32:0:1:0:40:2:0.2:0:2 -4 68264833 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=0;LSEQ=GATTCTGTCTACTTTTTATA;RSEQ=GAAGATATTTCCTTTTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:30.5:1:30.5:1:1:1.58:60:4:0.2:0:5 0/0:5:0:0,0:2,3:0:2,0:30.2:1:31.6:1:1:0:53.2:10:1:0:3.4 -4 68264840 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10989;SOR=Inf;LSEQ=TCTACTTTTTATACGAAGAT;RSEQ=TTTCCTTTTCTACTTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:26.2:1:29:1:1:0:42.8:18:1:0:4.9 0/1:5:2:1,1:1,2:0.4:2,2:20:0:33.5:1:1:1.73:53:4:0.4:0:2.5 -4 68264851 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TACGAAGATATTTCCTTTTC;RSEQ=ACTTTTGGCCTATAAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:23:1:30:1:1:1.29:60:4:0.2222:0:5 0/0:5:0:0,0:2,3:0:2,0:15.4:1:30.2:1:1:0:53.2:10:1:0:4.2 -4 68264854 . T A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATATTTCCTTTTCTAC;RSEQ=TTTGGCCTATAAGCGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:29.7:1:30.3:1:1:0:40.7:14:1:0:5.3 1/1:5:5:2,3:0,0:1:0,2:13.6:1:30:1:1:0:53.2:10:1:0:4.2 -4 68264864 . T A 78 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTTCTACTTTTGGCCTA;RSEQ=AAGCGCTTGAAATCTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:33.8:1:30.5:1:1:0:41.3:12:1:0:5.7 1/1:3:3:1,2:0,0:1:0,2:15.3:1:28.3:1:1:0:53.3:6:1:0:5.3 -4 68264883 . A C 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAAGCGCTTGAAATCTCCA;RSEQ=CTTCAAATATCACAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:30.5:1:32:1:1:0:41.8:8:0.8:0:6.5 1/1:2:2:1,1:0,0:1:0,2:20.5:1:30:1:1:0:50:4:1:0:6 -4 68264886 . T G 77 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCTTGAAATCTCCAACT;RSEQ=CAAATATCACAGAAAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:23.6:1:33.4:1:1:0:40.8:10:1:0:6.2 1/1:2:2:1,1:0,0:1:0,2:19:1:29:0:1:0:50:4:1:0:6 -4 68264898 . G A 49 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAACTTCAAATATCACA;RSEQ=AAAGAGTGTTTCACATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:22:1:31:0:1:0:35.7:6:1:0:6.7 1/1:1:1:0,1:0,0:1:0,0:23:0:28:0:1:0:40:2:1:0:6 -4 68264905 . T G 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAAATATCACAGAAAGAG;RSEQ=GTTTCACATCTGCTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:14.5:1:33:0:1:0:33.5:4:1:0:6.5 1/1:1:1:0,1:0,0:1:0,0:16:0:30:0:1:0:40:2:1:0:6 -4 68264989 . G C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTACTGAGAATTCTTT;RSEQ=TCCAGCAGTATATGAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:32.5:1:1:0:60:4:1:0:3.5 -4 68264994 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGAGAATTCTTTGTCCA;RSEQ=CAGTATATGAAGAAATCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:1:30.5:1:1:0:60:4:1:0:3.5 -4 68264997 . G T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAATTCTTTGTCCAGCA;RSEQ=TATATGAAGAAATCCCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39.5:1:30.5:1:1:0:60:4:1:0:3.5 -4 68265246 . TA GT 29 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATTCCACAAAAAGAGTG;RSEQ=TCAAATGTGCTCTGTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:31:1:1:0:60:4:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:28.5:1:29:1:1:0:50:4:0.6667:0:5 -4 68265271 . AGGTTCAAGTCTGTGAGTGGAATACACA CAGTTCACCTCTGTGAGTTGAGTAGAGG 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=AATGTGCTCTGTCTAAAGGA;RSEQ=CAACACAAAGAAGTTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35:0:32:0:1:0:60:4:1:0:5 1/0:4:2:1,1:1,1:0.5:2,2:31:1:29.1:1:1:1:21:4:0.6667:0.5:7 -4 68265274 . T G 31 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTCTGTCTAAAGGAAGG;RSEQ=TCAAGTCTGTGAGTGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:0:33:0:1:0:60:4:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:37.5:1:31:1:1:0:50:4:0.6667:0:5 -4 68265279 . G C 32 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTAAAGGAAGGTTCAA;RSEQ=TCTGTGAGTGGAATACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:0:34:0:1:0:60:4:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:36:1:32:1:1:0:50:4:0.6667:0:5 -4 68265285 . G C 32 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGAAGGTTCAAGTCTGT;RSEQ=AGTGGAATACACACAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:33:0:1:0:60:4:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:30:1:32.5:1:1:0:50:4:0.6667:0:5 -4 68265408 . C G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTGCGGACTATCCAAC;RSEQ=AGAGTGTTTCCACACTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:30.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 68265457 . T C 34 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAAAGGTTAAACTCTGTGAG;RSEQ=TGAACGCACACATCAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:45:1:30:1:1:0:60:4:1:0:2.5 1/0:3:2:2,0:1,0:0.6667:0,0:23:1:34:0:1:0:33.5:4:0.6667:0:7.5 -4 68265462 . C T 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GTTAAACTCTGTGAGTTGAA;RSEQ=GCACACATCAAAAAGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30.5:1:1:0:60:4:1:0:2.5 0/0:3:0:0,0:3,0:0:0,0:29.7:1:32.3:1:1:0:42.3:6:1:0:6.3 -4 68265463 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TTAAACTCTGTGAGTTGAAC;RSEQ=CACACATCAAAAAGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:39.5:1:31.5:1:1:0:60:4:1:0:2.5 1/0:3:2:2,0:1,0:0.6667:0,0:29:1:31:1:1:0:33.5:4:0.6667:0:7.5 -4 68265487 . A T 80 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=ACATCAAAAAGTAGTTTCTG;RSEQ=GAATGATTCTGTCTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:15.5:1:29:1:1:0:60:4:1:0:2.5 1/0:8:6:6,0:1,1:0.75:2,0:23.2:1:31.3:1:0.25:0:39.2:12:0.75:0:7.7 -4 68265492 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAGTAGTTTCTGAGAAT;RSEQ=ATTCTGTCTAATTTTTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10.5:1:30.5:1:1:0:60:4:1:0:2.5 0/1:9:2:1,1:7,0:0.2222:0,2:30.5:1:28.5:1:0.22222:0:60:4:0.2222:0:4 -4 68265503 . A G 121 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.15827;LSEQ=TCTGAGAATGATTCTGTCTA;RSEQ=TTTTTATACGAAGATATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,0:0.8:0,2:6:1:33.3:1:1:0:47.5:8:0.8:0:7.8 1/1:17:14:11,3:0,0:0.8235:0,2:14.8:1:31.9:1:1:0:47.3:28:0.8235:0:7.7 -4 68265506 . T G 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.63336;SOR=0.6367;LSEQ=GAGAATGATTCTGTCTAATT;RSEQ=TTATACGAAGATATTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:0.2857:2,0:7:1:31.5:1:1:0:47:4:0.2857:0:8 0/1:20:4:3,1:11,5:0.2:2,2:15.8:1:32.8:1:1:1.34:59.5:8:0.2105:0:8 -4 68265519 . A G 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAATTTTTATACGAAGAT;RSEQ=TTTCTTTTTCTACCATTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:1:0,2:17.2:1:33.7:1:1:0:48.7:18:1:0:7.7 1/1:31:29:20,9:1,1:0.9355:2,2:19.2:1:31.6:1:1:2.16:50.2:58:0.9355:0:7.5 -4 68265520 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTAATTTTTATACGAAGATA;RSEQ=TTCTTTTTCTACCATTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:8,1:0:2,0:18.2:1:31.6:1:1:0:48.7:18:1:0:7.7 0/1:32:2:1,1:21,9:0.0625:2,2:30:1:29.5:1:0.53427:2.26571:60:4:0.0625:0:4 -4 68265524 . T C 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTATACGAAGATATTTC;RSEQ=TTTTCTACCATTGGCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:1:0,2:22.2:1:32.8:1:1:0:48.7:18:1:0:7.7 1/1:31:29:20,9:1,1:0.9355:2,2:23.1:1:30:1:1:2.16:50.7:28:0.9333:0:7.5 -4 68265528 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATACGAAGATATTTCTTTT;RSEQ=CTACCATTGGCCTCAAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:0:2,0:23.7:1:31.6:1:1:0:48.8:20:1:0:7.6 0/1:41:2:1,1:26,13:0.0488:2,2:22:1:30.5:1:1:1.96402:60:4:0.05:0:4 -4 68265534 . A T 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATATTTCTTTTTCTACC;RSEQ=TTGGCCTCAAAGCGATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:9,2:0,0:1:0,2:27.1:1:31.5:1:1:0:48.6:22:1:0:7.5 1/1:44:42:28,14:0,1:0.9545:0,2:22.3:1:30.4:1:0.34884:0:51.4:84:0.9767:0:7 -4 68265539 . C T 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTTTTTCTACCATTGG;RSEQ=CTCAAAGCGATTGAAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:9,3:0,0:1:0,2:29.8:1:30.1:1:1:0:48.6:24:1:0:7.3 1/1:50:47:28,19:1,2:0.94:2,2:24.4:1:29.4:1:0.565:2.88:52.7:94:0.94:0:6.6 -4 68265545 . A T 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62165;SOR=0.59561;LSEQ=TTTTCTACCATTGGCCTCAA;RSEQ=GCGATTGAAATTTCCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:9,4:0.1333:2,2:45:1:32.5:1:1:2.12136:41.5:4:0.1333:0:8 0/1:60:5:3,2:31,24:0.0833:2,2:27.4:1:31.4:1:1:1.16:54.6:10:0.0833:0:6.6 -4 68265557 . T C 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTCAAAGCGATTGAAAT;RSEQ=TCCACATGGAAATTCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:10,5:0,0:1:0,2:35.1:1:31.7:1:1:0:49.5:30:1:0:6.6 1/1:69:65:34,31:2,2:0.942:2,2:28.2:1:31.9:1:1:1.10:49.9:130:0.942:0:6.3 -4 68265562 . CA AC 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CAAAGCGATTGAAATTTCCA;RSEQ=TGGAAATTCCACAAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:34.1:1:32.2:1:1:0:49.5:30:1:0:6.6 0/1:72:2:1,1:35,34:0.0278:2,2:24:0:29.8:1:1:1.029:43:4:0.0278:0:6.5 -4 68265570 . T C 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69767;LSEQ=TTGAAATTTCCACATGGAAA;RSEQ=TCCACAAAAAGAGTGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:17:10,7:1,1:0.8947:2,2:29.4:1:31.9:1:1:1.40:48.4:34:0.8947:0:6.6 1/1:76:65:31,34:3,4:0.8553:2,2:29:1:31.7:1:1:1.21:49.9:130:0.8667:0:6.2 -4 68265572 . C G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAATTTCCACATGGAAATT;RSEQ=CACAAAAAGAGTGTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:26.6:1:31.1:1:1:0:47.7:38:1:0:6.3 0/1:76:2:1,1:35,39:0.0263:2,2:33:0:32:1:1:1.11:43:4:0.027:0:6.5 -4 68265575 . C CA 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTCCACATGGAAATTCCA;RSEQ=AAAAAGAGTGTTTCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:26.1:1:31.7:1:1:0:47.7:38:1:0:6.3 0/1:79:2:1,1:36,41:0.0253:2,2:27.5:1:28:1:1:1.14:47:4:0.0253:0:7 -4 68265576 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCCACATGGAAATTCCAC;RSEQ=AAAAGAGTGTTTCAAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:25.9:1:29.9:1:1:0:47.7:38:1:0:6.3 0/1:80:2:1,1:35,42:0.025:2,2:24.5:1:29.5:1:1:1.20:53.5:4:0.0256:0:7.5 -4 68265579 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCACATGGAAATTCCACAAA;RSEQ=AGAGTGTTTCAAATCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:25.3:1:29.9:1:1:0:47.7:38:1:0:6.3 0/1:81:2:1,1:36,43:0.0247:2,2:33.5:1:28:1:1:1.19:43:4:0.0247:0:6.5 -4 68265582 . A G 92 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.34556;SOR=Inf;LSEQ=CATGGAAATTCCACAAAAAG;RSEQ=GTGTTTCAAATCTGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:24.2:1:30.1:1:1:0:47.7:38:1:0:6.3 0/1:85:8:3,5:35,42:0.0941:2,2:18.5:1:30.8:1:0.72642:1.38363:50.3:16:0.0952:0:5.1 -4 68265585 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAATTCCACAAAAAGAGT;RSEQ=TTTCAAATCTGCTCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:22.7:1:31.8:1:1:0:47.7:38:1:0:6.3 0/1:86:2:1,1:37,47:0.0233:2,2:5:0:31:1:1:1.27:42:4:0.0235:0:4 -4 68265589 . C A 78 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58884;SOR=Inf;LSEQ=ATTCCACAAAAAGAGTGTTT;RSEQ=AAATCTGCTCTGTCTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:20.8:1:31:1:1:0:47.7:38:1:0:6.3 0/1:86:6:2,4:36,44:0.0698:2,2:21.5:1:30.2:1:0.68966:1.62736:52.7:12:0.0698:0:4.7 -4 68265591 . A C 84 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58884;SOR=Inf;LSEQ=TCCACAAAAAGAGTGTTTCA;RSEQ=ATCTGCTCTGTCTAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:19.8:1:29.5:1:1:0:47.7:38:1:0:6.3 0/1:86:6:2,4:36,44:0.0698:2,2:23.5:1:32.7:1:0.68966:1.62736:52.7:12:0.0698:0:4.7 -4 68265601 . G T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20568;SOR=0.34201;LSEQ=GAGTGTTTCAAATCTGCTCT;RSEQ=TCTAAAGGAAAGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:6,5:1,1:0.8462:2,2:19.2:1:29.4:1:1:1.18:46.6:22:0.8462:0:7.3 1/0:60:39:14,25:6,7:0.65:2,2:23:1:29.4:1:0.52919:1.51774:44.3:78:0.65:0:6.6 -4 68265603 . C G 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60429;SOR=0.52694;LSEQ=GTGTTTCAAATCTGCTCTGT;RSEQ=TAAAGGAAAGTTCAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:30:0:33.5:1:1:1:42:4:0.1667:0:3 0/1:53:5:2,3:18,30:0.0943:2,2:20.4:1:31.8:1:1:1.11:38.8:10:0.0962:0:5 -4 68265605 . A G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.68255;LSEQ=GTTTCAAATCTGCTCTGTCT;RSEQ=AAGGAAAGTTCAACTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:3,5:1,1:0.8:2,2:23.5:1:31.6:1:1:1.58108:44.9:16:0.8:0:7 1/0:52:38:14,24:6,8:0.7308:2,2:23:1:30.4:1:0.75417:1.2794:45.8:76:0.7308:0:6.8 -4 68265608 . G T 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.18322;SOR=0.26392;LSEQ=TCAAATCTGCTCTGTCTAAA;RSEQ=GAAAGTTCAACTCTGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:25:0:31.5:1:0.46429:3.87:42:4:0.25:0:3 0/1:51:4:2,2:17,30:0.0784:2,2:29.5:1:31.8:1:0.62289:1.74:40:8:0.0784:0:4.3 -4 68265612 . A G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74783;LSEQ=ATCTGCTCTGTCTAAAGGAA;RSEQ=GTTCAACTCTGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:1,5:1,1:0.75:2,2:28.3:1:32.5:1:0.46429:3.87298:44.2:12:0.75:0:6.7 1/0:42:29:7,22:6,7:0.6905:2,2:25.1:1:29.7:1:0.17269:2.62509:43:28:0.6829:0:7.1 -4 68265618 . A T 104 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03627;LSEQ=TCTGTCTAAAGGAAAGTTCA;RSEQ=CTCTGTGAGTTGAATGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:2,5:0.3:2,2:10.7:1:29.7:1:1:1.22:42:6:0.3:0:7.7 0/1:39:12:2,10:10,16:0.3077:2,2:25.8:1:29.1:1:0.26806:3.03952:41.6:24:0.3077:0:7.7 -4 68265623 . G A 78 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31726;SOR=Inf;LSEQ=CTAAAGGAAAGTTCAACTCT;RSEQ=TGAGTTGAATGCACACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:15.5:1:32.4:1:1:0:43.5:20:1:0:6.2 0/1:37:6:2,4:8,23:0.1622:2,2:8.7:1:30.3:1:0.65274:1.42:52.7:12:0.1622:0:4.7 -4 68265634 . G A 124 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACTCTGTGAGTTGAAT;RSEQ=CACACAACAGAAATAAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:22.2:1:30:1:1:0:41.2:10:1:0:7.4 1/1:21:18:3,15:1,1:0.8571:2,2:23.8:1:29.9:1:0.36842:4.47215:40.1:36:0.9:0:6.9 -4 68265641 . A C 120 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGAGTTGAATGCACACA;RSEQ=CAGAAATAAGTTACTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:26:1:32.3:1:1:0:41.5:8:1:0:7.5 1/1:20:16:3,13:2,2:0.8:2,2:21:1:30.1:1:0.24871:3.95518:43.4:15:0.7895:0:6.8 -4 68265644 . G C 125 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTTGAATGCACACAACA;RSEQ=AAATAAGTTACTGAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:26:1:32:1:1:0:41.5:8:1:0:7.5 1/0:19:15:3,12:1,1:0.7895:2,2:17.4:1:32.1:1:0.42647:3.6058:42.7:30:0.7895:0:6.7 -4 68265671 . C G 105 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53782;SOR=3.07187;LSEQ=GTTACTGAGAATTCTTCTGT;RSEQ=TAACATTATACGAAGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:32:0:33.5:1:1:1:43:4:0.5:0:8 1/0:13:10:3,7:1,2:0.7692:2,2:9.8:1:31.7:1:1:1.15267:47.2:20:0.7692:0:5.3 -4 68265672 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21891;SOR=0.20694;LSEQ=TTACTGAGAATTCTTCTGTC;RSEQ=AACATTATACGAAGAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:27:0:32.5:1:1:1:47:4:0.5:0:4 0/1:13:2:1,1:3,8:0.1538:2,2:28:0:32.5:1:1:2.45:49:4:0.1538:0:4 -4 68265680 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52048;SOR=0.28074;LSEQ=AATTCTTCTGTCTAACATTA;RSEQ=ACGAAGAAATCACGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:0:33.5:1:1:1:47:4:0.5:0:4 0/1:10:2:1,1:3,5:0.2:2,2:26:0:33:1:1:1.58:49:4:0.2222:0:4 -4 68265682 . C T 64 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06061;SOR=0;LSEQ=TTCTTCTGTCTAACATTATA;RSEQ=GAAGAAATCACGTTTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:23.5:1:32:1:1:0:45:8:1:0:6 0/1:7:2:1,1:1,2:0.2857:2,2:6.5:1:30.5:1:1:1.73:51:4:0.2857:0:3 -4 68265685 . A G 30 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57576;SOR=0.437;LSEQ=TTCTGTCTAACATTATACGA;RSEQ=GAAATCACGTTTCCAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:18:0:33.5:1:1:1:43:4:0.5:0:8 0/1:7:2:1,1:2,3:0.2857:2,2:3.5:1:30.5:1:1:1.41:51:4:0.2857:0:3 -4 68265692 . A C 64 d7;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TAACATTATACGAAGAAATC;RSEQ=CGTTTCCAACGAAGGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:13.5:1:32.3:1:1:0:45:8:1:0:6 0/1:5:2:1,1:1,2:0.4:2,2:14:0:31:1:1:1.73:49:4:0.4:0:4 -4 68265736 . T A 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCCATATATCCACTTGC;RSEQ=GAATTTACAAGGAGAGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:0:29:1:1:0:60:4:1:0:1 -4 68265765 . G C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAGAGTGTCTCCAAACT;RSEQ=CTCAATCAAAAGAAAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:15:0:33:0:1:0:40:2:1:0:6 1/0:5:3:2,1:1,1:0.6:2,2:19.3:1:32.7:1:1:1.73:40:6:0.6:0:7 -4 68265769 . A C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGTCTCCAAACTGCTC;RSEQ=ATCAAAAGAAAGTTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:19:0:34:0:1:0:40:2:1:0:6 1/0:5:3:2,1:1,1:0.6:2,2:23.3:1:32.3:1:1:1.73:40:6:0.6:0:7 -4 68265782 . T G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCTCAATCAAAAGAAAG;RSEQ=TTAAACTCCGTGAATTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:32:0:34:0:1:0:40:2:1:0:6 1/1:3:3:2,1:0,0:1:0,2:36.3:1:32.7:1:1:0:40:6:1:0:7 -4 68265786 . A T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAATCAAAAGAAAGTTTA;RSEQ=ACTCCGTGAATTGAACGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:36:0:30:0:1:0:40:2:1:0:6 1/1:3:3:2,1:0,0:1:0,2:38:1:30.7:1:1:0:40:6:1:0:7 -4 68265791 . C T 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAAAGAAAGTTTAAACTC;RSEQ=GTGAATTGAACGCACCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:41:0:32:0:1:0:40:2:1:0:6 1/0:4:3:2,1:0,0:0.75:0,2:27:1:32.3:1:1:0:40:6:1:0:6.3 -4 68265807 . C A 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCGTGAATTGAACGCAC;RSEQ=CATCACAAAGTAGTTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:35:0:32:0:1:0:40:2:1:0:6 1/1:6:6:5,1:0,0:1:0,2:23.3:1:31:1:1:0:38.2:12:1:0:5.5 -4 68265843 . TA GT 120 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGAGAATGATTCTGTCTA;RSEQ=TTTTATACGAAGATATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:12.8:1:31.1:1:1:0:44.5:8:1:0:6.8 1/1:17:16:11,5:0,0:0.9412:0,2:12.4:1:30.1:1:1:0:37.1:32:1:0.5294:6.1 -4 68265873 . T A 146 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATATTTCCTTTTCTAC;RSEQ=TTTGGCGTATAAGCGCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:37.6:1:30.6:1:1:0:43.6:10:1:0:7 1/1:34:34:19,15:0,0:1:0,2:21.3:1:28.7:1:1:0:42.7:16:1:0:6.1 -4 68265880 . G C 152 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCTTTTCTACTTTTGGC;RSEQ=TATAAGCGCTCGAAATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:41.8:1:31.4:1:1:0:43.6:10:1:0:7 1/1:34:32:17,15:1,1:0.9412:2,2:26.8:1:30.5:1:1:1.13:42.2:31:0.9394:0:6.4 -4 68265883 . T A 155 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTTCTACTTTTGGCGTA;RSEQ=AAGCGCTCGAAATCTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:43:1:30.2:1:1:0:43.6:10:1:0:7 1/1:35:35:18,17:0,0:1:0,2:27.9:1:30.3:1:1:0:42.7:70:1:0:6.2 -4 68265891 . C T 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTGGCGTATAAGCGCT;RSEQ=GAAATCTCCAACTGCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:5,2:0,0:1:0,2:32.4:1:30.4:1:1:0:37.1:14:1:0:5.7 1/1:38:38:19,19:0,0:1:0,2:31.7:1:30.2:1:1:0:41.9:76:1:0:6 -4 68265896 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGGCGTATAAGCGCTCGAAA;RSEQ=CTCCAACTGCAAATATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:31.6:1:30.7:1:1:0:37.1:14:1:0:5.7 0/1:38:2:1,1:18,18:0.0526:2,2:10:0:31.5:1:1:1:21:4:0.0541:0:4 -4 68265902 . A C 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGCGCTCGAAATCTCCA;RSEQ=CTGCAAATATCACAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:1:0,2:25.5:1:30.6:1:1:0:37.5:16:1:0:6 1/1:38:38:19,19:0,0:1:0,2:32.6:1:31.5:1:1:0:41.9:76:1:0:6 -4 68265925 . T G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAATATCACAAAAAGAGG;RSEQ=TTTCACATCTGCTCCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:15.1:1:31:1:1:0:39.9:14:1:0:6.7 1/1:36:36:17,19:0,0:1:0,2:14.5:1:30.8:1:1:0:42.6:35:1:0:6 -4 68265940 . CT TG 49 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=AGAGGTTTTCACATCTGCTC;RSEQ=TCTAAAAGAAGGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24.3:1:31.3:1:1:0:38:6:1:0:6.7 0/1:5:2:1,1:0,0:0.4:0,2:5.5:1:29.8:1:1:0:27:4:0.4:0:6 -4 68265948 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCACATCTGCTCCTTCTAAA;RSEQ=GAAGGTTCAACTCTGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:0:31.5:1:1:0:37:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 68265951 . AG CA 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATCTGCTCCTTCTAAAAGA;RSEQ=GTTCAACTCTGTGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23:0:32.3:1:1:0:37:4:1:0:5.5 0/0:1:0:0,0:0,1:0:0,0:1:0:29:0:1:0:30:2:1:0:6 -4 68265958 . A C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTCTAAAAGAAGGTTCA;RSEQ=CTCTGTGAGTTGAATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,0:0.6667:0,0:17:0:32:1:1:0:37:4:0.6667:0:5.5 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 68265981 . AC GT 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=CTGTGAGTTGAATACACAGA;RSEQ=ACAAAGAAGTTACTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30.2:1:1:0:40.5:4:1:0.5:2.5 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 68266001 . A C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACACAAAGAAGTTACTGAGA;RSEQ=TTCTTCTGTCTAACATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:33:1:1:0:40.5:4:1:0:2.5 0/0:1:0:0,0:0,1:0:0,0:50:0:29:0:1:0:30:2:1:0:6 -4 68266143 . G A 115 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACTCTGTATGTTGAAC;RSEQ=CACACATCAAAAAGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:15:15:7,8:0,0:1:0,2:6.8:1:29.5:1:1:0:46.3:30:1:0:6.7 -4 68266152 . A G 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATGTTGAACGCACACATC;RSEQ=AAAAGTAGTTTCTCAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:3:1,2:7,7:0.1765:2,2:17.3:1:30.3:1:1:1.9219:46.7:6:0.1765:0:8 -4 68266158 . T A 123 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACGCACACATCAAAAAG;RSEQ=AGTTTCTCAGAATGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:17:17:8,9:0,0:1:0,2:20.8:1:30.2:1:1:0:46.1:34:1:0:6.5 -4 68266166 . CA GT 134 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCAAAAAGTAGTTTCT;RSEQ=GAATGATTCTGTCTAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:19:19:9,10:0,0:1:0,2:27.7:1:31.7:1:1:0:43.7:38:1:0.1053:5.6 -4 68266189 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGATTCTGTCTAGATTTT;RSEQ=TACGAAGATATTTCCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:20:2:1,1:8,10:0.1:2,2:25:0:33.5:1:1:1.24:45:4:0.1:0:6 -4 68266192 . C A 134 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCTGTCTAGATTTTATA;RSEQ=GAAGATATTTCCTTTTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:20:19:9,10:0,0:0.95:0,2:20.2:1:31.6:1:1:0:43.7:38:0.95:0:5.6 -4 68266199 . A G 134 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGATTTTATACGAAGAT;RSEQ=TTTCCTTTTCTACCCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:20:20:9,11:0,0:1:0,2:15.5:1:31.2:1:1:0:43.6:19:1:0:5.6 -4 68266214 . C G 47 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATATTTCCTTTTCTACC;RSEQ=TTGGCCAGAAAGAGCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:26:0:30:1:1:0:29.3:6:1:0:6 -4 68266216 . T A 47 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATTTCCTTTTCTACCCT;RSEQ=GGCCAGAAAGAGCTTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:24:0:29.7:1:1:0:29.3:6:1:0:6 -4 68266222 . G C 49 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTTTCTACCCTTGGCCA;RSEQ=AAAGAGCTTGAAATCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:18:0:31:1:1:0:29.3:6:1:0:6 -4 68266227 . A C 47 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTACCCTTGGCCAGAAAG;RSEQ=GCTTGAAATCTCTGCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:13:0:30:1:1:0:29.3:6:1:0:6 -4 68266352 . T G 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTGAGAATTCTTCTGTC;RSEQ=AGCATTACATGAAGAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:22:0:31:1:1:1:33:4:0.3333:0:4 -4 68266353 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGAGAATTCTTCTGTCT;RSEQ=GCATTACATGAAGAAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:20:0:33:1:1:1:60:4:0.3333:0:3 -4 68266354 . G A 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGAGAATTCTTCTGTCTA;RSEQ=CATTACATGAAGAAATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:24:0:29.5:1:1:1:33:4:0.3333:0:4 -4 68266360 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCTTCTGTCTAGCATTA;RSEQ=ATGAAGAAATCCCTTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:32:1:29.5:1:1:1:50:4:0.3333:0:2 -4 68266374 . T G 62 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTACATGAAGAAATCCC;RSEQ=TTTCTAAGGAAAGTCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:6.8:1:31:1:1:1:46.5:8:0.6667:0:3.5 -4 68266409 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCAAAGAGGTCCAAATATC;RSEQ=TCTTGCAGACTTTGAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:50:4:1:0:2 -4 68266465 . A T 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCATGAAAAGAAAGGTTA;RSEQ=ACTCTGTGAATTGAACGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:0,0:0.6667:0,0:14:1:32:0:1:0:30:4:0.6667:0:5 -4 68266500 . A T 46 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCACACATCACAAAGTAG;RSEQ=TTCTCAGAATGATTCTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:48:1:29.3:1:1:0:27.7:6:1:0:5 -4 68266505 . C G 49 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCACAAAGTAGATTCT;RSEQ=AGAATGATTCTGTATAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:45.3:1:31:1:1:0:27.7:6:1:0:5 -4 68266519 . A C 46 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCTCAGAATGATTCTGT;RSEQ=TAGTTTTTATACGAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:31.3:1:29.3:1:1:0:27.7:6:1:0:5 -4 68266540 . A T 42 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAGTTTTTATACGAAGATAT;RSEQ=TCCTTTTCTATCTTTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:1:0,0:10.3:1:27:1:1:0:27.7:6:1:0:5 -4 68266567 . T G 102 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTATCTTTGGCCTAAAAGC;RSEQ=CTACAAATCTCCACGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:12:11:6,5:0,1:0.9167:0,2:15.9:1:29.5:1:1:0:39.6:22:0.9167:0:6.3 -4 68266570 . AC TG 102 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTTGGCCTAAAAGCTCT;RSEQ=AAATCTCCACGTGCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:13:11:6,5:1,1:0.8462:2,2:19.9:1:29.7:1:1:1.18:39.6:22:0.8462:0:5.3 -4 68266582 . G C 149 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCTCTACAAATCTCCAC;RSEQ=TGCAAATATCACAAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:8.7:1:31:1:1:0:43.3:6:1:0:3.3 1/1:28:28:14,14:0,0:1:0,2:17.8:1:31:1:1:0:39.3:56:1:0:4.1 -4 68266593 . A C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATCTCCACGTGCAAATATC;RSEQ=CAAAAAGAGTATTTCACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:19.7:1:31:1:1:0:43.3:6:1:0:3.3 0/1:33:2:1,1:14,17:0.0606:2,2:17.5:1:29.5:1:1:1.21:45:4:0.0625:0:4 -4 68266603 . TA GG 153 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAATATCACAAAAAGAG;RSEQ=TTTCACATCTGCTCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:26:0:33:1:1:0:43.3:6:1:0:2.3 1/1:33:30:13,17:1,1:0.9091:2,2:24.2:1:31.3:1:1:1.29665:41:60:0.9375:0:2.9 -4 68266619 . TG T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGTATTTCACATCTGCTC;RSEQ=TCTAAAGGAAGTTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:10:0:34:0:1:0:39.8:8:1:0:1.8 0/1:37:2:1,1:15,19:0.0541:2,2:12:0:31.5:1:1:1.26:34:4:0.0541:0:3 -4 68266631 . GT AG 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCTCTGTCTAAAGGAA;RSEQ=TTCAACTCTATGAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:23:0:33:0:1:1.73:34:4:0.4:0:2 -4 68266636 . A C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGTCTAAAGGAAGTTTC;RSEQ=ACTCTATGAGTTGAATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:24:0:32:0:1:1.73:34:4:0.4:0:2 -4 68266721 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGAAATCCCGTTTCCAA;RSEQ=GAAGGCCTCAAAGAGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:0,2:1,1:0.5:2,0:23:0:31.5:1:1:0:31.5:4:0.6667:0:4.5 -4 68266726 . G A 25 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCCCGTTTCCAATGAAG;RSEQ=CCTCAAAGAGGTCCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:25:1:25:1:1:0:47:4:0.6667:0:4.5 -4 68266729 . T C 51 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGTTTCCAATGAAGGCC;RSEQ=CAAAGAGGTCCAAATATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:28:1:25.5:1:1:0:39.3:3:1:0:4.5 -4 68266733 . A T 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTCCAATGAAGGCCTCAA;RSEQ=GAGGTCCAAATATCCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:25:1:27:1:1:0:47:4:0.5:0:4.5 -4 68266748 . CT TG 59 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCAAAGAGGTCCAAATATC;RSEQ=CTTGCAGACTTTACAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:16.8:1:29.5:1:1:0:39.3:8:1:0.25:3.8 -4 68266765 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTCTTGCAGACTTTACA;RSEQ=ACAGAGTGTTTCCAGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:9:1:31.5:1:1:0:37:4:1:0:4.5 -4 69761100 . T TAC 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18659;SOR=Inf;LSEQ=GCTGACTCCCCTTTCTGAGT;RSEQ=AGTTATTTTCAAAATGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:29.3:1:29.3:1:1:0:60:46:1:0:0.4 0/1:18:2:1,1:9,7:0.1111:2,2:17:0:32.3:1:1:1.26772:49:4:0.1111:0:0 -4 69761131 . T C 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05249;SOR=0;LSEQ=AAAATGTCACATTTGTAGTT;RSEQ=CCATTTTCTTGTCTCTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:3,10:0.2778:2,2:18:1:31.6:1:0.58275:2.12:60:10:0.2778:0:1.2 0/0:14:0:0,0:7,7:0:2,0:14.3:1:29.5:1:1:0:60:28:1:0:0.1 -4 73526628 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5004;SOR=Inf;LSEQ=TAAGATGGGGGTAAGGTTCT;RSEQ=GCTAAGCTTGCTAAACTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:55,14:0:2,0:22.4:1:30:1:1:0:60:33.5:1:0:0.1 0/1:82:2:1,1:59,21:0.0244:2,2:7:1:28:1:0.46703:2.76809:60:4:0.0244:0:1 -4 73526674 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50618;SOR=Inf;LSEQ=GAAGGGTTCTTGTTGAAACT;RSEQ=GATATTACAAGGAAATGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:88,57:0:2,0:25.3:1:31.7:1:1:0:60:290:1:0:0.1 0/1:186:2:1,1:104,80:0.0108:2,2:26.5:1:29:1:1:1.29814:60:4:0.011:0:1.5 -4 73526723 . C A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10052;SOR=0;LSEQ=CTACGAGAAGGTTCAGGAGC;RSEQ=TGACTAATGTTTGGTCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:3:2,1:57,87:0.0204:2,2:23:1:30.3:1:0.56455:3.03:60:6:0.0205:0:1 0/0:168:0:0,0:67,101:0:2,0:25.1:1:30.9:1:1:0:60:83:1:0:0.1 -4 75662382 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18171;SOR=Inf;LSEQ=ACTCTCTCACCTATTAATTT;RSEQ=TCATCCGTTTTATAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:71,1:0:1,0:24.6:1:30.9:1:1:0:60:35:1:0:0.1 0/1:54:2:2,0:52,0:0.037:1,0:10.5:1:30.5:1:1:0:60:4:0.0377:0:1 -4 75662398 . AT A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.70135;SOR=0.65729;LSEQ=ATTTCTCATCCGTTTTATAG;RSEQ=TTTTTTTTACCAATAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:4:3,1:96,5:0.0381:1,2:17.8:1:29.5:1:0.21251:6.16927:60:8:0.0381:0.0095:0.3 0/1:79:2:2,0:71,5:0.0253:2,0:21:1:31.5:1:1:0:60:4:0.0263:0.0127:0.5 -4 75662446 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.79288;LSEQ=TCTCCTCTTTCCTCCTGGGA;RSEQ=GGATCTTGTCTAAAGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:19:12,7:143,79:0.0788:2,2:23.5:1:30.7:1:1:1.05567:60:38:0.0795:0:1.8 0/1:283:94:57,37:113,76:0.3322:2,2:25.1:1:30.8:1:1:1.04:60:93:0.3333:0:1.9 -4 75662515 . A T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=13.14884;LSEQ=CTGCTTTCCTAAGGTGGCCT;RSEQ=TATTAAAGATAAAGTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:29:15,14:129,178:0.0863:2,2:23:1:29.2:1:0.33194:1.48:60:28:0.0848:0:2.2 1/0:382:212:98,114:74,96:0.555:2,2:25.2:1:29.7:1:0.60662:1.11:60:69.667:0.5573:0:1.7 -4 75662524 . A G 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.86522;LSEQ=TAAGGTGGCCTATATTAAAG;RSEQ=TAAAGTGATTTATAATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:25:12,13:120,163:0.0812:2,2:24:1:31.9:1:0.67467:1.25:60:50:0.082:0:2.2 0/1:357:91:42,49:116,150:0.2549:2,2:23.5:1:30.7:1:0.71443:1.11:60:44.5:0.255:0:2.3 -4 75662594 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22972;SOR=Inf;LSEQ=TGTTTGCCTAACATAATAAT;RSEQ=CCAAGGTAATGGTTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:29,103:0:2,0:23.3:1:32:1:1:0:60:131:1:0:0.2 0/1:122:2:1,1:29,90:0.0164:2,2:36.5:1:29:1:0.43595:3.07:60:4:0.0165:0:1 -4 75662635 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00131;SOR=5.46711;LSEQ=AAATAGACTTAAAAATTCAC;RSEQ=AATAAAAGGGATACAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:5:1,4:6,53:0.0781:2,2:30.6:1:32.8:1:0.45084:2.17:60:10:0.0806:0:1.2 0/1:50:16:0,16:5,29:0.32:2,1:23.8:1:31.7:1:0.1626:0:60:32:0.32:0:1.2 -4 75662692 . C T 62 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02935;SOR=8.9847;LSEQ=CAGAGAATAAATCCCTTTAA;RSEQ=GGCAAGATTTGCTTGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:0,20:0.0909:1,2:21.5:1:29.5:1:0.09091:0:60:4:0.0909:0:1.5 1/0:8:4:0,4:0,4:0.5:0,0:27.3:1:31:1:1:0:60:8:0.5:0:1.8 -4 75662871 . A G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAGCTTGTGAGACAGCAG;RSEQ=AGAACCTAAGGAGTTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20.3:1:32.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 76957171 . C T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=2e-05;SOR=18.37565;LSEQ=TGCTGTTGCTGCTGGTGCTG;RSEQ=TGCTGCTACTTCAGCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:6,7:7,7:0.4815:2,2:31.5:1:30.3:1:1:1.16002:60:26:0.4815:0:1.2 1/1:38:36:16,20:1,1:0.9474:2,2:26.9:1:29.6:1:1:1.24262:60:72:0.9474:0:1.2 -4 78271425 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00183;SOR=Inf;LSEQ=TGACTATGTGAGCTTTCCTT;RSEQ=TATCTGCTTTATTGCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:39,1:0:1,0:22.1:1:32.3:1:1:0:60:39:1:0:0.2 0/1:12:4:4,0:8,0:0.3333:0,0:22.3:1:29.3:1:1:0:60:8:0.3333:0:1 -4 78271514 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23125;SOR=Inf;LSEQ=GTGGTCTTCTACATTGTGTT;RSEQ=AAACCAGGTTGCTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:95,34:0:2,0:21.9:1:31.5:1:1:0:60:128:1:0:0.2 0/1:120:2:1,1:83,35:0.0167:2,2:31:1:28:1:0.51176:2.35233:60:4:0.0168:0:1 -4 78271554 . C G 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=TCCCTTTCATCTTCATTTCT;RSEQ=TTAGCAAATTCAGGGCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:11:9,2:145,93:0.0438:2,2:24.3:1:32.6:1:0.21349:2.88:60:22:0.0442:0:1 0/0:306:0:0,0:178,126:0:2,0:23.5:1:31.4:1:1:0:60:151:0.9934:0:0.5 -4 78271576 . A G 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGCAAATTCAGGGCATAAC;RSEQ=TAATCTTCTAGGTTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:200,147:0:2,0:24.8:1:30.2:1:1:0:60:33.7:1:0:0.5 0/1:379:58:34,24:171,148:0.153:2,2:23.2:1:30.7:1:0.56686:1.23:60:57:0.1532:0:1.7 -4 78271612 . T A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99309;LSEQ=GGGAGTGGGAAAGGGCAGGC;RSEQ=GGTAACAAGAAGGGAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:89:51,38:157,161:0.2187:2,2:27.6:1:30.9:1:0.18984:1.38:60:178:0.2219:0:2 0/1:446:97:53,44:177,172:0.2175:2,2:25.1:1:29.9:1:0.566:1.17:60:31.333:0.2146:0:2 -4 78271620 . A G 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=2.19068;LSEQ=GAAAGGGCAGGCTGGTAACA;RSEQ=GAAGGGAAAAGCCCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:90:50,40:154,162:0.2217:2,2:26.6:1:31.9:1:0.28286:1.31:60:89:0.2208:0:2 0/1:424:163:90,73:132,127:0.3844:2,2:25.7:1:30.7:1:0.42381:1.19:60:53.333:0.3865:0:1.9 -4 78271705 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACCCAACCCTTTGTGTCT;RSEQ=TAGTGAAGTTTCCCACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:58,128:0:2,0:21.4:1:31.7:1:1:0:60:185:1:0:0.2 0/1:197:29:13,16:62,106:0.1472:2,2:22.6:1:28.4:1:0.41662:1.39:60:58:0.148:0:1.4 -4 78271850 . T A 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63047;SOR=2.22221;LSEQ=TATTGCCTGTGGTGCCAACA;RSEQ=GGCCTCCCAGCTCTTCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:0.3:2,0:19.7:1:31:1:1:0:60:6:0.3:0:1 1/0:8:4:0,4:0,4:0.5:0,0:12:1:32.3:1:1:0:60:8:0.5714:0:1 -4 78271858 . C CG 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.68385;LSEQ=GTGGTGCCAACATGGCCTCC;RSEQ=AGCTCTTCAAGTATCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:1,6:0.2222:2,0:19:1:32:1:1:0:60:4:0.2222:0:1 0/1:6:2:0,2:0,4:0.3333:0,0:20.5:1:32.4:1:1:0:60:4:0.3333:0.1667:1 -4 79792115 . ACAG A 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=1.28401;LSEQ=CAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:45,36:0.0233:2,2:32:1:31:1:1:1.24661:60:4:0.0238:0:0.5 0/1:101:3:2,1:53,43:0.0297:2,2:11.7:1:33:1:1:1.62:60:6:0.0306:0:0.3 -4 79792121 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50237;SOR=Inf;LSEQ=CAGCAGCAACAGCAACAGCA;RSEQ=CAGCAGCAACAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:49,42:0:2,0:21.5:1:31.7:1:1:0:59.5:29.333:1:0:0.3 0/1:112:2:1,1:61,48:0.0179:2,2:20:1:29:0:1:1.26806:38:4:0.0185:0:2.5 -4 79792217 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51301;SOR=Inf;LSEQ=GATGCTTATATGCAGCAGGT;RSEQ=ATTTTTTTGTTTCTTTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:0:1,0:30:1:30.1:1:1:0:60:46:1:0:0.1 0/1:35:2:1,1:5,28:0.0571:2,2:20.5:1:27:1:0.31765:5.20:60:4:0.0588:0:1 -4 82267196 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20648;SOR=0;LSEQ=ATTCTGCAGTTTCCTGGGGA;RSEQ=CCACTGTCCCCTGTGCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:22:0:32.5:1:1:1.26772:60:4:0.1333:0:1 0/0:21:0:0,0:14,7:0:2,0:22.1:1:31.2:1:1:0:60:42:1:0:0.2 -4 82267263 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.34441;LSEQ=GGTGGCGTGGCGACTCGACG;RSEQ=CAGAGAATCCCTGGCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:1,0:12,15:0.0357:2,0:1:0:30:0:0.46429:0:60:2:0.0385:0:1 0/1:42:2:1,1:16,24:0.0476:2,2:24.5:1:28.5:1:1:1.49:60:4:0.0488:0:1 -4 82267297 . T TG 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11343;SOR=0.23754;LSEQ=GCCAGGGCGGTGGCCCACTA;RSEQ=GGTGCACAACCAGTATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:2,3:6,6:0.2941:2,2:30.6:1:30.9:1:1:1.46472:60:10:0.2941:0.0588:0 0/1:23:2:0,2:6,15:0.087:2,0:25.5:1:31.5:1:1:0:60:4:0.087:0:0.5 -4 82931947 . C T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCTTTTCCTATACTTGC;RSEQ=TGCATTTTGGCTTTGATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:8,9:0,0:1:0,2:36.1:1:30.4:1:1:0:60:34:1:0:1.3 1/1:12:12:7,5:0,0:1:0,2:29.8:1:29.8:1:1:0:60:24:1:0:1.1 -4 82931981 . G T 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27277;SOR=0;LSEQ=TGATATCTTCTACAGAACTA;RSEQ=GTCCTTTTGGTGTTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:3,1:7,11:0.1818:2,2:19.3:1:30.5:1:0.29323:4.39:60:8:0.1818:0:1.5 0/0:12:0:0,0:5,7:0:2,0:25.1:1:29.5:1:1:0:60:24:1:0:0.8 -4 82932013 . GT G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTTCAGGGTTTTTTTCCT;RSEQ=TTTTTTTGAATAATTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:6,5:0,0:0.9167:0,2:30.5:1:32.3:1:1:0:60:22:0.9167:0:0.5 1/1:7:7:2,5:0,0:1:0,2:30:1:31.6:1:1:0:60:14:1:0:0.4 -4 82932267 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49848;SOR=0;LSEQ=AAAAGTTGCATATCCTTCTC;RSEQ=TCTTCATCTTCTGACTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:88,49:0.0144:2,2:26.5:1:29.5:1:1:1.78785:60:4:0.0144:0:1 0/0:132:0:0,0:85,47:0:2,0:24.4:1:31.2:1:1:0:60:264:1:0:0.1 -4 82932359 . C T 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00211;SOR=0.42889;LSEQ=ACTACACTTCAACCAGAAGA;RSEQ=CACAAGTGTTATTTTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:46:18,28:45,78:0.2722:2,2:23:1:30.2:1:0.85838:1.11:60:45:0.2695:0:1 0/1:174:24:10,14:59,90:0.1379:2,2:27.3:1:29.2:1:1:1.09:60:48:0.1404:0:1.1 -4 82932384 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24383;SOR=0;LSEQ=AGTGTTATTTTAAAGTCCTC;RSEQ=AGAGACAAAAGCAAAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:28,70:0.02:2,2:14.5:1:32:0:0.49798:2.47:60:4:0.0206:0:2 0/0:102:0:0,0:31,71:0:2,0:22.2:1:29:1:1:0:60:101:1:0:0.5 -4 82932387 . A G 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00989;SOR=0.44601;LSEQ=GTTATTTTAAAGTCCTCAAG;RSEQ=GACAAAAGCAAAAATTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:43:9,34:12,33:0.4886:2,2:23.9:1:30.7:1:0.62014:1.36878:60:42:0.4828:0:1.1 0/1:94:28:6,22:20,46:0.2979:2,2:23:1:29.2:1:0.45591:1.58664:60:27:0.2903:0:1.1 -4 82933477 . G C 76 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGATATTTTCAAAGTTG;RSEQ=CTGTGTTATTTTAATTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:27.8:1:29.6:1:1:0:60:10:1:0:1.2 1/1:6:5:3,2:1,0:0.8333:0,2:18.2:1:32.8:1:1:0:60:10:0.8333:0:1.2 -4 82933499 . G T 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09804;SOR=0;LSEQ=TGTGTTATTTTAATTAACCT;RSEQ=CCTTCATCATTTGTTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:14:1:29:1:1:2.45:60:4:0.3333:0:1.5 0/0:12:0:0,0:6,6:0:2,0:22.2:1:30.3:1:1:0:60:11:1:0:1 -4 82933572 . C CT 51 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30888;SOR=0.29632;LSEQ=CAGTCCCTCAACTGACTATT;RSEQ=TTTTTTTTTTTGAATCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:1,4:0.375:2,2:38.7:1:32.3:1:0.46429:5.78:60:6:0.4286:0:0 0/1:14:2:0,2:6,4:0.1429:2,0:34.5:1:31:1:0.45455:0:60:4:0.1538:0:0 -4 82934035 . TG T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.68017;SOR=1.62959;LSEQ=AGGCTGGGGAGGGGAGAGCA;RSEQ=GGGGGATAGGGAGAGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:29.8:1:33.3:1:1:0:60:8:0.3333:0:0 0/1:11:5:5,0:6,0:0.4545:0,0:10.8:1:31.2:1:1:0:60:10:0.4545:0.2727:0.6 -4 82934042 . A C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19928;SOR=Inf;LSEQ=GGAGGGGAGAGCATGGGGGG;RSEQ=TAGGGAGAGATTGGTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:12,0:0:0,0:26.8:1:29.4:1:1:0:60:24:1:0:0.1 0/1:11:2:2,0:9,0:0.1818:0,0:35.5:1:34:0:1:0:60:4:0.1818:0:1 -4 83255712 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19928;SOR=0;LSEQ=ACCATCTGTAGCTTGATGGC;RSEQ=TCAATCCTAGAGGAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:0.1818:2,2:18.5:1:31.5:1:1:1.87089:60:4:0.1818:0:1 0/0:13:0:0,0:9,4:0:2,0:24.1:1:30.4:1:1:0:60:26:1:0:0.1 -4 83255772 . TA T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5023;SOR=Inf;LSEQ=ATACAGGGCCCGAAGGCAAG;RSEQ=ACAGTAAGATGGCTGTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:0:2,0:21.1:1:29.2:1:1:0:60:54:1:0:0.1 0/1:36:2:1,1:20,14:0.0556:2,2:24:1:32:0:1:1.41419:60:4:0.0556:0:0 -4 83492301 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=AGTGAAACTGAGAAGCTAAG;RSEQ=AGTGAGGAGAACAGCAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:25.6:1:32.4:1:1:0:60:26:1:0:0.2 0/1:13:2:1,1:7,4:0.1538:2,2:25:1:25:1:1:1.67325:60:4:0.1667:0:1.5 -4 83492563 . A T 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37826;SOR=2.98519;LSEQ=GTCCCAGCTACTCGGGAGGC;RSEQ=GAGGCAGGAGAATGGCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:25.5:1:32:1:1:0:38:4:0.1667:0:1 0/1:13:5:5,0:8,0:0.3846:0,0:23.6:1:26.8:1:1:0:40:4:0.3333:0:1.2 -4 83493197 . G C 33 d7;v4;MAF0.05;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCAACATGGTGAAACC;RSEQ=CGTCTCTACTAAAAACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:40:0:33:0:1:0:44:4:1:0:1 1/0:2:1:0,1:0,1:0.5:0,0:31:0:32:0:1:0:60:2:0.5:0:1 -4 83493495 . C G 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATGTACATACATATATTCA;RSEQ=ATTTTAAAACAAAAAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:33.5:1:1:0:60:4:1:0:1 -4 83501194 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24925;SOR=Inf;LSEQ=GTCTTCACATAAACTTTCTT;RSEQ=CATCTGCTCTTGATCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:151,13:0:2,0:23:1:32.1:1:1:0:59.8:81:1:0:0.1 0/1:179:3:1,2:150,26:0.0168:2,2:7.7:1:28:1:0.06421:11.28002:47:6:0.017:0:1 -4 83501594 . G A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04619;SOR=0;LSEQ=GTTTGGGGAACATCAACGTC;RSEQ=CAGTCAACACCTTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:4:3,1:177,173:0.0113:2,2:16.5:1:27.5:1:0.62308:2.92:60:8:0.0115:0:1 0/0:409:0:0,0:207,202:0:2,0:25.8:1:30.7:1:1:0:60:80.8:1:0:0.1 -4 83501691 . G A 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06009;SOR=0;LSEQ=ACTGCAGTGCACCAAGACCG;RSEQ=CCCTGCATCCATGATGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:4:3,1:184,193:0.0105:2,2:17.3:1:28.5:1:0.36402:3.14:60:8:0.0106:0:1 0/0:388:0:0,0:184,204:0:2,0:24.4:1:31.2:1:1:0:60:63.667:1:0:0.2 -4 83501886 . T G 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.59689;LSEQ=GTCATGAGCGGCGCTTTCTT;RSEQ=GACGTTCCTAACACGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:179:97,82:203,189:0.3118:2,2:24.7:1:30.9:1:0.65162:1.10:52.4:28.833:0.3067:0:1.1 0/1:686:146:70,76:259,281:0.2128:2,2:26:1:30.5:1:1:1.00071:53:47.667:0.2112:0:1.1 -4 83501968 . C A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.12573;SOR=5.57221;LSEQ=ACACATTTACTCTTTCCTCT;RSEQ=TCCGCTTCTTTCATTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:1:1,0:162,238:0.0025:2,0:1:0:26:0:0.40648:0:47:2:0.0025:0:1 0/1:436:6:4,2:200,230:0.0138:2,2:5.8:1:25.5:1:0.42502:2.30:49.5:12:0.0139:0:1.3 -4 83502446 . A G 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCCAATGTTTCCACCATT;RSEQ=GATTCTTCTTGTAATGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:195,255:0:2,0:25.3:1:29.7:1:1:0:60:149:0.9978:0:0.1 0/1:491:22:9,13:216,253:0.0448:2,2:17.2:1:31:1:0.66853:1.23268:60:44:0.0454:0:1.2 -4 83502533 . A T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07627;SOR=1.4728;LSEQ=ATTTCAATTCCTGACAACGA;RSEQ=TCATTTATTCAGAAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:52:12,40:48,142:0.2149:2,2:22.4:1:29:1:0.85686:1.12623:60:25:0.2101:0:1.1 0/1:247:71:21,50:51,125:0.2874:2,2:22.4:1:27.7:1:1:1.03:60:70:0.2846:0:1.1 -4 83502544 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=TGACAACGAATCATTTATTC;RSEQ=GAAATCATTTATTTCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:37,156:0:2,0:21.3:1:30.9:1:1:0:60:192:1:0:0.3 0/1:194:2:1,1:49,143:0.0103:2,2:22.5:1:27.5:1:0.45003:2.90:60:4:0.0103:0:1 -4 83680084 . AAAC A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50046;SOR=Inf;LSEQ=ACATCCCCTACAATCCTGCG;RSEQ=AACAAGCACATCCCCTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:19.8:1:30.3:1:1:0:60:19:1:0:0.3 0/1:27:2:1,1:13,11:0.0741:2,2:24:1:28.5:1:1:1.17422:60:4:0.0769:0:0 -4 84383735 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17387;LSEQ=TTGGTTACTACTACCAGTAT;RSEQ=TGCTTTAGATCGTTTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:301:146,155:191,204:0.4319:2,2:25.6:1:30.3:1:1:1.01:60:300:0.4329:0:1.1 0/1:909:106:50,56:406,395:0.1166:2,2:25.6:1:30.1:1:0.53569:1.15101:60:212:0.118:0:1.1 -4 84383810 . C T 224 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGTCATCTAAGTCTAAGG;RSEQ=TTTATGCTTAATGATTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:0:0,0:406,394:0:2,0:25.7:1:32:1:1:0:59.9:79:1:0:0.1 0/1:989:208:105,103:386,395:0.2103:2,2:24:1:29.1:1:0.81511:1.04:60:68.333:0.21:0:1.1 -4 84384580 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27364;SOR=Inf;LSEQ=TAGGCGACAGAGCGAGACTC;RSEQ=GTCTCAAAAATAAATAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:162,25:0:2,0:21.2:1:31:1:1:0:60:374:1:0:0.1 0/1:271:3:1,2:222,46:0.0111:2,2:8.3:1:29.7:1:0.08195:9.52964:57:6:0.0112:0:1 -4 84384587 . AAAAT A 99 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03322;SOR=7.48944;LSEQ=CAGAGCGAGACTCCGTCTCA;RSEQ=AAATAAATAAATAAAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:1,0:211,38:0.004:2,0:38:0:32:0:1:0:60:2:0.0041:0:0 0/1:376:11:8,3:282,82:0.0293:2,2:28.3:1:28.9:1:0.71741:1.2887:60:22:0.0296:0.0053:0.4 -4 84388475 . C T 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACACATTTCTCAGAAGGTA;RSEQ=ATAGCCTTCATTAAGCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:115,1:0:1,0:23.7:1:31.9:1:1:0:60:57:1:0:0.1 0/1:93:25:24,1:68,0:0.2688:1,1:27.1:1:30.3:1:0.26882:0:60:50:0.2717:0:1 -4 84388494 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2273;SOR=0;LSEQ=ACATAGCCTTCATTAAGCAA;RSEQ=TCATAACTGTATAAATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:134,3:0.0144:1,2:20:1:29.5:1:0.05693:38.80706:60:4:0.0145:0:1 0/0:152:0:0,0:146,6:0:1,0:21.5:1:31.3:1:1:0:60:75:1:0:0.2 -4 84388757 . TATTC T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21021;SOR=Inf;LSEQ=TAATGATAAGGTGAAAAACT;RSEQ=ATTGTCAAGGACCAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:31,181:0:2,0:24:1:30.8:1:1:0:60:424:1:0:0.1 0/1:180:2:0,2:20,157:0.0111:2,0:14:1:32:0:1:0:60:4:0.0112:0:0 -4 84390088 . A G 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=TTTACTTGAGTAATGGATTA;RSEQ=TTTTCCCTTGAATTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:74,0:0:1,0:24.1:1:31:1:1:0:60:148:1:0:0 0/1:89:13:13,0:73,3:0.1461:1,1:20.8:1:32.7:1:1:0:60:26:0.1461:0:1 -4 84390446 . G A 34 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18195;LSEQ=TTTACTACTTATCCAAAATA;RSEQ=AATTTACTGACTTGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:3:0,3:1,43:0.0625:1,0:20.7:1:13.7:1:1:0:60:0:0:0:2 0/1:41:3:0,3:1,37:0.0732:1,0:28:1:21.7:1:1:0:60:2:0.0556:0:4.7 -4 84391410 . G A 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=24.83654;LSEQ=GATGAGTAGAGCAGCTTTCT;RSEQ=TTATTATACTTGGTGTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:482:1:1,0:251,230:0.0021:2,0:1:0:22:0:1:0:60:2:0.0021:0:1 0/1:549:27:13,14:262,259:0.0492:2,2:28.8:1:28.6:1:0.84632:1.08921:59.7:54:0.0497:0:1.1 -4 84391576 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21816;SOR=0;LSEQ=TACAGAATAAAAAGGATATA;RSEQ=ATCTTAATAGTTACAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:33,118:0.0131:2,2:29.5:1:30.5:1:0.3962:3.54:60:4:0.0132:0:1.5 0/0:174:0:0,0:40,134:0:2,0:23.3:1:31.3:1:1:0:60:173:1:0:0.1 -4 84393475 . C T 204 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATTAAAGGTATTTCAAATA;RSEQ=GCTAAAAATATAAGTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:55,153:0:2,0:22.8:1:30:1:1:0:60:40.6:1:0:0.2 0/1:255:119:33,86:34,102:0.4667:2,2:22.8:1:29.7:1:0.66978:1.15:60:58.5:0.4643:0:1.4 -4 84393476 . G A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03751;SOR=0;LSEQ=ATTAAAGGTATTTCAAATAC;RSEQ=CTAAAAATATAAGTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:4:3,1:49,145:0.0202:2,2:13.3:1:27.5:1:0.0563:8.76:60:8:0.0207:0:1 0/0:250:0:0,0:66,184:0:2,0:24.1:1:31.4:1:1:0:60:82.333:1:0:0.7 -4 84393485 . A G 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATTTCAAATACGCTAAAAAT;RSEQ=TAAGTAATTTTATTAGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:35,127:0:2,0:24:1:30.4:1:1:0:60:324:1:0:0.1 0/1:214:38:9,29:41,135:0.1776:2,2:21.1:1:31.5:1:1:1.02:60:76:0.1784:0:2.1 -4 84397590 . A C 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0142;SOR=Inf;LSEQ=GAAAGGTAATGAAGATCAGC;RSEQ=TTAAGTAATATAAATACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:0:1,0:23.1:1:30.8:1:1:0:60:40:1:0:0 0/1:17:5:5,0:11,1:0.2941:2,0:20.8:1:30.6:1:1:0:60:10:0.2941:0:2.2 -4 84397605 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21992;SOR=Inf;LSEQ=TCAGCATTAAGTAATATAAA;RSEQ=ACAGAGAAAGAACTGCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:29,1:0:1,0:21.1:1:31.5:1:1:0:60:60:1:0:0 0/1:27:2:1,1:24,1:0.0741:1,2:14.5:1:28.5:1:0.1453:17.31852:60:4:0.0741:0:2.5 -4 84397620 . G A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAATACAGAGAAAGAACT;RSEQ=CTAGGGTTGACAATACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:35,1:0:1,0:24.8:1:32.2:1:1:0:60:35:1:0:0 0/1:39:17:15,2:22,0:0.4359:1,2:25.6:1:28.6:1:0.18354:0:60:34:0.4359:0:1.4 -4 84397894 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.24463;SOR=Inf;LSEQ=TTCAGAATCACCTGAATGCT;RSEQ=CATATTGAGCCTTTACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:22,142:0:2,0:23.5:1:32.3:1:1:0:60:163:1:0:0 0/1:161:2:1,1:26,133:0.0124:2,2:6.5:1:27:1:0.30815:5.04:60:4:0.0126:0:1 -4 84403178 . G T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=AAAGTGCTGGGATTACAGGT;RSEQ=TGAGCCACCTTGCCCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:83,0:0:1,0:21.5:1:32.1:1:1:0:60:82:1:0:0.1 0/1:53:12:12,0:41,0:0.2264:1,0:21.3:1:29.1:1:1:0:60:24:0.2264:0:1.4 -4 84403476 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=TAACCGTATTTCCTGAGTAT;RSEQ=TTACTATGTATACAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:4,110:0:1,0:23.2:1:30.5:1:1:0:60:228:1:0:0.1 0/1:130:2:1,1:15,113:0.0154:2,2:11.5:1:29:1:0.23184:7.33:60:4:0.0156:0:1 -4 84403491 . A AG 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTATTTTACTATGTATACA;RSEQ=TATGTGCTACCAGTCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:1,78:0:1,0:26.2:1:30.9:1:1:0:60:38.5:1:0:0.1 0/1:81:30:0,30:3,48:0.3704:2,1:24:1:31.7:1:0.29167:0:60:60:0.375:0.0864:0.4 -4 84406052 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22129;SOR=Inf;LSEQ=CGGCGGCGTCGGGGGAGCGG;RSEQ=CGGGGACCGGAGCAACAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:81,13:0:2,0:18.3:1:31.6:1:1:0:60:46:1:0:0.1 0/1:84:2:1,1:65,17:0.0238:2,2:36.5:1:28.5:1:0.38468:3.74436:60:4:0.0244:0:1 -4 84406085 . G T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.32457;SOR=0.25938;LSEQ=CAACAGCGGGGAGGCAGGCC;RSEQ=CGCGCAGGGCTCTTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:181,53:0.0126:2,2:11.7:1:23:1:0.13535:6.75854:60:2:0.0084:0:1.3 0/0:305:1:0,1:222,81:0.0033:2,0:1:0:22:0:0.26974:0:60:2:0.0034:0:1 -4 84406267 . C T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.11432;SOR=0;LSEQ=ACAAGAGGACGAGGGCGGGG;RSEQ=GCGCGGAGGCAAGACCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:61,235:0.01:2,2:44.3:1:25.3:1:0.50331:1.92:60:2:0.0069:0:2.7 0/0:316:0:0,0:86,228:0:2,0:23:1:29.9:1:1:0:60:43.857:0.9935:0:0.2 -4 84406286 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=0;LSEQ=GCGCGCGGAGGCAAGACCCT;RSEQ=TGGTGGCAGCGAGGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:28,161:0.0105:2,2:34.5:1:31.5:1:0.28129:5.67:60:4:0.0105:0:1 0/0:188:0:0,0:37,150:0:2,0:21.6:1:31.3:1:1:0:60:61.333:0.9946:0:0.2 -4 84406289 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23785;SOR=Inf;LSEQ=CGCGGAGGCAAGACCCTGTG;RSEQ=TGGCAGCGAGGCGGGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:25,152:0:2,0:21.9:1:32.2:1:1:0:60:87.5:1:0:0.2 0/1:169:2:1,1:29,137:0.0118:2,2:5:1:29.5:1:0.32613:4.66:60:4:0.012:0:1 -4 87163499 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.96588;LSEQ=CAGTTGGGCGGCACGGGGAG;RSEQ=AGGACCCATTTAATGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:9,9:0.0526:2,0:1:0:23:0:1:0:60:2:0.0526:0:1 0/1:20:2:1,1:11,7:0.1:2,2:20.5:1:28:1:1:1.53525:60:4:0.1:0:1 -4 87163541 . G T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02707;SOR=0;LSEQ=TTTGTCCCTTGATGGAGAGG;RSEQ=TGTGCTTTGCTGAGGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:2,4:17,16:0.1538:2,2:13.7:1:28.2:1:0.66142:2.08513:60:5:0.1316:0:2 0/0:34:0:0,0:16,18:0:2,0:27.9:1:30.7:1:1:0:60:68:1:0:0.2 -4 87163749 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=CCCACTGAGGAAGGATGGGT;RSEQ=AGGGTTAGACCTGAAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:21.5:1:31.7:1:1:0:60:20:1:0:0.1 0/1:10:2:1,1:5,3:0.2:2,2:8.5:1:26.5:1:1:1.58108:60:4:0.2:0:1 -4 89983509 . C G 65 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTCCTGGATAATATCCT;RSEQ=AATTGTGTTTTCCAGCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:30.3:1:32.8:1:1:0:56.8:8:1:0:1 -4 89983727 . G C 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGTCAATTCAGCTGTTGATA;RSEQ=TTATGTATGCTTTACGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:9.5:1:33.5:1:1:0:60:4:1:0:1 1/1:4:4:2,2:0,0:1:0,2:9.3:1:30.3:1:1:0:60:8:1:0:1 -4 89984278 . G C 48 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27218;SOR=0.19788;LSEQ=TGTCACTCAAGGAGGCTGGA;RSEQ=AGCAGCAAAGATGGGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:1,5:0.3333:2,0:19.7:1:30.7:1:1:0:60:6:0.3333:0:1.3 0/1:12:1:1,0:7,4:0.0833:2,0:44:0:29:0:1:0:60:2:0.0833:0:1 -4 89984725 . C T 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.15611;LSEQ=CTGCCGACTGCCACAGCTGG;RSEQ=TTGTTGGGCTGTGGGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:0,2:0.75:0,2:17.8:1:29.3:1:0.46429:0:60:12:0.75:0:1.3 1/0:9:7:4,3:1,1:0.7778:2,2:24.9:1:28:1:1:1.29:60:14:0.7778:0:1.9 -4 89984747 . T C 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60839;SOR=2.12849;LSEQ=TGTTGGGCTGTGGGGACAAG;RSEQ=CGTGGGACCAAGCTGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,2:0.5714:2,2:18:1:31:1:1:1.41418:60:8:0.5714:0:1.5 1/0:8:6:2,4:1,1:0.75:2,2:14.5:1:29.5:1:1:1.8258:60:12:0.75:0:2.2 -4 94653647 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24565;SOR=0;LSEQ=CTTTAGTAGACTATCATTTT;RSEQ=TGCCTCTGCTGTTTACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:123,74:0.0101:2,2:14.5:1:32:0:1:1.65767:60:4:0.0101:0:1 0/0:202:0:0,0:131,70:0:2,0:24.1:1:31.3:1:1:0:60:402:1:0:0.3 -4 94653663 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25196;SOR=Inf;LSEQ=TTTTCTGCCTCTGCTGTTTA;RSEQ=AGGAATATATTTTATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:129,87:0:2,0:24.5:1:31.8:1:1:0:60:107:1:0:0.2 0/1:248:3:1,2:144,101:0.0121:2,2:26.7:1:27.7:1:0.57184:2.83944:60:6:0.0122:0:1.3 -4 94653694 . T C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=4.84389;LSEQ=TTTATTTCAAAAGCAAGATT;RSEQ=TTCTTGGCACTCAACTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:26:15,11:114,110:0.104:2,2:24.4:1:31.3:1:0.54101:1.31:60:52:0.104:0:1.2 0/1:294:106:60,46:96,92:0.3605:2,2:25.4:1:31.3:1:0.39524:1.25:60:105:0.3621:0:1.1 -4 94653779 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23193;SOR=Inf;LSEQ=TTTGTGTGGTTAAAATGGCT;RSEQ=AGGCTCTTTTATGTTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:50,126:0:2,0:25.1:1:31.4:1:1:0:60:175:1:0:0.1 0/1:164:2:1,1:54,108:0.0122:2,2:32.5:1:30:0:1:1.99:60:4:0.0122:0:1.5 -4 94653783 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49848;SOR=0;LSEQ=TGTGGTTAAAATGGCTGAGG;RSEQ=TCTTTTATGTTGTTCTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:44,116:0.0123:2,2:27:1:28.5:1:0.47964:2.62:60:4:0.0125:0:1 0/0:159:0:0,0:51,108:0:2,0:25:1:31.6:1:1:0:60:78.5:1:0:0.1 -4 94741469 . T TTGC 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.00113;SOR=0.17292;LSEQ=TGCCATTGCTGTTCTTGCTG;RSEQ=TGCTGCTGCTGCTGTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:21:10,11:7,4:0.6563:2,2:28:1:31.4:1:0.47191:1.88584:60:42:0.6563:0.0938:0.6 0/1:33:8:6,2:12,13:0.2424:2,2:30.9:1:32.6:1:0.24188:3.14:60:16:0.2424:0.0303:0.8 -4 94741522 . A C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15892;SOR=0.27953;LSEQ=GGTTCACCTTTCCTGAGCTA;RSEQ=CTCTTTTTCAACTTTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:18:7,11:1,2:0.8571:2,2:27.9:1:31.4:1:1:1.26:60:17:0.85:0:1.1 1/0:21:13:6,7:3,5:0.619:2,2:23.5:1:29.3:1:1:1.40:60:26:0.619:0:1.1 -4 96051136 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13904;SOR=0;LSEQ=TGAAAGTGTTCTTCACCACA;RSEQ=AGGAAGCCAGCTGGTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:4,7:0.1538:2,2:33.5:1:28.5:1:1:1.67:60:4:0.1538:0:1.5 0/0:21:0:0,0:9,12:0:2,0:26.9:1:31.9:1:1:0:60:42:1:0:0.1 -4 96052605 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15146;SOR=0;LSEQ=TGAAAAGTAAAAACATTCTG;RSEQ=TGAAGAAAAATGGAACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:19,12:0.0606:2,2:45:1:30:1:1:1.56069:60:4:0.0606:0:1 0/0:51:0:0,0:28,23:0:2,0:26.9:1:30.4:1:1:0:60:102:1:0:0.2 -4 98947326 . G A 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=AGTTAAAAAGAGGTGGAATC;RSEQ=TCCCAAAATGTCCCTTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:0:2,0:26.9:1:31.3:1:1:0:60:48:1:0:0.1 0/1:52:22:15,7:18,12:0.4231:2,2:24:1:30.3:1:0.57552:1.42:60:44:0.4231:0:1.5 -4 98947401 . T C 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCCCCTCAAGAGCTCAGGAG;RSEQ=GGGCTGCTGAGAGCTAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:0:2,0:18.8:1:29.1:1:1:0:60:34:1:0:0.1 1/0:36:22:9,13:3,11:0.6111:2,2:20.4:1:30.3:1:0.29248:2.48:60:44:0.6111:0:1.5 -4 99802204 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21711;SOR=Inf;LSEQ=CAACAAACCTATTTTTAGTG;RSEQ=TGGAGCCGCTCTTAGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:46,5:0:2,0:28.2:1:31.3:1:1:0:38.4:24.5:1:0:0 0/1:45:2:1,1:40,3:0.0444:2,2:11.5:1:28.5:1:0.17172:11.69064:50:4:0.0444:0:1.5 -4 99802236 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49805;SOR=0;LSEQ=TTAGTAGCTGTGTCTGCGTG;RSEQ=GACTGATAACCAATCACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:73,35:0.0182:2,2:14.5:1:29.5:1:0.54946:2.07063:50:4:0.0185:0:1.5 0/0:104:0:0,0:74,30:0:2,0:24.8:1:30.1:1:1:0:50:103:1:0:0.3 -4 99802289 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50032;SOR=Inf;LSEQ=TCCTAACCTTTCCTTGTATA;RSEQ=CCTCCTAGAAGAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:62,80:0:2,0:27.8:1:31:1:1:0:57.5:27.4:1:0:0.3 0/1:161:2:1,1:77,81:0.0124:2,2:27.5:1:31:1:1:1.05:60:4:0.0127:0:1.5 -4 99802300 . G GA 129 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.1919;SOR=0.59786;LSEQ=CCTTGTATACCCTCCTAGAA;RSEQ=AAAAAAAAAAAGAAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:19:5,14:50,62:0.1407:2,2:29.6:1:30.5:1:0.20806:2.24493:60:38:0.161:0:0.1 0/1:146:13:6,7:59,70:0.089:2,2:38.8:1:28.9:1:1:1.02:60:12:0.0909:0:0.5 -4 99802309 . A G 32 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.49813;SOR=0;LSEQ=CCCTCCTAGAAGAAAAAAAA;RSEQ=AAGAAGAAGAAAAAAGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:47,79:0.0156:2,2:48:0:32.5:1:1:1.67:60:4:0.0157:0:1 0/0:124:0:0,0:46,77:0:2,0:27.3:1:29.4:1:1:0:60:60.5:1:0:0.4 -4 99802395 . C T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.39289;SOR=1.72957;LSEQ=TTAGTCTTTATATTAAAAAA;RSEQ=ATAGACTTGAGAATAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:0,13:0,14:0.4815:1,1:24.6:1:29.5:1:1:0:60:26:0.4815:0:1 1/0:21:13:0,13:1,6:0.619:2,1:24.6:1:26.9:1:0.35:0:60:12:0.6:0:1.1 -4 99806215 . TA T 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09657;SOR=0.53031;LSEQ=TCCAATAAGGCACAGAAGCT;RSEQ=AAAAAAAATCCCAAATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:635:18:8,10:250,366:0.0283:2,2:26.7:1:30.2:1:0.80965:1.17:60:36:0.0286:0.0016:0.1 0/1:788:12:6,6:324,450:0.0152:2,2:27.7:1:30.9:1:0.57144:1.39:60:24:0.0154:0.0013:0.2 -4 99808136 . CTTAAA C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0;SOR=5.2451;LSEQ=CTAGTGTTGGGCATCCTTCT;RSEQ=TTAAGTAACAAATGTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:37:32,5:219,16:0.136:2,2:23.2:1:31.9:1:0.17963:2.13123:60:74:0.1365:0.0257:0.1 0/1:256:116:108,8:131,9:0.4531:2,2:26.1:1:31.4:1:1:1.07787:59.8:232:0.4531:0.0859:0.1 -4 99808254 . G A 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.05595;LSEQ=TCTAGCCAAAAGCGATCGAG;RSEQ=TCACTTCGTCTCTGCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1258:114:53,61:596,545:0.0906:2,2:27.2:1:30.2:1:0.27961:1.25841:53.9:113:0.0915:0:1.1 0/1:1506:622:304,318:441,442:0.413:2,2:27:1:29.2:1:0.71406:1.04368:55.3:61.2:0.4124:0:1.2 -4 99808693 . T C 102 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAATGAATGTCCCGTCCC;RSEQ=CTACCAACTGACAAAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:3,6:0,0:1:0,2:24.3:1:32.2:1:1:0:60:18:1:0:2.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 99808872 . T C 92 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12271;SOR=0.17799;LSEQ=TAACTCTCTCTCAATTTTTA;RSEQ=AAACAAATAGAATAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:7,0:21,2:0.2333:2,0:23.4:1:33:1:1:0:60:14:0.2333:0:1 0/1:20:1:1,0:16,3:0.05:2,0:17:0:26:0:1:0:60:2:0.05:0:2 -4 99808940 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20349;SOR=0;LSEQ=TTAAATTATCAGCCTATTCA;RSEQ=CACACTATCAAATATTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:2,0:65,5:0.0278:2,0:30:1:33.5:1:1:0:60:4:0.0282:0:1 0/0:87:0:0,0:82,5:0:2,0:24.1:1:30:1:1:0:60:174:1:0:0 -4 99808952 . A T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.61601;SOR=0.47784;LSEQ=CCTATTCATCACACTATCAA;RSEQ=TATTCCTAAGTTTATGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:87,13:0.0196:2,2:18:1:28.5:1:0.25684:6.48583:60:4:0.0198:0:1 0/0:106:1:0,1:90,15:0.0094:2,0:1:0:29:0:0.15094:0:60:2:0.0095:0:1 -4 99809176 . A T 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00154;SOR=Inf;LSEQ=AGGTGCTTACATATATATAC;RSEQ=TTTAGAACATATGATGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:31,127:0:2,0:22.5:1:31:1:1:0:60:78:1:0:0.1 0/1:201:12:4,8:42,147:0.0597:2,2:24.7:1:29.9:1:0.47621:1.74:60:24:0.0603:0:1.2 -4 99812300 . C A 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=CATTCATTAACTGTTTAACT;RSEQ=ACACTTCATTTTGTGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:226,17:0:2,0:24.2:1:31.3:1:1:0:60:47.6:1:0:0.1 0/1:307:20:18,2:264,22:0.0651:2,2:20.5:1:27.9:1:0.66285:1.33194:60:40:0.0654:0:1.1 -4 99822587 . T G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCAAACTCCTGACCTCAGG;RSEQ=GATCCGCCCGCCTCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:35:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:29:1:1:0:60:4:1:0:1 -4 99822905 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.46322;LSEQ=ATGGGTCATCCAAGTGAAAA;RSEQ=AGAACCCTCAACCTTAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:11:11,0:97,1:0.1009:1,0:26.3:1:32.8:1:1:0:60:22:0.1048:0:1.2 0/1:100:49:46,3:50,1:0.49:1,2:21.3:1:31.2:1:0.35739:3.22541:60:48:0.4848:0:1.1 -4 99823225 . AT A 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.31148;SOR=0.63422;LSEQ=CCTGAACTGATATGCTGATA;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:17:0,17:1,112:0.1308:1,1:32.6:1:32.3:1:1:0:60:34:0.1371:0.0077:0.1 0/1:115:10:0,10:1,104:0.087:1,0:21.2:1:29.3:1:1:0:60:9:0.0818:0.0174:0.5 -4 99849930 . T C 139 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75229;SOR=1.13592;LSEQ=CTATCATGAAGACACCATCC;RSEQ=CGCATACCCAGCCCAGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:21:21,0:166,7:0.1082:1,1:22.9:1:30.9:1:1:0:60:20:0.1064:0:1 0/1:198:24:23,1:164,10:0.1212:2,1:22.5:1:30.4:1:1:1.40:60:48:0.1231:0:1.8 -4 99850126 . A G 306 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.45879;LSEQ=GGAGGTCAGGTCCAACATGA;RSEQ=GGGGAAGGGGCGGCAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1146:426:214,212:346,373:0.3717:2,2:25:1:31.5:1:0.50154:1.09:60:141:0.3753:0:1.1 1/0:1472:989:489,500:251,230:0.6719:2,2:24:1:30.8:1:0.3447:1.11577:60:122.625:0.6738:0:1.2 -4 99850297 . A AG 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=39.25015;LSEQ=GATCGCACAACCGCTCCAGA;RSEQ=GGGGGGGTAAGAGGAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:1:1,0:321,408:0.0014:2,0:22:0:34:0:0.4411:0:60:2:0.0014:0:0 0/1:1098:56:26,30:464,577:0.051:2,2:28.3:1:31.1:1:0.78459:1.08:60:112:0.0519:0.0027:0.2 -4 99850341 . A G 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATTCAAACCGGATTGGCC;RSEQ=GCTTCTGGCCACGTGACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:99,214:0:2,0:23.3:1:30.3:1:1:0:60:30.3:1:0:0.1 0/1:444:30:11,19:137,276:0.0676:2,2:22.8:1:30.4:1:0.69226:1.17:60:60:0.0682:0:1.2 -4 100276461 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5098;SOR=0;LSEQ=CTCCCAGCATTTACAGGAAA;RSEQ=GGCTTCTGAAATCAGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:29,19:0.04:2,2:35:1:31:1:1:1.51306:60:4:0.04:0:1 0/0:35:0:0,0:20,15:0:2,0:24.4:1:30.4:1:1:0:56.5:70:1:0:0.2 -4 100276504 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50525;SOR=Inf;LSEQ=CTTTCAAACTCTTATACCAA;RSEQ=CTCTGGAGTTGGGCAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:24,26:0:2,0:30.1:1:30.9:1:1:0:55.1:24:1:0:0.3 0/1:66:2:1,1:34,30:0.0303:2,2:20.5:1:31:1:1:1.13118:60:4:0.0303:0:1.5 -4 100276569 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42105;SOR=Inf;LSEQ=GGCTGCCATTTGCTATTACT;RSEQ=GCCTTCAGGCCCTGTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:23:4,19:0,0:0.9583:0,2:15.5:1:29.7:1:1:0:58.3:46:1:0:1.2 1/1:33:33:13,20:0,0:1:0,2:21.1:1:29.4:1:1:0:58.8:32:1:0:1 -4 100276623 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03181;SOR=Inf;LSEQ=AAATTTGTTTCCTCTAGAAT;RSEQ=GAGGCCGTCAAGCTACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,12:0:2,0:24.8:1:31:1:1:0:57.6:34:1:0:0.8 0/1:14:4:1,3:1,9:0.2857:2,2:22.3:1:29.8:1:0.50549:2.74:43.5:8:0.2857:0:1.3 -4 100276859 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGATGGGGGATTGAGAG;RSEQ=TGAAGCCAGCTGGGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 103165485 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACAATCCCGAATAGACTTT;RSEQ=TGGCAGCAGTGACTCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:34:1:22:1:1:0:60:1:0.5:0:3.5 1/1:2:2:1,1:0,0:1:0,2:38.5:1:29.5:1:1:0:60:4:1:0:2 -4 103165513 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGACTCTCCAAAACCGCC;RSEQ=AGGCCTAGACGTCCTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:34.5:1:29:1:1:0:60:4:0.6667:0:3.5 1/1:2:2:1,1:0,0:1:0,2:28:1:31:1:1:0:60:4:1:0:2 -4 103165608 . A G 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63512;SOR=2.19746;LSEQ=CCAGTCAGGGATAGTACGAG;RSEQ=TGCCACCCAGCATTTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:6,2:0.2:2,0:28:1:30.5:1:1:0:60:4:0.2:0:1 0/1:11:4:2,2:6,1:0.3636:2,2:10.5:1:29.3:1:0.49091:4.9538:60:8:0.3636:0:1.3 -4 103165724 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51373;SOR=Inf;LSEQ=CCTTTCTAGGTCCCGTGGCA;RSEQ=CCATCTTGCTGTTACTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:7,13:0:2,0:19:1:31.9:1:1:0:53.7:40:1:0:0.1 0/1:31:2:1,1:14,15:0.0645:2,2:33.5:1:31.5:1:1:1.07:60:4:0.0667:0:1 -4 103165885 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCACCCCTGGACCAACCTG;RSEQ=TGGCACTTTCACCGGCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:18:0:34:0:1:0:60:2:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:29:1:1:1:60:4:0.5:0:2 -4 103165898 . C T 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACCTGCTGGCACTTTCAC;RSEQ=GGCCTAGAGAGCTCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:5:0:30:0:1:0:60:2:1:0:1 1/1:4:4:2,2:0,0:1:0,2:36.5:1:30:1:1:0:60:8:1:0:1.5 -4 103166193 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTTTGCTTGTGGGGAGG;RSEQ=GTGGAGGGAGAGGCATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:30:0:1:0:60:4:1:0:1.5 -4 103166437 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTCAGCTGCCTCCCTGC;RSEQ=AGGAAGGGCTCGGGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19.5:1:32:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 103166444 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCCTCCCTGCAAGGAAG;RSEQ=GCTCGGGACCTGCAGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:26.5:1:32:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 103166559 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACCAGGTCCCATCGACC;RSEQ=CCCAAGGGCTGAGGAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:39:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 103585509 . CT C 29 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCACTTTAAACATACATT;RSEQ=TTTTTTTTTTTTTGAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36:1:29.5:1:1:0:60:4:1:0:0 -4 105135443 . T C 256 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCATGACTGCTAATCATAT;RSEQ=GAATGTGGTGGTTTGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:334:334:153,181:0,0:1:0,2:27.8:1:30.6:1:1:0:60:82.5:1:0:1.1 0/1:416:184:85,99:111,120:0.4423:2,2:26.2:1:30.2:1:0.76664:1.07716:60:45:0.4423:0:1.1 -4 105409654 . T C 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00578;SOR=1.59177;LSEQ=TATTTCTTTTAGCCAAATAG;RSEQ=ATTCCGCTAATAATCTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:139:75,64:64,65:0.5167:2,2:24.1:1:32.3:1:0.54092:1.19:60:138:0.5169:0:1.1 1/0:319:201:107,94:55,61:0.6301:2,2:26.4:1:31.7:1:0.35144:1.26:60:66:0.6306:0:1.1 -4 105409678 . G A 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10729;SOR=0;LSEQ=CCGCTAATAATCTTAGCCTT;RSEQ=AAACACAGCCCATGCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:3,0:128,137:0.0112:2,0:10.7:1:20.3:1:0.11542:0:60:2:0.0076:0:2.3 0/0:296:0:0,0:130,166:0:2,0:25.1:1:31.1:1:1:0:60:295:1:0:0.7 -4 105409696 . T G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12437;SOR=Inf;LSEQ=TTGAAACACAGCCCATGCTC;RSEQ=GATAGAAGGGATCTGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:108,128:0:2,0:27.3:1:30.4:1:1:0:60:117:1:0:0.4 0/1:253:4:2,2:99,149:0.0158:2,2:12.8:1:31:0:1:1.50:60:8:0.016:0:1.5 -4 106111517 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50043;SOR=0;LSEQ=TCAAACTCTGTCTTCTCTAG;RSEQ=CTGGCAAACATTCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:129,23:0.013:2,2:24.5:1:27.5:1:0.28826:5.51192:60:4:0.0133:0:1 0/0:135:0:0,0:108,26:0:2,0:20.8:1:30.6:1:1:0:60:32.5:1:0:0.1 -4 106111673 . G T 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01852;SOR=Inf;LSEQ=TGAGCTGCTGGTAAGACAGT;RSEQ=GAGACAGTTGACACTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:169,249:0:2,0:26:1:31.3:1:1:0:60:58.714:1:0:0.1 0/1:510:7:2,5:224,279:0.0137:2,2:28.6:1:30.3:1:0.47112:2.00459:60:14:0.0138:0:1.1 -4 106111737 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49884;SOR=0;LSEQ=TGTAATGGTAATCTCTCTCC;RSEQ=AAACTTCAACTTCAAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:44,135:0.011:2,2:31:1:31:1:0.43646:3.05:60:4:0.0111:0:1 0/0:173:0:0,0:47,126:0:2,0:22.5:1:31.1:1:1:0:60:172:1:0:0.1 -4 106111758 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20736;SOR=Inf;LSEQ=AAACTTCAACTTCAAGTTAC;RSEQ=CTGCACCCTCTCAAATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:15,104:0:2,0:23.1:1:31.6:1:1:0:60:238:1:0:0.1 0/1:100:2:1,1:11,87:0.02:2,2:14.5:1:32:0:0.22667:7.62:60:4:0.0202:0:1 -4 106154990 . TATAGATAG T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=4;SSF=0;SOR=0.27369;LSEQ=TTAAGATATATTAGTATTTT;RSEQ=ATAGATAGATAGATAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:96:90,6:57,2:0.6194:1,2:27.7:1:30.4:1:0.71104:1.89282:60:47:0.6144:0.0903:0.1 0/1:114:35:33,2:75,4:0.307:2,2:25.4:1:30.6:1:1:1.13505:60:70:0.3125:0.0526:0.1 -4 106155037 . G T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1265;SOR=Inf;LSEQ=ATAAACACATTTTAATTTTT;RSEQ=TTTCCATGCTCTTTAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:260,70:0:2,0:22.2:1:31.9:1:1:0:60:81.5:1:0:0.1 0/1:371:4:1,3:282,85:0.0108:2,2:14.8:1:28.5:1:0.04299:9.87339:60:8:0.011:0:1 -4 106155185 . C G 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCCCATTTGCCAGACAGAAC;RSEQ=TCTGGCTACAAAGCTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:0:0,0:370,401:0:2,0:24.7:1:31.5:1:1:0:60:69.091:1:0:0.1 0/1:845:47:25,22:381,415:0.0556:2,2:22.7:1:29.3:1:0.54863:1.24:60:46:0.055:0:1.1 -4 106156163 . G A 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTGAAGAATTCTGTTCAG;RSEQ=TTCCAGCAGCAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:0:0,0:227,266:0:2,0:25.3:1:31.4:1:1:0:60:48.3:1:0:0.1 0/1:542:68:31,37:210,264:0.1255:2,2:26.3:1:28.8:1:0.89642:1.05:60:67:0.1241:0:1 -4 106156187 . C T 143 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=23.21707;LSEQ=CAGCAGCAATTTGCAAGCTC;RSEQ=TGGTGGCAGCTCTGAACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:1:1,0:222,249:0.0021:2,0:21:0:27:0:0.47246:0:60:2:0.0022:0:1 0/1:510:24:9,15:216,269:0.0471:2,2:24.5:1:31.2:1:0.53527:1.33754:60:48:0.0473:0:1 -4 106156288 . ACAC A 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03871;SOR=7.79819;LSEQ=ATTCCTTTTCTGCCACTACC;RSEQ=CACCACCACCATCACAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:1:0,1:361,326:0.0015:2,0:49:0:32:0:0.47529:0:60:2:0.0015:0:0 0/1:712:8:3,5:353,349:0.0112:2,2:22.5:1:28.5:1:0.50441:1.68454:60:16:0.0113:0.0028:0.3 -4 106158030 . G A 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGTCTTGCCATAGTCAGAT;RSEQ=CACAGGCCAATTAAGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:0:0,0:304,309:0:2,0:25.3:1:31.7:1:1:0:60:37.313:0.9983:0:0.1 0/1:721:49:26,23:378,294:0.068:2,2:18.9:1:28.2:1:0.65857:1.13716:60:98:0.0686:0:1.2 -4 106162473 . A T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.25216;SOR=Inf;LSEQ=TATAATTGAGGTCTAAAATA;RSEQ=TAATCTTCTATTATCTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:178,81:0:2,0:22.9:1:30.3:1:1:0:60:128.5:1:0:0.1 0/1:297:3:1,2:193,101:0.0101:2,2:13:1:26.7:1:0.27669:3.80305:60:6:0.0102:0:1 -4 106163925 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49861;SOR=0;LSEQ=TTATGCTCAAATGTTCAAAT;RSEQ=TTTTGATTGCCTCTTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:165,13:0.0111:2,2:24.5:1:27.5:1:0.14991:12.26775:60:4:0.0113:0:1 0/0:180:0:0,0:159,21:0:2,0:22.7:1:28:1:1:0:60:59:1:0:0.1 -4 106164284 . T G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32598;SOR=0.31895;LSEQ=TTGTATTTAATTGAAATAAT;RSEQ=TAGTGATGAGGAAGAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:1,8:1,3:0.6923:2,2:28.9:1:33.1:1:1:2.4495:60:18:0.6923:0:1 0/1:5:2:0,2:0,3:0.4:0,0:24:1:30.5:1:1:0:60:4:0.4:0:1 -4 106164673 . G A 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0151;SOR=Inf;LSEQ=ATCTGCTGCAAGTGACCCTT;RSEQ=TTTTGTTTTGGTTGGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:152,42:0:2,0:25.1:1:32.1:1:1:0:60:96:1:0:0.2 0/1:206:7:6,1:154,45:0.034:2,2:22.1:1:29.6:1:1:1.75:60:14:0.035:0:1.3 -4 106164922 . G A 45 q23 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04153;SOR=0;LSEQ=CGCTCACCAATCGCCGGTGT;RSEQ=CCTTGAATGAAGAGTAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:4:3,1:97,176:0.0144:2,2:11.5:1:22.5:1:0.13558:5.41:60:3:0.0112:0:1.3 0/0:336:0:0,0:115,221:0:2,0:23.8:1:31.5:1:1:0:60:83:1:0:0.2 -4 106164961 . CT C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23648;SOR=Inf;LSEQ=TGAAGCCCAGGGCCTCTCCC;RSEQ=CTTTGCGGCCACTGATAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:43,134:0:2,0:23.9:1:29.8:1:1:0:60:43.25:1:0:0.4 0/1:169:2:1,1:41,126:0.0118:2,2:18:0:33:1:0.43639:3.05:60:4:0.0123:0:1 -4 106164970 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22304;SOR=Inf;LSEQ=GGGCCTCTCCCCTCTTTGCG;RSEQ=CCACTGATAGGAAAGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:34,123:0:2,0:23.6:1:31.4:1:1:0:60:51.333:1:0:0.4 0/1:141:2:1,1:31,107:0.0142:2,2:24.5:1:28.5:1:0.40617:3.41:60:4:0.0147:0:1 -4 106164980 . G A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21124;SOR=0.65245;LSEQ=CCTCTTTGCGGCCACTGATA;RSEQ=GAAAGCCCAATCTTTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:32:6,26:18,81:0.2443:2,2:27.4:1:29.9:1:1:1.04:60:15:0.2381:0:1.2 0/1:115:20:5,15:18,77:0.1739:2,2:22.9:1:30.8:1:0.54564:1.42:60:40:0.1786:0:1.2 -4 106183474 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGATGTGTCAGATTTTGC;RSEQ=GATCTTCCTTTTTTGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25.5:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 106190740 . G A 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GAGTAAAACTAACTACTTTC;RSEQ=CATTCACACACACTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:0:0,0:296,178:0:2,0:26.1:1:30.5:1:1:0:60:78:0.9915:0:0.1 0/1:633:20:12,8:366,243:0.0316:2,2:27.6:1:29.4:1:1:1.00411:60:40:0.0321:0:1.2 -4 106190944 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=GCTTAGCAGCTGTTGAGTCT;RSEQ=TTCTCACACTGCTAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:30,146:0:2,0:26.2:1:32.3:1:1:0:60:175:1:0:0.1 0/1:196:2:1,1:39,155:0.0102:2,2:25:1:31.5:1:0.36735:3.94:60:4:0.0103:0:1 -4 106193334 . T C 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCGTAGAAAAAACTTT;RSEQ=AGCCTGTTTTTGAAGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:23.3:1:28.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 106193588 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.18118;SOR=Inf;LSEQ=TAGGATGGTTTTATGGTAAT;RSEQ=TATATGTCACTGATCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:28,1:0:1,0:21.9:1:27.7:1:1:0:60:58:1:0:0 0/1:22:2:2,0:19,1:0.0909:1,0:35:1:33:1:1:0:60:4:0.0952:0:1 -4 106193665 . C T 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.2062;SOR=0;LSEQ=GAGAAAGATACACACACACA;RSEQ=ACACGTTTTCTTTGGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:71,19:0.0217:2,2:33.5:1:30:1:0.38939:3.66809:60:4:0.0222:0:1 0/0:110:0:0,0:89,21:0:2,0:22.4:1:31.1:1:1:0:59.8:109:1:0:0.2 -4 106193666 . ACACGTTTTCTTTGGGACCTGTAGTTGAGGCTGTAATGTCTTACTTCCCTACCAGGTATGCACTCT A 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.50654;SOR=Inf;LSEQ=AGAAAGATACACACACACAC;RSEQ=CACTAGAGAAGACAATCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:70,20:0:2,0:26.6:1:32.1:1:1:0:60:180:1:0:0.3 0/1:119:2:1,1:95,22:0.0168:2,2:17:1:31:1:0.35052:4.24544:60:4:0.0168:0.0168:0 -4 106193695 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21832;SOR=0;LSEQ=CTTTGGGACCTGTAGTTGAG;RSEQ=CTGTAATGTCTTACTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:126,33:0.0124:2,2:5.5:1:29:1:0.3788:3.77651:60:4:0.0127:0:1 0/0:183:0:0,0:135,45:0:2,0:25.1:1:30.9:1:1:0:60:59:1:0:0.1 -4 106195987 . AT A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTTGGATGTTTATTAC;RSEQ=TTTTTTTTTCACTAAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:0.1429:0,0:37:1:32.5:1:1:0:60:4:0.1429:0:0 0/0:5:0:0,0:4,1:0:2,0:30:1:30.2:1:1:0:60:10:1:0:0.4 -4 106196092 . C T 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74617;SOR=0.77124;LSEQ=TATCTTTGCTTAATGGGTGT;RSEQ=GTATATCACTAGTGGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:52:50,2:5,0:0.9123:0,1:23.3:1:29.8:1:1:0:60:25:0.9091:0:1.1 1/1:45:40:39,1:4,0:0.8889:0,1:25:1:29:1:1:0:60:19:0.8837:0:1.1 -4 106196829 . T G 202 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTACATCATGTAGGGAAAT;RSEQ=GCCTCCTTATCCCACTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:0:0,0:365,344:0:2,0:23.8:1:30.1:1:1:0:60:353.5:1:0:0.1 0/1:868:100:49,51:370,395:0.1152:2,2:23.6:1:30.5:1:0.91568:1.03:60:49:0.1136:0:1.1 -4 106196951 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26884;LSEQ=AACATCATTCACCTTCTCAC;RSEQ=TAATCCATAACTACAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:613:332:164,168:131,148:0.5416:2,2:25:1:30.9:1:0.56994:1.10:60:109.667:0.5465:0:1.1 0/1:739:178:81,97:295,264:0.2409:2,2:27:1:30.5:1:0.10196:1.33761:60:177:0.2428:0:1.1 -4 106197000 . A G 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGTTCAACAGCTCTCTTC;RSEQ=TGCCCTGCATCTCCAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:0:0,0:291,303:0:2,0:25.3:1:30.3:1:1:0:60:58.4:1:0:0.4 0/1:692:40:20,20:308,343:0.0578:2,2:29.7:1:30.6:1:0.74747:1.11:60:80:0.0581:0:1.1 -4 106197257 . G A 74 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29443;SOR=2.66746;LSEQ=CTGACATTGGGGGAGTGGCC;RSEQ=TGGCTCCAACTCATGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:2:2,0:193,212:0.0049:2,0:4.5:1:28:1:0.22894:0:60:4:0.005:0:1 0/1:461:6:3,3:229,226:0.013:2,2:19:1:28.7:1:1:1.01325:60:12:0.013:0:1.2 -4 107004079 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06021;SOR=Inf;LSEQ=AGCACACTACCCAGCCAGGG;RSEQ=AAACTGTGCTTTTCAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:29.6:1:31.5:1:1:0:60:34:1:0:0.1 0/1:12:3:2,1:7,2:0.25:2,2:21.3:1:28.7:1:1:1.66417:60:6:0.25:0:1 -4 107004513 . A AC 67 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.22078;SOR=Inf;LSEQ=TTCAGGTCTAACCCTGACCC;RSEQ=CCTTCCTCAGTGGGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:32:1:31.3:1:1:0:60:8:1:0:0 1/0:10:5:2,3:3,2:0.5:2,2:21.2:1:29:1:1:2.06996:60:10:0.5:0.1:0.4 -4 107004868 . C G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGGTTGGTGCCCCTCAAGGT;RSEQ=AGAGGTCCCAGAAGATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:47:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:6:1:28:1:1:0:60:4:1:0:2 -4 107005093 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5502;SOR=Inf;LSEQ=ATAAAAACCCCATGCAAGGG;RSEQ=CAGCAGCCTCAAAGACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:27.1:1:30.9:1:1:0:60:56:1:0:0.1 0/1:56:2:1,1:26,28:0.0357:2,2:21:0:31.5:1:1:1.08:60:4:0.0357:0:1 -4 107005529 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19231;SOR=Inf;LSEQ=CCTTACTGAAATAAGACACA;RSEQ=AGACAAGTATAGAGAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:28.6:1:29.1:1:1:0:60:6:1:0:0 0/1:6:2:1,1:4,0:0.3333:0,2:34:1:32:1:0.33333:0:60:4:0.3333:0:1 -4 108124442 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23528;SOR=Inf;LSEQ=ATTGAGTGTGAAGGTTCCAC;RSEQ=GTTTTTTGAGCAAAGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:94,18:0:2,0:23.4:1:31.3:1:1:0:59.9:224:1:0:0.7 0/1:106:2:1,1:85,19:0.0189:2,2:20.5:1:29:1:0.34322:4.38599:60:4:0.0192:0:1 -4 108124443 . G A 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.40637;SOR=0.77945;LSEQ=TTGAGTGTGAAGGTTCCACC;RSEQ=TTTTTTGAGCAAAGTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:113:74:63,11:32,7:0.6549:2,2:23.3:1:30.4:1:0.78778:1.25:59.9:148:0.6607:0:1 1/0:109:65:53,12:34,9:0.5963:2,2:24.2:1:30:1:0.80642:1.17:60:130:0.5963:0:1 -4 108124583 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=Inf;LSEQ=TTGGATCTCTTTGTCAAACA;RSEQ=TGTTGAGGCCTCGCTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:224,168:0:2,0:25.4:1:32:1:1:0:60:129.667:1:0:0.1 0/1:333:10:5,5:168,155:0.03:2,2:28.4:1:30.2:1:1:1.08359:60:20:0.0302:0:1 -4 108124706 . G A 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02934;SOR=0.77997;LSEQ=TCTTCTCCTTCAGTTTCTCA;RSEQ=TCGTGTCTGTATCATCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:650:428:231,197:119,102:0.6585:2,2:25.5:1:30.1:1:1:1.01:59.8:60.143:0.6588:0:1.1 1/0:726:436:239,197:163,126:0.6006:2,2:26.5:1:29.4:1:0.70305:1.0662:59.7:28.067:0.5963:0:1.2 -4 108124872 . G A 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00699;SOR=1.38955;LSEQ=CACATCTGTTTGCGGATAGG;RSEQ=TAGGGGGCATAATCTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:669:458:230,228:121,90:0.6846:2,2:24.9:1:30.2:1:0.09577:1.33217:55:49.889:0.6824:0:1.1 1/0:711:534:275,259:93,82:0.7511:2,2:24.1:1:28.9:1:0.72787:1.06803:55.9:47.545:0.7504:0:1.1 -4 108125120 . G A 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03188;SOR=Inf;LSEQ=CGCAGGGGCAGCAGCAGGGC;RSEQ=CTGAGACCAGAAGCGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:0:0,0:160,360:0:2,0:27:1:31.1:1:1:0:60:64:1:0:0.4 0/1:572:6:3,3:211,355:0.0105:2,2:26.8:1:24:1:0.67628:1.68:60:2:0.0072:0:1 -4 108125157 . G A 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0449;SOR=0.68364;LSEQ=CGGGTACAAGGAATAAAAGT;RSEQ=TCAAGGGTAAAACCTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:279:178:15,163:8,92:0.638:2,2:23.2:1:30.7:1:1:1.06:60:43.5:0.635:0:1.1 1/0:227:124:15,109:5,98:0.5463:1,2:22.1:1:29.8:1:0.06268:2.69:60:248:0.5511:0:1.1 -4 108125170 . C A 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAAAGTGTCAAGGGTAAAA;RSEQ=CTCTAAAAGGTTAATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:11,194:0:2,0:23.4:1:31.4:1:1:0:60:50.25:1:0:0.7 0/1:162:34:1,33:5,123:0.2099:1,1:21.7:1:29.1:1:1:1.33921:60:33:0.2063:0:1.2 -4 108125279 . C G 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.05378;SOR=5.61694;LSEQ=TCTTACATCAGCCATCCCCC;RSEQ=CCAAATTGGGCATTTAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:0,4:0,24:0.1429:1,0:18.5:1:31.8:1:1:0:60:8:0.1481:0:1 1/0:8:4:0,4:0,4:0.5:0,0:33.8:1:33.5:1:1:0:60:8:0.5:0:1 -4 113485894 . A T 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATTTTTAAAAAATGATC;RSEQ=CAAATGCTTAATTTCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:20.5:1:31.3:1:1:0:60:8:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 113485940 . T C 63 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ACCACTTCATGAATGTCTTC;RSEQ=ATGTGATATACATTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:31.3:1:31.8:1:1:0:60:8:1:0:1.8 0/1:4:1:1,0:3,0:0.25:0,0:22:0:32:0:1:0:60:2:0.25:0:1 -4 113486045 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49668;SOR=Inf;LSEQ=TACTGAATTGTGTTCGCAGC;RSEQ=GCCACCGCGCCGCCGTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:41,3:0:2,0:24.4:1:29.9:1:1:0:60:43:1:0:0.1 0/1:50:2:2,0:44,4:0.04:2,0:12.5:1:30.5:1:1:0:60:4:0.0408:0:1 -4 113486054 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49608;SOR=Inf;LSEQ=GTGTTCGCAGCCGCCACCGC;RSEQ=CCGCCGTCGCTCTCCAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:50,3:0:2,0:22.6:1:28.6:1:1:0:60:16.667:1:0:0.1 0/1:57:2:1,1:52,3:0.0351:2,2:11.5:1:26:1:0.13659:15.15409:60:4:0.0357:0:1 -4 113486125 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25725;SOR=Inf;LSEQ=CCGAAGGAGAAATGAGGTAA;RSEQ=TAAGGAGGTCTCTGTACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:113,60:0:2,0:23.6:1:31.8:1:1:0:60:172:1:0:0.1 0/1:216:3:1,2:132,81:0.0139:2,2:10.3:1:30.7:1:0.56014:3.24098:60:6:0.0142:0:1 -4 113486180 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26097;SOR=Inf;LSEQ=AGACTGCCCACAAATCAACC;RSEQ=GTGGTAAACCACCCAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:108,101:0:2,0:28.3:1:30.2:1:1:0:60:68.667:1:0:0.1 0/1:271:3:2,1:137,131:0.0111:2,2:24:1:30:1:1:1.91:60:6:0.0112:0:1 -4 113486193 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26534;SOR=Inf;LSEQ=ATCAACCGGTGGTAAACCAC;RSEQ=CAGGAAGCAACTGGCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:103,101:0:2,0:25.2:1:30.7:1:1:0:59.3:50:1:0:0.1 0/1:276:3:2,1:140,133:0.0109:2,2:25.7:1:26:1:1:1.90:60:6:0.0111:0:1 -4 113486206 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40092;SOR=2.97014;LSEQ=AAACCACCCAGGAAGCAACT;RSEQ=GCTACAAAAGCCGCTCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:1,0:91,97:0.0053:2,0:1:0:27:0:0.48677:0:60:2:0.0054:0:1 0/1:258:4:3,1:127,127:0.0155:2,2:14.8:1:27:1:0.62211:2.99:60:8:0.0159:0:1 -4 113486566 . G A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07903;SOR=0;LSEQ=TGTGCTTTAGAATCCACTAT;RSEQ=ATGGGAAACATTTCATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:3:1,2:54,156:0.0141:2,2:24.3:1:23:1:1:1.44:60:2:0.012:0:3.3 0/0:282:0:0,0:77,202:0:2,0:21.9:1:28.2:1:1:0:59.6:4.471:1:0:0.6 -4 113486586 . C AA 33 v4;q23;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.09184;SOR=0;LSEQ=GATGGGAAACATTTCATTCT;RSEQ=AAAAAAAAAAAAAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:0,3:27,98:0.0222:2,0:37.7:1:21:1:1:0:56.7:6:0.039:0:5 0/0:163:0:0,0:48,110:0:2,0:26:0:19:0:1:0:60:0:0:0:2 -4 113486769 . T C 63 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCATCTGACAAAGGGCTAA;RSEQ=ATCCAGAATCTACGATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:28.3:1:31.5:1:1:0:43.3:8:1:0:1 1/1:1:1:0,1:0,0:1:0,0:40:0:34:0:1:0:42:2:1:0:1 -4 114756960 . C T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=ATTTTCAGCAGTTAGCACTT;RSEQ=TAGAATTGGCATCAGCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:33:1:31.3:1:1:0:60:6:0.4286:0:1 1/0:4:2:2,0:2,0:0.5:0,0:31:1:32:0:1:0:60:4:0.5:0:1 -4 114757200 . A T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24931;SOR=Inf;LSEQ=TTTCCACAAATATGCATGAA;RSEQ=ATCATGTTAAATATTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:97,99:0:2,0:24.6:1:29.9:1:1:0:60:195:1:0:0.6 0/1:212:3:1,2:115,94:0.0142:2,2:7.7:1:25:1:0.59101:2.43672:60:6:0.0143:0:1.3 -4 114757214 . T C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.1556;LSEQ=CATGAAAATCATGTTAAATA;RSEQ=TTTTTAAAGGCATTTGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:191:123:55,68:31,37:0.644:2,2:25.2:1:32.2:1:1:1.0357:60:246:0.644:0:1.2 0/1:224:49:26,23:88,87:0.2188:2,2:27.3:1:31:1:0.74918:1.12:60:98:0.2197:0:1.2 -4 114757257 . T G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50472;SOR=Inf;LSEQ=CTTGAGCGAAATTCTTGATA;RSEQ=TCTGCTCTTATAATATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:45,107:0:2,0:26.4:1:30.4:1:1:0:60:75:1:0:0.8 0/1:190:2:1,1:76,112:0.0105:2,2:17:0:33.5:1:1:1.47:60:4:0.0106:0:1.5 -4 114757297 . A G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.25225;LSEQ=CAAGGACAATAAAAAAGTAT;RSEQ=CGCTGTTTTCAAGGGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:47:9,38:6,24:0.6104:2,2:21.6:1:32.2:1:1:1.0548:60:94:0.6104:0:1.6 0/1:103:29:7,22:24,50:0.2816:2,2:23.6:1:31.9:1:0.47993:1.50277:60:28:0.2745:0:1.4 -4 114757327 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50834;SOR=Inf;LSEQ=CAAGGGCAATTGCTCATTAG;RSEQ=AGTGGAGCTGACATGTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:1,27:0:1,0:24.8:1:32.5:1:1:0:60:56:1:0:1 0/1:40:2:1,1:4,34:0.05:2,2:32:1:27:1:0.23718:7.71:60:4:0.0526:0:2 -4 114757343 . T G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.55745;SOR=1.56134;LSEQ=TTAGCAGTGGAGCTGACATG;RSEQ=CCAATTCAAAGCATTGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:15:0,15:0,9:0.625:0,1:21.3:1:31.7:1:1:0:60:30:0.625:0:1.7 1/0:29:21:2,19:1,7:0.7241:2,2:20.9:1:31.9:1:1:1.34216:60:42:0.7241:0:1.2 -4 115455964 . A G 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00856;SOR=Inf;LSEQ=AAGATGAGTAGAAAACTAGA;RSEQ=TGGGGTCCAAAGACTTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:100,5:0:1,0:24.7:1:30.7:1:1:0:60:210:1:0:0 0/1:68:5:5,0:59,4:0.0735:2,0:38.2:1:33:1:1:0:60:10:0.0746:0:1.2 -4 115455999 . C T 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03512;SOR=Inf;LSEQ=TTATTAGGTGTCCATAGATC;RSEQ=ATGGATTGATCATACAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:162,43:0:2,0:23.9:1:31.2:1:1:0:60:410:1:0:0.1 0/1:158:4:1,3:120,34:0.0253:2,2:5:1:26.3:1:0.04026:10.38255:60:8:0.0265:0:1 -4 115456111 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=26.89899;LSEQ=TGCCTCACTTCCCTCCATCT;RSEQ=CAGGAACCTCACAGTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:35:17,18:181,266:0.0725:2,2:26.5:1:30.5:1:0.37564:1.39:60:70:0.0731:0:1.1 1/0:504:342:150,192:71,91:0.6786:2,2:25.2:1:29:1:1:1.00:60:113:0.6835:0:1.1 -4 115456152 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15038;LSEQ=ACTTCTTTACTCATTTAAAT;RSEQ=CCATTCTTTAAAAAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:259:179:40,139:23,57:0.6911:2,2:22.8:1:29.2:1:0.27609:1.40035:60:43.75:0.689:0:1.1 0/1:259:65:20,45:52,142:0.251:2,2:23.2:1:28.3:1:0.52713:1.21:60:130:0.2549:0:1.1 -4 115456182 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.243;SOR=Inf;LSEQ=AAAAAGAAAAAAAGTCCCCC;RSEQ=TTAAGACTCTCTGGCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:16,109:0:2,0:23.1:1:30.2:1:1:0:60:40.667:0.9919:0:0.8 0/1:123:2:1,1:19,101:0.0163:2,2:21.5:1:29:1:0.30213:5.21:60:4:0.0165:0:2.5 -4 115456236 . C G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=28.38371;LSEQ=GCTATGGAAAACACCAGAGT;RSEQ=AATTTATAGTTGATGTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:7:0,7:0,38:0.1556:1,0:21.6:1:31.4:1:1:0:60:14:0.1591:0:1 1/1:33:28:1,27:0,5:0.8485:0,1:25.5:1:31.7:1:1:0:60:56:0.8485:0:1 -4 115461109 . G C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00266;SOR=0.18303;LSEQ=GACTAAACAGCTGTGAGACT;RSEQ=TGAGGTCCCTAAAGATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:13:8,5:19,9:0.3095:2,2:23.2:1:32.1:1:0.73374:1.31036:60:26:0.3171:0:1.4 0/1:67:5:4,1:39,23:0.0746:2,2:11.2:1:32:1:0.64731:2.33:60:10:0.0794:0:1.2 -4 115461155 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52065;SOR=Inf;LSEQ=TGAGGAACAGGCAGAAGGGG;RSEQ=AATAGTGAACAGCAATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:31,32:0:2,0:30.8:1:30:1:1:0:60:14.75:1:0:0.4 0/1:98:2:1,1:46,50:0.0204:2,2:19:1:28.5:1:1:1.09:60:4:0.0206:0:2 -4 115461158 . T G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.55045;LSEQ=GGAACAGGCAGAAGGGGGAA;RSEQ=AGTGAACAGCAATGACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:4:2,2:28,30:0.0645:2,2:32.5:1:31.3:1:1:1.07:60:8:0.0678:0:1 1/0:98:67:29,38:17,14:0.6837:2,2:30.6:1:31.3:1:0.38432:1.58349:60:134:0.6907:0:1.2 -4 115461170 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.519;SOR=Inf;LSEQ=AGGGGGAATAGTGAACAGCA;RSEQ=TGACAGATGATTCCACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:27,33:0:2,0:27.8:1:30.6:1:1:0:60:120:1:0:0.4 0/1:92:2:1,1:38,52:0.0217:2,2:42.5:1:30.5:1:1:1.36:60:4:0.0217:0:1 -4 115461265 . T C 55 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.31889;SOR=4.12333;LSEQ=TGTTACATAGGTAAATTGCA;RSEQ=GTCACTGAGGTCTGGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:0,9:0.1818:0,0:31.5:1:32:0:1:0:60:4:0.1818:0:1 1/0:8:4:0,4:0,4:0.5:0,0:24.8:1:27.8:1:1:0:60:8:0.5714:0:1 -4 117847288 . G C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49195;SOR=Inf;LSEQ=CTACGCGGTGCCCGGTGTCC;RSEQ=GCGGGGACGACTAGCGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:0:2,0:16.9:1:29.8:1:1:0:60:26:1:0:0.2 0/1:17:2:1,1:8,7:0.1176:2,2:29:1:27.5:1:1:1.13389:60:4:0.1176:0:1 -4 117847340 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26667;SOR=Inf;LSEQ=CTCGCTCCCCACATCCCCGC;RSEQ=GACACAGCTGGTGGCGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:0:2,0:30.2:1:29.5:1:1:0:60:15.5:1:0:0.2 0/1:48:3:1,2:20,25:0.0625:2,2:20.7:1:30:1:1:1.58499:60:6:0.0625:0:1 -4 118610163 . T A 69 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24242;SOR=0.1257;LSEQ=ACACCTGGAAAAAGCCATCC;RSEQ=TGAGAACTAACTCCCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:25.2:1:29.8:1:1:0:60:10:0.7143:0:1.6 0/1:5:1:1,0:4,0:0.2:0,0:11:0:31:0:1:0:60:2:0.2:0:2 -4 118610216 . C G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54687;SOR=0.64668;LSEQ=TCACAACTGTGATTTTTCTT;RSEQ=AGAGAGAGCAAAACTATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:9,0:14,0:0.3913:1,0:24.4:1:31:1:1:0:60:18:0.4091:0:1.3 0/1:24:7:6,1:17,0:0.2917:1,2:22.7:1:32:1:0.29167:0:60:14:0.2917:0:1.1 -4 118610301 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19658;SOR=0;LSEQ=TGAGGAGCAGACATACAGAA;RSEQ=AATGATTCACAAGAAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:72,41:0.0172:2,2:14:0:30.5:1:1:1.74699:60:4:0.0177:0:1 0/0:145:0:0,0:90,55:0:2,0:23.1:1:31.5:1:1:0:60:290:1:0:0.2 -4 118610383 . A C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36658;SOR=0.79874;LSEQ=ATTACTAGGGGAGAGCATCC;RSEQ=TCAGCTGACATGGTGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:57:24,33:53,64:0.3276:2,2:27.4:1:31.3:1:0.74632:1.13782:60:56:0.3256:0:1.1 0/1:200:56:27,29:65,79:0.28:2,2:25.9:1:31.2:1:0.7529:1.13:60:112:0.2814:0:1.1 -4 118610399 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50096;SOR=Inf;LSEQ=ATCCATCAGCTGACATGGTG;RSEQ=TGGCAGCATGGTCACAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:68,93:0:2,0:25.5:1:31.2:1:1:0:60:39.25:1:0:0.4 0/1:185:2:1,1:81,101:0.0108:2,2:20.5:1:26:1:1:1.25:60:4:0.011:0:2 -4 118610405 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25071;SOR=Inf;LSEQ=CAGCTGACATGGTGGTGGCA;RSEQ=CATGGTCACAACTGAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:65,92:0:2,0:24.5:1:31.7:1:1:0:60:156:1:0:0.4 0/1:178:3:2,1:76,99:0.0169:2,2:9:1:27.3:1:0.58222:2.59:60:6:0.017:0:1.7 -4 118610435 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22108;SOR=0;LSEQ=AACTGAGGTGCGGCTTCAGA;RSEQ=AGGAGAGCTTTTCAATAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:30,75:0.0187:2,2:40.5:1:31.5:1:0.49744:2.48:60:4:0.0187:0:1 0/0:120:0:0,0:38,82:0:2,0:25.5:1:29.9:1:1:0:60:240:1:0:0.4 -4 118610504 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26503;SOR=0.50225;LSEQ=TCAAATTCCCAGGAATGTAG;RSEQ=TAATAACAATTATGCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:1,10:1,14:0.4231:1,2:25.6:1:32.5:1:1:1.38:60:22:0.4231:0:2.1 0/1:30:8:0,8:1,21:0.2667:1,0:28.9:1:31.6:1:1:0:60:16:0.2667:0:2.4 -4 118610508 . T C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27303;SOR=0.52581;LSEQ=ATTCCCAGGAATGTAGATAA;RSEQ=AACAATTATGCCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:1,10:1,14:0.4231:1,2:23.1:1:32.3:1:1:1.38:60:22:0.4231:0:2.1 0/1:29:8:0,8:1,20:0.2759:1,0:28.9:1:32.5:1:1:0:60:16:0.2759:0:2.4 -4 118862907 . T A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTGTGAGTCTCAGTGCTGG;RSEQ=TGCTGCCCCTCCCCCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:16.5:1:29:1:1:0:60:4:0.6667:0:1 1/1:2:2:1,1:0,0:1:0,2:16.5:1:28:1:1:0:60:4:1:0:1 -4 118862978 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTGTGCTGGTTGCCCCT;RSEQ=CCCGTGGGAGTTCAGTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:17.5:1:28.5:1:1:1.29:60:4:0.2222:0:1 0/0:2:0:0,0:1,1:0:2,0:25.5:1:32.5:1:1:0:60:4:1:0:0.5 -4 118863268 . A G 48 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATGGGTCACGCCAGCGTTCT;RSEQ=GTCAGTTTTGGTGAGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:28:1:1:0:60:4:1:0:0 1/1:3:3:0,3:0,0:1:0,0:29.7:1:30.3:1:1:0:60:6:1:0:1 -4 119555489 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCTCTAGGCCCAGCTTGGGC;RSEQ=TCCTGGCGGCCTCTGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:29.5:1:1:0:29:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 119555497 . GG AT 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGCTTGGGCCTCCTGGC;RSEQ=CCTCTGCAGGCCCAAATCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:29:1:1:0:29:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 119557176 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48571;SOR=Inf;LSEQ=TGTTGAGGCAGGGCTGGGGT;RSEQ=TCCCCTTCCAACCAGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:7.3:1:32.3:1:1:0:37.7:12:1:0:0.2 0/1:9:2:1,1:5,2:0.2222:2,2:31.5:1:27.5:1:1:2.23609:42:4:0.2222:0:1 -4 119557325 . C T 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10851;SOR=3.91245;LSEQ=GCAGCAGTGGACCCGCTATG;RSEQ=ACACATCTTCTTCTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:2,1:17,5:0.12:2,2:25:1:30.7:1:1:1.66053:37.7:6:0.125:0:1.7 0/1:14:5:4,1:7,2:0.3571:2,2:17.6:1:28.6:1:1:1.13:39:10:0.3571:0:2.2 -4 119557333 . T A 88 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01569;SOR=6.10787;LSEQ=GGACCCGCTATGCACACATC;RSEQ=TCTTCTCCAAGGTTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:3,0:19,5:0.1111:2,0:27:1:30:1:1:0:43.7:6:0.125:0:1.7 0/1:18:8:5,3:8,2:0.4444:2,2:17:1:29.4:1:0.60784:2.28225:40.6:16:0.4444:0:1.9 -4 119557394 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2344;SOR=Inf;LSEQ=GCCCCAGCAGCTTCAGTTGG;RSEQ=ACCTGCCCCAGTCCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:30,26:0:2,0:23.9:1:31.4:1:1:0:50.8:27:0.9818:0:0.2 0/1:54:2:1,1:31,21:0.037:2,2:13.5:1:27.5:1:1:1.46529:49:4:0.037:0:1 -4 119557562 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13853;SOR=Inf;LSEQ=CTGAGGCTCCTCCCACTGGA;RSEQ=CGTCACCCAACTGGCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:13,30:0:2,0:25.2:1:31.5:1:1:0:53.1:86:1:0:1.1 0/1:26:2:1,1:11,13:0.0769:2,2:6.5:1:28:1:1:1.17:59.5:4:0.08:0:1.5 -4 119557567 . A C 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCTCCCACTGGACCGTC;RSEQ=CCCAACTGGCACCACTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:10,31:0,0:1:0,2:25.9:1:30.7:1:1:0:52.7:40:1:0:1.2 1/1:22:22:9,13:0,0:1:0,2:28:1:29.9:1:1:0:50.3:21:1:0:1.5 -4 119557718 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19346;SOR=Inf;LSEQ=GGGCTGGGAGTCAGGGCAGG;RSEQ=GCAGAACAAACCTTGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,10:0:2,0:23.8:1:30.6:1:1:0:47.5:42:1:0:0 0/1:17:2:1,1:7,8:0.1176:2,2:8:0:31.5:1:1:1.13:44:4:0.1176:0:1 -4 119557831 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21647;SOR=0;LSEQ=AGCTGCATGATCAGGGCCGG;RSEQ=ACTGGTCCAGGGCGCGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:12,10:0.0833:2,2:23:1:26.5:1:1:1.19087:54.5:4:0.0833:0:1 0/0:27:0:0,0:15,12:0:2,0:28.7:1:31.7:1:1:0:49.6:26:1:0:0.1 -4 119557950 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22575;SOR=0;LSEQ=AGCTGTCCCCATCACACATG;RSEQ=CACACTTGGGGGTGTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:20,12:0.0588:2,2:24.5:1:29:1:1:1.64076:40:4:0.0588:0:1 0/0:37:0:0,0:15,22:0:2,0:28.1:1:30.4:1:1:0:36:36:1:0:0 -4 119558263 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51094;SOR=Inf;LSEQ=GAAACAGGTCGCCTTGGAAG;RSEQ=TGTCCCTGGGCCCCCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:36,37:0:2,0:27.5:1:31.8:1:1:0:59.1:146:1:0:0.1 0/1:102:2:1,1:50,50:0.0196:2,2:24.5:1:26.5:1:1:1:57:4:0.0196:0:1 -4 119558273 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51486;SOR=Inf;LSEQ=GCCTTGGAAGGTGTCCCTGG;RSEQ=CCCCCATCCCCAGGGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:34,35:0:2,0:26.7:1:31.8:1:1:0:57.5:68:1:0:0.1 0/1:101:2:2,0:47,52:0.0198:2,0:13.5:1:26.5:1:0.23287:0:60:4:0.0198:0:1 -4 119558288 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18125;SOR=0;LSEQ=CCTGGGCCCCCATCCCCAGG;RSEQ=GTAGGGGCCGTAGGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:30,33:0.0308:2,2:45:0:31:1:1:1.10:60:4:0.0313:0:1.5 0/0:87:0:0,0:42,45:0:2,0:19.6:1:30.1:1:1:0:55.1:174:1:0:0.1 -4 119558577 . G A 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01087;SOR=0.28341;LSEQ=CCCTCTGGCTCCTCCCCAGA;RSEQ=TTGTCCCCACTCTCAGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:17:10,7:23,11:0.3333:2,2:25.2:1:28.8:1:0.55095:1.45245:44.6:16:0.32:0:1.2 0/1:57:7:4,3:32,18:0.1228:2,2:23.6:1:29.9:1:0.70056:1.32641:42.7:14:0.1273:0:1 -4 119558596 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50116;SOR=Inf;LSEQ=AGTTGTCCCCACTCTCAGTC;RSEQ=GTCACCCAGTCCTTGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:30,21:0:2,0:31.3:1:30.5:1:1:0:44.7:102:1:0:0.3 0/1:63:2:1,1:38,23:0.0317:2,2:8.5:1:28:1:1:1.63846:47:4:0.0317:0:1 -4 119558914 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49739;SOR=Inf;LSEQ=GGTCTATTTCCCTGCCATCC;RSEQ=GGCTGTGTACCCCCCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:45,34:0:2,0:23.5:1:30.5:1:1:0:54.6:158:1:0:0.1 0/1:84:2:1,1:44,38:0.0238:2,2:23.5:1:28:1:1:1.15587:54.5:4:0.0241:0:1 -4 119558927 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.50153;SOR=Inf;LSEQ=GCCATCCAGGCTGTGTACCC;RSEQ=CCTGTGGGTGAAGGCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:48,36:0:2,0:24.3:1:30.6:1:1:0:54:41:1:0:0.2 0/1:101:2:1,1:51,48:0.0198:2,2:18:0:31.5:1:1:1.06189:49:4:0.0198:0:1 -4 119558932 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2075;SOR=0;LSEQ=CCAGGCTGTGTACCCCCCTG;RSEQ=GGGTGAAGGCTTGGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:48,35:0.0235:2,2:14.5:1:28.5:1:1:1.36624:50:4:0.025:0:1 0/0:101:0:0,0:51,50:0:2,0:23:1:29.3:1:1:0:52.3:32.667:1:0:0.2 -4 119558948 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21244;SOR=0;LSEQ=CCTGTGGGTGAAGGCTTGGG;RSEQ=CAGGCTGAGCCAGGTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:45,39:0.0233:2,2:7.5:1:29:1:1:1.15192:60:4:0.0244:0:1.5 0/0:100:0:0,0:51,49:0:2,0:29.6:1:31.3:1:1:0:50.3:49:1:0:0.2 -4 119559057 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06729;SOR=Inf;LSEQ=GCAACTGACAGGAGTTCAGA;RSEQ=GACACCCCAGGGGCAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:38,32:0:2,0:25.4:1:31.6:1:1:0:40:34:1:0:0.1 0/1:49:3:1,2:25,21:0.0612:2,2:12.3:1:25.3:1:0.59428:2.34:28.3:6:0.0612:0:1 -4 119559101 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50063;SOR=0;LSEQ=GCCCGTCTCTGATATGCTCC;RSEQ=CTCCCACAAGCCCTTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:65,43:0.0182:2,2:14.5:1:31.5:1:1:1.50576:41:4:0.0183:0:1 0/0:94:0:0,0:57,37:0:2,0:23.9:1:30.1:1:1:0:39.9:93:1:0:0.1 -4 119559126 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.23217;SOR=0;LSEQ=CACAAGCCCTTGTTACACTC;RSEQ=TGCTAGCCCCTGGCTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:59,39:0.02:2,2:20.5:1:28:1:1:1.50636:42:4:0.0202:0:1 0/0:107:0:0,0:64,43:0:2,0:27.4:1:30.8:1:1:0:39.6:214:1:0:0.1 -4 119559217 . C T 106 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0397;SOR=0.29389;LSEQ=CTTCACCTGGAAGGCCAGGT;RSEQ=GTGGTATTTCTGCGTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:13:9,4:36,38:0.1494:2,2:18.8:1:28.9:1:0.2325:2.35:23.5:26:0.1512:0:1.3 0/1:82:4:3,1:37,41:0.0488:2,2:13:1:26.5:1:0.35349:3.28:36:8:0.0488:0:1.8 -4 119559280 . C T 140 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04177;SOR=0.44733;LSEQ=CTCGCTCAGCATCTGGCTGA;RSEQ=GGTCCGGTTATCCTGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:23:7,16:39,43:0.219:2,2:31.2:1:31:1:0.16157:2.05914:32:46:0.2233:0:1.4 0/1:108:12:3,9:50,46:0.1111:2,2:34.3:1:28.9:1:0.12397:3.22741:31.8:11:0.1048:0:1.7 -4 119559308 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49934;SOR=Inf;LSEQ=TTATCCTGGTTGGGGTGACC;RSEQ=TGGTGCGCCCTGCCAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:53,68:0:2,0:26.7:1:31.9:1:1:0:49.7:242:1:0:0.5 0/1:134:2:1,1:66,66:0.0149:2,2:31.5:1:27.5:1:1:1:25:4:0.0156:0:2 -4 119559314 . C T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59079;SOR=0.80044;LSEQ=TGGTTGGGGTGACCCTGGTG;RSEQ=GCCCTGCCAGGGCCTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:19:8,11:42,57:0.1583:2,2:26.4:1:30:1:1:1.01305:42.1:38:0.1597:0:1 0/1:130:17:6,11:61,51:0.1308:2,2:28.8:1:27.6:1:0.19336:2.1796:46.6:16:0.126:0:1.3 -4 119559382 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49772;SOR=Inf;LSEQ=CATGGGCCACTGGATGTGGT;RSEQ=CTTGTCCCATTTGTTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:45,62:0:2,0:21:1:31:1:1:0:51.4:106:1:0:0.1 0/1:109:2:1,1:50,57:0.0183:2,2:40.5:1:28.5:1:1:1.14:54.5:4:0.0183:0:1 -4 119559464 . C A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62197;SOR=2.82252;LSEQ=AGGGCACTGAGGGACTGGGC;RSEQ=TGACATCATCTGAGTGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:1:1,0:45,42:0.0114:2,0:1:0:26:0:1:0:46:2:0.0115:0:1 0/1:95:3:2,1:39,53:0.0316:2,2:13.3:1:27.3:1:0.57612:2.69:44.7:6:0.0323:0:1 -4 119559480 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22092;SOR=0;LSEQ=GGGCCTGACATCATCTGAGT;RSEQ=GTAGAGGCAACGGGGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:34,38:0.0267:2,2:24:1:28.5:1:1:1.12:50:4:0.0278:0:1 0/0:84:0:0,0:34,50:0:2,0:21.6:1:30.7:1:1:0:49.2:168:1:0:0.1 -4 120258955 . T G 101 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17178;SOR=0.15964;LSEQ=CCACAGAGGTGGGCTTCAGT;RSEQ=GGGCCTTGATGGGAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:9,0:8,0:0.5294:0,0:28.8:1:32.1:1:1:0:55.8:18:0.5294:0:1 0/1:7:1:1,0:5,1:0.1429:2,0:38:0:29:0:1:0:60:2:0.1429:0:1 -4 120259052 . A G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.05986;LSEQ=AAGTCAGGGAGGGAATAAAC;RSEQ=TCATCTGTTGGATAAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:16:15,1:50,0:0.2424:1,1:23.6:1:30.6:1:0.24242:0:46.8:32:0.2462:0:1 0/1:75:19:19,0:54,2:0.2533:1,1:21:1:30.2:1:1:0:47.2:38:0.2533:0:1.3 -4 120259212 . CA TG 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00767;SOR=0.5231;LSEQ=CAGTGAAGGCTTTTGGGAAA;RSEQ=GAGCATCATGCTAAGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:43:21,22:195,209:0.0958:2,2:24.6:1:30.6:1:1:1.02:44.4:86:0.0973:0.0067:1 0/1:629:33:16,17:273,319:0.0525:2,2:21.5:1:29.8:1:0.85841:1.10:49:66:0.0534:0.0048:1 -4 120259213 . A G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=3e-04;SOR=1.70112;LSEQ=AGTGAAGGCTTTTGGGAAAC;RSEQ=GAGCATCATGCTAAGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:91:47,44:149,161:0.2054:2,2:25.6:1:30.5:1:0.55366:1.15:47:90:0.2267:0:1.1 0/1:612:187:89,98:179,216:0.3056:2,2:26.7:1:30:1:0.65627:1.10:46.4:374:0.323:0:1.1 -4 120259304 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49988;SOR=Inf;LSEQ=GTGGGAAATTCAGATCTTAA;RSEQ=TCTAAATTTCCCAAGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:25,143:0:2,0:25.8:1:32.2:1:1:0:50.4:167:1:0:0.1 0/1:186:2:1,1:42,142:0.0108:2,2:25.5:1:31.5:1:0.40988:3.35:49:4:0.0108:0:1 -4 120324304 . C T 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00245;SOR=0;LSEQ=GGAGGAGGGGGTGATGATGT;RSEQ=ATTGCTGATGACGGCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:8:8,0:52,31:0.0879:2,0:13.8:1:30.9:1:0.04739:0:52.5:16:0.0879:0:1.1 0/0:98:0:0,0:53,45:0:2,0:22.1:1:30.8:1:1:0:49.1:31.667:1:0:0.2 -4 120324317 . G A 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00779;SOR=Inf;LSEQ=ATGATGTCATTGCTGATGAC;RSEQ=GCTTTAGCACCACTGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:56,34:0:2,0:22.2:1:30:1:1:0:46.4:89:1:0:0.2 0/1:104:8:4,4:50,46:0.0769:2,2:22.6:1:29.3:1:1:1.08608:42.9:16:0.0769:0:1.1 -4 120324424 . A T 128 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01735;SOR=0.33875;LSEQ=CAACAAGGGCTTTCATGGGA;RSEQ=GGTATTTGCACCTGTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:18:3,15:10,33:0.2951:2,2:25.8:1:30.8:1:0.7372:1.50538:58.8:36:0.3:0:1.2 0/1:73:9:4,5:24,40:0.1233:2,2:18.9:1:30.1:1:0.72515:1.33:52.7:18:0.1233:0:1.7 -4 120324432 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24394;SOR=Inf;LSEQ=GCTTTCATGGGAAGGTATTT;RSEQ=CACCTGTCATTCCTTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:12,44:0:2,0:20.4:1:32.2:1:1:0:59.6:27:1:0:0.4 0/1:59:3:2,1:22,34:0.0508:2,2:19:1:26:1:0.56074:3.03:60:6:0.0517:0:1 -4 120324476 . A G 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.85928;LSEQ=ACTCCTGCCGCCCCTTGCTG;RSEQ=ATCCTGAGCCCCCAGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:0,5:15,9:0.1724:2,0:18.4:1:31.6:1:0.01686:0:51.8:10:0.1724:0:1.6 0/1:33:5:3,2:12,16:0.1515:2,2:21.6:1:30:1:0.63899:1.96:46.8:10:0.1515:0:2 -4 120324546 . TCTC T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.88851;LSEQ=CTATGGTCCCACCCCGTCCT;RSEQ=CTACACATTCTCGGATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:4,2:24,9:0.1538:2,2:21.5:1:32.8:1:1:1.32314:49:12:0.1579:0:1 0/1:36:5:3,2:27,4:0.1389:2,2:27.8:1:31.2:1:0.18583:4.24589:56.4:10:0.1429:0:1 -4 120324591 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23567;SOR=0;LSEQ=CTCCTCAACCTTGGCACCCA;RSEQ=CTCCTTCTTACTGGGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:36,21:0.0339:2,2:49:0:31.5:1:1:1.6979:60:4:0.0339:0:1 0/0:62:0:0,0:35,27:0:2,0:27.2:1:30.3:1:1:0:47.5:61:1:0:0.2 -4 120324615 . C A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78496;SOR=1.27224;LSEQ=CTTCTTACTGGGCCCAGGAG;RSEQ=CTTCAAAGCCCAGGAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:7:4,3:28,30:0.1077:2,2:21.7:1:28.3:1:0.70847:1.42:44.9:14:0.1077:0:1.1 0/1:60:8:4,4:28,24:0.1333:2,2:18.1:1:29.8:1:1:1.16366:46.1:16:0.1379:0:1.4 -4 120324707 . T C 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49761;SOR=1.82969;LSEQ=CCCAGGGACGCCTTCCAAGG;RSEQ=GACCTGTTTCCTCCCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:3:2,1:18,28:0.0612:2,2:22.7:1:24.7:1:0.55927:3.04:36.3:2:0.0417:0:1.3 0/1:56:6:3,3:25,25:0.1071:2,2:5.2:1:27.8:1:1:1:52.2:12:0.1071:0:1.3 -4 120324738 . CTTCTGGTGCAAGAGA C 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27652;SOR=2.85368;LSEQ=CTCCCAATGGATCCTGCCAC;RSEQ=CCTGAAAGTGTGGGCGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:2,0:24,24:0.04:2,0:32.5:1:32.5:1:0.49061:0:48:4:0.04:0.02:0.5 0/1:56:6:2,4:26,24:0.1071:2,2:30.8:1:29.5:1:0.66946:2.13765:58:12:0.1091:0:0.8 -4 120324799 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28045;SOR=Inf;LSEQ=TACCAGGCCCCTCAGTCATT;RSEQ=TGGTCCCTCCCAACACTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:12,26:0:2,0:23.3:1:31.7:1:1:0:55.9:76:1:0:0.3 0/1:60:3:2,1:23,34:0.05:2,2:6.3:1:30:1:0.56531:2.90:41.7:6:0.0517:0:1 -4 120324918 . A G 77 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.37409;SOR=3.85381;LSEQ=GCAGAGGGAACCCCACGGAC;RSEQ=TGGATCCCGCACTGGCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:7,3:0.0909:2,0:18:0:32:0:1:0:57:2:0.0909:0:1 0/1:21:6:5,1:6,9:0.2857:2,2:21.2:1:29.8:1:0.14861:6.81:55:12:0.2857:0:1 -4 120325264 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0.69162;LSEQ=TGCCCTGACTCCCAGCCCTG;RSEQ=GGGGGTCCTGACCCCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:0,2:9,4:0.1333:2,0:46.5:1:31.5:1:0.14286:0:45:4:0.1429:0:2 0/1:21:2:2,0:10,9:0.0952:2,0:32:1:31.5:1:0.48571:0:40:4:0.0952:0:2 -4 120325273 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCCCAGCCCTGCGGGGGTCC;RSEQ=GACCCCACCTCACCTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:9,5:0.125:2,0:37.5:1:31:1:0.175:0:45:4:0.1333:0:2 0/1:24:3:3,0:12,9:0.125:2,0:22:1:31.3:1:0.2663:0:46.7:6:0.125:0:1.7 -4 120325345 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18362;SOR=0;LSEQ=CTGCCTCTGCCCGAGAGTCA;RSEQ=GTGAGGCTGAGAGTAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:16,8:0.0769:2,2:31.5:1:29:1:1:1.94371:50:4:0.08:0:1 0/0:34:0:0,0:22,12:0:2,0:22.5:1:29.7:1:1:0:55.3:68:1:0:0.2 -4 120325387 . TG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.24211;SOR=0;LSEQ=GGGGCAGCAGTGGTGCCAGT;RSEQ=GGGGGCGGTCCAGTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:32,13:0.0426:2,2:24.5:1:31:1:0.51156:2.40879:46:4:0.0426:0:0 0/0:48:0:0,0:26,22:0:2,0:28:1:30.6:1:1:0:55.5:96:1:0:0.2 -4 120325432 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.8051;SOR=1.26015;LSEQ=CTCAGCCTCGTGGGCTGTTC;RSEQ=GTGGGACTGATGACTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:8:5,3:36,20:0.125:2,2:22.8:1:30.3:1:1:1.07869:52.6:16:0.129:0:1.1 0/1:72:11:5,6:31,30:0.1528:2,2:18.2:1:31.4:1:1:1.2363:55.9:22:0.1528:0:1 -4 120325529 . G A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29893;SOR=0.50515;LSEQ=GTGCAGGGCCACTGGGAGCC;RSEQ=CTGCATGGTCCCAGAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:12:5,7:30,40:0.1463:2,2:26.4:1:30.5:1:1:1.04939:55.9:24:0.1463:0:1 0/1:63:5:2,3:27,31:0.0794:2,2:28.6:1:29.6:1:1:1.30099:51.4:10:0.0794:0:1 -4 120325559 . A C 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16372;SOR=Inf;LSEQ=CCCAGAGGCTGGACTGGGGC;RSEQ=GGTGCCAACTGAAGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:23,41:0:2,0:27.4:1:30.5:1:1:0:55.6:128:1:0:0.2 0/1:44:2:1,1:16,26:0.0455:2,2:36.5:1:24:1:1:1.61:57:4:0.0455:0:1 -4 120325630 . G A 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.67133;SOR=1.59864;LSEQ=AACCTTGGAGAAGAAAATGT;RSEQ=TGCATAGCGGGTCCACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:0,2:10,19:0.0645:2,0:15:1:30.5:1:1:0:50:4:0.0645:0:2 0/1:30:3:2,1:9,17:0.1:2,2:36.3:1:27.3:1:0.53941:3.60:44.7:6:0.1034:0:1 -4 120325654 . GC G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=1.2186;LSEQ=ATAGCGGGTCCACTGCTGCT;RSEQ=CCCTGCCCTGACTCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:1,3:15,18:0.1081:2,2:27:1:27.5:1:0.61844:2.44353:55:3:0.0857:0:1.5 0/1:31:4:1,3:11,16:0.129:2,2:25.5:1:31.5:1:1:2.01848:51.8:8:0.1333:0:1.5 -4 120325674 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23881;SOR=Inf;LSEQ=GCCCCTGCCCTGACTCCCAG;RSEQ=CCTGCCTGACCCCACCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:14,20:0:2,0:28.8:1:31.4:1:1:0:56.1:68:1:0:0.4 0/1:33:2:1,1:12,19:0.0606:2,2:5.5:1:26:1:1:1.56:60:4:0.0645:0:1 -4 120325732 . C A 43 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.83805;LSEQ=GCAACTCTGGGTGCCTTGCC;RSEQ=CTGCCTCTGCCCCAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:5,10:0.1667:2,2:5:1:27.3:1:1:1:60:6:0.1667:0:1 0/1:14:2:0,2:5,7:0.1429:2,0:3:1:25.5:1:0.50549:0:60:4:0.1429:0:2 -4 123792847 . T A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17647;SOR=0;LSEQ=CCTTGAGTAACATCTCCAGG;RSEQ=GCAGGAGCAAATCAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:18:0:31:0:1:0:60:2:1:0:1 0/1:16:2:1,1:7,7:0.125:2,2:26.5:1:29.5:1:1:1:60:4:0.125:0:1 -4 123792964 . GCAA G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.48617;SOR=0;LSEQ=AAAAAAAAAACTAGCAGAAA;RSEQ=CAACAACAGCATCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:9,2:0.1538:2,2:30:1:31.5:1:0.42308:3.87298:52.5:4:0.1818:0:1 0/0:10:0:0,0:4,6:0:2,0:23.8:1:30.7:1:1:0:60:9:1:0:0.5 -4 123793061 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10256;SOR=Inf;LSEQ=AAAATAGACAAACTCACAAA;RSEQ=ATGAGAAAGAAATCAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:0:2,0:27.3:1:31.7:1:1:0:60:36:1:0:0.5 0/1:9:2:1,1:4,3:0.2222:2,2:40:0:28.5:1:1:1.29098:60:4:0.2222:0:2 -4 123793070 . GA G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTCACAAAGATGAGAAA;RSEQ=AATCAACGAAAAAATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:6,12:0,0:1:0,2:24.4:1:31.6:1:1:0:60:36:1:0.1111:0.5 1/1:5:5:3,2:0,0:1:0,2:21.4:1:31.6:1:1:0:60:10:1:0.2:1.2 -4 123793087 . G T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2451;SOR=Inf;LSEQ=AAAGAAATCAACGAAAAAAT;RSEQ=ATGAAAACCCAAAAGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:2,6:2,4:0.5714:2,2:21.6:1:29.9:1:1:1.45647:60:16:0.5714:0:1.1 1/1:4:4:2,2:0,0:1:0,2:26.3:1:29.5:1:1:0:60:8:1:0:1.5 -4 124344600 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09994;SOR=0;LSEQ=GCTCTGTATTCCAGATATTG;RSEQ=TCCCTTAAGAGAGGAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:3:1,2:74,8:0.0353:2,2:12:1:27.7:1:0.03539:17.22203:60:6:0.0353:0:1.3 0/0:97:0:0,0:86,11:0:2,0:24.7:1:31.5:1:1:0:60:47.5:1:0:0.2 -4 124344636 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20034;SOR=0;LSEQ=AAGAGATTTTTCTCTTGTGA;RSEQ=ATTTGTTTATTCTACGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:143,37:0.011:2,2:14.5:1:28:1:0.3749:3.82698:60:4:0.0112:0:1 0/0:224:0:0,0:157,67:0:2,0:22.4:1:31.4:1:1:0:60:73.667:1:0:0.5 -4 124344650 . A T 168 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=55.75228;LSEQ=TTGTGAGATTTGTTTATTCT;RSEQ=CGAAACTCAAAAAGTCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:1:0,1:180,60:0.0041:2,0:33:0:27:0:0.25311:0:60:2:0.0042:0:1 0/1:280:53:34,19:149,78:0.1893:2,2:27.3:1:29.5:1:0.8732:1.06724:60:106:0.1927:0:1.1 -4 124344717 . T C 268 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09249;SOR=0.77743;LSEQ=CAGGTCACCAAGTAGTGCAG;RSEQ=CGTCAGCTGGGGTTCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:459:355:186,169:56,47:0.7734:2,2:27.5:1:31.6:1:0.73798:1.08238:60:176.5:0.7741:0:1.1 1/0:537:390:198,192:68,76:0.7263:2,2:26.4:1:31.2:1:0.49554:1.15:60:64:0.7273:0:1.1 -4 124344813 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23628;SOR=Inf;LSEQ=GAGTCCTCTTCAACCAAAGG;RSEQ=TGCTAGGATTGTTTCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:42,152:0:2,0:23.5:1:31.5:1:1:0:60:37.8:1:0:0.5 0/1:184:2:1,1:48,134:0.0109:2,2:35.5:1:30.5:1:0.46276:2.77:60:4:0.0112:0:1 -4 124344819 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10929;LSEQ=TCTTCAACCAAAGGCTGCTA;RSEQ=GATTGTTTCTGTAATCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:85:11,74:14,69:0.506:2,2:24:1:30.8:1:0.52078:1.36242:60:84:0.503:0:1.1 0/1:160:16:3,13:38,106:0.1:2,2:25.9:1:30.4:1:0.76332:1.54956:60:32:0.1006:0:1.1 -4 124344820 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24005;SOR=Inf;LSEQ=CTTCAACCAAAGGCTGCTAG;RSEQ=ATTGTTTCTGTAATCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:24,141:0:2,0:24:1:31.3:1:1:0:60:330:1:0:0.6 0/1:159:2:1,1:39,118:0.0126:2,2:35.5:1:29:1:0.44105:3.00:60:4:0.0127:0:1 -4 124344915 . C T 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0518;SOR=Inf;LSEQ=TCTCACTGTATTATAAGTTC;RSEQ=CCCAAAGGCTTGAGGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:0,22:0:1,0:19.9:1:30:1:1:0:60:21:1:0:0 0/1:25:5:0,5:0,20:0.2:1,0:28.2:1:29.6:1:1:0:60:10:0.2:0:1 -4 128734263 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23501;SOR=Inf;LSEQ=TCACCTTTCTTATAGATTCG;RSEQ=ATATACGTGGCCAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:45,65:0:2,0:26.9:1:32.4:1:1:0:49.6:54:1:0:0 0/1:104:2:1,1:39,63:0.0192:2,2:13:1:29:1:1:1.61:44.5:4:0.0194:0:1 -4 128734335 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.80048;LSEQ=ATATATCGGGTGCCTCTCCT;RSEQ=TTTCCCTTTGTGTTCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:0,1:69,60:0.0077:2,0:1:0:25:0:0.46923:0:60:2:0.0078:0:1 0/1:145:2:1,1:73,70:0.0138:2,2:13.5:1:29.5:1:1:1.04257:55:4:0.014:0:1 -4 130070827 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51234;SOR=Inf;LSEQ=TTCAGAATTCCCCAAATTGT;RSEQ=TAAACTTCTGGCCCCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:24,10:0:2,0:24.1:1:29.7:1:1:0:60:10.333:1:0:0.5 0/1:50:2:1,1:26,20:0.04:2,2:13:1:27.5:1:1:1.29283:60:4:0.0426:0:2 -4 130070886 . C T 146 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGGCAATGCTGGCTAACAA;RSEQ=GTTCATTGTGTGCTTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:11,16:0,0:1:0,2:32.9:1:30.9:1:1:0:60:54:1:0:1.1 1/0:40:20:8,12:7,12:0.5:2,2:26.9:1:29.8:1:1:1.14:60:40:0.5128:0:1.2 -4 130124405 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCGAGTAGTTGGGACTACAG;RSEQ=CGCCCACCACCACACCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:31:1:1:0:46:4:1:0:1.5 -4 130125306 . T C 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1106;SOR=1.29529;LSEQ=TTCAAACTAAAACCAGTTTA;RSEQ=GTAGAGGAAATCTTTATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:218:109,109:62,57:0.645:2,2:24.2:1:30.7:1:0.73344:1.08745:59.9:217:0.6458:0:1.1 1/0:379:266:118,148:54,59:0.7018:2,2:23.8:1:30:1:0.57364:1.14752:60:87.667:0.7032:0:1.1 -4 130125355 . C A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1045;SOR=0;LSEQ=GGAAAATGTTCTTGTCATAC;RSEQ=TATCCACCTAATCTACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:101,157:0.0115:2,2:34.3:1:30.3:1:1:1.28541:60:6:0.0116:0:1.3 0/0:292:0:0,0:111,181:0:2,0:24.8:1:30.5:1:1:0:59.8:35.5:1:0:0.8 -4 130125383 . CT C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.22945;SOR=Inf;LSEQ=CTAATCTACTGATTCTCCAC;RSEQ=TTTGTTTTCTTCTTTTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:54,125:0:2,0:21.7:1:29.8:1:1:0:59.9:28.833:0.9943:0:0.9 0/1:166:2:1,1:49,114:0.012:2,2:31.5:1:32.5:1:0.51552:2.31:60:4:0.0127:0:0 -4 130125405 . T TA 70 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.75765;SOR=0.7896;LSEQ=TTTGTTTTCTTCTTTTTAGC;RSEQ=AAAAAAAAAACACAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:6:1,5:23,72:0.0583:2,2:33.2:1:27.2:1:1:1.59072:60:5:0.0568:0:2.2 0/1:86:4:0,4:23,55:0.0465:2,0:25.3:1:32:0:0.57251:0:60:8:0.058:0:1.3 -4 130125415 . AC A 82 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.77891;SOR=1.28341;LSEQ=TCTTTTTAGCTAAAAAAAAA;RSEQ=ACAAAAAAAAAAACCTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:7:1,6:0,0:0.0886:0,2:20.3:1:29.7:1:1:0:60:14:0.0921:0.038:0.4 0/1:63:7:0,7:4,17:0.1111:2,0:13:1:29.3:1:0.5453:0:60:14:0.1207:0.0635:0.4 -4 130125416 . C A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.12664;LSEQ=CTTTTTAGCTAAAAAAAAAA;RSEQ=ACAAAAAAAAAAACCTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:70:12,58:0,0:0.8861:0,2:22.5:1:29.9:1:1:0:58.9:34:0.8947:0:1.6 0/1:63:31:6,25:4,17:0.4921:2,2:19.2:1:29.9:1:1:1.02:57.4:62:0.5345:0:1.8 -4 130125418 . C CA 98 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.09491;SOR=0.30141;LSEQ=TTTTAGCTAAAAAAAAAACA;RSEQ=AAAAAAAAAAACCTAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:12:1,11:8,50:0.1519:2,2:24.8:1:27.4:1:1:1.74786:58.3:11:0.1667:0.038:1.7 0/1:59:3:1,2:7,35:0.0508:2,2:27:1:30.7:1:0.45243:2.44:60:6:0.0612:0:1.3 -4 131217633 . TA T 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATTTTATGACTCAGTT;RSEQ=AAAAAAAAAAACAAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:12:1:28.5:1:1:0:60:4:0.3333:0.1667:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 131217680 . T C 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20455;SOR=0;LSEQ=GTGATTAACTTTCACTCTTA;RSEQ=AGCAACATTTATTTGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:3,1:0.4286:2,2:19.3:1:30.3:1:1:1.41418:60:6:0.4286:0:1.3 0/0:5:0:0,0:5,0:0:0,0:33.6:1:31.4:1:1:0:60:10:1:0:0 -4 134134156 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22092;SOR=Inf;LSEQ=GACACAGAGTCAGACCATAT;RSEQ=GATTATAAATGTCTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:30,1:0:1,0:19.6:1:31.8:1:1:0:60:62:1:0:0 0/1:28:2:2,0:26,0:0.0714:1,0:28:1:30:1:1:0:60:4:0.0714:0:1 -4 134134244 . T C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25256;SOR=Inf;LSEQ=ATTACATACTTAACAATGAT;RSEQ=TATATTTTAGAAGTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:120,59:0:2,0:25.3:1:29.8:1:1:0:60:43.75:1:0:0.7 0/1:209:3:1,2:132,74:0.0144:2,2:25.7:1:25.7:1:0.29961:3.54485:60:2:0.01:0:1.7 -4 134134309 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05561;LSEQ=TAATGATGTCAGTGTTTTTG;RSEQ=ATTTCCTATTTGAAGACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:239:221:107,114:8,10:0.9247:2,2:26.6:1:31.7:1:0.80976:1.17:60:35.833:0.9227:0:1.8 0/1:319:129:61,68:95,95:0.4044:2,2:25.8:1:31.5:1:0.64963:1.11437:60:42:0.4013:0:1.9 -4 134134331 . G A 231 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCCTATTTGAAGACTAAC;RSEQ=TGAGAATAATATTTGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:200:200:84,116:0,0:1:0,2:26.5:1:30.3:1:1:0:60:99:1:0:1.9 1/0:296:158:64,94:60,78:0.5338:2,2:24.4:1:29.2:1:0.63767:1.12934:60:51.667:0.5308:0:1.7 -4 134134348 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16468;SOR=0;LSEQ=AACGTGAGAATAATATTTGA;RSEQ=GGAAGGAGACAGATTGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:59,99:0.0124:2,2:10.5:1:29:1:1:1.67:60:4:0.0128:0:2 0/0:235:0:0,0:91,144:0:2,0:26.9:1:30:1:1:0:60:46:1:0:0.9 -4 134134495 . G GT 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.222;SOR=0.32577;LSEQ=CTCTTTTTAATAACATTCAT;RSEQ=TTTTTTCCAGAAAAATATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:1,15:0,5:0.7619:0,1:29.4:1:30.6:1:1:0:60:32:0.7619:0:0.1 1/0:10:5:0,5:0,5:0.5:0,0:30.4:1:31:1:1:0:60:10:0.5:0:0 -4 134635942 . G A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50525;SOR=1.16577;LSEQ=TAGAAAATTTCACTGTAGTC;RSEQ=CAAGCTCTAACATTTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:42:19,23:60,77:0.2346:2,2:24.1:1:29.8:1:1:1.06:60:84:0.2346:0:1.2 0/1:262:69:30,39:87,104:0.2634:2,2:26.9:1:28.9:1:0.77974:1.08713:60:22:0.2588:0:1.2 -4 135458997 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22;SOR=Inf;LSEQ=TAGAGCATGGCAGAGTTAAT;RSEQ=CTTTCTGAGGACTGTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:0:2,0:22.3:1:30.2:1:1:0:60:26:1:0:0 0/1:12:2:1,1:7,3:0.1667:2,2:10:1:29:1:1:2.16028:60:4:0.1667:0:1 -4 136777565 . CT C 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTCATCCCTCTTTACAATT;RSEQ=TTTCCTTGGGTATCTAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:24:20,4:55,7:0.2791:2,2:25.4:1:31.4:1:0.49141:1.56259:60:48:0.2791:0.0465:0 0/0:102:0:0,0:86,16:0:2,0:25.8:1:30.8:1:1:0:60:101:1:0:0 -4 136777610 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.18979;SOR=0;LSEQ=TGGAAAACAATGACAGACTT;RSEQ=CTTTCTGCCTAGTTTAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:130,53:0.0108:2,2:11:1:30:1:0.49971:2.43936:60:4:0.0111:0:1 0/0:239:0:0,0:162,77:0:2,0:23.9:1:29.7:1:1:0:60:478:1:0:0.2 -4 136777689 . A G 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0566;LSEQ=CCAGTGCAACTTAGAATCAG;RSEQ=GACAGAAAAGTGAAATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:336:304:148,156:17,15:0.9048:2,2:25.7:1:31.1:1:0.71142:1.19396:60:100.333:0.9066:0:1.1 0/1:436:152:71,81:132,151:0.3486:2,2:25:1:30.5:1:1:1.00:60:49.667:0.3457:0:1.2 -4 140619088 . C T 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=GCATTAATGCTTTACGTCTC;RSEQ=GCATTTATATTAAAAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:45.3:1:31:1:1:0:35:6:0.6:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:11:0:33:0:1:0:40:2:0.3333:0:1 -4 140619196 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.20353;SOR=Inf;LSEQ=TATACTTAGGTACCTTTTGA;RSEQ=CCCATGGAAAAAAATTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:53,6:0:2,0:23.5:1:32.2:1:1:0:43.7:58:1:0:0.1 0/1:49:2:1,1:42,5:0.0408:2,2:18.5:1:31.5:1:0.23214:7.75867:35.5:4:0.0408:0:1 -4 140619247 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50512;SOR=Inf;LSEQ=ACTACCAATAACAGGAAGAA;RSEQ=AGAAATTTTTTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:115,18:0:2,0:25:1:31.9:1:1:0:47.9:43.333:1:0:0.5 0/1:168:2:1,1:137,29:0.0119:2,2:10:1:25.5:1:0.32613:4.66169:35:4:0.0123:0:3 -4 140619252 . A AT 192 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.82308;SOR=0.93954;LSEQ=CAATAACAGGAAGAAGAGAA;RSEQ=TTTTTTTTTTTTTGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:142:74:57,17:55,5:0.5211:2,2:27.1:1:30.6:1:0.03342:3.25369:44.8:148:0.5481:0.0423:0.4 1/0:182:92:73,19:60,17:0.5055:2,2:26.1:1:29.5:1:0.85208:1.09:46.8:91:0.5028:0.033:0.5 -4 140619395 . A G 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=CACACAGGTTGGTGTCTTCA;RSEQ=AAAGGCCAACCAGATAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:110,192:0:2,0:22.3:1:29.8:1:1:0:43.7:74.5:1:0:0.1 0/1:362:13:7,6:136,213:0.0359:2,2:26.9:1:30.5:1:0.38683:1.82:42.4:26:0.0362:0:1 -4 140619644 . G A 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0287;SOR=Inf;LSEQ=TCTTGCGAGCGGCTTTTGTA;RSEQ=CCAGTTGCTTCCTGGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:58,63:0:2,0:22.6:1:32.1:1:1:0:32.8:120:1:0:0.1 0/1:119:5:1,4:46,68:0.042:2,2:21.4:1:28.6:1:0.647:2.68646:29.6:10:0.0427:0:1.2 -4 140619673 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10504;SOR=Inf;LSEQ=TTCCTGGGTGCTTTACCACC;RSEQ=GTCGATTTGCGGGCAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:101,49:0:2,0:26.2:1:30.3:1:1:0:35.2:49:1:0:0.1 0/1:135:3:3,0:88,44:0.0222:2,0:9.7:1:30.3:1:0.55067:0:40:6:0.0226:0:1 -4 140619686 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21453;SOR=Inf;LSEQ=TACCACCGGTCGATTTGCGG;RSEQ=CAGTCTGCTTTGTACGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:118,46:0:2,0:27:1:31.3:1:1:0:35.8:31.8:1:0:0.1 0/1:142:2:2,0:99,41:0.0141:2,0:10.5:1:29.5:1:1:0:40:4:0.0145:0:1 -4 140619764 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49846;SOR=Inf;LSEQ=TCGGCTGGAGCTCGGCGAGC;RSEQ=AGAGGCGGCGCTGGCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:37,110:0:2,0:24.7:1:30.1:1:1:0:51.3:294:1:0:0.1 0/1:152:2:1,1:45,105:0.0132:2,2:23:1:31.5:1:0.51507:2.32:33:4:0.0134:0:1 -4 140810637 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12925;LSEQ=GCCTGGAGCTGTGGAGGTGG;RSEQ=GGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:81:51,30:6,4:0.8265:2,2:27.2:1:30.3:1:1:1.13:59.7:162:0.8351:0:1.4 0/1:132:50:29,21:48,31:0.3788:2,2:27.1:1:28.8:1:0.85415:1.12025:60:49:0.3769:0:1.6 -4 140810678 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.2618;SOR=Inf;LSEQ=CTGCTGTTGCTGTTGCTGCT;RSEQ=CTGTTGCTGCTGCTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:71,64:0:2,0:24.6:1:32.2:1:1:0:59.8:134:1:0:1.1 0/1:178:3:2,1:86,89:0.0169:2,2:27:1:28:1:0.61864:2.06:60:6:0.0169:0:1.3 -4 140810700 . C T 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.89843;SOR=0.94178;LSEQ=TGTTGCTGCTGCTGGATATA;RSEQ=GGCATCAAGGGGTTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:60:27,33:23,30:0.5263:2,2:27:1:30:1:1:1.07:60:59:0.5221:0:1.5 1/0:133:68:27,41:30,34:0.5113:2,2:26.5:1:29.4:1:0.48259:1.33687:59.5:67:0.5115:0:1.4 -4 140811050 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13636;SOR=0;LSEQ=GGGAGACCAATTTGAAGTCT;RSEQ=ATTTGAGTGCTGTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:26,17:0.0444:2,2:22.5:1:28:1:1:1.51459:60:4:0.0444:0:1.5 0/0:76:0:0,0:48,28:0:2,0:22.9:1:30.5:1:1:0:58.5:75:1:0:1.5 -4 140811063 . TTGCTGCTGCTGC T 162 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=47;MSI=19.000;MSILEN=3;SSF=0.60672;SOR=0.82904;LSEQ=GAAGTCTGATTTGAGTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:31:16,15:9,10:0.5849:2,2:22.1:1:29.9:1:1:1.18:59.8:62:0.5849:0.1698:2.1 1/0:91:49:26,23:22,11:0.5385:2,2:16.2:1:29:1:0.25828:1.75698:58:48:0.5333:0.2198:2.2 -4 140811084 . C T 140 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=19.000;MSILEN=3;SSF=0.36753;SOR=1.43265;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:15:4,11:29,21:0.2308:2,2:16.1:1:31.1:1:0.04235:3.71966:60:30:0.2381:0:1.3 0/1:93:28:17,11:33,32:0.3011:2,2:21:1:29.3:1:0.49707:1.49:59.2:56:0.3043:0:1.7 -4 140811096 . C T 177 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=3;SSF=0.00061;SOR=0.29937;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:75:61:35,26:7,7:0.8133:2,2:25:1:30:1:0.76683:1.34:59.3:122:0.8133:0:2.1 1/0:101:57:26,31:28,16:0.5644:2,2:29:1:29.4:1:0.10709:2.07115:58.6:114:0.57:0:2.2 -4 140811135 . T C 201 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03426;LSEQ=TGCTGCTGTTGCTGTTGCTG;RSEQ=TTCTGCTGCATGAGTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:87:85:41,44:2,0:0.977:0,2:29:1:31.5:1:0.24138:0:59.3:27.333:0.988:0:2 1/0:117:69:28,41:24,24:0.5897:2,2:27:1:31.4:1:0.34806:1.45944:59.1:68:0.5965:0:2 -4 140811149 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50841;SOR=Inf;LSEQ=TTGCTGTTTCTGCTGCATGA;RSEQ=TTTGGCCCTTTGTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:35,42:0:2,0:26.9:1:31.1:1:1:0:60:18.25:1:0:1.9 0/1:104:2:1,1:45,57:0.0192:2,2:39.5:1:29.5:1:1:1.26:60:4:0.0198:0:2.5 -4 142367676 . G T 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62427;SOR=0.35067;LSEQ=AAGTAATGTCTTCTTACTGT;RSEQ=ATAGTATAAACAAAATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:197,95:0.0101:2,2:20:1:22.7:1:1:1.03669:60:2:0.0069:0:1.7 0/0:280:1:0,1:185,94:0.0036:2,0:1:0:22:0:0.33929:0:60:2:0.0036:0:1 -4 142367740 . G A 214 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGTGGCTATTTAAATAT;RSEQ=CACATGCAAACACACAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:215,242:0:2,0:25.4:1:31.8:1:1:0:60:64.286:1:0:0.1 0/1:584:172:85,87:211,201:0.2945:2,2:27.7:1:28.9:1:0.717:1.07431:60:171:0.2958:0:1.1 -4 142949864 . A C 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00368;SOR=Inf;LSEQ=TCATGACAATAAAAACAAAC;RSEQ=AAAAAGACCAAGGTGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:253,50:0:2,0:24.3:1:30.2:1:1:0:60:150.5:0.9967:0:0.1 0/1:306:9:8,1:232,64:0.0294:2,2:13.7:1:30.1:1:0.68985:2.20:60:18:0.0297:0:1 -4 142950186 . A AT 27 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.68225;LSEQ=TAACAAAGATTCAACTCTAC;RSEQ=TTTTTTTTTTCCACAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:1,36:0.05:1,0:9:1:27.8:1:1:0:60:4:0.0513:0.025:0.5 0/1:29:1:0,1:0,28:0.0345:1,0:20:0:26:0:1:0:60:2:0.037:0:1 -4 143002782 . A T 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGATAATGAGTTAGTTT;RSEQ=ATTTTGCAAGTACTCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:9.3:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 143003015 . T C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16763;SOR=0;LSEQ=AGATAGAGATGAAATCATTA;RSEQ=ACAGGTGGAGAAAATTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:31,0:0,0:1:0,1:24.1:1:32.4:1:1:0:60:62:1:0:1.1 1/1:22:20:20,0:2,0:0.9091:0,1:18.3:1:31.3:1:1:0:60:40:0.9091:0:1 -4 143003117 . G GA 118 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.72117;SOR=1.156;LSEQ=TCCAATAAAATATGTATTTT;RSEQ=AAAAAAAAAATAAAAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:15:14,1:171,38:0.0661:2,1:24.5:1:31.3:1:0.47866:3.10:60:30:0.0682:0.0088:0.1 0/1:238:18:13,5:177,42:0.0756:2,2:20.5:1:28.4:1:0.36505:1.61717:59.1:36:0.0773:0.0294:0.1 -4 143003155 . G GA 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=4e-05;SOR=0.35124;LSEQ=AACTCAAAATGACCTTAAAA;RSEQ=AAAAAAACTTGAAAAACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:430:409:287,122:15,3:0.9512:2,2:27.8:1:30.1:1:0.29635:2.12226:60:135.333:0.9598:0.1256:0.1 1/1:470:410:266,144:38,18:0.8723:2,2:28.8:1:29:1:0.76521:1.14257:60:81:0.8804:0.0234:0.1 -4 143003396 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24773;SOR=Inf;LSEQ=TGTAATACCGTAAAGTGTCG;RSEQ=CCTCCTCCAAACACTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:26,140:0:2,0:24:1:31.1:1:1:0:60:22.714:1:0:0.2 0/1:165:2:1,1:26,137:0.0121:2,2:8.5:1:28:1:0.30133:5.19:60:4:0.0123:0:1 -4 143003404 . CA C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49913;SOR=0;LSEQ=CGTAAAGTGTCGGCCTCCTC;RSEQ=AACACTTCTAGTCTAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:20,127:0.0134:2,2:11:1:29:1:0.26283:6.22:60:4:0.0141:0:0 0/0:137:0:0,0:14,123:0:2,0:20.9:1:30:1:1:0:60:67.5:1:0:0.1 -4 143003526 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTCATTTCAAAAGCCAAC;RSEQ=CAATGGACCCAATTTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1:0,1:24.8:1:32.9:1:1:0:60:26:1:0:1.2 1/1:6:6:0,6:0,0:1:0,0:23.3:1:30.8:1:1:0:60:12:1:0:1 -4 143003718 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAAAAACAAACAAACAA;RSEQ=CAACCAAAAAACTATATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:40.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 143007169 . C A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74218;SOR=1.29693;LSEQ=CAAGAGTAAAAATGCCTAAT;RSEQ=CATGGACTAATAGAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:4:4,0:52,0:0.0714:1,0:18.8:1:29:0:1:0:60:8:0.0727:0:2 0/1:55:5:5,0:49,1:0.0909:1,0:13.2:1:28.2:1:1:0:60:10:0.0926:0:2 -4 143007197 . C T 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01347;SOR=0;LSEQ=TAATAGAAGATGACACCTGG;RSEQ=AACCCAAAGTGCAGAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:95:93,2:0,0:1:0,1:24.7:1:30.4:1:1:0:60:94:1:0:1.1 1/1:93:87:87,0:6,0:0.9355:0,1:25.3:1:30.4:1:1:0:60:174:0.9355:0:1.1 -4 143007224 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49908;SOR=Inf;LSEQ=AAGTGCAGAGGTTGGACCCT;RSEQ=CACAGTAGAGAACTGATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:130,45:0:2,0:23.1:1:32.1:1:1:0:60:174:1:0:0.6 0/1:186:2:1,1:149,35:0.0108:2,2:5.5:1:29.5:1:0.35048:4.21166:60:4:0.0108:0:1 -4 143007419 . A G 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00482;SOR=0.52922;LSEQ=ATGTGAAATATCTGAAGGGG;RSEQ=AAAAACAAAGGAGAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:289:256:74,182:14,19:0.8858:2,2:25.8:1:31.1:1:0.15795:1.80829:60:512:0.8858:0:1.5 1/1:352:283:96,187:26,43:0.804:2,2:24.5:1:30.6:1:0.57439:1.17724:60:69.75:0.8064:0:1.5 -4 143007449 . A G 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.248;SOR=Inf;LSEQ=GGAGAAAAATAAAATGAGAC;RSEQ=GTGTTCACATTAAGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:40,148:0:2,0:23.5:1:30.9:1:1:0:60:187:1:0:1.5 0/1:187:2:1,1:44,141:0.0107:2,2:33:1:23.5:1:0.42436:3.18:60:4:0.011:0:1 -4 143007460 . T G 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03904;SOR=0.50343;LSEQ=AAATGAGACAGTGTTCACAT;RSEQ=AAGCTGCCCATGGAGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:149:132:22,110:5,12:0.8859:2,2:22.8:1:31.4:1:0.19576:2.07123:60:264:0.8859:0:1.9 1/0:147:117:22,95:7,23:0.7959:2,2:22.9:1:30.8:1:0.60989:1.31167:60:28.25:0.7902:0:1.9 -4 143007466 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24347;SOR=Inf;LSEQ=GACAGTGTTCACATTAAGCT;RSEQ=CCCATGGAGGTTTTTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:24,110:0:2,0:21.7:1:32.4:1:1:0:60:268:0.9926:0:1.7 0/1:132:2:1,1:23,107:0.0152:2,2:13.5:1:26.5:1:0.33171:4.58:60:4:0.0159:0:2.5 -4 143029211 . C T 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32862;SOR=0.26624;LSEQ=AAAGATTTATAATCAAGAAG;RSEQ=TATTATTGCTGTCTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:193,86:0.0106:2,2:8.7:1:21.7:1:0.2305:4.46176:60:2:0.0072:0:1 0/0:351:1:0,1:245,105:0.0028:2,0:1:0:27:0:0.30199:0:60:2:0.0029:0:1 -4 143029391 . A G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.22178;SOR=0.67673;LSEQ=TGGGTTATAAAACGGTACCA;RSEQ=AAAGTAACACATTTTACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:27:8,19:30,121:0.1517:2,2:19.1:1:31.7:1:0.3069:1.69:60:54:0.1543:0:1.1 0/1:204:22:5,17:34,148:0.1078:2,2:18.4:1:30.1:1:0.57916:1.28:60:44:0.11:0:1 -4 143029543 . CACCTCAAATATCCTCACAATCATCAAATGTGAACCTAGATAAAATACCATGTATAAA C 88 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00749;SOR=0;LSEQ=ATTTCACTAATCGCTTCTAA;RSEQ=ACAACAGTCTCTGTGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:28.6:1:31.4:1:1:0:60:14:1:0.5714:0.3 0/1:16:6:1,5:1,9:0.375:2,2:66.5:1:30.5:1:1:1.73:60:12:0.4:0.375:0.2 -4 143033641 . T C 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACATGGGACTTCTCATCATA;RSEQ=GCTTAAAAGGAACAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:283,99:0:2,0:24.5:1:30.5:1:1:0:60:75.4:1:0:0.1 0/1:438:18:12,6:296,124:0.0411:2,2:22.6:1:30.8:1:0.79314:1.19302:60:36:0.0418:0:1.3 -4 143043164 . G GA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49971;SOR=0;LSEQ=TTTCTTACCAAAAAGGAAAA;RSEQ=AAAAAAAACAAAAGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:2,0:117,1:0.0167:1,0:40.5:1:31:1:1:0:60:4:0.0172:0:0 0/0:106:0:0,0:104,2:0:1,0:18.8:1:32.2:1:1:0:60:105:1:0:0.1 -4 143043173 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.21;SOR=Inf;LSEQ=AAAAAGGAAAAGAAAAAAAA;RSEQ=AAAAGAAATATTCCCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:145,1:0:1,0:23.3:1:31.6:1:1:0:60:19.857:1:0:0.1 0/1:124:2:1,1:118,4:0.0161:1,2:29.5:1:30.5:1:0.07933:26.49731:60:4:0.0163:0:1.5 -4 143043397 . G A 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11451;LSEQ=TCTAGCATTCCAATTTCATC;RSEQ=CCTAAACAATAGAAAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:93:28,65:119,219:0.2158:2,2:26.8:1:29.6:1:0.38907:1.26075:60:45.5:0.2156:0:1.2 0/1:492:15:7,8:172,304:0.0305:2,2:15.5:1:28.4:1:0.42299:1.54:60:30:0.031:0:1.3 -4 143043404 . C T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22638;SOR=1.32477;LSEQ=TTCCAATTTCATCGCCTAAA;RSEQ=AATAGAAAAGGCACTTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:38:9,29:119,239:0.096:2,2:29.5:1:28.8:1:0.27611:1.60259:60:76:0.0969:0:1.2 0/1:446:55:18,37:131,260:0.1233:2,2:23.9:1:28.8:1:1:1.03561:60:110:0.1256:0:1.1 -4 143043452 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11667;SOR=Inf;LSEQ=AACATTTGAGGAAAATGTCA;RSEQ=TAGCTACTATGCCTCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:27,153:0:2,0:23.6:1:32.2:1:1:0:60:360:1:0:0.5 0/1:173:3:2,1:29,141:0.0173:2,2:5:1:28.3:1:0.08316:9.53:60:6:0.0175:0:1 -4 143043464 . C T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12966;LSEQ=AAATGTCACTAGCTACTATG;RSEQ=CTCCCTGCTGGAATTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:35:1,34:12,98:0.2414:2,1:26.4:1:30.3:1:0.18949:4.13508:60:70:0.2448:0:1.4 0/1:127:5:0,5:17,104:0.0394:2,0:22.6:1:29.4:1:1:0:60:10:0.04:0:1.8 -4 143044571 . G GA 120 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.04058;SOR=0.4021;LSEQ=ACAAACCAATCCAGCAAGCT;RSEQ=AAAAAAAAATATTGATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:17:6,11:104,316:0.0389:2,2:22.9:1:29.5:1:0.39102:1.66:60:34:0.0393:0.0046:0.4 0/1:500:8:2,6:154,334:0.016:2,2:28.9:1:29.6:1:1:1.38242:60:16:0.0162:0:0.8 -4 143044666 . A C 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35168;SOR=0.30233;LSEQ=GAGGCATCACAGATTCGATT;RSEQ=TCAGGTATGTATAACAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:59:1,58:0,0:0.9833:0,1:26.3:1:32.9:1:1:0:60:118:0.9833:0:1 1/1:56:53:2,51:0,3:0.9464:0,1:23.7:1:32.1:1:1:0:60:52:0.9455:0:1 -4 143045058 . T C 49 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCGACAGTTTGGTTAAAA;RSEQ=ATTCCCTTTTCCTAGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:40:1:31.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:1:0:29:0:1:0:60:2:1:0:1 -4 143045599 . G A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77118;SOR=0.7892;LSEQ=ATATTCAGCTGATATTTATC;RSEQ=TGAATAAGAAACATGGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:12,0:22,0:0.3529:1,0:28.6:1:30.5:1:1:0:60:24:0.3529:0:1 0/1:20:6:6,0:13,1:0.3:1,0:25:1:31:1:1:0:60:12:0.3:0:1 -4 143045690 . A T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.50225;SOR=Inf;LSEQ=TATTCATCATCAAGGATAGG;RSEQ=TGTTAACAATCCGGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:132,28:0:2,0:24.1:1:30.3:1:1:0:60:52.333:1:0:0.1 0/1:190:2:1,1:153,35:0.0105:2,2:13:1:24:1:0.34386:4.32436:60:4:0.0106:0:1 -4 143045938 . G A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12408;SOR=Inf;LSEQ=GGGAAGGGGGTGTAAGAACA;RSEQ=TGCAATAGATGAAGGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:116,270:0:2,0:24.3:1:31.7:1:1:0:60:54.143:0.9974:0:0.2 0/1:393:4:3,1:123,266:0.0102:2,2:22:1:27:1:0.09901:6.45:60:8:0.0103:0:1 -4 143046110 . A G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATAAGCAGCCACCCATC;RSEQ=GACCTCTCCAAGTGGATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:0,18:0,0:1:0,1:25.6:1:29.3:1:1:0:60:17:1:0:1 1/1:2:2:0,2:0,0:1:0,0:27.5:1:31.5:1:1:0:60:4:1:0:1 -4 143066925 . A AT 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39258;SOR=1.51628;LSEQ=GACTCCTCTTCTTCTATATC;RSEQ=TTTTTTTTTCACGAGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:9:7,2:143,18:0.0526:2,2:15.4:1:30.5:1:0.28611:2.25554:60:18:0.0533:0.0117:0.3 0/1:180:14:12,2:150,15:0.0778:2,2:26.4:1:30.8:1:0.62659:1.66103:60:28:0.0787:0.0167:0.1 -4 143066973 . G GA 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10249;SOR=0.17267;LSEQ=TTTACTCAGTAAATGATTGG;RSEQ=AAAAAAAATTATTTCTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:5:4,1:311,145:0.0108:2,2:14.6:1:26.3:1:1:1.86:60:4:0.0088:0.0022:0.2 0/0:530:1:1,0:352,177:0.0019:2,0:39:0:31:0:1:0:60:2:0.0019:0:0 -4 143067054 . G A 200 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.59528;LSEQ=TTTTCTCCATCATTGTTGCC;RSEQ=CCACTGCCTTCACTGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:974:3:2,1:532,437:0.0031:2,2:5:1:27.7:1:1:1.64:60:6:0.0031:0:1 0/1:1146:102:50,52:546,497:0.089:2,2:25.6:1:30:1:0.53481:1.1424:60:204:0.09:0:1.1 -4 143067196 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12331;SOR=0;LSEQ=TATTTTTGTCACAAAAACAA;RSEQ=ATAAGGCAAAGTCGGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:36,182:0.0136:2,2:17.3:1:28.3:1:0.07725:9.95:60:6:0.0137:0:1 0/0:222:0:0,0:46,175:0:2,0:22.7:1:31:1:1:0:60:109.5:0.9955:0:0.1 -4 143081836 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12672;SOR=0;LSEQ=ATGGTGGAAAAAGTACAGAC;RSEQ=CCAAGGAGAGAAAATGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:4:0,4:1,58:0.0635:1,0:14.3:1:30.5:1:1:0:60:8:0.0645:0:1 0/0:51:0:0,0:0,51:0:1,0:24.7:1:32.2:1:1:0:60:102:1:0:0.1 -4 143094991 . C A 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0506;SOR=0;LSEQ=ACAAAGATAAAAATAAGTTA;RSEQ=ACAAACAGCATAATGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:4:3,1:69,256:0.0122:2,2:8:1:27:1:0.03412:11.02:60:8:0.0122:0:1 0/0:363:0:0,0:96,267:0:2,0:23.9:1:31.2:1:1:0:60:120:1:0:0.1 -4 143095139 . C T 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.05699;SOR=0;LSEQ=TATGTAAGGTGACGAAAATG;RSEQ=TTTTTAAAACTAGGTAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:0.3529:0,0:19.5:1:30.7:1:1:0:60:12:0.375:0:1 0/0:10:0:0,0:0,10:0:0,0:26.4:1:33.2:1:1:0:60:20:1:0:0.3 -4 143095201 . C T 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=AGATTAACACTAATACTTGA;RSEQ=GTGATTACATATATGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:42.8:1:31.8:1:1:0:60:10:0.625:0:1 1/1:3:3:0,3:0,0:1:0,0:36.7:1:29.3:1:1:0:60:6:1:0:1 -4 143095271 . T A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTAATCATGTATGTCAAG;RSEQ=ATTAGTATTCAAAACAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:25:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 143113782 . A G 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCCCTAAGAAACAGAAC;RSEQ=TAGAATTCTGTATTGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:16.8:1:28.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 143114003 . T C 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26087;SOR=0;LSEQ=AATATCACCCCTTAGTCATA;RSEQ=GACTTCCAGAAGATTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:1:0,1:26.9:1:32.5:1:1:0:60:34:1:0:2.6 1/1:6:5:4,1:1,0:0.8333:0,2:13.6:1:32.8:1:1:0:60:10:0.8333:0:3 -4 143114011 . A G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTAGTCATATGACTTCC;RSEQ=GAAGATTTTCTGCCATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:1:0,1:28.8:1:30.8:1:1:0:60:34:1:0:2.8 1/1:6:6:5,1:0,0:1:0,2:16.8:1:31.2:1:1:0:60:12:1:0:2.8 -4 143114040 . A C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCCATCACAATGCCACT;RSEQ=ACTAAGCAAGACACTTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:34:34,0:0,0:1:0,1:22.2:1:32.1:1:1:0:60:68:1:0:1.8 1/1:10:10:9,1:0,0:1:0,2:24.1:1:31.9:1:1:0:60:20:1:0:2 -4 143114402 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23561;SOR=Inf;LSEQ=TGCAAACATTTATCTCCGTC;RSEQ=TGCTGTTTGCATTGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:22,163:0:2,0:24.6:1:31.2:1:1:0:60:370:1:0:0 0/1:175:2:1,1:27,146:0.0114:2,2:13:1:29:1:0.29517:5.33:60:4:0.0117:0:1 -4 143114548 . A G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1778;SOR=5.2797;LSEQ=AGCCACCTGTGCACCTAAAC;RSEQ=AGATATAATGTTTTCCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:0.4667:0,0:28.9:1:31.6:1:1:0:60:14:0.4667:0:3.1 1/1:6:5:0,5:0,1:0.8333:0,0:24.4:1:32.6:1:1:0:60:10:0.8333:0:2.8 -4 143114556 . A G 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3125;SOR=0;LSEQ=GTGCACCTAAACAAGATATA;RSEQ=TGTTTTCCTGATTTATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:23.5:1:33.1:1:1:0:60:22:1:0:2.8 1/1:5:4:0,4:0,1:0.8:0,0:21:1:32.5:1:1:0:60:8:0.8:0:3.3 -4 143114558 . G A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3125;SOR=0;LSEQ=GCACCTAAACAAGATATAAT;RSEQ=TTTTCCTGATTTATGACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:22.2:1:30.5:1:1:0:60:10:1:0:2.8 1/1:5:4:0,4:0,1:0.8:0,0:19:1:31.5:1:1:0:60:8:0.8:0:3.3 -4 143114598 . G C 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATCTTAATTACATGCTACA;RSEQ=TGTAGAACAGTGTGTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:24.3:1:32.8:1:1:0:60:8:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 143129292 . G A 42 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTCAAATGAGCTTAAAT;RSEQ=TTAACTATTAGCCACCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:31.3:1:26.7:1:1:0:60:6:0.375:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 143129490 . A G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00156;SOR=Inf;LSEQ=CAACTTTATATAATTGTTAA;RSEQ=CTTTTGAATTCTGCCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:92,3:0:1,0:23.4:1:29.9:1:1:0:60:22.75:1:0:0.1 0/1:80:8:7,1:69,3:0.1:1,2:25.5:1:32:1:0.34952:3.21323:60:16:0.1013:0:1.3 -4 143129539 . A T 31 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24856;SOR=0;LSEQ=TTTACAGAAGTACACACTGT;RSEQ=ACATAATTTGCTATTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:183,58:0.0123:2,2:15:1:20:1:0.15049:6.25061:60:2:0.0083:0:1 0/0:238:0:0,0:170,68:0:2,0:23.4:1:28.1:1:1:0:60:78.333:1:0:0.1 -4 143129980 . A AT 175 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.27441;LSEQ=CTACATAAAATCTATTTATT;RSEQ=TTTTTTTTTTCATTTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:57:45,12:158,21:0.2385:2,2:18.2:1:30.1:1:0.0834:1.99972:59.8:27.5:0.2361:0.0962:0.9 0/1:228:18:16,2:177,31:0.0789:2,2:31.3:1:30.5:1:1:1.40:60:36:0.0811:0:0.8 -4 143130034 . A T 263 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACTTTGAGTAAGTAGAG;RSEQ=AATTGCTTCCACACCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:583:583:380,203:0,0:1:0,2:26.9:1:29.1:1:1:0:60:82.286:1:0:1.1 1/1:618:617:372,245:1,0:0.9984:0,2:25.8:1:28.4:1:1:0:60:60.7:1:0:1.1 -4 143130219 . T A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.2068;LSEQ=AGAGAAACTTTATTTTTATC;RSEQ=TAAATCCATAAACGCATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:265:140:24,116:22,103:0.5283:2,2:23:1:30.5:1:1:1.03225:60:69:0.5287:0:1.1 1/0:253:198:41,157:9,46:0.7826:2,2:22.1:1:29.5:1:0.56806:1.33:60:48.5:0.7823:0:1.1 -4 143130233 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24816;SOR=0;LSEQ=TTTATCTTAAATCCATAAAC;RSEQ=CATAACCCTTAGTCAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:1,2:24,151:0.0168:2,2:9.3:1:28.3:1:0.36671:3.12:60:6:0.0172:0:2 0/0:172:0:0,0:16,155:0:2,0:24:1:31.6:1:1:0:60:27.5:0.994:0:0.8 -4 143158979 . A C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.03099;LSEQ=AAAATTTTTAAATGGTATAA;RSEQ=ATAATTAATATGAGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:98:77,21:98,22:0.4495:2,2:20.8:1:31.5:1:0.61003:1.21378:60:48:0.4486:0:1.1 0/1:204:5:3,2:152,46:0.0245:2,2:30.2:1:30.8:1:0.33834:2.19283:60:10:0.0249:0:1 -4 143159168 . G GA 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.41808;SOR=0.68976;LSEQ=TACTGGGTTCTTTAACACTG;RSEQ=AAAAAAAAAGAAAAAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:14:3,11:100,258:0.0376:2,2:28.6:1:30.8:1:0.7655:1.42:60:28:0.0386:0:0.4 0/1:419:11:3,8:134,273:0.0263:2,2:27.2:1:28.5:1:1:1.30815:60:22:0.0272:0:0.6 -4 143181484 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=8.04498;LSEQ=GTACATTTATCTTTCCTGTG;RSEQ=AATTGTACAATCTCCCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:32:32,0:32,0:0.5:1,1:26.7:1:30:1:1:0:60:31:0.5:0:1.1 1/1:46:41:41,0:5,0:0.8913:0,1:23.1:1:29.4:1:1:0:60:82:0.8913:0:1 -4 143181502 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17477;SOR=Inf;LSEQ=TGGAATTGTACAATCTCCCC;RSEQ=CATTCTGCTGGCCCCTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:87,0:0:1,0:25.3:1:28.5:1:1:0:60:16.4:1:0:0.4 0/1:63:2:2,0:61,0:0.0317:1,0:33:1:32:0:1:0:60:4:0.0323:0:1 -4 143181748 . T A 229 LongAT STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.96453;LSEQ=ATGTAAAAAAAAAAAAAAAA;RSEQ=TTTGAGAACAATCAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:129:28,101:40,113:0.3718:2,2:21.8:1:29.2:1:0.40506:1.27576:59:17.429:0.3765:0:1.5 1/0:397:253:69,184:20,25:0.6373:2,2:24.2:1:28.7:1:0.03266:2.12739:59.5:27.111:0.7011:0:1.8 -4 143191978 . CA C 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.0999;SOR=0;LSEQ=TAAGAAGCTTCTCTCTCCCC;RSEQ=AAAATATCCAAAACACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:1,2:32,196:0.0129:2,2:13:1:28:1:0.37163:3.04:60:6:0.0133:0.0043:1 0/0:268:0:0,0:49,219:0:2,0:24.1:1:29.6:1:1:0:60:37.286:1:0:0.1 -4 143192000 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23477;SOR=0;LSEQ=AAAATATCCAAAACACATTT;RSEQ=TTTCTGAAAACCACCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:13,150:0.0121:2,2:11.5:1:29:1:0.16297:11.16:60:4:0.0125:0:1 0/0:175:0:0,0:22,153:0:2,0:22.2:1:31.3:1:1:0:60:86.5:1:0:0.1 -4 143192178 . G A 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTGTAATGGC;RSEQ=TGATCTCAGCTCACCACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:22.3:1:32.3:1:1:0:55.3:6:1:0:2 1/1:2:2:0,2:0,0:1:0,0:16:1:31:0:1:0:60:4:1:0:1.5 -4 143192242 . GAG AA 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTCTGCCTCAGCCTCCC;RSEQ=TAGCTGGGATTACAGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:22:1:32.8:1:1:0:40.5:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 143192299 . G GT 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTACTTTTGTATTCTCCAT;RSEQ=TGGTCAGGCTGGTGTCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:35.3:1:31:0:1:0:51.7:6:1:0:0.7 1/1:2:2:1,1:0,0:1:0,2:22:0:30:1:1:0:60:4:1:0:1.5 -4 143226496 . A C 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01929;SOR=Inf;LSEQ=TGCAGTGGAGAACATTAGCT;RSEQ=TTTGAGAACTGACATCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:100,1:0:1,0:25:1:28.3:1:1:0:60:100:1:0:0.1 0/1:86:5:4,1:78,3:0.0581:1,2:25.2:1:32.8:1:0.21653:6.21665:60:10:0.0595:0:1.2 -4 143226512 . C T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00171;SOR=Inf;LSEQ=AGCTATTTGAGAACTGACAT;RSEQ=TAACATCTGCAAGAATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:126,6:0:1,0:24.6:1:31.4:1:1:0:60:65:1:0:0.1 0/1:112:8:8,0:95,9:0.0714:2,0:23.5:1:30.1:1:1:0:60:16:0.0721:0:1 -4 143226521 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49957;SOR=0;LSEQ=AGAACTGACATCTAACATCT;RSEQ=CAAGAATTGTGACTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:144,14:0.0125:2,2:29.5:1:30:1:0.17925:9.97142:60:4:0.0126:0:1 0/0:145:0:0,0:123,22:0:2,0:22.5:1:31.7:1:1:0:60:47.333:1:0:0.2 -4 143226768 . G T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.24018;LSEQ=TCACATCAATCAAACAAAAT;RSEQ=AGTCTTTAGAAGAATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:343:184:89,95:94,65:0.5364:2,2:23.9:1:29.1:1:0.0512:1.54164:60:91:0.5369:0:1.9 1/1:290:241:135,106:25,24:0.831:2,2:21.7:1:29.1:1:0.53269:1.22:60:59.25:0.8287:0:1.9 -4 143226784 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.86002;LSEQ=AAATGAGTCTTTAGAAGAAT;RSEQ=AAATATTAAATCTATTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:388:208:116,92:105,75:0.5361:2,2:24.2:1:29.1:1:0.68099:1.11004:60:68.333:0.5352:0:1.8 1/1:350:286:175,111:35,29:0.8171:2,2:21.9:1:28.9:1:0.39724:1.31:60:285:0.8213:0:1.8 -4 143235721 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12438;SOR=Inf;LSEQ=TCCATGCAATTCAGCAAATA;RSEQ=GTGACAGTGCCTCCTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:75,3:0:1,0:23.3:1:31.4:1:1:0:60:156:1:0:0.1 0/1:43:2:2,0:39,2:0.0465:1,0:18:1:32.5:1:1:0:60:4:0.0465:0:1 -4 143235799 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05257;SOR=Inf;LSEQ=AGTTACCAAGCAGGAGGCCA;RSEQ=AGAAAATCCAAATGATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:204,73:0:2,0:22.5:1:31.7:1:1:0:60:91.333:1:0:0.1 0/1:256:4:1,3:172,80:0.0156:2,2:15.8:1:24.3:1:0.10145:6.39976:60:8:0.0159:0:1 -4 143235865 . C G 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GAAACGTTAGAAACACTTAC;RSEQ=CCAACTTCTGGCGGGGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:572:0:0,0:286,286:0:2,0:27.2:1:30.8:1:1:0:60:51:1:0:0.1 0/1:603:17:8,9:310,276:0.0282:2,2:25.9:1:30.5:1:0.80627:1.26309:60:16:0.0271:0:1.4 -4 143236008 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22249;SOR=Inf;LSEQ=TTCAATTTCCTTCATCTCGC;RSEQ=TCAATTCAGACTCTGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:10,88:0:2,0:23.5:1:31.9:1:1:0:60:196:1:0:0 0/1:88:2:0,2:7,79:0.0227:2,0:31.5:1:31.5:1:1:0:60:4:0.0233:0:1 -4 143236139 . T C 94 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12727;SOR=0.09014;LSEQ=CTGGAACCTCACTCCATCTA;RSEQ=TTATCTAATACAGATATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:0,1:0.8889:0,0:20.3:1:31.6:1:1:0:60:16:0.8889:0:1 0/1:3:1:0,1:0,2:0.3333:0,0:1:0:29:0:1:0:60:2:0.3333:0:1 -4 143323915 . T G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03286;SOR=0.23949;LSEQ=AACTTTTGCTCCTAACCAAT;RSEQ=GCCAATTTGGCAACGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:16,0:6,0:0.7273:0,1:25.4:1:33.3:1:1:0:60:32:0.7273:0:1.1 0/1:21:8:7,1:13,0:0.381:1,2:16.9:1:32.1:1:0.38095:0:60:16:0.381:0:1 -4 143324036 . T C 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49173;SOR=0.84614;LSEQ=CAGTTACACAAAAAATCCAA;RSEQ=CGTGTGGAAAAGCATAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:157:105:84,21:43,9:0.6688:2,2:22.3:1:31.8:1:0.82994:1.1931:60:210:0.6731:0:1.6 1/0:176:111:90,21:47,18:0.6307:2,2:22.6:1:30.8:1:0.19182:1.64:60:110:0.6322:0:1.6 -4 143324094 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.40858;LSEQ=GAAGTACCAGTACTTACGGT;RSEQ=TCATGAGACTTATCCTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:423:266:174,92:101,54:0.6288:2,2:25:1:29.4:1:1:1.01:60:265:0.628:0:1.3 0/1:521:213:136,77:174,133:0.4088:2,2:27.2:1:28.6:1:0.10311:1.35:60:212:0.4109:0:1.4 -4 143325968 . T C 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TACAACTTTCTTTTTTTTCC;RSEQ=CAAAATAAATATTTATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:18:0:27:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:28.5:1:1:0:60:4:1:0:1 -4 143326120 . G T 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=0.26566;LSEQ=AAAAAAAGACAAGTTATTTT;RSEQ=TCATTTGTTCGTTCTAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:22.7:1:31:1:1:0:60:6:0.75:0:1 0/1:5:2:2,0:3,0:0.4:0,0:25:1:27.5:1:1:0:60:4:0.4:0:1 -4 143326265 . C G 52 v4;q23;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08467;SOR=7.14093;LSEQ=ATTCAAATCCAGAGATGGGG;RSEQ=GGGGGTGGGGGGGAGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:110,0:0.0089:1,0:5:0:33:0:0.00901:0:60:2:0.0095:0:2 0/1:82:5:2,3:77,0:0.061:1,2:10:1:22.8:1:0.00011:0:57:4:0.0519:0:4.8 -4 143326271 . T TGGGG 114 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=11.000;MSILEN=1;SSF=0.1322;SOR=0.37918;LSEQ=ATCCAGAGATGGGGCGGGGG;RSEQ=GGGGGGGAGGGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:14:7,7:112,0:0.1085:1,2:12.1:1:30.1:1:0:0:59.3:28:0.1186:0.0698:1.4 0/1:91:4:4,0:74,0:0.044:1,0:26:1:31.3:1:1:0:60:8:0.0476:0:1.5 -4 143326299 . C T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.24833;SOR=Inf;LSEQ=AGGGAGAGAGAGAGCAAGAG;RSEQ=GAGCGAGCCAGCAAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:153,29:0:2,0:25.2:1:30.2:1:1:0:59.9:13:1:0:0.3 0/1:190:3:1,2:145,41:0.0158:2,2:9.3:1:23.7:1:0.13019:6.97731:51.7:6:0.0172:0:2.7 -4 143326307 . C A 14 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90544;LSEQ=AGAGAGCAAGAGCGAGCGAG;RSEQ=CAGCAAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:156,35:0.0104:2,2:16.5:1:29:1:0.33905:4.40887:60:4:0.011:0:1 0/0:213:2:1,1:157,54:0.0094:2,2:40:1:14:0:0.45066:2.89006:60:0:0:0:6 -4 143326312 . AAGAG A 198 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=10.000;MSILEN=2;SSF=0.03748;SOR=0.67288;LSEQ=GCAAGAGCGAGCGAGCCAGC;RSEQ=AGAGAGAGAGAGAGAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:94:73,21:77,16:0.4393:2,2:28.9:1:30.3:1:0.46344:1.382:59.9:46:0.4423:0.0327:0.3 0/1:258:89:60,29:115,39:0.345:2,2:23.4:1:30:1:0.23813:1.42304:59.7:43.5:0.3522:0.0659:0.5 -4 143326545 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23365;SOR=Inf;LSEQ=TCAGGGAAAACTTCTGCGCC;RSEQ=GGCTGAAAGTGAACTTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:4,97:0:1,0:25.7:1:31.2:1:1:0:60:202:1:0:0 0/1:95:2:1,1:7,86:0.0211:2,2:20:1:28.5:1:0.16215:11.56:60:4:0.0215:0:1 -4 143326714 . T G 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTGCAGTTCATGCAAGTCTT;RSEQ=ACTGGTCTGAGATCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:24.3:1:31.8:1:1:0:60:12:0.75:0:1.3 0/0:1:0:0,0:0,1:0:0,0:19:0:12:0:1:0:60:0:0:0:0 -4 143352065 . T C 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=CTCTTAATATATATTCAAGA;RSEQ=ATTTAATCTTGTTATTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:27.5:1:29.5:1:1:0:60:4:0.3333:0:1 1/0:2:1:1,0:1,0:0.5:0,0:19:0:32:0:1:0:60:2:0.5:0:1 -4 143352246 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.49885;SOR=0;LSEQ=CTATGAATCTATGAATGCAT;RSEQ=TATGTATGTGTAAGTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:181,11:0.0103:2,2:20.5:1:29:1:0.12019:15.79154:60:4:0.0105:0:1 0/0:187:0:0,0:170,17:0:2,0:22.6:1:31.9:1:1:0:60:186:1:0:0.1 -4 143352425 . C A 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.91668;SOR=0.97288;LSEQ=ATTTCCATGATCAACCTTCA;RSEQ=AGTTTTAAAATTTTCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:49:17,32:191,339:0.0843:2,2:20.4:1:29.6:1:1:1.06046:60:48:0.0844:0:1.1 0/1:608:50:20,30:206,352:0.0822:2,2:22.9:1:29.6:1:0.65064:1.14:60:100:0.0832:0:1.1 -4 143352479 . G A 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0485;SOR=Inf;LSEQ=TGTCAGTTCTAGTGATTCCT;RSEQ=GTTTAATGTAGATGTATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:12,191:0:2,0:25:1:30.9:1:1:0:60:49.75:1:0:0.1 0/1:181:4:3,1:21,156:0.0221:2,2:5.3:1:25.5:1:0.00759:21.57:60:8:0.0226:0:1.3 -4 143352599 . T A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53021;SOR=0.55628;LSEQ=TTCAGTATAAAGCTAAAAAG;RSEQ=AAAGGTAAGTAGAGACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:0,17:1,13:0.5484:1,1:18.4:1:31:1:0.45161:0:60:34:0.5667:0:1.1 0/1:15:6:0,6:0,9:0.4:0,0:21.2:1:30.8:1:1:0:60:12:0.4:0:1.2 -4 145225888 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24375;SOR=Inf;LSEQ=ATGTATTTTCCTTGTTTTAC;RSEQ=TACTGCCTTTTATGTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:110,31:0:2,0:23.1:1:30.3:1:1:0:60:140:1:0:0.1 0/1:138:2:2,0:97,39:0.0145:2,0:13:1:31.5:1:1:0:60:4:0.0146:0:1 -4 145225889 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=TGTATTTTCCTTGTTTTACG;RSEQ=ACTGCCTTTTATGTCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:110,32:0.0139:2,2:26.5:1:30.5:1:0.40705:3.40028:60:4:0.0139:0:1 0/0:138:0:0,0:99,39:0:2,0:21.2:1:29.1:1:1:0:60:276:1:0:0.1 -4 145225998 . G A 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45623;SOR=0.87318;LSEQ=CTTATAGTTACAATGAATGT;RSEQ=TCAATTATTAAAATATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:131:57,74:79,100:0.4226:2,2:25.8:1:29.4:1:1:1.02554:60:42.667:0.4211:0:1.1 0/1:295:115:57,58:87,93:0.3898:2,2:24.6:1:28.7:1:0.90503:1.05:60:56.5:0.3897:0:1.1 -4 147770165 . G T 29 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCTTGAATCTCTATCTT;RSEQ=GTGCCTAGCCTGGTCCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:20,2:0.0833:2,2:10.5:1:29:1:0.23913:8.36492:60:4:0.087:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 147770229 . T G 168 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCTGCCCTCAGTATGCC;RSEQ=GAGTCAGCAGTCTCACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:28,26:0,0:1:0,2:26.5:1:29.2:1:1:0:60:17:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 148756033 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14329;SOR=0;LSEQ=CCCTCCCCATTTTCTCTCAC;RSEQ=GATGTTTCCCCTAATAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:0.1:2,2:14.5:1:29:1:1:1.23603:60:4:0.1:0:1 0/0:32:0:0,0:15,17:0:2,0:23.4:1:30.6:1:1:0:60:64:1:0:0.2 -4 149116035 . A G 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54337;SOR=1.72765;LSEQ=TGATTAAAATAATAAAAAAT;RSEQ=ACTGTTAAAATAGAGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:3,5:5,6:0.4211:2,2:37.5:1:31.9:1:1:1.36508:60:16:0.4211:0:1.1 1/0:25:14:6,8:3,8:0.56:2,2:24.4:1:30.2:1:0.67662:1.95:60:28:0.56:0:1 -4 151172408 . C A 30 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCACACATCCCCCACAC;RSEQ=CCACACATCCCCCACACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:0:30:0:1:0:35.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 151172417 . CCCC TCCCT 30 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=ATCCCCCACACCCCACACAT;RSEQ=CACACCCCCCACACCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:0:30.7:1:1:0:35.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 151172429 . C A 29 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACACATCCCCCACACCCC;RSEQ=CACACCACACATTCCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:0:29:1:1:0:35.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 151172455 . C A 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACATTCCCTCACACCCC;RSEQ=CACACCACACACCCCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:28.5:1:1:0:35.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 151172535 . CCCCACACA C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACCCTCCACACCACACAT;RSEQ=CCTCACACCCCCCACACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:30.5:1:1:0:60:4:1:0:4.5 -4 151172570 . A C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCCACACCCCCACACA;RSEQ=CCCACATCCCCCGCACCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:30:1:1:0:60:4:1:0:4.5 -4 151174195 . TG T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49505;SOR=0;LSEQ=TGGTCTGGGGCATGGTTGTG;RSEQ=GGGGAACTTGCGATGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:32,17:0.0392:2,2:12.5:1:30:1:1:1.85775:60:4:0.04:0:0.5 0/0:50:0:0,0:37,13:0:2,0:23.7:1:31.5:1:1:0:60:100:1:0:0.1 -4 151174249 . GTCCTCCTCA G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=3.000;MSILEN=1;SSF=7e-04;SOR=0.38614;LSEQ=TCGTCCTCCTCATCCTCCTC;RSEQ=TCCTCCTCATCCTCCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:100:58:26,32:23,18:0.58:2,2:31.6:1:31.2:1:0.31106:1.56537:60:116:0.58:0.01:0.1 0/1:124:43:21,22:44,37:0.3468:2,2:33.2:1:29.7:1:0.57675:1.2436:60:20.5:0.3417:0.0081:0.3 -4 151174258 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20239;SOR=0;LSEQ=TCATCCTCCTCGTCCTCCTC;RSEQ=TCCTCCTCATCCTCCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:0,2:21,17:0.0206:2,0:13.5:1:28.5:1:0.21923:0:60:4:0.0513:0:1.5 0/0:118:0:0,0:38,38:0:2,0:7:0:12:0:1:0:60:0:0:0:1 -4 151174287 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51464;SOR=Inf;LSEQ=ATCCTCCTCATCCTCCTCAC;RSEQ=TCACTGTGTGTCCTGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:29,43:0:2,0:30.3:1:30.5:1:1:0:60:35:1:0:0.1 0/1:105:2:1,1:45,58:0.019:2,2:40.5:1:29.5:1:1:1.29:60:4:0.0194:0:1 -4 152880761 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.21739;SOR=Inf;LSEQ=ATATCAGCAGGACATGTCTC;RSEQ=CTCTATCAGGACTAATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:3,9:0:2,0:22.2:1:29.4:1:1:0:60:11:1:0:0.4 0/1:11:2:1,1:4,5:0.1818:2,2:22.5:1:29:1:1:1.22:60:4:0.1818:0:1 -4 153243979 . A G 52 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3769;SOR=0.27859;LSEQ=TTTTTTCTTTTTGCAGGGGG;RSEQ=AGGGCAGGGAGTATATCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:4:4,0:237,41:0.0142:2,0:31.8:1:26:1:1:0:60:3:0.0108:0:1.5 0/0:251:1:0,1:193,56:0.004:2,0:3:0:28:0:0.228:0:60:2:0.0041:0:1 -4 153244352 . A G 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01454;SOR=Inf;LSEQ=GGTTAGAAATAATGGCTATG;RSEQ=GTTAGTTACATTATAATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:17,148:0:2,0:24.1:1:30.9:1:1:0:60:54:1:0:0.1 0/1:126:5:2,3:20,101:0.0397:2,2:16.4:1:31:1:0.20924:3.32:60:10:0.0397:0:1 -4 153245264 . CTA C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22032;SOR=Inf;LSEQ=GGTTGACTCTTTTTGTGATG;RSEQ=AGGCTCCATATTTCTCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:192,29:0:2,0:23.1:1:30.8:1:1:0:60:220:1:0:0.1 0/1:196:2:1,1:159,35:0.0102:2,2:21:1:34:0:0.33438:4.4934:60:4:0.0104:0:0 -4 153245521 . C G 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00093;SOR=0;LSEQ=GGATTGATGTATCAAGAGAT;RSEQ=CACTCACCACATGGATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:11:4,7:190,351:0.0198:2,2:30.8:1:31.7:1:1:1.06:60:22:0.0203:0:1.1 0/0:550:0:0,0:214,334:0:2,0:24.8:1:30.9:1:1:0:60:77.286:0.9963:0:0.1 -4 153247036 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15417;SOR=Inf;LSEQ=TTTAACGTATATAAAAACAG;RSEQ=AGAATAATCTGATTAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:58,0:0:1,0:28.6:1:32.2:1:1:0:60:57:1:0:0.1 0/1:38:2:2,0:35,1:0.0526:1,0:30.5:1:31:1:1:0:60:4:0.0541:0:1 -4 153247374 . G A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13139;SOR=5.18338;LSEQ=AGAGTGGCATCTCGAGAACC;RSEQ=CTAACAACTCTGCAGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:1:0,1:115,301:0.0024:2,0:39:0:31:0:1:0:60:2:0.0024:0:1 0/1:488:6:4,2:161,320:0.0123:2,2:18:1:25.2:1:0.18649:3.96:54:12:0.0127:0:2 -4 153248143 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACATTTGGTTCAACAT;RSEQ=AGCGCTATACTCTTCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 153249146 . T C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTTTCAAACAGGAAGC;RSEQ=GACAACACTAGCAAATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:18,0:0,0:1:0,1:30:1:31.6:1:1:0:60:36:1:0:1.2 1/1:5:5:5,0:0,0:1:0,0:22.6:1:31.8:1:1:0:60:10:1:0:1 -4 153250963 . AAT A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05299;SOR=Inf;LSEQ=AGAAAGATGTGCAGATTAGA;RSEQ=ATGTTAATTAAATTATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:43,208:0:2,0:21.9:1:30.7:1:1:0:60:61.75:1:0:0.1 0/1:233:4:1,3:53,176:0.0172:2,2:25.3:1:30:1:1:1.11:60:8:0.0172:0:0 -4 153251013 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50249;SOR=0;LSEQ=TACTGGTGAAGAGAAAAATG;RSEQ=AGGCATAAACAGGAACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:0,2:2,92:0.0208:1,0:32.5:1:32.5:1:1:0:60:4:0.0211:0:1 0/0:78:0:0,0:4,74:0:2,0:23.4:1:30.6:1:1:0:60:156:1:0:0.1 -4 153251788 . G C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09405;SOR=Inf;LSEQ=ACGGTTTTCTTTCTACAGAA;RSEQ=AGGAGTGTCATATTATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:210,13:0:2,0:24:1:32:1:1:0:60:36.167:1:0:0.1 0/1:187:3:3,0:161,23:0.016:2,0:12:1:32.3:1:1:0:60:6:0.0162:0:1 -4 153252061 . A G 220 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=231.56408;LSEQ=AGTAAATTGCCTTCACCAAT;RSEQ=ATAACAGTTATACATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:1:0,1:96,275:0.0027:2,0:31:0:33:0:1:0:60:2:0.0027:0:1 0/1:345:133:32,101:61,149:0.3855:2,2:23.9:1:31.2:1:0.32203:1.2912:60:132:0.3894:0:1.1 -4 153253991 . TA T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.03581;SOR=0;LSEQ=TAATTCTGCACTCTGATTTC;RSEQ=AAATTATGAAAGGCAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:7:0,7:0,29:0.1892:1,0:28.6:1:31.7:1:1:0:60:14:0.1892:0:0 0/0:24:0:0,0:0,24:0:1,0:21.9:1:31.1:1:1:0:60:48:1:0:0.1 -4 153258892 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24899;SOR=0;LSEQ=GCATGACAATGTTTAAAGGT;RSEQ=GTAGCTGTTGAGTTATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:2,1:231,46:0.0107:2,2:18.3:1:28.3:1:0.42503:2.50012:60:6:0.0108:0:1 0/0:268:0:0,0:210,58:0:2,0:22.7:1:31.3:1:1:0:60:133:1:0:0.1 -4 153259143 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61494;SOR=2.10882;LSEQ=ACAGATGTCCCAAATTACAG;RSEQ=CTTATAAAGGAAAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:27,159:0.0053:2,0:27:0:14:0:1:0:60:0:0:0:1 0/1:179:2:1,1:33,143:0.0112:2,2:18.5:1:27:1:0.34641:4.28:60:4:0.0113:0:1 -4 153267968 . A G 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGCAGAATGATTTCAAA;RSEQ=TTCATCCACAGTATACTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:80:80:80,0:0,0:1:0,1:22.1:1:32.1:1:1:0:60:39:1:0:1.1 1/1:59:59:57,2:0,0:1:0,1:20.9:1:32.4:1:1:0:60:118:1:0:1.1 -4 153270964 . A G 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27778;SOR=0;LSEQ=TTTAAATTTTTGTTCACAAG;RSEQ=TAATTTCTGCTTGTGTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:0.3571:0,0:28.6:1:32:1:1:0:60:10:0.3571:0:1 0/0:4:0:0,0:4,0:0:0,0:27.8:1:30.8:1:1:0:60:8:1:0:0 -4 153271338 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=CTAACTATCAAATCTTGAGT;RSEQ=AGCATGGTTAATATTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:28,145:0:2,0:22.9:1:31.9:1:1:0:60:346:1:0:0.1 0/1:141:2:1,1:22,117:0.0142:2,2:12:1:29.5:1:0.30061:5.22:60:4:0.0143:0:2 -4 153271348 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50957;SOR=0;LSEQ=AATCTTGAGTCAGCATGGTT;RSEQ=ATATTTTAAATTCTTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:15,123:0.0143:2,2:23.5:1:30:1:0.21624:7.97:60:4:0.0143:0:1 0/0:103:0:0,0:9,94:0:2,0:23.7:1:29.9:1:1:0:60:206:1:0:0.1 -4 153273893 . A G 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12461;SOR=Inf;LSEQ=GGACACACATACATACATGC;RSEQ=GCTTGACTGAGAAGAACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:62,210:0:2,0:24:1:30.8:1:1:0:60:53.4:1:0:0.1 0/1:292:4:2,2:84,204:0.0137:2,2:11.8:1:30.5:1:0.58386:2.42:60:8:0.0139:0:1.3 -4 153303292 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49927;SOR=Inf;LSEQ=TTTCACTAAAAGAGGCCAAG;RSEQ=TACTTCACTTAAATAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:144,39:0:2,0:23.7:1:31.2:1:1:0:60:90.5:1:0:0.1 0/1:196:2:1,1:154,40:0.0102:2,2:13:1:28.5:1:0.37546:3.81509:60:4:0.0103:0:1 -4 153332301 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17068;SOR=Inf;LSEQ=ATTTCTACTTGTAATACTTT;RSEQ=CATTACCTTCTGTAAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:0:1,0:24.2:1:31.7:1:1:0:60:98:1:0:0.1 0/1:35:2:2,0:31,2:0.0571:2,0:23:1:32.5:1:1:0:60:4:0.0571:0:1 -4 153332604 . TCTC T 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.49148;SOR=0.80022;LSEQ=ATCGTCACTCTCCTGGTCCA;RSEQ=CTCCTCCTCCTCATCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1166:29:16,13:583,551:0.0249:2,2:29.8:1:31:1:0.7113:1.16:60:28:0.0246:0.0043:0.6 0/1:1250:25:14,11:643,578:0.02:2,2:25.6:1:31.6:1:0.84071:1.14:60:50:0.0204:0.0016:0.1 -4 153332986 . C A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10522;SOR=Inf;LSEQ=CAGCTTGCTACTTCTTGGAC;RSEQ=TTGGCTAGACTATCAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:57,188:0:2,0:24.8:1:31.3:1:1:0:60:39.833:1:0:0.1 0/1:221:3:2,1:53,165:0.0136:2,2:16:1:21.7:1:0.15369:6.16:60:2:0.0092:0:3 -4 153333100 . T A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTCATGTTATATGTCTAC;RSEQ=TTCTAAATATCATTAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:0:1,0:28.1:1:30.2:1:1:0:60:29:1:0:0.1 1/0:11:8:0,8:0,3:0.7273:0,0:17.5:1:28.6:1:1:0:60:7:0.7:0:1.1 -4 155454109 . G A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACAATTTTAAATCAAGC;RSEQ=GAAAGCACACCCATTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:22.8:1:29.8:1:1:0:60:16:1:0:1 1/1:5:5:5,0:0,0:1:0,0:16.4:1:30.6:1:1:0:60:10:1:0:1 -4 155454265 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20745;SOR=0;LSEQ=TCAAGGAAAGAAAGACAGAA;RSEQ=TTCTCCATGAGAATTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:49,39:0.0222:2,2:9.5:1:32:1:1:1.25319:60:4:0.0222:0:1.5 0/0:107:0:0,0:65,42:0:2,0:23.1:1:30.3:1:1:0:60:106:1:0:0.4 -4 155454287 . T C 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.15998;LSEQ=TCTCCATGAGAATTCTGATT;RSEQ=TCAGCTTTGTAAATTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:72:40,32:11,11:0.766:2,2:27:1:31.2:1:0.80733:1.25:60:71:0.7634:0:1 0/1:123:42:22,20:43,38:0.3415:2,2:21.3:1:31:1:1:1.02848:60:84:0.3443:0:1.1 -4 155454335 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51409;SOR=Inf;LSEQ=TTTCAGGAGAAACTTCCTCT;RSEQ=ACCAAGTTAAGAAAGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:27,49:0:2,0:25.2:1:31.5:1:1:0:60:152:1:0:0.6 0/1:110:2:1,1:45,63:0.0182:2,2:18.5:1:28:1:1:1.40:60:4:0.0185:0:1 -4 155454489 . T C 34 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACGATTGTGCCACTGCA;RSEQ=TCCAGCCTGGGCAACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31:1:34:0:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:32:0:34:0:1:0:60:2:1:0:1 -4 155828547 . GCTGGGCCTGGGGGACCACTACCATCA G 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26573;SOR=6.78852;LSEQ=AAAGAAATAAAGAGAAGGCA;RSEQ=AGATGCAGAGACCAGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:3,1:0.2:2,0:35:0:33:0:1:0:54:2:0.2:0:1 1/0:9:6:5,1:3,0:0.6667:0,2:29.8:1:32:1:1:0:58.7:12:0.6667:0.1111:1.3 -4 155828610 . T C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27337;SOR=2.65905;LSEQ=AGTGGCCCCGAAAGGCTGGG;RSEQ=GCACTGATATTTATTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:7,1:4,4:0.5:2,2:25.4:1:31:1:0.28205:6.16:59.3:16:0.5:0:1.3 1/0:15:11:9,2:2,2:0.7333:2,2:22.8:1:32.2:1:0.51648:3.99:59.3:22:0.7333:0:2 -4 155828657 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00533;SOR=4.80835;LSEQ=AAGGGGGGCAGGGTAAGGAG;RSEQ=GTGAATCTTCTAAGTGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:4,3:13,9:0.2414:2,2:18.7:1:29.3:1:1:1.08034:60:14:0.2414:0:2.1 1/0:36:22:13,9:7,7:0.6111:2,2:25:1:28.5:1:0.73428:1.43:60:44:0.6111:0:2.4 -4 155828662 . A G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00685;SOR=4.3381;LSEQ=GGGCAGGGTAAGGAGGGTGA;RSEQ=TCTTCTAAGTGATCGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:4,3:13,9:0.2414:2,2:22.3:1:32.9:1:1:1.08034:60:14:0.2414:0:2.1 1/0:41:24:14,10:8,9:0.5854:2,2:25.9:1:31:1:0.53703:1.56:60:48:0.5854:0:2.3 -4 155828714 . G GC 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.04647;SOR=2.94717;LSEQ=CACGTGATCATAGGACAGTG;RSEQ=CCCCTTCCCTTTCAGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:10:5,5:9,11:0.3333:2,2:24.1:1:30:1:1:1.21:60:9:0.3103:0.0667:1.3 1/0:35:21:7,14:6,8:0.6:2,2:24.9:1:31.7:1:0.72406:1.48241:60:42:0.6:0.1714:1.4 -4 156646905 . G T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25341;SOR=0;LSEQ=ATCTCATGTATTTCAGCAGA;RSEQ=GACCACAACATGTTGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:1,2:172,84:0.0116:2,2:17.3:1:23.7:1:0.25667:4.07103:60:2:0.0078:0:1 0/0:220:0:0,0:138,82:0:2,0:23.2:1:30.7:1:1:0:60:43:1:0:0.5 -4 156646960 . G A 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16445;SOR=0.80215;LSEQ=GGACAATGCTCATGACTTAA;RSEQ=TCTTAGATTCACTGTATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:362:212:107,105:74,76:0.5856:2,2:27.3:1:30.2:1:0.91505:1.05:60:52:0.5843:0:1.1 1/0:320:170:85,85:81,69:0.5313:2,2:27.4:1:29.1:1:0.50232:1.17332:60:55.667:0.5318:0:1.2 -4 156647018 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21128;SOR=Inf;LSEQ=CACATATAGGTTTTTATAGC;RSEQ=TAGATGGTGTTATCTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:66,165:0:2,0:23.7:1:30.3:1:1:0:60:45.2:1:0:0.5 0/1:197:2:1,1:71,124:0.0102:2,2:20.5:1:32.5:1:1:1.74:60:4:0.0102:0:2 -4 156647025 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22941;SOR=Inf;LSEQ=AGGTTTTTATAGCATAGATG;RSEQ=TGTTATCTTTTAAATAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:51,141:0:2,0:25.1:1:31.6:1:1:0:60:95:1:0:0.4 0/1:177:2:1,1:61,114:0.0113:2,2:28:1:31:1:1:1.86:60:4:0.0116:0:1.5 -4 156647054 . C T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10123;SOR=Inf;LSEQ=TTTAAATAAATTTTTTATTA;RSEQ=TGTGGTAACACATGCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:23,94:0:2,0:23:1:31.8:1:1:0:60:116:1:0:0.1 0/1:104:3:1,2:26,75:0.0288:2,2:24.7:1:32:0:1:1.44:60:6:0.0291:0:1 -4 156647198 . G A 37 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AGTTACGTTTATATACACAT;RSEQ=CATGAATGACATTGAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:20.2:1:32.8:1:1:0:60:10:1:0:0 1/0:5:3:0,3:0,2:0.6:0,0:13:1:23.7:1:1:0:60:2:0.5:0:1 -4 157518984 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11335;SOR=Inf;LSEQ=TCCAAGAAGTCCATTTGGAT;RSEQ=CAACAAGTCACTAAAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:129,48:0:2,0:24.6:1:31.8:1:1:0:60:58:1:0:0.1 0/1:167:3:1,2:111,53:0.018:2,2:18:1:27.3:1:0.25258:4.14952:60:6:0.0185:0:1 -4 157519085 . T A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12414;SOR=Inf;LSEQ=CTTTATTTCATTGTATTCAC;RSEQ=GTTCATATTGAGATTGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:198,188:0:2,0:25.2:1:30.5:1:1:0:60:127.667:1:0:0.4 0/1:395:4:3,1:191,200:0.0101:2,2:11.8:1:29.3:1:0.36441:3.13:60:8:0.0102:0:1 -4 157519096 . A T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02295;SOR=0.68443;LSEQ=TGTATTCACTGTTCATATTG;RSEQ=GATTGCTTAAAGTCCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:119:58,61:130,138:0.3075:2,2:27.7:1:30.1:1:1:1.01:60:238:0.3115:0:1.1 0/1:382:89:39,50:140,152:0.233:2,2:24.3:1:29.4:1:0.5448:1.18032:60:88:0.2328:0:1.1 -4 157615331 . A G 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23365;LSEQ=CCTTTTACCTGTTTTTTCTC;RSEQ=CTTATTCCTTAAAGCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:14.3:1:29.8:1:1:0:60:8:0.4444:0:1 1/0:8:4:4,0:3,1:0.5:2,0:24.5:1:30.8:1:1:0:60:8:0.5:0:1.8 -4 157615435 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49806;SOR=0;LSEQ=AACAAGCCTCCAAATTTACA;RSEQ=TAATCCTGAGGAGCAGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:57,2:0.0328:1,2:7.5:1:30.5:1:0.09672:23.47392:60:4:0.0345:0:1 0/0:53:0:0,0:52,1:0:1,0:26.2:1:32.6:1:1:0:60:106:1:0:0 -4 157615446 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22327;SOR=Inf;LSEQ=AAATTTACAGTAATCCTGAG;RSEQ=AGCAGGATTCAAACCGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:68,4:0:2,0:24.3:1:31:1:1:0:60:23:1:0:0.2 0/1:65:2:1,1:57,5:0.0308:2,2:24:1:30.5:1:0.18006:10.49773:60:4:0.0317:0:1 -4 157615583 . T C 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26068;SOR=0.85284;LSEQ=TCAAGTTTGATAATTCACAG;RSEQ=CACTGGGAGGGGGAAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:400:211:100,111:91,97:0.5275:2,2:25.4:1:31.3:1:0.84168:1.04126:60:69.333:0.5253:0:1.1 0/1:406:198:99,99:104,104:0.4877:2,2:26.2:1:31:1:1:1:60:65:0.4912:0:1.2 -4 157615710 . G A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60599;SOR=0.68319;LSEQ=ACTGTCAGGAACTTGGTACC;RSEQ=TGAAGAGCAGAAATTTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:11:1,10:1,45:0.193:1,2:21.7:1:31.7:1:0.3515:4.34:60:22:0.193:0:1.1 0/1:50:7:0,7:2,41:0.14:1,0:27.9:1:30.6:1:1:0:60:14:0.14:0:1.1 -4 159958815 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTATGGTCCCAGCTACT;RSEQ=GGGAGGCTTAGGTGGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1 -4 159959946 . T G 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGTGGTGAGGGCATTTTG;RSEQ=GCAAAGGGCATAGCTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:11:1:33:0:1:0:60:4:0.6667:0:1 -4 159960118 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=GGACCCCTGATGGTTTTATA;RSEQ=TCTTATTTATTTATTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,9:0:2,0:17.1:1:31.9:1:1:0:60:30:1:0:0.2 0/1:28:2:1,1:11,15:0.0714:2,2:9:1:33.5:1:1:1.35:60:4:0.0714:0:1 -4 161588046 . A C 51 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04779;SOR=0;LSEQ=AAGTGTTGTTTTTACACTAA;RSEQ=CAGTCAGGGATAGTACGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:9,1:0.2308:2,0:7:1:32.7:1:1:0:36.7:6:0.2308:0:6.3 0/0:21:0:0,0:16,5:0:2,0:21.2:1:30.1:1:1:0:60:42:1:0:0.1 -4 161588051 . C G 53 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.27712;SOR=0.18365;LSEQ=TTGTTTTTACACTAAACAGT;RSEQ=AGGGATAGTACGAGATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:10,1:0.2143:2,0:12:1:33.7:1:1:0:36.7:6:0.2143:0:6.3 0/1:22:1:1,0:15,5:0.0455:2,0:5:0:32:0:1:0:41:2:0.0476:0:7 -4 161588062 . C T 62 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05095;SOR=0.11721;LSEQ=CTAAACAGTCAGGGATAGTA;RSEQ=GAGATGCCACCCGGCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:3,1:11,1:0.25:2,2:18.5:1:31.3:1:0.45:3.31654:35:8:0.25:0:6.3 0/1:28:1:1,0:19,8:0.0357:2,0:16:0:32:0:1:0:41:2:0.0357:0:7 -4 161588099 . A G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13562;SOR=0.25891;LSEQ=TTTACAGGAAAAGGCTTCTG;RSEQ=AATCAGACAACACCTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:6:3,3:18,11:0.1714:2,2:37.3:1:31.3:1:0.66446:1.61275:36.7:12:0.1765:0:6 0/1:40:2:1,1:26,12:0.05:2,2:42.5:1:31.5:1:1:2.12136:40.5:4:0.0513:0:6 -4 161588110 . C A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13277;SOR=0.24173;LSEQ=AGGCTTCTGAAATCAGACAA;RSEQ=ACCTTTCAAACTCTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:6:3,3:20,15:0.1463:2,2:36.5:1:30.2:1:1:1.32389:36.7:12:0.1463:0:6 0/1:51:2:1,1:31,18:0.0392:2,2:42.5:1:29.5:1:1:1.70303:40.5:4:0.0392:0:6 -4 161588129 . C T 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1329;SOR=0.23611;LSEQ=ACACCTTTCAAACTCTTATA;RSEQ=CAACCTCTGGAGTTAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:6:3,3:18,19:0.1395:2,2:21.5:1:30.7:1:1:1.05:36.7:12:0.1395:0:6 0/1:55:2:1,1:31,22:0.0364:2,2:26:1:28:1:1:1.40015:40.5:4:0.0364:0:6 -4 161588141 . G T 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65116;SOR=0.50671;LSEQ=CTCTTATACCAACCTCTGGA;RSEQ=TTAGGCAACATGGCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:0,3:19,21:0.0698:2,0:22.7:1:31.7:1:0.24252:0:36.7:6:0.0714:0:5.7 0/1:55:2:1,1:29,24:0.0364:2,2:14:1:28.5:1:1:1.20416:40.5:4:0.037:0:6 -4 161588144 . A G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65003;SOR=0.49739;LSEQ=TTATACCAACCTCTGGAGTT;RSEQ=GGCAACATGGCTTCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:0,3:19,21:0.0698:2,0:19.7:1:32.3:1:0.24252:0:36.7:6:0.0698:0:5.7 0/1:56:2:1,1:29,25:0.0357:2,2:11:1:30.5:1:1:1.15692:40.5:4:0.0364:0:6 -4 161588177 . T A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04175;SOR=Inf;LSEQ=TCTCCCCTTTCTAGGTCCCG;RSEQ=GACAGCTGTCTTGCTATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:26.3:1:30.3:1:1:0:60:54:1:0:0.1 0/1:46:7:4,3:17,22:0.1522:2,2:24.3:1:27.3:1:0.68567:1.70:60:14:0.1522:0:1.1 -4 161588273 . T A 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGGCCATCAAGCTATAGA;RSEQ=GATCTTACAAATGGAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:29.4:1:31.8:1:1:0:60:10:1:0:0 0/1:13:2:0,2:2,9:0.1538:2,0:36:1:33:0:1:0:60:4:0.1538:0:1 -4 165696972 . C T 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31663;SOR=0.24395;LSEQ=AGGGATGTTGGAACTTTTTC;RSEQ=AGTAAAACCCTTTTCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:173,106:0.0106:2,2:9.7:1:22.7:1:0.56043:3.2501:60:2:0.0072:0:2 0/0:383:1:0,1:233,147:0.0026:2,0:1:0:26:0:0.38845:0:60:2:0.0026:0:1 -4 165697040 . G T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.29948;LSEQ=CCATGTGTGTGCAGCTGAAA;RSEQ=GAAAGTTTCATAAACTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:107:56,51:156,148:0.2603:2,2:25.1:1:30.3:1:0.91059:1.04:60:52.5:0.2586:0:1.1 1/0:478:257:126,131:101,119:0.5377:2,2:25.6:1:29.7:1:0.52047:1.13:60:514:0.5399:0:1.1 -4 165933619 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18947;SOR=Inf;LSEQ=TGGAGCAGGCTGGCGCTTTA;RSEQ=TTGAACCCAGGTACCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:11,0:0:0,0:24.3:1:33.3:1:1:0:51.7:22:1:0:0.1 0/1:9:2:1,1:7,0:0.2222:0,2:12.5:1:28:1:0.22222:0:60:4:0.25:0:1.5 -4 165933704 . A G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4953;SOR=Inf;LSEQ=AGGAAGCTATCTCGGCTCAC;RSEQ=GTGTTTAATGTGCTCAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:40,2:0:1,0:25.3:1:30.1:1:1:0:58.6:41:1:0:0 0/1:46:2:1,1:36,8:0.0435:2,2:5.5:1:26.5:1:0.35652:4.30117:40:4:0.0444:0:1.5 -4 165933756 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50097;SOR=Inf;LSEQ=CTCTTGGCAAGAATCTTGCC;RSEQ=TTAACTTGTTTGTTTACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:80,32:0:2,0:21.8:1:30.7:1:1:0:44.2:111:0.9911:0:0 0/1:132:2:1,1:83,47:0.0152:2,2:33.5:1:28.5:1:1:1.75787:42.5:4:0.0154:0:1 -4 165933761 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50311;SOR=Inf;LSEQ=GGCAAGAATCTTGCCCTTAA;RSEQ=TTGTTTGTTTACAACAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:91,37:0:2,0:21.7:1:31.8:1:1:0:45.4:256:1:0:0.1 0/1:156:2:1,1:98,55:0.0128:2,2:14:1:28.5:1:1:1.77473:51:4:0.0129:0:1.5 -4 165933848 . C A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.2705;SOR=Inf;LSEQ=CTAACACTTGTGGGGCATTC;RSEQ=TTTTGAACAGTACCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:67,101:0:2,0:22:1:31.8:1:1:0:56.8:83:1:0:0.1 0/1:238:3:2,1:103,131:0.0126:2,2:9.7:1:22.3:1:0.58559:2.53:49.3:2:0.0085:0:1 -4 165933861 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51238;SOR=Inf;LSEQ=GGCATTCCTTTTGAACAGTA;RSEQ=CCATTCCCTTGGTGTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:41,86:0:2,0:23:1:31.4:1:1:0:60:254:1:0:0.1 0/1:178:2:1,1:70,106:0.0112:2,2:40.5:1:28.5:1:1:1.51:60:4:0.0114:0:1 -4 165934032 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50457;SOR=0;LSEQ=GGAAGATGGTGGCTCTGGCC;RSEQ=AAAGGCATAAAATTCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:17,23:0.0476:2,2:26:1:31.5:1:1:1.34:60:4:0.0476:0:1 0/0:31:0:0,0:12,19:0:2,0:26.1:1:30.5:1:1:0:60:62:1:0:0.1 -4 165934108 . C G 79 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.134;SOR=0.12753;LSEQ=GTTGACGGGGTTGGAGGGTG;RSEQ=GAGAGATGAACAGGAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:0.6:0,2:24.8:1:30.7:1:1:0:60:12:0.6:0:1.2 0/1:7:1:0,1:1,5:0.1429:2,0:21:0:32:0:1:0:60:2:0.1429:0:1 -4 166144709 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49961;SOR=Inf;LSEQ=GTTCATCCTGGGGAGTCTGT;RSEQ=CAGAAAAGGTTAGGAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:133,36:0:2,0:22.6:1:32.2:1:1:0:59.6:168:1:0:0.1 0/1:185:2:1,1:143,40:0.0108:2,2:28.5:1:27:1:0.39506:3.54322:60:4:0.0109:0:1 -4 166144712 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24817;SOR=Inf;LSEQ=CATCCTGGGGAGTCTGTGCA;RSEQ=AAAAGGTTAGGAAGCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:146,44:0:2,0:21.7:1:32:1:1:0:59.7:94:1:0:0.1 0/1:195:3:2,1:146,46:0.0154:2,2:21:1:23:1:0.56495:1.58279:60:2:0.0103:0:1 -4 166144830 . A G 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CTTTTGAGAAACGGAGCATC;RSEQ=TGCTAAGATTAATGATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:26:8,18:160,205:0.0665:2,2:28.3:1:31.4:1:0.22295:1.75369:60:52:0.0668:0:1.4 0/0:500:0:0,0:216,284:0:2,0:25.9:1:29.6:1:1:0:59.2:99:1:0:0.3 -4 166144875 . G A 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08922;SOR=0.73523;LSEQ=TGTGAAAGGATGGCTTTTAG;RSEQ=TCAGCAGTGCATCTCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:107:28,79:40,80:0.4714:2,2:24.3:1:30.6:1:0.24959:1.40856:56.5:52.5:0.4667:0:1.2 0/1:288:114:37,77:54,120:0.3958:2,2:23.5:1:29.1:1:0.79714:1.07:56.7:37:0.3908:0:1.1 -4 166310601 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50398;SOR=0;LSEQ=TCTCAAGAATGTTTTTTTCA;RSEQ=GAAGTTTTCTTGGGCTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:153,42:0.0102:2,2:13.5:1:31.5:1:0.38978:3.61164:60:4:0.0102:0:2 0/0:160:0:0,0:121,39:0:2,0:22.4:1:31.5:1:1:0:60:320:1:0:0.2 -4 166310679 . T C 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00192;SOR=0.65456;LSEQ=CCTTTGCTTTCAACAGAATG;RSEQ=TAACCGGATACCTTCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:197:113,84:129,122:0.4378:2,2:26.4:1:32.1:1:0.21586:1.27:60:97.5:0.4382:0:1.7 0/1:480:162:80,82:162,156:0.3375:2,2:25.8:1:32.1:1:0.77261:1.06426:60:324:0.3396:0:1.8 -4 166310721 . C A 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00032;SOR=0.60821;LSEQ=AGGTTACAACTTCATGGCTT;RSEQ=AAGTATTGGTTGTGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:446:202:95,107:111,133:0.4529:2,2:25.9:1:29:1:0.77511:1.06:60:49.5:0.451:0:1.7 0/1:466:156:70,86:138,172:0.3348:2,2:25.9:1:28.6:1:1:1.01:60:51:0.3326:0:1.8 -4 166311028 . T A 60 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCTCATTTCTTAAGGAG;RSEQ=CTTTTTCAAACTTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:31.8:1:30.3:1:1:0:60:8:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 168210641 . C A 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01282;SOR=0;LSEQ=GGCTTTTGTGGGGACTTTTT;RSEQ=TTTTTGTTGTTGTTGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:5,2:2,2:0.6364:2,2:25.4:1:27:1:0.57576:2.29:60:14:0.6364:0:1 0/0:7:0:0,0:5,2:0:2,0:7.7:1:29.1:1:1:0:60:6:1:0:0 -4 169529802 . G A 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCCATCTCTGATATCCAG;RSEQ=GCTGTTTGTTGTTATTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:29.7:1:30.4:1:1:0:60:18:1:0:0.3 1/0:26:17:11,6:6,2:0.6538:2,2:29.9:1:27.7:1:1:1.60542:60:16:0.6667:0:1 -4 169531708 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGAGCAGAAGTTTCTGC;RSEQ=TCACCACGTGCTCTTTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5.5:1:30:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 171735386 . C T 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27982;SOR=0;LSEQ=AAACTCTTGGATTTTATAGC;RSEQ=TAGGCAATTTGAAGTCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:0.2632:1,0:21.4:1:31.6:1:1:0:60:10:0.2632:0:1 0/0:8:0:0,0:8,0:0:0,0:28.1:1:28.3:1:1:0:60:7:1:0:0 -4 171735486 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50537;SOR=Inf;LSEQ=AAGTCAACTATTGCACTTAC;RSEQ=AGCCTATCTTATTAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:54,46:0:2,0:27.4:1:29.7:1:1:0:60:200:1:0:0.1 0/1:128:2:1,1:74,51:0.0156:2,2:30:0:32.5:1:1:1.44661:60:4:0.0156:0:1 -4 171735532 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50494;SOR=Inf;LSEQ=CCAGATTCTACTCTAGCAAC;RSEQ=CCTGCAAAAGCCAGCAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:45,59:0:2,0:25.7:1:29.3:1:1:0:60:33.667:1:0:0.1 0/1:132:2:1,1:60,70:0.0152:2,2:28:1:28:1:1:1.17:60:4:0.0153:0:1 -4 173291406 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=0;LSEQ=GTAAGACCTTCTGTATGTAG;RSEQ=TTGATGGCCTCGATTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:8,4:0.1429:2,2:31:1:32:1:1:1.89743:60:4:0.1429:0:1 0/0:9:0:0,0:6,3:0:2,0:19.6:1:30.1:1:1:0:60:8:1:0:0.1 -4 173291591 . G A 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.44828;SOR=Inf;LSEQ=TTGAGACCATTCTGGCTAAC;RSEQ=TGGTGAAACCCCATCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:4,8:0,0:0.9231:0,2:14.4:1:29.6:1:1:0:60:24:1:0:1.1 1/1:16:16:3,13:0,0:1:0,2:23.4:1:29.6:1:1:0:60:32:1:0:1.1 -4 173291655 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGCTAATTTTGGTGGTGGGC;RSEQ=CCTGTAGTCCCAGCTACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:25:1:28.7:1:1:0:60:2:1:0:0.7 1/0:4:2:0,2:0,2:0.5:0,0:11:1:27.5:1:1:0:60:4:0.5:0:2 -4 173291816 . A G 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAGAGTTTGAAAGGC;RSEQ=TTGTCTGACTTCGGAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:20:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:5:0:26.5:1:1:0:60:4:1:0:2 -4 173291864 . A G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATGCTGGGTGGCATCTC;RSEQ=TACTATCCGTGACTGGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:34.3:1:33:1:1:0:60:6:1:0:1.3 1/1:2:2:1,1:0,0:1:0,2:46.5:1:29.5:1:1:0:60:4:1:0:2 -4 173704071 . G A 114 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01912;SOR=2.99121;LSEQ=AGTGACTTTTCGAAGAGCTT;RSEQ=TTATGCATGGTCTAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:7:5,2:97,21:0.056:2,2:25.7:1:29.6:1:0.61161:1.83693:60:14:0.0565:0:1 0/1:119:18:15,3:75,26:0.1513:2,2:22.2:1:27.4:1:0.55633:1.73:60:17:0.1453:0:1.4 -4 173704096 . C T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62382;SOR=2.85291;LSEQ=GCATGGTCTAGAAAAAATGT;RSEQ=ACATGTATTTCCCAGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:1,0:141,62:0.0049:2,0:3:0:16:0:1:0:60:0:0:0:1 0/1:216:3:1,2:136,77:0.0139:2,2:5.7:1:25.3:1:0.55567:3.51092:60:6:0.0141:0:1.3 -4 173704182 . G C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.29563;LSEQ=AGCTAAAGTGTGTCTTATTT;RSEQ=TAAAACACTATCTCATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:117:57,60:114,138:0.3162:2,2:24.5:1:31.1:1:0.5754:1.15:60:57.5:0.3151:0:1.1 1/0:379:229:115,114:72,78:0.6042:2,2:27.1:1:31.4:1:0.67603:1.09:60:228:0.6032:0:1.1 -4 173704270 . G A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0647;SOR=0.42798;LSEQ=TTCTGAATTGGACCTGCCAC;RSEQ=GCAGGTCCAATTCCTAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:20:5,15:22,84:0.1587:2,2:20.8:1:30.4:1:0.76675:1.27:60:19:0.152:0:1.2 0/1:94:7:1,6:11,76:0.0745:2,2:27.9:1:31.3:1:1:1.15:60:14:0.0761:0:1 -4 173704391 . T A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.91151;LSEQ=AAGGACCTAAATAAATAAAG;RSEQ=AGTATACTATGTTCATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:0.5:0,0:20:1:30.5:1:1:0:60:12:0.5:0:1.5 1/0:3:2:0,2:0,1:0.6667:0,0:46:1:32:0:1:0:60:4:0.6667:0:2 -4 173704408 . G A 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AAGTAGTATACTATGTTCAT;RSEQ=GATTTGGAAGCTTTACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:23:1:30:1:1:0:60:8:0.6667:0:1.8 1/1:2:2:0,2:0,0:1:0,0:38:1:33:0:1:0:60:4:1:0:2 -4 175047506 . C CAT 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57673;SOR=0.7661;LSEQ=CAAACATGAAAAAATAGACA;RSEQ=CTTTCCCTTTCAGTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:28:25,3:41,3:0.3889:2,2:22:1:30.4:1:0.67157:1.6283:60:56:0.3944:0.0556:0.2 0/1:55:18:16,2:36,1:0.3273:1,2:17.8:1:29.9:1:0.24688:4.36511:60:36:0.3273:0.1455:0.2 -4 175047525 . G T 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61389;SOR=2.1173;LSEQ=ACCTTTCCCTTTCAGTGCCT;RSEQ=TTAAGAATCCAATGATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:1,0:78,24:0.0097:2,0:37:0:13:0:1:0:60:0:0:0:4 0/1:98:2:1,1:72,24:0.0204:2,2:21.5:1:32:0:0.44709:2.9597:60:4:0.0204:0:1 -4 175047534 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62173;SOR=0.49277;LSEQ=TTTCAGTGCCTGTTAAGAAT;RSEQ=CAATGATCAAAAGTAATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:82,31:0.0174:2,2:7:1:29:0:0.48085:2.61933:60:4:0.0179:0:1 0/0:116:1:1,0:77,38:0.0086:2,0:25:0:30:0:1:0:60:2:0.0086:0:1 -4 175047618 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11129;LSEQ=CACCAGGGCCTGATAGAACC;RSEQ=TAAAAATGAGTTTTGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:97:48,49:72,88:0.3774:2,2:24.1:1:30.4:1:0.52027:1.20:60:96:0.381:0:1.1 0/1:270:17:9,8:119,134:0.063:2,2:26.4:1:30.4:1:0.80278:1.27:60:34:0.063:0:1.2 -4 175047639 . A G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00793;SOR=1.64483;LSEQ=TAAAAATGAGTTTTGCAGAG;RSEQ=CATGCCAAGAAATATTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:136:57,79:51,63:0.544:2,2:24.9:1:31.6:1:0.70123:1.12145:60:44.333:0.5407:0:1.6 1/0:249:165:70,95:38,45:0.6627:2,2:25.9:1:31.1:1:0.68423:1.1454:60:54:0.6612:0:1.6 -4 175047669 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21084;SOR=Inf;LSEQ=AAATATTTGAAATCACTGAA;RSEQ=AGAATGGAGCTTCACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:77,125:0:2,0:24.1:1:30.3:1:1:0:60:201:1:0:1.2 0/1:172:2:1,1:67,103:0.0116:2,2:27:1:27:1:1:1.53:60:4:0.0119:0:3 -4 175047679 . C T 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00075;SOR=2.25345;LSEQ=AATCACTGAAAAGAATGGAG;RSEQ=TTCACTGAGCTGCCGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:173:87:30,57:29,55:0.5029:2,2:26.6:1:30:1:1:1.00181:60:174:0.5058:0:1.8 1/0:138:96:31,65:13,29:0.6957:2,2:22.5:1:29.1:1:1:1.06:60:31:0.694:0:1.9 -4 175047700 . T C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27486;SOR=0;LSEQ=TTCACTGAGCTGCCGAGTCC;RSEQ=CCAAATAATGAAAAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:2,1:42,93:0.0216:2,2:34.3:1:31.3:1:0.23841:4.38:60:6:0.0224:0:1.7 0/0:94:0:0,0:24,70:0:2,0:23.7:1:29.1:1:1:0:60:46:1:0:1.1 -4 175304981 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4902;SOR=Inf;LSEQ=CCGATAATGATCAATAAATA;RSEQ=TAAGGGAACTCAGAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:27.8:1:32.7:1:1:0:57.3:52:1:0:0.9 0/1:26:2:1,1:13,11:0.0769:2,2:30.5:1:32.5:1:1:1.17422:53.5:4:0.0769:0:1 -4 175304986 . G A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.05765;LSEQ=AATGATCAATAAATAGTAAG;RSEQ=GAACTCAGAGGCCGGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:17:7,10:5,4:0.6538:2,2:27.8:1:30.9:1:0.68284:1.74571:56.6:16:0.64:0:1.2 1/0:27:18:10,8:4,5:0.6667:2,2:28.8:1:30.4:1:0.69458:1.54:58.2:36:0.6667:0:1.2 -4 176934309 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACTTACAAGTGACAACATG;RSEQ=GATACTTGGTCTTCTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:31.5:1:1:0:60:4:1:0:1.5 -4 176935505 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50525;SOR=Inf;LSEQ=ACTGATGGTCTTTGCAGCCA;RSEQ=CTCTTTCCCAGTGAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:43,7:0:2,0:24.4:1:31.5:1:1:0:60:100:1:0:0.1 0/1:66:2:1,1:55,9:0.0303:2,2:12.5:1:28:1:0.28205:5.85001:60:4:0.0303:0:1 -4 176935553 . TA T 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54037;SOR=Inf;LSEQ=CAATTTCACCTTGGTGAAGT;RSEQ=CCCCCACTGATGGAGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:71,32:0:2,0:23.7:1:28.6:1:1:0:60:206:1:0:0.1 0/1:187:2:1,1:122,63:0.0107:2,2:20:0:33:0:1:1.92924:60:4:0.0108:0:0.5 -4 176935570 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.142;SOR=0;LSEQ=AGTTACCCCCACTGATGGAG;RSEQ=CAGTCGACTAAGGAGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:85,55:0.0141:2,2:22:1:29:1:1:1.54053:60:4:0.0142:0:2 0/0:234:0:0,0:146,88:0:2,0:25.5:1:31.1:1:1:0:60:45.8:1:0:0.4 -4 176935634 . G A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.38318;LSEQ=TGAATAGAGATGGCTGAGAG;RSEQ=CACTGCAGCATGTTGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:75:38,37:91,88:0.2953:2,2:26.1:1:30.2:1:1:1.00685:60:150:0.3:0:1.1 1/0:348:174:91,83:84,90:0.5:2,2:23.6:1:29:1:0.5201:1.17:60:86:0.4971:0:1.2 -4 176935814 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4873;SOR=Inf;LSEQ=CAAAAATAAAAAGTACCAGA;RSEQ=ATTAACAATAACTAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:0:1,0:23.6:1:31.6:1:1:0:60:34:1:0:0.4 0/1:19:2:1,1:0,17:0.1053:1,2:10.5:1:29.5:1:0.10526:0:60:4:0.1053:0:1 -4 176936014 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AAAAGAGAAAAAAAGCCAAA;RSEQ=AGATAAAAAGTTAACTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:15:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:28.5:1:1:0:60:4:1:0:1 -4 181796994 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTCTCCCTGTGGAGTTTTAC;RSEQ=CCCTGCTTCTCTCCCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:29.5:1:32.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:39:0:32:0:1:0:60:2:1:0:0 -4 181797393 . A G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13228;SOR=0.36143;LSEQ=ACAGTCTAGTCCTGCCTCCC;RSEQ=TCCACCGTGATGATCCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:18:18,0:14,0:0.5625:1,1:25.6:1:30.6:1:1:0:60:36:0.5625:0:1.1 0/1:16:5:5,0:10,1:0.3125:2,0:27.2:1:30.4:1:1:0:60:10:0.3125:0:1 -4 181797474 . A G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.19847;SOR=0;LSEQ=GCAGAACAATGCCTAACCAC;RSEQ=ATGTAGGTACCATCTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:101,14:0.0171:2,2:6:1:27.5:1:0.24094:7.00406:60:4:0.0174:0:1 0/0:145:0:0,0:129,16:0:2,0:23.6:1:30.1:1:1:0:60:144:1:0:0.1 -4 181797596 . A G 294 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00908;LSEQ=TCATGATTTCCTTGTCAACA;RSEQ=TTTCAACTTGTCAACCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:582:580:299,281:1,1:0.9966:2,2:26.2:1:32.1:1:1:1.06:60:115:0.9965:0:1.4 1/0:780:565:278,287:107,108:0.7244:2,2:25.7:1:31.2:1:0.93615:1.02279:60:140.25:0.7286:0:1.4 -4 181797669 . C T 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=0;LSEQ=TTTTTAACTTCATTAGACGT;RSEQ=CATTTGGCGGATTCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:350:350:105,245:0,0:1:0,2:24.1:1:30:1:1:0:60:86.5:1:0:1.8 1/1:413:398:133,265:4,11:0.9637:2,2:24.9:1:29:1:0.78171:1.38:60:78.6:0.9656:0:2 -4 181797677 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.27152;LSEQ=TTCATTAGACGTCCATTTGG;RSEQ=GGATTCTTCTCTTAATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:142:40,102:41,122:0.4656:2,2:23.4:1:30:1:0.6038:1.17:60:141:0.4653:0:2.3 1/0:347:257:76,181:28,60:0.7406:2,2:25.2:1:29.9:1:0.68855:1.11106:60:256:0.7464:0:2.3 -4 181797707 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49859;SOR=Inf;LSEQ=TCTTAATATTTTCTTCCATT;RSEQ=AATCAGCTGTGTCCTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:23,154:0:2,0:23.8:1:28.7:1:1:0:60:354:1:0:1.3 0/1:178:2:1,1:26,150:0.0112:2,2:16:1:30:1:0.28109:5.68:60:4:0.0114:0:1 -4 181797720 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23791;SOR=Inf;LSEQ=TTCCATTTAATCAGCTGTGT;RSEQ=CTTTCCTTATATCCCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:11,125:0:2,0:24.5:1:31.4:1:1:0:60:67:1:0:1.2 0/1:130:2:1,1:8,120:0.0154:2,2:16:1:28.5:1:0.13417:14.21:60:4:0.0156:0:3 -4 181797780 . T C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21857;SOR=1.97929;LSEQ=TCCCAGGATTTCAAAGGAAA;RSEQ=TCCTAATTCCTAAACTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:12:0,12:0,24:0.3333:1,0:19.2:1:32.9:1:1:0:60:24:0.3333:0:2.1 1/0:32:16:0,16:1,15:0.5:1,1:19.4:1:32.8:1:1:0:60:32:0.5:0:1.6 -4 181797798 . G T 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34188;SOR=0.49419;LSEQ=AATTCCTAATTCCTAAACTT;RSEQ=CACACACACAAATACAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:0.3913:1,0:24.4:1:30.2:1:1:0:60:18:0.3913:0:2.6 0/1:21:5:0,5:0,16:0.2381:1,0:26.4:1:28.8:1:1:0:60:10:0.25:0:2.2 -4 181797842 . T C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63325;SOR=2.38223;LSEQ=TGTCCCCTTCAAGTCTCATA;RSEQ=TGAAATGTAATCCCCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:0.5:0,0:25.5:1:33:1:1:0:60:12:0.5:0:2.8 1/0:7:5:0,5:0,2:0.7143:0,0:21.2:1:31.2:1:1:0:60:10:0.7143:0:2.2 -4 182443806 . C T 41 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30138;SOR=Inf;LSEQ=TATGTTGTAGCCATAGTTTT;RSEQ=AGAACCAAAATGCAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:90,36:0:2,0:25.3:1:31:1:1:0:60:41:1:0:0.1 0/1:228:4:1,3:149,75:0.0175:2,2:11:1:20.8:1:0.11707:5.91135:60:3:0.0133:0:2.3 -4 182443933 . G C 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGTAAATGGAGAACAACTG;RSEQ=ATCTGGATCCTGGTCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:40:23,17:149,123:0.1282:2,2:30.6:1:32.4:1:0.86509:1.12:60:80:0.1286:0:1.1 0/0:501:0:0,0:278,222:0:2,0:24.4:1:30.6:1:1:0:60:61.5:0.998:0:0.1 -4 182444038 . A G 228 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTGCTGTTATTGTGGTTGTG;RSEQ=TGATAGCAGTTGTTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:210,201:0:2,0:25.1:1:30.1:1:1:0:60:67.5:1:0:0.1 0/1:794:180:97,83:317,295:0.2267:2,2:25.1:1:30.5:1:0.6714:1.09:59.2:44:0.2271:0:1.2 -4 182444093 . T A 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATTTCCAGAAAGAAGAGAA;RSEQ=GGCAAAGTATGAGAAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:37:13,24:125,198:0.1025:2,2:26.5:1:31.1:1:0.72423:1.16499:60:74:0.1048:0:1 0/0:710:0:0,0:305,405:0:2,0:24.5:1:29.6:1:1:0:59.9:100.429:1:0:0.4 -4 182444131 . A G 221 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAGATAAAGGAGATGGGT;RSEQ=GGATGCATAGGGAACTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:83,179:0:2,0:25.5:1:30.2:1:1:0:60:64.5:1:0:0.5 0/1:477:157:51,106:113,205:0.3291:2,2:26.2:1:30.3:1:0.53931:1.14535:60:38.25:0.3262:0:1.1 -4 182444132 . G T 202 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGAGATAAAGGAGATGGGTA;RSEQ=GATGCATAGGGAACTCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:95:32,63:51,112:0.3668:2,2:26.2:1:30.8:1:0.78241:1.11:60:94:0.3701:0:1.1 0/0:463:0:0,0:157,305:0:2,0:12:0:16:0:1:0:60:0:0:0:2 -4 182444208 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.5256;SOR=Inf;LSEQ=GAAATCGCAAACGGACTCAG;RSEQ=TTACAAATGTATGAGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:5,64:0:2,0:27.1:1:31.3:1:1:0:60:138:1:0:0.1 0/1:112:2:1,1:19,91:0.0179:2,2:16:1:30.5:1:0.32658:4.69:60:4:0.0179:0:1 -4 183806463 . G T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCTTTTCTGATCAAAGG;RSEQ=ATAGCCAAGAGCAGAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:9.5:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:0:0,0:20:0:33:0:1:0:60:2:1:0:0 -4 183806775 . GA G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49923;SOR=0;LSEQ=TCAGAGGCTGGGGAAAGGCA;RSEQ=ATAAATCAAAAGGCTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:94,17:0.0177:2,2:15.5:1:27.1:1:0.29441:5.40222:60:4:0.0185:0.0088:0.5 0/0:101:0:0,0:84,17:0:2,0:22.5:1:29.4:1:1:0:60:202:1:0:0.1 -4 183806854 . G T 56 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02106;SOR=0;LSEQ=GAATGCCCATTTAAAACCTG;RSEQ=ACCAAATGGCATGTTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:5:2,3:182,155:0.0146:2,2:21.8:1:24.4:1:0.6654:1.75837:60:4:0.0119:0:1.4 0/0:397:0:0,0:228,169:0:2,0:26:1:30.7:1:1:0:60:65.167:1:0:0.4 -4 183806867 . G A 49 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04597;SOR=0;LSEQ=AAACCTGGACCAAATGGCAT;RSEQ=TTTAAGTTTCTAACAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:4:4,0:183,178:0.0109:2,0:6.5:1:24.5:1:0.1234:0:60:8:0.0109:0:1 0/0:425:0:0,0:229,196:0:2,0:25.6:1:31.2:1:1:0:60:140.667:1:0:0.5 -4 183806904 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=6.31476;LSEQ=TTTTCATTAACAAAAGTTAA;RSEQ=ATACAGAACTCCTACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:58:22,36:122,146:0.1774:2,2:24.9:1:29.4:1:0.31074:1.36607:60:116:0.1779:0:1.1 1/0:421:243:115,128:87,91:0.5772:2,2:25.4:1:28.6:1:0.76783:1.06395:60:242:0.5776:0:1.1 -4 183806977 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50403;SOR=Inf;LSEQ=GGTCAAGAAATCCACTAATC;RSEQ=GATGGGTTTCAGTGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:44,105:0:2,0:24.3:1:30.2:1:1:0:60:148:1:0:0.1 0/1:184:2:1,1:53,129:0.0109:2,2:8.5:1:32:1:0.50196:2.42:60:4:0.0109:0:1.5 -4 183806981 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50409;SOR=Inf;LSEQ=AAGAAATCCACTAATCGGAT;RSEQ=GGTTTCAGTGGAAACATCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:39,104:0:2,0:23.6:1:30.8:1:1:0:60:46.667:1:0:0.1 0/1:177:2:2,0:48,127:0.0113:2,0:8:1:25.5:1:0.07865:0:60:4:0.0115:0:1.5 -4 183807129 . T C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTAATCTCCTGTCTCTCT;RSEQ=AAAGATAAATGTGCCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:32:1:33.5:1:1:0:60:20:1:0:1 1/1:5:5:0,5:0,0:1:0,0:19:1:28.8:1:1:0:60:4:1:0:1.2 -4 183807884 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCCAGGGAATTAGTGTGG;RSEQ=GATGCATGTCCATAGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29.5:1:1:0:60:4:1:0:2 -4 183880764 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00043;SOR=0.21323;LSEQ=GCTAACTTTACTTAGAAGGG;RSEQ=TCTTTTTCTAAAACTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:26:9,17:3,7:0.7222:2,2:26.1:1:29.1:1:1:1.23:60:52:0.7222:0:1.1 0/1:68:24:7,17:14,29:0.3529:2,2:23.2:1:28.9:1:1:1.16966:60:23:0.3485:0:1.1 -4 183881396 . ACT A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCACACACACTCTCACAC;RSEQ=CTCTCACACACTCTCACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:30.5:1:1:0:60:4:1:0:0 -4 184234224 . G C 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AAGAGAACCCATCATGGAAG;RSEQ=ATGGCTGCAAGCTCCTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:23:1:32.5:1:1:0:60:4:0.5:0:1 0/0:2:0:0,0:2,0:0:0,0:44:1:30.5:1:1:0:60:4:1:0:0 -4 184234499 . G T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04153;SOR=Inf;LSEQ=GGGGATGGGTTTTATGTAGG;RSEQ=CAGATATCAGAGGCATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:216,130:0:2,0:24.9:1:31.1:1:1:0:60:25.615:1:0:0.4 0/1:469:6:3,3:277,186:0.0128:2,2:19.7:1:28:1:0.6889:1.48791:60:5:0.011:0:1.7 -4 184234587 . T C 271 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53721;SOR=1.12442;LSEQ=GGGAGGTTTGTGGGGGGCAG;RSEQ=GGCTGCCCTGTGGTGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:412:342:142,200:31,34:0.8301:2,2:24.6:1:30.6:1:0.41183:1.28336:60:170:0.8333:0:1.2 1/1:565:478:207,271:34,48:0.846:2,2:26.7:1:30.5:1:0.80973:1.08:60:158.333:0.8482:0:1.2 -4 184234592 . G A 52 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12588;SOR=0.26927;LSEQ=GTTTGTGGGGGGCAGTGGCT;RSEQ=CCCTGTGGTGCCAGCGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:5:3,2:152,211:0.0136:2,2:13.2:1:22.6:1:0.65369:2.08:60:4:0.011:0:2.8 0/0:542:2:2,0:230,308:0.0037:2,0:1:0:24.5:1:0.18413:0:60:4:0.0037:0:2 -4 184234602 . G A 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08522;SOR=Inf;LSEQ=GGCAGTGGCTGCCCTGTGGT;RSEQ=CCAGCGCTCGAGATGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:120,199:0:2,0:22.5:1:31.8:1:1:0:60:62.8:1:0:1 0/1:471:5:3,2:186,280:0.0106:2,2:11:1:27.2:1:0.39475:2.25:60:10:0.0108:0:1.6 -4 184234645 . G A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25472;SOR=Inf;LSEQ=CTGGGGAGCAGGGGTGTGGG;RSEQ=AGGATGCTGACCTCTGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:15,118:0:2,0:23.4:1:30.9:1:1:0:60:65.5:1:0:0.6 0/1:162:3:1,2:32,127:0.0185:2,2:7:1:29.3:1:0.49749:1.97:60:6:0.0189:0:2 -4 187367227 . C T 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGATTTGCTTTTCAAGCA;RSEQ=TCCAAGGTTGCTAATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:10.7:1:31.3:1:1:0:60:6:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 187367234 . G A 47 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TGCTTTTCAAGCACTCCAAG;RSEQ=TTGCTAATTATTTTCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:17.7:1:30:1:1:0:60:6:1:0:4 0/0:1:0:0,0:1,0:0:0,0:7:0:32:0:1:0:60:2:1:0:0 -4 187367298 . C T 53 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CAAACAAAACTTGTCTTTGG;RSEQ=GTATATTCTTTCTATTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:25.8:1:26.8:1:1:0:60:3:1:0:3.5 0/1:4:1:1,0:3,0:0.25:0,0:6:0:32:0:1:0:60:2:0.25:0:2 -4 187367319 . G A 59 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GTATATTCTTTCTATTCTTT;RSEQ=AAAATTTTGTACATTAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:15:1:25.6:1:1:0:60:4:1:0:3.2 0/1:5:2:2,0:3,0:0.4:0,0:23.5:1:30:0:1:0:60:4:0.4:0:1.5 -4 187367404 . T C 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05357;SOR=Inf;LSEQ=GGTTATTCTTACCAAAGATA;RSEQ=AGAGACCTTCCTTCAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:25,3:0:2,0:28.6:1:31.1:1:1:0:60:56:1:0:1 0/1:31:5:5,0:24,2:0.1613:2,0:11:1:31.4:1:1:0:60:10:0.1613:0:1.4 -4 187367442 . A G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.10328;LSEQ=AAACTATAAACATTTTCAGC;RSEQ=AATAACTAATCAGAGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:59:48:39,9:8,3:0.8136:2,2:24.8:1:29.6:1:0.67866:1.61:60:47:0.8103:0:1.8 1/1:64:53:43,10:10,1:0.8281:2,2:24:1:29.9:1:0.67222:2.3006:60:106:0.8281:0:1.9 -4 187367490 . T C 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.01574;SOR=0.42589;LSEQ=TTTTCCAAATATGCACAACT;RSEQ=ATAGTAGCAAAATATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:98:71,27:9,5:0.875:2,2:26.7:1:31.8:1:0.53726:1.46:60:196:0.875:0:2.1 1/0:139:104:73,31:23,12:0.7482:2,2:24.4:1:31.4:1:0.67432:1.23:60:208:0.7536:0:2.1 -4 187367511 . A T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25308;SOR=Inf;LSEQ=ATAGTAGCAAAATATTTGCA;RSEQ=ACTCAGTAATCATAAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:94,58:0:2,0:23.4:1:29.8:1:1:0:60:304:1:0:1.5 0/1:180:3:1,2:106,71:0.0167:2,2:25.3:1:22:1:0.5669:2.96763:60:2:0.0112:0:2.7 -4 187367539 . T C 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0.29569;LSEQ=AATCATAAGTTAAACCATAA;RSEQ=GATGATGACATATTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:197:175:95,80:12,10:0.8883:2,2:23.9:1:30.6:1:1:1.01047:60:86.5:0.8872:0:1.5 1/0:261:183:99,84:38,36:0.7011:2,2:24.5:1:30.2:1:0.78259:1.12:60:182:0.7027:0:1.5 -4 187367589 . C T 27 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.15461;SOR=0;LSEQ=GTTTAGTACCTTGAATATGC;RSEQ=ACACACTATCCTAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:74,104:0.0111:2,2:36:0:27:1:1:1.40:60:4:0.0113:0:1 0/0:277:0:0,0:115,162:0:2,0:27.5:1:30.6:1:1:0:60:29.778:1:0:0.6 -4 187367606 . GA G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.15684;SOR=0;LSEQ=TGCCACACACTATCCTAAAA;RSEQ=AAAAAAGTGAAGATTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:56,92:0.0133:2,2:31:1:32:1:1:1.64:60:4:0.0135:0:0 0/0:228:0:0,0:93,134:0:2,0:25.3:1:29:1:1:0:60:44.4:1:0:0.4 -4 187367637 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5122;SOR=Inf;LSEQ=AAGATTCAAAAGCAGTGAGA;RSEQ=AAAATTTCCCTGTACAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:20,65:0:2,0:22.8:1:31:1:1:0:60:41.5:1:0:0.2 0/1:120:2:1,1:36,82:0.0167:2,2:35.5:1:30:1:0.52339:2.26:60:4:0.0171:0:1 -4 187367804 . T C 67 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGGCATGTCAGCTAGATC;RSEQ=AGCATACAGTTTTTGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:20:1:33.5:1:1:0:60:8:0.8:0:1.3 1/1:1:1:0,1:0,0:1:0,0:25:0:31:0:1:0:60:2:1:0:1 -4 187367891 . G GCCCT 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=5.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTCCTTCCTTCCTTCCGCCT;RSEQ=CCCTCCCTCCCTCCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:30.9:1:1:0:60:4:1:0:0 1/0:2:1:1,0:1,0:0.5:0,0:28:0:24.5:0:1:0:60:2:0.5:0:0 -4 187509730 . TG T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.17383;SOR=0;LSEQ=TTCACTAAAGTCAGGCACTT;RSEQ=GGGGGAGTTGAGAGTCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:129,64:0.0103:2,2:35.5:1:32.5:1:1:2.00786:60:4:0.0103:0:0 0/0:272:0:0,0:174,98:0:2,0:23.6:1:30.6:1:1:0:60:89.667:1:0:0.2 -4 187509875 . G A 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCAGGCTGACACGTCAGA;RSEQ=CAGGAGGCGGTGGAGGCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:56:32,24:206,150:0.1353:2,2:27.4:1:29.5:1:1:1.02994:60:55:0.1361:0:1.4 0/0:611:0:0,0:320,289:0:2,0:26.4:1:31.6:1:1:0:60:120.8:0.9967:0:0.2 -4 187510319 . T C 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCATAGTTGGGGAACTC;RSEQ=TGTATGTCCGGCAGAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:0:0,0:177,299:0:2,0:24.1:1:30.2:1:1:0:60:94.2:0.9979:0:0.1 0/1:617:35:15,20:238,343:0.0567:2,2:21.1:1:30.7:1:0.8606:1.08:60:70:0.0569:0:1.1 -4 187510350 . C A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12998;SOR=Inf;LSEQ=GCAGAGGAACGCTTGGCATC;RSEQ=AATCTGATGTATCCCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:81,233:0:2,0:24.4:1:31.8:1:1:0:60:77.5:1:0:0.1 0/1:376:4:3,1:127,244:0.0106:2,2:6.5:1:26.5:1:0.12211:5.74:60:8:0.0106:0:1 -4 187516655 . T A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05235;SOR=0.11439;LSEQ=CAAGTTCAAACACCTATTCA;RSEQ=TAAGAACAGTTTGGCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:11,1:3,0:0.8:0,2:18.9:1:29.1:1:1:0:60:11:0.7857:0:1 0/1:7:2:2,0:5,0:0.2857:0,0:19:1:32:0:1:0:60:4:0.2857:0:1 -4 187516776 . A G 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06442;SOR=Inf;LSEQ=AGGGTAGATAGTGCGTCTAC;RSEQ=TTGTGAGATAACACAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:103,11:0:2,0:22.9:1:30.6:1:1:0:60:113:1:0:0.1 0/1:135:5:4,1:112,18:0.037:2,2:25.2:1:30.2:1:0.53738:1.54969:60:10:0.0373:0:1 -4 187516880 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.17264;LSEQ=TCGGACTGGAAGGAGCTCAG;RSEQ=GACTGCACTTCAGACAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:456:277:171,106:116,62:0.6075:2,2:24:1:30.6:1:0.48684:1.1594:60:38.571:0.6054:0:1.1 0/1:627:132:79,53:288,207:0.2105:2,2:25.7:1:29.6:1:0.76603:1.07:60:15.5:0.2039:0:1.2 -4 187517681 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50292;SOR=Inf;LSEQ=GACACTTTAGTGAGATGAAA;RSEQ=AGTGGCTCTTACTGTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:125,35:0:2,0:23.9:1:30.5:1:1:0:60:320:1:0:0.1 0/1:194:2:1,1:128,63:0.0103:2,2:39:1:32.5:1:1:2.02373:60:4:0.0104:0:1 -4 187518196 . C T 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGACACATACTGGTTGGG;RSEQ=GCAGCATCCTCGCAGTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:130,309:0:2,0:24.8:1:30.5:1:1:0:60:86.8:0.9977:0:0.2 0/1:599:31:11,20:207,359:0.0518:2,2:18.8:1:30.2:1:1:1.04829:60:62:0.0527:0:1.1 -4 187518259 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17096;SOR=0;LSEQ=TTGCAGTGATAGGAGCCGTG;RSEQ=GTGTTCTCACAGAGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:59,139:0.01:2,2:32:1:30.5:1:0.51106:2.34:60:4:0.0102:0:1 0/0:283:0:0,0:94,189:0:2,0:24.3:1:29.9:1:1:0:60:55.6:1:0:0.2 -4 187518265 . C T 102 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05069;SOR=4.1423;LSEQ=TGATAGGAGCCGTGCGTGTT;RSEQ=TCACAGAGGGCCCCGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:58,127:0.0107:2,2:20:0:32:0:0.53263:2.18:60:4:0.011:0:1 0/1:256:11:3,8:83,162:0.043:2,2:24.8:1:29.6:1:0.75534:1.36467:60:22:0.0437:0:1.1 -4 187518281 . T C 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18071;SOR=0;LSEQ=TGTTCTCACAGAGGGCCCCG;RSEQ=GCAGGCAAGGGTTTCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:48,106:0.0127:2,2:47:0:28:1:0.53093:2.20:60:4:0.0132:0:1 0/0:213:0:0,0:65,148:0:2,0:24.1:1:29.5:1:1:0:60:52.25:1:0:0.2 -4 187518326 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50552;SOR=Inf;LSEQ=CGTCGATATCACTCTGACAC;RSEQ=TGCCAAGGAAGTCAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:18,63:0:2,0:26.7:1:31.4:1:1:0:60:26:1:0:0.1 0/1:106:2:1,1:27,77:0.0189:2,2:34.5:1:31.5:1:0.46038:2.82:60:4:0.0189:0:1 -4 187518871 . G A 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCGAATCACACTGACAAAC;RSEQ=GCGCCATCCAAACTGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:667:0:0,0:380,287:0:2,0:25.9:1:30.1:1:1:0:60:73.111:1:0:0.1 0/1:870:49:26,23:442,376:0.0563:2,2:27:1:30.4:1:1:1.03986:60:98:0.0567:0:1.3 -4 187518976 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11125;LSEQ=AAGGAGAAACAGACATAAAC;RSEQ=TCATGATCCTATTGCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:277:83,194:37,82:0.6977:2,2:24.8:1:30.1:1:0.81279:1.05451:60:91.333:0.699:0:2 0/1:471:96:35,61:132,243:0.2038:2,2:23.3:1:29.4:1:0.81219:1.06:60:192:0.2065:0:2 -4 187518980 . T C 261 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAAACAGACATAAACCTCA;RSEQ=GATCCTATTGCAAATAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:370:113,257:0,0:1:0,2:24.8:1:30.6:1:1:0:60:369:1:0:1.8 1/0:441:221:69,152:84,134:0.5011:2,2:23.2:1:29.7:1:0.11049:1.37988:60:72.667:0.5:0:1.5 -4 187519206 . C G 298 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29518;LSEQ=GTGCCCCCATAGAGGCATGG;RSEQ=TTGGAGGAACACGGATTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:634:633:308,325:0,0:0.9984:0,2:24.8:1:31.2:1:1:0:60:62.3:1:0:1.1 1/1:821:820:424,396:0,0:0.9988:0,2:24.5:1:30.8:1:1:0:60:163:0.9988:0:1.2 -4 187521018 . A T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24899;SOR=Inf;LSEQ=CCTTAAATGTACACACGTGC;RSEQ=GCATTTTAAAGATGGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:210,57:0:2,0:24.8:1:30.2:1:1:0:60:266:1:0:0.8 0/1:279:3:0,3:206,70:0.0108:2,0:17.3:1:22:1:0.01737:0:60:2:0.0072:0:2.3 -4 187521037 . C A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10541;LSEQ=CAGCATTTTAAAGATGGCAA;RSEQ=ATTACGGAGCCCACCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:212:159,53:74,26:0.6795:2,2:27.5:1:29.9:1:0.88936:1.05:60:105:0.6796:0:1.1 0/1:379:69:50,19:208,101:0.1821:2,2:26.7:1:30:1:0.47525:1.28:60:138:0.186:0:1.2 -4 187522325 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49873;SOR=Inf;LSEQ=TGTGGAATTCAACCATTTCA;RSEQ=TTACTTTATTATCTGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:131,6:0:1,0:21.9:1:32.1:1:1:0:60:274:1:0:0 0/1:146:2:1,1:130,14:0.0137:2,2:17.5:1:29:1:0.19556:9.00529:60:4:0.0139:0:1 -4 187522658 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24631;SOR=Inf;LSEQ=AGTATGACTCCCCTGCACCC;RSEQ=TTGAGACTGATTTAGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:6,96:0:2,0:25.8:1:32.1:1:1:0:60:33:1:0:0.2 0/1:101:2:1,1:6,93:0.0198:2,2:34:1:28.5:1:0.13446:14.42:60:4:0.0198:0:1 -4 187522789 . T C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3712;SOR=0.38127;LSEQ=GAAAGAATAAATTTGACGAC;RSEQ=GCATCACAGAGAAATGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:0.7333:0,0:24:1:29.8:1:1:0:60:22:0.7333:0:1.8 1/0:8:4:1,3:0,4:0.5:0,2:11:1:30.3:1:1:0:60:8:0.5:0:1.3 -4 187525020 . A C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33208;LSEQ=TGAGTATTCTTCTCCAGAAG;RSEQ=GGTGATGAAAATCTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:460:286:111,175:78,96:0.6217:2,2:26.4:1:30.5:1:0.20594:1.28026:60:94.333:0.622:0:1.1 0/1:564:199:79,120:148,215:0.3528:2,2:23.8:1:30.3:1:0.85742:1.04556:60:98.5:0.3524:0:1.2 -4 187525058 . T C 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=GGGGCAAAATCGCAGGCGGA;RSEQ=AGATGCTCTCCTCAATTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:104,235:0:2,0:22.8:1:28.7:1:1:0:60:55.5:1:0:0.6 0/1:420:15:7,8:144,261:0.0357:2,2:26.2:1:31.7:1:0.41691:1.58:60:30:0.0361:0:1.1 -4 187525363 . C G 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.0982;LSEQ=GAATCAACAATGAGCTCCTT;RSEQ=AAACACAGCGGGATAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:28:25,3:18,2:0.5833:2,2:24.7:1:31.6:1:1:1.0783:60:27:0.5745:0:1.2 0/1:34:4:4,0:28,2:0.1176:2,0:17:1:31.8:1:1:0:60:8:0.125:0:1.3 -4 187525453 . C T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.249;SOR=Inf;LSEQ=TGTATGAAATGTAAGCTGTT;RSEQ=AAATAGAAGAGGGGAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:208,32:0:2,0:24.7:1:31.4:1:1:0:60:79:1:0:0.1 0/1:253:3:2,1:197,52:0.0119:2,2:16.3:1:21.3:1:0.50913:1.88852:60:2:0.0081:0:1.7 -4 187525910 . A T 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27761;SOR=0;LSEQ=GTGAGGAGGAGGGAAAGGAG;RSEQ=AGGGGTGTAGCGAAAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,11:0.3125:0,0:23.6:1:29.6:1:1:0:60:10:0.3125:0:1.8 0/0:5:0:0,0:0,5:0:0,0:25.8:1:30.4:1:1:0:60:10:1:0:0.4 -4 187525922 . G A 85 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56923;SOR=0.26046;LSEQ=GAAAGGAGAAGGGGTGTAGC;RSEQ=AAAAGGGAAGAAAAAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:0.5833:0,0:26.3:1:30.4:1:1:0:60:14:0.5833:0:2.3 0/1:4:1:0,1:0,3:0.25:0,0:3:0:27:0:1:0:60:2:0.25:0:2 -4 187525940 . AG CT 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAAAAGGGAAGAAAAAGG;RSEQ=GATGAAGGAAACATGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:27.5:1:32.5:1:1:0:60:4:0.2222:0:2 0/0:2:0:0,0:0,2:0:0,0:14.5:1:32.5:1:1:0:60:4:1:0:0 -4 187526002 . C A 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGAGGAGGGGAAGCAGA;RSEQ=ACGAGGAGGAGTGGGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:11.5:1:31:0:0.33333:0:60:4:0.6667:0:4.5 0/0:1:0:0,0:0,1:0:0,0:48:0:33:0:1:0:60:2:1:0:0 -4 187527039 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.59321;SOR=1.43265;LSEQ=AAAAATCAAAGCACGGAAAG;RSEQ=AAAGAGATAAAAGCTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:13:12,1:14,1:0.4643:1,1:17.2:1:29:1:1:1.16024:60:12:0.4444:0:1.4 1/0:27:15:15,0:12,0:0.5556:0,1:25.4:1:29.5:1:1:0:60:30:0.5769:0:1.1 -4 187527089 . T C 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AAATGCTCATCTTTTAATAC;RSEQ=GATAGCGACTTCTTGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:13:13,0:35,2:0.26:2,1:30.6:1:31.8:1:1:0:60:26:0.26:0:1.4 0/0:60:0:0,0:58,2:0:1,0:23.8:1:31.2:1:1:0:60:120:1:0:0.2 -4 187527164 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15298;SOR=0;LSEQ=ATAAGAAAGAAAAGCAACAG;RSEQ=GGCCAATGGAAAAGCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:141,47:0.0105:2,2:11:0:32.5:1:0.44244:2.97908:60:4:0.0106:0:1.5 0/0:295:0:0,0:195,99:0:2,0:22.6:1:29.4:1:1:0:60:293:0.9966:0:0.1 -4 187527300 . G T 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16714;SOR=0.17817;LSEQ=CGGACACATCGATGTTCACG;RSEQ=TCGTCGTGTTGACTCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:4:2,2:148,207:0.0111:2,2:29.3:1:29:1:1:1.40:60:8:0.0112:0:1 0/0:500:1:1,0:213,285:0.002:2,0:47:0:32:0:0.42886:0:60:2:0.002:0:1 -4 187527391 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22419;SOR=Inf;LSEQ=TTCAGGCAAAAGACAGAATG;RSEQ=ACGTTCATTTTCACAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:34,110:0:2,0:21.9:1:31.8:1:1:0:60:35:1:0:0.2 0/1:130:2:1,1:33,94:0.0154:2,2:8:0:28.5:1:0.45918:2.82:60:4:0.0155:0:1.5 -4 187527472 . A G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00515;SOR=0.14071;LSEQ=CGGGCAGGTCCCAGTGAGCT;RSEQ=CCACTATCTGTTGCATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:0,16:0,7:0.6667:0,1:27.3:1:32.3:1:1:0:60:15:0.6818:0:1.1 0/1:19:4:0,4:1,14:0.2105:1,0:23.5:1:33:1:1:0:60:8:0.2105:0:1 -4 187529904 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTATTTTATCTCACTCT;RSEQ=CTTTCTTCTTATGATTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:17.5:1:28:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 187530313 . C T 281 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGTGATTTGTAAACAA;RSEQ=GTAAATCAACCTTTTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:509:509:301,208:0,0:1:0,2:25.5:1:30.7:1:1:0:60:253.5:1:0:1.1 1/1:706:705:430,275:0,0:0.9986:0,2:25.7:1:29.8:1:1:0:60:87.125:0.9986:0:1.2 -4 187530402 . T C 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGTCAATTGTGAACGAGC;RSEQ=TCCTTGGTTGCCATCTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:0:0,0:366,350:0:2,0:24.9:1:30.5:1:1:0:60:142.2:1:0:0.2 0/1:995:58:26,32:455,481:0.0583:2,2:23.3:1:30.4:1:0.59118:1.16406:60:18.333:0.0558:0:1.3 -4 187530578 . G GT 87 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.75756;SOR=0.74888;LSEQ=AGCTGTTTCTTTTTGTTGTT;RSEQ=TTTTTTTTTTGAGATGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:7:0,7:2,66:0.0933:1,0:25.4:1:31.1:1:1:0:60:14:0.0946:0:0.4 0/1:56:4:0,4:0,51:0.0714:1,0:39.3:1:25:1:1:0:60:3:0.0566:0:0.3 -4 187530731 . T C 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.01373;SOR=0;LSEQ=CAGGCGCCCGCCACCACGCC;RSEQ=GGCTAATTTTTTTTTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:8,3:2,4:0.6471:2,2:12.5:1:29.8:1:0.16176:4.77:47.8:22:0.6471:0:1.6 0/0:6:0:0,0:4,2:0:2,0:25.8:1:29.2:1:1:0:58.5:5:1:0:0.2 -4 187531022 . A G 215 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00449;LSEQ=TGTAGGTGTCTTGGCTGAAC;RSEQ=CAGGGGTATTATCGTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:591:133:77,56:242,216:0.225:2,2:24.6:1:30.6:1:0.32396:1.23:60:43.333:0.2238:0:1.1 0/0:769:1:1,0:400,367:0.0013:2,0:18:0:23:0:1:0:60:2:0.0013:0:1 -4 187531122 . A G 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCTCTACTGTTAGGTAAT;RSEQ=CTCATGAGAGCTCTCATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:568:0:0,0:249,319:0:2,0:24.8:1:29:1:1:0:60:93.667:1:0:0.1 0/1:676:27:15,12:280,369:0.0399:2,2:28.7:1:31.6:1:0.23648:1.65:60:54:0.0405:0:1.3 -4 187533153 . C T 41 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TTTTGTATTTTTATTAGAGA;RSEQ=GGGGTTTCTCCATGTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:37:1:26.3:1:1:0:60:2:0.4:0:2.7 0/0:3:0:0,0:0,3:0:0,0:30:1:31.3:1:1:0:60:6:1:0:0 -4 187533998 . T G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAACACATCACTGATTAAT;RSEQ=CAATGGGATGTGAAGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:38.5:1:34:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 187534240 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2156;SOR=0;LSEQ=ATCTCAGTGAGCAGCGTCAG;RSEQ=CAAGAGCATTCCCGGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:149,48:0.0101:2,2:17:1:30:1:0.43277:3.08242:60:4:0.0104:0:1 0/0:229:0:0,0:178,51:0:2,0:21.4:1:30.6:1:1:0:60:56.25:1:0:0.1 -4 187534363 . G A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12892;LSEQ=TCGGCAGAGAATTCGGGGGC;RSEQ=TTATCGTTCACATCTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:667:490:263,227:91,86:0.7346:2,2:24.4:1:30.4:1:0.66052:1.09:60:80.667:0.7367:0:1.7 0/1:1001:263:142,121:379,357:0.2627:2,2:24.2:1:29.4:1:0.5177:1.11:60:64.75:0.2608:0:2 -4 187534375 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39618;LSEQ=TCGGGGGCGTTATCGTTCAC;RSEQ=TCTTCTAGCGTGAGCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:320:162,158:180,175:0.4734:2,2:24.7:1:30.4:1:1:1.00317:60:34.556:0.4705:0:2 0/1:1021:268:142,126:377,374:0.2625:2,2:24.5:1:29.8:1:0.47671:1.12:60:43.667:0.2607:0:2 -4 187534524 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20914;SOR=0;LSEQ=CAAAAACAAATGGACTCACT;RSEQ=GTAATTTAAGACGTGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:0,2:34,144:0.0111:2,0:10:1:30:1:1:0:60:4:0.0113:0:1 0/0:213:0:0,0:39,174:0:2,0:23.4:1:29.6:1:1:0:60:52.25:1:0:0.4 -4 187534542 . T C 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12215;SOR=0.68367;LSEQ=CTTGTAATTTAAGACGTGAC;RSEQ=TGCAGTTGTACATCTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:72:11,61:3,27:0.5143:2,2:25.6:1:32:1:0.75285:1.62:60:144:0.518:0:1 0/1:143:60:12,48:12,71:0.4196:2,2:21.6:1:31.7:1:0.49701:1.48:60:120:0.4196:0:1 -4 187534689 . G T 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00606;SOR=0;LSEQ=AGGTCTCCAACCCTGCCAGG;RSEQ=GCTAGCTCTTTAAGTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:18.6:1:31:1:1:0:60:16:1:0:1 0/0:3:0:0,0:0,3:0:0,0:17.3:1:30.3:1:1:0:60:6:1:0:0 -4 187535063 . T C 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03333;SOR=0;LSEQ=AAGCTTGAGTTATATTTTAA;RSEQ=TTCTGAGGGTTGTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:26.3:1:30.5:1:1:0:60:5:0.8333:0:1.2 0/0:3:0:0,0:3,0:0:0,0:28:1:31:1:1:0:60:6:1:0:0 -4 187535121 . T C 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.3043;SOR=0.18507;LSEQ=GCCTTCTAAATTTTAAATCC;RSEQ=TTTTTCAATTAGGTGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:25.6:1:30.8:1:1:0:60:10:0.5:0:1.8 0/1:7:1:1,0:6,0:0.1429:0,0:15:0:32:0:1:0:60:2:0.1429:0:2 -4 187535169 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51213;SOR=0.54558;LSEQ=TTTTTTAAAAAATCTCACCT;RSEQ=GAATTTTACGCACTAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:11,0:13,0:0.4583:1,0:27.2:1:31.4:1:1:0:60:22:0.4583:0:1.5 0/1:16:5:5,0:11,0:0.3125:0,0:25.4:1:30.8:1:1:0:60:10:0.3125:0:2 -4 187535178 . C T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29266;SOR=4.75314;LSEQ=AAATCTCACCTTGAATTTTA;RSEQ=GCACTAAATTGCTGGTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:1,0:31,0:0.0313:1,0:28:0:32:0:1:0:60:2:0.0313:0:3 0/1:22:3:3,0:19,0:0.1364:1,0:26:1:29.3:1:1:0:60:6:0.1429:0:2.7 -4 187535219 . C T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21439;SOR=2.32858;LSEQ=TTTCTAAGAGATGTCAACTT;RSEQ=GGAGCATCAGAATACATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:4:4,0:51,0:0.0727:1,0:26:1:30.5:1:1:0:60:8:0.0741:0:1.5 0/1:45:7:7,0:38,0:0.1556:1,0:16.9:1:30.4:1:1:0:60:14:0.1556:0:1.7 -4 187535519 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.21435;SOR=0;LSEQ=CTGCAAAGAGTTTAAACAAA;RSEQ=ACGTTACATAAAAGCATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:37,146:0.0108:2,2:15.5:1:31:1:0.36951:3.91:60:4:0.0112:0:1 0/0:214:0:0,0:68,146:0:2,0:26.1:1:29.4:1:1:0:60:106:1:0:0.1 -4 187535528 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50183;SOR=Inf;LSEQ=GTTTAAACAAAAACGTTACA;RSEQ=AAAAGCATTAACAGGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:29,130:0:2,0:23.7:1:28.9:1:1:0:60:158:1:0:0.2 0/1:187:2:1,1:57,128:0.0107:2,2:32:1:32:1:0.52527:2.23:60:4:0.0108:0:1 -4 187535588 . T C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00199;SOR=0.19296;LSEQ=GGAAAAGAAATCATTCATCT;RSEQ=TGACCACAGAAAACATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:19:0,19:0,31:0.38:1,1:27.8:1:32.8:1:1:0:60:38:0.38:0:1.1 0/1:48:5:0,5:3,40:0.1042:2,0:24.4:1:32.8:1:1:0:60:10:0.1042:0:1 -4 187535765 . T C 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.375;SOR=0;LSEQ=TACAAAATGCTATTATATGT;RSEQ=ATTAAGCTGATTTCATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:24.6:1:31.4:1:1:0:60:10:0.7143:0:1 0/0:1:0:0,0:0,1:0:0,0:8:0:28:0:1:0:60:2:1:0:0 -4 187538083 . G C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49913;SOR=0;LSEQ=CATGTGAATTACACCACAGC;RSEQ=CCAAATGATGGTCCCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:126,12:0.0143:2,2:9:0:32.5:1:0.1777:10.12807:60:4:0.0143:0:2 0/0:128:0:0,0:111,17:0:2,0:24.1:1:29.1:1:1:0:60:31:1:0:0.2 -4 187538133 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0;SOR=0.14643;LSEQ=GAAATTGAAATTCATAACAC;RSEQ=CAAATGTAAGGGAAGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:319:233:181,52:59,26:0.7304:2,2:23.4:1:30:1:0.14194:1.53:60:76.667:0.7302:0:1.1 0/1:367:104:77,27:176,87:0.2834:2,2:20.6:1:30.1:1:0.21128:1.41:59.8:103:0.2845:0:1.2 -4 187538330 . G A 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.35642;LSEQ=TCATTCTGTATAGTTTCAAC;RSEQ=GCAAACTGTCCTAAAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:635:331:128,203:122,181:0.5213:2,2:25.2:1:30.6:1:0.68514:1.06885:60:65.2:0.5208:0:1.1 0/1:680:190:84,106:208,282:0.2794:2,2:26.1:1:30.4:1:0.72993:1.07:60:380:0.2819:0:1.1 -4 187538465 . T C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93809;LSEQ=AATGTTATAGTTTAAAAGAA;RSEQ=TGAGTATTAAAAGAATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:6:0,6:0,60:0.0909:1,0:23.2:1:32.5:1:1:0:60:12:0.0938:0:1 0/1:35:3:0,3:0,32:0.0857:1,0:25.7:1:33.7:1:1:0:60:6:0.0857:0:1.3 -4 187538928 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00204;SOR=Inf;LSEQ=ATCCGTGGTACTTAAGATGG;RSEQ=AATCACCCCACCTTGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:807:0:0,0:473,334:0:2,0:25.1:1:31.8:1:1:0:60:49.438:1:0:0.8 0/1:874:10:3,7:494,369:0.0114:2,2:16.7:1:26.6:1:0.10999:3.11978:60:20:0.0116:0:1.5 -4 187538942 . T G 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.12968;LSEQ=AGATGGCAATCACCCCACCT;RSEQ=GGGGGTCATCCTCACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:851:635:349,286:121,94:0.7462:2,2:25.6:1:31.5:1:0.75149:1.05482:60:104.833:0.7461:0:1.1 0/1:972:268:156,112:348,273:0.2757:2,2:23.1:1:30.9:1:0.55614:1.09:60:133:0.2771:0:1.2 -4 187539205 . C T 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=47.57417;LSEQ=TGTGACTGATCCAGGCTATA;RSEQ=ATAACTTGGCCGTTGGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:700:1:0,1:361,337:0.0014:2,0:1:0:25:0:0.48355:0:60:2:0.0015:0:1 0/1:768:49:22,27:366,353:0.0638:2,2:23.9:1:28.9:1:0.46181:1.27207:60:48:0.0627:0:1.1 -4 187539588 . T C 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.41577;LSEQ=GAGATCTATCTCTGTTCCAA;RSEQ=AGGCACGTCCTCTGACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:67:29,38:244,255:0.1182:2,2:22.1:1:31.8:1:0.43548:1.25332:60:32.5:0.1173:0:1.1 0/1:512:27:15,12:242,243:0.0527:2,2:20.5:1:31.1:1:0.69329:1.25:60:54:0.0538:0:1.1 -4 187540042 . G A 185 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATCCTTAGCCATTAAACG;RSEQ=ACTGAGATCACTTTCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:74:36,38:314,320:0.1045:2,2:27.1:1:29.9:1:0.90283:1.03572:60:36:0.1043:0:1.1 0/0:917:0:0,0:475,442:0:2,0:26:0:13:0:1:0:60:0:0:0:4 -4 187540378 . C T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05392;SOR=Inf;LSEQ=TAAAATGGCTTCAGGGCGTG;RSEQ=CGGTGCAGGTTTGAGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:159,263:0:2,0:25.4:1:31.3:1:1:0:60:37.364:1:0:0.1 0/1:394:4:1,3:143,246:0.0102:2,2:30.3:1:27.8:1:1:1.74165:60:8:0.0104:0:1 -4 187540399 . G A 45 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2035;SOR=4.29173;LSEQ=CGGTGCAGGTTTGAGAGGGT;RSEQ=ATAATCCCTGTTGCACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:1:1,0:147,224:0.0027:2,0:1:0:24:0:0.39785:0:60:2:0.0027:0:2 0/1:351:4:2,2:136,211:0.0114:2,2:11.8:1:22.8:1:0.6475:1.55:60:3:0.0087:0:1 -4 187540996 . C T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18278;SOR=0.69018;LSEQ=CGTATGCTCAGCTTATATGC;RSEQ=GGGTGGGCCTCAAAGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:33:18,15:143,160:0.0982:2,2:24.5:1:30.7:1:0.46613:1.34:60:66:0.0991:0:1 0/1:415:29:14,15:204,182:0.0699:2,2:27.6:1:29.9:1:0.70169:1.20041:60:28:0.0685:0:1.1 -4 187541131 . G A 173 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=60.27017;LSEQ=TCCGGGCTGTTAGCCTGCAC;RSEQ=TGGACCACAGGGCTGTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:1:1,0:232,178:0.0024:2,0:1:0:26:0:1:0:60:2:0.0025:0:1 0/1:467:60:30,30:211,196:0.1285:2,2:23.7:1:29.4:1:0.89008:1.07634:60:29:0.1258:0:1.1 -4 187541598 . C G 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TGTCACTTCTACAACCACAT;RSEQ=AAACGCCTCCTGCTGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:14:5,9:208,273:0.0283:2,2:24.6:1:29.7:1:0.78543:1.37058:60:13:0.0269:0:1.1 0/0:555:0:0,0:267,288:0:2,0:23.8:1:31.2:1:1:0:60:68.375:1:0:0.1 -4 187541686 . G T 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTAAATCTGCGATCTGG;RSEQ=TTGAGGATGTGATAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:0:0,0:380,279:0:2,0:24.6:1:31.4:1:1:0:60:49.692:1:0:0.1 0/1:797:50:25,25:385,362:0.0627:2,2:23.3:1:29.4:1:0.88433:1.06349:60:49:0.0623:0:1.1 -4 187542094 . T C 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAGAGATGCTTCATATAA;RSEQ=GGCTTGGCAAACACAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:294,220:0:2,0:24.6:1:30.6:1:1:0:60:72.429:1:0:0.1 0/1:508:21:12,9:271,215:0.0413:2,2:26.5:1:29.6:1:1:1.06:60:20:0.0397:0:1.1 -4 187542755 . T C 240 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00369;LSEQ=ATGTAAACTTCGGAGAGGCG;RSEQ=TGTCAGCAATTGTGACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:180:90,90:290,318:0.2278:2,2:26:1:32.1:1:0.61095:1.10:60:59:0.2272:0:1.1 0/0:920:1:0,1:443,476:0.0011:2,0:17:0:34:0:1:0:60:2:0.0011:0:1 -4 187542899 . G A 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTTTAATAGAGCCCAAGACA;RSEQ=GATCAATCATAAAAGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:168,296:0:2,0:25.5:1:31.3:1:1:0:60:57:1:0:0.2 0/1:521:19:10,9:196,306:0.0365:2,2:26.7:1:31.4:1:0.24212:1.73:60:38:0.0368:0:1.1 -4 187542922 . A G 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAATCATAAAAGAATTTCC;RSEQ=ATATTTCCTGGAAGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:42:16,26:112,214:0.1141:2,2:23.7:1:30.1:1:0.73094:1.18:60:41:0.1139:0:1.1 0/0:402:0:0,0:147,255:0:2,0:24.5:1:29.5:1:1:0:60:99.5:1:0:0.2 -4 187542927 . T C 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=CATAAAAGAATTTCCAATAT;RSEQ=TCCTGGAAGGAGAGGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:114,233:0:2,0:25.7:1:29.9:1:1:0:60:68.4:1:0:0.2 0/1:379:14:5,9:130,235:0.0369:2,2:27.6:1:30.4:1:1:1.00:60:13:0.0349:0:1.1 -4 187542986 . G C 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CACAAGGGGCAGTAGTAGTA;RSEQ=TAGTTAGAGAAACAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:36:2,34:9,84:0.2791:2,2:27.8:1:32.4:1:0.72667:1.81396:60:72:0.2835:0:1.1 0/0:119:0:0,0:15,104:0:2,0:22.3:1:31.5:1:1:0:60:118:1:0:0.1 -4 187549364 . G A 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.54422;LSEQ=CTTTGTCCTTGTCCAGAGCC;RSEQ=TCACCTGCAACACAACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:841:3:2,1:442,394:0.0036:2,2:20.3:1:29.3:1:1:1.78:60:6:0.0036:0:1.3 0/1:1116:66:37,29:544,504:0.0591:2,2:25.6:1:30:1:0.52817:1.18:60:132:0.0599:0:1.2 -4 187549586 . G A 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=ACTAATTAAAAATCACGCTC;RSEQ=AACACACAAAGGCCTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:136,118:0:2,0:23.5:1:30.2:1:1:0:60:62.5:1:0:0.1 0/1:296:16:10,6:144,136:0.0541:2,2:22.4:1:30.2:1:0.44808:1.57:60:32:0.055:0:1.1 -4 187552855 . C A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CTCTGCTCTTCAATCCATCC;RSEQ=CGCGGTATCCTAGTGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:20.3:1:30.7:1:1:0:60:6:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:42.5:1:28.5:1:1:1:60:4:0.3333:0:1 -4 187553049 . C G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGCACCCCCCTCCCGCC;RSEQ=CCACCCAAATTCATATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:30:1:1:0:60:4:1:0:1 -4 187557113 . C G 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=GACTTGTGCCCAAAACTCAT;RSEQ=AAACCGTATGCAGGTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:18:12,6:161,31:0.0857:2,2:20.6:1:30.8:1:0.09839:2.58191:60:36:0.0865:0:2 0/0:193:0:0,0:151,42:0:2,0:22.8:1:30.9:1:1:0:60:63.333:1:0:0.1 -4 187557120 . T C 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14659;SOR=0.60521;LSEQ=GCCCAAAACTCATCAAACCG;RSEQ=ATGCAGGTTCTCCTCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:27:20,7:180,42:0.1084:2,2:25.3:1:32.2:1:0.44095:1.49732:60:54:0.1089:0:1.7 0/1:219:15:12,3:159,45:0.0685:2,2:22.5:1:28.8:1:1:1.13:60:6.5:0.0602:0:1.1 -4 187557420 . C A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.89218;LSEQ=TGGGCAGAGGGGATTAAAAA;RSEQ=AGCAAATCAGGAGTTACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:1:1,0:27,154:0.0055:2,0:1:0:26:0:0.15385:0:60:2:0.0055:0:1 0/1:193:2:1,1:42,149:0.0104:2,2:30:1:31:1:0.39686:3.52:60:4:0.0104:0:1 -4 187557600 . G A 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1558;SOR=6.00433;LSEQ=CTGATTCTCAAACGTTATCC;RSEQ=GCATTGCCTAATGGGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:1,0:39,6:0.0213:2,0:48:0:32:0:1:0:60:2:0.0222:0:1 0/1:34:4:4,0:26,4:0.1176:2,0:27.3:1:31:1:1:0:60:8:0.1176:0:1.3 -4 187557642 . G A 130 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00401;SOR=0.23481;LSEQ=AGGTCACAAACACTTCAGCC;RSEQ=TTTACAAAATAGAAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:20:18,2:50,3:0.274:2,2:27.3:1:30.2:1:0.6101:1.83447:60:40:0.2778:0:1.1 0/1:62:5:5,0:53,3:0.0806:2,0:29:1:30.8:1:1:0:60:10:0.082:0:1 -4 187557893 . T C 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13089;LSEQ=CCTTGTCGGTGGCTATGACG;RSEQ=GATAGAGCGGCTCCCGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:845:635:305,330:96,107:0.7515:2,2:25.7:1:30.6:1:0.87203:1.03:60:51.917:0.7561:0:1.1 0/1:1126:319:153,166:408,397:0.2833:2,2:24.5:1:30.7:1:0.4276:1.11492:60:158.5:0.2838:0:1.2 -4 187557908 . C T 192 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=23.39831;LSEQ=TGACGTGATAGAGCGGCTCC;RSEQ=GTCTGGCATTTCTTTCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:809:3:1,2:369,435:0.0037:2,2:8.3:1:28.7:1:1:1.69548:60:6:0.0038:0:1.3 0/1:1135:91:44,47:497,547:0.0802:2,2:25.1:1:29.6:1:0.9132:1.03:60:29.333:0.0791:0:1.2 -4 187558187 . CA C 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00051;SOR=0.07257;LSEQ=CATTTTGCAGGGCACGATGA;RSEQ=ACATACACAGCAGATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:14:1,13:0,9:0.6087:0,1:25.6:1:31.7:1:1:0:60:28:0.6087:0.0435:0.4 0/1:21:2:0,2:0,19:0.0952:1,0:34:1:28:1:1:0:60:4:0.0952:0:0 -4 187560860 . T TA 161 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.18268;SOR=0.74136;LSEQ=GAATCTTTAAGTATTAAAGA;RSEQ=AAAAAAAAAACTTACCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:46:24,22:249,165:0.0985:2,2:27.3:1:29.2:1:0.34301:1.38231:60:92:0.1022:0.0021:0.3 0/1:574:43:24,19:311,209:0.0749:2,2:29.7:1:29.1:1:0.63018:1.17768:60:86:0.0778:0:0.1 -4 187560995 . G A 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18041;SOR=0;LSEQ=AAGGTCAATTACAAAATACT;RSEQ=CAATTAAAATCACACTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:36,152:0.0105:2,2:16:1:24.5:1:0.35238:4.18:60:4:0.0106:0:2 0/0:258:0:0,0:59,199:0:2,0:22.4:1:31.4:1:1:0:60:35.857:1:0:0.1 -4 187561080 . A G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09506;LSEQ=CCCAGGGGGGTGGATTACTT;RSEQ=AGGTCAGGAGTTGGAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:28:0,28:0,17:0.6222:1,1:23.3:1:31.8:1:1:0:60:56:0.6364:0:1.1 0/1:38:5:0,5:0,33:0.1316:1,0:31.4:1:30.8:1:1:0:60:10:0.1351:0:1.2 -4 187584530 . G A 181 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01327;LSEQ=TGAGCTTGTCATTAGAGCTC;RSEQ=AATCTGGATCAAATGCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:650:66:37,29:347,237:0.1015:2,2:26.9:1:30.1:1:0.60007:1.14732:60:65:0.1009:0:1.1 0/0:669:1:1,0:376,290:0.0015:2,0:1:0:25:0:1:0:60:2:0.0015:0:1 -4 187584771 . C G 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04321;LSEQ=TGACGTCTCTATGACACCTA;RSEQ=AGAGAAAAAAGAAAAGCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:350:348:86,262:0,0:0.9943:0,2:22.4:1:31.3:1:1:0:60:86:0.9942:0:1.1 1/1:408:360:85,275:12,33:0.8824:2,2:22.4:1:31.2:1:0.71107:1.17595:60:119:0.8859:0:1.1 -4 187627096 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAAGTTAGTTCTAAGAA;RSEQ=TCATTTGCTTGTCCAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:39.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 187627576 . C CA 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=CTACAATACAGCAGCCGGGC;RSEQ=AAAAAAAATATTCACACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:73,1:0:1,0:24.5:1:30.4:1:1:0:60:36:1:0:0.2 0/1:83:2:2,0:76,5:0.0241:2,0:36:1:29.5:1:1:0:60:4:0.025:0:0 -4 187627593 . C T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35135;SOR=1.5197;LSEQ=GGCCAAAAAAAATATTCACA;RSEQ=GCACTTCTATACCGAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:12:12,0:92,1:0.1143:1,0:22.3:1:32.3:1:1:0:60:24:0.12:0:1.3 0/1:134:22:21,1:108,4:0.1642:1,1:23:1:29.8:1:1:1.28311:60:44:0.1667:0:1.2 -4 187627792 . T C 290 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01399;LSEQ=TCGGATCTCCCCATCTCTTC;RSEQ=GGCGTCCTCATCATGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:794:791:403,388:1,1:0.9962:2,2:24.1:1:30.2:1:1:1.04:60:86.889:0.9974:0:1.1 1/0:899:707:353,354:100,90:0.7864:2,2:24.3:1:29.3:1:0.5145:1.11412:60:43.188:0.7834:0:1.1 -4 187628054 . C G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTGCTCCACTGAGTTTATC;RSEQ=ACATCGAAGTTTCCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:0:0,0:333,334:0:2,0:23.3:1:31.4:1:1:0:60:65.7:0.997:0:0.1 0/1:765:20:12,8:372,372:0.0261:2,2:15.4:1:30.2:1:0.49781:1.50:60:40:0.0264:0:1.2 -4 187628352 . A T 197 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CCAGAGGGCGTGCGATGTTA;RSEQ=CAACACCCGTCACGCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:96:55,41:124,100:0.3:2,2:24.5:1:30:1:0.80627:1.08:60:31:0.2962:0:1.7 0/0:412:0:0,0:217,194:0:2,0:23:1:29.8:1:1:0:60:204.5:1:0:0.6 -4 187628398 . C G 277 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATGTGTCTGTGTCTGTAA;RSEQ=AATTGAGTACGTCACGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:423:423:266,157:0,0:1:0,2:25.7:1:31.8:1:1:0:60:69.5:1:0:1.2 1/0:479:357:212,145:71,49:0.7453:2,2:26.1:1:31.3:1:1:1.01:60:43.625:0.7441:0:1.1 -4 187629140 . G C 291 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGTTGGGGTTTAAACTAAA;RSEQ=AAATCCAGTTCATTTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:590:590:312,278:0,0:1:0,2:25.3:1:31.7:1:1:0:60:58:1:0:1.1 1/0:690:517:273,244:84,88:0.7493:2,2:25.1:1:31.3:1:0.37947:1.17:60:102.4:0.7518:0:1.1 -4 187629497 . G A 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22398;LSEQ=ATACTGTATGTCACGTACCC;RSEQ=TTCTCACCCTCATCAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:569:490:256,234:43,35:0.8612:2,2:23.8:1:30.5:1:0.71443:1.12276:60:80.667:0.8612:0:1.7 1/0:776:451:218,233:171,154:0.5812:2,2:24:1:29.5:1:0.24521:1.18653:60:74.167:0.5809:0:1.7 -4 187629538 . C T 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15878;LSEQ=TACGGCACTCAGGCTCATGA;RSEQ=AGTAGTACCAATGGGCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:620:543:285,258:37,40:0.8758:2,2:25.5:1:29.5:1:0.46811:1.19:60:89.5:0.8746:0:1.7 1/0:771:407:198,209:175,187:0.5279:2,2:24.9:1:28.6:1:0.94249:1.01:60:49.875:0.5243:0:1.7 -4 187629770 . A C 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16342;LSEQ=AATTTAGCTTTTCCAGGTGT;RSEQ=CTTTTAAAAACATACCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:880:775:371,404:49,55:0.8807:2,2:25.2:1:31.2:1:0.91699:1.03:60:69.455:0.8792:0:1.1 1/0:1043:570:259,311:222,251:0.5465:2,2:25.7:1:30.6:1:0.66239:1.06196:60:62.333:0.5441:0:1.1 -4 187630590 . G A 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14436;SOR=1.24898;LSEQ=GCACCCTGACCTTTGTTCGC;RSEQ=CCTCCACATTAGTATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:84:39,45:286,358:0.1152:2,2:22.4:1:29.6:1:0.72799:1.08:60:83:0.1161:0:1.1 0/1:972:136:61,75:386,449:0.1399:2,2:23.7:1:29.2:1:0.78153:1.05695:60:67:0.1397:0:1.2 -4 187630597 . C G 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GACCTTTGTTCGCGCCTCCA;RSEQ=ATTAGTATTTTTTTCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:697:0:0,0:321,374:0:2,0:24.2:1:32:1:1:0:60:114.833:0.9971:0:0.2 0/1:923:34:19,15:404,483:0.0368:2,2:26.6:1:31.4:1:0.29293:1.51:60:68:0.0374:0:1.1 -4 187630989 . C A 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02597;SOR=1.72657;LSEQ=AATGTCTCCCCATTGCTTAA;RSEQ=TGTCGGGAATCTGAAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:29:7,22:84,245:0.081:2,2:23.8:1:30.8:1:1:1.07733:60:28:0.0791:0:1.1 0/1:401:53:19,34:113,235:0.1322:2,2:24.5:1:29.9:1:0.63982:1.16:60:106:0.1332:0:1.1 -4 187631223 . C T 70 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=0.33624;LSEQ=ACTTCCTTTTCATTTTTGAA;RSEQ=GACAAGGTCCTCTCTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:18.8:1:30.4:1:1:0:60:10:0.625:0:1 0/1:3:1:0,1:0,2:0.3333:0,0:7:0:24:0:1:0:60:2:0.3333:0:1 -4 187631324 . A C 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTATATTTTTATATTTA;RSEQ=ATCGTTAAGGCAAATATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:21:1:32.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -4 189191971 . C G 119 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACACTCAGTCTCCAGCA;RSEQ=CAGCAGCAGCAGCCCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:31.7:1:32.3:1:1:0:60:6:1:0:1.3 1/1:17:16:8,8:1,0:0.9412:0,2:13:1:29.8:1:1:0:56:7:1:0:1.7 -4 189191989 . CCAGCACCAG C 32 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=7.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CACCAGCAGCAGCAGCCCCA;RSEQ=CAGCAGCAGCAGCAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:19.3:1:31:1:1:0:54.5:8:1:0:1.3 0/1:17:2:1,1:8,7:0.1176:2,2:20:1:32:1:1:1.13389:23:4:0.125:0:0.5 -4 189191998 . GCAGCAGCAGCAGCAGCAGCCC G 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.6749;SOR=0.5479;LSEQ=CAGCAGCCCCACCAGCACCA;RSEQ=CACCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:3,2:0.4444:2,2:14.5:1:28.2:1:1:1.43328:44.5:8:0.4444:0.4444:2 0/1:20:6:3,3:8,6:0.3:2,2:19.2:1:23.2:1:1:1.31413:54.3:8:0.1204:0.2784:2.3 -4 189192001 . G C 57 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.15284;SOR=Inf;LSEQ=CAGCCCCACCAGCACCAGCA;RSEQ=CAGCAGCAGCAGCAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,2:0:2,0:14.8:1:32.4:1:1:0:60:10:1:0:1.6 0/1:20:5:3,2:8,7:0.25:2,2:17.4:1:24.6:1:1:1.29:54.6:1.5:0.1765:0:2.4 -4 189192022 . C CCAG 72 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=8.000;MSILEN=3;SSF=0.40382;SOR=0.42767;LSEQ=CAGCAGCAGCAGCAGCCCCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:3,1:5,2:0.3636:2,2:19:1:29.8:1:1:1.18:45.8:8:0.4444:0.0909:2.5 0/1:26:5:4,1:9,10:0.1923:2,2:26.6:1:31.3:1:0.32712:4.19:57:10:0.2083:0.0385:1 -4 189192028 . G C 66 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.01115;SOR=0;LSEQ=CAGCAGCAGCCCCACCAGCA;RSEQ=CAGCAGCAGCAGCAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:3,1:5,5:0.25:2,2:21.5:1:33.3:1:0.58042:2.78:52:8:0.3636:0:2.3 0/0:30:0:0,0:17,13:0:2,0:23.2:1:30.1:1:1:0:53:6.5:1:0:1.3 -4 189192061 . CCAG C 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.64652;SOR=0.48817;LSEQ=CAGCCCCACCAGCACCAGCA;RSEQ=CAGCAGCAGCAGCCCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:2,1:15,14:0.0938:2,2:16.7:1:33:1:1:1.83:60:6:0.0938:0:0.3 0/1:42:2:1,1:21,19:0.0476:2,2:23.5:1:33:0:1:1.10263:55:4:0.05:0:2 -4 189192078 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49922;SOR=Inf;LSEQ=GCACCAGCAGCAGCAGCAGC;RSEQ=CCACCAGCAGCAGCACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:0:2,0:25:1:28.4:1:1:0:53.8:7:1:0:1.2 0/1:40:2:1,1:20,16:0.05:2,2:5.5:1:27.5:1:1:1.24262:60:4:0.0667:0:1.5 -4 189192088 . G C 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.08394;SOR=0.14568;LSEQ=CAGCAGCAGCCCCACCAGCA;RSEQ=CAGCACCAGCACCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:3,2:14,13:0.1563:2,2:9.4:1:28.2:1:1:1.38:52.4:4:0.1379:0:3.2 0/1:39:1:0,1:19,17:0.0256:2,0:47:0:29:0:0.48649:0:41:2:0.0313:0:6 -4 189192094 . C G 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11993;SOR=5.47776;LSEQ=CAGCCCCACCAGCAGCAGCA;RSEQ=CAGCACCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:1,0:15,13:0.0345:2,0:26:0:14:0:1:0:54:0:0:0:8 0/1:36:6:4,2:12,12:0.1667:2,2:26:1:28.2:1:0.6567:1.96:43.2:5:0.1923:0.0278:3.5 -4 189192100 . CCAG C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.6482;SOR=0.5171;LSEQ=CACCAGCAGCAGCACCAGCA;RSEQ=CAGCAGCAGCAGCCCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:1,2:13,10:0.1154:2,2:4:1:31.8:1:0.58:2.50674:60:4:0.107:0.0862:0.7 0/1:32:2:1,1:14,16:0.0625:2,2:28:0:33:0:1:1.14:60:4:0.0667:0:1.5 -4 189192121 . CCAG C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.18018;SOR=0;LSEQ=CAGCAGCAGCAGCAGCCCCA;RSEQ=CAGCAGCAGCAGCCTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:29.5:1:33.5:1:1:1:60:4:0.1538:0:1.5 0/0:21:0:0,0:10,11:0:2,0:18.6:1:29.4:1:1:0:53.7:42:1:0:1.5 -4 189192124 . G C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.62567;SOR=2.2833;LSEQ=CAGCAGCAGCAGCCCCACCA;RSEQ=CAGCAGCAGCAGCCTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:7,5:0.0667:2,0:47:0:33:0:0.46154:0:60:2:0.0909:0:5 0/1:21:3:1,2:9,9:0.1429:2,2:29.7:1:31.3:1:1:1.93674:52:6:0.15:0:3.3 -4 189192127 . G C 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.05139;SOR=8.17566;LSEQ=CAGCAGCAGCCCCACCAGCA;RSEQ=CAGCAGCAGCCTGGCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:7,7:0.0667:2,0:11:0:14:0:1:0:60:0:0:0:1 0/1:21:8:5,3:5,8:0.381:2,2:9.3:1:24.9:1:0.387:2.54:50.6:3:0.3529:0:1.4 -4 190093170 . C T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1395;SOR=Inf;LSEQ=CAGAGCAAGAGTGAGCCTTC;RSEQ=ACAGAGGTGTGCGCAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:151,99:0:2,0:24.4:1:30.9:1:1:0:60:34.714:1:0:0.5 0/1:336:4:1,3:192,140:0.0119:2,2:17.8:1:25.8:1:0.31599:4.0978:60:8:0.0121:0:1.5 -4 190093234 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01389;LSEQ=TAACGGGAGAAAAAATTCCC;RSEQ=GAAGCTGACACTCATCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:323:206:98,108:58,59:0.6378:2,2:25.3:1:30.6:1:0.81686:1.08309:60:412:0.6398:0:1.1 0/1:464:11:5,6:214,236:0.0237:2,2:26.5:1:27.7:1:1:1.0879:59.7:4.5:0.0196:0:2 -4 190093246 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.80012;LSEQ=AAATTCCCCGAAGCTGACAC;RSEQ=CATCCAGTGCCCAGTGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:33:14,19:131,140:0.1086:2,2:22.2:1:30.4:1:0.58228:1.2689:60:32:0.1077:0:1.2 0/1:451:220:105,115:103,127:0.4878:2,2:24.6:1:30.4:1:0.5707:1.13:60:219:0.4944:0:1.3 -4 190093296 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19021;SOR=0;LSEQ=TGTGTTTAAAATACTGCAGT;RSEQ=CTGTCACAACGGTTGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:67,121:0.0105:2,2:8:1:26.5:1:1:1.80:60:4:0.0107:0:1 0/0:245:0:0,0:90,155:0:2,0:26.4:1:31.3:1:1:0:60:34:1:0:0.8 -4 190093299 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26086;SOR=Inf;LSEQ=GTTTAAAATACTGCAGTGCT;RSEQ=TCACAACGGTTGTGGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:64,117:0:2,0:26.2:1:31.7:1:1:0:60:35.2:1:0:0.5 0/1:235:3:3,0:79,153:0.0128:2,0:9:1:26:1:0.04147:0:60:6:0.013:0:1.3 -4 190093329 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=13.00992;LSEQ=TTGTGGTGTATGTGGCTCTG;RSEQ=GGGTTCACACGCCGAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:11:2,9:31,86:0.0859:2,2:24.3:1:29.5:1:0.72747:1.61659:60:10:0.0794:0:1.4 1/0:152:84:26,58:17,51:0.5526:2,2:23.9:1:30.3:1:0.47139:1.34:60:83:0.5533:0:1.3 -4 190262203 . C T 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TCCTCATTTCTAACAAGCTC;RSEQ=CGTGCAATGCCATTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:37:1:33:0:1:0:60:4:0.3333:0:1 1/1:1:1:1,0:0,0:1:0,0:6:0:31:0:1:0:60:2:1:0:1 -4 190262402 . C T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.65258;SOR=2.01085;LSEQ=GAGACAATGCCGTACTAGTT;RSEQ=CATGGTTGACAACATGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:1:0,1:86,53:0.0071:2,0:1:0:25:0:0.38571:0:60:2:0.0072:0:2 0/1:210:3:1,2:131,76:0.0143:2,2:24.3:1:28.7:1:0.55677:3.42628:60:6:0.0144:0:1 -4 190262486 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33157;LSEQ=TTTATGTACATTTTATTTCC;RSEQ=AACATAAAAATATGTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:174:130:56,74:21,23:0.7471:2,2:26.2:1:30.3:1:0.6031:1.20521:60:129:0.7457:0:1.1 0/1:259:128:52,76:60,71:0.4942:2,2:25.8:1:29.8:1:0.45208:1.23409:60:127:0.4922:0:1.1 -4 190262598 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49206;SOR=Inf;LSEQ=GGATAGGGGACTTTGAATAA;RSEQ=ATTATAAAATAGGGAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:2,29:0:2,0:21.6:1:28.9:1:1:0:60:62:1:0:0.1 0/1:32:2:0,2:1,29:0.0625:1,0:31.5:1:33.5:1:1:0:60:4:0.0625:0:1 -5 30352 . A T 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55324;SOR=0;LSEQ=TCAAGTGTGGTGGATGCCTC;RSEQ=TCTAGGAAAGGCCCTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:0,3:87,52:0.0211:2,0:8.7:1:20.7:1:0.05616:0:60:2:0.0147:0:2 0/0:76:0:0,0:39,37:0:2,0:24.1:1:29.7:1:1:0:60:75:1:0:0.2 -5 30358 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12664;SOR=Inf;LSEQ=GTGGTGGATGCCTCATCTAG;RSEQ=AAAGGCCCTCACCACGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:99,63:0:2,0:25.7:1:30.7:1:1:0:60:31.4:1:0:0.2 0/1:90:2:1,1:46,42:0.0222:2,2:30.5:1:27.5:1:1:1.09413:60:4:0.0233:0:1 -5 30397 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54145;SOR=0;LSEQ=GACTCCTTCTACTCACTCAA;RSEQ=TGTACTTACTTCTCTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:79,83:0.0121:2,2:21.5:1:29:1:1:1.05:60:4:0.0123:0:1 0/0:90:0:0,0:42,48:0:2,0:26.8:1:31.5:1:1:0:60:89:1:0:0.2 -5 30414 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12326;SOR=Inf;LSEQ=CAACTGTACTTACTTCTCTT;RSEQ=TTCCTCTATGAACACTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:55,79:0:2,0:27.3:1:29.3:1:1:0:60:43.667:1:0:0.2 0/1:73:2:1,1:30,41:0.0274:2,2:12.5:1:29.5:1:1:1.36:60:4:0.0282:0:1.5 -5 218356 . T C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71291;SOR=1.15469;LSEQ=CCACTGCAGCCCCGCTCGAC;RSEQ=CCGGCGTGGTGCGCAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:25:24,1:92,12:0.1938:2,1:26.2:1:31.2:1:0.4608:3.11:60:24:0.189:0:1.1 0/1:69:15:13,2:49,5:0.2174:2,2:24.4:1:30.3:1:0.64092:1.49792:60:30:0.2174:0:1 -5 218381 . T TC 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.77423;SOR=1.10354;LSEQ=CGTGGTGCGCAGGCGCGGTA;RSEQ=CCCCCCTCCCCCGCCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:45:38,7:143,34:0.2018:2,2:22.2:1:30.9:1:0.6708:1.29:60:90:0.2074:0.0673:0.6 0/1:110:24:19,5:69,16:0.2182:2,2:26.3:1:30.2:1:0.77728:1.13351:59.8:48:0.2222:0.0636:0.8 -5 218466 . C T 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06143;SOR=4.79194;LSEQ=GGACTGCGCGGCGGCAACAG;RSEQ=AGACATGTCGGGGGTCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:923:2:0,2:401,517:0.0022:2,0:11.5:1:20:1:0.50769:0:60:1:0.0011:0:2 0/1:582:6:2,4:262,314:0.0103:2,2:22.2:1:27.3:1:0.69398:1.66738:60:12:0.0108:0:1 -5 218467 . A G 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=78.5778;LSEQ=GACTGCGCGGCGGCAACAGC;RSEQ=GACATGTCGGGGGTCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:926:1:1,0:401,523:0.0011:2,0:25:0:10:0:0.43459:0:60:0:0:0:6 0/1:586:46:22,24:242,296:0.0785:2,2:25.7:1:29.5:1:0.75863:1.12:60:92:0.082:0:1.2 -5 218598 . G A 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.73758;LSEQ=GCGGCGGTAGGAGCGGGACG;RSEQ=TCCCCAGCGGGTCCGAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:5,7:3,4:0.6316:2,2:23.8:1:28.8:1:1:1.04727:51.3:11:0.6111:0:1.4 1/0:9:5:3,2:2,2:0.5556:2,2:28.2:1:28:1:1:1.43:60:10:0.5556:0:2 -5 218600 . C A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08867;SOR=Inf;LSEQ=GGCGGTAGGAGCGGGACGGT;RSEQ=CCCAGCGGGTCCGAGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:20.9:1:30.5:1:1:0:53.7:19:1:0:0.9 0/1:9:2:1,1:4,3:0.2222:2,2:17:0:29:1:1:1.29098:50:4:0.2222:0:1.5 -5 223195 . C T 27 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02778;SOR=Inf;LSEQ=GGAAAGGGCTATGATGGAGC;RSEQ=AGTTAAAATGCTTCATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:19.9:1:27.7:1:1:0:52.6:6:1:0:1 1/1:2:2:1,1:0,0:1:0,2:24.5:1:27:1:1:0:30.5:4:1:0:2.5 -5 223214 . C T 38 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCAGTTAAAATGCTTCATTA;RSEQ=TTGCAAAATACCACATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:27.3:1:24.3:1:1:0:48.3:2:0.2857:0:2.3 1/1:2:2:1,1:0,0:1:0,2:31:1:27.5:1:1:0:30.5:4:1:0:2.5 -5 223408 . C A 25 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02745;SOR=Inf;LSEQ=TGGAAACGAGGACCTGGGGG;RSEQ=TCAGTCCTTCCTTGCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:75,3:0:1,0:22.8:1:31.4:1:1:0:54.7:38:1:0:1.2 0/1:16:2:1,1:12,2:0.125:2,2:9.5:1:25.5:1:0.35:5.09912:60:4:0.125:0:2 -5 223411 . A C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72905;SOR=0.60098;LSEQ=AAACGAGGACCTGGGGGCTC;RSEQ=GTCCTTCCTTGCCCCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:16:15,1:65,2:0.1928:1,1:21.5:1:31:1:0.47862:2.14221:53.9:32:0.1951:0:1.9 0/1:16:2:0,2:13,1:0.125:1,0:14:1:24.5:1:0.025:0:55.5:4:0.125:0:2.5 -5 223415 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02426;SOR=0.26771;LSEQ=GAGGACCTGGGGGCTCAGTC;RSEQ=TTCCTTGCCCCTTGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:87:74:72,2:12,1:0.8506:1,1:22.1:1:31:1:0.38842:2.95:54.3:36:0.8571:0:1.3 1/0:20:12:9,3:8,0:0.6:0,2:21.3:1:30.3:1:0.24211:0:55.9:24:0.6:0:1.3 -5 223646 . A T 155 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.0616;LSEQ=AGGTTTTCACTTCACTGTTG;RSEQ=TGGGAACAAGAGGGCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2200:2:0,2:1057,1140:9e-04:2,0:1:0:27.5:1:0.50052:0:56:4:9e-04:0:1 0/1:1266:37:18,19:615,613:0.0292:2,2:27.7:1:29.8:1:0.86944:1.05898:58.7:74:0.0296:0:1.2 -5 223807 . C T 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13197;SOR=1.56406;LSEQ=TTTCTCATAGGTATCCAATG;RSEQ=ATGCTGAAATTATTTTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:45:2,43:8,164:0.2074:1,1:22.3:1:27.8:1:1:1.04858:47.3:21.5:0.2009:0:1.1 0/1:86:25:0,25:3,58:0.2907:1,1:28.6:1:29.1:1:0.55296:0:46.3:50:0.2941:0:1 -5 223890 . G C 123 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42707;SOR=0.32963;LSEQ=TTACATTTTTACTTGTATCT;RSEQ=TTATGTATCTATAAACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:15:0,15:0,39:0.2778:1,1:22.1:1:31.7:1:1:0:53.3:14:0.2692:0:1.9 0/1:9:1:0,1:0,8:0.1111:0,0:22:0:30:0:1:0:60:2:0.1111:0:1 -5 223909 . GATTTAA G 88 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTATGTATCTATAAACTA;RSEQ=ATTTAGATCAAGTAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:7:0,7:1,32:0.175:1,0:26.7:1:31.7:1:1:0:58:14:0.1795:0.025:1.6 0/0:4:0:0,0:0,4:0:0,0:11.3:1:29.8:1:1:0:60:8:1:0:0.3 -5 223958 . T C 65 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAAAATAAAATGAACAG;RSEQ=GTCTGCTGTGATAGATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:0,5:4,14:0.2174:2,0:17.4:1:28.2:1:0.53924:0:60:10:0.2174:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 224105 . A AT 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTGTATTTAGTGAGCCT;RSEQ=TCTCTGTTGAAAAACTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:3,3:0.4:2,2:36.5:1:30.3:1:1:1:60:8:0.4:0:0.3 0/0:1:0:0,0:1,0:0:0,0:17:0:30:0:1:0:60:2:1:0:0 -5 224196 . A T 91 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30773;SOR=0;LSEQ=CTTGGCACCTTCTCAGGCAT;RSEQ=AGCATAGGCACGGCCCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:8:6,2:20,3:0.25:2,2:26.6:1:30.6:1:0.58308:2.15834:56.3:16:0.2667:0:3.6 0/0:7:0:0,0:5,2:0:2,0:21.6:1:26.6:1:1:0:56.7:6:1:0:0.3 -5 224207 . C T 100 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16449;SOR=0;LSEQ=CTCAGGCATAAGCATAGGCA;RSEQ=GGCCCTGAAGTAGAGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:7,2:21,3:0.2727:2,2:32.6:1:31.8:1:0.59705:1.95399:56.7:18:0.2813:0:3.6 0/0:8:0:0,0:6,2:0:2,0:28.8:1:31.4:1:1:0:57.1:16:1:0:0.3 -5 224211 . C T 96 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16753;SOR=0;LSEQ=GGCATAAGCATAGGCACGGC;RSEQ=CTGAAGTAGAGTTGTGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:9:7,2:22,3:0.2647:2,2:34.8:1:30.3:1:0.59084:2.04473:56.7:8:0.2424:0:3.6 0/0:8:0:0,0:6,2:0:2,0:32.1:1:31.3:1:1:0:57.1:16:1:0:0.3 -5 224268 . G A 110 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16051;SOR=0.20352;LSEQ=GGATAGACCCTCTACCATTC;RSEQ=TAGAATCTGATTGTCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:15:13,2:38,1:0.2778:1,2:24.2:1:28.2:1:0.18344:5.61939:58.9:6.5:0.2549:0:2 0/1:14:1:1,0:12,1:0.0714:1,0:23:0:32:0:1:0:60:2:0.0714:0:1 -5 224397 . A G 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCCTTTTATCTTTGTCA;RSEQ=GCTCTTTCACTGTCACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:362,72:0:2,0:22.7:1:29.9:1:1:0:55.7:26.125:1:0:0.3 0/1:221:17:14,3:162,42:0.0769:2,2:26.4:1:31.8:1:1:1.21:60:34:0.078:0:1.1 -5 224418 . T G 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17409;SOR=1.25022;LSEQ=GCTCTTTCACTGTCACAAGA;RSEQ=TCTTCATGTTTGGCATAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:137:104,33:355,107:0.2287:2,2:27.7:1:32.3:1:0.8189:1.05266:42.5:136:0.2305:0:1.1 0/1:329:89:62,27:182,58:0.2705:2,2:26.9:1:31.4:1:0.25998:1.36521:41.5:43.5:0.2677:0:1.2 -5 224633 . A G 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89637;SOR=1.02164;LSEQ=AGGTCACACACTGTTGCAGC;RSEQ=CAGGTAAGAGAAAGGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1167:183:68,115:374,608:0.1568:2,2:24.4:1:31.2:1:0.86829:1.04027:46.9:44.75:0.1552:0:1.2 0/1:714:114:47,67:247,351:0.1597:2,2:23.4:1:30.7:1:1:1.00315:48.3:56:0.1593:0:1.3 -5 224656 . C T 182 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.65426;LSEQ=GGTAAGAGAAAGGTGCCCCA;RSEQ=TGTGCTCCCACTCCGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:864:48:23,25:250,566:0.0556:2,2:28.2:1:29.9:1:0.0161:2.08:38.9:47:0.0552:0:1.4 0/1:518:70:34,36:161,284:0.1351:2,2:28.2:1:29.8:1:0.06283:1.66:42.5:69:0.135:0:1.4 -5 224692 . G T 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29356;SOR=1.24436;LSEQ=TGCAGGTCCCGCGCAGCCTC;RSEQ=CACTTTCTACCTGGGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:71:16,55:63,282:0.1695:2,2:25.9:1:29.5:1:0.40829:1.30:47.2:22.667:0.1655:0:1.7 0/1:237:48:14,34:52,132:0.2025:2,2:26.6:1:28.5:1:1:1.05:47.7:47:0.2017:0:1.8 -5 224713 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.52862;SOR=1.58855;LSEQ=CACTTTCTACCTGGGCAGCC;RSEQ=CCTGCCTCCTCCCCCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:7:0,7:30,254:0.024:2,0:8:1:31:1:1:0:28.6:14:0.0251:0:2 0/1:133:5:0,5:19,109:0.0376:2,0:10.8:1:30.2:1:1:0:27.4:10:0.0391:0:2 -5 224904 . T C 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3191;SOR=3.04568;LSEQ=TGCCTACTACCTTCCCCACC;RSEQ=ACCCCCGCCACCCCAACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:1,4:1,15:0.2381:1,2:19.6:1:33:1:0.42857:3.46:60:10:0.25:0:1.2 1/0:6:3:1,2:1,2:0.5:2,2:12.7:1:29.3:1:1:1:60:6:0.6:0:1 -5 225267 . C A 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29839;SOR=0;LSEQ=GTAGCCTTTCACTCACTGCT;RSEQ=CAGTCAGCCCTTCCTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:10:10,0:23,0:0.303:1,0:27.3:1:28:1:1:0:53:20:0.303:0:1.1 0/0:5:0:0,0:5,0:0:0,0:16.6:1:32.2:1:1:0:60:10:1:0:0 -5 225328 . A AG 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.07304;LSEQ=AGATGAGGAGACTGAGGCTA;RSEQ=GGATGGAATCACTGGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:11:11,0:60,3:0.1486:1,0:15.5:1:32.6:1:1:0:54.7:22:0.1549:0.0541:0.6 0/1:19:3:3,0:14,1:0.1579:1,0:35.7:1:33.7:1:1:0:60:6:0.1579:0:0 -5 225768 . G C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28365;LSEQ=AAGCAATTGAGGCGGATGTG;RSEQ=CAGCCAAAAGAATGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:324:193:31,162:16,114:0.5957:2,2:23.5:1:31.4:1:0.42177:1.36:60:95.5:0.6025:0:1.1 0/1:119:35:7,28:2,82:0.2941:1,2:25.4:1:30:1:0.00264:10.01:60:16.5:0.287:0:1 -5 225774 . A G 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15952;SOR=1.42294;LSEQ=TTGAGGCGGATGTGGCAGCC;RSEQ=AAAGAATGGTGATGAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:69:8,61:26,185:0.2464:2,2:25.7:1:31.1:1:1:1.07136:60:33.5:0.2436:0:1.8 0/1:107:34:0,34:6,67:0.3178:2,1:25.4:1:31.4:1:0.17361:0:60:68:0.3178:0:1.7 -5 225796 . T C 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88306;SOR=1.0484;LSEQ=AAGAATGGTGATGAGCAAAG;RSEQ=TCACAAGAAGAGTCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:54:7,47:29,128:0.2559:2,2:23.1:1:32.4:1:0.40815:1.51839:60:53:0.256:0:2 0/1:83:22:0,22:6,55:0.2651:2,1:26.6:1:32.5:1:0.33387:0:60:21:0.2561:0:2.1 -5 225941 . C T 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=2.30417;LSEQ=TGTTTAGTGTAGATTAGCTG;RSEQ=GAATATCTTGACTCCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:72:61,11:189,24:0.2526:2,2:24:1:30.1:1:0.40701:1.41822:58.8:144:0.2562:0:1.1 0/1:146:64:58,6:69,13:0.4384:2,2:20.9:1:29.3:1:0.32397:1.81:59.7:31:0.4336:0:1.1 -5 226069 . G C 125 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=14.57998;LSEQ=CAGCGTGCATTTGGTGGACA;RSEQ=AGCCTCAAGTTTGGAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1507:2:2,0:747,758:0.0013:2,0:5:1:31.5:1:0.24686:0:45.5:4:0.0013:0:1.5 0/1:841:16:8,8:394,428:0.019:2,2:41.5:1:31.3:1:1:1.09:37.1:32:0.0193:0:1.5 -5 226160 . A C 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00866;SOR=1.45517;LSEQ=TATTGCACACCTTATATGGA;RSEQ=GGGTAAGGCCGCCCCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:826:166:43,123:200,458:0.201:2,2:21.3:1:30.3:1:0.29484:1.24877:59.1:165:0.2017:0:1.3 0/1:403:108:42,66:90,205:0.268:2,2:24.1:1:29.6:1:0.12033:1.45:58.8:53:0.2657:0:1.3 -5 226222 . T C 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.21667;SOR=1.38749;LSEQ=GCTGGGGCTTATGGTGACAG;RSEQ=GGGGAATGGGTTAGCGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:50:3,47:39,212:0.1656:2,2:21.9:1:30:1:0.11457:2.87416:52.6:24:0.1616:0:2 0/1:125:27:4,23:21,77:0.216:2,2:26.8:1:30.1:1:0.59045:1.56298:49.6:54:0.2195:0:2 -5 226224 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08492;SOR=Inf;LSEQ=TGGGGCTTATGGTGACAGTG;RSEQ=GGAATGGGTTAGCGTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:40,252:0:2,0:24.4:1:31:1:1:0:57.1:57.4:0.9965:0:0.4 0/1:121:2:1,1:24,95:0.0165:2,2:22:0:32:1:0.3719:3.90:60:4:0.0169:0:1.5 -5 226264 . C T 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21347;SOR=1.83942;LSEQ=AGTGAGTCAGCCAGAGATTA;RSEQ=GTAAAAAGCAACAGAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:15:1,14:9,111:0.1111:2,1:22.4:1:29.3:1:1:1.13409:46.5:14:0.1069:0:2.1 0/1:48:9:0,9:6,33:0.1875:2,0:21.2:1:31:1:0.57774:0:47.7:18:0.1915:0:1.8 -5 226376 . A G 104 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77909;LSEQ=GGCAGTGTGTGACTTCTTGC;RSEQ=TCTATGTCAGAAAGTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:10:1,9:1,30:0.2439:1,2:33.2:1:31.6:1:0.43293:3.21:60:20:0.2439:0:1.7 0/1:5:1:0,1:1,3:0.2:2,0:9:0:33:0:1:0:60:2:0.2:0:1 -5 226453 . G A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.45455;SOR=0.2887;LSEQ=GTGACACTCAACATACAAGA;RSEQ=CAGAGCAAGCAGGCCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:0,1:0.8889:0,0:21.6:1:29.8:1:1:0:50.3:16:0.8889:0:1.1 1/0:3:2:1,1:0,1:0.6667:0,2:14:1:29.5:1:1:0:60:4:0.6667:0:1 -5 228071 . A C 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56125;SOR=0;LSEQ=AGTAGGAAATGTGTCACCAA;RSEQ=ATAGGAGCTGTTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:5,0:14,4:0.2174:2,0:27.6:1:33.8:1:0.53924:0:37.2:10:0.2174:0:2 0/0:4:0:0,0:3,1:0:2,0:23.5:1:31.8:1:1:0:60:8:1:0:0.5 -5 228129 . G A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24084;SOR=0.41263;LSEQ=CCTTGTCTGTACTGCTCGGC;RSEQ=TGGAATGCCTCTCGGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:16:15,1:36,1:0.3019:1,1:22.6:1:30.2:1:0.51669:2.35586:50.7:32:0.3077:0:1.3 0/1:20:3:3,0:16,1:0.15:1,0:41.3:1:31:1:1:0:60:6:0.15:0:1 -5 228221 . A G 172 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97704;LSEQ=TGGATCAAGTTCTTTCACCT;RSEQ=TTCACATGAGCAGATACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:38:36,2:191,7:0.161:1,2:25.5:1:32.8:1:0.64026:1.51284:47.1:76:0.1617:0:1 0/1:95:15:14,1:72,8:0.1579:2,1:21.1:1:31.5:1:1:1.55:46.7:30:0.1613:0:1.3 -5 228278 . CT C 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=3e-05;SOR=1.84077;LSEQ=TTGGCTTAACACTTCTTGCC;RSEQ=TTTTTTTTCCTTTCTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:737:128:100,28:477,129:0.1737:2,2:23.3:1:31.4:1:0.90568:1.0353:49.4:127:0.1728:0.0393:0.7 0/1:430:120:89,31:230,77:0.2791:2,2:23.3:1:30.9:1:0.90166:1.04031:48.4:59:0.277:0.0581:0.6 -5 228362 . T C 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00204;SOR=1.32663;LSEQ=TTGGATCTCCTGATGGAGAA;RSEQ=GGGGAGTGCCGTGGTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2018:379:225,154:873,765:0.1878:2,2:26.2:1:30.7:1:0.03424:1.28:57.5:46.375:0.1877:0:1.1 0/1:1133:266:130,136:464,402:0.2348:2,2:24.2:1:29.8:1:0.18303:1.20729:57:52.2:0.2339:0:1.2 -5 228687 . C A 72 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.40171;SOR=3.74166;LSEQ=AGTAGATGGTAGTGGTTGCC;RSEQ=TCAGGTTCACAGCTTACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:0,20:0.2:1,0:23.6:1:31.2:1:1:0:60:10:0.2:0:1 1/0:2:1:0,1:0,1:0.5:0,0:30:0:30:0:1:0:60:2:0.5:0:1 -5 228713 . A AT 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACAGCTTACCTCTCCCA;RSEQ=TTTAGATGAGGGAACTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:1,3:0,22:0.1538:1,2:24.5:1:30.2:1:0.15385:0:60:8:0.1538:0.0769:0.8 0/0:1:0:0,0:0,1:0:0,0:4:0:30:0:1:0:60:2:1:0:1 -5 230603 . G A 37 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATACAAAAATTAACTGGGC;RSEQ=TGGTGGTGCACACTGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:23:1:23.7:1:1:0:36.7:2:0.25:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 230704 . C G 63 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGCCGAGATCGCACCACT;RSEQ=TACTCCAGCCTGGTCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:0.2222:1,0:26:1:31.8:1:1:0:60:8:0.2222:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 230749 . T TAAATA 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=4.000;MSILEN=1;SSF=0.23842;SOR=3.18426;LSEQ=AGATCCTATCTCAAAATAAA;RSEQ=AAATAAAATACAAATGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:5,0:32,1:0.1316:1,0:25.8:1:28.8:1:1:0:60:10:0.1316:0.0526:2 0/1:6:2:2,0:4,0:0.3333:0,0:21.5:1:30.4:1:1:0:57:4:0.3333:0.1667:2 -5 230778 . T C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.35845;SOR=1.79362;LSEQ=TACAAATGGAAGTCCTTTCT;RSEQ=TGATCCCAGGCTTCTATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:14:14,0:57,2:0.1918:1,1:19.2:1:31.6:1:1:0:53.6:28:0.1918:0:2.9 0/1:20:6:5,1:14,0:0.3:1,2:19.2:1:31.8:1:0.3:0:54.8:12:0.3:0:2.8 -5 230822 . G C 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83422;SOR=1.11047;LSEQ=TGTGCAGGGTAGCAGCACCA;RSEQ=TGGCGCGGCCCCTAGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:27:27,0:109,5:0.1915:1,1:27.7:1:31.6:1:0.58323:0:53.9:26:0.1857:0:2.6 0/1:48:10:9,1:35,3:0.2083:2,2:25.7:1:31.6:1:1:1.28886:57.5:20:0.2128:0:2.6 -5 230828 . C T 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05579;LSEQ=GGGTAGCAGCACCAGTGGCG;RSEQ=GGCCCCTAGTGATATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:31:31,0:119,5:0.1987:1,1:25.2:1:30.1:1:0.58367:0:54.7:62:0.2039:0:2.5 0/1:53:11:10,1:39,3:0.2075:2,2:23.5:1:30.5:1:1:1.29316:57.7:22:0.2157:0:2.5 -5 230980 . A G 341 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00921;LSEQ=GTGTGCAGTCACTGCTCTCT;RSEQ=TTGTTTCCAGAGGCTACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1644:1642:953,689:1,0:0.9988:0,2:25.3:1:32:1:1:0:59.9:90.222:0.9988:0:1.1 1/1:914:807:462,345:59,46:0.8829:2,2:25.1:1:31.1:1:0.83481:1.04:59.4:79.7:0.8816:0:1.2 -5 231111 . T C 327 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34095;LSEQ=GAGTTTGTTCAGTTCCACCC;RSEQ=ACAGGTAGGGCAGGACGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1657:1452:591,861:73,127:0.8763:2,2:26:1:31.2:1:0.28164:1.19:56.8:49.069:0.8762:0:1.3 1/0:891:630:268,362:108,148:0.7071:2,2:27.9:1:30.3:1:0.94034:1.01:56.6:51.5:0.7063:0:1.4 -5 231143 . T C 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00134;SOR=1.45735;LSEQ=AGGACGCCTTGCCCGGCAGG;RSEQ=GTTTGGCTTGTGTGTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1146:239:73,166:279,626:0.2086:2,2:24.9:1:30.3:1:1:1.01347:56.3:118.5:0.2105:0:1.9 0/1:609:169:57,112:136,286:0.2775:2,2:25.4:1:29.4:1:0.77103:1.07:57.1:32.8:0.2729:0:2 -5 231260 . C T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.84764;SOR=1.0952;LSEQ=CTCTCAGGTCCTAACTTCAA;RSEQ=GTCATTTACCTAAGGAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:37:1,36:4,121:0.2284:1,1:23.4:1:30.6:1:1:1.18886:43.9:74:0.2284:0:3.1 0/1:49:12:0,12:3,34:0.2449:2,0:18.8:1:31.6:1:0.56622:0:48.7:24:0.2449:0:1.9 -5 231270 . C T 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94959;LSEQ=CTAACTTCAACGTCATTTAC;RSEQ=TAAGGAGACTTTTCCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:31:1,30:4,99:0.2313:1,1:24.5:1:29.8:1:1:1.21046:42.6:14.5:0.2231:0:3.5 0/1:36:8:0,8:3,25:0.2222:2,0:14.1:1:31:1:1:0:43:16:0.2286:0:2.4 -5 231286 . C G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24413;SOR=0.33769;LSEQ=TTACCTAAGGAGACTTTTCC;RSEQ=ACACTCCCCTTCCCCTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:23:1,22:3,78:0.2212:1,1:27.2:1:31.7:1:1:1.18:44.8:46:0.2277:0:4 0/1:23:2:0,2:2,19:0.087:2,0:12.5:1:32:1:1:0:43:4:0.0909:0:3.5 -5 231301 . C T 125 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.18274;SOR=0.20815;LSEQ=TTTCCCACACTCCCCTTCCC;RSEQ=TAAGGCAGTTTGGGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:17:1,16:2,61:0.2125:1,1:25.9:1:30.8:1:0.51666:1.89:48.5:34:0.2179:0:4.3 0/1:19:1:0,1:1,17:0.0526:1,0:9:0:31:0:1:0:46:2:0.0556:0:4 -5 231337 . A C 97 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56899;SOR=0;LSEQ=CACCGTCTTATGTATTTCTC;RSEQ=AGAGCGCTAAACCCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:0,29:0.2162:1,0:17.4:1:32.5:1:1:0:52.8:16:0.2222:0:3.9 0/0:4:0:0,0:0,4:0:0,0:24:1:30:1:1:0:56.5:8:1:0:0 -5 231463 . TCAGGAGTTCGAGAC T 64 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGGCGGATCACCTGAGG;RSEQ=CAGCCTGACCAACATGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:0,7:0.3636:0,0:24.3:1:32:1:1:0:53.8:8:0.3636:0.0909:0.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 233325 . G A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33766;SOR=0.19802;LSEQ=TACACTGGGCTGTAATCAGA;RSEQ=TATTGGCCAGAGGTCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:17,0:1,0:0.9444:0,1:27:1:30.1:1:1:0:49.5:16:0.9412:0:2.1 1/0:4:3:2,1:1,0:0.75:0,2:13:1:27.7:1:1:0:38:6:0.75:0:2 -5 233362 . T G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11522;SOR=0.15006;LSEQ=GTGGGCCGGCCTTTCTCCTC;RSEQ=CTGGGGACACCGCTCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:29:29,0:2,0:0.9355:0,1:23.3:1:30.1:1:1:0:50.9:58:0.9355:0:1.8 1/0:6:4:3,1:2,0:0.6667:0,2:35.8:1:30:1:1:0:38:8:0.6667:0:2.3 -5 233371 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06826;SOR=4.20573;LSEQ=CCTTTCTCCTCTCTGGGGAC;RSEQ=CCGCTCTGCCCCAGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:11:11,0:24,0:0.3143:1,0:22.2:1:30.4:1:1:0:45.7:22:0.3143:0:1.8 1/0:9:6:5,1:3,0:0.6667:0,2:30:1:30.5:1:1:0:39.8:12:0.75:0:1.7 -5 233473 . C T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.72254;SOR=1.14698;LSEQ=TCTTGCTGTGCAGTTTTGCA;RSEQ=ATAATGCCTTCTGCTTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:29:28,1:139,3:0.1696:1,1:21.4:1:31.9:1:0.52793:1.6491:60:58:0.1716:0:1.9 0/1:79:15:15,0:63,1:0.1899:1,1:25.9:1:31:1:1:0:59.3:30:0.1899:0:1.9 -5 233509 . CA C 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.31032;SOR=0;LSEQ=TATCTTTTTCCTCTTTCCCC;RSEQ=AAAAATGTCTTGAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:4:3,1:327,38:0.0108:2,2:26.5:1:30.3:1:0.36157:2.85639:60:8:0.011:0:0 0/0:176:0:0,0:146,30:0:2,0:22.3:1:29.6:1:1:0:60:43:1:0:0.6 -5 233517 . G A 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.0711;SOR=1.45882;LSEQ=TCCTCTTTCCCCCAAAAAAT;RSEQ=TCTTGAAAAAAATAATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:77:70,7:310,56:0.1734:2,2:24.2:1:28.4:1:0.20801:1.80:60:24.667:0.1713:0:2.2 0/1:209:49:40,9:124,36:0.2344:2,2:21.4:1:28.7:1:0.69153:1.29:60:48:0.2341:0:2 -5 233572 . A G 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00278;SOR=1.41935;LSEQ=TAGCAATTGTTAGGTAATAA;RSEQ=TATGTGTGGTTTTTTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1122:240:164,76:554,325:0.2139:2,2:26.7:1:32.4:1:0.14892:1.27:59.3:239:0.2173:0:1.4 0/1:628:175:104,71:266,184:0.2787:2,2:26.3:1:31.3:1:1:1.01:59.4:350:0.2836:0:1.4 -5 233734 . C G 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00247;SOR=1.51522;LSEQ=AGAGATGTGGTGTCTCGGTC;RSEQ=ATGACTCTGGAGATCCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:847:158:53,105:263,426:0.1865:2,2:24.3:1:30.6:1:0.31585:1.22281:59.4:78:0.1855:0:1.1 0/1:504:130:47,83:157,217:0.2579:2,2:25:1:30.3:1:0.25556:1.27706:59.5:129:0.2601:0:1.1 -5 233889 . T C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50252;SOR=1.49897;LSEQ=CAGCCACCTCTCTTAGCTGC;RSEQ=GGCAGGCGTCTGTTAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:9:1,8:1,60:0.1286:1,2:23.8:1:28:1:0.24224:7.13:48.7:8:0.1159:0:1 0/1:22:4:0,4:0,18:0.1818:1,0:24.3:1:31.3:1:1:0:49:8:0.1905:0:1 -5 234867 . AT CA 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATACTCTCCCATTTTAT;RSEQ=TAGGGACTTGAGCATCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:26:1:31.8:1:1:0:42:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 234989 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGCACTTACCAAGGACA;RSEQ=CTGCAGCAGGCTGTGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:0.1176:1,0:17.5:1:32.5:1:1:0:60:4:0.1176:0:1 0/0:1:0:0,0:1,0:0:0,0:5:0:32:0:1:0:60:2:1:0:0 -5 235118 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGCTTAGAAAAGATTTG;RSEQ=TGAGAGGGTGACCATACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:2,0:133,10:0.0137:2,0:39.5:1:31.5:1:1:0:60:4:0.0141:0:1 0/0:62:0:0,0:59,3:0:1,0:26.2:1:29.6:1:1:0:59.7:61:1:0:0.1 -5 235376 . C T 110 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=11.96748;LSEQ=ATGATCTTCGCTGGCGTGGA;RSEQ=GTCACGAAGGAGCCGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1861:2:0,2:913,946:0.0011:2,0:1:0:26:1:0.49991:0:60:4:0.0011:0:1 0/1:1022:13:6,7:476,531:0.0127:2,2:14.8:1:29.9:1:1:1.04579:45.7:26:0.0128:0:5.5 -5 235397 . T G 95 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTCACGAAGGAGCCGATCCC;RSEQ=GTCCTCCCCACCGTGCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1884:0:0,0:926,955:0:2,0:24.4:1:30.6:1:1:0:59.4:68.667:0.9989:0:0.2 0/1:1015:11:6,5:475,527:0.0108:2,2:29.1:1:27.7:1:0.76479:1.33:45.8:10:0.01:0:6.6 -5 235406 . C G 99 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GAGCCGATCCCTGTCCTCCC;RSEQ=ACCGTGCATTATAACATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1900:0:0,0:913,986:0:2,0:24.2:1:31.4:1:1:0:59.5:62.3:1:0:0.2 0/1:971:10:5,5:457,500:0.0103:2,2:21.4:1:30.1:1:1:1.09:44.4:20:0.0104:0:6.5 -5 235548 . T C 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=2.43857;LSEQ=TTAGATCTTACAGGAAAAGA;RSEQ=AGATGTTTCCTTCAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:60:5,55:9,211:0.2143:1,2:23.6:1:31.3:1:0.18818:2.12:60:19:0.2073:0:1.3 0/1:125:50:4,46:5,70:0.4:2,2:25:1:31.9:1:1:1.22:59.9:49:0.4016:0:1.2 -5 235608 . A G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.81415;SOR=1.17384;LSEQ=TTGCACTTTAAATTTCTATT;RSEQ=CCGGAGGATGGAGGGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:19:1,18:0,67:0.2209:1,1:19.2:1:31.5:1:0.22093:0:60:18:0.2118:0:1.9 0/1:36:9:0,9:1,26:0.25:1,0:25:1:32.7:1:1:0:59.7:18:0.25:0:1.7 -5 236142 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATACGGTCTTTACTTCCCT;RSEQ=TCTTTTTTTTTCTTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:42.5:1:29:1:1:0:41:4:0.5:0:2 0/0:1:0:0,0:0,1:0:0,0:38:0:33:0:1:0:60:2:1:0:0 -5 236144 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACGGTCTTTACTTCCCTCT;RSEQ=TTTTTTTTTCTTGGAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:42.5:1:29.5:1:1:0:41:4:0.5:0:2 0/0:1:0:0,0:0,1:0:0,0:36:0:33:0:1:0:60:2:1:0:0 -5 236288 . C T 86 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.582;LSEQ=TAGCTGGGATTACAGGCACC;RSEQ=GCCATTATGCCCCGCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:7,0:16,0:0.3043:1,0:14.7:1:30.9:1:1:0:50.9:14:0.3182:0:1 0/1:5:1:1,0:4,0:0.2:0,0:16:0:33:0:1:0:49:2:0.2:0:1 -5 236405 . C G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24948;SOR=1.46635;LSEQ=CACCTCAGCCTCCCAAAGTG;RSEQ=TGAGATTACAGGCGTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:46:46,0:148,4:0.2323:1,1:24.1:1:31.6:1:0.57508:0:59.8:45:0.2296:0:1.2 0/1:65:20:18,2:44,1:0.3077:1,2:22.6:1:30.8:1:0.22184:4.75445:60:19:0.2969:0:1 -5 236424 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57222;SOR=0;LSEQ=GCTGAGATTACAGGCGTGAG;RSEQ=CACCACGCCTGGCCTACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:262,9:0.0109:1,2:10:1:29:1:0.10591:14.09423:60:6:0.0111:0:1.3 0/0:95:0:0,0:91,4:0:1,0:24.9:1:32.5:1:1:0:60:190:1:0:0.3 -5 236458 . T C 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18623;SOR=5.27219;LSEQ=CTACTTCCCTCTCTCTGACC;RSEQ=GCAGCACAGACACCCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:527:1:1,0:450,75:0.0019:2,0:27:0:33:0:1:0:60:2:0.0019:0:1 0/1:201:2:1,1:168,31:0.01:2,2:28:0:30.5:1:0.29373:5.34996:60:4:0.01:0:1.5 -5 236587 . G T 144 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.27875;LSEQ=GATCAGATTGTGCCCGGCCT;RSEQ=TACGCCTGTGGGGAGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1780:2:1,1:977,801:0.0011:2,2:24.5:1:30:1:1:1.21958:50:4:0.0011:0:1 0/1:940:30:16,14:493,413:0.0319:2,2:27.8:1:29.4:1:1:1.04446:48.6:60:0.0324:0:1.1 -5 236617 . G T 122 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=5.95565;LSEQ=GGGGAGGCCGCCTGTGCCTC;RSEQ=GTACATGGTGCCAACCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1982:5:2,3:1032,943:0.0025:2,2:10.6:1:30.6:1:0.67454:1.64115:48.6:10:0.0025:0:3.4 0/1:1145:17:14,3:576,552:0.0148:2,2:13.3:1:30:1:0.01276:4.47:41.2:16:0.0141:0:5.9 -5 236619 . T C 148 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.93802;LSEQ=GGAGGCCGCCTGTGCCTCGG;RSEQ=ACATGGTGCCAACCGCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1999:4:4,0:1035,957:0.002:2,0:15.8:1:26.8:1:0.12589:0:41.5:3:0.0015:0:5.8 0/1:1164:25:20,5:583,556:0.0215:2,2:9.9:1:32:1:0.00426:3.81:42:50:0.0217:0:6.1 -5 236628 . C T 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.94618;LSEQ=CTGTGCCTCGGTACATGGTG;RSEQ=CAACCGCCTCGGGGCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2089:27:18,9:1042,1018:0.0129:2,2:7.7:1:29.4:1:0.12093:1.95:44.5:54:0.0132:0:4.8 0/1:1238:46:32,14:597,595:0.0372:2,2:13.3:1:28.7:1:0.01036:2.28:43.3:22:0.0361:0:5.4 -5 236649 . C T 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.00306;LSEQ=CAACCGCCTCGGGGCAAACT;RSEQ=GCTCTTGGACCTGGTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2024:51:26,25:955,1017:0.0252:2,2:20.5:1:30.3:1:0.7773:1.11:44.7:50:0.025:0:4.5 0/1:1249:90:50,40:559,599:0.0721:2,2:24:1:29.4:1:0.19057:1.34:46.3:21.5:0.0697:0:4.7 -5 236650 . G A 158 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.87755;LSEQ=AACCGCCTCGGGGCAAACTC;RSEQ=CTCTTGGACCTGGTTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2005:2:1,1:979,1022:0.001:2,2:29.5:1:14:0:1:1.04:46:0:0:0:4.5 0/1:1238:44:24,20:582,611:0.0355:2,2:26:1:29:1:0.53962:1.26:59.9:21:0.0345:0:1.1 -5 236653 . C A 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=3.32808;LSEQ=CGCCTCGGGGCAAACTCGCT;RSEQ=TTGGACCTGGTTGTCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2003:50:27,23:946,1004:0.025:2,2:25.2:1:29.6:1:0.47589:1.25:43.8:49:0.0248:0:4.6 0/1:1235:97:55,42:549,588:0.0785:2,2:24.9:1:28.5:1:0.11395:1.40:46.7:31.333:0.0778:0:4.6 -5 236676 . G A 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05149;SOR=1.61161;LSEQ=GGACCTGGTTGTCTTTGGTC;RSEQ=GGCATGTGCCCTGAGCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1918:39:20,19:804,1075:0.0203:2,2:35.4:1:30.5:1:0.32796:1.41:39.1:78:0.0205:0:4.6 0/1:1112:36:18,18:486,590:0.0324:2,2:36.2:1:29.3:1:0.61181:1.21:39.8:35:0.0319:0:4.9 -5 236678 . G A 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.12883;LSEQ=ACCTGGTTGTCTTTGGTCGG;RSEQ=CATGTGCCCTGAGCATCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1882:55:27,28:775,1051:0.0292:2,2:31:1:30.5:1:0.33574:1.31:43.5:110:0.0297:0:4.5 0/1:1094:121:61,60:431,542:0.1106:2,2:32:1:28.7:1:0.20904:1.28:46.5:242:0.1121:0:4.2 -5 236734 . G C 164 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.9698;LSEQ=GGTAAGTGTTTTCTTCAGGA;RSEQ=CCAGACTATTTGAGAAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1060:9:0,9:278,772:0.0085:2,0:15:1:30.3:1:0.12229:0:37.1:8:0.0077:0:4.1 0/1:518:37:9,28:142,339:0.0714:2,2:17.1:1:31.6:1:0.57713:1.30259:42.3:74:0.0727:0:3.9 -5 236745 . T G 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.57207;LSEQ=TCTTCAGGAGCCAGACTATT;RSEQ=GAGAAGGCGCAGGACGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:885:1:0,1:179,704:0.0011:2,0:5:0:14:0:1:0:40:0:0:0:4 0/1:427:17:4,13:97,310:0.0398:2,2:12.4:1:31.2:1:1:1.0169:46.8:34:0.0403:0:3.7 -5 236753 . C T 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14445;SOR=1.29854;LSEQ=AGCCAGACTATTTGAGAAGG;RSEQ=GCAGGACGTTAGAAAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:781:103:2,101:133,545:0.1319:2,1:21.7:1:30.5:1:0:12.30394:39.3:33.333:0.1299:0:1.9 0/1:358:59:4,55:68,230:0.1648:2,2:22.4:1:29.9:1:0.00403:4.05341:40.7:58:0.1643:0:1.8 -5 236778 . C CT 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.67291;SOR=0.45425;LSEQ=GACGTTAGAAAGTCTTTTTT;RSEQ=TTTTTTTTGAGAAAGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:5:1,4:52,370:0.0117:2,2:22.6:1:27.5:1:0.48623:1.78:44.4:4:0.0095:0.0023:0.2 0/0:187:1:0,1:26,160:0.0053:2,0:32:0:32:0:1:0:49:2:0.0054:0:0 -5 236926 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCACCACCACACCTGGCT;RSEQ=ATTTTTAAAAAAATTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:0,39:0.0488:1,0:8.5:1:32:0:1:0:53:4:0.0488:0:2 0/0:5:0:0,0:0,5:0:0,0:20.4:1:31:1:1:0:60:10:1:0:0.4 -5 236932 . T A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.12843;SOR=0.16737;LSEQ=CACCACACCTGGCTAATTTT;RSEQ=AAAAAAATTTATTTTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:32:0,32:0,5:0.8649:0,1:26.8:1:29:1:1:0:54.1:9.667:0.8529:0:1.4 1/0:4:2:0,2:0,2:0.5:0,0:20:1:29.5:1:1:0:60:4:0.5:0:1 -5 239294 . A G 34 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCATTTCATACATCCT;RSEQ=CCTCCTGCATGTATTACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:34:0:1:0:60:4:1:0:2.5 -5 239307 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATCCTACCTCCTGCATGT;RSEQ=TTACCTGTTGAAGAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:33.5:1:1:0:60:4:1:0:2.5 -5 240350 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10418;SOR=Inf;LSEQ=GCTGGCAGTGTGTTAGCTCA;RSEQ=GAGACTTACAGAGTTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:163,7:0:1,0:24.1:1:32.2:1:1:0:59.9:55.667:1:0:0.1 0/1:82:2:2,0:73,7:0.0244:2,0:24.5:1:31.5:1:1:0:60:4:0.0244:0:1 -5 240457 . CT C 127 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0019;SOR=3.53604;LSEQ=TTTCAAAAGTTAAATTCTAG;RSEQ=TTTTTTTGTTTTAGGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1228:9:5,4:741,478:0.0073:2,2:24.4:1:32.3:1:0.74392:1.23993:48.6:18:0.0074:0.0016:0.1 0/1:707:18:11,7:391,298:0.0255:2,2:23.2:1:30.6:1:0.81218:1.20:51.8:36:0.0259:0.0028:0.3 -5 240664 . A C 209 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCACTGGTTTTGTTTTTTA;RSEQ=AAACTAGATCTAGGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:88:8,80:7,105:0.44:2,2:23.5:1:32.4:1:0.59012:1.50:58:176:0.4422:0:1.1 0/0:85:0:0,0:10,75:0:2,0:25.9:1:29.7:1:1:0:53:27.333:1:0:0.2 -5 240750 . A C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.86868;LSEQ=GCTTTTCATGTACCCGTCAC;RSEQ=CAAGTCGTGTGTGTTGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:10:0,10:1,38:0.2041:1,0:24.2:1:31.1:1:1:0:36.9:9:0.1875:0:1.4 0/1:11:2:1,1:1,8:0.1818:2,2:34.5:1:29.5:1:0.34545:6.00:40:4:0.1818:0:1 -5 250922 . A C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.727;SOR=1.36866;LSEQ=GAAACATTTATTTATTCAGA;RSEQ=GCTTTAGTCAAAACTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:16:16,0:42,2:0.2667:1,1:23.4:1:32.9:1:1:0:58.9:32:0.2759:0:1 0/1:12:4:4,0:8,0:0.3333:0,0:17.3:1:32:1:1:0:60:8:0.3333:0:1 -5 251419 . C T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.621;SOR=1.16221;LSEQ=GGGCCCATGTGACTGGGTCC;RSEQ=GCCTGCCCCTGATGGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:43:29,14:160,40:0.177:2,2:21.7:1:31.4:1:0.10383:1.92523:37.3:86:0.1792:0:1.8 0/1:80:16:13,3:56,8:0.2:2,2:27:1:30.7:1:0.68458:1.60471:38.4:15:0.1899:0:1.8 -5 251469 . G A 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59018;SOR=1.12385;LSEQ=CCAGGAATGGTCTGGAACAC;RSEQ=GACCTGGTGGAGACCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:75:69,6:388,106:0.1316:2,2:23.1:1:30.6:1:0.00477:3.14:37.3:150:0.1337:0:1.8 0/1:268:39:37,2:174,55:0.1455:2,2:24.9:1:30.6:1:0.00549:5.82:39.1:38:0.1445:0:1.8 -5 251541 . A G 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=1.60539;LSEQ=ACCATCTACGGAGCAGAGGC;RSEQ=CGGAAGGAGTCACGGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1396:222:146,76:674,495:0.159:2,2:25.2:1:30.8:1:0.0256:1.41:55.5:221:0.1599:0:1.3 0/1:790:184:116,68:341,265:0.2329:2,2:27.4:1:30.2:1:0.10621:1.33:56.6:183:0.2337:0:1.2 -5 251680 . G T 120 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.01561;SOR=2.70776;LSEQ=TCTCTGCATTTTCTTTCGTT;RSEQ=CCCCAAAAGTAAATCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2360:10:5,5:1109,1236:0.0042:2,2:3.9:1:31.1:1:1:1.11:52:20:0.0043:0:2.6 0/1:1492:17:8,9:681,791:0.0114:2,2:5.5:1:29.4:1:1:1.03:41.4:34:0.0116:0:2.9 -5 251703 . TG T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65752;SOR=1.13567;LSEQ=CCAAAAGTAAATCCAAAAAA;RSEQ=CCTTTTTCCCCCCTGGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2095:28:11,17:780,943:0.0134:2,2:11.4:1:27.6:1:0.5709:1.27814:47:6:0.0117:0.0095:2 0/1:1320:20:10,10:432,552:0.0152:2,2:12.9:1:28.3:1:0.65222:1.28:44.3:19:0.0145:0.0106:2.1 -5 251704 . GCCT CCC 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.58959;LSEQ=CAAAAGTAAATCCAAAAAAT;RSEQ=TTTTCCCCCCTGGTAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2095:339:142,197:780,943:0.1618:2,2:25.4:1:31.2:1:0.2569:1.14744:46.7:55.5:0.1625:0.0391:0.5 0/1:1320:310:129,181:432,552:0.2348:2,2:26.8:1:30.7:1:0.51119:1.09799:46.3:102.333:0.2345:0.0545:0.5 -5 251707 . T C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15706;SOR=1.43238;LSEQ=AAGTAAATCCAAAAAATGCC;RSEQ=TTTTCCCCCCTGGTAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1805:36:13,23:783,976:0.0199:2,2:10.4:1:30.5:1:0.3973:1.4191:49.5:17:0.0192:0:2 0/1:1059:30:14,16:440,579:0.0283:2,2:10:1:29.9:1:0.71249:1.15:48.7:14:0.0268:0:1.9 -5 251712 . C T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.62231;SOR=1.1245;LSEQ=AATCCAAAAAATGCCTTTTT;RSEQ=CCCCCTGGTAACTTTGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1987:41:20,21:856,1079:0.0206:2,2:25.2:1:29.7:1:0.63446:1.20:49.7:19.5:0.02:0:2.3 0/1:1253:29:15,14:520,697:0.0231:2,2:26.9:1:30.7:1:0.3483:1.44:44.2:58:0.0233:0:2.7 -5 251748 . C T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.86294;SOR=1.07378;LSEQ=GATCCCTGGGTTCTCGCCAT;RSEQ=TTCTGGATCACTGTGACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1458:22:10,12:579,855:0.0151:2,2:15.8:1:30.8:1:0.66529:1.23:42:44:0.0153:0:2.8 0/1:865:14:7,7:358,491:0.0162:2,2:18.1:1:29.4:1:0.59356:1.37:45.6:28:0.0164:0:3.2 -5 251784 . C T 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00227;SOR=1.54584;LSEQ=ACCTTTTCCTTGCTTTGGGT;RSEQ=GGCATCCACTGATGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:871:141:39,102:208,522:0.1619:2,2:25.9:1:29.9:1:0.91878:1.0421:45.1:34.25:0.1608:0:1.4 0/1:487:112:41,71:129,243:0.23:2,2:25:1:29.6:1:0.73539:1.09:46.5:111:0.2322:0:1.4 -5 251792 . A G 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGCTTTGGGTCGGCATCC;RSEQ=CTGATGCCAGCAGTGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:790:0:0,0:199,589:0:2,0:23.2:1:29.7:1:1:0:50.6:111.571:0.9987:0:0.3 0/1:423:53:18,35:129,241:0.1253:2,2:22.2:1:30.2:1:1:1.04071:50.2:52:0.1238:0:1.3 -5 251809 . C A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03128;SOR=Inf;LSEQ=TCCACTGATGCCAGCAGTGG;RSEQ=ATCTCCAAGCCAATGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:613:0:0,0:108,505:0:2,0:23.5:1:31.8:1:1:0:49:46.154:1:0:0.2 0/1:283:3:2,1:75,205:0.0106:2,2:14:1:28.3:1:0.18084:5.43:49.7:6:0.0109:0:1.7 -5 251981 . A T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAGTAAGCCACCGTTTCA;RSEQ=ACCTGCCCTGTGGAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:6,34:0.0476:2,2:24:0:28.5:1:0.30894:5.32:22:4:0.0488:0:3.5 0/0:10:0:0,0:3,7:0:2,0:27.2:1:30.2:1:1:0:40.1:20:1:0:0.2 -5 252027 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84124;LSEQ=TTTATTAAATAACGAGTAAG;RSEQ=CACCGTTTCAAACCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:0.1667:2,2:30:1:31.5:1:1:2.16:22:4:0.1667:0:3.5 0/1:7:1:0,1:2,4:0.1429:2,0:1:0:24:0:1:0:20:2:0.1667:0:1 -5 252038 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=ACGAGTAAGCCACCGTTTCA;RSEQ=ACCTGCCCTGTGGAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:4,7:0.1538:2,2:19:1:31.5:1:1:1.67:22:4:0.1538:0:3.5 0/0:7:0:0,0:3,4:0:2,0:16:1:29.6:1:1:0:26:14:1:0:1.4 -5 252166 . T A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17828;SOR=5.67833;LSEQ=GTTTCAGACCTGCCCTGTGG;RSEQ=GGAAATGCCAGTTTATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:11:1:24:1:1:1.15:32.5:1:0.0833:0:1.5 1/0:4:2:1,1:1,1:0.5:2,2:9:0:30.5:1:1:1:49:4:0.6667:0:3 -5 252200 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12308;SOR=8.40058;LSEQ=TATTAAATAACGAGTAAGCC;RSEQ=CTGTTTCAAACCTGCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:7,12:0.05:2,0:29:0:29:0:1:0:60:2:0.05:0:2 0/1:6:2:1,1:3,1:0.3333:2,2:43:0:32:1:1:2.44949:49:4:0.3333:0:3 -5 252255 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15993;LSEQ=TTTATTAACGAGTAAGTCAC;RSEQ=GTTTCAAACCTGTCCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:2,11:0.1765:2,2:31.3:1:31.3:1:0.48929:2.55:60:6:0.1765:0:1.3 0/1:10:2:2,0:4,4:0.2:2,0:27.5:1:30.5:1:0.46667:0:60:4:0.2:0:1.5 -5 252263 . A G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21739;SOR=Inf;LSEQ=CGAGTAAGTCACTGTTTCAA;RSEQ=CCTGTCCTGTGGAGGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:3,9:0:2,0:20.7:1:29.9:1:1:0:56.6:24:1:0:0.4 0/1:11:2:1,1:5,4:0.1818:2,2:21.5:1:34:0:1:1.22474:60:4:0.1818:0:3.5 -5 252315 . A G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGAATAAGCCACCGTTTCA;RSEQ=ACCTGCCCTGTGAAGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:25:1:31:1:1:0:60:8:1:0:0.5 0/1:11:2:1,1:2,7:0.1818:2,2:27.5:1:30.5:1:0.49091:3.06:60:4:0.1818:0:3.5 -5 252328 . A G 71 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25824;SOR=Inf;LSEQ=CGTTTCAAACCTGCCCTGTG;RSEQ=AGGAAATGCCAGTTTATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:25.3:1:30.7:1:1:0:60:6:1:0:0.3 0/1:11:5:2,3:1,5:0.4545:2,2:25.8:1:31:1:0.54545:2.97:54.8:10:0.4545:0:2.6 -5 252353 . G C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AATGCCAGTTTATTAAATAA;RSEQ=GAGTAAGCCACCGTTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:14.3:1:27:1:1:0:46.8:3:1:0:0.8 1/0:4:2:0,2:1,1:0.5:2,0:16:0:32:0:1:0:47:4:0.5:0:2 -5 252370 . C A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGGAGTAAGCCACCGTTT;RSEQ=AAGCCTGCCCTGTGGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:22.5:1:29:1:1:2.45:47:4:0.3333:0:1.5 0/0:1:0:0,0:1,0:0:0,0:21:0:33:0:1:0:59:2:1:0:0 -5 252594 . A G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TAAATAACGAGTAAGCCACC;RSEQ=TTTCAAACCTGCCCTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:30.5:1:31:0:1:1:34:4:0.4:0:2.5 0/0:3:0:0,0:2,1:0:2,0:18.3:1:26.3:1:1:0:50:6:1:0:0.7 -5 252683 . G T 28 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGAGGAAATGCCAGTTTA;RSEQ=TAACGAGTAAGTCACCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:14:1:28.5:1:1:0:56.5:4:0.5:0:2 1/1:1:1:0,1:0,0:1:0,0:19:0:29:0:1:0:60:2:1:0:1 -5 252764 . G A 18 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.77001;LSEQ=TAAGCCACCGTTTCAAACCT;RSEQ=CCCTGTGGAGGAAGTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:24:1:30:1:1:1.7321:56.5:4:0.4:0:2.5 0/1:6:2:1,1:1,2:0.3333:2,2:41:1:18:1:1:1.73:60:1:0.25:0:2.5 -5 252797 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=AGTGCCAGTTTATTAAATAA;RSEQ=GAGTAAGTCACCGTTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:11:1:30:1:1:1.7321:31.5:4:0.4:0:4 0/0:5:0:0,0:2,3:0:2,0:19.8:1:26.4:1:1:0:58:4:1:0:2.2 -5 252805 . T C 27 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.55247;LSEQ=TTTATTAAATAATGAGTAAG;RSEQ=CACCGTTTCAAGCCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:15.5:1:27.5:1:1:0:41.5:4:0.5:0:3 0/1:3:1:0,1:1,1:0.3333:2,0:2:0:15:0:1:0:60:0:0:0:2 -5 252866 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAATAACGAGTAAGTCAC;RSEQ=GTTTCATACCTGCCCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:31:1:31:1:1:1.83:31.5:4:0.25:0:5 0/0:3:0:0,0:2,1:0:2,0:35.7:1:31.3:1:1:0:60:6:1:0:0 -5 252873 . TA AG 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAGTAAGTCACCGTTTCA;RSEQ=CCTGCCCTGTGGAGGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:0.1818:2,2:39:1:33.5:1:1:1.22:31.5:4:0.1818:0:4 0/0:5:0:0,0:3,2:0:2,0:22:1:30.6:1:1:0:56.8:10:1:0:0.2 -5 252879 . C T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCACCGTTTCATACCTG;RSEQ=CCTGTGGAGGAAATGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:0.1818:2,2:44:1:32:0:1:1.22:31.5:4:0.1818:0:4 0/0:5:0:0,0:3,2:0:2,0:23.2:1:33.2:1:1:0:56.8:10:1:0:0.2 -5 252910 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGCCAGTTTATTAACGA;RSEQ=TAAGCCACCGTTTCAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:26:1:30.5:1:1:1.58108:31.5:4:0.2:0:4 0/0:4:0:0,0:2,2:0:2,0:21.8:1:32.3:1:1:0:56:8:1:0:0.3 -5 254035 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACATAAAAAATGAGCCAGG;RSEQ=GTGGTGGTAGCACAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:20:1:29.5:1:1:0:42.5:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 254271 . CT TC 89 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCTTAGGTACATAAAGGATG;RSEQ=TAAGGGAACATGCGGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:7,0:28,0:0.2:1,0:19.9:1:31.8:1:1:0:27:14:0.2:0.0286:2.9 0/1:5:1:1,0:4,0:0.2:0,0:45:0:30.5:0:1:0:25:2:0.2:0:3 -5 254297 . A G 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80603;LSEQ=GGAACATGCGGACATGGATT;RSEQ=CTGTGGACTCACTGCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:14:14,0:45,0:0.2373:1,1:23.9:1:33.2:1:1:0:27:28:0.2414:0:2.4 0/1:10:2:2,0:8,0:0.2:0,0:26.5:1:31:1:1:0:26:4:0.2:0:2.5 -5 254322 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.92716;LSEQ=GGACTCACTGCTGGCTGCAC;RSEQ=CCCCCTGGCCAGCCATGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:16:16,0:63,0:0.2025:1,1:30.4:1:29.9:1:1:0:27:32:0.2078:0:2.2 0/1:21:4:4,0:17,0:0.1905:1,0:19:1:29.8:1:1:0:26.5:8:0.1905:0:1.8 -5 254442 . C T 290 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34738;SOR=0;LSEQ=CTCTTAGATCATGTTAATGT;RSEQ=TGCTGTGTTTTTTCTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:836:836:641,195:0,0:1:0,2:20.2:1:29.9:1:1:0:34.3:68.667:1:0:1.1 1/1:445:444:322,122:0,1:0.9978:0,2:20.5:1:29.5:1:0.2764:0:35.2:221:1:0:1.1 -5 254599 . A T 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06262;SOR=1.33281;LSEQ=GAGGAAGCACACCCTGTCCT;RSEQ=TGTGGACGTTGGCACTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:861:153:34,119:265,443:0.1777:2,2:20.5:1:30.1:1:0.00035:2.09199:30.7:75.5:0.1772:0:1.1 0/1:389:87:14,73:112,190:0.2237:2,2:20.9:1:29.9:1:0.00015:3.06603:32.8:174:0.226:0:1.1 -5 254636 . C T 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAAGGTCAGTGTGGAGCT;RSEQ=GTTCTCACCACAGCCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:0:0,0:174,401:0:2,0:24.5:1:30:1:1:0:36.7:81.143:1:0:0.2 0/1:251:32:11,21:65,154:0.1275:2,2:18.8:1:28.2:1:0.68071:1.24:42.3:64:0.128:0:1.1 -5 254706 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.79122;SOR=0.78738;LSEQ=TGGCCTTGCTGATGGTGAAC;RSEQ=GGGAAGAGCAGGCCAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:14:4,10:22,292:0.0427:2,2:17.9:1:30.3:1:0.01808:5.26:35.1:28:0.0433:0:1.9 0/1:118:4:1,3:11,103:0.0339:2,2:16.5:1:28.5:1:0.35265:3.08:40.5:8:0.0339:0:2.5 -5 254711 . A G 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.7913;SOR=0.7569;LSEQ=TTGCTGATGGTGAACGGGGA;RSEQ=GAGCAGGCCAGATTTAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:15:4,11:12,283:0.0484:1,2:19.4:1:29.3:1:0.00462:8.44:40.9:14:0.0459:0:1.9 0/1:108:4:1,3:6,98:0.037:2,2:21.5:1:28.5:1:0.23813:5.28:40.5:8:0.037:0:2.5 -5 254756 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGACAGATTCGAGGCACC;RSEQ=CTGAAAAAGGCACTCCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:0,2:7,139:0.0134:1,0:35.5:1:31:0:1:0:60:4:0.0138:0:1 0/0:41:0:0,0:2,39:0:1,0:26.3:1:32.3:1:1:0:58.1:82:1:0:0.4 -5 254861 . C G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61483;SOR=0.57871;LSEQ=AAGGGTTGCTCCGTGGTGTG;RSEQ=GCCAGATGGACGTCACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:22:2,20:0,5:0.8148:0,2:28.5:1:30.5:1:1:0:49.7:44:0.8148:0:1 1/0:7:5:1,4:0,2:0.7143:0,2:22.4:1:31.6:1:1:0:43.4:10:0.7143:0:1.2 -5 254996 . T C 34 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=ACCAGAAACCAGTCCCACGT;RSEQ=AAGGGAGCCCAGAAGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:32.5:1:34:0:1:0:42.5:4:0.25:0:1 1/1:1:1:0,1:0,0:1:0,0:23:0:34:0:1:0:60:2:1:0:1 -5 255254 . AG A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCAGCCGAGGGTGTGGT;RSEQ=GGGGGTCGCAGCCTTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:32.5:1:1:0:52:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 256109 . G C 66 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CTGAGCATCCCTAATCGGAA;RSEQ=ATCTGACTCCATAGCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:26.5:1:33:1:1:0:44.3:8:1:0:2 0/0:1:0:0,0:1,0:0:0,0:45:0:30:0:1:0:50:2:1:0:0 -5 256121 . T C 64 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=AATCGGAAGATCTGACTCCA;RSEQ=AGCACATTTCTTTTGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:26.8:1:32.3:1:1:0:44.3:8:1:0:2 0/0:1:0:0,0:1,0:0:0,0:33:0:27:0:1:0:50:2:1:0:0 -5 256350 . A G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.38398;SOR=2.14733;LSEQ=AATCTTAAAGTTCACATGCC;RSEQ=TAAATCTACTTTTATAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:4:4,0:229,15:0.0161:2,0:17:1:31.8:1:1:0:32.3:8:0.0163:0:4.3 0/1:88:3:3,0:78,6:0.0341:2,0:16:1:31.7:1:1:0:33.3:6:0.0341:0:4 -5 256374 . T A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.57064;SOR=1.31638;LSEQ=ATCTACTTTTATAGTTAAAA;RSEQ=TTTTCAAAAGGAACACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:9:9,0:337,66:0.0218:2,0:26.1:1:31.4:1:0.36561:0:35.6:18:0.0221:0:3.4 0/1:175:5:5,0:140,30:0.0286:2,0:29.8:1:30.4:1:0.58952:0:36:10:0.0286:0:3.6 -5 256379 . C T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61344;SOR=1.34761;LSEQ=CTTTTATAGTTAAAATTTTT;RSEQ=AAAAGGAACACAAGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:12:11,1:358,95:0.0258:2,2:23.9:1:30.7:1:0.47395:2.91:36.8:24:0.0263:0:3.2 0/1:203:7:7,0:155,41:0.0345:2,0:27.6:1:30.3:1:0.34864:0:37.9:14:0.0347:0:3 -5 256392 . A T 142 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54169;SOR=0.71208;LSEQ=AATTTTTCAAAAGGAACACA;RSEQ=GAGATGGCTTTTTGTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:635:22:22,0:450,163:0.0346:2,1:19.9:1:32:1:0.00203:0:36.3:44:0.0354:0:2.7 0/1:281:7:7,0:203,69:0.0249:2,0:23.4:1:30.7:1:0.19909:0:35:14:0.0252:0:2.9 -5 256434 . ACT A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00013;SOR=1.93955;LSEQ=TTGTGCTTAACTTACCACTG;RSEQ=CTTCTTTTCAAGGTCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1180:76:53,23:678,424:0.0644:2,2:24.3:1:31.4:1:0.17896:1.44:39:152:0.0654:0.0144:1.7 0/1:645:76:50,26:347,221:0.1178:2,2:19.3:1:30.4:1:0.45375:1.22:39:152:0.1186:0.0403:1.8 -5 256472 . G A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00064;SOR=1.39784;LSEQ=ACTCTGGAATATAGACCCGT;RSEQ=ATCGACAAAACTTTGAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1400:333:176,157:552,512:0.2379:2,2:27.7:1:28.7:1:0.80154:1.04:52.8:110:0.2386:0:1.8 0/1:846:257:137,120:310,279:0.3038:2,2:29.9:1:28.5:1:0.8811:1.03:51:84.667:0.3035:0:1.7 -5 256509 . G A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00926;SOR=0.72523;LSEQ=ACGAGGCTGACTGTGCCACC;RSEQ=TCCCGCCAGCCATTCGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1296:245:103,142:460,590:0.189:2,2:25:1:30.3:1:0.66771:1.07484:58.3:80.667:0.1889:0:1.8 0/1:823:119:53,66:310,393:0.1446:2,2:23:1:29.1:1:1:1.02:59:28.75:0.1422:0:1.7 -5 256514 . G C 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=2.19449;LSEQ=GCTGACTGTGCCACCGTCCC;RSEQ=CCAGCCATTCGCTCCTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1244:55:15,40:516,667:0.0442:2,2:21:1:31.6:1:0.01762:2.06182:40.3:110:0.0445:0:2.2 0/1:781:72:27,45:309,396:0.0922:2,2:18.1:1:30.5:1:0.32023:1.30007:39.6:71:0.0923:0:2.3 -5 256548 . TG CA 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20895;SOR=1.67922;LSEQ=CCTACTGATGAGACAAGATG;RSEQ=GTGATGACAGAATCAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:899:12:0,12:288,598:0.0133:2,0:12.8:1:31.4:1:0.01201:0:34.8:24:0.0135:0.0056:2.6 0/1:540:12:3,9:191,336:0.0222:2,2:15.8:1:29.8:1:0.55078:1.70381:35:24:0.0225:0.0074:2.8 -5 256573 . A G 110 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2034;SOR=1.72615;LSEQ=ATGACAGAATCAGCTTTTGT;RSEQ=ATTATGTATAATAGCTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:13:0,13:155,440:0.0214:2,1:26.7:1:29.8:1:0.04646:0:37.4:26:0.0215:0:2.7 0/1:330:12:1,11:83,235:0.0364:2,2:22.6:1:29.8:1:0.30841:3.87426:39.3:24:0.0365:0:3 -5 256578 . T C 111 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27964;SOR=1.62597;LSEQ=AGAATCAGCTTTTGTAATTA;RSEQ=GTATAATAGCTCATGCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:14:0,14:138,419:0.0245:2,1:29.6:1:29.4:1:0.02733:0:36.4:28:0.0249:0:2.7 0/1:280:11:1,10:60,209:0.0393:2,2:27:1:29.2:1:0.46579:2.86296:40.6:22:0.0399:0:3 -5 256624 . G A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58035;SOR=0;LSEQ=TGTCATAACTGTCTTCATAC;RSEQ=CTTCTGCACTCTGGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:4:1,3:13,211:0.0175:2,2:24:1:31:1:0.22525:5.33:45.3:8:0.0178:0:1.5 0/0:90:0:0,0:9,81:0:2,0:22.4:1:31.5:1:1:0:52.7:29:1:0:0.5 -5 256662 . A G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34248;SOR=2.86048;LSEQ=AGAAGGAGTACATTGAAGGG;RSEQ=GATTGGCACCTAGTGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:3:0,3:4,97:0.0288:1,0:12:1:32.3:1:1:0:38.7:6:0.0291:0:2.7 0/1:38:3:0,3:6,29:0.0789:2,0:22.3:1:31.7:1:1:0:30:6:0.0811:0:2.3 -5 256673 . T C 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05132;SOR=9.31653;LSEQ=ATTGAAGGGAGATTGGCACC;RSEQ=AGTGGCTGGGAGCTTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:0,1:4,85:0.0111:1,0:6:0:34:0:1:0:40:2:0.0115:0:2 0/1:31:3:0,3:6,22:0.0968:2,0:11.3:1:34:0:1:0:30:6:0.0968:0:2.3 -5 256681 . GGGAGCTTGCCAGGAACCCAGTGGCCA G 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02296;SOR=Inf;LSEQ=GAGATTGGCACCTAGTGGCT;RSEQ=GGGAGCGTGGCACTTACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:4,69:0:2,0:25.1:1:31.1:1:1:0:59.1:146:1:0:0.1 0/1:30:3:0,3:6,21:0.1:2,0:23:1:31.2:1:1:0:30:6:0.1071:0.1:2.3 -5 257801 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCCACCCCCTGCCAGAG;RSEQ=ATTACTGTGAGCTCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 420898 . C T 71 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTCCAGAAAGAGACACCTC;RSEQ=GCGCTGCACGCACGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:3,2:0.5:2,2:20.4:1:30.6:1:1:2.41:60:10:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 420915 . GCCACGCAGCCACCCAC G 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGCGCTGCACGCACGCA;RSEQ=CCACGCAGCCACCCACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:3,2:8,2:0.3333:2,2:24.8:1:32.3:1:0.56044:2.48238:60:10:0.3333:0.1333:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 420932 . C G 36 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56804;SOR=2.39328;LSEQ=GCAGCCACGCAGCCACCCAC;RSEQ=CACGCAGCCACCCACCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:10,5:0.1667:2,2:7:0:23.3:1:0.52819:3.68244:60:2:0.125:0:2.3 0/1:6:2:2,0:2,2:0.3333:2,0:7:0:30:1:0.46667:0:60:4:0.3333:0:2 -5 420941 . C ACGCACAG 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.01869;SOR=Inf;LSEQ=CAGCCACCCACCCACGCAGC;RSEQ=ACCCACCCACGCAGCACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:21.3:1:29:1:1:0:60:6.333:1:0:1.5 0/1:9:3:2,1:3,3:0.3333:2,2:15:1:29.7:1:1:1.85:60:6:0.3333:0.2222:1.7 -5 420948 . C G 50 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=3.000;MSILEN=1;SSF=0.01177;SOR=16.95308;LSEQ=CCACCCACGCAGCCACCCAC;RSEQ=CACGCAGCACGCACAGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:1,0:14,10:0.04:2,0:7:0:32:0:1:0:60:2:0.0455:0:1 0/1:9:4:2,2:3,2:0.4444:2,2:21.5:1:25.3:1:1:1.43328:60:3:0.375:0:2 -5 420961 . A C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.45974;SOR=0.46833;LSEQ=CACCCACCCACGCAGCACGC;RSEQ=CAGACCCACGCACGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:16:7,9:9,2:0.5926:2,2:27.6:1:25.8:1:0.10902:5.4061:58.6:3:0.5455:0:2.3 0/1:10:4:2,2:3,2:0.4:2,2:32:1:31:1:1:1.43328:60:8:0.5:0:2.3 -5 421000 . A C 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.71968;SOR=0.68485;LSEQ=CACCCACCCACGCAGCACGC;RSEQ=CAGACCCACGCACGCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:3,4:10,9:0.2692:2,2:15.7:1:27.7:1:1:1.45919:60:6:0.25:0:3.1 0/1:15:3:2,1:6,6:0.2:2,2:13:1:26.7:1:1:1.91:60:2:0.1667:0:2.7 -5 421057 . A C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.50549;SOR=4.64888;LSEQ=GCACACGCAGCCACCCACCC;RSEQ=CACAGGCGCACATACGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:2,6:0.2727:2,0:13.3:1:31.3:1:1:0:60:6:0.3:0:1.3 1/0:3:2:1,1:0,1:0.6667:0,2:27.5:1:29.5:1:1:0:60:4:0.6667:0:1 -5 820725 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50183;SOR=0;LSEQ=GCTGCACTCCACTTTCTGGC;RSEQ=ATGGTGGAGACTCTGACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:17,24:0.0455:2,2:14.5:1:31.5:1:1:1.40:60:4:0.0488:0:1 0/0:34:0:0,0:13,21:0:2,0:27.3:1:31.4:1:1:0:60:68:1:0:0.3 -5 820789 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17787;SOR=Inf;LSEQ=GGGGGCTGTGATGTGGTCCC;RSEQ=TCCCAATGGAAAGTGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:19.5:1:29.5:1:1:0:60:12:1:0:0.2 0/1:10:2:1,1:3,5:0.2:2,2:10.5:1:32:1:1:1.58:60:4:0.2:0:1 -5 1096009 . C A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGTGCAGGTCCTTGGTG;RSEQ=GACCATGAGTGACTGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1097411 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51652;SOR=0;LSEQ=CCAACATCCTTCCCGTCGCC;RSEQ=CCAACACTCCCAGCAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:14,7:0.087:2,2:23:1:31:0:1:1.93655:60:4:0.0909:0:1.5 0/0:14:0:0,0:9,5:0:2,0:27.2:1:31:1:1:0:60:28:1:0:0.5 -5 1097446 . G A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49979;SOR=0.5099;LSEQ=AGAAGCAACCCCTGCTCACC;RSEQ=CAGCGTCTCCTCTGCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:6,6:6,3:0.5714:2,2:22.8:1:29.8:1:0.66049:1.9345:60:24:0.5714:0:1.2 0/1:15:6:3,3:5,4:0.4:2,2:22.5:1:29.7:1:1:1.23147:60:12:0.4:0:1.2 -5 1098903 . A C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCTCTGCTCACCCAGCC;RSEQ=CCCTCTAACCCTCTGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:6:0:33:0:1:1:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1098920 . T A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACCCTCTAACCCTCTGC;RSEQ=CACCCAGCCGCGTCCCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23:0:32:0:1:1:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1218114 . ATCCTGG TCC 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCAGAGTTGGCGCCTCC;RSEQ=CGCCTCCTCCCGCCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:0.5:2,2:10:1:31.9:1:1:1:60:6:0.5:0.3333:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1218135 . A T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGGCGCCTCCTCCCGCC;RSEQ=CCTCCCACCACCTCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:10:1:32:1:1:1:60:4:0.25:0:1.5 0/0:2:0:0,0:1,1:0:2,0:15:0:31.5:1:1:0:60:4:1:0:0.5 -5 1219654 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06143;SOR=Inf;LSEQ=GGGACATTCCTCATTGGCTT;RSEQ=ATCTTCACGCTGAACTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:72,60:0:2,0:26.9:1:31.3:1:1:0:60:25.4:1:0:0.2 0/1:44:2:1,1:21,21:0.0455:2,2:23:0:31:1:1:1:60:4:0.0476:0:1 -5 1219710 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCTGGACAGCTATGCCG;RSEQ=CTCCATTCCCCTGCTCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:29,47:0.0256:2,2:21:1:28.5:1:1:1.61:60:4:0.026:0:2 0/0:20:0:0,0:8,12:0:2,0:23.7:1:31.6:1:1:0:60:40:1:0:0 -5 1252950 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCATCATCCCTGCCACCC;RSEQ=GGCCAGGCCCTCCATCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:47:1:31:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:9:0:32:0:1:0:60:4:1:0:1.5 -5 1253641 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGCTGGACACTCAGCC;RSEQ=TTGGCTGGACACTCGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:2,0:52,2:0.0357:1,0:23.5:1:31.5:1:1:0:60:4:0.0364:0:1 0/0:13:0:0,0:10,3:0:2,0:20.3:1:32:1:1:0:60:26:1:0:0.1 -5 1253744 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19358;LSEQ=CCTCAGACTCCCAGCGGTGC;RSEQ=GGCCTGGGTGTGGGCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:119:117,2:129,3:0.4722:1,1:25:1:30.5:1:1:1.36:60:58.5:0.4718:0:1.1 0/1:68:10:7,3:53,5:0.1471:2,2:24.6:1:30.2:1:0.08754:4.39917:60:20:0.1493:0:1.1 -5 1253760 . CG C 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01082;SOR=Inf;LSEQ=GTGCGGGCCTGGGTGTGGGC;RSEQ=CCCCTCCCTCCCTGGGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:324,6:0:1,0:24.4:1:29.8:1:1:0:60:81.5:1:0:0.4 0/1:95:3:2,1:84,8:0.0316:2,2:29:1:26.7:1:0.26063:5.08942:59:6:0.0316:0.0105:1 -5 1253818 . C T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20494;SOR=3.2086;LSEQ=GGGCTGCTGGTGTCTGCTCT;RSEQ=GGCCTGGCTGTGGGCGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:875:3:0,3:685,187:0.0034:2,0:1:0:26.3:1:0.01011:0:60:6:0.0035:0:1 0/1:366:4:1,3:275,87:0.0109:2,2:12.3:1:23.5:1:0.04756:9.40931:60:3:0.0083:0:1.8 -5 1254034 . C T 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.02259;SOR=Inf;LSEQ=CGTGTGGGTGGCCGGGCAGG;RSEQ=AGGGCCTGCACCTCGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:0:0,0:94,552:0:2,0:24.1:1:31.8:1:1:0:60:45.143:1:0:0.1 0/1:256:3:1,2:46,205:0.0117:2,2:22.3:1:28:1:0.4602:2.22:60:6:0.0118:0:1.7 -5 1254201 . T C 29 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.01731;SOR=Inf;LSEQ=AGCAGCCAGGGAAGAGGCTG;RSEQ=GAGAGGACACAGGTCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:18,38:0:2,0:25.8:1:29.2:1:1:0:60:17.667:1:0:0.2 0/1:9:2:1,1:3,4:0.2222:2,2:12:0:29:1:1:1.29:60:4:0.25:0:1 -5 1254335 . T C 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02899;SOR=Inf;LSEQ=GACACCAGCGTTTAATCACA;RSEQ=AGGGCTGCCAGCGTGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:123,11:0:2,0:23.4:1:31:1:1:0:60:268:1:0:0.2 0/1:28:2:2,0:26,0:0.0714:1,0:39.5:1:30.5:1:1:0:60:4:0.0714:0:1 -5 1254358 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGCCAGCGTGGCTCCAG;RSEQ=CCCCCAGGGTCAGGCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:2,1:170,5:0.0168:1,2:33.7:1:25.7:1:0.09829:16.07729:60:2:0.0116:0:1.7 0/0:46:0:0,0:46,0:0:1,0:23.5:1:30:1:1:0:60:14.333:1:0:0.2 -5 1254360 . C A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCAGCGTGGCTCCAGGC;RSEQ=CCCAGGGTCAGGCCCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:3:2,1:176,6:0.0162:1,2:34:1:24:1:0.10985:13.99623:60:2:0.011:0:1.7 0/0:48:0:0,0:48,0:0:1,0:23.5:1:30.2:1:1:0:60:96:1:0:0.2 -5 1254681 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06485;SOR=Inf;LSEQ=AGCTCCCCTCCCAGGAGACA;RSEQ=CGGAAAGCTGCCCACACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:461:0:0,0:92,369:0:2,0:22.5:1:30.9:1:1:0:60:45.1:1:0:0.1 0/1:158:2:1,1:32,124:0.0127:2,2:15.5:1:28:1:0.37515:3.83:60:4:0.0129:0:2 -5 1255297 . C A 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04145;SOR=0;LSEQ=GGTTAAACCACTTCCTGATG;RSEQ=GAAAAGGGGTAAGAACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:13:13,0:149,5:0.0778:1,1:25.4:1:30.7:1:1:0:60:26:0.0802:0:1.1 0/0:53:0:0,0:50,3:0:2,0:22.4:1:32.2:1:1:0:60:52:1:0:0 -5 1255520 . G A 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13698;LSEQ=GGGAGCTGCAGCACACATGC;RSEQ=TGAAACCTGAGAGGATGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:792:338:116,222:154,298:0.4268:2,2:25.1:1:30.5:1:0.93975:1.01:60:83.5:0.4277:0:1.1 0/1:357:33:8,25:129,195:0.0924:2,2:26:1:29.2:1:0.09207:2.06344:60:66:0.0935:0:1.1 -5 1256585 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCCTCTGCCTGAGCCCCCC;RSEQ=TGTACCTCATCTCACCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30.5:1:1:0:25:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1260195 . T C 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTGGGACCCCGTCTCA;RSEQ=CCTGTAAGGAGTGGCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:31.2:1:28.8:1:1:0:60:5:0.7143:0:2.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1260515 . G A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.76891;SOR=1.29168;LSEQ=TCAGCCTTGCAGGCACGCGC;RSEQ=CACACACACACACACATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:9:7,2:357,55:0.0209:2,2:24.8:1:30.9:1:0.34981:1.85116:60:18:0.0216:0:0.8 0/1:186:5:5,0:146,27:0.0269:2,0:21.4:1:31:1:1:0:60:10:0.0275:0:1 -5 1260752 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07149;SOR=7.63457;LSEQ=AATGTCAGACACAGGTGCCT;RSEQ=CCCCACACCCAGCCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:1:1,0:131,456:0.0017:2,0:1:0:23:0:0.22449:0:60:2:0.0017:0:1 0/1:233:3:2,1:51,178:0.0129:2,2:11.7:1:25.7:1:0.13147:6.90:60:6:0.013:0:1 -5 1261052 . G A 62 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTGGAGCCCTGGCTCCC;RSEQ=GGCGTCCCTCGAGTGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:1,3:0.5:2,0:29.8:1:31.3:1:1:0:60:8:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1264152 . A G 87 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCCCCAGGGTCTCGGGTTC;RSEQ=GAGGGACTCATGCCCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:0.7273:0,0:32.1:1:29:1:1:0:60:16:0.7273:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1264465 . A G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.08694;SOR=Inf;LSEQ=GGTGGACGCAACGGCCCTGC;RSEQ=GCAGCACCTGCCCCAGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:391:0:0,0:364,27:0:2,0:22.6:1:30.3:1:1:0:60:64.167:1:0:0.1 0/1:164:2:1,1:144,18:0.0122:2,2:26.5:1:26:1:0.21891:7.81342:60:4:0.0123:0:1 -5 1265204 . C T 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGAGTTCCTGCTCAGGCG;RSEQ=GGGACCTGGCTGGGCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:14:1:30.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1265373 . G A 53 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCTGCGGCCTCTGCTGT;RSEQ=GCCCCGGGCGTCCCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:26.8:1:26.5:1:1:0:60:3:1:0:3.3 1/1:1:1:1,0:0,0:1:0,0:36:0:27:0:1:0:60:2:1:0:1 -5 1265935 . G A 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTTAAAACAAGCCCACC;RSEQ=GCTCTGTGGGGCGCCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:23.3:1:30.5:1:1:0:60:8:0.8:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1266310 . A G 127 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAAGAGCAGCAGGAGCC;RSEQ=GGTCACCGCCTGCACTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:21,2:0,0:1:0,2:21.5:1:28.2:1:1:0:60:10.5:1:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1266322 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGCCAGGTCACCGCCT;RSEQ=CACTCACCACGTGTGTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:28,1:0.0645:1,2:41.5:1:28.5:1:0.12688:20.14946:60:4:0.069:0:2 0/0:1:0:0,0:1,0:0:0,0:2:0:30:0:1:0:60:2:1:0:0 -5 1266713 . G T 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02147;SOR=Inf;LSEQ=TTTACGTAGTATCTGTCTAC;RSEQ=AGGGACTGAATGTCAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:0:0,0:129,453:0:2,0:24.4:1:30.6:1:1:0:60:71.75:1:0:0.1 0/1:225:3:1,2:48,172:0.0133:2,2:25:1:28.3:1:0.52677:1.79:60:6:0.0137:0:1.3 -5 1268552 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07731;SOR=Inf;LSEQ=ACAGAGCAGTCATGGTCTCC;RSEQ=GAGCACCAGGAATATTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:394,111:0:2,0:22.4:1:30:1:1:0:60:71.143:1:0:0.1 0/1:195:2:1,1:155,38:0.0103:2,2:11:1:29:1:0.36082:4.03928:60:4:0.0103:0:1 -5 1268768 . G A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0011;SOR=Inf;LSEQ=CCTGGGGCGGGAAGACACAG;RSEQ=TGAGAGACGGGCAGGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:937:0:0,0:338,598:0:2,0:25:1:31.5:1:1:0:60:61.4:1:0:0.1 0/1:446:6:4,2:164,276:0.0135:2,2:11.2:1:26.3:1:0.20443:3.36:60:12:0.0137:0:1 -5 1268866 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0597;SOR=Inf;LSEQ=CAAACGACACGTCTACCATT;RSEQ=AGCCGGCAAACACCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:7,177:0:1,0:24.4:1:32.3:1:1:0:60:91:1:0:0.2 0/1:60:2:1,1:7,51:0.0333:2,2:14:1:26.5:1:0.25085:6.88:60:4:0.0339:0:1 -5 1271084 . C A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01009;SOR=Inf;LSEQ=GGCCTCGGGAGCCTGCAGCC;RSEQ=AGGAGCCGGAGGGGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:64,3:0:1,0:26.3:1:30.8:1:1:0:60:32.5:1:0:0.2 0/1:8:2:1,1:6,0:0.25:0,2:14:1:31:1:0.25:0:60:4:0.25:0:1 -5 1271150 . GA G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGCAGAAGGGCAGTGGG;RSEQ=AGGGGCAGGAGAGAGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:166,21:0.0106:2,2:16.5:1:30.4:1:0.2198:7.7461:60:4:0.0108:0.0053:0 0/0:62:0:0,0:55,7:0:2,0:23.4:1:29:1:1:0:60:30:1:0:0.2 -5 1271247 . G A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00652;SOR=Inf;LSEQ=GACTCACTTGCCCCTGATGC;RSEQ=CACGGCGTGGTGGCACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:0:0,0:378,300:0:2,0:24.7:1:30.7:1:1:0:60:83.75:1:0:0.1 0/1:393:5:3,2:220,168:0.0127:2,2:22.6:1:29:1:1:1.15:60:10:0.0128:0:1 -5 1271524 . T C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0482;SOR=Inf;LSEQ=GCAGAGTGTGTGACACAGAA;RSEQ=GTCTCCTCTGGGCCACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:0,12:0,14:0.4615:1,0:26.3:1:28.9:1:1:0:60:24:0.48:0:1 1/1:5:5:0,5:0,0:1:0,0:18.8:1:31:1:1:0:60:10:1:0:2 -5 1272019 . C T 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00833;SOR=Inf;LSEQ=GGCCTCAAGATCAAAACTGG;RSEQ=AGAGAAGACATTTAGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:13,1:0:1,0:22.5:1:32.9:1:1:0:60:28:1:0:0.1 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 -5 1272414 . G A 226 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03292;LSEQ=ACCTGCCGGCAGAGGAGAGG;RSEQ=CATGAGCCACAAATGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:906:205:73,132:240,461:0.2263:2,2:25.9:1:29.5:1:0.73867:1.06:60:67.333:0.2262:0:1.1 0/0:420:4:3,1:159,257:0.0095:2,2:3.3:1:23:1:0.16203:4.83:60:3:0.0073:0:1 -5 1272688 . C CCA 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACGACCGCCATCCACAGTCA;RSEQ=CACATCAGACCCTACGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:15:0:32.3:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:0,1:0:0,0:5:0:33:0:1:0:60:2:1:0:0 -5 1273215 . A G 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCACACATCAGACCCCAC;RSEQ=ACCGCCATCCACAGTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:27:1:1:0:56.5:4:1:0:2.5 -5 1277720 . TG T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCGCTGCAGCGGGGATG;RSEQ=GGGGGGGGTCTCCTGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1278556 . CCA C 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACCATGGACACACACGTG;RSEQ=CACACACACACACCACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:2,0:37,0:0.0513:1,0:38:1:32:1:1:0:60:4:0.0513:0:0 0/0:13:0:0,0:12,1:0:1,0:16.9:1:30.9:1:1:0:60:26:1:0:0.1 -5 1278584 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56913;SOR=0;LSEQ=ACACACACCACAAATATGCA;RSEQ=GCCACAGATACATGCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:3,0:57,0:0.05:1,0:19.3:1:31:0:1:0:60:6:0.0526:0:1 0/0:20:0:0,0:19,1:0:1,0:28.7:1:31.6:1:1:0:60:40:1:0:0.1 -5 1278975 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07573;SOR=Inf;LSEQ=ACTCAGACATCACCTCTGCC;RSEQ=TCAGGGCCTGGCCTGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:39,281:0:2,0:22.9:1:32:1:1:0:60:63:1:0:0.1 0/1:122:2:1,1:10,110:0.0164:2,2:28.5:1:28:0:0.17288:10.54:60:4:0.0169:0:1 -5 1279224 . T G 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGGTGCACAGTCGGCCCCA;RSEQ=GTGCTGCAGGAAAGGCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:3,1:63,9:0.0526:2,2:21.3:1:33:1:0.43824:2.2996:60:8:0.0533:0:1 0/0:11:0:0,0:11,0:0:0,0:22.7:1:30:1:1:0:60:22:1:0:0.1 -5 1279637 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07911;SOR=Inf;LSEQ=AAGTGGATCCGGCCAAGTGC;RSEQ=CACCCCACCATAGGGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:89,361:0:2,0:23:1:30.8:1:1:0:60:44:0.9977:0:0.1 0/1:177:2:1,1:39,135:0.0113:2,2:19.5:1:28.5:1:0.4039:3.43:60:4:0.0113:0:1 -5 1279658 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06998;SOR=Inf;LSEQ=CACCCCACCATAGGGACCCA;RSEQ=GGGAGAAGCAGCCCCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:30,280:0:2,0:24.9:1:31:1:1:0:60:37.75:1:0:0.1 0/1:112:2:1,1:14,95:0.0179:2,2:19.5:1:27.5:1:0.25307:6.59:60:4:0.0182:0:1 -5 1279790 . C T 116 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37649;SOR=0.2696;LSEQ=CACACGGGATCCTCATGCCA;RSEQ=ACCTCTGTCCACCTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:16:3,13:2,19:0.4324:2,2:22:1:29.2:1:0.63386:2.15:60:32:0.4324:0:1.1 0/1:6:1:0,1:1,4:0.1667:2,0:38:0:30:0:1:0:60:2:0.2:0:1 -5 1279964 . G C 116 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAGCGGAAGCGCACGGAG;RSEQ=CTGCGCACCACAGCAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:9,3:7,3:0.5455:2,2:21.3:1:32.6:1:1:1.27:60:24:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1280128 . T C 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26836;SOR=0.6851;LSEQ=CGGCACCTCGGCCACCTCAC;RSEQ=GTGCGCACAAATGGGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:94:93,1:71,1:0.5663:1,1:21.8:1:30.8:1:1:1.31:60:30.333:0.5583:0:1.4 0/1:53:25:25,0:27,0:0.4717:1,1:21.6:1:30.3:1:1:0:60:24:0.4615:0:1.1 -5 1280180 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.07484;SOR=Inf;LSEQ=GCCCTGGCTGTGTCCCGTGG;RSEQ=CCCTCCTCCGGGCCCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:369,19:0:1,0:24.2:1:31.9:1:1:0:60:63.667:1:0:0.5 0/1:147:2:1,1:131,14:0.0136:2,2:16:1:26.5:1:0.1943:9.0743:60:4:0.014:0:1 -5 1280190 . G A 202 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTCCCGTGGCCCCTCCTCC;RSEQ=GGCCCTTCATCTAAGCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:107:94,13:329,40:0.2243:2,2:25.5:1:30:1:0.7276:1.13716:60:20.4:0.2189:0:1.4 0/0:192:0:0,0:158,34:0:2,0:23.1:1:28.9:1:1:0:60:37.4:1:0:0.2 -5 1280434 . G A 55 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03726;SOR=8.69921;LSEQ=TTCCGACAGCTCCCGCAGCT;RSEQ=CACCCTCTTCAAGTGCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:1:0,1:188,514:0.0014:2,0:16:0:32:0:1:0:60:2:0.0015:0:1 0/1:327:4:3,1:98,225:0.0122:2,2:14:1:27.8:1:0.08925:6.84:60:8:0.0125:0:1.3 -5 1280477 . G A 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00686;SOR=0.42505;LSEQ=CAATAGAGAGCCCCTCAGGA;RSEQ=GCTTGCTCAGCCAGACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:72:10,62:48,227:0.2075:2,2:23.6:1:31.2:1:0.59487:1.31:60:144:0.2149:0:1.1 0/1:130:13:3,10:18,99:0.1:2,2:22.8:1:30.2:1:0.44041:1.64:60:26:0.1008:0:1 -5 1280830 . G C 68 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CAGCCACTGGGGTAGCCCAA;RSEQ=GCTGGCCCCAGGCAGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:18.6:1:29.6:1:1:0:60:10:1:0:1.2 0/0:1:0:0,0:0,1:0:0,0:16:0:32:0:1:0:60:2:1:0:0 -5 1280938 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAGCAGAATCAGCTCTC;RSEQ=TGAGCCCACCAGTCTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1282319 . C A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.67224;SOR=1.72372;LSEQ=TGCTTTACAAACCCTAGAGA;RSEQ=CACTTGGCACAAACTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:16:15,1:14,0:0.5333:1,1:30.1:1:29.8:1:1:0:60:15:0.5172:0:1.1 1/0:6:4:4,0:2,0:0.6667:0,0:30:1:31:1:1:0:60:8:0.6667:0:1 -5 1282414 . G A 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.72932;SOR=0.84577;LSEQ=ACTTGGACCAGGCCTGTGAC;RSEQ=GGGCCCCTGGCTCCCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:73:73,0:58,1:0.553:1,1:21.7:1:29.6:1:0.44697:0:60:17.25:0.5391:0:1.1 1/0:45:23:23,0:22,0:0.5111:1,1:22:1:30:1:1:0:60:46:0.5111:0:1 -5 1282755 . C G 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=38.32331;LSEQ=AACCCCTTAAACGAGAAGGA;RSEQ=ATGCCACATCCAGATCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:1:1,0:193,486:0.0015:2,0:1:0:31:0:0.28529:0:60:2:0.0015:0:1 0/1:336:18:3,15:105,211:0.0536:2,2:25.1:1:31.8:1:0.19672:2.48248:60:36:0.0542:0:1.2 -5 1282778 . G A 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02858;SOR=Inf;LSEQ=GCCACATCCAGATCACCGAG;RSEQ=GCCTGGTGACCTCACCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:0:0,0:113,356:0:2,0:24.5:1:30.7:1:1:0:60:28.313:1:0:0.2 0/1:208:3:2,1:56,149:0.0144:2,2:11:1:27:1:0.1886:5.27:60:6:0.0149:0:1 -5 1282796 . C A 54 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24507;SOR=2.40224;LSEQ=AGGGCCTGGTGACCTCACCC;RSEQ=GGACCTGCACCATCCGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:4:4,0:58,279:0.0117:2,0:8.3:1:23.3:1:0.00101:0:60:3:0.0089:0:2.3 0/1:144:4:3,1:31,109:0.0278:2,2:13.3:1:27:1:0.04102:10.33:60:8:0.0282:0:1 -5 1283104 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=GCAGGGCCTGGCGACCTCAC;RSEQ=CCGGACCTGCACCATCCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:3,7:0.2308:2,0:28.3:1:32.7:1:0.52797:0:53.3:6:0.3:0:2.3 1/1:2:2:1,1:0,0:1:0,2:37.5:1:32.5:1:1:0:60:4:1:0:2 -5 1283841 . A C 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCGACCTCACCCCAGAC;RSEQ=TGCACCATGCAGACACCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:29:1:31.5:1:1:0:60:8:1:0:1 1/1:2:2:1,1:0,0:1:0,2:25:0:30:1:1:0:60:4:1:0:1 -5 1284046 . T C 58 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTGCAGCAACCGGACAC;RSEQ=GCACAACCAGCTCACCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:24.8:1:31.3:1:1:0:60:8:1:0:1 1/1:4:4:2,2:0,0:1:0,2:28.8:1:29:1:1:0:60:8:1:0:1 -5 1284554 . TCTGGCGACCTCACCCCGGACCGGCACCATCCGGACTCCATACATCCAGCTCACCGAGGGC T 86 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=2.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=ATATCCAGCTCACAGCAGGG;RSEQ=CTGGCGACCTCACTCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:34.9:1:30.8:1:1:0:44.3:14:1:1:4.3 0/0:1:0:0,0:1,0:0:0,0:5:0:32:0:1:0:60:2:1:0:0 -5 1284638 . C T 57 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0.17288;LSEQ=GCGACCTCACTCCAGACCTG;RSEQ=ACCATCCAGACACCGCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:33:1:28.8:1:1:0:52.5:8:0.8:0:5.5 0/1:3:1:1,0:1,1:0.3333:2,0:43:0:31:0:1:0:60:2:0.3333:0:4 -5 1284668 . C A 59 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=ACACCGCACATCCAGCTCAC;RSEQ=GCAGGGTCTGGCGACCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:33:1:29.5:1:1:1:52.5:8:0.6667:0:5.5 0/1:3:1:1,0:1,1:0.3333:2,0:25:0:28:0:1:0:60:2:0.3333:0:4 -5 1284697 . T G 46 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TGGCGACCTCACCCCGGACC;RSEQ=GCACCATCTGGACACTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:2,1:0.5:2,2:9.3:1:29.3:1:1:3.10575:50:6:0.6:0:6 0/0:3:0:0,0:2,1:0:2,0:19:1:29.7:1:1:0:60:6:1:0:0 -5 1284976 . C T 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.32198;LSEQ=CGCATATCCAGCTCACCGCA;RSEQ=GGTCTGGCACCGTCTGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:27.5:1:29:1:1:0:60:4:0.6667:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:17:0:31:0:1:0:60:2:0.3333:0:1 -5 1291331 . A AC 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTACACGTGACAGGGAC;RSEQ=CCTGGGGCCGCGCCTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24:1:30.7:1:1:0:37:4:1:0.5:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1291510 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGGACACCCGGGGACAG;RSEQ=GCCTCACTCACCCTGCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:1:28.5:1:1:0:51:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1291522 . C G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGACAGCGCCTCACTCAC;RSEQ=CTGCACGGGACAGGGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:37:1:31:1:1:0:51:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:7:1:29:1:1:0:60:4:1:0:2 -5 1291591 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACAGGGACACCCGGGGA;RSEQ=GGCGCCTCACTCACCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:60:4:1:0:2 -5 1291801 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACAGGGACACCCGGGGG;RSEQ=CGCGCCTCACTCACCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1292983 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=ATATTGGCTGACCACGTGCA;RSEQ=CTGCAAAACCCTTACCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:13.5:1:33.5:1:1:0:60:8:1:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:29:1:1:0:60:4:1:0:1 -5 1293389 . C G 226 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGAGCCCCTACTGCATTCAG;RSEQ=TCTGGGGCCTGGGCCCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:154:127,27:235,48:0.3524:2,2:22.4:1:31.2:1:0.89484:1.04073:60:153:0.355:0:1.1 0/0:154:0:0,0:124,30:0:2,0:25:1:31.9:1:1:0:60:37.5:1:0:0.2 -5 1293760 . G A 58 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02583;SOR=10.02299;LSEQ=GGGTGACCGCAGCTCGCAGC;RSEQ=GGCAGTGCGTCTTGAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:955:1:1,0:536,417:0.001:2,0:1:0:28:0:1:0:60:2:0.0011:0:1 0/1:384:4:2,2:211,167:0.0104:2,2:23:1:29:1:1:1.26269:60:8:0.0106:0:1.3 -5 1293833 . G A 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=CAGCTCCAGAAACAGGGGCC;RSEQ=CATTTGCCAGTAGCGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1583:0:0,0:801,781:0:2,0:24.5:1:30.8:1:1:0:60:74.333:0.9994:0:0.2 0/1:665:7:4,3:354,303:0.0105:2,2:14.6:1:29.4:1:1:1.14:60:14:0.0107:0:1 -5 1294086 . C T 279 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33306;SOR=1.09604;LSEQ=CGCGATGTGGATGGGGGGCC;RSEQ=GCGTGGTGCTGGCGGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1438:582:271,311:395,458:0.4047:2,2:26:1:30.4:1:0.95702:1.01:60:63.667:0.4055:0:1.2 0/1:733:313:154,159:193,223:0.427:2,2:24.9:1:29.9:1:0.455:1.12:60:51.167:0.4264:0:1.1 -5 1294166 . C T 136 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=13.85498;LSEQ=CAAAGAGGTGGCTTCTTCGG;RSEQ=GGGTCTGGCAGGTGACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1310:4:0,4:609,696:0.0031:2,0:15.3:1:29.5:1:0.12805:0:60:8:0.0031:0:1 0/1:638:26:12,14:286,326:0.0408:2,2:21.2:1:29:1:1:1.02348:60:52:0.0411:0:1.2 -5 1294664 . CG C 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.26651;SOR=3.92577;LSEQ=CACGCTGGTGGTGAAGGCCT;RSEQ=GGGGGGCCCCCGCGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:1,0:100,164:0.0038:2,0:25:0:33:0:0.38113:0:60:2:0.0038:0:0 0/1:136:2:1,1:54,80:0.0147:2,2:20.5:1:30:1:1:1.48:60:4:0.015:0:0.5 -5 1294671 . GC G 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=7.000;MSILEN=1;SSF=0.55395;SOR=0;LSEQ=GTGGTGAAGGCCTCGGGGGG;RSEQ=CCCCGCGGGCCCCGTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:1,2:89,147:0.0124:2,2:27.3:1:33.7:1:1:1.2099:60:6:0.0127:0:0.3 0/0:125:0:0,0:51,73:0:2,0:26.1:1:30.3:1:1:0:60:19.667:0.9916:0:0.2 -5 1294709 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53628;SOR=0;LSEQ=CAGCAGCGCGAAGCCGAAGG;RSEQ=CAGCACGTTCTTCGCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:49,99:0.0133:2,2:20.5:1:31:0:1:2.01:60:4:0.0134:0:1 0/0:85:0:0,0:32,53:0:2,0:21.7:1:31:1:1:0:60:41.5:1:0:0.1 -5 1294879 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53114;SOR=0;LSEQ=CCGGACGCCGACCCCGGGGA;RSEQ=GCCCACCTGGCGGAAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:74,73:0.0134:2,2:25.5:1:30:0:1:1.01361:60:4:0.0138:0:1 0/0:88:0:0,0:43,45:0:2,0:18.1:1:29.6:1:1:0:60:28.333:1:0:0.3 -5 1294906 . C T 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=1;SOR=0.62546;LSEQ=CTGGCGGAAGGAGGGGGCGG;RSEQ=GGGGGGCGGCCGTGCGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:1,2:94,114:0.0142:2,2:13:1:30.7:1:1:1.64538:60:6:0.0146:0:1 0/0:112:1:0,1:53,57:0.0089:2,0:39:0:27:0:1:0:60:2:0.0095:0:1 -5 1294920 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55504;SOR=0;LSEQ=GGGCGGCGGGGGGCGGCCGT;RSEQ=CGTCCCAGGGCACGCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:1,2:118,130:0.012:2,2:29:1:28:1:1:1.81125:60:6:0.012:0:1 0/0:137:0:0,0:62,74:0:2,0:25.8:1:30.7:1:1:0:60:16:1:0:0.4 -5 1294934 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30007;SOR=0;LSEQ=GGCCGTGCGTCCCAGGGCAC;RSEQ=CACACCAGGCACTGGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:129,147:0.0108:2,2:8:1:28.7:1:1:1.75171:60:6:0.0112:0:1 0/0:163:0:0,0:79,82:0:2,0:23.6:1:29.7:1:1:0:60:16.889:0.987:0:0.4 -5 1294954 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16019;SOR=Inf;LSEQ=GCACACCAGGCACTGGGCCA;RSEQ=CAGCGCGCGGAAAGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:116,135:0:2,0:24.2:1:31.4:1:1:0:60:49.2:1:0:0.4 0/1:168:2:1,1:81,85:0.0119:2,2:41.5:1:31:1:1:1.05:60:4:0.0123:0:1.5 -5 1294969 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57342;SOR=2.81169;LSEQ=GGCCACCAGCGCGCGGAAAG;RSEQ=CGCCGGGTCCCCGCGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:1:0,1:111,129:0.0041:2,0:1:0:30:0:1:0:60:2:0.0042:0:1 0/1:173:2:1,1:86,85:0.0116:2,2:39:1:28:1:1:1.0117:60:4:0.0121:0:1 -5 1294978 . C T 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.54624;LSEQ=CGCGCGGAAAGCCGCCGGGT;RSEQ=CCCGCGCTGCACCAGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:115,119:0.0127:2,2:14:1:24.7:1:1:1.92761:60:2:0.0088:0:3.7 0/0:144:1:0,1:73,70:0.0069:2,0:1:0:25:0:0.49306:0:60:2:0.0071:0:1 -5 1294987 . G T 49 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65229;SOR=0.37814;LSEQ=AGCCGCCGGGTCCCCGCGCT;RSEQ=CACCAGCCGCCAGCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:4:2,2:120,118:0.0164:2,2:24.5:1:24.5:1:1:1.01688:60:3:0.013:0:3.3 0/0:160:1:0,1:80,78:0.0063:2,0:1:0:23:0:0.49686:0:60:2:0.0066:0:1 -5 1294996 . G T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTCCCCGCGCTGCACCAGCC;RSEQ=CCAGCCCTGGGGCCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:122,115:0.0125:2,2:15.7:1:30:1:0.61418:2.11531:60:6:0.013:0:1.3 0/1:160:2:1,1:79,77:0.0125:2,2:28:1:30.5:1:1:1.02581:60:4:0.0129:0:1 -5 1295010 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16559;SOR=Inf;LSEQ=CCAGCCGCCAGCCCTGGGGC;RSEQ=CCAGGCGCCGCACGAACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:124,107:0:2,0:23.5:1:30.1:1:1:0:60:20:1:0:0.4 0/1:159:2:1,1:84,73:0.0126:2,2:28:0:32:1:1:1.14966:60:4:0.013:0:1.5 -5 1295045 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19653;SOR=Inf;LSEQ=AACGTGGCCAGCGGCAGCAC;RSEQ=TCGCGGTAGTGGCTGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:128,120:0:2,0:25.1:1:31:1:1:0:60:30:1:0:0.4 0/1:198:2:1,1:96,100:0.0101:2,2:32:0:32:0:1:1.04:60:4:0.0103:0:1.5 -5 1295048 . G T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63524;SOR=0.42734;LSEQ=GTGGCCAGCGGCAGCACCTC;RSEQ=CGGTAGTGGCTGCGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:127,119:0.012:2,2:6:1:23:1:0.61312:2.12816:60:2:0.0082:0:1.7 0/0:194:1:0,1:94,98:0.0052:2,0:1:0:28:0:1:0:60:2:0.0054:0:1 -5 1295061 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26318;SOR=0;LSEQ=GCACCTCGCGGTAGTGGCTG;RSEQ=GCAGCAGGGAGCGCACGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:3:1,2:123,119:0.0121:2,2:25:1:28.3:1:0.61887:2.06131:60:6:0.0125:0:1 0/0:186:0:0,0:89,97:0:2,0:26.3:1:30.4:1:1:0:60:45.5:1:0:0.4 -5 1295088 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1787;SOR=Inf;LSEQ=GGGAGCGCACGGCTCGGCAG;RSEQ=GGGGAGCGCGCGGCATCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:116,110:0:2,0:23.9:1:30.8:1:1:0:60:44.2:1:0:0.3 0/1:166:2:1,1:85,79:0.012:2,2:30:0:31:1:1:1.07545:60:4:0.0125:0:1.5 -5 1295093 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18243;SOR=Inf;LSEQ=CGCACGGCTCGGCAGCGGGG;RSEQ=GCGCGCGGCATCGCGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:117,109:0:2,0:22.3:1:30.1:1:1:0:60:24.111:1:0:0.3 0/1:169:2:1,1:86,81:0.0118:2,2:9.5:1:30.5:1:1:1.06138:60:4:0.0122:0:1.5 -5 1295110 . G C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13677;SOR=Inf;LSEQ=GGGAGCGCGCGGCATCGCGG;RSEQ=GGTGGCCGGGGCCAGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:126,110:0:2,0:17.1:1:31.1:1:1:0:60:46.2:1:0:0.3 0/1:139:2:1,1:70,67:0.0144:2,2:5.5:1:27:1:1:1.04446:60:4:0.0144:0:1.5 -5 1295117 . CG C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.13521;SOR=Inf;LSEQ=CGCGGCATCGCGGGGGTGGC;RSEQ=GGGCCAGGGCTTCCCACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:137,94:0:2,0:17.4:1:30.1:1:1:0:60:76:0.9913:0:0.3 0/1:136:2:1,1:74,60:0.0147:2,2:41.5:1:29.5:1:1:1.23141:60:4:0.0147:0:0 -5 1295123 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0517;SOR=Inf;LSEQ=ATCGCGGGGGTGGCCGGGGC;RSEQ=AGGGCTTCCCACGTGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:138,86:0:2,0:19.2:1:31.4:1:1:0:60:43.8:1:0:0.3 0/1:134:3:1,2:74,56:0.0224:2,2:8.7:1:26.7:1:0.5801:2.6238:60:6:0.0226:0:1.3 -5 1295127 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55802;SOR=3.41295;LSEQ=CGGGGGTGGCCGGGGCCAGG;RSEQ=CTTCCCACGTGCGCAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:1:1,0:153,85:0.0042:2,0:1:0:23:0:1:0:60:2:0.0043:0:2 0/1:141:2:1,1:81,58:0.0142:2,2:26.5:1:27.5:1:1:1.39317:60:4:0.0144:0:1 -5 1295161 . T C 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03631;SOR=Inf;LSEQ=CAGCAGGACGCAGCGCTGCC;RSEQ=GAAACTCGCGCCGCGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:287,119:0:2,0:23.3:1:30.6:1:1:0:60:24.375:0.9974:0:0.3 0/1:203:3:1,2:120,79:0.0148:2,2:39.7:1:23:1:0.56549:3.02108:60:2:0.0103:0:2.3 -5 1295250 . G A 234 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGCTGGGCCGGGGACCCGG;RSEQ=AGGGGTCGGGACGGGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1241:290:175,115:570,377:0.2337:2,2:25.8:1:28.7:1:1:1.01:60:16.059:0.2306:0:1.3 0/0:602:0:0,0:332,267:0:2,0:25.5:1:29.7:1:1:0:60:25.043:0.9948:0:0.4 -5 1295349 . A G 298 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17984;LSEQ=CAGTCCCTCCGCCACGTGGG;RSEQ=AGCGCGGTCCTGGGCGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1060:778:260,518:95,184:0.734:2,2:24.8:1:31.1:1:0.88258:1.02863:60:69.727:0.7361:0:1.2 0/1:501:166:67,99:135,199:0.3313:2,2:27:1:30.8:1:1:1.0024:60:82:0.3327:0:1.1 -5 1295373 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGGTCCTGGGCGTCTGTGC;RSEQ=CGCGAATCCACTGGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:690:0:0,0:200,488:0:2,0:23.5:1:30.8:1:1:0:60:42:0.9985:0:0.9 0/1:322:11:5,6:115,196:0.0342:2,2:26.1:1:29.1:1:0.54611:1.42:60:22:0.0347:0:1.5 -5 1295381 . C A 31 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11344;SOR=5.95407;LSEQ=GGGCGTCTGTGCCCGCGAAT;RSEQ=CACTGGGAGCCCGGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:1:1,0:134,417:0.0018:2,0:1:0:24:0:0.24457:0:60:2:0.0018:0:2 0/1:280:3:2,1:95,182:0.0107:2,2:16:1:20:1:0.27614:3.81:60:2:0.0073:0:2 -5 1336626 . T A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61782;LSEQ=TGCCCCTGTCCACCATCTCC;RSEQ=GAATGCCTGCAAGGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:5,6:7,3:0.5238:2,2:32.2:1:30.9:1:0.387:2.66125:60:22:0.5238:0:1.1 0/1:5:2:1,1:2,1:0.4:2,2:16:1:28.5:1:1:1.7321:60:4:0.4:0:1 -5 1563875 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCACACCCAGTTGAGGGCC;RSEQ=GGTAAAGCAGCACCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:5:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31:1:1:0:60:4:1:0:1.5 -5 1564675 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAGGAGGGGCCGCTCCT;RSEQ=GTGTCACAGGGGAGGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:28.5:1:1:0:60:4:1:0:1 -5 1572205 . T C 111 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.29177;SOR=0.25703;LSEQ=TCCCAGCCTGGGTGCCAATC;RSEQ=CCCTTCAATGTACTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:11:11,0:84,3:0.1122:1,0:9.6:1:32.2:1:1:0:30.8:22:0.1146:0:4.3 0/1:32:1:1,0:29,2:0.0313:2,0:9:0:31:0:1:0:25:2:0.0313:0:4 -5 1572216 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08041;SOR=Inf;LSEQ=GTGCCAATCTCCCTTCAATG;RSEQ=ACTCCTTCTTCCCCGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:117,3:0:1,0:23:1:30.2:1:1:0:52.5:119:1:0:0.6 0/1:48:2:2,0:44,2:0.0417:1,0:25.5:1:30.5:1:1:0:54.5:4:0.0417:0:1 -5 1572231 . G A 148 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26885;SOR=1.53156;LSEQ=CAATGTACTCCTTCTTCCCC;RSEQ=GAGTGCAGAAGCGTATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:27:27,0:139,6:0.157:1,1:20.9:1:31.2:1:0.59149:0:35:54:0.1588:0:4.1 0/1:72:16:16,0:53,3:0.2222:2,1:11.4:1:31:1:1:0:33.8:32:0.2222:0:3.7 -5 1572243 . C T 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29847;SOR=0.58134;LSEQ=TCTTCCCCGGAGTGCAGAAG;RSEQ=GTATGAAGACAGTTATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:25:23,2:196,12:0.1073:2,2:21.4:1:30.6:1:0.65112:1.41788:39.1:50:0.1087:0:3.8 0/1:92:6:6,0:80,6:0.0652:2,0:13:1:31:1:1:0:41.8:12:0.0659:0:3.7 -5 1572275 . A G 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54804;SOR=1.17212;LSEQ=GTTATGACATGGACACATGC;RSEQ=TGAGCTATTATACATAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:59:50,9:351,73:0.1211:2,2:24:1:30.6:1:0.85356:1.16:44.5:118:0.1227:0:2.8 0/1:230:32:24,8:161,36:0.1391:2,2:18.7:1:30.4:1:0.34484:1.48791:49.2:64:0.1397:0:2.3 -5 1572289 . A G 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=1.66226;LSEQ=ACATGCATGAGCTATTATAC;RSEQ=TAATTACAAAAGCTGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:665:195:142,53:360,110:0.2932:2,2:21.8:1:30.3:1:0.32252:1.22111:45.7:64:0.2922:0:2.7 0/1:338:138:103,35:149,50:0.4083:2,2:21.4:1:29.8:1:1:1.01259:46.3:45:0.403:0:2.7 -5 1572294 . T C 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.05305;LSEQ=CATGAGCTATTATACATAAT;RSEQ=ACAAAAGCTGATTCTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:732:110:82,28:449,173:0.1503:2,2:22.8:1:32:1:0.64476:1.13:45:220:0.1511:0:3.1 0/1:394:105:76,29:206,83:0.2665:2,2:20.5:1:30.5:1:0.89973:1.06:44.2:34:0.2636:0:3 -5 1572318 . C T 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=1.84474;LSEQ=AAAGCTGATTCTGTCATCAC;RSEQ=GCATCTTGTCTCATCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1095:178:107,71:583,334:0.1626:2,2:26.9:1:30.4:1:0.39678:1.15807:47.6:88:0.1637:0:2.4 0/1:637:168:103,65:283,186:0.2637:2,2:26.1:1:30:1:0.85435:1.04:48.1:41:0.2611:0:2.4 -5 1572397 . C T 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74643;SOR=1.08203;LSEQ=GTTCAAAGTTTTGTCGATTA;RSEQ=GGGTCTATATCCCAGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1104:59:14,45:461,583:0.0534:2,2:10.6:1:30.2:1:0.0018:2.53963:48.2:28.5:0.0525:0:1.7 0/1:660:38:10,28:267,354:0.0576:2,2:10.6:1:30.8:1:0.06124:2.10962:50.8:76:0.0582:0:1.3 -5 1572408 . C T 187 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02136;SOR=1.54361;LSEQ=TGTCGATTACGGGTCTATAT;RSEQ=CCAGGGTGACCATGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:935:71:9,62:361,500:0.0759:2,2:13.6:1:30.5:1:0:4.96702:39.8:70:0.0767:0:2.6 0/1:524:59:7,52:203,261:0.1126:2,2:17.5:1:29.4:1:0:5.76235:38.3:118:0.1132:0:2.6 -5 1572413 . G A 165 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01271;SOR=1.8319;LSEQ=ATTACGGGTCTATATCCCAG;RSEQ=GTGACCATGAAAAGAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:885:38:1,37:339,503:0.0429:2,1:19.7:1:31.6:1:0:24.89065:34.2:18:0.0419:0:3 0/1:487:37:2,35:193,256:0.076:2,2:20.9:1:31.4:1:0:13.15126:30.1:74:0.0776:0:2.9 -5 1572585 . A G 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAAAAATGATCTACATGC;RSEQ=CAACAGGGGACTGTAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:46:3,43:0,0:0.9787:0,2:22.6:1:32.3:1:1:0:56.1:92:1:0:1.2 1/1:12:12:0,12:0,0:1:0,0:21:1:30.2:1:1:0:56.6:11:1:0:1.1 -5 1574146 . A G 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57373;SOR=0;LSEQ=CCCAAAGCCCAACTGCTGTC;RSEQ=GAGTGCCTTTTTCAGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:4:4,0:126,10:0.0284:2,0:18.8:1:28:1:1:0:43.5:8:0.029:0:1.8 0/0:48:0:0,0:45,3:0:2,0:21.4:1:29.6:1:1:0:58.7:23:1:0:0.7 -5 1574162 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07554;SOR=Inf;LSEQ=TGTCAGAGTGCCTTTTTCAG;RSEQ=GGTGCCTCAAATCTGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:176,10:0:2,0:22.2:1:31.5:1:1:0:58:30:1:0:1 0/1:71:2:2,0:65,4:0.0282:2,0:14:1:30.5:1:1:0:60:4:0.0286:0:2 -5 1574171 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22352;SOR=1.79123;LSEQ=GCCTTTTTCAGCGGTGCCTC;RSEQ=AATCTGTCGGGAGTTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:14:14,0:204,11:0.0611:2,1:10.4:1:29.5:1:1:0:40.1:13:0.0591:0:1.2 0/1:86:9:9,0:73,4:0.1047:2,0:9.9:1:31.4:1:1:0:32.1:18:0.1059:0:1.1 -5 1574179 . C T 237 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00022;SOR=0.34801;LSEQ=CAGCGGTGCCTCAAATCTGT;RSEQ=GGGAGTTGATTTAAATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:282:243:232,11:37,2:0.8617:2,1:21.9:1:30:1:0.69722:1.14:58.8:33.714:0.8582:0:1.1 1/0:98:67:64,3:30,1:0.6837:1,1:25.7:1:29.9:1:1:1.40168:59.2:32.5:0.6771:0:1.1 -5 1574251 . G T 37 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01952;SOR=Inf;LSEQ=CAGCCCGCAGGCCTGGGCGG;RSEQ=GCCGTGTGGGTGCTGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:692:0:0,0:528,164:0:2,0:27.2:1:30.3:1:1:0:46.1:42.25:1:0:0.3 0/1:256:3:1,2:188,65:0.0117:2,2:17:1:23.7:1:0.16855:5.7365:53.3:2:0.008:0:1.3 -5 1574523 . TCCA T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11506;LSEQ=GCCCTAGAACTCATTCCATT;RSEQ=CTTCAGCCCAGGAGGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:255:235:0,235:0,19:0.9216:1,1:25.3:1:32:1:1:0:28.1:77.333:0.9317:0.1843:0.1 1/0:103:59:0,59:0,44:0.5728:1,1:23.3:1:31.9:1:1:0:27:118:0.5728:0.1165:0.1 -5 1576000 . C G 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00125;SOR=0;LSEQ=AATAAACTGGCATTTACTTC;RSEQ=TGGTCATGCCACTCTAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:19:17,2:170,10:0.0955:2,2:21.9:1:30.3:1:0.32066:1.99118:57.3:38:0.0969:0:1 0/0:86:0:0,0:72,14:0:2,0:24.2:1:30:1:1:0:58.9:20.5:1:0:0.1 -5 1576094 . G A 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGGCATCAGTGGATGCC;RSEQ=ACCCAAAGCAAGGAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:778:0:0,0:546,232:0:2,0:24.2:1:30:1:1:0:52.2:85.444:1:0:0.1 0/1:380:41:27,14:222,117:0.1079:2,2:20.1:1:29.7:1:1:1.02:51.3:82:0.1088:0:1.3 -5 1576118 . G A 97 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00097;SOR=7.01178;LSEQ=CAAAGCAAGGAAAAGGTCAC;RSEQ=GTGATCCAGAAGATGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1079:3:2,1:678,398:0.0028:2,2:6.3:1:31.3:1:1:1.17:25:6:0.0028:0:2 0/1:573:11:6,5:346,215:0.0192:2,2:24.3:1:28.3:1:0.7564:1.34035:22.7:10:0.0177:0:2.5 -5 1576166 . A G 148 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00105;SOR=2.99736;LSEQ=GGATCAAAGTTACCAGGGGG;RSEQ=AAAAGGGATTTTTTGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1688:14:8,6:940,722:0.0083:2,2:24.2:1:29.4:1:1:1.02:33.4:6:0.0073:0:2.6 0/1:981:24:12,12:545,410:0.0245:2,2:26.3:1:32.3:1:0.53499:1.32886:26.3:48:0.0252:0:2.5 -5 1576191 . C T 210 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=25.78259;LSEQ=GGGATTTTTTGGATTTACTT;RSEQ=TGGGGCAACGAAATAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1989:10:5,5:1074,903:0.005:2,2:10.5:1:27.2:1:1:1.18926:36:4:0.0041:0:2.5 0/1:1153:133:68,65:537,481:0.1154:2,2:23.2:1:29.8:1:0.78192:1.06709:56:132:0.1158:0:1.3 -5 1576317 . T A 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=85.89868;LSEQ=GTAGCCTTCCCTGGCGTGCG;RSEQ=GCCCCGTGACTCCTTCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1330:1:1,0:546,777:8e-04:2,0:1:0:25:0:0.41314:0:60:2:8e-04:0:1 0/1:690:42:22,20:290,353:0.0609:2,2:24.7:1:29.8:1:0.42453:1.34:59.2:84:0.0614:0:1.2 -5 1576408 . C T 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=2.59661;LSEQ=TCCAGGGTCTCCACCAGGTC;RSEQ=GTGTTCCAGACCATTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:607:29:16,13:164,414:0.0478:2,2:17.3:1:30.1:1:0.00329:3.10:32:28:0.047:0:1.3 0/1:286:33:17,16:63,189:0.1154:2,2:18:1:29.8:1:0.00319:3.17:34.3:66:0.117:0:1.4 -5 1576457 . C T 72 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0161;SOR=7.17166;LSEQ=AAAGTTCCATCAGGGGCAGG;RSEQ=GGGACCCAGTCACATGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:2:0,2:44,213:0.0077:2,0:10.5:1:31.5:1:1:0:40:4:0.0079:0:1 0/1:94:5:0,5:10,79:0.0532:2,0:28.8:1:31.2:1:1:0:40:10:0.0556:0:1 -5 1576458 . G A 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.31145;SOR=2.08864;LSEQ=AAGTTCCATCAGGGGCAGGC;RSEQ=GGACCCAGTCACATGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:7:0,7:49,206:0.0267:2,0:27.6:1:30.7:1:0.35406:0:27:14:0.027:0:1.4 0/1:92:5:0,5:10,77:0.0543:2,0:22:1:29.6:1:1:0:25.8:4:0.0444:0:2.6 -5 1576820 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10661;SOR=Inf;LSEQ=AAACTTTTAATCCATAGAAG;RSEQ=AGCCATATCAAGAACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:53,309:0:2,0:23.4:1:32.1:1:1:0:60:89.5:1:0:0.1 0/1:176:2:1,1:34,140:0.0114:2,2:33.5:1:30:1:0.35909:4.07:60:4:0.0116:0:1 -5 1576823 . C A 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60102;SOR=2.05206;LSEQ=CTTTTAATCCATAGAAGCAG;RSEQ=CATATCAAGAACTGCTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:2:0,2:44,291:0.0059:2,0:6.5:1:28.5:1:1:0:60:4:0.0061:0:1 0/1:165:2:1,1:32,131:0.0121:2,2:12:1:26.5:1:0.36098:4.05:60:4:0.0124:0:1 -5 1576828 . T C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0301;SOR=Inf;LSEQ=AATCCATAGAAGCAGCCATA;RSEQ=CAAGAACTGCTTAATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:30,269:0:2,0:24.1:1:30.1:1:1:0:60:36.375:1:0:0.1 0/1:136:3:2,1:20,113:0.0221:2,2:9.7:1:30.3:1:0.06798:10.98:56.3:6:0.0222:0:1.3 -5 1576843 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09736;SOR=Inf;LSEQ=CCATATCAAGAACTGCTTAA;RSEQ=TTTTAGACCTGTTGTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:5,221:0:1,0:24.4:1:30.4:1:1:0:60:112:1:0:0 0/1:103:2:1,1:10,91:0.0194:2,2:24:1:27.5:1:0.20312:8.73:54.5:4:0.0198:0:1.5 -5 1587545 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTAAACTGACAACCTTCCAG;RSEQ=GTGGGCATCATGGCCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:14.5:1:29:1:1:0:60:4:0.6667:0:1 -5 1587716 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08615;SOR=Inf;LSEQ=GTCAGCAGAAAAATCCCTTC;RSEQ=CCCAACGAAACACATTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:0:2,0:27.1:1:31:1:1:0:60:36:1:0:0.1 0/1:8:2:1,1:3,3:0.25:2,2:32.5:1:29.5:1:1:1:60:4:0.25:0:1 -5 1588404 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCACTCTCCCTCTCTTCC;RSEQ=AGTATATTTAGGGCCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1589387 . C G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCATGCTGAGTCGCAGTTCT;RSEQ=ATGTTCTTATGCTTCCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:943:0:0,0:612,330:0:2,0:24.3:1:31.4:1:1:0:57.9:116.75:0.9989:0:0.1 0/1:441:17:12,5:262,162:0.0385:2,2:29.2:1:31.9:1:0.61235:1.48:39.4:34:0.0386:0:1 -5 1589487 . CA C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.27601;SOR=1.67451;LSEQ=AGGGACTTTATCTCCTAAAA;RSEQ=AAAAAAAGCTAGAATTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1173:13:6,7:467,692:0.0111:2,2:27.9:1:31.4:1:0.77819:1.27:53.8:26:0.0111:0:0.1 0/1:597:11:2,9:255,331:0.0184:2,2:21.4:1:31.7:1:0.12628:3.46067:45.9:22:0.0186:0.0017:0.1 -5 1589751 . A G 104 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06593;SOR=0;LSEQ=AAACTAGAAATCATCTCTAA;RSEQ=ATTAAAAAATTAAATGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:16.4:1:31.6:1:1:0:41.4:20:1:0:1.1 1/0:4:2:0,2:0,2:0.5:0,0:30.5:1:32:1:1:0:39.5:4:0.5:0:1 -5 1593155 . CA C 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.57628;SOR=0;LSEQ=AGCCTGGGCTGACCCTTTCT;RSEQ=AAAAAAAGAAAAAAGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:4:2,2:279,45:0.0121:2,2:17:1:31.3:1:0.09981:6.14394:49.8:8:0.0122:0.003:0.3 0/0:112:0:0,0:87,23:0:2,0:19.4:1:29.9:1:1:0:48.5:220:0.9821:0:0.2 -5 1593166 . A T 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00486;SOR=Inf;LSEQ=ACCCTTTCTCAAAAAAAAGA;RSEQ=AAAAGACTTTCTAACTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:399,93:0:2,0:18.9:1:30.4:1:1:0:48.1:97.4:1:0:0.2 0/1:178:4:1,3:128,45:0.0225:2,2:10.3:1:26.3:1:0.06137:8.41091:50.5:8:0.0227:0:1.5 -5 1593189 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58413;SOR=1.15797;LSEQ=AAGACTTTCTAACTTCCTGC;RSEQ=CCTTCTCAAATAGTCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:45:25,20:620,157:0.0547:2,2:30.1:1:29:1:0.00052:3.15343:42.1:21.5:0.053:0:1.3 0/1:350:22:10,12:236,92:0.0629:2,2:32.8:1:29.6:1:0.01412:3.06686:47.8:44:0.0638:0:1.3 -5 1593208 . C G 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.20215;LSEQ=CGCCTTCTCAAATAGTCTGG;RSEQ=TCCTGAAGAAAACACTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1032:23:12,11:736,271:0.0223:2,2:24.5:1:32:1:0.03331:2.487:36.6:46:0.0226:0:3.2 0/1:480:42:21,21:293,143:0.0875:2,2:21.5:1:31:1:0.0279:2.04569:34.9:84:0.0886:0:3.3 -5 1593246 . C T 183 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=69.90565;LSEQ=ACCAGGCCTGCATGACTCTT;RSEQ=GATGCTCAGGGCACATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1454:2:0,2:903,549:0.0014:2,0:19:1:20:1:0.14344:0:46.5:1:7e-04:0:2.5 0/1:806:71:44,27:429,305:0.0881:2,2:22.8:1:29.9:1:0.61473:1.16:50.8:142:0.0902:0:2.3 -5 1593261 . A T 127 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=4.65796;LSEQ=CTCTTCGATGCTCAGGGCAC;RSEQ=TGCCTGACCAAAGACAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1576:8:3,5:912,656:0.0051:2,2:17.4:1:30.1:1:0.29156:2.31584:36.8:16:0.0051:0:3.4 0/1:861:20:10,10:476,365:0.0232:2,2:19.4:1:29.6:1:0.64998:1.30369:38.6:19:0.0223:0:3.4 -5 1593264 . C T 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=3.73297;LSEQ=TTCGATGCTCAGGGCACATG;RSEQ=CTGACCAAAGACAACCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1591:28:14,14:898,665:0.0176:2,2:16.3:1:29.9:1:0.44631:1.3501:40.1:56:0.0179:0:2.9 0/1:861:54:27,27:455,350:0.0627:2,2:17.9:1:29.4:1:0.39606:1.29959:37.5:108:0.064:0:3.1 -5 1593266 . T C 188 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=28.48695;LSEQ=CGATGCTCAGGGCACATGCC;RSEQ=GACCAAAGACAACCAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1599:6:1,5:909,684:0.0038:2,2:3.3:1:30.2:1:0.09052:6.63714:38:12:0.0038:0:2.2 0/1:866:84:47,37:441,341:0.097:2,2:29:1:29.5:1:1:1.01808:52.9:41:0.0959:0:2.4 -5 1593326 . G A 201 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=244.64651;LSEQ=GCCGATTGGCACCATGTACC;RSEQ=AGGCACAGGCGGCCTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1754:1:1,0:868,885:6e-04:2,0:1:0:16:0:0.49544:0:60:0:0:0:1 0/1:897:110:57,53:399,388:0.1226:2,2:25:1:29.7:1:0.83934:1.05:55.6:220:0.1236:0:1.7 -5 1593488 . CAG C 73 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.67198;SOR=0.44666;LSEQ=AGGGTGTCTGTGCTGCAGGT;RSEQ=AGAGAGAGGGAAGTAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:5:0,5:39,366:0.0122:2,0:25:1:31.7:1:1:0:51:10:0.0124:0.0024:0.4 0/0:183:1:0,1:13,169:0.0055:2,0:23:0:32:0:1:0:51:2:0.0055:0:0 -5 1593498 . G A 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGCAGGTCAGAGAGAGA;RSEQ=GGAAGTAGGCCCGGCGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:21,322:0:2,0:21.6:1:31.3:1:1:0:59.8:113.333:1:0:0.1 0/1:143:12:2,10:3,128:0.0839:1,2:19.5:1:30.8:1:0.05622:8.27:60:24:0.0845:0:1.1 -5 1593803 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCAAGAAAAAAAAAAAA;RSEQ=GGGAAGTAAAGACCGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26:1:31:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1594542 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08123;SOR=Inf;LSEQ=CGCCAGGCGCGGAGCGCTCA;RSEQ=CAGGCGCGACAGGACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:140,76:0:2,0:27.4:1:31.8:1:1:0:59.8:42.2:0.9953:0:0.2 0/1:87:2:1,1:51,34:0.023:2,2:35:1:27.5:1:1:1.4928:60:4:0.0235:0:2 -5 1594550 . G A 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGGAGCGCTCAGCAGGCGC;RSEQ=ACAGGACCCAGACCGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:141,83:0:2,0:28.1:1:30:1:1:0:60:55:0.9955:0:0.2 0/1:91:10:5,5:47,34:0.1099:2,2:25.5:1:31:1:0.73945:1.37735:60:20:0.1111:0:1.3 -5 1594565 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07977;SOR=Inf;LSEQ=GGCGCGACAGGACCCAGACC;RSEQ=CCATGCCTGTAGTCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:142,91:0:2,0:27.3:1:29.8:1:1:0:60:28.125:0.9912:0:0.2 0/1:93:2:1,1:50,41:0.0215:2,2:38.5:1:30.5:1:1:1.21689:60:4:0.0225:0:1 -5 1594577 . G A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.56577;SOR=0;LSEQ=CCCAGACCGCCATGCCTGTA;RSEQ=TCGCCTCCGCGCAGTCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:2,1:134,105:0.0124:2,2:18:1:27.7:1:1:1.56:60:6:0.0127:0:1 0/0:90:0:0,0:45,45:0:2,0:28.1:1:30.7:1:1:0:60:29:1:0:0.4 -5 1594664 . C G 192 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TTGGGGGGCAGGAACCGCGG;RSEQ=GGGTGGGATGCCGCGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:70:10,60:0,0:1:0,2:21.9:1:31.4:1:1:0:60:140:1:0:1.1 1/0:16:10:2,8:0,6:0.625:0,2:22.6:1:31.3:1:0.5:0:60:20:0.625:0:1.2 -5 1594879 . C G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATCGCCCAGACCGAAAGG;RSEQ=CCCGAACGTCCAGATCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 1595305 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGTGTGTCTTTTTGTAA;RSEQ=ATATCTGAAATCTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:28:1:1:0:24:4:1:0:1.5 -5 2739230 . T C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCGAGGGGACTCAACGCGCT;RSEQ=TGTAGGGCCTGTGAAATCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:1,5:0.3333:2,2:17.7:1:30.3:1:1:2.24:60:6:0.375:0:1.3 0/1:6:2:1,1:0,4:0.3333:0,2:36.5:1:31.5:1:0.33333:0:60:4:0.3333:0:1.5 -5 2740500 . TG T 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTGTTCCCTGACCTGCGAC;RSEQ=TTCGGTTCTCCCGACTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:18:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:17:1:32.5:1:1:0:60:4:1:0:0 -5 2958096 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGCAACCTGGAGCCTCT;RSEQ=GTGAAGCCACTGGCCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:28.5:1:1:0:60:4:1:0:2 -5 2958127 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCCTTCTGCCACCTTTT;RSEQ=CCCACACAACTTTATTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:32:1:1:0:60:4:1:0:2 -5 2979710 . G A 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41288;LSEQ=GCTAAGTTTAAAGCTAACAA;RSEQ=TATTTTTCTTTTTGCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:438:224,214:262,284:0.4442:2,2:25.4:1:30.4:1:0.33636:1.13:60:72:0.444:0:1.1 0/1:504:125:68,57:190,189:0.248:2,2:26.5:1:29.9:1:0.41163:1.19:60:250:0.25:0:1.2 -5 2979811 . T A 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08786;SOR=Inf;LSEQ=CGATAAGCACCTTAATCATA;RSEQ=TGTGTTTATTTCTGTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:54,269:0:2,0:22.9:1:30.3:1:1:0:60:79.75:1:0:0.1 0/1:137:2:1,1:27,108:0.0146:2,2:8.5:1:23.5:1:0.36818:3.95:60:4:0.0148:0:1.5 -5 2979827 . ATTTG A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0;SOR=0.2012;LSEQ=CATATTGTGTTTATTTCTGT;RSEQ=TTTGGCCTACTGAAGTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:85:8,77:13,117:0.3953:2,2:28.2:1:31.2:1:1:1.06913:60:170:0.3953:0.0512:0.2 0/1:95:11:2,9:7,77:0.1158:2,2:21.4:1:30.6:1:0.27856:2.41:60:22:0.1183:0.0316:0.1 -5 4089089 . G T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5535;SOR=0;LSEQ=TACTTCCTCTCTGACATCCA;RSEQ=GGGGCTGTAAAGCCTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:3:1,2:124,31:0.019:2,2:12:1:27:1:0.11079:7.85514:60:6:0.0194:0:1 0/0:73:0:0,0:52,20:0:2,0:22.4:1:30.5:1:1:0:60:23:0.9857:0:0.1 -5 4089094 . C T 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64832;SOR=1.48284;LSEQ=CCTCTCTGACATCCAGGGGG;RSEQ=TGTAAAGCCTCACTCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:0,3:132,44:0.0168:2,0:1:0:25:1:0.01725:0:60:6:0.017:0:1 0/1:81:2:1,1:54,25:0.0247:2,2:10:1:28:1:0.54167:2.13762:60:4:0.0256:0:1 -5 4089148 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28817;SOR=3.6525;LSEQ=AAAACCCAGCAGGGCAAAAA;RSEQ=CATGTCAGCAGAAAAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:1:0,1:195,161:0.0028:2,0:1:0:26:0:0.45378:0:60:2:0.0028:0:3 0/1:197:2:1,1:111,84:0.0102:2,2:30.5:1:29:1:1:1.31952:60:4:0.0105:0:1 -5 4089201 . T A 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99815;LSEQ=GGAGTAACAGGCACATGCCC;RSEQ=GCAAGGCTTCCCTGCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:180:75,105:75,90:0.5217:2,2:25.3:1:30.3:1:0.51487:1.16614:60:35:0.5162:0:2 1/0:188:98:44,54:45,45:0.5213:2,2:26.1:1:30.2:1:0.55898:1.22592:60:196:0.5269:0:2.1 -5 4089206 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12404;SOR=Inf;LSEQ=AACAGGCACATGCCCTGCAA;RSEQ=GCTTCCCTGCAAGAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:139,193:0:2,0:24.8:1:31.1:1:1:0:60:65.4:1:0:1.1 0/1:181:2:1,1:84,95:0.011:2,2:10.5:1:30.5:1:1:1.13:60:4:0.0114:0:1 -5 4089211 . C T 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45302;SOR=1.17089;LSEQ=GCACATGCCCTGCAAGGCTT;RSEQ=CCTGCAAGAAGGAAGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:166:65,101:68,91:0.5092:2,2:23.6:1:29.5:1:0.57274:1.16058:60:26.667:0.5016:0:2.1 1/0:175:96:41,55:38,41:0.5486:2,2:25.3:1:29.1:1:0.54214:1.24175:60:31:0.5439:0:2.1 -5 4089228 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.13702;SOR=Inf;LSEQ=CTTCCCTGCAAGAAGGAAGA;RSEQ=ACCCTTGCCTTTGTTGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:99,186:0:2,0:23.5:1:31.8:1:1:0:60:56:1:0:0.9 0/1:168:2:1,1:68,98:0.0119:2,2:44.5:1:28.5:1:1:1.44:60:4:0.012:0:3.5 -5 4089499 . A G 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGAAAGAGGATGTGGAC;RSEQ=GAAGTAGAACAGAACTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9:1:29:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:7:0:32:0:1:0:60:2:1:0:2 -5 4089547 . G A 30 d7;v4;MAF0.05;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGTAACACTTGGCTAAG;RSEQ=GTTTCACAAGGGTCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:36:0:30.5:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:46:0:27:0:1:0:60:2:1:0:2 -5 4089687 . C G 52 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTCCTTCTTTCCTTCTTT;RSEQ=TTTTTCTTTCTTTCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:19.7:1:33:1:1:0:60:6:0.75:0:1 1/1:1:1:0,1:0,0:1:0,0:46:0:33:0:1:0:60:2:1:0:1 -5 4112464 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCTCCACAAAGTGTCAG;RSEQ=GAATGGCCTGACTACATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 4114269 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12354;SOR=Inf;LSEQ=CCTGCGATAATTAAAATCTG;RSEQ=GTGTGGCCTCAGCTGATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:52,67:0:2,0:26.4:1:30.5:1:1:0:60:58.5:1:0:0.2 0/1:65:2:1,1:24,39:0.0308:2,2:16.5:1:29.5:1:1:1.61:60:4:0.0308:0:1 -5 4114285 . A G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00867;SOR=Inf;LSEQ=TCTGCGTGTGGCCTCAGCTG;RSEQ=TGTCTCACTCTTGAGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:35,64:0:2,0:20.9:1:30.3:1:1:0:60:98:1:0:0.2 0/1:45:4:1,3:13,28:0.0889:2,2:20:1:30:1:1:1.3832:60:8:0.0889:0:1.3 -5 4577774 . G T 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0947;SOR=6.59999;LSEQ=ATCAGCTTGTGCTGTCTGTT;RSEQ=ATTGGTGTTGTGCTGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:1:0,1:265,84:0.0029:2,0:10:0:30:0:0.24286:0:60:2:0.0029:0:1 0/1:161:3:1,2:116,42:0.0186:2,2:5.3:1:23.7:1:0.18154:5.45413:60:6:0.0188:0:2 -5 4577842 . G A 253 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.94899;SOR=0.98855;LSEQ=ACTTTGGTAGCAGCATATGT;RSEQ=TGTCAGTGAATGCTGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:724:419:212,207:151,153:0.5787:2,2:24.6:1:29.1:1:0.82148:1.04:60:51.375:0.5764:0:1.1 1/0:382:220:114,106:82,80:0.5759:2,2:24.7:1:28.5:1:0.83644:1.05:60:219:0.5763:0:1.1 -5 4577917 . TTTA T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.22856;SOR=2.70851;LSEQ=GCATGCAGGATCAGCTTCGT;RSEQ=TTATTATTATTATTAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:3:1,2:121,285:0.0073:2,2:25:1:30.3:1:1:1.18:60:6:0.0074:0.0024:0 0/1:204:4:1,3:63,136:0.0196:2,2:22.5:1:27.3:1:1:1.38762:60:8:0.0197:0.0049:0.5 -5 4577920 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.11342;SOR=Inf;LSEQ=TGCAGGATCAGCTTCGTTTT;RSEQ=TTATTATTATTATTAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:109,274:0:2,0:23.1:1:29.9:1:1:0:60:62.833:1:0:0.5 0/1:196:2:1,1:59,132:0.0102:2,2:27:1:29:1:0.52623:2.23:60:4:0.0105:0:1 -5 4577968 . A G 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40238;SOR=1.30988;LSEQ=ACAAGTCAAACCACAACTGC;RSEQ=CTTTGCTTAGAATCATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:164:83:4,79:11,70:0.5061:2,1:27.2:1:32.8:1:0.06124:3.08324:60:166:0.5123:0:1.1 1/0:75:43:7,36:3,29:0.5733:2,2:26.3:1:31.3:1:0.50168:1.86:60:42:0.5676:0:1.2 -5 4578107 . C T 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAACCTCATTACGAGTTCAG;RSEQ=TTAGATGCTTTCCATCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:0.6667:0,0:33.7:1:30.8:1:1:0:60:12:0.6667:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:27.5:1:29.5:1:1:0:60:4:0.6667:0:1 -5 5319835 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53007;SOR=0;LSEQ=ACCTGGAGCCACCGCCGGAG;RSEQ=CAGCGTCATCTCTAGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:22,18:0.0476:2,2:36:1:29.5:1:1:1.21636:60:4:0.0488:0:1 0/0:24:0:0,0:12,12:0:2,0:26.2:1:31.2:1:1:0:60:48:1:0:0.3 -5 5319934 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05455;SOR=Inf;LSEQ=ATTCCTGCTAAGGTGCTTCT;RSEQ=TCTCTTTCAGATTCATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:24.9:1:29.5:1:1:0:60:7:1:0:0.1 1/0:3:2:0,2:0,1:0.6667:0,0:9:1:30:1:1:0:60:4:0.6667:0:1 -5 5492597 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21364;SOR=4.74112;LSEQ=CAGCAAGTTCAATATTTAAG;RSEQ=AACATGAAATAGAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:1:0,1:217,45:0.0038:2,0:1:0:23:0:0.1749:0:60:2:0.0039:0:1 0/1:112:2:1,1:92,18:0.0179:2,2:21:1:28:1:0.31178:5.0019:60:4:0.0183:0:1 -5 5492635 . A T 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03822;SOR=Inf;LSEQ=AATTCATACCTGGACTTGGA;RSEQ=AGAACTGCACTGTAGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:375,192:0:2,0:25:1:29.9:1:1:0:60:93.5:1:0:0.3 0/1:289:3:1,2:184,102:0.0104:2,2:14.7:1:25.3:1:0.29462:3.59102:60:6:0.0105:0:1.3 -5 5492718 . A T 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.53311;LSEQ=AGACAGGGAACCTTAACTGG;RSEQ=GAGGTCGTCTGGGTGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:802:533:257,276:133,136:0.6646:2,2:24.7:1:29.4:1:0.765:1.05021:60:65.625:0.6662:0:1.2 1/0:479:246:124,122:122,111:0.5136:2,2:24.3:1:29.3:1:0.71468:1.08119:60:40:0.5128:0:1.1 -5 5493023 . AAAG A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAAAAGAGAAAGAAAA;RSEQ=AGAAAGGAAAGAGAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,0:0.2857:0,0:8:1:31.5:1:1:0:60:4:0.2857:0.1429:0 0/0:3:0:0,0:0,1:0:0,0:11:1:31:1:1:0:60:2:0.3333:0:0 -5 5493025 . AG GAA 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0.81844;LSEQ=AGAAAAAGAGAAAGAAAAAA;RSEQ=AGAAAGGAAAGAGAAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,0:0.7143:0,0:27:1:30.6:1:1:0:57.6:10:0.7143:0:1.8 1/0:3:2:1,1:0,1:0.6667:0,2:31.5:1:27.3:1:1:0:60:4:0.6667:0:1 -5 5493037 . GAGAA G 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=AGAAAAAAAGAGAAAGGAAA;RSEQ=GGAAGGAGGGAGGGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:27.3:1:31.3:1:1:0:57:8:0.8:0.2:2 0/0:2:0:0,0:1,1:0:2,0:23:1:27:1:1:0:60:4:1:0:1 -5 6482092 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09804;SOR=Inf;LSEQ=CCTGTGGCTGTGAATGTGAC;RSEQ=TTATTTGAAAATAGGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:21.7:1:31:1:1:0:60:24:1:0:0.1 0/1:6:2:2,0:4,0:0.3333:0,0:8.5:1:31:1:1:0:60:4:0.3333:0:1 -5 6482179 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53112;SOR=0;LSEQ=TCCCTAATCCAATGACTGGT;RSEQ=TCACTGTAAGAAGAGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:20,22:0.0455:2,2:34:1:30.5:1:1:1.10:60:4:0.0455:0:1 0/0:25:0:0,0:11,14:0:2,0:29.4:1:30.9:1:1:0:60:50:1:0:0.3 -5 6482233 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07977;SOR=Inf;LSEQ=ACAGATTCACAGAGAACACC;RSEQ=TATGGCAATGGAGGCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:2,17:0:2,0:21:1:32.3:1:1:0:60:38:1:0:0.1 0/1:8:2:0,2:1,5:0.25:2,0:12.5:1:32:0:1:0:60:4:0.25:0:1 -5 6622789 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACCAACATGGAGAAACCC;RSEQ=GTCTCTACTAAAAATACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:30:1:1:0:60:4:1:0:1 -5 6624371 . C T 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.03162;SOR=0;LSEQ=ATCCAAGGTTTTGATTAAAG;RSEQ=ATTAAGTAAGATGGGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:15:15,0:5,0:0.75:0,1:25.5:1:29.9:1:1:0:60:14:0.7368:0:1.1 0/0:3:0:0,0:3,0:0:0,0:40:1:27.7:1:1:0:60:2:1:0:0 -5 6624395 . G A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23298;SOR=3.441;LSEQ=AAGTAAGATGGGGACATCCC;RSEQ=GCAGACAGTAACCAGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:27,0:0.1:1,0:31.7:1:30:1:1:0:60:6:0.1:0:1 0/1:7:2:2,0:5,0:0.2857:0,0:8:1:31:0:1:0:60:4:0.2857:0:1 -5 6624458 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGCCAGCTTTCCATAAC;RSEQ=CAGAGGTTATTGCCATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:66,39:0.0187:2,2:21.5:1:29:1:1:1.68356:60:4:0.0189:0:1 0/0:48:0:0,0:29,19:0:2,0:25.4:1:30.4:1:1:0:60:47:1:0:0.1 -5 6624472 . C T 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67294;LSEQ=CATAACCCAGAGGTTATTGC;RSEQ=ATTCATCTCAAGAGCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:1,2:78,55:0.0221:2,2:5.7:1:21.7:1:0.57171:2.81467:60:2:0.015:0:3.3 0/1:67:1:0,1:38,28:0.0149:2,0:1:0:25:0:0.43284:0:60:2:0.0149:0:1 -5 6624481 . C A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTTATTGCCATTCATCT;RSEQ=AAGAGCTCTCATCACGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:91,66:0.0126:2,2:37:0:30.5:1:1:1.37594:60:4:0.0127:0:1.5 0/0:79:0:0,0:45,34:0:2,0:23.5:1:31:1:1:0:60:158:1:0:0.2 -5 6790378 . ATG A 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.22949;SOR=4.76337;LSEQ=GTGTGCGCGTGTGTGTTTGC;RSEQ=TGTGTGTGTGGGGGGCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:9,16:0.0385:2,0:38:0:32:0:1:0:60:2:0.04:0:0 0/1:12:2:1,1:5,5:0.1667:2,2:38:0:31.5:1:1:1:60:4:0.1667:0:0.5 -5 6790691 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGGTGTGGTGAGCTGTTC;RSEQ=TATGCAGGAGAGGGACGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 6830890 . C CACAT 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGCACGCACCATGCACACA;RSEQ=GCATGCACACATACACACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:20:1:32.5:0:1:0:60:4:1:0:0.5 1/1:3:3:1,2:0,0:1:0,2:20.3:1:30.3:1:1:0:55.7:6:1:0.3333:1 -5 6831048 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49872;SOR=0;LSEQ=ATGCACACGCACACACAGAC;RSEQ=CATTCTTACACATGCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,12:0.087:2,2:41.5:1:30.5:1:1:1.32:60:4:0.087:0:1 0/0:17:0:0,0:8,9:0:2,0:14.9:1:30.2:1:1:0:60:34:1:0:0.3 -5 6831103 . ACT A 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=ATGCACGCACACACAGGCAC;RSEQ=CTCACACGTGCACGCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:6,10:0.2:2,2:16:0:33.8:1:1:1.62:60:8:0.2105:0:0.5 0/1:25:5:4,1:9,12:0.2:2,2:19.4:1:27.2:1:0.32174:5.01:60:4:0.16:0.12:1.2 -5 6831147 . T C 70 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACACACATGCACGCACA;RSEQ=ACAGGCACACTCTCACACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:28:1:31.7:1:1:0:60:6:1:0:1 1/1:5:5:2,3:0,0:1:0,2:27.8:1:30.2:1:1:0:60:10:1:0:1.6 -5 6831571 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGACAAAATGGTAAAATGA;RSEQ=ATGCACACACCTCAGACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 7869455 . TC T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.11797;LSEQ=GGTTCCCACGCCCTTCGGCC;RSEQ=CGGGGGTCGCCGCGGGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:5:5,0:39,3:0.1064:2,0:27.2:1:33:1:1:0:60:10:0.1087:0:0 0/1:17:2:2,0:14,1:0.1176:1,0:21:1:32.5:1:1:0:60:4:0.1176:0:0 -5 7869518 . TC T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.05975;SOR=Inf;LSEQ=TTTGGCCTTTGGCTTTGGTG;RSEQ=CCCGGGAGCGTGTCCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:88,60:0:2,0:26.9:1:30.5:1:1:0:60:28.6:1:0:0.2 0/1:96:3:1,2:57,36:0.0313:2,2:6:1:25.8:1:0.56037:3.12803:60:6:0.0313:0.0208:0.3 -5 7869546 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51244;SOR=0;LSEQ=AGCGTGTCCTTGGGCTCGGC;RSEQ=TCGGCCTCTGCCGCGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:69,81:0.0132:2,2:30.5:1:30.5:1:1:1.17:60:4:0.0133:0:2 0/0:108:0:0,0:57,51:0:2,0:26.7:1:30.3:1:1:0:59.5:107:1:0:0.3 -5 7869578 . C T 104 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00015;SOR=20.03309;LSEQ=CGCGGGAGGCCCCTGGGCGG;RSEQ=GTGGGGTCTCTCCTCATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:1:0,1:39,68:0.0091:2,0:43:0:29:0:1:0:60:2:0.0096:0:1 0/1:70:11:5,6:25,34:0.1571:2,2:23.5:1:30.2:1:1:1.13:60:22:0.1571:0:1.1 -5 8181426 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAGCTCAAGGCAGGGGAAG;RSEQ=GACAGAGAAAGAACAAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 8182721 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10526;SOR=Inf;LSEQ=TAATGATTTTCATCATTTGT;RSEQ=GTCATTTTAAGCCTCAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:18,8:0:2,0:19.3:1:31.7:1:1:0:60:52:1:0:0.3 0/1:13:2:1,1:9,2:0.1538:2,2:25.5:1:27.5:1:0.42308:3.87298:60:4:0.1667:0:1 -5 8182785 . AC A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50506;SOR=0;LSEQ=GGTCAGAGTTTAGAGTCGCC;RSEQ=CCCCACCCGCCACCCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:18,26:0.0435:2,2:22.5:1:31.5:1:1:1.43:60:4:0.0435:0:1.5 0/0:34:0:0,0:18,16:0:2,0:23.1:1:31:1:1:0:60:68:1:0:0.8 -5 8182799 . C T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.97009;LSEQ=GTCGCCACCCCCACCCGCCA;RSEQ=CCAGCAGGTGCACTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:22:6,16:9,11:0.5238:2,2:23.2:1:29.8:1:0.33566:2.1407:60:21:0.5122:0:1.1 1/0:31:16:7,9:8,7:0.5161:2,2:26.6:1:29.5:1:0.72443:1.45111:60:32:0.5161:0:1.5 -5 8306347 . G A 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=8.000;MSILEN=1;SSF=0.52381;SOR=0.26566;LSEQ=CCCACCTGAGAGAGAGAGAG;RSEQ=GGGGGGCAGGGGAATCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:12.3:1:31.3:1:1:0:60:6:0.6:0:1 0/1:4:1:1,0:2,1:0.25:2,0:44:0:31:0:1:0:60:2:0.25:0:1 -5 8306754 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=TGCTGGAGCCAGGGAGGCTG;RSEQ=ACAGCTTGGTCCCAAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:21:0:30.5:1:1:1:60:4:0.1667:0:1.5 0/0:12:0:0,0:6,6:0:2,0:27.3:1:30.7:1:1:0:58.5:24:1:0:0 -5 8307486 . G GA 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AGAAGAAATAAAGAAAAGAA;RSEQ=AAAAAAAAAGGGAAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:13.3:1:31:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:28.7:1:1:0:60:4:1:0.5:0 -5 8452726 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAAGTCACATGGTTGGC;RSEQ=TGTAATGAAAGTACCTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 8453517 . CT C 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=1.29191;LSEQ=TCAAACGCTTTACCACATGA;RSEQ=TTTTTTAGACCATTATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:3:2,1:249,100:0.0085:2,2:30.7:1:32.7:1:1:1.24423:60:6:0.0088:0:0 0/1:182:2:1,1:130,50:0.011:2,2:17:1:29:1:0.48303:2.58427:60:4:0.0111:0:0 -5 8453614 . AG A 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TTTCAAACACTAATTATTCT;RSEQ=TCTAAGTTATAACCAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:698:0:0,0:336,359:0:2,0:26.2:1:31.8:1:1:0:60:114.833:0.9971:0:0.9 0/1:422:28:13,15:194,200:0.0664:2,2:29.9:1:29.5:1:0.84617:1.11893:60:56:0.0675:0:1.1 -5 8453623 . T C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13865;LSEQ=CTAATTATTCTAGTCTAAGT;RSEQ=ATAACCAGCTCATCTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:681:497:220,277:90,94:0.7298:2,2:25.7:1:31.5:1:0.2989:1.20517:60:123.25:0.7304:0:1.3 0/1:419:114:54,60:150,155:0.2721:2,2:24.8:1:30.9:1:0.82623:1.07507:60:113:0.2749:0:1.3 -5 8453697 . C T 245 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAGTCAGATGATTATAT;RSEQ=TGATCAGTGAACATGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:267:267:42,225:0,0:1:0,2:23.9:1:30.4:1:1:0:60:266:1:0:1.4 1/1:150:150:31,119:0,0:1:0,2:23.4:1:29.7:1:1:0:60:74:1:0:1.3 -5 8453897 . T C 120 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTTATTGTACATTTTG;RSEQ=TTTATTGAGTTTCACAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1:0,1:26.9:1:32.5:1:1:0:60:26:1:0:1.1 1/1:1:1:0,1:0,0:1:0,0:10:0:34:0:1:0:60:2:1:0:1 -5 8453932 . CAT C 86 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGATACTGTATTTTATATA;RSEQ=ATATATATATATATAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,2:0.6667:0,0:37.2:1:33.5:1:1:0:60:12:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 8726406 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2601;SOR=Inf;LSEQ=GCTGACCGGGTCGCACGCTG;RSEQ=CTCCGGCTTCACCAACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:23:1:31.7:1:1:0:60:54:1:0:0.3 0/1:38:3:2,1:17,18:0.0789:2,2:21.7:1:28.3:1:1:2.08:60:6:0.0833:0:1.7 -5 8726429 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53846;SOR=Inf;LSEQ=CCGGCTTCACCAACACCTTG;RSEQ=ATGTTGTTTCTGTGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:30.7:1:31.5:1:1:0:60:17:1:0:0.4 0/1:34:2:1,1:15,17:0.0588:2,2:21:1:28:1:1:1.13:60:4:0.0588:0:2 -5 9535516 . G C 127 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01915;SOR=0;LSEQ=AAGCTGCAACAGCCAAGATG;RSEQ=GCTGCCTGGACACGCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:9,10:0,0:1:0,2:26:1:30.1:1:1:0:60:18:1:0:1.2 1/0:8:5:3,2:2,1:0.625:2,2:18.6:1:30.6:1:1:1.28664:60:10:0.625:0:1 -5 9594749 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71643;LSEQ=TGGTGGAGGTGGAAGATCTT;RSEQ=ATCAAATATAGACGAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:5,2:0.2222:2,0:32.5:1:29:1:1:0:60:4:0.25:0:1 0/1:6:1:1,0:5,0:0.1667:0,0:3:0:28:0:1:0:60:2:0.1667:0:1 -5 11504369 . TTGC T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.62107;SOR=1.78321;LSEQ=CATGGTCAGGTCTAATGCTG;RSEQ=TGCTGCTGCTGCCGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:61,66:0.0155:2,2:25:0:32:0:1:1.08:60:4:0.0155:0:0 0/1:73:2:1,1:40,32:0.0274:2,2:15.5:1:29.5:1:1:1.2462:60:4:0.0278:0.0137:0.5 -5 11504409 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52394;SOR=0;LSEQ=GCTGCTGATGATGATGACGA;RSEQ=GATGACTCAGCGTAATGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:37,62:0.0198:2,2:34:1:32.5:1:1:1.67:60:4:0.02:0:1 0/0:63:0:0,0:27,36:0:2,0:25.3:1:29.7:1:1:0:60:62:1:0:0.2 -5 12856955 . A G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57426;SOR=0;LSEQ=TAACCGGTCAGGGATAGTAC;RSEQ=CAATGCTGCCCGGCCGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:4:3,1:47,12:0.0635:2,2:18.8:1:31.8:1:1:1.29966:60:8:0.0656:0:1.3 0/0:25:0:0,0:19,6:0:2,0:23.6:1:29.8:1:1:0:60:50:1:0:0.2 -5 12856961 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCAGGGATAGTACACAATG;RSEQ=TGCCCGGCCGGTGTTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:49,16:0.0299:2,2:19.5:1:32:1:0.44595:3.00121:60:4:0.0303:0:1 0/0:27:0:0,0:21,6:0:2,0:25:1:31.3:1:1:0:60:26:1:0:0.3 -5 12857026 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5394;SOR=0;LSEQ=TGCCTTTCAAACTCTTACAC;RSEQ=AACCTCTGGAGTTGGGCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:101,88:0.0105:2,2:22.5:1:30.5:1:1:1.1469:60:4:0.0105:0:1 0/0:106:0:0,0:52,54:0:2,0:30.5:1:30.8:1:1:0:59.9:212:1:0:0.2 -5 12858465 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAGCCTGACAATGAGA;RSEQ=AGAAAAGAAAAACTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:32:1:1:0:60:4:1:0:1.5 -5 14007036 . T C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACAATGAGCTCCACTC;RSEQ=GAGCCTCCAGTGGCCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:17.6:1:29.4:1:1:0:60:16:1:0:1 1/1:2:2:1,1:0,0:1:0,2:24.5:1:27:1:1:0:60:4:1:0:1.5 -5 14008995 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12131;LSEQ=GGTAAACAGAAAAAGAAAGC;RSEQ=TTCATTCCACCAGTTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:88:65,23:34,8:0.6718:2,2:23.5:1:30.5:1:0.50962:1.49931:60:176:0.6769:0:1.3 0/1:66:13:9,4:35,18:0.197:2,2:26:1:29.5:1:1:1.15:60:26:0.197:0:1.2 -5 14009018 . CT C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12192;SOR=Inf;LSEQ=CATTCCACCAGTTCTATGCC;RSEQ=TCACCCCATGCATCGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:131,47:0:2,0:26:1:30.8:1:1:0:60:58.333:1:0:0.8 0/1:96:2:1,1:63,31:0.0208:2,2:23.5:1:31:1:1:2.01612:60:4:0.0211:0.0104:0 -5 14009050 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1157;SOR=Inf;LSEQ=CATCGGGCCTGGCCATGGGC;RSEQ=GGGCCTGCCCCTGCAAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:141,85:0:2,0:25.5:1:30.3:1:1:0:60:36.667:1:0:0.7 0/1:117:2:1,1:70,45:0.0171:2,2:19.5:1:30.5:1:1:1.54946:60:4:0.0171:0:1 -5 14009079 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14051;SOR=Inf;LSEQ=CCCTGCAAGGACAGGACAAA;RSEQ=TGATCCATGTCCTGTCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:148,118:0:2,0:24.3:1:31.9:1:1:0:60:532:1:0:0.8 0/1:160:2:1,1:96,62:0.0125:2,2:31.5:1:28:1:1:1.54398:60:4:0.0125:0:1.5 -5 14009085 . C T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19412;LSEQ=AAGGACAGGACAAACTGATC;RSEQ=ATGTCCTGTCTCGAAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:282:159:86,73:68,55:0.5638:2,2:22.8:1:29.5:1:0.90413:1.04932:60:38.75:0.5596:0:1.3 0/1:175:35:20,15:82,58:0.2:2,2:18.2:1:29.5:1:1:1.05998:60:70:0.2023:0:1.3 -5 14009089 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15465;SOR=Inf;LSEQ=ACAGGACAAACTGATCCATG;RSEQ=CCTGTCTCGAAGCTGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:155,142:0:2,0:23.6:1:29.5:1:1:0:60:48.5:1:0:0.7 0/1:193:2:1,1:107,84:0.0104:2,2:40:0:32.5:1:1:1.27219:60:4:0.0106:0:1 -5 14009175 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52268;SOR=0;LSEQ=GGTAGGTAACTCACTCTTGA;RSEQ=TTGAAGCCGTCGGTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:64,129:0.0102:2,2:25.5:1:32:1:1:2.01:60:4:0.0102:0:1 0/0:126:0:0,0:42,84:0:2,0:22.3:1:30.7:1:1:0:60:252:1:0:0.1 -5 14761059 . C T 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTATCTAGCCATAAGGTCA;RSEQ=TGCAGATATAACTGGTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:32:0:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:48:0:28:0:1:0:60:2:1:0:2 -5 14761178 . T G 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGATGCACACAGGGAGAAC;RSEQ=CAGTGTGAAGATGAACGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:13,3:0,0:1:0,2:30.8:1:30.8:1:1:0:60:32:1:0:2 1/1:6:6:4,2:0,0:1:0,2:20.8:1:31:1:1:0:60:12:1:0:1.8 -5 14761194 . C G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACTCAGTGTGAAGATGAA;RSEQ=GCAGAAACCGGGGTGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:12,8:0,0:1:0,2:26.7:1:31.6:1:1:0:60:40:1:0:1.8 1/1:7:7:4,3:0,0:1:0,2:24.9:1:31:1:1:0:60:14:1:0:1.9 -5 14761303 . G C 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=AGTCTTCCTCATATCTCTCA;RSEQ=AAGGAACCGCCCCTGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:0:2,0:25.9:1:30.5:1:1:0:60:11:1:0:0 1/0:4:2:0,2:0,2:0.5:0,0:42:1:32:0:1:0:60:4:0.5:0:1 -5 14869666 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCATGATAATCAGGTTAG;RSEQ=AATGTTTTAAGGATGAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:3,0:30,1:0.0882:1,0:24:1:30.7:1:1:0:60:6:0.0909:0:1 0/0:10:0:0,0:9,1:0:2,0:23.4:1:32.3:1:1:0:60:20:1:0:0.4 -5 14869709 . A G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00653;SOR=3.73918;LSEQ=ATTATTAGACCTGCGAGGAT;RSEQ=AACCATCTGGATAGTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:20:19,1:63,2:0.2353:1,1:19.5:1:32.5:1:0.55776:1.64688:60:40:0.2381:0:1.1 1/0:26:14:14,0:12,0:0.5385:0,1:22.4:1:32.9:1:1:0:60:28:0.5385:0:1 -5 14869915 . A G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.80446;LSEQ=TATCTCGATATGATTCTTAC;RSEQ=TGCACACAAACACACACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:191:76,115:287,376:0.2237:2,2:23.1:1:30.7:1:0.40701:1.1548:60:62.667:0.2225:0:1.1 0/1:463:207:89,118:118,136:0.4471:2,2:25.5:1:30:1:0.51004:1.15001:60:40.4:0.444:0:1.1 -5 14870158 . G GGAA 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.56923;SOR=3.3097;LSEQ=GCGGGTACAGGGTGGAGCAG;RSEQ=GAAGAAGCCCTTGGGGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:1,4:0,6:0.4545:0,2:23.2:1:29.8:1:0.45455:0:60:10:0.5:0.0909:1.6 1/0:4:3:1,2:0,1:0.75:0,2:16.7:1:28.8:1:1:0:60:6:0.75:0.5:0.7 -5 14870166 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05714;SOR=Inf;LSEQ=AGGGTGGAGCAGGGAAGAAG;RSEQ=CCTTGGGGTACCCTTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:23.8:1:30.7:1:1:0:60:22:1:0:0 1/0:4:2:1,1:0,2:0.5:0,2:8:0:28:1:1:0:60:4:0.5:0:1 -5 14870691 . G C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGAACGCAGCTGCATCCC;RSEQ=CTGGTGGCCCTGCCAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:32:0:1:0:60:4:1:0:1.5 -5 16590934 . C CAT 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.5;SOR=Inf;LSEQ=AAAACACACAGACATGCAAA;RSEQ=ACACACATGCAAACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:38:1:33.3:1:1:0:60:6:1:0:0.3 0/1:6:2:1,1:3,1:0.3333:2,2:29:0:31:0:1:2.44949:60:4:0.3333:0:1 -5 16590956 . C CACAA 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.28613;SOR=4.35427;LSEQ=CACACATGCAAACACACATG;RSEQ=ACACACAAAAAACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:0.2857:2,0:17:1:29.1:1:1:0:60:4:0.2857:0.1429:0 1/0:6:4:3,1:1,1:0.6667:2,2:3.2:1:28.4:1:1:2.45:60:4:0.5494:0.5055:0.8 -5 16590985 . TAC T 48 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=1;SOR=0.84709;LSEQ=AAAACACACACATGCAAACA;RSEQ=ACACACACGCACACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:3,2:0.375:2,2:20.7:1:30.6:1:1:1.29:60:6:0.375:0.125:0.3 0/1:3:1:1,0:2,0:0.3333:0,0:30:0:31:0:1:0:60:2:0.3333:0:0 -5 16591013 . A C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12644;SOR=Inf;LSEQ=CACGCACACACACATGCACA;RSEQ=ACACAAAAAAACACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:13,6:0:2,0:16.6:1:28.7:1:1:0:60:18:1:0:0.2 0/1:11:2:1,1:4,5:0.1818:2,2:5:0:32.5:1:1:1.22:60:4:0.1818:0:1.5 -5 16591023 . A AC 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.76111;SOR=1.2435;LSEQ=CACATGCACAAACACAAAAA;RSEQ=ACACACACATGCAAATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:12:8,4:11,4:0.4444:2,2:15.8:1:31.5:1:1:1.3587:60:24:0.4615:0.2222:0.6 1/0:16:8:5,3:3,5:0.5:2,2:15.8:1:29.5:1:0.61927:2.60:60:7:0.4667:0.1875:0.9 -5 16591070 . GCA G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.10013;SOR=Inf;LSEQ=ACGCACATGCAAACACACAT;RSEQ=CACACACACATATTTGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:46,35:0:2,0:29.2:1:32.6:1:1:0:60:80:1:0:0.2 0/1:38:2:1,1:19,17:0.0526:2,2:39:1:31.5:1:1:1.11437:60:4:0.0541:0:0 -5 16591093 . C T 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03915;SOR=Inf;LSEQ=CACACACACATATTTGCTTG;RSEQ=CTCCATAGCACTTATTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:38,32:0:2,0:30.5:1:31.3:1:1:0:60:34:1:0:0.2 0/1:37:3:2,1:17,17:0.0811:2,2:44:1:29.3:1:1:1.96:60:6:0.0811:0:1.3 -5 17463005 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGGTTATTCTAGTTAGC;RSEQ=ATTCCTCTAACCTTTTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 17463384 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATGGTCAGGTCCTTCCG;RSEQ=AGGGCTGCTGCAGTTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:0.0952:2,2:12.5:1:32.5:1:1:1.10554:60:4:0.0952:0:1 0/0:10:0:0,0:6,4:0:2,0:26.3:1:28.8:1:1:0:60:20:1:0:0.4 -5 17463669 . TG T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=GTGAAGGGGTTGTGCTTCTC;RSEQ=GGGGGGAACCCACTTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,1:0.7143:2,2:22.4:1:31.6:1:1:1.41418:60:10:0.7143:0.1429:0.2 1/1:6:6:1,5:0,0:1:0,2:22.8:1:31.4:1:1:0:60:12:1:0.1667:0 -5 17464034 . C T 78 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCCACCCAGGGAGCTTC;RSEQ=GTGTTAGGCAGTTGCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:24.5:1:30.5:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 17491212 . A G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCCACTTGACACTAGT;RSEQ=CCTTGGGAGCCTCAAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1:0,2:20.5:1:32.3:1:1:0:60:20:1:0:1.6 1/1:6:6:5,1:0,0:1:0,2:21.7:1:30:1:1:0:60:12:1:0:1.3 -5 17491269 . T C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCACACACAAACACAAC;RSEQ=GCCACCTGATTTCTGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:23,1:0,0:1:0,1:26.8:1:31.9:1:1:0:60:48:1:0:1.3 1/1:9:9:5,4:0,0:1:0,2:19.6:1:31:1:1:0:60:18:1:0:1.2 -5 17491448 . T A 194 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTCCTCTAGAGTGCAAGGT;RSEQ=TCCCAGGAGCGTGGGCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:114:95,19:317,45:0.2395:2,2:23:1:28.4:1:0.27078:1.40781:60:113:0.2399:0:1.1 0/0:263:0:0,0:215,48:0:2,0:23.7:1:29.8:1:1:0:60:86.667:1:0:0.1 -5 17491617 . G A 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66138;SOR=0.9099;LSEQ=TGCAGGGCGCCAATGGCCGC;RSEQ=CTCTGGAAGCGCAGGTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1174:104:5,99:469,600:0.0886:2,1:22.3:1:30.3:1:0:15.4567:28.2:51:0.0889:0:1.3 0/1:640:52:4,48:280,308:0.0813:2,2:17.7:1:29.9:1:0:10.87931:29:104:0.0825:0:1.2 -5 17491627 . C T 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.03133;LSEQ=CAATGGCCGCGCTCTGGAAG;RSEQ=GCAGGTCCGGGCTGATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1126:38:15,23:425,662:0.0337:2,2:27.2:1:29.2:1:1:1.02:48.2:37:0.0336:0:1.9 0/1:595:57:16,41:227,311:0.0958:2,2:23.9:1:29.6:1:0.04679:1.86852:50.4:114:0.0969:0:1.6 -5 17491659 . A G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.48039;LSEQ=CTGATGGCCTGGGCGATCTC;RSEQ=CGCACCAGACGCTGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:920:406:155,251:221,290:0.4413:2,2:27.2:1:30.6:1:0.13699:1.23377:40.8:32.833:0.4383:0:1.2 1/0:477:372:146,226:44,61:0.7799:2,2:28.5:1:30.7:1:0.65238:1.11629:40.7:73.4:0.7792:0:1.2 -5 17502240 . C T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=0.20977;LSEQ=CAATGGTAGCGCTCTGGAAG;RSEQ=GCAGGACCAGGATGATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:37:31,6:39,17:0.3978:2,2:23.4:1:29.9:1:0.14603:2.23:60:36:0.4091:0:1.1 0/1:58:7:6,1:34,17:0.1207:2,2:20.3:1:31.3:1:0.41714:2.95:60:14:0.125:0:1 -5 17502275 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18319;SOR=Inf;LSEQ=ATGGCCTAGGAGATCTTGCG;RSEQ=ACCAGGCGCTGGAAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:87,58:0:2,0:25.9:1:31.8:1:1:0:59.9:71.5:1:0:0.3 0/1:109:2:1,1:58,49:0.0183:2,2:18:1:28:1:1:1.18183:60:4:0.0185:0:1 -5 17502349 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15895;SOR=Inf;LSEQ=CTTTCTGATTTCGCACATTG;RSEQ=CAGGCCTGTAGCGGTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:52,86:0:2,0:24.9:1:31.4:1:1:0:60:137:1:0:0.1 0/1:92:2:1,1:40,50:0.0217:2,2:12.5:1:30:1:1:1.25:54.5:4:0.0217:0:1 -5 17502359 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13736;SOR=Inf;LSEQ=TCGCACATTGCCAGGCCTGT;RSEQ=GCGGTGAGGCTTCTTGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:50,85:0:2,0:23.6:1:29.6:1:1:0:59.9:44:1:0:0.1 0/1:80:2:1,1:31,47:0.025:2,2:45:1:31:1:1:1.51:60:4:0.0256:0:1 -5 17502367 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53394;SOR=0;LSEQ=TGCCAGGCCTGTAGCGGTGA;RSEQ=GCTTCTTGATCCCTCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:40,78:0.0167:2,2:21.5:1:29.5:1:1:1.94:60:4:0.0172:0:1 0/0:69:0:0,0:28,41:0:2,0:23:1:30:1:1:0:60:22:1:0:0.2 -5 17502472 . G T 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCTGGCTGTTGGCTTGG;RSEQ=GCATGCAGTGGCCTGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:1,17:0,0:1:0,1:30.2:1:29.7:1:1:0:56.8:17:1:0:1 1/1:14:14:0,14:0,0:1:0,1:22.2:1:30.8:1:1:0:57.8:28:1:0:1.1 -5 17602802 . C G 108 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.71352;LSEQ=ACAACACAGCAAAAGAGAAA;RSEQ=CATTAACAGAGAAAAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:10,0:7,0:0.5882:0,0:26.6:1:32.6:1:1:0:60:20:0.5882:0:1 1/0:2:1:1,0:1,0:0.5:0,0:13:0:33:0:1:0:60:2:0.5:0:1 -5 17602891 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05268;SOR=Inf;LSEQ=GGGCTCTTAAGCACCCTCTC;RSEQ=ACGGAGGCTGTGGGCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:24,26:0:2,0:22.5:1:31.4:1:1:0:60:100:1:0:0.1 0/1:31:3:2,1:18,10:0.0968:2,2:16.3:1:28.7:1:1:1.11:60:6:0.1:0:1 -5 17604343 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGTGCACACCCAGGGAGC;RSEQ=TCACAGCCCAGACCTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 17620724 . GT G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51332;SOR=0;LSEQ=CTGGCATGGATGACATACAG;RSEQ=TGGTGTCTTCAAAGAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:97,81:0.0111:2,2:29:1:31.5:1:1:1.19632:60:4:0.0112:0:0 0/0:127:0:0,0:67,60:0:2,0:25.4:1:29.6:1:1:0:60:41.333:1:0:0.1 -5 17620755 . G A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28483;SOR=0;LSEQ=CAAAGAGGCGCACCAGGTAG;RSEQ=CCTCATTGGTCCCCTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:3:3,0:82,82:0.018:2,0:14.3:1:21:1:0.24573:0:60:2:0.0122:0:1.3 0/0:106:0:0,0:52,54:0:2,0:27.9:1:31.1:1:1:0:60:52:1:0:0.1 -5 17620777 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18877;SOR=Inf;LSEQ=CTCATTGGTCCCCTGAAAGC;RSEQ=CCAACGGCCACGCTCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:58,65:0:2,0:23:1:29.8:1:1:0:60:122:1:0:0 0/1:95:2:1,1:43,50:0.0211:2,2:21.5:1:30.5:1:1:1.16:60:4:0.0213:0:1 -5 17620793 . TG T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50741;SOR=0;LSEQ=AAGCACCAACGGCCACGCTC;RSEQ=GAAGCCCAGGTCCCGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:45,62:0.0183:2,2:11.5:1:30:1:1:1.37:60:4:0.0187:0:1 0/0:82:0:0,0:36,46:0:2,0:24.3:1:29.9:1:1:0:60:26.333:1:0:0 -5 17625684 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCTCTCTGCCGAGTTGG;RSEQ=AGGCCAGCTGCATGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:8,1:0.1818:2,2:22:1:27.5:1:0.34545:6:60:4:0.1818:0:1.5 0/0:3:0:0,0:2,1:0:2,0:22.3:1:33.3:1:1:0:60:6:1:0:0.7 -5 17625744 . T C 111 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=TGGCATGGATAACACATAGG;RSEQ=TGATGTCTTTAAAGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:7,4:0,0:1:0,2:25.3:1:32.3:1:1:0:60:22:1:0:1.1 1/0:5:3:2,1:2,0:0.6:0,2:8:1:31.7:1:1:0:60:6:0.6:0:1 -5 17655069 . AGCTGAAGT A 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTTGAAAATTGATGTAG;RSEQ=GCTGAAACTCGCTCACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:36,2:0,0:1:0,2:22.8:1:32.1:1:1:0:59.7:76:1:0.2632:0.3 1/1:3:3:3,0:0,0:1:0,0:28:1:32:1:1:0:60:6:1:0:0 -5 17655339 . C T 277 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43325;LSEQ=AGGTTGGTGTCTTCAAAGAG;RSEQ=TGCACCAGGTAGGCCTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:637:634:289,345:0,1:0.9953:0,2:25.4:1:29.8:1:1:0:40.1:78.25:0.9968:0:1.1 1/1:304:303:131,172:0,0:0.9967:0,2:25.3:1:29.9:1:1:0:40.8:150.5:1:0:1.1 -5 17655383 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19263;SOR=3.69897;LSEQ=CTCCTGCAGGGCGCCAATGG;RSEQ=CGCACTCTGGAAGCGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:702:2:0,2:289,411:0.0028:2,0:19.5:1:21:1:0.51491:0:60:1:0.0015:0:1 0/1:382:4:2,2:188,188:0.0105:2,2:27.3:1:28.5:1:1:1:50:8:0.0106:0:1.5 -5 17655498 . C T 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30197;SOR=0;LSEQ=TTCTGGTACTTTCTGATTTC;RSEQ=CGCAGCGCCAGGGTGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:4:2,2:82,236:0.0124:2,2:23.8:1:31.5:1:0.2796:2.87:48:8:0.0126:0:1.3 0/0:181:0:0,0:49,131:0:2,0:21.5:1:29.9:1:1:0:53.7:44:0.9944:0:0.1 -5 17655589 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05461;SOR=Inf;LSEQ=CGGCTGCTTTGGTGGCCAGG;RSEQ=GCTTCCTGGGGGCCTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:27,73:0:2,0:25:1:30.7:1:1:0:58:49:1:0:0.1 0/1:31:2:1,1:5,24:0.0645:2,2:39.5:1:30:1:0.35484:4.47:60:4:0.0667:0:1.5 -5 17670092 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54118;SOR=0;LSEQ=ACAGTCACTACCTGTGATTT;RSEQ=TGCTTATGTTTCCACTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:0.2857:0,0:23.8:1:30.3:1:1:0:60:8:0.3077:0:1 0/0:3:0:0,0:3,0:0:0,0:19.3:1:31:1:1:0:60:6:1:0:0 -5 17670208 . G GA 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.13863;SOR=2.06486;LSEQ=TACCAGTAACTGAAAGAAGA;RSEQ=AAAAAAAAAACACAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:12:12,0:108,3:0.0968:1,0:24.8:1:31.3:1:1:0:60:24:0.0984:0.0161:0.9 0/1:55:10:9,1:41,4:0.1818:2,2:22.5:1:29.5:1:1:1.13613:60:20:0.1818:0.0364:0.6 -5 17670396 . G T 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=TCAAAGAGGCGCACCAGGTA;RSEQ=GCCTTGCTGGGCTCCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:23:9,14:321,477:0.028:2,2:21.9:1:30.1:1:1:1.04677:60:46:0.0284:0:1 0/0:487:0:0,0:200,287:0:2,0:25.5:1:30.4:1:1:0:60:59.875:1:0:0.2 -5 17670555 . G T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08295;LSEQ=CTGATTTTGCAGAGTGCCAG;RSEQ=GTGCCAGACCTGTAGCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:27,128:0.0127:2,2:30:1:31:1:0.32582:4.67:60:4:0.0129:0:1 0/1:73:1:0,1:19,53:0.0137:2,0:1:0:25:0:1:0:60:2:0.0137:0:1 -5 17670570 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGGGTGCCAGACCTGTA;RSEQ=CCGTGGGGCTTCTTGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:16,107:0.016:2,2:22:1:27.5:1:0.25445:6.52:60:4:0.0161:0:2 0/0:55:0:0,0:10,45:0:2,0:19.5:1:31.7:1:1:0:60:54:1:0:0.1 -5 17670600 . C A 161 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=0.05177;LSEQ=TTCTTGATCCCTCCTGTAGG;RSEQ=GGCGCCCTCTTGCTGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:36:5,31:5,37:0.4615:2,2:22.4:1:31.2:1:1:1.19:60:17:0.4658:0:1.1 0/1:24:1:0,1:5,18:0.0417:2,0:44:0:29:0:1:0:60:2:0.0417:0:1 -5 17670818 . T C 71 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAGCCTGTGAGTTGAGATC;RSEQ=GTGCAGAAGACGCAACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:25.2:1:31:1:1:0:60:10:1:0:1 1/1:1:1:0,1:0,0:1:0,0:50:0:29:0:1:0:60:2:1:0:1 -5 18119214 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTAGAAGGCTGGCATGA;RSEQ=CCATGGAGAGAAGGAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:32:0:33:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:27:1:29.5:1:1:0:60:4:1:0:1 -5 18119944 . T C 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49;SOR=0.37048;LSEQ=TCCCCAGCAAAATACACCCT;RSEQ=TCCACCAAGGGACAAAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:11,6:1,0:0.9444:0,2:24.5:1:31.4:1:1:0:60:34:0.9444:0:1.1 1/1:7:6:3,3:0,1:0.8571:0,2:7.8:1:31.7:1:1:0:60:12:0.8571:0:1.5 -5 18119968 . G A 63 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02228;SOR=13.45809;LSEQ=ACCAAGGGACAAAGTGCTTC;RSEQ=TAAAATGGGTTCTGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:11,8:0.05:2,0:19:0:32:0:0.45:0:60:2:0.05:0:2 0/1:9:4:2,2:2,3:0.4444:2,2:22.5:1:31.5:1:1:1.43:60:8:0.4444:0:1.8 -5 18120256 . G GACA 130 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=8.000;MSILEN=3;SSF=0.39529;SOR=0.56619;LSEQ=GAAAGAAACAAGCAGAAAGT;RSEQ=ACAACAACAACAACAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:19:12,7:7,2:0.5938:2,2:22.8:1:30.8:1:0.67003:1.99246:60:38:0.5938:0.1875:0.3 0/1:20:9:4,5:5,0:0.45:0,2:19.8:1:29:1:0.08591:0:60:8:0.4211:0.2:0.4 -5 18120390 . T C 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0129;SOR=Inf;LSEQ=AATGTGGAAAACCCAAAAGG;RSEQ=CAGAGTGCCTCTTGTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:20.7:1:29.3:1:1:0:60:54:1:0:0 1/0:4:2:1,1:0,2:0.5:0,2:12:1:33:0:1:0:60:4:0.5:0:1.5 -5 18120489 . C A 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCACAGAAGTAGGCTTC;RSEQ=GAAGATGGATAATAACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:24.3:1:31.5:1:1:0:60:8:0.8:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 18120548 . A G 61 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGTGTTCTAACCCAATGCAA;RSEQ=GAAGCTAAGAACCATGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:14.3:1:30.8:1:1:0:60:8:1:0:1.8 1/1:1:1:1,0:0,0:1:0,0:12:0:32:0:1:0:60:2:1:0:1 -5 18123234 . CA TG 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACTGGCAAATTGAATC;RSEQ=GCAGCACATCAAAGAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:0:32.3:1:1:0:60:4:1:0:1.5 -5 21758500 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGAGACTCTGACTTTCTTTG;RSEQ=CTAATCATTGTAGCAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31:1:29.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:38.5:1:31:1:1:0:60:4:1:0:0 -5 21759524 . CTAAA C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=5.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AACCATGTCTCTCCCTCCCT;RSEQ=TAAATAAATAAATAAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:30.5:1:1:0:60:4:1:0:0.5 -5 21760602 . C A 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2984;LSEQ=TTCAAAGAAAAGTATTGATT;RSEQ=CTCCCTTTGTGCCTTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:637:570:286,284:32,34:0.8948:2,2:26.8:1:28.9:1:0.89665:1.07:60:141.5:0.8942:0:1.1 1/0:304:218:105,113:43,42:0.7171:2,2:25.3:1:28.3:1:0.7982:1.10146:60:53.5:0.7181:0:1.2 -5 21760731 . T C 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=GGTGATAATCTAAAGGAGAA;RSEQ=TGTTGCCCAGCAGGTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:3,114:0:1,0:25.5:1:30.4:1:1:0:60:234:1:0:0 0/1:41:5:0,5:1,35:0.122:1,0:27:1:33.2:1:1:0:60:10:0.122:0:1 -5 21824695 . C A 279 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28967;LSEQ=ACACAGCCTTGTTCTCTTTT;RSEQ=CTTTCTCTGCTGTTTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:961:870:375,495:34,53:0.9053:2,2:24.7:1:28.6:1:0.49697:1.18:60:71.5:0.9051:0:1.1 1/0:550:404:182,222:59,87:0.7345:2,2:22.9:1:28.4:1:0.3812:1.21:60:133.667:0.7385:0:1.1 -5 21825081 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACCGGCCTGGCCAACAT;RSEQ=GTGAAACTCCATCTCTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:27:1:30:1:1:0:53.7:6:1:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 22934322 . T G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGCTATAGGAACCAGAA;RSEQ=AGCCAGTTTATCTATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:10:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 22934438 . A G 84 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCCAAATAGACTCTTTG;RSEQ=CAGCAGTGACTCTCCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:23.2:1:32.8:1:1:0:53.8:12:1:0:1 1/1:4:4:4,0:0,0:1:0,0:13.5:1:27.3:1:1:0:54.8:3:1:0:1 -5 22934579 . G T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.20604;LSEQ=ACACCACCTGGCATTTATAG;RSEQ=ACAGGCTTCTGAAATCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:93:75:51,24:12,6:0.8065:2,2:21.8:1:29:1:1:1.06:59.7:74:0.8043:0:1.2 0/1:61:28:15,13:21,12:0.459:2,2:27.1:1:29.1:1:0.44718:1.50621:60:56:0.459:0:1 -5 22934613 . C G 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08034;SOR=2.50429;LSEQ=ATCAGACAATGCCTTTCAAA;RSEQ=TCTTATACCAACCTCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:8:5,3:74,64:0.0544:2,2:29.6:1:30.3:1:0.72662:1.44:60:7:0.0486:0:1.8 0/1:87:11:5,6:40,36:0.1264:2,2:30.8:1:29.7:1:0.75259:1.32892:60:10:0.1163:0:1.7 -5 22934638 . G T 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01471;SOR=0;LSEQ=ATACCAACCTCTGGAGTTGG;RSEQ=TGACATGGCTTCTCCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:10:4,6:63,66:0.0719:2,2:30.5:1:28.5:1:0.74633:1.42816:59:9:0.0667:0:1.7 0/0:84:0:0,0:36,48:0:2,0:28.4:1:30.1:1:1:0:60:83:1:0:0.5 -5 22934642 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52939;SOR=0;LSEQ=CAACCTCTGGAGTTGGGTGA;RSEQ=ATGGCTTCTCCCCTTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:63,72:0.0146:2,2:26:0:32:0:1:1.14:60:4:0.0148:0:1.5 0/0:82:0:0,0:31,51:0:2,0:27.8:1:31:1:1:0:60:164:1:0:0.5 -5 22934660 . T C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59475;SOR=1.35882;LSEQ=GACATGGCTTCTCCCCTTTC;RSEQ=AGTTCTCGTGACGGCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:9:3,6:44,68:0.0744:2,2:21.8:1:31:1:1:1.29144:60:18:0.0763:0:1.7 0/1:71:7:1,6:24,40:0.0986:2,2:24.7:1:30.1:1:0.40856:3.54787:60:14:0.0986:0:1.9 -5 23145691 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49365;SOR=0;LSEQ=CTAGTTTCGGTCTTTGAGGC;RSEQ=GCTGACCCTTGGATGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:14,15:0.0645:2,2:31:1:29.5:1:1:1.07:60:4:0.0667:0:1 0/0:27:0:0,0:13,14:0:2,0:27.1:1:30.1:1:1:0:60:54:1:0:0.2 -5 23146100 . G A 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06912;SOR=0;LSEQ=AGGGTGTGTTTCGCTGGGGG;RSEQ=AAACCCACTTGTCTGTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:3,3:8,8:0.2727:2,2:29.7:1:31:1:1:1:60:12:0.2727:0:1 0/0:12:0:0,0:5,7:0:2,0:26.9:1:26.4:1:1:0:60:11:1:0:0.5 -5 23146227 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGAGAGATCTGAATTCT;RSEQ=TCCCTGAGCCTCTGGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:16,10:0.0714:2,2:6.5:1:28:1:1:1.57244:60:4:0.0714:0:1.5 0/0:11:0:0,0:7,4:0:2,0:18.7:1:31.2:1:1:0:60:22:1:0:0.3 -5 23303287 . C A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCACAATGAGGAAAAAAA;RSEQ=TTAAACTGGTTAAGGTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:27.5:1:32:0:1:0:58.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 23303312 . GA G 67 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGTTAAGGTTATAAAAA;RSEQ=AAAAAAAAAGCCTATTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:18.8:1:33.5:1:1:0:59.3:8:0.8:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 23303757 . G A 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCTGCACAGGGTGGCGTT;RSEQ=GAGTACAAGGCAGGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1168:93:42,51:476,597:0.0796:2,2:25.8:1:29.6:1:0.91359:1.03:60:92:0.0803:0:1.1 0/0:640:0:0,0:283,357:0:2,0:25.8:1:30.3:1:1:0:60:57.182:1:0:0.3 -5 23303772 . A C 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.10974;LSEQ=GCGTTGGAGTACAAGGCAGG;RSEQ=GGGGGCTCTGATCTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1130:674:298,376:193,258:0.5965:2,2:26.2:1:30.4:1:0.66778:1.06:60:47.143:0.5995:0:1.1 0/1:660:92:41,51:252,316:0.1394:2,2:24.1:1:30.2:1:1:1.01:60:45:0.1391:0:1.1 -5 23303943 . C A 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGCTTCTGTCTGGACCATC;RSEQ=CTGACCTCTGAGACCGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1116:60:38,22:552,504:0.0538:2,2:24.6:1:30.2:1:0.11061:1.58:59.8:120:0.0543:0:1.2 0/0:619:0:0,0:320,299:0:2,0:25.8:1:30.2:1:1:0:59.9:60.9:1:0:0.1 -5 23304111 . C T 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.17473;LSEQ=GCCCTGCATCCGTGATGCTC;RSEQ=CCTGCTTATGGTACACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:863:550:293,257:169,143:0.6373:2,2:23.8:1:30.4:1:0.8313:1.03658:59.9:54:0.6406:0:1.1 0/1:456:107:59,48:178,169:0.2346:2,2:25.8:1:29.6:1:0.50813:1.17:59.5:52.5:0.2376:0:1.2 -5 23304211 . G T 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12834;LSEQ=AAAGTGATATTGCCCGACCG;RSEQ=TCTCTCCATATTCCCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:972:855:453,402:61,53:0.8796:2,2:24.2:1:29.9:1:0.92086:1.02135:60:170:0.8854:0:2 0/1:515:249:124,125:145,120:0.4835:2,2:25.7:1:29.6:1:0.28928:1.2176:60:123.5:0.4881:0:1.7 -5 23304235 . T C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15585;LSEQ=CTCCATATTCCCTGGTCCAA;RSEQ=CTTTGAAAGTTCAAGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1016:656:341,315:201,158:0.6457:2,2:24.4:1:31.4:1:0.23639:1.17497:60:108.333:0.6533:0:2.6 0/1:525:116:61,55:231,178:0.221:2,2:23.9:1:31.2:1:0.46084:1.16975:60:232:0.2235:0:2.6 -5 23304261 . G A 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.16009;LSEQ=AAAGTTCAAGTTCTCTTAGT;RSEQ=TATAGTCATGAGCTGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1137:702:350,352:233,199:0.6174:2,2:26.5:1:29.4:1:0.19892:1.17737:59.9:77:0.6182:0:2.2 0/1:624:128:66,62:260,235:0.2051:2,2:23.5:1:28.1:1:0.92096:1.03928:60:31:0.202:0:2.2 -5 23304368 . A C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1326;LSEQ=ACACATTTACTCTTTCCTCT;RSEQ=TCCACTTCTTTTGTTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:985:618:295,323:161,205:0.6274:2,2:24.4:1:31.7:1:0.26153:1.16:57.9:308:0.6351:0:1.7 0/1:543:99:51,48:203,241:0.1823:2,2:26.4:1:31.3:1:0.3172:1.26:58.1:32:0.1815:0:1.7 -5 23304401 . G T 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14174;LSEQ=GTTGTCATGACAATCACTCG;RSEQ=GAGTTTTCTTGGAACTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:906:567:274,293:147,191:0.6258:2,2:25.2:1:30:1:0.16854:1.21:59.9:188:0.6288:0:1.8 0/1:465:89:44,45:171,205:0.1914:2,2:24.8:1:29.3:1:0.55482:1.17:60:88:0.1934:0:1.8 -5 23304501 . C T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16658;LSEQ=TGGGCTTTGAATTGTTGCAC;RSEQ=TGGTTTCAAATTCAGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:867:579:309,270:154,133:0.6678:2,2:24:1:30.5:1:0.94244:1.01174:59.3:71.375:0.6671:0:1.8 0/1:423:106:53,53:175,140:0.2506:2,2:23.2:1:30.3:1:0.36748:1.24932:59.5:105:0.2518:0:1.8 -5 23304559 . C T 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14636;LSEQ=GTAATCTGAAACAGGCTCAT;RSEQ=GGGATCACCGTCGTGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1070:742:365,377:152,176:0.6935:2,2:25.9:1:29.8:1:0.42599:1.12:59.1:48.467:0.6924:0:2.2 0/1:495:123:58,65:182,190:0.2485:2,2:26.9:1:30:1:0.7557:1.07333:59.6:246:0.2505:0:2.2 -5 23304569 . G A 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00293;SOR=Inf;LSEQ=ACAGGCTCATCGGGATCACC;RSEQ=TCGTGTAGGACAACCCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1041:0:0,0:501,540:0:2,0:26.1:1:30.7:1:1:0:59.2:42.375:1:0:1.5 0/1:473:5:4,1:225,242:0.0106:2,2:10.6:1:24:1:0.20363:4.29:56:4:0.0087:0:1.8 -5 23304587 . A C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14746;LSEQ=CCGTCGTGTAGGACAACCCT;RSEQ=GTATGATCAAAGGGTAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:997:673:319,354:154,169:0.675:2,2:24.3:1:30.2:1:0.94604:1.01121:57.5:36.389:0.6725:0:2 0/1:491:115:53,62:189,187:0.2342:2,2:21.8:1:29.7:1:0.45682:1.18192:57.9:56.5:0.2354:0:2 -5 23304724 . G C 326 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08221;LSEQ=TTCCCAAAAGCCTTGTTTGA;RSEQ=TTTGTCTGTGGTCTCAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1394:1234:594,640:77,82:0.8852:2,2:24.7:1:31.8:1:1:1.01174:55.5:111.182:0.8862:0:1.5 0/1:761:295:143,152:216,249:0.3876:2,2:24.7:1:31.3:1:0.6023:1.08:54.8:146.5:0.3865:0:1.6 -5 23304772 . T C 315 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.10099;LSEQ=TAGTTCTCGAACTCTGCTTT;RSEQ=TATTTCAGCAGCATTTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1126:984:412,572:62,80:0.8739:2,2:26.1:1:31.7:1:0.71643:1.0759:54.3:108.333:0.8729:0:1.6 0/1:603:248:109,139:150,205:0.4113:2,2:26.2:1:31.5:1:0.73813:1.07:53.5:81.667:0.4104:0:1.6 -5 23304880 . TT CC 230 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTAATGTTCTTCAAGATCTG;RSEQ=AAAGAATCAAACCGTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:946:152:73,79:404,388:0.1607:2,2:27.4:1:31.8:1:0.53566:1.12667:59.6:304:0.162:0.0053:1.8 0/0:482:0:0,0:243,239:0:2,0:26.6:1:29.5:1:1:0:60:79.333:1:0:0.7 -5 23304881 . T C 275 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09069;SOR=0.82391;LSEQ=TAATGTTCTTCAAGATCTGT;RSEQ=AAAGAATCAAACCGTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:420:216,204:192,189:0.443:2,2:26.2:1:31.6:1:0.77756:1.04:59.9:139:0.5259:0:1.8 0/1:485:192:94,98:152,141:0.3959:2,2:26:1:31.3:1:0.57755:1.12361:59.9:95:0.395:0:1.5 -5 23304911 . G A 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18661;LSEQ=AACCGTTCTCCTCCACCAAC;RSEQ=TCATATTTCAGTTCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1045:624:329,295:210,207:0.5971:2,2:24.2:1:30.5:1:0.48635:1.10:59.9:155:0.5985:0:1.7 0/1:522:113:60,53:200,208:0.2165:2,2:24.1:1:29.9:1:0.45845:1.18:59.8:112:0.2179:0:1.8 -5 23305275 . T C 315 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.15047;LSEQ=CCTCCCGCCCTCCAGCTCTG;RSEQ=GACGGACCCGCTGCTTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1912:1231:550,681:283,394:0.6438:2,2:26.4:1:30.7:1:0.22825:1.12:59.9:75.938:0.6442:0:1.9 0/1:1137:243:115,128:390,500:0.2137:2,2:26.7:1:30.4:1:0.34431:1.15:59.8:39.5:0.2109:0:1.9 -5 23305303 . A G 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16014;LSEQ=CCGCTGCTTGCTCAGGCTCC;RSEQ=CTGGGCTGGGTCACATCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1437:912:371,541:200,325:0.6347:2,2:26.9:1:31:1:0.34181:1.11:59.9:81.909:0.6372:0:2.3 0/1:846:184:75,109:246,416:0.2175:2,2:25.7:1:30.4:1:0.39099:1.16:59.7:35.8:0.2164:0:2.3 -5 23305356 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13579;LSEQ=AGGCCTACTCGGGACCAGAC;RSEQ=AGGAGACAGAGCCAGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:581:388:52,336:20,172:0.6678:2,2:22.9:1:30:1:0.34996:1.33:60:54.429:0.6661:0:2.1 0/1:243:52:11,41:22,169:0.214:2,2:24.6:1:29.9:1:0.10702:2.05:60:51:0.2125:0:2.2 -5 23305427 . GC G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.20779;LSEQ=ATCCCAGAGACTGTGCAGCC;RSEQ=CCCCCCCGGTCCGGCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:209:111:2,109:7,90:0.5311:2,1:27.6:1:32.6:1:0.08533:4.21188:60:222:0.5441:0.0335:0.8 0/1:58:11:1,10:4,43:0.1897:2,2:28:1:32.6:1:1:1.07:60:22:0.193:0.0172:0.5 -5 23305435 . C GCCG 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.0113;SOR=Inf;LSEQ=GACTGTGCAGCCGCCCCCCC;RSEQ=GGTCCGGCTTGCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:8,189:0:1,0:24.1:1:31:1:1:0:60:23.625:1:0:0.6 0/1:58:3:0,3:5,50:0.0517:2,0:17.7:1:28:1:1:0:60:6:0.0517:0.0345:1 -5 23305484 . T C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03202;SOR=0.30896;LSEQ=TTTTGTACTTTTAGTGGAGA;RSEQ=GGGGTTTCTCACTTTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:46:0,46:0,22:0.6765:1,1:22.7:1:30.5:1:1:0:60:45:0.6716:0:1 0/1:18:7:0,7:1,10:0.3889:2,0:36.4:1:29:1:1:0:60:14:0.3889:0:1.1 -5 23396653 . G C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50786;SOR=0;LSEQ=GCCAGGCTTTTTAATCTTCT;RSEQ=CTAGGCCCATCTGTGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:16,10:0.0714:2,2:27:0:33:0:1:1.57244:60:4:0.0714:0:1 0/0:19:0:0,0:11,8:0:2,0:21.9:1:30.9:1:1:0:60:38:1:0:0.1 -5 23396678 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1301;SOR=Inf;LSEQ=GCCCATCTGTGCAGTTCCTT;RSEQ=CAAATTCCAGTTTTAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:0:2,0:32.4:1:31.7:1:1:0:60:30:1:0:0.2 0/1:18:2:1,1:8,8:0.1111:2,2:18.5:1:29:1:1:1:60:4:0.1111:0:1 -5 23396822 . G A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TTGGCCTGTCTTCAGCAAGC;RSEQ=TCATGTTTGAGCAGTTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:44.3:1:32.7:1:1:0:60:6:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:12:0:31.5:1:1:1:60:4:0.3333:0:1.5 -5 24364917 . C A 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGAGGTAGGACAATGTTG;RSEQ=ATACCCCTAAGACAGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:3,11:0.125:2,2:35:1:30:0:0.45:3.32:60:4:0.125:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 24400400 . T C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTTCTGAAATCAGACAA;RSEQ=GCCTTTCGAACTCTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:5,5:0,0:1:0,2:24.3:1:31.6:1:1:0:57.4:20:1:0:1.1 1/1:7:7:5,2:0,0:1:0,2:27.1:1:30.4:1:1:0:56.7:14:1:0:1.1 -5 24400471 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTCTAGATCCCATGAC;RSEQ=GCCATCTTGCTATTACTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:18:0:32:1:1:1.13389:60:4:0.1176:0:1.5 0/0:6:0:0,0:3,3:0:2,0:25.2:1:30.2:1:1:0:60:12:1:0:0.2 -5 26148813 . A G 79 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGGGGAGGGGGTGGGGC;RSEQ=ACCAGCACTGCCTGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:0,1:0.8571:0,2:28.7:1:30.8:1:0.28571:0:60:12:0.8571:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 26149087 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11392;SOR=Inf;LSEQ=CAGGTCTAACCCTGACCCAT;RSEQ=CTTCCTCAGTGGGTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,27:0:2,0:23.8:1:31.1:1:1:0:59.8:51:1:0:0.2 0/1:27:2:1,1:13,12:0.0741:2,2:22.5:1:28.5:1:1:1.0801:60:4:0.0741:0:2 -5 26149197 . C T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12797;SOR=0;LSEQ=CCCTTAGGAGTAGGGGTGGC;RSEQ=ACAGTCGCTGTGGACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:1,4:2,6:0.3846:2,2:29.8:1:25.6:1:1:1.30472:60:4:0.3333:0:1.4 0/0:6:0:0,0:1,5:0:2,0:26.7:1:31.5:1:1:0:60:12:1:0:0.2 -5 26149350 . C T 80 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19231;SOR=0;LSEQ=GGCCCTGCTCCCTATGACAC;RSEQ=CAACTGGGTGATATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:3,4:2,2:0.6364:2,2:30:1:28.7:1:1:1.29868:60:6:0.6:0:1.4 0/0:3:0:0,0:2,1:0:2,0:15:1:28:1:1:0:60:6:1:0:0 -5 26149627 . C CACA 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=1;SOR=0.87042;LSEQ=ACAACAGCATCATCATCAAC;RSEQ=ACAACAACAACAACAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:3,3:7,6:0.3158:2,2:20.3:1:28.3:1:1:1.15722:60:5:0.2778:0.0526:0.3 0/1:14:4:1,3:6,4:0.2857:2,2:20.8:1:29.6:1:0.55944:4.03195:60:8:0.3077:0.0714:0.3 -5 26149754 . A AGGCCCATAGTGCCTCTTCTCCTCCAAAGATCACAATGTCTGTCCATCAAG 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0119;SOR=0;LSEQ=AAAACTGCTGAAAATACAAA;RSEQ=GGCCCAGAATCGGATAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:33:1:28.4:1:1:0:60:6:1:1:0 0/0:6:0:0,0:2,4:0:2,0:3.5:1:29.5:1:1:0:60:12:1:0:0.3 -5 26150118 . A T 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.00058;SOR=0;LSEQ=ATGAACAAAGCTTCCAAGAA;RSEQ=TATGGGACTTCATAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:14:8,6:8,8:0.4667:2,2:28.1:1:30.1:1:0.73001:1.32:54.4:28:0.4667:0:1.2 0/0:17:0:0,0:12,5:0:2,0:22.9:1:30.8:1:1:0:60:34:1:0:0.2 -5 26150150 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16393;SOR=Inf;LSEQ=ATAAAAAGACTGAACCTATG;RSEQ=TGACTGGAGTACCAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:0:2,0:29.4:1:30.9:1:1:0:57.8:72:1:0:0.5 0/1:25:2:1,1:12,11:0.08:2,2:24:1:28:1:1:1.0871:60:4:0.08:0:0 -5 26150155 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5082;SOR=0;LSEQ=AAGACTGAACCTATGATTGA;RSEQ=TGGAGTACCAGAAGGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:0.0556:2,2:30:1:29.5:1:1:1:60:4:0.0556:0:1.5 0/0:25:0:0,0:13,12:0:2,0:27.5:1:31.6:1:1:0:60:50:1:0:0.1 -5 26669768 . G T 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04166;SOR=Inf;LSEQ=GTCCCTGGGGTTTAGCAGCC;RSEQ=CTCTGGGCAGCCATGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:556:0:0,0:439,117:0:2,0:26.4:1:30:1:1:0:60:36.067:1:0:0.1 0/1:296:3:1,2:213,80:0.0101:2,2:18.3:1:28:1:0.1868:5.28955:60:6:0.0102:0:1 -5 26670194 . A C 105 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07548;SOR=0;LSEQ=AATAATATATCTTTAATTTT;RSEQ=CTTAGATTACAAAACAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:12:0,12:0,196:0.0577:1,0:31.1:1:29.4:1:1:0:60:24:0.0583:0:1.1 0/0:65:0:0,0:1,64:0:1,0:23.6:1:29.8:1:1:0:60:64:1:0:0 -5 26678490 . G T 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67033;SOR=0.44167;LSEQ=AGAGATCAACTAACTTATTT;RSEQ=AGGTCACATAGGTAATAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:5:2,3:164,63:0.0216:2,2:15.8:1:28.4:1:0.14082:3.8779:60:10:0.0217:0:1.4 0/0:104:1:0,1:69,34:0.0096:2,0:1:0:23:0:0.33654:0:60:2:0.0096:0:2 -5 26678537 . A G 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCATTCTACATTACTGTC;RSEQ=CAAAGTAGGTTTTTGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:223,171:0:2,0:27.1:1:29.9:1:1:0:60:130.333:1:0:0.1 0/1:187:26:14,12:86,75:0.139:2,2:25:1:31.1:1:1:1.02:60:52:0.1405:0:1.9 -5 26678559 . T C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03258;SOR=Inf;LSEQ=AAAGTAGGTTTTTGAAGATA;RSEQ=ATGCTATCATACTGACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:221,218:0:2,0:24.9:1:29.5:1:1:0:60:145.333:1:0:0.2 0/1:207:3:2,1:104,100:0.0145:2,2:26.3:1:30.7:1:1:1.92:60:6:0.0147:0:3.7 -5 26678572 . T C 87 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0021;SOR=8.99271;LSEQ=GAAGATATATGCTATCATAC;RSEQ=GACATTCTCATGGTCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:2:1,1:194,217:0.0048:2,2:24:0:32:0:1:1.12:60:4:0.0049:0:1.5 0/1:191:8:4,4:86,97:0.0419:2,2:28.4:1:29.3:1:1:1.13:60:16:0.0423:0:2.9 -5 26678593 . T G 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.7647;LSEQ=GACATTCTCATGGTCTTAAA;RSEQ=AAATGCTATATCTTGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:22:9,13:138,196:0.0618:2,2:24.4:1:31.1:1:1:1.01696:60:44:0.0629:0:1.2 0/1:167:40:19,21:56,71:0.2395:2,2:27.2:1:31:1:0.7192:1.15:60:80:0.2395:0:1.7 -5 28498907 . G A 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=0.38343;LSEQ=CTGCCATCCTTCTGAGCTAC;RSEQ=CAATGGTGAGTAGTACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:410:374:263,111:26,10:0.9122:2,2:25.3:1:29.9:1:1:1.0971:60:92.5:0.9113:0:1.5 1/0:214:171:112,59:24,12:0.7991:2,2:23.7:1:29:1:1:1.05331:60:33.2:0.7943:0:1.5 -5 28498983 . T C 290 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30327;LSEQ=GTTTCAAAAACACTGTGCAT;RSEQ=AATTACATACAGTGAGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:647:583:269,314:30,33:0.9011:2,2:25:1:31.6:1:0.89438:1.06104:60:290.5:0.9008:0:1.3 1/0:406:298:146,152:54,54:0.734:2,2:26.3:1:31.4:1:0.91069:1.04101:60:98.333:0.732:0:1.3 -5 28499031 . A G 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATGTTGCAAAACCTAATGC;RSEQ=TGGGGAGTTTCTTCAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:0:0,0:189,333:0:2,0:25.3:1:30.5:1:1:0:60:129.5:1:0:0.7 0/1:303:29:11,18:107,167:0.0957:2,2:32.1:1:30.1:1:1:1.04829:60:28:0.0946:0:1.2 -5 28499097 . GTA G 53 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.7256;LSEQ=TTCCTGAGAAGCAGAAAAAA;RSEQ=TATATATATATTTGTATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:3:0,3:22,128:0.0196:2,0:28:1:33.7:1:1:0:60:6:0.0199:0:0 0/1:70:1:0,1:9,60:0.0143:2,0:43:0:31:0:1:0:60:2:0.0143:0:0 -5 28499161 . A C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03557;SOR=0.23046;LSEQ=TTATGGAAGAGGAAGCCCCA;RSEQ=AGTTGAGGTGAAAGTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:57:0,57:0,8:0.8769:0,1:24.4:1:32.1:1:1:0:60:27.5:0.873:0:1.2 1/0:13:8:0,8:0,5:0.6154:0,0:25.3:1:31.5:1:1:0:60:16:0.6154:0:1 -5 28499327 . T A 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCTGCTCTTAAGAGTGAA;RSEQ=AAAAGCTCACAAGTGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:16.6:1:26.4:1:1:0:60:4:1:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 29070817 . C T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21739;SOR=0;LSEQ=GTACTATTCTTGAGTGAGCT;RSEQ=GCTTAAGAATGAATATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:4,5:0.25:2,0:25.3:1:31.7:1:0.20455:0:60:6:0.25:0:1 0/0:12:0:0,0:9,3:0:2,0:16.3:1:29.3:1:1:0:60:24:1:0:0.1 -5 29954863 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50515;SOR=0;LSEQ=AGTTTATGAGCCAATTTTCA;RSEQ=TTATTATCTCATCATAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:74,22:0.0204:2,2:21:1:29.5:1:0.41616:3.31182:60:4:0.0206:0:1 0/0:76:0:0,0:57,19:0:2,0:22.3:1:28.8:1:1:0:60:152:1:0:0.1 -5 29954903 . A T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19467;SOR=Inf;LSEQ=GAATAAGCTTAAAAATATGA;RSEQ=GCTACTCTAATCACATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:112,71:0:2,0:27.7:1:30.4:1:1:0:60:182:1:0:0.3 0/1:145:2:1,1:85,58:0.0138:2,2:44:0:30:1:1:1.46153:60:4:0.0141:0:1.5 -5 29954926 . A T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57542;SOR=2.76065;LSEQ=TACTCTAATCACATTATCTA;RSEQ=ACATTATAACATATTACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:1:0,1:135,103:0.0042:2,0:1:0:24:0:0.43515:0:60:2:0.0042:0:1 0/1:174:2:1,1:95,77:0.0115:2,2:27.5:1:29:1:1:1.23226:60:4:0.0118:0:3.5 -5 29954930 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17287;SOR=Inf;LSEQ=CTAATCACATTATCTAAACA;RSEQ=TATAACATATTACAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:139,109:0:2,0:25.3:1:30.7:1:1:0:60:247:1:0:0.4 0/1:177:2:1,1:95,80:0.0113:2,2:31.5:1:31:1:1:1.18634:60:4:0.0115:0:3.5 -5 29954963 . T C 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.756;SOR=0.9234;LSEQ=CAGCAGTTCATCTATATTAG;RSEQ=TACACTTTTTAGCATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:77:41,36:97,92:0.2884:2,2:26.1:1:31.9:1:0.78839:1.08:60:154:0.2917:0:1.7 0/1:202:55:31,24:71,76:0.2723:2,2:24.8:1:31.5:1:0.34477:1.38:60:110:0.2736:0:1.8 -5 29954999 . T C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56953;SOR=1.15687;LSEQ=CAAATTAAATATAAATGACT;RSEQ=CATGAGTGAATGGAACCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:69:25,44:77,98:0.2828:2,2:25:1:31.1:1:0.31375:1.38103:60:138:0.2911:0:1.8 0/1:150:47:20,27:41,61:0.3133:2,2:29.9:1:30.5:1:0.85825:1.10:60:22.5:0.3103:0:1.8 -5 29955160 . GA G 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.24895;SOR=0;LSEQ=GATGTTTTAAGAATTTTTGG;RSEQ=AAGGAAAATAGAAAATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:0,8:0.3846:0,0:33.6:1:31:1:1:0:60:10:0.4167:0:1.2 0/0:5:0:0,0:0,5:0:0,0:17:1:30.6:1:1:0:60:10:1:0:0.2 -5 29955205 . TGT G 51 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAATCTGTACTTTTTTTT;RSEQ=TTTTTTTTTAAAGATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:25.3:1:32.2:1:1:0:60:6:0.375:0:0.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 30031540 . T TA 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGTTAAATGTACTTTGT;RSEQ=AAAAAAAAAAAAAGGATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:29.5:1:28.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 30031802 . A G 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.89345;SOR=0.93313;LSEQ=ATTGTGGCACTAGCATACTA;RSEQ=TATACTCTTTGTAAGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:68:63,5:104,9:0.3757:2,2:24.4:1:32.2:1:1:1.09:60:67:0.3785:0:1 0/1:89:32:31,1:48,9:0.3596:2,1:23.1:1:33:1:0.0881:5.73:60:64:0.3596:0:1.1 -5 30031845 . A AT 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.04473;SOR=1.76717;LSEQ=AAGCCAGGTATGTAATTTAT;RSEQ=TTTTTCTTTTCTATCAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:32:22,10:272,103:0.0784:2,2:24.2:1:29.9:1:0.68199:1.19976:60:31:0.0777:0.0172:0.9 0/1:214:28:19,9:127,59:0.1308:2,2:20.9:1:28.8:1:1:1.01954:60:27:0.1286:0.0327:0.9 -5 30031915 . T C 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.01771;SOR=1.34925;LSEQ=CTCTTCATGTAAGGTTATGA;RSEQ=GATTCCCCAAATATTACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:764:219:98,121:276,269:0.2866:2,2:28.7:1:30.8:1:0.15011:1.26642:60:108.5:0.2882:0:1.2 0/1:492:173:81,92:165,153:0.3516:2,2:26.8:1:29.9:1:0.29961:1.22437:60:85.5:0.3526:0:1.3 -5 30031998 . A G 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01273;SOR=1.76834;LSEQ=AATGTCTTCTTAATGATCAT;RSEQ=AGAAAGTAAAACATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:65:10,55:30,155:0.26:2,2:23.7:1:31.6:1:1:1.06426:60:64:0.2591:0:1.5 0/1:146:56:13,43:12,78:0.3836:2,2:21.5:1:31.2:1:0.17437:1.96:60:112:0.3862:0:1.5 -5 30032075 . A C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.82648;LSEQ=CTGTTTATTAACTCATATTT;RSEQ=CACCAGACTCCTCCATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:19:0,19:0,47:0.2879:1,1:24.9:1:31.9:1:1:0:60:38:0.2923:0:1.4 0/1:16:4:0,4:0,12:0.25:0,0:17:1:26.8:1:1:0:60:3:0.2:0:1.5 -5 30204405 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16757;SOR=Inf;LSEQ=CCTTTCAAACTCTTATACCA;RSEQ=CTACTGGAGTCAGGCGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:20,24:0:2,0:32:1:30:1:1:0:60:43:1:0:0.1 0/1:31:2:1,1:12,17:0.0645:2,2:35.5:1:29.5:1:1:1.40:60:4:0.0645:0:1 -5 30204626 . G T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=ACTGACCCACTGACCCTTTG;RSEQ=CTGGCCTAGAGAGATCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:4:0:29:0:1:0:60:2:1:0:0 0/1:5:2:1,1:0,2:0.4:0,2:23:1:27:1:1:0:60:4:0.4:0:1 -5 30708931 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19096;SOR=Inf;LSEQ=TAGAGAGTCGCCACTGTGGC;RSEQ=CTGCCTTGGAACTGTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:22,16:0:2,0:26.7:1:30.3:1:1:0:60:76:1:0:1.1 0/1:30:2:1,1:13,15:0.0667:2,2:20.5:1:30:0:1:1.15:60:4:0.0667:0:2 -5 30708938 . T C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGCCACTGTGGCACTGCCT;RSEQ=GGAACTGTTGAGGTGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:21,16:0,0:1:0,2:28.5:1:30.6:1:1:0:60:36:1:0:1.1 1/1:29:29:12,17:0,0:1:0,2:24.9:1:30.3:1:1:0:60:28:1:0:1.3 -5 30708947 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18363;SOR=Inf;LSEQ=TGGCACTGCCTTGGAACTGT;RSEQ=GAGGTGGGAACCACTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:0:2,0:26.7:1:29.8:1:1:0:60:37:1:0:1.1 0/1:29:2:1,1:11,16:0.069:2,2:26.5:1:28:1:1:1.44:60:4:0.069:0:2 -5 31061347 . C T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54023;SOR=0;LSEQ=AAAACATGAACCCTCTGATT;RSEQ=TGACAACTTCAAATATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:23:1:31.7:1:1:0:60:6:0.1429:0:1 0/0:8:0:0,0:8,0:0:0,0:15.3:1:32.1:1:1:0:60:16:1:0:0 -5 31061463 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05397;SOR=2.36161;LSEQ=GACTTAGCAAGCATTTAAGG;RSEQ=GCCTTAACGTCAATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:12:9,3:115,14:0.0851:2,2:18.7:1:30.6:1:0.16061:2.71188:60:24:0.0863:0:1 0/1:83:15:11,4:52,16:0.1807:2,2:19.9:1:29.6:1:0.74996:1.17935:60:30:0.1829:0:1.1 -5 31061575 . C T 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=1.92191;LSEQ=TGCAGGGAATTCCTATGACA;RSEQ=GCATACATTAAACTGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:389:197:80,117:91,100:0.5064:2,2:25.6:1:29.9:1:0.1839:1.32987:60:20.889:0.496:0:1.1 1/0:229:152:69,83:38,38:0.6638:2,2:26.5:1:29.7:1:0.57395:1.20192:60:49.667:0.6622:0:1.1 -5 31061706 . G GA 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.57047;SOR=0;LSEQ=ATGGATATTGCCAACGATAG;RSEQ=AAAAAAAAACAGGGCAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:4:0,4:5,59:0.058:2,0:29.8:1:29.3:1:1:0:60:8:0.0597:0:0 0/0:25:0:0,0:5,20:0:2,0:19.4:1:30.4:1:1:0:60:50:1:0:0.1 -5 31652486 . G A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TAAGGTTTGCCAACAATGGC;RSEQ=GTCCTGCAGATAGGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:38.7:1:29.3:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:30.5:1:1:0:60:4:1:0:1 -5 31652673 . G T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20624;SOR=Inf;LSEQ=ATCCAACTAATGTTTATTTA;RSEQ=CACATGCCACATAGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:96,26:0:2,0:24.2:1:32:1:1:0:60:121:1:0:0.1 0/1:102:2:1,1:74,26:0.0196:2,2:7:0:26.5:1:0.46127:2.81176:60:4:0.0198:0:1 -5 31652765 . A C 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04489;SOR=0.68998;LSEQ=TGCCTTGAATTATCAATTGC;RSEQ=TCAAATTGTTTGGCTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:310:219:101,118:45,46:0.7065:2,2:26.8:1:31.4:1:0.61872:1.14242:60:53.75:0.7096:0:1.1 1/0:242:151:68,83:43,48:0.624:2,2:28:1:30.7:1:0.79046:1.09304:60:74.5:0.6234:0:1.1 -5 31652931 . A G 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTCGAGACCAGCCTGGCC;RSEQ=ACATGGTGAAACCCCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:0,25:0,0:1:0,1:26.2:1:31.3:1:1:0:54.7:24:1:0:1.2 1/1:9:9:0,9:0,0:1:0,0:23.8:1:32.1:1:1:0:53.3:18:1:0:1 -5 31840606 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=TAACAGTAGCTATTTTGCCA;RSEQ=GAATTCATAGGGAATGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:26:1:31.5:1:1:0:60:8:1:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:30.5:1:1:0:60:4:1:0:1.5 -5 31840805 . T C 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0163;SOR=Inf;LSEQ=AGTGCTTAATGTGCTCAATA;RSEQ=GCACATTAATTCTCTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:32,5:0:2,0:24:1:30.5:1:1:0:56.3:36:1:0:0.1 0/1:31:5:4,1:20,6:0.1613:2,2:33.6:1:30.6:1:1:1.19:47.4:10:0.1613:0:1 -5 31848168 . C A 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92115;LSEQ=GTTGAAAAGCAGAGGTGGAA;RSEQ=TATCCCAAAATGTCCCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:4:3,1:32,22:0.069:2,2:23:1:30.5:1:1:2.04:60:8:0.069:0:1.3 0/1:47:3:2,1:26,18:0.0638:2,2:6.7:1:32:0:1:1.38:60:6:0.0652:0:1.3 -5 32553710 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82277;LSEQ=CAAGGAGGTTAAAAATACAA;RSEQ=GCCCAAAGGCGAGTAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:8,3:8,1:0.55:2,2:22.3:1:32.6:1:0.59133:2.84745:49.2:22:0.5789:0:1 1/0:16:8:5,3:7,1:0.5:2,2:26.4:1:29.6:1:0.56923:3.83897:53.5:16:0.5:0:1 -5 32553853 . A G 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18467;LSEQ=TCCTGTAAATGCCGGGTGGC;RSEQ=TCTTGTACTATCCCTGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:3,4:4,11:0.3182:2,2:20:1:30.6:1:0.63022:1.99:60:14:0.3182:0:1.3 0/1:14:5:0,5:3,6:0.3571:2,0:12:1:29.2:1:0.25824:0:57.2:10:0.3846:0:1.2 -5 32673983 . T A 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.55944;SOR=0.36341;LSEQ=TAAGACCATCTGTAGCATGA;RSEQ=GACCTTGATTCTAGAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:17.5:1:29:1:1:2.44949:60:4:0.3333:0:1 0/1:7:1:1,0:6,0:0.1429:0,0:46:0:32:0:1:0:60:2:0.1429:0:1 -5 32674283 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4697;SOR=Inf;LSEQ=AGCAGTTTTGGAGAGTCACT;RSEQ=CTGCCAAAGAGTCTATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:17.4:1:32.6:1:1:0:55.2:10:1:0:0 0/1:7:2:1,1:2,3:0.2857:2,2:26.5:1:27:1:1:1.41:60:4:0.2857:0:1 -5 33816874 . T A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGTACATCAACTGAGGA;RSEQ=GAGAAGCTGAAGAGCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:25.5:1:30.5:1:1:0:60:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 33816914 . A C 53 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTCTAAGAGTGAGTAGG;RSEQ=TTGTTCTGAATCAGATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:19.8:1:26.8:1:1:0:60:3:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 33816922 . G C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGAGTAGGATTGTTCT;RSEQ=AATCAGATTTTAACTTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:41:1:31.5:1:1:0:60:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 33817078 . T A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44525;SOR=2.24676;LSEQ=CCCTCAGTAAGTGTGTAGTT;RSEQ=ACGGTGCTTCCTCTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:21:21,0:16,0:0.5676:1,1:20:1:28.6:1:1:0:60:42:0.5676:0:2 1/0:8:6:6,0:2,0:0.75:0,0:25:1:29:1:1:0:60:12:0.75:0:2.2 -5 33817083 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45109;SOR=2.3935;LSEQ=AGTAAGTGTGTAGTTTACGG;RSEQ=GCTTCCTCTCCAGGGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:23,0:16,0:0.5897:1,1:20.7:1:32.8:1:1:0:60:46:0.6053:0:2.1 1/0:9:7:7,0:2,0:0.7778:0,0:24.9:1:32.3:1:1:0:60:14:0.7778:0:2.1 -5 33817174 . A G 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26377;SOR=1.48705;LSEQ=AAGCTGTATCCTTAAAAAAT;RSEQ=TTAATCAGACTTCTACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:147:88:88,0:58,1:0.5986:1,1:25:1:32.5:1:0.40136:0:60:87:0.5959:0:1.1 1/0:58:40:40,0:18,0:0.6897:1,1:21.3:1:32.9:1:1:0:60:80:0.7018:0:1.2 -5 33817339 . A G 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.6563;LSEQ=CTACAGGTAGTAAGTAGTCT;RSEQ=TGTTTTACAAGAGACATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:890:526:230,296:152,211:0.591:2,2:24.7:1:31.9:1:0.62953:1.08:60:86.667:0.5889:0:1.3 1/0:594:419:188,231:78,95:0.7054:2,2:24.2:1:31.3:1:1:1.00883:60:418:0.7085:0:1.3 -5 33817367 . T C 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45556;SOR=1.12595;LSEQ=CAAGAGACATTAACTTGAAC;RSEQ=TTAGTGGAAACTGCCTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:139:50,89:206,361:0.1969:2,2:24.3:1:31.8:1:1:1.01571:60:278:0.1986:0:1.8 0/1:453:98:33,65:141,214:0.2163:2,2:26.9:1:31.2:1:0.29313:1.29705:60:48:0.2138:0:1.9 -5 33817593 . T C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.60435;SOR=2.62691;LSEQ=GGAGTTCTTTATATTGTTAT;RSEQ=ATGGAAAATACCAAACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:0,11:0,10:0.5238:0,0:19:1:32.7:1:1:0:60:22:0.55:0:1 1/0:4:3:0,3:0,1:0.75:0,0:15.3:1:33.7:1:1:0:60:6:0.75:0:1 -5 33841375 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=TTGTCTGCAGCTACTCCCTC;RSEQ=TTCCTTTTCATCCTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:2,8:0.1667:2,2:25:1:32:0:0.45455:3.46:60:4:0.1667:0:1 0/0:6:0:0,0:2,4:0:2,0:18.7:1:27.3:1:1:0:60:5:1:0:0.7 -5 33997097 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08511;SOR=Inf;LSEQ=CATTAAATTATTTAAAATGT;RSEQ=CAGTATTTTTTTTTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:170,23:0:2,0:19.7:1:31.1:1:1:0:60:63.333:1:0:0.1 0/1:80:2:1,1:72,6:0.025:2,2:13:1:31:1:0.16835:11.18701:60:4:0.025:0:1 -5 33997102 . A AT 85 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.44251;SOR=0.3066;LSEQ=AATTATTTAAAATGTCCAGT;RSEQ=TTTTTTTTTAATTTTACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:7:5,2:171,28:0.034:2,2:28.6:1:30.4:1:0.27032:2.42914:60:14:0.0343:0.0049:0.7 0/1:94:1:1,0:81,12:0.0106:2,0:29:0:32:0:1:0:60:2:0.0106:0:0 -5 33997283 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09683;SOR=Inf;LSEQ=CTTAGCAATTCTGCTGTTTT;RSEQ=TCATACCCTATATGAGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:100,210:0:2,0:24.3:1:32:1:1:0:60:50.667:0.9967:0:0.1 0/1:141:2:1,1:51,88:0.0142:2,2:8.5:1:26.5:1:1:1.72:60:4:0.0144:0:1 -5 33997291 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08937;SOR=Inf;LSEQ=TTCTGCTGTTTTGTCATACC;RSEQ=TATATGAGGGTTGAGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:105,193:0:2,0:23.7:1:31.6:1:1:0:60:48.667:1:0:0.1 0/1:128:2:1,1:49,76:0.0156:2,2:27:0:32.5:1:1:1.55:60:4:0.0156:0:1.5 -5 33997307 . A C 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00415;SOR=0;LSEQ=TACCCTATATGAGGGTTGAG;RSEQ=GCTGTCACCAGCATTAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:16:6,10:113,148:0.0578:2,2:24.4:1:31.2:1:0.79658:1.27143:60:32:0.0597:0:1 0/0:119:0:0,0:53,66:0:2,0:23.6:1:30.1:1:1:0:60:58.5:1:0:0.1 -5 34487059 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGCACAGTATCAGTTGT;RSEQ=TGTCCTCATGACTTTGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:27.5:1:1:0:60:4:1:0:1.5 -5 34487707 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTATTAATACTTCAGTTG;RSEQ=AAGTTACAGAAACAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:12,1:0.1333:1,2:28:0:31.5:1:0.25714:8.83176:60:4:0.1333:0:1.5 0/0:5:0:0,0:5,0:0:0,0:26.4:1:33:1:1:0:60:10:1:0:0 -5 34487850 . A G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01184;SOR=Inf;LSEQ=CTACTGCAGTCCTGCCATTC;RSEQ=CGTAACTCATTGGTGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:30,38:0:2,0:27.4:1:29.8:1:1:0:60:136:1:0:0.1 0/1:35:4:2,2:13,18:0.1143:2,2:22.5:1:30:1:1:1.37:60:8:0.1143:0:1 -5 34487998 . T C 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAAAAGTGAGATCACA;RSEQ=AGGTTATTTCTTGTTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:18.7:1:33:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 34489182 . G C 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGATAGCAGAGCCACCCCC;RSEQ=CCCCACCACCACCCTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:27:1:1:0:60:4:1:0:5 -5 34489187 . A C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGCAGAGCCACCCCCGCCCC;RSEQ=CCACCACCCTGTGTTACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29:1:1:0:60:4:1:0:5 -5 34605325 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.2281;LSEQ=GGATAAAAGAACATGGATCA;RSEQ=TCAGTGCACACTCATCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:93:53,40:174,149:0.222:2,2:26.1:1:30.3:1:0.63726:1.13:60:45.5:0.2203:0:1.1 0/1:371:178:96,82:103,89:0.4798:2,2:25.4:1:29.8:1:1:1.01:60:177:0.4836:0:1.1 -5 34605375 . C A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41597;SOR=2.48021;LSEQ=AAATAACTTGAAAGCTATAT;RSEQ=ATACAAATGGTGGGTTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:2:2,0:149,226:0.0053:2,0:1:0:24:1:0.15979:0:60:4:0.0054:0:1 0/1:306:4:3,1:128,174:0.0131:2,2:22:1:27.5:1:0.31699:4.06:60:8:0.0133:0:1 -5 35856997 . C T 22 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30041;SOR=3.51466;LSEQ=ATCTAAGCTTCTCTGTCTTC;RSEQ=TCCCTCCCTCCCTTCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:1:0,1:310,27:0.0029:2,0:2:0:14:0:0.08284:0:60:0:0:0:1 0/1:195:2:1,1:167,26:0.0103:2,2:18:1:22.5:1:0.25837:6.32186:60:4:0.0106:0:1.5 -5 35857055 . ACT A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1.04651;LSEQ=ACACACTGGCTCACACATCT;RSEQ=CTCTCTCTCTATCTCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:893:9:5,4:543,341:0.0101:2,2:17:1:30.2:1:0.74022:1.27353:60:18:0.0103:0.0034:0.4 0/1:664:7:6,1:402,255:0.0105:2,2:29.3:1:31.3:1:0.25873:3.80:60:14:0.0108:0:0.3 -5 35857177 . G C 275 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.76749;SOR=0.95934;LSEQ=AAATGGTGAGTCATTTCTAA;RSEQ=TTTTCTTATGGATTTTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:687:392:129,263:86,208:0.5706:2,2:24.5:1:32:1:0.31926:1.19:60:55:0.5678:0:1.3 1/0:505:283:98,185:77,144:0.5604:2,2:23.2:1:31.5:1:1:1.00941:60:93.333:0.5589:0:1.3 -5 35857207 . C T 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.44614;LSEQ=GGATTTTGGATTATCTGTAG;RSEQ=ATGGTTTCAGGTTATTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:124:23,101:56,214:0.3147:2,2:25:1:28.3:1:0.6852:1.14869:60:40.333:0.3119:0:1 0/1:259:44:13,31:48,167:0.1699:2,2:22.9:1:27.8:1:0.33097:1.46:60:88:0.1712:0:1.1 -5 35857235 . C G 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99786;LSEQ=CAGGTTATTCAGTTCCCTAA;RSEQ=AGACCTGAGTCAGGCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:124:11,113:10,106:0.5167:2,2:23.8:1:31.5:1:1:1.03:60:123:0.5146:0:2.3 1/0:124:64:6,58:5,55:0.5161:2,2:25.3:1:31.4:1:1:1.14:60:128:0.5161:0:2.3 -5 35857262 . A G 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76696;SOR=0.88355;LSEQ=GAGTCAGGCACTGGGTTTGA;RSEQ=TGCAGTTTGAGAATTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:136:78:1,77:2,56:0.5735:1,1:25.1:1:32.4:1:0.57523:2.72969:60:77:0.5704:0:2.3 1/0:70:38:0,38:0,32:0.5429:1,1:24.9:1:31.6:1:1:0:60:76:0.5429:0:2.3 -5 35857294 . A AT 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54992;SOR=0;LSEQ=AATTTCCCACATATTCAGTC;RSEQ=TTTTTTTTAATGTTTAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:3:0,3:1,76:0.0375:1,0:20.7:1:30.3:1:1:0:60:6:0.0375:0.0125:2 0/0:39:0:0,0:0,39:0:1,0:24.1:1:29.6:1:1:0:60:18.5:1:0:0.9 -5 35857308 . T TC 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46749;SOR=1.52948;LSEQ=TCAGTCATTTTTTTTAATGT;RSEQ=TAACCACCATGACAGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:41:1,40:0,21:0.6613:1,1:23.4:1:32.2:1:1:0:60:82:0.6613:0.1613:1.1 1/0:28:21:0,21:0,7:0.75:0,1:25.7:1:31.8:1:1:0:60:42:0.75:0.1071:0.7 -5 35860637 . A G 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=AAAAACTCCAGTTTAAATAC;RSEQ=GAAAAGAATGTGTTCAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:22.3:1:18.7:1:1:0:60:0.5:0.2:0:3 1/1:3:3:2,1:0,0:1:0,2:16.3:1:30:1:1:0:60:6:1:0:1 -5 35860710 . AT A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTTACTCATTATGATGG;RSEQ=TTTTTTTTTCTATTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:12,1:0.1333:1,0:10.5:1:31.7:1:1:0:60:4:0.1333:0.0667:0 0/0:5:0:0,0:4,1:0:2,0:14.2:1:29.2:1:1:0:60:10:1:0:0.4 -5 35860873 . C T 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATGTCTGCCACAGAGTCTG;RSEQ=TATTTTATTAAGGTCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:55:50,5:109,6:0.3235:2,2:22.4:1:29.6:1:0.33707:1.80989:60:54:0.3253:0:1.1 0/0:111:0:0,0:95,16:0:2,0:20:1:31.9:1:1:0:60:222:1:0:0.1 -5 35861068 . T C 280 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.95967;SOR=0.99096;LSEQ=TGAGGACCCAGATGTCAACA;RSEQ=CACCAATCTGGAATTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:907:485:180,305:165,256:0.5347:2,2:26.4:1:31.4:1:0.53742:1.09202:60:79.833:0.5346:0:1.1 1/0:693:369:163,206:153,170:0.5325:2,2:25.1:1:30.8:1:0.40153:1.13721:60:72.8:0.5322:0:1.2 -5 35861149 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29984;SOR=3.5229;LSEQ=CTCTGTCTCTCTTTTCATAT;RSEQ=CTCTTTTTAATAGCCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:0,1:38,257:0.0034:2,0:39:0:30:0:1:0:60:2:0.0034:0:1 0/1:169:2:1,1:20,147:0.0118:2,2:21.5:1:28:1:0.23373:7.20:60:4:0.0118:0:1 -5 35861152 . C G 148 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00037;SOR=3.25306;LSEQ=TGTCTCTCTTTTCATATGCT;RSEQ=TTTTTAATAGCCACAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:16:1,15:31,230:0.0578:2,1:21.8:1:32.9:1:0.7037:2.01771:60:32:0.0584:0:1.6 0/1:162:27:3,24:13,122:0.1667:2,2:23.1:1:31.3:1:0.73245:1.17:60:54:0.1698:0:1.3 -5 35861159 . A G 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00241;SOR=Inf;LSEQ=CTTTTCATATGCTCTTTTTA;RSEQ=TAGCCACAAAAGAAAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:25,213:0:2,0:23.7:1:30.7:1:1:0:60:38.667:1:0:0.2 0/1:140:6:1,5:9,125:0.0429:2,2:26.3:1:30.8:1:0.36436:2.75:60:12:0.0435:0:1.2 -5 35861268 . T G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66449;SOR=0.51409;LSEQ=ACCAAAAACACTCATACAAA;RSEQ=CTCCTCTCACGGTTCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:0,12:0,6:0.6667:0,0:18.9:1:31.3:1:1:0:60:24:0.7059:0:1 1/0:8:4:0,4:0,4:0.5:0,0:33.3:1:33:1:1:0:60:8:0.5:0:1 -5 35867343 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14176;SOR=Inf;LSEQ=ATACATCAATGTGCATATGA;RSEQ=ACTATTCCACTGCATACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:185,46:0:2,0:23.3:1:30.4:1:1:0:60:114.5:1:0:0.1 0/1:140:2:1,1:110,28:0.0143:2,2:12:1:33:0:0.37256:3.87775:60:4:0.0144:0:1.5 -5 35867351 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16018;SOR=Inf;LSEQ=ATGTGCATATGATACTATTC;RSEQ=ACTGCATACAGGAACTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:199,61:0:2,0:24.3:1:30.9:1:1:0:60:51:1:0:0.1 0/1:174:2:1,1:129,43:0.0115:2,2:24:1:25:1:0.44289:2.97718:60:4:0.0119:0:1 -5 35870814 . A C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCTTCTCCCAGCAGTATT;RSEQ=GGGGCACTTTCCATCTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:26:1:29:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 35870979 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07895;SOR=Inf;LSEQ=AAGGCCACACCCCACTGCAA;RSEQ=AGAGGCTGGAGAATGCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:0:1,0:25.9:1:32.1:1:1:0:60:28:1:0:0.2 0/1:6:2:1,1:4,0:0.3333:0,2:13.5:1:26.5:1:0.33333:0:60:4:0.3333:0:1 -5 35871190 . G A 252 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19577;SOR=1.16359;LSEQ=CTCCTTTTGACCTGAGTGTC;RSEQ=TCTATCGGGAAGGAGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:717:332:213,119:238,147:0.463:2,2:24.6:1:30.1:1:0.53575:1.11:60:65.4:0.4665:0:1.1 1/0:567:284:172,112:170,112:0.5009:2,2:26.2:1:29.8:1:1:1.01:60:93.667:0.5:0:1.1 -5 35871273 . C T 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGTAAAAGTTTTAATGCA;RSEQ=GATGTAGCTTACCGCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:843:0:0,0:336,505:0:2,0:25.7:1:30.3:1:1:0:60:63.692:0.9988:0:0.3 0/1:621:63:26,37:221,337:0.1014:2,2:28:1:29.1:1:0.78788:1.07:60:30.5:0.0997:0:1.2 -5 35871291 . G A 194 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01498;LSEQ=CACGATGTAGCTTACCGCCA;RSEQ=GAAAAGGATGAAAACAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:78:30,48:218,411:0.1103:2,2:27.3:1:30.9:1:0.53041:1.18:60:156:0.1116:0:1.1 0/0:540:1:1,0:203,336:0.0019:2,0:3:0:27:0:0.37778:0:60:2:0.0019:0:1 -5 35871460 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATCTCCCAATATTGGCC;RSEQ=CATGAAAACCTGGATCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:0,24:0.0769:1,2:24:1:31.5:1:0.07692:0:60:4:0.08:0:1 0/0:11:0:0,0:0,11:0:0,0:23.5:1:31.9:1:1:0:60:22:1:0:0 -5 35873872 . T G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0.17324;LSEQ=GACACCCTTGGAGGGCACTC;RSEQ=TACACTTTCTTTGGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:57:1,56:1,56:0.5:1,1:22:1:32.3:1:1:1:60:56:0.4956:0:1.1 0/1:41:6:1,5:0,35:0.1463:1,2:12.7:1:30.3:1:0.14634:0:60:12:0.1463:0:1 -5 35874575 . C T 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00068;SOR=1.60559;LSEQ=GATGGATCCTATCTTACTAA;RSEQ=CATCAGCATTTTGAGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1712:112:54,58:807,793:0.0654:2,2:24.9:1:30:1:0.69614:1.09297:60:55:0.0651:0:1.1 0/1:1138:115:56,59:519,500:0.1011:2,2:24:1:28.8:1:0.69427:1.09352:60:18.167:0.0971:0:1.1 -5 35875134 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATTACAAATACCCTAAT;RSEQ=TGAAAAGTACTGCCTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,1:0.4:2,0:26.5:1:33:0:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 35875428 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCTCTGGTCCAACCCCT;RSEQ=CTTGAATTGATAGGGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:48,0:0.04:1,2:29:1:31.5:1:0.04:0:60:4:0.04:0:1 0/0:13:0:0,0:11,2:0:2,0:23.9:1:31.3:1:1:0:60:26:1:0:0 -5 35875518 . C T 152 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTAGAGCCAAGACTAGAAAT;RSEQ=TGTTCTTCTGATTCCAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:35:33,2:131,9:0.2:2,2:23.1:1:29.8:1:1:1.13:60:34:0.1965:0:1.7 0/0:105:0:0,0:96,9:0:2,0:22.9:1:31.4:1:1:0:60:104:1:0:0.2 -5 35875593 . A T 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.53488;LSEQ=CTCTGCCATTCACTTCATCT;RSEQ=TCAATGTTCTCTGATTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:694:389:277,112:213,89:0.5605:2,2:24:1:30:1:0.86613:1.03:60:388:0.5681:0:1.1 0/1:444:180:123,57:176,86:0.4054:2,2:24.6:1:29.8:1:0.83641:1.05:60:179:0.4068:0:1.1 -5 35876274 . A G 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.40355;LSEQ=GCCCATCTGAGGATGTAGTC;RSEQ=TCACTCCAGAAAGCTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1080:511:244,267:272,297:0.4731:2,2:24.7:1:30.5:1:1:1.00215:60:62.875:0.471:0:1.1 0/1:707:188:87,101:236,283:0.2659:2,2:25.2:1:30.6:1:0.86462:1.03:60:376:0.2674:0:1.1 -5 35876623 . G A 41 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03089;SOR=Inf;LSEQ=AGACTGAACTTACCGTGAGC;RSEQ=ACAAAGATGATTTAAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:47,222:0:2,0:24:1:30.5:1:1:0:60:25.9:1:0:0.1 0/1:124:3:2,1:30,91:0.0242:2,2:17:1:26.3:1:0.16313:5.96:60:6:0.0248:0:1.3 -5 36367860 . C T 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCTTAGCTGGCTGTGCTC;RSEQ=TCGGCTGTGTTTAACCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:38:1:33:1:1:0:60:4:0.4:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 36367987 . T G 123 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTTGGGGAATATTCAAT;RSEQ=GTTCATGTTTGGATCTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:14,0:3,1:0.7778:2,1:25.9:1:32.4:1:0.22222:0:60:28:0.7778:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 36368082 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03443;SOR=0.35074;LSEQ=AACAACTACTGATGATTCCT;RSEQ=TTATCTCTTTCCCAGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:50:50,0:20,0:0.7143:1,1:24.2:1:32.1:1:1:0:60:49:0.7206:0:1.2 0/1:28:13:13,0:15,0:0.4643:1,1:28.5:1:30.6:1:1:0:60:12:0.4444:0:1.4 -5 36368227 . G T 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16506;SOR=5.82097;LSEQ=TAGCAACATTCACATGTGCT;RSEQ=TAACTCTCCCCCACCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:1:0,1:282,236:0.0019:2,0:1:0:26:0:0.45665:0:60:2:0.0019:0:2 0/1:360:4:2,2:188,168:0.0111:2,2:34:1:29.5:1:1:1.1187:60:8:0.0112:0:1.5 -5 36368254 . T C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25641;LSEQ=TCCCCCACCATGCCTGATGC;RSEQ=GATTTCTAACCATCAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:571:440:213,227:58,73:0.7706:2,2:24.8:1:30:1:0.4264:1.18:60:54:0.7701:0:1.1 0/1:385:178:89,89:96,111:0.4623:2,2:24:1:29.8:1:0.53942:1.16:60:58.333:0.4617:0:1.2 -5 36368354 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53768;SOR=0;LSEQ=TCCTCCTTCCCCTGTCTCTG;RSEQ=GCCTCAGTCAGGTATCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:43,140:0.0108:2,2:7:1:29:1:0.42009:3.23:60:4:0.0109:0:1 0/0:104:0:0,0:24,80:0:2,0:21.2:1:29.2:1:1:0:60:51:1:0:0.1 -5 36370268 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGTGTCCATATGTACTCA;RSEQ=TGTTTAACTCCCCCTAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 36391256 . ACAG A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.23881;SOR=0;LSEQ=ATATTCACCCACCAGCAGCA;RSEQ=CAGCAGCAGCCCCTAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:0.0606:2,2:33:1:31:1:1:1.06462:60:4:0.0625:0:0 0/0:34:0:0,0:16,18:0:2,0:24.3:1:31.4:1:1:0:60:33:1:0:0.5 -5 37743328 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCCTCCCCCAAGCTAA;RSEQ=GGAGGCGGTGAGTGAACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:25.5:1:31:1:1:1.41:60:4:0.2857:0:1.5 0/0:1:0:0,0:1,0:0:0,0:28:0:34:0:1:0:60:2:1:0:0 -5 37743917 . A C 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGTGGCCTTAGTCTTTGC;RSEQ=GACCAACAGACTTTGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:1:0,2:26.2:1:31.3:1:1:0:60:22:1:0:1.1 1/1:18:17:10,7:1,0:0.9444:0,2:20.4:1:29.8:1:1:0:60:34:0.9444:0:1.1 -5 37744238 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18617;SOR=Inf;LSEQ=TGGGAGCGAATCAGATGAAT;RSEQ=GAGCCTGAAGTGAACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,15:0:2,0:25.1:1:30.4:1:1:0:60:54:1:0:0.1 0/1:21:2:1,1:10,9:0.0952:2,2:49:0:30:1:1:1.10554:60:4:0.0952:0:1 -5 37744444 . GA G 70 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTCAACAAAAAAATGCT;RSEQ=AAACCCACAAGGCCAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:0.625:2,2:25:1:30.4:1:1:2.60168:60:10:0.625:0.125:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38942090 . T C 90 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTGTTCCACTGTCATTA;RSEQ=GCTTTTAAAATGAAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:24.1:1:30.1:1:1:0:60:7:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38942628 . T C 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17451;SOR=0;LSEQ=AATGTTGCCATCTTTGTTCA;RSEQ=TGCAACCTCTGAGTCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:6:1,5:8,41:0.1091:2,2:17.2:1:32:1:1:1.02:60:12:0.1154:0:1 0/0:22:0:0,0:0,22:0:1,0:22.7:1:30.4:1:1:0:59.5:44:1:0:0.2 -5 38943156 . T C 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=GGTATCACTTACTTTAAAAA;RSEQ=AGATTTCCCTACAGATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:0,147:0:1,0:25.2:1:28.5:1:1:0:60:72.5:1:0:0 0/1:56:5:1,4:2,49:0.0893:1,2:21.4:1:32.2:1:0.24874:5.77:60:10:0.0893:0:2 -5 38943260 . G GT 93 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.31889;SOR=0.23522;LSEQ=CTTAGACATTCTGAGTTTGG;RSEQ=TTTTTTTTTAAAAAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:0,2:0.5333:0,0:31.3:1:31.1:1:1:0:60:16:0.5714:0:0 0/1:5:1:0,1:0,2:0.2:0,0:40:0:30:0:1:0:60:2:0.2:0:1 -5 38943269 . T TA 49 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54118;SOR=0;LSEQ=TCTGAGTTTGGGTTTTTTTT;RSEQ=AAAAAAAATGATTATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:0,4:0,10:0.2857:0,0:19.3:1:24.5:1:1:0:55:3:0.2308:0.0714:2 0/0:3:0:0,0:0,3:0:0,0:13.7:1:30:1:1:0:60:6:1:0:2.3 -5 38944534 . C T 74 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03196;SOR=5.6575;LSEQ=AAACAAATAATACTCATGCA;RSEQ=ATAGTTTACTCACGTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1023:2:0,2:663,358:0.002:2,0:1:0:19:1:0.12361:0:60:1:0.001:0:1 0/1:638:7:2,5:383,246:0.011:2,2:20:1:26.7:1:0.11912:3.88395:60:14:0.0111:0:1.1 -5 38945854 . T A 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35698;SOR=2.67727;LSEQ=TAAGTAAATATAAAACATAA;RSEQ=CCAATAAAGATAATACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:2:2,0:75,263:0.0059:2,0:1:0:26:1:0.05077:0:60:4:0.006:0:1 0/1:192:3:2,1:39,150:0.0156:2,2:9.3:1:22.7:1:0.1158:7.58:60:2:0.011:0:1 -5 38945855 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1283;SOR=Inf;LSEQ=AAGTAAATATAAAACATAAT;RSEQ=CAATAAAGATAATACTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:68,258:0:2,0:22.8:1:31:1:1:0:60:64.2:0.9969:0:0.1 0/1:183:2:1,1:37,144:0.0109:2,2:30:1:25:1:0.37309:3.85:60:4:0.011:0:1 -5 38945919 . C T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=6.28133;LSEQ=TTTTAAAGAAAGCTTAAGCA;RSEQ=ATTTTATGACTCAAAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:12:0,12:1,86:0.1212:1,0:22.6:1:28.7:1:1:0:60:24:0.1237:0:1.1 0/1:47:22:0,22:0,25:0.4681:1,1:27.2:1:28.4:1:1:0:60:44:0.4783:0:1 -5 38947098 . AT A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATAAATTTCTACAGAGA;RSEQ=ATATGGATAAAGAAATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:15,2:0,0:1:0,2:27:1:30.8:1:1:0:60:34:1:0.1176:0.2 1/1:3:3:2,1:0,0:1:0,2:22:1:31:1:1:0:60:6:1:0.3333:0 -5 38947185 . C G 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02056;SOR=0;LSEQ=AAGGACTAAATAAAAGAGTA;RSEQ=AGAGTAGTTGAAAAGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:9,0:25,1:0.2571:1,0:17.1:1:31.6:1:1:0:60:18:0.2647:0:1.4 0/0:18:0:0,0:17,1:0:1,0:20.2:1:31.3:1:1:0:60:36:1:0:0.1 -5 38947288 . G T 34 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03933;SOR=Inf;LSEQ=TGGTGCCCACCCTAAATTAT;RSEQ=ATTTCTAGTAAGCAGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:244,49:0:2,0:23.6:1:31.8:1:1:0:60:57.6:1:0:0 0/1:152:3:1,2:121,28:0.0197:2,2:8.3:1:21.7:1:0.09956:8.46848:60:2:0.0134:0:1.3 -5 38949632 . C T 150 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAGGATTTTCTTCCCCCCT;RSEQ=GCAGCTGCAAGAATCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:36:9,27:34,83:0.2353:2,2:27.1:1:29.1:1:0.67842:1.22729:60:11:0.2245:0:1.1 0/0:70:0:0,0:13,57:0:2,0:24.9:1:30.2:1:1:0:60:140:1:0:0.1 -5 38949775 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02916;SOR=Inf;LSEQ=TATTTAAATTTGTTAAAATG;RSEQ=AACCATTATTGGTCACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:0:0,0:419,144:0:2,0:23.4:1:32:1:1:0:60:79.429:1:0:0.1 0/1:398:4:2,2:280,114:0.0101:2,2:14.3:1:29.8:1:0.58345:2.44985:60:8:0.0101:0:1 -5 38950776 . G A 281 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGATATCAAGGAAAAATGT;RSEQ=CTAGTAGAGCTGCTGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:793:792:278,514:0,0:0.9987:0,2:26.1:1:29.2:1:1:0:60:98:0.9987:0:1.1 1/1:550:550:194,356:0,0:1:0,2:26.2:1:28.8:1:1:0:60:90.667:1:0:1.1 -5 38950905 . AT A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACATCACATTTCAGGAA;RSEQ=TTTTTTTTAGTCATCTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:2,114:0.0169:1,0:39:0:31:1:1:0:60:4:0.0171:0:0 0/0:31:0:0,0:0,31:0:1,0:28.5:1:29.7:1:1:0:60:30:1:0:0.2 -5 38951829 . T C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCACAAATCATTTTATATA;RSEQ=AACTATTTTTGTTACTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38952655 . GA G 151 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.27243;SOR=0.50231;LSEQ=CCAAAATGGTTGCGTTTGTG;RSEQ=AAAAAAAAAACTTATTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:31:5,26:0,13:0.6889:1,2:27.3:1:30.6:1:0.30051:0:60:62:0.6889:0.0222:0.1 1/0:21:11:0,11:0,8:0.5238:0,0:29.7:1:31:1:1:0:60:22:0.5238:0:0.1 -5 38952825 . A T 133 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGAACAGCTGGGTTAC;RSEQ=GGAATACTGGAGTATCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:19,1:0,0:1:0,1:25.1:1:31:1:1:0:60:40:1:0:1.1 1/1:1:1:1,0:0,0:1:0,0:12:0:33:0:1:0:60:2:1:0:1 -5 38953427 . T C 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGAGATAATACACTTATAT;RSEQ=GGCAGGAACAATCCAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:101:100:93,7:0,0:0.9901:0,2:23.6:1:30.9:1:1:0:60:99:0.99:0:1.9 1/1:40:40:38,2:0,0:1:0,2:27:1:31.4:1:1:0:60:80:1:0:2.1 -5 38953447 . T A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCAGGAACAATCCAGTCT;RSEQ=AAATATTAATCTAATAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:125:125:117,8:0,0:1:0,2:24.2:1:28.3:1:1:0:60:40.667:1:0:1.7 1/1:69:69:68,1:0,0:1:0,1:20.3:1:28.4:1:1:0:60:68:1:0:1.7 -5 38953503 . G GA 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.65574;SOR=1.26496;LSEQ=TTTATCTATTTAGTATAAAT;RSEQ=AAAAAAAAACTTAAAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:11:8,3:256,90:0.0306:2,2:15.8:1:30.6:1:1:1.06648:60:22:0.0309:0.0111:0.5 0/1:260:10:7,3:187,60:0.0385:2,2:27.6:1:29.9:1:0.71059:1.33411:60:20:0.0398:0.0077:0.1 -5 38953661 . G GA 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.15046;SOR=0;LSEQ=TTCTGTAATAATATTCTGGA;RSEQ=AAAGAAAAAAAAATACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:4:1,3:102,283:0.0103:2,2:23:1:30.5:1:1:1.08106:60:8:0.011:0.0026:2.3 0/0:266:0:0,0:65,199:0:2,0:22.4:1:30.2:1:1:0:60:23:0.9961:0:0.1 -5 38953665 . G GA 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.01995;SOR=0.6481;LSEQ=GTAATAATATTCTGGAGAAA;RSEQ=AAAAAAAAATACCATGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:360:274:57,217:29,37:0.7611:2,2:27.6:1:30.1:1:0.00023:2.97252:60:136:0.764:0.0444:0.2 1/0:242:163:29,134:19,40:0.6736:2,2:25.1:1:30.1:1:0.02688:2.18623:60:162:0.6778:0.0537:0.1 -5 38954825 . G GT 139 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.13765;SOR=1.60155;LSEQ=TTTAGCAATGTTAAGATTTT;RSEQ=TTTTTTTTTTACTATTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:24:21,3:237,81:0.0694:2,2:24.4:1:30.3:1:0.21866:2.39:60:48:0.0712:0.0029:0.1 0/1:253:27:21,6:165,61:0.1067:2,2:24.6:1:29.3:1:0.81764:1.29:59.6:54:0.1093:0.0237:0.2 -5 38954994 . T C 261 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61957;LSEQ=AAAGATGATTACTATATCTC;RSEQ=TGGCTAATTTAAATATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:287:286:52,234:1,0:0.9965:0,2:25:1:32:1:0.18467:0:60:94.333:0.9965:0:1 1/1:178:177:37,140:0,0:0.9944:0,2:24.6:1:31.5:1:1:0:60:87.5:0.9943:0:1.1 -5 38955796 . G A 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00207;SOR=1.39588;LSEQ=CAATCAAGTCAACATATTTG;RSEQ=AGTTGTATTCCTAGAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:899:387:133,254:167,344:0.4305:2,2:24.9:1:29.8:1:0.61734:1.08:60:42:0.4295:0:1.1 1/0:557:286:95,191:106,165:0.5135:2,2:23.7:1:29.2:1:0.15838:1.291:60:56.2:0.5147:0:1.1 -5 38956039 . G T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACATTTTCAAGCCATCAC;RSEQ=TGGTTACTGCACAGACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:1:0,1:19.7:1:30.2:1:1:0:60:30:1:0:1.5 1/1:2:2:0,2:0,0:1:0,0:32.5:1:32:0:1:0:60:4:1:0:1.5 -5 38958167 . A G 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAACATGGTGAAACTCC;RSEQ=ACTCTACTAAAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:23.5:1:30.6:1:1:0:58:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38958386 . T TA 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.29583;SOR=0;LSEQ=TATGAACAGACCAAAAAAAT;RSEQ=AAAAAAAAAGAAAAACCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:3,0:71,3:0.039:1,0:22.7:1:28.7:1:1:0:60:6:0.0395:0.013:0.3 0/0:45:0:0,0:44,1:0:1,0:23.4:1:30:1:1:0:60:90:1:0:0.3 -5 38958750 . A G 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01166;SOR=1.45518;LSEQ=AAAAATTTAAGTATTAAATT;RSEQ=TAAAAAATGAACCTTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:139:97,42:335,169:0.2158:2,2:23.4:1:32.3:1:0.47719:1.16:60:138:0.2163:0:1.1 0/1:402:115:76,39:185,101:0.2861:2,2:20.7:1:31.4:1:0.81771:1.06:60:114:0.2843:0:1.2 -5 38958968 . A C 251 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=0.31091;SOR=0.74169;LSEQ=GAATACATTAAAAAAAAAAA;RSEQ=AACTTCAGCATAAATAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:255:51,204:6,0:0.8586:0,2:21.7:1:31.4:1:9e-05:0:60:22.182:0.8683:0:1.2 1/1:132:108:17,91:3,0:0.8182:0,2:23.4:1:31.2:1:0.00514:0:60:35:0.8268:0:1.3 -5 38959123 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTATCTAGCAGCTTCT;RSEQ=CCCCCGATACAAAAATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:67,22:0.0217:2,2:6.5:1:32:1:0.44371:3.00065:60:4:0.0227:0:1 0/0:22:0:0,0:17,5:0:2,0:29.1:1:29.7:1:1:0:60:21:1:0:0.1 -5 38959431 . G GA 146 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01962;LSEQ=AAGATTAAGGAGACTTAAAA;RSEQ=AAAAAAAAAATAAGAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:27:4,23:96,358:0.0558:2,2:29:1:30.9:1:0.6252:1.54063:60:54:0.0591:0.0041:0.2 0/1:264:15:2,13:56,191:0.0568:2,2:27.2:1:30.2:1:0.53334:1.90191:60:30:0.0591:0.0076:0 -5 38959794 . T C 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54848;SOR=Inf;LSEQ=ATAAAACTTAACCAAACACA;RSEQ=GTACACAGAATAAAAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:223:221:205,16:0,1:0.991:0,2:25.2:1:31.4:1:0.07658:0:60:30.571:0.9953:0:1.1 1/1:116:116:107,9:0,0:1:0,2:23.6:1:31:1:1:0:60:37.667:1:0:1.1 -5 38960325 . T TA 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATAACTTGCCCAGTCTCA;RSEQ=AACTAGTGACTAAGTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:39,5:0,0:1:0,2:22.4:1:29:1:1:0:60:43:0.9773:0.25:0.2 1/1:10:10:10,0:0,0:1:0,0:25.1:1:28.2:1:1:0:60:20:1:0.2:0.1 -5 38960854 . CAT C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGTTCCCATAATCCCCA;RSEQ=GTCATGAAAGGGACCTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:0,18:0,0:1:0,1:30.6:1:31.2:1:1:0:60:17:1:0.1111:0.2 1/1:2:2:0,2:0,0:1:0,0:29:1:31.5:1:1:0:60:4:1:0:0 -5 38962277 . AT A 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATAAGACTATATTAAAA;RSEQ=ATATATGAGTACCTATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:95:94,1:0,0:1:0,1:26.7:1:30.6:1:1:0:60:94:1:0.1474:0.1 1/1:36:36:36,0:0,0:1:0,1:24.2:1:30.2:1:1:0:60:72:1:0.1944:0.1 -5 38962325 . G T 24 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61278;SOR=1.88163;LSEQ=TTGTTAAAATGTATGTATAT;RSEQ=TCTTTAAAATTATTACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:180,17:0.01:2,2:17.5:1:28.5:1:0.17314:10.31853:60:4:0.0102:0:1 0/1:107:2:0,2:97,8:0.0187:2,0:1:0:24:0:0.00794:0:60:4:0.0187:0:1 -5 38962543 . A G 300 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.52914;SOR=Inf;LSEQ=TAATTACGTTATAATTAATA;RSEQ=TAAAATTAAAGACAAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:667:665:402,263:0,0:0.997:0,2:24.2:1:32:1:1:0:60:82.125:0.997:0:1.1 1/1:406:406:230,176:0,0:1:0,2:23.8:1:31.4:1:1:0:60:100.5:1:0:1.1 -5 38962656 . T C 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00197;SOR=0;LSEQ=TGTTGAAGGACTTGGCTATC;RSEQ=CTAAGGTTAATTAAAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:12:4,8:419,554:0.0122:2,2:19.2:1:29.3:1:0.57002:1.51202:60:11:0.0114:0:1.2 0/0:706:0:0,0:306,400:0:2,0:25.5:1:29.5:1:1:0:60:57.833:1:0:0.2 -5 38964811 . A AT 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCATAACCTATCCATACT;RSEQ=TTTTTTTTAAAAAGAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:2,0:132,7:0.0142:2,0:23:1:32.5:1:1:0:60:4:0.0144:0:0 0/0:68:0:0,0:66,2:0:1,0:25.3:1:27.8:1:1:0:60:21.667:1:0:0 -5 38966903 . A ATT 138 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0.04765;SOR=1.84179;LSEQ=CATCAGATTTATTTTTCAAA;RSEQ=TTTTTTTTTTTTTTTTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:32:0,32:10,84:0.172:2,1:27.7:1:27.6:1:0.06387:0:59.4:7:0.1667:0:1.1 0/1:101:28:0,28:4,44:0.2772:2,1:25.6:1:27.7:1:0.29019:0:58.6:13:0.2708:0.0396:1.4 -5 38968584 . AA C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATACTTTAAAAAACAAAAC;RSEQ=AAAAAAAAAAAGCCCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,0:0.4:0,0:25.5:1:32.8:1:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38971649 . A ATT 44 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCCAGCTAATTTTTGT;RSEQ=TTTTTTTTTTTTTTAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:2,1:0.3333:2,0:24.3:1:28:1:1:0:51.3:6:0.375:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38971865 . A G 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03013;SOR=1.47188;LSEQ=TTCTGTATTTTAAAAATATG;RSEQ=TCTAGATTAACAACTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:151:146,5:196,3:0.4314:1,1:23.1:1:31.4:1:0.29839:2.23229:60:74.5:0.4331:0:1.7 1/0:216:114:109,5:97,5:0.5278:1,1:21.2:1:31.1:1:1:1.12:60:37:0.5236:0:1.8 -5 38971912 . T A 284 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCACCTGAAATAATTT;RSEQ=TTTTTTATAATTAATTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:910:910:651,259:0,0:1:0,2:24:1:28.9:1:1:0:60:302.333:1:0:1.2 1/1:643:643:434,209:0,0:1:0,2:23.8:1:28.2:1:1:0:60:106.167:1:0:1.2 -5 38972078 . G GA 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.99816;LSEQ=ATACCTAAAGAGGACAGAAA;RSEQ=AAAAAAAAATCACTGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:14:3,11:155,503:0.0207:2,2:25.1:1:30.8:1:1:1.12969:60:28:0.0214:0.0015:0.1 0/1:436:9:1,8:108,315:0.0206:2,2:27.2:1:30.2:1:0.45988:2.73818:60:18:0.0211:0:0.2 -5 38972335 . T C 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGAGTCTGACTGCCTGA;RSEQ=GAACTCTTCTCTGGGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:14.1:1:28.9:1:1:0:60:18:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38975458 . T C 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.79189;SOR=1.15591;LSEQ=ATTAGCTAATTCCTATTGAC;RSEQ=ATTACAAATTTCCTTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:17:17,0:32,0:0.3469:1,1:21.9:1:31.5:1:1:0:60:34:0.3469:0:1.1 0/1:21:8:8,0:13,0:0.381:1,0:19.8:1:30.8:1:1:0:60:16:0.381:0:1 -5 38975955 . C T 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTTCTATATTCCTGCTC;RSEQ=CTGAAAACTATTCTTAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1:0,1:33.3:1:30.8:1:1:0:60:26:1:0:1.2 1/1:2:2:0,2:0,0:1:0,0:19:1:31:0:1:0:60:4:1:0:1 -5 38976082 . G C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTTTAATCACACACACT;RSEQ=TTTACTTCACAATCTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38978257 . GATA G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATTATACTGTCTCATTTCTA;RSEQ=ATAATATTTACTCTATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:9:1:29.3:1:1:0:60:4:0.6667:0.3333:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38978758 . TA T 181 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.65983;SOR=0.88299;LSEQ=GGGTGCTAAAATTCTCTATT;RSEQ=AAAAAAAAAAGGAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:598:61:14,47:183,349:0.102:2,2:28:1:30.6:1:0.08485:1.75879:60:122:0.1037:0.0033:0.2 0/1:384:35:6,29:132,210:0.0911:2,2:27.5:1:30.8:1:0.01549:3.03046:59.4:70:0.0931:0.0078:0.3 -5 38978782 . T A 38 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70495;SOR=1.35134;LSEQ=AAAAAAAAGGAAGAAAAGAG;RSEQ=CTTTATTTTAAAATGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:4:4,0:64,328:0.0101:2,0:7.5:1:19.3:1:0.00081:0:60:1:0.0053:0:2.3 0/1:221:3:2,1:54,164:0.0136:2,2:14.3:1:20.7:1:0.1588:6.01:60:2:0.0096:0:1.3 -5 38982220 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTTTAAAACTTAATTGC;RSEQ=TTTCTGACTTGAAAAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:2,156:0.0125:1,2:20:1:32:0:0.03726:63.90:60:4:0.0128:0:1 0/0:58:0:0,0:0,58:0:1,0:22.6:1:32.4:1:1:0:60:116:1:0:0 -5 38990779 . G T 65 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATATCAGATATATATCA;RSEQ=ATATATCATATATATGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:8.5:1:32.5:1:1:0:59.3:8:0.6667:0:5.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990786 . C G 67 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGATATATATCAGATATAT;RSEQ=ATATATATGATATATATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:15.5:1:33.5:1:1:0:59.3:8:0.6667:0:5.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990793 . AT CA 64 NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATCAGATATATCATATAT;RSEQ=GATATATATCAGATATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:2,0:0.5714:0,0:23.5:1:32.3:1:1:0:59.3:8:0.6667:0:4.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990810 . TG T 30 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATGATATATATCAGATA;RSEQ=ATATATATGATATATATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:36.5:1:30:1:1:0:58.5:4:0.2222:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990818 . A C 30 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATATCAGATATGATATAT;RSEQ=TGATATATATCATATATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:30.5:1:30:1:1:0:58.5:4:0.2222:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990820 . G C 89 NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAGATATGATATATAT;RSEQ=ATATATATCATATATATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:37.7:1:32:1:1:0:57.1:14:0.7778:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990829 . C G 52 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGATATATATGATATATAT;RSEQ=ATATATATGATATATATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:0.25:0,0:17:1:33:0:1:0:60:6:0.25:0:3.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990834 . ATA C 30 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATATGATATATATCATAT;RSEQ=TGATATATATGAGATATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:16.5:1:30.7:1:1:0:58.5:4:0.1667:0.0833:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990836 . AT CA 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATGATATATATCATATAT;RSEQ=GATATATATGAGATATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:30:1:31.5:1:1:0:60:4:0.2:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990847 . G C 33 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCATATATATGATATATAT;RSEQ=AGATATATGATATATATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:11,0:0.1538:0,0:32:1:33:0:1:0:50:4:0.1538:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990849 . G T 51 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATATATATGATATATATGA;RSEQ=ATATATGATATATATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:10,0:0.2308:0,0:29:1:32.7:1:1:0:53.3:6:0.2308:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990867 . G T 32 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGATATATGATATATATGA;RSEQ=ATATATGATATATATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:13,1:0.125:1,0:23:1:32.5:1:1:0:35:4:0.125:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990876 . T G 109 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.51703;SOR=Inf;LSEQ=GATATATATGAGATATATGA;RSEQ=ATATATGAGATATATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:9,1:6,0:0.625:0,2:23.2:1:33.1:1:1:0:57.7:20:0.625:0:2.6 1/1:3:3:2,1:0,0:1:0,2:3.3:1:31:1:1:0:60:6:1:0:3 -5 38990892 . GAGATATATGAT G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGATATATATGAGATATAT;RSEQ=ATATATGAGATATATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:20,0:0.1304:1,2:24.3:1:32:1:0.13043:0:58.3:6:0.1304:0:3 0/0:6:0:0,0:5,1:0:2,0:14.5:1:29.3:1:1:0:60:12:1:0:2.5 -5 38990901 . GAT G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=0.16219;SOR=Inf;LSEQ=ATGAGATATATGAGATATAT;RSEQ=ATATATGAGATATATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:19:19,0:2,0:0.76:0,1:23.3:1:32.1:1:1:0:58.8:38:0.9048:0.16:2.2 1/1:9:9:8,1:0,0:1:0,2:17.2:1:31.9:1:1:0:60:18:1:0.3333:2.4 -5 38990903 . T G 31 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGATATATGAGATATATGA;RSEQ=ATATATGAGATATATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:0,0:0.0952:0,0:33.5:1:31:1:1:0:43.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 38990930 . TATATGAGATATATG T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00998;SOR=0;LSEQ=GAGATATATGAGATATATGA;RSEQ=AGATATATGATATATATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:16:16,0:58,1:0.2133:1,1:7.4:1:30.9:1:1:0:59.7:32:0.2133:0.2133:2 0/0:26:0:0,0:25,1:0:1,0:21.7:1:28.9:1:1:0:60:52:1:0:2.2 -5 38990946 . G TAT 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TATGATATATGAGATATATG;RSEQ=ATATATGATATATATATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:80:81:80,1:0,0:1:0,1:20.6:1:31:1:1:0:59.6:162:1:0.284:2.1 1/1:30:39:38,1:0,0:1:0,1:21.7:1:29.6:1:1:0:59.9:78:1:0.2564:2.1 -5 38990957 . T G 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATATATGAGATATATGATA;RSEQ=ATATATGATAGATATATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:105,1:0,0:1:0,1:22.7:1:32.6:1:1:0:59.9:105:1:0:1.8 1/1:53:53:52,1:0,0:1:0,1:23.5:1:32.4:1:1:0:59.2:106:1:0:1.8 -5 38991272 . T C 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.00218;SOR=Inf;LSEQ=TAGTTAATAACAGAATAAGA;RSEQ=CCAGAATAAGATCTAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:1,110:0:1,0:26:1:30.2:1:1:0:60:36:1:0:0.1 0/1:65:6:0,6:0,59:0.0923:1,0:25.2:1:32.8:1:1:0:60:12:0.0938:0:1 -5 38996638 . A G 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTCTAGTAACTTATCAA;RSEQ=GCAGTAACTACATTTACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:0.2727:0,0:26.7:1:32.7:1:1:0:60:6:0.2727:0:1.3 0/0:2:0:0,0:2,0:0:0,0:24.5:1:30.5:1:1:0:60:4:1:0:0 -5 38996986 . T A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00516;SOR=Inf;LSEQ=CTGTTGTATGTCAATGCACC;RSEQ=AAACAATACACAAAATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:830:0:0,0:331,499:0:2,0:25.3:1:29:1:1:0:60:68.167:1:0:0.1 0/1:593:6:5,1:232,355:0.0101:2,2:10.7:1:27.3:1:0.04003:7.63:60:12:0.0103:0:1 -5 38997022 . C A 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04659;SOR=Inf;LSEQ=TATTAATCATTGATAAAATT;RSEQ=TATTAAACAACTTTTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:114,361:0:2,0:23.2:1:31.8:1:1:0:60:58.375:1:0:0.1 0/1:268:3:1,2:62,203:0.0112:2,2:7.7:1:25.7:1:0.55398:1.63:60:2:0.0075:0:2.3 -5 38997170 . G A 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32415;SOR=0;LSEQ=ATCTCGAGGGATAAATATCT;RSEQ=TCATTTAAAAGACCAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:1,28:0.2162:1,0:16.1:1:30.1:1:1:0:60:16:0.2162:0:1 0/0:9:0:0,0:1,8:0:2,0:13.3:1:31.4:1:1:0:60:18:1:0:0 -5 39002271 . CAAA C 53 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATGAAATGTTACACAG;RSEQ=AAAAAAAAAAAAAAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:32:1:34:0:1:0:60:6:0.75:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 39002504 . A G 135 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.1694;SOR=0.386;LSEQ=TTGTGTGTGTGTGTGTGTGT;RSEQ=TATATATATATATACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:19:19,0:36,0:0.2923:1,1:31.5:1:31.9:1:1:0:60:38:0.3455:0:1.8 0/1:22:3:3,0:15,0:0.1364:1,0:30.7:1:28.3:1:1:0:60:6:0.1667:0:1.3 -5 39002513 . TATATAC T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTGTGTGTATATATATA;RSEQ=ACACACACAAAATTCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:3:3,0:71,1:0.04:1,0:29.7:1:32:1:1:0:60:6:0.0405:0:0 0/0:22:0:0,0:22,0:0:1,0:24.4:1:27.6:1:1:0:60:44:1:0:0.6 -5 39002515 . TATAC T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0.13774;SOR=2.78266;LSEQ=TGTGTGTGTATATATATATA;RSEQ=ACACACACAAAATTCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:7:7,0:67,1:0.0897:1,0:21.1:1:31.1:1:1:0:60:14:0.0946:0:0 0/1:23:5:5,0:18,0:0.2174:1,0:23.2:1:29:1:1:0:60:10:0.2174:0.0435:0.2 -5 39002517 . TAC T 74 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=1.21374;LSEQ=TGTGTGTATATATATATATA;RSEQ=ACACACACAAAATTCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:5:5,0:64,2:0.0617:1,0:34.8:1:32:1:1:0:60:10:0.0704:0:0.6 0/1:27:2:2,0:21,0:0.0741:1,0:22.5:1:32:0:1:0:60:4:0.087:0:0 -5 39002519 . C T 157 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGTGTATATATATATATATA;RSEQ=ACACACACAAAATTCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:40:39,1:25,2:0.4878:2,1:25.2:1:29.6:1:0.56038:3.07:60:19:0.5938:0:1.4 0/0:32:0:0,0:9,0:0:0,0:17.4:1:30.1:1:1:0:60:18:1:0:0.3 -5 39002808 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.127;SOR=Inf;LSEQ=ATACAAGTTTTGCTGCACAG;RSEQ=TTTCAAATACACACAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:65,261:0:2,0:23.7:1:31.7:1:1:0:60:64.2:1:0:0.1 0/1:181:2:1,1:32,147:0.011:2,2:22:1:26:1:0.33223:4.54:60:4:0.0112:0:3 -5 39003212 . G A 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGCCAATAGCAGGCACA;RSEQ=ACCTTTTATATCAATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:1,4:0.375:2,2:10.3:1:31:1:0.46429:5.78:60:6:0.375:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 39021088 . G T 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01414;SOR=Inf;LSEQ=GGTCAAGAAACATTTAGTAA;RSEQ=TGTGGTAAGGAACAAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:331,95:0:2,0:24:1:31.8:1:1:0:60:37.727:1:0:0.1 0/1:319:5:3,2:220,94:0.0157:2,2:16.4:1:29.2:1:0.63906:1.55794:60:10:0.0159:0:1 -5 39021369 . G A 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28384;SOR=0.53802;LSEQ=TTACCCTCCACCCCAAATCT;RSEQ=TTAATTTAAATGACTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:46:1,45:0,13:0.7797:1,1:23.2:1:30.6:1:1:0:60:45:0.7759:0:1.1 1/0:26:17:1,16:0,9:0.6538:0,1:24.3:1:30.1:1:1:0:60:34:0.6538:0:1 -5 39021493 . G A 83 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACAAAATCTTAAATCTT;RSEQ=CTATTATTTGAATGTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:0.5385:0,0:13.3:1:29.6:1:1:0:60:14:0.5385:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 39074202 . C T 56 v4;q23;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07977;SOR=4.04739;LSEQ=CCCTCGCGGCGCCCGCGGCG;RSEQ=CCCGCGTTACCTCGGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:792:2:0,2:550,240:0.0025:2,0:1:0:25.5:1:0.0931:0:60:4:0.0025:0:1 0/1:591:6:0,6:378,207:0.0102:2,0:5.8:1:21.8:1:0.00209:0:60:5:0.0085:0:1.5 -5 39074207 . C T 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11576;SOR=3.00387;LSEQ=GCGGCGCCCGCGGCGCCCCG;RSEQ=GTTACCTCGGGTCAGATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:870:3:0,3:595,272:0.0034:2,0:1:0:28.3:1:0.03135:0:60:6:0.0035:0:1 0/1:680:7:2,5:423,249:0.0103:2,2:7.1:1:24.7:1:0.1092:4.23773:60:6:0.009:0:1.7 -5 39074296 . G C 279 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.52282;LSEQ=ACACAGCCCCAATTAGGATT;RSEQ=GCTCGCAGGCCAGCTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1403:593:327,266:462,342:0.4227:2,2:25.4:1:30.3:1:0.41289:1.0988:60:58.3:0.4271:0:1.1 1/0:1066:562:312,250:268,232:0.5272:2,2:25.2:1:30:1:0.53756:1.08:60:61.444:0.5277:0:1.2 -5 39074559 . G A 49 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.82841;LSEQ=CCTCCCCGCGCGCCGCGCCC;RSEQ=CCCCCCGCGGCACCTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:4:3,1:71,293:0.0107:2,2:12:1:24.5:1:0.02688:12.27:60:3:0.0086:0:2 0/0:226:2:2,0:45,176:0.0088:2,0:5.5:1:20:1:0.04367:0:60:1:0.0047:0:2 -5 39074575 . C T 40 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.28152;SOR=0;LSEQ=GCCCGCCCCCCGCGGCACCT;RSEQ=CCCCGCCCCCTCGGCGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:3:1,2:20,182:0.0146:2,2:13:0:25.3:1:0.27813:4.49:60:2:0.0101:0:3 0/0:134:0:0,0:23,110:0:2,0:12.8:1:31.2:1:1:0:60:132:1:0:0.2 -5 39074580 . G C 39 v4;pSTD;NM4;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.28402;SOR=0;LSEQ=CCCCCCGCGGCACCTCCCCC;RSEQ=CCCCCTCGGCGGCGACGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:3:3,0:10,146:0.0188:2,0:6:0:24.7:1:0.00044:0:60:6:0.0195:0:5.3 0/0:102:0:0,0:11,88:0:2,0:8:0:8:0:1:0:60:0:0:0:1 -5 40456871 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAAAATAAATTGAGATAG;RSEQ=TTTCAGGGAAGAGATCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 40457232 . T A 81 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.64552;LSEQ=CGTTGTGGAAATTCCATTTT;RSEQ=TAACACACTGTTAGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:0.6154:0,0:24.1:1:27:1:1:0:60:7:0.5833:0:1 1/0:2:1:1,0:1,0:0.5:0,0:21:0:30:0:1:0:60:2:0.5:0:1 -5 40457347 . A T 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACATCCTTCTCAGACCA;RSEQ=GTGCCAGAATCTTTGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:157:139,18:0,0:1:0,2:24.4:1:30.6:1:1:0:60:77.5:1:0:1.5 1/1:85:85:67,18:0,0:1:0,2:23.6:1:29.9:1:1:0:60:170:1:0:1.2 -5 40457379 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2819;SOR=3.73039;LSEQ=TTTGGAAAGGAACATAATAT;RSEQ=CCTAATTGGAAAAGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:1:0,1:212,78:0.0034:2,0:1:0:27:0:0.27148:0:60:2:0.0035:0:1 0/1:157:2:0,2:107,48:0.0127:2,0:18.5:1:27.5:1:0.10003:0:60:4:0.0127:0:1.5 -5 40457403 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1259;LSEQ=AATTGGAAAAGGCTCTGCAC;RSEQ=CACCCTGCTTCAGAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:415:208:140,68:131,76:0.5012:2,2:24.6:1:30.6:1:0.41048:1.19:60:40.6:0.4975:0:1.9 0/1:250:28:23,5:133,86:0.112:2,2:23.4:1:29.9:1:0.03602:2.96:60:27:0.1089:0:2 -5 40457459 . G A 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.56966;LSEQ=TTTGGAAGACCACATAATGG;RSEQ=TCTTTAATCAACAACACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:580:311:161,150:136,132:0.5362:2,2:26.2:1:30.3:1:0.86759:1.04:60:102.667:0.5375:0:1.5 0/1:393:156:81,75:126,110:0.3969:2,2:26.9:1:28.5:1:0.83633:1.06043:60:30.2:0.3912:0:1.3 -5 40457488 . G A 146 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04799;LSEQ=CAACAACACACTGCAGGACC;RSEQ=ATATATTTTCCTTGCCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:30:15,15:240,299:0.0527:2,2:20.5:1:29.8:1:0.57653:1.25:60:60:0.0533:0:1.2 0/0:376:1:1,0:174,201:0.0027:2,0:1:0:26:0:0.46543:0:60:2:0.0027:0:1 -5 40457560 . T A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12571;SOR=Inf;LSEQ=TCTTCCCCCATATCCTGCTA;RSEQ=TCTCACAAAACGTATGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:47,176:0:2,0:23.1:1:30.1:1:1:0:60:43.6:1:0:0.1 0/1:123:2:1,1:24,97:0.0163:2,2:14:1:25:1:0.36652:3.98:60:4:0.0163:0:1 -5 40457629 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.2969;SOR=0;LSEQ=ACAAAATATCTCAACCAGAA;RSEQ=CAAGCAACTGAAGTTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:4:0,4:0,56:0.0667:1,0:12:1:30.5:1:1:0:60:8:0.0678:0:1 0/0:30:0:0,0:1,29:0:1,0:22.1:1:32.5:1:1:0:60:60:1:0:0.1 -5 40457889 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGATATTTTATTAATT;RSEQ=TACATTTTAGTAAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18.5:1:31:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 40457892 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATATTTTATTAATTCTA;RSEQ=ATTTTAGTAAAGCATTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21.5:1:27:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 42116639 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTAAAGAAAAAAGTGTA;RSEQ=CCTATTCCTTTAAAAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 42117027 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49524;SOR=Inf;LSEQ=CCTTTCTAGGTCCCGTGGCA;RSEQ=CCATGTTACTGTTACTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:21,31:0:2,0:25.8:1:32:1:1:0:58.5:51:1:0:0.2 0/1:53:2:1,1:22,29:0.0377:2,2:26:1:26.5:1:1:1.31:50:4:0.0377:0:1 -5 42384740 . A G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09388;SOR=0;LSEQ=CAGACTTTAGCATGAAGGTG;RSEQ=TGGTTAATTCAGAGGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:5,21:0,0:1:0,2:24.3:1:31.8:1:1:0:60:52:1:0:1 1/1:12:10:1,9:0,2:0.8333:0,2:22.8:1:30.9:1:1:0:60:20:0.8333:0:1 -5 42384876 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATACACATATAAGATTTAT;RSEQ=TAAGTAGGTGCAGGTTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,0:0.75:0,0:28:1:29.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 43981410 . G A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTAGGTGGATACCCACAC;RSEQ=TCTGGGCTGGCCGGATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:7:1:32:1:1:0:60:4:1:0:0 0/1:5:2:1,1:0,3:0.4:0,2:24.5:1:32:0:0.4:0:60:4:0.4:0:1 -5 44273551 . TTTTG T 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.95818;LSEQ=CTTAAGAGTTTGAAACTGTT;RSEQ=TTTGTTTGTTTGTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:5:4,1:172,29:0.0244:2,2:18.2:1:27:1:0.54859:1.47953:60:4:0.02:0.0098:0.4 0/1:171:4:3,1:141,26:0.0234:2,2:22.5:1:30.3:1:0.50047:1.80019:60:8:0.0237:0.0058:0.3 -5 44273622 . G T 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00205;SOR=0.43344;LSEQ=TTTGGGAGATGAGTTGGGGA;RSEQ=ATGAAAAGACTGAATTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:54:33,21:325,224:0.0896:2,2:25.9:1:29.9:1:0.88478:1.08:60:108:0.0903:0:1.6 0/1:465:19:10,9:252,194:0.0409:2,2:24.3:1:28.9:1:0.81512:1.16867:60:38:0.041:0:1.6 -5 44273673 . A T 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.60229;LSEQ=AAACTTTCACTTTGACTGTT;RSEQ=CTTTTTAACTAAAACAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:300:147,153:194,206:0.4286:2,2:24.7:1:30.2:1:0.93912:1.02:60:299:0.429:0:1.2 0/1:524:163:71,92:172,189:0.3111:2,2:26.2:1:29.2:1:0.396:1.17885:60:80.5:0.309:0:1.2 -5 44273923 . A G 63 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=2.12136;LSEQ=AATTATGTATTATGACAACA;RSEQ=CTAAGCATATTAAAAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:0,9:0.3077:0,0:28:1:31.5:1:1:0:60:8:0.3077:0:1.3 1/0:2:1:0,1:0,1:0.5:0,0:29:0:34:0:1:0:60:2:0.5:0:1 -5 44274058 . C A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGGTCAATGGATATAC;RSEQ=TGCCAAACAGGTAAGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:19:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 44275948 . C G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTCTGAATTGCTTACA;RSEQ=GGTAAACGAATTATTAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:0:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 50979093 . G T 55 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCTCCTTTCATAATGTTA;RSEQ=AGTTTGCAGTGATATCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:32.3:1:27.8:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 50979220 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48649;SOR=Inf;LSEQ=GGCGATGTTCAGTTATTTAA;RSEQ=GTACCAATGCATCAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:14,4:0:2,0:12.8:1:30.5:1:1:0:60:36:1:0:0.1 0/1:19:2:1,1:12,5:0.1053:2,2:32:1:30:0:1:2.28037:60:4:0.1053:0:1 -5 50979299 . TC T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23964;SOR=0;LSEQ=TGCTGCCCAGGAGTCAGCGT;RSEQ=CCTTTTTACTCACACAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:30,27:0.0339:2,2:19:0:32.5:1:1:1.10912:60:4:0.0351:0:0.5 0/0:61:0:0,0:28,33:0:2,0:25:1:31.2:1:1:0:60:122:1:0:0.1 -5 51977648 . G C 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24268;SOR=Inf;LSEQ=TCTCATCTTCATGAGTTTGT;RSEQ=TAGTTTGGTCTTTGAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:23.8:1:32.7:1:1:0:60:36:1:0:0.1 0/1:23:3:2,1:11,9:0.1304:2,2:11:1:29.3:1:1:1.60:60:6:0.1304:0:1 -5 51977894 . C G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=0;LSEQ=AGCAAAGATGGGTGCCTGCT;RSEQ=CTTCTTCTGGGACCTCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:20.5:1:33:1:1:1:60:4:0.1667:0:1 0/0:10:0:0,0:6,4:0:2,0:29.6:1:30.2:1:1:0:60:20:1:0:0 -5 51977947 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18347;SOR=Inf;LSEQ=CAGCCTGATGCCAATAGGAT;RSEQ=GCTCCTGTATAAGGTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:13,5:0:2,0:16.9:1:29.9:1:1:0:60:36:1:0:0.4 0/1:14:2:1,1:7,5:0.1429:2,2:8.5:1:27.5:1:1:1.36624:60:4:0.1667:0:2 -5 51977971 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20814;SOR=Inf;LSEQ=CCTGTATAAGGTGCCTGACA;RSEQ=CCCCTATTGGAGGGTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:17,11:0:2,0:22.4:1:32.2:1:1:0:60:56:1:0:0.3 0/1:24:2:1,1:11,11:0.0833:2,2:23.5:1:33:0:1:1:60:4:0.087:0:1 -5 51978028 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23523;SOR=Inf;LSEQ=GAGAGCAGGACCCATTTAAC;RSEQ=AAGCACTTTGTCCCTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:0:2,0:26.6:1:30.1:1:1:0:60:86:1:0:0.3 0/1:41:2:1,1:18,21:0.0488:2,2:11.5:1:32:0:1:1.16:60:4:0.0488:0:2 -5 51978040 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49463;SOR=0;LSEQ=CATTTAACGAAGCACTTTGT;RSEQ=CCTTGGTGGAGAGAGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:19,18:0.0513:2,2:6:1:27:1:1:1.05412:60:4:0.0526:0:2 0/0:35:0:0,0:17,18:0:2,0:27.1:1:31.1:1:1:0:60:70:1:0:0.1 -5 51978302 . T C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAGAGGCACTCTGGTTGAA;RSEQ=ACTGCCACAGCCAGTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:29.5:1:28:1:1:0:60:4:1:0:0 0/1:7:2:1,1:2,3:0.2857:2,2:28:1:30:1:1:1.41:60:4:0.2857:0:1.5 -5 51978411 . C A 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCTGGAGCTATAGAAATGGG;RSEQ=ACCATCCTTCCCCCACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:31.5:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:31:0:33:0:1:0:60:2:1:0:0 -5 52074333 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGTGTGGTGGCTCACAAA;RSEQ=TTTTTTCTAACAAATCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:1:0:31:0:1:0:60:2:0.5:0:2 1/1:2:2:2,0:0,0:1:0,0:22.5:1:33.5:1:1:0:60:4:1:0:1 -5 52074401 . T G 65 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20635;SOR=0.09168;LSEQ=ATTGCTGTTTTCCCCCCACT;RSEQ=TGTTTAGGTTATACTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:35.8:1:32.5:1:1:0:60:8:0.8:0:1.3 0/1:5:1:1,0:4,0:0.2:0,0:7:0:34:0:1:0:60:2:0.2:0:1 -5 52074527 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5051;SOR=Inf;LSEQ=CTTATTTTTATTGTTGTCTG;RSEQ=TGTTGCTGTTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:36,36:0:2,0:32.3:1:32.6:1:1:0:60:144:1:0:0 0/1:93:2:1,1:46,45:0.0215:2,2:22.5:1:29:1:1:1.02198:60:4:0.0217:0:1.5 -5 52074533 . C CTGT 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=2e-05;SOR=0.1556;LSEQ=TTTATTGTTGTCTGCTGTTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:25:10,15:26,24:0.3333:2,2:28.9:1:30.8:1:0.4625:1.61445:60:50:0.3333:0.04:0.2 0/1:98:7:3,4:44,47:0.0714:2,2:20.9:1:28.7:1:1:1.24542:60:14:0.0722:0.0306:0.4 -5 52074551 . C CTGA 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.13395;SOR=Inf;LSEQ=TGCTGTTGTTGCTGCTGCTG;RSEQ=TGATGATGATAATGATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:32,39:0:2,0:26.1:1:32.4:1:1:0:60:142:1:0:0.1 0/1:93:4:0,4:39,48:0.043:2,0:25.5:1:32:1:0.13207:0:60:8:0.0435:0.0108:0.3 -5 52665229 . GTCT AGAC 209 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACACATTATGAATAAAACAA;RSEQ=AGATGATGCAAGAGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:108:71,37:110,56:0.3899:2,2:26.9:1:31:1:1:1.02356:60:216:0.3942:0.0939:1.4 0/0:329:0:0,0:203,125:0:2,0:24.5:1:31.6:1:1:0:60:108.333:0.9969:0:0.4 -5 52665299 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.65276;LSEQ=TGTTTGTTTCCATTACATCC;RSEQ=CAGTGCCAGTTTTAGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:154:76,78:161,167:0.3182:2,2:25.8:1:30.4:1:1:1.01:60:29.8:0.3157:0:1.3 1/0:508:348:177,171:72,87:0.685:2,2:24.6:1:30.3:1:0.25206:1.25:60:57:0.6826:0:1.1 -5 52665368 . G T 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=AAGACATTAGACTTCCTATT;RSEQ=CAGTGGTTTATAACAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:15:5,10:83,196:0.051:2,2:23.1:1:30.3:1:0.77606:1.18:60:30:0.0523:0:1.1 0/0:312:0:0,0:122,190:0:2,0:25.3:1:31.4:1:1:0:60:51:1:0:0.5 -5 52665396 . A G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATAACAAAACCTCTTCTA;RSEQ=TGGATATTAGCATTAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:33,150:0:2,0:22.3:1:31:1:1:0:60:366:1:0:0.1 0/1:185:19:6,13:46,120:0.1027:2,2:17.1:1:31.5:1:0.78869:1.20:60:38:0.1027:0:1.4 -5 52665731 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCTCCCACGAGAATTATGT;RSEQ=CACTTGACTTGGCACAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:23:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 53875170 . T TA 27 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGAGAGAGCCAGACCCTGT;RSEQ=AAAAAAAAAAGAAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:22.5:1:27:1:1:0:60:4:0.6667:0.3333:2 1/1:1:1:1,0:0,0:1:0,0:11:0:29:0:1:0:60:2:1:0:0 -5 53875320 . A T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74802;LSEQ=TATAGAATCATGAGCCAACA;RSEQ=GTTGATTTAATAAATGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:63:61,2:0,0:0.9844:0,1:23.1:1:31.5:1:1:0:60:126:0.9844:0:1 1/1:48:47:43,4:1,0:0.9792:0,2:21.7:1:29.9:1:1:0:60:22.5:0.9783:0:1 -5 53875373 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2223;SOR=Inf;LSEQ=CCTCCTTCATCCATCTATTT;RSEQ=CAGAGTCACTGGTTCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:149,41:0:2,0:25.1:1:28.3:1:1:0:60:62.333:1:0:0.3 0/1:170:2:1,1:126,42:0.0118:2,2:35.5:1:31:1:0.44302:2.97664:60:4:0.0118:0:1 -5 53875375 . A G 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22718;SOR=Inf;LSEQ=TCCTTCATCCATCTATTTAC;RSEQ=GAGTCACTGGTTCACTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:151,45:0:2,0:25.1:1:30.3:1:1:0:60:97:1:0:0.3 0/1:179:2:1,1:129,47:0.0112:2,2:11:0:26.5:1:0.46772:2.72645:60:4:0.0114:0:1.5 -5 53875481 . G C 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.03536;LSEQ=CTAGTAAACAGGAATACAGA;RSEQ=AGAAGTACACATGTGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:343:325:149,176:7,10:0.9475:2,2:25.8:1:31.8:1:0.80551:1.21:60:64:0.9496:0:1.2 0/1:376:146:61,85:104,125:0.3883:2,2:25.7:1:31.4:1:0.5229:1.15889:60:292:0.3904:0:1.2 -5 53875569 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05799;LSEQ=TGGAAAGAGAAGCTCATCAA;RSEQ=GATGGGAACAAATTTTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:115:20,95:1,8:0.9274:2,2:25.9:1:30.7:1:1:1.68:60:56.5:0.9262:0:1.2 0/1:109:46:9,37:13,50:0.422:2,2:25.9:1:31:1:1:1.06826:60:92:0.4299:0:1.2 -5 53875603 . T A 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22018;SOR=2.28635;LSEQ=TTTAGAAGGTTCCCAAGAGG;RSEQ=TAGGCATAGCAAGGTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:6:1,5:4,71:0.0741:2,2:14.3:1:30.5:1:0.32637:3.46:60:12:0.075:0:1.5 0/1:45:7:1,6:5,33:0.1556:2,2:27:1:30.1:1:1:1.10:60:14:0.1591:0:1.4 -5 53875646 . A G 51 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21076;SOR=3.63026;LSEQ=AGGGTGGGGCTGGCCTTAGG;RSEQ=ATATTGCAAAGTGCATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:0,3:0,34:0.0811:1,0:41.7:1:32.3:1:1:0:60:6:0.0833:0:2 0/1:8:2:0,2:0,6:0.25:0,0:3:1:30:1:1:0:60:4:0.25:0:2 -5 53876988 . G T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTTGTGCTGCACCTTT;RSEQ=AATTCTGTGACTGCAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 54380840 . G A 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGCAAGATGGCTGTCACA;RSEQ=GACCTAGAAAGAGGAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:44,28:0:2,0:24.6:1:31.6:1:1:0:60:144:0.9863:0:0.2 0/1:85:19:13,6:36,29:0.2235:2,2:26.6:1:29.9:1:0.42895:1.73:60:38:0.2235:0:1.1 -5 54380851 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50502;SOR=Inf;LSEQ=GCTGTCACAGGACCTAGAAA;RSEQ=AGGAGAAGCCATGTCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:52,38:0:2,0:24.9:1:31.6:1:1:0:60:89:1:0:0.2 0/1:115:2:1,1:62,51:0.0174:2,2:5:0:30:0:1:1.21361:60:4:0.0175:0:1 -5 54380854 . G T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19258;SOR=0;LSEQ=GTCACAGGACCTAGAAAGAG;RSEQ=AGAAGCCATGTCACCCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:52,38:0.0217:2,2:13:0:30.5:1:1:1.36367:60:4:0.022:0:1.5 0/0:117:0:0,0:63,54:0:2,0:26.4:1:30.1:1:1:0:60:22.4:1:0:0.4 -5 54579474 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=Inf;LSEQ=TCTCTTATTTTCAGAATGCT;RSEQ=TTGTTGCTGCTGTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:24:1:32.5:1:1:0:60:32:1:0:0.1 0/1:17:2:1,1:7,8:0.1176:2,2:15.5:1:31.5:1:1:1.13:60:4:0.1176:0:1 -5 54913071 . G A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0393;SOR=Inf;LSEQ=TTATACCAACCTCTGGAGTT;RSEQ=GGCAACATGGCTTCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:30.3:1:31.3:1:1:0:55.5:60:1:0:0.1 0/1:43:6:3,3:19,18:0.1395:2,2:35.2:1:25:1:1:1.05426:32.3:5:0.119:0:1.3 -5 54913108 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53634;SOR=Inf;LSEQ=CCCTTTCTAGGTCCCGTGAC;RSEQ=GCCATCTTGCTATTACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:24.5:1:31.6:1:1:0:55.1:40:1:0:0.1 0/1:37:2:1,1:16,19:0.0541:2,2:6.5:1:28:1:1:1.18:60:4:0.0541:0:1.5 -5 54914089 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTCTAGGACAATGAGTA;RSEQ=AAGTTTACTGCATTGGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:1:31.5:1:1:0:60:4:1:0:1 -5 56110233 . G A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCACCTTCTCACGTAGA;RSEQ=TCCAGGGACTAGGAGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:32:0:1:0:60:4:1:0:1.5 -5 56111307 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49967;SOR=0;LSEQ=CTCACGCAGTTGGCGCAGGA;RSEQ=GCCTTACGCTGGCGGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:155,14:0.0117:2,2:14.5:1:29:1:0.16821:10.73065:60:4:0.0119:0:1 0/0:155:0:0,0:139,16:0:2,0:23.4:1:32:1:1:0:60:154:1:0:0.1 -5 56111314 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22977;SOR=Inf;LSEQ=AGTTGGCGCAGGAGGCCTTA;RSEQ=GCTGGCGGCGCAGTGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:176,32:0:2,0:23:1:31.9:1:1:0:60:103:1:0:0.1 0/1:192:2:1,1:160,30:0.0104:2,2:37.5:1:30.5:1:0.29756:5.26309:60:4:0.0106:0:1.5 -5 56111330 . C T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.06378;SOR=Inf;LSEQ=CTTACGCTGGCGGCGCAGTG;RSEQ=CCGCCCCCTGCGCTCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:225,71:0:2,0:25.5:1:31.4:1:1:0:60:36:1:0:0.1 0/1:334:5:3,2:233,96:0.015:2,2:14.8:1:28.2:1:0.63265:1.61553:60:10:0.0152:0:1 -5 56111402 . TGGC T 108 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.07282;SOR=3.32386;LSEQ=ATGTAGCCCGCGAGAGAAAA;RSEQ=GGCGGCGGCGGGGAATCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:3:1,2:370,409:0.0038:2,2:37.3:1:31.3:1:1:1.80797:60:6:0.0039:0:0 0/1:1028:13:5,8:484,529:0.0126:2,2:25.6:1:29.3:1:0.58414:1.46336:60:26:0.0128:0.0039:0.5 -5 56111508 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18697;SOR=0;LSEQ=GCCCTCAAGGCGAGCAGCGC;RSEQ=CCCGCGGCTGCCGCGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:44,116:0.0123:2,2:7.5:1:28.5:1:0.47964:2.62:60:4:0.0126:0:1 0/0:212:0:0,0:76,136:0:2,0:19.9:1:31.1:1:1:0:60:52:1:0:0.2 -5 56111553 . C T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4059;SOR=0.46228;LSEQ=CGGGAGGCGGGCAGCGGGGG;RSEQ=CGCGAGCGGGCGGACTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:1,2:132,66:0.0149:2,2:9:1:27.7:1:0.26482:3.97015:60:6:0.0155:0:1 0/0:288:2:0,2:177,109:0.0069:2,0:1:0:23.5:1:0.14772:0:60:4:0.0071:0:1 -5 56111575 . C T 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=1.18328;LSEQ=GCGAGCGGGCGGACTGGCGG;RSEQ=GGCGGCAGCTGCGCAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:4:1,3:234,125:0.011:2,2:5.5:1:28.5:1:0.12773:5.58861:60:8:0.0112:0:1.3 0/1:461:6:3,3:276,179:0.013:2,2:18.2:1:27.8:1:0.6846:1.54036:60:12:0.0133:0:1.2 -5 56111730 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70498;SOR=1.81018;LSEQ=GGCTTCCAGCCTGTGGCGGT;RSEQ=CCGCCGCCCCACGGAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:2:2,0:76,181:0.0077:2,0:1:0:26.5:1:0.08988:0:60:4:0.008:0:1 0/1:361:5:3,2:127,229:0.0139:2,2:18.2:1:24.6:1:0.35543:2.70:60:10:0.0142:0:1.8 -5 56111734 . C A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.40897;SOR=3.69754;LSEQ=TCCAGCCTGTGGCGGTGCCG;RSEQ=CGCCCCACGGAGCCGCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:1,0:66,160:0.0044:2,0:1:0:25:0:0.29515:0:60:2:0.0046:0:1 0/1:310:5:4,1:109,196:0.0161:2,2:17.4:1:25:1:0.061:7.15:60:10:0.0164:0:1 -5 56111749 . G A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.65382;SOR=2.44821;LSEQ=TGCCGCCGCCCCACGGAGCC;RSEQ=CGAGCCGCGGCGGCGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:1,0:39,98:0.0072:2,0:1:0:29:0:0.28986:0:60:2:0.0076:0:1 0/1:229:4:2,2:84,141:0.0175:2,2:26.8:1:29.3:1:0.6323:1.67:60:8:0.0183:0:2.3 -5 56111751 . G C 225 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03548;LSEQ=CCGCCGCCCCACGGAGCCGC;RSEQ=AGCCGCGGCGGCGCCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:134:132:37,95:1,1:0.9851:2,2:14.9:1:31.5:1:0.48827:2.54687:60:65:1:0:1.2 1/0:223:156:58,98:28,38:0.6996:2,2:21.3:1:30.9:1:0.5468:1.24375:60:51:0.7083:0:1.3 -5 56111758 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53025;SOR=Inf;LSEQ=CCCACGGAGCCGCGAGCCGC;RSEQ=GCGGCGCCCACCTTACCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:31,74:0:2,0:13.6:1:29.9:1:1:0:60:25.25:1:0:1.2 0/1:176:2:1,1:70,103:0.0114:2,2:9.5:1:30.5:1:1:1.47:60:4:0.0118:0:2.5 -5 56111761 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGGAGCCGCGAGCCGCGGC;RSEQ=GCGCCCACCTTACCGAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:24,53:0:2,0:16.5:1:30.4:1:1:0:60:76:1:0:1.2 0/1:169:2:1,1:72,95:0.0118:2,2:12.5:1:29:1:1:1.32:60:4:0.0123:0:3 -5 56111830 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.55199;SOR=Inf;LSEQ=GTCCCGCAGCGGCCGAGCCC;RSEQ=GGGAGAAGCGGGCGCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:22,20:0:2,0:18.7:1:31:1:1:0:60:84:0.9767:0:0.4 0/1:77:3:2,1:38,36:0.039:2,2:15.3:1:28.3:1:1:1.88:60:6:0.04:0:1.3 -5 56111892 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12919;SOR=0;LSEQ=GCCCCCGCCGGGTGAGCAGC;RSEQ=CGGCCGGGGTCGCGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:13,13:0.0714:2,2:46:1:31.5:1:1:1:60:4:0.0741:0:2 0/0:49:0:0,0:27,22:0:2,0:20.9:1:29.4:1:1:0:60:98:1:0:0.6 -5 56111927 . C T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51339;SOR=1.79885;LSEQ=GCGGGGACTTGGAGAGCGGG;RSEQ=AGAGGGCAATGAATGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:4,4:4,5:0.4706:2,2:28:1:27.6:1:1:1.23:60:7:0.4375:0:1.4 1/0:21:13:6,7:5,3:0.619:2,2:18.8:1:26.7:1:0.65944:1.88324:60:26:0.619:0:1.2 -5 56152416 . C A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.1842;LSEQ=CTCATTTTATTTGTTTCTGC;RSEQ=TGCATTTTAGTCGTGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:79:65,14:78,26:0.4293:2,2:26.7:1:30.1:1:0.28059:1.54:60:78:0.4333:0:1.1 1/0:211:149:107,42:45,17:0.7062:2,2:25.5:1:29.9:1:1:1.03885:60:73.5:0.7136:0:1.1 -5 56155804 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20104;SOR=0;LSEQ=TTAGCTTCATTTATAACAAA;RSEQ=AAAAGACTGGCCAGCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:26,118:0.0137:2,2:17:1:31.5:1:0.3367:4.47:60:4:0.0137:0:1 0/0:179:0:0,0:37,142:0:2,0:22:1:30.6:1:1:0:60:88.5:1:0:0.1 -5 56155870 . TG T 72 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20243;SOR=5.1742;LSEQ=GATCTGCAGACCCCTGAGGA;RSEQ=GGGGGGGTGGTTCCTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:0,1:0,40:0.0244:1,0:24:0:27:0:1:0:60:2:0.025:0:0 0/1:43:5:0,5:0,38:0.1163:1,0:24.4:1:31.2:1:1:0:60:10:0.119:0:0 -5 56160541 . T TA 104 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.02252;SOR=0.29111;LSEQ=GAAATGAGAAACGTACCTAA;RSEQ=AAAAAAAAATGTTGTGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:12:10,2:209,56:0.0433:2,2:26.4:1:29.2:1:1:1.34:60:24:0.0446:0.0036:0.5 0/1:385:5:4,1:274,104:0.013:2,2:20.2:1:26.9:1:1:1.52:60:10:0.0133:0.0026:0.8 -5 56161787 . G A 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04104;LSEQ=TCATCATCTAGTACTTCTAC;RSEQ=TCTAGTTCAGAAAACAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:575:573:220,353:0,1:0.9965:0,2:25.9:1:30.4:1:1:0:60:113.6:0.9982:0:1.1 1/1:739:681:264,417:26,31:0.9215:2,2:25.4:1:29.9:1:0.32518:1.32424:60:112.5:0.9221:0:1.1 -5 56161975 . C T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77608;LSEQ=GTTCGCTGGGCATGGTGGCT;RSEQ=GTGCCTGTAATCCCAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:13:2,11:0,8:0.619:0,2:15.5:1:29.8:1:0.50476:0:60:26:0.619:0:1.1 1/0:9:5:0,5:0,4:0.5556:0,0:23.6:1:31:1:1:0:60:10:0.5556:0:1 -5 56168571 . G A 215 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAATAATTTTGAAATGATAC;RSEQ=GATATGTTTAATTTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:134:79,55:95,88:0.4227:2,2:21.1:1:30.5:1:0.25326:1.33:60:66:0.419:0:1 0/0:460:0:0,0:258,200:0:2,0:22.6:1:29.7:1:1:0:60:228:0.9956:0:0.1 -5 56168712 . C T 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGCTGCACAGCAGCAAAC;RSEQ=GTACAGCAGCAGCCTTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:606:0:0,0:296,310:0:2,0:25.9:1:30.4:1:1:0:60:150.5:1:0:0.1 0/1:777:61:30,31:358,357:0.0785:2,2:24:1:30.3:1:1:1.03619:60:60:0.0781:0:1.1 -5 56170813 . C G 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTCAAAATGCTCTGGGTC;RSEQ=ATAAGCTTTTCTTTACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:235,108:0:2,0:25.5:1:31.1:1:1:0:60:67.6:0.9971:0:0.1 0/1:398:22:15,7:251,125:0.0553:2,2:23:1:29.7:1:1:1.07:60:44:0.0566:0:1.1 -5 56171171 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17192;SOR=0;LSEQ=TTCCATAATCATATCATTAT;RSEQ=GGTTTGGGGTTTTTTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:39,154:0.0102:2,2:23:1:28.5:1:0.36902:3.91:60:4:0.0103:0:1 0/0:276:0:0,0:69,207:0:2,0:24.2:1:29.9:1:1:0:60:45:1:0:0.1 -5 56171191 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5104;SOR=Inf;LSEQ=GGGTTTGGGGTTTTTTGATG;RSEQ=TTCGTAGATAGTGTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:9,125:0:2,0:23.8:1:32:1:1:0:60:268:1:0:0 0/1:183:2:1,1:24,156:0.0109:2,2:13.5:1:31.5:1:0.25651:6.39:60:4:0.0111:0:1 -5 56175226 . A G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCGATAAGAACAGTAGTTG;RSEQ=CATTTATATCTATAAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:11:0:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 56176306 . T C 78 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55944;SOR=0.24802;LSEQ=GTACTTGCAAAGAGCCATTG;RSEQ=TGAAAATTCTGTGCTTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:6,0:4,0:0.6:0,0:20.2:1:30.3:1:1:0:60:5:0.5556:0:2.2 0/1:4:1:1,0:3,0:0.25:0,0:18:0:27:0:1:0:60:2:0.25:0:1 -5 56176446 . C T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03935;SOR=Inf;LSEQ=TCCTGAAAACATTATTTCTC;RSEQ=ACTTTTTCACAAGGCATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:90,4:0:1,0:21.1:1:31.6:1:1:0:60:188:1:0:0 0/1:77:4:4,0:63,10:0.0519:2,0:24:1:32.5:1:1:0:60:8:0.0526:0:1 -5 56176474 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.60158;SOR=2.27967;LSEQ=CACAAGGCATTACATTACTC;RSEQ=TCTAATATTGTATAGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:1:0,1:134,26:0.0062:2,0:1:0:26:0:0.1677:0:60:2:0.0063:0:1 0/1:142:2:1,1:108,32:0.0141:2,2:20.5:1:29:1:0.41205:3.33877:60:4:0.0144:0:1 -5 56176642 . C A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08956;SOR=0;LSEQ=AAAAGCTGGTAATAACTTTT;RSEQ=ACTTAAAAGGAATATAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:89,177:0.0112:2,2:13.3:1:21:1:0.26508:3.96:60:2:0.0075:0:1.7 0/0:331:0:0,0:119,212:0:2,0:24.1:1:31.4:1:1:0:60:109.333:1:0:0.1 -5 56177148 . A G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.1098;LSEQ=TGTATCTTCCTACCCTCCCT;RSEQ=CACCCTCCTCAAGAATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:110:65:18,47:10,35:0.5909:2,2:22.4:1:31.1:1:0.6569:1.34:60:20.667:0.6019:0:1.1 0/1:118:16:5,11:22,80:0.1356:2,2:25.1:1:32.7:1:0.52141:1.65:60:32:0.1368:0:1 -5 56177369 . T C 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=12.37913;LSEQ=TTTTCAGTAATTGGAACTTA;RSEQ=ATGGTAATGAATGTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:2:2,0:235,66:0.0066:2,0:29.5:1:13:0:1:0:60:0:0:0:5.5 0/1:328:25:18,7:220,83:0.0762:2,2:27.6:1:32.1:1:1:1.0307:60:50:0.0772:0:1 -5 56177382 . G GT 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04871;SOR=0;LSEQ=GAACTTATATGGTAATGAAT;RSEQ=TTTTTTTCTTTCAGGTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:4:2,2:271,96:0.0108:2,2:13.5:1:29.1:1:0.28532:2.81357:60:8:0.0109:0.0054:1 0/0:417:0:0,0:289,128:0:2,0:24:1:31.4:1:1:0:60:138:1:0:0.5 -5 56177443 . G A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.37255;LSEQ=CCTTTGCTTTGCAGTCCATT;RSEQ=ATAATTCCCACTCAATGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:321:179,142:226,156:0.456:2,2:27:1:28.9:1:0.39944:1.14903:60:52.5:0.4532:0:1.1 1/0:864:575:320,255:154,133:0.6655:2,2:25.4:1:28.4:1:0.61128:1.08:60:70.875:0.6624:0:1.1 -5 56177743 . G A 277 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGTTCCCCTGAGTGCACA;RSEQ=TCCATTTAGAGAAAACTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:532:532:251,281:0,0:1:0,2:25.8:1:30.7:1:1:0:60:132:1:0:1.1 1/0:627:494:251,243:69,63:0.7879:2,2:24.7:1:29.6:1:0.76983:1.06026:60:69.571:0.788:0:1.1 -5 56177848 . TCAA T 272 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=1e-05;SOR=0.56377;LSEQ=TTTCAGTAGGACCTTCTAGT;RSEQ=CAACAACAACAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:549:414:243,171:71,32:0.7541:2,2:27.7:1:31.3:1:0.07089:1.56003:60:81.8:0.756:0.0984:0.1 1/0:652:413:221,192:119,83:0.6334:2,2:25.6:1:30.8:1:0.22693:1.24515:59.9:102.25:0.6341:0.1212:0.2 -5 56177913 . C G 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCAAACAAAAGGCAGACC;RSEQ=CACAGTCAGTGTTTGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:799:0:0,0:420,377:0:2,0:24.7:1:31:1:1:0:60:112.857:0.9975:0:0.1 0/1:1083:33:15,18:564,481:0.0305:2,2:23.9:1:30.7:1:0.37748:1.40661:60:66:0.0311:0:1.2 -5 56178111 . A G 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCGCAAGTTTTCTCTACA;RSEQ=TTCCACAGAAACTGTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:0:0,0:282,246:0:2,0:24.7:1:30.5:1:1:0:60:74.429:1:0:0.1 0/1:618:43:20,23:301,273:0.0696:2,2:28.7:1:31.7:1:0.52747:1.26745:60:86:0.07:0:1 -5 56178217 . A C 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01987;LSEQ=TACACAGGCCAAAGCCATCT;RSEQ=GACCTACCCCAGGTAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:719:716:350,366:0,0:0.9958:0,2:25.1:1:30.2:1:1:0:60:78.556:0.9958:0:1.1 1/1:854:705:360,345:72,76:0.8255:2,2:25:1:30:1:0.65129:1.10:60:87.125:0.8258:0:1.1 -5 56179212 . C T 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02233;SOR=0;LSEQ=ATTACTTTTGCATTTGCTGT;RSEQ=GGTCACAAATACCTTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:41,1:0,0:1:0,1:25:1:30.1:1:1:0:60:41:1:0:1.1 1/1:28:24:23,1:4,0:0.8571:0,1:23.7:1:30.2:1:1:0:60:48:0.8571:0:1 -5 56179341 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.18706;LSEQ=ACAGTAAAAAGATTGCTTTC;RSEQ=TTTAATATGTAGACACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:158:117,41:125,55:0.4675:2,2:24.2:1:30.2:1:0.3978:1.25:60:316:0.4702:0:1.1 0/1:405:57:40,17:234,114:0.1407:2,2:24.1:1:29.4:1:0.76054:1.15:60:56:0.1404:0:1.1 -5 56179573 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49968;SOR=Inf;LSEQ=TGAAGCATGTTCAGTAAAAA;RSEQ=AATAAAGGATATGTCCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:3,86:0:1,0:23.1:1:31.6:1:1:0:60:88:0.9888:0:0 0/1:103:2:0,2:6,95:0.0194:2,0:14:1:26.5:1:1:0:60:4:0.0194:0:2 -5 56180112 . T G 41 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTTTCAACAGTGTACTTG;RSEQ=GCGGTGCCATCTTGGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:22.7:1:26:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 56180419 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24717;SOR=Inf;LSEQ=TGCTAATAAAGTGCTAGTTT;RSEQ=CATTTGTTCATTTTAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:104,28:0:2,0:21.9:1:31.7:1:1:0:60:65:1:0:0.4 0/1:133:3:1,2:104,26:0.0226:2,2:14:1:23.7:1:0.11209:7.82851:60:6:0.0226:0:1.3 -5 56180420 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49817;SOR=Inf;LSEQ=GCTAATAAAGTGCTAGTTTG;RSEQ=ATTTGTTCATTTTAGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:107,29:0:2,0:21.7:1:31.8:1:1:0:60:67:1:0:0.4 0/1:137:2:2,0:106,29:0.0146:2,0:25:1:31.5:1:1:0:60:4:0.0146:0:1 -5 56180480 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14326;LSEQ=AAAACTTTGTGAACGTGTTT;RSEQ=TTTGAAACAGGTGACTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:276:158:103,55:78,39:0.5725:2,2:26.5:1:32.2:1:0.89775:1.06767:60:78:0.5714:0:1 0/1:349:56:41,15:179,114:0.1605:2,2:23.3:1:31.2:1:0.09724:1.74:60:55:0.1585:0:1.1 -5 56180691 . G A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11474;SOR=0;LSEQ=ATTACAAAATAGTAGTACGT;RSEQ=GATTTAACTTTCTGCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:2,1:38,150:0.0157:2,2:6.7:1:21.3:1:0.11168:7.78:60:2:0.0107:0:1 0/0:201:0:0,0:58,143:0:2,0:22.4:1:30.4:1:1:0:60:32.5:1:0:0.1 -5 56181215 . GTTC G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTTCTCTTTACCAGTCA;RSEQ=TTAAGTATGTTATCTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:20.5:1:33.5:1:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 56181982 . GT AC 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17208;SOR=Inf;LSEQ=GGCTCACACCTGTAATCCCA;RSEQ=ACTTTGGGAGGTGAAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:0,67:0:1,0:22.8:1:32.1:1:1:0:60:66:1:0:0.1 0/1:48:2:0,2:0,46:0.0417:1,0:15:1:31.5:1:1:0:60:4:0.0417:0:2.5 -5 56182589 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTAGGTCCCATTATTTT;RSEQ=CTTATCCTTTTCTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:27:0:32:0:1:0:60:2:1:0:1 1/1:2:2:0,2:0,0:1:0,0:23:1:30:1:1:0:60:4:1:0:1 -5 56183542 . C T 102 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03612;SOR=0;LSEQ=CCTTGGCAATATTCAAAAAA;RSEQ=AGGTTTTAATAGATTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:1:0,0:20.4:1:28.7:1:1:0:60:24:1:0:1.1 1/0:7:4:0,4:0,3:0.5714:0,0:12:1:29.3:1:1:0:60:8:0.5714:0:1 -5 56183637 . G C 74 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAACTCAAAGTGCACATAA;RSEQ=AAATTTTTAAAAATATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:16.8:1:32.2:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 56183743 . T G 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16667;SOR=0;LSEQ=ATTGTTCTTCTGACTCAGCT;RSEQ=CTTCTGTCGTGTTCATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,1:0.7143:2,2:21.6:1:32.4:1:1:1.41418:60:10:0.7143:0:1 0/0:2:0:0,0:1,1:0:2,0:13.5:1:27.5:1:1:0:60:4:1:0:0 -5 56183941 . C G 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=ATTAGGTAGTCCACAGAATT;RSEQ=CTGTTTGTACCAGTTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:63,2:0,0:1:0,1:23:1:31.7:1:1:0:60:20.667:1:0:1.1 1/1:45:36:36,0:9,0:0.8:0,1:22.1:1:32.9:1:1:0:60:72:0.8:0:1 -5 56184247 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.78656;LSEQ=ACAGCAGAATTTGGCAGGAG;RSEQ=CAAATTTTGATGGGTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:1:0,1:14,114:0.0078:2,0:21:0:32:0:1:0:60:2:0.0078:0:2 0/1:145:2:0,2:15,128:0.0138:2,0:42.5:1:29.5:1:1:0:60:4:0.0139:0:1.5 -5 56184444 . T C 92 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGATACACTGGTGATGC;RSEQ=AGGCAGTGGCAGCGAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:26.3:1:30.9:1:1:0:60:7:1:0:1.1 1/1:1:1:1,0:0,0:1:0,0:12:0:31:0:1:0:60:2:1:0:1 -5 56184610 . C T 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTAAGCTATAATGTTTGG;RSEQ=AGGTTAGGTGTATTAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:35.6:1:28.4:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 56185143 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTAGCTGAGACTACAGGCAC;RSEQ=CGCCACCATGCCCAGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:39.3:1:29.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 56188977 . G A 68 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTAATCTAAATAGCTCT;RSEQ=TATGCTGAAGAAATAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:27.2:1:29.4:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 56189554 . G GAA 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.12265;SOR=Inf;LSEQ=AAACAGGATGCTCAACAAGA;RSEQ=AAAAAAAACTTGTGGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:23,136:0:2,0:24.2:1:31.2:1:1:0:60:30.8:0.9935:0:0.2 0/1:160:4:2,2:28,128:0.025:2,2:18.5:1:28.9:1:0.15983:4.51:60:8:0.0256:0.0125:0.5 -5 56525768 . G GCGTCCCGTCCCGTCC 109 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=31;MSI=9.000;MSILEN=5;SSF=0.05488;SOR=0.39655;LSEQ=CCATCCCGTTGCATCGCATC;RSEQ=CGTCCCGTCCCGTCCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:13:7,6:7,4:0.4333:2,2:23.3:1:30.2:1:0.69683:1.47477:59.2:26:0.4333:0.2:0.2 0/1:65:15:7,8:27,17:0.2308:2,2:18.3:1:28.1:1:0.37377:1.79643:59.7:30:0.2419:0.1385:0.5 -5 56525851 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGCAACCTCCCCGCCTCCC;RSEQ=GGTTCAAGCGATTCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:0:2,0:23.1:1:30.8:1:1:0:60:18:1:0:0.2 0/1:24:2:0,2:6,16:0.0833:2,0:16.5:1:29.5:1:1:0:57.5:4:0.0952:0:1.5 -5 56527347 . A G 34 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACCTCAGGTGATCCACCT;RSEQ=CCTCAGCCTCCCAAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:34:0:1:0:60:4:1:0:1 -5 57750267 . A C 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04145;SOR=0;LSEQ=CTTAGCCTGTTCTGGTTCCA;RSEQ=CCAGTCCAGCAGGCCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:76:74,2:0,0:1:0,1:24.7:1:32.3:1:1:0:60:75:1:0:1.3 1/1:64:60:60,0:4,0:0.9375:0,1:23.7:1:31.6:1:1:0:60:120:0.9375:0:1.1 -5 57750305 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23391;SOR=Inf;LSEQ=AGGGGAATTGTTTTCGTACC;RSEQ=CCACATGTCCATCTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:146,4:0:1,0:21.7:1:30.4:1:1:0:60:149:1:0:0.8 0/1:141:2:1,1:134,5:0.0142:1,2:24.5:1:27:1:0.08359:24.55647:60:4:0.0145:0:1.5 -5 57750350 . C G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33206;LSEQ=ACTCTAGATCATTCTTTTGG;RSEQ=TTCCCTGTAGATCTCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:366:188:139,49:129,48:0.5137:2,2:22.9:1:31.4:1:0.90568:1.06:60:93:0.5152:0:1.1 0/1:401:104:72,32:198,99:0.2594:2,2:24.8:1:31.1:1:0.71574:1.12:60:103:0.2594:0:1 -5 57751274 . G GA 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.65036;SOR=0.74581;LSEQ=GAACGAAAGGGAGAGAAGAG;RSEQ=AAAAAAAAATAGAAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:11:7,4:127,158:0.0369:2,2:30.7:1:30.3:1:0.23354:2.17:60:22:0.0377:0:0.1 0/1:324:9:4,5:124,191:0.0278:2,2:16.9:1:29.8:1:0.7433:1.23:60:18:0.0288:0.0062:0.1 -5 57751443 . A G 196 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTCTGAGAGCTGGTACCC;RSEQ=AAGCCATATTTGTTAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:991:0:0,0:536,455:0:2,0:24.1:1:30:1:1:0:60:81.583:1:0:0.1 0/1:996:97:50,47:470,427:0.0974:2,2:24.3:1:29.7:1:0.91496:1.03464:60:47.5:0.0967:0:1.2 -5 57751651 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20816;SOR=Inf;LSEQ=CAAGTTATACAATATTTTAG;RSEQ=AATAAAACCTCAGGCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:45,188:0:2,0:23.8:1:32.1:1:1:0:60:115.5:1:0:0.1 0/1:196:2:1,1:37,157:0.0102:2,2:9:0:30.5:1:0.35097:4.20:60:4:0.0104:0:1.5 -5 57751836 . G A 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=AGTTTCATTATTTAAAATAC;RSEQ=ATTGACAACCACTTACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:598:0:0,0:436,162:0:2,0:22.8:1:30.1:1:1:0:60:148.5:1:0:0.1 0/1:590:12:10,2:414,164:0.0203:2,2:19.1:1:30.8:1:0.52441:1.98:60:24:0.0205:0:1.2 -5 57752252 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20553;SOR=Inf;LSEQ=CCATGATAATCATAGTCCAA;RSEQ=TGCTAATTAATAAAGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:173,35:0:2,0:24.2:1:32.1:1:1:0:60:68.333:1:0:0.1 0/1:173:2:1,1:150,21:0.0116:2,2:21.5:1:28.5:1:0.23881:7.00185:60:4:0.0118:0:1.5 -5 57752504 . T C 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=ATTTTCTCCTTCTTGCATTA;RSEQ=TGACCAACTTATGAGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:14,69:0:2,0:25:1:29.9:1:1:0:60:40.5:1:0:0.2 0/1:44:8:1,7:3,33:0.1818:2,2:24.4:1:32.4:1:0.56608:1.55:60:16:0.1818:0:1.8 -5 57752526 . G A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00158;SOR=Inf;LSEQ=GACCAACTTATGAGCATCCT;RSEQ=GGCAAAAATAGCATTTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:13,49:0:2,0:20.3:1:31.1:1:1:0:60:30:1:0:0.2 0/1:26:5:2,3:1,20:0.1923:1,2:17.6:1:29.2:1:0.08462:11.33:60:10:0.2083:0:2.4 -5 57752563 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09504;SOR=Inf;LSEQ=TACCTTTGCCTTTAGCTGCA;RSEQ=CTACCCCCAAAAGCCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:28.9:1:31.9:1:1:0:60:17.5:1:0:0.4 0/1:17:2:1,1:6,9:0.1176:2,2:22.5:1:31.5:1:1:1.46:60:4:0.1176:0:2.5 -5 57752593 . C G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56222;SOR=0.60748;LSEQ=AAAGCCCTCTTTAGTGTTTG;RSEQ=AAAATAAAAAGCTATCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:14:9,5:15,12:0.3415:2,2:26.6:1:28.4:1:0.74171:1.43:60:13:0.325:0:1 0/1:21:5:4,1:13,3:0.2381:2,2:29.2:1:31.2:1:1:1.07915:60:10:0.2381:0:1.2 -5 57752811 . CA C 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00888;SOR=0;LSEQ=TGCTTTGTCTTTTTTGCCAC;RSEQ=AAAAGAGCAGCAGCTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:6:3,3:219,209:0.0138:2,2:30.8:1:31.2:1:1:1.04775:60:12:0.014:0:0.2 0/0:518:0:0,0:249,269:0:2,0:25.6:1:29.7:1:1:0:60:128.5:1:0:0.1 -5 57752965 . G A 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=AGTAACCTGTCAGGTAACTG;RSEQ=GATCAATACCAGGTAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:267,165:0:2,0:22.6:1:31:1:1:0:60:60.714:1:0:0.1 0/1:394:14:8,6:234,146:0.0355:2,2:16.1:1:27.3:1:0.78357:1.20147:60:6:0.0316:0:1.1 -5 57752983 . TA T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.78747;SOR=1.07729;LSEQ=TGGGATCAATACCAGGTAAT;RSEQ=AAAAAAAAAGATAGTGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:545:28:17,11:329,188:0.0514:2,2:26.2:1:30.4:1:0.84075:1.13209:60:56:0.0517:0.0073:0.1 0/1:526:29:16,13:297,193:0.0551:2,2:28.5:1:30.1:1:0.56387:1.24976:60:58:0.0566:0.0019:0.2 -5 57753011 . C CA 103 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03019;SOR=0.25446;LSEQ=AAAGATAGTGCACCAACCTG;RSEQ=AAAAAAAAGTCATGTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:11:7,4:428,284:0.0151:2,2:23.6:1:30:1:1:1.16:60:22:0.0157:0.0027:0.1 0/0:772:3:0,3:432,333:0.0039:2,0:31.3:1:30:1:0.08332:0:60:6:0.0041:0:0 -5 57753116 . C T 192 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=90.22886;LSEQ=GCAGGAGCCAGCAATGAGGA;RSEQ=GGCATTGTATACCTTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:1:0,1:302,422:0.0014:2,0:29:0:31:0:1:0:60:2:0.0014:0:1 0/1:803:89:36,53:320,393:0.1108:2,2:23.3:1:29.7:1:0.49743:1.19849:60:43.5:0.1092:0:1.8 -5 57753149 . A G 192 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGCTTCCCTTATGCACCT;RSEQ=TAAGTTTCTTTGAGATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:657:0:0,0:276,381:0:2,0:25.4:1:29.7:1:1:0:60:130.4:1:0:0.1 0/1:676:74:31,43:248,354:0.1095:2,2:25.3:1:31:1:0.90121:1.03:60:73:0.1101:0:1.9 -5 57753251 . T A 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAATGGTCATAAAGCAAC;RSEQ=CTTTTCAAGTGTTAAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:144,177:0:2,0:23.5:1:30.2:1:1:0:60:44.857:1:0:0.1 0/1:303:21:8,13:155,127:0.0693:2,2:21.6:1:30:1:0.17384:1.97882:60:42:0.07:0:1.1 -5 57753413 . G A 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06975;SOR=6.7774;LSEQ=GGGGTACCACATATCGTTCT;RSEQ=GAAAGACAAAATATTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:1:0,1:206,304:0.002:2,0:10:0:30:0:1:0:60:2:0.002:0:6 0/1:533:7:4,3:220,304:0.0131:2,2:14.7:1:25.3:1:0.46247:1.84:60:6:0.0115:0:1.3 -5 57753437 . G A 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=12.57781;LSEQ=AGACAAAATATTGAGATCGT;RSEQ=TTAGGAACTATTCCACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:2:1,1:133,260:0.0051:2,2:6:0:21.5:1:1:1.95:60:1:0.0026:0:2 0/1:398:24:7,17:130,244:0.0603:2,2:22:1:29:1:0.66229:1.29311:60:23:0.0587:0:1.8 -5 57753456 . C T 247 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00321;LSEQ=TGTTAGGAACTATTCCACTA;RSEQ=TTAAACTTGGTTCTCTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:286:285:78,207:1,0:0.9965:0,2:24.5:1:30.3:1:0.27622:0:60:94:1:0:1.1 0/1:284:135:39,96:37,112:0.4754:2,2:22.6:1:29.7:1:0.50259:1.23:60:44:0.4731:0:1.2 -5 57753937 . C T 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGTTCCAAGGGTTCTAG;RSEQ=CTGGCTGCCAGACCGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:0:0,0:368,393:0:2,0:26.2:1:31.4:1:1:0:60:94.125:0.9987:0:0.4 0/1:838:55:29,26:359,422:0.0656:2,2:27.7:1:28.8:1:0.40154:1.31:60:54:0.0653:0:1.4 -5 57754004 . C T 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.84737;LSEQ=TAATAAAAAAGTTCCCTAGA;RSEQ=GATAAACAAAACAAAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:182:60,122:77,151:0.4428:2,2:22.7:1:30.3:1:0.91619:1.03679:60:181:0.4458:0:1.1 1/0:442:263:87,176:63,114:0.595:2,2:26.1:1:29.8:1:0.60893:1.11768:60:51.6:0.5917:0:1.4 -5 57754005 . G A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23972;LSEQ=AATAAAAAAGTTCCCTAGAC;RSEQ=ATAAACAAAACAAAATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:402:226:75,151:58,118:0.5622:2,2:24.9:1:29.9:1:1:1.01:60:36.667:0.5612:0:1.1 0/1:434:102:30,72:115,217:0.235:2,2:25:1:30:1:0.34021:1.2712:60:204:0.2367:0:1 -5 57754007 . T G 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAAAAAGTTCCCTAGACGA;RSEQ=AAACAAAACAAAATGTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:130,259:0:2,0:24.3:1:28.8:1:1:0:60:54.571:1:0:1.1 0/1:416:34:11,23:127,255:0.0817:2,2:25.4:1:30.4:1:1:1.04126:60:16:0.0777:0:2.6 -5 57754040 . G A 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTGAATCCCTTTGAAAAT;RSEQ=CGTTCTAACCAAGTACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:59,176:0:2,0:23.9:1:31.8:1:1:0:60:116.5:1:0:0.9 0/1:227:19:3,16:63,145:0.0837:2,2:20.8:1:30.1:1:0.29006:2.31002:60:38:0.0841:0:2.8 -5 57754132 . G C 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAAAGCAAGATTGCAGACAC;RSEQ=AGATCCCAATTAAGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:157:91,66:0,0:1:0,2:22.4:1:31.5:1:1:0:60:38.25:1:0:1.1 1/1:115:97:65,32:11,6:0.8435:2,2:20.7:1:30.2:1:1:1.11:60:47.5:0.8407:0:1 -5 57754159 . T TA 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.60762;SOR=0.73128;LSEQ=CAATTAAGAACATTAATATG;RSEQ=AAAAAAAAACAGAGAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:9:4,5:134,60:0.0443:2,2:21.4:1:28.4:1:0.14877:2.77597:60:18:0.0457:0.0099:0.6 0/1:183:6:3,3:136,41:0.0328:2,2:32:1:29.7:1:0.1512:3.29017:60:12:0.0331:0:0.7 -5 57754461 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.26123;SOR=0;LSEQ=TTAACTTTGCAGTGTAAGTG;RSEQ=TGCCACAGCTAAAATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:163,75:0.0124:2,2:6.7:1:28.7:1:1:1.08628:60:6:0.0127:0:1 0/0:185:0:0,0:122,63:0:2,0:23.2:1:32.2:1:1:0:60:370:1:0:0.1 -5 57754489 . ACT A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05193;LSEQ=GCTAAAATCCCAGATAAAAT;RSEQ=CTTTGAATACCATGTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:145:108,37:127,68:0.4265:2,2:24.4:1:32.2:1:0.07517:1.56:60:290:0.4315:0.0618:0.1 0/1:324:12:7,5:205,107:0.037:2,2:20.2:1:29.8:1:0.75812:1.36706:60:24:0.0372:0.0123:0.2 -5 57754808 . G A 278 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00446;LSEQ=ACTTTACTCAAGAGTCATAC;RSEQ=CACCTTTTCCCTTTGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:621:618:361,257:0,0:0.9952:0,2:25:1:30:1:1:0:60:122.6:0.9951:0:1.4 0/1:768:367:206,161:215,184:0.4779:2,2:23.6:1:29.5:1:0.56113:1.09:60:90.75:0.4783:0:1.4 -5 57754851 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21637;LSEQ=TTAGCTACTCTGCTGTGAGG;RSEQ=ATAATTTTTGCGGCGTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:756:318:161,157:226,210:0.4206:2,2:26.3:1:31.1:1:0.76815:1.04942:60:62.6:0.4201:0:1.7 0/1:951:129:63,66:412,407:0.1356:2,2:27.6:1:30.8:1:0.77689:1.06045:60:128:0.1359:0:1.8 -5 57754972 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23025;SOR=Inf;LSEQ=GATGGCACAAAAATGGACGG;RSEQ=AGATATTTTAAATAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:26,174:0:2,0:24:1:31.6:1:1:0:60:24:1:0:0.2 0/1:185:2:1,1:35,148:0.0108:2,2:10:1:30:1:0.35217:4.18:60:4:0.0116:0:1 -5 57755703 . C T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31945;LSEQ=GGCCGCTTCTTCTTCGAGTC;RSEQ=GCTCCGCAACCCTTGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:736:375:184,191:166,194:0.5095:2,2:24.8:1:30.6:1:0.46014:1.13:60:124:0.511:0:1.1 0/1:747:186:90,96:263,297:0.249:2,2:25.9:1:30.2:1:0.79935:1.06:60:92:0.2497:0:1.2 -5 57755774 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50663;SOR=1.94315;LSEQ=TGGCTGGTAGGTGATAGTCC;RSEQ=CAAAAGCTCCATGGTCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:3:2,1:229,329:0.0053:2,2:8:1:21.3:1:0.57157:2.87:60:2:0.0037:0:2 0/1:580:6:4,2:260,313:0.0103:2,2:17.3:1:26.8:1:0.41914:2.40:60:5:0.0087:0:1.5 -5 57755827 . G C 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00189;SOR=Inf;LSEQ=CTGCCCGCTGCCACCCCCTA;RSEQ=GCGCGGTCACACGTCCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:91,207:0:2,0:26.4:1:30.5:1:1:0:60:26.091:1:0:0.1 0/1:318:10:1,9:110,198:0.0314:2,2:22.9:1:30.9:1:0.17383:4.98168:60:20:0.0323:0:1 -5 57755840 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11795;SOR=Inf;LSEQ=CCCCCTAGGCGCGGTCACAC;RSEQ=TCCGAGCCGGCCGTGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:70,195:0:2,0:23.1:1:31:1:1:0:60:65.25:1:0:0.1 0/1:257:3:2,1:74,180:0.0117:2,2:8.3:1:28:1:0.20963:4.83:60:6:0.012:0:1.7 -5 57755843 . C T 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTAGGCGCGGTCACACGTC;RSEQ=GAGCCGGCCGTGGTCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:68,190:0:2,0:22.3:1:29.7:1:1:0:60:128:0.9961:0:0.1 0/1:241:67:17,50:50,124:0.278:2,2:22.9:1:29.1:1:0.63417:1.18512:60:21.333:0.2723:0:1.2 -5 57755865 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21268;SOR=Inf;LSEQ=AGCCGGCCGTGGTCCTCGCA;RSEQ=CCTTGCCTCTGGTGCCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:30,140:0:2,0:22.5:1:30.4:1:1:0:60:23.286:1:0:0.1 0/1:146:2:1,1:19,125:0.0137:2,2:25:0:32:0:0.25602:6.44:60:4:0.014:0:1 -5 57755901 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50456;SOR=0;LSEQ=CGACTAGCACCCAACACCCC;RSEQ=GTCCACTTGTGCGAGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:0,2:0,89:0.022:1,0:42.5:1:29.5:1:1:0:60:4:0.022:0:1 0/0:71:0:0,0:1,70:0:1,0:22.1:1:30.5:1:1:0:60:70:1:0:0.6 -5 57755923 . C T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00253;SOR=Inf;LSEQ=TCCACTTGTGCGAGTGAGAG;RSEQ=GCTCGGCGAAGTCTTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:0,64:0:1,0:22.7:1:30.2:1:1:0:60:63:1:0:0.2 0/1:40:6:0,6:0,34:0.15:1,0:20.5:1:31.3:1:1:0:60:12:0.1538:0:1.2 -5 57755936 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00215;SOR=Inf;LSEQ=GTGAGAGCGCTCGGCGAAGT;RSEQ=TTATATACGGGGAGGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:0,53:0:1,0:19.8:1:32.6:1:1:0:60:106:1:0:0.2 0/1:24:5:0,5:0,19:0.2083:1,0:10.6:1:31.2:1:1:0:60:10:0.2083:0:1.2 -5 57755944 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=GCTCGGCGAAGTCTTATATA;RSEQ=GGGGAGGCGGGAAGGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,38:0:1,0:23.1:1:30:1:1:0:60:76:0.9744:0:0.3 0/1:16:2:0,2:0,14:0.125:1,0:27:1:30.5:1:1:0:60:4:0.125:0:1.5 -5 57755983 . T C 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31078;SOR=5.28626;LSEQ=CGGAGACTCGATACGCGACA;RSEQ=CACGTCACGGCCTATGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:0.4118:0,0:26.6:1:32.4:1:1:0:60:14:0.4118:0:1.1 1/1:5:4:0,4:0,1:0.8:0,0:20:1:31.5:1:1:0:60:8:0.8:0:1.5 -5 57756109 . T G 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAAACGCCGGCCGCCGAGA;RSEQ=CTCTTGCGGCCGCGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:14:1:32:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 58088168 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67163;SOR=0.64288;LSEQ=AACAATAACAGCCCTATGGC;RSEQ=ATGGGGGCAAAACCTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:21:21,0:4,0:0.84:0,1:23.5:1:31.9:1:1:0:60:42:0.875:0:1 1/0:13:10:9,1:3,0:0.7692:0,2:19.5:1:31:1:1:0:60:20:0.7692:0:1 -5 58088265 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26193;SOR=Inf;LSEQ=TGAAGAAGGAACCAAGTGCA;RSEQ=GGAAAAAAGCAAGAAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:136,50:0:2,0:24.4:1:31.1:1:1:0:60:92:1:0:0.3 0/1:244:3:1,2:159,82:0.0123:2,2:10.3:1:30.3:1:0.27308:3.85486:60:6:0.0125:0:1 -5 58088276 . A G 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.25718;SOR=Inf;LSEQ=CCAAGTGCACGGAAAAAAGC;RSEQ=AGAAATTTTACAAAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:159,79:0:2,0:23:1:29.7:1:1:0:60:38.667:1:0:0.4 0/1:295:3:2,1:180,112:0.0102:2,2:22.7:1:22.7:1:1:1.24:60:2:0.0069:0:1 -5 58088350 . G C 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01718;SOR=0.64653;LSEQ=GATGCAAATGCAAGGGACTA;RSEQ=TACAGTGCAGTGGAAATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:362:302:139,163:28,32:0.8343:2,2:25.6:1:31.9:1:1:1.02601:60:150:0.8333:0:1.1 1/0:438:335:156,179:44,57:0.7648:2,2:24.8:1:31.2:1:0.6491:1.13:60:334:0.7696:0:1.1 -5 58088388 . G A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35587;SOR=0.30741;LSEQ=TAGAGCCAGAGGCGGAAGCT;RSEQ=TGAACCACACATGGAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:105,173:0.0107:2,2:12:1:29:1:0.55982:3.28:60:6:0.0109:0:1.7 0/0:303:1:1,0:120,182:0.0033:2,0:1:0:21:0:0.39934:0:60:2:0.0033:0:2 -5 58088425 . G A 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.02933;LSEQ=ACATTGATTTTGGTGAGGGA;RSEQ=GGGGGAGATGAAGGGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:45,130:0.0113:2,2:18:1:21.5:1:0.45333:2.87:60:1:0.0057:0:2.5 0/1:172:2:1,1:52,118:0.0116:2,2:46:0:31.5:1:0.52258:2.26:60:4:0.0118:0:1.5 -5 58088523 . G A 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32538;SOR=0.47575;LSEQ=TAGATGGCCAAGCTATTTTC;RSEQ=TTAATAATTGTGATGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:22:0,22:0,8:0.7333:0,1:28.9:1:30.9:1:1:0:60:21:0.7241:0:1 1/0:16:9:0,9:0,7:0.5625:0,0:23.2:1:31.2:1:1:0:60:18:0.5625:0:1 -5 58205384 . G A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23171;SOR=0;LSEQ=ATTCATTATCATCATTTCAT;RSEQ=AATAAAAGCCATTTGAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:10.7:1:26.7:1:1:0:60:6:0.1429:0:1 0/0:20:0:0,0:19,1:0:1,0:22:1:32.9:1:1:0:60:40:1:0:0 -5 58205481 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4978;SOR=0;LSEQ=GGATTTAGTTTTAGAAAAAA;RSEQ=TCACCACATTTGCTTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:76,36:0.0175:2,2:17:1:28.5:1:0.54572:2.09609:60:4:0.0177:0:1 0/0:114:0:0,0:80,34:0:2,0:23.9:1:31.4:1:1:0:60:228:1:0:0.1 -5 58205509 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21426;SOR=0;LSEQ=ATTTGCTTACATTTTCATTT;RSEQ=ACCTCACATCAGCACTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:107,63:0.0116:2,2:34:1:31:1:1:1.69287:60:4:0.0116:0:1 0/0:199:0:0,0:115,84:0:2,0:23.2:1:28.6:1:1:0:60:198:1:0:0.3 -5 58205580 . T C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=10.61564;LSEQ=GCCCGTTTAAGCTCACGCCT;RSEQ=CTGTCATTCTCATACAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:18:8,10:82,99:0.0905:2,2:24.1:1:31.2:1:1:1.03518:60:36:0.0928:0:1.1 1/0:270:139:61,78:63,68:0.5148:2,2:26.9:1:31.1:1:0.54168:1.18392:60:68.5:0.5112:0:1.1 -5 58205668 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49803;SOR=Inf;LSEQ=AACTACCTGTCCCAAATAAA;RSEQ=GACATCCAAAGGTCATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:6,53:0:2,0:24.4:1:31.1:1:1:0:60:28.5:1:0:0 0/1:67:2:1,1:15,50:0.0299:2,2:6.5:1:27:1:0.42334:3.26:60:4:0.0303:0:3 -5 58988107 . CT C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.17516;SOR=Inf;LSEQ=GGGAGGGTCTTAAGGATCCG;RSEQ=TTTTATTGTTGTATTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:67,24:0:2,0:23:1:30.7:1:1:0:60:182:1:0:0.1 0/1:66:2:1,1:47,17:0.0303:2,2:22.5:1:32:1:0.47413:2.71525:60:4:0.0303:0:0 -5 58988151 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50104;SOR=0;LSEQ=CATGTAATTTGTGCTGCTTG;RSEQ=CTTGGTTTGACCATGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:89,59:0.0133:2,2:15:1:27.5:1:1:1.50419:60:4:0.0133:0:1 0/0:129:0:0,0:77,52:0:2,0:24.1:1:31.7:1:1:0:60:258:1:0:0.1 -5 58988192 . G T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5956;SOR=1.1585;LSEQ=ATAGCAAAGCAGAATTCCAA;RSEQ=GGGATTGGGTGAAAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:34:22,12:77,98:0.1627:2,2:12.6:1:30.2:1:0.03802:2.32:48.1:68:0.165:0:3.1 0/1:185:34:23,11:78,73:0.1838:2,2:16:1:30.3:1:0.12653:1.95:47.8:68:0.1838:0:3.4 -5 58988200 . G C 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00212;SOR=Inf;LSEQ=GCAGAATTCCAAGGGGATTG;RSEQ=GTGAAAGAAGAACTCTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:98,124:0:2,0:24.8:1:30.7:1:1:0:58.2:73:1:0:0.7 0/1:195:8:2,6:94,93:0.041:2,2:12.5:1:30.4:1:0.27926:3.01648:53.6:16:0.0412:0:3.9 -5 58988214 . T C 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59729;SOR=1.13194;LSEQ=GGATTGGGTGAAAGAAGAAC;RSEQ=CTTAAGTTATGGCTGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:65:25,40:55,89:0.3095:2,2:24.9:1:30.3:1:1:1.01:53.7:130:0.314:0:2.6 0/1:199:67:31,36:63,69:0.3367:2,2:25.1:1:30.4:1:0.88135:1.05996:53.7:66:0.3333:0:2.8 -5 58988216 . T C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52825;SOR=1.16564;LSEQ=ATTGGGTGAAAGAAGAACTC;RSEQ=TAAGTTATGGCTGGTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:66:25,41:56,89:0.3128:2,2:26.5:1:31:1:1:1.03176:53.8:132:0.3173:0:2.5 0/1:199:69:31,38:61,69:0.3467:2,2:25.8:1:31.1:1:0.8814:1.08324:53.9:138:0.3467:0:2.7 -5 58988237 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.2367;SOR=Inf;LSEQ=TAAGTTATGGCTGGTTTTCC;RSEQ=AGAACCAGTTTCTTAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:65,135:0:2,0:28.9:1:31.8:1:1:0:57.2:199:1:0:1 0/1:190:2:1,1:70,118:0.0105:2,2:37.5:1:30:1:1:1.68:60:4:0.0106:0:1 -5 58988316 . A C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48785;SOR=0.67566;LSEQ=AGTAATCTCTTTAAGAGTAA;RSEQ=CCCCATCACCTCATATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:16:0,16:1,25:0.381:1,1:14.7:1:32.4:1:1:0:44.3:32:0.3902:0:1.3 0/1:41:12:1,11:1,28:0.2927:1,2:17.3:1:32.2:1:0.50488:2.48:47.1:24:0.2927:0:1.6 -5 58988342 . G A 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10559;SOR=3.07502;LSEQ=TCACCTCATATTACTCTCAC;RSEQ=TACTGAGCTTTTAATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:6:0,6:2,24:0.1875:2,0:14.7:1:32.5:1:1:0:38.2:12:0.1875:0:2 0/1:19:8:0,8:1,10:0.4211:2,0:18.4:1:30.3:1:1:0:42.1:16:0.4211:0:1.5 -5 58988358 . A G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCACGTACTGAGCTTTTAAT;RSEQ=TACATCAAGAAGATTAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:1,21:0.0833:1,0:40.5:1:34:0:1:0:36:4:0.0833:0:2 0/0:8:0:0,0:1,7:0:2,0:27.4:1:29.1:1:1:0:55:16:1:0:0.4 -5 59017895 . A G 157 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CTTACTCCCTTTTGGATAAC;RSEQ=AAACAGCAGAAGACACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:33,5:0,0:1:0,2:17.7:1:30.1:1:1:0:60:37:1:0:1.1 1/0:32:19:15,4:12,1:0.5938:1,2:19.8:1:29.7:1:0.62467:3.09787:60:38:0.5938:0:1 -5 59018033 . A G 239 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAATAAGGCAAGAAAGCAC;RSEQ=ACTTTAGGACAATGCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:232:232:122,110:0,0:1:0,2:26.2:1:30.5:1:1:0:60:115:1:0:1.7 1/0:329:219:121,98:58,52:0.6657:2,2:24.8:1:30.3:1:0.7251:1.11:60:438:0.6677:0:1.5 -5 59018067 . C G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04193;LSEQ=GCCAAAAATGGCCTTCGTTT;RSEQ=TCGTCTTTTGACATAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:204:191:79,112:6,7:0.9363:2,2:27.3:1:31.6:1:0.77665:1.21401:60:46.75:0.935:0:1.9 0/1:282:107:50,57:75,98:0.3794:2,2:25:1:30.6:1:0.62154:1.15:60:106:0.3772:0:1.9 -5 59018098 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1859;SOR=0;LSEQ=ACATAAATAAGATGCTTTTG;RSEQ=TCATATTAATGAGTGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:47,94:0.014:2,2:29.5:1:29.5:1:1:1.99:60:4:0.0143:0:2 0/0:188:0:0,0:65,123:0:2,0:23.8:1:29.3:1:1:0:60:187:1:0:0.8 -5 61496655 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATGCAAATTAAAGGAG;RSEQ=CACTTCTCTTTGTTTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 61496821 . T G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48988;SOR=Inf;LSEQ=ATGCTAAGACTAGATTAAGC;RSEQ=TCACACAAGAATTTTATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:13,5:0:2,0:21.3:1:29.9:1:1:0:60:36:1:0:0 0/1:21:2:1,1:15,4:0.0952:2,2:19:0:32.5:1:0.42857:3.46389:60:4:0.1:0:1.5 -5 62835307 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCACTTTGGGAGGCCAA;RSEQ=GTGGGCAGATCAGGGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:34:1:30.8:1:1:0:60:8:0.5714:0:1 0/0:1:0:0,0:1,0:0:0,0:15:0:34:0:1:0:60:2:1:0:0 -5 62835401 . AT A 48 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.66352;SOR=0.5692;LSEQ=AGTACGGTGGGGATTAACTT;RSEQ=TTTTTTTTTTATTTTTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:2,1:13,9:0.12:2,2:11:1:30.2:1:1:1.37:60:6:0.1304:0.04:0.7 0/1:42:3:2,1:25,14:0.0714:2,2:16:1:30.3:1:1:1.12:60:6:0.0732:0:0.7 -5 62835420 . G A 120 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03112;LSEQ=TATTTTTTTTTTTATTTTTC;RSEQ=GAAGAAATAGGTATGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:16:8,8:18,11:0.3556:2,2:18.7:1:30.1:1:0.53364:1.61817:60:32:0.3556:0:1.2 0/1:61:1:1,0:35,25:0.0164:2,0:38:0:32:0:1:0:60:2:0.0167:0:1 -5 62835498 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49376;SOR=Inf;LSEQ=GGAATGCTGTGTGTTTCTAG;RSEQ=GGGAAATGGGATGTAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:13,21:0:2,0:19.5:1:30:1:1:0:60:68:1:0:0.3 0/1:37:2:1,1:11,24:0.0541:2,2:26:1:29:1:1:2.13:60:4:0.0541:0:1 -5 62836591 . T C 141 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03294;LSEQ=AGTGATATTACTTTTAAAAA;RSEQ=CACCAAGTGTAAGCACAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:22:22,0:31,0:0.4151:1,1:27.8:1:31.8:1:1:0:60:21:0.4118:0:1 0/1:45:1:1,0:41,3:0.0222:2,0:12:0:32:0:1:0:60:2:0.0227:0:1 -5 62836669 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58668;SOR=0.39639;LSEQ=AAGATCTTTCAGAAAGACAG;RSEQ=ATACCTGTAACTGCTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:2,0:154,43:0.0101:2,0:24:1:30.5:1:1:0:60:4:0.0104:0:1.5 0/0:250:1:0,1:170,77:0.004:2,0:1:0:23:0:0.31452:0:60:2:0.0041:0:1 -5 62836715 . C G 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00309;SOR=Inf;LSEQ=TGATCGTAAGTTTCCAAATC;RSEQ=ACAGTGGCACTGCAGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:223,134:0:2,0:24.6:1:31.3:1:1:0:60:70.4:0.9972:0:0.5 0/1:453:10:5,5:256,186:0.0221:2,2:23.5:1:30.7:1:0.74911:1.37534:60:20:0.0225:0:2 -5 62836726 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03212;LSEQ=TTCCAAATCCACAGTGGCAC;RSEQ=GCAGATTCAAAGCACTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:182:110,72:118,92:0.4631:2,2:25.2:1:30.1:1:0.41285:1.19:60:59.667:0.4602:0:1.1 0/1:484:13:7,6:268,202:0.0269:2,2:22.5:1:30.5:1:1:1.13689:60:26:0.0272:0:1.8 -5 62836848 . AT A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.11434;SOR=0;LSEQ=ACCTGAATGTGCTAAATATT;RSEQ=TTTTTTAAGTATGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:2,1:43,153:0.015:2,2:17.7:1:29:1:0.12882:7.02:60:6:0.0152:0.005:0.3 0/0:211:0:0,0:55,155:0:2,0:22.7:1:29.6:1:1:0:60:69:1:0:0.1 -5 62836972 . C CA 31 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.5453;SOR=1.84904;LSEQ=AGCTCCCCTATTCGTGATAG;RSEQ=AAAAAAAAAAGAAAGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:0,15:0.0952:1,0:24:1:31.5:1:1:0:60:4:0.1111:0:0 0/1:6:1:0,1:0,5:0.1667:0,0:33:0:31:0:1:0:60:2:0.2:0:0 -5 67151556 . A G 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.85377;LSEQ=TCTAAATTGTGTGTGGGTTG;RSEQ=GGAATGCCGCAAATAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:1,0:119,36:0.0064:2,0:32:0:33:0:1:0:60:2:0.0065:0:1 0/1:170:2:1,1:117,50:0.0118:2,2:18:1:28.5:1:0.51374:2.32685:60:4:0.0119:0:1 -5 67151564 . C T 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34158;SOR=0.28704;LSEQ=GTGTGTGGGTTGAGGAATGC;RSEQ=GCAAATAGAAAAGTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:1,2:127,49:0.0168:2,2:6:1:26.7:1:0.19579:5.12822:58:6:0.0172:0:2.3 0/0:206:1:0,1:136,69:0.0049:2,0:1:0:24:0:0.33981:0:60:2:0.0049:0:1 -5 67151565 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTGGGTTGAGGAATGCC;RSEQ=CAAATAGAAAAGTTTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:133,51:0:2,0:22.9:1:29.9:1:1:0:60:91:1:0:0.1 0/1:211:21:15,6:125,65:0.0995:2,2:29.7:1:30.1:1:0.80825:1.30:60:42:0.1005:0:1.1 -5 67151660 . G T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22059;SOR=4.5505;LSEQ=CAAATTTAGCCCGGCTGTGA;RSEQ=AACTTACAAAGGGAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:0,1:241,120:0.0028:2,0:1:0:24:0:0.33425:0:60:2:0.0028:0:1 0/1:401:5:2,3:247,149:0.0125:2,2:21.6:1:27:1:0.37181:2.48069:60:10:0.0127:0:1.2 -5 67151668 . A G 226 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCGGCTGTGAGAACTTAC;RSEQ=AAGGGAAGGTCAGAGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:233,126:0:2,0:23.7:1:29.9:1:1:0:60:70.8:1:0:0.1 0/1:424:192:117,75:150,81:0.4528:2,2:23:1:29.9:1:0.41904:1.1866:60:95:0.4545:0:1.1 -5 67151832 . C AA 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.68538;SOR=1.5123;LSEQ=TGAAACCCCTTTTTAAAATT;RSEQ=AAAAAAAAAAAAAAAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:2:0,2:58,161:0.009:2,0:18:1:20.5:1:1:0:55:4:0.0115:0:1 0/1:222:3:0,3:62,149:0.0135:2,0:28:1:24.3:1:0.55822:0:59:6:0.018:0:3 -5 67522722 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17995;LSEQ=GGGGACTTTCCGGGAACTTA;RSEQ=GTAGAATATATTGGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:228:99,129:118,138:0.4711:2,2:23.4:1:30.6:1:0.58334:1.11394:60:113:0.4728:0:1.1 0/1:667:92:43,49:284,290:0.1379:2,2:22.9:1:29.1:1:0.65432:1.11577:60:45:0.1378:0:1.2 -5 67522851 . A C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2362;LSEQ=CAACAAGGTCAGTATTGATA;RSEQ=GTGGTTGCTTAATGACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:121:35,86:46,109:0.4384:2,2:23.2:1:30.5:1:1:1.03683:60:120:0.4412:0:1.1 0/1:309:48:13,35:77,184:0.1553:2,2:25.2:1:30.3:1:0.86309:1.12626:60:96:0.1558:0:1.2 -5 67569342 . T C 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTAGAGGGCATCAGTTCCT;RSEQ=TGTTCTACCCTTATTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:19:6,13:75,277:0.0512:2,2:23.2:1:32.1:1:0.26864:1.70:60:38:0.0512:0:1.2 0/0:361:0:0,0:85,275:0:2,0:24.1:1:29.6:1:1:0:60:50.429:0.9972:0:0.2 -5 67569391 . A C 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00056;SOR=0.4179;LSEQ=TATTTGTCTCTTGTGCATTC;RSEQ=TTAAGTAAATTTCCTACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:63:4,59:7,80:0.42:2,2:23.4:1:32.5:1:0.76155:1.28848:60:126:0.4286:0:1.1 0/1:151:35:3,32:13,103:0.2318:2,2:23.3:1:32:1:1:1.34376:60:34:0.2329:0:1.1 -5 67569479 . A G 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.75462;SOR=1.37413;LSEQ=AGTACTGGGAAAAATGTCTC;RSEQ=GTCTATAATTTCTAACTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:1,12:1,13:0.4815:1,1:22.6:1:29.6:1:1:1.08:60:26:0.4815:0:1.3 1/0:16:9:2,7:1,6:0.5625:2,2:12:1:31.4:1:1:1.66:60:18:0.5625:0:1.4 -5 67569602 . A G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02506;SOR=0.2442;LSEQ=ATGGTTTTGCCAAAATTATC;RSEQ=ACATGCCAGGTAAGATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:14:12,2:16,0:0.4667:1,2:23.4:1:29.7:1:0.2092:0:60:28:0.4828:0:1 0/1:29:5:5,0:23,1:0.1724:1,0:31:1:28.4:1:1:0:60:10:0.1724:0:1 -5 67569739 . A T 48 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18941;SOR=0.21588;LSEQ=GAGAGCTGTGTTTTGCATAC;RSEQ=TGGTCTGTGGTCTGTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:4:1,3:222,140:0.0109:2,2:8.8:1:24.3:1:0.30376:4.73724:60:3:0.0083:0:1.3 0/0:421:1:0,1:258,162:0.0024:2,0:1:0:23:0:0.38717:0:60:2:0.0024:0:1 -5 67569746 . G A 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.00034;SOR=0.60171;LSEQ=GTGTTTTGCATACATGGTCT;RSEQ=TGGTCTGTTTTGTGTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:180:111,69:121,86:0.4627:2,2:27.3:1:29.3:1:0.53423:1.14:60:89:0.4611:0:1.1 0/1:466:159:97,62:181,124:0.3412:2,2:23.8:1:28.5:1:0.76509:1.07:60:52:0.3414:0:1.1 -5 67569909 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.49834;SOR=0;LSEQ=CTTTCTGTTTCAGGTAATGC;RSEQ=CACACACAAAATTGAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:20,111:0.015:2,2:28.5:1:32.5:1:0.29187:5.44:60:4:0.0152:0:1 0/0:127:0:0,0:16,111:0:2,0:21.2:1:30:1:1:0:60:254:1:0:0.1 -5 67569969 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19821;SOR=Inf;LSEQ=TTTAAAGGGAACTCAAATCA;RSEQ=GTACAGTTCTCCCTGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:0,38:0:1,0:26.2:1:31.1:1:1:0:60:76:1:0:0 0/1:31:2:0,2:0,29:0.0645:1,0:37:1:26.5:1:1:0:60:4:0.0667:0:1 -5 67575281 . C T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.5311;LSEQ=CCTACAAGAAGTACGGCTAA;RSEQ=GAATACTTTGTGTCTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:2,0:36,1:0.0513:1,0:9.5:1:32:0:1:0:60:4:0.0513:0:1.5 0/1:26:2:2,0:22,2:0.0769:2,0:33:1:30.5:1:1:0:60:4:0.0769:0:3 -5 67575323 . ATT A 140 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=0.09591;SOR=1.90697;LSEQ=TATCCTCATATTGCTTCCTT;RSEQ=TTTTTTTTTTTTTGTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:17:17,0:33,0:0.2297:1,1:20.8:1:30.6:1:1:0:60:34:0.2297:0.0946:0.9 0/1:66:24:23,1:24,1:0.3636:1,1:23.2:1:30.7:1:1:1.04259:59.6:48:0.3636:0.0909:1.1 -5 67575344 . A G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77564;SOR=0.91802;LSEQ=TTTTTTTTTTTTTTTGTCAC;RSEQ=TGTGAGTCAAATTGTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:39:37,2:71,5:0.3362:2,2:20.1:1:27.3:1:1:1.30:59.7:8.75:0.3608:0:1.3 0/1:104:33:30,3:65,5:0.3173:2,2:22.2:1:28.2:1:0.70883:1.29652:60:32:0.3368:0:1.3 -5 67575642 . A G 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17818;SOR=0.68581;LSEQ=ATATGTCTTGCATATATAGA;RSEQ=ATAGTGGTTAGAAAATAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:50:3,47:4,79:0.3759:1,2:21.5:1:31.9:1:1:1.26:60:100:0.3759:0:1.1 0/1:113:33:0,33:7,73:0.292:2,1:22.2:1:31.8:1:0.10408:0:60:66:0.2973:0:1 -5 67576345 . T A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2529;SOR=0;LSEQ=TTTCTCTTTTTTTTTTTTTT;RSEQ=AAACTTGTAGAAGTACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:2,1:194,69:0.0112:2,2:9.7:1:21:1:1:1.40386:60:2:0.0083:0:1.7 0/0:229:0:0,0:166,63:0:2,0:22.5:1:27.7:1:1:0:59.9:18.083:1:0:0.7 -5 67576346 . A T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66456;SOR=1.78245;LSEQ=TTCTCTTTTTTTTTTTTTTT;RSEQ=AACTTGTAGAAGTACAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:2:0,2:203,72:0.0072:2,0:1:1:25:1:0.07066:0:60:6:0.0055:0:1 0/1:235:3:2,1:166,66:0.0128:2,2:25.3:1:29:1:1:1.25633:60:6:0.0132:0:1.3 -5 67576682 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50668;SOR=0;LSEQ=CAGATGCTATCACACACATT;RSEQ=ACTTGAGTGTATATAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:109,79:0.0105:2,2:24.5:1:27.5:1:1:1.37735:60:4:0.0108:0:1 0/0:147:0:0,0:91,56:0:2,0:23.4:1:30.9:1:1:0:60:146:1:0:0.1 -5 67576688 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.19331;SOR=Inf;LSEQ=CTATCACACACATTCACTTG;RSEQ=GTGTATATAAATGAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:118,84:0:2,0:24.6:1:30:1:1:0:60:27.857:1:0:0.1 0/1:159:2:1,1:98,59:0.0126:2,2:19:1:29.5:1:1:1.65543:60:4:0.013:0:1 -5 67576819 . C T 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20194;SOR=0.23116;LSEQ=TCTCAACTGAATGGAATGAA;RSEQ=GACAGCCTGCACCAGGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:4:2,2:100,137:0.0166:2,2:14.5:1:28.5:1:1:1.37:60:8:0.0167:0:2.5 0/0:258:1:0,1:102,155:0.0039:2,0:10:0:30:0:1:0:60:2:0.004:0:2 -5 67576835 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22957;SOR=0;LSEQ=TGAACGACAGCCTGCACCAG;RSEQ=TAATGCTTTTTGAGCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:70,118:0.0105:2,2:8:1:31:0:1:1.68:60:4:0.0106:0:1 0/0:206:0:0,0:71,133:0:2,0:25.1:1:31.1:1:1:0:60:203:0.9951:0:0.2 -5 67584357 . A G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=GGGACGAGCCGAGCCGAGCC;RSEQ=AGCGGAGCTGGGCCACTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:7,1:0.2727:2,0:28.7:1:31.3:1:1:0:60:6:0.2727:0:1 0/0:6:0:0,0:6,0:0:0,0:18.3:1:31:1:1:0:60:12:1:0:0.2 -5 67584512 . AT A 169 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.19808;SOR=1.39291;LSEQ=GTGGAAGAACAGCTTTGGGG;RSEQ=TTTTTTTTTTTCATTGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:32:28,4:207,46:0.1096:2,2:24.3:1:31.4:1:0.62148:1.55:60:64:0.1123:0.024:0.1 0/1:362:53:43,10:231,70:0.1464:2,2:23.9:1:29.6:1:0.59392:1.30:59.7:52:0.1457:0.0359:0.3 -5 67584739 . G A 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00389;SOR=Inf;LSEQ=CTCCCCCTGTCCTCGAGGGG;RSEQ=ACAGTGGCTGGGAAAGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:0,104:0:1,0:25:1:31.9:1:1:0:60:208:1:0:0.3 0/1:89:7:0,7:0,82:0.0787:1,0:34.3:1:31.1:1:1:0:60:14:0.0795:0:1.9 -5 67584758 . A G 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37416;SOR=0.71316;LSEQ=GGACAGTGGCTGGGAAAGAT;RSEQ=GGGTTTAGGTTGGAATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:31:0,31:0,42:0.4189:1,1:23.8:1:31.1:1:1:0:60:30:0.411:0:1 0/1:59:20:0,20:0,39:0.339:1,1:23.5:1:29.8:1:1:0:60:19:0.3276:0:1.7 -5 67586680 . T A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2486;SOR=Inf;LSEQ=CAGGTAATACTGCAGTATTA;RSEQ=TGTAGAGAGTTAGTTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:64,188:0:2,0:24.2:1:30.2:1:1:0:60:125:1:0:0.1 0/1:257:3:2,1:82,172:0.0117:2,2:7.3:1:27:1:0.24976:4.17:60:6:0.0117:0:1 -5 67586727 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50689;SOR=0;LSEQ=TTTTTAATTTTTCGAAAGCT;RSEQ=CTGTAAAAGATCCTTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:9,101:0.0179:2,2:24.5:1:30:1:0.17133:10.70:60:4:0.0179:0:1 0/0:85:0:0,0:8,77:0:2,0:23.1:1:29.8:1:1:0:60:170:1:0:0 -5 67587984 . G T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.60746;LSEQ=AACTAATGCTATATATTTCA;RSEQ=TTACTCTAACTTTTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:81,5:0.0227:2,2:16:1:30.5:1:0.13245:14.8795:60:4:0.023:0:1 0/1:72:1:1,0:67,4:0.0139:2,0:5:0:30:0:1:0:60:2:0.0139:0:1 -5 67587994 . C T 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.074;SOR=0.60372;LSEQ=ATATATTTCAGTTACTCTAA;RSEQ=TTTTTATTTTTTTAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:55:50,5:47,6:0.5093:2,2:27.8:1:31.1:1:0.75886:1.27:60:54:0.5047:0:1.2 0/1:104:40:36,4:59,5:0.3846:2,2:20.1:1:30.6:1:0.73039:1.3076:60:80:0.3922:0:1.2 -5 67588000 . A G 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.04697;SOR=Inf;LSEQ=TTCAGTTACTCTAACTTTTT;RSEQ=TTTTTTTAAAGTAAAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:111,17:0:2,0:23.7:1:28.7:1:1:0:60:127:1:0:0.6 0/1:113:4:4,0:97,11:0.0354:2,0:27.3:1:33.5:1:1:0:60:8:0.036:0:2 -5 67588001 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.21549;SOR=Inf;LSEQ=TCAGTTACTCTAACTTTTTA;RSEQ=TTTTTTAAAGTAAAAGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:113,18:0:2,0:23.5:1:31:1:1:0:60:130:1:0:0.6 0/1:114:2:1,1:101,11:0.0175:2,2:20:1:29.5:1:0.20028:8.83537:60:4:0.0175:0:2 -5 67588025 . C T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=Inf;LSEQ=TTTAAAGTAAAAGTATTCAT;RSEQ=TAAAGAAATTTAGTTCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:161,36:0:2,0:23.8:1:31.6:1:1:0:60:196:1:0:0.4 0/1:197:2:1,1:155,40:0.0102:2,2:8:0:26.5:1:0.37377:3.83978:60:4:0.0104:0:1.5 -5 67588148 . G A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27822;SOR=1.3841;LSEQ=AACGGTATGAATAACAATAT;RSEQ=TCCTTACAAGATGCTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:23:10,13:186,248:0.0503:2,2:22:1:29.4:1:1:1.03:60:46:0.0511:0:1 0/1:512:35:15,20:206,270:0.0684:2,2:23.6:1:29.1:1:1:1.01725:60:70:0.0692:0:1.2 -5 67588162 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06404;SOR=Inf;LSEQ=CAATATGTCCTTACAAGATG;RSEQ=TGAATGGTACTGGGGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:170,255:0:2,0:24.1:1:31.9:1:1:0:60:52.125:1:0:0.2 0/1:479:5:2,3:200,274:0.0104:2,2:17.4:1:25:1:1:1.09471:60:4:0.0086:0:1 -5 67589038 . G A 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=9.22904;LSEQ=TTACACTAAGGTAAGCCAGG;RSEQ=AATATAGCTGAAATTAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:2:1,1:184,218:0.005:2,2:20.5:1:23:1:1:1.18:60:1:0.0025:0:1.5 0/1:432:19:8,11:180,230:0.044:2,2:19:1:28.7:1:1:1.07593:60:38:0.0444:0:1.1 -5 67589188 . C T 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CGAGATGGGAAATATGGCTT;RSEQ=TCTGACCCATTAACCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:773:0:0,0:422,350:0:2,0:25.8:1:31.5:1:1:0:60:84.778:1:0:0.1 0/1:824:25:14,11:417,382:0.0303:2,2:25.8:1:29.8:1:0.83951:1.17:60:50:0.0306:0:1.1 -5 67590558 . C A 89 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19685;SOR=3.3211;LSEQ=TAACCAAAATCCTCTAAAAC;RSEQ=ATTTAAAGATGATCTCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:2:2,0:47,171:0.0091:2,0:11.5:1:19.5:1:0.04882:0:60:1:0.0046:0:1.5 0/1:270:8:3,5:52,210:0.0296:2,2:18.4:1:29.8:1:0.20886:2.41:60:16:0.0299:0:1 -5 67590615 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4963;SOR=Inf;LSEQ=TCACGTGGACACAGGAAGGG;RSEQ=AATATCACTCTGGGGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:1,66:0:1,0:23.3:1:28.4:1:1:0:59.7:3.467:1:0:0.4 0/1:68:2:1,1:1,63:0.0294:1,2:27:0:31:1:0.06014:44.90:60:4:0.037:0:1.5 -5 67590797 . AAAAAT A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAGTATAATAAAAATAA;RSEQ=AAAATAAAATAAAATATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:3,0:18,7:0.1071:2,0:21:1:31.7:1:0.55128:0:49:6:0.1071:0:0 0/0:5:0:0,0:5,0:0:0,0:25.8:1:29.8:1:1:0:59:10:1:0:0.4 -5 67591525 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=ATTTATTTTTACTCATAATG;RSEQ=TGTGAAACAACTCTCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:21.8:1:33:1:1:0:60:10:1:0:0 0/1:7:2:1,1:0,5:0.2857:0,2:28.5:1:29.5:1:0.28571:0:60:4:0.2857:0:1 -5 67592281 . G A 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40901;SOR=2.44954;LSEQ=ATAGTTTTAGTCTTGAATAA;RSEQ=CTTACAGTACAATAATGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:0,2:0,47:0.0408:1,0:34.5:1:27.5:1:1:0:60:4:0.0435:0:1 0/1:42:4:0,4:2,36:0.0952:2,0:21.5:1:29.5:1:1:0:60:8:0.1:0:1 -5 67592293 . A C 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.45929;LSEQ=TTGAATAAGCTTACAGTACA;RSEQ=TAATGTAGAAGAGAAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:0,2:0,44:0.0435:1,0:21:1:24.5:1:1:0:60:1:0.0222:0:1 0/1:32:2:0,2:2,28:0.0625:2,0:25.5:1:33.5:1:1:0:60:4:0.0645:0:1.5 -5 67593016 . T C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64993;LSEQ=CAAAGTAACTGTATTACATG;RSEQ=ATTTTACTATTGTCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:11,0:6,0:0.6111:0,0:23.5:1:33.2:1:1:0:60:22:0.6471:0:1 1/0:4:2:2,0:2,0:0.5:0,0:16.5:1:31.5:1:1:0:60:4:0.5:0:1 -5 67593363 . T C 171 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=48.93617;LSEQ=CATTACCAACACACCTCCCT;RSEQ=GTGCAGCACAACGACTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:848:1:0,1:348,498:0.0012:2,0:27:0:27:0:1:0:60:2:0.0012:0:1 0/1:1006:55:25,30:382,568:0.0547:2,2:26.7:1:29.6:1:0.48093:1.24:60:110:0.0556:0:1.2 -5 67593523 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18086;SOR=Inf;LSEQ=AGTCTGATCTGTGAATTGAG;RSEQ=TGCAGAAACGAAGCCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:2,73:0:1,0:21.8:1:32:1:1:0:60:24:1:0:0.1 0/1:56:2:0,2:1,53:0.0357:1,0:40:1:28.5:1:1:0:60:4:0.0364:0:1.5 -5 68390203 . C G 107 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00098;SOR=0.03358;LSEQ=AAGGCAGCGACCGGCCGGGT;RSEQ=GCTCAGGATGCACTTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:6,5:2,1:0.7857:2,2:18.1:1:31.1:1:1:1.60839:60:22:0.7857:0:1.4 0/1:11:1:0,1:7,3:0.0909:2,0:49:0:29:0:0.36364:0:60:2:0.0909:0:1 -5 68390284 . C T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54505;SOR=1.61366;LSEQ=GGGTCGGCGCGCCCTCTCCC;RSEQ=CTGCCTGCCTCCCTGCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:6,6:4,4:0.6:2,2:18.2:1:30.5:1:1:1:60:24:0.6:0:1.3 1/0:31:22:12,10:4,5:0.7097:2,2:27.8:1:29:1:0.70425:1.48:60:21:0.7:0:1 -5 72671623 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.26758;SOR=0;LSEQ=AGCCTCCTGAGAGGCGAAAT;RSEQ=GGCCTCACATGAGTCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:1,2:165,29:0.0152:2,2:10.7:1:24.3:1:0.06509:11.1501:60:2:0.0103:0:1 0/0:142:0:0,0:111,31:0:2,0:22.7:1:30.9:1:1:0:60:46.333:1:0:0.1 -5 72671651 . G A 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=CATGAGTCTCTTCCATAGGG;RSEQ=CTCATTAAAGAGGGATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:216,78:0:2,0:23.7:1:31:1:1:0:60:48:1:0:0.1 0/1:253:11:7,4:166,76:0.0435:2,2:27.1:1:30:1:0.74605:1.24695:60:22:0.044:0:1.2 -5 72671738 . G T 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GATCTTCAGGTGATGTGTGC;RSEQ=CATTTTCTTCAGGGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:643:0:0,0:299,340:0:2,0:24.5:1:30.7:1:1:0:60:44.643:0.9952:0:0.1 0/1:621:75:36,39:260,283:0.1208:2,2:25.4:1:30:1:1:1.00:60:150:0.122:0:1.1 -5 72671819 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22681;SOR=Inf;LSEQ=GAGCAGCTTGCTTGCAATAA;RSEQ=AATAATAAAAACAACAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:45,170:0:2,0:21.3:1:31.8:1:1:0:60:70.667:1:0:0.1 0/1:196:2:1,1:47,147:0.0102:2,2:42.5:1:30:1:0.43077:3.11:60:4:0.0104:0:1 -5 72742882 . T C 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCGGCGGACGAGGAGAC;RSEQ=GAGGAGGCGGCGGCGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:33.3:1:29.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 72743299 . G GGC 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AAGGCGGCGGCGGCGGCGGC;RSEQ=CGCTGCGGCGGCGAAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:33:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 72743539 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49738;SOR=Inf;LSEQ=CCGCTTGAAGCGCTTCCTCC;RSEQ=GCGCAGGAAGCTGCCGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:54,15:0:2,0:23.8:1:29.3:1:1:0:60:68:1:0:0 0/1:75:2:1,1:53,20:0.0267:2,2:5:1:29:1:0.48432:2.61042:60:4:0.0267:0:1 -5 72743581 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50093;SOR=Inf;LSEQ=GAACATGTCGGCGGACTCCG;RSEQ=GTCCAGCGTCCAGTAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:71,34:0:2,0:25.6:1:30.6:1:1:0:60:34:1:0:0.1 0/1:123:2:1,1:82,39:0.0163:2,2:37:0:29.5:1:0.54645:2.08879:60:4:0.0168:0:1 -5 73011081 . T C 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03543;SOR=Inf;LSEQ=TGTCCAAGGTGGAGTCTGGC;RSEQ=CTGGTGCTGTTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:24.9:1:30.8:1:1:0:60:56:1:0:0.1 0/1:23:4:2,2:10,9:0.1739:2,2:37.5:1:30.5:1:1:1.10603:60:8:0.1739:0:1 -5 75111183 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGCTCTGTCTATATGAG;RSEQ=GGGAGGTGCATTCTAGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:8:1:29:1:1:0:60:6:0.3:0:1.3 0/0:2:0:0,0:2,0:0:0,0:28.5:1:32.5:1:1:0:60:4:1:0:0 -5 75111304 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49882;SOR=0;LSEQ=ATGGGATTAAGTATAGATTT;RSEQ=TTTGCTTAATTCTCCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:60,23:0.0235:2,2:26:1:31.5:1:0.48739:2.57497:60:4:0.0244:0:1.5 0/0:75:0:0,0:55,20:0:2,0:24:1:27.8:1:1:0:60:36.5:1:0:0.2 -5 75111343 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23262;SOR=Inf;LSEQ=TAGCCTTTTACAGTTAGCAG;RSEQ=TTGTCAGTACATGCTGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:80,59:0:2,0:25.5:1:31.8:1:1:0:60:33.75:1:0:0.3 0/1:130:2:2,0:86,42:0.0154:2,0:21:1:27.5:1:1:0:60:4:0.0156:0:1.5 -5 75111365 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23917;SOR=0;LSEQ=TGTCAGTACATGCTGCTATG;RSEQ=TGTATTAGCTGTGCAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:86,80:0.0119:2,2:45:1:30.5:1:1:1.07451:60:4:0.0123:0:1 0/0:175:0:0,0:105,70:0:2,0:23.1:1:29:1:1:0:60:174:1:0:0.3 -5 75111374 . C T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37204;SOR=3.90024;LSEQ=ATGCTGCTATGATGTATTAG;RSEQ=TGTGCAGGGGAGAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:0,1:94,86:0.0055:2,0:1:0:28:0:0.48066:0:60:2:0.0057:0:1 0/1:188:4:1,3:108,76:0.0213:2,2:11.8:1:28:1:0.31119:4.23165:60:8:0.0217:0:1.5 -5 75111376 . G T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36155;SOR=0.3153;LSEQ=GCTGCTATGATGTATTAGCT;RSEQ=TGCAGGGGAGAAAAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:1,2:94,88:0.0161:2,2:12.7:1:28:1:0.61294:2.12789:60:6:0.0166:0:2 0/0:195:1:0,1:113,81:0.0051:2,0:1:0:25:0:0.42051:0:60:2:0.0052:0:1 -5 75111378 . GCAGGGG CAGGGGA 23 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24049;SOR=0;LSEQ=TGCTATGATGTATTAGCTGT;RSEQ=AGAAAAAAATTATACTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:99,91:0.0104:2,2:19.5:1:23.8:1:1:1.08742:60:4:0.0107:0.0052:4 0/0:199:0:0,0:115,83:0:2,0:23:1:31.5:1:1:0:60:65:0.9949:0:0.4 -5 75111397 . T C 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15415;SOR=1.42879;LSEQ=TGCAGGGGAGAAAAAAATTA;RSEQ=ACTTTTGTGTTCCCTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:38:19,19:78,83:0.19:2,2:22.8:1:32.2:1:1:1.06:60:76:0.1939:0:1.2 0/1:211:53:29,24:86,72:0.2512:2,2:25.6:1:30.7:1:1:1.01:60:25.5:0.2452:0:1.3 -5 75111451 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52031;SOR=Inf;LSEQ=CCACACAATTATAGAAGATT;RSEQ=TTGTTCATCTCCAAGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:44,75:0:2,0:22.2:1:31.9:1:1:0:60:58.5:1:0:0.3 0/1:182:2:1,1:73,106:0.011:2,2:21.5:1:31:0:1:1.45:60:4:0.0112:0:2 -5 75926812 . G A 69 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAACATAATTTGATGACAAC;RSEQ=AATTGTAATTTAATATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:24.6:1:29.8:1:1:0:60:10:0.7143:0:1.2 1/1:1:1:1,0:0,0:1:0,0:39:0:32:0:1:0:60:2:1:0:1 -5 75926863 . G A 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.89743;LSEQ=GTACGTGTAAGAAAAAAAGA;RSEQ=AAAGCATCCGTGTCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:12:1:31.3:1:1:0:60:8:0.3333:0:2.3 1/0:2:1:1,0:1,0:0.5:0,0:24:0:32:0:1:0:60:2:0.5:0:2 -5 75926873 . G A 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.89743;LSEQ=GAAAAAAAGAGAAAGCATCC;RSEQ=TGTCTCCCTTCTCTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:22:1:31:1:1:0:60:8:0.3333:0:2.3 1/0:2:1:1,0:1,0:0.5:0,0:34:0:31:0:1:0:60:2:0.5:0:2 -5 75927027 . G A 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCTTACCTGGAATTAA;RSEQ=GTGGGAAATAATTCACTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:64:62,2:0,0:1:0,1:24.2:1:30.5:1:1:0:60:31:1:0:1.6 1/1:49:49:48,1:0,0:1:0,1:21.1:1:29.7:1:1:0:60:23.5:1:0:1.3 -5 75927069 . A G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00131;SOR=0.43999;LSEQ=TAACTTTCCTTAGGCAACCA;RSEQ=GAGTTTAATGTGTTTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:145:79:69,10:56,10:0.5448:2,2:27.7:1:32.5:1:0.80963:1.23:60:158:0.5486:0:1.4 0/1:122:42:32,10:70,10:0.3443:2,2:23.2:1:31.2:1:0.12693:2.17246:60:84:0.35:0:1.3 -5 75927086 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2367;SOR=Inf;LSEQ=CCAAGAGTTTAATGTGTTTT;RSEQ=TTAATGAGGAGGGGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:155,45:0:2,0:23.7:1:32.3:1:1:0:60:400:1:0:0.6 0/1:190:2:1,1:143,45:0.0105:2,2:6:0:31:1:0.42657:3.15401:60:4:0.0106:0:1 -5 75927188 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.40962;LSEQ=CCGTTGCACATATCCACCAG;RSEQ=TCTGCCTTTCTAGAACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:174:81,93:147,160:0.3602:2,2:24.7:1:30:1:0.84931:1.05478:60:348:0.3633:0:1.8 1/0:540:311:138,173:110,119:0.5759:2,2:25.1:1:29.5:1:0.43192:1.15849:60:102.667:0.5768:0:1.7 -5 75927222 . T G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=2.57334;LSEQ=AACACTTGTTTAGGTTGTTT;RSEQ=TGACAATCTTGCTAAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:125:44,81:87,153:0.3425:2,2:23.8:1:31.6:1:0.90858:1.04667:60:61.5:0.3465:0:2.3 1/0:356:204:79,125:60,91:0.573:2,2:24.7:1:30.9:1:0.91248:1.04317:60:101:0.5771:0:2.2 -5 75927274 . T C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.06694;LSEQ=CAAGAGAATACCAGGATTTC;RSEQ=GTAACTTAAAAAGGATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:61:6,55:15,91:0.3631:2,2:21.7:1:30.8:1:0.4764:1.50743:60:122:0.3653:0:2.1 1/0:124:79:16,63:7,38:0.6371:2,2:23.2:1:29.5:1:0.63358:1.38:60:78:0.6341:0:2.1 -5 75927295 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17765;SOR=Inf;LSEQ=GTAACTTAAAAAGGATTTTG;RSEQ=TTATCCTAAAGTAAACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:8,97:0:2,0:23.4:1:32.6:1:1:0:60:104:1:0:0.6 0/1:77:2:1,1:13,62:0.026:2,2:21.5:1:31:0:0.33254:4.63:60:4:0.0267:0:2.5 -5 75927595 . C G 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATGTTTGATACTAATG;RSEQ=ATTCCTAAAACGTTGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:15.3:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 77168090 . G A 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=2.02904;LSEQ=GGCTCTCCCCACACTTAGCT;RSEQ=TGTTCTCCACAGAGCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:65:31,34:139,158:0.1786:2,2:27.8:1:29.4:1:1:1.04:60:130:0.1826:0:1.5 0/1:382:117:59,58:129,135:0.3063:2,2:26.3:1:28.8:1:0.82449:1.06:60:116:0.3069:0:1.5 -5 77168145 . G A 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02014;SOR=1.71778;LSEQ=ACCCTATGTGAGCCTAGGAC;RSEQ=ATAGTAAACTTTTTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:36:9,27:59,133:0.1572:2,2:20.8:1:29.7:1:0.55626:1.32921:60:35:0.1549:0:1.9 0/1:280:68:25,43:78,134:0.2429:2,2:25:1:29.3:1:1:1.00119:60:136:0.2455:0:1.8 -5 77168161 . TA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19705;SOR=0;LSEQ=GGACGATAGTAAACTTTTTT;RSEQ=AAAAAAATTATTTTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:31,104:0.0146:2,2:46:1:31.5:1:0.41391:3.32:60:4:0.0147:0:0 0/0:171:0:0,0:57,114:0:2,0:26:1:28.4:1:1:0:60:27.5:1:0:0.5 -5 77168181 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18307;SOR=0;LSEQ=TAAAAAAAATTATTTTCAGA;RSEQ=AGTTCTTTCCTCAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:13,73:0.0227:2,2:33:1:32.5:1:0.29441:5.45:60:4:0.0233:0:2 0/0:117:0:0,0:31,86:0:2,0:23.4:1:29.4:1:1:0:60:22.4:1:0:0.4 -5 77570405 . G C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51301;SOR=Inf;LSEQ=ATAAAACTACACCAGGTACA;RSEQ=CATAGTCAAACTGCTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:0:2,0:27.4:1:32.1:1:1:0:60:46:1:0:0.1 0/1:35:2:1,1:17,16:0.0571:2,2:30:0:30:1:1:1.06069:60:4:0.0571:0:1.5 -5 78516069 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACTTCACCTCCCAGGTT;RSEQ=AAATGATTCTCCTGCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 78517050 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTGAGAACCAGGAAGAT;RSEQ=CACCTACTCTAAAAATTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:5,15:0.0909:2,2:40:1:28.5:1:0.48052:2.83:60:4:0.0909:0:1 0/0:10:0:0,0:3,7:0:2,0:25.1:1:29.9:1:1:0:60:9:1:0:0.1 -5 78517143 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATAGGTGAATTTTGAAGCCT;RSEQ=CGTGAATATATCCATATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:28.5:1:30:0:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:0,2:0:0,0:23:1:28.5:1:1:0:60:4:1:0:0 -5 79172055 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.10747;SOR=Inf;LSEQ=TGGTCACTCCTCACTCTGTG;RSEQ=CCCCAAAGCCTGCTGTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:158,109:0:2,0:24.7:1:31.2:1:1:0:60:88:1:0:0.1 0/1:243:3:1,2:146,94:0.0123:2,2:19.7:1:28.3:1:0.56386:3.09167:60:6:0.0124:0:1.3 -5 79172136 . A G 221 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCTCAACTGGACTATAAA;RSEQ=TTCTCCAGGGTAGAGATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:143,186:0:2,0:25.5:1:30.3:1:1:0:60:53.833:1:0:0.2 0/1:294:140:62,78:69,85:0.4762:2,2:24.6:1:31:1:1:1.02119:60:69:0.4726:0:1.1 -5 79172158 . C T 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCCAGGGTAGAGATTGTG;RSEQ=CTGATTCATGTAGCTTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:25:11,14:88,134:0.1012:2,2:25.6:1:29.6:1:0.67307:1.20:60:50:0.1029:0:1.2 0/0:216:0:0,0:87,129:0:2,0:26.4:1:30.7:1:1:0:60:53:1:0:0.5 -5 79172193 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18232;SOR=Inf;LSEQ=TTAGCAGAGAGGCTGGCCTG;RSEQ=AGCCTCTGTGCAGGAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:40,115:0:2,0:22.1:1:31.9:1:1:0:60:76.5:1:0:0.1 0/1:116:2:1,1:32,82:0.0172:2,2:22:1:27.5:1:0.48981:2.54:60:4:0.0175:0:2 -5 79172312 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAGAAGCTTTGCTTCTAAT;RSEQ=TCACTTGGACAATACTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:0,19:0.0952:1,0:18.5:1:30.5:1:1:0:60:4:0.0952:0:1 0/0:9:0:0,0:0,9:0:0,0:28.1:1:30:1:1:0:60:18:1:0:0 -5 84761041 . G A 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03906;SOR=Inf;LSEQ=TAAAAAGAAGAGGTGGAACC;RSEQ=TCCCAAAATGTCCCTTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:26,14:0:2,0:23.4:1:30.7:1:1:0:60:80:1:0:0.1 0/1:57:7:4,3:32,18:0.1228:2,2:20.6:1:29:1:0.70056:1.32641:60:14:0.125:0:1 -5 84761079 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51194;SOR=Inf;LSEQ=CTCAGAAGAAAGATGGGGTA;RSEQ=CTCAAAAGAAGGCAAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:25,23:0:2,0:24.6:1:32.3:1:1:0:60:96:1:0:0.1 0/1:69:2:1,1:34,33:0.029:2,2:22.5:1:28:1:1:1.02986:60:4:0.029:0:1 -5 86564230 . C T 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.53423;LSEQ=CTGGTGGCCCCTGGGGCTCC;RSEQ=GGGCGGGCAGGGTAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:122,23:0.0136:2,2:17.5:1:32:1:0.30081:5.21402:60:4:0.0141:0:1 0/0:137:1:1,0:98,37:0.0073:2,0:36:0:32:0:1:0:60:2:0.0075:0:1 -5 86564237 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.20933;SOR=Inf;LSEQ=CCCCTGGGGCTCCCGGGCGG;RSEQ=CAGGGTAGGGCAGAGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:146,36:0:2,0:23.3:1:30.9:1:1:0:60:35.4:1:0:0.2 0/1:154:2:1,1:108,44:0.013:2,2:28.5:1:28:1:0.50038:2.43834:60:4:0.0133:0:1 -5 86564245 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24172;SOR=Inf;LSEQ=GCTCCCGGGCGGGCAGGGTA;RSEQ=GGCAGAGTAGAGCGGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:155,43:0:2,0:24.4:1:31.5:1:1:0:60:32:1:0:0.2 0/1:192:2:1,1:130,60:0.0104:2,2:20:1:28:1:0.53561:2.15713:60:4:0.0106:0:1 -5 86564995 . T A 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26399;SOR=0.84013;LSEQ=CAGGCATACTACCTGGCGTC;RSEQ=TCCTACATTTATTGCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:139:91,48:128,92:0.3872:2,2:23.1:1:30.5:1:0.18346:1.36:60:278:0.3938:0:1.1 0/1:424:147:90,57:179,98:0.3467:2,2:23.9:1:29.8:1:0.52545:1.1564:60:72.5:0.3452:0:1.1 -5 86565170 . G A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.00037;SOR=Inf;LSEQ=TAGTGTATATTAACTTGTGT;RSEQ=TGTTACTTGATAAAGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:90,264:0:2,0:23.5:1:31.7:1:1:0:60:87.5:1:0:0.1 0/1:423:13:5,8:99,310:0.0307:2,2:18.7:1:28.9:1:0.32273:1.95:60:26:0.0309:0:1.2 -5 86626521 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13116;SOR=0;LSEQ=TTAAACTGAGAGCAAGAAGG;RSEQ=TGAAGGGACAAAGGTGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:0.3077:0,0:15:1:30.3:1:1:0:60:8:0.3077:0:1 0/0:8:0:0,0:8,0:0:0,0:21.9:1:32.4:1:1:0:60:16:1:0:0 -5 86628504 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50219;SOR=Inf;LSEQ=TTCAAAACTTTATTTTTTCA;RSEQ=TACAATAATGGTTTTAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:26,102:0:2,0:25.1:1:31.8:1:1:0:60:63:1:0:0.1 0/1:153:2:1,1:33,116:0.0131:2,2:13:0:31.5:1:0.40079:3.48:60:4:0.0131:0:1.5 -5 86628891 . G A 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.04824;LSEQ=ACTGCTTATATTTAAAATAT;RSEQ=ATTTTCATAAAAACAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:6,1:4,1:0.5833:2,2:27.9:1:28.7:1:1:1.45:60:14:0.5833:0:1 1/0:4:3:3,0:1,0:0.75:0,0:40:1:28.3:1:1:0:60:6:0.75:0:1 -5 86629039 . TA T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.18304;SOR=0;LSEQ=TACCTCTTTTGACTTTAAGA;RSEQ=AAAAGACTATCTTTTTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:140,23:0.0121:2,2:15:1:26:1:0.27051:5.98006:60:4:0.0122:0.0061:0.5 0/0:220:0:0,0:185,34:0:2,0:23.3:1:28.2:1:1:0:60:108.5:0.9954:0:0.2 -5 86629061 . CT C 167 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.11216;SOR=0.66818;LSEQ=AAAAGACTATCTTTTTAAAT;RSEQ=TTTTTTTTTTATGGTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:40:27,13:179,77:0.1347:2,2:25.3:1:31.4:1:0.85352:1.11885:60:80:0.1351:0.0236:0.2 0/1:393:37:25,12:231,122:0.0941:2,2:24.4:1:30.2:1:0.8574:1.10:60:74:0.0946:0.0229:0.1 -5 86633730 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25112;SOR=Inf;LSEQ=TCCTATTTTGTGGTATATGA;RSEQ=TATTCTAATCTCTGTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:118,13:0:2,0:23.4:1:32.5:1:1:0:60:262:1:0:0.1 0/1:151:3:1,2:138,10:0.0199:2,2:16:1:26.3:1:0.0167:25.99829:60:6:0.0203:0:1 -5 86633973 . G A 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66307;SOR=1.11513;LSEQ=TATAAATTTGGATCTTGTCC;RSEQ=TAATCAGAGAAAGTAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:82:4,78:3,70:0.529:1,1:22.3:1:30.5:1:1:1.20:60:26.333:0.5197:0:1.1 1/0:187:104:6,98:5,78:0.5561:2,2:21.3:1:30.3:1:1:1.04678:60:208:0.5561:0:1 -5 86637050 . AT A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.23165;SOR=0;LSEQ=TACGATTTTCATGAATTTTA;RSEQ=AAAAATTGATTAATAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:132,66:0.01:2,2:37:1:29.5:1:1:1.99258:60:4:0.0102:0:0 0/0:215:0:0,0:151,64:0:2,0:25.1:1:29:1:1:0:60:214:1:0:0.1 -5 86637164 . G GA 181 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.67948;SOR=1.09309;LSEQ=TTTGTGTTAATTATTAAAAT;RSEQ=AAAAAAAAAATCTATATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:64:25,39:43,85:0.3153:2,2:29.5:1:29.7:1:0.52254:1.27:60:31:0.3116:0:0.1 0/1:221:74:24,50:48,91:0.3348:2,2:25.6:1:29.3:1:0.87919:1.0984:59.8:36:0.3364:0.0136:0.3 -5 86644898 . T TA 59 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.12273;SOR=Inf;LSEQ=AAATTTGAAAGAAATTATCT;RSEQ=AAAAAAAAAACAAGTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:38,0:0:1,0:19:1:31:1:1:0:60:76:0.9744:0:0.3 0/1:47:4:4,0:43,0:0.0851:1,0:12:1:29.7:1:1:0:60:8:0.0851:0.0426:0.3 -5 86648120 . T TAC 32 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAGATAACATACTTGAAGA;RSEQ=ACACACACACACACATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:0:32.3:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 86648931 . GT G 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.25305;SOR=Inf;LSEQ=ATATTTTTAAAGATTTTGCA;RSEQ=TTTATGAGACAGATTAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:167,64:0:2,0:25.8:1:29.4:1:1:0:60:76:1:0:0 0/1:270:3:2,1:195,71:0.0111:2,2:24.7:1:29.3:1:1:1.37151:60:6:0.0113:0:0 -5 86649101 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.10498;SOR=0;LSEQ=TTAGCATTTTATTTTAAAAT;RSEQ=CATTTTGGTGGTATGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:2,1:44,146:0.0155:2,2:12:1:28.3:1:0.14185:6.55:60:6:0.0156:0:1 0/0:215:0:0,0:54,161:0:2,0:23:1:31.3:1:1:0:60:70.667:1:0:0.1 -5 86649123 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49988;SOR=Inf;LSEQ=ATTTTGGTGGTATGTTTTTG;RSEQ=ACACATTTGTACAATTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:12,99:0:2,0:23.6:1:31.9:1:1:0:60:222:1:0:0.1 0/1:127:2:0,2:10,113:0.0157:2,0:38.5:1:27.5:1:1:0:60:4:0.0161:0:1 -5 86658548 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49892;SOR=0;LSEQ=CGTTGTAAATATGGAGCTCC;RSEQ=AACTTATTGTGATATATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:38,144:0.0108:2,2:19:1:31.5:1:0.3799:3.75:60:4:0.011:0:1.5 0/0:176:0:0,0:38,138:0:2,0:22:1:30.3:1:1:0:60:43:1:0:0.1 -5 86658723 . CT C 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTTTCTTTCTTTCTTT;RSEQ=TTTTTTTTTTTGAGGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:1,8:0.1818:2,0:49:1:32:1:1:0:60:4:0.1818:0:0 0/0:2:0:0,0:0,2:0:0,0:17.5:1:31.5:1:1:0:60:4:1:0:0 -5 86659147 . A AT 139 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.24331;SOR=0.66581;LSEQ=TGTTTGGCTAAGAGAAAACA;RSEQ=TTTTTTTTTTTAAACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:22:18,4:200,46:0.0818:2,2:24.7:1:31.2:1:1:1.03:60:44:0.0833:0.0037:0.1 0/1:286:16:14,2:208,61:0.0559:2,2:28.8:1:30:1:0.53625:2.05:60:15:0.0534:0.0105:0.2 -5 86659159 . A T 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0129;SOR=0;LSEQ=AGAAAACAATTTTTTTTTTT;RSEQ=AACAGGCAAAGGAAAACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:6:5,1:248,80:0.018:2,2:23.2:1:26.2:1:1:1.61:60:5:0.0155:0:2 0/0:353:0:0,0:259,94:0:2,0:24.4:1:28.2:1:1:0:60:69.6:1:0:0.2 -5 86665476 . CT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.4958;SOR=0;LSEQ=TCTAAAATATATATAGCTGA;RSEQ=TTTTTTTAGTAATGATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:17,1:0.1:1,0:33:1:33.5:1:1:0:60:4:0.1:0:0.5 0/0:15:0:0,0:15,0:0:1,0:19.8:1:31.9:1:1:0:60:30:1:0:0 -5 86665775 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.221;SOR=0;LSEQ=TGTTAGCCCATGTTTTCTTA;RSEQ=TAACTGGAATAGAAAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:35,164:0.01:2,2:9.5:1:29:1:0.32687:4.63:60:4:0.01:0:1 0/0:226:0:0,0:51,173:0:2,0:25:1:29.7:1:1:0:60:111:0.9955:0:0 -5 86667856 . G GA 204 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.35113;SOR=1.27048;LSEQ=AGGAAAAAATTGTTGAATTT;RSEQ=AAAAAAAAAACCTAACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:151:98:89,9:19,2:0.649:2,2:28.3:1:30.4:1:1:1.04:60:196:0.6533:0:0.3 1/0:191:134:114,20:22,2:0.7016:2,2:28.7:1:29:1:0.53209:1.92319:60:21.333:0.7191:0:0.3 -5 86667872 . C T 50 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07398;SOR=Inf;LSEQ=ATTTGAAAAAAAAAACCTAA;RSEQ=TGATGATTTGGAAGCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:203,58:0:2,0:21.9:1:30.7:1:1:0:60:15.313:1:0:0.2 0/1:348:5:2,3:253,89:0.0144:2,2:11.2:1:21.6:1:0.11856:4.24239:60:1.5:0.0092:0:1.8 -5 86670546 . G GT 100 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.46504;SOR=1.49135;LSEQ=GGTTTTAGGTCTAGCACACT;RSEQ=TTTTTTTTTTTAAAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:8:7,1:97,5:0.0714:1,2:18.5:1:29.7:1:0.37132:2.73406:58.1:7:0.0642:0.0357:0.4 0/1:97:10:10,0:83,3:0.1031:1,0:29.3:1:30.2:1:1:0:60:20:0.1042:0.0103:0.5 -5 86670582 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24861;SOR=Inf;LSEQ=CAGAAATAGGGGGTTTATTT;RSEQ=ATACTAGAACTAAAGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:169,60:0:2,0:22.3:1:30.9:1:1:0:59.9:21.9:1:0:0.1 0/1:237:3:2,1:163,70:0.0127:2,2:20.7:1:22.7:1:1:1.1635:60:2:0.0088:0:1 -5 86670643 . C G 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTGTTAATTCTTTTTCT;RSEQ=CTTGCTCCTTTAGTGATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:0:0,0:268,235:0:2,0:25.7:1:31.1:1:1:0:60:54.889:1:0:0.1 0/1:652:28:15,13:333,289:0.0429:2,2:27.1:1:31.5:1:1:1.00:60:56:0.0433:0:1.1 -5 86672192 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49975;SOR=Inf;LSEQ=CTCTTTTTAAACAATAATTG;RSEQ=TTGTTTTTCTTCCCAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:130,36:0:2,0:23.9:1:32.1:1:1:0:60:54.333:1:0:0.1 0/1:183:2:1,1:137,44:0.0109:2,2:31.5:1:29.5:1:0.43235:3.08982:60:4:0.0112:0:1 -5 86675708 . T A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10966;SOR=Inf;LSEQ=TTGACAAGAAATTGTGTATC;RSEQ=ATGTCTTCAGAAATTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:31,140:0:2,0:21.5:1:28.7:1:1:0:60:84.5:1:0:0 0/1:158:3:2,1:29,126:0.019:2,2:6:1:29.7:1:0.09853:8.52:60:6:0.0196:0:1 -5 86676220 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23458;SOR=Inf;LSEQ=ACTTTTTTGGGTAAAAGGCC;RSEQ=GTTTTATTGAACTGTGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:104,3:0:1,0:25.5:1:30.5:1:1:0:60:214:1:0:0 0/1:101:2:2,0:94,5:0.0198:2,0:17.5:1:28:1:1:0:60:4:0.0198:0:1 -5 86679466 . T C 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05073;SOR=Inf;LSEQ=TTCTGTTTATATATATTGTT;RSEQ=TAATGTAACACATTATATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:79,9:0:2,0:21.5:1:30.7:1:1:0:59.7:87:1:0:1.1 0/1:81:4:4,0:69,8:0.0494:2,0:10.3:1:31.3:1:1:0:60:8:0.05:0:3.3 -5 86679617 . T A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09211;SOR=0;LSEQ=GGTAATCAGCTTTTGATACA;RSEQ=TTTGAAATTCAAAATATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:104,188:0.0102:2,2:8:1:21.3:1:0.29389:3.60:60:2:0.0069:0:3.3 0/0:357:0:0,0:142,214:0:2,0:25.3:1:29.4:1:1:0:60:177:0.9972:0:0.1 -5 86681045 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24641;SOR=Inf;LSEQ=CAGTAAAGAAATATTAAAGT;RSEQ=CTAAATTTATAATGGTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:144,31:0:2,0:24.5:1:31.8:1:1:0:60:57.333:1:0:0.1 0/1:173:2:1,1:142,29:0.0116:2,2:31:1:28.5:1:0.31758:4.83125:60:4:0.0116:0:1 -5 86682545 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=ATTTGGTGCAATAGTAATTG;RSEQ=AGTTTTTGCTGTTAACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:131,6:0:1,0:23.5:1:32.3:1:1:0:60:136:1:0:0.1 0/1:140:2:2,0:127,11:0.0143:2,0:35.5:1:31:0:1:0:60:4:0.0146:0:1 -5 86682803 . A G 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21965;SOR=Inf;LSEQ=ATTTAAGCAGCAATCTTTAG;RSEQ=AAGATTTTCTATCCAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:4,102:0:1,0:25.7:1:30.3:1:1:0:60:105:1:0:0.1 0/1:94:2:1,1:7,85:0.0213:2,2:13:0:29:1:0.16381:11.43:60:4:0.0217:0:1.5 -5 86685123 . GG AA 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50612;SOR=Inf;LSEQ=ATGCCATTGCATTTCAGCCT;RSEQ=GCAACAAGAGCGAAACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:82,8:0:2,0:26.9:1:31.7:1:1:0:59.8:29:1:0:0.1 0/1:117:2:1,1:109,6:0.0171:2,2:8.5:1:27.8:1:0.11656:16.8953:60:4:0.0171:0.0085:0.5 -5 86685148 . C CA 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.58256;SOR=0.38421;LSEQ=ACAAGAGCGAAACTCTGTCT;RSEQ=AAAAAAAACAAAAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:150,44:0.0102:2,2:15.5:1:28:1:0.40738:3.38215:60:4:0.0105:0:0 0/0:254:1:1,0:197,56:0.0039:2,0:18:0:31:0:1:0:42:2:0.004:0:0 -5 86685157 . CA C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.98101;LSEQ=AAACTCTGTCTCAAAAAAAA;RSEQ=AAAAAAAAGAAGATTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:6:5,1:211,69:0.021:2,2:16.2:1:32.4:1:1:1.63:60:12:0.0211:0.0105:0 0/1:340:7:4,3:236,96:0.0206:2,2:27.4:1:31.7:1:0.42095:1.83998:60:14:0.0208:0.0029:0.3 -5 86686570 . G A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12224;SOR=Inf;LSEQ=CAGGTTCCCATCCTGAAATT;RSEQ=CTGACCGAGCTTTCATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:205,66:0:2,0:23.5:1:32.2:1:1:0:60:134.5:1:0:0.1 0/1:269:3:2,1:190,76:0.0112:2,2:24.3:1:29.3:1:1:1.24896:60:6:0.0112:0:1 -5 86686797 . A G 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24612;SOR=Inf;LSEQ=CTCTTGCCAAAAAATAGCAC;RSEQ=CTTTTCCACATTCCAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:2,89:0:1,0:23.3:1:29.7:1:1:0:60:29.333:1:0:0.1 0/1:94:3:0,3:4,87:0.0319:1,0:16.3:1:34:0:1:0:60:6:0.0319:0:1.3 -5 87428845 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49853;SOR=0;LSEQ=CAACAGTAACCGAATTGTAG;RSEQ=ACCTCAGCATTTACTAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:111,51:0.0122:2,2:17.5:1:29.5:1:0.53494:2.16517:60:4:0.0123:0:1 0/0:160:0:0,0:107,52:0:2,0:21.7:1:31.6:1:1:0:60:158:0.9937:0:0.2 -5 87428853 . C T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68343;SOR=1.53023;LSEQ=ACCGAATTGTAGCACCTCAG;RSEQ=ATTTACTAGATGTTACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:122,70:0.0103:2,2:27.5:1:28:1:1:1.73753:60:4:0.0104:0:1 0/1:191:3:0,3:125,63:0.0157:2,0:1:0:23:1:0.04003:0:60:6:0.0158:0:1 -5 87428855 . TTTACTAGATG T 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CGAATTGTAGCACCTCAGCA;RSEQ=TTACTAGATGTTACTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:130,76:0:2,0:23.8:1:29.8:1:1:0:60:50.5:1:0:0.1 0/1:204:14:9,5:120,70:0.0686:2,2:23:1:29.7:1:1:1.05:59.6:28:0.07:0.0098:0.1 -5 87428894 . CTGT C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.09637;SOR=2.12766;LSEQ=TGTTACTGCTGCTGTTGCTG;RSEQ=TGTTGTTGTTGTTGCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:8:5,3:157,154:0.0251:2,2:22.9:1:31.4:1:0.72335:1.63:60:16:0.0256:0:0.1 0/1:308:16:9,7:145,146:0.0519:2,2:28.6:1:31.9:1:0.79832:1.29:60:32:0.0523:0:0.1 -5 87428897 . T C 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TACTGCTGCTGTTGCTGCTG;RSEQ=TGTTGTTGTTGTTGCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:152,157:0:2,0:28.3:1:29.9:1:1:0:60:153.5:1:0:0.1 0/1:312:28:14,14:132,136:0.0897:2,2:25.8:1:31.9:1:1:1.03:60:56:0.0959:0:1.9 -5 87428912 . C T 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGTTGTTGTTGTTGTTG;RSEQ=TTAAATTGAAGTATAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:138,170:0:2,0:26.9:1:32:1:1:0:60:76:1:0:0.1 0/1:304:23:10,13:125,156:0.0757:2,2:24.6:1:30.3:1:1:1.04154:60:46:0.0757:0:2.1 -5 87428969 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51095;SOR=0;LSEQ=GGGTTAGAGACACCAGCCTC;RSEQ=CAGGCAGTTGAAAATTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:24,103:0.0155:2,2:6:1:28.5:1:0.35126:4.23:60:4:0.0156:0:1.5 0/0:93:0:0,0:17,76:0:2,0:20.9:1:31.1:1:1:0:60:92:1:0:0.2 -5 87429684 . AG GA 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GAAAGAAAGAAAGAAAGAAA;RSEQ=AAAGAAAAAGAAAGAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:5.5:1:28:1:1:0:60:4:0.6667:0:1 -5 87898719 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49648;SOR=Inf;LSEQ=GCTTCATTGTTACAGGCCTC;RSEQ=TAGTGAGGCACGATTCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:19,13:0:2,0:22.9:1:30.3:1:1:0:60:64:1:0:0.1 0/1:38:2:1,1:22,14:0.0526:2,2:18:1:28.5:1:1:1.55221:60:4:0.0556:0:1 -5 87898886 . A T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62366;SOR=2.93572;LSEQ=CACCCACCTGTGTGCTATCC;RSEQ=TGCCAAACGTGTAACAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:0,1:158,92:0.004:2,0:1:0:28:0:0.37052:0:60:2:0.004:0:1 0/1:258:3:1,2:153,102:0.0116:2,2:27:1:29.3:1:0.56691:2.98711:60:6:0.0118:0:1 -5 87898888 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24869;SOR=Inf;LSEQ=CCCACCTGTGTGCTATCCAT;RSEQ=CCAAACGTGTAACAATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:160,97:0:2,0:26:1:32.1:1:1:0:59.7:127.5:1:0:0.1 0/1:264:3:2,1:152,109:0.0114:2,2:23.7:1:29.3:1:1:1.43:60:6:0.0116:0:1 -5 87898894 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62406;SOR=2.8791;LSEQ=TGTGTGCTATCCATGCCAAA;RSEQ=GTGTAACAATTATGCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:1:0,1:162,111:0.0036:2,0:1:0:25:0:0.40876:0:60:2:0.0037:0:1 0/1:287:3:2,1:158,126:0.0105:2,2:5.7:1:30.7:1:1:1.59:60:6:0.0106:0:1.3 -5 87898981 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2418;SOR=Inf;LSEQ=GCTTAAAAATCCACTATGAT;RSEQ=GGAAACATTTCATTCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:43,126:0:2,0:22:1:30.8:1:1:0:60:83.5:1:0:0.1 0/1:164:2:0,2:43,119:0.0122:2,0:5:1:30:1:1:0:60:4:0.0125:0:1 -5 87898997 . T TA 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.33276;SOR=3.64487;LSEQ=TGATGGGAAACATTTCATTC;RSEQ=AAAAAAAAATTATCTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:1:0,1:18,92:0.009:2,0:13:0:31:0:1:0:60:2:0.0092:0:0 0/1:93:3:1,2:15,75:0.0323:2,2:29.3:1:29:1:0.43629:2.47:60:6:0.0326:0.0108:0.3 -5 87899069 . C T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14144;SOR=0;LSEQ=TTCTCCCCGCCCGCCCCCTC;RSEQ=CCCGGCCCCATGGGGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:0,5:1,22:0.1786:1,0:26.4:1:30.6:1:1:0:60:10:0.1786:0:1.4 0/0:16:0:0,0:1,15:0:1,0:17.7:1:30.7:1:1:0:60:32:1:0:0.1 -5 88100495 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52533;SOR=Inf;LSEQ=AAGCACTTTGTCCATGTCGG;RSEQ=GCTGGCATACTGGAACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:74,35:0:2,0:24.9:1:30:1:1:0:60:218:1:0:0.1 0/1:175:2:1,1:117,56:0.0114:2,2:21.5:1:30:1:0.5466:2.07976:60:4:0.0115:0:1 -5 88100578 . G C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06675;SOR=0;LSEQ=ACAGCACGCTCAGCTCATAA;RSEQ=CCTTCTTCATCAACCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:1,2:69,101:0.0173:2,2:39.3:1:25.3:1:1:1.36396:60:2:0.0118:0:2.7 0/0:252:0:0,0:105,147:0:2,0:26.9:1:31.5:1:1:0:60:49.4:1:0:0.1 -5 88100618 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50749;SOR=Inf;LSEQ=TTTCCTCTTTGTAAATGTCA;RSEQ=CTAGAAAAAAGAAAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:36,74:0:2,0:24.4:1:31.2:1:1:0:60:220:1:0:0.2 0/1:145:2:1,1:35,108:0.0138:2,2:16.5:1:30:1:0.43621:3.06:60:4:0.0144:0:1 -5 88365778 . G A 201 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTATTGTCTTTAGCTTCA;RSEQ=TTTTGTTTTCTTTTCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:0:0,0:189,248:0:2,0:26.7:1:32:1:1:0:60:86.4:1:0:0.1 0/1:530:113:48,65:192,225:0.2132:2,2:26.9:1:29.6:1:0.524:1.15524:60:55.5:0.2114:0:1.2 -5 88365829 . CA C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09728;SOR=0.43022;LSEQ=CATCTCATCAGATTGACATG;RSEQ=AAAAAAAAGTCTAAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:12:2,10:58,145:0.0548:2,2:27.3:1:32.4:1:0.51696:1.99449:60:24:0.0561:0.0046:0.1 0/1:247:6:2,4:72,169:0.0243:2,2:37.7:1:31:1:1:1.17:60:12:0.0246:0:0.3 -5 93018597 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52972;SOR=Inf;LSEQ=ATAGCCTCTTGGTTAGTCAT;RSEQ=CGGAAGCAATTCTTCACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:70,30:0:2,0:25.9:1:31:1:1:0:58.4:49:1:0:0.1 0/1:167:2:1,1:106,59:0.012:2,2:14:1:30.5:1:1:1.78986:56:4:0.012:0:1 -5 93019214 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50688;SOR=Inf;LSEQ=TGCCAGTGTTACTTTAATTG;RSEQ=ACTGCCTTCGTAATTCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:52,89:0:2,0:22.4:1:31:1:1:0:58.1:46:1:0:0.1 0/1:183:2:1,1:74,107:0.0109:2,2:5.5:1:24:1:1:1.44:57:4:0.011:0:1.5 -5 93019512 . C A 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02124;SOR=0;LSEQ=AGCCGCGCAGGACGGAATCA;RSEQ=ACCAGGCAAAAAGTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:4:3,1:121,239:0.011:2,2:15:1:27.3:1:0.11649:5.90:60:8:0.0114:0:1 0/0:587:0:0,0:202,384:0:2,0:19.9:1:30.6:1:1:0:60:40.857:0.9983:0:0.3 -5 93019525 . G GT 131 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.29852;SOR=0.69302;LSEQ=GGAATCACACCAGGCAAAAA;RSEQ=TTTTTTTTTTAAAGATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:17:3,14:54,153:0.0756:2,2:26.3:1:29.3:1:0.57043:1.64378:60:34:0.0762:0.0089:0.6 0/1:392:21:2,19:93,275:0.0536:2,2:26.6:1:29.9:1:0.12167:3.20591:60:42:0.0544:0.0026:0.6 -5 93019536 . A T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34355;SOR=0.48641;LSEQ=AGGCAAAAAGTTTTTTTTTT;RSEQ=AAGATATATATTTTGAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:6:2,4:24,145:0.0343:2,2:12:1:28:1:0.21837:2.99:60:12:0.0343:0:1.5 0/1:295:5:0,5:48,242:0.0169:2,0:12.2:1:29:1:1:0:60:10:0.0169:0:1.2 -5 93019574 . T C 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGAGATGAAAATGAATTC;RSEQ=TTTTAAGATGTAAAAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:83:83:0,83:0,0:1:0,1:25.8:1:32.3:1:1:0:60:82:1:0:1.1 1/1:131:131:2,129:0,0:1:0,1:23.8:1:32.6:1:1:0:60:262:1:0:1.1 -5 93019685 . TTTAA T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63287;SOR=0.52218;LSEQ=TTGTCAATGTTATTAATTAC;RSEQ=TTATGTCTAGTACTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:39.2:1:30.2:1:1:0:60:10:0.5:0:0.2 0/1:6:2:0,2:0,4:0.3333:0,0:19:1:30.3:1:1:0:60:4:0.3333:0.1667:0 -5 93537742 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=TAAGATAATCAGATATTAAA;RSEQ=ATAGGGGGTTCTGGCTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:13,2:0.1176:2,2:15:1:26:1:0.33088:5.50762:60:4:0.1176:0:1 0/0:16:0:0,0:13,3:0:2,0:19.3:1:32.3:1:1:0:60:32:1:0:0.1 -5 96383427 . CA AG 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCAGAGGAGGATGTTTC;RSEQ=CTTAAAAATCCCACAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:22.5:1:32.5:0:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:0:0,0:25:0:32:0:1:0:60:2:1:0:0 -5 96383496 . C T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60784;SOR=2.28225;LSEQ=TTATGGCATGTGTCAACCTG;RSEQ=GTCCTCCTGTGGGATCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:20.8:1:30.2:1:1:0:60:10:0.3846:0:1.2 1/0:5:3:3,0:2,0:0.6:0,0:23.7:1:30.3:1:1:0:60:6:0.6:0:1 -5 96383670 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25098;SOR=Inf;LSEQ=ACTAAACCTCAGTGAAGAGT;RSEQ=CATGTCCTTAGGTGGATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:147,80:0:2,0:23.2:1:31.7:1:1:0:60:55.75:1:0:0.3 0/1:255:3:1,2:173,79:0.0118:2,2:22.7:1:27.7:1:0.23766:4.35166:60:6:0.0119:0:1.3 -5 96383752 . A G 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.52222;SOR=0.9047;LSEQ=TTACACACAGAAGCATTCGC;RSEQ=GAGAGTAGAAAGAGTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:183:76,107:84,114:0.4791:2,2:26:1:30.2:1:0.91732:1.03731:60:182:0.4802:0:1.1 0/1:414:188:84,104:105,121:0.4541:2,2:24.1:1:29.6:1:0.76645:1.07419:60:93:0.4559:0:1.1 -5 96383880 . T A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5056;SOR=0.72143;LSEQ=CTCCCTCAAAGATGTCCATG;RSEQ=CCTAATCCCTGGAACCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:28:1,27:2,16:0.6087:2,1:23:1:30.2:1:0.55178:3.28381:60:56:0.6087:0:1.1 1/0:36:19:3,16:0,17:0.5278:1,2:17.1:1:28.2:1:0.23095:0:60:38:0.5278:0:1 -5 97303829 . C A 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10657;SOR=Inf;LSEQ=AATTCATTGTGGTAAAATTA;RSEQ=TCAAGGGACTAAACTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:168,157:0:2,0:26:1:31.9:1:1:0:60:80.25:1:0:0.2 0/1:294:3:2,1:143,148:0.0102:2,2:23.3:1:23.7:1:0.61864:2.06:60:2:0.0069:0:2.3 -5 97303834 . G T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=27.04848;LSEQ=ATTGTGGTAAAATTACTCAA;RSEQ=GGACTAAACTCAGAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:14:9,5:156,158:0.0427:2,2:29.1:1:29.6:1:0.41377:1.82:60:13:0.0402:0:1.6 1/0:292:160:76,84:66,64:0.5479:2,2:27.4:1:29.9:1:0.63694:1.13929:60:159:0.5502:0:1.1 -5 98004209 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GAGAACCACAAGAGGAAGAT;RSEQ=ACCCCTCACCCCCAGCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:30.1:1:31:1:1:0:60:16:1:0:0.1 0/1:8:2:1,1:4,2:0.25:2,2:42.5:1:30:0:1:1.8258:60:4:0.25:0:1 -5 98004831 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTAGAGGGAGGGATGGTC;RSEQ=CAGTCTCTCTGCACCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:19:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 98005437 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02601;SOR=0;LSEQ=ACAATGTCTCTCCATGAAGG;RSEQ=CGCAGAACAACAGGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:2,3:0.4444:2,2:38.8:1:31:1:1:1.43:60:8:0.4444:0:1 0/0:11:0:0,0:3,8:0:2,0:25.9:1:32.1:1:1:0:60:22:1:0:0.1 -5 101265568 . A C 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8165;LSEQ=TAGTCATACAAATATCTACT;RSEQ=GTCTACTCATCTGGAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:38.8:1:30.8:1:1:0:60:10:0.5556:0:1.2 1/0:2:1:1,0:1,0:0.5:0,0:32:0:32:0:1:0:60:2:0.5:0:1 -5 101265670 . T C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10922;SOR=Inf;LSEQ=GCCTTGAGGAATGAAAAAAA;RSEQ=ACAATAATTTAAAGCCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:0:1,0:24:1:31.2:1:1:0:60:23:1:0:0 0/1:23:3:3,0:19,1:0.1304:1,0:11.7:1:31.7:1:1:0:60:6:0.1304:0:1.3 -5 101265723 . AT A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=TTTAAAATGCAGACTTCAAC;RSEQ=TTTTGTAGGTAATAGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:52,2:0.0357:1,2:13.5:1:31.5:1:0.10519:21.43217:60:4:0.0364:0.0179:0.5 0/0:72:0:0,0:67,5:0:2,0:25.7:1:30.1:1:1:0:60:144:1:0:0.1 -5 101265865 . C T 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.35324;SOR=0.82984;LSEQ=GACAGGATTACATTTTATAA;RSEQ=TTTCAATAAACCTCCTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:89:47,42:65,72:0.3938:2,2:27.9:1:30.4:1:0.49632:1.24:60:88:0.3929:0:1.3 0/1:277:97:37,60:77,103:0.3502:2,2:27.8:1:29.9:1:0.52251:1.21144:60:194:0.3514:0:1.5 -5 101265926 . C A 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.90118;SOR=0.96012;LSEQ=CTTAGTTATATGATCAAGAG;RSEQ=ATTAACGCTTCAGTATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:50:12,38:24,56:0.3846:2,2:21.9:1:29.7:1:0.54726:1.354:60:100:0.3846:0:1.6 0/1:144:54:18,36:23,67:0.375:2,2:25.1:1:29.8:1:0.34427:1.45:60:53:0.3732:0:1.6 -5 110749262 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGCCTGGGTGACAGAGC;RSEQ=ACACTCCATCTCAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:32.5:1:1:0:60:4:1:0:2.5 -5 110749264 . C G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTGGGTGACAGAGCAA;RSEQ=ACTCCATCTCAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:32.5:1:1:0:60:4:1:0:2.5 -5 110750079 . TCAG T 49 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.24822;SOR=Inf;LSEQ=TTTCCCCACTTCTCCACCTC;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:30,20:0:2,0:25.5:1:31.2:1:1:0:60:100:1:0:0.2 0/1:59:3:1,2:26,30:0.0508:2,2:38:1:31:1:1:1.71787:60:6:0.0517:0:0 -5 110750082 . G T 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.20885;SOR=0;LSEQ=CCCCACTTCTCCACCTCTCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:29,20:0.0392:2,2:39.5:1:32:1:1:1.43922:60:4:0.04:0:1 0/0:60:0:0,0:27,30:0:2,0:26.4:1:30.7:1:1:0:60:27.5:1:0:0.2 -5 110858691 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTGTTGGGATTACAGGC;RSEQ=TGAGCCACTGCAGCATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 111982886 . A G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.86596;LSEQ=TCATCAATTCTATGGCTTAG;RSEQ=TTAGCCAGTGATAGCTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:7:7,0:46,0:0.1321:1,0:19.7:1:32.1:1:1:0:60:14:0.1321:0:1 0/1:43:5:5,0:38,0:0.1163:1,0:29.6:1:30:1:1:0:60:10:0.119:0:1.4 -5 111982962 . TA T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16064;SOR=0.53285;LSEQ=TTTATTTCATTTCCATTCCT;RSEQ=AAAAAAAAATACGATGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:16:13,3:141,37:0.0825:2,2:21.3:1:30.1:1:1:1.14:60:32:0.0829:0.0155:0.3 0/1:241:11:7,4:160,69:0.0456:2,2:30.5:1:28.5:1:0.73945:1.32346:60:22:0.0462:0:0.6 -5 111982982 . A T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07872;SOR=0;LSEQ=TAAAAAAAAAATACGATGAT;RSEQ=TAATTAGAGAACTTGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:1,2:175,75:0.0119:2,2:15:1:23.7:1:0.22051:4.63465:60:2:0.0082:0:2.3 0/0:336:0:0,0:217,119:0:2,0:22:0:14:0:1:0:60:0:0:0:3 -5 111983041 . C A 243 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31038;SOR=1.14165;LSEQ=GATTTTTCAGGATAAGCAGA;RSEQ=ATACTCTCCACCTCCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:194:102,92:120,113:0.4501:2,2:26.8:1:30:1:0.84616:1.04:60:31.333:0.4476:0:1.1 0/1:592:286:147,139:153,152:0.4831:2,2:26.1:1:29.8:1:0.80504:1.05:60:94.333:0.4838:0:1.2 -5 111983052 . C T 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45203;SOR=0.90957;LSEQ=ATAAGCAGACATACTCTCCA;RSEQ=CTCCTAAAACAGCCCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:443:232:118,114:100,109:0.5237:2,2:26.9:1:29.7:1:0.56745:1.13:60:24.778:0.5174:0:1.2 1/0:594:297:145,152:146,151:0.5:2,2:26.4:1:28.8:1:1:1.01354:60:41.429:0.4966:0:1.1 -5 111983180 . T C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00085;SOR=Inf;LSEQ=TAGTCTTACTCCTATCAAAG;RSEQ=CTTCTATAAGCCAGCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:0,73:0:1,0:26.2:1:30.4:1:1:0:60:146:1:0:0.1 0/1:55:8:0,8:2,45:0.1455:1,0:27.1:1:31.3:1:1:0:60:16:0.1455:0:1.3 -5 112043072 . A G 41 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGGCTGCCTAGGCAGCA;RSEQ=TGGCTCACGGGACAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:27.7:1:26.3:1:1:0:60:2:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 112043282 . CG GT 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.00523;SOR=0;LSEQ=CCGGAAGCCTAGCCGCTGCT;RSEQ=GGGGGGACCTGCGGGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:10:9,1:76,0:0.1163:1,2:26.3:1:31.2:1:0.11628:0:60:20:0.119:0:1 0/0:63:0:0,0:44,1:0:1,0:27.6:1:31.4:1:1:0:60:90:0.7258:0:0.1 -5 112043384 . T G 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00145;SOR=1.96759;LSEQ=TGGTGAGGAAGGTGAAGCAC;RSEQ=CAGTTGCCTTCTCGGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:35:27,8:326,178:0.0648:2,2:25.5:1:29.8:1:0.14571:1.84:60:70:0.0659:0:1.1 0/1:658:79:53,26:351,226:0.1201:2,2:21.7:1:30.2:1:0.32445:1.31:60:158:0.1221:0:1.1 -5 112043548 . G A 50 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18494;SOR=0.20984;LSEQ=GAAGAGCCCGGGCGGCGCTC;RSEQ=TACTTCTGGCCACTGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:4:3,1:126,272:0.01:2,2:22:1:25:1:0.09928:6.44:60:3:0.0076:0:1.3 0/0:476:1:1,0:174,301:0.0021:2,0:1:0:24:0:0.36765:0:60:2:0.0021:0:1 -5 112043635 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49793;SOR=0;LSEQ=GCAAAGCTTCCTCGGCTTTG;RSEQ=CCCGCCGCTGCTCGGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:23,93:0.0169:2,0:31:1:29.5:1:1:0:60:4:0.0172:0:1 0/0:115:0:0,0:21,94:0:2,0:23:1:31.1:1:1:0:60:114:1:0:0.1 -5 112089282 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTCAACCAAAGACTT;RSEQ=TGTAGGTGATCCCTGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43:0:32.5:1:1:0:60:4:1:0:1 -5 112090379 . CT C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATTTCATTTATCTTGAA;RSEQ=AAGACTCCACTGTTTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:3,0:16,0:0.1579:1,0:42.3:1:32.7:1:1:0:60:6:0.1579:0:0 0/0:2:0:0,0:2,0:0:0,0:16.5:1:32:1:1:0:60:4:1:0:0 -5 112090779 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49828;SOR=0;LSEQ=TTTTTATTCAGTATTCCCTC;RSEQ=TGTAAACTTGAGGTAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:17,116:0.0148:2,2:8:1:28.5:1:0.24975:6.66:60:4:0.0149:0:1 0/0:130:0:0,0:17,113:0:2,0:23.6:1:29.8:1:1:0:60:64:1:0:0 -5 112101793 . C A 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22797;SOR=Inf;LSEQ=AATGTATCTTAAATGTGTTT;RSEQ=TAATACCTTGCACAGAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:24.6:1:29:1:1:0:60:10:0.5556:0:1 1/1:4:4:3,1:0,0:1:0,2:17.5:1:29:1:1:0:60:8:1:0:1 -5 112101970 . T C 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=TGTCAAGAAATACAGAATCA;RSEQ=GTCTTGAAGTTATTTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:206,56:0:2,0:23.9:1:30.5:1:1:0:60:51.4:1:0:0.1 0/1:277:14:10,4:190,73:0.0505:2,2:23.1:1:29.7:1:1:1.04095:60:28:0.0507:0:1.1 -5 112111070 . G A 28 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATATGAAGAAAGCCTTT;RSEQ=GTGAAGTGTAAGTATTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23.5:1:28:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:44:0:27:0:1:0:60:2:1:0:1 -5 112111450 . G A 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66163;SOR=0.54196;LSEQ=AAAATGTAAGTAACTTGGCA;RSEQ=TACAACTTATTTGAAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:84,197:0.0106:2,2:16.7:1:28.3:1:0.21867:4.66:60:6:0.0108:0:1 0/0:348:2:2,0:115,231:0.0057:2,0:1:0:25.5:1:0.11239:0:60:4:0.0058:0:1 -5 112116436 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12146;SOR=Inf;LSEQ=TATGCTTTTTTGCTTTTACT;RSEQ=ATTAACGTAAATACAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:130,29:0:2,0:25.6:1:31.8:1:1:0:60:78.5:1:0:0.1 0/1:157:3:1,2:117,37:0.0191:2,2:13.7:1:28.3:1:0.15264:6.23153:60:6:0.0192:0:1.3 -5 112116632 . C T 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02232;SOR=2.05182;LSEQ=GTTTCTAAGTGATAAAACAG;RSEQ=GAAGAGCTATTAGGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:17:5,12:46,146:0.081:2,2:22.4:1:29.9:1:0.56857:1.32:60:34:0.0821:0:1 0/1:261:40:12,28:64,156:0.1533:2,2:23.9:1:29.5:1:1:1.04:60:80:0.1538:0:1.1 -5 112116773 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66992;SOR=0.49289;LSEQ=GCAACATAATCAATATTCAC;RSEQ=TAGTTGTGTCTTTACCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:0.5833:0,0:19.1:1:32.7:1:1:0:60:14:0.5833:0:1 0/1:10:4:0,4:0,6:0.4:0,0:17.5:1:31:1:1:0:60:8:0.4:0:1 -5 112151551 . G T 26 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGAGGCATGAGAATAGTT;RSEQ=GAACCCAGGAGGCAGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:30:1:26.5:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:0,1:0:0,0:30:0:26:0:1:0:60:2:1:0:0 -5 112154544 . C CG 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.39598;SOR=0.66913;LSEQ=GTTTTTTGTTTTTTTTTTGG;RSEQ=GGGGGGGGTTGTTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:18:18,0:28,1:0.3103:1,1:28.9:1:28.6:1:1:0:60:36:0.375:0.0517:0.8 0/1:52:12:12,0:31,0:0.2308:1,0:20.1:1:24.8:1:1:0:60:5:0.2439:0.0577:0.9 -5 112154571 . G C 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60655;SOR=1.39246;LSEQ=GGTTGTTTTGTTTTTTTAGA;RSEQ=TTATAGTAAATATCCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:6:5,1:73,3:0.0723:1,2:20.7:1:31.2:1:0.26648:4.70169:60:12:0.0857:0:1 0/1:102:10:7,3:85,7:0.098:2,2:19.5:1:29.5:1:0.05699:5.06891:60:9:0.0968:0:1.9 -5 112154604 . GT G 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=1.96001;LSEQ=TCCCATTCATCACTTAATTG;RSEQ=TTTTGGCTTTTGGATATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:1:1,0:122,37:0.0063:2,0:22:0:32:0:1:0:60:2:0.0063:0:0 0/1:246:3:1,2:171,71:0.0122:2,2:15:1:30:1:0.21239:4.78173:60:6:0.0123:0:1 -5 112162713 . G GT 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.33077;SOR=3.68079;LSEQ=CATATATTCTCATTGATTGA;RSEQ=TTTTTTTTTCCTAGTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:1,0:88,1:0.0111:1,0:32:0:31:0:1:0:60:2:0.0111:0:0 0/1:75:3:2,1:66,6:0.04:2,2:22.3:1:26.7:1:0.25782:5.28009:60:6:0.04:0.0133:0.3 -5 112162854 . T C 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0.63704;LSEQ=CAAGTGGACTGTGAAATGTA;RSEQ=GGGCTTACTAATGACCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:588:324:181,143:150,113:0.551:2,2:25.6:1:30.8:1:0.80206:1.04869:60:161:0.5561:0:1.1 0/1:636:279:153,126:190,167:0.4387:2,2:24.8:1:30.3:1:0.68946:1.07:60:278:0.4406:0:1.1 -5 112163027 . C CT 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.25151;SOR=0;LSEQ=AAATACATTTTACTGATTTT;RSEQ=TTTTTTTTCACTCTCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:3:0,3:2,106:0.027:1,0:27.7:1:31.7:1:1:0:60:6:0.0275:0:0 0/0:94:0:0,0:0,94:0:1,0:20.9:1:32.4:1:1:0:60:93:1:0:0.1 -5 112163238 . G GT 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGATCCATTACTAGAGAA;RSEQ=TTTAACTGTGTAGAATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:22:1:31:0:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 112163772 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18897;SOR=0;LSEQ=GGCAGGGTCTCACTCTGTCA;RSEQ=CCAGGCTTAGAGGGCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:9,111:0.0164:2,2:21.5:1:30:1:0.15784:11.75:60:4:0.0164:0:1 0/0:158:0:0,0:18,139:0:2,0:21.6:1:31.1:1:1:0:60:77.5:0.9936:0:0 -5 112164238 . C T 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCACAGTAACCTCAAG;RSEQ=TCCTGGGATCCTCCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:24:1:29.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 112164561 . G A 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27295;SOR=1.18782;LSEQ=ATTAATTTGCAGGTTATTGC;RSEQ=AGTGTTTTGAGGAATTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:286:159:99,60:87,40:0.5559:2,2:24.3:1:29.8:1:0.31831:1.3169:60:38.75:0.5536:0:1.1 1/0:398:238:156,82:100,60:0.598:2,2:24.6:1:29.7:1:0.59378:1.14:60:78.333:0.5995:0:1.1 -5 112164716 . C CT 70 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.08912;SOR=0.15067;LSEQ=AATATGAATTTCATGTTTGG;RSEQ=TTTTTTTTGCTGCCTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:5:1,4:7,97:0.0459:2,2:29.4:1:30.4:1:0.32201:3.40:60:10:0.0467:0:0 0/0:140:1:0,1:27,112:0.0071:2,0:42:0:30:0:1:0:60:2:0.0072:0:0 -5 112164747 . A G 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02619;SOR=Inf;LSEQ=TGCCTTCTTTTAGCCATGAG;RSEQ=TTTCCTAATTTCTTACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:0,60:0:1,0:26.8:1:31.5:1:1:0:60:120:1:0:0 0/1:58:5:0,5:2,51:0.0862:1,0:22.4:1:33:0:1:0:60:10:0.0862:0:1 -5 112164862 . G A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77001;LSEQ=AATTTCTTTTTTGAGATGGG;RSEQ=TCTCTTTCTCTCGCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:26.5:1:31.5:1:1:0:60:4:0.4:0:1 0/1:6:2:0,2:1,3:0.3333:2,0:45.5:1:29:1:1:0:60:4:0.3333:0:1 -5 112170358 . G A 61 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTCATAATGCACATCA;RSEQ=TTGTGCCTCATATTCTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:22.5:1:30.5:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 112170490 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15;SOR=Inf;LSEQ=TAAATACTATTTGGTATTTT;RSEQ=TGAACATTTTTCTAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:33,1:0:1,0:25.1:1:28.1:1:1:0:60:68:1:0:0.1 0/1:22:2:2,0:19,1:0.0909:1,0:18.5:1:33.5:1:1:0:60:4:0.0909:0:1 -5 112172930 . T C 81 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAACATAGGATTTCATGATA;RSEQ=AGTTTTTAAATTGGGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:0.8571:0,2:16.5:1:31.5:1:1:0:60:12:0.8571:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 112173106 . T TAGAA 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.22039;SOR=2.63494;LSEQ=CATTAAACATTACATGAAAT;RSEQ=AGAACAAAAGGAGATGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:19:19,0:17,0:0.5278:1,1:18.8:1:30:1:1:0:60:38:0.5278:0.1944:0 1/0:16:12:11,1:4,0:0.75:0,2:21.8:1:29.4:1:1:0:60:24:0.75:0:0.3 -5 112173849 . A T 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.04776;SOR=0.1283;LSEQ=TGAAAAAGATAGAAGTTTGG;RSEQ=GAGAGAACGCGGAATTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:6:0,6:211,227:0.0135:2,0:8.2:1:27.8:1:0.03134:0:60:12:0.0139:0:1 0/0:571:1:0,1:287,283:0.0018:2,0:1:0:24:0:0.49737:0:60:2:0.0018:0:1 -5 112175031 . C T 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05813;SOR=0;LSEQ=TGGTCAGCCTCAAAAGGCTG;RSEQ=CACTTGCAAAGTTTCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:4:2,2:177,217:0.0101:2,2:23.5:1:29.3:1:1:1.23:60:8:0.0103:0:1 0/0:411:0:0,0:194,216:0:2,0:25:1:31.1:1:1:0:60:81:0.9975:0:0.1 -5 112175617 . T A 194 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTAAAACACCTCCACCACC;RSEQ=CCTCAAACAGCTCAAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:881:93:48,45:391,394:0.1056:2,2:27.8:1:29.7:1:0.82651:1.07:60:30:0.1056:0:1.1 0/0:1272:0:0,0:617,653:0:2,0:23:0:14:0:1:0:60:0:0:0:4 -5 112175770 . G A 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.88636;SOR=0.976;LSEQ=ACTTTATTACATTTTGCCAC;RSEQ=GAAAGTACTCCAGATGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:357:209:96,113:75,73:0.5854:2,2:26.8:1:30.6:1:0.39136:1.20868:60:51.25:0.5824:0:1.1 1/0:459:266:128,138:91,102:0.5795:2,2:23.8:1:30.3:1:0.85034:1.04:60:87.667:0.578:0:1.1 -5 112176325 . G A 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06346;SOR=1.25297;LSEQ=GGAGAAGGAGTTAGAGGAGG;RSEQ=GCACAGTCAGGTGAATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:228:99,129:113,146:0.4682:2,2:23.4:1:30.5:1:1:1.00849:60:37:0.4693:0:1.1 1/0:652:342:139,203:136,174:0.5245:2,2:23.9:1:29.8:1:0.42759:1.14125:60:67.4:0.5299:0:1.1 -5 112176559 . T G 239 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68077;SOR=0.94428;LSEQ=GTCCAGCAAGCATCTGCGTC;RSEQ=TCTTCTGCACCCAACAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:391:207:114,93:109,75:0.5294:2,2:24.8:1:30.6:1:0.41492:1.18509:60:68:0.5299:0:1.1 1/0:464:239:118,121:116,109:0.5151:2,2:24.1:1:30.3:1:0.64363:1.09107:60:238:0.5152:0:1.1 -5 112176756 . T A 263 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTGAAAAATAATTCCAAGG;RSEQ=CTTCAATGATAAGCTCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:467:467:253,214:0,0:1:0,2:25:1:29.7:1:1:0:60:50.889:1:0:1.1 1/0:575:385:206,179:107,83:0.6696:2,2:22.2:1:28.8:1:0.53454:1.11997:60:76:0.6702:0:1.1 -5 112177171 . G A 256 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32534;SOR=1.12922;LSEQ=TTTGCTATTGAAAATACTCC;RSEQ=GTTTGCTTTTCTCATAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:458:246:99,147:88,124:0.5371:2,2:24.5:1:30.7:1:0.84883:1.05362:60:60.5:0.5378:0:1.1 1/0:640:363:137,226:113,164:0.5672:2,2:23.4:1:30.2:1:0.46208:1.13641:60:71.6:0.5647:0:1.1 -5 112177863 . G GA 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01359;SOR=0;LSEQ=AAGTAAAGGAATCAAAGGAG;RSEQ=AAAAAAAGTTTATAAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:5:3,2:262,206:0.0105:2,2:20.4:1:30.1:1:1:1.18:60:10:0.0107:0.0063:0.4 0/0:643:0:0,0:353,289:0:2,0:23.6:1:30.6:1:1:0:60:63.2:0.9984:0:0.1 -5 112179789 . G A 77 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.3126;SOR=2.74682;LSEQ=TGGAACCCAAAGTCCTAAGC;RSEQ=CCATTCTGGGTCTTACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:2:2,0:156,246:0.0049:2,0:1:0:29:0:0.15236:0:60:4:0.005:0:1 0/1:520:7:6,1:207,305:0.0135:2,2:13.4:1:27.7:1:0.02098:8.81:60:14:0.0138:0:1 -5 112179909 . C A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12801;SOR=Inf;LSEQ=TCAAATGAAACTTTAAAAGA;RSEQ=TGAAAAATTTTGTAAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:0:1,0:24.1:1:32:1:1:0:60:18.5:1:0:0.2 0/1:50:4:0,4:0,45:0.08:1,0:33.3:1:26.8:1:1:0:60:8:0.0816:0:1 -5 112213678 . CTGTGTGTG C 257 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=20.000;MSILEN=2;SSF=0;SOR=0.01801;LSEQ=ATTGAGAGTTACAGGTTACT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:283:153,130:184,179:0.3086:2,2:31.7:1:31.6:1:0.42748:1.14:59.3:93.333:0.3135:0.0142:0.4 0/0:1130:9:5,4:272,260:0.008:2,2:23.4:1:29.7:1:1:1.19:60:18:0.0082:0.0018:0 -5 112213747 . GTAAC G 295 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=4.000;MSILEN=4;SSF=0.00446;SOR=1.28;LSEQ=CCGATTTATCACTAGAGTGA;RSEQ=TAACTAACTAACTGCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1011:530:258,272:249,224:0.5242:2,2:26.6:1:31.9:1:0.22943:1.17174:59.6:74.714:0.5386:0.0376:0.8 1/0:1186:694:339,355:244,247:0.5852:2,2:26.9:1:31.3:1:0.81352:1.03447:59.7:137.8:0.5945:0.0278:0.7 -5 112213805 . C G 313 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.962;LSEQ=TATTCATATGCCATATACTA;RSEQ=GGAAACAACCAGGCCAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1345:789:386,403:263,291:0.5866:2,2:26.7:1:31.6:1:0.61787:1.06:60:86.667:0.5856:0:1.1 1/0:1548:1139:554,585:206,201:0.7358:2,2:24.7:1:30.9:1:0.52526:1.08217:60:80.357:0.7343:0:1.2 -5 112213906 . G A 51 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06242;SOR=0;LSEQ=TTATTTAGTAGACCACACCA;RSEQ=CACAATGGTTCCTCCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:5:3,2:94,323:0.0118:2,2:15:1:22.2:1:0.08221:5.13:60:1.5:0.0073:0:1 0/0:395:0:0,0:85,310:0:2,0:22.3:1:31.7:1:1:0:60:64.833:1:0:0.1 -5 112214093 . C T 90 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.51487;LSEQ=TTATATAAAATTGTACATTA;RSEQ=AGGAAGTAGAACCATAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:0,10:0,10:0.5:0,0:22.5:1:27.3:1:1:0:60:20:0.5:0:1.1 0/1:3:1:0,1:1,1:0.3333:2,0:26:0:30:0:1:0:60:2:0.3333:0:1 -5 112227799 . A G 280 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1581;SOR=0.89038;LSEQ=CTGAAAATGATTTAGAAAAT;RSEQ=GTACCACATGGCAAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1207:433:228,205:425,349:0.3587:2,2:27.1:1:31.4:1:0.47013:1.09484:56.6:71.167:0.3573:0:1.1 0/1:1564:520:279,241:561,482:0.3325:2,2:27:1:31.1:1:1:1.00537:56.6:259:0.3335:0:1.1 -5 112227939 . T C 273 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30945;SOR=0.91789;LSEQ=AAACATAATTTCCCAACATC;RSEQ=AGTCCTACCCTTCTTATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1276:443:222,221:420,412:0.3472:2,2:24.9:1:31.3:1:0.90649:1.01482:50.9:43.3:0.3442:0:1.1 0/1:1442:473:223,250:476,489:0.328:2,2:24.9:1:30.8:1:0.46545:1.09121:52:66.571:0.3275:0:1.1 -5 112227998 . G A 190 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01064;LSEQ=TGGAATGGAGCAGTGCAGGA;RSEQ=GGATGACTATGACCCTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1357:79:42,37:637,638:0.0582:2,2:23.3:1:30.2:1:0.64319:1.14:52.2:38.5:0.0575:0:1.2 0/0:1523:1:1,0:790,729:7e-04:2,0:1:0:22:0:1:0:60:2:7e-04:0:2 -5 112228595 . G A 232 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=52.02364;LSEQ=CAAACGCACATCAAAGAGTC;RSEQ=GGAGAGGCACAATTCACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1097:3:3,0:500,594:0.0027:2,0:1:0:27.3:1:0.09609:0:60:6:0.0028:0:1 0/1:1625:203:104,99:704,714:0.1249:2,2:24.2:1:30.3:1:0.70769:1.07:59.6:100.5:0.1252:0:1.4 -5 112228667 . G A 261 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31459;SOR=0.91206;LSEQ=CCAGGGCCGCCGGAGCCAGA;RSEQ=CCGCAGGAGCCACCGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:855:319:172,147:259,276:0.3731:2,2:24:1:30:1:0.12047:1.25:60:318:0.379:0:1.2 0/1:1316:463:233,230:433,417:0.3518:2,2:23.9:1:29.5:1:0.86245:1.02499:60:76.167:0.3568:0:1.3 -5 112228765 . C A 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.65554;LSEQ=ACAGAACTGTTCAGAGTCCC;RSEQ=AATCCAAATAAACTAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:788:352:140,212:172,264:0.4467:2,2:22.6:1:29.7:1:0.94169:1.01:59:24.143:0.4525:0:1.7 0/1:1208:418:191,227:351,439:0.346:2,2:24.9:1:28.7:1:0.71527:1.05:59.1:14.481:0.3442:0:1.7 -5 112228815 . G A 81 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46639;SOR=1.56603;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AATGGACCAGGCCAGGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:5:5,0:16,201:0.0222:2,0:5.8:1:13.4:1:0:0:60:0.25:0.0049:0:2.4 0/1:378:13:11,2:27,334:0.0344:2,2:5.1:1:22.1:1:0:66.14:58.5:3.333:0.0289:0:1.4 -5 112675951 . C A 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTATGGAAGAGCTGTTGTG;RSEQ=ATCTTCTAGTAATTAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:177,73:0:2,0:26.3:1:32.3:1:1:0:60:249:1:0:0.1 0/1:219:83:58,25:96,40:0.379:2,2:25.2:1:28.9:1:1:1.03435:60:82:0.3779:0:1.5 -5 112676024 . C G 222 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGAGTCTACTCTGGTCTC;RSEQ=ATGAGAGTGAAGTCCCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:206,200:0:2,0:25.9:1:31.3:1:1:0:60:57:0.9975:0:0.1 0/1:460:167:85,82:150,143:0.363:2,2:26.8:1:30.1:1:1:1.01191:60:166:0.3617:0:1.4 -5 112676127 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49839;SOR=0;LSEQ=CAATAAAGAAGACAATACCC;RSEQ=ATATGTCCCCTGGAGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:16,131:0.0134:2,2:17.5:1:28.5:1:0.21585:7.97:60:4:0.0137:0:1 0/0:145:0:0,0:33,111:0:2,0:20.8:1:29.9:1:1:0:60:47:0.993:0:0.1 -5 112676130 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49818;SOR=0;LSEQ=TAAAGAAGACAATACCCGAT;RSEQ=TGTCCCCTGGAGCACAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:14,121:0.0146:2,2:34:1:31.5:1:0.20771:8.38:60:4:0.0149:0:1 0/0:135:0:0,0:29,106:0:2,0:20.7:1:28.7:1:1:0:60:32.75:1:0:0.1 -5 112676191 . A G 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00116;SOR=Inf;LSEQ=ACAGACAGGCCGAAATATGT;RSEQ=TTCCATGAACCAAAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,43:0:1,0:19.4:1:31.6:1:1:0:60:86:1:0:0.1 0/1:36:8:0,8:1,27:0.2222:1,0:24.6:1:31.5:1:1:0:60:16:0.2222:0:1 -5 113064928 . A T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACAGCTTCGACCATAAA;RSEQ=GACGGCCGCCCCGCGAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:29:1:1:0:60:4:1:0:1 -5 113066014 . G GT 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=TGGCCTTTTGGATTCTTGGT;RSEQ=TTTTTTTGGTTGATTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:0.1818:2,2:22.5:1:29.1:1:0.49091:3.05504:60:4:0.1818:0.0909:0 0/0:8:0:0,0:5,3:0:2,0:20.5:1:31:1:1:0:60:16:1:0:0.1 -5 113066133 . T G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTGTGGATGCTGTTGTT;RSEQ=TTGCTTTCTGTTTGTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:3,8:0,0:1:0,2:13.9:1:32.1:1:1:0:55.2:22:1:0:1.5 1/1:5:5:3,2:0,0:1:0,2:18:1:30:1:1:0:59.8:10:1:0:1.8 -5 113066151 . A G 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTGCTTTCTGTTTGTTT;RSEQ=TTTTTCTTTCAATGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:26.2:1:31:1:1:0:51.2:12:1:0:2 1/1:4:4:2,2:0,0:1:0,2:29.5:1:30.8:1:1:0:59.8:8:1:0:2 -5 113066262 . G A 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCTGGAGATGTCACTCA;RSEQ=TAAGGCTGGAGAACAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:26.5:1:1:0:60:4:1:0:1 1/1:4:4:1,3:0,0:1:0,2:8.8:1:30:1:1:0:60:8:1:0:1 -5 113066568 . G C 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCATAGAGACTGTGGGCA;RSEQ=CTCTCCCCCTAGGGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38:1:32.5:1:1:0:60:4:1:0:2 1/1:4:4:2,2:0,0:1:0,2:17:1:31.8:1:1:0:60:8:1:0:2 -5 113066577 . C A 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGTGGGCAGCTCTCCCC;RSEQ=TAGGGGTCAGGCCCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38:1:31:1:1:0:60:4:1:0:2 1/1:4:4:2,2:0,0:1:0,2:12.5:1:30.3:1:1:0:60:8:1:0:2 -5 113066747 . A G 70 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTTGGGCTGTGGGGGAC;RSEQ=TATCTTGGGACCAAGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22.5:1:26:0:1:0:60:4:1:0:1 1/0:7:5:2,3:1,1:0.7143:2,2:24.6:1:30.2:1:1:1.41418:60:10:0.7143:0:1.2 -5 113697880 . AGCC A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=1.1321;LSEQ=GCGCGGCTTCTTCCCAGAGC;RSEQ=GCCGCCGCCGCCGCGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:44:0:34:0:1:0:60:2:0.2:0:0 0/1:9:2:1,1:6,1:0.2222:2,2:36.5:1:31.5:1:0.41667:4.58262:60:4:0.2222:0:1 -5 113698201 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTGCTCGTCGCGCCGGG;RSEQ=CAGCCAGCTCAATGTGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 113698411 . C A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCACCACCACCCGCACCCGG;RSEQ=GCACCACCAGCACCACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:0:29.5:1:1:0:60:4:1:0:0.5 0/1:6:2:1,1:2,2:0.3333:2,2:27.5:1:27.5:1:1:1:60:4:0.3333:0:1 -5 114100938 . T G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=CACTCCAATCAATCATAGGC;RSEQ=CAGTCTTTTTATGAAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:34.5:1:31:1:1:1.73:60:4:0.4:0:1 0/0:3:0:0,0:1,2:0:2,0:32.3:1:31.7:1:1:0:60:6:1:0:0.3 -5 114334447 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49336;SOR=Inf;LSEQ=CCAGTCAGGGATAGTATGAG;RSEQ=TGCCACCCGGAGTTTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:19,5:0:2,0:22.8:1:29.2:1:1:0:58.8:48:0.96:0:0.3 0/1:29:2:1,1:20,7:0.069:2,2:7:1:29:1:0.48276:2.73861:60:4:0.069:0:1 -5 114334452 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2147;SOR=Inf;LSEQ=CAGGGATAGTATGAGATGCC;RSEQ=CCCGGAGTTTACAGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:21,12:0:2,0:18:1:29.2:1:1:0:58.8:66:1:0:0.5 0/1:29:2:1,1:20,7:0.069:2,2:14:1:33:1:0.48276:2.73861:21:4:0.0714:0:2 -5 114334458 . A C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20913;SOR=Inf;LSEQ=TAGTATGAGATGCCACCCGG;RSEQ=GTTTACAGGAAAAGGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:22,13:0:2,0:18.7:1:29.7:1:1:0:57.7:34:1:0:0.6 0/1:30:2:1,1:20,8:0.0667:2,2:20:1:33:1:0.51724:2.41524:21:4:0.069:0:2 -5 114334522 . G A 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19436;SOR=0.5891;LSEQ=CTCTTATACCAACCTCTGGA;RSEQ=TTGGGCAACATGGCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:34:20,14:11,11:0.6071:2,2:30.5:1:30.1:1:0.58804:1.42:52.4:68:0.6071:0:1.2 0/1:61:29:14,15:18,14:0.4754:2,2:26.1:1:28.6:1:0.61191:1.37028:54:13.5:0.4576:0:1.1 -5 114334543 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23758;SOR=Inf;LSEQ=TTGGGCAACATGGCTTCTCC;RSEQ=CTTTCTAGGTCCTGTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:0:2,0:27.8:1:30.6:1:1:0:53.9:102:1:0:0.7 0/1:49:2:1,1:18,29:0.0408:2,2:24.5:1:29:1:1:1.59:59.5:4:0.0417:0:1.5 -5 114725764 . C G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGAGTCGAGCAGGCCGG;RSEQ=CTTGCTTGCAGGCCGAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:30.5:1:1:0:60:4:1:0:1 -5 115106241 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50437;SOR=0;LSEQ=ACCTCTCACTCGCTGAGCTC;RSEQ=AGCCTAAGGAGAAGGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:79,17:0.0204:2,2:30.5:1:29.5:1:0.33516:4.54464:60:4:0.0206:0:1 0/0:77:0:0,0:56,21:0:2,0:26.1:1:29.8:1:1:0:60:24.667:1:0:0.2 -5 115106267 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49842;SOR=Inf;LSEQ=AAGGAGAAGGGGGGTAAGTA;RSEQ=GGAGGTCTCTATACCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:104,55:0:2,0:22.3:1:30.3:1:1:0:60:318:1:0:0.1 0/1:159:2:1,1:103,54:0.0126:2,2:21:1:29:1:1:1.89921:60:4:0.0128:0:1.5 -5 115106722 . C CA 136 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.63862;SOR=1.17463;LSEQ=GATGGGAAACATTTCATTCT;RSEQ=AAAAAAAAAAATTATCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:19:4,15:49,164:0.0805:2,2:29.5:1:30.1:1:1:1.11989:60:38:0.0833:0:0.2 0/1:268:25:6,19:59,176:0.0933:2,2:24.4:1:29.4:1:1:1.06131:58.8:24:0.0934:0.0112:0.5 -5 116414876 . C A 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TCTAAGAAAACATATCTTGC;RSEQ=TTGTCTCTAGTCCTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:26.7:1:31.3:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:26.5:1:1:0:60:4:1:0:1 -5 116415112 . TTC T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.499;SOR=0;LSEQ=AAATTGCTAGCTTTGTGTTT;RSEQ=TCTCAGTTTGGCCTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:168,16:0.0108:2,2:21.5:1:28:1:0.17489:10.21682:60:4:0.011:0:2 0/0:176:0:0,0:160,16:0:2,0:23.8:1:30.3:1:1:0:60:87:1:0:1 -5 116415123 . T C 246 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99165;LSEQ=TTTGTGTTTTTCTCTCAGTT;RSEQ=GGCCTCTCCTTGGTTACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:240:239:198,41:0,0:0.9958:0,2:22.5:1:31.2:1:1:0:60:118.5:0.9958:0:1.1 1/1:238:237:198,39:1,0:0.9958:0,2:23.1:1:30.9:1:1:0:60:117.5:0.9958:0:1 -5 116415244 . A T 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00954;SOR=0.74825;LSEQ=ACCTTTTTTCCTTTCTACCA;RSEQ=CCCAAGTAATAAGCCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:590:286:120,166:122,182:0.4847:2,2:26.7:1:29.7:1:0.67588:1.08:60:21:0.4748:0:1.1 0/1:765:316:148,168:201,246:0.4131:2,2:24.8:1:29:1:0.6581:1.08:60:78:0.4132:0:1.1 -5 117054836 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21863;SOR=Inf;LSEQ=AGTTGTTAGTTAAAAGTTAA;RSEQ=AAGGACTTCTCAAGTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:28,9:0:2,0:25.4:1:31.9:1:1:0:60:74:1:0:0.1 0/1:33:2:1,1:21,10:0.0606:2,2:8.5:1:27:1:1:2.04944:60:4:0.0606:0:1.5 -5 117055037 . G T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28002;SOR=1.90492;LSEQ=CATTGTGTTCTGTATGTTTT;RSEQ=ATGGTCTGGAAGATATCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:6:2,4:22,16:0.1364:2,2:34.2:1:28:1:0.38713:2.68715:60:12:0.1364:0:1.3 0/1:43:10:6,4:12,21:0.2326:2,2:16.6:1:29.3:1:0.27535:2.56:60:20:0.2326:0:1.2 -5 117055145 . C A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.21624;SOR=2.04029;LSEQ=TCACATTACAGTGAACTGAA;RSEQ=TGGGTCCATCTTGACCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:29:21,8:11,8:0.6042:2,2:21.8:1:29.9:1:0.35677:1.88:60:28:0.5957:0:1.2 1/0:29:22:11,11:4,3:0.7586:2,2:26:1:30.2:1:1:1.32019:60:44:0.7586:0:1.2 -5 117055315 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50489;SOR=0;LSEQ=ATGACTTTAAATTCCCTTGT;RSEQ=ATAAACTATGGCATGTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:107,73:0.011:2,2:19.5:1:28:1:1:1.46257:60:4:0.0111:0:1.5 0/0:145:0:0,0:86,59:0:2,0:23.4:1:31.5:1:1:0:60:290:1:0:0.1 -5 117055390 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49961;SOR=0;LSEQ=CTTGTGGATTATTCTGCTGG;RSEQ=CAGTATTGGTGACATTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:75,107:0.0108:2,2:29:1:29:1:1:1.42:60:4:0.0114:0:1 0/0:169:0:0,0:69,100:0:2,0:24.2:1:30.4:1:1:0:60:23.143:1:0:0.1 -5 117057428 . A AAT 49 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.04315;SOR=Inf;LSEQ=TAGAACTTAAAGTGTAATAA;RSEQ=ATATATATATATAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:19,5:0:2,0:18.3:1:30.5:1:1:0:60:48:1:0:0.1 0/1:14:3:2,1:8,3:0.2143:2,2:33.3:1:31:1:1:1.30524:60:6:0.2143:0:0 -5 117057746 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22552;SOR=Inf;LSEQ=TTTTTTCATGCTTGATTCTT;RSEQ=CCAACATGGCATCTATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:26,42:0:2,0:28.4:1:29.7:1:1:0:60:67:1:0:0.1 0/1:62:2:1,1:23,37:0.0323:2,2:37.5:1:26.5:1:1:1.60:60:4:0.0323:0:1 -5 117759448 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49368;SOR=Inf;LSEQ=GGAGCTGGCTTTTTGTAAAA;RSEQ=TTAATAAAATAGACCACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:13,24:0:2,0:17.6:1:31.9:1:1:0:60:74:1:0:0.1 0/1:39:2:1,1:12,25:0.0513:2,2:5:1:27.5:1:1:2.04:60:4:0.0526:0:1.5 -5 118882170 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATTTGAAGTGAGGTTGA;RSEQ=CAGCTCTATACACCTTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 118882820 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTCTTTTATTTTTTTAA;RSEQ=ACCTACTATGCCATGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:26.5:1:29.5:1:0.33333:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:0:0,0:1:0:30:0:1:0:60:2:1:0:0 -5 118883014 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49742;SOR=0;LSEQ=ATCTTGGCTCTTAGAGTGCT;RSEQ=AATGTGTTCAATAAGCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:44,7:0.0377:2,2:18:1:30:1:0.28157:5.94621:60:4:0.0377:0:1 0/0:46:0:0,0:33,13:0:2,0:27:1:29:1:1:0:60:45:1:0:0.1 -5 118883086 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23863;SOR=Inf;LSEQ=TTGTTTGTTTACAATAAGGC;RSEQ=AACAGCATGCCAGGTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:115,74:0:2,0:22.9:1:31.1:1:1:0:60:36.8:1:0:0.1 0/1:181:2:1,1:109,70:0.011:2,2:23.5:1:28.5:1:1:1.55317:60:4:0.011:0:1 -5 118883091 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49911;SOR=0;LSEQ=TGTTTACAATAAGGCCAACA;RSEQ=CATGCCAGGTAACATTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:120,79:0.01:2,2:9.5:1:29:1:1:1.5157:60:4:0.0101:0:1.5 0/0:190:0:0,0:119,71:0:2,0:26.3:1:31.5:1:1:0:60:37:1:0:0.2 -5 118883106 . T C 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00094;SOR=Inf;LSEQ=CAACAGCATGCCAGGTAACA;RSEQ=TGTAGACTCTTCCAGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:125,99:0:2,0:28.1:1:30.6:1:1:0:59.9:111:1:0:0.1 0/1:242:11:6,5:137,94:0.0455:2,2:30.4:1:32:1:0.76275:1.21354:60:22:0.0458:0:1.2 -5 118883138 . C A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41292;LSEQ=CCAGTTTTGCCATGATAACA;RSEQ=TTGTGGGGCATTCCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:2:1,1:109,121:0.0086:2,2:17:1:32.5:1:1:1.11:60:4:0.0088:0:1 0/1:247:3:2,1:122,122:0.0121:2,2:21.7:1:28.7:1:1:1.99:54:6:0.0123:0:1.7 -5 118883167 . C A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.30754;LSEQ=CATTCCTTTTTGAGCAGTAC;RSEQ=CATTCCCTTGATGTCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:2,0:67,97:0.012:2,0:1:0:27.5:1:0.1713:0:55.5:4:0.0125:0:1 0/1:191:3:1,2:82,105:0.0157:2,2:15.3:1:32:0:1:1.55839:60:6:0.016:0:1 -5 118883215 . A G 157 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00064;SOR=0.27565;LSEQ=TTTCTTATAGATTTGCATAT;RSEQ=CATGGCCAAAGGAAAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:31:5,26:8,35:0.4189:2,2:26.5:1:31.8:1:1:1.18583:60:30:0.4167:0:1.1 0/1:79:13:1,12:13,53:0.1646:2,1:20.1:1:30.4:1:0.4445:2.9125:60:5.5:0.1467:0:1.5 -5 125065999 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTGAGCTCCCTGTGGAA;RSEQ=GTGTAGCAGCCATCACTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:29:1:1:0:60:4:1:0:1 -5 125066527 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=GTAGGCTTAGTTTTCCCCCT;RSEQ=CTAGCCCTGAGGAATCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:24.5:1:32.7:1:1:0:60:30:1:0:0.3 0/1:28:2:1,1:14,12:0.0714:2,2:41.5:1:29:1:1:1.16024:60:4:0.0714:0:1 -5 125066642 . T C 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGGTCCTGGTTCCCATGC;RSEQ=CCCAACTGGGTGAGACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:16.2:1:32.6:1:1:0:60:10:1:0:1 1/1:6:6:2,4:0,0:1:0,2:29.5:1:31.3:1:1:0:60:12:1:0:1 -5 125564245 . GA G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16194;SOR=0;LSEQ=ATGCCACCCTGCATTTGCAG;RSEQ=AAAGGTTTCTGAAATCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:0.125:2,2:22.5:1:31.5:1:1:1.73197:60:4:0.125:0:0.5 0/0:23:0:0,0:15,8:0:2,0:23.3:1:29.3:1:1:0:59.3:46:1:0:0.3 -5 125564266 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23065;SOR=Inf;LSEQ=AAAAGGTTTCTGAAATCAGA;RSEQ=AACGCCTTTCAAACTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,14:0:2,0:21.6:1:31.5:1:1:0:54.3:64:0.9697:0:0.1 0/1:31:2:1,1:18,11:0.0645:2,2:30:0:32:0:1:1.60957:52:4:0.0645:0:1.5 -5 125564339 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50355;SOR=Inf;LSEQ=CCCCTTTCTAGGTCCCATGG;RSEQ=AGCCATCTTGCTGTTACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:20.9:1:32.2:1:1:0:55.2:40:1:0:0 0/1:28:2:1,1:12,14:0.0714:2,2:20:0:31.5:1:1:1.16:51:4:0.0714:0:1 -5 125564480 . G T 44 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AACTAACGACTTCTACTGAG;RSEQ=ACCCCTGGACCAAACCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:7:0:32:0:1:0:60:2:1:0:0 1/0:4:3:0,3:0,1:0.75:0,0:29:1:28:1:1:0:60:6:0.75:0:1.3 -5 126841002 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49829;SOR=Inf;LSEQ=AGAGCCAGCCCTTGTTAAAT;RSEQ=ATTCCAGTGCCTGATACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:106,17:0:2,0:24.8:1:31.9:1:1:0:60:60.5:1:0:0.1 0/1:129:2:1,1:109,18:0.0155:2,2:19.5:1:27:1:0.27386:5.92105:60:4:0.0155:0:1 -5 126841016 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=TTAAATGATTCCAGTGCCTG;RSEQ=TACTCACTTGAAATAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:131,27:0:2,0:23.7:1:30.2:1:1:0:60:78:1:0:0.1 0/1:165:2:1,1:128,35:0.0121:2,2:7:1:28:1:0.3898:3.61967:60:4:0.0122:0:1 -5 126841120 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06404;LSEQ=AAAAGGAGTTGGAGAATAGA;RSEQ=GAATGCAGCATCATGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:458:392:170,222:28,36:0.8559:2,2:25.8:1:30.1:1:1:1.01566:60:48:0.8571:0:1.1 0/1:593:163:76,87:196,232:0.2749:2,2:24.5:1:29.4:1:0.92645:1.03:60:26.167:0.2712:0:1.2 -5 126841209 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49985;SOR=Inf;LSEQ=AGTCAGGCCAGGCGCAGTGG;RSEQ=TCACCCCTGTAATCCTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:23,90:0:2,0:20.3:1:30.1:1:1:0:60:226:0.9912:0:0.4 0/1:129:2:1,1:29,97:0.0155:2,2:33.5:1:33:1:0.41523:3.31:60:4:0.0156:0:5 -5 126841213 . CC TG 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4992;SOR=Inf;LSEQ=AGGCCAGGCGCAGTGGTTCA;RSEQ=CCTGTAATCCTAGCATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:20,86:0:2,0:19:1:30.9:1:1:0:60:52:1:0:0.3 0/1:118:2:1,1:24,92:0.0169:2,2:28.5:1:32.3:1:0.38027:3.78:60:4:0.0171:0:4 -5 126841225 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50077;SOR=Inf;LSEQ=GTGGTTCACCCCTGTAATCC;RSEQ=AGCATTTTGGGAGGCCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:6,66:0:2,0:21.1:1:28.5:1:1:0:60:35:1:0:0.1 0/1:86:2:1,1:13,71:0.0233:2,2:17.5:1:32:0:0.30068:5.30:60:4:0.0233:0:4 -5 126841230 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49897;SOR=Inf;LSEQ=TCACCCCTGTAATCCTAGCA;RSEQ=TTTGGGAGGCCGAGGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:4,61:0:2,0:21.6:1:29.9:1:1:0:59.4:20.667:1:0:0.2 0/1:75:2:1,1:9,64:0.0267:2,2:12.5:1:33:0:0.25045:6.80:60:4:0.0267:0:4 -5 127195983 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17595;SOR=Inf;LSEQ=ATACTCCATAAATGTTTGTT;RSEQ=AATAGAACTAAATTATTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:125,39:0:2,0:24.1:1:31.8:1:1:0:60:163:1:0:0.1 0/1:119:2:1,1:92,25:0.0168:2,2:31:1:27.5:1:0.39069:3.62849:60:4:0.0168:0:1 -5 127196035 . C T 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12588;SOR=0;LSEQ=AACAAGCTCTTTCTAATGAG;RSEQ=TGTATCCTCTCTTAAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:4:1,3:179,161:0.0116:2,2:17.8:1:27.3:1:0.35103:3.32464:60:8:0.0117:0:1.5 0/0:310:0:0,0:168,142:0:2,0:24.5:1:31.6:1:1:0:60:43.286:1:0:0.5 -5 127196066 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.09244;LSEQ=CTTAAAATTTTCTCTGCTTT;RSEQ=GAAAGTTTAACCCGGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:21:12,9:171,184:0.0559:2,2:25.2:1:29.9:1:0.50314:1.43:60:42:0.0572:0:1.1 0/1:371:169:89,80:99,103:0.4555:2,2:27.6:1:29:1:0.53185:1.16:60:338:0.458:0:1.1 -5 127792031 . G A 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GGAGGGGTGGCTGCAGTCTC;RSEQ=GGATCAGCAGACTTAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:35:1:32:0:1:1.7321:60:4:0.4:0:1 0/0:3:0:0,0:3,0:0:0,0:24:1:28:1:1:0:60:6:1:0:0.3 -5 129976931 . A G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAGTTTGCAAGAAATAAC;RSEQ=AAATCTATCCTTACTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:16.5:1:31:0:1:0:60:4:1:0:0 0/1:5:2:1,1:2,1:0.4:2,2:33:1:30.5:1:1:1.7321:50:4:0.4:0:2 -5 129976933 . A C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTTTGCAAGAAATAACAA;RSEQ=ATCTATCCTTACTCTACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:18.5:1:31:0:1:0:60:4:1:0:0 0/1:5:2:1,1:2,1:0.4:2,2:35:1:31:1:1:1.7321:50:4:0.4:0:2 -5 129977114 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21871;SOR=0;LSEQ=ACTGACCGGCATTTACAGGA;RSEQ=AAGGCTTCTGAAATCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:37,23:0.0323:2,2:24:1:28.5:1:1:1.59591:51:4:0.0333:0:1 0/0:70:0:0,0:39,31:0:2,0:24.6:1:31:1:1:0:60:140:1:0:0.1 -5 129977136 . A T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21217;SOR=0;LSEQ=AGGCTTCTGAAATCAGACAA;RSEQ=GCCTTTCAAACTCTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:2,0:54,41:0.0206:2,0:12.5:1:32.5:1:0.50687:0:25:4:0.0211:0:4.5 0/0:113:0:0,0:61,52:0:2,0:23.6:1:30.1:1:1:0:59.2:112:1:0:0.2 -5 129977167 . A G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19685;SOR=0;LSEQ=CTCTTATACCAACCTCTGGA;RSEQ=TTGGGCAACATGGCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:2,0:42,53:0.0206:2,0:42.5:1:33.5:1:0.20318:0:25:4:0.0206:0:4.5 0/0:121:0:0,0:55,66:0:2,0:28.7:1:29.7:1:1:0:58:39.333:1:0:0.2 -5 129977171 . G A 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08778;SOR=0;LSEQ=TATACCAACCTCTGGAATTG;RSEQ=GCAACATGGCTTCTCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:3:2,1:41,53:0.0309:2,2:29.7:1:30:1:0.58266:2.56:26:6:0.0313:0:4 0/0:120:0:0,0:55,65:0:2,0:28.1:1:30.6:1:1:0:58:119:1:0:0.2 -5 129977173 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19822;SOR=0;LSEQ=TACCAACCTCTGGAATTGGG;RSEQ=AACATGGCTTCTCCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:40,53:0.0208:2,2:37:1:26:1:1:1.32:60:4:0.0211:0:1.5 0/0:119:0:0,0:54,65:0:2,0:27.6:1:32:1:1:0:58:118:1:0:0.2 -5 129977185 . TC T 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.08258;SOR=0;LSEQ=GAATTGGGCAACATGGCTTC;RSEQ=CCCTTTCTAGGTCCCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:3:2,1:32,47:0.0366:2,2:30.3:1:32:1:0.56694:2.90:26:6:0.037:0:4 0/0:105:0:0,0:44,61:0:2,0:24.4:1:30.8:1:1:0:57.6:104:1:0:0.3 -5 129977203 . T C 60 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11999;SOR=0;LSEQ=TCTCCCCTTTCTAGGTCCCA;RSEQ=GGCAGCCATCTTGCTATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:4:2,2:28,42:0.0541:2,2:22:1:30:1:1:1.49:25:8:0.0556:0:4.5 0/0:72:0:0,0:30,41:0:2,0:21.4:1:29.9:1:1:0:58.4:142:1:0:0.1 -5 129977226 . A G 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24098;SOR=0;LSEQ=CAGCCATCTTGCTATTACTC;RSEQ=CCTTTGGGCCCTGTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:3:1,2:8,30:0.0732:2,2:28:1:30:1:0.53471:1.84:26:6:0.0732:0:4.3 0/0:39:0:0,0:14,25:0:2,0:16.6:1:28.7:1:1:0:56.3:38:1:0:0.2 -5 131281244 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51538;SOR=Inf;LSEQ=ACGGGTGCCTCTGGACTCTC;RSEQ=ATGGCCTGCCTTCCTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:0:2,0:24.2:1:30.1:1:1:0:60:84:1:0:0.1 0/1:63:2:1,1:35,26:0.0317:2,2:25.5:1:28.5:1:1:1.33971:60:4:0.0317:0:1.5 -5 131281346 . G T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.23333;SOR=0;LSEQ=CTAATCGAGCGAAAGCAAAA;RSEQ=CCCCAGAACTGGAGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:6,14:0.0909:2,2:20:0:29.5:1:1:2.24:60:4:0.0952:0:1 0/0:23:0:0,0:7,16:0:2,0:16.3:1:32:1:1:0:60:46:1:0:0.3 -5 131892979 . G A 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05698;LSEQ=CCTCAGTTAAGCCTTTGTGG;RSEQ=CTCCAGGTCCCTGGTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:458:456:341,115:1,0:0.9956:0,2:24.7:1:29.4:1:1:0:60:40.455:0.9978:0:1.1 1/1:484:482:322,160:0,0:0.9959:0,2:23:1:28.7:1:1:0:60:119.5:0.9979:0:1.1 -5 131893329 . T C 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAGTTTGCCTGAAGCAGTC;RSEQ=CGGAAGGATGTCCGGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:0,26:0,0:1:0,1:18.3:1:31.4:1:1:0:60:25:1:0:1 1/1:2:2:0,2:0,0:1:0,0:32.5:1:30.5:1:1:0:60:4:1:0:1 -5 131911401 . CT C 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.58965;SOR=2.46112;LSEQ=TTGGGTAAGATTGCTTATGC;RSEQ=TTTTCTCAGAACCAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:1:1,0:114,12:0.0079:2,0:47:0:33:0:1:0:60:2:0.0079:0:0 0/1:104:2:1,1:92,10:0.0192:2,2:33.5:1:30.5:1:0.20127:8.82052:60:4:0.0194:0:0 -5 131911426 . C T 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.12288;SOR=0;LSEQ=TCTCAGAACCAACACTGGTG;RSEQ=TTATTAAAGTAACATAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:4:1,3:131,39:0.023:2,2:10.8:1:27.3:1:0.04411:9.90643:60:8:0.0234:0:1.3 0/0:171:0:0,0:136,35:0:2,0:23.5:1:32:1:1:0:60:342:1:0:0.1 -5 131911847 . G C 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACAGCCTCCTCCACTAT;RSEQ=AACATTTGATTTTTTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:0.25:0,0:19.3:1:31.7:1:1:0:60:6:0.3:0:1 0/0:2:0:0,0:0,2:0:0,0:22:1:24:1:1:0:54.5:1:1:0:3.5 -5 131914904 . CT C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.67106;SOR=1.70354;LSEQ=TAACGGGATAGGTGAAGGGC;RSEQ=TTTTTTTTATTCTTTTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:3:3,0:77,0:0.0375:1,0:20.3:1:32:1:1:0:60:6:0.0375:0.0125:0.3 0/1:48:3:3,0:45,0:0.0625:1,0:6.3:1:31.6:1:1:0:60:6:0.0625:0.0417:0 -5 131915213 . G A 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00076;SOR=0.49882;LSEQ=AGGTTTGTAACCCTTAAATA;RSEQ=ACTTTGTAGTCCATTAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:88:25,63:79,149:0.2785:2,2:25.9:1:30.1:1:0.35003:1.33491:60:28.333:0.2733:0:1.1 0/1:279:45:16,29:82,152:0.1613:2,2:24.1:1:28.2:1:1:1.02:60:14:0.1533:0:1.1 -5 131915317 . T C 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15636;SOR=0.36756;LSEQ=TCATCAGTTACTACCTCTCA;RSEQ=CCAGCAGCAACCATTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:14:1,13:2,37:0.2642:2,1:23.6:1:31.5:1:1:1.41:60:28:0.2692:0:1.5 0/1:26:3:0,3:1,22:0.1154:1,0:31.3:1:32.7:1:1:0:60:6:0.12:0:1.3 -5 131915526 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19524;SOR=Inf;LSEQ=CATAATTTACTTTGCCAGAA;RSEQ=TTTGATTTTTGTTTCATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:123,33:0:2,0:23.4:1:30.5:1:1:0:60:77:1:0:0.1 0/1:124:2:1,1:90,32:0.0161:2,2:30.5:1:33:0:0.46302:2.7849:60:4:0.0163:0:1 -5 131923393 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.34771;SOR=3.37993;LSEQ=AATGGAAAAGGTTTGTGGTG;RSEQ=TAGAATTTTGTTCTGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:1,0:102,178:0.0036:2,0:1:0:25:0:0.36655:0:60:2:0.0036:0:1 0/1:251:3:1,2:102,146:0.012:2,2:30.7:1:29:1:1:1.39547:60:6:0.0121:0:1 -5 131923408 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21822;SOR=Inf;LSEQ=TGGTGGTAGAATTTTGTTCT;RSEQ=CTTCAAAATTTTGGGATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:69,154:0:2,0:25.6:1:32.3:1:1:0:60:222:1:0:0.1 0/1:196:2:1,1:65,129:0.0102:2,2:8:0:30.5:1:1:1.98:60:4:0.0103:0:1.5 -5 131923532 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53226;SOR=0;LSEQ=AAAATGAAGGATATTGAATA;RSEQ=GGTTTGGTTTATATTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:111,34:0.0136:2,2:17:1:33.5:1:0.42074:3.23218:60:4:0.0142:0:1 0/0:86:0:0,0:68,18:0:2,0:23:1:30.5:1:1:0:60:42:1:0:0.1 -5 131923555 . T C 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58645;SOR=2.52375;LSEQ=TTTGGTTTATATTTGATACC;RSEQ=CAAAGTGATCATATTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:1,0:145,41:0.0053:2,0:6:0:15:0:1:0:60:0:0:0:4 0/1:149:2:1,1:113,34:0.0134:2,2:19.5:1:28:1:0.41584:3.29014:60:4:0.0136:0:1 -5 131923604 . G T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04774;SOR=Inf;LSEQ=ACATTAAAGCTTTTTATTTT;RSEQ=GTGTTACACAGGTTTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:260,111:0:2,0:23.9:1:31.6:1:1:0:60:45.375:1:0:0.1 0/1:328:4:1,3:209,115:0.0122:2,2:17.3:1:28:1:0.13459:5.4235:60:8:0.0123:0:1 -5 131924341 . C T 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0153;SOR=9.22635;LSEQ=TATCTCAACTTTTTAAGCAC;RSEQ=AGTTGAAAAAAAAATTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:1,0:109,13:0.0081:2,0:46:0:16:0:1:0:60:0:0:0:7 0/1:113:8:6,2:93,12:0.0708:2,2:18.3:1:28.4:1:0.25815:2.55455:60:16:0.0721:0:1 -5 131924346 . G GA 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.06481;LSEQ=CAACTTTTTAAGCACCAGTT;RSEQ=AAAAAAAAATTATGAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:2,0:113,18:0.015:2,0:40.5:1:29.5:1:1:0:60:4:0.0154:0:0 0/1:125:2:1,1:106,16:0.016:2,2:11:0:31:0:0.25636:6.45744:60:4:0.0163:0:1 -5 131924362 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.2482;SOR=Inf;LSEQ=AGTTGAAAAAAAAATTATGA;RSEQ=ATTTTTTTTTTAAAAGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:144,32:0:2,0:23.8:1:31.5:1:1:0:60:34.2:1:0:0.3 0/1:184:3:1,2:142,39:0.0163:2,2:22:1:25.3:1:0.12524:7.17795:60:6:0.0167:0:1.7 -5 131924363 . A AT 104 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.64031;SOR=1.33533;LSEQ=GTTGAAAAAAAAATTATGAG;RSEQ=TTTTTTTTTTAAAAGGTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:8:7,1:138,32:0.0442:2,2:25.6:1:31.9:1:1:1.62:60:16:0.0471:0.0055:0 0/1:189:11:8,3:137,41:0.0582:2,2:20.5:1:30.1:1:0.7199:1.25148:60:22:0.0615:0.0053:0.2 -5 131924374 . A T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00537;SOR=0;LSEQ=AATTATGAGATTTTTTTTTT;RSEQ=AAAGGTCGTCTACAGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:7:3,4:175,48:0.0304:2,2:9.7:1:24.6:1:0.04787:4.81737:60:6:0.0271:0:1 0/0:252:0:0,0:181,70:0:2,0:21.7:1:27.9:1:1:0:59.9:49.2:0.996:0:0.2 -5 131924620 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49902;SOR=Inf;LSEQ=TATTTTGTTTGCATCATATT;RSEQ=TCTACTTGAATTGTTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:39,143:0:2,0:22.6:1:31.9:1:1:0:60:90:1:0:0.1 0/1:192:2:1,1:46,144:0.0104:2,2:36:1:28.5:1:0.43063:3.11:60:4:0.0105:0:1 -5 131925174 . A C 102 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05485;SOR=0.12688;LSEQ=CACAATGATAAAATTGCCTA;RSEQ=TGATGCATTTCTTGGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:13,0:0.4091:1,0:28.2:1:32.2:1:1:0:60:18:0.4091:0:2 0/1:13:1:1,0:12,0:0.0769:0,0:6:0:32:0:1:0:60:2:0.0769:0:1 -5 131925187 . T C 93 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11941;SOR=0.16676;LSEQ=TTGCCTAATGATGCATTTCT;RSEQ=GGAATATATCCCTGCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:8,0:18,0:0.3077:1,0:31.6:1:31.1:1:1:0:60:16:0.3077:0:2.1 0/1:15:1:1,0:14,0:0.0667:1,0:13:0:32:0:1:0:60:2:0.0667:0:1 -5 131925599 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52459;SOR=0;LSEQ=GAAGTATTTTGTCTATTTTT;RSEQ=ATCCTAAGATTATAGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:7,113:0.0164:2,2:6.5:1:27.5:1:0.12735:15.17:60:4:0.0165:0:1 0/0:76:0:0,0:5,71:0:2,0:24.5:1:31.3:1:1:0:60:152:1:0:0 -5 131927191 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15266;SOR=Inf;LSEQ=AGACTATAAGGTATTAAGTT;RSEQ=GTATTGACTATATTTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:3,135:0:1,0:25.2:1:31.3:1:1:0:60:137:1:0:0 0/1:89:2:1,1:0,87:0.0225:1,2:6:1:29.5:1:0.02247:0:60:4:0.0225:0:1 -5 131927550 . AT A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.0639;SOR=2.07101;LSEQ=ATAGACTTTATTTTTAAAAG;RSEQ=TTTTTTTTTACCTATAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:14:10,4:174,65:0.0551:2,2:31.6:1:31.9:1:1:1.07048:60:28:0.0558:0:0 0/1:176:19:17,2:114,43:0.108:2,2:24.9:1:30.8:1:0.16332:3.19:60:38:0.1086:0.0284:0.2 -5 131931451 . TA T 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16707;SOR=1.72865;LSEQ=CAAGTCAACAGAATCAGAGC;RSEQ=AAAAAAAAGGAAAAGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:12:7,5:177,276:0.0258:2,2:31.7:1:31.3:1:0.23294:2.18:60:24:0.0265:0:0.1 0/1:525:23:8,15:217,285:0.0438:2,2:22:1:31:1:0.52038:1.42669:60:46:0.0442:0.0057:0.1 -5 131938959 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24955;SOR=0;LSEQ=TCTAACTGTGAGAAACATCA;RSEQ=ATACTTTATTTTTAATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:3:1,2:122,41:0.0181:2,2:9:1:27.3:1:0.16484:5.87312:60:6:0.0185:0:1 0/0:150:0:0,0:101,49:0:2,0:21.9:1:31.1:1:1:0:60:74:1:0:0.1 -5 131939240 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1676;SOR=Inf;LSEQ=CCATGGTGGCTTGAATTTGA;RSEQ=GTGTGAGAGTTAAAAATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:37,183:0:2,0:23.2:1:30.8:1:1:0:60:43:1:0:0.1 0/1:153:2:1,1:20,131:0.0131:2,2:23.5:1:29.5:1:0.25645:6.42:60:4:0.0133:0:1 -5 131939904 . T G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09603;SOR=0.33029;LSEQ=CTTCTCTTTGTTCTCTTACT;RSEQ=TGCACAACAGATTTTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:16:0,16:1,25:0.381:1,1:26:1:28.9:1:1:0:60:4.333:0.3421:0:1.1 0/1:24:4:0,4:0,20:0.1667:1,0:15:1:31.8:1:1:0:60:8:0.1667:0:1 -5 131944129 . G A 54 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76351;LSEQ=TTCTCTGTGTCTGTTTGCTC;RSEQ=TTTGAAATATAGGACTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:27.3:1:27:1:1:0:60:3:0.3333:0:1.5 0/1:6:2:2,0:4,0:0.3333:0,0:22:1:32:0:1:0:60:4:0.4:0:1 -5 131944381 . C CA 78 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24173;SOR=2.27285;LSEQ=GAAAAAGAAGAATTAATCAA;RSEQ=AAAAAAAATACAAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:3:3,0:175,191:0.0081:2,0:13.7:1:28:1:0.11127:0:60:6:0.0082:0.0027:2 0/1:437:8:4,4:206,223:0.0183:2,2:17.6:1:26.3:1:1:1.08:60:7:0.0164:0.0069:1 -5 131944452 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22775;SOR=Inf;LSEQ=ATATATTTACTTATCAAATA;RSEQ=CTGTATTAAACTTATGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:37,118:0:2,0:25.6:1:30.1:1:1:0:60:310:1:0:0.1 0/1:142:2:1,1:33,106:0.0141:2,2:23:1:27.5:1:0.42543:3.18:60:4:0.0149:0:1 -5 131944592 . A G 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01742;SOR=Inf;LSEQ=TAGAACAAGGATTTGATGTA;RSEQ=ATTATTTTGCTGCTTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:16,20:0:2,0:28.2:1:30.7:1:1:0:60:72:1:0:0 0/1:6:2:0,2:1,3:0.3333:2,0:28:1:33:0:1:0:60:4:0.3333:0:1 -5 131944771 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49837;SOR=0;LSEQ=CTCCTGTTATGTGCCCTTAA;RSEQ=TACAACCAGTGTAAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:2,0:100,45:0.0136:2,0:32.5:1:32.5:1:1:0:60:4:0.0138:0:1 0/0:143:0:0,0:96,47:0:2,0:25.3:1:31.5:1:1:0:60:70.5:1:0:0.1 -5 131944806 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62486;SOR=2.76746;LSEQ=ATTTAATGAATATTTTTCTA;RSEQ=AGCTGAATGATATTAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:133,99:0.0043:2,0:1:0:23:0:0.42918:0:60:2:0.0043:0:1 0/1:254:3:1,2:146,105:0.0118:2,2:11.3:1:27.7:1:0.57458:2.7698:60:6:0.0119:0:1 -5 131944811 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24997;SOR=Inf;LSEQ=ATGAATATTTTTCTACAGCT;RSEQ=AATGATATTAAAGAGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:145,113:0:2,0:22.4:1:31.6:1:1:0:60:516:1:0:0.1 0/1:281:3:1,2:157,121:0.0107:2,2:18:1:28:1:0.58302:2.58637:60:6:0.0108:0:1.3 -5 131945121 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06066;SOR=Inf;LSEQ=TGCTTATGATATCACTTACA;RSEQ=CTATGACATTCTTTTCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:30,137:0:2,0:21.8:1:31.4:1:1:0:60:54.667:0.982:0:0.1 0/1:169:4:1,3:35,130:0.0237:2,2:22:1:29.5:1:1:1.24:60:8:0.024:0:1 -5 131951880 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51541;SOR=0;LSEQ=CTTTATTACTGGAATGTGAA;RSEQ=AATATTAAATACCTGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:0,2:14,117:0.015:2,0:32.5:1:29.5:1:1:0:60:4:0.0152:0:1 0/0:91:0:0,0:13,78:0:2,0:20.4:1:31.2:1:1:0:60:182:1:0:0 -5 131951996 . T C 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.26632;SOR=0;LSEQ=CATGGCCTTAAGAACTTTAT;RSEQ=ACTGAAGAAGTGATATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:0.3333:0,0:14.8:1:31.6:1:1:0:60:10:0.3333:0:1.4 0/0:5:0:0,0:0,5:0:0,0:18.8:1:29.6:1:1:0:60:10:1:0:0.2 -5 131952072 . C T 69 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTATTGAACATGCTTAG;RSEQ=CCCCATACATCTGCTAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:18.8:1:30:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 131953510 . A G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAACTTTATCAGTGATC;RSEQ=CATGCTATGAGGGTTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:30.5:1:31.5:1:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:1,0:0:0,0:12:0:25:0:1:0:60:2:1:0:0 -5 131954027 . T A 42 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05266;SOR=0;LSEQ=TTTCTTATTGCAGTTAATAT;RSEQ=AACTAACATACTTTAGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:4:3,1:32,154:0.0211:2,2:8.8:1:21.3:1:0.02028:14.14:60:3:0.0161:0:1.3 0/0:205:0:0,0:45,160:0:2,0:23.2:1:28.4:1:1:0:60:204:1:0:0.1 -5 131972916 . A G 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTACCATGGTGTATCACAA;RSEQ=TGCTCTTTCCAAAGCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:0:0,0:179,315:0:2,0:25.5:1:30.5:1:1:0:60:122.5:1:0:0.1 0/1:424:25:11,14:156,243:0.059:2,2:24.8:1:31.6:1:0.67547:1.22:60:50:0.0594:0:1.2 -5 131973004 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1511;SOR=Inf;LSEQ=CTGGACCCCTTTCTAAGCAT;RSEQ=TCTTTGAGATTTTCTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:1,102:0:1,0:27.1:1:32.9:1:1:0:60:206:1:0:0.1 0/1:66:2:0,2:1,63:0.0303:1,0:7:1:28:1:1:0:60:4:0.0308:0:1 -5 131973221 . C CT 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTTTTTTTTTTCTTTTT;RSEQ=TTTTTTTTTTTTCCAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:20.5:1:30.3:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 131973663 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69573;SOR=0.81963;LSEQ=CACACCAGCCATTGTTTTCC;RSEQ=CTGGTAATGTCAGCCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:22:22,0:37,0:0.3729:1,1:18.7:1:31.5:1:1:0:60:44:0.386:0:1 0/1:55:18:18,0:36,1:0.3273:1,1:28.3:1:30.2:1:1:0:60:17:0.3148:0:1.1 -5 131973683 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23983;SOR=Inf;LSEQ=TCTGGTAATGTCAGCCTCAT;RSEQ=TGTTGTTCCTAGGCTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:79,8:0:2,0:23.2:1:31.3:1:1:0:60:28:1:0:0.2 0/1:84:2:1,1:74,8:0.0238:2,2:17.5:1:30.5:1:0.20396:8.78103:60:4:0.0241:0:1 -5 131974063 . T A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10861;LSEQ=TGAATCAGGCTCAGCTACTA;RSEQ=TATTACACTCTCCTGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:0,9:0,19:0.3103:1,0:23.3:1:30.7:1:1:0:60:18:0.3214:0:1.2 0/1:18:6:0,6:0,12:0.3333:0,0:24.2:1:30.7:1:1:0:60:12:0.3333:0:1 -5 131976302 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23409;LSEQ=GAAAAGATCATGTCAGGACT;RSEQ=CTTGCCTGCCATGAGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:3:2,1:231,69:0.0099:2,2:19.3:1:29.3:1:0.54664:1.6707:60:6:0.01:0:1 0/1:246:3:1,2:185,58:0.0122:2,2:18:1:28:1:0.14828:6.31879:60:6:0.0123:0:1 -5 131976594 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50666;SOR=0;LSEQ=CAAGAGAGTTCTGTGATGAA;RSEQ=ACGTTCTCTAGCTGTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:5,164:0.0117:1,2:6.5:1:31:0:0.06914:30.03:60:4:0.012:0:1 0/0:132:0:0,0:5,126:0:1,0:22.1:1:30.3:1:1:0:60:64.5:1:0:0 -5 131977963 . T C 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTTTTAGGACGTTCTGAATA;RSEQ=GTGGAGAAATTCTACAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:698:0:0,0:326,371:0:2,0:23.9:1:30.5:1:1:0:60:98.571:0.9986:0:0.1 0/1:629:26:16,10:299,304:0.0413:2,2:26.7:1:30.8:1:0.31668:1.63:60:52:0.0416:0:1.2 -5 131978076 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10025;SOR=Inf;LSEQ=AAAATATCCAAGATTTAAAT;RSEQ=CCATAGAAATGTAGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:73,213:0:2,0:22.6:1:31.7:1:1:0:60:70.5:0.9965:0:0.1 0/1:250:3:1,2:69,177:0.012:2,2:25.3:1:28.7:1:1:1.28:60:6:0.0123:0:1 -5 133478341 . G A 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGCACACTCTAGGCCCAC;RSEQ=CTAGAGGAGGAGGCTGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:12:1:31.7:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 133478359 . A C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=ACGCTAGAGGAGGAGGCTGC;RSEQ=ATTAGGTGGGCACTCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18:1:33:0:1:0:60:6:1:0:2.3 0/0:2:0:0,0:2,0:0:0,0:12:1:31.5:1:1:0:60:4:1:0:0 -5 133478475 . C T 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=CCAACCATCAAGAAGCCCCT;RSEQ=AATGCCTTCATGCTGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:10,2:2,0:0.8571:0,2:22.8:1:29.8:1:1:0:60:24:0.8571:0:1.2 0/0:10:0:0,0:6,4:0:2,0:20.6:1:31.3:1:1:0:60:20:1:0:0 -5 133478708 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=ACGCGCTGTCGCGAGAAGAG;RSEQ=AGGCCAAGTACTATGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:25.3:1:32.4:1:1:0:60:22:1:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:28.5:1:26.5:1:1:2.44949:60:4:0.3333:0:1 -5 133908289 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50904;SOR=0;LSEQ=AAGACCCTGGTGGGACCCAG;RSEQ=ATTCAAGCTGAGCAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:94,43:0.0144:2,2:35:1:32:1:0.53446:2.17257:60:4:0.0145:0:1 0/0:103:0:0,0:71,31:0:2,0:23:1:30.5:1:1:0:60:101:1:0:0.6 -5 133908311 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50323;SOR=0;LSEQ=TTCAAGCTGAGCAGCTTTGG;RSEQ=CAACTGTCCCTGATAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:115,70:0.0107:2,2:8:1:29.5:1:1:1.63826:60:4:0.011:0:2 0/0:154:0:0,0:90,64:0:2,0:23.9:1:30.9:1:1:0:60:50.333:1:0:0.9 -5 133908361 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=18.26316;LSEQ=CTGTGCTGAAGACCAAGGAA;RSEQ=TGTCTCAAGGGAGGGGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:90:49,41:96,91:0.3249:2,2:25:1:30.4:1:0.70027:1.13:60:89:0.3236:0:1.9 1/1:207:186:89,97:9,12:0.8986:2,2:25:1:29.9:1:0.81838:1.22:60:185:0.8981:0:1.8 -5 133908378 . G C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.3328;LSEQ=GAAGTGTCTCAAGGGAGGGG;RSEQ=CTTGGTCTTGGCTTCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:91:45,46:87,95:0.3333:2,2:23.7:1:30.9:1:0.79892:1.07:60:21.75:0.3271:0:1.9 1/0:211:132:61,71:34,43:0.6256:2,2:25:1:31.6:1:0.88557:1.09:60:65:0.628:0:2.1 -5 133908395 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18536;SOR=Inf;LSEQ=GGGGCTTGGTCTTGGCTTCA;RSEQ=AAGTGTGGCCTGCCCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:111,137:0:2,0:26.5:1:31.8:1:1:0:60:247:1:0:0.7 0/1:188:2:1,1:76,110:0.0106:2,2:36:0:30.5:1:1:1.44:60:4:0.0107:0:3 -5 133908406 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17789;SOR=Inf;LSEQ=TTGGCTTCAGAAGTGTGGCC;RSEQ=GCCCTGAGAGCAGCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:96,135:0:2,0:25.3:1:30.4:1:1:0:60:76:1:0:0.6 0/1:169:2:1,1:65,102:0.0118:2,2:16:1:28:1:1:1.56:60:4:0.012:0:2 -5 133908443 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1704;SOR=Inf;LSEQ=GGGAGGGATGGCCCACTGGG;RSEQ=TAAGGTGCCAGGTGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:33,99:0:2,0:23.3:1:31.9:1:1:0:60:264:0.9925:0:0.4 0/1:94:2:1,1:28,64:0.0213:2,2:33.5:1:28:1:0.52414:2.26:60:4:0.0215:0:1.5 -5 133908456 . T A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50472;SOR=0;LSEQ=CACTGGGGTAAGGTGCCAGG;RSEQ=GGGCAGGCAGTAGCATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:17,82:0.0198:2,2:14:1:27:1:0.32614:4.72:60:4:0.0204:0:1.5 0/0:79:0:0,0:23,56:0:2,0:22.1:1:28.7:1:1:0:59.8:25.333:1:0:0.6 -5 134389581 . C T 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30842;SOR=4.43119;LSEQ=CACTGGGGTTGCGCAGAGAG;RSEQ=TGGTGGCAGATCCAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:1,0:202,47:0.004:2,0:17:0:12:0:1:0:60:0:0:0:3 0/1:171:3:2,1:115,52:0.0175:2,2:26:1:24.3:1:1:1.1051:60:2:0.012:0:2.3 -5 134389689 . G T 207 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTAGGGGATGTGCAGGCT;RSEQ=CTGTGGTGGTGACCCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:612:0:0,0:277,334:0:2,0:27.1:1:31.9:1:1:0:60:75.375:0.9983:0:0.1 0/1:520:139:64,75:183,197:0.2673:2,2:27.5:1:29.2:1:0.69222:1.08841:60:68.5:0.266:0:1.1 -5 134389729 . C A 44 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18008;SOR=4.93099;LSEQ=GAGGCCAGGTGGGGGAAGCC;RSEQ=TTGTGTCTGCCTGGTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:1:1,0:124,286:0.0024:2,0:1:0:26:0:0.30414:0:60:2:0.0025:0:1 0/1:336:4:3,1:117,215:0.0119:2,2:12.8:1:22:1:0.13204:5.48:60:3:0.0091:0:1.3 -5 134389752 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17945;SOR=Inf;LSEQ=GTGTCTGCCTGGTGCCTGTA;RSEQ=TATATTTGAATTATCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:56,209:0:2,0:23.9:1:30.8:1:1:0:60:131.5:1:0:0.1 0/1:196:2:1,1:51,143:0.0102:2,2:19:1:29.5:1:0.46122:2.79:60:4:0.0103:0:1 -5 135406459 . G C 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00555;SOR=0.13968;LSEQ=CTGAGAAAGGTCACCCCTGG;RSEQ=TCAGCAGGCCCCAACTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:39:39,0:3,0:0.9286:0,1:24.6:1:31.6:1:1:0:60:38:0.9268:0:1.5 1/0:22:14:13,1:8,0:0.6364:0,1:26.1:1:33.4:1:1:0:60:28:0.6364:0:1.3 -5 135406534 . A G 216 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03341;LSEQ=TGATGAGTCACACTGCAGAA;RSEQ=GGCTGCTTCATCTTTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:125:102,23:5,1:0.9542:2,2:21:1:31.1:1:1:1.12645:60:30.25:0.9528:0:1.2 0/1:123:50:38,12:56,17:0.4065:2,2:26.3:1:31.9:1:1:1.03994:60:100:0.4065:0:1.2 -5 135406560 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24808;SOR=Inf;LSEQ=CTTCATCTTTAGCAGGTGAC;RSEQ=CCACCCTCTAACCCTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:134,62:0:2,0:24.8:1:30.3:1:1:0:60:64.333:1:0:0.7 0/1:195:2:1,1:129,64:0.0103:2,2:23:0:32.5:1:1:2.00786:60:4:0.0104:0:1.5 -5 135406658 . G A 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03779;LSEQ=GAAGAAAGTCTGAGATTTGG;RSEQ=AGTAGCAGAGACAGAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:307:294:131,163:6,7:0.9577:2,2:24.4:1:30:1:1:1.06628:60:97:0.9572:0:1.1 0/1:385:177:82,95:96,110:0.4597:2,2:22.2:1:28.7:1:1:1.01106:60:58:0.4579:0:1.1 -5 135406781 . C T 139 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=75.54612;LSEQ=GTGGGGCGGGTGAGTCCCTG;RSEQ=GGCTTCTTGGCAACAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:0,1:10,81:0.0109:2,0:29:0:27:0:1:0:60:2:0.0111:0:1 0/1:52:24:2,22:4,24:0.4615:2,2:19.3:1:30.4:1:0.67431:1.81273:60:48:0.4615:0:1.1 -5 135406894 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.19118;SOR=0.15819;LSEQ=CCAGAATCGGAGGGTGAGGG;RSEQ=AAAAGCCCTGCTAGAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:0,11:0,1:0.9167:0,0:28.8:1:30.5:1:1:0:60:10:0.9091:0:1.3 1/0:5:3:0,3:0,2:0.6:0,0:21.3:1:28.3:1:1:0:60:6:0.6:0:1.3 -5 135535192 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTAGAAAGACTTGGTCTG;RSEQ=GTCAGCAATAAGCTCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:17,5:0.0833:2,2:15.5:1:29.5:1:0.44565:3.19373:60:4:0.087:0:1.5 0/0:9:0:0,0:7,2:0:2,0:35.1:1:29.3:1:1:0:60:18:1:0:0 -5 135535242 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19522;SOR=Inf;LSEQ=TGCCTTCTCTCTGCATCCTC;RSEQ=GGAGTCAGCGGTCTGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:41,18:0:2,0:29.6:1:30.6:1:1:0:60:58:0.9831:0:0.2 0/1:48:2:1,1:30,16:0.0417:2,2:43:0:31:1:1:1.84915:60:4:0.0417:0:1.5 -5 135535267 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50899;SOR=0;LSEQ=TCAGCGGTCTGGGCCAGCCT;RSEQ=CGGCGGGCTGAAGCTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:36,30:0.0294:2,2:35.5:1:30:1:1:1.19677:60:4:0.0303:0:1 0/0:49:0:0,0:26,23:0:2,0:28.6:1:30.8:1:1:0:60:23.5:1:0:0.2 -5 135535272 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17707;SOR=Inf;LSEQ=GGTCTGGGCCAGCCTGCGGC;RSEQ=GGCTGAAGCTGGGAGAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:35,29:0:2,0:25.9:1:29.8:1:1:0:60:63:1:0:0.1 0/1:47:2:1,1:24,21:0.0426:2,2:26.5:1:28:1:1:1.1396:60:4:0.0444:0:1 -5 136191507 . C T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20567;SOR=Inf;LSEQ=GGCTTTGTATACAATGAGGA;RSEQ=TAAGAAAAGTGTTAGTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:117,27:0:2,0:23.3:1:32:1:1:0:60:71:1:0:0.1 0/1:120:2:1,1:90,28:0.0167:2,2:7:0:27:1:0.42647:3.17587:60:4:0.0168:0:1.5 -5 136191512 . A G 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTATACAATGAGGACTAAG;RSEQ=AAAGTGTTAGTTCATTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:121,35:0:2,0:23.5:1:29.7:1:1:0:60:38:0.9935:0:0.1 0/1:136:43:30,13:65,26:0.3162:2,2:25.3:1:31.1:1:0.84131:1.08268:60:86:0.3209:0:1.1 -5 136191583 . A G 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGTGAGAACAACTGAATG;RSEQ=GGTAGGGAATTTAAATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:195,168:0:2,0:26.1:1:30:1:1:0:60:35.3:1:0:0.1 0/1:327:17:10,7:150,160:0.052:2,2:33.4:1:29.6:1:0.46107:1.52:60:16:0.0494:0:1.8 -5 136191604 . T A 43 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04343;SOR=Inf;LSEQ=GGTAGGGAATTTAAATGCAT;RSEQ=GTTTGAAATTTCATTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:190,187:0:2,0:25.5:1:30.1:1:1:0:60:74.4:1:0:0.1 0/1:319:4:3,1:149,166:0.0125:2,2:15.5:1:21.5:1:0.35062:3.33:60:3:0.0096:0:2.3 -5 136191624 . A G 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTTGAAATTTCATTAATG;RSEQ=GGTGCATTTAATGACAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:172,201:0:2,0:24.9:1:30.5:1:1:0:60:73.6:1:0:0.1 0/1:280:77:33,44:93,109:0.275:2,2:22.2:1:30.2:1:0.68724:1.13709:60:76:0.2754:0:1.2 -5 136191628 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.077;SOR=Inf;LSEQ=TGAAATTTCATTAATGAGGT;RSEQ=CATTTAATGACAGTGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:168,198:0:2,0:25:1:32:1:1:0:60:121:1:0:0.1 0/1:272:3:2,1:119,150:0.011:2,2:17.3:1:25.3:1:0.58688:2.51:60:2:0.0075:0:2.7 -5 136191651 . G A 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAATGACAGTGGGAACAT;RSEQ=CATAAAGGAGACTTAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:130,196:0:2,0:24.6:1:31.9:1:1:0:60:107.667:1:0:0.1 0/1:210:20:8,12:73,117:0.0952:2,2:21.2:1:28.6:1:1:1.07:60:40:0.0962:0:1.1 -5 137222330 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50317;SOR=0;LSEQ=ATACAAACACAGACACACCC;RSEQ=AGTGAATGACAGGGACCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:108,83:0.0103:2,2:36:0:31:1:1:1.2994:60:4:0.0105:0:1 0/0:161:0:0,0:91,70:0:2,0:25.1:1:29.7:1:1:0:60:79.5:1:0:0.2 -5 137222354 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.61177;SOR=2.14722;LSEQ=GAATGACAGGGACCATCAGG;RSEQ=GACAGATTGAAGAGCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:1:0,1:92,107:0.005:2,0:7:0:14:0:1:0:60:0:0:0:3 0/1:187:2:1,1:91,94:0.0107:2,2:35.5:1:29:1:1:1.03:60:4:0.0108:0:1.5 -5 137222379 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=0;LSEQ=GATTGAAGAGCAGAGGGAGA;RSEQ=AGCACCCAAGGGGGGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:61,115:0.0112:2,2:21:1:28:1:1:1.88:60:4:0.0114:0:1 0/0:172:0:0,0:72,100:0:2,0:25.7:1:31:1:1:0:60:85:1:0:0.2 -5 137222393 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.49836;SOR=0;LSEQ=GGGAGACAGCACCCAAGGGG;RSEQ=GATGTTTAATTCAAGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:47,100:0.0133:2,2:21:0:31.5:1:0.54199:2.12:60:4:0.0139:0:1.5 0/0:147:0:0,0:56,90:0:2,0:21.3:1:30:1:1:0:60:292:0.9932:0:0.2 -5 137431453 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19467;SOR=0;LSEQ=TTCCCTACCACTGAAGGCAA;RSEQ=CAGAGCCTGGAGGAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:101,86:0.0105:2,2:33.5:1:29.5:1:1:1.17341:60:4:0.0108:0:2.5 0/0:240:0:0,0:131,109:0:2,0:25.1:1:31.8:1:1:0:60:79:1:0:0.4 -5 137431501 . C T 225 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03963;LSEQ=CCCCTATCAGCACGTGAGAT;RSEQ=GCAGAGGAGCAAAGAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:187:178:73,105:3,6:0.9519:2,2:27:1:30.1:1:0.74053:1.39:60:58.333:0.9511:0:1.2 0/1:265:116:57,59:66,79:0.4377:2,2:25.9:1:29.5:1:0.6181:1.16:60:57:0.4335:0:1.1 -5 137431507 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17543;SOR=0;LSEQ=TCAGCACGTGAGATCGCAGA;RSEQ=GAGCAAAGAGTAGACTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:73,110:0.0108:2,2:34.5:1:29.5:1:1:1.50:60:4:0.0109:0:2 0/0:256:0:0,0:120,136:0:2,0:24.4:1:30.8:1:1:0:60:84.333:1:0:0.6 -5 137801686 . G A 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.48943;SOR=0;LSEQ=CGGCGGGGGCGGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,9:0.087:2,2:22:0:28.5:1:1:1.21106:60:4:0.0952:0:1 0/0:21:0:0,0:10,11:0:2,0:24:1:32.6:1:1:0:60:42:1:0:0 -5 137802404 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCGTCCTCCAGTGATTG;RSEQ=TTTCCAGTAACCAGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 138890495 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=CGCCTTTCAAACTCTTATAC;RSEQ=AACCTCTGGAGTTGGGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:10,16:0:2,0:28.8:1:31.5:1:1:0:52:25:1:0:0.1 0/1:30:2:1,1:15,13:0.0667:2,2:11:1:28:1:1:1.14834:45:4:0.0714:0:1 -5 138890548 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51684;SOR=Inf;LSEQ=CTTTCTAGGTCCCATGGCAG;RSEQ=CATCTTGCTATTACTCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:24.1:1:29.9:1:1:0:55.1:7:1:0:0.2 0/1:26:2:1,1:12,12:0.0769:2,2:25:1:26.5:1:1:1:54.5:4:0.08:0:1.5 -5 138890770 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGCAAGGCCCCTTCTTC;RSEQ=CCCCCATCCAGCAGGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:22:1:31.5:1:1:0:53.5:4:0.6667:0:3.5 -5 138890772 . C A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAGGCCCCTTCTTCGC;RSEQ=CCCATCCAGCAGGAAGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:24:1:31:0:1:0:53.5:4:0.6667:0:3.5 -5 138890775 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGCCCCTTCTTCGCCCC;RSEQ=ATCCAGCAGGAAGTAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:27:1:30.5:1:1:0:53.5:4:0.6667:0:3.5 -5 138991568 . C A 35 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64345;SOR=0.47635;LSEQ=TTTTTTTTTTTTTTTTTGAA;RSEQ=ATGAAATGTTTCCCAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:3,0:18,6:0.1111:2,0:43:1:22.3:1:1:0:60:2:0.1:0:6.3 0/1:36:2:2,0:21,13:0.0556:2,0:25:1:20.5:1:0.5254:0:60:1:0.0417:0:5.5 -5 138991655 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21271;SOR=Inf;LSEQ=CATACTTGTTACATATTTGG;RSEQ=ATGAGTTACACATAAGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:30,36:0:2,0:22.6:1:31.3:1:1:0:60:132:1:0:0.1 0/1:57:2:1,1:25,30:0.0351:2,2:15:1:27:1:1:1.20:60:4:0.0364:0:1 -5 139061857 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=CGCAAATGTCCAGAATGGTT;RSEQ=GAAAACAACAGTGGTATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:0.1538:2,2:11:0:31.5:1:1:2.4495:60:4:0.1538:0:1 0/0:14:0:0,0:8,6:0:2,0:18.9:1:30.4:1:1:0:60:28:1:0:0.6 -5 139061927 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=6;SSF=0.50128;SOR=0;LSEQ=CAACCCCAGCCCCAGCCCCA;RSEQ=CCCCAGCCCCAGCCCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:21,15:0.0513:2,2:18.5:1:30.5:1:1:1.38742:60:4:0.0571:0:1.5 0/0:30:0:0,0:14,16:0:2,0:27.6:1:26.8:1:1:0:60:3.286:1:0:0.8 -5 139061932 . A AGCCCCC 24 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=5.000;MSILEN=1;SSF=0.19096;SOR=Inf;LSEQ=CCAGCCCCAGCCCCAGCCCC;RSEQ=GCCCCAGCCCTTCCATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:21,16:0:2,0:21.8:1:28:1:1:0:60:8.25:1:0:0.3 0/1:30:2:2,0:11,16:0.0667:2,0:44.5:1:24.1:1:0.19212:0:60:4:0.08:0:4.5 -5 139517048 . A G 215 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=223.50539;LSEQ=TGTTAGAAGGTATTCAAACT;RSEQ=ACATATGTTGTGCCAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:534:1:1,0:233,300:0.0019:2,0:37:0:33:0:0.4382:0:60:2:0.0019:0:1 0/1:422:125:60,65:134,163:0.2962:2,2:21.7:1:31:1:0.59457:1.12:60:124:0.2959:0:1.1 -5 139517197 . T C 104 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=73.21385;LSEQ=CCTCACTTGAATGCTTGGTA;RSEQ=GTAGTTTGGTACTTAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:1:0,1:1,71:0.0137:1,0:32:0:25:0:1:0:60:2:0.0139:0:1 1/0:21:11:0,11:0,10:0.5238:0,0:22:1:30.1:1:1:0:60:22:0.55:0:1 -5 139781699 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13846;SOR=Inf;LSEQ=ACCGTGAGGCTCTTTGGGGA;RSEQ=GCCGGGCCAGCGTCGGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:0:2,0:21.6:1:32.8:1:1:0:60:32:1:0:0.3 0/1:10:2:1,1:4,4:0.2:2,2:17.5:1:31.5:1:1:1:60:4:0.2:0:1.5 -5 140012528 . AGCG A 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=TGGTCGCAGAGACGTGCACC;RSEQ=GCAGCAGCAGCAGCAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:11.5:1:33:0:1:1.11:60:4:0.0952:0:0.5 0/0:21:0:0,0:10,11:0:2,0:30.5:1:29.6:1:1:0:60:20:1:0:0.2 -5 140012586 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47826;SOR=Inf;LSEQ=CTGGGGAGAGAGCAGAGGTC;RSEQ=AGGAGGCCCCATCCAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:30.8:1:29.1:1:1:0:60:22:1:0:0.1 0/1:12:2:1,1:2,8:0.1667:2,2:25.5:1:26:1:0.45455:3.46:60:4:0.1667:0:1.5 -5 140174865 . G C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCGGAATGTAGCATCCAC;RSEQ=TGGAGGTGATCGTGGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 140176506 . G T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GCCTACTCGTGCTGGTGAAG;RSEQ=ACCACGGCGAACCAGCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:13.2:1:30.4:1:1:0:60:10:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:28.5:1:29:1:1:1:60:4:0.5:0:1 -5 140188401 . A G 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCTCGCGATGCCGGCGTGCC;RSEQ=CCTCTGGGCAGCAACGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:12.5:1:31:0:1:0:60:4:1:0:1 0/1:4:1:1,0:3,0:0.25:0,0:40:0:27:0:1:0:49:2:0.25:0:2 -5 140188575 . G C 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=CGCGCGGTGGATGCTGACTC;RSEQ=GGCTACAACGCGTGGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:11,13:0,0:1:0,2:19.3:1:31:1:1:0:60:48:1:0:1.1 1/1:24:22:9,13:1,1:0.9167:2,2:24.5:1:30.9:1:1:1.42202:60:44:0.9167:0:1.3 -5 140256920 . G C 243 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCGGTCGGCGCGCACATCCC;RSEQ=TTCCACGTGGGGCTGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:218:85,133:58,102:0.5767:2,2:22.7:1:31.3:1:0.59361:1.12:60:71.667:0.5749:0:1.1 0/0:333:0:0,0:115,217:0:2,0:22.3:1:29.6:1:1:0:60:40.5:0.9969:0:0.1 -5 140346468 . T A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02198;SOR=0;LSEQ=CTGCTGCTGCTACCTGGCCC;RSEQ=GCGGCCTCCCAGCTGCGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:23:1:29.3:1:1:1.73:60:6:0.6:0:1.3 0/0:10:0:0,0:4,6:0:2,0:26.1:1:30.2:1:1:0:60:20:1:0:0.3 -5 141876089 . T C 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28737;SOR=Inf;LSEQ=AGATAATTATTTGTTGGAGG;RSEQ=GGTGGCGGCGGTGGCGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:19,4:0:2,0:18:1:29.2:1:1:0:60:46:1:0:0.1 0/1:38:4:2,2:20,14:0.1053:2,2:29.8:1:31.3:1:1:1.41496:60:8:0.1053:0:1.3 -5 142328796 . AG A 31 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=17.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAGAGAGAGGAGAGAGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:18:1:31.8:1:1:0:53.5:4:0.5:0.25:0 0/0:1:0:0,0:1,0:0:0,0:3:0:31:0:1:0:60:2:1:0:0 -5 142328893 . T TTCCTCTC 64 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=2;SSF=1;SOR=0.5163;LSEQ=GAGGCCAAGTGATGAATATG;RSEQ=TCCTCTCTATGAACAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:0.2857:0,0:17.8:1:32.1:1:1:0:57.5:8:0.3333:0.1429:0.5 0/1:6:1:1,0:5,0:0.1667:0,0:15:1:31.5:1:1:0:60:2:0.1667:0.1667:1 -5 142328966 . C T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29915;SOR=0.60682;LSEQ=TAAGCCTTCATTTTTGCCAC;RSEQ=GTCATCTCTCTAACCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:29:28,1:43,0:0.4028:1,1:27.8:1:32.1:1:0.40278:0:59.7:58:0.4028:0:1 0/1:38:11:11,0:26,1:0.2895:1,0:26.6:1:31.4:1:1:0:60:22:0.2895:0:1 -5 142329033 . C T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05512;SOR=Inf;LSEQ=TTGCTATTCTTTGGTTGGGG;RSEQ=CAATATTAATGCATCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:158,67:0:2,0:23.8:1:31.2:1:1:0:60:74:1:0:0.1 0/1:213:4:1,3:160,49:0.0188:2,2:19.3:1:26:1:0.04593:9.66329:60:8:0.0193:0:1 -5 142329054 . C T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03052;SOR=0;LSEQ=CAATATTAATGCATCAGAAT;RSEQ=AGTGTTTGGAAGTTCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:5:2,3:195,118:0.0157:2,2:11.6:1:24.4:1:0.37254:2.47144:60:4:0.0128:0:1 0/0:319:0:0,0:216,103:0:2,0:25.2:1:31:1:1:0:60:78.75:1:0:0.2 -5 142329145 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11668;LSEQ=TCTTTGGCTCAAGACTTTTC;RSEQ=GTACAATGTTCTAAACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:188:88,100:74,99:0.5208:2,2:26.5:1:30.2:1:0.45987:1.18:60:376:0.5251:0:1.1 0/1:401:45:20,25:138,218:0.1122:2,2:28.3:1:29.1:1:0.5181:1.26:60:21.5:0.1091:0:1 -5 142329273 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.30455;SOR=0;LSEQ=ATGAGGGGCAGAGTGGGAGG;RSEQ=AGGTAGCTGGAATGTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:0,4:2,67:0.0548:1,0:25:1:30.8:1:1:0:60:8:0.0563:0:1 0/0:34:0:0,0:1,33:0:1,0:22.2:1:30.9:1:1:0:60:68:1:0:0.1 -5 142689039 . T A 27 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGATATTTGGAGCGCTT;RSEQ=GAGGCCTACGGTGGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:27:1:1:0:60:4:1:0:3 -5 142689062 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCCTACGGTGGAAAAGGTA;RSEQ=TATCTTCACATAAAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:32:1:1:0:60:4:1:0:3 -5 144227881 . T C 134 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00468;SOR=0.06238;LSEQ=GAGGTTAAAAATGCAGGGCC;RSEQ=GAATGTGAGTAATAGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:20:15,5:0,1:0.9524:0,2:25.2:1:31.2:1:0.28571:0:58.9:40:0.9524:0:1 1/0:15:8:5,3:6,1:0.5333:2,2:22.3:1:30.6:1:0.56923:3.3097:57.9:16:0.5333:0:1 -5 144228002 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49772;SOR=0;LSEQ=CTGATTTCAGAAGGCTTTTC;RSEQ=TGTAATGCCAGGTGGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:15,23:0.05:2,2:29:1:31:1:1:1.52:53.5:4:0.05:0:1 0/0:33:0:0,0:10,23:0:2,0:19.8:1:31.6:1:1:0:59.1:66:1:0:0.1 -5 144228069 . A G 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00482;SOR=Inf;LSEQ=AAAACAACACTCTTACCCTA;RSEQ=GAAGGTGCGGAGTCCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:19.5:1:31.8:1:1:0:60:22:1:0:0.1 1/0:8:5:2,3:1,2:0.625:2,2:36:1:31.8:1:1:1.29:60:10:0.625:0:1.2 -5 144755084 . TG T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.22;SOR=Inf;LSEQ=GTGGAGAGGGTGTGCTTTGC;RSEQ=GGGGTAAACTCGCTCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:0:2,0:26.3:1:31.2:1:1:0:60:26:1:0:0 0/1:12:2:1,1:3,7:0.1667:2,2:38:0:32.5:1:1:2.16:60:4:0.1667:0:0.5 -5 145122906 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTGCTTGAACCCAAGAGGC;RSEQ=GAGGCTGCAGTGAGCTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:31.5:1:1:0:60:4:1:0:1.5 -5 145123287 . G C 55 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAAACCACGCTACAGAGG;RSEQ=CTGGGGTCCCAACCCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:25.8:1:27.8:1:1:0:60:3:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 145123812 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTAGCCTTTTCTCCTGC;RSEQ=GACCAGCAGACTTAGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:1:0,2:22.6:1:30.9:1:1:0:60:16:1:0:1 1/1:2:2:1,1:0,0:1:0,2:25:1:32:0:1:0:60:4:1:0:1 -5 145123948 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19918;SOR=0;LSEQ=AAATGGGTCCCGTTCCCTGT;RSEQ=CCACTCAACTGGGTGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:16,22:0.05:2,2:30.5:1:31:0:1:1.36:60:4:0.0513:0:1.5 0/0:49:0:0,0:24,25:0:2,0:32.5:1:31.5:1:1:0:60:48:1:0:0.2 -5 145123957 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19918;SOR=0;LSEQ=CCGTTCCCTGTGCCACTCAA;RSEQ=TGGGTGAGACCCTCCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:16,22:0.05:2,2:27.5:1:29.5:1:1:1.36:60:4:0.0526:0:2 0/0:49:0:0,0:23,26:0:2,0:29.6:1:31.4:1:1:0:60:98:1:0:0.1 -5 145124401 . T C 34 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACGTTTCTCCAGCAAGGG;RSEQ=GCATAATTGGACAGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:27.5:1:34:0:1:0:60:4:1:0:1.5 -5 145124434 . T A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGATGAGATGGAAGAAT;RSEQ=GACAGAAGTAGGTTTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:1:28:1:1:0:60:4:1:0:1.5 -5 145124755 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGAATGAACAAAGCCT;RSEQ=CAAGAAATATGGGACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 146257931 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18995;SOR=Inf;LSEQ=CCTCCGCTGCCTCCGGGTGC;RSEQ=AAGATACGCCGTGCCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:0:2,0:28:1:30.8:1:1:0:60:32:1:0:0.2 0/1:26:2:1,1:10,14:0.0769:2,2:8.5:1:27.5:1:1:1.38:60:4:0.08:0:1.5 -5 146386270 . T C 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CTCTTTGGCAGCAGTGATTC;RSEQ=CCAAAACCACCGAGGCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:27.8:1:31.8:1:1:0:60:8:1:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:28:1:1:0:60:4:1:0:1 -5 146386506 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19714;SOR=Inf;LSEQ=ACTCTTATACCATCCTCTGG;RSEQ=GTTGGGCAACATGGCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:33,39:0:2,0:30.4:1:30.8:1:1:0:57.9:144:1:0:0.2 0/1:58:2:1,1:26,30:0.0345:2,2:14:0:32.5:1:1:1.15:60:4:0.0351:0:1.5 -5 147496166 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15235;SOR=Inf;LSEQ=AAGTTTCTCCTTAAGGTTGC;RSEQ=GGGTAAGATATCAGCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:80,2:0:1,0:26.9:1:30.8:1:1:0:60:164:1:0:0 0/1:53:2:1,1:47,4:0.0377:2,2:25:1:31.5:1:0.18142:10.62088:60:4:0.0377:0:1 -5 147496188 . TC T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14875;SOR=Inf;LSEQ=GGTAAGATATCAGCACATTT;RSEQ=ACTGCTCTGGGGTTCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:119,14:0:2,0:22.1:1:31.4:1:1:0:60:132:1:0:0.1 0/1:84:2:1,1:66,15:0.0238:2,2:10.5:1:28.9:1:0.35028:4.29244:60:4:0.0247:0.0119:0 -5 147496226 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16245;SOR=Inf;LSEQ=TTTGGATTTCTTTACACCTT;RSEQ=AAATAATTAACAATATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:177,76:0:2,0:24.8:1:31.7:1:1:0:60:125.5:0.996:0:0.3 0/1:172:2:1,1:109,60:0.0116:2,2:20:1:27.5:1:1:1.80986:60:4:0.0117:0:1 -5 147496307 . G A 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03152;SOR=1.34129;LSEQ=TAGACCTCATATCAATAATC;RSEQ=TTCTCATCAGTATCACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:552:306:145,161:117,127:0.5543:2,2:26.7:1:30.1:1:0.93159:1.02288:60:60.2:0.5574:0:1.7 1/0:387:242:123,119:69,76:0.6253:2,2:26.4:1:29.6:1:0.59962:1.14:60:120:0.6234:0:1.7 -5 147496345 . T C 255 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13715;SOR=1.25199;LSEQ=TGCTCTTCATTTTCTTTCAT;RSEQ=ATTCTTTCTTGCCTTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:469:266:96,170:72,131:0.5672:2,2:25.8:1:31.7:1:0.92273:1.03:60:87.667:0.5705:0:1.9 1/0:309:192:76,116:50,67:0.6214:2,2:26.1:1:31.5:1:0.63357:1.13856:60:384:0.6275:0:1.9 -5 147496415 . G T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGATCCAAGGCAGCATGATA;RSEQ=GACAAAAGAGCACAGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:19,105:0.0159:2,2:20:1:30:1:0.29333:5.41:60:4:0.0161:0:1 0/1:63:1:0,1:9,53:0.0159:2,0:9:0:30:0:1:0:60:2:0.0159:0:1 -5 147496483 . G C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55873;SOR=1.55725;LSEQ=CCTACTACCTGGACTTGTGA;RSEQ=ACATTGAGTAAATTACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:0,16:0,16:0.5:1,1:28.1:1:32.5:1:1:0:60:32:0.5:0:1.1 1/0:18:11:0,11:0,7:0.6111:0,0:21.9:1:31.7:1:1:0:60:22:0.6111:0:1.1 -5 148140339 . C T 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAAAACTCAGCTGTATA;RSEQ=GCTGACCAATCAAAACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:19:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 148140697 . T G 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06447;LSEQ=CAAAGATCAGTGGGTAAGCC;RSEQ=GGCCCTAACCACACATAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:511:473:221,252:18,20:0.9256:2,2:26.1:1:30.3:1:1:1.0262:60:156.667:0.9252:0:1.1 0/1:513:228:116,112:144,138:0.4444:2,2:25.4:1:29.6:1:1:1.00748:60:113:0.4466:0:1.1 -5 148140858 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06822;LSEQ=TCAAGGAACAGAAAAAATGC;RSEQ=AGCCTAAATTTGCCTGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:57:2,55:0,4:0.9344:0,1:20.9:1:31.1:1:1:0:60:27.5:0.9322:0:1.2 0/1:29:14:0,14:0,15:0.4828:1,1:23.4:1:32.1:1:1:0:60:28:0.4828:0:1.1 -5 148367981 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51613;SOR=0;LSEQ=TGTATAACCAATAAAATATA;RSEQ=CAGATGTGACACTGTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:26:1:31.5:1:1:1:60:4:0.1111:0:1 0/0:12:0:0,0:8,4:0:2,0:32:1:31.9:1:1:0:60:24:1:0:0.1 -5 149137124 . C G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCAGAGTAGCCCTGCCAG;RSEQ=CTGTCCTGACGGATGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:5,4:2,1:0.75:2,2:27.2:1:30.7:1:1:1.53983:60:8:0.7273:0:1.3 1/1:3:3:2,1:0,0:1:0,2:31.3:1:32:1:1:0:60:6:1:0:1 -5 149433400 . G GC 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.04568;SOR=Inf;LSEQ=CCATGAGAACAGTAGGGGAG;RSEQ=GGGGGGTGAGGGCTCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:25:25,0:11,0:0.6944:0,1:23:1:31.5:1:1:0:60:24:0.7059:0.0833:0.1 1/1:11:11:11,0:0,0:1:0,0:22.4:1:31.4:1:1:0:60:22:1:0.2727:0.2 -5 149433596 . TG GA 298 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.24756;LSEQ=CATGGAGGAGTTGAAGTTTG;RSEQ=GGAGGGGAGAGTGGTACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:908:883:539,344:0,1:0.9725:0,2:27.5:1:30.5:1:0.39027:0:60:1766:0.9955:0.0099:1.1 1/1:740:664:382,282:40,28:0.8973:2,2:27.1:1:29.9:1:0.89781:1.05454:60:331:0.9044:0.0149:1.1 -5 149433597 . G A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3959;SOR=0.75426;LSEQ=ATGGAGGAGTTGAAGTTTGT;RSEQ=GGAGGGGAGAGTGGTACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:908:32:16,16:0,0:0.0352:0,2:18.3:1:26.7:1:1:0:60:3:0.9231:0:2.4 0/1:746:20:9,11:42,28:0.0268:2,2:5.2:1:29.4:1:0.30742:1.82077:60:19:0.2159:0:1.7 -5 149433731 . ACTG A 96 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.80886;SOR=1.2114;LSEQ=GAGCTCTCCTCCTCCAGCTC;RSEQ=CTGCTGCTGCCGCTGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:862:8:4,4:382,472:0.0093:2,2:12:1:29.1:1:1:1.24:58.8:16:0.0094:0.0058:1 0/1:802:9:6,3:350,441:0.0112:2,2:20.4:1:30.6:1:0.19705:2.52:60:18:0.0113:0.0037:0.3 -5 149433752 . A G 115 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00049;SOR=15.39676;LSEQ=CTGCTGCTGCTGCCGCTGCC;RSEQ=CCGCTTCTGCTGCTGCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:826:1:1,0:378,446:0.0012:2,0:22:0:10:0:0.45939:0:60:0:0:0:1 0/1:709:13:5,8:299,396:0.0183:2,2:32:1:31.1:1:0.78627:1.20776:60:26:0.0185:0:1 -5 149433939 . G A 186 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=121.39113;LSEQ=AGGAAGGAGCAGATCTGCTG;RSEQ=AAGGTGGGTCTGTGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:902:1:1,0:450,451:0.0011:2,0:1:0:26:0:1:0:60:2:0.0011:0:1 0/1:740:88:44,44:310,337:0.1189:2,2:27.5:1:28.9:1:0.73411:1.09:60:28.333:0.1164:0:1.1 -5 149434518 . C A 87 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTATGATTGCACACATCA;RSEQ=TGCGCTCCAGCCCGGGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:4,1:0.6154:2,0:19.9:1:29.1:1:0.38462:0:60:7:0.5833:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149434684 . T G 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00738;SOR=Inf;LSEQ=TGTGTCCACTATGGGAGAGA;RSEQ=AAAGTCTGACCCTGGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:234,3:0:1,0:22.6:1:31:1:1:0:60:46.4:1:0:0.1 0/1:144:5:5,0:137,2:0.0347:1,0:20:1:33.2:1:1:0:60:10:0.0352:0:1 -5 149434722 . C T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03217;SOR=Inf;LSEQ=CATTTTGGACAGGGAAAGAT;RSEQ=AGGGCCACACGGCCTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:384,103:0:2,0:24.3:1:31.3:1:1:0:60:47.7:1:0:0.1 0/1:360:4:2,2:286,70:0.0111:2,2:20.8:1:24:1:0.17994:4.06412:60:3:0.0086:0:1.5 -5 149434954 . C T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTGTCTTCTCCCCATTCC;RSEQ=GCACACCCACACACATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:37,289:0:2,0:21.5:1:29.7:1:1:0:60:107.667:1:0:0.1 0/1:162:17:2,15:23,122:0.1049:2,2:22.5:1:30.4:1:1:1.41118:60:34:0.1056:0:1.1 -5 149435293 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTAGTAGTAGAGAGCTGC;RSEQ=TCTTCAAGGGTCTGTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:38:1:30:1:1:1.55:60:4:0.1333:0:1 0/0:1:0:0,0:1,0:0:0,0:29:0:29:0:1:0:60:2:1:0:0 -5 149435759 . G A 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.91625;LSEQ=TTCACCCCCTCCCCAGCCTG;RSEQ=CCCAAGCCCTCCCAGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:995:528:268,260:242,224:0.5307:2,2:24.8:1:29.6:1:0.75059:1.04809:60:43:0.5336:0:1.2 1/0:833:570:279,291:119,140:0.6843:2,2:24.3:1:28.7:1:0.45345:1.13:60:50.818:0.6901:0:1.2 -5 149435996 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28471;SOR=0;LSEQ=GAGGGCCCCACATGGCTTTG;RSEQ=AGTCCCTGCTGGAGTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:1,2:5,131:0.0216:1,2:18.7:1:21.7:1:0.12485:12.40:60:2:0.015:0:2.7 0/0:88:0:0,0:11,77:0:2,0:24.8:1:31.4:1:1:0:60:176:1:0:0.1 -5 149436545 . G A 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTATCATCCCCACCAGACC;RSEQ=CGTGCTTTATGAGCAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:32.5:1:31.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149436598 . A T 90 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATACACTATTTAGTAAAA;RSEQ=CGAATGAAGAAAGCCTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:8,0:8,0:0.5:0,0:24.3:1:30:1:1:0:60:16:0.5:0:1.4 0/0:1:0:0,0:1,0:0:0,0:23:0:32:0:1:0:60:2:1:0:0 -5 149437190 . C G 282 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01968;LSEQ=GGGTTGGGGGGCAGAGGTCA;RSEQ=TCATCATCACTGCACTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:453:452:108,344:0,0:0.9978:0,2:24.3:1:32:1:1:0:60:149.667:0.9978:0:1.1 1/1:316:284:78,206:11,21:0.8987:2,2:23.8:1:30.9:1:0.41216:1.3819:60:283:0.9042:0:1.1 -5 149438822 . G T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACCTTGTTGGTAAGGCTG;RSEQ=TCTCGAACTCCCATCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30:1:30.5:1:1:0:59.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149439044 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25881;SOR=3.36185;LSEQ=CCCTCCACACTCCCAGAACA;RSEQ=GGTAGGTGTTCAAATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:15:15,0:13,0:0.5357:1,1:27.9:1:30.4:1:1:0:60:30:0.5357:0:1.2 1/1:10:8:8,0:2,0:0.8:0,0:28.3:1:30.6:1:1:0:60:16:0.8:0:1.1 -5 149439045 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCACACTCCCAGAACAC;RSEQ=GTAGGTGTTCAAATATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:26,0:0.0714:1,0:23:1:32:0:1:0:60:4:0.0714:0:1 0/0:12:0:0,0:12,0:0:0,0:21.5:1:31.2:1:1:0:60:24:1:0:0.8 -5 149439458 . T G 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGTGTGGGGTGAGGGAGG;RSEQ=GCTGAGTGCTCCCCTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:165,356:0:2,0:24.6:1:29.7:1:1:0:60:103.2:1:0:0.3 0/1:385:25:10,15:128,232:0.0649:2,2:17.8:1:30:1:0.67012:1.21:60:24:0.0633:0:1.2 -5 149439494 . C A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22737;LSEQ=CCATGAACAGGAGCATGAGA;RSEQ=TGGGGGCAGTGAGGCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:95:11,84:25,130:0.38:2,2:24.8:1:30.5:1:0.35828:1.46635:60:22.75:0.3792:0:1.1 0/1:164:20:5,15:30,114:0.122:2,2:20.8:1:29.3:1:0.77081:1.26:60:40:0.1258:0:1.3 -5 149439588 . T C 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22973;SOR=0;LSEQ=TTGTGCCTCAGTAGTTCCAT;RSEQ=TGTTTAAAACAGATGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:57:0,57:0,0:1:0,1:24:1:32.7:1:1:0:60:56:1:0:1.2 1/1:17:16:0,16:0,1:0.9412:0,1:16.5:1:31.8:1:1:0:60:32:0.9412:0:1.1 -5 149440114 . C T 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCTTCATAAGAGGTAGG;RSEQ=GGGGGGCTTCACTCCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:19.5:1:31.3:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149440334 . G A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=Inf;LSEQ=ACTTGGAGCAGTAGGATCCT;RSEQ=AGAAGGAGAAGACGGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:261,13:0:1,0:24.4:1:32.4:1:1:0:60:273:1:0:0.1 0/1:142:8:7,1:114,20:0.0563:2,2:19.6:1:29.5:1:1:1.23:60:16:0.058:0:1.1 -5 149440343 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13243;SOR=Inf;LSEQ=AGTAGGATCCTGAGAAGGAG;RSEQ=AGACGGAACAAGGTAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:286,33:0:2,0:24.3:1:29.9:1:1:0:60:52.167:1:0:0 0/1:183:2:1,1:147,34:0.0109:2,2:5:1:30:1:0.34678:4.27579:60:4:0.0112:0:1 -5 149440644 . C T 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.86503;SOR=0.89735;LSEQ=AGGGGAGAAAGCAGGGCATA;RSEQ=CCCAAGACCCGGAGTGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:64:2,62:2,42:0.5926:1,1:24.3:1:30.1:1:1:1.47071:59.9:20.333:0.581:0:1.2 1/0:53:30:1,29:2,12:0.566:2,1:21:1:28.9:1:0.23362:4.64088:60:60:0.566:0:1.1 -5 149440708 . CAG C 31 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.15598;SOR=6.50459;LSEQ=AAATGCAGACACACAGATGG;RSEQ=AGAGAGAGAGAGGAGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:1,0:15,16:0.0313:2,0:33:0:34:0:1:0:60:2:0.0333:0:0 0/1:11:2:1,1:0,9:0.1818:0,2:8:1:31.3:1:0.18182:0:60:4:0.1818:0.0909:0.5 -5 149440721 . AGG A 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.41204;SOR=2.88615;LSEQ=CAGATGGCAGAGAGAGAGAG;RSEQ=AGGGATGAGCCTGTCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:2,0:14,15:0.0625:2,0:20.5:1:31.5:1:0.48387:0:60:4:0.0667:0:0 0/1:6:1:0,1:1,4:0.1667:2,0:11:0:31:0:1:0:60:2:0.1667:0:1 -5 149440723 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1983;SOR=0.28534;LSEQ=GATGGCAGAGAGAGAGAGAG;RSEQ=AGGGATGAGCCTGTCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:20:8,12:7,2:0.6452:2,2:24.5:1:28.9:1:0.10865:4.94883:59.4:19:0.7037:0:1.7 0/1:6:2:0,2:1,2:0.3333:2,0:26:1:31:1:1:0:60:4:0.4:0:1.5 -5 149440739 . A G 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00504;SOR=Inf;LSEQ=AGAGGAGGGATGAGCCTGTC;RSEQ=CTGAGCTGGTCTTCAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:18,14:0:2,0:26.3:1:29.4:1:1:0:59.6:15:1:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:46:1:31.5:1:1:0:60:4:0.6667:0:1.5 -5 149441015 . CA C 104 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0.96813;LSEQ=AGCCCACCCCCAGCATCTAC;RSEQ=CCCCCCATCCCTTCCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:773:14:14,0:466,268:0.0181:2,1:28.7:1:27.4:1:0.00313:0:60:13:0.0235:0:3.6 0/1:570:10:9,1:340,206:0.0175:2,2:23.8:1:27.8:1:0.09967:5.44:58:20:0.0226:0:3.9 -5 149441016 . AC A 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00263;SOR=1.3912;LSEQ=GCCCACCCCCAGCATCTACC;RSEQ=CCCCCATCCCTTCCCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:783:366:218,148:292,124:0.4674:2,2:27.6:1:30.2:1:0.00204:1.59768:60:14.25:0.5:0.0128:0.6 1/0:582:320:191,129:171,88:0.5498:2,2:27.1:1:29.9:1:0.12112:1.31178:60:23.615:0.5938:0.0172:0.7 -5 149447628 . A G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77629;LSEQ=CAGAGGCCACCCAGCAGCTG;RSEQ=CTCATGTTGGCATACAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:13,0:10,0:0.5652:0,1:24.2:1:29.1:1:1:0:60:12:0.5455:0:1 1/0:6:3:3,0:3,0:0.5:0,0:29.3:1:31.3:1:1:0:60:6:0.5:0:1 -5 149447720 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52499;SOR=0;LSEQ=TGAATCCATGCAGCCTGGGG;RSEQ=TACCATCCAAATCTGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:148,15:0.0121:2,2:43:1:33:1:0.18507:9.58559:60:4:0.0124:0:1 0/0:103:0:0,0:89,14:0:2,0:23.9:1:31.7:1:1:0:60:102:1:0:0.2 -5 149447744 . A G 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18918;SOR=Inf;LSEQ=CATCCAAATCTGGCTCACTC;RSEQ=GGCACCTGGCAGCCCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:184,31:0:2,0:26.6:1:29.9:1:1:0:60:52.75:1:0:0.1 0/1:166:2:1,1:137,27:0.012:2,2:24:0:29:1:0.30975:5.00094:60:4:0.0123:0:1 -5 149447771 . G A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCAGCCCCACTCCGCTCC;RSEQ=GCTCACCTGCTTATACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:0:0,0:278,82:0:2,0:21.9:1:29.3:1:1:0:60:29:1:0:0.1 0/1:263:18:14,4:186,58:0.0684:2,2:21.3:1:29.8:1:1:1.09:60:36:0.07:0:1.1 -5 149447775 . C T 52 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40912;SOR=0.2817;LSEQ=AGCCCCACTCCGCTCCGGCT;RSEQ=ACCTGCTTATACTTGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:5:1,4:303,95:0.0124:2,2:12:1:22.6:1:0.01407:12.66005:60:4:0.01:0:1 0/0:284:1:0,1:206,77:0.0035:2,0:1:0:20:0:0.27465:0:60:2:0.0036:0:1 -5 149447805 . GAGC G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.0837;SOR=0.45099;LSEQ=TACTTGTACAATAGCAGCAG;RSEQ=AGCAGCAGCAGCAAGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:22:13,9:439,210:0.0326:2,2:24.9:1:31.4:1:0.48812:1.44645:59.5:44:0.0335:0.0119:0.2 0/1:468:7:5,2:282,179:0.015:2,2:19.3:1:30.1:1:0.7115:1.59:60:14:0.0153:0.0043:0.1 -5 149447970 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1377;SOR=Inf;LSEQ=GTCAGGCCTGCACACTGCCT;RSEQ=GAACACAGTGGGTGCTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:51,260:0:2,0:22.9:1:31.1:1:1:0:60:102.667:1:0:0.1 0/1:184:2:2,0:36,146:0.0109:2,0:23:1:26:1:0.04176:0:60:4:0.011:0:1 -5 149448427 . T C 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTATACTACTAGTTCTAG;RSEQ=GATGTTTTGGAGAACATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:28.3:1:29.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149449389 . C G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.69444;SOR=1.17317;LSEQ=GCCGCCTAAAGGAGCAGGGG;RSEQ=GGGGGGCGGGCGGGGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:15:0,15:171,0:0.0802:1,1:5.1:1:23.1:1:0:0:60:2.75:0.0625:0:2.5 0/1:140:13:0,13:122,4:0.0929:1,1:5.2:1:22.8:1:0:0:59.8:3.333:0.0781:0:2.6 -5 149449396 . C G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.26988;SOR=1.44331;LSEQ=AAAGGAGCAGGGGCGGGGGG;RSEQ=GGGCGGGGGGGCGGTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:22:0,22:191,4:0.1009:1,1:10.4:1:26.2:1:0:0:59.5:6.333:0.0955:0:2.3 0/1:172:24:0,24:142,4:0.1395:1,1:8.5:1:20.2:1:0:0:59.9:2:0.1046:0:2.5 -5 149449400 . C G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.33152;SOR=1.33671;LSEQ=GAGCAGGGGCGGGGGGCGGG;RSEQ=GGGGGGGCGGTGCGGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:30:2,28:203,6:0.1245:1,2:12.6:1:25.2:1:0:422.79407:59.6:4:0.1086:0:2.1 0/1:194:31:0,31:156,5:0.1598:1,1:11.8:1:25.3:1:0:0:59.9:6.75:0.1467:0:2.3 -5 149449762 . G T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.00445;SOR=Inf;LSEQ=TACCTATCAGTGTGGCCACT;RSEQ=CACTGCAGCCATGTCACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:694:0:0,0:419,275:0:2,0:24.6:1:31.5:1:1:0:60:32.048:1:0:0.1 0/1:476:6:2,4:297,173:0.0126:2,2:5.7:1:27.2:1:0.20141:3.42428:60:12:0.0129:0:1.3 -5 149449923 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0584;SOR=Inf;LSEQ=CCCGCCACCTCCCAATCTCC;RSEQ=AGTACCTACTTCCCTGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:165,282:0:2,0:22.4:1:31.7:1:1:0:60:62.857:0.9977:0:0.1 0/1:285:3:2,1:106,176:0.0105:2,2:26.3:1:28.7:1:0.55936:3.31:60:6:0.0106:0:1 -5 149450027 . G T 64 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01397;SOR=Inf;LSEQ=CCCAGCACTCACATCGAAGG;RSEQ=TGAGCTCAAACGTCAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:614:0:0,0:362,252:0:2,0:25:1:31.4:1:1:0:60:46.231:1:0:0.2 0/1:457:5:0,5:278,174:0.0109:2,0:6.8:1:27.8:1:0.00891:0:60:10:0.0112:0:1 -5 149450132 . T C 184 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=44.51942;LSEQ=GCAGAGAGAGGGTGAAGGTG;RSEQ=GCCTGCAGGAGAGAATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:823:2:1,1:347,473:0.0024:2,2:42:1:20.5:1:1:1.36:60:1:0.0012:0:1 0/1:664:65:27,38:263,334:0.0979:2,2:25.6:1:30.6:1:0.79259:1.10803:60:64:0.0977:0:1.1 -5 149450142 . A G 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGTGAAGGTGTGCCTGCAGG;RSEQ=GAGAATCAGGTGGTGTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:0:0,0:283,447:0:2,0:25.9:1:30.2:1:1:0:60:47.667:1:0:0.1 0/1:618:40:19,21:240,338:0.0647:2,2:21.1:1:29.9:1:0.50885:1.27:60:80:0.0657:0:1.2 -5 149450187 . G A 112 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0334;SOR=0.22084;LSEQ=CCCAGCCTAGTATGGCCCCT;RSEQ=CCAGGATTGCAGTCAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:13:2,11:90,317:0.031:2,2:25.4:1:30.4:1:0.74223:1.56002:60:26:0.0315:0:1 0/0:286:2:2,0:76,208:0.007:2,0:1:0:18.5:1:0.07368:0:60:1:0.0036:0:1 -5 149450258 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0672;SOR=Inf;LSEQ=TAAAATATTCAGGGCCCAAC;RSEQ=GCCTTGGGTAAGCCAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:1,89:0:1,0:23.5:1:30.7:1:1:0:60:44:1:0:0.1 0/1:32:2:0,2:0,30:0.0625:1,0:25.5:1:30:1:1:0:60:4:0.0645:0:1 -5 149452793 . C T 175 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=29.7791;LSEQ=AGGTTGGGACATGAGCCAAG;RSEQ=GTCCTGATGCTTGCTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:4:2,2:372,54:0.0093:2,2:14.3:1:27.5:1:0.08411:6.83519:60:8:0.0094:0:1 0/1:292:64:54,10:186,42:0.2192:2,2:22.9:1:29.3:1:0.713:1.22:60:63:0.2195:0:1.1 -5 149453450 . T C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCTTCTGGTCATAAAT;RSEQ=AGTCAATGCGGCTTCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:9.7:1:32.7:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149454981 . G A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTTTTTCTCACTCTCTCCCC;RSEQ=CAGCCACACTGGCCCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:0:33:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:27:0:31:1:1:0:60:4:1:0:2.5 -5 149455029 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACATGGCAAGCACAGTCCC;RSEQ=CTGCAGGATGGAGCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:28:1:1:0:60:4:1:0:2.5 -5 149456771 . CT AA 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=3e-05;SOR=0.63279;LSEQ=TCCCTGACATCAGCTTCCTC;RSEQ=CAAAACCCTTCTGCTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:750:420:231,189:182,137:0.56:2,2:27.4:1:30.1:1:0.60098:1.0868:60:840:0.5676:0:1.1 0/1:639:285:169,116:190,152:0.446:2,2:25.4:1:29.5:1:0.37279:1.17:60:284:0.453:0.0391:1 -5 149456772 . T A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.69201;SOR=1.22535;LSEQ=CCCTGACATCAGCTTCCTCC;RSEQ=CAAAACCCTTCTGCTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:752:13:6,7:181,138:0.0173:2,2:10.7:1:28:1:0.57095:1.52818:60:12:0.0369:0:1.8 0/1:616:13:6,7:190,152:0.0211:2,2:14.1:1:26.7:1:0.57618:1.45675:60:12:0.0343:0:2.2 -5 149456811 . G A 192 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCCTGCAGGATCCCTACC;RSEQ=ACTGTCCACCACCACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:859:0:0,0:466,392:0:2,0:25.7:1:30.3:1:1:0:60:56.2:1:0:0.5 0/1:742:89:48,41:362,291:0.1199:2,2:19.9:1:29.8:1:0.82072:1.06246:60:88:0.1221:0:1.2 -5 149457019 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08597;SOR=Inf;LSEQ=CTGCAGCCAGAAGGAATGGA;RSEQ=ATGTTATACCAAGGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:64,298:0:2,0:24.1:1:31.5:1:1:0:60:71.4:1:0:0.1 0/1:287:3:2,1:54,230:0.0105:2,2:20:1:27.7:1:0.09835:8.43:60:6:0.0106:0:1.7 -5 149457041 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17573;SOR=Inf;LSEQ=TGTTATACCAAGGTAGTTTA;RSEQ=GGATTAGAAAGATCTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:20,219:0:2,0:25.6:1:31.4:1:1:0:60:238:1:0:0.1 0/1:173:2:1,1:13,158:0.0116:2,2:22:1:28:1:0.15573:11.75:60:4:0.0116:0:1 -5 149457493 . A G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=CGGCACAAGCATGAGTCCTG;RSEQ=TTCTGTGTCAGCTACTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:0:1,0:23.8:1:29.5:1:1:0:60:19.333:1:0:0.4 0/1:18:6:5,1:12,0:0.3333:0,2:13.7:1:32.2:1:0.33333:0:60:12:0.3529:0:1.2 -5 149457678 . G A 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.58633;LSEQ=GATCTGCAGGGACTGACCTT;RSEQ=GTGTTGTTGTGTTGGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:947:534:272,262:212,200:0.5639:2,2:26.9:1:29.5:1:0.89572:1.02101:60:58.333:0.5639:0:1.1 0/1:835:360:184,176:261,209:0.4311:2,2:26.9:1:28.9:1:0.20725:1.19425:60:39:0.4301:0:1.1 -5 149458110 . C T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTGCCTCCCTCCAAGCCCCC;RSEQ=ACACCTAGATTCTTCACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:32:0:29:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:1:0,2:7:0:27.5:1:1:0:60:4:1:0:2 -5 149458128 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACACCTAGATTCTTCAC;RSEQ=AAAGTGACCTCTTACAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27.5:1:32:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:25:0:30:1:1:0:60:4:1:0:2 -5 149459381 . T C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39742;SOR=0.41128;LSEQ=TTTGTAGCATGTCCAATGAC;RSEQ=TGAGATGACCTTGCCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:20:20,0:8,0:0.7143:0,1:20.8:1:30.8:1:1:0:60:40:0.7143:0:1.5 1/0:8:4:4,0:4,0:0.5:0,0:31.5:1:32:0:1:0:60:8:0.5:0:1 -5 149459538 . C T 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8329;LSEQ=CCCCCATCACACCCAGTCCC;RSEQ=AGTCACCACCCATGTGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:1,2:247,44:0.0102:2,2:15.3:1:21.7:1:0.06485:11.07471:60:2:0.0071:0:2.7 0/0:235:2:1,1:188,45:0.0085:2,2:23.5:1:14.5:1:0.35385:4.14309:60:0:0:0:5.5 -5 149459574 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15653;LSEQ=GGCCGCCGGCTCTCTGTCCC;RSEQ=ACTCTTCAGGCCTGGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:534:203:131,72:222,109:0.3801:2,2:25.3:1:29.4:1:0.57265:1.11917:60:28:0.3762:0:1.3 0/1:446:39:26,13:249,157:0.0874:2,2:29.6:1:29.1:1:0.60593:1.26:60:78:0.0888:0:1.1 -5 149459915 . G A 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37901;SOR=0.28492;LSEQ=AGGGTCTAGAGTAGAGGAGG;RSEQ=CACAGGGTTACAACTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:4:3,1:120,235:0.0111:2,2:17:1:28.3:1:0.11828:5.84:60:8:0.0116:0:1.3 0/0:313:1:1,0:119,193:0.0032:2,0:1:0:26:0:0.38339:0:60:2:0.0033:0:1 -5 149460176 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=CCGACTTGCAGGGTTGTTGT;RSEQ=AGGACTGCATTACATTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:49,7:0:2,0:24.5:1:31.4:1:1:0:60:17.667:1:0:0.1 0/1:15:4:4,0:10,1:0.2667:2,0:23.8:1:29:1:1:0:60:8:0.2667:0:1 -5 149460271 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13492;SOR=Inf;LSEQ=TTACGATTGTTAATTTTAGG;RSEQ=CCCATTGTAGTGGGGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:196,14:0:2,0:24.8:1:31.2:1:1:0:60:41:1:0:0 0/1:123:2:2,0:109,12:0.0163:2,0:28.5:1:32:0:1:0:60:4:0.0164:0:1 -5 149460291 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14545;SOR=Inf;LSEQ=GCCCATTGTAGTGGGGCCTG;RSEQ=CGGGTCAGGCCTCTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:279,30:0:2,0:23.6:1:32.3:1:1:0:60:308:1:0:0.1 0/1:191:2:1,1:164,25:0.0105:2,2:23:1:28:1:0.25434:6.45219:60:4:0.0105:0:1 -5 149460334 . G T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01398;SOR=Inf;LSEQ=GGCTCAGACTCCTCACCTTT;RSEQ=ACATAGAGGTGGATGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:622:0:0,0:420,202:0:2,0:25.1:1:31.6:1:1:0:60:55.545:1:0:0.1 0/1:463:5:2,3:300,158:0.0108:2,2:13.4:1:24.6:1:0.34734:2.84118:60:4:0.0088:0:1.2 -5 149460553 . A G 263 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29213;SOR=0.88744;LSEQ=CCTGGCTTCACGACCAGCTC;RSEQ=GGGACACTGGGCTCTATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:706:403:148,255:121,180:0.5708:2,2:25.6:1:30.4:1:0.38853:1.15797:60:99.75:0.5716:0:1.1 1/0:617:334:139,195:105,177:0.5413:2,2:26.1:1:29.6:1:0.28307:1.20:60:110.333:0.5417:0:1.2 -5 149460627 . G A 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=0;LSEQ=GCAGACAGAAGTGAGGTCTA;RSEQ=GATGCGCCCCTTGGGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:22:5,17:44,201:0.0824:2,2:23.5:1:31:1:0.56881:1.34:60:44:0.0827:0:1.2 0/0:152:0:0,0:34,118:0:2,0:22.8:1:30.8:1:1:0:60:151:1:0:0.4 -5 149460645 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11725;SOR=Inf;LSEQ=TAGGATGCGCCCCTTGGGCC;RSEQ=TCCTGACTCTGAGATGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:23,170:0:2,0:23.8:1:31.7:1:1:0:60:192:1:0:0.3 0/1:101:2:1,1:18,81:0.0198:2,2:11:1:32.5:1:0.34238:4.41:60:4:0.0202:0:1 -5 149460953 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AACCCTGTGTACAAAGTGGA;RSEQ=GTATTTCTACCACCGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:16.7:1:29:1:1:0:60:6:1:0:1 0/0:2:0:0,0:1,1:0:2,0:9:0:32.5:1:1:0:60:4:1:0:0 -5 149466072 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13612;SOR=Inf;LSEQ=TCAGCTACTAGCTCCGCAGG;RSEQ=ATCGGGACACTGGACACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:38,281:0:2,0:24:1:31.1:1:1:0:60:62.8:1:0:0.1 0/1:187:2:1,1:35,150:0.0107:2,2:22:1:28.5:1:0.3488:4.24:60:4:0.0107:0:1 -5 149495050 . T C 94 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAAGCCTAACTTTCCCAT;RSEQ=TTACATATGGGAAAACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:31.1:1:31.5:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149495253 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23231;LSEQ=CTGGCTGACAGGAAGCCCGG;RSEQ=CAGGCCAGGCCAGGAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:191:161:130,31:24,6:0.8429:2,2:23.2:1:32:1:1:1.05:60:79.5:0.8413:0:1.5 1/0:112:62:44,18:38,12:0.5536:2,2:23.7:1:31.3:1:0.66868:1.29247:60:124:0.5536:0:1.4 -5 149495285 . A AG 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.63134;SOR=1.68665;LSEQ=AGGAGATGCTGGGTGCTGGC;RSEQ=GGGGGGGAGCTTCAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:2:1,1:250,86:0.0059:2,2:49:1:32:1:0.44911:2.89608:60:4:0.0061:0:2 0/1:201:2:2,0:132,66:0.01:2,0:13:1:32.5:1:1:0:60:4:0.0103:0.005:1.5 -5 149495287 . G C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=0.26406;LSEQ=GAGATGCTGGGTGCTGGCAG;RSEQ=GGGGGAGCTTCAGGCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:119:98,21:159,68:0.3439:2,2:24.9:1:32.2:1:0.01388:1.99:60:118:0.3491:0:1.6 0/1:206:25:20,5:114,59:0.1214:2,2:25.9:1:31.5:1:0.17827:2.06:60:50:0.1225:0:1.8 -5 149495395 . T C 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14063;LSEQ=TCCGGCAACTGTTCCAGCTC;RSEQ=GGCTCCGGCTCCACCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1009:881:552,329:80,45:0.8731:2,2:24.2:1:30.3:1:0.84333:1.05953:60:61.929:0.8731:0:1.1 0/1:828:407:248,159:249,171:0.4915:2,2:22.9:1:29.8:1:0.67009:1.07:60:80.4:0.4896:0:1.2 -5 149495770 . G A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCAGCTGGCTCCAAAGCTC;RSEQ=TTTCTCACCCACCAGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:1,12:0,2:0.8667:0,1:30.2:1:29.8:1:1:0:60:12:0.8571:0:1.2 1/1:2:2:0,2:0,0:1:0,0:37.5:1:31.5:1:1:0:60:4:1:0:1.5 -5 149496321 . A G 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTGCACTTCACTCCTCTGC;RSEQ=CCATCCACTGGGACTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:27:0:26:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:6:1:26.5:1:1:0:60:4:1:0:1 -5 149497099 . GCGCGCGCGCACACA G 183 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=17.000;MSILEN=2;SSF=0.0063;SOR=0.43157;LSEQ=GCAAACCTGGCAGCGCGCGC;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:59:50,9:169,11:0.2235:2,2:22.2:1:31.2:1:0.05328:2.75139:60:118:0.2278:0.0947:0.6 0/1:136:15:12,3:104,7:0.1103:2,2:24.1:1:31.7:1:0.09842:3.6574:59.3:30:0.1154:0:0.5 -5 149497109 . A G 178 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=2;SSF=0.03904;SOR=0.58733;LSEQ=CAGCGCGCGCGCGCGCGCGC;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:67:61,6:63,6:0.2557:2,2:15.8:1:29.4:1:1:1.03255:59.4:66:0.4459:0:2.5 0/1:155:26:23,3:63,4:0.1677:2,2:17.7:1:27.5:1:0.3948:2.03664:60:12:0.2637:0:2.1 -5 149497177 . T C 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17145;LSEQ=TTGGCCCCAGGCCAGGGTGG;RSEQ=TACCTGGCTAGGCTGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:743:644:393,251:54,44:0.8668:2,2:25.5:1:31.1:1:0.26988:1.28:59.9:19.774:0.8634:0:1.7 1/0:558:294:173,121:145,117:0.5269:2,2:25.6:1:31.1:1:0.43989:1.15:60:35.75:0.5287:0:1.5 -5 149497184 . G T 57 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04691;SOR=8.02992;LSEQ=CAGGCCAGGGTGGTTACCTG;RSEQ=CTAGGCTGGGGGAACCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:793:1:1,0:470,322:0.0013:2,0:15:0:13:0:1:0:60:0:0:0:5 0/1:597:6:2,4:333,258:0.0101:2,2:15.3:1:22.3:1:0.41248:2.57736:57.5:5:0.0087:0:2.7 -5 149497228 . G A 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.32954;LSEQ=GGGCCCTCGTCAGCAACCTC;RSEQ=GGTTTGGGGTCAGGCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1011:351:186,165:330,328:0.3472:2,2:24.9:1:30.4:1:0.42759:1.12:60:49.143:0.3464:0:1.5 0/1:785:117:61,56:318,347:0.149:2,2:26.3:1:29.8:1:0.42276:1.19:60:22.4:0.1451:0:1.6 -5 149497419 . C A 42 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22753;SOR=2.97899;LSEQ=CACCTGCTGGTACTTCTGCT;RSEQ=CCGGGGCAGGGAGAACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:2:1,1:174,345:0.0038:2,2:24:1:18.5:1:1:1.98:60:1:0.002:0:2 0/1:352:4:3,1:127,221:0.0114:2,2:9:1:21:1:0.14437:5.20:60:3:0.0086:0:2 -5 149497672 . C T 66 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAACTCTTCCCCCACTT;RSEQ=AGAGCAGACAGGCACAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:16:1:28.6:1:1:0:60:10:0.625:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149497815 . A G 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGTGGGGGTGAGAAATG;RSEQ=ACCCAAAGAAGGAGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:32.3:1:30.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149498064 . C G 92 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAGCAGGACAGACAGTGCT;RSEQ=TAGGCCCCCTCCCTGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:6,1:12,0:0.3684:0,2:31.3:1:33:1:0.36842:0:60:14:0.3684:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149498151 . G A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53412;SOR=0.71672;LSEQ=TGCTAAAATAAACTCACAGC;RSEQ=CCAGCCCATCCCCTCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:28:28,0:32,0:0.4667:1,1:25.4:1:29.9:1:1:0:60:27:0.4576:0:1.1 0/1:39:15:15,0:24,0:0.3846:1,1:21.1:1:30.5:1:1:0:60:30:0.3947:0:1.2 -5 149498193 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13082;SOR=Inf;LSEQ=CCAGCAGGGAAACTGAGGCC;RSEQ=AGAGAGGACAAAGGGTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:133,2:0:1,0:24.3:1:31.3:1:1:0:60:270:1:0:0.3 0/1:77:2:1,1:75,0:0.026:1,2:20.5:1:28.5:1:0.02597:0:60:4:0.026:0:1 -5 149498759 . A T 29 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTGGGACTTTTGCTGGC;RSEQ=CTATGGAGCAAGCAGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:12,3:0.1176:2,2:21.5:1:29:1:0.42647:3.6058:60:4:0.125:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149498821 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCATTTGGGCAATGCTGG;RSEQ=CTGAAAATGAGGCCACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:22,2:0.0769:2,0:23:1:29.5:1:1:0:60:4:0.08:0:1.5 0/0:6:0:0,0:6,0:0:0,0:29.7:1:31.8:1:1:0:60:12:1:0:0.3 -5 149498871 . AG A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09599;SOR=0.42631;LSEQ=GAGCTCAGGGCTAGAACAAG;RSEQ=GTTCCTGATGCCATCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:32:31,1:26,1:0.5424:1,1:21.7:1:31.9:1:1:1.19:60:64:0.5517:0.1356:0 0/1:24:8:7,1:16,0:0.3333:1,2:24.6:1:30.9:1:0.33333:0:60:16:0.3478:0.0417:0 -5 149499672 . T C 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.29807;LSEQ=CTCTCCGGAGCCATCCACTT;RSEQ=AAAGGCAAAAAGGTCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:761:432:170,262:119,209:0.5677:2,2:25.6:1:31.6:1:0.40714:1.14:60:85.4:0.5671:0:1.1 0/1:683:192:83,109:196,294:0.2811:2,2:27.6:1:30.8:1:0.48856:1.14:60:47:0.2781:0:1.2 -5 149499733 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07779;SOR=Inf;LSEQ=AGTGCAAGGAAGGACCTCAG;RSEQ=CCCACTCTGCACCTGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:51,239:0:2,0:24.7:1:31.2:1:1:0:60:71.5:1:0:0.4 0/1:217:3:1,2:44,170:0.0138:2,2:17:1:27.3:1:0.50384:1.92:60:6:0.0142:0:1 -5 149499796 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11721;SOR=Inf;LSEQ=CCACCCACAACCACTTCTCC;RSEQ=TCCCATTCCCTGTGAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:1,96:0:1,0:22.6:1:32:1:1:0:60:47.5:1:0:0.1 0/1:51:2:0,2:1,48:0.0392:1,0:43.5:1:30:1:1:0:60:4:0.0392:0:1 -5 149500236 . C T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.69075;SOR=0.56096;LSEQ=CCATTATAGCCAGCCCTCCC;RSEQ=GCCGCTATACTTGCTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:10,0:11,0:0.4762:0,0:25.8:1:29.8:1:1:0:60:9:0.45:0:2.2 0/1:9:3:2,1:6,0:0.3333:0,2:27.3:1:32.7:1:0.33333:0:60:6:0.3333:0:1 -5 149500363 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51732;SOR=0;LSEQ=GCCCCACACAGATTTCCTAT;RSEQ=AGCTGCAGCCACACTGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:168,8:0.0112:1,2:17:1:28:1:0.09884:19.85928:60:4:0.0114:0:1 0/0:120:0:0,0:107,13:0:2,0:21.3:1:32:1:1:0:60:119:1:0:0.1 -5 149500402 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0684;SOR=Inf;LSEQ=CAGGAGGGAATCTGTTCCTG;RSEQ=GGTCACAGGCACTGTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:299,110:0:2,0:23.4:1:31.2:1:1:0:60:203.5:1:0:0.1 0/1:284:3:1,2:207,74:0.0106:2,2:17.3:1:26.3:1:0.17554:5.55392:60:6:0.0106:0:1 -5 149500423 . C T 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.08744;SOR=7.11319;LSEQ=GGTCACAGGCACTGTGACTG;RSEQ=CCTGCAGGGGCCAGGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:1:0,1:381,192:0.0017:2,0:1:0:27:0:0.33624:0:60:2:0.0018:0:1 0/1:407:5:2,3:262,140:0.0123:2,2:20.6:1:25.8:1:0.34942:2.79952:60:10:0.0126:0:1 -5 149500434 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00576;SOR=Inf;LSEQ=CTGTGACTGCCCTGCAGGGG;RSEQ=CAGGGAAGGTACTCACGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:672:0:0,0:429,243:0:2,0:25.5:1:31.2:1:1:0:60:28.217:1:0:0.1 0/1:496:6:1,5:298,191:0.0121:2,2:12.7:1:25.7:1:0.03822:7.77004:60:12:0.0124:0:1 -5 149500514 . C T 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAGGCCAAAGTCACAGAT;RSEQ=TTGACCAGCTTGCCTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1020:0:0,0:508,509:0:2,0:26.1:1:31.5:1:1:0:60:58.824:0.998:0:0.2 0/1:827:32:14,18:382,413:0.0387:2,2:29.8:1:30.4:1:0.71941:1.18896:60:64:0.0393:0:1.2 -5 149500934 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16425;SOR=Inf;LSEQ=ATCTTATATCTCCTTCTGGC;RSEQ=CACAGGACCCCTGCCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:52,207:0:2,0:23.8:1:30.9:1:1:0:60:42.167:1:0:0.1 0/1:177:2:1,1:48,127:0.0113:2,2:14.5:1:29:1:0.47817:2.63:60:4:0.0115:0:1 -5 149501751 . A C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73297;SOR=0.79716;LSEQ=AGGAAAGCCTGTGGATCAAG;RSEQ=CTTTTCAACCAACCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:34:0,34:0,18:0.6538:1,1:22:1:29.7:1:1:0:60:10.333:0.6327:0:1.4 1/0:10:6:0,6:0,4:0.6:0,0:27.2:1:31.8:1:1:0:60:12:0.6:0:1.3 -5 149501803 . C T 82 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19087;LSEQ=CACTGAGGCTACCAAAATGA;RSEQ=AGTTAGAACCCAGAGAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:0,10:1,11:0.4545:2,0:20.9:1:24.9:1:1:0:60:4:0.4211:0:1.9 1/0:2:1:0,1:0,1:0.5:0,0:21:0:30:0:1:0:60:2:0.5:0:2 -5 149502529 . C A 41 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03276;SOR=Inf;LSEQ=TCACAGCCTCAGCTTCCCCT;RSEQ=CTGGACAAAAGGAGGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:95,7:0:2,0:25.3:1:31.5:1:1:0:60:204:1:0:0 0/1:49:3:3,0:40,6:0.0612:2,0:27.7:1:26:1:1:0:60:6:0.0625:0:1 -5 149502576 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15666;SOR=Inf;LSEQ=TGCTCCTCAGGTATCCCAAA;RSEQ=ATTCAGTCCCTGGCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:197,48:0:2,0:22.3:1:32.3:1:1:0:60:490:1:0:0.1 0/1:161:2:1,1:128,31:0.0124:2,2:32:1:30.5:1:0.35901:4.07985:60:4:0.0126:0:1 -5 149502838 . G C 208 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAGGCCATGAGGCTAATCA;RSEQ=GGGCTGGATGTGGGAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:220:121:11,110:6,93:0.55:2,2:24.4:1:30.2:1:0.45585:1.55:60:120:0.5556:0:1.1 0/0:104:0:0,0:16,88:0:2,0:21.8:1:30.4:1:1:0:60:208:1:0:0.1 -5 149502881 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09545;SOR=Inf;LSEQ=TTTGGCATGACGGCTAGGAG;RSEQ=CTTTAGTGCCTTGCAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:0,104:0:1,0:22.7:1:32.3:1:1:0:60:51:1:0:0.5 0/1:47:2:1,1:1,44:0.0426:1,2:30.5:1:28.5:1:0.08418:31.47:60:4:0.0426:0:1 -5 149503670 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=0.26543;LSEQ=CCCCACCGCCCTCTGGGACC;RSEQ=CGCAGTGAGGGCGCTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:81:76,5:53,1:0.6:1,2:24.5:1:30.2:1:0.40133:3.46039:60:39.5:0.6031:0:1.1 0/1:60:17:17,0:42,1:0.2833:1,1:22.1:1:30.1:1:1:0:60:34:0.2931:0:1 -5 149503739 . AG A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.57521;SOR=0.63907;LSEQ=GTGCTGTTGTGCAAGGCCTG;RSEQ=GGGGGGGTAGGCGGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:9:5,4:346,88:0.0203:2,2:22.9:1:31.3:1:0.09397:3.13484:60:18:0.0206:0.0045:0.3 0/1:306:4:4,0:216,86:0.0131:2,0:36.3:1:33:1:0.57971:0:60:8:0.0132:0:0 -5 149503974 . A G 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55631;SOR=0;LSEQ=CAGTCATGGAGGCTCCATGG;RSEQ=GGCCCCACCACAGGAGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:38,236:0.0108:2,2:20.3:1:24.3:1:0.05558:12.23:60:2:0.0074:0:1 0/0:157:0:0,0:24,133:0:2,0:20.9:1:30.7:1:1:0:60:77.5:1:0:0.1 -5 149504115 . A T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00165;SOR=0.24646;LSEQ=GCAGGCCGAGGAGGCCAGGG;RSEQ=GAGGAACGCTCTTTCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:78:63,15:39,11:0.6094:2,2:20.7:1:30.7:1:0.82236:1.18:60:156:0.624:0:1.8 0/1:29:8:8,0:18,3:0.2759:2,0:25.8:1:28.8:1:0.54023:0:60:16:0.2857:0:1.6 -5 149504155 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGACCCAGACTCGGGAG;RSEQ=AGTGCCTGCTGCAGTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:172,12:0.0108:2,2:28.5:1:29:1:0.13525:13.811:60:4:0.0109:0:3 0/0:75:0:0,0:70,5:0:2,0:20.9:1:32.6:1:1:0:60:150:1:0:0.6 -5 149504158 . T C 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08558;SOR=0.62126;LSEQ=AGACCCAGACTCGGGAGCAG;RSEQ=GCCTGCTGCAGTGTGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:195:117:107,10:74,4:0.6:2,2:25.2:1:31.8:1:0.41229:1.72441:60:38:0.6:0:1.6 0/1:83:40:39,1:39,4:0.4819:2,1:18.8:1:32.6:1:0.36118:3.94:60:80:0.4819:0:1.4 -5 149504167 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09489;SOR=Inf;LSEQ=CTCGGGAGCAGTGCCTGCTG;RSEQ=AGTGTGATGGCCCCTCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:214,14:0:2,0:24.3:1:31.9:1:1:0:60:44.6:1:0:0.9 0/1:102:2:1,1:96,4:0.0196:1,2:29.5:1:30.5:1:0.0961:21.5779:60:4:0.0198:0:2 -5 149504192 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1159;SOR=Inf;LSEQ=TGATGGCCCCTCTAGTGCCT;RSEQ=CAAATCAGCATCAGGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:259,49:0:2,0:24.2:1:31.8:1:1:0:60:43:1:0:0.6 0/1:160:2:2,0:138,20:0.0125:2,0:21.5:1:30:0:1:0:60:4:0.0125:0:1 -5 149504348 . C T 131 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00045;SOR=4.61475;LSEQ=GAATGGCTCAGGCCATGAGC;RSEQ=GTGGCCTCCACCACCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:987:6:1,5:463,516:0.0061:2,2:7.8:1:24:1:0.22204:4.48071:60:5:0.0052:0:1 0/1:728:20:8,12:320,386:0.0275:2,2:31.6:1:30.5:1:0.82048:1.24315:60:40:0.0278:0:1.1 -5 149505174 . G A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=CCCAGGAATTAGTTATCAGA;RSEQ=GGAGTCTCAGGCCCTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:858:0:0,0:286,572:0:2,0:24.7:1:31.2:1:1:0:60:121.571:1:0:0.1 0/1:620:8:6,2:216,395:0.0129:2,2:7.9:1:24.8:1:0.02788:5.47:60:7:0.0115:0:1.5 -5 149505259 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.03294;SOR=Inf;LSEQ=AGGCCCAGAGAGGGGCAGGG;RSEQ=CATATTTGAAGTCACACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:3,139:0:1,0:25.4:1:32.4:1:1:0:60:70:1:0:0.3 0/1:68:3:0,3:2,63:0.0441:1,0:15:1:30:1:1:0:60:6:0.0441:0:1 -5 149505291 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08475;SOR=Inf;LSEQ=TCACACAGCAAGTGCTCAAC;RSEQ=GAGCCAAGGTCTTCGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:2,82:0:1,0:23.5:1:29.9:1:1:0:60:20:1:0:0.6 0/1:35:2:1,1:1,32:0.0571:1,2:18:1:26.5:1:0.11261:22.98:60:4:0.0571:0:1.5 -5 149505306 . G A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63372;SOR=1.29608;LSEQ=TCAACTGAGCCAAGGTCTTC;RSEQ=TGGGCTCGGAGGGAACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:32:0,32:0,32:0.5:1,1:19:1:31.1:1:1:0:60:64:0.5161:0:1 1/0:23:13:1,12:0,10:0.5652:0,1:27.3:1:30.5:1:1:0:60:26:0.5652:0:1.2 -5 149505327 . A G 128 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05041;SOR=0.14775;LSEQ=TGGGCTCGGAGGGAACAGGG;RSEQ=CCAAGGGGCCCCAGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:16:0,16:0,30:0.3478:1,1:21.3:1:32.1:1:1:0:60:32:0.3478:0:1.4 0/1:14:1:0,1:1,12:0.0714:1,0:1:0:30:0:1:0:60:2:0.0714:0:1 -5 149509111 . C T 49 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04513;SOR=8.1767;LSEQ=ATATTCATATCCATGGCTTA;RSEQ=AGACTTGTGTTTGTACACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:26,1:0.1:1,0:31.7:1:31.3:1:1:0:60:6:0.1034:0:1 1/0:6:3:3,0:3,0:0.5:0,0:23.7:1:31:1:1:0:60:6:0.5:0:1 -5 149509243 . A T 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03703;SOR=Inf;LSEQ=TCCTTTGGCCTGCTGTGGGT;RSEQ=CATGGGCACATTACCAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:197,33:0:2,0:22.8:1:28.2:1:1:0:60:229:1:0:0.2 0/1:116:3:1,2:86,27:0.0259:2,2:8:1:25.3:1:0.15378:6.24361:60:6:0.0259:0:1.7 -5 149509270 . A G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.5999;LSEQ=CACATTACCAATTAGGCAGG;RSEQ=TTAAGGTAGGGATTGGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:42:31,11:245,92:0.1108:2,2:21.9:1:30.4:1:1:1.06:60:20:0.1096:0:1 1/0:240:131:84,47:69,36:0.5458:2,2:22.7:1:30.9:1:0.89099:1.07208:60:64.5:0.5536:0:1.2 -5 149509290 . C A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATTAAGGTAGGGATTGGGAT;RSEQ=GTCAGGGGCCACTGAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:314,147:0:2,0:27:1:30.7:1:1:0:60:152.667:0.9978:0:0.2 0/1:344:14:8,6:214,116:0.0407:2,2:32.1:1:30.4:1:0.57637:1.38221:60:28:0.0417:0:1.8 -5 149509619 . C T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=ACTGGTGGAAGGAGGCAGGA;RSEQ=GTGTCCAGTTCCTATGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:2,106:0:1,0:25:1:30.5:1:1:0:60:216:1:0:0.1 0/1:53:6:1,5:0,47:0.1132:1,2:23.7:1:31:1:0.11321:0:60:12:0.1154:0:1 -5 149510290 . A C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=AGTTAACAGGACAGGTCCTC;RSEQ=GGGGAGGACCTGGCCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:39,206:0:2,0:24:1:30.8:1:1:0:60:121.5:1:0:0.1 0/1:165:11:3,8:37,117:0.0667:2,2:19.1:1:27.2:1:0.72881:1.18:60:10:0.0613:0:1.1 -5 149511666 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03984;SOR=Inf;LSEQ=TCTGACACATACCTGGGGAG;RSEQ=AGGAAAGGCAGCTGTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:121,366:0:2,0:25:1:31.7:1:1:0:60:31.467:0.9916:0:0.1 0/1:398:4:2,2:120,274:0.0101:2,2:15.3:1:29.5:1:0.58937:2.28:60:8:0.0102:0:1 -5 149511792 . G A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5646;SOR=0;LSEQ=TCGGCATTGGTAGCAGAGCC;RSEQ=GGACTCAAACCAGGTCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:4:0,4:1,44:0.0816:1,0:20.3:1:31.3:1:1:0:60:8:0.0833:0:1 0/0:16:0:0,0:1,15:0:1,0:18.1:1:30.1:1:1:0:60:32:1:0:0.1 -5 149512042 . G A 32 v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCCCAGTCATCTGCCC;RSEQ=TTTACTTCTTGGCTGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:6,0:0.25:0,2:30:0:32:1:0.25:0:60:4:0.25:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 149512258 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16158;SOR=Inf;LSEQ=CTGAAAGCCGAGGGCTGCCT;RSEQ=GCGGCTGCAAAGAAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:129,22:0:2,0:25.4:1:32.1:1:1:0:60:150:1:0:0.2 0/1:102:2:1,1:85,15:0.0196:2,2:20.5:1:26.5:1:0.29043:5.51898:60:4:0.0198:0:1 -5 149512501 . G A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4902;SOR=1.81977;LSEQ=CCCAGGAGCCGCACGTAGCC;RSEQ=CTCTCTGCAAGGGGTGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:3:1,2:126,251:0.0079:2,2:24.7:1:28.7:1:1:1.00397:60:6:0.008:0:1 0/1:350:5:3,2:125,220:0.0143:2,2:8.6:1:24.2:1:0.35978:2.63:60:1.5:0.0087:0:1 -5 149513072 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.49877;LSEQ=AAAATGCAACTCTCACCATC;RSEQ=CTCTGCACCCAGCAAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:6:6,0:214,37:0.0233:2,0:25:1:30:1:0.59773:0:60:12:0.0236:0:1 0/1:209:69:59,10:116,23:0.3301:2,2:20.8:1:30.5:1:0.84085:1.17:60:68:0.3333:0:1.1 -5 149513626 . T G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15378;SOR=2.05875;LSEQ=TCACCACCAGCCACTAGCAC;RSEQ=TCAGCTTGGGGATAGGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:9:1,8:30,181:0.0409:2,2:29.2:1:32.7:1:1:1.32442:60:18:0.0413:0:1 0/1:136:11:2,9:24,100:0.0809:2,2:27.4:1:30.5:1:1:1.0794:60:22:0.0809:0:1.1 -5 149514660 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54823;SOR=0;LSEQ=TGCTGTGTGGCAAGTCATTT;RSEQ=CCATCTCTGGCCCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:12,182:0.0102:2,2:24.5:1:28:1:0.12857:14.61:60:4:0.0104:0:1 0/0:102:0:0,0:11,91:0:2,0:24.4:1:31.7:1:1:0:60:101:1:0:0.1 -5 149514958 . T G 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCAGACCAAGGAGTGGG;RSEQ=GCGAACACACTCCCCGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:51,3:0,0:1:0,2:23:1:31.3:1:1:0:60:108:1:0:1 1/1:16:16:16,0:0,0:1:0,1:24.3:1:32.3:1:1:0:60:32:1:0:1 -5 149515074 . G A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=12.78334;LSEQ=TTCCCCTGATGCCTCCAGTT;RSEQ=ACAAGAGGGGTAAGGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:16:13,3:312,86:0.0386:2,2:25.3:1:28.3:1:1:1.19:60:32:0.0391:0:1 0/1:315:107:79,28:157,51:0.3397:2,2:24.7:1:27.7:1:0.78437:1.09078:60:25.75:0.3411:0:1.1 -5 149515397 . T A 136 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=39.1857;LSEQ=GACGACCAGGCCCTGAGAGA;RSEQ=CTGTGGTTCCAGAAGTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:664:1:1,0:269,393:0.0015:2,0:23:0:14:0:0.40724:0:60:0:0:0:3 0/1:483:27:13,14:190,266:0.0559:2,2:21.7:1:28.8:1:0.55046:1.30:60:26:0.0552:0:1.2 -5 149515468 . A G 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29077;SOR=3.62878;LSEQ=GAGAGGAGGTATCAGACATC;RSEQ=GGAAACAGGGGCTTCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:0,1:39,205:0.0041:2,0:47:0:31:0:1:0:60:2:0.0041:0:1 0/1:136:2:1,1:38,96:0.0147:2,2:31:1:28.5:1:0.49281:2.51:60:4:0.0149:0:1 -5 149515577 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10204;SOR=Inf;LSEQ=CCTTTATCCGACAGACTGGG;RSEQ=CTCTCCAGCCATGGCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:0:1,0:23:1:31.8:1:1:0:60:32:1:0:0.2 0/1:16:2:1,1:1,13:0.125:1,2:5.5:1:26:1:0.24167:9.54:60:4:0.1333:0:1.5 -5 149516480 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.65611;LSEQ=GCAGTGTGCCTGGTGCTTCA;RSEQ=GCCCTGCCACCAGCACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:501:25:20,5:372,104:0.0499:2,2:27.4:1:30.5:1:1:1.12:60:50:0.0504:0:1.1 0/1:370:96:70,26:184,90:0.2595:2,2:19.9:1:30.2:1:0.30975:1.32:60:192:0.263:0:1.2 -5 149516738 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11872;SOR=Inf;LSEQ=CCAGCCTTCATGTCCGAGGG;RSEQ=CTGAAGTCAAAAGCCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:8,206:0:1,0:25:1:31.7:1:1:0:60:25.75:1:0:0.1 0/1:113:2:1,1:11,100:0.0177:2,2:16.5:1:27:1:0.20196:8.75:60:4:0.0177:0:1 -5 149516774 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10036;SOR=Inf;LSEQ=ACCACGTCCCAAGCCTGAAA;RSEQ=GGCACTCATGACCACAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:2,122:0:1,0:24:1:30.8:1:1:0:60:19.667:1:0:0.2 0/1:58:2:0,2:3,53:0.0345:2,0:13:1:30:1:1:0:60:4:0.0351:0:1 -5 149782814 . C T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2616;SOR=0;LSEQ=CCGTTCTCGTCGCACTTGGG;RSEQ=CTGAATGAACCCGGGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:2,1:267,31:0.01:2,2:8.3:1:29.3:1:0.28708:4.27215:60:6:0.0103:0:1 0/0:231:0:0,0:194,37:0:2,0:23.2:1:31.5:1:1:0:60:76:1:0:0.1 -5 149783188 . G A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0385;SOR=Inf;LSEQ=TCTTAGCACTTTGGGAGGCC;RSEQ=AGGTGGGCGGATCACTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:45,309:0:2,0:23.7:1:31.1:1:1:0:57.2:117:1:0:0.1 0/1:283:4:2,2:37,242:0.0141:2,2:10:1:29.5:1:0.0928:6.47:60:8:0.0143:0:1.5 -5 149783361 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1763;SOR=Inf;LSEQ=GAACCCGGGAGGCTGAGGTT;RSEQ=CAGTGAGCTGAGATCGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:230,18:0:2,0:26.8:1:32.2:1:1:0:59.5:30:1:0:0.1 0/1:180:2:1,1:173,5:0.0111:1,2:20.5:1:31:1:0.06574:31.67413:57:4:0.0112:0:2.5 -5 149783694 . G A 202 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=73.25062;LSEQ=CCTTTGACCTTCTACTTCAG;RSEQ=ACCCTGAATCCTAGAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1813:2:2,0:873,938:0.0011:2,0:1:0:20.5:1:0.23279:0:60:1:6e-04:0:1 0/1:1682:126:67,59:771,784:0.0749:2,2:23.3:1:29:1:0.45955:1.15:60:62:0.0744:0:1.2 -5 149783879 . G A 213 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=37.48889;LSEQ=TGGCGCCCTCACTGGATTGC;RSEQ=GGCAGCACTGGGGCAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1599:4:2,2:766,825:0.0025:2,2:11.3:1:25.8:1:1:1.08:60:3:0.0019:0:1.8 0/1:1513:130:63,67:660,723:0.0859:2,2:26.1:1:30.4:1:0.92689:1.03:60:129:0.0861:0:1.2 -5 149784087 . G GGA 118 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.26815;SOR=1.54894;LSEQ=AAACCAAGAAGGAACAGACA;RSEQ=GAGAGAGAGAGAAGTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1078:11:6,5:512,555:0.0102:2,2:20.7:1:30.3:1:0.76624:1.30:60:22:0.0104:0.0019:0.4 0/1:1145:18:9,9:554,570:0.0157:2,2:17.6:1:28.4:1:1:1.03:60:8:0.0142:0.0061:0.4 -5 149784414 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13664;SOR=Inf;LSEQ=TTTGCCCCTGGGGACAGAAA;RSEQ=ATGCAGGGCCAAATAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:0:1,0:21.3:1:32.4:1:1:0:60:46:1:0:0.2 0/1:14:2:0,2:0,12:0.1429:0,0:9.5:1:30:0:1:0:60:4:0.1429:0:1 -5 150229723 . C A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.026;SOR=Inf;LSEQ=GCTGCTGAAGGGTCCTATTT;RSEQ=TTTTCCTTTCTTTCATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:96,18:0:2,0:20.5:1:31.2:1:1:0:60:113:1:0:0.1 0/1:78:4:4,0:61,13:0.0513:2,0:21:1:28.5:1:1:0:60:8:0.0513:0:1 -5 150229801 . A C 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=5.03583;LSEQ=CATACGTAATTTAAAAAAAT;RSEQ=TGTATGGCAGTAAAAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:7:4,3:159,146:0.0224:2,2:22:1:32.4:1:1:1.22:60:14:0.0224:0:1.1 0/1:260:27:14,13:127,106:0.1038:2,2:27.5:1:31.7:1:0.84009:1.11208:60:54:0.1042:0:1 -5 150777720 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CAGTCGTTGGATTAACTGAC;RSEQ=CAGCAACCATTGCCCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:26.1:1:29.9:1:1:0:60:14:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:12.5:1:28.5:1:1:0:60:4:0.6667:0:1.5 -5 150777953 . C T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.38055;LSEQ=CCCGCAGTAATGCAGGTGTG;RSEQ=GGGCTGAAATATAATTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:42:19,23:154,133:0.1277:2,2:29.3:1:29.9:1:0.3252:1.4002:60:41:0.1262:0:1.7 0/1:341:113:62,51:124,104:0.3314:2,2:27.7:1:29:1:1:1.02:60:55.5:0.3333:0:1.8 -5 150777997 . A G 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=3.29258;LSEQ=CCTTTTGCTTGGGGTGTTAA;RSEQ=AAGAAAGTATCATATGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:37:14,23:129,155:0.1153:2,2:21.4:1:31.7:1:0.48233:1.36597:60:74:0.1164:0:1.9 0/1:366:110:56,54:120,135:0.3005:2,2:23.8:1:31.7:1:0.56831:1.17:60:220:0.3064:0:1.9 -5 150778076 . C T 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00245;SOR=2.86762;LSEQ=AGTAGATACTGTACTGGAAC;RSEQ=AGAACTGAAGAAACCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:15:4,11:11,87:0.1327:2,2:26.8:1:27.9:1:0.1127:2.84:60:14:0.1261:0:1.3 0/1:98:30:3,27:12,56:0.3061:2,2:25.4:1:28.1:1:0.54328:1.9169:60:29:0.3021:0:1.6 -5 150778145 . A T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27572;SOR=2.70643;LSEQ=AGAAAAAGCTCCAATTGCTC;RSEQ=TCCTTTATTCCAGCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:0,4:0,24:0.1429:1,0:32:1:31.3:1:1:0:60:8:0.1429:0:1.5 0/1:19:6:0,6:1,12:0.3158:1,0:16.8:1:31.2:1:1:0:60:12:0.3158:0:1.8 -5 151755922 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00111;SOR=Inf;LSEQ=TCAACCAGGAGGGTCTCCTC;RSEQ=GTGGAGAACAGTCAGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:101,13:0:2,0:25.6:1:30.9:1:1:0:60:113:1:0:0.2 0/1:105:9:8,1:85,11:0.0857:2,2:21.9:1:31.6:1:1:1.03:60:18:0.0874:0:1.2 -5 151755945 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49866;SOR=0;LSEQ=GGAGAACAGTCAGAAGTGGG;RSEQ=GCAGCAAGAGTGGAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:131,48:0.011:2,2:33:1:29:1:0.46924:2.71147:60:4:0.0111:0:1.5 0/0:177:0:0,0:126,51:0:2,0:23.8:1:30.3:1:1:0:60:28.5:1:0:0.5 -5 151755961 . TA T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.24984;SOR=Inf;LSEQ=TGGGGGCAGCAAGAGTGGAA;RSEQ=AAAAAATAAAAACCGGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:181,81:0:2,0:22.1:1:28.5:1:1:0:60:86.333:1:0:0.7 0/1:284:3:1,2:190,89:0.0106:2,2:15:1:29:1:0.24436:4.2455:60:6:0.0107:0.0035:0.3 -5 151756016 . G T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1612;LSEQ=AGACCAGGTGGGAGAAGAAG;RSEQ=TAGCTTGGATTAGAGTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:564:496:275,221:41,27:0.8794:2,2:26.7:1:29.6:1:0.51534:1.21991:60:81.667:0.8781:0:1.1 1/0:600:324:172,152:150,125:0.54:2,2:26.5:1:29:1:0.74264:1.06034:60:63.8:0.537:0:1.2 -5 151756225 . G C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0018;SOR=0.07592;LSEQ=GTGGCTTTCCTGGAGCAATG;RSEQ=AAAGAAAAGCCTGAGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:1,24:0,4:0.8621:0,1:22.6:1:32:1:1:0:60:50:0.8621:0:1.2 0/1:10:3:0,3:1,6:0.3:2,0:37.7:1:33.3:1:1:0:60:6:0.3:0:1 -5 151756309 . G T 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAGATTGATGCAATTTT;RSEQ=CTAGTAAAAAAGAAGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:15.8:1:30.8:1:1:0:60:8:0.5714:0:1.8 0/0:1:0:0,0:0,1:0:0,0:5:0:32:0:1:0:60:2:1:0:0 -5 151756408 . A G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATATTATTTTTAAAACAAC;RSEQ=CACAAAAGATAGGAAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:9:1:33.3:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 153690374 . T C 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0263;SOR=0.47541;LSEQ=CTTAAATCAGCTCTTCTCCT;RSEQ=TGAAATTAAATGACTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:132:116:89,27:11,5:0.8788:2,2:21.9:1:31.3:1:0.53629:1.49:60:232:0.8788:0:1.5 1/0:142:110:77,33:20,12:0.7746:2,2:23.1:1:31.1:1:0.51766:1.40:60:220:0.7746:0:1.7 -5 153690415 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24961;SOR=Inf;LSEQ=CTGAACAGTGGTGTTTCTTC;RSEQ=ACGATAACAGTTATTGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:164,107:0:2,0:25.3:1:31.2:1:1:0:60:53.2:1:0:1.2 0/1:291:3:2,1:169,119:0.0103:2,2:32:1:28.3:1:1:1.41:60:6:0.0104:0:2 -5 153690417 . C A 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01322;SOR=1.51639;LSEQ=GAACAGTGGTGTTTCTTCCA;RSEQ=GATAACAGTTATTGATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:140:84,56:89,59:0.4861:2,2:25.1:1:30.4:1:1:1.00563:60:280:0.4878:0:2 1/0:302:178:106,72:70,54:0.5894:2,2:24.9:1:29.8:1:0.63575:1.14:60:58.333:0.5853:0:2 -5 153690473 . C G 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.04836;LSEQ=GATTTAAAGGTGCTCATATA;RSEQ=CTTAAAATAAAATGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:178:91,87:100,103:0.4648:2,2:25.1:1:32.4:1:0.75836:1.08:60:177:0.4683:0:1.6 1/0:367:235:118,117:69,62:0.6403:2,2:27.1:1:31.6:1:0.66415:1.10317:60:77.333:0.6409:0:1.5 -5 153690516 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11437;SOR=Inf;LSEQ=AACATTTCTTACATTGACTT;RSEQ=TTTTCTCTAATTTTTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:114,168:0:2,0:25.1:1:31.5:1:1:0:60:55.4:1:0:0.4 0/1:267:3:1,2:109,155:0.0112:2,2:31.7:1:29:1:1:1.40472:60:6:0.0113:0:2.7 -5 154109263 . T A 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGTGGCATAATAGGTATT;RSEQ=AAAAAATACCTCTAGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:28.3:1:30.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 154193735 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGTGCCCAGTCCCAGGA;RSEQ=AGGGGACAATGAAGGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21:1:31:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 154194093 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2044;SOR=Inf;LSEQ=CAGCCCACAAGAAGGCCCTG;RSEQ=GGGCCCCCCCATTGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:77,46:0:2,0:25.2:1:30.4:1:1:0:60:29.75:1:0:0.1 0/1:102:2:1,1:54,46:0.0196:2,2:24.5:1:26:1:1:1.17206:60:4:0.0204:0:1.5 -5 154194111 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50268;SOR=0;LSEQ=TGCGGGCCCCCCCATTGCCC;RSEQ=GCACTGTCTCATAGAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:80,54:0.0147:2,2:10.5:1:30:1:1:1.47706:60:4:0.0154:0:1 0/0:112:0:0,0:58,54:0:2,0:26.2:1:29.4:1:1:0:60:36.333:1:0:0.3 -5 154194208 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23337;SOR=Inf;LSEQ=ATCACCATATTTTCTCCCTG;RSEQ=TGTTCCCACCATGCCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:90,101:0:2,0:27:1:32.2:1:1:0:60:190:1:0:0.1 0/1:179:2:1,1:93,83:0.0112:2,2:25:1:28.5:1:1:1.11976:60:4:0.0116:0:1 -5 154194283 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50691;SOR=0;LSEQ=AAACTGGGGTTTGGGGGAAG;RSEQ=TTTCAGCCTCTCCCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:40,84:0.0159:2,2:22.5:1:28.5:1:0.54667:2.09:60:4:0.0164:0:1 0/0:96:0:0,0:36,58:0:2,0:22.3:1:30.4:1:1:0:60:46:0.9787:0:0.1 -5 154194290 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50741;SOR=0;LSEQ=GGTTTGGGGGAAGGTTTCAG;RSEQ=CTCTCCCCACTCCCCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:32,75:0.0183:2,2:18:1:28.5:1:0.5158:2.32:60:4:0.0185:0:1 0/0:82:0:0,0:27,54:0:2,0:21.6:1:30.3:1:1:0:60:19.25:0.9872:0:0.1 -5 154504661 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08276;SOR=Inf;LSEQ=CTCTGGAAAGGAGAACTTAA;RSEQ=GCCTTGGCTCTGTCTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:20,1:0:1,0:18.9:1:29.9:1:1:0:60:20:1:0:0.2 0/1:9:2:2,0:7,0:0.2222:0,0:33.5:1:32:1:1:0:60:4:0.2222:0:2 -5 154504680 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09677;SOR=Inf;LSEQ=AAGCCTTGGCTCTGTCTTTT;RSEQ=AGTGGGTGGGTTGAGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:20,1:0:1,0:29.2:1:30:1:1:0:60:42:1:0:0.2 0/1:10:2:2,0:8,0:0.2:0,0:33.5:1:29.5:1:1:0:60:4:0.2222:0:2 -5 154504784 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51628;SOR=0;LSEQ=AAATTTCCCAGGAAATTAGG;RSEQ=TAGCTGAGTCAGGTGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:114,24:0.0143:2,2:5:1:29.5:1:0.32631:4.67443:60:4:0.0144:0:1 0/0:95:0:0,0:74,21:0:2,0:20.5:1:31.5:1:1:0:60:94:1:0:0.1 -5 154504827 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25623;SOR=0;LSEQ=AGTGTTCTCTTTTGCTTTCT;RSEQ=CATTTTCCCCAGCGACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:3:2,1:192,94:0.0104:2,2:18.7:1:28.3:1:1:1.02122:60:6:0.0104:0:1.7 0/0:236:0:0,0:142,94:0:2,0:25.6:1:31.7:1:1:0:60:58:1:0:0.4 -5 154504902 . C T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.07656;LSEQ=ACTTCTCAATTTCATCCACT;RSEQ=TCTGGAAGCTCACCTTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:381:361:167,194:8,11:0.9475:2,2:26.1:1:29.5:1:0.81568:1.18:60:44.125:0.9489:0:1.1 1/0:328:190:89,101:66,71:0.5793:2,2:24.4:1:29.4:1:0.82327:1.05472:60:94:0.5802:0:1.2 -5 154504947 . C T 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCTCAGGGCACATAAGCACC;RSEQ=ACATGTTGTCAGACATCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:65,171:0:2,0:24.3:1:31.4:1:1:0:60:46.2:1:0:0.8 0/1:169:19:7,12:50,100:0.1124:2,2:19.7:1:28.6:1:0.79928:1.17:60:38:0.1145:0:1.2 -5 154504952 . G A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2758;SOR=0;LSEQ=GGGCACATAAGCACCCACAT;RSEQ=TTGTCAGACATCAATTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:3:1,2:57,159:0.0136:2,2:32.7:1:23.3:1:1:1.39:60:2:0.0094:0:1.7 0/0:149:0:0,0:47,102:0:2,0:24.7:1:30.6:1:1:0:60:73.5:1:0:0.7 -5 154505054 . CAGA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.04625;SOR=0;LSEQ=GTGTGCGCATGTGAGTGAAT;RSEQ=TGTTAATCTGCTTTGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:9:0,9:0,27:0.2308:1,0:21.2:1:32.9:1:1:0:60:18:0.2432:0.1026:1.4 0/0:16:0:0,0:1,12:0:1,0:17.4:1:30.4:1:1:0:60:26:0.8125:0:0.3 -5 154505097 . G T 72 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06061;SOR=0;LSEQ=AACCTTTTTCAAACACAACC;RSEQ=AATTCCTAAAGAACCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:22.7:1:28.2:1:1:0:60:12:1:0:1.8 0/1:5:2:0,2:0,3:0.4:0,0:18:1:29:0:1:0:60:4:0.4:0:1 -5 154505672 . T C 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTTGCTTCCTTCCTTGC;RSEQ=TCCTTCCTTCCTTCCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:32.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:25:0:28:0:1:0:60:2:1:0:1 -5 154936066 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68795;LSEQ=ACCAATGGTAAACAAAGATG;RSEQ=CTCTTTGTGAGCCTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:120,5:0.0157:1,0:26.5:1:29:1:1:0:60:4:0.0161:0:1 0/1:92:1:1,0:81,10:0.0109:2,0:50:0:31:0:1:0:60:2:0.0112:0:1 -5 154936095 . TA T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.81356;SOR=1.17875;LSEQ=GAGCCTTTAAAATTTCAAGT;RSEQ=AAAAAAAAAGACCCAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:10:9,1:163,25:0.05:2,2:31.7:1:31:1:1:1.38:60:20:0.0508:0:0 0/1:154:9:8,1:113,30:0.0584:2,2:18.8:1:30.9:1:0.68684:2.12:60:18:0.0592:0.0065:0.2 -5 154936207 . T C 219 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAAAGTGGGTACTGTCAT;RSEQ=TGACCCCCACCCAAATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:812:0:0,0:426,386:0:2,0:25.3:1:30:1:1:0:60:134.333:1:0:0.1 0/1:758:127:65,62:331,299:0.1675:2,2:26.3:1:31.4:1:0.84567:1.05589:60:254:0.1687:0:1.2 -5 154936211 . C T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGTGGGTACTGTCATTTGA;RSEQ=CCCCACCCAAATGTTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:809:0:0,0:412,397:0:2,0:25.8:1:31.4:1:1:0:60:100.125:1:0:0.1 0/1:771:18:7,11:390,363:0.0233:2,2:23.8:1:27.4:1:0.34286:1.68716:60:8:0.0211:0:1.9 -5 154936212 . C T 207 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTGGGTACTGTCATTTGAC;RSEQ=CCCACCCAAATGTTGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:808:0:0,0:407,401:0:2,0:25.9:1:30.7:1:1:0:60:56.714:1:0:0.1 0/1:778:130:64,66:333,314:0.1671:2,2:24:1:29.5:1:0.70071:1.09352:60:42.333:0.1656:0:1.1 -5 154936488 . T TC 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00714;SOR=Inf;LSEQ=TTTCAGAAATATTTGCTGTT;RSEQ=CCTTTAATCCTTGCTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:0:0,0:16.4:1:30.5:1:1:0:60:24:1:0:0.2 1/0:4:3:1,2:0,1:0.75:0,2:24:1:30.4:1:1:0:60:6:0.75:0.25:0 -5 161253208 . A G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGGTGTTCCTACTATT;RSEQ=CATGTTTCCTGTGGGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:32.3:1:31.5:1:1:0:60:8:0.5:0:1 0/0:1:0:0,0:1,0:0:0,0:40:0:29:0:1:0:60:2:1:0:0 -5 161253295 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68913;SOR=0.59337;LSEQ=TACATTCATTCCTAATCCCC;RSEQ=GGTACCAAAGGGTATGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:10,1:3,0:0.7333:0,2:18.1:1:28.2:1:1:0:60:10:0.7692:0:1.9 1/0:13:8:8,0:5,0:0.6154:0,0:27.1:1:28.1:1:1:0:60:16:0.6154:0:1.8 -5 161253358 . A G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01441;SOR=0.35314;LSEQ=TTTTCCGTTCTGAGCCATTT;RSEQ=AGGGCCAATATCCAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:37:30,7:17,2:0.6607:2,2:26.1:1:30.6:1:0.70265:1.9612:59.3:8.25:0.6346:0:1.6 0/1:42:17:15,2:21,3:0.4048:2,2:20.1:1:28.9:1:1:1.07:58.8:7.5:0.375:0:2 -5 161253422 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.501;SOR=Inf;LSEQ=AAAAAAAAAAAGTAGACAGA;RSEQ=GAGGCAACCAGCTGAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:89,79:0:2,0:19.3:1:28.8:1:1:0:59.7:9.5:0.9935:0:1.2 0/1:194:2:1,1:95,97:0.0103:2,2:18.5:1:29.5:1:1:1.02:60:4:0.0112:0:2.5 -5 161253451 . A T 215 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.46718;LSEQ=CAGCTGAGACTTTCAGGCTC;RSEQ=TGGATTCCAGAAATGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:225:132:63,69:41,52:0.5867:2,2:28.9:1:30.6:1:0.68389:1.16:60:65:0.5991:0:1.3 0/1:236:94:45,49:63,79:0.3983:2,2:31.1:1:30.1:1:0.68901:1.15:59.9:93:0.4115:0:1.2 -5 161253677 . A G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCATTTACAGGGATTCA;RSEQ=TTCTAGATGTTTCCCTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:12:1:33.5:1:1:0:60:4:0.4:0:1.5 0/0:2:0:0,0:1,1:0:2,0:13.5:1:27.5:1:1:0:60:4:1:0:0.5 -5 161322652 . G GT 60 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.56375;SOR=0;LSEQ=TATGAACTGGCATCATGTAT;RSEQ=TTTTTTTTTTTCTTTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:4:4,0:34,0:0.1053:1,0:33.5:1:30.3:1:1:0:60:8:0.1053:0.0263:0 0/0:14:0:0,0:14,0:0:1,0:18.8:1:32.6:1:1:0:60:28:1:0:0.4 -5 161322654 . T C 52 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=11.000;MSILEN=1;SSF=0.62655;SOR=1.64973;LSEQ=TGAACTGGCATCATGTATGT;RSEQ=TTTTTTTTTCTTTACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:3,0:35,0:0.0789:1,0:21.7:1:33:0:1:0:60:6:0.0789:0:1 0/1:16:2:2,0:14,0:0.125:1,0:5:1:30.5:1:1:0:60:4:0.125:0:1 -5 161322889 . G A 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.11768;LSEQ=GAAAAGGTAAATGCTTTAAT;RSEQ=GTCACTGTAGTACATCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:765:381:170,211:179,205:0.498:2,2:24.2:1:29.6:1:0.61152:1.08364:60:94.25:0.5013:0:1.1 1/0:698:473:220,253:107,117:0.6777:2,2:25:1:29.5:1:0.80745:1.0516:60:156.667:0.6802:0:1.2 -5 161323930 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGTGTTGTACTTCTTGAT;RSEQ=GCAAAAGGCTATTAAATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:31.5:1:1:0:60:4:1:0:1 -5 162712457 . A G 67 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTAAAGGTCCTGAGGCA;RSEQ=GAATAAGCTTGGTGTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:1,0:0.6667:0,0:17.3:1:33.8:1:1:0:60:8:0.6667:0:1 1/1:2:2:1,1:0,0:1:0,2:17:0:33:1:1:0:60:4:1:0:1 -5 162712583 . G A 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTGGAATCTAGGATGTTA;RSEQ=TGGTTGTCTGCATCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:57,0:0:1,0:24.2:1:32.6:1:1:0:60:114:1:0:0.1 0/1:53:18:17,1:34,1:0.3396:1,1:22.4:1:28.7:1:1:1.97209:60:17:0.3269:0:1.1 -5 162712737 . C T 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03754;SOR=0.74741;LSEQ=GGTGGTTAAACTTATATTGA;RSEQ=TTAAATGTACTATGAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:162:78,84:123,139:0.3821:2,2:24.1:1:30.4:1:0.84165:1.05:60:53:0.3786:0:1.1 0/1:500:158:72,86:167,175:0.316:2,2:28.3:1:29.9:1:0.50222:1.13954:60:316:0.3198:0:1.1 -5 165332375 . A AT 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10502;SOR=0;LSEQ=TTGTTGTAAACAAGCAAGTT;RSEQ=AGGGCAAGGTTCCTGCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:2,2:6,9:0.2105:2,2:18.3:1:29.6:1:1:1.47:60:8:0.2105:0.1053:0 0/0:18:0:0,0:8,10:0:2,0:32.5:1:29.2:1:1:0:60:36:1:0:0.4 -5 165332462 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=ATAGCTTCCTGAAACCCATG;RSEQ=AGGAAAATGATCAGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:0:2,0:25:1:27.6:1:1:0:60:6:1:0:0.1 0/1:6:2:1,1:1,3:0.3333:2,2:5:1:29:1:1:2.45:60:4:0.3333:0:1 -5 165488576 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49245;SOR=Inf;LSEQ=ATCCTGCTAAAAGGAAAACT;RSEQ=TGATTTGGGTAGGTCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:0:2,0:21.8:1:30:1:1:0:60:18:1:0:0.5 0/1:23:2:1,1:14,7:0.087:2,2:9.5:1:27:1:1:1.93655:60:4:0.087:0:1.5 -5 167024749 . CTT C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGCTATCTTACTTTCAAA;RSEQ=ATATATGCATGTCATATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:45.5:1:33.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 169531898 . G T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCGTGTGCGCGTGTGTGGGC;RSEQ=TGCGCGTGTGCGTGTGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:60:2:1:0:1 -5 169531949 . T G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGCGCGTACGCGTGTGTGCG;RSEQ=GTATGTGTGTGTTGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27.5:1:20.5:1:1:0:60:1:1:0:1 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30:1:1:0:60:4:1:0:2 -5 169533195 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCACCCTACCTGCCCGG;RSEQ=CCCAACGCCAGCCCCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44:0:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 169533606 . T C 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64663;SOR=1.75443;LSEQ=TCCTCCCCAAGACCCCATTC;RSEQ=AGAAAGTTCTGACTAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:0,5:0,12:0.2941:0,0:26:1:34:0:1:0:60:10:0.2941:0:1 0/1:7:3:0,3:0,4:0.4286:0,0:26.7:1:33:1:1:0:60:6:0.4286:0:1 -5 170187643 . T C 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CTACCTACAGAGACCCCTAC;RSEQ=ACTCCCCAGGCTCAACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:32.5:1:30.5:1:1:0:60:4:0.4:0:1 1/1:1:1:1,0:0,0:1:0,0:13:0:25:0:1:0:60:2:1:0:1 -5 170448963 . A G 90 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=TGAATGGGGTTTTTCTGTGG;RSEQ=CTTTTTTGTTGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:23:1:32.3:1:1:0:60:14:1:0:2.4 1/0:7:5:3,2:1,1:0.7143:2,2:41.8:1:31:1:1:1.41:60:10:0.7143:0:2.8 -5 170448971 . G T 84 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.46154;SOR=0;LSEQ=GTTTTTCTGTGGACTTTTTT;RSEQ=TTGTTGTTGTTGATGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:21.4:1:30:1:1:0:60:14:1:0:2.4 1/0:7:5:3,2:1,1:0.7143:2,2:38:1:29:1:1:1.41:60:10:0.7143:0:2.8 -5 170449000 . A G 58 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGATGCTCCTGTTGTTGC;RSEQ=TTGTTTGTTTGTTTGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:22.3:1:32.5:1:1:0:60:8:1:0:2.5 1/1:4:4:2,2:0,0:1:0,2:13.5:1:29.3:1:1:0:60:8:1:0:3 -5 170449265 . A T 148 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00065;SOR=0;LSEQ=TGCCAACCCCTGTTGGAGGG;RSEQ=CTCACCCAGTTGGGTGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:16,16:0,0:1:0,2:26.6:1:29.7:1:1:0:60:64:1:0:1.2 1/0:25:17:8,9:5,3:0.68:2,2:29.6:1:28.4:1:0.67277:1.82828:60:16:0.6667:0:1.1 -5 170449442 . G C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AGACTGTGGCCATCCTTCCC;RSEQ=CTAGGGGCTCAGGCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:33.7:1:31.7:1:1:0:60:6:1:0:1 0/0:2:0:0,0:0,2:0:0,0:22.5:1:33.5:1:1:0:60:4:1:0:0 -5 170449872 . C G 84 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCTGAGAGGCGGTTGA;RSEQ=AATCTGTAGGGCTCTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:20.2:1:32:1:1:0:60:10:1:0:1 1/1:8:7:4,3:1,0:0.875:0,2:18.3:1:30.1:1:1:0:60:14:0.875:0:1.3 -5 170814849 . C T 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.74857;LSEQ=ATATAAGCGCGGGGAGCCTG;RSEQ=GTCCTTTCCCTGGTGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:5:1,4:344,131:0.0104:2,2:6.4:1:26:1:0.02362:10.4463:60:10:0.0106:0:1 0/1:438:37:23,14:279,122:0.0845:2,2:18.5:1:29.2:1:0.35739:1.39094:60:74:0.0847:0:1.2 -5 170815125 . G T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00283;SOR=0.50611;LSEQ=GTGGAGACCGCCAGACCGAC;RSEQ=GGAGGCCTGAGCGGGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:189:121:5,116:3,65:0.6402:1,1:25.4:1:30.1:1:1:1.07038:60:39.333:0.6344:0:1.4 0/1:150:71:4,67:5,74:0.4733:2,2:22.5:1:29.8:1:1:1.13083:60:142:0.4797:0:1.5 -5 170816401 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGGAGTGAGAGTAGACA;RSEQ=ATGTATTCAAAACATTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:47.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170816498 . G C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTGATAACTATCGGAAA;RSEQ=AACCCTCCTTGTCTTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170816969 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.10604;SOR=Inf;LSEQ=AGTGAAAAACTAGTTCAAAA;RSEQ=TTAGACCTGACCTTTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:236,70:0:2,0:20.4:1:31.6:1:1:0:60:42.714:1:0:0.1 0/1:276:3:1,2:204,69:0.0109:2,2:13.3:1:27:1:0.16346:5.86644:60:6:0.011:0:2 -5 170817555 . C T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGCCAAGATCACAAAA;RSEQ=CTGAGGACAACATTGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:41:0:30:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170817947 . C CA 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGTTGTCCAGGCTGGTCT;RSEQ=AAACTCCTGACCTCATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:28.3:1:30.7:1:1:0:60:6:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170818290 . AT A 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08852;SOR=0.77255;LSEQ=AACTCAAAAGTTGAAGTAGT;RSEQ=TTTTTTTTTGTTCACAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1597:100:48,52:776,708:0.0626:2,2:27.2:1:31.1:1:0.41041:1.18725:59.9:99:0.0634:0.0056:0.3 0/1:1936:95:52,43:935,897:0.0491:2,2:30.1:1:30.3:1:0.52815:1.16:60:190:0.0498:0:0.2 -5 170818897 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00128;SOR=0.38139;LSEQ=TAAAGCATGGGTATAGTACT;RSEQ=CTGTCTTTTTAATAGGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:119:77:1,76:0,42:0.6471:1,1:23:1:32.2:1:1:0:60:76:0.6552:0:1.9 0/1:78:32:1,31:1,45:0.4103:1,1:23.9:1:32:1:1:1.44:60:31:0.4133:0:1.9 -5 170818906 . T A 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.25381;SOR=0.68243;LSEQ=GGTATAGTACTACTGTCTTT;RSEQ=TAATAGGTTCCAATGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:62:0,62:0,34:0.6458:1,1:25.8:1:31.6:1:1:0:60:124:0.6526:0:2.2 1/0:65:36:0,36:1,28:0.5538:1,1:24.9:1:30.5:1:0.44615:0:60:72:0.5714:0:1.8 -5 170818966 . GGGA TGGGGG 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.18679;SOR=0.36504;LSEQ=AAATAAATTTTTGGGGCGGG;RSEQ=GAGGAAATCTTGCTGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:21:0,21:0,14:0.5833:1,1:21:1:31.4:1:1:0:60:42:0.5833:0.1667:2.1 0/1:12:4:0,4:1,7:0.3333:2,0:18.8:1:30.3:1:1:0:60:8:0.3333:0.0833:2.3 -5 170819122 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGTTGCGTTTCATAGTT;RSEQ=TAGTAGAGAAGGGGTTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170819590 . CTTT C 175 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=17.000;MSILEN=1;SSF=0.21285;SOR=0.66877;LSEQ=AGTTCCTTTTCCCATGTGCT;RSEQ=TTTTTTTTTTTTTTAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:48:47,1:22,0:0.4848:1,1:23.1:1:31.4:1:1:0:59.3:47:0.4947:0.1313:1.8 0/1:70:27:27,0:33,0:0.3857:1,1:24.7:1:31.8:1:1:0:60:54:0.3913:0.0571:1.2 -5 170819607 . T A 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04894;SOR=0.53973;LSEQ=GCTCTTTTTTTTTTTTTTTT;RSEQ=AAATAGAATAGAAGTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:113:79:74,5:32,2:0.6991:2,2:26.2:1:27.2:1:1:1.08034:59.6:12.167:0.7019:0:1.7 1/0:81:45:43,2:33,3:0.5556:2,1:25.4:1:27.6:1:0.65109:1.94:60:90:0.5844:0:1.2 -5 170819654 . C CT 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17084;SOR=0.47881;LSEQ=GAGTATTTACTATCAGTGTT;RSEQ=TTTTTTTTTCTGACTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:13:8,5:200,69:0.0435:2,2:16:1:28.8:1:0.33612:1.80726:60:26:0.0504:0.0134:0.1 0/1:329:7:5,2:206,109:0.0213:2,2:36.4:1:29.4:1:1:1.32:60:14:0.0232:0:0.1 -5 170819887 . G A 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.4934;LSEQ=TTGGTGATAGAACAGCTCTT;RSEQ=TTCATGAGTACGTATCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:675:438:192,246:99,137:0.6489:2,2:23.6:1:29.9:1:0.68371:1.08:60:108.5:0.6468:0:1.1 0/1:755:360:156,204:185,210:0.4768:2,2:24.3:1:28.9:1:0.3421:1.1518:60:179:0.4773:0:1.1 -5 170820024 . G A 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=0.55895;LSEQ=TGATATACTTCCGGAATCTT;RSEQ=ACAAAAAAAGGAATTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:414:272:89,183:44,98:0.657:2,2:22.8:1:29.5:1:0.7407:1.08:60:544:0.6586:0:1.1 1/0:385:199:74,125:64,122:0.5169:2,2:23.1:1:28.8:1:0.59595:1.13:60:65.333:0.5158:0:1.1 -5 170826687 . A ATT 71 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTCTATTTAGGTCTTTA;RSEQ=TTTTTTTTTTTAACACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,0:0.7143:0,2:31.6:1:30.9:1:1:0:60:10:0.7143:0:0.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170827115 . C A 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00165;SOR=0.57956;LSEQ=TCAATTCTTGTGTCTACTCC;RSEQ=AAATTTTGAAAGTGCTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:293:169:123,46:86,38:0.5768:2,2:26.7:1:30.3:1:0.60116:1.18:60:83.5:0.5759:0:2.1 0/1:263:116:87,29:108,39:0.4411:2,2:25.9:1:29.6:1:0.88731:1.08:60:232:0.4411:0:2.1 -5 170827118 . A G 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00197;SOR=0.58913;LSEQ=ATTCTTGTGTCTACTCCCAA;RSEQ=TTTTGAAAGTGCTTAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:295:171:125,46:85,39:0.5797:2,2:27.4:1:32.1:1:0.43534:1.25:60:56:0.5813:0:2.1 0/1:279:125:93,32:113,41:0.448:2,2:25.3:1:31.3:1:0.89155:1.05:60:61.5:0.4473:0:2 -5 170827156 . GTGA G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.80768;SOR=0.80016;LSEQ=GTCTTGACATTTCATTTGTA;RSEQ=TGATGATGATGATTTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:9:6,3:325,214:0.0164:2,2:20.1:1:32.9:1:1:1.32:60:18:0.0166:0.0036:0.1 0/1:608:8:5,3:373,227:0.0132:2,2:27.6:1:32.6:1:1:1.01:60:16:0.0134:0.0016:0 -5 170827311 . T TGGGAGATCATCTCATACTGA 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00804;SOR=0.58604;LSEQ=GTAGTTAAGGGAAGCTGGTG;RSEQ=GGGAGATCATCTCATACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:90:1,89:28,140:0.3448:2,1:27.6:1:30.8:1:4e-05:17.68778:59.8:180:0.3462:0.092:0.1 0/1:242:57:0,57:34,149:0.2355:2,1:26.4:1:30.8:1:6e-05:0:59.9:114:0.2355:0.0785:0.1 -5 170827459 . C T 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=CCAAGTGGTTGCTGCTTTTT;RSEQ=CTTCCTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:1,10:2,6:0.55:2,2:22.1:1:27.1:1:0.54592:3.12168:59.1:4.5:0.5294:0:1.6 0/0:1:0:0,0:0,1:0:0,0:25:0:32:0:1:0:60:2:1:0:0 -5 170827464 . CT C 76 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTTGCTGCTTTTTCCTTC;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:0,6:0.3125:0,2:34.2:1:32.8:1:0.18182:0:58:10:0.3125:0:3.2 0/0:1:0:0,0:0,1:0:0,0:19:0:30:0:1:0:60:2:1:0:0 -5 170827654 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04581;SOR=Inf;LSEQ=CATTTTTAGTAGACCACCAT;RSEQ=TCGGCCAGGCTGGTCTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:0:1,0:21.9:1:32.6:1:1:0:60:122:1:0:0 0/1:35:3:3,0:32,0:0.0857:1,0:20:1:29.7:1:1:0:60:6:0.0857:0:1 -5 170828123 . G A 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11149;SOR=0;LSEQ=TCCCAGCACTTTGGGAGGGA;RSEQ=GCCAAGGTGGGTGGGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:0,4:0,24:0.1429:1,0:22:1:32:1:1:0:60:8:0.1429:0:1 0/0:28:0:0,0:0,28:0:1,0:17.2:1:30.9:1:1:0:60:27:1:0:0.1 -5 170828170 . C T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61752;SOR=0.44089;LSEQ=TCAGGAGTTTGAGACTAGCC;RSEQ=GGCCAACATCGTGAAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:0.6111:0,0:17.5:1:30.9:1:1:0:60:22:0.6111:0:1 0/1:5:2:0,2:0,3:0.4:0,0:37.5:1:32:0:1:0:60:4:0.4:0:1 -5 170831875 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GCACTGAGTGAACGAGACTC;RSEQ=GTCTGCCCTGATTTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:17.5:1:31.5:1:1:0:42.5:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170831912 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTGAACTGACTTAGTA;RSEQ=TGTGCATAAAAGCAAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:32.5:1:30.5:1:1:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170831942 . C CT 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAAACTCCCAAGTTACT;RSEQ=TTTTTTTTTTTATTTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:21:1:29.5:1:1:0:60:4:0.2857:0:2 0/0:1:0:0,0:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 -5 170832092 . C A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01474;SOR=Inf;LSEQ=GCTGGGATTACAGGCATGCA;RSEQ=CACCATGCCTAGCTAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:42,0:0:1,0:22.9:1:32.2:1:1:0:60:41:1:0:0.1 0/1:24:4:4,0:20,0:0.1667:1,0:21:1:30.5:1:1:0:60:8:0.1667:0:1.5 -5 170832187 . G A 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3099;SOR=1.37913;LSEQ=TATTGATGATAATTCCAGTT;RSEQ=TATAATTAGCTTTATAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:27:26,1:274,2:0.0891:1,1:27.7:1:28.7:1:0.24495:5.21617:60:54:0.0894:0:1.1 0/1:227:27:27,0:200,0:0.1189:1,1:26:1:27:1:1:0:60:26:0.1161:0:1.1 -5 170832243 . A G 289 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.63147;LSEQ=TTTGAGGAAATCCAGATAGA;RSEQ=TGGGTTTTAATTAGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:860:543:364,179:200,115:0.6314:2,2:24.3:1:31.9:1:0.29709:1.17:60:134.75:0.6297:0:1.1 1/0:870:452:285,167:262,154:0.5195:2,2:24:1:31.2:1:1:1.00:60:904:0.5207:0:1.1 -5 170832637 . C T 72 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTCCATTATGCAAGGAA;RSEQ=GTAGTGCACTGGTTGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:26:1:31.4:1:1:0:60:10:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170832767 . TACAA T 69 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATGAGACTTCATTAAAAT;RSEQ=ACAGCTGGAAAAGTAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:21.8:1:29.8:1:1:0:60:10:0.8333:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170833005 . A G 45 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GGAAGAGGGTTAGGTCTCTC;RSEQ=TCTGCTTGACTGGGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29.3:1:29:1:1:0:60:6:1:0:2.3 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 170834890 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52167;SOR=0;LSEQ=TTAAAAAGTTCCTAACCACA;RSEQ=ATAATATTTCATTTAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:0,2:0,129:0.0153:1,0:25.5:1:29.5:1:1:0:60:4:0.0155:0:1 0/0:84:0:0,0:1,83:0:1,0:25:1:31.7:1:1:0:60:168:1:0:0 -5 170837222 . C CAG 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GCCAACTCTAAAGCTGATCT;RSEQ=GGGAGATGAAGTTGGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:18:1:31.7:1:1:0:60:6:1:0.6667:0 0/0:1:0:0,0:1,0:0:0,0:19:0:33:0:1:0:60:2:1:0:0 -5 170837279 . T G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14229;SOR=Inf;LSEQ=TCTCTGTTCTTTCTGTTGAT;RSEQ=TCCTTAAGTAAATAATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:0:1,0:14.5:1:30.5:1:1:0:60:28:1:0:0 0/1:9:2:2,0:7,0:0.2222:0,0:17:1:34:0:1:0:60:4:0.2222:0:1 -5 170837457 . A G 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02272;SOR=1.64186;LSEQ=AATAGATGTTGAACTATGCA;RSEQ=AGAGACATTTAATTTATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:37:22,15:204,145:0.0954:2,2:25.8:1:31.5:1:1:1.04:60:36:0.094:0:1.2 0/1:481:71:46,25:237,173:0.1476:2,2:26:1:31.2:1:0.29766:1.34:59.9:34.5:0.1456:0:1.2 -5 170837509 . A AT 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.10699;SOR=0.45898;LSEQ=TGTTGTGGTTCCTTAACCAC;RSEQ=TTTCTTTTTTTTTTTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:12:0,12:174,197:0.0302:2,0:38:1:28.2:1:0.00066:0:60:11:0.0332:0:2.3 0/1:498:7:0,7:227,247:0.0141:2,0:33:1:26.1:1:0.01597:0:58.6:6:0.0145:0:2 -5 170837733 . CT C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GAATGTGTTGTCCAAAATGC;RSEQ=GTTTAGTTTTTAAAGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:33:1:32.7:1:1:0:42:6:0.75:0:0 0/0:3:0:0,0:0,3:0:0,0:19.7:1:32:0:1:0:40:6:1:0:0.3 -5 170883125 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51153;SOR=Inf;LSEQ=CTCCTGAACCTTCTCTTATG;RSEQ=CCATCTGTGCACTTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,15:0:2,0:33.4:1:31.4:1:1:0:60:26:1:0:0 0/1:40:2:1,1:18,20:0.05:2,2:33.5:1:28.5:1:1:1.11:60:4:0.05:0:1 -5 172084989 . C G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09962;SOR=Inf;LSEQ=GCTGACATATGCTGCCTTCT;RSEQ=TGTCTGCTTCAGCTACCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:22.6:1:31.1:1:1:0:58.7:14:1:0:0.3 0/1:14:3:2,1:8,3:0.2143:2,2:15.7:1:30:1:1:1.30524:60:6:0.2143:0:1 -5 172123916 . A T 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.498;SOR=0;LSEQ=CCCAGGAAAGAAACACCAGG;RSEQ=TGTTCCCAGGAACCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:74,31:0.0187:2,2:18.5:1:24:1:0.51067:2.36534:60:4:0.0187:0:1 0/0:101:0:0,0:69,32:0:2,0:16.5:1:29.2:1:1:0:60:49.5:1:0:0.2 -5 172123938 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09845;SOR=0;LSEQ=GTTCCCAGGAACCCTCTCTG;RSEQ=CTTCCCCATCTGCCCGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:1,2:110,57:0.0176:2,2:21:1:27.7:1:0.2765:3.82675:60:6:0.018:0:2 0/0:197:0:0,0:121,75:0:2,0:22.2:1:31.4:1:1:0:60:64.333:1:0:0.2 -5 172123950 . G A 19 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.85313;LSEQ=CCTCTCTGGCTTCCCCATCT;RSEQ=CCCGCAGTTTCCCACGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:121,76:0.0101:2,2:17.5:1:26.5:1:1:1.5882:60:4:0.0101:0:1 0/0:233:2:2,0:137,94:0.0086:2,0:36.5:1:19:1:0.51658:0:60:1:0.0044:0:1 -5 172124010 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50165;SOR=Inf;LSEQ=TGCCACCCCACCCCTGATCA;RSEQ=CACAAAAAGAGTTCCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:57,90:0:2,0:24.6:1:31.2:1:1:0:60:35.75:0.9795:0:0.1 0/1:176:2:1,1:76,98:0.0114:2,2:18:1:30:1:1:1.29:60:4:0.0118:0:1 -5 172573673 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=CTTTTATATTAATTCAACAT;RSEQ=AATCTAAAAAGGAATGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:85,41:0:2,0:25.4:1:28.6:1:1:0:60:20:1:0:0.1 0/1:150:2:1,1:103,45:0.0133:2,2:27:1:31.5:1:0.52072:2.27487:60:4:0.0134:0:1 -5 172573767 . T C 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11084;SOR=1.35964;LSEQ=AGGATGAATTATAGTTAGTA;RSEQ=GTTAATATTAGTTGGTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:246:143:71,72:49,54:0.5813:2,2:23.9:1:30.4:1:0.7965:1.09:60:70.5:0.5802:0:1.1 1/0:234:153:63,90:30,51:0.6538:2,2:25.1:1:29.7:1:0.57624:1.19:60:50:0.6494:0:1.2 -5 172573834 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18004;SOR=Inf;LSEQ=GTCATTTCATTTCATTGCCT;RSEQ=GAGAAAGGCCTTTCATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:26,90:0:2,0:24.6:1:30.2:1:1:0:60:115:1:0:0.4 0/1:86:2:1,1:22,62:0.0233:2,2:22.5:1:28.5:1:0.46566:2.78:60:4:0.0233:0:1 -5 172658139 . C A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATAGAGGAGCTGGAGGTC;RSEQ=GGTCCCAGCACCTGCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:29:1:31:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 172659905 . AGGC A 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.64137;SOR=1.59275;LSEQ=GGCACCGCGATCCTGCGGGC;RSEQ=GGCGGCGGCGGCGGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:62,2:0.0303:1,0:20:1:33.5:1:1:0:60:4:0.0308:0:0.5 0/1:42:2:2,0:39,1:0.0476:1,0:13:1:32.5:1:1:0:60:4:0.0476:0.0238:0.5 -5 172659907 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.52458;SOR=0;LSEQ=CACCGCGATCCTGCGGGCAG;RSEQ=CGGCGGCGGCGGCGGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:62,1:0.0299:1,2:27.5:1:30:1:0.06106:44.19295:60:4:0.0323:0:1 0/0:41:0:0,0:39,1:0:1,0:24.9:1:30.6:1:1:0:60:39:1:0:0.2 -5 172659915 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.14609;SOR=Inf;LSEQ=TCCTGCGGGCAGGCGGCGGC;RSEQ=GCGGCGGGGGCAGCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:75,5:0:2,0:22.6:1:29:1:1:0:60:25.667:1:0:0.2 0/1:50:2:1,1:42,6:0.04:2,2:11:1:30:1:0.26286:6.55744:60:4:0.0408:0:1.5 -5 172659920 . CG C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.16159;SOR=Inf;LSEQ=CGGGCAGGCGGCGGCGGCGG;RSEQ=GGGGCAGCCCCACCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:80,10:0:2,0:21.7:1:29.3:1:1:0:60:29:1:0:0.1 0/1:61:2:1,1:46,13:0.0328:2,2:12.5:1:31.4:1:0.40929:3.44648:60:4:0.0328:0.0164:0 -5 172660010 . G T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59396;SOR=2.39736;LSEQ=AACCAGATCTTGACCTGCGT;RSEQ=GACGTGAGTTTCAGCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:1:0,1:111,127:0.0042:2,0:27:0:15:0:1:0:60:0:0:0:1 0/1:201:2:1,1:90,109:0.01:2,2:22.5:1:31.5:1:1:1.21:60:4:0.0102:0:1 -5 172660050 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50564;SOR=0;LSEQ=TGGCCAGCTGGTCGCGTTCG;RSEQ=GGGCCGACAGGTACCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:63,102:0.012:2,2:32:1:29:1:1:1.61:60:4:0.0121:0:1 0/0:131:0:0,0:52,79:0:2,0:21.2:1:29.6:1:1:0:60:31.75:1:0:0.1 -5 172660056 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17965;SOR=Inf;LSEQ=GCTGGTCGCGTTCGGGGGCC;RSEQ=ACAGGTACCGCTGCTGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:59,98:0:2,0:25:1:29.9:1:1:0:60:51.333:1:0:0.1 0/1:116:2:1,1:45,69:0.0172:2,2:6:0:27:1:1:1.53:60:4:0.0175:0:1 -5 172660089 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51206;SOR=0;LSEQ=GCTGCTTGAAGCGCCGCTCC;RSEQ=GCTCATAGACCTGCGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:25,75:0.0196:2,2:29.5:1:31:0:0.44671:2.96:60:4:0.02:0:1 0/0:72:0:0,0:25,47:0:2,0:24.9:1:30.3:1:1:0:60:71:1:0:0.1 -5 172774626 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGGTACCCCTTTTGTACTTA;RSEQ=TGGGCTCTCCCTCAGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:1 -5 172775066 . GCAA G 146 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.00023;SOR=9.92309;LSEQ=ATCTCCAACAAACAACAACA;RSEQ=CAGCAGCAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:1,2:11,10:0.125:2,2:43.7:1:33.7:1:1:2.13045:60:6:0.125:0:0.3 1/0:42:25:10,15:8,9:0.5952:2,2:28.5:1:31.6:1:0.75491:1.32415:60:50:0.5952:0.0238:0.7 -5 172775079 . C T 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.70426;SOR=1.68033;LSEQ=AACAACAGCAACAGCAGCAG;RSEQ=AGCAACAACAACAACAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:0.0833:2,2:8.5:1:27.5:1:1:1:25:4:0.0833:0:1.5 0/1:45:6:3,3:15,24:0.1333:2,2:8:0:25:1:0.67033:1.58:23.7:5:0.122:0:1 -5 172775097 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGCAACAACAACAACAA;RSEQ=GAAACAGTAATCTAAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:21.6:1:30.3:1:1:0:60:14:1:0:0.3 0/1:33:2:1,1:11,20:0.0606:2,2:36:1:28.5:1:1:1.78:60:4:0.0645:0:1 -5 173763325 . A C 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCAGGATCAGGAGGCTGAG;RSEQ=CGTGATCTGGAAGTGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:195:118,77:0,0:0.9949:0,2:24.6:1:31.3:1:1:0:60:38:0.9948:0:1.7 1/1:121:121:68,53:0,0:1:0,2:24:1:31.1:1:1:0:60:242:1:0:2.6 -5 173763340 . G T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20513;LSEQ=CTGAGACGTGATCTGGAAGT;RSEQ=AGTGCCCATCCATACACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:249:150:81,69:48,42:0.6024:2,2:25.2:1:29.3:1:1:1.03:60:300:0.6098:0:1.8 0/1:165:39:24,15:8,7:0.2364:2,2:22:1:28.8:1:0.75818:1.39:60:78:0.2364:0:1.7 -5 173763344 . G T 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56597;SOR=3.03956;LSEQ=GACGTGATCTGGAAGTGAGT;RSEQ=CCCATCCATACACCTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:0,1:138,118:0.0039:2,0:1:0:26:0:0.46304:0:60:2:0.0039:0:2 0/1:170:2:1,1:96,72:0.0118:2,2:35:0:31:0:1:1.33103:60:4:0.0119:0:3.5 -5 173763356 . A C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=22.06199;LSEQ=AAGTGAGTGCCCATCCATAC;RSEQ=CCTTCCCCAGCTTTGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:14:10,4:128,131:0.0513:2,2:24.8:1:29.2:1:0.16859:2.55:60:13:0.05:0:2.2 1/0:196:107:58,49:49,40:0.5459:2,2:25:1:29.8:1:1:1.03475:60:34.667:0.5445:0:2.5 -5 173763567 . G A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23352;SOR=Inf;LSEQ=ACAGCATCATCCTGAGTCAT;RSEQ=TTTGAACCTGAGGTAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:0.5:0,0:19.8:1:31.8:1:1:0:60:12:0.5:0:1 1/1:4:4:1,3:0,0:1:0,2:22.3:1:26.8:1:1:0:60:8:1:0:1 -5 173764643 . C G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGGGAACAGGCCTCCCC;RSEQ=CTTCTGTTTCCAGAAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:32.5:1:1:0:60:4:1:0:1 -5 174291096 . T C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTGATTCTTTCTCATCTT;RSEQ=GCGAGTTTGTCTGTTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:44:0:32:0:1:0:60:2:1:0:0 0/1:7:2:1,1:2,3:0.2857:2,2:36:1:29.5:1:1:1.41:60:4:0.2857:0:1 -5 174291231 . T C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40097;SOR=2.88728;LSEQ=TTCTTTCAATAGTCAGGTCC;RSEQ=TCTTCTGTAGTGCTTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:6,4:3,3:0.625:2,2:20:1:31.9:1:1:1.46:60:20:0.625:0:1.1 1/1:12:10:5,5:1,1:0.8333:2,2:22.3:1:31.5:1:1:1:60:20:0.8333:0:1.1 -5 174291450 . T C 77 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04977;SOR=11.63911;LSEQ=ACCTCTGCTGGAGGGTCTCA;RSEQ=CCAGTTGGGTGGCACAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:4,3:0.125:2,0:17:0:34:0:1:0:60:2:0.125:0:1 1/0:9:6:4,2:3,0:0.6667:0,2:22.5:1:30:1:0.5:0:60:12:0.6667:0:1.2 -5 174291455 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=TGCTGGAGGGTCTCATCCAG;RSEQ=TGGGTGGCACAGGGAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:37.6:1:31.4:1:1:0:60:14:1:0:0.3 0/1:10:2:2,0:5,3:0.2:2,0:34.5:1:32.5:1:1:0:60:4:0.2:0:1 -5 174291542 . G A 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14861;SOR=6.08068;LSEQ=TGCTAGGCGGAAACCCACTT;RSEQ=TCTGGGTTGCCTGGATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:3,7:0.0909:2,0:14:0:32:0:1:0:60:2:0.0909:0:1 0/1:10:4:1,3:2,4:0.4:2,2:23.5:1:30:1:1:1.44135:60:8:0.4:0:1.5 -5 174291575 . G T 24 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.45455;SOR=Inf;LSEQ=GGATTCCTCAGAACTACCAG;RSEQ=AGGAGAGGCTAAGTCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:25.2:1:30.4:1:1:0:60:10:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:29.5:1:24:1:1:1:60:4:0.3333:0:1.5 -5 174914787 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49202;SOR=Inf;LSEQ=CTGCCTCCTGGGTGCCTCAC;RSEQ=CTTACTCCGTGCAAATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:30.8:1:31:1:1:0:60:50:1:0:0.4 0/1:28:2:1,1:11,15:0.0714:2,2:22:0:32:0:1:1.35:60:4:0.0741:0:1.5 -5 174914837 . A T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2031;SOR=3.82314;LSEQ=CTTCTCCCTCGGCCCTCTCC;RSEQ=CCTCCAGTTTTTCCAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:2,4:2,5:0.4615:2,2:24.8:1:30.8:1:1:1.23:60:12:0.4615:0:1 1/0:9:7:1,6:0,2:0.7778:0,2:32.3:1:28.7:1:1:0:60:14:0.7778:0:1 -5 176295825 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACCTGGTGGACCCGTCCC;RSEQ=GGACCCCAATGTATACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:6,0:0.25:0,2:20:1:29.5:1:0.25:0:60:4:0.25:0:1 0/0:2:0:0,0:2,0:0:0,0:14:1:31.5:1:1:0:60:4:1:0:0 -5 176516631 . G A 226 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0082;LSEQ=TGCTGCTGGCCCTGTTGGGG;RSEQ=TCCTGCTGAGTGTGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:171:80,91:291,277:0.2311:2,2:23:1:30.6:1:0.33749:1.1947:60:170:0.2326:0:1.1 0/0:815:2:2,0:395,418:0.0025:2,0:13:1:29:1:0.23698:0:60:4:0.0025:0:1 -5 176516760 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18456;SOR=Inf;LSEQ=GGCACCAGGAGGGGGCTGCT;RSEQ=GGCTGAGCAAAGCTGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:45,192:0:2,0:22.9:1:30.3:1:1:0:60:20.545:1:0:0.1 0/1:179:2:1,1:44,133:0.0112:2,2:7:1:27.5:1:0.44065:3.00:60:4:0.0115:0:1 -5 176516953 . A G 90 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCTGGTGGTGAGCTCCTT;RSEQ=CCTGGGTGTGTGTGCGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:1,6:0,0:0.875:0,2:29.3:1:32.3:1:1:0:60:14:1:0:1 1/1:1:1:0,1:0,0:1:0,0:50:0:34:0:1:0:60:2:1:0:1 -5 176517136 . C CGTGT 49 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=12.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGTATGTGTGTGTGTGTATG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:2,1:0.3333:2,0:16.3:1:31.5:1:1:0:60:6:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 176517170 . G A 105 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTGTCTTGGCCACTGTC;RSEQ=TGTGCACTAAATGCTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:1:0,2:29.5:1:29.4:1:1:0:59.2:11:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 176517292 . A G 178 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=0.03731;LSEQ=GCTCCTTCAGCATGCGTTGC;RSEQ=AAGTGCTTGTGCCCTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:63:57,6:1,0:0.9844:0,2:27.9:1:29.8:1:1:0:60:62:0.9841:0:2 1/0:26:18:17,1:8,0:0.6923:0,1:24.9:1:30.8:1:1:0:60:36:0.6923:0:2.1 -5 176517326 . T C 214 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01571;LSEQ=CTGCATGTGCGGTGTGTTCT;RSEQ=TGTACACAGGAGGCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:121:109,12:1,0:0.9918:0,2:20.4:1:31:1:1:0:60:120:1:0:1.6 1/0:60:39:31,8:20,1:0.65:1,2:23.2:1:31:1:0.14166:5.05196:60:78:0.65:0:1.5 -5 176517383 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14739;SOR=Inf;LSEQ=TCTGCTGACCTCTGCCCTCT;RSEQ=CCCACAGAGCCCTGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:200,72:0:2,0:25.8:1:31.7:1:1:0:60:37.857:1:0:0.7 0/1:170:2:1,1:121,47:0.0118:2,2:18.5:1:28:1:0.48618:2.55802:60:4:0.012:0:1.5 -5 176517461 . T G 284 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01137;LSEQ=GCCCTTGGGCAGCCTGTGCG;RSEQ=CTGTGCTGTGGGCGGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:537:533:313,220:0,4:0.9926:0,2:24.2:1:31.4:1:0.0298:0:60:75.143:0.9925:0:1.1 1/0:485:292:159,133:109,84:0.6021:2,2:25.1:1:31.6:1:0.70921:1.08525:60:145:0.6029:0:1.2 -5 176517797 . C T 310 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.00698;LSEQ=CCCCAAGTCCCATAGGGACC;RSEQ=CTCGAATAGGCACAGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1179:1175:520,655:1,2:0.9966:2,2:25.8:1:30.4:1:1:1.59:60:60.842:0.9983:0:1.2 1/0:1002:673:293,380:153,174:0.6717:2,2:24.8:1:29.5:1:0.34296:1.14025:60:83.125:0.6786:0:1.1 -5 176517801 . G A 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTCCCATAGGGACCCCTC;RSEQ=AATAGGCACAGTTACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1169:52:24,28:504,612:0.0445:2,2:26.3:1:30.2:1:0.88779:1.04:60:104:0.045:0:2.1 0/0:993:0:0,0:443,550:0:2,0:25:1:30.2:1:1:0:60:75.385:1:0:0.8 -5 176518315 . A C 132 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=CTCTCAGCCTCAGCAACTCC;RSEQ=TTTGTAAAGGGAGAAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:2,16:0,0:1:0,2:23.7:1:31.8:1:1:0:60:17:1:0:1.4 1/0:4:3:0,3:0,1:0.75:0,0:26:1:32.7:1:1:0:60:6:0.75:0:1.3 -5 176518426 . T C 92 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCTGTCATGAGGCAACTGAG;RSEQ=CTCAGAGAAGGCAAGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:1:0,2:25.9:1:30.9:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 176518633 . G T 19 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.17022;LSEQ=ATCTAGCCTCCTGGTCCTCT;RSEQ=GCCCCCTTGGTGGACATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:2,0:110,27:0.0144:2,0:39.5:1:30.5:1:1:0:60:4:0.0146:0:1 0/1:119:2:1,1:92,25:0.0168:2,2:5.5:1:19.5:1:0.39069:3.62849:60:1:0.0088:0:1 -5 176518642 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19167;SOR=Inf;LSEQ=CCTGGTCCTCTGGCCCCCTT;RSEQ=GTGGACATGGTCCGGTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:133,41:0:2,0:22.2:1:31.4:1:1:0:60:42.5:1:0:0.1 0/1:136:2:1,1:102,32:0.0147:2,2:31:0:31.5:1:0.42778:3.15418:60:4:0.015:0:1.5 -5 176518651 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.25273;SOR=0;LSEQ=CTGGCCCCCTTGGTGGACAT;RSEQ=GTCCGGTGGTCCCGGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:3:1,2:147,46:0.0153:2,2:18.7:1:29.7:1:0.14909:6.31524:60:6:0.0157:0:1 0/0:167:0:0,0:124,43:0:2,0:23.8:1:30.8:1:1:0:60:40.75:1:0:0.1 -5 176518784 . C T 271 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01933;LSEQ=AACGCTGTGGGCAGCATCCG;RSEQ=TATAACTACCTGCTAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:562:557:264,293:0,0:0.9911:0,2:25.9:1:29.8:1:1:0:60:78.571:0.9946:0:1.2 1/0:532:363:169,194:75,94:0.6823:2,2:24.9:1:29.4:1:0.70863:1.09:60:180.5:0.6811:0:1.2 -5 176519285 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03231;SOR=Inf;LSEQ=ACAGGGTGCTTCTATGGGTG;RSEQ=CGGTGGTCAGGGTTGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:247,92:0:2,0:25.6:1:31.6:1:1:0:60:36.667:1:0:1.1 0/1:251:4:2,2:161,86:0.0159:2,2:21.5:1:29.8:1:0.61381:1.86719:60:8:0.0163:0:1.8 -5 176519287 . G A 255 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00823;LSEQ=AGGGTGCTTCTATGGGTGCC;RSEQ=GTGGTCAGGGTTGACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:348:347:252,95:1,0:0.9971:0,2:25.7:1:30.3:1:1:0:60:42.375:0.9971:0:1.1 1/0:261:193:129,64:41,25:0.7395:2,2:26.1:1:29.9:1:0.54856:1.23:60:63.333:0.7393:0:1.2 -5 176519730 . C T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGCGAGTACACCTGCCT;RSEQ=GCAGGCAATTCCATCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:0:0,0:346,218:0:2,0:24.8:1:30.4:1:1:0:60:50.273:1:0:0.1 0/1:534:31:19,12:285,218:0.0581:2,2:27.8:1:28.7:1:0.70999:1.21:60:30:0.0575:0:1.3 -5 176520223 . C T 73 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05785;SOR=6.69321;LSEQ=GTCGGGCTCCCTGGCCTTGG;RSEQ=TGTGCTCCTGCTGCTGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:1:1,0:335,322:0.0015:2,0:26:0:27:0:1:0:60:2:0.0016:0:2 0/1:596:6:2,4:307,282:0.0101:2,2:17.2:1:28.3:1:0.43466:2.17456:60:12:0.0104:0:1.7 -5 176520243 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.24682;LSEQ=CTGTGCTCCTGCTGCTGGCC;RSEQ=GGCTGTATCGAGGGCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:613:450:225,225:80,82:0.7341:2,2:25.8:1:30.1:1:0.9271:1.02:60:33.615:0.7357:0:1.1 0/1:563:228:118,110:169,165:0.405:2,2:25.7:1:29.4:1:0.79717:1.05:60:37:0.3993:0:1.2 -5 176520839 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50309;SOR=0;LSEQ=CACTTTAGGAGGCTGAGGGT;RSEQ=GGAGGATCGCTTGAATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:25,162:0.0105:2,2:27:1:28.5:1:0.25684:6.37:60:4:0.0107:0:1 0/0:157:0:0,0:23,134:0:2,0:22.9:1:30.2:1:1:0:60:77.5:1:0:0.1 -5 176520848 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49949;SOR=0;LSEQ=AGGCTGAGGGTGGGAGGATC;RSEQ=CTTGAATCCAGGAATTCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:7,133:0.0141:2,2:8:1:26.5:1:0.10988:17.84:60:4:0.0144:0:1 0/0:128:0:0,0:14,113:0:2,0:23.3:1:31.6:1:1:0:60:126:1:0:0.1 -5 176520904 . C CA 52 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.18984;SOR=3.64191;LSEQ=ATGGCAAGACTTCATCTCTA;RSEQ=AAAAAAAAAATAAGAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:0,2:0,50:0.0385:1,0:36.5:1:30.5:1:1:0:60:4:0.0408:0:0 0/1:31:4:0,4:1,26:0.129:1,0:25:1:26.3:1:1:0:60:3:0.1034:0:1 -5 176522036 . C T 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCCTGCTCCGAGCTCTTCCC;RSEQ=TCTCTCCTGTGTCCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:37.4:1:32:1:1:0:60:10:0.625:0:1 1/1:2:2:2,0:0,0:1:0,0:28.5:1:32.5:1:1:0:60:4:1:0:1 -5 176522260 . T A 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00137;SOR=Inf;LSEQ=TGGTCCAGTGCTGCTTGTCC;RSEQ=GCACCTGCCTCTGCATGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:162,14:0:2,0:24.1:1:31.3:1:1:0:60:352:1:0:0.1 0/1:141:8:7,1:115,18:0.0567:2,2:20.3:1:30.5:1:1:1.10:60:16:0.0576:0:2 -5 176522263 . A T 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00169;SOR=Inf;LSEQ=TCCAGTGCTGCTTGTCCTGC;RSEQ=CCTGCCTCTGCATGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:163,16:0:2,0:24.5:1:30.2:1:1:0:60:178:1:0:0.1 0/1:151:8:7,1:121,21:0.053:2,2:22.5:1:31.3:1:1:1.21:60:16:0.0537:0:2 -5 176522273 . G T 31 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34052;SOR=3.5035;LSEQ=CTTGTCCTGCACCTGCCTCT;RSEQ=CATGCTCCCTCGTGCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:1,0:182,29:0.0047:2,0:43:0:15:0:1:0:60:0:0:0:1 0/1:184:3:1,2:146,35:0.0163:2,2:12:1:20:1:0.10346:8.20767:60:2:0.0109:0:3 -5 176522728 . C T 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTGGAGTCCCGGAAGGTA;RSEQ=AGGCGCTAGGGCTCTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:619:619:218,401:0,0:1:0,2:23.4:1:28.7:1:1:0:60:46.615:1:0:1.1 1/0:574:353:141,212:85,135:0.615:2,2:24:1:28.3:1:0.7923:1.06:60:69.6:0.6127:0:1.1 -5 176522903 . A G 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5618;SOR=0;LSEQ=CACCCTTCCCCAGAGGGGAG;RSEQ=GGGGACGCAGGAGAAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:2,1:33,29:0.0455:2,2:31.3:1:24.3:1:1:1.74:60:2:0.0317:0:3.3 0/0:24:0:0,0:12,12:0:2,0:23.5:1:29.8:1:1:0:60:23:1:0:0.2 -5 176523067 . C T 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32109;SOR=2.24213;LSEQ=GCTCCCTGCAGTGTATCCAC;RSEQ=GGGACCTGGCTGCCCGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:3:0,3:345,235:0.0051:2,0:1.3:1:26.7:1:0.06753:0:60:6:0.0052:0:1 0/1:523:6:1,5:322,195:0.0115:2,2:19.8:1:25.3:1:0.03264:8.22775:60:5:0.0097:0:1 -5 176523422 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32346;SOR=3.88792;LSEQ=AAGGCACTGCCCAAAGTCAC;RSEQ=TGGCCCCAGGAGTCATGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:1,0:130,231:0.0028:2,0:1:0:29:0:0.36188:0:60:2:0.0028:0:1 0/1:281:3:2,1:96,181:0.0107:2,2:21.3:1:28:1:0.28101:3.75:60:6:0.0109:0:1 -5 176523545 . G A 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=TCATGTCTGTGGGGTCCCCC;RSEQ=TCCTAGCCCCGGTCGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:465:0:0,0:344,120:0:2,0:21.5:1:29.9:1:1:0:60:57:1:0:1.7 0/1:357:10:6,4:250,97:0.028:2,2:24.5:1:29.6:1:0.47766:1.71532:60:20:0.0284:0:2.5 -5 176523562 . C A 268 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCGTCCTAGCCCCGGTCGT;RSEQ=GGGAGGGCGCTGAGCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:647:647:449,198:0,0:1:0,2:21.3:1:28.8:1:1:0:60:63.7:1:0:1.9 1/0:518:378:244,134:88,48:0.7297:2,2:21.5:1:28.6:1:1:1.00682:60:74.6:0.7271:0:1.9 -5 176523597 . A G 315 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00555;LSEQ=CCACACTGAGCCCTGGCCCT;RSEQ=CCTCCAGGTGGTCTTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:958:955:548,407:2,1:0.9969:2,2:26.7:1:31.9:1:1:1.48481:60:62.667:0.9979:0:1.7 1/0:848:541:297,244:170,137:0.638:2,2:28.1:1:31.6:1:0.94275:1.01942:60:59.111:0.6364:0:1.7 -5 176523778 . GTCC G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.60199;SOR=1.44279;LSEQ=GCCCTCGACCCCACTTTCCA;RSEQ=TCCTCCTCCTCTGCCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:7:2,5:124,337:0.015:2,2:24.1:1:32.4:1:1:1.09:60:14:0.0156:0.0021:0 0/1:373:8:3,5:113,247:0.0214:2,2:23.4:1:29.2:1:0.71082:1.31:60:16:0.0225:0.0027:0.3 -5 176523861 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.28111;SOR=3.75951;LSEQ=AACAACAACTCCTCGTCCTC;RSEQ=TCCTCCTCTTCCTCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:3,137:0.0071:1,0:6:0:25:0:1:0:40:2:0.0074:0:2 0/1:76:2:0,2:3,71:0.0263:1,0:27.5:1:28.5:1:1:0:60:4:0.027:0:2 -5 176523870 . T C 51 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01745;LSEQ=TCCTCGTCCTCCTCCTCCTC;RSEQ=TCCTCTTCCTCCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:4:0,4:2,114:0.0333:1,0:17.8:1:25.8:1:1:0:42.3:3:0.0265:0:3 0/1:59:2:0,2:3,53:0.0339:2,0:18.5:1:33:0:1:0:60:4:0.0357:0:2 -5 176523876 . TTCC T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0.95312;LSEQ=TCCTCCTCCTCCTCTTCCTC;RSEQ=TCCTCCTCCTCTTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:0,2:2,99:0.0194:1,0:17:1:30.5:1:1:0:60:4:0.0206:0:2 0/1:54:1:0,1:3,50:0.0185:2,0:19:0:30:0:1:0:60:2:0.0204:0:2 -5 176523906 . T C 40 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55261;SOR=0;LSEQ=TCCTCTTCCTCCTCCTCCTC;RSEQ=TCCTCCTCCTCTTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:3:1,2:0,43:0.0625:1,2:23.3:1:25.3:1:0.06522:0:38.3:2:0.05:0:4.3 0/0:19:0:0,0:0,19:0:1,0:20.1:1:28.4:1:1:0:58.1:8.5:1:0:1.2 -5 176523918 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44108;SOR=0.52746;LSEQ=TCCTCCTCTTCCTCCTCCTC;RSEQ=TCCTCCTCCTCCTCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:26:1,25:0,6:0.8125:0,1:19.2:1:32.2:1:1:0:55.5:25:0.8333:0:2.3 1/0:13:9:0,9:1,3:0.6923:2,0:13.8:1:32.7:1:0.30769:0:60:18:0.6923:0:1.8 -5 176523921 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=2e-05;SOR=Inf;LSEQ=TCCTCTTCCTCCTCCTCTTC;RSEQ=TCCTCCTCCTCTTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:1,8:0:2,0:33.6:1:30.4:1:1:0:38.8:8:1:0:3.6 1/0:11:7:0,7:1,3:0.6364:2,0:14:1:30.1:1:0.36364:0:60:14:0.6364:0:2 -5 176523956 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=2.60168;LSEQ=CTCCTCCTCCTCTTCCTCCT;RSEQ=CTCCTCCTGCTCCTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:17:1:33:0:1:0:42.5:4:0.4:0:3.5 1/0:3:2:0,2:1,0:0.6667:0,0:9:1:32:1:0.33333:0:41.5:4:0.6667:0:3 -5 176523963 . C T 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1;LSEQ=TCCTCTTCCTCCTTCTCCTC;RSEQ=TGCTCCTCTTCCTCCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:10:1:31:0:1:0:42.5:4:0.5:0:3.5 1/0:2:1:0,1:1,0:0.5:0,0:6:0:30:0:1:0:40:2:0.5:0:3 -5 176523965 . G C 32 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTCTTCCTCCTTCTCCTCCT;RSEQ=CTCCTCTTCCTCCTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:8:1:32:0:1:0:42.5:4:0.5:0:3.5 1/0:2:1:0,1:1,0:0.5:0,0:4:0:32:0:1:0:40:2:0.5:0:3 -5 176523983 . T C 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=CTGCTCCTCTTCCTCCTCCT;RSEQ=CTCTTCCTCCTCCTCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:11:1:29:1:1:0:26:4:0.6667:0:2.5 0/0:2:0:0,0:1,1:0:2,0:21:1:22:1:1:0:33:1:1:0:2.5 -5 176524082 . T C 27 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=CTCCTTCTCTTCCTCCTCCT;RSEQ=CTCTTCCTCCTCCTCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12.5:1:27.5:1:1:0:43.5:4:1:0:6 0/0:1:0:0,0:1,0:0:0,0:39:0:31:0:1:0:60:2:1:0:0 -5 176524086 . T C 52 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TTCTCTTCCTCCTCCTTCTC;RSEQ=TCCTCCTCCTCCTCCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:9.3:1:26:1:1:0:51.8:3:0.75:0:5 0/0:2:0:0,0:2,0:0:0,0:23:1:31:1:1:0:60:4:1:0:0.5 -5 176524101 . C T 106 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.05252;SOR=0.07721;LSEQ=TTCTCTTCCTCCTCCTCCTC;RSEQ=TGCTCCTCTTCCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:10,1:1,1:0.8462:2,2:13:1:30.7:1:0.29487:7.42:60:10:0.9091:0:3.4 0/1:4:1:1,0:3,0:0.25:0,0:4:0:32:0:1:0:60:2:0.25:0:3 -5 176524103 . G C 114 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03741;SOR=0.09902;LSEQ=CTCTTCCTCCTCCTCCTCCT;RSEQ=CTCCTCTTCCTCCTCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:10,2:0,0:0.8571:0,2:16.6:1:31.9:1:1:0:57.3:24:0.8571:0:3.7 0/1:6:2:2,0:4,0:0.3333:0,0:3.5:1:32:1:1:0:60:4:0.3333:0:2.5 -5 176524110 . T C 135 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04894;SOR=0;LSEQ=TCCTCCTCCTCCTGCTCCTC;RSEQ=TCCTCCTCCTCCTCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:17,2:0,0:1:0,2:17.9:1:31.9:1:1:0:58.3:38:1:0:2.7 1/0:12:9:8,1:3,0:0.75:0,2:7.9:1:31.7:1:1:0:60:18:0.75:0:1.4 -5 176524465 . C T 158 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05646;LSEQ=GGCCTCATCTGGCCTGACCG;RSEQ=GTGGACATGCGCCCCGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:902:42:20,22:435,424:0.0466:2,2:26.7:1:29.4:1:0.75331:1.12839:60:41:0.0464:0:1.1 0/0:728:2:0,2:381,345:0.0027:2,0:4.5:1:26.5:1:0.22685:0:60:4:0.0028:0:1 -5 176524734 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13861;SOR=Inf;LSEQ=GCCTTGGGCCTTGGGGCTCA;RSEQ=CCACAGCCTGACACAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:40,207:0:2,0:23.4:1:32.2:1:1:0:60:81.333:1:0:0.1 0/1:147:2:1,1:25,120:0.0136:2,2:26:1:28:1:0.32346:4.73:60:4:0.0138:0:1 -5 176525029 . G C 31 d7;v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=CCCCTGCTGCTGCTGCCCCA;RSEQ=CGTCTTGACGGGAGCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:28:1:28:1:1:0:60:5:1:0:1 1/1:2:2:1,1:0,0:1:0,2:24:0:31:1:1:0:60:4:1:0:1.5 -5 176562041 . C T 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63129;SOR=0.40872;LSEQ=GCCATTTTAAAGAGTCGAGT;RSEQ=AGATGGCCTATTAACTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:1,2:166,42:0.0142:2,2:5.7:1:22:1:0.11094:7.79825:56:2:0.0097:0:1.3 0/0:171:1:0,1:148,22:0.0058:2,0:1:0:22:0:0.1345:0:60:2:0.0059:0:1 -5 176562558 . C A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27007;SOR=2.72616;LSEQ=CTATCAAGAATGGCTTTCTG;RSEQ=ACTTTGAGAATTTTACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:2:2,0:210,327:0.0037:2,0:1:0:26:1:0.15426:0:60:4:0.0038:0:1 0/1:497:5:4,1:198,294:0.0101:2,2:13.4:1:23.6:1:0.16363:5.92:60:4:0.0082:0:2 -5 176619202 . GT G 31 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATGATTTAAACCTTCTCTCA;RSEQ=TTTTTTTTTTTGTTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:0,24:0.0769:1,0:22.5:1:31:1:1:0:60:4:0.08:0:3.5 0/1:13:1:0,1:0,12:0.0769:0,0:36:0:28:0:1:0:60:2:0.0769:0:0 -5 176621075 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGTGAGCCACCACACCTG;RSEQ=CTGATATTAATATATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 176630984 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00032;SOR=0.1463;LSEQ=TTTTCCTTGTGTATGATCTA;RSEQ=TCTAGGTTGTCTAGTTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:63:62,1:6,0:0.9:0,1:22.1:1:32:1:1:0:60:62:0.8986:0:1.1 1/0:32:18:18,0:14,0:0.5625:1,1:24.1:1:31.5:1:1:0:60:36:0.5806:0:1.1 -5 176636546 . G A 132 LongAT STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11281;LSEQ=TCTCAAAAAAAAAAAAAAAA;RSEQ=GAATAAAAAAAAAAGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:32:30,2:33,1:0.2909:1,2:9.4:1:26.4:1:0.60769:2.17462:56.9:3.571:0.3623:0:1.6 0/1:114:5:3,2:95,10:0.0439:2,2:20.6:1:17.8:1:0.09096:6.1479:60:0.667:0.0217:0:2 -5 176636550 . T TA 48 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.43647;SOR=0.46698;LSEQ=AAAAAAAAAAAAAAAAGGAA;RSEQ=AAAAAAAAAAGCTTCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:4:4,0:112,5:0.0317:1,0:19.5:1:24.3:1:1:0:60:3:0.0345:0:2 0/1:133:2:2,0:108,17:0.015:2,0:28.5:1:18.5:1:1:0:60:1:0.0116:0:2 -5 176636882 . C T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03834;LSEQ=GATGAGAAGGAAAAGCCTTG;RSEQ=GCTAAATCTCGAGCCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:470:338:161,177:57,73:0.7191:2,2:24.8:1:29.9:1:0.47105:1.16:60:111.667:0.7267:0:1.1 0/1:438:39:15,24:193,205:0.089:2,2:20.4:1:29.4:1:0.24465:1.50494:60:78:0.0899:0:1.1 -5 176637149 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01349;LSEQ=ACTGCAAAGAAAGAATTTGA;RSEQ=ACTTCAAATGGTGACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:254:134,120:68,56:0.672:2,2:25.9:1:30:1:0.74236:1.08718:60:30.75:0.6685:0:1.1 0/1:449:12:7,5:226,211:0.0267:2,2:22.5:1:29.2:1:0.77335:1.31:60:11:0.0249:0:1.3 -5 176637240 . G T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.01739;LSEQ=ATAAACCCCAACGAAGCCTG;RSEQ=TGTGTGGTTCAAAAGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:613:390:200,190:107,114:0.6362:2,2:24.5:1:29.8:1:0.50189:1.12:60:77:0.6385:0:1.2 0/1:646:19:10,9:298,329:0.0294:2,2:28.4:1:29.7:1:0.81645:1.23:60:38:0.0296:0:1.1 -5 176637576 . T C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02042;LSEQ=CAGAGCCTGGAACCGAGACG;RSEQ=CTCAGGTTAATCTCTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:433:264:145,119:89,79:0.6097:2,2:23.5:1:31.8:1:0.69343:1.08:60:87:0.6185:0:1.1 0/1:455:14:7,7:251,190:0.0308:2,2:24.7:1:30.7:1:0.78526:1.32022:60:28:0.031:0:1 -5 176639031 . G T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02892;SOR=Inf;LSEQ=CAGAGCATAGAACTCCTTCA;RSEQ=CAAGCATACTTGAGGAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:496:0:0,0:194,301:0:2,0:24.2:1:31.8:1:1:0:60:60.875:0.998:0:0.2 0/1:483:5:3,2:216,261:0.0104:2,2:26.6:1:29.6:1:0.66302:1.81:60:10:0.0106:0:1.4 -5 176639105 . T C 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TCAGCTGGGCCACGGTTAAA;RSEQ=GTTTGTGATAAATCCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:109,188:0:2,0:23.6:1:30.1:1:1:0:60:36.125:1:0:0.1 0/1:340:15:4,11:140,183:0.0441:2,2:22.5:1:28.9:1:0.28666:2.09953:60:14:0.0424:0:1.3 -5 176639170 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49862;SOR=0;LSEQ=GCCAGGAATTCCCAGTTTGA;RSEQ=ACCACAGGCTGAGCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:46,123:0.0117:2,2:25.5:1:28.5:1:0.47534:2.66:60:4:0.012:0:1 0/0:166:0:0,0:54,112:0:2,0:26.6:1:31:1:1:0:60:54.333:1:0:0.2 -5 176639304 . C G 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.72376;LSEQ=TAAAGTGAAGTATAAACTAG;RSEQ=GGGGAAGAATCATCACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:0,14:0,1:0.9333:0,1:24.2:1:28:1:1:0:60:6:0.9231:0:1.2 1/1:11:10:0,10:0,1:0.9091:0,0:27.4:1:30.7:1:1:0:60:20:0.9091:0:1 -5 176662828 . G A 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05781;SOR=Inf;LSEQ=TTATCATCTTTTAGCTGTGC;RSEQ=GTCAGAGAAGAAACGCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:247,162:0:2,0:24.6:1:30.2:1:1:0:60:135.333:1:0:0.1 0/1:395:4:2,2:230,160:0.0101:2,2:22.3:1:32.3:1:1:1.43612:60:8:0.0103:0:1.3 -5 176666691 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19787;SOR=Inf;LSEQ=TTCATTTTGTGTGGTATACA;RSEQ=ATTTTTTAAAAATTAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:210,34:0:2,0:23:1:32.1:1:1:0:60:488:1:0:0.1 0/1:196:2:1,1:160,33:0.0102:2,2:24.5:1:27.5:1:0.31906:4.79162:60:4:0.0103:0:1 -5 176671142 . A T 43 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12436;SOR=Inf;LSEQ=AGACTTTGGCATATAAAGTA;RSEQ=AGGGTTTATTTTTTCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:248,73:0:2,0:24.8:1:30:1:1:0:60:79.25:1:0:0.1 0/1:338:4:1,3:234,99:0.0118:2,2:8.3:1:21.8:1:0.08448:7.04523:60:3:0.0091:0:1.8 -5 176675110 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50165;SOR=0;LSEQ=TAATGGCTAGACAAATAGCA;RSEQ=CCCAGAGGGAGGGGGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:135,13:0.0133:2,2:11.5:1:29:1:0.17852:10.0439:60:4:0.0135:0:1 0/0:127:0:0,0:113,14:0:2,0:23.5:1:32.3:1:1:0:60:41.333:1:0:0.2 -5 176675394 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50297;SOR=0;LSEQ=AAGGGAAACCCACTCCATCT;RSEQ=TTTATGATGGTTTCTTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:21,163:0.0108:2,2:20.5:1:31.5:1:0.22313:7.61:60:4:0.0109:0:1.5 0/0:154:0:0,0:17,136:0:2,0:25:1:31.7:1:1:0:60:37.25:0.9933:0:0.1 -5 176675423 . A G 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04095;SOR=Inf;LSEQ=GGTTTCTTGGTAGAATAACA;RSEQ=TGCTTTTGGATGATTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:2,105:0:1,0:27.5:1:31.4:1:1:0:60:52.5:1:0:0.1 0/1:89:4:0,4:2,83:0.0449:1,0:20.3:1:31.3:1:1:0:60:8:0.0455:0:1 -5 176678609 . G T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58316;SOR=2.55514;LSEQ=ATCTACAACTACGGGCCCTT;RSEQ=CCTCTTTCTCACCTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:1,0:56,2:0.0169:1,0:41:0:15:0:1:0:60:0:0:0:1 0/1:47:2:2,0:45,0:0.0426:1,0:12:1:31.5:1:1:0:60:4:0.0435:0:1 -5 176678625 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50488;SOR=0;LSEQ=CCTTGCCTCTTTCTCACCTC;RSEQ=TTTTCTGCCACTTTTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:83,4:0.0225:1,2:7.5:1:30.5:1:0.10981:18.66298:60:4:0.0225:0:1 0/0:69:0:0,0:68,1:0:1,0:19.9:1:30.2:1:1:0:60:68:1:0:0.1 -5 176687248 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50497;SOR=0;LSEQ=ATTGGAACAAAAATACTTTT;RSEQ=ATCATATTGCCACTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:0,2:10,147:0.0126:2,0:14:1:28.5:1:1:0:60:4:0.0126:0:1 0/0:126:0:0,0:9,117:0:2,0:21.1:1:31.3:1:1:0:60:125:1:0:0.1 -5 176691923 . C T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.71651;LSEQ=GTACTCTTCAAAAAGGAATG;RSEQ=CCCACAAGTGTTATCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:154,107:0.0114:2,2:17.3:1:28.7:1:0.57092:2.86696:60:6:0.0117:0:1 0/0:245:2:0,2:148,95:0.0082:2,0:1:0:25.5:1:0.15577:0:54.5:4:0.0084:0:1 -5 176691965 . G A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.67887;SOR=0.63226;LSEQ=AAACTGGAAGAGTCTACAGT;RSEQ=TTACCCAGCATGCTGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:2,1:119,134:0.0117:2,2:10.3:1:28.7:1:0.60397:2.25:52.7:6:0.0119:0:1.3 0/0:269:2:1,1:130,137:0.0074:2,2:16:1:29:1:1:1.05:60:4:0.0075:0:1 -5 176692006 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=ATTGTTGTAAACAAACAAGG;RSEQ=CAAGATTCTTGCCAAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:43,95:0:2,0:20.8:1:31.6:1:1:0:59.8:137:1:0:0 0/1:147:2:1,1:48,97:0.0136:2,2:41.5:1:29:1:1:2.01:60:4:0.014:0:1 -5 176694479 . AAT A 94 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.76676;SOR=0.67587;LSEQ=CTTTTAGTGAAGAGAAAGAA;RSEQ=ATATATATATATGTGTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:8:7,1:153,9:0.0471:2,2:22:1:31.6:1:0.3908:2.41046:60:16:0.0473:0.0176:0.3 0/1:124:4:3,1:103,18:0.0323:2,2:25.3:1:30:1:0.48741:1.89532:60:8:0.0323:0.0081:0.3 -5 176696503 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.5082;SOR=0;LSEQ=AAGATGGACTTTAATGTGGA;RSEQ=AGACAGACATTGCTAATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:96,7:0.019:2,2:15.5:1:27:1:0.14725:12.89524:60:4:0.0192:0:1.5 0/0:78:0:0,0:74,4:0:2,0:23.8:1:31.2:1:1:0:60:77:1:0:0.1 -5 176696836 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50027;SOR=Inf;LSEQ=TATCCTTTTTGTTTCTCAGG;RSEQ=AAACACAGACCTCTGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:40,134:0:2,0:25.2:1:32.2:1:1:0:60:173:1:0:0.1 0/1:195:2:1,1:54,139:0.0103:2,2:28.5:1:31:0:0.48559:2.56:60:4:0.0104:0:1.5 -5 176697155 . A AGTCTT 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=8.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=GAGCTACATTTGCTCCAAGG;RSEQ=GTCTTGTCTTGTCTTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:23:1:24.2:1:1:0:60:2:0.5:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:31.2:1:1:0:60:4:1:0:0 -5 176700613 . G T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24872;SOR=Inf;LSEQ=GGAAAAAGTAAAAAATAAGT;RSEQ=AATAAATAAGTAATTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:225,65:0:2,0:22.9:1:32:1:1:0:60:144:1:0:0.1 0/1:292:3:2,1:199,90:0.0103:2,2:17.7:1:21.3:1:1:1.10516:60:2:0.0069:0:3.3 -5 176700812 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19393;SOR=Inf;LSEQ=AGAAAATCTTGGGGGACCTT;RSEQ=TCTAGAAGAGAAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:56,181:0:2,0:22.7:1:31.5:1:1:0:60:32.857:1:0:0.1 0/1:187:2:1,1:51,134:0.0107:2,2:13:1:31:1:0.4799:2.61:60:4:0.0109:0:1 -5 176700885 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=35.95033;LSEQ=CGGAAGCACAAGCATAGTTC;RSEQ=TTTTAGGTAGAGGTATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:20:0,20:0,44:0.3125:1,1:28.4:1:31:1:1:0:60:19:0.3016:0:1 1/1:36:34:0,34:0,2:0.9444:0,1:22.1:1:30.6:1:1:0:60:68:0.9444:0:1.1 -5 176701997 . A T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCGCCACAGCCTCCCAA;RSEQ=GTGCTGGGATTACAGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29:1:1:0:55:4:1:0:1 -5 176707483 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50268;SOR=0;LSEQ=AAATGTGGCTGCAACTTCAA;RSEQ=GAAAAAAAGTTTGCCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:2,0:128,6:0.0147:1,0:17.5:1:32:0:1:0:60:4:0.0149:0:1 0/0:112:0:0,0:100,12:0:2,0:23.1:1:31.3:1:1:0:60:36.333:1:0:0.1 -5 176707544 . G A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=GCTGACTTGTTTTATGCGGT;RSEQ=TACTTTGTGTTACTTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:303,158:0:2,0:25.7:1:32:1:1:0:60:152.667:0.9978:0:0.1 0/1:397:14:12,2:243,140:0.0353:2,2:21.3:1:28.4:1:0.1526:3.45:60:28:0.0356:0:1 -5 176710547 . C G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.24176;SOR=5.20669;LSEQ=ACGCAGAATGCTGCACCCCA;RSEQ=AGTCTCTGCTTTAGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:0.25:0,0:28:1:30.7:1:1:0:60:6:0.25:0:1 1/0:3:2:2,0:1,0:0.6667:0,0:25.5:1:34:0:1:0:60:4:0.6667:0:1 -5 176710684 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21066;SOR=Inf;LSEQ=TCTTTTCTCTGAGAGGTTCA;RSEQ=TCTTTACAAATAGAAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:121,1:0:1,0:22.6:1:32.3:1:1:0:60:60:1:0:0.1 0/1:104:2:2,0:98,4:0.0192:1,0:26.5:1:30.5:1:1:0:60:4:0.0196:0:1 -5 176710956 . C A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10388;SOR=5.72642;LSEQ=ATCATTTCAGGATTCTGCAG;RSEQ=TGACATCTGAATTTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:1:1,0:129,362:0.002:2,0:1:0:26:0:0.26423:0:60:2:0.0021:0:1 0/1:433:5:4,1:126,301:0.0115:2,2:6.4:1:25.2:1:0.03034:9.50:60:10:0.0117:0:1 -5 176719227 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19899;SOR=Inf;LSEQ=CTCAGGGTCTCATGCCATTT;RSEQ=CATCAGCCTTGAAGAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:13,118:0:2,0:24.3:1:31.7:1:1:0:60:42.667:1:0:0.1 0/1:106:2:0,2:13,91:0.0189:2,0:25.5:1:32:0:1:0:60:4:0.0192:0:1 -5 176720766 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=2.38564;LSEQ=CCACACCTTCGGACTGTAGC;RSEQ=TAGCCTTGGCCCATGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:66:61,5:139,17:0.2973:2,2:22.3:1:30.2:1:0.6239:1.49:60:65:0.3009:0:1 1/0:173:87:77,10:74,11:0.5029:2,2:22.2:1:30.1:1:0.81904:1.14:60:86:0.5:0:1 -5 176720770 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20605;SOR=Inf;LSEQ=ACCTTCGGACTGTAGCATAG;RSEQ=CTTGGCCCATGTGATATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:209,31:0:2,0:23.3:1:31.9:1:1:0:60:47:1:0:0.3 0/1:200:2:1,1:166,32:0.01:2,2:26:1:29.5:1:0.30347:5.12379:60:4:0.0101:0:1 -5 176721119 . G A 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGCTCAGGCACCCAAAAT;RSEQ=TCAGATAAACCTCCTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:196,251:0:2,0:23.8:1:32:1:1:0:60:62.857:1:0:0.2 0/1:311:16:6,10:140,155:0.0514:2,2:25.5:1:29.9:1:0.6084:1.50343:60:32:0.0525:0:1.5 -5 176721151 . T C 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TCCTGCTGACACCAACCAGA;RSEQ=GCTGTCGCTCTCCAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:202,221:0:2,0:23.8:1:30.5:1:1:0:60:140:1:0:0.3 0/1:287:11:5,6:145,131:0.0383:2,2:19.7:1:29.3:1:0.76214:1.32692:60:22:0.04:0:2 -5 176721198 . T C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=55.5162;LSEQ=CAGGGACTTGTCAGAGGCCA;RSEQ=TGCTACCTGAAAGACCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:162:82,80:155,144:0.3514:2,2:26.3:1:32:1:0.84541:1.05006:60:80:0.3509:0:1.2 1/1:406:393:214,179:7,6:0.968:2,2:25:1:31.3:1:1:1.02:60:97.25:0.9677:0:1.3 -5 176721272 . G C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.63321;LSEQ=AAGGTCAGAGACCTCGCTGG;RSEQ=TCAGGGACCAAATCCCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:25:15,10:248,169:0.0563:2,2:23.7:1:32.5:1:1:1.02:60:50:0.0573:0:1.2 0/1:446:192:107,85:147,106:0.4305:2,2:22.8:1:31.7:1:0.62987:1.10142:60:63:0.4295:0:1.4 -5 176722005 . G A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TTTCTCAGCCTCCTGCCAAG;RSEQ=CCTTTTTATATGAGCCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:581:0:0,0:303,277:0:2,0:25.2:1:31.3:1:1:0:60:43.615:0.9982:0:0.1 0/1:598:15:7,8:283,299:0.0251:2,2:21.1:1:29.9:1:1:1.08153:60:30:0.0255:0:1.2 -5 176722514 . AG A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18157;SOR=Inf;LSEQ=CCCCAGGGTACCATTTGGGG;RSEQ=GGGAAATCTTTTCTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:27,239:0:2,0:23.7:1:31.1:1:1:0:60:43.333:1:0:0.1 0/1:198:2:1,1:33,163:0.0101:2,2:6:1:28.5:1:0.31467:4.88:60:4:0.0103:0.0051:0.5 -5 176722542 . T TA 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.63594;SOR=1.28989;LSEQ=TCTTTTCTTTCTTTCCCCCT;RSEQ=AAAAAAAAACACATCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:11:0,11:4,126:0.0775:1,0:24.7:1:29.3:1:1:0:60:10:0.0719:0.007:0.4 0/1:92:9:0,9:3,80:0.0978:1,0:28.6:1:31.3:1:1:0:60:18:0.0989:0:0.2 -5 178012535 . A G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGTCCCTGGATGACGCTGG;RSEQ=GTAACACTCCACAGCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:19:1:32.5:1:0.33333:0:37.5:4:0.6667:0:2 1/1:2:2:1,1:0,0:1:0,2:11.5:1:28.5:1:1:0:46.5:4:1:0:4.5 -5 178012604 . A G 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2;SOR=0;LSEQ=CTGGATGGCGCTGGGGTAAC;RSEQ=CTCCACAGCCCTGGATGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:0,2:0.5:0,2:25.7:1:31:1:0.4:0:27.3:6:0.6:0:3.7 0/0:4:0:0,0:2,2:0:2,0:19.5:1:28:1:1:0:46.8:8:1:0:2.5 -5 178012606 . T C 63 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07619;SOR=0;LSEQ=GGATGGCGCTGGGGTAACAC;RSEQ=CCACAGCCCTGGATGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:0,2:0.6667:0,2:27:1:31.5:1:0.4:0:28.8:8:0.6667:0:4 0/0:4:0:0,0:2,2:0:2,0:19.5:1:25.8:1:1:0:46.8:3:1:0:2.5 -5 178012608 . C T 62 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07619;SOR=0;LSEQ=ATGGCGCTGGGGTAACACTC;RSEQ=ACAGCCCTGGATGGCGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:0,2:0.6667:0,2:29:1:31:1:0.4:0:28.8:8:0.6667:0:4 0/0:4:0:0,0:2,2:0:2,0:19.5:1:30:1:1:0:46.8:8:1:0:2.5 -5 178012665 . CA TG 99 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.56434;LSEQ=CCTGGATGGCGCTGGGGTAA;RSEQ=CTCCACAGCCCTGGATGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:8,1:9,8:0.3103:2,2:29.1:1:31.3:1:0.0977:6.64:42.4:18:0.36:0:3.8 0/1:5:1:1,0:1,3:0.2:2,0:19:0:33:0:0.4:0:60:2:0.2:0:3 -5 178012668 . T C 113 MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20929;SOR=0.21302;LSEQ=GGATGGCGCTGGGGTAACAC;RSEQ=CCACAGCCCTGGATGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:13:8,5:9,7:0.4483:2,2:33.3:1:30.8:1:1:1.24:44.1:26:0.4643:0:4.5 0/1:7:1:1,0:2,4:0.1429:2,0:21:0:32:0:0.42857:0:60:2:0.1429:0:3 -5 178012670 . C T 100 MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20267;SOR=0.20032;LSEQ=ATGGCGCTGGGGTAACACTC;RSEQ=ACAGCCCTGGATGGCGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:13:8,5:8,7:0.4643:2,2:35:1:27.1:1:0.71768:1.38:44.1:3.333:0.4:0:4.5 0/1:7:1:1,0:2,4:0.1429:2,0:23:0:33:0:0.42857:0:60:2:0.1429:0:3 -5 178012712 . A T 81 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55906;SOR=0;LSEQ=GTAATGCCCTACAGCCCTGG;RSEQ=TGGCGCTGGGGTAACACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:4,3:11,10:0.25:2,2:25.3:1:29:1:1:1.20:37.6:14:0.28:0:3.6 0/0:5:0:0,0:2,3:0:2,0:19.6:1:30:1:1:0:55.6:10:1:0:1.6 -5 178012715 . GC AT 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGCCCTACAGCCCTGGATG;RSEQ=GCTGGGGTAACACTCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:2,3:12,10:0.1852:2,2:28.2:1:30.7:1:0.64831:1.76109:36.8:10:0.1923:0:2.4 0/0:4:0:0,0:2,2:0:2,0:20.8:1:33.3:1:1:0:54.5:8:1:0:1.5 -5 178012716 . C T 32 v4;q23;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCTACAGCCCTGGATGG;RSEQ=GCTGGGGTAACACTCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:3,0:9,9:0.1154:2,0:16.7:1:20.7:1:0.22857:0:43.3:2:0.1111:0:4 0/0:4:0:0,0:2,2:0:2,0:19.8:1:32.3:1:1:0:54.5:8:1:0:1.5 -5 178012719 . T TG 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACAGCCCTGGATGGCGC;RSEQ=GGGGTAACACTCCACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:2,3:12,9:0.1923:2,2:24.2:1:32:1:0.63478:1.94676:36.8:10:0.2083:0:3.4 0/0:4:0:0,0:2,2:0:2,0:16.8:1:31.5:1:1:0:54.5:8:1:0:1.5 -5 178012735 . AG GT 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTGGGGTAACACTCCAC;RSEQ=CCCTGGCTGACCCTGTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,7:0.1333:2,2:5:1:27.3:1:1:1.37:44:4:0.1429:0.0667:5.5 0/0:2:0:0,0:1,1:0:2,0:9.5:1:32:1:1:0:60:4:1:0:2.5 -5 178095692 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49786;SOR=Inf;LSEQ=GCCTGCCTGGCTTCTCGTGG;RSEQ=TTGCTGGCAAGCTTTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:55,52:0:2,0:26.1:1:30.1:1:1:0:60:106:1:0:0.2 0/1:111:2:1,1:61,48:0.018:2,2:36:1:28.5:1:1:1.26806:60:4:0.0182:0:1 -5 178095709 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24433;SOR=0;LSEQ=TGGTTTGCTGGCAAGCTTTG;RSEQ=CATTCCTCGGCTTCTAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:52,55:0.0183:2,2:36:1:31.5:1:1:1.06:60:4:0.0185:0:1 0/0:111:0:0,0:53,58:0:2,0:28.2:1:31.4:1:1:0:60:54.5:1:0:0.2 -5 178095757 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50015;SOR=Inf;LSEQ=CCAATCTCCACCCTCATCTT;RSEQ=ATGTGGTATTCTCCCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:18,35:0:2,0:23.5:1:31:1:1:0:60:25.5:1:0:0.1 0/1:64:2:1,1:18,44:0.0313:2,2:32.5:1:28:1:0.50893:2.41:60:4:0.0313:0:1 -5 178095779 . C CA 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.03182;LSEQ=TGTGGTATTCTCCCTATCTC;RSEQ=AACTTCCCCTTTTTATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:1,6:9,19:0.2:2,2:27.3:1:31.1:1:0.64446:2.77057:60:14:0.2188:0.0286:0.1 0/1:39:8:2,6:5,26:0.2051:2,2:20.1:1:30.5:1:0.61704:1.71:60:16:0.2051:0.0769:0.1 -5 178267705 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGAAAAAGGTTCTTCAG;RSEQ=CCAGGCTCCAGTATCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:22:1:33.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 178267755 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGGAGGAGGAGTTTCCT;RSEQ=TAATCCAGAAGGGGAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:29:1:29.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 178268093 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49855;SOR=Inf;LSEQ=CTGAGAAGCGGGACACCCTG;RSEQ=CCCTGCTGCAGAAGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:39,21:0:2,0:25.9:1:31.1:1:1:0:60:59:1:0:1.6 0/1:69:2:1,1:43,24:0.029:2,2:44:0:30.5:1:1:1.77567:60:4:0.0294:0:1 -5 178268107 . G C 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=0.20541;LSEQ=ACCCTGCCCCTGCTGCAGAA;RSEQ=CAGCCATCCCAGCAGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:51:30,21:11,6:0.75:2,2:25.8:1:31.2:1:0.77852:1.27869:60:102:0.7727:0:2.4 0/1:74:28:15,13:28,18:0.3784:2,2:28:1:30.4:1:0.62933:1.34264:60:56:0.3889:0:2.2 -5 178268132 . A G 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24184;SOR=0.65798;LSEQ=CATCCCAGCAGCCAGCAGGC;RSEQ=AGGTCTGAGCTCAGGACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:54:29,25:11,10:0.72:2,2:29.7:1:30.2:1:1:1.05:60:108:0.7397:0:2.4 1/0:86:54:27,27:19,13:0.6279:2,2:28.7:1:30.1:1:0.50328:1.45507:60:26:0.619:0:1.9 -5 178268174 . C T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49991;SOR=Inf;LSEQ=CCGAGGCCCTCTATGGCCAG;RSEQ=AACCATGTCAGACACAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:25,43:0:2,0:25.8:1:31.7:1:1:0:60:21.667:1:0:1.5 0/1:80:2:1,1:32,46:0.025:2,2:7.5:1:24:1:1:1.43:60:4:0.025:0:1.5 -5 178268179 . A G 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00266;SOR=0.35265;LSEQ=GCCCTCTATGGCCAGCAACC;RSEQ=TGTCAGACACAGCACCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:40:13,27:11,17:0.5882:2,2:22.9:1:30.4:1:0.61269:1.33798:60:39:0.6:0:2.2 0/1:78:26:9,17:21,31:0.3333:2,2:22.9:1:29.9:1:0.8054:1.27556:60:52:0.3377:0:2.4 -5 178268227 . T C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00078;SOR=Inf;LSEQ=GCCAGATGCCTCTGCTGGAG;RSEQ=CAGCACTCCAAACCTATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:9,26:0:2,0:24.6:1:30.3:1:1:0:60:70:1:0:0.6 0/1:33:9:2,7:4,20:0.2727:2,2:19.3:1:29.7:1:1:1.41:60:8:0.25:0:2.1 -5 178268271 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=AAAATGGTGACCCCCACCCT;RSEQ=GCCAGGGCTCCTGGGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:0,12:0.1429:0,2:12.5:1:28.5:1:0.14286:0:60:4:0.1429:0:1.5 0/0:7:0:0,0:0,7:0:0,0:15.1:1:31.1:1:1:0:60:14:1:0:0.9 -5 178268295 . G A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=AGGGCTCCTGGGCCTTTGAC;RSEQ=TCTTTTAGGCTGGTCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:0,7:0.125:0,0:5:0:32:0:1:0:60:2:0.125:0:1 1/0:4:2:0,2:0,2:0.5:0,0:14:1:28:1:1:0:60:4:0.5:0:2 -5 178268306 . T C 69 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.63248;LSEQ=GCCTTTGACGTCTTTTAGGC;RSEQ=GGTCTGTGTGGGACAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:25.4:1:29.8:1:1:0:60:10:0.8333:0:1 1/0:4:3:0,3:0,1:0.75:0,0:15.3:1:21.7:1:1:0:60:2:0.6667:0:1.7 -5 178996349 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25008;SOR=0;LSEQ=TGATGGAGGAAGAAGGGATG;RSEQ=TGATTGTTGGTCTGCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:1,2:149,90:0.0124:2,2:15.7:1:28.7:1:0.5593:3.29425:60:6:0.0124:0:1 0/0:220:0:0,0:138,82:0:2,0:22.6:1:30.7:1:1:0:60:72.333:1:0:0.2 -5 178996435 . A G 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGATTCTCAGGTAAAATG;RSEQ=AATTTTGGCTCTAGATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:119,167:0:2,0:25.5:1:30.1:1:1:0:60:94.333:1:0:0.1 0/1:332:81:36,45:111,140:0.244:2,2:25.8:1:30.7:1:1:1.01:60:80:0.2439:0:1.1 -5 178996554 . G A 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACTGGTAGAGGACCCCAGG;RSEQ=ATGCAGCTGGGGAAGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:28:0,28:1,16:0.6222:1,1:23.1:1:30.5:1:0.37778:0:60:56:0.6222:0:1 0/0:28:0:0,0:2,26:0:2,0:19.8:1:31.1:1:1:0:60:27:1:0:0.1 -5 179545228 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17557;SOR=Inf;LSEQ=CCAAAGGGCCCCAAGTGGGG;RSEQ=GGAGCCTGGAAACTGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:72,41:0:2,0:23.9:1:30:1:1:0:60:55.5:1:0:0.7 0/1:82:2:1,1:44,36:0.0244:2,2:33.5:1:29:1:1:1.21921:60:4:0.0253:0:1.5 -5 179545252 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15565;LSEQ=GCCTGGAAACTGTAGTGTGG;RSEQ=AGGGCAGGTCTGGGGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:79,69:0.0133:2,2:12.5:1:30.5:1:1:1.14389:60:4:0.0133:0:3 0/1:130:2:1,1:66,62:0.0154:2,2:6:0:31:1:1:1.06404:60:4:0.0156:0:2 -5 179545299 . TG CA 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.3915;SOR=1.521;LSEQ=GGAGAAGAGAGGAGAGGCCA;RSEQ=GGGGCTCTGAAGAACTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:120:105:44,61:7,7:0.875:2,2:27.2:1:31.7:1:0.57909:1.38248:60:210:0.8898:0.1:1 1/1:105:96:43,53:4,5:0.9143:2,2:25.9:1:30.7:1:1:1.01:60:192:0.9231:0.0667:1.1 -5 179545318 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50327;SOR=0;LSEQ=ATGGGGGCTCTGAAGAACTG;RSEQ=TGAGCAGAAGACGAAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:34,59:0.0211:2,2:12.5:1:28.5:1:1:1.72:60:4:0.0211:0:2.5 0/0:76:0:0,0:29,47:0:2,0:21.4:1:30.4:1:1:0:60:75:1:0:1 -5 179545346 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12783;SOR=Inf;LSEQ=AAGACGAAGTGGCCTCACTC;RSEQ=TGTGGCCCCCCAAGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:6,47:0:2,0:19.7:1:31:1:1:0:60:52:1:0:0.7 0/1:30:2:1,1:2,26:0.0667:2,2:16:1:28.5:1:0.1931:10.82:60:4:0.0667:0:2.5 -5 180029879 . G A 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGTGATGAAAGGAGGTC;RSEQ=CCAAAGAGACATTCCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:23.3:1:29.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180030038 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCCTTGGGCCTGGAGTC;RSEQ=TGCTCTTCCTAGCTGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:2,0:50,0:0.0385:1,0:10:1:31:0:1:0:60:4:0.04:0:1 0/0:24:0:0,0:23,1:0:1,0:24.6:1:30.3:1:1:0:60:48:1:0:0 -5 180030313 . C A 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03858;LSEQ=CCTGGCCTCCTCGGGCCCCC;RSEQ=GCTCAGGCCGCCGCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1334:1121:538,583:104,103:0.8403:2,2:23.9:1:30.2:1:0.59631:1.09409:60:45.708:0.8387:0:1.2 0/1:1098:185:92,93:458,454:0.1685:2,2:23.2:1:29.8:1:0.9358:1.01976:60:45.25:0.1676:0:1.2 -5 180035262 . TTC T 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=1.01071;LSEQ=AAATGCTGACGTATGCTGCC;RSEQ=TCTCTCTCTGCTTCAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:6:3,3:98,43:0.0408:2,2:12.2:1:30.7:1:0.37734:2.26498:59.8:12:0.0414:0.0204:0.3 0/1:97:4:2,2:65,28:0.0412:2,2:8.5:1:29:1:0.58522:2.29911:60:8:0.0426:0.0309:0 -5 180035274 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16026;SOR=Inf;LSEQ=ATGCTGCCTTCTCTCTCTCT;RSEQ=CTTCAGCTACCTAAGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:118,67:0:2,0:23.5:1:31.6:1:1:0:60:36:1:0:0.2 0/1:124:2:1,1:76,46:0.0161:2,2:13:1:28:1:1:1.64515:60:4:0.0163:0:1 -5 180035347 . C T 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=59.05652;LSEQ=CACCTTATCAATCACTTGAA;RSEQ=GACTCACCCTCCTGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:1,0:131,155:0.0035:2,0:14:0:32:0:0.45993:0:60:2:0.0036:0:1 0/1:250:43:20,23:98,108:0.172:2,2:27:1:29.6:1:1:1.04335:60:86:0.1734:0:1.4 -5 180035504 . C T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29032;SOR=0;LSEQ=TCTTGTGTCTTTCTTTCTTA;RSEQ=GATCTCTTATCTCCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:1,21:0,0:1:0,1:19.1:1:30.2:1:1:0:60:21:1:0:1.5 1/1:9:8:1,7:0,0:0.8889:0,2:26.4:1:31:1:1:0:60:16:1:0:1.3 -5 180035792 . C T 129 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.04236;SOR=0.27526;LSEQ=ATGTGACAGGGAGGGGCTCC;RSEQ=GCGGTGCTGTAGGTCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:19:19,0:45,4:0.2754:2,1:27.2:1:30.4:1:0.57016:0:60:18:0.2769:0:1.1 0/1:32:3:3,0:27,2:0.0938:2,0:28.7:1:32.3:1:1:0:60:6:0.0938:0:1 -5 180036791 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54602;SOR=0;LSEQ=TCACCCTGGACTTGCACTTT;RSEQ=AAAGGACAGTCGTTGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:172,4:0.0112:1,2:16.5:1:30.5:1:0.05554:38.5548:60:4:0.0115:0:1 0/0:94:0:0,0:93,1:0:1,0:20.6:1:31.3:1:1:0:60:93:1:0:0 -5 180037058 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23631;SOR=2.87085;LSEQ=ATCAGAAGGTGCTGAGGAAC;RSEQ=CGCTGCAGCAACCCTCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:2:2,0:141,418:0.0036:2,0:1:0:25.5:1:0.06464:0:60:4:0.0036:0:1 0/1:393:4:3,1:121,268:0.0102:2,2:17.3:1:27:1:0.09481:6.61:60:8:0.0102:0:1 -5 180037231 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGCCCCAGCAGCACCCT;RSEQ=GGCTGTGTTTCCTCCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:0,20:0.0909:1,2:20:1:27.5:1:0.09091:0:60:4:0.0952:0:1 0/0:2:0:0,0:0,2:0:0,0:34.5:1:31:1:1:0:60:4:1:0:0.5 -5 180038248 . T TC 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.08871;LSEQ=GACGTCGCATGATTTGCTTT;RSEQ=CCCCGATGACGCAGAGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:195:191:163,28:3,0:0.9795:0,2:21.4:1:31.1:1:1:0:60:62.667:0.9792:0.1744:0.2 1/1:104:84:68,16:18,2:0.8077:2,2:21.9:1:30.7:1:0.51412:2.10472:60:83:0.8058:0.1538:0.2 -5 180038678 . CCT C 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGCTTGGGCTCCTGACC;RSEQ=GAGATAGGGCCCTAACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:2,12:0,0:1:0,2:27.9:1:32.3:1:1:0:60:28:1:0.2143:0.6 1/1:2:2:0,2:0,0:1:0,0:35:1:33:0:1:0:60:4:1:0:0 -5 180039187 . A G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCACCAGGTGAAGGAAT;RSEQ=CATCATGACGATGCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:26.3:1:32.9:1:1:0:60:24:1:0:1.1 1/1:2:2:1,1:0,0:1:0,2:40.5:1:31.5:1:1:0:60:4:1:0:1 -5 180039606 . C T 174 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=21.50615;LSEQ=ACCAGCAGTTCAGCATGATG;RSEQ=GGCGTCTGCAGGATCACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1007:4:2,2:424,579:0.004:2,2:18.8:1:28.5:1:1:1.37:60:8:0.004:0:1 0/1:784:62:28,34:306,415:0.0791:2,2:27.2:1:29.3:1:0.68997:1.12:60:124:0.0802:0:1.3 -5 180039715 . C T 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.03421;SOR=Inf;LSEQ=TCACCCACTCTGCCCTCCTC;RSEQ=TGACACGTCTCCCACTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:5,176:0:1,0:25.6:1:32.5:1:1:0:60:89.5:1:0:0.2 0/1:88:3:0,3:3,82:0.0341:1,0:14.3:1:29:1:1:0:60:6:0.0341:0:1 -5 180040270 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACCCGACTGTGCTCTAC;RSEQ=TGGGACCTGTGGGCAAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:2,73:0.026:1,2:28:1:29.5:1:0.0769:30.00:60:4:0.0278:0:1 0/0:22:0:0,0:0,22:0:1,0:25.7:1:31.3:1:1:0:60:21:1:0:0.2 -5 180040457 . T C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACAAAGCCTCTCTTGC;RSEQ=TCTCGCTGCTTCTCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:1:33:1:1:0:60:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:19:0:33:1:1:0:60:4:1:0:1 -5 180040918 . G A 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00269;SOR=8.96819;LSEQ=CCAGGCTGGGGAGAGGTGGG;RSEQ=GGCCCTTGGTGGCCCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:13:13,0:52,0:0.2:1,1:24.5:1:30.9:1:1:0:60:26:0.2031:0:1.5 1/0:10:7:7,0:3,0:0.7:0,0:32.9:1:29.9:1:1:0:60:14:0.7:0:1.7 -5 180041001 . G C 252 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.34398;LSEQ=AGTCCCTTACTCCAGCAGGG;RSEQ=CGGTCATGTAACCTGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:231:229:212,17:0,0:0.9913:0,2:24.8:1:32.2:1:1:0:60:458:0.9913:0:2.1 1/1:155:154:139,15:0,0:0.9935:0,2:23:1:32.2:1:1:0:60:308:1:0:2.1 -5 180041008 . T C 256 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41595;SOR=0;LSEQ=TACTCCAGCAGGGGCGGTCA;RSEQ=GTAACCTGCCGCCAGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:271:271:241,30:0,0:1:0,2:23.4:1:31.7:1:1:0:60:66.75:1:0:2 1/1:193:192:167,25:0,0:0.9948:0,2:22.6:1:31:1:1:0:60:191:0.9948:0:1.9 -5 180041200 . T G 79 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1739;SOR=2.33587;LSEQ=CTGGGGAGACAGAGGGAAGC;RSEQ=TGTCCCGTGGTGGATGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:666:5:0,5:235,425:0.0075:2,0:7.4:1:27.6:1:0.16736:0:47:10:0.0077:0:2.8 0/1:518:9:0,9:184,325:0.0174:2,0:5.6:1:25:1:0.03013:0:41.3:8:0.0157:0:3 -5 180041208 . T C 271 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13157;LSEQ=ACAGAGGGAAGCTTGTCCCG;RSEQ=GGTGGATGGGGAGACGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:567:547:182,365:2,15:0.9647:2,2:24.9:1:29.9:1:0.0692:3.73:59.9:27.789:0.9724:0:1.3 1/0:427:334:114,220:29,62:0.7822:2,2:24.8:1:29.5:1:0.7094:1.11:60:32.4:0.7864:0:1.3 -5 180041242 . T C 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00119;SOR=0.39626;LSEQ=ACGGAGGGAAGCGTGTCCCG;RSEQ=GGTGGATGGGGAGACGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:54:8,46:58,217:0.1622:2,2:23:1:26.3:1:0.35516:1.53503:57.3:9.8:0.1612:0:2.4 0/1:239:17:5,12:57,163:0.0711:2,2:30.2:1:29.1:1:0.77668:1.19:50.8:34:0.0742:0:2.6 -5 180041258 . G A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01024;SOR=Inf;LSEQ=CCCGTGGTGGATGGGGAGAC;RSEQ=GAGGGAAGCGTGTCCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:34,215:0:2,0:26.5:1:30.3:1:1:0:58.2:26.667:1:0:1.9 0/1:168:5:4,1:35,128:0.0298:2,2:24.4:1:26.6:1:0.01065:14.33:60:10:0.0301:0:3 -5 180041268 . G T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02074;SOR=Inf;LSEQ=ATGGGGAGACGGAGGGAAGC;RSEQ=TGTCCTGCGGTGGATGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:26,188:0:2,0:26.2:1:31.1:1:1:0:57.9:25.75:1:0:2.1 0/1:133:4:2,2:25,104:0.0301:2,2:41:1:23.8:1:0.1831:4.10:60:3:0.0227:0:3.3 -5 180041274 . T C 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACGGAGGGAAGCGTGTCC;RSEQ=GCGGTGGATGGGGAGACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:198:197:23,174:0,0:0.9949:0,2:25.4:1:29.2:1:1:0:57.8:18.7:0.9947:0:2.1 1/1:124:124:24,100:0,0:1:0,2:23.3:1:30.1:1:1:0:57.8:248:1:0:2 -5 180041276 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=ACGGAGGGAAGCGTGTCCTG;RSEQ=GGTGGATGGGGAGACGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:22,171:0:2,0:25:1:29.3:1:1:0:57.7:18.3:1:0:2.1 0/1:121:9:0,9:23,88:0.0744:2,0:17.6:1:31.7:1:0.20394:0:59.3:18:0.0756:0:2 -5 180041310 . T C 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14303;SOR=0.49553;LSEQ=ACGGAGGGAAGCGTGTCCCG;RSEQ=GGTGGATGGGAAGAGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:25:2,23:12,62:0.2525:2,2:6.6:1:29.5:1:0.50787:2.21051:51.6:24:0.25:0:2.5 0/1:49:7:2,5:14,28:0.1429:2,2:5.4:1:28.9:1:1:1.24446:54.4:14:0.1458:0:2 -5 180041316 . A G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.58939;SOR=2.22716;LSEQ=GGAAGCGTGTCCCGTGGTGG;RSEQ=TGGGAAGAGAGGGCTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:0,2:13,70:0.0235:2,0:24:0:34:0:1:0:60:4:0.0241:0:3 0/1:39:2:0,2:11,26:0.0513:2,0:44:1:31.5:1:1:0:60:4:0.0526:0:2 -5 180041637 . G A 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCTGAGGCATCTCCGCC;RSEQ=CCGGCTGTCTCTCTCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:25.3:1:27:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180041662 . G A 54 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTCTCTCCCTCTCATG;RSEQ=TCTCTACCTGGGAGCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:31:1:27:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180041999 . G T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACATACTGCACCAAGC;RSEQ=GGTCCATCTCCAGGACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29.5:1:1:0:60:4:1:0:1 -5 180042507 . C T 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TCGGAGCACTGGGGCCCCGC;RSEQ=GGTCACCTCCCTTCTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:24:0:31.5:1:1:0:55:4:0.5:0:1 0/0:2:0:0,0:1,1:0:2,0:19.5:1:30.5:1:1:0:53:4:1:0:0.5 -5 180042545 . G GGC 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTTCCTTTCGGAGCACTGG;RSEQ=CCCGCCGGTCACCTCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:29:0:1:0:43:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:33.5:0:1:0:53:4:1:0:0.5 -5 180043093 . TGCC CCGCT 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TCCTTTCGGAGCACTGGGCC;RSEQ=GGTCACCTCCCTTCTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:4:4,0:0,0:2:0,0:9.8:1:32.3:1:1:0:44.5:8:1:1:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180043388 . G A 217 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=123.08337;LSEQ=CTGCCCTTGCGGACGTAGTC;RSEQ=GGGTCTTTGTAGATGTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1089:2:2,0:550,536:0.0018:2,0:1:0:29:0:0.49965:0:60:4:0.0019:0:1 0/1:811:150:79,71:337,321:0.185:2,2:25.4:1:30.1:1:0.78623:1.06:60:74:0.1862:0:1.1 -5 180043538 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14434;SOR=Inf;LSEQ=TGTCAGTGCAGGCCCCTGGG;RSEQ=TAATACCCACACCCGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:49,195:0:2,0:22.9:1:31.7:1:1:0:60:80.333:1:0:0.1 0/1:150:2:1,1:31,117:0.0133:2,2:8:1:29:1:0.38228:3.73:60:4:0.0135:0:1 -5 180043731 . C A 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=GCTGCTGACCAGCCAAGAGA;RSEQ=CTTGGGAGGTCAACTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:101,7:0:2,0:26.6:1:32.4:1:1:0:60:216:1:0:0.1 0/1:45:7:7,0:37,1:0.1556:1,0:31:1:30.9:1:1:0:60:14:0.1556:0:1 -5 180044769 . G A 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGCCTCTGGTACACCCAC;RSEQ=TCCTATTCCAGAGCACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:6:0:32:0:1:0:25:2:1:0:1 1/1:3:3:2,1:0,0:1:0,2:19:1:28:1:1:0:38.7:6:1:0:1.3 -5 180044870 . G A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89765;LSEQ=TCAACCTCTGGGACACCCAC;RSEQ=TCCTATTCCAGAGCACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:2,2:0.4286:2,2:36.3:1:30:1:1:1.81:40.3:6:0.4286:0:2 0/1:5:2:1,1:1,2:0.4:2,2:48:1:29:1:1:1.73:40:4:0.4:0:2 -5 180044891 . T A 42 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=TCCTATTCCAGAGCACCCTC;RSEQ=CCTGCCACTCAGCCTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:2,1:0.5714:2,2:27:1:21.3:1:1:1.81007:37.5:1:0.4:0:1.8 1/0:3:2:1,1:0,1:0.6667:0,2:30.5:1:28:1:1:0:40:4:0.6667:0:2 -5 180045700 . G GGGTTACCCTA 243 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.03254;LSEQ=CCCGCTGAGGACCCCAGGCT;RSEQ=GGGTGCCTGATCACGGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:290:287:244,43:3,0:0.9897:0,2:21:1:29.8:1:1:0:59.8:94.667:0.9861:0.4414:0.2 1/0:176:133:107,26:30,10:0.7557:2,2:22.2:1:29.5:1:0.50652:1.37:59.8:266:0.7688:0.3466:0.1 -5 180045715 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05429;SOR=Inf;LSEQ=AGGCTGGGGTGCCTGATCAC;RSEQ=GGATATAACCGGGCCCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:305,120:0:2,0:18.1:1:29.4:1:1:0:59.9:59.714:1:0:0.2 0/1:260:3:2,1:185,72:0.0115:2,2:15:1:27:1:1:1.28345:60:6:0.0117:0:1 -5 180045944 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12277;SOR=Inf;LSEQ=CGGATGCACGAAGCTGGCTC;RSEQ=AGGGCGCCCAGTCGTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:53,238:0:2,0:25.9:1:31.2:1:1:0:60:96:0.9965:0:0.1 0/1:158:2:1,1:30,126:0.0127:2,2:24:1:27:1:0.35491:4.15:60:4:0.0128:0:1 -5 180046002 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20776;SOR=Inf;LSEQ=CCCCCGCCGCCCGCGGCGCC;RSEQ=CGCAGGCCGCCCGCTCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:78,79:0:2,0:19.9:1:31.2:1:1:0:60:156:1:0:0.1 0/1:132:2:1,1:61,69:0.0152:2,2:25:1:28:1:1:1.13:60:4:0.0155:0:1.5 -5 180046012 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49975;SOR=0;LSEQ=CCGCGGCGCCCCGCAGGCCG;RSEQ=CCGCTCACCGCGCAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:95,85:0.0109:2,2:42:1:30:1:1:1.11696:60:4:0.0112:0:1 0/0:166:0:0,0:90,76:0:2,0:22.6:1:31.1:1:1:0:60:40.5:1:0:0.3 -5 180046031 . C T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.4458;LSEQ=GCCCGCTCACCGCGCAGGGG;RSEQ=TGAAGGCGTCCCGCTTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:2:1,1:139,106:0.0081:2,2:31.5:1:30:1:1:1.30985:60:4:0.0082:0:1 0/1:257:3:1,2:141,113:0.0117:2,2:21.7:1:26:1:0.58827:2.48687:60:6:0.012:0:1 -5 180046107 . G A 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.62662;SOR=0.37626;LSEQ=CTCCACGATCACCATGAGGG;RSEQ=GCCTGCGGCGGGACCGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:3,0:124,169:0.0101:2,0:8.7:1:21.7:1:0.07792:0:60:2:0.0069:0:2 0/0:261:1:0,1:122,138:0.0038:2,0:7:0:31:0:1:0:60:2:0.0039:0:1 -5 180046111 . T G 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25327;SOR=0;LSEQ=ACGATCACCATGAGGGGGCC;RSEQ=GCGGCGGGACCGGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:116,158:0.0108:2,2:20:1:24:1:1:1.4664:60:2:0.0074:0:1.3 0/0:238:0:0,0:108,128:0:2,0:22.4:1:30:1:1:0:60:46.2:0.9914:0:0.3 -5 180046126 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18266;SOR=Inf;LSEQ=GGGCCTGCGGCGGGACCGGG;RSEQ=GGCGGCCGTGCGTTCGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:82,125:0:2,0:24.3:1:30.4:1:1:0:60:33.5:1:0:0.3 0/1:155:2:1,1:64,89:0.0129:2,2:33.5:1:31:0:1:1.39:60:4:0.014:0:1.5 -5 180046127 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18472;SOR=Inf;LSEQ=GGCCTGCGGCGGGACCGGGC;RSEQ=GCGGCCGTGCGTTCGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:79,121:0:2,0:24.3:1:30.3:1:1:0:60:39:0.9949:0:0.3 0/1:152:2:1,1:62,88:0.0132:2,2:7:1:28:1:1:1.42:60:4:0.0137:0:1 -5 180046137 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51027;SOR=0;LSEQ=GGGACCGGGCGGCGGCCGTG;RSEQ=GTTCGGAACCCGGGGCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:60,105:0.0119:2,2:11.5:1:28.5:1:1:1.74:60:4:0.0122:0:1.5 0/0:123:0:0,0:46,76:0:2,0:19.9:1:29.8:1:1:0:60:39.667:1:0:0.3 -5 180046209 . C T 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=0;LSEQ=CCCTCCCGCCCGCGGCGCCC;RSEQ=GCGCCCGGGGTCTCGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:123:123:109,14:0,0:1:0,2:15.8:1:31.6:1:1:0:60:122:1:0:1.2 1/1:92:79:63,16:10,3:0.8587:2,2:14.4:1:30.9:1:0.72747:1.18:60:78:0.8667:0:1.3 -5 180046234 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66903;SOR=1.70754;LSEQ=CCGGGGTCTCGCCGTCCCAG;RSEQ=GGGCCGCCCGCTCCGTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:2:0,2:194,59:0.0078:2,0:1:0:25:0:0.05651:0:60:4:0.008:0:1 0/1:225:3:1,2:150,72:0.0133:2,2:11:1:27.7:1:0.25234:4.13785:60:6:0.0136:0:1 -5 180046238 . C T 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62888;SOR=0.39247;LSEQ=GGTCTCGCCGTCCCAGCGGG;RSEQ=CGCCCGCTCCGTACCCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:212,76:0.0103:2,2:30:1:30.3:1:1:1.39303:60:6:0.0105:0:2 0/0:246:1:0,1:161,84:0.0041:2,0:1:0:29:0:0.34553:0:60:2:0.0041:0:1 -5 180046344 . G C 292 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00404;LSEQ=AGCTCCGACATCAGCGCGCG;RSEQ=TGCTCGCTGGCCGTGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:583:582:296,286:0,0:0.9983:0,2:25.7:1:31.9:1:1:0:59.9:63.667:1:0:1.2 1/0:478:335:168,167:76,65:0.7008:2,2:25.5:1:31.5:1:0.48287:1.1619:59.9:82.75:0.7058:0:1.2 -5 180046426 . C CTGGCCGCTTAGCTAAGGCACAG 273 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.04506;LSEQ=CAGGTCCCCGTTCCCCGCCA;RSEQ=CCGGCGCTTTTGGGAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:503:496:273,223:0,0:0.9861:0,2:23.7:1:30.6:1:1:0:59.3:495:0.99:0.5924:0.4 1/0:343:261:126,135:40,40:0.7609:2,2:24.5:1:30.5:1:0.79954:1.0712:59.5:522:0.7676:0.449:0.5 -5 180046492 . CAG C 303 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.06101;LSEQ=TCCTGCCGGCCCCACTGAGG;RSEQ=AGGGGGTTCGGGTGGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:722:702:382,320:12,8:0.9723:2,2:26.2:1:32.1:1:0.65663:1.25615:59.9:139.4:0.9721:0.1343:0.2 1/0:502:342:189,153:84,75:0.6813:2,2:26.9:1:31.8:1:0.63072:1.10:59.9:341:0.6834:0.0876:0.2 -5 180046495 . A G 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCGGCCCCACTGAGGCAG;RSEQ=GGGGGTTCGGGTGGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:691:0:0,0:378,306:0:2,0:26.3:1:30.6:1:1:0:59.9:75:0.997:0:0.2 0/1:487:16:10,6:249,210:0.0329:2,2:14.2:1:27.6:1:0.61406:1.40:59.4:7:0.0294:0:3.1 -5 180046499 . GGT T 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00479;SOR=Inf;LSEQ=GGCCCCACTGAGGCAGAGGG;RSEQ=TCGGGTGGTCCCTCGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:399,321:0:2,0:26.5:1:31.1:1:1:0:59.9:71:1:0:0.2 0/1:504:6:5,1:267,224:0.0119:2,2:11:1:26.2:1:0.22852:4.18:59.2:12:0.0122:0.002:2 -5 180046784 . GG A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.03005;SOR=Inf;LSEQ=CTCTCCCTGTCGGGGCAGGG;RSEQ=CCAGTTGCAGGTGAGCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:118,254:0:2,0:25.2:1:30.8:1:1:0:60:52.143:0.9918:0:0.1 0/1:269:4:3,1:74,189:0.0149:2,2:13.5:1:26.5:1:0.07367:7.60:60:8:0.015:0.0074:1 -5 180046839 . G A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGACAGGTGGGCGGCGGGG;RSEQ=AGCCCCGTGCAGAGGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:18,123:0:2,0:22.8:1:31.2:1:1:0:60:69.5:1:0:0.1 0/1:66:14:2,12:5,47:0.2121:2,2:20.7:1:30.5:1:0.63402:1.55:60:28:0.2188:0:1.2 -5 180046846 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGCGGCGGGGGAGCCCC;RSEQ=TGCAGAGGTCCAGGAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:0,2:17,109:0.0156:2,0:5.5:1:31.5:1:1:0:60:4:0.016:0:1 0/0:52:0:0,0:6,46:0:2,0:20.8:1:30.8:1:1:0:60:25:1:0:0.5 -5 180046934 . G T 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.22214;LSEQ=AGAGGTGGACAGGAGGCCGC;RSEQ=CATCCTCCCGGGTAGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:25:9,16:9,14:0.5208:2,2:28:1:30.2:1:1:1.13968:60:24:0.5217:0:1.4 1/0:7:4:1,3:0,3:0.5714:0,2:17.8:1:31.3:1:1:0:60:8:0.5714:0:1 -5 180047412 . T C 243 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGATGGCACTTCCTGCGGGG;RSEQ=TCTCAGTCAAGGAGGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:183:181:17,164:0,0:0.9891:0,2:26.3:1:32.5:1:1:0:60:44.25:1:0:1.1 1/1:86:86:5,81:0,0:1:0,2:25:1:31.6:1:1:0:60:42:1:0:1.1 -5 180047615 . C T 58 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04965;SOR=7.48386;LSEQ=GGAGGGACACTCACCCTCCT;RSEQ=ATGTTACAGAAGATGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:678:1:0,1:421,256:0.0015:2,0:1:0:24:0:0.37906:0:60:2:0.0015:0:1 0/1:548:6:1,5:326,215:0.0109:2,2:5.3:1:22.7:1:0.04113:7.55469:60:5:0.0092:0:1.8 -5 180047793 . G C 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGCAGCACCCCTTCTGGT;RSEQ=GCCACGACTTGCCCAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:0:0,0:163,230:0:2,0:23.3:1:31.4:1:1:0:60:38.3:1:0:0.4 0/1:297:53:20,33:97,147:0.1785:2,2:19.1:1:29.7:1:0.87709:1.0885:60:16.667:0.1761:0:1.4 -5 180047863 . C G 285 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.46113;LSEQ=AAGGGAGTTGAGGGGTGCAG;RSEQ=CTGAGGCCAGACCTTCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:563:561:306,255:0,1:0.9964:0,2:24.5:1:31.3:1:0.45552:0:60:42.154:0.9964:0:1.1 1/1:411:410:228,182:0,0:0.9976:0,2:25.8:1:31.1:1:1:0:60:57.571:1:0:1.2 -5 180048056 . C T 198 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=159.68041;LSEQ=CCACCTGGGTTTGGGATCGT;RSEQ=GGCCTCGCGGGCCTCCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:667:1:0,1:331,335:0.0015:2,0:1:0:27:0:1:0:60:2:0.0015:0:1 0/1:547:106:55,51:228,213:0.1938:2,2:21.5:1:29.5:1:1:1.01:60:34.333:0.1914:0:1.1 -5 180048315 . G T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30213;SOR=0;LSEQ=AGCAGGAGGACCCTCTTTGG;RSEQ=CTGGGAGCAGAGGTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:1,2:23,172:0.0152:2,2:7.3:1:31:0:0.32277:3.70:60:6:0.0155:0:1.3 0/0:114:0:0,0:12,100:0:2,0:22.5:1:32.1:1:1:0:60:111:0.9823:0:0.1 -5 180048487 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52831;SOR=0;LSEQ=CCACGCCGGGGCAAAGGCAG;RSEQ=GGCAGCTACTGCTAGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:67,18:0.023:2,2:25:1:30.5:1:0.39107:3.65023:60:4:0.0241:0:1 0/0:52:0:0,0:45,7:0:2,0:21.1:1:29.6:1:1:0:60:51:1:0:0.1 -5 180048581 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08801;SOR=Inf;LSEQ=CTTGTGGCAGTGCTTGTCAT;RSEQ=GCTGCGCCGGTCTTGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:204,133:0:2,0:27.4:1:31.4:1:1:0:60:66.4:1:0:0.1 0/1:271:3:2,1:160,108:0.0111:2,2:11.7:1:23.3:1:1:1.35:60:2:0.0075:0:3.7 -5 180048954 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.15267;SOR=Inf;LSEQ=CTGCCCTGGGAGTTTGCTCC;RSEQ=CCATCCACCTGCCGCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:25,205:0:2,0:23.2:1:30.9:1:1:0:59.9:27.75:1:0:0.1 0/1:148:2:1,1:24,121:0.0135:2,2:7.5:1:28:1:0.31218:4.96:60:4:0.014:0:2 -5 180048958 . T C 45 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07116;SOR=6.66274;LSEQ=CCTGGGAGTTTGCTCCCCCA;RSEQ=CCACCTGCCGCCCCGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:1:0,1:20,191:0.0047:2,0:23:0:12:0:1:0:60:0:0:0:1 0/1:130:4:2,2:20,106:0.0308:2,2:16.5:1:22.8:1:0.13279:5.20:58.8:3:0.0238:0:1.5 -5 180048972 . C A 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.06423;SOR=4.16132;LSEQ=CCCCCATCCACCTGCCGCCC;RSEQ=GGGGTCTCCTCCTGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:3:0,3:8,147:0.019:2,0:27:1:32.3:1:1:0:60:6:0.0195:0:1 0/1:80:6:1,5:4,70:0.075:2,2:17.2:1:30.3:1:0.32992:3.42:60:12:0.0759:0:1 -5 180048986 . G GCCTC 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=5.000;MSILEN=4;SSF=0.04142;SOR=0.49075;LSEQ=CCGCCCCGGGGTCTCCTCCT;RSEQ=CCTCCCTCCCTCCCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:125:85:2,83:0,40:0.68:1,1:29.1:1:30.4:1:1:0:59.7:20.25:0.6694:0.144:0.3 1/0:53:27:1,26:0,26:0.5094:1,1:28.8:1:31:1:1:0:59.8:54:0.5192:0.0755:0.3 -5 180049003 . T C 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00132;SOR=Inf;LSEQ=CCTGCCTCCCTCCCTCCCTC;RSEQ=CTCCTGGAGGGGCCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:2,81:0:1,0:23.8:1:29.5:1:1:0:59.7:26.667:1:0:0.2 0/1:36:5:0,5:1,30:0.1389:1,0:11.2:1:26.8:1:1:0:60:4:0.1143:0:1 -5 180049212 . C T 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TCTTGTCTCTCTGGTCACTT;RSEQ=TGGTCAGGCTCCTGTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:20:1:32.5:1:1:0:60:8:1:0:0.5 1/0:4:2:1,1:1,1:0.5:2,2:16:0:32:0:1:1:60:4:0.5:0:1.5 -5 180049525 . T C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGGGAGGAGCCCCAGGG;RSEQ=TGGGGACAGAGGATGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:28,1:0,0:1:0,1:26.2:1:31.4:1:1:0:60:28:1:0:1.4 1/1:7:7:6,1:0,0:1:0,2:19.9:1:33.7:1:1:0:60:14:1:0:1.1 -5 180049618 . A G 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09092;LSEQ=TTTTCCTGTCTACAACCGGT;RSEQ=GGCCTTGGATCTCTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:216:206:206,0:9,0:0.9537:0,1:21.7:1:32:1:1:0:60:28.429:0.9522:0:1.1 1/0:120:78:75,3:42,0:0.65:1,1:21.9:1:31.1:1:0.5509:0:60:25:0.641:0:1.1 -5 180049923 . GCAC G 73 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.40512;SOR=0.27394;LSEQ=TTCTGCAAGGAGGTCGCTGT;RSEQ=CACCCCCCCCAATCATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:5:0,5:9,125:0.0357:2,0:30.8:1:31.8:1:1:0:60:10:0.0455:0:0 0/1:100:1:0,1:3,92:0.01:1,0:48:0:34:0:1:0:60:2:0.0127:0:0 -5 180049926 . CCA C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=1;SOR=1.41342;LSEQ=TGCAAGGAGGTCGCTGTGCA;RSEQ=CCCCCCCCAATCATGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:0,2:5,84:0.0156:2,0:35.5:1:33:0:1:0:60:4:0.023:0:0 0/1:91:2:0,2:2,70:0.022:1,0:33.5:1:32:1:1:0:60:4:0.027:0:0 -5 180049927 . CA C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.47416;SOR=1.52255;LSEQ=GCAAGGAGGTCGCTGTGCAC;RSEQ=CCCCCCCCAATCATGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:10:0,10:0,5:0.0775:0,0:29.9:1:33:1:1:0:60:20:0.1124:0:0.5 0/1:88:10:0,10:0,1:0.1136:0,0:27.9:1:31.3:1:1:0:60:20:0.1493:0:0.4 -5 180049928 . A C 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.25997;SOR=1.38987;LSEQ=CAAGGAGGTCGCTGTGCACC;RSEQ=CCCCCCCCAATCATGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:129:75:5,70:0,5:0.5814:0,2:20.4:1:31.2:1:1:0:59.5:150:0.8427:0:2.2 1/0:88:58:2,56:0,1:0.6591:0,1:22.1:1:30.7:1:1:0:59.7:28:0.8358:0:2 -5 180050148 . T C 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTCTGGCCGTGGCTATG;RSEQ=TGAGGGGGCACCAGCGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:28:1:30:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180050208 . A G 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGCCTGGGTCACAGCAAA;RSEQ=GCCAGTCACTTCTGGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:27.3:1:30:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180051003 . T C 301 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04904;LSEQ=GGGGTTCACGGCATCCTGCG;RSEQ=GGTCACCGCCCTCCAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1066:926:409,517:64,73:0.8687:2,2:26.4:1:30.6:1:0.58181:1.10811:60:70.231:0.8704:0:1.1 0/1:916:224:96,128:321,369:0.2445:2,2:26:1:30.2:1:0.35486:1.1597:60:43.8:0.2433:0:1.2 -5 180051120 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.15139;SOR=Inf;LSEQ=CAGGCAGGAAGGGCCCACAT;RSEQ=GGGGGCGGGGTCAAGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:40,212:0:2,0:24.3:1:31.2:1:1:0:60:83:1:0:0.2 0/1:161:2:1,1:30,129:0.0124:2,2:6:1:27:1:0.34899:4.25:60:4:0.0127:0:1 -5 180051296 . A G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGCAATGGCACAATCTC;RSEQ=GCTCACCGAAACCTCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:31.7:1:30.3:1:1:0:60:6:1:0:1.3 1/1:2:2:0,2:0,0:1:0,0:16:1:29.5:1:1:0:50:4:1:0:2 -5 180053307 . A G 271 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0.81607;LSEQ=GGGCCCATACAGATCCCACC;RSEQ=CAGCCCCAACCTCATGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:431:429:117,312:1,0:0.9954:0,2:24.7:1:31:1:0.27442:0:60:41.9:0.9952:0:1.1 1/1:352:350:113,237:2,0:0.9943:0,2:23.8:1:30.4:1:0.10611:0:60:57.333:0.9942:0:1.3 -5 180053387 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=8.73038;LSEQ=GGCAGGAGTGCAGGGTAGGA;RSEQ=GGGGAACACTGGTCTGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:7:0,7:0,96:0.068:1,0:14.9:1:31.3:1:1:0:60:14:0.07:0:1.7 0/1:56:22:0,22:0,34:0.3929:1,1:17.5:1:29.5:1:1:0:60:44:0.3929:0:1.5 -5 180054220 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGATACACCACTGTGTCC;RSEQ=GGGAGAGGCACAGCCCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:20:1:30.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180055773 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53487;SOR=0;LSEQ=CCCCCGCCATGCCTGGTCTC;RSEQ=GTGTGCAGGTCCTGACGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:174,5:0.011:1,2:14.5:1:31:0:0.06538:31.8554:60:4:0.0114:0:2 0/0:104:0:0,0:98,5:0:1,0:23.1:1:30.1:1:1:0:60:33.333:0.9901:0:0.2 -5 180055862 . T G 296 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.0135;LSEQ=AAGGGTATCGGCGGGGTCGG;RSEQ=GGGGAGCCAGGGCTGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:800:794:489,305:1,0:0.9925:0,2:27.6:1:30.8:1:1:0:60:38.7:0.9949:0:2.2 1/0:693:444:260,184:138,111:0.6407:2,2:27.2:1:30.1:1:0.42474:1.14:60:33.154:0.658:0:2.3 -5 180055864 . G A 274 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.04761;LSEQ=GGGTATCGGCGGGGTCGGTG;RSEQ=GGAGCCAGGGCTGTTACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:814:792:480,312:11,1:0.973:2,2:27.4:1:28.5:1:0.03448:7.13959:60:8.9:0.9903:0:2.2 1/0:713:450:261,189:147,112:0.6311:2,2:26.7:1:27.9:1:0.75291:1.05:60:9.465:0.6176:0:2.2 -5 180055946 . C T 89 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01319;SOR=4.62364;LSEQ=CTTCACCAGCTCGTCTCCTG;RSEQ=CGTGGCCTCCAGGATGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1242:3:0,3:594,645:0.0024:2,0:1:0:26.7:1:0.25081:0:60:6:0.0025:0:1 0/1:993:11:3,8:464,517:0.0111:2,2:23.6:1:26:1:0.2328:2.39124:60:4.5:0.0092:0:1.1 -5 180056044 . G A 203 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=307.44438;LSEQ=AAATCCAGGACTGACCCGTC;RSEQ=TGGACTGACCAGGGACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:1:0,1:217,393:0.0016:2,0:2:0:31:0:1:0:60:2:0.0017:0:1 0/1:351:118:42,76:86,147:0.3362:2,2:23:1:29.6:1:0.9066:1.05848:60:58:0.3362:0:1.1 -5 180056071 . G C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09642;SOR=Inf;LSEQ=GACCAGGGACTCCCCCCACG;RSEQ=CCCCTGCAGCCCCGGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:109,293:0:2,0:22.7:1:31.4:1:1:0:60:29.923:1:0:0.1 0/1:182:2:1,1:46,133:0.011:2,2:10:1:28.5:1:0.45298:2.87:60:4:0.0114:0:1.5 -5 180056103 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07409;SOR=Inf;LSEQ=CCGGCAGCCGGACATCCGCA;RSEQ=ACTGGGGCTGGCCATGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:81,169:0:2,0:23.5:1:31.6:1:1:0:60:61.5:1:0:0.2 0/1:94:2:1,1:18,74:0.0213:2,2:15.5:1:29:1:0.36513:4.03:60:4:0.0215:0:2 -5 180056192 . T C 269 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGCTGGACTCCTGAGTGC;RSEQ=CAAGGGCACCGTGAGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:403:403:303,100:0,0:1:0,2:24.1:1:31.1:1:1:0:60:79.6:1:0:1.1 1/0:211:141:116,25:57,13:0.6682:2,2:23.3:1:30.2:1:1:1.06:60:46:0.6667:0:1.1 -5 180056215 . C T 58 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.7187;SOR=1.55177;LSEQ=AGGGCACCGTGAGCTCTGGG;RSEQ=CCAGGCCCACAGGGCACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:580:4:2,2:405,171:0.0069:2,2:11.3:1:23:1:0.5865:2.36448:60:3:0.0053:0:1.5 0/1:375:4:2,2:264,107:0.0107:2,2:25.5:1:29:1:0.58307:2.46054:60:8:0.0109:0:1.3 -5 180056434 . G A 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16266;SOR=0;LSEQ=TTACCCCGCTCTGCCTGCCC;RSEQ=CACCCAGGGAAGCCCCGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:5:3,2:122,333:0.0109:2,2:26.4:1:28.6:1:0.12658:4.08:60:10:0.0112:0:1 0/0:284:0:0,0:92,192:0:2,0:24.8:1:31:1:1:0:60:70:1:0:0.1 -5 180056457 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14457;SOR=Inf;LSEQ=CCCAGGGAAGCCCCGCGTCA;RSEQ=CAGGCGGGCTCCTGCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:58,246:0:2,0:24.1:1:31.9:1:1:0:60:42.429:1:0:0.1 0/1:187:2:1,1:51,134:0.0107:2,2:25:1:27.5:1:0.4799:2.61:60:4:0.0109:0:1 -5 180056620 . G A 247 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGGCCCACACATCCTCCAC;RSEQ=CGGAGGCCCAGTGTGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:293:292:244,48:1,0:0.9966:0,2:24:1:30.2:1:1:0:60:96.333:1:0:1.1 1/1:174:174:147,27:0,0:1:0,2:23.7:1:29.7:1:1:0:60:57:1:0:1.1 -5 180056863 . C T 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CACGCACACAGTGACTCCCA;RSEQ=GCCCTCACAGGACGACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:786:0:0,0:373,413:0:2,0:24.4:1:30.8:1:1:0:60:97.25:1:0:0.1 0/1:490:11:5,6:236,243:0.0224:2,2:23.8:1:30.5:1:1:1.16507:60:22:0.0228:0:1 -5 180056924 . C T 81 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13722;SOR=2.53098;LSEQ=GACAGCCCCGTTACTGGGAA;RSEQ=GGGGCACAGCCCTGTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:975:4:2,2:492,478:0.0041:2,2:14.5:1:28.5:1:1:1.02926:60:8:0.0041:0:1.3 0/1:678:7:2,5:358,313:0.0103:2,2:21.1:1:28.9:1:0.26205:2.85522:60:14:0.0105:0:1.4 -5 180057167 . C T 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02366;SOR=Inf;LSEQ=CTCCTGGCCAGACAGGCGGC;RSEQ=GCCTTTCCCAGGGGTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:238,254:0:2,0:23.6:1:29.4:1:1:0:60:22.429:1:0:0.2 0/1:319:4:1,3:152,163:0.0125:2,2:8.5:1:27.8:1:0.62389:2.78916:60:8:0.0134:0:1.3 -5 180057293 . T C 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACATGGCGTCCTTCCTGT;RSEQ=GACCAAGAGCGTGTCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:0:0,0:426,455:0:2,0:26:1:29.9:1:1:0:60:47.944:0.9988:0:0.2 0/1:646:65:35,30:291,288:0.1006:2,2:26.9:1:30.2:1:0.60312:1.15:60:64:0.0995:0:1.4 -5 180057375 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.06943;SOR=Inf;LSEQ=GCTGTTGGGGAAGGGACGTG;RSEQ=CGGCCAGGCTGGGGGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:167,250:0:2,0:24:1:31.2:1:1:0:60:25.063:1:0:0.1 0/1:292:3:1,2:99,188:0.0103:2,2:8:1:23:1:1:1.05301:60:2:0.007:0:3 -5 180057504 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=4.000;MSILEN=1;SSF=0;SOR=10.96734;LSEQ=ACAGGCTGGGGGCGGTGTGG;RSEQ=CCCCAGCTGCCCGGGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:25:18,7:366,140:0.047:2,2:18.1:1:28.8:1:1:1.01664:60:24:0.0464:0:1.2 0/1:364:128:97,31:166,69:0.3516:2,2:23.9:1:28.4:1:0.32647:1.30:60:41.667:0.3501:0:1.1 -5 180058008 . C A 95 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGGGGCTGGCCTGTGG;RSEQ=CAAGCACAGGCCTTGGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:1:0,2:24.3:1:28.6:1:1:0:60:9:1:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180058189 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=CCATATGAAATGCTGATGGG;RSEQ=TGGGCTGGGCACAGTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:21:1:31.3:1:1:0:60:8:1:0:1 0/0:4:0:0,0:1,3:0:2,0:27:1:31:1:1:0:60:8:1:0:0 -5 180058451 . T C 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTGCACTCCAGCCTGGG;RSEQ=GACAGAGTGAGACTCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:32.8:1:33.3:1:1:0:55.4:22:1:0:1.9 1/1:2:2:2,0:0,0:1:0,0:26.5:1:31.5:1:1:0:38:4:1:0:1 -5 180058474 . GA G 50 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTGAGACTCCATCTCA;RSEQ=AAAAAAAAAAGAAATGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:21,0:0.125:1,0:18:1:31.7:1:1:0:55:6:0.125:0:0.3 0/0:4:0:0,0:4,0:0:0,0:15.8:1:30.3:1:1:0:55:8:1:0:0.3 -5 180058567 . CACTCTGCCCTG C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1336;SOR=Inf;LSEQ=AGACCACACGGCCCCGAGGC;RSEQ=ACTCTGCCCTGGGAGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:131,6:0:1,0:22.6:1:29.8:1:1:0:60:44.667:1:0:0.1 0/1:80:2:1,1:72,6:0.025:2,2:24.5:1:30.5:1:0.16835:11.18701:60:4:0.0256:0:0 -5 180058591 . G A 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79644;SOR=1.17332;LSEQ=CTGCCCTGACTCTGCCCTGG;RSEQ=AGGGGGCTGCCATCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:9:8,1:152,8:0.0533:2,2:14.8:1:25.1:1:0.39646:2.35805:60:2:0.0368:0:1.1 0/1:113:7:7,0:98,8:0.0619:2,0:26.6:1:28.7:1:1:0:60:14:0.0648:0:1.3 -5 180058913 . GCGTGGCCTGGCCTCA C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0;SOR=10.90074;LSEQ=CTCAGGTTCTCAGCCAGCAC;RSEQ=CCATGTGCGCCGTGAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:11:1,10:1,61:0.1507:1,2:22.4:1:31.2:1:0.28044:5.86:59.5:22:0.1549:0.0548:0.8 1/0:27:18:1,17:1,5:0.6667:2,1:26.4:1:30.7:1:0.44565:3.19373:60:36:0.72:0.1111:0.7 -5 180058928 . A C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00213;SOR=Inf;LSEQ=GCACCGCGTGGCCTGGCCTC;RSEQ=CCATGTGCGCCGTGAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:1,45:0:1,0:25.6:1:30:1:1:0:60:92:1:0:0.3 0/1:8:3:0,3:1,4:0.375:2,0:33:1:30.7:1:1:0:60:6:0.375:0:3 -5 180058963 . G A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=18.72485;LSEQ=AGCAGCACCAGCTCCCAGGC;RSEQ=CCAAGACAGCCACGAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:0,8:2,25:0.2286:2,0:17:1:29.3:1:1:0:60:16:0.2353:0:1.6 1/1:14:12:0,12:0,2:0.8571:0,0:24.2:1:29.1:1:1:0:60:24:0.8571:0:2.4 -5 180059042 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAGCTACACACCGGCCC;RSEQ=GGACCTAACCCCAACCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:20.5:1:29.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180059230 . A C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCCCAGGTCCTCCCCG;RSEQ=ACCACGCAGGCCTCGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180073373 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCTGCTGGCACTGCCGC;RSEQ=TCTCCAGCCTCGTTTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:35.3:1:32:1:1:0:60:6:1:0:1 1/1:2:2:1,1:0,0:1:0,2:11.5:1:29.5:1:1:0:60:4:1:0:2.5 -5 180073385 . G A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ACTGCCGCATCTCCAGCCTC;RSEQ=TTTCCCCTACCTCCCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:47.3:1:24:1:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30:1:1:0:60:4:1:0:2.5 -5 180074544 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50337;SOR=0;LSEQ=AGGCTTCTGGCCTGCTCCCA;RSEQ=CGGACCAGCTGCCCTGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:7,14:0.087:2,2:17:1:27:0:1:1.94:60:4:0.0909:0:1.5 0/0:16:0:0,0:8,8:0:2,0:23.3:1:31:1:1:0:60:32:1:0:0.3 -5 180074627 . T C 65 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TGCAGCTGAGGGCTTGTGCT;RSEQ=CCGCCATGGCATCCCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:14.8:1:32.5:1:1:0:60:8:1:0:1.5 0/1:3:1:0,1:0,2:0.3333:0,0:28:0:33:0:1:0:60:2:0.3333:0:1 -5 180075730 . A AT 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTCCCCGCCAGAGCCAC;RSEQ=TCCCAACACAAACCGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:27.5:1:1:0:60:4:1:0:0 -5 180076403 . C T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4648;SOR=1.7628;LSEQ=CCCGCCCGTACCCGGCGGAG;RSEQ=GGTCTCAGCGCCCGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:4:3,1:47,8:0.0678:2,2:13.5:1:30.3:1:0.49399:1.93153:60:8:0.069:0:1 0/1:35:4:3,1:26,5:0.1143:2,2:11.3:1:31.5:1:0.54639:1.7024:60:8:0.1176:0:1.3 -5 180076445 . G T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66637;SOR=1.74444;LSEQ=TGCGCGGTACCCCCTCCCCG;RSEQ=CCAGCCCCACGCTCGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:0,2:118,80:0.01:2,0:15:1:16:1:0.16688:0:60:0:0:0:1.5 0/1:173:3:1,2:103,66:0.0173:2,2:27.7:1:21.3:1:0.56295:3.10023:60:2:0.012:0:1 -5 180076468 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09773;SOR=Inf;LSEQ=AGCCCCACGCTCGGGCGGGT;RSEQ=GCCCGTTCGCCGCGCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:172,143:0:2,0:25.8:1:31.3:1:1:0:60:77.75:1:0:0.2 0/1:270:3:1,2:146,121:0.0111:2,2:22.3:1:29.7:1:0.59314:2.40554:60:6:0.0113:0:1.3 -5 180076529 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.67099;SOR=1.68075;LSEQ=GCCACAGTCGCAGGCACAGC;RSEQ=CGGCGCCCCGCTGCATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:2:2,0:127,159:0.0069:2,0:1:0:26:0:0.19977:0:60:4:0.0071:0:1 0/1:258:3:2,1:114,141:0.0116:2,2:21.7:1:28.7:1:0.58952:2.47:60:6:0.0118:0:1.3 -5 180076550 . G A 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17889;SOR=4.96194;LSEQ=CGGCGCCCCGCTGCATCTCC;RSEQ=GCCGCTGCGCGTGGGTCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:1:1,0:80,117:0.005:2,0:2:0:26:0:0.40909:0:60:2:0.0052:0:1 0/1:163:4:3,1:66,93:0.0245:2,2:16:1:24:1:0.31187:4.19:60:3:0.0186:0:1.3 -5 180076574 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2047;SOR=Inf;LSEQ=GCTGCGCGTGGGTCCGACCC;RSEQ=AGCGGCCGCGGCTCGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:31,64:0:2,0:17.2:1:30.6:1:1:0:60:22.75:1:0:0.3 0/1:79:2:1,1:27,50:0.0253:2,2:26:1:28:1:1:1.84:60:4:0.0263:0:1 -5 180525809 . G GT 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCAGACAATCTGAAGTT;RSEQ=TTTTTTTTTTCTTTGAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,0:0.5:0,0:29:1:32:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180525845 . T G 85 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGGAGTCTTGCTTTGTT;RSEQ=CCAGGCTGGAGTGCAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:29.5:1:28.4:1:1:0:53:3:1:0:1.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180525899 . C G 98 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAATCTCCGCCTCCCA;RSEQ=GTTCAAGCGATTCTTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:29.2:1:31.1:1:1:0:52.6:18:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -5 180526117 . A T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25972;SOR=0;LSEQ=CCAGCCGATGAAGTACTTTT;RSEQ=AGTGTAGCGGGCTCACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:178,60:0.0124:2,2:40:1:23:1:1:1.48069:60:2:0.0084:0:1 0/0:188:0:0,0:139,49:0:2,0:21.7:1:28.1:1:1:0:60:376:1:0:0.1 -5 180526302 . G A 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16839;SOR=5.5184;LSEQ=TCCAAGGGCTCAGTGAGCAT;RSEQ=CCGTCCAAGTCACTTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:1:0,1:297,235:0.0019:2,0:12:0:31:0:0.44278:0:60:2:0.0019:0:1 0/1:389:4:3,1:199,186:0.0103:2,2:16.8:1:26.3:1:0.62419:2.80:60:8:0.0104:0:1.3 -5 180526819 . T C 307 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16289;LSEQ=TCTGGGGCAAAGGGCTCATG;RSEQ=TGGACTGGCCCTACGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:842:795:469,326:27,19:0.9442:2,2:24.7:1:31.9:1:1:1.01:60:78.5:0.9446:0:1.1 1/0:604:443:250,193:105,56:0.7334:2,2:23.9:1:31.6:1:0.06141:1.44662:59.9:39.273:0.7285:0:1.2 -5 180526837 . T C 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTGGACTGGCCCTACGTC;RSEQ=GTTTTTTGCAGTTTGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:940:0:0,0:561,379:0:2,0:23.8:1:30.6:1:1:0:60:103.444:1:0:0.8 0/1:712:22:14,8:402,288:0.0309:2,2:29:1:28.6:1:0.66669:1.25:60:21:0.0299:0:2.9 -5 180526839 . T G 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=26.15914;LSEQ=TTGGACTGGCCCTACGTCTG;RSEQ=TTTTTGCAGTTTGGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:940:1:1,0:552,386:0.0011:2,0:6:0:13:0:1:0:60:0:0:0:2 0/1:737:20:12,8:416,297:0.0271:2,2:29.3:1:30.3:1:1:1.07:60:40:0.0277:0:2.9 -5 180527070 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13756;SOR=Inf;LSEQ=TGGCGGGTACCCCACAGAAT;RSEQ=TGCGTCCCCATCTCCAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:186,149:0:2,0:25.2:1:32.3:1:1:0:60:334:1:0:0.1 0/1:198:2:1,1:110,85:0.0101:2,2:29.5:1:30:1:1:1.2924:60:4:0.0102:0:1 -5 180527309 . C A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19347;LSEQ=AGCTTGACTTAGGCTCCGAG;RSEQ=GCATTTGCTGCTGCTGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:261:243:74,169:5,13:0.931:2,2:24.4:1:30.9:1:1:1.14:60:59.75:0.93:0:2 1/0:144:104:22,82:6,34:0.7222:2,2:25.1:1:31:1:0.4862:1.52:60:208:0.7222:0:1.8 -5 180527344 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14176;LSEQ=TGTCCATGGATGCAGCTCTT;RSEQ=TCCTAAGAGATCTCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:225:208:97,111:6,10:0.9244:2,2:25.9:1:29.9:1:0.60545:1.45:60:207:0.9324:0:2.6 1/0:128:81:34,47:21,26:0.6328:2,2:21.3:1:29.5:1:0.85351:1.11555:60:162:0.6328:0:2.4 -5 180527367 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11567;LSEQ=CTAAGAGATCTCCCACCCTT;RSEQ=CCGCCCTCTGGATCCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:256:236:122,114:11,8:0.9219:2,2:23.2:1:28.4:1:0.64098:1.28358:60:58:0.9243:0:2.3 1/0:139:80:49,31:34,25:0.5755:2,2:24.1:1:28.7:1:0.72765:1.16:60:79:0.5725:0:2.2 -5 180527433 . C T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03374;SOR=Inf;LSEQ=TCATTCTGCGCGCGAGTCAG;RSEQ=TTGCTGTGTAGGGACAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:0:0,0:233,137:0:2,0:25.2:1:32:1:1:0:60:45.25:1:0:1.1 0/1:279:4:2,2:178,97:0.0143:2,2:6.8:1:27.3:1:0.617:1.83089:60:8:0.0145:0:1.5 -5 180527440 . T C 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0321;SOR=Inf;LSEQ=GCGCGCGAGTCAGCTTGCTG;RSEQ=GTAGGGACAGAAGATGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:244,145:0:2,0:24.9:1:29.7:1:1:0:60:63.833:1:0:1.1 0/1:287:4:2,2:180,102:0.0139:2,2:28.8:1:28.8:1:0.62347:1.76093:60:8:0.0141:0:1 -5 180527455 . T C 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16783;LSEQ=TGCTGTGTAGGGACAGAAGA;RSEQ=GACGAAGTGAATTCCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:417:388:239,149:13,16:0.9305:2,2:25.2:1:30.9:1:0.07995:1.97:60:54.429:0.9315:0:1.2 1/0:311:215:137,78:55,41:0.6913:2,2:25.7:1:30.3:1:0.313:1.31:60:214:0.6948:0:1.2 -5 180527577 . G A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1767;SOR=3.04184;LSEQ=TTCTCCGCCGAGCTCTCGTC;RSEQ=GCCCTGGTGCTGAGGTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:2:2,0:190,357:0.0036:2,0:1:0:25.5:1:0.12189:0:60:4:0.0037:0:1 0/1:545:6:5,1:210,329:0.011:2,2:7.5:1:25.5:1:0.03766:7.80:60:5:0.0093:0:1 -5 180527614 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25076;SOR=0;LSEQ=CGGCGTGGGACAGGCTGCGC;RSEQ=ACGCGGTGCGACGGGACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:70,226:0.01:2,2:6.7:1:21.7:1:0.14507:6.41:60:2:0.0068:0:1.3 0/0:270:0:0,0:70,200:0:2,0:25:1:30.3:1:1:0:60:66.5:1:0:0.2 -5 180527742 . C T 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09797;SOR=0.43294;LSEQ=CCTGCAGCAGGCTCGGGTTG;RSEQ=TCATGAAGTCGGCGCTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:19:10,9:6,7:0.5938:2,2:29.4:1:29.5:1:1:1.29:60:38:0.5938:0:1.7 0/1:39:15:8,7:13,11:0.3846:2,2:32.3:1:28.3:1:1:1.03322:60:14:0.3684:0:2.1 -5 180527769 . A G 148 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTCGGCGCTGACGGGCGGG;RSEQ=CTGGAGGTGGCCGCGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:10,14:0,0:1:0,2:20:1:32.3:1:1:0:60:48:1:0:1.6 0/1:39:14:7,7:11,14:0.359:2,2:24.4:1:29.4:1:0.74957:1.26:60:13:0.3514:0:2.1 -5 180527792 . C CGCGGAACTCCCGCCCGGGCG 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09118;SOR=0.26355;LSEQ=GGAGGTGGCCGCGTGGGACC;RSEQ=GCGACTGGAAATCCGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:3,7:0,1:0.7692:0,2:15.9:1:30.8:1:1:0:60:20:0.7692:0.6154:1.4 0/1:24:11:4,7:5,8:0.4583:2,2:15.7:1:27.9:1:1:1.08968:60:22:0.4583:0.4583:2.1 -6 142840 . T C 106 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09778;SOR=0;LSEQ=AATGGGACAAGGACCACATC;RSEQ=GGTGGCCCATGAGTGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:9,4:0,0:1:0,2:14.8:1:28.7:1:1:0:22:26:1:0:1 1/0:14:10:6,4:1,3:0.7143:2,2:14.8:1:26.9:1:0.55944:4.03:21.2:20:0.7143:0:1.3 -6 142893 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21587;SOR=Inf;LSEQ=CAAGCGGCACCAGGCCCTGG;RSEQ=GGGGCGCACCAGGGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:33.1:1:29.3:1:1:0:21.4:8.5:1:0:0.3 0/1:17:2:0,2:4,11:0.1176:2,0:12.5:1:29:1:1:0:21:4:0.1176:0:2.5 -6 143944 . G A 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GGGGATGGGGGCCCAGGGAC;RSEQ=CCTTCCAAGGTGGCCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:34.7:1:31.3:1:1:0:20:6:0.75:0:1 0/0:2:0:0,0:0,2:0:0,0:13:1:33.5:1:1:0:20.5:4:1:0:0 -6 393170 . C T 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0102;SOR=10.05999;LSEQ=GGCATGAACCTGGAGGGCGG;RSEQ=GGCCGAGGCGGAGAGTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:955:1:0,1:593,361:0.001:2,0:47:0:32:0:0.37906:0:60:2:0.0011:0:1 0/1:670:7:4,3:394,268:0.0104:2,2:24.7:1:28.7:1:1:1.10245:60:14:0.0106:0:1.3 -6 393205 . G C 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCGGCATGAGCGCGGTGA;RSEQ=CTGCGGCAACGGGAAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1168:0:0,0:659,505:0:2,0:25.5:1:31.9:1:1:0:60:54.429:0.9974:0:0.1 0/1:850:31:17,14:442,373:0.0365:2,2:22.2:1:30.8:1:1:1.02:60:62:0.0371:0:1.2 -6 393409 . GC G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19942;SOR=Inf;LSEQ=GCGGGGGCGCGCCGGGGAGG;RSEQ=CCAGAGACAGAGCCCGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:40,205:0:2,0:25.8:1:31.3:1:1:0:60:29.625:0.9958:0:0.1 0/1:199:2:1,1:35,161:0.0101:2,2:12:1:30.5:1:0.33133:4.55:60:4:0.0103:0.005:0.5 -6 394711 . T A 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00165;SOR=Inf;LSEQ=GCTGCGGTGAGCTATCATCG;RSEQ=GCCACTGTACTCTAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:75,6:0:2,0:21.7:1:29.9:1:1:0:60:162:1:0:0.1 0/1:45:6:5,1:37,2:0.1333:2,2:27:1:29.2:1:0.35595:3.54565:60:12:0.1333:0:1 -6 394950 . C T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10812;SOR=5.54759;LSEQ=AACTGGTTGAGCGGAGCCAG;RSEQ=TGGACATCTCAGACCCGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:1:1,0:241,309:0.0018:2,0:39:0:32:0:0.4392:0:60:2:0.0018:0:1 0/1:500:5:2,3:222,273:0.01:2,2:19:1:27.2:1:1:1.2193:60:10:0.0102:0:1 -6 394967 . G A 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01369;SOR=Inf;LSEQ=CAGCTGGACATCTCAGACCC;RSEQ=TACAAAGTGTACAGGATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:206,299:0:2,0:25.3:1:31:1:1:0:60:504:1:0:0.1 0/1:486:6:3,3:210,270:0.0123:2,2:30.7:1:29.8:1:1:1.29:60:12:0.0126:0:1.2 -6 395000 . CA C 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.48827;SOR=1.84182;LSEQ=AGGATTGTTCCTGAGGGAGC;RSEQ=AAAAAGGTAGGGGCTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:3:0,3:113,231:0.0086:2,0:19.7:1:31:1:0.55378:0:60:6:0.0088:0.0029:0.3 0/1:316:5:2,3:118,193:0.0158:2,2:36.8:1:29.8:1:1:1.09:60:10:0.0161:0:0 -6 395031 . T C 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.587;SOR=2.51628;LSEQ=GGGGCTCTCCTGAATTTGGG;RSEQ=CACCTAACAGAGGCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:1,0:55,177:0.0043:2,0:46:0:14:0:0.24034:0:60:0:0:0:2 0/1:186:2:1,1:55,128:0.0108:2,2:25.5:1:30:1:0.51492:2.32:60:4:0.0109:0:1 -6 395042 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50284;SOR=0;LSEQ=GAATTTGGGTCACCTAACAG;RSEQ=GGCAGCCAGATCCTTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:36,144:0.011:2,2:33.5:1:29:1:0.36616:3.96:60:4:0.0111:0:1 0/0:151:0:0,0:38,113:0:2,0:22.8:1:30:1:1:0:60:36.75:1:0:0.1 -6 395980 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05409;SOR=Inf;LSEQ=CTGAGGGCGAGGCTGTGTGG;RSEQ=CCAGCTGCCCACATGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:97,365:0:2,0:23.8:1:31.4:1:1:0:60:45.2:1:0:0.1 0/1:282:3:2,1:63,216:0.0106:2,2:16:1:27:1:0.13387:6.80:60:6:0.0108:0:1 -6 395988 . C A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05076;SOR=Inf;LSEQ=GAGGCTGTGTGGGCCAGCTG;RSEQ=CCACATGGCCAGAGAACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:66,331:0:2,0:24.4:1:31.2:1:1:0:60:65.167:0.9974:0:0.1 0/1:235:3:2,1:46,185:0.0128:2,2:16:1:20.3:1:0.10772:7.94:60:2:0.0087:0:1 -6 396003 . A G 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1233;SOR=Inf;LSEQ=AGCTGCCCACATGGCCAGAG;RSEQ=ACCACAGCAGCCCAGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:28,300:0:2,0:23.3:1:30.2:1:1:0:60:108.333:1:0:0.1 0/1:178:2:0,2:26,150:0.0112:2,0:26:1:25:1:1:0:60:4:0.0114:0:2.5 -6 396121 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07792;SOR=Inf;LSEQ=ACGGTGCTGCCATTGGTGTG;RSEQ=ATTTTAAGTTGGGGAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:0,40:0:1,0:22.4:1:31.6:1:1:0:60:80:1:0:0.1 0/1:16:2:0,2:0,14:0.125:1,0:26:1:33.5:1:1:0:60:4:0.125:0:1 -6 396611 . C T 74 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09341;SOR=0;LSEQ=CGTCTCGATGCCAGTGCTTC;RSEQ=TATCTCAGCCTCTCCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:11:1:29:1:1:0:49.8:10:1:0:1.6 0/1:11:5:2,3:3,3:0.4545:2,2:17.2:1:32:1:1:1.44544:46.6:10:0.4545:0:1 -6 396923 . C T 47 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84312;LSEQ=CGTCTCAATGCCAGTGCTTC;RSEQ=TATCTCAGCCTCTCCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:2,1:16,13:0.0938:2,2:5:1:29.7:1:1:1.60:24.3:6:0.1154:0:1 0/1:25:2:0,2:16,7:0.08:2,0:3:1:21:1:0.12:0:23.5:4:0.08:0:1 -6 396958 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50057;SOR=0;LSEQ=CTGCACTCCTTTACCCCCGT;RSEQ=TCGATGCCAGTGCTTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:54,13:0.029:2,2:13.5:1:28.5:1:0.36701:4.03964:29:4:0.0294:0:1.5 0/0:57:0:0,0:40,17:0:2,0:23.3:1:31.4:1:1:0:37.8:56:1:0:0.6 -6 396961 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=CACTCCTTTACCCCCGTCTC;RSEQ=ATGCCAGTGCTTCTTATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:60,14:0:2,0:25.4:1:28.6:1:1:0:39.2:11.333:1:0:0.4 0/1:65:2:2,0:46,17:0.0308:2,0:26:1:30:1:1:0:45:4:0.0351:0:4 -6 396993 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58586;SOR=2.52679;LSEQ=TCTTATCTCAGCCTCTCCTG;RSEQ=ACTCCTTTACCCCCGTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:0,1:105,13:0.0084:2,0:1:0:23:0:0.11765:0:36:2:0.0087:0:1 0/1:95:2:1,1:79,14:0.0211:2,2:24.5:1:28.5:1:0.29227:5.48599:36:4:0.0215:0:1.5 -6 397013 . G A 56 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32437;SOR=1.95407;LSEQ=CACTCCTTTACCCCCGTCTC;RSEQ=ATGCCAGTGCTTCCTATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:4:4,0:174,14:0.0208:2,0:20.3:1:22:1:1:0:35:1:0.0116:0:1.3 0/1:125:5:5,0:104,16:0.04:2,0:13.8:1:24.4:1:1:0:48.2:1.5:0.0261:0:2.2 -6 397027 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50242;SOR=1.37589;LSEQ=CGTCTCGATGCCAGTGCTTC;RSEQ=TATCTCAGCCTCTCCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:12:10,2:217,15:0.049:2,2:12.4:1:24.4:1:0.19955:2.87465:33.5:2:0.0354:0:1.1 0/1:151:10:8,2:129,12:0.0662:2,2:18.3:1:25.3:1:0.23348:2.66302:29.5:4:0.0556:0:1.3 -6 397038 . TCTCCTGCACTCCTTTAC T 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGTGCTTCCTATCTCAGCC;RSEQ=CCCCGTCTCAATGCCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:240,29:0:2,0:25.1:1:31.4:1:1:0:53.1:52.8:1:0:0.2 0/1:182:17:13,4:141,23:0.0934:2,2:14:1:30.6:1:0.28972:1.87853:59.4:34:0.0944:0.0385:0.3 -6 397290 . T C 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGAAATAGAAGAGCTAA;RSEQ=TGCTAATGTGGCCATGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:53,293:0:2,0:22.4:1:30:1:1:0:60:85.5:1:0:0.1 0/1:232:20:6,14:42,169:0.0862:2,2:24.8:1:31.6:1:0.38442:1.72:60:40:0.0873:0:1.1 -6 398775 . G A 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACACCCCAGGAAGCCCCGC;RSEQ=GTGCGTCGGACTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:605:0:0,0:420,183:0:2,0:22.6:1:29.9:1:1:0:59.9:119.6:0.9967:0:0.1 0/1:554:52:34,18:325,175:0.0939:2,2:22:1:29.9:1:1:1.02:60:104:0.0945:0:1.1 -6 399079 . T A 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.02267;SOR=0;LSEQ=AGATGTAGACACATCCTGTG;RSEQ=GTGAGGTGACCAGGGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:0,43:0,0:1:0,1:21.5:1:30.1:1:1:0:60:9.75:1:0:1.2 1/1:18:15:1,14:0,3:0.8333:0,1:26.5:1:31.2:1:1:0:60:30:0.8333:0:1 -6 401509 . C T 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=130.486;LSEQ=CCCGAGGGCTGCCGGATCTC;RSEQ=CATGGACATACGTATGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:712:1:0,1:401,310:0.0014:2,0:2:0:26:0:0.4368:0:60:2:0.0014:0:1 0/1:547:85:47,38:243,219:0.1554:2,2:27.1:1:29.7:1:0.72302:1.11:60:84:0.1556:0:1.2 -6 401878 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15888;SOR=Inf;LSEQ=CACCCCAGGCTGAGGTCTTC;RSEQ=TCCTGTTGACTTCGGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:17,112:0:2,0:22.7:1:31.5:1:1:0:60:42:1:0:0.1 0/1:86:2:1,1:9,75:0.0233:2,2:25.5:1:29.5:1:0.22025:7.96:60:4:0.0235:0:1 -6 404973 . G A 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TTTAACCTGGTGTGTTCGGT;RSEQ=ATGAGGGTTTCTGAACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:0:0,0:376,138:0:2,0:23.3:1:31.7:1:1:0:60:72.429:1:0:0.1 0/1:362:28:18,10:233,99:0.0773:2,2:26.9:1:28.9:1:0.52468:1.30655:60:56:0.0791:0:1.1 -6 405162 . G A 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00321;SOR=Inf;LSEQ=GTTACACTCCTACCATAGTG;RSEQ=CTTCCTGTTCTTTGTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:152,377:0:2,0:23.7:1:31.5:1:1:0:60:51.9:1:0:0.1 0/1:420:7:5,2:121,288:0.0167:2,2:13.6:1:26.3:1:0.02889:5.92:60:6:0.0146:0:1 -6 407656 . G A 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTTTTTTTTTGATACGG;RSEQ=GATACGGGGTCTTGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:23,179:0:2,0:17.9:1:28.6:1:1:0:57.7:7.783:0.9944:0:1.6 0/1:164:60:7,53:16,85:0.3659:2,2:20.1:1:26:1:0.64198:1.42218:56:2.333:0.3158:0:3.2 -6 407882 . T C 86 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTACTGTTTTGAGGAA;RSEQ=TCAGAAGTGGAGATTTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:36.5:1:33.3:1:1:0:60:12:1:0:1.5 1/1:1:1:0,1:0,0:1:0,0:18:0:32:0:1:0:60:2:1:0:1 -6 408012 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGCATTTCTTGTGTTCT;RSEQ=TAGACTGCCATCATTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 408385 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGGGTCCCTCTGCCCC;RSEQ=CCCTCCTTCCCATTGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 432393 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.53846;SOR=0;LSEQ=AGAAAAGTCAGAGCGCCACA;RSEQ=AACAGAACCAATGCAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,9:0.1111:2,2:32.5:1:31:1:1:1.27:60:4:0.1111:0:1.5 0/0:9:0:0,0:6,3:0:2,0:31.7:1:32:1:1:0:60:18:1:0:0.4 -6 432451 . G A 42 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.11403;LSEQ=TATCAGGAGATGTGGGCTTG;RSEQ=AGAGCCACATCTTTTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:35.5:1:30.5:1:1:1.73:60:4:0.4:0:1 0/1:7:3:2,1:1,3:0.4286:2,2:20.3:1:27:1:0.48571:4.45:60:6:0.4286:0:1 -6 1313117 . A C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGCGGCGGCGCCAGAGAT;RSEQ=CGCAGGGCGACGGCGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:32:1:1:0:60:4:1:0:2 -6 1313121 . A C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCGGCGCCAGAGATACGC;RSEQ=GGGCGACGGCGAACAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:31.5:1:1:0:60:4:1:0:2 -6 1390276 . CCCGCCGCCG C 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=9.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=CCGCCCTGATGAGCCCGCCG;RSEQ=CCGCCGCCGCCGCCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30:1:1:0:60:4:1:0:0 -6 1390636 . C A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49701;SOR=Inf;LSEQ=AGAACTCGGTGCGCCACAAT;RSEQ=TCTCGCTCAACGAGTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:52,32:0:2,0:25.8:1:31.6:1:1:0:60:168:1:0:0.1 0/1:84:2:1,1:45,37:0.0238:2,2:16:0:27.5:1:1:1.21336:60:4:0.0244:0:1 -6 1390652 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49732;SOR=0;LSEQ=CAATCTCTCGCTCAACGAGT;RSEQ=CTTCATCAAGCTGCCTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:43,42:0.023:2,2:21.5:1:29.5:1:1:1.02354:60:4:0.0233:0:1.5 0/0:83:0:0,0:42,41:0:2,0:28.2:1:31.2:1:1:0:60:26.667:1:0:0.3 -6 1390668 . TA T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24222;SOR=Inf;LSEQ=GAGTGCTTCATCAAGCTGCC;RSEQ=AGGGCCTCGGGCGGCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:36,45:0:2,0:26.4:1:28.7:1:1:0:60:39.5:1:0:0.1 0/1:79:2:1,1:35,42:0.0253:2,2:27:1:32.5:1:1:1.20:60:4:0.026:0:0 -6 1390718 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20556;SOR=Inf;LSEQ=CTACTGGACCATCGACCCGG;RSEQ=CAGCGAGTTCATGTTCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:12,32:0:2,0:22.4:1:31:1:1:0:60:43:1:0:0.1 0/1:37:2:1,1:9,26:0.0541:2,2:20.5:1:27.5:1:0.47297:2.79:60:4:0.0541:0:1 -6 1390722 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18192;SOR=Inf;LSEQ=TGGACCATCGACCCGGCCAG;RSEQ=GAGTTCATGTTCGAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:10,31:0:2,0:21.6:1:28.9:1:1:0:60:12.667:1:0:0.1 0/1:31:2:1,1:5,24:0.0645:2,2:11.5:1:31.5:1:0.35484:4.47:60:4:0.0645:0:1 -6 1391252 . C G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCAGCCGCCTGCCCTGACGC;RSEQ=CAGCAGCAACCCCGCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:38.5:1:32:0:1:0:60:4:1:0:0.5 -6 1611038 . C T 63 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09007;SOR=4.07982;LSEQ=CCTTCTACCGGGACAACAAG;RSEQ=AGGGCTGGCAGAACAGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:2:0,2:366,193:0.0036:2,0:1:0:23:0:0.12042:0:60:4:0.0036:0:1.5 0/1:486:7:1,6:311,168:0.0144:2,2:8.7:1:22.7:1:0.00976:11.05778:58.1:6:0.0127:0:1 -6 1611183 . TGCG T 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.70954;SOR=1.3108;LSEQ=GTTCGAGAACGGCAGCTTCC;RSEQ=GCGGCGGCGGCGCTTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:4:1,3:81,253:0.0118:2,2:31.5:1:32:1:1:1.04:60:8:0.012:0:0 0/1:194:3:1,2:45,144:0.0155:2,2:33.3:1:31:1:0.56248:1.60:60:6:0.0156:0:0 -6 1611220 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09839;SOR=Inf;LSEQ=TTCAAGAAGAAGGACGCGGT;RSEQ=AAGGACAAGGAGGAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:16,146:0:2,0:23.2:1:31.7:1:1:0:60:80:0.9938:0:0.2 0/1:75:2:1,1:8,65:0.0267:2,2:33.5:1:27.5:1:0.22703:7.72:60:4:0.0267:0:1 -6 2872045 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGGGTTGCAGTGAGCTGA;RSEQ=ATCACGCCACCGCAATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:31.5:1:1:0:60:4:1:0:1 -6 2873722 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52862;SOR=Inf;LSEQ=CGCCCTGCCCAGCACTCAGC;RSEQ=CCTTCCCTTACGCTGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:0:2,0:27.5:1:29.8:1:1:0:60:40:1:0:0.2 0/1:35:2:1,1:18,15:0.0571:2,2:28:0:33:1:1:1.19373:60:4:0.0571:0:1.5 -6 2873791 . C T 42 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12821;SOR=0.15773;LSEQ=CCAGAACCATCGCCTCTGCC;RSEQ=CAAACACCTGCATTAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:0.3:2,0:14:1:26.7:1:1:0:60:6:0.3:0:1.3 0/1:17:1:0,1:4,12:0.0588:2,0:42:0:29:0:1:0:60:2:0.0588:0:1 -6 3797630 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08615;SOR=Inf;LSEQ=ACAATGGGCTCCCACAAGCC;RSEQ=GGGAAAGCCAGCTATGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:18,0:0:1,0:22.6:1:29.6:1:1:0:60:17:1:0:0.2 0/1:8:2:2,0:6,0:0.25:0,0:16.5:1:31.5:1:1:0:60:4:0.25:0:1 -6 3797857 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41781;LSEQ=ACACTCAAGCTTAGTCCCAA;RSEQ=GGGAACACACCCCTCCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:387:254:121,133:60,73:0.6563:2,2:23.3:1:31.2:1:0.66865:1.11:60:62.5:0.6579:0:1.1 0/1:354:157:74,83:102,94:0.4435:2,2:25.8:1:30.8:1:0.3921:1.21639:60:38.25:0.4397:0:1.2 -6 4289703 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19615;SOR=Inf;LSEQ=TGGCAGAGTTGGTTCCTTCT;RSEQ=AGGGCTGGGAGGGAGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:26.4:1:30.9:1:1:0:60:21:1:0:0.3 0/1:18:2:1,1:10,6:0.1111:2,2:37.5:1:29.5:1:1:1.61828:60:4:0.1111:0:1.5 -6 4289773 . G A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24026;SOR=0;LSEQ=GATTGCTGGCAAGCTTTGAC;RSEQ=TTCCTTGGCTAGCAGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:2,8:0.2308:2,2:15:1:32:1:1:1.89:60:6:0.2308:0:1 0/0:9:0:0,0:3,6:0:2,0:23.2:1:30.6:1:1:0:60:18:1:0:0.4 -6 4291026 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAGGTCACTGCAACCTC;RSEQ=GCCTCCTGGGTTCAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:28.5:1:1:0:60:4:1:0:1.5 -6 4405966 . A AG 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATTCTCAACAGCCCCTC;RSEQ=CTGGAATCTGCTTAAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:23.1:1:32.7:1:1:0:60:14:1:0:0 1/1:4:4:1,3:0,0:1:0,2:31.3:1:32.8:1:1:0:60:8:1:0:0.3 -6 4406121 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=AACACACTAAGCTCCCTGAG;RSEQ=GGGGGAAGGGCAGAAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:35:1:31.3:1:1:0:60:8:1:0:1.3 0/1:8:2:2,0:3,3:0.25:2,0:18:1:29.5:1:0.46429:0:60:4:0.25:0:1 -6 4406129 . G A 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=AAGCTCCCTGAGCGGGGGAA;RSEQ=GGCAGAAGCCATTTCTATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:31:1:32.3:1:1:0:60:8:1:0:1.3 0/0:4:0:0,0:2,2:0:2,0:19:1:31.8:1:1:0:60:8:1:0:0.5 -6 4406150 . T TTC 69 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGAAGCCATTTCTATAG;RSEQ=CAGGCCGCACTTTTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:15.2:1:30.1:1:1:0:60:10:1:0.6:1.2 1/1:4:4:2,2:0,0:1:0,2:21.3:1:28.6:1:1:0:60:8:1:0.5:0.8 -6 4406229 . T C 87 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCCCCCACAGCCCAACA;RSEQ=ACCAGCTGTGGCAGACTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:27.3:1:31:1:1:0:60:14:1:0:1.1 1/1:1:1:0,1:0,0:1:0,0:14:0:34:0:1:0:60:2:1:0:1 -6 4406310 . T C 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTGGGCAGGGCTTCCC;RSEQ=GCAGGAACTCCAACAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:8.5:1:24.5:1:1:1:60:4:0.2222:0:2.5 0/0:1:0:0,0:0,1:0:0,0:38:0:32:0:1:0:60:2:1:0:0 -6 4406601 . A G 33 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84709;LSEQ=CAGGGGTTGTCAGAGAGCCT;RSEQ=TACAGGAGTGATACTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:31.5:1:33:1:1:1.41:60:4:0.2857:0:3 0/1:4:1:0,1:1,2:0.25:2,0:33:0:28:0:1:0:60:2:0.25:0:3 -6 4406607 . G A 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15267;LSEQ=TTGTCAGAGAGCCTATACAG;RSEQ=AGTGATACTACTGGCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:25.5:1:31.5:1:1:1.29:60:4:0.2222:0:3 0/1:4:1:0,1:1,2:0.25:2,0:39:0:27:0:1:0:60:2:0.25:0:3 -6 4406615 . C T 29 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.66417;LSEQ=GAGCCTATACAGGAGTGATA;RSEQ=TACTGGCATCAGGTTAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:17.5:1:29.5:1:1:1.29098:60:4:0.2222:0:3 0/1:3:1:0,1:0,2:0.3333:0,0:47:0:28:0:1:0:60:2:0.3333:0:3 -6 4407325 . A G 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.5321;LSEQ=AGACATGCAGACAAGATTAC;RSEQ=GAGAAAAGAATGCAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:13.8:1:25.3:1:1:0:60:3:0.75:0:1 1/0:6:4:4,0:2,0:0.6667:0,0:18:1:31.8:1:1:0:60:8:0.6667:0:1 -6 4407421 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48506;SOR=Inf;LSEQ=ACTGGAGTACCTGAAGGAGA;RSEQ=GGGGAGAATGGAAACAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:25.1:1:30.5:1:1:0:58.3:28:1:0:0.3 0/1:16:2:0,2:7,7:0.125:2,0:27.5:1:32:0:0.475:0:60:4:0.125:0:1.5 -6 4407450 . T C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15611;LSEQ=TGGAAACAAGCTGGAAAACA;RSEQ=ACTTCAGGATATTATCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:1.5:1:30.5:1:1:2.24:48:4:0.2222:0:1 0/1:8:2:1,1:4,2:0.25:2,2:11:1:29.5:1:1:1.8258:60:4:0.25:0:1.5 -6 5042052 . G T 95 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTGCTAATAAACTATAAGAA;RSEQ=CAAGGAAAATTAGGGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:1:0,2:24.9:1:30.2:1:1:0:53.1:18:1:0:1.3 1/0:3:2:1,1:1,0:0.6667:0,2:30:1:29:1:1:0:60:4:0.6667:0:1 -6 5042179 . G T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04105;SOR=Inf;LSEQ=GTGCCACACAATGATTTAAG;RSEQ=TATTTGTTTTCTATAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:73,7:0:2,0:21:1:31.7:1:1:0:59.7:160:1:0:0.1 0/1:67:4:3,1:57,6:0.0597:2,2:26.5:1:29.3:1:0.3638:3.08774:60:8:0.0606:0:1 -6 5042363 . C T 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.24127;LSEQ=AGACTTTTATTTTTGTGTGT;RSEQ=ATCAAATATAGGTAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:187:172:55,117:4,10:0.9198:2,2:21.4:1:28.7:1:1:1.17:59.5:171:0.9194:0:1.7 1/0:169:124:44,80:15,30:0.7337:2,2:24:1:28:1:0.85653:1.10:59.5:61:0.7305:0:1.6 -6 5042388 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16535;LSEQ=AATATAGGTAAAAATAATTG;RSEQ=GCAATTCTGCTGTTTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:120:33,87:3,8:0.916:2,2:25.8:1:29.8:1:1:1.01:59.2:119:0.9154:0:2 1/0:120:77:22,55:9,34:0.6417:2,2:25.6:1:29.6:1:0.39324:1.51:58.9:76:0.6387:0:2 -6 5042389 . G A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0011;SOR=Inf;LSEQ=ATATAGGTAAAAATAATTGC;RSEQ=CAATTCTGCTGTTTAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:35,95:0:2,0:25.9:1:31.6:1:1:0:59.2:31.5:1:0:1.8 0/1:119:9:3,6:27,83:0.0756:2,2:22.6:1:30.2:1:0.69012:1.53:60:18:0.0763:0:1.2 -6 5042420 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1715;SOR=Inf;LSEQ=GTTTAAACAGGAACTATTGG;RSEQ=CTCCTTGGCCCTAAATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:16,71:0:2,0:26.4:1:30.9:1:1:0:59:42.5:1:0:1.6 0/1:62:2:1,1:9,51:0.0323:2,2:19:1:27.5:1:0.29878:5.43:60:4:0.0345:0:2.5 -6 5042488 . A G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59705;SOR=0.51177;LSEQ=ATTGTAAAATAATCCAACCT;RSEQ=ATTTTTTTTAATTTGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:21:3,18:0,3:0.875:0,2:22.8:1:30.9:1:1:0:58.5:20:0.8696:0:1.3 1/0:9:7:0,7:0,2:0.7778:0,0:28.1:1:32.4:1:1:0:60:14:0.7778:0:1 -6 5042668 . C A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGCTGCTGTGTTCTGTT;RSEQ=ATTGCCTCCTTCAACAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:9:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 5043276 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCCTAGTGACTTCTACT;RSEQ=TATGCTCCAGCTTTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:26.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 5106731 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13793;SOR=Inf;LSEQ=TGGTGGGGCTTGAGATTAAC;RSEQ=GGAGAGGCTGTGGATGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:55,0:0:1,0:24.9:1:30:1:1:0:60:54:1:0:0.1 0/1:33:2:2,0:31,0:0.0606:1,0:25.5:1:32:0:1:0:60:4:0.0606:0:1.5 -6 5106788 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0779;SOR=Inf;LSEQ=CTACTTAGTTAGCAGCAGGA;RSEQ=GGAGTATACCTAAAGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:132,33:0:2,0:21.2:1:31.2:1:1:0:59.8:54:1:0:0.4 0/1:124:3:2,1:86,35:0.0242:2,2:22:1:27.3:1:1:1.22641:60:6:0.0246:0:1 -6 5106807 . T C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.24095;SOR=1.34753;LSEQ=ACGGAGTATACCTAAAGCAA;RSEQ=CTAGCCAATTCTTTCAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:50:37,13:123,54:0.2203:2,2:24.7:1:31.8:1:0.60127:1.25:60:100:0.2283:0:1.2 0/1:174:48:30,18:78,48:0.2759:2,2:24.8:1:30.6:1:1:1.03:60:47:0.2733:0:1.3 -6 5106899 . T G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.06754;LSEQ=GTGCAAGATCTCCCAGCTAT;RSEQ=ATGTCATGACAGCCAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:150:55,95:91,116:0.4202:2,2:24.3:1:31.4:1:0.19086:1.35385:60:49:0.4188:0:1.1 1/0:265:159:72,87:47,57:0.6:2,2:26.1:1:31:1:1:1.00:60:30.8:0.5923:0:1.2 -6 5106916 . C T 39 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08156;SOR=Inf;LSEQ=TATTATGTCATGACAGCCAG;RSEQ=CCAGCCCAGAGCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:101,183:0:2,0:23.8:1:30.9:1:1:0:60:30.556:0.9964:0:0.5 0/1:220:3:1,2:92,125:0.0136:2,2:8:1:25:1:1:1.46951:60:2:0.0093:0:4 -6 5106962 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58168;SOR=2.60936;LSEQ=CTAGGATATAGCCTTGCTCG;RSEQ=CCAATGAGTTCTGCCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:1:0,1:27,104:0.0076:2,0:38:0:31:0:1:0:60:2:0.0077:0:1 0/1:102:2:1,1:29,71:0.0196:2,2:38:1:28.5:1:0.50379:2.42:60:4:0.0202:0:1 -6 5603804 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15766;SOR=0;LSEQ=CTTCTGAGGATCTGTTTTGT;RSEQ=CCTCCTTCACCTCCAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:0.1333:2,2:30.5:1:31:1:1:1.54914:60:4:0.1333:0:2 0/0:22:0:0,0:13,9:0:2,0:24:1:31.8:1:1:0:60:44:1:0:1.1 -6 5603835 . A G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.163;LSEQ=CTCCAGTGGTTTGCTGGCAC;RSEQ=CTTTGGCATTCCTGGGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:18:10,8:4,3:0.72:2,2:27.2:1:31.1:1:1:1.06395:60:36:0.72:0:1.7 1/0:24:18:9,9:3,3:0.75:2,2:35.8:1:31.7:1:1:1:60:36:0.75:0:1.8 -6 5603872 . G C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.75264;SOR=1.2615;LSEQ=CTTGCAGGAGCGTTATCCCA;RSEQ=CCTCTGGCTTCATCTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:13:4,9:3,6:0.5909:2,2:28.1:1:30.9:1:1:1.11896:60:26:0.5909:0:1.6 1/0:17:11:5,6:3,3:0.6471:2,2:19.8:1:31.3:1:1:1.18716:60:22:0.6471:0:2.1 -6 6269168 . C G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00036;SOR=Inf;LSEQ=CCTGACCTCAGGTGTTCCCC;RSEQ=CCGCCTCAGCCTCCCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:65,0:0:1,0:28.5:1:30.2:1:1:0:60:31.5:1:0:0.1 0/1:34:7:7,0:27,0:0.2059:1,0:14.6:1:30.9:1:1:0:60:14:0.2059:0:1.4 -6 6269225 . A AT 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20429;SOR=Inf;LSEQ=TGAGCCACCATGCCTGGCAA;RSEQ=TTGTTTTTTTTTTTTAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:161,53:0:2,0:21:1:30:1:1:0:59.9:41.8:1:0:0.4 0/1:177:2:0,2:133,42:0.0113:2,0:13.5:1:24:1:0.06073:0:60:4:0.0114:0.0056:3 -6 6269228 . GT G 125 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.93477;LSEQ=GCCACCATGCCTGGCAAATT;RSEQ=TTTTTTTTTTTAAGTATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:15:13,2:166,62:0.0598:2,2:22.1:1:32.2:1:0.36575:2.42:60:30:0.0607:0.0239:0.1 0/1:214:12:9,3:143,57:0.0561:2,2:18.6:1:30.3:1:1:1.19:57.9:24:0.0566:0.014:1.4 -6 6269240 . T A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2548;SOR=0;LSEQ=GGCAAATTGTTTTTTTTTTT;RSEQ=AAGTATAACTTCTACTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:2,1:206,92:0.01:2,2:15.3:1:24.3:1:1:1.11913:60:2:0.0067:0:1 0/0:251:0:0,0:171,80:0:2,0:23.1:1:28.9:1:1:0:59.7:250:1:0:0.8 -6 6269298 . G C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.29957;LSEQ=GAAGGGGTGATTTCTTTTTT;RSEQ=CTCTCTGGTTCTGAATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:113:69,44:264,226:0.1874:2,2:29.2:1:30.7:1:0.17398:1.34:60:36.667:0.189:0:1.1 1/0:536:295:154,141:121,119:0.5504:2,2:24.6:1:30.6:1:0.72806:1.07:59.8:72.75:0.5564:0:1.2 -6 6270236 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACAGGCATGAGCCACTG;RSEQ=GCCCAGCCTACCTACTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:28.5:1:1:0:60:4:1:0:1 -6 6728508 . GC G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10686;SOR=Inf;LSEQ=AGGAGCCCTTCCTTGTGAGG;RSEQ=CCAGCTCTGATATTCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:37,25:0:2,0:26.2:1:31.7:1:1:0:60:61:1:0:0 0/1:57:3:2,1:25,29:0.0526:2,2:22:1:29.9:1:0.5986:2.29:60:6:0.0545:0.0175:0 -6 6728616 . G A 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGCCTAGGCCTTCACAGCA;RSEQ=GGGGCAAGGGGGATGTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:20:5,15:2,10:0.625:2,2:23:1:30.8:1:0.68332:1.64:60:40:0.625:0:1.1 0/0:29:0:0,0:13,16:0:2,0:19.7:1:30.1:1:1:0:60:58:1:0:0.2 -6 7516670 . GTA G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.15;SOR=Inf;LSEQ=TCACAACGGTGGCAATAACT;RSEQ=TATATATATATGTCTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:34,0:0:1,0:21.1:1:30.5:1:1:0:59.4:68:1:0:0.4 0/1:22:2:2,0:19,1:0.0909:1,0:16:1:33:1:1:0:60:4:0.0909:0:0 -6 7516674 . A ATATATACATATATATATATATATATG 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=4e-05;SOR=0;LSEQ=AACGGTGGCAATAACTGTAT;RSEQ=TATATATATGTCTATAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:18,0:21,0:0.4286:1,1:18.6:1:31.1:1:1:0:60:36:0.439:0.1905:1.1 0/0:26:0:0,0:21,1:0:1,0:17.7:1:28.6:1:1:0:60:44:0.8462:0:0 -6 7516700 . T A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0208;SOR=0.4172;LSEQ=ATATGTCTATAAACTTACAA;RSEQ=AAAGATAAACTCTAGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:52:52,0:46,0:0.5306:1,1:17.7:1:30.9:1:1:0:59.6:104:0.5306:0:1.2 0/1:47:15:15,0:30,2:0.3191:2,1:15.5:1:30.1:1:1:0:60:30:0.3191:0:1.1 -6 7516833 . G T 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42877;LSEQ=TCCTCAGCCCAGGTATGAAC;RSEQ=TAAAGTTTGGCCTGAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:780:497:277,220:175,108:0.6372:2,2:26.4:1:30.5:1:0.09788:1.28651:59.7:61.125:0.6384:0:1.1 0/1:687:295:170,125:223,169:0.4294:2,2:26.7:1:30.4:1:0.87633:1.03:59.7:97.333:0.4282:0:1.1 -6 7517131 . A T 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.49157;LSEQ=GGCCTTTCTGGTACATGCAG;RSEQ=AGTGACGGGTTACAGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:798:479:235,244:143,176:0.6003:2,2:25.9:1:28.8:1:0.24768:1.19:60:67.429:0.599:0:1.1 0/1:603:256:132,124:182,165:0.4245:2,2:25.6:1:28.5:1:0.86909:1.03614:59.8:63:0.4257:0:1.2 -6 7517239 . G A 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCCATACCCTTGGGCCACA;RSEQ=AGTCTGACTGCATGTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:0:0,0:324,335:0:2,0:25.6:1:31.6:1:1:0:60:93.143:0.9985:0:0.1 0/1:552:75:39,36:230,245:0.1359:2,2:24.3:1:28.8:1:0.61965:1.15:60:36.5:0.1342:0:1.2 -6 7517509 . T C 215 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGTGTGCAAAATCTTCGA;RSEQ=TGACTTATCTTGATTATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:799:0:0,0:414,385:0:2,0:23.7:1:30.3:1:1:0:60:78.9:1:0:0.1 0/1:645:119:66,53:261,265:0.1845:2,2:24.1:1:31.3:1:0.26515:1.26:60:58.5:0.1834:0:1.1 -6 7518105 . A AT 201 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.03266;SOR=0.6648;LSEQ=TAAACCTTGAAAGTGAATCA;RSEQ=TTTTTTTTTTTTTCTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:105:12,93:50,144:0.3163:2,2:25.6:1:30:1:0.00423:2.68272:59.3:25.25:0.3186:0.0181:0.5 0/1:251:59:9,50:44,125:0.2351:2,2:25.4:1:30.1:1:0.10815:1.95031:59.3:58:0.2367:0.0239:0.5 -6 7518127 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51389;SOR=0;LSEQ=TTTTTTTTTTTTCTGAGACG;RSEQ=AGTTTTGCTCTTGTTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:12,163:0.0113:2,2:6:1:27:1:0.14188:13.09:60:4:0.0116:0:1 0/0:124:0:0,0:7,116:0:2,0:20.4:1:30.9:1:1:0:59.1:60.5:1:0:0.5 -6 7518144 . C A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGGAGTTTTGCTCTTGTTG;RSEQ=CCAGGCTGGAGTGCAATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:0,111:0:1,0:24.5:1:31.6:1:1:0:59.5:54.5:1:0:0.4 0/1:67:14:0,14:0,53:0.209:1,1:23.9:1:30.3:1:1:0:60:28:0.209:0:1.2 -6 7518659 . A G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAAAAAGCTATGCAACT;RSEQ=TAATTCTTTTCCAAACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21:1:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 8313973 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTGTAGGTGACCTGGG;RSEQ=TTTCTCTGTGGCTGCCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 8314164 . G A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.72471;SOR=0.70817;LSEQ=TGAAGTGTGTTTTCCACCTT;RSEQ=TTTCCATTATCCCCATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:5,2:5,2:0.5:2,2:20.7:1:30.3:1:1:1:60:14:0.5:0:1.1 0/1:17:7:5,2:4,6:0.4118:2,2:28:1:29.4:1:0.33484:3.46:55:14:0.4118:0:1.3 -6 8314545 . G T 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTTTTTTTATTACCCAT;RSEQ=TTCTGAAGCCTACTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:19.3:1:31.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 8314616 . G A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCTCTTGAAGGAGAGAC;RSEQ=TTGCAGTCATTTGGAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:3,1:0.5:2,0:25:1:30.5:1:1:0:55:8:0.5714:0:1.3 0/0:1:0:0,0:1,0:0:0,0:27:0:32:0:1:0:60:2:1:0:0 -6 8314742 . GT G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.48276;SOR=0;LSEQ=GCTGCTGACTCTTGCATGGG;RSEQ=TTTTTTTTTGGCAGCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:0.1333:2,2:25:1:28.5:1:1:1.55:60:4:0.1333:0.0667:1 0/0:14:0:0,0:9,5:0:2,0:28.7:1:29.2:1:1:0:60:28:1:0:0.4 -6 8314762 . T TTTG 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.4467;LSEQ=GTTTTTTTTTTGGCAGCTTT;RSEQ=TTGTTGTTGATGCTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:3,7:1,3:0.7143:2,2:21.8:1:29.7:1:1:1.26:60:20:0.7143:0.0714:0.8 1/0:14:11:6,5:2,1:0.7857:2,2:31.2:1:29.6:1:1:1.60839:60:22:0.7857:0.0714:0.5 -6 8315463 . T C 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATCTATGGAGATGGCTG;RSEQ=CACCCTTCCCCCACCTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:26.7:1:31.3:1:1:0:60:6:1:0:1 1/1:3:3:3,0:0,0:1:0,0:27:1:27.7:1:1:0:60:2:1:0:1.7 -6 8315773 . C G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.07395;SOR=0.15127;LSEQ=CTGGCTGTGTAGCGTGCTCA;RSEQ=TCACCACCTCCCTTGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:1,1:0.8182:2,0:24.7:1:31.7:1:0.18182:0:60:18:0.8182:0:1.2 0/1:8:3:1,2:1,4:0.375:2,2:29.3:1:31.7:1:1:1.83:60:6:0.375:0:1 -6 8909370 . CT AC 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=TTTTCTTAGTTTAGATTCCC;RSEQ=TGAAATAGACCCTCAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:0:2,0:21.4:1:28.4:1:1:0:60:10:1:0:1.3 0/1:6:2:1,1:3,1:0.3333:2,2:6.5:1:29.3:1:1:2.44949:60:4:0.3333:0.1667:0.5 -6 8909371 . T C 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=0;LSEQ=TTTCTTAGTTTAGATTCCCC;RSEQ=TGAAATAGACCCTCAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:8,3:0,0:1:0,2:21.8:1:28.5:1:1:0:60:10:1:0:1.3 0/0:5:0:0,0:3,1:0:2,0:15.3:1:31.5:1:1:0:60:8:1:0:0.3 -6 10214548 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.51301;SOR=0;LSEQ=CCATGTTTTCTAAAAGGCCT;RSEQ=GAGAACATACATTGGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:18,15:0.0571:2,2:11.5:1:31.5:1:1:1.19373:41:4:0.0588:0:1 0/0:23:0:0,0:12,11:0:2,0:16.3:1:28.9:1:1:0:60:22:1:0:0.3 -6 10214590 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49503;SOR=Inf;LSEQ=CTTCTCTTTCCCTTTGTGTT;RSEQ=GTCATCTTGGCAAATTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,17:0:2,0:25.3:1:30.4:1:1:0:60:37:1:0:1 0/1:43:2:1,1:21,20:0.0465:2,2:29.5:1:29:1:1:1.04883:60:4:0.0465:0:1 -6 10214600 . G A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05578;LSEQ=CCTTTGTGTTCGTCATCTTG;RSEQ=CAAATTACTGGAAGATGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:34:19,15:1,2:0.9189:2,2:26.7:1:29.5:1:0.5843:2.47:60:33:0.9167:0:1.2 0/1:45:17:9,8:13,15:0.3778:2,2:28.2:1:29.4:1:0.7631:1.29:60:34:0.3864:0:1.1 -6 10575131 . T C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.63512;SOR=0.40612;LSEQ=TTTCTTTTTCTGATCGTTTT;RSEQ=CTTCAAGCGTTTCAGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:5,4:1,1:0.8182:2,2:33.8:1:30.6:1:1:1.22:59.1:18:0.8182:0:1.1 1/0:11:7:4,3:3,1:0.6364:2,2:19.6:1:30.9:1:1:2.09375:58.4:14:0.6364:0:1 -6 10575346 . T C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16809;SOR=0.30774;LSEQ=CATTCCCTTGATGCCTGCAA;RSEQ=GTCACCTTTCTTATAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:5,3:11,5:0.3333:2,2:30.6:1:31.1:1:1:1.30452:60:16:0.3333:0:1 0/1:23:3:2,1:13,7:0.1304:2,2:38:1:31.7:1:1:1.07:60:6:0.1364:0:1 -6 12518463 . T G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25178;SOR=0.31741;LSEQ=TTTTACATTGCATGCCTGTA;RSEQ=CAAAACATCTCATGTACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:13,0:5,0:0.4815:0,1:22.8:1:32.4:1:1:0:60:12:0.4615:0:2.4 0/1:9:2:2,0:0,0:0.2222:0,0:17:1:30.5:1:1:0:60:4:0.2222:0:2 -6 12518500 . A G 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19101;LSEQ=CCCCATAAATATATACACCT;RSEQ=CTATGTACCTATGAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:43:43,0:7,0:0.86:0,1:25.6:1:32.4:1:1:0:60:42:0.8571:0:2.5 1/1:25:22:22,0:3,0:0.88:0,1:15.9:1:32.4:1:1:0:60:44:0.88:0:2 -6 12518544 . A T 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.84774;SOR=1.17081;LSEQ=ATTAAAAAAAATTAAAAATT;RSEQ=AACAAACACTTGCAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:118:113,5:21,0:0.8489:1,1:21.4:1:30.3:1:1:0:60:38.333:0.8456:0:1.5 1/1:91:79:71,8:12,0:0.8681:0,2:23.8:1:30:1:0.5907:0:60:158:0.8681:0:1.2 -6 12518585 . C T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04433;SOR=Inf;LSEQ=ATCAAATGTGTGTTCTCCCA;RSEQ=CATGTGTAAATCATCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:209,77:0:2,0:26.3:1:31.5:1:1:0:60:94.333:1:0:0.5 0/1:244:4:1,3:162,78:0.0164:2,2:7.8:1:25.8:1:0.10807:6.18137:60:8:0.0165:0:1 -6 12518688 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2793;LSEQ=GAAAATGTTTCTGGAGTTAG;RSEQ=TTAGAAGAATGTGTGGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:434:373:149,224:24,36:0.8594:2,2:25.2:1:29.7:1:1:1.00223:60:92.25:0.8601:0:1.1 1/0:376:237:98,139:64,75:0.6303:2,2:24.8:1:29.5:1:0.38974:1.20971:60:117.5:0.6317:0:1.1 -6 12518742 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07406;SOR=Inf;LSEQ=TGAGTGTACTTCTTTTTCTG;RSEQ=TCATGTGACAATAAATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:69,181:0:2,0:25.3:1:31.4:1:1:0:60:61.5:1:0:0.7 0/1:182:3:2,1:61,118:0.0165:2,2:13.3:1:27.3:1:0.27535:3.84:60:6:0.0168:0:1 -6 13521823 . G T 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCAAGGGTCACTTTGCT;RSEQ=TACATTGTATTACACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:14.5:1:30.3:1:1:0:60:8:1:0:1 1/1:3:3:3,0:0,0:1:0,0:20.3:1:31:1:1:0:60:6:1:0:1.3 -6 13686333 . C T 32 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAATTTCCAAAATTTCTT;RSEQ=CCCCCCCCCCCCCCGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 16463818 . G A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AGTAGTGAATATCCAAAACC;RSEQ=CCAAGGCCTAGACCTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:19:1:28.7:1:1:0:60:6:1:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:16:1:32:0:1:2.44949:60:4:0.3333:0:1.5 -6 16945029 . A G 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20789;SOR=0;LSEQ=TTTTTCTAGCAGCTTTCAAG;RSEQ=TGTTTTTGTTTTAATCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:20,6:0.069:2,2:16:0:34:0:0.44444:3.16227:60:4:0.0714:0:1.5 0/0:34:0:0,0:20,14:0:2,0:25.3:1:29.1:1:1:0:60:68:1:0:0.1 -6 16945103 . G T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01044;SOR=0.17912;LSEQ=TGGTTTTCTTTGTGTTTATT;RSEQ=TTTATCATCTTTGGGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:14:5,9:9,13:0.3889:2,2:18.5:1:29.2:1:1:1.23859:60:28:0.3889:0:1.3 0/1:30:3:1,2:11,16:0.1:2,2:20.7:1:28.3:1:1:1.36092:60:6:0.1034:0:1 -6 17627494 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.13681;LSEQ=ATTAGACCCTATCATGTTTT;RSEQ=GTTGCTTTCCAAATAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:44:34,10:23,9:0.5789:2,2:22.2:1:30:1:0.60347:1.33:60:13.667:0.5775:0:1 0/1:64:10:8,2:42,12:0.1563:2,2:24.7:1:30.9:1:1:1.14:60:20:0.1563:0:1 -6 17627535 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24068;SOR=Inf;LSEQ=TAATTTTAGTTTTGATTTTG;RSEQ=CTTTATATTTCTAAGTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:107,42:0:2,0:23.4:1:29.9:1:1:0:60:48.667:1:0:0.5 0/1:144:2:1,1:99,43:0.0139:2,2:13.5:1:29.5:1:0.51923:2.28751:60:4:0.0139:0:2 -6 17627590 . T C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.3974;LSEQ=AAACTGCTCATAGCTATTTG;RSEQ=TGAATTCCATACTTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:72:38,34:97,78:0.2915:2,2:24.6:1:31.3:1:0.77879:1.1122:60:23:0.2887:0:1.1 1/0:284:214:116,98:37,32:0.7535:2,2:26.2:1:31.6:1:1:1.02:60:106:0.7544:0:1.1 -6 17729006 . G T 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAGGGAGAGGCGCCGCG;RSEQ=GGAACTGGGGCTGTGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44:0:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 17729816 . T C 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01945;SOR=Inf;LSEQ=AATCTGGTTGGGTTGCTTTC;RSEQ=GTGTTATGAGGGCTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:34.6:1:30.4:1:1:0:60:20:1:0:0.5 0/1:36:9:4,5:10,17:0.25:2,2:21:1:27.9:1:0.71151:1.35:60:8:0.2353:0:1.9 -6 17729829 . C G 80 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07079;SOR=Inf;LSEQ=TGCTTTCTGTGTTATGAGGG;RSEQ=TTTGTGTTTTTTTGTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:31.9:1:31.4:1:1:0:60:19:1:0:0.6 0/1:32:6:3,3:9,17:0.1875:2,2:14.2:1:31:1:0.64713:1.85:60:12:0.2:0:2.3 -6 17729851 . C T 86 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05246;SOR=0.12258;LSEQ=TTGTGTTTTTTTGTTCTTTA;RSEQ=GTTAAAACTTGTTGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:7,7:0.3636:2,2:16.1:1:28.9:1:0.67492:1.62835:60:16:0.3636:0:1.9 0/1:16:1:1,0:4,10:0.0625:2,0:26:0:32:0:0.33333:0:60:2:0.0667:0:2 -6 17729871 . C G 69 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36898;SOR=0.30006;LSEQ=CGTTAAAACTTGTTGCTGCT;RSEQ=CCTTTGTGAGTTACATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:2,3:3,7:0.3333:2,2:23.8:1:29.8:1:1:1.51:60:10:0.3333:0:2 0/1:8:1:1,0:0,7:0.125:0,0:6:0:32:0:0.125:0:60:2:0.1429:0:2 -6 18657237 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15766;SOR=Inf;LSEQ=TCCCCCAGCAAAGCACACCC;RSEQ=CCTCCACCAGGGGACATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,8:0:2,0:21.1:1:30.1:1:1:0:60:20:1:0:0 0/1:15:2:1,1:5,7:0.1333:2,2:36.5:1:30:1:1:1.37:60:4:0.1429:0:1.5 -6 18657579 . A G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CAGAAAGCAACAACAATAGC;RSEQ=TCAACAATAACAAAAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:43.5:1:30:0:1:1:60:4:0.5:0:1 0/0:5:0:0,0:1,4:0:2,0:22:1:30.4:1:1:0:60:10:1:0:0.2 -6 19144021 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51334;SOR=0;LSEQ=CCTTTGGCCACATATATGCG;RSEQ=ATCTATAAGAAAGGTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:30,91:0.0163:2,2:24.5:1:28:1:0.44209:3.00:60:4:0.0167:0:1 0/0:86:0:0,0:17,69:0:2,0:25.7:1:30:1:1:0:60:172:1:0:0.1 -6 19144202 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=GTGCGTATTGAGCACATTAA;RSEQ=CACTCTAAGAGCTGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:29.9:1:32.8:1:1:0:58.2:38:1:0:0 0/1:20:2:1,1:6,12:0.1:2,2:46:0:31:1:1:1.93:60:4:0.1:0:1.5 -6 19349172 . T C 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02767;SOR=Inf;LSEQ=ATCCAGTCTATGAGAAGAAG;RSEQ=CCGAGAAAGAAGTTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:13,3:0:2,0:22.6:1:30.1:1:1:0:60:32:1:0:0 0/1:8:3:3,0:4,1:0.375:2,0:19:1:31.3:1:1:0:60:6:0.4286:0:1.7 -6 19349215 . T C 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01055;SOR=Inf;LSEQ=GAAGTGGAACCATCTGAAAA;RSEQ=GTCCCTTGCCCAGAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:26,17:0:2,0:22.4:1:30.2:1:1:0:60:42:1:0:0.1 0/1:31:5:3,2:15,11:0.1613:2,2:11.8:1:28.8:1:1:1.10:60:10:0.1613:0:2 -6 19349227 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17647;SOR=Inf;LSEQ=TCTGAAAATGTCCCTTGCCC;RSEQ=GAAGAAAGATCAGGTAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:27,22:0:2,0:25.1:1:30.2:1:1:0:60:48:1:0:0.1 0/1:36:2:1,1:19,15:0.0556:2,2:22.5:1:30:1:1:1.2583:60:4:0.0556:0:2.5 -6 19728835 . G C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02621;SOR=0.34835;LSEQ=TAACCAACTGGCAACCATGG;RSEQ=TGTTTTCATTACTTGGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:34:34,0:26,0:0.5667:1,1:22:1:30.8:1:1:0:60:10.333:0.5439:0:1.1 0/1:29:9:9,0:19,1:0.3103:1,0:16:1:31.7:1:1:0:60:18:0.3103:0:1 -6 19729003 . T G 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.51866;LSEQ=CAATATGTGGAATCAAGAAC;RSEQ=TTGGTTATTTGTCGGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:536:378:185,193:79,78:0.7052:2,2:26.7:1:30.6:1:0.77667:1.05648:60:53:0.7094:0:1.1 1/0:448:248:119,129:97,102:0.5536:2,2:24.9:1:30.1:1:0.92419:1.03084:60:123:0.5553:0:1.1 -6 19729078 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17903;SOR=Inf;LSEQ=ATCACTTGGTTTGCAAAATT;RSEQ=CCAAGGGACTAAATGACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:56,171:0:2,0:24:1:31.6:1:1:0:60:36.833:1:0:0.4 0/1:167:2:1,1:42,123:0.012:2,2:10:1:29:1:0.44982:2.91:60:4:0.0123:0:1 -6 19729381 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGCACTGTATTGAGAAG;RSEQ=AAGCCGATTTCACTAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:33:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 20402239 . T C 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03158;SOR=Inf;LSEQ=CATCCCCGCTTGGGGCCCGA;RSEQ=ATCCGTGCGGCCGGGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:14,2:0:2,0:24.1:1:31.1:1:1:0:60:32:1:0:0 1/0:4:2:2,0:1,1:0.5:2,0:25.5:1:30.5:1:1:0:60:4:0.5:0:1.5 -6 20402594 . TCGC T 135 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.04032;SOR=2.02014;LSEQ=ACTGCTAGCCAGCCCCGGCT;RSEQ=CGCCGCCGCCGCCGCTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:835:15:10,5:508,310:0.018:2,2:21:1:31.5:1:0.79466:1.22:60:30:0.0182:0.0048:0.2 0/1:589:21:14,7:349,217:0.0357:2,2:23.1:1:30.9:1:0.81978:1.24:60:42:0.036:0.0034:0.3 -6 20402610 . C T 127 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.08068;SOR=0.38996;LSEQ=GGCTTCGCCGCCGCCGCCGC;RSEQ=GCTGCCGCCGCCCCGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1056:17:11,6:642,396:0.0161:2,2:27.6:1:31.1:1:1:1.13:60:34:0.0163:0:1.1 0/0:789:5:3,2:478,306:0.0063:2,2:24.4:1:29.4:1:1:1.04137:60:10:0.0064:0:1 -6 20402765 . C A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01432;SOR=Inf;LSEQ=CGCCGGCAGCCTCCTCTACA;RSEQ=CACGCCGCACGGACCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:94,396:0:2,0:23.9:1:31.6:1:1:0:60:121.5:0.9979:0:0.2 0/1:369:5:4,1:89,275:0.0136:2,2:16.4:1:27.6:1:0.01546:12.26:60:10:0.0137:0:1 -6 20402799 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06663;SOR=Inf;LSEQ=CCCTCCAGCAGAGCCGGGCT;RSEQ=CTGCAGCAGCCACCAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:32,165:0:2,0:20.9:1:32.7:1:1:0:60:64.667:0.9949:0:0.2 0/1:136:3:1,2:21,112:0.0221:2,2:9.3:1:29.7:1:0.41356:2.64:60:6:0.0224:0:1.3 -6 20402836 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.15349;SOR=Inf;LSEQ=CGCTGGGACGCGGCGGCAGC;RSEQ=GCGGCGGCGGCGGCCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:17,35:0:2,0:20.5:1:30.6:1:1:0:60:104:1:0:0.3 0/1:34:2:1,1:11,20:0.0588:2,2:30:0:32.5:1:1:1.78:60:4:0.0625:0:1.5 -6 20403936 . AC A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.53812;SOR=0;LSEQ=ACCCTCCCTCTCCTCTCCCC;RSEQ=CCCCCCACCGGCGCCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:2,0:158,8:0.0119:1,0:8:1:32.3:1:1:0:60:4:0.0123:0.006:0 0/0:94:0:0,0:88,5:0:2,0:19.4:1:30.8:1:1:0:60:22.25:0.9889:0:1.1 -6 20403953 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1624;SOR=Inf;LSEQ=CCCACCCCCCCACCGGCGCC;RSEQ=GCCCTCGCCCTGCGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:235,25:0:2,0:22.9:1:30.8:1:1:0:59.9:42.333:1:0:0.6 0/1:176:2:1,1:158,16:0.0114:2,2:25.5:1:26:1:0.18435:9.61044:60:4:0.0116:0:1 -6 20403978 . G T 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47708;SOR=0.43035;LSEQ=TCGCCCTGCGCCGCCGGTCT;RSEQ=TTCGGCCCTCCGGGCCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:6:2,4:356,128:0.0122:2,2:17.8:1:23.7:1:0.04771:5.53916:60:2:0.0088:0:1.8 0/0:378:2:0,2:280,96:0.0053:2,0:1:0:26:0:0.06671:0:60:4:0.0056:0:1 -6 20404345 . A AG 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGGCGATAGAAAACCGG;RSEQ=GGGGGCTTCTCGCCAATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:20:1:32.3:1:1:0:60:4:0.3333:0.125:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 20481404 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03036;SOR=Inf;LSEQ=TTCTTTACCTTTCCCCCTAT;RSEQ=CCCCACCCGCTCGGTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:202,60:0:2,0:25.9:1:31.4:1:1:0:60:86.333:1:0:0.1 0/1:261:5:2,3:182,74:0.0192:2,2:15.6:1:27.2:1:0.15449:3.66834:60:10:0.0195:0:1 -6 20481678 . G C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=2.57415;LSEQ=TGAGTAGGAGTCCTCCCCAT;RSEQ=CCCCGGCTCTGAGGGGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:68:23,45:128,295:0.1385:2,2:24.3:1:30.4:1:0.57257:1.18:60:67:0.1396:0:1.1 0/1:437:128:45,83:112,194:0.2929:2,2:23.8:1:29.7:1:0.82691:1.0647:60:31:0.2925:0:1.3 -6 20481758 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16803;SOR=Inf;LSEQ=CCACGCCCACACGTTCTTTT;RSEQ=TTTTCTCTCCTACTGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:2,111:0:1,0:23.6:1:32.7:1:1:0:60:226:1:0:0.2 0/1:79:2:1,1:4,73:0.0253:2,2:5:0:33.5:1:0.12334:16.43:60:4:0.0263:0:1.5 -6 20481825 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00392;SOR=7.2757;LSEQ=CAGCTTCTAAGCCAGAAGTT;RSEQ=GAAGTCTCTTTACAAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:15:0,15:1,19:0.4286:1,1:18.5:1:30.7:1:1:0:60:30:0.4412:0:1 1/1:20:17:1,16:1,2:0.85:2,1:19.8:1:31:1:0.28421:6.73285:60:34:0.85:0:1.1 -6 20482573 . G GT 28 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGATGGGTTGTTTTTTT;RSEQ=TTTTTTTTTTTTTTTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:15:1:28.6:1:1:0:60:4:0.5:0.25:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 20482821 . G GAA 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.05983;SOR=Inf;LSEQ=AAGTGCAGAACTGTATTTAT;RSEQ=AAAAAAAAAATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:19,0:0:1,0:18.2:1:32.7:1:1:0:58.7:38:0.95:0:1.1 0/1:7:2:2,0:4,0:0.2857:0,0:16.5:1:31.8:1:1:0:60:4:0.2857:0.1429:2 -6 20482830 . A T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0.75549;LSEQ=ACTGTATTTATGAAAAAAAA;RSEQ=ATATATATATATATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:7,0:15,0:0.25:1,0:23.4:1:31.7:1:1:0:57.1:14:0.2593:0:1.4 0/1:10:2:2,0:6,0:0.2:0,0:13:1:32:0:1:0:60:4:0.2:0:1.5 -6 20482851 . A G 69 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=11.000;MSILEN=2;SSF=0.00085;SOR=Inf;LSEQ=ATATATATATATATATATAT;RSEQ=TGTGTAAATGTTCTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:24,0:0:1,0:20.3:1:29.2:1:1:0:59.8:48:0.8:0:0.6 0/1:14:5:5,0:9,0:0.3571:0,0:24.4:1:30:1:1:0:60:4:0.3077:0:1.4 -6 20482958 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10146;SOR=Inf;LSEQ=CTCCTTCCCCTCCCTCCCAT;RSEQ=AGTAGCCATGAAGAGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:224,45:0:2,0:22.8:1:31.7:1:1:0:60:28.889:0.9962:0:0.1 0/1:237:3:2,1:171,63:0.0127:2,2:10:1:28.3:1:1:1.35528:60:6:0.0129:0:1 -6 20483230 . A G 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01612;SOR=Inf;LSEQ=TGACAATCTGACTTATGCAC;RSEQ=AGGTAGATTATTATTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:21,174:0:2,0:21.4:1:30.4:1:1:0:60:96.5:1:0:0.1 0/1:154:5:1,4:14,135:0.0325:2,2:13.6:1:31.4:1:0.40521:2.39:60:10:0.0329:0:1.2 -6 20483265 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51357;SOR=0;LSEQ=TCTGATGTCATGCAAATGAG;RSEQ=ACCTGTGTGCCTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:0,92:0.0213:1,2:29.5:1:31.5:1:0.02128:0:60:4:0.0215:0:1.5 0/0:65:0:0,0:0,65:0:1,0:25.7:1:28:1:1:0:60:31.5:1:0:0.1 -6 20483286 . ATG A 33 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.51597;SOR=0;LSEQ=ACCTGTGTGCCTGTGTGTGT;RSEQ=TGTGTGTGTGTGCACGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:1,69:0.0278:1,0:22.5:1:33:0:1:0:60:4:0.0278:0:0 0/0:48:0:0,0:0,48:0:1,0:21.4:1:29.3:1:1:0:60:15:1:0:0.1 -6 20483407 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09341;SOR=13.74787;LSEQ=ATTTTGATACCAGGTGGGAA;RSEQ=TGTTTTTTAAAGCATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:0,10:0.0909:0,0:47:0:32:0:1:0:60:2:0.1:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:5.5:1:29.5:1:1:0:60:4:0.6667:0:1 -6 20486754 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00038;SOR=Inf;LSEQ=ACCTCATGATCCACCCGCCT;RSEQ=GGCCTCCCAAAGTGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:34,0:0:1,0:19.2:1:31.3:1:1:0:59:33:1:0:0.3 0/1:24:8:8,0:16,0:0.3333:1,0:13.4:1:29.5:1:1:0:58.4:16:0.3333:0:1 -6 20486794 . C T 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04034;SOR=0;LSEQ=ATTACAGGTGTGAGCCACCG;RSEQ=GCCCGGCCACATATGCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:7:7,0:61,0:0.1029:1,0:26.9:1:28.3:1:1:0:60:6:0.0909:0:1.4 0/0:46:0:0,0:46,0:0:1,0:27.3:1:32.6:1:1:0:60:92:1:0:0.6 -6 20486798 . C T 134 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04149;SOR=2.36304;LSEQ=CAGGTGTGAGCCACCGCGCC;RSEQ=GGCCACATATGCATACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:15:15,0:61,1:0.1948:1,1:20:1:31.2:1:1:0:60:30:0.2027:0:1 0/1:52:19:19,0:33,0:0.3654:1,1:25.2:1:31.6:1:1:0:60:38:0.3654:0:1.1 -6 20487054 . G A 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTAAGGAGACAGCGTCTTT;RSEQ=TTCATCTGCAAAGATCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:111,312:0:2,0:23.6:1:31.9:1:1:0:60:83.6:0.9976:0:0.1 0/1:414:23:5,18:130,260:0.0556:2,2:23.4:1:28.8:1:0.36019:1.7977:60:22:0.0541:0:1.3 -6 20487250 . T G 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.64992;SOR=1.80535;LSEQ=TGACCTAGCAGGATGTTCAG;RSEQ=TCAAAGTGGTATATGATGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:1,6:0.4167:2,0:24.2:1:32.8:1:1:0:60:10:0.4545:0:1.2 1/0:7:4:0,4:1,2:0.5714:2,0:29.5:1:32.5:1:0.42857:0:60:8:0.5714:0:1 -6 20488234 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00075;SOR=3.03224;LSEQ=GTTGGACTAGTAGGGAAAAA;RSEQ=CAAGTGAAAAACGAACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:32:31,1:72,0:0.3077:1,1:20.7:1:30.4:1:0.30769:0:60:64:0.3077:0:1 1/0:66:38:38,0:28,0:0.5758:1,1:20:1:30.3:1:1:0:60:76:0.5758:0:1.1 -6 20488897 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTTATTTTCCCCCCCA;RSEQ=TGAGATGGGGAGAGGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22:1:33.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 20490321 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17179;SOR=Inf;LSEQ=TACATGCTTTTTTCTAACAG;RSEQ=AACATATACATTCTTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:187,3:0:1,0:22.5:1:32.4:1:1:0:60:62.333:1:0:0.1 0/1:135:2:1,1:126,7:0.0148:2,2:16.5:1:27.5:1:0.11542:16.9034:60:4:0.0152:0:1 -6 20490390 . T G 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=Inf;LSEQ=TTTTGTTTCCATCAATGTTT;RSEQ=CTTTTCAGACTTGGCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:681:0:0,0:454,227:0:2,0:25.4:1:30:1:1:0:60:96.286:1:0:0.1 0/1:612:23:15,8:371,218:0.0376:2,2:21.2:1:31.6:1:1:1.10:60:46:0.0383:0:1.1 -6 22054082 . AGTG A 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.04336;SOR=Inf;LSEQ=TAAAATTAGAGGATGACAGC;RSEQ=GTGGTGGTGGTGGTGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:0:2,0:25.5:1:32:1:1:0:60:48:1:0:0.1 0/1:44:8:5,3:21,15:0.1818:2,2:30:1:32.5:1:1:1.19:60:16:0.186:0:0.3 -6 22054141 . G GGCCCTTTCATCTATTTCTTCACTATCTCCC 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14132;SOR=0;LSEQ=TTTGTCTTCTTCCTTTTCCT;RSEQ=ATTAGCTTGATAGATTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:9,13:0.0833:2,2:22:1:30.1:1:1:1.42:60:4:0.087:0.0833:0 0/0:39:0:0,0:16,23:0:2,0:22.1:1:30.3:1:1:0:60:18.5:1:0:0.3 -6 22054191 . G T 94 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02374;SOR=11.25228;LSEQ=GGCATTTTCCACATCAGGCT;RSEQ=TAGTTCTTTATTTTTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:35:1:30.5:1:1:0:60:4:0.25:0:1 1/1:11:9:0,9:0,2:0.8182:0,0:27.9:1:29.9:1:1:0:60:18:0.8182:0:1.9 -6 23515364 . G A 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29644;SOR=0;LSEQ=AAAACTTTAGTCAGGTTTCT;RSEQ=AACCTTCTCCTAGGTCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:5,2:12,7:0.2692:2,2:22.7:1:27:1:1:1.44:60:14:0.2692:0:1 0/0:6:0:0,0:4,2:0:2,0:26.7:1:30.8:1:1:0:60:12:1:0:0 -6 25092335 . A G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2031;SOR=3.82314;LSEQ=GTAAGACTCAAATGCTCTTA;RSEQ=ATGATAGATGATAGGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:7,0:0.4615:0,0:27.5:1:33.2:1:1:0:60:12:0.4615:0:1.2 1/0:9:7:7,0:2,0:0.7778:0,0:29.1:1:31.4:1:1:0:60:14:0.7778:0:1 -6 25092425 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAGTCTATATTAGCAAAAC;RSEQ=GCTTCATGTCACTAACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:34:25,9:36,4:0.4595:2,2:23.4:1:31.1:1:0.07485:3.18828:60:68:0.4595:0:1.8 1/1:58:58:54,4:0,0:1:0,2:23.4:1:30.3:1:1:0:60:57:1:0:1.9 -6 25092465 . C T 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGTATACAGCTGGTTAT;RSEQ=GCTATCTGAAGTACTATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:117,44:0:2,0:23.8:1:31.2:1:1:0:60:79.5:1:0:0.8 0/1:129:30:21,9:74,25:0.2326:2,2:24.3:1:29.6:1:0.63955:1.26621:60:60:0.2362:0:1.6 -6 25092466 . G A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.07476;LSEQ=AATGTATACAGCTGGTTATC;RSEQ=CTATCTGAAGTACTATTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:67:47,20:71,27:0.4061:2,2:25.9:1:30.2:1:0.86075:1.11822:60:134:0.4061:0:1.8 1/0:133:98:72,26:24,11:0.7368:2,2:25.1:1:29.3:1:0.66124:1.27:60:48:0.7442:0:1.9 -6 25092479 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19557;SOR=Inf;LSEQ=GGTTATCGCTATCTGAAGTA;RSEQ=TATTAGTAATGAGACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:141,69:0:2,0:23.3:1:32.2:1:1:0:60:420:1:0:0.7 0/1:167:2:1,1:107,58:0.012:2,2:9:1:28.5:1:1:1.83773:60:4:0.0122:0:2.5 -6 25092539 . A C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.88557;LSEQ=GGTGAGGAAATAAATGTGAG;RSEQ=TGTTTCTCATTGTCATATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:110:51,59:100,104:0.3503:2,2:26.1:1:31.6:1:0.72266:1.11199:60:54:0.3462:0:1.3 1/0:295:214:94,120:39,42:0.7254:2,2:28.3:1:31.8:1:0.51591:1.18472:60:70.333:0.7301:0:1.4 -6 25092612 . GT G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.5076;SOR=0;LSEQ=TTTATAAAAAACTGTCAAAA;RSEQ=TTTTCTCTTTTTCATACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:28,86:0.0171:2,2:44.5:1:30:1:0.43913:3.04:60:4:0.0171:0:0.5 0/0:88:0:0,0:15,73:0:2,0:22.6:1:29.7:1:1:0:60:43:1:0:0.4 -6 25261412 . CA C 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.13563;SOR=0;LSEQ=AGAAGCAAGAAAATGTGACC;RSEQ=AAAACAAAACCAGCCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:4:2,2:119,86:0.0191:2,2:28.8:1:30.8:1:1:1.38152:60:8:0.0194:0:0.3 0/0:161:0:0,0:98,63:0:2,0:24.1:1:29.7:1:1:0:60:52.667:1:0:0.1 -6 25261601 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22407;SOR=Inf;LSEQ=ATTGCAGACATCAAGGGAAG;RSEQ=GGTACTGTTCAAAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:100,73:0:2,0:22.2:1:31.1:1:1:0:59.9:85.5:1:0:0.3 0/1:156:2:1,1:91,63:0.0128:2,2:32:1:31.5:1:1:1.44094:60:4:0.0129:0:1 -6 25261662 . A T 187 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCAAAACTGGAAGAGTCTAC;RSEQ=ATTTTACCCAGCATGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:84:38,46:64,76:0.375:2,2:26.6:1:29.4:1:1:1.01931:59.7:83:0.3739:0:1.1 0/0:227:0:0,0:106,121:0:2,0:28.3:1:29.4:1:1:0:60:74.667:1:0:0.1 -6 25261697 . C A 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.89575;LSEQ=GCTTTTGGCATTGTTTTAAA;RSEQ=AAACAAGTTAAGGGCAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:1:1,0:40,93:0.0075:2,0:1:0:25:0:0.30597:0:60:2:0.0075:0:2 0/1:142:2:1,1:51,89:0.0141:2,2:13:1:25.5:1:1:1.74:60:4:0.0141:0:1 -6 25261964 . TAAAAT G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=8;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAATAGGTGTTAAAGAAA;RSEQ=AAAAGACCTCTGGACTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:21:1:32:0:1:0:60:4:0.2857:0:0.5 0/0:1:0:0,0:0,1:0:0,0:24:0:31:0:1:0:60:2:1:0:0 -6 25606558 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15114;SOR=Inf;LSEQ=AGGTGGCTTCCCAGAGCCAG;RSEQ=TGGATCAGACTCTGCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:125,22:0:2,0:25.7:1:32:1:1:0:60:146:1:0:0.1 0/1:94:2:1,1:73,19:0.0213:2,2:11.5:1:28:1:0.38206:3.77038:60:4:0.0215:0:1 -6 25606644 . G T 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38546;SOR=0.30317;LSEQ=GGGGATCACAAGAAACCTAT;RSEQ=CAAAGCTGTGAAAGTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:4:2,2:202,177:0.0104:2,2:22.3:1:30.5:1:1:1.14085:60:8:0.0105:0:1.3 0/0:314:1:0,1:164,149:0.0032:2,0:1:0:27:0:0.47771:0:60:2:0.0032:0:1 -6 25606672 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13043;LSEQ=GTGAAAGTGATGAGAGCTGA;RSEQ=GGATTCTTTTATTTAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:128:55,73:127,121:0.3404:2,2:24.3:1:29.9:1:0.15679:1.39184:60:41.667:0.3369:0:1.9 0/1:302:19:9,10:131,150:0.0629:2,2:16:1:28.7:1:1:1.03:60:18:0.0608:0:2 -6 25606678 . C T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.67074;SOR=0.91772;LSEQ=GTGATGAGAGCTGACGGATT;RSEQ=TTTTATTTAATGCAGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:119:51,68:125,120:0.326:2,2:25.1:1:29.9:1:0.14813:1.38762:60:118:0.3278:0:2 0/1:283:87:44,43:86,109:0.3074:2,2:24.6:1:29.3:1:0.36552:1.30:60:28:0.3:0:1.3 -6 25727517 . G A 83 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12159;SOR=6.31813;LSEQ=ACTAAGTACACCAGCTCCAA;RSEQ=TAAGCCTGCTAAGTAAACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:9,16:0.0385:2,0:36:0:31:0:1:0:60:2:0.0385:0:1 0/1:34:7:4,3:12,15:0.2059:2,2:34.1:1:29.6:1:0.68146:1.64:60:14:0.2059:0:1.3 -6 25727527 . T A 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27677;SOR=0.36841;LSEQ=CCAGCTCCAAGTAAGCCTGC;RSEQ=AAGTAAACGTCATTTCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:1,5:8,13:0.2222:2,2:28:1:31:1:0.62785:2.96583:60:12:0.2222:0:1.2 0/1:32:3:1,2:13,16:0.0938:2,2:37.7:1:29.3:1:1:1.60139:60:6:0.0938:0:1 -6 25732302 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTTTGCGGCATCTCTT;RSEQ=CGCTTTTTGTCCTCCTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:36.5:1:32.5:1:1:0:60:4:0.3333:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 25732331 . A G 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCTCCTTCGAGTTTTAGC;RSEQ=ACTGCCTTCTTAAAGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:8.7:1:29.3:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 25795460 . A T 23 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51342;SOR=0;LSEQ=CAACCAGGTAAACAAAGGAG;RSEQ=ATGGAGGAAATTCTACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:103,39:0.0139:2,2:20.5:1:23.5:1:0.4798:2.62044:60:4:0.0139:0:4.5 0/0:101:0:0,0:75,26:0:2,0:24.5:1:28.5:1:1:0:60:32.667:1:0:0.1 -6 25795577 . A T 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00301;SOR=1.9361;LSEQ=TTGATATTTTGGAAGGAGAA;RSEQ=AAAAGCAGAAAAAGAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:41:15,26:107,134:0.1454:2,2:26.6:1:28.8:1:0.39658:1.38251:60:40:0.1429:0:1.1 0/1:250:62:28,34:83,105:0.248:2,2:24.4:1:28.5:1:1:1.04:60:124:0.25:0:1 -6 25795612 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.50043;SOR=0;LSEQ=AATATAGCATGTAAATAGAA;RSEQ=AAATGAACACATTTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:60,133:0.0103:2,2:30.5:1:31:1:0.52889:2.21:60:4:0.0104:0:1 0/0:173:0:0,0:61,112:0:2,0:25.9:1:30.1:1:1:0:60:172:1:0:0.3 -6 25795614 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.222;SOR=Inf;LSEQ=TATAGCATGTAAATAGAAAA;RSEQ=ATGAACACATTTTCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:60,128:0:2,0:24.4:1:30.4:1:1:0:60:376:1:0:0.3 0/1:168:2:1,1:59,107:0.0119:2,2:10.5:1:27:1:1:1.81:60:4:0.0119:0:1 -6 25795682 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51489;SOR=0;LSEQ=ATTTAAAATATTCTACAAAT;RSEQ=TAAATTGCTAGAGTCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:5,50:0.0351:2,2:6.5:1:28:1:0.20113:9.22:60:4:0.0357:0:1.5 0/0:38:0:0,0:4,34:0:2,0:20:1:32:1:1:0:60:76:1:0:0.1 -6 26020431 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGCTGAGGCGGGAAGATC;RSEQ=TTTGAGCCCAAGTTTAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:13,0:0.2353:1,0:24.8:1:30.3:1:1:0:60:8:0.2353:0:1 0/0:3:0:0,0:2,1:0:2,0:17.3:1:29.7:1:1:0:60:6:1:0:0.3 -6 26021044 . C T 219 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=94.9669;LSEQ=GGGCTATTTGAGGACACTAA;RSEQ=CTGTGCGCCATCCACGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2984:2:0,2:1566,1414:7e-04:2,0:1:0:28:1:0.2254:0:60:4:7e-04:0:1 0/1:3038:182:95,87:1486,1364:0.0599:2,2:21.6:1:29.3:1:1:1.00:60:90:0.0598:0:1.2 -6 26021124 . C T 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.31655;LSEQ=CCGCATCCGCGGAGAGAGGG;RSEQ=GTGATTACTGTGGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2521:4:0,4:1031,1480:0.0016:2,0:1:0:26.8:1:0.14917:0:60:8:0.0016:0:1 0/1:2407:121:54,67:1007,1275:0.0503:2,2:25.9:1:29.5:1:0.92539:1.02:60:120:0.0505:0:1.2 -6 26021147 . C T 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=87.75195;LSEQ=GATTACTGTGGTCTCTCTGA;RSEQ=GGTCCAAGCAAAGGCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1994:1:0,1:680,1313:5e-04:2,0:12:0:31:0:1:0:60:2:5e-04:0:1 0/1:1777:75:23,52:625,1074:0.0422:2,2:22.8:1:29.8:1:0.32737:1.31547:60:150:0.0424:0:1.1 -6 26021327 . G A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11453;SOR=2.09587;LSEQ=GCCTGTAATTCAAGCACTTT;RSEQ=AGAGGCTGAGGCGGGCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:21:0,21:0,56:0.2692:1,1:25.6:1:30.1:1:1:0:60:20:0.2597:0:1 0/1:32:14:0,14:0,18:0.4375:1,1:15.3:1:30.1:1:1:0:60:28:0.4375:0:1.3 -6 26021456 . C G 51 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAGCGCTTGTAATCCCAG;RSEQ=TACACTCTGAAGGCTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:0.2727:0,0:23.3:1:32.3:1:1:0:60:6:0.2727:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 26026599 . G C 245 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.71688;SOR=0.95266;LSEQ=TAACCGCCAGTCCTACTCCA;RSEQ=AGAAGGGGGAGGTGACGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:193:74,119:211,324:0.2647:2,2:26.2:1:32.3:1:0.79713:1.0472:60:386:0.2673:0:1.2 0/1:693:177:74,103:215,298:0.2554:2,2:25.9:1:31.2:1:1:1.00421:60:176:0.2577:0:1.2 -6 26031613 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTAATCATAGCAAGCTA;RSEQ=AGGCCTGAATGATAGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:25,0:0.0741:1,0:9:1:32:1:1:0:60:4:0.0741:0:1.5 0/0:2:0:0,0:1,1:0:2,0:15.5:1:31:1:1:0:60:4:1:0:0 -6 26031720 . C G 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00441;SOR=0;LSEQ=AAACCGTTATTTCTGTTAAT;RSEQ=AACTTTAAGACCATAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:14:14,0:61,0:0.1842:1,1:22.7:1:31.2:1:1:0:60:13:0.1757:0:1.1 0/0:36:0:0,0:36,0:0:1,0:24.4:1:31.4:1:1:0:60:35:1:0:0.2 -6 26031855 . C T 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGCCTTTGGGTTTTAAGA;RSEQ=TGATGAAAAAGTGACTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:791:0:0,0:594,197:0:2,0:23.3:1:32:1:1:0:60:130.833:1:0:0.4 0/1:771:37:26,11:540,194:0.048:2,2:22:1:29.5:1:0.70322:1.17735:60:36:0.0471:0:2.2 -6 26031868 . G A 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.08156;LSEQ=TTTAAGACTGATGAAAAAGT;RSEQ=ACTTTACATTTACGCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1005:362:250,112:456,187:0.3602:2,2:23.7:1:28.6:1:0.56547:1.09235:60:180:0.3607:0:1.1 1/0:1005:778:535,243:159,63:0.7741:2,2:23.6:1:28.4:1:0.45762:1.14614:60:128.667:0.7751:0:1.2 -6 26032428 . T A 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.67499;SOR=1.71993;LSEQ=GCCCTTCTTGGATTGGTCCA;RSEQ=CTCTGTGCCTGGTTGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:5:0,5:2,50:0.0877:1,0:24.8:1:30.4:1:1:0:60:10:0.0877:0:1 0/1:21:3:0,3:3,15:0.1429:2,0:33:1:31:1:1:0:60:6:0.1579:0:1 -6 26032847 . G C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTTATCACGCCGCTGCACT;RSEQ=CAGCTTGGGCGAGAGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:11:0:33:0:1:0:60:2:0.5:0:1 1/1:2:2:1,1:0,0:1:0,2:36.5:1:30.5:1:1:0:60:4:1:0:2 -6 26036092 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CACTCCAGCCTGGGCAAGAG;RSEQ=GAAACTCCATTTCAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:14.3:1:30.7:1:1:0:60:6:0.375:0:1.7 0/0:8:0:0,0:6,2:0:2,0:23.4:1:28.4:1:1:0:60:7:1:0:0.6 -6 26036476 . T C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=8.68466;LSEQ=AGCAGTGCACGTTCTGCATA;RSEQ=AAAATAAAGATTTTGAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:50:8,42:14,91:0.3226:2,2:20.9:1:32.2:1:0.63227:1.24:60:100:0.3247:0:1 1/1:119:96:14,82:3,20:0.8067:2,2:23.9:1:31.4:1:1:1.14:60:95:0.8051:0:1.1 -6 26043661 . C T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.54753;LSEQ=GCCAGGCGAGAAGCCTCGCC;RSEQ=GCGATGCGCTCGAAGATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:0,2:135,64:0.01:2,0:22.5:1:27.5:1:0.10672:0:60:4:0.0101:0:1 0/0:183:1:0,1:120,62:0.0055:2,0:34:0:32:0:0.34426:0:60:2:0.0056:0:1 -6 26043670 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11619;SOR=Inf;LSEQ=GAAGCCTCGCCCGCGATGCG;RSEQ=TCGAAGATGTCGTTGACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:148,86:0:2,0:25.5:1:31.7:1:1:0:59.9:38:1:0:0.1 0/1:224:3:1,2:139,82:0.0134:2,2:9.7:1:28.3:1:0.55778:3.37113:60:6:0.0135:0:1 -6 26043776 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22904;SOR=Inf;LSEQ=TGTACACATAGATAGAATAG;RSEQ=TCTCCTTGCGGCTGCGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:91,122:0:2,0:24.7:1:32.1:1:1:0:60:70:1:0:0.1 0/1:196:2:1,1:73,121:0.0102:2,2:19.5:1:30.5:1:1:1.65:60:4:0.0104:0:1.5 -6 26043834 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16104;SOR=Inf;LSEQ=CTTCTGCGCCTTAGTGATAG;RSEQ=CTTCTTAGAACCCTTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:64,74:0:2,0:25.6:1:31.3:1:1:0:60:45:1:0:0 0/1:93:2:1,1:34,57:0.0215:2,2:17:1:27.5:1:1:1.67:60:4:0.022:0:1 -6 26044064 . G A 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.22581;LSEQ=GGTGGGGTTTATGCAAATAT;RSEQ=GAATTTATGTTATCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:673:53:17,36:261,357:0.0788:2,2:25.9:1:30:1:0.19064:1.54722:60:52:0.0783:0:1.2 0/1:674:179:74,105:216,277:0.2656:2,2:24.4:1:29.3:1:0.59763:1.10628:60:88.5:0.2662:0:1.1 -6 26044155 . A C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0435;SOR=Inf;LSEQ=CAGCCTTGCAGTTTGTATAA;RSEQ=AGGATTTGTTCAGGCGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:15,145:0:2,0:22.9:1:30.2:1:1:0:60:52.333:1:0:0.1 0/1:136:4:0,4:18,114:0.0294:2,0:16:1:32.3:1:1:0:60:8:0.0296:0:2 -6 26044174 . A G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03679;SOR=Inf;LSEQ=AAAGGATTTGTTCAGGCGCC;RSEQ=TTCCAGCTTGCTTGTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:6,105:0:2,0:24.4:1:31.1:1:1:0:60:110:1:0:0.1 0/1:88:4:0,4:6,78:0.0455:2,0:21.5:1:31.8:1:1:0:60:8:0.0465:0:1.8 -6 26044729 . T C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTTTTGAGACAGTCTAG;RSEQ=TCTGTCACCCAGGCTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:18.3:1:33.7:1:1:0:60:6:0.4286:0:1.3 0/0:1:0:0,0:1,0:0:0,0:26:0:32:0:1:0:60:2:1:0:0 -6 26044812 . T A 49 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.59564;LSEQ=CTTCACGCGGTTCTCATGCC;RSEQ=CAGCCTCCTGTGTACTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:21.3:1:31.3:1:1:0:60:6:0.375:0:1.3 1/0:4:2:2,0:2,0:0.5:0,0:17:1:23:1:1:0:60:1:0.3333:0:3.5 -6 26044956 . C CA 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00394;SOR=Inf;LSEQ=ATCGTCCCATCTCGCCCTCC;RSEQ=AAAATGCTGGGATTACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:154,40:0:2,0:22.6:1:31:1:1:0:60:96:1:0:0.1 0/1:164:7:6,1:119,37:0.0427:2,2:20.7:1:30.1:1:1:1.86:60:14:0.0427:0.0122:0.3 -6 26044967 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21427;SOR=Inf;LSEQ=TCGCCCTCCCAAAATGCTGG;RSEQ=ATTACAGGCGTGAGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:166,62:0:2,0:23.4:1:30.9:1:1:0:60:56:1:0:0.1 0/1:197:2:1,1:140,55:0.0102:2,2:8.5:1:27.5:1:0.48876:2.53163:60:4:0.0104:0:1 -6 26044975 . G T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02539;SOR=Inf;LSEQ=CCAAAATGCTGGGATTACAG;RSEQ=CGTGAGCCACCGCCCCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:179,77:0:2,0:24.3:1:30.8:1:1:0:60:31:1:0:0.1 0/1:238:5:1,4:161,72:0.021:2,2:9.4:1:28.2:1:0.0371:8.85817:60:10:0.0214:0:1 -6 26044987 . G GC 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00063;SOR=Inf;LSEQ=GATTACAGGCGTGAGCCACC;RSEQ=CCCCCCTAGCCTAATGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:212,106:0:2,0:24.8:1:30.4:1:1:0:60:78.5:0.9968:0:0.1 0/1:297:10:6,4:181,104:0.0337:2,2:21.1:1:31.2:1:1:1.15965:60:20:0.0342:0.0067:0.1 -6 26045737 . C G 193 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTAAGAGCGCTCCGGCCAC;RSEQ=GGTGGCGTGAAGAAACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2298:0:0,0:1180,1114:0:2,0:24.4:1:30.4:1:1:0:60:98.739:0.9987:0:0.1 0/1:2095:87:46,41:985,1014:0.0415:2,2:22.8:1:30:1:0.51376:1.15:60:174:0.0419:0:1.1 -6 26045905 . G C 219 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCGTTTCCAGAGCTCTGC;RSEQ=GTGATGGCGCTGCAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2652:0:0,0:1338,1312:0:2,0:24.9:1:30.4:1:1:0:59.9:84.484:0.9992:0:0.4 0/1:2554:175:86,89:1175,1201:0.0685:2,2:23.8:1:29.4:1:0.93778:1.01248:59.9:42.75:0.0679:0:1.9 -6 26045929 . T C 335 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.5947;LSEQ=ATGGCGCTGCAGGAGGCTTG;RSEQ=GAGGCCTACCTGGTGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2645:923:454,469:860,860:0.349:2,2:26.1:1:30.8:1:0.71347:1.03304:59.9:60.533:0.3458:0:1.2 1/0:2436:1899:933,966:271,255:0.7796:2,2:25.2:1:30.8:1:0.34924:1.10029:59.9:98.947:0.7804:0:1.2 -6 26046158 . T C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12612;SOR=1.56716;LSEQ=ATGTTAGTTTCCAGGAGATA;RSEQ=AAAGGTGATAACTACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:31:0,31:4,247:0.1099:1,1:22.4:1:32.7:1:1:0:60:62:0.1111:0:1.1 0/1:191:31:1,30:4,156:0.1623:1,1:24.5:1:32.2:1:0.59173:1.30:60:62:0.164:0:1 -6 26046265 . T TA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTACTGTTTTGCCCTTGT;RSEQ=AAAAAATTCCTAGGGGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:0,2:2,54:0.0345:1,0:22:1:31.5:1:1:0:60:4:0.0345:0:0 0/0:9:0:0,0:0,9:0:0,0:22.6:1:29.3:1:1:0:60:18:1:0:0.1 -6 26046565 . G A 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATAGATTTATGTAACAA;RSEQ=TACACAAGACTTGCGTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:26:1:26.7:1:1:0:60:2:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 26049819 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACACACCAGATTTCAAAGA;RSEQ=CTAGTAAAATAACAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:32.5:1:31:1:1:0:60:4:0.25:0:1 0/0:2:0:0,0:2,0:0:0,0:18:1:30.5:1:1:0:60:4:1:0:0 -6 26049924 . T C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68166;SOR=1.95409;LSEQ=ATTAAAATAGATTTCTTTTT;RSEQ=CACTTTTTAAAATGTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:10,0:12,0:0.4545:0,0:24.2:1:31.6:1:1:0:60:20:0.4545:0:1 1/0:8:5:5,0:3,0:0.625:0,0:23.2:1:31.4:1:1:0:60:10:0.625:0:1 -6 26050295 . GT CC 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.23946;LSEQ=TGTAGTTTTCATCAGTATGT;RSEQ=ATGTTCAAATGGAGATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:48:1,47:3,85:0.3453:1,1:23.7:1:32.3:1:1:1.65316:60:96:0.3478:0.0288:0.9 1/0:117:81:6,75:2,29:0.6923:2,2:19.6:1:31.4:1:1:1.16:60:80:0.6957:0.1282:0.9 -6 26055865 . G GTC 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.56984;SOR=0.39516;LSEQ=CCAACCCCGTCACCCAATTC;RSEQ=TCTGATACCTCAGTAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:26:25,1:2,0:0.9286:0,1:29.7:1:30.4:1:1:0:60:52:0.9286:0.0357:0 1/1:12:10:9,1:2,0:0.8333:0,2:21.1:1:30.6:1:1:0:60:20:0.8333:0.25:0.6 -6 26055962 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59527;SOR=2.37478;LSEQ=TTATCCAGCTCTTTTATTGA;RSEQ=ATCAGTGGTGGCTCTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:1:1,0:158,36:0.0051:2,0:22:0:14:0:1:0:60:0:0:0:1 0/1:165:2:1,1:127,36:0.0121:2,2:12:1:28:1:0.39926:3.49328:60:4:0.0123:0:1 -6 26055968 . TG T 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2239;SOR=Inf;LSEQ=AGCTCTTTTATTGAGATCAG;RSEQ=GTGGCTCTGAAAAGAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:174,47:0:2,0:25.5:1:31.8:1:1:0:60:54.25:1:0:0.1 0/1:199:2:1,1:143,50:0.0101:2,2:19:1:33.5:1:0.45567:2.84171:60:4:0.0104:0:0.5 -6 26056065 . C T 66 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21733;SOR=0.20204;LSEQ=CTTGACAACCTTGGGCTTAG;RSEQ=GGCCTTGGGCTTCACAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:5:2,3:279,183:0.0107:2,2:22.8:1:28.8:1:0.39148:2.28274:60:10:0.0109:0:1 0/0:459:1:0,1:261,197:0.0022:2,0:1:0:25:0:0.43137:0:60:2:0.0022:0:2 -6 26056072 . G C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.96444;LSEQ=ACCTTGGGCTTAGCGGCCTT;RSEQ=GGCTTCACAGCCTTAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:23:10,13:282,191:0.0464:2,2:29.3:1:31.1:1:0.13399:1.91682:60:46:0.0481:0:1 0/1:465:130:74,56:192,141:0.2796:2,2:26.3:1:30:1:0.91688:1.03043:60:64:0.2783:0:1.1 -6 26056399 . G A 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGTGCCCTTGCTCACCAG;RSEQ=CTCTTGAGACCAAGTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:0:0,0:230,362:0:2,0:27.2:1:31.8:1:1:0:60:64.778:0.9966:0:0.1 0/1:567:26:12,14:238,303:0.0459:2,2:22.8:1:29.4:1:0.84232:1.09:60:52:0.0465:0:1.3 -6 26056477 . A C 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAACGCTTTTTTCAGAGC;RSEQ=GCCAGAGAAACTCCGCTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:162,187:0:2,0:23.9:1:30.3:1:1:0:60:57.167:1:0:0.2 0/1:316:17:12,5:130,169:0.0538:2,2:25.5:1:29.7:1:0.04262:3.11:60:34:0.054:0:1.5 -6 26056541 . G T 50 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.05602;SOR=0;LSEQ=TGGTGATGAGCTCTGACACC;RSEQ=GGGGACCAGACGCCTTACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:4:2,2:145,186:0.0119:2,2:18.3:1:25.3:1:1:1.28:60:3:0.0091:0:1.8 0/0:352:0:0,0:164,187:0:2,0:23.7:1:29.4:1:1:0:60:57.5:1:0:0.8 -6 26056549 . A G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.66326;LSEQ=AGCTCTGACACCGGGGGACC;RSEQ=GACGCCTTACGAGGCGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:107:48,59:102,132:0.3129:2,2:24.7:1:30.3:1:0.90646:1.05:60:52.5:0.3144:0:1.1 1/0:355:256:121,135:41,58:0.7211:2,2:24.9:1:29.2:1:0.34344:1.27:60:84.333:0.7208:0:1.2 -6 26056637 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=GAGGCGCGGCAGCGGGAGCG;RSEQ=CAGGAGCAGTCTCGGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:54,134:0.0105:2,2:25:1:30.5:1:0.49624:2.47:60:4:0.0106:0:1 0/0:176:0:0,0:60,116:0:2,0:22.7:1:31.2:1:1:0:60:175:1:0:0.3 -6 26056646 . G A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10606;SOR=Inf;LSEQ=CAGCGGGAGCGGCAGGAGCA;RSEQ=TCTCGGACATGTTGAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:43,125:0:2,0:24.8:1:31.7:1:1:0:60:55:1:0:0.1 0/1:152:3:3,0:49,100:0.0197:2,0:14:1:21.7:1:0.03852:0:60:2:0.0134:0:1.7 -6 26056708 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00026;SOR=7.60176;LSEQ=AAAGCGCCGATGAAGCAGCG;RSEQ=CTGGGCAGGGCCGCTGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:4:0,4:6,54:0.0625:2,0:28:1:30.8:1:1:0:60:8:0.0656:0:1 0/1:44:15:3,12:8,21:0.3409:2,2:29.4:1:28.7:1:0.72221:1.50978:60:14:0.3333:0:1.1 -6 26061649 . CT C 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0275;SOR=8.31523;LSEQ=CCTGGCTTCAGCCCCATAAA;RSEQ=TTTTTTTAACATATAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:1:0,1:181,420:0.0017:2,0:17:0:34:0:1:0:60:2:0.0017:0:0 0/1:513:7:3,4:160,345:0.0136:2,2:16.6:1:30.4:1:0.68483:1.62:60:14:0.0139:0.0039:0.3 -6 26061769 . G C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00056;SOR=6.53198;LSEQ=CTCACCTCAAGGGCTGAGAC;RSEQ=AAAGTTACTGCATCTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:21:1,20:0,37:0.3621:1,1:25.6:1:32.4:1:0.36207:0:60:42:0.3621:0:1.1 1/0:24:19:0,19:0,5:0.7917:0,1:19.3:1:31.5:1:1:0:60:18:0.7826:0:1.1 -6 26065976 . AAC A 84 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.20911;SOR=0.3918;LSEQ=TTGTAAACCACATTCCCTTA;RSEQ=ACACACACACCTCAAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:684:7:5,2:454,222:0.0102:2,2:25.9:1:30.1:1:1:1.22:60:14:0.0103:0.0029:0 0/0:744:3:3,0:446,295:0.004:2,0:13.3:1:28.1:1:0.28117:0:60:6:0.0041:0.0027:0 -6 26066088 . TA T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.85907;SOR=1.09139;LSEQ=TTGTGTATTAATCTGTGAAC;RSEQ=AAAAAAAATTTCATTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:732:16:8,8:251,464:0.0219:2,2:27.6:1:30.6:1:0.28976:1.85:60:32:0.0221:0.0014:0.1 0/1:672:16:6,10:264,392:0.0238:2,2:25.1:1:29.3:1:1:1.12229:60:15:0.0226:0.003:0.3 -6 26066198 . A G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12649;SOR=1.7094;LSEQ=TTAACTTTTAGATTTTTCAA;RSEQ=GCTAGCAGAACTGCTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:22:1,21:3,71:0.2292:1,1:23.8:1:31.6:1:1:1.13:60:44:0.2292:0:1 0/1:77:26:0,26:1,50:0.3377:1,1:21.2:1:30.3:1:1:0:60:52:0.3377:0:1 -6 26123539 . G C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACAACGAATTGACCCCAAA;RSEQ=CCATTTTTAATGGCTGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:29.3:1:32.7:1:1:0:60:6:0.75:0:1 1/1:3:3:2,1:0,0:1:0,2:25:1:32.7:1:1:0:60:6:1:0:1.7 -6 26123629 . T C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19794;SOR=2.68522;LSEQ=CCACCCCTCTCCAGTTCCTA;RSEQ=ATTCTAATACCCCTCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:17:17,0:10,0:0.6296:0,1:16.8:1:32.1:1:1:0:60:34:0.6538:0:1.1 1/1:17:14:14,0:3,0:0.8235:0,1:23.8:1:30.3:1:1:0:60:13:0.8125:0:1.1 -6 26123737 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09537;SOR=0;LSEQ=TTGGGGTTAGGTGTTAAGAC;RSEQ=CTTACTTGGAATGTTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:153,92:0.012:2,2:32.7:1:28:1:0.55906:3.30948:60:6:0.0124:0:1 0/0:296:0:0,0:178,116:0:2,0:26:1:29.8:1:1:0:60:48:0.9931:0:0.2 -6 26123802 . C A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12666;SOR=Inf;LSEQ=CTTGGTGCCCTCCGACACGG;RSEQ=GTGCTTGGCCAGCTCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:112,156:0:2,0:25.7:1:30.1:1:1:0:59.6:37.286:1:0:0.2 0/1:304:4:3,1:131,168:0.0132:2,2:30.5:1:24.8:1:0.32501:3.83:60:3:0.0102:0:1.3 -6 26123809 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12409;SOR=Inf;LSEQ=CCCTCCGACACGGCGTGCTT;RSEQ=GCCAGCTCTCCGGGAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:102,142:0:2,0:24.3:1:31:1:1:0:59.3:39.667:0.9958:0:0.2 0/1:261:4:3,1:108,149:0.0153:2,2:18.3:1:25.3:1:0.31503:4.12:60:8:0.0157:0:1 -6 26123827 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24801;SOR=0;LSEQ=TTGGCCAGCTCTCCGGGAAG;RSEQ=AGCAGGCGCACGGCCGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:69,117:0.0159:2,2:24.3:1:22.7:1:1:1.17852:60:2:0.0108:0:1.3 0/0:189:0:0,0:69,120:0:2,0:23.3:1:31.5:1:1:0:59.6:62:1:0:0.1 -6 26123834 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2417;SOR=Inf;LSEQ=GCTCTCCGGGAAGCAGCAGG;RSEQ=GCACGGCCGTCTGGATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:58,109:0:2,0:20.5:1:29.9:1:1:0:58.7:32.4:1:0:0.2 0/1:162:2:1,1:50,110:0.0123:2,2:15.5:1:29:1:0.53186:2.19:60:4:0.0126:0:1 -6 26123835 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23851;SOR=Inf;LSEQ=CTCTCCGGGAAGCAGCAGGC;RSEQ=CACGGCCGTCTGGATCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:59,106:0:2,0:20.4:1:30.4:1:1:0:58.7:22.571:1:0:0.2 0/1:158:2:1,1:48,108:0.0127:2,2:28:1:31.5:1:0.52544:2.24:60:4:0.013:0:1 -6 26124018 . A T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59962;SOR=2.30974;LSEQ=CACCTTGTACACGTACACAG;RSEQ=GTAACTCTCCTTGCGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:0,1:111,95:0.0048:2,0:1:0:27:0:0.46377:0:60:2:0.005:0:1 0/1:180:2:1,1:106,72:0.0111:2,2:17:1:27:1:1:1.46895:60:4:0.0112:0:1 -6 26124032 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50179;SOR=0;LSEQ=ACACAGAGTAACTCTCCTTG;RSEQ=GGCTGCGCTTGCGCTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:100,95:0.0102:2,2:23.5:1:29.5:1:1:1.05238:60:4:0.0105:0:1 0/0:168:0:0,0:98,70:0:2,0:27:1:31.1:1:1:0:60:336:1:0:0.1 -6 26124046 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49888;SOR=0;LSEQ=TCCTTGCGGCTGCGCTTGCG;RSEQ=TTCTTGCCATCTTTCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:92,96:0.0105:2,2:20.5:1:29.5:1:1:1.04:60:4:0.0108:0:1 0/0:182:0:0,0:94,88:0:2,0:24.7:1:31.7:1:1:0:60:90:1:0:0.1 -6 26124243 . G A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00386;SOR=0.0798;LSEQ=AGTTAATTGGAAGACAAACT;RSEQ=CACAGTTGTCATCCGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:15:0,15:1,5:0.7143:2,1:25.7:1:30.8:1:0.28571:0:60:30:0.7143:0:1 0/1:13:2:0,2:0,11:0.1538:0,0:23:1:31.5:1:1:0:60:4:0.1538:0:1 -6 26124303 . T C 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02424;SOR=Inf;LSEQ=ATGAAAGTACAGCTTTTCTA;RSEQ=TGGCTATCTGACTAGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:18.7:1:30.6:1:1:0:60:14:1:0:0.3 1/0:4:3:0,3:0,1:0.75:0,0:12.7:1:33.7:1:1:0:60:6:0.75:0:1 -6 26127759 . A G 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00027;SOR=0.56507;LSEQ=AGCATAGAACTTGGCATACA;RSEQ=GAGACACTTGGCTGTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:344:217:163,54:95,32:0.6308:2,2:24.2:1:31.6:1:1:1.02:60:107.5:0.6287:0:1.1 0/1:334:164:118,46:119,51:0.491:2,2:24:1:31.4:1:0.71881:1.10:59.9:81:0.4954:0:1.1 -6 26127813 . CT C 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00645;SOR=1.38467;LSEQ=TGAACTGAATGAATCAATGA;RSEQ=TAGGCAGCCAGGAAGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:683:433:232,201:127,121:0.634:2,2:26.4:1:31.8:1:0.57702:1.10:60:143.333:0.6333:0.101:0.4 1/0:605:427:224,203:100,78:0.7058:2,2:25.8:1:31:1:0.4217:1.16157:59.9:426:0.7088:0.1041:0.4 -6 26128007 . G GGT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.08452;SOR=Inf;LSEQ=GAGGTGGGTAGATCACCTGA;RSEQ=GTCAGGAGTTTGAGACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:7,104:0:2,0:23:1:31.4:1:1:0:59.6:110:1:0:0 0/1:46:2:0,2:2,42:0.0435:1,0:37:1:31.8:1:1:0:54:4:0.0444:0:0 -6 26128226 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCGACAAAGTGAAACTC;RSEQ=GTCTCAAAAAAAAACCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:10.5:1:28:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 26128632 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCTAAGCAAAGGACATT;RSEQ=CTCGTAGCTCTGTCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:31:1:1:0:60:4:1:0:1.5 -6 26153159 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07848;SOR=Inf;LSEQ=CCAATATATGGTCATATTCA;RSEQ=CATGGATATCTTTTCTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:88,294:0:2,0:22:1:32:1:1:0:60:75.4:1:0:0.1 0/1:287:3:2,1:71,213:0.0105:2,2:18.7:1:27.3:1:0.1602:5.95:60:6:0.0106:0:1 -6 26156918 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50056;SOR=Inf;LSEQ=GTGCAGACCAAGGGCACCGG;RSEQ=GCGTCGGGTTCCTTCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:32,63:0:2,0:27:1:30.2:1:1:0:60:46.5:1:0:0.1 0/1:112:2:1,1:43,67:0.0179:2,2:5.5:1:28.5:1:1:1.55:60:4:0.0187:0:1 -6 26156981 . A G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=GAAGCCAAGCCTAAGGCTAA;RSEQ=AAGGCAGGCGCGGCCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:6,21:0:2,0:23.4:1:30.6:1:1:0:60:54:1:0:0 0/1:28:3:0,3:2,23:0.1071:2,0:27.7:1:31.3:1:1:0:60:6:0.1111:0:1 -6 26158328 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18817;SOR=Inf;LSEQ=TGAATACCGCATCTATAAAT;RSEQ=AACAGGGCCTCGGCGGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:166,20:0:2,0:22.3:1:32.2:1:1:0:60:92:1:0:0.1 0/1:143:2:1,1:118,22:0.014:2,2:23.5:1:25.5:1:0.29867:5.26803:60:4:0.0142:0:1 -6 26158562 . C T 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTCCATCCCGACACCGGCAT;RSEQ=TCTTCCAAGGCAATGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:0:0,0:269,332:0:2,0:26.8:1:31.6:1:1:0:60:65.778:1:0:0.1 0/1:624:65:28,37:252,307:0.1042:2,2:24.8:1:29.6:1:0.79334:1.08458:60:64:0.1032:0:1.2 -6 26158615 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11766;SOR=5.21864;LSEQ=CGTCAACGACATCTTCGAGC;RSEQ=CATCGCAGGCGAGGCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:1:0,1:178,259:0.0023:2,0:7:0:25:0:1:0:47:2:0.0023:0:1 0/1:423:5:2,3:176,240:0.0118:2,2:22.8:1:30:1:1:1.09978:60:10:0.012:0:1 -6 26158685 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24873;SOR=Inf;LSEQ=ATCACCTCCAGGGAGATCCA;RSEQ=ACGGCCGTGCGCCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:159,106:0:2,0:24.2:1:31.6:1:1:0:56.7:65.25:1:0:0.1 0/1:273:3:2,1:165,105:0.011:2,2:13.7:1:24.7:1:1:1.27:56.3:2:0.0074:0:1 -6 26158690 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24903;SOR=Inf;LSEQ=CTCCAGGGAGATCCAGACGG;RSEQ=CGTGCGCCTGCTGCTTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:173,112:0:2,0:23.4:1:31.3:1:1:0:56.9:46.5:1:0:0.1 0/1:297:3:1,2:176,118:0.0101:2,2:20:1:27.7:1:0.56757:2.97198:60:6:0.0102:0:1 -6 26158993 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9643;LSEQ=TAGAAATTGAGTGCTATGGG;RSEQ=ACGTATTAGATCGTTAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:0.1875:1,0:18.3:1:32.3:1:1:0:60:6:0.1875:0:1 0/1:11:2:0,2:0,9:0.1818:0,0:16.5:1:31.5:1:1:0:60:4:0.1818:0:1 -6 26165446 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGGGAATCCGAAATACC;RSEQ=AAATGTCTGTTTTCCACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:38.5:1:29.5:1:1:1.73:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 26172150 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19012;SOR=Inf;LSEQ=TCAACCCTCGCCAAAAACGC;RSEQ=GGCCCCCTCATAGGGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:43,184:0:2,0:24.1:1:30:1:1:0:60:44.4:1:0:0.1 0/1:176:2:1,1:39,134:0.0114:2,2:36.5:1:30.5:1:0.40591:3.41:60:4:0.0116:0:1.5 -6 26172219 . C T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.39779;SOR=2.07787;LSEQ=AGAGCCACACGTTACGCCGC;RSEQ=GCCCCGTTACGCCCATCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:0,3:3,64:0.0429:1,0:16:1:31.7:1:1:0:60:6:0.0441:0:1 0/1:35:3:0,3:1,31:0.0857:1,0:30:1:30.3:1:1:0:60:6:0.0857:0:1 -6 26184082 . C G 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00049;SOR=Inf;LSEQ=GGGCTCCAAGAAGGCCGTGA;RSEQ=CAAGGCGCAGAAGAAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:94,77:0:2,0:24.6:1:30.9:1:1:0:59.3:23.429:1:0:0.2 0/1:133:9:6,3:66,58:0.0677:2,2:27.4:1:31.4:1:0.50676:1.75:58.3:18:0.0687:0:1.1 -6 26184086 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19831;SOR=Inf;LSEQ=TCCAAGAAGGCCGTGACCAA;RSEQ=GCGCAGAAGAAGGACGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:94,81:0:2,0:25.2:1:31.5:1:1:0:58.9:86.5:1:0:0.2 0/1:141:2:1,1:75,64:0.0142:2,2:28.5:1:29.5:1:1:1.17055:60:4:0.0147:0:1 -6 26184098 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20761;SOR=Inf;LSEQ=GTGACCAAGGCGCAGAAGAA;RSEQ=GACGGCAAGAAGCGCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:93,88:0:2,0:26:1:31.2:1:1:0:57.9:35.2:1:0:0.2 0/1:152:2:1,1:78,72:0.0132:2,2:27.5:1:30:1:1:1.08274:60:4:0.0133:0:1 -6 26184102 . G A 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00325;SOR=3.14626;LSEQ=CCAAGGCGCAGAAGAAGGAC;RSEQ=GCAAGAAGCGCAAGCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:10:5,5:88,83:0.0552:2,2:20.4:1:29.2:1:1:1.05993:60:9:0.0511:0:1.4 0/1:154:24:11,13:69,61:0.1558:2,2:23:1:30:1:0.65727:1.33428:58.2:23:0.1513:0:1.3 -6 26184107 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49981;SOR=0;LSEQ=GCGCAGAAGAAGGACGGCAA;RSEQ=AAGCGCAAGCGCAGCCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:2,0:87,84:0.0116:2,0:13:1:28:0:0.49751:0:56:4:0.012:0:1 0/0:156:0:0,0:78,78:0:2,0:25.3:1:31.3:1:1:0:57.6:77:1:0:0.3 -6 26184183 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.193;SOR=0;LSEQ=AACAGGTCCACCCCGACACC;RSEQ=GCATCTCCTCTAAAGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:54,73:0.0155:2,2:26.5:1:30:1:1:1.35:60:4:0.0161:0:1.5 0/0:164:0:0,0:80,84:0:2,0:26.1:1:29.3:1:1:0:58.8:53.667:1:0:0.1 -6 26184188 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5041;SOR=Inf;LSEQ=GTCCACCCCGACACCGGCAT;RSEQ=TCCTCTAAAGCCATGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:57,76:0:2,0:25.1:1:30.5:1:1:0:58.6:25.6:1:0:0.2 0/1:165:2:1,1:79,84:0.0121:2,2:14:0:31:0:1:1.06:60:4:0.0123:0:1.5 -6 26184235 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50021;SOR=Inf;LSEQ=TTCCTTTGTCAACGACATCT;RSEQ=CGAGCGCATCGCCGGCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:36,86:0:2,0:25.3:1:29.6:1:1:0:57.5:29.5:1:0:0.2 0/1:139:2:1,1:57,80:0.0144:2,2:21:0:33:0:1:1.40:53.5:4:0.0146:0:1 -6 26184268 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49879;SOR=Inf;LSEQ=CGGCGAGGCTTCCCGCCTGG;RSEQ=GCATTACAACAAGCGCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:27,52:0:2,0:24.8:1:29.4:1:1:0:54.7:18.75:1:0:0.1 0/1:89:2:1,1:32,54:0.0225:2,2:5:0:28.5:1:1:1.68:60:4:0.0227:0:1 -6 26184412 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49782;SOR=Inf;LSEQ=CAGCTCCAAGTAAACTTGTC;RSEQ=CTGCAACTGCCTTAGTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:40,49:0:2,0:23.6:1:30.9:1:1:0:60:88:0.9888:0:0.1 0/1:96:2:1,1:36,57:0.0208:2,2:12:0:28:1:1:1.58:60:4:0.0213:0:1 -6 26197493 . C A 194 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=55.25876;LSEQ=AGCCATTGCGAACTTCTAAA;RSEQ=CCTGCTAAATGACGAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1600:2:1,1:587,1011:0.0013:2,2:17.5:1:30.5:1:1:1.72:60:4:0.0013:0:1 0/1:1637:106:41,65:601,930:0.0648:2,2:26.3:1:28.9:1:1:1.02451:60:105:0.0648:0:1.2 -6 26198064 . A ACT 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTCATCCTCATATGAAAGC;RSEQ=CTCTTATCTTTTACAAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:32.5:1:32.3:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 26199822 . A G 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=AAGTCCGCTCCTGCTCCAAA;RSEQ=AAGGGCTCCAAAAAGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:80,55:0:2,0:27.6:1:30.1:1:1:0:60:270:1:0:0.1 0/1:184:17:10,7:105,62:0.0924:2,2:25.6:1:31.8:1:0.79529:1.18436:60:34:0.0939:0:1.2 -6 26199903 . C T 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=AGCCGCAAGGAGAGCTATTC;RSEQ=GTGTACGTGTACAAGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:89,84:0:2,0:26.9:1:30.5:1:1:0:60:172:1:0:0.1 0/1:186:13:6,7:74,99:0.0699:2,2:28.6:1:29.8:1:1:1.15:60:26:0.0699:0:1 -6 26199933 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=TACAAGGTGCTAAAGCAGGT;RSEQ=CACCCCGACACCGGCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:91,98:0.0105:2,2:6.5:1:30:1:1:1.08:60:4:0.0107:0:1.5 0/0:176:0:0,0:72,104:0:2,0:21.8:1:30.5:1:1:0:59.8:57.667:1:0:0.3 -6 26199939 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50372;SOR=0;LSEQ=GTGCTAAAGCAGGTCCACCC;RSEQ=GACACCGGCATCTCATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:94,100:0.0102:2,2:25:1:32.5:1:1:1.06:60:4:0.0103:0:1 0/0:160:0:0,0:66,93:0:2,0:23.1:1:28.9:1:1:0:59.8:25.5:0.9935:0:0.3 -6 26200050 . C G 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.05901;SOR=0;LSEQ=GCGCATTACAACAAGCGCTC;RSEQ=ACCATCACCTCCAGGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:5:2,3:51,30:0.0581:2,2:25:1:31.8:1:0.36737:2.52106:49.2:10:0.0595:0:1.4 0/0:83:0:0,0:48,35:0:2,0:22.5:1:30.4:1:1:0:58:166:1:0:0.4 -6 26200080 . C T 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06289;SOR=2.25072;LSEQ=TCCAGGGAGATCCAGACGGC;RSEQ=GTACGCCTGCTGCTGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:10:7,3:63,42:0.087:2,2:29:1:30.5:1:0.73792:1.55:60:20:0.0885:0:1.4 0/1:96:17:10,7:44,35:0.1771:2,2:21.8:1:30.1:1:1:1.13:60:34:0.1809:0:1.2 -6 26200083 . A G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=4.31589;LSEQ=AGGGAGATCCAGACGGCCGT;RSEQ=CGCCTGCTGCTGCCCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:11:8,3:65,46:0.0902:2,2:21.5:1:33:1:0.52267:1.88:55.5:22:0.0909:0:1.3 0/1:103:31:19,12:37,33:0.301:2,2:20.5:1:30:1:0.51704:1.41:56:14.5:0.2871:0:1.1 -6 26200089 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.2137;SOR=Inf;LSEQ=ATCCAGACGGCCGTACGCCT;RSEQ=CTGCTGCCCGGGGAGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:80,58:0:2,0:21.3:1:32:1:1:0:59.6:276:0.9928:0:0.3 0/1:120:2:1,1:68,50:0.0167:2,2:22:1:30.5:1:1:1.35645:60:4:0.0169:0:2 -6 26200106 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22776;SOR=Inf;LSEQ=CCTGCTGCTGCCCGGGGAGC;RSEQ=GGCTAAGCACGCCGTGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:95,82:0:2,0:24:1:30.4:1:1:0:59.7:87.5:1:0:0.3 0/1:163:2:1,1:86,75:0.0123:2,2:12.5:1:28.5:1:1:1.1457:60:4:0.0124:0:1 -6 26200117 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24808;SOR=0;LSEQ=CCGGGGAGCTGGCTAAGCAC;RSEQ=CCGTGTCAGAGGGCACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:102,91:0.0103:2,2:38.5:1:31:1:1:1.12022:60:4:0.0106:0:2 0/0:196:0:0,0:103,93:0:2,0:24.9:1:30:1:1:0:59.9:38.2:1:0:0.4 -6 26200175 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23301;SOR=0;LSEQ=CAGCTCTAAGTAATTCTAAC;RSEQ=TCTTCATACCCAATCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:67,106:0.0114:2,2:31.5:1:30.5:1:1:1.58:60:4:0.0115:0:1 0/0:187:0:0,0:85,102:0:2,0:25.3:1:29.4:1:1:0:59.9:22.375:1:0:0.2 -6 26200215 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.229;SOR=Inf;LSEQ=AGGCTCTTTTAAGAGCCACC;RSEQ=ACTTTTTCAGCTATAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:20,59:0:2,0:19.2:1:31.8:1:1:0:60:158:1:0:0 0/1:73:2:1,1:18,53:0.0274:2,2:12:1:27.5:1:0.45548:2.89:60:4:0.0286:0:1 -6 26200256 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49183;SOR=Inf;LSEQ=GTAATTACCTGCATATTTTC;RSEQ=GTGTTTACCACCAACAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:0:1,0:26.3:1:30.5:1:1:0:60:56:1:0:0 0/1:30:2:0,2:1,27:0.0667:1,0:30:1:30.5:1:1:0:60:4:0.0667:0:1.5 -6 26216656 . T C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00269;SOR=Inf;LSEQ=GAAGCCTCGCCTGCGATGCG;RSEQ=TCGAAGATGTCGTTAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:48,27:0:2,0:23:1:30.2:1:1:0:60:150:1:0:0.1 0/1:72:8:4,4:37,27:0.1111:2,2:31.1:1:31.6:1:0.71856:1.36428:60:16:0.1127:0:1.1 -6 26216806 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50388;SOR=Inf;LSEQ=TTCTTGCCATCCTTCTTCTG;RSEQ=GCCTTGGTCACAGCCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:31,40:0:2,0:26.5:1:31.3:1:1:0:60:142:1:0:0.1 0/1:90:2:1,1:44,44:0.0222:2,2:10:1:27.5:1:1:1:60:4:0.0222:0:2 -6 26216819 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50064;SOR=Inf;LSEQ=TCTTCTGCGCCTTGGTCACA;RSEQ=CCTTCTTGGAACCCTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:27,38:0:2,0:25.9:1:32.2:1:1:0:60:64:1:0:0.1 0/1:78:2:1,1:37,39:0.0256:2,2:20:1:28:1:1:1.05:60:4:0.026:0:1 -6 26216866 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49521;SOR=Inf;LSEQ=GGAGCTGACTTAGCTGGTTC;RSEQ=GGCATGCTGTCAGAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:9,32:0:2,0:21.2:1:30:1:1:0:60:40:1:0:0 0/1:45:2:1,1:10,33:0.0444:2,2:7.5:1:30.5:1:0.43333:3.19:60:4:0.0444:0:1 -6 26219312 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19615;SOR=Inf;LSEQ=CCACACGGAAGTCCACTGGT;RSEQ=GCAGACAGCCTCCTAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:26.1:1:30.8:1:1:0:60:44:1:0:0 0/1:18:2:1,1:11,5:0.1111:2,2:34:1:31:1:1:2.09766:60:4:0.1176:0:1 -6 26219319 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18937;SOR=Inf;LSEQ=GAAGTCCACTGGTGGCAGAC;RSEQ=GCCTCCTAAGCAGCTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:25.2:1:30.3:1:1:0:60:48:1:0:0.1 0/1:19:2:1,1:11,6:0.1053:2,2:38:0:31.5:1:1:1.77272:60:4:0.1053:0:1.5 -6 26219337 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20854;SOR=Inf;LSEQ=ACAGCCTCCTAAGCAGCTGG;RSEQ=CACCAAGGCAGCCAGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:0:2,0:28.5:1:32.3:1:1:0:60:44:1:0:0.1 0/1:19:2:1,1:10,7:0.1053:2,2:27:1:27.5:1:1:1.40151:60:4:0.1053:0:1 -6 26219384 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48276;SOR=Inf;LSEQ=TGGCCACCAGCAGCTTGAAG;RSEQ=TGTCCCTCAGATATAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:0:2,0:25.4:1:31.8:1:1:0:60:28:1:0:0.1 0/1:15:2:1,1:3,10:0.1333:2,2:40:1:28:1:0.47619:3.03:60:4:0.1333:0:1 -6 26225381 . C G 218 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATTTACTTTGCAGATGAA;RSEQ=TATGGCGCGTACTAAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1789:0:0,0:1045,742:0:2,0:25.1:1:32:1:1:0:60:80.227:0.9989:0:0.1 0/1:2089:118:71,47:1121,846:0.0565:2,2:27.3:1:31.7:1:0.5657:1.14:60:236:0.0571:0:1.1 -6 26226032 . C G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25366;SOR=2.9409;LSEQ=GCTGTTCTCCATTGGTTTAG;RSEQ=TGGCTTTGTTTTGCTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:0,3:3,51:0.0526:2,0:29.7:1:32.3:1:1:0:60:6:0.0526:0:1.3 0/1:14:2:0,2:1,11:0.1429:2,0:14:1:32.5:1:1:0:60:4:0.1538:0:1 -6 26234734 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49652;SOR=Inf;LSEQ=TCTTCGGGGTAGCGGCGCCA;RSEQ=CCACCTTCTTGGGCTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:25,12:0:2,0:28.4:1:32.4:1:1:0:60:74:1:0:0 0/1:43:2:1,1:21,20:0.0465:2,2:16.5:1:28:1:1:1.04883:60:4:0.0476:0:1 -6 26234883 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51216;SOR=Inf;LSEQ=GTACCTTTGGTCTGCACCAG;RSEQ=GTACCTTTGCTCACCAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:35,34:0:2,0:28:1:30.6:1:1:0:60:68:1:0:0.1 0/1:98:2:1,1:48,48:0.0204:2,2:20:0:32.5:1:1:1:60:4:0.0206:0:1.5 -6 26249518 . G T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CTACTCGGGAGGCTGAGGCA;RSEQ=GAGAATCGCTTGAACCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:44.5:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:1,1:0:2,0:36.5:1:31.5:1:1:0:60:4:1:0:0 -6 26250254 . C G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.93849;LSEQ=TTTGAAGACAATGGCCAAGA;RSEQ=ACAAAAGCCTAGTTTAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:13:13,0:121,3:0.0949:1,1:18.8:1:32.3:1:1:0:60:26:0.0963:0:1 0/1:67:6:6,0:60,1:0.0896:1,0:22.2:1:29.5:1:1:0:60:5:0.0758:0:1.2 -6 26251905 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24737;SOR=Inf;LSEQ=GATCCAGCTAAGTCCGCTCC;RSEQ=GCCCCGAAGAAGGGCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:83,60:0:2,0:27.1:1:30.4:1:1:0:60:70.5:1:0:0.1 0/1:142:2:1,1:81,59:0.0141:2,2:37.5:1:31:1:1:1.36975:60:4:0.0141:0:1 -6 26251911 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24093;SOR=0;LSEQ=GCTAAGTCCGCTCCCGCCCC;RSEQ=AAGAAGGGCTCCAAGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:83,63:0.0135:2,2:40:0:31:1:1:1.31497:60:4:0.0136:0:2 0/0:153:0:0,0:87,66:0:2,0:26.4:1:29.5:1:1:0:59.9:29.6:1:0:0.2 -6 26251944 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49848;SOR=0;LSEQ=AAGAAGGCGGTGACCAAGGC;RSEQ=CAGAAGAAGGATGGCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:79,84:0.0121:2,2:18:1:29:1:1:1.06:60:4:0.0122:0:1 0/0:165:0:0,0:80,85:0:2,0:24.8:1:30.3:1:1:0:59.7:164:1:0:0.2 -6 26251959 . C A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49841;SOR=0;LSEQ=AAGGCGCAGAAGAAGGATGG;RSEQ=AAGAAGCGTAAACGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:2,0:80,75:0.0127:2,0:8.5:1:25.5:1:0.4978:0:60:4:0.0129:0:1 0/0:155:0:0,0:76,79:0:2,0:24.1:1:31.3:1:1:0:59.6:76.5:1:0:0.2 -6 26251979 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24166;SOR=Inf;LSEQ=CAAGAAGCGTAAACGCAGCC;RSEQ=CAAGGAGAGCTACTCCGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:70,66:0:2,0:24.9:1:30.8:1:1:0:60:135:1:0:0.1 0/1:132:2:1,1:64,66:0.0152:2,2:39.5:1:28.5:1:1:1.03:60:4:0.0152:0:1 -6 26252035 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5032;SOR=0;LSEQ=TGAAGCAAGTCCACCCCGAC;RSEQ=CCGGCATCTCCTCCAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:77,82:0.0124:2,2:28:1:30.5:1:1:1.06:60:4:0.0125:0:1 0/0:132:0:0,0:63,69:0:2,0:23.3:1:29:1:1:0:59.9:65:1:0:0.1 -6 26252104 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.99294;LSEQ=ATATCTTCGAGCGCATCGCC;RSEQ=GCGAGGCTTCCCGCCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:1,0:36,57:0.0106:2,0:1:0:29:0:0.39362:0:60:2:0.0109:0:1 0/1:95:2:1,1:41,52:0.0211:2,2:16.5:1:29:1:1:1.27:60:4:0.0211:0:1 -6 26252240 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22209;SOR=0;LSEQ=GGGCACTAAGGCCGTCACCA;RSEQ=GTACACCAGCTCCAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:48,53:0.0194:2,2:30.5:1:32:1:1:1.10:60:4:0.0194:0:1 0/0:115:0:0,0:57,58:0:2,0:27.1:1:29.9:1:1:0:60:56.5:1:0:0.1 -6 26270961 . T C 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39906;SOR=2.97532;LSEQ=TTCCACTACCAAATCGAAGC;RSEQ=CCAAACCCCTAAAAGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:3,0:27,1:0.0968:1,0:16.3:1:31.3:1:1:0:60:6:0.1034:0:1 0/1:4:1:0,1:2,1:0.25:2,0:16:0:33:0:1:0:60:2:0.25:0:1 -6 26271241 . G A 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.59294;LSEQ=ATGCGGCGAGCGAGCTGAAT;RSEQ=TCCTTGGGCATGATAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2583:186:104,82:1320,1074:0.072:2,2:24.8:1:29.3:1:0.87845:1.03:60:92:0.0719:0:1.1 0/1:2645:291:163,128:1199,1154:0.11:2,2:25.3:1:28.4:1:0.10632:1.23:60:71.75:0.1094:0:1.1 -6 26271713 . A T 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.44076;LSEQ=GCCTTGTTGATTTTCAAAAG;RSEQ=CCCGCGCAACAAAACCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:46:1,45:8,294:0.1322:1,1:23.3:1:29.5:1:1:1.22383:60:22:0.1275:0:1.3 0/1:241:83:2,81:10,147:0.3444:2,1:23.1:1:29.4:1:0.22626:2.74547:60:166:0.3458:0:1.1 -6 26273283 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24935;SOR=Inf;LSEQ=CAAGGCACAGAAGAAGGATG;RSEQ=CAAGAAGCGCAAGCGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:139,142:0:2,0:25.6:1:31.5:1:1:0:59.1:69.25:1:0:0.1 0/1:298:3:2,1:151,143:0.0101:2,2:12.7:1:31.3:1:1:1.89:57.3:6:0.0103:0:1 -6 26273435 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49971;SOR=Inf;LSEQ=TCGAGCGCATTGCAGGCGAG;RSEQ=CTTCCCGCCTGGCGCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:32,74:0:2,0:22.8:1:31.6:1:1:0:60:105:1:0:0 0/1:120:2:1,1:38,80:0.0167:2,2:30.5:1:31.5:1:0.54622:2.09:60:4:0.0172:0:2 -6 26273522 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12163;SOR=Inf;LSEQ=GCCTGCTGCTACCCGGGGAG;RSEQ=TGGCCAAACACGCGGTGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:51,50:0:2,0:24.1:1:31.7:1:1:0:60:49.5:1:0:0.1 0/1:105:4:1,3:59,42:0.0381:2,2:8:1:26.5:1:0.31129:4.15912:60:8:0.0381:0:1 -6 26273525 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49795;SOR=Inf;LSEQ=TGCTGCTACCCGGGGAGCTG;RSEQ=CCAAACACGCGGTGTCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:53,53:0:2,0:24:1:31.1:1:1:0:60:52:1:0:0.1 0/1:111:2:1,1:62,47:0.018:2,2:10:0:27.5:1:1:1.31581:60:4:0.0182:0:1 -6 26273560 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49913;SOR=Inf;LSEQ=TCGGAGGGCACCAAGGCGGT;RSEQ=ACCAAGTACACCAGCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:61,72:0:2,0:26.8:1:31.7:1:1:0:59.8:43.333:1:0:0.1 0/1:145:2:1,1:72,71:0.0138:2,2:30:0:31:1:1:1.01399:60:4:0.0139:0:1.5 -6 26273574 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49931;SOR=Inf;LSEQ=GGCGGTCACCAAGTACACCA;RSEQ=CTCCAAGTAAACTAGTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:54,73:0:2,0:26.7:1:32:1:1:0:59.8:41.333:1:0:0.1 0/1:140:2:1,1:61,77:0.0143:2,2:35.5:1:29.5:1:1:1.26:60:4:0.0143:0:1 -6 26322023 . G GA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49808;SOR=0;LSEQ=GGTACCTTTTGACCCCATGG;RSEQ=AAAAAAAATAACGTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:2,0:103,7:0.0179:2,0:34.5:1:31:1:1:0:60:4:0.0183:0:0.5 0/0:106:0:0,0:96,9:0:2,0:22.4:1:30.8:1:1:0:60:51.5:0.9904:0:0.1 -6 26322115 . C T 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGATTCTTAAGCACGTT;RSEQ=TCCACGTATGCGGCGTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:0:0,0:433,279:0:2,0:27.6:1:31.4:1:1:0:59:100.714:1:0:0.1 0/1:628:52:29,23:334,242:0.0828:2,2:28.2:1:29.2:1:0.771:1.09445:54.5:51:0.0824:0:1.9 -6 26322153 . A G 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAGCTGGATGTCTTTTGGC;RSEQ=TAATTGTTACACGTTTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:780:0:0,0:403,377:0:2,0:26.9:1:30.2:1:1:0:59:44.882:1:0:0.1 0/1:652:60:28,32:292,300:0.092:2,2:25:1:30:1:0.78664:1.1122:52.2:59:0.0915:0:1.8 -6 26322444 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21851;SOR=Inf;LSEQ=TCTTGCGAGAGGCTTTTGTA;RSEQ=CCAGTTGCTTCCCGGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:102,123:0:2,0:22.4:1:32:1:1:0:60:74:1:0:0.3 0/1:198:2:1,1:102,93:0.0101:2,2:11.5:1:24.5:1:1:1.09626:60:4:0.0102:0:1 -6 26322473 . G A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.62501;LSEQ=TTCCCGGGTGCTTTGCCACC;RSEQ=GTCGATTTGCCGGTCGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:8:5,3:108,123:0.0333:2,2:32.1:1:30.6:1:0.48145:1.89:60:16:0.034:0:1 0/1:212:53:27,26:78,79:0.25:2,2:29.3:1:30.1:1:1:1.05:60:106:0.2524:0:1.2 -6 26322500 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20385;SOR=Inf;LSEQ=TTGCCGGTCGATTTGCGGGC;RSEQ=GTCGGCTTTCTACGAGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:98,131:0:2,0:27.8:1:30.2:1:1:0:60:37.167:1:0:0.4 0/1:189:2:1,1:85,102:0.0106:2,2:40:1:30.5:1:1:1.20:60:4:0.0106:0:3 -6 26322501 . G A 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCCGGTCGATTTGCGGGCA;RSEQ=TCGGCTTTCTACGAGCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:57:22,35:76,93:0.2522:2,2:26.6:1:30.2:1:0.44195:1.2986:60:56:0.25:0:1.1 0/0:188:0:0,0:84,104:0:2,0:26.5:1:31.6:1:1:0:60:187:1:0:0.4 -6 26322526 . A G 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTTTCTACGAGCCGTGGTAT;RSEQ=GAGACCTCCTTACTTACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:59,112:0:2,0:21.7:1:29.9:1:1:0:60:84.5:1:0:0.4 0/1:127:16:7,9:43,68:0.126:2,2:19.6:1:29.4:1:0.78657:1.23:60:15:0.119:0:1.1 -6 26322624 . G T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97535;LSEQ=AGCGACGGCAGGACGGCTGC;RSEQ=GCTACGAACACAATTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:0,5:4,35:0.1136:2,0:17.8:1:26.2:1:1:0:60:1.5:0.0732:0:1 0/1:27:3:0,3:1,23:0.1111:1,0:20.7:1:31.3:1:1:0:60:6:0.1111:0:1 -6 27100347 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25225;SOR=Inf;LSEQ=TTCACAAACGAATTCATGAT;RSEQ=CCCATGGCCTTGGACGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:62,15:0:2,0:25.8:1:31.8:1:1:0:60:37.5:1:0:0.1 0/1:93:3:1,2:63,27:0.0323:2,2:11.7:1:25:1:0.2284:4.5803:60:6:0.0333:0:1 -6 27100413 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24072;SOR=Inf;LSEQ=AGAACCTTGTACACATAGAT;RSEQ=GAATAGCTCTCCTTGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:126,78:0:2,0:26.7:1:31.8:1:1:0:60:101:1:0:0.1 0/1:197:2:1,1:113,82:0.0102:2,2:17.5:1:30.5:1:1:1.37575:60:4:0.0103:0:1 -6 27100458 . C A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24875;SOR=0;LSEQ=TTGCGCTTCTTGCCGTCTTT;RSEQ=TTCTGCGCCTTAGTCACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:3:2,1:129,111:0.0123:2,2:5.3:1:27:1:1:1.72:60:6:0.0125:0:1 0/0:233:0:0,0:118,115:0:2,0:27.6:1:31:1:1:0:60:37.833:1:0:0.1 -6 27101644 . G C 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=Inf;LSEQ=TGTTCCACGCGGGCCAGGGC;RSEQ=GCATGAAGAAGTCCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:124,28:0:2,0:20.8:1:29.8:1:1:0:60:75:1:0:0.1 0/1:156:12:11,1:105,37:0.0769:2,2:24.1:1:30.1:1:0.29569:3.85:60:24:0.0789:0:1 -6 27101761 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24024;SOR=Inf;LSEQ=TCCTGCGAGAGCTCGGCGGT;RSEQ=ACGCCGCTGCACGAGAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:54,140:0:2,0:22.3:1:31.2:1:1:0:60:63.667:1:0:0.1 0/1:187:2:1,1:52,133:0.0107:2,2:21.5:1:27:1:0.48761:2.54:60:4:0.0108:0:1 -6 27114052 . G T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87078;LSEQ=CTGCATGCATTACTCAGTGT;RSEQ=ATAAGATCATGATAATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:13,0:0.4091:1,0:30:1:29.9:1:1:0:60:18:0.4091:0:1.1 0/1:8:3:3,0:5,0:0.375:0,0:10:1:30.7:1:1:0:60:6:0.375:0:1 -6 27114150 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49832;SOR=0;LSEQ=ATCGATAATTTAAGTGGCTC;RSEQ=TAAAAGAGCCTTTGGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:85,35:0.0164:2,2:18:0:33:1:0.50481:2.40867:60:4:0.0168:0:1.5 0/0:115:0:0,0:84,31:0:2,0:20.8:1:30.3:1:1:0:60:114:1:0:0.1 -6 27114233 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5959;SOR=0.42271;LSEQ=TACTTGGTGACGGCCTTGGT;RSEQ=CCCTCGGACACGGCGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:75,103:0.0111:2,2:10:1:29:1:1:1.37:60:4:0.0112:0:1 0/0:212:1:0,1:95,116:0.0047:2,0:3:0:27:0:1:0:60:2:0.0048:0:1 -6 27114240 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25614;SOR=Inf;LSEQ=TGACGGCCTTGGTGCCCTCG;RSEQ=ACACGGCGTGCTTGGCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:62,91:0:2,0:24.7:1:31.1:1:1:0:52.7:50:1:0:0.2 0/1:189:3:1,2:79,107:0.0159:2,2:31.7:1:22.7:1:1:1.47371:47:2:0.011:0:2.3 -6 27114242 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20442;SOR=0;LSEQ=ACGGCCTTGGTGCCCTCGGA;RSEQ=ACGGCGTGCTTGGCCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:60,92:0.013:2,2:31:1:31.5:1:1:1.53:60:4:0.0131:0:1 0/0:186:0:0,0:79,107:0:2,0:22.9:1:30.9:1:1:0:51.8:61:1:0:0.2 -6 27114268 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23371;SOR=0;LSEQ=GTGCTTGGCCAACTCCCCGG;RSEQ=CAGCAGCAGGCGCACGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:43,65:0.0182:2,2:23:1:29:1:1:1.51:50:4:0.0183:0:1 0/0:117:0:0,0:41,76:0:2,0:16:0:13:0:1:0:21:0:0:0:3 -6 27114342 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20387;SOR=Inf;LSEQ=TGTTGTAATGCGCCAGGCGG;RSEQ=AAGCCTCACCCGCGATGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:53,46:0:2,0:23.8:1:31.1:1:1:0:55.2:98:1:0:0.1 0/1:82:2:1,1:36,44:0.0244:2,2:11.5:1:29:1:1:1.22:60:4:0.0244:0:1.5 -6 27114416 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19422;SOR=Inf;LSEQ=CCCATGGCCTTAGAGGAGAT;RSEQ=CCGGTGTCGGGGTGGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:91,67:0:2,0:24.4:1:31.9:1:1:0:39.8:78:1:0:0.2 0/1:125:2:1,1:73,50:0.016:2,2:18.5:1:31:1:1:1.45545:27:4:0.0161:0:1 -6 27114421 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18576;SOR=Inf;LSEQ=GGCCTTAGAGGAGATGCCGG;RSEQ=GTCGGGGTGGACCTGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:95,72:0:2,0:23.9:1:29.8:1:1:0:39.4:82.5:1:0:0.3 0/1:127:2:1,1:76,49:0.0157:2,2:31:1:29:1:1:1.54545:27:4:0.016:0:1 -6 27114425 . G A 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19549;SOR=0.66482;LSEQ=TTAGAGGAGATGCCGGTGTC;RSEQ=GGGTGGACCTGCTTCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:41:30,11:74,66:0.2265:2,2:22.8:1:30.4:1:0.03035:2.42:34.4:82:0.2278:0:1 0/1:129:21:15,6:64,44:0.1628:2,2:23.8:1:28.4:1:0.3373:1.71:34.4:20:0.1613:0:1.1 -6 27114488 . G C 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00134;SOR=0;LSEQ=CTCTCCTTGCGGCTGCGCTT;RSEQ=CGCTTCTTGCCGTCCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:11:3,8:83,112:0.0534:2,2:28.8:1:31.2:1:0.36604:1.97012:45.2:22:0.0537:0:1.1 0/0:169:0:0,0:77,92:0:2,0:27.5:1:31.2:1:1:0:45.9:27.167:1:0:0.3 -6 27114569 . T C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28136;SOR=0.36135;LSEQ=GCGGGAGCGGACTTCGCTGG;RSEQ=TCCGGCATGTTGAAGGCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:6:0,6:8,49:0.0952:2,0:10.7:1:33.3:1:1:0:28:12:0.0952:0:1.2 0/1:55:2:0,2:10,43:0.0364:2,0:11.5:1:32.5:1:1:0:27:4:0.0377:0:2.5 -6 27775248 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21943;SOR=Inf;LSEQ=GAGCGAACCAGCTCTTCTTT;RSEQ=GATAATAGTGAGTGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:67,13:0:2,0:22:1:28.1:1:1:0:60:39:1:0:0 0/1:71:2:2,0:54,15:0.0282:2,0:25.5:1:31.5:1:1:0:60:4:0.0294:0:1 -6 27775315 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18584;SOR=0;LSEQ=CTTGAGAATTTACTTGGAGC;RSEQ=GGTGTACTTGGTGACGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:110,84:0.0102:2,2:33.5:1:29.5:1:1:1.30769:60:4:0.0103:0:1 0/0:258:0:0,0:136,121:0:2,0:26.7:1:29.9:1:1:0:59.9:41.833:1:0:0.1 -6 27775370 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5035;SOR=Inf;LSEQ=ACCGCGTGCTTGGCCAGCTC;RSEQ=CCCGGAAGCAGCAGGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:64,79:0:2,0:25.9:1:31:1:1:0:58.9:142:1:0:0.1 0/1:175:2:1,1:73,100:0.0114:2,2:24.5:1:31.5:1:1:1.37:60:4:0.0117:0:1 -6 27775446 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.84139;LSEQ=GCTTGTTGTAGTGCGCCAGG;RSEQ=GGGAAGCCTCGCTTGCGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:0,1:61,47:0.0092:2,0:1:0:25:0:0.44037:0:60:2:0.0092:0:1 0/1:119:2:1,1:60,57:0.0168:2,2:12:1:28.5:1:1:1.0522:60:4:0.0171:0:1 -6 27775486 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23935;SOR=Inf;LSEQ=GCGCTCGAAGATGTCGTTGA;RSEQ=GAAGGAGTTCATGATTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:100,78:0:2,0:26.4:1:30.6:1:1:0:59.1:34.6:1:0:0.1 0/1:171:2:1,1:98,71:0.0117:2,2:21:0:31:1:1:1.37762:60:4:0.0118:0:1.5 -6 27775562 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18397;SOR=0;LSEQ=TGCTTCAGCACCTTGTACAC;RSEQ=TACACGGAGTAGCTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:92,85:0.0111:2,2:12:1:30.5:1:1:1.08186:42:4:0.0111:0:1.5 0/0:239:0:0,0:128,111:0:2,0:25.3:1:30.4:1:1:0:57.9:238:1:0:0.1 -6 27775672 . C T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.07967;SOR=0;LSEQ=CGGGGCGGGAGCAGACTTGG;RSEQ=CAGCTCGGGCATAATGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:1,2:45,95:0.021:2,2:29.7:1:28.3:1:1:1.06:60:6:0.0217:0:1 0/0:188:0:0,0:66,122:0:2,0:24.6:1:31:1:1:0:60:187:1:0:0.4 -6 27775674 . A G 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGGCGGGAGCAGACTTGGCC;RSEQ=GCTCGGGCATAATGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:43,95:0:2,0:25:1:30.4:1:1:0:60:45:1:0:0.2 0/1:180:20:9,11:50,110:0.1111:2,2:27.4:1:29.9:1:0.21861:1.79:60:40:0.1124:0:2.1 -6 27775697 . G C 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGGGCATAATGAAACAATA;RSEQ=TGGCAAAACCAAAACAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:16,74:0:2,0:21.3:1:32.3:1:1:0:60:180:0.989:0:0.2 0/1:116:20:7,13:22,74:0.1724:2,2:25:1:31:1:0.26648:1.80:60:40:0.1739:0:2.1 -6 27775707 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25296;SOR=Inf;LSEQ=TGAAACAATAGTGGCAAAAC;RSEQ=AAAACAAGAAGTCGGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:12,58:0:2,0:20.3:1:32.2:1:1:0:60:140:0.9859:0:0.1 0/1:87:3:2,1:14,70:0.0345:2,2:16.7:1:28.7:1:0.08566:9.61:60:6:0.0349:0:2 -6 27778097 . C T 256 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=464.45348;LSEQ=GCGCAGGACTTCAAGACCGA;RSEQ=TTGCGCTTCCAGAGCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2832:1:0,1:1456,1375:4e-04:2,0:1:0:25:0:0.48588:0:60:2:4e-04:0:1 0/1:2784:394:198,196:1232,1156:0.1415:2,2:24.7:1:29.7:1:0.62492:1.05499:60:77.8:0.141:0:1.2 -6 27783042 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50136;SOR=0;LSEQ=CAACGACATCTTTGAGCGTA;RSEQ=CGCCGGAGAAGCGTCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:41,125:0.0119:2,2:12.5:1:28.5:1:0.43862:3.02:60:4:0.012:0:1 0/0:144:0:0,0:54,90:0:2,0:23.7:1:29:1:1:0:60:35:1:0:0.2 -6 27783144 . C T 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.68877;LSEQ=ACTGCTACCCGGGGAATTGG;RSEQ=CAAGCACGCCGTGTCCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:1:1,0:35,37:0.0137:2,0:22:0:31:0:0.49315:0:60:2:0.0141:0:1 0/1:87:2:1,1:43,42:0.023:2,2:21:0:30.5:1:1:1.02354:60:4:0.023:0:1 -6 27783199 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.521;SOR=Inf;LSEQ=ACCAAGTATACCAGCTCCAA;RSEQ=TGAGCCTCTCGCTGCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:32,42:0:2,0:27:1:31.1:1:1:0:60:23.667:1:0:0.2 0/1:115:2:1,1:52,59:0.0174:2,2:42.5:1:30.5:1:1:1.13:60:4:0.0174:0:1 -6 27806434 . C A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01325;SOR=Inf;LSEQ=CAATTTTCCGGCAGTTACTC;RSEQ=CAGTCATGCCCGAGCCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:56,11:0:2,0:23:1:30.8:1:1:0:60:134:1:0:0 0/1:66:6:5,1:51,9:0.0909:2,2:18:1:29.7:1:1:1.13114:60:12:0.0923:0:1 -6 27806492 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61379;SOR=2.12186;LSEQ=GAAGAAAGGCTCCAAGAAGG;RSEQ=AGTGACAAAGGCCCAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:1:0,1:103,65:0.0059:2,0:1:0:27:0:0.39053:0:60:2:0.006:0:1 0/1:160:2:1,1:92,66:0.0125:2,2:33.5:1:28:1:1:1.39098:60:4:0.0126:0:1 -6 27806519 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23074;SOR=Inf;LSEQ=AAAGGCCCAGAAGAAGGACG;RSEQ=CAAGAAGCGCAAGCGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:114,91:0:2,0:26.5:1:31.5:1:1:0:59.1:101.5:1:0:0.1 0/1:190:2:1,1:98,90:0.0105:2,2:20.5:1:27.5:1:1:1.08839:60:4:0.0106:0:1 -6 27806523 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.22947;SOR=Inf;LSEQ=GCCCAGAAGAAGGACGGCAA;RSEQ=AAGCGCAAGCGCAGCCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:113,92:0:2,0:26.8:1:31.4:1:1:0:59:40:1:0:0.1 0/1:189:2:1,1:95,92:0.0106:2,2:22:1:28:1:1:1.03244:60:4:0.0106:0:1 -6 27806557 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21864;SOR=Inf;LSEQ=GCCGCAAGGAGAGCTACTCC;RSEQ=TGTACGTGTACAAGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:95,98:0:2,0:26.2:1:31:1:1:0:58.9:192:1:0:0.1 0/1:170:2:1,1:72,96:0.0118:2,2:48:0:30.5:1:1:1.33:60:4:0.0119:0:1 -6 27806562 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50112;SOR=0;LSEQ=AAGGAGAGCTACTCCGTGTA;RSEQ=GTGTACAAGGTGCTGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:0,2:96,100:0.0101:2,0:9.5:1:26.5:1:0.49792:0:55:4:0.0103:0:1 0/0:172:0:0,0:75,97:0:2,0:24.9:1:30.1:1:1:0:58.8:171:1:0:0.1 -6 27806565 . G C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22368;SOR=Inf;LSEQ=GAGAGCTACTCCGTGTACGT;RSEQ=TACAAGGTGCTGAAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:90,100:0:2,0:25.4:1:31.6:1:1:0:58.8:26.143:1:0:0.1 0/1:171:2:1,1:73,96:0.0117:2,2:6:0:33.5:1:1:1.31:48.5:4:0.0117:0:1.5 -6 27806748 . GC G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.22949;SOR=Inf;LSEQ=ACGGCCGTGCGCCTGCTGCT;RSEQ=CAGGGGAGCTGGCCAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:86,56:0:2,0:22.6:1:31.5:1:1:0:58.8:70:0.9929:0:0.1 0/1:132:2:1,1:82,48:0.0152:2,2:10:1:30.2:1:1:1.70101:60:4:0.0154:0.0076:0 -6 27806755 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49891;SOR=0;LSEQ=TGCGCCTGCTGCTGCCAGGG;RSEQ=AGCTGGCCAAGCACGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:92,68:0.0123:2,2:28.5:1:28:1:1:1.35037:60:4:0.0127:0:1 0/0:152:0:0,0:91,61:0:2,0:23.8:1:29.7:1:1:0:59.7:15.889:1:0:0.2 -6 27806762 . C T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23764;SOR=0;LSEQ=GCTGCTGCCAGGGGAGCTGG;RSEQ=CAAGCACGCGGTGTCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:89,74:0.012:2,2:8.5:1:25.5:1:1:1.20135:54.5:4:0.0123:0:1 0/0:174:0:0,0:101,73:0:2,0:24.8:1:31.2:1:1:0:59.7:57:1:0:0.2 -6 27806839 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.89973;LSEQ=GAGCCCGCCCACCGCGGAAC;RSEQ=TTCGGTCAGTCTCGGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:2,0:68,102:0.0116:2,0:1:0:28:1:0.16422:0:60:4:0.0118:0:1 0/1:191:2:1,1:80,109:0.0105:2,2:25.5:1:27:1:1:1.36:60:4:0.0105:0:1.5 -6 27835012 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50632;SOR=0;LSEQ=CAGAAGCACCAGTGCCCTTG;RSEQ=TCTGCACCAGGGTGCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:43,56:0.0198:2,2:37:1:30.5:1:1:1.30:60:4:0.0202:0:1 0/0:77:0:0,0:36,41:0:2,0:48:0:13:0:1:0:60:0:0:0:1 -6 27835026 . G A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0452;SOR=Inf;LSEQ=CCCTTGGTCTGCACCAGGGT;RSEQ=CCCTTGCTCACCAAGCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:41,62:0:2,0:28.1:1:31.4:1:1:0:60:50.5:1:0:0.1 0/1:58:3:1,2:26,29:0.0517:2,2:29.7:1:29.3:1:1:1.77582:60:6:0.0517:0:1 -6 27835094 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52314;SOR=0;LSEQ=CTTCTCCACGTCGTAGCCAC;RSEQ=GGCCGCTAAGGCCTTCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:0,2:1,29:0.0625:1,0:28.5:1:31.5:1:1:0:60:4:0.0645:0:1 0/0:19:0:0,0:3,16:0:2,0:26.1:1:28.9:1:1:0:60:38:1:0:0.2 -6 27839184 . C T 43 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTAGCTGGGACTACAGGCG;RSEQ=GTGCCACCACGGCCGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:10.7:1:27.3:1:1:0:57.7:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 27839746 . T C 270 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAGGCATAATAGTGACGCG;RSEQ=TTGGCGTGAATGGCGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2731:0:0,0:1435,1291:0:2,0:24.7:1:29.9:1:1:0:60:99.963:0.9993:0:0.2 0/1:2822:367:197,170:1262,1190:0.13:2,2:23.4:1:31.8:1:0.43363:1.09:60:51.429:0.129:0:1.2 -6 27840221 . C A 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00252;SOR=0;LSEQ=CGTCTCACACACGGAATTGG;RSEQ=TCCCAGTTTAATCTGCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:13:0,13:5,192:0.0619:1,1:23.9:1:31.2:1:1:0:60:26:0.0644:0:1 0/0:125:0:0,0:2,123:0:1,0:23.1:1:31.9:1:1:0:60:61.5:1:0:0.1 -6 27840322 . CA C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAAAACAAAAACGGAAA;RSEQ=AAAAAAAATCCCCCAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:3:0,3:1,41:0.0667:1,0:12:1:32.5:1:1:0:60:6:0.0698:0.0222:0 0/0:13:0:0,0:2,11:0:2,0:29:1:30.4:1:1:0:60:26:1:0:0.2 -6 27858040 . A G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00144;SOR=Inf;LSEQ=CCAGTTTATCCCTGCTTTAA;RSEQ=GTTGATTTAAGACAGTCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:219,3:0:1,0:23:1:30.4:1:1:0:60:110:1:0:0.1 0/1:179:8:7,1:164,7:0.0447:1,2:21.8:1:32:1:0.31155:3.30993:60:16:0.0449:0:1.1 -6 27858421 . A G 268 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTGATAACGGCGGATCTC;RSEQ=CGCAAGGCCACGGTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2203:0:0,0:1086,1117:0:2,0:25:1:30.1:1:1:0:60:128.588:1:0:0.1 0/1:2064:438:209,229:799,824:0.2122:2,2:26.1:1:30.6:1:0.59039:1.06239:60:86.6:0.212:0:1.2 -6 27858837 . T C 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=CTCCCGGGTTCAAGCGATTC;RSEQ=GCCTCAGCCTCCGGAGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:39.3:1:27.3:1:1:0:58.7:6:0.3:0:1.7 1/1:2:2:0,2:0,0:1:0,0:13.5:1:28.5:1:1:0:60:4:1:0:1 -6 27858904 . C T 45 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGGCTAATTTTTTTTTAG;RSEQ=AGAGAAGGGGTTTCACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:0,5:0.375:0,2:28:1:29:1:0.375:0:60:6:0.4286:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 27861326 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20194;SOR=Inf;LSEQ=CCAGAAAAAGGACGGCAAGA;RSEQ=GCGCAAGCGCAGCCGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:41,27:0:2,0:28.3:1:29.6:1:1:0:60:21.667:1:0:0.1 0/1:56:2:1,1:29,25:0.0357:2,2:25.5:1:29:1:1:1.15692:60:4:0.0357:0:1 -6 27861571 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50555;SOR=0;LSEQ=CCGGGGAGCTGGCCAAGCAC;RSEQ=CCGTGTCCGAGGGCACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:2,0:40,33:0.0267:2,0:16.5:1:26:1:0.50054:0:53.5:4:0.0274:0:1 0/0:57:0:0,0:32,25:0:2,0:21.4:1:29.6:1:1:0:58.6:114:1:0:0.2 -6 27861643 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22804;SOR=Inf;LSEQ=CTCTCGCAGCTGCCAGCAAT;RSEQ=CAAAGGCTCTTTTCAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:25,39:0:2,0:24.3:1:30.5:1:1:0:60:31:1:0:0.1 0/1:59:2:1,1:21,36:0.0339:2,2:8.5:1:27.5:1:1:1.70:60:4:0.0339:0:1 -6 27861670 . G A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45239;SOR=0.47638;LSEQ=CTCTTTTCAGAGCCACTCAC;RSEQ=CTTCCAGAGAAAGAGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:0,5:9,24:0.1316:2,0:15.6:1:28.4:1:0.31207:0:60:10:0.1316:0:1 0/1:30:2:1,1:5,23:0.0667:2,2:20.5:1:27.5:1:0.36552:4.29:60:4:0.069:0:1 -6 28067099 . C T 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54247;SOR=0;LSEQ=CCCAACTGGGTAAGACCCTG;RSEQ=AAGAGGGGTAGTCAGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:1,3:5,11:0.2:2,2:21.3:1:29.3:1:1:1.34348:60:8:0.2:0:1.3 0/0:6:0:0,0:3,3:0:2,0:26.2:1:30.2:1:1:0:60:12:1:0:0.2 -6 28067196 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAGAGGAAGGAGCAGACACC;RSEQ=ATCTTGTGCTCTCCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:36.5:1:33:1:1:0:60:4:0.6667:0:1 1/0:3:2:0,2:1,0:0.6667:0,0:22:1:32:0:0.33333:0:60:4:0.6667:0:1 -6 28067537 . G A 49 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GATACTAGACAAATTCATGA;RSEQ=GATGAGAAAGAATCAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:19:0:33:0:1:0:60:2:1:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:17:1:24.8:1:1:1:60:3:0.6:0:1.3 -6 28954286 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49496;SOR=0;LSEQ=TTCCTCCTAGCTGTGAAGGT;RSEQ=AGGACCGCCGGTGTCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:24,23:0.0408:2,2:20.5:1:26:1:1:1.04259:60:4:0.0408:0:1 0/0:47:0:0,0:23,24:0:2,0:27:1:30.7:1:1:0:60:46:1:0:0.1 -6 29230100 . T TA 30 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTTCTTTTTTTATTTT;RSEQ=TTTTTTGTTTGTTTTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30:1:1:0:60:4:1:0:0.5 -6 29230520 . A C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0.13102;LSEQ=TGGGAGTAACAATGGAGTAA;RSEQ=ATATATGGAGAAGTTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:37:36,1:72,0:0.3394:1,1:24.1:1:32.5:1:0.33945:0:60:74:0.3491:0:1.1 0/1:64:4:4,0:60,0:0.0625:1,0:14.3:1:30.8:1:1:0:60:8:0.0625:0:1 -6 29230577 . C A 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06283;SOR=0.72295;LSEQ=TGTTTCCTGGCTCTATATAC;RSEQ=TATATCTAACAGTCCCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:318:184:136,48:109,24:0.5786:2,2:23.6:1:30.2:1:0.10381:1.60059:60:60.333:0.5783:0:1.1 0/1:253:126:87,39:98,28:0.498:2,2:23.7:1:29.7:1:0.15362:1.56613:60:125:0.5:0:1.1 -6 29230683 . T C 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23286;LSEQ=CTTGATCTTGAGTACAGCCA;RSEQ=AGCAATGAAGCCATATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:564:493:195,298:29,41:0.8741:2,2:25.1:1:31.9:1:0.7948:1.08077:58.1:81.167:0.8743:0:1.1 1/0:502:310:132,178:82,109:0.6175:2,2:25.6:1:31:1:1:1.01443:59.7:50.667:0.6179:0:1.1 -6 29236102 . TTTTTATTATAA T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATTCGGCTTAATTATAA;RSEQ=TTTTATTATATTTTTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:34.5:1:30.5:1:1:0:54:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29236155 . TAGACAATTTAT A 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TATTATCTTTATCTCAGGTG;RSEQ=TTACAAAATAAATTGTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:22.7:1:33:0:1:0:60:6:0.6:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29236581 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=0;LSEQ=AGAGGAACAAGAACTATAAT;RSEQ=AGGCACATGGCAAATGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:12,124:0.0145:2,2:5:1:28.5:1:0.18015:9.97:60:4:0.0147:0:1 0/0:126:0:0,0:23,103:0:2,0:47:0:13:0:1:0:60:0:0:0:7 -6 29236588 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12518;LSEQ=CAAGAACTATAATCAGGCAC;RSEQ=TGGCAAATGTGGTTACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:36:1,35:6,78:0.3:2,1:25.5:1:32.3:1:0.67305:2.67444:60:72:0.3:0:1.1 0/1:99:5:1,4:11,83:0.0505:2,2:20.6:1:30.8:1:0.48339:1.87:60:10:0.051:0:1 -6 29236645 . G T 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.00495;SOR=Inf;LSEQ=CACATGCAATCTTGAATCTT;RSEQ=ATCATTGCAGACATTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:1,38:0:1,0:18:1:31:1:1:0:60:38:1:0:0.4 0/1:30:6:0,6:0,24:0.2:1,0:23.2:1:26.3:1:1:0:60:12:0.2:0:1 -6 29236722 . G A 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.06347;SOR=8.88906;LSEQ=CGAGGAAGACTCGTGGCATA;RSEQ=GGGGAAGGTATGATGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,9:0.3333:0,0:16.2:1:29.8:1:1:0:60:10:0.3571:0:1 1/1:6:5:0,5:0,1:0.8333:0,0:25:1:30.2:1:1:0:60:10:0.8333:0:1 -6 29491195 . G GC 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.19087;LSEQ=TTCCTGTTTTATCCTAAACA;RSEQ=CTTCTTTCCTAAATAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:3,2:6,3:0.3571:2,2:20.2:1:29.5:1:1:1.30579:60:10:0.3571:0.2143:0 0/1:10:4:3,1:5,1:0.4:2,2:33:1:32.1:1:1:1.58108:60:8:0.4:0.1:0 -6 29491263 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.18149;SOR=Inf;LSEQ=AAGATTTCTTTGTTGTTGCT;RSEQ=CTGTTGTTGCTGCTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:15,18:0:2,0:26.6:1:32.2:1:1:0:60:32:1:0:0.2 0/1:25:2:1,1:10,13:0.08:2,2:37:1:30.5:1:1:1.29:60:4:0.08:0:1 -6 29491297 . GTC G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.50046;SOR=0;LSEQ=TGTTGTTTCCTTGAGACAAG;RSEQ=TCTCTCTCTGTGTCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:24:1:30.5:1:1:1.0801:60:4:0.0769:0:0 0/0:20:0:0,0:8,12:0:2,0:29.9:1:29.9:1:1:0:60:40:1:0:0.2 -6 29691019 . G A 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64241;SOR=2.05177;LSEQ=GAGGCGGTGTCTGGGGTTGG;RSEQ=AGGCTCAGTATTGAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:0.2727:0,0:36.7:1:24.3:1:1:0:60:2:0.2222:0:1.7 0/1:9:4:4,0:5,0:0.4444:0,0:24.3:1:25.5:1:1:0:60:3:0.375:0:1.8 -6 29691090 . T A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=9.71141;LSEQ=CAACCCGTGTCAGGTCCTTC;RSEQ=TCCTGGATACTCATAACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:6:6,0:58,2:0.0909:1,0:25.3:1:30.2:1:1:0:60:12:0.0909:0:1.2 1/0:34:17:16,1:14,2:0.5:2,1:19.4:1:30.5:1:0.60117:2.23:60:34:0.5152:0:1.2 -6 29691097 . A T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01619;SOR=Inf;LSEQ=TGTCAGGTCCTTCTTCCTGG;RSEQ=TACTCATAACGCGGCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:70,3:0:1,0:22.8:1:29.8:1:1:0:60:23.333:1:0:0.2 0/1:42:4:3,1:35,3:0.0952:2,2:22:1:29.5:1:0.34053:3.70283:60:8:0.1026:0:2 -6 29691140 . C G 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=CTCACTCCCATTGGGCGTCG;RSEQ=GTTTCTAGAGAAGCCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:123,6:0:1,0:25.3:1:31.9:1:1:0:60:42:1:0:0.1 0/1:97:12:10,2:78,7:0.1237:2,2:28.3:1:31.8:1:0.30782:2.20542:60:24:0.1304:0:1.4 -6 29691166 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19271;SOR=Inf;LSEQ=TAGAGAAGCCAATCAGTGTC;RSEQ=CCGCAGTTCCCAGGTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:179,21:0:2,0:22.7:1:29.4:1:1:0:60:39:1:0:0.2 0/1:157:2:1,1:137,18:0.0127:2,2:12:1:27:1:0.22807:7.43509:60:4:0.0132:0:1.5 -6 29691303 . G A 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=46.98423;LSEQ=GCCCTGACCGATACTTGGGC;RSEQ=GGTGAGTGCGGGGTCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:544:1:1,0:230,311:0.0018:2,0:1:0:28:0:0.4262:0:60:2:0.0019:0:2 0/1:438:35:13,22:162,241:0.0799:2,2:21.5:1:30.6:1:0.85758:1.1372:60:70:0.0805:0:1.1 -6 29691390 . CT GC 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=5.59672;LSEQ=CGCAGGACTCAGGGAGCCGC;RSEQ=CCGGAGGAGGGTCTGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:103:41,62:74,101:0.364:2,2:23.8:1:31.2:1:0.70687:1.10754:60:206:0.3718:0.0601:1 1/0:156:119:63,56:17,18:0.7628:2,2:23.2:1:30.7:1:0.70269:1.19:59.9:238:0.7778:0.0769:1.1 -6 29691391 . T C 42 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.46178;SOR=1.84223;LSEQ=GCAGGACTCAGGGAGCCGCC;RSEQ=CCGGAGGAGGGTCTGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:4:1,3:73,103:0.015:2,2:18.3:1:27.5:1:0.64463:2.11816:60:3:0.0173:0:2.5 0/1:146:4:1,3:17,18:0.0274:2,2:12.8:1:21:1:0.60937:2.7643:60:1:0.0556:0:1.8 -6 29691396 . A G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30214;SOR=0;LSEQ=ACTCAGGGAGCCGCCTCCGG;RSEQ=GGAGGGTCTGGCGGGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:4:2,2:113,161:0.0143:2,2:15.3:1:31.5:1:1:1.42:60:8:0.0148:0:2 0/0:169:0:0,0:86,83:0:2,0:22.4:1:29.4:1:1:0:60:32.8:1:0:0.9 -6 29691408 . C T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.566;SOR=3.04365;LSEQ=GCCTCCGGAGGAGGGTCTGG;RSEQ=GGGTCTCAGCCCCTCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:1:0,1:138,164:0.0033:2,0:1:0:26:0:1:0:60:2:0.0033:0:1 0/1:200:2:1,1:109,89:0.01:2,2:6.5:1:24.5:1:1:1.22347:60:4:0.0103:0:1.5 -6 29691473 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26331;SOR=0;LSEQ=ATTTCAGCACCGCTGTGTCG;RSEQ=GGCCCGGCCGCGGGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:138,156:0.0101:2,2:8.3:1:22.3:1:1:1.76597:60:2:0.0069:0:1.7 0/0:224:0:0,0:108,116:0:2,0:25.3:1:30.1:1:1:0:60:111:1:0:0.3 -6 29691487 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26603;SOR=0;LSEQ=GTGTCGCGGCCCGGCCGCGG;RSEQ=GAGCCCCGCTACATCGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:2,1:125,147:0.0109:2,2:15:1:28:1:0.59704:2.34:60:6:0.0111:0:1.3 0/0:202:0:0,0:89,113:0:2,0:23.6:1:29.8:1:1:0:60:39.4:1:0:0.2 -6 29691524 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16943;SOR=Inf;LSEQ=CCGTGGAGTACGTAGACGAC;RSEQ=CGCAATTCCTGCGGTTCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:95,143:0:2,0:22.9:1:29.4:1:1:0:60:58.5:1:0:0.2 0/1:167:2:1,1:71,94:0.012:2,2:29.5:1:30.5:1:1:1.32:60:4:0.0123:0:1.5 -6 29691551 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21603;SOR=Inf;LSEQ=TCCTGCGGTTCGACAGCGAC;RSEQ=CCGCGATTCCGAGGATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:83,126:0:2,0:28.8:1:31:1:1:0:60:40.8:1:0:0.1 0/1:182:2:1,1:88,92:0.011:2,2:27:0:31.5:1:1:1.05:60:4:0.0113:0:1.5 -6 29691592 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49862;SOR=Inf;LSEQ=CCGCGGGAGCCGTGGGTGGA;RSEQ=CAAGAGGGGCCGCAGTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:76,103:0:2,0:22.7:1:32.1:1:1:0:60:178:1:0:0.1 0/1:181:2:1,1:96,83:0.011:2,2:30.5:1:29:1:1:1.15569:60:4:0.0111:0:3 -6 29691604 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49906;SOR=Inf;LSEQ=TGGGTGGAGCAAGAGGGGCC;RSEQ=CAGTATTGGGAGTGGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:77,90:0:2,0:22.4:1:30.9:1:1:0:60:166:1:0:0.1 0/1:178:2:1,1:95,80:0.0112:2,2:33.5:1:28:1:1:1.18634:60:4:0.0114:0:1 -6 29691648 . A G 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19985;SOR=0;LSEQ=GTACGCCAAGGCCAACGCAC;RSEQ=GACTGACCGAGTGGCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:74,87:0.0123:2,2:20:1:26:0:1:1.17:60:4:0.0123:0:1 0/0:201:0:0,0:90,111:0:2,0:26.1:1:30:1:1:0:60:49.25:1:0:0.2 -6 29691713 . A C 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02413;SOR=Inf;LSEQ=AGAGCGAGGCTGGTGAGTGA;RSEQ=CCCGGCCGGGGGCGCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:32,62:0:2,0:22.2:1:29.5:1:1:0:60:188:1:0:0.2 0/1:87:5:1,4:23,59:0.0575:2,2:24:1:28.8:1:1:1.55213:60:10:0.0581:0:2 -6 29691736 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50041;SOR=0;LSEQ=CGGCCGGGGGCGCAGGTCAC;RSEQ=ACCACCCCCCATCCGCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:14,45:0.0328:2,2:37:1:30:1:0.43443:3.14:60:4:0.0333:0:2 0/0:50:0:0,0:13,37:0:2,0:23.4:1:30.3:1:1:0:60:100:1:0:0.7 -6 29691740 . AC A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.18733;SOR=Inf;LSEQ=CGGGGGCGCAGGTCACGACC;RSEQ=CCCCCATCCGCCACGGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:11,46:0:2,0:22.2:1:31.8:1:1:0:60:114:1:0:0.2 0/1:44:2:0,2:11,31:0.0455:2,0:38.5:1:31:1:1:0:60:4:0.0488:0:0.5 -6 29691744 . C G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.07371;SOR=Inf;LSEQ=GGCGCAGGTCACGACCACCC;RSEQ=CCATCCGCCACGGACCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:9,45:0:2,0:22.9:1:31.7:1:1:0:60:108:1:0:0.2 0/1:40:3:0,3:9,28:0.075:2,0:39.3:1:31.7:1:1:0:60:6:0.0769:0:2.3 -6 29691772 . T C 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00034;SOR=7.64131;LSEQ=CCACGGACCGCCCGGGTCCC;RSEQ=CAGAGTCTCCGGATCCGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:6:1,5:9,29:0.1364:2,2:17.8:1:32.2:1:1:1.5377:60:12:0.1395:0:1.3 1/0:27:15:4,11:0,12:0.5556:0,2:26.9:1:30.1:1:0.10598:0:60:14:0.5385:0:1.7 -6 29691774 . A C 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00074;SOR=Inf;LSEQ=ACGGACCGCCCGGGTCCCTC;RSEQ=GAGTCTCCGGATCCGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:11,32:0:2,0:24.2:1:31.1:1:1:0:60:86:1:0:0.3 0/1:27:7:3,4:1,19:0.2593:1,2:34.3:1:31.1:1:0.04188:12.39:60:14:0.2593:0:2.1 -6 29691857 . C G 96 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=15.66999;LSEQ=GAGTCCCAGGCGCCTTTACC;RSEQ=AGGTTCATTTTCAGTTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:2,1:19,15:0.0811:2,2:22.7:1:28.7:1:1:1.56:60:6:0.0833:0:1.3 1/0:15:9:4,5:5,1:0.6:2,2:27.8:1:30.6:1:0.28671:5.514:60:18:0.6:0:1.1 -6 29691936 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.13729;SOR=Inf;LSEQ=TAGCTGGGCGGGGCTGACTG;RSEQ=GGGGACCGGCTAGGGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:43,19:0:2,0:24.5:1:30.5:1:1:0:60:30:1:0:0 0/1:37:2:1,1:26,9:0.0541:2,2:46.5:1:30:1:0.47297:2.79285:60:4:0.0541:0:1 -6 29691992 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1978;SOR=Inf;LSEQ=GAATGGCTGCGACATGGGGC;RSEQ=CGACGGACGCCTCCTCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:51,47:0:2,0:24.8:1:30.8:1:1:0:60:97:1:0:0.1 0/1:79:2:1,1:47,30:0.0253:2,2:24:0:32:1:1:1.55745:60:4:0.026:0:1.5 -6 29692000 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.21057;SOR=Inf;LSEQ=GCGACATGGGGCCCGACGGA;RSEQ=GCCTCCTCCGCGGGTATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:54,48:0:2,0:25.7:1:30.4:1:1:0:60:50:1:0:0.1 0/1:87:2:1,1:52,33:0.023:2,2:11.5:1:28:1:1:1.56722:60:4:0.0241:0:1 -6 29692050 . C A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24438;SOR=0;LSEQ=TACGACGGCAAGGATTACAT;RSEQ=TCCCTGAACGAGGACCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:45,63:0.0182:2,2:36:0:30.5:1:1:1.40:60:4:0.0183:0:1.5 0/0:112:0:0,0:53,59:0:2,0:26.6:1:31.3:1:1:0:60:224:1:0:0.2 -6 29692305 . A G 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52381;SOR=4.91839;LSEQ=CAAGGTTGGGAGGAAAGTGG;RSEQ=CCCAATGCTAGGATATCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,2:0.25:2,0:12:0:32:0:1:0:60:2:0.25:0:1 1/0:6:4:0,4:0,2:0.6667:0,0:30.5:1:33.3:1:1:0:60:8:0.6667:0:1 -6 29692433 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACAATTAAGGGATGAAAT;RSEQ=TCTGAGGGAATGGAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:25:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:26:1:32:1:1:0:60:4:1:0:1 -6 29692562 . A G 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCACACTCAATGTGTTTG;RSEQ=GGCTCTGATTCCAGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:28.5:1:31:1:1:0:60:4:0.5:0:1.5 1/1:1:1:1,0:0,0:1:0,0:14:0:26:0:1:0:60:2:1:0:1 -6 29692634 . T G 36 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03333;SOR=Inf;LSEQ=TGCTCCCCCCTCAGAGACTC;RSEQ=AACTTTCCAAGGAATAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:0.1429:2,0:17:0:26:0:1:0:60:2:0.1429:0:2 1/1:3:3:3,0:0,0:1:0,0:12.7:1:23:1:1:0:60:2:1:0:1.3 -6 29692852 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4985;SOR=0;LSEQ=ACCACCCCATCTCTGACCAT;RSEQ=AGGCCACCCTGAGGTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:48,53:0.0194:2,2:18.5:1:30:1:1:1.10:60:4:0.02:0:1 0/0:94:0:0,0:37,57:0:2,0:21.9:1:30.9:1:1:0:59.8:188:1:0:0.1 -6 29692880 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50221;SOR=0;LSEQ=CCTGAGGTGCTGGGCCCTGG;RSEQ=CTTCTACCCTGCGGAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:0,2:26,35:0.0317:2,0:35.5:1:32:0:0.50742:0:39:4:0.0333:0:3 0/0:50:0:0,0:15,35:0:2,0:21.3:1:31.1:1:1:0:59.6:100:1:0:0.1 -6 29693011 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.91367;LSEQ=GGGCCGCTGTGGTGGTGCCT;RSEQ=CTGGAGAGGAACAGAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:118:87,31:121,44:0.417:2,2:21.4:1:29.3:1:1:1.02:59.8:58:0.4218:0:1.1 1/0:217:160:116,44:38,19:0.7373:2,2:21.3:1:29.7:1:0.40157:1.32:60:159:0.743:0:1.1 -6 29693113 . C T 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGATGGGTAAAGAGGGGAA;RSEQ=GAGGGGTCATGTCTTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:416:0:0,0:189,226:0:2,0:23.2:1:30.4:1:1:0:60:50.875:0.9975:0:0.1 0/1:347:24:14,10:134,187:0.0692:2,2:19.1:1:29.7:1:0.13576:1.95:60:23:0.0673:0:1.2 -6 29693183 . G A 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGCAGGGTCAGGGCTGAG;RSEQ=CCTGGAGATCAGGGCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:116:62,54:166,111:0.2944:2,2:22.4:1:29.4:1:0.26288:1.30162:60:57:0.2992:0:1.2 0/0:326:0:0,0:192,132:0:2,0:21.5:1:31:1:1:0:60:63.8:0.9969:0:0.2 -6 29693370 . T A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10357;SOR=Inf;LSEQ=GGTGAGGAGTGGAGTCTGAG;RSEQ=TTTCTTGTCCCACTGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:81,207:0:2,0:22.2:1:29.8:1:1:0:60:71:1:0:0.1 0/1:256:3:3,0:79,174:0.0117:2,0:9.3:1:23:1:0.03205:0:59.7:2:0.008:0:3.7 -6 29693392 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17308;SOR=5.19327;LSEQ=TTCTTGTCCCACTGGGGGTT;RSEQ=CAAGCCCCAAGTAGAAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:1:0,1:32,134:0.006:2,0:39:0:31:0:1:0:60:2:0.006:0:1 0/1:132:4:2,2:27,101:0.0303:2,2:13.5:1:27.3:1:0.20962:3.69:60:8:0.031:0:1 -6 29693499 . A G 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03636;SOR=Inf;LSEQ=CAGCACCTACTCATTTGTAA;RSEQ=GCTCCTGTGAAAATGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:4,32:0:2,0:21.7:1:30.9:1:1:0:60:35:1:0:0.1 0/1:9:2:0,2:1,6:0.2222:2,0:29:1:28:1:1:0:60:4:0.2222:0:2 -6 29693680 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1369;SOR=Inf;LSEQ=GATCCTGCCCTGGATCTACA;RSEQ=TTACACTTTTCTGGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:33,7:0:2,0:24.7:1:32.5:1:1:0:60:80:1:0:0 0/1:24:2:2,0:20,2:0.0833:2,0:32.5:1:31:1:1:0:60:4:0.0909:0:1 -6 29693726 . G T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01092;SOR=Inf;LSEQ=GGATCAAAGACTAGGGGTTT;RSEQ=CTCTAGGACCTTATGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:79,33:0:2,0:23.2:1:32:1:1:0:60:55:1:0:0 0/1:79:5:4,1:54,20:0.0633:2,2:18.4:1:30:1:1:1.47:60:10:0.0641:0:1 -6 29693811 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23213;SOR=Inf;LSEQ=GAAACAGAGGGAGCTACTCT;RSEQ=AGGCTGCAGGTAAGATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:84,94:0:2,0:24.8:1:31.7:1:1:0:60:177:1:0:0.1 0/1:166:2:1,1:89,75:0.012:2,2:33:1:27.5:1:1:1.18544:60:4:0.0123:0:1 -6 29693815 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2334;SOR=Inf;LSEQ=CAGAGGGAGCTACTCTCAGG;RSEQ=TGCAGGTAAGATGAAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:82,94:0:2,0:25.5:1:31.9:1:1:0:60:57.667:1:0:0.1 0/1:165:2:1,1:87,76:0.0121:2,2:5.5:1:28:0:1:1.1438:60:4:0.0123:0:1 -6 29693833 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49865;SOR=0;LSEQ=GGCTGCAGGTAAGATGAAGG;RSEQ=GGCTGATCCCTGAGATTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:72,86:0.0125:2,2:26.5:1:29:1:1:1.19:60:4:0.0131:0:1 0/0:153:0:0,0:73,80:0:2,0:27.8:1:29.1:1:1:0:60:16:1:0:0.2 -6 29693938 . G A 114 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02152;SOR=2.7053;LSEQ=GTGGGCTCTGACCAGGTCCT;RSEQ=TTTTTGTTCTACCCCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:9:3,6:51,77:0.0657:2,2:24.1:1:29.6:1:1:1.32204:60:18:0.0667:0:1 0/1:106:17:4,13:40,49:0.1604:2,2:27:1:28:1:0.11553:2.63066:60:7.5:0.1456:0:1.2 -6 29693952 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18367;SOR=Inf;LSEQ=GGTCCTGTTTTTGTTCTACC;RSEQ=CAATCACTGACAGTGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:50,84:0:2,0:26.5:1:30.8:1:1:0:60:43.667:1:0:0.4 0/1:101:2:1,1:39,60:0.0198:2,2:49.5:1:29:1:1:1.53:60:4:0.0198:0:2 -6 29693966 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19524;SOR=Inf;LSEQ=TCTACCCCAATCACTGACAG;RSEQ=GCCCAGGGCTCTGGGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:43,65:0:2,0:25:1:29.6:1:1:0:60:53:1:0:0.5 0/1:86:2:1,1:34,50:0.0233:2,2:26:0:33:1:1:1.46:60:4:0.0233:0:1 -6 29693969 . C T 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00723;SOR=0.34209;LSEQ=ACCCCAATCACTGACAGTGC;RSEQ=CAGGGCTCTGGGGTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:31:12,19:29,48:0.287:2,2:26.4:1:30.1:1:1:1.04:60:62:0.2925:0:1.2 0/1:83:10:2,8:31,42:0.1205:2,2:28.9:1:29.7:1:0.30187:2.9184:60:20:0.1235:0:1.1 -6 29759729 . C T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CAGAAGTAGCGGGGTCAGGG;RSEQ=GAAGTCCCAGGGCCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:18.5:1:31.5:1:0.33333:0:60:4:0.3333:0:2.5 0/0:3:0:0,0:3,0:0:0,0:24:1:32.3:1:1:0:60:6:1:0:1 -6 29759750 . G A 80 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68231;LSEQ=GAAGTCCCAGGGCCTCAGGC;RSEQ=TGGCTCTCAGGATCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:5,1:8,0:0.4286:0,2:19.2:1:31.3:1:0.42857:0:60:12:0.4286:0:3.5 0/1:3:1:1,0:2,0:0.3333:0,0:31:0:32:0:1:0:60:2:0.5:0:3 -6 29759811 . C G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23234;SOR=2.17066;LSEQ=TGGGGAGGCCCAGCGCTGGG;RSEQ=ATTCCCCATCTTTGCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:12:12,0:32,1:0.2667:1,0:30.2:1:31.4:1:1:0:60:24:0.2727:0:3.6 0/1:18:8:6,2:9,1:0.4444:2,2:20:1:31:1:0.55882:2.81935:59.3:16:0.4444:0:4.5 -6 29759823 . TT CC 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16797;SOR=2.17202;LSEQ=GCGCTGGGCATTCCCCATCT;RSEQ=GCAGGGTTTCTCTTCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:12:12,0:38,2:0.2264:2,0:24:1:30.2:1:1:0:60:24:0.24:0.0189:2.4 0/1:23:9:7,2:11,2:0.3913:2,2:25.7:1:30.7:1:1:1.53863:59.3:18:0.3913:0:3.6 -6 29759824 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTGGGCATTCCCCATCTT;RSEQ=GCAGGGTTTCTCTTCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:2,0:38,2:0.0377:2,0:10.5:1:31.5:1:1:0:60:4:0.05:0:3 0/0:23:0:0,0:11,2:0:2,0:19.4:1:29.3:1:1:0:60:26:1:0:0.2 -6 29759876 . G A 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16061;SOR=1.5457;LSEQ=TGTCGGGTCCTTCTTCCTGG;RSEQ=TACTCACCGGGCTGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:37:34,3:98,10:0.2552:2,2:32:1:29.7:1:1:1.16:60:36:0.2571:0:1.4 0/1:75:26:23,3:42,6:0.3467:2,2:21.8:1:29.3:1:1:1.09:59.8:52:0.3562:0:3.2 -6 29759885 . G A 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCTTCCTGGGTACTCACC;RSEQ=GGCTGCCCCAGTTCTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:153,15:0:2,0:25.7:1:29.9:1:1:0:60:83:1:0:0.4 0/1:102:36:32,4:58,7:0.3529:2,2:19:1:30:1:1:1.03538:59.8:72:0.3564:0:2.9 -6 29759894 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15226;SOR=Inf;LSEQ=GGGTACTCACCGGGCTGCCC;RSEQ=AGTTCTCACTCCCATTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:175,18:0:2,0:25.7:1:31.5:1:1:0:59.8:386:1:0:0.4 0/1:124:2:1,1:112,10:0.0161:2,2:21:1:28.5:1:0.17021:10.72653:60:4:0.0167:0:1 -6 29759912 . A G 40 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26755;SOR=0;LSEQ=CCCAGTTCTCACTCCCATTG;RSEQ=GTGTCGGGTTTCTAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:3:2,1:207,20:0.013:2,2:29.3:1:25.3:1:0.25066:5.10817:49.7:2:0.009:0:7.3 0/0:167:0:0,0:151,15:0:2,0:24.5:1:28.7:1:1:0:60:19.75:0.9937:0:0.8 -6 29759920 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17205;SOR=Inf;LSEQ=TCACTCCCATTGAGTGTCGG;RSEQ=TTTCTAGAGAAGCCAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:244,29:0:2,0:23.9:1:31.1:1:1:0:59.9:67.25:1:0:0.5 0/1:194:2:1,1:172,20:0.0103:2,2:16:1:27.5:1:0.20528:8.41571:60:4:0.0105:0:1 -6 29759923 . T C 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCCATTGAGTGTCGGGTT;RSEQ=CTAGAGAAGCCAATCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:248,32:0:2,0:24:1:30.3:1:1:0:59.9:92.333:1:0:0.4 0/1:206:69:60,9:123,14:0.335:2,2:25.5:1:30.8:1:0.63998:1.31599:60:22:0.3267:0:2.1 -6 29759996 . T C 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00597;SOR=1.30624;LSEQ=CCCACCGGGACTCCGATTCT;RSEQ=CCCAGTCGCCGAGGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:294:170,124:370,306:0.3031:2,2:26.9:1:30.9:1:0.39897:1.13:59.9:48:0.3035:0:1.2 0/1:966:350:191,159:338,278:0.3623:2,2:27.1:1:30.5:1:0.94644:1.01212:60:57.333:0.361:0:1.3 -6 29760029 . G C 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATGGTGTCATGGCGCCCC;RSEQ=AACCCTGCTTCTGCTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1128:0:0,0:551,573:0:2,0:25.3:1:30.2:1:1:0:60:47.87:0.9964:0:0.4 0/1:1113:48:21,27:508,555:0.0431:2,2:30:1:30.8:1:0.65843:1.17666:60:96:0.044:0:1.1 -6 29760050 . CG C 98 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.01961;SOR=5.26683;LSEQ=AACCCTGCTTCTGCTGCTCT;RSEQ=GGGGCCCTGGTCCTGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:955:2:1,1:431,519:0.0021:2,2:19:1:33:0:1:1.20:60:4:0.0021:0:0 0/1:914:10:5,5:391,511:0.0109:2,2:24:1:29.8:1:0.75386:1.31:60:20:0.0111:0.0011:0.1 -6 29760111 . G C 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7612;SOR=0.94571;LSEQ=GGGGTCGGGAGGGAAACGGC;RSEQ=TCTGTGGGGAGTAGCTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:150:41,109:88,207:0.3371:2,2:24.6:1:31.7:1:0.65859:1.12988:60:49:0.3349:0:1.9 0/1:348:113:32,81:71,163:0.3247:2,2:23.6:1:30.9:1:0.8021:1.10223:60:55.5:0.3236:0:1.3 -6 29760132 . G T 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTGTGGGGAGTAGCTAGGG;RSEQ=CCTGCCCGGCGGGGGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:108:25,83:59,168:0.3224:2,2:25.2:1:29.6:1:0.5931:1.16541:60:53:0.3242:0:2.3 0/0:240:0:0,0:70,168:0:2,0:23.4:1:31.1:1:1:0:60:78.333:1:0:0.5 -6 29760149 . G T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00942;SOR=Inf;LSEQ=GGGGCCTGCCCGGCGGGGGC;RSEQ=CAGGAACCCGGTTGCGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:74,200:0:2,0:24.4:1:31.1:1:1:0:60:33.25:0.9925:0:0.7 0/1:181:5:2,3:52,123:0.0276:2,2:35:1:30:1:0.63697:1.57:60:10:0.0279:0:2.4 -6 29760188 . G A 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62157;SOR=1.14214;LSEQ=GCCGGGAGGAGGGTCGGGAG;RSEQ=GTCTCAGCCCCCTCCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:61:23,38:44,90:0.3096:2,2:22.9:1:31.3:1:0.51925:1.24:60:122:0.3211:0:1.8 0/1:121:41:10,31:20,60:0.3388:2,2:21:1:30.5:1:1:1.03306:60:82:0.3388:0:1.5 -6 29760299 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67007;LSEQ=CTCTCCGTGGGCGACGTGGA;RSEQ=GACACGCAGTGCGTGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:90,84:0.0114:2,2:19:1:29:1:1:1.07098:60:4:0.0116:0:1 0/0:131:1:1,0:74,56:0.0076:2,0:1:0:23:0:1:0:60:2:0.0079:0:1 -6 29760311 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50496;SOR=0;LSEQ=GACGTGGACGACACGCAGTG;RSEQ=GTGCGGCTCGACAGCGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:84,84:0.0118:2,2:13:1:30.5:1:1:1:60:4:0.012:0:2 0/0:135:0:0,0:75,60:0:2,0:26:1:30.2:1:1:0:60:44:1:0:0.2 -6 29760317 . G C 163 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACGACACGCAGTGCGTGCG;RSEQ=CTCGACAGCGACGCCACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:40:12,28:74,54:0.2381:2,2:24.5:1:30.7:1:0.00342:3.17518:59.6:19:0.2331:0:1.1 0/0:141:0:0,0:80,61:0:2,0:25.4:1:29.9:1:1:0:60:14.667:1:0:0.2 -6 29760341 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50271;SOR=0;LSEQ=GACAGCGACGCCACGAGTCC;RSEQ=AGGATGGAGCCGCGGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:85,98:0.0108:2,2:25:1:29:1:1:1.15:60:4:0.0112:0:1 0/0:154:0:0,0:89,65:0:2,0:34:0:14:0:1:0:60:0:0:0:2 -6 29760351 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50342;SOR=0;LSEQ=CCACGAGTCCCAGGATGGAG;RSEQ=CGCGGGCGCCGTGGATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:80,101:0.0109:2,2:49.5:1:29:0:1:1.26:60:4:0.0112:0:1.5 0/0:150:0:0,0:82,68:0:2,0:25.7:1:31.1:1:1:0:60:49:1:0:0.2 -6 29760352 . CGCGGGCGCCGTGGATGGAGCA C 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33498;SOR=1.3247;LSEQ=CACGAGTCCCAGGATGGAGC;RSEQ=GGAGGGGCCGGAATATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:32:12,20:65,81:0.1798:2,2:28.8:1:31:1:0.55618:1.33529:59.5:64:0.1818:0.0225:0.9 0/1:151:34:21,13:63,54:0.2252:2,2:25.5:1:30.4:1:0.43988:1.38:59.9:68:0.2267:0.053:0.2 -6 29760364 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21561;SOR=Inf;LSEQ=GATGGAGCCGCGGGCGCCGT;RSEQ=GATGGAGCAGGAGGGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:65,76:0:2,0:25.9:1:31.2:1:1:0:60:69.5:1:0:0.2 0/1:147:2:1,1:67,52:0.0136:2,2:28:0:30.5:1:1:1.28573:60:4:0.0168:0:1.5 -6 29760365 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.22278;SOR=Inf;LSEQ=ATGGAGCCGCGGGCGCCGTG;RSEQ=ATGGAGCAGGAGGGGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:62,75:0:2,0:26.7:1:31.4:1:1:0:60:274:1:0:0.2 0/1:148:2:1,1:67,53:0.0135:2,2:20:1:26.5:1:1:1.2617:60:4:0.0164:0:1 -6 29760399 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.20704;SOR=Inf;LSEQ=GGCCGGAATATTGGGAAGAG;RSEQ=AGACAGGGACCGCCAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:102,107:0:2,0:21.5:1:31.1:1:1:0:60:103.5:1:0:0.3 0/1:175:2:1,1:95,78:0.0114:2,2:23:1:31:0:1:1.21656:60:4:0.0114:0:1 -6 29760462 . T C 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=ACCTGCGGACCCTGAGCGGC;RSEQ=ACTACAACCAGAGTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:35:18,17:88,107:0.1522:2,2:30.7:1:31:1:0.58142:1.29:60:34:0.1491:0:1.5 0/0:244:0:0,0:107,137:0:2,0:29.7:1:29:1:1:0:60:60:1:0:0.4 -6 29760504 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23376;SOR=0;LSEQ=GTGAGTGACACCGGCCGGGG;RSEQ=CGCAGGTCACTACCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:48,75:0.016:2,2:22.5:1:28:1:1:1.56:60:4:0.0164:0:1 0/0:133:0:0,0:50,83:0:2,0:21.6:1:30.9:1:1:0:60:43.333:1:0:0.8 -6 29760510 . G A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=3.58691;LSEQ=GACACCGGCCGGGGGCGCAG;RSEQ=TCACTACCCCTCCACATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:17:4,13:40,52:0.156:2,2:20.3:1:30.6:1:0.17892:2.48049:60:34:0.1604:0:1.9 0/1:115:46:17,29:24,45:0.4:2,2:22.9:1:29.2:1:0.84433:1.10:60:92:0.4035:0:2 -6 29760523 . C T 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGCGCAGGTCACTACCCCTC;RSEQ=ACATCCCCCACGGACCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:29,58:0:2,0:22.7:1:31.3:1:1:0:60:28:1:0:0.4 0/1:81:35:12,23:17,29:0.4321:2,2:22.3:1:28.3:1:0.81993:1.12195:60:34:0.425:0:2.3 -6 29760536 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18831;SOR=Inf;LSEQ=ACCCCTCCACATCCCCCACG;RSEQ=ACCGCCCGGGTCTCCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:26,49:0:2,0:22.5:1:31.1:1:1:0:60:74:1:0:0.3 0/1:58:2:0,2:16,40:0.0345:2,0:18.5:1:31.5:1:1:0:60:4:0.0345:0:1 -6 29760590 . G A 106 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03325;SOR=2.69944;LSEQ=GATCCACGCCGAGGCAGCGG;RSEQ=ACCTGGAGACCCTTGACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:13:10,3:33,27:0.1781:2,2:32.3:1:28:1:0.21568:2.69:60:5.5:0.1571:0:2.3 0/1:35:13:7,6:11,11:0.3714:2,2:23.1:1:28.8:1:1:1.16:60:26:0.3824:0:2.6 -6 29760605 . G T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32684;SOR=1.68504;LSEQ=AGCGGGACCTGGAGACCCTT;RSEQ=ACCCGGGAGAGGCCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:14:12,2:40,24:0.1795:2,2:26.5:1:28.1:1:0.12396:3.55:60:13:0.1688:0:2.3 0/1:37:10:6,4:16,11:0.2703:2,2:26.8:1:28.5:1:1:1.03:60:20:0.2857:0:2.4 -6 29760677 . A G 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37397;SOR=1.28027;LSEQ=CCCGCAGGTTGGTCCTGGCG;RSEQ=GGGCGGGGCTCGGTGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:44:34,10:138,20:0.2167:2,2:20.8:1:30:1:0.14756:2.02134:60:13.667:0.2113:0:1.6 0/1:149:39:35,4:93,17:0.2617:2,2:22.2:1:31.5:1:0.59367:1.59:60:78:0.2708:0:1.3 -6 29760730 . AC A 210 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGCGGGGCCAGGGTCTCAC;RSEQ=CCATCTAGAGGATGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:99:62,37:224,163:0.2037:2,2:27.7:1:31.8:1:0.42428:1.22:60:198:0.2054:0.0226:1.6 0/0:469:0:0,0:266,202:0:2,0:25:1:30.6:1:1:0:60:45.8:0.9978:0:0.3 -6 29760765 . C A 201 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCTGTCTGCGACGTGGGGT;RSEQ=GGACGGGCGCCTACTCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:118:64,54:228,251:0.1977:2,2:25.6:1:29.3:1:0.21769:1.30:60:236:0.2014:0:2 0/0:575:0:0,0:278,296:0:2,0:27.5:1:30.1:1:1:0:60:94.667:0.9982:0:0.3 -6 29760799 . T C 194 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCGCGGGTATCACCAGCT;RSEQ=GCTTACGATGGCAAGGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:93:45,48:119,204:0.2236:2,2:25.1:1:29.8:1:0.05385:1.61:60:30:0.2217:0:2.3 0/0:423:0:0,0:181,241:0:2,0:24.8:1:29.7:1:1:0:60:421:0.9976:0:0.3 -6 29760819 . A C 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTTACGATGGCAAGGATT;RSEQ=CATCGTCCTGAACGAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:117,229:0:2,0:22.3:1:29:1:1:0:60:114.333:0.9971:0:0.6 0/1:307:74:25,49:93,140:0.241:2,2:20.4:1:30.4:1:0.41081:1.3009:60:36:0.2361:0:1.1 -6 29760854 . G A 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56846;SOR=2.95263;LSEQ=AGGACCTGTGCTCCTTGACA;RSEQ=CCGCAGACACGGCGGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:54,174:0.0044:2,0:1:0:29:0:0.24017:0:60:2:0.0044:0:2 0/1:156:2:1,1:40,114:0.0128:2,2:41:0:31:1:0.45782:2.83:60:4:0.0128:0:2 -6 29760856 . C T 186 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACCTGTGCTCCTTGACAGC;RSEQ=GCAGACACGGCGGCTCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:77:21,56:31,117:0.3422:2,2:23.9:1:29.7:1:0.31871:1.41:60:37.5:0.3363:0:1.7 0/0:153:0:0,0:38,115:0:2,0:24.8:1:29:1:1:0:60:37.25:1:0:0.3 -6 29760900 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05805;SOR=Inf;LSEQ=CCAGCTCAAGTGGGAGGCGG;RSEQ=CCGGGGGGCGGAGGTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:40,123:0:2,0:25.3:1:31.3:1:1:0:60:53.333:1:0:0.3 0/1:104:3:1,2:26,75:0.0288:2,2:15.7:1:27.3:1:1:1.44:60:6:0.0291:0:1.7 -6 29761062 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CGCGGGACACACCTCAGAGG;RSEQ=AAGGGGATGAAGCGTGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:18.8:1:32:1:1:0:60:8:0.5714:0:2 1/0:4:2:0,2:0,2:0.5:0,0:25.5:1:30:1:1:0:60:4:0.5:0:3.5 -6 29761080 . T G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22619;SOR=7.11489;LSEQ=GGAAAGGGGATGAAGCGTGG;RSEQ=CCATGACCATGGCACCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,5:0.1667:0,0:29:0:33:0:1:0:60:2:0.2:0:5 1/0:3:2:0,2:0,1:0.6667:0,0:25.5:1:29.5:1:1:0:60:4:0.6667:0:3.5 -6 29761835 . A G 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69794;SOR=1.54582;LSEQ=AGTGACTGGTCACAGCAGGC;RSEQ=TTAAGGCAAGCCATTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:7,4:0.3125:2,2:27.6:1:31.4:1:1:1.15538:60:10:0.3125:0:2.6 0/1:12:5:2,3:4,3:0.4167:2,2:35.6:1:31.6:1:1:1.88578:60:10:0.4167:0:2.2 -6 29761880 . T C 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09463;SOR=5.21634;LSEQ=CACGGGACTCCTCTGATGGC;RSEQ=AACTGTAGCTGGAAGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:6,8:0.2632:2,2:28.6:1:31.2:1:1:1.11808:60:10:0.2632:0:3.2 1/0:9:6:3,3:1,2:0.6667:2,2:16:1:31.7:1:1:1.85:60:12:0.6667:0:2.5 -6 29761896 . A G 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12874;SOR=5.91384;LSEQ=TGGCTAACTGTAGCTGGAAG;RSEQ=CTCCTCCACGGCCTTGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:4,6:0.2308:2,2:39:1:32.7:1:1:1.30472:60:6:0.2308:0:4 1/0:6:4:1,3:0,2:0.6667:0,2:17.8:1:32.8:1:1:0:60:8:0.6667:0:2.8 -6 29761906 . G A 41 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=TAGCTGGAAGACTCCTCCAC;RSEQ=GCCTTGCTCAACTCTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:5,6:0.2143:2,2:33.3:1:26.3:1:1:1.60839:60:2:0.1538:0:4 0/0:5:0:0,0:2,3:0:2,0:28.6:1:31:1:1:0:60:10:1:0:1 -6 29762440 . T TC 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTATTTTTGAACATTT;RSEQ=AAATTTTGTCTTTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29768344 . T C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAAAAGGCGGCTCAGATGTT;RSEQ=TGGAGGAGGAACATGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:41:1:28.5:1:1:0:60:4:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:11:1:32.5:1:1:0:60:4:0.6667:0:1.5 -6 29768816 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCTCTTCTGAGTCCCT;RSEQ=GGCCTCCACTCAGGTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:16.5:1:31.5:1:1:0:60:4:0.5:0:8 0/0:1:0:0,0:0,1:0:0,0:9:0:32:0:1:0:60:2:1:0:0 -6 29768831 . T C 33 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TCCCTCGGCCTCCACTCAGG;RSEQ=CAGGACCAGAAATCTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:31.5:1:33.5:1:1:0:60:4:0.5:0:8 0/0:2:0:0,0:1,1:0:2,0:13.5:1:29:1:1:0:60:4:1:0:0 -6 29768835 . GA AG 33 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TCGGCCTCCACTCAGGTCAG;RSEQ=CCAGAAATCTCTGTTTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:36.5:1:33:0:1:0:60:4:0.5:0:7 0/0:2:0:0,0:1,1:0:2,0:17.5:1:33:0:1:0:60:4:1:0:0 -6 29768852 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CAGGACCAGAAATCTCTGTT;RSEQ=CCGCCTCAGACACTAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:38:1:29.5:1:0.33333:0:60:4:0.6667:0:7 0/0:3:0:0,0:2,1:0:2,0:25.7:1:31:0:1:0:60:6:1:0:0 -6 29768861 . G A 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=AAATCTCTGTTTCCGCCTCA;RSEQ=ACACTAGAACTTTCCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:38:1:31:1:0.33333:0:60:4:0.6667:0:7 0/0:5:0:0,0:3,2:0:2,0:21:1:31.6:1:1:0:60:10:1:0:0.2 -6 29768885 . A G 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17157;SOR=0.14538;LSEQ=CTAGAACTTTCCAAGGAATA;RSEQ=GAGATTATCCCAGGTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:15.5:1:29:0:1:0:60:4:0.4:0:7 0/1:13:1:1,0:7,5:0.0769:2,0:24:0:32:0:1:0:49:2:0.0769:0:6 -6 29768908 . T G 73 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00296;SOR=0;LSEQ=GATTATCCCAGGTGCCTGTG;RSEQ=CCAGAATGTTGTCTGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:1,1:0.5556:2,2:13.6:1:31.8:1:1:3.16:43.8:10:0.5556:0:7.2 0/0:15:0:0,0:8,6:0:2,0:26.9:1:29.6:1:1:0:60:28:0.9333:0:0.6 -6 29768917 . T G 65 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02767;SOR=0.07715;LSEQ=AGGTGCCTGTGTCCAGAATG;RSEQ=TGTCTGGGTTCTGTGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:3,1:3,1:0.5:2,2:24.8:1:32.5:1:1:1:39.8:8:0.5:0:7.3 0/1:16:1:1,0:7,6:0.0625:2,0:31:0:26:0:1:0:49:2:0.0625:0:5 -6 29768948 . CAGATGTCCCATCCAT AGGTTTCCCGTCCTA 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00383;SOR=0;LSEQ=CTGTGCTCCCTTCCCCACCC;RSEQ=TCTCAGGATGGTCACATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:4,1:0.5:2,2:49:1:29:1:1:1:40.8:4:0.4444:0.1:2 0/0:16:0:0,0:8,8:0:2,0:25.6:1:30.3:1:1:0:59.3:15:1:0:1.1 -6 29768951 . A G 63 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53044;SOR=Inf;LSEQ=TGCTCCCTTCCCCACCCCAG;RSEQ=TGTCCCATCCATTCTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:31:1:28.8:1:1:0:60:10:1:0:2.2 0/1:15:4:2,2:5,6:0.2667:2,2:21.5:1:31.5:1:1:1.19:60:8:0.2667:0:2.5 -6 29768957 . CA TG 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00387;SOR=0;LSEQ=CTTCCCCACCCCAGATGTCC;RSEQ=TCCATTCTCAGGATGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:2,0:0.6667:0,2:32.5:1:30.8:1:1:0:60:8:0.6667:0:1.8 0/0:13:0:0,0:6,7:0:2,0:29.6:1:30.5:1:1:0:60:26:1:0:0.8 -6 29768958 . A G 61 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.25542;SOR=Inf;LSEQ=TTCCCCACCCCAGATGTCCC;RSEQ=TCCATTCTCAGGATGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,0:0:0,0:12:1:28.5:1:1:0:60:4:1:0:0 0/1:13:4:2,2:4,5:0.3077:2,2:21.5:1:30.8:1:1:1.23:60:8:0.3077:0:2.5 -6 29769063 . T A 79 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03512;SOR=7.18247;LSEQ=CCTGAAGGCACAGGTAACCC;RSEQ=CCACCCCATCTCCAACTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:13,5:0.1:2,0:3.5:1:27.5:1:1:0:60:4:0.1:0:1.5 0/1:13:6:5,1:4,3:0.4615:2,2:23.5:1:30.7:1:0.55944:3.39:60:12:0.4615:0:1 -6 29769077 . A G 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51923;SOR=0;LSEQ=TAACCCTCCACCCCATCTCC;RSEQ=ACTATGAGGCCACGCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:17,6:0.08:2,2:10:0:29.5:1:0.49:2.69921:35:4:0.0833:0:8 0/0:15:0:0,0:10,5:0:2,0:22.3:1:29.4:1:1:0:60:14:1:0:0.6 -6 29769080 . T C 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=CCCTCCACCCCATCTCCAAC;RSEQ=ATGAGGCCACGCTGAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:18,6:0.0769:2,2:13:0:31:1:0.47385:2.85369:35:4:0.08:0:8 0/0:14:0:0,0:9,5:0:2,0:25:1:30.5:1:1:0:60:28:1:0:0.6 -6 29769091 . G C 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5298;SOR=0;LSEQ=ATCTCCAACTATGAGGCCAC;RSEQ=CTGAGGTGCTGGGCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:22,8:0.0625:2,2:24:0:30.5:1:0.48992:2.651:35:4:0.0625:0:8 0/0:18:0:0,0:13,5:0:2,0:25.7:1:31:1:1:0:60:36:1:0:0.4 -6 29769099 . G T 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52481;SOR=0;LSEQ=CTATGAGGCCACGCTGAGGT;RSEQ=CTGGGCCCTGGGCTTCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:24,8:0.0588:2,2:32:0:29.5:1:0.46524:2.88652:35:4:0.0588:0:8 0/0:20:0:0,0:15,5:0:2,0:25.3:1:32.6:1:1:0:60:40:1:0:0.4 -6 29769111 . G T 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53634;SOR=0;LSEQ=GCTGAGGTGCTGGGCCCTGG;RSEQ=CTTCTACCCTCTGGAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:25,10:0.0541:2,2:44:0:29:0:0.51201:2.43088:35:4:0.0541:0:8 0/0:20:0:0,0:14,6:0:2,0:26.1:1:32.3:1:1:0:60:40:1:0:0.3 -6 29769122 . C G 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.54488;LSEQ=GGGCCCTGGGCTTCTACCCT;RSEQ=TGGAGATCACACTGACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:2,1:24,10:0.0811:2,2:26:1:31.3:1:1:1.19389:32.3:6:0.0811:0:8 0/1:22:1:1,0:13,8:0.0455:2,0:5:0:32:0:1:0:21:2:0.0455:0:8 -6 29769134 . C G 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62483;SOR=0.40986;LSEQ=TCTACCCTCTGGAGATCACA;RSEQ=TGACCCAGGAGCGGGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:2,1:23,11:0.0811:2,2:22:1:32:1:1:1.04419:32.3:6:0.0811:0:8 0/1:29:1:1,0:17,11:0.0345:2,0:17:0:34:0:1:0:21:2:0.0345:0:8 -6 29769143 . G C 62 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64236;SOR=0.35772;LSEQ=TGGAGATCACACTGACCCAG;RSEQ=AGCGGGATGGGGAGGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:2,2:28,13:0.0889:2,2:15:1:31.3:1:0.59126:2.11436:34.3:8:0.0889:0:7.8 0/1:30:1:1,0:18,11:0.0333:2,0:26:0:34:0:1:0:21:2:0.0333:0:8 -6 29769169 . G A 45 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61744;SOR=0.35498;LSEQ=GATGGGGAGGACCAAATTCA;RSEQ=GATGCAGAGTTTGTGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:1,2:30,10:0.0698:2,2:33.3:1:29:1:0.18362:5.70339:35.7:6:0.0698:0:7 0/1:39:1:1,0:24,14:0.0256:2,0:49:0:29:0:1:0:21:2:0.0256:0:8 -6 29769172 . T G 48 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61706;SOR=0.34533;LSEQ=GGGGAGGACCAAATTCAGGA;RSEQ=GCAGAGTTTGTGGAGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:3:1,2:32,10:0.0667:2,2:35.3:1:30.3:1:0.16899:6.07938:35.7:6:0.0667:0:7 0/1:42:1:1,0:26,15:0.0238:2,0:46:0:30:0:1:0:21:2:0.025:0:8 -6 29769179 . T C 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62113;SOR=0.37566;LSEQ=ACCAAATTCAGGATGCAGAG;RSEQ=TTGTGGAGACCAGACTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:1,2:36,12:0.0588:2,2:37.7:1:31.7:1:0.17916:5.74827:35.7:6:0.0612:0:7 0/1:44:1:1,0:28,15:0.0227:2,0:39:0:29:0:1:0:21:2:0.0233:0:8 -6 29769186 . A G 45 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61897;SOR=0.36019;LSEQ=TCAGGATGCAGAGTTTGTGG;RSEQ=GACCAGACTTGCAGGGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:3:1,2:35,11:0.0612:2,2:39.7:1:28.7:1:0.16793:6.07129:35.7:6:0.0625:0:7 0/1:44:1:1,0:27,16:0.0227:2,0:32:0:27:0:1:0:21:2:0.0233:0:8 -6 29769195 . T C 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61794;SOR=0.34382;LSEQ=AGAGTTTGTGGAGACCAGAC;RSEQ=TGCAGGGTACAGAACCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:1,2:36,12:0.0588:2,2:32.7:1:32:1:0.17916:5.74827:35.7:6:0.0638:0:7 0/1:48:1:1,0:30,17:0.0208:2,0:23:0:25:0:1:0:21:2:0.0217:0:8 -6 29769225 . C T 28 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5058;SOR=0;LSEQ=CAGAACCTTCCAGAAGTGGG;RSEQ=AGCTGCAGTGGTGTCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:0,2:63,24:0.0225:2,0:6:0:28.5:1:0.08299:0:40:4:0.023:0:6.5 0/0:68:0:0,0:48,20:0:2,0:22.7:1:32.1:1:1:0:60:136:1:0:0.4 -6 29769226 . A G 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5058;SOR=0;LSEQ=AGAACCTTCCAGAAGTGGGC;RSEQ=GCTGCAGTGGTGTCTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:62,25:0.0225:2,2:5:0:28.5:1:0.50128:2.45139:60:4:0.0233:0:0 0/0:68:0:0,0:48,20:0:2,0:22.9:1:30.2:1:1:0:60:136:1:0:0.4 -6 29769246 . G A 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGCTGCAGTGGTGTCTTCTG;RSEQ=AGAGAAGCAGAGGTACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:45:28,17:59,23:0.3543:2,2:22:1:29.4:1:0.31871:1.5518:60:90:0.3571:0:1.2 0/0:109:0:0,0:69,40:0:2,0:21.1:1:31.1:1:1:0:60:218:1:0:0.8 -6 29769280 . C T 185 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACACATGCCATGTGCAGCA;RSEQ=GAGGGGTTGCCTGAGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:99,70:0:2,0:31:1:30.7:1:1:0:60:32.8:1:0:0.4 1/0:139:74:39,35:40,25:0.5324:2,2:32.1:1:29.8:1:0.3088:1.43213:60:148:0.5362:0:1.7 -6 29769332 . G A 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGTAAGGAGACGAATGAG;RSEQ=GGTCATGTCTCTTCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:88,74:0:2,0:21.4:1:30.8:1:1:0:60:80:1:0:0.3 1/0:116:63:26,37:27,26:0.5431:2,2:18.1:1:29.4:1:0.35116:1.47277:60:62:0.5536:0:1.8 -6 29769497 . A C 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTGCTGGCCTGGTTCTTCT;RSEQ=GTTGCTGTAATCACTGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:89,184:0:2,0:24.1:1:29.4:1:1:0:60:26.3:1:0:0.6 0/1:212:103:42,61:43,66:0.4858:2,2:24.3:1:29.9:1:0.88893:1.06:60:102:0.488:0:2.5 -6 29769507 . A T 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00283;SOR=1.87566;LSEQ=TGGTTCTTCTAGTTGCTGTA;RSEQ=TCACTGTAGCTGTAGTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:72:25,47:38,121:0.3103:2,2:23.8:1:29.8:1:0.11038:1.69:60:35:0.3111:0:1.9 0/1:179:82:30,52:35,62:0.4581:2,2:23.9:1:29.6:1:1:1.02:60:81:0.4551:0:2.7 -6 29769521 . A G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=6;SSF=0;SOR=3.33464;LSEQ=GCTGTAATCACTGTAGCTGT;RSEQ=GTCGCTGCTGTGATGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:80:16,64:17,82:0.4469:2,2:21.6:1:30.8:1:0.69967:1.20:60:39:0.4457:0:1.8 1/0:126:92:30,62:7,27:0.7302:2,2:21.4:1:30:1:0.27038:1.86:60:29.667:0.7295:0:2.3 -6 29769529 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50633;SOR=0;LSEQ=CACTGTAGCTGTAGTCGCTG;RSEQ=TGTGATGTGGAGGAATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:20,118:0.0143:2,2:16.5:1:32:0:0.27842:5.78:60:4:0.0149:0:2 0/0:108:0:0,0:26,82:0:2,0:18.7:1:31.8:1:1:0:60:216:1:0:1.7 -6 29769621 . A T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74857;SOR=1.27674;LSEQ=TTCAAGCCCCAGGTAGGAGT;RSEQ=GGCTCATATCTTGCCTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:0,10:0,9:0.5263:0,0:31.8:1:30.6:1:1:0:60:20:0.5556:0:1.3 1/0:17:10:0,10:0,7:0.5882:0,0:18.5:1:30:1:1:0:60:20:0.5882:0:1.3 -6 29769696 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAGAGGCCCTGTCTATCAAC;RSEQ=CTTACTCTTTTGTAAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:6:1:30.7:1:1:0:60:6:0.5:0:2 1/0:4:2:0,2:0,2:0.5:0,0:24:1:28.5:1:1:0:60:4:0.5:0:3 -6 29770158 . C G 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20455;SOR=0;LSEQ=TGTTCCACCCCAAACAGGAA;RSEQ=AGTACCCAGGGCTCTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:3,1:0.5556:2,2:22:1:30.8:1:0.52381:3.76419:60:10:0.5556:0:1 0/0:3:0:0,0:1,2:0:2,0:46:1:31.3:1:1:0:60:6:1:0:1 -6 29770187 . A C 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01471;SOR=Inf;LSEQ=GGGCTCTGATGTGTCTCTCA;RSEQ=GGCTTGTAAAAGTGACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:27.1:1:31.2:1:1:0:58.2:24:1:0:0.5 1/0:5:3:1,2:1,1:0.6:2,2:22.3:1:32.3:1:1:1.7321:60:6:0.6:0:1 -6 29770255 . A G 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCAGAGGGGACACAACTA;RSEQ=GCTCTGGAGATTCTTTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:0,3:0.5714:0,2:16.5:1:31.3:1:0.42857:0:60:8:0.5714:0:1.3 0/0:1:0:0,0:0,1:0:0,0:18:0:30:0:1:0:40:2:1:0:0 -6 29770423 . A G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.11403;LSEQ=CTCCTCTTTGTGACATTAAG;RSEQ=GCCTCTGGCTTCTCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:0,3:0.5714:0,2:23.8:1:31.8:1:0.42857:0:60:8:0.5714:0:1.5 1/0:5:3:1,2:1,1:0.6:2,2:19:1:30.7:1:1:1.7321:60:6:0.6:0:1.7 -6 29770450 . G C 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GGCTTCTCTTTCTGCCAAAG;RSEQ=GTCTGAATGTGTCTATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:0.6:0,2:21.3:1:30.3:1:1:0:60:6:0.6:0:1.7 0/0:4:0:0,0:1,1:0:2,0:21:1:28.5:1:1:0:60:4:0.5:0:0 -6 29794443 . A G 47 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGAAAGAATTCCAAAGCAGC;RSEQ=GAACTCTTAGGTTTAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:9.8:1:23.8:1:1:0:60:3:1:0:1.8 -6 29795222 . G A 53 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GGAGTCCAGTTCAGGGACAG;RSEQ=GATTCCGGGATGAAAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:22.8:1:26.8:1:1:0:50.8:3:1:0:3.3 0/0:1:0:0,0:0,1:0:0,0:16:0:25:0:1:0:60:2:1:0:1 -6 29795231 . G A 61 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=TTCAGGGACAGGGATTCCGG;RSEQ=ATGAAAAGTGAAGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:27.3:1:30.5:1:1:0:50.8:8:1:0:3.3 0/0:1:0:0,0:0,1:0:0,0:25:0:27:0:1:0:60:2:1:0:1 -6 29795253 . C A 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=TGAAAAGTGAAGGGAGAGGG;RSEQ=CAGGGACCTTGCCGAGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:2,0:0.7143:0,2:27.4:1:30.2:1:1:0:52.6:10:0.7143:0:2.8 0/0:1:0:0,0:0,1:0:0,0:47:0:29:0:1:0:60:2:1:0:1 -6 29795421 . G A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00094;SOR=Inf;LSEQ=GCCCCACAGGCGGTGTATGG;RSEQ=TTGGGGAGGCCCCGCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:35,1:0:1,0:24.5:1:31.4:1:1:0:60:35:1:0:0 0/1:14:5:5,0:8,1:0.3571:2,0:29.2:1:26.4:1:1:0:60:4:0.3077:0:1 -6 29795551 . C T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07962;SOR=Inf;LSEQ=AGGTTTTTAGAGAAGCCAAT;RSEQ=AGCGTCGCCGCGGTCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:269,29:0:2,0:24.6:1:31.4:1:1:0:60:98.333:1:0:0.4 0/1:226:3:1,2:186,37:0.0133:2,2:15.3:1:24.7:1:0.07781:9.89543:60:6:0.0134:0:1.3 -6 29795566 . C T 208 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02273;LSEQ=CCAATCAGCGTCGCCGCGGT;RSEQ=CTGGTTCTAAAGTCCTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:140:107,33:272,87:0.2806:2,2:21.4:1:29.3:1:0.90773:1.04:60:22.333:0.2746:0:1.1 0/0:342:3:1,2:243,96:0.0088:2,2:9.7:1:19:1:0.1985:5.03468:60:2:0.006:0:2 -6 29795636 . G A 256 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAGGATGGTGGTCATGGC;RSEQ=CCCCGAACCCTCTTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1086:0:0,0:538,547:0:2,0:26.9:1:30.5:1:1:0:60:50.667:1:0:0.3 0/1:973:411:206,205:270,291:0.4224:2,2:26.7:1:29.5:1:0.55917:1.08:59.9:101.75:0.4266:0:2.1 -6 29795657 . G A 245 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=820.1573;LSEQ=CCCCGAACCCTCTTCCTGCT;RSEQ=CTCTCGGGGGCCCTGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1064:1:1,0:479,582:9e-04:2,0:1:0:24:0:0.45198:0:60:2:0.001:0:1 0/1:912:401:183,218:229,280:0.4397:2,2:24.2:1:28.4:1:0.8933:1.03:59.9:99.25:0.4411:0:2.2 -6 29795720 . A G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.80269;LSEQ=TGCGGGGTCAGGAGGGAAAC;RSEQ=GCCCCTGCGCGGAGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:186:59,127:137,236:0.3316:2,2:25.5:1:30.3:1:0.2598:1.24907:59.1:36.2:0.3291:0:1.4 1/0:369:274:98,176:30,65:0.7425:2,2:23.5:1:29.5:1:0.532:1.21:60:53.8:0.7431:0:2.2 -6 29795747 . G C 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCGGAGGAGGGAGGGGCC;RSEQ=GCCCGGCGGGGGCGCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:0:0,0:174,256:0:2,0:23.4:1:30.2:1:1:0:60:46.778:1:0:0.6 0/1:237:67:24,43:62,108:0.2827:2,2:25:1:28.9:1:1:1.02843:60:32.5:0.2778:0:2.9 -6 29795751 . C T 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGAGGGAGGGGCCGGCC;RSEQ=GGCGGGGGCGCAGGACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:180,250:0:2,0:22.4:1:29.7:1:1:0:60:25.875:1:0:0.6 0/1:228:66:26,40:63,98:0.2895:2,2:24:1:30.1:1:1:1.01:60:32:0.2883:0:2.7 -6 29795768 . T C 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=2.12853;LSEQ=GCCCGGCGGGGGCGCAGGAC;RSEQ=CGGCAGCCGCGCCGGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:98:45,53:144,178:0.2328:2,2:20.3:1:30.9:1:0.90775:1.05:60:48:0.237:0:1.7 0/1:219:86:46,40:57,75:0.3927:2,2:22:1:31:1:0.16528:1.51:60:172:0.3963:0:2.1 -6 29795788 . A G 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.04707;SOR=Inf;LSEQ=TCGGCAGCCGCGCCGGGAGG;RSEQ=GGGTCGGGCGGGTCTCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:0:0,0:211,241:0:2,0:22.8:1:29.9:1:1:0:59.9:24.111:1:0:0.4 0/1:257:3:1,2:134,120:0.0117:2,2:13:1:23.3:1:0.60536:2.22658:53.3:2:0.0078:0:2.3 -6 29795809 . C T 206 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTCGGGCGGGTCTCAACC;RSEQ=CTCCTCGCCCCCAGGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:293,258:0:2,0:25.5:1:31:1:1:0:59.9:54.1:1:0:0.3 0/1:349:123:73,50:133,93:0.3524:2,2:22.8:1:29.7:1:1:1.02:59.4:40:0.3499:0:1.6 -6 29795913 . A T 218 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0077;LSEQ=CCATGGGCTACGTGGACGAC;RSEQ=CGCAGTTCGTGCGGTTCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:516:142:90,52:217,157:0.2752:2,2:26:1:30.6:1:0.31538:1.25:60:46.333:0.2742:0:1.2 0/0:344:1:0,1:176,167:0.0029:2,0:1:0:24:0:0.48837:0:60:2:0.003:0:1 -6 29795931 . G A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01961;SOR=Inf;LSEQ=ACACGCAGTTCGTGCGGTTC;RSEQ=ACAGCGACTCGGCGTGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:0:0,0:346,214:0:2,0:25:1:30.4:1:1:0:59.9:92.333:0.9982:0:0.4 0/1:337:4:2,2:182,150:0.0119:2,2:19.3:1:28.5:1:1:1.21263:60:8:0.012:0:1.3 -6 29795993 . G A 226 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGTGGAGCAGGAGGGGCC;RSEQ=GAGTATTGGGAAGAGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:919:0:0,0:519,400:0:2,0:24.8:1:30.2:1:1:0:60:182.8:1:0:0.2 0/1:615:186:103,83:238,191:0.3024:2,2:26.3:1:30.1:1:1:1.00411:60:61:0.301:0:1.1 -6 29796103 . T C 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.07665;LSEQ=GAGCGAGGCCAGTGAGTAAC;RSEQ=CCGGCCCAGGGAGCAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:168:56,112:159,298:0.2684:2,2:25.5:1:30.7:1:0.77608:1.06702:60:55:0.2714:0:3.5 0/1:467:202:85,117:88,172:0.4325:2,2:22.8:1:30:1:0.08111:1.42:60:49.5:0.4333:0:2 -6 29796106 . G T 220 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGAGGCCAGTGAGTAACTCC;RSEQ=GCCCAGGGAGCAGATCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:160:51,109:145,274:0.2754:2,2:25.9:1:30.1:1:0.55703:1.13077:60:79:0.2782:0:3.6 0/0:427:0:0,0:157,269:0:2,0:23.7:1:29.5:1:1:0:60:105.5:0.9976:0:1 -6 29796115 . A C 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00055;SOR=1.66259;LSEQ=TGAGTAACTCCGGCCCAGGG;RSEQ=GCAGATCACGACCCCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:143:43,100:111,245:0.2866:2,2:25.7:1:30.2:1:0.83111:1.05353:60:142:0.291:0:3.8 0/1:357:143:59,84:65,149:0.4006:2,2:23.4:1:30:1:0.04112:1.61:60:46.667:0.4046:0:2.4 -6 29796126 . A AC 200 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCCAGGGAGCAGATCACG;RSEQ=CCCCCACCTCCATGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:107,298:0:2,0:24.4:1:29.5:1:1:0:60:66.5:1:0:1.3 0/1:280:97:30,67:57,123:0.3464:2,2:23.8:1:30.4:1:1:1.03484:60:47.5:0.3493:0.0357:2.4 -6 29796128 . C A 200 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCAGGGAGCAGATCACGAC;RSEQ=CCCACCTCCATGCCCCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:123:29,94:74,204:0.306:2,2:25:1:28.9:1:0.53854:1.17532:60:23.6:0.3041:0:3.9 0/0:275:0:0,0:84,191:0:2,0:20.8:1:29.7:1:1:0:59.9:33.375:1:0:1.1 -6 29796132 . A C 55 v4;q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.01719;SOR=9.34427;LSEQ=GGGAGCAGATCACGACCCCC;RSEQ=CCTCCATGCCCCACGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:1:1,0:90,284:0.0027:2,0:4:0:7:0:0.24267:0:60:0:0:0:1 0/1:246:6:3,3:67,172:0.0244:2,2:8.2:1:21.3:1:0.35712:2.56:60:2:0.0173:0:3.3 -6 29796152 . G C 183 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCCATGCCCCACGGACG;RSEQ=CCCGGGTACTCCCGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:49,213:0:2,0:21.3:1:31.3:1:1:0:60:28.111:1:0:1.1 0/1:150:62:11,51:14,73:0.4133:2,2:22.3:1:30.9:1:0.82641:1.12:59.8:61:0.4266:0:2.4 -6 29796234 . CA C 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTCTACCTGGGAGAACCC;RSEQ=AGGCGCCTTTACCAAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:64,63:0:2,0:23.5:1:30.4:1:1:0:59.8:62.5:1:0:0.5 0/1:47:18:6,12:16,13:0.383:2,2:18.2:1:31.4:1:0.2293:2.41392:60:36:0.383:0.1064:1.4 -6 29796257 . C T 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07886;SOR=1.87363;LSEQ=GGCGCCTTTACCAAAATCCC;RSEQ=GCGGGTGGGTCCGGGCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:34:27,7:52,41:0.2677:2,2:24.5:1:31.5:1:0.0222:3.02:60:68:0.2742:0:2 0/1:54:22:15,7:26,6:0.4074:2,2:19.2:1:30.7:1:0.33828:1.99504:60:21:0.3962:0:2 -6 29796265 . G T 163 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACCAAAATCCCCGCGGGTG;RSEQ=GTCCGGGCGAGGGCGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:41:32,9:65,49:0.2645:2,2:22.5:1:30.5:1:0.02328:2.66:60:82:0.268:0:1.9 0/0:59:0:0,0:46,13:0:2,0:23.8:1:30.8:1:1:0:60:118:1:0:0.8 -6 29796306 . G A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGTGGGCGGGGCTGACCGA;RSEQ=GGGGTGGGGCCAGGTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:139,117:0:2,0:26.8:1:31.3:1:1:0:60:63:0.9921:0:0.4 0/1:135:38:24,14:61,36:0.2815:2,2:22.9:1:29:1:1:1.01:60:37:0.2803:0:2.2 -6 29796312 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.11706;SOR=Inf;LSEQ=GCGGGGCTGACCGAGGGGGT;RSEQ=GGGCCAGGTTCTCACACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:148,126:0:2,0:27.7:1:31.3:1:1:0:60:67.5:1:0:0.3 0/1:143:2:1,1:88,53:0.014:2,2:6.5:1:27:1:1:1.65418:60:4:0.0142:0:1.5 -6 29796327 . C T 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGGTGGGGCCAGGTTCTCA;RSEQ=ACCCTCCAGTGGATGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:149,150:0:2,0:28.8:1:31.8:1:1:0:60:58.8:1:0:0.3 0/1:163:17:10,7:87,59:0.1043:2,2:26.6:1:28.5:1:1:1.03202:60:34:0.1049:0:2.2 -6 29796369 . A T 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCGACCTGGGGTCCGACGG;RSEQ=CGCCTCCTCCGCGGGTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:123,126:0:2,0:23.9:1:29.2:1:1:0:60:34.571:1:0:0.2 0/1:162:17:7,10:72,73:0.1049:2,2:23.1:1:29.1:1:0.61141:1.40604:60:34:0.1076:0:1.7 -6 29796376 . C A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=Inf;LSEQ=TGGGGTCCGACGGACGCCTC;RSEQ=TCCGCGGGTATGAACAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:114,120:0:2,0:22.5:1:31.2:1:1:0:60:57.5:1:0:0.2 0/1:156:12:5,7:72,72:0.0769:2,2:22.6:1:29.6:1:0.76548:1.397:60:24:0.0779:0:1.3 -6 29796434 . AC A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0027;SOR=Inf;LSEQ=TTACCTCGCCCTGAACGAGG;RSEQ=CTGCGCTCCTGGACCGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:172,63:0:2,0:25.1:1:31.7:1:1:0:60:32.571:1:0:0.1 0/1:180:7:4,3:111,61:0.0389:2,2:25.1:1:30.3:1:0.70176:1.36225:60:14:0.0393:0.0111:0 -6 29796640 . T C 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0467;SOR=2.11186;LSEQ=CCTGATCTCCTGTAGACCTC;RSEQ=CAGCCTGGCCTAGCACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:30:1,29:6,63:0.303:2,1:22.2:1:30.9:1:0.67161:2.73907:60:29:0.2959:0:1.5 0/1:50:24:1,23:3,23:0.48:2,1:26.9:1:30.8:1:0.61051:2.93967:60:48:0.48:0:1.5 -6 29796656 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTCAGCCTGGCCTAGCA;RSEQ=AAGGAGAGGAGGAAAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:5,76:0.0241:2,2:24.5:1:28.5:1:0.14017:13.97:60:4:0.0244:0:1 0/0:40:0:0,0:4,36:0:2,0:28.1:1:31.7:1:1:0:60:39:1:0:0.8 -6 29796675 . G T 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00169;SOR=0;LSEQ=ACAAGGAGAGGAGGAAAATG;RSEQ=GACCAACACTAGAATATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:15:1,14:2,39:0.2679:1,1:23.5:1:29.9:1:1:1.38:60:30:0.2679:0:1.8 0/0:28:0:0,0:2,26:0:2,0:27.5:1:30.5:1:1:0:60:27:1:0:1 -6 29796685 . T C 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGAAAATGGGACCAACAC;RSEQ=AGAATATCGCCCTCCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:3,41:0:2,0:24.6:1:28.1:1:1:0:60:88:1:0:0.5 0/1:25:12:1,11:2,11:0.48:2,2:26.4:1:32.8:1:1:1.94684:60:24:0.48:0:2 -6 29796877 . GGCACC G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGACCCCACAGCAGCCTT;RSEQ=AGGACTTTTCCCCTCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:31:1:32.5:1:1:3.1622:60:4:0.2857:0:0 0/0:1:0:0,0:1,0:0:0,0:43:0:30:0:1:0:60:2:1:0:2 -6 29796986 . G A 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01587;SOR=Inf;LSEQ=CCTCCACTCAGGTCAGAACC;RSEQ=GAGGTCCCTGCTCCCCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:22,2:0:2,0:26.8:1:30.6:1:1:0:60:48:1:0:0.2 1/0:4:2:1,1:2,0:0.5:0,2:29.5:1:32.5:1:1:0:60:4:0.5:0:1 -6 29797155 . G C 214 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GCTGCTGGAGTGTCCCATGA;RSEQ=AGATGCAAAGTGCTTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:111:77,34:143,95:0.3171:2,2:22.4:1:31.6:1:0.0974:1.50:60:54.5:0.3178:0:2.7 0/0:237:0:0,0:143,94:0:2,0:23.6:1:30.9:1:1:0:60:38.5:1:0:0.5 -6 29797169 . T C 83 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48536;SOR=0.4917;LSEQ=CCATGAGAGATGCAAAGTGC;RSEQ=TGAATTTTCTGACTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:3,3:266,185:0.0131:2,2:9.8:1:32.2:1:0.69367:1.43664:52.3:12:0.0133:0:2.7 0/0:308:2:1,1:175,131:0.0065:2,2:9.5:1:30:1:1:1.33459:60:4:0.0066:0:3.5 -6 29797173 . A G 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17278;SOR=1.23221;LSEQ=GAGAGATGCAAAGTGCTTGA;RSEQ=TTTTCTGACTCTTCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:152:93,59:191,143:0.3121:2,2:24.3:1:31.7:1:0.42828:1.18:59.5:75:0.3125:0:2.7 0/1:329:118:64,54:122,89:0.3587:2,2:27:1:31:1:0.56297:1.15608:60:236:0.362:0:1.2 -6 29797211 . C T 229 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGACCCCCCCAAGACACA;RSEQ=GTGACCCACCACCCTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:547:180:87,93:170,197:0.3291:2,2:27.9:1:30.6:1:0.71545:1.08:60:360:0.3321:0:2.2 0/0:385:0:0,0:173,210:0:2,0:27.5:1:30.1:1:1:0:59.9:94.75:0.9948:0:0.4 -6 29797302 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54826;SOR=0;LSEQ=AGATCATACTGACCTGGCAG;RSEQ=GGGATGGGGAGGACCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:45,111:0.0127:2,2:32:1:28:1:0.49883:2.45:60:4:0.0128:0:1 0/0:82:0:0,0:31,51:0:2,0:23.4:1:29.9:1:1:0:60:26.333:1:0:0.1 -6 29797354 . C G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16193;SOR=Inf;LSEQ=GCTCGTGGAGACCAGGCCTG;RSEQ=AGGGGATGGAACCTTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:65,59:0:2,0:23.9:1:31.5:1:1:0:53.9:30:1:0:0.1 0/1:84:2:1,1:49,33:0.0238:2,2:20.5:1:28:0:1:1.47767:60:4:0.0253:0:1 -6 29797389 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51044;SOR=0;LSEQ=TCCAGAAGTGGGCAGCTGTG;RSEQ=TGGTGCCTTCTGGAGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:98,63:0.0123:2,2:19:1:29:1:1:1.55116:37:4:0.0126:0:5 0/0:119:0:0,0:80,39:0:2,0:24:1:30.8:1:1:0:54.9:28.75:1:0:0.3 -6 29797420 . C T 107 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00141;SOR=8.48002;LSEQ=TGGAGAGGAGCAGAGATACA;RSEQ=GTGCCATGTGCAGCATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:2:0,2:130,117:0.008:2,0:1:0:25:0:0.22739:0:60:4:0.0081:0:1 0/1:186:12:5,7:103,71:0.0645:2,2:20.7:1:29.9:1:0.24545:2.02311:55.5:24:0.0659:0:1 -6 29797430 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18932;SOR=Inf;LSEQ=CAGAGATACACGTGCCATGT;RSEQ=CAGCATGAGGGGCTGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:131,128:0:2,0:27.2:1:32:1:1:0:57.6:63.75:1:0:0.2 0/1:200:2:1,1:111,87:0.01:2,2:23.5:1:29.5:1:1:1.27429:21:4:0.0102:0:5.5 -6 29797436 . T C 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96171;LSEQ=TACACGTGCCATGTGCAGCA;RSEQ=GAGGGGCTGCCGGAGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:4:2,2:130,128:0.0152:2,2:26.5:1:32.5:1:1:1.01557:48.5:8:0.0153:0:3.5 0/1:205:3:2,1:107,95:0.0146:2,2:27.3:1:29.3:1:1:1.77:22:6:0.0149:0:4.3 -6 29797452 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19461;SOR=Inf;LSEQ=AGCATGAGGGGCTGCCGGAG;RSEQ=CCCTCATGCTGAGATGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:127,127:0:2,0:29.9:1:31.3:1:1:0:59.8:49.8:1:0:0.2 0/1:201:2:1,1:98,101:0.01:2,2:34.5:1:29.5:1:1:1.03:60:4:0.0103:0:1.5 -6 29797456 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.19061;SOR=Inf;LSEQ=TGAGGGGCTGCCGGAGCCCC;RSEQ=CATGCTGAGATGGAGTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:124,127:0:2,0:29.5:1:30.3:1:1:0:59.8:40.833:1:0:0.2 0/1:195:2:1,1:94,99:0.0103:2,2:12:1:32.5:1:1:1.05:60:4:0.0105:0:1 -6 29797459 . TG CC 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86345;LSEQ=GGGGCTGCCGGAGCCCCTCA;RSEQ=CTGAGATGGAGTAAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:3:1,2:120,126:0.012:2,2:11:1:32.3:1:1:1.90002:52.3:6:0.0121:0.004:3 0/1:192:2:1,1:93,97:0.0104:2,2:24:0:32.8:1:1:1.04:21:4:0.0106:0:4.5 -6 29797553 . G C 201 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAACAGGGTCGGTGGTGAGG;RSEQ=CTGGGGGTCAGAGACCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:109,73:0:2,0:23.2:1:31.2:1:1:0:60:35.4:0.9944:0:0.2 1/0:150:85:46,39:41,24:0.5667:2,2:22.1:1:31.5:1:0.31774:1.44477:60:84:0.5753:0:1.3 -6 29797554 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19596;SOR=Inf;LSEQ=AACAGGGTCGGTGGTGAGGG;RSEQ=TGGGGGTCAGAGACCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:115,77:0:2,0:22.3:1:31.3:1:1:0:60:26.429:1:0:0.2 0/1:153:2:1,1:86,65:0.0131:2,2:21.5:1:30.5:1:1:1.32061:60:4:0.0136:0:1 -6 29797558 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50221;SOR=0;LSEQ=GGGTCGGTGGTGAGGGCTGG;RSEQ=GGTCAGAGACCCTCACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:119,78:0.0101:2,2:12:1:27.5:1:1:1.52227:60:4:0.0102:0:1.5 0/0:168:0:0,0:93,75:0:2,0:22.2:1:29.9:1:1:0:60:55:1:0:0.8 -6 29797564 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09364;SOR=Inf;LSEQ=GTGGTGAGGGCTGGGGGTCA;RSEQ=AGACCCTCACCTTCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:133,93:0:2,0:22.9:1:31.4:1:1:0:60:44.2:1:0:0.2 0/1:189:3:1,2:104,82:0.0159:2,2:16.7:1:27.3:1:0.58585:2.52432:60:6:0.0162:0:2 -6 29797639 . C T 191 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=210.03178;LSEQ=ATCATGGGTATCGTTGCTGG;RSEQ=CTGGTTGTCCTTGCAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:1:1,0:147,153:0.0033:2,0:4:0:13:0:0.49169:0:60:0:0:0:2 0/1:249:103:59,44:73,73:0.4137:2,2:21.1:1:28.6:1:0.30257:1.34:60:50.5:0.4156:0:1.7 -6 29797642 . G A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25417;SOR=0;LSEQ=ATGGGTATCGTTGCTGGCCT;RSEQ=GTTGTCCTTGCAGCTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:3,0:144,150:0.0101:2,0:7.7:1:26.7:1:0.12:0:60:6:0.0102:0:1 0/0:250:0:0,0:132,117:0:2,0:22.4:1:30.4:1:1:0:60:82:0.996:0:0.8 -6 29797653 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09675;SOR=Inf;LSEQ=TGCTGGCCTGGTTGTCCTTG;RSEQ=AGCTGTAGTCACTGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:141,162:0:2,0:21.5:1:31.7:1:1:0:60:49.5:0.9966:0:0.3 0/1:259:3:1,2:132,124:0.0116:2,2:13.7:1:27:0:0.61358:2.12302:60:6:0.0119:0:1.7 -6 29797696 . A G 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=2.12255;LSEQ=GTCGCTGCTGTGCTGTGGAG;RSEQ=AAGAAGAGCTCAGGTAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:93:38,55:53,96:0.3843:2,2:29.9:1:31:1:0.41665:1.25:60:92:0.3833:0:1.1 1/0:242:138:63,75:37,67:0.5702:2,2:29:1:30.4:1:0.14678:1.52:60:68:0.5763:0:1.5 -6 29797719 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24831;SOR=0;LSEQ=GAAGAGCTCAGGTAAGGAAG;RSEQ=GGTGACAAGTGGGGTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:2,1:71,137:0.0142:2,2:8.7:1:22:1:0.27526:3.83:60:2:0.0098:0:1 0/0:206:0:0,0:73,133:0:2,0:26.7:1:29.9:1:1:0:60:205:1:0:0.9 -6 29797763 . C A 31 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25668;SOR=0;LSEQ=TCTTGTCCCACTGGGGGTTT;RSEQ=AAGCCCCAGGTAGAAGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:3:2,1:17,83:0.0291:2,2:10:1:20:1:0.0867:9.44:60:2:0.0198:0:2.3 0/0:81:0:0,0:12,69:0:2,0:22.1:1:31.5:1:1:0:60:39.5:1:0:0.9 -6 29797779 . G A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17388;SOR=Inf;LSEQ=GTTTCAAGCCCCAGGTAGAA;RSEQ=TGTGCCCTGCCTGGTTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:9,63:0:2,0:24.7:1:32.1:1:1:0:59.3:71:1:0:0.3 0/1:52:2:1,1:3,47:0.0385:2,2:12:0:30.5:1:0.14932:13.71:51:4:0.0392:0:4.5 -6 29797782 . T C 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCAAGCCCCAGGTAGAAGTG;RSEQ=GCCCTGCCTGGTTACTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:9,59:0:2,0:24.8:1:30.4:1:1:0:59.3:33:1:0:0.3 1/0:46:26:2,24:1,19:0.5652:1,2:24.3:1:29.5:1:1:1.57:60:25:0.5556:0:1.3 -6 29797792 . G C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14413;SOR=Inf;LSEQ=GGTAGAAGTGTGCCCTGCCT;RSEQ=GTTACTGGGAAGCACCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:7,51:0:2,0:23.7:1:30.9:1:1:0:58.6:28:1:0:0.2 0/1:36:2:1,1:2,32:0.0556:2,2:25:0:31.5:1:0.1619:13.27:51:4:0.0556:0:4.5 -6 29797816 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11458;SOR=Inf;LSEQ=ACTGGGAAGCACCATCCACA;RSEQ=TCATGGGCCTACCCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:6,36:0:2,0:23.1:1:32.7:1:1:0:57.4:84:1:0:0.2 0/1:22:2:1,1:2,18:0.0909:2,2:26.5:1:29.5:1:0.25974:7.55:51:4:0.0909:0:4.5 -6 29797818 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12216;SOR=Inf;LSEQ=TGGGAAGCACCATCCACACT;RSEQ=ATGGGCCTACCCAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:5,35:0:2,0:23.6:1:32.5:1:1:0:57.2:80:1:0:0.2 0/1:22:2:1,1:2,18:0.0909:2,2:24.5:1:28.5:1:0.25974:7.55:51:4:0.0952:0:4.5 -6 29797899 . T C 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01;SOR=Inf;LSEQ=ACAATGAAGGACAGATTTAT;RSEQ=ACCTTGATGATTGTAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:27.7:1:29.7:1:1:0:58.8:44:1:0:0 1/0:3:2:0,2:0,1:0.6667:0,0:44:1:32.5:1:1:0:60:4:0.6667:0:2 -6 29797933 . C T 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00342;SOR=Inf;LSEQ=TAGTGATGGGGACCTGATCC;RSEQ=AGTAATCACAGGTCAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:17,5:0:2,0:27.5:1:31.6:1:1:0:60:44:1:0:0 1/0:5:3:1,2:2,0:0.6:0,2:8:1:29:1:0.4:0:60:6:0.6:0:2.3 -6 29798039 . G A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTCCTGATCCCGCCCTG;RSEQ=GTCTGCAGTCACACATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:77,1:0:1,0:22.5:1:30.8:1:1:0:60:18.5:1:0:0.1 1/0:29:16:13,3:13,0:0.5517:1,2:28.6:1:29.5:1:0.23153:0:60:32:0.5517:0:1.4 -6 29798083 . C T 83 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=21.88883;LSEQ=AACTTCTCGAGGGTCCAAGA;RSEQ=TAGGAGGTTCCTCTAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:159,28:0.0053:2,0:1:0:27:0:0.15426:0:60:2:0.0054:0:1 0/1:66:7:7,0:50,9:0.1061:2,0:24.1:1:29.7:1:0.58064:0:60:14:0.1061:0:2.1 -6 29798092 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08854;SOR=Inf;LSEQ=AGGGTCCAAGACTAGGAGGT;RSEQ=CCTCTAGGACCTCATGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:178,38:0:2,0:24.6:1:29.9:1:1:0:60:71:1:0:0.1 0/1:92:2:1,1:76,14:0.0217:2,2:30.5:1:32.5:1:0.301:5.279:60:4:0.0222:0:1.5 -6 29798140 . A G 203 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCTGGCCTCTCACAGGAC;RSEQ=TTTTCTTCCCACAGATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:274,168:0:2,0:24.9:1:30.2:1:1:0:59.8:72.667:1:0:0.1 0/1:290:112:69,43:113,64:0.3862:2,2:25.2:1:29.9:1:0.70938:1.09995:57.6:224:0.3958:0:1.1 -6 29798280 . G A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16594;SOR=5.67605;LSEQ=ACCCCACAATTCCTCCTCTG;RSEQ=CCACATCTCCTGTGGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:1:0,1:128,178:0.0033:2,0:8:0:13:0:1:0:60:0:0:0:5 0/1:219:4:2,2:90,125:0.0183:2,2:25.8:1:29.8:1:1:1.39:60:8:0.0187:0:1 -6 29798312 . G A 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GTGGTCTCTGACCAGGTGCT;RSEQ=TTTTTGTTCTACTCTAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:150,196:0:2,0:25.7:1:31.9:1:1:0:60:68.2:1:0:0.1 0/1:238:10:4,6:103,124:0.042:2,2:16.2:1:29.4:1:1:1.24483:60:20:0.0424:0:1 -6 29798419 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTGTGGGTTGTTGAGGG;RSEQ=AACAGGGGACATAGCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:24,89:0:2,0:24.1:1:31:1:1:0:60:55.5:1:0:0.7 0/1:74:27:6,21:12,35:0.3649:2,2:17.2:1:29:1:1:1.19708:59.3:26:0.3611:0:2.1 -6 29798425 . G T 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62812;SOR=1.20111;LSEQ=TGGGTTGTTGAGGGGAACAG;RSEQ=GGACATAGCTGTGCTATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:38:10,28:9,57:0.3654:2,2:25.8:1:30.6:1:0.12102:2.24:60:76:0.3762:0:1.6 0/1:66:27:8,19:8,31:0.4091:2,2:20.9:1:29.5:1:0.56001:1.62:59:54:0.4219:0:2.3 -6 29798459 . C G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40218;SOR=1.51121;LSEQ=CTATGAGGTTTCTTTGACTT;RSEQ=AATGTATTGAGCATGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:29:12,17:11,33:0.3973:2,2:24.7:1:31.2:1:0.19827:2.10:56.9:28:0.3944:0:1.8 1/0:34:17:5,12:3,14:0.5:2,2:29.9:1:31.1:1:0.68802:1.91:58.4:34:0.5:0:2.4 -6 29798581 . G GATTTGTTCATGCCT 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11481;SOR=1.69362;LSEQ=TGTGTGGGACTGAGTGGCAA;RSEQ=TCCCTTTGTGACTTCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:59:30,29:23,26:0.5463:2,2:22.3:1:30.3:1:0.7036:1.17:56.2:118:0.5463:0.2778:1.9 1/0:67:45:27,18:12,8:0.6716:2,2:24.7:1:29.4:1:1:1:54.5:90:0.6923:0.3433:1.4 -6 29798610 . C T 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03036;SOR=2.32615;LSEQ=TGACTTCAAGAACCCTGACT;RSEQ=CTCTTTGTGCAGAGACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:89:50:19,31:15,24:0.5618:2,2:26.2:1:29.6:1:1:1.01952:58.6:100:0.5618:0:2.5 1/0:52:39:19,20:5,8:0.75:2,2:22.4:1:28.2:1:0.74903:1.51:56.2:38:0.7451:0:2.1 -6 29798617 . G C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27496;SOR=1.58355;LSEQ=AAGAACCCTGACTCCTCTTT;RSEQ=TGCAGAGACCAGCCCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:43:17,26:15,26:0.5119:2,2:27.2:1:31.7:1:0.82496:1.13:59.1:86:0.5119:0:2.7 1/0:48:30:13,17:7,11:0.625:2,2:23.1:1:30.6:1:1:1.20:58.2:29:0.6304:0:2.5 -6 29798634 . C A 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=TTTGTGCAGAGACCAGCCCA;RSEQ=CCCTGTGCCCACCATGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:16,47:0:2,0:25.7:1:31.1:1:1:0:59.4:62:1:0:1.6 0/1:34:7:1,6:5,22:0.2059:2,2:29.9:1:28.7:1:1:1.35206:54.3:14:0.2059:0:3.7 -6 29798642 . C T 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01101;SOR=0.27503;LSEQ=GAGACCAGCCCACCCCTGTG;RSEQ=CCACCATGACCCTCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:32:5,27:5,21:0.5517:2,2:23.3:1:29.7:1:0.74037:1.2801:59:31:0.5536:0:2.8 0/1:28:7:1,6:2,19:0.25:2,2:26.4:1:27.4:1:1:1.56:54.3:14:0.25:0:3.7 -6 29798749 . C G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62848;SOR=0.39418;LSEQ=CTCTGTCTCAAATTTGTGGT;RSEQ=CACTGAGCTATAACTTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:0,2:0.8:0,0:27.5:1:32.8:1:1:0:60:16:0.8:0:1.3 1/0:10:6:1,5:0,4:0.6:0,2:25.5:1:31.8:1:1:0:60:12:0.6:0:1.3 -6 29855241 . C T 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCTTGGCACAGGAGGAG;RSEQ=GGGGTCAGGGCGAAGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:2,1:16,1:0.15:1,2:27:1:31.3:1:0.28421:6.73285:50.3:6:0.15:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29855296 . C T 84 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTCAGGGTCTCAGGCCC;RSEQ=GAAGGCGGTGTATGGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:6:6,0:34,3:0.1395:2,0:25.5:1:32.8:1:1:0:34.7:12:0.1463:0:6.5 0/0:5:0:0,0:5,0:0:0,0:20.6:1:30.6:1:1:0:60:10:1:0:2.2 -6 29855320 . T G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00884;SOR=6.75517;LSEQ=GGCGGTGTATGGATTGGGGA;RSEQ=GCCCCGCCTTAGGGATTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:14:14,0:40,2:0.25:1,1:33.9:1:33.1:1:1:0:50.6:28:0.2545:0:4.4 1/0:10:7:7,0:3,0:0.7:0,0:21.6:1:32:1:1:0:60:14:0.7:0:4 -6 29855325 . C A 72 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.57467;SOR=0;LSEQ=TGTATGGATTGGGGATGCCC;RSEQ=GCCTTAGGGATTCGCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:5,0:48,2:0.0909:1,0:36.2:1:31.4:1:1:0:33.8:10:0.0909:0:7.4 0/0:13:0:0,0:13,0:0:1,0:21.2:1:30.2:1:1:0:60:26:1:0:3.5 -6 29855328 . C G 71 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5762;SOR=0;LSEQ=ATGGATTGGGGATGCCCCGC;RSEQ=TTAGGGATTCGCCACCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:5,0:52,2:0.0847:1,0:34.4:1:30.6:1:1:0:33.8:10:0.0893:0:7.4 0/0:15:0:0,0:15,0:0:1,0:20.5:1:30.8:1:1:0:60:30:1:0:3.4 -6 29855331 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0011;SOR=15.35153;LSEQ=GATTGGGGATGCCCCGCCTT;RSEQ=GGGATTCGCCACCTCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:32:30,2:35,1:0.4706:1,2:25.1:1:32.1:1:0.59773:2.30511:56.2:31:0.4627:0:2.4 1/1:15:14:14,0:1,0:0.9333:0,1:23.6:1:32.3:1:1:0:60:28:0.9333:0:3.6 -6 29855336 . T C 66 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57707;SOR=0;LSEQ=GGGATGCCCCGCCTTAGGGA;RSEQ=TCGCCACCTCCGCAGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:4,0:66,3:0.0548:1,0:34.5:1:33.3:1:1:0:29.3:8:0.0556:0:8 0/0:19:0:0,0:18,1:0:1,0:20.5:1:29.2:1:1:0:60:18:1:0:3.2 -6 29855339 . G C 64 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.73209;LSEQ=ATGCCCCGCCTTAGGGATTC;RSEQ=CCACCTCCGCAGTTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:4:4,0:70,3:0.0519:1,0:31.5:1:32.3:1:1:0:29.3:8:0.0533:0:8 0/1:26:1:1,0:24,1:0.0385:1,0:2:0:32:0:1:0:55:2:0.0385:0:8 -6 29855343 . C T 64 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.70031;LSEQ=CCCGCCTTAGGGATTCGCCA;RSEQ=CTCCGCAGTTTCTCTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:4:4,0:79,2:0.0471:1,0:27.5:1:32:1:1:0:29.3:8:0.0488:0:8 0/1:30:1:1,0:28,1:0.0333:1,0:6:0:32:0:1:0:55:2:0.0333:0:8 -6 29855355 . CTCT C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.34078;SOR=0.55542;LSEQ=ATTCGCCACCTCCGCAGTTT;RSEQ=TCTTCTCACAACCTGCGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:21:20,1:85,1:0.1963:1,1:24:1:31.9:1:0.35549:4.1719:60:42:0.2019:0.0467:0.7 0/1:42:5:5,0:36,1:0.119:1,0:22.8:1:31.3:1:1:0:60:10:0.122:0.0238:0.4 -6 29855376 . A T 57 pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50141;LSEQ=TCTTCTTCTCACAACCTGCG;RSEQ=CGGGTCCTTCTTCCTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:4:4,0:136,3:0.0278:1,0:33:0:28.8:1:1:0:45.8:8:0.029:0:6.3 0/1:71:1:1,0:67,3:0.0141:1,0:39:0:31:0:1:0:55:2:0.0143:0:8 -6 29855378 . G T 59 pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.50133;LSEQ=TTCTTCTCACAACCTGCGAC;RSEQ=GGTCCTTCTTCCTTGATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:4:4,0:143,3:0.0263:1,0:35:0:29.8:1:1:0:45.8:8:0.027:0:6.3 0/1:75:1:1,0:71,3:0.0133:1,0:41:0:31:0:1:0:55:2:0.0133:0:8 -6 29855380 . G C 54 pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66223;SOR=0.47079;LSEQ=CTTCTCACAACCTGCGACGG;RSEQ=TCCTTCTTCCTTGATACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:4:4,0:151,3:0.0253:1,0:37:0:27.3:1:1:0:45.8:3:0.0197:0:6.3 0/1:83:1:1,0:78,4:0.012:1,0:41:0:32:0:1:0:55:2:0.0125:0:8 -6 29855386 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=17.44002;LSEQ=ACAACCTGCGACGGGTCCTT;RSEQ=TTCCTTGATACTCACGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:19:18,1:154,3:0.1073:1,1:22.3:1:30.6:1:0.36943:2.82734:60:38:0.1124:0:3.2 1/0:97:66:62,4:30,1:0.6804:1,2:22:1:30.4:1:1:1.92393:60:65:0.6771:0:3.8 -6 29855392 . T G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.2942;LSEQ=TGCGACGGGTCCTTCTTCCT;RSEQ=GATACTCACGAAGCGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:19:18,1:171,4:0.0955:1,1:25.2:1:32.8:1:0.4061:2.36039:60:38:0.0969:0:3.1 1/0:105:73:69,4:28,1:0.6952:1,2:23.1:1:31.9:1:1:1.61626:60:35.5:0.6893:0:3.6 -6 29855401 . C G 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTCTTCCTTGATACTCA;RSEQ=GAAGCGGACACAGTTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:222,6:0:1,0:24:1:32.1:1:1:0:59.8:113:1:0:0.6 0/1:130:41:38,3:85,4:0.3154:1,2:24.5:1:32.1:1:0.6778:1.67049:60:82:0.3203:0:3.7 -6 29855404 . A C 56 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.65762;SOR=0.43877;LSEQ=TTCTTCCTTGATACTCACGA;RSEQ=GCGGACACAGTTCTCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:4:4,0:234,6:0.0164:1,0:16.5:1:28:1:1:0:45.8:8:0.0169:0:6.3 0/0:138:1:1,0:130,7:0.0072:2,0:17:0:28:0:1:0:55:2:0.0074:0:8 -6 29855409 . A G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=17.17293;LSEQ=CCTTGATACTCACGAAGCGG;RSEQ=CACAGTTCTCATTCCCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:29:28,1:234,5:0.1082:1,1:23.4:1:31:1:0.50044:1.66756:60:28:0.1089:0:2.3 1/0:149:101:95,6:46,2:0.6779:1,2:25:1:30.7:1:1:1.44923:60:32.667:0.6712:0:3 -6 29855411 . A C 43 q23;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65955;SOR=0.44973;LSEQ=TTGATACTCACGAAGCGGAC;RSEQ=CAGTTCTCATTCCCACTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:4:4,0:265,7:0.0144:1,0:9.5:1:21.5:1:1:0:45.8:3:0.0113:0:6.3 0/0:153:1:1,0:144,8:0.0065:2,0:10:0:26:0:1:0:55:2:0.0067:0:8 -6 29855431 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05358;SOR=Inf;LSEQ=ACAGTTCTCATTCCCACTAG;RSEQ=TGTCGGGTTTCTAGAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:347,43:0:2,0:23.7:1:30.9:1:1:0:59.7:31.5:1:0:0.5 0/1:237:3:1,2:210,23:0.0127:2,2:6:1:24.7:1:0.03033:17.78438:60:6:0.013:0:1 -6 29855435 . C T 129 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04749;SOR=0.32868;LSEQ=TTCTCATTCCCACTAGGTGT;RSEQ=GGGTTTCTAGAGAAGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:19:12,7:351,45:0.0458:2,2:6.2:1:30.4:1:0.00498:4.52405:50.6:38:0.0466:0:6.9 0/1:258:4:4,0:219,34:0.0155:2,0:4:1:30:1:1:0:42.5:8:0.0157:0:7.3 -6 29855457 . G A 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02533;SOR=0.43692;LSEQ=GGTTTCTAGAGAAGCCAATC;RSEQ=GTGCCGCCGCGGTCCCGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:33:19,14:451,168:0.0505:2,2:22.6:1:31:1:0.07175:1.97583:50.9:66:0.0517:0:6.8 0/1:441:10:8,2:305,126:0.0227:2,2:21:1:32.1:1:0.73067:1.65:45.9:20:0.023:0:6.5 -6 29855461 . C T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09189;SOR=0.55626;LSEQ=TCTAGAGAAGCCAATCGGTG;RSEQ=CGCCGCGGTCCCGGTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:702:33:19,14:468,201:0.047:2,2:26.6:1:30:1:0.17405:1.71421:50.9:32:0.0466:0:6.8 0/1:487:13:8,5:314,160:0.0267:2,2:19.5:1:28.9:1:0.76968:1.22601:49.2:12:0.0252:0:5.2 -6 29855463 . GC AT 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05105;SOR=0.51346;LSEQ=TAGAGAAGCCAATCGGTGCC;RSEQ=CGCGGTCCCGGTTCTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:35:19,16:477,213:0.0479:2,2:28:1:30.4:1:0.09155:1.88413:50.5:70:0.049:0.0027:5.8 0/1:516:13:9,4:328,174:0.0252:2,2:21.8:1:30:1:1:1.19:49.2:26:0.0257:0.0058:4.7 -6 29855492 . C A 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01233;SOR=0.64326;LSEQ=CCGGTTCTAAAGTCCCCACG;RSEQ=ACCCACCGGGACTCAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1214:111:45,66:648,453:0.0914:2,2:28.3:1:30:1:0.00026:2.09673:51:54.5:0.0914:0:5.3 0/1:839:51:24,27:439,345:0.0608:2,2:26:1:29.6:1:0.24531:1.43088:49.9:102:0.0613:0:5 -6 29855500 . G C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01562;SOR=0.65017;LSEQ=AAAGTCCCCACGCACCCACC;RSEQ=GGACTCAGATTCTCCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1327:110:44,66:685,530:0.0829:2,2:31.5:1:30.6:1:0.00127:1.93773:50.9:220:0.0837:0:5.3 0/1:919:51:24,27:472,394:0.0555:2,2:30.6:1:29.1:1:0.31456:1.34726:49.9:16:0.053:0:5 -6 29855533 . T C 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07131;SOR=0.6818;LSEQ=TCCCCAGACGCCGAGGATGG;RSEQ=GCTCATGGCGCCCCGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1544:70:21,49:740,733:0.0453:2,2:26.2:1:31.3:1:9e-04:2.35438:50:140:0.046:0:5.5 0/1:1148:36:13,23:540,571:0.0314:2,2:22.6:1:31.4:1:0.17501:1.67244:48.9:72:0.0317:0:5.4 -6 29855535 . C G 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07671;SOR=0.67369;LSEQ=CCCAGACGCCGAGGATGGTG;RSEQ=TCATGGCGCCCCGAACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1547:65:19,46:735,743:0.042:2,2:26.1:1:32.4:1:0.00137:2.39371:49.3:130:0.0424:0:5.5 0/1:1150:33:11,22:543,574:0.0287:2,2:22.5:1:31.8:1:0.11061:1.89097:48.7:66:0.0291:0:5.5 -6 29855538 . A G 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09553;SOR=0.69085;LSEQ=AGACGCCGAGGATGGTGCTC;RSEQ=TGGCGCCCCGAACCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1563:65:19,46:737,759:0.0416:2,2:23.1:1:32:1:0.00147:2.34967:49.3:130:0.0421:0:5.5 0/1:1134:33:11,22:531,570:0.0291:2,2:19.5:1:31.6:1:0.11138:1.86217:48.7:66:0.0293:0:5.5 -6 29855564 . G A 133 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08666;SOR=0.46686;LSEQ=CCCCGAACCCTCCTCCTGCT;RSEQ=CTCTCAGGGGCCCTGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1304:22:3,19:580,701:0.0169:2,2:6.2:1:30:1:0.00382:5.23489:47:44:0.0171:0:6 0/0:881:7:1,6:401,473:0.0079:2,2:5.3:1:28.3:1:0.13355:5.07925:43.1:14:0.0081:0:6 -6 29855570 . AG A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0.20374;LSEQ=ACCCTCCTCCTGCTGCTCTC;RSEQ=GGGCCCTGGCCCTGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1176:66:39,27:479,630:0.0561:2,2:15.5:1:31.3:1:0.01483:1.90:59.7:132:0.0569:0.0043:0.6 0/1:836:10:5,5:379,447:0.012:2,2:13.3:1:30.3:1:1:1.18:60:20:0.0121:0.0024:0.6 -6 29855571 . GGGGCCCT G 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14468;LSEQ=CCCTCCTCCTGCTGCTCTCA;RSEQ=GGCCCTGACCCTGACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1172:276:115,161:392,502:0.2355:2,2:29.9:1:31.6:1:0.53253:1.09312:59.7:275:0.2391:0.0316:1.1 0/1:821:35:17,18:354,427:0.0426:2,2:33:1:31.3:1:0.73124:1.14:58.7:70:0.044:0.0024:1.3 -6 29855574 . GCCCTGGCCCTGA G 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00145;SOR=0.5381;LSEQ=TCCTCCTGCTGCTCTCAGGG;RSEQ=CCCTGACCCAGACCTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1101:98:44,54:329,435:0.089:2,2:28.2:1:31.7:1:0.74616:1.08:59.9:97:0.114:0.0091:0.2 0/1:761:38:18,20:305,381:0.0499:2,2:28.5:1:31.1:1:0.74017:1.12:59.9:76:0.0531:0.0053:0.2 -6 29855580 . GCCCTGA G 268 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=2.000;MSILEN=6;SSF=0;SOR=1151.95896;LSEQ=TGCTGCTCTCAGGGGCCCTG;RSEQ=CCCTGACCCAGACCTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1039:1:0,1:389,559:0.001:2,0:49:0:34:0:1:0:60:2:0.0011:0:0 1/0:697:372:166,206:127,164:0.5337:2,2:27.9:1:31.4:1:0.81354:1.04:59.5:61:0.5657:0.076:0.3 -6 29855586 . A G 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.27663;LSEQ=TCTCAGGGGCCCTGGCCCTG;RSEQ=CCCTGACCCAGACCTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:982:270:104,166:253,369:0.2749:2,2:29.8:1:31.9:1:0.55287:1.09425:59.7:269:0.306:0:1.1 0/1:664:63:24,39:111,132:0.0949:2,2:19.7:1:30.8:1:0.32:1.36509:59.3:62:0.2081:0:1.7 -6 29855662 . G C 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCGAGGGGCCCGCCCGGC;RSEQ=GGGGCGCAGGACCCGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:181,246:0:2,0:23.9:1:30.5:1:1:0:59.9:60:0.9976:0:0.4 0/1:255:25:8,17:95,135:0.098:2,2:27.1:1:28.3:1:0.40008:1.4931:60:24:0.0956:0:3.1 -6 29855677 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=19.09187;LSEQ=CCGGCGGGGGCGCAGGACCC;RSEQ=GGGATCCGCGCAGGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:45:20,25:188,217:0.1:2,2:24.3:1:30.4:1:0.87529:1.08272:60:44:0.0993:0:2.7 1/0:257:175:77,98:42,39:0.6809:2,2:21.4:1:30.5:1:0.28147:1.36891:59.9:350:0.6809:0:3 -6 29855682 . T G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=19.6017;LSEQ=GGGGGCGCAGGACCCGGGGA;RSEQ=CCGCGCAGGGAGGAGGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:46:19,27:197,212:0.1011:2,2:25.7:1:32:1:0.43723:1.3197:59.2:45:0.102:0:2.9 1/0:251:173:79,94:41,37:0.6892:2,2:21.9:1:31.6:1:0.34076:1.31704:59.9:172:0.6964:0:3 -6 29855706 . C G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=17.53094;LSEQ=CGCAGGGAGGAGGGTCGGGC;RSEQ=GGTCTCAGCTCCTCCTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:58:27,31:259,233:0.1051:2,2:23.8:1:30.6:1:0.40659:1.27569:59.4:116:0.1076:0:2.4 1/0:316:213:110,103:60,41:0.6741:2,2:23.3:1:29.6:1:0.2258:1.3689:59.7:426:0.6762:0:2.4 -6 29855726 . T C 118 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00691;SOR=3.42353;LSEQ=CGGTCTCAGCTCCTCCTCGC;RSEQ=CCCAGGCTCCCACTCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:658:7:4,3:339,311:0.0106:2,2:7.6:1:32:1:1:1.22:31.9:14:0.0109:0:3.4 0/1:422:15:9,6:214,193:0.0355:2,2:10.2:1:30.3:1:0.60978:1.35:37.9:30:0.0359:0:3.1 -6 29855733 . C T 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTCCTCCTCGCTCCCAGG;RSEQ=TCCCACTCCATGAGGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:0:0,0:350,329:0:2,0:26.5:1:32:1:1:0:59.6:74.444:1:0:0.3 0/1:461:23:13,10:224,214:0.0499:2,2:22.7:1:29.9:1:0.67268:1.24:60:46:0.0505:0:2.9 -6 29855761 . A G 165 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=3.69565;LSEQ=CCATGAGGTATTTCTACACC;RSEQ=CCATGTCCCGGCCCGGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:680:16:8,8:315,348:0.0235:2,2:30.6:1:32.1:1:1:1.10:39.6:32:0.0238:0:2.3 0/1:452:37:20,17:207,208:0.0819:2,2:32.9:1:31.7:1:0.73205:1.18:40.6:74:0.0833:0:3 -6 29855800 . T A 113 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=12.78299;LSEQ=GCGGGGAGCCCCGCTTCATC;RSEQ=CCGTCGGCTACGTGGACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:2:1,1:251,259:0.0039:2,2:18:1:28.5:1:1:1.03:33:4:0.004:0:4.5 0/1:335:16:9,7:149,170:0.0478:2,2:20.8:1:28.3:1:0.60922:1.47:41.1:32:0.0483:0:4.4 -6 29855805 . C G 110 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00093;SOR=7.11292;LSEQ=GAGCCCCGCTTCATCTCCGT;RSEQ=GGCTACGTGGACGATACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:3:1,2:237,250:0.0061:2,2:11.3:1:30.3:1:1:1.89362:33:6:0.0062:0:4.7 0/1:309:13:8,5:135,161:0.0421:2,2:20.9:1:29.8:1:0.27361:1.90:38.2:26:0.0426:0:5 -6 29855818 . G T 153 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00433;SOR=0.374;LSEQ=TCTCCGTCGGCTACGTGGAC;RSEQ=ATACGCAGTTCGTGCGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:41:20,21:206,206:0.0905:2,2:23.2:1:28.6:1:1:1.04991:60:40:0.0901:0:1.1 0/1:279:10:4,6:119,150:0.0358:2,2:16.6:1:30.1:1:1:1.18927:60:20:0.0366:0:1.3 -6 29855820 . T C 71 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00822;SOR=Inf;LSEQ=TCCGTCGGCTACGTGGACGA;RSEQ=ACGCAGTTCGTGCGGTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:0:0,0:226,219:0:2,0:23.6:1:29.4:1:1:0:60:73.167:1:0:0.2 0/1:278:5:3,2:121,152:0.018:2,2:22.4:1:30.8:1:0.65891:1.88:32.4:10:0.0182:0:6.4 -6 29855825 . A T 67 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00842;SOR=Inf;LSEQ=CGGCTACGTGGACGATACGC;RSEQ=GTTCGTGCGGTTCGACAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:416:0:0,0:203,212:0:2,0:24.8:1:30.4:1:1:0:60:45.111:1:0:0.2 0/1:262:5:3,2:114,143:0.0191:2,2:17.4:1:29.2:1:0.6589:1.88:32.4:10:0.0193:0:6.4 -6 29855833 . C A 41 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05424;SOR=Inf;LSEQ=TGGACGATACGCAGTTCGTG;RSEQ=GGTTCGACAGCGACGACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:195,198:0:2,0:25.4:1:30.5:1:1:0:60:34.727:0.9974:0:0.3 0/1:241:3:2,1:109,128:0.0124:2,2:16.7:1:26.3:1:0.59723:2.34:29.3:6:0.0125:0:7.3 -6 29855849 . A C 167 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CGTGCGGTTCGACAGCGACG;RSEQ=CGCGAGTCCGAGAGAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:215,187:0:2,0:24.9:1:29.4:1:1:0:59.9:32.5:1:0:0.3 0/1:238:39:23,16:99,100:0.1639:2,2:18.7:1:31.7:1:0.30046:1.45:39.6:78:0.166:0:4.1 -6 29855856 . T C 140 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCGACAGCGACGACGCGAG;RSEQ=CCGAGAGAGGAGCCGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:211,195:0:2,0:24.6:1:29.4:1:1:0:59.9:35.909:1:0:0.3 0/1:227:23:14,9:101,103:0.1013:2,2:25.6:1:31:1:0.38044:1.58:38.1:22:0.0991:0:5.8 -6 29855858 . C A 132 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGACAGCGACGACGCGAGTC;RSEQ=GAGAGAGGAGCCGCGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:216,197:0:2,0:24.3:1:30.1:1:1:0:59.9:67.833:0.9975:0:0.3 0/1:224:21:12,9:101,102:0.0938:2,2:27.2:1:30.2:1:0.64786:1.34:37.9:42:0.0942:0:6.1 -6 29855862 . AGA GAT 130 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AGCGACGACGCGAGTCCGAG;RSEQ=GGAGCCGCGGGCGCCGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:217,191:0:2,0:24.6:1:30:1:1:0:59.9:30.385:1:0:0.4 0/1:216:20:12,8:97,98:0.0926:2,2:26.8:1:30.1:1:0.48302:1.51:37.5:40:0.0939:0.0046:4.4 -6 29855901 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=18.7437;LSEQ=TGGATGGAGCGGGAGGGGCC;RSEQ=GAGTATTGGGACCGGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:43:12,31:218,208:0.0907:2,2:29.3:1:31:1:0.00383:2.70207:58.9:42:0.0905:0:2.2 1/0:311:203:100,103:46,62:0.6527:2,2:25.9:1:29.6:1:0.2841:1.31:57.5:202:0.6558:0:1.9 -6 29855902 . G A 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATGGAGCGGGAGGGGCCA;RSEQ=AGTATTGGGACCGGAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:231,241:0:2,0:25.5:1:31.4:1:1:0:59.9:156.333:1:0:0.4 0/1:314:14:4,10:144,156:0.0446:2,2:22.5:1:29.9:1:0.17994:2.30178:60:28:0.0456:0:1.2 -6 29855930 . G T 73 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00508;SOR=Inf;LSEQ=GGACCGGAACACACAGATCT;RSEQ=CAAGGCCCAGGCACAGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:461:0:0,0:192,269:0:2,0:27.4:1:31.7:1:1:0:59.9:75.833:1:0:0.3 0/1:329:6:1,5:143,180:0.0182:2,2:27:1:28.3:1:0.23638:3.95857:45:12:0.0186:0:8 -6 29855935 . G A 85 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00098;SOR=Inf;LSEQ=GGAACACACAGATCTGCAAG;RSEQ=CCCAGGCACAGACTGAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:175,275:0:2,0:27.1:1:31.3:1:1:0:59.9:55.25:1:0:0.3 0/1:330:8:2,6:135,187:0.0242:2,2:32.9:1:28.5:1:0.47699:2.16117:47:16:0.0251:0:7.9 -6 29855938 . C A 88 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00099;SOR=Inf;LSEQ=ACACACAGATCTGCAAGGCC;RSEQ=AGGCACAGACTGAACGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:0:0,0:170,275:0:2,0:26.7:1:31.3:1:1:0:59.9:48.444:1:0:0.3 0/1:328:8:2,6:133,187:0.0244:2,2:35.9:1:29.5:1:0.47821:2.12922:47:16:0.0247:0:7.9 -6 29855940 . G A 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.32853;LSEQ=ACACAGATCTGCAAGGCCCA;RSEQ=GCACAGACTGAACGAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:25:5,20:159,253:0.0569:2,2:22.1:1:31.8:1:0.08707:2.50922:59:50:0.0577:0:3 0/1:318:66:20,46:103,134:0.2075:2,2:25:1:30.1:1:0.06532:1.76468:60:32:0.2051:0:2.9 -6 29855945 . A G 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.48507;LSEQ=GATCTGCAAGGCCCAGGCAC;RSEQ=GACTGAACGAGAGAACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:24:5,19:148,256:0.0561:2,2:19.6:1:30.5:1:0.13028:2.19332:60:23:0.0546:0:3.1 0/1:361:62:19,43:116,183:0.1717:2,2:24.6:1:29.4:1:0.25096:1.43318:60:30:0.1695:0:3 -6 29855950 . G T 115 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=7.76468;LSEQ=GCAAGGCCCAGGCACAGACT;RSEQ=AACGAGAGAACCTGCGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:3:1,2:144,275:0.0071:2,2:9:0:28.7:1:1:1.04716:47.7:6:0.0072:0:5.3 0/1:360:19:4,15:126,214:0.0528:2,2:23.7:1:27.3:1:0.22049:2.20366:45.3:18:0.0513:0:5.1 -6 29855952 . A C 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.42061;LSEQ=AAGGCCCAGGCACAGACTGA;RSEQ=CGAGAGAACCTGCGGATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:6:2,4:142,273:0.0143:2,2:12.5:1:29:1:1:1.0402:42.8:5:0.0121:0:4.7 0/1:362:73:21,52:106,182:0.2017:2,2:14.8:1:29.4:1:0.21887:1.44076:44:17.25:0.196:0:3.1 -6 29855960 . A G 140 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00686;SOR=2.7927;LSEQ=GGCACAGACTGAACGAGAGA;RSEQ=CCTGCGGATCGCGCTCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:10:4,6:127,256:0.0254:2,2:8.9:1:32.3:1:0.73685:1.34:35.2:20:0.0258:0:2.9 0/1:338:23:8,15:104,211:0.068:2,2:17.6:1:31:1:0.82297:1.08:39:22:0.0665:0:3.3 -6 29855967 . G C 75 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48023;SOR=1.97818;LSEQ=ACTGAACGAGAGAACCTGCG;RSEQ=ATCGCGCTCCGCTACTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:3:1,2:114,246:0.0083:2,2:26:0:33.3:1:1:1.08:47.7:6:0.0085:0:5.3 0/1:308:5:1,4:94,209:0.0162:2,2:24.2:1:32.6:1:1:1.79603:47.6:10:0.0164:0:5 -6 29855969 . T C 74 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47998;SOR=1.98339;LSEQ=TGAACGAGAGAACCTGCGGA;RSEQ=CGCGCTCCGCTACTACAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:3:1,2:112,243:0.0084:2,2:28:0:32.3:1:1:1.08:47.7:6:0.0087:0:5.3 0/1:303:5:1,4:93,205:0.0165:2,2:26.2:1:32:1:1:1.8115:47.6:10:0.0172:0:5 -6 29855978 . G T 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GAACCTGCGGATCGCGCTCC;RSEQ=CTACTACAACCAGAGCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:97,212:0:2,0:24.9:1:30.9:1:1:0:59:37.625:1:0:0.3 0/1:273:14:4,10:81,178:0.0513:2,2:27.3:1:29.6:1:1:1.13711:59:28:0.0528:0:1.7 -6 29855999 . G A 97 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00373;SOR=0.09055;LSEQ=CTACTACAACCAGAGCGAGG;RSEQ=CGGTGAGTGACCCCGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:12:5,7:48,160:0.0538:2,2:34.9:1:27.1:1:0.16644:2.37:36.2:5:0.0463:0:3.1 0/0:196:1:1,0:31,92:0.0051:2,0:1:0:24:0:0.25806:0:60:2:0.0053:0:2 -6 29856022 . G A 147 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=21.04824;LSEQ=GTGAGTGACCCCGGCCCGGG;RSEQ=CGCAGGTCACGACCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:0,3:45,122:0.0175:2,0:22.3:1:29:1:0.56647:0:60:6:0.0181:0:2.3 0/1:109:30:3,27:17,62:0.2752:2,2:23.9:1:30:1:0.26692:2.4501:60:60:0.2885:0:1.4 -6 29856034 . ACCC A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02008;SOR=Inf;LSEQ=GGCCCGGGGCGCAGGTCACG;RSEQ=CTCCCCATCCCCCACGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:35,100:0:2,0:22.2:1:31.3:1:1:0:58.6:44:1:0:0.4 0/1:83:4:0,4:18,61:0.0482:2,0:13:1:33.5:1:0.57214:0:39:8:0.0506:0:2.8 -6 29856037 . CCTCCC TCT 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CCGGGGCGCAGGTCACGACC;RSEQ=CATCCCCCACGGAGGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:35,94:0:2,0:22.4:1:30.8:1:1:0:58.7:24.8:1:0:0.4 0/1:77:9:1,8:15,49:0.1169:2,2:10.2:1:26.5:1:0.6732:2.42478:49.3:8:0.1159:0.0779:3.3 -6 29856039 . TCCC T 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.66801;SOR=1.84469;LSEQ=GGGGCGCAGGTCACGACCCC;RSEQ=CATCCCCCACGGAGGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:3:0,3:32,92:0.0236:2,0:12:1:34:1:0.57141:0:38.7:6:0.0244:0:2.7 0/1:70:3:0,3:13,51:0.0429:2,0:11.3:1:33:1:1:0:50.3:6:0.0462:0:2.3 -6 29856058 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCATCCCCCACGGAGG;RSEQ=CCGGGTCGCCTCGAGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:44,67:0.0177:2,2:11:0:31.5:1:1:1.52:60:4:0.018:0:1.5 0/0:40:0:0,0:14,26:0:2,0:23.6:1:32.1:1:1:0:60:80:1:0:0.9 -6 29856092 . A T 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=20.29012;LSEQ=AGTCTCTGGGTCCGAGATCC;RSEQ=CCCCGAAACCGCGGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:8:6,2:71,44:0.065:2,2:16.6:1:30.6:1:0.70878:1.85:59.6:16:0.0672:0:1.5 1/0:32:19:12,7:8,5:0.5938:2,2:27.3:1:30.8:1:1:1.07:60:38:0.5938:0:1.3 -6 29856151 . CG C 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00754;SOR=Inf;LSEQ=GAGGCCCAGGCGCCTTTACC;RSEQ=GTTTCATTTTCAGTTTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:187,20:0:2,0:24.9:1:29.7:1:1:0:59.8:50.75:1:0:0.4 0/1:88:4:4,0:80,4:0.0455:1,0:28:1:31.3:1:1:0:60:8:0.046:0.0114:2 -6 29856178 . C T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=4.37396;LSEQ=ATTTTCAGTTTAGGCCAAAA;RSEQ=CCCCGCGGGTTGGTCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:109:97,12:171,29:0.3516:2,2:21.5:1:30.7:1:0.48336:1.37:60:108:0.3529:0:1.2 1/0:169:119:108,11:44,5:0.7041:2,2:23.7:1:30:1:1:1.11:59.5:118:0.7024:0:1.6 -6 29856194 . G C 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAACCCCCGCGGGTTGGTC;RSEQ=GGGCAGGGCGGGGCTCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:339,92:0:2,0:22.3:1:29.8:1:1:0:60:85.2:1:0:0.4 0/1:255:41:27,14:167,47:0.1608:2,2:24:1:27.6:1:0.11024:1.83758:60:7.2:0.1446:0:1.7 -6 29856197 . G A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00726;SOR=Inf;LSEQ=ACCCCCGCGGGTTGGTCGGG;RSEQ=CAGGGCGGGGCTCGGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:343,105:0:2,0:22.9:1:31.1:1:1:0:60:55:1:0:0.4 0/1:269:5:4,1:197,67:0.0186:2,2:19.6:1:26.6:1:1:1.36:60:4:0.0153:0:2.4 -6 29856198 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08843;SOR=0;LSEQ=CCCCCGCGGGTTGGTCGGGG;RSEQ=AGGGCGGGGCTCGGGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:6:3,3:344,105:0.0132:2,2:15.5:1:23.3:1:0.1486:3.26554:60:5:0.0112:0:1.2 0/0:276:0:0,0:204,72:0:2,0:23.5:1:31.3:1:1:0:59.3:45:1:0:1 -6 29856199 . A G 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=58.13443;LSEQ=CCCCGCGGGTTGGTCGGGGC;RSEQ=GGGCGGGGCTCGGGGGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:1:0,1:357,115:0.0021:2,0:3:0:30:0:0.24524:0:40:2:0.0021:0:4 0/1:282:31:24,7:184,67:0.1099:2,2:19:1:29.3:1:0.82882:1.25:53.4:30:0.1095:0:2.9 -6 29856204 . G T 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGTTGGTCGGGGCAGGGC;RSEQ=GGGCTCGGGGGACCGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:368,147:0:2,0:22.9:1:29.8:1:1:0:60:45.818:1:0:0.4 0/1:314:29:22,7:197,88:0.0924:2,2:19.1:1:30.5:1:0.52947:1.40:58.1:58:0.0942:0:2.3 -6 29856219 . G GGGCTGACCGCGGTCCAGAGGATGTAT 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00139;SOR=Inf;LSEQ=AGGGCGGGGCTCGGGGGACC;RSEQ=GGCTGACCGCGGGGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:644:0:0,0:414,230:0:2,0:24.5:1:29.8:1:1:0:60:79.5:1:0:0.3 0/1:416:7:4,3:259,147:0.0168:2,2:15.3:1:29.3:1:0.70811:1.32047:53.1:14:0.0172:0.0168:2.3 -6 29856234 . G T 120 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=5;SSF=0;SOR=Inf;LSEQ=GGACCGGGCTGACCGCGGGG;RSEQ=CGGGGCCAGGTTCTCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:813:0:0,0:489,324:0:2,0:25.6:1:30.9:1:1:0:60:37.714:1:0:0.3 0/1:521:16:8,8:294,211:0.0307:2,2:21.3:1:30.1:1:0.60933:1.39244:50.5:32:0.0312:0:4.4 -6 29856236 . G C 121 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGGGCTGACCGCGGGGGC;RSEQ=GGGCCAGGTTCTCACACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:842:0:0,0:504,337:0:2,0:25.5:1:29.7:1:1:0:60:48.471:0.9988:0:0.3 0/1:541:15:8,7:307,218:0.0277:2,2:22.2:1:31.2:1:0.79235:1.23173:49.9:30:0.0282:0:4.6 -6 29856248 . T C 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=0.34496;LSEQ=GCGGGGGCGGGGCCAGGTTC;RSEQ=CACACCATGCAGGTGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:74:42,32:518,382:0.076:2,2:26.6:1:30.9:1:0.90317:1.03314:60:23.667:0.0744:0:1.3 0/1:653:18:10,8:349,285:0.0276:2,2:25.5:1:29.9:1:1:1.02:60:36:0.0282:0:1.3 -6 29856255 . A G 95 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0038;SOR=12.06154;LSEQ=CGGGGCCAGGTTCTCACACC;RSEQ=TGCAGGTGATGTATGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1029:1:1,0:560,467:0.001:2,0:49:0:11:0:1:0:60:0:0:0:4 0/1:689:8:4,4:359,321:0.0116:2,2:21.6:1:31.8:1:1:1.1182:55.8:16:0.0118:0:6.1 -6 29856257 . G C 108 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00031;SOR=16.67367;LSEQ=GGGCCAGGTTCTCACACCAT;RSEQ=CAGGTGATGTATGGCTGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1030:1:1,0:555,473:0.001:2,0:11:0:32:0:1:0:60:2:0.001:0:3 0/1:689:11:6,5:354,322:0.016:2,2:16.5:1:31.5:1:1:1.09:49.1:22:0.0161:0:5.8 -6 29856279 . G T 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTGATGTATGGCTGCGAC;RSEQ=TGGGGCCCGACGGGCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1129:0:0,0:557,571:0:2,0:25.8:1:30.7:1:1:0:60:52.714:0.9991:0:0.4 0/1:803:38:18,20:381,382:0.0473:2,2:25.6:1:30.1:1:0.86829:1.10806:60:37:0.0467:0:1.4 -6 29856285 . C T 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTATGGCTGCGACGTGGGG;RSEQ=CCGACGGGCGCTTCCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1104:0:0,0:527,576:0:2,0:26.3:1:31.4:1:1:0:60:43.12:0.9991:0:0.4 0/1:767:32:18,14:356,379:0.0417:2,2:19.5:1:28.8:1:0.47076:1.37:54.8:31:0.0413:0:2.6 -6 29856287 . C G 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGGCTGCGACGTGGGGCC;RSEQ=GACGGGCGCTTCCTCCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1103:0:0,0:522,580:0:2,0:26.2:1:30.1:1:1:0:60:60.222:0.9991:0:0.4 0/1:754:31:18,13:349,373:0.0411:2,2:22.1:1:29.9:1:0.3595:1.48:54.6:62:0.0416:0:2.5 -6 29856303 . C T 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGCCCGACGGGCGCTTCCTC;RSEQ=GCGGGTATGAACAGCACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1058:0:0,0:501,557:0:2,0:25.5:1:30.1:1:1:0:60:54.684:1:0:0.4 0/1:730:93:47,46:307,330:0.1274:2,2:28.4:1:29.9:1:0.73921:1.10:60:45.5:0.126:0:1.6 -6 29856330 . G A 201 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=45.11689;LSEQ=ATGAACAGCACGCCTACGAC;RSEQ=GCAAGGATTACATCGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:877:4:4,0:393,479:0.0046:2,0:5.3:1:27.3:1:0.04184:0:60:8:0.0046:0:1.3 0/1:612:105:47,58:236,268:0.1716:2,2:21.1:1:30:1:0.74739:1.08652:60:104:0.1725:0:1.9 -6 29856347 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.2497;LSEQ=GACGGCAAGGATTACATCGC;RSEQ=CTGAACGAGGACCTGCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:763:301:119,182:203,257:0.3945:2,2:24.6:1:29.7:1:0.23005:1.20775:59.9:22.154:0.3887:0:1.1 1/0:518:308:143,165:90,120:0.5946:2,2:23.1:1:29.3:1:0.47185:1.16:59.9:76:0.5938:0:1.6 -6 29856363 . C A 87 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15729;SOR=0.21772;LSEQ=TCGCCCTGAACGAGGACCTG;RSEQ=GCTCCTGGACCGCGGCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:683:7:4,3:293,381:0.0102:2,2:17.1:1:31.1:1:0.47695:1.73:44:14:0.0106:0:1.3 0/0:445:1:0,1:202,242:0.0022:2,0:44:0:33:0:1:0:60:2:0.0023:0:2 -6 29856368 . C T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAACGAGGACCTGCGCTC;RSEQ=TGGACCGCGGCGGACATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:676:0:0,0:288,387:0:2,0:23.9:1:31.2:1:1:0:59.7:47.214:1:0:0.4 0/1:441:15:7,8:194,232:0.034:2,2:21.9:1:30.6:1:1:1.05:44.5:30:0.0343:0:2.9 -6 29856389 . A G 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=TGGACCGCGGCGGACATGGC;RSEQ=GCTCAGATCACCAAGCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:0:0,0:299,347:0:2,0:23.7:1:30.5:1:1:0:59.9:70.778:0.9984:0:0.4 0/1:439:9:4,5:205,225:0.0205:2,2:18.1:1:29.9:1:1:1.13855:41.9:18:0.0207:0:3.1 -6 29856402 . A C 87 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03666;SOR=5.11363;LSEQ=ACATGGCAGCTCAGATCACC;RSEQ=AGCGCAAGTGGGAGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:637:2:2,0:286,349:0.0031:2,0:7:1:32:0:0.20402:0:38.5:4:0.0032:0:5 0/1:441:7:2,5:205,229:0.0159:2,2:18.7:1:31.3:1:0.4556:2.23409:39.3:14:0.0162:0:3.6 -6 29856421 . C T 64 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06428;SOR=4.61442;LSEQ=CAAGCGCAAGTGGGAGGCGG;RSEQ=CCGTCGGGCGGAGCAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:2:0,2:269,361:0.0032:2,0:16:1:29:1:0.51029:0:60:4:0.0033:0:1 0/1:415:6:3,3:186,223:0.0145:2,2:31.5:1:25:1:1:1.20:42:5:0.0123:0:5.2 -6 29856426 . CG GT 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0145;SOR=0.51979;LSEQ=GCAAGTGGGAGGCGGCCCGT;RSEQ=GGCGGAGCAGCTGAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:616:56:25,31:239,320:0.0909:2,2:29.2:1:31:1:0.77927:1.08:58.3:112:0.092:0.0049:1.4 0/1:405:20:7,13:176,200:0.0494:2,2:19.7:1:31.3:1:0.36167:1.63231:59.4:40:0.0499:0.0074:1.5 -6 29856427 . G A 201 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=221.71015;LSEQ=CAAGTGGGAGGCGGCCCGTC;RSEQ=GGCGGAGCAGCTGAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:613:1:1,0:242,315:0.0016:2,0:1:0:27:0:0.43548:0:60:2:0.0018:0:1 0/1:405:108:53,55:126,150:0.2667:2,2:24.5:1:29.8:1:0.57069:1.15:59.9:26:0.2781:0:1.4 -6 29856439 . T G 194 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=188.73769;LSEQ=GGCCCGTCGGGCGGAGCAGC;RSEQ=GAGAGCCTACCTGGAGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:1:1,0:262,339:0.0017:2,0:31:0:9:0:0.43688:0:60:0:0:0:3 0/1:388:93:43,50:126,168:0.2397:2,2:27.9:1:29.7:1:0.63162:1.15:58.8:186:0.2422:0:2.3 -6 29856445 . C T 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGGGCGGAGCAGCTGAGAG;RSEQ=CTACCTGGAGGGCGAGTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:593:0:0,0:258,334:0:2,0:26:1:31.3:1:1:0:59.7:36:1:0:0.3 0/1:392:97:45,52:128,167:0.2474:2,2:25.8:1:28.7:1:0.6382:1.13:58.9:96:0.2474:0:2.3 -6 29856463 . T G 131 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02923;SOR=2.4164;LSEQ=AGCCTACCTGGAGGGCGAGT;RSEQ=CGTGGAGTGGCTCCGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:11:6,5:200,304:0.0214:2,2:32.4:1:31.1:1:0.36064:1.82:47:10:0.0201:0:2.1 0/1:339:17:8,9:133,188:0.0501:2,2:30.4:1:32.2:1:0.80157:1.26:51.9:34:0.0512:0:1.4 -6 29856480 . A G 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22019;SOR=3.08138;LSEQ=AGTTCGTGGAGTGGCTCCGC;RSEQ=GATACCTGGAGAACGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:2:1,1:142,287:0.0046:2,2:25:1:30:0:0.55401:2.02:60:4:0.0048:0:1.5 0/1:282:4:2,2:98,180:0.0142:2,2:41.5:1:30:1:0.61685:1.83:54:8:0.0142:0:2 -6 29856531 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12763;SOR=Inf;LSEQ=AGCGCGCGGGTACCAGGGGC;RSEQ=ACAGGGCGCCTCCCGGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:31,165:0:2,0:24.4:1:31.8:1:1:0:60:48:1:0:0.1 0/1:110:2:1,1:25,83:0.0182:2,2:10:1:28.5:1:0.41852:3.28:60:4:0.0189:0:1 -6 29856546 . G T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03892;SOR=Inf;LSEQ=GGGGCCACAGGGCGCCTCCC;RSEQ=GATCGCCTGTAGATCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:17,140:0:2,0:25.5:1:31.3:1:1:0:60:156:0.9936:0:0.1 0/1:82:3:1,2:16,63:0.0366:2,2:24.7:1:30.3:1:0.50678:1.95:60:6:0.037:0:1.3 -6 29856550 . C G 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACAGGGCGCCTCCCGGAT;RSEQ=GCCTGTAGATCTCCGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:17,134:0:2,0:25.2:1:29.9:1:1:0:60:36.75:1:0:0.1 0/1:73:33:2,31:9,31:0.4521:2,2:25.2:1:30.4:1:0.09718:4.41758:60:66:0.4648:0:1.3 -6 29856552 . C T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00119;SOR=Inf;LSEQ=ACAGGGCGCCTCCCGGATCG;RSEQ=CTGTAGATCTCCGGGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:16,128:0:2,0:25.8:1:31.1:1:1:0:60:27.8:1:0:0.1 0/1:72:6:0,6:11,55:0.0833:2,0:24.7:1:30.3:1:0.58115:0:60:12:0.0833:0:2 -6 29856633 . T C 111 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=36.6935;LSEQ=ATATCGCCCTCCCTCTGGTC;RSEQ=TGAGGGAGAAGAATCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:3,23:0.037:2,0:32:0:33:0:1:0:60:2:0.0385:0:1 1/0:18:11:1,10:2,5:0.6111:2,2:20.5:1:32.3:1:0.52819:3.68244:60:22:0.6111:0:1.7 -6 29856655 . G C 103 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05911;SOR=0.13365;LSEQ=GAGGGAGAAGAATCCTCCTG;RSEQ=GTTTCCAGAGAGTGACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:3,7:3,11:0.4167:2,2:20.5:1:31.3:1:0.66533:1.54:60:20:0.4167:0:1 0/1:12:1:0,1:2,8:0.0833:2,0:28:0:26:0:1:0:60:2:0.0909:0:1 -6 29856843 . G C 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=CTGCTTCACACTCAATGTGC;RSEQ=TGGGGGTCTGAGTCCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:21,4:0:2,0:19.2:1:30.9:1:1:0:53.4:50:1:0:0.1 1/0:7:4:4,0:3,0:0.5714:0,0:23:1:31.8:1:1:0:38:8:0.5714:0:2 -6 29856862 . T A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56073;SOR=2.77635;LSEQ=CGTGGGGGTCTGAGTCCAGC;RSEQ=CTTCTGAGTCCCTCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:21,2:0.08:2,0:14.5:1:32:1:1:0:43:4:0.08:0:1.5 0/1:10:2:2,0:8,0:0.2:0,0:28:1:30.5:1:1:0:49.5:4:0.2:0:2 -6 29856917 . T C 114 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=18.73042;LSEQ=CCAGAAGTCGCTGTTCCCTC;RSEQ=TCAGGGACTAGAATTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:3,0:71,4:0.0385:2,0:19:1:30.7:1:1:0:53:6:0.039:0:2 0/1:32:14:14,0:14,4:0.4375:2,1:22.5:1:30.1:1:0.11293:0:52.9:28:0.4375:0:1.5 -6 29856930 . A G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.97793;LSEQ=TTCCCTCTTCAGGGACTAGA;RSEQ=TTTTCCACGGAATAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:5:5,0:84,4:0.0538:1,0:18.6:1:32.2:1:1:0:53.4:10:0.0543:0:2 0/1:38:2:2,0:32,4:0.0526:2,0:16:1:32:1:1:0:59:4:0.0526:0:2.5 -6 29856965 . G C 73 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00273;SOR=Inf;LSEQ=GGAGATTATCCCAGGTGCCT;RSEQ=TGTCCAGGCTGTTGTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:171,5:0:1,0:25.2:1:32.3:1:1:0:58.9:43:1:0:0.4 0/1:80:5:5,0:71,4:0.0625:2,0:10:1:31.6:1:1:0:53.2:10:0.0625:0:4 -6 29856977 . T G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9702;LSEQ=AGGTGCCTGTGTCCAGGCTG;RSEQ=TGTCTGGGTTCTGTGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:16:14,2:200,4:0.0727:1,2:25.3:1:30.3:1:0.06276:7.011:56.6:15:0.0688:0:1.8 0/1:99:7:5,2:90,2:0.0707:1,2:15.6:1:27.7:1:0.02422:16.64368:60:6:0.0619:0:1.3 -6 29857005 . C T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51392;SOR=0.52903;LSEQ=GTTCTGTGCTCCCTTCCCCA;RSEQ=CCCAGGCATCCTGTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:8:8,0:287,11:0.0261:1,0:8.4:1:28.3:1:1:0:53.3:16:0.0268:0:2.5 0/1:143:2:1,1:140,1:0.014:1,2:9.5:1:24.5:1:0.02787:99.34961:50:4:0.0143:0:3.5 -6 29857012 . CA TG 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7404;LSEQ=GCTCCCTTCCCCACCCCAGG;RSEQ=TCCTGTCCATTCTCAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:6:6,0:319,14:0.0177:1,0:5.8:1:28.8:1:1:0:51.5:12:0.0182:0.0118:2.3 0/1:152:2:1,1:143,7:0.0132:1,2:22:1:29:1:0.10282:19.18576:45:4:0.0134:0:3.5 -6 29857013 . A G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.31927;LSEQ=CTCCCTTCCCCACCCCAGGC;RSEQ=TCCTGTCCATTCTCAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:23:20,3:304,12:0.0673:1,2:30.8:1:29.8:1:0.0726:3.77561:47.3:46:0.0693:0:1.8 0/1:153:69:64,5:79,3:0.451:1,2:29.3:1:29.3:1:0.4701:2.04754:43.4:68:0.4595:0:2 -6 29857021 . C A 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCACCCCAGGCATCCTGTC;RSEQ=ATTCTCAAGATGGCCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:353,40:0:2,0:23.9:1:30.6:1:1:0:57.7:23.563:1:0:0.3 0/1:164:15:12,3:136,13:0.0915:2,2:27.4:1:29.1:1:0.1667:2.59476:48.9:30:0.0932:0:2.5 -6 29857042 . C T 67 Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27495;SOR=2.04156;LSEQ=ATTCTCAAGATGGCCACATG;RSEQ=GTGCTGGAGGAGTGTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:616:6:1,5:443,166:0.0097:2,2:11:1:26:1:0.00739:13.27927:47:5:0.0083:0:4.8 0/1:203:4:0,4:153,46:0.0197:2,0:12:1:26:1:0.00335:0:50:8:0.0201:0:3.3 -6 29857050 . A T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=15.70912;LSEQ=GATGGCCACATGCGTGCTGG;RSEQ=GGAGTGTCCCATGACAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:714:21:13,8:474,219:0.0294:2,2:19:1:28.1:1:0.63466:1.33141:39:20:0.0289:0:2 0/1:235:76:57,19:100,59:0.3234:2,2:27.7:1:27.4:1:0.07604:1.77:38.4:75:0.3304:0:2.2 -6 29857099 . C T 119 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.42636;LSEQ=CTGAATTTTCTGACTCTTCC;RSEQ=GTCAGACCCCCCCCAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1445:7:1,6:757,681:0.0048:2,2:22.3:1:29.9:1:0.05829:6.66227:43.4:14:0.0049:0:6.3 0/1:458:16:3,13:220,222:0.0349:2,2:21.6:1:29.8:1:0.01979:4.28217:35:32:0.0355:0:2.3 -6 29857105 . A AC 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09304;SOR=1.32095;LSEQ=TTTCTGACTCTTCCCGTCAG;RSEQ=CCCCCCCCAAGACACATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1497:157:77,80:696,634:0.1049:2,2:28.8:1:31.4:1:0.44818:1.14046:23.4:51.333:0.1053:0.002:0.5 0/1:470:63:32,31:184,218:0.134:2,2:32.4:1:31.1:1:0.49816:1.22:22.3:126:0.1382:0:0.4 -6 29857132 . C T 73 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.03044;SOR=3.74459;LSEQ=CCAAGACACATATGACCCAC;RSEQ=ACCCCATCTCTGACCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1320:5:0,5:595,720:0.0038:2,0:10:1:28.8:1:0.06811:0:31:10:0.0039:0:1.6 0/1:427:6:0,6:175,243:0.0141:2,0:22.3:1:28.3:1:0.0447:0:35.7:12:0.0146:0:1.3 -6 29857177 . G A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.86124;SOR=1.03596;LSEQ=CCCTGAGGTGCTGGGCCCTG;RSEQ=GCTTCTACCCTGCGGAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:41:9,32:222,419:0.0601:2,2:15.1:1:31.1:1:0.12471:1.88228:25:82:0.0614:0:1.2 0/1:177:11:3,8:47,119:0.0621:2,2:15:1:29.6:1:1:1.05292:43.3:22:0.0632:0:1 -6 29857236 . GG C 171 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=17.1283;LSEQ=GATGGGGAGGACCAGACCCA;RSEQ=ACACGGAGCTCGTGGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:14:13,1:139,202:0.0393:2,1:34.1:1:32:1:1e-04:18.78:33.9:28:0.0395:0:0 0/1:111:46:40,6:32,30:0.4144:2,2:20.3:1:31:1:0.00016:6.14:33.3:45:0.4206:0.1171:0.7 -6 29857264 . G A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24418;LSEQ=AGCTCGTGGAGACCAGGCCT;RSEQ=CAGGGGATGGAACCTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:124:74,50:162,69:0.3493:2,2:24.7:1:29:1:0.05894:1.58418:35.3:61:0.3496:0:1.1 0/1:147:17:13,4:113,16:0.1156:2,2:26.3:1:28.7:1:0.25403:2.15895:33.5:34:0.1156:0:1.1 -6 29857359 . C A 264 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1243.6434;LSEQ=GTGCAGCATGAGGGTCTGCC;RSEQ=GAGCCCCTCACCCTGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1213:1:1,0:640,570:8e-04:2,0:1:0:31:0:1:0:60:2:8e-04:0:1 1/0:853:437:233,204:214,201:0.5123:2,2:27.8:1:30.2:1:0.63122:1.07:49.6:144.667:0.5142:0:1.8 -6 29857410 . T C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=13.23451;LSEQ=GGAGATGGGGGTGTCATGTC;RSEQ=CTTAGGGAAAGCCGGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:999:111:56,55:381,507:0.1111:2,2:25.7:1:31.2:1:0.15518:1.35:57.2:222:0.1141:0:1.1 1/0:683:426:199,227:106,146:0.6237:2,2:23.5:1:30.2:1:0.26357:1.21:55.9:84.2:0.6293:0:2 -6 29857424 . G A 208 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGTCTCTTAGGGAAAGCC;RSEQ=GAGCCTCTCTGGAGAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:841:0:0,0:361,480:0:2,0:24.3:1:30.2:1:1:0:59.3:51.563:1:0:0.3 0/1:589:130:60,70:204,255:0.2207:2,2:24.4:1:29.7:1:0.76477:1.07:59.2:31.5:0.2165:0:2.7 -6 29857473 . C T 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGTCCCTCACCTTCCCC;RSEQ=CTTTTCCCAGAGCCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:560:0:0,0:218,342:0:2,0:25.5:1:30.9:1:1:0:59.9:61.222:1:0:0.5 0/1:467:46:23,23:187,234:0.0985:2,2:26.3:1:29.4:1:0.53323:1.25:59:45:0.0978:0:2.8 -6 29857502 . A C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=16.11493;LSEQ=AGAGCCATCTTCCCAGCCCA;RSEQ=CGTCCCCATCGTGGGCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:516:76:28,48:169,270:0.1473:2,2:27.3:1:31.2:1:0.89836:1.07289:59.1:24.333:0.1446:0:3 1/0:425:313:141,172:58,54:0.7365:2,2:26.7:1:30.8:1:0.22693:1.30937:59.5:38.125:0.7332:0:2.3 -6 29857504 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=11.55284;LSEQ=AGCCATCTTCCCAGCCCAAC;RSEQ=TCCCCATCGTGGGCATCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:513:72:27,45:172,269:0.1404:2,2:27.4:1:30.7:1:0.89639:1.06556:59.1:71:0.142:0:3 1/0:428:280:128,152:70,76:0.6542:2,2:26.4:1:29.5:1:0.68312:1.09352:59.4:34:0.6538:0:2.5 -6 29857522 . G A 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0157;SOR=0.56445;LSEQ=ACGTCCCCATCGTGGGCATC;RSEQ=TTGCTGGCCTGGTTCTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:65:25,40:160,280:0.1287:2,2:22.2:1:30.5:1:0.78322:1.09:58.5:130:0.1316:0:3.1 0/1:390:30:14,16:159,201:0.0769:2,2:21:1:28.8:1:0.8494:1.11:59.2:60:0.0781:0:2.9 -6 29857570 . G A 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01274;SOR=0.49722;LSEQ=TGGTCACTGGAGCTGTGGTC;RSEQ=CTGCTGTAATGTGGAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:47:15,32:106,211:0.1291:2,2:24.5:1:29.7:1:1:1.07153:58.9:46:0.1285:0:2.2 0/1:277:19:7,12:97,161:0.0686:2,2:25.5:1:28.9:1:1:1.03271:60:38:0.0693:0:2.4 -6 29857646 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14821;SOR=Inf;LSEQ=CTGAGATTTCTTGTCTCACT;RSEQ=AGAGTTCCAAGCCCCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:30,97:0:2,0:23.5:1:31.3:1:1:0:60:41.333:1:0:0.3 0/1:80:2:1,1:13,65:0.025:2,2:14.5:1:28.5:1:0.3212:4.86:60:4:0.026:0:1 -6 29857649 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14322;SOR=Inf;LSEQ=AGATTTCTTGTCTCACTGAG;RSEQ=GTTCCAAGCCCCAGGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:30,94:0:2,0:22.7:1:31:1:1:0:60:123:1:0:0.3 0/1:76:2:1,1:11,63:0.0263:2,2:22.5:1:28:1:0.29263:5.53:27:4:0.027:0:6 -6 29857658 . C A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12891;SOR=Inf;LSEQ=GTCTCACTGAGAGTTCCAAG;RSEQ=CCCAGGTAGAAGTGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:25,83:0:2,0:21.7:1:30.9:1:1:0:59.6:26:1:0:0.3 0/1:61:2:1,1:7,52:0.0328:2,2:31.5:1:26.5:1:0.24699:7.02:27:4:0.0339:0:6 -6 29857671 . T G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20881;SOR=0.31974;LSEQ=TTCCAAGCCCCAGGTAGAAG;RSEQ=GCCCTGCCTGGTTACTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:10:1,9:15,58:0.1205:2,2:19.8:1:30.1:1:0.67822:2.30859:58:20:0.122:0:1.6 0/1:48:2:0,2:6,40:0.0417:2,0:23:1:25.5:1:1:0:60:4:0.0417:0:2 -6 29857681 . G C 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11538;SOR=Inf;LSEQ=CAGGTAGAAGTGCCCTGCCT;RSEQ=GTTACTGGGAAGCACCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:11,58:0:2,0:25.4:1:31.1:1:1:0:57.9:68:1:0:0.5 0/1:36:2:1,1:5,29:0.0556:2,2:34:0:29.5:1:0.30952:5.39:27:4:0.0571:0:6 -6 29857699 . T C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10833;SOR=Inf;LSEQ=CTGGTTACTGGGAAGCACCA;RSEQ=CCACACTCATGGGCCTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:7,47:0:2,0:26.1:1:29.9:1:1:0:56.6:108:1:0:0.6 0/1:27:2:1,1:5,20:0.0741:2,2:16:0:31.5:1:0.40171:3.74:27:4:0.08:0:6 -6 29857730 . G C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.06501;SOR=3.90068;LSEQ=GGGCCTACCCAGCCTGGGCC;RSEQ=TGTGTGCCAGCACTTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:19:1,18:3,16:0.5:2,1:23.6:1:32.3:1:0.60386:3.27486:51.3:38:0.5:0:1.8 1/1:15:12:3,9:1,2:0.8:2,2:23.5:1:29.4:1:1:1.45761:48:11:0.8462:0:1.8 -6 29857753 . T C 108 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13208;SOR=0.18063;LSEQ=TGTGCCAGCACTTACTCTTT;RSEQ=GTAAAGCACCTGTTACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:4,8:5,16:0.3636:2,2:17.4:1:30.3:1:0.69046:1.58:48.9:24:0.3636:0:1.7 0/1:11:1:0,1:4,6:0.0909:2,0:17:0:32:0:1:0:42:2:0.0909:0:2 -6 29857852 . A G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00374;SOR=9.03157;LSEQ=AGTCACAGGGGAAGGTCCCC;RSEQ=AGGACAGACCTCAGAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:16,1:22,7:0.3696:2,1:26.4:1:28.8:1:0.2263:4.95:60:16:0.3556:0:2.2 1/1:13:11:9,2:1,1:0.8462:2,2:21.4:1:30.6:1:0.42308:3.87:60:22:0.8462:0:2.5 -6 29857890 . T C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.34803;LSEQ=GGCGGTTGGTCCAGGACCCA;RSEQ=ATCTGCTTTCTTCATGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:6:6,0:72,10:0.0682:2,0:26.7:1:33.3:1:1:0:55.7:12:0.069:0:3.8 1/0:48:32:30,2:16,0:0.6667:1,2:19.2:1:31.6:1:0.5461:0:55.8:64:0.6667:0:3.4 -6 29857901 . T C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.26915;LSEQ=CAGGACCCATATCTGCTTTC;RSEQ=TCATGTTTCCTGATCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:7:7,0:92,9:0.0642:2,0:30.3:1:32:1:1:0:54.6:14:0.0642:0:3.7 1/0:56:28:27,1:27,1:0.5:1,1:25.2:1:30.8:1:1:1:54.1:27:0.4909:0:3.8 -6 29857905 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00069;SOR=0.18107;LSEQ=ACCCATATCTGCTTTCTTCA;RSEQ=GTTTCCTGATCCCACCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:33:30,3:74,6:0.292:2,2:21.6:1:32.2:1:0.71905:1.23093:60:66:0.2946:0:1.3 0/1:58:4:4,0:52,2:0.069:1,0:26.8:1:32.5:1:1:0:60:8:0.069:0:1.5 -6 29857918 . CA TG 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13082;SOR=Inf;LSEQ=TTCTTCATGTTTCCTGATCC;RSEQ=CCCTGGGTCTGCAGTTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:126,9:0:2,0:26.4:1:31.5:1:1:0:59.7:66.5:1:0:0.5 0/1:77:2:2,0:72,3:0.026:1,0:28.5:1:32.3:1:1:0:54.5:4:0.0263:0:4 -6 29857919 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=16.0364;LSEQ=TCTTCATGTTTCCTGATCCC;RSEQ=CCCTGGGTCTGCAGTTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:11:10,1:117,9:0.0803:2,2:23.8:1:30.3:1:0.57984:1.29727:56.4:22:0.0809:0:3 1/0:80:47:43,4:31,0:0.5875:1,2:26.8:1:30.3:1:0.1471:0:56.7:94:0.6026:0:3 -6 29857959 . G A 115 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18679;SOR=0.38949;LSEQ=CATTTCTGGAAACTTCTCTG;RSEQ=GGTCCGAGACTTGGAGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:13:13,0:230,47:0.0447:2,1:11:1:31.1:1:0.13729:0:36.9:26:0.0455:0:5 0/1:168:3:3,0:127,37:0.0179:2,0:15:1:30.3:1:1:0:29:6:0.0185:0:5 -6 29857965 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=7.00449;LSEQ=TGGAAACTTCTCTGGGGTCC;RSEQ=AGACTTGGAGGTTCCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:45:40,5:232,60:0.1335:2,2:19.3:1:30.7:1:0.15851:2.07:49.5:90:0.1351:0:2.9 1/0:198:103:78,25:68,26:0.5202:2,2:21.8:1:29.5:1:0.62739:1.19:57.5:102:0.5178:0:1.9 -6 29857971 . TG AC 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05573;SOR=0;LSEQ=CTTCTCTGGGGTCCGAGACT;RSEQ=GAGGTTCCTCTAGGACCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:8:8,0:295,92:0.0203:2,0:6:1:31:1:0.20667:0:38.1:16:0.0205:0.0101:3.9 0/0:220:0:0,0:156,64:0:2,0:21.4:1:29.7:1:1:0:58.8:440:1:0:1 -6 29857993 . T A 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0183;SOR=0.56637;LSEQ=GAGGTTCCTCTAGGACCTTA;RSEQ=GGCCCTGGCTTCTTTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:68:65,3:338,167:0.1187:2,1:20:1:30.3:1:0:10.68:38:21.667:0.115:0:3.8 0/1:353:25:23,2:199,129:0.0708:2,2:15.5:1:31:1:0.00106:7.42:38.1:50:0.0716:0:3.6 -6 29858001 . G A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TCTAGGACCTTATGGCCCTG;RSEQ=CTTCTTTCTGGCATCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:651:0:0,0:431,219:0:2,0:24.7:1:31.3:1:1:0:57:64:1:0:0.7 0/1:418:10:6,4:248,160:0.0239:2,2:7.9:1:28.6:1:1:1.03327:44.7:20:0.0242:0:3.4 -6 29858004 . T C 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03495;SOR=0.6883;LSEQ=AGGACCTTATGGCCCTGGCT;RSEQ=CTTTCTGGCATCTCACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:118:95,23:355,209:0.173:2,2:19:1:31.4:1:0.00018:2.43:42.4:117:0.1731:0:3.6 0/1:445:56:39,17:224,165:0.1258:2,2:14.6:1:31.1:1:0.10931:1.69:44.3:55:0.1242:0:3.3 -6 29858013 . C T 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01159;SOR=0.67881;LSEQ=TGGCCCTGGCTTCTTTCTGG;RSEQ=ATCTCACAGGACATTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:158:119,39:362,237:0.2087:2,2:21.1:1:29.7:1:0.00056:2.00:44.4:316:0.2121:0:3.2 0/1:494:75:51,24:231,188:0.1518:2,2:18.8:1:29.4:1:0.04275:1.73:47.2:150:0.1534:0:2.9 -6 29858090 . C A 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42875;LSEQ=GCAAGTAAGTATGAAGGAGG;RSEQ=TGATCCCTGAAATCCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:842:204:96,108:261,377:0.2423:2,2:22.9:1:30.1:1:0.12309:1.28:43.6:50:0.241:0:4.9 0/1:556:67:29,38:223,266:0.1205:2,2:20.4:1:29.2:1:0.79394:1.09831:47.3:134:0.122:0:4.5 -6 29858095 . C G 108 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00027;SOR=17.10873;LSEQ=TAAGTATGAAGGAGGCTGAT;RSEQ=CCTGAAATCCTTTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:1:0,1:325,466:0.0013:2,0:1:0:16:0:1:0:21:0:0:0:4 0/1:520:11:7,4:228,281:0.0212:2,2:5.1:1:31.5:1:0.23626:2.15:47:22:0.0215:0:1.7 -6 29858097 . CT AA 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39127;LSEQ=AGTATGAAGGAGGCTGATCC;RSEQ=GAAATCCTTTGGATATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:738:122:46,76:209,338:0.1653:2,2:30.6:1:30.7:1:1:1.02158:41.6:244:0.1674:0:5.7 0/1:487:35:9,26:189,235:0.0719:2,2:28.6:1:30.8:1:0.03334:2.31939:46.9:70:0.0731:0:5.8 -6 29858105 . CT AC 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.39858;LSEQ=GGAGGCTGATCCCTGAAATC;RSEQ=TTGGATATTGTGTTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:690:106:34,72:220,359:0.1536:2,2:29.4:1:31.5:1:0.27472:1.29724:40.5:212:0.1563:0:4.9 0/1:445:30:8,22:183,231:0.0674:2,2:26.6:1:31.3:1:0.08434:2.17498:46.2:60:0.0686:0:5.1 -6 29858108 . T G 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.42174;LSEQ=GGCTGATCCCTGAAATCCTT;RSEQ=GGATATTGTGTTTGGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:108:35,73:218,359:0.1577:2,2:27.6:1:31.8:1:0.32857:1.26611:40.6:216:0.1598:0:4.9 0/1:424:31:8,23:173,219:0.0731:2,2:26:1:31:1:0.05869:2.26699:46:62:0.0743:0:5.2 -6 29858123 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.693;SOR=0.77652;LSEQ=TCCTTTGGATATTGTGTTTG;RSEQ=GAGCCCATGGGGGAGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:609:19:7,12:201,388:0.0312:2,2:5.8:1:29.3:1:0.80915:1.13:42.9:18:0.0304:0:5.1 0/1:369:9:2,7:139,221:0.0244:2,2:9.1:1:30.4:1:0.49176:2.1972:44.2:18:0.0247:0:5.7 -6 29858128 . C A 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41114;SOR=1.62514;LSEQ=TGGATATTGTGTTTGGGAGC;RSEQ=CATGGGGGAGCTCACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:7:1,6:189,358:0.0126:2,2:12.1:1:29.7:1:0.43135:3.16244:42.6:14:0.0129:0:6.1 0/1:344:7:2,5:130,207:0.0203:2,2:8.1:1:27.7:1:0.71185:1.56812:43.6:14:0.0208:0:6 -6 29858130 . A G 187 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00096;SOR=0.42182;LSEQ=GATATTGTGTTTGGGAGCCC;RSEQ=TGGGGGAGCTCACCCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:66:17,49:167,300:0.1238:2,2:17.5:1:31:1:0.12836:1.60317:39.3:65:0.1236:0:5.1 0/1:338:19:6,13:127,192:0.0562:2,2:21.4:1:31:1:0.63024:1.43169:42.8:38:0.0565:0:5.2 -6 29858158 . T C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.29066;SOR=0.64883;LSEQ=GCTCACCCACCCCACAATTC;RSEQ=TCCTCTAGCCACATCTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:24:0,24:122,243:0.0617:2,1:19:1:33.3:1:0.00013:0:34.8:48:0.0623:0:5.2 0/1:269:11:4,7:102,156:0.0409:2,2:21.2:1:31.9:1:1:1.14371:40.5:22:0.0418:0:5.5 -6 29858175 . A T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.91181;LSEQ=TTCTTCCTCTAGCCACATCT;RSEQ=CTGTGGGATCTGACCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:10:0,10:122,229:0.0277:2,0:18.2:1:30:1:0.01849:0:32.1:9:0.0254:0:4.1 0/1:237:6:3,3:98,133:0.0253:2,2:13:1:28.7:1:0.70184:1.36:40.8:12:0.0254:0:5 -6 29858201 . T C 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07348;SOR=Inf;LSEQ=GGATCTGACCAGGTCCTGTT;RSEQ=TTATTCTACTCGAGGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:136,197:0:2,0:24.2:1:29.9:1:1:0:59.9:46.571:1:0:0.5 0/1:241:3:2,1:104,134:0.0124:2,2:9:1:25:1:0.58386:2.57:60:2:0.0085:0:3.3 -6 29858213 . G C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.90269;LSEQ=GTCCTGTTTTTATTCTACTC;RSEQ=AGGCAGCAACAGTGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:117:54,63:89,104:0.3774:2,2:25.7:1:31.4:1:1:1.00:60:57.5:0.3795:0:1.3 1/0:223:167:76,91:25,30:0.7489:2,2:27.6:1:30.3:1:1:1.00:60:54.667:0.7593:0:2.5 -6 29858218 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.99923;LSEQ=GTTTTTATTCTACTCGAGGC;RSEQ=GCAACAGTGCCCAGGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:21:8,13:137,153:0.0675:2,2:26.8:1:30.4:1:0.50009:1.45334:60:42:0.0693:0:2.5 1/0:215:122:55,67:42,47:0.5674:2,2:28:1:29.2:1:0.78118:1.08815:60:39.667:0.5777:0:3 -6 29858253 . G A 138 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTCTGATGTGTCTCTCAC;RSEQ=GCTTGAAAGGTGAGACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:121,130:0:2,0:26.1:1:29.9:1:1:0:60:26.889:1:0:0.9 0/1:148:33:14,19:52,63:0.223:2,2:29.5:1:27.4:1:0.84397:1.11933:60:3.714:0.1912:0:4.3 -6 29858256 . T G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.10254;LSEQ=TCTGATGTGTCTCTCACGGC;RSEQ=TGAAAGGTGAGACCTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:9:3,6:119,113:0.0372:2,2:19.7:1:27.3:1:0.32942:2.09988:60:3.5:0.031:0:3.4 1/0:144:79:33,46:31,33:0.5486:2,2:25.3:1:30.3:1:0.4994:1.30696:60:158:0.5683:0:3.6 -6 29858294 . A G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.67985;LSEQ=GGGGGCCTGATGTGTGGGGG;RSEQ=TGTTGGGGGGGAACAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:13:8,5:102,62:0.0695:2,2:18:1:26.4:1:1:1.02808:60:2.25:0.0682:0:2 0/1:94:46:23,23:23,21:0.4894:2,2:17.5:1:29.9:1:0.83655:1.09413:59.6:22:0.5789:0:2.9 -6 29858296 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5386;SOR=0;LSEQ=GGGCCTGATGTGTGGGGGAT;RSEQ=TTGGGGGGGAACAGTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:104,75:0.011:2,2:12:1:27.5:1:1:1.3841:60:4:0.0124:0:1.5 0/0:101:0:0,0:46,55:0:2,0:16.1:1:28.4:1:1:0:59.6:7.417:1:0:1.8 -6 29858357 . A G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00077;SOR=Inf;LSEQ=TTGAATTTGATGTTTTGAGC;RSEQ=TGCGATGGGCTGCCAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:143,53:0:2,0:24.1:1:29.9:1:1:0:60:27:1:0:0.4 0/1:113:7:6,1:78,28:0.0619:2,2:22.3:1:29.9:1:0.67545:2.14:60:14:0.0625:0:1.4 -6 29858395 . A G 61 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9283;LSEQ=GTGTCATCCATTACTGGGAC;RSEQ=GATATGAATTTGTTCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:4:4,0:241,95:0.0118:2,0:5.3:1:30.5:1:0.57954:0:54:8:0.0119:0:4.8 0/1:183:2:2,0:127,53:0.0109:2,0:4.5:1:29.5:1:1:0:41:4:0.011:0:4.5 -6 29858407 . G C 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27809;SOR=1.41016;LSEQ=ACTGGGACAGATATGAATTT;RSEQ=TTCATGAATATTTTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:440:28:23,5:284,127:0.0636:2,2:10.4:1:31.9:1:0.20062:2.05:53.5:56:0.0648:0:3.1 0/1:240:21:12,9:146,73:0.0875:2,2:8.9:1:31.5:1:0.47042:1.4974:44.7:42:0.0882:0:3 -6 29858468 . G T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.60193;LSEQ=TGTGGGACTGAGAGGCAAGA;RSEQ=TTGTTCCTGCCTTCCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:931:29:13,16:460,442:0.0311:2,2:30.9:1:30.8:1:0.57393:1.28055:45.2:58:0.0315:0:4.4 0/1:432:110:56,54:156,165:0.2546:2,2:28.1:1:29.8:1:0.74044:1.10:42.9:35.667:0.2512:0:3.8 -6 29858475 . CTG ACA 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.5496;LSEQ=CTGAGAGGCAAGAGTTGTTC;RSEQ=CCTTCCCTTTGTGACTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:933:38:16,22:438,457:0.0407:2,2:24.5:1:30.3:1:0.50801:1.31744:48.3:76:0.0414:0.0118:2.3 0/1:432:105:50,55:152,170:0.2431:2,2:27.6:1:30.2:1:1:1.02:42.9:210:0.2494:0.0532:2.2 -6 29858476 . T C 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.03342;LSEQ=TGAGAGGCAAGAGTTGTTCC;RSEQ=GCCTTCCCTTTGTGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:913:98:54,44:375,413:0.1073:2,2:29.4:1:30.3:1:0.16524:1.35:50.4:97:0.1109:0:4 0/1:407:80:39,41:113,128:0.1966:2,2:30.6:1:29.4:1:0.79709:1.08:50.7:79:0.2453:0:3.8 -6 29858483 . C T 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=1.94764;LSEQ=CAAGAGTTGTTCCTGCCTTC;RSEQ=CTTTGTGACTTGAAGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:898:95:52,43:367,435:0.1058:2,2:28.4:1:30.2:1:0.1036:1.43:51.2:30.667:0.1045:0:4.1 0/1:411:77:37,40:152,180:0.1873:2,2:28.5:1:29.5:1:0.79988:1.10:51:76:0.1872:0:3.9 -6 29858506 . ACTTT A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0;SOR=8.42767;LSEQ=TTGTGACTTGAAGAACCCTG;RSEQ=CTTTCTACAAAGGCACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:30:11,19:235,376:0.0424:2,2:25.9:1:31.4:1:1:1.07943:53:60:0.0432:0.0042:3.3 0/1:301:82:34,48:61,104:0.2724:2,2:23.5:1:30.8:1:0.57873:1.21:45.4:164:0.2752:0.0365:3.4 -6 29858507 . C A 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=2.15752;LSEQ=TGTGACTTGAAGAACCCTGA;RSEQ=TTTCTTTCTACAAAGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:65:29,36:235,376:0.0919:2,2:25.4:1:31:1:0.35104:1.29:48.2:130:0.0937:0:4.5 0/1:301:54:26,28:61,104:0.1794:2,2:19.1:1:29:1:0.15287:1.58:51.9:53:0.1779:0:4.2 -6 29858517 . A G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.16207;LSEQ=AGAACCCTGACTTTCTTTCT;RSEQ=CAAAGGCACCTGAATGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:605:83:32,51:180,342:0.1372:2,2:22.5:1:32.6:1:0.46087:1.19:49.5:166:0.1386:0:4.3 0/1:257:116:44,72:54,87:0.4514:2,2:21.6:1:31.4:1:1:1.01562:48:57:0.4488:0:3.7 -6 29858530 . A C 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52887;SOR=1.2321;LSEQ=TCTTTCTACAAAGGCACCTG;RSEQ=ATGTGTCTGTGTTCCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:33:12,21:108,301:0.0747:2,2:16.3:1:33:1:0.22538:1.59:42.6:66:0.0757:0:5.2 0/1:199:18:4,14:60,121:0.0905:2,2:15.4:1:32.5:1:0.43424:1.73116:43.3:36:0.0914:0:5.3 -6 29858554 . T C 51 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66083;SOR=1.39524;LSEQ=TGTCTGTGTTCCTGTAGGCA;RSEQ=AATGTGTGGAGGAGGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:1,2:29,214:0.0122:2,2:4.7:1:32.7:1:0.32421:3.66:52.3:6:0.0123:0:6.7 0/1:118:2:0,2:21,95:0.0169:2,0:6:0:33:1:1:0:51:4:0.0174:0:7 -6 29858567 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54555;SOR=0;LSEQ=GTAGGCATAATGTGTGGAGG;RSEQ=GGGGAGACCAACCCACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:0,2:5,176:0.0109:1,0:20:1:30:1:1:0:60:4:0.011:0:1 0/0:97:0:0,0:14,83:0:2,0:23.7:1:30.7:1:1:0:58.6:194:1:0:0.6 -6 29858660 . A C 66 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00129;SOR=27.51706;LSEQ=TCTTTCCTGTTCCAGAGAGG;RSEQ=GGGGCTGAGATGTCTCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:0,1:1,36:0.0263:1,0:14:0:31:0:1:0:60:2:0.0263:0:1 0/1:11:5:1,4:0,6:0.4545:0,2:25.4:1:28.8:1:0.45455:0:60:10:0.4545:0:1 -6 29858842 . A C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGACAAAATAAATGGAACAC;RSEQ=TGAGAACCTTCCAGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28.5:1:31.5:1:1:0:46:4:1:0:3 0/0:1:0:0,0:0,1:0:0,0:23:0:32:0:1:0:60:2:1:0:1 -6 29863766 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCTCCTCACCTCTCAGAC;RSEQ=GGGCGGCCGGGGAGAGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:29:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29864315 . T G 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24242;SOR=7.95544;LSEQ=AGGAGGTGTCTGGGTTCTGT;RSEQ=CTCCCTTCCCCACCCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:2,2:0.2:2,0:16:0:34:0:1:0:23:2:0.2:0:3 1/0:7:5:3,2:1,1:0.7143:2,2:35:1:31:1:1:1.41:60:10:0.7143:0:1.2 -6 29864379 . G A 77 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25359;SOR=0;LSEQ=CACATGGGTGCTGCTGGAGT;RSEQ=TCCCATGAGGAATGCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:6,2:5,5:0.4444:2,2:32.1:1:25.8:1:0.36652:2.82:30.9:7:0.4118:0:2.8 0/0:4:0:0,0:2,2:0:2,0:9.3:1:33.3:1:1:0:60:8:1:0:2.3 -6 29864404 . G C 64 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=ATGAGGAATGCAAAGTGCCT;RSEQ=AATTTTCTTACTCTTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:0:2,0:16.9:1:30.6:1:1:0:48.4:19:1:0:1.2 1/1:4:4:3,1:0,0:1:0,2:23.5:1:32:1:1:0:60:8:1:0:4 -6 29864413 . T G 85 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25359;SOR=0;LSEQ=GCAAAGTGCCTGAATTTTCT;RSEQ=ACTCTTCCCCTCAGAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:6,2:7,3:0.4444:2,2:12.4:1:28.5:1:1:1.27:30.9:7:0.4118:0:2.8 0/0:4:0:0,0:3,1:0:2,0:31.8:1:30.8:1:1:0:60:8:1:0:4 -6 29864421 . C T 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26749;SOR=0;LSEQ=CCTGAATTTTCTTACTCTTC;RSEQ=CCTCAGAATCCCAGAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:7,3:0.375:2,2:6.8:1:30.3:1:1:1.15538:32:12:0.375:0:3 0/0:4:0:0,0:3,1:0:2,0:35.5:1:27:1:1:0:60:3:1:0:4 -6 29864423 . C T 60 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=TGAATTTTCTTACTCTTCCC;RSEQ=TCAGAATCCCAGAATACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:0:2,0:18.9:1:31.2:1:1:0:49.5:32:1:0:1.1 1/1:4:4:3,1:0,0:1:0,2:35.5:1:30.3:1:1:0:60:8:1:0:4 -6 29864446 . G T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AGAATCCCAGAATACATGTG;RSEQ=GATCCACTACCCCATCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,4:0:2,0:27.7:1:32.3:1:1:0:60:28:1:0:0 1/1:7:6:4,2:1,0:0.8571:0,2:25.7:1:30:1:1:0:60:12:0.8571:0:3.3 -6 29864478 . A G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00058;SOR=Inf;LSEQ=CCATCTCGGACCATGAGGCC;RSEQ=CCCTGAGGTGCTGGGTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:11,3:0:2,0:27.4:1:29.6:1:1:0:60:28:1:0:0 1/0:13:8:6,2:4,1:0.6154:2,2:22.3:1:28.9:1:1:1.30472:60:16:0.6154:0:2.8 -6 29864556 . T C 33 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67024;LSEQ=GGGATGGGGAGGACCAAATT;RSEQ=AGGACACAGAGCTTGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:28,12:0.0476:2,0:20:1:33:0:1:0:47:4:0.0488:0:6 0/1:31:1:1,0:21,9:0.0323:2,0:18:0:32:0:1:0:47:2:0.0333:0:6 -6 29864558 . G A 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.64424;LSEQ=GATGGGGAGGACCAAATTTA;RSEQ=GACACAGAGCTTGTGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:29,12:0.0465:2,0:22:1:32:0:1:0:47:4:0.0476:0:6 0/1:33:1:1,0:23,9:0.0303:2,0:20:0:29:0:1:0:47:2:0.0313:0:6 -6 29864561 . CA GG 33 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.60671;LSEQ=GGGGAGGACCAAATTTAGGA;RSEQ=CAGAGCTTGTGGGGACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:29,12:0.0465:2,0:26:1:33.5:0:1:0:47:4:0.0488:0:5 0/1:35:1:1,0:25,9:0.0286:2,0:24:0:32.5:0:1:0:47:2:0.0286:0:5 -6 29864562 . A G 129 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=27.9608;LSEQ=GGGAGGACCAAATTTAGGAC;RSEQ=CAGAGCTTGTGGGGACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:2,0:28,12:0.0455:2,0:28:1:31.5:1:1:0:60:4:0.0488:0:1 1/0:36:21:14,7:11,3:0.5833:2,2:18.1:1:29.5:1:0.70412:1.80255:60:20:0.5882:0:1.8 -6 29864594 . T C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28176;SOR=0.36557;LSEQ=GGGACCAGACCTGCAGGGTA;RSEQ=AGAACCTTCCAGAAGTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:6:5,1:39,11:0.1071:2,2:31:0:33.5:1:1:1.40:53.7:12:0.1111:0:3 0/1:48:2:2,0:36,10:0.0417:2,0:31:0:33:0:1:0:34:4:0.0417:0:3.5 -6 29864599 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20434;SOR=Inf;LSEQ=CAGACCTGCAGGGTATAGAA;RSEQ=CTTCCAGAAGTGGGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:47,13:0:2,0:26.2:1:32.2:1:1:0:59.4:59:1:0:0.5 0/1:50:2:1,1:38,10:0.04:2,2:26:0:31:1:0.3951:3.67078:60:4:0.0408:0:2.5 -6 29864613 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23157;SOR=Inf;LSEQ=ATAGAACCTTCCAGAAGTGG;RSEQ=CAGCTGTGGTGCTGTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:62,14:0:2,0:21.4:1:31.5:1:1:0:59.5:37:1:0:0.4 0/1:71:2:1,1:46,23:0.0282:2,2:8.5:1:29:1:1:1.97912:60:4:0.0286:0:4 -6 29864614 . C T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27708;SOR=0.33559;LSEQ=TAGAACCTTCCAGAAGTGGG;RSEQ=AGCTGTGGTGCTGTCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:6:5,1:56,15:0.0779:2,2:11:0:31.5:1:1:1.33:53.7:12:0.0811:0:3 0/1:73:2:2,0:46,25:0.0274:2,0:11:0:30.5:1:0.54338:0:34:4:0.0278:0:3.5 -6 29864622 . G A 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCAGAAGTGGGCAGCTGTG;RSEQ=TGCTGTCTTCTAGAGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:70,22:0:2,0:19.3:1:31.3:1:1:0:59.6:91:1:0:0.3 1/0:80:41:27,14:23,16:0.5125:2,2:24:1:29.1:1:0.64497:1.34:60:40:0.5128:0:1.5 -6 29864625 . CTGTCTTCTAGAGAC GTCTCTTATGTAAAG 147 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02809;SOR=0.41599;LSEQ=AGAAGTGGGCAGCTGTGGTG;RSEQ=AAGTAGAGATACACATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:27:24,3:61,24:0.2411:2,2:16:1:31:1:0.07708:3.12:42.3:54:0.2432:0.2411:6 0/1:86:10:7,3:46,30:0.1163:2,2:13.9:1:29.3:1:0.73469:1.51:37.4:20:0.1163:0.1163:6.5 -6 29864650 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19554;SOR=Inf;LSEQ=TTCTAGAGACAAGTAGAGAT;RSEQ=CACATGCCATGTGCAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:102,50:0:2,0:23:1:28.8:1:1:0:57.1:151:1:0:1 0/1:121:2:1,1:71,48:0.0165:2,2:27:1:32.5:1:1:1.47423:60:4:0.0167:0:1 -6 29864669 . G C 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05309;SOR=0.43393;LSEQ=TACACATGCCATGTGCAGCA;RSEQ=GAGGCACTGCCAGAGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:22:20,2:81,63:0.1325:2,2:29.5:1:32.6:1:0.00177:7.71:40:44:0.1333:0:6.7 0/1:129:8:5,3:65,56:0.062:2,2:30:0:31.3:1:0.72622:1.43:38.3:16:0.0635:0:7.1 -6 29864673 . GCA AGG 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00393;SOR=0.33159;LSEQ=CATGCCATGTGCAGCAGGAG;RSEQ=CTGCCAGAGCCCCTCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:33:25,8:77,66:0.1875:2,2:26.5:1:31.3:1:0.03042:2.66:42.4:66:0.1897:0.0625:5.1 0/1:127:9:5,4:63,55:0.0709:2,2:32.1:1:31.4:1:1:1.09:40.7:18:0.0714:0.0079:5.3 -6 29864686 . C T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00066;SOR=Inf;LSEQ=GCAGGAGGCACTGCCAGAGC;RSEQ=CCTCACACTGAGATGGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:100,85:0:2,0:30.1:1:30.7:1:1:0:56.7:91.5:1:0:1.2 0/1:127:8:4,4:57,62:0.063:2,2:21.6:1:30:1:1:1.09:60:16:0.064:0:2.5 -6 29864693 . A C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10088;SOR=0.58882;LSEQ=GCACTGCCAGAGCCCCTCAC;RSEQ=CTGAGATGGGCTAAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:40:26,14:70,78:0.2128:2,2:24.5:1:30.8:1:0.05169:2.06:44.9:80:0.2174:0:5.3 0/1:124:17:9,8:47,60:0.1371:2,2:25.4:1:30.6:1:0.60192:1.43:43.5:34:0.1405:0:5.3 -6 29864704 . C G 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13455;SOR=0.59986;LSEQ=GCCCCTCACACTGAGATGGG;RSEQ=TAAGGAGATGAATGAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:42:26,16:64,81:0.2246:2,2:22.6:1:30.6:1:0.05364:2.05:45.6:41:0.2253:0:5.3 0/1:115:17:9,8:41,57:0.1478:2,2:25.2:1:31.4:1:0.43526:1.56:43.5:34:0.1491:0:5.3 -6 29864724 . C T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1117;SOR=0.57421;LSEQ=CTAAGGAGATGAATGAGGGG;RSEQ=CATGTCTCTTCTCAGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:40:18,22:35,75:0.2667:2,2:22.9:1:29.3:1:0.17615:1.75:47.4:80:0.2797:0:5.9 0/1:87:15:7,8:29,43:0.1724:2,2:21.1:1:29.4:1:0.77488:1.29:45.5:30:0.1744:0:5.6 -6 29864730 . C G 163 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02893;SOR=0.44244;LSEQ=AGATGAATGAGGGGCCATGT;RSEQ=TCTTCTCAGGGAAAGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:40:13,27:30,71:0.2837:2,2:22.6:1:30.8:1:0.83958:1.14:48.3:39:0.2826:0:6.3 0/1:74:11:5,6:26,37:0.1486:2,2:23.8:1:32.1:1:1:1.18:47.1:22:0.1507:0:5.7 -6 29864736 . T A 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01947;SOR=0.38749;LSEQ=ATGAGGGGCCATGTCTCTTC;RSEQ=CAGGGAAAGCAGGAGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:35:7,28:24,63:0.2869:2,2:26.3:1:29.8:1:0.49238:1.51879:50.9:70:0.3017:0:6.5 0/1:67:9:3,6:21,37:0.1343:2,2:23.7:1:30.6:1:1:1.13305:48.7:18:0.1385:0:5.7 -6 29864745 . G A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34662;SOR=2.8264;LSEQ=CATGTCTCTTCTCAGGGAAA;RSEQ=CAGGAGCCTTTCTGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:0,2:22,88:0.0179:2,0:40:1:30:1:1:0:60:4:0.0182:0:2 0/1:61:3:2,1:15,43:0.0492:2,2:24.7:1:28.3:1:0.18516:5.54:60:6:0.05:0:2 -6 29864754 . T C 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03492;SOR=2.17063;LSEQ=TCTCAGGGAAAGCAGGAGCC;RSEQ=TTCTGGAGGCCTTCAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:42:6,36:7,48:0.433:2,2:25.4:1:31.8:1:1:1.14:52.7:84:0.4375:0:6.2 1/0:48:30:5,25:3,15:0.625:2,2:22.2:1:31.9:1:1:1:59.2:60:0.6383:0:2.4 -6 29864792 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.02594;SOR=0.31593;LSEQ=AGGGTCAGGGCTGAGGCCTG;RSEQ=GGGTCAGGACCCCTCACGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:31:2,29:8,34:0.4247:2,2:29.8:1:32.2:1:0.1739:3.36096:52.5:62:0.4247:0:6.5 0/1:32:6:1,5:5,21:0.1875:2,2:26.5:1:28.5:1:1:1.18422:60:12:0.1875:0:6.2 -6 29864801 . A G 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10467;SOR=0.42247;LSEQ=GCTGAGGCCTGGGGGTCAGG;RSEQ=CCCCTCACGTTCCCCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:30:2,28:11,33:0.4054:2,2:26.6:1:33:1:0.06131:4.58382:52.2:60:0.4054:0:6.6 0/1:27:6:1,5:6,15:0.2222:2,2:26.7:1:30.5:1:1:1.95426:60:12:0.2222:0:6.2 -6 29864810 . G A 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13243;SOR=0.39734;LSEQ=TGGGGGTCAGGACCCCTCAC;RSEQ=TTCCCCTCCTTTCTTAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:23:0,23:10,28:0.377:2,1:28.3:1:31.8:1:0.00942:0:53.5:46:0.377:0:6.7 0/1:26:5:1,4:5,16:0.1923:2,2:32.8:1:29.8:1:1:1.2397:60:10:0.2:0:6.2 -6 29864814 . CC TG 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20127;SOR=0.45642;LSEQ=GGTCAGGACCCCTCACGTTC;RSEQ=CTCCTTTCTTAGGGCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:21:0,21:10,28:0.3559:2,1:27.1:1:32.1:1:0.00998:0:54.5:42:0.3559:0:5.7 0/1:25:5:1,4:5,15:0.2:2,2:33.8:1:29.7:1:1:1.31882:60:10:0.2:0:5.2 -6 29864846 . C T 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.78475;LSEQ=AGGGCCATCTTCCCAGCCCA;RSEQ=ATTCCCCATCGTGGGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:7:0,7:9,21:0.1842:2,0:21.1:1:28.9:1:0.15996:0:56.7:14:0.1892:0:5.3 0/1:20:3:1,2:4,13:0.15:2,2:31.3:1:30.7:1:1:1.58:60:6:0.15:0:5.3 -6 29864852 . C T 86 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00044;SOR=23.74803;LSEQ=ATCTTCCCAGCCCACATTCC;RSEQ=CATCGTGGGCATTGTTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:0,1:9,26:0.0278:2,0:13:0:31:0:1:0:60:2:0.0278:0:2 0/1:19:8:2,6:3,8:0.4211:2,2:25.4:1:28.9:1:1:1.11808:60:16:0.4211:0:4.1 -6 29864857 . G A 88 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=24.47975;LSEQ=CCCAGCCCACATTCCCCATC;RSEQ=TGGGCATTGTTACTGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:9,24:0.0294:2,0:8:0:32:0:1:0:60:2:0.0303:0:2 0/1:18:8:2,6:3,7:0.4444:2,2:25:1:29.5:1:1:1.26799:60:16:0.4706:0:4.1 -6 29864865 . T C 82 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=ACATTCCCCATCGTGGGCAT;RSEQ=GTTACTGTCCTGGTTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:25.4:1:29.8:1:1:0:58.6:27:1:0:0.7 0/1:17:7:2,5:3,7:0.4118:2,2:26.3:1:29.3:1:1:1.06713:60:14:0.4375:0:4.4 -6 29864871 . T C 85 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=CCCATCGTGGGCATTGTTAC;RSEQ=GTCCTGGTTGTTCTAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:22.7:1:30.4:1:1:0:58.6:54:1:0:0.7 0/1:17:8:2,6:3,6:0.4706:2,2:22.6:1:28.4:1:1:1.46472:60:16:0.4706:0:4 -6 29864879 . T C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14444;SOR=Inf;LSEQ=GGGCATTGTTACTGTCCTGG;RSEQ=TGTTCTAGGTGCTGTGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:0:2,0:21.9:1:29.5:1:1:0:58.2:44:1:0:0.5 0/1:14:2:1,1:4,8:0.1429:2,2:47:0:32.5:1:1:1.90:60:4:0.1429:0:5.5 -6 29864886 . A T 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7348;LSEQ=GTTACTGTCCTGGTTGTTCT;RSEQ=GGTGCTGTGGTCACTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:5,11:0.1111:2,2:20:1:31.5:1:1:2.10:40.5:4:0.1176:0:4 0/1:12:1:1,0:3,8:0.0833:2,0:3:0:27:0:0.33333:0:60:2:0.0909:0:6 -6 29864889 . T TGCTGTGGTCCCCTGA 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=ACTGTCCTGGTTGTTCTAGG;RSEQ=GCTGTGGTCACTGCTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:15.5:1:32.1:1:1:1.62:40.5:4:0.125:0.0556:4 0/0:12:0:0,0:4,8:0:2,0:25.2:1:29.6:1:1:0:60:24:1:0:2.1 -6 29865155 . A G 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCTGACTCCCAGCAGTCACA;RSEQ=GTCAGGAGAATGTTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:29:1:1:1:51:4:0.5:0:8 0/0:4:0:0,0:3,1:0:2,0:37:1:30.5:1:1:0:60:8:1:0:0.3 -6 29865169 . T C 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GTCACAAGTCAGGAGAATGT;RSEQ=CCTGCTGAGGACAGATGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:42:1:30.5:1:1:0:51:4:0.6667:0:8 0/0:4:0:0,0:3,1:0:2,0:37:1:31:1:1:0:60:8:1:0:0.3 -6 29865395 . A G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AGTGTGGTAGGGGTGGGAGA;RSEQ=TGATTCCTGAGATCCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:36.2:1:30.6:1:1:0:60:10:1:0:0 1/0:4:2:2,0:1,1:0.5:2,0:35.5:1:32.5:1:1:0:60:4:0.5:0:2.5 -6 29865444 . CACAG GTCA 66 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=GACAGGAGCCCATGGGGGAG;RSEQ=CCACCCCAAAATTCCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:12.4:1:30:1:1:0:60:10:1:0:0 1/1:6:5:4,1:0,1:0.8333:0,2:23.8:1:28.8:1:0.33333:0:52.6:10:0.8333:0.3333:2.2 -6 29865457 . A C 61 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=GGGGGAGCACAGCCACCCCA;RSEQ=AATTCCTCCTTTAGTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:14.3:1:27.5:1:1:0:55:8:1:0:0 1/1:5:4:3,1:0,1:0.8:0,2:29.8:1:30.5:1:0.4:0:50.8:8:0.8:0:3.3 -6 29865572 . G A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCTCAAGTCTTGTAAAAGTG;RSEQ=CACCTTAGAGGGCCTGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:38.7:1:30.7:1:1:0:60:6:1:0:0.3 1/0:3:2:0,2:1,0:0.6667:0,0:9:1:30.5:1:0.33333:0:49:4:0.6667:0:1 -6 29865725 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTGTTCATGACTATTTT;RSEQ=TTTCTAAGACTGCCTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29865903 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCCACCATGACCCCTGATA;RSEQ=TGTTTGGATCTGTGTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:17:0:34:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:35.5:1:30.5:1:1:0:60:4:0.6667:0:1.5 -6 29892834 . G T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGAAAGGGACAGAGGGAA;RSEQ=GGCTGGAGAAGCAGGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:1:29.5:1:1:0:60:4:1:0:2 -6 29892854 . T G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCTGGAGAAGCAGGAGGT;RSEQ=AGGAAAAGGAGCAGAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:30:1:1:0:60:4:1:0:2 -6 29893919 . G C 64 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGACTCAGGGAGACATTGA;RSEQ=ACAGAGCGCTTGGCACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:0.2857:0,0:25.3:1:32:1:1:0:57.5:8:0.2857:0:4 0/0:1:0:0,0:1,0:0:0,0:35:0:32:0:1:0:60:2:1:0:0 -6 29893922 . A T 67 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTCAGGGAGACATTGAGAC;RSEQ=GAGCGCTTGGCACAGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:0.3571:0,0:23.8:1:29.2:1:1:0:58:10:0.3571:0:4.2 0/0:1:0:0,0:1,0:0:0,0:38:0:30:0:1:0:60:2:1:0:0 -6 29893960 . T C 75 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60268;SOR=0.35166;LSEQ=GGAGCGGGGTCAGGGCGAAG;RSEQ=CCTATGGCCCCAGGCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:27.8:1:29.3:1:1:0:58.3:5:0.3846:0:4.5 0/1:5:1:1,0:4,0:0.2:0,0:10:0:34:0:1:0:60:2:0.2:0:4 -6 29893982 . C T 89 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20112;SOR=0.20713;LSEQ=CTATGGCCCCAGGCGTGGCT;RSEQ=TCAGGGTTTCAGGCCCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:11,0:0.4211:0,0:18.4:1:29.9:1:1:0:58.8:16:0.4211:0:4 0/1:8:1:1,0:6,1:0.125:2,0:32:0:31:0:1:0:60:2:0.125:0:4 -6 29894007 . A T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44628;SOR=0.45077;LSEQ=GGTTTCAGGCCCCGAAGGCG;RSEQ=TGTATTGATTGGGGAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:11:10,1:16,1:0.3929:1,2:18.9:1:30.2:1:1:1.57244:60:22:0.3929:0:2.6 0/1:9:2:2,0:5,2:0.2222:2,0:24.5:1:27.5:1:1:0:60:4:0.2222:0:3 -6 29894016 . T C 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0.65525;LSEQ=CCCCGAAGGCGATGTATTGA;RSEQ=TGGGGAGGCCCAGGGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:6,1:24,1:0.2188:1,2:24.4:1:31.9:1:0.39516:3.77964:60:14:0.2188:0:2.7 0/1:13:2:2,0:8,3:0.1538:2,0:24.5:1:30.5:1:1:0:60:4:0.1538:0:3 -6 29894030 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10345;SOR=Inf;LSEQ=TATTGATTGGGGAGGCCCAG;RSEQ=GTTGGGGATTCCCCATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:37,2:0:2,0:24.7:1:31.6:1:1:0:60:38:1:0:0.7 0/1:19:2:2,0:12,5:0.1053:2,0:9.5:1:33.5:1:1:0:60:4:0.1053:0:1 -6 29894128 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=5.30103;LSEQ=GATGTGGACTCAGTTCTCAC;RSEQ=CCCATTTGGTGTCGGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:17:17,0:215,4:0.072:1,1:29.6:1:31.5:1:1:0:60:34:0.0739:0:1.2 0/1:147:43:42,1:100,4:0.2925:1,1:24.1:1:31:1:1:1.67:60:86:0.2945:0:1.5 -6 29894152 . C A 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTGGTGTCGGGTTTCTAG;RSEQ=GAAGCCAATCGGCGTCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:319,36:0:2,0:23.5:1:31.6:1:1:0:60:43.375:1:0:0.3 0/1:243:24:17,7:186,33:0.0988:2,2:16:1:28:1:0.0861:2.31095:60:48:0.0992:0:1.4 -6 29894205 . T C 217 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAAGTCCCCGCGAACCCA;RSEQ=TGGGACTCAGATTCTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:963:0:0,0:558,405:0:2,0:26:1:30.3:1:1:0:60:59.188:1:0:0.5 0/1:769:128:80,48:378,263:0.1664:2,2:22.6:1:31:1:0.49072:1.16:60:256:0.1684:0:2.9 -6 29894211 . C T 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.64371;LSEQ=TCCCCGCGAACCCATTGGGA;RSEQ=TCAGATTCTCCCCAGACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1036:340:195,145:395,299:0.3282:2,2:27.6:1:30.4:1:0.94669:1.02:60:84:0.3294:0:1.4 0/1:832:199:113,86:364,269:0.2392:2,2:25.4:1:29.3:1:0.86975:1.02982:60:65.333:0.2396:0:1.4 -6 29894226 . G T 215 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=281.5521;LSEQ=TGGGACTCAGATTCTCCCCA;RSEQ=ACGCCGAGGATGGGGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1201:1:1,0:623,577:8e-04:2,0:45:0:13:0:1:0:60:0:0:0:7 0/1:949:180:98,82:404,365:0.1897:2,2:26:1:28.8:1:0.67867:1.08:60:179:0.1919:0:2.8 -6 29894243 . C T 221 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=158.71816;LSEQ=CCAGACGCCGAGGATGGGGT;RSEQ=ATGGCGTCCCGAACCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1291:2:0,2:632,656:0.0015:2,0:14.5:1:19.5:1:0.49982:0:60:1:8e-04:0:2 0/1:1021:202:100,102:398,421:0.1978:2,2:27.5:1:28.9:1:0.87515:1.04:60:66.333:0.1974:0:2.6 -6 29894250 . T A 177 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=25.75043;LSEQ=CCGAGGATGGGGTCATGGCG;RSEQ=CCCGAACCCTCCTCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1272:4:2,2:611,655:0.0031:2,2:5.5:1:20:1:1:1.07:60:1:0.0016:0:3 0/1:1024:77:39,38:453,493:0.0752:2,2:27:1:28.4:1:0.72223:1.12:59.8:24.667:0.0738:0:2.2 -6 29894254 . G A 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33074;LSEQ=GGATGGGGTCATGGCGTCCC;RSEQ=AACCCTCCTCCTGCTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1252:106:50,56:539,606:0.0847:2,2:23.9:1:30:1:1:1.00:60:212:0.0859:0:1.8 0/1:1011:30:14,16:462,517:0.0297:2,2:26.4:1:30.3:1:1:1.02126:60:60:0.0302:0:1.9 -6 29894269 . T C 183 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=95.35648;LSEQ=GTCCCGAACCCTCCTCCTGC;RSEQ=GCTCTTGGGGGCCCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1143:1:0,1:513,629:9e-04:2,0:29:0:26:0:1:0:60:2:9e-04:0:4 0/1:946:73:35,38:394,477:0.0772:2,2:22.3:1:29.7:1:0.71395:1.11:59.1:146:0.0784:0:2.4 -6 29894297 . G A 68 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0247;SOR=9.13495;LSEQ=GGGGCCCTGGCCCTGACCGA;RSEQ=ACCTGGGCGGGTGAGTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:879:1:1,0:371,507:0.0011:2,0:1:0:29:0:0.42321:0:60:2:0.0012:0:1 0/1:679:7:3,4:272,400:0.0103:2,2:8.9:1:24.4:1:1:1.10:60:6:0.009:0:2.4 -6 29894299 . C A 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25214;LSEQ=GGCCCTGGCCCTGACCGAGA;RSEQ=CTGGGCGGGTGAGTGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:855:233:104,129:248,374:0.2725:2,2:24.9:1:29.7:1:0.21268:1.22:59.7:76.667:0.2741:0:1.6 0/1:661:57:24,33:240,364:0.0862:2,2:22.1:1:29.2:1:0.77775:1.10:59.7:114:0.0885:0:1.7 -6 29894324 . GA G 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGGGTGAGTGCGGGATCCG;RSEQ=GGGAAATGGCCTCTGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:220,389:0:2,0:25.1:1:30.2:1:1:0:60:32.833:1:0:0.8 0/1:442:22:6,16:144,275:0.0498:2,2:28.5:1:30.6:1:0.64564:1.39536:60:44:0.0512:0.0068:2.2 -6 29894332 . T A 156 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=26.55798;LSEQ=GTGCGGGATCCGGAGGGAAA;RSEQ=GGCCTCTGCGGGGAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:2:1,1:185,370:0.0036:2,2:5:1:29:1:1:2.00:60:4:0.0036:0:3 0/1:389:34:12,22:119,236:0.0874:2,2:22.2:1:30.7:1:0.8506:1.08:60:68:0.0892:0:4.4 -6 29894334 . G A 146 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=17.74674;LSEQ=GCGGGATCCGGAGGGAAATG;RSEQ=CCTCTGCGGGGAGGAGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:3:2,1:174,366:0.0055:2,2:3:1:27.7:1:0.24664:4.19:60:6:0.0056:0:2 0/1:378:34:12,22:115,229:0.0899:2,2:22.1:1:28.8:1:0.85015:1.09:60:33:0.0897:0:4.4 -6 29894344 . G C 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGGAAATGGCCTCTGCGG;RSEQ=GAGGAGGTAGGGGCCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:150,318:0:2,0:25.2:1:30.8:1:1:0:59.9:57.5:1:0:1 0/1:318:20:7,13:97,200:0.0629:2,2:22.6:1:31.2:1:0.80982:1.11:60:40:0.0641:0:2.4 -6 29894349 . AGGTAGGGGCCC A 152 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGGCCTCTGCGGGGAGG;RSEQ=GCGCACTGGGGCGCAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:133,309:0:2,0:24.5:1:31.4:1:1:0:59.9:48.111:1:0:1.1 0/1:282:26:8,18:80,176:0.0922:2,2:28.3:1:32.5:1:1:1.02265:60:52:0.0949:0.0035:5 -6 29894351 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.17341;LSEQ=ATGGCCTCTGCGGGGAGGAG;RSEQ=TAGGGGCCCGCGCACTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:171:47,124:82,179:0.394:2,2:24.9:1:31.8:1:0.39228:1.20808:60:33.2:0.3934:0:2.4 1/0:276:186:60,126:17,48:0.6739:2,2:21.9:1:31.2:1:0.43519:1.34:60:30:0.7407:0:1.9 -6 29894389 . A C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.87887;LSEQ=GGGCGCAGGACCCGGGGAGC;RSEQ=GCGCAAGGAGGAGGGTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:107:29,78:52,123:0.3794:2,2:25.1:1:30.5:1:0.68536:1.13657:60:106:0.3799:0:2.9 1/0:141:90:26,64:12,39:0.6383:2,2:26.4:1:30.5:1:0.5568:1.32:60:89:0.6357:0:3.7 -6 29894392 . G T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0713;SOR=1.47699;LSEQ=CGCAGGACCCGGGGAGCAGC;RSEQ=CAAGGAGGAGGGTCGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:105:28,77:48,119:0.386:2,2:24.9:1:30.8:1:0.78183:1.10881:60:210:0.3903:0:2.9 0/1:137:66:18,48:18,53:0.4818:2,2:25:1:30:1:0.84746:1.10:60:32:0.4776:0:3 -6 29894393 . C G 140 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGACCCGGGGAGCAGCG;RSEQ=AAGGAGGAGGGTCGGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:77,195:0:2,0:23.3:1:31.6:1:1:0:60:29.222:1:0:1.2 0/1:139:23:8,15:29,86:0.1655:2,2:26.3:1:31.1:1:0.43902:1.58:60:46:0.1691:0:5.8 -6 29894406 . CG AA 132 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAGCGCAAGGAGGAGGGT;RSEQ=GACGGGTCTCAGCCCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:85,182:0:2,0:23.2:1:30.2:1:1:0:60:132.5:1:0:1 0/1:130:19:5,14:36,73:0.1462:2,2:27.6:1:31.1:1:0.79044:1.37749:60:38:0.1484:0.0231:5.5 -6 29894410 . C T 167 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=146.32729;LSEQ=GCGCAAGGAGGAGGGTCGGA;RSEQ=GGGTCTCAGCCCCTCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:1,0:87,170:0.0039:2,0:30:0:33:0:0.34109:0:60:2:0.004:0:3 0/1:131:48:20,28:27,56:0.3664:2,2:22.8:1:30:1:0.34593:1.48:60:23:0.3594:0:3.8 -6 29894439 . A T 173 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=249.56594;LSEQ=GCCCCTCCTCGCCCCCAGGT;RSEQ=CCCACTCCATAAGGTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:1,0:113,146:0.0038:2,0:42:0:33:0:0.43846:0:60:2:0.0039:0:3 0/1:123:61:29,32:30,31:0.4959:2,2:24.4:1:29.3:1:1:1.06727:60:60:0.4959:0:3.2 -6 29894449 . T A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=GCCCCCAGGTACCCACTCCA;RSEQ=AAGGTATTTCAGCACCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:113,147:0:2,0:26.7:1:29:1:1:0:60:31.5:1:0:0.3 0/1:116:6:2,4:57,53:0.0517:2,2:25.2:1:29:1:0.43462:2.13721:60:12:0.0526:0:1.3 -6 29894456 . T G 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=224.0673;LSEQ=GGTACCCACTCCATAAGGTA;RSEQ=TTCAGCACCGCCGTGTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:1,0:107,151:0.0039:2,0:25:0:34:0:0.41699:0:60:2:0.004:0:3 0/1:117:55:27,28:35,27:0.4701:2,2:30.7:1:31.4:1:0.46194:1.34088:60:110:0.4701:0:3 -6 29894495 . C T 38 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04808;SOR=Inf;LSEQ=CGGCCGGGTCGCGGGGAGCC;RSEQ=CGGTACATCGCAGTGGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:124,120:0:2,0:23.7:1:30.8:1:1:0:60:60:1:0:0.2 0/1:141:3:1,2:81,57:0.0213:2,2:10:1:24.3:1:0.57154:2.82109:60:2:0.0145:0:2 -6 29894505 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13523;SOR=Inf;LSEQ=GCGGGGAGCCCCGGTACATC;RSEQ=CAGTGGGCTACGTGGACGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:134,111:0:2,0:23.9:1:30.5:1:1:0:60:39.833:1:0:0.2 0/1:143:2:1,1:80,61:0.014:2,2:29:1:30:1:1:1.30895:60:4:0.0143:0:2.5 -6 29894523 . G A 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGCAGTGGGCTACGTGGAC;RSEQ=ACACGCAGTTCGTGCGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:144,117:0:2,0:24.1:1:30:1:1:0:60:36.286:1:0:0.3 0/1:154:20:12,8:72,62:0.1299:2,2:25.5:1:28.8:1:0.63856:1.29:60:19:0.1275:0:2.8 -6 29894548 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15602;SOR=Inf;LSEQ=GCAGTTCGTGCGGTTCGACA;RSEQ=CGACGCGGCGACTCCGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:169,109:0:2,0:24.9:1:32:1:1:0:60:54.6:1:0:0.5 0/1:182:2:1,1:106,74:0.011:2,2:9:1:27.5:1:1:1.42952:60:4:0.0112:0:1 -6 29894567 . G A 126 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=46.94111;LSEQ=AGCGACGCGGCGACTCCGAG;RSEQ=ATGTAGCCGCAGTCGCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:1:1,0:207,117:0.0031:2,0:1:0:26:0:1:0:60:2:0.0032:0:1 0/1:213:27:14,13:110,76:0.1268:2,2:22.1:1:26.7:1:0.53348:1.34207:60:8:0.1165:0:3.1 -6 29894569 . T C 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGACGCGGCGACTCCGAGGA;RSEQ=GTAGCCGCAGTCGCCGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:205,127:0:2,0:23.1:1:30.3:1:1:0:60:46.429:1:0:0.6 0/1:224:16:8,8:118,89:0.0714:2,2:24.7:1:29.6:1:0.60989:1.32413:60:32:0.0717:0:1.4 -6 29894580 . T G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.69182;LSEQ=CTCCGAGGATGTAGCCGCAG;RSEQ=CGCCGTGGTTGGAGCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:150:85,65:128,94:0.4032:2,2:22.7:1:30.9:1:0.91497:1.04122:60:36.5:0.4044:0:1.3 1/0:252:180:102,78:41,31:0.7143:2,2:22.6:1:30.2:1:1:1.01134:60:21.5:0.7078:0:1.7 -6 29894584 . C A 105 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=21.57;LSEQ=GAGGATGTAGCCGCAGTCGC;RSEQ=GTGGTTGGAGCAGGAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:1:1,0:214,170:0.0026:2,0:2:0:21:0:1:0:60:2:0.0027:0:2 0/1:263:14:9,5:137,112:0.0532:2,2:15.4:1:27.6:1:0.58759:1.47:60:6:0.0469:0:2.5 -6 29894595 . C T 82 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0088;SOR=7.10435;LSEQ=CGCAGTCGCCGTGGTTGGAG;RSEQ=AGGAGGGACCGGAGTATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:2:0,2:234,187:0.0047:2,0:1:0:18:1:0.19905:0:60:1:0.0025:0:1.5 0/1:275:9:5,4:146,119:0.0327:2,2:24.9:1:26:1:1:1.02:60:18:0.0332:0:2.6 -6 29894600 . G T 105 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=18.58692;LSEQ=TCGCCGTGGTTGGAGCAGGA;RSEQ=GGACCGGAGTATTGGGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:1:0,1:227,191:0.0024:2,0:1:0:28:0:0.45823:0:60:2:0.0024:0:1 0/1:281:12:7,5:146,123:0.0427:2,2:19.3:1:29.3:1:1:1.18:60:24:0.0432:0:2.3 -6 29894603 . A G 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGTGGTTGGAGCAGGAGGG;RSEQ=CCGGAGTATTGGGACCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:226,194:0:2,0:27:1:29.6:1:1:0:60:51.5:1:0:0.5 0/1:287:37:20,17:135,115:0.1289:2,2:24.3:1:30.2:1:1:1.00:60:17.5:0.1254:0:2.5 -6 29894629 . G C 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.87863;SOR=0.9048;LSEQ=GTATTGGGACCGGAGCACAC;RSEQ=GAACATCAGGCCCGCGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:30:9,21:183,203:0.0721:2,2:29.5:1:30.1:1:0.08617:2.09987:60:60:0.0732:0:1.9 0/1:274:18:6,12:120,136:0.0657:2,2:30.3:1:28.8:1:0.3315:1.76117:60:36:0.0662:0:1.6 -6 29894630 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06275;SOR=Inf;LSEQ=TATTGGGACCGGAGCACACG;RSEQ=AACATCAGGCCCGCGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:188,223:0:2,0:28.4:1:30.7:1:1:0:60:57.714:0.9951:0:0.4 0/1:274:3:2,1:124,147:0.0109:2,2:16.3:1:25.7:1:0.59581:2.36:60:2:0.0074:0:1.7 -6 29894636 . C CA 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACCGGAGCACACGGAACAT;RSEQ=AGGCCCGCGCACAGACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:171,225:0:2,0:27.8:1:31.3:1:1:0:60:65:1:0:0.4 0/1:267:35:14,21:104,127:0.1311:2,2:27.7:1:30.1:1:0.71547:1.2274:60:70:0.1336:0.015:1.5 -6 29894756 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07338;SOR=Inf;LSEQ=ACGACCCCTCCTCATCCCCC;RSEQ=CGGACGTCCCGGGTCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:23,50:0:2,0:21.3:1:29.4:1:1:0:60:17.25:0.9857:0:0.6 0/1:28:2:0,2:5,21:0.0714:2,0:29.5:1:33:0:1:0:60:4:0.08:0:2 -6 29894763 . T C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.90377;LSEQ=CTCCTCATCCCCCACGGACG;RSEQ=CCCGGGTCCCCCCCGCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:18:7,11:16,36:0.2571:2,2:22.8:1:32.4:1:0.56854:1.42:60:36:0.2687:0:1.8 0/1:21:5:1,4:5,11:0.2381:2,2:30.2:1:32.8:1:1:1.77078:60:10:0.2381:0:1.8 -6 29894794 . A G 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=8.32206;LSEQ=CCCCGCGAGTCTCCGGCTCC;RSEQ=AGATCCACCCCGAGGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:15:7,8:21,22:0.2586:2,2:24.9:1:31.4:1:1:1.08927:60:30:0.2679:0:2.3 1/0:20:15:11,4:2,2:0.75:2,2:15.3:1:29.9:1:0.55728:2.59:60:30:0.75:0:2.4 -6 29894798 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06162;SOR=Inf;LSEQ=GCGAGTCTCCGGCTCCAAGA;RSEQ=CCACCCCGAGGCTGCGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:29,27:0:2,0:26.4:1:29.9:1:1:0:60:13:1:0:0.8 0/1:19:2:1,1:12,5:0.1053:2,2:11.5:1:33:0:1:2.28037:60:4:0.1111:0:2.5 -6 29894813 . C G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08208;SOR=Inf;LSEQ=CAAGATCCACCCCGAGGCTG;RSEQ=GGGACCCGCCAGATCCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:36,25:0:2,0:25.7:1:30.9:1:1:0:60:29.5:1:0:0.7 0/1:25:2:1,1:17,6:0.08:2,2:14:1:28.5:1:0.49:2.69921:60:4:0.0833:0:4 -6 29894851 . C A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07948;SOR=2.05225;LSEQ=CGACCCGGGAGAGGCCCAGG;RSEQ=GCCTTTACCAGGTTTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:18:13,5:49,15:0.2169:2,2:23.2:1:30.2:1:0.75923:1.25284:60:36:0.2222:0:1.6 0/1:55:20:16,4:27,8:0.3636:2,2:27.6:1:28.2:1:1:1.18:60:19:0.3654:0:2.1 -6 29894853 . C T 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACCCGGGAGAGGCCCAGGCG;RSEQ=CTTTACCAGGTTTCATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:64,18:0:2,0:22.8:1:31.8:1:1:0:60:40:1:0:0.6 0/1:56:12:11,1:33,11:0.2143:2,2:30.8:1:26.9:1:0.4274:3.60:60:11:0.2075:0:2.6 -6 29894863 . G A 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGCCCAGGCGCCTTTACCAG;RSEQ=TTTCATTTTCCGTTTAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:79,18:0:2,0:22.1:1:30.9:1:1:0:60:23.25:1:0:0.7 0/1:68:12:9,3:47,9:0.1765:2,2:24.5:1:28.1:1:0.4319:1.72487:60:11:0.1719:0:2.8 -6 29894874 . C A 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTACCAGGTTTCATTTTC;RSEQ=GTTTAGGCCAAAATCCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:97,17:0:2,0:23:1:30.2:1:1:0:60:15.286:0.9907:0:0.5 0/1:78:32:27,5:39,7:0.4103:2,2:25.8:1:28.7:1:1:1.03135:60:7:0.3836:0:2.3 -6 29894909 . G A 69 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00686;SOR=Inf;LSEQ=CCCCGCGGGTTGGTCGGGGC;RSEQ=GGGGCGGGGCTCGGTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:193,40:0:2,0:24.3:1:29.7:1:1:0:60:45.6:0.9956:0:0.6 0/1:139:5:4,1:96,38:0.036:2,2:9.6:1:29.8:1:1:1.58:60:10:0.0365:0:4.8 -6 29894914 . C T 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGTTGGTCGGGGCGGGGG;RSEQ=GGGGCTCGGTGGGCGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:202,39:0:2,0:25.5:1:29.3:1:1:0:60:6.774:0.9953:0:0.5 0/1:153:19:14,5:93,29:0.1242:2,2:21.9:1:26:1:0.77869:1.14417:60:3.75:0.124:0:2.2 -6 29894933 . C T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16652;SOR=2.206;LSEQ=GCGGGGCTCGGTGGGCGGGG;RSEQ=TGACCGCGGGGGCGGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:6:2,4:260,126:0.0153:2,2:13.8:1:27.5:1:0.09678:4.11071:60:12:0.0161:0:2.5 0/1:241:8:5,3:147,86:0.0332:2,2:21.1:1:28.4:1:1:1.02549:60:16:0.0351:0:4.8 -6 29894938 . C A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=12;MSI=2.000;MSILEN=2;SSF=0;SOR=8.33068;LSEQ=GCTCGGTGGGCGGGGCTGAC;RSEQ=GCGGGGGCGGGGCCAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:36:27,9:256,133:0.0843:2,2:24.3:1:28.4:1:0.35572:1.56:60:6.2:0.0769:0:1.5 0/1:269:117:71,46:91,59:0.4349:2,2:20.3:1:28.1:1:1:1.00:60:5.5:0.4024:0:2.5 -6 29894953 . A T 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGACCGCGGGGGCGGGGCC;RSEQ=GGGTCTAACACCCTCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:332,202:0:2,0:24.6:1:29.8:1:1:0:60:43.5:0.9962:0:0.4 0/1:379:14:6,8:201,164:0.0369:2,2:23.8:1:29.1:1:0.41984:1.63199:60:28:0.0373:0:3.6 -6 29894964 . C A 111 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=19.7743;LSEQ=GGCGGGGCCAGGGTCTAACA;RSEQ=CCTCCAGATAATGTATGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:1:0,1:339,247:0.0017:2,0:25:0:13:0:0.42249:0:60:0:0:0:5 0/1:428:14:8,6:219,194:0.0327:2,2:26.6:1:29.3:1:0.79307:1.18:60:28:0.033:0:3.6 -6 29894966 . C T 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGGCCAGGGTCTAACACC;RSEQ=TCCAGATAATGTATGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:0:0,0:343,258:0:2,0:25.9:1:30.9:1:1:0:60:53.636:1:0:0.4 0/1:437:37:20,17:211,189:0.0847:2,2:22.6:1:30.4:1:1:1.05:60:74:0.0855:0:2.6 -6 29894991 . T C 193 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=144.23624;LSEQ=GATAATGTATGGCTGCGACT;RSEQ=GGGGCTGGAAGGGCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:1:0,1:292,301:0.0017:2,0:25:0:31:0:1:0:60:2:0.0017:0:6 0/1:464:91:46,45:190,183:0.1961:2,2:28.5:1:29.8:1:1:1.01565:60:44.5:0.1943:0:2.7 -6 29894998 . G A 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09267;SOR=6.4064;LSEQ=TATGGCTGCGACTTGGGGCT;RSEQ=GAAGGGCGCCTCCTCCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:1:1,0:267,299:0.0018:2,0:1:0:27:0:0.47266:0:60:2:0.0018:0:1 0/1:446:5:3,2:224,216:0.0112:2,2:33.8:1:28.2:1:1:1.45:60:10:0.0114:0:2.6 -6 29895002 . G C 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGCGACTTGGGGCTGGAA;RSEQ=GGCGCCTCCTCCGCGGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:0:0,0:266,297:0:2,0:27:1:31.2:1:1:0:60:61.556:0.9964:0:0.3 0/1:435:83:42,41:162,162:0.1908:2,2:28.7:1:30.1:1:1:1.02:60:166:0.1939:0:2.7 -6 29895005 . C T 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGACTTGGGGCTGGAAGGG;RSEQ=GCCTCCTCCGCGGGTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:255,296:0:2,0:26.7:1:30.5:1:1:0:60:90.833:0.9963:0:0.3 0/1:425:26:14,12:200,199:0.0612:2,2:32.3:1:29.4:1:0.84017:1.16:60:52:0.0628:0:2.8 -6 29895032 . G C 158 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.5564;LSEQ=TCCGCGGGTATGAACAGCAC;RSEQ=CCAACGATGGCAAGGATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:1:1,0:194,245:0.0023:2,0:21:0:14:0:0.44318:0:60:0:0:0:8 0/1:321:39:19,20:138,142:0.1215:2,2:19.1:1:30:1:1:1.02291:60:78:0.1254:0:1.5 -6 29895039 . A C 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTATGAACAGCACGCCAACG;RSEQ=TGGCAAGGATTACATAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:182,235:0:2,0:21.6:1:30.5:1:1:0:60:58.571:1:0:0.1 0/1:299:24:11,13:136,139:0.0803:2,2:19.5:1:30.9:1:0.83255:1.15575:60:23:0.0788:0:2.8 -6 29895099 . C A 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGACCGCGGCGGACATGG;RSEQ=GGCTCAGATCACCAAGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:254,234:0:2,0:26:1:30.9:1:1:0:59.9:68.714:0.9979:0:0.2 0/1:376:48:24,24:175,149:0.1277:2,2:26.1:1:30:1:0.64361:1.17398:60:96:0.129:0:1.4 -6 29895111 . C T 125 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.25493;LSEQ=GGACATGGCGGCTCAGATCA;RSEQ=CAAGCGCAAGTGGGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:1:0,1:267,252:0.0019:2,0:49:0:16:0:0.48654:0:60:0:0:0:3 0/1:404:23:11,12:197,184:0.0569:2,2:22.7:1:27.7:1:0.83078:1.16753:60:22:0.0557:0:1.2 -6 29895215 . C T 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGAGAACGGGAAGGAGA;RSEQ=GCTGCAGCTCACGGGTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:52,159:0:2,0:25.2:1:30.3:1:1:0:60:104.5:0.9952:0:0.2 1/0:135:78:20,58:13,44:0.5778:2,2:24.6:1:30.2:1:0.83973:1.17:60:156:0.5778:0:1.3 -6 29895228 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16544;SOR=Inf;LSEQ=AAGGAGACGCTGCAGCTCAC;RSEQ=GGTACCAGGGAACACAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:30,137:0:2,0:24.9:1:30.8:1:1:0:60:54.667:1:0:0.3 0/1:115:2:0,2:28,85:0.0174:2,0:41.5:1:31.5:1:1:0:60:4:0.0175:0:2 -6 29895235 . A G 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00098;SOR=Inf;LSEQ=CGCTGCAGCTCACGGGTACC;RSEQ=GGGAACACAAGACGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:24,133:0:2,0:23.2:1:31:1:1:0:60:51.333:1:0:0.3 0/1:96:7:1,6:19,70:0.0729:2,2:24.9:1:29.1:1:1:1.62126:60:14:0.0745:0:1 -6 29895250 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00048;SOR=2.92754;LSEQ=GTACCAGGGAACACAAGACG;RSEQ=CTCCCTGATCGCCTGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:39:5,34:9,80:0.3047:2,2:18.6:1:30.1:1:0.7595:1.30:60:78:0.3145:0:1.1 1/0:71:40:2,38:8,23:0.5634:2,2:20.8:1:28.1:1:0.017:6.43642:60:19:0.5507:0:1.6 -6 29895649 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01186;SOR=0.0621;LSEQ=CTGTTCCCTCCTCAGGGACT;RSEQ=GAATTTTCCACGGAATTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:15,0:0,1:0.9375:0,1:16.4:1:29.1:1:0.0625:0:53.6:30:0.9375:0:3.9 0/1:9:4:4,0:4,1:0.4444:2,0:15.8:1:28:1:1:0:58.3:8:0.4444:0:4.3 -6 29895664 . ATTC TA 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43177;SOR=0.43461;LSEQ=GGACTGGAATTTTCCACGGA;RSEQ=GGAGATTATCCCAGATACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:16,1:3,1:0.8095:2,1:24.5:1:31:1:0.35238:4.76:54.2:34:0.85:0.0476:2.8 1/0:14:9:9,0:3,1:0.6429:2,0:17:1:30.7:1:0.30769:0:52.2:18:0.75:0.2143:3 -6 29895682 . A G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35894;SOR=0.55519;LSEQ=GAATTCGGAGATTATCCCAG;RSEQ=TACCTGTGTCCAGGTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:25:24,1:6,2:0.7576:2,1:24:1:30.3:1:0.13856:7.35:55.2:11.5:0.7667:0:3.3 1/0:19:12:12,0:5,2:0.6316:2,0:22:1:31.3:1:0.12281:0:54.2:24:0.6316:0:3.3 -6 29895697 . T C 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01227;SOR=Inf;LSEQ=CCCAGATACCTGTGTCCAGG;RSEQ=TGGTGTCTGGGTTCTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:34,4:0:2,0:28.3:1:30.3:1:1:0:57.9:76:1:0:2.1 0/1:21:4:4,0:15,2:0.1905:2,0:30.5:1:33:1:1:0:47.5:8:0.1905:0:2.5 -6 29895701 . T C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43944;SOR=0.62003;LSEQ=GATACCTGTGTCCAGGTTGG;RSEQ=GTCTGGGTTCTGTGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:26:25,1:13,3:0.619:2,1:31.2:1:31.2:1:0.14634:5.52:56.9:12:0.6154:0:3 1/0:24:12:12,0:8,4:0.5:2,0:26.3:1:31.8:1:0.09317:0:58.3:24:0.5:0:2.8 -6 29895816 . A T 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55568;SOR=1.1722;LSEQ=AAGTGCCTGAATTTTCTGAC;RSEQ=CTTCCTGTTAGACCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:269:222:130,92:28,19:0.8253:2,2:28.8:1:29.5:1:1:1.04276:59.4:10.684:0.8185:0:3.8 1/1:255:216:114,102:20,18:0.8471:2,2:27:1:29.1:1:1:1.01:59.6:29.857:0.8462:0:4.3 -6 29895822 . T C 38 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2489;SOR=0;LSEQ=CTGAATTTTCTGACACTTCC;RSEQ=GTTAGACCTCTCCCCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:1,2:152,113:0.0112:2,2:15:1:24.3:1:0.57847:2.68043:53.3:2:0.0078:0:5.7 0/0:257:0:0,0:133,124:0:2,0:28.4:1:30.1:1:1:0:59.7:50.4:1:0:3.8 -6 29895830 . CTCTCCCCC ACCCCCCTCCA 129 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=Inf;LSEQ=TCTGACACTTCCTGTTAGAC;RSEQ=AGACACATATGATCCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:149,117:0:2,0:30.9:1:31.1:1:1:0:59.5:16.733:1:0:3.2 0/1:256:18:10,8:118,119:0.0703:2,2:36.1:1:31:1:0.80766:1.26:60:36:0.0717:0:5.8 -6 29895831 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.20173;LSEQ=CTGACACTTCCTGTTAGACC;RSEQ=CTCCCCCAGACACATATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:254:200:105,95:31,22:0.7874:2,2:32.1:1:31.1:1:0.53571:1.27367:59.5:49:0.7871:0:4.2 0/1:239:102:44,58:17,17:0.4268:2,2:32:1:30.5:1:0.55234:1.31547:59.8:204:0.7445:0:4.7 -6 29895833 . T C 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.9139;SOR=0.97619;LSEQ=GACACTTCCTGTTAGACCTC;RSEQ=CCCCCAGACACATATGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:253:197:102,95:33,22:0.7787:2,2:32.2:1:30.8:1:0.28954:1.39521:59.5:31.833:0.7828:0:4.2 1/0:235:182:82,100:12,13:0.7745:2,2:31.9:1:29.9:1:0.83233:1.12506:59.5:25:0.875:0:4.2 -6 29895836 . CCC ACCA 178 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=Inf;LSEQ=ACTTCCTGTTAGACCTCTCC;RSEQ=AGACACATATGATCCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:135,123:0:2,0:31.1:1:31.2:1:1:0:59.5:128:1:0:3.3 0/1:236:63:26,37:70,77:0.2669:2,2:33:1:29.9:1:0.45092:1.29212:60:126:0.2972:0.0085:5 -6 29895837 . CC GCA 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.09793;LSEQ=CTTCCTGTTAGACCTCTCCC;RSEQ=AGACACATATGATCCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:126:66,60:68,60:0.4884:2,2:32:1:31.5:1:1:1.0302:60:252:0.4961:0.0155:4.4 0/1:235:20:9,11:63,67:0.0851:2,2:34.9:1:31.6:1:0.8142:1.14819:60:40:0.1351:0:4.2 -6 29895838 . C CCA 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1e-04;SOR=0.25798;LSEQ=TTCCTGTTAGACCTCTCCCC;RSEQ=AGACACATATGATCCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:38:17,21:35,23:0.1467:2,2:30.2:1:29.1:1:0.1482:1.86726:57.7:18:0.2748:0.0077:3.9 0/1:236:10:5,5:18,17:0.0424:2,2:35.8:1:27.1:1:1:1.05751:60:4:0.0625:0:4.9 -6 29895862 . G A 208 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=493.53186;LSEQ=CACATATGATCCACCATTCC;RSEQ=TCTCTGACTATAAGGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:1:1,0:105,131:0.0042:2,0:1:0:29:0:0.44726:0:60:2:0.0044:0:4 1/0:209:142:49,93:29,37:0.6794:2,2:24.6:1:29.2:1:0.21928:1.48463:59.8:27.4:0.6782:0:5 -6 29895877 . G A 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09748;SOR=Inf;LSEQ=ATTCCGTCTCTGACTATAAG;RSEQ=CCACCCTGAGGTGCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:78,112:0:2,0:21:1:31:1:1:0:59.6:26.143:1:0:2.7 0/1:163:3:2,1:54,105:0.0184:2,2:13.3:1:27:1:0.27456:3.85:60:6:0.0189:0:4.3 -6 29895878 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20804;SOR=Inf;LSEQ=TTCCGTCTCTGACTATAAGG;RSEQ=CACCCTGAGGTGCTGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:78,111:0:2,0:20.9:1:31.1:1:1:0:59.6:46.25:1:0:2.7 0/1:159:2:1,1:53,104:0.0126:2,2:25:1:30.5:1:1:1.95:60:4:0.0127:0:2 -6 29895888 . G C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11366;LSEQ=GACTATAAGGCCACCCTGAG;RSEQ=TGCTGGGCCCTGGGCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:83:34,49:26,23:0.494:2,2:20.3:1:31.7:1:0.2073:1.62301:59.9:166:0.5155:0:3.6 0/1:131:13:2,11:37,76:0.0992:2,2:28.8:1:31.6:1:0.34171:2.66021:60:26:0.1024:0:3.2 -6 29895913 . G A 117 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCCTGGGCTTCTACCCT;RSEQ=TGGAGATCACACTGGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:62,71:0:2,0:28.6:1:32.3:1:1:0:59.9:132:1:0:1.6 0/1:75:18:2,16:17,40:0.24:2,2:22.8:1:28.2:1:0.13322:3.35397:59.7:8:0.2192:0:4.7 -6 29895928 . G A 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.88324;SOR=0.95731;LSEQ=ACCCTGTGGAGATCACACTG;RSEQ=CCTGGCAGCAGGATGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:76:24,52:39,16:0.5802:2,2:27.3:1:29.1:1:1e-05:5.20698:60:14.2:0.568:0:2.5 1/0:72:41:15,26:9,6:0.5694:2,2:20.1:1:29.5:1:0.13837:2.554:59.9:40:0.5797:0:2.5 -6 29895939 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10696;SOR=Inf;LSEQ=ATCACACTGGCCTGGCAGCA;RSEQ=GATGGAGAGGACCAGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:79,64:0:2,0:24.2:1:32:1:1:0:60:142:1:0:1.4 0/1:70:2:0,2:34,34:0.0286:2,0:9:1:31.5:1:0.49317:0:60:4:0.029:0:3 -6 29895944 . G A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTGGCCTGGCAGCAGGATG;RSEQ=AGAGGACCAGACTCGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:86,60:0:2,0:23.4:1:31.7:1:1:0:60:292:1:0:1.3 0/1:72:12:5,7:34,26:0.1667:2,2:22.7:1:30.2:1:0.36331:1.81524:60:24:0.169:0:3.2 -6 29895958 . C A 78 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00521;SOR=13.34011;LSEQ=AGGATGGAGAGGACCAGACT;RSEQ=GGGACATGGAGCTTCTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:1,0:110,53:0.0061:2,0:43:0:27:0:1:0:60:2:0.0062:0:3 0/1:79:6:4,2:46,27:0.0759:2,2:20.7:1:30.2:1:1:1.17:60:12:0.0769:0:2.3 -6 29895959 . G A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19203;SOR=0.39861;LSEQ=GGATGGAGAGGACCAGACTC;RSEQ=GGACATGGAGCTTCTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:15:5,10:107,42:0.0915:2,2:20.3:1:30.9:1:0.00624:5.03713:60:30:0.092:0:3.3 0/1:78:3:3,0:48,27:0.0385:2,0:44.3:1:31.7:1:0.54749:0:60:6:0.0385:0:4 -6 29895973 . C G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.96507;LSEQ=AGACTCGGGACATGGAGCTT;RSEQ=TAGAGACCAGGCCTGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:66:37,29:95,14:0.3771:2,2:21.8:1:32.2:1:1e-05:5.26079:55.9:65:0.3779:0:3.1 1/0:99:70:52,18:23,6:0.7071:2,2:21:1:31.6:1:0.7972:1.32325:56.5:140:0.7143:0:2.5 -6 29896001 . C A 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.15301;SOR=0.71241;LSEQ=CAGGCCTGCAGGGGATGGAA;RSEQ=CTTCCAGAAGTGGGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:87:59,28:127,25:0.364:2,2:23:1:30.1:1:0.006:2.40136:54.1:86:0.3675:0:3.1 0/1:152:44:35,9:85,22:0.2895:2,2:23.4:1:30:1:1:1.01:55.2:88:0.2973:0:3 -6 29896015 . G A 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06829;SOR=Inf;LSEQ=ATGGAACCTTCCAGAAGTGG;RSEQ=CAGCTGTGGTGGTGCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:223,86:0:2,0:23.7:1:31.3:1:1:0:58.3:76.25:1:0:1.2 0/1:216:3:2,1:158,54:0.0139:2,2:31:1:23.7:1:1:1.46015:60:2:0.0096:0:1.7 -6 29896045 . CAG C 175 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGGTGCCTTCTGGAGAGGAA;RSEQ=AGATACCCGTGCCATGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:0:0,0:315,213:0:2,0:24.2:1:30.1:1:1:0:58.9:65:0.9981:0:1.2 0/1:366:53:38,15:193,119:0.1448:2,2:28.2:1:30.6:1:0.21735:1.56:56.2:106:0.1476:0.0301:4 -6 29896054 . CC AT 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00967;SOR=1.43067;LSEQ=CTGGAGAGGAACAGAGATAC;RSEQ=GTGCCATGTGCAGCATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:195:114,81:212,153:0.3476:2,2:27.4:1:30.5:1:1:1.02:57.1:390:0.3501:0.0053:2.1 0/1:386:167:111,56:103,71:0.4326:2,2:28.2:1:29.7:1:0.17971:1.37:56.7:166:0.4427:0.0104:2.7 -6 29896055 . C T 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10107;SOR=3.41576;LSEQ=TGGAGAGGAACAGAGATACC;RSEQ=GTGCCATGTGCAGCATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:560:3:1,2:211,154:0.0054:2,2:7:1:29.7:1:0.57648:2.7328:60:6:0.0083:0:1.3 0/1:387:7:3,4:129,88:0.0181:2,2:22.6:1:23.9:1:0.44938:1.94859:60:2.5:0.0228:0:3.1 -6 29896084 . A G 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCAGCATGAGGGGTTGCCC;RSEQ=AGCCCCTCACCCTGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:694:0:0,0:352,342:0:2,0:27.3:1:30.1:1:1:0:59.9:76.111:1:0:0.7 0/1:499:113:65,48:198,186:0.2265:2,2:25.1:1:29.3:1:0.28471:1.27:57.2:21.6:0.2218:0:3.2 -6 29896105 . G A 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0.54618;LSEQ=AGCCCCTCACCCTGAGATGG;RSEQ=GTAAGGCAGGAGATGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:222:101,121:181,219:0.3558:2,2:27.1:1:30.3:1:1:1.01:59.9:30.714:0.3536:0:1.8 0/1:449:104:51,53:159,185:0.2316:2,2:25.1:1:29:1:0.65437:1.12:59.8:16.333:0.2243:0:2.5 -6 29896108 . A T 154 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=69.67331;LSEQ=CCCTCACCCTGAGATGGGGT;RSEQ=AGGCAGGAGATGAGTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:1:0,1:272,346:0.0016:2,0:42:0:14:0:1:0:60:0:0:0:4 0/1:423:43:20,23:173,207:0.1017:2,2:24:1:28.4:1:1:1.04:59.5:42:0.1007:0:3.5 -6 29896112 . C T 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCCTGAGATGGGGTAAGG;RSEQ=AGGAGATGAGTGGAGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:264,344:0:2,0:25.1:1:31.9:1:1:0:60:59.8:1:0:0.6 0/1:408:39:18,21:162,207:0.0956:2,2:24.7:1:27.9:1:0.86578:1.09:60:38:0.0962:0:3.6 -6 29896114 . G A 200 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=189.52439;LSEQ=CCCTGAGATGGGGTAAGGCA;RSEQ=GAGATGAGTGGAGGGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:605:1:1,0:260,344:0.0017:2,0:3:0:27:0:0.4314:0:60:2:0.0017:0:1 0/1:405:97:43,54:133,175:0.2395:2,2:24.9:1:30.4:1:0.90659:1.05:58.5:194:0.2431:0:3.4 -6 29896120 . G T 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=54.46898;LSEQ=GATGGGGTAAGGCAGGAGAT;RSEQ=AGTGGAGGGGGGGTCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:3:1,2:236,332:0.0053:2,2:16:1:26.3:1:1:1.42084:60:6:0.0053:0:1.3 0/1:384:86:37,49:125,173:0.224:2,2:25.8:1:28.3:1:0.9016:1.04:59.2:85:0.2249:0:3.4 -6 29896125 . G A 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=52.01063;LSEQ=GGTAAGGCAGGAGATGAGTG;RSEQ=AGGGGGGGTCATGTCTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:1,0:226,308:0.0019:2,0:1:0:27:0:0.4243:0:60:2:0.0019:0:1 0/1:360:32:10,22:142,186:0.0889:2,2:24.8:1:29.3:1:0.26032:1.67725:60:64:0.0909:0:2.3 -6 29896126 . A AG 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=GTAAGGCAGGAGATGAGTGG;RSEQ=GGGGGGGTCATGTCTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:223,304:0:2,0:23.1:1:30.2:1:1:0:60:51.7:1:0:0.6 0/1:359:9:2,7:150,200:0.0251:2,2:24.2:1:30.8:1:0.31188:2.61876:59.9:18:0.0256:0:3 -6 29896128 . G T 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCAGGAGATGAGTGGAG;RSEQ=GGGGGTCATGTCTCTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:220,299:0:2,0:22.8:1:30.8:1:1:0:60:102.8:1:0:0.6 0/1:348:31:9,22:135,180:0.0891:2,2:24.6:1:29.8:1:0.18101:1.8303:60:62:0.0906:0:2.3 -6 29896145 . A AG 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10713;SOR=1.30575;LSEQ=GAGGGGGGGTCATGTCTCTT;RSEQ=GGAAAGCAGGAGCCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:151:66,85:104,159:0.3647:2,2:21.5:1:30.9:1:0.40886:1.19:60:74.5:0.3634:0.0894:0.9 0/1:266:114:41,73:61,87:0.4286:2,2:25.1:1:30.7:1:0.44359:1.24733:60:113:0.428:0.0376:1.2 -6 29896147 . G GT 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGGGGTCATGTCTCTTAG;RSEQ=AAAGCAGGAGCCTCTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:163,235:0:2,0:22.3:1:31.1:1:1:0:60:98.5:1:0:0.4 0/1:256:53:18,35:78,124:0.207:2,2:23:1:28.8:1:0.63325:1.22217:60:106:0.2095:0.043:2.4 -6 29896210 . G GCT 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGGGCTGAGGGTCAGGGAC;RSEQ=CTCACCTTCCCCTTTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:187,190:0:2,0:24.3:1:30.7:1:1:0:60:187.5:0.9921:0:0.1 0/1:270:18:9,9:127,125:0.0667:2,2:19.5:1:29.5:1:1:1.01594:60:17:0.0639:0.0185:2.1 -6 29896257 . C T 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTCTTCTCAGCCCACCATC;RSEQ=CCATCGTGGGTATCGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:175,230:0:2,0:26.5:1:31:1:1:0:60:100.25:1:0:0.2 0/1:315:21:11,10:134,160:0.0667:2,2:26.7:1:29.4:1:0.65196:1.31:60:42:0.068:0:2.8 -6 29896268 . T C 218 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=139.59095;LSEQ=CCCACCATCCCCATCGTGGG;RSEQ=ATCGTTGCTGGCCTGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:2:1,1:155,216:0.0054:2,2:8:1:32:1:1:1.39:60:4:0.0054:0:2 0/1:285:123:57,66:69,93:0.4316:2,2:28.5:1:31.5:1:0.54885:1.16:59.1:60.5:0.4291:0:2.3 -6 29896272 . G A 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=47.39677;LSEQ=CCATCCCCATCGTGGGTATC;RSEQ=TTGCTGGCCTGGTTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:1,0:150,211:0.0028:2,0:1:0:26:0:0.41713:0:60:2:0.0028:0:1 0/1:275:32:13,19:104,139:0.1164:2,2:27:1:29.3:1:0.85151:1.09321:59.6:31:0.114:0:2.1 -6 29896275 . G A 172 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=52.50354;LSEQ=TCCCCATCGTGGGTATCGTT;RSEQ=CTGGCCTGGTTCTCCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:2:1,1:141,203:0.0058:2,2:15:1:27:1:1:1.44:60:4:0.0059:0:2 0/1:277:65:29,36:89,121:0.2347:2,2:27.4:1:28.6:1:0.77557:1.09:58.5:64:0.237:0:2.1 -6 29896280 . C T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0816;SOR=Inf;LSEQ=ATCGTGGGTATCGTTGCTGG;RSEQ=CTGGTTCTCCTTGGAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:133,196:0:2,0:25.5:1:31.1:1:1:0:60:46:1:0:0.1 0/1:253:3:0,3:105,145:0.0119:2,0:14.3:1:25:1:0.26877:0:60:6:0.0122:0:1.7 -6 29896291 . T C 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTTGCTGGCCTGGTTCTCC;RSEQ=TGGAGCTGTAGTCACTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:105,178:0:2,0:25:1:30.1:1:1:0:60:39.429:1:0:0.1 0/1:240:20:10,10:88,130:0.0833:2,2:25.4:1:30.3:1:0.47856:1.47:60:40:0.0851:0:2.7 -6 29896336 . GGAA G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.80618;SOR=1.13525;LSEQ=GGTTTCTGCTGTGATGTGCA;RSEQ=GAAGAACTCAGGTAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:9:2,7:39,99:0.0612:2,2:32.7:1:31.2:1:1:1.37602:60:18:0.0621:0:0 0/1:116:8:2,6:33,75:0.069:2,2:31.9:1:32.1:1:1:1.31704:60:16:0.0702:0:0 -6 29896636 . C T 80 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22857;SOR=0;LSEQ=ACCTCAGGAGGGCAGTTGGT;RSEQ=CAGGACCCACACCTGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:5,1:0.5:2,0:22.2:1:31.2:1:1:0:60:12:0.5:0:1.3 0/0:3:0:0,0:1,2:0:2,0:14:1:25:1:1:0:60:2:1:0:0 -6 29896713 . G A 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12837;SOR=0.23307;LSEQ=CACTTTCAGGAAACTTCTCT;RSEQ=GGATCAAAGGCTAGGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:10,0:9,1:0.5:2,0:19.1:1:28.2:1:1:0:60:20:0.5:0:1.9 0/1:11:2:2,0:8,1:0.1818:2,0:32.5:1:30:0:1:0:60:4:0.2:0:1.5 -6 29896773 . C T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=0.16834;LSEQ=CTGACTCCTTTCTGGCCTCT;RSEQ=ATAGGACATTTTCTTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:29:23,6:26,6:0.4754:2,2:24.2:1:29.6:1:1:1.12816:60:58:0.4754:0:1.7 0/1:46:6:5,1:32,8:0.1304:2,2:24.2:1:30.5:1:1:1.24:60:12:0.1364:0:1.5 -6 29896847 . T TGA 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=29.31382;LSEQ=GTATGAAGTGGGCTGATCCC;RSEQ=GATCCTTGGGATATTGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:10:5,5:48,33:0.0714:2,2:20.1:1:29.5:1:0.73633:1.44842:57.5:20:0.0719:0.0429:1.9 1/0:122:85:47,38:0,6:0.6967:0,2:23.5:1:30:1:0.01059:0:60:170:0.9551:0.3934:0.9 -6 29896850 . TCC GATCT 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=TGAAGTGGGCTGATCCCTGA;RSEQ=TTGGGATATTGTGGTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:49:30,19:48,33:0.35:2,2:30.7:1:31.6:1:0.85534:1.08:60:98:0.3525:0.0071:1.3 0/0:122:0:0,0:0,6:0:0,0:36:1:31.3:1:1:0:60:8:0.0449:0:-9.5 -6 29896852 . C T 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00072;SOR=0;LSEQ=AAGTGGGCTGATCCCTGATC;RSEQ=TTGGGATATTGTGGTCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:12:7,5:46,31:0.0876:2,2:17.2:1:27.4:1:1:1.0592:57.9:5:0.1163:0:1.9 0/0:110:0:0,0:38,39:0:2,0:26.1:1:30.5:1:1:0:60:37.5:1:0:0.4 -6 29896872 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21827;SOR=Inf;LSEQ=CTTGGGATATTGTGGTCGGG;RSEQ=GCCCATGGGGGAGCTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:78,56:0:2,0:24.3:1:29.6:1:1:0:59.8:25.8:1:0:0.9 0/1:118:2:1,1:62,54:0.0169:2,2:40:0:31.5:1:1:1.1468:60:4:0.0172:0:1.5 -6 29896883 . G A 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00709;SOR=Inf;LSEQ=GTGGTCGGGAGCCCATGGGG;RSEQ=AGCTCACCCAACCCCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:82,57:0:2,0:22.3:1:30.5:1:1:0:59.8:33.75:1:0:1 0/1:111:6:4,2:55,48:0.0541:2,2:26:1:28.3:1:0.68535:1.74:60:12:0.0561:0:1.3 -6 29896914 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20412;SOR=Inf;LSEQ=ACCCCAGATTCCTCCTCTAG;RSEQ=CGCATCTCCTCTGGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:84,61:0:2,0:26:1:31.5:1:1:0:59.8:47.333:1:0:1.3 0/1:120:2:1,1:72,46:0.0167:2,2:35.5:1:27.5:1:1:1.55914:60:4:0.0171:0:2 -6 29896922 . C T 148 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01309;SOR=0.38479;LSEQ=TTCCTCCTCTAGCCGCATCT;RSEQ=CTCTGGGCTCTGACCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:27:16,11:66,51:0.1875:2,2:35.6:1:31.2:1:0.83231:1.12:60:54:0.1915:0:3 0/1:123:10:7,3:65,48:0.0813:2,2:21.9:1:28.9:1:0.52065:1.72:60:20:0.0826:0:2.7 -6 29896925 . C G 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33536;SOR=1.28027;LSEQ=CTCCTCTAGCCGCATCTCCT;RSEQ=TGGGCTCTGACCAAGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:75:49,26:35,38:0.4902:2,2:29.9:1:32.2:1:0.04612:2.04:60:74:0.4901:0:2.4 1/0:125:69:44,25:31,25:0.552:2,2:26.2:1:31:1:0.36374:1.42:60:138:0.552:0:2.1 -6 29896959 . C A 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59635;SOR=2.35819;LSEQ=AGTCCTGTTTTTGTTCTACC;RSEQ=CAGGCAGCGACCATGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:1,0:101,93:0.0051:2,0:47:0:28:0:1:0:60:2:0.0053:0:3 0/1:167:2:1,1:86,79:0.012:2,2:48:0:30.5:1:1:1.08804:60:4:0.0124:0:3 -6 29896967 . C T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02374;SOR=0.59924;LSEQ=TTTTGTTCTACCCCAGGCAG;RSEQ=GACCATGCGCAGGGTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:81:42,39:67,60:0.3894:2,2:23.1:1:29:1:1:1.03674:60:80:0.3902:0:2.2 0/1:181:50:27,23:65,65:0.2762:2,2:22.9:1:30.1:1:0.73947:1.17:60:100:0.2809:0:3 -6 29896968 . G A 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.21006;LSEQ=TTTGTTCTACCCCAGGCAGC;RSEQ=ACCATGCGCAGGGTTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:41:23,18:83,81:0.2:2,2:22.3:1:28.5:1:0.60153:1.25:60:12.667:0.19:0:2.9 0/1:181:9:4,5:89,83:0.0497:2,2:34.4:1:30:1:0.74184:1.33819:60:18:0.0503:0:2.7 -6 29896977 . C T 92 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=CCCCAGGCAGCGACCATGCG;RSEQ=AGGGTTCTGATGTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:105,107:0:2,0:23.5:1:31.2:1:1:0:60:29.286:1:0:1.5 0/1:189:9:4,5:91,89:0.0476:2,2:26.1:1:29.1:1:0.74718:1.27643:60:18:0.0497:0:4.7 -6 29896980 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2282;SOR=Inf;LSEQ=CAGGCAGCGACCATGCGCAG;RSEQ=GTTCTGATGTGTCTCTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:98,107:0:2,0:24.5:1:30.2:1:1:0:60:28.286:1:0:1.5 0/1:188:2:1,1:94,92:0.0106:2,2:34.5:1:28.5:1:1:1.02163:60:4:0.0109:0:2 -6 29896991 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23904;SOR=Inf;LSEQ=CATGCGCAGGGTTCTGATGT;RSEQ=TCTCTCACGGCTTGTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:92,104:0:2,0:26.8:1:30.8:1:1:0:60:18.6:1:0:1.6 0/1:188:2:0,2:98,87:0.0106:2,0:15.5:1:30:1:0.22517:0:60:4:0.011:0:2 -6 29896999 . C T 136 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTTCTGATGTGTCTCTCA;RSEQ=GGCTTGTAAAGGTGAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:95,103:0:2,0:26.9:1:29.7:1:1:0:60:27.286:1:0:1.6 0/1:191:25:10,15:83,82:0.1309:2,2:26.4:1:29.3:1:0.39405:1.51497:60:50:0.1374:0:4.4 -6 29897017 . CA AG 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACGGCTTGTAAAGGTGAGA;RSEQ=CTGGGGGACCTGATGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:85,105:0:2,0:27.1:1:29.8:1:1:0:60:14.833:1:0:1.7 0/1:168:43:19,24:59,62:0.256:2,2:28.1:1:31.2:1:0.72254:1.20069:59.5:86:0.2792:0.006:2.7 -6 29897018 . A G 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.44392;SOR=0.83237;LSEQ=ACGGCTTGTAAAGGTGAGAC;RSEQ=CTGGGGGACCTGATGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:187:119:48,71:35,33:0.6364:2,2:27.3:1:29.9:1:0.16894:1.56494:60:13.875:0.6236:0:2.5 1/0:167:99:45,54:12,13:0.5928:2,2:28.7:1:30.2:1:0.82645:1.10678:60:98:0.8167:0:2 -6 29897030 . G A 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGTGAGACACTGGGGGACCT;RSEQ=ATGTGGGGGGGTGTTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:77,102:0:2,0:25.6:1:30.7:1:1:0:59.9:13.917:1:0:1.7 0/1:151:15:7,8:59,77:0.0993:2,2:26.1:1:23.7:1:1:1.14:58.5:2:0.0725:0:2.7 -6 29897035 . G GT 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00129;SOR=2.15265;LSEQ=GACACTGGGGGACCTGATGT;RSEQ=GGGGGGTGTTGGGGGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:171:91:31,60:41,38:0.5322:2,2:27.9:1:28.8:1:0.02057:2.07904:59.8:10.375:0.5188:0:2.4 1/0:152:108:39,69:21,20:0.7105:2,2:23.3:1:28:1:0.13401:1.84976:60:12.5:0.7143:0.1118:2.5 -6 29897036 . G T 106 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00058;SOR=0;LSEQ=ACACTGGGGGACCTGATGTG;RSEQ=GGGGGTGTTGGGGGCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:12:6,6:65,96:0.0686:2,2:10.1:1:29.7:1:0.55346:1.47:60:24:0.0719:0:2.6 0/0:149:0:0,0:54,80:0:2,0:23.5:1:29.2:1:1:0:59.8:15.75:0.9921:0:2.1 -6 29897050 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51161;SOR=0;LSEQ=GATGTGGGGGGGTGTTGGGG;RSEQ=CAATAGTGGACGCAGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:67,90:0.0125:2,2:8:1:29:1:1:1.34:55:4:0.013:0:2.5 0/0:115:0:0,0:47,68:0:2,0:30:0:15:0:1:0:60:0:0:0:7 -6 29897051 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18097;SOR=Inf;LSEQ=ATGTGGGGGGGTGTTGGGGG;RSEQ=AATAGTGGACGCAGCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:65,91:0:2,0:22.8:1:31.3:1:1:0:59.8:14.6:1:0:1.6 0/1:116:2:0,2:48,66:0.0172:2,0:7:1:27:1:0.51064:0:60:4:0.0182:0:2 -6 29897061 . C T 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01915;LSEQ=GTGTTGGGGGCAATAGTGGA;RSEQ=GCAGCTGTGCTATGGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:144:78:29,49:37,28:0.5417:2,2:23.6:1:29.8:1:0.02817:2.21989:59.6:38:0.539:0:2.7 1/0:97:53:17,36:22,20:0.5464:2,2:21.1:1:29.5:1:0.05946:2.30803:60:25.5:0.5484:0:3.1 -6 29897102 . G A 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02406;SOR=1.96941;LSEQ=CTTTGAATTGGATGTATTGA;RSEQ=CATGTGATGGGCTGTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:57:31,26:50,18:0.456:2,2:24.4:1:30:1:0.0381:2.31352:59.4:56:0.4516:0:2.5 1/0:85:53:28,25:22,10:0.6235:2,2:24.5:1:30.2:1:0.1768:1.9488:60:52:0.6265:0:2.5 -6 29897112 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52006;SOR=0;LSEQ=GATGTATTGAGCATGTGATG;RSEQ=GCTGTTTAAAGTGTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:2,0:91,39:0.0152:2,0:47.5:1:29.5:1:1:0:60:4:0.0155:0:2.5 0/0:86:0:0,0:57,29:0:2,0:24.5:1:30.5:1:1:0:59.8:20.5:1:0:1.4 -6 29897129 . C T 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00033;SOR=2.48457;LSEQ=ATGGGCTGTTTAAAGTGTCA;RSEQ=CCCTCACTGTGACGGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:55:33,22:84,27:0.3313:2,2:23.4:1:30.7:1:0.04689:2.06444:59.9:110:0.3354:0:1.9 1/0:114:63:42,21:34,17:0.5526:2,2:21.8:1:28.8:1:1:1:60:20:0.5405:0:1.9 -6 29897138 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08363;SOR=Inf;LSEQ=TTAAAGTGTCACCCCTCACT;RSEQ=TGACGGATATGAATTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:127,57:0:2,0:21.8:1:31.6:1:1:0:60:35.8:1:0:0.6 0/1:144:3:1,2:93,48:0.0208:2,2:19.7:1:29:1:0.2765:3.83597:60:6:0.021:0:1 -6 29897196 . G C 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00965;SOR=0.36882;LSEQ=TAGTGTGAGACAGCTGCCTT;RSEQ=TGTGGGACTGAGAGGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:27:13,14:231,179:0.0618:2,2:26.3:1:31.9:1:0.42941:1.3887:60:54:0.0631:0:1.1 0/1:380:9:6,3:202,169:0.0237:2,2:33:1:32.1:1:0.52045:1.67:60:18:0.0239:0:1.1 -6 29897226 . G A 141 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=7.16319;LSEQ=GAGAGGCAAGATTTGTTCAC;RSEQ=CCTTCCCTTTGTGACTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:4:1,3:187,221:0.0097:2,2:40.5:1:30:1:0.62893:2.5332:36:8:0.0099:0:3.8 0/1:365:24:12,12:161,180:0.0658:2,2:32.7:1:30.9:1:0.8348:1.12:45.9:48:0.0665:0:3.2 -6 29897232 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0456;SOR=Inf;LSEQ=CAAGATTTGTTCACGCCTTC;RSEQ=CTTTGTGACTTCAAAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:181,220:0:2,0:28.7:1:30.8:1:1:0:59.6:99.25:1:0:0.2 0/1:346:4:2,2:156,186:0.0116:2,2:19.5:1:24.8:1:1:1.19:60:3:0.0087:0:1 -6 29897244 . C G 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=6e-05;SOR=7.08387;LSEQ=ACGCCTTCCCTTTGTGACTT;RSEQ=AAAAACCCTGACTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:4:1,3:144,206:0.0113:2,2:38.3:1:33.3:1:0.64725:2.09312:36:8:0.0115:0:3.8 0/1:293:22:11,11:114,155:0.0751:2,2:32.5:1:31.9:1:0.50901:1.36:45.4:44:0.0751:0:3.4 -6 29897247 . A G 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=8e-05;SOR=6.81789;LSEQ=CCTTCCCTTTGTGACTTCAA;RSEQ=AACCCTGACTCTCTTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:4:1,3:138,208:0.0114:2,2:36:1:33:1:1:1.98684:36:8:0.0115:0:3.8 0/1:273:20:10,10:104,149:0.0733:2,2:33:1:31.6:1:0.48467:1.43:44.9:40:0.0738:0:3.5 -6 29897255 . ACTCT A 130 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.00042;SOR=5.23662;LSEQ=TTGTGACTTCAAAAACCCTG;RSEQ=CTTTCTGCAAAGGCACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:5:2,3:108,194:0.0163:2,2:21.8:1:32.4:1:1:1.20:40.8:10:0.0167:0.0033:3.2 0/1:225:18:9,9:76,131:0.08:2,2:27.3:1:31.2:1:0.31355:1.72:44.8:36:0.08:0:3.5 -6 29897259 . T A 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GACTTCAAAAACCCTGACTC;RSEQ=CTTTCTGCAAAGGCACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:93,184:0:2,0:23.9:1:29.8:1:1:0:60:38.571:1:0:0.1 0/1:211:34:11,23:60,99:0.1611:2,2:24.8:1:29.2:1:0.69568:1.2657:60:33:0.1728:0:1.1 -6 29897285 . C T 76 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03822;SOR=5.03117;LSEQ=TGCAAAGGCACCTGAATGTG;RSEQ=CTGTGTTCCTGTAGGCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:19,140:0.0124:2,0:9:1:30.5:1:1:0:35:4:0.0127:0:4 0/1:117:7:2,5:17,93:0.0598:2,2:10.4:1:27.1:1:0.31779:2.17:42.7:6:0.0531:0:4 -6 29897301 . C T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00113;SOR=Inf;LSEQ=TGTGCCTGTGTTCCTGTAGG;RSEQ=ATAATATGAGGAGGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:1,93:0:1,0:26:1:33:1:1:0:60:188:1:0:0.1 0/1:74:8:0,8:2,64:0.1081:1,0:18.1:1:29.1:1:1:0:60:16:0.1081:0:1.5 -6 29897322 . G T 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04413;SOR=Inf;LSEQ=ATAATATGAGGAGGTGGGGA;RSEQ=ACCAACCCACCCCCATGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:1,73:0:1,0:23.6:1:31.6:1:1:0:60:36:1:0:0.1 0/1:42:3:0,3:1,38:0.0714:1,0:19:1:29.3:1:1:0:60:6:0.075:0:2 -6 29897350 . C T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01033;SOR=Inf;LSEQ=CACCCCCATGTCCACCATGA;RSEQ=CCTCTTCCCTCATGCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:1,47:0:1,0:24.6:1:30.9:1:1:0:60:23:1:0:0.3 0/1:24:4:0,4:0,20:0.1667:1,0:15.3:1:29:1:1:0:60:8:0.1739:0:2 -6 29897379 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06388;SOR=Inf;LSEQ=CTCATGCTGACCTGTGTTCC;RSEQ=TCTCCAATAATTAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:1,30:0:1,0:27.5:1:32.6:1:1:0:60:62:1:0:0.4 0/1:11:2:0,2:0,9:0.1818:0,0:38.5:1:33.5:1:1:0:60:4:0.1818:0:2 -6 29897412 . G C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47778;LSEQ=AATCATTCCTGCTCCATAGA;RSEQ=GTGAGGCTGAGATGTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:0,11:1,10:0.5:2,0:21.3:1:30.4:1:1:0:60:22:0.5:0:1.2 1/0:5:3:0,3:0,2:0.6:0,0:18.3:1:30.7:1:1:0:60:6:0.6:0:1 -6 29897868 . C A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGCTGGGCCCGGGGGAC;RSEQ=ACTGCCATCAAGATGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:22:1:31.5:1:1:2.45:50.5:4:0.4:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29897872 . G A 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGCCCGGGGGACCACT;RSEQ=CCATCAAGATGCGGAGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:0,2:0.6667:0,2:27.8:1:28:1:0.46667:0:52.5:8:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29897885 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCACTGCCATCAAGATGC;RSEQ=GAGACCGGTAGTGGCCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:26:1:31:1:1:2.45:54.5:4:0.4:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29897944 . A G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTATTGCATACAAGACAA;RSEQ=GGGCAGGGTAAGGAAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:23:1:32.5:1:1:0:50.5:4:0.5:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29901783 . A T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00438;SOR=Inf;LSEQ=GCTTACAGAGGCCAGGGAAT;RSEQ=AACCTGGACAAATTATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:0:1,0:25.2:1:28:1:1:0:60:66:1:0:0.5 0/1:13:4:4,0:9,0:0.3077:0,0:30.3:1:30.8:1:1:0:60:8:0.3077:0:1 -6 29901806 . C T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02056;LSEQ=CCTGGACAAATTATGCCCCA;RSEQ=GGTGGAATCACTGGGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:12,0:35,0:0.2553:1,0:24.2:1:30.8:1:1:0:60:24:0.2609:0:1.7 0/1:27:7:7,0:20,0:0.2593:1,0:19.3:1:30.9:1:1:0:60:14:0.2692:0:1.9 -6 29901865 . G C 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31003;SOR=1.30649;LSEQ=CTCCCCATTCTCTGTAAAAA;RSEQ=GATTCTCTGTAAAAAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:62:62,0:97,7:0.3735:2,1:23.3:1:32.6:1:0.0464:0:60:124:0.3758:0:2.6 0/1:105:46:45,1:52,7:0.4381:2,1:22.6:1:31.4:1:0.0765:5.98:60:92:0.4466:0:2.8 -6 29901898 . CC GG 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGATTACATCGCCCTAAA;RSEQ=AGGACCTGAGCTCTTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:254,73:0:2,0:23:1:31.4:1:1:0:59.6:64.4:1:0:1.1 0/1:205:48:39,9:123,34:0.2341:2,2:25.6:1:31.4:1:0.83968:1.20:58.4:96:0.2376:0:2.1 -6 29901899 . C G 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00148;SOR=1.7708;LSEQ=AAGATTACATCGCCCTAAAC;RSEQ=AGGACCTGAGCTCTTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:132:104,28:158,47:0.3917:2,2:21.8:1:29.8:1:0.78885:1.10:59:131:0.3922:0:2.7 1/0:212:113:87,26:40,11:0.533:2,2:23.6:1:29.5:1:1:1.0862:59.6:55.5:0.6894:0:2.8 -6 29901917 . A G 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCAGGACCTGAGCTCTTGG;RSEQ=CTGCGGCGGCCATGGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:286,137:0:2,0:24.9:1:29.2:1:1:0:59.6:41.3:1:0:1.1 0/1:306:23:16,7:194,89:0.0752:2,2:26.6:1:30.7:1:1:1.05:59.1:22:0.0733:0:3.7 -6 29901919 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=4.61361;LSEQ=CAGGACCTGAGCTCTTGGAC;RSEQ=GCGGCGGCCATGGCGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:175:117,58:169,86:0.407:2,2:25.5:1:30:1:0.91752:1.03:58.9:57.333:0.4086:0:2.6 1/0:313:238:163,75:51,23:0.7604:2,2:24.6:1:29.6:1:1:1.02021:59:78.333:0.763:0:2.6 -6 29901921 . C T 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=29.9598;LSEQ=GGACCTGAGCTCTTGGACTG;RSEQ=GGCGGCCATGGCGGCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:1:0,1:289,156:0.0022:2,0:1:0:28:0:0.35202:0:60:2:0.0023:0:3 0/1:332:21:12,9:211,100:0.0633:2,2:20.3:1:29.7:1:0.34075:1.58021:60:42:0.0648:0:3 -6 29901987 . C G 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.80654;LSEQ=CCATGAGGCGGAGCAGCAGA;RSEQ=AGCCTACCTGGAGGGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:237:104,133:151,217:0.3911:2,2:27.1:1:31.6:1:0.5008:1.12:56.6:78:0.3926:0:2.6 1/0:531:377:168,209:70,83:0.71:2,2:28.5:1:31.1:1:0.84732:1.04907:55.7:61.833:0.7121:0:2.6 -6 29901997 . G A 102 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=GAGCAGCAGACAGCCTACCT;RSEQ=GAGGGCAGGTGCGTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:0:0,0:215,343:0:2,0:26.4:1:31.1:1:1:0:58.2:78.714:1:0:1.1 0/1:476:11:4,7:197,268:0.0231:2,2:29.5:1:29.5:1:0.76672:1.28571:55.1:22:0.0233:0:4.4 -6 29902004 . A C 71 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01891;SOR=Inf;LSEQ=AGACAGCCTACCTGGAGGGC;RSEQ=GGTGCGTGGAGTGGCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:185,330:0:2,0:25.4:1:30.7:1:1:0:58.1:102:0.998:0:1.1 0/1:428:5:3,2:172,251:0.0117:2,2:38.6:1:30.8:1:0.40315:2.18:46.6:10:0.012:0:5.2 -6 29902005 . G C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.34287;LSEQ=GACAGCCTACCTGGAGGGCA;RSEQ=GTGCGTGGAGTGGCTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:37:10,27:170,301:0.0727:2,2:21.1:1:30.9:1:0.29046:1.52372:56:74:0.0736:0:2.6 0/1:420:198:78,120:92,130:0.4714:2,2:26.3:1:30.1:1:0.69124:1.08854:54:197:0.4747:0:2.8 -6 29902011 . T A 97 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=CTACCTGGAGGGCAGGTGCG;RSEQ=GGAGTGGCTCCGCAGATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:165,303:0:2,0:24.1:1:29.8:1:1:0:58:57.5:1:0:1.1 0/1:393:10:4,6:152,231:0.0254:2,2:22.8:1:29.5:1:1:1.01:54.6:20:0.0256:0:4.5 -6 29902016 . T A 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21928;LSEQ=TGGAGGGCAGGTGCGTGGAG;RSEQ=GGCTCCGCAGATACCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:121:43,78:103,211:0.2775:2,2:24.1:1:30.6:1:0.65052:1.13:53.3:59.5:0.2774:0:3 0/1:361:28:12,16:129,202:0.0776:2,2:20.9:1:30.1:1:0.69145:1.17:58.1:56:0.0787:0:2.9 -6 29902040 . A G 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15699;SOR=0.69784;LSEQ=TCCGCAGATACCTGGAGAAC;RSEQ=GGAAGGAGACACTGCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:62:13,49:44,134:0.2583:2,2:20.3:1:31.2:1:0.60662:1.23657:46.4:61:0.2574:0:3.9 0/1:174:34:7,27:36,104:0.1954:2,2:11.4:1:30.7:1:0.65957:1.33301:48.9:68:0.1977:0:3.4 -6 29902050 . CA TG 116 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGAGAACAGGAAGGAGA;RSEQ=CTGCAGCACACCTGTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:37,148:0:2,0:20.7:1:32.1:1:1:0:55.7:60.667:1:0:1.2 0/1:104:12:0,12:21,67:0.1154:2,0:15.9:1:32.6:1:0.06592:0:39.6:24:0.12:0:5 -6 29902051 . A G 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=45.96574;LSEQ=CTGGAGAACAGGAAGGAGAC;RSEQ=CTGCAGCACACCTGTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:0,3:32,139:0.0172:2,0:3:1:31.3:1:1:0:40:6:0.0175:0:4 0/1:91:41:10,31:7,31:0.4505:2,2:21.4:1:31.1:1:0.59075:1.42:56.4:40:0.5195:0:2.1 -6 29902059 . A G 131 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.21896;SOR=1.67345;LSEQ=CAGGAAGGAGACACTGCAGC;RSEQ=CACCTGTACCAGGGACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:17:3,14:17,91:0.136:2,2:20.5:1:32.2:1:0.73534:1.15:34.1:34:0.1382:0:6.1 0/1:67:14:1,13:11,42:0.209:2,1:10.2:1:31.6:1:0.43513:3.35727:40.7:28:0.209:0:5.5 -6 29902063 . CT TG 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62502;SOR=1.29032;LSEQ=AAGGAGACACTGCAGCACAC;RSEQ=GTACCAGGGACCACGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:13:0,13:16,89:0.1102:2,1:21.1:1:31.9:1:0.2105:0:31.1:26:0.1121:0:5.8 0/1:58:8:1,7:9,41:0.1379:2,2:10.1:1:31.4:1:1:1.52635:36.1:16:0.1404:0:5.5 -6 29902073 . GA AG 104 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05712;SOR=0;LSEQ=TGCAGCACACCTGTACCAGG;RSEQ=CCACGGGCGCCTCCCTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:9:0,9:12,74:0.0947:2,0:17.3:1:33.1:1:0.59717:0:24.4:18:0.0947:0:5.1 0/0:44:0:0,0:6,38:0:2,0:16.5:1:30.8:1:1:0:56.4:88:1:0:1.3 -6 29902078 . C CG 96 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.0555;SOR=0;LSEQ=CACACCTGTACCAGGGACCA;RSEQ=GGGCGCCTCCCTGATCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:8:0,8:8,67:0.0964:2,0:13.8:1:32:1:1:0:22.5:16:0.0988:0:7 0/0:38:0:0,0:6,31:0:2,0:17.2:1:29.4:1:1:0:60:74:1:0:0.7 -6 29902101 . A AG 87 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00401;SOR=8.86887;LSEQ=GCGCCTCCCTGATCGCCTGT;RSEQ=ATCTCCCGGGCTGGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:4,44:0.04:2,0:12.5:1:27.2:1:1:0:40.5:4:0.0408:0.02:2 0/1:29:8:0,8:2,19:0.2759:2,0:18.1:1:29.1:1:1:0:36.8:16:0.2857:0.0345:2.3 -6 29902129 . TG GA 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46234;SOR=2.07823;LSEQ=GGGCTGGCCTCCCACAAGGA;RSEQ=GGAGACAGATGGGACCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:4:0,4:0,32:0.1111:1,0:31:1:30:1:1:0:44.3:8:0.1176:0:2.3 0/1:24:5:0,5:2,12:0.2083:2,0:31.2:1:29.9:1:1:0:47.4:10:0.2083:0.0417:1.8 -6 29902135 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17293;SOR=Inf;LSEQ=GCCTCCCACAAGGATGGGAG;RSEQ=CAGATGGGACCAACACTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:0:1,0:25.8:1:30:1:1:0:58.1:66:1:0:0.4 0/1:24:2:1,1:1,21:0.0833:1,2:33:1:32.5:1:0.16304:15.20:60:4:0.0833:0:1 -6 29902168 . C T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06387;SOR=Inf;LSEQ=ACACTAGAATATCACCCTCC;RSEQ=TCTGGTCCTGAGGGAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:1,29:0:1,0:25:1:32.5:1:1:0:55.7:60:1:0:0.7 0/1:21:3:0,3:2,16:0.1429:2,0:10.3:1:31.7:1:1:0:60:6:0.15:0:1 -6 29902189 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGGTCCTGAGGGAGAAGA;RSEQ=TCCTCCTCAGTTTCCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:0,22:0.0833:1,2:34.5:1:33:1:0.08333:0:33:4:0.0833:0:3.5 0/0:6:0:0,0:1,5:0:2,0:29.8:1:28.8:1:1:0:52.2:5:1:0:2 -6 29902197 . CA GG 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02653;SOR=11.25399;LSEQ=TGAGGGAGAAGAATCCTCCT;RSEQ=GTTTCCAGATCCTGTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:1,5:0,14:0.2857:1,2:29.2:1:30.8:1:0.3:0:47.2:12:0.3158:0:1.8 1/1:6:5:1,4:0,1:0.8333:0,2:24.6:1:31.3:1:1:0:50.6:10:0.8333:0.1667:1.6 -6 29902294 . G T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGAGGCAATGACGGGAAGAC;RSEQ=CAATTAAGGGATAAAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:31.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:17:0:33:0:1:0:60:2:1:0:0 -6 29909745 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCTCATGCACTCAGGC;RSEQ=CAACTTTTCCGGATTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:27:1:30:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29909756 . G C 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCAGGCACAACTTTTCC;RSEQ=GATTAAAAACAAAAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:27:0:30.5:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29909988 . C T 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTGTTTCTCAGACAGCTC;RSEQ=TGGGCCAAGACTCAGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:44.5:1:32.5:1:1:0:50:4:0.5:0:3 1/1:1:1:1,0:0,0:1:0,0:47:0:33:0:1:0:42:2:1:0:2 -6 29910027 . C G 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59615;SOR=2.46453;LSEQ=GACATTGAGACAGAGCGCTT;RSEQ=GCACAGGAGCAGAGGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:16.8:1:32.5:1:1:0:48.8:8:0.4:0:3 1/0:5:3:2,1:1,1:0.6:2,2:11.3:1:31:1:1:1.73:40.7:6:0.6:0:2.7 -6 29910057 . C A 81 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.38051;SOR=0.29658;LSEQ=CAGAGGGGTCAGGGCGAAGT;RSEQ=CCAGGGCCCCAGGCGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:7,0:13,1:0.3333:1,0:20.3:1:29.1:1:1:0:56.4:14:0.3333:0:2.3 0/1:8:1:1,0:5,2:0.125:2,0:12:0:30:0:1:0:60:2:0.125:0:2 -6 29910083 . A G 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47658;SOR=1.76128;LSEQ=GCCCCAGGCGTGGCTCTCAG;RSEQ=GTCTCAGGCCCCGAAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:14:12,2:20,0:0.4118:1,2:27.8:1:30.5:1:0.16221:0:55.4:13:0.4063:0:2.5 1/0:9:5:4,1:4,0:0.5556:0,2:35.4:1:31.6:1:1:0:50.2:10:0.5556:0:2 -6 29910167 . C G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69425;SOR=1.19269;LSEQ=GCAGTTTCTTTTCTCCCTCT;RSEQ=CCAACCTACGTAGGGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:21:21,0:163,2:0.1129:1,1:22.4:1:32.8:1:1:0:60:42:0.1141:0:3 0/1:91:12:12,0:78,1:0.1319:1,0:24.6:1:32.2:1:1:0:60:24:0.1319:0:3 -6 29910176 . C T 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90819;SOR=1.04667;LSEQ=TTTCTCCCTCTCCCAACCTA;RSEQ=GTAGGGTCCTTCATCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:89:88,1:132,2:0.3973:1,1:20.7:1:30.8:1:1:1.33:60:28.667:0.3945:0:2.2 0/1:120:49:48,1:70,1:0.4083:1,1:20.9:1:30.4:1:1:1.45362:60:98:0.4118:0:2.4 -6 29910189 . A T 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.83936;SOR=1.05497;LSEQ=CAACCTACGTAGGGTCCTTC;RSEQ=TCCTGGATACTCACGACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:127:124,3:162,2:0.4364:1,1:21.1:1:31.7:1:0.65624:1.95508:58.4:126:0.4421:0:2.8 0/1:149:67:63,4:81,1:0.4497:1,2:22:1:31.3:1:0.1745:5.09216:59.4:32.5:0.4452:0:2.5 -6 29910194 . G A 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16859;SOR=0.45244;LSEQ=TACGTAGGGTCCTTCATCCT;RSEQ=GATACTCACGACGCGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:18:17,1:299,8:0.0554:1,1:11.6:1:29.3:1:0.40513:2.19108:49:36:0.0561:0:6.2 0/1:155:4:4,0:147,4:0.0258:1,0:12:0:28.5:1:1:0:49.5:8:0.026:0:5.8 -6 29910195 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1031;SOR=Inf;LSEQ=ACGTAGGGTCCTTCATCCTG;RSEQ=ATACTCACGACGCGGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:324,9:0:1,0:23.3:1:31.5:1:1:0:59.3:46.571:1:0:1.2 0/1:158:2:2,0:152,4:0.0127:1,0:39:1:30:1:1:0:60:4:0.0131:0:2 -6 29910225 . C G 132 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05641;SOR=0.37636;LSEQ=ACGCGGACCCAGTTCTCACT;RSEQ=CCATTGGGTGTCGGGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:19:18,1:401,38:0.0414:2,1:40.7:1:31.3:1:1:1.70:47.8:18:0.04:0:6.2 0/1:313:5:5,0:282,26:0.016:2,0:38:1:27.8:1:1:0:51.6:4:0.0129:0:5.8 -6 29910237 . C T 126 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0424;SOR=0.39068;LSEQ=TTCTCACTCCCATTGGGTGT;RSEQ=GGGTTTCCAGAGAAGCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:527:19:18,1:430,78:0.0361:2,1:36.1:1:29.7:1:0.33383:3.26:47.8:38:0.0365:0:6.2 0/1:417:6:6,0:330,81:0.0144:2,0:35.3:1:28.2:1:0.60169:0:53:12:0.0146:0:5 -6 29910245 . C T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05228;SOR=0.4137;LSEQ=CCCATTGGGTGTCGGGTTTC;RSEQ=AGAGAAGCCAATCAGTGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:21:19,2:469,130:0.0339:2,2:26:1:29.7:1:0.27666:2.63:49:42:0.0342:0:5.7 0/1:490:7:6,1:359,124:0.0143:2,2:21.6:1:28.4:1:0.68422:2.07:54:14:0.0144:0:4.6 -6 29910265 . G T 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAGAAGCCAATCAGTGTC;RSEQ=TCGCGGTCGCTGTTCTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:864:0:0,0:584,266:0:2,0:22.1:1:29.7:1:1:0:60:46.222:0.9835:0:0.9 0/1:700:61:39,22:405,230:0.0871:2,2:23.9:1:30.4:1:1:1.01:60:122:0.0883:0:3.5 -6 29910274 . G C 115 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13861;SOR=0.38776;LSEQ=CAATCAGTGTCGTCGCGGTC;RSEQ=CTGTTCTAAAGCCCGCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1027:13:11,2:641,372:0.0127:2,2:7.5:1:31.2:1:0.14985:3.19:40:26:0.013:0:7.8 0/0:809:4:2,2:482,321:0.0049:2,2:6:1:28:1:1:1.50074:44.8:8:0.0051:0:7.5 -6 29910276 . T G 260 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30007;SOR=1.10704;LSEQ=ATCAGTGTCGTCGCGGTCGC;RSEQ=GTTCTAAAGCCCGCACGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1073:410:259,151:420,242:0.3821:2,2:22.6:1:30:1:0.94805:1.01183:58.9:101.5:0.3856:0:2.4 0/1:844:343:208,135:289,212:0.4064:2,2:25.9:1:29.3:1:0.39396:1.13:59.2:170.5:0.4064:0:2.4 -6 29910277 . G C 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGTGTCGTCGCGGTCGCT;RSEQ=TTCTAAAGCCCGCACGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1099:0:0,0:689,403:0:2,0:22.1:1:31.5:1:1:0:59.4:83:0.9936:0:1 0/1:856:68:39,29:466,321:0.0794:2,2:26.3:1:31.1:1:0.79775:1.07938:59.7:67:0.0788:0:3.6 -6 29910286 . C T 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.24726;LSEQ=TCGCGGTCGCTGTTCTAAAG;RSEQ=CCGCACGCACCCACCGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1242:490:289,201:452,300:0.3945:2,2:22.9:1:29.6:1:0.72262:1.04782:58.3:53.444:0.3943:0:2.5 1/0:985:669:388,281:181,135:0.6792:2,2:25.6:1:28.9:1:0.83609:1.03:59.4:73.333:0.6783:0:2.2 -6 29910289 . G C 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=0.36698;LSEQ=CGGTCGCTGTTCTAAAGCCC;RSEQ=CACGCACCCACCGGGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1314:57:36,21:735,520:0.0434:2,2:10:1:30.9:1:0.58253:1.21:44.8:114:0.0444:0:6.2 0/1:1039:17:11,6:573,443:0.0164:2,2:9.6:1:30.7:1:0.62425:1.42:49.8:34:0.0166:0:6.2 -6 29910294 . C A 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.00129;SOR=0.5219;LSEQ=GCTGTTCTAAAGCCCGCACG;RSEQ=ACCCACCGGGACTCAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1422:84:50,34:759,576:0.0591:2,2:11.3:1:30.1:1:0.6514:1.12:48.2:83:0.0595:0:5.5 0/1:1135:36:21,15:610,487:0.0317:2,2:9.2:1:29.3:1:0.86499:1.12:53.7:35:0.0313:0:4.9 -6 29910302 . G C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00059;SOR=0.57104;LSEQ=AAAGCCCGCACGCACCCACC;RSEQ=GGACTCAGATTCTCCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1567:120:66,54:791,650:0.0766:2,2:15:1:30.1:1:1:1.00:50.4:59:0.0767:0:4.8 0/1:1283:58:35,23:652,568:0.0452:2,2:12.8:1:30.4:1:0.34626:1.33:55.4:116:0.0458:0:4.3 -6 29910324 . G C 202 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTCAGATTCTCCCCAGAC;RSEQ=CCGAGGATGGCCGTCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2027:0:0,0:1036,984:0:2,0:26.2:1:30.7:1:1:0:59.3:58.412:0.9975:0:1 0/1:1561:102:49,53:726,728:0.0653:2,2:25.6:1:30.3:1:0.75897:1.07858:59.8:50:0.0647:0:2.5 -6 29910336 . C G 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.5771;LSEQ=CCCCAGACGCCGAGGATGGC;RSEQ=GTCATGGCGCCCCGAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2188:260:136,124:964,955:0.1188:2,2:29.9:1:30.3:1:0.55227:1.09:55.3:85.667:0.119:0:3.4 0/1:1676:121:62,59:756,794:0.0722:2,2:29:1:30.3:1:0.63734:1.10:57.3:242:0.0731:0:3.2 -6 29910340 . A G 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.58193;LSEQ=AGACGCCGAGGATGGCCGTC;RSEQ=TGGCGCCCCGAACCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2221:274:139,135:970,976:0.1234:2,2:30:1:30.9:1:0.79661:1.04:55.6:67.5:0.124:0:3.3 0/1:1678:127:66,61:750,800:0.0757:2,2:29.3:1:30.6:1:0.46086:1.15:57.4:126:0.076:0:3.1 -6 29910358 . C G 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=209.06588;LSEQ=TCATGGCGCCCCGAACCCTC;RSEQ=TCCTGCTACTCTCGGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2240:4:2,2:1072,1159:0.0018:2,2:26.5:1:30:1:1:1.08:60:8:0.0018:0:2.3 0/1:1626:443:208,235:577,603:0.2724:2,2:25.4:1:30.3:1:0.50367:1.08103:59.9:87.6:0.2724:0:2.3 -6 29910371 . C T 276 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.27885;LSEQ=AACCCTCCTCCTGCTACTCT;RSEQ=GGGGGCCCTGGCCCTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2095:598:271,327:695,799:0.2854:2,2:25.2:1:30:1:0.62771:1.04958:59.7:53.364:0.2856:0:1.9 0/1:1517:152:73,79:649,712:0.1002:2,2:26.6:1:29.7:1:1:1.01:60:75:0.0997:0:1.8 -6 29910378 . C T 231 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=98.95157;LSEQ=CTCCTGCTACTCTCGGGGGC;RSEQ=CTGGCCCTGACCCAGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1983:4:2,2:896,1080:0.002:2,2:34.5:1:27.8:1:1:1.21:58.8:3:0.0016:0:2.5 0/1:1420:237:108,129:571,610:0.1669:2,2:25.4:1:29.4:1:0.47627:1.11799:59.9:46.4:0.1673:0:2.9 -6 29910402 . G A 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=28.44343;LSEQ=GCCCTGACCCAGACCTGGGC;RSEQ=GGTGAGTGCGGGGTCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1626:2:2,0:703,918:0.0012:2,0:1:0:28:1:0.18854:0:55.5:4:0.0012:0:1.5 0/1:1181:40:17,23:534,606:0.0339:2,2:21.9:1:30.2:1:0.63132:1.19202:59.6:80:0.0342:0:3.1 -6 29910419 . GGA TG 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19825;LSEQ=GGCGGGTGAGTGCGGGGTCG;RSEQ=GGGAAACCGCCTCTGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1312:385:159,226:394,526:0.2934:2,2:24:1:30.2:1:0.6236:1.06467:59.6:54:0.2935:0.064:3.3 0/1:947:72:35,37:392,463:0.076:2,2:22.9:1:29.9:1:0.7123:1.12:59.1:71:0.0765:0.0095:3.7 -6 29910420 . GA G 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00099;SOR=0.33741;LSEQ=GCGGGTGAGTGCGGGGTCGG;RSEQ=GGGAAACCGCCTCTGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:951:36:21,15:392,519:0.0379:2,2:8.2:1:29.1:1:0.08601:1.85:59.1:35:0.0378:0.0326:2.4 0/1:840:11:2,9:376,450:0.0131:2,2:13.9:1:28.8:1:0.12369:3.75492:60:22:0.0135:0.0083:3 -6 29910429 . C G 225 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=98.8217;LSEQ=TGCGGGGTCGGGAGGGAAAC;RSEQ=GCCTCTGCGGGGAGAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1161:4:3,1:484,673:0.0034:2,2:16:1:23.5:1:0.31511:4.17:33.8:3:0.0026:0:7.3 0/1:803:205:87,118:273,321:0.2553:2,2:24.9:1:29.4:1:0.41581:1.1533:58.6:67.333:0.2567:0:4.7 -6 29910437 . C T 209 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=138.75556;LSEQ=CGGGAGGGAAACCGCCTCTG;RSEQ=GGGGAGAAGCAAGGGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1055:2:0,2:443,610:0.0019:2,0:13.5:1:26.5:1:0.51237:0:60:4:0.0019:0:4.5 0/1:713:149:64,85:268,293:0.209:2,2:26.7:1:29:1:0.31061:1.21447:58.3:36.25:0.208:0:5.2 -6 29910439 . G A 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00329;SOR=0.62009;LSEQ=GGAGGGAAACCGCCTCTGCG;RSEQ=GGAGAAGCAAGGGGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1033:137:50,87:391,505:0.1326:2,2:18.8:1:30.7:1:0.13766:1.34682:58:33.25:0.131:0:3.3 0/1:693:60:27,33:297,336:0.0866:2,2:14.1:1:29.1:1:0.78852:1.0802:57.8:19:0.0841:0:2.4 -6 29910444 . AAGCAAGGGGCCCTCCT GAGCGGGCTGCCCGCCC 190 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAACCGCCTCTGCGGGGAG;RSEQ=GGCGGGGGCGCAGGACCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1015:76:27,49:388,483:0.0749:2,2:13:1:30.5:1:0.14816:1.45729:52.4:152:0.0764:0.0739:1.6 0/0:632:0:0,0:274,304:0:2,0:24.1:1:29:1:1:0:59.2:56.8:0.9147:0:2.3 -6 29910448 . AA GG 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00149;SOR=0.40664;LSEQ=CCGCCTCTGCGGGGAGAAGC;RSEQ=GGGGCCCTCCTGGCGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:906:53:19,34:391,460:0.0585:2,2:32.2:1:31.5:1:0.15825:1.52036:55.2:106:0.0593:0:6.2 0/1:609:15:8,7:280,314:0.0246:2,2:32.6:1:29.6:1:0.79466:1.28:55.3:14:0.0233:0:6.3 -6 29910450 . G C 196 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTCTGCGGGGAGAAGCAA;RSEQ=GGGCCCTCCTGGCGGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:888:0:0,0:392,492:0:2,0:23.7:1:31.3:1:1:0:59:54.25:0.9988:0:1.9 0/1:591:95:35,60:240,254:0.1607:2,2:25.7:1:29.9:1:0.04298:1.61848:58.9:94:0.1621:0:5.8 -6 29910451 . G C 179 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00218;SOR=0.4167;LSEQ=CCTCTGCGGGGAGAAGCAAG;RSEQ=GGCCCTCCTGGCGGGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:880:53:19,34:372,453:0.0602:2,2:30.4:1:31.4:1:0.20227:1.46887:55.2:106:0.062:0:6.2 0/1:577:15:8,7:263,297:0.026:2,2:30.6:1:30.9:1:0.7944:1.29:55.3:30:0.0264:0:6.3 -6 29910457 . T G 252 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38533;SOR=1.11136;LSEQ=CGGGGAGAAGCAAGGGGCCC;RSEQ=CCTGGCGGGGGCGCAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:839:266:107,159:270,301:0.317:2,2:24.5:1:31.3:1:0.06217:1.33247:56.7:52.2:0.321:0:5.7 0/1:570:194:85,109:181,194:0.3404:2,2:26.4:1:30.7:1:0.33038:1.19604:56.4:388:0.3464:0:6.1 -6 29910460 . T C 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38867;LSEQ=GGAGAAGCAAGGGGCCCTCC;RSEQ=GGCGGGGGCGCAGGACCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:828:261:106,155:269,295:0.3152:2,2:23.4:1:30.7:1:0.06046:1.33291:56.6:522:0.3206:0:5.8 0/1:567:86:38,48:227,253:0.1517:2,2:27.2:1:29.1:1:0.63962:1.1331:55.3:85:0.1521:0:6.2 -6 29910468 . G A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21499;SOR=0.6859;LSEQ=AAGGGGCCCTCCTGGCGGGG;RSEQ=CGCAGGACCGGGGGAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:819:39:17,22:361,419:0.0476:2,2:22.6:1:29.7:1:0.86954:1.11481:56.5:38:0.0475:0:6.1 0/1:543:18:9,9:246,279:0.0331:2,2:24.2:1:29.2:1:0.81472:1.13:53.6:36:0.0336:0:6.3 -6 29910473 . G A 127 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCTCCTGGCGGGGGCGCA;RSEQ=GACCGGGGGAGCCGCGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:834:0:0,0:387,446:0:2,0:22.1:1:31:1:1:0:57.6:36.864:0.9988:0:1.9 0/1:543:21:11,10:245,276:0.0387:2,2:22.6:1:29.1:1:0.66155:1.24:51.4:20:0.0377:0:6.7 -6 29910478 . G C 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=6e-05;SOR=1.68226;LSEQ=CCTGGCGGGGGCGCAGGACC;RSEQ=GGGGAGCCGCGCCGGGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:830:165:80,85:313,346:0.1988:2,2:22.5:1:30.4:1:0.86175:1.04:51.4:330:0.2022:0:6.6 0/1:533:157:66,91:187,187:0.2946:2,2:20.7:1:29.5:1:0.10566:1.37794:52.4:77.5:0.2941:0:6.8 -6 29910482 . G T 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39213;LSEQ=GCGGGGGCGCAGGACCGGGG;RSEQ=AGCCGCGCCGGGACGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:848:154:73,81:330,364:0.1816:2,2:22.6:1:29:1:1:1.00594:50.4:308:0.1855:0:6.8 0/1:550:44:19,25:196,197:0.08:2,2:22.6:1:27.6:1:0.42989:1.3083:53.1:21:0.0788:0:6.4 -6 29910491 . C A 173 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03383;SOR=0.56078;LSEQ=CAGGACCGGGGGAGCCGCGC;RSEQ=GGGACGAGGGTCGGGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:52:29,23:395,433:0.059:2,2:14.8:1:30.5:1:0.31668:1.38:37.8:104:0.06:0:7.5 0/1:560:19:14,5:262,279:0.0339:2,2:10.3:1:30:1:0.03578:2.98:39.9:38:0.0344:0:6.7 -6 29910492 . G T 110 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=20.86119;LSEQ=AGGACCGGGGGAGCCGCGCC;RSEQ=GGACGAGGGTCGGGCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:885:1:0,1:432,452:0.0011:2,0:1:0:26:0:1:0:60:2:0.0012:0:1 0/1:563:13:4,9:275,272:0.0231:2,2:23.8:1:29.8:1:0.26122:2.27165:52.6:12:0.0218:0:7.1 -6 29910496 . C G 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.80998;LSEQ=CCGGGGGAGCCGCGCCGGGA;RSEQ=GAGGGTCGGGCAGGTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:908:218:117,101:327,361:0.2401:2,2:20.1:1:31.7:1:0.12039:1.28:43.1:217:0.2425:0:7 1/0:596:386:196,190:109,100:0.6477:2,2:22:1:30.7:1:0.79671:1.0565:54.1:63.333:0.6452:0:4.1 -6 29910506 . G T 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCGCCGGGACGAGGGTCGG;RSEQ=CAGGTCTCAGCCACTGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:972:0:0,0:494,478:0:2,0:24.5:1:31.3:1:1:0:55.6:47.6:1:0:1.8 0/1:672:65:34,31:325,282:0.0967:2,2:22.5:1:29.3:1:0.89625:1.05074:59.9:130:0.0988:0:3 -6 29910507 . CA TG 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00421;SOR=0.36513;LSEQ=GCGCCGGGACGAGGGTCGGG;RSEQ=GGTCTCAGCCACTGCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:981:38:18,20:479,459:0.0387:2,2:20.1:1:30.5:1:0.74138:1.15935:43.6:76:0.0394:0.0031:5.6 0/1:690:10:6,4:366,314:0.0145:2,2:12.7:1:29.5:1:0.75969:1.29:45.2:20:0.0147:0.0058:5.4 -6 29910508 . A G 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=1.63725;LSEQ=CGCCGGGACGAGGGTCGGGC;RSEQ=GGTCTCAGCCACTGCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:984:207:124,83:366,375:0.2104:2,2:21.9:1:30.5:1:0.00756:1.53:41.6:206:0.2201:0:6.7 0/1:688:209:115,94:255,216:0.3038:2,2:19.5:1:30:1:0.8676:1.04:47.9:208:0.3109:0:5.9 -6 29910510 . G A 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20914;LSEQ=CCGGGACGAGGGTCGGGCAG;RSEQ=TCTCAGCCACTGCTCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1021:125:75,50:454,441:0.1224:2,2:23.1:1:30.7:1:0.05614:1.46:43.8:250:0.1256:0:6.6 0/1:706:20:13,7:373,313:0.0283:2,2:18:1:28.9:1:0.37318:1.56:47.6:19:0.0274:0:6.3 -6 29910516 . G A 140 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00043;SOR=0.16277;LSEQ=CGAGGGTCGGGCAGGTCTCA;RSEQ=CCACTGCTCGCCCCCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1103:26:7,19:560,514:0.0236:2,2:34.5:1:29.9:1:0.01565:2.95447:32.1:52:0.0242:0:7.5 0/0:767:3:0,3:412,349:0.0039:2,0:36:1:31.7:1:0.09735:0:36.3:6:0.004:0:7.7 -6 29910519 . A C 155 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0.17512;LSEQ=GGGTCGGGCAGGTCTCAGCC;RSEQ=CTGCTCGCCCCCAGGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1138:32:10,22:571,532:0.0281:2,2:30.7:1:31.1:1:0.02999:2.35957:32.8:64:0.0286:0:7.1 0/0:794:4:1,3:422,366:0.005:2,2:33.5:1:32.8:1:0.34348:3.454:35:8:0.0051:0:7.3 -6 29910522 . G C 265 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09146;SOR=1.1775;LSEQ=TCGGGCAGGTCTCAGCCACT;RSEQ=CTCGCCCCCAGGCTCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1172:375:210,165:394,399:0.32:2,2:21.2:1:31:1:0.04501:1.29:45.6:74:0.322:0:5.5 0/1:819:292:159,133:276,248:0.3565:2,2:22.2:1:31.2:1:0.6607:1.07:50:145:0.3607:0:5.1 -6 29910527 . C T 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.77932;LSEQ=CAGGTCTCAGCCACTGCTCG;RSEQ=CCCCAGGCTCCCACTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1251:135:83,52:564,551:0.1079:2,2:20.5:1:29.4:1:0.01774:1.56:45.1:44:0.1078:0:5.2 0/1:878:221:122,99:343,314:0.2517:2,2:26.2:1:29.4:1:0.48331:1.13:50:72.667:0.2526:0:5.1 -6 29910530 . C T 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.82796;SOR=0.93293;LSEQ=GTCTCAGCCACTGCTCGCCC;RSEQ=CAGGCTCCCACTCCATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1295:55:26,29:644,596:0.0425:2,2:19.3:1:30.5:1:0.58166:1.20504:39.8:110:0.0434:0:6.7 0/1:906:36:20,16:459,410:0.0397:2,2:9.6:1:30.4:1:0.86505:1.12:48:72:0.0403:0:5.6 -6 29910538 . C T 223 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=91.21702;LSEQ=CACTGCTCGCCCCCAGGCTC;RSEQ=CACTCCATGAGGTATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1366:3:0,3:704,659:0.0022:2,0:1:0:28:1:0.11355:0:56.3:6:0.0022:0:2.3 0/1:1015:170:91,79:439,406:0.1675:2,2:26.8:1:30.2:1:0.73681:1.07:54.1:169:0.1687:0:4.3 -6 29910549 . G A 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04487;SOR=0.49943;LSEQ=CCCAGGCTCCCACTCCATGA;RSEQ=GTATTTCTTCACATCCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1462:32:16,16:720,709:0.0219:2,2:22.3:1:31.2:1:1:1.01551:46.2:64:0.0223:0:4.2 0/1:1086:12:6,6:557,517:0.011:2,2:20.8:1:30:1:1:1.07727:43:24:0.0112:0:4.2 -6 29910557 . TT AC 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26735;LSEQ=CCCACTCCATGAGGTATTTC;RSEQ=CACATCCGTGTCCCGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1470:321:177,144:573,567:0.2184:2,2:27.8:1:30.8:1:0.12944:1.22:53.1:159.5:0.2212:0.0122:2.5 0/1:1094:76:40,36:535,481:0.0695:2,2:32:1:30.6:1:1:1.00104:56.1:152:0.0706:0.0018:2.2 -6 29910558 . T C 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0323;SOR=1.22568;LSEQ=CCACTCCATGAGGTATTTCT;RSEQ=CACATCCGTGTCCCGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1456:314:153,161:424,415:0.2157:2,2:27.8:1:30.9:1:0.5971:1.07503:45.3:103.667:0.2738:0:4.7 0/1:1083:273:145,128:342,313:0.2521:2,2:27.3:1:30.5:1:0.82885:1.04:51.5:33.125:0.2671:0:4.4 -6 29910562 . A C 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCATGAGGTATTTCTTCAC;RSEQ=TCCGTGTCCCGGCCCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1486:0:0,0:771,715:0:2,0:26.5:1:30.4:1:1:0:55:45.438:1:0:1.7 0/1:1092:78:44,34:536,478:0.0714:2,2:24.2:1:30.4:1:0.55856:1.15:54.1:38:0.0714:0:2.6 -6 29910572 . C T 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.57265;LSEQ=ATTTCTTCACATCCGTGTCC;RSEQ=GGCCCGGCCGCGGGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1459:221:105,116:666,572:0.1515:2,2:29.8:1:30.4:1:0.0925:1.28608:44.9:109.5:0.1527:0:4.3 0/1:1100:102:51,51:531,466:0.0927:2,2:27.5:1:30:1:0.53414:1.13935:47.4:204:0.094:0:4.1 -6 29910577 . C T 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07257;SOR=0.51787;LSEQ=TTCACATCCGTGTCCCGGCC;RSEQ=GGCCGCGGGGAGCCCCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1450:28:14,14:764,658:0.0193:2,2:29.9:1:31.1:1:0.70662:1.16097:46.4:56:0.0197:0:4.5 0/1:1090:11:5,6:576,502:0.0101:2,2:32:1:29.3:1:0.76347:1.37648:41.5:10:0.0093:0:4.9 -6 29910581 . C A 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.30469;LSEQ=CATCCGTGTCCCGGCCCGGC;RSEQ=GCGGGGAGCCCCGCTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1418:78:43,35:731,607:0.055:2,2:32.4:1:31.2:1:1:1.02:48.1:156:0.056:0:5.3 0/1:1048:124:66,58:493,429:0.1183:2,2:27.5:1:29.7:1:1:1.00988:52.6:61:0.1187:0:5.1 -6 29910583 . C T 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.21748;LSEQ=TCCGTGTCCCGGCCCGGCCG;RSEQ=GGGGAGCCCCGCTTCATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1404:78:43,35:727,599:0.0556:2,2:32.3:1:30.6:1:1:1.01:48.1:156:0.0564:0:5.3 0/1:1031:119:61,58:488,424:0.1154:2,2:28.1:1:29.2:1:0.69622:1.09424:52.4:238:0.1172:0:5.1 -6 29910586 . G A 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=4e-05;SOR=1.77681;LSEQ=GTGTCCCGGCCCGGCCGCGG;RSEQ=GAGCCCCGCTTCATCGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1407:105:57,48:721,576:0.0746:2,2:29.9:1:30.9:1:0.83844:1.05402:47.7:51.5:0.0744:0:5 0/1:1037:130:67,63:488,418:0.1254:2,2:27.1:1:29.6:1:0.63904:1.09767:51.5:129:0.1267:0:5.1 -6 29910602 . G T 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.44096;SOR=1.41159;LSEQ=GCGGGGAGCCCCGCTTCATC;RSEQ=CCGTGGGCTACGTGGACGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1351:14:6,8:762,571:0.0104:2,2:24.7:1:30.9:1:0.29282:1.77853:37.8:28:0.0106:0:5.1 0/1:961:14:9,5:505,437:0.0146:2,2:19.9:1:29.8:1:0.59109:1.56:40.9:13:0.0138:0:4.3 -6 29910604 . C A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.22241;LSEQ=GGGGAGCCCCGCTTCATCGC;RSEQ=GTGGGCTACGTGGACGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1355:282:119,163:648,425:0.2081:2,2:23.4:1:30.3:1:0:2.08732:47.1:46:0.2074:0:4 0/1:968:357:185,172:336,274:0.3688:2,2:25.4:1:29.9:1:0.34951:1.13995:54.7:38.667:0.3686:0:3.1 -6 29910622 . C T 140 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=20.83862;LSEQ=GCCGTGGGCTACGTGGACGA;RSEQ=ACGCAGTTCGTGCGGTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1273:2:0,2:724,547:0.0016:2,0:1:0:23.5:1:0.1858:0:60:4:0.0016:0:1 0/1:944:30:19,11:497,417:0.0318:2,2:14.7:1:28.6:1:0.35774:1.45:51.8:60:0.0323:0:3 -6 29910640 . C T 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31446;SOR=0.84334;LSEQ=GACACGCAGTTCGTGCGGTT;RSEQ=GACAGCGACGCCGCGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1317:114:72,42:666,537:0.0866:2,2:23.8:1:30:1:0.11495:1.38:59.6:228:0.0882:0:2.3 0/1:973:72:41,31:485,415:0.074:2,2:21.8:1:29.4:1:0.62584:1.13:59.8:71:0.0743:0:2 -6 29910658 . C T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09866;SOR=1.77841;LSEQ=TTCGACAGCGACGCCGCGAG;RSEQ=CAGAGGATGGAGCCGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1474:16:6,10:804,640:0.0109:2,2:16.6:1:27.9:1:0.2052:2.09271:42.9:4.333:0.0091:0:4.6 0/1:1149:22:10,12:588,539:0.0191:2,2:11:1:26.2:1:0.66756:1.30878:46:10:0.0178:0:4.7 -6 29910660 . A C 108 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68066;SOR=1.26429;LSEQ=CGACAGCGACGCCGCGAGCC;RSEQ=GAGGATGGAGCCGCGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1504:12:8,4:820,667:0.008:2,2:20:1:26.8:1:0.56394:1.63:41.1:3:0.0062:0:5.4 0/1:1192:12:7,5:608,568:0.0101:2,2:16.3:1:30.4:1:0.77498:1.31:38.6:24:0.0103:0:6.5 -6 29910663 . G A 217 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCGACGCCGCGAGCCAGA;RSEQ=GATGGAGCCGCGGGCGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1541:0:0,0:844,695:0:2,0:24.1:1:31.4:1:1:0:59.6:89.529:1:0:1 0/1:1219:155:85,70:541,518:0.1272:2,2:22.1:1:29.9:1:0.39093:1.16:60:310:0.1287:0:2 -6 29910669 . A C 114 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07818;SOR=2.12043;LSEQ=CGCCGCGAGCCAGAGGATGG;RSEQ=GCCGCGGGCGCCGTGGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1587:10:5,5:845,730:0.0063:2,2:25.5:1:32:1:1:1.15743:34.6:20:0.0065:0:6.1 0/1:1281:17:9,8:644,615:0.0133:2,2:20.4:1:27.9:1:1:1.07:42.7:7.5:0.012:0:6 -6 29910673 . G C 114 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11271;SOR=1.96197;LSEQ=GCGAGCCAGAGGATGGAGCC;RSEQ=CGGGCGCCGTGGATAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1591:10:5,5:829,749:0.0063:2,2:29.5:1:32:1:1:1.10674:34.6:20:0.0064:0:6.1 0/1:1305:16:8,8:657,630:0.0123:2,2:24.4:1:28.7:1:1:1.04284:39.2:15:0.0117:0:5.9 -6 29910679 . G A 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.31248;LSEQ=CAGAGGATGGAGCCGCGGGC;RSEQ=CCGTGGATAGAGCAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1660:162:88,74:764,731:0.0976:2,2:25.7:1:29.8:1:0.4571:1.14:60:39.5:0.0966:0:3.4 0/1:1377:45:21,24:666,664:0.0327:2,2:27.5:1:29.9:1:0.76216:1.14618:60:90:0.0332:0:3.4 -6 29910682 . G A 123 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10122;SOR=1.9238;LSEQ=AGGATGGAGCCGCGGGCGCC;RSEQ=TGGATAGAGCAGGAGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1728:12:6,6:880,835:0.0069:2,2:31.8:1:31.3:1:1:1.05388:38.8:24:0.007:0:5.3 0/1:1431:19:9,10:700,709:0.0133:2,2:29.4:1:29:1:1:1.09692:42.5:38:0.0134:0:5.5 -6 29910688 . A G 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05821;SOR=1.36805;LSEQ=GAGCCGCGGGCGCCGTGGAT;RSEQ=GAGCAGGAGGGGCCGGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1810:74:27,47:894,842:0.0409:2,2:22:1:31.1:1:0.0125:1.84761:55.4:36:0.0403:0:2.3 0/1:1488:82:35,47:707,697:0.0551:2,2:24.2:1:30.4:1:0.21121:1.36184:54.8:19.5:0.0531:0:2.5 -6 29910693 . A G 152 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=24.46909;LSEQ=GCGGGCGCCGTGGATAGAGC;RSEQ=GGAGGGGCCGGAGTATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1875:2:1,1:951,920:0.0011:2,2:34:1:21:1:1:1.03369:60:1:5e-04:0:2.5 0/1:1570:40:20,20:761,767:0.0255:2,2:20.8:1:28.6:1:1:1.01:53.1:9:0.0233:0:2.9 -6 29910698 . G A 275 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.44131;LSEQ=CGCCGTGGATAGAGCAGGAG;RSEQ=GGCCGGAGTATTGGGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1962:520:273,247:708,733:0.265:2,2:25.2:1:30.5:1:0.20094:1.14:60:85.667:0.2667:0:3.2 0/1:1610:221:109,112:686,697:0.1373:2,2:25.2:1:29.8:1:0.9424:1.0113:60:220:0.1379:0:2.8 -6 29910699 . G A 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48111;SOR=0.86082;LSEQ=GCCGTGGATAGAGCAGGAGG;RSEQ=GCCGGAGTATTGGGACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1982:60:20,40:968,952:0.0303:2,2:15.9:1:30.4:1:0.01214:2.0329:53.7:29:0.0298:0:2.4 0/1:1605:42:14,28:782,780:0.0262:2,2:15.2:1:29.9:1:0.04109:2.00428:55.9:41:0.0259:0:2.2 -6 29910700 . G T 227 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=170.27248;LSEQ=CCGTGGATAGAGCAGGAGGG;RSEQ=CCGGAGTATTGGGACCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1992:2:0,2:990,998:0.001:2,0:24:1:26.5:1:0.49976:0:60:4:0.001:0:3 0/1:1607:235:123,112:676,696:0.1462:2,2:26.1:1:28.9:1:0.39746:1.13:59.8:234:0.1469:0:4.8 -6 29910703 . G T 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.43918;LSEQ=TGGATAGAGCAGGAGGGGCC;RSEQ=GAGTATTGGGACCAGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2030:543:277,266:736,749:0.2675:2,2:24.9:1:30.6:1:0.58131:1.06:60:107.6:0.2685:0:3.3 0/1:1650:228:115,113:707,715:0.1382:2,2:25.5:1:30.3:1:0.88658:1.03:60:456:0.139:0:2.7 -6 29910716 . CA GG 242 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGCCGGAGTATTGGGAC;RSEQ=GGAGACACGGAATGTGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2169:0:0,0:1061,1101:0:2,0:24.1:1:31.5:1:1:0:59.7:73.552:0.9981:0:1.4 0/1:1756:272:143,129:692,713:0.1549:2,2:25.3:1:30:1:0.32118:1.14:58.7:271:0.1566:0.0091:4.3 -6 29910717 . A T 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33004;LSEQ=GGGGCCGGAGTATTGGGACC;RSEQ=GGAGACACGGAATGTGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2141:200:98,102:956,969:0.0934:2,2:26.8:1:30.5:1:0.88203:1.02685:60:39:0.0923:0:3.9 0/1:1703:56:26,30:633,627:0.0329:2,2:26.8:1:30.4:1:0.58814:1.16475:60:112:0.0393:0:3.9 -6 29910719 . G C 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.33117;LSEQ=GGCCGGAGTATTGGGACCAG;RSEQ=AGACACGGAATGTGAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2153:200:100,100:973,978:0.0929:2,2:26.8:1:32.2:1:1:1.01:59.9:65.667:0.0926:0:3.9 0/1:1738:57:30,27:788,779:0.0328:2,2:27.3:1:31.6:1:0.78801:1.10:60:27.5:0.0319:0:3.9 -6 29910721 . G C 215 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCGGAGTATTGGGACCAGGA;RSEQ=ACACGGAATGTGAAGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2193:0:0,0:1085,1103:0:2,0:24.3:1:31.6:1:1:0:59.9:71.933:0.9981:0:1.4 0/1:1774:115:59,56:829,825:0.0648:2,2:28.2:1:31.5:1:0.8473:1.05:59:114:0.0648:0:5.3 -6 29910725 . C G 189 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=84.79473;LSEQ=AGTATTGGGACCAGGAGACA;RSEQ=GGAATGTGAAGGCCCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2239:1:0,1:1104,1128:4e-04:2,0:26:0:33:0:1:0:60:2:5e-04:0:3 0/1:1779:65:36,29:843,866:0.0365:2,2:28.2:1:31.5:1:0.37712:1.28:56.5:130:0.037:0:4.1 -6 29910730 . T A 258 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=299.00767;LSEQ=TGGGACCAGGAGACACGGAA;RSEQ=GTGAAGGCCCAGTCACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2229:2:1,1:1106,1121:9e-04:2,2:25:1:22.5:1:1:1.01:60:1:5e-04:0:2 0/1:1762:372:195,177:684,704:0.2111:2,2:24:1:30.3:1:0.29357:1.13:59.3:92:0.2106:0:4.3 -6 29910731 . G A 234 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=196.99345;LSEQ=GGGACCAGGAGACACGGAAT;RSEQ=TGAAGGCCCAGTCACAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2225:2:2,0:1106,1117:9e-04:2,0:1:0:24.5:1:0.24787:0:60:4:9e-04:0:3 0/1:1759:265:131,134:746,746:0.1507:2,2:23:1:29.1:1:0.89401:1.02289:60:264:0.1513:0:3.8 -6 29910742 . G C 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.15416;LSEQ=ACACGGAATGTGAAGGCCCA;RSEQ=TCACAGACTGACCGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2166:581:279,302:770,814:0.2682:2,2:26.2:1:32.2:1:0.80853:1.02392:60:144.25:0.2692:0:3.5 1/0:1708:916:452,464:390,400:0.5363:2,2:23.6:1:31.5:1:1:1.00088:59.5:129.857:0.5379:0:4.1 -6 29910750 . C T 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23266;LSEQ=TGTGAAGGCCCAGTCACAGA;RSEQ=TGACCGAGTGGACCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2127:564:267,297:756,805:0.2652:2,2:26.5:1:30.5:1:0.65855:1.04465:60:69.5:0.2649:0:3.6 0/1:1679:130:60,70:761,784:0.0774:2,2:26:1:29.4:1:0.52329:1.13236:60:129:0.078:0:3.6 -6 29910752 . G C 261 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAAGGCCCAGTCACAGACT;RSEQ=ACCGAGTGGACCTGGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2128:0:0,0:1018,1109:0:2,0:25.6:1:31.6:1:1:0:59.9:74.964:0.9995:0:1.4 0/1:1643:324:165,159:639,676:0.1972:2,2:25.3:1:31.4:1:0.45731:1.10:59.9:323:0.1993:0:4.1 -6 29910759 . T C 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.19411;LSEQ=CCAGTCACAGACTGACCGAG;RSEQ=GGACCTGGGGACCCTGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2084:180:84,96:900,1002:0.0864:2,2:26.2:1:30.5:1:0.87623:1.02651:58.4:44:0.0855:0:4 0/1:1513:351:162,189:559,586:0.232:2,2:25.9:1:30.8:1:0.39314:1.11283:58.3:174.5:0.2333:0:4.9 -6 29910761 . G A 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.32036;LSEQ=AGTCACAGACTGACCGAGTG;RSEQ=ACCTGGGGACCCTGCGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2044:177:81,96:877,989:0.0866:2,2:26.4:1:29.7:1:0.81319:1.05096:58.4:34.4:0.0855:0:4 0/1:1474:353:165,188:550,571:0.2395:2,2:25.7:1:29.4:1:0.46402:1.09742:58:116.667:0.2409:0:4.9 -6 29910801 . C A 225 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=87.39725;LSEQ=CTACTACAACCAGAGCGAGG;RSEQ=CGGTGAGTGACCCCGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1369:5:3,2:553,811:0.0037:2,2:3.8:1:26.4:1:0.40135:2.20:56.6:10:0.0037:0:2.6 0/1:962:234:97,137:315,411:0.2432:2,2:23.2:1:28.7:1:0.64875:1.08236:56.7:468:0.2468:0:4.2 -6 29910816 . G A 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29007;LSEQ=CGAGGCCGGTGAGTGACCCC;RSEQ=GCCGGGGGCGCAGGTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1074:267:93,174:286,520:0.2486:2,2:24.4:1:30.7:1:0.88266:1.02901:59.7:132.5:0.2514:0:4.8 0/1:697:61:27,34:223,413:0.0875:2,2:24.1:1:29.6:1:0.16352:1.47:59.6:29.5:0.086:0:4.2 -6 29910820 . G C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=3.16003;LSEQ=GCCGGTGAGTGACCCCGGCC;RSEQ=GGGGCGCAGGTCAGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:979:336:103,233:215,426:0.3432:2,2:24.6:1:29.9:1:0.3886:1.14153:58.7:66.2:0.3441:0:4.7 1/0:626:390:125,265:83,149:0.623:2,2:24.7:1:29.2:1:0.37959:1.18061:57.3:129:0.6242:0:3.9 -6 29910834 . G C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.57921;LSEQ=CCGGCCGGGGGCGCAGGTCA;RSEQ=GACCCCTCATCCCCCACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:282:74,208:151,367:0.3525:2,2:23.5:1:30.4:1:0.41089:1.15628:58.7:69.5:0.3523:0:4.9 1/0:486:347:96,251:41,98:0.714:2,2:23.9:1:29.6:1:0.73801:1.09365:57:68.4:0.714:0:3.5 -6 29910839 . C T 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.9505;SOR=0.99102;LSEQ=CGGGGGCGCAGGTCAGGACC;RSEQ=CTCATCCCCCACGGACGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:735:266:65,201:128,341:0.3619:2,2:22.5:1:30.3:1:0.43281:1.16052:58.8:87.667:0.3643:0:4.9 0/1:453:163:48,115:76,213:0.3598:2,2:21.7:1:28.7:1:0.51048:1.17:59.1:31.6:0.3583:0:3.8 -6 29910852 . G C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59205;SOR=0.65327;LSEQ=CAGGACCCCTCATCCCCCAC;RSEQ=GACGGGCCAGGTCGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:600:11:6,5:123,466:0.0183:2,2:27.1:1:31.3:1:0.01577:4.53:56.6:22:0.0185:0:3.7 0/1:332:4:2,2:68,259:0.012:2,2:22:1:25.8:1:0.1978:3.79:54.8:3:0.0091:0:4 -6 29910856 . G A 224 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCCTCATCCCCCACGGAC;RSEQ=GGCCAGGTCGCCCACAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:153:34,119:74,324:0.2777:2,2:23.3:1:30.9:1:0.33981:1.25:59.8:75.5:0.2761:0:4.8 0/0:309:0:0,0:61,248:0:2,0:22.1:1:29.9:1:1:0:58.8:102:1:0:2.2 -6 29910861 . A G 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30268;SOR=0.73067;LSEQ=TCATCCCCCACGGACGGGCC;RSEQ=GGTCGCCCACAGTCTCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:52:14,38:86,377:0.101:2,2:26.6:1:31.3:1:0.19356:1.61:57.6:104:0.1018:0:3.7 0/1:277:21:5,16:43,212:0.0758:2,2:28.4:1:30:1:0.38105:1.54:54.7:42:0.0772:0:3.5 -6 29910865 . C G 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCCACGGACGGGCCAGGT;RSEQ=GCCCACAGTCTCCGGGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:85,394:0:2,0:24.9:1:30.7:1:1:0:59.7:158.667:1:0:1.8 0/1:255:22:6,16:31,202:0.0863:2,2:21.4:1:31:1:0.1056:2.43:57:44:0.0876:0:2.9 -6 29910866 . G A 211 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.15923;LSEQ=CCCCACGGACGGGCCAGGTC;RSEQ=CCCACAGTCTCCGGGTCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:136:25,111:58,269:0.2937:2,2:24.6:1:29.8:1:0.89446:1.04:59.8:33:0.2927:0:4.6 0/1:242:15:1,14:34,193:0.062:2,1:16.1:1:28.6:1:0.70325:2.4595:60:14:0.0581:0:3.4 -6 29910892 . A G 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=146.19869;LSEQ=AGTCTCCGGGTCCGAGATCC;RSEQ=CCCCGAAGCCGCGGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:1:1,0:97,289:0.0026:2,0:35:0:26:0:0.25323:0:60:2:0.0026:0:1 0/1:188:52:14,38:40,95:0.2766:2,2:22.9:1:31.7:1:0.85728:1.14202:60:51:0.2742:0:2.5 -6 29910910 . C T 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACCCCGAAGCCGCGGGAC;RSEQ=CCGAGACCCTTGCCCCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:137,211:0:2,0:23.9:1:31.1:1:1:0:59.2:42.5:1:0:1 0/1:167:20:9,11:62,85:0.1198:2,2:28.8:1:30.8:1:0.81426:1.12:60:40:0.1235:0:2.3 -6 29910923 . C A 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.53299;SOR=0.72807;LSEQ=GCGGGACCCCGAGACCCTTG;RSEQ=CCCGGGAGAGGCCCAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:20:16,4:152,164:0.0595:2,2:26.5:1:29.4:1:0.00951:4.30:42.1:19:0.0576:0:3.2 0/1:159:7:5,2:64,68:0.044:2,2:24.1:1:29.9:1:0.27464:2.64:59.6:14:0.0452:0:2.6 -6 29910947 . T A 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGAGGCCCAGGCGCCTT;RSEQ=ACCCGGTTTCATTTTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:270,112:0:2,0:23:1:30.1:1:1:0:58.1:190:1:0:0.9 0/1:199:12:7,5:138,49:0.0603:2,2:22.6:1:27.5:1:0.31335:2.00378:59.3:11:0.0567:0:1.6 -6 29910970 . G A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57564;SOR=0.77902;LSEQ=CCGGTTTCATTTTCAGTTTA;RSEQ=GCCAAAAATCCCCCCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:21:19,2:377,93:0.0427:2,2:31.8:1:29.4:1:0.39532:2.34:31.7:20:0.0417:0:3.2 0/1:298:10:6,4:227,60:0.0336:2,2:36.2:1:28.1:1:0.23075:2.51258:51.4:9:0.0307:0:3.5 -6 29910980 . C T 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCAGTTTAGGCCAAAAAT;RSEQ=CCCCCGGGTTGGTCGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:597:0:0,0:458,139:0:2,0:23.1:1:31:1:1:0:59:41.643:1:0:1.2 0/1:360:14:12,2:259,86:0.0389:2,2:23.1:1:29.2:1:0.53132:1.99:60:28:0.0395:0:1.2 -6 29910984 . C G 111 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.84654;SOR=0.90504;LSEQ=AGTTTAGGCCAAAAATCCCC;RSEQ=CGGGTTGGTCGGGGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:637:18:17,1:470,147:0.0283:2,1:29.7:1:26.8:1:0.08894:5.31:31.3:8:0.0258:0:3.4 0/1:390:10:6,4:288,92:0.0256:2,2:36.9:1:27.9:1:0.26989:2.08245:51.4:9:0.0233:0:3.5 -6 29910986 . G A 188 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=173.49231;LSEQ=TTTAGGCCAAAAATCCCCCC;RSEQ=GGTTGGTCGGGGCTGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:661:1:0,1:499,161:0.0015:2,0:13:0:17:0:0.24508:0:48:0:0:0:7 0/1:412:86:66,20:240,86:0.2087:2,2:22.7:1:29.4:1:0.6775:1.18:55:16.2:0.2005:0:4.8 -6 29911000 . T C 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00016;SOR=0.62856;LSEQ=CCCCCCGGGTTGGTCGGGGC;RSEQ=GGGCGGGGCTCGGGGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:828:287:204,83:358,171:0.3466:2,2:25.2:1:30:1:0.34235:1.17:59.9:40:0.3448:0:3.5 0/1:544:136:94,42:123,54:0.25:2,2:24.6:1:29.8:1:1:1.01768:59.6:67:0.2519:0:3.3 -6 29911003 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26767;LSEQ=CCCGGGTTGGTCGGGGCTGG;RSEQ=CGGGGCTCGGGGGACTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:866:310:220,90:369,187:0.358:2,2:24.6:1:29.3:1:0.17196:1.24:59.9:43.286:0.3577:0:3.5 0/1:578:75:53,22:330,171:0.1298:2,2:26.3:1:29.2:1:0.43477:1.25:59.6:150:0.1318:0:3.6 -6 29911005 . G A 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGTTGGTCGGGGCTGGGC;RSEQ=GGGCTCGGGGGACTGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:926:0:0,0:605,318:0:2,0:23.7:1:29.5:1:1:0:59.6:39.13:0.9967:0:1.4 0/1:607:47:33,14:362,196:0.0774:2,2:25.6:1:29.9:1:0.52544:1.28:59.7:46:0.0764:0:3.3 -6 29911011 . C T 170 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=42.8305;LSEQ=GGTCGGGGCTGGGCGGGGCT;RSEQ=GGGGGACTGGGCTGACCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1015:2:0,2:645,367:0.002:2,0:1:0:25.5:1:0.1322:0:60:4:0.002:0:3 0/1:666:52:35,17:387,227:0.0781:2,2:25.6:1:29.9:1:0.65327:1.21:60:104:0.0795:0:3.1 -6 29911019 . T C 222 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=416.8475;LSEQ=CTGGGCGGGGCTCGGGGGAC;RSEQ=GGGCTGACCGCGGGGTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1136:1:0,1:707,428:9e-04:2,0:46:0:28:0:0.37764:0:48:2:9e-04:0:7 0/1:778:208:122,86:355,212:0.2674:2,2:24.5:1:28.9:1:0.31871:1.18014:55.2:40.6:0.2647:0:5.8 -6 29911029 . G T 155 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.47862;LSEQ=CTCGGGGGACTGGGCTGACC;RSEQ=CGGGGTCGGGGCCAGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1289:4:1,3:757,528:0.0031:2,2:2:1:26.3:1:0.31207:4.29646:60:3:0.0024:0:1.3 0/1:900:49:27,22:498,353:0.0544:2,2:23.2:1:27.7:1:0.65694:1.14933:53.7:11.25:0.0509:0:5.9 -6 29911030 . C T 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.29444;LSEQ=TCGGGGGACTGGGCTGACCG;RSEQ=GGGGTCGGGGCCAGGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1301:502:305,197:458,338:0.3859:2,2:24.8:1:29.4:1:0.27136:1.14:59.7:44.636:0.386:0:3.1 0/1:910:142:91,51:439,329:0.156:2,2:22.5:1:28.8:1:0.13849:1.34:59.6:34.5:0.1563:0:3.3 -6 29911037 . G C 234 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=234.79773;LSEQ=ACTGGGCTGACCGCGGGGTC;RSEQ=GGGCCAGGTTCTCACACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1400:2:1,1:801,594:0.0014:2,2:20:1:28.5:1:1:1.34818:48.5:4:0.0015:0:5.5 0/1:1001:252:137,115:436,307:0.2517:2,2:26.8:1:29.4:1:0.2386:1.19192:56:125:0.253:0:6 -6 29911056 . A G 234 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=89.17188;LSEQ=CGGGGCCAGGTTCTCACACC;RSEQ=TCCAGATAATGTATGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1602:4:2,2:853,743:0.0025:2,2:20.3:1:25:1:1:1.14795:57:3:0.0019:0:5.5 0/1:1264:231:117,114:524,448:0.1828:2,2:26.8:1:29.9:1:0.37956:1.13953:56.9:76:0.1831:0:6.3 -6 29911063 . TA GG 250 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=86.26842;LSEQ=AGGTTCTCACACCATCCAGA;RSEQ=ATGTATGGCTGCGACGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1669:5:2,3:857,804:0.003:2,2:20.4:1:31.6:1:0.67796:1.59842:53.4:10:0.0031:0:4.6 0/1:1324:273:134,139:544,498:0.2062:2,2:28.2:1:31:1:0.3768:1.13302:56.4:546:0.2078:0.0053:5.3 -6 29911064 . A G 294 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42183;LSEQ=GGTTCTCACACCATCCAGAT;RSEQ=ATGTATGGCTGCGACGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1697:664:337,327:537,490:0.3913:2,2:25.5:1:31.4:1:0.55011:1.06334:60:54.333:0.3921:0:2.8 0/1:1327:283:153,130:399,373:0.2133:2,2:25.2:1:31.1:1:0.53132:1.10:59.8:282:0.2678:0:3.4 -6 29911069 . A T 177 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=41.01866;LSEQ=TCACACCATCCAGATAATGT;RSEQ=TGGCTGCGACGTGGGGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1752:2:0,2:887,863:0.0011:2,0:1:0:26:0:0.24362:0:60:4:0.0012:0:2 0/1:1385:62:30,32:677,646:0.0448:2,2:26.4:1:29.8:1:0.69804:1.11776:60:61:0.0447:0:4.8 -6 29911086 . T C 272 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=122.40851;LSEQ=TGTATGGCTGCGACGTGGGG;RSEQ=CGGACGGGCGCTTCCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1745:6:4,2:850,886:0.0034:2,2:24.7:1:32.7:1:0.44373:2.08:56.5:12:0.0035:0:1.7 0/1:1409:419:204,215:480,507:0.2974:2,2:26.6:1:31.3:1:1:1.00:58.9:68.833:0.2969:0:2.3 -6 29911092 . G T 240 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=95.27868;LSEQ=GCTGCGACGTGGGGTCGGAC;RSEQ=GGCGCTTCCTCCGCGGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1718:4:1,3:844,865:0.0023:2,2:23.3:1:28:1:0.6247:2.92572:60:8:0.0024:0:4 0/1:1378:251:116,135:542,583:0.1821:2,2:22.5:1:30.2:1:0.57711:1.08187:59.8:82.667:0.182:0:5.2 -6 29911098 . T C 179 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.91695;LSEQ=ACGTGGGGTCGGACGGGCGC;RSEQ=TCCTCCGCGGGTACCGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1659:3:1,2:819,837:0.0018:2,2:22.7:1:19.3:1:1:1.95622:60:0.5:6e-04:0:4 0/1:1342:58:29,29:610,673:0.0432:2,2:26.9:1:30.7:1:0.78846:1.10:57.1:57:0.0431:0:4.4 -6 29911112 . CCGG TGAA 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCGCTTCCTCCGCGGGTA;RSEQ=CAGGACGCCTACGACGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1536:0:0,0:754,780:0:2,0:25.8:1:31.5:1:1:0:60:68.727:0.9993:0:1 0/1:1215:38:14,24:552,623:0.0313:2,2:17.2:1:29:1:0.24934:1.5184:49.4:76:0.0317:0.0206:1 -6 29911114 . G A 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.59893;LSEQ=GCGCTTCCTCCGCGGGTACC;RSEQ=GCAGGACGCCTACGACGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1504:446:205,241:537,516:0.2965:2,2:27.3:1:30.5:1:0.07991:1.22328:60:48.556:0.2959:0:2.5 0/1:1161:234:113,121:314,352:0.2016:2,2:23.5:1:29.9:1:0.81946:1.05:59.8:45.8:0.2027:0:3.2 -6 29911119 . G T 222 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=178.95463;LSEQ=TCCTCCGCGGGTACCGGCAG;RSEQ=ACGCCTACGACGGCAAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1479:2:1,1:713,763:0.0014:2,2:28.5:1:29.5:1:1:1.07:60:4:0.0014:0:5 0/1:1101:215:100,115:405,464:0.1953:2,2:28.2:1:28.7:1:1:1.00377:58:106.5:0.1951:0:4.6 -6 29911124 . C T 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCGGGTACCGGCAGGACGC;RSEQ=TACGACGGCAAGGATTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1443:0:0,0:694,744:0:2,0:25.4:1:31.4:1:1:0:60:50.357:0.9979:0:0.9 0/1:1077:53:26,27:470,553:0.0492:2,2:22.7:1:30.3:1:0.67392:1.13:59.9:106:0.0498:0:3.7 -6 29911149 . C T 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39496;LSEQ=ACGGCAAGGATTACATCGCC;RSEQ=TGAACGAGGACCTGCGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1207:450:204,246:355,401:0.3728:2,2:23.4:1:30.4:1:0.59157:1.06747:59:63.286:0.3732:0:2.5 0/1:826:157:66,91:297,371:0.1901:2,2:23.7:1:30.3:1:0.59324:1.10363:58.7:156:0.1907:0:2.7 -6 29911154 . C A 224 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=86.44228;LSEQ=AAGGATTACATCGCCCTGAA;RSEQ=GAGGACCTGCGCTCTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1172:4:3,1:544,623:0.0034:2,2:16.5:1:29:1:0.34479:3.43:60:8:0.0035:0:1.3 0/1:799:183:86,97:264,351:0.229:2,2:21.1:1:29.9:1:0.35107:1.18:55.5:44.75:0.2272:0:4.3 -6 29911190 . G A 236 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGACCGCGGCGGACATGGC;RSEQ=GCTCAGATCACCAAGCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1053:0:0,0:479,574:0:2,0:24.2:1:30.1:1:1:0:58.6:60.941:1:0:1.2 0/1:645:222:94,128:193,230:0.3442:2,2:24.6:1:30.3:1:0.45336:1.14241:51.1:73:0.3422:0:4 -6 29911198 . T C 213 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCGGACATGGCGGCTCAGA;RSEQ=CACCAAGCGCAAGTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1037:0:0,0:464,572:0:2,0:25.1:1:30.1:1:1:0:58.3:42.167:1:0:1.2 0/1:622:136:62,74:214,271:0.2186:2,2:23.9:1:30.1:1:0.7704:1.06:54.6:26.2:0.2165:0:4.9 -6 29911203 . A C 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0023;SOR=0.70728;LSEQ=ACATGGCGGCTCAGATCACC;RSEQ=AGCGCAAGTGGGAGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1054:330:147,183:330,394:0.3131:2,2:26.1:1:31.5:1:0.78964:1.04266:53.9:164:0.3157:0:3.5 0/1:640:156:67,89:225,259:0.2438:2,2:25.1:1:30.3:1:0.46065:1.15372:51.7:38:0.2424:0:3.7 -6 29911207 . G A 210 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=104.30919;LSEQ=GGCGGCTCAGATCACCAAGC;RSEQ=CAAGTGGGAGGCGGCCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1038:3:1,2:466,569:0.0029:2,2:9.7:1:23.7:1:1:1.63721:60:2:0.002:0:1 0/1:627:146:71,75:215,264:0.2329:2,2:24.8:1:29.3:1:0.4486:1.16:56.2:292:0.2362:0:4.7 -6 29911218 . G A 148 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=66.16129;LSEQ=TCACCAAGCGCAAGTGGGAG;RSEQ=CGGCCCATGAGGCGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1070:1:1,0:468,598:9e-04:2,0:3:0:17:0:0.43955:0:60:0:0:0:2 0/1:633:37:16,21:278,318:0.0585:2,2:28:1:28.5:1:0.73627:1.14716:52.2:36:0.0584:0:4.3 -6 29911222 . C T 135 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGCGCAAGTGGGAGGCGG;RSEQ=CCATGAGGCGGAGCAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1072:0:0,0:469,602:0:2,0:25.5:1:31.2:1:1:0:57.1:35.931:0.999:0:1.2 0/1:644:25:9,16:289,330:0.0388:2,2:21.6:1:29.2:1:0.31464:1.55586:44.4:50:0.0396:0:4.5 -6 29911225 . A G 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.46831;LSEQ=GCGCAAGTGGGAGGCGGCCC;RSEQ=TGAGGCGGAGCAGTTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1060:288:116,172:355,417:0.2717:2,2:27.3:1:31:1:0.10995:1.26202:50.4:287:0.2739:0:3.8 0/1:639:95:39,56:252,292:0.1487:2,2:25.7:1:29.9:1:0.37265:1.23878:47.1:46.5:0.1498:0:4 -6 29911227 . GA TG 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAAGTGGGAGGCGGCCCAT;RSEQ=GGCGGAGCAGTTGAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1056:0:0,0:467,587:0:2,0:25.9:1:31.6:1:1:0:57.1:69.267:1:0:1.2 0/1:637:16:8,8:279,340:0.0251:2,2:34.6:1:31:1:0.801:1.22:41.8:32:0.0256:0:3.8 -6 29911228 . A T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.04168;LSEQ=CAAGTGGGAGGCGGCCCATG;RSEQ=GGCGGAGCAGTTGAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1049:283:113,170:355,411:0.2698:2,2:27.2:1:29.9:1:0.06892:1.29911:50.4:140.5:0.2718:0:3.7 1/0:631:334:147,187:103,121:0.5293:2,2:25.8:1:29.4:1:0.6648:1.08271:55.5:54.667:0.5458:0:3.9 -6 29911239 . TT CA 222 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=15.98235;LSEQ=CGGCCCATGAGGCGGAGCAG;RSEQ=GAGAGCCTACCTGGATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1052:19:18,1:446,586:0.0181:2,1:21.4:1:32.2:1:0:23.60:37.7:38:0.0182:0.0019:4.1 0/1:620:141:67,74:205,256:0.2274:2,2:23.3:1:31.2:1:0.56218:1.13:52.3:282:0.23:0.0145:3.1 -6 29911240 . T G 158 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=35.29084;LSEQ=GGCCCATGAGGCGGAGCAGT;RSEQ=GAGAGCCTACCTGGATGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1055:2:1,1:445,586:0.0019:2,2:32.5:1:33:0:1:1.32:43:4:0.002:0:4 0/1:604:38:16,22:186,231:0.0629:2,2:22.7:1:30.2:1:0.86508:1.10687:50.8:76:0.0839:0:4.6 -6 29911246 . C T 112 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGGCGGAGCAGTTGAGAG;RSEQ=CTACCTGGATGGCACGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1036:0:0,0:451,584:0:2,0:25.2:1:31.2:1:1:0:57:35.964:0.999:0:1.1 0/1:629:18:6,12:274,337:0.0286:2,2:8.9:1:26.9:1:0.47146:1.6249:46.4:36:0.0292:0:5.4 -6 29911256 . T G 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.20039;LSEQ=CAGTTGAGAGCCTACCTGGA;RSEQ=GGCACGTGCGTGGAGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:979:295:119,176:286,394:0.3013:2,2:24.1:1:31:1:0.62137:1.07347:49.5:48.167:0.3014:0:3.2 1/0:588:379:166,213:89,119:0.6446:2,2:24.1:1:30.6:1:0.86188:1.04:51.8:74.8:0.6493:0:3.6 -6 29911260 . AC CG 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGAGCCTACCTGGATGGC;RSEQ=GTGCGTGGAGTGGCTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:964:0:0,0:402,562:0:2,0:25.3:1:29.8:1:1:0:56.7:159.667:1:0:1 0/1:578:57:17,40:224,295:0.0986:2,2:23.8:1:29.3:1:0.06536:1.78492:48.6:114:0.1004:0.0121:3.7 -6 29911261 . C G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3854;SOR=1.53876;LSEQ=GAGAGCCTACCTGGATGGCA;RSEQ=GTGCGTGGAGTGGCTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:949:12:10,2:383,550:0.0126:2,2:28.1:1:32.2:1:0.00527:7.17:37.5:24:0.0129:0:6 0/1:569:11:4,7:221,287:0.0193:2,2:31.1:1:23.9:1:0.76373:1.3468:42.3:2.667:0.0157:0:4.7 -6 29911271 . GT CG 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGATGGCACGTGCGTGGA;RSEQ=GGCTCCGCAGATACCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:889:0:0,0:357,529:0:2,0:25.6:1:31.7:1:1:0:56.5:45.632:0.9966:0:1 0/1:538:29:11,18:207,301:0.0539:2,2:23:1:29.5:1:0.8473:1.12513:52.8:58:0.0545:0.0074:3.5 -6 29911272 . T A 126 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00658;SOR=0.2128;LSEQ=TGGATGGCACGTGCGTGGAG;RSEQ=GGCTCCGCAGATACCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:887:23:13,10:343,519:0.0259:2,2:22.3:1:27.9:1:0.13145:1.97:44.1:10.5:0.0241:0:5.2 0/0:533:3:0,3:205,300:0.0056:2,0:23.7:1:28.3:1:0.27649:0:33.7:6:0.006:0:6 -6 29911296 . G A 154 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=61.55006;LSEQ=TCCGCAGATACCTGGAGAAC;RSEQ=GGAAGGAGACGCTGCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:664:1:1,0:220,443:0.0015:2,0:1:0:29:0:0.33283:0:60:2:0.0015:0:1 0/1:434:37:14,23:141,256:0.0853:2,2:31:1:29.6:1:0.85793:1.10:51.1:74:0.086:0:3.7 -6 29911306 . C T 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGAGAACGGGAAGGAGA;RSEQ=GCTGCAGCGCACGGGTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:186,417:0:2,0:24.7:1:29.8:1:1:0:57.3:32.5:1:0:0.9 0/1:390:33:11,22:118,239:0.0846:2,2:31.2:1:28.9:1:1:1.01:52.6:66:0.0855:0:3.8 -6 29911307 . G A 150 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.20044;LSEQ=CTGGAGAACGGGAAGGAGAC;RSEQ=CTGCAGCGCACGGGTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:594:37:14,23:166,390:0.0623:2,2:29:1:28.9:1:0.35574:1.43:50.1:74:0.064:0:4.4 0/1:381:5:0,5:126,250:0.0131:2,0:36.8:1:29.4:1:0.17547:0:44.2:10:0.0134:0:4.8 -6 29911319 . G T 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00076;SOR=1.83377;LSEQ=AAGGAGACGCTGCAGCGCAC;RSEQ=GGTACCAGGGGCCACGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:73:21,52:115,315:0.1451:2,2:29.1:1:29.8:1:0.77575:1.11:51.6:35.5:0.144:0:3.4 0/1:341:81:22,59:73,182:0.2375:2,2:25.8:1:29.9:1:0.88764:1.07546:51.7:162:0.2382:0:3.3 -6 29911326 . A G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.59975;SOR=0.77723;LSEQ=CGCTGCAGCGCACGGGTACC;RSEQ=GGGGCCACGGGGCGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:24:8,16:97,335:0.0526:2,2:18.9:1:29.6:1:0.21865:1.72:59.4:23:0.0509:0:1.9 0/1:290:12:6,6:72,206:0.0414:2,2:17.3:1:28.5:1:0.09192:2.85:60:24:0.0417:0:2.1 -6 29911329 . G A 156 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00018;SOR=0.20347;LSEQ=TGCAGCGCACGGGTACCAGG;RSEQ=GCCACGGGGCGCCTCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:35:9,26:78,313:0.0822:2,2:30.5:1:30.5:1:0.38919:1.39:51.4:34:0.0817:0:4.4 0/1:280:5:0,5:73,202:0.0179:2,0:30.2:1:29.4:1:0.33124:0:44.2:4:0.0144:0:4.8 -6 29911344 . C A 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00033;SOR=Inf;LSEQ=CCAGGGGCCACGGGGCGCCT;RSEQ=CCTGATCGCCTGTAGATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:43,280:0:2,0:24:1:30.8:1:1:0:58.8:34.889:1:0:0.8 0/1:191:8:0,8:30,145:0.0419:2,0:26:1:29.9:1:0.35678:0:60:16:0.0419:0:2.8 -6 29911360 . A G 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00088;SOR=Inf;LSEQ=GCCTCCCTGATCGCCTGTAG;RSEQ=TCTCCCGGGCTGGCCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:6,221:0:1,0:25.8:1:31:1:1:0:59.1:44.4:1:0:0.8 0/1:134:7:0,7:15,112:0.0522:2,0:23.1:1:27.9:1:1:0:60:6:0.0462:0:2.4 -6 29911365 . C G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.13252;SOR=Inf;LSEQ=CCTGATCGCCTGTAGATCTC;RSEQ=CGGGCTGGCCTCCCACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:5,209:0:1,0:24.8:1:31.3:1:1:0:59.2:52.5:1:0:0.8 0/1:123:2:0,2:14,107:0.0163:2,0:10:1:33.5:1:1:0:51.5:4:0.0164:0:4 -6 29911367 . G A 128 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00576;SOR=2.92757;LSEQ=TGATCGCCTGTAGATCTCCC;RSEQ=GGCTGGCCTCCCACAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:13:0,13:3,192:0.0625:1,1:30.2:1:32.2:1:1:0:55.9:26:0.0637:0:3.8 0/1:116:19:2,17:10,87:0.1638:2,2:25.9:1:30.3:1:1:1.02:52.9:38:0.1696:0:4.4 -6 29911388 . G A 132 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22567;SOR=1.64325;LSEQ=GGCTGGCCTCCCACAAGGAG;RSEQ=GGAGACAATTGGGACCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:17:0,17:4,123:0.1172:1,1:21.5:1:32.4:1:1:0:52.7:34:0.1197:0:4.2 0/1:78:14:1,13:8,56:0.1795:2,1:26.2:1:31.6:1:1:1.84476:50.5:28:0.1795:0:4.6 -6 29911396 . AT GA 133 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0013;SOR=3.53164;LSEQ=TCCCACAAGGAGGGGAGACA;RSEQ=TGGGACCAACACTAGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:13:0,13:3,108:0.1048:1,1:18.2:1:32.2:1:1:0:50.5:26:0.1048:0.0161:3.5 0/1:68:20:2,18:7,41:0.2941:2,2:21.6:1:30.9:1:1:1.52757:48.4:40:0.2941:0.0147:3.1 -6 29911419 . A G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00509;SOR=4.36716;LSEQ=GGGACCAACACTAGAATATC;RSEQ=CCCTCCCTCTGGTCCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:8:0,8:4,67:0.1013:2,0:26:1:32.9:1:1:0:55.3:16:0.1053:0:1.1 0/1:33:11:2,9:1,21:0.3333:1,2:20.7:1:31.8:1:0.25202:4.43:58.2:22:0.3333:0:1.5 -6 29911444 . G A 62 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03035;SOR=7.13949;LSEQ=CCCTCTGGTCCTGAGGGAGA;RSEQ=GAATCCTCCTGGGTTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:0,2:5,54:0.0328:2,0:18.5:1:26.5:1:1:0:40:4:0.0339:0:2 0/1:20:4:0,4:0,16:0.2:1,0:16.8:1:31:1:1:0:38:8:0.2:0:3.8 -6 29911457 . G GT 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0163;SOR=5.04122;LSEQ=AGGGAGAGGAATCCTCCTGG;RSEQ=TTCCAGATCCTGTACCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:12:0,12:5,34:0.2353:2,0:33.8:1:30.8:1:0.32305:0:51.1:24:0.2449:0:0.8 1/0:13:8:0,8:0,5:0.6154:0,0:31:1:30.1:1:1:0:53.9:16:0.6154:0:1.1 -6 29911495 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTGACTCTGAGGTTCC;RSEQ=CCCTGCTCTCTGACACAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:0,2:2,26:0.0667:2,0:30.5:1:31.5:1:1:0:40:4:0.0667:0:2 0/0:8:0:0,0:0,8:0:0,0:26.5:1:33.3:1:1:0:60:16:1:0:0.6 -6 29911505 . C G 53 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=1.10712;LSEQ=CTGAGGTTCCGCCCTGCTCT;RSEQ=TGACACAATTAAGGGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:2,18:0.1304:2,0:19.3:1:34:0:1:0:48.7:6:0.1429:0:1.3 0/1:7:1:0,1:1,4:0.1429:2,0:9:0:32:0:1:0:60:2:0.1667:0:1 -6 29911538 . G A 30 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42308;SOR=3.87298;LSEQ=GGGATAAAATCTCTGAAGGA;RSEQ=TGACGGGAAGACGATCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:3,6:0.1818:2,0:36.5:1:30.5:1:1:0:55:4:0.2:0:1.5 1/0:2:1:0,1:1,0:0.5:0,0:5:0:30:0:1:0:60:2:0.5:0:1 -6 29911583 . G GACAC 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTGATGAGTGGTTCCCTTT;RSEQ=ACACCGGCAGCAGCCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:8,2:0.2857:2,2:20.8:1:32.2:1:0.09491:9.51263:51.5:8:0.3077:0.0714:0.8 0/0:1:0:0,0:1,0:0:0,0:19:0:27:0:1:0:60:2:1:0:0 -6 29911684 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=GAGTCCAGCACTTCTGAGTC;RSEQ=CTCAGCCTCCACTCAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:34,2:0:2,0:25.5:1:30.7:1:1:0:56.9:35:1:0:0 1/0:6:4:3,1:1,1:0.6667:2,2:25.5:1:31.5:1:1:2.45:56:8:0.6667:0:1.8 -6 29911740 . A G 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55011;SOR=0;LSEQ=GTTCCCTTCTCAGGGAATAG;RSEQ=AGATTATCCCAGGTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:3,0:71,3:0.039:1,0:7.7:1:32:0:1:0:39.7:6:0.039:0:4 0/0:36:0:0,0:36,0:0:1,0:21:1:29.2:1:1:0:60:35:1:0:0.1 -6 29911790 . T C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16837;SOR=0.52378;LSEQ=GGTGTCTGGGTTCTGTGCTC;RSEQ=CTTCCCCATCCCGGGTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:22:22,0:155,6:0.1202:1,1:30.8:1:31.1:1:1:0:43.1:21:0.1167:0:5.4 0/1:120:8:8,0:108,4:0.0667:1,0:20.8:1:29.4:1:1:0:39.1:7:0.0593:0:5 -6 29911799 . T C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06938;SOR=Inf;LSEQ=GTTCTGTGCTCTCTTCCCCA;RSEQ=CCCGGGTGTCCTGTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:199,6:0:1,0:26.3:1:31:1:1:0:57.8:50.25:1:0:0.8 0/1:144:3:3,0:135,5:0.0208:1,0:9.7:1:31.7:1:1:0:23:6:0.0216:0:3.7 -6 29911803 . G A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.73641;SOR=0.83651;LSEQ=TGTGCTCTCTTCCCCATCCC;RSEQ=GGTGTCCTGTCCATTCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:26:26,0:192,8:0.115:1,1:31.3:1:31.2:1:0.60124:0:40.9:52:0.1161:0:5.3 0/1:153:15:15,0:133,5:0.098:1,1:19.9:1:30.5:1:1:0:40.7:30:0.098:0:4.5 -6 29911806 . T C 125 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=13.54358;LSEQ=GCTCTCTTCCCCATCCCGGG;RSEQ=GTCCTGTCCATTCTCAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:2:2,0:229,13:0.0082:2,0:4.5:1:31.5:1:1:0:36.5:4:0.0083:0:1.5 0/1:178:18:17,1:153,7:0.1011:1,1:5.3:1:30.1:1:0.58152:1.28373:44.1:17:0.0971:0:2 -6 29911815 . C A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10443;SOR=Inf;LSEQ=CCCATCCCGGGTGTCCTGTC;RSEQ=ATTCTCAAGATGGCCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:252,30:0:2,0:24:1:31:1:1:0:56.6:55.4:1:0:0.8 0/1:252:3:3,0:218,30:0.0119:2,0:6.3:1:30.7:1:1:0:45:6:0.0121:0:1 -6 29911827 . G A 150 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=0.32405;LSEQ=GTCCTGTCCATTCTCAAGAT;RSEQ=GCCACATGCGTGCTGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:38:35,3:254,78:0.1027:2,2:22.9:1:28.6:1:0.03603:3.57:38.9:76:0.105:0:6.2 0/1:364:13:13,0:265,83:0.0357:2,1:27.6:1:28.3:1:0.04509:0:40.8:26:0.0363:0:6.1 -6 29911836 . C T 170 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.37058;LSEQ=ATTCTCAAGATGGCCACATG;RSEQ=GTGCTGGTGGAGTGTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:54:42,12:288,120:0.1169:2,2:17.5:1:29.6:1:0.33666:1.46:34.6:53:0.117:0:6.9 0/1:471:22:18,4:315,134:0.0467:2,2:24.3:1:29.2:1:0.33804:1.91:41.3:44:0.0474:0:5.5 -6 29911837 . G A 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=23.79267;LSEQ=TTCTCAAGATGGCCACATGC;RSEQ=TGCTGGTGGAGTGTCCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:1:0,1:345,138:0.0021:2,0:23:0:13:0:0.28719:0:60:0:0:0:3 0/1:490:23:18,5:328,138:0.0469:2,2:20.6:1:29.3:1:0.48984:1.51:59.5:46:0.0476:0:1 -6 29911844 . T A 182 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20923;LSEQ=GATGGCCACATGCGTGCTGG;RSEQ=GGAGTGTCCCATGACAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:565:71:52,19:333,161:0.1257:2,2:17.3:1:29.6:1:0.34423:1.32:34.5:34.5:0.1259:0:6.6 0/1:583:17:15,2:368,198:0.0292:2,2:26.5:1:28.5:1:0.06647:4.03:36.2:16:0.0281:0:6.7 -6 29911857 . G T 176 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1765;LSEQ=GTGCTGGTGGAGTGTCCCAT;RSEQ=ACAGATGCAAAATGCCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:66:42,24:389,237:0.0954:2,2:22.6:1:29.2:1:0.89404:1.07:36.2:132:0.0968:0:6.8 0/1:767:14:9,5:462,291:0.0183:2,2:22.4:1:25.4:1:1:1.13:42.7:6:0.016:0:5.1 -6 29911879 . T G 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.15621;LSEQ=CAGATGCAAAATGCCTGAAT;RSEQ=TTCTGACTCTTCCCGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:950:90:51,39:487,372:0.0947:2,2:30.2:1:31.9:1:1:1.00111:38.3:44:0.094:0:7.3 0/1:1182:19:14,5:651,511:0.0161:2,2:25.7:1:29.7:1:0.16232:2.20:37.8:38:0.0162:0:7.5 -6 29911893 . C T 254 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.86601;LSEQ=CTGAATTTTCTGACTCTTCC;RSEQ=GTCAGACCCCCCCAAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1128:105:49,56:553,469:0.0931:2,2:25.9:1:30.5:1:0.15153:1.34718:40.2:210:0.094:0:7.2 0/1:1403:319:182,137:588,496:0.2274:2,2:25.9:1:30.6:1:0.40544:1.12:52.1:318:0.2293:0:1.7 -6 29911895 . T A 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17377;LSEQ=GAATTTTCTGACTCTTCCCG;RSEQ=CAGACCCCCCCAAGACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1159:99:47,52:576,484:0.0854:2,2:26.9:1:29.8:1:0.20652:1.31636:39.7:98:0.0858:0:7.6 0/1:1441:23:11,12:772,644:0.016:2,2:21.7:1:27.3:1:0.53475:1.30748:39.9:46:0.0163:0:7.9 -6 29911912 . A G 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.1783;LSEQ=CCGTCAGACCCCCCCAAGAC;RSEQ=CATATGACCCACCACCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1195:105:47,58:535,554:0.0879:2,2:23.9:1:30.7:1:0.41465:1.19154:39.3:51.5:0.0881:0:7.5 0/1:1422:24:10,14:688,710:0.0169:2,2:25.8:1:29.8:1:0.53944:1.35633:38.8:48:0.0172:0:7.8 -6 29911921 . C T 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.17872;LSEQ=CCCCCCAAGACACATATGAC;RSEQ=CACCACCCCATCTCTGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1131:95:37,58:495,539:0.084:2,2:24.2:1:30.3:1:0.10727:1.43914:40.8:94:0.0849:0:7.4 0/1:1303:21:7,14:617,662:0.0161:2,2:30.6:1:28.4:1:0.19315:1.86318:40.8:42:0.0164:0:7.8 -6 29911925 . C T 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.37295;LSEQ=CCAAGACACATATGACCCAC;RSEQ=ACCCCATCTCTGACCATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1090:113:56,57:452,524:0.1037:2,2:28:1:29.5:1:0.55057:1.14:50.3:112:0.1047:0:1.1 0/1:1258:52:25,27:564,640:0.0413:2,2:25.4:1:28.9:1:0.88788:1.05:50.7:104:0.0418:0:1.2 -6 29911928 . C G 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.23008;LSEQ=AGACACATATGACCCACCAC;RSEQ=CCATCTCTGACCATGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1027:59:19,40:457,509:0.0574:2,2:35.7:1:30.9:1:0.03072:1.88905:43.7:28.5:0.0563:0:7.5 0/1:1230:17:5,12:562,648:0.0138:2,2:37.6:1:30.8:1:0.22116:2.08026:43.1:34:0.0141:0:7.8 -6 29911930 . CA TG 182 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24086;LSEQ=ACACATATGACCCACCACCC;RSEQ=TCTCTGACCATGAGGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1011:57:18,39:442,508:0.0564:2,2:36.5:1:31.3:1:0.02887:1.88403:43.4:56:0.0561:0:6.6 0/1:1199:17:5,12:539,639:0.0142:2,2:38.1:1:30.5:1:0.22351:2.02325:43.1:34:0.0144:0:6.8 -6 29911951 . C T 143 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=31.25824;LSEQ=ATCTCTGACCATGAGGCCAC;RSEQ=CTGAGGTGCTGGGCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:798:1:0,1:325,469:0.0013:2,0:17:0:13:0:1:0:40:0:0:0:3 0/1:847:32:12,20:330,483:0.0378:2,2:25.9:1:28.7:1:0.85482:1.13851:45.6:31:0.0374:0:2.2 -6 29911957 . G A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.12598;LSEQ=GACCATGAGGCCACCCTGAG;RSEQ=TGCTGGGCCCTGGGCTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:729:3:3,0:283,441:0.0041:2,0:1:0:22:1:0.0605:0:56.7:2:0.0028:0:1.3 0/1:771:31:12,19:285,454:0.0402:2,2:23.3:1:28.5:1:1:1.01:45.4:30:0.0399:0:2.2 -6 29911970 . G A 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.31877;LSEQ=CCCTGAGGTGCTGGGCCCTG;RSEQ=GCTTCTACCCTGCGGAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:62:27,35:173,333:0.1088:2,2:23.4:1:30.4:1:0.15971:1.48:38:61:0.1099:0:3.9 0/1:588:22:10,12:184,381:0.0374:2,2:20.8:1:30.7:1:0.24822:1.72:36:44:0.0385:0:3.6 -6 29912041 . C T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.28876;SOR=1.48589;LSEQ=CAGACCCAGGACACGGAGCT;RSEQ=GTGGAGACCAGGCCTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:19:18,1:225,124:0.0516:2,1:22.9:1:30.7:1:0.00515:9.88:30.4:38:0.0523:0:2.6 0/1:227:17:13,4:124,86:0.0749:2,2:21.9:1:29.6:1:0.20143:2.25:36.1:7.5:0.0676:0:2.6 -6 29912068 . A G 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCAGGCCTGCAGGGGATGG;RSEQ=ACCTTCCAGAAGTGGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:0:0,0:409,116:0:2,0:22.9:1:30:1:1:0:36.7:57.333:1:0:0.9 0/1:308:20:18,2:217,70:0.0649:2,2:29.3:1:31.8:1:0.17864:2.90:34.3:40:0.0669:0:2.9 -6 29912087 . G T 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=0.58634;LSEQ=GAACCTTCCAGAAGTGGGCG;RSEQ=CTGTGGTGGTGCCTTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:723:330:273,57:263,127:0.4564:2,2:22.3:1:29.5:1:0:2.31:40:54:0.457:0:2.3 0/1:473:156:118,38:228,89:0.3298:2,2:20.8:1:28.5:1:0.44028:1.21:40:38:0.3312:0:2.3 -6 29912108 . G C 284 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.92324;SOR=1.00981;LSEQ=CTGTGGTGGTGCCTTCTGGA;RSEQ=AGGAGCAGAGATACACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1018:499:344,155:327,189:0.4902:2,2:23.6:1:31.7:1:0.06357:1.28:42.3:61.375:0.4895:0:2.1 0/1:745:367:236,131:237,141:0.4926:2,2:23.8:1:30.9:1:0.70359:1.07:42.7:121.333:0.4939:0:2.2 -6 29912147 . C T 229 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=106.69626;LSEQ=GCCATGTGCAGCATGAGGGT;RSEQ=TGCCCAAGCCCCTCACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1569:3:0,3:876,689:0.0019:2,0:1:0:26.3:1:0.08575:0:57:6:0.0019:0:2 0/1:1283:218:114,104:570,495:0.1699:2,2:28.4:1:29.5:1:0.76592:1.05049:48.7:42.6:0.1696:0:2.7 -6 29912149 . G C 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19471;LSEQ=CATGTGCAGCATGAGGGTCT;RSEQ=CCCAAGCCCCTCACCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1595:338:197,141:686,568:0.2119:2,2:26.8:1:31.1:1:0.24224:1.16:50.1:66.6:0.2117:0:2.4 0/1:1307:65:35,30:656,585:0.0497:2,2:25.5:1:31.2:1:0.89926:1.04:48.3:130:0.0506:0:2.5 -6 29912188 . T C 238 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATGGGGTAAGGAGGGAGA;RSEQ=GGGGGTGTCATGTCTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1609:0:0,0:778,830:0:2,0:25.9:1:30.1:1:1:0:54.7:46.294:1:0:0.9 0/1:1224:250:109,141:466,502:0.2042:2,2:23.5:1:30:1:0.20191:1.20063:53:82.333:0.2083:0:2.7 -6 29912204 . C T 286 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02012;SOR=0.83218;LSEQ=GAGATGGGGGTGTCATGTCT;RSEQ=TTAGGGAAAGCAGGAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1533:761:371,390:388,380:0.4964:2,2:24.8:1:29.9:1:0.50622:1.07329:57.4:53.357:0.4957:0:1.8 0/1:1114:502:236,266:298,307:0.4506:2,2:22.1:1:29.4:1:0.4689:1.09399:56.5:32.467:0.4497:0:2.2 -6 29912208 . G C 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGGTGTCATGTCTCTTA;RSEQ=GGAAAGCAGGAGCCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1519:0:0,0:741,778:0:2,0:24.1:1:31.3:1:1:0:57.9:53.25:1:0:1 0/1:1088:38:23,15:503,543:0.0349:2,2:23.5:1:29.5:1:0.14016:1.65:58.3:18:0.0337:0:2.3 -6 29912227 . TGGA T 275 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.05906;SOR=1.18364;LSEQ=AGGGAAAGCAGGAGCCTCTC;RSEQ=GACCTTTAGCAGGGTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1419:444:223,221:451,520:0.3129:2,2:23.9:1:31.3:1:0.18777:1.16:59.8:110:0.3127:0.0557:1.6 0/1:1005:352:174,178:312,337:0.3502:2,2:23.5:1:30.9:1:0.69155:1.06:59.7:351:0.3542:0.0657:1.8 -6 29912234 . C G 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.46149;LSEQ=GCAGGAGCCTCTCTGGAGAC;RSEQ=TTTAGCAGGGTCAGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1380:277:126,151:538,563:0.2007:2,2:23.6:1:31.2:1:0.34637:1.14508:59.9:554:0.2029:0:2.5 0/1:992:103:39,64:447,439:0.1038:2,2:22.1:1:30.6:1:0.01664:1.67006:60:102:0.1041:0:2.6 -6 29912268 . T C 121 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4354;SOR=1.42552;LSEQ=GGGCCCCTCACCTTCCCCTC;RSEQ=TTTCCCAGAGCTGTCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1464:13:7,6:706,745:0.0089:2,2:22.9:1:32.8:1:0.78504:1.23:43.6:26:0.0089:0:2.7 0/1:1110:14:7,7:569,525:0.0126:2,2:21.8:1:31.9:1:1:1.08371:40:28:0.0128:0:3.4 -6 29912280 . T C 290 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30595;SOR=0.92124;LSEQ=TTCCCCTCTTTTCCCAGAGC;RSEQ=GTCTTCCCAGCCCACCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1486:765:356,409:354,365:0.5148:2,2:26.5:1:30.3:1:0.29906:1.11417:58.5:126.5:0.517:0:3 0/1:1139:563:288,275:271,254:0.4943:2,2:26.4:1:29.8:1:0.90343:1.01876:58.1:69.375:0.4925:0:2.5 -6 29912297 . A G 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTGTCTTCCCAGCCCACC;RSEQ=TCCCCATCGTGGGCATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1448:0:0,0:680,765:0:2,0:25.3:1:30.1:1:1:0:59:39.139:1:0:1.8 0/1:1093:41:24,17:532,518:0.0375:2,2:25.8:1:29.6:1:0.34342:1.37:59.9:82:0.0384:0:2.2 -6 29912315 . A C 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.52794;LSEQ=CCATCCCCATCGTGGGCATC;RSEQ=TTGCTGGCCTGGTTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1336:213:83,130:527,590:0.1594:2,2:25.5:1:31.5:1:0.02956:1.39866:59.3:105.5:0.1616:0:3.9 0/1:1011:92:44,48:455,463:0.091:2,2:22.6:1:30.6:1:0.827:1.07195:58:29.667:0.0895:0:3.7 -6 29912326 . G A 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.40157;LSEQ=GTGGGCATCATTGCTGGCCT;RSEQ=GTTCTCCTTGGAGCTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1280:353:143,210:431,494:0.2758:2,2:24.2:1:29.4:1:0.05151:1.281:56.8:43.125:0.2747:0:4.9 0/1:988:131:56,75:429,427:0.1326:2,2:23.2:1:28.8:1:0.13316:1.34515:55.3:25.2:0.1296:0:5 -6 29912333 . C T 271 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.93151;SOR=1.00794;LSEQ=TCATTGCTGGCCTGGTTCTC;RSEQ=TTGGAGCTGTGATCACTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1280:524:200,324:357,397:0.4094:2,2:23.2:1:30:1:0.00131:1.45632:57.4:36.429:0.407:0:4.9 0/1:992:408:184,224:288,296:0.4113:2,2:23.1:1:30:1:0.19685:1.18428:58.1:407:0.4128:0:3.8 -6 29912342 . G A 137 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTGGTTCTCCTTGGAGCT;RSEQ=TGATCACTGGAGCTGTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1244:0:0,0:530,714:0:2,0:23.9:1:31.8:1:1:0:58.9:53.087:1:0:2.1 0/1:999:28:10,18:461,510:0.028:2,2:24.4:1:28.5:1:0.25236:1.62628:53.1:56:0.0283:0:6.5 -6 29912345 . A T 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35455;LSEQ=TGGTTCTCCTTGGAGCTGTG;RSEQ=TCACTGGAGCTGTGGTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1216:289:107,182:408,519:0.2377:2,2:23.3:1:29.9:1:0.04073:1.33683:55.6:95.333:0.2391:0:5.8 0/1:985:98:36,62:428,458:0.0995:2,2:24.2:1:29:1:0.03283:1.60864:55.3:48:0.0989:0:6.1 -6 29912348 . A G 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43358;LSEQ=TTCTCCTTGGAGCTGTGATC;RSEQ=CTGGAGCTGTGGTCGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1193:435:155,280:349,409:0.3646:2,2:23.8:1:31.2:1:0.00051:1.54087:57:71.5:0.3633:0:5.3 0/1:984:196:80,116:374,411:0.1992:2,2:25.9:1:29.8:1:0.09286:1.31909:57.1:20.778:0.194:0:5.1 -6 29912368 . C T 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00651;SOR=1.28433;LSEQ=ACTGGAGCTGTGGTCGCTGC;RSEQ=GTGATGTGGAGGAGGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1167:378:127,251:359,426:0.3239:2,2:24.1:1:30.4:1:8e-05:1.66479:57.4:62:0.3246:0:5.3 0/1:987:376:156,220:281,329:0.381:2,2:26.5:1:30.1:1:0.16622:1.20427:58:46:0.3786:0:3.7 -6 29912373 . T G 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.31846;LSEQ=AGCTGTGGTCGCTGCCGTGA;RSEQ=GTGGAGGAGGAAGAGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1137:233:76,157:401,503:0.2049:2,2:24.1:1:31.4:1:0.00134:1.64617:56.5:76.667:0.2066:0:6 0/1:976:74:23,51:406,496:0.0758:2,2:24.4:1:29.9:1:0.0208:1.81398:55.9:17.5:0.0731:0:6.1 -6 29912386 . G C 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGTGATGTGGAGGAGGAA;RSEQ=AGCTCAGGTGGAGAAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1136:0:0,0:461,674:0:2,0:25.2:1:31.6:1:1:0:59.5:69.938:0.9991:0:1.6 0/1:979:71:33,38:385,519:0.0725:2,2:26:1:31.8:1:0.53564:1.17:59.7:142:0.0733:0:2.1 -6 29912395 . T TGG 106 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=TGGAGGAGGAAGAGCTCAGG;RSEQ=GGAGAAGGGGTGAAGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1105:14:4,10:382,527:0.0127:2,2:15.1:1:27.9:1:0.41666:1.81105:51.2:28:0.0129:0.0072:6.4 0/0:944:0:0,0:380,502:0:2,0:24.7:1:29.2:1:1:0:59.5:66.846:0.9344:0:1.1 -6 29912398 . A GGT 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.34666;LSEQ=GGAGGAGGAAGAGCTCAGGT;RSEQ=GAAGGGGTGAAGGGTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1105:181:55,126:382,527:0.1638:2,2:27.5:1:31.2:1:0.00361:1.65983:57.8:362:0.1673:0.019:5.5 0/1:944:60:20,40:380,502:0.0636:2,2:24.8:1:30.3:1:0.17669:1.5133:55.5:120:0.0645:0.0117:5.6 -6 29912405 . G A 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0416;SOR=1.55961;LSEQ=AGAGCTCAGGTGGAGAAGGG;RSEQ=TGAAGGGTGGGGTCTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1030:40:13,27:395,595:0.0388:2,2:25.1:1:30.7:1:0.41123:1.37838:54.4:80:0.0395:0:6.5 0/1:877:52:15,37:349,473:0.0593:2,2:26.5:1:29.3:1:0.05955:1.81883:55.7:104:0.06:0:5.4 -6 29912410 . G A 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=82.09856;LSEQ=TCAGGTGGAGAAGGGGTGAA;RSEQ=GGTGGGGTCTGAGATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:975:1:1,0:382,591:0.001:2,0:1:0:25:0:0.39322:0:60:2:0.001:0:1 0/1:822:64:23,41:314,443:0.0779:2,2:24.7:1:30.2:1:0.42875:1.26317:60:63:0.0778:0:1.2 -6 29912413 . TG T 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.01146;SOR=0.74437;LSEQ=GGTGGAGAAGGGGTGAAGGG;RSEQ=GGGTCTGAGATTTCTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:926:237:73,164:287,400:0.2559:2,2:26.3:1:31.7:1:0.00328:1.61109:58.2:474:0.2596:0.0292:4.7 0/1:785:160:49,111:269,354:0.2038:2,2:25.2:1:30.4:1:0.00389:1.72021:57.8:159:0.2057:0.0204:4.3 -6 29912451 . C A 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25276;SOR=0.81949;LSEQ=GTCTCACTGAGGGTTCCAAG;RSEQ=CCCAGCTAGAAATGTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:529:120:24,96:140,268:0.2268:2,2:22.4:1:29.6:1:0.00338:2.08683:55.2:59:0.2282:0:5.3 0/1:387:75:15,60:108,204:0.1938:2,2:23.2:1:29.3:1:0.01837:2.11388:54.3:36.5:0.1947:0:5.4 -6 29912457 . C G 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09932;SOR=0.73646;LSEQ=CTGAGGGTTCCAAGCCCCAG;RSEQ=TAGAAATGTGCCCTGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:111:23,88:122,250:0.2293:2,2:20:1:31.4:1:0.01795:1.86488:54:54.5:0.2295:0:5.5 0/1:345:62:12,50:97,186:0.1797:2,2:24.2:1:31.3:1:0.02364:2.16851:53.2:124:0.1818:0:5.8 -6 29912463 . A G 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98536;LSEQ=GTTCCAAGCCCCAGCTAGAA;RSEQ=TGTGCCCTGTCTCATTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:58:8,50:114,267:0.1321:2,2:20.8:1:31.6:1:0.01124:2.66357:51.6:28:0.1299:0:6.2 0/1:322:42:6,36:88,192:0.1304:2,2:24.3:1:31.6:1:0.02782:2.74279:51:84:0.1308:0:6.3 -6 29912473 . T C 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.39095;SOR=0.82439;LSEQ=CCAGCTAGAAATGTGCCCTG;RSEQ=CTCATTACTGGGAAGCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:70:6,64:65,220:0.1961:2,2:21.4:1:31.1:1:0.00716:3.14346:48.8:69:0.1966:0:6.2 0/1:239:40:3,37:49,150:0.1674:2,2:24.4:1:31.6:1:0.01936:4.01157:48.2:80:0.1695:0:6.7 -6 29912477 . A G 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42518;SOR=0.81257;LSEQ=CTAGAAATGTGCCCTGTCTC;RSEQ=TTACTGGGAAGCACCGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:62:4,58:52,197:0.1994:2,2:22:1:31.6:1:0.00878:3.81513:47.1:61:0.1981:0:6.3 0/1:214:36:3,33:42,135:0.1682:2,2:24.2:1:31.8:1:0.04365:3.40712:47.5:72:0.1706:0:6.8 -6 29912493 . G A 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01202;SOR=1.88782;LSEQ=TCTCATTACTGGGAAGCACC;RSEQ=TCCACAATCATGGGCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:45:3,42:20,153:0.2055:2,2:21.8:1:30.9:1:0.42509:1.82574:43:90:0.2074:0:6.1 0/1:137:45:4,41:3,41:0.3285:2,2:26.6:1:30.4:1:1:1.33:51.5:90:0.3333:0:4.1 -6 29912502 . C T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97225;LSEQ=TGGGAAGCACCGTCCACAAT;RSEQ=ATGGGCCTACCCAGTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:41:3,38:9,145:0.2103:2,2:22.6:1:27.4:1:0.71845:1.27:43:19.5:0.2053:0:5.8 0/1:107:22:0,22:1,84:0.2056:1,1:18.3:1:28.2:1:1:0:41:44:0.2075:0:6.7 -6 29912510 . T G 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGTCCACAATCATGGGCC;RSEQ=ACCCAGTCTGGGCCCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:12,175:0:2,0:25.8:1:28.5:1:1:0:56.5:92.5:1:0:1.2 0/1:93:38:1,37:0,55:0.4086:1,1:26.9:1:31.2:1:0.4086:0:57.6:37:0.4022:0:3.2 -6 29912517 . T C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.47083;LSEQ=ACAATCATGGGCCTACCCAG;RSEQ=CTGGGCCCTGTGTGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:34:3,31:12,126:0.1977:2,2:24.8:1:30.9:1:1:1.02:43.8:16:0.1939:0:5.4 1/0:84:59:1,58:0,25:0.7024:1,1:24.6:1:31.5:1:1:0:54.3:118:0.7024:0:3.7 -6 29912562 . T G 48 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01561;SOR=Inf;LSEQ=CTCTTTTGTAAAGCACCTGT;RSEQ=AAAATGAAGGACAGATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:19,65:0:2,0:23.8:1:29.1:1:1:0:57.9:83:1:0:0.8 0/1:29:3:1,2:0,26:0.1034:1,2:28.7:1:30.7:1:0.10345:0:37.3:6:0.1034:0:5 -6 29912564 . A C 50 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01474;SOR=Inf;LSEQ=CTTTTGTAAAGCACCTGTTA;RSEQ=AATGAAGGACAGATTTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:21,59:0:2,0:24.2:1:30.4:1:1:0:58.1:39:1:0:0.8 0/1:27:3:1,2:0,24:0.1111:1,2:28:1:32:1:0.11111:0:37.3:6:0.12:0:5 -6 29912594 . C T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.029;SOR=3.51451;LSEQ=CAGATTTATCACCTTGATTA;RSEQ=GGCGGTGATGGGACCTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:12:8,4:31,28:0.169:2,2:21.3:1:30.7:1:0.52714:1.79:54.1:24:0.169:0:3.1 0/1:19:8:4,4:2,9:0.4211:2,2:15.5:1:30.8:1:0.31889:4.12:46.3:16:0.4444:0:4 -6 29912595 . G A 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00853;SOR=Inf;LSEQ=AGATTTATCACCTTGATTAC;RSEQ=GCGGTGATGGGACCTGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:41,29:0:2,0:21:1:30.4:1:1:0:58.3:69:1:0:1 0/1:19:3:2,1:4,12:0.1579:2,2:19.3:1:32.3:1:0.22188:5.36:60:6:0.1765:0:2 -6 29912649 . G C 71 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00152;SOR=Inf;LSEQ=TCACAGGGGAAGGTCCCTGA;RSEQ=GACAGACCTCAGGAGGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:72,13:0:2,0:26:1:32.2:1:1:0:56.8:84:1:0:1.3 0/1:34:5:3,2:27,2:0.1471:2,2:13.6:1:31:1:0.09391:8.07089:58.2:10:0.1563:0:4.6 -6 29912652 . CAGA C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.83886;LSEQ=CAGGGGAAGGTCCCTGAGGA;RSEQ=CCTCAGGAGGGCTATTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:9:8,1:49,9:0.0882:2,2:8.3:1:29.8:1:1:1.46:59.4:18:0.0891:0.0784:3.1 0/1:40:3:3,0:22,2:0.075:2,0:10.3:1:25.1:1:1:0:60:2:0.0513:0.05:3.7 -6 29912653 . AGACC CT 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.9222;LSEQ=AGGGGAAGGTCCCTGAGGAC;RSEQ=TCAGGAGGGCTATTGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:35:29,6:49,9:0.3431:2,2:23.1:1:31.9:1:1:1.12498:52:70:0.3465:0.0196:2.1 0/1:40:13:12,1:22,2:0.325:2,1:29.8:1:31.6:1:1:1.09:54.5:26:0.3333:0.025:2.3 -6 29912656 . C T 67 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0018;SOR=Inf;LSEQ=GGAAGGTCCCTGAGGACAGA;RSEQ=CTCAGGAGGGCTATTGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:60,11:0:2,0:21.3:1:31.5:1:1:0:59.9:70:1:0:0.6 0/1:30:5:3,2:25,0:0.1667:1,2:12.2:1:29:1:0.02299:0:58.2:10:0.1724:0:4.6 -6 29912657 . C T 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38388;SOR=0.46221;LSEQ=GAAGGTCCCTGAGGACAGAC;RSEQ=TCAGGAGGGCTATTGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:14:13,1:50,10:0.1892:2,1:6.1:1:29.1:1:0.67815:2.57:59.6:6:0.1714:0:3.2 0/1:31:3:3,0:26,2:0.0968:2,0:8:1:31:1:1:0:60:6:0.1:0:3.7 -6 29912668 . TA GG 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62804;SOR=0.82571;LSEQ=AGGACAGACCTCAGGAGGGC;RSEQ=TTGGTCCAGGACCCACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:59:52,7:61,10:0.447:2,2:18.9:1:31.1:1:0.79734:1.22:54.5:118:0.4609:0.0455:2.1 0/1:55:22:21,1:29,0:0.4:1,1:22.2:1:30.5:1:0.43137:0:56.8:44:0.4074:0.0364:2.1 -6 29912680 . A G 64 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00844;SOR=Inf;LSEQ=AGGAGGGCTATTGGTCCAGG;RSEQ=CCCACACCTGCTTTCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:135,11:0:2,0:22.7:1:29.9:1:1:0:57.8:35.5:1:0:1 0/1:65:4:3,1:59,2:0.0615:1,2:29.3:1:32.3:1:0.17605:9.06016:60:8:0.0625:0:5 -6 29912687 . C T 77 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00133;SOR=Inf;LSEQ=CTATTGGTCCAGGACCCACA;RSEQ=CTGCTTTCTTCATGTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:143,9:0:2,0:24.6:1:32:1:1:0:58.2:49.667:1:0:1 0/1:78:6:5,1:70,2:0.0769:1,2:22.5:1:30:1:0.21605:6.65592:60:12:0.0769:0:4 -6 29912713 . C T 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=TTCTTCATGTTTCCTGATCC;RSEQ=GCCCTGGGTCTGCAGTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:240,10:0:1,0:24.2:1:31.3:1:1:0:58.9:124:1:0:0.9 0/1:130:8:7,1:117,5:0.0615:1,2:25.8:1:31.1:1:0.32218:3.29347:60:16:0.062:0:3.3 -6 29912754 . G A 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03161;SOR=1.37877;LSEQ=CATTTCTGGAAACTTCTCTG;RSEQ=GGTCCAAGACTAGGAGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:172:123,49:287,83:0.3162:2,2:22.4:1:29.8:1:0.13321:1.37672:58.5:56.333:0.3177:0:2.5 0/1:321:125:93,32:141,53:0.3894:2,2:24.1:1:29.5:1:0.7958:1.09:59:250:0.3918:0:2.9 -6 29912766 . A T 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00305;SOR=1.49612;LSEQ=CTTCTCTGGGGTCCAAGACT;RSEQ=GGAGGTTCCTCTAGGACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:680:191:125,66:347,142:0.2809:2,2:25.2:1:29.4:1:0.16583:1.28972:56.4:46.75:0.2812:0:2.6 0/1:412:152:105,47:175,85:0.3689:2,2:25.6:1:29.8:1:0.74353:1.08:56.7:75:0.3704:0:3 -6 29912767 . G C 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00063;SOR=0.50225;LSEQ=TTCTCTGGGGTCCAAGACTA;RSEQ=GAGGTTCCTCTAGGACCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:109:79,30:395,179:0.1591:2,2:25.2:1:31.4:1:0.49714:1.19:57.3:218:0.1608:0:1.9 0/1:415:36:21,15:260,118:0.0867:2,2:24.7:1:27.4:1:0.19762:1.57204:56.9:8:0.0782:0:2 -6 29912796 . G A 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=83.2212;LSEQ=TCTAGGACCTTAAGGCCCTG;RSEQ=CTCCTTTCTGGTATCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:948:2:1,1:550,391:0.0021:2,2:10.5:1:29.5:1:1:1.40611:60:4:0.0022:0:1 0/1:640:96:61,35:321,221:0.15:2,2:28.2:1:29:1:0.49807:1.20:51.8:47:0.1497:0:3.7 -6 29912830 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.18101;LSEQ=TCTCACAGGACATTTTCTTC;RSEQ=CACAGATAGAAAAGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1088:289:117,172:447,352:0.2656:2,2:25.4:1:30.8:1:1e-05:1.86579:47.8:35.125:0.2658:0:3 1/0:837:504:258,246:179,151:0.6022:2,2:24:1:29.9:1:0.39576:1.13013:51:55:0.6015:0:2.4 -6 29912852 . T C 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.41223;LSEQ=ACAGATAGAAAAGGAGGGAG;RSEQ=TACACTCAGGCTGCAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1080:187:72,115:474,419:0.1731:2,2:22.3:1:31.9:1:0.00029:1.80586:40.3:36.4:0.1706:0:3.4 0/1:840:282:131,151:301,255:0.3357:2,2:25.1:1:31.2:1:0.0405:1.36008:40.9:55.4:0.3345:0:3.3 -6 29912856 . A T 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.70893;LSEQ=ATAGAAAAGGAGGGAGTTAC;RSEQ=CTCAGGCTGCAAGTAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1072:172:64,108:483,416:0.1604:2,2:22:1:30.4:1:8e-05:1.95808:38.7:56.333:0.1599:0:3.3 0/1:844:288:132,156:300,256:0.3412:2,2:25.5:1:29.4:1:0.02929:1.38439:41:71:0.3393:0:3.2 -6 29912918 . G A 157 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.13011;LSEQ=TCCTTGGGATATTGTGTTTG;RSEQ=GAGCCCATGGGGGAGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:942:38:34,4:461,443:0.0403:2,2:14.2:1:30:1:0:8.15:39.6:18:0.0388:0:6.2 0/0:736:4:3,1:357,375:0.0054:2,2:14:1:28.5:1:0.36343:3.15:40:8:0.0055:0:6 -6 29912923 . C A 166 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.17597;LSEQ=GGGATATTGTGTTTGGGAGC;RSEQ=CATGGGGGAGCCCACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:920:43:39,4:453,421:0.0467:2,2:17.3:1:30.6:1:0:9.05:39.7:86:0.0477:0:6 0/0:702:6:5,1:343,353:0.0085:2,2:13.2:1:30.2:1:0.12053:5.14:43.5:12:0.0087:0:5 -6 29912925 . A G 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21136;SOR=1.19553;LSEQ=GATATTGTGTTTGGGAGCCC;RSEQ=TGGGGGAGCCCACCCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:942:134:91,43:431,377:0.1423:2,2:20.1:1:30.7:1:0.00189:1.85:42:268:0.1435:0:3.5 0/1:701:116:60,56:292,291:0.1655:2,2:23.4:1:30.2:1:0.7613:1.07:44.3:115:0.1659:0:3.8 -6 29912927 . G T 171 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.15942;LSEQ=TATTGTGTTTGGGAGCCCAT;RSEQ=GGGGAGCCCACCCACCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:944:49:43,6:486,408:0.0519:2,2:19:1:30.6:1:0:6.01:40.9:48:0.0514:0:5.7 0/0:694:6:4,2:350,338:0.0086:2,2:16.5:1:29.7:1:0.68653:1.93:38:12:0.0087:0:5.5 -6 29912935 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.45816;LSEQ=TTGGGAGCCCATGGGGGAGC;RSEQ=CACCCACCTCACAATTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:938:209:150,59:380,347:0.2228:2,2:22.5:1:30.5:1:0:2.32:43.7:51.25:0.2243:0:3.9 1/0:644:439:237,202:95,110:0.6817:2,2:23.1:1:29.5:1:0.07581:1.36:47.2:32.769:0.6805:0:2.7 -6 29912938 . C A 140 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=37.8646;LSEQ=GGAGCCCATGGGGGAGCCCA;RSEQ=CCACCTCACAATTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:946:1:1,0:539,404:0.0011:2,0:1:0:29:0:1:0:60:2:0.0011:0:1 0/1:648:25:12,13:321,301:0.0386:2,2:23.9:1:30.2:1:0.83898:1.15506:47.1:50:0.0392:0:3.5 -6 29912944 . T C 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.50571;LSEQ=CATGGGGGAGCCCACCCACC;RSEQ=CACAATTCCTCCTCTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:952:256:177,79:366,329:0.2689:2,2:23.1:1:30.8:1:0:2.01:46.7:63:0.2692:0:3.7 1/0:660:442:242,200:96,119:0.6697:2,2:23.4:1:30.3:1:0.01598:1.50:48:62.143:0.6723:0:2.6 -6 29912961 . G T 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00093;SOR=0.55755;LSEQ=ACCTCACAATTCCTCCTCTA;RSEQ=CCACATCTTCTGTGGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1071:118:84,34:533,420:0.1102:2,2:24.3:1:30.4:1:0.00153:1.95:50.6:117:0.1107:0:3.7 0/1:759:49:30,19:379,331:0.0646:2,2:20.6:1:29.3:1:0.30349:1.38:51.8:48:0.0643:0:2.6 -6 29912968 . C G 173 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATTCCTCCTCTAGCCACAT;RSEQ=TTCTGTGGGATCTGACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1100:0:0,0:636,462:0:2,0:24.3:1:31.6:1:1:0:56.9:108.8:0.9982:0:1.2 0/1:797:50:28,22:413,333:0.0627:2,2:20.7:1:30.8:1:1:1.03:51.9:49:0.0625:0:4 -6 29913001 . T C 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.57851;LSEQ=TGACCAGGTTCTGTTTTTGT;RSEQ=CTACCCCAGGCAGTGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1387:330:202,128:583,474:0.2379:2,2:25.7:1:31.2:1:0.05637:1.28:55.7:109:0.2387:0:4.1 0/1:1033:158:85,73:492,382:0.153:2,2:23.3:1:30.1:1:0.60161:1.10602:54.1:18.75:0.1482:0:4.3 -6 29913007 . C T 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTCTGTTTTTGTTCTACC;RSEQ=CAGGCAGTGACAGTGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1450:0:0,0:819,630:0:2,0:25:1:31:1:1:0:58.6:62:0.9993:0:1.6 0/1:1065:48:29,19:572,445:0.0451:2,2:24.8:1:30.1:1:0.65568:1.19:57.7:96:0.0454:0:3 -6 29913037 . G A 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.53256;LSEQ=ACAGTGCCCAGGGCTCTGAT;RSEQ=TGTCCCTCACAGCTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1820:490:268,222:684,645:0.2692:2,2:24.1:1:29.5:1:0.22415:1.14:59.2:121.5:0.2705:0:5.1 0/1:1311:215:109,106:593,501:0.164:2,2:24.6:1:28.7:1:0.36961:1.15093:59.7:214:0.1645:0:5.2 -6 29913042 . C T 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.18939;LSEQ=GCCCAGGGCTCTGATGTGTC;RSEQ=CTCACAGCTTGTAAAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1845:773:412,361:545,526:0.419:2,2:24.7:1:30.4:1:0.32136:1.10:59.2:50.533:0.4172:0:4.9 1/0:1340:934:497,437:217,189:0.697:2,2:24.6:1:29.7:1:0.95254:1.00953:59.7:61.267:0.6946:0:3.6 -6 29913067 . T C 301 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.97152;SOR=0.99666;LSEQ=CAGCTTGTAAAGGTGAGAGC;RSEQ=TGGAGGACCTAATGTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1924:781:376,405:534,560:0.4059:2,2:28.2:1:31.4:1:0.77877:1.02711:59.6:59.077:0.4046:0:5.3 0/1:1407:570:276,294:425,412:0.4051:2,2:27:1:30.8:1:0.41532:1.09875:59.8:56:0.4037:0:4.8 -6 29913070 . G C 197 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CTTGTAAAGGTGAGAGCTTG;RSEQ=AGGACCTAATGTGTGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1894:0:0,0:824,838:0:2,0:26.4:1:31.1:1:1:0:59.9:91.333:0.9994:0:1.8 0/1:1411:76:35,41:668,667:0.0539:2,2:31.9:1:31.6:1:0.55589:1.17305:59.1:37:0.0531:0:5.8 -6 29913074 . A G 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.47291;LSEQ=TAAAGGTGAGAGCTTGGAGG;RSEQ=CCTAATGTGTGTTGGGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1863:755:355,400:540,564:0.4053:2,2:29.1:1:31.4:1:0.44958:1.07877:59.7:57.077:0.4068:0:5.3 1/0:1375:863:436,427:250,253:0.6276:2,2:27.7:1:31.3:1:0.77933:1.03:59.9:52.938:0.6302:0:4.3 -6 29913078 . A G 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.60223;LSEQ=GGTGAGAGCTTGGAGGACCT;RSEQ=ATGTGTGTTGGGTGTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1849:757:353,404:527,562:0.4094:2,2:28.6:1:31.6:1:0.47739:1.07315:59.8:83.111:0.4112:0:5.3 1/0:1377:886:445,441:241,250:0.6434:2,2:27.2:1:31.2:1:0.69401:1.05:59.9:62.286:0.6416:0:4.3 -6 29913098 . C A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.46952;LSEQ=AATGTGTGTTGGGTGTTGGG;RSEQ=GGAACAGTGGACACAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1705:239:92,147:647,816:0.1402:2,2:23.6:1:30.4:1:0.10553:1.26673:59.8:46.8:0.14:0:5 0/1:1252:89:41,48:461,543:0.0711:2,2:22.7:1:29.7:1:1:1.01:59.6:43.5:0.0705:0:4.8 -6 29913111 . A G 269 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.57544;LSEQ=TGTTGGGCGGAACAGTGGAC;RSEQ=CAGCTGTGCTATGGGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1487:414:173,241:431,641:0.2784:2,2:24.8:1:31:1:0.59619:1.07:59.2:68:0.2776:0:4.7 0/1:1101:200:85,115:374,527:0.1817:2,2:24.3:1:30.3:1:0.81233:1.04:59.3:49:0.1798:0:4.6 -6 29913135 . G C 208 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGCTATGGGGTTTCTTT;RSEQ=CATTGGATGTATTGAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1032:0:0,0:360,669:0:2,0:24.3:1:31.8:1:1:0:59.3:53.158:0.997:0:1.7 0/1:751:113:39,74:243,394:0.1505:2,2:22.9:1:30.5:1:0.52742:1.16999:59.6:36.667:0.1482:0:3.7 -6 29913137 . A G 202 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGCTATGGGGTTTCTTTGC;RSEQ=TTGGATGTATTGAGCATGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1021:0:0,0:352,669:0:2,0:23.9:1:30.2:1:1:0:59.2:39.84:1:0:1.7 0/1:725:103:39,64:228,394:0.1421:2,2:25.6:1:30.3:1:0.826:1.05:60:102:0.1429:0:3.1 -6 29913171 . G A 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16903;SOR=1.18101;LSEQ=GCATGCGATGGGCTGTTTAA;RSEQ=GTGTGACCCCTCACTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:289:106,183:136,261:0.4207:2,2:23.8:1:30.8:1:0.5185:1.11:53.9:40.286:0.419:0:3.9 0/1:483:223:95,128:90,170:0.4617:2,2:22.3:1:30.2:1:0.07522:1.40:55.1:30.857:0.4586:0:3.8 -6 29913179 . C T 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=9e-05;SOR=0.55868;LSEQ=TGGGCTGTTTAAGGTGTGAC;RSEQ=CCTCACTGTGATGGATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:186:74,112:170,298:0.2844:2,2:24:1:30.5:1:0.4209:1.16:53.7:45.5:0.2871:0:4.6 0/1:457:83:31,52:151,223:0.1816:2,2:25.1:1:29.8:1:0.71021:1.13551:53.6:82:0.1834:0:4.7 -6 29913191 . TG CA 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.82943;LSEQ=GGTGTGACCCCTCACTGTGA;RSEQ=GATATGAATTTGTTCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:179:77,102:161,231:0.2741:2,2:24.8:1:31.5:1:0.7145:1.08:53.6:358:0.2797:0.0413:3.9 0/1:482:197:93,104:110,139:0.4087:2,2:22.3:1:30.8:1:0.56591:1.13:54.6:196:0.4144:0.0788:3.1 -6 29913192 . G A 71 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.76964;SOR=1.17518;LSEQ=GTGTGACCCCTCACTGTGAT;RSEQ=GATATGAATTTGTTCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:6:3,3:196,273:0.0096:2,2:12:1:27.7:1:0.69844:1.39:53.7:5:0.0107:0:4.5 0/1:446:5:3,2:124,157:0.0112:2,2:11.2:1:27.8:1:0.65836:1.89:58:10:0.0176:0:2.8 -6 29913197 . T C 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04792;SOR=1.29476;LSEQ=ACCCCTCACTGTGATGGATA;RSEQ=GAATTTGTTCATGAATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:664:193:89,104:212,258:0.2907:2,2:23.4:1:30.6:1:0.86371:1.04:54.2:192:0.2945:0:3.6 0/1:499:173:91,82:153,172:0.3467:2,2:23:1:30.1:1:0.2592:1.25:55.9:85.5:0.3462:0:3.1 -6 29913201 . T G 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=43.01986;LSEQ=CTCACTGTGATGGATATGAA;RSEQ=TTGTTCATGAATATTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:1:1,0:320,361:0.0015:2,0:45:0:16:0:0.47067:0:60:0:0:0:5 0/1:522:31:16,15:251,240:0.0594:2,2:21.1:1:31.5:1:1:1.02:47.2:62:0.0601:0:2.4 -6 29913204 . G C 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00081;SOR=0.45863;LSEQ=ACTGTGATGGATATGAATTT;RSEQ=TTCATGAATATTTTTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:70:30,40:304,312:0.1019:2,2:28.9:1:31.5:1:0.31556:1.29865:44.2:69:0.1021:0:3 0/1:526:26:11,15:268,228:0.0494:2,2:30.2:1:31.1:1:0.31357:1.6014:39.2:52:0.0502:0:2.9 -6 29913213 . TA T 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATATGAATTTGTTCATGAA;RSEQ=TTTTTTTCTATAGTGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:745:0:0,0:374,369:0:2,0:23:1:29.2:1:1:0:56.9:48.533:0.9973:0:1.3 0/1:593:43:22,21:294,256:0.0725:2,2:19.5:1:30:1:0.87414:1.09607:49.1:86:0.073:0.027:1.9 -6 29913214 . AT A 187 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00231;SOR=0.48916;LSEQ=ATATGAATTTGTTCATGAAT;RSEQ=TTTTTTCTATAGTGTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:752:66:35,31:346,340:0.0878:2,2:28.7:1:31.1:1:0.70112:1.11:41.1:132:0.0886:0.0106:2.6 0/1:601:27:11,16:311,263:0.0449:2,2:27.1:1:30.2:1:0.23569:1.71844:39.3:54:0.0451:0.01:2.5 -6 29913266 . G T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33172;LSEQ=TGTGGGACTGAGAGGCAAGA;RSEQ=TTGTTCCTGCCCTTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:969:351:176,175:305,313:0.3622:2,2:29.5:1:30.1:1:0.84117:1.03:58.5:30.909:0.3568:0:2.2 0/1:934:148:71,77:381,405:0.1585:2,2:28.1:1:29.8:1:0.92876:1.02022:59:73:0.1585:0:1.9 -6 29913274 . TGCCCTTCC CGCCTTCT 154 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00046;SOR=0.28674;LSEQ=TGAGAGGCAAGAGTTGTTCC;RSEQ=CTTTGTGACTTGAAGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:987:33:12,21:458,495:0.0334:2,2:27.1:1:30.7:1:0.21639:1.61841:37.8:66:0.034:0.0061:3.3 0/0:917:9:2,7:433,472:0.0098:2,2:19:1:30.8:1:0.1821:3.20696:34.6:18:0.0099:0.0033:3.2 -6 29913294 . G C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7251;SOR=0.87481;LSEQ=TGCCCTTCCCTTTGTGACTT;RSEQ=AAGAACCCTGACTTTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:857:18:10,8:354,485:0.021:2,2:12.7:1:31.1:1:0.33569:1.71:46.7:36:0.0214:0:1.4 0/1:760:14:7,7:323,423:0.0184:2,2:17.9:1:29.4:1:0.78669:1.31:44.7:6:0.0162:0:1.6 -6 29913298 . A T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18003;LSEQ=CTTCCCTTTGTGACTTGAAG;RSEQ=ACCCTGACTTTGTTTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:817:235:92,143:241,341:0.2876:2,2:21.9:1:28.2:1:0.58232:1.09839:59.8:116.5:0.2909:0:2.2 0/1:709:48:21,27:275,386:0.0677:2,2:25.5:1:27.9:1:0.76439:1.09:60:47:0.0673:0:2.3 -6 29913306 . C A 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00064;SOR=0.2841;LSEQ=TGTGACTTGAAGAACCCTGA;RSEQ=TTTGTTTCTGCAAAGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:32:11,21:271,425:0.044:2,2:29:1:29.8:1:0.71179:1.21699:42.3:31:0.0432:0:5.3 0/1:621:8:3,5:239,374:0.0129:2,2:29:1:28:1:1:1.06496:44.6:16:0.0131:0:5.6 -6 29913309 . TG CTC 96 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.046;SOR=3.93513;LSEQ=GACTTGAAGAACCCTGACTT;RSEQ=TTTCTGCAAAGGCACCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:699:3:0,3:263,432:0.0043:2,0:14.3:1:32.9:1:0.29453:0:35.3:6:0.0044:0:2.7 0/1:599:10:5,5:224,361:0.0167:2,2:7.3:1:29:1:0.51909:1.61:42.7:20:0.0171:0.0117:1.5 -6 29913310 . G C 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00103;SOR=0.29201;LSEQ=ACTTGAAGAACCCTGACTTT;RSEQ=TTTCTGCAAAGGCACCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:32:10,22:240,404:0.0469:2,2:28.1:1:31.5:1:0.576:1.30642:41.7:64:0.0478:0:5.5 0/1:565:8:3,5:208,341:0.0142:2,2:30:1:28.5:1:1:1.01659:41.3:7:0.0128:0:5.8 -6 29913344 . G T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00089;SOR=0.53519;LSEQ=ACCTGCATGTGTCTGTGTTC;RSEQ=TGTAGGCATAATGTGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:121:16,105:44,204:0.3087:2,2:25:1:30.1:1:0.29609:1.41416:60:59.5:0.3091:0:2 0/1:275:53:13,40:42,155:0.1927:2,2:24.5:1:29.8:1:0.70882:1.20:60:52:0.1912:0:1.7 -6 29913353 . T C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1184;SOR=0.48915;LSEQ=TGTCTGTGTTCGTGTAGGCA;RSEQ=AATGTGAGGAGGTGGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:22:0,22:36,288:0.0636:2,1:25.8:1:32.5:1:0.14717:0:49.9:44:0.0641:0:7.3 0/1:218:7:0,7:36,175:0.0321:2,0:20.9:1:32.3:1:0.60305:0:49.9:14:0.0323:0:7.3 -6 29913355 . A G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11946;SOR=0.49606;LSEQ=TCTGTGTTCGTGTAGGCATA;RSEQ=TGTGAGGAGGTGGGGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:22:0,22:30,283:0.0657:2,1:25.6:1:32.5:1:0.24002:0:49.9:44:0.0667:0:7.3 0/1:208:7:0,7:31,169:0.0337:2,0:20.6:1:31.4:1:0.59741:0:49.9:14:0.0338:0:7.3 -6 29913367 . G A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51965;SOR=0.68909;LSEQ=TAGGCATAATGTGAGGAGGT;RSEQ=GGGAGACCACCCCACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:18:0,18:9,229:0.07:1,1:28.2:1:31.3:1:1:0:53.2:36:0.0706:0:7.2 0/1:142:7:0,7:7,128:0.0493:2,0:21.1:1:31.7:1:1:0:52.6:14:0.05:0:6.9 -6 29913374 . C G 115 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=24.36192;LSEQ=AATGTGAGGAGGTGGGGAGA;RSEQ=CACCCCACCCCCATGTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:1:0,1:2,217:0.0045:1,0:18:0:27:0:1:0:60:2:0.0048:0:3 0/1:119:12:0,12:2,105:0.1008:1,0:23.8:1:32.1:1:1:0:60:24:0.1017:0:1.6 -6 29913377 . C T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.37542;SOR=0.59415;LSEQ=GTGAGGAGGTGGGGAGACCA;RSEQ=CCCACCCCCATGTCCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:18:0,18:2,192:0.0849:1,1:26.4:1:30.3:1:1:0:54.4:36:0.0861:0:7.1 0/1:115:6:0,6:0,109:0.0522:1,0:24.5:1:30:1:1:0:54.7:12:0.055:0:6.7 -6 29913383 . C T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49482;SOR=0.65105;LSEQ=AGGTGGGGAGACCACCCCAC;RSEQ=CCCATGTCCACCATGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:17:0,17:2,173:0.0885:1,1:26.6:1:30.4:1:1:0:54.2:34:0.0909:0:7 0/1:101:6:0,6:0,94:0.0594:1,0:24.5:1:29.5:1:1:0:54.7:12:0.0612:0:6.7 -6 29913386 . C G 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=TGGGGAGACCACCCCACCCC;RSEQ=ATGTCCACCATGACCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:2,187:0:1,0:25:1:32.4:1:1:0:59.5:62:1:0:1 0/1:95:8:0,8:0,86:0.0842:1,0:29.6:1:30.4:1:1:0:60:16:0.086:0:1.6 -6 29913396 . A C 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79607;SOR=0.78085;LSEQ=ACCCCACCCCCATGTCCACC;RSEQ=TGACCCTCTTCCCACGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:13:0,13:3,141:0.0828:1,1:27.6:1:33.1:1:1:0:54.7:26:0.0833:0:6.2 0/1:76:5:0,5:0,71:0.0658:1,0:30.4:1:32.4:1:1:0:58:10:0.0667:0:5.4 -6 29913430 . C T 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGCTGACCTGTGCTCCCTC;RSEQ=CCAATCATCTTTCCTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:1,74:0:1,0:21.8:1:31:1:1:0:59.5:74:1:0:0.8 0/1:34:11:0,11:0,23:0.3235:1,0:19.4:1:29.8:1:1:0:60:22:0.3333:0:1.9 -6 29913449 . C G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07775;SOR=Inf;LSEQ=CCCCAATCATCTTTCCTGTT;RSEQ=CAGAGAGGTGGGGCTGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:1,52:0:1,0:24:1:30.9:1:1:0:59:52:1:0:0.6 0/1:21:2:0,2:0,19:0.0952:1,0:11:1:33.5:1:1:0:60:4:0.1:0:1 -6 29913468 . G A 80 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66394;SOR=0.45429;LSEQ=TCCAGAGAGGTGGGGCTGAG;RSEQ=TGTCTCCATCTCTGTCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:6:0,6:1,34:0.1463:1,0:30.8:1:31.2:1:1:0:51:12:0.15:0:3.2 0/1:14:1:0,1:0,13:0.0714:1,0:28:0:31:0:1:0:60:2:0.0769:0:3 -6 29913483 . T C 100 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32275;SOR=0;LSEQ=CTGAGGTGTCTCCATCTCTG;RSEQ=CTCAACTTCATGGTGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:9:1,8:0,30:0.2308:1,2:21.8:1:31.6:1:0.23077:0:60:18:0.2308:0:1 0/0:8:0:0,0:0,8:0:0,0:20.9:1:28.8:1:1:0:60:16:1:0:1.8 -6 29913495 . G A 75 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07779;LSEQ=CATCTCTGTCTCAACTTCAT;RSEQ=GTGCACTGAGCTGTAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:0,5:0,27:0.1563:1,0:30.8:1:32.6:1:1:0:49.2:10:0.1563:0:3.4 0/1:6:1:0,1:0,5:0.1667:0,0:1:0:31:0:1:0:60:2:0.2:0:3 -6 29913518 . C A 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGAGCTGTAACTTCTT;RSEQ=CTTCCCTATTAAAATTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:0,6:0,21:0.2222:1,0:17:1:30.5:1:1:0:42.3:12:0.24:0:3.5 0/0:1:0:0,0:0,1:0:0,0:34:0:32:0:1:0:60:2:1:0:0 -6 29913526 . A G 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTAACTTCTTCCTTCCCT;RSEQ=TTAAAATTAGAACCTTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:0,6:0,19:0.24:1,0:16.2:1:32:1:1:0:41:12:0.24:0:3.3 0/0:1:0:0,0:0,1:0:0,0:26:0:18:0:1:0:60:0:0:0:0 -6 29913542 . T G 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4902;SOR=2.79285;LSEQ=CCCTATTAAAATTAGAACCT;RSEQ=AGTATAAATTTACTTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:0,4:0,12:0.25:0,0:28.8:1:30.3:1:1:0:38.3:8:0.25:0:3 1/0:2:1:0,1:0,1:0.5:0,0:1:0:28:0:1:0:45:2:0.5:0:2 -6 29915102 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACACTGGGGCTTACAGA;RSEQ=GCCAGGGAATAAACCTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:30.5:1:31.5:1:1:1:60:4:0.5:0:2.5 -6 29915122 . T C 61 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAGGGAATAAACCTAGA;RSEQ=ACATTATGCCCCATGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:16.3:1:30.8:1:1:0:60:8:1:0:2.5 -6 29915124 . C A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGAATAAACCTAGATA;RSEQ=ATTATGCCCCATGGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:22:1:29.5:1:1:1:60:4:0.5:0:2.5 -6 29917583 . C T 27 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATAGTATGTGCCCAGAGA;RSEQ=AAGCAGGTGAGAAGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:27.5:1:1:0:60:4:1:0:4 -6 29917589 . G T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTGCCCAGAGACAAGCA;RSEQ=GTGAGAAGAGGAGGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15:0:29:1:1:0:60:4:1:0:4 -6 29917610 . C G 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAGAAGAGGAGGAGGCAG;RSEQ=GCTGCTATCACACAATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36:0:31:1:1:0:60:4:1:0:4 -6 29917635 . G C 34 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CTATCACACAATGAGGGCAG;RSEQ=AGAAGTGTGTGTGGAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:4.5:1:31.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:34:0:1:0:60:4:1:0:4 -6 29917701 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TTCCCTTGTCCGTTGTGTGA;RSEQ=CGGAATCATCCAGCAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:31:1:31.8:1:1:0:60:8:1:0:0.8 1/0:3:2:1,1:1,0:0.6667:0,2:26.5:1:29:1:1:0:60:4:0.6667:0:2.5 -6 29917703 . G A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=CCCTTGTCCGTTGTGTGAGC;RSEQ=GAATCATCCAGCAACCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:29.5:1:30:1:1:0:60:4:0.5:0:1.5 1/0:3:2:1,1:1,0:0.6667:0,2:28.5:1:29.5:1:1:0:60:4:0.6667:0:2.5 -6 29917801 . G A 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14256;SOR=0;LSEQ=ACTCCTAGGTAATGTCCCAC;RSEQ=TCTCTGCTTCTGTGCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:4,1:21,0:0.1923:1,2:27.4:1:29.8:1:0.19231:0:59.4:10:0.2083:0:1.4 0/0:14:0:0,0:14,0:0:1,0:24.5:1:29.5:1:1:0:60:28:1:0:0.2 -6 29917881 . C T 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=22.96964;LSEQ=AGTTGTTCCCAGCCAGTGAC;RSEQ=GGTCACAGCAAGCACACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:1,0:63,36:0.01:2,0:5:0:33:0:1:0:60:2:0.0102:0:5 0/1:100:19:14,5:52,29:0.19:2,2:20.7:1:29.9:1:0.59208:1.55:60:38:0.1939:0:1.1 -6 29917899 . T C 134 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00205;SOR=0.27961;LSEQ=ACCGGTCACAGCAAGCACAC;RSEQ=AAGGCAGGCCATTACTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:23:13,10:59,41:0.187:2,2:25:1:29.8:1:0.81942:1.10602:60:22:0.1849:0:1 0/1:133:8:7,1:73,52:0.0602:2,2:32.3:1:31.4:1:0.1445:4.94:60:16:0.0615:0:1 -6 29917940 . G A 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=GACATGGGACTCCTCTGATG;RSEQ=CCAAATGTGGCTCCAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:52,69:0:2,0:26.6:1:31.3:1:1:0:60:120:1:0:0.2 0/1:128:14:8,6:48,66:0.1094:2,2:27.1:1:29.6:1:0.39313:1.82:60:28:0.112:0:1 -6 29917941 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23897;SOR=0;LSEQ=ACATGGGACTCCTCTGATGG;RSEQ=CAAATGTGGCTCCAGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:51,68:0.0165:2,2:33.5:1:31:1:1:1.33:60:4:0.0167:0:1.5 0/0:126:0:0,0:56,70:0:2,0:27.5:1:30.8:1:1:0:60:125:1:0:0.4 -6 29917974 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23132;SOR=0;LSEQ=CAGGACTCCTCCATGCCCTT;RSEQ=CTCAACTCTCCTTAGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:21,46:0.0286:2,2:17:1:31.5:1:0.53922:2.16:60:4:0.029:0:3.5 0/0:75:0:0,0:25,50:0:2,0:21.9:1:30.2:1:1:0:60:74:1:0:0.2 -6 29918022 . C T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11742;SOR=Inf;LSEQ=CTAGGATGCGTCGAACAGAC;RSEQ=TTGTCTCCTTCTGTCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:1,19:0:1,0:20.6:1:32.7:1:1:0:60:40:1:0:0.3 0/1:25:4:0,4:0,21:0.16:1,0:24.8:1:28.3:1:1:0:60:8:0.16:0:2 -6 29918059 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21053;SOR=Inf;LSEQ=AGCACTTGGGGTCACACTTG;RSEQ=ATCATTGTCTGCCGCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:0:0,0:15.8:1:31.5:1:1:0:60:20:1:0:0.3 0/1:9:2:0,2:0,7:0.2222:0,0:27:1:29.5:1:1:0:60:4:0.2222:0:3 -6 29918072 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20588;SOR=Inf;LSEQ=ACACTTGCATCATTGTCTGC;RSEQ=GCCTTTTCCAGGGATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:23.8:1:29.3:1:1:0:60:16:1:0:0.6 0/1:9:3:0,3:0,6:0.3333:0,0:10.3:1:30.7:1:1:0:60:6:0.3333:0:2.3 -6 29918684 . G T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAGTAAAGAAAAGGAAG;RSEQ=TATTAATGGAATATGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:0:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29924822 . G A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCCTGCACTCTGGGACA;RSEQ=TTAAAGGATGTAGTCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:24:1:30.5:1:1:0:50.5:4:0.4:0:2.5 0/0:1:0:0,0:1,0:0:0,0:47:0:31:0:1:0:60:2:1:0:1 -6 29924833 . T A 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGGGACAGTTAAAGGATG;RSEQ=AGTCTCTGAGGGAAAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:0.6:2,0:29.3:1:30:1:0.4:0:53.7:6:0.6:0:2 1/1:1:1:1,0:0,0:1:0,0:43:0:27:0:1:0:60:2:1:0:1 -6 29925086 . T G 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.73779;SOR=1.2499;LSEQ=AAGATTGCCCCAGGTGCCTG;RSEQ=GTCTAGACTGGTGTCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:5:5,0:71,1:0.0649:1,0:18.6:1:32.4:1:1:0:60:10:0.0649:0:1 0/1:50:4:4,0:45,1:0.08:1,0:27.5:1:32:1:1:0:60:8:0.08:0:1 -6 29925127 . G A 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCTCCCTTCCCCACTTCAG;RSEQ=TGTCCCGTCAATTTTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:140,2:0:1,0:27.3:1:31.1:1:1:0:60:27.4:1:0:0.5 0/1:112:22:22,0:89,1:0.1964:1,1:25.4:1:28.6:1:1:0:60:21:0.1892:0:1.1 -6 29925134 . G A 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14578;LSEQ=TTCCCCACTTCAGGTGTCCC;RSEQ=TCAATTTTCAGGATGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:59:58,1:97,3:0.3711:1,1:26.9:1:30.5:1:1:1.79:60:118:0.3806:0:1 0/1:127:10:10,0:114,3:0.0787:1,0:21.2:1:31.1:1:1:0:60:20:0.0794:0:1 -6 29925209 . C T 90 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07591;SOR=0.16541;LSEQ=CCTGAATTTTCTGACTCTTC;RSEQ=CCTCAGAACCCCAAAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:635:7:7,0:342,284:0.011:2,0:34.1:1:32.1:1:0.01858:0:36.6:14:0.0112:0:5.7 0/0:544:1:1,0:298,245:0.0018:2,0:42:0:33:0:1:0:22:2:0.0019:0:6 -6 29925217 . A TC 93 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.04383;SOR=0.14547;LSEQ=TTCTGACTCTTCCCCTCAGA;RSEQ=CCCCAAAGACTCACATGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:645:8:6,2:327,310:0.0124:2,2:35:1:31.1:1:0.2881:2.84:30.5:16:0.0127:0.0031:6.8 0/0:549:1:1,0:287,261:0.0018:2,0:43:0:32.5:0:1:0:22:2:0.0018:0:6 -6 29925221 . C CA 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.01401;SOR=1.33856;LSEQ=GACTCTTCCCCTCAGAACCC;RSEQ=AAAGACTCACATGACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:661:251:124,127:209,201:0.3797:2,2:30.8:1:29.6:1:0.74857:1.06484:60:30.375:0.3756:0.0318:0.2 0/1:555:250:124,126:152,148:0.4505:2,2:32.5:1:29.7:1:0.86404:1.04354:60:61.5:0.4514:0.0234:0.2 -6 29925228 . T A 96 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0264;SOR=0.13261;LSEQ=CCCCTCAGAACCCCAAAGAC;RSEQ=CACATGACCCACCACCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:673:9:6,3:313,348:0.0134:2,2:33.7:1:30.4:1:0.32168:2.22:32.1:18:0.0137:0:6.9 0/0:558:1:1,0:256,300:0.0018:2,0:31:0:32:0:0.4614:0:22:2:0.0019:0:6 -6 29925235 . A T 94 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02802;SOR=0.12196;LSEQ=GAACCCCAAAGACTCACATG;RSEQ=CCCACCACCCCATCTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:686:10:6,4:305,370:0.0146:2,2:29.6:1:28.5:1:0.52465:1.82:34.9:9:0.0134:0:6.3 0/0:556:1:1,0:242,309:0.0018:2,0:24:0:32:0:0.44022:0:22:2:0.0019:0:6 -6 29925243 . C G 100 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12447;SOR=0.26913;LSEQ=AAGACTCACATGACCCACCA;RSEQ=CCCATCTCTGACCATGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:666:9:6,3:279,378:0.0135:2,2:28.7:1:31.8:1:0.18181:2.71:32.1:18:0.0137:0:6.9 0/0:545:2:1,1:224,319:0.0037:2,2:19.5:1:24:1:1:1.42:41:1:0.0019:0:5 -6 29925252 . T C 93 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24434;SOR=0.40994;LSEQ=ATGACCCACCACCCCATCTC;RSEQ=GACCATGAGGCCACCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:9:6,3:249,363:0.0145:2,2:25.7:1:29.6:1:0.17104:2.91:32.1:18:0.0149:0:6.9 0/0:501:3:1,2:193,304:0.006:2,2:26.3:1:31:1:1:1.26913:47.3:6:0.0061:0:3 -6 29925268 . C A 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=62.21054;LSEQ=TCTCTGACCATGAGGCCACC;RSEQ=TGAGGTGCTGGGCTCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:1:1,0:171,297:0.0021:2,0:1:0:25:0:0.36674:0:60:2:0.0022:0:1 0/1:331:39:12,27:99,193:0.1178:2,2:24.4:1:29.7:1:0.8569:1.15369:60:78:0.1204:0:1.3 -6 29925275 . G T 69 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70749;SOR=0.59006;LSEQ=CCATGAGGCCACCCTGAGGT;RSEQ=CTGGGCTCTGGGCTTCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:5:2,3:129,269:0.0124:2,2:23.2:1:29.8:1:0.66179:1.39:31.2:10:0.0127:0:7.4 0/0:272:2:1,1:78,192:0.0074:2,2:26:1:27.5:1:0.49729:2.45:60:4:0.0075:0:1 -6 29925281 . C G 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=GGCCACCCTGAGGTGCTGGG;RSEQ=TCTGGGCTTCTACCCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:95,250:0:2,0:23.9:1:32.1:1:1:0:59.7:56.5:1:0:0.2 0/1:249:12:1,11:63,174:0.0482:2,2:30.1:1:30:1:0.3065:3.96767:60:11:0.0453:0:1 -6 29925331 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60634;SOR=0.66394;LSEQ=TGACCCAGTAGTGGGATGGA;RSEQ=AGGACCAAATGTAGGATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:12:4,8:42,98:0.0789:2,2:16:1:28.8:1:0.75487:1.17:60:11:0.0748:0:1.7 0/1:93:5:2,3:23,65:0.0538:2,2:19.6:1:29.6:1:0.60825:1.87:60:10:0.0543:0:1 -6 29925438 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08002;LSEQ=TCTGGAGAGGAGCAGAGATA;RSEQ=ACATGCCATGTGCAGCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:105:63,42:132,109:0.3035:2,2:24.1:1:29.1:1:0.4098:1.24:60:104:0.3023:0:1.2 0/1:268:9:6,3:149,110:0.0336:2,2:29.1:1:29.9:1:0.73788:1.47:60:18:0.0338:0:1 -6 29925441 . A G 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00123;SOR=Inf;LSEQ=GGAGAGGAGCAGAGATACAC;RSEQ=TGCCATGTGCAGCACGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:193,158:0:2,0:24.3:1:30.1:1:1:0:59.4:69.2:1:0:0.7 0/1:272:8:4,4:149,114:0.0294:2,2:13.5:1:31.3:1:0.73144:1.3057:26.5:16:0.0296:0:3.9 -6 29925456 . C T 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.8327;LSEQ=TACACATGCCATGTGCAGCA;RSEQ=GATGGGCTGCCAGAGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:0,1:190,178:0.0027:2,0:1:0:28:0:0.48509:0:60:2:0.0027:0:1 0/1:304:20:11,9:149,135:0.0658:2,2:31.3:1:30.1:1:1:1.11:60:40:0.0664:0:1.2 -6 29925459 . TG GA 107 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15788;SOR=0.35263;LSEQ=ACATGCCATGTGCAGCACGA;RSEQ=GGCTGCCAGAGCCCCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:10:1,9:187,171:0.0272:2,2:30.2:1:32.3:1:0.00932:9.79612:37.5:20:0.0278:0:2.7 0/0:308:3:1,2:156,141:0.0097:2,2:30.3:1:31.8:1:0.60693:2.2071:47.3:6:0.0099:0:3 -6 29925473 . C T 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00144;SOR=0.3848;LSEQ=GCACGATGGGCTGCCAGAGC;RSEQ=CCTCACCCTGAGATGGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:43:21,22:158,167:0.1168:2,2:32.6:1:30.7:1:1:1.01:60:86:0.1204:0:2.1 0/1:310:15:5,10:148,147:0.0484:2,2:33:1:28.7:1:0.2903:2.0092:60:14:0.0465:0:1.7 -6 29925487 . T TG 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.02491;SOR=8.94441;LSEQ=CAGAGCCCCTCACCCTGAGA;RSEQ=GGGTAAGGAAGGGGATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:1:0,1:170,198:0.0027:2,0:34:0:32:0:1:0:29:2:0.0028:0:7 0/1:295:7:3,4:126,162:0.0237:2,2:29.7:1:31.4:1:1:1.03691:30:14:0.0242:0:3.7 -6 29925497 . A G 80 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00655;SOR=Inf;LSEQ=CACCCTGAGATGGGTAAGGA;RSEQ=GGGGATGAGGGGTCATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:157,185:0:2,0:24.6:1:30.5:1:1:0:60:84.5:0.9971:0:0.6 0/1:264:6:3,3:109,149:0.0227:2,2:22.7:1:31.3:1:0.7008:1.37:25:12:0.0232:0:4.2 -6 29925500 . G A 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00341;SOR=0.4033;LSEQ=CCTGAGATGGGTAAGGAAGG;RSEQ=GATGAGGGGTCATGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:44:20,24:133,160:0.1306:2,2:25.5:1:29.5:1:1:1.00:60:13.667:0.1246:0:2.1 0/1:263:15:4,11:104,144:0.057:2,2:24.7:1:30.3:1:0.28984:1.98131:60:30:0.0579:0:1.7 -6 29925533 . AGGAGCCCTTCT A 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=1.000;MSILEN=1;SSF=0.01132;SOR=0.2837;LSEQ=TGTCTCTTCTCACGGGAACT;RSEQ=GGAGCCCTTCAGCAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:20:10,10:82,99:0.0995:2,2:29.1:1:31.9:1:0.81397:1.21:60:40:0.102:0.0149:1.3 0/1:165:5:0,5:77,83:0.0303:2,0:35.4:1:32:1:0.06147:0:60:10:0.0305:0:1.4 -6 29925558 . AAGGTCAGGG A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTTCTGGAGCCCTTCAGC;RSEQ=TTTGAGGCCTGATGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:113,110:0:2,0:21.9:1:30.2:1:1:0:60:43.6:0.9954:0:0.4 0/1:165:23:13,10:74,68:0.1394:2,2:29.5:1:30.3:1:0.82275:1.19:59.8:46:0.142:0.0303:0.7 -6 29925584 . C G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00439;SOR=Inf;LSEQ=AGGGTTTGAGGCCTGATGGT;RSEQ=AGGGCCCCTCACGTTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:165,129:0:2,0:24:1:31.6:1:1:0:60:57.8:1:0:0.5 0/1:254:7:5,2:132,113:0.0276:2,2:16.6:1:30.9:1:0.45927:2.13:60:14:0.0278:0:2.1 -6 29925596 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11091;SOR=Inf;LSEQ=CTGATGGTCAGGGCCCCTCA;RSEQ=GTTCCCCTCCTTTCTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:175,143:0:2,0:27.4:1:30.9:1:1:0:60:62.6:1:0:0.6 0/1:296:3:1,2:158,135:0.0101:2,2:21.3:1:27:1:0.59781:2.3342:60:6:0.0102:0:1.7 -6 29925636 . G T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=4.65118;LSEQ=GCTGTCTTCCCAGCCCACCA;RSEQ=CCCCATCATGGGCATCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:348:186:86,100:71,91:0.5345:2,2:28.4:1:29.6:1:0.66712:1.10:60:25.571:0.5359:0:1.1 1/1:324:273:127,146:23,28:0.8426:2,2:27.1:1:28.7:1:0.87952:1.06:60:33.125:0.8439:0:1.2 -6 29925653 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19091;SOR=4.59016;LSEQ=CCAGCCCCATCATGGGCATC;RSEQ=TTACTGTCCTGGTTGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:1:1,0:121,185:0.0033:2,0:1:0:27:0:0.39739:0:60:2:0.0033:0:2 0/1:270:4:2,2:113,153:0.0148:2,2:34:1:28.5:1:1:1.35:60:8:0.015:0:2 -6 29925682 . TT GG 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.654;SOR=2.05271;LSEQ=CTGGTTGTTCTTGGTGCTGT;RSEQ=TCACCAGAGCTGTGGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:42,150:0.0103:2,2:26:1:33.8:1:0.39506:3.54:60:4:0.0105:0:3.5 0/1:143:3:1,2:42,98:0.021:2,2:28.7:1:28.5:1:1:1.17:54.3:6:0.021:0:3.3 -6 29925686 . A C 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40133;SOR=2.19994;LSEQ=TTGTTCTTGGTGCTGTTTTC;RSEQ=CCAGAGCTGTGGTCACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:33,142:0.0113:2,2:29:1:33:0:0.34816:4.25:60:4:0.0116:0:3.5 0/1:122:3:1,2:28,91:0.0246:2,2:31.7:1:29:1:0.56047:1.62:54.3:6:0.0246:0:3.3 -6 29925689 . A T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.38903;SOR=2.30487;LSEQ=TTCTTGGTGCTGTTTTCACC;RSEQ=GAGCTGTGGTCACTGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:31,137:0.0118:2,2:32:1:32.5:1:0.34194:4.37:60:4:0.012:0:3.5 0/1:112:3:1,2:23,86:0.0268:2,2:34.7:1:28.7:1:0.51853:1.86:54.3:6:0.0268:0:3.3 -6 29925713 . T TG 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01169;SOR=2.31497;LSEQ=CTGTGGTCACTGCTGTGATG;RSEQ=GAAGAATAAGAGCCCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:49:4,45:8,39:0.4623:2,2:27:1:31.5:1:0.22794:2.28799:59.6:48:0.5053:0.1604:0.8 1/0:66:44:3,41:0,18:0.6667:1,2:21.9:1:30.4:1:0.54976:0:59.6:88:0.7097:0.2424:1 -6 29925719 . A G 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55296;SOR=0;LSEQ=TCACTGCTGTGATGTGAAGA;RSEQ=TAAGAGCCCAGGTAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:0,3:8,68:0.0337:2,0:30.7:1:32.3:1:1:0:60:6:0.0385:0:2 0/0:50:0:0,0:2,44:0:1,0:25.5:1:30.6:1:1:0:59.6:92:1:0:0.6 -6 29925817 . A G 41 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94642;LSEQ=GGCTTGTATCCTGCCTAGTC;RSEQ=TGAGGCACCATCTCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:0,17:0.15:1,0:23.3:1:26.3:1:1:0:60:2:0.1053:0:1 0/1:7:1:0,1:0,6:0.1429:0,0:10:0:32:0:1:0:60:2:0.1429:0:1 -6 29926220 . AG GA 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=TAGACAGGAGCCCATGGGGG;RSEQ=CTCACCACCCCAAAATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:34.8:1:32.3:1:1:0:53.3:12:1:0:0.7 0/1:6:2:1,1:3,1:0.3333:2,2:47:0:30.8:1:1:2.44949:52:4:0.4:0:2 -6 29926227 . C CA 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=Inf;LSEQ=GAGCCCATGGGGGAGCTCAC;RSEQ=ACCCCAAAATTCCTCCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:34.8:1:33.5:1:1:0:53.3:12:1:0:0.7 0/1:8:2:1,1:4,2:0.25:2,2:40:0:30:1:1:1.8258:52:4:0.2857:0:3 -6 29926234 . A C 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=TGGGGGAGCTCACCACCCCA;RSEQ=AATTCCTCCTTTAGTCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:33:1:31.7:1:1:0:53.3:12:1:0:0.7 0/1:7:2:1,1:3,2:0.2857:2,2:33:0:31:1:1:1.41418:52:4:0.2857:0:3 -6 29926300 . AGGGACAGTACCCAGG A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03612;SOR=Inf;LSEQ=GTTTTTGTTCCACCCGAAAC;RSEQ=GCTCTGATGTGTCTCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:24.7:1:32.9:1:1:0:60:24:1:0:0.1 0/1:7:3:1,2:3,1:0.4286:2,2:21.3:1:30.5:1:0.48571:4.4496:60:6:0.4286:0.1429:0 -6 29926597 . T C 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02407;SOR=Inf;LSEQ=GTCTTCTCTTTCTGCCAAGG;RSEQ=GTCTGAATGTGTCTACATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:9,18:0:2,0:25.1:1:29.5:1:1:0:60:54:1:0:0.1 0/1:12:3:0,3:2,7:0.25:2,0:28:1:31.7:1:1:0:60:6:0.25:0:1 -6 29926668 . C G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CCCACCCTCATGTCCACCAT;RSEQ=ACCCCTGATATTGTTTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:0.2:0,0:1:0:31:0:1:0:60:2:0.2:0:2 1/1:2:2:0,2:0,0:1:0,0:19.5:1:32.5:1:1:0:60:4:1:0:1 -6 29973526 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACAGAAACTCAGGGCTA;RSEQ=GGAATAAAGGTAAATTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:30:1:1:0:60:4:1:0:1 -6 29973978 . A G 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCCGGATGAAAAGTGAA;RSEQ=GGAGAGGGACGGGGCCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:5,1:0.25:2,0:31.5:1:32.5:1:1:0:46:4:0.25:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29973989 . G C 31 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGTGAAAGGAGAGGGAC;RSEQ=GGGCCCAAGCTGAGGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:34:1:31:1:1:0:46:4:0.25:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29974000 . T C 38 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGGGACGGGGCCCAAGC;RSEQ=GAGGGTTTCTTCCTGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:25.3:1:24.3:1:1:0:49.7:2:0.25:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 29974083 . CG C 77 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGTTTGTCACAGGAGGAG;RSEQ=GGGTCAGGGCGAAGTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:5,1:7,1:0.4286:2,2:31:1:29.8:1:1:1.36624:59.5:5:0.4167:0:0.7 0/0:1:0:0,0:1,0:0:0,0:9:0:24:0:1:0:60:2:1:0:1 -6 29974191 . CAG C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.11579;SOR=Inf;LSEQ=TTGGGGATTCCCCATCTCCG;RSEQ=AGTTTCTCTTCTCCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:61,2:0:1,0:19.8:1:30.1:1:1:0:60:62:1:0:0.1 0/1:33:2:2,0:27,3:0.0606:2,0:10.5:1:32:1:1:0:60:4:0.0625:0.0303:0 -6 29974294 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14053;SOR=Inf;LSEQ=CTGAGTGTCGGGTTTCTAGG;RSEQ=AAGCCAATCAGCGTCGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:282,37:0:2,0:24.1:1:30.9:1:1:0:60:28:0.9968:0:0.3 0/1:193:2:1,1:161,29:0.0104:2,2:32.5:1:29:1:0.28878:5.47542:60:4:0.0107:0:1 -6 29974346 . G C 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.343;LSEQ=AAAGTCCCCACGCACCCACC;RSEQ=GGACTCGGAGTCTCCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:943:301:179,122:392,247:0.3192:2,2:24.2:1:30.4:1:0.61642:1.08158:60:149.5:0.3215:0:1.2 0/1:650:90:52,38:319,239:0.1385:2,2:28.5:1:29.3:1:1:1.03:60:89:0.1384:0:1.2 -6 29974500 . A G 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10844;SOR=0.74857;LSEQ=CCGTGAGGAGCGAAAGGTCC;RSEQ=CCTGGCTGGGGCGCAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:131:54,77:140,191:0.2823:2,2:23.5:1:31.4:1:0.91675:1.0451:60:130:0.2838:0:1.1 0/1:299:68:28,40:94,137:0.2274:2,2:20.4:1:30.8:1:1:1.02:59.4:67:0.2264:0:1.3 -6 29974506 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06005;SOR=Inf;LSEQ=GGAGCGAAAGGTCCACCTGG;RSEQ=TGGGGCGCAGGACCCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:207,256:0:2,0:23.6:1:32.1:1:1:0:59.8:65.143:1:0:0.4 0/1:299:3:1,2:123,173:0.01:2,2:19:1:27.7:1:1:1.42035:60:6:0.0101:0:2 -6 29974507 . T G 101 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25792;SOR=1.72993;LSEQ=GAGCGAAAGGTCCACCTGGC;RSEQ=GGGGCGCAGGACCCGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:10:7,3:205,253:0.0214:2,2:3.2:1:29.2:1:0.19691:2.87:42.5:20:0.0217:0:4.4 0/1:302:11:6,5:122,169:0.0364:2,2:5.8:1:29.3:1:0.53684:1.66:44.7:22:0.0367:0:5.1 -6 29974525 . G T 141 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02155;SOR=0.42271;LSEQ=GCTGGGGCGCAGGACCCGGG;RSEQ=AGCCGCGCCGGGAGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:32:15,17:217,256:0.0634:2,2:15.4:1:28.3:1:1:1.04:39.7:64:0.0645:0:3.5 0/1:324:9:3,6:133,163:0.0278:2,2:12.3:1:23.2:1:0.73591:1.62938:45.8:8:0.0251:0:3.7 -6 29974547 . G T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.30448;SOR=0.4927;LSEQ=GCCGCGCCGGGAGGAGGGTC;RSEQ=GGCGGGTCTCAGCCCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:12:5,7:281,266:0.0214:2,2:30.3:1:29.4:1:0.56916:1.47791:43.3:24:0.0217:0:1.6 0/1:375:4:2,2:171,200:0.0107:2,2:39:1:30.5:1:1:1.17:48.8:8:0.0109:0:2 -6 29974550 . C T 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30541;SOR=0.50305;LSEQ=GCGCCGGGAGGAGGGTCGGG;RSEQ=GGGTCTCAGCCCCTCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:12:6,6:290,265:0.0212:2,2:33.7:1:30.5:1:1:1.09416:42.8:24:0.0217:0:3.3 0/1:372:4:1,3:176,192:0.0108:2,2:29.5:1:27.8:1:0.62474:2.74305:41.5:8:0.0109:0:2.8 -6 29974553 . G A 144 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01106;SOR=0.33515;LSEQ=CCGGGAGGAGGGTCGGGCGG;RSEQ=TCTCAGCCCCTCCTCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:589:27:12,15:297,264:0.0458:2,2:38.5:1:30.3:1:0.4336:1.40542:39:54:0.0468:0:3.2 0/1:379:6:2,4:180,192:0.0158:2,2:39.5:1:28:1:0.6863:1.872:51:12:0.016:0:3.8 -6 29974562 . C A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26233;SOR=1.32272;LSEQ=GGGTCGGGCGGGTCTCAGCC;RSEQ=CTCCTCGCCCCCAGGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:616:39:18,21:300,277:0.0633:2,2:35.8:1:29.9:1:0.51123:1.26305:40.2:78:0.0641:0:3.2 0/1:402:33:14,19:179,190:0.0821:2,2:35.2:1:29.7:1:0.58672:1.27779:43.9:32:0.0808:0:4 -6 29974570 . C T 132 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGTCTCAGCCCCTCCTCG;RSEQ=CCCCAGGCTCCCACTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:0:0,0:335,304:0:2,0:26.2:1:31.4:1:1:0:58:41.6:1:0:0.4 0/1:424:21:10,11:196,207:0.0495:2,2:28.5:1:30.1:1:1:1.04146:41.7:42:0.0501:0:4.2 -6 29974581 . C T 112 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCCTCCTCGCCCCCAGGCTC;RSEQ=CACTCCATGAGGTATTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:650:0:0,0:330,320:0:2,0:26.7:1:30.8:1:1:0:58.1:33.211:1:0:0.4 0/1:428:13:6,7:205,210:0.0304:2,2:16.6:1:30.5:1:1:1.13854:48.2:26:0.0307:0:4.7 -6 29974608 . C G 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ATGAGGTATTTCAGCACCGC;RSEQ=GTTTCCTGGCCGGGCCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:576:0:0,0:301,274:0:2,0:25.9:1:30.5:1:1:0:60:94.833:0.9982:0:0.1 0/1:335:21:12,9:157,157:0.0627:2,2:27.5:1:29.3:1:0.65342:1.33:60:20:0.0608:0:1.2 -6 29974672 . T G 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTACGTGGACGACACGCAG;RSEQ=TCGTGCGGGTCGACAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:350,201:0:2,0:25.1:1:30.1:1:1:0:60:136.75:1:0:0.1 0/1:309:33:19,14:160,114:0.1068:2,2:19.9:1:30.6:1:1:1.03407:60:66:0.1082:0:1.2 -6 29974675 . G A 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00205;SOR=Inf;LSEQ=ACGTGGACGACACGCAGTTC;RSEQ=TGCGGGTCGACAGTGACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:566:0:0,0:364,202:0:2,0:25.1:1:30.5:1:1:0:60:50.455:1:0:0.1 0/1:316:6:4,2:181,129:0.019:2,2:27.2:1:30.8:1:1:1.42:60:12:0.0194:0:1.3 -6 29975047 . G T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06736;SOR=3.08161;LSEQ=ATCTCCGCAGGTTGCTAGGG;RSEQ=CCGGGCCAGGGCTCGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:6:5,1:54,30:0.0667:2,2:18.8:1:31:1:0.66009:2.75:60:12:0.069:0:1 0/1:44:8:7,1:27,9:0.1818:2,2:15.5:1:30.4:1:0.65852:2.30:60:16:0.2:0:1 -6 29975049 . C G 70 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00329;SOR=Inf;LSEQ=CTCCGCAGGTTGCTAGGGGC;RSEQ=GGGCCAGGGCTCGGTGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:61,33:0:2,0:22.7:1:29.7:1:1:0:60:17.8:1:0:0.2 0/1:46:5:4,1:31,10:0.1087:2,2:14.4:1:30.2:1:1:1.28:60:10:0.1136:0:4 -6 29975055 . A G 69 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00496;SOR=Inf;LSEQ=AGGTTGCTAGGGGCCGGGCC;RSEQ=GGGCTCGGTGGGCGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:67,35:0:2,0:21.8:1:30:1:1:0:60:24.5:1:0:0.2 0/1:56:5:4,1:38,13:0.0893:2,2:20.4:1:29.8:1:1:1.36:60:10:0.0909:0:4 -6 29975093 . A T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=CTGACCGCGGGAACTGGGCC;RSEQ=GGGTATCACATCCTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:95,51:0:2,0:26.3:1:30:1:1:0:60:47.667:1:0:0.2 0/1:96:10:6,4:60,26:0.1042:2,2:30.9:1:30.4:1:0.49819:1.53117:60:20:0.1075:0:3.1 -6 29975095 . G C 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=GACCGCGGGAACTGGGCCAG;RSEQ=GTATCACATCCTCCAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:95,53:0:2,0:26.5:1:30.8:1:1:0:60:48.333:1:0:0.2 0/1:100:10:6,4:62,28:0.1:2,2:31.7:1:31.3:1:0.72222:1.47018:60:20:0.102:0:3.1 -6 29975105 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51028;SOR=0;LSEQ=ACTGGGCCAGGGTATCACAT;RSEQ=CTCCAGGGAATGTTTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:98,64:0.0122:2,2:6.5:1:28.5:1:1:1.52711:60:4:0.0124:0:1 0/0:120:0:0,0:77,43:0:2,0:26.5:1:30.5:1:1:0:60:39:1:0:0.4 -6 29975193 . ATCGCCCTGAA CGT 166 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00241;SOR=0.3914;LSEQ=CCTACGACGGCAAGGATTAC;RSEQ=CGAGGACCTGCGCTCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:40:16,24:98,102:0.1667:2,2:23.4:1:31.2:1:0.38608:1.43899:59.9:80:0.1695:0.0458:0.3 0/1:207:15:10,5:93,99:0.0725:2,2:29.3:1:30.3:1:0.19202:2.12:59.7:30:0.0735:0.0048:0.3 -6 29975230 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12085;SOR=Inf;LSEQ=CCTGCGCTCCTGGACCGCCG;RSEQ=GGATACCGCGGCTCAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:92,88:0:2,0:24.1:1:30.5:1:1:0:59.7:35:0.9943:0:0.2 0/1:178:3:1,2:86,87:0.0169:2,2:19.3:1:27:1:1:1.96965:60:6:0.0169:0:1 -6 29975231 . G A 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36059;SOR=3.1846;LSEQ=CTGCGCTCCTGGACCGCCGC;RSEQ=GATACCGCGGCTCAGATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:1:1,0:93,88:0.0055:2,0:1:0:27:0:1:0:60:2:0.0055:0:1 0/1:173:3:2,1:84,86:0.0173:2,2:19:1:26.3:1:0.62063:2.04:60:6:0.0174:0:1 -6 29975304 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51093;SOR=0;LSEQ=AGCAAAGGAGAGCCTACCTG;RSEQ=AGGGCACCTGCATGGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:84,105:0.0105:2,2:16:1:28.5:1:1:1.25:60:4:0.0105:0:1 0/0:139:0:0,0:58,81:0:2,0:26.2:1:31:1:1:0:60:278:1:0:0.2 -6 29975453 . C A 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0.75739;LSEQ=AGGAGGGGAAGAAAATGGAA;RSEQ=CACCACCAGAATATCGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:1,7:1,11:0.4:2,2:24.5:1:30:1:1:1.54:60:16:0.4211:0:1.1 0/1:9:3:1,2:1,5:0.3333:2,2:16:1:29.3:1:1:2.24:60:6:0.3333:0:1 -6 29975719 . T C 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATGTGTCGGAGTCTGAC;RSEQ=CCAGCTCCTCTGAGTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:3,1:3,1:0.5:2,2:27.3:1:31:1:1:1:58.5:8:0.5:0:3.3 0/0:1:0:0,0:0,1:0:0,0:37:0:30:0:1:0:60:2:1:0:0 -6 29975766 . G C 109 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=CACTCAGATCAGGACCAGAA;RSEQ=TCCCTGCTACCCTGCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:9,2:6,1:0.6111:2,2:24.3:1:31.6:1:1:1.3127:59.5:22:0.6471:0:2.5 0/0:2:0:0,0:1,1:0:2,0:10.5:1:32.5:1:1:0:60:4:1:0:0 -6 29975775 . A C 103 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=CAGGACCAGAAGTCCCTGCT;RSEQ=CCCTGCTCAGAGACTAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:9,2:6,1:0.6111:2,2:26.5:1:29.8:1:1:1.3127:59.5:10:0.625:0:2.3 0/0:2:0:0,0:1,1:0:2,0:10.5:1:27.5:1:1:0:60:4:1:0:0 -6 29975950 . C T 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=0.47449;LSEQ=TGCAAAGTGCCTGAGTTTTC;RSEQ=GACTCTTCCTTTCAGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:243:148:78,70:59,36:0.6091:2,2:29.3:1:30.6:1:0.18494:1.46844:56.2:147:0.6151:0:2.1 0/1:179:76:44,32:61,42:0.4246:2,2:25.1:1:30.1:1:0.87898:1.05594:56.1:152:0.427:0:2.2 -6 29975966 . AC A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.24283;LSEQ=TTTCCGACTCTTCCTTTCAG;RSEQ=CCCCCCCAAGACACACGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:144:65,79:57,47:0.576:2,2:30.6:1:31.8:1:0.15706:1.47163:56.1:288:0.6025:0.012:2.3 0/1:194:48:24,24:79,67:0.2474:2,2:30.6:1:30.6:1:0.73907:1.1781:53.5:96:0.2623:0.0052:2.3 -6 29975968 . C A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.08066;SOR=Inf;LSEQ=TCCGACTCTTCCTTTCAGAC;RSEQ=CCCCCCAAGACACACGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:126,129:0:2,0:28.6:1:30.8:1:1:0:57.7:35.429:1:0:1.6 0/1:195:3:2,1:100,92:0.0154:2,2:26.3:1:25:1:1:1.83:60:2:0.0109:0:1.3 -6 29975994 . C A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=5e-05;SOR=0.44268;LSEQ=CAAGACACACGTGACCCACC;RSEQ=CCCTCTCTGAACATGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:237:137:55,82:42,57:0.5781:2,2:25.2:1:29.6:1:0.78894:1.09813:55.9:33.25:0.5783:0:2.4 0/1:183:69:26,43:50,64:0.377:2,2:25.8:1:28.8:1:0.442:1.29026:55.8:138:0.392:0:2.5 -6 29975997 . C CTG 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00011;SOR=0.45241;LSEQ=GACACACGTGACCCACCCCC;RSEQ=TCTCTGAACATGAGGCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:238:128:49,79:50,60:0.5378:2,2:25.5:1:30.9:1:0.29242:1.34184:55.8:256:0.5447:0.1008:2.4 0/1:180:62:25,37:49,68:0.3444:2,2:26.9:1:29.9:1:0.87435:1.06605:55.7:61:0.3547:0.05:2.5 -6 29976024 . C G 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17833;SOR=0.69893;LSEQ=AACATGAGGCATAACGAGGT;RSEQ=CTGGGTTCTGGGCTTCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:85:28,57:41,48:0.4885:2,2:21.1:1:31.6:1:0.08915:1.7333:58.2:20.25:0.488:0:2.4 0/1:110:44:17,27:20,45:0.4:2,2:21.1:1:30.8:1:0.41649:1.41:58.5:43:0.4019:0:2.4 -6 29976161 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1505;SOR=Inf;LSEQ=AGAAGTGGGCGGTTGTGGTA;RSEQ=TGCCTTCTGGAGAGGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:196,71:0:2,0:21.9:1:31.8:1:1:0:60:65.75:0.9925:0:0.1 0/1:171:2:1,1:129,40:0.0117:2,2:13:1:28.5:1:0.42312:3.19774:60:4:0.012:0:1 -6 29976193 . C T 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16704;SOR=5.61393;LSEQ=GAGGAACAGAGATACACATG;RSEQ=CATGTGCAGCACAAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:1:0,1:271,179:0.0022:2,0:9:0:14:0:0.39911:0:60:0:0:0:1 0/1:324:4:1,3:196,124:0.0123:2,2:9.3:1:26.8:1:0.30368:4.71959:60:8:0.0127:0:1.5 -6 29976253 . TG T 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATGGGGTAAGGAGAGAGA;RSEQ=GGGGCGGCCATGTCTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:0:0,0:214,281:0:2,0:24.6:1:31.3:1:1:0:60:122.75:1:0:0.4 0/1:362:14:6,8:144,204:0.0387:2,2:20.4:1:31.1:1:1:1.06:60:28:0.0393:0.0055:0.2 -6 29976262 . C T 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25383;SOR=0.82147;LSEQ=AAGGAGAGAGATGGGGGCGG;RSEQ=CATGTCTCTTAGGGAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:129:57,72:130,183:0.2912:2,2:24.3:1:29.9:1:0.672:1.11:59.9:63.5:0.294:0:1.1 0/1:329:83:31,52:98,148:0.2523:2,2:21.6:1:28.9:1:0.79497:1.11035:60:82:0.2539:0:1.2 -6 29976312 . C G 106 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00021;SOR=18.11768;LSEQ=CTGGAGACCTTTAGCAGGGT;RSEQ=GGGGCTGGGTCCTGGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:1,0:117,142:0.0038:2,0:49:0:34:0:0.45385:0:60:2:0.004:0:1 0/1:168:11:5,6:59,97:0.0655:2,2:22.8:1:30.7:1:0.75031:1.37:60:22:0.0663:0:1.8 -6 29976419 . TTGGAGCTGTGGTCAC T 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTGCTGGCCTGGTTCTCC;RSEQ=TGGAGCTGTGGTCACTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:0:0,0:295,247:0:2,0:23.7:1:30:1:1:0:60:134.5:1:0:0.2 0/1:431:20:9,11:228,182:0.0464:2,2:28.1:1:30.9:1:0.36725:1.52958:59.3:40:0.0469:0.007:0.8 -6 29976432 . C T 52 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25694;SOR=2.97823;LSEQ=GTTCTCCTTGGAGCTGTGGT;RSEQ=ACTGGAGCTGTGGTCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:572:2:0,2:305,265:0.0035:2,0:1:0:27:1:0.21745:0:58.5:4:0.0036:0:1 0/1:483:5:1,4:243,218:0.0104:2,2:17.2:1:22.8:1:0.19664:4.44562:60:4:0.0087:0:1.2 -6 29976499 . C G 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.3924;LSEQ=GTGGGGAAGGGGTGAGGAGT;RSEQ=GGGTTTGAGTTTTCTTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:149:54,95:100,179:0.3481:2,2:23.9:1:31.2:1:1:1.02:60:148:0.3491:0:1.1 0/1:312:54:17,37:87,169:0.1731:2,2:21.4:1:30.1:1:0.75414:1.12006:59.9:53:0.1743:0:1.3 -6 29976741 . A G 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60927;SOR=1.80741;LSEQ=AAGGTCCCTGCTGAGGACAG;RSEQ=CCTTAGGAGGGCAGTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:2,2:23,10:0.1081:2,2:22.5:1:33.3:1:0.5821:2.24385:60:8:0.1081:0:1 0/1:11:2:2,0:9,0:0.1818:0,0:26.5:1:33:0:1:0:60:4:0.2:0:1 -6 29976789 . T C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00274;SOR=Inf;LSEQ=CACATCTGCTTTCCTTGTTT;RSEQ=TCCTGATCCTGCCCTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:44,10:0:2,0:23.1:1:30.4:1:1:0:57.6:108:1:0:0.6 0/1:26:5:5,0:20,1:0.1923:1,0:25:1:32.6:1:1:0:60:10:0.2:0:1.4 -6 29976838 . A G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00082;SOR=3.06816;LSEQ=CACATTTCTGGAAACTTCTC;RSEQ=AGGTTCCAAGACTAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:52:48,4:62,3:0.4444:1,2:23.8:1:30.6:1:0.6983:1.71412:54.6:104:0.4522:0:1.6 1/0:59:42:35,7:16,1:0.7119:1,2:21:1:28.8:1:0.41741:3.14969:56.5:20:0.7018:0:1.7 -6 29976842 . T G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.86178;SOR=1.11503;LSEQ=TTTCTGGAAACTTCTCAAGG;RSEQ=TCCAAGACTAGGAGGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:33:30,3:86,4:0.2683:1,2:24.6:1:31.8:1:0.38401:2.13483:51.8:66:0.2727:0:2 0/1:62:18:14,4:38,6:0.2903:2,2:21.9:1:30.7:1:0.45697:1.79095:52.8:36:0.2903:0:2.4 -6 29976857 . G C 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00386;SOR=Inf;LSEQ=CAAGGTTCCAAGACTAGGAG;RSEQ=TTCCTCTAGGACCTCATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:148,9:0:2,0:25.2:1:31.3:1:1:0:58.2:77.5:1:0:0.6 0/1:79:5:5,0:62,12:0.0633:2,0:20.2:1:33.8:1:1:0:57.6:10:0.0649:0:2.4 -6 29976904 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0672;SOR=Inf;LSEQ=ACCTTCCTGGCCTCTCACAG;RSEQ=ACGTTTTCTTCCCGCAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:254,108:0:2,0:23.2:1:30.8:1:1:0:59.4:44.25:1:0:0.3 0/1:249:3:1,2:161,85:0.012:2,2:16:1:26:1:0.2801:3.76709:60:6:0.0125:0:1 -6 29976906 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02841;SOR=Inf;LSEQ=CTTCCTGGCCTCTCACAGGA;RSEQ=GTTTTCTTCCCGCAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:260,114:0:2,0:23.2:1:31:1:1:0:59.4:73.8:1:0:0.3 0/1:262:4:1,3:165,93:0.0153:2,2:11.5:1:24.5:1:0.14093:5.28829:59:3:0.0116:0:1.3 -6 29976971 . C A 96 NM4;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01251;SOR=0;LSEQ=GCAAGTAAGTATGAAGGAGG;RSEQ=TGATCCCTGAGATCCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:9:9,0:349,297:0.0137:2,0:25:1:30.4:1:0.00491:0:39.4:18:0.014:0:6.1 0/0:484:0:0,0:245,239:0:2,0:27.6:1:31.6:1:1:0:59.5:68.143:1:0:0.2 -6 29976978 . CT AA 86 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02185;SOR=0;LSEQ=AGTATGAAGGAGGCTGATCC;RSEQ=GAGATCCTTGGGATATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:638:7:7,0:335,296:0.011:2,0:32.3:1:30.9:1:0.01681:0:42.6:14:0.0111:0.0016:6.1 0/0:482:0:0,0:239,243:0:2,0:26.7:1:30.7:1:1:0:59.6:79.333:1:0:0.2 -6 29976982 . G A 82 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0236;SOR=0;LSEQ=TGAAGGAGGCTGATCCCTGA;RSEQ=ATCCTTGGGATATTGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:7:7,0:329,293:0.0111:2,0:35.9:1:29.3:1:0.01663:0:42.6:6:0.0098:0:6.1 0/0:459:0:0,0:224,235:0:2,0:27.1:1:31.3:1:1:0:59.6:113.75:1:0:0.2 -6 29977000 . G T 115 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06601;SOR=0.35432;LSEQ=GAGATCCTTGGGATATTGTG;RSEQ=TTGGGAGCCCATGGGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:16:8,8:319,297:0.0253:2,2:20.3:1:28.8:1:1:1.07393:38.5:15:0.0244:0:5.4 0/0:439:4:2,2:211,224:0.0091:2,2:11:1:29:1:1:1.06:33.3:8:0.0092:0:3.8 -6 29977004 . G A 91 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05442;SOR=0.15879;LSEQ=TCCTTGGGATATTGTGGTTG;RSEQ=GAGCCCATGGGGGAGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:9:3,6:317,301:0.0144:2,2:8.3:1:29:1:0.33112:2.10388:43.2:18:0.0149:0:4.8 0/0:434:1:0,1:208,224:0.0023:2,0:17:0:25:0:1:0:40:2:0.0023:0:6 -6 29977008 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01116;SOR=Inf;LSEQ=TGGGATATTGTGGTTGGGAG;RSEQ=CCATGGGGGAGCTCACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:612:0:0,0:307,304:0:2,0:23:1:31:1:1:0:59:37.188:1:0:0.3 0/1:422:5:1,4:200,216:0.0118:2,2:16.8:1:26.2:1:0.37458:3.69358:54:10:0.012:0:1.8 -6 29977009 . C A 94 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.259;SOR=0.42667;LSEQ=GGGATATTGTGGTTGGGAGC;RSEQ=CATGGGGGAGCTCACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:10:1,9:306,296:0.0163:2,2:11.9:1:28.4:1:0.01091:9.27895:38.9:20:0.0166:0:5.3 0/0:428:3:2,1:204,219:0.007:2,2:8:1:25.3:1:0.61213:2.14:53.3:6:0.0072:0:2.7 -6 29977011 . A G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05684;SOR=0.36811;LSEQ=GATATTGTGGTTGGGAGCCC;RSEQ=TGGGGGAGCTCACCCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:19:8,11:304,288:0.031:2,2:15.6:1:29.5:1:0.48925:1.4505:39.7:38:0.0317:0:4.2 0/1:430:5:3,2:203,222:0.0116:2,2:7.6:1:28.6:1:0.67392:1.64:49.4:10:0.0118:0:2.8 -6 29977047 . G T 135 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00309;SOR=0.19433;LSEQ=ACCCCACAATTCCTCCTCTA;RSEQ=CCACATCTCCTGTGGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:607:22:5,17:267,318:0.0362:2,2:34.3:1:30.3:1:0.04735:2.85019:41.3:44:0.037:0:4 0/0:414:3:1,2:206,205:0.0072:2,2:34:1:30.3:1:1:2.00649:43.3:6:0.0074:0:3.7 -6 29977056 . C T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14898;SOR=1.47522;LSEQ=TTCCTCCTCTAGCCACATCT;RSEQ=CTGTGGGATCTGACCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:32:5,27:262,317:0.0523:2,2:37.2:1:30.2:1:8e-04:4.45401:39.9:64:0.0532:0:3.8 0/1:425:32:15,17:200,193:0.0753:2,2:34.2:1:30.3:1:0.71537:1.17399:46.9:64:0.0766:0:2.1 -6 29977068 . G C 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACATCTCCTGTGGGATCT;RSEQ=ACCAGGTTCTGTTTTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:0:0,0:275,343:0:2,0:25.4:1:31.6:1:1:0:58.8:55.182:0.9984:0:0.4 0/1:458:30:13,17:222,205:0.0655:2,2:22.8:1:31.6:1:0.45041:1.41505:59.5:60:0.0664:0:1.1 -6 29977087 . T C 107 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08012;SOR=0.26216;LSEQ=TGACCAGGTTCTGTTTTTGT;RSEQ=CTACCCCAGGCAGCCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:594:10:1,9:254,330:0.0168:2,2:11.8:1:32.4:1:0.04931:6.91114:39:20:0.0171:0:3.3 0/0:448:2:1,1:225,221:0.0045:2,2:4:0:32.5:1:1:1.01806:49.5:4:0.0046:0:2.5 -6 29977101 . CC TG 104 Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00327;SOR=0;LSEQ=TTTTGTTCTACCCCAGGCAG;RSEQ=AAAGTGCCCAGGGCTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:568:10:0,10:253,302:0.0176:2,0:6.8:1:31.4:1:0.00276:0:36.4:20:0.018:0.0141:3.9 0/0:443:0:0,0:219,218:0:2,0:25:1:31:1:1:0:60:47.556:0.9862:0:0.3 -6 29977145 . G C 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00075;SOR=2.27199;LSEQ=GTCTCTCACGGCTTGTAAAG;RSEQ=TGAGACCCTGGGGAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:30:15,15:162,246:0.0685:2,2:23.3:1:31.6:1:0.33529:1.52:60:29:0.0678:0:1.1 0/1:342:49:15,34:128,165:0.1433:2,2:23.5:1:31.2:1:0.11697:1.75559:60:15.333:0.1386:0:1.3 -6 29977299 . AT A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.13154;SOR=1.79589;LSEQ=ATATGAATTTGTTCATGAAT;RSEQ=TTTTTCTATAGTGTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:12:9,3:258,167:0.0275:2,2:13.6:1:31.4:1:0.38236:1.94:44.8:24:0.0276:0.0137:4.3 0/1:352:17:11,6:203,132:0.0483:2,2:10.1:1:29.4:1:0.80431:1.19:53.4:34:0.0484:0.0227:4.1 -6 29977308 . A G 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06768;SOR=1.82673;LSEQ=TGTTCATGAATATTTTTTCT;RSEQ=TAGTGTGAGACAGCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:18:12,6:271,192:0.0374:2,2:14.8:1:33.4:1:0.62764:1.42:47.7:36:0.0382:0:4.3 0/1:422:28:15,13:236,158:0.0664:2,2:12.5:1:30.6:1:0.553:1.29369:54.5:56:0.0673:0:4.1 -6 29977317 . G A 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07543;SOR=1.73611;LSEQ=ATATTTTTTCTATAGTGTGA;RSEQ=ACAGCTGCCTTGTGTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:19:12,7:300,211:0.0358:2,2:22.8:1:30.8:1:0.81446:1.21:48.3:38:0.0361:0:4.2 0/1:478:29:15,14:257,190:0.0607:2,2:21:1:28.6:1:0.56597:1.26182:54.7:13.5:0.0574:0:4.1 -6 29977327 . T C 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10464;SOR=1.59732;LSEQ=TATAGTGTGAGACAGCTGCC;RSEQ=TGTGTGGGACTGAGAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:24:12,12:313,250:0.0408:2,2:26.9:1:31.9:1:0.67655:1.25151:50.4:48:0.0419:0:3.8 0/1:534:34:16,18:275,225:0.0637:2,2:27.6:1:30.4:1:0.37967:1.37416:55.5:68:0.065:0:3.8 -6 29977342 . A T 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02901;SOR=1.77532;LSEQ=CTGCCTTGTGTGGGACTGAG;RSEQ=GGCAAGATTTGTTCATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:25:12,13:298,310:0.0395:2,2:34.8:1:30.2:1:1:1.04134:50.8:50:0.0401:0:3.7 0/1:573:39:17,22:266,268:0.0681:2,2:35.2:1:29.2:1:0.50882:1.2839:56.1:78:0.0684:0:3.5 -6 29977350 . T G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.24333;LSEQ=TGTGGGACTGAGAGGCAAGA;RSEQ=TTGTTCATGCCTTCCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:199:94,105:197,226:0.3199:2,2:25:1:31.7:1:0.93138:1.03:48.8:65.333:0.3213:0:2 0/1:575:59:29,30:241,275:0.1026:2,2:24.1:1:31.3:1:0.78352:1.10:49.9:118:0.1035:0:2.1 -6 29977357 . A C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24918;LSEQ=CTGAGAGGCAAGATTTGTTC;RSEQ=TGCCTTCCCTTTGTGACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:186:86,100:186,232:0.3069:2,2:27.4:1:31.4:1:0.72341:1.07:48.5:92:0.3082:0:2.1 0/1:554:55:27,28:227,270:0.0993:2,2:27.5:1:30.7:1:0.67017:1.15:49.5:110:0.1002:0:2.1 -6 29977358 . TG CA 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.78788;LSEQ=TGAGAGGCAAGATTTGTTCA;RSEQ=CCTTCCCTTTGTGACTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:9:5,4:265,329:0.0149:2,2:19.9:1:29.3:1:0.52327:1.55:50.2:18:0.0151:0.0017:1.9 0/1:545:44:20,24:228,270:0.0807:2,2:29.9:1:30.1:1:1:1.01331:41.3:88:0.0815:0:2.1 -6 29977359 . G GC 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.26693;LSEQ=GAGAGGCAAGATTTGTTCAT;RSEQ=CCTTCCCTTTGTGACTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:187:86,101:180,233:0.3051:2,2:27.9:1:31.2:1:0.59545:1.10:48.9:45.75:0.3096:0.0408:2 0/1:544:57:27,30:200,241:0.1048:2,2:28.9:1:30.9:1:0.77942:1.08:49.5:56:0.1131:0.0074:2.1 -6 29977377 . C G 158 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=11.61612;LSEQ=ATGCCTTCCCTTTGTGACTT;RSEQ=AAGAACCCTGACTTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:4:2,2:217,319:0.0074:2,2:15:1:33.3:1:1:1.47:44.8:8:0.0075:0:2.3 0/1:463:37:16,21:179,247:0.0799:2,2:18.4:1:30.4:1:1:1.05:40.5:36:0.0791:0:2.3 -6 29977388 . ACTTCT A 128 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=11.33622;LSEQ=TTGTGACTTCAAGAACCCTG;RSEQ=CTTTCTGCAAAGGCATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:2:1,1:159,297:0.0044:2,2:9.5:1:29.5:1:1:1.87:50:4:0.0044:0.0022:2.5 0/1:380:18:5,13:130,230:0.0474:2,2:14.9:1:30.9:1:0.61663:1.46815:34.5:36:0.0477:0.0184:3.3 -6 29977400 . G A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31861;SOR=4.03344;LSEQ=GAACCCTGACTTCTCTTTCT;RSEQ=CAAAGGCATCTGAATGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:1:1,0:123,268:0.0025:2,0:1:0:23:0:0.31633:0:60:2:0.0026:0:1 0/1:294:3:2,1:90,200:0.0102:2,2:20:1:26.7:1:0.23303:4.42:60:6:0.0104:0:1 -6 29977402 . AAAGGCATCTGAATGTGTCTGTGTCCCTATAGGCATAATGTGAGGTGGTGGG A 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04535;SOR=0;LSEQ=ACCCTGACTTCTCTTTCTGC;RSEQ=GAGACCAGCCCACACCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:7:0,7:110,253:0.0189:2,0:69:1:32:1:0.10904:0:58.7:14:0.0192:0.0189:2.1 0/0:263:0:0,0:79,184:0:2,0:20.7:1:29.6:1:1:0:57.8:86.667:1:0:0.6 -6 29977409 . T C 90 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00877;SOR=10.55806;LSEQ=CTTCTCTTTCTGCAAAGGCA;RSEQ=CTGAATGTGTCTGTGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:0,1:82,238:0.003:2,0:3:0:30:0:1:0:40:2:0.0032:0:4 0/1:223:7:0,7:52,161:0.0314:2,0:13.6:1:32.4:1:0.20258:0:31.9:14:0.0326:0:4 -6 29978916 . T A 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAGTGCTGTGTGGCAGGTGA;RSEQ=CCAGAGGGTGGGCTGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:29:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:32:0:30.5:1:1:0:60:4:1:0:1 -6 29979560 . A G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAGCTGCTGTCAGTGGAGAT;RSEQ=GGGAGACTCTGGCAGGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:33:0:1:0:60:4:1:0:2.5 0/0:2:0:0,0:1,1:0:2,0:44.5:1:29.5:1:1:0:60:4:1:0:0 -6 29979579 . T C 34 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TAGGGAGACTCTGGCAGGAG;RSEQ=ACACAGAGGAGAGGGCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:34:0:1:0:60:4:1:0:2.5 0/0:2:0:0,0:1,1:0:2,0:30:1:27:1:1:0:60:4:1:0:0 -6 30227246 . T A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18673;SOR=2.00935;LSEQ=TTTTGGTTCTCCCAACCTTC;RSEQ=TCCTGGATACTTGTGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:10:10,0:53,1:0.1563:1,0:19.2:1:30.4:1:1:0:60:20:0.1563:0:1 0/1:33:9:9,0:24,0:0.2727:1,0:21.7:1:30.3:1:1:0:60:18:0.2813:0:1 -6 30227322 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1355;SOR=Inf;LSEQ=TAGAGAAGCCAATCAGCTTC;RSEQ=CCGCGATCCCGGCACTACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:207,5:0:1,0:25.6:1:29.6:1:1:0:60:69.667:1:0:0.1 0/1:124:2:2,0:116,6:0.0161:1,0:28.5:1:30:1:1:0:60:4:0.0171:0:1 -6 30227340 . C A 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=TCGCCGCGATCCCGGCACTA;RSEQ=GATCCCGGCACTACAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:246,48:0:2,0:22.9:1:31.4:1:1:0:60:293:1:0:0.2 0/1:192:7:6,1:150,34:0.0365:2,2:12.7:1:29.7:1:1:1.36:60:14:0.0372:0:1 -6 30227397 . C T 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.93349;LSEQ=CTCAGATTCTCCCCAAACGC;RSEQ=AAGGATGGGGGTCATGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:698:58:31,27:358,282:0.0831:2,2:25.3:1:28.7:1:0.78286:1.10554:60:18.333:0.0812:0:1.2 0/1:571:120:69,51:253,197:0.2102:2,2:25.7:1:28.9:1:0.83626:1.05:60:29:0.2094:0:1.2 -6 30227399 . A G 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00538;SOR=0.53593;LSEQ=CAGATTCTCCCCAAACGCCA;RSEQ=GGATGGGGGTCATGGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:65:38,27:354,289:0.0918:2,2:31.3:1:30.7:1:0.69479:1.15:60:15.25:0.0882:0:1.2 0/1:584:30:15,15:310,244:0.0514:2,2:27.4:1:29.8:1:0.57386:1.26996:60:29:0.0508:0:1.2 -6 30227412 . T C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70624;SOR=1.16508;LSEQ=AACGCCAAGGATGGGGGTCA;RSEQ=GGCTCCCCGAACCCTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:811:14:8,6:414,382:0.0173:2,2:6.6:1:30.2:1:0.79133:1.23:38.5:28:0.0176:0:6 0/1:698:14:7,7:355,328:0.0201:2,2:9.6:1:27.5:1:1:1.08218:44.7:13:0.0189:0:6.2 -6 30227416 . T G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.28583;SOR=1.49593;LSEQ=CCAAGGATGGGGGTCATGGC;RSEQ=CCCCGAACCCTCCTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:831:14:9,5:421,393:0.0168:2,2:11.4:1:29.6:1:0.42493:1.68:43.9:28:0.0173:0:6.2 0/1:720:18:9,9:355,346:0.025:2,2:10.4:1:26.8:1:1:1.02598:43.3:5:0.0216:0:6.4 -6 30227425 . C G 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGTCATGGCTCCCCGAAC;RSEQ=CTCCTCCTGCTGCTCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:880:0:0,0:436,444:0:2,0:24.8:1:30.6:1:1:0:59.4:37.261:1:0:0.5 0/1:769:48:23,25:352,367:0.0624:2,2:26.1:1:30.5:1:1:1.04249:60:47:0.0622:0:1.2 -6 30227442 . T G 155 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03689;SOR=1.70395;LSEQ=AACCCTCCTCCTGCTGCTCT;RSEQ=GGGGGCCCTGGCCCTGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:828:28:13,15:369,430:0.0338:2,2:28.3:1:31:1:1:1.01:43.2:27:0.0336:0:5.3 0/1:746:42:20,22:328,376:0.0563:2,2:25.1:1:28.8:1:1:1.04:48.3:20:0.0545:0:6.2 -6 30227449 . CC AG 162 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01001;SOR=2.0144;LSEQ=CTCCTGCTGCTCTTGGGGGC;RSEQ=TGGCCCTGACCGAGACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:785:23:11,12:344,418:0.0293:2,2:31.8:1:31.9:1:0.83402:1.11:43.7:46:0.0298:0.0025:4.9 0/1:715:41:20,21:310,359:0.0573:2,2:32:1:30.4:1:0.8721:1.10:48:82:0.0586:0:5.2 -6 30227473 . C T 78 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0061;SOR=Inf;LSEQ=GCCCTGACCGAGACCTGGGC;RSEQ=GGTGAGTGCGGGGTCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:627:0:0,0:270,356:0:2,0:25.7:1:29.7:1:1:0:59.2:33.778:1:0:0.4 0/1:588:7:3,4:254,325:0.0119:2,2:26.4:1:28.1:1:1:1.04198:40:6:0.0105:0:5.9 -6 30227486 . G A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61211;SOR=0.73699;LSEQ=CCTGGGCCGGTGAGTGCGGG;RSEQ=TCGGGAGGGAAAGGGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:545:9:4,5:221,315:0.0165:2,2:11.9:1:30.3:1:1:1.14:48.6:18:0.0168:0:5.3 0/1:491:6:4,2:194,291:0.0122:2,2:11.5:1:27.5:1:0.22655:2.99:52.8:12:0.0124:0:4.8 -6 30227491 . G C 71 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.02184;SOR=Inf;LSEQ=GCCGGTGAGTGCGGGGTCGG;RSEQ=AGGGAAAGGGCCTCTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:526:0:0,0:216,308:0:2,0:22.6:1:31.2:1:1:0:59.2:103.8:0.9981:0:0.4 0/1:460:5:2,3:180,274:0.0109:2,2:12.4:1:30.8:1:1:1.01:38.8:10:0.011:0:6.4 -6 30227499 . G T 145 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02335;SOR=2.06647;LSEQ=GTGCGGGGTCGGGAGGGAAA;RSEQ=GGCCTCTGCGGGGAGAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:17:7,10:168,274:0.037:2,2:10.8:1:31.4:1:0.80323:1.14:41.6:34:0.0372:0:4.8 0/1:408:30:13,17:149,228:0.0735:2,2:14.8:1:29.7:1:0.70156:1.17:49.3:14:0.0695:0:5.3 -6 30227508 . C T 129 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00364;SOR=3.175;LSEQ=CGGGAGGGAAAGGGCCTCTG;RSEQ=GGGGAGAAGCGAGTGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:9:3,6:141,237:0.0233:2,2:7.6:1:30.4:1:1:1.18939:45.2:18:0.0236:0:5.1 0/1:341:24:11,13:122,194:0.0704:2,2:8.7:1:28.2:1:0.51938:1.34:50:11:0.0659:0:5.1 -6 30227527 . C T 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=GCGGGGAGAAGCGAGTGGCC;RSEQ=GCCCGGCCCGGGGAGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:113,198:0:2,0:23.3:1:29.9:1:1:0:60:61.2:1:0:0.2 0/1:232:23:9,14:81,128:0.0991:2,2:24.9:1:29.6:1:1:1.02:60:22:0.0969:0:1 -6 30227583 . C G 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11747;SOR=1.5662;LSEQ=GGCGGGTCTCAGCCTCTCCT;RSEQ=GCCTCCAGGCTCCCACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:26:17,9:150,168:0.0754:2,2:23:1:32.1:1:0.10143:2.11:60:52:0.0767:0:1.1 0/1:256:29:13,16:114,113:0.1133:2,2:23.4:1:30.4:1:0.69417:1.24061:60:28:0.1107:0:1.1 -6 30227838 . G T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02465;SOR=Inf;LSEQ=GAACCTGCGGACCCTGCTCC;RSEQ=CTATTACAACCAGAGCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:108,290:0:2,0:20.9:1:31:1:1:0:60:48.75:0.9949:0:0.1 0/1:264:4:1,3:74,185:0.0152:2,2:21.3:1:31:1:1:1.19919:60:8:0.0153:0:1 -6 30227912 . CG TT 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04422;SOR=Inf;LSEQ=CGATCCCTCCCCATCCCCCA;RSEQ=GACAGCCCAGGTCCCGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:19,86:0:2,0:20.5:1:30.5:1:1:0:60:51.5:0.9904:0:0.1 0/1:59:3:2,1:12,43:0.0508:2,2:29.7:1:29.3:1:0.14156:6.86:60:6:0.0508:0:2 -6 30227915 . A T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01588;SOR=Inf;LSEQ=TCCCTCCCCATCCCCCACGG;RSEQ=CAGCCCAGGTCCCGGGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:20,79:0:2,0:21.2:1:30.1:1:1:0:60:98:1:0:0.2 0/1:56:4:2,2:12,40:0.0714:2,2:28.5:1:29.3:1:0.25767:3.25:60:8:0.0714:0:2 -6 30227955 . AC A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.52027;SOR=0;LSEQ=GAGTCTCCGGTCTGAGATCC;RSEQ=CCCGAGGCTGCGGGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:21,40:0.0317:2,2:34:1:31:1:1:1.88:60:4:0.0317:0:0 0/0:40:0:0,0:18,22:0:2,0:24:1:30.4:1:1:0:60:39:1:0:0.5 -6 30228038 . CA C 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.57048;SOR=2.87635;LSEQ=GGTTTAATTTCAGTTTAGGC;RSEQ=AAATCCCCGCGGGTTGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:1:1,0:116,26:0.0069:2,0:40:0:31:0:1:0:60:2:0.007:0:0 0/1:101:2:1,1:80,19:0.0198:2,2:35.5:1:28.5:1:0.35842:4.12948:60:4:0.0202:0:3.5 -6 30228063 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18245;SOR=Inf;LSEQ=TCCCCGCGGGTTGGTCGGGG;RSEQ=GGGAGCGGGGCTCGGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:161,69:0:2,0:22.9:1:30.9:1:1:0:60:75.667:1:0:0.2 0/1:172:2:1,1:115,55:0.0116:2,2:19:1:29:1:0.54644:2.0812:60:4:0.0117:0:1 -6 30228073 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.26509;SOR=0;LSEQ=TTGGTCGGGGCGGGAGCGGG;RSEQ=CTCGGTGTTCGGGGCTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:1,2:196,91:0.0103:2,2:25:1:25.3:1:0.24175:4.28378:60:2:0.0071:0:1.7 0/0:215:0:0,0:140,75:0:2,0:22.9:1:30.5:1:1:0:60:29.714:1:0:0.2 -6 30228138 . G A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06541;SOR=0.5032;LSEQ=CACCATCCAGAGGAAGCATG;RSEQ=CTGCGACGTGGGCCCGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:26:11,15:175,191:0.0663:2,2:24.6:1:31:1:0.68597:1.2487:60:52:0.0675:0:1.2 0/1:348:12:8,4:159,177:0.0345:2,2:29.8:1:28.4:1:0.24364:2.22:60:24:0.0346:0:1.1 -6 30228224 . A T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=TTACATCGCCCTGAACGAGG;RSEQ=CCTGCACTCCTGGACCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:54,122:0.0112:2,2:25.5:1:26:0:0.52371:2.25:60:4:0.0113:0:1 0/0:155:0:0,0:56,99:0:2,0:25.8:1:29:1:1:0:60:50.667:1:0:0.4 -6 30228225 . C A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.60042;SOR=2.29699;LSEQ=TACATCGCCCTGAACGAGGA;RSEQ=CTGCACTCCTGGACCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:1:1,0:53,122:0.0057:2,0:1:0:26:0:0.30682:0:60:2:0.0058:0:1 0/1:154:2:1,1:54,98:0.013:2,2:30:1:31:0:1:1.81:60:4:0.0132:0:1 -6 30228230 . A C 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00474;SOR=2.30512;LSEQ=CGCCCTGAACGAGGACCTGC;RSEQ=CTCCTGGACCGCCGCGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:24:6,18:45,102:0.1404:2,2:19.3:1:31.4:1:0.63943:1.32142:60:48:0.1404:0:1.2 0/1:146:40:14,26:38,68:0.274:2,2:25.1:1:29.9:1:1:1.03756:59.9:39:0.269:0:1.2 -6 30228241 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21491;SOR=Inf;LSEQ=AGGACCTGCACTCCTGGACC;RSEQ=CCGCGAACACAGCGGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:44,107:0:2,0:23.8:1:31.5:1:1:0:60:150:1:0:0.2 0/1:131:2:1,1:48,81:0.0153:2,2:22.5:1:26:1:1:1.68:60:4:0.0153:0:1 -6 30228379 . A G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47933;SOR=1.48448;LSEQ=CGGGAAGGAGACGCTGCAGC;RSEQ=CGCGGGTACCAGGGGCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:14:3,11:17,38:0.2029:2,2:19.3:1:31.1:1:0.74247:1.62937:58.6:28:0.2029:0:1.9 0/1:40:11:4,7:12,17:0.275:2,2:20:1:31.2:1:1:1.22884:60:22:0.2821:0:1.3 -6 30228384 . G C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53512;SOR=0;LSEQ=AGGAGACGCTGCAGCACGCG;RSEQ=GTACCAGGGGCCACGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:19,45:0.0303:2,2:22:1:27.5:1:0.51748:2.33:60:4:0.0313:0:1.5 0/0:37:0:0,0:13,24:0:2,0:25.5:1:29.9:1:1:0:59.7:74:1:0:0.4 -6 30228395 . CCACGGGGGCG TCACGGGGCA 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54974;SOR=0;LSEQ=CAGCACGCGGGTACCAGGGG;RSEQ=CCTCCCTCATTTCCTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:3:2,1:13,41:0.0517:2,2:29:1:29:1:0.16627:6.06:57:6:0.0556:0.0172:2.3 0/0:32:0:0,0:10,22:0:2,0:23.2:1:30.4:1:1:0:59.7:31:1:0:0.3 -6 30228398 . CG C 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52687;SOR=1.70212;LSEQ=CACGCGGGTACCAGGGGCCA;RSEQ=GGGGCGCCTCCCTCATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:7:1,6:12,32:0.1373:2,2:21.4:1:31.1:1:0.66183:2.21983:59.7:14:0.1373:0.0392:1.9 0/1:28:6:1,5:7,15:0.2143:2,2:21.3:1:30:1:0.63991:2.27148:60:12:0.2143:0:1.5 -6 30228416 . T C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CACGGGGGCGCCTCCCTCAT;RSEQ=TCCTGTAGATTTCCCGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:6:2,4:6,26:0.1579:2,2:38:1:32.5:1:0.58704:2.12:58.2:12:0.1667:0:2.7 0/1:19:3:0,3:4,12:0.1579:2,0:35.3:1:31.7:1:1:0:60:6:0.1579:0:2 -6 30228712 . AG A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=TTGTTCTCTCCCTCACACTC;RSEQ=TGTGTCCGTGGCTCCGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:2,3:0.375:2,0:9.3:1:31.2:1:0.19643:0:60:6:0.375:0.125:1.3 1/1:3:3:2,1:0,0:1:0,2:21.3:1:28.8:1:1:0:60:6:1:0.3333:1.3 -6 30228721 . G A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCCTCACACTCAGTGTGTCC;RSEQ=TGGCTCCGATTCCAGCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:0.4286:2,0:14.3:1:31.3:1:1:0:60:6:0.4286:0:1.3 1/1:2:2:1,1:0,0:1:0,2:37.5:1:31:0:1:0:60:4:1:0:1 -6 30228879 . C T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16511;SOR=2.13721;LSEQ=GGGTTCTGTGCTCCCTTCCC;RSEQ=ATCCCAGGTGTCCTGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:10:9,1:71,7:0.1136:2,2:28.2:1:31.6:1:1:1.12536:60:20:0.1136:0:2.5 0/1:37:8:7,1:24,5:0.2162:2,2:21.1:1:31.4:1:1:1.44:60:16:0.2162:0:2.9 -6 30228880 . AT A 52 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.5536;SOR=0;LSEQ=GGTTCTGTGCTCCCTTCCCC;RSEQ=CCCAGGTGTCCTGTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:3:3,0:71,7:0.033:2,0:26.7:1:33.3:1:1:0:40:6:0.0333:0:8 0/0:39:0:0,0:25,5:0:2,0:25:1:28.9:1:1:0:60:29:0.7632:0:0.1 -6 30228881 . T C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10262;SOR=2.41151;LSEQ=GTTCTGTGCTCCCTTCCCCA;RSEQ=CCCAGGTGTCCTGTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:10:9,1:71,7:0.1099:2,2:28.3:1:32.9:1:1:1.12536:60:20:0.1111:0:2.5 0/1:39:9:8,1:25,5:0.2308:2,2:19.9:1:31.7:1:1:1.58:60:18:0.2368:0:2.8 -6 30228889 . G T 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55106;SOR=0;LSEQ=CTCCCTTCCCCATCCCAGGT;RSEQ=TCCTGTCCATTCTCAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:3:3,0:87,9:0.03:2,0:33.7:1:31:0:1:0:40:6:0.0306:0:8 0/0:50:0:0,0:43,7:0:2,0:21.2:1:30.4:1:1:0:60:15.667:1:0:0.7 -6 30228893 . T C 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55179;SOR=0;LSEQ=CTTCCCCATCCCAGGTGTCC;RSEQ=GTCCATTCTCAGGATGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:3:3,0:95,12:0.0273:2,0:37.7:1:32:0:1:0:40:6:0.0275:0:8 0/0:52:0:0,0:45,7:0:2,0:22:1:30.7:1:1:0:60:51:1:0:0.6 -6 30228898 . AT TA 60 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30744;SOR=0;LSEQ=CCATCCCAGGTGTCCTGTCC;RSEQ=TCTCAGGATGGTCACATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:4:4,0:103,12:0.0336:2,0:34.3:1:30.3:1:1:0:40:8:0.0339:0:7 0/0:56:0:0,0:48,8:0:2,0:22.7:1:29.7:1:1:0:60:55:1:0:0.6 -6 30228918 . TA GG 117 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01149;SOR=0.11024;LSEQ=ATTCTCAGGATGGTCACATG;RSEQ=TGCTGCTGGAGTGTCCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:14:9,5:128,24:0.0843:2,2:15.5:1:30.8:1:0.07264:2.93784:36.9:28:0.0843:0.0361:4.3 0/1:100:1:1,0:80,18:0.01:2,0:20:0:33:0:1:0:31:2:0.0101:0:6 -6 30228932 . G A 120 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00395;SOR=0.14588;LSEQ=CACATGTATGCTGCTGGAGT;RSEQ=TCCTATGAGGAATGCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:18:10,8:149,59:0.0796:2,2:19.7:1:29:1:0.17997:2.01345:39.6:36:0.08:0:4.1 0/1:161:2:1,1:106,52:0.0124:2,2:22:1:28.5:1:1:2.0287:38:4:0.0127:0:4.5 -6 30228936 . T C 135 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00381;SOR=0.18962;LSEQ=TGTATGCTGCTGGAGTGTCC;RSEQ=ATGAGGAATGCAAAGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:20:11,9:151,67:0.084:2,2:20.4:1:31.3:1:0.21381:1.83893:38.9:40:0.0858:0:3.9 0/1:176:3:2,1:111,61:0.017:2,2:22:1:20:1:1:1.10:45.3:0.5:0.0058:0:4 -6 30228938 . T C 168 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00517;SOR=2.07738;LSEQ=TATGCTGCTGGAGTGTCCTA;RSEQ=GAGGAATGCAAAGTGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:32:22,10:147,72:0.1275:2,2:23.4:1:29:1:1:1.08:60:7:0.1157:0:2 0/1:193:45:30,15:94,54:0.2332:2,2:21.2:1:30.7:1:0.72657:1.15:60:90:0.2381:0:1.9 -6 30228957 . G T 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04082;SOR=Inf;LSEQ=ATGAGGAATGCAAAGTGCCT;RSEQ=AATTTTCTGACTCTTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:209,136:0:2,0:24.3:1:31.5:1:1:0:58.6:37.333:1:0:0.6 0/1:284:4:1,3:166,114:0.0141:2,2:14:1:26.8:1:0.30943:4.34658:60:8:0.0145:0:1.3 -6 30228974 . C T 133 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00028;SOR=0.11094;LSEQ=CCTGAATTTTCTGACTCTTC;RSEQ=CCTCAGATCCCCCAAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:20:9,11:192,150:0.0552:2,2:23.6:1:31:1:0.36133:1.56246:37:40:0.0559:0:3.5 0/0:311:2:1,1:172,136:0.0064:2,2:23.5:1:20.5:1:1:1.26373:38:1:0.0033:0:4.5 -6 30228992 . G A 132 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=0.10835;LSEQ=TCCCCTCAGATCCCCCAAAG;RSEQ=CACATGTGACCCAGCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:20:9,11:167,167:0.0565:2,2:6.9:1:30.6:1:0.81867:1.22153:37:40:0.0583:0:3.5 0/0:311:2:1,1:157,152:0.0064:2,2:5.5:1:19:1:1:1.0328:38:1:0.0034:0:4.5 -6 30229012 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10228;SOR=Inf;LSEQ=GCACATGTGACCCAGCACCC;RSEQ=ATCTCTGACCATGAGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:140,181:0:2,0:24.3:1:31:1:1:0:59.9:159.5:1:0:0.4 0/1:283:3:1,2:119,160:0.0106:2,2:5.7:1:26:1:1:1.48549:56.3:6:0.0109:0:1 -6 30229013 . A G 179 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03402;SOR=1.59988;LSEQ=CACATGTGACCCAGCACCCC;RSEQ=TCTCTGACCATGAGGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:48:24,24:115,153:0.1514:2,2:22.8:1:30.2:1:0.43025:1.33:59.9:96:0.1529:0:1.6 0/1:279:62:25,37:92,125:0.2222:2,2:23:1:30.2:1:0.88409:1.08892:60:61:0.2251:0:1.5 -6 30229027 . G A 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04605;SOR=Inf;LSEQ=CACCCCATCTCTGACCATGA;RSEQ=GCCACCCTGAGGTGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:93,159:0:2,0:21.6:1:31:1:1:0:59.9:30.5:1:0:0.3 0/1:219:4:3,1:88,127:0.0183:2,2:5.5:1:23:1:0.30985:4.30:60:3:0.0141:0:2.5 -6 30229034 . C CT 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00357;SOR=2.04882;LSEQ=TCTCTGACCATGAGGCCACC;RSEQ=TGAGGTGCTGGGCCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:35:15,20:73,126:0.1489:2,2:22.8:1:29.4:1:0.57087:1.29:59.9:34:0.1472:0.0298:1.2 0/1:193:51:21,30:54,87:0.2642:2,2:18:1:29.5:1:0.73984:1.13:59.7:102:0.2684:0.0933:0.9 -6 30229102 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17773;SOR=Inf;LSEQ=TGGCAGCAGGATGGGGAGGA;RSEQ=CAGACCCAGGACACGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:66,76:0:2,0:24.1:1:31.2:1:1:0:59.7:27.4:1:0:0.1 0/1:104:2:1,1:43,59:0.0192:2,2:15.5:1:29:1:1:1.37:60:4:0.0198:0:1.5 -6 30229206 . T C 103 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.04854;SOR=3.65359;LSEQ=CGGAGAGGAGCAGAGATACA;RSEQ=GTGCCATGTGCAGCATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:3:2,1:244,172:0.0072:2,2:5.7:1:31:1:1:1.41:45:6:0.0073:0:2.3 0/1:389:10:5,5:225,154:0.0257:2,2:9.8:1:31.1:1:0.74633:1.45955:33.4:20:0.0261:0:2.6 -6 30229222 . T C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15504;SOR=2.12443;LSEQ=TACATGTGCCATGTGCAGCA;RSEQ=GAGGGGCTGCCAGAGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:6:2,4:246,209:0.013:2,2:18.3:1:29.2:1:0.42173:2.34981:48.2:5:0.0109:0:2.2 0/1:440:12:6,6:237,191:0.0273:2,2:24:1:31.3:1:0.7738:1.24022:35.3:24:0.0276:0:2.5 -6 30229267 . G C 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGAGATGGGGTAAGGAGGG;RSEQ=TGTAAGTTGTCTCCTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:187,224:0:2,0:25:1:31.3:1:1:0:59.9:67.5:1:0:0.5 0/1:401:22:11,11:183,196:0.0549:2,2:24.7:1:31.4:1:1:1.07:60:21:0.0528:0:1.5 -6 30229280 . CC AT 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.21933;LSEQ=AGGAGGGGTGTAAGTTGTCT;RSEQ=TCTCAGGGAAAGCAGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:60:27,33:142,156:0.1676:2,2:22.8:1:30.4:1:0.77736:1.1122:60:120:0.1681:0.0112:1.7 0/1:330:102:46,56:115,113:0.3091:2,2:22.1:1:29.2:1:0.40506:1.23813:60:204:0.311:0.0303:1.6 -6 30229306 . A G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=3.57373;LSEQ=AGGGAAAGCAGGAGACCTTC;RSEQ=GCAGGGCAGGGCTGAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:47:22,25:109,132:0.1632:2,2:21.6:1:30.4:1:0.87373:1.07:60:94:0.1661:0:1.7 0/1:248:102:55,47:70,76:0.4113:2,2:22.3:1:29.8:1:0.36907:1.27:60:50:0.4098:0:1.7 -6 30229374 . T C 82 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.53058;SOR=1.6682;LSEQ=CCTTTCCCAGAGCCGTCTTC;RSEQ=CAGCCCACCATCCCCATCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:4:2,2:235,199:0.0091:2,2:24.5:1:29.3:1:1:1.18045:38:3:0.0071:0:2.5 0/1:396:6:3,3:201,189:0.0152:2,2:19.2:1:32:1:1:1.06336:46.5:12:0.0152:0:1.7 -6 30229401 . C T 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=32.28049;LSEQ=ACCATCCCCATCGTGGGCAT;RSEQ=GTTGCTGGCCTGTTTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:1:0,1:221,233:0.0022:2,0:1:0:28:0:1:0:60:2:0.0022:0:1 0/1:437:29:14,15:191,217:0.0664:2,2:22.4:1:30.2:1:1:1.06:60:58:0.0673:0:1.2 -6 30229457 . C T 182 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01969;SOR=1.59036;LSEQ=TGGAGCTGTGGTTGCTGCTG;RSEQ=GATGTGGAGGAAGAAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:59:21,38:103,175:0.1751:2,2:25.7:1:29.8:1:0.88268:1.06485:59.7:118:0.1777:0:2.4 0/1:301:76:28,48:95,130:0.2525:2,2:29.8:1:29.2:1:0.42209:1.25182:59.8:75:0.2551:0:2.4 -6 30229463 . G A 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02188;SOR=1.60313;LSEQ=TGTGGTTGCTGCTGCGATGT;RSEQ=GAGGAAGAAAAGCTCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:55:20,35:89,165:0.178:2,2:26.7:1:30.1:1:0.87699:1.06:59.7:110:0.1827:0:2.5 0/1:287:74:26,48:86,127:0.2578:2,2:29.4:1:29.1:1:0.48981:1.24919:59.8:36:0.2562:0:2.5 -6 30229504 . G A 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0287;SOR=1.83604;LSEQ=GGGAAGGGGTGAGAGGTGGG;RSEQ=TCTGGGTTTTCTTGTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:33:7,26:31,106:0.1941:2,2:21.5:1:31.1:1:1:1.08574:60:66:0.1988:0:2.6 0/1:127:39:11,28:29,59:0.3071:2,2:17.8:1:29.2:1:0.68118:1.24898:60:38:0.3016:0:2.8 -6 30229583 . G C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13418;SOR=2.26856;LSEQ=CATCACTGGGAAGCACCGTC;RSEQ=ACACACAGGCCGACCTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:12:0,12:0,36:0.25:1,0:25.6:1:32.3:1:1:0:60:24:0.25:0:1.3 0/1:30:13:1,12:0,17:0.4333:1,1:21.6:1:32.6:1:0.43333:0:60:26:0.4333:0:1.5 -6 30229869 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGCTGTTTCCTTAAGGAC;RSEQ=TCATGCCCCATGTCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:33:0:34:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:1:0,2:33.5:1:30:1:1:0:60:4:1:0:1 -6 30229989 . C T 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05276;SOR=Inf;LSEQ=AGAGGGCTGCTCCCTGAGAT;RSEQ=GTTGGGACAGTGTAGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:19,6:0:2,0:21.5:1:31.1:1:1:0:60:50:1:0:0.2 0/1:28:5:4,1:17,6:0.1786:2,2:16.4:1:29:1:1:1.40:60:10:0.1786:0:1 -6 30229990 . G A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.21233;SOR=2.7122;LSEQ=GAGGGCTGCTCCCTGAGATC;RSEQ=TTGGGACAGTGTAGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:4,0:15,6:0.16:2,0:38.5:1:30.3:1:0.5404:0:60:8:0.16:0:1 0/1:29:10:8,2:14,5:0.3448:2,2:21.3:1:30.1:1:1:1.41:60:20:0.3448:0:1.5 -6 30230066 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49745;SOR=Inf;LSEQ=CAGTTCCTATTTTTGTTCTA;RSEQ=CCCAGGCAGCAATTGTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:19,22:0:2,0:26.4:1:31.4:1:1:0:60:82:1:0:0.3 0/1:48:2:1,1:20,26:0.0417:2,2:12.5:1:29:1:1:1.29:60:4:0.0435:0:1 -6 30230085 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00898;SOR=4.76351;LSEQ=ACCCCAGGCAGCAATTGTGC;RSEQ=CAGTACTCTGATGCATCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:0,4:15,13:0.125:2,0:36.5:1:31.8:1:0.10414:0:60:8:0.125:0:1.5 0/1:39:16:4,12:8,15:0.4103:2,2:17.4:1:27.8:1:0.72618:1.58106:60:7:0.3784:0:2 -6 30230128 . T C 52 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.10577;SOR=4.74507;LSEQ=ATACTTGTAAAGGTGAGACA;RSEQ=GGGGGGGCCTGAAGTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:2,13:0.1176:2,0:14.5:1:31:1:1:0:60:4:0.1429:0:2 0/1:15:6:0,6:0,9:0.4:0,0:31.7:1:20.2:1:1:0:60:1:0.3333:0:3 -6 30457216 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12531;SOR=Inf;LSEQ=TCATTCCCAATGGGTGTCGG;RSEQ=TTTCTAGAGAAGCCAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:45,7:0:2,0:25.4:1:31:1:1:0:60:51:1:0:0.1 0/1:29:2:1,1:18,9:0.069:2,2:9.5:1:27:1:1:1.94942:60:4:0.069:0:1 -6 30457604 . C T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10775;SOR=Inf;LSEQ=TGGACGACACCCAGTTCGTG;RSEQ=GCTTCGACAACGACGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:138,155:0:2,0:25.8:1:30.3:1:1:0:60:35.625:1:0:0.1 0/1:267:3:0,3:120,144:0.0112:2,0:11:1:24.3:1:0.25488:0:60:2:0.0077:0:1 -6 30457732 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.45004;LSEQ=GCACAGATTTTCCGAGTGAA;RSEQ=CTGCGGACGCTGCGCGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:102:39,63:62,95:0.3938:2,2:26.9:1:31.5:1:0.89653:1.05406:60:101:0.3961:0:1.1 1/0:273:203:86,117:29,41:0.7436:2,2:26:1:30.7:1:1:1.04:60:49.75:0.7425:0:1.1 -6 30457739 . A T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24883;SOR=Inf;LSEQ=TTTTCCGAGTGAATCTGCGG;RSEQ=CGCTGCGCGGCTACTACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:105,148:0:2,0:25.6:1:29.4:1:1:0:60:35.143:1:0:0.5 0/1:263:3:0,3:109,151:0.0114:2,0:14.3:1:23:1:0.26918:0:60:2:0.0078:0:2 -6 30457792 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24239;SOR=0;LSEQ=GGTGAGTGACCCCGGCCAGG;RSEQ=GAGCAGGTCACGACCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:44,99:0.0138:2,2:25.5:1:29.5:1:0.52586:2.24:60:4:0.0141:0:1 0/0:149:0:0,0:50,99:0:2,0:22.1:1:29.9:1:1:0:60:73.5:1:0:0.6 -6 30458015 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.54724;SOR=0;LSEQ=ACTGACTAAGGGGCGGGGCC;RSEQ=GGGTCTCACACCCTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:103,50:0.0129:2,2:23:1:29.5:1:0.55124:2.04964:60:4:0.0135:0:1 0/0:81:0:0,0:58,22:0:2,0:24.1:1:29.9:1:1:0:60:79:0.9875:0:0.5 -6 30458039 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5188;SOR=0;LSEQ=TCTCACACCCTGCAGTGGAT;RSEQ=CATGGCTGCGAGCTGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:111,87:0.01:2,2:30.5:1:30.5:1:1:1.27429:60:4:0.0102:0:2 0/0:133:0:0,0:81,52:0:2,0:26.3:1:31.4:1:1:0:60:65.5:1:0:0.7 -6 30458058 . C T 53 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1437;SOR=0;LSEQ=TGCATGGCTGCGAGCTGGGG;RSEQ=CCGACGGGCGCTTCCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:4:0,4:105,109:0.0183:2,0:11.8:1:26.8:1:0.12256:0:60:8:0.0193:0:1.5 0/0:156:0:0,0:89,66:0:2,0:28.8:1:30.3:1:1:0:60:18.375:1:0:0.7 -6 30458064 . G A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=8.58128;LSEQ=GCTGCGAGCTGGGGCCCGAC;RSEQ=GGCGCTTCCTCCGCGGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:33:16,17:91,102:0.1454:2,2:25.7:1:30.3:1:1:1.05:60:66:0.1507:0:1.1 1/0:163:97:55,42:37,29:0.5951:2,2:30.2:1:29.6:1:1:1.03:60:23.25:0.6:0:1.1 -6 30458099 . C T 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.64317;LSEQ=GGGTATGAACAGTTCGCCTA;RSEQ=GACGGCAAGGATTATCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:73,120:0.0102:2,2:20.5:1:32:1:1:1.64:60:4:0.0104:0:1 0/0:152:1:1,0:70,81:0.0066:2,0:7:0:32:0:0.46711:0:60:2:0.0068:0:1 -6 30458100 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50532;SOR=0;LSEQ=GGTATGAACAGTTCGCCTAC;RSEQ=ACGGCAAGGATTATCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:72,118:0.0104:2,2:9.5:1:28:1:1:1.63:60:4:0.0105:0:2 0/0:152:0:0,0:70,82:0:2,0:25.1:1:29.6:1:1:0:60:29.4:1:0:0.6 -6 30458160 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50118;SOR=Inf;LSEQ=CCTGGACCGCGGTGGACACG;RSEQ=CGGCTCAGATCTCCGAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:16,50:0:2,0:21.6:1:32:1:1:0:60:132:1:0:0.1 0/1:80:2:1,1:28,50:0.025:2,2:21:1:29.5:1:1:1.77:60:4:0.026:0:1.5 -6 30458172 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50323;SOR=Inf;LSEQ=TGGACACGGCGGCTCAGATC;RSEQ=CCGAGCAAAAGTCAAATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:14,41:0:2,0:23.7:1:30.5:1:1:0:60:110:1:0:0.1 0/1:70:2:1,1:24,44:0.0286:2,2:13:1:28.5:1:1:1.82:60:4:0.0303:0:1 -6 30458248 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21601;SOR=Inf;LSEQ=AGACACATGCGTGGAGTGGC;RSEQ=CCACAAATACCTGGAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:18,39:0:2,0:28.7:1:30.2:1:1:0:60:56:1:0:0.1 0/1:50:2:1,1:17,31:0.04:2,2:33:1:29.5:1:1:1.80:60:4:0.0408:0:1 -6 30458260 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22697;SOR=Inf;LSEQ=GGAGTGGCTCCACAAATACC;RSEQ=GGAGAAGGGGAAGGAGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:16,34:0:2,0:27.2:1:30.5:1:1:0:60:100:1:0:0.1 0/1:46:2:1,1:16,28:0.0435:2,2:24.5:1:31.5:1:1:1.73:60:4:0.0444:0:1 -6 30458322 . T A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=0;LSEQ=TCCACAGGGCTACTCTCCCA;RSEQ=CTCCTTCTTGGGCTAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:1,11:0.1429:2,0:25:1:31:1:1:0:60:4:0.1429:0:1 0/0:8:0:0,0:1,7:0:2,0:28:1:29.9:1:1:0:60:16:1:0:0 -6 30458735 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5148;SOR=0;LSEQ=TGGGCTAGCTCATCCCGATT;RSEQ=TAGAACTTTCCAAGGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:23,2:0.0741:2,2:41.5:1:29.5:1:0.21368:9.59167:60:4:0.0769:0:1 0/0:17:0:0,0:17,0:0:1,0:18.9:1:32.3:1:1:0:60:34:1:0:0.1 -6 30458802 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20202;SOR=Inf;LSEQ=GGCTGGTGTCAAGGTTTTGT;RSEQ=CTCTTCTCCTACTATAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:79,0:0:1,0:24.5:1:30.7:1:1:0:60:25.333:1:0:0.1 0/1:65:2:1,1:59,4:0.0308:2,2:24:1:28:1:0.14904:13.30416:60:4:0.0313:0:1 -6 30458838 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20947;SOR=Inf;LSEQ=AATTGTCCTCTTCCTTCTCA;RSEQ=GATGGTCACATGGGTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:140,17:0:2,0:21.9:1:31.5:1:1:0:59.4:30.4:1:0:0.3 0/1:133:2:1,1:111,20:0.015:2,2:6.5:1:30.5:1:0.29187:5.44067:60:4:0.0153:0:1 -6 30458865 . G A 83 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09889;SOR=0.2671;LSEQ=CACATGGGTGCTGCTGGAGT;RSEQ=TCCCATGAGAGATACAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:7:7,0:179,70:0.0272:2,0:25.6:1:29.6:1:0.19484:0:33.3:14:0.0283:0:6.3 0/0:270:2:2,0:174,94:0.0074:2,0:42:1:30:0:0.54443:0:46.5:4:0.0075:0:4.5 -6 30458875 . AG GA 89 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03191;SOR=0.13012;LSEQ=CTGCTGGAGTGTCCCATGAG;RSEQ=ATACAAAGTGCCTGAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:7:7,0:205,102:0.0222:2,0:36.6:1:31.8:1:0.10071:0:33.3:14:0.0233:0:5.3 0/0:340:1:1,0:206,133:0.0029:2,0:45:0:32:0:1:0:33:2:0.003:0:7 -6 30458879 . A G 92 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03285;SOR=0.13193;LSEQ=TGGAGTGTCCCATGAGAGAT;RSEQ=CAAAGTGCCTGAATTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:7:7,0:215,124:0.0202:2,0:39.6:1:33:1:0.05287:0:33.3:14:0.0205:0:5.3 0/0:370:1:1,0:217,150:0.0027:2,0:48:0:34:0:1:0:33:2:0.0027:0:7 -6 30458907 . C T 90 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01627;SOR=0.11214;LSEQ=CCTGAATTTTCTGACTCTTC;RSEQ=CCTCAGAGCCCCCAAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:8:7,1:235,202:0.018:2,2:24:1:30.3:1:0.07625:6.00:33.3:16:0.0182:0:5.6 0/0:489:1:1,0:254,234:0.002:2,0:25:0:33:0:1:0:33:2:0.0021:0:7 -6 30458915 . G T 89 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01532;SOR=0.10923;LSEQ=TTCTGACTCTTCCCCTCAGA;RSEQ=CCCCCAAAGACACACGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:8:7,1:217,212:0.0183:2,2:18:1:29.8:1:0.0685:6.82:33.3:16:0.0189:0:5.6 0/0:494:1:1,0:244,249:0.002:2,0:17:0:32:0:0.49595:0:33:2:0.002:0:7 -6 30458961 . G A 46 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20807;SOR=0.23814;LSEQ=ACCCCATCTCTGACCATGAG;RSEQ=CCACCCTGAGGTGCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:4:4,0:110,197:0.0128:2,0:6.5:1:23:1:0.01745:0:59.8:3:0.0101:0:2.5 0/0:325:1:1,0:122,202:0.0031:2,0:1:0:23:0:0.37846:0:60:2:0.0032:0:1 -6 30458974 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35888;SOR=3.20918;LSEQ=CCATGAGGCCACCCTGAGGT;RSEQ=CTGGGCCCTGGGCTTCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:80,172:0.0039:2,0:25:0:11:0:0.32016:0:60:0:0:0:5 0/1:239:3:2,1:77,159:0.0126:2,2:22.7:1:28.3:1:0.2546:4.10:52.3:6:0.0128:0:1 -6 30459130 . A T 55 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06031;SOR=0;LSEQ=GGTGCCTTCTGGAGAGGAGC;RSEQ=GAGATACACGTGCCATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:4:1,3:253,107:0.011:2,2:11.5:1:27.5:1:0.08422:7.05111:55:8:0.0111:0:1 0/0:369:0:0,0:228,141:0:2,0:24.7:1:29.9:1:1:0:56.5:72.8:1:0:0.2 -6 30459165 . C T 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGTGCAGCATGAGGGGCTA;RSEQ=CCGAGCCCGTCACCCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:46:24,22:247,188:0.0956:2,2:28.6:1:30.4:1:0.63953:1.20387:59.6:92:0.0973:0:1.2 0/0:501:0:0,0:264,237:0:2,0:27.9:1:30.6:1:1:0:59.2:82.5:1:0:0.2 -6 30459450 . G A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24964;SOR=Inf;LSEQ=GGTGGGGAAGGGAGAAGGGT;RSEQ=GGGTCTGAGTTTTCTTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:63,197:0:2,0:25.3:1:30.8:1:1:0:60:36.143:1:0:0.1 0/1:280:3:2,1:97,180:0.0107:2,2:9.3:1:25:1:0.28591:3.69:60:6:0.0108:0:1 -6 30459475 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=CTGAGTTTTCTTGTCCCACT;RSEQ=GGTGTTTCAAGCCCTAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:32,136:0.0118:2,2:23.5:1:29:1:0.35148:4.20:60:4:0.0119:0:1.5 0/0:157:0:0,0:40,117:0:2,0:23:1:30.3:1:1:0:60:156:1:0:0.1 -6 30460232 . C T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00068;SOR=Inf;LSEQ=GTGTAAGTGCGGGGCGGGAG;RSEQ=GTGGAGGAGCTCGCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:51,15:0:2,0:24:1:30.1:1:1:0:60:12.2:1:0:0.2 0/1:57:9:7,2:40,8:0.1579:2,2:25.7:1:27.7:1:0.65047:1.41894:60:8:0.1429:0:1.3 -6 30460300 . GT G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.05221;SOR=Inf;LSEQ=GTGGGCTCTGACCAGGTCTT;RSEQ=TTTTGTTCTACCCCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:95,88:0:2,0:27.9:1:29.4:1:1:0:60:60:1:0:0.2 0/1:170:4:2,2:91,75:0.0235:2,2:29.5:1:31.4:1:1:1.21194:60:8:0.0241:0.0059:0 -6 30460318 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60614;SOR=2.21879;LSEQ=TTGTTTTTGTTCTACCCCAG;RSEQ=GAGCGACAGTGCCCAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:1,0:86,103:0.0053:2,0:34:0:31:0:0.45789:0:60:2:0.0053:0:1 0/1:172:2:0,2:84,86:0.0116:2,0:21.5:1:27:1:0.49735:0:60:4:0.0118:0:1 -6 30460323 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23346;SOR=Inf;LSEQ=TTTGTTCTACCCCAGGGAGC;RSEQ=ACAGTGCCCAGGGGTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:87,105:0:2,0:27.5:1:30.1:1:1:0:60:95:1:0:0.2 0/1:180:2:1,1:84,93:0.0111:2,2:38.5:1:28:0:1:1.11:60:4:0.0112:0:1 -6 30460341 . G T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06157;LSEQ=GCGACAGTGCCCAGGGGTCT;RSEQ=AGTCTCACAGCTTGTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:69,102:0.0115:2,2:23.5:1:28.5:1:1:1.47:60:4:0.0118:0:1 0/1:164:2:1,1:68,93:0.0122:2,2:31:1:27.5:1:1:1.36:60:4:0.0123:0:1 -6 30545661 . GAGC G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.20777;SOR=0;LSEQ=AGAAAGTGCTCAAGGAGAAG;RSEQ=AGCAGCAGCAGCAACAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:34,29:0.0308:2,2:16.5:1:33.5:1:1:1.16953:60:4:0.0313:0:0 0/0:77:0:0,0:38,39:0:2,0:24.9:1:29.6:1:1:0:60:76:1:0:0.2 -6 30545707 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50051;SOR=Inf;LSEQ=GCAGGTACAAGTGCCACAGG;RSEQ=CCCACCAATCCTGGGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:20,29:0:2,0:26.3:1:31.4:1:1:0:60:98:1:0:0.1 0/1:60:2:1,1:23,35:0.0333:2,2:27.5:1:30.5:1:1:1.51:60:4:0.0339:0:1.5 -6 30545737 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49514;SOR=0;LSEQ=CCTGGGAGGCATCTGGGTTC;RSEQ=ACCAACCCCTTTCCAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:7,25:0.0588:2,2:31:1:28:1:0.42068:3.41:60:4:0.0606:0:1 0/0:29:0:0,0:10,19:0:2,0:21.6:1:30.4:1:1:0:60:58:1:0:0.1 -6 30668071 . C G 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01632;SOR=Inf;LSEQ=AACAAACAAACAAAAAACAA;RSEQ=CTGTGGCTTCCAAATCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:44,3:0:2,0:27.1:1:31.9:1:1:0:60:46:1:0:0.3 0/1:17:3:3,0:13,1:0.1765:1,0:14.7:1:33.3:1:1:0:60:6:0.1765:0:1 -6 30668143 . A C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06777;SOR=Inf;LSEQ=CCCACCCATGTTCCAGGACA;RSEQ=GTTGTATCAATATACCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:122,15:0:2,0:23.1:1:30.2:1:1:0:60:67.5:0.9926:0:0.2 0/1:96:3:3,0:81,12:0.0313:2,0:27:1:32.7:1:1:0:60:6:0.033:0:1 -6 30668159 . C T 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00718;SOR=Inf;LSEQ=GACAAGTTGTATCAATATAC;RSEQ=CCAATCCTTTCTAACGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:147,26:0:2,0:24.9:1:30.7:1:1:0:60:42.25:1:0:0.1 0/1:138:6:3,3:107,25:0.0435:2,2:22.5:1:29.3:1:0.09788:4.21934:60:12:0.0444:0:1.5 -6 30668226 . A G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCGTGGTCTGGGAGGGAA;RSEQ=AGGGTAGTGGAGTTCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:0:0,0:467,195:0:2,0:25.1:1:30.2:1:1:0:60:93.571:1:0:0.1 0/1:526:25:17,8:314,185:0.0475:2,2:26.7:1:31.3:1:0.67596:1.25:60:24:0.0465:0:1.4 -6 30668374 . G A 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=86.15569;LSEQ=AGTGGAATGGAGCAATGAGG;RSEQ=AAGTCCTGAGGGCATGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1260:1:1,0:573,684:8e-04:2,0:1:0:25:0:0.45628:0:60:2:8e-04:0:1 0/1:1076:69:37,32:495,511:0.0641:2,2:22.9:1:29.8:1:0.5343:1.19:60:138:0.0648:0:1.2 -6 30668447 . A G 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=8.54738;LSEQ=AAGGCAAAATCAGGTGAAAA;RSEQ=GAATCCTAGAAATGGGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:3:1,2:160,447:0.0049:2,2:25.7:1:32.7:1:1:1.40:60:6:0.005:0:1 0/1:542:22:7,15:171,349:0.0406:2,2:26.3:1:30.3:1:1:1.04985:60:44:0.0406:0:1.4 -6 30668488 . C G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.43378;SOR=0.84529;LSEQ=GGACCCACTAACCAGTCTTA;RSEQ=CATCACTAAAATAATACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:101:8,93:16,156:0.37:2,2:23:1:31.9:1:0.82608:1.19153:60:49.5:0.368:0:1.1 0/1:196:65:5,60:11,120:0.3316:2,2:22.4:1:32.5:1:1:1.09948:60:130:0.3368:0:1.1 -6 30668679 . C CA 29 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=22.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGTCTCTACTAAAAATA;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,2:0.2857:0,0:35:1:29.5:1:1:0:38.5:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 30669956 . T C 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AGGCTGAGGCAGGAGAATGG;RSEQ=GTGAACCCAGGAGGCGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:27:1:18.5:1:1:0:58:1:1:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:33:1:1:0:60:4:1:0:1 -6 30670292 . C T 143 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07962;LSEQ=AGCCACCTCTTTAACTGCCA;RSEQ=TGCCACCTCACCCAGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:744:28:17,11:466,250:0.0376:2,2:23.7:1:29.9:1:0.68773:1.20579:60:56:0.0379:0:1 0/0:645:2:0,2:382,261:0.0031:2,0:12:1:28.5:1:0.16589:0:60:4:0.0031:0:1 -6 30670674 . G A 85 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39685;SOR=0.56479;LSEQ=ACTAAGGACGGCAGCAGTCA;RSEQ=CATCAAAGCTCAGCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:8:4,4:227,368:0.0133:2,2:19.5:1:28.6:1:0.4899:1.62:60:7:0.0119:0:1 0/0:531:4:3,1:198,329:0.0075:2,2:20.3:1:27.3:1:0.15449:4.97:60:8:0.0076:0:1.3 -6 30670700 . A C 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCTCAGCCCAGCCCCTCA;RSEQ=TCAGCTCTGCTGCCTAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:138,308:0:2,0:24.2:1:30.3:1:1:0:60:36.167:1:0:0.1 0/1:357:62:19,43:99,196:0.1737:2,2:20.4:1:31.3:1:0.76674:1.14274:60:61:0.1723:0:1.1 -6 30670842 . G A 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCACTATATGAGCAGTCTT;RSEQ=CCACTATATCGGTCTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:636:0:0,0:400,236:0:2,0:24.2:1:31.7:1:1:0:60:36.412:1:0:0.1 0/1:524:33:23,10:314,176:0.063:2,2:26.5:1:28.2:1:0.57723:1.29:60:66:0.0643:0:1.2 -6 30671312 . A C 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGTTTTGGAGTCACGAC;RSEQ=TCCTGAGATTGAGAAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:828:0:0,0:344,484:0:2,0:22.4:1:30.5:1:1:0:60:81.8:1:0:0.1 0/1:613:27:11,16:230,356:0.044:2,2:17.8:1:30.6:1:1:1.06:60:54:0.0444:0:1 -6 30671452 . T C 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCTTCCTTGATAATCAC;RSEQ=GTCTTCTGGGAGACTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1108:0:0,0:577,530:0:2,0:25.2:1:30.5:1:1:0:60:84.154:1:0:0.1 0/1:997:38:25,13:512,446:0.0381:2,2:26.9:1:29.9:1:0.13974:1.67:60:76:0.0385:0:1.1 -6 30671588 . A T 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGATCTACCTGCTGGTTCC;RSEQ=CCTTTTGGATCTGGGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1072:0:0,0:515,557:0:2,0:24.6:1:29.8:1:1:0:60:66:1:0:0.2 0/1:979:48:20,28:454,473:0.049:2,2:25.3:1:29.4:1:0.37508:1.34335:60:47:0.0489:0:1.2 -6 30671650 . A G 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27422;LSEQ=TGGGGAGAGGCAGGCTCAGG;RSEQ=ATGGCTGTAAGGGATTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:942:219:105,114:357,365:0.2325:2,2:25.5:1:31.1:1:0.7005:1.06182:60:35.5:0.2323:0:1.1 0/1:822:63:27,36:378,381:0.0766:2,2:20.8:1:30.7:1:0.29769:1.32238:60:30.5:0.0758:0:1.1 -6 30671726 . G C 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=44.78104;LSEQ=CCTGGGATTTAGGTTCCAAG;RSEQ=GTGCAGAGCAAGGCTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:863:1:0,1:427,434:0.0012:2,0:19:0:7:0:1:0:60:0:0:0:8 0/1:707:35:17,18:326,345:0.0495:2,2:24.9:1:31.1:1:1:1.00051:60:34:0.0489:0:1.1 -6 30671760 . C T 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.31151;LSEQ=CTTATGGTCAATGGGAGCTG;RSEQ=GAGGGAGCCAGGGTTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:844:3:1,2:412,429:0.0036:2,2:7.3:1:29:1:1:1.91931:60:6:0.0036:0:1 0/1:683:31:13,18:325,326:0.0454:2,2:23.9:1:29.3:1:0.46326:1.37971:60:30:0.0445:0:1.3 -6 30671969 . G C 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACGGACTGGTCTGTGGGG;RSEQ=TAAAAGGCTCAAGATCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1332:0:0,0:696,633:0:2,0:24.8:1:31.3:1:1:0:60:50.115:0.9977:0:0.2 0/1:1188:38:20,18:601,547:0.032:2,2:27.9:1:31.2:1:1:1.01:60:76:0.0323:0:1.1 -6 30671989 . G C 218 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAAAAGGCTCAAGATCAGA;RSEQ=GCTGCTGGTTCAACTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1468:0:0,0:769,695:0:2,0:25.5:1:31.4:1:1:0:60:51.286:0.9986:0:0.2 0/1:1295:149:82,67:572,573:0.1151:2,2:25.1:1:30.2:1:0.25816:1.23:60:73.5:0.1143:0:1.1 -6 30672326 . T C 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0983;LSEQ=TGGGCTCAGGGGTGACAGGT;RSEQ=GGTCTGTGGAGGTGGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1810:666:320,346:556,587:0.368:2,2:25.1:1:29.8:1:0.80757:1.02414:59.9:36:0.3686:0:2 0/1:1571:85:38,47:746,739:0.0541:2,2:24.1:1:29.4:1:0.37241:1.24838:59.6:41.5:0.0541:0:2 -6 30672342 . A G 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.49785;LSEQ=AGGTTGGTCTGTGGAGGTGG;RSEQ=AGGCTGGAGCTCAGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1754:661:306,355:527,562:0.3769:2,2:26.5:1:30.8:1:0.40169:1.08783:59.9:37.882:0.374:0:2 0/1:1530:354:173,181:577,597:0.2314:2,2:25.3:1:30.8:1:0.95167:1.01119:60:69.8:0.2338:0:1.4 -6 30672433 . C A 202 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=54.65648;LSEQ=CTAGTGGTCCGAGATGTGGG;RSEQ=TCAGAGGTGACAGGCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1300:3:1,2:660,634:0.0023:2,2:33.3:1:31.7:1:0.61761:2.08087:60:6:0.0023:0:1 0/1:1076:121:66,55:493,462:0.1125:2,2:24.6:1:29.2:1:0.56347:1.12:60:39.333:0.1117:0:1.2 -6 30672463 . G A 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=96.83615;LSEQ=ACAGGCTGGTCTGTGGAGGC;RSEQ=GAAGCCTGTAGCTCAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1460:1:1,0:748,711:7e-04:2,0:1:0:31:0:1:0:60:2:7e-04:0:1 0/1:1268:79:42,37:602,586:0.0623:2,2:24.7:1:30.2:1:0.72778:1.10:60:158:0.0631:0:1.1 -6 30672718 . G A 177 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=19.79672;LSEQ=TCTGTGGAAGTGGAAGGCTC;RSEQ=AGCTTAGGGGCTGTGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2061:4:3,1:980,1074:0.0019:2,2:14.8:1:27.8:1:0.3538:3.29:60:8:0.002:0:1.3 0/1:1780:66:35,31:832,880:0.0371:2,2:29:1:29.3:1:0.53108:1.19:60:65:0.0369:0:1.1 -6 30672757 . G A 192 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=47.92219;LSEQ=ACAAGTGTTTCAGGGGTCTT;RSEQ=CCAGAGGATCTATTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1791:3:3,0:876,909:0.0017:2,0:1:0:24.7:1:0.11861:0:60:6:0.0017:0:1.3 0/1:1462:109:61,48:650,701:0.0746:2,2:16.9:1:28.4:1:0.13489:1.37:60:53.5:0.0738:0:1.2 -6 30673013 . A G 191 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=105.59435;LSEQ=CAGGGGTCTTGACAGAGGAC;RSEQ=TATTTGTCCTGCTCCTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1596:1:1,0:823,765:6e-04:2,0:26:0:9:0:1:0:50:0:0:0:5 0/1:1416:88:46,42:680,645:0.0621:2,2:23.7:1:29.7:1:0.91249:1.04:60:87:0.0629:0:1.2 -6 30673064 . C T 191 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=25.04616;LSEQ=TGGGCTTGGGGGTGACAGGT;RSEQ=GGTCTGTGGAGGTGGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1887:5:1,4:902,979:0.0026:2,2:5.2:1:27.2:1:0.37659:3.68302:40.4:10:0.0027:0:1.2 0/1:1650:103:52,51:793,752:0.0624:2,2:25.1:1:28.7:1:0.91903:1.03423:56.6:19.6:0.0611:0:1.8 -6 30673113 . G T 197 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=145.65782;LSEQ=AGGGGCTGTGGGCACAACTG;RSEQ=TTCAGGGGTCTTGACAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1715:1:0,1:815,896:6e-04:2,0:6:0:32:0:1:0:60:2:6e-04:0:1 0/1:1416:111:54,57:615,686:0.0784:2,2:25.2:1:29:1:0.84313:1.06:53.3:110:0.0791:0:2.2 -6 30673163 . T G 184 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.0263;LSEQ=TTCTTCCCCTAGTAGCCTGA;RSEQ=ATGTGGGCTCAGAAGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1711:8:5,3:921,778:0.0047:2,2:21.6:1:18.4:1:0.73377:1.41:50.4:0.333:0.0013:0:2 0/1:1422:64:31,33:696,661:0.045:2,2:23.9:1:30.8:1:0.70195:1.12079:40.1:31:0.0457:0:3.5 -6 30673177 . A G 180 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=17.41254;LSEQ=GCCTGATATGTGGGCTCAGA;RSEQ=GTGACAGGCTGGTCTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1824:5:1,4:960,858:0.0027:2,2:20.8:1:21:1:0.19557:4.4718:47.8:0.667:0.0012:0:2.4 0/1:1576:72:39,33:764,738:0.0457:2,2:23.7:1:29.2:1:0.63019:1.14:39.6:9.286:0.0426:0:3.5 -6 30673185 . GC AT 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGGGCTCAGAAGTGACAG;RSEQ=TGGTCTGTGGAGGTGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1896:0:0,0:995,896:0:2,0:26.3:1:31.2:1:1:0:58.8:36.82:0.9984:0:0.2 0/1:1625:31:13,18:813,772:0.0191:2,2:26:1:29.4:1:0.36536:1.4578:38.2:62:0.0196:0.0025:2.7 -6 30673186 . C T 152 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.95442;LSEQ=GTGGGCTCAGAAGTGACAGG;RSEQ=TGGTCTGTGGAGGTGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1887:12:1,11:981,893:0.0064:2,2:16.1:1:18.9:1:0.00239:12.07003:53.1:0.714:0.0028:0:1.4 0/1:1626:50:26,24:796,753:0.0308:2,2:20.4:1:27:1:1:1.02:45.2:9:0.0292:0:2.6 -6 30673288 . G T 204 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=79.01702;LSEQ=CTTCCCCTAGTAGCCTGAGA;RSEQ=GTGGGTTCAGAGGTGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2328:2:0,2:1213,1110:9e-04:2,0:38:1:15.5:1:0.22864:0:56:0:0:0:3.5 0/1:2026:129:66,63:978,913:0.0637:2,2:26.8:1:29.1:1:0.92761:1.0225:53.7:20.5:0.0619:0:2.1 -6 30673340 . A G 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=32.13515;LSEQ=AGGTGGAAGGCTGGAGCTCA;RSEQ=GGGCTGTGGGCACAACTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2405:4:1,3:1167,1232:0.0017:2,2:23:1:21.5:1:0.62527:2.84037:51.3:1:9e-04:0:3.8 0/1:2026:103:54,49:946,971:0.0508:2,2:21.7:1:30.3:1:0.54604:1.13:47.7:33.333:0.0506:0:3 -6 30673351 . C G 184 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=13.54547;LSEQ=TGGAGCTCAAGGGCTGTGGG;RSEQ=ACAACTGTTTCAGGGGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2242:7:3,4:1078,1156:0.0031:2,2:31.9:1:18.7:1:1:1.24325:55:0.4:9e-04:0:3.1 0/1:1842:75:36,39:859,900:0.0407:2,2:23.2:1:29.7:1:0.90664:1.03397:43.3:17.75:0.0394:0:3.2 -6 30673359 . T G 175 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=8.89293;LSEQ=AAGGGCTGTGGGCACAACTG;RSEQ=TTCAGGGGTCTTGACAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2126:9:7,2:1005,1109:0.0042:2,2:24.6:1:17.2:1:0.09538:3.86:56.1:0.286:0.001:0:2.7 0/1:1756:64:30,34:812,880:0.0364:2,2:22.7:1:29.2:1:0.89906:1.04574:42.7:11.8:0.0345:0:3.2 -6 30673385 . C T 120 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=2e-05;SOR=11.51979;LSEQ=GGGTCTTGACAGAGGATCTA;RSEQ=TTTTTCTTCCCCTAGTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1771:2:1,1:833,935:0.0011:2,2:12.5:1:29.5:1:1:1.12:46.5:4:0.0012:0:2 0/1:1477:19:11,8:702,753:0.0129:2,2:24.2:1:28.4:1:0.49077:1.47:35.6:18:0.0124:0:3.6 -6 30673403 . A G 163 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.95998;LSEQ=TACTTTTTCTTCCCCTAGTA;RSEQ=CCTGAGATGTGGGCTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1734:10:1,9:871,849:0.0058:2,2:26.8:1:15.8:1:0.01091:9.22446:44.4:0.111:6e-04:0:1.7 0/1:1501:42:21,21:713,739:0.028:2,2:20.9:1:30.4:1:1:1.04:41:13:0.0267:0:3.2 -6 30673422 . A G 223 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=94.10332;LSEQ=AACCTGAGATGTGGGCTCAG;RSEQ=GGTGACAGGCTGGTCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1836:2:1,1:904,927:0.0011:2,2:30.5:1:31:0:1:1.03:40:4:0.0011:0:1 0/1:1664:155:79,76:736,773:0.0931:2,2:23.7:1:30.7:1:0.61369:1.09:59.7:154:0.0947:0:1.5 -6 30673431 . GC AT 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGGGCTCAGAGGTGACAG;RSEQ=TGGTCTGTGGAGGTGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1917:0:0,0:961,951:0:2,0:25.9:1:31.4:1:1:0:58.9:43.465:0.9973:0:0.2 0/1:1688:50:25,25:806,830:0.0296:2,2:25.8:1:29.7:1:1:1.03:44.3:100:0.0301:0:2.1 -6 30673432 . C T 117 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=7.62111;LSEQ=GTGGGCTCAGAGGTGACAGG;RSEQ=TGGTCTGTGGAGGTGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1913:3:0,3:960,949:0.0016:2,0:11.3:1:17.3:1:0.12324:0:58.3:0.5:5e-04:0:1.3 0/1:1690:20:8,12:799,818:0.0118:2,2:25.4:1:27.3:1:0.50165:1.46481:46.9:9:0.0113:0:2.2 -6 30673489 . G C 218 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGGGACAACTGGTTCAGG;RSEQ=GTCTTGACAGAGGACCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1854:0:0,0:937,916:0:2,0:23.6:1:30.9:1:1:0:59.3:55.152:0.9995:0:0.2 0/1:1494:152:78,74:671,666:0.1017:2,2:23.9:1:30.1:1:0.79803:1.05:59.8:49.667:0.1018:0:1.5 -6 30673625 . G A 196 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=114.38794;LSEQ=GAAAGGGTGTCATTCTGGAG;RSEQ=ACTTCCGAGTTCTAATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1606:1:1,0:691,912:6e-04:2,0:1:0:25:0:0.43142:0:60:2:6e-04:0:1 0/1:1532:102:51,51:684,746:0.0666:2,2:23.2:1:29.4:1:0.68289:1.09:60:101:0.0668:0:2 -6 30673662 . G C 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAGGCTTTGGGTGGAAAG;RSEQ=CTCCAGCTCTGAGGACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1241:0:0,0:511,729:0:2,0:24.7:1:31.5:1:1:0:60:50.667:0.9992:0:0.1 0/1:1098:64:29,35:478,552:0.0583:2,2:23.9:1:31.8:1:0.89781:1.04507:60:128:0.0593:0:2.7 -6 30673681 . G A 176 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=67.46996;LSEQ=GGCTCCAGCTCTGAGGACAA;RSEQ=GGAGCCTCTGGAGCTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1135:1:1,0:461,671:9e-04:2,0:1:0:26:0:0.40777:0:60:2:9e-04:0:1 0/1:978:55:24,31:395,527:0.0562:2,2:20.9:1:30.6:1:1:1.03:60:110:0.0568:0:2.6 -6 30673888 . A G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04397;SOR=Inf;LSEQ=TGATCGCCCTAGGGAGAAAC;RSEQ=GAAGCAAGTGAGGGGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:76,229:0:2,0:26:1:31.1:1:1:0:60:100.667:0.9967:0:0.2 0/1:260:4:2,2:80,175:0.0154:2,2:24:1:30:1:0.59327:2.18:60:8:0.0157:0:1 -6 30675036 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12244;SOR=Inf;LSEQ=GAATAGAAGCCAATCAAGGC;RSEQ=TGACAAAAATGGAAGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:193,3:0:1,0:24.8:1:30.3:1:1:0:60:392:1:0:0 0/1:106:2:2,0:102,2:0.0189:1,0:13.5:1:31.5:1:1:0:60:4:0.0189:0:1 -6 30675135 . T C 195 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATAGAGATGACTTGTGGAA;RSEQ=AGGAGGTAGAAAAAGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:947:0:0,0:560,387:0:2,0:25.8:1:29.6:1:1:0:60:156.833:1:0:0.1 0/1:826:81:49,32:410,334:0.0981:2,2:26.3:1:30.8:1:0.41003:1.25:60:39.5:0.0974:0:1.2 -6 30675605 . T G 225 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=185.36613;LSEQ=GCTACTGGTCTCTCTACTTC;RSEQ=CTCTCAAATGCTTTGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1518:1:1,0:740,774:7e-04:2,0:15:0:9:0:0.48911:0:60:0:0:0:2 0/1:1480:161:79,82:646,670:0.1088:2,2:24.9:1:30.7:1:1:1.00079:60:79.5:0.1085:0:1.1 -6 30676046 . C G 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTCCATAGGCCTCAAGGTG;RSEQ=GTGTCAAAAGGCTGGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:833:0:0,0:331,502:0:2,0:24.7:1:30.3:1:1:0:60:42.842:1:0:0.1 0/1:705:62:30,32:272,369:0.0879:2,2:22.7:1:30:1:0.42051:1.27:60:61:0.0884:0:1.2 -6 30676152 . AAG A 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.63342;SOR=0.71668;LSEQ=TACCTGGAAGGGGAGGAAGG;RSEQ=AGAGAGAGAGGGAGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:13:2,11:57,213:0.0459:2,2:29.9:1:30.5:1:1:1.47:60:26:0.0471:0.0071:0.2 0/1:180:6:1,5:46,128:0.0333:2,2:29:1:30.7:1:1:1.79186:60:12:0.0343:0:0.5 -6 30676173 . A G 23 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13253;SOR=Inf;LSEQ=AGAGAGAGAGAGGGAGAGGG;RSEQ=GAGAAAAGAGGGAGAGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:35,172:0:2,0:22.2:1:30.7:1:1:0:60:68:1:0:0.1 0/1:119:2:1,1:18,99:0.0168:2,2:17:0:23:1:0.29497:5.38:60:4:0.0171:0:1.5 -6 30679134 . G GA 97 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01143;SOR=9.88528;LSEQ=ATCCAGCCTGAGTGACAGAG;RSEQ=AAAAAAAAGAGAATGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:592:1:1,0:476,114:0.0017:2,0:34:0:27:0:1:0:60:2:0.0017:0:0 0/1:607:10:7,3:421,173:0.0165:2,2:17.3:1:29.4:1:1:1.04287:60:20:0.0167:0.0066:0 -6 30679289 . G C 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGCTCTGGACTGCTGTACA;RSEQ=GAAAAGATGGCCTAAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1031:0:0,0:373,658:0:2,0:25.5:1:31.2:1:1:0:60:63.438:1:0:0.1 0/1:833:59:23,36:286,488:0.0708:2,2:23.5:1:30.1:1:0.78061:1.09:60:118:0.0713:0:1.5 -6 30679333 . T C 205 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=176.41939;LSEQ=CCTCCATACTACTGTAGGGT;RSEQ=CCATTCCTGGTCTCCTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:676:1:0,1:269,406:0.0015:2,0:29:0:15:0:1:0:60:0:0:0:1 0/1:467:97:41,56:142,227:0.2077:2,2:17.6:1:31.2:1:0.55928:1.17:60:194:0.2095:0:1.4 -6 30679628 . T A 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=78.78958;LSEQ=CCTGGTTGATTTCAGAGGTC;RSEQ=AGGAAGGAAGGCCAGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1154:986:547,439:90,76:0.8544:2,2:26.6:1:29.9:1:0.80034:1.05:60:88.636:0.8545:0:1.1 1/1:928:926:497,429:0,1:0.9978:0,2:26.3:1:29.4:1:0.46386:0:60:53.471:0.9978:0:1.1 -6 30680562 . G A 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCCAGAGGGACAGCCTGT;RSEQ=GGGCCTTGCCTTCTTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:780:0:0,0:424,354:0:2,0:23.7:1:31.5:1:1:0:60:85.444:0.9987:0:0.1 0/1:617:59:29,30:292,264:0.0956:2,2:24.7:1:29.4:1:0.68165:1.14395:60:118:0.097:0:1.8 -6 30680608 . C T 187 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=116.86249;LSEQ=ATCACTACCAGCCTGGCTCT;RSEQ=CTGCAGATGGGCCAGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:882:1:1,0:495,386:0.0011:2,0:13:0:13:0:1:0:60:0:0:0:2 0/1:699:82:43,39:327,290:0.1173:2,2:22.7:1:29.5:1:1:1.02267:60:81:0.1179:0:1.5 -6 30680916 . C T 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=88.19009;LSEQ=TGACTTTTGTATCATTGTCC;RSEQ=TCTCCTTCACTAAAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1482:1:0,1:668,810:7e-04:2,0:2:0:28:0:1:0:60:2:7e-04:0:1 0/1:1440:81:37,44:634,721:0.0563:2,2:24.4:1:30:1:0.9089:1.04567:60:162:0.0568:0:1.2 -6 30681315 . G T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05239;LSEQ=CTGAGTGAATGAATATGTAT;RSEQ=GTTCCCCAGCCCCAACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:19:16,3:119,11:0.1275:2,2:14.9:1:30.3:1:0.39046:2.01664:60:38:0.1293:0:1 0/1:90:12:11,1:74,4:0.1333:2,2:25.7:1:28.8:1:0.51965:1.67039:60:11:0.1264:0:1 -6 30681359 . T C 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01594;SOR=9.01101;LSEQ=ATAATCATCTCTTTTAGAGA;RSEQ=TGATCCTCCAGCCCCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:1:1,0:234,62:0.0034:2,0:22:0:13:0:1:0:60:0:0:0:5 0/1:270:8:6,2:195,67:0.0296:2,2:22.8:1:31.3:1:1:1.03:60:16:0.0299:0:1 -6 30681477 . G A 151 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=44.1215;LSEQ=CCTTGATTTTTTTACCATAC;RSEQ=CCTTTCAGAAAGAAAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:1:1,0:450,432:0.0011:2,0:1:0:25:0:1:0:60:2:0.0012:0:1 0/1:796:38:22,16:375,383:0.0477:2,2:27.6:1:28.9:1:0.324:1.40:60:76:0.0481:0:1.2 -6 30681980 . A G 121 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTAAGAATTAGAGAGGTAG;RSEQ=TAAGCTCCAAGATCAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:24,119:0:2,0:25.1:1:31:1:1:0:60:142:1:0:0 0/1:110:16:5,11:23,71:0.1455:2,2:32.7:1:30.4:1:0.54767:1.40:60:32:0.1455:0:1.8 -6 30682007 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0675;SOR=Inf;LSEQ=CCAAGATCAGAGTCCTGGCC;RSEQ=GTCATTAGGAAAAAGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:13,86:0:2,0:24.4:1:30.3:1:1:0:60:98:1:0:0 0/1:69:3:1,2:13,53:0.0435:2,2:12.3:1:30.3:1:0.49927:2.01:60:6:0.0455:0:2.7 -6 30682700 . G GA 113 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.21588;SOR=0.46785;LSEQ=GCCCCATCTCTTCCATTCAT;RSEQ=AAAAAAAAAAATTCACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:14:14,0:177,2:0.0711:1,1:24.5:1:29.9:1:1:0:60:28:0.0725:0.0152:0.1 0/1:116:4:3,1:109,2:0.0345:1,2:20.3:1:30:1:0.10162:16.66065:60:8:0.0351:0:0 -6 30683058 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02495;SOR=Inf;LSEQ=GTAAACTGGATCATTATGAA;RSEQ=GTTGATGCTTCTCTTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:1,154:0:1,0:26.2:1:30.3:1:1:0:60:310:1:0:0.1 0/1:65:3:1,2:2,60:0.0462:1,2:27.3:1:31.3:1:0.13416:13.33:60:6:0.0462:0:1 -6 30683117 . A AT 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00962;SOR=Inf;LSEQ=CCTTCTGAAGCACTTAAAAC;RSEQ=TTTTTTTCTTTTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:0:1,0:19.2:1:31.2:1:1:0:60:47:1:0:0.1 0/1:14:3:0,3:0,11:0.2143:0,0:15:1:29:1:1:0:60:6:0.2143:0.1429:0 -6 30865058 . C T 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66992;SOR=0.61559;LSEQ=ATGTACGCTGGGGGTGGGGA;RSEQ=GCCTGGTCTGCCTGAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:0.4545:0,0:27.4:1:32.6:1:1:0:60:10:0.4545:0:1.6 0/1:9:3:3,0:6,0:0.3333:0,0:28.3:1:24.7:1:1:0:60:2:0.25:0:1 -6 30865115 . G A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17058;SOR=0.26506;LSEQ=CGCGGGGGAAGGTGCAGGCC;RSEQ=CCCACTCGGCATTCCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:10:8,2:19,3:0.3125:2,2:21.9:1:30.6:1:0.63675:1.55946:60:20:0.3226:0:1.3 0/1:19:2:2,0:13,4:0.1053:2,0:16.5:1:30.5:1:1:0:60:4:0.1053:0:1 -6 30865204 . A C 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=0.18322;LSEQ=ATGTCGAGGCTCAAGGACCC;RSEQ=AACATCATTCGGCTGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:22:9,13:39,37:0.2245:2,2:25.3:1:32.2:1:0.47085:1.516:60:44:0.2245:0:1.3 0/1:120:6:3,3:55,59:0.05:2,2:16.2:1:30.8:1:1:1.07:60:12:0.0508:0:1.3 -6 30865225 . CGT C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=0.50634;SOR=Inf;LSEQ=AACATCATTCGGCTGCTGGG;RSEQ=GTGTGTGCAGGACGACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:31,42:0:2,0:27:1:31:1:1:0:60:146:1:0:0.3 0/1:96:2:1,1:41,52:0.0208:2,2:23:0:33.5:1:1:1.27:60:4:0.0211:0:0.5 -6 30865230 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.17382;SOR=0;LSEQ=CATTCGGCTGCTGGGCGTGT;RSEQ=TGTGCAGGACGACCCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:26,39:0.0299:2,2:31.5:1:28:1:1:1.49:60:4:0.0303:0:1 0/0:93:0:0,0:40,53:0:2,0:23.6:1:31:1:1:0:60:186:1:0:0.2 -6 30865279 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01478;SOR=Inf;LSEQ=ACTGACTACATGGAGAACGG;RSEQ=GACCTCAACCAGTTCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:5,28:0:2,0:23.5:1:29.4:1:1:0:60:66:1:0:0.1 0/1:27:5:1,4:1,21:0.1852:1,2:32.6:1:29.8:1:0.34188:4.81:60:10:0.1852:0:1 -6 30865991 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10638;SOR=Inf;LSEQ=ATCAAAATCGCAGACTTTGG;RSEQ=ATGAGCCGGAACCTCTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:21,11:0:2,0:21.8:1:31.9:1:1:0:60:64:1:0:0.1 0/1:16:2:1,1:9,5:0.125:2,2:23.5:1:26.5:1:1:1.73197:60:4:0.125:0:1.5 -6 30866035 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54338;SOR=0;LSEQ=GGACTATTACCGTGTGCAGG;RSEQ=CCGGGCAGTGCTGCCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:26,20:0.0417:2,2:11:0:31.5:1:1:1.29283:60:4:0.0426:0:1 0/0:25:0:0,0:11,14:0:2,0:33.4:1:31.4:1:1:0:60:50:1:0:0.2 -6 30954245 . T C 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTCTGAGTTCAGCACAG;RSEQ=GTCCAGTGGGATCAGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:2,0:0.7143:0,2:33:1:32.2:1:1:0:60:10:0.7143:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 30954873 . G A 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=0;LSEQ=ACCAACTCTGAGTCCAGTAC;RSEQ=ACCTCCAGTGGGGCCAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:25.5:1:29.5:1:1:0:60:4:0.4:0:1.5 0/0:9:0:0,0:4,5:0:2,0:26.8:1:31:1:1:0:60:18:1:0:0.4 -6 31052539 . C CT 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATGTCCTGCCTCCTCCT;RSEQ=TTTTTTTTTCTTCTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:29.3:1:1:0:60:4:1:0.5:0.5 -6 31053131 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23101;SOR=0;LSEQ=AGAGTAAAGGATGAAGTCCC;RSEQ=TTTAGAGAGATACACTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:2,0:94,10:0.0189:2,0:29:1:32:0:1:0:60:4:0.019:0:1 0/0:114:0:0,0:99,15:0:2,0:23.7:1:30.7:1:1:0:60:56:1:0:0.1 -6 31053257 . A C 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01688;SOR=1.33208;LSEQ=AAATGCCACTGGTTTAAATT;RSEQ=GGTAGAAAATGTTTTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:242:128,114:160,146:0.4416:2,2:26.3:1:30.5:1:0.9314:1.02:60:79.667:0.4401:0:1.1 1/0:573:294:140,154:132,147:0.5131:2,2:27.2:1:30.3:1:1:1.01:60:588:0.514:0:1.2 -6 31053348 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58224;SOR=2.60696;LSEQ=GACCTGCTCTATCATTCCCC;RSEQ=AACTTATAGGACAAAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:1:1,0:44,169:0.0047:2,0:1:0:26:0:0.21028:0:60:2:0.0047:0:1 0/1:165:2:1,1:35,128:0.0121:2,2:19.5:1:28:1:0.3898:3.62:60:4:0.0123:0:1 -6 31053360 . CA C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.17137;SOR=Inf;LSEQ=CATTCCCCCAACTTATAGGA;RSEQ=AAAAGTCCGAGAAGCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:22,150:0:2,0:23.6:1:29.9:1:1:0:60:85:1:0:0.1 0/1:122:2:1,1:18,102:0.0164:2,2:12.5:1:32:0:0.28831:5.54:60:4:0.0165:0:0.5 -6 31053516 . G C 82 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTCCTCCTGGGGCCATC;RSEQ=TCCCAGGGGTTATGCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:23.2:1:31.8:1:1:0:60:12:0.3529:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31053521 . A G 81 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTGGGGCCATCGTCCC;RSEQ=GGGGTTATGCCTCGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:22.3:1:31.7:1:1:0:60:12:0.3333:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31162154 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAGAAATTCATGTTCTG;RSEQ=ATTCTGAGCAATGCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:28:1:1:0:60:4:1:0:1 -6 31162384 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAACCTTGAGCGCAAGGG;RSEQ=GGTTTGGTTCCTCTTACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:36.5:1:31.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31162520 . T C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00057;SOR=0.092;LSEQ=GAAAGCGGAATGAAAGCAGG;RSEQ=CAAAAGTGGCTGGGAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:14,0:5,1:0.7:2,1:26.5:1:32.9:1:0.3:0:60:28:0.7:0:1 0/1:24:4:4,0:14,6:0.1667:2,0:20:1:31.8:1:0.53924:0:60:8:0.1667:0:1 -6 31162648 . C A 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00557;SOR=Inf;LSEQ=CATCCCTGCCCTCCAGAGCC;RSEQ=ACTTAGTCACACACTACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:23,34:0:2,0:24.4:1:30.8:1:1:0:60:27.5:1:0:0.1 0/1:44:6:2,4:17,21:0.1364:2,2:33.2:1:30.7:1:0.68428:1.60194:60:12:0.1364:0:1.2 -6 31162662 . C T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51605;SOR=0;LSEQ=AGAGCCCACTTAGTCACACA;RSEQ=TACCTTTCAGGACTACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:16,31:0.0408:2,2:9:1:32:0:1:1.91:46.5:4:0.0408:0:6.5 0/0:32:0:0,0:10,22:0:2,0:26.9:1:31.6:1:1:0:60:64:1:0:0.3 -6 31162676 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50913;SOR=0;LSEQ=CACACACTACCTTTCAGGAC;RSEQ=ACCTTCCACATCAGCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:11,30:0.0465:2,2:23:1:32:1:0.48505:2.65:46.5:4:0.0465:0:6.5 0/0:30:0:0,0:8,22:0:2,0:21.8:1:28.4:1:1:0:60:60:1:0:0.3 -6 31162680 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50554;SOR=0;LSEQ=CACTACCTTTCAGGACTACC;RSEQ=TCCACATCAGCCAGGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:8,30:0.05:2,2:27:1:31.5:1:0.40385:3.59:46.5:4:0.0526:0:6.5 0/0:29:0:0,0:7,22:0:2,0:20.4:1:30.3:1:1:0:60:58:1:0:0.2 -6 31162682 . C T 28 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50909;SOR=0;LSEQ=CTACCTTTCAGGACTACCTT;RSEQ=CACATCAGCCAGGTGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:8,29:0.0513:2,2:27:0:28:1:0.41296:3.48:46.5:4:0.0526:0:6.5 0/0:27:0:0,0:6,20:0:2,0:21.7:1:31.2:1:1:0:60:52:0.963:0:0.2 -6 31162685 . C G 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.51084;SOR=0;LSEQ=CCTTTCAGGACTACCTTCCA;RSEQ=ATCAGCCAGGTGCAAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:7,28:0.0541:2,2:24:0:32.5:1:0.39039:3.81:46.5:4:0.0541:0:6.5 0/0:25:0:0,0:6,19:0:2,0:21.3:1:31.8:1:1:0:60:50:1:0:0.2 -6 31162688 . C T 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50273;SOR=0;LSEQ=TTCAGGACTACCTTCCACAT;RSEQ=AGCCAGGTGCAAACCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:6,27:0.0571:2,2:21:0:29:1:0.36471:4.24:46.5:4:0.0588:0:6.5 0/0:26:0:0,0:6,20:0:2,0:19.5:1:31.4:1:1:0:60:52:1:0:0.2 -6 31162839 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATTAGGGAAATAGTGT;RSEQ=TACATTTCAAAAGAGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:38.5:1:30.5:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:0,1:0:0,0:33:0:33:0:1:0:60:2:1:0:0 -6 31193144 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACCCTGAGAAGAAAGAG;RSEQ=AACTTGACTGTCTGAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:0.125:2,2:15:1:28:1:1:1.73197:60:4:0.1333:0:3.5 0/0:5:0:0,0:3,2:0:2,0:27:1:26.4:1:1:0:60:4:1:0:1.6 -6 31193155 . T C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07849;SOR=0.1408;LSEQ=AAGAAAGAGGAACTTGACTG;RSEQ=CTGAAGGCTCTTGGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:9,7:2,0:0.8889:0,2:23.1:1:30:1:0.49673:0:60:15:0.8824:0:3.1 1/0:6:3:2,1:2,1:0.5:2,2:30.7:1:30.3:1:1:1:60:6:0.5:0:2.3 -6 31193164 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05619;SOR=0.19946;LSEQ=GAACTTGACTGTCTGAAGGC;RSEQ=CTTGGGTGGTGTTTAAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:16:9,7:2,1:0.8421:2,2:28.9:1:30.9:1:1:1.52085:60:32:0.8421:0:3.1 1/0:12:6:4,2:3,3:0.5:2,2:16.2:1:29.5:1:1:1.89:60:12:0.5:0:2.5 -6 31193211 . C T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=CACTGTGTCCTGGCTGAATG;RSEQ=ATACATGCAGATGGAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:26:13,13:1,1:0.9286:2,2:26.8:1:29.1:1:1:1:60:52:0.9286:0:2.7 1/1:15:15:7,8:0,0:1:0,2:37.9:1:28.9:1:1:0:60:30:1:0:1.8 -6 31193239 . CT C 32 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.57307;SOR=2.63458;LSEQ=CAGATGGAATCTCTTTCTTT;RSEQ=TTTTTTTTTTGAGACGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:6,9:0.0625:2,0:26:0:29:0:1:0:60:2:0.0625:0:1 0/1:13:2:1,1:6,5:0.1538:2,2:34.5:1:32.5:1:1:1.18321:60:4:0.1538:0:2 -6 31193255 . C T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11599;SOR=0.24391;LSEQ=CTTTCTTTTTTTTTTTGAGA;RSEQ=GGAGTCTCGCTCTGTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:4,6:1,3:0.7143:2,2:14.9:1:30:1:1:1.91:58:20:0.7143:0:2.6 0/1:11:4:2,2:3,3:0.3636:2,2:13.3:1:30.5:1:1:1:60:8:0.3636:0:2.5 -6 31234911 . A G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTGGAGTTGTCTGCCCA;RSEQ=CTGCCACCCCAGCTCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:32:1:1:0:60:4:1:0:3.5 -6 31234948 . C A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACCTGCATTCCTAGTAG;RSEQ=CATGTCCTCCACTGAGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:27.5:1:1:0:60:4:1:0:3.5 -6 31234952 . G C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCATTCCTAGTAGCCAT;RSEQ=TCCTCCACTGAGTGCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:30.5:1:1:0:60:4:1:0:3.5 -6 31236034 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCCCACACCAACCGCCC;RSEQ=GCACACTGCAGCACACGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:49:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:18:0:30.5:1:1:0:60:4:1:0:1 -6 31236853 . G A 57 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.30792;LSEQ=AGGAACGCAGACACATTCAG;RSEQ=TGCCTTTGCAGAAAGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:2,2:0.5:2,0:30.3:1:30.8:1:0.42857:0:60:8:0.5:0:1.3 1/0:7:4:3,1:1,0:0.5714:0,2:21.5:1:28.8:1:1:0:60:8:0.5714:0:1.3 -6 31236998 . C T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14328;SOR=0.13275;LSEQ=TTCAGGTCAGTCATGGTAAG;RSEQ=GATGACACTCTGAACGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:11,6:0,1:0.9444:0,2:20.7:1:29.7:1:0.38889:0:60:34:0.9444:0:4.8 1/0:6:4:3,1:1,1:0.6667:2,2:24.3:1:29:1:1:2.45:60:8:0.6667:0:3.8 -6 31237002 . G C 41 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07211;SOR=9.12257;LSEQ=GGTCAGTCATGGTAAGCGAT;RSEQ=ACACTCTGAACGGCCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:11,6:0.0556:2,0:14:0:32:0:1:0:60:2:0.0556:0:7 0/1:8:3:3,0:3,2:0.375:2,0:11.7:1:26:1:0.46429:0:60:2:0.2857:0:6 -6 31237014 . G A 123 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.083;SOR=0;LSEQ=TAAGCGATGACACTCTGAAC;RSEQ=GCCCACCACACACTCGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:11,5:0,0:1:0,2:26.1:1:30.9:1:1:0:60:32:1:0:5.3 1/0:7:5:5,0:1,1:0.7143:2,0:21:1:30.4:1:0.28571:0:60:10:0.7143:0:5.2 -6 31237016 . C T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=AGCGATGACACTCTGAACGG;RSEQ=CCACCACACACTCGAAACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:28.3:1:32.6:1:1:0:60:30:1:0:5.5 0/1:7:2:2,0:4,1:0.2857:2,0:29:1:32:0:1:0:60:4:0.2857:0:4 -6 31237017 . C T 123 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02273;SOR=0;LSEQ=GCGATGACACTCTGAACGGC;RSEQ=CACCACACACTCGAAACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:10,5:0,0:1:0,2:28.5:1:31.6:1:1:0:60:30:1:0:5.5 1/0:7:4:4,0:2,1:0.5714:2,0:13:1:30.5:1:0.42857:0:60:8:0.5714:0:5.5 -6 31237027 . C T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08079;SOR=0.11635;LSEQ=TCTGAACGGCCCACCACACA;RSEQ=TCGAAACGTCCCAATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:12,4:1,0:0.9412:0,2:29.5:1:31.5:1:1:0:60:32:0.9412:0:5.4 1/0:8:5:5,0:2,1:0.625:2,0:15.2:1:30.2:1:0.375:0:60:10:0.625:0:5.2 -6 31237048 . A G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1256;SOR=0.29144;LSEQ=TCGAAACGTCCCAATCAAAG;RSEQ=ATCCCCATTACCCAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:18,2:4,0:0.8333:0,2:25.6:1:32:1:1:0:60:40:0.8333:0:4.8 1/0:12:7:7,0:4,1:0.5833:2,0:30.9:1:32:1:0.41667:0:60:14:0.5833:0:4.6 -6 31237061 . C T 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27541;SOR=0.43678;LSEQ=ATCAAAGAATCCCCATTACC;RSEQ=AGGCCTTTTCCCTCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:28:25,3:5,0:0.8235:0,2:18.6:1:31.4:1:1:0:60:56:0.8485:0:3.8 1/0:15:10:7,3:5,0:0.6667:0,2:20.8:1:29.5:1:0.50549:0:60:20:0.6667:0:3.5 -6 31237087 . C A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55246;SOR=0.62018;LSEQ=TTTTCCCTCTGCCCCACCCC;RSEQ=GACCACTTCAGCTCCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:9:5,4:33,17:0.1525:2,2:18.6:1:30:1:0.7078:1.54098:60:18:0.1525:0:3.4 0/1:40:4:2,2:22,14:0.1:2,2:31.8:1:28.5:1:1:1.55321:60:8:0.1:0:3.5 -6 31237110 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50322;SOR=0;LSEQ=CCACTTCAGCTCCCCAGAAT;RSEQ=TCACCTTTACAAGTGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:48,39:0.0225:2,2:18.5:1:30:0:1:1.22788:60:4:0.0227:0:3.5 0/0:71:0:0,0:42,29:0:2,0:23.7:1:31.1:1:1:0:60:70:1:0:1.6 -6 31237124 . T C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05386;SOR=0.48756;LSEQ=CAGAATCTCACCTTTACAAG;RSEQ=GATGAGAGACTCATCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:77:37,40:11,7:0.8105:2,2:30.5:1:30.3:1:0.43347:1.6894:60:37.5:0.8152:0:2.3 1/0:80:54:29,25:17,9:0.675:2,2:28.5:1:31.2:1:0.34649:1.61851:60:108:0.6835:0:2.2 -6 31237148 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24315;SOR=Inf;LSEQ=GAGAGACTCATCAGAGCCCT;RSEQ=GGCACTGTTGCTGCCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:41,51:0:2,0:28.5:1:31.6:1:1:0:60:45:1:0:1.8 0/1:90:2:1,1:43,45:0.0222:2,2:20.5:1:30:1:1:1.05:60:4:0.0225:0:2.5 -6 31237162 . C G 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03943;SOR=0.47435;LSEQ=AGCCCTGGGCACTGTTGCTG;RSEQ=CTGGGGTAGAACAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:83:66:22,44:9,8:0.7952:2,2:24:1:31.6:1:0.16506:2.22679:60:65:0.7927:0:2.4 1/0:85:55:27,28:15,15:0.6471:2,2:25:1:31.7:1:1:1.03661:60:110:0.6548:0:2.2 -6 31237174 . CA C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.03009;LSEQ=TGTTGCTGCCTGGGGTAGAA;RSEQ=AAAAAAAAGACCTGGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:24,44:0.0286:2,2:33:1:32.5:1:1:1.82:60:4:0.029:0:1.5 0/1:68:2:1,1:32,34:0.0294:2,2:42.5:1:31:1:1:1.06:60:4:0.0294:0:2 -6 31237230 . A G 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.542;SOR=0.6135;LSEQ=TGGGACAAGAGGAATTATGG;RSEQ=GTAGGTGAGCTCCTCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:15:2,13:2,5:0.6818:2,2:27.9:1:31.7:1:0.56459:2.4775:60:30:0.6818:0:3.3 1/0:23:13:4,9:1,9:0.5652:2,2:23.3:1:30.2:1:0.33936:3.78:60:26:0.5652:0:3.2 -6 31237233 . A G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53026;SOR=0.55798;LSEQ=GACAAGAGGAATTATGGAGT;RSEQ=GGTGAGCTCCTCCACACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:2,12:2,5:0.6667:2,2:27.2:1:32.1:1:0.57427:2.29323:60:28:0.6667:0:3.4 1/0:21:11:4,7:1,9:0.5238:2,2:27:1:30.3:1:0.31078:4.77:60:22:0.5238:0:3.4 -6 31237255 . G A 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92526;LSEQ=GTGAGCTCCTCCACACGCCC;RSEQ=CCGCCATCACTTACACGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:3,10:1,5:0.6842:2,2:14.2:1:30.4:1:1:1.47:60:26:0.6842:0:3.2 1/0:15:10:4,6:0,5:0.6667:0,2:23.7:1:29:1:0.23077:0:60:20:0.7143:0:3.5 -6 31237323 . A G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33308;SOR=3.9895;LSEQ=CTGTGGGAAGAAAATGCCCT;RSEQ=TGAGGGGACTGGGAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:3,4:1,4:0.5833:2,2:19:1:31.3:1:0.57576:2.74:60:14:0.5833:0:3 1/1:7:6:2,4:0,1:0.8571:0,2:25.5:1:33:1:1:0:60:12:0.8571:0:3.7 -6 31237333 . T A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58462;SOR=2.80823;LSEQ=AAAATGCCCTATGAGGGGAC;RSEQ=GGGAGGAGGCAGGGCCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:0,3:0.6667:0,2:21.2:1:29.5:1:0.46429:0:60:12:0.6667:0:3.2 1/1:7:6:2,4:0,1:0.8571:0,2:25.5:1:32.3:1:1:0:60:12:0.8571:0:3.7 -6 31237342 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=TATGAGGGGACTGGGAGGAG;RSEQ=CAGGGCCATGTGATCTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:23.2:1:31.6:1:1:0:60:18:1:0:1.9 0/1:11:2:0,2:3,6:0.1818:2,0:11:1:27.5:1:1:0:60:4:0.1818:0:3.5 -6 31237353 . T C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.31198;LSEQ=TGGGAGGAGGCAGGGCCATG;RSEQ=GATCTTAGGGGAACCTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:0,2:0.75:0,2:23.3:1:31:1:0.46429:0:59.8:12:0.75:0:3 1/1:10:8:2,6:1,1:0.8:2,2:21.3:1:28.8:1:1:2.64575:60:16:0.8:0:3.4 -6 31237405 . C T 86 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=AAGAGAAGTTTCCAGAACTA;RSEQ=GACTGCAGACCCAGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:35.3:1:31.3:1:1:0:59.7:6:1:0:2.7 1/0:11:7:3,4:2,2:0.6364:2,2:21.6:1:30.7:1:1:1.29868:60:14:0.6364:0:3.7 -6 31237437 . T C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCAGGATCAGGAAACA;RSEQ=GGGGAAAGCAGTTGTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:15:0:27:0:1:0:59:2:1:0:4 1/0:5:3:2,1:1,1:0.6:2,2:37.7:1:32.3:1:1:1.73:60:6:0.6:0:4.3 -6 31237449 . T C 53 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAACATGGGGAAAGCAG;RSEQ=TGTGGGTTCTGGACCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:3:0:29:0:1:0:59:2:1:0:4 1/1:3:3:2,1:0,0:1:0,2:25.7:1:34:0:1:0:60:6:1:0:4.3 -6 31237463 . C G 53 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAGTTGTGGGTTCTGGA;RSEQ=CAACTGCCCTCCTAAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:11.7:1:34:0:1:0:60:6:1:0:4.3 -6 31237526 . C CA 50 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTCATGAATGCTGGAAT;RSEQ=AGGACCCCAACACCATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:37:1:25.3:1:1:0:41.3:3:1:0:1.8 1/0:4:3:2,1:1,0:0.75:0,2:17.3:1:30.7:1:1:0:60:6:0.75:0.25:2 -6 31237563 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64552;LSEQ=AATCATCAAGGTGATACATC;RSEQ=GTCCTTCATTGTCACATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:7,1:1,0:0.8889:0,2:19.1:1:29.9:1:1:0:48.1:16:0.8889:0:2.5 1/1:6:5:3,2:1,0:0.8333:0,2:26.4:1:30:1:1:0:58:10:0.8333:0:2 -6 31237575 . TCA T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.4714;LSEQ=GATACATCCGTCCTTCATTG;RSEQ=CATGTGCTTCACAAAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:8,1:1,0:0.9:0,2:20.6:1:30.3:1:1:0:53.7:18:0.9:0.1:2.6 1/1:5:4:3,1:1,0:0.8:0,2:39.5:1:29.8:1:1:0:57.5:8:0.8:0:2.3 -6 31237592 . A C 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTCACATGTGCTTCACAA;RSEQ=AGAGTAAGTGCTGGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:13,1:1,0:0.9333:0,1:19.8:1:30.9:1:1:0:57.2:13:0.9286:0:3.1 1/1:6:6:4,2:0,0:1:0,2:24.2:1:30.7:1:1:0:58.3:12:1:0:2.5 -6 31237605 . G A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55829;SOR=2.71122;LSEQ=TTCACAAAAGAGTAAGTGCT;RSEQ=GCACACAGGGTCCCAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:0.1053:1,0:31:1:28:1:1:0:50:4:0.1053:0:5 0/1:8:2:2,0:4,2:0.25:2,0:7:1:28:1:1:0:60:4:0.25:0:4 -6 31237660 . A G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.18367;SOR=0;LSEQ=TGGATGGTGCTTCCAGTAAC;RSEQ=AGGCGGGGCACACTTCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:37,3:0,0:1:0,2:24.4:1:28.5:1:1:0:60:39:1:0:3.8 1/1:9:8:7,1:1,0:0.8889:0,2:24.9:1:30.9:1:1:0:60:16:0.8889:0:4 -6 31237664 . C T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18868;SOR=0;LSEQ=TGGTGCTTCCAGTAACAAGG;RSEQ=GGGGCACACTTCTACCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:39,4:0,0:1:0,2:23.7:1:28.7:1:1:0:60:20.5:1:0:3.8 1/1:10:9:8,1:1,0:0.9:0,2:22.6:1:30:1:1:0:60:18:0.9:0:3.9 -6 31237703 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00055;SOR=0.14253;LSEQ=GGGCTTGAAACTCCCAGTGG;RSEQ=ACAAGAAAACCCAGACCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:50:41,9:15,0:0.7692:1,2:31.5:1:29.8:1:0.10334:0:54.8:49:0.8033:0:3.9 0/1:19:6:6,0:13,0:0.3158:1,0:27.7:1:29.3:1:1:0:50.7:12:0.3158:0:3.7 -6 31237723 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9382;LSEQ=GACAAGAAAACCCAGACCCC;RSEQ=CTCTTCACCCCTTCCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:48:39,9:16,1:0.7273:1,2:31.6:1:28.5:1:0.27048:3.63547:54.1:11:0.7097:0:3.9 1/0:21:15:15,0:6,0:0.7143:0,1:32.9:1:30.2:1:1:0:49.8:30:0.7143:0:3 -6 31237727 . T C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.79735;SOR=0.8885;LSEQ=AGAAAACCCAGACCCCGCTC;RSEQ=TCACCCCTTCCCTACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:71:52:42,10:18,1:0.7324:1,2:27.3:1:30.5:1:0.267:4.22023:53.8:51:0.7286:0:4.2 1/0:24:17:17,0:7,0:0.7083:0,1:28.4:1:30.2:1:1:0:51:34:0.7083:0:3.6 -6 31237760 . CAC TGT 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13155;SOR=Inf;LSEQ=TACCTGAGCTCTTCCTCCTA;RSEQ=ATCATAGCGGTGACCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:83,11:0:2,0:20.8:1:30.8:1:1:0:56.1:12.429:1:0:4.6 0/1:54:2:1,1:47,5:0.037:2,2:27:1:32.2:1:0.21174:8.67357:49.5:4:0.037:0:6 -6 31237765 . C A 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55466;SOR=3.49721;LSEQ=GAGCTCTTCCTCCTACACAT;RSEQ=ATAGCGGTGACCACAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:1,0:81,9:0.011:2,0:1:0:27:0:1:0:60:2:0.0119:0:4 0/1:53:2:2,0:45,6:0.0377:2,0:37:1:29.5:1:1:0:60:4:0.0385:0:8 -6 31237767 . T C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34607;SOR=0.66895;LSEQ=GCTCTTCCTCCTACACATCA;RSEQ=AGCGGTGACCACAGCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:45:41,4:29,1:0.6:1,2:30.2:1:32.6:1:0.64236:2.79541:58.3:44:0.5946:0:7.8 1/0:46:23:19,4:21,2:0.5:2,2:31.4:1:31.1:1:0.66515:2.17346:58.2:22:0.4889:0:7.7 -6 31237769 . G A 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19793;SOR=0.5994;LSEQ=TCTTCCTCCTACACATCATA;RSEQ=CGGTGACCACAGCTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:43:40,3:31,1:0.5658:1,2:33.2:1:30.5:1:0.6315:2.30131:58.5:42:0.5753:0:7.9 0/1:48:21:18,3:23,4:0.4375:2,2:33.3:1:30:1:1:1.04:59:42:0.4375:0:7.9 -6 31237771 . G A 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20634;SOR=0.62193;LSEQ=TTCCTCCTACACATCATAGC;RSEQ=GTGACCACAGCTCCAAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:44:40,4:31,1:0.5789:1,2:34.8:1:30.8:1:0.39046:3.06009:58.5:43:0.5811:0:7.9 0/1:50:23:19,4:24,3:0.46:2,2:35.4:1:29.8:1:0.68883:1.66656:58.2:22:0.449:0:7.7 -6 31237773 . TG CC 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03049;SOR=0.44162;LSEQ=CCTCCTACACATCATAGCGG;RSEQ=ACCACAGCTCCAAGGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:42:38,4:30,1:0.5676:1,2:37.7:1:32.5:1:0.38694:3.11483:58.5:84:0.5915:0:6.9 0/1:52:19:16,3:24,5:0.3654:2,2:37.4:1:31.4:1:1:1.11:59.2:38:0.3878:0:6.9 -6 31237774 . G C 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73948;SOR=0.60722;LSEQ=CTCCTACACATCATAGCGGT;RSEQ=ACCACAGCTCCAAGGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:7:6,1:29,1:0.0886:1,2:12:1:28.6:1:0.34685:4.55132:60:6:0.1667:0:6.3 0/1:54:3:3,0:25,6:0.0556:2,0:31:1:24.3:1:1:0:58.3:2:0.0588:0:7.7 -6 31237776 . C T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17833;SOR=2.68214;LSEQ=CCTACACATCATAGCGGTGA;RSEQ=CACAGCTCCAAGGACAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:4:4,0:122,36:0.0247:2,0:44.8:1:32:1:0.57616:0:60:8:0.025:0:7.3 0/1:94:6:6,0:66,22:0.0638:2,0:37.8:1:29.7:1:0.33007:0:59.2:12:0.0645:0:6.7 -6 31237779 . C T 175 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00211;SOR=0.41617;LSEQ=ACACATCATAGCGGTGACCA;RSEQ=AGCTCCAAGGACAGCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:56:41,15:100,29:0.3027:2,2:11:1:30.3:1:0.57447:1.25991:58.3:112:0.3043:0:4.6 0/1:131:20:17,3:79,32:0.1527:2,2:6.4:1:30.2:1:0.27536:2.28:60:40:0.1538:0:4.6 -6 31237786 . A T 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00325;SOR=0.47077;LSEQ=ATAGCGGTGACCACAGCTCC;RSEQ=AGGACAGCTAGGACAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:238:202:141,61:31,5:0.8487:2,2:16.2:1:30.2:1:0.04525:2.67295:58.9:66.333:0.8468:0:4.9 1/0:160:116:78,38:33,11:0.725:2,2:15.6:1:29.6:1:0.44278:1.45818:59.6:232:0.7342:0:4.6 -6 31237802 . A G 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00087;SOR=0.47947;LSEQ=CTCCAAGGACAGCTAGGACA;RSEQ=CCAGGACAGCCAGGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:350:305:188,117:33,11:0.8714:2,2:20.3:1:31.8:1:0.09577:1.86391:57.8:42.571:0.8713:0:4.7 1/0:242:185:114,71:37,19:0.7645:2,2:19.9:1:31.6:1:0.63684:1.21188:58.9:60.667:0.7615:0:4.4 -6 31237813 . CA TG 80 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00225;SOR=Inf;LSEQ=GCTAGGACAACCAGGACAGC;RSEQ=GGCCAGCAACGATGCCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:255,173:0:2,0:23.9:1:31.3:1:1:0:57.3:213:1:0:3.9 0/1:311:7:3,4:179,121:0.0225:2,2:19.3:1:28.5:1:0.44846:1.96801:54:14:0.0228:0:6.7 -6 31237821 . C A 107 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AACCAGGACAGCCAGGCCAG;RSEQ=AACGATGCCCATGATGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:0:0,0:270,200:0:2,0:26.3:1:31.9:1:1:0:56.8:77.333:1:0:3.9 0/1:349:14:9,5:198,137:0.0401:2,2:17.6:1:28.2:1:0.78705:1.24:56.1:28:0.0408:0:6.9 -6 31237833 . T C 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.38783;LSEQ=CAGGCCAGCAACGATGCCCA;RSEQ=GATGGGGATGGTGGGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:554:480:268,212:39,35:0.8664:2,2:27.4:1:30.7:1:0.61783:1.13:56.1:67.571:0.8647:0:4.2 1/0:404:289:168,121:50,45:0.7153:2,2:27.6:1:30.1:1:0.4035:1.25:58.2:40.286:0.7103:0:3.7 -6 31237835 . A T 121 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.32947;LSEQ=GGCCAGCAACGATGCCCATG;RSEQ=TGGGGATGGTGGGCTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:586:1:0,1:325,258:0.0017:2,0:1:0:25:0:0.44349:0:60:2:0.0018:0:2 0/1:418:20:12,8:223,174:0.0478:2,2:22.7:1:28:1:0.81993:1.17:56:19:0.0459:0:6.6 -6 31237858 . T C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28067;LSEQ=GGGATGGTGGGCTGGGAAGA;RSEQ=GGCTCTGGGAAAGGAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:650:502:255,247:73,75:0.7723:2,2:27.1:1:30.5:1:0.77944:1.06:56.2:49.2:0.7773:0:4.2 0/1:476:232:120,112:117,126:0.4874:2,2:27:1:29.6:1:0.46328:1.15:57.4:45.4:0.483:0:4.3 -6 31237862 . T C 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTGGGCTGGGAAGATGGC;RSEQ=CTGGGAAAGGAGGAGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:0:0,0:310,319:0:2,0:28.2:1:30:1:1:0:56.9:25.208:1:0:3.5 0/1:471:27:14,13:217,227:0.0573:2,2:32.9:1:30.3:1:0.84393:1.13:59.8:54:0.0584:0:3.1 -6 31237876 . A G 281 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00038;SOR=0.5293;LSEQ=GATGGCTCTGGGAAAGGAGG;RSEQ=GAAGGTGAGGGGCCCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:620:552:261,291:27,41:0.8903:2,2:27.6:1:30.9:1:0.24892:1.36:56.6:109.4:0.8909:0:3.7 1/1:450:365:168,197:35,50:0.8111:2,2:27:1:29.7:1:0.46835:1.22:58.2:39.556:0.8091:0:3.5 -6 31237893 . G T 126 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGAGAAGGTGAGGGGCCCT;RSEQ=ACCCCCAAGCCTCAGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:534:0:0,0:233,299:0:2,0:26:1:31.2:1:1:0:56.7:52.2:0.9981:0:3 0/1:389:22:10,12:159,208:0.0566:2,2:32.1:1:28.4:1:1:1.09:59:44:0.0573:0:5.5 -6 31237896 . C A 129 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAGGTGAGGGGCCCTGAC;RSEQ=CCCAAGCCTCAGCCCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:0:0,0:225,289:0:2,0:25.6:1:31:1:1:0:56.8:45.727:1:0:3 0/1:368:22:10,12:146,200:0.0598:2,2:30.5:1:29.1:1:0.82561:1.14:59:44:0.0604:0:5.5 -6 31237897 . C T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.14326;LSEQ=GAAGGTGAGGGGCCCTGACC;RSEQ=CCAAGCCTCAGCCCTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:507:361:158,203:65,81:0.712:2,2:26.3:1:30.2:1:0.92138:1.03097:55.8:59.167:0.7157:0:3.6 0/1:360:94:41,53:113,152:0.2611:2,2:27.9:1:28.7:1:0.90375:1.04:57.4:30.333:0.2578:0:3.7 -6 31237917 . C T 159 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=3.24488;LSEQ=CCCAAGCCTCAGCCCTGACC;RSEQ=GGCTGAAGGGCTCCAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:19:10,9:148,199:0.0516:2,2:19.2:1:29.4:1:0.47748:1.49:56.5:18:0.0496:0:3.3 0/1:266:40:15,25:87,139:0.1504:2,2:22.1:1:29.9:1:1:1.04301:58.2:80:0.1527:0:3.5 -6 31237931 . CAGA C 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=0.45149;LSEQ=CTGACCCGGCTGAAGGGCTC;RSEQ=AGGACTTCTGCTTTCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:196:73,123:21,30:0.7903:2,2:16.4:1:31.6:1:0.62959:1.17865:58.5:64.333:0.7975:0.1653:3 1/0:197:124:35,89:31,42:0.6294:2,2:22.7:1:31.6:1:0.04395:1.87069:57.1:248:0.6294:0.0609:3.7 -6 31237950 . T C 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.88277;SOR=0.92415;LSEQ=CCAGAAGGACTTCTGCTTTC;RSEQ=CTGATAAGAGATGTGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:159:128:40,88:10,21:0.805:2,2:7.6:1:31.7:1:1:1.04731:58.2:256:0.805:0:2.9 1/0:130:103:25,78:15,12:0.7923:2,2:14.9:1:31:1:0.00409:3.85276:56.6:50.5:0.7891:0:3.9 -6 31237955 . TAAGAGATGTGACCCCCCATT GAAGACACATCACCCCTCATC 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGACTTCTGCTTTCTCTGA;RSEQ=CCCCTCCTTACCCCAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:90:29,61:0,0:1:0,2:18.8:1:31:1:1:0:55.7:180:0.75:1:2 0/0:75:0:0,0:16,12:0:2,0:24.7:1:30.2:1:1:0:60:56:0.3733:0:0.1 -6 31237960 . G C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0465;SOR=2.34733;LSEQ=TTCTGCTTTCTCTGATAAGA;RSEQ=ATGTGACCCCCCATTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:14:5,9:11,20:0.3111:2,2:18.9:1:32.3:1:1:1.01:53.2:28:0.3182:0:6.6 1/0:60:31:10,21:17,12:0.5167:2,2:29:1:31.1:1:0.06834:2.91874:51.2:30:0.5172:0:7.4 -6 31237962 . TG CA 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00536;SOR=3.68983;LSEQ=CTGCTTTCTCTGATAAGAGA;RSEQ=TGACCCCCCATTCCCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:8:4,4:11,20:0.2051:2,2:28.8:1:31.9:1:0.68566:1.79:48.1:16:0.2105:0:6.6 0/1:57:28:10,18:18,11:0.4912:2,2:29:1:31.1:1:0.06496:2.88747:50.2:56:0.4912:0:6.5 -6 31237971 . C T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0506;SOR=2.302;LSEQ=CTGATAAGAGATGTGACCCC;RSEQ=CATTCCCCTCCTTACCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:15:5,10:10,19:0.3409:2,2:14.7:1:29.2:1:1:1.05142:44.1:14:0.3333:0:6.2 1/0:66:36:14,22:19,11:0.5455:2,2:18.1:1:29.6:1:0.08278:2.67169:47.1:72:0.5455:0:6.3 -6 31237975 . T C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07681;SOR=2.1333;LSEQ=TAAGAGATGTGACCCCCCAT;RSEQ=CCCCTCCTTACCCCAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:15:5,10:10,17:0.3571:2,2:14.5:1:31.2:1:1:1.17195:44.1:30:0.3846:0:6.2 1/0:68:37:15,22:19,12:0.5441:2,2:15.5:1:30.8:1:0.14351:2.2928:46.9:36:0.5373:0:6.2 -6 31237987 . C T 56 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17049;SOR=0.19052;LSEQ=CCCCCCATTCCCCTCCTTAC;RSEQ=CCAGCTCAGGGTGAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:4:0,4:18,37:0.0678:2,0:8.5:1:28:1:0.30274:0:32.5:8:0.0702:0:7 0/1:74:1:0,1:40,33:0.0135:2,0:7:0:30:0:0.45946:0:58:2:0.0135:0:8 -6 31237991 . G T 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3824;SOR=0.7291;LSEQ=CCATTCCCCTCCTTACCCCA;RSEQ=CTCAGGGTGAGGGGCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:33:9,24:10,17:0.55:2,2:15.5:1:29.5:1:0.57772:1.5567:36.1:66:0.569:0:5.8 0/1:68:32:17,15:21,14:0.4706:2,2:14.9:1:29.1:1:0.62702:1.31796:40.7:15:0.4545:0:5.8 -6 31237992 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=Inf;LSEQ=CATTCCCCTCCTTACCCCAG;RSEQ=TCAGGGTGAGGGGCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:18,41:0:2,0:21.8:1:31.3:1:1:0:46.6:58:1:0:3.3 0/1:69:2:1,1:36,30:0.029:2,2:18:1:27:1:1:1.19677:60:4:0.0303:0:1 -6 31238001 . AG CA 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24461;SOR=Inf;LSEQ=CCTTACCCCAGCTCAGGGTG;RSEQ=GGGCTCTTGCAGCCCCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:19,48:0:2,0:23:1:29.9:1:1:0:45.1:21.333:1:0:3.4 0/1:69:3:0,3:35,31:0.0435:2,0:14.3:1:30.7:1:0.11421:0:57.7:6:0.0435:0:5 -6 31238009 . TT CG 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.17153;LSEQ=CAGCTCAGGGTGAGGGGCTC;RSEQ=GCAGCCCCTCGTGCTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:30:8,22:13,27:0.4286:2,2:24.2:1:29.5:1:0.79262:1.3188:35.2:60:0.4286:0.0143:4.6 0/1:71:8:4,4:29,30:0.1127:2,2:17.9:1:29.9:1:1:1.03:37.8:16:0.1143:0.0141:3.6 -6 31238010 . T G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24875;SOR=1.67869;LSEQ=AGCTCAGGGTGAGGGGCTCT;RSEQ=GCAGCCCCTCGTGCTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:15:5,10:8,16:0.2174:2,2:30.1:1:29.9:1:1:1:39.3:6.5:0.3611:0:4.6 0/1:69:22:10,12:19,21:0.3188:2,2:30.2:1:29.5:1:1:1.08427:37.8:10:0.3448:0:4.4 -6 31238027 . C A 120 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.05417;LSEQ=TCTTGCAGCCCCTCGTGCTG;RSEQ=ATATGGCACGTGTATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:16:4,12:21,44:0.1975:2,2:28.9:1:30.1:1:0.76451:1.42576:41.8:32:0.2:0:4.5 0/1:77:1:0,1:32,44:0.013:2,0:31:0:32:0:1:0:37:2:0.0133:0:4 -6 31238029 . T C 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02911;SOR=0.46025;LSEQ=TTGCAGCCCCTCGTGCTGCA;RSEQ=ATGGCACGTGTATCTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:79:58:18,40:7,14:0.7342:2,2:30.1:1:31.6:1:1:1.10961:40.2:57:0.76:0:4.2 1/0:77:43:14,29:17,17:0.5584:2,2:29.3:1:30.6:1:0.16142:2.0514:40.2:42:0.5526:0:3.8 -6 31238048 . C T 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.12131;SOR=Inf;LSEQ=ATATGGCACGTGTATCTCTG;RSEQ=TCTTGTCCAGAAGGCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:28,57:0:2,0:26.4:1:31.3:1:1:0:45.4:20.25:1:0:3.2 0/1:90:4:0,4:33,53:0.0444:2,0:28.5:1:29.5:1:0.29232:0:58.3:8:0.046:0:4.5 -6 31238053 . G C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00069;SOR=0.29328;LSEQ=GCACGTGTATCTCTGCTCTT;RSEQ=TCCAGAAGGCACCACCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:65:24,41:3,11:0.8228:2,2:28.3:1:31.8:1:0.35911:2.13:42.1:130:0.8333:0:3.9 1/0:87:50:21,29:10,26:0.5747:2,2:27:1:31.5:1:0.25497:1.87:38.8:100:0.5747:0:3.1 -6 31238068 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11383;LSEQ=CTCTTGTCCAGAAGGCACCA;RSEQ=CACAGCTGCCCACTTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:31:13,18:16,31:0.3974:2,2:26.7:1:30.2:1:0.63256:1.39:45.2:62:0.4133:0:3.6 0/1:87:6:2,4:28,53:0.069:2,2:30:1:30.2:1:1:1.05594:37.5:12:0.069:0:3.5 -6 31238076 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49708;SOR=Inf;LSEQ=CAGAAGGCACCACCACAGCT;RSEQ=CCCACTTCTGGAAGGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:33,47:0:2,0:23.7:1:32.1:1:1:0:48.1:79:1:0:2.9 0/1:83:2:1,1:26,55:0.0241:2,2:6.5:1:24:1:0.54746:2.09:40.5:4:0.025:0:3 -6 31238126 . G A 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13882;SOR=4.01448;LSEQ=GGCCTGGTCTCCACAAGCTC;RSEQ=GTGTCCTGGGTCTGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:42,35:0.0253:2,2:13:1:32.5:1:1:1.19722:44.5:4:0.0263:0:3 0/1:63:6:4,2:28,29:0.0952:2,2:7.3:1:29.5:1:0.67187:2.05:33.3:12:0.0952:0:3 -6 31238135 . G A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00288;SOR=0.3174;LSEQ=TCCACAAGCTCGGTGTCCTG;RSEQ=GTCTGGTCCTCCCCATCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:56:31,25:11,6:0.7671:2,2:26.3:1:30.1:1:0.5821:1.47071:47.4:27:0.7606:0:3.3 1/0:57:29:15,14:16,12:0.5088:2,2:25:1:29.4:1:0.79208:1.23966:43:28:0.5:0:3.2 -6 31238138 . C T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0054;SOR=0.34438;LSEQ=ACAAGCTCGGTGTCCTGGGT;RSEQ=TGGTCCTCCCCATCCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:59:32,27:11,6:0.7763:2,2:25.1:1:30.2:1:0.58087:1.53815:47.1:118:0.7763:0:3.3 1/0:59:32:17,15:16,11:0.5424:2,2:23.5:1:30.1:1:0.79306:1.27799:42.7:64:0.5517:0:3.3 -6 31238147 . C G 127 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00667;SOR=3.63611;LSEQ=GTGTCCTGGGTCTGGTCCTC;RSEQ=CCATCCCGCTGCCAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:8:4,4:43,33:0.0952:2,2:31.5:1:27.5:1:0.7266:1.29888:36:7:0.0864:0:3.8 0/1:61:17:10,7:29,15:0.2787:2,2:28.8:1:31.1:1:0.76705:1.34646:36.9:34:0.2881:0:3.4 -6 31238155 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11619;LSEQ=GGTCTGGTCCTCCCCATCCC;RSEQ=CTGCCAGGTCAGTGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:85:59:32,27:16,9:0.6941:2,2:22.9:1:30.3:1:0.47481:1.49283:46.7:118:0.7108:0:3.2 0/1:68:14:11,3:37,17:0.2059:2,2:21.9:1:29.7:1:0.53185:1.67:47:28:0.2154:0:3.4 -6 31238194 . G T 26 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.92679;LSEQ=CTCCGCAGGGTAGAAGCCCA;RSEQ=GGCCCAGCACCTCAGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:92,48:0.0071:2,0:32:0:15:0:0.34752:0:21:0:0:0:6 0/1:147:2:1,1:106,39:0.0136:2,2:17.5:1:26:1:0.47153:2.69639:46.5:4:0.0136:0:4 -6 31238230 . G C 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=4e-05;SOR=0.47506;LSEQ=GGTGGCCTCATGGTCAGAGA;RSEQ=GGGGTGGTGGGTCACGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:256:181:99,82:41,33:0.707:2,2:24.7:1:30.3:1:1:1.02897:54.8:59.333:0.7149:0:4.3 1/0:296:158:99,59:75,61:0.5338:2,2:24.6:1:30.2:1:0.23401:1.36:57:157:0.5377:0:4.1 -6 31238232 . G A 90 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00219;SOR=Inf;LSEQ=TGGCCTCATGGTCAGAGAGG;RSEQ=GGTGGTGGGTCACGTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:144,117:0:2,0:25.4:1:30.4:1:1:0:56.3:36.286:1:0:3.1 0/1:299:10:5,5:169,119:0.0334:2,2:29.6:1:27.1:1:0.74633:1.41844:52.1:9:0.0304:0:4.4 -6 31238234 . G A 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=2e-05;SOR=0.46966;LSEQ=GCCTCATGGTCAGAGAGGGG;RSEQ=TGGTGGGTCACGTGTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:262:186:102,84:42,34:0.7099:2,2:25.8:1:29.4:1:1:1.01724:55.1:25.571:0.7075:0:4.3 1/0:305:163:100,63:77,65:0.5344:2,2:26:1:28.6:1:0.24487:1.34:57.2:162:0.5364:0:4.1 -6 31238259 . G T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.43086;LSEQ=GGGTCACGTGTGTCTTTGGG;RSEQ=GTTCTGACGGGAAGAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:275:187:95,92:46,42:0.68:2,2:32:1:30.1:1:0.89721:1.06039:57.6:374:0.6825:0:4.5 0/1:335:160:83,77:71,77:0.4776:2,2:30.1:1:29.2:1:0.56859:1.17:59:79:0.4788:0:4.3 -6 31238267 . C T 172 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1367;LSEQ=TGTGTCTTTGGGGGTTCTGA;RSEQ=GGGAAGAGTCAGAAAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:55:27,28:105,111:0.203:2,2:32.1:1:29.8:1:1:1.02:55.2:17.333:0.197:0:5.2 0/1:328:11:6,5:147,170:0.0335:2,2:30.9:1:27.2:1:0.76065:1.39:58.7:4.5:0.0285:0:5 -6 31238297 . C T 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00418;SOR=0.54688;LSEQ=CAGAAAATTCAGACACTTTG;RSEQ=ATCTCTCTTGGGACACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:200:148:56,92:23,28:0.74:2,2:22.9:1:28.6:1:0.40796:1.3474:59.3:73:0.7449:0:4.9 1/0:235:143:53,90:31,60:0.6085:2,2:24.4:1:27.8:1:0.67669:1.14:59.7:70.5:0.613:0:4.7 -6 31238308 . G C 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13786;SOR=0.7068;LSEQ=GACACTTTGCATCTCTCTTG;RSEQ=GACACTCCAGCAGCGCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:118:42,76:18,28:0.7152:2,2:21.1:1:30.6:1:0.71973:1.16218:59.2:236:0.7239:0:4.9 1/0:183:117:38,79:20,45:0.6393:2,2:22.4:1:30.1:1:0.86908:1.08:60:116:0.648:0:4.9 -6 31238318 . G A 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02976;SOR=0.57532;LSEQ=ATCTCTCTTGGGACACTCCA;RSEQ=CAGCGCCCATGTGACCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:92:29,63:14,29:0.6815:2,2:21.7:1:29.8:1:1:1.04837:59.6:91:0.6894:0:4.8 1/0:156:86:21,65:24,45:0.5513:2,2:21.5:1:29:1:0.21245:1.64532:59.8:85:0.5556:0:4.8 -6 31238322 . C T 103 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00101;SOR=Inf;LSEQ=CTCTTGGGACACTCCAGCAG;RSEQ=GCCCATGTGACCATCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:39,86:0:2,0:20.5:1:30.3:1:1:0:59.7:124:1:0:3.2 0/1:143:11:1,10:35,96:0.0769:2,2:16.4:1:30:1:0.2902:3.6214:58.6:22:0.0775:0:5.4 -6 31238323 . G A 25 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.77398;LSEQ=TCTTGGGACACTCCAGCAGC;RSEQ=CCCATGTGACCATCCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:1:1,0:38,82:0.0083:2,0:1:0:27:0:0.32231:0:60:2:0.0084:0:1 0/1:137:2:1,1:34,101:0.0146:2,2:16.5:1:25.5:1:0.44708:2.94:57.5:4:0.015:0:4 -6 31238345 . T C 111 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00563;SOR=4.70506;LSEQ=CCATGTGACCATCCTGAGAA;RSEQ=GGACAGGACACCTGGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:1,3:11,61:0.0526:2,2:23.3:1:30.8:1:0.50476:1.83:60:8:0.0526:0:4.8 0/1:67:14:4,10:5,48:0.209:2,2:29.4:1:29.4:1:0.08265:3.74:59.6:28:0.209:0:5 -6 31238364 . G A 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09169;SOR=Inf;LSEQ=ATGGACAGGACACCTGGGGT;RSEQ=GGGAAGGCGGCAGAGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:6,50:0:2,0:24.7:1:30.6:1:1:0:59.6:17.667:1:0:2.6 0/1:47:3:1,2:4,40:0.0638:2,2:12.3:1:30.3:1:0.29201:4.72:60:6:0.0638:0:4.7 -6 31238372 . C G 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63321;SOR=1.2804;LSEQ=GACACCTGGGGTGGGGAAGG;RSEQ=GGCAGAGAACCCAGACGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:36:5,31:0,13:0.7347:1,2:23.9:1:31.1:1:0.30636:0:59.3:72:0.7347:0:3.4 1/0:41:32:4,28:1,8:0.7805:2,2:25.6:1:31:1:1:1.14:59.3:64:0.7805:0:4.3 -6 31238377 . G C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00469;SOR=12.42231;LSEQ=CTGGGGTGGGGAAGGCGGCA;RSEQ=AGAACCCAGACGCCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:33:6,27:0,12:0.7333:0,2:24.7:1:31.8:1:0.17139:0:59:66:0.7333:0:3.2 1/1:36:35:4,31:0,1:0.9722:0,2:22.7:1:32.2:1:1:0:59.4:70:0.9722:0:3.5 -6 31238406 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14787;SOR=Inf;LSEQ=GACGCCAGCCTGGACACAGG;RSEQ=ACCTGGGATAATCTCCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:5,31:0:2,0:22.5:1:29.3:1:1:0:59.1:5:1:0:1.6 0/1:23:2:1,1:2,19:0.087:2,2:41.5:1:30.5:1:0.24901:7.96:60:4:0.087:0:5 -6 31238428 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07051;SOR=Inf;LSEQ=CCTGGGATAATCTCCTATTC;RSEQ=TTGGAAAGTTCTAGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:3,26:0:2,0:24.8:1:29.7:1:1:0:59.3:13.5:1:0:1.8 0/1:11:2:1,1:0,9:0.1818:0,2:24:1:29:1:0.18182:0:60:4:0.1818:0:5 -6 31238490 . T C 111 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09701;SOR=0.08933;LSEQ=GTCCTGACCTGAGTGGAGGC;RSEQ=GCAGGACTCAGAAAAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:0,14:0,2:0.875:0,1:24.6:1:29.3:1:1:0:60:13:0.8667:0:3.1 0/1:3:1:0,1:0,2:0.3333:0,0:2:0:27:0:1:0:60:2:0.3333:0:1 -6 31238492 . C A 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05;SOR=0;LSEQ=CCTGACCTGAGTGGAGGCTG;RSEQ=AGGACTCAGAAAAGCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:0,12:0,2:0.8571:0,0:27.3:1:31:1:1:0:60:24:0.8571:0:2.9 0/0:2:0:0,0:0,2:0:0,0:15:1:33.5:1:1:0:60:4:1:0:0 -6 31238524 . G A 72 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCTGGAATCAAACCTTCA;RSEQ=ACACATTGAGTGTGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:19.8:1:31.2:1:1:0:60:10:0.8333:0:4.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31238535 . T C 64 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACCTTCAGACACATTGAG;RSEQ=GTGAGGCAGAGAACAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:14.5:1:32.3:1:1:0:60:8:0.8:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31238613 . A G 98 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGTCAAAGTGGTCAAAGG;RSEQ=GACCCCTGATCAGTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:9,1:1,0:0.9091:0,2:16.4:1:29.6:1:1:0:50.4:9:0.9:0:2.9 1/1:1:1:1,0:0,0:1:0,0:16:0:32:0:1:0:60:2:1:0:3 -6 31238632 . C T 51 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=2.73861;LSEQ=GAGACCCCTGATCAGTATTC;RSEQ=AGGGACTGTCTTCCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:8,1:0.25:2,0:28.7:1:32.7:1:1:0:35:6:0.25:0:4 1/0:2:1:1,0:1,0:0.5:0,0:3:0:30:0:1:0:40:2:0.5:0:3 -6 31238661 . GA AG 121 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5;SOR=0.37796;LSEQ=TCTTCCCCTCCATTTCCTCA;RSEQ=GACTTCATCCCTTAATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:14,0:3,0:0.7368:0,1:29.4:1:31.9:1:1:0:53.6:28:0.8235:0.0526:2.1 1/0:2:1:1,0:1,0:0.5:0,0:36:0:27:0:1:0:60:2:0.5:0:2 -6 31238666 . T G 50 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52688;SOR=1.93621;LSEQ=CCCTCCATTTCCTCAGAGAC;RSEQ=TCATCCCTTAATTGTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:0.1429:1,0:19:1:31.7:1:1:0:56:6:0.1429:0:2 0/1:4:1:1,0:3,0:0.25:0,0:37:0:31:0:1:0:40:2:0.25:0:3 -6 31238691 . C A 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.63601;SOR=1.54338;LSEQ=CCCTTAATTGTCCTAGAGAG;RSEQ=AGAGGGGGCCCTCAGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:4,0:25,0:0.1379:1,0:39.3:1:30.8:1:1:0:52:8:0.1429:0:2.5 0/1:10:2:2,0:7,1:0.2:2,0:30.5:1:28.5:1:1:0:40:4:0.2:0:3.5 -6 31238728 . G C 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31059;SOR=0.50929;LSEQ=GGAAACTCAGGAAAACTCAT;RSEQ=CCATTCTCCATTCAAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:35:35,0:8,0:0.814:0,1:24:1:31.4:1:1:0:53:70:0.814:0:3.4 1/0:16:11:10,1:5,0:0.6875:0,2:29.3:1:30.9:1:1:0:54.4:22:0.6875:0:3.5 -6 31238759 . C T 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60279;SOR=0.75842;LSEQ=TTCAAGGGAGGGCGATATTC;RSEQ=AGTGCTGATCCCATTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:43:42,1:13,0:0.7679:1,1:27:1:31:1:1:0:52.6:86:0.7679:0:3.9 1/0:28:20:19,1:7,1:0.7143:2,1:20.7:1:30.2:1:0.49735:2.60:55.8:40:0.7143:0:3.6 -6 31238762 . T C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.08988;LSEQ=AAGGGAGGGCGATATTCCAG;RSEQ=GCTGATCCCATTTTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:44:43,1:13,1:0.7586:1,1:26.6:1:32.3:1:0.42771:3.22:52.5:88:0.7586:0:4 1/0:31:24:22,2:7,0:0.7742:0,2:20.9:1:31.7:1:1:0:56.5:48:0.7742:0:3.4 -6 31238782 . C T 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.85386;LSEQ=TGCTGATCCCATTTTCCTCC;RSEQ=CTCCTCGTGGGAGGCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:2,0:82,5:0.0225:2,0:6.5:1:32.5:1:1:0:39.5:4:0.0227:0:6 0/1:52:1:1,0:49,2:0.0192:1,0:5:0:30:0:1:0:39:2:0.0192:0:6 -6 31238785 . C T 62 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.88249;LSEQ=TGATCCCATTTTCCTCCCCT;RSEQ=CTCGTGGGAGGCCATCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:4:4,0:90,7:0.0396:2,0:5.5:1:31:0:1:0:39.8:8:0.04:0:5.5 0/1:57:2:2,0:53,2:0.0351:1,0:4.5:1:31:0:1:0:39.5:4:0.0351:0:5.5 -6 31238797 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.14175;SOR=Inf;LSEQ=CCTCCCCTCCTCGTGGGAGG;RSEQ=CATCCCGGGAGATCTATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:122,8:0:2,0:21.7:1:31.7:1:1:0:56.2:31.5:1:0:3.3 0/1:79:2:1,1:71,6:0.0253:2,2:18:1:26.5:1:0.1704:11.03273:60:4:0.0256:0:2.5 -6 31238801 . C G 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00026;SOR=0.16817;LSEQ=CCCTCCTCGTGGGAGGCCAT;RSEQ=CCGGGAGATCTATAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:31:30,1:105,8:0.2138:2,1:21.5:1:31.7:1:0.6841:2.28:57.5:30:0.2158:0:4.3 0/1:92:4:4,0:81,7:0.0435:2,0:28:1:32.5:1:1:0:60:8:0.044:0:4.5 -6 31238804 . G C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5427;SOR=0.72619;LSEQ=TCCTCGTGGGAGGCCATCCC;RSEQ=GGAGATCTATAGGAGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:20:19,1:124,11:0.1274:2,1:12.5:1:30.4:1:1:1.68:36.5:9:0.1184:0:4.6 0/1:94:9:9,0:77,8:0.0957:2,0:11.3:1:31.2:1:1:0:42.7:18:0.0978:0:4.4 -6 31238807 . A C 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24626;SOR=0.58189;LSEQ=TCGTGGGAGGCCATCCCGGG;RSEQ=GATCTATAGGAGATGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:23:22,1:129,12:0.1402:2,1:13.8:1:32.5:1:0.69597:2.04:39.5:46:0.1484:0:4.3 0/1:104:9:9,0:85,10:0.0865:2,0:14.3:1:33.1:1:0.59485:0:42.7:18:0.0865:0:4.4 -6 31238814 . TA CG 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.22081;LSEQ=AGGCCATCCCGGGAGATCTA;RSEQ=GGAGATGGGGAAGGCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:215:109:96,13:73,6:0.507:2,2:24:1:31.3:1:0.46313:1.64337:58:218:0.5166:0.0605:2.4 0/1:141:26:21,5:60,9:0.1844:2,2:22.3:1:30.3:1:0.5193:1.57904:58.8:52:0.1844:0.0284:2.3 -6 31238815 . A G 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0124;SOR=0;LSEQ=GGCCATCCCGGGAGATCTAT;RSEQ=GGAGATGGGGAAGGCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:9:7,2:96,8:0.0431:2,2:9.8:1:26.4:1:0.18136:3.37311:58.9:8:0.0727:0:3.3 0/0:143:0:0,0:104,16:0:2,0:20.2:1:29.2:1:1:0:57.1:59:1:0:1.8 -6 31238851 . T C 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32873;LSEQ=TCCCCACTGCCCCTGGTACC;RSEQ=GCGCGCTGCAGCGTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:469:424:311,113:31,11:0.9041:2,2:25.3:1:30.4:1:1:1.02393:54.4:46.111:0.9041:0:2.3 1/0:352:266:194,72:57,25:0.7557:2,2:24.8:1:30.1:1:0.57419:1.18:52.5:132:0.7586:0:2.7 -6 31238853 . C T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.75106;SOR=1.35542;LSEQ=CCCACTGCCCCTGGTACCTG;RSEQ=GCGCTGCAGCGTCTCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:5:3,2:350,129:0.0103:2,2:5.6:1:30.8:1:0.61567:1.80625:40.2:10:0.0105:0:2.6 0/1:359:5:4,1:254,100:0.0139:2,2:8:1:30.2:1:1:1.57:39:10:0.014:0:5.2 -6 31238859 . G C 136 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCCTGGTACCTGCGCGCT;RSEQ=CAGCGTCTCCTTCCCGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:0:0,0:401,153:0:2,0:24.7:1:32.1:1:1:0:54.6:91.333:0.9982:0:2.2 0/1:426:19:15,4:275,129:0.0446:2,2:23.2:1:32.1:1:0.44959:1.76:41.6:38:0.045:0:4.6 -6 31238864 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01471;SOR=Inf;LSEQ=TGGTACCTGCGCGCTGCAGC;RSEQ=TCTCCTTCCCGTTCTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:0:0,0:427,188:0:2,0:24.4:1:30:1:1:0:53.6:40:1:0:2.2 0/1:466:5:3,2:314,146:0.0107:2,2:11.6:1:27.4:1:0.65539:1.43264:48.4:10:0.011:0:3.8 -6 31238866 . C G 149 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.19115;LSEQ=GTACCTGCGCGCTGCAGCGT;RSEQ=TCCTTCCCGTTCTCCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:1:1,0:431,194:0.0016:2,0:35:0:15:0:1:0:48:0:0:0:4 0/1:475:24:19,5:305,146:0.0505:2,2:24.5:1:32.5:1:0.26996:1.82:42.8:48:0.051:0:4.8 -6 31238868 . C T 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=32.88255;LSEQ=ACCTGCGCGCTGCAGCGTCT;RSEQ=CTTCCCGTTCTCCAGGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:638:1:0,1:436,200:0.0016:2,0:1:0:27:0:0.31554:0:60:2:0.0016:0:1 0/1:488:24:16,8:314,150:0.0492:2,2:30:1:29.5:1:1:1.04657:50.6:48:0.0499:0:2.8 -6 31238875 . G A 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15878;SOR=1.61568;LSEQ=CGCTGCAGCGTCTCCTTCCC;RSEQ=TTCTCCAGGTATCTGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:678:19:12,7:443,214:0.028:2,2:24.3:1:29.6:1:0.80456:1.20719:51.4:38:0.0283:0:4.8 0/1:539:24:15,9:330,185:0.0445:2,2:24.7:1:29.6:1:1:1.07013:46:23:0.0432:0:5.3 -6 31238880 . C T 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16018;SOR=1.58987;LSEQ=CAGCGTCTCCTTCCCGTTCT;RSEQ=CAGGTATCTGCGGAGCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:709:19:12,7:450,240:0.0268:2,2:26.5:1:28:1:0.81257:1.09361:51.4:8.5:0.0243:0:4.9 0/1:572:24:14,10:336,212:0.042:2,2:27.3:1:29.5:1:0.83167:1.13182:45.1:48:0.0425:0:5.4 -6 31238886 . A G 176 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=67.23985;LSEQ=CTCCTTCCCGTTCTCCAGGT;RSEQ=TCTGCGGAGCCACTCCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:729:1:1,0:460,268:0.0014:2,0:30:0:30:0:1:0:60:2:0.0014:0:4 0/1:590:50:34,16:321,217:0.0847:2,2:21.4:1:31.2:1:0.29118:1.44:54.3:100:0.0865:0:2.9 -6 31238889 . T C 87 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00164;SOR=Inf;LSEQ=CTTCCCGTTCTCCAGGTATC;RSEQ=GCGGAGCCACTCCACGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:747:0:0,0:465,282:0:2,0:27.1:1:30.6:1:1:0:51:92.375:1:0:2.3 0/1:611:8:2,6:358,243:0.0131:2,2:16.9:1:29.1:1:0.06878:4.40932:47.6:16:0.0133:0:4.4 -6 31238897 . C G 144 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=35.32512;LSEQ=TCTCCAGGTATCTGCGGAGC;RSEQ=ACTCCACGCACGTGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:813:1:1,0:475,335:0.0012:2,0:46:0:11:0:1:0:60:0:0:0:5 0/1:671:28:19,9:362,280:0.0417:2,2:28.4:1:30.1:1:0.24917:1.63:43.6:56:0.0422:0:4.6 -6 31238909 . GT AG 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0036;SOR=0.68024;LSEQ=TGCGGAGCCACTCCACGCAC;RSEQ=GCCCTCCAGGTAGGCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:799:185:110,75:323,281:0.2315:2,2:28.2:1:30.8:1:0.17663:1.28:45:370:0.2348:0.01:3 0/1:688:117:67,50:294,256:0.1701:2,2:27.9:1:30.4:1:0.47575:1.17:44.8:116:0.1708:0:3.4 -6 31238925 . C T 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=GCACGTGCCCTCCAGGTAGG;RSEQ=TCTCAGCTGCTCCGCCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:775:0:0,0:398,377:0:2,0:25.8:1:31.8:1:1:0:48:69.455:1:0:2.5 0/1:643:15:9,6:316,312:0.0233:2,2:27.1:1:27.9:1:0.60323:1.48:57.7:6.5:0.0206:0:3.1 -6 31238929 . CAG GTC 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGCCCTCCAGGTAGGCTCT;RSEQ=CTGCTCCGCCGCACGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:0:0,0:381,374:0:2,0:25.7:1:31.3:1:1:0:47.8:106.857:1:0:2.5 0/1:626:80:45,35:270,275:0.1278:2,2:31.5:1:30.8:1:0.28259:1.31:46.3:160:0.129:0.008:3.5 -6 31238930 . A C 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42975;LSEQ=TGCCCTCCAGGTAGGCTCTC;RSEQ=GCTGCTCCGCCGCACGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:746:204:88,116:281,242:0.2735:2,2:25.1:1:30:1:0.01062:1.52969:46.6:101:0.273:0:2.8 0/1:618:86:40,46:191,186:0.1392:2,2:25.3:1:29.3:1:0.55044:1.18049:44.3:85:0.1583:0:2.8 -6 31238931 . G A 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42966;SOR=0.78188;LSEQ=GCCCTCCAGGTAGGCTCTCA;RSEQ=CTGCTCCGCCGCACGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:37:19,18:344,342:0.0503:2,2:30.2:1:29.6:1:1:1.05:40.6:17.5:0.0494:0:3 0/1:604:24:11,13:239,245:0.0397:2,2:33.7:1:29.3:1:0.83539:1.15255:33.3:23:0.0461:0:3.1 -6 31238942 . G T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.36004;LSEQ=AGGCTCTCAGCTGCTCCGCC;RSEQ=CACGGGCCGCCTCCAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:678:351:146,205:45,41:0.5177:2,2:24.9:1:30.2:1:0.08918:1.53951:46.1:69.2:0.5203:0:2.8 0/1:560:156:66,90:79,96:0.2786:2,2:25:1:29.3:1:0.65743:1.12177:42.8:51:0.2777:0:3.3 -6 31238945 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00182;SOR=Inf;LSEQ=CTCTCAGCTGCTCCGCCGCA;RSEQ=GGGCCGCCTCCAACTTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:0:0,0:307,356:0:2,0:24.9:1:30.4:1:1:0:46:81.875:1:0:2.7 0/1:556:8:3,5:253,295:0.0144:2,2:15.5:1:28.1:1:0.73148:1.42848:47.9:7:0.0128:0:3 -6 31238951 . G A 70 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35766;SOR=1.85383;LSEQ=GCTGCTCCGCCGCACGGGCC;RSEQ=CCTCCAACTTGCGCTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:4:3,1:282,339:0.0064:2,2:5:1:26.5:1:0.33575:3.60:47:8:0.0065:0:3.3 0/1:509:6:4,2:225,278:0.0118:2,2:15.3:1:27.2:1:0.41604:2.47:52.3:5:0.0099:0:2 -6 31238957 . A C 279 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.52553;LSEQ=CCGCCGCACGGGCCGCCTCC;RSEQ=ACTTGCGCTGGGTGATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:566:476:193,283:41,49:0.841:2,2:24.5:1:31.4:1:0.41437:1.22646:40.5:78.333:0.8408:0:3.2 1/0:476:350:151,199:52,74:0.7353:2,2:21.6:1:30.4:1:0.75323:1.08:43.7:86.5:0.7346:0:3.3 -6 31238963 . C A 88 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56212;SOR=0.59753;LSEQ=CACGGGCCGCCTCCAACTTG;RSEQ=GCTGGGTGATCTGAGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:8:2,6:204,312:0.0153:2,2:32.9:1:29.4:1:0.48979:1.95925:40.3:16:0.0154:0:5.1 0/0:436:4:1,3:174,258:0.0092:2,2:23.5:1:32.5:1:0.65214:2.0203:42.3:8:0.0093:0:4 -6 31238970 . T A 85 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00131;SOR=Inf;LSEQ=CGCCTCCAACTTGCGCTGGG;RSEQ=GATCTGAGCCGCGGTGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:195,323:0:2,0:23.3:1:29.7:1:1:0:43:56.556:1:0:2.8 0/1:405:8:4,4:150,247:0.0198:2,2:16.3:1:28.6:1:0.48564:1.64:37.4:16:0.0198:0:4.4 -6 31238983 . G C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56361;SOR=1.12655;LSEQ=CGCTGGGTGATCTGAGCCGC;RSEQ=GTGTCCGCGGCGGTCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:77:32,45:156,257:0.1568:2,2:17.8:1:30.2:1:0.52653:1.17:37:154:0.1584:0:3.6 0/1:329:57:25,32:110,156:0.1733:2,2:18.5:1:28.6:1:0.76821:1.11:38.8:27.5:0.1708:0:3.1 -6 31238992 . G C 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.8222;SOR=0.9595;LSEQ=ATCTGAGCCGCGGTGTCCGC;RSEQ=GCGGTCCAGGAGCGCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:217:71,146:100,131:0.4833:2,2:23.1:1:30.2:1:0.02517:1.5681:40.5:107.5:0.481:0:3.9 0/1:296:140:52,88:75,80:0.473:2,2:25.2:1:29.4:1:0.05976:1.584:42.8:139:0.476:0:3.8 -6 31238995 . G A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01045;SOR=Inf;LSEQ=TGAGCCGCGGTGTCCGCGGC;RSEQ=GTCCAGGAGCGCAGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:179,267:0:2,0:23.6:1:30.4:1:1:0:42.9:73.333:0.9977:0:2.8 0/1:302:5:3,2:127,170:0.0166:2,2:26.6:1:32:1:0.65492:2.00:47.6:10:0.0168:0:2 -6 31239006 . G T 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07971;SOR=0.7571;LSEQ=GTCCGCGGCGGTCCAGGAGC;RSEQ=CAGGTCCTCGTTCAGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:190:63,127:135,134:0.4121:2,2:23.1:1:29.9:1:0.00028:2.02777:39.5:37:0.4084:0:4 0/1:300:104:39,65:98,98:0.3467:2,2:26.7:1:29.3:1:0.05111:1.6638:42.9:51:0.3446:0:3.8 -6 31239010 . G A 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=0.49406;LSEQ=GCGGCGGTCCAGGAGCGCAG;RSEQ=TCCTCGTTCAGGGCGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:93:65,28:142,233:0.1979:2,2:23.3:1:30.8:1:0:3.80:42.8:45.5:0.1978:0:4.1 0/1:304:33:24,9:119,152:0.1086:2,2:22.7:1:30:1:0.00266:3.39:41.1:66:0.1096:0:3.8 -6 31239016 . G A 112 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.49361;LSEQ=GTCCAGGAGCGCAGGTCCTC;RSEQ=TTCAGGGCGATGTAATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:1:0,1:218,261:0.0021:2,0:5:0:32:0:1:0:27:2:0.0021:0:5 0/1:328:16:7,9:150,162:0.0488:2,2:23.7:1:28.2:1:0.8017:1.18985:49.1:15:0.046:0:3.8 -6 31239049 . GG TA 137 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05421;SOR=0.47356;LSEQ=TAATCCTTGCCGTCGTAGGC;RSEQ=ACTGGTCATACCCGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:25:0,25:276,259:0.0446:2,1:26.9:1:29.6:1:0:0:35.6:50:0.0455:0.0036:5.1 0/1:416:9:4,5:210,197:0.0216:2,2:31.8:1:28.9:1:0.74506:1.33156:50.7:18:0.0218:0:3.3 -6 31239050 . G A 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.5552;LSEQ=AATCCTTGCCGTCGTAGGCG;RSEQ=ACTGGTCATACCCGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:559:284:156,128:60,67:0.5081:2,2:25.6:1:30:1:0.16515:1.36:50.3:283:0.531:0:4.3 0/1:420:153:84,69:98,104:0.3643:2,2:24.8:1:29.2:1:0.24032:1.29:51.9:152:0.3725:0:4.3 -6 31239057 . C T 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07782;SOR=1.26154;LSEQ=GCCGTCGTAGGCGGACTGGT;RSEQ=ATACCCGCGGAGGAGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:204:105,99:171,205:0.3517:2,2:27:1:29:1:0.19157:1.27:51.2:67:0.3514:0:4.4 0/1:438:178:94,84:133,127:0.4064:2,2:24.6:1:28.6:1:0.77057:1.07:52.1:177:0.4088:0:4.3 -6 31239060 . A G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.23038;LSEQ=GTCGTAGGCGGACTGGTCAT;RSEQ=CCCGCGGAGGAGGCGCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:587:163:64,99:211,212:0.2777:2,2:25.5:1:31.8:1:0.02132:1.53843:47.3:53.333:0.2778:0:4.5 0/1:443:36:19,17:211,194:0.0813:2,2:30.9:1:32.1:1:1:1.03:53.7:72:0.0824:0:3.5 -6 31239082 . G C 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.5543;LSEQ=CCGCGGAGGAGGCGCCCGTC;RSEQ=GGCCCCAGGTCGCAGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:201:101,100:155,223:0.3466:2,2:29:1:30.2:1:0.03519:1.45:54:99.5:0.351:0:4.4 0/1:480:109:56,53:180,188:0.2271:2,2:28.5:1:29.6:1:0.66416:1.10:51.5:218:0.2334:0:4.5 -6 31239090 . G C 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.12105;LSEQ=GAGGCGCCCGTCGGGCCCCA;RSEQ=GTCGCAGCCAGACATCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:26:13,13:226,315:0.0457:2,2:23.8:1:31.4:1:0.42265:1.39:46:52:0.0468:0:4.5 0/1:492:97:51,46:180,214:0.1972:2,2:27.8:1:29.4:1:0.25631:1.32:44.7:23.25:0.1929:0:4.9 -6 31239101 . G T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.29013;LSEQ=CGGGCCCCAGGTCGCAGCCA;RSEQ=ACATCCTCTGGAGGGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:523:218:76,142:19,26:0.4168:2,2:26.6:1:28.9:1:0.39509:1.36368:53:217:0.4197:0:4.5 1/0:473:332:155,177:20,34:0.7019:2,2:25.2:1:28.5:1:0.23821:1.49:54.9:65.4:0.7032:0:3.6 -6 31239108 . T A 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12636;SOR=1.27365;LSEQ=CAGGTCGCAGCCAGACATCC;RSEQ=CTGGAGGGTGTGAGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:107:35,72:142,245:0.2166:2,2:26.7:1:28.8:1:0.49505:1.19188:58.1:25.75:0.2164:0:3.6 0/1:453:118:50,68:150,185:0.2605:2,2:25.8:1:29.2:1:0.66779:1.10246:56.5:58:0.2619:0:3.4 -6 31239114 . G T 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09542;SOR=1.27936;LSEQ=GCAGCCAGACATCCTCTGGA;RSEQ=GGTGTGAGACCCTGGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:138:45,93:106,217:0.2981:2,2:29:1:30.4:1:1:1.0095:52.1:276:0.3026:0:5.1 0/1:409:144:62,82:113,146:0.3521:2,2:26.6:1:29.4:1:0.91694:1.02359:51.3:47:0.349:0:5 -6 31239116 . G A 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00152;SOR=0.59738;LSEQ=AGCCAGACATCCTCTGGAGG;RSEQ=TGTGAGACCCTGGCCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:452:134:42,92:101,216:0.2965:2,2:29:1:30.4:1:1:1.0242:51.9:32.5:0.2941:0:5.2 0/1:398:80:37,43:134,184:0.201:2,2:25.4:1:28.5:1:0.52923:1.18:51.5:25.667:0.199:0:4.9 -6 31239124 . C A 164 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCTCTGGAGGGTGTGAGA;RSEQ=CCTGGCCCCGCCCCCGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:121,292:0:2,0:24.8:1:31.2:1:1:0:55.6:58:1:0:4 0/1:367:49:21,28:133,185:0.1335:2,2:24.9:1:29.3:1:1:1.04:50.6:98:0.1369:0:5.1 -6 31239133 . C G 58 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02099;SOR=Inf;LSEQ=AGGGTGTGAGACCCTGGCCC;RSEQ=GCCCCCGCGGTCAGCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:98,267:0:2,0:23.7:1:29.6:1:1:0:54.7:44.625:1:0:4 0/1:316:5:2,3:119,191:0.0158:2,2:37.8:1:25.4:1:1:1.07:42.2:4:0.0129:0:5.6 -6 31239135 . C G 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.36199;LSEQ=GGTGTGAGACCCTGGCCCCG;RSEQ=CCCCGCGGTCAGCCCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:83:18,65:74,192:0.2378:2,2:23.8:1:31.5:1:0.31851:1.39052:49.3:26.667:0.2339:0:5.4 0/1:296:30:10,20:102,160:0.1014:2,2:24.3:1:31.2:1:0.69245:1.27396:44.8:29:0.1007:0:5.4 -6 31239141 . C T 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15398;SOR=0.78436;LSEQ=AGACCCTGGCCCCGCCCCCG;RSEQ=GGTCAGCCCAGTCCCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:314:183:45,138:36,95:0.5828:2,2:22.5:1:29.9:1:0.60183:1.16154:55.1:60:0.5882:0:4.3 1/0:264:138:48,90:48,78:0.5227:2,2:23.3:1:28.6:1:0.6097:1.15322:55.5:26.6:0.5216:0:4.3 -6 31239151 . A C 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3009;SOR=1.22259;LSEQ=CCCGCCCCCGCGGTCAGCCC;RSEQ=GTCCCCCGAGCCCCGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:256:140:28,112:9,24:0.5469:2,2:21.7:1:29.6:1:0.35401:1.49623:51.4:22.333:0.5425:0:4.7 1/0:208:124:37,87:20,30:0.5962:2,2:23.3:1:29.6:1:0.21457:1.56344:52.6:40.333:0.599:0:4.6 -6 31239153 . T TC 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CGCCCCCGCGGTCAGCCCAG;RSEQ=CCCCCGAGCCCCGCCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:50,188:0:2,0:23.9:1:29.6:1:1:0:53.5:28.75:0.9957:0:3.9 0/1:195:12:1,11:61,120:0.0615:2,2:27.1:1:31.9:1:0.10749:5.5585:40.6:24:0.0649:0.0051:3.8 -6 31239157 . C G 75 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01583;SOR=Inf;LSEQ=CCCGCGGTCAGCCCAGTCCC;RSEQ=CGAGCCCCGCCCCGCCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:47,178:0:2,0:23.4:1:31.2:1:1:0:53.4:74:0.9955:0:3.9 0/1:177:5:0,5:55,117:0.0282:2,0:19.4:1:32.6:1:0.32615:0:58.2:10:0.0291:0:4.8 -6 31239170 . C CA 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=14.23037;LSEQ=CAGTCCCCCGAGCCCCGCCC;RSEQ=GCCCCGACCAACCCGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:17:4,13:19,49:0.0944:2,2:18.5:1:28.7:1:1:1.25686:54.4:7.5:0.0847:0.0389:3.6 1/0:130:78:19,59:8,24:0.6:2,2:20.8:1:28.9:1:1:1.03473:53.1:14.6:0.6887:0.3077:4.2 -6 31239171 . GC AGT 204 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=AGTCCCCCGAGCCCCGCCCC;RSEQ=CCCGACCAACCCGCGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:180:95:19,76:19,49:0.5278:2,2:23.5:1:31.1:1:0.2631:1.54671:51.9:190:0.5367:0.1:4.3 0/0:130:0:0,0:8,24:0:2,0:13.7:1:31.2:1:1:0:47.7:66:0.3113:0:3.3 -6 31239172 . C T 86 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0119;SOR=0;LSEQ=GTCCCCCGAGCCCCGCCCCG;RSEQ=CCCGACCAACCCGCGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:9:4,5:17,53:0.0577:2,2:7:1:27.2:1:0.23607:2.46:56.7:8:0.1067:0:3.8 0/0:108:0:0,0:20,68:0:2,0:21.2:1:30.2:1:1:0:50.2:11.571:1:0:3.8 -6 31239177 . A C 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00899;SOR=Inf;LSEQ=CCGAGCCCCGCCCCGCCCCG;RSEQ=CCAACCCGCGGGGATTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:35,120:0:2,0:22.1:1:29.5:1:1:0:52.3:18.375:1:0:3.5 0/1:101:5:0,5:23,73:0.0495:2,0:16.8:1:32.8:1:0.58581:0:49.4:10:0.0526:0:3.2 -6 31239205 . C T 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8183;SOR=0.9053;LSEQ=GCGGGGATTTTGGCCTAAAC;RSEQ=GAAAATGAAACCGGGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:105:47,58:10,9:0.8468:2,2:21.3:1:30.5:1:0.61967:1.36763:53:104:0.8525:0:3.8 1/1:48:40:10,30:3,5:0.8333:2,2:22.3:1:30.5:1:0.66448:1.77622:50.5:80:0.8333:0:3.6 -6 31239215 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCTAAACCGAAAATGAA;RSEQ=CCGGGTAAAGGCGACTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:71,51:0.0161:2,2:6.5:1:31:1:1:1.38836:30:4:0.0165:0:5.5 0/0:46:0:0,0:15,31:0:2,0:22:1:29.1:1:1:0:54.1:45:1:0:3.2 -6 31239227 . C T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02798;SOR=0.37558;LSEQ=AAAATGAAACCGGGTAAAGG;RSEQ=GACTGGGGCTCTCTCCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:133:116:72,44:15,2:0.8722:2,2:24:1:30.3:1:0.0531:4.54232:56.5:57:0.8702:0:3.9 1/0:39:28:11,17:4,7:0.7179:2,2:23.7:1:30.4:1:1:1.13:57:56:0.7179:0:3.9 -6 31239232 . G A 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.046;SOR=Inf;LSEQ=GAAACCGGGTAAAGGCGACT;RSEQ=GGGCTCTCTCCGGTCGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:98,43:0:2,0:24.1:1:31.8:1:1:0:57.7:34.25:1:0:3.4 0/1:39:2:0,2:18,19:0.0513:2,0:38.5:1:33:0:0.48988:0:52.5:4:0.0513:0:3 -6 31239246 . T C 84 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=GCGACTGGGGCTCTCTCCGG;RSEQ=CGAGGGTCTGGGCGGGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:114,37:0:2,0:27.1:1:30.1:1:1:0:58.8:29.2:1:0:3.2 0/1:50:6:3,3:29,15:0.12:2,2:18.2:1:32.5:1:0.65377:1.90656:57:12:0.12:0:4.2 -6 31239270 . GATCCA G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95791;LSEQ=GGGTCTGGGCGGGTTCCGCA;RSEQ=CCTTGGGGTGGATCTCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:18:15,3:27,3:0.1053:2,2:17.8:1:30.9:1:0.65832:1.77713:56.5:36:0.1065:0.0526:3.7 0/1:79:8:7,1:12,3:0.1013:2,2:11.6:1:31.6:1:1:1.71:58.1:16:0.1111:0.0886:3.5 -6 31239271 . ATCCACCTT CCTC 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3794;SOR=0.77436;LSEQ=GGTCTGGGCGGGTTCCGCAG;RSEQ=GGGGTGGATCTCAGACGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:171:122:98,24:27,3:0.7135:2,2:28.8:1:31.9:1:0.29022:2.19441:59.3:244:0.7219:0.0468:2.7 1/0:79:52:43,9:12,3:0.6582:2,2:21.6:1:30.8:1:1:1.19:59.4:16.333:0.6806:0.1899:3 -6 31239279 . T C 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGGGTTCCGCAGATCCACCT;RSEQ=GGGGTGGATCTCAGACGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:26:23,3:28,3:0.4483:2,2:12.1:1:28.3:1:1:1.21317:57.6:5.5:0.4231:0:3.9 0/0:28:0:0,0:15,3:0:2,0:24:1:30.4:1:1:0:60:36:1:0:0.6 -6 31239296 . G C 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12879;SOR=1.48678;LSEQ=CCTTGGGGTGGATCTCAGAC;RSEQ=GGGAGACTCTGGGCGACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:84:76,8:91,12:0.4492:2,2:23.5:1:30.6:1:0.81267:1.25:59.2:83:0.4536:0:4.7 1/0:93:51:44,7:39,1:0.5484:1,2:25.8:1:30.1:1:0.07408:6.1064:59.5:50:0.5495:0:3.9 -6 31239305 . CT TG 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00127;SOR=0.41073;LSEQ=GGATCTCAGACGGGGAGACT;RSEQ=GGGCGACCCGGGCCGTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:76:70,6:110,13:0.3762:2,2:21.3:1:30.8:1:0.62503:1.38:58.8:152:0.3858:0.0347:3.8 0/1:106:21:18,3:77,7:0.1981:2,2:23.7:1:30.7:1:0.41467:1.82114:59.6:42:0.2039:0.0094:4 -6 31239306 . T G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=2.9802;LSEQ=GATCTCAGACGGGGAGACTC;RSEQ=GGGCGACCCGGGCCGTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:95:84,11:30,4:0.4798:2,2:23.6:1:30:1:1:1.02:59.3:190:0.7422:0:2.3 1/0:109:80:72,8:9,0:0.7339:0,2:24.7:1:29.5:1:1:0:59.5:79:0.8977:0:2.2 -6 31239314 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12763;SOR=Inf;LSEQ=ACGGGGAGACTCTGGGCGAC;RSEQ=CGGGCCGTCCGTGGGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:187,28:0:2,0:22.8:1:30.5:1:1:0:59.2:42:1:0:2.3 0/1:120:2:1,1:106,12:0.0167:2,2:30.5:1:31.5:1:0.20574:8.52485:60:4:0.0171:0:3 -6 31239335 . G A 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00142;SOR=0.52487;LSEQ=CGGGCCGTCCGTGGGGGATG;RSEQ=GGAGGGGTCGTGACCTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:112:93,19:173,41:0.3404:2,2:20.8:1:29.8:1:0.65521:1.16:56.4:27:0.3375:0:3.1 0/1:216:46:37,9:139,31:0.213:2,2:18.3:1:29.2:1:0.83236:1.09022:56:92:0.216:0:3.2 -6 31239363 . C T 138 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=36.27685;LSEQ=TCGTGACCTGCGCCCCGGGC;RSEQ=GGGGTCACTCACCGTCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:1:1,0:394,143:0.0019:2,0:11:0:17:0:1:0:50:0:0:0:4 0/1:379:24:14,10:252,103:0.0633:2,2:20.7:1:30.1:1:0.24747:1.74471:57.5:48:0.065:0:4 -6 31239376 . C T 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=53.7524;LSEQ=CCCGGGCCGGGGTCACTCAC;RSEQ=GTCCTCGCTCTGGTTGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:666:1:1,0:456,209:0.0015:2,0:45:0:30:0:1:0:60:2:0.0015:0:3 0/1:520:39:27,12:325,156:0.075:2,2:28.3:1:30.8:1:1:1.08:52.7:78:0.0759:0:3.2 -6 31239378 . T G 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01371;SOR=1.33753;LSEQ=CGGGCCGGGGTCACTCACCG;RSEQ=CCTCGCTCTGGTTGTAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:249:166,83:305,140:0.3572:2,2:23.3:1:30.8:1:0.61231:1.08915:55.5:34.571:0.3548:0:2.3 0/1:544:232:159,73:204,108:0.4265:2,2:24.3:1:31:1:0.46263:1.15:55.4:76.333:0.4257:0:2.6 -6 31239407 . G T 269 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.66364;LSEQ=TGGTTGTAGTAGCCGCGCAG;RSEQ=TTCCGCAGGCTCACTCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1095:561:338,223:307,226:0.5123:2,2:24.3:1:29.5:1:0.38962:1.12:59.7:69.125:0.5101:0:2.2 0/1:857:352:202,150:290,215:0.4107:2,2:25.5:1:29.2:1:1:1.00161:59.5:116.333:0.4116:0:2.4 -6 31239417 . C T 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.71234;LSEQ=AGCCGCGCAGGTTCCGCAGG;RSEQ=TCACTCGGTCAGCCTGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1167:585:348,237:321,258:0.5013:2,2:25.7:1:29.6:1:0.17281:1.18:59.8:82.571:0.503:0:2.2 0/1:918:383:214,169:300,235:0.4172:2,2:26.5:1:29.4:1:1:1.00814:59.6:126.667:0.419:0:2.4 -6 31239430 . C T 261 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69191;SOR=0.96303;LSEQ=CCGCAGGCTCACTCGGTCAG;RSEQ=CTGTGCCTGGCGCTTGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1235:458:236,222:431,344:0.3709:2,2:27.4:1:29.6:1:0.17392:1.17842:57.8:40.636:0.3685:0:1.5 0/1:1008:365:197,168:338,305:0.3621:2,2:25.9:1:29.2:1:0.69377:1.06:57.4:90.25:0.3628:0:1.8 -6 31239449 . C G 211 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=145.3574;LSEQ=GCCTGTGCCTGGCGCTTGTA;RSEQ=TTCTGTGTCTCCCGGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1251:1:1,0:637,608:8e-04:2,0:42:0:28:0:1:0:60:2:8e-04:0:3 0/1:1026:107:50,57:470,443:0.1043:2,2:26.7:1:31.4:1:0.35971:1.20925:60:214:0.1058:0:1.2 -6 31239501 . G T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.34948;LSEQ=CCTCCTGCTCCACCCACGGC;RSEQ=CCCGCGGCTCCCCTCTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:362:153,209:239,313:0.3948:2,2:23.3:1:29.9:1:0.78477:1.04303:59.5:35.2:0.3924:0:2.5 0/1:733:136:64,72:273,323:0.1855:2,2:23.4:1:29.5:1:0.84887:1.05:59.5:44.333:0.1858:0:2.3 -6 31239506 . C G 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00017;SOR=1.82381;LSEQ=TGCTCCACCCACGGCGCCCG;RSEQ=GGCTCCCCTCTCGGACTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:868:76:31,45:330,459:0.0876:2,2:24.2:1:31.2:1:0.9035:1.0436:60:152:0.0889:0:1.3 0/1:698:104:44,60:263,331:0.149:2,2:24:1:30:1:0.74866:1.08341:60:103:0.1499:0:1.2 -6 31239518 . C T 245 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58102;SOR=0.93833;LSEQ=GGCGCCCGCGGCTCCCCTCT;RSEQ=GGACTCGCGGCGTCGCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:784:305:110,195:198,279:0.389:2,2:25:1:29.7:1:0.13404:1.25769:57.9:32.889:0.3854:0:2.6 0/1:623:233:98,135:170,218:0.374:2,2:23.5:1:29.8:1:0.67666:1.07409:59.1:57.25:0.373:0:2.1 -6 31239543 . C T 154 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=23.66606;LSEQ=TCGCGGCGTCGCTGTCGAAC;RSEQ=GCACGAACTGCGTGTCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:2:1,1:255,371:0.0032:2,2:19:1:15.5:1:1:1.45:54:0:0:0:4.5 0/1:497:35:13,22:207,255:0.0704:2,2:21:1:30.1:1:0.48075:1.37289:60:34:0.0691:0:2.7 -6 31239577 . A C 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.03016;LSEQ=GTCGTCCACGTAGCCCACTG;RSEQ=GATGAAGCGGGGCTCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:493:140:46,94:150,201:0.284:2,2:22.7:1:30.6:1:0.05231:1.52368:49.7:69:0.284:0:3.5 0/1:437:195:85,110:113,128:0.4462:2,2:21.7:1:29.7:1:0.50001:1.14211:54.2:26.857:0.4434:0:2.9 -6 31239585 . C T 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0054;SOR=1.95211;LSEQ=CGTAGCCCACTGAGATGAAG;RSEQ=GGGGCTCTCCGCGGCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:29:11,18:187,263:0.0605:2,2:24.4:1:30.5:1:0.8462:1.16312:46.5:58:0.0614:0:4.1 0/1:474:53:19,34:200,221:0.1118:2,2:24.1:1:30:1:0.14325:1.61781:46:106:0.1135:0:4.1 -6 31239593 . T C 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15608;SOR=0.78639;LSEQ=ACTGAGATGAAGCGGGGCTC;RSEQ=CCGCGGCCGGGCCGGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:94:26,68:172,192:0.2048:2,2:17.3:1:31.3:1:0.00067:2.33877:46:93:0.2067:0:3.7 0/1:487:82:32,50:196,209:0.1684:2,2:21.3:1:30.4:1:0.1452:1.46416:47:81:0.1698:0:3.8 -6 31239596 . G A 85 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25222;SOR=0.46801;LSEQ=GAGATGAAGCGGGGCTCTCC;RSEQ=CGGCCGGGCCGGGACACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:8:7,1:197,251:0.0175:2,2:17.8:1:28.5:1:0.02495:8.88:31.9:7:0.0156:0:6.3 0/0:483:4:3,1:223,256:0.0083:2,2:25.5:1:29.5:1:0.34438:3.44:27:8:0.0084:0:6.5 -6 31239598 . G T 82 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25685;SOR=0.4802;LSEQ=GATGAAGCGGGGCTCTCCGC;RSEQ=GCCGGGCCGGGACACGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:8:7,1:203,249:0.0174:2,2:18.3:1:27.4:1:0.02624:8.55:31.9:3:0.0132:0:6.3 0/0:475:4:3,1:220,250:0.0084:2,2:25.5:1:30:1:0.34642:3.40:27:8:0.0086:0:6.5 -6 31239602 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.10766;LSEQ=AAGCGGGGCTCTCCGCGGCC;RSEQ=GGCCGGGACACGGCGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:165:84,81:135,165:0.3548:2,2:20.8:1:30.4:1:0.24434:1.27:48.6:54:0.3553:0:4.2 0/1:484:27:9,18:218,239:0.0558:2,2:20.8:1:30.4:1:0.16778:1.82208:48.4:54:0.0564:0:4 -6 31239607 . G A 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.12285;LSEQ=GGGCTCTCCGCGGCCGGGCC;RSEQ=GGACACGGCGGTGTCGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:53:22,31:188,197:0.121:2,2:8:1:31.2:1:0.37932:1.34381:39.2:106:0.1241:0:5.2 0/1:482:8:2,6:226,247:0.0166:2,2:7.3:1:30.3:1:0.29031:2.73953:34.5:16:0.0168:0:4.6 -6 31239613 . C T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0862;SOR=1.77443;LSEQ=TCCGCGGCCGGGCCGGGACA;RSEQ=GGCGGTGTCGAAATACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:14:7,7:197,205:0.0337:2,2:13.6:1:30.9:1:1:1.04:46.6:28:0.0342:0:2.4 0/1:498:29:14,15:216,253:0.0582:2,2:25.6:1:30:1:0.84959:1.09:54.5:58:0.0585:0:2.6 -6 31239614 . G A 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13121;SOR=1.5079;LSEQ=CCGCGGCCGGGCCGGGACAC;RSEQ=GCGGTGTCGAAATACCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:25:10,15:195,195:0.0602:2,2:26.2:1:30.4:1:0.41067:1.49854:40.9:50:0.0616:0:4.4 0/1:499:44:15,29:214,239:0.0882:2,2:21.9:1:30.3:1:0.11331:1.72924:40.7:43:0.0874:0:4.5 -6 31239616 . CG AT 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08325;LSEQ=GCGGCCGGGCCGGGACACGG;RSEQ=GTGTCGAAATACCTCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:121:70,51:107,126:0.338:2,2:31.3:1:31:1:0.04348:1.61:42.6:242:0.3428:0:5.7 0/1:492:20:8,12:220,248:0.0407:2,2:33.9:1:29.2:1:0.64941:1.32987:40.1:40:0.0412:0:5.7 -6 31239621 . TC AA 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.089;LSEQ=CGGGCCGGGACACGGCGGTG;RSEQ=GAAATACCTCATGGAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:100:54,46:113,126:0.2747:2,2:33.9:1:31:1:0.28462:1.31:43.7:200:0.2762:0:4.5 0/1:492:16:6,10:221,250:0.0325:2,2:34.5:1:30.2:1:0.61199:1.47218:42.6:32:0.0329:0:4.4 -6 31239622 . C A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.81638;LSEQ=GGGCCGGGACACGGCGGTGT;RSEQ=GAAATACCTCATGGAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:41:19,22:95,104:0.1123:2,2:23.5:1:29.9:1:1:1.05747:43.7:82:0.1723:0:3.6 0/1:488:185:89,96:127,152:0.3791:2,2:28.1:1:29.3:1:0.63478:1.11:52.5:370:0.3996:0:2.5 -6 31239630 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08443;LSEQ=ACACGGCGGTGTCGAAATAC;RSEQ=TCATGGAGTGGGAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:137:72,65:174,156:0.2934:2,2:26.6:1:30.9:1:1:1.00693:44.1:136:0.2944:0:3.9 0/1:503:17:7,10:228,258:0.0338:2,2:31.5:1:30.5:1:0.80576:1.26188:42.6:34:0.0344:0:4.2 -6 31239649 . G A 97 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18136;SOR=0.4287;LSEQ=CCTCATGGAGTGGGAGCCTG;RSEQ=GGGCGAGGAGGGGCTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:10:5,5:254,260:0.0191:2,2:25.6:1:29.2:1:1:1.02:34.4:9:0.0175:0:6.1 0/0:484:4:2,2:221,259:0.0083:2,2:18.8:1:28:1:1:1.17:35.3:8:0.0084:0:4.8 -6 31239652 . G A 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19544;LSEQ=CATGGAGTGGGAGCCTGGGG;RSEQ=CGAGGAGGGGCTGAGACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:134:74,60:182,202:0.2572:2,2:25.4:1:29.7:1:0.13251:1.37:46.4:32.5:0.2584:0:4.2 0/1:474:30:19,11:199,245:0.0633:2,2:24:1:28.5:1:0.05849:2.12:52:29:0.0633:0:3.9 -6 31239660 . G T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.18946;LSEQ=GGGAGCCTGGGGGCGAGGAG;RSEQ=GGCTGAGACCCGCCCGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:527:159:83,76:182,186:0.3017:2,2:27.1:1:29.5:1:0.57056:1.12:47.1:38.75:0.3033:0:4.4 0/1:450:34:19,15:186,227:0.0756:2,2:26.4:1:28.9:1:0.28275:1.54:51.2:16:0.0727:0:4.3 -6 31239663 . C T 101 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13168;SOR=0.40568;LSEQ=AGCCTGGGGGCGAGGAGGGG;RSEQ=TGAGACCCGCCCGACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:12:5,7:261,257:0.0226:2,2:22.6:1:28.3:1:0.57552:1.42085:36.9:11:0.0212:0:6.1 0/0:430:4:1,3:196,229:0.0093:2,2:18.5:1:28:1:0.62826:2.5625:30.3:8:0.0094:0:6.3 -6 31239673 . C A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02788;SOR=Inf;LSEQ=CGAGGAGGGGCTGAGACCCG;RSEQ=CCGACCCACCTCCCTGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:0:0,0:265,264:0:2,0:26.2:1:31.1:1:1:0:52:34.267:1:0:3.1 0/1:367:4:4,0:177,185:0.0109:2,0:12.8:1:24.3:1:0.05881:0:58:8:0.0111:0:2.5 -6 31239681 . A T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.39385;LSEQ=GGCTGAGACCCGCCCGACCC;RSEQ=CCTCCCTGCGCGGCTCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:507:381:204,177:52,74:0.7515:2,2:27.2:1:29.8:1:0.01824:1.64:50:22.813:0.7464:0:4.2 1/0:335:182:96,86:69,84:0.5433:2,2:25.2:1:29.1:1:0.18819:1.36:53.6:17.2:0.5309:0:3.2 -6 31239688 . T G 68 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0374;SOR=7.80014;LSEQ=ACCCGCCCGACCCACCTCCC;RSEQ=GCGCGGCTCCCCGGGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:1:0,1:251,250:0.002:2,0:30:0:9:0:1:0:60:0:0:0:7 0/1:326:5:1,4:162,156:0.0153:2,2:8.2:1:29.4:1:0.21153:4.1375:45:10:0.0157:0:3.8 -6 31239701 . G C 66 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49479;SOR=0.45716;LSEQ=ACCTCCCTGCGCGGCTCCCC;RSEQ=GGTCCTGCGCCCTCGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:7:2,5:257,252:0.0135:2,2:26.6:1:23.7:1:0.28428:2.54535:41.1:2.5:0.0098:0:6 0/0:321:2:0,2:168,151:0.0062:2,0:32.5:1:31:1:0.2264:0:30.5:4:0.0064:0:6.5 -6 31239714 . T C 77 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49504;SOR=0.46328;LSEQ=GCTCCCCGGGTCCTGCGCCC;RSEQ=CGCCGGGAGGGCCCCTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:506:7:2,5:248,251:0.0138:2,2:17.3:1:27.6:1:0.45009:2.46613:35.4:6:0.0121:0:6.3 0/0:310:2:0,2:173,135:0.0065:2,0:19.5:1:32.5:1:0.19451:0:30.5:4:0.0065:0:6.5 -6 31239722 . A C 268 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17891;SOR=1.45437;LSEQ=GGTCCTGCGCCCTCGCCGGG;RSEQ=GGGCCCCTCGCTCCTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:496:441:230,211:21,31:0.8891:2,2:24.3:1:30.6:1:0.14194:1.61:57.2:43.1:0.8923:0:4.3 1/1:304:280:166,114:12,11:0.9211:2,2:24.4:1:30.7:1:0.51655:1.33:59.3:139:0.9236:0:3.1 -6 31239727 . C A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.14491;LSEQ=TGCGCCCTCGCCGGGAGGGC;RSEQ=CCTCGCTCCTCTCCGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:160:90,70:179,173:0.3113:2,2:25.3:1:30:1:0.29367:1.24:59.3:52.333:0.3178:0:4.6 0/1:326:20:12,8:181,125:0.0613:2,2:24.6:1:29.9:1:1:1.04:60:40:0.0631:0:4.7 -6 31239733 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17353;LSEQ=CTCGCCGGGAGGGCCCCTCG;RSEQ=TCCTCTCCGCAGAGGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:166:95,71:193,171:0.3126:2,2:25.6:1:30:1:0.39793:1.19:59.2:82:0.3154:0:4.7 0/1:356:26:15,11:205,125:0.073:2,2:21.2:1:28.8:1:0.67859:1.20202:60:52:0.0747:0:4.6 -6 31239742 . G C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31629;LSEQ=AGGGCCCCTCGCTCCTCTCC;RSEQ=CAGAGGCCGCTTCCCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:249:137,112:180,143:0.4338:2,2:22.9:1:30.9:1:0.86577:1.02901:55.1:40.5:0.4371:0:5 0/1:390:76:47,29:201,112:0.1949:2,2:24:1:29.9:1:0.69228:1.10704:55.7:75:0.1948:0:4.8 -6 31239752 . C T 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.39411;LSEQ=GCTCCTCTCCGCAGAGGCCG;RSEQ=TTCCCTCCCAACCCCGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:614:530:312,218:33,25:0.8632:2,2:23.4:1:29.4:1:0.78038:1.08:57.3:36.857:0.8629:0:4.6 1/0:446:318:198,120:46,29:0.713:2,2:22.7:1:28.9:1:0.8953:1.04:58.2:78.5:0.7153:0:4.1 -6 31239766 . C T 167 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=70.12463;LSEQ=AGGCCGCTTCCCTCCCAACC;RSEQ=CGCACTCACAGGCCCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:687:1:0,1:403,283:0.0015:2,0:1:0:24:0:0.41339:0:21:2:0.0015:0:6 0/1:527:49:28,21:290,188:0.093:2,2:24.7:1:29.9:1:0.64778:1.15659:60:98:0.094:0:4.2 -6 31239776 . A C 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00267;SOR=0.71688;LSEQ=CCTCCCAACCCCGCACTCAC;RSEQ=GGCCCAGGTCTCGGTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:775:352:206,146:245,176:0.4542:2,2:25.3:1:30:1:0.9417:1.01:53.8:49.286:0.4557:0:5.1 0/1:621:232:132,100:222,163:0.3736:2,2:24.3:1:29.5:1:0.86682:1.03175:55.2:76.333:0.3798:0:4.9 -6 31239790 . G A 157 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCACAGGCCCAGGTCTCG;RSEQ=TCAGGGCCAGGCCTCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:932:0:0,0:519,412:0:2,0:24.2:1:31.2:1:1:0:57.5:39.478:0.9989:0:4.3 0/1:726:44:24,20:379,302:0.0606:2,2:24.2:1:28.8:1:0.87726:1.04577:60:21:0.0592:0:4.8 -6 31239802 . C G 308 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.4836;LSEQ=AGGTCTCGGTCAGGGCCAGG;RSEQ=CTCCCGAGAGCAGCAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1029:927:517,410:51,45:0.9009:2,2:25.2:1:31.3:1:0.66645:1.11:57.3:45.35:0.9034:0:4.9 1/1:809:659:357,302:81,68:0.8146:2,2:25.5:1:30.7:1:1:1.00765:58.1:31.95:0.8119:0:4.9 -6 31239821 . G T 307 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0.33523;LSEQ=GCCTCCCGAGAGCAGCAGGA;RSEQ=GAGGGCTCGGGGCGCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1255:1132:597,535:66,56:0.902:2,2:25.2:1:30.3:1:0.84869:1.05615:57.6:48.217:0.9024:0:4.7 1/0:976:737:383,354:130,108:0.7551:2,2:24.8:1:29.3:1:0.50195:1.11244:58:34.095:0.7505:0:4.9 -6 31239827 . C T 303 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31699;LSEQ=CGAGAGCAGCAGGAGGAGGG;RSEQ=TCGGGGCGCCATGACCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1282:1161:597,564:63,56:0.9056:2,2:25.6:1:29.8:1:0.77334:1.06279:57.7:54.286:0.9084:0:4.6 1/0:1010:760:385,375:132,116:0.7525:2,2:24.8:1:29.1:1:0.51052:1.10826:58.2:43.706:0.7535:0:4.9 -6 31239829 . C T 185 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=98.63453;LSEQ=AGAGCAGCAGGAGGAGGGCT;RSEQ=GGGGCGCCATGACCCGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1292:1:1,0:658,629:8e-04:2,0:21:0:32:0:1:0:60:2:8e-04:0:5 0/1:999:71:38,33:472,456:0.0711:2,2:23.6:1:30.1:1:0.71255:1.11:60:142:0.0722:0:4.6 -6 31239855 . C G 313 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.49153;LSEQ=GCCATGACCCGCATCTCGGC;RSEQ=TCTGGGGAGAATGTGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1219:1105:511,594:49,61:0.9065:2,2:27:1:31:1:0.76416:1.07:58.7:121.778:0.9095:0:4.2 1/1:899:743:328,415:73,83:0.8265:2,2:26.9:1:30.3:1:0.59517:1.11267:58.9:105.143:0.8288:0:4.7 -6 31239868 . G C 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22452;LSEQ=TCTCGGCCTCTGGGGAGAAT;RSEQ=TGAGTCCGGGTGGGTGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1079:899:398,501:42,62:0.8332:2,2:26.9:1:31.7:1:0.46687:1.17:59.3:98.889:0.8341:0:4.1 1/0:776:410:181,229:60,73:0.5284:2,2:26.1:1:31:1:0.92004:1.03983:59.2:36.273:0.525:0:4.4 -6 31239888 . GGGGACTTT TC 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGAGTCCGGGTGGGTGACT;RSEQ=AGAACCGGGACTGCGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:878:0:0,0:338,539:0:2,0:25.2:1:31.3:1:1:0:59.9:72.083:0.9988:0:3.1 0/1:621:48:20,28:227,342:0.0773:2,2:27.5:1:30.6:1:0.87835:1.08:60:96:0.0783:0.0113:3.4 -6 31239896 . T C 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.09765;LSEQ=GGGTGGGTGACTGGGGACTT;RSEQ=AGAACCGGGACTGCGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:764:31:10,21:258,472:0.0406:2,2:22.2:1:31.7:1:0.84854:1.1477:60:62:0.0412:0:4.4 0/1:428:76:29,47:121,230:0.1776:2,2:24.6:1:31.3:1:0.59637:1.17:60:152:0.1788:0:4.2 -6 31239912 . G T 149 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTTTAGAACCGGGACTGCG;RSEQ=AGACGCTGATTGGCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:145,404:0:2,0:21.5:1:30.9:1:1:0:60:67.625:0.9963:0:1.8 0/1:333:37:12,25:74,222:0.1111:2,2:24.7:1:28.7:1:0.3252:1.44:60:74:0.1114:0:4.2 -6 31239937 . C T 129 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=4.61989;LSEQ=GCTGATTGGCTTCTCTAGAA;RSEQ=CCGACACCCAATGGGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:11:2,9:34,272:0.0347:2,2:23.6:1:30.3:1:0.36117:1.77:60:22:0.0351:0:2.8 0/1:161:23:0,23:14,124:0.1429:2,1:21.3:1:28.6:1:0.22312:0:60:22:0.1401:0:2.7 -6 31239951 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10937;SOR=Inf;LSEQ=CTAGAACCCGACACCCAATG;RSEQ=GAGTGGGAATTGGGGACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:18,238:0:2,0:26.1:1:30.9:1:1:0:60:84.333:1:0:0.3 0/1:127:2:1,1:8,117:0.0157:2,2:36.5:1:28:1:0.13723:13.85:60:4:0.0157:0:1 -6 31240010 . G GAGA 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.82944;SOR=0.87413;LSEQ=AAGGACCCGACGCAGGTTGG;RSEQ=AGAAGTGAAACTCAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:71:4,67:1,21:0.7634:1,2:24.6:1:30.9:1:1:1.25:59.4:70:0.7692:0.1398:0.6 1/0:42:31:3,28:2,8:0.7381:2,2:30:1:30.8:1:0.58013:2.278:59.1:62:0.7381:0.0714:1.1 -6 31240034 . A GAGTGGG 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.02245;SOR=Inf;LSEQ=AGTGAAACTCAGGGGAGTGG;RSEQ=GAATCCCCAACGCGGCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:0,53:0:1,0:20.1:1:30.8:1:1:0:59.2:25.5:1:0:1.2 0/1:35:4:0,4:4,27:0.1143:2,0:11.5:1:32.4:1:1:0:60:8:0.1143:0.1143:0 -6 31240035 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15309;SOR=Inf;LSEQ=GTGAAACTCAGGGGAGTGGA;RSEQ=AATCCCCAACGCGGCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:0,49:0:1,0:20.8:1:30.5:1:1:0:59.1:15.333:1:0:1.2 0/1:32:2:0,2:4,26:0.0625:2,0:7:1:31:1:1:0:60:4:0.0625:0.0625:0 -6 31240037 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14486;SOR=Inf;LSEQ=GAAACTCAGGGGAGTGGAGA;RSEQ=TCCCCAACGCGGCGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:0:1,0:20.5:1:29.6:1:1:0:59:11:1:0:1.3 0/1:30:2:0,2:4,24:0.0667:2,0:5:1:30:1:1:0:60:4:0.0667:0.0667:0 -6 31240041 . C T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15342;SOR=2.17997;LSEQ=CTCAGGGGAGTGGAGAATCC;RSEQ=CAACGCGGCGCCTCCCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:18:0,18:0,28:0.3913:1,1:20.8:1:29.2:1:1:0:57.7:17:0.3953:0:2.7 1/0:29:17:2,15:2,10:0.5862:2,2:21.2:1:30.2:1:1:1.47868:58.9:34:0.5862:0:1.8 -6 31240060 . A G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25524;SOR=0.37695;LSEQ=CCCAACGCGGCGCCTCCCCA;RSEQ=TGCAGACACGGCCCTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:26:0,26:0,3:0.8966:0,1:25.8:1:30.8:1:1:0:58.4:25:0.8929:0:2.2 1/0:21:16:2,14:1,4:0.7619:2,2:15.9:1:31.1:1:1:1.69906:58.9:32:0.7619:0:1.8 -6 31240096 . G A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.30312;SOR=2.85648;LSEQ=TGGAGCCTGAGACCCTGAGA;RSEQ=CCCCGCCCGGGACCTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:0,15:0.1429:1,0:17.7:1:28.3:1:1:0:58:6:0.1667:0:2.7 0/1:6:2:1,1:0,4:0.3333:0,2:12:1:29.5:1:0.33333:0:60:4:0.3333:0:3 -6 31240128 . C T 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.45926;LSEQ=ACCTGGGACTTCGTCCTGAT;RSEQ=CCTCTTCTCCTACACCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:0,7:0.3636:0,0:29.8:1:31:1:1:0:57:8:0.3636:0:2 0/1:5:1:0,1:0,4:0.2:0,0:14:0:31:0:1:0:60:2:0.2:0:2 -6 31240180 . A C 65 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.31624;LSEQ=ACTGTGTGCCTGAGTCCTGG;RSEQ=CAAGGATCTGTCTGTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:24.8:1:32.8:1:1:0:48.3:8:0.8:0:2 1/0:2:1:0,1:0,1:0.5:0,0:35:0:33:0:1:0:60:2:0.5:0:2 -6 31240307 . TACCTC T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCCACCCTTTGCCTTACCT;RSEQ=ACCTCAGGTAATATTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21.5:1:28:1:1:0:48:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31241032 . A G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCTGCCAGGCTCTTCT;RSEQ=CTGCTTTAGAATTCTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:19.7:1:32.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31241092 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGCTTCTCCAGCCCTTCT;RSEQ=TCTGCCCCTCTCATCCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31320467 . C T 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CATCCCACTCAGAGCAAAGG;RSEQ=CAGATCCAACCCCACTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:7:0:31.5:1:1:0:60:4:0.6667:0:3.5 0/0:2:0:0,0:1,1:0:2,0:5:0:33:0:1:0:60:4:1:0:0.5 -6 31320473 . C G 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACTCAGAGCAAAGGCCAGAT;RSEQ=CAACCCCACTCCCCTCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:13:0:33.5:1:1:0:60:4:0.6667:0:3.5 0/0:2:0:0,0:1,1:0:2,0:11:0:33:0:1:0:60:4:1:0:0.5 -6 31320538 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACCTCACCTCAGTTTCTCTC;RSEQ=GTCCAGCCCTCCTGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29:1:1:0:60:4:1:0:3.5 0/0:2:0:0,0:1,1:0:2,0:14.5:1:29:1:1:0:60:4:1:0:0.5 -6 31321807 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTGCAGCTCAGTGCAC;RSEQ=TAAAGTTGAGACAGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:31.5:1:31:1:1:0:60:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31321845 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGAGACATCCAGCCCCACC;RSEQ=CTCTGGAACAAGAAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:31.5:1:30:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31321856 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCCACCTCTCTGGAACA;RSEQ=GAAAGATGACTGGGGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:20.5:1:30:1:1:1.73:60:4:0.4:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31321883 . G A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTGGGGAGGAAACACAG;RSEQ=TCAGCATGGGAACAGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:40.5:1:30:1:1:0:60:4:0.5:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31321916 . AG CA 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGGTCACAGTGGACACA;RSEQ=GGTGGGCTGTCTCTCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:26.5:1:32.8:1:1:0:60:4:0.6667:0:3 0/0:1:0:0,0:1,0:0:0,0:5:0:31:0:1:0:59:2:1:0:2 -6 31321919 . G T 31 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGTCACAGTGGACACAAGG;RSEQ=TGGGCTGTCTCTCCACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:24.5:1:31.5:1:1:0:60:4:0.6667:0:3 1/1:1:1:1,0:0,0:1:0,0:8:0:14:0:1:0:59:0:0:0:2 -6 31322026 . C A 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTGAAGTCACAAAGGGGAGG;RSEQ=GTGAAGAAATCCTGCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:26:1:31.7:1:1:0:60:6:0.75:0:1.3 0/0:1:0:0,0:1,0:0:0,0:44:0:34:0:1:0:60:2:1:0:0 -6 31322121 . C T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13804;SOR=5.07211;LSEQ=TTCTGGTTAGTCATGGTAAG;RSEQ=GATGACACTCTAAACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:23:23,0:8,0:0.7419:0,1:22.4:1:29.8:1:1:0:59.3:46:0.7419:0:3.3 1/1:16:15:14,1:1,0:0.9375:0,1:31.4:1:30.9:1:1:0:60:30:0.9375:0:3 -6 31322129 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13158;SOR=Inf;LSEQ=AGTCATGGTAAGCGATGACA;RSEQ=TCTAAACAGCCCACCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:36,0:0:1,0:23.5:1:32.4:1:1:0:58.1:72:1:0:3.1 0/1:21:2:2,0:18,1:0.0952:1,0:33:1:32:0:1:0:60:4:0.1:0:5.5 -6 31322133 . A G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.87812;LSEQ=ATGGTAAGCGATGACACTCT;RSEQ=AACAGCCCACCACACACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:15:15,0:23,0:0.3947:1,1:25:1:32.9:1:1:0:58:30:0.4054:0:4.9 0/1:22:8:7,1:14,0:0.3636:1,2:25.3:1:32.4:1:0.36364:0:60:16:0.3636:0:3.4 -6 31322143 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02182;SOR=Inf;LSEQ=ATGACACTCTAAACAGCCCA;RSEQ=CACACACGCGAAACATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:0:1,0:23.9:1:31.8:1:1:0:58.4:43:1:0:2.9 0/1:29:4:4,0:24,1:0.1379:1,0:18:1:29.5:1:1:0:60:8:0.1379:0:2.8 -6 31322144 . C G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01512;SOR=0.20603;LSEQ=TGACACTCTAAACAGCCCAC;RSEQ=ACACACGCGAAACATCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:16,0:28,0:0.3636:1,1:27.5:1:29.6:1:1:0:58.1:32:0.3721:0:4.9 0/1:29:3:3,0:25,1:0.1034:1,0:23.7:1:31:1:1:0:60:6:0.1034:0:3.7 -6 31322174 . CC GT 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50321;SOR=0.56532;LSEQ=AAACATCCCAATCAAAGAAT;RSEQ=CCATTACCCAGGCCTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:6:6,0:54,0:0.1:1,0:25.8:1:31.2:1:1:0:60:12:0.1053:0.0167:2.3 0/1:51:3:3,0:48,0:0.0588:1,0:26.7:1:28.8:1:1:0:60:6:0.0588:0:1.3 -6 31322175 . C T 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.32283;SOR=1.8061;LSEQ=AACATCCCAATCAAAGAATC;RSEQ=CCATTACCCAGGCCTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:45:45,0:8,0:0.7759:0,1:26.6:1:31.3:1:1:0:58.3:44:0.8627:0:3.6 1/1:51:44:44,0:4,0:0.8627:0,1:22.3:1:30.9:1:1:0:60:88:0.9167:0:3 -6 31322197 . T A 137 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=32.27748;LSEQ=CATTACCCAGGCCTTTCCCC;RSEQ=CTGCCCCACCCACCCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:3:2,1:75,5:0.0357:2,2:10.3:1:24.3:1:0.20386:7.12716:60:2:0.0274:0:3.7 1/0:69:38:35,3:30,1:0.5507:1,2:18.9:1:26.2:1:0.62187:2.53941:59.1:8.5:0.5397:0:3.4 -6 31322204 . C CCT 74 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01617;SOR=0;LSEQ=CAGGCCTTTCCCCTCTGCCC;RSEQ=ACCCACCCCCAGACCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:7:7,0:46,5:0.0753:2,0:23.3:1:26.6:1:1:0:51.4:14:0.0795:0:5.9 0/0:78:0:0,0:65,13:0:2,0:12.9:1:28.9:1:1:0:59.1:18.5:1:0:2.3 -6 31322205 . A CTC 135 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=AGGCCTTTCCCCTCTGCCCC;RSEQ=CCCACCCCCAGACCCGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:25:19,6:46,5:0.2688:2,2:19.6:1:29.2:1:0.16212:2.86015:58.8:50:0.2841:0.1183:4.3 0/0:78:0:0,0:65,13:0:2,0:12.9:1:28.9:1:1:0:59.1:18.5:1:0:2.3 -6 31322208 . CACCCCCAGACCCGCCACCCCA ACCCCCCCCG 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.12365;SOR=0;LSEQ=CCTTTCCCCTCTGCCCCACC;RSEQ=CCCACTCTAGACCCCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:4:4,0:43,10:0.0571:2,0:15.3:1:28.1:1:1:0:60:8:0.0755:0.0429:2 0/0:60:0:0,0:43,15:0:2,0:17:1:26.3:1:1:0:59.4:5.444:1:0:2.5 -6 31322220 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2174;LSEQ=GCCCCACCCACCCCCAGACC;RSEQ=GCCACCCCACCCACTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:60:40,20:17,12:0.6383:2,2:20.1:1:27.3:1:0.48712:1.41:59.4:3.615:0.6267:0:3.4 0/1:98:27:15,12:43,28:0.2755:2,2:16.4:1:29:1:0.6539:1.22596:60:26:0.2766:0:1.6 -6 31322221 . G C 25 v4;q23;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30285;LSEQ=CCCCACCCACCCCCAGACCC;RSEQ=CCACCCCACCCACTCTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:3,0:53,32:0.0319:2,0:15.7:1:20.7:1:0.29781:0:60:2:0.0308:0:5 0/1:97:4:4,0:51,41:0.0412:2,0:21.5:1:12.8:1:0.13315:0:60:0:0:0:4.8 -6 31322224 . A C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.33551;SOR=1.76707;LSEQ=CACCCACCCCCAGACCCGCC;RSEQ=CCCCACCCACTCTAGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:7:6,1:54,35:0.0707:2,2:17.3:1:18.4:1:0.2501:3.85:57.9:0.75:0.0405:0:5 0/1:101:12:5,7:50,37:0.1188:2,2:13.8:1:23.9:1:0.3614:1.8796:60:2:0.093:0:3.8 -6 31322229 . A G 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01823;SOR=0.48362;LSEQ=ACCCCCAGACCCGCCACCCC;RSEQ=CCCACTCTAGACCCCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:38:15,23:55,38:0.2836:2,2:5.9:1:28.8:1:0.05355:2.20552:60:18:0.3158:0:1.1 0/1:131:21:8,13:58,48:0.1603:2,2:7.9:1:30.4:1:0.23187:1.95314:59.2:20:0.1802:0:1.8 -6 31322299 . G A 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69897;LSEQ=TCAGAGCCCTGGGCACTGTC;RSEQ=CTGCCTGGAGTAGAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:130,155:0.0104:2,2:26.3:1:30.3:1:0.59495:2.38:60:6:0.0108:0:2 0/0:274:2:2,0:115,157:0.0073:2,0:1:0:24:1:0.18144:0:60:4:0.0074:0:1.5 -6 31322303 . C G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22761;LSEQ=AGCCCTGGGCACTGTCGCTG;RSEQ=CTGGAGTAGAACAAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:274:194:82,112:38,40:0.708:2,2:28.9:1:31.6:1:0.34738:1.29629:60:63.667:0.71:0:1.3 0/1:262:93:38,55:72,95:0.355:2,2:29:1:31.4:1:0.79371:1.09656:60:92:0.358:0:1.4 -6 31322340 . G A 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=ACAGGACCTGGTCAGAGCCC;RSEQ=CAGGAGACGTGGGACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:61,121:0:2,0:23.3:1:30.7:1:1:0:60:59.667:1:0:0.7 0/1:153:12:7,5:46,91:0.0784:2,2:21:1:28.8:1:0.11596:2.75:60:11:0.0738:0:2.2 -6 31322341 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08759;SOR=Inf;LSEQ=CAGGACCTGGTCAGAGCCCG;RSEQ=AGGAGACGTGGGACAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:63,121:0:2,0:22.6:1:31.2:1:1:0:60:35.8:1:0:0.7 0/1:148:3:2,1:49,96:0.0203:2,2:16:1:28:1:0.27295:3.88:60:6:0.0204:0:1.3 -6 31322367 . T G 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00419;SOR=Inf;LSEQ=ACGTGGGACAGGAGGAATTA;RSEQ=GGGGTGGGTGAGCTCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:24,87:0:2,0:23.1:1:30:1:1:0:60:110:1:0:0.4 0/1:77:6:2,4:14,57:0.0779:2,2:24.3:1:29.5:1:0.59853:2.01:60:12:0.0789:0:1.8 -6 31322395 . A G 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00181;SOR=Inf;LSEQ=GTGAGCTCCTCCACACTCCC;RSEQ=CCCCCACCACTTACACGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:14,67:0:2,0:22.7:1:30.1:1:1:0:60:162:1:0:0.3 0/1:46:6:1,5:9,31:0.1304:2,2:19.2:1:31:1:1:1.44089:60:12:0.1333:0:2.2 -6 31322402 . C T 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCCACACTCCCACCCCCA;RSEQ=CACTTACACGCAGCCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:16,65:0:2,0:21.6:1:32:1:1:0:60:162:0.9878:0:0.4 0/1:45:11:1,10:9,25:0.2444:2,2:23.9:1:28.4:1:0.40874:3.51835:60:10:0.2381:0:2.1 -6 31322459 . T C 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02421;SOR=Inf;LSEQ=CCACCTGTGGGAAGAAAATG;RSEQ=CCTGTGAGGGCACTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:18,36:0:2,0:26.2:1:30.1:1:1:0:60:108:1:0:0.9 0/1:23:3:0,3:6,14:0.1304:2,0:20:1:32:1:0.53924:0:60:6:0.1364:0:2.7 -6 31322470 . C G 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.74022;SOR=1.51839;LSEQ=AAGAAAATGTCCTGTGAGGG;RSEQ=ACTGGGAGGAAGCAGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:36:13,23:3,7:0.766:2,2:26.8:1:31.6:1:1:1.31:60:72:0.766:0:1.5 1/1:18:15:6,9:0,3:0.8333:0,2:27.5:1:30.7:1:0.51471:0:60:14:0.8235:0:1.5 -6 31322487 . G A 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.17457;LSEQ=GGGCACTGGGAGGAAGCAGG;RSEQ=CCATGAGATCTTAGAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:0,2:12,21:0.0571:2,0:21.5:1:31.5:1:0.53613:0:60:4:0.0588:0:3 0/1:15:1:0,1:5,9:0.0667:2,0:13:0:25:0:1:0:60:2:0.0714:0:3 -6 31322513 . A C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19368;SOR=0.26156;LSEQ=AGATCTTAGAGGAACCTCCT;RSEQ=GTCTTGGACCCAAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:13:2,11:1,3:0.7647:2,2:25.1:1:29.8:1:1:1.76214:60:26:0.7647:0:2.3 0/1:9:4:1,3:1,4:0.4444:2,2:25.3:1:29:1:1:1.29:60:8:0.5:0:2.5 -6 31322559 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.55811;LSEQ=GAAGTATGACTACAGACCCA;RSEQ=GGCAGGATCAGGAAACACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:1,3:0.5556:2,0:21.8:1:31:1:0.44444:0:60:10:0.5556:0:2 0/1:5:2:1,1:1,2:0.4:2,2:24.5:1:29:1:1:1.73:60:4:0.4:0:2 -6 31322662 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01786;SOR=0;LSEQ=CCCCTGACTCATGAATGCTG;RSEQ=AATCAGGACCCCAACACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:9.3:1:28.7:1:1:0:48:6:1:0:2 0/0:5:0:0,0:3,2:0:2,0:24:1:32:1:1:0:51.8:10:1:0:0.8 -6 31322704 . A G 84 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCATCAAGGTGATACATCC;RSEQ=TCCTTCATTGTCACATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:5,2:1,0:0.875:0,2:32.6:1:30:1:1:0:44.1:14:0.875:0:2 1/1:1:1:0,1:0,0:1:0,0:7:0:33:0:1:0:49:2:1:0:2 -6 31322767 . G A 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11808;SOR=0;LSEQ=CACACAGGGTCCCAGGCTGC;RSEQ=TTAGCCCCTGTGTGCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:4,1:9,1:0.3333:2,2:23.4:1:30.2:1:1:2.12136:53.4:10:0.3333:0:2.4 0/0:9:0:0,0:8,1:0:2,0:27.1:1:30.6:1:1:0:60:18:1:0:0.9 -6 31322782 . C G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29055;SOR=0.39601;LSEQ=GCTGCGTTAGCCCCTGTGTG;RSEQ=ATGCTGCTTCCCAGTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:13:12,1:8,0:0.619:0,1:15.5:1:30.2:1:1:0:57.5:12:0.6:0:1.5 0/1:13:5:5,0:6,2:0.3846:2,0:31.6:1:31.8:1:0.48718:0:60:10:0.3846:0:1 -6 31322803 . G T 43 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04163;SOR=Inf;LSEQ=ATGCTGCTTCCCAGTAATGA;RSEQ=GCAGGGAACACTTCTACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:30,2:0:2,0:22.8:1:33.2:1:1:0:60:64:1:0:0.6 0/1:18:3:2,1:13,2:0.1667:2,2:28:1:27.3:1:0.4424:2.98763:60:6:0.1765:0:1 -6 31322835 . C T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.54332;SOR=0;LSEQ=TTCTACCTGGGGCTTGAAAC;RSEQ=CCCAGTGGGACAAGAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:45,12:0.0339:2,0:9:1:32:0:1:0:30.5:4:0.0339:0:7 0/0:31:0:0,0:26,5:0:2,0:22.4:1:30.9:1:1:0:60:62:1:0:1.2 -6 31322844 . G A 71 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.66324;SOR=0.36259;LSEQ=GGGCTTGAAACCCCCAGTGG;RSEQ=ACAAGAAAACCCAGACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:5:3,2:58,14:0.0649:2,2:7.6:1:30.6:1:0.2763:2.7167:34.4:10:0.0667:0:6.6 0/1:41:1:1,0:30,10:0.0244:2,0:7:0:31:0:1:0:27:2:0.0244:0:5 -6 31322854 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55986;SOR=3.20992;LSEQ=CCCCCAGTGGGACAAGAAAA;RSEQ=CCAGACCCCACCCCTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:0,1:70,19:0.0111:2,0:1:0:26:0:0.22222:0:60:2:0.0116:0:5 0/1:57:2:1,1:40,15:0.0351:2,2:17.5:1:31.5:1:0.48622:2.61407:60:4:0.0351:0:1 -6 31322855 . C T 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCCCAGTGGGACAAGAAAAC;RSEQ=CAGACCCCACCCCTCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:72,21:0:2,0:22.9:1:30.2:1:1:0:58:22.25:0.9889:0:1.8 0/1:58:11:7,4:34,13:0.1897:2,2:24.1:1:31:1:0.71465:1.48367:60:22:0.1897:0:2.1 -6 31322866 . C T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1271;SOR=0.27166;LSEQ=CAAGAAAACCCAGACCCCAC;RSEQ=CCTCACCCCTTCCCTACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:10:6,4:83,20:0.0877:2,2:24.4:1:31.4:1:0.21574:2.73604:37.3:20:0.0909:0:5.8 0/1:79:2:1,1:56,21:0.0253:2,2:20:1:31.5:1:0.48199:2.62852:27:4:0.026:0:4.5 -6 31322888 . A G 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33026;SOR=0.71975;LSEQ=CTCACCCCTTCCCTACCTGA;RSEQ=CTCTTCCTCCTACACATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:135:112:92,20:16,7:0.8296:2,2:28.3:1:32:1:0.24947:2.00:58:21.4:0.8231:0:2.4 1/0:108:84:58,26:18,6:0.7778:2,2:25.9:1:31.8:1:0.62345:1.34127:59.2:83:0.7905:0:1.7 -6 31322910 . G A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07588;SOR=0.25384;LSEQ=TCTTCCTCCTACACATCACA;RSEQ=CAGCGACCACAGCTCCGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:10:6,4:134,38:0.0549:2,2:16:1:30:1:0.24253:2.33776:37.3:20:0.0556:0:5.8 0/1:138:2:1,1:96,40:0.0145:2,2:17:0:28.5:1:0.50746:2.38288:27:4:0.0149:0:4.5 -6 31322911 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17782;LSEQ=CTTCCTCCTACACATCACAG;RSEQ=AGCGACCACAGCTCCGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:134:108,26:34,16:0.7283:2,2:24.3:1:29.6:1:0.07819:1.95:60:66:0.7293:0:2.4 0/1:140:45:33,12:66,29:0.3214:2,2:23.8:1:29:1:0.69468:1.21:60:90:0.3214:0:2.4 -6 31322915 . G C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07938;SOR=0.26334;LSEQ=CTCCTACACATCACAGCAGC;RSEQ=ACCACAGCTCCGATGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:10:6,4:150,39:0.0503:2,2:11:1:31.8:1:0.22762:2.54925:37.3:20:0.0518:0:5.8 0/1:146:2:1,1:101,42:0.0137:2,2:12:0:29.5:1:0.50661:2.38839:27:4:0.014:0:4.5 -6 31322920 . C T 78 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04083;SOR=0;LSEQ=ACACATCACAGCAGCGACCA;RSEQ=AGCTCCGATGACCACAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:6:4,2:156,46:0.0287:2,2:5.5:1:30.3:1:0.62346:1.6908:32.2:12:0.0288:0:6.3 0/0:154:0:0,0:104,50:0:2,0:25.1:1:30.6:1:1:0:59.6:37.5:1:0:1.3 -6 31322927 . GATGACCACAACTGCT TAGGACAGCTAGGACAGCC 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.37067;SOR=0.51071;LSEQ=ACAGCAGCGACCACAGCTCC;RSEQ=AGGACAGCCAGGCCAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:8:5,3:167,54:0.0346:2,2:11.6:1:30:1:0.41445:1.8498:41.4:16:0.0348:0.0346:5.4 0/1:167:3:2,1:112,51:0.018:2,2:17.3:1:29.9:1:1:1.09741:27:6:0.0182:0.018:4.3 -6 31322963 . A G 49 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69931;SOR=1.38595;LSEQ=AGGACAGCCAGGCCAGCAAC;RSEQ=ATGCCCACGATGGGGACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:3:3,0:219,136:0.0084:2,0:20:1:32:0:0.2913:0:23:6:0.0085:0:4.3 0/1:259:3:2,1:147,109:0.0116:2,2:14.3:1:31:1:1:1.48:40:6:0.0119:0:5.3 -6 31322973 . A T 43 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07033;SOR=Inf;LSEQ=GGCCAGCAACAATGCCCACG;RSEQ=TGGGGACGGTGGACTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:223,153:0:2,0:28.2:1:29.5:1:1:0:59.6:22.5:0.9972:0:2.3 0/1:266:3:1,2:143,119:0.0113:2,2:14.3:1:27.3:1:0.59374:2.39561:51:6:0.0119:0:5.3 -6 31322980 . C T 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21033;LSEQ=AACAATGCCCACGATGGGGA;RSEQ=GGTGGACTGGGAAGACGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:381:294:169,125:47,40:0.7717:2,2:29.7:1:30.2:1:0.62265:1.15:59.4:41:0.7715:0:2.9 0/1:270:112:62,50:80,78:0.4148:2,2:28.7:1:29.3:1:0.46036:1.21:59.3:111:0.4221:0:2.6 -6 31322987 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01086;SOR=Inf;LSEQ=CCCACGATGGGGACGGTGGA;RSEQ=TGGGAAGACGGCTCTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:216,184:0:2,0:28.7:1:31.5:1:1:0:59.6:32.333:1:0:2.3 0/1:274:5:3,2:137,132:0.0182:2,2:22:1:27.2:1:1:1.44:60:10:0.0187:0:2 -6 31322996 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25051;LSEQ=GGGACGGTGGACTGGGAAGA;RSEQ=GGCTCTGGGAAAGGAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:398:323:168,155:39,36:0.8116:2,2:28:1:30.4:1:1:1.00:59.8:160.5:0.8127:0:2.7 1/0:272:141:74,67:62,69:0.5184:2,2:29.2:1:29.2:1:0.46662:1.23:59.8:22.5:0.5094:0:2.2 -6 31323012 . G A 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGACGGCTCTGGGAAAGGA;RSEQ=GGGAAGATGAGGGGCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:202,194:0:2,0:25:1:31.2:1:1:0:59.7:48.5:1:0:2.1 0/1:273:43:18,25:109,120:0.1575:2,2:28.9:1:30.5:1:0.51015:1.2605:60:86:0.161:0:1 -6 31323019 . A G 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4494;SOR=1.97228;LSEQ=CTCTGGGAAAGGAGGGGAAG;RSEQ=TGAGGGGCCCTGACCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:3:3,0:190,195:0.0077:2,0:14.7:1:33:0:0.12211:0:23:6:0.008:0:4.3 0/1:264:4:2,2:121,139:0.0152:2,2:11:1:31.3:1:1:1.15:48.5:8:0.0153:0:3.5 -6 31323020 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04685;LSEQ=TCTGGGAAAGGAGGGGAAGA;RSEQ=GAGGGGCCCTGACCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:384:282:143,139:45,56:0.7344:2,2:23.5:1:30.5:1:0.2989:1.28:59.9:55.4:0.7328:0:2.6 0/1:263:30:13,17:112,121:0.1141:2,2:22.1:1:30.2:1:0.69971:1.20955:59.8:60:0.1154:0:2.6 -6 31323025 . G GGCCCTGACCCTCCAAGCCTCA 79 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08619;SOR=0;LSEQ=GAAAGGAGGGGAAGATGAGG;RSEQ=GCCCTGACCCTGCTGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:6:3,3:184,192:0.0157:2,2:10.8:1:30.6:1:1:1.04:27.7:12:0.0164:0.0157:4.3 0/0:258:0:0,0:122,135:0:2,0:21.5:1:29.8:1:1:0:59.7:31.125:0.996:0:1.2 -6 31323027 . C T 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGAGGGGAAGATGAGGGG;RSEQ=CCTGACCCTGCTGAAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:186,194:0:2,0:22.1:1:31.1:1:1:0:59.2:33.545:1:0:1.9 0/1:253:14:8,6:112,126:0.0553:2,2:19.4:1:29.6:1:0.58467:1.50:60:28:0.0567:0:2.4 -6 31323036 . T G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.69365;SOR=1.16892;LSEQ=AAGATGAGGGGCCCTGACCC;RSEQ=GCTGAAGGGCTCCTGCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:15:6,9:175,167:0.042:2,2:6.9:1:30:1:0.43923:1.56987:43.6:30:0.0427:0:5.1 0/1:246:12:7,5:116,117:0.0488:2,2:6.6:1:29.6:1:0.76871:1.41:49.3:24:0.0496:0:4.6 -6 31323039 . T TGAAGGGCTCCA 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33109;LSEQ=ATGAGGGGCCCTGACCCTGC;RSEQ=GAAGGGCTCCTGCTTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:433:263:138,125:82,87:0.6074:2,2:24.4:1:31:1:0.43193:1.17:59.7:262:0.6107:0.1663:1.3 0/1:266:90:45,45:90,84:0.3383:2,2:21.5:1:30.4:1:0.79665:1.07114:59.6:180:0.3409:0.1429:1.4 -6 31323041 . AAGGG TAGGGCTCCAGGA 91 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.0157;SOR=0;LSEQ=GAGGGGCCCTGACCCTGCTG;RSEQ=CTCCTGCTTTCCCTGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:9:4,5:218,211:0.0205:2,2:5.9:1:28.9:1:0.74836:1.29071:47.4:18:0.021:0.0205:6.9 0/0:268:0:0,0:139,129:0:2,0:18.8:1:31.2:1:1:0:58.8:66:1:0:1.2 -6 31323045 . G A 60 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02173;SOR=Inf;LSEQ=GGCCCTGACCCTGCTGAAGG;RSEQ=CTCCTGCTTTCCCTGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:0:0,0:220,206:0:2,0:19:1:31.3:1:1:0:58.7:70:1:0:1.5 0/1:272:4:2,2:141,127:0.0147:2,2:9.8:1:30:1:1:1.10981:45:8:0.0149:0:4.8 -6 31323048 . C CCAGGACTT 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00077;SOR=0.45893;LSEQ=CCTGACCCTGCTGAAGGGCT;RSEQ=CTGCTTTCCCTGAGAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:91:44,47:212,193:0.1831:2,2:12.8:1:30:1:0.56185:1.17296:44.4:182:0.1846:0.1227:5.9 0/1:279:26:14,12:130,123:0.0932:2,2:14.5:1:30.8:1:0.83966:1.10:45.5:52:0.0956:0.0143:5 -6 31323065 . G C 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.86618;LSEQ=GCTCCTGCTTTCCCTGAGAA;RSEQ=AGATATGACCCCTCATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:10:6,4:277,252:0.0186:2,2:11:1:33.2:1:0.75474:1.36:58.5:20:0.0187:0:1.6 0/1:350:35:16,19:164,151:0.1:2,2:21.3:1:31.3:1:0.48294:1.28879:59.2:70:0.1003:0:1.3 -6 31323067 . G C 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26373;SOR=0.82481;LSEQ=TCCTGCTTTCCCTGAGAAGA;RSEQ=ATATGACCCCTCATCCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:137:71,66:217,190:0.2518:2,2:21.4:1:32.2:1:0.76759:1.06154:45.1:136:0.2537:0:6.4 0/1:359:78:41,37:146,134:0.2173:2,2:23.3:1:31.8:1:1:1.02:48.6:156:0.2197:0:5.9 -6 31323069 . T C 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.20441;SOR=0.81204;LSEQ=CTGCTTTCCCTGAGAAGAGA;RSEQ=ATGACCCCTCATCCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:136:71,65:222,196:0.245:2,2:23.3:1:32:1:0.92126:1.03688:45.1:44.333:0.2427:0:6.4 0/1:374:78:41,37:158,138:0.2086:2,2:25.1:1:31.8:1:0.89933:1.03315:48.6:156:0.2097:0:5.9 -6 31323072 . G C 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=0.5213;LSEQ=CTTTCCCTGAGAAGAGATAT;RSEQ=ACCCCTCATCCCCCTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:134:68,66:242,201:0.231:2,2:25:1:31.9:1:0.43122:1.16825:45.6:268:0.2334:0:6.4 0/1:399:54:28,26:190,155:0.1353:2,2:23.6:1:31.4:1:0.6625:1.13788:49.1:108:0.1364:0:6.2 -6 31323094 . C T 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10478;SOR=0.72336;LSEQ=CCCCTCATCCCCCTCCTTAC;RSEQ=CCATCTCAGGGTGAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:755:82:34,48:350,322:0.1086:2,2:28.8:1:30.3:1:0.07924:1.53364:42.9:81:0.1093:0:6.2 0/1:531:43:20,23:261,227:0.081:2,2:29.3:1:28.8:1:0.42708:1.32154:53.4:42:0.0797:0:5.7 -6 31323115 . T C 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00671;SOR=0.69919;LSEQ=CCATCTCAGGGTGAGGGGCT;RSEQ=CGGCAGCCCCTCATGCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:747:216:92,124:251,268:0.2892:2,2:29:1:31.2:1:0.16787:1.26192:45.3:71:0.2902:0:5.8 0/1:533:118:55,63:193,198:0.2214:2,2:29.4:1:30.6:1:0.6744:1.11629:50.6:117:0.2216:0:5.3 -6 31323116 . C T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CATCTCAGGGTGAGGGGCTT;RSEQ=GGCAGCCCCTCATGCTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:741:0:0,0:338,392:0:2,0:28.5:1:30.4:1:1:0:55.6:120.667:1:0:1.8 0/1:528:13:7,6:241,253:0.0246:2,2:30.2:1:28.3:1:0.78392:1.22:60:12:0.024:0:1.2 -6 31323128 . A G 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12912;SOR=0.81032;LSEQ=AGGGGCTTCGGCAGCCCCTC;RSEQ=TGCTGTACATGGCATGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:205:89,116:218,259:0.3006:2,2:25.7:1:30.8:1:0.61489:1.0969:45.1:101.5:0.3016:0:5.9 0/1:484:125:60,65:167,192:0.2583:2,2:26.7:1:29.7:1:0.83525:1.06:48.3:124:0.2594:0:5.3 -6 31323134 . T C 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99751;LSEQ=TTCGGCAGCCCCTCATGCTG;RSEQ=ACATGGCATGTGTATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:110:48,62:208,256:0.1708:2,2:24.5:1:31.7:1:0.83198:1.04941:46.5:54:0.169:0:5.7 0/1:440:75:36,39:144,183:0.1705:2,2:26.7:1:31.3:1:0.60683:1.17:46.8:150:0.1708:0:5.1 -6 31323143 . T C 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49295;SOR=0.89546;LSEQ=CCCTCATGCTGTACATGGCA;RSEQ=GTGTATCTCTGCTCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:145:57,88:183,244:0.2531:2,2:24.9:1:30.5:1:0.49581:1.1576:44.4:47.333:0.2518:0:5.9 0/1:391:91:39,52:125,173:0.2327:2,2:23.5:1:30:1:0.90382:1.04:47.9:182:0.2376:0:5.3 -6 31323169 . G A 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41385;SOR=0.31604;LSEQ=TCTCTGCTCTTCTCCAGAAG;RSEQ=CACCACCACAGCTGCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:5:3,2:130,255:0.0128:2,2:17.4:1:24.6:1:0.34277:2.93:60:1.5:0.0079:0:3 0/0:245:1:1,0:84,160:0.0041:2,0:1:0:24:0:0.34694:0:59:2:0.0042:0:6 -6 31323175 . C T 153 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00088;SOR=0.23136;LSEQ=CTCTTCTCCAGAAGGCACCA;RSEQ=CACAGCTGCCCACTTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:34:9,25:97,217:0.0977:2,2:14.9:1:30.1:1:0.69696:1.24089:45.1:68:0.0991:0:5.1 0/1:205:5:2,3:56,144:0.0244:2,2:14.2:1:29:1:0.62297:1.71:42.4:10:0.0248:0:4.8 -6 31323191 . C A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28829;SOR=0;LSEQ=ACCACCACAGCTGCCCACTT;RSEQ=TGGAAGGTTCTATCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:2,1:62,180:0.0122:2,2:24.7:1:28.3:1:0.16792:5.76:50.3:6:0.0125:0:3 0/0:153:0:0,0:47,106:0:2,0:24.5:1:31.6:1:1:0:56.6:37.25:1:0:0.9 -6 31323202 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16671;SOR=1.60598;LSEQ=TGCCCACTTCTGGAAGGTTC;RSEQ=ATCTCCTGCTGGTCTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:20:0,20:69,124:0.0939:2,1:23.2:1:32.5:1:3e-04:0:33.6:40:0.0948:0:4.8 0/1:133:19:2,17:43,71:0.1429:2,2:27.2:1:31.8:1:0.01985:5.09921:37.6:38:0.1429:0:3.8 -6 31323203 . A G 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=GCCCACTTCTGGAAGGTTCT;RSEQ=TCTCCTGCTGGTCTGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:70,142:0:2,0:25.1:1:30:1:1:0:57.4:52:1:0:0.6 0/1:132:10:2,8:42,80:0.0758:2,2:22.5:1:31.4:1:0.49482:2.08964:60:20:0.0781:0:1.8 -6 31323215 . T C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.12218;SOR=1.82519;LSEQ=AAGGTTCTATCTCCTGCTGG;RSEQ=CTGGTCTCCACAAGCTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:15:0,15:90,101:0.0725:2,1:27.8:1:31.1:1:0.00017:0:33.9:30:0.0739:0:4.4 0/1:128:16:3,13:54,58:0.125:2,2:31.9:1:31.6:1:0.03201:3.99588:37.3:32:0.125:0:3.4 -6 31323225 . A G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.14636;SOR=Inf;LSEQ=CTCCTGCTGGTCTGGTCTCC;RSEQ=CAAGCTCAGTGTCCTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:109,100:0:2,0:23.2:1:30.5:1:1:0:58:208:1:0:0.7 0/1:130:2:1,1:65,63:0.0154:2,2:49:0:30.5:1:1:1.03151:60:4:0.0154:0:1 -6 31323233 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.21295;LSEQ=GGTCTGGTCTCCACAAGCTC;RSEQ=GTGTCCTGAGTTTGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:20:7,13:110,80:0.0952:2,2:27:1:30.3:1:0.05987:2.54212:45.6:40:0.0971:0:2.8 1/0:138:75:45,30:35,28:0.5435:2,2:23.5:1:29.5:1:0.6085:1.20:54:74:0.5441:0:2 -6 31323254 . G C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02376;LSEQ=GTGTCCTGAGTTTGGTCCTC;RSEQ=CCATCCCGCTGCCAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:10:0,10:152,62:0.0444:2,0:21:1:32.1:1:1e-05:0:34.7:20:0.0459:0:4.5 0/1:132:6:1,5:87,38:0.0455:2,2:24.5:1:30.2:1:0.01453:11.22779:33.8:12:0.0458:0:3.8 -6 31323262 . G A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.08977;LSEQ=AGTTTGGTCCTCGCCATCCC;RSEQ=CTGCCAGGTCAGTGTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:9:1,8:171,53:0.0386:2,2:17.8:1:30.7:1:0.00011:25.41513:35.6:18:0.0398:0:4.2 0/1:143:6:2,4:102,35:0.042:2,2:27.2:1:28:1:0.04716:5.74192:31.8:12:0.0423:0:3.8 -6 31323288 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06142;SOR=Inf;LSEQ=AGGTCAGTGTGATCTCCGCA;RSEQ=GGTAGAAACCCAGGGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:263,93:0:2,0:23:1:31.2:1:1:0:51.2:31.364:1:0:1.2 0/1:233:3:2,1:163,67:0.0129:2,2:7.3:1:23.3:1:1:1.21532:49.7:2:0.0088:0:3.3 -6 31323296 . A G 265 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.04035;SOR=1.58637;LSEQ=GTGATCTCCGCAGGGTAGAA;RSEQ=CCCAGGGCCCAGCACCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:395:326:235,91:45,24:0.8253:2,2:23.7:1:31.8:1:0.30698:1.38:49.9:53.333:0.8312:0:1.5 1/1:289:255:169,86:24,10:0.8824:2,2:19.4:1:31.7:1:0.70088:1.22045:49.5:84:0.8842:0:1.8 -6 31323321 . G A 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCCAGCACCTCAGGGTG;RSEQ=CCTCATGGTCAGAGATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:612:0:0,0:368,242:0:2,0:23.6:1:31.2:1:1:0:54.6:75.25:0.9967:0:1.1 0/1:494:68:37,31:247,176:0.1377:2,2:21.8:1:28.6:1:0.5971:1.17543:52.9:67:0.1387:0:2.8 -6 31323337 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.28961;LSEQ=GGTGGCCTCATGGTCAGAGA;RSEQ=GGGGTGGTGGGTCACGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:761:249:146,103:291,221:0.3272:2,2:24.8:1:30.1:1:0.69611:1.08:53.4:23.9:0.3243:0:2 0/1:689:85:52,33:337,267:0.1234:2,2:21.4:1:29.6:1:0.4136:1.25:57.8:20.25:0.1196:0:1.8 -6 31323353 . G A 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=19.90008;LSEQ=GAGATGGGGTGGTGGGTCAC;RSEQ=TGTGTCTTTGGGGGGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:843:35:21,14:440,366:0.0415:2,2:28.8:1:29.8:1:0.60447:1.25:58.4:34:0.041:0:1.9 0/1:790:366:197,169:236,187:0.4633:2,2:27.8:1:29.9:1:0.61568:1.08255:55.7:60:0.4627:0:2.1 -6 31323409 . T C 280 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05921;SOR=1.40349;LSEQ=AATTCAGGCGCTTTGCATCT;RSEQ=TCATGGGACACCCTAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:580:484:174,310:36,59:0.8345:2,2:23.1:1:31.4:1:0.72733:1.08692:60:59.5:0.8336:0:1.8 1/1:517:453:193,260:26,37:0.8762:2,2:21.6:1:30.6:1:0.8923:1.06:60:36.75:0.8733:0:1.8 -6 31323414 . G A 216 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01479;LSEQ=AGGCGCTTTGCATCTTTCAT;RSEQ=GGACACCCTAGGACCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:161:55,106:125,245:0.3032:2,2:21.4:1:29.5:1:1:1.02:60:39.25:0.3025:0:2.1 0/0:471:3:3,0:195,273:0.0064:2,0:6.7:1:15.7:1:0.07364:0:60:0.5:0.0022:0:3.3 -6 31323416 . G C 187 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCTTTGCATCTTTCATGG;RSEQ=ACACCCTAGGACCACCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:0:0,0:166,337:0:2,0:22.3:1:30.7:1:1:0:60:44.727:1:0:1.5 0/1:448:73:29,44:153,221:0.1629:2,2:20.7:1:30.3:1:0.89687:1.05029:60:23.333:0.1598:0:2.1 -6 31323455 . A G 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00571;SOR=Inf;LSEQ=TGTGACCAGCCTGAGAATGG;RSEQ=CAGGACACCTGGGGTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:10,216:0:1,0:23.1:1:30.2:1:1:0:60:225:1:0:1.2 0/1:168:6:0,6:11,151:0.0357:2,0:28.8:1:32:1:1:0:60:12:0.0361:0:1.8 -6 31323468 . G T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0.26002;LSEQ=AGAATGGACAGGACACCTGG;RSEQ=GTGGGGAAGGGGCACAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:60:2,58:2,114:0.3409:1,1:28.2:1:31:1:0.60634:1.96:60:120:0.3488:0:1.6 0/1:127:15:1,14:4,108:0.1181:1,1:27.7:1:29.3:1:0.47232:1.92:60:30:0.1181:0:1.5 -6 31323480 . G A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=ACACCTGGGGTGGGGAAGGG;RSEQ=CACAGAACCCAGACACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:4,147:0:1,0:24.4:1:32.2:1:1:0:60:49.333:1:0:0.9 0/1:111:11:0,11:4,96:0.0991:1,0:27.3:1:30.5:1:1:0:60:22:0.1:0:1.7 -6 31323501 . CTGGAC GGAT 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CACAGAACCCAGACACCAGC;RSEQ=GCAGGCACCTGGGATAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:2,106:0:1,0:25.8:1:32.4:1:1:0:60:53:1:0:0.6 0/1:72:12:0,12:1,59:0.1667:1,0:21.3:1:31.8:1:1:0:60:24:0.1739:0.0417:0.8 -6 31323524 . TCTC T 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=GACGCAGGCACCTGGGATAA;RSEQ=CTATTCATTGGAAAGTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:2,67:0:1,0:25.7:1:32.6:1:1:0:60:68:1:0:0.3 0/1:37:7:1,6:0,30:0.1892:1,2:14.4:1:32.6:1:0.18919:0:60:14:0.1892:0.027:0.7 -6 31323707 . G A 63 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGCTGCAGGGGTCAAAG;RSEQ=GGACCCCTGATCAGTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:3,6:0.3077:2,0:25.5:1:31.8:1:0.4965:0:60:8:0.3077:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31323766 . T C 64 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCCTCAGAGACGTCAT;RSEQ=CCTTAATTGTCTAGAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:2,1:0.5:2,2:19.8:1:32.3:1:0.48571:4.4496:55.5:8:0.5714:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31323776 . T TC 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACGTCATTCCTTAATTG;RSEQ=CTAGAGAGAAGAGGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:3,2:0.375:2,2:15.7:1:30.7:1:1:1.29:41:6:0.375:0.25:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31323838 . C G 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66846;SOR=2.09479;LSEQ=TCATGCCATTCTCCATTCAA;RSEQ=GGAGGGCGACATTCTAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:33:30,3:6,1:0.825:2,2:24.2:1:32.7:1:0.55225:1.64:55.6:66:0.825:0:1.2 1/1:11:10:9,1:1,0:0.9091:0,2:23.4:1:33:1:1:0:58.1:20:0.9091:0:1.5 -6 31323875 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00948;SOR=Inf;LSEQ=GCGCTGATCCCATTTTCCTC;RSEQ=TCTTCTCGTGGGAGGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:71,5:0:2,0:25.1:1:30.9:1:1:0:56:75:1:0:1.4 0/1:36:4:4,0:30,2:0.1111:2,0:12:1:31.8:1:1:0:40.8:8:0.1111:0:3.5 -6 31323945 . A C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51198;SOR=1.30323;LSEQ=TCCCCACTGCCCCTGGTACC;RSEQ=GCGCGCTCCAGCTTGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:36:28,8:32,15:0.4337:2,2:21.5:1:29.4:1:0.45853:1.63:47.5:35:0.4268:0:3.1 1/0:68:34:25,9:24,7:0.5:2,2:29.1:1:27.6:1:0.77898:1.2303:49.5:33:0.4925:0:3.2 -6 31323949 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50924;SOR=0;LSEQ=CACTGCCCCTGGTACCAGCG;RSEQ=GCTCCAGCTTGTCCTTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:59,26:0.0227:2,2:24:0:32.5:1:0.52686:2.24564:60:4:0.0233:0:1.5 0/0:64:0:0,0:48,16:0:2,0:27:1:30.3:1:1:0:54.4:63:1:0:1.7 -6 31323953 . C G 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07683;SOR=0.49634;LSEQ=GCCCCTGGTACCAGCGCGCT;RSEQ=CAGCTTGTCCTTCCCGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:32:23,9:39,22:0.3441:2,2:18.2:1:29.7:1:0.49426:1.44:44:9.667:0.3222:0:3.8 0/1:68:14:12,2:34,20:0.2059:2,2:19.9:1:29.6:1:0.12384:3.47:44.4:28:0.2154:0:3.9 -6 31323958 . T G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10945;SOR=1.72417;LSEQ=TGGTACCAGCGCGCTCCAGC;RSEQ=TGTCCTTCCCGTTCTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:31:21,10:42,23:0.3229:2,2:15.9:1:29.2:1:0.82147:1.15:42:30:0.3158:0:4.4 0/1:73:33:22,11:25,15:0.4521:2,2:22.3:1:28.1:1:0.80787:1.20:48.7:66:0.4648:0:3.6 -6 31323960 . G C 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01035;SOR=0.38063;LSEQ=GTACCAGCGCGCTCCAGCTT;RSEQ=TCCTTCCCGTTCTCCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:36:26,10:42,23:0.3564:2,2:13.2:1:30.7:1:0.51001:1.42:41.7:72:0.3564:0:4.2 0/1:75:13:11,2:38,24:0.1733:2,2:14.6:1:29:1:0.19809:3.42:41.5:26:0.1781:0:4.4 -6 31323969 . G A 30 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58994;SOR=2.45863;LSEQ=CGCTCCAGCTTGTCCTTCCC;RSEQ=TTCTCCAGGTATCTGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:1,0:104,44:0.0067:2,0:9:0:31:0:1:0:60:2:0.0069:0:4 0/1:122:2:2,0:76,44:0.0164:2,0:6.5:1:30.5:1:0.53502:0:46.5:4:0.0169:0:5.5 -6 31323974 . C T 56 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17914;SOR=4.94963;LSEQ=CAGCTTGTCCTTCCCGTTCT;RSEQ=CAGGTATCTGCGGAGCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:1,0:121,53:0.0057:2,0:14:0:14:0:1:0:60:0:0:0:4 0/1:144:4:3,1:86,54:0.0278:2,2:6.5:1:28:1:1:1.88:47.5:8:0.0284:0:4.8 -6 31323980 . A G 84 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04944;SOR=7.4652;LSEQ=GTCCTTCCCGTTCTCCAGGT;RSEQ=TCTGCGGAGCCACTCCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:1,0:136,64:0.005:2,0:27:0:14:0:1:0:60:0:0:0:2 0/1:166:6:4,2:101,59:0.0361:2,2:12.5:1:32.8:1:1:1.17:37:12:0.0364:0:4.3 -6 31323983 . T C 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CTTCCCGTTCTCCAGGTATC;RSEQ=GCGGAGCCACTCCACGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:150,75:0:2,0:18.7:1:30.8:1:1:0:49.7:74:1:0:1.9 0/1:181:13:8,5:106,62:0.0718:2,2:9.1:1:29.7:1:1:1.06815:45.1:12:0.0678:0:3.6 -6 31323985 . C T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.85336;LSEQ=TCCCGTTCTCCAGGTATCTG;RSEQ=GGAGCCACTCCACGCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:0,3:153,85:0.0124:2,0:1:0:26.3:1:0.04763:0:56.3:6:0.0126:0:1.7 0/1:188:2:1,1:115,71:0.0106:2,2:13:1:28.5:1:1:1.61535:60:4:0.0108:0:2.5 -6 31323991 . C G 60 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03991;SOR=Inf;LSEQ=TCTCCAGGTATCTGCGGAGC;RSEQ=ACTCCACGCACTCGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:173,105:0:2,0:20.7:1:31.3:1:1:0:50.3:38.714:0.9963:0:1.9 0/1:227:4:2,2:136,87:0.0176:2,2:25.3:1:30.3:1:0.64598:1.55999:39.5:8:0.018:0:5 -6 31324003 . TC GT 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43277;LSEQ=TGCGGAGCCACTCCACGCAC;RSEQ=GCCCTCCAGGTAGGCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:325:165:117,48:65,56:0.5077:2,2:26:1:30.6:1:0.00411:2.09:46:330:0.5189:0:1.4 0/1:266:82:49,33:63,52:0.3083:2,2:22.4:1:30.6:1:0.55987:1.22:49.8:164:0.3228:0:2.2 -6 31324004 . C T 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.76176;SOR=0.68956;LSEQ=GCGGAGCCACTCCACGCACT;RSEQ=GCCCTCCAGGTAGGCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:7:2,5:65,56:0.0213:2,2:10.4:1:28.4:1:0.25673:2.87876:54.6:14:0.0534:0:1.7 0/1:271:4:3,1:63,53:0.0148:2,2:13.3:1:27.3:1:0.62634:2.51:53.5:8:0.0339:0:3 -6 31324023 . CCG GTC 100 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=TCGCCCTCCAGGTAGGCTCT;RSEQ=CTGCTCCGCCTCACGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:262,195:0:2,0:28.2:1:31.2:1:1:0:51.3:75.167:1:0:1.4 0/1:375:9:4,5:202,164:0.024:2,2:30.9:1:31.8:1:0.73684:1.53783:37.1:18:0.0247:0:4 -6 31324024 . C A 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.30894;LSEQ=CGCCCTCCAGGTAGGCTCTC;RSEQ=GCTGCTCCGCCTCACGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:58:29,29:233,166:0.1266:2,2:32:1:30.8:1:0.25646:1.40253:40.5:57:0.1261:0:3.5 0/1:379:123:73,50:129,115:0.3245:2,2:29.7:1:29.7:1:0.26684:1.30:47.3:60.5:0.3315:0:3 -6 31324025 . G A 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.21927;LSEQ=GCCCTCCAGGTAGGCTCTCC;RSEQ=CTGCTCCGCCTCACGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:57:29,28:240,173:0.121:2,2:25.1:1:29.4:1:0.31974:1.33858:52.2:56:0.1212:0:2.4 0/1:380:89:50,39:154,127:0.2342:2,2:27.5:1:29.1:1:0.90276:1.06:55.3:21.25:0.2342:0:2.1 -6 31324036 . T A 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.69865;LSEQ=AGGCTCTCCGCTGCTCCGCC;RSEQ=CACGGGCCGCCTCCCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:41:20,21:281,216:0.0762:2,2:32.4:1:30.3:1:0.41348:1.36516:40.4:82:0.0777:0:3.9 0/1:428:78:48,30:184,160:0.1822:2,2:25.7:1:29.5:1:0.20961:1.39:45.7:156:0.1853:0:3.2 -6 31324039 . C T 64 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09375;SOR=6.31713;LSEQ=CTCTCCGCTGCTCCGCCTCA;RSEQ=GGGCCGCCTCCCACTTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:1:0,1:302,245:0.0018:2,0:1:0:27:0:0.44891:0:60:2:0.0018:0:2 0/1:438:5:2,3:237,196:0.0114:2,2:25.2:1:27.6:1:0.66285:1.81129:42.6:4:0.0092:0:5 -6 31324051 . C A 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGCCTCACGGGCCGCCTCC;RSEQ=ACTTGCGCTGGGTGATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:577:0:0,0:316,261:0:2,0:26.4:1:31.4:1:1:0:50.4:63.111:1:0:1.4 0/1:463:28:15,13:239,196:0.0605:2,2:20.9:1:29.1:1:1:1.05665:46.5:56:0.0614:0:3.6 -6 31324057 . C A 135 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00321;SOR=0.27377;LSEQ=CACGGGCCGCCTCCCACTTG;RSEQ=GCTGGGTGATCTGAGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:26:16,10:284,254:0.0461:2,2:23.3:1:28.8:1:0.42606:1.43:40.2:52:0.0464:0:4.2 0/1:460:6:3,3:247,207:0.013:2,2:25.5:1:29.8:1:1:1.19277:44.3:12:0.0133:0:4.2 -6 31324064 . T A 138 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.33874;LSEQ=CGCCTCCCACTTGCGCTGGG;RSEQ=GATCTGAGCCGCCGTGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:1:1,0:278,271:0.0018:2,0:1:0:27:0:1:0:49:2:0.0018:0:2 0/1:454:26:12,14:226,202:0.0573:2,2:18.7:1:29.4:1:0.54882:1.30451:46.6:52:0.0582:0:3.8 -6 31324077 . C G 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00098;SOR=0.58866;LSEQ=CGCTGGGTGATCTGAGCCGC;RSEQ=GTGTCCGCGGCGGTCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:138:71,67:168,191:0.2771:2,2:25.7:1:30.4:1:0.36826:1.20:39:137:0.279:0:2.8 0/1:413:76:52,24:162,175:0.184:2,2:24.5:1:29.6:1:0.00144:2.34:36.6:24.333:0.1794:0:3.6 -6 31324078 . G A 94 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1991;SOR=0.30133;LSEQ=GCTGGGTGATCTGAGCCGCC;RSEQ=TGTCCGCGGCGGTCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:8:4,4:236,254:0.0161:2,2:5.8:1:31.5:1:1:1.08:40.6:16:0.0162:0:2 0/0:409:2:1,1:196,178:0.0049:2,2:10:0:32:0:1:1.10084:33:4:0.0049:0:3.5 -6 31324086 . G C 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.32428;LSEQ=ATCTGAGCCGCCGTGTCCGC;RSEQ=GCGGTCCAGGAGCGCAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:96:65,31:158,204:0.2096:2,2:23.2:1:30.3:1:3e-05:2.70:41.5:31:0.209:0:4.1 0/1:380:145:88,57:102,133:0.3816:2,2:24.5:1:29.6:1:0.00149:2.01:44.1:47.333:0.3787:0:3.5 -6 31324089 . G A 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=TGAGCCGCCGTGTCCGCGGC;RSEQ=GTCCAGGAGCGCAGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:218,232:0:2,0:24.5:1:30.1:1:1:0:50:111.5:0.9978:0:1.8 0/1:375:10:3,7:183,182:0.0267:2,2:26.1:1:31:1:0.33726:2.34111:51.7:20:0.027:0:1.7 -6 31324100 . G T 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00438;SOR=1.54534;LSEQ=GTCCGCGGCGGTCCAGGAGC;RSEQ=CAGGTCCTCGTTCAGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:122:78,44:118,181:0.2898:2,2:20.8:1:30.7:1:1e-05:2.71:42.6:244:0.2912:0:4.3 0/1:380:147:90,57:102,130:0.3868:2,2:23.4:1:29.6:1:0.00111:2.01:46.8:35.75:0.3824:0:3.6 -6 31324104 . G A 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.44423;LSEQ=GCGGCGGTCCAGGAGCGCAG;RSEQ=TCCTCGTTCAGGGCGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:134:42,92:154,134:0.3175:2,2:25.3:1:30:1:3e-05:2.51188:50.2:25.8:0.3123:0:2 0/1:409:70:27,43:179,159:0.1711:2,2:24.1:1:28.7:1:0.03526:1.79033:50.1:34:0.1696:0:2.1 -6 31324110 . G A 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCAGGAGCGCAGGTCCTC;RSEQ=TTCAGGGCGATGTAATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:184,217:0:2,0:22.9:1:30.7:1:1:0:48.8:56.286:1:0:2.3 0/1:433:20:6,14:217,194:0.0462:2,2:23.9:1:29.7:1:0.06501:2.6044:52.9:40:0.0463:0:3.3 -6 31324128 . C T 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00045;SOR=Inf;LSEQ=TCGTTCAGGGCGATGTAATC;RSEQ=TTGCCGTCGTAGGCGTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:175,213:0:2,0:23.5:1:31.6:1:1:0:48.1:96:1:0:2.7 0/1:480:13:7,6:232,235:0.0271:2,2:22.6:1:30.2:1:0.78698:1.18:52.4:26:0.0274:0:3.7 -6 31324143 . GT TA 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04971;LSEQ=TAATCCTTGCCGTCGTAGGC;RSEQ=ACTGGTCATGCCCGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:118:71,47:100,127:0.3401:2,2:33:1:29.3:1:0.0047:1.91:41.8:117:0.3401:0.0115:4.3 0/1:482:12:8,4:230,239:0.0249:2,2:35:1:30:1:0.25644:2.08:46.7:24:0.0253:0:3.8 -6 31324144 . T A 182 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0098;SOR=0.59973;LSEQ=AATCCTTGCCGTCGTAGGCG;RSEQ=ACTGGTCATGCCCGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:64:20,44:60,61:0.1888:2,2:21.9:1:30.4:1:0.01948:2.15495:42.2:128:0.287:0:4.2 0/1:482:59:19,40:170,155:0.1224:2,2:25.4:1:29.8:1:0.00468:2.30408:45.4:118:0.1266:0:3.9 -6 31324145 . A C 219 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCTTGCCGTCGTAGGCGT;RSEQ=CTGGTCATGCCCGCGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:166,170:0:2,0:27.6:1:29.8:1:1:0:49.1:111:1:0:2.7 0/1:487:145:82,63:156,184:0.2977:2,2:26.7:1:30.6:1:0.03713:1.53:52.3:144:0.3:0:4.6 -6 31324151 . C T 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01646;SOR=0.70384;LSEQ=GCCGTCGTAGGCGTACTGGT;RSEQ=ATGCCCGCGGAGGAGGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:147:69,78:97,92:0.4362:2,2:31.7:1:29.3:1:0.44299:1.19124:42.2:72.5:0.4394:0:4.3 0/1:488:172:83,89:135,143:0.3525:2,2:27.9:1:28.7:1:1:1.01228:53:85:0.3505:0:2.8 -6 31324154 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.97006;LSEQ=GTCGTAGGCGTACTGGTCAT;RSEQ=CCCGCGGAGGAGGCGCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:39:0,39:168,131:0.1154:2,1:18.4:1:29.7:1:0:0:38.3:38:0.1155:0:4 0/1:480:189:87,102:151,140:0.3938:2,2:29.5:1:28.2:1:0.22518:1.2639:49.3:46.25:0.3945:0:4.3 -6 31324176 . C G 145 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16806;LSEQ=CCGCGGAGGAGGCGCCCGTC;RSEQ=GGCCCCACGTCGCAGCCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:30:23,7:144,145:0.094:2,2:25.1:1:29.6:1:0.00647:3.30:36.8:14:0.0897:0:6.2 0/1:526:9:0,9:255,262:0.0171:2,0:20:1:31.1:1:0.00377:0:34.1:18:0.0172:0:4 -6 31324184 . C G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04548;LSEQ=GAGGCGCCCGTCCGGCCCCA;RSEQ=GTCGCAGCCGTACATGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:132:79,53:75,93:0.4385:2,2:16.2:1:31.2:1:0.01049:1.84:42.1:25.4:0.4349:0:4.8 0/1:527:18:8,10:243,266:0.0342:2,2:11.6:1:29:1:0.81519:1.14163:46.9:17:0.0328:0:4.6 -6 31324194 . G A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36209;LSEQ=TCCGGCCCCACGTCGCAGCC;RSEQ=TACATGCTCTGGAGGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:107:66,41:70,78:0.4163:2,2:13.3:1:30.1:1:0.03041:1.79:41.2:106:0.419:0:4.9 0/1:478:98:50,48:166,209:0.205:2,2:19.9:1:29.7:1:0.25541:1.31:46.1:97:0.2046:0:5 -6 31324200 . GCTCTGGAGG CGTCTGCCAA 190 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCACGTCGCAGCCGTACAT;RSEQ=GTGTGAGACCCTGGCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:96:41,55:18,33:0.4248:2,2:15.9:1:29:1:0.47985:1.36:44.8:47:0.4273:0.4248:3.3 0/0:429:0:0,0:70,98:0:2,0:27.2:1:31.3:1:1:0:60:41:0.3877:0:0.7 -6 31324202 . T A 90 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29435;SOR=3.38143;LSEQ=CACGTCGCAGCCGTACATGC;RSEQ=CTGGAGGGTGTGAGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:0,1:90,84:0.0057:2,0:2:0:26:0:0.48571:0:39:2:0.0059:0:5 0/1:419:8:6,2:168,229:0.0191:2,2:27:1:30.1:1:0.07942:4.08:30.5:16:0.0201:0:4.3 -6 31324208 . G T 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01577;SOR=1.71199;LSEQ=GCAGCCGTACATGCTCTGGA;RSEQ=GGTGTGAGACCCTGGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:33:26,7:62,75:0.193:2,2:29.8:1:30.2:1:0.00079:4.46:38.7:15.5:0.189:0:6.3 0/1:375:109:43,66:112,151:0.2907:2,2:26.4:1:29.9:1:0.64422:1.13806:56.6:218:0.293:0:4.6 -6 31324210 . G A 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00219;SOR=1.96487;LSEQ=AGCCGTACATGCTCTGGAGG;RSEQ=TGTGAGACCCTGGCCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:34:27,7:71,108:0.1596:2,2:29.1:1:30:1:2e-05:5.82:39:33:0.1587:0:6.2 0/1:375:102:39,63:114,159:0.272:2,2:26.2:1:29.3:1:0.55704:1.15775:56.9:50:0.2681:0:4.7 -6 31324227 . C A 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05489;SOR=0.55339;LSEQ=AGGGTGTGAGACCCTGGCCC;RSEQ=GGCCCCGCGGTCAGCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:29:11,18:70,115:0.1355:2,2:23.8:1:30.3:1:1:1.00:58.6:28:0.1366:0:3 0/1:301:24:8,16:102,175:0.0797:2,2:23.9:1:30.8:1:0.82745:1.16509:57.2:48:0.0814:0:3 -6 31324229 . G C 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02474;SOR=2.38489;LSEQ=GGTGTGAGACCCTGGCCCCG;RSEQ=CCCCGCGGTCAGCCCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:9:0,9:79,125:0.0421:2,0:20.2:1:27:1:0.02802:0:34.9:8:0.0394:0:4.7 0/1:295:28:9,19:96,171:0.0949:2,2:21.1:1:29.8:1:0.83627:1.18448:39.3:56:0.0959:0:3.7 -6 31324235 . C T 56 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03593;SOR=0;LSEQ=AGACCCTGGCCCCGGCCCCG;RSEQ=GGTCAGCCCAGTCCCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:4:0,4:72,136:0.0189:2,0:28:1:28:1:0.30204:0:36.3:8:0.0198:0:4.8 0/0:273:0:0,0:91,182:0:2,0:23.1:1:29.3:1:1:0:55.7:33.125:1:0:2.3 -6 31324243 . C A 60 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13131;SOR=Inf;LSEQ=GCCCCGGCCCCGCGGTCAGC;RSEQ=CAGTCCCCCGAGCCCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:56,139:0:2,0:24.6:1:30.1:1:1:0:53.2:26.857:1:0:1.8 0/1:240:4:0,4:75,161:0.0167:2,0:34:0:30:1:0.31251:0:44.3:8:0.017:0:2 -6 31324245 . A C 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=2.28887;LSEQ=CCCGGCCCCGCGGTCAGCCC;RSEQ=GTCCCCCGAGCCCCGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:194:130:36,94:18,43:0.6701:2,2:26.3:1:28.8:1:0.86353:1.09251:50.4:42.333:0.6755:0:2.4 1/1:232:191:55,136:16,25:0.8233:2,2:22.2:1:29:1:0.1977:1.57926:55.3:46.75:0.8238:0:2.6 -6 31324247 . T TC 197 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGCCCCGCGGTCAGCCCAG;RSEQ=CCCCCGAGCCCCGCCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:52,138:0:2,0:26:1:28.1:1:1:0:53.5:14.833:1:0:1.7 0/1:219:91:29,62:37,89:0.4155:2,2:24.5:1:30.3:1:0.76528:1.12:52.3:29.333:0.4171:0.0274:2.3 -6 31324251 . C CA 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.2528;SOR=Inf;LSEQ=CCCGCGGTCAGCCCAGTCCC;RSEQ=CGAGCCCCGCCCCGCCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:45,135:0:2,0:28:1:30.1:1:1:0:53.6:21.5:1:0:1.5 0/1:211:3:2,1:55,153:0.0142:2,2:10.7:1:20.7:1:0.1782:5.51:59:2:0.0097:0.0095:3.3 -6 31324254 . A AGCCCC 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=4.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=GCGGTCAGCCCAGTCCCCCG;RSEQ=GCCCCGCCCCGCCCCGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:43,132:0:2,0:29:1:29.7:1:1:0:53.4:13.583:0.9939:0:1.5 0/1:196:2:0,2:51,142:0.0102:2,0:32.5:1:25.4:1:1:0:46.5:4:0.0107:0:2 -6 31324264 . C CA 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49906;SOR=0;LSEQ=CAGTCCCCCGAGCCCCGCCC;RSEQ=GCCCCGACCAACCCGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:0,2:38,135:0.0112:2,0:40:1:31.5:1:1:0:39:4:0.0114:0:4.5 0/0:168:0:0,0:37,130:0:2,0:22.2:1:29.2:1:1:0:54.9:40.75:0.9939:0:1.9 -6 31324265 . GC AGT 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.49906;SOR=0;LSEQ=AGTCCCCCGAGCCCCGCCCC;RSEQ=CCCGACCAACCCGCGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:0,2:38,135:0.0112:2,0:45.5:1:31.8:1:1:0:33.5:4:0.0114:0:5 0/0:168:0:0,0:37,130:0:2,0:22.2:1:29.2:1:1:0:54.9:40.75:0.9939:0:1.9 -6 31324269 . C T 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.00019;SOR=Inf;LSEQ=CCCCGAGCCCCGCCCCGCCC;RSEQ=GACCAACCCGCGGGGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:35,140:0:2,0:27.8:1:29.3:1:1:0:54.2:28.167:1:0:1.3 0/1:154:11:2,9:29,112:0.0714:2,2:26.2:1:28.5:1:1:1.16405:52.6:4.5:0.0604:0:3.7 -6 31324271 . A C 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00169;SOR=Inf;LSEQ=CCGAGCCCCGCCCCGCCCCG;RSEQ=CCAACCCGCGGGGATTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:35,139:0:2,0:27.4:1:29:1:1:0:54.1:20.75:1:0:1.3 0/1:146:8:1,7:28,110:0.0548:2,2:28.5:1:29.8:1:1:1.7758:46.5:16:0.0576:0:1.6 -6 31324290 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50977;SOR=0;LSEQ=GACCAACCCGCGGGGATTTT;RSEQ=GCCTCAACTGAAAATGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:26,119:0.0136:2,2:6:0:32:0:0.33464:4.51:60:4:0.0139:0:1.5 0/0:108:0:0,0:16,92:0:2,0:23.7:1:30.3:1:1:0:55.4:26:1:0:1.3 -6 31324295 . C A 73 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15995;SOR=0;LSEQ=ACCCGCGGGGATTTTGGCCT;RSEQ=AACTGAAAATGAAACCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:5:0,5:29,110:0.0345:2,0:14.4:1:31.6:1:0.58319:0:37:10:0.0352:0:4.4 0/0:95:0:0,0:16,79:0:2,0:25.9:1:31.5:1:1:0:57:46.5:1:0:1.2 -6 31324348 . C T 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15606;SOR=2.87021;LSEQ=GGCTCTCGCCGGTCGAGGGT;RSEQ=TGGGCGGGTCCCGCGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:2,1:74,30:0.028:2,2:18.3:1:32:0:1:1.23078:60:6:0.0288:0:1.3 0/1:65:5:2,3:32,28:0.0769:2,2:26.2:1:24.2:1:0.66312:1.70016:60:4:0.0635:0:1.6 -6 31324369 . AGGGA GGG 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGCGGGTCCCGCGGCCTC;RSEQ=GGCGGATCTCGGACCCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:110,19:0:2,0:25:1:30.2:1:1:0:60:24.8:0.992:0:0.2 0/1:67:14:8,6:39,12:0.209:2,2:24.1:1:29.8:1:0.18471:2.40038:60:28:0.209:0.0448:0.4 -6 31324373 . A G 102 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=10.36987;LSEQ=CGGGTCCCGCGGCCTCAGGG;RSEQ=GGCGGATCTCGGACCCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:3,0:116,16:0.0222:2,0:26:1:32.3:1:1:0:60:6:0.0233:0:2 0/1:57:11:7,4:38,8:0.193:2,2:17.3:1:29.5:1:0.21852:2.65847:60:10:0.1786:0:1.5 -6 31324415 . A C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=16.45675;LSEQ=CTCGGGGCGACCCGGGCCGT;RSEQ=CGTGGGGGATGGGGAGTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:11:10,1:211,41:0.0418:2,2:25:1:30.1:1:1:1.94:52.2:10:0.0386:0:1.5 0/1:107:45:38,7:56,6:0.4206:2,2:23.3:1:30.6:1:0.38395:1.71035:58.9:90:0.4245:0:1.2 -6 31324448 . G A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13489;SOR=1.85728;LSEQ=GGAGTCGTGACCTGCGCCCC;RSEQ=GGCCGGGGTCACTCACCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:12:8,4:301,108:0.0285:2,2:20.8:1:29.9:1:0.52807:1.39234:60:24:0.0294:0:1.8 0/1:232:12:8,4:147,72:0.0517:2,2:23.1:1:30.2:1:1:1.02076:58.9:24:0.0529:0:1.8 -6 31324452 . C T 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.13927;SOR=3.07589;LSEQ=TCGTGACCTGCGCCCCGGGC;RSEQ=GGGGTCACTCACCGGCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:3:1,2:330,134:0.0064:2,2:8:1:24:1:0.20448:4.90605:60:2:0.0044:0:2.7 0/1:256:5:2,3:167,84:0.0195:2,2:11.2:1:28.8:1:0.34055:2.96832:44.4:10:0.02:0:3.4 -6 31324489 . C G 128 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTCGCTCTGGTTGTAGTAGC;RSEQ=GCGCAGGTTCCGCAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:773:0:0,0:456,316:0:2,0:24.7:1:30.1:1:1:0:59.6:44.412:0.9987:0:1.2 0/1:388:24:19,5:203,161:0.0619:2,2:31.6:1:28:1:0.03178:3.01:47.7:23:0.0599:0:5.3 -6 31324491 . C A 127 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CGCTCTGGTTGTAGTAGCCG;RSEQ=GCAGGTTCCGCAGGCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:802:0:0,0:465,334:0:2,0:24.5:1:30.8:1:1:0:59.7:56.071:0.9962:0:1.3 0/1:397:24:18,6:204,169:0.0605:2,2:30.5:1:27.8:1:0.05801:2.48:47.7:23:0.0588:0:5.6 -6 31324496 . G T 68 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01894;SOR=9.85387;LSEQ=TGGTTGTAGTAGCCGCGCAG;RSEQ=TTCCGCAGGCTCTCTCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:834:1:1,0:478,354:0.0012:2,0:3:0:25:0:1:0:60:2:0.0012:0:3 0/1:427:5:3,2:235,185:0.0117:2,2:11.6:1:29.4:1:1:1.18:44.4:10:0.0118:0:2.2 -6 31324497 . T G 157 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTGTAGTAGCCGCGCAGG;RSEQ=TCCGCAGGCTCTCTCGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:835:0:0,0:477,357:0:2,0:25.1:1:29.7:1:1:0:59.7:68.5:1:0:1.4 0/1:427:38:26,12:213,176:0.089:2,2:18.5:1:30:1:0.12415:1.79:47.8:37:0.0877:0:5.3 -6 31324506 . CT TC 148 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AGCCGCGCAGGTTCCGCAGG;RSEQ=CTCTCGGTCAGTCTGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:878:0:0,0:490,386:0:2,0:25.6:1:32:1:1:0:59.8:86.6:0.9977:0:1.5 0/1:452:33:23,10:219,186:0.073:2,2:17.2:1:29.4:1:0.10136:1.95:51.8:66:0.0737:0.0044:5.2 -6 31324509 . T A 117 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.00896;SOR=2.99402;LSEQ=CGCGCAGGTTCCGCAGGCTC;RSEQ=CTCGGTCAGTCTGTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:10:5,5:500,393:0.0111:2,2:18.1:1:30.4:1:0.75632:1.27191:49.4:20:0.0113:0:1.6 0/1:462:15:8,7:247,200:0.0325:2,2:17.8:1:30:1:1:1.08044:47.1:30:0.0329:0:1.4 -6 31324516 . C A 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.496;LSEQ=GTTCCGCAGGCTCTCTCGGT;RSEQ=AGTCTGTGCCTGGGCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:929:268:156,112:354,306:0.2885:2,2:25:1:29:1:0.2163:1.20:59.8:37.286:0.2887:0:5 0/1:478:80:43,37:209,189:0.1674:2,2:20.7:1:28.9:1:0.90252:1.05:57.2:160:0.1709:0:4.9 -6 31324525 . CC TG 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=1.72249;LSEQ=GCTCTCTCGGTCAGTCTGTG;RSEQ=TGGGCCTTGTAGATCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:183:111,72:318,282:0.2143:2,2:34.2:1:31.4:1:0.07493:1.37:60:366:0.2168:0:5.7 0/1:416:133:71,62:144,136:0.3197:2,2:31:1:30.3:1:0.75224:1.08:58.6:266:0.3252:0:4.9 -6 31324528 . G T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.83973;LSEQ=CTCTCGGTCAGTCTGTGCCT;RSEQ=GGCCTTGTAGATCTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:855:185:111,74:347,323:0.2164:2,2:34.2:1:30.3:1:0.05532:1.40:60:60.667:0.2167:0:5.7 0/1:423:186:97,89:119,117:0.4397:2,2:28.1:1:29.4:1:0.76881:1.07:58:36.2:0.4351:0:4.9 -6 31324531 . C T 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=1.81992;LSEQ=TCGGTCAGTCTGTGCCTGGG;RSEQ=CTTGTAGATCTGTGTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:863:198:119,79:340,322:0.2294:2,2:32.1:1:29.8:1:0.03469:1.43:60:48.5:0.2285:0:5.6 0/1:421:148:83,65:136,137:0.3515:2,2:29.7:1:28.7:1:0.22248:1.29:58.3:36:0.347:0:4.9 -6 31324536 . T A 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02845;SOR=0.75916;LSEQ=CAGTCTGTGCCTGGGCCTTG;RSEQ=AGATCTGTGTGTTCCGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:992:285:156,129:357,327:0.2873:2,2:22.2:1:29.9:1:0.48074:1.11:60:56:0.286:0:5.2 0/1:525:123:70,53:116,112:0.2343:2,2:24.8:1:29.2:1:0.31354:1.27:57.9:122:0.236:0:3.8 -6 31324547 . G C 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=12.0603;LSEQ=TGGGCCTTGTAGATCTGTGT;RSEQ=TTCCGGTCCCAATACTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1038:23:10,13:532,479:0.0222:2,2:19.1:1:31.1:1:0.40643:1.44332:47.4:46:0.0225:0:5.4 0/1:577:124:64,60:240,212:0.2149:2,2:21.1:1:30.8:1:0.83916:1.06119:50.3:40.333:0.2119:0:5.4 -6 31324549 . T C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.1918;LSEQ=GGCCTTGTAGATCTGTGTGT;RSEQ=CCGGTCCCAATACTCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1033:24:11,13:526,483:0.0232:2,2:18.8:1:30.6:1:0.6802:1.28671:47.5:48:0.0236:0:5.5 0/1:582:131:67,64:240,211:0.2251:2,2:21.4:1:30.3:1:0.69187:1.08635:51:31.75:0.2216:0:5.4 -6 31324562 . C T 167 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=84.01352;LSEQ=TGTGTGTTCCGGTCCCAATA;RSEQ=TCCGGCCCCTCCTGCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1022:1:0,1:522,499:0.001:2,0:1:0:25:0:0.48924:0:60:2:0.001:0:7 0/1:643:49:24,25:302,292:0.0762:2,2:26:1:29.9:1:0.88212:1.07719:59.9:98:0.0767:0:3 -6 31324574 . C T 117 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCCCAATACTCCGGCCCCTC;RSEQ=TGCTCTATCCACGGCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:960:0:0,0:477,483:0:2,0:24.7:1:31.7:1:1:0:58.8:239:1:0:2.1 0/1:646:16:7,9:303,326:0.0248:2,2:26.2:1:29.4:1:0.80357:1.19467:60:15:0.0234:0:5.8 -6 31324586 . C T 254 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=0.68003;LSEQ=GGCCCCTCCTGCTCTATCCA;RSEQ=GGCGCCCGCGGCTCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:881:336:168,168:258,286:0.3814:2,2:25.9:1:30.3:1:0.48767:1.11:57:41:0.3796:0:5.4 0/1:623:184:88,96:207,229:0.2953:2,2:28.6:1:29.8:1:1:1.01:47.9:91:0.2959:0:5.9 -6 31324595 . C G 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.41603;LSEQ=TGCTCTATCCACGGCGCCCG;RSEQ=GGCTCCTCTCTCGGACTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:776:289:143,146:223,263:0.3724:2,2:28.1:1:30.8:1:0.33469:1.15:57.9:40.286:0.3715:0:5.6 0/1:571:113:59,54:212,245:0.1979:2,2:29.8:1:30.2:1:0.29333:1.26:53.8:55.5:0.1975:0:5.7 -6 31324599 . T G 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56453;SOR=1.2037;LSEQ=CTATCCACGGCGCCCGCGGC;RSEQ=CCTCTCTCGGACTCGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:27:15,12:344,384:0.0357:2,2:38.2:1:29.3:1:0.43665:1.39:42.8:8:0.0327:0:6.9 0/1:563:24:16,8:250,288:0.0426:2,2:39.4:1:30.5:1:0.06097:2.30:46.1:48:0.0436:0:6.9 -6 31324602 . TCT GTC 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0;SOR=0.43983;LSEQ=TCCACGGCGCCCGCGGCTCC;RSEQ=CTCGGACTCGCGGCGTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:712:205:93,112:217,251:0.2879:2,2:30.3:1:30.7:1:0.8666:1.04112:59.3:410:0.295:0:3.4 0/1:550:83:40,43:201,240:0.1509:2,2:29:1:30.2:1:0.71911:1.11:55.5:166:0.1537:0.0127:3.6 -6 31324603 . CT TC 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=2.29512;LSEQ=CCACGGCGCCCGCGGCTCCT;RSEQ=CTCGGACTCGCGGCGTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:763:62:28,34:217,251:0.0813:2,2:12.3:1:29.3:1:0.89283:1.04972:57.5:61:0.1166:0.076:1.7 0/1:539:91:44,47:158,188:0.1688:2,2:28:1:30:1:0.72316:1.11:41.8:90:0.2088:0:5.4 -6 31324615 . C T 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.54314;LSEQ=CGGCTCCTCTCTCGGACTCG;RSEQ=GGCGTCGCTGTCGAACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:26:11,15:310,392:0.0357:2,2:23.4:1:28.5:1:1:1.0783:41.9:25:0.0351:0:4.5 0/1:528:103:48,55:197,227:0.1951:2,2:23.8:1:29.4:1:1:1.01:42.6:50.5:0.1957:0:5.6 -6 31324641 . T A 196 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCTGTCGAACCTCACGAAC;RSEQ=GGGTGTCGTCCACGTAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:259,343:0:2,0:24.7:1:30.3:1:1:0:56.2:49.167:1:0:2.2 0/1:410:90:38,52:151,169:0.2195:2,2:25.9:1:30.2:1:0.47285:1.22207:44.1:44:0.2195:0:5.3 -6 31324643 . G C 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0032;SOR=1.4865;LSEQ=CTGTCGAACCTCACGAACTG;RSEQ=GTGTCGTCCACGTAGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:194:72,122:189,218:0.3228:2,2:26.5:1:30:1:0.03469:1.46809:51.7:31.333:0.3203:0:2.4 0/1:405:168:71,97:114,120:0.4148:2,2:25.2:1:30.4:1:0.22377:1.29703:49.3:27:0.4112:0:3.5 -6 31324647 . T C 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.00072;SOR=Inf;LSEQ=CGAACCTCACGAACTGGGTG;RSEQ=CGTCCACGTAGCCCACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:252,347:0:2,0:24.7:1:29.4:1:1:0:55.3:30.526:1:0:2.3 0/1:411:8:5,3:181,222:0.0195:2,2:17.6:1:32:1:0.47666:2.04:59.6:16:0.0197:0:2.8 -6 31324664 . T G 190 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.51624;LSEQ=GTGTCGTCCACGTAGCCCAC;RSEQ=GAGATGAAGCGGGGCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:600:27:6,21:243,330:0.045:2,2:30.2:1:31.3:1:0.04496:2.57363:44.2:54:0.0463:0:4.2 0/1:374:88:37,51:128,158:0.2353:2,2:27.4:1:29.5:1:0.71316:1.11633:40.7:28.333:0.2329:0:5.4 -6 31324666 . A C 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11878;LSEQ=GTCGTCCACGTAGCCCACTG;RSEQ=GATGAAGCGGGGCTCCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:600:429:181,248:54,87:0.715:2,2:24.3:1:30.5:1:0.43173:1.18:50.4:52.625:0.7172:0:3.1 0/1:371:85:45,40:78,117:0.2291:2,2:24.6:1:30.4:1:0.0501:1.68:53.6:84:0.2308:0:3.5 -6 31324674 . C T 69 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.03278;SOR=8.17245;LSEQ=CGTAGCCCACTGAGATGAAG;RSEQ=GGGGCTCCCCGCGGCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:612:1:0,1:251,360:0.0016:2,0:1:0:25:0:1:0:60:2:0.0017:0:2 0/1:378:5:2,3:166,207:0.0132:2,2:20.6:1:30:1:1:1.20232:48:10:0.0136:0:4 -6 31324682 . C T 97 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.77232;SOR=0.75835;LSEQ=ACTGAGATGAAGCGGGGCTC;RSEQ=CCGCGGCCGGGCCGGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:8:7,1:265,340:0.0131:2,2:18.9:1:32.4:1:0.02485:8.95:33.8:16:0.0134:0:6.9 0/0:403:4:4,0:177,222:0.0099:2,0:23.8:1:28.8:1:0.03995:0:31.8:3:0.0077:0:8 -6 31324687 . G T 84 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09973;SOR=3.5157;LSEQ=GATGAAGCGGGGCTCCCCGC;RSEQ=GCCGGGCCGGGACACGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:620:3:2,1:280,337:0.0048:2,2:26.7:1:32.3:1:0.5937:2.40:36.3:6:0.0049:0:8 0/1:416:7:5,2:182,227:0.0168:2,2:17.3:1:30:1:0.25117:3.11:33.4:14:0.0169:0:7.4 -6 31324691 . G A 113 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05378;SOR=0.23824;LSEQ=AAGCGGGGCTCCCCGCGGCC;RSEQ=GGCCGGGACACGGAGGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:12:6,6:280,334:0.0192:2,2:14.9:1:31.6:1:0.77827:1.19:36.9:24:0.0194:0:5.6 0/0:432:2:1,1:190,240:0.0046:2,2:26.5:1:28.5:1:1:1.26:41.5:4:0.0047:0:4.5 -6 31324702 . C T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21596;LSEQ=CCCGCGGCCGGGCCGGGACA;RSEQ=GGAGGTGTAGAAATACCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:602:435:198,237:75,91:0.7226:2,2:27.2:1:30.3:1:1:1.01:45.4:61.143:0.723:0:3.7 0/1:431:155:70,85:123,152:0.3596:2,2:25.2:1:29.4:1:1:1.02:45.4:310:0.3656:0:4 -6 31324705 . A C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32964;LSEQ=GCGGCCGGGCCGGGACACGG;RSEQ=GGTGTAGAAATACCTCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:597:425:197,228:76,95:0.7119:2,2:27.7:1:30.8:1:0.71644:1.08:45.3:140.667:0.7128:0:3.7 0/1:428:192:86,106:105,131:0.4486:2,2:24.4:1:30.1:1:1:1.01:46.3:63:0.45:0:3.7 -6 31324706 . G T 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.87521;SOR=0.92698;LSEQ=CGGCCGGGCCGGGACACGGA;RSEQ=GTGTAGAAATACCTCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:26:11,15:274,319:0.0419:2,2:25.2:1:29.9:1:0.84121:1.17098:35.3:52:0.0425:0:6.2 0/1:436:17:8,9:186,233:0.039:2,2:22.7:1:27.2:1:1:1.11:37.5:16:0.0372:0:6.1 -6 31324710 . T G 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13796;SOR=1.77458;LSEQ=CGGGCCGGGACACGGAGGTG;RSEQ=AGAAATACCTCATGGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:14:5,9:284,324:0.0221:2,2:25.7:1:30.6:1:0.58954:1.57665:36.1:28:0.0223:0:6.5 0/1:441:17:8,9:186,238:0.0385:2,2:25.6:1:30.2:1:0.80816:1.14:36.4:34:0.0392:0:6.4 -6 31324711 . A G 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCGGGACACGGAGGTGT;RSEQ=GAAATACCTCATGGAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:0:0,0:295,338:0:2,0:26.2:1:29.6:1:1:0:48.3:78.125:1:0:2.9 0/1:439:62:24,38:159,198:0.1412:2,2:27.4:1:30.6:1:0.40915:1.27074:49.5:124:0.1429:0:3.2 -6 31324719 . C T 109 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00106;SOR=0;LSEQ=ACACGGAGGTGTAGAAATAC;RSEQ=TCATGGAGTGGGAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:13:7,6:280,326:0.021:2,2:34.3:1:29.5:1:0.58986:1.36:36.2:12:0.0197:0:5.7 0/0:443:0:0,0:195,248:0:2,0:25.5:1:31:1:1:0:51.5:146.667:1:0:2.4 -6 31324738 . G A 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14022;SOR=1.77199;LSEQ=CCTCATGGAGTGGGAGCCTG;RSEQ=GGGTGAGGAGGGGCTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:15:6,9:262,320:0.0251:2,2:37.8:1:30.3:1:0.79634:1.22771:37.7:30:0.0255:0:6.1 0/1:389:17:8,9:157,215:0.0437:2,2:34.2:1:29.7:1:0.80316:1.22:36.4:34:0.044:0:6.4 -6 31324741 . GTG CA 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CATGGAGTGGGAGCCTGGGG;RSEQ=AGGAGGGGCTGAGACCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:271,330:0:2,0:26.4:1:31.3:1:1:0:48.2:74.125:0.9983:0:2.8 0/1:403:10:3,7:166,227:0.0248:2,2:32.5:1:30.4:1:0.53022:1.70418:48.3:20:0.025:0.0025:1.8 -6 31324742 . T C 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03462;SOR=0.73381;LSEQ=ATGGAGTGGGAGCCTGGGGG;RSEQ=GAGGAGGGGCTGAGACCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:575:417:187,230:60,73:0.7252:2,2:26.9:1:30:1:1:1.0109:44.9:26.8:0.7217:0:3.5 1/0:367:242:101,141:42,59:0.6594:2,2:27.6:1:30.2:1:1:1.01:48.7:79.667:0.662:0:3.1 -6 31324749 . G T 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGCCTGGGGGTGAGGAG;RSEQ=GGCTGAGACCCGCCCGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:246,307:0:2,0:26.1:1:30.9:1:1:0:49.1:60.444:1:0:2.7 0/1:366:17:7,10:149,199:0.0464:2,2:26.4:1:28.3:1:1:1.06945:51.5:7.5:0.042:0:2.9 -6 31324752 . C T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16855;SOR=1.78471;LSEQ=AGCCTGGGGGTGAGGAGGGG;RSEQ=TGAGACCCGCCCGACCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:547:13:4,9:240,293:0.0238:2,2:29.7:1:30.5:1:0.40196:1.84105:37.3:26:0.0244:0:6.4 0/1:360:15:6,9:149,196:0.0417:2,2:25.7:1:30:1:1:1.13987:38.4:30:0.0425:0:6.2 -6 31324756 . G A 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGGGGGTGAGGAGGGGCTGA;RSEQ=ACCCGCCCGACCCTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:0:0,0:243,299:0:2,0:25:1:31.2:1:1:0:50.3:30.882:1:0:2.7 0/1:352:31:16,15:137,184:0.0881:2,2:31.7:1:29.8:1:0.34948:1.43:53.9:62:0.0896:0:2.7 -6 31324764 . C A 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.23992;LSEQ=AGGAGGGGCTGAGACCCGCC;RSEQ=GACCCTCCTCCCGGCGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:144:59,85:174,202:0.2764:2,2:23.2:1:30.8:1:0.28064:1.24046:44.9:143:0.2793:0:4.4 0/1:334:28:14,14:134,172:0.0838:2,2:25.8:1:30.9:1:0.5558:1.28:47.1:56:0.0846:0:4.5 -6 31324776 . C A 96 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00125;SOR=14.49485;LSEQ=GACCCGCCCGACCCTCCTCC;RSEQ=GGCGCGGCTCCTCAGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:1:1,0:205,262:0.0021:2,0:14:0:31:0:0.44017:0:60:2:0.0022:0:6 0/1:300:9:2,7:138,153:0.03:2,2:6.7:1:30.6:1:0.18192:3.1459:50.8:18:0.0305:0:3.1 -6 31324777 . G T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.305;SOR=0.5819;LSEQ=ACCCGCCCGACCCTCCTCCC;RSEQ=GCGCGGCTCCTCAGGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:19:5,14:204,249:0.0403:2,2:6.3:1:30.4:1:0.15605:2.2902:36.4:38:0.0409:0:6 0/1:294:7:1,6:137,150:0.0238:2,2:10.3:1:30.7:1:0.12546:5.45469:35.9:14:0.0241:0:6.6 -6 31324788 . T C 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03064;SOR=1.4512;LSEQ=CCTCCTCCCGGCGCGGCTCC;RSEQ=CAGGTCCTGCGCCCCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:118:59,59:133,164:0.2843:2,2:26.5:1:30.8:1:0.38279:1.23:51.3:58:0.2864:0:4.6 0/1:246:90:48,42:76,79:0.3659:2,2:29.6:1:30.6:1:0.59617:1.19:51.8:89:0.3693:0:4.7 -6 31324790 . A G 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04646;SOR=1.41401;LSEQ=TCCTCCCGGCGCGGCTCCTC;RSEQ=GGTCCTGCGCCCCCGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:119:59,60:133,164:0.2861:2,2:26.5:1:30.1:1:0.38596:1.21:51.6:58.5:0.2875:0:4.5 0/1:246:89:50,39:77,78:0.3618:2,2:29.4:1:30.1:1:0.35333:1.30:52.4:178:0.3663:0:4.6 -6 31324819 . C T 56 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02186;SOR=Inf;LSEQ=GCCCCCGCCTGCGGTCCCCT;RSEQ=GCTCCTCCCGGCAGAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:208,201:0:2,0:24.6:1:30.4:1:1:0:57.5:50.125:1:0:2.7 0/1:257:4:2,2:148,104:0.0156:2,2:25:1:28:1:1:1.42105:60:8:0.0157:0:6.5 -6 31324820 . G T 145 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCCGCCTGCGGTCCCCTC;RSEQ=CTCCTCCCGGCAGAGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:214,193:0:2,0:24.8:1:30.6:1:1:0:57.3:39.7:1:0:2.7 0/1:252:30:17,13:134,88:0.119:2,2:25.4:1:29.7:1:0.6965:1.16372:53.3:14:0.1124:0:5.2 -6 31324829 . GG CA 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26309;LSEQ=GCGGTCCCCTCGCTCCTCCC;RSEQ=CAGAGGCCATTTCCCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:428:334:174,160:45,35:0.7804:2,2:25:1:30.8:1:0.5346:1.18179:54.8:333:0.7986:0.0771:2.8 0/1:259:125:78,47:73,50:0.4826:2,2:24.8:1:30.4:1:0.69647:1.14:54.6:250:0.4941:0.0077:3.6 -6 31324830 . G A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34018;SOR=0.58191;LSEQ=CGGTCCCCTCGCTCCTCCCG;RSEQ=CAGAGGCCATTTCCCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:13:10,3:46,37:0.0327:2,2:16.8:1:24.9:1:0.22638:2.66:49.5:2.25:0.1011:0:5.2 0/1:259:5:3,2:75,51:0.0193:2,2:18.4:1:27.2:1:1:1.02:53.8:4:0.0317:0:5.6 -6 31324847 . C G 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=7.19952;LSEQ=CCGGCAGAGGCCATTTCCCT;RSEQ=CCGACCCGCACTCACCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:14:10,4:254,180:0.0313:2,2:26.6:1:29.6:1:0.41549:1.77:55.1:6:0.0276:0:4.3 0/1:323:61:36,25:159,102:0.1889:2,2:25:1:31.3:1:0.77351:1.08225:55.6:60:0.1881:0:4.1 -6 31324851 . A AC 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18266;SOR=0.81758;LSEQ=CAGAGGCCATTTCCCTCCCG;RSEQ=CCCGCACTCACCGGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:176:104,72:140,101:0.3929:2,2:27:1:31.7:1:0.84133:1.04:51.9:87:0.4047:0.0268:3.9 0/1:344:119:82,37:109,88:0.3459:2,2:24:1:30.6:1:0.0179:1.79:49.3:58.5:0.3441:0.0727:5.3 -6 31324864 . G A 140 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCCCGACCCGCACTCACC;RSEQ=GCCCAGGTCTCGGTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:0:0,0:325,230:0:2,0:22.5:1:29.9:1:1:0:53.2:60.667:1:0:3.9 0/1:408:28:15,13:216,163:0.0686:2,2:19.7:1:29.2:1:0.84373:1.14807:54.9:27:0.0685:0:5.1 -6 31324884 . CCAGGGCCGCCG TCACTGCCCCCC 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCCAGGTCTCGGTCAGGG;RSEQ=AGAGCAGCAGGAGGACGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:0:0,0:364,278:0:2,0:24.3:1:31.4:1:1:0:54:57.364:1:0:4.4 0/1:596:62:27,35:289,240:0.104:2,2:10.8:1:28.6:1:0.10728:1.55975:58.6:61:0.1052:0.104:3.8 -6 31324887 . GG CT 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.50024;LSEQ=CCAGGTCTCGGTCAGGGCCA;RSEQ=GCCGCCGAGAGCAGCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:637:300:178,122:183,151:0.471:2,2:26:1:31.1:1:0.26142:1.20:52.7:600:0.4754:0.0487:5.3 0/1:526:162:95,67:185,171:0.308:2,2:27:1:30.8:1:0.18308:1.31:49.8:324:0.3109:0:6.3 -6 31324891 . CG TC 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00062;SOR=2.28291;LSEQ=GTCTCGGTCAGGGCCAGGGC;RSEQ=CCGAGAGCAGCAGGAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:616:27:15,12:334,254:0.0438:2,2:27.8:1:30.9:1:1:1.05185:53.4:54:0.0444:0.0032:3.7 0/1:538:51:27,24:262,223:0.0948:2,2:28.4:1:29.9:1:0.88387:1.04428:53.9:102:0.0966:0:4.2 -6 31324892 . G C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21007;LSEQ=TCTCGGTCAGGGCCAGGGCC;RSEQ=CCGAGAGCAGCAGGAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:610:424:244,180:86,72:0.6951:2,2:27.6:1:30.6:1:0.51147:1.13:51.4:41.4:0.725:0:5.7 0/1:541:175:104,71:161,153:0.3235:2,2:27.3:1:30:1:0.08888:1.39:50.4:57.333:0.3561:0:6.3 -6 31324895 . G C 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21063;LSEQ=CGGTCAGGGCCAGGGCCGCC;RSEQ=AGAGCAGCAGGAGGACGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:631:440:255,185:104,85:0.6973:2,2:27.5:1:31:1:0.5387:1.13:51.7:35.667:0.6937:0:5.7 0/1:576:188:105,83:202,186:0.3264:2,2:26.5:1:30.3:1:0.4232:1.16:51.1:93:0.3257:0:6.3 -6 31324911 . C G 249 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61859;SOR=0.94415;LSEQ=CGCCGAGAGCAGCAGGAGGA;RSEQ=GGTTCGGGGCGCCATGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:249:135,114:281,264:0.3136:2,2:26.3:1:31.4:1:0.49183:1.11:52.1:82:0.315:0:6.1 0/1:740:223:112,111:263,254:0.3014:2,2:24.5:1:30.4:1:0.8731:1.02616:54.2:54.75:0.2984:0:5.7 -6 31324921 . C T 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18154;LSEQ=AGCAGGAGGACGGTTCGGGG;RSEQ=GCCATGACCAGCATCTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:139:64,75:330,320:0.1759:2,2:26.4:1:29.7:1:0.35014:1.2082:51.5:45.333:0.1757:0:6.4 0/1:751:28:16,12:354,368:0.0373:2,2:27.7:1:29.8:1:0.44474:1.39:59.8:56:0.038:0:4.4 -6 31324925 . A G 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35997;LSEQ=GGAGGACGGTTCGGGGCGCC;RSEQ=TGACCAGCATCTCGGCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:784:596:285,311:93,94:0.7602:2,2:27.1:1:30.7:1:0.67534:1.07951:56.2:73.5:0.7597:0:5.3 1/0:747:398:195,203:169,180:0.5328:2,2:28.3:1:30:1:0.88361:1.02:56.3:55.857:0.5305:0:5.2 -6 31324931 . A C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34633;LSEQ=CGGTTCGGGGCGCCATGACC;RSEQ=GCATCTCGGCGTCTGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:786:603:272,331:90,93:0.7672:2,2:27.1:1:30:1:0.35222:1.17741:57.1:59.3:0.7681:0:5.3 1/0:747:398:190,208:164,180:0.5328:2,2:28.8:1:29.5:1:1:1.00:56.8:48.75:0.5342:0:5.2 -6 31324938 . C T 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCGCCATGACCAGCATCT;RSEQ=GGCGTCTGAGGAGACTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:760:0:0,0:331,429:0:2,0:27.4:1:30.2:1:1:0:58.5:107.571:1:0:4.1 0/1:730:60:26,34:310,359:0.0822:2,2:25.3:1:30.7:1:0.68691:1.12902:60:120:0.083:0:1.4 -6 31324941 . C T 209 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02012;LSEQ=CGCCATGACCAGCATCTCGG;RSEQ=GTCTGAGGAGACTCTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:750:130:51,79:268,350:0.1733:2,2:26.9:1:29.8:1:0.4353:1.18584:55.5:260:0.1754:0:6.3 0/0:716:3:0,3:326,387:0.0042:2,0:17.7:1:31:1:0.25495:0:53.3:6:0.0042:0:3 -6 31324953 . C T 261 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.26649;SOR=0.87991;LSEQ=CATCTCGGCGTCTGAGGAGA;RSEQ=TCTGAGTCCGGGTGGGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:684:417:165,252:101,165:0.6096:2,2:26.7:1:30:1:0.6882:1.07:59.8:58.571:0.6119:0:5 1/0:660:382:160,222:124,154:0.5788:2,2:26.2:1:29.8:1:0.5243:1.11702:58.7:381:0.5817:0:5.2 -6 31324955 . C T 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04687;SOR=1.82114;LSEQ=TCTCGGCGTCTGAGGAGACT;RSEQ=TGAGTCCGGGTGGGTGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:661:19:6,13:250,391:0.0287:2,2:24.1:1:30.7:1:0.63576:1.38468:59.5:38:0.0291:0:5.5 0/1:645:33:12,21:266,345:0.0512:2,2:26.5:1:30:1:0.47365:1.34866:60:66:0.0516:0:4.7 -6 31324996 . G C 249 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77205;SOR=1.05932;LSEQ=GGGACTTTAGAACTGGGACC;RSEQ=CGGCGACGCTGATTGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:351:275:50,225:17,56:0.7835:2,2:22.7:1:30.8:1:0.32086:1.36478:59.4:29.556:0.7824:0:5.1 1/0:290:230:64,166:14,38:0.7931:2,2:22.5:1:29.8:1:1:1.05:58.9:31.857:0.788:0:4.8 -6 31325004 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36986;LSEQ=AGAACTGGGACCGCGGCGAC;RSEQ=CTGATTGGCTTCTCTAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:294:233:34,199:11,50:0.7925:2,2:23.2:1:30.1:1:0.54942:1.28648:59.2:232:0.7918:0:5.3 1/0:241:141:34,107:22,78:0.5851:2,2:23.5:1:29.7:1:0.75815:1.13:57.7:140:0.5907:0:6.1 -6 31325023 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.07113;LSEQ=CGCTGATTGGCTTCTCTAGA;RSEQ=ATCCAATACCCAATGGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:52:4,48:17,125:0.268:2,2:30.3:1:32.3:1:0.60195:1.62826:56.3:104:0.2737:0:7.1 1/0:149:79:15,64:6,63:0.5302:2,2:31.5:1:32.2:1:0.09837:2.45:55.6:158:0.5302:0:7.1 -6 31325025 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.20295;LSEQ=CTGATTGGCTTCTCTAGATA;RSEQ=CCAATACCCAATGGGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:47:4,43:16,119:0.2582:2,2:33:1:30.6:1:0.78672:1.44267:55.9:14.667:0.2472:0:7.1 1/0:142:75:13,62:6,61:0.5282:2,2:32.5:1:31.5:1:0.21645:2.12:55.3:74:0.5401:0:7.1 -6 31325028 . A G 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00622;SOR=2.33784;LSEQ=ATTGGCTTCTCTAGATATCC;RSEQ=ATACCCAATGGGAGTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:122:14,108:3,41:0.7349:2,2:28.4:1:31:1:0.56354:1.77:58.4:39.667:0.7346:0:6 1/1:135:117:15,102:2,16:0.8667:2,2:29.3:1:31.2:1:1:1.18:57:38:0.8636:0:6.1 -6 31325030 . T C 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01814;SOR=2.08993;LSEQ=TGGCTTCTCTAGATATCCAA;RSEQ=ACCCAATGGGAGTGGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:160:121:14,107:3,36:0.7563:2,2:27.9:1:31.8:1:0.7653:1.57:58.4:23.2:0.7532:0:6 1/1:135:117:14,103:2,16:0.8667:2,2:28.4:1:31.8:1:1:1.09:57:22.4:0.8615:0:6.1 -6 31325049 . G A 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42527;SOR=0.79353;LSEQ=ATACCCAATGGGAGTGGGAA;RSEQ=TGGGGACGCGTCACGAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:142:90:10,80:3,29:0.6338:2,2:23.8:1:30.7:1:1:1.21:59.2:44:0.6377:0:5.7 1/0:102:59:12,47:0,27:0.5784:1,2:22.2:1:29.9:1:0.01503:0:57.9:58:0.5743:0:6.7 -6 31325090 . C T 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62434;SOR=0.77975;LSEQ=CCTGGAAGAAGGACCCGACA;RSEQ=AAGTTGGGAGAAGAAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:52:5,47:0,13:0.8:1,2:25.9:1:28.5:1:0.57391:0:58.1:104:0.8:0:5.9 1/0:37:28:7,21:0,9:0.7568:0,2:24.9:1:28.6:1:0.15996:0:54.9:56:0.7568:0:5.9 -6 31325092 . A G 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGAAGAAGGACCCGACACA;RSEQ=GTTGGGAGAAGAAGTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:52:5,47:0,13:0.8:1,2:25.1:1:31.3:1:0.57391:0:58.1:104:0.8:0:5.9 1/1:35:28:7,21:0,7:0.8:0,2:25.3:1:30.7:1:0.30091:0:55.5:56:0.8:0:5.8 -6 31325115 . AG GT 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24449;SOR=0.49118;LSEQ=TGGGAGAAGAAGTGAAACTC;RSEQ=GGGAGTGGGGAATCCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:35:2,33:0,8:0.814:0,2:24.6:1:31.4:1:1:0:58:70:0.814:0.093:4.7 1/0:25:17:1,16:0,6:0.68:0,1:24.8:1:29.2:1:1:0:58.6:34:0.7083:0.04:3.9 -6 31325151 . T A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00656;SOR=0.1226;LSEQ=CCCAACGCTGCGCCTCCCCA;RSEQ=TGCAGACGCGGCCCTCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:1,24:0,4:0.8621:0,1:20.9:1:30.5:1:1:0:50.9:24:0.8571:0:5 0/1:12:5:0,5:0,7:0.4167:0,0:5.2:1:29.6:1:1:0:60:10:0.4167:0:4 -6 31325159 . GC AA 127 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=0;LSEQ=TGCGCCTCCCCATTGCAGAC;RSEQ=GGCCCTCGGAGCCTGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:17:0,17:1,6:0.7083:2,1:21.1:1:31.2:1:0.29167:0:49.2:34:0.7083:0.1667:5.2 0/0:9:0:0,0:0,8:0:0,0:25:1:31.6:1:1:0:60:16:0.8889:0:0.9 -6 31325164 . C T 108 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00248;SOR=0;LSEQ=CTCCCCATTGCAGACGCGGC;RSEQ=CTCGGAGCCTGAGACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:13:0,13:1,6:0.65:2,1:24.8:1:29.2:1:0.35:0:47.8:12:0.6316:0:5.2 0/0:8:0:0,0:0,8:0:0,0:24.1:1:30.3:1:1:0:60:16:1:0:0.9 -6 31325193 . T C 74 MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35116;SOR=0.27199;LSEQ=CTGAGACCCTGAGAGCCCCG;RSEQ=CCGGGACCTGGGACTTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:0.3571:0,0:31.4:1:32.2:1:1:0:37.4:10:0.3571:0:5 0/1:8:1:0,1:1,6:0.125:2,0:18:0:31:0:1:0:60:2:0.125:0:3 -6 31325199 . A G 77 MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61262;SOR=0.31603;LSEQ=CCCTGAGAGCCCCGTCCGGG;RSEQ=CCTGGGACTTCGTCCTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:0.3571:0,0:25.4:1:33.4:1:1:0:37.4:10:0.3571:0:5 0/1:7:1:0,1:1,5:0.1429:2,0:12:0:34:0:1:0:60:2:0.1429:0:3 -6 31325201 . C A 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1235;SOR=0;LSEQ=CTGAGAGCCCCGTCCGGGAC;RSEQ=TGGGACTTCGTCCTGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:0.3571:0,0:18.2:1:32:1:1:0:51:10:0.3571:0:2.4 0/0:7:0:0,0:1,6:0:2,0:30.6:1:31.6:1:1:0:60:14:1:0:0.6 -6 31325235 . CA C 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.5286;LSEQ=TGATCCCTCTTCTCCTACAC;RSEQ=AGCCTCTTTGTCACACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:19.8:1:31.2:1:1:0:42.8:12:0.75:0.25:2.2 1/0:5:3:0,3:1,1:0.6:2,0:21.7:1:33.3:1:0.4:0:60:6:0.6:0:0 -6 31325270 . G C 52 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGTCTGCCTGAGTCCTG;RSEQ=ACAAGGATCTGTCTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:35.7:1:33.3:1:1:0:47.3:6:0.5:0:1.3 0/0:1:0:0,0:0,1:0:0,0:21:0:26:0:1:0:60:2:1:0:1 -6 31325403 . AC A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTCCTTACCTCTCCTCTTGG;RSEQ=TCTTGTGTAGGGAAACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31.5:1:29.5:1:1:0:56:4:1:0:6 0/0:1:0:0,0:0,1:0:0,0:25:0:34:0:1:0:60:2:1:0:0 -6 31326099 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCCTGCTCCTTTTCCTC;RSEQ=CCTCCTGCCTCTCCAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:1:31:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31326131 . C T 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCAGCCCTTCTGTCTGCCC;RSEQ=TCTCATCCCTCACACCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:0:29.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31326140 . C T 29 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCTGCCCCTCTCATCC;RSEQ=TCACACCCCCGCTCCCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:29:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31345229 . G A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTTGTATGGCTGTGGCT;RSEQ=TTCAGCCCCTACTTCTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:32.5:1:27.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31345237 . C G 49 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCTGTGGCTGTTCAGCC;RSEQ=CTACTTCTGATCCCCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:22:1:24.5:1:1:0:60:3:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31345270 . C T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTAGGACTGGGAGCAGCC;RSEQ=GCCTGGGGGAGACCATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:29:1:30.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31345441 . TGG T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00548;SOR=0.03659;LSEQ=GTCTGGCAGGACCCAGGCTC;RSEQ=GAGCTGATCCTCCCTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:0.8889:0,0:27.8:1:32.1:1:1:0:60:16:0.8889:0:0.6 0/1:11:2:2,0:9,0:0.1818:0,0:28:1:32.4:1:1:0:60:4:0.1818:0.0909:1 -6 31345484 . G A 111 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00023;SOR=0.04088;LSEQ=AAGGCCTGCTGCAGCCTCCC;RSEQ=CTGAGGTCTTGAAACCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:12,0:10,0:0.5455:0,0:21.8:1:31.2:1:1:0:60:24:0.5455:0:1 0/1:23:1:1,0:22,0:0.0435:1,0:41:0:29:0:1:0:60:2:0.0455:0:1 -6 31345486 . T A 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70078;SOR=1.81893;LSEQ=GGCCTGCTGCAGCCTCCCGC;RSEQ=GAGGTCTTGAAACCATCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:21,0:0.125:1,0:20.3:1:31.3:1:1:0:60:6:0.125:0:1 0/1:24:5:5,0:19,0:0.2083:1,0:24.4:1:31:1:1:0:60:10:0.2083:0:1.2 -6 31345513 . T G 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=TTGAAACCATCAGGAGCAGT;RSEQ=GTTCTTTGGCCTCCGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:40,13:0:2,0:20.9:1:29.8:1:1:0:60:25.5:1:0:0.3 0/1:46:11:10,1:25,9:0.2391:2,2:20.2:1:32.7:1:0.40874:3.52:60:22:0.2444:0:2.7 -6 31345523 . C T 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CAGGAGCAGTTGTTCTTTGG;RSEQ=CTCCGGGACACCGCAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:48,21:0:2,0:22.6:1:31.9:1:1:0:60:138:1:0:0.3 0/1:52:11:9,2:27,14:0.2115:2,2:25.1:1:30.8:1:0.46794:2.30:60:22:0.22:0:2.8 -6 31345535 . C T 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTTGGCCTCCGGGACAC;RSEQ=GCAGGGCTGAGTTGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:61,30:0:2,0:24.8:1:30.5:1:1:0:60:90:1:0:0.3 0/1:64:16:9,7:31,17:0.25:2,2:24.4:1:29.7:1:0.56532:1.41035:60:32:0.254:0:2.2 -6 31345596 . G A 148 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00066;SOR=0.2309;LSEQ=GGCCCACTGTCTGGGTCAAG;RSEQ=ATGGTGCAGAGCTGGTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:33:19,14:70,64:0.1976:2,2:28.9:1:29.4:1:0.69757:1.24:60:32:0.1951:0:1.1 0/1:112:6:3,3:50,56:0.0536:2,2:30.3:1:25.8:1:1:1.12:60:5:0.045:0:1 -6 31345602 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15609;SOR=Inf;LSEQ=CTGTCTGGGTCAAGGATGGT;RSEQ=CAGAGCTGGTGTCCTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:87,73:0:2,0:27.7:1:32.1:1:1:0:60:159:1:0:0.3 0/1:105:2:1,1:45,58:0.019:2,2:30:1:29:1:1:1.29:60:4:0.0194:0:1 -6 31345640 . C G 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGCATCCTGGTGGAGCC;RSEQ=CAGCAGCTGCAGGTGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:43,60:0:2,0:22.6:1:30.5:1:1:0:60:50.5:1:0:0.3 0/1:61:13:5,8:14,34:0.2131:2,2:23.2:1:31.1:1:0.51965:1.51:60:26:0.2167:0:1.1 -6 31345728 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13277;SOR=Inf;LSEQ=AGCATGAGCGGTGCCACTCA;RSEQ=TGTGCACATGACAGATGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:5,29:0:2,0:27.4:1:31.6:1:1:0:59.9:33:1:0:0.3 0/1:20:2:0,2:5,13:0.1:2,0:22.5:1:30:0:1:0:60:4:0.1:0:1.5 -6 31345771 . C CG 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.01485;SOR=4.65572;LSEQ=TCCTCAGGAGATGACAAAGA;RSEQ=GGGAGGACAAGGTGAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:4,4:4,23:0.2286:2,2:30.3:1:29.8:1:0.05958:5.39:60:16:0.2286:0.0286:0.1 1/0:17:10:4,6:3,4:0.5882:2,2:28:1:31.1:1:1:1.11721:60:20:0.625:0:0.2 -6 31345772 . G GT 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03872;SOR=0.24988;LSEQ=CCTCAGGAGATGACAAAGAC;RSEQ=GGAGGACAAGGTGAAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:19:4,15:4,11:0.5588:2,2:25.4:1:29.7:1:1:1.3511:59.7:38:0.5938:0.0882:1.4 0/1:17:4:2,2:5,8:0.2353:2,2:33.8:1:27.5:1:1:1.56:60:8:0.25:0:1.8 -6 31345783 . G GC 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20924;SOR=0.36337;LSEQ=GACAAAGACGGGAGGACAAG;RSEQ=TGAAGACACAGGTGCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:4,11:4,12:0.4839:2,2:27.8:1:32.2:1:1:1.09:60:30:0.4839:0.0968:1.7 0/1:16:4:2,2:5,7:0.25:2,2:33.8:1:31.8:1:1:1.37:60:8:0.25:0:1.8 -6 31345794 . G A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20644;SOR=0.39767;LSEQ=GAGGACAAGGTGAAGACACA;RSEQ=GTGCATCATCTCCTACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:2,10:4,10:0.4615:2,2:29.3:1:31.6:1:0.65217:1.94818:60:24:0.48:0:2 0/1:16:4:2,2:5,7:0.25:2,2:28.8:1:30.3:1:1:1.37:60:8:0.25:0:1.8 -6 31345801 . C A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48753;SOR=0.54293;LSEQ=AGGTGAAGACACAGGTGCAT;RSEQ=ATCTCCTACTCACCTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:2,8:4,8:0.4545:2,2:28.9:1:30.5:1:0.64617:1.93862:60:20:0.4545:0:2.2 0/1:13:4:1,3:4,5:0.3077:2,2:24.3:1:29:1:1:2.24915:60:8:0.3077:0:2 -6 31349805 . C A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTGAAGTCACAAAGGGG;RSEQ=GGCATGAAGAAATCCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,0:0.6:0,0:12.3:1:31:0:1:0:60:6:0.75:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31349819 . C A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=AAGGGGCGGCATGAAGAAAT;RSEQ=CTGCATCTCAGTCCCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:22.8:1:28.4:1:1:0:59.4:10:0.8333:0:2.6 0/0:3:0:0,0:2,1:0:2,0:6:1:32:1:1:0:60:6:1:0:0 -6 31349922 . C T 57 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23944;SOR=2.47577;LSEQ=AGCGTAACACTCTGAACTCC;RSEQ=CACTACACACTCAAAGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:4:4,0:68,2:0.0541:1,0:7.5:1:31.5:1:1:0:60:8:0.0548:0:1.3 0/1:32:4:3,1:27,1:0.125:1,2:15:1:28.8:1:0.2379:7.93681:60:8:0.125:0:1 -6 31349980 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1465;SOR=Inf;LSEQ=TCCAGTCTTGTCCCCTGTAC;RSEQ=CCATCCCCCTTCCACATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:169,35:0:2,0:22:1:30.8:1:1:0:60:50:1:0:0.2 0/1:127:2:1,1:99,26:0.0157:2,2:13:1:29.5:1:0.38133:3.75541:60:4:0.0161:0:1 -6 31349993 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18794;SOR=Inf;LSEQ=CCTGTACCCCATCCCCCTTC;RSEQ=ACATAAGGCCCTCCAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:186,59:0:2,0:23.4:1:31:1:1:0:60:80.667:1:0:0.2 0/1:188:2:1,1:131,55:0.0106:2,2:27:1:28:1:0.50814:2.36947:60:4:0.011:0:1 -6 31350090 . C T 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.46554;LSEQ=GGTAGAACAAAAACAGGACC;RSEQ=GGTCAGAGCCTGCAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:366:295:107,188:25,45:0.806:2,2:26.2:1:30.3:1:1:1.02:60:72.75:0.8039:0:1.1 1/0:302:199:78,121:40,63:0.6589:2,2:25.9:1:29.9:1:1:1.02:59.9:65.333:0.6577:0:1.2 -6 31350114 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07085;SOR=Inf;LSEQ=CAGAGCCTGCAGGAGATGTG;RSEQ=GAGAGGAGGAATTATGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:69,186:0:2,0:23.6:1:30.8:1:1:0:60:126.5:1:0:0.8 0/1:181:3:1,2:52,126:0.0166:2,2:6:1:30.7:1:1:1.21:60:6:0.0168:0:1.3 -6 31350154 . C T 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TAGGTGAGCTCCTCCACATC;RSEQ=GTCTCCCATAGTTACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:11,103:0:2,0:23.8:1:30:1:1:0:60:56:1:0:0.5 0/1:70:10:1,9:4,56:0.1429:2,2:18.5:1:29.9:1:0.54875:1.54:60:20:0.1493:0:1.1 -6 31350232 . A G 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.63035;SOR=0.63189;LSEQ=ATCCTGTGAGGGGCTAGGGA;RSEQ=GAGACAGGGCCATGAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:32:3,29:0,5:0.8649:0,2:26.6:1:31.1:1:1:0:60:64:0.8649:0:1.1 1/1:10:8:0,8:0,2:0.8:0,0:25:1:31.3:1:1:0:60:16:0.8:0:1 -6 31350303 . T G 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.55841;LSEQ=GAAGTTTCCAAAACTGTGAC;RSEQ=GCAGACCCAGGGCAGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:1,4:0,6:0.4545:0,2:19.4:1:31:1:0.45455:0:60:10:0.4545:0:2 1/0:7:4:2,2:1,2:0.5714:2,2:34.5:1:30.3:1:1:1.81:60:8:0.5714:0:2.5 -6 31350328 . A G 88 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06993;SOR=Inf;LSEQ=ACCCAGGGCAGGAAACATGA;RSEQ=GAAAGCAGGTGTGAGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:33.3:1:31:1:1:0:60:6:0.5:0:1.7 1/1:7:7:3,4:0,0:1:0,2:28:1:31.7:1:1:0:60:14:1:0:2.1 -6 31358630 . C TT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TGACCAGTTTCTTCCTTTTT;RSEQ=CTCTCTCAATTTGTGTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:23:1:31.6:1:1:0:30:4:0.2857:0.1429:1.5 0/0:2:0:0,0:1,1:0:2,0:20.5:1:28:1:1:0:50:4:1:0:0 -6 31358749 . T C 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0163;SOR=4.88327;LSEQ=CCCAGCTCCTCTTAAAACAA;RSEQ=GCCCTGCACACAGTAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:7:7,0:42,2:0.1373:1,0:22.7:1:32.6:1:1:0:51.4:14:0.1429:0:2.3 0/1:18:8:8,0:10,0:0.4444:0,0:23:1:31.6:1:1:0:57.5:16:0.4444:0:1.6 -6 31358754 . T C 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72516;LSEQ=CTCCTCTTAAAACAATGCCC;RSEQ=GCACACAGTAGGTATTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:4:4,0:50,2:0.0714:1,0:8.5:1:32:0:1:0:40:8:0.0727:0:3.8 0/1:19:1:1,0:18,0:0.0526:1,0:11:0:31:0:1:0:40:2:0.0526:0:6 -6 31358757 . A G 79 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66805;SOR=0.43716;LSEQ=CTCTTAAAACAATGCCCTGC;RSEQ=CACAGTAGGTATTTGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:6:6,0:50,2:0.1034:1,0:8.2:1:30.8:1:1:0:41.5:12:0.1034:0:3 0/1:21:1:1,0:20,0:0.0476:1,0:14:0:32:0:1:0:40:2:0.0476:0:6 -6 31358784 . C T 61 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05779;SOR=7.4304;LSEQ=AGGTATTTGATAAATGTTTA;RSEQ=CAAATGAAGGGATTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:1,0:96,0:0.0103:1,0:13:0:32:0:1:0:47:2:0.0105:0:5 0/1:55:4:4,0:50,1:0.0727:1,0:10:1:30.8:1:1:0:45.3:8:0.0727:0:5 -6 31358789 . T C 119 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=30.23551;LSEQ=TTTGATAAATGTTTACCAAA;RSEQ=GAAGGGATTGCCTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:1,0:116,0:0.0085:1,0:18:0:34:0:1:0:47:2:0.0087:0:5 0/1:62:13:13,0:48,1:0.2097:1,1:16.8:1:32.3:1:1:0:44.3:26:0.2097:0:4.3 -6 31358804 . G C 138 v4;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.95747;LSEQ=CCAAATGAAGGGATTGCCTG;RSEQ=AATGGCTTGGCAGACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:3:3,0:150,3:0.0192:1,0:19.3:1:33:0:1:0:42.3:6:0.0192:0:4.3 0/1:83:18:17,1:58,7:0.2169:2,1:25.9:1:33.2:1:0.6796:2.04:43.9:36:0.2195:0:4.1 -6 31358806 . A G 140 v4;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.45441;LSEQ=AAATGAAGGGATTGCCTGGA;RSEQ=TGGCTTGGCAGACAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:3:3,0:152,5:0.0188:1,0:21.3:1:27:1:1:0:42.3:2:0.0126:0:4.3 0/1:87:19:18,1:61,7:0.2184:2,1:26.3:1:33:1:0.6797:2.05:43.7:38:0.2184:0:4.1 -6 31358884 . A C 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00571;LSEQ=AGATTTTCCAAATCCTAGTG;RSEQ=TGGGCACAGGGCCCCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:93:78,15:300,170:0.1649:2,2:17.1:1:31.8:1:1e-04:2.94:41.3:45.5:0.164:0:5.7 0/1:338:56:50,6:154,116:0.1657:2,2:18.4:1:31.4:1:0:6.25:42.1:27:0.1607:0:6.4 -6 31358899 . C A 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.1364;SOR=1.26367;LSEQ=TAGTGATGGGCACAGGGCCC;RSEQ=CTAAAGTTCACTTTTGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:120:82,38:322,226:0.1794:2,2:21.9:1:30.5:1:0.06322:1.51:45.9:119:0.1806:0:6.9 0/1:425:92:68,24:180,151:0.2165:2,2:21.6:1:29.8:1:0.00077:2.37:46.8:184:0.219:0:6.9 -6 31358902 . A G 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18064;SOR=1.23874;LSEQ=TGATGGGCACAGGGCCCCCT;RSEQ=AAGTTCACTTTTGGAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:119:81,38:321,235:0.176:2,2:24.1:1:32.3:1:0.03975:1.56:46.3:118:0.1766:0:6.9 0/1:430:90:65,25:185,154:0.2093:2,2:23.7:1:31.7:1:0.00261:2.16:47.3:180:0.2108:0:7.1 -6 31358905 . G A 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13256;SOR=1.26036;LSEQ=TGGGCACAGGGCCCCCTAAA;RSEQ=TTCACTTTTGGAACCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:132:87,45:323,248:0.1867:2,2:24:1:30.5:1:0.05081:1.48:47.5:43:0.1859:0:6.7 0/1:450:101:71,30:188,160:0.2244:2,2:23.4:1:29.6:1:0.00413:2.01:48.5:100:0.2247:0:6.9 -6 31358914 . T C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.8512;SOR=1.03662;LSEQ=GGCCCCCTAAAGTTCACTTT;RSEQ=GGAACCTTCCCATCTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:792:75:40,35:395,322:0.0947:2,2:19.8:1:30.5:1:0.80786:1.07327:51.3:150:0.0955:0:5.8 0/1:552:54:31,23:270,228:0.0978:2,2:21.9:1:30.2:1:0.66932:1.14:51.8:26:0.0952:0:5.8 -6 31358918 . A G 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00006;LSEQ=CCCTAAAGTTCACTTTTGGA;RSEQ=CCTTCCCATCTGTCTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:837:130:79,51:377,329:0.1553:2,2:24.4:1:32.1:1:0.12614:1.35:52.3:260:0.1568:0:5.7 0/1:573:89:58,31:242,219:0.1553:2,2:21.6:1:31.5:1:0.03595:1.69:53.8:88:0.1547:0:5.6 -6 31358943 . T C 271 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06596;SOR=1.20898;LSEQ=CCCATCTGTCTTGTTCTCCT;RSEQ=TCATCAGGGACATCCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:951:387:194,193:283,280:0.4069:2,2:26.9:1:31.6:1:1:1.0055:55.8:386:0.4102:0:4.4 0/1:666:302:158,144:183,180:0.4535:2,2:27.2:1:31.1:1:0.64073:1.08:56.7:99.667:0.4537:0:4.4 -6 31358955 . A T 269 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=1.42424;LSEQ=GTTCTCCTTTCATCAGGGAC;RSEQ=TCCATGCCCCTCAAAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:953:452:212,240:246,255:0.4743:2,2:27.8:1:30.5:1:0.51649:1.09202:56.5:149.667:0.4756:0:3.9 1/0:697:392:197,195:146,156:0.5624:2,2:27.8:1:30:1:0.64619:1.08:57.2:77.4:0.5633:0:3.7 -6 31358975 . C A 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.02983;SOR=1.2603;LSEQ=ATCCATGCCCCTCAAAGCCC;RSEQ=CCTAGTCACACACTACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:865:337:140,197:222,306:0.3896:2,2:27.5:1:29.8:1:0.88788:1.02085:56.4:66.4:0.3906:0:4.1 0/1:637:284:131,153:157,195:0.4458:2,2:27.7:1:29.5:1:0.74867:1.06:56.8:93.667:0.4439:0:4 -6 31359023 . G A 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35121;SOR=1.21223;LSEQ=ACCTTCCAGATCAGCCAGGT;RSEQ=CAAATCCCACAGACTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:63:18,45:94,260:0.1507:2,2:18.7:1:29:1:0.75852:1.11:49.2:62:0.1527:0:3.1 0/1:288:51:19,32:78,159:0.1771:2,2:19.4:1:28.5:1:0.62452:1.21:46.3:102:0.1789:0:2.9 -6 31359025 . A T 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCAGATCAGCCAGGTGC;RSEQ=AATCCCACAGACTTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:104,302:0:2,0:23.3:1:29.7:1:1:0:54.8:49.75:1:0:1 0/1:283:30:14,16:80,173:0.106:2,2:22.1:1:29:1:0.10499:1.89:55.6:60:0.1071:0:2.8 -6 31359162 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07309;SOR=Inf;LSEQ=GAAGTAGTGTTTACATCTCA;RSEQ=AAGAGAAGACCGCGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:0,29:0:1,0:22.2:1:29.6:1:1:0:42.9:13.5:1:0:0.8 0/1:12:2:0,2:0,9:0.1667:0,0:13.5:1:33:0:1:0:40:4:0.1818:0:2 -6 31359176 . G T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29014;SOR=Inf;LSEQ=ATCTCAAAAGAGAAGACCGC;RSEQ=CCACCAGAAATGCAGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:17:0,17:0,6:0.7391:0,1:22.2:1:29.6:1:1:0:42.3:16:0.7273:0:1.5 1/1:7:7:0,7:0,0:1:0,0:15.4:1:30.1:1:1:0:39.7:14:1:0:1.3 -6 31360946 . T C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATGCCCGGCCGCATGAA;RSEQ=ATTTTTAAGCCTTCTCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:34:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31430010 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=GACACTCCAGCAGCACTCAC;RSEQ=TGACCATCCTGAGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:23.1:1:29.9:1:1:0:60:16:1:0:0.4 0/1:5:2:2,0:2,1:0.4:2,0:31.5:1:32:0:1:0:60:4:0.4:0:2 -6 31430065 . C T 56 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07619;SOR=Inf;LSEQ=GGGGAAGGGAGCACAGAACC;RSEQ=AGACACCAGCCTGGACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:27:1:32.3:1:1:0:60:8:1:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:28.5:1:28:1:1:1:60:8:0.6667:0:1.5 -6 31430143 . G C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GTATCTGAGGGAGGAACAGT;RSEQ=ACTTCTGGTCCTGACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:20:1:30.3:1:1:0:60:6:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:29.5:1:29.5:1:1:0:60:4:0.6667:0:1 -6 31430721 . A G 65 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01282;SOR=26.16533;LSEQ=AGCCAAGTCCCAGGGCCCGG;RSEQ=GCTTGGCTCTCTGGGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:10,0:0.0909:0,0:3:0:14:0:1:0:60:0:0:0:6 1/1:5:4:4,0:1,0:0.8:0,0:12.8:1:32.5:1:1:0:60:8:0.8:0:2.3 -6 31430752 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01722;SOR=Inf;LSEQ=CTGGGCTTCAGGCCCCGAGG;RSEQ=CGGTGCCTGGGATGGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:0:1,0:28:1:31.9:1:1:0:60:26:1:0:0.8 0/1:9:4:4,0:5,0:0.4444:0,0:33.8:1:29:1:1:0:60:8:0.4444:0:1.8 -6 31430799 . G T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37752;SOR=1.82687;LSEQ=TTTGGGGTTTCCCGAGCTCC;RSEQ=CTCTCTCTCTTCCACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:13:13,0:30,0:0.3023:1,1:13.8:1:31.5:1:1:0:60:26:0.3095:0:1 0/1:18:8:8,0:10,0:0.4444:0,0:31.8:1:31.3:1:1:0:60:16:0.4444:0:1 -6 31430951 . C T 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTAAAGTCCTCGCCGGCC;RSEQ=ACCGGGACTCAGATTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:0:0,0:461,256:0:2,0:24.4:1:30.8:1:1:0:60:36.737:1:0:0.1 0/1:527:36:23,13:305,186:0.0683:2,2:25.5:1:30.3:1:1:1.08:60:72:0.0694:0:1.1 -6 31431082 . A G 267 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.87476;SOR=1.03213;LSEQ=TGCGGGGTCGGGAGGGAAAA;RSEQ=GCCTCTGCGGGAAGGAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:510:388:98,290:36,86:0.7608:2,2:26.2:1:31.1:1:0.3483:1.23816:60:54.429:0.7605:0:1.1 1/0:394:302:85,217:32,60:0.7665:2,2:25.3:1:30.4:1:0.24168:1.36051:60:301:0.7659:0:1.1 -6 31431091 . G T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03241;SOR=Inf;LSEQ=GGGAGGGAAAAAGCCTCTGC;RSEQ=GGAAGGAGCGAGGGGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:116,346:0:2,0:25.3:1:30.5:1:1:0:60:76:1:0:0.9 0/1:342:4:1,3:98,240:0.0117:2,2:28.8:1:30.5:1:1:1.22429:60:8:0.0119:0:1.5 -6 31455603 . C T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=3.3097;LSEQ=TGCCTGAGCAAGACTGGGCA;RSEQ=GCCTTGAGGGCAAGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:5,1:0.1429:2,0:6:0:31:0:1:0:60:2:0.1667:0:3 0/1:8:3:3,0:3,2:0.375:2,0:23.3:1:31:1:0.46429:0:40:6:0.375:0:4.7 -6 31455630 . G C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65266;SOR=0.58398;LSEQ=AGGGCAAGGAGGGTTTATTT;RSEQ=CTCTTACCTCAGTTCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:13,1:3,1:0.7778:2,1:21.1:1:30.6:1:0.40523:3.89:50.8:13:0.7647:0:2.6 1/0:9:6:6,0:1,2:0.6667:2,0:29.5:1:32.3:1:0.08333:0:46.8:12:0.6667:0:3.7 -6 31455644 . T C 74 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00272;SOR=Inf;LSEQ=TTATTTGCTCTTACCTCAGT;RSEQ=CCAGCTCCTCTTAAAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:18,2:0:2,0:29.6:1:30.9:1:1:0:53.6:40:1:0:1.9 0/1:11:5:5,0:5,1:0.4545:2,0:24.2:1:32.2:1:1:0:40.4:10:0.5:0:5 -6 31455664 . T C 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52196;SOR=1.59759;LSEQ=TCCAGCTCCTCTTAAAACAA;RSEQ=GCCCCACGCACAGTAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:13,0:16,2:0.4194:2,1:27:1:33:1:0.49677:0:42.4:26:0.4483:0:3.6 1/0:13:7:7,0:5,1:0.5385:2,0:23.9:1:32.6:1:0.46154:0:46.7:14:0.5385:0:5.1 -6 31455670 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51593;SOR=1.63278;LSEQ=TCCTCTTAAAACAATGCCCC;RSEQ=CGCACAGTAGGTATTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:12,0:15,2:0.4138:2,0:32.1:1:29.5:1:0.49754:0:43.7:24:0.4138:0:3.8 1/0:13:7:7,0:5,1:0.5385:2,0:26.4:1:31.3:1:0.46154:0:46.7:14:0.5385:0:5.1 -6 31455671 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTAAAACAATGCCCCA;RSEQ=GCACAGTAGGTATTTGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:2,0:25,2:0.069:2,0:29.5:1:30:1:1:0:60:4:0.0741:0:2.5 0/0:13:0:0,0:12,1:0:1,0:24:1:32.2:1:1:0:52.8:26:1:0:2.9 -6 31455699 . C T 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69207;LSEQ=AGGTATTTGATAAATGTTTA;RSEQ=CAAATGAAGGGATTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:31,2:0.0833:2,0:26.7:1:31:1:1:0:42:6:0.0833:0:6 0/1:17:1:1,0:16,0:0.0588:1,0:40:0:27:0:1:0:60:2:0.0588:0:6 -6 31455704 . T C 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58901;SOR=2.16386;LSEQ=TTTGATAAATGTTTACCAAA;RSEQ=GAAGGGATTGCCTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:2,0:32,1:0.0571:1,0:34.5:1:33.5:1:1:0:43.5:4:0.0588:0:7 0/1:17:2:2,0:15,0:0.1176:1,0:36.5:1:28:0:1:0:58.5:4:0.125:0:5.5 -6 31455719 . G C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00075;SOR=7.96636;LSEQ=CCAAATGAAGGGATTGCCTG;RSEQ=AATGGCTTGGCAGACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:5:5,0:33,5:0.1163:2,0:27.4:1:33.6:1:1:0:41.4:10:0.119:0:4.6 1/0:23:12:12,0:11,0:0.5217:0,0:21:1:31.2:1:1:0:43.9:24:0.5217:0:3.9 -6 31455721 . A G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00114;SOR=7.13373;LSEQ=AAATGAAGGGATTGCCTGGA;RSEQ=TGGCTTGGCAGACAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:5:5,0:32,5:0.119:2,0:27.8:1:33.6:1:1:0:41.4:10:0.119:0:4.6 1/0:24:12:12,0:12,0:0.5:0,0:21.3:1:31.3:1:1:0:43.9:24:0.5217:0:3.9 -6 31455743 . A C 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18094;SOR=0.4133;LSEQ=GGCTTGGCAGACAGGAAAGC;RSEQ=GAATGAAAACCCACAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:15:12,3:37,6:0.2586:2,2:14.8:1:30.9:1:0.68226:1.52938:39.1:30:0.2632:0:2.9 0/1:32:4:2,2:23,2:0.125:2,2:10.3:1:30.3:1:0.08004:9.90496:54.8:8:0.125:0:3.5 -6 31455767 . A G 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.85147;SOR=1.10069;LSEQ=TGAAAACCCACAGGCCAAAA;RSEQ=TGGCTGGGAAAAGATTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:75:53,22:16,4:0.7813:2,2:23.3:1:32:1:0.57414:1.65214:46.4:74:0.7789:0:2.7 1/0:74:59:42,17:11,4:0.7973:2,2:21.2:1:30.5:1:1:1.11153:50.5:18.667:0.7887:0:2.7 -6 31455771 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6164;LSEQ=AACCCACAGGCCAAAAATGG;RSEQ=TGGGAAAAGATTTTCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:74,33:0.0183:2,2:28:1:30.5:1:0.52854:2.22411:60:4:0.0185:0:3 0/1:88:1:0,1:61,26:0.0114:2,0:1:0:25:0:0.30682:0:60:2:0.0116:0:5 -6 31455786 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50652;SOR=0;LSEQ=AATGGCTGGGAAAAGATTTT;RSEQ=CAAATCCTAGTGCTGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:97,54:0.0131:2,2:33:1:28.5:1:1:1.78895:54.5:4:0.0132:0:4.5 0/0:118:0:0,0:66,52:0:2,0:23.1:1:30.9:1:1:0:54.1:117:1:0:2.3 -6 31455799 . C G 64 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.03176;SOR=Inf;LSEQ=AGATTTTCCAAATCCTAGTG;RSEQ=TGGGCACAGGGCCCACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:107,73:0:2,0:26.2:1:32:1:1:0:49.6:59:1:0:2.2 0/1:133:4:2,2:67,62:0.0301:2,2:38:1:32:1:1:1.07999:45.5:8:0.031:0:5.3 -6 31455804 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19114;SOR=Inf;LSEQ=TTCCAAATCCTAGTGCTGGG;RSEQ=ACAGGGCCCACTGAAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:104,73:0:2,0:28.6:1:32:1:1:0:49.9:43.25:1:0:2.2 0/1:138:2:1,1:69,67:0.0145:2,2:24.5:1:29.5:1:1:1.02964:60:4:0.0149:0:1.5 -6 31455829 . C T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01536;LSEQ=GGCCCACTGAAATTCACTTT;RSEQ=GGAAACTTCCCATCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:37:16,21:80,53:0.2164:2,2:27.8:1:29.9:1:0.09097:1.973:44.3:74:0.2189:0:4.4 0/1:137:30:14,16:51,56:0.219:2,2:30:1:30:1:1:1.04053:52.7:60:0.2206:0:4.4 -6 31455833 . AA GC 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.8843;SOR=0.92181;LSEQ=CACTGAAATTCACTTTCGGA;RSEQ=CTTCCCATCTGTCTCGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:33:13,20:77,52:0.2012:2,2:24.6:1:31.8:1:0.0491:2.26627:42.8:66:0.2025:0:3.5 0/1:138:26:12,14:50,58:0.1884:2,2:25.1:1:31.8:1:1:1.0057:53.8:52:0.1898:0:3.3 -6 31455834 . A C 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90712;SOR=0.95073;LSEQ=ACTGAAATTCACTTTCGGAA;RSEQ=CTTCCCATCTGTCTCGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:97:58,39:19,13:0.5879:2,2:28.8:1:31.9:1:1:1.02:51.6:194:0.7462:0:2 1/0:139:80:34,46:17,12:0.5755:2,2:28.4:1:30.6:1:0.19219:1.90511:56.3:79:0.7315:0:1.8 -6 31455849 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00023;SOR=0.40695;LSEQ=CGGAAACTTCCCATCTGTCT;RSEQ=GTTCTCCTCTCATCAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:152:92:46,46:33,26:0.6053:2,2:15.8:1:29.9:1:0.50765:1.26722:46.3:91:0.6026:0:2.7 0/1:133:51:20,31:38,44:0.3835:2,2:14.9:1:29.9:1:0.47429:1.3357:50.8:50:0.3876:0:2.9 -6 31455867 . ATAG GACTTCCATGCCCCTCAA 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00011;SOR=0.35667;LSEQ=CTCGTTCTCCTCTCATCAGG;RSEQ=AGCCCACCTAGTCACACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:141:80:35,45:30,30:0.5674:2,2:13.5:1:29.6:1:0.49672:1.28338:44.4:160:0.5714:0.5674:2 0/1:107:34:8,26:30,43:0.3178:2,2:10.9:1:29.7:1:0.08694:2.25078:44.9:68:0.3178:0.3178:2.4 -6 31455922 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50426;SOR=0;LSEQ=CCACCTTCCAGATCAGCCAG;RSEQ=TACAAATCCCACAGACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:21,53:0.0263:2,2:19:0:31.5:1:0.49789:2.49:60:4:0.027:0:3 0/0:59:0:0,0:17,42:0:2,0:25.1:1:30.5:1:1:0:51.8:58:1:0:0.5 -6 31455924 . A G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13861;SOR=0;LSEQ=ACCTTCCAGATCAGCCAGGT;RSEQ=CAAATCCCACAGACTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:0,4:22,50:0.0526:2,0:16.8:1:31.8:1:0.31702:0:31.5:8:0.0526:0:1 0/0:55:0:0,0:15,40:0:2,0:25.6:1:28.9:1:1:0:53.6:110:1:0:0.5 -6 31455935 . A C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00462;SOR=4.59847;LSEQ=CAGCCAGGTACAAATCCCAC;RSEQ=GACTTCCTGCCTGTGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:6:1,5:14,48:0.0882:2,2:29.2:1:26:1:1:1.45093:51.8:5:0.0781:0:1.3 0/1:45:14:3,11:6,24:0.3111:2,2:20.7:1:28.6:1:1:1.09:55.8:28:0.3111:0:1.1 -6 31455952 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29382;SOR=3.66432;LSEQ=CACAGACTTCCTGCCTGTGG;RSEQ=TCCAAATGCTCAGCTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:1:0,1:8,46:0.0182:2,0:7:0:31:0:1:0:60:2:0.0185:0:1 0/1:31:2:0,2:6,23:0.0645:2,0:29:1:29:1:1:0:54.5:4:0.0645:0:1.5 -6 31456099 . T G 75 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCAGAAATGCAGAGTTTT;RSEQ=GTATGTGCGGGTCCGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:1,4:1,4:0.5:2,2:33.6:1:32.6:1:1:1:46.8:10:0.5:0:3.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31456104 . G A 72 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATGCAGAGTTTTTGTAT;RSEQ=TGCGGGTCCGGGGTCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:1,4:1,4:0.5:2,2:30.6:1:31.2:1:1:1:46.8:10:0.5:0:3.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31456108 . G A 73 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGAGTTTTTGTATGTGC;RSEQ=GGTCCGGGGTCTTCAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:1,4:1,4:0.5:2,2:28.2:1:31.8:1:1:1:46.8:10:0.5556:0:3.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 31457417 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTATACTGGTATTTCCTTG;RSEQ=TGGAATTTGACATCCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:19:1:31:1:1:1:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 32163274 . G A 165 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=54.16417;LSEQ=TGGAGGGCTGGGGGACCACA;RSEQ=TCAAGTTGAGGTGATCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1919:1:1,0:1001,917:5e-04:2,0:1:0:29:0:1:0:60:2:5e-04:0:1 0/1:1673:46:22,24:816,808:0.0275:2,2:24.8:1:29.9:1:0.76701:1.10164:60:45:0.0273:0:1.1 -6 32163541 . A C 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00293;SOR=1.59419;LSEQ=CCCGAGAGGCTCCGGCAATG;RSEQ=GAATAGGCCCCGCCCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:840:90:40,50:340,409:0.1071:2,2:26.3:1:30.6:1:0.91101:1.03908:60:180:0.1099:0:1.1 0/1:635:102:41,61:254,279:0.1606:2,2:24.3:1:30.5:1:0.19353:1.35384:60:204:0.1632:0:1.1 -6 32163799 . T C 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAGATCCCAGTGGTTACG;RSEQ=TGGTGAGCGACGTCCGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:795:0:0,0:390,405:0:2,0:25.7:1:29.5:1:1:0:60:40.842:1:0:0.2 0/1:665:18:8,10:306,340:0.0271:2,2:23:1:32.1:1:1:1.1248:60:36:0.0276:0:1.3 -6 32164265 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20198;SOR=Inf;LSEQ=CCTGGGTTCCGGTTTCCCAC;RSEQ=GGTTCTGGCCTTGGGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:16,150:0:2,0:24.2:1:31.1:1:1:0:60:82:1:0:0.1 0/1:136:2:1,1:19,115:0.0147:2,2:30.5:1:28.5:1:0.27342:5.92:60:4:0.0148:0:1 -6 32164535 . TG T 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20055;SOR=5.07536;LSEQ=GTGGTGTTGAGGGTGGGAGT;RSEQ=GGGGGGGAAACTCACGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:1,0:78,2:0.0123:1,0:28:0:34:0:1:0:60:2:0.0128:0:0 0/1:33:2:2,0:29,2:0.0606:2,0:10.5:1:32.2:1:1:0:60:4:0.0606:0.0303:0.5 -6 32164587 . C T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00263;SOR=Inf;LSEQ=ACCGCATCTCAGATTGACCG;RSEQ=CGTAACAGCAGGATGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:164,3:0:1,0:25.9:1:32:1:1:0:60:40.75:1:0:0.1 0/1:128:7:7,0:114,7:0.0547:2,0:33:1:31:1:1:0:60:14:0.0551:0:1.1 -6 32164615 . C T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09203;SOR=Inf;LSEQ=GCAGGATGAGAGGGAATGCC;RSEQ=CTCTGCTGCACCTATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:265,29:0:2,0:23.1:1:30.5:1:1:0:60:25.727:1:0:0.1 0/1:243:3:1,2:207,33:0.0123:2,2:21.3:1:21.3:1:0.05517:12.32029:60:2:0.0084:0:1 -6 32164665 . CT C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16338;LSEQ=CTCCCACCCCATCTGCTCAA;RSEQ=TCTCTATAGCATACATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:824:241:164,77:369,214:0.2925:2,2:25:1:31.8:1:0.20083:1.23:60:482:0.2972:0.0607:0.2 0/1:712:45:27,18:403,264:0.0632:2,2:22.8:1:30.9:1:1:1.01766:60:90:0.0644:0.014:0.2 -6 32164869 . G C 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.91922;LSEQ=GCTGGGGAGACAGAGGGCCA;RSEQ=TGACCCCTGGGGTACCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:12:3,9:81,239:0.0361:2,2:27.8:1:32.9:1:1:1.01669:60:24:0.0367:0:2.2 0/1:257:59:15,44:41,157:0.2296:2,2:22.8:1:31.7:1:0.47374:1.30:60:58:0.2292:0:1.8 -6 32164874 . C A 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=5.39594;LSEQ=GGAGACAGAGGGCCAGTGAC;RSEQ=CCTGGGGTACCTTGGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:12:3,9:72,215:0.0401:2,2:26.9:1:30.4:1:1:1.00464:60:24:0.0408:0:2.2 0/1:233:43:8,35:38,152:0.1845:2,2:19.6:1:29.7:1:1:1.09333:60:86:0.1861:0:2.2 -6 32165018 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.31572;SOR=4.11574;LSEQ=AAACTCTAGGGGATGCTTCT;RSEQ=TCCAGCTTTACTTGTAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:1:1,0:171,63:0.0043:2,0:2:0:14:0:1:0:60:0:0:0:3 0/1:173:3:1,2:131,38:0.0173:2,2:27.7:1:28:1:0.13541:6.79458:60:6:0.0174:0:1 -6 32165215 . AG A 92 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.07075;SOR=3.36109;LSEQ=AGAATCGGGCAGCCAGGTGC;RSEQ=GGGGGTCTCCCCAGTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:925:3:2,1:520,401:0.0032:2,2:21:1:33.3:1:1:1.54:60:6:0.0033:0:0 0/1:739:8:3,5:372,354:0.0108:2,2:30.9:1:30.9:1:0.49681:1.75009:60:16:0.0109:0.0027:0.4 -6 32165444 . A G 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01218;SOR=2.12591;LSEQ=GGGACAACATGTAAGCTCAG;RSEQ=GAGAATCAAAACCTGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:28:2,26:9,169:0.1353:2,2:19.3:1:31.1:1:0.64813:1.44:60:27:0.1317:0:1.1 0/1:128:32:2,30:5,91:0.25:2,2:20.4:1:29.8:1:1:1.21:60:31:0.248:0:1.2 -6 32165583 . G A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03623;SOR=Inf;LSEQ=TAATTCTCTGACATTCCAGG;RSEQ=CAGTGGTTTTCTCTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:0,19:0:1,0:17.8:1:32.8:1:1:0:58.9:38:1:0:0.9 0/1:5:2:0,2:0,3:0.4:0,0:17.5:1:31:1:1:0:57:4:0.4:0:1.5 -6 32166380 . C G 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAAGGTTGATTTGCCCTTT;RSEQ=ATCCCTTCCATCACCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1168:0:0,0:631,537:0:2,0:24.1:1:31.7:1:1:0:60:96.333:1:0:0.1 0/1:837:43:25,18:422,371:0.0514:2,2:23.6:1:30.7:1:0.63821:1.22:60:13.333:0.0483:0:1.2 -6 32166992 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53746;SOR=0;LSEQ=ATTACTATTGGGAGACCTTT;RSEQ=GACAAGTTTAGTAGCCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:8,94:0.0192:2,0:13.5:1:30.5:1:1:0:60:4:0.0192:0:1 0/0:58:0:0,0:9,49:0:2,0:22.7:1:30.4:1:1:0:60:57:1:0:0.6 -6 32167009 . G T 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61393;SOR=0.76405;LSEQ=TTTGGACAAGTTTAGTAGCC;RSEQ=GTCTTTGCCTCGGTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:62:2,60:1,13:0.8158:1,1:21.7:1:29.8:1:0.46202:2.27628:60:124:0.8267:0:1 1/0:35:27:2,25:0,8:0.7714:0,2:22.6:1:30.6:1:1:0:60:54:0.7941:0:1.1 -6 32168565 . G T 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.39229;SOR=0.31877;LSEQ=TGTTGCTAGCATGAGAGCTG;RSEQ=CCTGGGAACAGAGGTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:4:2,2:298,98:0.01:2,2:9:1:30:1:0.26119:3.03052:60:8:0.0102:0:1.3 0/0:312:1:0,1:209,102:0.0032:2,0:1:0:22:0:0.33013:0:60:2:0.0033:0:1 -6 32168771 . G T 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.87648;LSEQ=CGGGACAAATCCACACCCAT;RSEQ=ACCACCACAAACCTGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1335:132:60,72:590,610:0.0989:2,2:25.4:1:28.3:1:0.46323:1.16052:60:25.4:0.0973:0:1.1 0/1:1054:180:83,97:411,461:0.1708:2,2:26.3:1:28.4:1:0.80632:1.04189:60:59:0.1704:0:1.2 -6 32168932 . C T 155 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.69892;LSEQ=GTCTCCTTGCCCAGGGGCTG;RSEQ=GTTTGAGGGGCTGCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1731:8:1,7:888,835:0.0046:2,2:11.3:1:28.4:1:0.03409:7.43745:60:16:0.0047:0:1.3 0/1:1303:45:26,19:654,604:0.0345:2,2:22.6:1:28.3:1:0.54402:1.26:60:21.5:0.0333:0:1.1 -6 32169621 . T A 44 MAF0.05;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17241;SOR=Inf;LSEQ=GGCTTGAGACCTGAGTTCCT;RSEQ=CAACTCTTAGAGAGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:4,0:21,3:0.1429:2,0:26:1:22.3:1:1:0:60:3:0.1111:0:3.3 1/1:1:1:1,0:0,0:1:0,0:39:0:30:0:1:0:60:2:1:0:1 -6 32169795 . TTCC T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.0428;SOR=0;LSEQ=ACTCAGAGCCATCTACGTCC;RSEQ=TCCTCCTCTCACCCACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:6:1,5:418,113:0.0111:2,2:11.8:1:25.8:1:0.00237:18.36814:60:5:0.0094:0.0074:0.7 0/0:392:0:0,0:289,101:0:2,0:21:1:29.3:1:1:0:60:54.714:0.9974:0:0.1 -6 32170433 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.61142;LSEQ=GCATTATTCTTCCCGCTCTC;RSEQ=ATCAAGCAAACTCTTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:21:6,15:28,116:0.1273:2,2:27:1:27.9:1:0.38606:1.65:60:20:0.1235:0:1.1 1/0:106:56:12,44:12,38:0.5283:2,2:22.9:1:28.3:1:0.81836:1.15629:59.9:55:0.5288:0:1 -6 32170464 . AG A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=7.67739;LSEQ=CTCTTGGGTTAAGACGGTGC;RSEQ=AGGGTCCTAGATTCTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:13:1,12:3,70:0.1512:1,1:19.8:1:30.3:1:0.48745:1.93:60:12:0.1412:0.0349:1.1 1/0:55:32:1,31:2,21:0.5818:2,1:23.2:1:30.8:1:0.56516:2.89429:59.8:31:0.5849:0.1636:0.9 -6 32171415 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAGACACTTCCCACTGT;RSEQ=AGCTTGGCATGGCTTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:2,0:133,2:0.0144:1,0:37:1:31:1:1:0:60:4:0.0147:0:1 0/0:60:0:0,0:58,2:0:1,0:26.3:1:31.9:1:1:0:60:120:1:0:0.2 -6 32171427 . G A 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67649;LSEQ=CCCACTGTGAGCTTGGCATG;RSEQ=CTTTTTCCAATAATTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:152,2:0.0191:1,2:33.3:1:24.7:1:0.05659:33.5817:60:2:0.0132:0:1.3 0/1:77:1:1,0:72,4:0.013:2,0:43:0:27:0:1:0:60:2:0.0132:0:1 -6 32171476 . G A 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07189;SOR=Inf;LSEQ=TCACCCACAGTCCCTTCTGG;RSEQ=ATTCCAACTGAGGTATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:285,55:0:2,0:23.3:1:30.9:1:1:0:60:41.5:1:0:0.1 0/1:243:3:2,1:186,54:0.0123:2,2:26:1:23.7:1:0.5386:1.71784:60:2:0.0084:0:1.7 -6 32171538 . G A 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGAGAAGGCAGATTTGTG;RSEQ=TCACTTGCCTTGGGGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:888:0:0,0:552,336:0:2,0:25.4:1:31.1:1:1:0:60:45.737:1:0:0.1 0/1:678:64:37,27:364,247:0.0944:2,2:27.5:1:29.1:1:0.79043:1.07527:60:128:0.0958:0:1.1 -6 32171683 . T C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.55082;LSEQ=TAATTATGGGGGAGATTAGA;RSEQ=GTCACACACTGCATCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:631:88:21,67:151,391:0.1395:2,2:23.8:1:30.5:1:0.51911:1.23177:60:87:0.1401:0:1.1 1/0:419:216:67,149:61,139:0.5155:2,2:21.9:1:29.5:1:0.91578:1.02:60:53:0.5171:0:1.1 -6 32171831 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACCAGGTGACGGCTGCC;RSEQ=CATGGGTGGAGACTATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:2,0:107,42:0.0132:2,0:25:1:31.5:1:1:0:60:4:0.0136:0:1 0/0:73:0:0,0:57,16:0:2,0:22.9:1:29.8:1:1:0:60:72:1:0:0.2 -6 32172065 . T G 321 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21401;SOR=0.86273;LSEQ=GGAGGGCAGGCACAGTGGAA;RSEQ=CCTCCAGGTTTGGGAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1254:1082:560,522:84,85:0.8628:2,2:25.1:1:31.9:1:0.6208:1.09:60:76.286:0.8634:0:1.1 1/1:1054:890:454,436:84,78:0.8444:2,2:25:1:31.8:1:0.86461:1.0342:60:147.333:0.8476:0:1.2 -6 32178414 . TA T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.36244;SOR=2.58923;LSEQ=GTTAGTTGGGTGTGTGGGGT;RSEQ=AAAAAAATAAAAGGAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:2,0:112,6:0.0167:2,0:25.5:1:32:0:1:0:60:4:0.0171:0:0 0/1:71:3:2,1:64,4:0.0423:2,2:22.3:1:28.8:1:0.19937:7.51513:60:6:0.0423:0.0141:0 -6 32178773 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.80309;LSEQ=GGGGGCCGGGCGCCATGGCT;RSEQ=ACGCCTGTAATCCCAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:23:1,22:18,115:0.1474:2,1:21.1:1:31.4:1:0.31123:3.42454:60:22:0.1419:0:1.1 0/1:90:41:5,36:7,41:0.4556:2,2:24.8:1:30.7:1:1:1.22644:60:19.5:0.4483:0:1.1 -6 32180146 . A G 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7198;SOR=0.86666;LSEQ=TGTGTGGTTTTGATTCTCAG;RSEQ=TGGTTGTTTTGGCCAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:149:127:117,10:20,1:0.8523:1,2:23.4:1:31.6:1:1:1.70417:60:62.5:0.8562:0:1.1 1/1:96:80:77,3:15,1:0.8333:1,1:21.4:1:31.6:1:0.5239:1.70:60:160:0.8333:0:1.2 -6 32180172 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18015;SOR=Inf;LSEQ=GTTTTGGCCAAAAGCTGTGT;RSEQ=GAAGCCCACAGGAACGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:175,43:0:2,0:24.8:1:31.6:1:1:0:59.9:71.667:0.9954:0:0.6 0/1:162:2:1,1:131,29:0.0123:2,2:25:1:27.5:1:0.33701:4.45825:60:4:0.0126:0:1.5 -6 32180241 . C T 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCTCCAGTCAGTGCCGG;RSEQ=GTTGGTTACCTTGGCTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:690:0:0,0:439,248:0:2,0:26.5:1:31.1:1:1:0:60:56.25:0.9985:0:0.2 0/1:573:61:37,24:299,212:0.1065:2,2:24.2:1:29:1:0.78465:1.09:60:29.5:0.1044:0:1.1 -6 32180684 . A C 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=25.15236;LSEQ=GCAGGTTGCCCTATTCCTAC;RSEQ=GGGGCTGAACAAGACAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:872:1:0,1:385,486:0.0011:2,0:2:0:10:0:1:0:60:0:0:0:2 0/1:783:22:8,14:346,415:0.0281:2,2:27.4:1:28.5:1:0.5158:1.45835:60:21:0.0272:0:1.1 -6 32181113 . AC A 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.15682;SOR=Inf;LSEQ=ACACTGTACATAGGACATAC;RSEQ=CCCCCACCCCCATCAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:13,244:0:2,0:27.4:1:31.1:1:1:0:60:31.125:1:0:0.2 0/1:169:2:0,2:15,152:0.0118:2,0:35.5:1:33:0:1:0:60:4:0.0122:0:0 -6 32181182 . G A 84 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00325;SOR=14.57428;LSEQ=TATTTATATGATATTTTATT;RSEQ=TTTTTAGATAGGGTCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:1:0,1:11,51:0.0159:2,0:35:0:17:0:1:0:60:0:0:0:1 0/1:36:7:2,5:1,28:0.1944:1,2:17.9:1:30:1:0.0902:10.09:60:14:0.2121:0:1 -6 32181399 . A G 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07123;SOR=Inf;LSEQ=ATTTTAAAAAATATGACACA;RSEQ=GCATACCCTCCTTAGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:254,44:0:2,0:20.8:1:30.4:1:1:0:60:98.333:1:0:0.1 0/1:212:3:1,2:158,51:0.0142:2,2:16.3:1:26.7:1:0.15491:6.1298:60:2:0.0097:0:2.3 -6 32181517 . A C 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGCCCTGTGTGGCTTGG;RSEQ=GGGCAGGTGCAGTAGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:812:0:0,0:440,371:0:2,0:25.6:1:30.3:1:1:0:60:46.706:1:0:0.1 0/1:609:16:8,8:325,268:0.0263:2,2:30.8:1:29.7:1:0.80113:1.2123:60:15:0.0252:0:1.4 -6 32181669 . G A 61 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04062;SOR=7.56772;LSEQ=TGTCCTCCTTCCCTCCCTCC;RSEQ=CTCTCCTTCTCTTTCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:1:1,0:136,348:0.0021:2,0:1:0:26:0:0.28247:0:60:2:0.0021:0:1 0/1:324:5:4,1:94,223:0.0154:2,2:7.8:1:26.6:1:0.03137:9.42:60:10:0.0156:0:0.6 -6 32181738 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10984;SOR=Inf;LSEQ=ATTCTTTCCCATCAACCTCC;RSEQ=TTCTCACCACCTCCCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:118,115:0:2,0:23.4:1:30.6:1:1:0:60:45.6:1:0:0.2 0/1:116:2:1,1:61,53:0.0172:2,2:24:1:26:1:1:1.14954:60:4:0.0174:0:1.5 -6 32182175 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.07439;LSEQ=GTGACTTTGCTCTCAGCACC;RSEQ=CCCCCATCCTCCCCAACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:0,2:2,84:0.0227:1,0:25.5:1:29:1:1:0:60:4:0.023:0:1.5 0/1:41:1:0,1:2,38:0.0244:2,0:45:0:32:0:1:0:60:2:0.025:0:1 -6 32182243 . G GAT 88 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=10.000;MSILEN=2;SSF=0.1591;SOR=0;LSEQ=CATCTATATATCTAGTTGGA;RSEQ=ATATATATATATATATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:0,8:0,19:0.2759:1,0:36.9:1:29.5:1:1:0:60:16:0.2759:0.0345:0.1 0/0:9:0:0,0:0,9:0:0,0:16.3:1:31.1:1:1:0:60:18:1:0:0.2 -6 32182261 . T TATAC 30 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=9.000;MSILEN=2;SSF=0.01709;SOR=Inf;LSEQ=GAGATATATATATATATATA;RSEQ=ACACACATATATATTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,18:0:1,0:23.6:1:28.4:1:1:0:60:36:0.7826:0:0.1 1/0:4:2:0,2:0,1:0.5:0,0:35:1:30.3:1:1:0:60:4:0.5:0:0.5 -6 32182914 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54964;SOR=0;LSEQ=TCCCCATTGGTCATTTCTCA;RSEQ=AGACCTACATCTCACTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:167,27:0.0102:2,2:24.5:1:28.5:1:0.26593:6.09191:60:4:0.0105:0:1 0/0:101:0:0,0:80,21:0:2,0:22.3:1:31.1:1:1:0:60:100:1:0:0.1 -6 32183175 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.88597;LSEQ=GAGCTGGCCTGGGGTGGGAA;RSEQ=ATGGGTCAAAAAGAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:595:85:31,54:155,355:0.1429:2,2:23.6:1:29.8:1:0.25879:1.31:60:84:0.1426:0:1.1 0/1:512:230:77,153:90,190:0.4492:2,2:25.6:1:29.4:1:0.77647:1.06:60:75.667:0.4504:0:1.2 -6 32183193 . C G 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0351;SOR=Inf;LSEQ=AAGATGGGTCAAAAAGAAAA;RSEQ=AGCTCCTCCACATCCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:110,344:0:2,0:22.1:1:32:1:1:0:60:226:1:0:0.2 0/1:348:4:2,2:80,263:0.0115:2,2:6:1:30.5:1:0.23814:3.27:60:8:0.0116:0:2.3 -6 32183195 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01396;SOR=Inf;LSEQ=GATGGGTCAAAAAGAAAACA;RSEQ=CTCCTCCACATCCTTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:0:0,0:106,330:0:2,0:22.1:1:31.8:1:1:0:60:47.444:1:0:0.2 0/1:325:5:4,1:70,249:0.0154:2,2:6.2:1:26.2:1:0.01053:14.08:60:10:0.0158:0:1 -6 32183200 . T A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07597;SOR=Inf;LSEQ=GTCAAAAAGAAAACAGCTCC;RSEQ=CCACATCCTTCATTGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:85,306:0:2,0:22.3:1:29.6:1:1:0:60:54.857:1:0:0.2 0/1:289:3:2,1:60,226:0.0104:2,2:13:1:22.3:1:0.11732:7.46:60:2:0.0071:0:2.3 -6 32184526 . T C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53947;SOR=0;LSEQ=CACCATTTACACTGGGCCCA;RSEQ=GTGGGCCCTACGGTAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:2,0:197,1:0.01:1,0:25:1:27:1:1:0:60:4:0.0101:0:1 0/0:111:0:0,0:108,3:0:1,0:22:1:30.1:1:1:0:60:222:1:0:0.2 -6 32184543 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06558;SOR=Inf;LSEQ=CCATGTGGGCCCTACGGTAA;RSEQ=CCCTGCCCTTGTCCCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:247,8:0:1,0:23.2:1:31.8:1:1:0:60:62.75:0.996:0:0.1 0/1:174:3:2,1:159,12:0.0172:2,2:20:1:23.3:1:0.20892:6.47866:60:2:0.0116:0:1.3 -6 32184574 . G A 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCCCATGGTTGTACAATT;RSEQ=TGCAGGTTTTACACTAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:328,99:0:2,0:21.9:1:31.9:1:1:0:60:60:0.9976:0:0.1 0/1:389:56:41,15:253,80:0.144:2,2:22.3:1:29.1:1:0.73675:1.15655:60:112:0.1443:0:1.1 -6 32184705 . G A 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04602;SOR=0.80052;LSEQ=TATTCTGCCAGTTCTTTCCA;RSEQ=TGCCTCCCCTGTGAACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:971:774:367,407:94,100:0.7971:2,2:23.5:1:30.1:1:0.80983:1.04243:60:32.652:0.7939:0:1.2 1/0:916:695:308,387:112,108:0.7587:2,2:23.7:1:29.5:1:0.08846:1.30264:60:42.438:0.7578:0:1.1 -6 32185246 . T G 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00743;SOR=0;LSEQ=TGTGACTTTGGGCAAGCTGG;RSEQ=CAACCCTCTAGGCCCCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:2,7:0,19:0.3214:1,2:29.1:1:32.4:1:0.09524:0:60:18:0.3333:0:1.3 0/0:18:0:0,0:1,17:0:1,0:27.5:1:27.7:1:1:0:60:17:1:0:0.3 -6 32185593 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGATGAGAATGGGCAAG;RSEQ=AAGCAAGGGAAGATTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:57,0:0.0339:1,2:17.5:1:28.5:1:0.0339:0:60:4:0.0339:0:1 0/0:25:0:0,0:22,3:0:2,0:20.5:1:30.1:1:1:0:60:50:1:0:0.2 -6 32185796 . C T 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.01311;LSEQ=CAGGCAGATGCACTGGAAGC;RSEQ=GTTGAGCAGGTCATGGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1072:3:0,3:565,503:0.0028:2,0:1:0:26.3:1:0.10513:0:60:6:0.0028:0:1 0/1:965:44:22,22:488,433:0.0456:2,2:28:1:29.8:1:0.75814:1.12688:60:13.667:0.0434:0:1.3 -6 32185818 . C T 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTGAGCAGGTCATGGCAATC;RSEQ=GCGTGGTTCAGGCAGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1135:0:0,0:577,557:0:2,0:25.4:1:30:1:1:0:60:48.304:1:0:0.2 0/1:996:82:41,41:458,455:0.0823:2,2:24.5:1:29.8:1:1:1.00659:60:81:0.0831:0:1.4 -6 32185922 . CAG C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.39471;LSEQ=CATGAGGGCTGTGGCTCAGC;RSEQ=GTCTGCCTGGGAGACCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:53:14,39:94,306:0.1165:2,2:22.9:1:30.7:1:0.61094:1.17:59.9:52:0.1163:0.0308:0.2 0/1:346:144:40,104:65,137:0.4162:2,2:25.9:1:30.5:1:0.40784:1.23283:60:143:0.4194:0.0289:0.1 -6 32185973 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51976;SOR=0;LSEQ=TCGGCCCTGCTCCTGACTTG;RSEQ=CCCACTCAGGCGGTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:7,178:0.0107:1,2:17.5:1:28.5:1:0.08395:23.85:60:4:0.011:0:1 0/0:123:0:0,0:12,111:0:2,0:25.2:1:30.8:1:1:0:60:40:1:0:0.2 -6 32186050 . G A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01839;SOR=4.27922;LSEQ=CCCTGAGGCCCTGCTGCTTC;RSEQ=CAGTGTGTGGCCCTGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:10:1,9:0,32:0.2381:1,2:24.6:1:29:1:0.2381:0:60:20:0.2439:0:1 1/0:19:11:1,10:1,7:0.5789:2,2:30.3:1:30.8:1:1:1.40151:60:22:0.5789:0:1.2 -6 32186147 . C A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=AAGGCTTTCTGGTGGCCATT;RSEQ=CTGTGTATACAGAGGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:33.5:1:28.5:1:1:0:60:4:0.2222:0:1 1/1:2:2:0,2:0,0:1:0,0:26.5:1:31:1:1:0:60:4:1:0:1 -6 32187202 . T C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.48247;LSEQ=ATCTGTGGTAACCCCTCTCC;RSEQ=AGGGGTCTTGGGTGTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:3,1:35,1:0.1:1,2:34.3:1:31.3:1:0.19231:10.24701:60:8:0.1:0:1 1/0:16:12:12,0:4,0:0.75:0,0:20.6:1:30.3:1:1:0:60:24:0.75:0:1.1 -6 32187605 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=3.84376;LSEQ=GAGTCCACAGGGGTCAGGGC;RSEQ=GGAAGGGCAAGGAGGTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:53:20,33:51,189:0.1809:2,2:21.1:1:30.1:1:0.02018:2.24:60:25.5:0.1796:0:1.4 0/1:224:103:22,81:33,88:0.4598:2,2:22.5:1:29.4:1:0.35131:1.3787:60:33.333:0.4587:0:1.3 -6 32187637 . G T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16436;SOR=1.65592;LSEQ=GAGGTGAGACTGTCAGGGAA;RSEQ=GTGTGGGGGCCTGCGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:22:3,19:18,128:0.131:2,2:23.4:1:30:1:0.74126:1.12:60:44:0.1333:0:1.9 0/1:100:20:2,18:9,71:0.2:2,2:26.6:1:29.5:1:1:1.13939:60:19:0.1959:0:2.1 -6 32187721 . AC TT 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55807;SOR=1.51561;LSEQ=GAAAGGAAATAAGGGACCAA;RSEQ=TCATGGGGACTGAGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:12:4,8:31,38:0.1463:2,2:21.6:1:30.6:1:0.53934:1.62202:60:11:0.1429:0.0244:1 0/1:29:6:2,4:7,15:0.2069:2,2:22.5:1:28.5:1:1:1.07:60:12:0.2143:0:1 -6 32187722 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.5429;LSEQ=AAAGGAAATAAGGGACCAAA;RSEQ=TCATGGGGACTGAGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:4:2,2:29,34:0.0519:2,2:22.8:1:31.8:1:1:1.17:60:8:0.0606:0:1.3 1/0:30:15:5,10:3,6:0.5:2,2:19.8:1:30.1:1:1:1:60:30:0.625:0:1.1 -6 32187836 . G GCC 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0;SOR=5.10023;LSEQ=TTTAATTGGAAAAGCAATCT;RSEQ=CCCTTTTCTGTCTTCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:20:18,2:209,21:0.08:2,2:20.4:1:30.5:1:1:1.1054:60:19:0.0776:0.024:0.4 0/1:146:45:43,2:90,11:0.3082:2,1:21:1:31:1:0.34526:2.61:60:90:0.3125:0.0822:0.1 -6 32188099 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.98268;LSEQ=GGTGAGGCTCTCAAAGGCCA;RSEQ=TTGAAGCTCCTAGCAGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:27:14,13:230,318:0.047:2,2:19.5:1:29.7:1:0.32504:1.49:60:26:0.0457:0:1.1 0/1:428:121:45,76:119,186:0.2827:2,2:23.4:1:30.4:1:0.74189:1.08037:60:242:0.2827:0:1.2 -6 32188297 . G C 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=5.89692;LSEQ=TTCTCCTCACAGCTTGTGCC;RSEQ=CCCCAGCCACTCACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1501:77:37,40:728,689:0.0513:2,2:26.5:1:30.4:1:0.63994:1.14217:60:24.667:0.0503:0:1.3 0/1:1294:313:153,160:490,485:0.2419:2,2:23.9:1:30.1:1:0.69687:1.05652:60:61.6:0.2418:0:1.3 -6 32188383 . T C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.11228;LSEQ=GCAGTGAGGGGGACCCTGGG;RSEQ=CTCACACTCATCCACATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:827:124:47,77:253,447:0.1499:2,2:24.3:1:31.7:1:0.76142:1.08:60:248:0.1525:0:1.2 0/1:647:307:129,178:136,203:0.4745:2,2:25.3:1:31:1:0.63171:1.08:60:75.75:0.4742:0:1.2 -6 32188603 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.91155;LSEQ=CAAGTGCCCCCATTCTGACA;RSEQ=TGGTGGCTGACACAGTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1182:38:19,19:567,576:0.0321:2,2:26.4:1:30.9:1:1:1.02:60:76:0.0326:0:1.9 0/1:1040:295:143,152:373,371:0.2837:2,2:24.8:1:29.6:1:0.6309:1.06858:60:146.5:0.2842:0:2.3 -6 32188640 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.01169;LSEQ=TGTCTGGATTCACCTCACAG;RSEQ=CTGGGCCTATGAAACCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:956:31:12,19:411,513:0.0324:2,2:19.8:1:30.5:1:0.58456:1.26821:60:30:0.0321:0:2.6 0/1:823:222:102,120:270,330:0.2697:2,2:26.6:1:31.1:1:0.81335:1.04:60:36:0.2693:0:2.9 -6 32188642 . T C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=11.65872;LSEQ=TCTGGATTCACCTCACAGTC;RSEQ=GGGCCTATGAAACCTGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:947:29:12,17:403,514:0.0306:2,2:20.7:1:30.1:1:0.85084:1.11058:60:58:0.0309:0:2.6 0/1:813:219:101,118:271,323:0.2694:2,2:26.4:1:29.6:1:0.9368:1.02:60:53.75:0.2671:0:2.9 -6 32188678 . G A 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20155;SOR=1.24219;LSEQ=GACAGGGTCATGGATCAGCT;RSEQ=TGGGAGGAGGCTCCAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:86:36,50:262,357:0.1218:2,2:25.1:1:29.2:1:1:1.01927:60:42:0.121:0:1.1 0/1:517:76:33,43:199,242:0.147:2,2:23.2:1:28.7:1:0.80406:1.07139:60:152:0.1484:0:1.1 -6 32188713 . C G 238 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACGGAGACATCCTGCCCTG;RSEQ=CCAGAGAGAGGGGCGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:635:192:88,104:188,251:0.3024:2,2:22:1:31.5:1:0.48684:1.13:60:47:0.3042:0:1.1 0/0:443:0:0,0:213,227:0:2,0:23.7:1:31.2:1:1:0:60:54:0.9931:0:0.3 -6 32188823 . G A 246 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGGCAGGTGCCCCCATTC;RSEQ=AACAGCCCCTAGGAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:306:181,125:313,255:0.3493:2,2:25.1:1:29.9:1:0.25351:1.18:60:50:0.3497:0:1.1 0/0:680:0:0,0:361,319:0:2,0:25.4:1:30.1:1:1:0:60:96.143:1:0:0.2 -6 32189032 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=7.33127;LSEQ=TGGCACTGGATCTGGGGGTA;RSEQ=GTGGCCAGACACACCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1057:53:23,30:434,567:0.0501:2,2:24.2:1:30.2:1:1:1.00:60:52:0.0501:0:1.1 0/1:881:246:104,142:290,343:0.2792:2,2:24.7:1:29.9:1:0.36505:1.15422:60:60.5:0.2785:0:1.2 -6 32189192 . G A 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCACTCTGGATTATCTCT;RSEQ=GGTCTCATTTTCATATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:36:0,36:2,101:0.259:1,1:22.1:1:31.8:1:1:0:60:72:0.2609:0:1.3 0/0:76:0:0,0:6,70:0:2,0:25.7:1:30.3:1:1:0:60:75:1:0:0.1 -6 32190028 . A G 88 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAGATTAAAGGGGCTAG;RSEQ=ACAGGCATCAGGATGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:25.6:1:29.5:1:1:0:60:7:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 32190217 . T C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.05742;LSEQ=AGTTTCTCAGGCTCCAGTTC;RSEQ=ATCTTCCCCACCCACAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:8:8,0:80,6:0.0851:2,0:28.5:1:30.8:1:1:0:60:16:0.086:0:1.1 1/0:37:19:17,2:17,1:0.5135:1,2:25.7:1:29.5:1:1:1.96404:60:18:0.5:0:1.3 -6 32190302 . A T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06693;SOR=Inf;LSEQ=GCTTACCTGTCCATCCAGGC;RSEQ=TGCAGGAGCACTGTGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:0:0,0:289,105:0:2,0:24.5:1:30.2:1:1:0:60:130.333:1:0:0.2 0/1:271:3:1,2:179,89:0.0111:2,2:12.7:1:27.3:1:0.26173:4.00016:60:6:0.0114:0:1.7 -6 32190304 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06686;SOR=Inf;LSEQ=TTACCTGTCCATCCAGGCAT;RSEQ=CAGGAGCACTGTGGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:292,112:0:2,0:24.8:1:31.7:1:1:0:60:49.5:1:0:0.2 0/1:277:3:2,1:182,92:0.0108:2,2:6:1:26.7:1:1:1.01:60:6:0.0109:0:1 -6 32190390 . T G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.14487;LSEQ=AGGACAAGGGTCTTCAAGCT;RSEQ=GGCCTGGCATCTCTCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:945:137:79,58:450,357:0.145:2,2:24.7:1:31.5:1:0.71021:1.08:60:136:0.1459:0:1.9 0/1:799:278:158,120:287,233:0.3479:2,2:23.8:1:30.9:1:0.70846:1.07:60:45.333:0.3483:0:2 -6 32190406 . A G 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.19851;LSEQ=AGCTTGGCCTGGCATCTCTC;RSEQ=CCAGTGAAGCCAGGGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:993:110:60,50:482,400:0.1108:2,2:23.9:1:30.1:1:1:1.00416:60:26.5:0.1088:0:2 0/1:834:328:189,139:269,237:0.3933:2,2:24.7:1:30.7:1:0.22596:1.20:60:108.333:0.393:0:1.9 -6 32190484 . G A 283 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00067;LSEQ=CTGGGGAGCCCTAGGGGAGC;RSEQ=GGAAGCAGGGCTTGGCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:954:626:297,329:154,174:0.6562:2,2:25.8:1:30.5:1:0.89162:1.02:60:77.25:0.6581:0:1.1 0/0:803:1:1,0:383,417:0.0012:2,0:1:0:26:0:0.4794:0:60:2:0.0013:0:1 -6 32190620 . T C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=10.98747;LSEQ=AGGAAAACTCACATCACTGG;RSEQ=CCCTCTTCCTATTCTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:37:12,25:136,224:0.0927:2,2:27.9:1:31.2:1:0.59475:1.26415:60:36:0.0921:0:1.2 1/0:232:123:38,85:29,80:0.5302:2,2:21.7:1:31.5:1:0.56177:1.23:60:60.5:0.5261:0:1.1 -6 32190941 . G A 34 v4;q23;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.26485;SOR=0;LSEQ=TCTTCTAGGTGCTCCTGAGA;RSEQ=ACCTGCCCACAGCAGCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:3,0:51,246:0.01:2,0:7:1:21.7:1:0.00557:0:60:2:0.0068:0:1 0/0:223:0:0,0:60,163:0:2,0:22.5:1:30.9:1:1:0:60:54.75:1:0:0.1 -6 32190994 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53146;SOR=0;LSEQ=AACCACCTCTTCTTCACATC;RSEQ=GTCCCCACTCTCCACATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:0,2:2,121:0.0159:1,0:22.5:1:30.5:1:1:0:60:4:0.0163:0:2 0/0:74:0:0,0:2,72:0:1,0:24.9:1:29.8:1:1:0:60:73:1:0:0.2 -6 32191041 . G A 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19667;SOR=3.25892;LSEQ=CCCCAGCCCCAGTGCCCTCC;RSEQ=TCCCAGTTACTAATCCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:0,3:2,60:0.0462:1,0:12.7:1:32.3:1:1:0:60:6:0.0476:0:1 0/1:29:4:1,3:2,23:0.1379:2,2:28.8:1:31:1:0.37055:3.59:60:8:0.1379:0:1.5 -6 32191457 . G A 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACCCCTGGCACCAGGCCC;RSEQ=AAGCAGCTCCATGGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:197,0:0:1,0:24.1:1:29.3:1:1:0:60:23.625:1:0:0.1 0/1:82:25:24,1:55,2:0.3049:1,1:26.2:1:30.2:1:1:1.14387:60:50:0.3086:0:1 -6 32191544 . C T 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=72.39707;LSEQ=TCCATCCAGCATCCCTCACA;RSEQ=GGCCTGGGGCTTGGCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:965:1:0,1:676,288:0.001:2,0:1:0:28:0:0.29948:0:60:2:0.001:0:1 0/1:657:46:28,18:414,197:0.07:2,2:19.1:1:29:1:0.33309:1.35038:60:45:0.0689:0:1.2 -6 32191581 . T A 262 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=536.13483;LSEQ=CTCTTCCCCCACCCCACTGA;RSEQ=CATCCTCCTAAGGGAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1596:2:1,1:879,711:0.0013:2,2:38:1:31:1:1:1.23612:60:4:0.0013:0:1 0/1:1253:501:286,215:408,342:0.3998:2,2:25.9:1:29.3:1:0.35363:1.11:60:70.571:0.4023:0:1.5 -6 32191607 . C T 247 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=192.55094;LSEQ=TCCTAAGGGAGCTGGGTCCC;RSEQ=TCACCTCACCCACGCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2016:2:0,2:1002,1009:0.001:2,0:1:0:27:1:0.49976:0:60:4:0.001:0:1.5 0/1:1712:275:149,126:738,697:0.1606:2,2:25.4:1:30.6:1:0.42938:1.12:60:274:0.1612:0:1.8 -6 32191620 . C T 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.6434;LSEQ=GGGTCCCCTCACCTCACCCA;RSEQ=GCCATGCCTCACCTCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2052:227:112,115:863,958:0.1106:2,2:24.3:1:30.3:1:0.6219:1.08:60:112.5:0.1109:0:1.2 0/1:1790:443:219,224:685,661:0.2475:2,2:25.3:1:29.8:1:0.62209:1.0599:60:146.667:0.2489:0:1.2 -6 32191658 . TAGC T 286 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=10.000;MSILEN=3;SSF=0;SOR=0.4617;LSEQ=GGTCTGACCACTGAGACACA;RSEQ=AGCAGCAGCAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1682:615:257,358:451,565:0.3656:2,2:32.1:1:30.9:1:0.32745:1.11186:60:122:0.3686:0.0345:0.4 0/1:1518:319:149,170:475,491:0.2101:2,2:33.5:1:30.5:1:0.47739:1.10367:60:318:0.2106:0.0086:0.4 -6 32191730 . G A 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.7334;LSEQ=CAGCCCCTTCTCCAAGCCCC;RSEQ=GTCCCTGTCCCTCTTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:899:340:119,221:194,365:0.3782:2,2:24.9:1:30.6:1:0.94253:1.01:60:41.5:0.3768:0:1.2 1/0:752:386:132,254:132,234:0.5133:2,2:23.8:1:30.3:1:0.59371:1.08535:59.9:41.889:0.5095:0:1.2 -6 32191822 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0102;SOR=Inf;LSEQ=TGCCCCTCTTCTTCCTCCTC;RSEQ=GCCTGCTGCAAGCCTCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:4,201:0:1,0:24.2:1:31:1:1:0:60:50.25:1:0:0.2 0/1:97:4:1,3:3,90:0.0412:1,2:28.8:1:30.3:1:0.15732:9.42:60:8:0.0412:0:1 -6 32877073 . A G 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=0.21684;LSEQ=AATTTACTGAATGTTCATTC;RSEQ=TTTTAACTTTTTTAAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:32:20,12:126,34:0.1667:2,2:22.8:1:29.9:1:0.06797:2.21301:60:64:0.1675:0:1.1 0/1:169:7:5,2:111,50:0.0414:2,2:28.3:1:30.4:1:1:1.13:60:14:0.0414:0:1 -6 32877076 . T C 25 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.21274;SOR=Inf;LSEQ=TTACTGAATGTTCATTCATT;RSEQ=TAACTTTTTTAAGTGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:154,51:0:2,0:22.5:1:30.1:1:1:0:60:410:1:0:0.3 0/1:176:2:1,1:119,55:0.0114:2,2:10:0:25:1:0.53636:2.15327:60:4:0.0114:0:1 -6 32877173 . A G 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01302;SOR=0.70109;LSEQ=CATTCTTGAATATTCACTAT;RSEQ=AGCCTGATGCTATGCGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:203:108,95:121,106:0.471:2,2:23.5:1:31.1:1:1:1.0041:59.9:28:0.4656:0:1.2 0/1:380:146:74,72:116,118:0.3842:2,2:24.4:1:31.1:1:0.91603:1.05:60:72:0.384:0:1.2 -6 32877176 . C T 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06395;SOR=0;LSEQ=TCTTGAATATTCACTATAAG;RSEQ=CTGATGCTATGCGAGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:5:0,5:226,206:0.0114:2,0:6.4:1:24.4:1:0.0256:0:60:4:0.0094:0:2 0/0:388:0:0,0:191,197:0:2,0:23.5:1:31:1:1:0:60:54.429:1:0:0.5 -6 32877266 . G A 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38394;SOR=0.80889;LSEQ=TATGGCTGAGTTTTTAAAAT;RSEQ=TAATTCAAGCTTTTCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:90:18,72:37,91:0.4128:2,2:21.6:1:31:1:0.15563:1.62281:60:180:0.4186:0:1.2 0/1:149:54:15,39:24,71:0.3624:2,2:19.8:1:29.4:1:0.84653:1.14:60:108:0.3624:0:1.2 -6 32942572 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.50198;SOR=Inf;LSEQ=GACATTGGAGCCGGGGAGGT;RSEQ=TGGGATGAGCAAGAATGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:0:0,0:32.1:1:32:1:1:0:60:18:1:0:0 0/1:14:2:1,1:4,8:0.1429:2,2:9:1:27.5:1:1:1.90:60:4:0.1429:0:1 -6 32944987 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAGTTATAGGGTGGAAA;RSEQ=ACAGGCATAGGCCACCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:10.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 32945230 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15698;SOR=Inf;LSEQ=CTTCTGCAGCGGAAGATGGA;RSEQ=AACCGTGATTACCGGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:56,24:0:2,0:21.2:1:31.1:1:1:0:60:25.667:1:0:0.2 0/1:53:2:1,1:37,14:0.0377:2,2:29.5:1:27:1:0.48984:2.58752:60:4:0.0377:0:2 -6 32945235 . G T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56298;SOR=3.09216;LSEQ=GCAGCGGAAGATGGAGAACC;RSEQ=TGATTACCGGGATGCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:0,1:63,32:0.0104:2,0:1:0:26:0:0.34375:0:60:2:0.011:0:1 0/1:63:2:1,1:41,20:0.0317:2,2:25:1:31.5:1:1:2.0249:60:4:0.0323:0:1 -6 32945243 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1641;SOR=Inf;LSEQ=AGATGGAGAACCGTGATTAC;RSEQ=GGGATGCACAGGAGTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:68,36:0:2,0:22.3:1:30:1:1:0:60:33.667:0.9902:0:0.2 0/1:72:2:1,1:45,24:0.0278:2,2:41:1:29.5:1:1:1.85749:60:4:0.0286:0:2 -6 32945254 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19012;SOR=Inf;LSEQ=CGTGATTACCGGGATGCACA;RSEQ=GAGTTTGCTGCTGATGTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:67,41:0:2,0:26.8:1:31.4:1:1:0:60:26:1:0:0.2 0/1:84:2:1,1:48,34:0.0238:2,2:11:0:30.5:1:1:1.40585:60:4:0.0238:0:1 -6 32945296 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5021;SOR=0;LSEQ=CTTATGTTCTCCAACTGCTA;RSEQ=AAGTACAATCCCCCAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:50,64:0.0172:2,2:10.5:1:30.5:1:1:1.28:60:4:0.0177:0:1 0/0:96:0:0,0:40,56:0:2,0:25.1:1:27.9:1:1:0:60:47:1:0:0.2 -6 33286403 . A T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29179;SOR=0;LSEQ=TTAAGCTTTTTTTTTTTTTT;RSEQ=AAGAAACACCACCAAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:3:3,0:57,2:0.0469:1,0:21.3:1:24:1:1:0:53.3:2:0.0345:0:2.7 0/0:38:0:0,0:36,1:0:1,0:24.8:1:26.1:1:1:0:60:11.333:1:0:0.7 -6 33286430 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50472;SOR=0;LSEQ=CACCACCAAAAGGGGATTAG;RSEQ=TTAGTCCATCCCTTCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:2,0:100,10:0.0179:2,0:19.5:1:29.5:1:1:0:60:4:0.0204:0:3.5 0/0:88:0:0,0:80,8:0:2,0:37:0:14:0:1:0:60:0:0:0:8 -6 33286460 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=CCCTTCCTCAGTCATCTGCT;RSEQ=CCCACCTTCCTCCAAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:136,41:0:2,0:26.7:1:29.6:1:1:0:60:34.4:1:0:0.2 0/1:179:2:1,1:133,44:0.0112:2,2:29.5:1:26:0:0.44065:3.00017:60:4:0.0114:0:3 -6 33286501 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37439;SOR=3.77421;LSEQ=ATCCCAGAACATTCTGGAGG;RSEQ=AGGGAGAAGGGGAGGCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:1:0,1:199,112:0.0032:2,0:1:0:23:0:0.36218:0:60:2:0.0032:0:1 0/1:333:4:1,3:210,119:0.012:2,2:7.3:1:25:1:0.14126:5.26739:60:8:0.0123:0:1 -6 33287100 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07303;SOR=Inf;LSEQ=AGTTCCCCAGTATTGCTCTC;RSEQ=GAAAGTCCCCTGCAATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:207,123:0:2,0:22.8:1:30.5:1:1:0:60:65:1:0:0.1 0/1:238:3:1,2:156,79:0.0126:2,2:9:1:25.3:1:0.26773:3.92486:60:6:0.0127:0:1 -6 33287183 . T C 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTAATGGCCCTGATCCTGT;RSEQ=TGCTTCTTCTCCTTCCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:808:0:0,0:440,368:0:2,0:25.9:1:30.2:1:1:0:60:88.778:1:0:0.1 0/1:785:46:28,18:396,342:0.0586:2,2:25.5:1:31:1:0.36401:1.34:60:45:0.0583:0:1.1 -6 33287796 . G C 203 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CCCTTGACATACCTGCTGCT;RSEQ=CTTCTTCCTCTTCGTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1439:0:0,0:795,643:0:2,0:25.1:1:32:1:1:0:60:78.889:0.9993:0:0.1 0/1:1464:104:52,52:738,616:0.071:2,2:27.8:1:30.4:1:0.41423:1.1979:60:33.667:0.0699:0:1.1 -6 33287897 . TTCC T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.89443;SOR=0.95121;LSEQ=GTGGCCTCCTCCTCTTCTTC;RSEQ=TCCTCCTCCTCCTCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:30:12,18:409,548:0.0304:2,2:25.1:1:29.5:1:0.85242:1.11936:59.8:60:0.0311:0.0071:0.3 0/1:968:28:15,13:431,506:0.0289:2,2:21.8:1:31.2:1:0.44787:1.35:60:56:0.0295:0.0052:0.4 -6 33288067 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06872;SOR=Inf;LSEQ=GTTTGGTTCTTGCTTTCCTT;RSEQ=TCATGCTCCCCCATCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:0:0,0:146,223:0:2,0:23.5:1:31.7:1:1:0:60:45.125:1:0:0.5 0/1:257:3:1,2:91,162:0.0117:2,2:17:1:25.7:1:1:1.12297:60:2:0.008:0:2 -6 33288075 . C A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.30527;LSEQ=CTTGCTTTCCTTCTCATGCT;RSEQ=CCCCATCAGTCAACCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:163:73,90:71,109:0.4752:2,2:22.5:1:28.8:1:0.32634:1.24:60:39.75:0.4718:0:1.1 0/1:222:48:21,27:63,111:0.2162:2,2:22.7:1:29.3:1:0.40108:1.37:60:96:0.2222:0:1.1 -6 33288086 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1547;SOR=Inf;LSEQ=TCTCATGCTCCCCCATCAGT;RSEQ=AACCTGGACTCCCTGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:130,170:0:2,0:24.5:1:31.6:1:1:0:60:49:1:0:0.6 0/1:195:2:1,1:78,115:0.0103:2,2:7.5:1:28:1:1:1.47:60:4:0.0104:0:1 -6 33288271 . A G 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21755;LSEQ=CTTTTGTCTTGCAACATTGC;RSEQ=TATTTGGAGATGACCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:832:386:194,192:219,225:0.4639:2,2:26.8:1:30.5:1:0.83465:1.04:60:54.143:0.465:0:1.1 0/1:859:136:68,68:361,359:0.1583:2,2:28.4:1:29.7:1:1:1.00556:60:33:0.1562:0:1.1 -6 33288506 . C A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAGAGGCATCCCACCAAC;RSEQ=CCCTACCTGGCCTATAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:239,161:0:2,0:25.6:1:31:1:1:0:60:132.333:1:0:0.1 0/1:400:30:16,14:216,153:0.075:2,2:24.8:1:28.1:1:0.57123:1.23462:60:29:0.0734:0:1.3 -6 33289316 . G A 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45271;SOR=0.42393;LSEQ=GGACCACCTCAGGGTGGTCT;RSEQ=CTGTCTGCATCTTACAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:5:4,1:161,235:0.0124:2,2:9.8:1:26:1:0.16413:5.81:60:10:0.0127:0:1 0/0:377:2:2,0:156,219:0.0053:2,0:1:0:22.5:1:0.175:0:60:4:0.0053:0:1 -6 33289356 . A G 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13216;SOR=0;LSEQ=TTCAAGGAACTAGAAGGTTC;RSEQ=GGGGAAGAAGGAAGGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:4:3,1:140,185:0.0122:2,2:25.5:1:30.5:1:0.32074:3.95:60:8:0.0125:0:1 0/0:266:0:0,0:115,151:0:2,0:24.1:1:30.5:1:1:0:60:87.667:1:0:0.1 -6 33289411 . T A 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07587;SOR=Inf;LSEQ=GGGTTGAGAGAAAGGGGAGG;RSEQ=GGGGTTAGTGGGAAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:225,104:0:2,0:22.7:1:29.2:1:1:0:60:24.308:1:0:0.1 0/1:244:3:2,1:169,72:0.0123:2,2:20.3:1:23.7:1:1:1.1728:60:2:0.0084:0:1 -6 33289707 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72792;SOR=1.51613;LSEQ=TGTTAGCGGTGGCCATAGGG;RSEQ=ATCAAATCCCCCGGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:3:2,1:144,260:0.0074:2,2:14:1:19:1:0.29324:3.60:60:0.5:0.0025:0:2.7 0/1:450:5:4,1:172,273:0.0111:2,2:10.2:1:26:1:0.07922:6.32:60:10:0.0114:0:1 -6 33289739 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11439;SOR=Inf;LSEQ=CGGAGGGAGGAAGTGGTGGG;RSEQ=ATTTCAGAATTCCTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:71,194:0:2,0:24.4:1:31:1:1:0:60:131.5:1:0:0.1 0/1:251:3:1,2:70,178:0.012:2,2:20:1:28.3:1:1:1.27:60:6:0.0122:0:1 -6 33289931 . T TG 33 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGGGCCCTTCAAGTGGTG;RSEQ=GGGGGGGGGGCAAACCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:1,6:0.1818:2,2:30:1:33:1:0.41667:4.58:60:4:0.2:0:2 0/0:1:0:0,0:0,1:0:0,0:33:0:29:0:1:0:60:2:1:0:0 -6 33290402 . G A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4025;SOR=0.38064;LSEQ=AACTGATCAAAAGTCCCCCC;RSEQ=CACCGCGCTACGCTCTCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:13,0:12,0:0.52:0,1:22.1:1:27.2:1:1:0:60:3.333:0.5:0:1.2 0/1:7:2:1,1:5,0:0.2857:0,2:40:1:29:0:0.28571:0:60:4:0.2857:0:2 -6 33290547 . T A 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.08289;SOR=0.75476;LSEQ=GGACAGGAAGGTACCACAGC;RSEQ=TTCCCCTCAGACTCAGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:359:207:165,42:116,35:0.5766:2,2:24.3:1:28.4:1:0.51783:1.18:60:8.409:0.5799:0:1.7 1/0:296:150:123,27:120,25:0.5068:2,2:21.1:1:29.4:1:0.87978:1.0535:60:17.75:0.5145:0:1.7 -6 33290825 . A G 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54479;SOR=0.81377;LSEQ=GCTTCCTGTGGCCGGAGGTG;RSEQ=CAGTAGGCCCGCCCCGCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:112:61:3,58:1,50:0.5446:1,1:22.4:1:32.6:1:0.62432:2.57:60:122:0.5446:0:1.4 0/1:71:35:1,34:1,35:0.493:1,1:22.8:1:31.9:1:1:1.03:60:34:0.4857:0:1.3 -6 33290827 . A T 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15819;SOR=0;LSEQ=TTCCTGTGGCCGGAGGTGAC;RSEQ=GTAGGCCCGCCCCGCGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:5:0,5:4,102:0.045:1,0:17.8:1:30.4:1:1:0:60:10:0.0459:0:1 0/0:68:0:0,0:2,66:0:1,0:25.4:1:31.1:1:1:0:60:33:1:0:0.7 -6 33290872 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03206;SOR=0.2455;LSEQ=CAGTGCGGCCCACATAGTCA;RSEQ=CGGTCTCTTCCAGGTCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:21:0,21:0,24:0.4667:1,1:25.5:1:29.9:1:1:0:60:42:0.4884:0:2 0/1:23:4:0,4:0,19:0.1739:1,0:24:1:29.8:1:1:0:60:8:0.1818:0:3 -6 33290900 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCAGGTCGGAGTTTGTCT;RSEQ=CCCGAACCCAGGCGTCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:0,34:0.0556:1,0:22:1:26.5:1:1:0:60:4:0.0571:0:1.5 0/0:6:0:0,0:0,6:0:0,0:21.5:1:31.3:1:1:0:60:12:1:0:0.7 -6 34294906 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49717;SOR=Inf;LSEQ=GTCATCCAAATGATTGATAA;RSEQ=GTCAAGCAAGTCACATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:29,32:0:2,0:28.6:1:31.3:1:1:0:60:60:1:0:0.1 0/1:67:2:1,1:30,35:0.0299:2,2:42:1:29.5:1:1:1.16:60:4:0.0299:0:1 -6 34617036 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22835;SOR=0;LSEQ=TAGGTCACGTAACTCTGAAA;RSEQ=GGTCAAAGATATTGATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:115,39:0.0127:2,2:26.5:1:31.5:1:0.4483:2.92406:60:4:0.0129:0:1 0/0:171:0:0,0:121,50:0:2,0:23.3:1:30.1:1:1:0:60:170:1:0:0.1 -6 34617144 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05235;LSEQ=GAGAAGTATAATAGAACTGG;RSEQ=CTCCAAATTAAGTCTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:273:240:108,132:15,18:0.8791:2,2:24.3:1:31.4:1:1:1.01845:60:79:0.8778:0:1.1 0/1:248:68:25,43:79,100:0.2742:2,2:27.2:1:31.9:1:0.31565:1.35712:60:136:0.2753:0:1.1 -6 34617243 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51198;SOR=0;LSEQ=GTTTTATGACGTTCCTAGTT;RSEQ=AGTATCACAATCAAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:6,72:0.025:2,2:34:1:28:1:0.16835:11.19:60:4:0.025:0:1 0/0:56:0:0,0:9,47:0:2,0:23.1:1:29:1:1:0:60:112:1:0:0 -6 34803947 . C T 92 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00022;SOR=0;LSEQ=ATGTAGATCACTCCACCAGC;RSEQ=CCCAGTGCCCAGCAGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:1:0,2:19.1:1:30.8:1:1:0:60:16:1:0:1.1 0/1:19:4:3,1:10,5:0.2105:2,2:20:1:30.5:1:1:1.47:60:8:0.2222:0:1 -6 34804012 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.53529;SOR=Inf;LSEQ=GGGCAACAGCAACAGCAGCA;RSEQ=CAGCCGCCTCAGCCAGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:35.8:1:32.7:1:1:0:60:38:1:0:0.3 0/1:35:2:1,1:14,19:0.0571:2,2:38.5:1:29:1:1:1.35:60:4:0.0571:0:1 -6 35758334 . C G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAAGGAAGTTAGAATTTG;RSEQ=GGGTTATGTACCATCTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 35758979 . C T 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=Inf;LSEQ=TGGTCATTGGTAGAGGCTGC;RSEQ=GTTGTCAGAATCCAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:37:1:28.8:1:1:0:60:5:1:0:0 0/1:8:2:1,1:3,3:0.25:2,2:12:1:32:1:1:1:60:4:0.25:0:1.5 -6 35759063 . T C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57158;SOR=1.46714;LSEQ=GCTACATCCTGATAAACACA;RSEQ=TGTTTAAGTTGAAAATATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:1,5:6,9:0.2857:2,2:30.8:1:32.8:1:0.61262:3.16415:60:12:0.3158:0:1.2 0/1:35:13:6,7:12,10:0.3714:2,2:29.5:1:31.6:1:0.73322:1.38652:60:26:0.3714:0:1.2 -6 35759082 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51429;SOR=Inf;LSEQ=ATTGTTTAAGTTGAAAATAT;RSEQ=GTAAGTTGAAAATACGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:5,17:0:2,0:21.2:1:30.1:1:1:0:60:44:1:0:0.5 0/1:34:2:1,1:16,16:0.0588:2,2:12.5:1:28.5:1:1:1:60:4:0.0588:0:1 -6 36104803 . T C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=8.000;MSILEN=1;SSF=1;SOR=0.57733;LSEQ=ACTTTATTTAAATAACTGTC;RSEQ=TTTTTTTCTTAATGTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:33:1:33:0:1:0:60:4:0.6667:0:1 1/0:2:1:0,1:0,1:0.5:0,0:14:0:27:0:1:0:60:2:0.5:0:1 -6 36645466 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51422;SOR=1.62192;LSEQ=GGCATTTTTGTCATTTTGGA;RSEQ=CCACAGAAATAAAGGATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:6:6,0:84,0:0.0667:1,0:14.5:1:30.2:1:1:0:60:12:0.0674:0:2 0/1:48:5:5,0:43,0:0.1042:1,0:23.2:1:30.8:1:1:0:60:10:0.1064:0:1 -6 36645549 . G T 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03177;SOR=Inf;LSEQ=ACTATAGTCATTTCTTTGCT;RSEQ=CATGATCTGAGTTAGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:347,93:0:2,0:22.7:1:31.7:1:1:0:60:54:1:0:0.2 0/1:323:4:2,2:245,74:0.0124:2,2:16:1:27.8:1:0.2364:3.29547:60:8:0.0125:0:1.5 -6 36645588 . A C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.22022;LSEQ=ACCAGACTTCTCTGAGCCCC;RSEQ=GTTTCCCCAGCAGTGTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:791:35:22,13:481,272:0.0442:2,2:32.1:1:30.5:1:1:1.04488:60:70:0.045:0:1.1 0/1:642:161:96,65:307,174:0.2508:2,2:24.8:1:29.5:1:0.34762:1.19428:60:52.667:0.25:0:1.2 -6 36645696 . A G 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.76032;LSEQ=AAGCTGCTGCAACCACAGGG;RSEQ=TTTCTTCTGTTCAGGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:984:146:55,91:353,484:0.1484:2,2:26.1:1:31:1:0.31831:1.2065:60:47.667:0.1482:0:1.2 0/1:905:294:133,161:261,349:0.3249:2,2:25.3:1:30.9:1:0.51947:1.10:60:293:0.3281:0:1.2 -6 36648084 . C CGTGTGTGT 92 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=38;MSI=23.000;MSILEN=2;SSF=0.29123;SOR=0;LSEQ=CGCGTGCGTGTCTGCGCGGG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:8,0:13,0:0.3077:1,0:13.8:1:30.7:1:1:0:59.9:16:0.32:0.2308:1 0/0:5:0:0,0:5,0:0:0,0:23.8:1:26:1:1:0:56:4:1:0:1.2 -6 36648117 . G GTC 46 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=18.000;MSILEN=2;SSF=0.01087;SOR=Inf;LSEQ=GTGTGTGTGTGTGTGTGTGT;RSEQ=TGTGTCTGTGTCAGAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:35,0:0:1,0:18.9:1:32.2:1:1:0:58.4:34:1:0:0.7 0/1:11:3:3,0:8,0:0.2727:0,0:22:1:29.2:1:1:0:60:6:0.2727:0.1818:1 -6 36648275 . C CAG 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=5.95748;LSEQ=ACGCGCAGCCGGAGTGGAAG;RSEQ=AGTTTTGGCGGGCGAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:863:111:65,46:471,279:0.1286:2,2:26.5:1:30.2:1:0.40252:1.19445:59.9:110:0.1305:0.022:0.2 0/1:786:368:217,151:247,169:0.4682:2,2:26.2:1:30.3:1:0.942:1.017:60:367:0.4699:0.0814:0.3 -6 36648364 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.59369;LSEQ=TCTGCCCACGCACCTCCCAC;RSEQ=CCGCGCGTGATTTCCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1222:111:57,54:517,593:0.0908:2,2:25.1:1:30.6:1:0.36974:1.21:60:26.75:0.0902:0:1.2 0/1:1065:382:177,205:326,357:0.3587:2,2:26.5:1:30.2:1:0.70107:1.05753:60:41.444:0.3614:0:1.2 -6 36649593 . A G 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTAGCCAGGATGGTCTC;RSEQ=ATCTCCTGACCTCGTGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:27.5:1:1:0:50:4:1:0:1 -6 36650267 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=CCCTTTAAACTTGGTGTGAA;RSEQ=TTACCAAGAGCCTCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:0.1818:0,0:23.5:1:31.5:1:1:0:60:4:0.1818:0:1 0/0:8:0:0,0:7,1:0:2,0:20.8:1:30.9:1:1:0:60:16:1:0:0 -6 36650436 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0652;SOR=Inf;LSEQ=GAAACTGCAAGTTGGGACTT;RSEQ=TCCCTAGGAAAATCCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:249,39:0:2,0:23.7:1:32:1:1:0:60:71:1:0:0.1 0/1:195:3:1,2:164,28:0.0154:2,2:26:1:29.7:1:0.06232:11.46954:60:6:0.0155:0:1 -6 36650467 . C T 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00298;SOR=Inf;LSEQ=AATCCAGTTGCTGCCAAGGT;RSEQ=GTGCAGTCACTCAGCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:373,118:0:2,0:24.1:1:30.6:1:1:0:60:69.143:1:0:0.1 0/1:382:7:2,5:257,118:0.0183:2,2:5.3:1:27.3:1:0.03765:5.41829:60:14:0.0185:0:1.4 -6 36650547 . G A 224 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATGGGCAAACTCACTCTCC;RSEQ=TTTTCCCTCTCCTGAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1075:163:79,84:443,468:0.1516:2,2:26.1:1:30.5:1:1:1.00649:60:162:0.1523:0:1.1 0/0:938:0:0,0:470,465:0:2,0:25.4:1:30.2:1:1:0:60:132.571:0.9968:0:0.4 -6 36650565 . G C 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=4.61114;LSEQ=CCGTTTTCCCTCTCCTGAAG;RSEQ=GGGAGGAGAGGAGCCAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1101:56:25,31:483,559:0.0509:2,2:26.4:1:30.3:1:0.8908:1.07137:60:55:0.0507:0:1.1 0/1:1029:204:99,105:409,410:0.1983:2,2:22.7:1:30.5:1:0.75445:1.05799:60:101:0.1992:0:1.2 -6 36650659 . G A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10421;SOR=5.71163;LSEQ=GGCAACACGAGGCAGGGGCT;RSEQ=CCAGGTGTCTAGACTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:1:1,0:189,343:0.0019:2,0:1:0:21:0:0.35647:0:60:2:0.0019:0:1 0/1:470:5:4,1:156,309:0.0106:2,2:5.8:1:24:1:0.04795:7.89:60:10:0.0107:0:1 -6 36650706 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16442;SOR=Inf;LSEQ=GATGTGCCTGGCAGGATGTG;RSEQ=CTCAGCCTGGGAGAAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:8,198:0:1,0:25.2:1:32.1:1:1:0:60:33.333:1:0:0.1 0/1:141:2:0,2:8,131:0.0142:2,0:20:1:30:1:1:0:60:4:0.0144:0:1 -6 36651971 . C A 199 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.49362;LSEQ=GTGGACAGCGAGCAGCTGAG;RSEQ=CGCGACTGTGATGCGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:34:20,14:301,278:0.0555:2,2:25.1:1:30.2:1:0.48311:1.32:60:68:0.0576:0:1.2 0/1:579:121:72,49:256,200:0.209:2,2:24.5:1:28.8:1:0.53663:1.15:60:120:0.2109:0:1.1 -6 36652339 . C G 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.43773;LSEQ=GACAGGTGCGGACATGTGCA;RSEQ=GGAAGGACTTTGTAAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:81:33,48:130,200:0.1971:2,2:23.9:1:31.5:1:0.89922:1.06:60:80:0.198:0:1.2 0/1:347:130:51,79:84,133:0.3746:2,2:23.4:1:30.3:1:1:1.02:60:129:0.3772:0:1.2 -6 36652366 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17917;SOR=Inf;LSEQ=ACTTTGTAAGGGACCAGGAT;RSEQ=CTCAGAATCCATGGTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:96,169:0:2,0:24:1:29.7:1:1:0:60:65.25:1:0:0.3 0/1:195:2:1,1:55,138:0.0103:2,2:21.5:1:29.5:1:0.49294:2.50:60:4:0.0105:0:2 -6 36653438 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18918;SOR=Inf;LSEQ=CCATTGGCCCCAGGGAAGGG;RSEQ=GTCCTGGCCCCCCACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:191,37:0:2,0:24.8:1:29.9:1:1:0:60:227:1:0:0.1 0/1:176:2:1,1:140,33:0.0114:2,2:26:1:29:1:0.35172:4.19447:60:4:0.0116:0:1.5 -6 36653471 . C T 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43508;SOR=2.17228;LSEQ=CACTGTCTTCCTCAGTTGGG;RSEQ=AGCTCCGCCGCGTCCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:2:0,2:284,115:0.005:2,0:1:0:24.5:1:0.08461:0:60:4:0.005:0:1 0/1:371:4:1,3:254,113:0.0108:2,2:10:1:26.5:1:0.09244:6.70559:60:8:0.011:0:1.3 -6 36653597 . C T 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.99734;LSEQ=ATCCGCCCACAGGAAGCCTG;RSEQ=AGTCCTGGAAGCGCGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:17:6,11:229,386:0.0269:2,2:29.7:1:29.1:1:1:1.08752:60:34:0.0273:0:1.1 0/1:651:118:45,73:221,311:0.1813:2,2:26.1:1:28.3:1:0.5354:1.15252:60:58:0.181:0:1.2 -6 37137426 . C A 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGAGCCCTTGACCCAAAA;RSEQ=CCTCAGCGAAACGGAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:10:1:26.5:1:1:0:60:4:1:0:1 -6 37138023 . GGCA G 80 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=10.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCAGCGGCGGCGGCGGGACC;RSEQ=GCAGCAGCAGCAGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38.5:1:33:0:1:0:60:4:1:0:0.5 1/1:6:6:2,4:0,0:1:0,2:30:1:31.2:1:1:0:60:12:1:0:0.2 -6 37138220 . C G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23955;SOR=1.42231;LSEQ=CCTTCCGCGCCAGCCGCAGC;RSEQ=ACAGCCGCAACGCCACCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:39:39,0:60,1:0.39:1,1:25:1:30.5:1:1:0:60:78:0.3939:0:1.1 0/1:86:41:37,4:40,5:0.4767:2,2:26:1:30.3:1:1:1.15:60:82:0.4767:0:1.1 -6 37139322 . T C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2108;SOR=1.97885;LSEQ=CTCGGCCCGGCCCGGCCCAG;RSEQ=CCGGAGGCCTCGGCCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:14:3,11:3,23:0.35:2,2:25:1:32:1:0.64557:2.05:60:28:0.35:0:1.1 1/0:27:14:4,10:2,11:0.5185:2,2:18.9:1:30.6:1:0.64831:2.14:60:28:0.5185:0:1.1 -6 37140501 . C T 80 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21454;SOR=2.76386;LSEQ=GGCCTCAAGTTTTGGGTCTG;RSEQ=GGCCAGCTGTGTTTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:2:1,1:240,262:0.004:2,2:31:1:20:1:1:1.09:60:1:0.002:0:4.5 0/1:734:8:2,6:354,372:0.0109:2,2:15.5:1:26.9:1:0.28815:2.85137:60:16:0.0111:0:1.5 -6 37140599 . C T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11492;SOR=0;LSEQ=TGCTTTGGGTTGGAGAGATG;RSEQ=CGTAAGGTGCGCCTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:2,1:83,178:0.0113:2,2:27.7:1:23.7:1:0.24335:4.26:60:2:0.0078:0:3 0/0:279:0:0,0:82,197:0:2,0:24.7:1:30.8:1:1:0:60:38.857:1:0:0.2 -6 37140684 . T A 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.41617;SOR=2.43355;LSEQ=GAAGGGATTTTTTTTTTTTT;RSEQ=AAAAGAAAGAGTTATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:98,56:0.0127:2,2:10:1:29.5:1:1:1.74332:60:4:0.0129:0:1 0/1:131:4:1,3:86,35:0.0305:2,2:7.8:1:28.8:1:0.08335:7.24023:60:4:0.0258:0:1.5 -6 37140733 . C A 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=Inf;LSEQ=CTTCTTTGTGCTTGTTTTTG;RSEQ=TAAAAGTGTGTTTTCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:224,81:0:2,0:25.3:1:31.2:1:1:0:60:29.5:1:0:0.2 0/1:352:12:9,3:234,105:0.0341:2,2:26.1:1:28.8:1:0.76173:1.35:60:24:0.0354:0:1.3 -6 37141622 . T C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00117;SOR=Inf;LSEQ=TCCCTGGGACCCCAGACTTG;RSEQ=GGGCCTCTGAGAAGCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:122,15:0:2,0:22.6:1:29.8:1:1:0:60:67.5:1:0:0.1 0/1:107:8:7,1:89,10:0.0748:2,2:23.6:1:31.4:1:0.59319:1.26834:60:7:0.066:0:1.1 -6 37141696 . C A 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATTCATAACCTCGTCTAT;RSEQ=CTCCTTTCTGCAGAATGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:0:0,0:305,195:0:2,0:25.9:1:31.2:1:1:0:60:82.333:0.996:0:0.1 0/1:569:21:11,10:338,210:0.0369:2,2:20.8:1:30:1:0.49405:1.46215:60:42:0.037:0:1.2 -6 37141734 . G T 94 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04961;SOR=7.21788;LSEQ=TCAGCATCTCATTAGATGGT;RSEQ=CTTGGCCCTGAGACCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:1:0,1:355,276:0.0016:2,0:34:0:32:0:0.43829:0:60:2:0.0016:0:1 0/1:795:9:5,4:434,352:0.0113:2,2:22:1:29.7:1:1:1.01:60:18:0.0114:0:1.2 -6 37141962 . C A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02135;SOR=Inf;LSEQ=AGTACCAGTGACACGTCTCG;RSEQ=CAAGCAGGACAGTGCTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:2,64:0:1,0:26.5:1:30.9:1:1:0:60:15.5:1:0:0.2 0/1:59:5:0,5:0,54:0.0847:1,0:28.8:1:29.8:1:1:0:60:10:0.0862:0:1.2 -6 38591531 . G A 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05263;SOR=0;LSEQ=TTGCTATTACTTGCCTTTGG;RSEQ=CCCTGTATTTTTAAACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:16.5:1:28.5:1:1:1.73:60:4:0.5:0:1.5 0/0:15:0:0,0:6,9:0:2,0:25.9:1:32.1:1:1:0:60:30:1:0:0.1 -6 39189959 . C G 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AATCTGGGAAGGTCACCAAA;RSEQ=GGGAGACGGAATGTCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:20:1:32:1:1:0:60:6:0.6:0:1 0/0:4:0:0,0:4,0:0:0,0:21.3:1:27:1:1:0:60:3:1:0:1.3 -6 39190287 . T A 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0532;SOR=1.3077;LSEQ=CTACTTGAAAATTGCAAAAA;RSEQ=TTGATGGAGTTCAAATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:148:74,74:161,187:0.2984:2,2:26.2:1:30.4:1:0.4917:1.16:60:48.333:0.2977:0:1.1 0/1:456:163:86,77:143,150:0.3575:2,2:24.5:1:29.5:1:0.43555:1.17:60:162:0.356:0:1.1 -6 39338315 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50029;SOR=0;LSEQ=CATATATTGGAGTCAAAAGT;RSEQ=AGTTCTGAGACAGACCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:168,23:0.0104:2,2:17.5:1:31:1:0.23381:7.17128:60:4:0.0105:0:1 0/0:172:0:0,0:143,29:0:2,0:23.2:1:31.7:1:1:0:60:85:1:0:0.1 -6 39338368 . C T 65 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75207;SOR=1.26046;LSEQ=ACATTTTCAAAGTGAAATGG;RSEQ=GAGAGCTGGCTAGACAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:4:1,3:277,191:0.0085:2,2:2.5:1:27.3:1:0.31042:4.33774:60:8:0.0086:0:2 0/1:469:5:1,4:278,186:0.0107:2,2:10.2:1:28:1:0.16328:5.95741:60:10:0.0108:0:1.6 -6 39338435 . A G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0852;LSEQ=GGCCAAAATAAATGTTTGAC;RSEQ=AGAATTCCTTTAAAAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:597:563:257,306:13,21:0.943:2,2:26.4:1:30.6:1:0.4791:1.36:60:92.833:0.9441:0:1.1 1/0:602:352:161,191:112,138:0.5847:2,2:26.1:1:30.2:1:0.8681:1.04:60:87:0.5859:0:1.2 -6 39338532 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51258;SOR=0;LSEQ=TGCTTCTTCCTCCCTCAGGG;RSEQ=CAGTGAAGGAGCCCGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:20,132:0.0129:2,2:24:1:29.5:1:0.2549:6.47:60:4:0.0134:0:1 0/0:110:0:0,0:19,91:0:2,0:20.9:1:31.2:1:1:0:60:35.667:1:0:0.2 -6 40588076 . A G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36185;SOR=3.12593;LSEQ=TTACAGCTAGCTCCATTGCA;RSEQ=TGAGGAAGCCCTCGGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:27.5:1:33.8:1:1:0:60:8:0.3333:0:1 1/0:8:5:5,0:3,0:0.625:0,0:16:1:32.2:1:1:0:60:10:0.625:0:1.2 -6 40588223 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=6.58144;LSEQ=ACACAGGATAATCGTCCCCA;RSEQ=GTGACTCTTAGCATAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:207:131:101,30:56,19:0.6329:2,2:24.4:1:30.2:1:0.73509:1.14:60:64.5:0.6293:0:1.5 1/1:124:114:78,36:7,3:0.9194:2,2:24:1:30.5:1:1:1.07629:60:113:0.9262:0:1.5 -6 40588276 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05881;SOR=Inf;LSEQ=CCAGATTGCTTTGAGAGGCT;RSEQ=TTGCCTCAGGTGGGACCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:211,163:0:2,0:27.7:1:31.9:1:1:0:60:186:1:0:0.9 0/1:239:3:2,1:135,101:0.0126:2,2:17:1:26.3:1:1:1.49:60:6:0.0127:0:2.7 -6 40588295 . G T 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.23869;LSEQ=TGTTGCCTCAGGTGGGACCC;RSEQ=TGATCTCCCCAGTAAGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:167:89,78:102,101:0.4489:2,2:26.5:1:30.5:1:0.60164:1.13:60:166:0.4523:0:1.8 1/0:260:168:89,79:46,45:0.6462:2,2:26.1:1:30:1:0.79455:1.10:60:167:0.6473:0:1.7 -6 40588343 . C T 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.99225;LSEQ=AGGGATTTGGTGAGGCACCA;RSEQ=CCCTACCCACTATGCTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:108:36,72:58,93:0.417:2,2:25.8:1:29.6:1:0.43343:1.24625:60:26:0.4143:0:1.8 0/1:212:88:38,50:47,77:0.4151:2,2:25.2:1:28.8:1:0.47847:1.24:60:43:0.4095:0:1.7 -6 40588380 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=0;LSEQ=TCACAACCCAAGGGATGCAG;RSEQ=TGACAGAGCTGGTGAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:31,121:0.013:2,2:36:1:30.5:1:0.37348:3.86:60:4:0.0133:0:2 0/0:139:0:0,0:50,89:0:2,0:22.2:1:30.5:1:1:0:60:45.333:1:0:0.8 -6 40588404 . G A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAGCTGGTGAAGGTGATG;RSEQ=TGACCATGTCTGGCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:11,99:0:2,0:22.2:1:32.1:1:1:0:60:109:1:0:0.4 0/1:79:24:5,19:16,39:0.3038:2,2:19.7:1:29.9:1:0.58273:1.55059:60:48:0.3038:0:1.1 -6 40588579 . C T 80 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTTTCAGGTCCCCACTTG;RSEQ=GGGGGGCGGATGGGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:22.8:1:31:0:1:0:60:12:0.6:0:1 1/1:1:1:0,1:0,0:1:0,0:39:0:32:0:1:0:60:2:1:0:1 -6 40589430 . A G 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTACTATTACTGCACGCAC;RSEQ=CACACACACACACAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 41311545 . CT C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGAAGGTGAGATAAACAA;RSEQ=TGGTTTTGGCTTGGTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:10.5:1:32.5:1:1:0:60:4:0.4:0.2:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 41311635 . T C 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62114;LSEQ=GTGCAGGAGCTCAGTCTAAA;RSEQ=CAATGGCCTCTTATTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:0.8333:0,0:20.3:1:32.5:1:1:0:60:20:0.8333:0:3.4 1/0:4:3:3,0:1,0:0.75:0,0:24.7:1:32.7:1:1:0:60:6:0.75:0:3 -6 41311638 . A G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82769;LSEQ=CAGGAGCTCAGTCTAAATCA;RSEQ=TGGCCTCTTATTACTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:11,0:3,0:0.7857:0,0:20.2:1:28.5:1:1:0:60:4.5:0.75:0:3.3 1/0:4:3:3,0:1,0:0.75:0,0:27.7:1:33.3:1:1:0:60:6:0.75:0:3 -6 41311656 . G T 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72102;SOR=1.46437;LSEQ=CAATGGCCTCTTATTACTCT;RSEQ=ATTTAACACCCCAAATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:13,0:11,0:0.5417:0,1:25.7:1:29.1:1:1:0:60:12:0.5217:0:2.6 1/0:11:7:7,0:4,0:0.6364:0,0:22.7:1:29.4:1:1:0:60:14:0.6364:0:2.7 -6 41311790 . G T 44 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02667;SOR=Inf;LSEQ=AAGCCCCTTCACCTCACACT;RSEQ=GCACTCGGACCACTGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:220,82:0:2,0:23.7:1:30.9:1:1:0:60:26.455:1:0:0.6 0/1:207:4:1,3:138,65:0.0193:2,2:10.3:1:22:1:0.10471:6.30861:60:3:0.0146:0:2 -6 41311821 . A G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=3.34627;LSEQ=CACTGTGTCAGCCACCTAAC;RSEQ=GGGGGTCCTGTCTTCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:426:217:133,84:121,85:0.5094:2,2:26.5:1:29.5:1:0.62022:1.11:60:30:0.5072:0:1.4 1/0:336:261:162,99:42,33:0.7768:2,2:25.5:1:29.4:1:0.35086:1.28:60:51.2:0.7781:0:1.5 -6 41311892 . T C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=3.00201;LSEQ=CCTTCCCAACAATACCTCTG;RSEQ=GCATTTCTGCCACCCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:516:268:120,148:108,140:0.5194:2,2:26.8:1:30.5:1:0.79073:1.05:60:43.667:0.5188:0:1.4 1/0:463:354:163,191:52,56:0.7646:2,2:25.8:1:30.1:1:0.74142:1.08788:60:43.25:0.7621:0:1.4 -6 41312937 . C A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCAGAGAATCTAGGAGT;RSEQ=TAAGTGATTCTTAAAGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35.5:1:30.5:1:1:0:60:4:1:0:1 -6 41460161 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50666;SOR=0;LSEQ=GCCCCACCCGGCCCCGTGAT;RSEQ=GATGGCATCTGTCTTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:96,25:0.0163:2,2:19:1:28.5:1:0.37945:3.78499:60:4:0.0167:0:1 0/0:94:0:0,0:68,26:0:2,0:21.3:1:30.9:1:1:0:60:93:1:0:0.1 -6 41460186 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22835;SOR=Inf;LSEQ=GCATCTGTCTTCTGCTTTAT;RSEQ=AAACTCACGCCGCGGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:120,51:0:2,0:24.4:1:29.1:1:1:0:60:41.75:1:0:0.2 0/1:157:2:1,1:103,52:0.0127:2,2:23.5:1:26.5:1:1:1.97156:60:4:0.0129:0:1 -6 41460195 . G T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10848;SOR=Inf;LSEQ=TTCTGCTTTATTAAACTCAC;RSEQ=CCGCGGTTCAGCCCTGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:140,64:0:2,0:24.5:1:30.2:1:1:0:60:67:1:0:0.3 0/1:187:3:2,1:115,69:0.016:2,2:34.3:1:31.7:1:1:1.20:60:6:0.0161:0:1.7 -6 41460287 . C T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00018;SOR=1.80196;LSEQ=TTTCAGGGGGTTACCAAGAC;RSEQ=CAGACAGGAAACGGCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:120:60,60:139,163:0.2844:2,2:26:1:29.8:1:0.51681:1.17:60:23:0.2785:0:1.2 0/1:321:134:63,71:90,97:0.4174:2,2:26.3:1:29.5:1:0.90986:1.04554:60:66:0.4164:0:1.3 -6 41460300 . G A 138 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=32.90627;LSEQ=CCAAGACCCAGACAGGAAAC;RSEQ=GCTTTCACCCTGAGTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:1:1,0:177,226:0.0025:2,0:1:0:25:0:0.44059:0:60:2:0.0025:0:1 0/1:317:24:12,12:134,159:0.0757:2,2:28.4:1:30.3:1:0.83184:1.19:60:48:0.0762:0:1.3 -6 41634511 . A G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=CTGGTATAACATATTTGAAA;RSEQ=TTATTTTATAACTTTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:0.1429:0,0:15.5:1:34:0:1:0:60:4:0.1429:0:1 0/0:7:0:0,0:7,0:0:0,0:28:1:29:1:1:0:60:14:1:0:0 -6 41634620 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16491;SOR=Inf;LSEQ=TCTCCATCTGCCTTCTCTCC;RSEQ=ACCTAAGTGCGTGGCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:35,33:0:2,0:28.5:1:31.1:1:1:0:60:33:1:0:0.2 0/1:47:2:1,1:23,22:0.0426:2,2:30:1:28.5:1:1:1.04448:60:4:0.0426:0:1 -6 41634789 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2282;SOR=Inf;LSEQ=TCTTTAAGAACAGTCAGTTA;RSEQ=GGGGCTGGAGCAAAGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:81,42:0:2,0:26.4:1:30.9:1:1:0:60:122:1:0:0.1 0/1:113:2:1,1:61,50:0.0177:2,2:28:1:32.5:1:1:1.21784:60:4:0.0179:0:1 -6 41634834 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57837;LSEQ=CACATTGTTGAAGCAGAGGC;RSEQ=ATGAATTACAAAGGCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:95,47:0.0139:2,2:24:1:29.5:1:1:2.01067:60:4:0.0139:0:1 0/0:124:1:1,0:73,50:0.0081:2,0:1:0:27:0:1:0:60:2:0.0082:0:1 -6 41634890 . C T 52 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13857;SOR=0;LSEQ=GGCAACTTTGAAAATGTCTG;RSEQ=ACAACCAATGGTTTCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:4:1,3:140,96:0.0167:2,2:11.3:1:26.3:1:0.30901:4.34908:60:8:0.0172:0:1 0/0:180:0:0,0:103,77:0:2,0:27.8:1:31.7:1:1:0:60:59:1:0:0.1 -6 41635041 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51714;SOR=0;LSEQ=GGTGAAGAGGAGGAGGATGT;RSEQ=AAACTCTTAAGTACATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:56,76:0.0149:2,2:32:1:28:1:1:1.35:60:4:0.0154:0:1 0/0:90:0:0,0:40,50:0:2,0:23:1:31.5:1:1:0:60:44:1:0:0.1 -6 41635054 . A T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52958;SOR=0;LSEQ=AGGATGTGAAACTCTTAAGT;RSEQ=CATCTGGAAAGCAGTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:56,71:0.0155:2,2:34:0:30.5:1:1:1.27:60:4:0.0156:0:1 0/0:77:0:0,0:37,40:0:2,0:25.9:1:28.9:1:1:0:60:154:1:0:0.1 -6 41635073 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29074;SOR=0;LSEQ=TACATCTGGAAAGCAGTCTG;RSEQ=CCCTGGAAGTGGTAGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:3:2,1:58,67:0.0234:2,2:34.7:1:30:1:0.59962:2.30:60:6:0.0238:0:1 0/0:78:0:0,0:40,38:0:2,0:24.6:1:30.9:1:1:0:60:77:1:0:0.1 -6 41635118 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17534;SOR=Inf;LSEQ=ACAGAAAAGAAGTAAAACTT;RSEQ=CTGCTGATGAAGATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:79,73:0:2,0:25.6:1:32:1:1:0:60:151:1:0:0.1 0/1:110:2:1,1:57,50:0.0182:2,2:14:0:31:1:1:1.13863:60:4:0.0187:0:1.5 -6 41635129 . AGAT A 52 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.6404;SOR=0.45275;LSEQ=GTAAAACTTGCTGCTGATGA;RSEQ=GATGATGATGATGATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:3:1,2:77,72:0.0197:2,2:30.7:1:33:0:0.61272:2.12855:60:6:0.0197:0:0 0/0:111:1:0,1:57,53:0.009:2,0:50:0:30:0:0.48649:0:60:2:0.0091:0:0 -6 41635148 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.51185;SOR=0;LSEQ=AAGATGATGATGATGATGAT;RSEQ=AAGAAGATGATTTTGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:79,74:0.0129:2,2:7.5:1:28:1:1:1.06708:60:4:0.013:0:1.5 0/0:111:0:0,0:55,56:0:2,0:26.7:1:31.5:1:1:0:60:110:1:0:0.2 -6 41635181 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50336;SOR=0;LSEQ=TTGATGATGAGGAAACTGAA;RSEQ=AAGCGCCAGTGAAGAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:66,58:0.0159:2,2:18.5:1:32:1:1:1.13676:60:4:0.0163:0:1.5 0/0:102:0:0,0:54,48:0:2,0:21.6:1:30.7:1:1:0:60:50:1:0:0.1 -6 41635226 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49932;SOR=0;LSEQ=AAGACACTCCAGCCAGAAAT;RSEQ=CACAAAAGTCAGATCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:67,68:0.0146:2,2:43:1:29:1:1:1.01:60:4:0.0147:0:1 0/0:124:0:0,0:64,60:0:2,0:23.6:1:31.6:1:1:0:60:61:1:0:0.1 -6 41635266 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22493;SOR=Inf;LSEQ=TGGAAAAGTCTCAAAACCAT;RSEQ=ATCAACACCAAGATCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:96,93:0:2,0:26.5:1:31.4:1:1:0:60:46.25:1:0:0.1 0/1:171:2:1,1:89,80:0.0117:2,2:39:0:30.5:1:1:1.1118:60:4:0.0118:0:1 -6 41635420 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5018;SOR=0;LSEQ=GTCCTGGGCACTACTGGTAA;RSEQ=TTAAGCCCAAAGATGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:37,58:0.0206:2,2:25.5:1:31.5:1:1:1.56:60:4:0.0211:0:1.5 0/0:80:0:0,0:33,47:0:2,0:27.3:1:29.5:1:1:0:59.9:160:1:0:0.1 -6 41658829 . TTGC T 61 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.17621;SOR=0.20011;LSEQ=GGCCCTCCGAGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:2,2:14,15:0.1212:2,2:38.3:1:30.5:1:1:1.07:60:8:0.125:0:0.3 0/1:38:1:1,0:19,18:0.0263:2,0:45:0:32:0:1:0:60:2:0.0263:0:0 -6 41658889 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04275;SOR=0.19037;LSEQ=TGTTGCTGCATGCGCTCCCG;RSEQ=TGCTCCTCCTGCTGCGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:15:5,10:1,2:0.8333:2,2:15.7:1:29.9:1:1:1:60:30:0.8333:0:1.1 0/1:21:10:4,6:3,8:0.4762:2,2:22.3:1:29.9:1:0.65944:1.73:60:20:0.4762:0:1 -6 41903614 . C T 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66063;SOR=1.86537;LSEQ=TGTGGTGTGGTTCCTGGAGG;RSEQ=AGGGAGGTGGGTGGCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:2:0,2:266,44:0.0064:2,0:1:0:25:1:0.02133:0:60:4:0.0066:0:1.5 0/1:252:3:1,2:203,46:0.0119:2,2:11.7:1:23.7:1:0.09388:8.71676:60:6:0.0121:0:1 -6 41903782 . A C 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.57247;LSEQ=TGGGCTGGAGCTGGTCTGAG;RSEQ=GGCTTCCCTGAGGCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:930:165:67,98:329,435:0.1774:2,2:26:1:30.7:1:0.60285:1.10612:60:164:0.1794:0:1.1 0/1:846:302:134,168:236,289:0.357:2,2:25.7:1:30.3:1:0.88472:1.02379:60:74.5:0.3595:0:1.1 -6 41903959 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10914;SOR=Inf;LSEQ=GTCTGGGGAGGTTAGGCCAC;RSEQ=GCCCGGCCCCAGGAATCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:5,71:0:2,0:22.3:1:31:1:1:0:60:75:1:0:0.1 0/1:38:2:1,1:1,35:0.0526:1,2:17:0:32:0:0.10384:25.10:60:4:0.0526:0:1.5 -6 41904258 . A T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25213;SOR=0;LSEQ=TCAGGGCATAGCACTACTTT;RSEQ=TGAATGGAGAGGCTGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:3:1,2:128,34:0.0181:2,2:14.3:1:27.3:1:0.12026:7.40583:60:6:0.0186:0:1 0/0:142:0:0,0:107,35:0:2,0:24.3:1:27.7:1:1:0:60:34.5:1:0:0.1 -6 41904483 . C T 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.00032;LSEQ=GAAGGAAACCTGAAGGATAA;RSEQ=GGCCAGCATGGACTTCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:2:1,1:82,223:0.0065:2,2:30:1:30:1:0.46827:2.71:60:4:0.0066:0:1 0/1:245:31:6,25:60,154:0.1265:2,2:21.5:1:30.2:1:0.3892:1.62044:60:62:0.1292:0:1.1 -6 41905174 . T A 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46892;SOR=1.14725;LSEQ=GGGGTCAGTGGCTGGAGAAG;RSEQ=GAAGAGGAGGGAGCAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:288:183:43,140:23,81:0.6354:2,2:22.8:1:30.9:1:0.8842:1.08:60:366:0.6489:0:1.1 1/0:249:166:43,123:17,64:0.6667:2,2:21.9:1:30.1:1:0.43308:1.31:60:165:0.6707:0:1.1 -6 41905187 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1954;SOR=Inf;LSEQ=GGAGAAGTGAAGAGGAGGGA;RSEQ=CAAAGCAGAAGTCTCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:39,180:0:2,0:23.3:1:31.9:1:1:0:60:218:1:0:0.7 0/1:174:2:1,1:33,139:0.0115:2,2:29.5:1:28:1:0.35353:4.16:60:4:0.0116:0:2 -6 41905275 . G A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.02349;LSEQ=CTGTTTCTGATTTTAAGGCC;RSEQ=GGCACCATGGAGTTCAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:7:1,6:1,42:0.14:1,2:18.9:1:30.6:1:0.26286:6.56:60:6:0.1277:0:1.1 0/1:21:3:0,3:0,18:0.1429:1,0:14:1:29.3:1:1:0:60:6:0.15:0:1 -6 41908032 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52032;SOR=0;LSEQ=TCCAGGGGGCAGAAAGCCTC;RSEQ=GATATCTCAAGCTTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:163,11:0.0114:2,2:33:1:31:1:0.13208:14.23649:60:4:0.0115:0:1 0/0:115:0:0,0:99,16:0:2,0:22.9:1:30.4:1:1:0:60:37.333:1:0:0.1 -6 41908366 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16955;SOR=Inf;LSEQ=TGCTGGGTCTGGAGCGTGGG;RSEQ=AACACAGCAGCGGGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:22,202:0:2,0:23.1:1:30.6:1:1:0:60:19.364:0.9953:0:0.3 0/1:158:2:1,1:20,136:0.0127:2,2:30:1:28:1:0.24889:6.66:60:4:0.0133:0:1 -6 41908377 . CG C 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.26866;SOR=0;LSEQ=GAGCGTGGGGAACACAGCAG;RSEQ=GGGGGGTGGGAGCGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:0,3:15,156:0.0172:2,0:24.7:1:30.7:1:1:0:60:6:0.0175:0:0 0/0:124:0:0,0:13,109:0:2,0:24.8:1:28.9:1:1:0:60:29.5:0.9833:0:0.4 -6 41908561 . C A 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5542;SOR=0;LSEQ=GGAGTGGTAAAGCCAAGGAG;RSEQ=CCTTGCTCACGGAGGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:2,1:166,17:0.0161:2,2:16.3:1:26:1:0.26442:4.8098:60:6:0.0165:0:1 0/0:85:0:0,0:82,3:0:1,0:24.5:1:32.6:1:1:0:60:170:1:0:0 -6 41908563 . C A 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0695;LSEQ=AGTGGTAAAGCCAAGGAGCC;RSEQ=TTGCTCACGGAGGATTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:167,17:0.0108:2,2:5:0:33:0:0.18466:9.5753:60:4:0.011:0:1.5 0/1:87:1:1,0:83,3:0.0115:1,0:13:0:32:0:1:0:60:2:0.0116:0:1 -6 41908717 . G A 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=GAAGGGAGGAGGCTCCTGCC;RSEQ=CTGCCTCCTGCACTTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:904:0:0,0:418,485:0:2,0:23.5:1:30.8:1:1:0:60:63.5:1:0:0.1 0/1:856:10:6,4:402,444:0.0117:2,2:21.7:1:28.3:1:0.53146:1.66:60:20:0.0119:0:1.1 -6 41908810 . G A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01429;SOR=Inf;LSEQ=GAACCCCGCGAAAGACACAG;RSEQ=AACCGGCTCCCGGGCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:84,248:0:2,0:20.3:1:30.7:1:1:0:60:54.333:1:0:0.2 0/1:250:5:4,1:69,175:0.02:2,2:7.6:1:25.8:1:0.02697:10.04:60:10:0.0203:0:1.2 -6 41909028 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGGGCTCGGGAAAGCAAG;RSEQ=GAGGCAGCTGGCGTGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:72,6:0.0244:2,2:39:0:31.5:1:0.16835:11.18701:60:4:0.027:0:1.5 0/0:39:0:0,0:37,2:0:2,0:22.8:1:30.1:1:1:0:60:12:1:0:0.2 -6 41909422 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24908;SOR=Inf;LSEQ=CAGGCAGGGCGGGAGTGCGG;RSEQ=CTCGCGAGTCCCAAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:34,121:0:2,0:24.2:1:32.3:1:1:0:60:310:1:0:0.2 0/1:170:3:2,1:54,113:0.0176:2,2:24:1:27.3:1:0.2527:4.15:60:6:0.0182:0:2 -6 41909426 . G T 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=CAGGGCGGGAGTGCGGGCTC;RSEQ=CGAGTCCCAAGGCAGGCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:31,113:0:2,0:22.8:1:31.9:1:1:0:60:143:1:0:0.2 0/1:150:15:6,9:42,91:0.1:2,2:29.2:1:30.1:1:0.56483:1.44:60:30:0.1014:0:1.2 -6 41909432 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50179;SOR=Inf;LSEQ=GGGAGTGCGGGCTCGCGAGT;RSEQ=CCAAGGCAGGCGACGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:24,92:0:2,0:22.1:1:31.6:1:1:0:60:57:1:0:0.2 0/1:138:2:1,1:43,93:0.0145:2,2:9:0:28.5:1:0.53761:2.15:60:4:0.0149:0:2.5 -6 41909521 . CCG C 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCCCCAGCCCGCCCGCCGC;RSEQ=CGCGCGCGCGCCGCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12:0:32.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 42699907 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGTGCTGAAATTACAGT;RSEQ=TGAGCCACCACGCCCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:33.5:1:1:0:60:4:1:0:2 -6 42699921 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGTATGAGCCACCACGC;RSEQ=CAGCTGAGACTATTATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:32:1:1:0:60:4:1:0:2 -6 42701641 . G A 68 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GACAAAGAGATAAAGAGAAA;RSEQ=CAGCTGGGCCTGGGGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:16:1:29.6:1:1:0:60:10:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 42701676 . T C 63 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACCACTACCACCAAGACG;RSEQ=GGAGACGTAGTGGCCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:31.3:1:31.8:1:1:0:60:8:1:0:1.8 1/0:4:3:3,0:1,0:0.75:0,0:14:1:33.7:1:1:0:60:6:0.75:0:1 -6 42702973 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTCGCTCTGTTGCCCAG;RSEQ=CTGGAGTGAAGCGATACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 42703256 . A G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATCTACTTTCAATGTTCC;RSEQ=TAACTTTCTTCATTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 43738350 . C G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.15502;LSEQ=GGGCGTGCGAGCAGCGAAAG;RSEQ=GACAGGGGCAAAGTGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:83:80,3:13,1:0.8469:1,1:24.1:1:30.9:1:0.46964:2.03:60:26.667:0.8421:0:1 0/1:35:16:14,2:18,1:0.4571:1,2:25.1:1:29.2:1:0.58197:2.50361:60:15:0.4545:0:1.2 -6 43738423 . TC T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06181;SOR=Inf;LSEQ=GTGAGCCCTCCCCCTTGGGA;RSEQ=CCGCAGCTGACCAGTCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:173,142:0:2,0:23.1:1:30.4:1:1:0:60:62:1:0:0.3 0/1:207:3:1,2:120,84:0.0145:2,2:25.7:1:27.7:1:0.57146:2.84265:60:6:0.0151:0.0048:0.3 -6 43738436 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07288;SOR=Inf;LSEQ=CTTGGGATCCCGCAGCTGAC;RSEQ=AGTCGCGCTGACGGACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:180,195:0:2,0:25.1:1:30.7:1:1:0:60:36.5:1:0:0.2 0/1:270:3:1,2:143,124:0.0111:2,2:29.3:1:27:1:0.60011:2.29952:60:6:0.0114:0:1 -6 43738449 . GGACA G 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=4.000;MSILEN=4;SSF=1;SOR=1.01491;LSEQ=AGCTGACCAGTCGCGCTGAC;RSEQ=GACAGACAGACACCGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:5:2,3:177,248:0.0116:2,2:20.4:1:31.6:1:1:1.07041:60:10:0.0118:0.0047:0.8 0/1:339:4:2,2:159,175:0.0118:2,2:13.5:1:30:1:1:1.10:60:8:0.012:0.0029:0.3 -6 43738513 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65652;SOR=1.9795;LSEQ=TCCCCGGCCGGCGGCGGACA;RSEQ=TGGACGCGGCGGCGAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:2:2,0:86,210:0.0067:2,0:1:0:28:0:0.0865:0:60:4:0.0068:0:1 0/1:227:3:2,1:84,140:0.0132:2,2:14:1:27.3:1:0.55879:3.32:60:6:0.0135:0:1.3 -6 43738527 . G A 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63489;SOR=0.42521;LSEQ=CGGACAGTGGACGCGGCGGC;RSEQ=AGCCGCGGGCAGGGGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:3,0:117,152:0.011:2,0:6.3:1:22.7:1:0.08467:0:60:2:0.0075:0:1.3 0/0:213:1:1,0:97,115:0.0047:2,0:1:0:24:0:0.46009:0:60:2:0.0048:0:1 -6 43738530 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57444;SOR=2.78801;LSEQ=ACAGTGGACGCGGCGGCGAG;RSEQ=CGCGGGCAGGGGCCGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:0,1:132,146:0.0036:2,0:1:0:25:0:1:0:60:2:0.0037:0:1 0/1:201:2:1,1:90,108:0.01:2,2:11.5:1:27:1:1:1.20:60:4:0.0102:0:1 -6 43738535 . G T 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14646;SOR=0;LSEQ=GGACGCGGCGGCGAGCCGCG;RSEQ=GCAGGGGCCGGAGCCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:4:1,3:170,136:0.0129:2,2:18:1:29:1:0.32904:3.73503:60:8:0.0132:0:1.3 0/0:218:0:0,0:111,106:0:2,0:12.8:1:30.2:1:1:0:60:35.167:0.9953:0:0.3 -6 43738540 . G A 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07781;SOR=Inf;LSEQ=CGGCGGCGAGCCGCGGGCAG;RSEQ=GGCCGGAGCCCGCGCCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:208,139:0:2,0:12.4:1:31.3:1:1:0:60:85.75:0.9971:0:0.2 0/1:261:3:3,0:137,121:0.0115:2,0:12.3:1:20:1:0.25111:0:60:2:0.0079:0:1.3 -6 43738977 . C T 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03614;LSEQ=GCCGGCCCCGGTCGGGCCTC;RSEQ=GAAACCATGAACTTTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1457:1163:631,532:157,135:0.7982:2,2:24.7:1:30.5:1:0.8956:1.02:60:76.533:0.7967:0:1.2 0/1:1097:137:70,67:509,451:0.1249:2,2:25.7:1:30.4:1:0.7147:1.08015:60:136:0.1244:0:1.3 -6 43740595 . G A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAGGAGGGGGAGGAGTG;RSEQ=CTGCCTGGCCACAGTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:0:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 43740840 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=Inf;LSEQ=CAGGGGGTCCCTGCAGGAGC;RSEQ=GCAGTGGTAAGCTGTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:35.6:1:30:1:1:0:60:16:1:0:0.1 0/1:10:2:1,1:4,4:0.2:2,2:18:0:31.5:1:1:1:60:4:0.2222:0:1.5 -6 43742166 . C A 175 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=38.56318;LSEQ=GTTGGATGGGGTTCCCTGTC;RSEQ=TCTCAGGGGATGGGTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1922:2:2,0:849,1070:0.001:2,0:1:0:30:1:0.19612:0:60:4:0.0011:0:1 0/1:1528:59:29,30:668,801:0.0386:2,2:28.4:1:29.9:1:0.5961:1.16:60:118:0.0392:0:1.2 -6 43742419 . G C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27893;SOR=4.91736;LSEQ=GAGCAGGAAGACAGTGTTCA;RSEQ=GGATCCTAGGTGTTGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:0,8:0,14:0.3636:1,0:32.5:1:31.1:1:1:0:60:16:0.3636:0:1.1 1/0:4:3:0,3:0,1:0.75:0,0:17:1:28.3:1:1:0:60:6:0.75:0:1.3 -6 43745095 . C A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07097;LSEQ=TACGTTAGATTTTGGAAGGA;RSEQ=TTGCCTGATTCGGAAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:285:222:219,3:61,1:0.7789:1,1:24.4:1:30.3:1:1:1.20:60:43.4:0.7862:0:1.1 0/1:171:34:34,0:133,4:0.1988:1,1:24.4:1:29.8:1:0.58553:0:60:33:0.1941:0:1 -6 43745107 . G A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.98747;LSEQ=TGGAAGGACTTGCCTGATTC;RSEQ=GAAGCTCCAAAGAGTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:71:69,2:288,6:0.1945:1,1:25:1:30.5:1:0.65586:1.38992:60:70:0.1934:0:1.1 1/0:212:116:110,6:94,2:0.5472:1,2:24.8:1:30:1:0.29751:2.55319:60:57:0.5455:0:1.1 -6 43745577 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.71767;LSEQ=TGGAGAAGATGCTTCATTCC;RSEQ=AGCCCAGGTTCCCAGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:137:25,112:111,452:0.1957:2,2:21.5:1:28.4:1:0.80975:1.10004:60:44.667:0.1951:0:1.1 1/0:395:230:40,190:39,126:0.5823:2,2:23.6:1:28.4:1:0.1285:1.46874:60:114:0.5831:0:1 -6 43746169 . C T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=4.02309;LSEQ=TGGCTGGCTGGGTCACTAAC;RSEQ=TCTGTGATCTGCTTCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1018:194:124,70:505,317:0.1906:2,2:24.3:1:30.7:1:0.5653:1.11:60:96:0.192:0:1.1 0/1:787:383:225,158:233,171:0.4867:2,2:25.3:1:30:1:0.77282:1.05:60:53.714:0.4877:0:1.2 -6 43746352 . CT C 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.09435;SOR=0;LSEQ=CCAGGGTTAAGCATGCTGTA;RSEQ=TTTTGGCCCCCGTCCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:2,4:84,367:0.0131:2,2:25.7:1:32:1:0.31546:2.18:60:12:0.0133:0.0022:0.2 0/0:252:0:0,0:61,189:0:2,0:23:1:30.2:1:1:0:60:124:0.992:0:0.1 -6 43746360 . C T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12368;SOR=5.6737;LSEQ=AAGCATGCTGTACTTTTTGG;RSEQ=CCCCGTCCAGCTTCCCGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:1:0,1:72,331:0.0025:2,0:37:0:31:0:1:0:60:2:0.0026:0:1 0/1:216:3:1,2:49,163:0.0139:2,2:25.3:1:26:1:0.54993:1.66:60:2:0.0095:0:1 -6 43747783 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCCCAAGCCTCTCCTCCCCA;RSEQ=ACCTCCTTAACTCCCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:26:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:42.5:1:31:1:1:0:60:4:1:0:1.5 -6 43747962 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCGCAGTTGCAAATGA;RSEQ=GGCACAAGGCCTGATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:28.5:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 43748328 . C G 185 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATGCCTCCCCAGAGACCA;RSEQ=CTGCCTCCTGACACTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:56:54,2:81,4:0.3916:1,1:23.6:1:32:1:1:1.33:60:27:0.383:0:1.2 0/0:65:0:0,0:63,2:0:1,0:23:1:30.7:1:1:0:60:31.5:1:0:0.2 -6 43748350 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04893;SOR=Inf;LSEQ=TGCCTCCTGACACTTCCTCC;RSEQ=GGAAGCGGCCCTGTGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:181,7:0:1,0:25.8:1:30.1:1:1:0:60:93:0.9947:0:0.7 0/1:110:3:3,0:104,3:0.0273:1,0:13.7:1:32:0:1:0:60:6:0.0283:0:2 -6 43748357 . G A 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00038;SOR=Inf;LSEQ=TGACACTTCCTCCGGGAAGC;RSEQ=GCCCTGTGTGGCTTTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:196,6:0:1,0:26.5:1:30.2:1:1:0:60:201:1:0:0.8 0/1:124:8:8,0:112,3:0.0645:1,0:25.3:1:30.9:1:1:0:60:16:0.065:0:2.3 -6 43748643 . T C 304 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=5.60034;LSEQ=CTGCCTCCCTCCCCTGGTCC;RSEQ=TCCCTGGCTCTCATCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1030:836:205,631:50,142:0.8117:2,2:24.2:1:31.4:1:0.6445:1.08373:60:51.25:0.8127:0:1.1 1/1:654:628:176,452:7,17:0.9602:2,2:22.8:1:31:1:1:1.0574:60:61.8:0.9611:0:1.1 -6 43748697 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10749;SOR=Inf;LSEQ=CTCTCACTCTCTCACTCCAC;RSEQ=AATTGGCACCAACGGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:18,350:0:1,0:23.1:1:28.2:1:1:0:60:29.667:1:0:0.7 0/1:180:2:1,1:13,165:0.0111:2,2:18:1:29:1:0.14991:12.27:60:4:0.0115:0:1.5 -6 43748795 . C T 53 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02998;SOR=7.21367;LSEQ=GGAGGATTAAGGGAGGGGAC;RSEQ=CTGGCTTGGCTGGGCACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:0,2:1,55:0.0345:1,0:38.5:1:32:0:1:0:60:4:0.0357:0:1 0/1:19:4:0,4:0,15:0.2105:1,0:33:1:26.8:1:1:0:60:3:0.1875:0:2.8 -6 43749163 . T C 51 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGGGCAGCCTCTTCCTC;RSEQ=GGGTCGGAGGCTGTGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:24:1:32.3:1:1:0:60:6:1:0:1.7 1/1:1:1:0,1:0,0:1:0,0:16:0:23:0:1:0:60:2:1:0:2 -6 43749230 . C T 42 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCCTGGCCTGGGGACAC;RSEQ=GCCTCCGGGCTTAGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16:1:32:1:1:0:60:4:1:0:4.5 1/1:3:3:1,2:0,0:1:0,2:24.7:1:27:1:1:0:60:2:1:0:2 -6 43749612 . AG A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.05913;SOR=Inf;LSEQ=GGTGCAGCTGCGGACATGTT;RSEQ=GGGGTGTTGCATGGTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:362,24:0:2,0:22.2:1:31.8:1:1:0:60:47.25:0.9974:0:0.2 0/1:248:3:1,2:224,21:0.0121:2,2:19.3:1:28:1:0.02337:20.72187:60:6:0.0122:0.0081:0.3 -6 43749615 . G T 55 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.0353;SOR=7.9789;LSEQ=GCAGCTGCGGACATGTTAGG;RSEQ=GGTGTTGCATGGTGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:1:1,0:371,26:0.0025:2,0:11:0:12:0:1:0:60:0:0:0:4 0/1:253:5:1,4:226,22:0.0198:2,2:11:1:24:1:0.00042:39.74444:60:4:0.0163:0:1 -6 43749876 . GGA G 118 MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.63845;SOR=0.73608;LSEQ=GGGGCATCACACAGAGATGG;RSEQ=GAGAGAGAGAGAAAGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:638:13:1,12:142,483:0.0204:2,1:28.2:1:31.9:1:0.31624:3.52325:58.5:26:0.0206:0.0016:0.3 0/1:398:6:1,5:84,307:0.0151:2,2:34:1:31.8:1:1:1.36708:60:12:0.0152:0:0 -6 43749914 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.30227;SOR=0;LSEQ=AGAGTGAGCGAGCGAGCGAG;RSEQ=GGGAGAGCGCCTGAGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:3:0,3:12,256:0.011:1,0:20:1:30.7:1:1:0:53.3:6:0.0115:0:2 0/0:157:0:0,0:6,151:0:1,0:24.4:1:29.7:1:1:0:60:30.4:1:0:0.2 -6 43751669 . G C 38 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGAGGCCTACAGCCACA;RSEQ=TGGGAGGGGACATGGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:31:1:24.3:1:1:0:60:2:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 43751976 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTGGTATCCGTTCATTT;RSEQ=TTGCTTTGTAAAGTGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:2,0:20,0:0.0909:1,0:33:1:31:1:1:0:60:4:0.0952:0:1.5 0/0:4:0:0,0:4,0:0:0,0:22.8:1:31.5:1:1:0:60:8:1:0:0 -6 43752536 . C T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCGGGCGGGTGACCCAGCA;RSEQ=GGTCCCTCTTGGAATTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:2,208:0:1,0:23.6:1:30.2:1:1:0:60:104:1:0:0.1 0/1:107:21:0,21:1,85:0.1963:1,1:31:1:29.1:1:1:0:60:20:0.1905:0:1 -6 43752551 . T C 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03059;SOR=Inf;LSEQ=CAGCACGGTCCCTCTTGGAA;RSEQ=TGGATTCGCCATTTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:2,154:0:1,0:22.5:1:30.3:1:1:0:60:51:1:0:0.1 0/1:72:3:0,3:1,68:0.0417:1,0:19.7:1:33.7:1:1:0:60:6:0.0417:0:1 -6 45390281 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18076;SOR=Inf;LSEQ=TTTCCACCCTCCTCCCCCTC;RSEQ=CCCGGCCACTTCGCTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:19,6:0:2,0:20.5:1:31.4:1:1:0:60:50:1:0:0.6 0/1:19:2:1,1:11,6:0.1053:2,2:12:0:30.5:1:1:1.77272:60:4:0.1053:0:1.5 -6 45390400 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17053;SOR=Inf;LSEQ=GGCAAAATGAGCGACGTGAG;RSEQ=CCGGTGGTGGCTGCGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:37,49:0:2,0:25.9:1:30.8:1:1:0:59.9:27.667:1:0:0.2 0/1:61:2:1,1:25,33:0.0328:2,2:28.5:1:29:1:1:1.31:60:4:0.0339:0:1 -6 45390430 . ACAG A 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.16812;SOR=Inf;LSEQ=GCTGCGCAACAGCAGCAGCA;RSEQ=CAGCAGCAGCAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:38,62:0:2,0:27.5:1:32.3:1:1:0:59.9:200:1:0:0.3 0/1:70:2:1,1:28,40:0.0286:2,2:21:0:33:1:1:1.42:60:4:0.0299:0:0.5 -6 45390433 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51305;SOR=0;LSEQ=GCGCAACAGCAGCAGCAACA;RSEQ=CAGCAGCAGCAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:36,61:0.0202:2,2:14.5:1:28.5:1:1:1.68:60:4:0.0208:0:1 0/0:69:0:0,0:27,40:0:2,0:24.6:1:31.2:1:1:0:59.3:21.333:1:0:0.4 -6 45390445 . ACAG A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.15921;SOR=6.03585;LSEQ=CAGCAACAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:1:0,1:31,56:0.0114:2,0:25:0:34:0:1:0:60:2:0.0115:0:0 0/1:61:4:2,2:23,34:0.0656:2,2:25.5:1:29.8:1:1:1.47:60:8:0.069:0.0328:0.8 -6 45390448 . G A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=1;SOR=1.48701;LSEQ=CAACAGCAGCAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:29,55:0.023:2,2:25.5:1:29:1:1:1.88:60:4:0.0238:0:1 0/1:59:2:1,1:22,33:0.0339:2,2:1.1:1:27.6:1:1:1.49:60:4:0.0346:0:1.5 -6 45390461 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.15789;SOR=Inf;LSEQ=AGCAACAGCAGCAGCAGCAG;RSEQ=AGCAACAGCAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:22,47:0:2,0:24:1:32:1:1:0:59.9:68:1:0:0.3 0/1:46:2:1,1:16,28:0.0435:2,2:9:0:31:1:1:1.73:60:4:0.0444:0:1.5 -6 45390466 . ACAG A 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=1;SOR=0.49475;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:3:1,2:17,42:0.0484:2,2:38.3:1:31.3:1:1:1.23:60:6:0.05:0:0 0/1:41:1:0,1:14,26:0.0244:2,0:45:0:30:0:1:0:60:2:0.0244:0:0 -6 45390501 . C G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22;SOR=0;LSEQ=GCAGGAGGCGGCGGCGGCGG;RSEQ=TGCGGCGGCGGCGGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:1,9:0.1667:2,2:14:0:32.5:1:0.31818:6.71:60:4:0.1667:0:1.5 0/0:13:0:0,0:3,10:0:2,0:15:1:31.9:1:1:0:60:26:1:0:0.7 -6 45390595 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50315;SOR=0;LSEQ=ATGGTGGAGATCATCGCCGA;RSEQ=CACCCGGCCGAACTCGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:142,38:0.011:2,2:22.5:1:31.5:1:0.38358:3.70183:60:4:0.0112:0:1 0/0:150:0:0,0:110,40:0:2,0:19.4:1:30.8:1:1:0:60:74:1:0:0.1 -6 45390711 . C A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.62406;SOR=0.35211;LSEQ=CAAGGTAAGAGGCTACACCG;RSEQ=CCCCCGCCCCCGGCCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:2,1:83,151:0.0127:2,2:16.7:1:27.3:1:0.29279:3.62:60:6:0.0128:0:1 0/0:223:1:1,0:86,136:0.0045:2,0:1:0:25:0:0.39013:0:60:2:0.0046:0:1 -6 45390727 . G A 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36764;SOR=3.09094;LSEQ=ACCGCCCCCCGCCCCCGGCC;RSEQ=GGAGCGGCGGAACCTGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:38,115:0.0065:2,0:9:0:26:0:1:0:60:2:0.0066:0:1 0/1:151:3:2,1:44,104:0.0199:2,2:16.7:1:25:1:0.2202:4.67:60:2:0.0136:0:1 -6 45390733 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50116;SOR=0;LSEQ=CCCCGCCCCCGGCCGGGAGC;RSEQ=GCGGAACCTGCCCGCCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:32,111:0.0137:2,2:14.5:1:26:0:0.4046:3.43:60:4:0.0141:0:1 0/0:125:0:0,0:26,87:0:2,0:22.3:1:29.6:1:1:0:60:226:0.904:0:0.1 -6 45390808 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51637;SOR=0;LSEQ=TCCAAGACCTCCTGCCTTGG;RSEQ=GGCTCTAACCCCAGAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:1,36:0.0513:1,0:11:1:31:0:1:0:60:4:0.0526:0:1 0/0:25:0:0,0:2,22:0:2,0:21.4:1:29.2:1:1:0:59.8:48:1:0:0.4 -6 45390838 . C CCT 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.11997;SOR=Inf;LSEQ=CCCAGAAACCCCCGGCCGGG;RSEQ=CTCCCTCCGGATGCCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:0,14:0,4:0.7778:0,1:24:1:31:1:1:0:60:28:0.7778:0.2222:0 1/1:13:13:2,11:0,0:1:0,2:25.6:1:28:1:1:0:59.6:12:1:0.1538:1 -6 45391943 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTGCTCCGCAGGTTGAGG;RSEQ=TTTAGGATCTGGAGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29.5:1:1:0:60:4:1:0:1.5 -6 45459414 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=CAGAGAAGGTGTCTAGTATC;RSEQ=TGCCTCTCTATTGATGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:11,0:0:0,0:20.5:1:27.8:1:1:0:60:4.5:1:0:0.9 0/1:6:2:2,0:4,0:0.3333:0,0:32.5:1:32:0:1:0:60:4:0.3333:0:1 -6 45459534 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52126;SOR=0;LSEQ=AAAGCAATTTGAAATGGAAG;RSEQ=CATTATGTAGACAAGTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:83,9:0.0213:2,2:23.5:1:32:0:0.20247:8.80272:60:4:0.0215:0:1 0/0:60:0:0,0:53,7:0:2,0:26.7:1:31.9:1:1:0:60:120:1:0:0 -6 45459915 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10328;SOR=Inf;LSEQ=CTGGGGGTGAGGGGCTACCA;RSEQ=AGGAGATGTGTTCACTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:104,163:0:2,0:25.4:1:31.6:1:1:0:60:132.5:1:0:0.1 0/1:237:3:1,2:92,142:0.0127:2,2:24.7:1:26:1:1:1.2944:60:6:0.0129:0:1 -6 45459967 . A G 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21661;SOR=Inf;LSEQ=CTGTGAAGCGGCTTATTATT;RSEQ=AAGAATCAAGACTTGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:45,98:0:2,0:25.1:1:29.3:1:1:0:60:70.5:1:0:0.1 0/1:125:2:1,1:31,92:0.016:2,2:13.5:1:24:1:0.448:2.94:60:4:0.016:0:1 -6 45556069 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.01914;LSEQ=TAGACACATATATATTATCT;RSEQ=ATAATACCTAAACACATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:49:24,25:206,237:0.0996:2,2:24.7:1:29.2:1:0.76464:1.10:60:48:0.0994:0:1.3 0/1:377:165:79,86:103,108:0.4377:2,2:23.9:1:28.5:1:0.91724:1.03812:60:81.5:0.437:0:1.1 -6 45556152 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17027;SOR=Inf;LSEQ=AGGCAAAATGTGTGTATCTT;RSEQ=CATGGTGCTTAGCTCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:61,176:0:2,0:25.9:1:31:1:1:0:60:58.25:1:0:0.1 0/1:167:2:1,1:54,111:0.012:2,2:27.5:1:27.5:1:0.55155:2.05:60:4:0.0121:0:1 -6 45556263 . C A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08537;SOR=6.10095;LSEQ=TACACATTATGAATGTATAG;RSEQ=AAATTTAGAACATGTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:0,22:0.0833:1,0:32:1:28.5:1:1:0:60:4:0.0909:0:2 0/1:8:3:0,3:0,5:0.375:0,0:29.7:1:30:1:1:0:60:6:0.375:0:1.7 -6 45556291 . G A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.24871;SOR=3.95518;LSEQ=GAACATGTACATTATAGAGA;RSEQ=AATCTAGAAAATACACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:0.1875:1,0:23.7:1:29:1:1:0:60:6:0.2:0:1.7 1/0:4:2:0,2:0,2:0.5:0,0:14:1:32:0:1:0:60:4:0.5:0:2 -6 45768791 . A G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGCAGAGAGACCTCATAA;RSEQ=CTCATTTGCTAGCGTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:44.3:1:33:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 45768796 . T TC 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGAGACCTCATAAACTCA;RSEQ=TTGCTAGCGTAACATGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:38.3:1:31.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 45768804 . C T 40 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCATAAACTCATTTGCTAG;RSEQ=GTAACATGCGTCCAATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:30.3:1:25.7:1:1:0:60:2:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 45768935 . C T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATGGCAGGAATAAAATC;RSEQ=GTCTGGCCAGGGTGTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:27:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 45769257 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55802;SOR=0;LSEQ=GTTCCAAGTACCATGAATAG;RSEQ=CCCACCCGAGGGGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:3:3,0:154,6:0.0184:1,0:36:1:29:1:1:0:60:6:0.0185:0:1 0/0:67:0:0,0:66,1:0:1,0:22.4:1:32.1:1:1:0:60:66:1:0:0 -6 45769293 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11402;SOR=Inf;LSEQ=CAGTTTATGTGTGCAGAAAG;RSEQ=GCCCTGGGGTGAGTAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:254,51:0:2,0:23.2:1:31.2:1:1:0:60:60:1:0:0.1 0/1:156:2:1,1:131,23:0.0128:2,2:25.5:1:28:1:0.28486:5.59704:60:4:0.0131:0:1.5 -6 45769418 . G C 296 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34071;LSEQ=ATGTCCCTTGCGAATGCATC;RSEQ=TATTTTCTCGTTCAACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:686:658:286,372:12,16:0.9592:2,2:26.7:1:31.7:1:1:1.03:60:130.6:0.9603:0:1.8 1/1:576:512:225,287:31,32:0.8889:2,2:25.7:1:30.4:1:0.50207:1.23523:60:35.571:0.8877:0:1.8 -6 45769439 . G A 274 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00051;SOR=0.42566;LSEQ=TATTTTCTCGTTCAACCAGC;RSEQ=TCAAATGCAATCCTGGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:556:528:210,318:10,18:0.9496:2,2:24.9:1:30.4:1:0.84318:1.19:60:74.429:0.949:0:2 1/1:451:401:153,248:23,27:0.8891:2,2:25.1:1:29.6:1:0.28643:1.37973:60:79.2:0.8879:0:2 -6 45769869 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCCTTCGATGAGTGAAAC;RSEQ=TAGATTTGAGGGGGCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 46910123 . C T 105 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAATCCCTAACGCAGCA;RSEQ=GCTATTAGAGATGCTTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:24.3:1:30.4:1:1:0:60:10:1:0:2.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 46910144 . G A 122 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTATTAGAGATGCTTAAGA;RSEQ=GGTAAAAGCATGGGCTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:1:0,1:29.1:1:30.5:1:1:0:60:32:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 46910415 . C T 256 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00517;LSEQ=TCTGTCATGAGAAGCCTGCA;RSEQ=ATAGGACACTTTTCATTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:440:438:215,223:0,0:0.9955:0,2:26.8:1:29.2:1:1:0:60:61.571:0.9954:0:1.1 1/0:357:189:94,95:80,87:0.5294:2,2:24.9:1:29.1:1:0.75079:1.08:60:188:0.5311:0:1.1 -6 46910536 . A C 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTTTTTCTCTTTCTTTGAC;RSEQ=TACTACTTTACAAGTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:12,94:0:2,0:22.2:1:30.2:1:1:0:60:25.5:1:0:0.1 0/1:67:21:1,20:3,43:0.3134:2,1:20:1:32.5:1:1:1.38884:60:42:0.3134:0:1.1 -6 47074474 . A G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37071;SOR=2.72696;LSEQ=AGACTTCCAACCACCAAAAC;RSEQ=GTGAAACAATACATTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:1,9:0.4118:2,0:20.4:1:32.3:1:1:0:60:14:0.4118:0:1 1/0:6:4:0,4:0,2:0.6667:0,0:39.3:1:30.8:1:1:0:60:8:0.6667:0:1 -6 50726648 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49344;SOR=Inf;LSEQ=GGAGAAGGTTCAGAAGCCTG;RSEQ=CTAAAGTTTACTCAAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:12,20:0:2,0:25.7:1:31:1:1:0:60:31:1:0:0.1 0/1:35:2:1,1:11,21:0.0571:2,2:35.5:1:31:0:1:1.87:60:4:0.0588:0:1 -6 51716715 . C T 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03727;SOR=Inf;LSEQ=TAACTCCTTCAATTCTTCTC;RSEQ=GATCTTAGTTATTTCTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:21.3:1:30.4:1:1:0:60:24:1:0:0.3 0/1:12:5:2,3:4,3:0.4167:2,2:17:1:31.6:1:1:1.88578:60:10:0.4167:0:1.2 -6 51716738 . C A 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08772;SOR=0;LSEQ=TCTTAGTTATTTCTTGTCTT;RSEQ=TGCTGGCTTTTGGATTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:14.5:1:31.5:1:1:2.45:60:4:0.3333:0:1 0/0:13:0:0,0:7,6:0:2,0:18.8:1:31.2:1:1:0:59.1:26:1:0:0.4 -6 51718374 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12685;SOR=Inf;LSEQ=CTCCAATCAATCATAGGTTC;RSEQ=GTCTTTTTATGAAATCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:13,15:0:2,0:27.7:1:30.6:1:1:0:59.9:56:1:0:0.2 0/1:16:2:1,1:8,6:0.125:2,2:26.5:1:29.5:1:1:1.30929:53.5:4:0.125:0:3 -6 51719074 . A T 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=GAGATGTCACTCAAGGAGAC;RSEQ=GGAGTGCAGCAAAGATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:3,9:0,0:1:0,2:25.5:1:29.2:1:1:0:58.7:11:1:0:1 1/1:11:10:6,4:0,1:0.9091:0,2:20.7:1:30.6:1:0.45455:0:58.6:20:0.9091:0:1.2 -6 51719409 . G T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GGAGATATGAATTCTGTCCC;RSEQ=GAGCCTCTGGCTGGAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:9.8:1:31.4:1:1:0:60:10:1:0:0.2 1/0:3:2:1,1:0,1:0.6667:0,2:15.5:1:28:1:1:0:60:4:0.6667:0:1 -6 51719595 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCCAACAGGGAAAAAA;RSEQ=GCAGCCTAGAGCTATAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:14:1:29.5:1:1:1.41:60:4:0.2857:0:1 0/0:1:0:0,0:1,0:0:0,0:12:0:33:0:1:0:60:2:1:0:0 -6 54479334 . G A 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=ACTAGAAGCAGCACCGTTTC;RSEQ=AGGCTTCCACCGAAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:0.5:2,2:24.3:1:31.7:1:1:1:60:6:0.5:0:1.3 0/0:5:0:0,0:3,2:0:2,0:20:1:25.8:1:1:0:60:4:1:0:0 -6 54479426 . C T 45 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=CATCAAAATTGACTAGAAGG;RSEQ=TGGTGTGACCCACAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:24:1:28.7:1:1:1.7321:60:6:0.6:0:2 0/0:7:0:0,0:3,4:0:2,0:30.6:1:31.1:1:1:0:60:14:1:0:0.3 -6 54479457 . A G 48 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02424;SOR=0;LSEQ=CACAGAGAGAAGGAAGAACA;RSEQ=TGTGGTGTGGCAACCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:32.7:1:30.7:1:1:0:60:6:0.75:0:2 0/0:7:0:0,0:3,4:0:2,0:17.1:1:29.1:1:1:0:60:14:1:0:0.3 -6 54479836 . T G 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GCTTCCTGGGCAGGGGAAGG;RSEQ=TGGCACCCATTTCTGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:6:0:33:0:1:0:60:4:0.3333:0:1 0/0:5:0:0,0:2,3:0:2,0:30.2:1:29.6:1:1:0:60:10:1:0:0.2 -6 54480057 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=ACCAGAGGCTCAGAGAGAGA;RSEQ=TTCAGATCTCCTTGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:23.2:1:30.4:1:1:0:60:18:1:0:0.1 0/1:9:2:1,1:3,4:0.2222:2,2:41.5:1:29.5:1:1:1.29:60:4:0.2222:0:1 -6 54480148 . A G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=CTCTCCTCCTGGTATTTCTG;RSEQ=GAAATCCAGGCAGCCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:8,1:0.25:2,2:20.7:1:31:1:0.12727:11.0937:60:6:0.25:0:1 0/0:6:0:0,0:4,2:0:2,0:23.7:1:30.8:1:1:0:60:12:1:0:0.3 -6 54480190 . AAC A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.71951;LSEQ=AGTGGTTTTGCCCCAAGCAA;RSEQ=ACACTCTCTTCACCAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:5,2:15,10:0.2188:2,2:23.3:1:29.9:1:0.68332:1.64:60:14:0.2188:0.0313:0.9 0/1:12:2:2,0:7,3:0.1667:2,0:30:1:32:0:1:0:60:4:0.1667:0:1 -6 54480220 . G C 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91427;LSEQ=CTTCACCAAGGGACAAAGTG;RSEQ=TTCGTTAAATGGGTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:3,2:21,14:0.125:2,2:33.6:1:32.6:1:1:1:60:10:0.1282:0:1.2 0/1:26:3:2,1:13,10:0.1154:2,2:30.7:1:31.3:1:1:1.51:60:6:0.12:0:1 -6 54480393 . T G 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32397;LSEQ=TGCTGTTCTCTAGCCTCCTT;RSEQ=AGTGACATCTCCAGGCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:4,2:13,15:0.1765:2,2:23.3:1:32:1:0.65618:2.25:60:12:0.1765:0:2.2 0/1:9:2:1,1:3,4:0.2222:2,2:6.5:1:29.5:1:1:1.29:60:4:0.2222:0:2 -6 54480396 . T G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60588;SOR=1.83492;LSEQ=TGTTCTCTAGCCTCCTTTAG;RSEQ=GACATCTCCAGGCACGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:4,2:13,15:0.1765:2,2:24.3:1:31.2:1:0.65618:2.25:60:12:0.1765:0:2.2 0/1:7:2:1,1:2,3:0.2857:2,2:9.5:1:28:1:1:1.41:60:4:0.2857:0:2 -6 54480521 . A G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07441;SOR=0;LSEQ=ACAAGCAGAAAGCATCAGCA;RSEQ=CAGCAAAAACATCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:8,6:0.1765:2,0:20.3:1:33.3:1:0.20588:0:60:6:0.1765:0:1 0/0:22:0:0,0:11,11:0:2,0:25.8:1:29.5:1:1:0:60:44:1:0:0 -6 54480573 . G T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.48775;LSEQ=CACAAAAACCCCATCCAAGG;RSEQ=TCAGCAGCTTCAAAGACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:9,13:0.0833:2,0:24.5:1:26:1:0.51087:0:60:4:0.087:0:1.5 0/1:25:3:2,1:9,13:0.12:2,2:18:1:28.7:1:0.56478:2.77:60:6:0.12:0:1 -6 54480935 . CAA C 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACCTTGTGAAGCCAAATCGA;RSEQ=AGTGGAAGAAAGGATATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,2:0.6667:0,2:26:1:32:1:1:0:60:4:0.6667:0.3333:1.5 0/0:2:0:0,0:2,0:0:0,0:15:1:31:1:1:0:60:4:1:0:0 -6 54635157 . T C 79 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATAAAATGAATCTTTAGTG;RSEQ=TTGACATTATCCTGCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:0.8571:0,2:20:1:30.7:1:1:0:60:12:0.8571:0:1 1/1:1:1:1,0:0,0:1:0,0:14:0:34:0:1:0:60:2:1:0:1 -6 54635275 . G C 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19858;SOR=0.36062;LSEQ=ATACTGGTTTAGATGAAGCT;RSEQ=GGCCAGTACTCCCGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:31:31,0:4,0:0.8857:0,1:21.6:1:32:1:1:0:60:62:0.8857:0:1.3 1/0:30:22:22,0:8,0:0.7333:0,1:25.5:1:30.9:1:1:0:60:21:0.7241:0:1.1 -6 54635342 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=1;SOR=0.85915;LSEQ=CGCAGGCACTGAAGGCGGCG;RSEQ=CAGGGCCAGAGGCTCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:73,18:0.0215:2,2:26.5:1:29:1:0.36863:3.97433:60:4:0.0217:0:1.5 0/1:108:2:1,1:87,19:0.0185:2,2:41:1:29:1:0.33749:4.4886:60:4:0.0187:0:1 -6 54635362 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19639;SOR=0;LSEQ=GCAGGGCCAGAGGCTCAGCG;RSEQ=CTCCCAGACCTGCTGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:99,34:0.0148:2,2:26:1:29.5:1:0.45274:2.88435:60:4:0.0149:0:1.5 0/0:169:0:0,0:122,46:0:2,0:22.2:1:30.7:1:1:0:60:83:0.994:0:0.5 -6 54635398 . T TG 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.24338;LSEQ=AAAATGACTGAATATAAACT;RSEQ=GCGGTAGTTGGAGCTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:267:240:153,87:14,12:0.8989:2,2:26:1:31.5:1:0.39345:1.50:59.9:47:0.9004:0.1386:1.1 1/0:319:218:130,88:68,33:0.6834:2,2:24.3:1:30.8:1:0.21534:1.39343:60:217:0.6867:0.1254:1.1 -6 54635417 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18448;LSEQ=TTGCGGTAGTTGGAGCTGGT;RSEQ=GCGTAAGCAAAAGTGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:328:301:191,110:14,12:0.9177:2,2:25.8:1:29.3:1:0.3986:1.49:60:99.333:0.9226:0:1.1 1/0:409:275:157,118:82,52:0.6724:2,2:25.2:1:28.9:1:0.45551:1.18471:60:90.667:0.6733:0:1.2 -6 54635439 . C T 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13727;SOR=4.92779;LSEQ=CGTAAGCAAAAGTGTCTTGA;RSEQ=GATACAGCTAATTCAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:1:0,1:241,161:0.0025:2,0:1:0:29:0:0.40199:0:54:2:0.0025:0:1 0/1:496:6:2,4:269,221:0.0121:2,2:16.7:1:29.2:1:0.41762:2.43012:59.5:12:0.0122:0:1.5 -6 54635573 . A G 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAACAGGTCAAGAAGAGTAC;RSEQ=ATGCAATGAGGACCAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:235,215:0:2,0:25.7:1:30:1:1:0:59.9:111.5:1:0:0.7 0/1:337:13:9,4:182,142:0.0386:2,2:29.6:1:28.9:1:0.4057:1.75:60:12:0.0367:0:1.1 -6 54635601 . T TG 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.27478;SOR=0.56998;LSEQ=GAGGACCAGTACATGAGGAC;RSEQ=GGGCGGGGGGGGGGGGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:16:7,9:205,199:0.0381:2,2:12.3:1:31.6:1:0.61942:1.32359:60:32:0.0397:0:0.2 0/1:272:6:3,3:167,97:0.0221:2,2:13:1:31.7:1:0.67326:1.71794:60:12:0.0242:0:0.5 -6 54635605 . CGGGGGGGG GC 253 MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=16.000;MSILEN=1;SSF=0;SOR=0.15697;LSEQ=AGGACCAGTACATGAGGACT;RSEQ=GGGGGGGGCTTTCTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:422:270:122,148:29,17:0.6398:2,2:29.8:1:31.4:1:0.02643:2.06469:59.9:540:0.6459:0.0403:0.1 0/1:285:62:26,36:53,15:0.2175:2,2:23.7:1:28.8:1:3e-05:4.82707:59:9.333:0.2074:0.0737:0.4 -6 54635879 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19529;SOR=Inf;LSEQ=AGTTTGAGAAATAAAAGATG;RSEQ=GCAAAGATGGTAAGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:78,153:0:2,0:23.8:1:30.6:1:1:0:60:37.5:1:0:0.1 0/1:185:2:1,1:72,110:0.0108:2,2:28.5:1:28:1:1:1.52:60:4:0.0112:0:1.5 -6 54870777 . C CA 75 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.0345;SOR=Inf;LSEQ=GTCTATTGTGTTAATTTTTT;RSEQ=AAAAAAAAAAACAACTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:1,0:0.4:0,2:24.3:1:29.3:1:1:0:60:8:0.4:0:0.3 1/1:7:7:4,3:0,0:1:0,2:34:1:26.9:1:1:0:60:6:1:0.1429:0 -6 54872205 . A T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCCCCACATATGTGTGAAT;RSEQ=TGATCCTGTCATCATTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:31:1:1:0:60:4:1:0:2 -6 54872251 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGTTTTGCACACTACTC;RSEQ=ATGCAGTTTCTTCGTAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:1:29:1:1:0:60:4:1:0:2 -6 54872748 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=CTGTTAGGTTGAGGAAGTTC;RSEQ=CCTGGATAATATCCCGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:16.6:1:31.4:1:1:0:60:18:1:0:0.3 0/1:9:2:1,1:3,4:0.2222:2,2:5.5:1:30:1:1:1.29:50:4:0.2222:0:1.5 -6 54872871 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52569;SOR=0;LSEQ=ATATTTCTTGGAGGATTTGT;RSEQ=CATTCCTTTTCATTCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:4,9:0.1333:2,2:23.5:1:28:1:1:2.12:56:4:0.1333:0:2 0/0:8:0:0,0:4,4:0:2,0:18:1:27.9:1:1:0:58.5:16:1:0:0.3 -6 54872899 . T C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77722;LSEQ=TTTCATTCATTTTTCTCTAT;RSEQ=CTTGTCTGTATGTCTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:34.5:1:33:0:1:0:60:4:0.4:0:2.5 0/1:3:1:0,1:0,2:0.3333:0,0:42:0:33:0:1:0:60:2:0.3333:0:2 -6 54872912 . T C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.32198;LSEQ=TCTCTATTCTTGTCTGTATG;RSEQ=CTTATTTCAGTAAGGTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:34.5:1:33:0:1:0:60:4:0.6667:0:2.5 0/1:3:1:0,1:0,2:0.3333:0,0:46:0:33:0:1:0:60:2:0.3333:0:2 -6 54873271 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.2634;LSEQ=AACAGAAACTCTGGCCTTTT;RSEQ=GGTTTTCAGCATTTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:26:0:29:0:1:0:60:2:0.25:0:1 0/1:10:3:3,0:4,3:0.3:2,0:21.7:1:30.3:1:0.475:0:60:6:0.3:0:1 -6 54873564 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23333;SOR=Inf;LSEQ=AGCAAAGATGGGTGCCTCCT;RSEQ=CTTCTTCCGGGACCTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:7,16:0:2,0:19.4:1:31.1:1:1:0:60:46:1:0:0.2 0/1:23:3:0,3:4,16:0.1304:2,0:9.7:1:31:0:1:0:60:6:0.1304:0:1 -6 54873667 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48791;SOR=0;LSEQ=GTTGGAGGGTCTCACCCAGT;RSEQ=GGGAGGCACAGGGAGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:0.1:2,2:31:0:32.5:1:1:1.54:60:4:0.1:0:1.5 0/0:18:0:0,0:9,9:0:2,0:25.9:1:29.9:1:1:0:60:36:1:0:0.3 -6 54873715 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAAGCACTTTGTCCCTT;RSEQ=GTGGAGAGGGTGTGTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:22,18:0.0476:2,2:33:1:31.5:1:1:1.21636:60:4:0.0488:0:1 0/0:12:0:0,0:4,8:0:2,0:32.6:1:30.1:1:1:0:60:24:1:0:0.4 -6 54873758 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11724;SOR=3.66296;LSEQ=GGGGGAAACCCACTTGTCTG;RSEQ=GCTGCCTGGATTCCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:11:7,4:10,15:0.3056:2,2:28.8:1:29.5:1:0.28142:2.55:60:10:0.303:0:1.6 1/0:8:5:1,4:0,3:0.625:0,2:13.8:1:30.6:1:1:0:60:10:0.625:0:1 -6 54873784 . A G 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGATTCCTCAGAACTACC;RSEQ=GGAGTAGAGGCTAAGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:5,1:7,10:0.2609:2,2:22:1:29.5:1:0.15495:6.57:60:12:0.2609:0:2.3 0/0:2:0:0,0:1,1:0:2,0:36.5:1:30:1:1:0:60:4:1:0:1 -6 54873908 . G A 86 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=GAGTTATTGGAGATCCTGCA;RSEQ=GAAAGCCCCACCCACTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:4,4:0.4667:2,2:25.1:1:30.9:1:0.60839:2.34872:60:14:0.4667:0:1 0/0:2:0:0,0:0,2:0:0,0:15.5:1:32:0:1:0:60:4:1:0:0 -6 54874109 . C T 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.3705;LSEQ=TTCCCCCCGCCCAGGGAGCT;RSEQ=AGCGTGTTAGGCAGTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:3,2:3,4:0.4167:2,2:24.8:1:29:1:1:1.89:60:10:0.4167:0:2 1/0:4:2:0,2:1,1:0.5:2,0:18:1:30:0:1:0:60:4:0.5:0:1 -6 54874135 . A G 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAGGCAGTTGCAAGTCCC;RSEQ=GTGCTGGCTGCTACCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:0.4545:2,2:17.8:1:29.4:1:1:1.30:60:10:0.5:0:2.2 0/0:1:0:0,0:0,1:0:0,0:5:0:31:0:1:0:60:2:1:0:0 -6 54874302 . G A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TTGGGAAGCTAGGTCCCAGT;RSEQ=GCGTGGGTTCGTGAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:25.5:1:28.5:1:1:1.73:60:4:0.4:0:1 0/0:5:0:0,0:2,3:0:2,0:21.6:1:31.4:1:1:0:60:10:1:0:0.2 -6 54874413 . G T 59 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=CCGCCTTCCTTGGCTTGTGG;RSEQ=GACAGGGTACCCCTTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:22.3:1:29.8:1:1:0:60:8:0.8:0:1 1/0:4:2:1,1:2,0:0.5:0,2:27:1:32:0:1:0:60:4:0.5:0:1 -6 54874576 . T C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94088;LSEQ=CGCTTATTATGTTTTTTTTT;RSEQ=CTATGGTAGACTCCAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:4,4:2,1:0.6154:2,2:12.4:1:29.5:1:1:1.87936:60:7:0.5833:0:1 1/0:5:3:1,2:1,1:0.6:2,2:22.3:1:31.3:1:1:1.7321:60:6:0.6:0:1 -6 54874637 . A AT 47 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGCCCCACCCGAAGTTA;RSEQ=TTTTTTTTTTCTTTTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:24.3:1:29.7:1:1:0:60:6:0.6:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 55804858 . A AT 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49939;SOR=Inf;LSEQ=TTCTGATTTGACTTTTGTGC;RSEQ=TTTTTGGCTGGAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:0:2,0:25.1:1:30.5:1:1:0:60:82:1:0:0.1 0/1:50:2:1,1:27,21:0.04:2,2:26.5:1:29.5:1:1:1.2792:60:4:0.04:0:0 -6 55804954 . A T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.49591;SOR=Inf;LSEQ=TCTTCATTATCATCATCATC;RSEQ=TCTTCAGCAGCATCAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:21,21:0:2,0:30.3:1:30.2:1:1:0:60:84:1:0:0 0/1:47:2:1,1:20,25:0.0426:2,2:27:1:32:0:1:1.24:60:4:0.0426:0:1 -6 55805131 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23772;SOR=0;LSEQ=CACACTTCAACTGTAAGACC;RSEQ=TGGGTGGTGTTATTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:71,55:0.0156:2,2:26:0:32:1:1:1.2883:60:4:0.0159:0:1.5 0/0:134:0:0,0:76,58:0:2,0:27.3:1:29.8:1:1:0:60:66:1:0:0.2 -6 55805151 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.50068;SOR=Inf;LSEQ=ATGGGTGGTGTTATTTCAAA;RSEQ=CCCCCAAGGGAAACTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:69,65:0:2,0:29.6:1:32.1:1:1:0:60:66:1:0:0.1 0/1:154:2:1,1:78,74:0.013:2,2:36.5:1:29.5:1:1:1.05372:60:4:0.0133:0:1.5 -6 55805211 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4966;SOR=Inf;LSEQ=GTTGCCAGTGTTACTTAATT;RSEQ=GACTGCCTTCATAACTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:25,49:0:2,0:22:1:30.1:1:1:0:60:148:1:0:0.1 0/1:74:2:1,1:27,44:0.027:2,2:19.5:1:27:1:1:1.62:60:4:0.0274:0:1 -6 55805272 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49543;SOR=0;LSEQ=CAATTCATCTTTTCCACAGG;RSEQ=CCCTAAACTTACCATTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:16,21:0.0513:2,2:9.5:1:29.5:1:1:1.30:60:4:0.0526:0:1 0/0:34:0:0,0:16,18:0:2,0:20:1:31.7:1:1:0:60:33:1:0:0.2 -6 55805282 . T G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20658;SOR=Inf;LSEQ=TTTCCACAGGGCCCTAAACT;RSEQ=ACCATTCTTAAAGATAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:21,24:0:2,0:22.8:1:29.2:1:1:0:60:44:1:0:0.2 0/1:38:2:1,1:19,17:0.0526:2,2:25.5:1:33.5:1:1:1.11437:60:4:0.0541:0:1 -6 55805422 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49738;SOR=Inf;LSEQ=CATGTCCATTGAATCTTCCA;RSEQ=GGGTGGTGGCACTCACTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:45,38:0:2,0:21.5:1:31.7:1:1:0:60:166:1:0:0.1 0/1:89:2:1,1:48,39:0.0225:2,2:17.5:1:29.5:1:1:1.22788:60:4:0.0225:0:0 -6 58774414 . T A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=TCTCAGAAACAACTTTGTGA;RSEQ=GTGTGCGTTGAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29:1:1:0:50:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:22:0:30.5:1:1:0:60:4:1:0:1.5 -6 58774557 . A G 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TCTTCACATAAAAGGCAGAC;RSEQ=GAAGTGTTCTCAGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22.3:1:32.3:1:1:0:42.8:8:1:0:0.8 0/1:8:2:1,1:3,3:0.25:2,2:34.5:1:31.5:1:1:1:45:4:0.25:0:2 -6 58774984 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCAGTTTCCAAACACTC;RSEQ=TTTGTAGAATTTGCAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:31:1:1:0:21:4:1:0:4 -6 58775010 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATTTGCAAGGGTACATT;RSEQ=AGAGCGCATTCAGTCCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:33.5:1:1:0:21:4:1:0:4 -6 58775018 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGGTACATTTAGAGCGC;RSEQ=TTCAGTCCTATGGTACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:32.5:1:1:0:21:4:1:0:4 -6 58775024 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATTTAGAGCGCATTCAG;RSEQ=CCTATGGTACAAAAGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:33.5:1:1:0:21:4:1:0:4 -6 58775527 . A T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TGCAAGTGGATATTTGGAAC;RSEQ=CTTTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:21:0:26:0:1:0:42:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:30.5:1:1:0:37:4:1:0:1 -6 58776251 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6348;SOR=0.34026;LSEQ=TTTCTTCATGTTACTCTAGA;RSEQ=AGAAGAATTCTCAAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:18:14,4:1,0:0.9474:0,2:28.7:1:32.5:1:1:0:40.4:36:0.9474:0:2.1 1/1:28:24:17,7:3,1:0.8571:2,2:18.3:1:32.5:1:1:1.22629:44.3:48:0.8571:0:2.4 -6 58776274 . A G 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01151;SOR=0;LSEQ=AAGAATTCTCAAACACTGCT;RSEQ=TGTGATGTTTGCATTCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:2,2:13,5:0.1818:2,2:30.3:1:31.5:1:0.56459:2.4775:48:8:0.1905:0:3.5 0/0:42:0:0,0:26,16:0:2,0:26:1:28.7:1:1:0:43.3:41:1:0:2 -6 58776276 . G A 81 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04432;SOR=Inf;LSEQ=GAATTCTCAAACACTGCTAT;RSEQ=TGATGTTTGCATTCAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,7:0:2,0:32:1:32.6:1:1:0:40.9:44:1:0:2.1 0/1:40:7:4,3:21,12:0.175:2,2:31.4:1:29.1:1:1:1.30339:44.9:14:0.175:0:4.3 -6 58776289 . T G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37529;SOR=1.90916;LSEQ=CTGCTATGTGATGTTTGCAT;RSEQ=CAAGTCACAGAGTGCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:2,2:12,5:0.1818:2,2:30.3:1:31.8:1:0.57427:2.29323:48:8:0.1818:0:3.5 0/1:40:12:8,4:16,12:0.3:2,2:38.1:1:31.5:1:0.7294:1.49:41.1:24:0.3:0:3.6 -6 58776297 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52632;SOR=Inf;LSEQ=TGATGTTTGCATTCAAGTCA;RSEQ=AGAGTGCAACATTCCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:14,7:0:2,0:28.5:1:31.8:1:1:0:39.3:42:1:0:2.1 0/1:36:2:1,1:21,13:0.0556:2,2:30.5:1:30.5:1:1:1.5932:47.5:4:0.0588:0:4.5 -6 58776318 . AC GT 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00072;SOR=0.08345;LSEQ=AGAGTGCAACATTCCTCTTG;RSEQ=AGAGCAGTTGGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:5,4:3,4:0.5625:2,2:21.4:1:29.3:1:1:1.61:41.4:18:0.5625:0.125:1.6 0/1:33:3:2,1:17,13:0.0909:2,2:24.3:1:30.3:1:1:1.51:41.7:6:0.0938:0:1.3 -6 58776319 . C T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00529;SOR=8.74612;LSEQ=GAGTGCAACATTCCTCTTGA;RSEQ=AGAGCAGTTGGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:3,4:0,0:0.5:0,2:20.9:1:29.6:1:1:0:33:14:1:0:2.3 1/1:31:28:16,12:0,0:0.9032:0,2:23.7:1:27.8:1:1:0:38.6:56:1:0:2.4 -6 58776335 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50968;SOR=Inf;LSEQ=TTGACAGAGCAGTTGGGAAA;RSEQ=ACTCCTTTTGTAGAATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:19.4:1:31.8:1:1:0:35.9:24:1:0:1.9 0/1:19:2:1,1:9,8:0.1053:2,2:24:1:27.5:1:1:1.11803:27:4:0.1053:0:2.5 -6 58776352 . T C 33 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58647;SOR=0.41768;LSEQ=AAACACTCCTTTTGTAGAAT;RSEQ=TGCAATGGGATATTTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:1,7:0.2:2,2:16.5:1:33:0:0.37778:5.29:27:4:0.2:0:3 0/1:11:1:1,0:3,7:0.0909:2,0:9:0:25:0:0.36364:0:27:2:0.0909:0:2 -6 58776377 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=ATGGGATATTTGGACTTCTT;RSEQ=GAGGCCTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:32.5:1:31:1:1:2.24:27:4:0.2222:0:4 0/0:8:0:0,0:2,6:0:2,0:10.9:1:29.4:1:1:0:27:16:1:0:1.8 -6 58776411 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47368;SOR=0;LSEQ=GAAACGGGATTTCTTCGTAT;RSEQ=AATCTAGACAGAAGAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:5,5:0,0:1:0,2:25.7:1:31.8:1:1:0:28.3:20:1:0:3 1/1:10:8:4,4:1,1:0.8:2,2:33.6:1:32.3:1:1:1:28.6:16:0.8:0:2 -6 58776416 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19481;SOR=0;LSEQ=GGGATTTCTTCGTATAAATC;RSEQ=AGACAGAAGAATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,2:0.2:2,2:34:1:32.5:1:1:1.8258:27:4:0.2:0:3.5 0/0:12:0:0,0:6,6:0:2,0:31.1:1:30.1:1:1:0:28.1:24:1:0:1.7 -6 58776442 . T C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.51096;LSEQ=GAAGAATTCTCAGAAACTTC;RSEQ=TTGTGATGTGTGCATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:8,6:1,0:0.9333:0,2:17.1:1:31.1:1:1:0:31.1:28:0.9333:0:2.3 1/1:16:14:8,6:0,2:0.875:0,2:25.6:1:30.6:1:0.46667:0:29.5:28:0.875:0:1.6 -6 58776487 . A C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49298;SOR=0;LSEQ=CGAGTGGCACCTTCCTTTGG;RSEQ=TACAGCAGTTTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:20,13:0.0571:2,2:25.5:1:30.5:1:1:1.51907:27:4:0.0588:0:3 0/0:33:0:0,0:18,15:0:2,0:23.9:1:29.6:1:1:0:42:32:1:0:0.8 -6 58776492 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49275;SOR=Inf;LSEQ=GGCACCTTCCTTTGGATACA;RSEQ=CAGTTTTGAAACACTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:0:2,0:22.1:1:31.9:1:1:0:43.1:68:1:0:0.7 0/1:35:2:1,1:18,15:0.0571:2,2:39.5:1:32:1:1:1.19373:60:4:0.0571:0:2.5 -6 58776517 . G C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48759;SOR=0.50364;LSEQ=TTTGAAACACTGTTTTTGTA;RSEQ=TATTTCCAAGCGGATATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:4,2:24,18:0.125:2,2:31.5:1:32.8:1:1:1.49:51.5:12:0.125:0:1.2 0/1:45:3:2,1:23,18:0.0667:2,2:25:1:33.3:1:1:1.55:54.7:6:0.0667:0:2 -6 58776537 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49683;SOR=Inf;LSEQ=GTATTTCCAAGCGGATATTT;RSEQ=GAGCGCCTTGAAGCCTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,21:0:2,0:31.5:1:29.5:1:1:0:50.8:48:1:0:0.8 0/1:55:2:1,1:27,26:0.0364:2,2:11.5:1:33:1:1:1.03776:60:4:0.037:0:1 -6 58776542 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49745;SOR=Inf;LSEQ=TCCAAGCGGATATTTAGAGC;RSEQ=CCTTGAAGCCTATGCTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:29,22:0:2,0:29.8:1:30.8:1:1:0:51:102:1:0:0.8 0/1:58:2:1,1:30,26:0.0345:2,2:44.5:1:30.5:1:1:1.15099:49:4:0.0357:0:1.5 -6 58776551 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49643;SOR=Inf;LSEQ=ATATTTAGAGCGCCTTGAAG;RSEQ=CTATGCTAGAAATGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:31,21:0:2,0:27.4:1:31.3:1:1:0:51.5:25:1:0:0.8 0/1:57:2:1,1:28,27:0.0351:2,2:36.5:1:29.5:1:1:1.03639:54:4:0.0351:0:1 -6 58776555 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12463;SOR=0.48691;LSEQ=TTAGAGCGCCTTGAAGCCTA;RSEQ=GCTAGAAATGGAAATATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:17:9,8:22,15:0.3148:2,2:23.8:1:31.7:1:0.76941:1.29724:49.8:34:0.34:0:1.1 0/1:55:10:5,5:24,21:0.1818:2,2:18.5:1:29.9:1:1:1.14008:55.9:20:0.1852:0:1.5 -6 58776569 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49596;SOR=Inf;LSEQ=AGCCTATGCTAGAAATGGAA;RSEQ=TATCTCCCCATAAAACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:29,22:0:2,0:23.4:1:30.1:1:1:0:53.4:24.5:1:0:0.7 0/1:55:2:1,1:30,23:0.0364:2,2:36.5:1:32.5:1:1:1.29798:60:4:0.037:0:2.5 -6 58776575 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49648;SOR=Inf;LSEQ=TGCTAGAAATGGAAATATCT;RSEQ=CCCATAAAACCAAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:29,24:0:2,0:21.9:1:31:1:1:0:54.4:52:1:0:0.7 0/1:58:2:1,1:32,24:0.0345:2,2:24:0:30:0:1:1.32664:60:4:0.0351:0:1.5 -6 58776580 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49694;SOR=Inf;LSEQ=GAAATGGAAATATCTCCCCA;RSEQ=AAAACCAAGACAGAAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:29,24:0:2,0:21.4:1:28.4:1:1:0:54.9:12.25:1:0:0.7 0/1:59:2:1,1:33,24:0.0339:2,2:28:1:31:1:1:1.36746:60:4:0.0345:0:2 -6 58776592 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50178;SOR=Inf;LSEQ=TCTCCCCATAAAACCAAGAC;RSEQ=GAAGCAATCTCAGAAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:29,23:0:2,0:22.1:1:29.2:1:1:0:56.7:16.333:0.98:0:0.7 0/1:66:2:1,1:34,30:0.0303:2,2:23:1:29:1:1:1.13118:50:4:0.0303:0:1 -6 58776598 . A C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.74432;LSEQ=CATAAAACCAAGACAGAAGC;RSEQ=ATCTCAGAAACTAATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:24,24:0.0392:2,2:35:1:29.5:1:1:1:60:4:0.04:0:1.5 0/1:68:2:1,1:33,33:0.0294:2,2:26.5:1:29.5:1:1:1:60:4:0.0299:0:2 -6 58776614 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21332;SOR=0;LSEQ=AAGCAATCTCAGAAACTAAT;RSEQ=TGTGATGGCTGCATTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:23,27:0.0385:2,2:13.5:1:31:1:1:1.17:53.5:4:0.0392:0:1 0/0:60:0:0,0:30,30:0:2,0:28.1:1:31.1:1:1:0:54.6:59:1:0:0.4 -6 58776624 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49811;SOR=Inf;LSEQ=AGAAACTAATGTGTGATGGC;RSEQ=GCATTCCACACACACGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:22,27:0:2,0:27.6:1:30:1:1:0:49.9:23.5:1:0:0.4 0/1:57:2:1,1:28,27:0.0351:2,2:36.5:1:29.5:1:1:1.03639:53.5:4:0.0351:0:1 -6 58776645 . A C 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38369;SOR=3.2126;LSEQ=GCATTCCACACACACGGTGG;RSEQ=CCATTTCTCTTGATAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:1:1,0:18,25:0.0227:2,0:38:0:34:0:0.43182:0:60:2:0.0233:0:1 0/1:57:4:1,3:26,27:0.0702:2,2:23.8:1:31:1:0.61347:2.83997:60:8:0.0702:0:1.5 -6 58776656 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50614;SOR=Inf;LSEQ=ACACGGTGGACCATTTCTCT;RSEQ=GATAGAGCAGTTTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:19,24:0:2,0:24:1:29.9:1:1:0:48.8:20.5:1:0:0.4 0/1:58:2:1,1:27,29:0.0345:2,2:13:1:32.5:1:1:1.07:60:4:0.0345:0:1 -6 58776735 . C T 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.35285;SOR=0.30399;LSEQ=CTAGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTCCATCTAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:3:1,2:25,21:0.0612:2,2:29.7:1:26.7:1:0.59428:2.34:60:2:0.0417:0:3.3 0/1:52:1:0,1:28,23:0.0192:2,0:6:0:32:0:0.46154:0:57:2:0.0196:0:3 -6 58776745 . C T 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTTGGAAACGGGATTTCT;RSEQ=CATCTAAACCTACAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:23,19:0,0:1:0,2:26.1:1:29.7:1:1:0:54.2:20:1:0:2 1/1:41:41:21,20:0,0:1:0,2:25.1:1:29:1:1:0:55.8:40:1:0:2 -6 58776748 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49398;SOR=Inf;LSEQ=TTGGAAACGGGATTTCTCCA;RSEQ=CTAAACCTACAGAGAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:0:2,0:26.2:1:30.3:1:1:0:54.2:41:1:0:2 0/1:42:2:1,1:21,19:0.0476:2,2:9.5:1:28.5:1:1:1.10263:60:4:0.0488:0:2 -6 58776750 . T G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49398;SOR=0;LSEQ=GGAAACGGGATTTCTCCATC;RSEQ=AAACCTACAGAGAAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:22,18:0.0476:2,2:33:0:32:0:1:1.21636:60:4:0.0488:0:3 0/0:41:0:0,0:21,20:0:2,0:25.2:1:29:1:1:0:55.9:40:1:0:2 -6 58776753 . A C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24118;SOR=0;LSEQ=AACGGGATTTCTCCATCTAA;RSEQ=CCTACAGAGAAGAATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:21,19:0.0476:2,0:26.5:1:33:0:0.49245:0:54:4:0.0476:0:3 0/0:43:0:0,0:23,20:0:2,0:23.6:1:28.4:1:1:0:56.1:13.333:1:0:2 -6 58776782 . A T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGAATTCTCAGTAACTTC;RSEQ=TCGGATGTGTGCATTCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:20,17:0,0:1:0,2:27.5:1:30.6:1:1:0:54.4:74:1:0:2.1 1/1:45:45:22,23:0,0:1:0,2:23.8:1:30.4:1:1:0:56.7:90:1:0:2.4 -6 58776798 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4985;SOR=Inf;LSEQ=CTTCATCGGATGTGTGCATT;RSEQ=GACTCACAGAATGGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:20,19:0:2,0:24.4:1:30.5:1:1:0:55.5:78:1:0:1.8 0/1:47:2:1,1:21,24:0.0426:2,2:38.5:1:31:1:1:1.14:50:4:0.0426:0:2.5 -6 58776802 . T G 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12455;SOR=Inf;LSEQ=ATCGGATGTGTGCATTCGAC;RSEQ=CACAGAATGGAACATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:0:2,0:25.1:1:30.6:1:1:0:55.3:76:1:0:1.8 0/1:47:4:1,3:21,22:0.0851:2,2:21.3:1:31.8:1:0.61147:2.80523:57:8:0.0851:0:2.5 -6 58776809 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50397;SOR=Inf;LSEQ=GTGTGCATTCGACTCACAGA;RSEQ=TGGAACATTCCCTTTGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:25.4:1:31.1:1:1:0:55.2:74:1:0:1.6 0/1:49:2:1,1:22,24:0.0408:2,2:13:1:29.5:1:1:1.09:59:4:0.0408:0:3.5 -6 58776817 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17321;SOR=0;LSEQ=TCGACTCACAGAATGGAACA;RSEQ=TCCCTTTGATAGAGCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:16,21:0.0513:2,2:20:1:31:1:1:1.30:59:4:0.0513:0:2.5 0/0:54:0:0,0:25,29:0:2,0:23.7:1:29.5:1:1:0:57.7:108:1:0:1.9 -6 58776821 . C G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46559;SOR=1.55478;LSEQ=CTCACAGAATGGAACATTCC;RSEQ=TTTGATAGAGCAGTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:8:4,4:12,18:0.2105:2,2:30.4:1:31:1:0.69845:1.48:60:16:0.2162:0:1.6 0/1:51:15:7,8:16,20:0.2941:2,2:26.5:1:30.9:1:1:1.09:56.7:30:0.3:0:2.6 -6 58776824 . T C 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50366;SOR=Inf;LSEQ=ACAGAATGGAACATTCCCTT;RSEQ=GATAGAGCAGTTTTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:16,22:0:2,0:23.2:1:30.4:1:1:0:55.4:76:1:0:1.5 0/1:50:2:1,1:21,27:0.04:2,2:11.5:1:25.5:1:1:1.28:59:4:0.0408:0:2.5 -6 58776826 . A G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92181;LSEQ=AGAATGGAACATTCCCTTTG;RSEQ=TAGAGCAGTTTTGAGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:2,3:14,19:0.1316:2,2:13.4:1:32.4:1:1:1.10234:55.2:10:0.1351:0:2.4 0/1:49:6:3,3:19,24:0.1224:2,2:29.7:1:32.2:1:1:1.26:60:12:0.1277:0:1.8 -6 58776828 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50252;SOR=Inf;LSEQ=AATGGAACATTCCCTTTGAT;RSEQ=GAGCAGTTTTGAGACACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:16,21:0:2,0:22.8:1:29.6:1:1:0:55.7:74:1:0:1.4 0/1:48:2:1,1:21,25:0.0417:2,2:30.5:1:31.5:1:1:1.19:60:4:0.0435:0:2.5 -6 58776835 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51513;SOR=Inf;LSEQ=CATTCCCTTTGATAGAGCAG;RSEQ=TTTGAGACACCGTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:15,18:0:2,0:24.8:1:29.8:1:1:0:58.2:66:1:0:1 0/1:50:2:1,1:23,24:0.04:2,2:30.5:1:31:1:1:1.04:60:4:0.0426:0:2.5 -6 58776849 . T G 86 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07218;SOR=6.20983;LSEQ=GAGCAGTTTTGAGACACCGT;RSEQ=TTTGTAGAATTCCCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:1,0:16,20:0.0263:2,0:37:0:14:0:0.45946:0:60:0:0:0:2 0/1:48:7:3,4:21,20:0.1458:2,2:17:1:30.7:1:1:1.39024:60:14:0.1522:0:2.7 -6 58776855 . A G 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03942;SOR=Inf;LSEQ=TTTTGAGACACCGTTTTTGT;RSEQ=GAATTCCCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:0:2,0:25.9:1:29.6:1:1:0:58.3:66:1:0:0.6 0/1:47:6:2,4:20,21:0.1277:2,2:33.5:1:30.3:1:0.67013:1.87954:60:12:0.1277:0:1.7 -6 58776887 . A G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26646;SOR=Inf;LSEQ=TGGATATTTAGAGCACTTTG;RSEQ=AGTCTCTGCTAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:0:2,0:26.7:1:29.7:1:1:0:58.4:35:1:0:0.6 0/1:52:3:1,2:28,20:0.0577:2,2:14:1:32.3:1:0.57109:2.74398:60:6:0.0588:0:1.7 -6 58776909 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53422;SOR=Inf;LSEQ=GTCTCTGCTAGAAAAGGAAA;RSEQ=ATCTTCATGTAAAAAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:15,17:0:2,0:27.3:1:32.5:1:1:0:58.3:64:1:0:0.8 0/1:57:2:1,1:33,22:0.0351:2,2:46:1:30:1:1:1.48905:60:4:0.037:0:2 -6 58776910 . A T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12957;SOR=0;LSEQ=TCTCTGCTAGAAAAGGAAAC;RSEQ=TCTTCATGTAAAAAGTAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:14,16:0.0625:2,2:47:0:31:1:1:1.14:60:4:0.0645:0:1 0/0:56:0:0,0:34,22:0:2,0:27.3:1:29.6:1:1:0:59.2:55:1:0:1.1 -6 58776918 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54408;SOR=Inf;LSEQ=AGAAAAGGAAACATCTTCAT;RSEQ=TAAAAAGTAGATAGAATCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:0:2,0:25.5:1:31.5:1:1:0:58.3:32:1:0:1 0/1:63:2:1,1:37,24:0.0317:2,2:12:1:28:1:1:1.53075:60:4:0.0317:0:1.5 -6 58776930 . T G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51627;SOR=Inf;LSEQ=ATCTTCATGTAAAAAGTAGA;RSEQ=AGAATCGTTCTCAGAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:0:2,0:19.5:1:29.8:1:1:0:58.1:86:1:0:1.3 0/1:65:2:1,1:35,28:0.0308:2,2:18.5:1:33:0:1:1.24568:60:4:0.0317:0:3 -6 58776932 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14202;SOR=0;LSEQ=CTTCATGTAAAAAGTAGATA;RSEQ=AATCGTTCTCAGAAAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:18,18:0.0526:2,2:40:1:30:1:1:1:60:4:0.0541:0:3 0/0:62:0:0,0:36,24:0:2,0:26.3:1:31.3:1:1:0:60:59:0.9672:0:1.3 -6 58776942 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15417;SOR=0;LSEQ=AAAGTAGATAGAATCGTTCT;RSEQ=AGAAAGTGCTTAGTGACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:19,17:0.0526:2,2:30:1:28.5:1:1:1.11437:60:4:0.0541:0:3 0/0:58:0:0,0:32,26:0:2,0:28.2:1:30.9:1:1:0:59.9:28:1:0:1.5 -6 58776950 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52514;SOR=Inf;LSEQ=TAGAATCGTTCTCAGAAAGT;RSEQ=CTTAGTGACGTGTGCGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,18:0:2,0:26.1:1:32.9:1:1:0:59.9:72:1:0:1.5 0/1:61:2:1,1:33,26:0.0328:2,2:6:0:31:1:1:1.26423:60:4:0.0339:0:1.5 -6 58776958 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=TTCTCAGAAAGTGCTTAGTG;RSEQ=CGTGTGCGTTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:20,20:0:2,0:24.9:1:29.6:1:1:0:56.1:19:1:0:1.6 0/1:65:2:1,1:34,28:0.0308:2,2:17:0:31.5:1:1:1.21058:60:4:0.0313:0:1.5 -6 58776965 . C T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42258;SOR=0.70574;LSEQ=AAAGTGCTTAGTGACGTGTG;RSEQ=GTTCAACTCACAGAGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:26:13,13:9,7:0.619:2,2:23.2:1:28.8:1:0.75808:1.27803:55.1:12:0.6:0:2.2 1/0:60:32:16,16:13,15:0.5333:2,2:23:1:28.9:1:0.8017:1.15:57.3:31:0.5254:0:2.3 -6 58776982 . G T 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10816;SOR=0.36114;LSEQ=GTGCGTTCAACTCACAGAGT;RSEQ=TAACGTTTCTTTTGATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:37:21,16:2,2:0.9024:2,2:23.6:1:29.3:1:1:1.30:51.9:11.333:0.9189:0:1.8 1/0:56:43:20,23:6,6:0.7679:2,2:22.8:1:28.8:1:1:1.14707:52.4:42:0.7636:0:2.2 -6 58776984 . A T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26031;SOR=Inf;LSEQ=GCGTTCAACTCACAGAGTGT;RSEQ=ACGTTTCTTTTGATAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:24,17:0:2,0:24.9:1:29.4:1:1:0:51.3:82:1:0:1.8 0/1:56:3:1,2:25,28:0.0536:2,2:15.3:1:30.7:1:1:1.76801:60:6:0.0536:0:1.7 -6 58776985 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50687;SOR=Inf;LSEQ=CGTTCAACTCACAGAGTGTA;RSEQ=CGTTTCTTTTGATAGAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:24,17:0:2,0:24.9:1:30.2:1:1:0:51.3:82:1:0:1.8 0/1:56:2:1,1:25,29:0.0357:2,2:30.5:1:28:1:1:1.16:48.5:4:0.0357:0:3.5 -6 58776992 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24908;SOR=Inf;LSEQ=CTCACAGAGTGTAACGTTTC;RSEQ=TTTGATAGAGCGTTTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:23,18:0:2,0:24.2:1:30.2:1:1:0:50.3:82:1:0:1.8 0/1:50:3:2,1:20,27:0.06:2,2:22.7:1:28:1:0.57571:2.65:59:6:0.06:0:3.3 -6 58777020 . T G 93 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06773;SOR=7.33217;LSEQ=GAGCGTTTCTGAAACACCCT;RSEQ=CTTGTAGTAGCTGCAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:1,0:15,14:0.0323:2,0:17:0:34:0:1:0:40:2:0.0345:0:3 0/1:40:8:2,6:13,19:0.2:2,2:27.5:1:31:1:0.68566:2.01822:46.3:16:0.2:0:2.8 -6 58777039 . G A 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1157;SOR=Inf;LSEQ=TTCTTGTAGTAGCTGCAAGT;RSEQ=GATATTTGGACCTATTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:19,15:0:2,0:22.9:1:30.8:1:1:0:47.7:33:1:0:2.1 0/1:37:4:1,3:13,20:0.1081:2,2:21.5:1:31.3:1:1:1.91784:45:8:0.1143:0:2.3 -6 58777056 . G T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10823;SOR=0.15985;LSEQ=AGTGGATATTTGGACCTATT;RSEQ=GAGGCCTTCTTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:32:17,15:0,0:0.9697:0,2:22.2:1:30.3:1:1:0:48.4:64:1:0:2.3 1/1:36:30:13,17:3,2:0.8333:2,2:20:1:29.4:1:0.64181:1.92382:45.9:29:0.8286:0:2.4 -6 58777064 . T C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59923;SOR=0.43737;LSEQ=TTTGGACCTATTGGAGGCCT;RSEQ=CTTTGGAAACGGGATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:16,15:0.0588:2,2:22.5:1:31:1:1:1.06462:60:4:0.0625:0:4 0/1:38:1:1,0:18,19:0.0263:2,0:11:0:32:0:1:0:60:2:0.0263:0:4 -6 58777071 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49335;SOR=Inf;LSEQ=CTATTGGAGGCCTTCTTTGG;RSEQ=AACGGGATTTCTTCATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:17,18:0:2,0:23.4:1:29.6:1:1:0:52.3:34:1:0:2.1 0/1:37:2:1,1:17,18:0.0541:2,2:18:1:31:1:1:1.06:60:4:0.0556:0:3 -6 58777074 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11507;SOR=Inf;LSEQ=TTGGAGGCCTTCTTTGGAAA;RSEQ=GGGATTTCTTCATGTAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:18,20:0:2,0:22.4:1:29.2:1:1:0:52.9:11.667:1:0:2 0/1:37:3:1,2:16,18:0.0811:2,2:28.7:1:29.3:1:1:1.75132:52.3:6:0.0833:0:1.7 -6 58777094 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49444;SOR=Inf;LSEQ=CGGGATTTCTTCATGTAACT;RSEQ=TAGATTGAAGAATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:16,23:0:2,0:26.4:1:31.6:1:1:0:57.2:38:1:0:2 0/1:42:2:1,1:19,21:0.0476:2,2:33.5:1:28:1:1:1.10:60:4:0.0488:0:3.5 -6 58777098 . A T 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62788;SOR=1.39426;LSEQ=ATTTCTTCATGTAACTCTAG;RSEQ=TTGAAGAATTCTCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:10:3,7:15,14:0.2564:2,2:29.7:1:29.9:1:0.2898:2.44266:55.9:20:0.2564:0:3.1 0/1:43:14:8,6:13,16:0.3256:2,2:22.8:1:29.4:1:0.5256:1.62:53:28:0.3333:0:3.1 -6 58777106 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49574;SOR=Inf;LSEQ=ATGTAACTCTAGATTGAAGA;RSEQ=TTCTCAGAAACTCCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:18,21:0:2,0:29:1:30.5:1:1:0:59.2:38:1:0:2 0/1:44:2:0,2:21,21:0.0455:2,0:27:1:32.5:1:0.48943:0:58.5:4:0.0455:0:2 -6 58777108 . TC CT 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49512;SOR=Inf;LSEQ=GTAACTCTAGATTGAAGAAT;RSEQ=TCAGAAACTCCTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:19,21:0:2,0:28.6:1:30:1:1:0:59.3:39:1:0:2 0/1:44:2:1,1:20,22:0.0455:2,2:18.5:1:32.3:1:1:1.10:60:4:0.0455:0:1.5 -6 58777109 . C T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7304;SOR=1.42249;LSEQ=TAACTCTAGATTGAAGAATT;RSEQ=TCAGAAACTCCTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:35:17,18:2,3:0.875:2,2:30.5:1:30.3:1:1:1.40:59.4:70:0.875:0:2.1 1/1:44:40:20,20:0,2:0.9091:0,2:28:1:29.3:1:0.48897:0:56.9:39:0.9512:0:2.4 -6 58777121 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24118;SOR=Inf;LSEQ=GAAGAATTCTCAGAAACTCC;RSEQ=TTGTGATGTGTGCATTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:22,21:0:2,0:26.3:1:30.5:1:1:0:60:42:1:0:1.9 0/1:42:2:1,1:20,20:0.0476:2,2:40.5:1:31.5:1:1:1:60:4:0.0476:0:3.5 -6 58777135 . A C 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.50369;LSEQ=AACTCCTTTGTGATGTGTGC;RSEQ=TTCAATTCAAAGAGTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:21,23:0.0435:2,2:16:0:33.5:1:1:1.09:60:4:0.0435:0:2.5 0/1:45:1:0,1:22,22:0.0222:2,0:19:0:33:0:1:0:60:2:0.0227:0:4 -6 58777156 . C G 83 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07837;SOR=4.40738;LSEQ=TTCAATTCAAAGAGTGAAAC;RSEQ=TCCCTTTTCACAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:20,21:0.0465:2,0:45:1:30.5:1:0.48837:0:60:4:0.0476:0:3 0/1:39:7:3,4:15,17:0.1795:2,2:19.6:1:29.9:1:1:1.1716:60:14:0.1795:0:2.9 -6 58777164 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49438;SOR=0;LSEQ=AAAGAGTGAAACCTCCCTTT;RSEQ=CACAGAGCAGTTTGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:21,22:0.0444:2,2:8:1:29.5:1:1:1.05:60:4:0.0444:0:2 0/0:45:0:0,0:22,23:0:2,0:19.2:1:29.1:1:1:0:60:90:1:0:1.9 -6 58777178 . G T 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6548;LSEQ=CCCTTTTCACAGAGCAGTTT;RSEQ=GAAACACTGTTTTTGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:45:25,20:0,0:0.9574:0,2:21.6:1:29.9:1:1:0:58.8:44:0.9565:0:1.6 1/1:47:44:23,21:1,2:0.9362:2,2:21.5:1:29.6:1:0.60851:2.16:58.2:88:0.9362:0:1.8 -6 58777185 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49554;SOR=Inf;LSEQ=CACAGAGCAGTTTGGAAACA;RSEQ=TGTTTTTGTAGGATTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:26,19:0:2,0:24.2:1:32.2:1:1:0:58.8:90:1:0:1.5 0/1:49:2:1,1:24,23:0.0408:2,2:31.5:1:29.5:1:1:1.04259:60:4:0.0408:0:3.5 -6 58777231 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22986;SOR=0;LSEQ=TATTTATAGCGCATTGAGCC;RSEQ=ACGGCAGAAAAAGAAACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:30,21:0.0377:2,2:18.5:1:31.5:1:1:1.41877:60:4:0.0385:0:1 0/0:57:0:0,0:29,28:0:2,0:24.7:1:29.6:1:1:0:59.2:56:1:0:1.4 -6 58777233 . C T 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39924;SOR=1.75352;LSEQ=TTTATAGCGCATTGAGCCTA;RSEQ=GGCAGAAAAAGAAACATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:4,1:26,21:0.0962:2,2:34.2:1:31.2:1:0.38138:3.17:60:10:0.0962:0:2.2 0/1:57:9:6,3:23,25:0.1579:2,2:26.2:1:29.2:1:0.47026:2.15:58.6:8:0.1455:0:2.6 -6 58777237 . A G 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1259;SOR=Inf;LSEQ=TAGCGCATTGAGCCTACGGC;RSEQ=GAAAAAGAAACATCTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:29,19:0:2,0:22:1:30.6:1:1:0:58.6:96:1:0:1.5 0/1:59:4:2,2:28,27:0.0678:2,2:10.5:1:30:1:1:1.03641:57.5:8:0.069:0:3.3 -6 58777245 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17749;SOR=0;LSEQ=TGAGCCTACGGCAGAAAAAG;RSEQ=AACATCTTCCTATAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:24,16:0.0476:2,2:6:0:33:0:1:1.48518:60:4:0.0476:0:2.5 0/0:57:0:0,0:28,29:0:2,0:22.5:1:29.3:1:1:0:57.4:18:1:0:1.7 -6 58777276 . A C 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08774;SOR=Inf;LSEQ=TATAAAAACTAGACAGAATA;RSEQ=TTCTCAGAATCTGCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,26:0:2,0:22.1:1:30.4:1:1:0:54:90:1:0:2.5 0/1:37:3:2,1:16,18:0.0811:2,2:43:1:31.7:1:0.60386:2.20:56.7:6:0.0811:0:4 -6 58777281 . C G 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24481;SOR=0;LSEQ=AAACTAGACAGAATAATTCT;RSEQ=AGAATCTGCTTTGTGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:1,2:17,24:0.0682:2,2:8:1:30.7:1:1:1.40587:50.7:6:0.0682:0:3.7 0/0:38:0:0,0:18,20:0:2,0:25.3:1:31.6:1:1:0:53.6:76:1:0:2.3 -6 58777295 . T C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42169;SOR=0;LSEQ=AATTCTCAGAATCTGCTTTG;RSEQ=GATGTGTGCGTTCAACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:22,26:0,0:1:0,2:22.4:1:31.1:1:1:0:53.9:96:1:0:3.2 1/1:35:34:16,18:1,0:0.9714:0,2:24.3:1:31:1:0.48571:0:52.9:68:0.9714:0:3 -6 58777300 . T G 86 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01396;SOR=0;LSEQ=TCAGAATCTGCTTTGTGATG;RSEQ=GTGCGTTCAACTCATAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:7:2,5:16,23:0.1522:2,2:24.3:1:30.9:1:0.68785:1.71934:60:14:0.1522:0:4.4 0/0:39:0:0,0:19,20:0:2,0:21:1:30.1:1:1:0:53.8:78:1:0:3 -6 58777312 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03491;SOR=0.33306;LSEQ=TTGTGATGTGTGCGTTCAAC;RSEQ=CATAGAGTAAAACTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:35:14,21:2,7:0.7955:2,2:29.1:1:31.7:1:0.4501:2.29:52.1:70:0.7955:0:3.9 1/0:41:23:12,11:8,10:0.561:2,2:19:1:31.1:1:0.75574:1.35:53.4:46:0.561:0:3.5 -6 58777315 . T C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24138;SOR=0;LSEQ=TGATGTGTGCGTTCAACTCA;RSEQ=AGAGTAAAACTTTTCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:16,28:0,0:1:0,2:29.6:1:32.9:1:1:0:53.3:88:1:0:3.7 1/1:43:41:19,22:0,1:0.9535:0,2:21:1:31.5:1:1:0:55.4:82:0.9762:0:3.2 -6 58777334 . T A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38031;SOR=3.28695;LSEQ=ATAGAGTAAAACTTTTCTTT;RSEQ=GATAGAGCAGTTTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:1:1,0:19,25:0.0222:2,0:49:0:28:0:0.44444:0:48:2:0.0222:0:7 0/1:57:4:3,1:25,26:0.0702:2,2:10.3:1:27.3:1:0.61098:3.06:52.5:8:0.0702:0:3 -6 58777335 . G C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19324;SOR=0;LSEQ=TAGAGTAAAACTTTTCTTTT;RSEQ=ATAGAGCAGTTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:19,25:0.0435:2,2:43:1:32:1:1:1.31:60:4:0.0435:0:5.5 0/0:58:0:0,0:28,30:0:2,0:22.5:1:30.8:1:1:0:55.9:57:1:0:2.5 -6 58777365 . AATATTTGCATGTGT GGAAAATGCAAGTGG 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08151;SOR=0;LSEQ=TTTTGAAACACTCTTTTTGT;RSEQ=ATATTTAGAGCGCATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:1,2:26,20:0.06:2,2:22:1:32:1:0.58087:2.55027:58.7:6:0.0612:0.04:1.7 0/0:64:0:0,0:33,31:0:2,0:27.8:1:29.4:1:1:0:57.3:128:1:0:2.2 -6 58777366 . A G 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.17391;SOR=Inf;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=TATTTGCATGTGTATATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:45:26,19:0,0:0.9574:0,2:21:1:31.7:1:1:0:57.5:90:1:0:3.2 1/1:65:65:34,31:0,0:1:0,2:27.3:1:31.4:1:1:0:57.3:64:1:0:2.2 -6 58777393 . A T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7674;LSEQ=CATGTGTATATTTAGAGCGC;RSEQ=TTGAAGCCCACAGTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:2,0:25,24:0.0392:2,0:21.5:1:33:1:0.49176:0:60:4:0.0392:0:2.5 0/1:66:2:1,1:37,27:0.0303:2,2:31.5:1:29:1:1:1.36372:60:4:0.0308:0:4 -6 58777397 . A G 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.49492;LSEQ=TGTATATTTAGAGCGCATTG;RSEQ=AGCCCACAGTAGAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:1,0:26,22:0.0204:2,0:30:0:32:0:1:0:60:2:0.0204:0:4 0/1:66:2:1,1:36,28:0.0303:2,2:27.5:1:29:1:1:1.28077:60:4:0.0308:0:4 -6 58777401 . C A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40202;SOR=0.37232;LSEQ=TATTTAGAGCGCATTGAAGC;RSEQ=CACAGTAGAAAAGGAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:4:3,1:27,21:0.0769:2,2:26:1:31.3:1:0.62883:2.30:60:8:0.0816:0:2 0/1:67:2:1,1:38,27:0.0299:2,2:4.5:1:26:1:1:1.40009:60:4:0.0303:0:2 -6 58777419 . T C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08768;LSEQ=GCCCACAGTAGAAAAGGAAA;RSEQ=AACTTCACCTAAAACCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:33:17,16:16,8:0.5789:2,2:21.4:1:31.3:1:0.2885:1.86149:59.6:15.5:0.5741:0:1.7 0/1:57:6:4,2:29,22:0.1053:2,2:23.5:1:31.8:1:1:1.51:55.5:12:0.1053:0:2.3 -6 58777461 . C T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13891;SOR=0.28529;LSEQ=AGAAGCAATCTCAGAAACTA;RSEQ=TTTGTGATGTGTACATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:5:3,2:25,27:0.0862:2,2:16.6:1:30:1:0.67013:1.61:60:10:0.0877:0:1.8 0/1:77:2:1,1:43,32:0.026:2,2:15:0:28:1:1:1.33852:60:4:0.0263:0:1 -6 58777486 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51496;SOR=Inf;LSEQ=TGATGTGTACATTCAACTCA;RSEQ=AGAGTGGAACTTTCCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:20,25:0:2,0:29.4:1:32.2:1:1:0:56.8:90:1:0:1 0/1:67:2:1,1:29,36:0.0299:2,2:14.5:1:29:1:1:1.24:60:4:0.0299:0:1.5 -6 58777500 . C T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54783;SOR=0.67455;LSEQ=AACTCACAGAGTGGAACTTT;RSEQ=CTCTTTATAGAGCAGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:6:3,3:18,23:0.1277:2,2:24:1:29.2:1:1:1.27:53.3:12:0.1277:0:2 0/1:67:6:3,3:24,36:0.0896:2,2:25:1:28:1:0.68225:1.49:60:5:0.0781:0:1.7 -6 58777502 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51496;SOR=Inf;LSEQ=CTCACAGAGTGGAACTTTCC;RSEQ=CTTTATAGAGCAGTGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:18,27:0:2,0:26.8:1:30:1:1:0:54.5:44:1:0:1.2 0/1:67:2:1,1:26,39:0.0299:2,2:16.5:1:30:1:1:1.49:60:4:0.0299:0:2 -6 58777506 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15252;SOR=0;LSEQ=CAGAGTGGAACTTTCCTCTT;RSEQ=ATAGAGCAGTGTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:0,2:18,26:0.0435:2,0:34.5:1:31:1:0.51304:0:50:4:0.0444:0:2 0/0:71:0:0,0:28,40:0:2,0:24.6:1:28.2:1:1:0:55:33:0.9565:0:1 -6 58777508 . T G 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00934;SOR=0;LSEQ=GAGTGGAACTTTCCTCTTTA;RSEQ=AGAGCAGTGTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:2,3:16,25:0.1087:2,2:26.8:1:32.4:1:1:1.04:57.8:10:0.1087:0:1.6 0/0:68:0:0,0:28,38:0:2,0:24.4:1:28.3:1:1:0:54.4:65:0.9701:0:1.1 -6 58777546 . G A 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTCTTTTTGTAGAAACTGCA;RSEQ=GTGGATATTTGGACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:45:22,23:1,1:0.9574:2,2:24.8:1:31.3:1:1:1.04448:54.1:90:0.9574:0:2 1/1:47:45:15,30:1,1:0.9574:2,2:24.8:1:29.9:1:1:1.96856:52.6:14:0.9545:0:1.9 -6 58777573 . C T 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77568;LSEQ=ATTTGGACCTCTTTGAGGCC;RSEQ=TCGTTGGAAACGGGATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:53:28,25:1,0:0.9815:0,2:26.8:1:30.9:1:1:0:55.3:106:0.9815:0:1.8 1/1:42:41:19,22:1,0:0.9762:0,2:21.9:1:29.6:1:0.47619:0:52.9:40:0.9756:0:1.8 -6 58777575 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24871;SOR=0;LSEQ=TTGGACCTCTTTGAGGCCCT;RSEQ=GTTGGAAACGGGATTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:3:2,1:27,23:0.0566:2,2:37:1:31.3:1:1:1.69:60:6:0.0577:0:2.7 0/0:44:0:0,0:21,23:0:2,0:21.2:1:29.9:1:1:0:53.4:43:1:0:1.8 -6 58777583 . A G 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63072;LSEQ=CTTTGAGGCCCTCGTTGGAA;RSEQ=CGGGATTTCTTCCTATAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:28,25:0.0357:2,2:22:1:31:1:1:1.11769:50:4:0.0357:0:2.5 0/1:44:1:0,1:21,22:0.0227:2,0:28:0:34:0:1:0:57:2:0.0238:0:3 -6 58777634 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50187;SOR=0;LSEQ=GAATTTTCAGAAACCTCATT;RSEQ=TGATGTGTGCGTTCATCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:26,30:0.0345:2,2:21.5:1:29:1:1:1.15:60:4:0.0345:0:1 0/0:46:0:0,0:23,23:0:2,0:21.4:1:31.6:1:1:0:59.6:92:1:0:0.6 -6 58777666 . C G 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17379;SOR=5.09312;LSEQ=TTCATCTCACAGAGTGGAGT;RSEQ=TTCCGTTTGATAGAGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:1:0,1:25,28:0.0185:2,0:47:0:31:0:1:0:60:2:0.0185:0:1 0/1:45:4:2,2:20,21:0.0889:2,2:27.3:1:32:1:1:1.05:60:8:0.0909:0:1.3 -6 58777684 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49821;SOR=0;LSEQ=GTCTTCCGTTTGATAGAGAA;RSEQ=TTTTGAAACCCTGTTCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:23,28:0.0377:2,2:24.5:1:33.5:1:1:1.21:60:4:0.0377:0:1 0/0:45:0:0,0:27,18:0:2,0:24.3:1:32:1:1:0:60:90:1:0:0.4 -6 58777685 . T C 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.59393;LSEQ=TCTTCCGTTTGATAGAGAAG;RSEQ=TTTGAAACCCTGTTCTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:24,28:0.037:2,2:26:1:31.5:1:1:1.16:60:4:0.037:0:1 0/1:45:1:0,1:27,17:0.0222:2,0:39:0:33:0:0.4:0:60:2:0.0227:0:1 -6 58777715 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50621;SOR=Inf;LSEQ=CTGTTCTTGTAGGATTTCCA;RSEQ=GTGGATATTTAGACCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:17,22:0:2,0:26.4:1:30.9:1:1:0:59.4:78:1:0:0.3 0/1:53:2:0,2:29,22:0.0377:2,0:22:1:27.5:1:0.20029:0:60:4:0.0377:0:2 -6 58777726 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1684;SOR=0;LSEQ=GGATTTCCAAGTGGATATTT;RSEQ=GACCACTTTGAAGCCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:0.0556:2,2:18.5:1:33.5:1:1:1:57:4:0.0556:0:1 0/0:51:0:0,0:28,23:0:2,0:23.9:1:28.9:1:1:0:57.6:102:1:0:0.4 -6 58777739 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19589;SOR=0;LSEQ=GATATTTAGACCACTTTGAA;RSEQ=CCTATGATAGAAAAGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:19,20:0.0488:2,2:19.5:1:30:1:1:1.05:50:4:0.0488:0:1 0/0:51:0:0,0:27,24:0:2,0:24.2:1:31.1:1:1:0:56.8:50:1:0:0.5 -6 58777764 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4966;SOR=Inf;LSEQ=TGATAGAAAAGGAAACATCT;RSEQ=CATGGAAAACATAGATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:21,20:0:2,0:22.3:1:29.5:1:1:0:55.7:40:1:0:0.6 0/1:47:2:1,1:23,22:0.0426:2,2:25:1:31:1:1:1.04448:51:4:0.0444:0:1.5 -6 58777766 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20274;SOR=0;LSEQ=ATAGAAAAGGAAACATCTTC;RSEQ=TGGAAAACATAGATAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:19,18:0.0513:2,2:23:1:29.5:1:1:1.05412:60:4:0.0526:0:1 0/0:47:0:0,0:24,23:0:2,0:25.5:1:29.8:1:1:0:56.7:94:1:0:1 -6 58777775 . A C 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00864;SOR=Inf;LSEQ=GAAACATCTTCATGGAAAAC;RSEQ=TAGATAGAATCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:25.4:1:30:1:1:0:55.3:36:1:0:0.7 0/1:48:8:4,4:19,21:0.1667:2,2:28.9:1:31.8:1:1:1.10:54.1:16:0.1667:0:2.1 -6 58777785 . T C 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50442;SOR=1.85316;LSEQ=CATGGAAAACATAGATAGAA;RSEQ=CATTCTCAGAAACAACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:1,2:17,15:0.0857:2,2:17.3:1:32.7:1:0.6026:2.21548:53.3:6:0.0882:0:2 0/1:47:7:3,4:16,24:0.1489:2,2:29.7:1:31.3:1:1:1.12:57.6:14:0.1522:0:1.7 -6 58777789 . T C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26287;SOR=Inf;LSEQ=GAAAACATAGATAGAATCAT;RSEQ=CTCAGAAACAACTTTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:19,15:0:2,0:28.9:1:30.1:1:1:0:54.9:68:1:0:0.9 0/1:48:3:1,2:18,27:0.0625:2,2:32.7:1:31.3:1:1:1.32561:60:6:0.0625:0:1.7 -6 58777790 . C G 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07135;SOR=Inf;LSEQ=AAAACATAGATAGAATCATT;RSEQ=TCAGAAACAACTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:0:2,0:29.7:1:31.9:1:1:0:54.7:66:1:0:0.9 0/1:46:5:2,3:16,25:0.1087:2,2:21.8:1:31.4:1:1:1.04:53.8:10:0.1087:0:2.2 -6 58777814 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23487;SOR=Inf;LSEQ=GAAACAACTTTGTGATGTGT;RSEQ=CGTTGAACTCACCGTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:20,22:0:2,0:22.9:1:32:1:1:0:56.4:84:1:0:1.1 0/1:40:2:1,1:15,23:0.05:2,2:24.5:1:30:1:1:1.52:50:4:0.05:0:4 -6 58777827 . C A 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.03398;LSEQ=GATGTGTGCGTTGAACTCAC;RSEQ=GTCTTTAAACTTTCTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:0,1:19,21:0.0244:2,0:16:0:33:0:1:0:60:2:0.0244:0:3 0/1:41:2:1,1:17,22:0.0488:2,2:24.5:1:28.5:1:1:1.29:50:4:0.0488:0:4 -6 58777828 . G A 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20164;SOR=5.18383;LSEQ=ATGTGTGCGTTGAACTCACC;RSEQ=TCTTTAAACTTTCTTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:1:0,1:19,19:0.0256:2,0:29:0:28:0:1:0:60:2:0.0263:0:2 0/1:41:5:2,3:16,20:0.122:2,2:25:1:29.2:1:1:1.19473:57.2:10:0.122:0:3 -6 58777836 . A C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49367;SOR=Inf;LSEQ=GTTGAACTCACCGTCTTTAA;RSEQ=CTTTCTTTTGGTAGAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:38:17,21:1,1:0.95:2,2:22.1:1:31.1:1:1:1.22874:58.8:37:0.9487:0:1.4 1/1:40:40:19,21:0,0:1:0,2:21.7:1:30.7:1:1:0:59.1:80:1:0:1.8 -6 58777939 . G A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4926;SOR=Inf;LSEQ=GGAAAAGGGAATGTCTTCAC;RSEQ=TAAAAGGCAGACAGAAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:11,11:2,0:0.9167:0,2:22.6:1:30:1:0.48188:0:47.8:44:0.9167:0:1.9 1/1:20:20:12,8:0,0:1:0,2:25.3:1:30.5:1:1:0:39.3:40:1:0:2 -6 58777952 . A G 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0432;SOR=Inf;LSEQ=TCTTCACGTAAAAGGCAGAC;RSEQ=GAAGTGTTCTCAGAAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:17,11:0:2,0:22.3:1:31.1:1:1:0:50:56:1:0:2.2 0/1:25:4:2,2:13,8:0.16:2,2:24.8:1:30.5:1:1:1.59276:37.8:8:0.1667:0:2 -6 58777953 . G C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=CTTCACGTAAAAGGCAGACA;RSEQ=AAGTGTTCTCAGAAACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:16,10:0.0714:2,2:21:1:31:1:1:1.57244:43:4:0.0741:0:4 0/0:27:0:0,0:15,12:0:2,0:21.3:1:31.2:1:1:0:44.1:26:1:0:2.2 -6 58777960 . T C 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02372;SOR=0;LSEQ=TAAAAGGCAGACAGAAGTGT;RSEQ=CTCAGAAACTGCTTTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:4,1:13,11:0.1724:2,2:11.4:1:31.8:1:0.37013:3.26:56:10:0.1786:0:3 0/0:30:0:0,0:16,14:0:2,0:21.6:1:29.1:1:1:0:45.3:29:1:0:2.1 -6 58777971 . G C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49895;SOR=Inf;LSEQ=CAGAAGTGTTCTCAGAAACT;RSEQ=CTTTGTGATGTCTGTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:19,15:0:2,0:25.2:1:31.6:1:1:0:51.9:16:1:0:2.4 0/1:42:2:1,1:23,17:0.0476:2,2:6.5:1:32:0:1:1.34309:59.5:4:0.0476:0:7 -6 58777983 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49419;SOR=Inf;LSEQ=CAGAAACTGCTTTGTGATGT;RSEQ=TGTGTTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:20,17:0:2,0:26.2:1:31.4:1:1:0:52.5:36:1:0:2.5 0/1:40:2:1,1:22,16:0.05:2,2:18.5:1:32.5:1:1:1.36391:59.5:4:0.05:0:7 -6 58777995 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49654;SOR=Inf;LSEQ=TGTGATGTCTGTGTTCAACT;RSEQ=ACAGAGTTTAACATTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:19,19:0:2,0:27.2:1:31.3:1:1:0:55.3:18:1:0:2.9 0/1:44:2:1,1:24,18:0.0455:2,2:44:1:29:1:1:1.32452:60:4:0.0455:0:5 -6 58778001 . G A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.07062;LSEQ=GTCTGTGTTCAACTCACAGA;RSEQ=TTTAACATTTCCTTTGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:18,17:0.0541:2,2:23:1:30:1:1:1.05721:60:4:0.0541:0:1.5 0/1:52:3:2,1:26,23:0.0577:2,2:21.3:1:29:1:1:1.75:34:6:0.0588:0:4 -6 58778003 . T G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50979;SOR=Inf;LSEQ=CTGTGTTCAACTCACAGAGT;RSEQ=TAACATTTCCTTTGATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:0:2,0:28.4:1:30.2:1:1:0:56.2:37:1:0:3.3 0/1:54:2:1,1:28,24:0.037:2,2:49:1:32:1:1:1.16333:60:4:0.0385:0:5 -6 58778004 . T G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51145;SOR=Inf;LSEQ=TGTGTTCAACTCACAGAGTT;RSEQ=AACATTTCCTTTGATAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:0:2,0:28.6:1:29.6:1:1:0:56.8:76:1:0:3.4 0/1:55:2:1,1:28,25:0.0364:2,2:12.5:1:29:1:1:1.11769:21:4:0.037:0:4.5 -6 58778008 . A C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50548;SOR=Inf;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCCTTTGATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:0:2,0:27:1:30.9:1:1:0:57:82:1:0:3.5 0/1:55:2:1,1:28,25:0.0364:2,2:43.5:1:32:1:1:1.11769:59.5:4:0.037:0:7 -6 58778011 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50649;SOR=Inf;LSEQ=AACTCACAGAGTTTAACATT;RSEQ=CCTTTGATAGAGCAGTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:22,20:0:2,0:26.7:1:29.7:1:1:0:57.1:20:1:0:3.6 0/1:57:2:1,1:28,27:0.0351:2,2:5.5:1:29:1:1:1.03639:21:4:0.0357:0:4.5 -6 58778013 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49981;SOR=Inf;LSEQ=CTCACAGAGTTTAACATTTC;RSEQ=TTTGATAGAGCAGTTTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:23,24:0:2,0:24.1:1:31.7:1:1:0:56.5:94:1:0:4 0/1:57:2:1,1:27,26:0.0351:2,2:48.5:1:31:1:1:1.03776:59.5:4:0.0364:0:7 -6 58778017 . G C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49515;SOR=Inf;LSEQ=CAGAGTTTAACATTTCCTTT;RSEQ=ATAGAGCAGTTTAGTAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:25,24:0:2,0:23.6:1:31.7:1:1:0:57:48:1:0:4 0/1:51:2:1,1:24,25:0.0392:2,2:48.5:1:31.5:1:1:1.04:59.5:4:0.0408:0:7 -6 58778019 . T G 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11187;SOR=0.38235;LSEQ=GAGTTTAACATTTCCTTTGA;RSEQ=AGAGCAGTTTAGTAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:44:23,21:2,3:0.898:2,2:24.3:1:32.3:1:0.6671:1.63:56.7:88:0.898:0:4.3 1/0:52:40:19,21:7,5:0.7692:2,2:26.5:1:30.4:1:0.74316:1.5344:56.7:19:0.76:0:4 -6 58778025 . A G 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73262;SOR=1.41942;LSEQ=AACATTTCCTTTGATAGAGC;RSEQ=GTTTAGTAACACTGTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:43:24,19:2,3:0.8958:2,2:25.1:1:30.6:1:0.64924:1.87:57.5:86:0.8958:0:4.4 1/1:53:49:25,24:1,2:0.9245:2,2:25.9:1:29.8:1:1:2.06:57.4:48:0.9231:0:4 -6 58778039 . G C 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGCAGTTTAGTAACACT;RSEQ=TCTTTGTAGAATTTGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:27,25:0,0:1:0,2:25.1:1:31.5:1:1:0:59.2:25:1:0:4.3 1/1:57:57:28,29:0,0:1:0,2:25.3:1:31.5:1:1:0:58.3:114:1:0:4 -6 58778058 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23567;SOR=Inf;LSEQ=TGTCTTTGTAGAATTTGGAA;RSEQ=TGTATACTAAGAGCGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:32,30:0:2,0:24.2:1:32.4:1:1:0:57.3:61:1:0:4.1 0/1:59:2:1,1:28,29:0.0339:2,2:26.5:1:28.5:1:1:1.04:59:4:0.0345:0:5.5 -6 58778081 . TT GC 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24348;SOR=0;LSEQ=TATACTAAGAGCGCTTTGAG;RSEQ=CTATGGTAGAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:58:30,28:0,0:1:0,2:27:1:31.9:1:1:0:56.1:116:1:0.0345:3.3 1/1:58:55:31,24:0,0:0.9483:0,2:23:1:31.3:1:1:0:55.9:54:0.9818:0.1034:3.1 -6 58778082 . T C 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACTAAGAGCGCTTTGAGT;RSEQ=CTATGGTAGAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:52:2:0,2:0,1:0.0385:0,0:28:1:27:0:1:0:60:4:0.6667:0:5.5 -6 58778086 . T C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4958;SOR=0;LSEQ=TAAGAGCGCTTTGAGTTCTA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:30,28:0.0333:2,2:29:1:31.5:1:1:1.07017:60:4:0.0333:0:4.5 0/0:60:0:0,0:31,29:0:2,0:22.4:1:28.9:1:1:0:54.5:29:1:0:3 -6 58778093 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49625;SOR=Inf;LSEQ=GCTTTGAGTTCTATGGTAGA;RSEQ=AAGGAAATATCTTTGCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:30,26:0:2,0:25.7:1:30.1:1:1:0:55.4:112:1:0:3.1 0/1:60:2:1,1:29,29:0.0333:2,2:31:0:33:0:1:1:45:4:0.0333:0:4 -6 58778097 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49602;SOR=Inf;LSEQ=TGAGTTCTATGGTAGAAAAG;RSEQ=AAATATCTTTGCATAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:26,25:0:2,0:27.4:1:30.9:1:1:0:55:50:0.9804:0:3 0/1:56:2:1,1:28,26:0.0357:2,2:21.5:1:30:1:1:1.07547:46:4:0.037:0:5.5 -6 58778100 . A T 86 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.32809;SOR=2.2241;LSEQ=GTTCTATGGTAGAAAAGGAA;RSEQ=TATCTTTGCATAAAAGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:1,2:25,23:0.0588:2,2:21:1:30:1:0.60984:2.142:60:6:0.0588:0:4.3 0/1:57:7:3,4:26,24:0.1228:2,2:30.1:1:30.7:1:0.7057:1.43516:55.7:14:0.125:0:3.9 -6 58778108 . G C 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GTAGAAAAGGAAATATCTTT;RSEQ=CATAAAAGCTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:48:23,25:0,0:0.9796:0,2:25.3:1:31.1:1:1:0:54.6:96:0.9796:0:2.8 1/1:56:56:30,26:0,0:1:0,2:27.3:1:29.9:1:1:0:53.3:17.667:1:0:2.5 -6 58778142 . C A 25 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51418;SOR=Inf;LSEQ=CAGAAGCAATCTCAGAAACT;RSEQ=CTTTGTGATGTCTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:18,21:0:2,0:22.4:1:30.4:1:1:0:57.6:78:1:0:1.6 0/1:58:2:1,1:30,26:0.0345:2,2:7.5:1:25:1:1:1.15099:60:4:0.0345:0:4 -6 58778145 . T C 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50352;SOR=0.60328;LSEQ=AAGCAATCTCAGAAACTCCT;RSEQ=TGTGATGTCTGCATTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:2,3:15,18:0.1316:2,2:34.8:1:28.2:1:1:1.24275:55.6:4:0.1143:0:2.8 0/1:60:5:3,2:28,27:0.0833:2,2:20.8:1:30.6:1:1:1.44:57:10:0.0847:0:2.2 -6 58778148 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51939;SOR=Inf;LSEQ=CAATCTCAGAAACTCCTTTG;RSEQ=GATGTCTGCATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:17,22:0:2,0:22.1:1:29.3:1:1:0:57.6:78:1:0:1.6 0/1:61:2:1,1:31,28:0.0328:2,2:32.5:1:29.5:1:1:1.10529:56:4:0.0333:0:3 -6 58778190 . T G 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67686;SOR=1.98479;LSEQ=GAGTGGAACATTCCTCTTGA;RSEQ=AGAGCAGTTTGGAAACGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:0,2:18,23:0.0465:2,0:8.5:1:31:1:0.50166:0:54.5:4:0.0476:0:2.5 0/1:45:4:2,2:21,20:0.0889:2,2:17:1:32.8:1:1:1.04888:56.3:8:0.0889:0:2.3 -6 58778193 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49425;SOR=0;LSEQ=TGGAACATTCCTCTTGATAG;RSEQ=GCAGTTTGGAAACGCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:18,24:0.0455:2,2:29.5:1:30.5:1:1:1.32:60:4:0.0488:0:3 0/0:44:0:0,0:23,21:0:2,0:24.4:1:30:1:1:0:59.3:88:1:0:1.7 -6 58778202 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22051;SOR=Inf;LSEQ=CCTCTTGATAGAGCAGTTTG;RSEQ=AAACGCTCTTTCTGTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:20,28:0:2,0:29:1:31.2:1:1:0:60:47:1:0:2 0/1:43:2:1,1:22,19:0.0465:2,2:19.5:1:29.5:1:1:1.15394:60:4:0.0465:0:2.5 -6 58778207 . G A 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=TGATAGAGCAGTTTGGAAAC;RSEQ=CTCTTTCTGTAGAATCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:21,27:0,0:1:0,2:29.9:1:30.5:1:1:0:60:96:1:0:2 1/1:44:43:22,21:0,0:0.9773:0,2:24.5:1:29.6:1:1:0:60:86:0.9773:0:1.9 -6 58778244 . A T 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.48454;SOR=0;LSEQ=AGCTTGTTTGTATTTGGACC;RSEQ=CCTTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:50:25,25:0,0:1:0,2:21:1:31:1:1:0:60:100:1:0:2 1/1:47:46:26,20:0,0:0.9787:0,2:24.6:1:29.6:1:1:0:59.7:22:1:0:1.9 -6 58778284 . AC A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1876;SOR=0;LSEQ=AACGGGTTTTCATCTTATAA;RSEQ=CCAGACAGAAGAATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:21,18:0.0488:2,2:25:1:30:1:1:1.16227:60:4:0.0488:0:0.5 0/0:53:0:0,0:26,26:0:2,0:24.8:1:31.3:1:1:0:59.6:104:1:0:1.2 -6 58778289 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50728;SOR=Inf;LSEQ=GTTTTCATCTTATAAACCCA;RSEQ=ACAGAAGAATTCTCAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:21,19:0:2,0:23.2:1:32:1:1:0:60:80:1:0:0.8 0/1:55:2:1,1:27,26:0.0364:2,2:28:1:28:1:1:1.03776:60:4:0.0364:0:1 -6 58778290 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50414;SOR=Inf;LSEQ=TTTTCATCTTATAAACCCAG;RSEQ=CAGAAGAATTCTCAGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:21,20:0:2,0:22.8:1:30.1:1:1:0:60:82:1:0:0.7 0/1:54:2:1,1:27,25:0.037:2,2:9:0:31:1:1:1.07844:60:4:0.037:0:1 -6 58778308 . T A 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.29451;SOR=Inf;LSEQ=AGACAGAAGAATTCTCAGAG;RSEQ=CTTCTTTGTGATGTGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:22,18:0:2,0:26.8:1:30.2:1:1:0:60:80:1:0:0.4 0/1:67:4:3,1:31,32:0.0597:2,2:16.8:1:28.3:1:0.61355:3.05:55:8:0.0645:0:3.3 -6 58778325 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52221;SOR=Inf;LSEQ=GAGTCTTCTTTGTGATGTGT;RSEQ=CTTTCAACTCACCGAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:0:2,0:24.7:1:32.2:1:1:0:60:102:1:0:0.7 0/1:81:2:1,1:41,38:0.0247:2,2:21.5:1:28.5:1:1:1.07791:60:4:0.0253:0:1.5 -6 58778338 . C T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00317;SOR=Inf;LSEQ=GATGTGTGCTTTCAACTCAC;RSEQ=GAGATAAAGATTTCTCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:0:2,0:25.5:1:30:1:1:0:60:50:1:0:0.9 0/1:77:11:6,5:31,35:0.1429:2,2:26.1:1:30.1:1:0.74959:1.35:58.2:22:0.1467:0:2.5 -6 58778339 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51429;SOR=Inf;LSEQ=ATGTGTGCTTTCAACTCACC;RSEQ=AGATAAAGATTTCTCTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:0:2,0:25.5:1:29.8:1:1:0:60:24.5:1:0:0.9 0/1:75:2:1,1:36,37:0.0267:2,2:28.5:1:28:1:1:1.03:60:4:0.0278:0:2.5 -6 58778354 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52665;SOR=Inf;LSEQ=TCACCGAGATAAAGATTTCT;RSEQ=TTGATAGAGCAATTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:0:2,0:25.7:1:31.1:1:1:0:60:23.5:1:0:1 0/1:81:2:1,1:40,39:0.0247:2,2:15:1:32:1:1:1.02533:60:4:0.025:0:3 -6 58778360 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53953;SOR=Inf;LSEQ=AGATAAAGATTTCTCTTGAT;RSEQ=GAGCAATTTGGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:22,25:0:2,0:25.4:1:29.3:1:1:0:60:46:1:0:1.1 0/1:86:2:1,1:42,42:0.0233:2,2:30:1:29:1:1:1:60:4:0.0241:0:2.5 -6 58778392 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACACTCTTTTTGTAGAAT;RSEQ=TGCAAGGGTACCCTGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:0:2,0:23.3:1:30.2:1:1:0:59.9:34:1:0:2.6 0/1:76:2:1,1:37,37:0.0263:2,2:7:0:31:1:1:1:60:4:0.0263:0:1 -6 58778394 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACTCTTTTTGTAGAATTT;RSEQ=CAAGGGTACCCTGAGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:19,17:0:2,0:22:1:32.4:1:1:0:59.9:35:1:0:2.8 0/1:73:2:1,1:34,37:0.0274:2,2:20:1:28.5:1:1:1.09:60:4:0.0278:0:2.5 -6 58778404 . CC AT 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGAATTTGCAAGGGTAC;RSEQ=TGAGAGTGCTTTCAGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:16,17:0,0:1:0,2:21.2:1:31:1:1:0:59.9:66:1:0.0606:2.2 1/1:60:60:31,29:0,0:1:0,2:23.7:1:29.1:1:1:0:60:120:1:0.1333:2.3 -6 58778412 . T C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAAGGGTACCCTGAGAG;RSEQ=GCTTTCAGGCCTATGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:14,15:0,0:1:0,2:22.4:1:30.9:1:1:0:60:58:1:0:2.7 1/1:59:59:31,28:0,0:1:0,2:23.8:1:29.3:1:1:0:60:18.667:1:0:2.5 -6 58778448 . C A 45 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30584;SOR=Inf;LSEQ=GTAGAAAAGGGAATATCTTT;RSEQ=CATAAAAGGTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:0:2,0:28.1:1:31.2:1:1:0:60:58:1:0:2.7 0/1:64:4:3,1:28,32:0.0625:2,2:5:1:22.5:1:0.34738:3.37:56.8:3:0.0484:0:3.8 -6 58778452 . A C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.07422;LSEQ=AAAAGGGAATATCTTTCCAT;RSEQ=AAAGGTAGACAGAAGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:24:13,11:4,3:0.7742:2,2:29:1:31.7:1:1:1.12384:60:48:0.7742:0:2.8 0/1:61:12:4,8:24,25:0.1967:2,2:31.3:1:31.4:1:0.51946:1.89996:58.9:24:0.2:0:3.1 -6 58778456 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54826;SOR=Inf;LSEQ=GGGAATATCTTTCCATAAAA;RSEQ=GTAGACAGAAGCAATCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:17,14:0:2,0:27.7:1:31.8:1:1:0:60:62:1:0:2.7 0/1:61:3:2,1:27,31:0.0492:2,2:18:1:29.7:1:0.60033:2.27:60:6:0.0526:0:2 -6 58778468 . C A 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATAAAAGGTAGACAGAAG;RSEQ=AATCTCAGAAACTGCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:30.4:1:32.4:1:1:0:60:56:1:0:2.6 0/1:63:2:1,1:26,35:0.0317:2,2:15:0:27:1:1:1.34:60:4:0.0328:0:5 -6 58778482 . G A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54133;SOR=0;LSEQ=CAGAAGCAATCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:16,16:0,0:1:0,2:24.9:1:29.1:1:1:0:60:64:1:0:2.3 1/1:60:58:25,33:1,1:0.9667:2,2:28:1:27.9:1:1:1.31382:59.8:18.333:0.9821:0:2.1 -6 58778489 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55001;SOR=Inf;LSEQ=AATCTCAGAAACTGCTTTGT;RSEQ=ATGTGTGCATTCAACTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:16,17:0:2,0:22.4:1:31.7:1:1:0:60:66:0.9706:0:2 0/1:62:3:1,2:25,34:0.0484:2,2:28:1:22.3:1:1:1.4618:60:2:0.0333:0:3 -6 58778519 . A G 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49158;SOR=2.05353;LSEQ=TTCAACTCACCGAGTGCAAC;RSEQ=TTCCTCTTGATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:14,17:0.0606:2,0:19.5:1:31.5:1:0.22727:0:60:4:0.0606:0:2 0/1:68:8:4,4:27,32:0.1176:2,2:11.1:1:30.4:1:1:1.18:58.4:16:0.1212:0:3.8 -6 58778530 . TA CC 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57025;SOR=1.58706;LSEQ=GAGTGCAACATTCCTCTTGA;RSEQ=GAGCAGTTTGGAAACATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:2,2:13,13:0.1333:2,2:27:1:31.3:1:1:1:60:8:0.1379:0:1.8 0/1:66:13:7,6:26,26:0.197:2,2:25.2:1:29.1:1:1:1.16:60:26:0.2:0.0152:2.3 -6 58778577 . T A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29907;SOR=1.62403;LSEQ=TAGAATCTGCAAGTGGATAT;RSEQ=TGGACCTCTTTGAGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:12:7,5:11,13:0.3333:2,2:23.8:1:29.3:1:0.72467:1.63:60:24:0.3429:0:2 0/1:69:31:16,15:20,18:0.4493:2,2:22.9:1:28.4:1:1:1.04107:60:62:0.4559:0:2.7 -6 58778582 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11327;SOR=0;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=CTCTTTGAGGCCTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:18,15:0.0571:2,2:30:1:30:0:1:1.19373:60:4:0.0588:0:1.5 0/0:68:0:0,0:36,32:0:2,0:22.9:1:29.7:1:1:0:59.8:21.667:1:0:1.8 -6 58778584 . T G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05074;LSEQ=TGCAAGTGGATATTTGGACC;RSEQ=CTTTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:21:11,10:8,6:0.6:2,2:26.2:1:31.3:1:1:1.20548:60:42:0.6:0:1.7 1/0:67:41:23,18:12,13:0.6119:2,2:22.8:1:30.3:1:0.61415:1.38:60:82:0.6308:0:2.4 -6 58778598 . G A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03001;LSEQ=TGGACCTCTTTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:1,0:17,16:0.0286:2,0:1:0:26:0:1:0:60:2:0.0294:0:2 0/1:68:2:1,1:33,33:0.0294:2,2:12.5:1:29:1:1:1:60:4:0.0299:0:2 -6 58778606 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52811;SOR=Inf;LSEQ=TTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCCTATAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:23,18:0:2,0:22:1:30.7:1:1:0:58.4:82:1:0:1 0/1:69:2:1,1:33,34:0.029:2,2:30:0:29:1:1:1.03:60:4:0.0294:0:3 -6 58778610 . A T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50765;SOR=Inf;LSEQ=AGGCCTTCGTTGGAAACGGG;RSEQ=TTTCTTCCTATAAACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:25,21:0:2,0:20.4:1:28.9:1:1:0:58.6:22:1:0:0.9 0/1:63:2:1,1:30,31:0.0317:2,2:35:0:29.5:1:1:1.03:60:4:0.0328:0:2 -6 58778614 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.5052;SOR=Inf;LSEQ=CTTCGTTGGAAACGGGATTT;RSEQ=TTCCTATAAACCCAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:25,21:0:2,0:21.2:1:31.3:1:1:0:58.6:92:1:0:0.9 0/1:61:2:1,1:28,31:0.0328:2,2:35.5:1:30:1:1:1.11:42.5:4:0.0333:0:6 -6 58778617 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50609;SOR=Inf;LSEQ=CGTTGGAAACGGGATTTCTT;RSEQ=CTATAAACCCAGACAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:26,21:0:2,0:21.3:1:30.4:1:1:0:58.6:22.5:1:0:0.9 0/1:63:2:1,1:28,33:0.0317:2,2:30.5:1:30:1:1:1.18:60:4:0.0317:0:4 -6 58778618 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50338;SOR=Inf;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TATAAACCCAGACAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,21:0:2,0:20.6:1:31.1:1:1:0:58.7:98:1:0:0.9 0/1:63:2:1,1:28,33:0.0317:2,2:7.5:1:29:1:1:1.18:60:4:0.0317:0:1 -6 58778624 . A T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50398;SOR=Inf;LSEQ=AACGGGATTTCTTCCTATAA;RSEQ=CCCAGACAGAAGAATTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:28,23:0:2,0:21.2:1:29.8:1:1:0:58.7:102:1:0:0.8 0/1:66:2:1,1:29,35:0.0303:2,2:24:1:27:0:1:1.20:60:4:0.0317:0:4 -6 58778627 . CA AG 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49867;SOR=Inf;LSEQ=GGGATTTCTTCCTATAAACC;RSEQ=GACAGAAGAATTCTCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:30,24:0:2,0:20.7:1:30.8:1:1:0:58.8:26:1:0:0.7 0/1:63:2:1,1:27,34:0.0317:2,2:35.5:1:31.5:1:1:1.25:42.5:4:0.0317:0:5 -6 58778636 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2066;SOR=0;LSEQ=TCCTATAAACCCAGACAGAA;RSEQ=AATTCTCAGAGACTTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:28,23:0.0377:2,2:38:0:31.5:1:1:1.21285:60:4:0.0392:0:1.5 0/0:63:0:0,0:27,36:0:2,0:24.5:1:31.8:1:1:0:58.9:126:1:0:1.5 -6 58778647 . G A 32 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.80424;LSEQ=CAGACAGAAGAATTCTCAGA;RSEQ=ACTTCTTTGTGATGTGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:1,0:33,25:0.0169:2,0:1:0:31:0:1:0:60:2:0.0172:0:1 0/1:66:2:1,1:26,36:0.0303:2,2:17.5:1:32:0:1:1.38:42.5:4:0.0303:0:5 -6 58778649 . C T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00708;SOR=3.02761;LSEQ=GACAGAAGAATTCTCAGAGA;RSEQ=TTCTTTGTGATGTGTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:11:5,6:28,20:0.1864:2,2:26.4:1:31.1:1:0.51148:1.66499:60:22:0.1897:0:1.6 0/1:68:28:12,16:18,22:0.4118:2,2:21:1:29.6:1:1:1.08951:60:56:0.4118:0:2 -6 58778655 . T A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24476;SOR=0;LSEQ=AGAATTCTCAGAGACTTCTT;RSEQ=GTGATGTGTGAATTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:1,2:36,26:0.0462:2,2:6.7:1:29.7:1:0.57308:2.72623:60:6:0.0462:0:1.3 0/0:61:0:0,0:28,32:0:2,0:23.6:1:30.3:1:1:0:59.4:120:1:0:1.4 -6 58778664 . T G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.00976;SOR=Inf;LSEQ=AGAGACTTCTTTGTGATGTG;RSEQ=GAATTCAACTCACAGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:38,30:0:2,0:25.8:1:30.3:1:1:0:59.2:136:1:0:0.6 0/1:61:6:4,2:22,33:0.0984:2,2:17.8:1:32.2:1:0.38705:2.95:60:12:0.0984:0:1.5 -6 58778666 . AA CT 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21871;SOR=Inf;LSEQ=AGACTTCTTTGTGATGTGTG;RSEQ=TTCAACTCACAGTGTGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:38,32:0:2,0:25.3:1:30.4:1:1:0:59.2:140:1:0:0.6 0/1:62:2:1,1:26,31:0.0323:2,2:7:0:33:1:1:1.19:60:4:0.0323:0:1.5 -6 58778686 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21592;SOR=Inf;LSEQ=AATTCAACTCACAGTGTGGA;RSEQ=CCTTCCTTTTGATAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:37,35:0:2,0:25.5:1:30.4:1:1:0:59.7:71:1:0:0.5 0/1:63:2:1,1:31,29:0.0317:2,2:22.5:1:29.5:1:1:1.06778:60:4:0.0323:0:2 -6 58778690 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49673;SOR=0;LSEQ=CAACTCACAGTGTGGATCCT;RSEQ=CCTTTTGATAGAGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:35,33:0.0286:2,2:38:0:32.5:1:1:1.05974:60:4:0.0286:0:1 0/0:66:0:0,0:34,32:0:2,0:23.1:1:29.7:1:1:0:59.7:132:1:0:0.9 -6 58778699 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24453;SOR=0;LSEQ=GTGTGGATCCTTCCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:33,33:0.0294:2,2:5:0:32:1:1:1:60:4:0.0294:0:2.5 0/0:69:0:0,0:34,35:0:2,0:24.2:1:28.9:1:1:0:59.8:68:1:0:0.9 -6 58778707 . T G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49624;SOR=Inf;LSEQ=CCTTCCTTTTGATAGAGCAG;RSEQ=TTTGAAACACTGTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:32,34:0:2,0:26:1:29.4:1:1:0:60:65:1:0:0.8 0/1:67:2:1,1:29,34:0.0299:2,2:21:1:33:0:1:1.17:60:4:0.0299:0:2 -6 58778715 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24453;SOR=Inf;LSEQ=TTGATAGAGCAGTTTTGAAA;RSEQ=ACTGTTTTTGTAGTATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:36,33:0:2,0:24.3:1:31.9:1:1:0:60:138:1:0:0.9 0/1:68:2:1,1:34,32:0.0294:2,2:29:1:32:0:1:1.06158:60:4:0.0294:0:2 -6 58778716 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23733;SOR=Inf;LSEQ=TGATAGAGCAGTTTTGAAAC;RSEQ=CTGTTTTTGTAGTATTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:36,34:0:2,0:23.8:1:29.5:1:1:0:60:69:1:0:0.9 0/1:67:2:0,2:35,30:0.0299:2,0:27:1:32.5:1:0.22433:0:60:4:0.0299:0:1 -6 58778718 . T C 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42504;SOR=1.776;LSEQ=ATAGAGCAGTTTTGAAACAC;RSEQ=GTTTTTGTAGTATTTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:4,2:29,32:0.0896:2,2:29.8:1:30.7:1:0.42748:2.18:60:12:0.0909:0:1.7 0/1:67:10:5,5:30,27:0.1493:2,2:30.3:1:28.8:1:1:1.10936:60:20:0.1493:0:2.5 -6 58778727 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22166;SOR=0;LSEQ=TTTTGAAACACTGTTTTTGT;RSEQ=GTATTTCCAAGCGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:28,31:0.0328:2,2:15:1:28.5:1:1:1.11:60:4:0.0328:0:3.5 0/0:68:0:0,0:36,32:0:2,0:26:1:29.2:1:1:0:59.8:67:1:0:1.1 -6 58778739 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.7865;LSEQ=GTTTTTGTAGTATTTCCAAG;RSEQ=GGATATTTGGAACGCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:1:1,0:29,31:0.0161:2,0:36:0:27:0:0.4918:0:60:2:0.0161:0:1 0/1:70:2:1,1:34,34:0.0286:2,2:25.5:1:28.5:1:1:1:60:4:0.0286:0:2 -6 58778740 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66186;SOR=0.56285;LSEQ=TTTTTGTAGTATTTCCAAGC;RSEQ=GATATTTGGAACGCCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:1,2:28,30:0.0492:2,2:27:1:30.3:1:1:1.84836:60:6:0.0492:0:2.3 0/1:71:2:1,1:35,34:0.0282:2,2:7.5:1:29.5:1:1:1.029:57.5:4:0.0286:0:3 -6 58778752 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21329;SOR=0;LSEQ=TTCCAAGCGGATATTTGGAA;RSEQ=GCCTTGAAGCGTATGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:27,29:0.0345:2,2:36.5:1:31.5:1:1:1.07:60:4:0.0345:0:1.5 0/0:67:0:0,0:33,34:0:2,0:24.5:1:31:1:1:0:59.6:134:1:0:1.3 -6 58778764 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2073;SOR=0;LSEQ=ATTTGGAACGCCTTGAAGCG;RSEQ=ATGGTAGAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:26,25:0.037:2,2:33:1:29:1:1:1.03924:60:4:0.0377:0:2.5 0/0:64:0:0,0:31,33:0:2,0:24.5:1:28.5:1:1:0:59.6:63:1:0:1.5 -6 58778765 . A G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81099;LSEQ=TTTGGAACGCCTTGAAGCGT;RSEQ=TGGTAGAAAAGGAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:26,25:0.0377:2,2:47.5:1:32.5:1:1:1.03924:60:4:0.0377:0:3.5 0/1:65:2:1,1:31,32:0.0308:2,2:9.5:1:33:1:1:1.03:60:4:0.0308:0:3 -6 58778766 . T A 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13002;SOR=5.12788;LSEQ=TTGGAACGCCTTGAAGCGTA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:26,25:0.0192:2,0:42:0:32:0:1:0:60:2:0.0196:0:2 0/1:65:6:4,2:28,31:0.0923:2,2:22.2:1:27.7:1:0.42665:2.19:60:12:0.0923:0:2 -6 58778769 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20954;SOR=0;LSEQ=GAACGCCTTGAAGCGTATGG;RSEQ=AGAAAAGGAAATATCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:27,23:0.0385:2,2:8.5:1:31.5:1:1:1.17028:60:4:0.0392:0:2.5 0/0:61:0:0,0:30,30:0:2,0:25.4:1:28.6:1:1:0:59.6:59:0.9833:0:1.6 -6 58778783 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50634;SOR=Inf;LSEQ=GTATGGTAGAAAAGGAAATA;RSEQ=CTTCTCATAAAACCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:26,24:0:2,0:23.9:1:30.2:1:1:0:59.9:49:1:0:1.9 0/1:67:2:1,1:35,30:0.0299:2,2:20:0:32:0:1:1.16397:57.5:4:0.0303:0:3 -6 58778787 . CT GC 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50105;SOR=Inf;LSEQ=GGTAGAAAAGGAAATATCTT;RSEQ=CATAAAACCTAGACAGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:27,25:0:2,0:22.8:1:30.9:1:1:0:59.9:51:1:0:1.9 0/1:64:2:1,1:31,31:0.0313:2,2:40.5:1:31.3:1:1:1:60:4:0.0317:0:1 -6 58778788 . T C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49807;SOR=0;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=CATAAAACCTAGACAGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:25,27:0,0:1:0,2:22.8:1:31:1:1:0:59.9:104:1:0:2 1/1:60:58:30,28:0,0:0.9667:0,2:23.2:1:30.7:1:1:0:59.5:116:1:0:1.8 -6 58778799 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50094;SOR=Inf;LSEQ=AATATCTTCTCATAAAACCT;RSEQ=GACAGAACCAATCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:27,26:0:2,0:22.5:1:29.1:1:1:0:59.9:25.5:1:0:2.1 0/1:65:2:1,1:34,29:0.0308:2,2:27:0:32:0:1:1.16953:60:4:0.0313:0:2 -6 58778809 . A C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96572;LSEQ=CATAAAACCTAGACAGAACC;RSEQ=ATCTCAGAAACGACTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:27:13,14:11,12:0.54:2,2:27.4:1:30.6:1:1:1.01:59.9:26:0.5306:0:2.3 1/0:64:34:18,16:17,13:0.5313:2,2:23.6:1:30.9:1:0.80566:1.15966:59.4:68:0.5313:0:1.9 -6 58778827 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50826;SOR=Inf;LSEQ=CCAATCTCAGAAACGACTTT;RSEQ=TGATGTCTGCATTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:23,28:0:2,0:24.6:1:31.5:1:1:0:59.6:102:1:0:1.8 0/1:70:2:1,1:33,35:0.0286:2,2:14.5:1:28:1:1:1.06:60:4:0.029:0:2.5 -6 58778828 . T A 101 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00384;SOR=0.12262;LSEQ=CAATCTCAGAAACGACTTTG;RSEQ=GATGTCTGCATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:10:4,6:18,22:0.1961:2,2:28.2:1:30.7:1:1:1.22229:60:20:0.2:0:1.9 0/1:70:2:1,1:33,35:0.0286:2,2:5:1:28:1:1:1.06:60:4:0.0286:0:2 -6 58778836 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17631;SOR=0;LSEQ=GAAACGACTTTGTGATGTCT;RSEQ=CATTCAACTCACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:20,27:0.0408:2,2:32.5:1:29.5:1:1:1.34:60:4:0.0417:0:1.5 0/0:67:0:0,0:33,34:0:2,0:27.7:1:31.3:1:1:0:59.7:66:1:0:1.3 -6 58778844 . C G 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07229;SOR=Inf;LSEQ=TTTGTGATGTCTGCATTCAA;RSEQ=TCACAGAGTTGAACATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:24,28:0:2,0:24.1:1:32.2:1:1:0:59.7:104:1:0:1.7 0/1:71:5:2,3:31,35:0.0704:2,2:41.6:1:30.8:1:1:1.32333:60:10:0.0704:0:1.4 -6 58778864 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50153;SOR=Inf;LSEQ=CTCACAGAGTTGAACATTTC;RSEQ=CTTGATAGAGCAGTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:25,30:0:2,0:22.7:1:30.7:1:1:0:59.7:54:1:0:1.5 0/1:68:2:1,1:32,34:0.0294:2,2:15:1:29:1:1:1.06:60:4:0.0299:0:2.5 -6 58778865 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19792;SOR=0;LSEQ=TCACAGAGTTGAACATTTCT;RSEQ=TTGATAGAGCAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:23,30:0.0364:2,2:22.5:1:31:1:1:1.30:60:4:0.0364:0:3 0/0:68:0:0,0:33,35:0:2,0:24.6:1:31.1:1:1:0:60:136:1:0:1.1 -6 58778872 . G A 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1229;SOR=Inf;LSEQ=GTTGAACATTTCTCTTGATA;RSEQ=AGCAGTTTTGAAACCCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:25,32:0:2,0:22.3:1:31.9:1:1:0:59.7:114:1:0:1.5 0/1:66:4:2,2:28,34:0.0606:2,2:24.8:1:30.5:1:1:1.21:60:8:0.0606:0:1.3 -6 58778897 . A T 26 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.80854;LSEQ=GTTTTGAAACCCTCTTTCTG;RSEQ=AGGATCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:1,0:24,26:0.0196:2,0:45:0:28:0:0.4902:0:60:2:0.0196:0:2 0/1:57:2:1,1:23,32:0.0351:2,2:12.5:1:26.5:1:1:1.38:60:4:0.0351:0:4 -6 58778902 . T G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0776;SOR=0.22116;LSEQ=GAAACCCTCTTTCTGAAGGA;RSEQ=CTGCAAGTGGATATTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:7:3,4:21,21:0.1429:2,2:40.1:1:32.3:1:1:1.32555:60:14:0.1458:0:2.4 0/1:57:2:0,2:24,31:0.0351:2,0:14.5:1:30.5:1:0.50376:0:60:4:0.037:0:3 -6 58778906 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.22911;SOR=0;LSEQ=CCCTCTTTCTGAAGGATCTG;RSEQ=AAGTGGATATTTGGACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:25,24:0.0392:2,2:40:1:29:1:1:1.04085:60:4:0.0392:0:2 0/0:55:0:0,0:22,32:0:2,0:25.4:1:32:1:1:0:60:53:1:0:1.5 -6 58778908 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22066;SOR=0;LSEQ=CTCTTTCTGAAGGATCTGCA;RSEQ=GTGGATATTTGGACCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:25,24:0.0392:2,2:31.5:1:32:1:1:1.04085:60:4:0.0408:0:2.5 0/0:57:0:0,0:24,33:0:2,0:24.9:1:30.6:1:1:0:60:114:1:0:1.6 -6 58778919 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23253;SOR=0;LSEQ=GGATCTGCAAGTGGATATTT;RSEQ=GACCTCCTTTGGGTCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:26,19:0.0417:2,2:35.5:1:30.5:1:1:1.35916:60:4:0.0417:0:2 0/0:51:0:0,0:23,28:0:2,0:29.2:1:31:1:1:0:59.8:50:1:0:1.9 -6 58778922 . C A 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23732;SOR=Inf;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=CTCCTTTGGGTCTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:46:26,20:0,0:0.9583:0,2:29.2:1:29.6:1:1:0:60:45:0.9574:0:1.9 1/1:50:50:22,28:0,0:1:0,2:30.1:1:29.7:1:1:0:59.8:100:1:0:2 -6 58778948 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49558;SOR=Inf;LSEQ=TTGGGTCTTCGTTGGAAACG;RSEQ=GATTTCTTCGTATAAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:30,26:0:2,0:19.1:1:30.4:1:1:0:60:55:1:0:2.4 0/1:57:2:1,1:28,27:0.0351:2,2:25.5:1:29:0:1:1.03639:60:4:0.0357:0:3 -6 58778961 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19799;SOR=0;LSEQ=GGAAACGGGATTTCTTCGTA;RSEQ=AAATCTAGACAGAAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:23,22:0.0426:2,2:28:1:32.5:1:1:1.04448:60:4:0.0435:0:4.5 0/0:58:0:0,0:28,26:0:2,0:21.5:1:28.7:1:1:0:59.9:108:0.931:0:2.8 -6 58778967 . T C 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04423;LSEQ=GGGATTTCTTCGTATAAATC;RSEQ=AGACAGAAGAATTCTCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:35:19,16:8,7:0.7:2,2:22.1:1:30.8:1:1:1.04:60:34:0.6939:0:3.1 1/0:55:39:20,19:8,8:0.7091:2,2:23.3:1:31:1:1:1.05:59.8:78:0.7091:0:3.1 -6 58778989 . T C 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAAGAATTCTCCGAAA;RSEQ=TTCTTTGGTTGTGTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:21,23:0,0:1:0,2:30.7:1:31.6:1:1:0:60:43:1:0:3.1 1/1:47:47:25,22:0,0:1:0,2:27.1:1:31.4:1:1:0:59.8:46:1:0:3.1 -6 58779007 . C T 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTCTTTGGTTGTGTGCA;RSEQ=TCAAGTCACAGAGTGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:46:24,22:0,0:1:0,2:26.7:1:30.3:1:1:0:60:45:1:0:2.8 1/1:57:57:30,27:0,0:1:0,2:22.5:1:29.7:1:1:0:59.9:114:1:0:2.7 -6 58779019 . A G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.03886;LSEQ=TGTGTGCACTCAAGTCACAG;RSEQ=GTGGAACCTTCCTTTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:3:1,2:30,22:0.0536:2,2:38.7:1:32:1:0.57461:2.67813:60:6:0.0556:0:4.7 0/1:54:3:2,1:25,26:0.0556:2,2:21.3:1:30.7:1:1:2.05:60:6:0.0588:0:4.7 -6 58779032 . T G 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06193;SOR=0;LSEQ=GTCACAGAGTGGAACCTTCC;RSEQ=TTGGATAGAGCAGTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:2,3:31,24:0.0833:2,2:10.2:1:31.4:1:0.64935:1.91607:60:10:0.0862:0:2.6 0/0:50:0:0,0:25,25:0:2,0:24.1:1:30:1:1:0:60:49:1:0:2.1 -6 58779037 . A G 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70457;SOR=1.54079;LSEQ=AGAGTGGAACCTTCCTTTGG;RSEQ=TAGAGCAGTTTGAAACGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:1,2:30,28:0.0492:2,2:26.3:1:33:0:0.61239:2.11706:60:6:0.0508:0:4.7 0/1:54:4:1,3:24,25:0.0741:2,2:26.3:1:29.3:1:0.61274:2.82767:60:8:0.0769:0:3.5 -6 58779057 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4956;SOR=0;LSEQ=ATAGAGCAGTTTGAAACGCT;RSEQ=TGGTTGTAGTATTTCCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:27,25:0.037:2,2:19.5:1:33:0:1:1.07844:60:4:0.037:0:4.5 0/0:51:0:0,0:23,28:0:2,0:24.3:1:30.2:1:1:0:60:16:1:0:1.4 -6 58779077 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11056;SOR=Inf;LSEQ=GTGGTTGTAGTATTTCCAAG;RSEQ=GGATATTAGAGCGCCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,27:0:2,0:28.2:1:30.8:1:1:0:60:104:1:0:0.8 0/1:49:3:1,2:19,27:0.0612:2,2:22.7:1:30.7:1:1:1.39796:60:6:0.0625:0:1.3 -6 58779089 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49619;SOR=0;LSEQ=TTTCCAAGCGGATATTAGAG;RSEQ=GCCTTGAAGCCTATGGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:23,25:0.0385:2,2:25.5:1:31:1:1:1.09:60:4:0.0408:0:1.5 0/0:47:0:0,0:16,21:0:2,0:26.1:1:30.5:1:1:0:60:74:0.7872:0:1 -6 58779097 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.22196;LSEQ=CGGATATTAGAGCGCCTTGA;RSEQ=GCCTATGGTAGAAAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:2,2:19,24:0.0851:2,2:36.8:1:32.3:1:1:1.26:60:8:0.0909:0:2 1/0:45:26:14,12:8,11:0.5778:2,2:22.5:1:30.6:1:0.5499:1.59:60:25:0.5682:0:1.6 -6 58779103 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24242;SOR=0;LSEQ=TTAGAGCGCCTTGAAGCCTA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:21,26:0.0408:2,2:26.5:1:28:1:1:1.23:60:4:0.0417:0:1 0/0:50:0:0,0:25,25:0:2,0:20.8:1:30.1:1:1:0:59.6:49:1:0:1 -6 58779121 . C T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12689;SOR=0;LSEQ=TATGGTAGAAAAGGAAATAT;RSEQ=TTCCCATAAAACCTAGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:4:0,4:22,28:0.0741:2,0:27.8:1:28.8:1:0.13684:0:60:8:0.0755:0:1.3 0/0:43:0:0,0:23,20:0:2,0:23.9:1:32.4:1:1:0:59.5:86:1:0:0.8 -6 58779124 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08294;SOR=Inf;LSEQ=GGTAGAAAAGGAAATATCTT;RSEQ=CCATAAAACCTAGACGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:21,32:0:2,0:20.6:1:30.3:1:1:0:59.9:25.5:1:0:0.4 0/1:42:3:2,1:21,18:0.0714:2,2:30.3:1:25.3:1:1:1.69:53.3:2:0.0488:0:1.7 -6 58779157 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.23382;SOR=Inf;LSEQ=GACGGAAGCAATCTCAGAAA;RSEQ=TACTGTGTGATGGCTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:26,29:0:2,0:24:1:31.7:1:1:0:59.4:26.5:1:0:0.3 0/1:52:2:1,1:30,20:0.0385:2,2:25.5:1:29.5:1:1:1.48801:60:4:0.0385:0:1 -6 58779180 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.2312;SOR=Inf;LSEQ=CTGTGTGATGGCTGCATTCC;RSEQ=CACACACGGTGGAACATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:31,30:0:2,0:23.2:1:30.1:1:1:0:58.3:29.5:1:0:0.3 0/1:57:2:1,1:30,25:0.0351:2,2:18.5:1:32.5:1:1:1.19614:60:4:0.0351:0:3 -6 58779186 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.22654;SOR=Inf;LSEQ=GATGGCTGCATTCCACACAC;RSEQ=CGGTGGAACATTTCTCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:31,29:0:2,0:24.7:1:30.1:1:1:0:58.2:59:1:0:0.3 0/1:55:2:1,1:27,26:0.0364:2,2:24.5:1:31.5:1:1:1.03776:60:4:0.0364:0:3 -6 58779211 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21212;SOR=Inf;LSEQ=GGAACATTTCTCTTGATAGA;RSEQ=CAGTTTTGAAACACTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:33,32:0:2,0:24.4:1:31.4:1:1:0:57.4:15.25:1:0:0.4 0/1:56:2:1,1:27,27:0.0357:2,2:45:0:30.5:1:1:1:60:4:0.0357:0:1 -6 58779214 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49804;SOR=0;LSEQ=ACATTTCTCTTGATAGAGCA;RSEQ=TTTTGAAACACTCTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:32,31:0.0308:2,2:14:1:32.5:1:1:1.03176:60:4:0.0313:0:1 0/0:57:0:0,0:28,28:0:2,0:29:1:31.2:1:1:0:57.5:112:0.9825:0:0.5 -6 58779254 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49589;SOR=0;LSEQ=TAGAATCTGCAAGTGGATAA;RSEQ=TGGACCGCCTTGAGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:27,29:0.0345:2,2:37.5:1:31.5:1:1:1.07:60:4:0.0345:0:2 0/0:55:0:0,0:24,31:0:2,0:20.7:1:30.4:1:1:0:57.3:110:1:0:0.8 -6 58779260 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49568;SOR=0;LSEQ=CTGCAAGTGGATAATTGGAC;RSEQ=GCCTTGAGGCCTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:0,2:27,26:0.0364:2,0:12.5:1:32:0:0.49091:0:60:4:0.037:0:1 0/0:52:0:0,0:21,31:0:2,0:21:1:30.4:1:1:0:55.9:104:1:0:1 -6 58779272 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18634;SOR=Inf;LSEQ=AATTGGACCGCCTTGAGGCC;RSEQ=TCGTTGGAAACGGGATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,27:0:2,0:25.5:1:30.1:1:1:0:58.5:51:1:0:1 0/1:40:2:0,2:16,22:0.05:2,0:24:1:29:1:0.50769:0:50:4:0.05:0:3 -6 58779283 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCATGTTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:20,23:0.0444:2,2:8.5:1:28.5:1:1:1.15:60:4:0.0455:0:2 0/0:36:0:0,0:15,21:0:2,0:28:1:30.8:1:1:0:54.4:72:1:0:1.4 -6 58779308 . T C 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.71194;SOR=0.701;LSEQ=TTTCTTCATGTTACTCTAGA;RSEQ=AGAAGAATTCTCAAACACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:33:11,22:2,1:0.8919:2,2:19.5:1:31.5:1:0.53936:3.83719:53.2:32:0.8889:0:1.8 1/1:27:23:6,17:2,2:0.8519:2,2:27.8:1:30.9:1:0.55829:2.71122:50.3:46:0.8519:0:2.4 -6 58779321 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49321;SOR=0;LSEQ=CTCTAGATAGAAGAATTCTC;RSEQ=AACACTACTATGTGATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:6,20:0.0714:2,2:23:1:31:1:0.44444:3.16:47.5:4:0.0714:0:5 0/0:24:0:0,0:6,18:0:2,0:24.1:1:29.7:1:1:0:49.5:48:1:0:2.4 -6 58779326 . C G 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23803;SOR=0;LSEQ=GATAGAAGAATTCTCAAACA;RSEQ=TACTATGTGATGTTTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:2,1:5,20:0.1071:2,2:30:1:30.3:1:0.1453:7.24:56.3:6:0.1071:0:1 0/0:25:0:0,0:6,19:0:2,0:20.4:1:31.3:1:1:0:49.2:50:1:0:2.4 -6 58779328 . A G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05015;SOR=Inf;LSEQ=TAGAAGAATTCTCAAACACT;RSEQ=CTATGTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:20:2,18:3,2:0.8:2,2:22:1:32.3:1:0.03766:11.414:48.1:40:0.8:0:2.7 1/1:25:25:6,19:0,0:1:0,2:19.4:1:30.8:1:1:0:49.2:24:1:0:2.4 -6 58779330 . T G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4898;SOR=0;LSEQ=GAAGAATTCTCAAACACTAC;RSEQ=ATGTGATGTTTGCATTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:4,19:0.08:2,2:32:1:31.5:1:0.36667:4.36:47.5:4:0.08:0:5 0/0:24:0:0,0:6,18:0:2,0:19.1:1:28.1:1:1:0:48.7:48:1:0:2.5 -6 58779346 . T G 65 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35531;SOR=0.28447;LSEQ=CTACTATGTGATGTTTGCAT;RSEQ=CAAGTCACAGAGTGCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:1,3:1,11:0.25:2,2:28.5:1:32.5:1:0.45:3.32:45.8:8:0.25:0:4.5 0/1:12:1:0,1:1,10:0.0833:2,0:35:0:33:0:1:0:40:2:0.0833:0:5 -6 58779375 . AC GT 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37652;SOR=2.52553;LSEQ=AGAGTGCAACATTCCTCTTG;RSEQ=AGAGCAGTTGGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:0,4:1,7:0.3333:2,0:22.5:1:30.9:1:1:0:40:8:0.3333:0.0833:2.8 1/0:7:4:0,4:0,3:0.5714:0,0:27.8:1:30.4:1:1:0:40:8:0.5714:0:2.5 -6 58779376 . C T 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3322;SOR=0.3037;LSEQ=GAGTGCAACATTCCTCTTGA;RSEQ=AGAGCAGTTGGGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:1,7:0,0:0.7273:0,2:23.1:1:28.9:1:1:0:41.9:16:1:0:3.5 0/1:7:3:0,3:0,0:0.4286:0,0:20.3:1:30:0:1:0:40:6:1:0:3.7 -6 58779409 . T C 63 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.54771;LSEQ=AAACACTCCTTTTGTAGAAT;RSEQ=TGCAATGGGATATTTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:20.5:1:31.8:1:1:0:42:8:0.8:0:3.5 1/0:3:2:0,2:0,1:0.6667:0,0:27.5:1:34:0:1:0:40:4:0.6667:0:2.5 -6 58779468 . A G 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACGGGATTTCTTCGTAT;RSEQ=AATCTAGACAGAAGAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:25:1:33:1:1:0:40:4:1:0:2 1/1:1:1:0,1:0,0:1:0,0:21:0:33:0:1:0:40:2:1:0:1 -6 58779802 . C T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTGGAAACGGGATTTCT;RSEQ=CATCTAAACCTACAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:32:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 58779807 . T G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAACGGGATTTCTCCATC;RSEQ=AAACCTACAGAGAAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:0:32:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 63788281 . G A 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3322;SOR=3.29271;LSEQ=AGAAGCCTTTTCCTGTAAAC;RSEQ=GCCGGTGGCATCTCATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:8.3:1:31.7:1:1:1.81007:60:6:0.4286:0:1 1/0:11:8:3,5:1,2:0.7273:2,2:13.1:1:30:1:1:1.18:60:16:0.7273:0:1 -6 63790107 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGGGACCCCTGAGCTGT;RSEQ=GATCCCGCAGTTTCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:1:29.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 63790142 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGGGGGTGTCCAAACTT;RSEQ=AACTTGGGTGTGGTGAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:1:32.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 63790169 . A C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGTGTGGTGAATCCAAGATT;RSEQ=CACTCCTGCCACCTTAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:1:31:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 64740380 . C T 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AACTGCCGAGGACTAGACCT;RSEQ=CTCACTGCTGAGAAAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:22.8:1:31.4:1:1:0:60:10:1:0:0 1/0:4:2:1,1:2,0:0.5:0,2:5.5:1:26:1:1:0:60:4:0.5:0:1.5 -6 64740517 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48988;SOR=Inf;LSEQ=AATCAGATGCCTTTCAAATT;RSEQ=TTATACCAACCTCTGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:27.1:1:31.7:1:1:0:59.1:36:1:0:0.1 0/1:21:2:1,1:9,10:0.0952:2,2:32:1:28.5:1:1:1.11:60:4:0.0952:0:1 -6 64741118 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATGAGTTCTGGGTGGGC;RSEQ=TGGGCTTGGCCAGCTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 65096797 . T G 272 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01047;LSEQ=CACTTTGGTTGCTATCAGAG;RSEQ=GAACATAGCATGATGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:459:456:207,249:0,0:0.9935:0,2:26:1:30.8:1:1:0:60:64.143:0.9956:0:1.1 1/0:465:285:128,157:85,95:0.6129:2,2:26.5:1:29.9:1:0.63412:1.09723:60:27.5:0.6057:0:1.1 -6 65096877 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18442;SOR=Inf;LSEQ=GTATGTAATGTATAGTATAT;RSEQ=TATATGGCAGCAATATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:40,148:0:2,0:23.8:1:31.3:1:1:0:60:22.5:1:0:1 0/1:142:2:1,1:31,109:0.0141:2,2:20:1:31.5:1:0.40116:3.48:60:4:0.0141:0:2 -6 65096906 . C T 191 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCAATATGTAAATATATAC;RSEQ=ATTTTGCATTTTACATAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:112:13,99:0,0:1:0,2:25.3:1:28.1:1:1:0:60:27:1:0:1.1 1/0:65:40:8,32:2,23:0.6154:2,2:29.3:1:28.7:1:0.29393:2.83:60:80:0.6154:0:1.1 -6 65097066 . T C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACCTTTCCATTACCTAAG;RSEQ=CTGTGTATATGTAATATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20.3:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 68164879 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.17058;SOR=Inf;LSEQ=GGCATTAGAAAAGTCAGTGA;RSEQ=CATTAAGGTGTTGATTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:139,82:0:2,0:26.2:1:30.3:1:1:0:60:35.833:1:0:0.1 0/1:156:2:1,1:93,61:0.0128:2,2:47:0:31:1:1:1.52031:60:4:0.013:0:1 -6 68164889 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19472;SOR=Inf;LSEQ=AAGTCAGTGATCATTAAGGT;RSEQ=TTGATTTGGCAACAAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:141,104:0:2,0:27.3:1:32:1:1:0:60:121.5:1:0:0.2 0/1:194:2:1,1:108,84:0.0103:2,2:41:1:29.5:1:1:1.28402:60:4:0.0104:0:1 -6 68164958 . T G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.25256;LSEQ=ACTCACATCCCTTCTAGAGA;RSEQ=AAATATTTAATAATGTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:44:18,26:95,130:0.163:2,2:22.6:1:30.7:1:1:1.05536:60:43:0.161:0:1.1 0/1:206:80:34,46:57,69:0.3883:2,2:25.9:1:31.2:1:0.77382:1.11704:60:39:0.3824:0:1.2 -6 68431386 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATTCATGAGGGATTTTA;RSEQ=TCTGTAGTTTTTTTATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 68433219 . C T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTGCACCCCACCATGCC;RSEQ=GAACCTCCCCCATGCCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:41:1:30:1:1:1:60:4:0.5:0:2 -6 68433236 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCGAACCTCCCCCATGCC;RSEQ=TGGGCTCCTGCGCGGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:43:1:31:1:1:1:60:4:0.5:0:2 -6 70415267 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21914;SOR=0;LSEQ=TCATATAATTGATGAACTTG;RSEQ=CTTCCACTTTGGGAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:2,0:72,55:0.0155:2,0:20.5:1:29:1:0.50703:0:60:4:0.0156:0:1 0/0:146:0:0,0:80,66:0:2,0:27.4:1:31.2:1:1:0:56.6:292:1:0:0.1 -6 70415327 . T C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11448;SOR=Inf;LSEQ=CTTGCATTTTTGCTTTAATG;RSEQ=CTTCTACAGAACTAGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:64,42:0:2,0:23:1:30.2:1:1:0:54.6:105:1:0:0 0/1:102:3:1,2:50,49:0.0294:2,2:9:1:32.7:1:1:2.02708:60:6:0.0294:0:1 -6 70415352 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24648;SOR=Inf;LSEQ=TACAGAACTAGGTCCTTTTG;RSEQ=TGTTTTAGGAGATTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:61,46:0:2,0:22.4:1:31.7:1:1:0:55.8:214:1:0:0.1 0/1:106:2:1,1:57,47:0.0189:2,2:38:1:31:1:1:1.21054:60:4:0.0189:0:1 -6 70415407 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19513;SOR=0;LSEQ=TCTTACCCGTTTGATCTTGG;RSEQ=ATTGATGATGGTTTTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:89,82:0.0116:2,2:21.5:1:29.5:1:1:1.08484:59.5:4:0.0116:0:2 0/0:218:0:0,0:124,94:0:2,0:22.3:1:28.3:1:1:0:59.1:108:1:0:0.7 -6 70415435 . T C 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGTTTTGAGTCTTTTCCA;RSEQ=TCTGATTTGGCTTTTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:101,104:0:2,0:26.8:1:30.4:1:1:0:58.7:67.333:1:0:0.6 0/1:271:25:15,10:127,119:0.0923:2,2:23.7:1:31:1:0.52962:1.40:58.3:50:0.0926:0:2 -6 70415475 . A G 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=3.96016;LSEQ=ATTTTTGGCTGGAGTATCTC;RSEQ=TATAGATTTCTTCACTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:216:164:83,81:24,28:0.7593:2,2:25.6:1:30.8:1:0.6343:1.19:58:81:0.7606:0:1.1 1/1:257:238:113,125:9,10:0.9261:2,2:26.9:1:30.3:1:1:1.00:57.1:78.333:0.9252:0:1.2 -6 70415528 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20161;SOR=Inf;LSEQ=TTTCCTTATTATCAAAATCA;RSEQ=CATTATCACCATCTTCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:74,80:0:2,0:24.8:1:30.3:1:1:0:60:76:1:0:0.5 0/1:126:2:1,1:59,65:0.0159:2,2:9:1:29:1:1:1.10:46:4:0.0161:0:2 -6 70415550 . TATC T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.35436;SOR=0.50121;LSEQ=ATTATCACCATCTTCATCAT;RSEQ=ATCATCATCATCATCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:7:4,3:62,78:0.0476:2,2:29.1:1:31.4:1:0.70094:1.67:60:14:0.0486:0:0 0/1:123:3:1,2:56,63:0.0244:2,2:20.3:1:30:1:1:1.76975:60:6:0.0244:0.0081:0.7 -6 70415581 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49864;SOR=0;LSEQ=TCATCATCTTCATCAGTAGC;RSEQ=AGTTTTACTTTTTTCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:75,90:0.012:2,2:29:1:29.5:1:1:1.20:60:4:0.0123:0:1 0/0:161:0:0,0:73,86:0:2,0:24:1:29.3:1:1:0:60:52:0.9873:0:0.2 -6 70415615 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50243;SOR=Inf;LSEQ=TCTGTGGAACCTTGCTACCA;RSEQ=CTCCAGGGACAGACCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:77,78:0:2,0:28.5:1:31.7:1:1:0:59.7:76.5:1:0:0.1 0/1:185:2:1,1:85,98:0.0108:2,2:26.5:1:28:1:1:1.15:60:4:0.0109:0:1.5 -6 70415637 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50178;SOR=Inf;LSEQ=TCCAGGGACAGACCACTTTC;RSEQ=AGATATACTTAAGAGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:69,77:0:2,0:26.3:1:31.8:1:1:0:59.8:145:1:0:0.1 0/1:172:2:1,1:78,92:0.0116:2,2:20.5:1:29.5:1:1:1.18:60:4:0.0118:0:1 -6 70415662 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.50026;SOR=Inf;LSEQ=ATACTTAAGAGTTTCACATC;RSEQ=TCCTCCTCTTCATCTACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:60,59:0:2,0:21.8:1:30.9:1:1:0:60:28.75:1:0:0.1 0/1:136:2:1,1:61,73:0.0147:2,2:24:1:27.5:1:1:1.20:60:4:0.0149:0:1 -6 70415663 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50032;SOR=Inf;LSEQ=TACTTAAGAGTTTCACATCC;RSEQ=CCTCCTCTTCATCTACTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:58,58:0:2,0:22.1:1:29.8:1:1:0:60:28:1:0:0.1 0/1:133:2:1,1:61,70:0.015:2,2:27.5:1:27.5:1:1:1.15:60:4:0.015:0:1 -6 70415667 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.49962;SOR=Inf;LSEQ=TAAGAGTTTCACATCCTCCT;RSEQ=CTCTTCATCTACTGACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:58,55:0:2,0:21.7:1:30.7:1:1:0:60:55.5:1:0:0.1 0/1:127:2:1,1:58,66:0.0157:2,2:22.5:1:30:1:1:1.14:60:4:0.016:0:1 -6 70415731 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22367;SOR=Inf;LSEQ=TTGTTCACTAATATGCACTG;RSEQ=CCCTGAACCACACTTCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:49,63:0:2,0:27.2:1:31.3:1:1:0:59.9:36.333:1:0:0.1 0/1:101:2:0,2:47,52:0.0198:2,0:11.5:1:26.5:1:0.49743:0:60:4:0.0204:0:1 -6 70415946 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19975;SOR=Inf;LSEQ=ATAACTAGTGCTCATTTTCA;RSEQ=CATTATCCACCTTAAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:42,44:0:2,0:24.5:1:30.7:1:1:0:60:85:1:0:0.1 0/1:70:2:1,1:34,34:0.0286:2,2:26.5:1:29.5:1:1:1:60:4:0.029:0:1 -6 70416053 . C G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8383;LSEQ=ATGTCCATCAAATCTTCCAT;RSEQ=AGGTGGCAGCACACACTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:2,1:17,24:0.0682:2,2:22.3:1:31:1:0.56962:2.76:60:6:0.0682:0:1 0/1:52:3:1,2:24,25:0.0577:2,2:31.7:1:31.7:1:1:1.8969:60:6:0.0588:0:1 -6 72501102 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14655;SOR=Inf;LSEQ=CCCAGCATTTACAGGAAAAG;RSEQ=CTTCTGAAATCAGACAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:33,21:0:2,0:20:1:30.3:1:1:0:58.2:26:1:0:0.1 0/1:34:2:1,1:18,14:0.0588:2,2:7.5:1:28:1:1:1.27615:56:4:0.0606:0:1 -6 72501165 . C T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0036;SOR=Inf;LSEQ=TCTGGAGTTGGGCAACGTGG;RSEQ=TTCTCCCCTTTCTAGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:31,35:0:2,0:28.4:1:31.4:1:1:0:58.1:65:1:0:0.1 0/1:45:6:3,3:18,21:0.1333:2,2:34.8:1:30:1:1:1.16:60:12:0.1333:0:1.2 -6 72501263 . T C 67 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=0.27349;LSEQ=AAATTTGTTTCCTGTAGAAT;RSEQ=GAGGCCATCAAGCTACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:23.8:1:29.2:1:1:0:60:10:0.5:0:1 0/1:5:1:0,1:1,3:0.2:2,0:8:0:31:0:1:0:60:2:0.2:0:1 -6 72558460 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.50555;SOR=0;LSEQ=AAAATAAAGCTGCATTTTGA;RSEQ=GAGAGAATAGATTTTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:135,31:0.0119:2,2:38:1:31.5:1:0.34559:4.3021:60:4:0.012:0:1 0/0:132:0:0,0:107,25:0:2,0:20.7:1:30:1:1:0:60:131:1:0:0.1 -6 72558580 . G C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.56706;LSEQ=AAATATAACGATGAAAATTA;RSEQ=GTACCTCATGTGATAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:112:53,59:171,192:0.2353:2,2:24.1:1:31.2:1:1:1.01:60:224:0.2378:0:1.1 1/0:431:252:117,135:83,91:0.5847:2,2:25.2:1:30.4:1:0.84357:1.05225:60:504:0.586:0:1.2 -6 72558584 . C T 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=0.54204;LSEQ=ATAACGATGAAAATTAGGTA;RSEQ=CTCATGTGATAAATTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:164:77,87:142,167:0.346:2,2:26.7:1:30.4:1:0.84691:1.04:60:53.667:0.3455:0:1.1 0/1:431:96:46,50:153,182:0.2227:2,2:25:1:29.3:1:0.72837:1.09:60:95:0.2241:0:1 -6 72558773 . A T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00136;SOR=7.54043;LSEQ=TTATGCAATGATTATTAAAG;RSEQ=TATACTGTGAATTATTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:0,4:0,29:0.1212:1,0:38.5:1:28.5:1:1:0:60:8:0.129:0:2 1/0:25:13:1,12:1,11:0.52:2,1:15.2:1:30.8:1:1:1.0871:60:26:0.5417:0:1.5 -6 72558820 . A C 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37148;SOR=2.87218;LSEQ=GCAATTGAGTTTTAAAACTG;RSEQ=TAAAACTAAACTAATAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:0,4:0,15:0.2105:1,0:15.5:1:33.5:1:1:0:60:8:0.2105:0:1.8 0/1:9:4:1,3:0,5:0.4444:0,2:37.5:1:32.5:1:0.44444:0:60:8:0.4444:0:2.5 -6 76277769 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGTGGTGTGGCAGCCCA;RSEQ=CTGAAAGCCACACAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:22:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29:1:1:0:60:4:1:0:1 -6 76295861 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=TCATACAAAGCAAACTGCCT;RSEQ=CAAATCGACCAGTGACAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:30.8:1:32.8:1:1:0:60:16:1:0:0.4 0/1:18:2:1,1:8,8:0.1111:2,2:6.5:1:27.5:1:1:1:60:4:0.1111:0:1 -6 76295914 . C T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06978;SOR=0.12265;LSEQ=AAATGGCTAAAAAAGCCACT;RSEQ=GAGAGGGAGTGTACCCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:3,4:1,1:0.7778:2,2:21.6:1:29.7:1:1:1.29098:60:14:0.7778:0:1 0/1:11:3:1,2:4,4:0.2727:2,2:31.7:1:31:1:1:1.87936:60:6:0.2727:0:1 -6 76296115 . G A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00105;SOR=0.14226;LSEQ=AGCACAGCTATTGGTGTTTT;RSEQ=CAGGAGGCAAGTGAAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:22:18,4:7,2:0.7097:2,2:25.5:1:27.8:1:1:1.27:60:44:0.7333:0:1.3 0/1:24:6:4,2:14,4:0.25:2,2:31:1:26.3:1:0.61806:1.70678:60:12:0.25:0:1.5 -6 76296176 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18831;SOR=Inf;LSEQ=ACACCAAATTGTGTGCTATC;RSEQ=ATGTGTAACAAATTATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:44,31:0:2,0:23.1:1:30.8:1:1:0:60:36.5:1:0:0.2 0/1:58:2:1,1:36,20:0.0345:2,2:18.5:1:26.5:1:1:1.78076:60:4:0.0351:0:1 -6 76296999 . C CTCTTT 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCCTTTTTCTTTTCTCTT;RSEQ=TCTTTTCTTTTCTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29.5:1:1:0:60:4:1:0:0 -6 76598904 . A G 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=1.85483;LSEQ=TGGAGGAAAATGAAAATGCT;RSEQ=TAAATAGACTCAGCTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:121:59,62:168,139:0.2827:2,2:26.9:1:31.6:1:0.28329:1.26937:60:39.333:0.2803:0:1.1 0/1:400:169:85,84:114,115:0.4225:2,2:28.6:1:31.1:1:1:1.02:60:83.5:0.4239:0:1.1 -6 76598991 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.15578;SOR=Inf;LSEQ=ATTAAAATTAACCCACCCAC;RSEQ=TTTTTGAAGGCTAATTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:40,154:0:2,0:23.3:1:30.2:1:1:0:60:96:1:0:0.1 0/1:127:2:1,1:29,96:0.0157:2,2:21.5:1:28.5:1:0.41807:3.27:60:4:0.0161:0:0 -6 79720867 . T A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.42994;LSEQ=TCCTGCCAATGCCAAACAAA;RSEQ=GTGGGCTTACTAAGTTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:536:303:136,167:111,122:0.5653:2,2:27.1:1:30.4:1:0.54154:1.11699:60:49.5:0.5646:0:1.1 0/1:452:162:79,83:131,159:0.3584:2,2:25.5:1:30:1:0.49185:1.15:60:324:0.3657:0:1.1 -6 79720958 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57819;SOR=2.68647;LSEQ=AAATATCCAAATATATACTA;RSEQ=ATTTCCTCTGAATACTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:1,0:22,129:0.0066:2,0:1:0:28:0:0.15132:0:60:2:0.0066:0:1 0/1:114:2:1,1:20,92:0.0175:2,2:9:1:27.5:1:0.33582:4.51:60:4:0.0177:0:1 -6 80346379 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51923;SOR=0;LSEQ=TCAGGGAGTTGGTGGGGTTG;RSEQ=TTCCTTCTGAGGGCTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:16,7:0.08:2,2:27.5:1:28:1:1:2.20393:60:4:0.08:0:1 0/0:15:0:0,0:12,3:0:2,0:24.4:1:31.5:1:1:0:60:30:1:0:0.1 -6 80346398 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49796;SOR=0;LSEQ=GCTTCCTTCTGAGGGCTGTG;RSEQ=GGGAGAGTCCTTTCCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:22,12:0.0541:2,2:40.5:1:30.5:1:1:1.8009:60:4:0.0541:0:1 0/0:30:0:0,0:19,10:0:2,0:20.5:1:29.5:1:1:0:60:58:0.9667:0:0.1 -6 80346560 . A G 65 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58042;SOR=0.27349;LSEQ=CCCAAATGTTCTGTTTTTAT;RSEQ=AGGACACAGCCATACTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:24:1:32.8:1:1:0:60:8:0.4444:0:1 0/1:6:1:0,1:0,5:0.1667:0,0:50:0:30:0:1:0:60:2:0.1667:0:1 -6 80563236 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTTCAGCAATACCCCA;RSEQ=AAGCACAGGCAACCAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 80564836 . C T 76 d7;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00466;SOR=0;LSEQ=CAGTTTCCCAAGCAGGACTT;RSEQ=CCCTAAACCAGAAGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:15:1:29.7:1:1:0:60:12:1:0:1.3 0/1:7:1:1,0:5,1:0.1429:2,0:22:0:32:0:1:0:60:2:0.1667:0:1 -6 80564945 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48617;SOR=Inf;LSEQ=CTTTCTACAGAATCTGAGAT;RSEQ=TGGCCCATCAGATGAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:19.9:1:30.3:1:1:0:60:20:1:0:0 0/1:13:2:1,1:5,6:0.1538:2,2:8:0:33:0:1:1.18:60:4:0.1538:0:1 -6 80565248 . T C 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68277;SOR=1.68366;LSEQ=AAAGACTTTCATACCAAATG;RSEQ=GATGAAATTTTTCTAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:11,4:0.25:2,2:37.2:1:31.4:1:1:1.43:60:10:0.25:0:1 0/1:11:4:4,0:5,2:0.3636:2,0:22.5:1:33.3:1:0.49091:0:60:8:0.3636:0:1 -6 82466944 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13406;SOR=Inf;LSEQ=CAACATTCCTGTCCTGCTTT;RSEQ=GGTCTTTCCACACCAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:103,0:0:1,0:24:1:30.5:1:1:0:60:102:1:0:0.2 0/1:60:2:1,1:55,3:0.0333:2,2:24:1:29.5:1:0.12994:16.02469:60:4:0.0333:0:1 -6 82466991 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17145;SOR=Inf;LSEQ=TGTCTCTCTTGATTTTCCAC;RSEQ=TCTACCACTTCTGCTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:239,14:0:2,0:24:1:31:1:1:0:60:49.6:0.996:0:0.1 0/1:180:2:1,1:160,18:0.0111:2,2:19.5:1:30.5:1:0.2005:8.68078:60:4:0.0111:0:0 -6 82467107 . T C 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=0.66456;LSEQ=ATTTGAGTACTCCCCCACCC;RSEQ=TGTCTGTCCCCCACCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1307:328:163,165:487,491:0.251:2,2:27.1:1:30.9:1:1:1.00402:60:31.8:0.2506:0:1.1 0/1:1049:191:94,97:427,431:0.1821:2,2:24.2:1:30.8:1:0.93626:1.02232:60:190:0.1839:0:1.2 -6 82609926 . C G 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65394;SOR=0.43997;LSEQ=TTGATGTGCCTTGACATTTT;RSEQ=CTTTATTAGAAAATATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:14:14,0:12,0:0.5385:0,1:22.1:1:32.4:1:1:0:60:28:0.5833:0:1 0/1:6:2:2,0:4,0:0.3333:0,0:37:1:30:1:1:0:60:4:0.3333:0:1 -6 82610040 . A T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.24311;LSEQ=TGGGATGAGACATACTACTC;RSEQ=GTGTGAATTCCTAAGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:69:67,2:34,2:0.6571:2,1:24.4:1:31.2:1:0.60542:1.96:60:68:0.6538:0:1.1 0/1:57:18:17,1:39,0:0.3158:1,1:15.2:1:30.3:1:0.31579:0:60:17:0.3091:0:1.1 -6 82610066 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14532;SOR=Inf;LSEQ=AATTCCTAAGACTGAATGAG;RSEQ=GCTTTGAATTTGAATAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:149,19:0:2,0:23:1:31.1:1:1:0:60:55:1:0:0.4 0/1:104:2:2,0:87,15:0.0192:2,0:31.5:1:30.5:1:1:0:60:4:0.0198:0:2 -6 82610188 . A T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43157;LSEQ=GAGGGCTTCGTGGTTTATGA;RSEQ=CAGATTAGTCTATTTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:631:370:172,198:126,135:0.5864:2,2:26:1:30.4:1:0.68592:1.0743:60:51.857:0.5893:0:1.1 0/1:651:247:119,128:197,207:0.3794:2,2:25:1:29.1:1:0.93562:1.02364:60:48.4:0.3799:0:1.2 -6 82610327 . G A 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.17715;LSEQ=AAAATCTAATAAAGGCAGTC;RSEQ=GTTTGAGAGACACTAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:83:55:0,55:0,28:0.6627:1,1:26:1:31:1:1:0:60:54:0.6585:0:1 0/1:47:12:0,12:1,34:0.2553:1,0:17.4:1:31.1:1:1:0:60:24:0.2553:0:1 -6 82679396 . C A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCATAAAAAAAAAAAAAAA;RSEQ=CACTTATAATAAGCATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:1:19:1:1:0:60:1:1:0:2 1/1:2:2:0,2:0,0:1:0,0:20.5:1:30.5:1:1:0:58:4:1:0:3 -6 82679654 . G T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCGGAAGATCCCACTCGC;RSEQ=AACCCACGCCACCAGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:32.4:1:30.6:1:1:0:60:10:1:0:0.2 0/1:19:2:1,1:6,11:0.1053:2,2:39.5:1:29.5:1:1:1.77:60:4:0.1053:0:1 -6 82679990 . G GGGCTGTGGCA 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=ACAGCCCAAAAAAACCACAC;RSEQ=GGCTGTGGCAGGCTGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:16.5:1:28.5:1:1:0:60:4:1:0:0 1/0:5:3:0,3:1,1:0.6:2,0:23.3:1:30.2:1:0.4:0:60:6:0.75:0.4:0 -6 82680358 . T C 92 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATACCCTATAAAGGAGTGA;RSEQ=CCTACTGACATCAGGTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:14.8:1:31.5:1:1:0:60:12:1:0:1.2 1/1:9:9:5,4:0,0:1:0,2:20.4:1:29.2:1:1:0:60:8:1:0:1.1 -6 82680523 . G A 59 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAGAAAACTGAAGCAGCCCT;RSEQ=CAGAAGAGGGTCCTGACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:0.8:0,2:17.8:1:29.8:1:1:0:60:8:0.8:0:1.3 0/0:1:0:0,0:1,0:0:0,0:47:0:30:0:1:0:60:2:1:0:0 -6 82680878 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAACCCAATGCAAAGAAG;RSEQ=TAAGAACCTTGATAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 82852407 . AAAATAAATAAAT A 116 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=10.000;MSILEN=4;SSF=0.00012;SOR=0;LSEQ=GTGAGACCCTGTCCCCCCAA;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:13:12,1:42,2:0.2167:1,1:21.2:1:31.4:1:0.54737:1.73063:58.8:26:0.2241:0.05:0.4 0/0:57:0:0,0:17,1:0:1,0:15.6:1:30.1:1:1:0:60:36:0.3158:0:0.1 -6 82852449 . G T 38 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62329;SOR=0.34552;LSEQ=AATAAATAAATAAATAAATA;RSEQ=AGTCTCAGTTGGTGTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:1,2:138,45:0.0161:2,2:22.7:1:24.3:1:0.15776:6.05936:55:2:0.0109:0:2 0/0:178:1:0,1:118,59:0.0056:2,0:1:0:23:0:0.33708:0:60:2:0.0057:0:1 -6 82852544 . A G 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=2.08596;LSEQ=AGAGAAAGTACATTGAGATG;RSEQ=GGCAAAACCAATCAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:50:18,32:88,123:0.1916:2,2:25.1:1:30.9:1:0.52333:1.27075:60:100:0.1931:0:1.1 0/1:296:98:48,50:93,105:0.3311:2,2:23.9:1:29.9:1:0.80494:1.08:60:196:0.3356:0:1.1 -6 85805288 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50826;SOR=0;LSEQ=ACCCACCTCTGGAGTTGGAC;RSEQ=ACATGGCTTCTCCCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:34,34:0.0286:2,2:10:0:31.5:1:1:1:60:4:0.029:0:1.5 0/0:51:0:0,0:23,28:0:2,0:33:1:30.6:1:1:0:60:102:1:0:0.2 -6 85805584 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAGCTAGAGTGGTCATC;RSEQ=CCCAGTTCCCAATAGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:26:1:29:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 85995785 . G A 50 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=AAGAAGGAAGCGGGGGAGGA;RSEQ=GAAGAAGGATGCGGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:5,0:0.1667:0,0:6:0:32:0:1:0:60:2:0.1667:0:1 1/1:3:3:3,0:0,0:1:0,0:16.7:1:31.7:1:1:0:60:6:1:0:1 -6 85995875 . G GGACACAGCA 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05442;LSEQ=GGTGGTGGAGCGGACACAGC;RSEQ=GACACAGCAGACACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:18:10,8:4,0:0.75:0,2:26.4:1:30.4:1:0.25359:0:58.3:36:0.75:0.2083:0.8 1/0:25:19:11,8:2,0:0.76:0,2:27.6:1:30.6:1:0.50476:0:60:38:0.76:0.24:0.4 -6 86578833 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00821;SOR=Inf;LSEQ=TCTGGGTGTATGAGATACAA;RSEQ=TGGACAAGAAGATTACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:25,6:0:2,0:26.2:1:32:1:1:0:60:62:1:0:0.3 0/1:42:9:6,3:23,10:0.2143:2,2:27.1:1:29.6:1:1:1.14611:60:18:0.225:0:1 -6 86578870 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54162;SOR=Inf;LSEQ=ACAGGTGGACAGATTATGAC;RSEQ=CCCACCCCCGTTCCTATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:27,11:0:2,0:24.6:1:30.3:1:1:0:60:18:1:0:0.1 0/1:71:2:1,1:43,26:0.0282:2,2:14.5:1:29:1:1:1.64163:60:4:0.0294:0:1.5 -6 86578881 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTATGACCCCCACCCCCG;RSEQ=TCCTATCCACAAACAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:27,14:0:2,0:24.9:1:29.4:1:1:0:60:82:1:0:0 0/1:83:2:1,1:51,30:0.0241:2,2:22.5:1:29:1:1:1.6886:60:4:0.025:0:1 -6 86578949 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51412;SOR=Inf;LSEQ=TCCTGCGTCATTAGAAAATG;RSEQ=CCATGCCAAGTGGTGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:61,47:0:2,0:24.9:1:29.7:1:1:0:60:107:1:0:0.2 0/1:155:2:1,1:93,60:0.0129:2,2:31:0:31:0:1:1.54544:60:4:0.0129:0:1 -6 86578969 . G T 18 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76093;LSEQ=TCCATGCCAAGTGGTGTCCT;RSEQ=AAGTGCAGCACCATTGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:69,60:0.0152:2,2:20:1:29.5:1:1:1.14877:60:4:0.0154:0:1.5 0/1:173:2:0,2:97,74:0.0116:2,0:1:0:18.5:1:0.19156:0:60:1:0.006:0:1 -6 87383938 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGATACAAAGCCAACAG;RSEQ=AATTTGCCAGGGAAGGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:44.5:1:29.5:1:1:0:60:4:1:0:1 -6 87821903 . C T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGTTTTTTTGTTTTTTATG;RSEQ=TTTTGAGACAGAGTCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:0:32:0:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 87821941 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCTTTCACCCAGGCTGCA;RSEQ=TGCAGTGGCATGACTATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38.5:1:31:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 87822418 . A T 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.87089;LSEQ=CAGGATCAAAATCCTAAATT;RSEQ=AGTGGTTTTGGCCTGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:5,1:0.3333:2,2:25.3:1:31:1:1:2.23609:60:6:0.3333:0:1 1/0:2:1:1,0:1,0:0.5:0,0:40:0:32:0:1:0:60:2:0.5:0:1 -6 87822526 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49306;SOR=Inf;LSEQ=GTAAATGATTAGGCTTATTT;RSEQ=GTAAATTGAATGGGAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:24:1:32.2:1:1:0:60:46:1:0:0.1 0/1:27:2:1,1:12,13:0.0741:2,2:31.5:1:29:1:1:1.08:60:4:0.0741:0:1 -6 89786309 . G GA 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAAGTCTATATAAAGAG;RSEQ=AAAAAAGACATTCAGGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35:0:29:1:1:0:60:4:1:0:0.5 -6 89787305 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50629;SOR=0;LSEQ=AGGGCAAACATGAAGCCTAC;RSEQ=CTTAAGGCCTCAAAATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:3,160:0.0121:1,2:27.5:1:29:1:0.04804:46.34:60:4:0.0126:0:1.5 0/0:128:0:0,0:2,126:0:1,0:22.7:1:29.6:1:1:0:60:63:1:0:0.2 -6 89787349 . C T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08587;SOR=0.506;LSEQ=TATACACATAATTACTCCAA;RSEQ=AATCACCCAAGAAATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:42:0,42:0,21:0.6563:1,1:27.2:1:28.1:1:1:0:60:41:0.6613:0:1.1 0/1:49:24:1,23:1,24:0.4898:1,1:23.4:1:27:1:1:1.04:60:11:0.4783:0:1.1 -6 89790201 . A G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCAGGGGCGTGCTGGGGAGG;RSEQ=GTAAAGAGGGTGGGGCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:28:1:32.5:1:1:0:60:4:1:0:1 -6 89790559 . CTTCA C 273 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0.06308;SOR=1.33781;LSEQ=CGCCACCCTATCTTCACTGG;RSEQ=TTCACCTTCTCCTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:457:340:261,79:101,16:0.744:2,2:25.3:1:32:1:0.03402:1.90822:60:112.333:0.7489:0.1182:0.1 1/0:484:385:297,88:78,21:0.7955:2,2:28.1:1:31.8:1:0.78836:1.10032:60:127.333:0.7992:0.0331:0.1 -6 89790979 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49953;SOR=Inf;LSEQ=CAGTACCAGCAGCACCGGCC;RSEQ=AGTCTGGAGGGCGGCCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:32,121:0:2,0:25.2:1:31.1:1:1:0:60:75.5:1:0:0.2 0/1:168:2:1,1:46,119:0.0119:2,2:5:0:31:1:0.48489:2.57:60:4:0.0122:0:1.5 -6 89790991 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22627;SOR=0;LSEQ=CACCGGCCGAGTCTGGAGGG;RSEQ=GGCCGGAGCCCCGCGACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:25,85:0.0177:2,2:8:1:31:0:0.412:3.35:60:4:0.0179:0:1 0/0:124:0:0,0:36,88:0:2,0:25.6:1:30:1:1:0:60:123:1:0:0.2 -6 89791003 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49877;SOR=Inf;LSEQ=CTGGAGGGCGGCCGGAGCCC;RSEQ=GCGACCGGCCCGAGCGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:15,68:0:2,0:23.5:1:29.7:1:1:0:60:26.667:1:0:0.2 0/1:93:2:1,1:26,65:0.0215:2,2:47:1:30.5:1:0.4986:2.47:60:4:0.0217:0:1 -6 89791012 . C T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24584;SOR=Inf;LSEQ=GGCCGGAGCCCCGCGACCGG;RSEQ=CCGAGCGGAGCGCAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:11,52:0:2,0:21.3:1:30.8:1:1:0:60:20:1:0:0.2 0/1:69:3:1,2:17,49:0.0435:2,2:7:1:21.3:1:1:1.43:60:2:0.0303:0:1 -6 89791015 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49803;SOR=Inf;LSEQ=CGGAGCCCCGCGACCGGCCC;RSEQ=AGCGGAGCGCAGGAGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:10,48:0:2,0:20.3:1:31.1:1:1:0:60:28:1:0:0.2 0/1:66:2:1,1:17,47:0.0303:2,2:12.5:1:26.5:1:0.47413:2.72:60:4:0.0308:0:2 -6 89791123 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14282;SOR=0;LSEQ=CTTGCCCCGCTGCGGCCCGC;RSEQ=GCTCCCGGCCAAACCCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:33,22:0.0351:2,2:36.5:1:30.5:1:1:1.48905:60:4:0.0357:0:1 0/0:93:0:0,0:55,38:0:2,0:28.2:1:29.8:1:1:0:60:92:1:0:0.4 -6 89791128 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52492;SOR=Inf;LSEQ=CCCGCTGCGGCCCGCGGCTC;RSEQ=CGGCCAAACCCCCCTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:33,25:0:2,0:27.9:1:30.8:1:1:0:60:28:1:0:0.3 0/1:94:2:1,1:53,38:0.0213:2,2:10:0:32:1:1:1.38965:60:4:0.0217:0:1.5 -6 89791134 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52543;SOR=Inf;LSEQ=GCGGCCCGCGGCTCCCGGCC;RSEQ=AACCCCCCTCAGGAAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:33,26:0:2,0:27.2:1:30.2:1:1:0:60:58:1:0:0.3 0/1:96:2:1,1:53,40:0.0208:2,2:25:0:31.5:1:1:1.32102:60:4:0.0213:0:1.5 -6 89791136 . AC A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.13972;SOR=0;LSEQ=GGCCCGCGGCTCCCGGCCAA;RSEQ=CCCCCTCAGGAAAGAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:32,25:0.0339:2,2:22.5:1:32.5:1:1:1.2746:60:4:0.0345:0:1 0/0:98:0:0,0:54,44:0:2,0:26.4:1:30.6:1:1:0:60:31.667:1:0:0.3 -6 89792120 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=CATTGAATTAGAGATTTGCG;RSEQ=TTTATCTGTGCCCTTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:142,17:0.0124:2,0:23.5:1:28.5:1:1:0:60:4:0.0126:0:3 0/0:159:0:0,0:138,21:0:2,0:25:1:30.7:1:1:0:60:78.5:1:0:0.1 -6 89792138 . GA G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.25114;SOR=Inf;LSEQ=CGGTTTATCTGTGCCCTTGG;RSEQ=AAAAATTTGCCCACCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:186,52:0:2,0:21.9:1:30:1:1:0:60:78.333:0.9958:0:0.1 0/1:269:3:2,1:204,61:0.0112:2,2:12:1:29.7:1:0.54739:1.66851:60:6:0.0113:0.0037:0.3 -6 89792392 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50018;SOR=0;LSEQ=TGCAGTGATCTAGTGGATTA;RSEQ=CTTACGCTTTTCCATCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:10,159:0.0117:2,2:10:1:29:1:0.12487:15.21:60:4:0.012:0:1 0/0:152:0:0,0:15,137:0:2,0:21.6:1:30.7:1:1:0:60:37:1:0:0.1 -6 89793894 . G C 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGCAGTACACTTAAAAAC;RSEQ=CTCCTCAAAGTTCAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:67,164:0:2,0:26.2:1:31.1:1:1:0:60:32:0.9956:0:0.1 0/1:279:59:16,43:81,139:0.2115:2,2:25.8:1:30.6:1:0.21782:1.56368:60:58:0.2101:0:1.1 -6 89795085 . T C 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.98283;LSEQ=ATTTTAGCTTTTGTTAGTAA;RSEQ=GTGTTGTAAATATTAATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:63:61,2:57,0:0.525:1,1:26.2:1:32.7:1:0.49706:0:60:126:0.5294:0:1 1/0:121:63:63,0:58,0:0.5207:1,1:25.7:1:31.4:1:1:0:60:126:0.5207:0:1 -6 89795288 . G C 272 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8391;SOR=0.97871;LSEQ=TCCAACATTTCTCAGCTCTT;RSEQ=TCATTTTGAGCAGTATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:711:366:140,226:141,202:0.5148:2,2:26.1:1:31.5:1:0.44343:1.12661:60:44.75:0.5136:0:1.9 1/0:852:434:169,265:184,232:0.5094:2,2:24.9:1:31.1:1:0.1258:1.24329:60:71.333:0.5089:0:1.5 -6 89795303 . A G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34079;LSEQ=CTCTTGTCATTTTGAGCAGT;RSEQ=TGTCTGCAGTTTAATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:615:316:115,201:108,189:0.5138:2,2:25.2:1:32:1:1:1.00:60:104.333:0.514:0:2 0/1:718:190:65,125:207,321:0.2646:2,2:23.8:1:30.7:1:0.25694:1.23975:60:62.333:0.2638:0:2 -6 89795551 . G C 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACACCTTAGAAAGTAACA;RSEQ=TGAGTTGAGCTGGGCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:15:1:32.2:1:1:0:60:10:0.5:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 90009187 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50044;SOR=0;LSEQ=TTTGTGTCCTGATTCTCCTT;RSEQ=CCTGCTCTTATATTTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:112,14:0.0156:2,2:36:1:27.5:1:0.22146:7.76299:60:4:0.016:0:2 0/0:111:0:0,0:93,18:0:2,0:20.9:1:31.5:1:1:0:60:222:1:0:0.9 -6 90009199 . A T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=3.65959;LSEQ=TTCTCCTTGCCTGCTCTTAT;RSEQ=TTTGTAGGACAAAAAAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:108:87,21:48,9:0.6506:2,2:23.9:1:30.4:1:0.67307:1.28544:60:216:0.6626:0:1.1 1/1:149:130:101,29:12,7:0.8725:2,2:21.7:1:29.8:1:0.24836:2.02:60:260:0.8725:0:1.1 -6 90009220 . G A 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTGTAGGACAAAAAAGTTG;RSEQ=CAGCTGCAGGGCCTGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:21:12,9:150,68:0.0879:2,2:17.3:1:28.3:1:0.32887:1.65073:60:20:0.0858:0:1.7 0/0:217:0:0,0:142,75:0:2,0:25.5:1:30.8:1:1:0:60:71.333:1:0:0.8 -6 90009311 . T C 241 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22216;SOR=1.19391;LSEQ=CCCTCTCCACTACTTCCTGC;RSEQ=CTTTTCTCCTTGGGAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:417:236:108,128:70,110:0.5659:2,2:25.5:1:30.7:1:0.16337:1.32:60:77.667:0.5697:0:1.1 1/0:381:232:102,130:64,83:0.6089:2,2:25.8:1:30.2:1:1:1.02:60:76.333:0.6123:0:1.1 -6 90009410 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52474;SOR=0;LSEQ=AGCGCTGTGCCAGAGGGAGC;RSEQ=AGAGAGGGCAGCACATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:10,85:0.0206:2,2:14.5:1:28.5:1:0.21499:8.15:60:4:0.0211:0:1.5 0/0:60:0:0,0:9,51:0:2,0:23.6:1:32:1:1:0:60:59:1:0:0.2 -6 90009427 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15472;SOR=Inf;LSEQ=AGCCAGAGAGGGCAGCACAT;RSEQ=ACATCCCTGGGGCCAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:4,60:0:2,0:25:1:32.6:1:1:0:60:128:1:0:0.1 0/1:42:2:0,2:4,36:0.0476:2,0:37.5:1:27:1:1:0:60:4:0.0488:0:1 -6 90012435 . G A 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.37616;SOR=0.39312;LSEQ=GGCAGTGGCCACCGTGTTCC;RSEQ=GGGCTGCCTGTCCATGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:24.3:1:30.3:1:1:0:60:8:0.4444:0:1.5 0/1:13:3:3,0:8,2:0.2308:2,0:14.7:1:31.7:1:1:0:60:6:0.2308:0:1.3 -6 90012463 . C A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65879;SOR=0.59813;LSEQ=CTGTCCATGAAGGAGGTGGA;RSEQ=GAGCAGATGCTGTCCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:7,3:0.2308:2,2:26:1:30.7:1:1:1.15267:60:6:0.2308:0:1.7 0/1:20:3:1,2:10,7:0.15:2,2:27.3:1:30.3:1:0.56579:2.70974:60:6:0.15:0:1.3 -6 90012496 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49826;SOR=Inf;LSEQ=TCCATCCAGAGCAAGAACAG;RSEQ=AGCTACTTCGTGGAGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:24.9:1:31.6:1:1:0:60:36:1:0:0.3 0/1:24:2:1,1:11,10:0.0833:2,2:44:0:30:1:1:1.09544:60:4:0.0833:0:1 -6 92525675 . C T 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCTGAACACTTCATGTA;RSEQ=CCCAAAGAGCCAATTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:719:0:0,0:367,352:0:2,0:26.9:1:31.4:1:1:0:60:58.917:1:0:0.2 0/1:660:33:17,16:326,299:0.05:2,2:27.1:1:28.8:1:1:1.02613:60:66:0.0505:0:1.1 -6 92525884 . C T 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99119;LSEQ=TAAACTCTCAGGGTTGTCAA;RSEQ=GGAGAACACATAACATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:102:44,58:134,203:0.2323:2,2:24.3:1:30.6:1:0.56612:1.15:60:101:0.2343:0:1.1 0/1:377:87:37,50:120,168:0.2308:2,2:20.8:1:29.4:1:0.90181:1.04:60:86:0.2318:0:1.1 -6 92525977 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.16692;LSEQ=TCCCACAAAGTCAGCTCTAC;RSEQ=CTTTCCCATCCACCTCGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:161:78,83:77,91:0.4879:2,2:24.7:1:30.3:1:0.65959:1.11:60:31.2:0.4921:0:1.1 0/1:358:49:24,25:154,155:0.1369:2,2:23.5:1:30.6:1:1:1.03486:60:98:0.1392:0:1.2 -6 92526096 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49904;SOR=0;LSEQ=GTCTTGCCACAGACTCTGTC;RSEQ=CCGACAATTACCAGCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:56,140:0.0101:2,2:40:1:29:1:0.49392:2.49:60:4:0.0101:0:2 0/0:188:0:0,0:68,120:0:2,0:24.1:1:29.1:1:1:0:60:376:1:0:0.2 -6 92526109 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5008;SOR=0;LSEQ=CTCTGTCACCGACAATTACC;RSEQ=GCTTCTTCTGGACGGGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:47,122:0.0117:2,2:33.5:1:31.5:1:0.4838:2.58:60:4:0.0121:0:2 0/0:149:0:0,0:51,98:0:2,0:21.9:1:29.8:1:1:0:60:48.667:1:0:0.1 -6 92526266 . A AGC 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.30975;LSEQ=CCGCAAGTCGCAAGCTGGGA;RSEQ=AGCAGGGCTGATAACTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:25.2:1:32:1:1:0:60:12:0.6:0.3:0 1/0:6:4:0,4:0,2:0.6667:0,0:14.5:1:32.6:1:1:0:60:8:0.6667:0.3333:0 -6 93108565 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1431;SOR=Inf;LSEQ=TTGAGATTCCATACATATGG;RSEQ=TTAGGAATGAAGTCATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:97,9:0:2,0:24.7:1:32:1:1:0:60:105:1:0:0.1 0/1:65:2:1,1:54,9:0.0308:2,2:33:1:28.5:1:0.28606:5.74461:60:4:0.0313:0:1 -6 93108691 . A T 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03261;SOR=0.69083;LSEQ=CCACTATGTTTCTATGCTAG;RSEQ=ACTGTGTTATAAGTGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:280:159:64,95:49,72:0.5679:2,2:27.9:1:29.1:1:1:1.01016:60:158:0.5683:0:1.1 0/1:267:127:60,67:62,78:0.4757:2,2:24.8:1:28.6:1:0.71221:1.13:60:126:0.4773:0:1.1 -6 93108758 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20837;SOR=Inf;LSEQ=AATAATTCTAAAATTGAAGT;RSEQ=CCATTCATTTGATTAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:31,97:0:2,0:24.3:1:32:1:1:0:60:41.667:1:0:0.3 0/1:108:2:1,1:28,78:0.0185:2,2:16.5:1:27:1:0.46677:2.75:60:4:0.0189:0:1 -6 93108854 . T TTTAA 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.7366;SOR=0.7471;LSEQ=TCACTTATTTTGTTTTCTAT;RSEQ=TTAAAGTTAACATTTTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:9:0,9:0,12:0.4286:0,0:23:1:29.8:1:1:0:60:18:0.4286:0.0476:0 0/1:14:5:0,5:0,9:0.3571:0,0:26.2:1:29.9:1:1:0:60:10:0.3571:0.0714:0 -6 93109029 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCCAGATGTTTTGCACTCTT;RSEQ=TGCACATAGCCACAGGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:22:1:29:1:1:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 93109113 . T G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACTTCAAGCGGGAAACT;RSEQ=CCATAAACACTTTAATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:24:1:32.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 93589500 . G T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTTGGGGAGGGCAGCAGCCA;RSEQ=CACTGGGACTCAAAACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 93590442 . G C 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGCTTCTCTGCAGGAACT;RSEQ=CAATAACCCCAGCCAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:1:32:1:1:0:60:4:1:0:2 1/1:1:1:0,1:0,0:1:0,0:50:0:30:0:1:0:60:2:1:0:1 -6 93590467 . G A 61 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=AACCCCAGCCAGAGGCTCAG;RSEQ=GACAGAACCCCGATCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:23:1:30.5:1:1:0:60:8:1:0:1.5 0/0:1:0:0,0:0,1:0:0,0:26:0:32:0:1:0:60:2:1:0:1 -6 93591455 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAACACTCCAAGAAATAT;RSEQ=GGACTTATTAAAAAGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29.5:1:1:0:60:4:1:0:1.5 -6 93592984 . T C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TAACTAAGATTAGAGCAGAA;RSEQ=TGAAGGAGATAGAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:2,0:0:0,0:11.5:1:26.5:1:1:0:57.5:4:1:0:0.5 -6 93954830 . A G 114 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65232;SOR=0.44051;LSEQ=TATTGTTGTGAAGGTTAAAA;RSEQ=GGTAATATGTTTAAAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:12:12,0:26,0:0.3158:1,0:23.4:1:31.9:1:1:0:60:24:0.3243:0:1.8 0/1:6:1:1,0:5,0:0.1667:0,0:19:0:34:0:1:0:60:2:0.1667:0:1 -6 93954871 . C T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28528;SOR=0.47689;LSEQ=ATTTAGTATAATGCCTGGTA;RSEQ=GCAGTAAGAACTTGTTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:23:23,0:49,0:0.3194:1,1:23.7:1:32:1:1:0:60:46:0.3239:0:1.5 0/1:22:4:4,0:18,0:0.1818:1,0:16:1:31.5:1:1:0:60:8:0.1818:0:1 -6 93954896 . AT A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGAACTTGTTAAAGAAGT;RSEQ=TTTTTTTATCTTGATTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:2,0:106,0:0.0185:1,0:19.5:1:31:1:1:0:60:4:0.0187:0:1.5 0/0:53:0:0,0:52,1:0:1,0:22.4:1:30.7:1:1:0:60:106:1:0:0.1 -6 93955304 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53012;SOR=0;LSEQ=GTACATAATAAAAAATACAT;RSEQ=GATATGCTAATAAAAACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:0,2:1,153:0.0128:1,0:21.5:1:30.5:1:1:0:60:4:0.0131:0:1 0/0:93:0:0,0:2,91:0:1,0:21.7:1:29.8:1:1:0:60:92:1:0:0.1 -6 93956769 . T C 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=0.542;LSEQ=TTATAATAAACCAAATTTCC;RSEQ=GGTAGGCAAAATGATTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:479:372:59,313:16,91:0.7766:2,2:22.4:1:30.1:1:0.88105:1.07:60:185:0.7757:0:1 1/0:320:209:32,177:15,95:0.6531:2,2:22.7:1:29.4:1:0.74203:1.14:60:103.5:0.653:0:1.1 -6 93957161 . C T 46 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATATGAATGTACTATGA;RSEQ=AGAAAATATTACCAAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:0.3:2,0:36.3:1:29.3:1:1:0:60:6:0.3:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 93964187 . C T 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.73112;SOR=0.71695;LSEQ=TGATTATTCAAAATGAAAGC;RSEQ=AAAATAATAAAATTAGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:63:63,0:9,0:0.875:0,1:22.8:1:31.4:1:1:0:60:62:0.8732:0:1.1 1/1:24:20:20,0:4,0:0.8333:0,1:28.1:1:31.7:1:1:0:60:40:0.8333:0:1.1 -6 93964319 . C T 275 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.56419;LSEQ=CATGTTCCAGTAATACTGGC;RSEQ=ATTAATGTATTCAATCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:699:547:432,115:118,34:0.7825:2,2:26.1:1:30.3:1:0.7374:1.08:60:67.375:0.7823:0:1.1 1/0:515:345:245,100:129,40:0.6699:2,2:24.3:1:29.8:1:0.24594:1.31564:60:85.25:0.6726:0:1 -6 93964787 . T C 58 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=ACAAACAATGACAGGCTGGG;RSEQ=GCTGTGGCTCACATCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:17.3:1:29.3:1:1:0:60:8:0.5714:0:1 1/0:2:1:0,1:0,1:0.5:0,0:17:0:32:0:1:0:60:2:0.5:0:1 -6 93965458 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15436;SOR=Inf;LSEQ=GCTCAATTTGCTTCATTTCT;RSEQ=CTGTTTAGTTTTACATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:292,7:0:1,0:26.8:1:31.3:1:1:0:60:58.8:1:0:0.1 0/1:194:2:1,1:178,14:0.0103:2,2:22:1:27.5:1:0.14903:12.31775:60:4:0.0104:0:1.5 -6 93965492 . G A 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTATTAGGTCCTGCTTTC;RSEQ=TGGTAGAAAAATCTTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:0:0,0:458,87:0:2,0:23.2:1:30:1:1:0:60:180.667:0.9982:0:0.1 0/1:418:28:22,6:302,88:0.067:2,2:24.6:1:30:1:1:1.07:60:56:0.068:0:1 -6 93966205 . G T 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACGGGGGAAATATTTGAG;RSEQ=CAAAATGAAGAGAAACTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:19.3:1:31.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 93967249 . TA T 193 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.17436;SOR=1.26704;LSEQ=ATGACTGGTTTCCCTAAAAT;RSEQ=AAAAAAAAAAGTTTCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:79:20,59:269,533:0.0889:2,2:29.2:1:30.7:1:0.16682:1.4882:60:78:0.09:0.0022:0.3 0/1:700:77:27,50:215,399:0.11:2,2:27.1:1:30:1:1:1.00:59.7:154:0.1127:0.0057:0.4 -6 93967319 . C T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01933;SOR=Inf;LSEQ=TTTCTCATCCCCCAATAAAA;RSEQ=ACATGGTGTTCTTTTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:5,233:0:1,0:25.9:1:32.4:1:1:0:60:78.333:1:0:0.1 0/1:143:4:0,4:2,137:0.028:1,0:26:1:29:1:1:0:60:8:0.0282:0:1 -6 93967851 . C T 317 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.48716;LSEQ=CCTTCCAAATGGACAACATT;RSEQ=GGGTGGTCAAACTGCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1965:1536:862,674:246,180:0.7817:2,2:27:1:30:1:0.58085:1.06859:60:101.4:0.7812:0:1.1 1/0:1800:1144:613,531:350,305:0.6356:2,2:26.1:1:29.9:1:0.96085:1.01:60:162.429:0.6356:0:1.1 -6 93968070 . G T 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16356;SOR=6.02033;LSEQ=ATTTTCTTTTAAGAGTAAAT;RSEQ=CGTTGAATTATTTTTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:1:0,1:56,392:0.0022:2,0:29:0:31:0:1:0:60:2:0.0023:0:1 0/1:301:4:2,2:50,247:0.0133:2,2:11.3:1:29.8:1:0.13935:4.90:60:8:0.0134:0:1 -6 93968162 . C T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00189;SOR=0.24441;LSEQ=GTAAAGCCCTGTGAGTTACA;RSEQ=TGAATACATTCCCATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:59:0,59:0,15:0.7973:1,1:29:1:30.3:1:1:0:60:118:0.831:0:1 0/1:37:18:0,18:0,19:0.4865:1,1:21.3:1:30.9:1:1:0:60:36:0.5:0:1 -6 93968294 . A ACTGT 79 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAAGTTACGCTTTCCTAA;RSEQ=CTGTTAAACAGGCTACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:25.3:1:30.9:1:1:0:60:12:0.3333:0.1111:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 93973569 . A G 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCATAATAAAGAAAAGCCA;RSEQ=ACACTTACAATGAAAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1640:0:0,0:912,726:0:2,0:25.4:1:30:1:1:0:60:62:0.9988:0:0.1 0/1:1297:33:18,15:706,558:0.0254:2,2:24.5:1:31.5:1:1:1.05429:60:66:0.0258:0:1.2 -6 93973658 . A G 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=35.71222;LSEQ=AAGAAAGCAAATTTGTGACA;RSEQ=TCTCAGTCATTTTACTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1196:1:0,1:434,761:8e-04:2,0:48:0:33:0:1:0:60:2:9e-04:0:1 0/1:1103:32:13,19:423,648:0.029:2,2:23.5:1:31.8:1:1:1.05:60:64:0.0295:0:1.4 -6 93973686 . A C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.68967;LSEQ=CATTTTACTTTATATATTTA;RSEQ=TATTCAGTACAATGTACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:722:199:49,150:139,384:0.2756:2,2:21.1:1:32.1:1:0.63569:1.10797:60:198:0.2762:0:1.2 1/0:670:339:101,238:103,227:0.506:2,2:23.6:1:31.4:1:0.73702:1.0691:60:338:0.5113:0:1.1 -6 93973735 . T C 175 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACAACTTACTAGAGTTAAA;RSEQ=TTACTGTTCATAGTTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:43:1,42:8,239:0.1483:1,1:22.8:1:32.4:1:1:1.40438:60:86:0.1498:0:1.8 0/0:192:0:0,0:9,183:0:1,0:22.7:1:30.2:1:1:0:60:384:1:0:0.5 -6 93973784 . G T 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1796;SOR=0;LSEQ=GTAATAATATAGCGATTCAC;RSEQ=ATTAAAATTGCAAAGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:6:0,6:3,126:0.0444:1,0:27.2:1:24.8:1:1:0:60:5:0.0379:0:1.5 0/0:61:0:0,0:1,60:0:1,0:21.9:1:32.1:1:1:0:60:122:1:0:0.1 -6 93979090 . A T 185 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=2.28126;LSEQ=TACATATATATTTATTTGTA;RSEQ=ATGTAAAAATTATGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:68:66,2:194,2:0.2576:1,1:24.1:1:30.5:1:0.27382:2.92487:60:33:0.2548:0:1 0/1:156:69:69,0:87,0:0.4423:1,1:23:1:30.4:1:1:0:60:68:0.4416:0:1.1 -6 93979780 . A G 63 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAAGTTATTCAGCAAGA;RSEQ=AAAAAGCCAGATGCTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:0.5714:0,0:32:1:31.5:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 93982124 . A G 318 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03626;LSEQ=ACTCTCTCCTTCATTACTCC;RSEQ=CTCACTTGCGAGGGAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1235:1227:518,709:3,0:0.9935:0,2:24.7:1:31:1:0.07574:0:60:71.176:0.9983:0:1.1 1/1:1121:950:407,543:78,90:0.8475:2,2:25.7:1:30.7:1:0.39929:1.15611:60:58.375:0.8499:0:1.1 -6 94065703 . T C 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATTACAAAGATCATAGTC;RSEQ=ATGTAGTAAAAAATTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16:1:27.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 94065942 . A G 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCCTGTTTTTTTTTTTCC;RSEQ=GAGACAAGAGTCTTAGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 94066172 . C T 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52632;SOR=0;LSEQ=ACCTTGTGATCTGCCCGCCT;RSEQ=GGCCTCCCAAAATGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:0.3333:0,0:23.3:1:31.8:1:1:0:60:12:0.3333:0:1 0/0:3:0:0,0:3,0:0:0,0:21.7:1:30.7:1:1:0:60:6:1:0:0.7 -6 94066191 . G A 103 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60513;SOR=0.37656;LSEQ=TCGGCCTCCCAAAATGCTGG;RSEQ=ATTACAGGTGTGAGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:11,0:12,0:0.4783:0,0:25.6:1:29.8:1:1:0:60:22:0.4783:0:1 0/1:4:1:1,0:3,0:0.25:0,0:39:0:30:0:1:0:60:2:0.25:0:1 -6 94066446 . G T 189 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02742;LSEQ=AAAACATACCTGCTTGACCA;RSEQ=TGGTGATACTGACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1535:77:48,29:869,589:0.0502:2,2:24.5:1:30.2:1:0.72086:1.12:60:76:0.05:0:1.2 0/0:1384:2:1,1:822,560:0.0014:2,2:7:1:30:1:1:1.46741:60:4:0.0015:0:1 -6 94066811 . G GA 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.69465;SOR=0.8779;LSEQ=TAAGTAAATAAGCAAAAATA;RSEQ=AAAAAAAAACATACAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:848:35:6,29:183,623:0.0413:2,2:25.2:1:29.9:1:0.53849:1.41918:60:34:0.0411:0:0.2 0/1:714:26:6,20:198,480:0.0364:2,2:26:1:29.6:1:0.66035:1.37447:60:52:0.0374:0.0014:0 -6 94066934 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAACATTTCATTACCTTT;RSEQ=CTAGAGAAGCTGTATAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:0,85:0.023:1,2:26:1:29:1:0.02299:0:60:4:0.0233:0:1 0/0:29:0:0,0:0,29:0:1,0:21.8:1:29.3:1:1:0:60:28:1:0:0.2 -6 94067373 . C CT 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATGCAAGACCCTAATAA;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:2,0:0.5:0,0:12:1:31.3:1:0.33333:0:60:4:0.5:0.25:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 94067497 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCCTGCTTCAGTCTTCC;RSEQ=CGTAGCTGGGATTACAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:41.5:1:30.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 94067846 . A C 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATTTTATCTTAATATTTT;RSEQ=AAATAATTTTAATATTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:123,0:0:1,0:22.6:1:28.5:1:1:0:60:122:1:0:0.5 0/1:69:15:15,0:54,0:0.2174:1,1:22.3:1:31.3:1:1:0:60:30:0.2174:0:1 -6 94067861 . T G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25988;LSEQ=ATTTTAAAATAATTTTAATA;RSEQ=TTAAGTATAATTAAGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:87:87,0:90,0:0.4915:1,1:22.4:1:32.3:1:1:0:60:28:0.4828:0:1 0/1:100:20:20,0:79,1:0.2:1,1:21.7:1:32.2:1:1:0:60:40:0.202:0:1 -6 94067981 . C T 292 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01798;SOR=1.21563;LSEQ=TAATACAACTCACTTGTGCA;RSEQ=GCAACGTATGGTGGGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1382:795:476,319:358,227:0.5753:2,2:25:1:30.4:1:0.65592:1.05691:60:60.154:0.5742:0:1.1 1/0:1138:708:417,291:246,182:0.6221:2,2:25.9:1:29.7:1:0.66388:1.06:60:77.667:0.6208:0:1.1 -6 94068181 . T TA 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.66978;SOR=1.22584;LSEQ=CATGAGAGCAAATCGATCTT;RSEQ=AAAAAAAAATTGTATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:11:2,9:116,482:0.0179:2,2:27.5:1:30.4:1:1:1.08283:60:22:0.0185:0.0016:0 0/1:502:11:1,10:111,373:0.0219:2,2:24.9:1:30.1:1:0.46952:2.97121:60:22:0.022:0.004:0.1 -6 94068208 . G C 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATTGTATTATTTAGCAAG;RSEQ=AATCAAATATTAAATGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:28:6,22:32,299:0.078:2,2:25.7:1:32:1:0.0993:2.54:60:56:0.0791:0:1.1 0/0:259:0:0,0:22,237:0:2,0:23.8:1:31.1:1:1:0:60:50.8:1:0:0.1 -6 94068364 . G C 118 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07552;SOR=0.13317;LSEQ=TGCACCTGCAGTTGGCACCA;RSEQ=GCCAAAGTCTGGAGCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:1,15:0,10:0.6154:0,1:26:1:29.5:1:1:0:60:32:0.6154:0:1.1 0/1:6:1:0,1:0,5:0.1667:0,0:40:0:27:0:1:0:60:2:0.1667:0:1 -6 94119750 . A G 59 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATTCTAAAAGTTTGTAAAT;RSEQ=TATTCGTTTATGCCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:23.5:1:29.5:1:1:0:60:8:0.4:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 94120192 . G A 267 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78651;SOR=1.02768;LSEQ=GAAATTTAAAAAGGCAAAGT;RSEQ=GAGTTTTAATAGGACACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1109:610:405,205:322,177:0.55:2,2:26.4:1:28.9:1:0.52583:1.09:60:42.571:0.5508:0:1.1 1/0:898:500:313,187:236,158:0.5568:2,2:25.6:1:28.7:1:0.44663:1.12:60:124:0.5567:0:1.1 -6 94124157 . G T 79 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTAATTAGTTAGCATTTACA;RSEQ=CCTGGACCCTGAGGTATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:6,0:0.5:0,0:21.5:1:30.8:1:1:0:60:12:0.5:0:1 1/0:2:1:1,0:1,0:0.5:0,0:35:0:31:0:1:0:60:2:0.5:0:1 -6 94124370 . G T 66 v4;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04778;SOR=7.80217;LSEQ=ACCCTGGAGGGAAGGGAAAC;RSEQ=TTTTGTTTCTTATTTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:1:0,1:525,159:0.0015:2,0:1:0:25:0:0.23358:0:60:2:0.0015:0:1 0/1:532:6:0,6:391,135:0.0113:2,0:6.5:1:25.8:1:0.00032:0:60:12:0.0115:0:1 -6 94124530 . C A 268 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38604;SOR=0.91009;LSEQ=TATGTTACATGAAACACTTA;RSEQ=GCACACATGTAGACATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:819:433:112,321:102,284:0.5287:2,2:24.7:1:30.6:1:0.87362:1.02934:60:143.333:0.5322:0:1.1 1/0:582:294:68,226:90,194:0.5052:2,2:24.1:1:30.4:1:0.02495:1.54065:60:48:0.5017:0:1.1 -6 94128872 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.50469;SOR=0;LSEQ=GGGTCGCCCGGCGCCGGAGG;RSEQ=GCGGCCGGCAGCGCCGCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:124,3:0.0155:1,2:17:1:30.5:1:0.06129:35.9361:60:4:0.0157:0:1 0/0:102:0:0,0:93,8:0:2,0:16.8:1:32:1:1:0:60:32.667:0.9899:0:0.2 -6 94129194 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52756;SOR=0;LSEQ=CTCGGTCCCCGATCGGCTGC;RSEQ=CCACGTTTAGCTTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:0,2:3,188:0.0104:1,0:13:1:28:1:1:0:60:4:0.0107:0:1 0/0:118:0:0,0:2,116:0:1,0:19.6:1:28.9:1:1:0:60:38.333:1:0:0.1 -6 95221894 . C G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GACAAGTGGATTTCCTCCCA;RSEQ=TGAAGCATACCCCCTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:24:1:32.4:1:1:0:60:10:1:0:1 0/1:5:2:1,1:2,1:0.4:2,2:20.5:1:29.5:1:1:1.7321:60:4:0.4:0:2 -6 95221943 . A G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCAAGGTGCTTCGTTAAAT;RSEQ=TGTCCTGTTTCCCGTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:12,10:0,0:1:0,2:24.5:1:32.3:1:1:0:60:44:1:0:1 1/1:8:8:4,4:0,0:1:0,2:34.4:1:32:1:1:0:60:16:1:0:1.3 -6 96823954 . ACAG A 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.0652;SOR=0;LSEQ=ATTAAATCAATGATGCTGGC;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:2,1:15,14:0.0938:2,2:23.3:1:33.7:1:1:1.83:60:6:0.0938:0:0 0/0:46:0:0,0:24,22:0:2,0:27.8:1:30:1:1:0:60:14.333:1:0:0.2 -6 97729953 . C A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.59484;LSEQ=AAAAATTAGTGCCCAGCTCC;RSEQ=TACAGTAAGGGAACATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:247:134,113:136,118:0.492:2,2:24.9:1:30.4:1:0.92861:1.03:60:246:0.494:0:1.1 0/1:602:220:121,99:191,190:0.3654:2,2:28.1:1:29.8:1:0.27093:1.22:60:219:0.3656:0:1.2 -6 98417064 . A G 25 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18703;SOR=Inf;LSEQ=AGTCTTTTACAAAAGTATCT;RSEQ=ATCCTATTCTAGTGTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:153,55:0:2,0:22.5:1:28.8:1:1:0:60:103:1:0:0.2 0/1:159:2:1,1:108,49:0.0126:2,2:5:0:25.5:1:0.53141:2.19205:60:4:0.0127:0:1.5 -6 98417147 . A T 208 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.19384;LSEQ=CAGCCAGCTACCTGAGGAGA;RSEQ=GGGAAGTGGGAGAGACTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:88:42,46:180,169:0.2014:2,2:27:1:30.2:1:0.55196:1.16611:60:87:0.2023:0:1.1 0/1:376:134:71,63:115,127:0.3564:2,2:24.1:1:29.5:1:0.33339:1.24:60:43.667:0.3531:0:1.1 -6 98417252 . AT A 141 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.03607;LSEQ=CGGCATCACACTGGGATTCA;RSEQ=TTTTTTTTTCTCTCTATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:23:4,19:11,88:0.1885:2,2:29.7:1:31.3:1:0.47991:1.68:60:46:0.1917:0.0082:0.3 0/1:67:13:1,12:10,44:0.194:2,1:31.5:1:29.1:1:0.67722:2.69504:60:26:0.194:0.0299:0.3 -6 99282579 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.47059;SOR=0;LSEQ=GGCGGCGGCGGCAGCAGCAG;RSEQ=AGTAATAGCAGGAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:18.5:1:29:1:1:1.29:60:4:0.25:0:1.5 0/0:8:0:0,0:4,4:0:2,0:17:1:31.4:1:1:0:60:16:1:0:0 -6 99282584 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=CGGCGGCAGCAGCAGCAGTA;RSEQ=TAGCAGGAGCAGCAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:23.5:1:31.5:1:1:1.58:60:4:0.2222:0:1.5 0/0:7:0:0,0:3,4:0:2,0:15.7:1:30.1:1:1:0:60:14:1:0:0 -6 99282962 . CG C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTCCCACGGCGGCGGCGG;RSEQ=GGGGCGGTGGCGGCGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:14:0:32:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:10:0:33:1:1:0:60:4:0.6667:0:0.5 -6 99283061 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50416;SOR=0;LSEQ=CTGGGCCAGCCGGACATCAA;RSEQ=CCCTCGGTGGTGGTGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:2,0:82,4:0.0227:1,0:46:0:31:0:1:0:60:4:0.023:0:1 0/0:69:0:0,0:65,4:0:2,0:24.6:1:32.1:1:1:0:60:33.5:1:0:0.2 -6 99283107 . G T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02994;SOR=Inf;LSEQ=GCCGCGGAGACGAGCTGCAC;RSEQ=GGCCAGGCGCCCTGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:161,91:0:2,0:24.3:1:29.3:1:1:0:60:30.5:1:0:0.2 0/1:181:4:2,2:110,67:0.0221:2,2:17.8:1:30:1:0.6364:1.63705:60:8:0.0229:0:1 -6 99283111 . C G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18555;SOR=Inf;LSEQ=CGGAGACGAGCTGCACGGGC;RSEQ=AGGCGCCCTGCAGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:162,98:0:2,0:25.1:1:30.4:1:1:0:60:27.889:0.996:0:0.2 0/1:198:2:1,1:119,75:0.0101:2,2:11.5:1:28:1:1:1.58275:60:4:0.0103:0:1 -6 99283120 . TGCA T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.04414;SOR=Inf;LSEQ=GCTGCACGGGCCAGGCGCCC;RSEQ=GCAGCAGCATCAGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:163,119:0:2,0:27.4:1:31.5:1:1:0:60:30.333:0.9964:0:0.2 0/1:241:4:1,3:136,101:0.0166:2,2:20.8:1:28.3:1:0.31798:4.01741:60:8:0.0169:0.0083:0.8 -6 99283127 . G T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.66043;SOR=1.86982;LSEQ=GGGCCAGGCGCCCTGCAGCA;RSEQ=CAGCATCAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:2:1,1:175,132:0.0065:2,2:32.5:1:32:0:1:1.32452:60:4:0.0066:0:1 0/1:249:3:2,1:134,111:0.012:2,2:47.7:1:30.3:1:1:1.65:60:6:0.0123:0:1 -6 99283133 . T C 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09547;SOR=Inf;LSEQ=GGCGCCCTGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:190,145:0:2,0:27.2:1:29.9:1:1:0:60:24.769:1:0:0.2 0/1:283:3:2,1:151,129:0.0106:2,2:24.3:1:24.3:1:1:1.71:60:2:0.0073:0:1.3 -6 99283172 . ACAG A 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.35161;SOR=1.48714;LSEQ=CAGCAGCAGCAACAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:13:8,5:186,200:0.0324:2,2:26.3:1:32.2:1:0.40554:1.72:60:26:0.0327:0.0075:0.2 0/1:358:17:8,9:163,178:0.0475:2,2:29.8:1:31.5:1:1:1.03012:58.2:34:0.0479:0:0.2 -6 99283175 . G A 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.01143;SOR=Inf;LSEQ=CAGCAGCAACAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:180,196:0:2,0:23.5:1:32.1:1:1:0:59.7:93:1:0.0026:0.2 0/1:353:6:3,3:159,171:0.017:2,2:20:1:29.8:1:1:1.08:60:12:0.0185:0:1.2 -6 99283182 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.05128;SOR=Inf;LSEQ=AACAGCAGCAACAGCAGCAG;RSEQ=AGCAGCAGCAACAGCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:163,178:0:2,0:26.2:1:32.2:1:1:0:59.8:67.2:0.997:0.0029:0.2 0/1:312:4:2,2:146,160:0.0128:2,2:32:1:29.8:1:1:1.10:60:8:0.013:0:1.3 -6 99283198 . G A 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.358;SOR=3.22189;LSEQ=GCAGCAGCAGCAGCAACAGC;RSEQ=GCCGCCGCATCTGGTGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:1:1,0:129,154:0.0035:2,0:1:0:27:0:0.45775:0:60:2:0.0036:0:1 0/1:266:3:3,0:120,143:0.0113:2,0:14.7:1:22.3:1:0.09757:0:60:2:0.0078:0:2.3 -6 99283376 . T G 74 d7;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGGCGGGCAGCCGGCCGG;RSEQ=CTGCACCACCACGGCCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:16.2:1:29:1:1:0:60:5:1:0:1 1/1:2:2:0,2:0,0:1:0,0:4:0:32:1:1:0:60:4:1:0:1.5 -6 99708653 . T A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGAACTGACCACATATA;RSEQ=TTCACAAATCAGACAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 99710241 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49025;SOR=Inf;LSEQ=GGAGGTTGGTATAAGAGTTT;RSEQ=AAAGGCGTTGTCTGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:0:2,0:32.1:1:31.5:1:1:0:59.1:22:1:0:0.1 0/1:25:2:1,1:10,13:0.08:2,2:42:1:27.5:1:1:1.29:57:4:0.0833:0:1 -6 99710546 . AACTTT A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACACTATTAACTTTTAGCA;RSEQ=ACTTTAGTTGAAAACCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:36.5:1:28:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 100302134 . T A 27 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CTCTTTTCTTTTTCTTTCTT;RSEQ=TTTTCTCCCCTTCCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:15.5:1:27:1:1:0:60:4:0.3333:0:2 0/0:6:0:0,0:5,1:0:2,0:22.2:1:31.3:1:1:0:60:12:1:0:0.2 -6 100302409 . A G 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=0.60014;LSEQ=ACATTTATGTTGTTTGAGGT;RSEQ=GAAAATAGACTTTCAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:473:330:149,181:68,73:0.6977:2,2:25.6:1:31.6:1:0.54654:1.13126:60:164:0.6979:0:1.1 1/0:422:245:116,129:87,89:0.5806:2,2:25:1:30.4:1:0.69328:1.08686:60:80.667:0.5776:0:1.1 -6 100302494 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23734;SOR=Inf;LSEQ=TATTATCTCTTGGTAATTCA;RSEQ=CATTTTTTTTAAGAGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:61,129:0:2,0:24:1:31.8:1:1:0:60:30.667:1:0:0.3 0/1:181:2:1,1:56,123:0.011:2,2:25:1:27.5:1:0.53186:2.19:60:4:0.0113:0:1.5 -6 100302496 . A AT 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.06994;LSEQ=TTATCTCTTGGTAATTCAGC;RSEQ=TTTTTTTTAAGAGGCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:0,2:59,124:0.0108:2,0:18.5:1:31.5:1:1:0:60:4:0.011:0:0 0/1:173:2:0,2:51,119:0.0116:2,0:10:1:29.4:1:1:0:60:4:0.0117:0.0058:0 -6 100302541 . T C 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=0;LSEQ=CTCTGTCACCCAGGCTGGAG;RSEQ=GCAGTGGTGCTCACTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:7,55:0.0313:2,2:29:1:25.5:1:0.23611:7.42:60:4:0.0317:0:1 0/0:55:0:0,0:4,51:0:2,0:22.5:1:29.8:1:1:0:60:54:1:0:0.1 -6 100303613 . A C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCATCAGTCTACTCCCTCTC;RSEQ=CACCCCGCTGCCTCCTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:45:0:30:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:18.5:1:30.5:1:1:0:60:4:1:0:1 -6 100314801 . CA C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.08772;SOR=Inf;LSEQ=AGTTCAGTAGATACTACCTA;RSEQ=AAAAAAAGTTTAGCATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:0:1,0:25.7:1:30.5:1:1:0:60:26:1:0:0.2 0/1:6:2:2,0:3,1:0.3333:2,0:26:1:32.5:1:1:0:60:4:0.3333:0:0 -6 100314973 . A G 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTATATAATAAGAAATAGA;RSEQ=GTATAGGCATAAAATTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:246:245:158,87:0,0:0.9959:0,2:23.1:1:31.7:1:1:0:60:244:0.9959:0:1.2 1/1:183:183:121,62:0,0:1:0,2:24.8:1:31:1:1:0:60:44.75:1:0:1.4 -6 100315027 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.89712;LSEQ=GCTAAGATAGACTATAGCAC;RSEQ=TAACCTCAAGACAGGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:68:30,38:163,152:0.1775:2,2:28.1:1:31.2:1:0.2856:1.35724:60:67:0.1754:0:1.5 0/1:352:161:83,78:90,101:0.4574:2,2:25:1:29.9:1:0.45405:1.19:60:79.5:0.4556:0:1.5 -6 100315078 . G T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10988;SOR=Inf;LSEQ=CCTTTAGTGATGTTGGTTTT;RSEQ=TATCACATGTTCAAGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:106,179:0:2,0:24.4:1:31.8:1:1:0:60:56:1:0:0.2 0/1:263:3:2,1:103,157:0.0114:2,2:22.3:1:24.3:1:0.56552:3.04:60:2:0.0077:0:2.3 -6 100498318 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=TCATCCACAAGCAATTCTTC;RSEQ=CATAATTGATGAACTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:80,31:0.0177:2,2:32:0:32.5:1:0.48799:2.55583:60:4:0.0177:0:1 0/0:84:0:0,0:57,27:0:2,0:24.7:1:30:1:1:0:60:83:1:0:0.1 -6 100498343 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19998;SOR=Inf;LSEQ=ATTGATGAACTTGGCTTCCA;RSEQ=TTTGAGAAGAGAACCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:85,38:0:2,0:23.5:1:32.1:1:1:0:60:122:1:0:0 0/1:100:2:1,1:71,27:0.02:2,2:23:1:32:0:0.48364:2.60037:60:4:0.02:0:1 -6 100498364 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.23278;SOR=Inf;LSEQ=TTTGAGAAGAGAACCACCTT;RSEQ=TTCTATACTTGCATTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:100,55:0:2,0:21:1:30.5:1:1:0:60:154:1:0:0 0/1:145:2:1,1:103,40:0.0138:2,2:14:1:31:1:0.48697:2.55573:60:4:0.0138:0:1 -6 100498524 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24655;SOR=Inf;LSEQ=CAAAAGGCTTTGAGTCTTTT;RSEQ=CATTCTAGTTTGACTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:66,116:0:2,0:24.4:1:31.3:1:1:0:60:181:1:0:0.1 0/1:180:2:0,2:58,119:0.0111:2,0:24.5:1:25.5:1:1:0:60:4:0.0113:0:1 -6 100498557 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23123;SOR=Inf;LSEQ=ACTTTTGTGCATTTTTGGCT;RSEQ=GAGTATCTCCTATAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:61,95:0:2,0:27.7:1:31.6:1:1:0:60:155:1:0:0.1 0/1:145:2:1,1:52,91:0.0138:2,2:28:1:32.5:1:1:1.74:60:4:0.0139:0:1 -6 100498638 . G T 96 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0286;SOR=0.11955;LSEQ=CACCATCATCATCATCTTCG;RSEQ=CATTATCATCATCATCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:11:4,7:29,57:0.1134:2,2:26.5:1:27.8:1:1:1.12:60:4.5:0.0947:0:1.5 0/1:67:1:0,1:31,35:0.0149:2,0:28:0:31:0:1:0:60:2:0.0152:0:1 -6 100498642 . TATC T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=1e-05;SOR=4.63077;LSEQ=ATCATCATCATCTTCGGCAT;RSEQ=ATCATCATCTTATTCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:25:9,16:26,49:0.25:2,2:28.7:1:30.7:1:1:1.06:60:50:0.2525:0.01:0.6 1/0:64:39:21,18:11,14:0.6094:2,2:30.4:1:30.2:1:0.60884:1.48:60:78:0.619:0.0156:0.8 -6 100498662 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16745;SOR=Inf;LSEQ=TATCATCATCATCTTATTCA;RSEQ=CAGCAGCAAGTTTTACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:42,67:0:2,0:24.7:1:29.9:1:1:0:60:35.333:1:0:0.8 0/1:76:2:1,1:39,35:0.0263:2,2:11:1:26:1:1:1.1127:60:4:0.0263:0:2 -6 100498693 . G T 204 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTACTTTTCTCTGTGGAA;RSEQ=CTTGCTACCACCTCCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:111:111:45,66:0,0:1:0,2:25.7:1:30.1:1:1:0:60:36:1:0:1.1 1/1:85:85:45,40:0,0:1:0,2:22.9:1:29.3:1:1:0:59.9:41.5:1:0:1.3 -6 100498754 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22993;SOR=Inf;LSEQ=CTTAAGAGTTTCACATCCTC;RSEQ=TCCTCTTCATCTTCTGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:54,54:0:2,0:22.3:1:31.7:1:1:0:60:107:1:0:0.5 0/1:100:2:1,1:53,45:0.02:2,2:11.5:1:24.5:1:1:1.17584:60:4:0.0204:0:1.5 -6 100498756 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22158;SOR=Inf;LSEQ=TAAGAGTTTCACATCCTCCT;RSEQ=CTCTTCATCTTCTGACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:56,57:0:2,0:21.5:1:31.4:1:1:0:60:226:1:0:0.5 0/1:101:2:1,1:52,46:0.0198:2,2:12.5:1:29.5:1:1:1.12905:60:4:0.02:0:1 -6 100498976 . C T 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTGCTTCAACAATGTGCAA;RSEQ=TTATCCTTCGCACCAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:33:17,16:93,73:0.1658:2,2:25.1:1:30.9:1:0.70296:1.19793:60:66:0.1667:0:1.3 0/0:226:0:0,0:114,112:0:2,0:27.7:1:31.6:1:1:0:60:452:1:0:0.1 -6 100499026 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5014;SOR=0;LSEQ=CGTTCTTCAAGATAACTGGT;RSEQ=CTCATTTTCATCATTATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:77,97:0.0114:2,2:33:1:31:1:1:1.26:60:4:0.0118:0:1 0/0:151:0:0,0:63,88:0:2,0:25:1:31.8:1:1:0:59.2:74.5:1:0:0.1 -6 100499087 . GA G 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.70756;SOR=0.66068;LSEQ=TTGGCCTTCAGTTCACAATT;RSEQ=AAAAGATAGTTCTGGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:74:23,51:1,2:0.961:2,2:25.5:1:31.6:1:1:1.10718:58.1:73:0.9605:0.1169:0 1/1:69:65:27,38:2,2:0.942:2,2:25.2:1:31:1:1:1.40031:58.1:130:0.9559:0.1159:0.1 -6 100499101 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.2066;SOR=Inf;LSEQ=ACAATTGAAAAAGATAGTTC;RSEQ=GGGCCTCAGGGTCATGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:24,51:0:2,0:20.6:1:30.7:1:1:0:58.1:24:1:0:0 0/1:63:2:1,1:25,36:0.0317:2,2:31.5:1:29.5:1:1:1.43:51:4:0.0317:0:3 -6 100977863 . AT A 60 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCATCATTAAATCGTG;RSEQ=TTTTTTTTTTTTCTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:11.3:1:30.2:1:1:0:60:8:0.4:0.1818:0.5 0/0:2:0:0,0:2,0:0:0,0:36:1:31.5:1:1:0:60:4:1:0:0.5 -6 100977940 . T C 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00192;SOR=0;LSEQ=TATTCTGGTATAATTTGGTA;RSEQ=TTAACATACATTAATTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:16,0:11,0:0.5714:0,1:29.4:1:30:1:1:0:60:7:0.5385:0:1.3 0/0:10:0:0,0:10,0:0:0,0:10:0:15:0:1:0:60:0:0:0:5 -6 100978351 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19495;LSEQ=TGGAAAGGAAGAAGTTAGAA;RSEQ=AACTGTACAATAGAGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:376:224:109,115:70,82:0.5957:2,2:23.7:1:29.3:1:0.67408:1.11:60:55:0.593:0:1.1 0/1:238:53:28,25:92,93:0.2227:2,2:23.2:1:29.1:1:0.75613:1.13:59.8:106:0.2236:0:1.1 -6 100978570 . C T 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15984;LSEQ=GCATAGAAAAACTAAAGGCC;RSEQ=AGATACCCAAGATGTAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:914:510:259,251:202,201:0.558:2,2:25:1:29.8:1:0.89396:1.03:59.7:101:0.5586:0:1.1 0/1:781:131:70,61:340,309:0.1677:2,2:23.5:1:29.4:1:0.84834:1.04:60:130:0.1686:0:1.1 -6 100978829 . C T 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=25.99057;LSEQ=AGTACAGTGATTGCAAATCA;RSEQ=GTGTCTAATTATGATGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:678:1:1,0:366,309:0.0015:2,0:28:0:14:0:1:0:52:0:0:0:8 0/1:513:19:12,7:270,224:0.037:2,2:20.6:1:28.8:1:0.49285:1.42:60:38:0.0375:0:1.5 -6 100979222 . A G 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01961;SOR=Inf;LSEQ=CCATAAGTCCTAGAAGCTTT;RSEQ=TGGTGATTATTTTGAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:0,15:0:1,0:29.5:1:31.8:1:1:0:50.3:30:1:0:0.1 1/0:3:2:1,1:0,1:0.6667:0,2:26:1:30:1:1:0:60:4:0.6667:0:1 -6 100979445 . A AT 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTATTTTGGTTTGGGGGGA;RSEQ=TTTTTTTTTTTCCTGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:23.5:1:29.5:1:1:0:51:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 101337371 . G A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23913;SOR=0;LSEQ=CTGCTGGTGCTGTTGCCGCC;RSEQ=CTGCTCTCGCTGCAGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:2,1:18,14:0.0857:2,2:22:1:28.3:1:1:1.54:60:6:0.0857:0:1 0/0:35:0:0,0:16,19:0:2,0:27.7:1:30.3:1:1:0:60:34:1:0:0.2 -6 104473752 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23361;SOR=Inf;LSEQ=GGAGTTTTCTTCAGTTTCCT;RSEQ=ATCATCAAAATTATTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:16.6:1:29.6:1:1:0:60:32:1:0:0.1 0/1:19:3:2,1:9,7:0.1579:2,2:6.3:1:30.7:1:1:1.52:60:6:0.1579:0:1 -6 104473941 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17612;SOR=Inf;LSEQ=AAAGTGCTGTCTACTAATAT;RSEQ=CACAAGGTCTGAACTACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:30,26:0:2,0:23.5:1:30.8:1:1:0:60:27:1:0:0.2 0/1:41:2:1,1:17,22:0.0488:2,2:33:1:27:1:1:1.29:60:4:0.0488:0:1 -6 104474026 . AT A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03476;SOR=Inf;LSEQ=AAACAGTTGGCTGTACAGAC;RSEQ=TTTTTTTTAACATTGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:2,17:0:2,0:21.3:1:29.4:1:1:0:60:18:1:0:0.5 0/1:16:4:2,2:4,8:0.25:2,2:21:1:29.3:1:0.6044:1.91:58.8:8:0.25:0.0625:0.3 -6 106051185 . A C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATTCCTAAGCATGGTAA;RSEQ=AATTTGGTGCCCCAAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:13:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 106051358 . AG A 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACTTTGATAGCAGAACA;RSEQ=TATTCTTAGTAATTAGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:42.5:1:32:1:1:0:60:8:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 106051478 . G A 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10131;SOR=0;LSEQ=GCTGAAATATATCAGTAACA;RSEQ=TATTAAATAATGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:6,1:6,0:0.5385:0,2:28.1:1:31.6:1:1:0:60:14:0.5385:0:1 0/0:5:0:0,0:5,0:0:0,0:22.2:1:33.8:1:1:0:60:10:1:0:0 -6 106051695 . A G 216 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTTCAGAAGACTTTTGATC;RSEQ=TAATTTTGGGGTTAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:136:74,62:116,98:0.3886:2,2:25.1:1:30.5:1:1:1.01:60:135:0.3879:0:1.7 0/0:390:0:0,0:205,183:0:2,0:25.7:1:29.7:1:1:0:60:76.6:0.9948:0:0.4 -6 106051738 . T C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.21162;LSEQ=TAAAATCAATATATGGTAGC;RSEQ=TTGAGTAAGAGACAAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:346:270:119,151:35,41:0.7803:2,2:25.9:1:31.4:1:0.7946:1.08296:60:53:0.7794:0:1.4 0/1:378:162:70,92:99,116:0.4286:2,2:23.4:1:31:1:0.60223:1.12133:60:39.5:0.427:0:1.1 -6 106534362 . C T 65 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98609;LSEQ=CGCCGAGGTGCGCGTCTGTG;RSEQ=GGCTCAGCCTGGCGGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:4:0,4:270,70:0.0116:2,0:1:0:27:1:0.00201:0:60:8:0.0118:0:1 0/1:436:5:2,3:334,97:0.0115:2,2:16.4:1:28.4:1:0.08178:5.13966:60:10:0.0116:0:1 -6 106534484 . AT A 168 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.14857;SOR=0.72537;LSEQ=GACCTTGGTAAGGAACTTGA;RSEQ=TTTTTTTTTTTAATTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:45:14,31:202,332:0.0769:2,2:28.6:1:30.6:1:0.42451:1.34658:59.9:90:0.078:0.0103:0.4 0/1:737:42:18,24:267,423:0.057:2,2:28.4:1:29.6:1:0.62651:1.19:60:41:0.0569:0.0054:0.1 -6 106534554 . AT A 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=2.00911;LSEQ=CTTTATTGTTATTATTATTA;RSEQ=TTTTTTTGGCTAATGTCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:1:0,1:1,145:0.0068:1,0:25:0:27:0:1:0:60:2:0.0068:0:0 0/1:148:2:0,2:1,145:0.0135:1,0:26.5:1:32:0:1:0:60:4:0.0135:0:0 -6 106535812 . CT C 52 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATTGTTCAGAGGTGATT;RSEQ=TTTTTTTTTTTTCCTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:22:1:33:0:1:0:60:6:0.3333:0:0 0/0:1:0:0,0:1,0:0:0,0:11:0:33:0:1:0:60:2:1:0:0 -6 106535936 . C T 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96539;LSEQ=CAGTTTACTTTATACGGCTT;RSEQ=TTGGCTCTTTCTCAACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:38:36,2:5,0:0.8837:0,2:24.4:1:30.8:1:1:0:60:76:0.9048:0:1.2 1/1:25:22:22,0:3,0:0.88:0,1:21.6:1:29.1:1:1:0:60:21:0.875:0:1.3 -6 106536046 . G T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06177;SOR=Inf;LSEQ=ACAGGAACGGCGGGACAATG;RSEQ=GGATTAAAGGCCTTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:289,119:0:2,0:24.4:1:30.9:1:1:0:60:50:1:0:0.2 0/1:414:5:1,4:278,131:0.0121:2,2:18.4:1:24.6:1:0.04083:8.44338:60:4:0.0099:0:1.2 -6 106536253 . G A 178 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=63.46204;LSEQ=GGGATTCTGGTGCTGATGGC;RSEQ=GTACTTCGGTTCAGGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:768:1:0,1:314,453:0.0013:2,0:42:0:32:0:1:0:60:2:0.0013:0:1 0/1:797:61:24,37:322,413:0.0765:2,2:23.1:1:30.1:1:0.59117:1.2017:60:122:0.0771:0:1.1 -6 106543405 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49905;SOR=Inf;LSEQ=CATTGTTAGTTGTATTACTA;RSEQ=TTGACAGTCCAATTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:87,1:0:1,0:24.9:1:32.5:1:1:0:60:176:1:0:0 0/1:99:2:1,1:88,9:0.0202:2,2:18:1:30:1:0.19274:9.32857:60:4:0.0208:0:1 -6 106543620 . G A 178 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01293;LSEQ=TTTTTGGAGGGTAAGTAAGG;RSEQ=AAATTTCTTCAGACCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:61:19,42:88,183:0.1837:2,2:26.2:1:30.1:1:0.88068:1.0628:60:60:0.1835:0:1.2 0/0:346:1:1,0:134,211:0.0029:2,0:1:0:23:0:0.39017:0:60:2:0.0029:0:2 -6 106543695 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23715;SOR=Inf;LSEQ=TGGCTCACCTTTCTCATCCT;RSEQ=TGCTGAGAAATGCTGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:2,67:0:1,0:25.2:1:32.3:1:1:0:60:138:1:0:0.1 0/1:66:2:1,1:2,62:0.0303:1,2:12.5:1:27.5:1:0.08951:25.52:60:4:0.0308:0:1 -6 106546865 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.506;SOR=Inf;LSEQ=AGTAGCAAAAGTAGTACTCT;RSEQ=TGGTGGGTTAATCGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:99,32:0:2,0:25.3:1:32:1:1:0:60:130:1:0:0.1 0/1:168:2:1,1:123,43:0.0119:2,2:25:0:29:1:0.45637:2.83924:60:4:0.012:0:1 -6 106546886 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19595;SOR=0;LSEQ=TGGTGGGTTAATCGGTTTGA;RSEQ=GCAGCTCCTTAAATGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:125,53:0.0111:2,2:20:1:30.5:1:0.51117:2.3459:60:4:0.0112:0:1 0/0:226:0:0,0:157,69:0:2,0:25.1:1:31.6:1:1:0:60:112:1:0:0.1 -6 106547372 . C G 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00379;SOR=0.542;LSEQ=CTTGTGTGGTATTGTCGGGA;RSEQ=TTTGCAGAAAGGCTTCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:62:26,36:248,365:0.0919:2,2:26.4:1:32.3:1:0.8922:1.06:60:124:0.0935:0:1.2 0/1:770:40:16,24:327,402:0.0519:2,2:29.2:1:31.3:1:0.62535:1.21984:60:80:0.0524:0:1.1 -6 106547453 . T A 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.06665;SOR=Inf;LSEQ=TGGATTACAGAACAAAAAAA;RSEQ=AAAAAATGCCAGTAATGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:46,195:0:2,0:24:1:28.3:1:1:0:60:39.167:1:0:0.1 0/1:290:5:3,2:59,226:0.0172:2,2:5.8:1:29.6:1:0.06737:5.70:60:10:0.0175:0:1 -6 106547470 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23211;SOR=0;LSEQ=AAATAAAAAATGCCAGTAAT;RSEQ=TCGGTTCTGCCCCTTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:27,149:0.0112:2,2:19.5:1:30.5:1:0.29061:5.44:60:4:0.0114:0:1 0/0:192:0:0,0:29,163:0:2,0:23.4:1:31.2:1:1:0:60:384:1:0:0.1 -6 106553096 . G A 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CAAGAGCTCCAGCCCTCACA;RSEQ=CAGCCCTGGGAATACGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:949:92:40,52:382,474:0.0969:2,2:27.8:1:29.3:1:0.91219:1.04764:60:29.667:0.0956:0:1.2 0/0:920:0:0,0:421,499:0:2,0:24.4:1:31.4:1:1:0:60:60.333:1:0:0.2 -6 106553383 . C T 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00125;SOR=Inf;LSEQ=TGTGCCCTGTCTACAGCAAT;RSEQ=TCCTCGGTGGGGGCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:165,256:0:2,0:24.5:1:31.3:1:1:0:60:29.071:1:0:0.1 0/1:386:9:3,6:162,215:0.0233:2,2:23:1:30.3:1:0.73812:1.50544:60:18:0.0237:0:1.1 -6 106553385 . C A 43 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05458;SOR=Inf;LSEQ=TGCCCTGTCTACAGCAATCT;RSEQ=CTCGGTGGGGGCAGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:161,250:0:2,0:24.7:1:30.8:1:1:0:60:50.375:1:0:0.1 0/1:386:4:3,1:164,218:0.0104:2,2:8.8:1:21.5:1:0.32004:3.97:60:3:0.0079:0:1 -6 106553911 . GC G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.53009;SOR=0;LSEQ=TTGCATTTGCAGTAGTATGA;RSEQ=CCCCGGTTGGGGATAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:5,111:0.0169:1,0:38:1:34:1:1:0:60:4:0.0175:0:0 0/0:70:0:0,0:1,69:0:1,0:22.6:1:31.2:1:1:0:60:34:1:0:0 -6 106554163 . A G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00077;SOR=Inf;LSEQ=GCTTTTCTTAAGATATTTGC;RSEQ=TCAACACTTGAGTCTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:187,11:0:2,0:23.9:1:30.1:1:1:0:60:32:1:0:0.1 0/1:140:8:8,0:129,3:0.0571:1,0:24:1:28.8:1:1:0:60:16:0.0576:0:1 -6 106554191 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07944;SOR=Inf;LSEQ=TTGAGTCTTGGAGCAGAAAT;RSEQ=TTAGGTCTCAGAGCCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:267,46:0:2,0:23.9:1:32.3:1:1:0:60:312:1:0:0.1 0/1:237:3:1,2:202,32:0.0127:2,2:16:1:29.7:1:0.05472:12.39144:60:6:0.0128:0:1.7 -6 106554732 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51937;SOR=0;LSEQ=CCTCCCGTTGGCAACTCTTA;RSEQ=TCTTCTGGCCTTCCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:136,11:0.0134:2,2:21.5:1:31:1:0.15509:11.88091:60:4:0.0138:0:1 0/0:98:0:0,0:91,7:0:2,0:24.5:1:30:1:1:0:60:97:1:0:0.2 -6 106554760 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17037;SOR=Inf;LSEQ=GCCTTCCTGTCTCCCTTCCC;RSEQ=GCTGTCTCTCTCCCCTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:191,52:0:2,0:26:1:30.6:1:1:0:60:47.6:1:0:0.1 0/1:172:2:1,1:132,38:0.0116:2,2:28:1:30:1:0.4031:3.44171:60:4:0.0118:0:1 -6 106554762 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18511;SOR=Inf;LSEQ=CTTCCTGTCTCCCTTCCCTG;RSEQ=TGTCTCTCTCCCCTACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:190,52:0:2,0:26.9:1:31.8:1:1:0:60:59.5:1:0:0.1 0/1:184:2:1,1:135,47:0.0109:2,2:34:1:28.5:1:0.45474:2.85277:60:4:0.011:0:1 -6 106554806 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.43995;SOR=2.11877;LSEQ=GTCTGCCACAAGAGATTTAG;RSEQ=AGCACCAGCAATCTCAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:2:0,2:269,135:0.0049:2,0:1:0:23.5:1:0.11331:0:60:4:0.0051:0:1 0/1:385:4:1,3:234,147:0.0104:2,2:15.5:1:25:1:0.30366:4.75645:60:8:0.0104:0:1.3 -6 106555025 . G A 213 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=157.28537;LSEQ=GGGAACTGCGCTGCGGCCCC;RSEQ=GCGCCTGGGCTGCCCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:1:1,0:251,251:0.002:2,0:1:0:25:0:1:0:60:2:0.002:0:1 0/1:569:136:65,71:215,218:0.239:2,2:22.7:1:30.1:1:0.76815:1.07712:60:272:0.2424:0:1.1 -6 107090222 . C T 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0.77722;LSEQ=ATTACAGGCGTGAGCCACCC;RSEQ=GCCCCGCCGACTCTTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:21.5:1:32.5:1:1:0:60:4:0.4:0:2 0/1:3:1:1,0:2,0:0.3333:0,0:23:0:33:0:1:0:60:2:0.3333:0:2 -6 107090228 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=GGCGTGAGCCACCCCGCCCC;RSEQ=CCGACTCTTGTTTCTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:21.5:1:31.5:1:1:0:60:4:0.4:0:2 1/0:4:2:2,0:2,0:0.5:0,0:16.5:1:31:1:1:0:60:4:0.5:0:1.5 -6 107090369 . A G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10736;SOR=0.48278;LSEQ=GGGAAAGAGGAGAGGCACCC;RSEQ=ATATGTGTTTTCTAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:27:23,4:16,2:0.6:2,2:22.3:1:29.9:1:1:1.38141:59.3:26:0.5909:0:2.1 0/1:55:23:18,5:24,8:0.4182:2,2:20.6:1:30.2:1:1:1.20:60:46:0.4259:0:2 -6 107090393 . C G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27719;SOR=0.63826;LSEQ=TGTGTTTTCTAGGCCTTTTA;RSEQ=AAAACAGGGAGTTGTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:30:25,5:28,3:0.4918:2,2:29.3:1:31.9:1:0.47293:1.84778:59.4:60:0.5:0:2 0/1:63:24:20,4:31,8:0.381:2,2:30.7:1:32.2:1:1:1.29:60:48:0.381:0:2 -6 107090441 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49813;SOR=0;LSEQ=TGTGAACCTATAAGAAAGGT;RSEQ=ATGTGGACATCAAGGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:94,37:0.015:2,2:18.5:1:28.5:1:0.49134:2.5202:60:4:0.0152:0:2 0/0:131:0:0,0:90,41:0:2,0:20.6:1:31.1:1:1:0:60:130:1:0:0.3 -6 107090462 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24806;SOR=0;LSEQ=ATGTGGACATCAAGGGAATG;RSEQ=GTATTGTTCAAAAAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:118,73:0.0104:2,2:20.5:1:29.5:1:1:1.61221:60:4:0.0105:0:1.5 0/0:194:0:0,0:111,83:0:2,0:21.5:1:30.1:1:1:0:59.9:63.667:1:0:0.2 -6 107090513 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2492;SOR=Inf;LSEQ=GTTACCATGGCAAAACTGGA;RSEQ=AGTACACAGTGTTCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:132,139:0:2,0:28.6:1:31.6:1:1:0:60:89.333:1:0:0.2 0/1:286:3:2,1:133,150:0.0105:2,2:29.3:1:28.3:1:0.60373:2.25:60:6:0.0106:0:1 -6 107090588 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24551;SOR=Inf;LSEQ=AGATTCTTGCCAAGAGAATG;RSEQ=ATGTGCATATTGAGCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:3,81:0:1,0:26.3:1:30.3:1:1:0:60:41:1:0:0.2 0/1:83:2:1,1:7,74:0.0241:2,2:30:1:30.5:1:0.18454:9.96:60:4:0.0247:0:1 -6 107090614 . C A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05548;SOR=0.36311;LSEQ=CATATTGAGCACAGTAAGTA;RSEQ=TGTAAGAGCCGAGATAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:15:1,14:1,44:0.25:1,1:24.9:1:31.9:1:0.44068:3.07:60:30:0.2542:0:1.1 0/1:56:6:0,6:5,45:0.1071:2,0:17.2:1:30.5:1:1:0:60:12:0.1071:0:1 -6 108424797 . AG A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATAATAAAAAGAAAAAA;RSEQ=AAACAAGTTCACTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:35.5:1:29:1:1:0:60:4:1:0:0 -6 108425743 . C T 57 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCTCGATCGCCTGACCT;RSEQ=GTGATCCGCCTGCCTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:41:0:32:0:1:0:40:2:1:0:1 1/1:4:4:4,0:0,0:1:0,0:26.3:1:28.8:1:1:0:55:8:1:0:1 -6 108425786 . A G 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CCAAAGTGCTGGGATTACAG;RSEQ=CATGAGCCACTGCGCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:39.5:1:32.5:1:1:0:60:4:1:0:1 0/0:3:0:0,0:2,1:0:2,0:15.3:1:31:0:1:0:60:6:1:0:0.3 -6 108425807 . CTTA C 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CATGAGCCACTGCGCCCGGC;RSEQ=TTATTATTATTTTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:19.2:1:32.4:1:1:0:60:10:1:0:0.8 0/1:13:2:1,1:7,4:0.1538:2,2:22:0:30.5:1:1:1.67325:60:4:0.1538:0:0 -6 108425822 . T G 51 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.29551;SOR=0.25881;LSEQ=CCGGCCTTATTATTATTATT;RSEQ=TTTTTGAGATAGGGTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,1:0.3:2,0:14.3:1:32.7:1:1:0:60:6:0.3:0:1 0/1:21:2:1,1:13,6:0.0952:2,2:4.5:1:31:1:1:2.08171:60:4:0.0952:0:1 -6 108425901 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52344;SOR=Inf;LSEQ=AGTAGGAGCTCTGGAAAGAG;RSEQ=AAATAGGAGGTAAGAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:0:2,0:23.3:1:30.3:1:1:0:60:25:1:0:0.2 0/1:43:2:1,1:18,23:0.0465:2,2:5.5:1:27.5:1:1:1.27:60:4:0.0465:0:1 -6 108882647 . TCGGCGG T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=3;SSF=0.47059;SOR=Inf;LSEQ=GGCCGGCTCGGCCATGGCGA;RSEQ=CGGCGGCGGGAGCGGCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:32.7:1:31.2:1:1:0:57.4:18:1:0:0.2 0/1:9:2:1,1:4,3:0.2222:2,2:11.5:1:26.6:1:1:1.29098:50:4:0.2222:0.1111:0 -6 108883054 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25115;SOR=0;LSEQ=TGCGTACCCACCCCGGGCTG;RSEQ=CAGCAGGACCCGCCGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:73,180:0.0117:2,2:12.7:1:29.3:1:1:1.23:60:6:0.0121:0:1 0/0:227:0:0,0:76,150:0:2,0:23.9:1:30.7:1:1:0:60:44.2:0.9955:0:0.2 -6 108883133 . A T 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02218;SOR=Inf;LSEQ=GCGCTTGCGGGCTCCAGGGC;RSEQ=AGGGGTTGGCAGGGGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:0,66:0:1,0:22.3:1:30.6:1:1:0:60:132:1:0:0.1 0/1:43:4:0,4:0,39:0.093:1,0:24.3:1:25.8:1:1:0:60:3:0.0769:0:1.3 -6 110255274 . T C 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCCCCATGTGTTGTTCTGCA;RSEQ=TGACCTGTGACCCTGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:28:1:31.5:1:1:0:60:4:0.4:0:1 1/1:2:2:0,2:0,0:1:0,0:26.5:1:27.5:1:1:0:60:4:1:0:1 -6 110699712 . C T 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCTTGGGCCCCCTCACTCAC;RSEQ=GCCTCCCTCCTCCAGCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:30:0:32:1:1:0:60:4:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:9:0:28:1:1:1:60:4:0.5:0:1 -6 110699863 . T C 100 pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01099;SOR=0;LSEQ=AGCATCCTAACCGTGGAACA;RSEQ=GCAGATTTTTGAGGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:1:0,2:26.6:1:31.7:1:1:0:60:18:1:0:1.1 0/1:6:2:1,1:2,2:0.3333:2,2:38:0:32:0:1:1:60:4:0.3333:0:1 -6 110700046 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCTCCTGGGCAGGGGAAT;RSEQ=GCGGCACCCATCTCTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:24:1:32.4:1:1:0:60:16:1:0:1.3 1/1:5:5:2,3:0,0:1:0,2:22.8:1:30.6:1:1:0:60:10:1:0:1 -6 110700201 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22711;SOR=Inf;LSEQ=CAGGTCTAACCCATCTTTCC;RSEQ=AATTGGGCGGGGCTACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:24.4:1:28:1:1:0:60:13:1:0:0.5 0/1:26:2:1,1:12,12:0.0769:2,2:29:1:29:1:1:1:60:4:0.0769:0:1 -6 110700229 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.01522;LSEQ=CGGGGCTACCCTGCAGGATC;RSEQ=CCAATAATGCCAGCCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:7,9:0,0:0.9412:0,2:24.6:1:29.1:1:1:0:60:15:0.9375:0:1.1 0/1:13:2:0,2:5,6:0.1538:2,0:22:1:29.5:1:0.48718:0:60:4:0.1538:0:1 -6 110700656 . A G 79 d7;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00466;SOR=0;LSEQ=ATGAATAGGGCCTGAAGTGA;RSEQ=CCCCCAGCAACCTGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1:0,2:27.8:1:30.8:1:1:0:60:12:1:0:1.2 0/1:7:1:1,0:4,2:0.1429:2,0:47:0:34:0:1:0:60:2:0.1429:0:1 -6 110700703 . G GA 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.52923;SOR=Inf;LSEQ=AGAAGAGGGGCCTGACTATT;RSEQ=AAAAAAAAACAAGCCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,4:0:2,0:19.8:1:31.1:1:1:0:60:16:1:0:0.6 0/1:17:2:1,1:11,4:0.1176:2,2:19.5:1:28:1:0.51471:2.56905:60:4:0.1176:0:0 -6 110700892 . T C 29 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TCTCCTCCAAATGATTGCAA;RSEQ=GTCTCTCCATCAGGGGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:30:0:29.5:1:1:0:60:4:0.6667:0:1.5 0/0:5:0:0,0:2,3:0:2,0:27:1:30.4:1:1:0:60:10:1:0:0 -6 110701451 . A G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAACACCATTAAGATGCTCT;RSEQ=TGAGAAGATCAATCCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:43:0:29:0:1:0:60:2:1:0:0 -6 111995666 . A G 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGTGTCAAAAAAGCCTCC;RSEQ=ATCTCAGGCCCATGTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:793:0:0,0:582,211:0:2,0:23.9:1:30.1:1:1:0:60:131.167:1:0:0.1 0/1:783:32:23,9:509,241:0.0409:2,2:24.1:1:28.5:1:0.70282:1.21:60:15:0.039:0:1.1 -6 111996251 . G T 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACTGAGCTGCTCCCAGG;RSEQ=TGGGGACAACTGGATACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:35:1:32:0:1:0:60:6:0.6:0:1.7 0/0:1:0:0,0:1,0:0:0,0:47:0:33:0:1:0:60:2:1:0:1 -6 112015373 . T C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0.10368;LSEQ=ACCCACCCACCAAAAACCAA;RSEQ=ATCTCATCCCTCCACTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:47:46,1:7,0:0.8704:0,1:23.6:1:32.3:1:1:0:60:46:0.8679:0:1.1 0/1:20:8:7,1:11,1:0.4:2,2:12:1:31:1:1:1.53525:60:16:0.4:0:1.1 -6 112017435 . C T 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.67383;SOR=0.94916;LSEQ=ATTTCTCTCCCCTAAACAAC;RSEQ=CCTTAAGGCACTGTGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:672:241:170,71:304,127:0.3586:2,2:23.3:1:30.1:1:1:1.00:60:39.167:0.3577:0:1.1 0/1:548:190:133,57:251,107:0.3467:2,2:23.2:1:29:1:1:1.00533:60:16.273:0.3352:0:1.2 -6 112021529 . A G 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=AGCAGAACACATGTAATGAC;RSEQ=ACACTCATAAGTGTAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:0:0,0:48,322:0:2,0:23.6:1:29.9:1:1:0:60:40.111:1:0:0.2 0/1:312:10:2,8:41,261:0.0321:2,2:15.9:1:28.7:1:0.63336:1.59:60:9:0.029:0:1.1 -6 112024350 . TAC T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.56086;SOR=3.22196;LSEQ=CAAGGATGCACACACACATG;RSEQ=ACACACACAGCATCTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:0,1:2,155:0.0063:1,0:25:0:31:0:1:0:60:2:0.0064:0:0 0/1:99:2:0,2:2,94:0.0202:1,0:10:1:31.5:1:1:0:60:4:0.0204:0.0101:0.5 -6 112025063 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51665;SOR=0;LSEQ=TAGAGCCTGGAGGGAAGACT;RSEQ=AAAACAGGACTCCACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:137,3:0.0141:1,0:40:1:31.5:1:1:0:60:4:0.0144:0:1 0/0:96:0:0,0:94,2:0:1,0:20.9:1:32.6:1:1:0:60:192:1:0:0.1 -6 112025352 . C A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09954;SOR=5.94145;LSEQ=TATTTTGAAATAGTCATTTA;RSEQ=AAAATGCAACAGCATAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:1:1,0:77,417:0.002:2,0:1:0:26:0:0.15758:0:60:2:0.0021:0:1 0/1:420:5:3,2:79,336:0.0119:2,2:9:1:24.2:1:0.05325:6.34:60:4:0.0096:0:1.6 -6 112025371 . CT C 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.37793;SOR=1.89162;LSEQ=ACAAAATGCAACAGCATAGG;RSEQ=TTTTTTTTGCCCATGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:5:0,5:13,313:0.0151:1,0:25:1:30.9:1:1:0:60:10:0.0155:0.003:0 0/1:248:7:0,7:14,227:0.0282:2,0:20.4:1:32.6:1:1:0:60:14:0.0288:0.0081:0.3 -6 112026587 . C TTT 25 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=GTGTTCATCATCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:25.8:1:1:0:35:4:1:0.5:2 -6 112029020 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08797;SOR=Inf;LSEQ=CTGAAAAACTCAGCCTTAAT;RSEQ=ACTGCTGTGAATTTCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:204,2:0:1,0:26.1:1:31.1:1:1:0:60:67.667:1:0:0.1 0/1:166:3:3,0:157,6:0.0181:1,0:29.7:1:29.3:1:1:0:60:6:0.0183:0:3 -6 112029331 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=3.03088;LSEQ=ACCTAATCATCCTGCCACCC;RSEQ=ATTTCTCCAACCTATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:34:0,34:3,135:0.1977:1,1:30.6:1:30.7:1:1:0:60:68:0.2:0:1.1 0/1:105:45:1,44:1,59:0.4286:1,1:29.9:1:30.6:1:1:1.34:60:90:0.4286:0:1.2 -6 112029402 . C T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01216;SOR=4.03628;LSEQ=AAGGTCAGAAGGTTCCAGTT;RSEQ=GAGTCAGCCATGAGATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:8:0,8:1,41:0.16:1,0:21:1:30.1:1:1:0:60:16:0.1633:0:1.5 0/1:25:11:1,10:0,14:0.44:1,2:14:1:31.1:1:0.44:0:60:22:0.4583:0:1.7 -6 112029505 . G C 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTCTTGGTAGGGGGCATTTT;RSEQ=CTTGGTTAGTGTCCTTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:28:1:30.3:1:1:0:60:12:0.8571:0:1 0/0:1:0:0,0:1,0:0:0,0:41:0:33:0:1:0:60:2:1:0:0 -6 112035002 . A G 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTCATTCAAGAGTGGGT;RSEQ=AAATCACTTCTTCTAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:25.8:1:32.5:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 112041359 . T C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.54042;LSEQ=GAGTAATTGACAAGGCTCAC;RSEQ=GTTGGCTATTTCAGGCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:48:0,48:5,227:0.1714:1,1:21.1:1:28.6:1:0.59198:0:60:11:0.1618:0:1.1 1/0:185:99:1,98:2,84:0.5351:1,1:24.4:1:29.4:1:0.59817:2.32295:60:98:0.5385:0:1 -6 112042878 . C G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGCCTCCCAAAGTACTGG;RSEQ=ATTACAGGCGTGAACCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:31.5:1:1:0:60:4:1:0:1 -6 112111363 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49701;SOR=Inf;LSEQ=AAGATATCCAGCTAGCACAC;RSEQ=ACATACCTGGAGAATCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:31,52:0:2,0:27.2:1:30.9:1:1:0:60:19.75:1:0:0.1 0/1:84:2:1,1:31,51:0.0238:2,2:26:1:31.5:1:1:1.63:60:4:0.0241:0:1 -6 112111450 . TACAC T 50 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=47;MSI=25.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTAGTTCTGAACCTTAGA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,3:0.25:0,0:37:1:31.7:1:1:0:60:6:0.25:0:0 0/0:3:0:0,0:0,2:0:0,0:24:1:31.5:1:1:0:60:4:0.6667:0:0 -6 115553700 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TGGGGTTCCATTTGTAAGAC;RSEQ=ATCTGTAGCTTGATGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:19:1:29.5:1:1:2.23609:44.5:4:0.2222:0:2 0/0:5:0:0,0:5,0:0:0,0:22.2:1:30.8:1:1:0:44.6:10:1:0:0 -6 115553830 . C T 111 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00024;SOR=0.04802;LSEQ=AAGGGAGAGGCAATGTTGCC;RSEQ=AACTCCAGAGGTTGGTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:7,7:10,8:0.4375:2,2:30.9:1:29.4:1:1:1.24128:60:28:0.4375:0:1.1 0/1:29:1:1,0:15,13:0.0345:2,0:43:0:31:0:1:0:60:2:0.037:0:1 -6 115553884 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.50906;SOR=Inf;LSEQ=ATTGTCTGATTTCGGAAGCC;RSEQ=TTTCCTGTAAACGCCAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:0:2,0:20.9:1:30:1:1:0:59.4:23:1:0:0.5 0/1:35:2:1,1:14,19:0.0571:2,2:34:1:29:1:1:1.35:60:4:0.0571:0:1 -6 116233469 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21438;SOR=Inf;LSEQ=AAAATTATTAAGAAGAAACA;RSEQ=CAAGGGTAAGGGGGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:51,47:0:2,0:26.8:1:30.9:1:1:0:60:31.667:1:0:0.2 0/1:85:2:1,1:40,43:0.0235:2,2:9:1:31.5:1:1:1.07:60:4:0.0241:0:1 -6 116417095 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49884;SOR=Inf;LSEQ=AAAGGCTTCTGATATCAGAC;RSEQ=ATGCCTTTCAAACTCTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:84,50:0:2,0:23.3:1:30:1:1:0:59.7:43.667:1:0:0.2 0/1:144:2:1,1:80,61:0.0139:2,2:37.5:1:31:1:1:1.30895:60:4:0.0144:0:1 -6 116417316 . G C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22862;LSEQ=ACAACTTCTACCGAGGACCC;RSEQ=TGGACAAACCCACTGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:0,5:0.2857:0,2:44:1:31:1:0.28571:0:60:4:0.2857:0:1 0/1:6:2:1,1:1,3:0.3333:2,2:29.5:1:32.5:1:1:2.45:60:4:0.3333:0:1 -6 116470561 . A G 230 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07917;SOR=1.28517;LSEQ=TAGACAGTGTGTCTTTACCA;RSEQ=ACTGGCTCTGCATTTTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:152:75,77:139,144:0.3494:2,2:26.5:1:31.2:1:1:1.01:60:37:0.3507:0:1.1 0/1:426:174:84,90:126,125:0.4085:2,2:25.8:1:31:1:0.76731:1.0798:60:57:0.4091:0:1.1 -6 117609387 . T C 100 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGGGAGAAGGGAGAGCAG;RSEQ=GTTTCCCTTCCAGACTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:0.8889:0,0:39.3:1:33.5:1:1:0:60:16:0.8889:0:1 1/1:1:1:1,0:0,0:1:0,0:42:0:34:0:1:0:60:2:1:0:1 -6 117609529 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0.17702;LSEQ=CAGAACCAAGATTAGAAATC;RSEQ=GGAACGTTGCATTGTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:48:48,0:20,0:0.7059:1,1:22.3:1:30.2:1:1:0:60:96:0.7059:0:1 0/1:34:10:10,0:24,0:0.2941:1,0:19.6:1:31:1:1:0:60:20:0.303:0:1 -6 117609569 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.50831;SOR=0;LSEQ=TTGGAGTTATAGACCACCAT;RSEQ=ACATTTATCATTCTAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:134,12:0.0135:2,2:23:1:28.5:1:0.16851:10.76875:60:4:0.0137:0:1.5 0/0:111:0:0,0:101,10:0:2,0:21.2:1:32.1:1:1:0:60:222:1:0:0.2 -6 117622028 . A G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08168;SOR=1.88152;LSEQ=ATGATGACAAAGGTGCCAGT;RSEQ=TATTATTCTTTTTGCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:22:22,0:115,2:0.1583:1,1:16.2:1:32.7:1:1:0:60:44:0.1594:0:1.1 0/1:84:22:22,0:59,3:0.2619:1,1:21.6:1:32:1:0.56339:0:60:44:0.2651:0:1.1 -6 117622184 . G C 213 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=136.98844;LSEQ=TGTTGTTTGCTTCATCTCTG;RSEQ=ACTTATAAATGCTATTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:876:1:1,0:483,391:0.0011:2,0:23:0:14:0:1:0:60:0:0:0:5 0/1:745:101:58,43:361,283:0.1356:2,2:26.2:1:32:1:0.82977:1.06:60:202:0.1369:0:2.6 -6 117622188 . T G 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTTTGCTTCATCTCTGGACT;RSEQ=ATAAATGCTATTTAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:872:0:0,0:470,399:0:2,0:23.9:1:29.1:1:1:0:60:85.9:0.9965:0:0.1 0/1:751:106:61,45:356,286:0.1411:2,2:25.1:1:31.6:1:0.75175:1.09:60:212:0.1423:0:2.6 -6 117622233 . C T 214 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=240.67423;LSEQ=TCTGAATAACTGAAGTTGGT;RSEQ=CTGAATTCTATGAAAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1111:1:0,1:560,549:9e-04:2,0:1:0:26:0:0.4955:0:60:2:9e-04:0:1 0/1:1006:179:90,89:424,402:0.1779:2,2:24.3:1:28.6:1:0.80517:1.04298:60:34.8:0.1765:0:1.8 -6 117622521 . T A 27 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.03623;SOR=Inf;LSEQ=CTTTTGAAAAGCTGACATTA;RSEQ=TTTAACAGTTATTATTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:1,18:0:1,0:21.7:1:29:1:1:0:60:18:1:0:0.3 0/1:5:2:0,2:0,3:0.4:0,0:21.5:1:27:0:1:0:60:4:0.4:0:1 -6 117629650 . A T 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=GTGTGTATACTCTCTCTCTC;RSEQ=CACACACACACATACACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:28.7:1:31.8:1:1:0:60:12:0.75:0:1.5 0/0:1:0:0,0:1,0:0:0,0:49:0:32:0:1:0:60:2:1:0:0 -6 117629661 . CAT C 65 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCACACACACACA;RSEQ=ACACTCGGAGTGCTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:6,0:0.3636:0,0:25.3:1:32.8:1:1:0:60:8:0.4:0:0.5 0/0:1:0:0,0:1,0:0:0,0:37:0:32:0:1:0:60:2:1:0:0 -6 117629663 . T C 85 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTCACACACACACACA;RSEQ=ACACTCGGAGTGCTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:0,0:0.5455:0,0:19.7:1:33.2:1:1:0:60:12:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:36:0:32:0:1:0:60:2:1:0:0 -6 117630188 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10515;SOR=Inf;LSEQ=TTTCCTGGGGCTAGCAGGGT;RSEQ=TACTTTGTCAGTGTATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:3,171:0:1,0:25.9:1:32.4:1:1:0:60:33.8:1:0:0.1 0/1:84:2:1,1:3,79:0.0238:1,2:26.5:1:30:0:0.09352:22.95:60:4:0.0241:0:1.5 -6 117631157 . TA T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.19836;SOR=Inf;LSEQ=GGTCTTCTGTTTTCTCACAT;RSEQ=AAAAAGCAAGATTAGATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:205,25:0:2,0:21.9:1:28.5:1:1:0:60:75.667:0.9956:0:0.1 0/1:186:2:1,1:157,27:0.0108:2,2:15:1:27.5:1:0.2791:5.72824:60:4:0.0108:0.0054:0.5 -6 117631431 . T G 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30226;LSEQ=CACGGAAACAAGGCAATTTC;RSEQ=AGCTGCCAGATCCCTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:239:100,139:210,318:0.3112:2,2:24:1:30.4:1:0.63371:1.09:60:238:0.3148:0:1.1 0/1:633:76:36,40:234,322:0.1201:2,2:23.4:1:29.5:1:0.38958:1.24:60:152:0.1218:0:1.2 -6 117631463 . TTAA T 174 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0;SOR=30.75091;LSEQ=CCCTGTGGCAGAAGTTATAT;RSEQ=TAATAATAATAATAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:3:2,1:108,336:0.0067:2,2:33.7:1:31.3:1:0.15123:6.19:60:6:0.0068:0:0 0/1:355:61:15,46:91,202:0.1718:2,2:30:1:29.5:1:0.35889:1.38031:60:122:0.1728:0.0254:0.3 -6 117631479 . T C 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.01228;SOR=0;LSEQ=ATATTTAATAATAATAATAA;RSEQ=AACAACAATAAAGTTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:9:1,8:65,286:0.0249:2,2:17.1:1:32.9:1:1:1.81566:60:18:0.0264:0:1.3 0/0:273:0:0,0:61,204:0:2,0:28.4:1:27.3:1:1:0:59.9:23.091:0.9922:0:0.2 -6 117631500 . A T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17368;SOR=Inf;LSEQ=AACAACAATAAAGTTCCAGA;RSEQ=ATCAAAGAAGTAGCCCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:20,255:0:2,0:26.2:1:30.1:1:1:0:60:67.75:1:0:0.4 0/1:197:2:1,1:29,166:0.0102:2,2:24.5:1:24.5:1:0.28204:5.64:60:4:0.0102:0:1 -6 117631558 . AC TT 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTATTTTTTTTTTTTTT;RSEQ=TTTAAGTTCTGGATTACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:1,94:0.0202:1,0:5:0:32.5:0:1:0:60:4:0.0208:0:1 0/0:41:0:0,0:0,40:0:1,0:19.9:1:30.5:1:1:0:59.4:80:1:0:1 -6 117631666 . T C 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTCATCTAGATTTTAAGCCC;RSEQ=GCCTGCATTAGGTATTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:0,5:0.375:0,2:16.7:1:30:1:0.375:0:60:6:0.375:0:1 0/0:2:0:0,0:0,2:0:0,0:24.5:1:31.5:1:1:0:60:4:1:0:0 -6 117632139 . G T 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCACTACAGGTGATTATT;RSEQ=TGCCAATATCCGTAATAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:509:0:0,0:358,151:0:2,0:25:1:31.9:1:1:0:60:71.714:1:0:0.1 0/1:358:24:15,9:232,102:0.067:2,2:24.9:1:29.3:1:0.49702:1.3635:60:48:0.068:0:1 -6 117638124 . G A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35153;SOR=0.44647;LSEQ=CGGGCTCACATGACCAGAAA;RSEQ=TGCCAGAATGTTAGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:13:13,0:20,0:0.3939:1,1:29.5:1:29.5:1:1:0:60:26:0.3939:0:1.1 0/1:18:4:4,0:13,1:0.2222:1,0:29.5:1:31.3:1:1:0:60:8:0.2222:0:1 -6 117638493 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16463;SOR=Inf;LSEQ=GAAGCAGGAGTCCTAGCCGA;RSEQ=GGTCTTTATGGAGTACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:22,216:0:2,0:23.8:1:31.1:1:1:0:60:38.667:1:0:0 0/1:163:2:0,2:21,140:0.0123:2,0:12:1:32:0:1:0:60:4:0.0125:0:1.5 -6 117638495 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1636;SOR=Inf;LSEQ=AGCAGGAGTCCTAGCCGAGG;RSEQ=TCTTTATGGAGTACAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:16,210:0:2,0:24.2:1:32.3:1:1:0:60:112:1:0:0 0/1:154:2:1,1:17,135:0.013:2,2:21:1:27:1:0.22078:7.75:60:4:0.0132:0:1 -6 117638546 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04724;SOR=Inf;LSEQ=TAGTTTCCTTCAAAACCCCT;RSEQ=ACTTAGTGTCTCTAACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:1,82:0:1,0:24.1:1:31.5:1:1:0:60:82:1:0:0.1 0/1:48:3:0,3:0,45:0.0625:1,0:17:1:31.7:1:1:0:60:6:0.0625:0:1 -6 117639026 . C T 64 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCATTTGAGAGAACTCTCT;RSEQ=TTACTGGGTATACTTGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:5,1:0.4:2,0:25.5:1:32:1:1:0:60:8:0.4444:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 117639104 . T C 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAACAGCTTCAGAATTCA;RSEQ=TTGCAAAACATGCTCCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:15,1:0,0:1:0,1:24.6:1:32.1:1:1:0:60:32:1:0:1.3 1/1:4:4:4,0:0,0:1:0,0:28:1:32.5:1:1:0:60:8:1:0:1 -6 117639153 . T C 132 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08176;SOR=0.15516;LSEQ=AAAGAAAGGAGAACCTTTTG;RSEQ=CTGAGGATTGCCTGTACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:18:18,0:29,1:0.375:1,1:24.1:1:31.7:1:1:0:60:17:0.3617:0:1.3 0/1:12:1:1,0:11,0:0.0833:0,0:14:0:29:0:1:0:60:2:0.0909:0:1 -6 117639262 . G A 131 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=0.10731;LSEQ=TGTTGTTTTAGTCATGATCC;RSEQ=TTAAGTCATGTCATTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:22:19,3:191,36:0.0884:2,2:28.9:1:29.6:1:1:1.19:60:44:0.0894:0:1.1 0/1:195:2:2,0:158,35:0.0103:2,0:27:1:29.5:1:1:0:60:4:0.0103:0:1 -6 117639266 . A T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31056;LSEQ=GTTTTAGTCATGATCCGTTA;RSEQ=GTCATGTCATTTTGGGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:89:76,13:143,31:0.3384:2,2:23.3:1:31.1:1:0.60167:1.27:60:88:0.3424:0:1 0/1:212:29:23,6:146,37:0.1368:2,2:22.4:1:29.7:1:1:1.02924:60:28:0.1346:0:1.1 -6 117639301 . C T 123 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=20.95554;LSEQ=GGTGTTAAAAATAAGTCAAG;RSEQ=GGACTTAAAACTTCTTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:1:0,1:336,148:0.0021:2,0:1:0:26:0:0.30722:0:60:2:0.0021:0:1 0/1:457:19:14,5:278,160:0.0416:2,2:22.3:1:29.1:1:0.46788:1.61:60:38:0.0419:0:1.1 -6 117639419 . T C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.28051;LSEQ=GAACCCTTCTTCAAAGTCTA;RSEQ=ACAACATAAAAACAAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:797:260:110,150:213,323:0.3262:2,2:25:1:31.9:1:0.48976:1.11:60:85.667:0.3257:0:1.1 0/1:703:84:29,55:273,346:0.1195:2,2:23.6:1:31.4:1:0.10131:1.49557:60:83:0.1189:0:1.2 -6 117639516 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13627;SOR=Inf;LSEQ=TTGTTCTGTAATATCTACCC;RSEQ=GAAAGCTGGAAACAGATCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:13,169:0:2,0:24.1:1:30.2:1:1:0:60:90:1:0:0.1 0/1:107:2:1,1:10,95:0.0187:2,2:24.5:1:32:0:0.19591:9.11:60:4:0.0192:0:2 -6 117639620 . G T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07585;SOR=0.1936;LSEQ=AAGAATATGCAAAATAAGAG;RSEQ=TCTAGTAATGTTTACACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:0,14:0,13:0.5185:1,1:24.1:1:31:1:1:0:60:28:0.5185:0:1 0/1:12:2:0,2:0,10:0.1667:0,0:29.5:1:32:0:1:0:60:4:0.1667:0:1 -6 117640388 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACATTAAGTATACTAT;RSEQ=ATAAATAATCATGTAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:25:1:30:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 117641246 . C A 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28427;LSEQ=CTCCACATATATAGGGTGTA;RSEQ=AAGTTTGTGTTGGTATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2156:694:352,342:753,709:0.3219:2,2:24.6:1:30.2:1:0.74697:1.03188:60:137.8:0.3241:0:1.2 0/1:1977:235:122,113:903,838:0.1189:2,2:24.3:1:30:1:1:1.00:60:470:0.12:0:1.2 -6 117641330 . C T 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26401;LSEQ=ATTGTGTGTTTTATGTGACA;RSEQ=GGTGATGTGGAACTTTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1883:606:284,322:586,691:0.3218:2,2:23.6:1:30.3:1:0.69262:1.04:60:54.091:0.3204:0:1.3 0/1:1851:206:101,105:769,874:0.1113:2,2:24.3:1:29.6:1:0.55443:1.09:60:67.667:0.1107:0:1.3 -6 117641474 . G A 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30115;LSEQ=ATTGCCTCAACACTTTTATT;RSEQ=TAGCTTGTTGAGTCAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1200:397:221,176:420,383:0.3308:2,2:25:1:29.4:1:0.29583:1.14:60:98.25:0.3311:0:1.1 0/1:965:125:57,68:451,388:0.1295:2,2:24.7:1:28.9:1:0.10244:1.3862:60:40.667:0.1282:0:1.1 -6 117641819 . T G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28657;LSEQ=CTCTAAACAGCTGATTTAGA;RSEQ=CACCTTTGTGTCTACTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1504:483:237,246:493,526:0.3211:2,2:25.3:1:32:1:0.82512:1.03:60:119.75:0.3236:0:1.1 0/1:1324:158:82,76:569,597:0.1193:2,2:25.5:1:32.1:1:0.49789:1.13:60:316:0.1209:0:1.1 -6 117642070 . TA T 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27418;LSEQ=TTGACTTAAGGCTGACCACG;RSEQ=ACACAAGGCTCTCAAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1670:517:243,274:532,621:0.3096:2,2:26.2:1:30:1:0.75043:1.04:60:257.5:0.3102:0.0317:0.1 0/1:1398:153:72,81:565,676:0.1094:2,2:24.1:1:29.9:1:0.73149:1.06:60:306:0.1105:0.0172:0.2 -6 117643433 . T C 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.33547;LSEQ=TTTTCCAACTTGAAATGTTC;RSEQ=CACCACCTCGCTTCACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1415:433:226,207:500,482:0.306:2,2:24.2:1:31.1:1:0.68633:1.05:60:107.25:0.3062:0:1.1 0/1:1180:152:75,77:500,526:0.1288:2,2:24.1:1:30:1:0.93079:1.02:60:49.667:0.1276:0:1.1 -6 117643659 . C G 290 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.31051;LSEQ=GTCTTCCCACACAGGCATGT;RSEQ=TTAACTCCCTCATTAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1675:532:279,253:597,540:0.3176:2,2:25.2:1:32.1:1:1:1.00253:60:52.2:0.3171:0:1.1 0/1:1418:179:94,85:606,632:0.1262:2,2:25.5:1:31.2:1:0.38016:1.15:60:178:0.1266:0:1.1 -6 117643865 . A C 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACAATACAAATTTTAAAAT;RSEQ=ATTGTGACTGTTTTGTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:758:0:0,0:395,363:0:2,0:24:1:29.4:1:1:0:60:188.5:1:0:0.2 0/1:583:30:15,15:284,269:0.0515:2,2:22.8:1:32:1:1:1.05569:60:60:0.052:0:1.1 -6 117643897 . A G 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.44218;LSEQ=TTTGTTATTTTAATTACTCA;RSEQ=TCTTTTCTCATGCACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:888:184:113,71:413,291:0.2072:2,2:24.4:1:32.2:1:0.55546:1.12:60:91:0.2071:0:1.1 0/1:676:70:43,27:354,251:0.1036:2,2:25.9:1:31.8:1:0.70114:1.13:60:140:0.1061:0:1.1 -6 117644018 . C A 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=63.69979;LSEQ=ATTTCAAACAGAATAAAGAC;RSEQ=TTTAAGTCCTGAGAAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1424:1:1,0:694,727:7e-04:2,0:1:0:26:0:0.48875:0:60:2:7e-04:0:1 0/1:1142:49:24,25:529,563:0.0429:2,2:21.3:1:30.1:1:1:1.02:60:98:0.0433:0:1.1 -6 117644054 . T C 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20407;LSEQ=AGTCAGATATCCATAGGATG;RSEQ=CTTGGAAGCACAATAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1431:467:226,241:508,455:0.3263:2,2:24.9:1:31.4:1:0.12791:1.19044:60:50.889:0.3248:0:1.3 0/1:1101:99:48,51:484,518:0.0899:2,2:25.4:1:31.3:1:1:1.01:60:98:0.0896:0:1.3 -6 117644065 . C CAAT 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CATAGGATGTCTTGGAAGCA;RSEQ=AATAGGTTGTCTGAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1453:0:0,0:743,708:0:2,0:24.4:1:32:1:1:0:60:110.615:0.9986:0:0.5 0/1:1116:48:26,22:518,547:0.043:2,2:25.7:1:29.3:1:0.46484:1.25:60:96:0.0434:0.009:1.2 -6 117644132 . C T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21924;LSEQ=GTTTAAACAATGGTGATGTA;RSEQ=AAGAAAGCAAGCAAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1555:507:263,244:543,504:0.326:2,2:24.8:1:29.6:1:1:1.00:60:252.5:0.3271:0:1.3 0/1:1325:127:65,62:611,585:0.0958:2,2:23.8:1:28.8:1:1:1.00:60:126:0.0958:0:1.2 -6 117644797 . T C 173 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=54.00526;LSEQ=AAATAAACAAGAATGTATGA;RSEQ=CACTGTGATAACTCTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1662:1:0,1:804,857:6e-04:2,0:17:0:19:0:1:0:60:0:0:0:1 0/1:1459:46:24,22:709,703:0.0315:2,2:27.2:1:31.4:1:0.88119:1.08:60:45:0.0313:0:1.3 -6 117644841 . C T 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.26081;LSEQ=AATCAGTACTTGACCATTCC;RSEQ=TTTGAGGTTTTTACTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1547:473:203,270:482,589:0.3058:2,2:26.3:1:30.6:1:0.47021:1.08836:60:117.25:0.3065:0:1.8 0/1:1272:131:58,73:542,598:0.103:2,2:25.6:1:30.4:1:0.51812:1.14064:60:130:0.103:0:1.8 -6 117644866 . T C 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.35333;LSEQ=AGGTTTTTACTGCATTTTAT;RSEQ=ATCATTAAAGTAAATCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1285:397:172,225:393,494:0.3089:2,2:22.7:1:31.6:1:0.76125:1.04067:60:98.25:0.3082:0:1.9 0/1:1034:141:66,75:405,486:0.1364:2,2:24.6:1:31.4:1:0.78534:1.06:60:140:0.1362:0:1.8 -6 117645041 . C T 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25104;LSEQ=CTTCTGCAAAAGAGGCCCTA;RSEQ=TCATTCCAAACCAGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1763:547:287,260:646,570:0.3103:2,2:26.3:1:30.4:1:0.83658:1.02671:60:59.778:0.309:0:1.1 0/1:1400:142:78,64:657,598:0.1014:2,2:24.7:1:29.6:1:0.59518:1.11:60:141:0.1014:0:1.1 -6 117645120 . T C 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGGCCTCCCATTAATTCTA;RSEQ=ACTTTTTTCTGTACCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1710:0:0,0:773,937:0:2,0:24.9:1:29.4:1:1:0:60:84.5:1:0:0.2 0/1:1398:41:18,23:648,708:0.0293:2,2:26.7:1:31:1:0.63832:1.16936:60:82:0.0297:0:1.1 -6 117645239 . C T 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.28431;LSEQ=AAGAAACCTAAAAGTTGGTG;RSEQ=CCTTGCAAGTAGTTTTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1315:394:180,214:456,465:0.2996:2,2:25.4:1:30:1:0.20655:1.16574:60:97.5:0.3009:0:1.1 0/1:1061:115:55,60:449,495:0.1084:2,2:23.7:1:29:1:1:1.01:60:230:0.1107:0:1.1 -6 117645778 . C CT 135 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05777;SOR=0.48902;LSEQ=TCAAAAGCAAGGTGTTTTTG;RSEQ=TTTTTTTTGCAGAGAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1405:24:12,12:666,714:0.0171:2,2:26.8:1:29.5:1:1:1.07:60:23:0.0166:0.005:0.3 0/0:1187:10:6,4:565,609:0.0084:2,2:31:1:31:1:0.53498:1.62:60:20:0.0085:0:0.2 -6 117646289 . A G 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27077;LSEQ=GTAGCAAACTTCTGTACACA;RSEQ=CTAACTAGATAACTAACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1119:352:174,178:375,390:0.3146:2,2:25.4:1:31.8:1:0.94865:1.02:60:38.111:0.3127:0:1.1 0/1:860:95:43,52:386,379:0.1105:2,2:24.9:1:31.5:1:0.38438:1.23134:60:190:0.1115:0:1.1 -6 117646772 . T C 282 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41152;LSEQ=CTGTCAGCAGTATGCGTAAG;RSEQ=CAAGGGCACAGGCAAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1575:477:245,232:548,550:0.3029:2,2:24.9:1:31.7:1:0.62171:1.06:60:94.4:0.303:0:1.1 0/1:1385:210:103,107:584,589:0.1516:2,2:26.3:1:31.7:1:0.88095:1.03:60:104:0.1518:0:1.1 -6 117647124 . A G 176 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=73.16861;LSEQ=TTGGAAGCCTAATTAGGAGC;RSEQ=TGGAATTGATGTGGTAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2048:1:1,0:958,1087:5e-04:2,0:1:0:31:0:0.46872:0:60:2:5e-04:0:1 0/1:1737:60:33,27:802,870:0.0345:2,2:23.8:1:29.9:1:0.29569:1.33:60:59:0.0343:0:1.2 -6 117647253 . AT A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05155;SOR=0.44599;LSEQ=TTAATAGTTTGGATAATAAG;RSEQ=TATATATATATATATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:27:24,3:200,205:0.0464:2,2:19.7:1:30.7:1:4e-05:8.17:60:54:0.0655:0:0 0/1:377:8:6,2:150,159:0.0212:2,2:16.5:1:28.3:1:0.16825:3.17:58.3:7:0.0217:0:0 -6 117647313 . G T 73 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07995;SOR=2.93404;LSEQ=CACCATTATCTATTGCTAAT;RSEQ=TTAAGAATGTACTGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:945:4:4,0:546,394:0.0042:2,0:19.8:1:13.5:1:0.14478:0:60:0:0:0:3.8 0/1:649:8:5,3:357,284:0.0123:2,2:20.4:1:24.5:1:1:1.33:56.1:1.667:0.0084:0:3.6 -6 117647581 . C CA 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTTGAAGTGCTCTTTCTG;RSEQ=AAAAAATAATAAATACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1526:0:0,0:766,759:0:2,0:25:1:32:1:1:0:60:94.313:0.9993:0:0.1 0/1:1285:49:30,19:584,647:0.0381:2,2:26.4:1:29.8:1:0.07921:1.75:60:98:0.0385:0.0078:0.1 -6 117647643 . GATC G 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTATTTCTAGTTGTTCATA;RSEQ=TTCTTAGTGACTGAACGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1697:0:0,0:891,806:0:2,0:25.4:1:30.5:1:1:0:60:83.85:1:0:0.1 0/1:1249:39:17,22:636,572:0.0312:2,2:30.8:1:31.5:1:0.32861:1.43848:60:78:0.0317:0.0016:0.2 -6 117647938 . T G 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTTTCCATTTTCTCAAT;RSEQ=TTCAGTCTTTTACATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1429:0:0,0:699,728:0:2,0:25.7:1:30.3:1:1:0:60:157.556:0.9993:0:0.1 0/1:1162:37:17,20:584,539:0.0318:2,2:26.5:1:30.8:1:0.50651:1.27442:60:36:0.0312:0:1.1 -6 117648064 . C T 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24623;LSEQ=TTATATCTGAGATTCTGAGG;RSEQ=TCGTTGCTTCCTTTTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1662:483:227,256:593,585:0.2906:2,2:24.8:1:30:1:0.23452:1.14308:60:160:0.2911:0:1.1 0/1:1463:134:63,71:665,662:0.0916:2,2:24.9:1:29.8:1:0.52624:1.13199:60:268:0.0924:0:1.1 -6 117648215 . T C 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAAGGCAAGCTCAAGGTCT;RSEQ=CCATTATGTCTTCTCTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1400:101:57,44:666,632:0.0721:2,2:24.4:1:30.7:1:0.35273:1.23:60:32.667:0.071:0:1.1 0/0:1205:0:0,0:639,564:0:2,0:23.8:1:29.4:1:1:0:60:91.538:0.9992:0:0.1 -6 117648340 . C T 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23906;LSEQ=TGGGAGAATCTGGTTCTATT;RSEQ=CTGCTAATTGACTCATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2027:649:330,319:711,662:0.3202:2,2:25.5:1:30:1:0.7032:1.03822:60:80.125:0.32:0:1.1 0/1:1720:174:90,84:772,772:0.1012:2,2:25.6:1:29.4:1:0.68972:1.07:60:173:0.1017:0:1.2 -6 117648481 . A C 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGAGCTGAGGGTCCCTTT;RSEQ=AGGACCATCCTGAGCAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1735:0:0,0:847,883:0:2,0:24.8:1:29.1:1:1:0:60:77.636:0.9971:0:0.1 0/1:1542:68:32,36:732,739:0.0441:2,2:24.8:1:30.9:1:0.71058:1.11426:60:67:0.0439:0:1.2 -6 117649173 . C T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23609;LSEQ=TCCCGCTGATACGTTGGTTT;RSEQ=AGACTTCTAACCTCTAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1805:621:318,303:584,594:0.344:2,2:24.2:1:29.4:1:0.51942:1.07:60:1242:0.3463:0:1.1 0/1:1607:177:90,87:704,725:0.1101:2,2:23.8:1:28.9:1:0.74999:1.07:60:176:0.1101:0:1.2 -6 117649988 . T C 294 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29304;LSEQ=TTTCAGTCCCTGGGAACACA;RSEQ=TGCAAACTGTAATCTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1838:578:284,294:609,647:0.3145:2,2:24.1:1:32.1:1:0.8017:1.03:60:191.667:0.317:0:1.1 0/1:1663:197:100,97:714,749:0.1185:2,2:23.3:1:31.5:1:0.64891:1.08:60:97.5:0.1183:0:1.2 -6 117650131 . A T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2378;LSEQ=GAGAGTATTCACCTTGCTAA;RSEQ=GCAAATTATCATCAGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1650:572:291,281:525,552:0.3467:2,2:25.3:1:30.5:1:0.43771:1.09:60:189.667:0.3489:0:1.1 0/1:1384:155:76,79:606,621:0.112:2,2:25.8:1:29.7:1:1:1.01436:60:310:0.1127:0:1.1 -6 117650800 . G A 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.4108;LSEQ=AAACCATAATAAGTGTGTGA;RSEQ=TCCTTCACCGGCAAGGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:587:154:68,86:198,234:0.2624:2,2:23.7:1:30.3:1:0.77747:1.06998:60:153:0.2647:0:1.1 0/1:471:60:31,29:188,223:0.1274:2,2:23.8:1:29.2:1:0.40855:1.27:60:29:0.1255:0:1.2 -6 117650964 . G T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01752;SOR=Inf;LSEQ=GCGAGCGAGCAGGCTACCCA;RSEQ=CCGGGGAAATTGCTTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:309,290:0:2,0:25.7:1:31.8:1:1:0:60:38.933:1:0:0.1 0/1:483:5:1,4:241,237:0.0104:2,2:13:1:23.4:1:0.21583:4.05692:60:4:0.0084:0:1.6 -6 117651024 . G A 123 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=10.64167;LSEQ=GATTGGAAGATCCCACTCTC;RSEQ=ATCCCATGCCACCGAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:2:1,1:296,320:0.0032:2,2:7.5:1:29.5:1:1:1.08:60:4:0.0033:0:1 0/1:539:18:8,10:237,284:0.0334:2,2:23:1:29.6:1:1:1.04306:60:36:0.0338:0:1.2 -6 117651145 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5332;SOR=0;LSEQ=GGGGTGACCAGCACAGGCTT;RSEQ=TGCTGCCTGCTGTCTAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:58,122:0.011:2,2:13:1:28.5:1:0.54447:2.09:60:4:0.0111:0:1 0/0:106:0:0,0:36,70:0:2,0:20.8:1:31.8:1:1:0:60:105:1:0:0.2 -6 117651172 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12619;SOR=Inf;LSEQ=CTGCTGTCTAAGCCCTTTGA;RSEQ=CTCCTTGAGGGAGGGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:59,98:0:2,0:23.3:1:32:1:1:0:60:77.5:1:0:0.1 0/1:87:2:1,1:39,46:0.023:2,2:23.5:1:27.5:1:1:1.18:60:4:0.0233:0:1 -6 117651192 . C A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00219;SOR=Inf;LSEQ=GCTCCTTGAGGGAGGGGCAG;RSEQ=AGCCAGCACTGGGACTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:76,97:0:2,0:24.4:1:31.9:1:1:0:60:85.5:1:0:0.1 0/1:100:6:2,4:47,47:0.06:2,2:26.5:1:29.7:1:0.67814:1.98662:60:12:0.0612:0:1 -6 117651240 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16779;SOR=Inf;LSEQ=AACACGCTAATCTCCCTGGG;RSEQ=GGCGGGGAGAAATGCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:118,109:0:2,0:24.9:1:31.1:1:1:0:60:74.667:1:0:0.2 0/1:158:2:1,1:83,72:0.0127:2,2:39:0:31.5:1:1:1.15173:60:4:0.0129:0:1.5 -6 117651285 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50114;SOR=0;LSEQ=TTCTATAGCTCCAGGCTGTG;RSEQ=TTTTCCCCTGCGGGAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:100,84:0.0107:2,2:28:1:29.5:1:1:1.18935:60:4:0.0109:0:1.5 0/0:162:0:0,0:89,73:0:2,0:23.3:1:31.3:1:1:0:59.9:31.4:1:0:0.2 -6 117651307 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19289;SOR=Inf;LSEQ=TTTCCCCTGCGGGAGCCAGC;RSEQ=AGGCTGGACAGCTTGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:98,98:0:2,0:23.3:1:30.1:1:1:0:60:64.333:1:0:0.3 0/1:154:2:1,1:83,68:0.013:2,2:25.5:1:25.5:1:1:1.21898:60:4:0.0133:0:1 -6 117651314 . G T 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.625;LSEQ=TGCGGGAGCCAGCGAGGCTG;RSEQ=ACAGCTTGGTCCCAAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:95,100:0.0101:2,2:15.5:1:26:1:1:1.05:60:4:0.0103:0:1 0/0:158:1:0,1:82,75:0.0063:2,0:1:0:22:0:0.48101:0:60:2:0.0066:0:2 -6 117651344 . A G 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.25239;LSEQ=TCCCAAGACTTGTCGCCACA;RSEQ=CCCAACACACCAGCTGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:49:21,28:58,73:0.2707:2,2:26.3:1:32.2:1:1:1.05905:59.8:98:0.2784:0:1.2 0/1:164:14:9,5:70,79:0.0854:2,2:22.9:1:30.7:1:0.26862:2.02:60:28:0.0859:0:1.1 -6 117651345 . C T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.55612;LSEQ=CCCAAGACTTGTCGCCACAA;RSEQ=CCAACACACCAGCTGTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:78,103:0.0109:2,2:37.5:1:27.5:1:1:1.32:60:4:0.011:0:1.5 0/0:164:1:0,1:78,85:0.0061:2,0:1:0:26:0:1:0:60:2:0.0062:0:1 -6 117651372 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21025;SOR=Inf;LSEQ=CACCAGCTGTGGTAGTCAGC;RSEQ=GCCAGAGTGCCTCTTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:76,97:0:2,0:24.3:1:30.2:1:1:0:59.9:33.6:1:0:0.4 0/1:147:2:1,1:63,82:0.0136:2,2:21.5:1:30:1:1:1.30:60:4:0.0139:0:1.5 -6 117651379 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21615;SOR=Inf;LSEQ=TGTGGTAGTCAGCGGCCAGA;RSEQ=TGCCTCTTCAGGTCTAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:74,90:0:2,0:23.6:1:32.1:1:1:0:59.9:81:1:0:0.4 0/1:143:2:1,1:61,80:0.014:2,2:7.5:1:28:1:1:1.31:60:4:0.0141:0:1.5 -6 117651529 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28549;SOR=0;LSEQ=AGGGGTGGCTGCAGTCTCTG;RSEQ=GGACCAACAGACTTAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:1,2:77,55:0.0222:2,2:10.3:1:29.7:1:0.57313:2.77874:60:6:0.0227:0:1 0/0:85:0:0,0:57,28:0:2,0:18.9:1:30.2:1:1:0:60:84:1:0:0.2 -6 117651651 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20812;SOR=Inf;LSEQ=ACAAAGTGCTTCGTTAAATG;RSEQ=GTCCTCCTCCTGGTGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:120,119:0:2,0:24.8:1:31.2:1:1:0:60:78.667:1:0:0.2 0/1:201:2:1,1:88,111:0.01:2,2:30:1:28:1:1:1.26:60:4:0.0104:0:1 -6 117651724 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15215;SOR=Inf;LSEQ=AGGACACCCTATACAGGAGC;RSEQ=ATCCTACTGGCATCAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:63,66:0:2,0:23.1:1:30.5:1:1:0:60:258:1:0:0.1 0/1:83:2:1,1:41,40:0.0241:2,2:11.5:1:29.5:1:1:1.0247:60:4:0.0244:0:1 -6 117651762 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52392;SOR=0;LSEQ=TTGGTGCCCCTTGAAGTCAG;RSEQ=GGTCCCAGAAGAAGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:66,72:0.0143:2,2:15:1:30:1:1:1.09:60:4:0.0145:0:1 0/0:88:0:0,0:53,35:0:2,0:19.6:1:29.2:1:1:0:60:176:1:0:0.1 -6 117651764 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15897;SOR=Inf;LSEQ=GGTGCCCCTTGAAGTCAGAG;RSEQ=TCCCAGAAGAAGGAGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:69,72:0:2,0:25:1:31.6:1:1:0:60:69.5:1:0:0.1 0/1:94:2:1,1:55,37:0.0213:2,2:30.5:1:27:1:1:1.48004:60:4:0.0213:0:1 -6 117651772 . A T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.98672;LSEQ=TTGAAGTCAGAGGTCCCAGA;RSEQ=GAAGGAGCAGACACCCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:0,3:77,71:0.0199:2,0:14.3:1:23:1:0.11525:0:60:2:0.0137:0:1 0/1:102:2:0,2:58,42:0.0196:2,0:1:0:26:1:0.18365:0:60:4:0.0198:0:1 -6 117651880 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23947;SOR=Inf;LSEQ=AAGTGAACCCCAGCAAACTG;RSEQ=AGCAGCCCTACAGAAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:97,106:0:2,0:24.2:1:32.1:1:1:0:60:100.5:0.995:0:0.3 0/1:196:2:1,1:101,92:0.0102:2,2:25:1:27.5:1:1:1.0973:60:4:0.0103:0:1 -6 117651888 . C G 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11225;SOR=Inf;LSEQ=CCCAGCAAACTGCAGCAGCC;RSEQ=TACAGAAGAGGGAAGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:87,103:0:2,0:23.5:1:31.4:1:1:0:60:189:0.9947:0:0.4 0/1:179:3:2,1:89,87:0.0168:2,2:14.3:1:22:1:1:1.95:60:2:0.0114:0:1.3 -6 117651926 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.3653;LSEQ=ACTATTGAAAGAAAAACAAA;RSEQ=AAGCAGAAAGTGACAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:172:91:51,40:43,38:0.5291:2,2:23:1:32:1:0.75965:1.13:60:182:0.5353:0:1.1 0/1:155:45:16,29:59,49:0.2903:2,2:25.2:1:30.3:1:0.03475:2.17122:59.7:21.5:0.2829:0:1.2 -6 117651947 . A G 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=AAGCAGAAAGTGACAACAAC;RSEQ=GCATCATCATCAACAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:131,88:0:2,0:22.5:1:30.5:1:1:0:60:35.5:0.9953:0:0.5 0/1:185:12:6,6:94,79:0.0649:2,2:21.8:1:27.3:1:0.77471:1.18875:60:11:0.0618:0:1.2 -6 117651957 . TCAA T 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=1.15275;LSEQ=TGACAACAACAGCATCATCA;RSEQ=CAACAACAACAAGGGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:5:2,3:137,104:0.0203:2,2:25:1:32.2:1:0.65534:1.97042:60:10:0.0208:0:0.4 0/1:214:5:3,2:112,96:0.0234:2,2:24.4:1:33.4:1:1:1.28:60:10:0.0237:0:0 -6 117651975 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.3503;SOR=3.33814;LSEQ=CATCAACAACAACAACAAGG;RSEQ=CCCCCACAAAAAACCCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:1:0,1:162,128:0.0034:2,0:1:0:15:0:0.4433:0:60:0:0:0:3 0/1:264:3:1,2:133,128:0.0114:2,2:14:1:28.3:1:0.61791:2.07256:60:6:0.0117:0:1 -6 117652005 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.20243;SOR=4.31464;LSEQ=AAAACCCATACAAGGGTCAG;RSEQ=AGCCTCAAAGACCACAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:1:0,1:168,166:0.003:2,0:1:0:23:0:0.49851:0:60:2:0.003:0:1 0/1:313:4:1,3:156,152:0.0128:2,2:23:1:27.8:1:0.36938:3.06893:60:8:0.0129:0:1 -6 117652037 . G A 86 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03318;SOR=7.55319;LSEQ=CCACAACTAGACAAACTCAC;RSEQ=AAGGTGAGAAAGAACCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:1:1,0:136,154:0.0034:2,0:1:0:26:0:0.47079:0:60:2:0.0035:0:1 0/1:275:7:6,1:134,134:0.0255:2,2:26.6:1:30.9:1:0.12065:5.97:60:14:0.0258:0:1 -6 117652187 . T C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07161;LSEQ=CAGAAGTAGGCTTCACAAGA;RSEQ=GGGTAGAAAAAACTATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:48:21,27:26,60:0.3582:2,2:25:1:30.3:1:0.13333:1.79:60:47:0.3588:0:1.2 0/1:105:4:1,3:37,64:0.0381:2,2:20.3:1:27.3:1:1:1.72606:60:8:0.0396:0:1 -6 117652632 . G T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02882;SOR=Inf;LSEQ=CTAGCAAGACAGGCCAACAT;RSEQ=CAAATTCGGCAAACACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:62,344:0:2,0:23.1:1:31.7:1:1:0:60:39.6:1:0:0.1 0/1:286:4:0,4:45,236:0.014:2,0:11:1:30:1:1:0:60:8:0.0141:0:1.3 -6 117653900 . G A 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTGAACAACTTGCTCCT;RSEQ=AATGGCTCCTGGGTAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:4,1:12,0:0.2941:0,2:27.2:1:28.4:1:0.29412:0:58.4:10:0.2941:0:1.2 0/0:1:0:0,0:1,0:0:0,0:2:0:28:0:1:0:56:2:1:0:4 -6 117654044 . TT AG 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10401;SOR=Inf;LSEQ=CATAGCACTAAATGCCCACA;RSEQ=AGAAAGCCAGAAAGATCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:167,0:0:1,0:22.8:1:31.3:1:1:0:59.9:82.5:1:0:0.1 0/1:80:2:2,0:78,0:0.025:1,0:9.5:1:31.4:1:1:0:60:4:0.0256:0.0125:1.5 -6 117654053 . CA AG 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00377;SOR=Inf;LSEQ=AAATGCCCACATTAGAAAGC;RSEQ=GAAAGATCTCAAATCGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:195,0:0:1,0:23.3:1:31.6:1:1:0:60:194:1:0:0 0/1:97:5:5,0:92,0:0.0515:1,0:8.2:1:30.9:1:1:0:60:10:0.0521:0.0309:0.6 -6 117654104 . G A 62 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.71964;SOR=1.5137;LSEQ=ACAATTAAAAGAGCTAGAGA;RSEQ=GCAAGAGCAAACTAATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:4:4,0:450,18:0.0085:1,0:6.5:1:31.5:1:1:0:60:8:0.0086:0:2 0/1:313:4:4,0:287,21:0.0128:2,0:11.3:1:31.3:1:1:0:60:8:0.0129:0:2.5 -6 117654130 . G A 110 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=9.53415;LSEQ=AGCAAACTAATCCAAAAGCT;RSEQ=GCAGAAGACAAGAAATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:853:2:2,0:607,244:0.0023:2,0:5:1:29.5:1:1:0:60:4:0.0024:0:1.5 0/1:638:14:9,5:437,184:0.0219:2,2:8.6:1:28.9:1:0.57026:1.31887:57:28:0.0224:0:1.9 -6 117654138 . A G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=5e-04;SOR=Inf;LSEQ=AATCCAAAAGCTGGCAGAAG;RSEQ=CAAGAAATAACTAAGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1016:0:0,0:663,351:0:2,0:21.9:1:29.6:1:1:0:60:91.182:0.998:0:0.1 0/1:771:9:4,5:483,278:0.0117:2,2:14.6:1:30.6:1:0.30091:2.16948:55.3:18:0.0118:0:2.8 -6 117654196 . C CA 123 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00967;SOR=2.74188;LSEQ=CAAAGACACAAAAAGCCCTC;RSEQ=AAAAAAAATCAACACATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2100:9:5,4:1023,1065:0.0043:2,2:30.6:1:30.6:1:0.74898:1.30:60:18:0.0044:0:0.2 0/1:1800:21:10,11:883,890:0.0117:2,2:27.9:1:28.1:1:1:1.09127:60:20:0.0113:0.0022:0.4 -6 117654231 . T A 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATCCAGGAGCCGTTTTTTT;RSEQ=AAAAAATAAAATAAATAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1602:0:0,0:676,922:0:2,0:26:1:29:1:1:0:60:132.167:0.9994:0:0.2 0/1:1352:61:30,31:561,720:0.0451:2,2:25.5:1:28.8:1:0.43022:1.24:60:122:0.0456:0:1.2 -6 117654308 . C CA 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.56244;SOR=3.18868;LSEQ=AGAGAAGAATCAAATAGACA;RSEQ=AAAAAAAATGATAAAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:1:0,1:4,312:0.0031:1,0:31:0:32:0:1:0:60:2:0.0032:0:0 0/1:201:2:0,2:1,197:0.01:1,0:37.5:1:32:0:1:0:60:4:0.0101:0:0 -6 117657368 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52031;SOR=0;LSEQ=CTGGGGTACATGTGCAGGAC;RSEQ=TGAAGGTTTGTTACATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:23,155:0.011:2,2:20:1:33:0:0.24953:6.62:60:4:0.011:0:1 0/0:119:0:0,0:21,97:0:2,0:22.7:1:30.9:1:1:0:60:117:0.9915:0:0.1 -6 117657686 . A G 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28007;SOR=0;LSEQ=TCATTCCTTTTTATGGCTGC;RSEQ=TAGTATGCCATGGTGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:3,2:12,1:0.2778:1,2:25.2:1:30:1:0.17157:6.87863:60:10:0.2778:0:1 0/0:6:0:0,0:5,1:0:2,0:26.5:1:30.3:1:1:0:60:12:1:0:0.2 -6 117658193 . G C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18995;LSEQ=CAAGGTCTCCTATATTTTCT;RSEQ=AATTTCTTCATTCAAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:233:136,97:248,193:0.3452:2,2:24.2:1:31.7:1:0.62399:1.09:60:115.5:0.3479:0:1.1 0/1:484:44:26,18:238,202:0.0909:2,2:26:1:31:1:0.63429:1.23:60:43:0.0905:0:1.1 -6 117659005 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTTTTCCTCCTAACAC;RSEQ=CTCTTCAGACATGTAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:26.5:1:30:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 117662453 . C T 199 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.033;LSEQ=ACTCTCTGTACACCACATTT;RSEQ=CTCAGAGTGGCAGGCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:945:103:53,50:386,456:0.109:2,2:30:1:29.8:1:0.29646:1.25:60:102:0.1093:0:1.1 0/0:747:3:0,3:356,388:0.004:2,0:1:0:23.7:1:0.25064:0:60:6:0.0041:0:1 -6 117662944 . C T 102 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22933;SOR=0.23263;LSEQ=AAGTCAGCCTCTTCTATAAT;RSEQ=GTAGGTTAACAGACTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:10:0,10:2,16:0.3571:2,0:28.1:1:30.8:1:0.52381:0:60:20:0.3571:0:1.3 0/1:9:1:0,1:0,8:0.1111:0,0:1:0:31:0:1:0:60:2:0.1111:0:1 -6 117663364 . A G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30762;SOR=0.36273;LSEQ=TCCTAGTTGCTTTCTATTTT;RSEQ=ATAGAATATTATTAGTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:14:14,0:30,0:0.3182:1,1:26.7:1:32.2:1:1:0:60:28:0.3182:0:1.1 0/1:14:2:2,0:12,0:0.1429:0,0:30.5:1:31:0:1:0:60:4:0.1429:0:1 -6 117663499 . A G 227 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3397;LSEQ=GATTTTAAAAAATAAACATC;RSEQ=ACATACACAGCACATATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:188:138,50:278,103:0.3304:2,2:22.8:1:30.1:1:1:1.02:60:93:0.3316:0:1.1 0/1:495:71:45,26:298,125:0.1434:2,2:21.6:1:29.1:1:0.26534:1.37653:60:22.667:0.1391:0:1.1 -6 117665115 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06562;LSEQ=ATTAGCTGTAAAAAAGTTGC;RSEQ=TACTAGTCCATTTCAGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:35:35,0:52,0:0.4023:1,1:21.8:1:30.6:1:1:0:60:34:0.3953:0:1 0/1:48:2:2,0:44,2:0.0417:1,0:37.5:1:29.5:1:1:0:60:4:0.0417:0:1 -6 117665635 . G C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1049;SOR=0;LSEQ=CTTGATACTGTGTGTAGTAT;RSEQ=TGTAGTATGTACTGCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:30.3:1:26.8:1:1:0:60:3:0.4286:0:1 0/0:5:0:0,0:1,4:0:2,0:10.4:1:30.8:1:1:0:60:10:1:0:0 -6 117674087 . G A 160 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGACAGCCTTGGAGAAGGA;RSEQ=ATGTTATGAGATTTTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:200,17:0:2,0:23:1:32.1:1:1:0:60:42.4:0.9953:0:0.1 0/1:137:43:40,3:84,10:0.3139:2,2:18.7:1:29.5:1:0.75441:1.58:60:86:0.3139:0:1.1 -6 117674434 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51786;SOR=0;LSEQ=ATTATAATTGCTAAATTTTG;RSEQ=ATCTATTATTTCAACATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:0,111:0.0177:1,2:27:1:32.5:1:0.0177:0:60:4:0.0179:0:1 0/0:75:0:0,0:2,73:0:1,0:22.5:1:30.6:1:1:0:60:74:1:0:0 -6 117678083 . A G 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.11047;LSEQ=TGTCCAATACAAGCGACTAT;RSEQ=GAGGAAAAAAAAGTCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:522:474:80,394:12,34:0.908:2,2:24:1:31.1:1:0.1537:1.73611:60:42.091:0.9132:0:1.1 1/0:357:186:42,144:41,130:0.521:2,2:23.4:1:30.4:1:0.80244:1.08108:60:92:0.5212:0:1.1 -6 117678087 . G GA 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16404;SOR=5.95068;LSEQ=CAATACAAGCGACTATAGAG;RSEQ=AAAAAAAAGTCCCCCCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:1:0,1:79,395:0.0021:2,0:28:0:32:0:1:0:60:2:0.0021:0:1 0/1:326:4:1,3:71,251:0.0123:2,2:13.5:1:30.6:1:1:1.18:60:8:0.0124:0.0061:0.5 -6 117678900 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5247;SOR=0;LSEQ=GTCTTCTACTATTAAACCAA;RSEQ=GACATTACATTAAATATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:140,10:0.0132:2,2:15:1:30.5:1:0.13994:13.39609:60:4:0.0137:0:1 0/0:95:0:0,0:86,9:0:2,0:25.1:1:30.5:1:1:0:60:190:1:0:0 -6 117680945 . T C 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAATACTTCACTTCCTTTA;RSEQ=TTCGGAAGAATTACATAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:253,63:0:2,0:23.8:1:30.6:1:1:0:60:51.667:1:0:0.1 0/1:240:22:15,7:152,66:0.0917:2,2:26.5:1:31:1:1:1.07442:60:44:0.0924:0:1.1 -6 117681386 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11833;SOR=Inf;LSEQ=GGTCAAAAACATGTTTTTGA;RSEQ=CTAAACTTTAGCAAAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:106,17:0:2,0:23.5:1:32.3:1:1:0:59.8:122:1:0:0.1 0/1:65:2:1,1:57,6:0.0308:2,2:19:1:27.5:1:0.20529:8.87273:60:4:0.0313:0:1 -6 117681423 . A C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18832;SOR=Inf;LSEQ=AGACAGTGTTCATATCCCTA;RSEQ=AGACACCAATGGGACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:193,32:0:2,0:24.6:1:29.9:1:1:0:59.9:27.125:1:0:0.3 0/1:173:2:2,0:141,30:0.0116:2,0:27:1:31.5:1:1:0:57.5:4:0.0119:0:1 -6 117681436 . G GACAC 227 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=15.000;MSILEN=2;SSF=0;SOR=0.28956;LSEQ=ATCCCTAAAGACACCAATGG;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:277:169:132,37:44,7:0.6101:2,2:24.8:1:30.7:1:0.23527:1.75779:59.2:168:0.6131:0.1733:0.5 0/1:196:61:50,11:58,14:0.3112:2,2:25.9:1:30.3:1:1:1.10:59.7:122:0.3211:0.0255:0.3 -6 117681655 . C G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.50044;SOR=0;LSEQ=TGAGAGATTACTAAATGTTT;RSEQ=ATTTCATACTCCTGATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:18,173:0.0103:2,2:21:0:33:1:0.18766:9.38:60:4:0.0104:0:1.5 0/0:172:0:0,0:30,142:0:2,0:20.7:1:31.9:1:1:0:60:171:1:0:0.1 -6 117681661 . A C 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.00046;SOR=Inf;LSEQ=ATTACTAAATGTTTCATTTC;RSEQ=TACTCCTGATACACAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:10,158:0:2,0:24.4:1:31.3:1:1:0:60:336:1:0:0.1 0/1:150:10:2,8:23,117:0.0667:2,2:19.5:1:32.1:1:0.67316:1.27:60:20:0.0671:0:1.1 -6 117683821 . G A 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGTTGAAAAGACATCACT;RSEQ=AGGGAGTGACATTGACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:759:0:0,0:440,318:0:2,0:25.8:1:31.6:1:1:0:60:150.6:1:0:0.1 0/1:650:55:32,23:331,260:0.0846:2,2:23.9:1:28.1:1:0.77835:1.09:60:54:0.084:0:1.2 -6 117686192 . T C 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00421;SOR=Inf;LSEQ=AAAGTGAGATTCTGCTTTTT;RSEQ=AAGAAAAAAGACAGATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:256,97:0:2,0:24:1:29.4:1:1:0:60:87.25:1:0:0.1 0/1:301:7:4,3:206,88:0.0233:2,2:21.4:1:31.9:1:0.43551:1.75204:60:14:0.0234:0:1 -6 117686693 . A T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06863;SOR=Inf;LSEQ=AGTGTGGGCAAGGCTGACAC;RSEQ=GATGGTACAGTCTGTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:289,112:0:2,0:22.9:1:30.1:1:1:0:60:132.667:1:0:0.1 0/1:279:3:1,2:188,88:0.0108:2,2:24.3:1:29.3:1:0.2442:4.24827:60:6:0.0108:0:1 -6 117686701 . C T 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03262;SOR=Inf;LSEQ=CAAGGCTGACACAGATGGTA;RSEQ=AGTCTGTTTGGGAAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:297,138:0:2,0:24.6:1:31.9:1:1:0:60:107.75:1:0:0.1 0/1:323:4:1,3:213,106:0.0124:2,2:5.3:1:25.3:1:0.11342:5.99317:60:8:0.0124:0:1.3 -6 117686781 . A G 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATTCTACACTGTAGAAAACT;RSEQ=CACCCCAGTCTACCGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:803:0:0,0:446,357:0:2,0:25.4:1:28.8:1:1:0:60:88.222:1:0:0.1 0/1:636:27:14,13:344,264:0.0425:2,2:29.2:1:31:1:0.69346:1.20958:60:54:0.0427:0:1.1 -6 117686918 . CA C 123 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01096;SOR=0.10711;LSEQ=AAGTTCCCTACAGGATGAAA;RSEQ=AAAAAAAGAAATAGGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:13:3,10:184,382:0.0225:2,2:37.3:1:33.5:1:0.56332:1.60439:60:26:0.0226:0:0.1 0/0:408:1:1,0:134,273:0.0025:2,0:12:0:33:0:0.33088:0:60:2:0.0025:0:0 -6 117686943 . A T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.75166;LSEQ=AAAAGAAATAGGAGAAAAAA;RSEQ=TGGGGATTATTGACCAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:26:5,21:79,275:0.0684:2,2:23.3:1:29.9:1:0.81167:1.20597:60:52:0.0697:0:1 0/1:242:88:21,67:38,115:0.3636:2,2:23.7:1:29.7:1:1:1.05403:60:87:0.3625:0:1.1 -6 117687002 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11654;SOR=Inf;LSEQ=ATAGCAATTACTAATAATTA;RSEQ=AACTGAAACAAAATTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:10,99:0:2,0:24.9:1:31.8:1:1:0:60:218:1:0:0.1 0/1:57:2:0,2:3,52:0.0351:2,0:11.5:1:30:1:1:0:60:4:0.0351:0:2 -6 117687159 . G GA 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.02252;LSEQ=TCTTAAAACTTAATTCTTAA;RSEQ=AAAAAAAAATATCCCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:7:6,1:227,44:0.0251:2,2:25.3:1:30.7:1:1:1.16:60:14:0.0252:0:0 0/1:234:6:6,0:189,39:0.0256:2,0:12.8:1:29.2:1:0.59289:0:60:12:0.026:0.0128:0.3 -6 117687535 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02229;SOR=Inf;LSEQ=AAGTAGTCATGAGAATATAT;RSEQ=TTTGTGAGTATCTGTACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:4,154:0:1,0:24:1:31.6:1:1:0:60:21.571:1:0:0.1 0/1:101:4:0,4:6,91:0.0396:2,0:17.3:1:30:1:1:0:60:8:0.04:0:1 -6 117687553 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13506;SOR=Inf;LSEQ=ATGTTTGTGAGTATCTGTAC;RSEQ=CATTTGTGTACATTAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:1,110:0:1,0:23.9:1:31.9:1:1:0:60:21.2:1:0:0.1 0/1:65:2:0,2:0,63:0.0308:1,0:14:1:31:0:1:0:60:4:0.0313:0:1 -6 117699831 . C T 32 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02778;SOR=Inf;LSEQ=GATCAGGACAGGGGGATAAG;RSEQ=TTGAGGACACAGATCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:0:0,0:34.4:1:31.6:1:1:0:60:14:1:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:32:0:1:0:60:4:1:0:1 -6 117699988 . A G 77 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACACTTCCTGGGCTCTTA;RSEQ=GCAGCATTCTCCTGAGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,1:0.2:1,0:27.8:1:33.4:1:1:0:60:10:0.2:0:1 0/0:1:0:0,0:1,0:0:0,0:26:0:32:0:1:0:60:2:1:0:0 -6 117700393 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15091;SOR=Inf;LSEQ=AACTTTGTGAACAGGTCACA;RSEQ=TTAAGCTATAGATTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:12,195:0:2,0:25.7:1:31.9:1:1:0:60:50.75:1:0:0.1 0/1:132:2:1,1:10,120:0.0152:2,2:12:1:29.5:1:0.16031:11.49:60:4:0.0153:0:1 -6 117704316 . GC TT 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0189;SOR=5.57781;LSEQ=TTGTGACCATCAAATAAGGC;RSEQ=TTTTTTTTCAAATAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:5,0:33,1:0.1282:1,0:28.6:1:30:1:1:0:60:10:0.1316:0:1 0/1:13:6:5,1:7,0:0.4615:0,2:30.3:1:30.3:1:0.46154:0:60:12:0.4615:0:1 -6 117704607 . T C 176 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=59.79749;LSEQ=CTGAATCCACCACCATGTCA;RSEQ=TCACCAATAGCTTCACGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1079:1:0,1:458,620:9e-04:2,0:47:0:14:0:1:0:60:0:0:0:2 0/1:988:52:28,24:423,513:0.0526:2,2:20.7:1:30.9:1:0.25324:1.41:60:104:0.0531:0:1.2 -6 117706683 . G GA 71 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.76335;LSEQ=GAAATTGTGTCTCAAAAAAA;RSEQ=AAAAAAAAAATGTTTAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:5:5,0:58,0:0.0781:1,0:16.2:1:30.8:1:1:0:60:10:0.0794:0.0313:0.4 0/1:33:2:2,0:30,1:0.0606:1,0:24.5:1:30:1:1:0:60:4:0.0606:0.0303:0 -6 117706757 . AT A 68 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4075;SOR=0.28832;LSEQ=AGCATAAGTGGTGCACAGGT;RSEQ=TTAAAAAAAAAAAAGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:5:4,1:191,15:0.0236:2,2:16.8:1:29.4:1:0.3285:3.15585:60:10:0.0244:0.0142:0.6 0/0:145:1:1,0:138,6:0.0069:1,0:27:0:32:0:1:0:60:2:0.007:0:0 -6 117706760 . TA T 162 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.25164;SOR=0.70485;LSEQ=ATAAGTGGTGCACAGGTATT;RSEQ=AAAAAAAAAAAGAAATTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:38:36,2:161,19:0.1667:2,2:22.2:1:31:1:0.54345:2.12:60:76:0.1696:0.0307:0.6 0/1:162:20:18,2:130,6:0.1235:1,2:25.5:1:30.1:1:0.27264:2.38958:60:40:0.125:0.0123:0.2 -6 117707038 . G A 211 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01126;LSEQ=TCCATGTCTCAAAATAAAGT;RSEQ=AATGATTAGCAGTTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:506:152:42,110:88,265:0.3004:2,2:23.4:1:29.2:1:0.57917:1.15:60:37:0.299:0:1.1 0/0:417:2:2,0:119,296:0.0048:2,0:1:0:24:0:0.0837:0:60:4:0.0048:0:1.5 -6 117707912 . C A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03064;SOR=Inf;LSEQ=TTTCTTAACAGAATCACTGG;RSEQ=AGTAGAGTTCAGTCAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:90,0:0:1,0:28.9:1:31.8:1:1:0:60:29:1:0:0 0/1:42:3:3,0:38,1:0.0714:1,0:16.3:1:30.3:1:1:0:60:6:0.075:0:1 -6 117708692 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATCAATTATAGTGTTTC;RSEQ=TTAAAAAATATCTTGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:13,1:0.125:1,0:29:1:31:1:1:0:60:4:0.125:0:1 0/0:2:0:0,0:2,0:0:0,0:13:1:30.5:1:1:0:60:4:1:0:0 -6 117708971 . C T 189 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=92.64475;LSEQ=AGGGTAGTACCCACTGAGGG;RSEQ=TCTGACCAGGGGCCTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:816:1:1,0:461,354:0.0012:2,0:21:0:31:0:1:0:60:2:0.0012:0:1 0/1:861:88:52,36:426,347:0.1022:2,2:26.6:1:29.3:1:0.49888:1.18:60:87:0.1026:0:1.1 -6 117710369 . C CT 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54987;SOR=0;LSEQ=ATGCAGAACAAATGTATAAA;RSEQ=TTTTTTTTTAGCTAAGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:3,0:59,1:0.0476:1,0:18.7:1:31.8:1:1:0:60:6:0.0484:0.0317:0 0/0:28:0:0,0:26,2:0:2,0:18.2:1:32.2:1:1:0:60:56:1:0:0 -6 117710447 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49937;SOR=0;LSEQ=TCAAAATTGAATCACAACGC;RSEQ=AAGCAGTTCAAACCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:153,32:0.0107:2,2:16:1:28.5:1:0.32258:4.72366:60:4:0.0109:0:2 0/0:173:0:0,0:133,40:0:2,0:20.7:1:29.8:1:1:0:60:42.25:1:0:0.1 -6 117710476 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11997;SOR=Inf;LSEQ=CAAACCTTCCTCTTATTCCA;RSEQ=CAAGGCCAGTAACCACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:215,83:0:2,0:22.2:1:31.4:1:1:0:60:32.111:1:0:0.1 0/1:291:3:1,2:191,97:0.0103:2,2:21:1:28.3:1:0.26772:3.91818:60:6:0.0104:0:1 -6 117711059 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12891;SOR=Inf;LSEQ=GATTCAGTCCAAAGGTTGAT;RSEQ=AGTAACCTCCTCAGCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:12,96:0:2,0:21.8:1:31.1:1:1:0:60:107:1:0:0.1 0/1:61:2:0,2:6,53:0.0328:2,0:5.5:1:29.5:1:1:0:60:4:0.0339:0:1 -6 117714346 . C G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.76072;LSEQ=TTTCTCAAAGATTATTTATT;RSEQ=CCAATGGAAGAGAATTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:49:35,14:269,104:0.1161:2,2:20:1:31.8:1:1:1.03451:60:98:0.1181:0:1.1 0/1:353:136:100,36:155,60:0.3853:2,2:24.4:1:31.4:1:0.80665:1.08:60:272:0.3864:0:1.1 -6 117717021 . AG T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAGGGATTAGGGCAGAAA;RSEQ=TTATATGTATCCCTTAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:5,0:0.25:0,0:19.5:1:30.3:1:1:0:60:4:0.25:0.125:0 0/0:3:0:0,0:2,1:0:2,0:10.3:1:28.7:1:1:0:60:6:1:0:0.7 -6 117717342 . G GA 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGCTAAAGGAAGAAGCCT;RSEQ=ACCCATACCTGCTGAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:738:0:0,0:415,323:0:2,0:24.8:1:31.5:1:1:0:60:72.8:1:0:0.1 0/1:686:44:28,16:376,265:0.0641:2,2:25.4:1:29:1:0.635:1.23:60:88:0.0649:0.0131:0.1 -6 117718303 . A G 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0907;SOR=1.58555;LSEQ=GAAGAGATAATGGTGACATA;RSEQ=TGAGCAGAAAAATGTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:32:7,25:80,243:0.0901:2,2:31.2:1:32:1:0.83146:1.17525:60:64:0.0914:0:1.2 0/1:265:36:9,27:74,155:0.1358:2,2:26.6:1:31.5:1:0.4432:1.43042:60:72:0.1364:0:1.1 -6 117718359 . G GT 105 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.80001;SOR=0.76623;LSEQ=ATAAGATGGAAAAAAGTCTT;RSEQ=TTTTTTTTTTTGAAAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:12:1,11:4,96:0.1062:1,2:26:1:29.4:1:0.4388:2.16:58.3:24:0.1143:0.0088:0.9 0/1:72:6:0,6:1,63:0.0833:1,0:28.2:1:30.3:1:1:0:60:12:0.0923:0:0.2 -6 117724207 . G A 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0069;SOR=0;LSEQ=TTGAATGGATCGATTAATAG;RSEQ=AAGGAATAGATTTATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:8:7,1:92,5:0.0762:2,2:11.1:1:31:1:0.38598:2.59429:60:16:0.0777:0:1.1 0/0:100:0:0,0:90,10:0:2,0:21.2:1:31:1:1:0:60:99:1:0:0.1 -6 117724277 . C T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17093;SOR=5.35229;LSEQ=GCTTTGGAATAATGTCCTTT;RSEQ=ATAAGAAATGTGTGCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:1:0,1:398,126:0.0019:2,0:1:0:27:0:0.2419:0:60:2:0.0019:0:1 0/1:395:4:1,3:269,122:0.0101:2,2:8.5:1:26:1:0.09558:6.58052:60:8:0.0103:0:1 -6 117724379 . C T 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27231;LSEQ=CTGTGAAGATCCAAACCACT;RSEQ=GGAAAATGTACTCAGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:963:91:41,50:395,475:0.0945:2,2:28.2:1:29.6:1:1:1.01411:60:44.5:0.0933:0:1.2 0/1:869:24:8,16:405,440:0.0276:2,2:30:1:30.1:1:0.21334:1.83966:59.9:23:0.0267:0:1.3 -6 117724462 . C A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=3.49816;LSEQ=TAGATCAAGGAGTGATCAAT;RSEQ=ATCAGCATTATAGAATCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:37:12,25:81,288:0.0911:2,2:17.5:1:29.4:1:0.15406:1.70:60:74:0.092:0:1.6 0/1:350:91:25,66:79,180:0.26:2,2:23.5:1:29.1:1:0.68931:1.15816:60:90:0.2594:0:1.4 -6 117724489 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17159;SOR=Inf;LSEQ=ATTATAGAATCAGCACCCCA;RSEQ=ATTGGGACTAAAAAGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:28,223:0:2,0:22.9:1:32.3:1:1:0:60:124.5:1:0:0.2 0/1:178:2:1,1:25,151:0.0112:2,2:6.5:1:28:1:0.2715:5.94:60:4:0.0114:0:1.5 -6 117724498 . TA T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=TCAGCACCCCACATTGGGAC;RSEQ=AAAAGCATAGATTAATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:7,180:0.01:1,2:11:0:32:1:0.08308:24.12:60:4:0.0101:0:0.5 0/0:130:0:0,0:8,81:0:2,0:21.3:1:30:1:1:0:60:88:0.6875:0:0.2 -6 117724499 . A C 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=7.86127;LSEQ=CAGCACCCCACATTGGGACT;RSEQ=AAAAGCATAGATTAATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:11:0,11:7,180:0.055:1,0:29.2:1:32.1:1:1:0:60:22:0.0553:0:1.9 0/1:130:41:5,36:8,81:0.3154:2,2:23.7:1:31.3:1:0.54672:1.40:60:40:0.3125:0:1.8 -6 117724504 . G T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=CCCCACATTGGGACTAAAAA;RSEQ=CATAGATTAATTTGTAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:6,170:0:1,0:23.5:1:32.1:1:1:0:60:34.2:1:0:0.2 0/1:120:9:2,7:11,100:0.075:2,2:16.1:1:28.7:1:0.25188:2.57:60:18:0.0769:0:1.1 -6 117725399 . T A 74 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4656;SOR=1.57168;LSEQ=GTCTCAAAAAAAAAAAAAAA;RSEQ=TGGGAAGGGGTCTGGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:6:6,0:355,173:0.0112:2,0:20.5:1:16.3:1:0.1841:0:50:0.5:0.004:0:3.3 0/1:629:11:9,2:360,257:0.0175:2,2:13.4:1:21.6:1:0.13551:3.21:54.1:1.75:0.012:0:1.6 -6 117725448 . T G 211 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGCAGCCTTTCATACCTTAG;RSEQ=ATAAGTCCAGCTTCCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:893:0:0,0:497,396:0:2,0:27.3:1:28.4:1:1:0:60:37.826:1:0:0.2 0/1:947:120:61,59:425,400:0.1267:2,2:26:1:30.6:1:0.92229:1.02764:59.8:59:0.1281:0:1.4 -6 117725578 . T A 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.60527;LSEQ=GAAGCAAAGGGAGCAGTTGG;RSEQ=AGGTCTGCATTTTCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:63:26,37:213,321:0.1055:2,2:26.2:1:29.8:1:0.89205:1.06:60:62:0.1054:0:1.5 0/1:529:158:67,91:147,220:0.2987:2,2:26.1:1:29.2:1:0.62927:1.10:60:78:0.2989:0:1.2 -6 117725622 . G A 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04861;SOR=0.44714;LSEQ=AACAAGATTTCACTCACCAC;RSEQ=CACTCCTGTCCATCAGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:25:4,21:94,195:0.0796:2,2:21.1:1:29.5:1:0.11476:2.52451:60:24:0.0777:0:1.9 0/1:242:9:4,5:75,158:0.0372:2,2:13.4:1:27.6:1:0.47885:1.68:60:18:0.0386:0:2.1 -6 117725763 . ATCAG A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.01862;SOR=Inf;LSEQ=CAGTTTATTTTAAAAAATCA;RSEQ=TCAGTCTGTCAGTCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:0:1,0:23.7:1:29.4:1:1:0:60:19.5:1:0:0.4 0/1:7:2:0,2:0,5:0.2857:0,0:12:1:31:1:1:0:60:4:0.2857:0.1429:0.5 -6 117730403 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATAAATAAATAAAAAAGA;RSEQ=AGAAAAAAAACTGGCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:8.5:1:30.5:1:1:0:51.5:4:0.2857:0:2.5 0/0:3:0:0,0:1,2:0:2,0:37.7:1:28.3:1:1:0:60:6:1:0:0 -6 117730592 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=4.62432;LSEQ=TTTATCAGAATGGCCTATAC;RSEQ=TTTGAAATTATTGAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:17:17,0:139,3:0.1069:1,1:25.6:1:30.7:1:1:0:60:34:0.1076:0:1.1 0/1:81:29:29,0:52,0:0.358:1,1:20.6:1:29.4:1:1:0:60:28:0.35:0:1.1 -6 117730673 . G A 188 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=110.73547;LSEQ=GATGTTTTGAGAGGTGTTTC;RSEQ=TTATCTTTACATAAGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:775:1:1,0:528,245:0.0013:2,0:48:0:30:0:1:0:60:2:0.0013:0:1 0/1:638:80:54,26:365,189:0.1254:2,2:23.7:1:29.8:1:0.80212:1.08:60:160:0.1268:0:1.1 -6 117730819 . G A 192 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCCCGCTGTGGAAGACAG;RSEQ=GAGCATGACAGTCAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:0:0,0:207,480:0:2,0:24.5:1:30.4:1:1:0:60:35.158:1:0:0.1 0/1:514:78:19,59:149,287:0.1518:2,2:23.6:1:30.7:1:0.11519:1.61073:60:77:0.1522:0:1.1 -6 117730899 . T G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15763;SOR=0.43685;LSEQ=TAAAATCCGAATGCCTAATA;RSEQ=GCAAGTATATCTTTGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:15:0,15:8,141:0.0915:2,1:22.2:1:30.2:1:1:0:60:14:0.0875:0:1 0/1:119:5:0,5:10,103:0.042:2,0:23.4:1:28.6:1:1:0:60:10:0.0424:0:1 -6 117737337 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20927;SOR=Inf;LSEQ=CAAACTAGTTGAAAGCCAAT;RSEQ=GAAATGCAAATGGGAATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:179,40:0:2,0:24.4:1:31.9:1:1:0:60:72:0.9954:0:0.1 0/1:186:2:1,1:151,33:0.0108:2,2:12.5:1:27.5:1:0.33298:4.52288:60:4:0.0108:0:2 -6 117737390 . G A 185 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCTTGAAAGAAACATCA;RSEQ=TATCAAAATAGAAATCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:308,181:0:2,0:23.9:1:32.2:1:1:0:60:488:1:0:0.1 0/1:463:80:47,33:234,148:0.1728:2,2:20.9:1:29.4:1:0.70639:1.10987:60:160:0.1735:0:1.1 -6 117739772 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5657;SOR=3.03292;LSEQ=GAAATAACGTTGCCTCCTCC;RSEQ=CATTTTGTAACTCTAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:8,161:0.0059:1,0:48:0:32:0:1:0:60:2:0.006:0:1 0/1:113:2:1,1:15,96:0.0177:2,2:7:1:27:1:0.26422:6.23:60:4:0.0179:0:1 -6 117746637 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1707;SOR=5.35123;LSEQ=AACAATTCTATCAGTTATAA;RSEQ=AAGCTGAATGCTACATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:1:0,1:278,72:0.0028:2,0:1:0:23:0:0.20798:0:60:2:0.0029:0:1 0/1:265:4:1,3:205,56:0.0151:2,2:8.8:1:24.3:1:0.03561:10.8488:60:8:0.0153:0:1 -6 117746851 . G A 105 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00082;SOR=14.29581;LSEQ=TGGCAGATTTTTAGATGGCC;RSEQ=GTCTAATTTTCTCCATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:1:0,1:138,329:0.0021:2,0:35:0:19:0:1:0:60:0:0:0:5 0/1:371:11:4,7:115,245:0.0296:2,2:22.7:1:30.5:1:0.75028:1.22:60:22:0.0298:0:1 -6 117746919 . A T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00504;SOR=Inf;LSEQ=TTCAATTGGAGGAGTAGCTG;RSEQ=TGGATTTTGCTTTGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:1,139:0:1,0:25.6:1:31.1:1:1:0:60:69:1:0:0.1 0/1:77:5:0,5:0,72:0.0649:1,0:22.8:1:27.2:1:1:0:60:4:0.0533:0:1.8 -6 117747602 . CCT C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTTCCTGCCTGCCTTCCTT;RSEQ=CTCTCTCTCTCTCTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:42.5:1:32.5:1:1:1:60:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 118629787 . G T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36364;SOR=3.14348;LSEQ=GCCAAAGAGTTAAAAATATG;RSEQ=GAAAGTTTAATTACATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:0,1:159,71:0.0043:2,0:1:0:27:0:0.31169:0:60:2:0.0043:0:1 0/1:222:3:1,2:152,67:0.0135:2,2:11:1:26:1:0.22865:4.50281:60:6:0.0136:0:1 -6 118629865 . G T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1244;LSEQ=CATGGTTATTATGGTCACCT;RSEQ=ATGGCCACATATCCTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:411:364:174,190:24,23:0.8856:2,2:26.1:1:28.9:1:0.7569:1.13907:60:120.333:0.8848:0:1.1 0/1:400:196:91,105:102,102:0.49:2,2:24.3:1:28.5:1:0.48524:1.15343:60:64.333:0.4886:0:1.1 -6 119108265 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22032;SOR=Inf;LSEQ=ATCTCAGATCCTTCATAGTT;RSEQ=TTGACATTGTTCTCTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:112,30:0:2,0:23.5:1:31.6:1:1:0:60:34.5:0.9928:0:0.2 0/1:127:2:1,1:100,25:0.0157:2,2:11.5:1:33.5:1:0.36883:3.94189:60:4:0.016:0:1 -6 119108363 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.163;LSEQ=ATAAAGATAAAGGCACATCA;RSEQ=GTGGCTAATGTGAGATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:399:334:174,160:28,36:0.8371:2,2:26.3:1:30.7:1:0.27488:1.40:60:166:0.8363:0:1.1 0/1:503:229:115,114:140,133:0.4553:2,2:26.8:1:30.2:1:0.85784:1.04342:60:113.5:0.4577:0:1.2 -6 119748114 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49811;SOR=Inf;LSEQ=CAGGCAGTCTACAAAGACTG;RSEQ=TGTTTTGTCAGTACCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:114,18:0:2,0:21.8:1:31.8:1:1:0:60:32:1:0:0 0/1:133:2:0,2:110,21:0.015:2,0:7:1:28:1:0.02882:0:60:4:0.0152:0:1 -6 119748232 . A G 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00791;SOR=1.42077;LSEQ=TTAGTTTTTGAAAACGAAAT;RSEQ=TAACATGATAAACTGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:210:100,110:135,113:0.4585:2,2:24.4:1:31.5:1:0.15976:1.31336:60:51.5:0.4558:0:1.8 1/0:498:272:134,138:108,116:0.5462:2,2:26.2:1:30.8:1:0.85688:1.04:60:23.727:0.5426:0:1.8 -6 119748259 . G A 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0532;SOR=1.31697;LSEQ=GATAAACTGGAAGAAGAGAG;RSEQ=GTCCTACACGTATATCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:193:80,113:110,106:0.4707:2,2:25:1:30.1:1:0.05965:1.46439:60:31.167:0.4663:0:1.9 1/0:430:232:103,129:82,114:0.5395:2,2:23.1:1:29.7:1:0.62501:1.11:60:115:0.5463:0:1.9 -6 120904528 . A T 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAAACCCTGATATCCTT;RSEQ=CTTCTACTTGGTTGATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:20.8:1:29.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 120905648 . G T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CAGCCTGGAGCTATAGAAAA;RSEQ=GGTGCCACCCTTCCCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:22.8:1:32.3:1:1:0:60:8:1:0:0.3 0/1:6:2:1,1:2,2:0.3333:2,2:17.5:1:29:1:1:1:60:4:0.3333:0:1.5 -6 121788574 . T A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02411;SOR=4.62141;LSEQ=CAAGGAAAGAAATTACTTTA;RSEQ=AGTAAACCACTGGGACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:5,0:24,0:0.1724:1,0:16.2:1:30.8:1:1:0:60:10:0.1724:0:1 1/0:18:9:9,0:9,0:0.5:0,0:25.9:1:30.7:1:1:0:60:18:0.5:0:1 -6 121788627 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=TAAATACTGTGAAGGAGAAT;RSEQ=GCACTTCTGTGATTTAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:58,15:0.0267:2,2:14.5:1:29:1:0.38342:3.77602:60:4:0.0274:0:1 0/0:65:0:0,0:51,14:0:2,0:23:1:30:1:1:0:60:130:1:0:0.2 -6 121788731 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0.43616;LSEQ=TGAAGCTAGAGATAAAAATG;RSEQ=TTATGAAATCAAGGTAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:180:101:49,52:39,40:0.5611:2,2:25.6:1:29.3:1:1:1.03451:60:19.2:0.5486:0:1.2 0/1:207:74:36,38:68,65:0.3575:2,2:26:1:29.1:1:0.77284:1.10374:60:148:0.3575:0:1.1 -6 121788786 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4986;SOR=Inf;LSEQ=ATTGATTTAGAAACCTTGAT;RSEQ=AAGAAGGAACAGAATAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:49,84:0:2,0:25.9:1:31.4:1:1:0:60:43.333:1:0:0.5 0/1:141:2:2,0:47,92:0.0142:2,0:47:1:32.5:1:0.11915:0:60:4:0.0143:0:1.5 -6 122329143 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49879;SOR=Inf;LSEQ=TACTCTGTACCTATTATACA;RSEQ=TCACCAAAAGCAGAGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:106,12:0:2,0:23.6:1:32:1:1:0:60:117:1:0:0.1 0/1:128:2:1,1:107,19:0.0156:2,2:24:1:28:1:0.28912:5.51465:60:4:0.0159:0:1 -6 122329217 . C T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATTTAAGTATTAAAATTAAC;RSEQ=TTGAGCATCAAATAGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:242,139:0:2,0:23.8:1:31.2:1:1:0:60:62.5:1:0:0.8 0/1:433:19:13,6:255,159:0.0439:2,2:21.5:1:30.1:1:0.63497:1.35:60:38:0.0443:0:1 -6 122329267 . A G 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08828;LSEQ=CACAGAGTGAGGTTGTTTGG;RSEQ=TGGAAATTGAGGAAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:596:540:276,264:23,29:0.906:2,2:27.5:1:31:1:0.38488:1.32:60:48.091:0.9074:0:1.2 0/1:638:293:140,153:173,171:0.4592:2,2:29.6:1:30.8:1:0.57786:1.10546:60:145.5:0.4619:0:1.2 -6 122329438 . C CT 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03476;SOR=Inf;LSEQ=AGTTCTGGGATTTGATAACA;RSEQ=TTTTTTTTTCTTTTTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:0:1,0:23.7:1:32.3:1:1:0:60:96:1:0:0.1 0/1:38:4:0,4:0,34:0.1053:1,0:12.8:1:31.5:1:1:0:60:8:0.1053:0:0 -6 122329923 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24099;SOR=Inf;LSEQ=CACATTGTTATGTAGCAGAG;RSEQ=CAAACAGCAGTGAGGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:123,31:0:2,0:22.6:1:29.5:1:1:0:60:153:1:0:0.7 0/1:149:2:1,1:104,43:0.0134:2,2:11.5:1:30:1:0.50481:2.40245:60:4:0.0135:0:1.5 -6 122329938 . G GA 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.95202;LSEQ=CAGAGACAAACAGCAGTGAG;RSEQ=AAAAAAAAAATTAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:8:6,2:148,48:0.0388:2,2:24:1:29.1:1:1:1.02764:60:16:0.0398:0.0049:1.1 0/1:216:8:5,3:136,71:0.037:2,2:25.6:1:29.4:1:1:1.14853:60:16:0.0379:0:0.3 -6 122329970 . C A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08565;LSEQ=TAAAAAATTCATTCCACTAG;RSEQ=CTTCATTGTTGTGTAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:378:338:218,120:24,16:0.8942:2,2:24.3:1:29.4:1:0.60339:1.21:60:36.556:0.894:0:1.1 0/1:439:184:121,63:155,99:0.4191:2,2:22.8:1:28.6:1:0.31808:1.23:60:29.667:0.4159:0:1.1 -6 122330162 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00172;SOR=0.15846;LSEQ=GAATATAATAAGGAAATAGA;RSEQ=ACATTTCCTATGGTATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:42:0,42:0,6:0.875:0,1:23.5:1:32.9:1:1:0:60:84:0.875:0:1.1 1/0:27:14:0,14:0,13:0.5185:1,1:21:1:33:1:1:0:60:28:0.5185:0:1 -6 122330339 . C T 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCCTGCCAAGGCAACCC;RSEQ=TGGTCTATGATCCCCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 125257962 . A G 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GATGAAATTCTGTTGCTTTT;RSEQ=TAACTAAATTCTTGAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:54,2:0:1,0:25.1:1:28.9:1:1:0:60:112:1:0:0.3 0/1:34:10:9,1:23,1:0.2941:1,2:24.8:1:32.4:1:0.50802:2.47657:60:20:0.2941:0:1.1 -6 125258040 . G T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.35021;LSEQ=TATAACACCTCAAACATTAT;RSEQ=ATATGGGACGGAACTGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:194:146:108,38:35,13:0.7526:2,2:25.5:1:29.4:1:1:1.06:60:35.5:0.7474:0:1.1 1/0:134:69:50,19:47,18:0.5149:2,2:24:1:29.4:1:1:1.01:60:138:0.5149:0:1.1 -6 125258137 . C T 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.49677;LSEQ=CAACTGTTTCAAATTATTAA;RSEQ=GGGAGACTTTAAAAACCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:443:298:139,159:73,72:0.6727:2,2:25.9:1:30.2:1:0.47946:1.15938:60:48.667:0.6713:0:1.1 1/0:402:203:100,103:93,103:0.505:2,2:26.9:1:29.7:1:0.76395:1.08:60:66.667:0.5025:0:1.2 -6 128960860 . T A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20908;SOR=Inf;LSEQ=TAATTTTTTAATTTAAAAAT;RSEQ=TCTAATGATTCTACTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:68,151:0:2,0:21.7:1:29.8:1:1:0:60:72:1:0:0.1 0/1:185:2:1,1:61,122:0.0108:2,2:15:1:24.5:1:1:1.99:60:4:0.011:0:1 -6 129478893 . A G 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.49154;LSEQ=GGATCACTCGGTACCATGTT;RSEQ=TAATATGGCAATTGGTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1048:107:105,2:443,498:0.1021:2,1:23.1:1:31.6:1:0:58.82:33.3:25.75:0.1009:0:2 0/1:926:49:46,3:417,460:0.0529:2,2:20.1:1:31.5:1:0:16.89:31.7:98:0.0534:0:2 -6 129478911 . G C 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.47158;LSEQ=TTATAATATGGCAATTGGTA;RSEQ=TCTTCCACGATCCCTCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1091:197:165,32:417,476:0.1806:2,2:19.3:1:31.5:1:0:5.88:38.8:38.4:0.1801:0:2 0/1:967:91:71,20:412,463:0.0941:2,2:18.8:1:31.3:1:0:3.98:36.6:182:0.0953:0:1.9 -6 129478980 . A G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATTAGGCCGAAGCTGTAGAT;RSEQ=TCAGCCATGATGTAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1407:0:0,0:694,713:0:2,0:25.5:1:29.3:1:1:0:52.3:86.938:1:0:0.6 0/1:1109:18:16,2:528,562:0.0162:2,2:17.1:1:31.3:1:0.00055:8.50:38.3:36:0.0164:0:1.2 -6 129478995 . G A 278 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.40885;LSEQ=TAGATATCAGCCATGATGTA;RSEQ=GGCTGGAAGTGGTTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1330:591:298,293:336,401:0.4444:2,2:24.3:1:30.3:1:0.08663:1.21:49.6:72.875:0.443:0:1.3 0/1:1023:252:130,122:365,403:0.2463:2,2:25.1:1:30.3:1:0.27637:1.18:49.5:62:0.2453:0:1.3 -6 129479220 . CG AA 106 Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12256;SOR=0.39527;LSEQ=GGCTTTCCTTGGGTGCCATA;RSEQ=TTTCTGTGTGCAGGTGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1029:11:0,11:514,504:0.0107:2,0:13.5:1:30.9:1:0.00093:0:33.8:22:0.0108:0.0068:0.5 0/0:941:4:0,4:449,487:0.0043:2,0:11:1:29.9:1:0.1257:0:33.3:8:0.0043:0.0032:0.5 -6 129479382 . A G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58541;SOR=0.76831;LSEQ=CAGGAACCTGTACCTTTAAT;RSEQ=TCTGCCGCTATGAAACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:885:19:13,6:470,395:0.0215:2,2:30.9:1:32.7:1:0.25194:1.82:27.3:38:0.0217:0:1 0/1:724:12:8,4:396,315:0.0166:2,2:10.6:1:29.3:1:0.56392:1.59:23:11:0.0154:0:1.3 -6 129479397 . A AC 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAATATCTGCCGCTATGAA;RSEQ=CCAAGTATGTTTTCATGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:940:0:0,0:514,425:0:2,0:24.3:1:29.9:1:1:0:53.7:103.333:1:0:0.1 0/1:773:19:11,8:424,330:0.0246:2,2:24.6:1:30.4:1:1:1.07:52.7:38:0.0248:0.0052:0.2 -6 129479522 . G A 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21777;LSEQ=GCCATGCCATTTGCCCATCC;RSEQ=TACTTCTCCATATCGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1269:431:215,216:442,396:0.3396:2,2:27.6:1:30.2:1:0.34305:1.12125:43.3:52.875:0.3379:0:1.2 0/1:1341:135:60,75:608,597:0.1007:2,2:27.4:1:29.5:1:0.20402:1.2728:43.2:44:0.0995:0:1.2 -6 129480304 . G A 98 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00511;SOR=10.64982;LSEQ=CCTGTGTACTGTCACCTTTA;RSEQ=TAATTGGTCTTGCTACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:872:1:1,0:333,538:0.0011:2,0:1:0:26:0:0.38303:0:47:2:0.0012:0:1 0/1:827:10:1,9:328,489:0.0121:2,2:17:1:29.7:1:0.05814:6.02709:26.4:20:0.0122:0:1.3 -6 131790227 . G T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0142;SOR=0;LSEQ=CACAAAGGGAAAGAGGAGAG;RSEQ=CACCGATACGTGTTCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:3,2:39,2:0.1087:1,2:22:1:28.2:1:0.05279:11.59891:60:10:0.1163:0:1 0/0:59:0:0,0:52,7:0:2,0:23.3:1:31.5:1:1:0:60:118:1:0:0.1 -6 131790416 . C A 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64155;SOR=2.20175;LSEQ=GTTACCCAGCATGCTATTGG;RSEQ=TTTGTTGTAAACAAACAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:1,0:81,127:0.0048:2,0:1:0:26:0:0.39234:0:60:2:0.0049:0:1 0/1:286:3:1,2:102,181:0.0105:2,2:17.7:1:23.7:1:1:1.12663:60:2:0.0071:0:1 -6 132626885 . G C 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=4.91839;LSEQ=TGAAGTGAACACCCAGCAAA;RSEQ=TGCAGCAGCCCTACAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:0.25:2,0:11:0:33:0:1:0:60:2:0.25:0:1 1/0:6:4:2,2:1,1:0.6667:2,2:9.5:1:33.5:1:1:1:60:8:0.6667:0:1.3 -6 132627132 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATCGCTCCATCAAGGGTG;RSEQ=AGAACTAGATGGAGGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:3,2:0.2857:2,2:33.5:1:27.5:1:1:1.41418:60:4:0.2857:0:1 -6 132840195 . G C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11136;SOR=0.34247;LSEQ=ATCTTGGCAAGAATCATGCC;RSEQ=TTAACTTGTTTGTTTACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:21:15,6:5,2:0.75:2,2:24.5:1:31.3:1:1:1:60:42:0.75:0:1.1 1/0:16:8:5,3:4,4:0.5:2,2:33.6:1:30.8:1:1:1.61:60:16:0.5:0:1.6 -6 132840197 . T A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00285;SOR=Inf;LSEQ=CTTGGCAAGAATCATGCCGT;RSEQ=AACTTGTTTGTTTACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:23,8:0:2,0:23.1:1:29.6:1:1:0:60:62:1:0:0.7 0/1:16:5:3,2:6,5:0.3125:2,2:38.8:1:29.4:1:1:1.23:60:10:0.3125:0:2 -6 132840201 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGAATCATGCCGTTAAC;RSEQ=TGTTTGTTTACAACAGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:23,10:0.0571:2,2:11:1:30.5:1:0.53613:2.24016:60:4:0.0571:0:1.5 0/0:17:0:0,0:10,7:0:2,0:26.3:1:31.2:1:1:0:60:34:1:0:0.9 -6 132840339 . G A 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00056;SOR=Inf;LSEQ=ACGGTATAACCTTTCTTGTA;RSEQ=ATTCGCATGTATGTGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,14:0:2,0:28.3:1:31:1:1:0:60:44:0.9565:0:0 0/1:23:10:5,5:6,7:0.4348:2,2:26.7:1:29.2:1:1:1.16:60:20:0.4348:0:1.2 -6 132840396 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49675;SOR=Inf;LSEQ=TTTCTAAAAGGCCTAGAGAA;RSEQ=ATGTATCAGGTGCCTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:23.9:1:32.8:1:1:0:60:50:1:0:0.1 0/1:31:2:1,1:14,15:0.0645:2,2:16:1:27:1:1:1.07:60:4:0.0645:0:1.5 -6 133309056 . C T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12449;SOR=0;LSEQ=AGTCCTGTAGCTGAAGTCAG;RSEQ=CATAAGTGAAGTCCAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:4:1,3:84,58:0.0274:2,2:16.5:1:29.5:1:0.30862:4.30279:60:8:0.0278:0:1 0/0:131:0:0,0:73,58:0:2,0:21.1:1:31.2:1:1:0:60:262:1:0:0.2 -6 134758313 . A T 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATACTTAAGATTTGTTAA;RSEQ=CCTTATCCCTGGTCAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:0:0,0:236,231:0:2,0:25.5:1:29.7:1:1:0:60:65.714:1:0:0.1 0/1:492:34:14,20:232,225:0.0691:2,2:24.6:1:29.9:1:0.29259:1.47185:60:68:0.0697:0:1.1 -6 134758428 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17765;SOR=Inf;LSEQ=ATTTTTGTAATTCCTTTTAT;RSEQ=TAATGGAACTATTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:7,98:0:2,0:22.1:1:32.7:1:1:0:60:104:1:0:0 0/1:77:2:1,1:6,69:0.026:2,2:28.5:1:26:1:0.17464:10.72:60:4:0.0263:0:1 -6 135130050 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGATCACCAGGTCAGGAGA;RSEQ=CGAGACCATCCTGCCTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:31:1:1:0:53:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 136294983 . C T 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0068;LSEQ=TTAGAAGATGCCCATTTGAA;RSEQ=GGTAACACTTTAGTTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:110:59,51:129,117:0.309:2,2:27.4:1:30.3:1:0.9086:1.05:60:109:0.307:0:1.1 0/1:364:113:55,58:120,131:0.3104:2,2:26.3:1:29.8:1:0.91001:1.04:60:226:0.3148:0:1.1 -6 136295052 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19389;SOR=Inf;LSEQ=CATCAGCTGCATGTGCTGCC;RSEQ=TGCTATTCATGCCCCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:57,147:0:2,0:22.1:1:30.3:1:1:0:60:203:1:0:0.3 0/1:161:2:1,1:47,112:0.0124:2,2:23.5:1:29:1:0.5087:2.37:60:4:0.0126:0:1 -6 136359280 . C CG 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0.5286;LSEQ=CGAAGCTGGAGAGGATCTTA;RSEQ=GGGGGTTCGCTTTTCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:0.4:2,0:11:1:31:1:0.4:0:60:4:0.4:0.2:0.5 0/1:8:2:2,0:5,1:0.25:2,0:25.5:1:30.9:1:1:0:60:4:0.25:0.125:0 -6 136359300 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48;SOR=0;LSEQ=CGGGGGTTCGCTTTTCCCTG;RSEQ=CTGGGAAGAATTTCCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:0.1538:2,2:10.5:1:28:1:1:1.67325:60:4:0.1538:0:1.5 0/0:12:0:0,0:8,4:0:2,0:14.2:1:30.7:1:1:0:60:24:1:0:0.1 -6 136359323 . TAGCAGC T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=6.000;MSILEN=3;SSF=0.22857;SOR=Inf;LSEQ=GGGAAGAATTTCCCCTGTGG;RSEQ=AGCAGCAGCAGCAGAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:27.3:1:29.1:1:1:0:60:36:1:0:0.3 0/1:18:3:1,2:8,7:0.1667:2,2:13.3:1:28.3:1:1:2.18465:60:6:0.1667:0.0556:0.7 -6 136359350 . AAACAGCAGCAGCAGC A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=4.000;MSILEN=3;SSF=0.23529;SOR=0;LSEQ=AGCAGCAGCAGCAGAAGCAG;RSEQ=AACAGCAGCAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:1,2:14,9:0.1154:2,2:26.7:1:31.7:1:0.55577:2.97549:60:6:0.1154:0:0 0/0:26:0:0,0:13,13:0:2,0:26.3:1:30.1:1:1:0:60:52:1:0:0.5 -6 136359367 . ACAG A 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.23585;SOR=Inf;LSEQ=CAGAAACAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,12:0:2,0:26.2:1:32.8:1:1:0:60:50:0.9615:0:0.2 0/1:27:3:1,2:12,12:0.1111:2,2:38.7:1:33:1:1:1.95076:60:6:0.1111:0:0.3 -6 136359446 . A C 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23636;SOR=0;LSEQ=AGAATGCCTGTGCTAGAGCG;RSEQ=TATTTCCACCCAGCAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:0,4:0.4286:0,2:19.7:1:33.3:1:0.42857:0:60:6:0.4286:0:1 0/0:4:0:0,0:0,4:0:0,0:22.8:1:28.3:1:1:0:60:8:1:0:0 -6 137519127 . C T 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=AATTAAAGCAGAAAACTGTC;RSEQ=AGGAAAATCAGACTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:275,122:0:2,0:25.5:1:31.1:1:1:0:60:55.714:1:0:0.1 0/1:417:14:9,5:269,134:0.0336:2,2:25.4:1:29.6:1:1:1.11496:60:28:0.0341:0:1 -6 137519154 . C T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03247;SOR=Inf;LSEQ=ATCAGACTTCAAAGTTGGTG;RSEQ=AACTTAGCTGATCTCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:0:0,0:334,190:0:2,0:25.5:1:32:1:1:0:60:73.857:0.9981:0:0.1 0/1:591:6:2,4:356,229:0.0102:2,2:17.5:1:26.5:1:0.21875:3.1031:60:12:0.0103:0:1 -6 137519504 . ACT A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.07266;SOR=2.2733;LSEQ=TTACTACTTAAAGGTGAAGA;RSEQ=CTCTCTCTCTATTGGAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:8:4,4:380,266:0.0122:2,2:29.1:1:31.9:1:0.72344:1.42775:60:16:0.0124:0.0015:0.1 0/1:657:18:10,8:358,279:0.0274:2,2:24.8:1:29.7:1:1:1.02649:60:17:0.0263:0.0076:0.5 -6 137519588 . A C 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31567;LSEQ=GTCACCACTTCTGTTATACT;RSEQ=GAAAGTTCTTCTGTATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:270:129,141:360,339:0.2784:2,2:25.2:1:30.5:1:0.31606:1.16055:60:540:0.2818:0:1.1 0/1:931:101:51,50:429,400:0.1085:2,2:23.3:1:30.4:1:0.83354:1.05144:60:100:0.1087:0:1.1 -6 137519780 . T C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.04488;LSEQ=CTTCTTACCACAGAGATCTA;RSEQ=GGGGAGAAAAATTGATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:124:38,86:37,112:0.4542:2,2:25.5:1:30.2:1:0.34061:1.34:60:61:0.4569:0:1.2 0/1:307:11:3,8:106,190:0.0358:2,2:19.3:1:30.1:1:0.75207:1.48591:60:22:0.0364:0:1 -6 137519834 . C CA 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.06049;SOR=0;LSEQ=TAAGCTTAAGTGCCTACCCT;RSEQ=AAAAAAAACAAAGGTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:0,5:15,94:0.0439:2,0:32.4:1:31:1:1:0:60:10:0.0446:0.0088:0.4 0/0:106:0:0,0:20,85:0:2,0:23:1:31.9:1:1:0:60:210:1:0:0.1 -6 137521825 . TA T 105 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.52222;LSEQ=ACCGTGTTTTTCCCTGAGAA;RSEQ=AAAAAAAAAACAAAATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:10,0:4,0:0.6667:0,0:22.9:1:31.8:1:1:0:59.5:20:0.6667:0:0.1 1/0:2:1:1,0:1,0:0.5:0,0:19:0:32:0:1:0:60:2:0.5:0:1 -6 137522190 . T C 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10439;SOR=Inf;LSEQ=TTACAATTAAGATGGAATAC;RSEQ=GCTATTATCTATCAAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:52,174:0:2,0:22.4:1:30:1:1:0:60:55.5:1:0:0.1 0/1:203:3:1,2:54,146:0.0148:2,2:10.7:1:22:1:1:1.35:60:2:0.0101:0:2.3 -6 137524613 . G GA 78 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.319;SOR=2.26657;LSEQ=TACTGCTCCCTCTATATTTA;RSEQ=AAAAAAAATGGCAAGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:3:2,1:265,105:0.008:2,2:16.3:1:31.7:1:1:1.26112:60:6:0.0081:0.0027:1 0/1:333:6:4,2:218,106:0.018:2,2:38.5:1:30.2:1:1:1.02824:60:12:0.0182:0:0 -6 137524760 . C T 142 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=28.69482;LSEQ=TTCAGTGAGGATACTGGAAT;RSEQ=GCTAACTGGCACTGAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:1:0,1:281,422:0.0014:2,0:1:0:29:0:1:0:60:2:0.0014:0:1 0/1:663:26:15,11:295,341:0.0392:2,2:23:1:30.3:1:0.3171:1.58:60:52:0.0395:0:1.1 -6 137524803 . G A 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06195;SOR=Inf;LSEQ=CACAATCATCTTCCTTCTGC;RSEQ=TGAGTATTTTATACTGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:0:0,0:149,332:0:2,0:26.4:1:31.2:1:1:0:60:47.1:1:0:0.1 0/1:493:5:2,3:172,316:0.0101:2,2:19.6:1:28.2:1:1:1.22:60:4:0.0083:0:1.4 -6 137524851 . G A 37 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62388;SOR=0.34586;LSEQ=AAAAAGAAAACAGTGAAAAT;RSEQ=CACAGCTTCTTTTAATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:66,195:0.0114:2,2:15.3:1:23.7:1:1:1.47:60:2:0.0081:0:3.3 0/0:253:1:1,0:70,182:0.004:2,0:1:0:22:0:0.28063:0:60:2:0.0041:0:1 -6 137525423 . G T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01793;SOR=Inf;LSEQ=TACAGAAAGGAACAACTTTT;RSEQ=CTAGCTACACAAGAATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:314,75:0:2,0:23.1:1:32:1:1:0:60:76.8:1:0:0.1 0/1:317:5:2,3:228,83:0.0158:2,2:27.4:1:27:1:0.12653:4.09838:60:10:0.0159:0:1 -6 137527446 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11151;SOR=Inf;LSEQ=TCCATTCTGAATTCTTAACA;RSEQ=TAAAAAGAATAAAAAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:44,206:0:2,0:25.9:1:32.3:1:1:0:60:82.333:1:0:0.1 0/1:233:3:1,2:48,182:0.0129:2,2:32.3:1:24.3:1:0.50922:1.89:60:2:0.0087:0:1.7 -6 137527456 . TA T 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.0481;SOR=Inf;LSEQ=ATTCTTAACACTAAAAAGAA;RSEQ=AAAAAATGCGAAGATAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:36,178:0:2,0:25.2:1:30.1:1:1:0:60:428:1:0:0.1 0/1:190:4:2,2:37,149:0.0211:2,2:12.5:1:32:0:0.18733:3.99:60:8:0.0211:0:0.3 -6 137536262 . T G 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2437;SOR=Inf;LSEQ=TCCCGTGAGGGAGACAATGT;RSEQ=ACCATACATATTTTACCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:0:1,0:25.1:1:30.6:1:1:0:60:58:1:0:0.1 0/1:60:3:3,0:56,1:0.05:1,0:21.3:1:33:1:1:0:60:6:0.05:0:1 -6 137536455 . G A 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50506;LSEQ=ATTTTCTGGTGACTTCAAAA;RSEQ=CATCTGCTTCAGGTAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:173:73,100:181,217:0.303:2,2:26.2:1:29.6:1:0.52137:1.14234:60:172:0.306:0:1.1 0/1:578:104:52,52:210,263:0.1799:2,2:23.8:1:29.5:1:0.32813:1.25:60:103:0.1807:0:1.1 -6 137536517 . G A 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18517;SOR=4.75443;LSEQ=ACAATTATATTATGGCCACT;RSEQ=CAAAAGTTGAACAATGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:1:0,1:40,202:0.0041:2,0:46:0:29:0:1:0:60:2:0.0042:0:5 0/1:207:4:2,2:42,161:0.0193:2,2:11:1:25.8:1:0.19897:3.80:60:8:0.0196:0:1 -6 137536519 . A G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.60123;SOR=2.28717;LSEQ=AATTATATTATGGCCACTGC;RSEQ=AAAGTTGAACAATGCATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:0,1:33,195:0.0044:2,0:44:0:15:0:1:0:60:0:0:0:5 0/1:201:2:1,1:42,157:0.01:2,2:41:1:30:1:0.38294:3.71:60:4:0.01:0:1 -6 137539423 . AAAAAG A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0;SOR=0.12064;LSEQ=GAATCATAAATCATAATAAA;RSEQ=AAAACTGAATTGAAAAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:48:48,0:45,1:0.5161:1,1:22.8:1:30.6:1:0.48936:0:60:96:0.5161:0.1183:0.8 0/1:71:8:8,0:63,0:0.1127:1,0:17:1:30.4:1:1:0:60:16:0.1127:0.0423:0.8 -6 137539505 . C G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26576;LSEQ=TGCACTTCAGAAAAGCCACC;RSEQ=TCAACATTTGTTTTCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:173:126,47:142,61:0.4601:2,2:24.3:1:30.4:1:0.56869:1.15:60:172:0.4636:0:1.1 0/1:423:78:59,19:230,114:0.1844:2,2:24.8:1:29.5:1:0.13996:1.54:60:156:0.1866:0:1.1 -6 137539726 . TC T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22056;SOR=1.96269;LSEQ=CCTACCCTAAGCACTTTGAG;RSEQ=CCCCCCCCCACCCCCGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:8:0,8:1,93:0.0769:1,0:35.3:1:32.5:1:1:0:60:16:0.087:0:0.6 0/1:78:11:0,11:3,64:0.141:1,0:25.4:1:30.8:1:1:0:60:22:0.1507:0:1.5 -6 137539810 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.39513;SOR=2.458;LSEQ=TGCTGATCAGGACACTCACA;RSEQ=TCATGCGTCACTTAACGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:0.2083:1,0:18:1:30.6:1:1:0:60:10:0.2083:0:1.2 0/1:10:4:0,4:0,6:0.4:0,0:22.8:1:30.3:1:1:0:60:8:0.4:0:1.5 -6 137539947 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCATGAACCTGTACAGC;RSEQ=TGTCACTGCACTGAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:27:1:30.5:1:1:1.7321:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 137540335 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.13883;LSEQ=CTGGGGCGGATCCCTCCCTC;RSEQ=CTCTCGTCCCGACCCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:262:183,79:235,100:0.4389:2,2:23.2:1:29.9:1:1:1.01446:60:20.833:0.431:0:2 0/1:450:44:36,8:281,125:0.0978:2,2:21.9:1:30.6:1:0.08506:2.00:60:43:0.0971:0:2.2 -6 137540370 . A G 297 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42903;LSEQ=CGGCCGCAGCCCTGCCGCGA;RSEQ=CGACGGTACCTGAGGACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:920:649:373,276:160,109:0.7054:2,2:26.2:1:31.8:1:0.60725:1.08604:60:48.923:0.7051:0:1.5 1/0:902:457:259,198:251,190:0.5067:2,2:25.5:1:31.3:1:0.94639:1.00991:60:34.154:0.504:0:1.3 -6 137540481 . G A 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15447;SOR=3.5003;LSEQ=CCATGCTGCTACCGACGGTC;RSEQ=CTGGCTCCAACCCCGAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:2:2,0:166,362:0.0038:2,0:1:0:25:0:0.10007:0:60:4:0.0038:0:1 0/1:458:6:4,2:153,299:0.0131:2,2:15:1:26:1:0.18747:3.90:60:5:0.011:0:1 -6 137540520 . A G 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.45481;LSEQ=GCCTGCGGGACCAGCCCAGC;RSEQ=CTGCCCTCCAGCCCCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:273:189:27,162:9,75:0.6923:2,2:24.4:1:31.5:1:0.56122:1.39:60:36.8:0.6891:0:1.4 1/0:188:95:20,75:12,80:0.5053:2,2:26.2:1:31.3:1:0.17559:1.77:60:46.5:0.5:0:1.1 -6 137540536 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08232;LSEQ=CAGCACTGCCCTCCAGCCCC;RSEQ=GCCTTACGTCACTTCCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:67:5,62:22,125:0.3131:2,2:26.1:1:30.6:1:0.18184:2.17539:60:21.333:0.3048:0:2.1 0/1:139:5:0,5:14,120:0.036:2,0:20.6:1:31.6:1:1:0:60:10:0.0362:0:1.8 -6 137723086 . C T 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGATCCCTTTCTTTGTTA;RSEQ=AGGAATGTTGTTGCCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:19.7:1:30.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 137723110 . T C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTTGTTGCCTTAAATTA;RSEQ=TCTTGTTAATGCTATGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:27.7:1:32:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 137723291 . C T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AATTATATCTTCTTATAATC;RSEQ=TTGTCTTTATTTTTTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:7,0:7,0:0.5:0,0:18.9:1:32.3:1:1:0:60:14:0.5:0:1 1/0:4:2:2,0:2,0:0.5:0,0:17:0:33:0:1:0:60:4:0.5:0:1 -6 137723535 . G GT 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01281;SOR=0.57174;LSEQ=TTTATGTTTAAACAAACACG;RSEQ=TTTTTTTTAATAATGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:62:26,36:114,133:0.1956:2,2:28.4:1:30:1:0.57138:1.18616:59.6:61:0.1955:0:1.2 0/1:328:40:19,21:118,113:0.122:2,2:30.9:1:29.2:1:0.73344:1.15356:60:39:0.1207:0:1.3 -6 137723544 . A T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19304;LSEQ=AAACAAACACGGTTTTTTTT;RSEQ=ATAATGAAATTGAGTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:307:270:115,155:14,20:0.8795:2,2:25.1:1:29:1:1:1.06:59.9:134:0.8816:0:1.2 1/0:303:177:81,96:33,32:0.5842:2,2:26.6:1:28.9:1:0.56156:1.2212:60:176:0.5867:0:1.3 -6 137723575 . T C 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGTTTCCTCCTGCACATA;RSEQ=TTGATTTTTATGTTCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:91,154:0:2,0:24.1:1:30.2:1:1:0:60:80.667:1:0:0.7 0/1:236:22:10,12:86,128:0.0932:2,2:26.7:1:30.3:1:0.65402:1.24:60:21:0.0913:0:2.2 -6 137723595 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23086;SOR=Inf;LSEQ=TTTGATTTTTATGTTCATCT;RSEQ=TGCACTTGCCTAAACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:63,130:0:2,0:25.5:1:31.8:1:1:0:60:31.167:1:0:0.6 0/1:179:2:1,1:65,111:0.0112:2,2:18:0:28.5:1:1:1.70:60:4:0.0114:0:3.5 -6 137723722 . T C 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04435;SOR=Inf;LSEQ=TTCAGAAAAAAAGGTTTGAA;RSEQ=AGACAAGCACTATTGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:1,19:0:1,0:21.6:1:28.3:1:1:0:60:40:1:0:0.1 0/1:12:3:0,3:0,9:0.25:0,0:22:1:31:1:1:0:60:6:0.25:0:1.3 -6 138026354 . G A 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAGAGGTCTAGCTACCCT;RSEQ=CCAGCCAGCCACTGAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:30:1:26.2:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 138026532 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49761;SOR=0;LSEQ=GAAAGTCCACATCTGTGGAC;RSEQ=TTCTGTGCTGAAGTTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:58,25:0.0235:2,2:6.5:1:30:1:0.52073:2.2945:60:4:0.0238:0:1.5 0/0:79:0:0,0:56,22:0:2,0:24:1:30.2:1:1:0:60:77:0.9872:0:0.1 -6 138026552 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50006;SOR=0;LSEQ=TTTCTGTGCTGAAGTTTTCC;RSEQ=GGTTTTCTCATGTGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:80,35:0.0171:2,2:29:0:32:0:0.52255:2.26782:60:4:0.0175:0:1.5 0/0:102:0:0,0:69,33:0:2,0:26.7:1:29.8:1:1:0:60:204:1:0:0.1 -6 138026868 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1905;SOR=Inf;LSEQ=CACTGTGTGGATGGTTTTGA;RSEQ=AAGGTCAATGTTGCAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:101,154:0:2,0:22.2:1:31.7:1:1:0:60:126.5:1:0:0.1 0/1:198:2:1,1:81,114:0.0101:2,2:12:1:30:1:1:1.40:60:4:0.0102:0:1 -6 138026895 . T A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.19094;SOR=Inf;LSEQ=AATGTTGCAGTTAATACCTT;RSEQ=CTCTCTGATGATGTCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:118,112:0:2,0:24.3:1:30.1:1:1:0:60:56.5:1:0:0.1 0/1:179:2:1,1:82,94:0.0112:2,2:21:0:28:1:1:1.15:60:4:0.0114:0:1 -6 138027115 . C A 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49558;LSEQ=ACCGTTCTCGCCATATTCCC;RSEQ=TGGAGTACAGCTTGTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:407:237:105,132:72,97:0.5823:2,2:26.4:1:30.4:1:0.76129:1.07:60:58.25:0.5825:0:1.7 0/1:382:156:64,92:90,135:0.4084:2,2:23.9:1:29.4:1:0.91549:1.04:60:51:0.408:0:1.8 -6 138027145 . C T 255 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTTGTCCAACCTTTGAAAA;RSEQ=TTAAGTTCTCTTAGCATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:329:329:144,185:0,0:1:0,2:25.5:1:30.5:1:1:0:60:81.25:1:0:1.5 1/0:280:159:70,89:42,79:0.5679:2,2:24:1:29.6:1:0.13949:1.48:60:25.5:0.5604:0:1.7 -6 138027229 . C T 198 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCATATTCTTGTAGAGCATC;RSEQ=TCTTCAGACCAGTATTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:122,135:0:2,0:24.2:1:31.7:1:1:0:60:127.5:1:0:0.2 0/1:230:90:52,38:82,58:0.3913:2,2:22.1:1:30.6:1:1:1.03303:60:89:0.3904:0:1 -6 138027662 . A G 300 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAATTTGCTTAGTTCTCAA;RSEQ=CTCTGCTTTCTATTTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:670:670:305,365:0,0:1:0,2:25.3:1:32:1:1:0:59.9:59.909:1:0:1.1 1/0:704:394:182,212:152,156:0.5597:2,2:25.4:1:31.6:1:0.44641:1.13476:59.8:77.8:0.5638:0:1.1 -6 138027772 . G A 277 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.43434;LSEQ=TTCTTCTTGTAATGTTCCAC;RSEQ=AGATCCGTCAAAGAATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:601:598:292,306:0,0:0.995:0,2:26.2:1:30.1:1:1:0:59.9:84.429:0.9949:0:1.1 1/1:574:572:267,305:0,1:0.9965:0,2:26.1:1:30:1:1:0:60:285:0.9965:0:1.1 -6 138027910 . A G 212 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGTGCGCACAGAGAGAAC;RSEQ=AAATCTCCAGGGTGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:134:62,72:228,269:0.212:2,2:28.8:1:30.1:1:1:1.02:60:32.5:0.2107:0:1.1 0/0:594:0:0,0:285,308:0:2,0:26.5:1:29.8:1:1:0:60:147.25:0.9983:0:0.2 -6 138028127 . G T 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATACTGGACCAACTCAGCC;RSEQ=AAGTGGCAAACTTTTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:738:0:0,0:378,359:0:2,0:25.9:1:30.4:1:1:0:60:104.286:0.9986:0:0.1 0/1:660:60:32,28:297,301:0.0909:2,2:26.6:1:29.4:1:0.68484:1.16:59.8:120:0.0922:0:1.9 -6 138028152 . C T 214 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=73.28187;LSEQ=GGCAAACTTTTCCCCCCAAA;RSEQ=GGGTCCTAGTAATCACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:713:3:1,2:361,348:0.0042:2,2:12.7:1:27:1:0.61823:2.07265:60:6:0.0043:0:1 0/1:637:151:72,79:250,235:0.237:2,2:26.5:1:29.7:1:0.45601:1.16697:60:302:0.2389:0:1.4 -6 138028543 . A C 77 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTAACCGGGAGTGGAGGCTG;RSEQ=GGCGGGAGGATCACTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:24.2:1:29.8:1:1:0:60:12:1:0:1.2 1/0:2:1:0,1:0,1:0.5:0,0:50:0:29:0:1:0:60:2:0.5:0:2 -6 138192324 . CT C 124 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.1368;SOR=1.91758;LSEQ=AAGTCAGGCTAATAGAATGG;RSEQ=TTTTTTTTTTCCTTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:12:11,1:116,6:0.0896:1,2:31.3:1:31.5:1:0.48967:1.74852:60:11:0.084:0:0.2 0/1:88:14:12,2:68,5:0.1591:2,2:24.6:1:32.7:1:0.31331:2.24031:60:28:0.1628:0.0114:0.3 -6 138192335 . TC T 42 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.27649;SOR=0;LSEQ=ATAGAATGGCTTTTTTTTTT;RSEQ=CTTTCCTTTTCAGGTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:3:3,0:140,19:0.0183:2,0:28:1:26.5:1:1:0:60:6:0.0194:0.0061:1.7 0/0:110:0:0,0:95,14:0:2,0:24.8:1:29.9:1:1:0:60:17.167:1:0:0.2 -6 138192670 . T C 189 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=54.78191;LSEQ=AAAACGAACGGTAAGACTTG;RSEQ=TCTGTTGTGTTTCTTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:1,0:128,234:0.0027:2,0:24:0:13:0:0.35537:0:60:0:0:0:4 0/1:510:67:22,45:173,266:0.1314:2,2:26.7:1:31.2:1:0.34653:1.32958:60:32.5:0.1305:0:1.1 -6 138192728 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49843;SOR=Inf;LSEQ=CTGCTGGATCCCCATTCATG;RSEQ=AGCTTTAATAGGACAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:24,120:0:2,0:24.7:1:29.8:1:1:0:60:47:1:0:0.2 0/1:149:2:1,1:20,127:0.0134:2,2:7:1:28:1:0.26283:6.22:60:4:0.0138:0:1 -6 138192730 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23513;SOR=0;LSEQ=GCTGGATCCCCATTCATGAA;RSEQ=CTTTAATAGGACAAGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:20,115:0.0146:2,2:24.5:1:29:1:0.28403:5.64:60:4:0.0148:0:1 0/0:145:0:0,0:20,125:0:2,0:21.7:1:31.5:1:1:0:60:28:1:0:0.3 -6 138192745 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24647;SOR=Inf;LSEQ=ATGAAGCTTTAATAGGACAA;RSEQ=CCCAAACTCAAATCAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:6,90:0:2,0:28.4:1:31.9:1:1:0:60:31:1:0:0.1 0/1:100:3:0,3:6,91:0.03:2,0:29:1:29.7:1:1:0:60:6:0.03:0:2 -6 138192761 . A G 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.33426;SOR=3.60719;LSEQ=ACAAGCCCAAACTCAAATCA;RSEQ=TCTTGAGATTTAGTATTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:1,0:1,79:0.0123:1,0:1:0:30:0:0.02469:0:60:2:0.013:0:1 0/1:69:3:0,3:1,65:0.0435:1,0:13:1:32:1:1:0:60:6:0.0441:0:2 -6 138195402 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTAATTCCGTGTTGTCAA;RSEQ=ACGACTTTCCACACCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27.5:1:29.5:1:1:0:60:4:1:0:2.5 -6 138195418 . A G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATACGACTTTCCACACC;RSEQ=GGAGAGGAAACTCCCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:28:1:1:0:60:4:1:0:2.5 -6 138195693 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAACTTAAGGAATTTCC;RSEQ=CCAGGTCACCTAAACTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:14:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 138195961 . TCTC T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26624;LSEQ=TAACTTGACTTTCCTTCTCT;RSEQ=CTCCTTTCTGTCCTCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:292:247:182,65:36,11:0.8459:2,2:25.5:1:31.5:1:0.85585:1.16825:60:246:0.8454:0.1473:0.2 1/0:354:210:145,65:102,43:0.5932:2,2:24.6:1:31:1:0.81541:1.0632:60:420:0.5949:0.0989:0.3 -6 138196066 . T G 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTACTGAGGAAGGCGCTGT;RSEQ=CAGCACGCTCAAGGAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:0:0,0:388,325:0:2,0:24.3:1:29.8:1:1:0:60:78.222:0.9986:0:0.1 0/1:804:40:22,18:417,347:0.0498:2,2:29.1:1:31.1:1:1:1.02:60:19:0.0483:0:1.2 -6 138196723 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19733;SOR=Inf;LSEQ=TGAAAGGGGAAAAAATAAGC;RSEQ=GAGTTATATAAATGAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:130,12:0:2,0:24.8:1:30.7:1:1:0:60:16.75:1:0:0 0/1:114:2:1,1:107,5:0.0175:1,2:15.5:1:30.5:1:0.10293:19.63123:60:4:0.0179:0:1 -6 138196799 . CT C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.06877;LSEQ=GAGTACAGGATACATTCAAG;RSEQ=TTTTTTTCACCCCGCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:7:3,4:345,189:0.0129:2,2:23.4:1:32.4:1:0.25435:2.42961:60:14:0.013:0:0.1 0/1:579:8:5,3:362,209:0.0138:2,2:22.6:1:31.6:1:1:1.03914:60:16:0.0139:0.0035:0.5 -6 138196993 . G A 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGAGATGCCTGCAGATCAC;RSEQ=GATCTGTACTTAAATGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:121,237:0:2,0:24.2:1:30.6:1:1:0:60:88.5:1:0:0.1 0/1:337:17:6,11:114,206:0.0504:2,2:16.4:1:29.6:1:1:1.01452:60:16:0.0489:0:1.1 -6 138197331 . A C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14474;LSEQ=AACTGCATTAATTCACATCT;RSEQ=TAACTAGACACTGAAACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:339:313:68,245:4,22:0.9233:2,2:24.6:1:31.6:1:0.61883:1.52:60:103.333:0.9226:0:1.1 1/0:323:205:53,152:33,85:0.6347:2,2:24.8:1:31.8:1:0.69634:1.11305:60:204:0.6335:0:1.1 -6 138197824 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCATTTTTATCCTTTTAGCA;RSEQ=TCTTGTGAGATGTAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 138198413 . C A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12242;SOR=0;LSEQ=AGTAAGCAGTTTATGTTCAG;RSEQ=TCTCTCCTGTGTCATCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:58,155:0.0139:2,2:15.7:1:30.3:1:0.18736:5.30:60:6:0.0141:0:1 0/0:218:0:0,0:70,148:0:2,0:23.3:1:31.4:1:1:0:60:53.5:1:0:0.1 -6 138199417 . G T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42884;SOR=0.4984;LSEQ=TCATGTTGCGTGAAAAGTGT;RSEQ=AGCTCTTCATCACAGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:23:23,0:5,0:0.8214:0,1:25.9:1:30.2:1:1:0:60:22:0.8148:0:1.3 1/0:13:9:9,0:4,0:0.6923:0,0:20.3:1:30:1:1:0:60:18:0.6923:0:1.2 -6 138199768 . A T 254 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00198;LSEQ=CGCCCAACTGCCCCTTCTTC;RSEQ=TGTCTGTGAACACCCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1125:328:160,168:388,408:0.2916:2,2:25.3:1:30.5:1:1:1.00:60:45.857:0.2887:0:1.1 0/0:1240:1:0,1:621,617:8e-04:2,0:1:0:24:0:0.49879:0:60:2:8e-04:0:1 -6 138199922 . C T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0284;SOR=Inf;LSEQ=AGAAGCCTATGAGCCCTTGG;RSEQ=GTGGAACCCTGAGGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:178,253:0:2,0:24.9:1:30.3:1:1:0:60:46.889:1:0:0.1 0/1:417:5:3,2:188,224:0.012:2,2:15.8:1:28:1:0.66419:1.78:60:4:0.0096:0:1.6 -6 138200369 . G T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03088;SOR=Inf;LSEQ=CTGCCTGTCTCAAGCTGCAC;RSEQ=GACTCCTGGGGACAGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:226,262:0:2,0:25.9:1:30:1:1:0:60:39.667:1:0:0.2 0/1:503:6:4,2:247,248:0.0119:2,2:24.8:1:25.7:1:0.68562:2.01:60:2:0.0082:0:1.5 -6 138200522 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23973;SOR=Inf;LSEQ=TTGACTTCCTAACACAGCGG;RSEQ=TGCTGTCCAGAAGGGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:49,160:0:2,0:22.8:1:31.8:1:1:0:60:33.833:1:0:0.1 0/1:201:2:1,1:44,154:0.01:2,2:24:1:28.5:1:0.40025:3.47:60:4:0.0101:0:1 -6 138200529 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60602;SOR=2.21996;LSEQ=CCTAACACAGCGGCTGCTGT;RSEQ=CAGAAGGGGTTTTGTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:0,1:37,141:0.0056:2,0:25:0:32:0:1:0:60:2:0.0057:0:1 0/1:162:2:1,1:28,132:0.0123:2,2:30.5:1:27.5:1:0.32689:4.65:60:4:0.0127:0:1 -6 138201076 . CAT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.54783;SOR=0;LSEQ=TTTATAGACTTAAACATATA;RSEQ=ATATATATTTCTATACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:2,0:73,1:0.0263:1,0:37.5:1:33.5:1:1:0:60:4:0.027:0:2.5 0/0:39:0:0,0:39,0:0:1,0:24.7:1:30.5:1:1:0:60:78:1:0:0.1 -6 138201452 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50994;SOR=Inf;LSEQ=ATGCTTTTTGCTGGAGCGTT;RSEQ=TCTACCGACAGTGACAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:10,97:0:2,0:24.1:1:30.3:1:1:0:60:34.667:1:0:0.1 0/1:146:2:1,1:28,116:0.0137:2,2:18:1:30:1:0.3589:4.09:60:4:0.014:0:1 -6 138201783 . GGCCT G 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGACAGAGCTTCCCAGG;RSEQ=GCCTCCACCTAATGGCGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:28.7:1:29:1:1:0:60:6:1:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 138202155 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12587;SOR=Inf;LSEQ=CTGACTTTTTAATGATCTGC;RSEQ=TGTTCTTTCCACTCAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:251,100:0:2,0:23.7:1:31.3:1:1:0:60:86.75:1:0:0.1 0/1:388:4:1,3:261,122:0.0103:2,2:12.5:1:26.5:1:0.101:6.38503:60:8:0.0105:0:1 -6 138202350 . AC A 91 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.11914;SOR=3.43598;LSEQ=GGGTGAGCCTGCCCCCGAAG;RSEQ=CCCCCCAAGCAGCGTTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:627:2:1,1:287,336:0.0032:2,2:43.5:1:31.5:1:1:1.17:60:4:0.0034:0:0 0/1:735:8:4,4:368,356:0.0109:2,2:29:1:30.5:1:1:1.03367:60:16:0.0115:0.0014:0.4 -6 138202447 . G A 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTTTCAGTTCAAGCAGAT;RSEQ=TATGGCTAACCGGAAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:202,303:0:2,0:24.4:1:32:1:1:0:60:100:1:0:0.1 0/1:589:21:7,14:233,335:0.0357:2,2:23.5:1:29.9:1:0.652:1.39029:60:42:0.036:0:1.1 -6 138202498 . G A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11417;SOR=Inf;LSEQ=CCTGCAAGAAGTGGGGCCTC;RSEQ=AGCTGTCAGTCATCATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:72,205:0:2,0:24:1:30.5:1:1:0:60:54.4:1:0:0.1 0/1:262:3:3,0:78,181:0.0115:2,0:8:1:21.3:1:0.02879:0:60:2:0.0077:0:1.3 -6 139292582 . T G 134 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00692;SOR=0.31153;LSEQ=CCAGGCACACTGGAACTCTG;RSEQ=AGAAGTTTTGCCTCATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:20:17,3:31,10:0.3226:2,2:26.6:1:31.1:1:0.51589:1.81:60:19:0.3167:0:1 0/1:78:10:9,1:53,15:0.1282:2,2:21.1:1:31.1:1:0.67756:2.52:60:20:0.1282:0:1 -6 139292609 . GA G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.0265;LSEQ=TTTGCCTCATTATATTTTAT;RSEQ=AAAAAAAAAGTATACGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:5:3,2:74,37:0.0431:2,2:27.6:1:31.2:1:1:1.32985:60:10:0.0442:0.0086:0.8 0/1:181:8:7,1:115,58:0.0442:2,2:14.4:1:31.2:1:0.27719:3.51:60:16:0.0449:0.0221:0.1 -6 139292620 . G T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14057;SOR=Inf;LSEQ=ATATTTTATGAAAAAAAAAA;RSEQ=TATACGCTATAGTGCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:96,61:0:2,0:21:1:31.1:1:1:0:60:21.429:0.9934:0:0.4 0/1:215:4:2,2:141,70:0.0186:2,2:5.8:1:25.3:1:0.60311:2.00726:60:3:0.0147:0:3.3 -6 139292658 . A T 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=27.06257;LSEQ=AGGTGTCCAGATTCTACCAT;RSEQ=ATTTATTTCTTTAGTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:1:0,1:137,97:0.0043:2,0:13:0:12:0:0.41702:0:60:0:0:0:1 0/1:356:37:21,16:177,142:0.1039:2,2:24.4:1:28.1:1:1:1.05:59.9:36:0.102:0:1.4 -6 139292683 . A G 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.37869;LSEQ=ATTTCTTTAGTTGCCAATAA;RSEQ=TTATCAGTTTTTAAAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:65:37,28:100,95:0.249:2,2:25.5:1:32.1:1:0.47468:1.25:60:64:0.25:0:1 0/1:368:41:19,22:175,152:0.1114:2,2:25.7:1:31.4:1:0.41051:1.33205:60:82:0.1129:0:1.1 -6 139292727 . TA T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.38522;SOR=3.28821;LSEQ=TACAATTACTCTGCTATAGA;RSEQ=AAAAAAAGTGGGGGTAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:77,115:0.0052:2,0:32:0:32:0:1:0:60:2:0.0052:0:0 0/1:237:4:1,3:81,152:0.0169:2,2:28.3:1:31.5:1:1:1.59577:60:8:0.017:0:0.3 -6 139292767 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24485;SOR=Inf;LSEQ=TAAGGGAAAAAGATCCTGAA;RSEQ=GGGAGGGAGGGGAAAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:29,92:0:2,0:25.1:1:30.8:1:1:0:60:59.5:1:0:0.1 0/1:120:2:1,1:22,96:0.0167:2,2:18.5:1:30:1:0.3479:4.29:60:4:0.0167:0:1 -6 139309070 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49491;SOR=Inf;LSEQ=TGCGGCTGCGGCTGCGACTA;RSEQ=GGCTCCGGCTCCGGCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:14,7:0:2,0:23.8:1:30.3:1:1:0:60:20:1:0:0.1 0/1:26:2:1,1:14,10:0.0769:2,2:31.5:1:28.5:1:1:1.38168:60:4:0.08:0:1.5 -6 139320432 . GT G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.52809;SOR=Inf;LSEQ=GCACTTCCTTGTAAAATCCA;RSEQ=TTTAGCAAAGAACATGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:11,14:0:2,0:24.5:1:29.2:1:1:0:60:24:1:0:0.3 0/1:43:2:1,1:19,22:0.0465:2,2:17.5:1:31.5:1:1:1.15:60:4:0.0465:0:0.5 -6 139320458 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51052;SOR=Inf;LSEQ=GCAAAGAACATGCTAAGTCA;RSEQ=TTTAGCAAGAAGCCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:0:2,0:20.2:1:31.8:1:1:0:60:34:1:0:0.5 0/1:26:2:1,1:9,15:0.0769:2,2:32.5:1:29:1:1:1.63:60:4:0.0769:0:2 -6 139320470 . G C 104 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02734;SOR=9.39347;LSEQ=CTAAGTCAGTTTAGCAAGAA;RSEQ=CCCCCACCCTCAATATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:4,7:0.0833:2,0:38:0:33:0:1:0:60:2:0.0833:0:7 0/1:21:10:3,7:5,6:0.4762:2,2:24.8:1:31.4:1:0.65944:1.88324:60:20:0.4762:0:1.4 -6 139320493 . G A 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CCCACCCTCAATATGTGATC;RSEQ=ACCTGGAAAATCTGACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:35.7:1:31.8:1:1:0:60:12:1:0:1.3 0/1:10:2:0,2:2,6:0.2:2,0:22.5:1:32:0:1:0:60:4:0.2:0:2 -6 143236425 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19843;SOR=0;LSEQ=GATGTAATTAGTTAGGATGA;RSEQ=ATCACACTGTAGTAGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:10,11:0.087:2,2:14.5:1:29:1:1:1.10:60:4:0.087:0:1 0/0:28:0:0,0:13,15:0:2,0:24.4:1:29.9:1:1:0:60:13:1:0:0.3 -6 147728025 . A G 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00845;SOR=Inf;LSEQ=TGTCAGGGGTGGGAGAAGCC;RSEQ=TGGATCCCGGGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:55,67:0:2,0:25.1:1:30.1:1:1:0:60:121:1:0:0.1 0/1:144:8:3,5:67,69:0.0556:2,2:30:1:30.5:1:0.71957:1.61305:60:16:0.0567:0:1.3 -6 147728034 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50121;SOR=Inf;LSEQ=TGGGAGAAGCCATGGATCCC;RSEQ=GGCAGCAGCAACTGCCTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:53,78:0:2,0:24.2:1:29.4:1:1:0:60:25.2:0.9921:0:0.2 0/1:154:2:2,0:69,83:0.013:2,0:18.5:1:28.5:1:0.21093:0:60:4:0.0131:0:1 -6 147728037 . C A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.09609;SOR=0;LSEQ=GAGAAGCCATGGATCCCGGG;RSEQ=AGCAGCAACTGCCTCAACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:1,2:48,81:0.0227:2,2:27:1:28:1:1:1.18373:60:6:0.0236:0:1.3 0/0:155:0:0,0:67,88:0:2,0:26.7:1:31.7:1:1:0:60:154:1:0:0.2 -6 147728079 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60103;SOR=2.28263;LSEQ=CCCCCCAGGGCCAAGGGCAG;RSEQ=CACCGGCGCAGCGCCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:0,1:35,67:0.0097:2,0:43:0:14:0:1:0:60:0:0:0:6 0/1:91:2:1,1:31,58:0.022:2,2:25:1:31:1:1:1.86:60:4:0.022:0:1 -6 147728092 . GC G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.57284;SOR=2.79404;LSEQ=AGGGCAGCCACCGGCGCAGC;RSEQ=CCCCCAGGGGCAGGGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:0,1:33,57:0.011:2,0:42:0:34:0:1:0:60:2:0.0114:0:0 0/1:66:2:1,1:20,44:0.0303:2,2:27:1:30.5:1:0.53846:2.17:60:4:0.0303:0:0 -6 147728099 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51299;SOR=0;LSEQ=CCACCGGCGCAGCGCCCCCC;RSEQ=GGGGCAGGGCCCGCGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:35,55:0.0217:2,2:18.5:1:31.5:1:1:1.56:60:4:0.0227:0:1.5 0/0:64:0:0,0:26,38:0:2,0:20.3:1:30.4:1:1:0:60:63:1:0:0.1 -6 147728117 . C T 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCAGGGGCAGGGCCCGCGGT;RSEQ=CAGACCAGGGCACCCGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:21:11,10:44,29:0.2234:2,2:20.4:1:30.5:1:0.6172:1.3745:60:42:0.2234:0:1.2 0/0:69:0:0,0:42,27:0:2,0:15.4:1:31.7:1:1:0:60:68:1:0:0.1 -6 147728866 . C A 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11447;SOR=5.3194;LSEQ=CAGTGAAACAGCCACCACCC;RSEQ=TGGTTCCCCAGAGCCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:1:1,0:235,253:0.002:2,0:1:0:26:0:0.48262:0:60:2:0.0021:0:1 0/1:463:5:3,2:200,258:0.0108:2,2:12.8:1:29:1:0.65783:1.93:60:10:0.011:0:1.2 -6 147729477 . T G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00049;SOR=0.15896;LSEQ=CTGTTCATAGTTGTAGCTTG;RSEQ=GGTGGTTATTGTAGTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:41:1,40:2,16:0.6949:2,1:28.5:1:31.2:1:0.21806:4.84566:56.7:82:0.6949:0:1 0/1:23:6:1,5:1,16:0.2609:1,2:25.2:1:30.5:1:0.46245:3.01:56.3:12:0.2609:0:1 -6 148266173 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATCTAAACTCCATAGTG;RSEQ=TCCACTGGAAGCCTTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17.5:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 148266417 . T C 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTGCCTTGCTCAAGATA;RSEQ=CCACAGCCAGAACTGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:13:1:32.3:1:1:0:60:8:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 148266419 . C A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCTGCCTTGCTCAAGATATC;RSEQ=ACAGCCAGAACTGACCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:13.3:1:31:1:1:0:60:6:0.75:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 148266575 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5841;SOR=2.52788;LSEQ=TCAGATTTTTAACCCCCAAA;RSEQ=GTTATTTATCCGTGTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:1,0:46,0:0.0213:1,0:13:0:32:0:1:0:60:2:0.0213:0:2 0/1:38:2:2,0:34,2:0.0526:2,0:22.5:1:31:0:1:0:60:4:0.0541:0:2 -6 148266586 . C T 163 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01357;LSEQ=ACCCCCAAACGTTATTTATC;RSEQ=GTGTATAAATACATGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:35:35,0:20,0:0.6364:1,1:25.9:1:31.9:1:1:0:60:70:0.6364:0:2.1 0/1:45:1:1,0:41,2:0.0222:1,0:11:0:33:0:1:0:60:2:0.0227:0:2 -6 148266603 . C A 180 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCCGTGTATAAATACATGT;RSEQ=AGATGCTCATTTAAAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:82,0:0,0:1:0,1:24.6:1:28.4:1:1:0:60:164:1:0:1.5 1/0:61:44:42,2:16,1:0.7213:1,1:26.6:1:28:1:1:1.31:60:21:0.7119:0:1.2 -6 148266753 . C T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.6778;LSEQ=AGGGTGATGAATAAAAGTGA;RSEQ=GCTATTGGAGAGGGATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:246:123,123:262,235:0.3311:2,2:22.9:1:30.3:1:0.53264:1.11473:60:122:0.3311:0:1.1 1/0:657:459:231,228:102,96:0.6986:2,2:25.3:1:29.7:1:0.79906:1.04865:60:64.571:0.6954:0:1.2 -6 148266755 . C T 137 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=5.90749;LSEQ=GGTGATGAATAAAAGTGACG;RSEQ=TATTGGAGAGGGATGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:742:5:0,5:380,357:0.0067:2,0:1:0:26.8:1:0.02725:0:60:10:0.0069:0:1 0/1:674:26:12,14:329,318:0.0386:2,2:25.9:1:29.2:1:0.69224:1.20668:60:52:0.0392:0:2.3 -6 148266965 . A G 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=GTTCCTACCTTGTGCCAGGC;RSEQ=CTAGGGTTATGCAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:23:0,23:0,15:0.6053:1,1:24.5:1:31.3:1:1:0:60:22:0.5946:0:1.2 0/0:15:0:0,0:0,15:0:1,0:26.4:1:30.7:1:1:0:60:30:1:0:0 -6 148267180 . T A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTATAAAAGACTCCTAA;RSEQ=TTAAAATTAGCTACCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 149159629 . A G 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23548;SOR=0.75671;LSEQ=GGAAGCCTGGCAGGGCCTGA;RSEQ=ATTCTGCATTTCTAACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:82:56,26:60,33:0.4686:2,2:24.1:1:31.3:1:0.63325:1.18:60:40:0.4651:0:1.1 0/1:175:70:42,28:67,37:0.4:2,2:22.3:1:30.6:1:0.63213:1.20588:60:22.333:0.3964:0:1.1 -6 149159687 . C A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24873;SOR=Inf;LSEQ=TGTTGCTGTTGCTGTTGCTG;RSEQ=TGGTCCATAGACGTCACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:107,148:0:2,0:27.9:1:31.9:1:1:0:60:41.5:1:0:0.4 0/1:263:3:2,1:115,145:0.0114:2,2:19:1:29.3:1:0.58683:2.51:60:6:0.0116:0:1.3 -6 149159725 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=TGTCAGTGTCAAGGCTCTCC;RSEQ=TCTCCTTTAAAATGATCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:55,116:0:2,0:23.5:1:30:1:1:0:60:170:1:0:0.2 0/1:143:2:1,1:49,92:0.014:2,2:11.5:1:29:1:1:1.87:60:4:0.0145:0:1 -6 149215481 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23469;SOR=0;LSEQ=ATGAAGATGAGGTCATACTG;RSEQ=AGAAGGGTGGACCCTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:15,7:0.0833:2,2:18:0:31:1:1:2.07024:60:4:0.0833:0:1.5 0/0:25:0:0,0:14,11:0:2,0:20.4:1:30.6:1:1:0:60:24:1:0:0.1 -6 149307085 . C G 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=AAGGAGGCAGGAAGAGCCAT;RSEQ=AAACCCATAGTAGATCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:28.5:1:33.5:1:1:0:60:4:0.5:0:1 0/0:6:0:0,0:6,0:0:0,0:33.2:1:31.3:1:1:0:60:12:1:0:0 -6 149982813 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21225;SOR=0;LSEQ=CTCTCAGAACCTCAAAACAC;RSEQ=TCGCATTTCAGGCCCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:127,21:0.0133:2,2:41.5:1:31:1:0.27266:5.93182:60:4:0.0136:0:1 0/0:175:0:0,0:124,50:0:2,0:22.9:1:30.1:1:1:0:60:28:0.9941:0:0.2 -6 149983216 . G A 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.56676;LSEQ=TGTCTCAGGTCACTGGAGAA;RSEQ=TCAATTGTTTTAAAAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:504:157:69,88:162,185:0.3115:2,2:26:1:30.5:1:0.62948:1.11656:60:77.5:0.3094:0:1.1 0/1:598:122:66,56:223,253:0.204:2,2:22.4:1:29.8:1:0.15677:1.34:60:60:0.2034:0:1.1 -6 149997233 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16776;SOR=Inf;LSEQ=CCTAGGCTCAAGCAATCCTC;RSEQ=TGCCTCAGCCTCCCAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:79,1:0:1,0:24.7:1:31.5:1:1:0:60:160:1:0:0 0/1:56:2:2,0:54,0:0.0357:1,0:10.5:1:28:1:1:0:60:4:0.0357:0:1 -6 149997283 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.97487;LSEQ=TGGGTGTGAGCCACTGCACC;RSEQ=GGCCCAAGTTCATTCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:0,1:146,37:0.0054:2,0:1:0:26:0:0.20652:0:60:2:0.0056:0:1 0/1:187:2:1,1:149,36:0.0107:2,2:8:1:30.5:1:0.35743:4.09625:60:4:0.0108:0:1 -6 149997343 . C A 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGTACTAATAAATAAAAGT;RSEQ=AATGATGTAGCAACTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:0:0,0:353,201:0:2,0:24.1:1:31.5:1:1:0:60:91.333:0.9982:0:0.1 0/1:657:51:27,24:366,238:0.0776:2,2:20.9:1:28.6:1:0.29989:1.36625:60:50:0.077:0:1.2 -6 149997512 . C A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12442;SOR=Inf;LSEQ=CTGTGTGTATCCTAAAATAA;RSEQ=AAAGTTATTTATAAGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:86,232:0:2,0:24.3:1:32.1:1:1:0:60:158:1:0:0.1 0/1:336:4:2,2:106,225:0.0119:2,2:12.5:1:26.5:1:0.59689:2.12:60:8:0.012:0:1 -6 149997620 . A G 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2225;SOR=Inf;LSEQ=TTATTATAAGCCTGAAAAAT;RSEQ=AGGCATATTCTAGTGTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:149,61:0:2,0:22.4:1:29.2:1:1:0:60:420:1:0:0.4 0/1:188:2:1,1:122,64:0.0106:2,2:26:0:30.5:1:1:1.89933:60:4:0.0106:0:1 -6 149997657 . T C 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05292;SOR=0.71801;LSEQ=CGTTTTGGCTGGTCTAAAGG;RSEQ=CTACTGAGAATATATATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:114:69,45:134,58:0.3725:2,2:26.8:1:31.3:1:0.10504:1.50463:60:56:0.3746:0:1.1 0/1:328:98:66,32:140,90:0.2988:2,2:28.1:1:31.3:1:0.31819:1.32:60:31.667:0.295:0:1.2 -6 149997665 . G T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12532;SOR=Inf;LSEQ=CTGGTCTAAAGGTCTACTGA;RSEQ=AATATATATGAAAGAAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:216,117:0:2,0:26.4:1:31.7:1:1:0:60:110:1:0:0.4 0/1:363:4:2,2:223,136:0.011:2,2:26.5:1:28.3:1:0.63671:1.63732:60:8:0.0111:0:1.5 -6 149997936 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16678;SOR=Inf;LSEQ=CAGTAAACCTGAAGTCTATT;RSEQ=AATCTTCTGACATCGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:16,118:0:2,0:21.4:1:28.4:1:1:0:60:268:1:0:0.1 0/1:93:2:1,1:10,81:0.0215:2,2:5:1:26:1:0.2237:7.77:60:4:0.0215:0:1.5 -6 150000946 . T C 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49809;SOR=0;LSEQ=AGTGATGATACCATCTTATA;RSEQ=TTTACTACATCAATAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:115,11:0.0156:2,2:5:0:29.5:1:0.17938:10.05293:60:4:0.0157:0:1 0/0:125:0:0,0:108,17:0:2,0:21:1:29.8:1:1:0:60:40.667:1:0:0.1 -6 150004027 . A C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54297;SOR=0.58486;LSEQ=ATAGGAAATTCTGAATAAAT;RSEQ=TTGAAATACTAAAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:9,0:24,0:0.2727:1,0:26.2:1:30.6:1:1:0:60:8:0.25:0:2 0/1:28:5:5,0:21,2:0.1786:2,0:17.2:1:31.2:1:1:0:60:10:0.1852:0:1 -6 150004779 . A G 226 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01017;SOR=0.70472;LSEQ=ATTGCAGTGACTGTTGTAGC;RSEQ=GAAGGCTGAGAATTAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:176:90,86:158,191:0.3352:2,2:25:1:30.3:1:0.2288:1.26:60:175:0.3378:0:1.1 0/1:515:135:54,81:164,216:0.2621:2,2:25.7:1:29.3:1:0.54427:1.1386:60:26:0.2574:0:1.1 -6 150005615 . T C 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATCTGTCTGTGAGTTGGGAC;RSEQ=CTCAGAATGATAGGCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:176,255:0:2,0:24.4:1:30.3:1:1:0:60:42.1:1:0:0.1 0/1:537:26:13,13:216,294:0.0484:2,2:25.9:1:31:1:0.54288:1.36:60:52:0.0494:0:1.3 -6 150005739 . A G 105 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01472;SOR=9.05601;LSEQ=TGCACATTCCCTATGGTTAT;RSEQ=AGAGAGATAAAGAGAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:38,113:0.0065:2,0:30:0:33:0:1:0:60:2:0.0066:0:1 0/1:196:11:3,8:58,127:0.0561:2,2:14:1:30.5:1:1:1.21664:60:22:0.0561:0:1.1 -6 150016376 . TA T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.5454;SOR=1.7187;LSEQ=TCCTGATATGAATTGAAGTT;RSEQ=AAAAAAAAGAAACAAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:4:0,4:64,223:0.0137:2,0:19.5:1:32:0:0.5793:0:60:8:0.014:0:0 0/1:301:7:1,6:80,214:0.0233:2,2:23.4:1:30.3:1:0.67894:2.23809:60:14:0.0233:0:0 -6 150016576 . G A 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=0;LSEQ=TCAAGCCACTTTGGGAGGCC;RSEQ=AGGTGGTCAGATCACTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:0,7:0.3636:0,0:33.8:1:28.8:1:1:0:60:8:0.3636:0:1 0/0:4:0:0,0:0,4:0:0,0:17.3:1:32.5:1:1:0:60:8:1:0:0.3 -6 150022869 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22925;SOR=Inf;LSEQ=CACCCAAAAAGTGTTATGTA;RSEQ=CATAAGGTAAGAAGAATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:137,29:0:2,0:21.3:1:32.2:1:1:0:60:54.333:1:0:0.1 0/1:153:2:1,1:121,30:0.0131:2,2:28:1:29:1:0.36524:3.98411:60:4:0.0133:0:1 -6 150023348 . C G 135 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04111;SOR=0.27182;LSEQ=TGAGCAAAAGTGAAAATGAT;RSEQ=CTTCAAGGAAGTCCCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:18:0,18:0,50:0.2647:1,1:25.1:1:32.6:1:1:0:60:36:0.2769:0:1.2 0/1:34:3:0,3:0,31:0.0882:1,0:15.3:1:33:0:1:0:60:6:0.0909:0:1 -6 151176771 . C T 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0258;SOR=0;LSEQ=TTTGGGCCCTGTATTTTTAA;RSEQ=CTTCTTGTCAAATTTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:3,5:3,7:0.4444:2,2:21.6:1:31.6:1:1:1.37:52.5:16:0.4444:0:1 0/0:9:0:0,0:2,7:0:2,0:34.9:1:31:1:1:0:53.9:18:1:0:0.1 -6 152128937 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16144;SOR=Inf;LSEQ=TCGCGTGTCGGCGGGACATG;RSEQ=GCTGCGTCGCCTCTAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:160,6:0:1,0:23.1:1:31.5:1:1:0:60:32.2:1:0:0.1 0/1:112:2:2,0:102,8:0.0179:2,0:27.5:1:32:0:1:0:60:4:0.0179:0:1 -6 152129063 . C T 193 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=105.15131;LSEQ=GGACCATGACCATGACCCTC;RSEQ=ACACCAAAGCATCTGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1294:1:0,1:713,578:8e-04:2,0:1:0:24:0:0.44814:0:60:2:8e-04:0:2 0/1:1262:95:58,37:620,545:0.0753:2,2:24.8:1:29.5:1:0.16405:1.38:60:46.5:0.0748:0:2.1 -6 152129077 . T C 299 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.6447;LSEQ=ACCCTCCACACCAAAGCATC;RSEQ=GGGATGGCCCTACTGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1394:995:530,465:213,183:0.7138:2,2:25.2:1:30.1:1:0.9052:1.02118:60:44.227:0.7133:0:1.2 1/0:1335:823:441,382:266,244:0.6165:2,2:24.2:1:29.7:1:0.61195:1.06:60:81.3:0.6168:0:1.3 -6 152129308 . G C 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03415;LSEQ=GGCCCCGGGTCTGAGGCTGC;RSEQ=GCGTTCGGCTCCAACGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1053:801:355,446:111,136:0.7607:2,2:25:1:30.1:1:0.88369:1.02538:60:56.214:0.7663:0:1.2 0/1:870:85:37,48:357,423:0.0977:2,2:22.8:1:29.3:1:0.73168:1.09474:60:41.5:0.0971:0:1.2 -6 152129488 . G A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19248;SOR=4.54844;LSEQ=GTGCGCGAGGCCGGCCCGCC;RSEQ=GCATTCTACAGGTACCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:0,1:71,189:0.0038:2,0:8:0:32:0:1:0:60:2:0.0038:0:1 0/1:232:4:2,2:77,151:0.0172:2,2:7:1:29.5:1:0.60687:1.95:60:8:0.0176:0:1 -6 152129545 . AGGAG A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=6.000;MSILEN=4;SSF=0.34952;SOR=3.33923;LSEQ=GGGTGGCCGCCGCGCCCGGC;RSEQ=GGAGGGAGGGAGGGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:1:0,1:7,47:0.0182:2,0:44:0:33:0:1:0:60:2:0.0182:0:0 0/1:51:3:1,2:13,34:0.0588:2,2:35.7:1:31.7:1:1:1.30:60:6:0.06:0:1 -6 152129588 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0068;SOR=Inf;LSEQ=AGAAGGGAGAGCCTAGGGAG;RSEQ=TGCGGGAGCCGCGGGACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:0,16:0:1,0:18.8:1:33.3:1:1:0:60:32:1:0:0.1 0/1:16:7:1,6:1,8:0.4375:2,2:29:1:30.1:1:1:1.31:59.3:14:0.4375:0:1.1 -6 152163335 . T C 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTTCCAAATGTCCCAGC;RSEQ=GTTTTATGCTTTGTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:31:1:32:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 152164026 . A G 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00373;SOR=0;LSEQ=GAATCAGCCATTTGTACAAA;RSEQ=CATGAATCCCTAGTAGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:12:0,12:2,98:0.1071:1,0:25.8:1:32.2:1:1:0:60:24:0.1091:0:1 0/0:73:0:0,0:0,73:0:1,0:22.8:1:29.8:1:1:0:60:72:1:0:0.1 -6 152164239 . C T 43 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGTTGTCTGTGCCCTGA;RSEQ=TGGGGAATGCCAGATGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:26:1:27.7:1:1:0:60:6:0.75:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 152201853 . G T 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00799;SOR=0;LSEQ=TGATAAAAACAGGAGGAAGA;RSEQ=CTGCCAGGCCTGCCGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:589:8:4,4:287,293:0.0136:2,2:23.9:1:29.8:1:1:1.02:60:16:0.0137:0:1.8 0/0:542:0:0,0:254,288:0:2,0:24.6:1:31.5:1:1:0:60:48.273:1:0:0.9 -6 152201875 . T C 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=93.91628;LSEQ=TGCCAGGCCTGCCGGCTCCG;RSEQ=AAATGCTACGAAGTGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:484:401:194,207:39,44:0.8285:2,2:25.5:1:32.1:1:0.90402:1.06:60:132.667:0.8292:0:1.1 1/1:456:455:211,244:0,0:0.9978:0,2:24.8:1:31.4:1:1:0:60:112.75:1:0:1.2 -6 152201963 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50098;SOR=0;LSEQ=CCTGGCCACCGCCCAGTGCT;RSEQ=GCTCTACCCATTGGAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:35,158:0.0103:2,2:23:1:31:1:0.33592:4.47:60:4:0.0103:0:1 0/0:170:0:0,0:42,128:0:2,0:23.8:1:30.3:1:1:0:60:169:1:0:0.5 -6 152202007 . T C 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64156;SOR=1.28817;LSEQ=ATGGGAATTTTGTGTTTTTT;RSEQ=CTTTTAATTGTTTTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:68:0,68:0,13:0.8395:1,1:22.8:1:31.7:1:1:0:60:67:0.8375:0:1 1/1:62:54:0,54:0,8:0.871:0,1:24.8:1:31.1:1:1:0:60:53:0.8689:0:1 -6 152265282 . A AT 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16891;SOR=0.79196;LSEQ=CACGGGAAAAAAATAAACTA;RSEQ=TTTTTTTTTCCACCTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:358:251:185,66:71,29:0.7011:2,2:22.5:1:30.7:1:0.59755:1.14:60:124.5:0.7054:0.1508:0.1 1/0:340:221:155,66:84,32:0.65:2,2:23:1:29.5:1:0.70599:1.11736:60:43.2:0.6448:0.1676:0.2 -6 152265522 . G C 276 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04115;SOR=0.73458;LSEQ=TTGTTGGATGCTGAGCCCCC;RSEQ=ATACTCTATTCCGAGTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:538:435:200,235:43,58:0.8086:2,2:23.6:1:31.5:1:0.57978:1.15:60:71.5:0.8094:0:1.1 1/0:566:428:204,224:59,76:0.7562:2,2:24.8:1:30.9:1:0.4306:1.17:60:141.667:0.7576:0:1.1 -6 152332921 . C G 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGTTTGCTCCTAACTTGCT;RSEQ=TTGGACAGGTAAGTGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:50:16,34:167,370:0.085:2,2:25.1:1:31.8:1:0.87446:1.04:60:49:0.0848:0:1.1 0/0:529:0:0,0:180,347:0:2,0:25:1:31.6:1:1:0:60:262.5:0.9962:0:0.1 -6 152333032 . A G 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00353;SOR=0;LSEQ=GTGAAGCTTCAGAGAACTTT;RSEQ=TTAGGTATGTTTACTTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:12:0,12:1,74:0.1379:1,0:23.6:1:32.6:1:1:0:60:24:0.1379:0:1 0/0:53:0:0,0:1,52:0:1,0:18.2:1:29.6:1:1:0:60:52:1:0:0.1 -6 152381781 . C G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=TTTAGAATATAGTAGCAGAT;RSEQ=AATATACGTGTATTAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:33.5:1:32:1:1:0:60:8:1:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:29:1:1:0:60:4:1:0:1.5 -6 152382089 . TTTTA T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.21925;SOR=Inf;LSEQ=GATTTTCTGTTTTTTAATCT;RSEQ=TTTATTTATTTATTTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:162,18:0:2,0:21.3:1:30.1:1:1:0:60:29:1:0:0.1 0/1:159:2:1,1:136,21:0.0126:2,2:16:1:25:1:0.25834:6.35052:60:4:0.0127:0.0063:1 -6 152382382 . G A 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00152;SOR=Inf;LSEQ=GAAAGAAACTACTGACACAC;RSEQ=TTTTAAAATAACCTACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:2,45:0:1,0:21.4:1:31.4:1:1:0:60:22.5:1:0:0.1 0/1:54:10:0,10:0,44:0.1852:1,0:27.5:1:30.7:1:1:0:60:20:0.1887:0:1.3 -6 152414420 . CA C 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTGTCTCAAAAAAAAAA;RSEQ=AAAAAAAAAAACTAAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:29.9:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 152415753 . C A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25773;SOR=0;LSEQ=AGACATAAAGAAAACATGCC;RSEQ=CCAAACCTATGTGACAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:1,2:45,168:0.0139:2,2:17.3:1:24.7:1:0.51433:1.86:60:2:0.0093:0:1.7 0/0:172:0:0,0:47,125:0:2,0:22.1:1:30.7:1:1:0:60:85:1:0:0.1 -6 152415776 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52416;SOR=0;LSEQ=AAACCTATGTGACAGCTGGC;RSEQ=GGGAAGGACTGGTGCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:0,2:11,132:0.0138:2,0:8:1:29:1:1:0:60:4:0.0138:0:1 0/0:91:0:0,0:13,77:0:2,0:22.3:1:29.8:1:1:0:60:44:0.9888:0:0.1 -6 152419807 . A G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06812;SOR=Inf;LSEQ=CTTCCCCTTCTAGGGATTTC;RSEQ=GCACTCCTGGGGCTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:169,28:0:2,0:26.7:1:30.2:1:1:0:60:196:1:0:0.1 0/1:137:3:2,1:113,20:0.0219:2,2:31.3:1:29.7:1:0.39785:2.79596:60:6:0.0221:0:1 -6 152420095 . G A 205 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=59.63035;LSEQ=GCAGAGGGTTTCCCTGCCAC;RSEQ=GTCTGAGAGCTCCCTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:2:2,0:233,393:0.0032:2,0:1:0:26.5:1:0.13966:0:60:4:0.0032:0:1 0/1:661:106:45,61:237,318:0.1604:2,2:22.4:1:30.6:1:1:1.01026:60:212:0.1621:0:1.2 -6 153023013 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05141;SOR=Inf;LSEQ=ATAATTTTCAATATTGTCCC;RSEQ=TAACCCTAGAGCTGCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:46,0:0:1,0:24.2:1:29.9:1:1:0:60:45:1:0:0.1 0/1:14:2:2,0:12,0:0.1429:0,0:35:1:30:0:1:0:60:4:0.1429:0:1 -6 153023151 . G A 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00385;SOR=1.67015;LSEQ=GATACCCAAGGGTTCTCAGA;RSEQ=CGGCTTGCCATCTTTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:90:48,42:94,88:0.3309:2,2:25.6:1:29.7:1:0.79811:1.07:60:89:0.3333:0:1.7 0/1:274:124:73,51:83,67:0.4526:2,2:27.8:1:29.5:1:0.62418:1.15:60:61:0.4552:0:1.9 -6 153023184 . A G 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=1.83722;LSEQ=TTTCCCAGGAAGCTGGAAAT;RSEQ=AGTACCAGTTCCTCTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:90:40,50:85,105:0.3214:2,2:25.4:1:31.9:1:1:1.01186:60:180:0.3226:0:1.7 0/1:305:142:74,68:82,80:0.4656:2,2:24.5:1:30.8:1:0.81879:1.06:60:141:0.4653:0:1.8 -6 153023257 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11471;SOR=Inf;LSEQ=GGCTGGAGAGTGATGCTTCC;RSEQ=TTCTCCAAAACCCTTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:46,118:0:2,0:23.3:1:31.3:1:1:0:60:53.667:1:0:0.2 0/1:156:3:2,1:51,102:0.0192:2,2:12.7:1:29:1:0.26644:3.96:60:6:0.0195:0:1.3 -6 153023277 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49789;SOR=Inf;LSEQ=CTTCTCCAAAACCCTTACAG;RSEQ=TCGTATTCTATATAGCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:22,90:0:2,0:24.2:1:31.4:1:1:0:60:36.333:0.9909:0:0.1 0/1:116:2:1,1:28,86:0.0172:2,2:25:1:25.5:1:0.43913:3.04:60:4:0.018:0:1 -6 153082870 . C G 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10294;SOR=0;LSEQ=AGGCACCGCAGACCAGGTGT;RSEQ=TCAAACAAAGAAATCAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:19.8:1:32.3:1:1:0:60:8:0.4444:0:1 0/0:7:0:0,0:6,1:0:2,0:29.4:1:32.1:1:1:0:60:14:1:0:0 -6 153269698 . G A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20705;SOR=0.36195;LSEQ=CAGCAGGCTGTAGATGCCTC;RSEQ=CACGCTGACTCCACACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:7,2:11,9:0.3103:2,2:19.2:1:31.1:1:0.41183:2.77:60:18:0.3103:0:2.6 0/1:29:4:2,2:12,13:0.1379:2,2:32:1:31.3:1:1:1.08:60:8:0.1379:0:2.5 -6 153269715 . A G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.2231;SOR=0.406;LSEQ=CTCGCACGCTGACTCCACAC;RSEQ=GCAGAGCCTTCAGAGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:10:7,3:11,12:0.303:2,2:23.2:1:30.7:1:0.2828:2.47:60:20:0.303:0:2.5 0/1:27:4:2,2:10,13:0.1481:2,2:31.8:1:31.8:1:1:1.29:60:8:0.1481:0:2.5 -6 153269782 . T A 118 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03162;SOR=0;LSEQ=ATCTCAAGGGATAATATCAG;RSEQ=GTTAGCAATCTTAGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:1:0,2:19.9:1:30.3:1:1:0:60:30:1:0:1.9 1/0:8:5:0,5:0,3:0.625:0,0:21.8:1:30.6:1:1:0:60:10:0.625:0:1.4 -6 153269819 . C T 72 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATAATTTTAAGTAAAAA;RSEQ=ATATTTATCAGCGTGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:29.2:1:28:1:1:0:60:12:1:0:2.2 1/1:4:4:1,3:0,0:1:0,2:31:1:24.5:1:1:0:60:3:1:0:1.5 -6 153412390 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17977;SOR=Inf;LSEQ=AGGAAAACAATCTAAAGGCA;RSEQ=AAGTGATTCTAAAATACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:178,74:0:2,0:23.3:1:31.9:1:1:0:60:125:1:0:0.1 0/1:186:2:1,1:129,55:0.0108:2,2:19.5:1:30:1:0.51264:2.33343:60:4:0.0108:0:1.5 -6 153412476 . CA TG 219 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.02426;LSEQ=TAATGGCTAGTTTGGAGAAC;RSEQ=TCTCAAATGATTTTGCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:68:29,39:214,225:0.1336:2,2:28.1:1:31.1:1:0.36416:1.27846:60:136:0.1371:0.0098:1 0/1:421:134:68,66:135,151:0.3183:2,2:24.4:1:31.1:1:0.5304:1.15:60:268:0.3183:0.0333:1 -6 155699472 . TA T 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03278;SOR=0;LSEQ=AATAAGTAAAATGCAAATAT;RSEQ=AAAAAAAATCTGAAATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:5,1:75,1:0.0732:1,2:19.2:1:30:1:0.14182:13.78406:60:12:0.0741:0.0244:0 0/0:67:0:0,0:61,5:0:2,0:19.8:1:28.4:1:1:0:60:65:1:0:0.1 -6 155699620 . T C 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96366;LSEQ=TTCATGATATTTAGTGTATG;RSEQ=TCTTTCAGGTCAAAAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:28:11,17:166,194:0.0718:2,2:30.8:1:32:1:0.55736:1.32146:60:27:0.0701:0:1.1 0/1:346:24:12,12:149,172:0.0694:2,2:26.7:1:30.9:1:0.83296:1.15:60:23:0.0674:0:1.1 -6 155699667 . AAT A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04606;SOR=Inf;LSEQ=TTTTGATTTTTTATTCTCAA;RSEQ=GACTTGTAAGAGTAATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:94,180:0:2,0:25.4:1:30.5:1:1:0:60:273:1:0:0.2 0/1:238:4:4,0:94,140:0.0168:2,0:7.3:1:24:1:0.02771:0:60:3:0.0128:0.0126:1.5 -6 155699732 . A G 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.78869;LSEQ=TTCCTCTGGGTCCTCAGAAC;RSEQ=AGCCTTTTTTTTTTTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:5:0,5:10,74:0.0562:2,0:8.8:1:31.6:1:1:0:60:10:0.0575:0:1 0/1:67:3:1,2:10,54:0.0448:2,2:13.7:1:31.3:1:0.42135:2.65:60:6:0.0462:0:1.3 -6 155699736 . CT C 90 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.97554;LSEQ=TCTGGGTCCTCAGAACAAGC;RSEQ=TTTTTTTTTTAATTTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:7:0,7:5,61:0.0959:2,0:23.9:1:32.1:1:1:0:60:14:0.1:0.0137:0.1 0/1:64:6:0,6:7,50:0.0938:2,0:30.2:1:32.5:1:1:0:60:12:0.1:0:0.3 -6 156983276 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18947;SOR=0;LSEQ=AGCCGCTCGCAGAGTGCGCC;RSEQ=TCTACCGGAGGGGTGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:33:1:29.5:1:1:2.23609:60:4:0.2222:0:1 0/0:11:0:0,0:7,4:0:2,0:30.1:1:29.8:1:1:0:60:10:1:0:0.4 -6 156983504 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14154;SOR=0;LSEQ=TGAAGACATTAACTTGTGTG;RSEQ=TGTCTATGCCAAACGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:10.5:1:28:1:1:1.62:60:4:0.1111:0:1 0/0:29:0:0,0:9,20:0:2,0:23.6:1:32.1:1:1:0:60:58:1:0:0.1 -6 156983856 . G A 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAAAATGTTTCAGTGAAC;RSEQ=AGTTTCAGCAGTTCAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18.5:1:26.5:1:1:0:50.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 157098952 . CGCG C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGGAGGCGGGGGCGCGCGG;RSEQ=GCGGCGGCGGCGGCGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:32.5:1:1:0:60:4:1:0:0.5 -6 157099165 . GTCC G 184 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.92096;SOR=0.96479;LSEQ=GGTGGAAGCGCCGCCGCGCT;RSEQ=TCCTCCTCCTCCTCCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:792:56:37,19:462,269:0.0707:2,2:26.5:1:31.8:1:0.77379:1.13:60:112:0.0717:0.0126:0.1 0/1:775:53:33,20:443,269:0.0684:2,2:23.2:1:30.5:1:1:1.00:60:106:0.0699:0.0194:0.2 -6 157099282 . C T 110 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00877;SOR=3.93899;LSEQ=CACAAACTGAAAACCGTTGG;RSEQ=GAAGCCCCCGCCGCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1448:4:0,4:726,708:0.0028:2,0:4.3:1:28.8:1:0.05985:0:60:8:0.003:0:1 0/1:1667:18:6,12:843,802:0.0108:2,2:13.5:1:26.4:1:0.15752:2.10132:60:17:0.0108:0:1.3 -6 157099312 . GCAC G 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=0.98974;LSEQ=GCCGCGCCGCCCCACCAGCA;RSEQ=CACCACCACCACCATGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1213:33:15,18:538,641:0.0272:2,2:33:1:31.9:1:1:1.00717:60:66:0.0278:8e-04:0.3 0/1:1448:39:22,17:656,750:0.0269:2,2:24.8:1:31.9:1:0.25663:1.48:60:78:0.0277:0.0041:0.3 -6 157099332 . CCCA C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.35118;SOR=0.76416;LSEQ=GCACCACCACCACCACCATG;RSEQ=CCACCACCACCACCATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1003:31:10,21:413,559:0.0309:2,2:32.9:1:30.2:1:0.27455:1.55087:60:30:0.0309:0.002:0.4 0/1:1135:27:9,18:499,600:0.0238:2,2:32.7:1:31.1:1:0.24398:1.66261:60:54:0.0244:9e-04:0.4 -6 157099402 . CCAG C 162 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.04236;SOR=1.74346;LSEQ=CAGCAGCAGCTAAACCAGTT;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:24:8,16:274,323:0.0383:2,2:23.9:1:30.6:1:0.29645:1.6952:58.8:23:0.0377:0.0096:0.5 0/1:647:42:24,18:285,315:0.0649:2,2:25.8:1:30.1:1:0.26438:1.47:59:20:0.0637:0.0201:0.6 -6 157099426 . ACAG A 142 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.05516;SOR=2.08995;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:772:11:8,3:372,388:0.0142:2,2:27.5:1:32.3:1:0.13802:2.78:60:22:0.0145:0.0039:0 0/1:784:23:8,15:394,365:0.0293:2,2:32.3:1:31.5:1:0.13778:2.02218:60:46:0.0298:0.0051:0.3 -6 157099429 . G A 122 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=1;SOR=0.95427;LSEQ=CAGCAGCAGCAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:19:8,11:360,383:0.0247:2,2:13.5:1:28.9:1:0.64717:1.29199:53.9:38:0.0252:0:1.7 0/1:806:19:8,11:397,368:0.0236:2,2:12.5:1:28.8:1:0.48814:1.4826:53.2:18:0.0234:0:1.7 -6 157099563 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06299;SOR=Inf;LSEQ=AGGCGCCAAGGACAGTGCTG;RSEQ=GGGCGGCCAGGCCGACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:156,284:0:2,0:21.4:1:30.4:1:1:0:60:47.889:0.9954:0:0.3 0/1:482:5:1,4:175,301:0.0104:2,2:8.2:1:25.8:1:0.65684:2.32208:60:10:0.0107:0:1 -6 157099591 . G T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13057;SOR=Inf;LSEQ=CAGGCCGACCCCCCGGGCCC;RSEQ=CCGCTGCTGAGCAAGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:138,141:0:2,0:24.4:1:30:1:1:0:60:20.462:0.9925:0:0.4 0/1:340:4:1,3:166,168:0.0118:2,2:13.3:1:26.8:1:0.62287:2.9558:60:3:0.009:0:1 -6 157099646 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14665;SOR=0;LSEQ=CGCCGCCCAAGATGGGGGAG;RSEQ=CGGCGGGCGGCCGCTACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:65,75:0.0141:2,2:14:0:31.5:1:1:1.15:60:4:0.0145:0:1.5 0/0:228:0:0,0:106,122:0:2,0:25.3:1:30.8:1:1:0:60:27.5:1:0:0.4 -6 157099697 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15769;SOR=0;LSEQ=TGGGCGCCCTGGGCACGCAG;RSEQ=AGCCGCCGGTCGCCGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:17,21:0.0476:2,2:5.5:1:28.5:1:1:1.23:60:4:0.0488:0:1 0/0:63:0:0,0:26,35:0:2,0:9.1:1:30.8:1:1:0:60:29.5:0.9672:0:0.4 -6 157099712 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.50695;SOR=Inf;LSEQ=CGCAGCAGCCGCCGGTCGCC;RSEQ=TGCCCGGGGGCGGCGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:68,23:0:2,0:8.4:1:29.8:1:1:0:60:44.5:0.9889:0:0.3 0/1:121:2:1,1:80,38:0.0165:2,2:10.5:1:30:1:0.54622:2.0911:60:4:0.0168:0:1.5 -6 157099715 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19435;SOR=0;LSEQ=AGCAGCCGCCGGTCGCCGTG;RSEQ=CCGGGGGCGGCGGCGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:77,23:0.0194:2,2:11:1:29.5:1:0.41701:3.29852:60:4:0.0196:0:1 0/0:130:0:0,0:90,40:0:2,0:10.6:1:31.4:1:1:0:60:129:1:0:0.3 -6 157099725 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.20036;SOR=0;LSEQ=GGTCGCCGTGCCCGGGGGCG;RSEQ=CGGCGGCCCGGCGGCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:2,0:131,31:0.0121:2,0:18:1:27:1:1:0:60:4:0.0123:0:1 0/0:203:0:0,0:139,64:0:2,0:14.7:1:31.6:1:1:0:60:100.5:1:0:0.3 -6 157099726 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.19869;SOR=0;LSEQ=GTCGCCGTGCCCGGGGGCGG;RSEQ=GGCGGCCCGGCGGCCGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:137,32:0.0117:2,2:17.5:1:30.5:1:0.34964:4.23125:60:4:0.0118:0:1.5 0/0:212:0:0,0:145,67:0:2,0:15.1:1:31.5:1:1:0:60:52:1:0:0.3 -6 157099732 . C T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06717;SOR=Inf;LSEQ=GTGCCCGGGGGCGGCGGCGG;RSEQ=CCGGCGGCCGTCCCGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:174,43:0:2,0:17:1:32.3:1:1:0:60:53.25:1:0:0.2 0/1:264:5:1,4:175,84:0.0189:2,2:7.6:1:23.4:1:0.0437:8.26487:60:4:0.0156:0:1.2 -6 157099871 . TCCG T 173 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.00011;SOR=2.82081;LSEQ=TGGGGATGATGCACTCCGCC;RSEQ=CCGCCGCCGCCGGGGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1518:17:11,6:732,766:0.0112:2,2:27.9:1:31.3:1:0.22768:1.92:60:34:0.0114:7e-04:0.1 0/1:1647:51:27,24:784,804:0.031:2,2:30.7:1:30.5:1:0.67059:1.15:60:102:0.0315:0.0024:0.3 -6 157099945 . G A 203 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=50.68893;LSEQ=GAAGGGTACCCCAACAGCCA;RSEQ=TGCAACCATTATCCGGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1329:2:1,1:562,765:0.0015:2,2:17.5:1:19.5:1:1:1.36:60:1:8e-04:0:3 0/1:1563:111:53,58:667,781:0.071:2,2:22.9:1:29.9:1:0.76735:1.07:60:222:0.0723:0:1.3 -6 157100054 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.50436;SOR=Inf;LSEQ=GAGGAGGAGGAGGAGCAGGA;RSEQ=CAGGAGGAGCAGGAGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:23,135:0:2,0:23.8:1:32.8:1:1:0:60:316:1:0:0.2 0/1:196:2:1,1:41,153:0.0102:2,2:46:1:29.5:1:0.38352:3.70:60:4:0.0104:0:1 -6 157100092 . CGCG C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.17223;SOR=0;LSEQ=GGAGCTGTGGCGGCGGCGGC;RSEQ=GCGGCGGCGGCAGCAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:15,36:0.0377:2,2:49.5:1:32.5:1:0.51669:2.36:60:4:0.0377:0:1 0/0:74:0:0,0:31,43:0:2,0:12.9:1:31.1:1:1:0:60:73:1:0:0.5 -6 157100100 . C T 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=1.58378;LSEQ=GGCGGCGGCGGCCGCGGCGG;RSEQ=GGCGGCAGCAGCAGGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:26,32:0.0169:2,0:1:0:25:0:1:0:60:2:0.0175:0:1 0/1:75:2:1,1:34,39:0.0267:2,2:10:0:30.5:1:1:1.14:60:4:0.027:0:2 -6 157100103 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.1112;SOR=Inf;LSEQ=GGCGGCGGCCGCGGCGGCGG;RSEQ=GGCAGCAGCAGGAGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:34,34:0:2,0:8.7:1:29.8:1:1:0:60:33:1:0:0.5 0/1:64:3:1,2:32,29:0.0469:2,2:9:1:28.7:1:0.60714:2.18054:60:6:0.0469:0:1.7 -6 157100116 . AGGC A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.32229;SOR=0.46173;LSEQ=GCGGCGGCGGCAGCAGCAGG;RSEQ=GGCGGCGGCGGCGGCTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:6:2,4:49,42:0.0612:2,2:14.2:1:30.2:1:0.41835:2.31347:60:12:0.0612:0.0204:0.7 0/1:103:3:1,2:54,43:0.0291:2,2:8.3:1:29.7:1:0.58673:2.48897:60:6:0.03:0.0194:0.7 -6 157100139 . G T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.32495;SOR=0.26032;LSEQ=CGGCGGCGGCGGCGGCTATG;RSEQ=GGGCTCGTCCGCGGGGTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:1,2:102,88:0.0155:2,2:27:1:29.7:1:0.59922:2.30837:60:6:0.0155:0:1.3 0/0:245:1:0,1:130,114:0.0041:2,0:1:0:29:0:0.46939:0:60:2:0.0041:0:1 -6 157100164 . G T 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03867;SOR=Inf;LSEQ=TCGTCCGCGGGGTACGGGGT;RSEQ=CTGAGCTCCCCCCGGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:136,134:0:2,0:26.9:1:31.9:1:1:0:60:32.75:0.9962:0:0.4 0/1:353:6:1,5:175,172:0.017:2,2:9.5:1:26.5:1:0.21475:5.06741:60:12:0.017:0:1.2 -6 157100170 . C T 43 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78079;LSEQ=GCGGGGTACGGGGTGCTGAG;RSEQ=TCCCCCCGGCAGCAGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:0,3:145,143:0.0103:2,0:9:1:21.7:1:0.24742:0:60:2:0.007:0:1 0/0:372:3:0,3:186,183:0.0081:2,0:1:0:27.3:1:0.24798:0:60:6:0.0081:0:1 -6 157100171 . TC T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.13624;SOR=Inf;LSEQ=CGGGGTACGGGGTGCTGAGC;RSEQ=CCCCCGGCAGCAGGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:148,147:0:2,0:26.2:1:30.9:1:1:0:60:31.778:1:0:0.4 0/1:383:4:2,2:191,188:0.0104:2,2:34.8:1:32.5:1:1:1.01592:60:8:0.0106:0:0.3 -6 157100178 . G A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39053;SOR=3.17396;LSEQ=CGGGGTGCTGAGCTCCCCCC;RSEQ=GCAGCAGGGCGGCGGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:1:1,0:149,149:0.0033:2,0:1:0:27:0:1:0:60:2:0.0034:0:1 0/1:379:4:3,1:189,185:0.0106:2,2:16.3:1:28:1:0.62319:2.93:60:8:0.0107:0:1 -6 157100212 . GGGCGGCGGGGCCGCGAGCCTCAGCAAGGCGGCCGCCGGCTC G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11007;SOR=0;LSEQ=GGCATGATGATGGGCCCCGG;RSEQ=GGCGGCGGGGGGCTTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:2,1:114,115:0.0129:2,2:64.3:1:31:1:1:2.01:60:6:0.0133:0.0129:0 0/0:251:0:0,0:122,127:0:2,0:20.3:1:30.6:1:1:0:59.9:82:0.9919:0:0.4 -6 157100229 . G T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37897;SOR=3.49812;LSEQ=CGGGGGCGGCGGGGCCGCGA;RSEQ=CCTCAGCAAGGCGGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:1:0,1:152,92:0.004:2,0:1:0:27:0:0.37959:0:60:2:0.0041:0:1 0/1:287:4:1,3:167,116:0.0139:2,2:12:1:28.5:1:0.31053:4.29781:60:8:0.0141:0:1.3 -6 157100246 . G T 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.14791;LSEQ=CGAGCCTCAGCAAGGCGGCC;RSEQ=CCGGCTCGGCGGCGGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:3:0,3:209,97:0.0096:2,0:1:0:25.3:1:0.03321:0:60:6:0.0098:0:1 0/1:364:4:1,3:222,138:0.011:2,2:5:1:26:1:0.30307:4.80552:60:8:0.0111:0:1 -6 157100255 . G T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.02205;SOR=0;LSEQ=GCAAGGCGGCCGCCGGCTCG;RSEQ=CGGCGGGGGGCTTCCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:5:1,4:244,126:0.0133:2,2:14.6:1:27.2:1:0.05101:7.70377:60:10:0.0136:0:1.2 0/0:428:0:0,0:271,157:0:2,0:20.8:1:31.6:1:1:0:60:52.5:1:0:0.3 -6 157100260 . G T 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.84744;LSEQ=GCGGCCGCCGGCTCGGCGGC;RSEQ=GGGGGCTTCCAGCGCTTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:5:2,3:265,139:0.0122:2,2:7.6:1:28.6:1:0.34667:2.85181:60:10:0.0125:0:1.4 0/1:483:5:1,4:299,178:0.0104:2,2:12:1:27.8:1:0.0699:6.69365:60:10:0.0104:0:1 -6 157100396 . GCGC G 83 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.50811;SOR=1.85715;LSEQ=CCGAGTACAGCAGCCCCAGC;RSEQ=CGCCGCCGCCGCCGTCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:3:1,2:104,208:0.0094:2,2:13:1:30:1:1:1:60:6:0.0096:0.0063:1 0/1:346:6:2,4:122,216:0.0173:2,2:30:1:32.3:1:1:1.12926:60:12:0.0175:0:0 -6 157100398 . G A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.12514;SOR=Inf;LSEQ=GAGTACAGCAGCCCCAGCGC;RSEQ=CCGCCGCCGCCGCCGTCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:102,209:0:2,0:22:1:31.4:1:1:0:60:154.5:1:0:0.2 0/1:339:4:3,1:119,210:0.0118:2,2:11.3:1:26.8:1:0.14126:5.27:60:8:0.0122:0:1 -6 157100410 . G A 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.72454;SOR=1.61265;LSEQ=CCCAGCGCGCCGCCGCCGCC;RSEQ=CCGTCGCAGCCCCAGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:59,157:0.0137:2,2:16.7:1:24:1:1:1.33:60:2:0.0093:0:2 0/1:228:5:4,1:67,155:0.0219:2,2:8.8:1:29:1:0.03426:9.16:60:10:0.022:0:1 -6 157100469 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60332;SOR=0.44372;LSEQ=GGCGGCGGGCGGCCAGCAGG;RSEQ=GGCCGCGGGCATGGGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:86,29:0.0171:2,2:6:1:28.5:1:0.44872:2.93244:60:4:0.0177:0:1 0/0:131:1:0,1:92,38:0.0076:2,0:1:0:25:0:0.29771:0:60:2:0.0079:0:1 -6 157100470 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22217;SOR=0;LSEQ=GCGGCGGGCGGCCAGCAGGC;RSEQ=GCCGCGGGCATGGGCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:94,32:0.0156:2,2:34:0:32:0:0.45066:2.90822:60:4:0.0159:0:1.5 0/0:143:0:0,0:103,40:0:2,0:11.4:1:29.2:1:1:0:60:27.6:1:0:0.3 -6 157100482 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25244;SOR=Inf;LSEQ=CAGCAGGCGGCCGCGGGCAT;RSEQ=GGCTTGGGCAAGGACATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:167,71:0:2,0:15.7:1:31.9:1:1:0:60:58.5:1:0:0.3 0/1:275:3:1,2:187,85:0.0109:2,2:9.7:1:22.7:1:0.23606:4.37371:60:2:0.0073:0:1.3 -6 157100505 . C T 53 v4;Bias;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07041;SOR=Inf;LSEQ=CTTGGGCAAGGACATGGGCG;RSEQ=CCAGTACGCCGCTGCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:267,128:0:2,0:24.5:1:31.9:1:1:0:60:78:0.9974:0:0.2 0/1:501:5:0,5:323,172:0.01:2,0:9.2:1:23:1:0.00536:0:60:4:0.0082:0:1.2 -6 157150145 . G A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.38002;LSEQ=TTTAGTCTAGAGCTCTCTTA;RSEQ=TTGTTAAAAACTCCTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:10,0:4,0:0.7143:0,0:17.7:1:30.3:1:1:0:60:20:0.7143:0:1.2 1/0:9:7:7,0:2,0:0.7778:0,0:31:1:29.9:1:1:0:60:14:0.7778:0:1 -6 157150230 . A G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.08219;LSEQ=GTCTTGCTGGATGTTTTGTC;RSEQ=GGTCATTGTTTTTAATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:32:31,1:59,2:0.3441:1,1:23.4:1:29.8:1:1:1.05:60:64:0.3441:0:1.1 0/1:49:2:2,0:47,0:0.0408:1,0:23.5:1:28:1:1:0:60:4:0.0426:0:1 -6 157150529 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02125;SOR=Inf;LSEQ=GTCGGACTCCCGGGGCCATG;RSEQ=CCGGAATGCAGTACCCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:175,353:0:2,0:26.2:1:31.5:1:1:0:60:47:1:0:0.1 0/1:457:5:3,2:172,279:0.0109:2,2:23.6:1:27.4:1:0.37658:2.43:60:10:0.0112:0:1 -6 157150546 . T A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1927;SOR=4.54368;LSEQ=ATGGCCGGAATGCAGTACCC;RSEQ=CAGCAGCAGGTTTGTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:1:1,0:119,310:0.0023:2,0:1:0:27:0:0.27907:0:60:2:0.0024:0:1 0/1:381:4:3,1:123,254:0.0105:2,2:6:1:28.3:1:0.10762:6.16:60:8:0.0108:0:1 -6 157150583 . T C 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=CTGGTCCCCCGACCCGCTGC;RSEQ=TTTTTGTAATAGTTTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:31,185:0:2,0:22.9:1:30.7:1:1:0:60:107:0.9953:0:0.1 0/1:185:10:4,6:33,142:0.0541:2,2:27.5:1:31:1:0.11495:2.85:60:20:0.0556:0:1.1 -6 157222269 . A T 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03636;SOR=Inf;LSEQ=CCACCTTTATGATATTATCA;RSEQ=TAGTTTCTATCTGATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:0:1,0:26.1:1:29.9:1:1:0:60:28:1:0:0 0/1:8:3:3,0:5,0:0.375:0,0:13.7:1:28:1:1:0:60:6:0.4286:0:1 -6 157222396 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50553;SOR=0;LSEQ=AAGAGAGGATTAGAAATATT;RSEQ=AGTTTAGTTGCTTAGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:2,0:134,1:0.0146:1,0:24.5:1:29.5:1:1:0:60:4:0.0146:0:1 0/0:107:0:0,0:103,4:0:1,0:20.9:1:31.8:1:1:0:60:106:1:0:0.1 -6 157222436 . A T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24878;SOR=Inf;LSEQ=GAACCCCCTTCATGTTGCTG;RSEQ=ATTGAAACCATATTTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:237,40:0:2,0:21.6:1:29.9:1:1:0:60:137.5:1:0:0.1 0/1:284:3:1,2:228,53:0.0106:2,2:27:1:25.7:1:0.09697:8.51026:60:6:0.0106:0:1 -6 157222761 . G GA 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.51134;SOR=0;LSEQ=TTAAAAATTATGTTCTGGTG;RSEQ=AAAAAAAATTAGTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:3,87:0.0215:1,0:30.5:1:31.5:1:1:0:60:4:0.022:0:0 0/0:66:0:0,0:1,65:0:1,0:24.1:1:31.2:1:1:0:60:65:1:0:0 -6 157256508 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19044;SOR=Inf;LSEQ=ACAGGCATGAGCCACTGTGC;RSEQ=CAGCCAAGCTTTTGTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:138,6:0:1,0:25:1:31.3:1:1:0:59.9:143:1:0:0.2 0/1:112:2:2,0:101,9:0.0179:2,0:41:1:28:1:1:0:60:4:0.018:0:1 -6 157256511 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50442;SOR=0;LSEQ=GGCATGAGCCACTGTGCCCA;RSEQ=CCAAGCTTTTGTTTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:2,0:140,7:0.0134:1,0:20.5:1:30.5:1:1:0:60:4:0.014:0:1 0/0:119:0:0,0:106,13:0:2,0:22.4:1:31.9:1:1:0:60:58.5:1:0:0.1 -6 157256588 . G GT 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50144;SOR=1.24688;LSEQ=ATGAAGTGCTTTGTGTTTGT;RSEQ=TTTTTTTTTAGGACATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:24:15,9:385,215:0.0383:2,2:24.7:1:30:1:0.83223:1.07429:60:48:0.0397:0.0032:0.3 0/1:719:34:19,15:418,264:0.0473:2,2:28.5:1:29.4:1:0.58991:1.24959:60:33:0.0467:0.0028:0.1 -6 157403542 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06672;SOR=Inf;LSEQ=GTCCAGTAATCAAGTTAAAT;RSEQ=TAAAGTTTCACCAGCTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:18.2:1:29.8:1:1:0:60:38:1:0:0.1 0/1:14:3:1,2:4,7:0.2143:2,2:12.3:1:30.7:1:1:1.1321:60:6:0.2143:0:1.3 -6 157405270 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGTGAGACTTCATCACC;RSEQ=CCCCCCCAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:32.5:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 157405495 . GC TT 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCTGTCTGTGTTGTGTG;RSEQ=ATTTTGAACAGGTCTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:13.5:1:32:0:1:0:60:4:0.5:0:1 0/0:2:0:0,0:1,1:0:2,0:19:1:29.5:1:1:0:60:4:1:0:0 -6 157405761 . G A 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.09536;SOR=1.30944;LSEQ=GATGAGATATTCATCCAAAC;RSEQ=TGTCACTCTATAAATACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:116:87,29:157,45:0.3625:2,2:22.8:1:30.2:1:0.58414:1.1624:60:115:0.3651:0:1 0/1:342:146:104,42:139,57:0.4269:2,2:25.5:1:30:1:1:1.02:60:292:0.4294:0:1.1 -6 157405930 . G A 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02463;SOR=1.24464;LSEQ=TCGCCTTTCTCCCCACATGC;RSEQ=TCCCCTCATCTCTCCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:930:317:171,146:350,261:0.3409:2,2:24:1:30.3:1:0.36457:1.14477:60:38.625:0.3414:0:1.1 0/1:955:374:212,162:325,251:0.3916:2,2:24.2:1:29.6:1:0.94669:1.01:60:73.8:0.3913:0:1.1 -6 157406462 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTCTAAAACATTTCTAC;RSEQ=GTCTATACTTATCAGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:17:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 157431259 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCCCACCTGGAGACTCA;RSEQ=GTAAGAGTCAGGAGGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:29.5:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 157431876 . T G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64045;SOR=2.02759;LSEQ=GAGGAGGGAGGATGCTTTCT;RSEQ=GTAGGTTGGGTGAAGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:1,21:0.0833:1,0:26:1:31:1:1:0:60:4:0.087:0:1 0/1:19:3:0,3:0,16:0.1579:1,0:22.7:1:32:0:1:0:60:6:0.1579:0:1 -6 157454046 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6516;SOR=0.7539;LSEQ=TTAGCTATTTTTTAGGAGAA;RSEQ=CTTATGGTACCAGCCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:14:14,0:109,3:0.1111:1,1:23.2:1:32.4:1:1:0:60:28:0.1138:0:1.1 0/1:93:8:8,0:84,1:0.086:1,0:23.5:1:31.3:1:1:0:60:16:0.0879:0:1 -6 157454082 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20566;SOR=Inf;LSEQ=TTCTCCCCTGCCACCTGCCA;RSEQ=ATCAGTCCATGTCCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:212,26:0:2,0:24.7:1:32.1:1:1:0:60:118:1:0:0.1 0/1:198:2:1,1:172,24:0.0101:2,2:21.5:1:32:0:0.23714:7.0422:60:4:0.0102:0:1 -6 157468351 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGCCTCCGGCCCTGCCC;RSEQ=CCGTCCCTCACCTCCGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:1:31.5:1:1:0:39.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 157468359 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGCCCTGCCCTCCGTCCC;RSEQ=CACCTCCGACCCTGCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:1:33:0:1:0:39.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 157468361 . A ACCCCCG 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCCCTGCCCTCCGTCCCTC;RSEQ=CCTCCGACCCTGCCGTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29:1:1:0:39.5:4:1:0.5:2.5 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 157468710 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCCCTCCGTCCCTCACC;RSEQ=CCGCCTCCGGCCCTGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:14.5:1:32.5:1:1:0:26.5:4:1:0:5.5 0/0:1:0:0,0:0,1:0:0,0:27:0:15:0:1:0:54:0:0:0:2 -6 157468729 . G T 27 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGCCTCCGGCCCTGCCC;RSEQ=CCGTCCCCCACCCCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,0:0.5:0,0:17.5:1:27.5:1:1:0:37:4:0.6667:0:4.5 0/0:1:0:0,0:0,1:0:0,0:8:0:33:0:1:0:54:2:1:0:2 -6 157468798 . C T 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCCGACCCTGCCCGCCAG;RSEQ=CCTCACCCCCGCCTCCGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:17:0:31:0:1:0:51:2:0.5:0:5 1/1:2:2:1,1:0,0:1:0,2:19.5:1:26.5:1:1:0:60:4:1:0:4.5 -6 157469563 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52577;SOR=0;LSEQ=GGGGCTGTCTGTATTTGAGT;RSEQ=ACTCTCTGAGGGCCTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:43,2:0.0426:1,2:24.5:1:27.5:1:0.12488:17.75462:60:4:0.0426:0:1 0/0:28:0:0,0:27,1:0:1,0:22.6:1:31.6:1:1:0:60:56:1:0:0.2 -6 157470120 . G A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15035;SOR=0;LSEQ=AGCACGCCCCGGGCAGGTAC;RSEQ=CTGTGTGTCTACCCGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:4:1,3:9,80:0.043:2,2:11.8:1:29.8:1:0.37062:2.91:60:8:0.0435:0:1 0/0:62:0:0,0:9,53:0:2,0:20.4:1:31.5:1:1:0:60:61:1:0:0.2 -6 157488140 . C T 81 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59283;SOR=1.49784;LSEQ=CCACTGCTAATGTGCATGGT;RSEQ=GGTATATGTGTGCTGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:851:6:0,6:518,327:0.0071:2,0:1:0:26.3:1:0.00349:0:60:12:0.0072:0:1 0/1:760:8:2,6:447,305:0.0105:2,2:9.5:1:27.3:1:0.06927:4.38844:60:16:0.0106:0:1.3 -6 157495331 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17262;SOR=Inf;LSEQ=TTCTCTCTTCACTGGTGTTG;RSEQ=CCGACACTTTTTTTTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:21,164:0:2,0:24.4:1:31.5:1:1:0:60:45.25:1:0:0.2 0/1:132:2:1,1:12,118:0.0152:2,2:11:0:27:1:0.18795:9.49:60:4:0.0155:0:1.5 -6 157495338 . CT C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50965;SOR=0;LSEQ=TTCACTGGTGTTGGCCGACA;RSEQ=TTTTTTTCATTTGGTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:0,2:13,145:0.0125:2,0:36.5:1:31.5:1:1:0:60:4:0.0128:0:0 0/0:118:0:0,0:8,110:0:2,0:21.7:1:29.8:1:1:0:60:38.333:1:0:0.1 -6 157496153 . G GT 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16283;SOR=1.554;LSEQ=AAGCCCTGTAAGTGGCTCTG;RSEQ=TTTTTTTTTGTTTTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:595:19:4,15:144,431:0.0319:2,2:26.6:1:30.5:1:1:1.25244:60:38:0.0326:0.0034:0 0/1:492:24:8,16:147,320:0.0488:2,2:28.4:1:29.4:1:0.825:1.09:59.8:23:0.0475:0.002:0.5 -6 157496163 . G GT 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14938;SOR=3.72907;LSEQ=AGTGGCTCTGGTTTTTTTTT;RSEQ=TTTTTTTTGTTTTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:2:0,2:118,359:0.0042:2,0:18.5:1:31.5:1:1:0:60:4:0.0042:0:0.5 0/1:390:6:1,5:112,272:0.0154:2,2:29:1:27.2:1:0.67696:2.05562:60:5:0.0131:0:0.5 -6 157502370 . T C 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTGGATAAGTTCTTACAG;RSEQ=GGCTTTCTTTGAATGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:40,180:0:2,0:22.6:1:29.3:1:1:0:60:30.429:1:0:0.1 0/1:145:31:2,29:14,100:0.2138:2,2:25.6:1:29.9:1:0.52334:2.02167:60:62:0.2153:0:1.1 -6 157510619 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08124;SOR=Inf;LSEQ=AATAGAAAAGCAACGAATTT;RSEQ=ACAACATCATTATCAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:77,2:0:1,0:25.8:1:30.4:1:1:0:60:78:1:0:0.1 0/1:32:2:2,0:30,0:0.0625:1,0:25:1:30:1:1:0:60:4:0.0625:0:1.5 -6 157511319 . G A 126 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=0.10393;LSEQ=ATGCCCTATGAGCCCAACAA;RSEQ=GACCCCTTTGGGGGAATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:18:5,13:135,329:0.0373:2,2:21.4:1:30.4:1:1:1.06673:60:36:0.0382:0:1 0/0:500:2:2,0:181,317:0.004:2,0:1:0:27.5:1:0.13349:0:60:4:0.004:0:1 -6 157517575 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13356;SOR=Inf;LSEQ=GTGTCCCCTTTCCTGTGAAA;RSEQ=TAAAGAGGCAATGGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:0,46:0:1,0:22.9:1:32.6:1:1:0:60:92:1:0:0.1 0/1:27:2:0,2:1,24:0.0741:1,0:25:1:29.5:1:1:0:60:4:0.0741:0:1 -6 157519832 . A G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00089;SOR=Inf;LSEQ=TTGTCGGAGGGGTGCGCAGT;RSEQ=AAAGCCACACAGAGCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:97,2:0:1,0:23.8:1:28.2:1:1:0:60:98:1:0:0.1 0/1:74:8:8,0:66,0:0.1081:1,0:30.4:1:32.8:1:1:0:60:16:0.1096:0:1 -6 157519938 . A G 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGTTTTCTTTGAATGCCTC;RSEQ=TTCCAGGCATGAACCTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:743:0:0,0:466,276:0:2,0:27.6:1:30.4:1:1:0:60:81.444:1:0:0.1 0/1:642:96:56,40:337,208:0.1495:2,2:24:1:30.3:1:0.57011:1.15701:60:192:0.1517:0:1.3 -6 157522360 . G A 168 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=14.93474;LSEQ=CCGTCCTACCAGACGCCACC;RSEQ=TCACTGCCAAATCACATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:882:5:3,2:426,451:0.0057:2,2:13:1:27.2:1:0.67871:1.59:60:10:0.0058:0:1 0/1:751:59:32,27:345,344:0.0786:2,2:23.7:1:28.7:1:0.58851:1.18:60:18.667:0.0758:0:1.1 -6 157522675 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50213;SOR=0;LSEQ=ATTCCAGTTGCAGTGTAGAA;RSEQ=TTTAATTTTAGTAAAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:1,167:0.0118:1,2:17.5:1:29:1:0.02346:118.34:60:4:0.0121:0:1 0/0:143:0:0,0:7,136:0:1,0:21.6:1:30.1:1:1:0:60:46.667:1:0:0.2 -6 157524934 . G T 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=32.33899;LSEQ=TTATTTTTTCTTACTCTTTC;RSEQ=TTAACTTTCGTTCTTTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:1:0,1:357,76:0.0023:2,0:1:0:27:0:0.17742:0:60:2:0.0023:0:1 0/1:374:26:21,5:277,70:0.0695:2,2:27.3:1:30:1:1:1.06:60:12:0.0647:0:1.1 -6 157527280 . TCTC T 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.11762;SOR=0.19136;LSEQ=TGTACCTGTTCTTTCTTTCT;RSEQ=CTCCTCCTCCTCTCCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:5:5,0:205,46:0.0196:2,0:25.2:1:32.2:1:0.58886:0:60:10:0.0199:0.0039:0.2 0/0:263:1:0,1:193,66:0.0038:2,0:15:0:34:0:0.25769:0:60:2:0.0038:0:0 -6 157527482 . A C 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGAGGAGGAAGATGCTG;RSEQ=ATGTATTGATGACGACGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:818:0:0,0:379,438:0:2,0:23.9:1:29.9:1:1:0:60:73.273:1:0:0.1 0/1:855:39:20,19:373,443:0.0456:2,2:23.9:1:31.1:1:0.51466:1.25:60:18.5:0.044:0:1.2 -6 157527492 . TGAC T 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GAAGATGCTGAATGTATTGA;RSEQ=GACGAGGAAGACGAGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:805:0:0,0:366,439:0:2,0:25.2:1:31.5:1:1:0:60:88.444:1:0:0.1 0/1:846:28:13,15:364,449:0.0331:2,2:24.8:1:31:1:1:1.07:60:56:0.0337:0.0059:0.2 -6 158190377 . C A 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48571;SOR=0.22474;LSEQ=AATTTTTGCAGAGTTCTACT;RSEQ=TGATGCAGGCGCAGGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:19.3:1:30.7:1:1:0:60:6:0.75:0:1.3 0/1:3:1:0,1:0,2:0.3333:0,0:20:0:32:0:1:0:60:2:0.3333:0:1 -6 158411364 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.43328;LSEQ=CTGCCCACTCTCTCATGCCT;RSEQ=CTTCTCCTTCTCCTTGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:19.5:1:27.5:1:1:0:60:4:0.4:0:1 1/0:4:2:2,0:1,1:0.5:2,0:8.5:1:31:1:1:0:60:4:0.5:0:1 -6 158411645 . A G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=13.68192;LSEQ=TGTTAGCGGCTGCTGCTCAG;RSEQ=CCCAGCGGAGGACCGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:19:9,10:103,130:0.0748:2,2:30.4:1:31.8:1:0.81421:1.14:60:38:0.0769:0:1.1 1/0:283:149:68,81:58,76:0.5265:2,2:25.9:1:30.7:1:0.72032:1.10:60:36.25:0.5216:0:1.1 -6 159215375 . G T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02277;SOR=0;LSEQ=ACCACCACCACCAGGCTTTG;RSEQ=CAATTGAGAAAACACATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:14,14:0.1515:2,2:29.4:1:30:1:1:1.48182:60:10:0.1515:0:1 0/0:35:0:0,0:15,20:0:2,0:28.6:1:31.3:1:1:0:60:34:1:0:0.3 -6 159215408 . C T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.04885;SOR=0.23444;LSEQ=CACATCTAAATCCCAACTTT;RSEQ=CATTTTATTATCAGGGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:6,6:3,4:0.6316:2,2:17.5:1:29.8:1:1:1.31:60:24:0.6316:0:1.5 0/1:18:5:2,3:6,7:0.2778:2,2:27.6:1:29.6:1:1:1.26799:60:10:0.2778:0:1 -6 159215413 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=CTAAATCCCAACTTTCCATT;RSEQ=TATTATCAGGGTGTTAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,8:0.125:2,2:9.5:1:30:1:1:1.31:60:4:0.125:0:2.5 0/0:16:0:0,0:7,9:0:2,0:16.3:1:29.6:1:1:0:60:32:1:0:0.4 -6 159947173 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05455;SOR=Inf;LSEQ=TCTCTGGGTGGAGCAGGCTG;RSEQ=CGCTTTAGCTGAACCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:30:1:31.9:1:1:0:57.3:16:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:39.5:1:29:1:1:0:60:4:0.6667:0:3 -6 159947207 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06494;SOR=Inf;LSEQ=CCCAGGTACCTTTCTCTTTG;RSEQ=CTTCTTTCTTTTTCTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:13,3:0:2,0:27.3:1:32.1:1:1:0:58.6:32:1:0:0 0/1:6:2:1,1:4,0:0.3333:0,2:27.5:1:31.5:1:0.33333:0:60:4:0.3333:0:3 -6 159947273 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10383;SOR=Inf;LSEQ=TATCTCGGCTCTTAGAGTGC;RSEQ=TAATGTGCTCAATACGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:37,4:0:2,0:21.4:1:30.4:1:1:0:53.2:82:1:0:0 0/1:20:2:2,0:17,1:0.1:1,0:8.5:1:27.5:1:1:0:40:4:0.1:0:1.5 -6 159947367 . C T 93 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00051;SOR=Inf;LSEQ=AACAGCATGCTGGGGAACAT;RSEQ=GTAGACTCCCAGTTTTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:89,71:0:2,0:27.8:1:30.4:1:1:0:59.8:79:1:0:0.1 0/1:105:8:8,0:51,46:0.0762:2,0:34.1:1:31:1:0.00889:0:33.8:16:0.0769:0:1.1 -6 159947375 . C CTT 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GCTGGGGAACATCGTAGACT;RSEQ=CCAGTTTTGCCATGGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:82,78:0:2,0:30.6:1:31.2:1:1:0:60:159:1:0:0.1 0/1:112:10:9,1:52,50:0.0893:2,2:28.5:1:29.8:1:0.02073:8.53:39:20:0.0901:0.0268:1.2 -6 159947377 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16796;SOR=Inf;LSEQ=TGGGGAACATCGTAGACTCC;RSEQ=AGTTTTGCCATGGTGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:83,79:0:2,0:30.8:1:31.3:1:1:0:60:39.5:1:0:0.1 0/1:113:2:1,1:60,51:0.0177:2,2:39:0:31:1:1:1.17477:60:4:0.018:0:1 -6 159947467 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCACCTTTCTTATAGATTC;RSEQ=CATATACGTGGCCAAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:37,42:0:2,0:24.5:1:31.1:1:1:0:59.6:78:1:0:0.2 0/1:68:23:10,13:22,23:0.3382:2,2:27.1:1:29.3:1:0.79862:1.2395:53.3:46:0.3433:0:1.2 -6 159947476 . T TG 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTATAGATTCGCATATACG;RSEQ=GGCCAAAGGAGCAACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:45,41:0:2,0:23.2:1:29.8:1:1:0:59.7:42:1:0:0.2 0/1:69:23:11,12:24,22:0.3333:2,2:25.7:1:30.6:1:0.80154:1.18708:54.3:46:0.3382:0.058:1.1 -6 159947526 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20401;SOR=Inf;LSEQ=AAGGCCTAGAGAACATATGT;RSEQ=AGGTGCCTCTCCTCTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:76,62:0:2,0:22.8:1:31.5:1:1:0:59.8:137:0.9928:0:0.3 0/1:115:2:1,1:65,48:0.0174:2,2:38.5:1:28:1:1:1.35053:60:4:0.0175:0:1.5 -6 159947566 . C T 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.07723;LSEQ=CTTTGTGTTCGTCATTTTGG;RSEQ=GAATTACCGGAAGATGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:1,0:97,95:0.0052:2,0:10:0:30:0:1:0:60:2:0.0053:0:1 0/1:167:29:13,16:73,65:0.1737:2,2:30:1:29.2:1:0.54047:1.37955:58.8:28:0.1697:0:1.7 -6 159947590 . C T 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19381;SOR=1.36741;LSEQ=TTACCGGAAGATGGCGGTTC;RSEQ=GGCCAAAAGACCAAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:49:22,27:58,79:0.262:2,2:27.8:1:30.6:1:0.86664:1.11:59.8:98:0.2649:0:1.2 0/1:159:52:22,30:47,60:0.327:2,2:27.8:1:29.8:1:0.8663:1.06771:59.3:104:0.3312:0:1.1 -6 159947592 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21871;SOR=Inf;LSEQ=ACCGGAAGATGGCGGTTCCG;RSEQ=CCAAAAGACCAAAATATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:77,100:0:2,0:27:1:31.3:1:1:0:59.8:43.25:1:0:0.4 0/1:156:2:1,1:66,88:0.0128:2,2:17:1:27:1:1:1.33:60:4:0.013:0:1.5 -6 159947597 . A G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.5933;SOR=2.40475;LSEQ=AAGATGGCGGTTCCGGCCAA;RSEQ=AGACCAAAATATGATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:0,1:74,96:0.0058:2,0:34:0:15:0:1:0:60:0:0:0:3 0/1:143:2:1,1:60,81:0.014:2,2:42:1:30:1:1:1.35:60:4:0.0144:0:3 -6 159947617 . T A 116 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=23.10072;LSEQ=AAGACCAAAATATGATTTTT;RSEQ=AATAAGCAGTATACATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:1,0:43,81:0.008:2,0:1:0:23:0:0.352:0:60:2:0.008:0:1 0/1:101:16:5,11:33,52:0.1584:2,2:16.6:1:29.1:1:0.77937:1.39169:60:32:0.1584:0:2.2 -6 159947648 . G T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.01631;SOR=Inf;LSEQ=ATACATCTCCTCTGGGAAAA;RSEQ=AAAAGGGGACTTTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:2,51:0:1,0:24.8:1:31.5:1:1:0:60:106:1:0:0.2 0/1:31:4:0,4:2,25:0.129:2,0:30.5:1:28:1:1:0:60:8:0.129:0:2.3 -6 159947789 . C T 48 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01786;SOR=Inf;LSEQ=AAATTCTGCTTACATGTCTC;RSEQ=TATACACCTGGGTAGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:29.8:1:31.8:1:1:0:60:10:1:0:0.2 1/1:3:3:2,1:0,0:1:0,2:38:1:30.3:1:1:0:60:6:1:0:3.7 -6 159947800 . G T 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=ACATGTCTCCTATACACCTG;RSEQ=GTAGGAGACCTGAGAGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:45:0:16:0:1:0:60:0:0:0:1 1/1:3:3:2,1:0,0:1:0,2:27:1:28:1:1:0:60:6:1:0:3.7 -6 159947807 . G A 44 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02857;SOR=Inf;LSEQ=TCCTATACACCTGGGTAGGA;RSEQ=ACCTGAGAGTAGCCTAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:32.8:1:31.8:1:1:0:60:8:1:0:0.3 1/1:3:3:2,1:0,0:1:0,2:20:1:28:1:1:0:60:6:1:0:3.7 -6 159948256 . CA TG 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGTGGGAGGATTGCTTG;RSEQ=CTAAGGTGGTTGAGGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:29.5:1:1:0:60:4:1:0:2.5 -6 159948268 . T C 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCTTGCACTAAGGTGGT;RSEQ=GAGGTTGCAGTGAGCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:29.5:1:1:0:60:4:1:0:2.5 -6 160639390 . G C 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33716;SOR=0.51291;LSEQ=AGCAATAGAAGCAGCAGCAG;RSEQ=AACAACAAAAGCAAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:6,0:19,14:0.1538:2,0:9:0:31.5:1:0.07054:0:39.8:12:0.1579:0:3.7 0/1:59:5:5,0:30,24:0.0847:2,0:9:0:32.6:1:0.07333:0:39.6:10:0.0847:0:4 -6 160639405 . G C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93802;LSEQ=AGCAGGAACAACAAAAGCAA;RSEQ=AACAGCAGCAACAGTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:7:7,0:20,15:0.1667:2,0:18:1:30.6:1:0.03816:0:39:14:0.1707:0:3.3 0/1:76:12:12,0:32,31:0.1579:2,0:17:1:31.6:1:0.00096:0:35.2:24:0.1622:0:2.3 -6 160639408 . C T 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32546;SOR=0.45452;LSEQ=AGGAACAACAAAAGCAAGAA;RSEQ=AGCAGCAACAGTAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:6:6,0:22,17:0.1333:2,0:16:1:28.5:1:0.06905:0:39.8:12:0.1333:0:3.7 0/1:77:5:5,0:40,32:0.0649:2,0:21:0:30:1:0.07203:0:39.6:10:0.0667:0:4 -6 160639417 . C T 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72025;SOR=0.67789;LSEQ=AAAAGCAAGAACAGCAGCAA;RSEQ=AGTAGCAGCAATAGTAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:4:4,0:22,18:0.0909:2,0:10.5:1:27.8:1:0.13267:0:39.8:8:0.0909:0:4 0/1:79:5:5,0:41,33:0.0633:2,0:12:0:29:1:0.07135:0:39.6:10:0.0649:0:4 -6 160639440 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53772;SOR=Inf;LSEQ=TAGCAGCAATAGTAGCAACA;RSEQ=CAGCAACAACAGTAATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:0:2,0:27.3:1:32.1:1:1:0:60:68:1:0:0 0/1:62:2:1,1:32,26:0.0323:2,2:10:0:31:1:1:1.22648:60:4:0.0323:0:1 -6 160639443 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53608;SOR=Inf;LSEQ=CAGCAATAGTAGCAACAGCA;RSEQ=CAACAACAGTAATTACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:0:2,0:25.5:1:32.2:1:1:0:60:70:1:0:0 0/1:63:2:1,1:34,27:0.0317:2,2:16:1:27:1:1:1.25461:60:4:0.0317:0:1.5 -6 160639492 . C G 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00709;SOR=Inf;LSEQ=AATAGCAACAGTAGAAGCAT;RSEQ=AGTGACAACAGCAGCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,18:0:2,0:27.1:1:32:1:1:0:60:78:1:0:0.1 0/1:33:6:4,2:14,13:0.1818:2,2:18.7:1:31.2:1:0.66478:1.82:60:12:0.1818:0:1 -6 160639494 . GTGACAACAGCAGCAGTAA G 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47795;SOR=1.83843;LSEQ=TAGCAACAGTAGAAGCATCA;RSEQ=CAACAACAAAAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:2,1:22,18:0.0698:2,2:7:1:29.6:1:1:1.62:56.7:6:0.0714:0.0698:7 0/1:41:5:2,3:20,16:0.122:2,2:5.8:1:29.2:1:0.6486:1.84631:57.4:10:0.122:0.122:7.2 -6 160639499 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49586;SOR=0;LSEQ=ACAGTAGAAGCATCAGTGAC;RSEQ=ACAGCAGCAGTAACAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:21,20:0.0435:2,2:40:1:30:1:1:1.04883:60:4:0.0476:0:1 0/0:41:0:0,0:20,17:0:2,0:22.5:1:28.9:1:1:0:60:36:1:0:0.3 -6 160639530 . GC AT 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.27098;SOR=2.10273;LSEQ=TAACAACAACAAAAGCAACA;RSEQ=AGCAACAATAGTAATAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:3,2:27,27:0.0833:2,2:18:1:29.9:1:1:1.49:53.2:10:0.0877:0:6 0/1:62:10:4,6:22,30:0.1613:2,2:16.8:1:29.3:1:1:1.09829:46:20:0.1613:0:6.1 -6 160639532 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1;LSEQ=ACAACAACAAAAGCAACAGC;RSEQ=GCAACAATAGTAATAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:0,2:32,27:0.0328:2,0:7:0:30.5:1:0.22186:0:40:4:0.0333:0:6 0/1:61:2:0,2:26,33:0.0328:2,0:7:0:32:0:0.50273:0:40:4:0.0328:0:6 -6 160639536 . A G 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19917;SOR=2.07298;LSEQ=CAACAAAAGCAACAGCAGCA;RSEQ=CAATAGTAATAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:6:4,2:31,27:0.0938:2,2:22.5:1:31.5:1:0.68102:1.73:51:12:0.0938:0:6.2 0/1:62:11:4,7:22,29:0.1774:2,2:20.1:1:31.6:1:0.74792:1.32163:45.3:22:0.1774:0:5.7 -6 160639540 . T C 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42962;SOR=2.19367;LSEQ=AAAAGCAACAGCAGCAACAA;RSEQ=AGTAATAGCAACAGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:0,2:36,26:0.0303:2,0:15:0:32.5:1:0.1875:0:40:4:0.0323:0:6 0/1:62:4:1,3:24,34:0.0645:2,2:14:1:33:1:0.64184:2.09441:50:8:0.0645:0:5.3 -6 160639543 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24013;SOR=Inf;LSEQ=AGCAACAGCAGCAACAATAG;RSEQ=AATAGCAACAGCAACAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:34,29:0:2,0:25.6:1:29:1:1:0:58.2:30.5:1:0:0.9 0/1:62:2:1,1:24,36:0.0323:2,2:16:0:33:1:1:1.49:60:4:0.0323:0:4.5 -6 160639545 . AT GC 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60311;SOR=1.50452;LSEQ=CAACAGCAGCAACAATAGTA;RSEQ=AGCAACAGCAACAGTAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:7:5,2:29,26:0.1111:2,2:28.1:1:32.7:1:0.44194:2.21:49.4:14:0.1129:0:4.9 0/1:63:10:4,6:22,31:0.1587:2,2:30.7:1:32.1:1:1:1.06348:46:20:0.1587:0:5.1 -6 160639546 . T C 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67981;SOR=2.05627;LSEQ=AACAGCAGCAACAATAGTAA;RSEQ=AGCAACAGCAACAGTAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:0,2:29,24:0.0317:2,0:21:0:32.5:1:0.21886:0:40:4:0.037:0:6 0/1:63:4:1,3:21,27:0.0635:2,2:20:1:33:1:0.62883:2.29882:50:8:0.0755:0:5.3 -6 160639551 . A G 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.68053;SOR=1.95779;LSEQ=CAGCAACAATAGTAATAGCA;RSEQ=CAGCAACAGTAACAGTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:0,2:34,26:0.0317:2,0:26:0:32.5:1:0.19989:0:40:4:0.0323:0:6 0/1:66:4:1,3:27,35:0.0606:2,2:25:1:33.3:1:0.63129:2.28762:50:8:0.0606:0:5.3 -6 160639553 . AG CA 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.60535;SOR=1.40481;LSEQ=GCAACAATAGTAATAGCAAC;RSEQ=CAACAGTAACAGTAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:4,2:37,37:0.0732:2,2:22.8:1:31.7:1:0.6758:1.98:51:12:0.0769:0:3.7 0/1:100:10:4,6:40,50:0.1:2,2:24:0:30.7:1:1:1.19784:46:20:0.1031:0:4.1 -6 160639555 . C T 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66974;SOR=0.59633;LSEQ=AACAATAGTAATAGCAACAG;RSEQ=AACAGTAACAGTAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:0,3:49,41:0.0319:2,0:15.7:1:27.3:1:0.10206:0:46.7:6:0.0337:0:4.3 0/1:104:2:0,2:49,52:0.0192:2,0:23:0:30:0:0.49629:0:40:4:0.0194:0:6 -6 160639570 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.83561;LSEQ=AACAGCAACAGTAACAGTAG;RSEQ=AGCAACAGATATGGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:53,38:0.0215:2,0:8:0:29.5:1:0.18233:0:40:4:0.0222:0:6 0/1:111:2:0,2:56,53:0.018:2,0:8:0:29.5:1:0.24324:0:40:4:0.018:0:6 -6 160639579 . ATATGGCAACAGTAATACCATC CATCAGCCACAACACTAACAGCGGCAACAACAGTAACAGCAGCAGTAACAGTAACAGTAGTAGCAACAACAGCAACGTCAGAAAA 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00284;SOR=Inf;LSEQ=AGTAACAGTAGCAGCAACAG;RSEQ=AGCAGCAACAGCAATAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:33,20:0:2,0:24.8:1:32.2:1:1:0:59.3:52:1:0:0.1 0/1:77:11:7,4:36,30:0.1429:2,2:28.2:1:29.6:1:0.74612:1.45:46.7:22:0.1429:0.1429:0.5 -6 160639597 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49656;SOR=Inf;LSEQ=AGATATGGCAACAGTAATAC;RSEQ=ATCAGCAGCAACAGCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:39,23:0:2,0:23.5:1:31:1:1:0:60:30:1:0:0.1 0/1:66:2:1,1:38,26:0.0303:2,2:32.5:1:30.5:1:1:1.45294:60:4:0.0308:0:1 -6 160639602 . G GCAGCAACAGCAATAGCAAGAAGCAGCAACAGCAGCAGCAGCAAGAGCAGCAACAACGGTAGCTGTAACAATAACAAAAGCAACGATAGCAACAGTATCAGCAA 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=3.000;MSILEN=6;SSF=0.244;SOR=Inf;LSEQ=TGGCAACAGTAATACCATCA;RSEQ=CAGCAACAGCAATAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:41,21:0:2,0:23.7:1:32.2:1:1:0:59.7:124:0.9841:0:0.1 0/1:63:3:2,1:37,23:0.0476:2,2:53:1:29.9:1:1:1.24:35:6:0.0484:0.0476:0 -6 160639684 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23612;SOR=Inf;LSEQ=ACGAGCAACAGCAGCAGCAA;RSEQ=AATAGTATCAGTAATAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:74,63:0:2,0:23.3:1:32:1:1:0:60:136:1:0:0.1 0/1:130:2:1,1:75,53:0.0154:2,2:29.5:1:27.5:1:1:1.41122:60:4:0.0155:0:1 -6 160639708 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49961;SOR=0;LSEQ=AGTATCAGTAATAGCAATAG;RSEQ=AACAGTAACAGCATCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:94,89:0.0108:2,2:5:0:32.5:1:1:1.05589:20.5:4:0.0109:0:3 0/0:169:0:0,0:92,77:0:2,0:25.8:1:28.4:1:1:0:60:41.25:1:0:0.2 -6 160639722 . T A 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48729;SOR=0.91063;LSEQ=CAATAGTAACAGTAACAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:531:337:185,152:101,92:0.6347:2,2:7.5:1:30:1:0.58768:1.11:45.2:66.4:0.636:0.0019:2.2 1/0:537:329:172,157:103,92:0.6127:2,2:7.6:1:29.6:1:0.92805:1.02189:45.9:35.556:0.613:0.0037:2.1 -6 160639728 . G T 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TAACAGTAACAGCATCAGCA;RSEQ=CAGCAGCAACAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:580:0:0,0:304,268:0:2,0:17.6:1:32.1:1:1:0:49.3:43:1:0.0052:1.4 0/1:595:26:13,13:294,275:0.0437:2,2:7.3:1:29.7:1:1:1.06894:21.8:52:0.0441:0:2.5 -6 160639732 . C T 101 Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.11097;SOR=0.38298;LSEQ=AGTAACAGCATCAGCAGCAG;RSEQ=AGCAACAGCAACAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:10:10,0:300,275:0.0171:2,0:10.4:1:30.5:1:0.00211:0:33.4:20:0.0175:0:2.6 0/0:605:4:2,2:310,291:0.0066:2,2:9:0:28.8:1:1:1.06521:22.5:8:0.0067:0:2.5 -6 160639734 . G A 260 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.76214;SOR=1.0447;LSEQ=TAACAGCATCAGCAGCAGCA;RSEQ=CAACAGCAACAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:589:377:205,172:105,106:0.6401:2,2:18.4:1:30.3:1:0.30195:1.20:43.8:187.5:0.6443:0.0085:2.1 1/0:603:392:203,189:107,104:0.6501:2,2:18.2:1:30.2:1:0.86438:1.04:43.3:195:0.6522:0.005:2 -6 160639737 . A ATAAGAGCAGCAACAACAGCAACAGTAG 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97684;LSEQ=CAGCATCAGCAGCAGCAGCA;RSEQ=CAGCAACAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:9:2,7:304,277:0.015:2,2:30.1:1:30.2:1:0.09584:3.83356:31.1:18:0.0152:0.015:2 0/1:613:9:2,7:308,296:0.0147:2,2:18.4:1:27.2:1:0.10325:3.63538:35:8:0.0131:0.0147:2.1 -6 160639744 . C TAATAATAGAAACAGCAACATAGCAGTAGCAGCAACAACAGCAGCAGCAACAGCAATGTCAGCAACAGGT 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=AGCAGCAGCAGCAACAGCAA;RSEQ=AGCAGCAGCAACAATAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:631:29:11,18:300,285:0.046:2,2:40:1:29.6:1:0.1851:1.72097:24:58:0.0481:0.046:0 0/0:622:0:0,0:302,305:0:2,0:21.5:1:29.8:1:1:0:48.9:74.875:0.982:0:1.4 -6 160639749 . G A 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.28787;SOR=0.67101;LSEQ=CAGCAGCAACAGCAACAGCA;RSEQ=CAGCAACAATAACAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:19:6,13:309,289:0.0307:2,2:9.5:1:29.6:1:0.10381:2.31359:36.2:38:0.0314:0:2 0/1:625:13:5,8:303,306:0.0208:2,2:9.8:1:27.4:1:0.5772:1.58315:35.4:26:0.0211:0:1.9 -6 160639753 . CAACAATAACAAAAGCAACAGAAACAGT C 255 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0;LSEQ=AGCAACAGCAACAGCAGCAG;RSEQ=AACAACAAAACCAACAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:629:329:175,154:150,150:0.5231:2,2:31.3:1:30.5:1:0.42589:1.14:44.6:658:0.5324:0.5231:2 0/0:622:0:0,0:309,313:0:2,0:14.1:1:29.8:1:1:0:47.6:68.111:1:0:1.4 -6 160639764 . AA GC 46 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25169;SOR=0;LSEQ=CAGCAGCAGCAACAATAACA;RSEQ=AGCAACAGAAACAGTAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:3,0:121,129:0.0115:2,0:8:0:29.3:1:0.11628:0:42.3:6:0.012:0:4 0/0:228:0:0,0:102,125:0:2,0:21.5:1:28.9:1:1:0:54.5:27.375:0.9955:0:0.4 -6 160639774 . A C 61 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12273;SOR=0;LSEQ=AACAATAACAAAAGCAACAG;RSEQ=AACAGTAACAACAAAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:4:3,1:71,82:0.0252:2,2:8.3:1:30.8:1:0.34355:3.44:43.3:8:0.0263:0:5 0/0:155:0:0,0:67,88:0:2,0:38:0:18:0:1:0:60:0:0:0:5 -6 160639780 . T A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62228;SOR=2.02441;LSEQ=AACAAAAGCAACAGAAACAG;RSEQ=AACAACAAAACCAACAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:1,0:58,76:0.0072:2,0:48:0:16:0:0.43704:0:60:0:0:0:1 0/1:138:2:1,1:54,81:0.0145:2,2:6:1:28.5:1:1:1.50:60:4:0.0146:0:1 -6 160639821 . T G 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00197;SOR=Inf;LSEQ=CAACAACAGCAGCAACAATT;RSEQ=TAGCAATAGCAGCAACAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:29,53:0:2,0:23.2:1:29.7:1:1:0:60:26.333:1:0:0.1 0/1:74:8:4,4:23,43:0.1081:2,2:20.3:1:31.8:1:0.45223:1.85:60:16:0.1111:0:1 -6 160639881 . G A 127 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.40197;SOR=1.48007;LSEQ=CACAATTAAGAGCAACAACA;RSEQ=CAGCAACAATAGCCACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:12:11,1:29,30:0.169:2,2:5:0:31:1:0.00901:11.08:38.1:24:0.169:0:7.3 0/1:69:16:16,0:25,28:0.2319:2,1:5:0:31.9:1:7e-05:0:39.1:32:0.2353:0:7.3 -6 160639893 . G C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07866;SOR=0.28815;LSEQ=CAACAACAGCAGCAACAATA;RSEQ=CCACAGAAATAGCAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:10:10,0:31,29:0.1429:2,0:14:1:29.6:1:0.00391:0:40:20:0.1449:0:1.7 0/1:66:3:3,0:37,26:0.0455:2,0:16:0:26.7:1:0.27273:0:40:6:0.0455:0:2 -6 160639900 . A C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94289;LSEQ=AGCAGCAACAATAGCCACAG;RSEQ=AATAGCAAAATCAGCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:21:20,1:21,29:0.2958:2,1:17:1:31.3:1:2e-05:26.54:38.9:42:0.2958:0:4.9 0/1:67:19:19,0:22,26:0.2836:2,1:21.6:1:32.3:1:1e-05:0:39.2:38:0.2836:0:6.4 -6 160639903 . T C 129 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52595;SOR=1.43021;LSEQ=AGCAACAATAGCCACAGAAA;RSEQ=AGCAAAATCAGCAGTAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:12:11,1:30,27:0.1739:2,2:27:0:32.9:1:0.02061:9.65:38.1:24:0.1739:0:7.3 0/1:69:16:16,0:25,28:0.2319:2,1:27:0:32.3:1:7e-05:0:39.1:32:0.2319:0:7.3 -6 160639909 . A C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52544;SOR=1.33008;LSEQ=AATAGCCACAGAAATAGCAA;RSEQ=ATCAGCAGTAGCAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:12:11,1:20,25:0.2105:2,2:33:0:32.3:1:0.00366:13.23:38.1:24:0.2143:0:7.3 0/1:61:16:16,0:21,24:0.2623:2,1:33:0:31.9:1:7e-05:0:39.1:32:0.2623:0:7.3 -6 160639911 . T G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5221;SOR=1.35941;LSEQ=TAGCCACAGAAATAGCAAAA;RSEQ=CAGCAGTAGCAACAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:12:11,1:21,25:0.2069:2,2:35:0:32.4:1:0.00726:12.62:38.1:24:0.2143:0:7.3 0/1:61:16:16,0:21,24:0.2623:2,1:35:0:32.6:1:7e-05:0:39.1:32:0.2623:0:7.3 -6 160639920 . GCAA G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.83031;SOR=1.14537;LSEQ=AAATAGCAAAATCAGCAGTA;RSEQ=CAACAGAAGTCGCAGCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:12:11,1:20,23:0.2182:2,2:34.9:1:31.8:1:0.00721:12.17:38.1:24:0.2222:0:7.3 0/1:66:16:16,0:25,25:0.2424:2,1:34.6:1:32.3:1:0.00019:0:39.1:32:0.2424:0:7.3 -6 160639932 . G A 118 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0925;LSEQ=CAGCAGTAGCAACAACAGAA;RSEQ=TCGCAGCAATAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:12:11,1:22,19:0.2264:2,2:26.9:1:29:1:0.01966:9.18:38.1:24:0.2264:0:7.3 0/1:66:16:16,0:24,26:0.2424:2,1:26.6:1:29.7:1:8e-05:0:39.1:32:0.2424:0:7.3 -6 160639934 . C T 29 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58756;SOR=0.40301;LSEQ=GCAGTAGCAACAACAGAAGT;RSEQ=GCAGCAATAACAGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:2,0:31,21:0.037:2,0:25:0:29.5:1:0.51572:0:24:4:0.0377:0:8 0/1:66:1:1,0:39,26:0.0152:2,0:25:0:26:0:1:0:24:2:0.0152:0:8 -6 160639935 . G A 44 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62798;SOR=2.45046;LSEQ=CAGTAGCAACAACAGAAGTC;RSEQ=CAGCAATAACAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:32,19:0.0192:2,0:24:0:31:0:1:0:24:2:0.0196:0:8 0/1:65:3:3,0:37,25:0.0462:2,0:24:0:28:1:0.27885:0:24:6:0.0462:0:8 -6 160639939 . C T 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.82873;SOR=1.16161;LSEQ=AGCAACAACAGAAGTCGCAG;RSEQ=AATAACAGCAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:12:11,1:23,18:0.2264:2,2:19.9:1:28.2:1:0.03785:8.34:38.1:24:0.2308:0:7.3 0/1:63:16:16,0:24,23:0.254:2,1:19.6:1:29.4:1:2e-04:0:39.1:32:0.254:0:7.3 -6 160639944 . ACAG A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.22905;SOR=0;LSEQ=CAACAGAAGTCGCAGCAATA;RSEQ=CAGCAGCAGCAACAGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:0,2:40,20:0.0323:2,0:33.5:1:32.5:1:0.12216:0:60:4:0.0333:0:0 0/0:67:0:0,0:43,24:0:2,0:23.9:1:31:1:1:0:54.4:134:1:0:2.3 -6 160639948 . C T 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.40478;SOR=1.46897;LSEQ=AGAAGTCGCAGCAATAACAG;RSEQ=AGCAGCAGCAACAGAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:12:11,1:31,21:0.1875:2,2:10.9:1:27.6:1:0.04486:7.28:38.1:24:0.1875:0:7.3 0/1:67:17:16,1:26,24:0.2537:2,1:12.4:1:29.3:1:0.0015:14.32:40.3:34:0.2537:0:6.9 -6 160639954 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.79816;SOR=0.8308;LSEQ=CGCAGCAATAACAGCAGCAG;RSEQ=AGCAACAGAAGTAGCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:9:5,4:37,19:0.1385:2,2:11.8:1:28.9:1:0.70938:1.5469:48.7:18:0.1385:0:5.1 0/1:68:8:6,2:38,22:0.1176:2,2:9.8:1:29.4:1:0.70264:1.72:55:16:0.1176:0:5.8 -6 160639956 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.49624;SOR=Inf;LSEQ=CAGCAATAACAGCAGCAGCA;RSEQ=CAACAGAAGTAGCAGTAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:44,23:0:2,0:19.6:1:31.5:1:1:0:54.4:134:1:0:2.2 0/1:67:2:1,1:44,21:0.0299:2,2:21.5:1:28:1:1:2.07025:60:4:0.0303:0:1 -6 160639965 . GTAGCAGT ATAGC 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01876;SOR=0;LSEQ=CAGCAGCAGCAGCAACAGAA;RSEQ=AGTAATAGCAGCAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:5:4,1:29,18:0.0862:2,2:16.6:1:30.8:1:0.64102:2.45:35.6:10:0.0877:0.0345:3.4 0/0:68:0:0,0:24,20:0:2,0:23.6:1:31.3:1:1:0:60:88:0.8148:0:0.2 -6 160639967 . A C 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=1.73449;LSEQ=GCAGCAGCAGCAACAGAAGT;RSEQ=GCAGTAGTAATAGCAGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:2,1:30,18:0.0526:2,2:24.3:1:30.7:1:1:1.20:60:6:0.0577:0:5 0/1:68:6:4,2:24,17:0.0882:2,2:15.8:1:31.2:1:1:1.41:60:12:0.1111:0:6.7 -6 160639974 . GTAATAGCAGCAACAGC ATAACAGT 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.09685;SOR=0;LSEQ=CAGCAACAGAAGTAGCAGTA;RSEQ=AGCAGCAGCAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:2,1:36,23:0.0476:2,2:32.3:1:30.3:1:1:1.27:60:6:0.0476:0:4 0/0:73:0:0,0:23,20:0:2,0:20.2:1:31.1:1:1:0:59.2:86:0.7679:0:0.2 -6 160639980 . G A 68 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.10447;SOR=0.17481;LSEQ=CAGAAGTAGCAGTAGTAATA;RSEQ=CAGCAACAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:2,3:37,23:0.0725:2,2:16.6:1:29.4:1:0.3815:2.37935:60:10:0.082:0.0145:4.8 0/1:75:1:0,1:23,20:0.0133:2,0:1:1:27:1:0.47727:0:60:2:0.0213:0.0133:0 -6 160639984 . C T 105 DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01787;SOR=0.27993;LSEQ=AGTAGCAGTAGTAATAGCAG;RSEQ=AACAGCAGCAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:16:4,12:40,23:0.2:2,2:8.9:1:26.4:1:0.00983:5.10486:60:32:0.2051:0:4.5 0/1:77:5:3,2:23,20:0.0649:2,2:2.6:1:26.2:1:1:1.30:60:10:0.1042:0:4 -6 160639986 . A ACAGCAGCAGCAGCAGCAGCAGCAATCATTACCATAGTAGCAACAACAGTAGCAGCAACTAACAATGGAAGCATCGGCAACAACAATAGCAAGAGCATCACAGTCAACAACAGCAACAGCAGCAACAATAGCCACAGCAACAGCAACAGCAGCAGTAGCAACAGAAATCACAGTAATAACAGTAG 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGCAGTAGTAATAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:42:27,15:64,54:0.2428:2,2:41.4:1:29.9:1:0.28155:1.51:52.8:84:0.25:0.2428:1.1 0/0:142:0:0,0:65,45:0:2,0:8:1:29.4:1:1:0:58.6:220:1:0.007:1.3 -6 160639987 . C CAATAGCCACAGCAACAGCAACAGCAGCAGTAGCAACAGAAATCACAGTAATAACAGT 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3105;SOR=2.40747;LSEQ=AGCAGTAGTAATAGCAGCAA;RSEQ=AGCAGCAGCAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:1,2:93,76:0.0169:2,2:31.7:1:27.5:1:0.59088:2.43492:60:6:0.0176:0.0169:0.3 0/1:151:6:1,5:73,57:0.0397:2,2:55.7:1:28.6:1:0.09233:6.32633:60:12:0.0448:0.0397:0 -6 160639989 . G A 121 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.15474;SOR=0.52453;LSEQ=CAGTAGTAATAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:18:5,13:98,69:0.0947:2,2:5.2:1:29.2:1:0.02227:3.66699:60:17:0.0939:0:3.5 0/1:154:8:3,5:78,66:0.0519:2,2:7.9:1:29.9:1:0.47422:1.96097:60:16:0.0526:0:2.8 -6 160639990 . C T 175 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.08029;SOR=1.47026;LSEQ=AGTAGTAATAGCAGCAACAG;RSEQ=AGCAGCAGCAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:68:42,26:64,63:0.3417:2,2:5.9:1:28.6:1:0.135:1.59:58.3:33:0.3492:0:2.2 0/1:157:68:43,25:38,46:0.4331:2,2:5.8:1:28.9:1:0.03373:2.07:58.2:136:0.4503:0:2 -6 160639992 . G A 31 v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.20268;SOR=Inf;LSEQ=TAGTAATAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:112,94:0:2,0:13:1:32:1:1:0:58.6:67.667:1:0:1.7 0/1:170:2:1,1:88,75:0.0118:2,2:24:0:31:1:1:1.17219:60:4:0.0121:0:1.5 -6 160639993 . C T 144 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.37217;SOR=0.75472;LSEQ=AGTAATAGCAGCAACAGCAG;RSEQ=AGCAGCAGCAGCAGCAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:32:14,18:101,79:0.1502:2,2:6.7:1:28.8:1:0.24825:1.63984:56.8:64:0.1561:0:3.2 0/1:170:20:12,8:77,68:0.1176:2,2:5.9:1:27.9:1:0.63697:1.32:60:40:0.122:0:2.5 -6 160640012 . C A 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32649;SOR=0.81337;LSEQ=GCAGCAGCAGCAGCAGCAAT;RSEQ=ATTACCATAGTAGCAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:69:38,31:220,140:0.1605:2,2:17:1:28.1:1:0.35107:1.28118:59.7:22:0.1587:0:1.7 0/1:394:53:30,23:195,144:0.1345:2,2:16.5:1:28.1:1:1:1.03812:58.2:106:0.1359:0:1.4 -6 160640035 . T C 122 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68134;SOR=0.79807;LSEQ=TACCATAGTAGCAACAACAG;RSEQ=AGCAGCAACACCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:577:14:14,0:341,221:0.0243:2,1:11.2:1:32.2:1:0.00136:0:41.4:13:0.0231:0:1.2 0/1:514:10:9,1:298,205:0.0195:2,2:12.6:1:30.1:1:0.05583:6.18:42:9:0.018:0:1.6 -6 160640055 . G A 270 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.523;SOR=0.91932;LSEQ=TAGCAGCAACACCAGCAGCA;RSEQ=TAGCAGCAGCAATAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:660:491:305,186:86,83:0.7439:2,2:24.6:1:30.3:1:0.01117:1.58:59.9:69.143:0.7492:0:2.6 1/0:602:438:268,170:80,83:0.7276:2,2:25.5:1:29.8:1:0.00918:1.63:59.4:72:0.7273:0:2.2 -6 160640059 . C T 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.16797;SOR=1.17773;LSEQ=AGCAACACCAGCAGCAGTAG;RSEQ=AGCAGCAATAGCAACAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:694:235:147,88:256,202:0.3386:2,2:23.5:1:29.1:1:0.10383:1.32:60:77.333:0.3402:0:3.2 0/1:630:237:145,92:217,176:0.3762:2,2:23.8:1:28.7:1:0.1575:1.28:58.7:58.25:0.3776:0:2.9 -6 160640064 . G GCAATAGCAACAGTAATAGTAGCAGCAACAGCAATAGCAACAGTAGCAGCATCAGCAACAATAACAGCAAGTAAAAACAGCAACAGCAGCAGCAACAATAATAGCAGCCACAGCATCAGTAGCAGCAGCAGCAACAAGAGCAACAATAACAA 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=69;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCAGCAGCAGTAGCAGCA;RSEQ=CAATAGCAACAGTAATAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:739:0:0,0:423,309:0:2,0:24.3:1:31.8:1:1:0:59.7:51.286:0.9903:0:2.3 0/1:685:71:39,32:349,262:0.1036:2,2:14.1:1:28.9:1:0.80031:1.09283:59.5:70:0.1046:0.1036:2.1 -6 160640068 . T TAGCAACAGTAATAGTAGCAGCAACAGCAATAGCAACAGTAGCAGCATCAGGCAACAAGAGCAACAATAGCAGCAGTAACAACAGCAACAGCAGCAGCAACAATAGGAGCAGCCGC 137 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=50;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=4.49723;LSEQ=AGCAGCAGTAGCAGCAGCAA;RSEQ=AGCAACAGTAATAGTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:772:6:1,5:440,324:0.0078:2,2:46.3:1:29.4:1:0.08911:6.77448:33.7:12:0.0079:0.0078:5 0/1:734:25:13,12:401,308:0.0341:2,2:35.9:1:29.7:1:0.68519:1.20149:36.6:50:0.0347:0.0341:2.2 -6 160640080 . T TAGCAGCCACAGCATCAGTAGCAGCAGCAGCAACAAGAGCAACAATAACAAAAGCAACAATAGCAAC 183 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCAGCAATAGCAACAGTAA;RSEQ=AGTAGCAGCAACAGCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:65:30,35:470,341:0.0721:2,2:34.7:1:30.5:1:0.06909:1.60709:42:130:0.0744:0.0721:0.1 0/0:883:0:0,0:404,302:0:2,0:19.9:1:28.3:1:1:0:58:43.125:0.8005:0:2.2 -6 160640083 . T C 90 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4233;SOR=0.57505;LSEQ=AGCAATAGCAACAGTAATAG;RSEQ=AGCAGCAACAGCAATAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:902:9:4,5:504,388:0.01:2,2:15.9:1:28.7:1:0.51427:1.6228:52.1:3.5:0.0079:0.0011:4.8 0/0:868:5:4,1:472,391:0.0058:2,2:12.4:1:32.2:1:0.38526:3.31:52:10:0.0058:0.0012:3.6 -6 160640085 . G GCAGCAACAGCAATAGCAACAGTAGCAGCATCAGCAACAATAACAGCAAGTAAAAACAGCAACAGCAGCAGCAACAACAACAGTAGCAGCAGCAGCAACAACAGCAACAATAACAAAAGCAACGATAGCAACAGTATCAGCAA 238 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=48;MSI=3.000;MSILEN=6;SSF=0;SOR=0;LSEQ=CAATAGCAACAGTAATAGTA;RSEQ=CAGCAACAGCAATAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1101:246:122,124:474,372:0.2234:2,2:31:1:30:1:0.08089:1.29476:54.9:81:0.2263:0.2234:2.5 0/0:1031:0:0,0:473,393:0:2,0:20.9:1:31.4:1:1:0:55.7:36.652:0.8371:0.001:1.9 -6 160640104 . CAGT C 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.31301;SOR=0.85377;LSEQ=AGCAGCAACAGCAATAGCAA;RSEQ=AGCAGCATCAGCAACAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1104:98:37,61:531,475:0.0888:2,2:15.9:1:32.5:1:0.00569:1.84198:41.9:196:0.0897:0:0.2 0/1:1068:82:39,43:507,479:0.0768:2,2:15.8:1:32:1:0.56571:1.16684:42.1:164:0.0776:0:0.2 -6 160640107 . T C 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63132;SOR=1.06599;LSEQ=AGCAACAGCAATAGCAACAG;RSEQ=AGCAGCATCAGCAACAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1071:162:84,78:430,380:0.1513:2,2:20.5:1:31.5:1:0.79628:1.05073:54.9:22.143:0.1628:0:3.4 0/1:1046:167:84,83:411,385:0.1597:2,2:19.9:1:31.8:1:0.79851:1.0548:53.3:82.5:0.1726:0.0019:3.2 -6 160640115 . T G 88 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50125;SOR=0.72443;LSEQ=CAATAGCAACAGTAGCAGCA;RSEQ=CAGCAACAATAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:990:11:2,9:496,480:0.0111:2,2:13.2:1:25.6:1:0.036:4.64352:31.9:1.75:0.0074:0:5.3 0/0:991:8:1,7:500,478:0.0081:2,2:9:1:33.4:1:0.03555:7.31054:34.8:16:0.0083:0:4.5 -6 160640117 . A G 173 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20579;LSEQ=ATAGCAACAGTAGCAGCATC;RSEQ=GCAACAATAACAGCAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:981:57:35,22:455,469:0.0581:2,2:7.2:1:29.8:1:0.07765:1.64:59.2:56:0.0582:0:2.2 0/1:958:12:8,4:473,473:0.0125:2,2:5.3:1:28.8:1:0.3847:2.00:51.3:24:0.0127:0:1.8 -6 160640124 . ATAACAGCAACAGAAGCAATAACAGC GCAATAGTATCACAATTAACAACAGCAACAATAGCCACAGCAACAGCAACAGCAGCAGTAGCAACAGCAATAGCAGTAATAGCAGCAGCAGCAGTAGCAGCAATAATTACAACAATAGCAGCAAT 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=CAGTAGCAGCATCAGCAACA;RSEQ=AGCAGCAACAACAGCAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:934:98:32,66:420,407:0.1049:2,2:32.1:1:30.4:1:0.00085:2.1267:41.4:196:0.1063:0.1049:0.2 0/0:887:0:0,0:391,407:0:2,0:11.9:1:29.7:1:1:0:54.9:71.545:0.8984:0:2.4 -6 160640125 . T CAGC 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1e-05;SOR=0.62065;LSEQ=AGTAGCAGCATCAGCAACAA;RSEQ=AACAGCAACAGAAGCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:282:150,132:257,267:0.3431:2,2:33:1:32:1:0.26874:1.18:54.7:564:0.3525:0:5.1 0/1:805:197:101,96:129,140:0.2447:2,2:34.9:1:31.2:1:0.51196:1.14:54.4:196:0.2503:0:5.2 -6 160640127 . A G 220 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGCAGCATCAGCAACAATA;RSEQ=CAGCAACAGAAGCAATAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:0:0,0:220,205:0:2,0:22.6:1:30:1:1:0:56:69.833:1:0.0018:3.8 0/1:452:138:62,76:156,157:0.3053:2,2:13.4:1:31:1:0.35842:1.21746:54.3:22:0.2986:0.0221:3.5 -6 160640128 . C G 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29194;SOR=0.76302;LSEQ=AGCAGCATCAGCAACAATAA;RSEQ=AGCAACAGAAGCAATAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:49:27,22:255,245:0.0886:2,2:8.4:1:31.8:1:0.6541:1.18:58.1:48:0.0886:0:2.2 0/1:449:31:15,16:197,213:0.069:2,2:9.4:1:31.5:1:1:1.01:55.5:62:0.0698:0:2.3 -6 160640133 . AC GT 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21106;SOR=1.39971;LSEQ=CATCAGCAACAATAACAGCA;RSEQ=AGAAGCAATAACAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:34:13,21:109,115:0.0608:2,2:31.4:1:29.9:1:0.27469:1.5286:45.7:68:0.1298:0:7 0/1:433:36:14,22:97,97:0.0831:2,2:31:1:29.4:1:0.27638:1.56836:45:72:0.0843:0:7 -6 160640134 . CAGAAGCAATAACAGCAGCAGCAACAACAGCAGTACGAACACCAGCAGTAA TAATAACAGCAACAACAACAGCAACAGCAGCAACAACAGCAACAATAACAAAAGCAACGATAGCAACAGTATCAGCAACAG 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00335;SOR=0;LSEQ=ATCAGCAACAATAACAGCAA;RSEQ=CAACAGCAGCAGCAACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:10:1,9:109,115:0.0179:2,2:49.7:1:26.7:1:0.02102:8.47271:39.8:20:0.0382:0.0179:2.8 0/0:433:0:0,0:97,97:0:2,0:4.5:1:29.4:1:1:0:56.1:96:0.4496:0:0.7 -6 160640136 . G A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45825;SOR=1.22383;LSEQ=CAGCAACAATAACAGCAACA;RSEQ=AAGCAATAACAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:37:15,22:194,185:0.0877:2,2:28.5:1:29.8:1:0.23221:1.53642:46.9:74:0.0907:0:6.8 0/1:342:36:14,22:154,150:0.1053:2,2:29:1:29.3:1:0.21814:1.61107:45:35:0.1048:0:7 -6 160640137 . A C 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03443;SOR=0.7244;LSEQ=AGCAACAATAACAGCAACAG;RSEQ=AGCAATAACAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:416:274:144,130:63,73:0.6587:2,2:20.7:1:31.7:1:0.24968:1.28:54.6:29.444:0.6709:0:5.1 1/0:338:197:96,101:69,70:0.5828:2,2:22.6:1:31.3:1:0.91195:1.03696:54.2:31.833:0.5859:0:5.2 -6 160640139 . G A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01332;SOR=0.66967;LSEQ=CAACAATAACAGCAACAGAA;RSEQ=CAATAACAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:293:151,142:51,55:0.7252:2,2:20.6:1:29.4:1:0.57209:1.15:53.3:35.625:0.7403:0:5.5 1/0:332:212:98,114:64,54:0.6386:2,2:23.4:1:29.2:1:0.16997:1.37732:52.1:52:0.65:0:5.7 -6 160640142 . AT GC 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3198;SOR=1.29361;LSEQ=CAATAACAGCAACAGAAGCA;RSEQ=AACAGCAGCAGCAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:35:13,22:175,171:0.0897:2,2:20.9:1:31.8:1:0.15646:1.72942:46.7:70:0.0926:0:5.7 0/1:327:37:15,22:145,138:0.1131:2,2:20.6:1:31.4:1:0.29418:1.53898:46.4:74:0.1156:0:5.7 -6 160640145 . A AGAG 236 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00945;SOR=0.66908;LSEQ=TAACAGCAACAGAAGCAATA;RSEQ=CAGCAGCAGCAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:379:213:107,106:55,67:0.562:2,2:15.9:1:30.6:1:0.42655:1.23:53.2:70:0.625:0.3166:5.2 0/1:314:145:73,72:60,61:0.4618:2,2:19.4:1:30.7:1:1:1.03:52.4:144:0.5393:0.2261:5.5 -6 160640160 . A G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.42444;SOR=1.32168;LSEQ=CAATAACAGCAGCAGCAACA;RSEQ=CAGCAGTACGAACACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:19:11,8:123,148:0.0653:2,2:5.5:1:30.7:1:0.34487:1.65:50:38:0.0657:0:6.7 0/1:272:23:13,10:113,134:0.0846:2,2:7:1:31:1:0.38457:1.54:49.3:46:0.0858:0:7.1 -6 160640163 . G A 182 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAACAGCAGCAGCAACAACA;RSEQ=CAGTACGAACACCAGCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:78:34,44:82,105:0.291:2,2:5.4:1:29.1:1:1:1.0106:46.8:77:0.295:0:5.5 0/0:253:0:0,0:87,100:0:2,0:18.3:1:31.5:1:1:0:55.8:45.75:0.9946:0:1.4 -6 160640179 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49867;SOR=Inf;LSEQ=AACAGCAGTACGAACACCAG;RSEQ=AGTAACAACAGCAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:83,80:0:2,0:23.6:1:31.9:1:1:0:59.7:53.333:1:0.0061:0.3 0/1:171:2:1,1:85,84:0.0117:2,2:20.5:1:28.5:1:1:1.01184:60:4:0.0119:0:1.5 -6 160640193 . G T 91 Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.0197;SOR=0.11966;LSEQ=CACCAGCAGTAACAACAGCA;RSEQ=CAGCAACATCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:8:0,8:83,78:0.0473:2,0:9:0:30.4:1:0.00663:0:38.5:16:0.0485:0:3 0/0:170:1:0,1:81,88:0.0059:2,0:9:0:30:0:1:0:40:2:0.006:0:3 -6 160640196 . G A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=1.49823;LSEQ=CAGCAGTAACAACAGCAGCA;RSEQ=CAACATCAGCAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:2,0:82,86:0.0118:2,0:11.5:1:29.5:1:0.24267:0:60:4:0.0118:0:5 0/1:171:3:3,0:79,89:0.0175:2,0:5.7:1:29:1:0.10816:0:60:6:0.018:0:3 -6 160640202 . T A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08416;SOR=0.31606;LSEQ=TAACAACAGCAGCAGCAACA;RSEQ=CAGCAACAACAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:9:0,9:78,75:0.0549:2,0:18:0:28.3:1:0.00326:0:37.6:8:0.0503:0:3 0/1:167:3:0,3:75,87:0.018:2,0:16.3:1:31.3:1:0.25166:0:34.7:6:0.0183:0:3 -6 160640205 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24781;SOR=Inf;LSEQ=CAACAGCAGCAGCAACATCA;RSEQ=CAACAACAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:81,91:0:2,0:22.9:1:32:1:1:0:58.5:42:1:0:0.5 0/1:171:2:1,1:76,93:0.0117:2,2:27:0:30.5:1:1:1.22:60:4:0.0121:0:1.5 -6 160640211 . A G 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.62275;SOR=2.02013;LSEQ=CAGCAGCAACATCAGCAACA;RSEQ=CAGCAGCAACAACAGTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:1:0,1:77,87:0.006:2,0:13:0:13:0:1:0:30:0:0:0:3 0/1:167:2:0,2:76,89:0.012:2,0:13:0:32.5:1:0.50105:0:32:4:0.0124:0:3 -6 160640212 . C T 86 Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01968;SOR=0.10696;LSEQ=AGCAGCAACATCAGCAACAA;RSEQ=AGCAGCAACAACAGTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:9:0,9:76,83:0.0536:2,0:8.6:1:27.2:1:0.00428:0:40.9:8:0.0497:0:3.6 0/0:167:1:0,1:76,90:0.006:2,0:8:0:30:0:1:0:40:2:0.0061:0:3 -6 160640215 . C CAGCAACAACAGT 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.35636;SOR=1.2554;LSEQ=AGCAACATCAGCAACAACAG;RSEQ=AGCAACAACAGTAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:164:100:47,53:27,36:0.6098:2,2:27:1:29.8:1:0.6311:1.18:59.5:99:0.6111:0.1646:0.4 1/0:160:106:50,56:21,31:0.6625:2,2:26.3:1:29.6:1:0.49679:1.32:60:105:0.6646:0.2313:0.3 -6 160640217 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49844;SOR=0;LSEQ=CAACATCAGCAACAACAGCA;RSEQ=CAACAACAGTAGCAGCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:73,86:0.0124:2,0:6.5:1:26.5:1:0.50124:0:47.5:4:0.0127:0.0062:1.5 0/0:160:0:0,0:71,88:0:2,0:20.8:1:31.6:1:1:0:59.4:38.75:0.9936:0:0.3 -6 160640268 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.12625;SOR=0.3872;LSEQ=CAATAATTATAACAGCAGCA;RSEQ=CAACAACAGTAACAACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:15:7,8:26,36:0.1948:2,2:6:0:29.5:1:0.77744:1.21:27.9:30:0.1948:0:1 0/1:47:4:2,2:18,25:0.0851:2,2:6:0:30:1:1:1.38:26:8:0.087:0:1 -6 160640308 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20579;SOR=Inf;LSEQ=AGAAATAAGTACAATAGCAA;RSEQ=AACAACAGTAATAGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:35,21:0:2,0:21.3:1:29.9:1:1:0:60:112:1:0:0.2 0/1:47:2:1,1:28,17:0.0426:2,2:5:0:31:1:1:1.62892:60:4:0.0426:0:0 -6 160640350 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5008;SOR=Inf;LSEQ=AAAAACAATAGCAGCAGTAA;RSEQ=AATAACAACAGCAATAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:53,46:0:2,0:23.7:1:31.9:1:1:0:57.5:198:1:0:0.3 0/1:116:2:1,1:69,45:0.0172:2,2:32:0:30:1:1:1.52748:60:4:0.0174:0:3 -6 160640353 . T C 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3397;SOR=0.5988;LSEQ=AACAATAGCAGCAGTAACAA;RSEQ=AACAACAGCAATAGCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:11:0,11:56,36:0.1068:2,0:21:0:31:1:9e-05:0:37.5:22:0.1068:0:2 0/1:120:8:1,7:71,41:0.0667:2,2:23:1:31.4:1:0.00676:11.89744:38.8:16:0.0672:0:2.3 -6 160640355 . A G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.33727;SOR=0.58447;LSEQ=CAATAGCAGCAGTAACAATA;RSEQ=CAACAGCAATAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:11:0,11:57,36:0.1058:2,0:19:0:31.2:1:8e-05:0:37.5:22:0.1058:0:2 0/1:124:8:1,7:71,45:0.0645:2,2:21:1:32:1:0.00943:10.85644:38.8:16:0.0656:0:2.3 -6 160640362 . CAAT C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.23913;SOR=0.55948;LSEQ=AGCAGTAACAATAACAACAG;RSEQ=AGCAGCAACAACAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:11:0,11:60,39:0.1:2,0:11:0:31.7:1:9e-05:0:37.5:22:0.1009:0:2 0/1:137:8:1,7:80,49:0.0584:2,2:13:1:32.1:1:0.00808:11.24844:38.8:16:0.0584:0:2.3 -6 160640365 . T TAGCAGCAACAATAGGAGCAGCCGCAGCAACAGCAACAGTAGCAGC 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.21888;SOR=0.50069;LSEQ=AGTAACAATAACAACAGCAA;RSEQ=AGCAGCAACAACAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:11:0,11:63,28:0.0973:2,0:44.4:1:31.1:1:1e-05:0:37.5:22:0.1089:0.0973:2 0/1:137:7:0,7:79,43:0.0511:2,0:32.4:1:30.7:1:0.001:0:35.7:14:0.0547:0.0511:1.9 -6 160640420 . A T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.17971;SOR=0;LSEQ=GCAGCAGCAACAACAGCAGC;RSEQ=GCAGCAACAACATCAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:70,72:0.0139:2,2:38:0:29.5:1:1:1.03:60:4:0.0139:0:1 0/0:195:0:0,0:95,100:0:2,0:27:1:30.2:1:1:0:59.8:96.5:1:0:0.2 -6 160640422 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50925;SOR=Inf;LSEQ=AGCAGCAACAACAGCAGCAG;RSEQ=AGCAACAACATCAGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:71,75:0:2,0:28.8:1:31.8:1:1:0:60:35.5:1:0:0.1 0/1:196:2:0,2:95,99:0.0102:2,0:13:0:30:0:0.49791:0:60:4:0.0103:0:1 -6 160640424 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.2635;SOR=Inf;LSEQ=CAGCAACAACAGCAGCAGCA;RSEQ=CAACAACATCAGCCACCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:67,78:0:2,0:28.7:1:32:1:1:0:60:47.333:1:0:0.1 0/1:194:3:2,1:91,100:0.0155:2,2:15.7:1:28.7:1:0.60802:2.19:60:6:0.0155:0:1.7 -6 160640426 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18403;SOR=0;LSEQ=GCAACAACAGCAGCAGCAGC;RSEQ=ACAACATCAGCCACCGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:66,79:0.0136:2,2:36.5:1:29.5:1:1:1.20:60:4:0.0137:0:1 0/0:195:0:0,0:91,104:0:2,0:26:1:29.6:1:1:0:59.8:96.5:1:0:0.2 -6 160640435 . A C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50592;SOR=Inf;LSEQ=GCAGCAGCAGCAACAACATC;RSEQ=GCCACCGGTGAGTGACTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:62,78:0:2,0:27.3:1:30.6:1:1:0:60:139:1:0:0.1 0/1:179:2:1,1:76,101:0.0112:2,2:14:1:28:1:1:1.33:60:4:0.0114:0:1.5 -6 160640437 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50691;SOR=Inf;LSEQ=AGCAGCAGCAACAACATCAG;RSEQ=CACCGGTGAGTGACTACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:60,77:0:2,0:27.3:1:31.6:1:1:0:60:136:1:0:0.1 0/1:178:2:1,1:75,101:0.0112:2,2:30:0:28.5:1:1:1.34:60:4:0.0116:0:1.5 -6 160640476 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49674;SOR=0;LSEQ=AACTAAATACCAAGCACTGC;RSEQ=ACGGGTGCTTCGTCGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:18,54:0.027:2,2:12.5:1:27:1:0.4502:2.95:60:4:0.0274:0:1 0/0:71:0:0,0:19,52:0:2,0:24.9:1:29.8:1:1:0:60:34.5:1:0:0.2 -6 160640494 . C T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00701;SOR=Inf;LSEQ=GCGACGGGTGCTTCGTCGCA;RSEQ=TGTCCCATTCATGAGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:4,40:0:2,0:25.5:1:32.1:1:1:0:60:43:1:0:0 0/1:52:8:3,5:7,37:0.1538:2,2:21.1:1:30:1:0.17097:3.08:60:16:0.1538:0:1 -6 161771025 . C T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.22192;SOR=4.41529;LSEQ=AAACTTGAAGAGTGTGTGTG;RSEQ=GCGCGCGCGCGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:153,18:0.0058:2,0:3:0:25:0:1:0:60:2:0.006:0:1 0/1:198:5:4,1:171,20:0.0253:2,2:18.2:1:26.8:1:0.43609:2.12663:60:10:0.0265:0:1 -6 161771035 . CGTGT C 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=7.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGTGTGTGTGCGCGCGCGCG;RSEQ=GTGTGTGTGTTTGAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:20:14,6:158,29:0.093:2,2:8.3:1:30.8:1:0.11671:2.32321:60:40:0.0943:0.0419:0.1 0/0:262:0:0,0:203,39:0:2,0:22.7:1:29.7:1:1:0:60:79:0.9186:0:0.2 -6 161771037 . T C 173 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGTGTGTGCGCGCGCGCGCG;RSEQ=GTGTGTGTGTGTTTGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:52:46,6:117,25:0.2441:2,2:24.7:1:30.4:1:0.38024:1.63:60:12:0.2595:0:2 0/0:270:0:0,0:208,43:0:2,0:22.3:1:28.2:1:1:0:60:34.857:1:0:0.2 -6 161771039 . T C 177 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGTGTGCGCGCGCGCGCGTG;RSEQ=GTGTGTGTGTTTGAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:54:48,6:122,28:0.25:2,2:23.6:1:30.9:1:0.28658:1.83:60:26:0.268:0:2 0/0:273:0:0,0:223,49:0:2,0:23.1:1:28.1:1:1:0:60:26.2:1:0:0.3 -6 161771361 . T C 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3637;SOR=1.88738;LSEQ=GAGCGAATAATCACAAGCAA;RSEQ=ACAAGGGCAGAGAGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:5:0,5:1,60:0.0758:1,0:26.2:1:33.4:1:1:0:60:10:0.082:0:1 0/1:52:7:0,7:1,44:0.1346:1,0:28.4:1:32.7:1:1:0:60:14:0.1346:0:1.1 -6 161807664 . G C 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00203;SOR=Inf;LSEQ=ACACTGTGCCCCAAGGAGGG;RSEQ=AGTCATTCTGGGAGAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:74,1:0:1,0:25.6:1:31.5:1:1:0:60:74:1:0:0.1 0/1:44:6:6,0:37,1:0.1364:1,0:31.8:1:33.2:1:1:0:60:12:0.1429:0:1 -6 161807855 . C G 259 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTCCTGAGGCTTCAAATA;RSEQ=GGCACTGCACTCCCCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:978:0:0,0:468,509:0:2,0:25.7:1:30.8:1:1:0:60:96.7:0.999:0:0.1 0/1:1078:341:174,167:354,381:0.3163:2,2:24.2:1:30.9:1:0.39471:1.12:60:169.5:0.3168:0:1.1 -6 161807975 . CT C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.24378;SOR=0;LSEQ=TTGGCAATAACACATTTTTC;RSEQ=TTTCCAAATTCATTATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:14,162:0.0112:2,2:28:1:27:1:0.16187:11.21:60:4:0.0114:0:0 0/0:182:0:0,0:24,158:0:2,0:23.7:1:29.5:1:1:0:60:29.333:1:0:0.1 -6 161966036 . T C 67 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCGGAAGACCACCCAGG;RSEQ=ACATGGTCGTGGGTGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:28.8:1:33.5:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:1:0,0:15:0:34:0:1:0:60:2:1:0:1 -6 161966374 . T A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2502;SOR=0;LSEQ=CTGGAACTCTGTAATTCTTC;RSEQ=ATAGCTTTGCTACCAATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:2,1:219,44:0.0113:2,2:32.3:1:30:1:0.42783:2.47754:60:6:0.0114:0:1 0/0:242:0:0,0:183,59:0:2,0:22.5:1:29.9:1:1:0:60:484:1:0:0.1 -6 161966410 . G T 67 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4515;SOR=0.40561;LSEQ=ATGACTTTTCCTTGAACGAT;RSEQ=TATTGAATGAGGCACTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:5:1,4:293,169:0.0107:2,2:9.8:1:29.2:1:0.06521:6.9071:60:10:0.0108:0:1.2 0/0:458:2:0,2:280,176:0.0044:2,0:1:0:25.5:1:0.15053:0:60:4:0.0044:0:1 -6 161970150 . ATGTG A 163 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=11.000;MSILEN=2;SSF=0.15091;SOR=0.62742;LSEQ=CAGTTTCAGTAAAATAATGC;RSEQ=TGTGTGTGTGTGTGTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:44:0,44:5,99:0.2588:1,1:33.4:1:30:1:0.32225:0:59.9:43:0.259:0.0176:0.3 0/1:117:21:2,19:2,78:0.1795:1,2:32:1:30:1:0.19006:4.03:60:42:0.1842:0.0171:0.3 -6 161970231 . T A 164 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=ACGAATATGGTTCAATGCAG;RSEQ=AAAAGTCTACCAAATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:46:1,45:0,0:1:0,1:22.2:1:29.7:1:1:0:60:22:1:0:1.1 1/0:19:11:1,10:0,8:0.5789:0,2:21.5:1:30.5:1:1:0:60:22:0.5789:0:1.4 -6 161990286 . A G 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02255;SOR=Inf;LSEQ=TTCCCCATTTCAGGGCACCC;RSEQ=GGGTCAGGAGACATACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:104,9:0:2,0:24.1:1:30.5:1:1:0:60:55.5:1:0:0.1 0/1:73:4:4,0:65,4:0.0548:2,0:24.8:1:29.8:1:1:0:60:8:0.0571:0:1 -6 161990339 . G A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=GCCCAAACTGTCTCATTAGC;RSEQ=TCTATCTTTCATGACAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:239,73:0:2,0:24.5:1:30.6:1:1:0:60:155:0.9968:0:0.1 0/1:238:11:11,0:170,57:0.0462:2,0:35.4:1:30.7:1:0.07065:0:60:22:0.0474:0:1.1 -6 161990401 . G A 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCACCTGCTCTTCTCCCA;RSEQ=AATCCTGAAGTGATGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:674:0:0,0:384,290:0:2,0:24.7:1:31.4:1:1:0:60:95.286:1:0:0.2 0/1:568:38:25,13:300,230:0.0669:2,2:22.7:1:30.2:1:0.31071:1.47:60:76:0.0677:0:1.2 -6 161990483 . C T 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24264;SOR=0.86475;LSEQ=AATTAATCACAAAAACGTCA;RSEQ=TTTCACTCTGTGTGGTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:229:76,153:124,172:0.4354:2,2:25.2:1:30.1:1:0.04631:1.4503:60:113.5:0.4382:0:1.6 0/1:560:224:84,140:141,195:0.4:2,2:25.5:1:29.7:1:0.3332:1.20472:60:111:0.4007:0:1.6 -6 161990516 . G C 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73971;SOR=1.06993;LSEQ=TGGTTATATGTTCTTACACA;RSEQ=AGTTATGACTATCAACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:130:24,106:42,113:0.4545:2,2:23.6:1:31.9:1:0.09228:1.63875:60:64:0.4523:0:1.9 0/1:297:140:34,106:49,107:0.4714:2,2:23.3:1:31.5:1:0.19579:1.42598:60:139:0.4744:0:1.8 -6 161990678 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37049;SOR=2.52834;LSEQ=AGAAAACAGTTGCATGTGAC;RSEQ=CTGGCCAGGCTTTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:0,8:0,14:0.3636:1,0:20.1:1:29.9:1:1:0:60:16:0.381:0:1 1/0:5:3:0,3:1,1:0.6:2,0:27.7:1:30:1:0.4:0:60:6:0.6:0:1 -6 162136980 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53265;SOR=0;LSEQ=AGAAACTCAAATTATGATAC;RSEQ=CCACCCTAGACAGACTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:190,1:0.0104:1,2:22.5:1:29.5:1:0.02067:134.63168:60:4:0.0105:0:1 0/0:113:0:0,0:109,4:0:1,0:21.3:1:31.3:1:1:0:60:226:1:0:0.1 -6 162137099 . CATCTT C 222 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=193.33272;LSEQ=CCACCATGCTGTGCTGGGCC;RSEQ=ACCGACTCCTCTCCTGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1150:1:1,0:640,507:9e-04:2,0:45:0:30:0:1:0:60:2:9e-04:0:0 0/1:1146:165:90,75:545,435:0.144:2,2:27.9:1:30.2:1:0.80017:1.04405:60:81.5:0.1437:0.0096:0.5 -6 162137107 . C A 200 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01854;LSEQ=CTGTGCTGGGCCCATCTTAC;RSEQ=GACTCCTCTCCTGAATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1196:99:47,52:604,491:0.0828:2,2:26.8:1:30.3:1:0.17043:1.36064:60:98:0.0829:0:1.1 0/0:1199:2:2,0:644,552:0.0017:2,0:1:0:25.5:1:0.50266:0:60:4:0.0017:0:1 -6 162137147 . C T 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAGAGCTCCTCTAAGCAC;RSEQ=ACTGTGTCTCCAGTTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1196:0:0,0:545,650:0:2,0:25.5:1:31.4:1:1:0:60:58.75:0.9991:0:0.2 0/1:1199:103:46,57:519,574:0.0859:2,2:22.6:1:29.1:1:0.60694:1.12029:60:102:0.086:0:1.2 -6 162138301 . C A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCAGCCCATGATGGAATG;RSEQ=GGACGGGCAAGAGGACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:28.5:1:1:0:60:4:1:0:1.5 -6 162169954 . T C 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00125;SOR=Inf;LSEQ=AGAAATTCCCTTGCCTGTCA;RSEQ=GTGTATTCCACAACGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:180,89:0:2,0:25.3:1:30.5:1:1:0:60:52.8:1:0:0.1 0/1:248:9:6,3:153,86:0.0363:2,2:26.8:1:28.4:1:1:1.12:60:8:0.0331:0:1.3 -6 162169968 . C T 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTCATGTGTATTCCACAA;RSEQ=GCATGAAAAGACCAGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:194,110:0:2,0:27.8:1:31.2:1:1:0:60:75:1:0:0.1 0/1:314:26:18,8:178,110:0.0828:2,2:25.2:1:27.8:1:0.53017:1.39:60:7.667:0.0754:0:1 -6 162170039 . C T 213 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCAGCTGGGAAACATTT;RSEQ=GAAGGGCTGGGAGAGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:229,228:0:2,0:25.5:1:30.4:1:1:0:60:75.167:1:0:0.1 0/1:475:157:72,85:153,165:0.3305:2,2:24.1:1:29.3:1:0.69619:1.09449:60:38.25:0.3269:0:1.2 -6 162170045 . G T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06281;SOR=Inf;LSEQ=GCTGGGAAACATTTCGAAGG;RSEQ=CTGGGAGAGATGGAAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:222,225:0:2,0:26.4:1:31.4:1:1:0:60:43.7:0.9977:0:0.1 0/1:485:5:1,4:226,254:0.0103:2,2:15.8:1:28.2:1:0.37755:3.55089:60:10:0.0105:0:1 -6 162170083 . G T 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGCAAAACCAAGGGGAGG;RSEQ=GGTCCTTGTACTTGGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:157,245:0:2,0:25.9:1:30.6:1:1:0:60:32.5:1:0:0.3 0/1:367:29:8,21:135,203:0.079:2,2:26.9:1:30:1:0.23554:1.7432:60:58:0.0803:0:1.2 -6 162170097 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09855;SOR=Inf;LSEQ=GGGAGGGGGTCCTTGTACTT;RSEQ=GTGAACAGATGACTCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:121,218:0:2,0:25.8:1:31.3:1:1:0:60:83.75:1:0:0.3 0/1:292:3:2,1:101,188:0.0103:2,2:14.3:1:27.7:1:0.2848:3.71:60:6:0.0104:0:2.3 -6 162170141 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=0.33673;LSEQ=AAGGATTCAGGGCCGGGAGG;RSEQ=GGGCAAGCAGGTACGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:84:11,73:10,54:0.5676:2,2:24.6:1:30.3:1:0.81263:1.22722:60:168:0.5753:0:1 0/1:108:33:7,26:15,60:0.3056:2,2:24.8:1:29.4:1:1:1.08:60:32:0.3107:0:1.1 -6 162206873 . A T 196 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCATTGAGTCTTGTCACAC;RSEQ=GTATAAGTGGAAACAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:672:82:34,48:263,325:0.122:2,2:26.1:1:30.9:1:0.63563:1.14222:60:164:0.1237:0:1.1 0/0:795:0:0,0:360,435:0:2,0:23.9:1:30.2:1:1:0:60:87.333:1:0:0.2 -6 162206881 . T C 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTCTTGTCACACAGTATAAG;RSEQ=GGAAACAGTCTAAGCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:649:0:0,0:280,367:0:2,0:24.9:1:29.9:1:1:0:60:160.75:1:0:0.2 0/1:762:18:8,10:319,424:0.0236:2,2:24.5:1:31.6:1:1:1.06:60:36:0.0237:0:1.2 -6 162393121 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGAGACCAGCCTGACCAA;RSEQ=ATGAAGAAACCCCCGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 162394272 . GCTATTTTTAGATCCTTACCTCACGTCCGTGGAGGGAAGTGACA G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=1.000;MSILEN=1;SSF=0.21408;SOR=Inf;LSEQ=AGTAAGGAGGGGGGAGTGAT;RSEQ=CTATTTTTAGATCCTTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:171,27:0:2,0:21.9:1:31.7:1:1:0:60:38.6:1:0:0.1 0/1:171:2:1,1:139,30:0.0117:2,2:19.5:1:28.1:1:0.33058:4.57438:60:4:0.0118:0.0117:0 -6 162394295 . C T 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35631;SOR=3.24649;LSEQ=ATTTTTAGATCCTTACCTCA;RSEQ=GTCCGTGGAGGGAAGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:1:0,1:204,79:0.0035:2,0:1:0:28:0:0.28169:0:60:2:0.0036:0:1 0/1:264:3:1,2:195,64:0.0114:2,2:26.3:1:29.3:1:0.15732:6.04173:60:6:0.0116:0:1.3 -6 162394500 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2365;SOR=0;LSEQ=TGGATCCCGGCTGCTCATTT;RSEQ=TCCTCTAAATGTTTCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:19,166:0.0107:2,2:13.5:1:28:1:0.20298:8.54:60:4:0.0108:0:1 0/0:197:0:0,0:37,160:0:2,0:22:1:29.7:1:1:0:60:196:1:0:0.1 -6 162473060 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18947;SOR=Inf;LSEQ=CCAAAGATACCAGGAATGAC;RSEQ=GTGTTATTAGATGAGATCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:24.9:1:30.8:1:1:0:60:22:1:0:0.2 0/1:9:2:1,1:6,1:0.2222:2,2:12.5:1:29:1:0.41667:4.58262:60:4:0.2222:0:1.5 -6 162474893 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06462;SOR=Inf;LSEQ=GTTTAAATTGGCACATTTCC;RSEQ=CACGGTCCCCCCAAATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:18,1:0:1,0:27.3:1:30.8:1:1:0:60:38:1:0:0.1 0/1:7:2:2,0:5,0:0.2857:0,0:33.5:1:27.5:1:1:0:60:4:0.2857:0:1 -6 162475245 . T A 44 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.68865;SOR=1.81338;LSEQ=ATATATGCTTATATGAGTTA;RSEQ=AATAGAAATGTACTCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:2:2,0:71,272:0.0058:2,0:1:0:25.5:1:0.04429:0:60:4:0.0059:0:1 0/1:382:4:3,1:103,275:0.0105:2,2:6.3:1:22:1:0.06665:7.96:60:3:0.008:0:2.5 -6 162475434 . A C 114 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATATTTGACATTTTGCTCC;RSEQ=AACCTGTTCGTTTTCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:0,13:0,6:0.6842:0,1:24.7:1:31:1:1:0:60:12:0.6667:0:1.5 1/1:1:1:0,1:0,0:1:0,0:14:0:34:0:1:0:60:2:1:0:1 -6 162622197 . C T 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGTTGCCTGCCTGCAGGTG;RSEQ=TGCACTGTACCCTGAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:833:0:0,0:437,395:0:2,0:25.4:1:31.8:1:1:0:60:63:1:0:0.2 0/1:800:18:9,9:414,367:0.0225:2,2:27.6:1:30.1:1:0.81601:1.12789:60:36:0.023:0:1.2 -6 162622304 . A G 270 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GCTGGAGAAGAAAAAGCAGA;RSEQ=GAAGTGGCTAATAATGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:428:428:123,305:0,0:1:0,2:25.3:1:31:1:1:0:60:141.667:1:0:1.1 1/0:393:295:89,206:35,63:0.7506:2,2:23.3:1:30.5:1:0.31746:1.28501:60:146.5:0.7494:0:1.1 -6 162683474 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.178;SOR=Inf;LSEQ=ACGTATCATAAACTAAATAT;RSEQ=CACCCGGTGAGGCCATGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:171,27:0:2,0:22.4:1:32.3:1:1:0:60:396:1:0:0.1 0/1:145:2:1,1:122,21:0.0138:2,2:15.5:1:28:1:0.28132:5.69922:60:4:0.014:0:1 -6 162683876 . C T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1592;LSEQ=GCGAGATAGAGTTTAACTTG;RSEQ=CCTCCGTGGTAGAAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:88:78:1,77:0,10:0.8864:0,1:23.8:1:30.3:1:1:0:60:156:0.8864:0:1.7 1/0:69:38:0,38:0,31:0.5507:1,1:25.1:1:29:1:1:0:60:37:0.5522:0:1.5 -6 162864276 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.356;SOR=3.25038;LSEQ=CAGGCATGAATGTCAGATTG;RSEQ=CAGCGCAGGCGGCATGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:0,1:201,26:0.0044:2,0:2:0:15:0:0.11842:0:60:0:0:0:2 0/1:212:3:1,2:175,34:0.0142:2,2:19.7:1:28:1:0.07538:10.11791:60:6:0.0144:0:1 -6 162864289 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05335;SOR=Inf;LSEQ=CAGATTGGCAGCGCAGGCGG;RSEQ=ATGAGCAATGGAGCTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:236,52:0:2,0:23.5:1:31.7:1:1:0:60:71:1:0:0.1 0/1:268:4:1,3:211,53:0.0149:2,2:13.5:1:24:1:0.02971:11.79678:60:8:0.015:0:1 -6 162864317 . A G 199 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=102.50521;LSEQ=ATGGAGCTGGCGGCATCCCA;RSEQ=GAACGGCCGCCAAGGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:1:0,1:308,141:0.0022:2,0:14:0:25:0:0.31556:0:60:2:0.0023:0:5 0/1:484:90:63,27:259,135:0.186:2,2:20.6:1:30.8:1:0.4606:1.22:60:89:0.185:0:1.1 -6 162864566 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=CACTCGAAGCCCTTAAATGG;RSEQ=GATAGCAACATTTCTCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:22,184:0:2,0:23.3:1:30.1:1:1:0:59.9:205:0.9951:0:0.1 0/1:173:2:1,1:28,143:0.0116:2,2:28:1:27:1:0.30797:5.04:60:4:0.0116:0:1 -6 162992348 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0089;SOR=Inf;LSEQ=GCCTGGGCAACAGAGAAAAA;RSEQ=TCATTTCAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:0:1,0:16.8:1:32.1:1:1:0:54:44:1:0:1.6 0/1:21:6:5,1:15,0:0.2857:1,2:6.8:1:28.2:1:0.28571:0:57.5:12:0.2857:0:1.7 -6 162992355 . CAA C 92 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.09325;SOR=3.7017;LSEQ=CAACAGAGAAAAACTCATTT;RSEQ=AAAAAAAAAAAAAAGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:24,0:0.1:1,0:23:1:32:1:1:0:60:6:0.1:0:1.3 0/1:27:8:7,1:12,0:0.2963:0,2:12.4:1:30.7:1:0.4:0:60:16:0.2963:0.0741:1 -6 162992419 . G T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53415;LSEQ=TGTATCCTATAAATATACAC;RSEQ=CATACTATGTACCCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:90,23:0.0172:2,2:23.5:1:30.5:1:0.37529:3.85188:60:4:0.0182:0:1.5 0/0:108:1:0,1:89,18:0.0093:2,0:1:0:24:0:0.17593:0:60:2:0.0102:0:1 -6 162992532 . C G 190 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=34.28833;LSEQ=ATTAAAACTGCTTTGACAAA;RSEQ=TTTTGGCAGATAAAATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:2:1,1:102,150:0.0079:2,2:24.5:1:31.5:1:1:1.47:60:4:0.008:0:1.5 0/1:331:71:30,41:108,152:0.2145:2,2:24.5:1:31:1:1:1.03:60:142:0.2158:0:1.2 -6 162992556 . T A 21 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21012;SOR=0;LSEQ=TGGCAGATAAAATTTGTGAT;RSEQ=GGTTGAATGTAGGCACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:54,129:0.0108:2,2:14.5:1:21.5:1:0.50734:2.38:60:4:0.0109:0:1.5 0/0:218:0:0,0:70,148:0:2,0:23.2:1:29.2:1:1:0:60:53.5:1:0:0.3 -6 162992560 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50112;SOR=Inf;LSEQ=AGATAAAATTTGTGATTGGT;RSEQ=GAATGTAGGCACTCAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:47,125:0:2,0:23.3:1:29.9:1:1:0:60:171:1:0:0.1 0/1:198:2:1,1:58,136:0.0101:2,2:21.5:1:28.5:1:0.51251:2.33:60:4:0.0103:0:1.5 -6 162992704 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=Inf;LSEQ=GGATGTAAAGTACCCGTGGG;RSEQ=TGTCCAAGTTGAGGGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:22.8:1:31.9:1:1:0:60:16:1:0:0 0/1:10:2:0,2:1,7:0.2:2,0:20:1:29.5:1:1:0:60:4:0.2222:0:1 -6 163092488 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51642;SOR=Inf;LSEQ=ATGCAGTGAGCCGAGATTGC;RSEQ=CCACTGCACTCCAGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:71,8:0:2,0:22:1:27.5:1:1:0:56.3:12.167:1:0:0.6 0/1:120:2:2,0:105,12:0.0167:2,0:34:1:28.5:1:1:0:56.5:4:0.0182:0:2.5 -6 163092643 . G A 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTTTGAAACATTTGTGCA;RSEQ=TAATCAAAAATTCCGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:86,164:0:2,0:19.2:1:31.5:1:1:0:60:500:1:0:0.1 0/1:292:40:13,27:82,170:0.137:2,2:21.9:1:29:1:1:1.0018:60:80:0.1375:0:1.1 -6 163092678 . C G 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12573;SOR=Inf;LSEQ=GAAATCATAGAAGAATTTAC;RSEQ=AGTCAATCATACCAGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:1,108:0:1,0:27.5:1:32.8:1:1:0:60:218:1:0:0.1 0/1:126:4:1,3:2,120:0.0317:1,2:11.3:1:28.8:1:0.09296:18.33:60:8:0.0317:0:1 -6 163092867 . C T 69 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCAGATGTCAAATTGTA;RSEQ=AGTCAAAGAATAAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,1:0.8333:0,2:21.4:1:29.8:1:1:0:60:10:0.8333:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 163092968 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGGTGACGGAGGCAGAC;RSEQ=CCAGGGCTGCAGACTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:29:1:1:0:60:4:1:0:1.5 -6 163148559 . CG C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51098;SOR=0;LSEQ=GGGAGCCCGGCGGCGCGGGC;RSEQ=GGGACGGCACGGGCACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:2,0:145,5:0.0132:1,0:28:1:33:0:1:0:60:4:0.0136:0:0 0/0:110:0:0,0:105,4:0:1,0:23.1:1:30.2:1:1:0:60:108:0.9908:0:0.1 -6 163148803 . G A 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03935;SOR=Inf;LSEQ=TCCTGGGTTAAATCCTCCAG;RSEQ=CCTCCCCGCCCCCGCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:71,292:0:2,0:23.7:1:32:1:1:0:60:71.6:1:0:0.1 0/1:293:4:3,1:64,223:0.0137:2,2:6:1:26:1:0.03928:10.34:60:8:0.0139:0:1 -6 163516710 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTCCCGCCCCATCTTCAT;RSEQ=TGGCCTTTTTTCCTGTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:20.3:1:29.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 163517035 . T A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21648;LSEQ=TCACATTGCTGTAACTAGTG;RSEQ=TACTGAGCCTGCTCTGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:516:288:133,155:104,122:0.5581:2,2:26.4:1:30.4:1:1:1.01:60:143:0.5619:0:1.1 0/1:471:101:52,49:172,198:0.2144:2,2:27.2:1:28.9:1:0.4315:1.22:60:49.5:0.2115:0:1.1 -6 163528662 . G A 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATTTGGCTGTCTGGACC;RSEQ=GGCCTCTCTGCTTCATGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:25.3:1:29:1:1:0:60:8:0.4444:0:1 0/0:1:0:0,0:1,0:0:0,0:1:0:29:0:1:0:60:2:1:0:0 -6 163528776 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.13574;LSEQ=AAAATCAGGTACAAGGCAGA;RSEQ=CTTTTCTTTGTTGGATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:29:29,0:27,0:0.5179:1,1:23.9:1:31:1:1:0:60:58:0.5179:0:2 0/1:48:6:6,0:40,2:0.125:1,0:32:1:31.2:1:1:0:60:12:0.125:0:2 -6 163528806 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09271;LSEQ=GTTGGATTCCAAATGTACAA;RSEQ=GACTCAATCTTGATTACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:83:77,6:24,1:0.7685:1,2:23:1:30.5:1:1:1.86098:60:82:0.7736:0:1.4 0/1:86:20:20,0:63,3:0.2326:1,1:23.6:1:30.2:1:1:0:60:40:0.2326:0:1.4 -6 163528910 . C T 188 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTATAAATTTCTCCAAAAT;RSEQ=CTAACATGTTGTTTGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:76:41,35:183,171:0.1763:2,2:25.6:1:30.1:1:0.80042:1.09:60:152:0.178:0:1.8 0/0:543:0:0,0:271,271:0:2,0:27.2:1:30.7:1:1:0:60:66.75:0.9981:0:0.3 -6 163528948 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10007;LSEQ=ATTTGGTTGTTTCTTCTTAT;RSEQ=CAAGTTTGCATTTCAAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:399:321:129,192:35,42:0.8045:2,2:25.5:1:29:1:0.4399:1.23962:60:106:0.8051:0:1.2 0/1:481:140:65,75:138,203:0.2911:2,2:22.7:1:28.3:1:0.26364:1.27:60:45.667:0.2878:0:1.2 -6 163529076 . T C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00087;SOR=0.21013;LSEQ=TAGGTTTGACATAAGGGAGG;RSEQ=GGTTTGAGGCTGAAGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:38:4,34:0,15:0.717:1,2:24:1:30.2:1:0.56786:0:60:76:0.717:0:1.6 0/1:35:12:2,10:2,21:0.3429:2,2:23:1:29.1:1:0.59412:2.05:60:11:0.3235:0:2 -6 163529109 . G T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.09804;SOR=0.30953;LSEQ=AAGCCGTCTGATGTGGTTTG;RSEQ=CTTTGTGTCCCTACCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:20:0,20:0,8:0.7143:0,1:23.3:1:29.8:1:1:0:60:19:0.7037:0:2.1 0/1:14:6:0,6:0,8:0.4286:0,0:21.8:1:29.3:1:1:0:60:12:0.4615:0:2.2 -6 163529169 . C G 87 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86755;LSEQ=ACCCATGTTGGAGGAGGGGC;RSEQ=AGGTGGGAGGTGATTGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:0.7:0,0:12.9:1:31.1:1:1:0:60:14:0.7:0:2.1 1/0:3:2:0,2:0,1:0.6667:0,0:4:1:29:0:1:0:60:4:0.6667:0:3.5 -6 163529226 . A G 84 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.25;SOR=0;LSEQ=TTCTTTCTGTTCTCATGATG;RSEQ=TGAGTGAGCTCTCACGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:31.2:1:32.7:1:1:0:60:12:0.8571:0:2 0/0:1:0:0,0:0,1:0:0,0:7:0:32:0:1:0:60:2:1:0:1 -6 163529269 . A C 51 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GGTTGTTTAAAAATCTGTAG;RSEQ=ACCACCCACTTTGCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:27.3:1:32.3:1:1:0:60:6:0.75:0:1.7 0/0:1:0:0,0:0,1:0:0,0:28:0:27:0:1:0:60:2:1:0:0 -6 163529910 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGATCTTTATGTATTCATC;RSEQ=AAATCAATACATCAAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:16:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 164341042 . C A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.28818;LSEQ=AATGAAGTGTTTCTATGTGC;RSEQ=TATTTCTCTAGGGTTTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:14:14,0:43,1:0.2414:1,1:24.4:1:30.5:1:1:0:60:28:0.2414:0:1.1 1/0:33:26:26,0:7,0:0.7879:0,1:24.3:1:30.5:1:1:0:60:52:0.7879:0:1 -6 164341106 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4995;SOR=0;LSEQ=CCTGATGAACATATCACTTC;RSEQ=TTTGAACTCTGTGGGTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:132,44:0.0112:2,2:8.5:1:28:1:0.44277:2.97768:60:4:0.0113:0:1 0/0:163:0:0,0:127,36:0:2,0:19:1:30.3:1:1:0:60:80.5:1:0:0.2 -6 164341214 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.3417;LSEQ=CCCCGTGACCTGTTACCTGT;RSEQ=GCTGAACCTTGTTCCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:102:50,52:161,188:0.2262:2,2:28.2:1:30.1:1:0.65235:1.12:60:50:0.2237:0:2.4 1/0:416:284:125,159:66,66:0.6827:2,2:25.2:1:29.8:1:0.29062:1.27125:60:93.667:0.6804:0:2.6 -6 164341220 . A C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=7.34035;LSEQ=GACCTGTTACCTGTTGCTGA;RSEQ=CCTTGTTCCAGTGCACAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:97:46,51:153,187:0.222:2,2:27.9:1:31.4:1:0.72908:1.10:60:96:0.2217:0:2.5 1/0:403:273:118,155:66,62:0.6774:2,2:25.1:1:30.3:1:0.13267:1.3971:60:33.125:0.6726:0:2.7 -6 164341228 . C T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTGTTGCTGAACCTTGTT;RSEQ=CAGTGCACAGCGGCCTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:169,242:0:2,0:25.8:1:30.9:1:1:0:60:40.1:1:0:0.7 0/1:381:18:5,13:165,196:0.0472:2,2:26.7:1:27.4:1:0.15259:2.1845:60:36:0.0481:0:3.8 -6 164341235 . A G 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGAACCTTGTTCCAGTGC;RSEQ=CAGCGGCCTCTCGCGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:159,238:0:2,0:24.9:1:29.5:1:1:0:60:55.714:1:0:0.7 0/1:367:17:5,12:147,203:0.0463:2,2:24.6:1:31.1:1:0.45032:1.73546:60:34:0.047:0:3.5 -6 164341262 . A C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.45037;LSEQ=CCTCTCGCGCATCCCCACCC;RSEQ=CCCGTCGGGTTGGGAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:64:20,44:85,142:0.2192:2,2:23.8:1:30.8:1:0.38111:1.31568:60:31:0.2183:0:2.4 1/0:279:189:60,129:31,58:0.6774:2,2:24.5:1:30.4:1:0.68131:1.14855:60:62:0.6813:0:2.6 -6 164341291 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.49926;SOR=0;LSEQ=GTTGGGAACTGGTCAAAACC;RSEQ=TCATCCTTCCGTTTTGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:51,134:0.0107:2,2:26:1:30:1:0.4799:2.61:60:4:0.0109:0:1.5 0/0:174:0:0,0:43,131:0:2,0:24.4:1:29.7:1:1:0:60:86:1:0:1.5 -6 164341302 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.22591;SOR=Inf;LSEQ=GTCAAAACCATCATCCTTCC;RSEQ=TTTTGCCATCATGGCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:36,118:0:2,0:24.2:1:31.4:1:1:0:60:50.333:1:0:0.4 0/1:140:2:1,1:30,108:0.0143:2,2:34:1:31:1:0.39507:3.56:60:4:0.0146:0:2.5 -6 164341347 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22528;SOR=Inf;LSEQ=TATTTAGGGTTTGGAGTTCG;RSEQ=TGAATTTAAACTGATACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:2,55:0:1,0:25.3:1:30.5:1:1:0:60:114:1:0:0.1 0/1:52:2:0,2:5,45:0.0385:2,0:25.5:1:33:1:1:0:60:4:0.04:0:1 -6 165677269 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=TATAGGGTGACAGAAGGCAG;RSEQ=GCAGAGTCTGCGGCCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:20,10:0.0625:2,2:10.5:1:28:1:1:1.95408:60:4:0.0625:0:1.5 0/0:31:0:0,0:21,10:0:2,0:19.9:1:30.8:1:1:0:60:62:1:0:0.2 -6 165677286 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22761;SOR=0;LSEQ=CAGCGCAGAGTCTGCGGCCA;RSEQ=AGGCCAAGCTGAACCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:21,14:0.0541:2,2:32.5:1:30:1:1:1.4832:60:4:0.0556:0:1 0/0:40:0:0,0:23,17:0:2,0:24.3:1:31:1:1:0:60:39:1:0:0.2 -6 165677365 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51637;SOR=Inf;LSEQ=ACACTCTGCTCTAGGTGTGC;RSEQ=CCTTTTCAAGGAAGCTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:8,17:0:2,0:23.4:1:30.7:1:1:0:60:50:1:0:0.1 0/1:39:2:1,1:14,23:0.0513:2,2:34:1:30.5:1:1:1.62:60:4:0.0526:0:1 -6 166653608 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCTCTCTTTTGAATATTC;RSEQ=CTCGATCATAAGACACCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:11.5:1:32:0:1:0:59.5:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 166653638 . A G 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGACACCAATAACACACAA;RSEQ=CAGTTTCATCTTCATAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:33:1:33.7:1:1:0:52:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 166653737 . T TA 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=ATTGTACACAAATGTACAAT;RSEQ=AAAAAAAAAAGTTTGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:8:1:29.3:1:1:0:60:4:0.1667:0.0833:2.5 0/0:6:0:0,0:6,0:0:0,0:14.2:1:30:1:1:0:60:12:1:0:0.2 -6 166653792 . A C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11793;SOR=0.42304;LSEQ=ATTTTACTACAAAAAGGAAT;RSEQ=GAATTTCTGGGTCTGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:24:24,0:13,0:0.6486:1,1:25.9:1:31.6:1:1:0:60:23:0.6389:0:1.1 0/1:23:10:10,0:13,0:0.4348:1,0:23.7:1:31.7:1:1:0:60:20:0.4348:0:1 -6 166653885 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.79246;LSEQ=AGACAATTGTTTAAAGTCTG;RSEQ=AGCTGCCTGGGAAACTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:0,1:108,50:0.0063:2,0:1:0:23:0:0.32075:0:60:2:0.0063:0:3 0/1:178:2:1,1:123,53:0.0112:2,2:18.5:1:28.5:1:0.5159:2.30852:60:4:0.0114:0:1 -6 166653963 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38239;LSEQ=CACTTTCTTCATAGCTGCGA;RSEQ=GCTGGAGGAAGCCAACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:261:144:69,75:66,51:0.5517:2,2:26.1:1:30.6:1:0.21291:1.40478:60:143:0.5564:0:1.1 0/1:366:117:53,64:125,124:0.3197:2,2:26.7:1:29.6:1:0.43271:1.21663:60:57.5:0.323:0:1.1 -6 166654047 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2315;SOR=Inf;LSEQ=GTCATAGGGGGCCAGAAAAT;RSEQ=GAGAGCATTCTCACATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:47,124:0:2,0:25.2:1:30.9:1:1:0:60:56:0.9941:0:0.7 0/1:160:2:1,1:39,118:0.0125:2,2:5.5:1:27.5:1:0.44105:3.00:60:4:0.0127:0:2 -6 166654085 . T C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13254;SOR=0.58049;LSEQ=CCTACCATGGGCTGGACGTT;RSEQ=CCAAAGCAGGCAGAAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:45:3,42:2,41:0.5114:1,2:23.2:1:31.5:1:1:1.46:60:44:0.5057:0:2 0/1:61:23:1,22:3,35:0.377:2,1:24.2:1:31:1:1:1.86785:60:46:0.3898:0:2 -6 166654087 . C G 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22582;SOR=0.63776;LSEQ=TACCATGGGCTGGACGTTTC;RSEQ=AAAGCAGGCAGAAATTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:43:3,40:2,39:0.5119:1,2:23.8:1:31.8:1:1:1.46:60:86:0.5119:0:2 0/1:55:22:1,21:2,31:0.4:2,1:25.2:1:31:1:1:1.34762:60:44:0.4:0:2 -6 167628441 . G A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCATGTTGGTCAGGCTG;RSEQ=TCTTAAACTCCCGACCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:32:1:1:0:36:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 167628451 . C G 34 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCAGGCTGGTCTTAAACT;RSEQ=CCGACCTCAGGTGATATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:34:1:1:0:36:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 167628477 . T C 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGGTGATATGCCTGCCT;RSEQ=GGCCTCCCAAAGTGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:30:1:1:0:36:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 167628496 . G A 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGCCTCCCAAAGTGCTGG;RSEQ=ATTACAGGCGTGAGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:28.5:1:1:0:36:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 167628506 . G A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTGCTGGGATTACAGGC;RSEQ=TGAGCCACCGTGCCTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:1:29.5:1:1:0:36:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 167630110 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCCTTGATCCCGACGAG;RSEQ=CAGAGTGTGGCGCTGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,1:0.2:2,0:40.5:1:32:1:1:0:60:4:0.2:0:1 0/0:1:0:0,0:1,0:0:0,0:29:0:34:0:1:0:60:2:1:0:0 -6 167630297 . A C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=3.10605;LSEQ=ACCAGGAAGACAAGAAAGGA;RSEQ=GTGCCTGGAGTGTTCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:54:52,2:26,3:0.4576:2,1:24.8:1:32.3:1:0.33728:2.96:56:53:0.4609:0:2.1 1/0:80:58:55,3:11,1:0.725:2,2:24.7:1:31.3:1:0.53728:1.65:58.2:116:0.725:0:2.1 -6 167630301 . C G 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05622;SOR=2.10905;LSEQ=GGAAGACAAGAAAGGAAGTG;RSEQ=CTGGAGTGTTCAGTCCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:125:94:87,7:27,4:0.752:2,2:25.8:1:31.9:1:0.46342:1.83:57:93:0.7686:0:2 1/1:89:77:72,5:11,1:0.8652:2,2:24.2:1:30.1:1:1:1.30:58.4:14.4:0.8571:0:2 -6 167630439 . C T 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.73775;LSEQ=TTTTTCCATTTTCTAAGCCC;RSEQ=GAGTGTTTGCCAGATAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:243:106,137:118,152:0.4718:2,2:26.7:1:29.9:1:1:1.00335:44.3:33.714:0.4683:0:1.1 1/0:503:306:144,162:94,103:0.6083:2,2:26.9:1:29.6:1:0.92718:1.02666:43.3:26.818:0.602:0:1.2 -6 167630896 . C A 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCACCAATAAATGTTATC;RSEQ=TCAATAAATGTTAATTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:19.3:1:30.3:1:1:0:50.7:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 167721910 . A T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGACGGGGCTCTGGGGC;RSEQ=TCCTGGGCAGTGGTGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:29.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -6 167722946 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11109;SOR=Inf;LSEQ=GCCCAAAGAGGCAAGACTGC;RSEQ=TGTCTAAGAGATGCTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:72,1:0:1,0:26.4:1:30.3:1:1:0:34.8:146:1:0:0.1 0/1:37:2:2,0:34,1:0.0541:1,0:28.5:1:30:1:1:0:27:4:0.0541:0:1 -6 167723177 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17385;SOR=Inf;LSEQ=GGATAAAGAGCACATGTGAC;RSEQ=TCAGATCGCGGACAGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:54,197:0:2,0:21.8:1:31.8:1:1:0:57.7:82.667:1:0:0 0/1:180:2:1,1:40,138:0.0111:2,2:40.5:1:29:1:0.40466:3.42:60:4:0.0114:0:1 -6 167723184 . C T 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAGCACATGTGACCTCAGAT;RSEQ=GCGGACAGAACACTCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:34,187:0:2,0:21.4:1:29.9:1:1:0:60:72.667:1:0:0 0/1:150:28:8,20:22,100:0.1867:2,2:25.4:1:28.3:1:0.29292:1.81:59.9:27:0.1837:0:1.2 -6 167723225 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52571;SOR=0;LSEQ=ACGTCCTTTCTTGTCTTCCT;RSEQ=GTGGGTTGCGTATCCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:3,96:0.0198:1,2:23.5:1:31.5:1:0.07802:27.86:60:4:0.0198:0:1 0/0:62:0:0,0:1,61:0:1,0:25.2:1:30.4:1:1:0:58.2:61:1:0:0.3 -6 167723364 . C T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TGAAGCTCTTCACCAAAATG;RSEQ=GTGTGTACTTGGCCCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:29.5:1:30:1:1:0:44.5:4:0.3333:0:1 0/0:3:0:0,0:0,3:0:0,0:21.3:1:20.7:1:1:0:50.7:2:1:0:0 -6 168672824 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18354;SOR=0;LSEQ=CCACAGGCGTGTGGCAAATG;RSEQ=AGGCAGGCCTGGGCTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:6.5:1:27:1:1:1.13389:60:4:0.1176:0:2 0/0:22:0:0,0:8,14:0:2,0:20.8:1:31.4:1:1:0:60:44:1:0:0.3 -6 169642695 . A C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCAAATTCCCACCTTCCCAC;RSEQ=TTCCCACCTTCCCACCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:33:0:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:37:0:30:0:1:0:59:2:1:0:3 -6 169643133 . G A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CACCTTCCCACCTTCCCACC;RSEQ=CTCCCACCTTCCCACCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:14.5:1:28.5:1:1:0:44:4:1:0:2.5 0/0:2:0:0,0:0,2:0:0,0:34:1:21:1:1:0:44:1:1:0:3 -6 169643158 . A G 39 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4;SOR=0;LSEQ=CACCTTCCCACCTTCCCACC;RSEQ=CTCCCACCTTCCCACCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:38.7:1:24.7:1:1:0:36.7:2:1:0:3 1/0:2:1:0,1:1,0:0.5:0,0:40:0:33:0:1:0:34:2:0.5:0:2 -6 169643879 . T C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=0.08928;LSEQ=GCTCTGACAGGAATGTAGTT;RSEQ=TACCTGGTAGTAAAACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:39:38,1:77,4:0.325:1,1:23.9:1:31.8:1:1:1.96:60:78:0.325:0:1.1 0/1:49:2:2,0:45,2:0.0408:1,0:37:1:33:0:1:0:60:4:0.0408:0:1 -6 169643986 . C T 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02155;SOR=1.36031;LSEQ=TCTTCACAAGGTTACTCTCA;RSEQ=TTTTAACAAACAGTGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:195:115,80:199,160:0.352:2,2:25.6:1:30.3:1:0.47275:1.16:60:47.75:0.3505:0:1.8 0/1:440:187:105,82:138,115:0.425:2,2:25:1:29.7:1:0.7715:1.07:60:45.75:0.4207:0:1.8 -6 169644032 . C T 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=1.67487;LSEQ=TGTCATTACCAAGAACCAAT;RSEQ=CATGAACTAGCTGTTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:226:101,125:198,235:0.3429:2,2:28.1:1:29.8:1:0.80533:1.04272:60:55.5:0.3442:0:1.7 0/1:523:244:122,122:130,148:0.4665:2,2:24.9:1:29.1:1:0.48316:1.14:60:39.667:0.463:0:1.7 -6 169644086 . TGAA T 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.00099;SOR=Inf;LSEQ=CTTAAGTCTGACATAACCAG;RSEQ=GAAGAAGTCTTTGTTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:127,255:0:2,0:23.3:1:31.4:1:1:0:60:75.4:0.9869:0:0.4 0/1:285:8:2,6:110,167:0.0281:2,2:19.3:1:32.3:1:0.48704:1.97176:60:16:0.0288:0.007:0.4 -6 169644148 . C T 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14542;SOR=1.58516;LSEQ=GGACATTGGCATCCACCTGG;RSEQ=TTTGAGTAGACTAACTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:45:6,39:5,72:0.3689:2,2:21:1:30.1:1:0.32546:2.20:60:90:0.3689:0:1.2 0/1:81:39:4,35:7,35:0.4815:2,2:21.7:1:29.9:1:0.52197:1.73813:60:78:0.4815:0:1.1 -6 169644190 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05062;SOR=Inf;LSEQ=GTGATTGCCACATATGGTCC;RSEQ=GTAGATATATGTATATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:0,63:0:1,0:26:1:31.7:1:1:0:60:126:1:0:0.5 0/1:38:3:0,3:0,35:0.0789:1,0:31:1:31.3:1:1:0:60:6:0.0833:0:1.7 -6 170137581 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51386;SOR=Inf;LSEQ=TTGGTCTTTGAGGCTGCTGA;RSEQ=CCTTAGATGGGGTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:0:2,0:33:1:32:1:1:0:60:74:1:0:0.1 0/1:55:2:1,1:26,27:0.0364:2,2:40.5:1:29.5:1:1:1.04:60:4:0.0364:0:1 -6 170137584 . T G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51566;SOR=Inf;LSEQ=GTCTTTGAGGCTGCTGACCC;RSEQ=TAGATGGGGTTTTTGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:0:2,0:33.2:1:30.4:1:1:0:60:36:1:0:0.1 0/1:56:2:1,1:26,28:0.0357:2,2:28.5:1:32:0:1:1.08:60:4:0.0364:0:1 -6 170138104 . G GA 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTCCCTGAGCCTCTGGCTG;RSEQ=AGTTATTGGAGATCCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:16.7:1:30.7:1:1:0:60:6:1:0:0 0/1:9:2:1,1:4,3:0.2222:2,2:20.5:1:29:1:1:1.29098:60:4:0.2222:0.1111:0 -6 170508532 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20979;SOR=Inf;LSEQ=CAACCCAGAAACACCAACGG;RSEQ=CACAAATAGAAGCAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:0:2,0:29.1:1:31.4:1:1:0:60:41:1:0:0.1 0/1:36:2:1,1:21,13:0.0556:2,2:35:1:27.5:1:1:1.5932:60:4:0.0588:0:1 -6 170508585 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23944;SOR=0;LSEQ=CTCTGCAGCCAAGGCCCTGG;RSEQ=GGGGCCGCCCAGAAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:14,19:0.0571:2,2:37.5:1:30:1:1:1.35:60:4:0.0606:0:1 0/0:36:0:0,0:14,22:0:2,0:25.8:1:29.6:1:1:0:60:35:1:0:0.1 -6 170508601 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22273;SOR=Inf;LSEQ=CTGGAGGGGCCGCCCAGAAG;RSEQ=AGCCCCGGCAAACGCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:12,21:0:2,0:21.6:1:31.6:1:1:0:60:66:1:0:0.2 0/1:30:2:1,1:9,19:0.0667:2,2:20.5:1:30.5:1:1:2.05:60:4:0.0667:0:1 -6 170798799 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=CAAGGGGCGTATAAGTCCAG;RSEQ=TAATCGAACTCTTACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:125,66:0:2,0:24.7:1:29.7:1:1:0:60:94.5:1:0:0.2 0/1:192:2:1,1:118,72:0.0104:2,2:32.5:1:30.5:1:1:1.63444:60:4:0.0105:0:1 -6 170798821 . G A 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18697;SOR=0.56969;LSEQ=AATCGAACTCTTACTCCACC;RSEQ=CTTTTTCATTCTTAAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:19:14,5:140,90:0.0763:2,2:30.9:1:30.7:1:0.33147:1.80:60:38:0.0772:0:1.5 0/1:245:11:6,5:137,97:0.0449:2,2:22.9:1:29.8:1:1:1.17618:60:22:0.0464:0:1.7 -6 170798856 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24875;SOR=Inf;LSEQ=AGGCCTGAAGTTGGAGAAAA;RSEQ=GAGGAAAGCGGAGCAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:155,130:0:2,0:26.1:1:31.5:1:1:0:60:141.5:1:0:0.7 0/1:290:3:1,2:146,141:0.0103:2,2:10:1:25.3:1:0.61855:2.0659:60:6:0.0105:0:1.7 -6 170798891 . C T 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.46823;LSEQ=AGCCATGGGTCTTTGCAAAA;RSEQ=GAACAGAGCTCAGAGATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:130:59,71:74,74:0.4659:2,2:24.5:1:30.2:1:0.47163:1.20258:60:64:0.4655:0:1.9 0/1:283:82:41,41:89,111:0.2898:2,2:23.7:1:29.6:1:0.43143:1.25:60:81:0.2914:0:2 -6 170798912 . G A 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=0.44292;LSEQ=GAACAGAGCTCAGAGATAGC;RSEQ=AGATCCCAGGCACAGGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:125:45,80:67,78:0.463:2,2:24.4:1:30.1:1:0.1074:1.52463:60:124:0.4662:0:1.9 0/1:250:69:32,37:76,104:0.276:2,2:26.4:1:29.9:1:0.57043:1.18:60:33.5:0.2724:0:2 -6 170871004 . G A 57 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.70096;SOR=0.63059;LSEQ=GAGCAACAAAGGCAGCAGCA;RSEQ=CAACAACAACAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:1,3:22,17:0.0889:2,2:7.5:1:28.8:1:0.32347:3.76689:60:8:0.0889:0:3 0/1:52:3:1,2:29,20:0.0577:2,2:7.7:1:29.3:1:0.56697:2.84084:60:6:0.06:0:2 -6 170871013 . A ACAG 154 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=9.000;MSILEN=3;SSF=5e-05;SOR=0.17421;LSEQ=AGGCAGCAGCAGCAACAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:30:16,14:8,7:0.6667:2,2:32.1:1:31.5:1:1:1:60:60:0.6667:0.1333:0.6 0/1:55:14:6,8:21,12:0.2545:2,2:40.6:1:31.3:1:0.2143:2.28993:60:28:0.2692:0:0.1 -6 170871040 . ACAGCAACAGCAGCAG GCAACAGCAA 107 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=26.000;MSILEN=3;SSF=0.01052;SOR=0.18676;LSEQ=AGCAGCAGCAGCAGCAGCAG;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:12:4,8:22,16:0.2353:2,2:8:1:29.9:1:0.19016:2.69404:59.2:24:0.24:0.2157:1.9 0/1:56:3:2,1:25,28:0.0536:2,2:18:1:28:1:0.60455:2.21:58.3:6:0.0556:0.0179:0.3 -6 170871046 . A G 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.73802;SOR=0.75005;LSEQ=CAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:5:2,3:24,18:0.1042:2,2:4:1:31.2:1:0.64405:1.97043:58:10:0.1064:0:3.6 0/1:50:4:2,2:21,23:0.08:2,2:19.5:1:31.5:1:1:1.09:60:8:0.0833:0:3 -7 58384 . C A 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTGCATTTGGGGGAAC;RSEQ=AGAAGTGAGCTGATCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:3,0:0.5:0,2:19.7:1:29.3:1:1:0:60:6:0.5:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 58414 . C G 82 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGATCTGCATATAGGCCAG;RSEQ=CTTTCTGCATAGGGCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:4,2:2,1:0.6667:2,2:20.3:1:31.8:1:1:1:60:12:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 58421 . G T 31 v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATATAGGCCAGCCTTTCT;RSEQ=CATAGGGCACAGCGTATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:11:0:31.5:1:1:2.23609:60:4:0.2222:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 59118 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATACCAGGCAAGGCCATG;RSEQ=GGGAAAGCACCAGCTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 60033 . C T 99 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01562;SOR=0.09863;LSEQ=ACTCCAAGCTCCCCCAGACC;RSEQ=GGTGGAAACGCAGACTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:4,6:9,8:0.3704:2,2:27.7:1:29.9:1:0.69458:1.65488:60:9:0.3462:0:1.6 0/1:19:1:0,1:11,7:0.0526:2,0:21:0:32:0:0.42105:0:60:2:0.0556:0:1 -7 60046 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16944;SOR=Inf;LSEQ=CCAGACCCGGTGGAAACGCA;RSEQ=ACTCCTTGGCTAACACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:0:2,0:23.3:1:31.8:1:1:0:60:50:1:0:1.8 0/1:18:2:1,1:8,8:0.1111:2,2:21:1:29.5:1:1:1:60:4:0.1111:0:2 -7 60055 . G T 116 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=0.04495;LSEQ=GTGGAAACGCAGACTCCTTG;RSEQ=CTAACACTGCCATGGGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:7,8:3,7:0.6:2,2:19.9:1:29.7:1:0.67846:1.98:60:30:0.6:0:1.9 0/1:17:1:0,1:8,8:0.0588:2,0:39:0:31:0:1:0:60:2:0.0625:0:2 -7 60061 . A G 133 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=0;LSEQ=ACGCAGACTCCTTGGCTAAC;RSEQ=CTGCCATGGGAGTAGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:8,12:0,0:1:0,2:18.4:1:30.9:1:1:0:60:40:1:0:2 0/1:15:5:2,3:5,5:0.3333:2,2:40.2:1:31.2:1:1:1.46001:60:10:0.3333:0:1.6 -7 60086 . C G 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00272;SOR=Inf;LSEQ=CATGGGAGTAGAACCCACCA;RSEQ=AAGCCCCCTACACTCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:24:1:31.6:1:1:0:60:20:1:0:1.3 1/0:13:8:3,5:2,3:0.6154:2,2:30.6:1:31.3:1:1:1.10211:60:16:0.6154:0:1 -7 173163 . G T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCAGTGCGGAGGGAGAG;RSEQ=GCCCAGGTCAGCCCAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:17.5:1:27:1:1:0:60:4:0.6667:0:1.5 -7 330676 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54221;SOR=0;LSEQ=CCCGCGGGGAGGGTGACCCT;RSEQ=TCCGGCATCTACGACTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:118,34:0.0129:2,2:22.5:1:27.5:1:0.40404:3.435:60:4:0.0132:0:1 0/0:84:0:0,0:69,15:0:2,0:20.1:1:31:1:1:0:60:27:1:0:0.1 -7 330781 . C A 38 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03754;SOR=Inf;LSEQ=CTGTCCCTCAACAGCTGCTT;RSEQ=GTCAAGGTGAGCGCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:99,197:0:2,0:24.3:1:29.9:1:1:0:60:73:1:0:0.5 0/1:150:3:2,1:50,97:0.02:2,2:14:1:24:1:0.2758:3.84:60:6:0.0205:0:1.7 -7 330808 . GC G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.09951;SOR=Inf;LSEQ=GTGAGCGCCGCCCCCGACGG;RSEQ=CCCGGGTGTCCCAGCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:40,125:0:2,0:22.5:1:31.1:1:1:0:60:54:0.9939:0:1 0/1:77:2:1,1:11,62:0.026:2,2:19:1:30.5:1:0.29622:5.44:60:4:0.026:0:2.5 -7 330822 . A C 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=0.10237;LSEQ=CGACGGGCCCCGGGTGTCCC;RSEQ=GCGTGGCGACACCTGCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:119:18,101:0,3:0.9754:0,2:22.5:1:29.3:1:1:0:60:22.8:0.9744:0:1.4 1/1:55:44:5,39:1,10:0.8:2,2:21.7:1:29.6:1:1:1.28:60:21:0.7925:0:1.3 -7 330834 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09486;SOR=Inf;LSEQ=GGTGTCCCAGCGTGGCGACA;RSEQ=CTGCGCCAGGGCCTCGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:3,79:0:1,0:25.1:1:31.7:1:1:0:60:81:1:0:1.4 0/1:37:2:0,2:2,33:0.0541:2,0:6:1:30:1:1:0:60:4:0.0588:0:2.5 -7 330882 . T G 128 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=GGGAGGGCACCGCGGCGGCT;RSEQ=CAGGGAGGTCCGTCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:1:0,1:20.1:1:32.8:1:1:0:60:30:1:0:2.9 1/0:7:5:0,5:0,2:0.7143:0,0:19:1:32.4:1:1:0:60:10:0.7143:0:2.8 -7 330884 . A G 122 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GAGGGCACCGCGGCGGCTTC;RSEQ=GGGAGGTCCGTCCTCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:1:0,1:19.7:1:32.1:1:1:0:60:28:1:0:2.9 1/0:7:5:0,5:0,2:0.7143:0,0:17.8:1:30.4:1:1:0:60:10:0.7143:0:2.8 -7 331086 . G A 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTACTGGACGTTCGCGGGC;RSEQ=GCTGCGAGTCGCTGCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:19.5:1:30.3:1:1:0:60:8:1:0:1.3 1/1:3:3:1,2:0,0:1:0,2:30.7:1:29.3:1:1:0:60:6:1:0:1 -7 384385 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.23443;SOR=4.80832;LSEQ=AGATGGGGAGGGCCAGAGTC;RSEQ=CCCCCACAGCGGCCACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:10,8:0.0526:2,0:26:0:32:0:1:0:60:2:0.0526:0:2 0/1:9:2:1,1:3,4:0.2222:2,2:43.5:1:31:1:1:1.29:60:4:0.2857:0:1.5 -7 384439 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GGACAGTGGCTGAACCCAGT;RSEQ=CCAGGTGCCAGGTGCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,2:0.2222:2,2:11.5:1:29:1:1:1.8258:60:4:0.2222:0:1 0/0:5:0:0,0:2,3:0:2,0:29.4:1:30.6:1:1:0:60:10:1:0:0 -7 385269 . T G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGGCTGTGGATATGTTAG;RSEQ=GGGTAACGATTACTCTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:32:0:1:0:60:4:1:0:1.5 -7 385345 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTATGTGATCTCCTGAGCT;RSEQ=GTGATCCACCCACCTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 602992 . C G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGCTGCCTCTGCAGACA;RSEQ=CATTCCTTAGGCCAGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45.5:1:32:1:1:0:60:4:1:0:2 -7 603002 . G T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCAGACACCATTCCTTA;RSEQ=GCCAGAAGGGAAAGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45.5:1:29:1:1:0:60:4:1:0:2 -7 604190 . T C 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.32198;LSEQ=CAGGTCCCCGCCCCACCGCA;RSEQ=TCAGGCCCTCGACTCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:16:1:33.5:1:1:0:60:4:0.6667:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:12:0:32:0:1:0:60:2:0.3333:0:2 -7 606189 . T C 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCACCACCATCACCATCA;RSEQ=TGTCATCACCTTCACATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:6:1:26.7:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 606306 . T A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCACCATCATCACCATCACC;RSEQ=TCATCACCATCACCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,1:0:0,0:11:0:32:0:1:0:42:2:1:0:8 1/1:2:2:1,1:0,0:1:0,2:6:0:32:0:1:0:50.5:4:1:0:4 -7 606311 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=ATCATCACCATCACCTTCAT;RSEQ=ACCATCACCATCATCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,1:0:0,0:16:0:32:0:1:0:42:2:1:0:8 1/1:2:2:1,1:0,0:1:0,2:11:0:31:1:1:0:50.5:4:1:0:4 -7 606336 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCACCATCATCACCATCACC;RSEQ=TCATCATCATCACCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:40:0:29:0:1:0:60:2:1:0:4 1/1:2:2:1,1:0,0:1:0,2:36:0:31.5:1:1:0:50.5:4:1:0:4 -7 1055639 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=0;LSEQ=ATCTAGTGTCTGAGGTGTCA;RSEQ=ATGAGGATCCCAGACAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:21:1:31.5:1:1:1.8258:60:4:0.25:0:1 0/0:4:0:0,0:3,1:0:2,0:27.5:1:32.5:1:1:0:60:8:1:0:1 -7 1055674 . G GT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAACACGCTCCCCCTCCG;RSEQ=TGTCACGCCAGCACACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:6,6:0.1429:2,0:30:1:31:1:0.47253:0:48:4:0.1538:0:2.5 0/0:6:0:0,0:3,3:0:2,0:23.8:1:31.2:1:1:0:60:12:1:0:0.3 -7 1055717 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACGCCAGCGCACAGCAGC;RSEQ=CACAGCAGCGCACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:5,9:0.125:2,0:19.5:1:28.5:1:0.175:0:48:4:0.125:0:2.5 0/0:4:0:0,0:2,2:0:2,0:26.8:1:31.8:1:1:0:60:8:1:0:0.3 -7 1056124 . C A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.45455;SOR=0;LSEQ=CATAGCAGCACAGCAGCACA;RSEQ=AGCAGCGCACAGCAGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:12.5:1:30:1:1:2.45:60:4:0.3333:0:2 0/0:5:0:0,0:3,2:0:2,0:40:1:30.8:1:1:0:60:10:1:0:0 -7 1056145 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.46154;SOR=0;LSEQ=AGCAGCGCACAGCAGCACAG;RSEQ=AGCGCACAGCAGCACACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:33.5:1:28:1:1:3.16:60:4:0.2857:0:2 0/0:7:0:0,0:4,3:0:2,0:25:1:29.3:1:1:0:60:6:1:0:0.9 -7 1056183 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11813;SOR=7.63506;LSEQ=ACCAGCACAAAGCAGCGCAC;RSEQ=CCAGCGCACAGCAGCGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:4,5:0.1:2,0:13:0:31:0:1:0:60:2:0.1:0:2 1/0:6:3:2,1:1,2:0.5:2,2:32.3:1:30.3:1:1:3.11:51.7:6:0.5:0:3.3 -7 1056188 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.09874;SOR=8.45755;LSEQ=CACAAAGCAGCGCACGCCAG;RSEQ=GCACAGCAGCGCACACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:4,6:0.0909:2,0:8:0:31:0:1:0:60:2:0.1:0:2 1/0:6:3:2,1:1,2:0.5:2,2:30.7:1:29.7:1:1:3.11:51.7:6:0.5:0:3.3 -7 1056203 . A G 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04912;SOR=Inf;LSEQ=GCCAGCGCACAGCAGCGCAC;RSEQ=CCAGTACACAGCAGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:0:2,0:19.9:1:30.3:1:1:0:60:24:1:0:0.8 0/1:8:3:2,1:2,3:0.375:2,2:25.7:1:30.3:1:1:2.60:51.7:6:0.375:0:3.3 -7 1056229 . ACACAGCAGCGTACAGCAGCGCACGCCAGAG A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0.21429;SOR=Inf;LSEQ=ACACAGCAGCACACAGCACC;RSEQ=CACAGTAGCGCACGCCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:28.4:1:31.5:1:1:0:60:10:1:0:0.7 0/1:10:2:1,1:4,4:0.2:2,2:8.5:1:29.4:1:1:1:43.5:4:0.2:0.2:3.5 -7 1056239 . G A 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.64241;SOR=0.5175;LSEQ=ACACAGCACCACACAGCAGC;RSEQ=TACAGCAGCGCACGCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:4,3:0.3636:2,2:14.8:1:31.3:1:1:1.29868:60:8:0.4:0:1.5 0/1:9:2:1,1:2,3:0.2222:2,2:34.5:1:30.5:1:1:1.41:60:4:0.2857:0:3 -7 1056265 . T C 61 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02564;SOR=Inf;LSEQ=CAGCGCACGCCAGAGCACAG;RSEQ=AGCGCACGCCAGCGCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:17.3:1:28.8:1:1:0:60:16:1:0:0.3 1/0:7:4:2,2:1,2:0.5714:2,2:9:1:30.5:1:1:1.81:45.5:8:0.5714:0:4 -7 1056349 . GCACAGCAGCA G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCATGCCAGCACACGCCAGC;RSEQ=CACAGCAGCACACGCCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:6,5:0.1429:2,0:16.5:1:34:0:0.48718:0:60:4:0.1538:0:1.5 0/0:1:0:0,0:1,0:0:0,0:6:0:33:0:1:0:60:2:1:0:2 -7 1056437 . AG GC 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CACAGCACACAGCAGCACAC;RSEQ=CAGCACACACCAGCGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,6:0.1111:2,2:32.5:1:29.3:1:1:1.46382:54.5:4:0.1429:0:5.5 0/0:6:0:0,0:4,2:0:2,0:18.7:1:28.2:1:1:0:56.2:5:1:0:2.2 -7 1056457 . AG GC 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGCAGCACACACCAGCGCAC;RSEQ=CAGCGCACAGCAGCGCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:9,9:0.1:2,0:22:1:27.8:1:0.47895:0:46:4:0.1176:0.05:5 0/0:4:0:0,0:3,1:0:2,0:37.8:1:30:1:1:0:54.3:8:1:0:2.5 -7 1056463 . G A 49 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=1.5538;LSEQ=ACACACCAGCGCACAGCAGC;RSEQ=CACAGCAGCGCACGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:1,2:8,10:0.1364:2,2:16:1:31.3:1:1:1.56568:47:6:0.1429:0:5.3 0/1:5:1:1,0:2,2:0.2:2,0:41:0:29:0:1:0:37:2:0.2:0:6 -7 1056477 . G A 46 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55128;SOR=0;LSEQ=AGCAGCGCACAGCAGCGCAC;RSEQ=CCAGCACACAGCAGCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:9,9:0.1429:2,2:20.7:1:29.3:1:1:1.94:37.7:6:0.15:0:4 0/0:7:0:0,0:4,3:0:2,0:25.1:1:21.3:1:1:0:52.9:1.333:1:0:2.4 -7 1056483 . A G 35 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0913;SOR=6.14705;LSEQ=GCACAGCAGCGCACGCCAGC;RSEQ=CACAGCAGCACACAGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:28:1:30:1:1:1:55:4:0.1053:0:4.5 0/1:7:3:2,1:2,1:0.4286:2,2:17.3:1:22.7:1:1:1:43.3:2:0.5:0:4.3 -7 1056493 . A G 52 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.94642;LSEQ=GCACGCCAGCACACAGCAGC;RSEQ=CACAGCACACAGCAGCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:8,9:0.15:2,2:7.3:1:33.3:1:1:1.72884:60:6:0.1579:0:1.3 0/1:7:1:1,0:3,2:0.1429:2,0:28:0:24:0:1:0:60:2:0.2:0:2 -7 1056524 . A G 53 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=1.42172;LSEQ=AGCAGCGCACAGCAGCACAC;RSEQ=CCAGCGCACAGCAGCACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:4,2:5,8:0.3158:2,2:30.5:1:20.8:1:0.34985:3.00:52.7:1:0.2143:0:3.8 0/1:5:2:1,1:1,2:0.4:2,2:38:0:26:1:1:1.73:46.5:4:0.4:0:3.5 -7 1056530 . GC AT 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCACAGCAGCACACACCAGC;RSEQ=ACAGCAGCACACGCCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:6,9:0.1053:2,2:24:1:28.8:1:1:1.46:46:4:0.1176:0:4.5 0/0:5:0:0,0:1,2:0:2,0:22.7:1:32.3:1:1:0:60:6:0.6:0:2 -7 1056540 . A G 46 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53247;SOR=0;LSEQ=ACACACCAGCGCACAGCAGC;RSEQ=CACGCCAGCGCACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:6,7:0.1875:2,2:15.7:1:29.3:1:1:2.21:50.7:6:0.1875:0:4.3 0/0:6:0:0,0:2,4:0:2,0:17.8:1:24.7:1:1:0:55.5:2:1:0:2.5 -7 1056565 . GCAGCACACGC G 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CCAGCGCACAGCAGCACACA;RSEQ=CAGCACACGCCAGCGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:3,4:0.3:2,2:14:1:33:1:1:1.44135:58:6:0.3:0.2:0.3 0/0:4:0:0,0:2,2:0:2,0:23.8:1:31.5:1:1:0:53.3:8:1:0:3.5 -7 1056600 . A G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.16667;SOR=Inf;LSEQ=ACACGCCAGCGCACAGCAGC;RSEQ=CACGCCAGCACACACCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:23:1:28.2:1:1:0:55:10:1:0:1.6 1/0:4:2:1,1:1,1:0.5:2,2:30.5:1:28.5:1:1:1:60:4:0.6667:0:3 -7 1056610 . ACACACCAGCG A 59 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.00476;SOR=Inf;LSEQ=GCACAGCAGCACACGCCAGC;RSEQ=CACAGCAGCGCACAGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:20:1:32:1:1:0:56.8:12:1:0:1 1/1:4:4:2,2:0,0:1:0,2:23.5:1:29.8:1:1:0:60:8:1:0.5:3.3 -7 1056636 . G C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05455;SOR=Inf;LSEQ=CAGCGCACAGCAGCGCACAG;RSEQ=AGCACACAGCAGCACACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:4,4:0.1111:2,0:8:0:20:0:1:0:41:2:0.1111:0:6 1/1:2:2:1,1:0,0:1:0,2:44.5:1:32.5:1:1:0:60:4:1:0:3 -7 1056645 . G C 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02222;SOR=Inf;LSEQ=GCAGCGCACAGGAGCACACA;RSEQ=CAGCACACAGCAGCGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:27.3:1:32:1:1:0:60:16:1:0:0.1 1/1:2:2:1,1:0,0:1:0,2:35.5:1:32.5:1:1:0:60:4:1:0:3 -7 1056911 . A T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAAGGAGCTCCCTGCTCA;RSEQ=ATTGGAGCTGCGGGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:36:1:29:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 1270880 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1489;SOR=Inf;LSEQ=GCGCCGTCCCCTCCTCTCCC;RSEQ=CAAGGAGAGACAAGAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:41,33:0:2,0:27.6:1:30.5:1:1:0:60:73:1:0:0.1 0/1:47:2:1,1:25,20:0.0426:2,2:26.5:1:29:1:1:1.24403:60:4:0.0435:0:1 -7 1270955 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54198;SOR=0;LSEQ=ACGACCTTCAGTTAGGAACA;RSEQ=GGCCAGACTGTGGGTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:22,29:0.0377:2,2:44.5:1:29.5:1:1:1.31:60:4:0.0392:0:1 0/0:28:0:0,0:9,19:0:2,0:23.6:1:30:1:1:0:60:56:1:0:0.1 -7 1345000 . T C 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24195;SOR=2.80936;LSEQ=TAGCTTAAAATTGGCCTTGG;RSEQ=GGGAGTATTTACACCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:6,8:0.1765:2,2:22.7:1:31:1:1:1.46561:60:6:0.1875:0:1 0/1:13:5:3,2:4,4:0.3846:2,2:26.2:1:30.4:1:1:1.45:60:10:0.3846:0:1.2 -7 1672522 . G T 52 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42391;SOR=0.34545;LSEQ=GTGGCTTCTGCCTCAGTGGG;RSEQ=AGGTGGACAGAGCTGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:5:1,4:268,184:0.0109:2,2:8.2:1:22.8:1:0.16443:5.80554:60:4:0.0089:0:1.4 0/0:263:1:0,1:155,107:0.0038:2,0:1:0:21:0:0.41065:0:60:2:0.0038:0:2 -7 1672540 . C T 243 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06594;SOR=0.75249;LSEQ=GGGAGGTGGACAGAGCTGAG;RSEQ=ACAAAGAAATCAATGGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:512:341:183,158:86,83:0.666:2,2:25.5:1:28.9:1:0.57279:1.12:60:340:0.6693:0:1.1 1/0:290:174:103,71:65,51:0.6:2,2:26.4:1:28.5:1:0.62816:1.14:60:173:0.5986:0:1.1 -7 1672759 . C G 52 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.94642;LSEQ=GCAAGGGTTGGACCATGGGG;RSEQ=GGGGGCAGGGAAAGGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:0,16:0.15:1,0:34.7:1:33:0:1:0:60:6:0.1579:0:1 0/1:7:1:0,1:1,4:0.1429:2,0:49:0:29:0:1:0:60:2:0.1667:0:1 -7 2020877 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCAAAGTGCTGGGATGA;RSEQ=AAGCGTGAGCCGGTGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:80,16:0.0204:2,2:15.5:1:28.5:1:0.31833:4.88103:60:4:0.0206:0:1.5 0/0:43:0:0,0:34,9:0:2,0:25.1:1:29.4:1:1:0:60:13.333:1:0:0.3 -7 2020882 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1023;SOR=Inf;LSEQ=AAAGTGCTGGGATGACAAGC;RSEQ=TGAGCCGGTGTGCCCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:83,18:0:2,0:23.6:1:30:1:1:0:60:100:1:0:0.2 0/1:48:2:1,1:34,12:0.0417:2,2:17:1:27.5:1:0.47252:2.76192:60:4:0.0435:0:3 -7 2020904 . G C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53314;SOR=1.31673;LSEQ=GAGCCGGTGTGCCCGGCCAG;RSEQ=AGTGTGGATTCTAACTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:21:14,7:109,42:0.1221:2,2:22.6:1:31.5:1:0.61115:1.29561:60:20:0.1183:0:1 0/1:71:11:7,4:37,23:0.1549:2,2:30.3:1:31.4:1:1:1.09:60:22:0.1594:0:1.4 -7 2020995 . G A 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69814;SOR=0.92785;LSEQ=CAGGAGCCAGAACGGACTGC;RSEQ=GGCTCAAGGAAGAGCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:219:109,110:67,75:0.6066:2,2:25.8:1:30.2:1:0.667:1.11:60:108.5:0.6045:0:1.1 1/0:158:93:40,53:30,35:0.5886:2,2:24.7:1:30:1:0.74605:1.1348:60:45.5:0.5871:0:1.1 -7 2021162 . T C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACAGGATCCGATGGGTT;RSEQ=AGGGAGGTAAATCCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:1:0,1:20.4:1:32.7:1:1:0:60:40:1:0:1.1 1/1:4:4:0,4:0,0:1:0,0:25.3:1:33.5:1:1:0:60:8:1:0:1 -7 2021248 . C T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCAGCTCACTCCGTCA;RSEQ=GAAGGGAGGAGGAAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:31.5:1:31:0:1:0:60:4:0.3333:0:1 0/0:2:0:0,0:1,1:0:2,0:24:1:29:1:1:0:60:4:1:0:0 -7 2160931 . T C 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGCCTCTCCCAACCTCTG;RSEQ=TCAGCGTCAGAGCGAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:39.5:1:34:0:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2160997 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACCGTGGGGACAGGCAG;RSEQ=GATGAGGGAGGCTGCGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:0.1429:0,0:27:1:33.5:1:1:0:60:4:0.1429:0:1 0/0:1:0:0,0:1,0:0:0,0:38:0:28:0:1:0:60:2:1:0:0 -7 2161099 . A G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47484;SOR=0.64191;LSEQ=CCCACGGGAGGGTCGTTAAC;RSEQ=GAGTCCCGGTGGCCAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:23:18,5:25,6:0.4259:2,2:21.3:1:29.6:1:1:1.15425:60:46:0.434:0:1 0/1:28:9:8,1:15,4:0.3214:2,2:22.7:1:30.1:1:1:2.08:60:18:0.3214:0:1 -7 2161239 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGGGCAGGACTATGCTG;RSEQ=AGATCACGGCATCCTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:9,43:0.0364:2,2:35.5:1:30:1:0.33892:4.59:60:4:0.0377:0:1 0/0:14:0:0,0:0,14:0:1,0:21.7:1:32:1:1:0:60:28:1:0:0 -7 2166233 . T C 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGATGCCGCCAGCCTTCC;RSEQ=TGGGACCAAGCACAACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:0.2857:2,0:26:1:30.5:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2166259 . G C 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGCACAACCCAGGCCCA;RSEQ=CCCAGCTCTGAAAGGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:5,2:0.2222:2,0:38.5:1:32.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2166319 . T G 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04923;SOR=6.0033;LSEQ=CTCTGGGGACCGGCCTCTTC;RSEQ=GTCACTCAGAGTTTTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:6,1:15,0:0.3182:1,2:17.9:1:30.7:1:0.31818:0:60:14:0.3182:0:1 1/0:8:6:6,0:2,0:0.75:0,0:19.2:1:30.3:1:1:0:60:12:0.75:0:1.2 -7 2166451 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09683;SOR=Inf;LSEQ=CCGCCAGGCAGGTGCTCACT;RSEQ=ACACTGTCCCCATGGGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:231,111:0:2,0:23:1:31.5:1:1:0:60:341:1:0:0.3 0/1:155:2:1,1:104,47:0.0129:2,2:16.5:1:31:1:0.53044:2.20014:60:4:0.013:0:1 -7 2166514 . T C 243 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.55606;SOR=0.9117;LSEQ=TCAGAATGAATAACCCCCTC;RSEQ=CACACTGCCAGGCAAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:230:113,117:160,177:0.4035:2,2:26.9:1:31:1:0.73234:1.07:60:75.667:0.4112:0:1.2 0/1:291:111:54,57:86,93:0.3814:2,2:26.1:1:29.7:1:1:1.02:60:26.75:0.3808:0:1.2 -7 2166580 . C T 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGTAGGGCATTTTAAACAA;RSEQ=GGCAGATTACAACTGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:56:20,36:73,166:0.1886:2,2:26.1:1:29.6:1:0.52294:1.26:60:27:0.1862:0:1.1 0/0:135:0:0,0:42,93:0:2,0:22.1:1:29.6:1:1:0:60:44:1:0:0.4 -7 2166583 . C T 45 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00931;SOR=Inf;LSEQ=TAGGGCATTTTAAACAACGG;RSEQ=AGATTACAACTGAGAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:85,195:0:2,0:23.1:1:31.8:1:1:0:60:45.667:0.9928:0:0.6 0/1:129:4:1,3:39,86:0.031:2,2:31.8:1:22.8:1:1:1.35745:60:3:0.0236:0:2.3 -7 2166601 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09179;SOR=Inf;LSEQ=GGCAGATTACAACTGAGAAC;RSEQ=TGGGATAAAGCCAGCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:40,159:0:2,0:23.5:1:31.5:1:1:0:60:48.75:1:0:0.5 0/1:87:2:1,1:16,68:0.023:2,2:35:1:29:1:0.35814:4.15:60:4:0.0235:0:1 -7 2166654 . C A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTCAGTCACGAAGCACAT;RSEQ=CGAGGCCTCGTTCCCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:2,75:0.025:1,2:21:1:25.5:1:0.07498:30.85:60:4:0.0256:0:1 0/0:27:0:0,0:1,26:0:1,0:20.5:1:31:1:1:0:60:54:1:0:0.2 -7 2166714 . A G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGATGAAGACATCTGAAC;RSEQ=CTCTCCTGGAGGGGGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:0,25:0,0:1:0,1:26:1:32.2:1:1:0:60:50:1:0:1 1/1:4:4:0,4:0,0:1:0,0:24.8:1:32.5:1:1:0:60:8:1:0:1 -7 2639587 . A C 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGCACACACCACCATGC;RSEQ=CAGCTAATTTTTGTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:27.5:1:1:0:50:4:1:0:3 -7 2640196 . C G 129 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11208;SOR=0.17318;LSEQ=ACTCCTCGTCCTCCCGAAAG;RSEQ=GTGGGAGAAAACTTAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:16:16,0:61,2:0.2025:1,1:23.9:1:32.4:1:1:0:60:32:0.2078:0:1 0/1:24:1:1,0:21,2:0.0417:2,0:22:0:33:0:1:0:60:2:0.0417:0:1 -7 2640258 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.23321;SOR=4.40801;LSEQ=ATGCTGGCTTGTCTGTCTGT;RSEQ=TCACTCTTATTCAGTGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:0,1:205,54:0.0038:2,0:1:0:27:0:0.21154:0:60:2:0.0039:0:1 0/1:119:2:1,1:94,23:0.0168:2,2:14.5:1:29.5:1:0.36405:4.02213:60:4:0.0168:0:1 -7 2640306 . G T 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01021;SOR=Inf;LSEQ=TTGCTTCCATCGTATATTCT;RSEQ=CTGGTCCTTGTACTCAGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:326,189:0:2,0:25:1:32.1:1:1:0:60:102:1:0:0.1 0/1:345:5:2,3:216,124:0.0145:2,2:24:1:24:1:0.36172:2.60524:60:4:0.0118:0:1.8 -7 2640378 . A C 217 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=124.46251;LSEQ=TACAGTAGTACAAATGTGGG;RSEQ=CGTGCACTCTGATGTACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:731:3:1,2:342,386:0.0041:2,2:20.7:1:30.7:1:1:1.77069:60:6:0.0042:0:1 0/1:411:140:66,74:116,155:0.3406:2,2:24.1:1:30.5:1:0.40438:1.19:60:69:0.345:0:1.2 -7 2640450 . T TGGCATC 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=6;SSF=0.00148;SOR=Inf;LSEQ=TAAGTGCACATTGATTAACT;RSEQ=GGCATCAACATCTGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:107,249:0:2,0:25:1:30:1:1:0:60:177:1:0:0.1 0/1:184:6:2,4:57,119:0.0326:2,2:21:1:28.9:1:1:1.04:60:12:0.0331:0.0109:0 -7 2640485 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGAGGACTTCGCTCACATC;RSEQ=ATAAGAACACATGCTCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:21,154:0.0113:2,2:30.5:1:31:1:0.23376:7.19:60:4:0.0114:0:1 0/0:81:0:0,0:12,69:0:2,0:22.3:1:28.3:1:1:0:60:80:1:0:0.2 -7 2640533 . C T 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00481;SOR=5.36026;LSEQ=CTCTACTGATTGTGACGCTG;RSEQ=GTGTCAGCTGCAGCCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:10:0,10:1,54:0.1538:1,0:26.3:1:29.6:1:1:0:60:20:0.1563:0:1.1 1/0:20:10:0,10:1,9:0.5:2,0:18.2:1:30.8:1:1:0:60:20:0.5:0:1 -7 2641473 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAATTACAGGCGTGAGCCAC;RSEQ=GCGCCCGGCAAGTCCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2642115 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAGGAGAGGACCCCGCC;RSEQ=CAGTCACTCAGAGCTGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:30:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2642142 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCAGAGCTGGCGCTGGGCC;RSEQ=CAGGGCTTCTCACGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:39.5:1:32:1:1:0:60:4:0.6667:0:3 1/1:2:2:1,1:0,0:1:0,2:17.5:1:33:1:1:0:60:4:1:0:2 -7 2642187 . A C 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCTCACCCACAGCTGCTTCT;RSEQ=AGTGGCAGGGCAGACTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:16.5:1:30:1:1:1:60:4:0.5:0:3 1/1:4:4:2,2:0,0:1:0,2:32.5:1:31.5:1:1:0:60:8:1:0:1.8 -7 2732326 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53247;SOR=0;LSEQ=TCTGAGAGGTTGCAGGGGGT;RSEQ=CTGCCTCCACACGCTGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:19,15:0.0556:2,2:9:0:30.5:1:1:1.2583:60:4:0.0606:0:1.5 0/0:20:0:0,0:13,7:0:2,0:22.3:1:31.8:1:1:0:60:40:1:0:0.3 -7 2732378 . C A 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.28545;SOR=0;LSEQ=AGGGCAGGAGTACCCCACCC;RSEQ=TTGGCCACAAGCCCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:2,2:14,15:0.1212:2,2:7:1:30:1:1:1.07:60:8:0.125:0:1.3 0/0:17:0:0,0:8,9:0:2,0:22.5:1:28.9:1:1:0:60:16:1:0:0.3 -7 2732414 . C T 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05491;SOR=9.05283;LSEQ=GCAGCGGTTCCCCACCTCAC;RSEQ=CAGAGCAAAGGTTAAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:4,11:0.0625:2,0:23:0:32:0:1:0:60:2:0.0625:0:1 0/1:10:4:0,4:0,6:0.4:0,0:29.5:1:30.3:1:1:0:60:8:0.4:0:1 -7 2770789 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08339;SOR=Inf;LSEQ=AGCCGTGGGGGCTGCTCAAC;RSEQ=ACGACAAACCCCGGGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:18,0:0:1,0:17.8:1:30.9:1:1:0:60:36:1:0:0.1 0/1:15:3:2,1:10,2:0.2:2,2:9:1:29.7:1:0.51648:2.32631:60:6:0.2308:0:1.3 -7 2770861 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50464;SOR=0;LSEQ=TCTCCTGCAGGATGGTGTCT;RSEQ=TCACAGCATGGAACACGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:40,32:0.027:2,2:20.5:1:31:1:1:1.2462:60:4:0.027:0:1 0/0:57:0:0,0:32,25:0:2,0:31.7:1:29:1:1:0:60:27.5:1:0:0.2 -7 2772261 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCACTCAGGCAGCTTCT;RSEQ=GCCAAAACACCAAACACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:0:32:1:1:0:60:4:1:0:2.5 -7 2772290 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAAACACGGACATGATCA;RSEQ=GCCTCGATCTAGAGGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:32.5:1:1:0:60:4:1:0:2.5 -7 2881639 . G GAGGGAGGGAGGAAGGAAGAA 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAGGGTAGAGAGGTAGG;RSEQ=AGGGAGGGAGAAAGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:27.5:1:1:0:60:4:1:0.5:0.5 -7 2883502 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10414;SOR=Inf;LSEQ=GTCACCTTGAGGATGTTGTC;RSEQ=AAGATGGTGTCGCGGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:43,21:0:2,0:20.5:1:30.2:1:1:0:60:63:1:0:0.3 0/1:31:2:1,1:22,7:0.0645:2,2:9.5:1:29:1:0.45591:3.00588:60:4:0.0667:0:1 -7 2883515 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55294;SOR=0;LSEQ=TGTTGTCGAAGATGGTGTCG;RSEQ=GGAACTCCAGCAGCGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:1,2:46,28:0.039:2,2:20:1:27.7:1:0.55666:3.23384:60:6:0.04:0:1 0/0:44:0:0,0:28,16:0:2,0:20.4:1:30.8:1:1:0:60:43:1:0:0.1 -7 2883523 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52815;SOR=0;LSEQ=AAGATGGTGTCGCGGAACTC;RSEQ=AGCAGCGCCTTCTGGTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:59,34:0.0211:2,2:49.5:1:29.5:1:1:1.72467:60:4:0.0211:0:2 0/0:57:0:0,0:33,24:0:2,0:21.5:1:30.8:1:1:0:60:114:1:0:0.2 -7 2944263 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAAAGCAGCATTGCTCA;RSEQ=GGGCTCTTGGAGGGAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:28.5:1:1:0:60:4:1:0:1.5 -7 2946179 . G T 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02001;SOR=Inf;LSEQ=GGGCAGCTCTGTGGGCCACA;RSEQ=GATCCCCCCGCACCCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:245,26:0:2,0:24.3:1:32.1:1:1:0:60:53.2:1:0:0.1 0/1:102:3:1,2:90,9:0.0294:2,2:10.7:1:27:1:0.03011:18.74937:60:6:0.0294:0:1 -7 2946188 . C T 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00252;SOR=Inf;LSEQ=TGTGGGCCACAGGATCCCCC;RSEQ=GCACCCACTGCATCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:262,45:0:2,0:24.6:1:30.6:1:1:0:60:50.167:1:0:0.1 0/1:135:5:4,1:109,21:0.037:2,2:17:1:30.4:1:1:1.29491:60:10:0.037:0:1.4 -7 2946461 . T C 317 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04996;LSEQ=AACTCCTCCTCCGTCTCAGG;RSEQ=CGGGGCAGCAGCTTTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1209:1148:470,678:23,33:0.9495:2,2:24.3:1:31.2:1:1:1.00541:60:40:0.9532:0:1.2 0/1:721:349:149,200:163,206:0.484:2,2:25.2:1:30.8:1:0.7069:1.06199:60:42.625:0.4837:0:1.2 -7 2946552 . C A 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-04;SOR=0.39658;LSEQ=GGCACCACCTGTCCGGCCAC;RSEQ=CCTGACTGCCGTGGTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:84:8,76:21,202:0.2727:2,2:24:1:29.9:1:1:1.01:60:83:0.2776:0:1.3 0/1:147:19:3,16:17,111:0.1293:2,2:24.2:1:30.4:1:0.72482:1.22:60:38:0.1329:0:1.2 -7 2946741 . T C 70 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.44721;LSEQ=TGAGTGCAGTGGCACTTTCT;RSEQ=GGCTCACTGCAACCTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:33.6:1:30.4:1:1:0:49.6:10:0.7143:0:1.2 1/0:2:1:0,1:0,1:0.5:0,0:25:0:28:0:1:0:60:2:0.5:0:1 -7 2948456 . TTTTTG T 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGTCCTTTCGTTTTTTTT;RSEQ=TTTTTTTTTTTCTGAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:30.5:1:1:0:50:4:1:0.5:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2949143 . G C 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.59564;LSEQ=CCCCTCCGCCCCTCACCCCT;RSEQ=CGCCCCTCACCCCTCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:17.5:1:26.5:1:1:1:50:4:0.5:0:2 1/0:8:5:3,2:1,2:0.625:2,2:9:1:27.8:1:1:2.60:56.4:4:0.6667:0:1.6 -7 2950020 . C T 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=GGCAGAGATGAGGCCCCGGA;RSEQ=GGGGTGAACCAGGTGGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:0,7:0,19:0.2692:1,0:20.1:1:30.9:1:1:0:60:14:0.2692:0:1.6 1/1:2:2:1,1:0,0:1:0,2:22.5:1:28.5:1:1:0:60:4:1:0:1 -7 2950622 . A C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAATCCCAGCACTTTGGG;RSEQ=GGTGGGAGGATTGCTTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2951244 . G A 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAAGGTCAGCGTCCACCAC;RSEQ=GAGCCAGCCCCCGGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:33.5:1:30:1:1:0:60:4:0.6667:0:2 1/1:1:1:0,1:0,0:1:0,0:11:0:32:0:1:0:60:2:1:0:1 -7 2951256 . C G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACCACGGAGCCAGCCCC;RSEQ=GGCAGCTGGGGGAGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21.5:1:29.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2951346 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTCAACGCTTAGGTCAC;RSEQ=TTGTCTGGCTCCAAAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:41:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2951650 . C G 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06803;SOR=2.29036;LSEQ=GGGTGCAGAGAGGGAGTTAA;RSEQ=ACGGGGCAGCTGCTGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:26:26,0:83,0:0.2385:1,1:21.5:1:32.1:1:1:0:60:25:0.2358:0:1 0/1:31:13:13,0:16,2:0.4194:2,1:23.6:1:32.8:1:0.49677:0:60:26:0.4194:0:1.1 -7 2951726 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09947;SOR=Inf;LSEQ=AAACAACTCTTCATCCCACC;RSEQ=TTGTCCCTGGCCCAGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:357,50:0:2,0:22.1:1:31:1:1:0:60:80.4:1:0:0.2 0/1:188:2:1,1:164,22:0.0106:2,2:9.5:1:27.5:1:0.23029:7.31445:60:4:0.0107:0:1.5 -7 2951763 . C T 148 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.89807;LSEQ=TGGCCTCATGAGGATCATCA;RSEQ=GGAGGGTCCTGGCCCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:5:0,5:517,231:0.0066:2,0:5:1:26.4:1:0.00294:0:60:10:0.0068:0:1 0/1:412:35:24,11:259,118:0.085:2,2:23.4:1:29:1:1:1.00599:60:34:0.0842:0:1.3 -7 2951934 . C T 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=ATCTCTTGTGACGATATCTG;RSEQ=AGAGAGAGGGGCCAGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:22:5,17:255,426:0.0313:2,2:27.3:1:28.9:1:0.18408:2.03337:60:44:0.0318:0:1 0/0:477:0:0,0:161,315:0:2,0:24:1:31.4:1:1:0:59.9:78.333:0.9979:0:0.1 -7 2952037 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01097;SOR=Inf;LSEQ=GCTCTACAGAACTCGATGTC;RSEQ=GATCCCCTTCCAGCCATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:4,143:0:1,0:24.8:1:29.8:1:1:0:60:146:1:0:0.1 0/1:43:3:0,3:0,40:0.0698:1,0:21.7:1:31.3:1:1:0:60:6:0.0732:0:1 -7 2952241 . C T 61 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCACCAGTCTAAATAAAT;RSEQ=TCCTGTTCCACCCACCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:1,3:0,6:0.4:0,2:15:1:30.5:1:0.4:0:60:8:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2952624 . GGGA G 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGGGGGAGGAGGGGTGATG;RSEQ=GGAGGAGGAGGGAAGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:30:1:32.5:1:1:0:60:4:0.2857:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2952802 . A AGAGGGAAGAGAAGAGGGGAG 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=0;LSEQ=GAAAGAGGGAAGAGGAGGAA;RSEQ=GAGGGAAGAGAAGAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:49:49,0:70,2:0.405:1,1:15.1:1:30.2:1:0.51405:0:58.8:48:0.4103:0.314:0.2 0/0:23:0:0,0:18,1:0:1,0:13.3:1:31.6:1:1:0:60:38:0.8261:0:0.2 -7 2952879 . G A 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0817;SOR=Inf;LSEQ=GGAAGTCGTCCTGGTTCATG;RSEQ=CTCCCGCGGGGCTCCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:339,87:0:2,0:25.4:1:31.1:1:1:0:59.9:41.6:1:0:0.3 0/1:171:2:1,1:136,33:0.0117:2,2:18:0:26.5:1:0.35906:4.07505:60:4:0.012:0:1 -7 2952886 . C T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01709;SOR=1.69934;LSEQ=GTCCTGGTTCATGGCTCCCG;RSEQ=GGGGCTCCCCAGGTGGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:70:52,18:315,98:0.1446:2,2:22.2:1:30:1:0.7624:1.11238:60:140:0.1452:0:1.2 0/1:197:44:34,10:114,39:0.2234:2,2:28.7:1:28.8:1:0.84373:1.16:60:13.667:0.2135:0:1.1 -7 2952915 . G A 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00025;SOR=0;LSEQ=CCAGGTGGCCGTGGCTCGCC;RSEQ=CTCACCTGACTTGCAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:21:13,8:417,237:0.0311:2,2:29.7:1:28.9:1:0.82262:1.08264:60:20:0.0303:0:1 0/0:336:0:0,0:208,127:0:2,0:23.1:1:29.9:1:1:0:60:166.5:0.997:0:0.3 -7 2953168 . GC G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GACCTTCCACGGAGGACGGG;RSEQ=CCCTGGGCTGGGTCCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:18,219:0:2,0:24.4:1:31.1:1:1:0:60:28.625:1:0:0.1 0/1:83:2:1,1:8,73:0.0241:2,2:22:1:27.8:1:0.20629:8.66:60:4:0.0244:0.012:0 -7 2954801 . T C 281 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09832;SOR=0;LSEQ=CTCACAAGGACCGATGTTCC;RSEQ=CCAGGTGAGGGTGAGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:544:544:435,109:0,0:1:0,2:22.7:1:31:1:1:0:60:107.8:1:0:1.1 1/1:249:247:186,61:2,0:0.992:0,2:22.2:1:29.8:1:1:0:60:40.167:0.9918:0:1.2 -7 2955084 . G T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03847;SOR=Inf;LSEQ=CAGGGTGCTGCCCTCAACCC;RSEQ=GCAAAGCCAGACCTTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:13,245:0:2,0:25.2:1:30.4:1:1:0:60:24.8:1:0:0.3 0/1:133:3:1,2:5,125:0.0226:1,2:16:1:29.7:1:0.13026:11.84:60:6:0.0226:0:1 -7 2955097 . C T 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01607;SOR=0.46458;LSEQ=TCAACCCGGCAAAGCCAGAC;RSEQ=TTGTTCAAATCCCTGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:60:1,59:2,144:0.2913:1,1:25.4:1:29.6:1:1:1.22:60:19:0.2938:0:1.2 0/1:100:16:0,16:0,84:0.16:1,1:27.1:1:30.3:1:1:0:60:32:0.16:0:1.3 -7 2956759 . G A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01911;SOR=Inf;LSEQ=GTCTACCCACCTGTCACTGA;RSEQ=AGGATAAAACGGGACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:50,2:0:1,0:26.6:1:32.4:1:1:0:60:104:1:0:0.1 0/1:20:3:3,0:17,0:0.15:1,0:32.3:1:31:1:1:0:60:6:0.1579:0:1 -7 2956858 . TG T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.23028;SOR=4.44676;LSEQ=ATTCGGGTGTCTCTTCTCAG;RSEQ=GGGAGAGGGCAGGGCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:1,0:290,78:0.0027:2,0:19:0:34:0:1:0:60:2:0.0028:0:6 0/1:167:2:1,1:128,36:0.012:2,2:23.5:1:28:1:0.39715:3.52065:60:4:0.012:0:0 -7 2956918 . C A 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGGTAGGTGCTCCGGAGAG;RSEQ=CTTACCTGAAGGAGCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:816:0:0,0:479,334:0:2,0:25.9:1:31.6:1:1:0:60:80.3:0.9963:0:0.2 0/1:424:80:48,32:197,145:0.1887:2,2:25.3:1:28.9:1:0.7081:1.10:60:160:0.1923:0:1.3 -7 2956926 . G T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10439;SOR=4.59131;LSEQ=TGCTCCGGAGAGCCTTACCT;RSEQ=AAGGAGCTGGCCAAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:846:2:1,1:475,369:0.0024:2,2:8.5:1:27.5:1:1:1.28687:60:4:0.0024:0:3.5 0/1:464:5:2,3:255,204:0.0108:2,2:20.8:1:25:1:0.6601:1.87243:60:4:0.0088:0:2.6 -7 2957005 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.70021;LSEQ=CTTGTTGAAAGCGCTTCTTC;RSEQ=GGCTGCAGGGTGTTCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:763:91:37,54:287,384:0.1193:2,2:26.2:1:30:1:0.73565:1.0907:60:44.5:0.1185:0:1.1 0/1:449:150:60,90:121,178:0.3341:2,2:24.5:1:29.7:1:1:1.01962:60:149:0.3341:0:1.3 -7 2957113 . G GC 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00823;SOR=Inf;LSEQ=AACTGGAGACCTGTCCTCAA;RSEQ=CCCCTCCATGCTAACGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:9,156:0:2,0:22.9:1:32.1:1:1:0:60:164:0.9939:0:0.1 0/1:43:3:0,3:2,38:0.0698:2,0:21.3:1:31.7:1:1:0:60:6:0.0732:0:0 -7 2958013 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00181;SOR=Inf;LSEQ=TTCCCTAGAATTCATCATCC;RSEQ=AATACGGATGGATTGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:149,3:0:1,0:28.6:1:31.5:1:1:0:60:304:1:0:0.1 0/1:62:5:5,0:54,3:0.0806:2,0:35.6:1:31.4:1:1:0:60:10:0.0806:0:1 -7 2958194 . C T 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01804;SOR=6.04957;LSEQ=CCTCGGTGCATCAGGCGCTG;RSEQ=AGTTTCACCAGGAGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1042:2:1,1:465,574:0.0019:2,2:29.5:1:26.5:1:1:1.23:60:4:0.0019:0:1 0/1:695:8:4,4:327,360:0.0115:2,2:19:1:28.6:1:1:1.10:60:16:0.0118:0:1.3 -7 2958274 . G A 44 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04361;SOR=Inf;LSEQ=AAATTCAGGGGCCAAGCACC;RSEQ=GGAAGCCAGCGGGGCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:89,316:0:2,0:23.1:1:30.6:1:1:0:60:80:1:0:0.2 0/1:221:3:2,1:51,167:0.0136:2,2:16.3:1:28:1:0.14365:6.48:60:6:0.014:0:1 -7 2958298 . C T 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00786;SOR=1.94377;LSEQ=AGCCAGCGGGGCCGCAGCAC;RSEQ=GCACTGGCATGGGTGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:46:9,37:20,189:0.1804:2,2:22.4:1:30.4:1:0.07033:2.29:60:92:0.1818:0:1.3 0/1:140:42:1,41:14,84:0.3:2,1:22.2:1:30.5:1:0.03913:6.77225:60:84:0.3022:0:1.1 -7 2958337 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06645;SOR=Inf;LSEQ=CGCGTGTCCGACTCTGCGTA;RSEQ=GGATGGCCCTGTGGCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:9,122:0:2,0:26.6:1:31:1:1:0:60:42.667:1:0:0.2 0/1:46:2:0,2:1,43:0.0435:1,0:21:1:32:0:1:0:60:4:0.0435:0:1 -7 2958484 . TCTC T 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CGAACCCCTCTGAGCCACGG;RSEQ=CTCCTCTGTAAATCTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:0,12:0.2:0,0:33.3:1:32.3:1:1:0:60:6:0.2:0:0.3 0/0:1:0:0,0:0,1:0:0,0:45:0:33:0:1:0:60:2:1:0:1 -7 2959172 . G A 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCTGGCTGGAGATGTTCA;RSEQ=GTTCAGCCGGATGTAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1510:0:0,0:714,795:0:2,0:24.4:1:31.4:1:1:0:60:67.591:0.9993:0:0.2 0/1:852:139:62,77:356,356:0.1631:2,2:24.2:1:29.8:1:0.26612:1.24162:60:138:0.1643:0:1.2 -7 2959278 . C A 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12699;SOR=5.58058;LSEQ=AAGATGCTCCAGCTGTCTAT;RSEQ=AGTATGGGGTCCCCCGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:1:1,0:114,408:0.0019:2,0:1:0:25:0:0.21989:0:60:2:0.0019:0:1 0/1:283:3:2,1:87,193:0.0106:2,2:6.3:1:24.7:1:0.23365:4.41:60:2:0.0072:0:1.7 -7 2959287 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05204;SOR=7.60158;LSEQ=CAGCTGTCTATCAGTATGGG;RSEQ=TCCCCCGACCATCAGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:1,0:63,345:0.0024:2,0:1:0:25:0:0.15648:0:60:2:0.0025:0:1 0/1:218:4:3,1:54,159:0.0183:2,2:17:1:27:1:0.0565:8.73:60:8:0.0186:0:1 -7 2961066 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGCAGCTCCGGGCTTTGG;RSEQ=GGTGCTGCCCACATCATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:29.5:1:1:0:60:4:1:0:1 -7 2961909 . A C 100 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAAGCCCGAGAGAGGAGG;RSEQ=AACTTCCACTTACCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:27.5:1:33.4:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2962014 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07326;SOR=12.4481;LSEQ=TGTGACCCGGCGGGCAGCCC;RSEQ=AGACACCTGGGCAGGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:22,0:0.0435:1,0:22:0:31:0:1:0:60:2:0.0455:0:1 0/1:5:2:2,0:3,0:0.4:0,0:12:1:27.5:1:1:0:60:4:0.4:0:1 -7 2962036 . C T 89 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3248;SOR=0;LSEQ=GACACCTGGGCAGGTGAGTG;RSEQ=AGACGTGGCCAAAGAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:8:8,0:31,0:0.2051:1,0:17.3:1:29.9:1:1:0:60:16:0.2162:0:1 0/0:7:0:0,0:7,0:0:0,0:28.3:1:33.6:1:1:0:60:14:1:0:0.3 -7 2962183 . G T 39 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03612;SOR=Inf;LSEQ=GAACAGACGAGCAAGCAGAG;RSEQ=CTCTAGGCGGCGAGGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:0:0,0:393,91:0:2,0:22.5:1:31:1:1:0:60:36.231:1:0:0.2 0/1:240:3:1,2:183,53:0.0125:2,2:6.7:1:25:1:0.13329:6.83308:60:6:0.0126:0:1 -7 2962201 . A C 163 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCTCTAGGCGGCGAGGTC;RSEQ=CTTGTCCAGGTCAGAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:37:27,10:504,187:0.0508:2,2:25.1:1:31.3:1:1:1.00:60:74:0.0514:0:1.1 0/0:387:0:0,0:267,118:0:2,0:22:1:29.7:1:1:0:60:76:0.9948:0:0.2 -7 2962241 . G A 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04319;SOR=0.73323;LSEQ=CGCCTCCCTGGCCAAGGGTC;RSEQ=CTCCAGACGGTGGAGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1261:161:102,59:669,430:0.1277:2,2:25.7:1:30.2:1:0.60354:1.11:60:79.5:0.1278:0:1.1 0/1:743:72:43,29:380,290:0.0969:2,2:23.2:1:29.4:1:0.70739:1.13:60:144:0.0976:0:1.2 -7 2962293 . C G 221 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=358.03598;LSEQ=TGGTTGACCTTGTAGTGCAG;RSEQ=GTGACGGGGCCGCTGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1640:1:0,1:841,793:6e-04:2,0:1:0:15:0:0.48563:0:60:0:0:0:1 0/1:939:168:84,84:393,373:0.1789:2,2:23.1:1:29.9:1:0.7984:1.05359:60:23:0.1754:0:1.2 -7 2962556 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTCAGGGGGGTGCACCT;RSEQ=CCTCCTGCCTGCACCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:37,64:0.0194:2,2:9.5:1:31.5:1:1:1.72:60:4:0.0206:0:1 0/0:19:0:0,0:7,12:0:2,0:20.8:1:31.7:1:1:0:60:38:1:0:0.1 -7 2962753 . G A 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.56802;LSEQ=TTGCAGCCACCTCCCTTGCC;RSEQ=CCATCCCCTCACCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:802:614:373,241:117,68:0.7656:2,2:24.9:1:30:1:0.60547:1.11152:60:121.8:0.768:0:1.1 1/0:431:280:181,99:93,58:0.6497:2,2:26.6:1:29.7:1:0.53113:1.14:60:279:0.6503:0:1.1 -7 2963056 . C T 43 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04409;SOR=Inf;LSEQ=CGGGGGTTGGTGGTGGGCGC;RSEQ=AGGACCCCGGTGGCATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:3,105:0:1,0:24.5:1:32:1:1:0:60:53:1:0:0.1 0/1:60:3:0,3:1,56:0.05:1,0:32.3:1:27.3:1:1:0:60:6:0.0508:0:1 -7 2963120 . C T 71 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.78333;LSEQ=GTGTCCTGGCTCCGAGAAGG;RSEQ=CCTTAATGGCTAAGGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:0,5:0,37:0.1136:1,0:19.6:1:30.8:1:1:0:60:10:0.122:0:1 0/1:11:1:0,1:1,9:0.0909:2,0:13:0:31:0:1:0:60:2:0.0909:0:1 -7 2963494 . GC CT 27 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATCATAGCTCACTGCAG;RSEQ=TCAACCTCCTGGGCTCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:0.25:2,2:25.5:1:27.8:1:0.46429:3.87298:42.5:4:0.2857:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2963521 . G T 75 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTGGGCTCAAGTGATCC;RSEQ=CCTGCCTCAGCCTCCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:27.3:1:29.2:1:1:0:50:5:0.8333:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2963744 . T C 116 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07528;SOR=0;LSEQ=CTGACTCGGGAATGCTACAA;RSEQ=TCTGGTTCTGGCTCTAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:12:12,0:181,2:0.0615:1,0:20:1:32.5:1:1:0:60:24:0.0625:0:1.2 0/0:53:0:0,0:53,0:0:1,0:24.2:1:30.3:1:1:0:60:52:1:0:0 -7 2963940 . GGGA G 145 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.12237;SOR=0.4823;LSEQ=ATCCAGGCCCTCGGATTGGT;RSEQ=GGAGGAGGAGGAGTGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2001:24:11,13:992,983:0.012:2,2:25:1:31.7:1:0.6873:1.19253:60:48:0.0122:0.003:0.2 0/0:1031:6:4,2:509,512:0.0058:2,2:36.2:1:31.3:1:0.45152:2.01:60:12:0.0059:0:0 -7 2964011 . C T 219 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTGTCATCTGCAGAGGGA;RSEQ=GAGGGCCCATCAGTACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1819:0:0,0:814,1005:0:2,0:25.1:1:30.5:1:1:0:60:52.5:1:0:0.2 0/1:977:166:68,98:379,429:0.1699:2,2:23.3:1:29.7:1:0.17183:1.27289:60:40.5:0.1695:0:1.2 -7 2964267 . AT A 31 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGTATCTGGTTTTTAAG;RSEQ=TTTTTTTTTTTGAGAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:0,2:0,35:0.0541:1,0:24.5:1:31:1:1:0:60:4:0.0541:0.027:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2966138 . G A 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46904;SOR=1.73812;LSEQ=TAAAAGCCCAGACCTAGCTC;RSEQ=CACCCTCTGCACAGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:9:9,0:62,0:0.125:1,0:19.9:1:31:1:1:0:60:18:0.1324:0:1 0/1:20:4:3,1:15,1:0.2:1,2:7.3:1:29.8:1:0.36842:4.47215:60:8:0.2:0:1 -7 2966334 . G A 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGTGACCCTCTGTGACCC;RSEQ=TCCTACCCAGGACCCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1788:0:0,0:998,783:0:2,0:25.3:1:30:1:1:0:60:31.382:0.9988:0:0.2 0/1:962:50:28,22:506,404:0.052:2,2:26.8:1:29.8:1:1:1.02:60:49:0.0524:0:1.3 -7 2966445 . T G 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00056;SOR=1.37309;LSEQ=GCTGCAAGACACAAGGGAGG;RSEQ=GGGGGAAAGCATGCATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1451:488:191,297:368,581:0.3363:2,2:26.7:1:30.4:1:0.90909:1.02:60:29.5:0.3384:0:1.2 0/1:792:325:141,184:178,245:0.4104:2,2:24.6:1:30.2:1:0.76553:1.05:60:80.25:0.4202:0:1.3 -7 2966465 . AGT A 172 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.78759;SOR=1.08925;LSEQ=TGGGGGAAAGCATGCATGTG;RSEQ=GTGTGTGTGTGTGCACACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1099:40:9,31:364,690:0.0364:2,2:26.9:1:32.4:1:0.12825:1.81618:59.5:80:0.037:0.0036:0.5 0/1:582:23:8,15:203,351:0.0395:2,2:23.7:1:30.4:1:1:1.08426:60:22:0.0383:0.0069:0.6 -7 2966520 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0936;SOR=Inf;LSEQ=GAGAAGCTTCTGGAAGGTTC;RSEQ=AGGCTTCCGAGTGGCCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:22,358:0:2,0:22.8:1:31.9:1:1:0:59.9:41.222:1:0:0.3 0/1:168:2:1,1:11,154:0.0119:2,2:13.5:1:30:0:0.13895:13.45:60:4:0.012:0:1 -7 2968093 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAGCCTCCTCATCTGTA;RSEQ=AATGAGCAGTACCCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:2,0:189,7:0.0101:1,0:14:0:31:1:1:0:60:4:0.0102:0:1.5 0/0:64:0:0,0:62,2:0:1,0:22.2:1:31.5:1:1:0:60:128:1:0:0.2 -7 2968105 . C A 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATCTGTACAATGAGCAGTA;RSEQ=CCTGCCTTTCAGGGTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:239,9:0:1,0:24.1:1:32.3:1:1:0:60:81.667:1:0:0.1 0/1:85:10:9,1:72,3:0.1176:1,2:25.7:1:29.1:1:0.39971:2.62452:60:20:0.1176:0:1 -7 2968195 . G A 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGCTTGGCATGGTGGCAC;RSEQ=GGGCAAAAGCCCAGTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1149:0:0,0:707,437:0:2,0:24.5:1:29.8:1:1:0:60:46.667:0.9956:0:0.1 0/1:579:54:35,19:318,204:0.0933:2,2:22.1:1:29.5:1:0.6605:1.18:60:108:0.0947:0:1.1 -7 2968289 . T C 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TGGAGTCGTTTCCCGGGGGC;RSEQ=CGGCGGTGATTGACATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1598:26:8,18:662,906:0.0163:2,2:22:1:30.6:1:0.31709:1.64355:60:25:0.0162:0:1.3 0/0:937:0:0,0:418,517:0:2,0:23.9:1:29.3:1:1:0:60:45.75:0.9978:0:0.2 -7 2968359 . C T 107 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=14.04928;LSEQ=ACACAGACACACACACGTTA;RSEQ=GGGTGCATAAATATTACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:664:2:0,2:166,494:0.003:2,0:33:1:29.5:1:1:0:60:4:0.0031:0:1 0/1:294:12:3,9:74,207:0.0408:2,2:15.3:1:30:1:1:1.07221:60:24:0.0408:0:1.1 -7 2968361 . G A 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.23722;SOR=1.28084;LSEQ=ACAGACACACACACGTTACG;RSEQ=GTGCATAAATATTACACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:76:18,58:137,413:0.1212:2,2:22.1:1:30.4:1:0.88789:1.06876:60:75:0.123:0:1.2 0/1:273:41:9,32:58,174:0.1502:2,2:16.1:1:30.4:1:0.84417:1.18445:60:40:0.1481:0:1.1 -7 2968486 . G C 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48247;SOR=1.89614;LSEQ=GGCTGGAGGAGGCTTGTGCT;RSEQ=AGCCCGGAGCGGCCGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:23:0,23:1,43:0.3433:1,1:24.2:1:32.5:1:1:0:60:46:0.3594:0:1.1 1/0:10:5:0,5:0,5:0.5:0,0:12.4:1:31:1:1:0:60:10:0.5:0:1 -7 2968548 . G A 110 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCGCACATCTGCTCACAGG;RSEQ=AGGACGCAGGCGGGAGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:0,12:0,11:0.5217:0,0:21.2:1:30.9:1:1:0:60:24:0.5455:0:1.3 0/0:1:0:0,0:0,1:0:0,0:39:0:33:0:1:0:60:2:1:0:1 -7 2969496 . G A 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03266;SOR=Inf;LSEQ=TCCCTGGATGGCATTCTGCA;RSEQ=GGGGAGAGGGTGGTGGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:163,7:0:1,0:22.4:1:32.1:1:1:0:60:33:1:0:0.3 0/1:38:2:2,0:35,1:0.0526:1,0:22:1:30:0:1:0:60:4:0.0541:0:1 -7 2969508 . G A 139 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00499;SOR=2.66542;LSEQ=ATTCTGCAGGGGGAGAGGGT;RSEQ=GTGGGGATGAGCTCTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:35:32,3:157,7:0.1759:1,2:24.7:1:27.1:1:0.38518:2.09314:60:16.5:0.1701:0:1.1 0/1:55:20:19,1:33,2:0.3636:2,1:21.1:1:27.9:1:1:1.15:60:40:0.3774:0:1.1 -7 2969583 . A T 43 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00862;SOR=Inf;LSEQ=ACACTCTTCTGCAGGGGGAG;RSEQ=CAATGGAGGGGACCTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:745:0:0,0:563,181:0:2,0:24:1:29.6:1:1:0:60:45.5:1:0:0.2 0/1:328:4:1,3:228,96:0.0122:2,2:7.5:1:21.8:1:0.08381:7.07765:60:3:0.0096:0:1.3 -7 2969660 . C A 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTTGGTGATGGGCAGAGAT;RSEQ=CGCAGGAGCTAGGGCTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1605:77:41,36:739,789:0.048:2,2:26.3:1:28.5:1:0.41571:1.22:60:76:0.0479:0:1.2 0/0:862:0:0,0:440,421:0:2,0:25.3:1:30.7:1:1:0:60:85.1:0.9988:0:0.4 -7 2969680 . G A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.94834;LSEQ=CCGCAGGAGCTAGGGCTGGC;RSEQ=TCCGTGCCTTCTTCCTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1591:248:114,134:618,720:0.1559:2,2:24.7:1:30.2:1:1:1.00891:60:48.6:0.1543:0:1.1 0/1:888:235:112,123:320,333:0.2646:2,2:25.1:1:29.6:1:0.76096:1.05531:60:46:0.2635:0:1.2 -7 2969983 . C T 112 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCTCCTCTTGCTTTTTAT;RSEQ=AAATTTTTTATAGAGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:0,15:0,4:0.7895:0,1:22.9:1:28.7:1:1:0:60:30:0.7895:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2971977 . T TG 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.54849;SOR=Inf;LSEQ=AGAGGGGACCTTTCAGCAGT;RSEQ=GGGCTCCTGCCTGCTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:61:59,2:2,0:0.9683:0,1:23.5:1:31.1:1:1:0:60:19.333:0.9831:0.2063:0.2 1/1:32:32:31,1:0,0:1:0,1:21.7:1:30.7:1:1:0:60:15:1:0.2813:0.3 -7 2972031 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.08625;SOR=Inf;LSEQ=TAATTGCTATTTGGATGGAC;RSEQ=CCCACCACTCCGAGACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:192,4:0:1,0:25.6:1:31:1:1:0:60:31.667:1:0:0.3 0/1:82:2:1,1:77,3:0.0244:1,2:37.5:1:29.5:1:0.09575:22.37217:60:4:0.0247:0:2.5 -7 2972072 . A G 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00063;SOR=2.04137;LSEQ=GAGAACCCGCCACGTTTACC;RSEQ=CGCAGGATTGTTCGTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:72:58,14:286,54:0.1748:2,2:24.8:1:29.4:1:0.48508:1.27761:60:35:0.1728:0:1.1 0/1:192:58:45,13:98,35:0.3021:2,2:23.2:1:28.5:1:0.71701:1.23:60:18.333:0.2957:0:1.1 -7 2973685 . TTTTTC T 69 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACAATGCCTGGCTGTTT;RSEQ=TTTTCTTTTCTTTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:34.8:1:26.8:1:1:0:60:5:1:0.1667:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 2973920 . G A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03784;SOR=Inf;LSEQ=AAATGAGTAAGAAGCGAGTC;RSEQ=CAGGATTTCCAGCTTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:59,1:0:1,0:23.5:1:30.1:1:1:0:60:120:1:0:0 0/1:15:2:2,0:12,1:0.1333:1,0:24.5:1:31:1:1:0:60:4:0.1429:0:1 -7 2973979 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTCTGGGCACCCAAGAC;RSEQ=CACCCAGAAGCAGGCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:2,0:151,7:0.0125:1,0:20.5:1:32:0:1:0:60:4:0.0132:0:1 0/0:61:0:0,0:54,7:0:2,0:25.8:1:30.9:1:1:0:60:122:1:0:0.1 -7 2974165 . C T 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=66.26454;LSEQ=CTGTCTTCAGGTGACTCCTC;RSEQ=GAGGTGGAAGAATCGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1703:2:0,2:914,787:0.0012:2,0:1.5:1:28.5:1:0.2145:0:60:4:0.0012:0:1 0/1:952:69:33,36:459,419:0.0725:2,2:28.6:1:29.5:1:0.53208:1.19483:60:22:0.0705:0:1.1 -7 2974494 . C A 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.21839;SOR=4.17601;LSEQ=GGTCCAGTCTCCCAAACAAG;RSEQ=CCCGGTCTTCTTGTACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:0,4:0,18:0.1818:1,0:17:1:31:0:1:0:60:8:0.1818:0:1 1/0:4:2:1,1:0,2:0.5:0,2:39:1:26.5:1:1:0:60:4:0.5:0:1 -7 2976520 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06167;SOR=Inf;LSEQ=GGTTTGGGGCCCCACAGGGA;RSEQ=GTGGCGACTGGTCACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:0:1,0:22.3:1:31.6:1:1:0:60:28.5:1:0:0.1 0/1:20:2:1,1:16,2:0.1:2,2:9:0:32.5:1:0.28421:6.73285:60:4:0.1:0:3 -7 2976522 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06013;SOR=Inf;LSEQ=TTTGGGGCCCCACAGGGAGG;RSEQ=GGCGACTGGTCACAGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:59,1:0:1,0:22.4:1:29.9:1:1:0:60:120:1:0:0.1 0/1:20:2:1,1:16,2:0.1:2,2:11:0:33:1:0.28421:6.73285:60:4:0.1053:0:3 -7 2976572 . G A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=CAGGGGGCACCTGGCTTCAG;RSEQ=TGTGGGTCTCCACGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:135,0:0:1,0:24:1:31.2:1:1:0:60:44:1:0:0.1 0/1:53:9:7,2:40,4:0.1698:2,2:19.6:1:29.6:1:0.26677:2.78562:60:18:0.1765:0:1.4 -7 2976767 . G A 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=1.63504;LSEQ=ACCATCTCGATCCTCATCTC;RSEQ=TCGTTCTTCTCCTCCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1876:272:128,144:815,788:0.145:2,2:25.9:1:30.2:1:0.26507:1.16345:60:33:0.1435:0:1.2 0/1:1239:269:141,128:491,479:0.2171:2,2:25.1:1:29.6:1:0.62969:1.07:60:66.25:0.2165:0:1.2 -7 2977488 . C T 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17127;SOR=0;LSEQ=GGAGCCGGTGGTCTGGGGTG;RSEQ=GGGCCCCGCTGTGCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:5:3,2:383,99:0.0103:2,2:9.8:1:26.4:1:0.27756:2.57285:60:10:0.0104:0:1 0/0:254:0:0,0:187,67:0:2,0:21.6:1:30.9:1:1:0:60:41.333:1:0:0.2 -7 2977732 . T C 155 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=64.76218;LSEQ=AGGTCAGGACTGAAAGCTGT;RSEQ=CTCTGCTCGTGCCTTCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:1:0,1:20,271:0.0034:2,0:40:0:13:0:1:0:60:0:0:0:2 0/1:186:34:2,32:13,139:0.1828:2,2:20.1:1:30.6:1:1:1.49348:60:33:0.1833:0:1.1 -7 2977768 . G T 84 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05018;SOR=0;LSEQ=CCCGCCAGCTGGCTGGAGCT;RSEQ=GCCTGTCCCTCCCTAAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:7:0,7:2,147:0.0446:1,0:35.7:1:30.1:1:1:0:60:14:0.0467:0:1 0/0:90:0:0,0:0,90:0:1,0:21.1:1:29.9:1:1:0:60:21.5:1:0:0.2 -7 2978226 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10224;SOR=Inf;LSEQ=TGGAAAGGAGTGTGGGGTCA;RSEQ=GGAGGTCCTGCTGACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:247,20:0:2,0:22.8:1:32.2:1:1:0:60:266:1:0:0.1 0/1:126:2:1,1:119,5:0.0159:1,2:29.5:1:28.5:1:0.09333:21.8176:60:4:0.0163:0:1 -7 2978506 . G A 56 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04803;SOR=7.84182;LSEQ=TTCAGAGGGTCAGGGTCGGG;RSEQ=TGGGGAGCCAGGTGGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:665:1:1,0:201,463:0.0015:2,0:1:0:25:0:0.30376:0:60:2:0.0015:0:1 0/1:342:4:2,2:108,230:0.0117:2,2:10.3:1:28:1:0.59652:2.12:60:8:0.0119:0:1.8 -7 2978543 . A T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09754;SOR=Inf;LSEQ=CCTGGAGGGCAGGGGACAGA;RSEQ=GAACCAGCAACAGATACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:29,320:0:2,0:22.5:1:31.3:1:1:0:60:173.5:1:0:0.1 0/1:159:2:1,1:21,136:0.0126:2,2:20:0:30:1:0.25834:6.35:60:4:0.0126:0:1.5 -7 2985351 . C A 92 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05672;SOR=0;LSEQ=TCACAGCTTAAGAACCATGC;RSEQ=ACTACTGAGGACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:8:8,0:233,5:0.0325:1,0:24.8:1:30.8:1:1:0:60:16:0.0342:0:1.3 0/0:121:0:0,0:114,5:0:1,0:22.4:1:30:1:1:0:60:28.75:0.9829:0:0.3 -7 2985361 . GAC G 212 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=13.000;MSILEN=2;SSF=0.00182;SOR=0.49439;LSEQ=AGAACCATGCCACTACTGAG;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:105:103,2:114,3:0.386:1,1:32.2:1:31.7:1:1:1.35:60:210:0.3992:0:0.2 0/1:152:36:36,0:94,9:0.2368:2,1:25.6:1:31.7:1:0.11148:0:59.4:72:0.2416:0.0197:0.2 -7 2985391 . C G 76 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.08685;SOR=0;LSEQ=CACACACACACACACACAGA;RSEQ=ACACACACACACACGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:6:5,1:343,78:0.0135:2,2:6.8:1:29.5:1:1:1.14:60:5:0.012:0:1.5 0/0:283:0:0,0:211,59:0:2,0:22.7:1:30.4:1:1:0:59.9:44:1:0:0.4 -7 2985639 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12663;SOR=Inf;LSEQ=GAATACATATCTGATGGAAC;RSEQ=CAAGTCTCTGTGGCTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:30,237:0:2,0:25.5:1:32.1:1:1:0:60:88:1:0:0.1 0/1:148:2:1,1:19,127:0.0135:2,2:9.5:1:25:0:0.2528:6.54:60:4:0.0135:0:1 -7 2985643 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12473;SOR=Inf;LSEQ=ACATATCTGATGGAACGCAA;RSEQ=TCTCTGTGGCTGGTCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:26,224:0:2,0:25.4:1:32.1:1:1:0:60:49:1:0:0.1 0/1:137:2:1,1:16,119:0.0146:2,2:26.5:1:28.5:1:0.23358:7.24:60:4:0.0147:0:1 -7 2985857 . G C 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01818;SOR=Inf;LSEQ=ATTGCCGCCCCAGTTTTGAA;RSEQ=AGTTTCCCAACTGACCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:0:0,0:21.7:1:32:1:1:0:60:18:1:0:0.2 1/1:2:2:1,1:0,0:1:0,2:27.5:1:33:0:1:0:60:4:1:0:1 -7 2987515 . TA T 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.92359;LSEQ=ACCTCTAGAATATATTAAGT;RSEQ=AAAAAAAGTCCTGTACACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:0,3:3,238:0.0123:1,0:28.3:1:31.7:1:1:0:60:6:0.0124:0:0.3 0/1:88:1:0,1:1,86:0.0114:1,0:42:0:28:0:1:0:60:2:0.0114:0:0 -7 2998044 . A G 114 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.30659;LSEQ=CTGCAGTATGTTATGATCAC;RSEQ=TCACTGCACTCCAGCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:1,0:319,49:0.0027:2,0:22:0:26:0:1:0:60:2:0.0027:0:1 0/1:175:15:12,3:137,23:0.0857:2,2:15.3:1:29.3:1:0.47061:1.48534:60:30:0.0877:0:1 -7 3371961 . T G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTAGCAGGGCTCCATCC;RSEQ=TTAATGTCAGTGCCGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:23.3:1:32:0:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 3372172 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11177;SOR=Inf;LSEQ=AAGGCATGATAATGGAGTCT;RSEQ=TTATCTATTTGGAAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:138,86:0:2,0:25.8:1:31.7:1:1:0:60:55:1:0:0.3 0/1:113:2:1,1:67,44:0.0177:2,2:19:1:28.5:1:1:1.51687:60:4:0.018:0:1 -7 3372198 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0981;SOR=Inf;LSEQ=TATTTGGAAAAACAACTTTT;RSEQ=TTGCCATTTATAATAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:153,120:0:2,0:25.3:1:29:1:1:0:60:38:1:0:0.4 0/1:125:2:1,1:63,60:0.016:2,2:19.5:1:29.5:1:1:1.04961:60:4:0.0163:0:2 -7 3372228 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22707;SOR=4.50538;LSEQ=ATAATAAATGTAAATGGCCT;RSEQ=CCATTTATTTTAGAATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:0,1:149,135:0.0035:2,0:1:0:28:0:0.47719:0:60:2:0.0036:0:1 0/1:128:2:1,1:63,62:0.0156:2,2:21.5:1:28.5:1:1:1.016:60:4:0.016:0:2.5 -7 3372238 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10576;SOR=Inf;LSEQ=TAAATGGCCTGCCATTTATT;RSEQ=TAGAATTACTCTGTTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:140,137:0:2,0:25:1:30.1:1:1:0:60:68.25:1:0:0.8 0/1:134:2:1,1:62,70:0.0149:2,2:11.5:1:28.5:1:1:1.13:60:4:0.0153:0:2.5 -7 3372249 . C G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=7e-05;SOR=0.40905;LSEQ=CCATTTATTTTAGAATTACT;RSEQ=TGTTTCTAGGCCCTAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:284:146:70,76:67,71:0.5141:2,2:24.5:1:32.3:1:1:1.02447:60:292:0.5252:0:1.5 0/1:126:38:16,22:39,48:0.3016:2,2:26.1:1:31.1:1:0.84597:1.1162:60:37:0.296:0:1.5 -7 3372308 . G C 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26817;SOR=0.71756;LSEQ=AAAGTTAGTAGAGGCTAGAA;RSEQ=AACTTATAGGAATGTCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:81:25,56:24,64:0.4765:2,2:25.4:1:31.9:1:0.61561:1.19:60:162:0.4821:0:1.7 0/1:76:30:11,19:17,29:0.3947:2,2:25.2:1:31.7:1:1:1.01237:60:29:0.3867:0:1.4 -7 3372409 . T C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.08567;SOR=0.23051;LSEQ=TAGTTCCAGATAACTTCTTT;RSEQ=CCCCCCAGGAATAGATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:0.3913:1,0:23:1:31.8:1:1:0:60:18:0.3913:0:1 0/1:16:2:0,2:1,13:0.125:1,0:21:1:30.5:1:1:0:60:4:0.1333:0:1 -7 3377718 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.49833;SOR=0;LSEQ=CTTAAAAAGTGGGGAAGGGC;RSEQ=TTTTGGCTGGAACCAACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:37,11:0.04:2,2:34.5:1:29.5:1:0.42612:3.26364:60:4:0.0426:0:1 0/0:42:0:0,0:25,17:0:2,0:22.6:1:29.7:1:1:0:60:41:1:0:0.2 -7 3377771 . A G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01308;SOR=Inf;LSEQ=TGCCAAAATGATGAACGACA;RSEQ=AGAGAAAAGGGAGAGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:60,29:0:2,0:22.6:1:30:1:1:0:60:88:1:0:0.2 0/1:47:4:3,1:18,25:0.0851:2,2:28.3:1:30.3:1:0.31124:4.05:60:8:0.0889:0:1 -7 3377822 . T C 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGGCCTTTTAGAAAACA;RSEQ=GGACTTGTTCTTTTGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:93,42:0.0146:2,2:12:1:26.5:1:0.53081:2.20016:60:4:0.0147:0:1 0/0:51:0:0,0:30,21:0:2,0:26.2:1:30.3:1:1:0:60:102:1:0:0.3 -7 3377882 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13165;SOR=Inf;LSEQ=AAAGATGATATTGGAGACAT;RSEQ=AAGGGAATGGGTACTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:169,82:0:2,0:23.4:1:31.1:1:1:0:60:34.857:0.9959:0:0.1 0/1:144:2:2,0:91,51:0.0139:2,0:15.5:1:26:1:0.53934:0:60:4:0.014:0:1 -7 3377886 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12677;SOR=Inf;LSEQ=ATGATATTGGAGACATCAAG;RSEQ=GAATGGGTACTGTTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:183,91:0:2,0:23:1:30.6:1:1:0:60:29.444:1:0:0.1 0/1:152:2:1,1:94,56:0.0132:2,2:33.5:1:30.5:1:1:1.67254:60:4:0.0136:0:1 -7 3377896 . C T 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55891;SOR=3.37526;LSEQ=AGACATCAAGGGAATGGGTA;RSEQ=TGTTCAGAAAGGAAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:1:0,1:194,119:0.0032:2,0:1:0:28:0:0.38217:0:60:2:0.0032:0:1 0/1:187:2:1,1:113,72:0.0107:2,2:13:0:31.5:1:1:1.56549:60:4:0.0109:0:1.5 -7 3378026 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08948;SOR=Inf;LSEQ=TTGCCAAGAGAACTAATGTG;RSEQ=GTGTTGAGCACATTAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:8,115:0:2,0:25.8:1:29.8:1:1:0:60:40:1:0:0 0/1:53:2:0,2:3,48:0.0377:2,0:8:1:28.5:1:1:0:60:4:0.0377:0:1 -7 3378162 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.175;SOR=Inf;LSEQ=GCCAGCCTGTTCCCAGAGAA;RSEQ=CACACTTTGTGAGAAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:28.2:1:32.2:1:1:0:60:18:1:0:0.1 0/1:7:2:1,1:2,3:0.2857:2,2:36:1:30:1:1:1.41:60:4:0.3333:0:1.5 -7 4382226 . G T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCCTCCACCCAGTCTT;RSEQ=AGGACCGAGAGCAACCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 4407814 . A G 47 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02692;SOR=21.88909;LSEQ=CTGCTCCTCCTGGGAGCCAG;RSEQ=AACCCCTCCTGGGAAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:5,6:0.0833:2,0:21:0:32:0:1:0:60:2:0.0833:0:1 1/0:4:3:1,2:0,1:0.75:0,2:12.3:1:30:1:1:0:60:6:0.75:0:1 -7 4798533 . G C 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=AGGCTGGGTTCAGGTTACGG;RSEQ=GGCGTTTCTCACCGTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:0:0,0:221,288:0:2,0:25.8:1:30.6:1:1:0:60:49.9:0.998:0:0.1 0/1:331:11:4,7:137,183:0.0332:2,2:29.2:1:31.2:1:0.76431:1.30906:60:22:0.0335:0:1.2 -7 4798579 . G A 117 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=24.7667;LSEQ=AGGACAGAGACGAGCTCCAG;RSEQ=GAGCGTGGGCGGGTGACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:1:0,1:98,222:0.0031:2,0:47:0:13:0:1:0:60:0:0:0:2 0/1:194:14:4,10:63,117:0.0722:2,2:24.6:1:30.9:1:0.77448:1.34418:60:28:0.0729:0:1.1 -7 4799576 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCTGAGGGAGGAGAAT;RSEQ=GCTTGAAGCCTGGAGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:32:0:1:0:60:4:1:0:1.5 -7 6012930 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55336;SOR=0;LSEQ=GTGATGTGTATTTTTTTTAA;RSEQ=TAGCAGGTTCATTTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:2,1:156,6:0.0182:1,2:23:1:23.3:1:0.12266:12.41086:53.7:2:0.0123:0:2.3 0/0:87:0:0,0:76,11:0:2,0:24.6:1:31.9:1:1:0:41.3:42.5:1:0:0.1 -7 6012958 . G T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55525;SOR=0;LSEQ=TTCATTTTAAAACAAAAAAG;RSEQ=TTAGTGAAGACTCTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:3:2,1:149,30:0.0165:2,2:11.3:1:21.3:1:0.43084:2.46724:43.3:2:0.0112:0:2.3 0/0:102:0:0,0:80,22:0:2,0:30.2:1:30:1:1:0:41:50:1:0:0.1 -7 6012999 . TA T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.53233;SOR=0;LSEQ=CAAAACATAAAAATCTGCGA;RSEQ=AAACCAATTATTCCATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:88,84:0.0115:2,2:11.5:1:27:1:1:1.04736:39:4:0.0115:0.0057:0 0/0:102:0:0,0:50,52:0:2,0:21.2:1:28:1:1:0:40.3:204:1:0:0.3 -7 6013049 . C G 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=9.8856;LSEQ=GTCAGTTCTGAGAAATGACA;RSEQ=CCAGGTTGGCGATGTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:12:0,12:0,106:0.1017:1,0:24.8:1:31.9:1:1:0:39:24:0.1034:0:1 1/0:62:33:0,33:0,29:0.5323:1,1:28.8:1:32:1:1:0:38.8:66:0.541:0:1 -7 6017523 . A G 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77981;SOR=1.16317;LSEQ=CACTTTGGGAGGCTGAGGCC;RSEQ=GCGGATCATGAGGTCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:11:0,11:1,46:0.1897:1,0:25.4:1:29.6:1:1:0:58.4:10:0.1786:0:1.2 0/1:28:6:0,6:0,22:0.2143:1,0:15.5:1:30.2:1:1:0:60:12:0.2143:0:1.3 -7 6017902 . G A 29 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACAAGAATCTATAGTTCT;RSEQ=ATTTTTTTTTTTTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,0:0.4:0,0:28.5:1:29.5:1:1:0:41.5:4:0.4:0:1 1/1:1:1:0,1:0,0:1:0,0:45:0:28:0:1:0:44:2:1:0:4 -7 6018058 . C G 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02398;SOR=Inf;LSEQ=ATTACAGGCACCCGCCACCA;RSEQ=GCCCGGCTACTTTTTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:32,0:0:1,0:21:1:30.3:1:1:0:50.2:9.667:1:0:0 0/1:14:3:3,0:11,0:0.2143:0,0:15.3:1:33.7:1:1:0:27:6:0.2143:0:1 -7 6018101 . C G 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02127;SOR=Inf;LSEQ=CAGTAGAGATGGGGTTTCAC;RSEQ=ATGTTAGCCAGGCTGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:72,0:0:1,0:25.3:1:30.6:1:1:0:46.5:23:1:0:0 0/1:46:4:4,0:42,0:0.087:1,0:25:1:29:1:1:0:43.5:8:0.087:0:1 -7 6018318 . AGT C 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.00047;SOR=Inf;LSEQ=TTAACAGCAGTTAAGTTGAG;RSEQ=CTGAGGTCTGAAAAACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:508:0:0,0:195,311:0:2,0:22.8:1:31:1:1:0:35.7:41.167:0.996:0:0.1 0/1:446:10:2,8:184,250:0.0224:2,2:22.8:1:31.5:1:0.20379:2.93781:36.2:20:0.0228:0.009:0 -7 6018444 . A G 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5854;SOR=2.52847;LSEQ=TCATGTCAAAATAACAACAC;RSEQ=AATAACAACACTACTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:0,1:0,88:0.0111:1,0:46:0:15:0:1:0:60:0:0:0:1 0/1:72:2:0,2:0,70:0.0278:1,0:20.5:1:33:0:1:0:53.5:4:0.0286:0:1 -7 6022626 . C T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08491;SOR=1.85123;LSEQ=CTGCAAACATCGTTTTACTG;RSEQ=AGGTAGAAAATGTTAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:20:7,13:61,52:0.1504:2,2:19.9:1:26.3:1:0.14765:2.16595:39.5:5.667:0.136:0:1 0/1:93:23:11,12:40,30:0.2473:2,2:22.3:1:26.8:1:0.47617:1.44861:39.6:22:0.2391:0:1.1 -7 6022629 . G A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89891;LSEQ=CAAACATCGTTTTACTGCAG;RSEQ=TAGAAAATGTTAATTATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:14:9,5:55,61:0.1077:2,2:25.5:1:30.2:1:0.26869:1.99:39.2:28:0.1094:0:1 0/1:92:9:6,3:42,41:0.0978:2,2:21.1:1:27.9:1:0.4892:1.94:39.6:18:0.1011:0:1 -7 6022673 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.18716;SOR=Inf;LSEQ=TTTTACAAGATTATTTTTCT;RSEQ=ATTATGTTATAGAACACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:18,102:0:2,0:30.3:1:29.9:1:1:0:43.7:19:1:0:0.2 0/1:92:2:1,1:18,72:0.0217:2,2:32.5:1:27.5:1:0.37219:3.92:42.5:4:0.023:0:1 -7 6022712 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.12991;SOR=Inf;LSEQ=GTAATAAAAAAAAAGTCAAA;RSEQ=AATACAAAAACAAAATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:3,115:0:1,0:24.5:1:32.2:1:1:0:46.4:38.333:1:0:0.2 0/1:67:2:0,2:1,64:0.0299:1,0:19:1:28.5:1:1:0:48:4:0.0299:0:1.5 -7 6022752 . CT C 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54688;SOR=1.71796;LSEQ=GTCCCTAGCCATCCCGCTTT;RSEQ=TTTTTTTTGAAACAGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:0,2:1,51:0.037:1,0:25.5:1:31.5:1:1:0:39:4:0.0377:0:0 0/1:16:1:0,1:1,14:0.0625:1,0:20:0:27:0:1:0:27:2:0.0625:0:0 -7 6026222 . C CTGA 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.06388;SOR=Inf;LSEQ=AATCCCAGCTACTCAGGAGG;RSEQ=TGAGGCAGGAGAAACGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:0:1,0:30.7:1:32.2:1:1:0:57.9:62:1:0:0 0/1:11:2:2,0:9,0:0.1818:0,0:20.5:1:31.8:1:1:0:60:4:0.1818:0.0909:1 -7 6026384 . C T 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAAAGTAAAAAATTAAAA;RSEQ=TTTACCTTATCTCTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:0:0,0:586,194:0:2,0:26.2:1:31.9:1:1:0:56.3:69.909:1:0:0.1 0/1:520:56:37,19:313,151:0.1077:2,2:25.2:1:29.5:1:0.88039:1.06431:56.1:112:0.1085:0:1.1 -7 6026530 . C T 183 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTCGTTTAGCTAAAGAACT;RSEQ=ATAGAAAAGTCCAGGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1618:85:37,48:752,779:0.0525:2,2:23.6:1:28.7:1:0.37263:1.25216:59.3:84:0.0526:0:1 0/0:1097:0:0,0:536,561:0:2,0:24.9:1:31.3:1:1:0:59.7:83.385:1:0:0.1 -7 6026775 . T C 316 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05795;LSEQ=TGAAAAAGAGTCGTCAGTTT;RSEQ=AGGCGCTTTCTCCTGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1095:1087:507,580:1,1:0.9927:2,2:23.3:1:31.4:1:1:1.14384:48.6:66.938:0.9954:0:1.1 1/1:718:637:286,351:37,43:0.8872:2,2:22.4:1:31.3:1:0.90519:1.05592:48.4:126.4:0.8876:0:1.1 -7 6026942 . G T 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCCACCTCCGCTCTGTCC;RSEQ=TAGGGTCACTGGGTCCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:976:0:0,0:523,451:0:2,0:24.7:1:30.5:1:1:0:55.3:50.263:0.9979:0:0.5 0/1:656:53:27,26:329,272:0.0808:2,2:25.9:1:29.4:1:0.66656:1.16448:56:25.5:0.0787:0:1.1 -7 6026958 . C T 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCGTAGGGTCACTGGGTC;RSEQ=GTGACTGGAACTCACTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1013:0:0,0:537,475:0:2,0:25.3:1:30.3:1:1:0:56.7:55.222:0.999:0:0.6 0/1:664:65:42,23:312,286:0.0979:2,2:26.8:1:30.3:1:0.06656:1.67:56.1:130:0.0988:0:1.1 -7 6026988 . G A 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38571;LSEQ=ACTCACTGCCTCTTTCTGAG;RSEQ=TCTCAGGACGCCTTTGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1043:715:379,336:178,148:0.6855:2,2:25.1:1:30.3:1:0.63972:1.06615:57.7:43.688:0.686:0:1.1 0/1:703:321:164,157:199,181:0.4566:2,2:25.2:1:29.4:1:0.76179:1.05241:58.1:106:0.4562:0:1.1 -7 6027308 . C T 64 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01917;SOR=10.03405;LSEQ=ATCCTGAAATGGTGAGAGGA;RSEQ=GTGCTTATGTGAACAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:1:0,1:11,133:0.0069:2,0:12:0:25:0:1:0:27:2:0.007:0:1 0/1:76:5:2,3:5,66:0.0658:2,2:9.2:1:27.8:1:0.06413:8.32:27:10:0.0658:0:1 -7 6029348 . C CA 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.61676;SOR=1.83424;LSEQ=AAGAGACTTTGTTTTCATGT;RSEQ=AAAAAAAAGTTTACTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:2,0:180,13:0.0103:2,0:22.5:1:31.5:1:1:0:60:4:0.0104:0:0 0/1:107:2:2,0:92,13:0.0187:2,0:35.5:1:31:1:1:0:60:4:0.0189:0:3.5 -7 6029690 . G GT 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=0.17661;LSEQ=ACTCTGTCGCCTAGGCTGGA;RSEQ=TGCAGTGGCGCGATCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:81:42:1,41:0,39:0.5185:1,1:22.4:1:31:1:1:0:59.7:84:0.5185:0.1358:0.3 0/1:38:6:0,6:1,31:0.1579:1,0:17.2:1:31.4:1:1:0:60:12:0.1579:0.0263:0.2 -7 6029748 . C T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30466;SOR=0.40508;LSEQ=TCCTGGGTTCAAGTGATTCT;RSEQ=CCTGCCTCAGCCTCCGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:1,22:0,16:0.5897:1,1:25.8:1:29.7:1:1:0:60:22:0.5789:0:1.1 0/1:11:4:0,4:1,6:0.3636:2,0:21:1:30.3:1:1:0:60:8:0.3636:0:1.3 -7 6031101 . TA T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTCCCTTGGTTGACAT;RSEQ=AAAAAAATTACATTTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:33.5:1:30.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6031469 . C CA 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.65105;SOR=1.46192;LSEQ=GACAGAGCAAGACCCCGTCT;RSEQ=AAAAAAAAACAAAAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:3,0:141,4:0.0203:1,0:13.7:1:31:1:1:0:60:6:0.0204:0.0068:0 0/1:68:2:2,0:65,1:0.0294:1,0:11:1:26.4:1:1:0:60:4:0.0299:0.0147:0.5 -7 6031479 . CAAAAAC AAAA 73 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.00319;SOR=Inf;LSEQ=GACCCCGTCTCAAAAAAAAA;RSEQ=AAAAAACTTACATGACCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:188,4:0:1,0:20:1:30.8:1:1:0:60:95:1:0:0.1 0/1:91:5:5,0:84,1:0.0549:1,0:8.8:1:31.5:1:1:0:33:10:0.0568:0.044:2 -7 6031744 . G A 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.67448;SOR=1.72683;LSEQ=ACAAATGTTCCCAGCCCCCC;RSEQ=CATTCTAACAACATTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:3:1,2:78,338:0.0071:2,2:16.3:1:16.7:1:0.46658:2.16:60:0.5:0.0025:0:4 0/1:246:3:1,2:50,191:0.0122:2,2:11.3:1:27.7:1:0.50673:1.90:60:6:0.013:0:2 -7 6031956 . TC T 32 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=20.000;MSILEN=1;SSF=1;SOR=1.22183;LSEQ=TTACAGGCAGGATTTTTTTT;RSEQ=TTTTTTTTTTTCAACGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,4:0.2857:0,0:27.5:1:32:0:1:0:56:4:0.3333:0:2 0/1:3:1:1,0:0,0:0.3333:0,0:15:0:32:0:1:0:60:2:0.3333:0:0 -7 6034818 . AA GC 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGGGATTACAGGCGTGG;RSEQ=CACCATGCCTGGTTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:18.7:1:31.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6035065 . A C 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTAAAGCCATGTTTCTCA;RSEQ=AGTCCCGAGCTCCACGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:194,3:0:1,0:25.2:1:30.6:1:1:0:60:394:1:0:0.1 0/1:78:13:13,0:65,0:0.1667:1,1:28.5:1:32.2:1:1:0:60:26:0.1667:0:2 -7 6035081 . G A 128 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAAAGTCCCGAGCTCCAC;RSEQ=TAAACTGCCTATTATCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:240,4:0:1,0:26:1:30:1:1:0:60:60:1:0:0.1 0/1:124:18:18,0:106,0:0.1452:1,1:27.8:1:30.8:1:1:0:60:36:0.1463:0:1.7 -7 6035373 . T C 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01254;SOR=Inf;LSEQ=AAACAAAACACCAGGTGACA;RSEQ=GCTGATAAGGATCACTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:4,164:0:1,0:25.6:1:30.3:1:1:0:60:83:1:0:0.3 0/1:86:4:0,4:4,77:0.0465:1,0:32:1:26:1:1:0:60:8:0.0471:0:1 -7 6035428 . A C 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.61166;SOR=0.72734;LSEQ=CTGTGCTCCAAATCTTGATG;RSEQ=GTCATCAAAGAACCAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:46:1,45:0,20:0.697:1,1:24.8:1:29.8:1:1:0:60:45:0.6923:0:1.1 1/0:24:15:1,14:0,9:0.625:0,1:20.6:1:29.9:1:1:0:60:30:0.625:0:1.1 -7 6035944 . A G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGTAATTCCAGAGCCTTG;RSEQ=GAGGCCAAGGTGGGTGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:20.7:1:31.3:1:1:0:53.3:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6036802 . A G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07753;SOR=3.30404;LSEQ=TTGCAGTGAGCCAAGATAGC;RSEQ=CCATTGCACTCCAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:5:5,0:67,0:0.0694:1,0:16:1:30:1:1:0:60:10:0.0704:0:1.8 0/1:30:6:6,0:24,0:0.2:1,0:17.8:1:28.8:1:1:0:60:12:0.2:0:1.7 -7 6036895 . TA T 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.34884;SOR=1.6055;LSEQ=AGCCTTAGAATCACTATCTT;RSEQ=AAAAAAAAGCTCTCAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:9:7,2:363,77:0.02:2,2:34:1:29.7:1:0.66176:1.34596:60:8:0.0184:0.0022:0.2 0/1:315:10:7,3:232,73:0.0317:2,2:28:1:28.7:1:0.70865:1.3606:60:20:0.0331:0.0063:0.3 -7 6036980 . G C 300 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00047;SOR=0.56609;LSEQ=AAAAGATTATGCAGAGCATC;RSEQ=GAACAGCTCAAACCGTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1149:1075:563,512:40,32:0.9356:2,2:25.2:1:29.8:1:0.62753:1.13664:60:37.393:0.9357:0:1.1 1/1:876:781:409,372:49,41:0.8916:2,2:25.5:1:29.6:1:0.73899:1.08688:60:77.1:0.8924:0:1.2 -7 6037075 . T A 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95;LSEQ=CTGAAAAAAAAAAAAAAAAA;RSEQ=TCACAGTTACTTCCTAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:566:6:1,5:116,443:0.0106:2,2:7.5:1:29:1:1:1.30867:60:12:0.0113:0:2.5 0/1:397:4:3,1:98,294:0.0101:2,2:6.3:1:29:1:0.05276:8.94:60:8:0.0106:0:1.8 -7 6037153 . CA C 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.55352;SOR=0;LSEQ=AGCTATTGACATTACAAGCG;RSEQ=AAAAAAATTAAAAGAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:0,3:0,132:0.0222:1,0:48.3:1:33.3:1:1:0:60:6:0.0224:0:0 0/0:61:0:0,0:2,58:0:1,0:22.3:1:30:1:1:0:60:29:1:0:0.1 -7 6037232 . A G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29187;SOR=3.2706;LSEQ=ATTGCCCAGGCTGGAGTACA;RSEQ=TGGCTCAATCATACCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:0.125:1,0:13.5:1:33.5:1:1:0:60:4:0.125:0:1.5 0/1:6:2:0,2:0,4:0.3333:0,0:10:1:32.5:1:1:0:60:4:0.3333:0:1 -7 6038324 . CAA C 32 d7;v4;pSTD;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=14.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=AACAGAGCAAGACTCCAGCT;RSEQ=AAAAAAAAAAAACCGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:10.8:1:29.4:1:1:0:60:10:1:0:0 1/1:2:2:1,1:0,0:1:0,2:30:0:32:0:1:0:60:4:1:0:0.5 -7 6038620 . CA C 196 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.58987;SOR=1.16599;LSEQ=AGCAGTGCGAGACTCCCTCT;RSEQ=AAAAAAAAAAAAAAATCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:76:73,3:79,2:0.4:1,1:23.1:1:31.4:1:0.67378:1.61832:59.2:75:0.4032:0.0895:0.5 0/1:80:35:34,1:28,0:0.4375:1,1:22.5:1:30.8:1:1:0:59.2:70:0.443:0.1125:0.8 -7 6038703 . G A 128 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.47311;LSEQ=AACCCGCTATAATCACTAGA;RSEQ=CAATAAGAGGCGTTGAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:947:2:2,0:626,314:0.0021:2,0:3.5:1:20:1:0.55508:0:60:1:0.0011:0:1.5 0/1:637:24:14,10:374,237:0.0377:2,2:26.4:1:28:1:0.83223:1.12697:60:23:0.0373:0:1.2 -7 6038722 . T C 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.34753;LSEQ=AGCAATAAGAGGCGTTGAAG;RSEQ=AACCGGCCATCACTACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1191:792:487,305:232,167:0.665:2,2:26.1:1:32:1:0.28607:1.15:60:78.2:0.6638:0:1.1 0/1:816:333:192,141:279,204:0.4081:2,2:25.8:1:31.6:1:1:1.00436:60:46.571:0.4055:0:1.2 -7 6038919 . C A 46 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00971;SOR=Inf;LSEQ=GCATACTCCTGTTTAAAAAA;RSEQ=ACAAACACAATATTCTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:748:0:0,0:245,503:0:2,0:25.4:1:32:1:1:0:60:92.5:1:0:0.1 0/1:492:5:4,1:180,307:0.0102:2,2:12.2:1:20.2:1:0.06754:6.80:60:1.5:0.0061:0:2 -7 6039129 . T C 91 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCACTTCCCAATGTGCCA;RSEQ=GCATCCTGGTAAAACAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:0.4:0,0:20.4:1:30.5:1:1:0:60:16:0.4444:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6041836 . T A 45 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGCCCAGTAAATTTTTTTT;RSEQ=AAAATTTTTCATAGAGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:30:1:28.7:1:1:0:60:6:0.6:0:2 1/1:1:1:1,0:0,0:1:0,0:19:0:29:0:1:0:60:2:1:0:2 -7 6042522 . C T 82 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.64552;LSEQ=TCGTTTTTCAGGTTGAACTG;RSEQ=AAAACCATAAATGATCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:0.6154:0,0:10.3:1:27.6:1:1:0:57.1:7:0.5833:0:1.1 1/0:2:1:0,1:0,1:0.5:0,0:34:0:29:0:1:0:60:2:0.5:0:1 -7 6043112 . C T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01048;SOR=0.14057;LSEQ=GTTTTAATAAGGGTAACCAT;RSEQ=TTTTTAACAATACTATTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:28:27,1:10,0:0.7368:0,1:26:1:31.5:1:1:0:57.8:56:0.7568:0:1 0/1:11:3:2,1:8,0:0.2727:0,2:29.3:1:30.3:1:0.27273:0:55.7:6:0.2727:0:1 -7 6043386 . G A 154 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.12784;LSEQ=GTTTCAACCTGAGTTAGGTC;RSEQ=GCAAACTCTTGAATCTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1366:4:3,1:586,774:0.0029:2,2:13:1:26.8:1:0.32131:3.96:54.3:8:0.003:0:1 0/1:942:35:16,19:395,512:0.0372:2,2:22.9:1:30.1:1:0.86277:1.09:53.5:70:0.0375:0:1.2 -7 6043797 . C G 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAAGAGTCATAACTATAC;RSEQ=TTTAGTTAAACATACTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:8,203:0:1,0:24.8:1:32.4:1:1:0:60:210:1:0:0.1 0/1:92:17:3,14:4,71:0.1848:2,2:25.2:1:30.7:1:0.11476:3.73:60:34:0.1889:0:1 -7 6043964 . CTG C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAAGGAACAAAAAAAAT;RSEQ=TAACTGGTGGTGATCAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:2,18:0.0909:2,0:23.5:1:32:1:1:0:60:4:0.0952:0.0455:0 0/0:1:0:0,0:0,1:0:0,0:13:0:32:0:1:0:60:2:1:0:0 -7 6044650 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTCAAGCAATTCTCCTCC;RSEQ=TCAGCGTCCTGAGGAGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45.5:1:31.5:1:1:0:60:4:1:0:1 -7 6045385 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00027;SOR=0.34163;LSEQ=GCTAAGTACTAGGCACATAA;RSEQ=AGGTGCTAACTTCAACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:125:87:79,8:34,2:0.696:2,2:25.1:1:32.3:1:0.72189:1.71469:55.2:86:0.7107:0:1 0/1:80:35:33,2:42,3:0.4375:2,2:21.1:1:31.9:1:1:1.18:55.3:70:0.4375:0:1 -7 6045627 . C T 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06896;SOR=0.75718;LSEQ=AAATCTGATGGACTGACTTC;RSEQ=GATCAATAGGTTTGATGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:989:157:49,108:245,587:0.1587:2,2:24.3:1:30.2:1:0.70343:1.09:58.3:156:0.1593:0:1.1 0/1:616:77:30,47:171,366:0.125:2,2:24.2:1:30.1:1:0.2425:1.37:58.4:76:0.1248:0:1.2 -7 6048359 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATGGGATGTGGGCAAGG;RSEQ=CTGTCTGGGACAGGCCGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:4,0:21,0:0.16:1,0:12.3:1:30:1:1:0:60:8:0.1667:0:1.5 0/0:5:0:0,0:5,0:0:0,0:15.8:1:32.8:1:1:0:59.8:10:1:0:0.4 -7 6048510 . G T 49 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17444;SOR=0;LSEQ=GCCACTCCGGGGCCTCCAGG;RSEQ=GGCTGCCTCGCCACGCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:5:3,2:235,43:0.0176:2,2:13:1:21.2:1:0.18038:3.61968:60:1.5:0.0109:0:2.8 0/0:142:0:0,0:113,29:0:2,0:22.7:1:30.5:1:1:0:60:70:1:0:0.3 -7 6048556 . G A 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00187;SOR=1.7296;LSEQ=ATGTTCCCCCCATTTCCAGG;RSEQ=AGGTTGGAATGCCGTGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:75:48,27:341,183:0.1252:2,2:24.3:1:29.3:1:0.89724:1.04806:60:24:0.1239:0:1.2 0/1:408:81:59,22:216,111:0.1985:2,2:24.8:1:29.1:1:0.28981:1.38:60:80:0.2005:0:1.2 -7 6048804 . G C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00589;SOR=Inf;LSEQ=ACTTCCCGTCTCTCCTTTTC;RSEQ=CCTATTGGCTCTGTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:2,135:0:1,0:23.2:1:32.2:1:1:0:60:67.5:1:0:0.1 0/1:54:4:0,4:1,49:0.0741:1,0:20.5:1:32:1:1:0:60:8:0.0755:0:1 -7 6048845 . A G 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01559;SOR=Inf;LSEQ=TCGACTTCGTGACGTCAAAG;RSEQ=GCCTGGGCCAATCAGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:2,58:0:1,0:24.6:1:30.6:1:1:0:60:14:1:0:0.1 0/1:21:3:0,3:0,18:0.1429:1,0:30.7:1:32:0:1:0:60:6:0.1429:0:1.3 -7 6048973 . C A 46 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCTTTGGCACGCGCTAC;RSEQ=CCCTTTTGCTTTGGTTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:22.7:1:29.3:1:1:0:60:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6348257 . A G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03931;SOR=0.1351;LSEQ=GTTAGAGCCTCTGGGAACCC;RSEQ=TACAATAGAATATTAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:6,5:1,3:0.7333:2,2:26.3:1:30.3:1:0.56923:3.31:60:22:0.7333:0:1 0/1:8:2:0,2:4,2:0.25:2,0:24.5:1:30:1:0.42857:0:60:4:0.25:0:1 -7 6348344 . G T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02158;SOR=Inf;LSEQ=TTTCTCCAAATTCCTTTTCA;RSEQ=GAAACTTTTGTTCACATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:32.8:1:31.2:1:1:0:60:40:1:0:0.1 0/1:14:4:2,2:4,6:0.2857:2,2:24.3:1:30.3:1:1:1.46:60:8:0.2857:0:1.5 -7 6414333 . TGCC T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.16564;SOR=1.79941;LSEQ=CGCTTCCTATCTCAGCGCCC;RSEQ=GCCGCCGCCGCGGCCCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:11:5,6:170,98:0.0391:2,2:19.1:1:30.6:1:0.33968:2.07591:56.2:22:0.0406:0.0142:0.4 0/1:234:16:9,7:135,82:0.0684:2,2:18.3:1:31:1:0.79057:1.27908:57.5:32:0.0699:0.0214:0.3 -7 6414344 . C T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.18145;SOR=4.88102;LSEQ=TCAGCGCCCTGCCGCCGCCG;RSEQ=CGCGGCCCAGCGAGCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:1:0,1:230,148:0.0026:2,0:1:0:29:0:0.39314:0:54:2:0.0027:0:1 0/1:314:4:1,3:183,127:0.0127:2,2:5:1:28.3:1:0.31057:4.30346:57.8:8:0.013:0:1.3 -7 6414355 . C T 63 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.73964;SOR=1.47232;LSEQ=CCGCCGCCGCCGCGGCCCAG;RSEQ=GAGCGGCCCTGATGCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:4:1,3:276,193:0.0085:2,2:11.3:1:25.8:1:0.31175:4.27748:59.5:8:0.0085:0:1.8 0/1:403:5:1,4:224,172:0.0124:2,2:15:1:27.2:1:0.17344:5.19048:60:10:0.0126:0:1.2 -7 6414424 . G A 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25955;SOR=2.9156;LSEQ=GAGTGCGCGGCCGGGGCCGG;RSEQ=CTGGAGGCCGCGGGATCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:581:2:2,0:256,322:0.0034:2,0:1:0:24.5:1:0.19745:0:60:4:0.0035:0:1 0/1:501:5:4,1:223,273:0.01:2,2:14.2:1:27.2:1:0.18125:4.88:60:10:0.0102:0:1 -7 6414442 . G A 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.37883;SOR=0.28402;LSEQ=GGGCTGGAGGCCGCGGGATC;RSEQ=GGCGCGGAGGGGGGTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:4:3,1:148,232:0.0104:2,2:15.8:1:30.3:1:0.30445:4.68:60:8:0.0105:0:1 0/0:336:1:1,0:139,196:0.003:2,0:1:0:25:0:0.41667:0:60:2:0.003:0:1 -7 6414450 . AG A 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.05191;SOR=Inf;LSEQ=GGCCGCGGGATCGGGCGCGG;RSEQ=GGGGGTTGGGCCCGGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:103,190:0:2,0:20:1:31.6:1:1:0:60:292:0.9966:0:0.2 0/1:270:4:2,2:106,160:0.0148:2,2:18.3:1:30.5:1:1:1.51:60:8:0.0152:0.0037:0.3 -7 6414482 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14791;SOR=Inf;LSEQ=CCCGGACTGGGGCCCAGGCA;RSEQ=GCCGGCGTCCGCCGCGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:12,48:0:2,0:10.6:1:31.9:1:1:0:60:120:1:0:0.2 0/1:38:2:1,1:5,31:0.0526:2,2:6.5:1:28:1:0.29445:5.75:60:4:0.0541:0:2 -7 6415128 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTCAGCCTCCAAAAGCGCTG;RSEQ=GGTGACACCGCGCCCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:24:0:33:0:1:0:60:2:1:0:0 -7 6415498 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTCCCATAGAAACAAGA;RSEQ=TCTCAGTGTAACCCGAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:49:0:32:1:1:0:60:4:1:0:1 -7 6426318 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCTACTTGGGAGGCTGA;RSEQ=GCAGGAGAATCGCTTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:26:1:31.5:1:1:0:48.5:4:0.6667:0:1 0/0:1:0:0,0:1,0:0:0,0:30:0:32:0:1:0:60:2:1:0:3 -7 6426419 . CA C 62 d7;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GACAGCACGAGACTCGGTCT;RSEQ=AAAAAAAAAAAAAAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:17.5:1:31.3:1:1:0:51:8:0.8:0.2:3 0/0:1:0:0,0:0,1:0:0,0:43:0:29:0:1:0:60:2:1:0:1 -7 6426892 . C T 167 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTTACACAACCAATGCATTT;RSEQ=CTGGAGAATATATCCCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1095:51:20,31:474,569:0.0466:2,2:24.6:1:29.6:1:0.47157:1.29091:59.9:24.5:0.0456:0:1.1 0/0:759:0:0,0:373,385:0:2,0:24:0:15:0:1:0:60:0:0:0:1 -7 6426908 . C G 189 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTTCCTGGAGAATATATCC;RSEQ=TACTGTGTAAGTATCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:983:73:30,43:375,534:0.0743:2,2:26.3:1:30.6:1:1:1.00655:60:72:0.0744:0:2 0/0:712:0:0,0:320,391:0:2,0:25.2:1:30.8:1:1:0:59.6:70.1:1:0:0.5 -7 6426941 . C T 267 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43036;LSEQ=ATCTTAAATTGGGAATTAAC;RSEQ=TGTTTGTGTTACGGGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:641:465:126,339:53,123:0.7254:2,2:23.9:1:30.2:1:0.48998:1.15903:60:76.5:0.7263:0:1.8 1/0:502:267:100,167:88,147:0.5319:2,2:23.6:1:29.7:1:1:1.00:60:43.5:0.5273:0:1.3 -7 6426954 . G A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14287;LSEQ=AATTAACCTGTTTGTGTTAC;RSEQ=GGTTTCACATTTCTTTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:522:306:75,231:54,161:0.5862:2,2:24.7:1:30.9:1:0.91799:1.033:60:305:0.5899:0:2.1 0/1:375:63:19,44:107,204:0.168:2,2:26.2:1:30.8:1:0.56125:1.21402:60:126:0.1698:0:1.9 -7 6429994 . A G 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAATTCCAGCACTTTGGG;RSEQ=AGCTGAGGTGGGCGCATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:0:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6431256 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTACCCTTATTTCTTCTGG;RSEQ=GATAAAAGTCTTAAACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:12.5:1:30.5:1:1:0:60:4:0.2857:0:1.5 0/0:1:0:0,0:1,0:0:0,0:34:0:33:0:1:0:60:2:1:0:0 -7 6431404 . G T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=0.22913;LSEQ=CCGCAAGTTTTGCCCGTGCC;RSEQ=CCTTCCTCCTTGTGCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:64:63,1:20,0:0.7619:1,1:22.5:1:31:1:1:0:60:63:0.759:0:1.3 0/1:50:21:20,1:29,0:0.42:1,1:20.7:1:31.3:1:0.42:0:60:42:0.4375:0:1.1 -7 6431420 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37466;SOR=2.44517;LSEQ=TGCCGCCTTCCTCCTTGTGC;RSEQ=TGCAGGGACATTTGCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:2,0:99,1:0.0196:1,0:20.5:1:18.5:1:1:0:60:1:0.0102:0:2 0/1:64:3:3,0:60,1:0.0469:1,0:23.7:1:26.7:1:1:0:60:2:0.0323:0:1.3 -7 6431457 . C G 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.16965;LSEQ=GGTGTGGCAGCCTCCAGGCC;RSEQ=GTCCCCAGCCTTTTTCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:35:33,2:160,10:0.1707:2,2:19.9:1:29.6:1:1:1.03:60:70:0.1716:0:1.4 0/1:119:4:4,0:105,10:0.0336:2,0:27.3:1:31.8:1:1:0:60:8:0.0339:0:1.5 -7 6431477 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12108;SOR=Inf;LSEQ=CGTCCCCAGCCTTTTTCTTG;RSEQ=CACACCTTCTCTAGGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:277,35:0:2,0:23:1:31.1:1:1:0:60:30.2:1:0:0.3 0/1:167:2:1,1:135,29:0.012:2,2:24.5:1:27:1:0.32968:4.59387:60:4:0.0124:0:1 -7 6431523 . C CT 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CAGTGACTTAGCTTCTACAC;RSEQ=TGTGACTAACCATTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:23:15,8:455,199:0.034:2,2:25.1:1:29.9:1:0.6498:1.21903:60:22:0.0329:0.0103:0.2 0/0:452:0:0,0:289,163:0:2,0:23.7:1:30.3:1:1:0:60:36.667:1:0:0.2 -7 6431690 . C T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.24539;LSEQ=ACAGTAAGGATTGCAGCTGA;RSEQ=TTTTAATGTGTCTTTTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:825:607:198,409:68,148:0.7358:2,2:24.1:1:30.2:1:0.79966:1.05:60:66.444:0.7337:0:1.1 0/1:567:230:87,143:124,213:0.4056:2,2:24.5:1:29.7:1:0.85959:1.04:60:75.667:0.4046:0:1.1 -7 6431759 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13746;SOR=Inf;LSEQ=CATGTTACCTATGGACTTGC;RSEQ=TATATTGCCATCATTTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:6,207:0:1,0:25.5:1:30.3:1:1:0:60:105.5:1:0:0.5 0/1:126:2:1,1:9,115:0.0159:2,2:13.5:1:29:1:0.15302:12.17:60:4:0.016:0:1 -7 6431933 . C G 93 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59764;LSEQ=AGAATAACCGTATGAAAGAG;RSEQ=TACTTTTTGTTTTTGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:0,7:0,4:0.6364:0,0:17.4:1:33.4:1:1:0:60:14:0.6364:0:1 1/0:2:1:0,1:0,1:0.5:0,0:38:0:32:0:1:0:60:2:0.5:0:1 -7 6432217 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCAGAAAAAAAAGTTTA;RSEQ=TTTTGCTTCTGTATCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:15:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6433607 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAGAACTGGATCTGGTA;RSEQ=TAACATGCTGGCACCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33:1:29:1:1:0:60:4:1:0:1 -7 6437843 . T TTGTC 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGTTCTGGGAGAGCCCT;RSEQ=TGGCAGGCATCATTTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:16:1:30.5:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6438217 . A G 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAAAATTCTAATAAAGA;RSEQ=TCGATAAGAGGTTATATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:482:0:0,0:407,75:0:2,0:23.5:1:29.9:1:1:0:60:47.2:1:0:0.1 0/1:284:26:19,7:207,51:0.0915:2,2:17.5:1:30.5:1:0.44281:1.49303:60:52:0.0925:0:1.1 -7 6438388 . C T 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00013;SOR=0;LSEQ=CCACTTCAGTTTCAAGCTTT;RSEQ=TCTGTTCTCTCATTTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:18:6,12:278,591:0.0202:2,2:26.9:1:30.7:1:1:1.06:60:36:0.0205:0:1 0/0:581:0:0,0:212,368:0:2,0:25.3:1:31.3:1:1:0:60:115:0.9983:0:0.1 -7 6439448 . A T 114 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTTATACTTGATTTTTTC;RSEQ=TTTTAGATAGTTAGGCGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:13,0:5,0:0.7222:0,1:20:1:31:1:1:0:60:26:0.7222:0:1 1/1:1:1:0,1:0,0:1:0,0:46:0:32:0:1:0:60:2:1:0:1 -7 6439945 . A G 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05822;SOR=0.52183;LSEQ=TTTTAGCAATTTGCTACTTA;RSEQ=GTACATGATTGGGTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:96:0,96:0,41:0.7007:1,1:23.7:1:29.6:1:1:0:60:8.6:0.6935:0:1.3 1/0:51:28:0,28:0,23:0.549:1,1:21.7:1:30:1:1:0:60:27:0.5625:0:1 -7 6439958 . G GT 113 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.04726;LSEQ=CTACTTAAGTACATGATTGG;RSEQ=TTTTTTTTTTTCTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:14:0,14:0,85:0.1373:1,1:18.4:1:29.7:1:1:0:60:28:0.1429:0.049:0.9 0/1:35:5:0,5:0,30:0.1429:1,0:24.2:1:27.9:1:1:0:60:10:0.1515:0.0571:1 -7 6439994 . G T 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0479;SOR=Inf;LSEQ=TGAGACGGAGGTCTCACTCT;RSEQ=TTGTGTCCAGGCTGGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:0:1,0:25.5:1:32:1:1:0:60:40:1:0:0.7 0/1:12:2:0,2:0,10:0.1667:0,0:11:1:30.5:1:1:0:60:4:0.1818:0:3 -7 6441229 . T TC 111 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTTTGTTTCTCTTCCCT;RSEQ=CCCCCCTTCCCCTGCGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:12,0:7,0:0.6316:0,0:31:1:31.1:1:1:0:60:24:0.6316:0:0.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6441688 . T C 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGTGTTTTTCCTCCTCCT;RSEQ=GTACCTCTTTTATTGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:0:0,0:110,374:0:2,0:23.3:1:30.4:1:1:0:60:79.667:1:0:0.1 0/1:326:21:7,14:84,220:0.0644:2,2:25.4:1:29.5:1:0.61701:1.31:60:20:0.0621:0:1.2 -7 6441799 . G C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00123;SOR=0.3317;LSEQ=GAACCAGCTGGCAAGGCCCT;RSEQ=TGGGTCTTAACGTCAGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:85:45,40:19,16:0.7083:2,2:24.8:1:32.3:1:1:1.05511:60:170:0.7143:0:1.1 0/1:54:24:13,11:13,17:0.4444:2,2:16.4:1:31.8:1:0.5843:1.53:60:48:0.4444:0:1.1 -7 6441887 . G T 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02422;SOR=Inf;LSEQ=AGGAGCTGCCTCCCGCTGGT;RSEQ=GTGTGATCAGAAGAGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:265,98:0:2,0:22:1:31.6:1:1:0:60:89.75:1:0:0.2 0/1:238:4:1,3:171,63:0.0168:2,2:11.3:1:28:1:0.06591:8.05917:60:8:0.0171:0:1 -7 6441993 . C G 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCGCTCACACAGCGAGGCCT;RSEQ=AAGACAGTGTTTGACGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:897:23:12,11:426,447:0.0256:2,2:27.1:1:31:1:0.834:1.14:57.6:22:0.0252:0:1.2 0/0:731:0:0,0:364,365:0:2,0:24.9:1:30.9:1:1:0:56.9:51.071:0.9986:0:0.2 -7 6442143 . C A 160 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.01422;SOR=0.40074;LSEQ=ACGCTTTGCTCAAAAAAAAA;RSEQ=AAAAAAAAAAAACAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:52:8,44:8,25:0.5417:2,2:13.3:1:28.2:1:0.39535:1.74795:46:12:0.6667:0:2.3 0/1:50:16:2,14:8,25:0.32:2,2:25.4:1:23.1:1:0.46359:2.20664:52.8:2.2:0.2973:0:2.9 -7 6442156 . C A 168 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAAAAACAAAAAAAAAAAA;RSEQ=AAAAAAAAAAAACAACGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:53:6,47:3,33:0.5761:2,2:18.7:1:29.4:1:0.73406:1.40:47.3:52:0.6118:0:2.5 0/0:41:0:0,0:1,22:0:1,0:24.5:1:27.7:1:1:0:57.1:4.75:0.8636:0:1 -7 6442371 . G A 56 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAAGCGCCCCCCCCATTCTT;RSEQ=TTCAGATTAAGAGTTGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:18.3:1:28.3:1:1:0:60:8:0.8:0:1.3 0/0:1:0:0,0:0,1:0:0,0:17:0:33:0:1:0:60:2:1:0:0 -7 6661256 . C G 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58252;SOR=2.52477;LSEQ=AGCAACAGCAGGAACAGTTA;RSEQ=AGCAGCAGCAGCTGCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:17,10:0.0357:2,0:16:0:33:0:0.39286:0:60:2:0.0357:0:1 0/1:23:2:1,1:11,10:0.087:2,2:38:1:29.5:1:1:1.09544:60:4:0.087:0:1 -7 6661979 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGGTGCTGCCCGCCGTG;RSEQ=CAGCGCCGGCCGTGGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6669111 . A T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGTGATCCGCCTGCTTC;RSEQ=GCCTCCCAAAGTACTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29:1:1:0:52:4:1:0:2.5 -7 6774643 . C CA 31 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGCGAGACTCCGTCT;RSEQ=AAAAAAAAAAAAAAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,0:0.2857:0,0:27:1:31:0:1:0:59:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 6774808 . C CA 49 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.76233;LSEQ=GACAAGGCGAGACCTTGTCT;RSEQ=AAAAAAAAAACCAAAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:3,0:56,1:0.05:1,0:20.3:1:31.1:1:1:0:60:6:0.05:0.0333:0 0/1:26:1:1,0:23,2:0.0385:2,0:32:0:25:0:1:0:60:2:0.0385:0:0 -7 6774871 . GT G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14324;SOR=Inf;LSEQ=GTTGGTTAGAATAGTATGTT;RSEQ=TAGAATGCAGGGGGTCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:240,40:0:2,0:26.3:1:29.8:1:1:0:60:69:1:0:0.1 0/1:171:2:1,1:143,26:0.0117:2,2:9:1:28.8:1:0.29164:5.41612:60:4:0.0119:0.0058:0.5 -7 6775045 . C G 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCCATTGGCATTTCAGTA;RSEQ=AACTAGTGACTAATGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:746:0:0,0:266,479:0:2,0:25.2:1:31.6:1:1:0:47.2:73.5:1:0:0.1 0/1:434:57:23,34:130,247:0.1313:2,2:28.8:1:31.2:1:0.45717:1.28:40.9:114:0.1326:0:1 -7 6775088 . A G 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATAAAATGAAATTCTACA;RSEQ=CTCTGCTATGACTGGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:89,386:0:2,0:25.3:1:29.7:1:1:0:50.1:78.167:1:0:0.1 0/1:234:37:8,29:40,157:0.1581:2,2:25:1:29.7:1:0.8269:1.08:39.3:8.25:0.1454:0:1.6 -7 6775132 . G GT 141 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.44866;SOR=0.68526;LSEQ=AACAATTTATGGTCATGTAA;RSEQ=TTTTTTTTTTTCTTTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:28:0,28:2,175:0.134:1,1:24.7:1:29.4:1:1:0:59.2:13:0.1294:0.0048:0.4 0/1:94:9:0,9:3,75:0.0957:1,0:34.2:1:30.2:1:1:0:58.9:18:0.1023:0:1 -7 6775144 . C T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATGTAAGTTTTTTTTTTT;RSEQ=TTTTTGAGACGGGGTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:2,164:0:1,0:19.8:1:32.7:1:1:0:59.7:82:1:0:0.2 0/1:77:18:1,17:1,56:0.2338:1,1:20.9:1:30.6:1:0.42486:3.23:50.8:36:0.24:0:2.3 -7 6776650 . G A 90 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=31.70095;LSEQ=GTATCTGTTCACATAAGCAC;RSEQ=TCCTCTCACCATTTCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:1:1,0:155,10:0.006:2,0:34:0:14:0:1:0:42:0:0:0:1 0/1:55:9:9,0:44,1:0.1636:1,0:23:1:28.6:1:1:0:37.8:8:0.1569:0:1.1 -7 6776731 . C G 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTAATAAAAATGCATGCAG;RSEQ=GGATTTGGAAAAGCCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:0:0,0:429,253:0:2,0:22.4:1:30.8:1:1:0:47.6:135.4:0.9985:0:0.1 0/1:329:14:10,4:194,119:0.0426:2,2:24.4:1:29.9:1:0.5807:1.53:43.9:13:0.0405:0:1.1 -7 6776825 . AGA G 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.00335;SOR=0;LSEQ=GTGTCCATTTCCAGACTGCG;RSEQ=GGCCTTTTCTCTTCGTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:14:7,7:522,436:0.0144:2,2:23.1:1:31.4:1:0.79142:1.19702:57:28:0.0146:0.0041:0.1 0/0:528:0:0,0:289,239:0:2,0:25.1:1:30:1:1:0:53.3:74.429:1:0:0.1 -7 6776906 . A G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=CCAAGAAGGAGCCCTCTAGG;RSEQ=CAGAAAAGGGGTATGTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1007:0:0,0:516,490:0:2,0:26.4:1:29.7:1:1:0:55.5:54.889:0.999:0:0.1 0/1:599:9:3,6:293,297:0.015:2,2:26.3:1:30.6:1:0.50477:1.9709:53.1:8:0.0136:0:1 -7 6776956 . A G 232 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=390.49293;LSEQ=TTCAGATGCCATCTCTGACA;RSEQ=AGGCGTCCTGAGACCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:990:1:1,0:458,531:0.001:2,0:10:0:29:0:0.46364:0:60:2:0.001:0:1 0/1:614:174:82,92:216,224:0.2834:2,2:23.9:1:31.2:1:0.72014:1.08174:57.7:57:0.2817:0:1.1 -7 6777218 . T C 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTCAGATGTGGACTGCCA;RSEQ=TCAAACCAGGAAGATACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1430:0:0,0:649,778:0:2,0:24.5:1:30.4:1:1:0:55.4:94.133:0.9993:0:0.2 0/1:1060:44:16,28:476,540:0.0415:2,2:26.7:1:30.7:1:0.21658:1.54197:56.7:13.667:0.0392:0:1.3 -7 6777369 . T C 235 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=182.1992;LSEQ=AATACTCAGAACGTGTCAGC;RSEQ=TCTCAGGTTGATGTAGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1092:2:1,1:657,433:0.0018:2,2:25.5:1:23.5:1:1:1.51668:60:1:9e-04:0:2.5 0/1:789:198:114,84:337,252:0.251:2,2:25.4:1:30.9:1:1:1.01:59.9:197:0.2513:0:1.1 -7 6777418 . A G 194 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAGAAAGTTGTGCCCCTG;RSEQ=ACTTTTCTGAGTTCTTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1399:0:0,0:755,642:0:2,0:25.5:1:30.1:1:1:0:59.9:81.176:0.9993:0:0.1 0/1:1015:88:41,47:499,428:0.0867:2,2:26.5:1:30.1:1:0.21902:1.33611:49.3:28.333:0.0852:0:1.1 -7 6777726 . T C 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01695;SOR=Inf;LSEQ=GGTTCAAGCGATTCTCCTGC;RSEQ=TCAGCCTCCTGAGTAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:0,52:0:1,0:24.5:1:30:1:1:0:58.2:25:1:0:0.3 0/1:19:3:0,3:0,16:0.1579:1,0:28:1:32.3:1:1:0:45.3:6:0.1579:0:1.7 -7 6777752 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06977;SOR=Inf;LSEQ=CTCCTGAGTAGCTGGGATTA;RSEQ=AGGTGCACGCCACCATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:0,31:0:1,0:28.9:1:28.2:1:1:0:56.7:30:1:0:0.2 0/1:12:2:0,2:0,10:0.1667:0,0:18.5:1:30:1:1:0:39.5:4:0.1667:0:5 -7 6777768 . T G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05121;SOR=Inf;LSEQ=ATTATAGGTGCACGCCACCA;RSEQ=GCCTGGCTAATTTTTATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:0:1,0:24.4:1:28:1:1:0:55.6:4.8:1:0:0.3 0/1:9:2:0,2:0,7:0.2222:0,0:18.5:1:28.5:1:1:0:39.5:4:0.2222:0:5 -7 6781190 . A G 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.00108;SOR=Inf;LSEQ=TCTGTTTCAAAAAAAAAGAA;RSEQ=GCGGGATGGCTAGGGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:65,2:0:1,0:20:1:29.9:1:1:0:39.9:32.5:1:0:0.2 0/1:25:5:4,1:20,0:0.2:1,2:38.6:1:31.8:1:0.2:0:46.8:10:0.2:0:1 -7 6781253 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51867;SOR=0;LSEQ=CTTTTTTTTATTACAGTGTT;RSEQ=TATAACATAATCAGAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:129,14:0.0138:2,2:14.5:1:28:1:0.19684:8.93663:39:4:0.0142:0:1 0/0:96:0:0,0:83,13:0:2,0:31.2:1:31.1:1:1:0:41.2:192:1:0:0.1 -7 6781491 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12391;SOR=Inf;LSEQ=AGAGGCTCATAGCGTGAGTG;RSEQ=GTTTAGTGTTCATTCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:195,151:0:2,0:26.9:1:29.3:1:1:0:36.5:114.333:1:0:0.1 0/1:189:2:1,1:94,93:0.0106:2,2:27.5:1:28.5:1:1:1.0107:27:4:0.0107:0:1 -7 6781566 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10723;SOR=Inf;LSEQ=GGCAGGAGGATCACAAGAGG;RSEQ=CAGGAGTTTGAGACCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:25,204:0:2,0:25.4:1:30.9:1:1:0:47.4:37.167:1:0:0.1 0/1:112:2:1,1:21,88:0.0179:2,2:5.5:1:26:1:0.35856:4.12:50:4:0.0187:0:1.5 -7 6781586 . T C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02233;SOR=Inf;LSEQ=CCAGGAGTTTGAGACCAGCC;RSEQ=GGACAACACAGCAAGACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:4,171:0:1,0:27.1:1:30.2:1:1:0:53:174:0.9943:0:0.1 0/1:70:3:0,3:7,60:0.0429:2,0:5.3:1:30.3:1:1:0:25:6:0.0435:0:1 -7 6785810 . G A 55 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04942;SOR=7.74332;LSEQ=ATGGCTTCGATTTTGTTATC;RSEQ=ATGAAAATGGTAAGTTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:767:1:1,0:312,454:0.0013:2,0:1:0:15:0:0.40808:0:50:0:0:0:2 0/1:399:4:3,1:165,230:0.01:2,2:11.5:1:27.8:1:0.31427:4.17:51.3:8:0.0102:0:1 -7 6785855 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11111;SOR=Inf;LSEQ=GAACTATAGCGGCTGGGTGT;RSEQ=GTGGCTCACGTCTGTAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:103,246:0:2,0:21.5:1:31.1:1:1:0:38.3:173.5:1:0:0.1 0/1:175:2:1,1:52,121:0.0114:2,2:36.5:1:27:1:0.51521:2.31:27:4:0.0115:0:1 -7 6785956 . A G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7695;SOR=1.18839;LSEQ=CGCTAACATGGTGAAACCCC;RSEQ=TCTCTACTGAAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:13:0,13:0,65:0.1667:1,1:18.8:1:32:1:1:0:50.4:26:0.1667:0:1 0/1:26:5:0,5:0,21:0.1923:1,0:26:1:30.6:1:1:0:44.6:10:0.1923:0:1.2 -7 6786286 . A AT 31 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTTTCAGATGTTCACT;RSEQ=TTTTTTTTTTTTTTCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:21.5:1:31.5:1:1:0:49:4:0.6667:0:0 0/0:1:0:0,0:0,1:0:0,0:47:0:27:0:1:0:60:2:1:0:0 -7 6786731 . C T 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00113;SOR=1.57537;LSEQ=AAAAGCTGGACCTTCGGACC;RSEQ=CAGGACGTCGATGAACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1260:154:80,74:550,555:0.1222:2,2:26.1:1:30.3:1:0.66727:1.09:40.2:153:0.1242:0:1.1 0/1:578:104:52,52:239,234:0.1799:2,2:26.5:1:29.8:1:1:1.02133:41.1:103:0.181:0:1.1 -7 6790900 . T C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08704;SOR=5.27818;LSEQ=GTGATGATTGGGACTGCTCT;RSEQ=AACACAAGCGAGATGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:17:17,0:37,0:0.3148:1,1:31.8:1:31.1:1:1:0:36.9:16:0.3019:0:1.1 1/0:7:5:5,0:2,0:0.7143:0,0:23.2:1:32.2:1:1:0:35.6:10:0.7143:0:1.2 -7 6791040 . G C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74199;SOR=1.10622;LSEQ=CTGACCGTAGTCACTGTATG;RSEQ=AATAATTGGTTTTATCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:26:16,10:126,94:0.1057:2,2:20.3:1:31.7:1:0.83421:1.19:40.3:52:0.1066:0:1 0/1:147:17:12,5:92,38:0.1156:2,2:24.6:1:31.1:1:1:1.00871:41:16:0.1103:0:1.1 -7 6791055 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12867;SOR=Inf;LSEQ=GTATGGAATAATTGGTTTTA;RSEQ=CGCAGATTTTTATGTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:111,167:0:2,0:22.5:1:29:1:1:0:41.3:54.6:1:0:0.2 0/1:156:2:1,1:81,73:0.0128:2,2:38:0:30.5:1:1:1.10885:21:4:0.0128:0:1 -7 6791096 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.11064;SOR=Inf;LSEQ=AAGACAGAGTCTTCACTAAC;RSEQ=TTTTTGTTTTAAAATGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:41,273:0:2,0:30:1:30.3:1:1:0:43.1:313:1:0:0.1 0/1:157:2:1,1:33,122:0.0127:2,2:32.5:1:30:1:0.38731:3.66:42.5:4:0.013:0:0 -7 6791126 . TA T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.65316;LSEQ=TTAAAATGAAACCTGCTACT;RSEQ=AAAAAAATACACATCACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:0,3:11,218:0.0129:1,0:35.7:1:31:1:1:0:49.7:6:0.013:0:0 0/0:118:1:0,1:7,110:0.0085:2,0:21:0:32:0:1:0:45:2:0.0086:0:0 -7 9291444 . A G 53 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTCCCCACAAAATCCCC;RSEQ=TCCAAGGATCAGCAGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:30.3:1:33.7:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:1:0,0:40:0:33:0:1:0:60:2:1:0:1 -7 10556727 . T C 29 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77151;LSEQ=TAAAAGAATGTCTATGAGTT;RSEQ=AGAGCACAGCAGTACTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:15,8:0.08:2,0:14.5:1:29.5:1:1:0:60:4:0.087:0:2 0/1:16:1:1,0:9,6:0.0625:2,0:13:0:33:0:1:0:60:2:0.0625:0:1 -7 10556795 . A T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04798;SOR=0.19452;LSEQ=CAAAACACACCCTCTCCACC;RSEQ=AAGGACAAAGTGCTTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:32:14,18:1,2:0.9143:2,2:24.5:1:28.3:1:1:1.54:60:15:0.9091:0:2.1 1/0:18:12:5,7:4,2:0.6667:2,2:25.3:1:29.2:1:0.61991:2.64037:60:24:0.6667:0:2.1 -7 10556797 . A C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01913;SOR=0.13958;LSEQ=AAACACACCCTCTCCACCAA;RSEQ=GGACAAAGTGCTTCATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:30:12,18:0,2:0.9375:0,2:25.9:1:30.4:1:0.51613:0:60:60:0.9375:0:2.2 1/0:18:12:5,7:4,2:0.6667:2,2:23.9:1:30.4:1:0.61991:2.64037:60:24:0.75:0:2.1 -7 10557126 . GA G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.19212;SOR=Inf;LSEQ=AACAACAGCATCAACAATAA;RSEQ=AAAAAAAAGGCCCCCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:28.1:1:30.7:1:1:0:56.3:32:1:0:0.1 0/1:13:2:1,1:6,5:0.1538:2,2:29:1:29.5:1:1:1.18321:60:4:0.1538:0:0 -7 10557265 . T C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1321;LSEQ=GAGTCCCTCTTCTCTCCAAA;RSEQ=GATCGCAACATCTCTCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:1,6:1,3:0.6364:2,2:20.4:1:29.7:1:1:1.87089:60:14:0.6364:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:21.5:1:29:1:1:0:60:4:0.6667:0:1 -7 10557347 . GA G 51 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=AGAGCTTAGATATAATCCGT;RSEQ=AATGCGAAGCAATTGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:13.7:1:32.3:1:1:0:60:6:1:0:0.7 0/0:1:0:0,0:0,1:0:0,0:23:0:32:0:1:0:60:2:1:0:1 -7 10563778 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGAGGCCAGGAAGGAGAGG;RSEQ=AGGAGGAGACCTGATGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:31:1:1:0:60:4:1:0:1 -7 10567455 . C T 45 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49255;SOR=2.02157;LSEQ=TGGGACTCACAACTGCCTAA;RSEQ=AGGCTAAGCTCCCTGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:1,2:19,12:0.0882:2,2:38.3:1:29:1:0.55548:3.05869:60:6:0.0882:0:1 0/1:6:1:1,0:3,2:0.1667:2,0:45:0:29:0:1:0:60:2:0.1667:0:1 -7 10567691 . G T 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31025;SOR=0.29158;LSEQ=TCTACAGGGAAGAGGCTAAC;RSEQ=ACAGCCAGAGGCTCAGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:25:8,17:1,2:0.8929:2,2:23.2:1:27.9:1:1:1.06018:60:24:0.8889:0:1.8 1/0:10:7:3,4:2,1:0.7:2,2:31.4:1:27.4:1:1:2.41422:60:14:0.7:0:2 -7 10567706 . A G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30923;SOR=0.29892;LSEQ=CTAACGACAGCCAGAGGCTC;RSEQ=GGGACAGAATTCAGATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:21:7,14:1,2:0.875:2,2:22.9:1:29.8:1:1:1:60:42:0.875:0:1.9 1/0:9:6:2,4:2,1:0.6667:2,2:27:1:29.8:1:0.52381:3.38757:60:12:0.6667:0:2.2 -7 10568055 . T G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15;SOR=Inf;LSEQ=TGCTCTCCAGCCTCCTTGAG;RSEQ=GACATCTCCAGGCATGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:19.3:1:29.7:1:1:0:42.6:30:1:0:0.9 0/1:10:2:1,1:6,2:0.2:2,2:13.5:1:28.5:1:1:2.64575:33:4:0.2:0:1.5 -7 10568077 . G A 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80019;LSEQ=ACATCTCCAGGCATGGGAGC;RSEQ=AATCAGATGAATAGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:11,6:2,1:0.85:2,2:24.5:1:29.9:1:1:1.08623:48.8:16:0.8421:0:1.1 1/1:11:9:4,5:2,0:0.8182:0,2:24.1:1:29.7:1:0.45455:0:47.1:18:0.8182:0:1.3 -7 10568196 . G GA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50588;SOR=0;LSEQ=AACAACAGCATCAACAGTAA;RSEQ=AAAAAAAAAGGCCCCCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:38.5:1:30:1:1:1.11:60:4:0.1111:0:0 0/0:14:0:0,0:9,5:0:2,0:25.9:1:32.1:1:1:0:55.8:28:1:0:0 -7 10711288 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09804;SOR=Inf;LSEQ=AATATTCAGGTCCCTCTTCT;RSEQ=TTGGGCTGCTGCAGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,4:0:2,0:14.7:1:32.1:1:1:0:56.1:22:1:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:13:0:32:0:1:1:60:4:0.3333:0:1.5 -7 10711493 . C CA 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.72467;SOR=1.63137;LSEQ=GACAACCCCTGTTGGAGGGT;RSEQ=CGTCCAGTTGAGTGGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:7,4:5,2:0.6111:2,2:25.4:1:30.8:1:1:1.40086:60:22:0.6111:0.1667:0.3 1/0:18:13:9,4:4,1:0.7222:2,2:24.7:1:29:1:1:1.7252:60:26:0.7222:0.1111:0.3 -7 10711573 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19481;SOR=Inf;LSEQ=GGATTGGGGTGTGTGTTTTG;RSEQ=TAGGGGGAACCCACTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:26.8:1:31.3:1:1:0:60:14.5:1:0:0.2 0/1:25:2:1,1:11,12:0.08:2,2:25:1:26:1:1:1.09:60:4:0.08:0:1 -7 10711893 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.48;SOR=Inf;LSEQ=TGGCCCCAGCAGGGGAAAAG;RSEQ=ACAGCCTGGAGCTATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:26.2:1:32.1:1:1:0:60:24:1:0:0.1 0/1:13:2:1,1:6,5:0.1538:2,2:30.5:1:28:1:1:1.18321:60:4:0.1667:0:1 -7 11297357 . G A 26 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02597;SOR=Inf;LSEQ=CTTGAACAGCTTCCTGGTCG;RSEQ=TCATCCAGAAGCAGTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:15,3:0:2,0:21.6:1:30.3:1:1:0:60:17:1:0:0.5 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:26:1:1:1:60:4:0.5:0:1 -7 11297388 . T C 91 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05728;SOR=0.0964;LSEQ=GCAGTCCTTCACGTGATTGA;RSEQ=AAATTTGGCTTCCACTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:7,1:3,1:0.6667:2,2:24.9:1:30.6:1:1:2.16:60:16:0.6667:0:1.1 0/1:7:1:0,1:3,3:0.1429:2,0:48:0:34:0:1:0:60:2:0.1429:0:1 -7 11297492 . G GT 28 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.11098;SOR=Inf;LSEQ=AAGGTCCTTTTGGTGTTTTA;RSEQ=TTTTTTTTTTCCCTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:22.3:1:30.3:1:1:0:60:12.5:1:0:1.5 0/1:14:2:1,1:7,5:0.1429:2,2:35.5:1:28.5:1:1:1.36624:60:4:0.1667:0:0.5 -7 11297507 . T G 71 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0.27207;SOR=0;LSEQ=TTTTAGTTTTTTTTTTCCCT;RSEQ=TTTTTTTTTTTTGAGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:2,3:4,6:0.2941:2,2:14.4:1:30.8:1:1:1:60:10:0.3571:0:1 0/0:7:0:0,0:2,3:0:2,0:25.8:1:27.8:1:1:0:60:10:1:0:1 -7 11297736 . C G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01527;SOR=0.30112;LSEQ=TTTCCTTTTTTTCTGTGGAA;RSEQ=CTCACTACCATTTCTAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:32:25,7:27,7:0.4848:2,2:23.3:1:31:1:1:1.07873:60:15:0.4688:0:1 0/1:32:7:4,3:19,6:0.2188:2,2:17:1:31.1:1:0.37018:2.30456:60:14:0.2258:0:1.3 -7 11297820 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16342;SOR=5.87853;LSEQ=CTCTTCATCTTCTCACTCTG;RSEQ=CTCTTCCTCCACAGCTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:0,1:131,85:0.0046:2,0:1:0:25:0:0.39631:0:60:2:0.0046:0:1 0/1:151:4:1,3:85,62:0.0265:2,2:10:1:29.3:1:0.31507:4.07626:60:8:0.0268:0:1.3 -7 11297830 . C T 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCTCACTCTGCCTCTTCCTC;RSEQ=ACAGCTACTAAGTGCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:146,107:0:2,0:26.3:1:31.1:1:1:0:60:62.25:1:0:0.2 0/1:175:25:13,12:84,66:0.1429:2,2:18.8:1:29:1:0.82855:1.17373:60:50:0.1445:0:1.2 -7 11297869 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.16147;SOR=Inf;LSEQ=CCACTAATATGCCCTGGCCC;RSEQ=GAACCACGCTTCAACCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:134,159:0:2,0:26.2:1:30.5:1:1:0:60:96.667:1:0:0.2 0/1:198:2:2,0:88,108:0.0101:2,0:19:1:31:0:0.20535:0:53.5:4:0.0102:0:1 -7 11297892 . C T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01966;SOR=Inf;LSEQ=ACCACGCTTCAACCATAAGA;RSEQ=CACGGGTGGTGGTATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:86,142:0:2,0:22.9:1:30.6:1:1:0:60:31.571:1:0:0.2 0/1:138:4:1,3:55,79:0.029:2,2:31:1:24:1:0.64639:2.07853:60:3:0.0222:0:1 -7 11297904 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.12728;SOR=Inf;LSEQ=CCATAAGACCACGGGTGGTG;RSEQ=TATTTCAAAGCCCCTAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:61,122:0:2,0:23.1:1:31.5:1:1:0:60:90.5:1:0:0.1 0/1:102:2:1,1:33,67:0.0196:2,2:5:0:30.5:1:1:2.02:60:4:0.0196:0:2 -7 11297930 . A G 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01623;SOR=Inf;LSEQ=CAAAGCCCCTAAGGGAAACC;RSEQ=CTGGCTGTATAGACATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:23,95:0:2,0:26.3:1:29.5:1:1:0:60:38.333:1:0:0.1 0/1:67:4:0,4:17,46:0.0597:2,0:8.5:1:32.8:1:0.56529:0:60:8:0.0597:0:1 -7 11298043 . G C 87 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00464;SOR=10.60442;LSEQ=CCTATGTATCAGCCCCTAAA;RSEQ=TGACTATTCTTAAAGATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:4,22:0.0714:2,2:28:1:34:0:0.33069:5.03:60:4:0.0714:0:1 0/1:15:7:3,4:3,5:0.4667:2,2:20.9:1:31.3:1:1:1.23:60:14:0.4667:0:1.1 -7 11691113 . A ACTAT 130 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=39;MSI=10.000;MSILEN=4;SSF=0.18547;SOR=0.40194;LSEQ=TATTATCTATCTATCTATCA;RSEQ=CTATCTATCTATCTATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:18:17,1:43,0:0.2951:1,1:21.9:1:31.4:1:0.29508:0:58.3:36:0.2951:0.082:0.3 0/1:28:4:4,0:21,0:0.1429:1,0:36.5:1:31.8:1:1:0:60:8:0.1429:0:0 -7 11691169 . T C 72 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00629;SOR=14.22233;LSEQ=TCTAGCACTACAATGAACTA;RSEQ=AGCCCACCCTTTTTTAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:1,0:150,20:0.0058:2,0:46:0:34:0:1:0:60:2:0.0059:0:2 0/1:64:5:5,0:52,7:0.0781:2,0:28.6:1:31.2:1:1:0:60:10:0.0781:0:1 -7 11691177 . C A 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACAATGAACTATAGCCCAC;RSEQ=CTTTTTTAGTCATGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:159,27:0:2,0:22.1:1:31.2:1:1:0:59.9:185:1:0:0.1 0/1:78:17:15,2:52,9:0.2179:2,2:19.6:1:29.2:1:1:1.29:60:34:0.2179:0:1 -7 11691247 . G T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05102;SOR=7.6428;LSEQ=ATATAGCAACATTACCTCAA;RSEQ=GTTCTAAGGAGTTAATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:694:1:1,0:426,267:0.0014:2,0:38:0:14:0:1:0:60:0:0:0:7 0/1:366:4:1,3:211,150:0.0109:2,2:7.3:1:28.8:1:0.31319:4.20408:60:8:0.0111:0:1.3 -7 11691296 . C T 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=2.33676;LSEQ=GCCTTGGGGAACTTTTAAAC;RSEQ=CCTTAGACCTAAAGGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:896:305:159,146:288,303:0.3404:2,2:25.6:1:30.1:1:0.35951:1.15:60:42.571:0.3394:0:1.1 1/0:459:251:129,122:99,109:0.5468:2,2:24.8:1:29:1:0.45347:1.16:60:24.1:0.5428:0:1.2 -7 12252540 . C G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29818;SOR=1.8075;LSEQ=TAATCTATTTTTAGGAACCG;RSEQ=TAAAAGACATATCAAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:17:17,0:31,0:0.3542:1,1:23.1:1:31.8:1:1:0:60:34:0.3542:0:1.1 1/0:22:11:10,1:10,1:0.5:2,2:29.6:1:31.7:1:1:1:60:22:0.5:0:1 -7 12252659 . G A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.94207;LSEQ=GCAGGGTGTATTATATGACT;RSEQ=TTAAGTTCTTTTCAGCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:103:75,28:247,124:0.2168:2,2:26:1:28.3:1:0.28278:1.34:60:33.333:0.2128:0:1.3 1/0:268:140:90,50:85,43:0.5224:2,2:25.1:1:28.4:1:0.79739:1.09781:60:139:0.5206:0:1.4 -7 12252741 . T G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.63395;LSEQ=CTGCAGAAGTTATTTTTGTG;RSEQ=AGGCACTAGTACTAATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:150:58,92:217,282:0.2311:2,2:28.3:1:30.8:1:0.30186:1.22022:60:49:0.2297:0:1.2 1/0:402:210:95,115:83,109:0.5224:2,2:26.5:1:30.7:1:0.68912:1.08:60:51.5:0.5176:0:1.6 -7 12252744 . G A 166 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=93.40423;LSEQ=CAGAAGTTATTTTTGTGTAG;RSEQ=CACTAGTACTAATTATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:648:1:0,1:272,374:0.0015:2,0:7:0:26:0:1:0:60:2:0.0016:0:1 0/1:395:50:24,26:147,197:0.1266:2,2:28.7:1:29.5:1:0.54214:1.24:60:100:0.1292:0:2.3 -7 12252893 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01453;SOR=3.3687;LSEQ=TATTTTGGAACATTGGCTTC;RSEQ=TAATTTTAACTGTCAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:18:0,18:0,44:0.2903:1,1:25.4:1:31.8:1:1:0:60:36:0.2903:0:1.3 1/0:24:14:0,14:0,10:0.5833:0,1:19.6:1:31.3:1:1:0:60:28:0.5833:0:1.2 -7 12252902 . A ACT 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.02978;SOR=3.28201;LSEQ=ACATTGGCTTCATAATTTTA;RSEQ=CTGTCAACTGTTGAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:15:0,15:0,41:0.2679:1,1:26.3:1:31:1:1:0:60:30:0.2727:0.0179:1 1/0:20:11:0,11:0,9:0.55:0,0:21.4:1:29.7:1:1:0:60:22:0.55:0.2:1.3 -7 12253050 . A C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAAAGGTGCGTGAATTTTC;RSEQ=GAGGCTGAAACGTACTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:18.5:1:27:0:1:0:60:4:0.25:0:1.5 0/0:1:0:0,0:0,1:0:0,0:5:0:31:0:1:0:60:2:1:0:0 -7 12462917 . A G 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.0241;SOR=Inf;LSEQ=CAAAATATTAGCCATACCCA;RSEQ=TAATCCTTCTGTGGCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:93,3:0:1,0:24.4:1:30.2:1:1:0:60:95:1:0:0.2 0/1:40:3:3,0:37,0:0.075:1,0:24.3:1:32:1:1:0:60:6:0.0811:0:3 -7 12462931 . G GCC 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.01147;SOR=0;LSEQ=TACCCAATAATCCTTCTGTG;RSEQ=CCCCCCCCTTATTTCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:13:13,0:99,3:0.1111:1,1:22.7:1:31.8:1:1:0:59.2:26:0.114:0.0256:1.4 0/0:48:0:0,0:43,0:0:1,0:25.2:1:31:1:1:0:60:20.5:0.8913:0:0.3 -7 12462937 . C A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00271;SOR=Inf;LSEQ=ATAATCCTTCTGTGGCCCCC;RSEQ=CCTTATTTCATTTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:119,3:0:1,0:28.3:1:31.2:1:1:0:59.9:121:1:0:0.2 0/1:56:5:5,0:49,2:0.0893:1,0:28:1:27.4:1:1:0:60:4:0.0727:0:2.2 -7 12463056 . G A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.85936;SOR=1.03931;LSEQ=CATTTACCCTCAAACTCTTC;RSEQ=TTGAATCCTTACTCTACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:92:55,37:384,313:0.1165:2,2:25.5:1:30.3:1:0.43522:1.21:60:91:0.1162:0:1.5 0/1:498:60:33,27:231,206:0.1205:2,2:29:1:30.1:1:0.78409:1.09:60:59:0.1204:0:1.6 -7 12463109 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.99108;LSEQ=CTGTATGGCCACACTGCTTA;RSEQ=GAGGAAAGCACTCAGCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:824:107:48,59:309,407:0.1299:2,2:28.3:1:30.1:1:0.75457:1.07:60:52.5:0.1296:0:1.5 0/1:515:220:102,118:135,160:0.4272:2,2:23.4:1:29.4:1:0.92887:1.02:60:54:0.4252:0:1.3 -7 12463189 . C T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00301;LSEQ=GTTACAGTGTCAGCATTCTC;RSEQ=TGAATTTTCAATGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:48:13,35:65,229:0.1395:2,2:24.9:1:29.8:1:0.46008:1.31:60:47:0.1374:0:1.4 0/1:193:27:6,21:53,113:0.1399:2,2:19:1:30.8:1:0.37322:1.63769:60:54:0.1414:0:1.6 -7 12463400 . C G 50 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACATAGATTGTGAAAGA;RSEQ=ATTTTTATATTGCTGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:0.3:0,0:13.7:1:32:1:1:0:60:6:0.3:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 13860395 . T C 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CCTTCCTTCCTTCCTTCCTT;RSEQ=CTTTCTTTCTTTTCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:29.5:1:1:0:60:4:1:0:1 -7 13861917 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1777;SOR=Inf;LSEQ=GCAGAATCTGTTCCATGTCT;RSEQ=TCCCCTGGCTTCTGGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:0:2,0:29.5:1:31.3:1:1:0:60:23:1:0:0.1 0/1:18:2:1,1:9,7:0.1111:2,2:21.5:1:29:1:1:1.26772:60:4:0.1111:0:1 -7 13935307 . C T 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=TTTAGATTACTCCCACCCAC;RSEQ=CTCAAATAAAGTGCACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:22:20,2:7,0:0.7586:0,2:22.9:1:29.9:1:1:0:60:10:0.7407:0:1.2 0/0:9:0:0,0:9,0:0:0,0:19:1:30.3:1:1:0:60:18:1:0:0.1 -7 13935468 . G T 52 q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07499;SOR=0;LSEQ=AAAAGGAAAAGCGCAAAAAC;RSEQ=CCCTGCTTGACTGTCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:5:2,3:323,161:0.0102:2,2:17.4:1:22.4:1:0.34024:3.00192:60:1.5:0.0063:0:1.4 0/0:366:0:0,0:240,125:0:2,0:25.4:1:29.9:1:1:0:60:35.5:1:0:0.2 -7 13935763 . GA G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11833;SOR=Inf;LSEQ=CCTCACCATCGCCAGATGGG;RSEQ=AGGACAGGAAGGAAAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:52,235:0:2,0:20.5:1:30:1:1:0:60:56.4:1:0:0.1 0/1:151:2:1,1:33,116:0.0132:2,2:31.5:1:30:1:0.40079:3.48:60:4:0.0134:0:1 -7 13935772 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11681;SOR=Inf;LSEQ=CGCCAGATGGGGAAGGACAG;RSEQ=AAGGAAAAAGCCAAAAACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:34,200:0:2,0:20.8:1:31.3:1:1:0:60:233:1:0:0.1 0/1:122:2:1,1:18,100:0.0164:2,2:24.5:1:26.5:1:0.29272:5.43:60:4:0.0168:0:1 -7 13935783 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54157;SOR=0;LSEQ=GAAGGACAGGAAGGAAAAAG;RSEQ=CAAAAACGTGGTTTAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:0,2:12,162:0.0114:2,0:32:1:30.5:1:1:0:60:4:0.0116:0:1 0/0:96:0:0,0:9,87:0:2,0:21.4:1:30.7:1:1:0:60:18.2:1:0:0.1 -7 13935861 . T TA 71 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.0446;SOR=4.24563;LSEQ=CAACTAATAGCAGATACACA;RSEQ=AAAAAAAAAAAAGTCTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:5:0,5:0,43:0.0943:1,0:35.6:1:31.2:1:1:0:60:10:0.125:0:0 0/1:16:5:0,5:0,11:0.3125:0,0:27:1:30.6:1:1:0:60:10:0.4167:0:0 -7 13945864 . C T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.39974;LSEQ=TTTGTAGGATTGTATACAAC;RSEQ=GGAAGGAACACGCAATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:8:8,0:17,0:0.32:1,0:13.4:1:32:1:1:0:60:16:0.3333:0:1 0/1:5:2:2,0:3,0:0.4:0,0:32.5:1:33:0:1:0:60:4:0.5:0:1 -7 13946266 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09043;SOR=Inf;LSEQ=TTTCTATTATTAGCAATACT;RSEQ=TGCTATCTTACATAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:22,221:0:2,0:22.9:1:30.9:1:1:0:60:120.5:1:0:0 0/1:105:2:1,1:13,90:0.019:2,2:18.5:1:30:1:0.25:6.71:60:4:0.019:0:1.5 -7 13946316 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=CAATCACTAATATGGTTAAA;RSEQ=CACAATCAACCACTTTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:0,90:0:1,0:24:1:31.2:1:1:0:60:44:1:0:0 0/1:30:6:0,6:0,24:0.2:1,0:28.3:1:27:1:1:0:60:5:0.1724:0:1.2 -7 13950777 . A T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.56317;SOR=3.15481;LSEQ=AATGATTTTTCCCAAATAAT;RSEQ=TAATGATTAATTAAATGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:1:0,1:247,55:0.0033:2,0:1:0:27:0:0.18482:0:60:2:0.0033:0:1 0/1:193:2:1,1:149,42:0.0104:2,2:38.5:1:29:1:0.39686:3.51767:60:4:0.0104:0:1 -7 13950838 . C T 170 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=87.08193;LSEQ=TATTCTGAACGGTATTTACA;RSEQ=GGAATTTCAGTGGTGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:824:1:0,1:487,335:0.0012:2,0:1:0:25:0:0.40826:0:60:2:0.0012:0:1 0/1:563:54:33,21:298,211:0.0959:2,2:25.2:1:29.6:1:0.7724:1.11:60:108:0.0969:0:1.2 -7 13970739 . C T 59 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTAAATGTTATAAGCAA;RSEQ=ATGTGACCTAGTTCAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:8.8:1:29.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 13971151 . G T 71 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05735;SOR=5.23449;LSEQ=GTCATATGCAAAATCTCTGG;RSEQ=TTCCTGTTTAATCATCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1036:2:0,2:649,384:0.0019:2,0:23:1:19:1:0.13886:0:60:1:0.001:0:1 0/1:598:6:2,4:366,226:0.01:2,2:21.7:1:27.5:1:0.21091:3.23241:60:12:0.0101:0:1.2 -7 13971669 . C CCA 48 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=14.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTTTGAGGATTTTACACAC;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:29.7:1:30.3:1:1:0:60:6:0.3333:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 13975472 . TG T 72 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.20274;SOR=2.34386;LSEQ=CACTGGCGTGCTGGATGGTG;RSEQ=GGGGGGTTGGAGGGCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:753:4:1,3:295,453:0.0053:2,2:31:1:30.8:1:1:1.95206:60:8:0.0054:0.0013:0.3 0/1:485:6:1,5:204,273:0.0124:2,2:16.8:1:28.1:1:0.2479:3.72793:60:12:0.0126:0.0041:0.8 -7 13975575 . A T 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=TTTCTTTGGAGCAATTTTTT;RSEQ=AAAAAGTTTCTAATCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:27,165:0:2,0:23.8:1:29.4:1:1:0:60:26.429:1:0:0.1 0/1:94:7:2,5:15,72:0.0745:2,2:18.9:1:27.4:1:0.60623:1.90:60:14:0.0745:0:1.3 -7 13978645 . C T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=16.74817;LSEQ=AGCTTGTTACATATTAAAGA;RSEQ=GTTACTCATAAAATATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:6:6,0:253,8:0.0225:1,0:28.7:1:31:1:1:0:60:12:0.0233:0:2.2 0/1:100:28:28,0:66,6:0.28:2,1:22.3:1:30.2:1:0.18122:0:60:56:0.2857:0:2.3 -7 13978648 . T A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=17.43444;LSEQ=TTGTTACATATTAAAGACGT;RSEQ=ACTCATAAAATATGACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:6:6,0:275,9:0.0207:1,0:29.7:1:28.8:1:1:0:60:12:0.0209:0:2.2 0/1:107:29:29,0:72,6:0.271:2,1:23:1:28.5:1:0.18698:0:60:58:0.2762:0:2.3 -7 13978683 . C G 107 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.45058;LSEQ=ACTTGAGATTTCATATTATT;RSEQ=TGGACTTTTTGATTCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:1:1,0:443,131:0.0017:2,0:9:0:15:0:1:0:60:0:0:0:6 0/1:245:12:10,2:177,55:0.049:2,2:23.1:1:30.1:1:0.73745:1.55:60:11:0.0455:0:1.8 -7 13978734 . G A 144 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTACATACATACACCTGGT;RSEQ=GCTTTACCTGACATTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1185:0:0,0:708,475:0:2,0:26.7:1:31.6:1:1:0:60:83.5:0.9983:0:0.1 0/1:622:33:19,14:345,243:0.0531:2,2:28.4:1:28.7:1:1:1.04602:60:66:0.0538:0:1.6 -7 13978809 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.20987;LSEQ=TTCTTGACTGCAGGCAGAGC;RSEQ=GATTTCTGAACATGGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1229:31:15,16:512,685:0.0252:2,2:25.6:1:29.3:1:0.58353:1.25:60:14.5:0.024:0:1.2 0/1:699:168:70,98:239,292:0.2403:2,2:26.3:1:29.3:1:0.47641:1.14567:60:83:0.2416:0:1.2 -7 14016939 . T C 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGCTGTAAGTTAAAAAGG;RSEQ=GCTGGTACAATGTAAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:164,11:0:2,0:22.1:1:30.1:1:1:0:60:174:1:0:0.1 1/0:87:56:54,2:30,1:0.6437:1,1:23.4:1:32.8:1:1:1.1098:60:112:0.6437:0:2.2 -7 14017007 . CC TG 234 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAAGAAGAAAGAAGGAAA;RSEQ=AGAAAGACAGAAAAATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:0:0,0:349,202:0:2,0:25.6:1:31.4:1:1:0:60:54.1:0.9982:0:0.1 1/0:340:204:136,68:83,46:0.6:2,2:26:1:30.5:1:0.72235:1.11:60:408:0.6108:0.0382:1.2 -7 14017008 . C G 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00089;SOR=Inf;LSEQ=GAAAGAAGAAAGAAGGAAAC;RSEQ=AGAAAGACAGAAAAATACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:0:0,0:351,209:0:2,0:25.5:1:31.2:1:1:0:60:69:0.9982:0:0.1 0/1:328:7:3,4:83,47:0.0213:2,2:22:1:25.4:1:0.42377:2.33911:60:2.5:0.0373:0:2.1 -7 14017126 . T TA 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAAGAAGAAAAAGAAAAT;RSEQ=AAAAAAAATTAAGAGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:57,211:0:2,0:22.5:1:28.4:1:1:0:60:43.667:1:0:0.2 1/0:171:88:14,74:19,63:0.5146:2,2:27.3:1:29.4:1:0.25009:1.58969:60:28.333:0.506:0.0117:0.3 -7 14025411 . T G 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=TCCAAAAGAAAAATTTCAAA;RSEQ=TATGAATGCCAACAGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:0:0,0:20.6:1:30.2:1:1:0:60:18:1:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:5:1:32:1:1:0:60:4:0.6667:0:2 -7 14025474 . A G 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=AGTTGTATAAAGCTTTATGA;RSEQ=GCAATCTCATTTTCCTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:0:1,0:23.5:1:30.4:1:1:0:60:23:1:0:0.4 1/0:7:5:4,1:2,0:0.7143:0,2:27.2:1:32.2:1:1:0:60:10:0.7143:0:1.4 -7 14025528 . C A 147 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=0.03805;LSEQ=AAAAGATATAACAGATTGCA;RSEQ=CACAAAATTTTAACAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:31:31,0:11,0:0.7381:0,1:28.4:1:29.8:1:1:0:60:30:0.7317:0:1.1 0/1:11:1:1,0:9,1:0.0909:2,0:4:0:30:0:1:0:60:2:0.0909:0:1 -7 14025640 . G A 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATAGCAAAGGTCAATTTCA;RSEQ=CAAACATAACATGAATAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:226,23:0:2,0:24.5:1:31.9:1:1:0:60:82:1:0:0.1 1/0:122:83:73,10:39,0:0.6803:1,2:23.8:1:30:1:0.02955:0:60:82:0.6833:0:1.2 -7 14025727 . C T 250 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1662.39731;LSEQ=AAACCCATAGATTTCCTAAG;RSEQ=ATTAGATACACACCTAACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1149:1:0,1:655,493:9e-04:2,0:1:0:23:0:0.42994:0:60:2:9e-04:0:1 1/0:697:419:242,177:157,119:0.6011:2,2:25.3:1:28.7:1:0.87544:1.04:60:103.75:0.605:0:1.9 -7 14025766 . T A 265 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCTGTGTTGTGAACAAGG;RSEQ=GGAAAGAAGACACTTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1386:0:0,0:697,688:0:2,0:25.3:1:29.6:1:1:0:60:114.417:1:0:0.1 1/0:841:500:247,253:172,168:0.5945:2,2:26.9:1:29.6:1:0.77862:1.04865:60:124:0.5976:0:1.7 -7 14026134 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21886;SOR=4.67043;LSEQ=ATCAGAGGCTCTAATGTATG;RSEQ=ATGACACATGAGGTGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:145,8:0.0065:2,0:1:0:24:0:0.05844:0:60:2:0.0066:0:1 0/1:67:2:2,0:62,3:0.0299:1,0:27:1:30:1:1:0:60:4:0.0299:0:1.5 -7 14026357 . A G 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00165;SOR=1.92861;LSEQ=ATAAGATTTGCAAATCTTTA;RSEQ=TCTTCATTAAATGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:349:239:51,188:28,82:0.6848:2,2:23.3:1:31.7:1:0.41063:1.25785:60:46.8:0.6862:0:1.1 1/1:213:172:55,117:16,25:0.8075:2,2:22.1:1:30.7:1:0.46123:1.35937:60:56.333:0.8048:0:1.1 -7 14026421 . C T 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00589;SOR=0;LSEQ=ATAAATTTAATTTCAAGAGA;RSEQ=GCAGTCAACATAAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:15:0,15:0,100:0.1304:1,1:17.3:1:30.3:1:1:0:60:30:0.1339:0:1.9 0/0:49:0:0,0:1,48:0:1,0:19.9:1:29.2:1:1:0:60:98:1:0:0.6 -7 14026438 . TA T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACGCAGTCAACATAAAAA;RSEQ=AAAAAAAGAGGCATAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:1,75:0:1,0:19.4:1:30.8:1:1:0:60:75:1:0:0.6 1/0:30:16:0,16:0,14:0.5333:1,1:25.8:1:29.8:1:1:0:60:32:0.5333:0:0.3 -7 14027477 . G A 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=CAAAACAATGATTAAAAGAA;RSEQ=GTTGTCATTGAGAAGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:0:1,0:20.8:1:32.2:1:1:0:60:37:1:0:0.5 1/0:6:4:3,1:2,0:0.6667:0,2:17.5:1:31.3:1:1:0:60:8:0.6667:0:1.5 -7 14027557 . G A 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.71225;SOR=0.86517;LSEQ=AGTCTCCCATGCAAACTGCC;RSEQ=CATTATGTAAATCGTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:152:116:115,1:35,0:0.7632:1,1:25.8:1:30.6:1:1:0:60:115:0.7667:0:1.1 1/0:53:39:39,0:14,0:0.7358:1,1:22.6:1:30.7:1:1:0:60:78:0.7358:0:1.3 -7 14027867 . G A 56 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=1;SOR=1.21598;LSEQ=ACACACACGCACACGCGCGC;RSEQ=CACACACACACACACAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:4:0,4:8,192:0.0194:1,0:34:1:28.3:1:1:0:60:8:0.0201:0:1 0/1:85:2:0,2:2,49:0.0235:1,0:21.5:1:31.5:1:1:0:60:4:0.0241:0:0.5 -7 14027991 . T C 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00081;SOR=Inf;LSEQ=TTTGACAGTGAAAGCTTATG;RSEQ=TAAGCAGGCAGGGAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:0:1,0:25.4:1:29.8:1:1:0:60:27:1:0:0.1 1/0:4:3:0,3:0,1:0.75:0,0:29.7:1:33:1:1:0:60:6:0.75:0:1 -7 14028220 . G GA 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAAAAGAGTAGAGAAAT;RSEQ=AAAAAAAAAAAAAAGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:17:1:29.8:1:1:0:60:4:0.5:0.25:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 14028544 . C T 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGTATCTGCAATCCCAACC;RSEQ=CCGTGCCCCCTCCCTTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:386,82:0:2,0:23.2:1:30.5:1:1:0:60:41.545:1:0:0.4 0/1:282:21:14,7:200,61:0.0745:2,2:25.5:1:28.6:1:0.29805:1.63617:60:20:0.0719:0:1.2 -7 14028575 . C T 199 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01282;LSEQ=TCCCTTCTCATTTTCTCCCT;RSEQ=TCCCCACCCCCGACGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:807:101:66,35:476,229:0.1252:2,2:23.4:1:29.9:1:0.65212:1.10215:60:202:0.13:0:1.1 0/0:547:1:0,1:342,204:0.0018:2,0:1:0:29:0:0.37477:0:60:2:0.0019:0:1 -7 14028707 . TA T 240 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCGCAAATCTCAGCTCAG;RSEQ=TTTTATATTTTGAGCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:659:0:0,0:189,470:0:2,0:24:1:30:1:1:0:60:72.222:1:0:0.1 1/0:432:261:89,172:60,111:0.6042:2,2:23:1:29.9:1:0.83676:1.0445:59.9:522:0.6056:0.1343:0.3 -7 14028794 . TA T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAAGATGGCTTTTAGGCT;RSEQ=AAAAAAAATCATGAATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:0,2:2,131:0.0148:1,0:17.5:1:32.5:1:1:0:60:4:0.0149:0:0 0/0:53:0:0,0:3,50:0:2,0:26.3:1:29.5:1:1:0:60:52:1:0:0.3 -7 14028860 . CA C 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CCCTCCGACAGTCCCATTCA;RSEQ=AAAATAACCCTCCCTACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:0,52:0:1,0:24.1:1:31:1:1:0:60:104:1:0:0.1 0/1:14:6:0,6:1,7:0.4286:2,0:21.2:1:31.8:1:1:0:60:12:0.4286:0:0 -7 14030093 . T G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGGGAGGAGGAGGGAG;RSEQ=GCTTGGGGTTGCTCGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 15146113 . A G 81 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03284;SOR=7.40131;LSEQ=TGTAAAATAGTAAGTGCTCA;RSEQ=AGATATTTCCTGTAATCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:12,8:0.1304:2,2:26.7:1:31.3:1:1:1.32:60:6:0.1304:0:1 1/0:11:6:5,1:4,1:0.5455:2,2:28:1:31.5:1:1:1.22:60:12:0.5455:0:1 -7 16584291 . A T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85937;LSEQ=CACATACATATAATCTTCTG;RSEQ=CTTTGCTCGTTACTTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:28:28,0:18,0:0.6087:1,1:28.3:1:30.3:1:1:0:60:56:0.6087:0:1 1/0:14:8:8,0:6,0:0.5714:0,0:24.1:1:31.3:1:1:0:60:16:0.5714:0:1 -7 16584370 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10597;SOR=Inf;LSEQ=ATAATATTGGTGCCACAATG;RSEQ=TAATATCCTTCTATTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:138,35:0:2,0:23.9:1:29.6:1:1:0:60:85.5:1:0:0.1 0/1:84:2:1,1:62,20:0.0238:2,2:17.5:1:31:1:0.43976:3.04948:60:4:0.0244:0:1 -7 16584389 . G T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.27387;LSEQ=GTTAATATCCTTCTATTTCT;RSEQ=GAAGTACGACAGTAGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:153,65:0.0136:2,2:8.3:1:31.3:1:1:1.17601:60:6:0.0138:0:2.3 0/1:116:2:1,1:73,41:0.0172:2,2:1:0:26.5:1:1:1.77108:60:4:0.0179:0:1.5 -7 16584413 . A G 35 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04354;SOR=Inf;LSEQ=GTACGACAGTAGCTTGGTAT;RSEQ=TTACATTTTGTCTCAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:184,120:0:2,0:25.2:1:29.1:1:1:0:60:151:1:0:0.5 0/1:166:3:2,1:98,65:0.0181:2,2:23:1:22.3:1:1:1.32:60:2:0.0121:0:1.3 -7 16584470 . A G 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00023;SOR=0.52544;LSEQ=CTCACCAAGCAAGTATTCAA;RSEQ=ATGGAATCTGGGTTTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:393:256:110,146:65,72:0.6514:2,2:26.8:1:31.4:1:0.39687:1.19767:60:63:0.6478:0:1.2 0/1:206:102:46,56:48,56:0.4951:2,2:26.6:1:31.2:1:0.88969:1.04329:60:101:0.4975:0:1.2 -7 16584588 . GAAT G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=8e-05;SOR=Inf;LSEQ=TATAAACATCATTATCTAAA;RSEQ=AATTGAGATATTTATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:7,69:0:2,0:22:1:29.8:1:1:0:60:24.333:1:0:0.2 0/1:30:7:1,6:1,22:0.2333:1,2:31.7:1:30.8:1:0.41839:3.47:60:14:0.2333:0.0333:0.1 -7 16584598 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTATCTAAAGAATAATTGA;RSEQ=ATATTTATAATAACATCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:5,57:0.0313:2,2:13.5:1:27.5:1:0.18006:10.50:60:4:0.0317:0:1 0/0:22:0:0,0:2,20:0:2,0:27.6:1:31.4:1:1:0:60:44:1:0:0.1 -7 16603332 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATAGAAGGAAAAAATAGA;RSEQ=TTAAAAATATGATTGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:34.5:1:31:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 16603629 . G T 44 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20952;SOR=3.25943;LSEQ=AGTTTTTAAATTTCCATATA;RSEQ=AAGTTACTTAACCAAGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:2:0,2:335,227:0.0035:2,0:1:0:24.5:1:0.16443:0:60:4:0.0036:0:1.5 0/1:349:4:0,4:191,153:0.0115:2,0:19.5:1:22.3:1:0.04056:0:60:3:0.0087:0:1.8 -7 16603660 . C G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=10.70973;LSEQ=ACCAAGGATTAGCAGAAAAA;RSEQ=CCAAGAAATGAAATGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:84:42,42:274,288:0.1296:2,2:23.4:1:32.1:1:0.90694:1.05:60:168:0.1302:0:1.1 1/0:364:224:106,118:71,68:0.6154:2,2:25.2:1:31.4:1:0.51776:1.16183:60:55:0.6128:0:1.1 -7 16603759 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52084;SOR=0;LSEQ=ATTGAAAGATGTTGGTATAT;RSEQ=TTCCATTAACGTCATATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:24,163:0.0106:2,2:14.5:1:28:1:0.24766:6.68:60:4:0.0106:0:1.5 0/0:123:0:0,0:26,96:0:2,0:20.9:1:29.8:1:1:0:60:121:0.9918:0:0.1 -7 18170622 . A T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTTTCTAGTTTCTTAT;RSEQ=ATCGAGTGTTTAGAAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:19.3:1:31.3:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 18170626 . G C 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTAGTTTCTTATAATC;RSEQ=AGTGTTTAGAAATCTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:23:1:32.3:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 18170898 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13456;SOR=Inf;LSEQ=TGCTTTAAAAATAGAACATT;RSEQ=ATGATTCAGTGCCCAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:168,20:0:2,0:21.4:1:31.8:1:1:0:60:187:0.9947:0:0.7 0/1:110:2:1,1:95,13:0.0182:2,2:15.5:1:33:1:0.23937:7.07866:60:4:0.0187:0:1 -7 18170920 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1411;LSEQ=TGATTCAGTGCCCAATATTT;RSEQ=TTAGTATGAACTTAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:290:193:155,38:77,19:0.6655:2,2:22.2:1:28.5:1:1:1.01:60:47.25:0.6655:0:1.1 0/1:174:38:29,9:107,29:0.2184:2,2:28.3:1:28.2:1:0.82472:1.14414:60:76:0.2184:0:1.2 -7 18171029 . G T 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17755;LSEQ=AAATGTTATGGTTAAAGAAC;RSEQ=AGTTTAGTAGCACTAATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:876:541:267,274:165,169:0.6176:2,2:25.7:1:29.5:1:1:1.00193:60:179.333:0.6191:0:1.1 0/1:566:126:57,69:215,224:0.2226:2,2:27.9:1:29:1:0.48017:1.16158:60:252:0.2254:0:1.1 -7 18171348 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAACAAGAGAGGAGGGTG;RSEQ=AGGTGAGGCGGTGAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:22.5:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 18182755 . T C 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1954;LSEQ=CTAGGGCAAAGATCTCCCCC;RSEQ=GCTTTTGTAAACTGGTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:940:622:280,342:152,163:0.6617:2,2:25.6:1:30:1:0.36743:1.13884:60:76.75:0.6638:0:1.4 0/1:561:155:76,79:202,204:0.2763:2,2:26.4:1:29.1:1:0.92485:1.02924:60:76.5:0.2777:0:1.9 -7 18182771 . T C 228 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24372;SOR=1.1739;LSEQ=CCCCTGCTTTTGTAAACTGG;RSEQ=CTATCCTGTGCACCTACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:849:157:64,93:298,393:0.1849:2,2:25.6:1:31.3:1:0.65507:1.10171:60:51.333:0.1838:0:2.2 0/1:561:118:48,70:214,229:0.2103:2,2:25.6:1:31:1:0.14726:1.36205:60:117:0.2108:0:2.2 -7 18182840 . G C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13992;LSEQ=GGCATATTTGTATTTTGTAG;RSEQ=AATTGCTGATAGTAATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:292:199:42,157:18,75:0.6815:2,2:23.1:1:31.9:1:0.7588:1.11:60:48.75:0.6794:0:1.5 0/1:196:45:12,33:40,111:0.2296:2,2:25.6:1:32:1:1:1.01:60:44:0.2292:0:1.6 -7 18988498 . C G 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01754;SOR=Inf;LSEQ=TGAAATAAGACAGAAATTTT;RSEQ=TAACAAGCTGTTTAAACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:14,2:0:2,0:20.9:1:31.6:1:1:0:60:32:1:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:20:1:33:1:1:0:60:4:0.6667:0:1 -7 18988707 . G GT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTTAGCGTTTTGGGAGG;RSEQ=TTTTTTTTCTGTTTTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:7,9:0.1111:2,0:9.5:1:31:1:0.49673:0:60:4:0.1111:0.0556:0.5 0/0:7:0:0,0:4,3:0:2,0:28.7:1:30.9:1:1:0:60:14:1:0:0 -7 18988818 . A G 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.3971;SOR=1.72395;LSEQ=AATTTTGGCTGGAGTATCTT;RSEQ=TATAGATTTCTTCACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:23:13,10:5,5:0.697:2,2:25.4:1:32.2:1:1:1.29:60:46:0.697:0:2 1/1:30:24:13,11:4,2:0.8:2,2:27.9:1:31.8:1:0.67247:1.66358:60:48:0.8:0:1.9 -7 18988836 . A G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.57856;SOR=1.56038;LSEQ=TTATATAGATTTCTTCACTG;RSEQ=GCTTTTTCTTCATCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:12,11:5,6:0.6765:2,2:29.2:1:30.6:1:1:1.30:60:22:0.6667:0:2 1/0:30:23:12,11:4,3:0.7667:2,2:25.1:1:30.7:1:1:1.2141:60:46:0.7667:0:2 -7 18988889 . CATT C 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.28118;SOR=0;LSEQ=GTCATCTTCATTGTCATCAT;RSEQ=ATCTTCATTAGCAGCAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:2,2:12,12:0.1429:2,2:33.8:1:32.3:1:1:1:60:8:0.1429:0:0 0/0:17:0:0,0:8,9:0:2,0:25.7:1:28.1:1:1:0:60:16:1:0:1.1 -7 18988916 . A T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02126;SOR=Inf;LSEQ=TTCATTAGCAGCAAGTTTTT;RSEQ=CTTTTTTTCTGTGGAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,8:0:2,0:26.2:1:28:1:1:0:60:23:1:0:0.2 0/1:17:4:1,3:6,7:0.2353:2,2:37.3:1:29:1:0.60294:2.43937:60:8:0.2353:0:1.3 -7 18989094 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCAACCATAAGACCATA;RSEQ=GTGGTGGTATTTCAAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:18,34:0.037:2,2:28:0:32:0:1:1.87:60:4:0.037:0:1.5 0/0:17:0:0,0:9,8:0:2,0:16.3:1:32.1:1:1:0:60:34:1:0:0.4 -7 18989154 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50913;SOR=0;LSEQ=GTACAGACATTTTCAAAGTT;RSEQ=CCAGTGTTACTTTTATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:17,24:0.0465:2,2:10:1:30:1:1:1.40:60:4:0.0476:0:1 0/0:30:0:0,0:14,15:0:2,0:23.9:1:31.8:1:1:0:60:58:0.9667:0:0.5 -7 18989156 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17505;SOR=Inf;LSEQ=ACAGACATTTTCAAAGTTGC;RSEQ=AGTGTTACTTTTATTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:18,23:0:2,0:17.2:1:31.4:1:1:0:60:82:1:0:0.3 0/1:30:2:1,1:14,14:0.0667:2,2:20.5:1:29:1:1:1:60:4:0.0667:0:1.5 -7 18989222 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.2092;SOR=Inf;LSEQ=TTCAACGATGTGCAATTCAT;RSEQ=ATAGGTACCAGCTCCTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:25.1:1:30.4:1:1:0:60:15:1:0:0.6 0/1:14:2:1,1:6,6:0.1429:2,2:28.5:1:26.5:1:1:1:60:4:0.1429:0:2 -7 18989232 . A G 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15195;SOR=3.3402;LSEQ=TGCAATTCATCATAGGTACC;RSEQ=GCTCCTGAACTGGCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:4,6:5,3:0.5556:2,2:20.7:1:29.7:1:0.63719:2.37182:60:20:0.5556:0:1.1 1/1:16:13:8,5:2,1:0.8125:2,2:17.4:1:30.6:1:1:1.23302:60:26:0.8125:0:1.2 -7 18989402 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=ATGGGTTTGTGGCACCCACT;RSEQ=TGGTGGGAGAGAAGGCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:17.2:1:32.2:1:1:0:60:12:1:0:0 0/1:6:2:1,1:0,4:0.3333:0,2:18:1:30:1:0.33333:0:60:4:0.3333:0:1 -7 19616137 . A C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=TTTATATCAATGTAGAAGAG;RSEQ=AACATTTGGGTTGAAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:38:1:33.7:1:1:0:60:6:0.4286:0:1.3 0/0:4:0:0,0:4,0:0:0,0:13.3:1:30.8:1:1:0:60:8:1:0:0 -7 19616316 . C T 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1979;SOR=0.71402;LSEQ=GAAAATGGCATATTTCTCTA;RSEQ=GTTTGAATTTGCATGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:113:90,23:47,8:0.6726:2,2:21.8:1:30.5:1:0.40454:1.49793:60:36.667:0.6707:0:2 1/0:106:63:42,21:29,14:0.5943:2,2:21.7:1:29.8:1:1:1.03538:60:62:0.5962:0:2 -7 19616327 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06454;SOR=Inf;LSEQ=ATTTCTCTACGTTTGAATTT;RSEQ=CATGTGTTACACATGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:160,52:0:2,0:23.1:1:32:1:1:0:60:69.667:1:0:1.2 0/1:143:3:1,2:92,48:0.021:2,2:9:1:29.7:1:0.27981:3.79474:60:6:0.0211:0:1.3 -7 19616340 . A G 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30677;SOR=0.80032;LSEQ=TGAATTTGCATGTGTTACAC;RSEQ=TGTGTAAGCAAGGGTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:179:125,54:62,26:0.6654:2,2:23.6:1:30.3:1:1:1.03004:60:58.667:0.6642:0:1.7 1/0:171:105:64,41:44,22:0.614:2,2:25.6:1:29.3:1:0.51602:1.2794:60:25.25:0.6159:0:1.7 -7 19616437 . T G 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01453;SOR=0.64863;LSEQ=TTTGTTTTAGATATTACACA;RSEQ=AGTAAAAGAAAAATCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:267:120,147:56,80:0.6609:2,2:24.8:1:31.4:1:0.52421:1.17:60:266:0.6683:0:1.1 1/0:215:120:56,64:45,50:0.5581:2,2:24.4:1:31.1:1:1:1.02845:60:59:0.5592:0:1.3 -7 19616522 . C T 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATCTTTAAAAAGTGTCAT;RSEQ=GATTTCCTAGCAGCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:42,131:0:2,0:22.2:1:30.1:1:1:0:60:346:1:0:0.5 0/1:92:34:12,22:12,46:0.3696:2,2:21.1:1:29:1:0.1448:2.07:60:68:0.3778:0:1.6 -7 19616550 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13372;SOR=Inf;LSEQ=TAGCAGCTTTTTTAAAAAGT;RSEQ=TCACTACAAACATATACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:9,89:0:2,0:22.1:1:32.1:1:1:0:60:97:1:0:0.5 0/1:57:2:1,1:7,48:0.0351:2,2:19.5:1:25.5:1:0.26316:6.48:60:4:0.0364:0:2.5 -7 19616566 . A T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00283;SOR=0.24324;LSEQ=AAGTCTCACTACAAACATAT;RSEQ=CACCAATTATAAAAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:52:1,51:0,14:0.7879:1,1:24.6:1:29.5:1:1:0:60:16.333:0.7778:0:1.1 0/1:34:16:0,16:1,17:0.4706:1,1:29:1:27.6:1:1:0:60:15:0.4545:0:1.8 -7 19616651 . G GT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCATGGAAGTATAGGAG;RSEQ=TTTTTTTTTGCTTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:0,11:0.1538:0,0:36:1:31.5:1:1:0:60:4:0.1667:0:0 0/0:2:0:0,0:0,2:0:0,0:19.5:1:30.5:1:1:0:60:4:1:0:0.5 -7 19694243 . T C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00424;SOR=Inf;LSEQ=ATACAGGGCCCAAAGGCGAG;RSEQ=AATAGCAAGATGGCTGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:69,36:0:2,0:19.8:1:28.6:1:1:0:59.9:210:1:0:0.1 0/1:55:5:4,1:31,18:0.0909:2,2:17.6:1:32.4:1:0.64611:2.29:60:10:0.0926:0:1 -7 19694269 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52524;SOR=0;LSEQ=CAAGATGGCTGTCAGGGGAC;RSEQ=TAGAAAGGGGAGAAGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:82,63:0.0135:2,2:45:1:31.5:1:1:1.29922:60:4:0.0138:0:1 0/0:92:0:0,0:55,36:0:2,0:24:1:30.8:1:1:0:59.5:182:1:0:0.2 -7 19694292 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5277;SOR=0;LSEQ=GAAAGGGGAGAAGCCATGTC;RSEQ=CCCAACTACAGAGGTTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:85,82:0.0118:2,2:31.5:1:29.5:1:1:1.03638:60:4:0.0121:0:1 0/0:103:0:0,0:56,47:0:2,0:28.8:1:30.5:1:1:0:59.5:50.5:1:0:0.2 -7 19694293 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14113;SOR=Inf;LSEQ=AAAGGGGAGAAGCCATGTCG;RSEQ=CCAACTACAGAGGTTGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:87,85:0:2,0:30.1:1:31.1:1:1:0:59.8:27.667:1:0:0.1 0/1:104:2:1,1:55,47:0.0192:2,2:31.5:1:30:1:1:1.16844:60:4:0.0194:0:1.5 -7 19694393 . G T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03066;SOR=Inf;LSEQ=CCTCGTACTATCCTTGACTG;RSEQ=TTAGTGTAAAAACAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:6,28:0:2,0:28.1:1:31.5:1:1:0:60:33:1:0:0.1 0/1:26:4:1,3:1,21:0.1538:1,2:10:1:30.3:1:0.28923:6.21:60:8:0.1538:0:1.5 -7 19695194 . T C 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCTCTTTGACTGTCTTT;RSEQ=CCCTCCTCCCCACCACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:27:1:1:0:60:4:1:0:1 -7 20042316 . G T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30343;SOR=4.66971;LSEQ=TCTGCAAATCTGACAAGTTG;RSEQ=CATCCAAGCAAAATTTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:0,1:111,30:0.007:2,0:1:0:25:0:0.21831:0:60:2:0.0071:0:1 0/1:93:3:1,2:63,27:0.0323:2,2:18.7:1:27.3:1:0.2284:4.5803:60:6:0.0326:0:1 -7 20042356 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16863;SOR=Inf;LSEQ=TGATCACCTTGCCCTTTCGG;RSEQ=CGGAACCGCCATCTTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:129,120:0:2,0:28.9:1:31.2:1:1:0:57.1:82:1:0:0.1 0/1:174:2:1,1:94,78:0.0115:2,2:15:0:30.5:1:1:1.20383:48:4:0.0117:0:1 -7 22987360 . A AGT 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.44661;SOR=0.68171;LSEQ=CTTTGTACTCTTAAAATTCT;RSEQ=TTTTTTATGAGGCTACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:84:69:65,4:13,2:0.8214:2,2:22:1:31.4:1:0.29036:2.47:59.9:138:0.8313:0.2262:0 1/0:33:25:24,1:8,0:0.7576:0,1:23.8:1:29.9:1:1:0:60:24:0.75:0.2121:0.2 -7 22987500 . G A 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28423;SOR=1.18013;LSEQ=TCATCTATTATTAACAGTAA;RSEQ=TATTAATGTGGCTGTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:157:77,80:167,161:0.3237:2,2:28.5:1:30.3:1:0.77099:1.07751:60:51.333:0.3222:0:1.1 0/1:313:113:58,55:103,97:0.361:2,2:22.6:1:29.6:1:1:1.00691:60:112:0.3601:0:1.1 -7 23293746 . A G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=16.82536;LSEQ=AATGTTTATGAACGAAAGGA;RSEQ=AAAGATGCTGGATCATCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:15:7,8:302,303:0.0242:2,2:28.6:1:32:1:1:1.13885:60:30:0.0244:0:1.1 0/1:366:108:56,52:119,138:0.2951:2,2:22.8:1:31.2:1:0.35952:1.25:60:53:0.2961:0:1.2 -7 23293803 . C A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05844;SOR=Inf;LSEQ=CCTAGGAGGCCGTGTGCAGG;RSEQ=GGTCCTGACCAGTGACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:102,226:0:2,0:25.2:1:30.6:1:1:0:60:163:1:0:0.2 0/1:209:3:2,1:76,130:0.0144:2,2:25.7:1:27.7:1:0.55716:3.40:60:6:0.0148:0:1 -7 23293814 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15845;SOR=Inf;LSEQ=GTGTGCAGGCGGTCCTGACC;RSEQ=GTGACTCACCAGCCCTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:77,202:0:2,0:24.6:1:30.8:1:1:0:60:68.75:1:0:0.1 0/1:185:2:1,1:64,119:0.0108:2,2:38.5:1:30:1:1:1.85:60:4:0.0109:0:1 -7 23662013 . G A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.125;SOR=Inf;LSEQ=GTTTATAGTATTCTCTGGTG;RSEQ=TAGTTTGTATTTCTGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:0.2857:0,0:26.8:1:29.5:1:1:0:60:8:0.2857:0:1 1/1:2:2:2,0:0,0:1:0,0:11:1:27.5:1:1:0:50:4:1:0:1 -7 23662135 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53508;SOR=0;LSEQ=AAAGCGAAACTGGATTTAGT;RSEQ=CAGTCAACGATGGACTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:103,35:0.0143:2,2:15.5:1:28.5:1:0.44954:2.9155:60:4:0.0147:0:1.5 0/0:80:0:0,0:60,20:0:2,0:26:1:32:1:1:0:60:79:1:0:0.1 -7 23662148 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52702;SOR=0;LSEQ=ATTTAGTGCAGTCAACGATG;RSEQ=ACTGTCTGTATGCCAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:113,53:0.0119:2,2:29.5:1:30:0:0.54085:2.12161:60:4:0.0122:0:1 0/0:103:0:0,0:69,34:0:2,0:26.2:1:30.7:1:1:0:60:102:1:0:0.1 -7 23662173 . C A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29492;SOR=0;LSEQ=TCTGTATGCCAGGTGTATCC;RSEQ=TTGTGTAACTGATTGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:3:2,1:124,98:0.0133:2,2:30.3:1:24:1:1:1.58:60:2:0.009:0:1.3 0/0:135:0:0,0:76,59:0:2,0:8:0:16:0:1:0:50:0:0:0:2 -7 23894809 . T C 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTGGCTTCACCTCTTAA;RSEQ=CCCCCTTCTAAACAGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:21:1:33.3:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 23894853 . T C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGCTGTTGGGAATTGGG;RSEQ=GATGACTGCTCTAGCTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:29.7:1:32:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 23895077 . A C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.06164;LSEQ=CAAATTTGACGAGGAGGTTA;RSEQ=AAATACAGGGCCCGAAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:32:23,9:9,7:0.6667:2,2:27.3:1:32:1:0.3387:1.96:58.4:64:0.6667:0:1 1/0:25:17:12,5:7,1:0.68:2,2:20.4:1:31.6:1:0.62372:2.80758:60:34:0.68:0:1.4 -7 23895205 . CT C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.13816;SOR=Inf;LSEQ=CATTGTCTGATTTCAGAAGC;RSEQ=TTTCCTGTAAACGCTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:22,38:0:2,0:21.7:1:30.4:1:1:0:60:120:1:0:0.2 0/1:36:2:1,1:13,21:0.0556:2,2:29:1:33.5:1:1:1.59:60:4:0.0556:0:0.5 -7 23895326 . T C 74 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGAGGAGGTCTAGGCCT;RSEQ=GGTGGTTTTGGAGAGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:34.8:1:28.8:1:1:0:37.2:12:1:0:1.5 1/1:2:2:0,2:0,0:1:0,0:40:1:32:0:1:0:40:4:1:0:1 -7 24164485 . A AT 70 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02308;SOR=6.42475;LSEQ=TAAAATGCTTGTATAGTCAG;RSEQ=TTTTTTTTAACTTTCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:2:2,0:194,8:0.0098:1,0:30:1:33:0:1:0:60:4:0.0101:0:0 0/1:83:5:5,0:73,5:0.0602:2,0:21:1:30.2:1:1:0:60:10:0.061:0.0241:0 -7 24164624 . T C 218 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=420.64974;LSEQ=TTTTGAGGCTGCAACCAGTA;RSEQ=GTACATGTTTTGGATTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:810:1:0,1:328,481:0.0012:2,0:1:0:31:0:1:0:60:2:0.0012:0:1 0/1:452:155:64,91:118,176:0.3429:2,2:25.6:1:30:1:0.84011:1.05:60:154:0.343:0:1.2 -7 24164678 . C T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03029;SOR=Inf;LSEQ=CCTTACTTCATATCAGGCTT;RSEQ=CACAGCTGGACACAGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:74,255:0:2,0:21.5:1:31.2:1:1:0:60:81.25:1:0:0.1 0/1:150:3:0,3:32,115:0.02:2,0:27.3:1:30.3:1:1:0:60:6:0.0204:0:1 -7 26196963 . G A 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCACCACTGCTTCTGGCT;RSEQ=ATTTTTTTTTTTTTTAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:0:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 26196964 . A AT 32 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCACCACTGCTTCTGGCTG;RSEQ=TTTTTTTTTTTTTTAATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38:0:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 27134260 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50035;SOR=0;LSEQ=CAGATCTTCACTTGGGTCTC;RSEQ=TTGAGCTGCAGGGATGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:29,41:0.0278:2,2:22.5:1:29:1:1:1.41:60:4:0.0282:0:1 0/0:60:0:0,0:30,30:0:2,0:29.1:1:29.6:1:1:0:60:19:1:0:0.1 -7 27135314 . C T 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTAGCCGGCTGGGGGTGG;RSEQ=GATGGTGGTGGTGGTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:21.7:1:30:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:28:0:28:0:1:0:60:2:1:0:1 -7 27141657 . C G 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCCACTCTCCCCTCCCCC;RSEQ=ACAGCCACTCTCGGGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:5,2:0.2222:2,0:16.5:1:30:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 27141768 . TGGC T 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.05;SOR=Inf;LSEQ=AGGGCCGGTGGCTGCGGCGG;RSEQ=GGCGGCGGCGGCGGCCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:27:1:31.4:1:1:0:60:38:1:0:0.3 0/1:6:2:1,1:2,2:0.3333:2,2:38.5:1:30:1:1:1:60:4:0.3333:0:0 -7 27141771 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCCGGTGGCTGCGGCGGTGG;RSEQ=GGCGGCGGCGGCGGCCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:6,11:0.1053:2,2:29.5:1:29:1:1:1.77:60:4:0.1053:0:1 0/0:6:0:0,0:2,2:0:2,0:15:1:33:1:1:0:60:8:1:0:0.3 -7 27201532 . C A 31 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGACTCCGCGGGGGTGG;RSEQ=GGGCGGTGCGAGGATGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31.5:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:10:0:15:0:1:0:60:0:0:0:2 -7 27203139 . G A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.56488;SOR=3.5981;LSEQ=AGGCTAGGGTGGGGGTGAGA;RSEQ=AAGGGAGAAGGCGGAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:20.5:1:32:1:1:0:60:8:0.5:0:1 1/1:5:4:4,0:1,0:0.8:0,0:16.5:1:29.8:1:1:0:60:8:0.8:0:1 -7 27203259 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.14697;SOR=Inf;LSEQ=GGTCTTTGTTGATTTTCTTC;RSEQ=TTTTCATCCTGCGGTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:64,50:0:2,0:26.6:1:29.9:1:1:0:60:56:1:0:0.1 0/1:72:2:1,1:38,31:0.0278:2,2:21.5:1:29:1:1:1.22227:60:4:0.0299:0:1 -7 27203278 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51256;SOR=0;LSEQ=CATTTTCATCCTGCGGTTCT;RSEQ=GAACCAGATCTTGACCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:53,59:0.0174:2,2:44.5:1:31:1:1:1.11:60:4:0.0174:0:1 0/0:81:0:0,0:38,43:0:2,0:27.8:1:30.8:1:1:0:60:80:1:0:0.2 -7 27203334 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15063;SOR=Inf;LSEQ=GCAGTCGAGCCACCTCGTAC;RSEQ=TGCGGTCCCTGGTGAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:21,46:0:2,0:22.4:1:31.7:1:1:0:60:134:1:0:0 0/1:43:2:1,1:14,27:0.0465:2,2:34:1:30:1:1:1.90:60:4:0.0476:0:1 -7 27203413 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=GTGTTTTGTATAGGGGCACC;RSEQ=CTTTTTCCGAGTGGAGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:0:1,0:16.4:1:32.1:1:1:0:60:26:1:0:0 0/1:8:2:1,1:0,6:0.25:0,2:35.5:1:27.5:1:0.25:0:60:4:0.25:0:1 -7 28996220 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGCCGACTCAGCCTTAG;RSEQ=GCGCTGCGGTTGCCTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42.5:1:30:1:1:0:60:4:1:0:1 -7 28996940 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCGCGGCCCGAGGTGCTG;RSEQ=AGGTTGTTGGCCGAGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:17,21:0.05:2,2:24.5:1:30.5:1:1:1.23:60:4:0.0513:0:2.5 0/0:4:0:0,0:2,2:0:2,0:32.3:1:31:1:1:0:60:8:1:0:1.3 -7 28996944 . T C 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCCCGAGGTGCTGCAGG;RSEQ=TGTTGGCCGAGAGGATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:18,22:0,0:1:0,2:28.3:1:32.3:1:1:0:60:39:1:0:1.5 1/1:4:4:2,2:0,0:1:0,2:32.3:1:31:1:1:0:60:8:1:0:1.3 -7 28997596 . G GC 50 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTCCGGGCACACGGGCTCG;RSEQ=CAGCGGCGGGAGCGCGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:1,0:0.75:0,0:29.7:1:32:1:0.25:0:60:6:0.75:0:0 1/1:1:1:0,1:0,0:1:0,0:15:0:33:0:1:0:60:2:1:0:0 -7 28997974 . G T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AGCAAGACCCGGCGCTTTTT;RSEQ=TTTGCAGCTGAGTCCGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:47.5:1:30.5:1:1:1:60:4:0.5:0:1 0/0:2:0:0,0:1,1:0:2,0:15.5:1:30:1:1:0:60:4:1:0:0.5 -7 29880530 . T G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGATCGGACATACCCTGG;RSEQ=GGTTGGTGAAGGATAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:36:1:32.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:34:1:27.5:1:1:0:60:4:1:0:0 -7 31287159 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05603;SOR=Inf;LSEQ=AAAAAGCAGCCCCAGGCCAA;RSEQ=GGCATTGGGAGTGCTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:223,140:0:2,0:24.4:1:31.3:1:1:0:60:71.6:1:0:0.2 0/1:226:3:1,2:130,93:0.0133:2,2:22.3:1:29.7:1:0.57389:2.78303:60:6:0.0133:0:1 -7 31287173 . C T 59 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04149;SOR=7.5154;LSEQ=GGCCAAGGGCATTGGGAGTG;RSEQ=TGGGGCAGGTGAGGTAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:1:0,1:237,176:0.0024:2,0:1:0:15:0:0.42754:0:60:0:0:0:1 0/1:279:5:1,4:151,123:0.0179:2,2:15.2:1:25.6:1:0.18086:4.88612:60:4:0.0147:0:1 -7 31287246 . C A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.76058;LSEQ=GCCCCAGGAGAAGATGAAAT;RSEQ=TTAAGCCCAGATTTGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:1:1,0:96,167:0.0038:2,0:1:0:26:0:0.36742:0:60:2:0.0038:0:1 0/1:175:33:14,19:50,92:0.1886:2,2:20.8:1:28.1:1:0.54763:1.35:60:32:0.185:0:1.1 -7 32159902 . G A 81 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=GGCCGCAGTCTCTGCAGACC;RSEQ=TCATACTTAGCCTTTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:5,2:6,2:0.4667:2,2:20.1:1:29.1:1:1:1.18545:60:14:0.4667:0:1.1 0/0:2:0:0,0:1,1:0:2,0:14:1:30:1:1:0:60:4:1:0:0 -7 32161232 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCAACCCAGAGTTTCAT;RSEQ=TCCAGCCAAACTAAGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 32894331 . G T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00642;SOR=5.60742;LSEQ=TTCGAATCACCCCATAAGGG;RSEQ=CAGAAGCATGTCTCAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:5,0:54,0:0.0847:1,0:26.8:1:29.6:1:1:0:60:10:0.0909:0:1 0/1:23:8:7,1:15,0:0.3478:1,2:30.1:1:26:1:0.34783:0:59.6:3:0.2857:0:2.1 -7 32894398 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53438;SOR=0;LSEQ=AGAGAAAATCTAGGTTTCAT;RSEQ=TGAAGAACTGCCATTTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:150,41:0.0103:2,2:32.5:1:28.5:1:0.38876:3.62636:60:4:0.0104:0:1 0/0:112:0:0,0:81,31:0:2,0:24.8:1:29.1:1:1:0:60:36.333:1:0:0.1 -7 32894503 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.2683;LSEQ=AGAAGAGCTTGGAAAAATGC;RSEQ=TGGCAGCCTGATGTCACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:199:90,109:144,149:0.4045:2,2:27.3:1:30.2:1:0.40887:1.17009:59.7:65.333:0.4033:0:1.1 1/1:295:239:114,125:23,32:0.8102:2,2:26.2:1:29.4:1:0.4568:1.27:60:58.75:0.8103:0:1.2 -7 32894601 . G A 119 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00333;SOR=3.50137;LSEQ=AGACTCAGACTCCTCAGACT;RSEQ=GGAACCAGGGGAGACTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:11:3,8:19,118:0.0743:2,2:18.3:1:30.5:1:0.21146:2.31:56.4:22:0.0753:0:1.1 0/1:68:15:4,11:7,46:0.2206:2,2:15:1:30.6:1:0.24264:2.35:58.5:30:0.2206:0:1.1 -7 33716528 . T C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATGAAATACTAGACATGAGA;RSEQ=TTTTTTTCTCTTTATTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32.5:1:31:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:9:0:31:0:1:0:60:2:1:0:0 -7 33716674 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=GTCAGCGGGCCTGGATGCAC;RSEQ=TCCCAGTTCTGCCTCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:24:1:29:1:1:1.12:60:4:0.1053:0:1.5 0/0:11:0:0,0:4,7:0:2,0:23.6:1:29.6:1:1:0:60:10:1:0:0.2 -7 34959604 . C T 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13949;SOR=0.55175;LSEQ=TTTTAGTCTCCCCTGGTTCC;RSEQ=AGTCTGAGGAGTCTGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:36:33,3:60,1:0.3711:1,2:26.5:1:31.3:1:0.1427:5.35796:53.8:72:0.3711:0:2 0/1:49:12:12,0:33,4:0.2449:2,0:28.2:1:31.1:1:0.55993:0:52.3:24:0.2553:0:2.1 -7 34959617 . C T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.02034;SOR=0.47024;LSEQ=TGGTTCCCAGTCTGAGGAGT;RSEQ=TGAGTCTGGGCTGCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:69:62,7:41,4:0.6053:2,2:24.1:1:30.1:1:1:1.15577:55:68:0.6018:0:1.5 0/1:67:28:25,3:31,8:0.4179:2,2:24.9:1:29.6:1:0.33662:2.13:55.6:56:0.4375:0:1.5 -7 34959661 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15799;SOR=Inf;LSEQ=AGTGTTTCAGCCCCTCTGCC;RSEQ=TGCTCACCTCTTGACCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:171,92:0:2,0:22.9:1:31.1:1:1:0:60:64.75:1:0:0.4 0/1:174:2:1,1:109,63:0.0115:2,2:32.5:1:29:1:1:1.72436:60:4:0.0118:0:2.5 -7 34959764 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1546;SOR=Inf;LSEQ=AGCTGTTCAGCTGAGTACTG;RSEQ=CTTGTGCTTCCCCAGCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:112,182:0:2,0:24.1:1:29.6:1:1:0:59.7:57.8:1:0:0.2 0/1:191:2:1,1:67,122:0.0105:2,2:26:1:31:1:1:1.81:60:4:0.0105:0:1 -7 34959828 . C G 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.44022;SOR=0.59762;LSEQ=ATGAAACCTAGATTTTCTCT;RSEQ=CCCATTTGAAACGAAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:14:0,14:4,61:0.1772:2,1:25.6:1:32.6:1:1:0:60:28:0.1842:0:2.2 0/1:44:5:0,5:5,34:0.1136:2,0:21.4:1:31.8:1:1:0:60:10:0.119:0:1.6 -7 34959833 . TTT A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.83001;SOR=0.83062;LSEQ=ACCTAGATTTTCTCTCCCCA;RSEQ=GAAACGAAAGCTCCACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:25:1,24:3,45:0.3378:2,1:22.8:1:32.1:1:1:1.5905:54.8:50:0.3472:0.0676:0.2 0/1:37:11:1,10:2,23:0.2973:2,2:18.3:1:29.8:1:1:1.15:56:10:0.2857:0.1351:0.3 -7 34959845 . G C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7502;SOR=0.61877;LSEQ=TCTCCCCATTTGAAACGAAA;RSEQ=CTCCACCAGAGGGTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:13:0,13:2,46:0.2131:1,1:19.6:1:30.3:1:1:0:60:12:0.2:0:2.3 0/1:21:3:0,3:1,17:0.1429:1,0:23.3:1:30.3:1:1:0:60:6:0.1429:0:2 -7 35458399 . A T 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0.15605;LSEQ=GAATTCCCAGAGGAGTGAGA;RSEQ=GATTGGGGTTGGAGTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:46.7:1:31.3:1:1:0:60:6:0.75:0:1 0/1:4:1:1,0:3,0:0.25:0,0:35:0:31:0:1:0:60:2:0.3333:0:3 -7 35458457 . T C 29 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.09524;SOR=0;LSEQ=CTCTTATTTCTCTCTGGTGG;RSEQ=GGTGGTGGTGGTGGCGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:6:0:29.5:1:1:2.24:22:4:0.25:0:5 0/0:19:0:0,0:9,9:0:2,0:28.8:1:25.2:1:1:0:60:8:1:0:1.1 -7 35458489 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0265;SOR=Inf;LSEQ=TGGCGGTGGTGATGGCGGTG;RSEQ=CGGTGACGGTGGCGGTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:24.1:1:30.4:1:1:0:56.5:10:1:0:1.1 0/1:27:6:3,3:11,10:0.2222:2,2:33.8:1:27.3:1:1:1.09612:60:12:0.25:0:1.2 -7 35458495 . A G 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20139;SOR=0;LSEQ=TGGTGATGGCGGTGGCGGTG;RSEQ=CGGTGGCGGTGGCGGTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:15,12:0.069:2,2:36:0:31.5:1:1:1.24034:22:4:0.0714:0:5 0/0:35:0:0,0:18,17:0:2,0:20.7:1:27.1:1:1:0:60:7.75:1:0:0.9 -7 35458499 . T TGGC 28 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0.19821;SOR=0;LSEQ=GATGGCGGTGGCGGTGACGG;RSEQ=GGCGGTGGCGGTGGCGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:0.0645:2,2:31:0:28.5:1:1:1.22249:22:4:0.0667:0:5 0/0:38:0:0,0:19,18:0:2,0:20.2:1:28.1:1:1:0:60:36:1:0:0.7 -7 35458520 . TGGC T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.21347;SOR=0;LSEQ=GGCGGTGGCGGTGGCGGTGG;RSEQ=GGCGGCGGCGGTGGCGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:18,14:0.0588:2,2:33.5:1:31.5:1:1:1.27615:60:4:0.0588:0:0.5 0/0:39:0:0,0:21,18:0:2,0:21.9:1:30:1:1:0:60:18.5:1:0:0.7 -7 35458532 . C A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.01329;SOR=0.22866;LSEQ=GGCGGTGGTGGCGGCGGCGG;RSEQ=GGTGGCGGTGGCGGGCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:7,6:11,7:0.4194:2,2:25.8:1:27.2:1:0.72695:1.33394:60:3.333:0.3846:0:1 0/1:36:5:2,3:16,15:0.1389:2,2:28.8:1:30:1:1:1.57936:60:10:0.1429:0:1.2 -7 35458551 . GT G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01355;SOR=5.31402;LSEQ=GCGGTGGCGGTGGCGGGCTA;RSEQ=AAGACCTCTGCGTGTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:10,3:6,5:0.5417:2,2:30.7:1:31.3:1:0.39045:2.66:60:26:0.5652:0.0417:0.7 1/1:30:26:12,14:3,1:0.8667:2,2:24.3:1:30.6:1:0.5977:3.36376:60:25:0.8621:0.1:0.7 -7 36541151 . G A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAATGGTTAAATGTACCC;RSEQ=GGGCTCAGTGAGGGTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:0:32.5:1:1:0:24:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 36858427 . G T 99 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21842;SOR=0;LSEQ=TCCACGTGCAAAAGAATGAA;RSEQ=TTGGACCCCTGCCTCACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:7,2:7,1:0.5294:2,2:14.3:1:31.3:1:1:1.9219:60:18:0.5294:0:1.1 0/0:3:0:0,0:3,0:0:0,0:27:1:31.3:1:1:0:60:6:1:0:0 -7 36858494 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52425;SOR=0;LSEQ=TGTGATTCCGTCCTGCATGG;RSEQ=TGTTCTCTTGAGCAGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:23,12:0.0541:2,2:37.5:1:29:1:1:1.88115:60:4:0.0556:0:1.5 0/0:22:0:0,0:13,9:0:2,0:21.6:1:31.9:1:1:0:60:44:1:0:0.2 -7 36858643 . A G 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=111.29329;LSEQ=TTGTGAACTAAAGGCTGACA;RSEQ=TCACTTTCAAGTGGATAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:1,0:103,34:0.0072:2,0:46:0:34:0:1:0:60:2:0.0074:0:1 0/1:66:30:23,7:26,10:0.4545:2,2:22.2:1:31.3:1:0.78099:1.26:60:29:0.4603:0:1 -7 36858807 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00704;SOR=Inf;LSEQ=CAACTTTGAAAATGTCTGTA;RSEQ=AGCCAACGGTTTCCCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:0:0,0:262,204:0:2,0:27.5:1:32.1:1:1:0:59:115.5:1:0:0.1 0/1:277:5:2,3:147,125:0.0181:2,2:24.6:1:26.8:1:0.66492:1.76038:51.6:10:0.0182:0:1.2 -7 36858858 . C T 127 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=17.97783;LSEQ=TAACACCACCAGTAGTCTTA;RSEQ=GGTTGAAGTGTGGTTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:2:1,1:276,268:0.0037:2,2:26:1:31:1:1:1.0298:60:4:0.0038:0:1 0/1:354:22:11,11:170,162:0.0621:2,2:17.4:1:28.7:1:1:1.04926:55.6:44:0.0632:0:1.5 -7 36859014 . C A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56807;SOR=2.96103;LSEQ=GAGGTGGTAGCAAGGTGCCA;RSEQ=AGAAAAAAGTAAAACTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:0,1:79,123:0.0049:2,0:30:0:16:0:1:0:60:0:0:0:1 0/1:138:2:1,1:56,80:0.0145:2,2:37.5:1:29:1:1:1.42:60:4:0.0148:0:1 -7 36859046 . A AGAT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.17471;SOR=Inf;LSEQ=AAACTTGCTGCTGATGAAGA;RSEQ=GATGATGATGATGATTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:76,89:0:2,0:24.4:1:30.4:1:1:0:60:54:1:0:0.1 0/1:119:2:1,1:54,63:0.0168:2,2:32.5:1:31.7:1:1:1.17:30:4:0.0171:0:0 -7 36859148 . G T 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55304;SOR=0;LSEQ=AATGCACAAAAGTCAAATCA;RSEQ=AATGGAAAAGACTCAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:1,2:83,91:0.0169:2,2:9.3:1:20.3:1:1:1.81823:49.7:2:0.0114:0:3 0/0:89:0:0,0:44,45:0:2,0:20.9:1:31.2:1:1:0:56:178:1:0:0.1 -7 36859217 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.53284;SOR=0;LSEQ=TCCTTCAAAAAACAGGAAAA;RSEQ=ATTCCTAAAACACCTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:56,88:0.0137:2,2:28.5:1:30.5:1:1:1.57:57:4:0.014:0:1 0/0:85:0:0,0:40,45:0:2,0:23:1:29.2:1:1:0:55.5:41.5:1:0:0.3 -7 36859286 . A G 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01182;SOR=0;LSEQ=AAAATGCAAGCAAGTATACA;RSEQ=AAAGCATATTGAACAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:10:2,8:13,34:0.1754:2,2:17:1:32.4:1:1:1.51882:55.6:20:0.1852:0:1.1 0/0:33:0:0,0:9,24:0:2,0:23.4:1:29.7:1:1:0:60:66:1:0:0.1 -7 36859510 . T C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=Inf;LSEQ=CACTTTTCTTCTGACTGCTG;RSEQ=GATTCAATGAACCTTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:0.3333:0,0:10:0:25:0:1:0:60:2:0.3333:0:1 1/1:3:3:2,1:0,0:1:0,2:28.3:1:30.7:1:1:0:60:6:1:0:1 -7 37220821 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16373;SOR=Inf;LSEQ=TAAAGTGTTAGATGGCAAAC;RSEQ=ATCAGCATGCCCAGTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:221,74:0:2,0:22:1:30.9:1:1:0:60:294:1:0:0.1 0/1:201:2:1,1:146,53:0.01:2,2:16.5:1:27:1:0.46612:2.73842:60:4:0.0102:0:1.5 -7 37220826 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07796;SOR=Inf;LSEQ=TGTTAGATGGCAAACCATCA;RSEQ=CATGCCCAGTGGCCACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:214,84:0:2,0:24.2:1:31.9:1:1:0:60:98.333:0.9966:0:0.1 0/1:224:3:2,1:153,68:0.0134:2,2:16.3:1:26:1:1:1.12439:60:6:0.0137:0:1 -7 37220932 . G A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.06493;LSEQ=GTACTCCAGGCTAAGTCACC;RSEQ=AGAAGGAGGATGCCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:598:557:243,314:19,19:0.9314:2,2:25.6:1:29.8:1:0.50066:1.29161:60:60.889:0.9368:0:1.1 0/1:389:182:75,107:90,114:0.4679:2,2:24.4:1:29.6:1:0.60675:1.12597:60:59.667:0.4723:0:1.2 -7 37220996 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13102;SOR=Inf;LSEQ=CACACCTGCCCTCTCTGTGG;RSEQ=CTACTCTTCACATTTTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:46,214:0:2,0:23.1:1:32:1:1:0:60:51:1:0:0.7 0/1:148:2:1,1:33,113:0.0135:2,2:16.5:1:27.5:1:0.40789:3.39:60:4:0.0136:0:2 -7 37221055 . T C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13415;SOR=0.3916;LSEQ=TGAGGCAGCTCTGTCTTGTA;RSEQ=TTGCAGATTGGATGGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:18:1,17:2,61:0.2222:1,1:23.1:1:32.4:1:0.53456:1.78:60:36:0.2222:0:1.1 0/1:40:4:0,4:3,33:0.1:2,0:24.8:1:32.3:1:1:0:60:8:0.1:0:1 -7 39479859 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TTGGGGAAGTTCTCCTGGAT;RSEQ=ATATCCTGAAGTGTGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:40:1:29.5:1:1:1:59.5:4:0.5:0:3 0/0:2:0:0,0:1,1:0:2,0:5.5:1:29.5:1:1:0:60:4:1:0:0 -7 39479863 . T A 30 d7;v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55247;LSEQ=GGAAGTTCTCCTGGATGATA;RSEQ=CCTGAAGTGTGTTTTCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:40:0:30:1:1:1:59.5:4:0.5:0:3 0/1:3:1:1,0:1,1:0.3333:2,0:4:0:30:0:1:0:60:2:0.3333:0:2 -7 39479901 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=AGCGTGTTTCCATTCTCCCT;RSEQ=TCTCATTCTGGTACTCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:12.5:1:32:1:1:1:59.5:4:0.5:0:3 0/1:6:2:1,1:2,2:0.3333:2,2:36:1:30.5:1:1:1:60:4:0.3333:0:1.5 -7 39480448 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTCTTTGAGGCTGCTGAT;RSEQ=GTTGGAGGGTTTTTGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:0.087:2,2:10:0:31.5:1:1:1.09544:60:4:0.0909:0:1 0/0:9:0:0,0:4,5:0:2,0:29.7:1:30.4:1:1:0:60:18:1:0:0.1 -7 39480470 . CTTG C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.52923;SOR=0;LSEQ=TTGGAGGGTTTTTGTGAGGG;RSEQ=TTGTTGTTGTTGATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:7,7:0.1765:2,2:34.3:1:33.7:1:1:1.9219:60:6:0.1875:0:0.7 0/0:9:0:0,0:5,4:0:2,0:29.1:1:29.4:1:1:0:60:8:1:0:0.6 -7 39480486 . A T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.52727;SOR=4.02871;LSEQ=AGGGCTTGTTGTTGTTGTTG;RSEQ=TGATGATGATGTTGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:6,7:0.0714:2,0:17:0:26:0:1:0:60:2:0.0769:0:3 0/1:8:2:2,0:2,4:0.25:2,0:31.5:1:30:0:0.42857:0:60:4:0.25:0:2 -7 39480585 . C T 48 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=GTTTGCTGGGAGGTTCACTT;RSEQ=AGGCCCTACTCATCCGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:26:1:33:1:1:0:60:8:1:0:0 1/1:3:3:1,2:0,0:1:0,2:39:1:30.3:1:1:0:60:6:1:0:2.3 -7 39480601 . G A 49 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=ACTTCAGGCCCTACTCATCC;RSEQ=ATTCACTCCCGTGCCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21.8:1:32.3:1:1:0:60:8:1:0:0 1/1:3:3:1,2:0,0:1:0,2:33.3:1:31:1:1:0:60:6:1:0:2.3 -7 39480649 . A C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TCAAGAAGTCTGGAGAACAG;RSEQ=AAAAATGGGTGCCTCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:28:0:34:0:1:0:60:2:0.2:0:1 1/1:2:2:1,1:0,0:1:0,2:18:1:31.5:1:1:0:60:4:1:0:2 -7 39480827 . CT C 26 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGTATTTTTAAAGCTTAG;RSEQ=TTTTTTTTTTTTTCAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:26:1:26:1:0.33333:0:60:4:0.6667:0.3333:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 39520306 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTATCGAAAGGACATAGC;RSEQ=GTGGCTCAGCTCTGACCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 39520802 . C G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCATGATGCACACCACCAC;RSEQ=CCAGGGGAGCTTAAGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:0:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 39521781 . A C 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAAGGATAATTTCACTGC;RSEQ=TCAAGAATTCCATGTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:0.3333:0,0:37:1:32.7:1:1:0:60:6:0.3333:0:1 0/0:1:0:0,0:1,0:0:0,0:29:0:32:0:1:0:60:2:1:0:0 -7 39521940 . C G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1199;SOR=Inf;LSEQ=CTGGTTGCTTTCAAGATTTT;RSEQ=TCTCACTGATTTTCTGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:49,52:0:2,0:26.7:1:31.7:1:1:0:60:49.5:1:0:0.2 0/1:54:2:1,1:27,25:0.037:2,2:38:0:31.5:1:1:1.07844:60:4:0.0385:0:1.5 -7 39835600 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.79698;LSEQ=GTCATCAGTCCCACGGAGCA;RSEQ=CCCGCGAGGCTGAGGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:33,37:0.0278:2,2:33:1:28.5:1:1:1.12:51:4:0.0278:0:1 0/1:45:1:1,0:21,23:0.0222:2,0:1:0:26:0:0.48889:0:60:2:0.0222:0:1 -7 39835668 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12685;SOR=Inf;LSEQ=CACTGCTGCCCCTGCCCCTA;RSEQ=TCTCAGCCTCATGTGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:9,19:0:2,0:22:1:32.2:1:1:0:38.6:56:1:0:0.1 0/1:16:2:1,1:2,12:0.125:2,2:11:1:27.5:1:0.35:5.10:44.5:4:0.125:0:1 -7 39835759 . G C 84 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01055;SOR=8.49305;LSEQ=GGGTCAGGACCCCCGCAGGG;RSEQ=TGGGAATCAGGGCAGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:1,2:10,12:0.1154:2,2:26.3:1:32.3:1:1:1.63407:52.3:6:0.12:0:1 1/0:11:6:5,1:4,1:0.5455:2,2:30.8:1:32.8:1:1:1.22:48:12:0.5455:0:1.2 -7 39835950 . C A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01299;SOR=Inf;LSEQ=TCGGTCTCCAGTTCCCTGAG;RSEQ=CCGTCCTCGGCTTCTTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:24.6:1:31.4:1:1:0:52.2:32:1:0:0.6 1/0:6:3:2,1:1,2:0.5:2,2:17:1:31:0:1:3.11:53.3:6:0.5:0:1 -7 39835960 . GCTT G 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.02632;SOR=Inf;LSEQ=GTTCCCTGAGCCCGTCCTCG;RSEQ=CTTCACCTGTACAGGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:19.1:1:31.7:1:1:0:51.1:28:1:0:0.7 0/1:7:3:2,1:2,2:0.4286:2,2:28:1:33.7:1:1:1.81:53.3:6:0.4286:0:1 -7 39835966 . T C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1;LSEQ=TGAGCCCGTCCTCGGCTTCT;RSEQ=CACCTGTACAGGCAAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:6,2:4,4:0.5:2,2:17.5:1:31.1:1:0.60839:2.79:46.5:16:0.5:0:1.4 1/0:6:3:2,1:2,1:0.5:2,2:15.3:1:32.3:1:1:1:56.3:6:0.5:0:1 -7 39836043 . C T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08697;SOR=3.75349;LSEQ=AGATGGAGCATCTTCTCATC;RSEQ=TGCATTTGGGCATGGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:5,2:8,3:0.3889:2,2:30:1:30.9:1:1:1.06284:54.1:14:0.4118:0:1 1/0:14:10:5,5:3,1:0.7143:2,2:32.9:1:30.6:1:0.58042:2.77987:55:20:0.7143:0:1.2 -7 39836177 . TA AG 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04703;SOR=Inf;LSEQ=GGCTCAGCCCAGCTCCTGCC;RSEQ=GGAAAGCCTTAGTGTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:53,21:0:2,0:25.6:1:30.2:1:1:0:45:73:1:0:0.1 0/1:21:2:1,1:13,6:0.0952:2,2:36:1:29.3:1:1:2.08171:59.5:4:0.0952:0:1 -7 39836251 . GTCTCTTGCACCACAA G 83 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00047;SOR=21.20377;LSEQ=CAGGTCGCCCACACTTTCAG;RSEQ=GGTGGCAGGATCCATTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:1,0:85,81:0.006:2,0:43:0:33:0:1:0:41:2:0.0061:0:0 0/1:61:7:4,3:27,27:0.1148:2,2:26.6:1:29.7:1:1:1.33:41:14:0.1148:0.0492:0.1 -7 39836318 . GC G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54841;SOR=0;LSEQ=GCCTTGGAAGGCGTCCCTGG;RSEQ=CCCCATCCCCAGGGGTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:56,64:0.0164:2,2:25.5:1:33.5:1:1:1.14:57:4:0.0165:0:0 0/0:63:0:0,0:33,30:0:2,0:23.1:1:31.3:1:1:0:47.7:126:1:0:0.1 -7 39836390 . G T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90623;LSEQ=CAGACTCCTGGGCTTTGAAG;RSEQ=CTCCTGGGCCCAGTAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:0,2:44,52:0.0204:2,0:19.5:1:31.5:1:0.50011:0:27:4:0.0213:0:1 0/1:54:1:0,1:22,31:0.0185:2,0:44:0:27:0:1:0:27:2:0.0192:0:2 -7 39836574 . A C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGAAGGAATGACAGGTGC;RSEQ=AATACCTTCCCACCAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:84,17:0.0194:2,2:27:0:33.5:1:0.32039:4.83053:40.5:4:0.0194:0:1.5 0/0:41:0:0,0:34,7:0:2,0:18.2:1:29.9:1:1:0:43.9:82:1:0:0.1 -7 39836727 . G T 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02459;SOR=0;LSEQ=ATCACCCCCTCCTCCTCATG;RSEQ=ATGACCATGTGCTCCTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:15:8,7:59,87:0.0932:2,2:19.7:1:29.7:1:0.41243:1.68:52.1:30:0.0943:0:1.1 0/0:52:0:0,0:24,28:0:2,0:25.1:1:30.9:1:1:0:51.3:51:1:0:0 -7 39836833 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07229;SOR=Inf;LSEQ=CCCACTGGTCACCTCCCTCA;RSEQ=CAGGGGCTGCAAAGTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:67,54:0:2,0:25.7:1:31.7:1:1:0:42.8:59.5:1:0:0.1 0/1:45:2:1,1:24,19:0.0444:2,2:12.5:1:28:1:1:1.25655:50:4:0.0455:0:1.5 -7 39836897 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGGCCAGAGTATGATG;RSEQ=AGTGCCAGACACCACCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:98,91:0.0105:2,0:19:1:26.5:1:0.23577:0:60:4:0.0106:0:1.5 0/0:86:0:0,0:42,44:0:2,0:27.9:1:31.5:1:1:0:49.5:172:1:0:0.1 -7 39836910 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.098;SOR=Inf;LSEQ=TATGATGCAGTGCCAGACAC;RSEQ=ACCTGTGTCAGTTCCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:102,90:0:2,0:29:1:31:1:1:0:53.8:47:1:0:0.1 0/1:88:2:1,1:41,44:0.0227:2,2:36:1:27.5:1:1:1.07:46:4:0.0233:0:1 -7 39837019 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.11635;SOR=Inf;LSEQ=TGAGCCAGGTTCCCTGACTG;RSEQ=GTGCAGCCGTTCTGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:104,93:0:2,0:26.1:1:30:1:1:0:43.4:97.5:1:0:0.1 0/1:103:2:1,1:61,40:0.0194:2,2:21.5:1:29:1:1:1.51854:43.5:4:0.0198:0:1 -7 39837099 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54206;SOR=0;LSEQ=GCTGCAACTGACAGGAGTTC;RSEQ=GAGGACACCCCAGGGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:74,97:0.0116:2,2:18:1:30.5:1:1:1.31:42:4:0.0116:0:1 0/0:94:0:0,0:45,49:0:2,0:24.4:1:30.4:1:1:0:50.5:188:1:0:0.1 -7 39837178 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12044;SOR=Inf;LSEQ=CCTTGTACACTCCTGCTAGC;RSEQ=CCTGGCTTGTGGGCTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:144,94:0:2,0:27.3:1:30.6:1:1:0:47.8:38.667:1:0:0.1 0/1:127:2:1,1:65,60:0.0157:2,2:48:1:30.5:1:1:1.08263:56:4:0.0159:0:1 -7 39837191 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11279;SOR=Inf;LSEQ=TGCTAGCCCCTGGCTTGTGG;RSEQ=CTTGGCCTCTGAGCTGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:163,101:0:2,0:26.6:1:30.9:1:1:0:46.2:23:1:0:0.2 0/1:134:2:1,1:69,63:0.0149:2,2:21.5:1:26.5:1:1:1.09449:23:4:0.0153:0:2 -7 39837213 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1151;SOR=Inf;LSEQ=TTGGCCTCTGAGCTGGACTT;RSEQ=TTTCGGTCCTTGTTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:160,137:0:2,0:25.3:1:30.6:1:1:0:43.5:20.214:1:0:0.2 0/1:153:2:1,1:72,79:0.0131:2,2:25.5:1:27.5:1:1:1.10:50:4:0.0132:0:1 -7 39837237 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11212;SOR=Inf;LSEQ=CGGTCCTTGTTGCAAGTGGG;RSEQ=CACCTTCACCTGGAAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:141,152:0:2,0:26.8:1:30.8:1:1:0:40.9:28.3:1:0:0.2 0/1:148:2:1,1:67,78:0.0135:2,2:36.5:1:28.5:1:1:1.16:23:4:0.0139:0:1 -7 39837257 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10959;SOR=Inf;LSEQ=CCACCTTCACCTGGAAGGCC;RSEQ=GGTCGTGGTACTTCTGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:123,168:0:2,0:25.9:1:30.6:1:1:0:44.4:290:1:0:0.2 0/1:145:2:1,1:67,76:0.0138:2,2:13.5:1:28.5:1:1:1.13:23:4:0.0139:0:2 -7 39837274 . C T 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59861;SOR=0.62291;LSEQ=GCCAGGTCGTGGTACTTCTG;RSEQ=GTCTCATTGGGCCCCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:13:3,10:108,161:0.0458:2,2:27.3:1:30:1:0.25907:2.23031:23:26:0.0481:0:1 0/1:138:4:2,2:61,73:0.029:2,2:27.3:1:25.8:1:1:1.20:30.3:3:0.0226:0:1 -7 39837303 . G A 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03565;SOR=Inf;LSEQ=GGGCCCCAGGGTGTACCACC;RSEQ=CTCGCTCAGGATCTGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:77,135:0:2,0:25.2:1:30.4:1:1:0:51.5:20.2:1:0:0.2 0/1:105:3:2,1:42,60:0.0286:2,2:26:1:27:1:0.57047:2.83:51:6:0.0288:0:1.3 -7 39837450 . A G 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02417;SOR=Inf;LSEQ=GTCCCATTTGTTGGGGCTGC;RSEQ=TCCATCCTTCTCAGAAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:63,55:0:2,0:23.9:1:29.8:1:1:0:42.4:18.667:1:0:0.1 0/1:49:3:1,2:25,21:0.0612:2,2:29:1:31:1:0.59428:2.34:46.7:6:0.0625:0:1 -7 39837490 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08337;SOR=Inf;LSEQ=GAGTCCTGTTCCTTGTGCAG;RSEQ=GCACTGAGGGACTGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:51,66:0:2,0:26.6:1:30.8:1:1:0:41.3:38:1:0:0.1 0/1:48:2:1,1:20,26:0.0417:2,2:19:1:27:1:1:1.29:48.5:4:0.0417:0:1 -7 39837858 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5111;SOR=0;LSEQ=TGCTAGGCCTCACGTGGCTG;RSEQ=AGGGAGGGGTCAGGAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:83,51:0.0147:2,2:26:1:27.5:1:1:1.62134:54.5:4:0.015:0:1 0/0:98:0:0,0:56,42:0:2,0:21.4:1:31.6:1:1:0:57.2:196:1:0:0.2 -7 39837870 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16937;SOR=Inf;LSEQ=CGTGGCTGCAGGGAGGGGTC;RSEQ=GGAAGGGGACAGAGTACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:96,61:0:2,0:23.7:1:30.2:1:1:0:54.8:156:0.9936:0:0.1 0/1:111:2:1,1:61,47:0.018:2,2:17:1:30:1:1:1.29476:55:4:0.0185:0:1 -7 39837939 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16556;SOR=Inf;LSEQ=CGTTCCTCCACACAAACATG;RSEQ=TGACGCCACCGGAGGCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:101,112:0:2,0:25.7:1:32:1:1:0:48.7:105.5:0.9906:0:0.1 0/1:148:2:1,1:76,70:0.0135:2,2:33:1:27:1:1:1.0851:49:4:0.0137:0:1 -7 40117685 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16149;SOR=Inf;LSEQ=AACACCATGAAACCAAAGAA;RSEQ=CAATATCGTCGAAAGTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:40,55:0:2,0:25.1:1:31.6:1:1:0:60:46.5:0.9894:0:0.2 0/1:65:2:1,1:24,39:0.0308:2,2:17:1:32:0:1:1.61:60:4:0.0313:0:1 -7 40117692 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.27034;SOR=0;LSEQ=TGAAACCAAAGAAGCAATAT;RSEQ=GTCGAAAGTTAAGAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:3:1,2:30,54:0.0345:2,2:32:1:31.3:1:1:1.1098:60:6:0.0353:0:1 0/0:60:0:0,0:23,37:0:2,0:20.4:1:30.1:1:1:0:60:120:1:0:0.1 -7 40117696 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51697;SOR=0;LSEQ=ACCAAAGAAGCAATATCGTC;RSEQ=AAAGTTAAGAGAAGAATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:27,51:0.025:2,2:25:1:29:1:1:1.87:60:4:0.0263:0:1 0/0:53:0:0,0:19,34:0:2,0:20.1:1:30.3:1:1:0:60:106:1:0:0.1 -7 41461200 . G A 247 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1576.6671;LSEQ=AACCACCCAGGGCCCTTTTA;RSEQ=TTCATGTAAGACCTAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:913:1:1,0:447,464:0.0011:2,0:1:0:27:0:0.49123:0:60:2:0.0011:0:1 1/0:539:337:149,188:92,109:0.6252:2,2:24.4:1:29.5:1:0.78811:1.06483:60:83.25:0.6271:0:1.1 -7 41461291 . C T 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTCTCAGAAGACAAGGAT;RSEQ=GAATCCTTCTAAGGGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:38,273:0:2,0:22.8:1:30:1:1:0:60:102.667:1:0:0.1 0/1:130:12:2,10:22,96:0.0923:2,2:22.8:1:30.6:1:1:1.14467:60:24:0.0938:0:1 -7 41461425 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTCTACTTTCCAGGTTG;RSEQ=AATCTCCCATCCTCCCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:0,23:0.08:1,2:45.5:1:29.5:1:0.08:0:60:4:0.08:0:1 0/0:2:0:0,0:0,2:0:0,0:33:1:27.5:1:1:0:60:4:1:0:1.5 -7 41726288 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGTTTCAAATAAAATAT;RSEQ=GAATTACATTTCTCTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:0,2:0,92:0.0213:1,0:18:1:31.5:1:1:0:60:4:0.0217:0:1 0/0:19:0:0,0:0,19:0:1,0:21.9:1:30.8:1:1:0:60:38:1:0:0.1 -7 41729111 . G GT 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=5e-04;SOR=0.36129;LSEQ=TTTGTTTTTAATTTACTTTT;RSEQ=TTTTTTTTTGTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:82:81,1:170,5:0.3118:1,1:20.2:1:30.5:1:0.66774:2.38:59.1:164:0.3166:0.0913:1.2 0/1:114:16:14,2:91,4:0.1404:1,2:29.8:1:29.5:1:0.20673:3.20199:60:32:0.1455:0:1.1 -7 41729121 . GT G 143 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.39805;SOR=0.63694;LSEQ=ATTTACTTTTGTTTTTTTTT;RSEQ=TTTTTTTTTTGTTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:22:22,0:286,6:0.0681:1,1:21.7:1:32.1:1:1:0:60:44:0.0701:0.0217:0.5 0/1:135:6:6,0:117,7:0.0444:2,0:23.7:1:31.6:1:1:0:60:12:0.0469:0.0074:0.5 -7 41729159 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00865;SOR=Inf;LSEQ=TTTTTAATTTCTATTTTTCT;RSEQ=GTTAACTCAGAAACCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:682,23:0:1,0:23.5:1:30.6:1:1:0:59.9:8.792:0.9984:0:0.4 0/1:313:4:4,0:285,22:0.0128:2,0:27.8:1:23.8:1:1:0:60:3:0.0103:0:2.3 -7 41729740 . TTTC T 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.5526;SOR=1.13979;LSEQ=TTCCCTTCCCCCTCCTCTTC;RSEQ=TTCTTCTTCTTGCCCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2909:64:34,30:1354,1487:0.022:2,2:27.7:1:30.3:1:0.44807:1.24:59.8:63:0.022:0.0041:0.3 0/1:1840:46:24,22:899,890:0.025:2,2:25.6:1:30.3:1:0.8816:1.08:60:92:0.0253:0.0071:0.2 -7 41729758 . CA AG 152 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTTTCTTCTTCTTCTTGCC;RSEQ=GGAGAACCAAGCTGGCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2532:28:13,15:1249,1247:0.0111:2,2:25.9:1:31.8:1:0.84972:1.15563:60:56:0.0113:4e-04:1.1 0/0:1564:0:0,0:781,780:0:2,0:24.9:1:30.5:1:1:0:60:56.815:0.9987:0:0.1 -7 41730289 . G C 173 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGCCCATGGGCTGAAACT;RSEQ=TTTCTGTACTGCCTGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:44:0,44:0,157:0.2189:1,1:25.5:1:31.8:1:1:0:60:21:0.2121:0:1.2 0/0:71:0:0,0:1,70:0:1,0:25.2:1:31.6:1:1:0:60:70:1:0:0.1 -7 41735034 . C T 340 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.69849;LSEQ=CAGGGTGCATTCTCTGAAGC;RSEQ=CTAACTTTGCATTTGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2915:2270:1195,1075:325,319:0.7787:2,2:25.6:1:30.5:1:0.34802:1.09:60:65.765:0.7796:0:1.1 1/0:1487:1057:553,504:224,203:0.7108:2,2:25.4:1:29.9:1:1:1.00567:60:104.7:0.7113:0:1.2 -7 41735646 . T TC 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATCTCTTTTCCCATCTT;RSEQ=CCCACCATTTCTCTCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,2:0.3333:2,0:8.5:1:32.5:1:1:0:60:4:0.4:0.1667:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 41739141 . G C 105 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCATTCCACTCCAATCCT;RSEQ=GTACATTCACCCCTCTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1:0,2:35.4:1:31.7:1:1:0:60:20:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 41740059 . A AT 100 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.57317;SOR=0.56238;LSEQ=AGGTTTTTTTGTGTGTGTGG;RSEQ=TTTTTTTATTTTTTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:12:0,12:60,635:0.0167:2,0:35.9:1:28.1:1:0.61284:0:60:24:0.018:0:4 0/0:317:3:0,3:42,268:0.0095:2,0:39.3:1:21:1:1:0:60:2:0.0069:0:3.3 -7 41740067 . AT A 146 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05489;SOR=1.79094;LSEQ=TTGTGTGTGTGGATTTTTTT;RSEQ=TTTTTTTTTTGGTGTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:592:28:0,28:25,537:0.0473:1,1:26.1:1:30.4:1:0.62408:0:59.3:27:0.0469:0.0034:0.5 0/1:257:21:0,21:14,222:0.0817:2,1:22.1:1:30.4:1:0.61315:0:59.9:42:0.0843:0.0117:0.7 -7 41740082 . G GT 152 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.87048;SOR=1.06783;LSEQ=TTTTTATTTTTTTTTTTGGT;RSEQ=TTTTTTTTTTCCTTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:33:1,32:11,422:0.0702:1,1:22.8:1:30.2:1:0.59031:1.20:59.4:32:0.0737:0.0106:1.2 0/1:201:15:0,15:6,179:0.0746:1,1:27.9:1:29:1:1:0:60:30:0.0802:0.005:1.1 -7 41740390 . G C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGAGGGAAAGAAGGGGGAGA;RSEQ=AGAGGGAGAGAGGGAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:40:0:30:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:13:0:33.5:1:1:0:60:4:1:0:1.5 -7 41741672 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAGCGTTCCTTCCCTCTC;RSEQ=GTTTCTTTCCCACACATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:11,0:0.1538:0,0:9.5:1:32:0:1:0:60:4:0.1538:0:1 0/0:2:0:0,0:1,1:0:2,0:25.5:1:31.5:1:1:0:60:4:1:0:0 -7 41742179 . A G 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTCACATATACAGTACCCA;RSEQ=AATGTTTTGCAGTTCAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:59,550:0:2,0:23.8:1:30.4:1:1:0:60:86:1:0:0.1 0/1:233:15:3,12:23,195:0.0644:2,2:16.7:1:30.5:1:0.22615:2.11:60:30:0.0647:0:1 -7 42426790 . G GGACCCTTCCTT 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTGCAGGTTTTAGGGAG;RSEQ=GACCCTTCCTTGCCCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:30.9:1:1:0:60:4:1:0:0 -7 42427292 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTAGGGCCCACCCTAAT;RSEQ=TAGTATGACCTCATCTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:9,15:0.0769:2,2:23.5:1:30:1:1:1.63:60:4:0.08:0:1 0/0:11:0:0,0:4,7:0:2,0:31.7:1:31.9:1:1:0:60:22:1:0:0 -7 43288295 . TTCCTCC T 99 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=10.000;MSILEN=3;SSF=0.0441;SOR=0;LSEQ=TCCTCCTCCTCCTCCTCCTT;RSEQ=TCCTCCTCCTCCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:8,1:14,0:0.25:1,2:10:1:31.4:1:0.3913:0:58.3:18:0.3:0.1111:1.1 0/0:15:0:0,0:5,0:0:0,0:12.6:1:27.4:1:1:0:59.4:10:0.3333:0:0.8 -7 43288365 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCTCTTCCCCCATCTCC;RSEQ=CGTTCTCCTCCTGTTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:2,0:148,43:0.0104:2,0:16:1:31.5:1:1:0:60:4:0.0106:0:1 0/0:87:0:0,0:70,17:0:2,0:26.5:1:29.9:1:1:0:60:42.5:1:0:0.4 -7 43288484 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28669;LSEQ=CTGTGTGCATGTGAGGCCAC;RSEQ=ACCTCTAGACCCCAGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:565:374:179,195:97,94:0.6619:2,2:26.6:1:30.3:1:0.53411:1.12392:60:61.333:0.6595:0:1.6 0/1:348:125:56,69:106,117:0.3592:2,2:24.4:1:29.7:1:0.65506:1.11595:60:30.25:0.3517:0:1.3 -7 43288513 . T G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1401;LSEQ=ACCCCAGTGACTTAGGGGCC;RSEQ=CCCTGCCTCCCCTCTAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:216:87,129:129,164:0.4244:2,2:27.9:1:30.8:1:0.41516:1.16596:60:53:0.424:0:2 0/1:289:27:10,17:115,146:0.0934:2,2:23.7:1:30.1:1:0.54487:1.33771:60:26:0.0919:0:2 -7 43299455 . A G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAAATGTGAGTAGTTGCA;RSEQ=TCCTAGAATAATGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:42.3:1:31.5:1:1:0:60:8:0.5714:0:1 0/0:1:0:0,0:1,0:0:0,0:29:0:30:0:1:0:60:2:1:0:1 -7 43299616 . T C 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACCACACCCAGGCACATCA;RSEQ=AGTCAAACTTCTGAAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:51:26:12,14:12,13:0.5098:2,2:30.5:1:32.6:1:1:1.07536:60:52:0.5098:0:1.1 0/0:68:0:0,0:32,36:0:2,0:30:1:28.3:1:1:0:60:33:1:0:0.1 -7 43299667 . GA G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.20139;SOR=0;LSEQ=AAATATAAAAGCAACCACAG;RSEQ=AAAAATGATATGTTGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:7,20:0.069:2,2:15.5:1:29.8:1:0.48276:2.74:60:4:0.0714:0.0345:1 0/0:35:0:0,0:13,22:0:2,0:21.2:1:28.7:1:1:0:60:70:1:0:0.1 -7 43316879 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5125;SOR=0;LSEQ=GCTTCCACTGACTCCCACTG;RSEQ=CACCTGCCGCCATGACGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:18,19:0.0513:2,2:37.5:1:29.5:1:1:1.05:60:4:0.0541:0:1 0/0:26:0:0,0:11,15:0:2,0:28.2:1:31.6:1:1:0:60:52:1:0:0.1 -7 43774403 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22711;SOR=Inf;LSEQ=AAGGGGGCAGGGTAAGGAGG;RSEQ=TGAATCTTCTAAGTGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:0:2,0:25.9:1:30.8:1:1:0:59.4:13:1:0:0.1 0/1:26:2:1,1:14,10:0.0769:2,2:15:1:27.5:1:1:1.38168:60:4:0.0769:0:1 -7 43774485 . CAG C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.48718;SOR=0;LSEQ=TCCCTCTTAGGTAGCCAAAG;RSEQ=AGAGAGAGAGAAGGCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:6,12:0.1:2,2:36:1:32.5:1:1:1.93:60:4:0.1:0:0 0/0:19:0:0,0:8,11:0:2,0:19.9:1:30.1:1:1:0:60:38:1:0:0.2 -7 43774515 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13043;SOR=Inf;LSEQ=GAGAAGGCAGCATACGTCAG;RSEQ=GTTTTCTTCTATGCACTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:5,10:0:2,0:23.3:1:31:1:1:0:57.3:30:1:0:0 0/1:9:2:1,1:2,5:0.2222:2,2:20:1:31.5:1:1:2.24:60:4:0.2222:0:1 -7 43975601 . G A 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26354;SOR=2.75183;LSEQ=CTTGTGCCTCAGCCTCCTGA;RSEQ=TAGCTGGTTATAGGCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:0,4:0,10:0.2857:0,0:24.5:1:32:1:1:0:60:8:0.2857:0:1 1/0:15:8:0,8:0,7:0.5333:0,0:16.8:1:30.4:1:1:0:60:16:0.5333:0:1 -7 44664306 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50026;SOR=Inf;LSEQ=ACCAACCACCGTATCTGTAT;RSEQ=GGACCCAGCATAGCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,15:0:2,0:24.5:1:30.6:1:1:0:60:54:1:0:0 0/1:35:2:1,1:16,17:0.0571:2,2:38.5:1:28:1:1:1.06:60:4:0.0606:0:1 -7 45127176 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55298;SOR=0;LSEQ=TTTCTCATCTACAAAGCAGA;RSEQ=CCAGGATTAGAGTTGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:2,1:75,15:0.0323:2,2:14:1:29:1:0.43629:2.46845:60:6:0.0326:0:1 0/0:52:0:0,0:40,12:0:2,0:21.3:1:31.9:1:1:0:60:104:1:0:0.1 -7 45127225 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15646;SOR=Inf;LSEQ=GGGGACCCTGTTGCCAGGCT;RSEQ=CTCCAGCTCCCCTCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:116,88:0:2,0:28.5:1:32:1:1:0:60:203:1:0:0.5 0/1:134:2:1,1:79,53:0.0149:2,2:14.5:1:24.5:1:1:1.48598:60:4:0.015:0:1.5 -7 45127231 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16598;SOR=Inf;LSEQ=CCTGTTGCCAGGCTGCTCCA;RSEQ=CTCCCCTCAGCAGCATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:119,96:0:2,0:28.6:1:31.9:1:1:0:60:106.5:0.9953:0:0.5 0/1:149:2:1,1:84,63:0.0134:2,2:12.5:1:32:0:1:1.33071:60:4:0.0135:0:1 -7 45127263 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.15593;SOR=Inf;LSEQ=AGCATCAGAGCCCTGAGCCC;RSEQ=GAACCACCAGCCAAAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:138,132:0:2,0:24.1:1:30.3:1:1:0:60:89:0.9926:0:0.7 0/1:178:2:1,1:86,90:0.0112:2,2:21:0:32:0:1:1.05:60:4:0.0112:0:1.5 -7 45127282 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31437;LSEQ=CTGAACCACCAGCCAAAACT;RSEQ=GTCACCCAAGGGCTTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:257:209:97,112:25,23:0.8132:2,2:24.6:1:30.4:1:0.52337:1.25392:60:103.5:0.8118:0:1.1 1/0:175:101:45,56:37,37:0.5771:2,2:28.1:1:30.3:1:0.54038:1.24288:60:202:0.5805:0:1.4 -7 45127332 . G A 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=3.9442;LSEQ=TGGGACATCCAGGGGGTCCT;RSEQ=AGACAAGGGGGTCCTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:18:8,10:79,108:0.0878:2,2:24.9:1:29.6:1:1:1.09:60:36:0.0891:0:1.7 0/1:105:29:12,17:31,45:0.2762:2,2:18.8:1:28.2:1:1:1.02:60:28:0.2718:0:1.8 -7 45381731 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49413;SOR=0;LSEQ=AGAACAGCAATACAGACTTG;RSEQ=AATGGGGTTACTTCCTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:24,16:0.0476:2,2:25.5:1:30:1:1:1.48518:60:4:0.0488:0:1.5 0/0:40:0:0,0:23,17:0:2,0:22.3:1:31.7:1:1:0:60:80:1:0:0.2 -7 45549709 . TT GG 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCCAGGTCTCAAGTAGG;RSEQ=CAGAAAATGCAAAACCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:33.5:1:27:1:1:0:60:4:0.6667:0:3 -7 45549712 . A T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGTCTCAAGTAGGTTC;RSEQ=GAAAATGCAAAACCCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:33.5:1:28:1:1:0:60:4:0.6667:0:3 -7 45551574 . A T 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54067;SOR=0;LSEQ=CCTCTTGTGATTTTCCATCC;RSEQ=CTGACCCTTGCAACCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:2,4:7,5:0.3333:2,2:26.2:1:29.7:1:0.61991:2.64037:60:12:0.3333:0:1 0/0:4:0:0,0:1,3:0:2,0:26.8:1:29.8:1:1:0:60:8:1:0:0 -7 45553520 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATCTCAGACTCCCAGCC;RSEQ=CTGGAACTGTGAGAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 45854001 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGTCTCTAGGCCCGACTC;RSEQ=GGCCTCCCAACAACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:1:31:1:1:0:53:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 45856020 . ATCT A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=1;SOR=1.01281;LSEQ=AGTGGACCCGCTATGCACAC;RSEQ=TCTTCTCCAAGGTTTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:22:19,3:18,8:0.4583:2,2:22.7:1:31.6:1:0.18866:2.76:40.1:44:0.4583:0.0417:0 0/1:26:12:10,2:8,6:0.4615:2,2:17.3:1:29.4:1:0.21638:3.56:43.7:24:0.48:0.1923:0.3 -7 45856070 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18917;SOR=Inf;LSEQ=ATCCTGCTCATGCTGCCCCA;RSEQ=CAGCTTCAGTTGGCACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:57,19:0:2,0:26.4:1:31.6:1:1:0:54:37:1:0:0.1 0/1:59:2:1,1:35,22:0.0339:2,2:7:0:30.5:1:1:1.57796:47:4:0.0339:0:1.5 -7 45856089 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51801;SOR=0;LSEQ=AGCAGCTTCAGTTGGCACCT;RSEQ=CTCCAGTCCAGCCTCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:61,34:0.0206:2,2:37.5:1:31:1:1:1.78264:60:4:0.0211:0:1 0/0:64:0:0,0:40,24:0:2,0:26.3:1:31.8:1:1:0:57.1:63:1:0:0.5 -7 45856117 . AG CC 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=CCAGCCTCTGGGACCCATGC;RSEQ=CGGCTCCCAGCGGCCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:56,59:0:2,0:25.6:1:30.6:1:1:0:53.8:230:1:0:0.1 0/1:94:11:7,4:47,36:0.117:2,2:21.7:1:30.7:1:0.75385:1.34:57.5:22:0.1183:0.0106:1 -7 45856119 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.25315;SOR=0;LSEQ=AGCCTCTGGGACCCATGCAG;RSEQ=GGCTCCCAGCGGCCCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:3:1,2:55,58:0.0259:2,2:24.3:1:29:1:1:1.88651:53.3:6:0.0261:0:1 0/0:96:0:0,0:53,43:0:2,0:21.8:1:29.7:1:1:0:52.7:31:1:0:0.4 -7 45856122 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21032;SOR=Inf;LSEQ=CTCTGGGACCCATGCAGCGG;RSEQ=TCCCAGCGGCCCTGCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:59,62:0:2,0:25.6:1:31.8:1:1:0:52.9:59.5:1:0:0.1 0/1:103:2:1,1:54,47:0.0194:2,2:14:1:28.5:1:1:1.14738:43:4:0.0196:0:1 -7 45856157 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5068;SOR=0;LSEQ=CACTCACCACCAGCATCCGT;RSEQ=TCACCTGCAGTTGAAGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:54,66:0.0164:2,2:40.5:1:29.5:1:1:1.22:45:4:0.0165:0:1 0/0:93:0:0,0:43,50:0:2,0:27.2:1:29.1:1:1:0:47.4:22.25:1:0:0.3 -7 45856302 . C T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07977;SOR=0.38677;LSEQ=TGCCTCTACTCTCAGCCTCA;RSEQ=GTGACTCTCGGGCAGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:21:10,11:5,12:0.5385:2,2:24:1:31.2:1:0.32637:2.14:44.9:42:0.5526:0:1.1 0/1:26:8:3,5:6,12:0.3077:2,2:21.3:1:28.5:1:1:1.19:48:7:0.28:0:1.1 -7 45856404 . A G 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10417;SOR=Inf;LSEQ=ACAGGGCTGGGAGTCAGGGC;RSEQ=GGGGCAGAACAAACCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:0:2,0:21.9:1:30.6:1:1:0:46:42:1:0:0.1 0/1:21:2:1,1:11,8:0.0952:2,2:30:1:25:1:1:1.35399:44.5:4:0.0952:0:1 -7 45856638 . T C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24386;SOR=0.48538;LSEQ=GCTGTCCCCATCACACATCG;RSEQ=ACACTTGTGGGTGTTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:12,11:6,5:0.6765:2,2:23:1:31.8:1:1:1.09692:44:46:0.6765:0:1.5 1/0:18:9:7,2:5,4:0.5:2,2:26.7:1:32:1:0.61991:2.64:40.2:18:0.5:0:1.4 -7 45856646 . T C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53298;SOR=0.58308;LSEQ=CATCACACATCGTACACTTG;RSEQ=GGGTGTTGGGCTTTGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:10:4,6:14,11:0.2778:2,2:25.5:1:30.6:1:0.47052:1.87378:34.3:20:0.2778:0:1.9 0/1:22:4:3,1:9,9:0.1818:2,2:21.8:1:29.8:1:0.59398:2.86:25.5:8:0.1905:0:1.8 -7 45856813 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCGGGTGGCTCAGCCCA;RSEQ=CTTCTGCCTAGGAAAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:39,22:0.0317:2,2:17:1:29.5:1:1:1.75576:60:4:0.0323:0:1 0/0:26:0:0,0:16,10:0:2,0:22:1:30.6:1:1:0:56.5:25:1:0:0.1 -7 45856831 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTTCTGCCTAGGAAAGC;RSEQ=TTAGTGTTGGGAGGGACCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:39,22:0.0317:2,2:25.5:1:29:1:1:1.75576:53.5:4:0.0323:0:1.5 0/0:27:0:0,0:15,12:0:2,0:21.3:1:30.5:1:1:0:55:54:1:0:0.2 -7 45856862 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGACCGTGATGACTGAG;RSEQ=GGCCTGGTAGCTCCAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:44,29:0.0267:2,2:23.5:1:29.5:1:1:1.50856:49.5:4:0.0278:0:1 0/0:33:0:0,0:17,16:0:2,0:28.2:1:31:1:1:0:52:66:1:0:0.3 -7 45856902 . T C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.011;SOR=0.36381;LSEQ=GCCCACACTTTCAGGTCTCT;RSEQ=GCACCAGAAGGTGGCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:36:19,17:20,24:0.45:2,2:27.6:1:29.7:1:0.65338:1.34:49.9:35:0.4487:0:1.2 0/1:57:13:6,7:23,21:0.2281:2,2:22.8:1:30.4:1:0.75983:1.27228:50.2:26:0.2281:0:1.2 -7 45856916 . G A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27898;SOR=1.96089;LSEQ=GTCTCTTGCACCAGAAGGTG;RSEQ=CAGGATCCATTGGGAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:7:4,3:28,41:0.0921:2,2:22.1:1:30.1:1:0.44562:1.93:55.6:14:0.0921:0:1 0/1:54:9:4,5:24,21:0.1667:2,2:34.1:1:27.7:1:0.72371:1.41913:47.6:8:0.1509:0:1.2 -7 45856963 . GC G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.19283;SOR=Inf;LSEQ=GCCTTGGAAGGCGTCCCTGG;RSEQ=CCCCATCCCCAGGGGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:16,37:0:2,0:23.7:1:31.3:1:1:0:52.7:52:1:0:0.5 0/1:42:2:1,1:17,23:0.0476:2,2:23:1:30:1:1:1.34:60:4:0.0476:0.0238:0 -7 45856989 . T TAGG 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCCCCAGGGGTGGGGGCCA;RSEQ=GGGCCCACTCTGCTGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:20:7,13:7,11:0.5263:2,2:18.3:1:29.9:1:1:1.17662:41.3:19:0.5278:0.2105:0.4 0/0:27:0:0,0:9,18:0:2,0:24:1:29.2:1:1:0:59.3:54:1:0:0.2 -7 45857101 . C T 78 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGTGTGTAGGAGGAGGA;RSEQ=GGGGTGGGACCATAGACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:3,3:4,5:0.4:2,2:22.5:1:30.5:1:1:1.23:38.8:12:0.4286:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 45857234 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55102;SOR=0;LSEQ=CCACCAAAGCCCTTGTTGCC;RSEQ=TCTGGCTCCTCCCCAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:48,16:0.0303:2,2:28.5:1:29:1:0.45175:2.94052:37:4:0.0303:0:1 0/0:33:0:0,0:25,8:0:2,0:29.1:1:30.5:1:1:0:40:66:1:0:0.1 -7 45857319 . G A 117 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0016;SOR=4.4305;LSEQ=GTGTCAGTGGTGCTAAAGCC;RSEQ=TCATCAGCAATGACATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:8:2,6:57,48:0.0708:2,2:25.1:1:30.5:1:0.14914:3.52492:42.3:16:0.0714:0:1 0/1:59:15:6,9:18,26:0.2542:2,2:27.9:1:30.1:1:1:1.03781:47.3:30:0.2542:0:1.1 -7 45857382 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09054;SOR=Inf;LSEQ=CCATGGGCTCCTCGTCACTC;RSEQ=CTGTGTCCTCACCGGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:51,64:0:2,0:25.2:1:30.6:1:1:0:47.9:37.333:1:0:0.4 0/1:50:2:1,1:26,22:0.04:2,2:27.5:1:29:0:1:1.17786:50:4:0.0408:0:1.5 -7 45857398 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGCTGTGTCCTCACCGG;RSEQ=CATGTGCTGGGAATGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:51,53:0.0189:2,2:21.5:1:28.5:1:1:1.04:53.5:4:0.0196:0:1 0/0:44:0:0,0:25,19:0:2,0:26:1:31.9:1:1:0:43.1:88:1:0:0.3 -7 45857415 . G A 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01952;SOR=0;LSEQ=CGGCCATGTGCTGGGAATGA;RSEQ=CAGCTCAGGTGGGCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:13:6,7:42,40:0.1368:2,2:27.2:1:30:1:0.77345:1.22238:46.3:26:0.1398:0:1.1 0/0:35:0:0,0:22,13:0:2,0:30.3:1:32.2:1:1:0:37.3:70:1:0:0.1 -7 45857456 . TC T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCTGCCCACTGGTCACC;RSEQ=CCTCACCAGGGGCTGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:38,30:0.0286:2,2:15.5:1:29.5:1:1:1.26235:23:4:0.0294:0:0 0/0:31:0:0,0:17,14:0:2,0:17.8:1:29.9:1:1:0:29.9:62:1:0:0 -7 45857543 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1134;SOR=Inf;LSEQ=GATGCAGTGCCAGACACCAC;RSEQ=TGTGTCAGTTCCTGTAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:66,63:0:2,0:28.3:1:31.3:1:1:0:44.2:128:1:0:0.2 0/1:66:2:0,2:33,31:0.0303:2,0:41.5:1:31:1:0.49231:0:24:4:0.0313:0:1 -7 45857545 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55102;SOR=0;LSEQ=TGCAGTGCCAGACACCACCT;RSEQ=TGTCAGTTCCTGTAGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:63,64:0.0154:2,2:31:1:32:0:1:1.02:60:4:0.0156:0:1 0/0:66:0:0,0:33,33:0:2,0:26.9:1:30.2:1:1:0:42.3:32:1:0:0.1 -7 45857663 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTGTGTGCAGCCGTCCT;RSEQ=CCCCACAGAAGCTGCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:72,76:0.0133:2,2:27.5:1:29.5:1:1:1.06:53.5:4:0.0137:0:1 0/0:65:0:0,0:31,34:0:2,0:26:1:31.7:1:1:0:55.4:130:1:0:0.1 -7 45857664 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGTGTGCAGCCGTCCTG;RSEQ=CCCACAGAAGCTGCTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:72,76:0.0133:2,2:40:1:29:1:1:1.06:52:4:0.0136:0:1 0/0:65:0:0,0:31,34:0:2,0:25.9:1:31.1:1:1:0:55.4:64:1:0:0.1 -7 45857752 . C T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54009;SOR=0;LSEQ=GGACACCCCAGGGGCAGTGG;RSEQ=AGTGCCCGTCTCTGATATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:64,48:0.0174:2,2:44:1:25.5:1:1:1.32991:60:4:0.0179:0:1.5 0/0:63:0:0,0:36,27:0:2,0:21.8:1:31.5:1:1:0:53.8:62:1:0:0.2 -7 45857779 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTCTCTGATATGCTCCGCT;RSEQ=CCACGAGCCCTTGTACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:98,60:0.0125:2,2:35.5:1:32.5:1:1:1.62807:60:4:0.0126:0:2 0/0:77:0:0,0:48,29:0:2,0:27.2:1:30.6:1:1:0:49.1:37.5:1:0:0.2 -7 45857807 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12909;SOR=Inf;LSEQ=CCCTTGTACACTCCTGCTAG;RSEQ=CCCTGGCTTGTGGGCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:103,78:0:2,0:28.4:1:31.2:1:1:0:46.3:59.333:1:0:0.4 0/1:102:2:1,1:58,42:0.0196:2,2:38.5:1:29:1:1:1.3765:41:4:0.02:0:1.5 -7 45857813 . G A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55591;SOR=0;LSEQ=TACACTCCTGCTAGCCCCTG;RSEQ=CTTGTGGGCTTGGCCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:3:2,1:105,80:0.016:2,2:11.7:1:27.7:1:1:1.52:49:6:0.0164:0:1 0/0:107:0:0,0:62,45:0:2,0:25.9:1:30.4:1:1:0:47.5:25.75:1:0:0.4 -7 45857848 . G A 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13366;SOR=0.6454;LSEQ=CTCTGAGCTGGACTTCTTTC;RSEQ=GTCCTTGTTGCAAGTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:59:28,31:66,74:0.2965:2,2:25.7:1:30.2:1:1:1.01:48.4:58:0.299:0:1.9 0/1:103:22:11,11:41,39:0.2136:2,2:28.3:1:29.8:1:1:1.05079:52.1:44:0.22:0:2 -7 45857884 . GC TT 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22357;SOR=0.66512;LSEQ=GGGCCACCTTCACTTGGAAG;RSEQ=CAGGTCGTAGCACTTCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:41:13,28:38,60:0.295:2,2:24.8:1:30.1:1:0.56298:1.3611:56.2:82:0.295:0.0216:1.8 0/1:92:20:10,10:30,41:0.2174:2,2:21.3:1:29.7:1:0.61385:1.36:56.6:40:0.2299:0.0435:1.5 -7 45857885 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15056;SOR=Inf;LSEQ=GGCCACCTTCACTTGGAAGG;RSEQ=CAGGTCGTAGCACTTCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:40,60:0:2,0:26.3:1:31.5:1:1:0:56.8:49:1:0:0.1 0/1:88:2:0,2:30,40:0.0227:2,0:36.5:1:28.5:1:0.50704:0:60:4:0.0282:0:3.5 -7 45857990 . C T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55463;SOR=0;LSEQ=GTTGGGGTGACCCTGGTGCG;RSEQ=CCTGCCAGAGCCTGGTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:0,3:71,61:0.0222:2,0:14.7:1:22:1:0.1039:0:45:2:0.0152:0:1.7 0/0:76:0:0,0:38,38:0:2,0:27.4:1:30.9:1:1:0:57.6:24.333:1:0:0.2 -7 45858021 . A C 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82424;LSEQ=CCTGGTGCCGCTTGCTGAAG;RSEQ=TCATGACCACCACTCATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:0,2:73,67:0.0141:2,0:10.5:1:32:1:0.23434:0:27:4:0.0142:0:2 0/1:86:1:0,1:42,43:0.0116:2,0:38:0:34:0:1:0:27:2:0.0118:0:1 -7 45858024 . AT A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13556;SOR=Inf;LSEQ=GGTGCCGCTTGCTGAAGATC;RSEQ=GACCACCACTCATGGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:73,72:0:2,0:26.7:1:30.9:1:1:0:54.5:290:1:0:0.2 0/1:85:2:1,1:42,41:0.0235:2,2:43.5:1:31:1:1:1.0241:60:4:0.0238:0:0.5 -7 45858047 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53884;SOR=0;LSEQ=ACCACCACTCATGGGCCACC;RSEQ=GATGTGGTCCTTGTCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:65,69:0.0146:2,2:26:1:30:1:1:1.06:53.5:4:0.0147:0:1 0/0:76:0:0,0:39,37:0:2,0:24.4:1:29.2:1:1:0:51.7:37:1:0:0.1 -7 45858079 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55039;SOR=0;LSEQ=TGTCCCATTTGTTGGGGCTG;RSEQ=ATCCATCCTTCTCAGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:58,54:0.0175:2,2:32:1:28:1:1:1.07337:37:4:0.0179:0:1 0/0:58:0:0,0:28,30:0:2,0:27.4:1:31.7:1:1:0:43.8:116:1:0:0.1 -7 45858117 . C T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGAGTCCTGTTCCTTGCG;RSEQ=AGGGCACTGAGGGACTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:51,69:0.0164:2,2:29:0:28:1:1:1.35:33:4:0.0168:0:1 0/0:56:0:0,0:28,28:0:2,0:24.9:1:31.2:1:1:0:39.4:55:1:0:0.3 -7 45858198 . T A 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18451;SOR=0.54722;LSEQ=GACATGACGGAGAGGAAAGC;RSEQ=TCATCGTGGTCATTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:52:15,37:8,14:0.7027:2,2:22.6:1:30:1:0.58726:1.40287:33.8:25:0.6944:0:1.1 1/0:32:18:5,13:6,7:0.5625:2,2:24.3:1:28:1:0.4491:2.16951:33.3:17:0.5667:0:1.6 -7 45858236 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0731;SOR=Inf;LSEQ=TGTCTCACTGTCCAGCAGGG;RSEQ=CTCCCCTGAGGGGCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:23,35:0:2,0:29:1:29.9:1:1:0:38.7:57:1:0:0.6 0/1:22:2:1,1:8,12:0.0909:2,2:10.5:1:32.5:1:1:1.47:48:4:0.0909:0:1 -7 45858273 . G A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3035;SOR=0;LSEQ=AGGGCTCCTCCTCCATGGTG;RSEQ=GAGGTGGGCTTTTACCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:4:2,2:23,26:0.0755:2,2:40.3:1:31:1:1:1.13:31:8:0.0755:0:1.5 0/0:24:0:0,0:10,14:0:2,0:20.9:1:30.2:1:1:0:39.1:48:1:0:0.3 -7 45858288 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54338;SOR=0;LSEQ=TGGTGGGAGGTGGGCTTTTA;RSEQ=CAGGTTCCACCACCCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:21,25:0.0417:2,2:47:0:31.5:1:1:1.19:31:4:0.0417:0:2 0/0:25:0:0,0:14,11:0:2,0:24.3:1:31:1:1:0:40.2:50:1:0:0.3 -7 45858358 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21201;SOR=Inf;LSEQ=AGGGCAGGTGGCTCCAGGGG;RSEQ=CCGCGCAGGGTCAACACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:37,21:0:2,0:28.9:1:31.8:1:1:0:41.7:57:1:0:0.4 0/1:50:2:1,1:28,20:0.04:2,2:32:1:25.5:1:1:1.39042:49:4:0.0408:0:1 -7 45858363 . G C 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03691;SOR=0.13187;LSEQ=AGGTGGCTCCAGGGGGCCGC;RSEQ=CAGGGTCAACACTCCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:8:7,1:30,21:0.1333:2,2:25:1:30.8:1:0.23723:4.80:40:16:0.1333:0:1.8 0/1:51:1:1,0:29,21:0.0196:2,0:1:0:29:0:1:0:40:2:0.0204:0:1 -7 45858505 . G T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11467;SOR=Inf;LSEQ=CTGCAGGGAGGGGTCAGGAA;RSEQ=GGGACGGAGTACCAGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:191,142:0:2,0:26.6:1:31.3:1:1:0:58:65.6:1:0:0.1 0/1:171:2:0,2:96,73:0.0117:2,0:7.5:1:23.5:1:0.19092:0:54.5:4:0.0119:0:1 -7 45858615 . AC A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06972;SOR=Inf;LSEQ=CGCAGGCCTGTGGGCCGAGT;RSEQ=TTGGTCCGGGCAGGGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:60,133:0:2,0:23:1:32:1:1:0:59.6:95.5:1:0:0.1 0/1:136:3:2,1:55,78:0.0221:2,2:15:1:26.3:1:0.57171:2.81:60:6:0.0222:0.0074:0.3 -7 46780610 . T C 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28527;SOR=0.8423;LSEQ=CTGCATCCAGAGAGAAATTT;RSEQ=AAGCATATTTGAAAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:171:95,76:148,128:0.3826:2,2:24.8:1:31.4:1:0.69724:1.08:60:170:0.3855:0:2 0/1:315:108:54,54:101,106:0.3429:2,2:26.8:1:30.6:1:0.90559:1.05:60:107:0.3429:0:2.1 -7 46780614 . C A 231 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10577;SOR=1.27628;LSEQ=ATCCAGAGAGAAATTTTAAG;RSEQ=ATATTTGAAAGCAGGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:220:126,94:121,115:0.4825:2,2:24.4:1:29.8:1:0.22168:1.27:60:54:0.4811:0:1.8 1/0:311:169:87,82:63,79:0.5434:2,2:27.1:1:28.8:1:0.25462:1.33:60:41.25:0.55:0:1.8 -7 46780714 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54149;SOR=0;LSEQ=CAGAGGGACATTGTCGAAAT;RSEQ=GTTTCCTACAGACAGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:44,147:0.0103:2,2:20:1:29:1:0.41289:3.31:60:4:0.0104:0:1 0/0:106:0:0,0:28,78:0:2,0:19.1:1:29.2:1:1:0:60:16.667:1:0:0.2 -7 46859675 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTTCCCTTTTAGGTAGC;RSEQ=GAAGCAGAGAGGAAAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:18,31:0.0392:2,2:27.5:1:30:1:1:1.70:60:4:0.0392:0:1 0/0:19:0:0,0:8,11:0:2,0:18.8:1:29.2:1:1:0:60:38:1:0:0.1 -7 47092258 . G GC 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.016;SOR=3.58508;LSEQ=TCTAGAGCGCTCCCTGCGGA;RSEQ=TCGGCCGCCCGCCTCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:29:29,0:65,2:0.3021:1,1:22.1:1:31:1:1:0:51.7:13.5:0.2903:0.0521:0.3 1/0:18:11:11,0:7,0:0.6111:0,0:29.1:1:32.9:1:1:0:51:22:0.6111:0.0556:0 -7 47092291 . G T 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01556;SOR=0;LSEQ=CTCTCCCCCAGGTCTCTCCC;RSEQ=ACGTCCCCACGCGGGGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:18:18,0:164,2:0.0978:1,1:24.6:1:31.9:1:1:0:58.6:36:0.1:0:1.1 0/0:51:0:0,0:51,0:0:1,0:20.8:1:29.9:1:1:0:58.1:50:1:0:0 -7 47092402 . C T 69 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09108;SOR=3.05594;LSEQ=CTCGGAGCCATGAGCTGCGG;RSEQ=CGCCCCCCTCCCGACGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1162:4:2,2:734,423:0.0034:2,2:19.8:1:23.5:1:0.62655:1.73427:51.3:3:0.0026:0:1.5 0/1:574:6:2,4:349,219:0.0105:2,2:8:1:26.8:1:0.21388:3.18063:49.7:12:0.0105:0:1 -7 47092580 . T G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.1568;LSEQ=TCGCCTTCGTCCGGTTTCAC;RSEQ=ACCGGAGCGACGCGCAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:239:74,165:138,269:0.3683:2,2:23.5:1:30.4:1:0.48766:1.14364:54.3:58.75:0.3707:0:1.1 1/0:307:199:77,122:40,68:0.6482:2,2:23.2:1:30.1:1:0.80649:1.07:54.6:38.8:0.6445:0:1.1 -7 47092677 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11149;SOR=Inf;LSEQ=GGCGCGCTATGGCCGCCGGG;RSEQ=CCTGCCTCGCAGCAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:120,272:0:2,0:24.3:1:29.6:1:1:0:59.6:77.4:1:0:0.1 0/1:197:2:1,1:72,123:0.0102:2,2:38.5:1:30.5:1:1:1.70:60:4:0.0103:0:3 -7 47092914 . C G 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31382;LSEQ=CAGGGGATCTCGCTACGGCC;RSEQ=ATCTCCCTACAGTCGATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:4,1:8,2:0.3333:2,2:26.2:1:31.2:1:1:1:46.8:10:0.3333:0:1 0/1:5:2:1,1:1,2:0.4:2,2:26:1:32:0:1:1.73:50:4:0.4:0:1 -7 47093009 . T C 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=10.55477;LSEQ=CTCGCTACAGGAGGTCTCCC;RSEQ=ACATCCGGTCTTCCCGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:3,2:53,2:0.0833:1,2:13.8:1:31:1:0.03159:15.71796:60:10:0.0847:0:1.2 1/0:22:11:11,0:11,0:0.5:0,0:21.7:1:31:1:1:0:60:22:0.5:0:1 -7 47272406 . C T 111 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00879;SOR=0;LSEQ=CACCCTAAGGGGCCCTAATC;RSEQ=GATATGACCATGTCCTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:18.2:1:32.1:1:1:0:60:22:1:0:1.1 0/1:4:1:1,0:3,0:0.25:0,0:15:0:32:0:1:0:60:2:0.25:0:1 -7 47272496 . AC A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52561;SOR=0;LSEQ=AAGGTCAGAGTTATGCCACC;RSEQ=AAGCCAAGGAATGCCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:36,28:0.0303:2,2:24:1:29.9:1:1:1.28077:60:4:0.0308:0.0152:1 0/0:40:0:0,0:22,18:0:2,0:30.1:1:31.8:1:1:0:60:80:1:0:0.1 -7 47467864 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTCAGCCCCATGCAGGC;RSEQ=CAGCTTTTAGCACCTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:28.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 47468573 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCACAGACCAGCAACAC;RSEQ=AGCAGGAGAAGCAGAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:32:1:30.5:1:1:1.12:60:4:0.1053:0:1 0/0:7:0:0,0:2,5:0:2,0:26.9:1:29:1:1:0:60:6:1:0:0.6 -7 47800327 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAAACAATCCAATTATAC;RSEQ=TTTAATTATTTTAAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 47802173 . GC G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATATTGGCAATACCATTT;RSEQ=ACAGGAACTCCTTGCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19.5:1:32.3:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 47802311 . C G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00838;SOR=0.12304;LSEQ=AAAAATCTTTCCAACTCCCA;RSEQ=CTGATTTCTGAAGGTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:29,0:3,1:0.8788:2,1:21.9:1:30.1:1:0.12121:0:60:8.667:0.8667:0:1.3 0/1:11:5:4,1:5,1:0.4545:2,2:20.6:1:33.2:1:1:1.22474:60:10:0.4545:0:1.2 -7 47802407 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12639;SOR=Inf;LSEQ=GCCTCCTTTAGTGAAGTCAG;RSEQ=TGCCTGAGGCTGGGCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:127,57:0:2,0:23.5:1:31.7:1:1:0:60:60.333:1:0:0.6 0/1:102:2:1,1:70,30:0.0196:2,2:29.5:1:28:1:0.51757:2.31175:60:4:0.0196:0:1 -7 47802472 . A G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.09104;LSEQ=GGGGGGCTGGGGTGGGTCAC;RSEQ=CTTATTCTACTGGATATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:324:287:139,148:17,19:0.8858:2,2:26.4:1:30.3:1:1:1.05:60:30.889:0.8825:0:1.8 0/1:223:92:45,47:66,65:0.4126:2,2:25.1:1:30.6:1:0.89201:1.06021:60:184:0.4163:0:1.8 -7 47802508 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09651;LSEQ=ATCACTGTTCCTGGGCCCTG;RSEQ=CACCACTCTCAGCCCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:295:266:114,152:12,17:0.9017:2,2:26.1:1:29.5:1:1:1.06:60:52.2:0.9:0:1.9 0/1:188:88:39,49:40,59:0.4681:2,2:27.4:1:28.9:1:0.65694:1.17:60:43:0.4674:0:1.8 -7 47802516 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56404;SOR=3.11571;LSEQ=TCCTGGGCCCTGCCACCACT;RSEQ=TCAGCCCTGGTGCTGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:1,0:111,167:0.0036:2,0:1:0:27:0:0.40143:0:60:2:0.0036:0:3 0/1:180:2:1,1:72,106:0.0111:2,2:19.5:1:27.5:1:1:1.47:60:4:0.0112:0:1 -7 47802635 . C T 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01094;SOR=0.13204;LSEQ=CTCACGGTAGCAGGTGGTGA;RSEQ=AGAGGACATGTCATTGTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:27:2,25:0,4:0.871:0,2:24.1:1:27.4:1:1:0:60:12.5:0.8621:0:1.8 0/1:11:5:0,5:0,6:0.4545:0,0:37:1:28.8:1:1:0:60:10:0.4545:0:2 -7 47802663 . G A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04916;SOR=0.14346;LSEQ=ATGTCATTGTCGCAGTCACT;RSEQ=AGGACACTGGTTCTCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:2,17:0,2:0.9048:0,2:22.7:1:30.7:1:1:0:60:38:0.9048:0:2.2 1/0:9:5:0,5:0,4:0.5556:0,0:15.8:1:29.6:1:1:0:60:10:0.5556:0:2 -7 47802710 . A G 107 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TCTGTGCCTGGACCTCAGCT;RSEQ=TAGGCCTGGCCCCATTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:21.8:1:32.5:1:1:0:60:20:1:0:2.4 1/0:2:1:0,1:0,1:0.5:0,0:50:0:30:0:1:0:60:2:0.5:0:2 -7 47802771 . C T 76 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTTGAGCTACCTGACT;RSEQ=TTCCCAGTTGGCCAGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:19:1:29.5:1:1:0:60:12:1:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 47802808 . T C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CACATCCCAGTGAATGATCA;RSEQ=CATCCTGCTCTCATCTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:41.3:1:31.7:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 47802835 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTCATCTCATAGCCAGC;RSEQ=GATCAGTCTGTTCACCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:17.7:1:31.3:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 48114609 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07977;SOR=Inf;LSEQ=ACTTGCTGAAGACAAGGCAA;RSEQ=GTGATAAGGTATCTAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:24.3:1:29.7:1:1:0:60:18:1:0:0 0/1:8:2:1,1:2,4:0.25:2,2:31:1:29:1:1:1.83:60:4:0.25:0:1 -7 49852999 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26667;SOR=0;LSEQ=CTGATCCAGAGGCTTGGCTG;RSEQ=GGCCTGAGAATTTGCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:1,2:24,6:0.0909:2,2:17.3:1:29.7:1:0.13856:7.35065:60:6:0.0938:0:1 0/0:22:0:0,0:17,5:0:2,0:21.5:1:30:1:1:0:60:21:1:0:0 -7 50358752 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17642;SOR=Inf;LSEQ=ATGAGAAAAGCTTCCCTGGG;RSEQ=CCGGAAGTCACAGTGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:72,179:0:2,0:25:1:31.3:1:1:0:60:82.667:0.996:0:0.1 0/1:183:2:1,1:61,119:0.0109:2,2:6.5:1:24.5:1:1:1.94:60:4:0.0112:0:1 -7 50367232 . A T 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08752;SOR=7.12221;LSEQ=CACACTTCTTCTTTCTCATC;RSEQ=GGGAAGGAAAGCCCCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:1:0,1:402,280:0.0015:2,0:1:0:26:0:0.41142:0:60:2:0.0015:0:1 0/1:483:5:1,4:285,190:0.0104:2,2:8.8:1:28.6:1:0.16318:5.97925:60:10:0.0107:0:1.2 -7 50367388 . A C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12413;SOR=Inf;LSEQ=AGCGGCCTCTGTGCCTGTGA;RSEQ=ACCTTTATCTCTTTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:62,279:0:2,0:22.8:1:30.1:1:1:0:60:55.833:1:0:0.1 0/1:186:2:1,1:43,141:0.0108:2,2:10:0:33.5:1:0.41813:3.25:60:4:0.0109:0:1 -7 50444040 . G A 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13723;SOR=0;LSEQ=TGTAACCCCAGGTGCATCCC;RSEQ=AGGCCTGCCACCGAAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:7,0:12,0:0.3684:0,0:31.7:1:28.4:1:1:0:60:6:0.3333:0:1.1 0/0:6:0:0,0:5,1:0:2,0:17.7:1:30.7:1:1:0:60:12:1:0:0 -7 50444181 . G GT 137 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.3933;SOR=1.37721;LSEQ=CTGCTGTGTTGTTTTGTTGA;RSEQ=TTTTTTTTTTGCAATGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:22:19,3:214,36:0.0806:2,2:22.7:1:30.9:1:1:1.07:59.1:44:0.0821:0:0.5 0/1:167:18:13,5:119,30:0.1078:2,2:20.2:1:28.9:1:0.53882:1.52141:60:36:0.1084:0.0419:0.2 -7 50450446 . C T 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGGGCTGTCTGGGTGTCC;RSEQ=GGGATTCCTCCACTCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:130,423:0:2,0:24:1:29.9:1:1:0:60:109.6:0.9982:0:0.2 0/1:296:38:12,26:82,176:0.1284:2,2:19.4:1:29.7:1:1:1.00944:60:76:0.1306:0:1.2 -7 50450456 . C A 37 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04025;SOR=Inf;LSEQ=CTGGGTGTCCCGGGATTCCT;RSEQ=CACTCTGCCCGCCTGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:98,370:0:2,0:23.5:1:31:1:1:0:60:65.857:1:0:0.1 0/1:245:3:2,1:69,172:0.0122:2,2:10.7:1:23.7:1:0.20367:4.95:60:6:0.0124:0:3.3 -7 50454452 . G A 26 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTATTATATAATGCAAAT;RSEQ=TAAGATATATTTATATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:30:1:26:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 50454648 . A G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGCATAGACTGAGGCCT;RSEQ=CTCTGGAGGCAAATCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:38.3:1:31.7:1:1:0:60:6:0.6:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 50454736 . A G 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGCATCCACGTTATAACAC;RSEQ=GCAGTGGCTCGTTTTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:4,0:0.4286:0,2:38:1:31.3:1:0.42857:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 50454939 . AT A 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50593;SOR=0.65624;LSEQ=TTTTAGCTCTCAAGGGTAGA;RSEQ=TTTTTTTTTAACTTTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:18:17,1:277,22:0.0568:2,1:24.2:1:30.9:1:1:1.35:60:36:0.0573:0.0063:0.6 0/1:158:6:5,1:143,9:0.038:2,2:21.5:1:29.7:1:0.32892:3.14114:60:12:0.038:0.0127:0.8 -7 50454980 . A T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27964;LSEQ=GTAATAATTGTATTGCATGC;RSEQ=TTCCCCTTACACAGAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:689:253:188,65:307,129:0.3672:2,2:23.9:1:30.5:1:0.29237:1.21:60:83.333:0.3687:0:1.2 0/1:423:59:44,15:251,113:0.1395:2,2:22.5:1:29.8:1:0.4464:1.32:60:18.667:0.1363:0:1.2 -7 50455179 . C A 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.02674;SOR=0;LSEQ=CTGTACCCAGGTAAGCGCTG;RSEQ=TGCTCGGAGGCCAGCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:8:2,6:142,308:0.0175:2,2:20.3:1:31.6:1:1:1.38223:60:16:0.0177:0:1.1 0/0:284:0:0,0:89,193:0:2,0:24:1:32.2:1:1:0:60:564:0.993:0:0.1 -7 50455209 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.1375;SOR=Inf;LSEQ=GCCAGCCTGGTGGGCTCTCC;RSEQ=CCCAGCACGGTGGGGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:60,231:0:2,0:23.2:1:30.9:1:1:0:60:40.571:1:0:0.1 0/1:172:2:1,1:37,133:0.0116:2,2:19.5:1:32:1:0.39406:3.56:60:4:0.0117:0:1 -7 50459320 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00012;SOR=0.22539;LSEQ=TAGAATTAATCTCTAGGAAG;RSEQ=GCCTGGCTCTTGTAGGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:56:56,0:119,3:0.3146:1,1:25.7:1:30.2:1:0.55275:0:60:112:0.3182:0:1.1 0/1:75:7:7,0:64,4:0.0933:2,0:14:1:29:1:1:0:60:14:0.0972:0:1 -7 50459588 . T TA 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.36814;SOR=1.53148;LSEQ=GTTAAATGTTTGCTGTCTCT;RSEQ=AAAAAAAAACTATGTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:12:5,7:147,365:0.0229:2,2:21.6:1:28.3:1:0.34271:1.77:60:24:0.0234:0.0057:0.3 0/1:289:10:2,8:82,196:0.0346:2,2:25.7:1:27.1:1:0.72881:1.6708:60:9:0.0316:0.0035:0.2 -7 50459624 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11702;SOR=Inf;LSEQ=GGGTGTTTTAGATGCAAGTA;RSEQ=AAATGAGTTGAGGGTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:33,268:0:2,0:23.7:1:31.3:1:1:0:60:36.625:1:0:0.1 0/1:157:2:1,1:24,130:0.0127:2,2:19:1:28.5:1:0.2957:5.33:60:4:0.0129:0:1.5 -7 50467583 . C T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGACCGGTTCCGGAGGTGGC;RSEQ=GCGCCCCACTCACTGTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:295,63:0:2,0:24.3:1:30.4:1:1:0:60:34.8:1:0:0.1 0/1:194:18:14,4:143,33:0.0928:2,2:21.4:1:30.5:1:0.75351:1.23666:60:17:0.0904:0:1.1 -7 50467767 . C A 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=0.48833;LSEQ=CGCCCGCTGGTGCAGACGCC;RSEQ=CCGGGCGGTTCCGAGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1358:498:226,272:390,467:0.3667:2,2:25:1:29.5:1:1:1.00509:60:54.333:0.3657:0:1.1 0/1:726:160:72,88:254,311:0.2204:2,2:24.8:1:29.5:1:1:1.00:60:159:0.2236:0:1.1 -7 50468384 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09689;SOR=Inf;LSEQ=CAGGAAAAGCACAAGGACTG;RSEQ=CGCCTTCTCGCTCCCGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:12,217:0:2,0:25.6:1:30.8:1:1:0:60:27.625:1:0:0.1 0/1:104:2:1,1:19,83:0.0192:2,2:7.5:1:27.5:1:0.34914:4.28:60:4:0.0198:0:1.5 -7 50493201 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15143;SOR=Inf;LSEQ=TGTTATTTTGGTAGAGCCAC;RSEQ=TGCTCCCCACACCTGCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:27,35:0:2,0:22.5:1:31.1:1:1:0:60:124:1:0:0.1 0/1:40:2:1,1:18,20:0.05:2,2:28:0:32:0:1:1.11:60:4:0.05:0:1.5 -7 50493208 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5175;SOR=0;LSEQ=TTGGTAGAGCCACCTGCTCC;RSEQ=CACACCTGCTACCCCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:24,31:0.0351:2,2:6.5:1:28.5:1:1:1.29:60:4:0.0357:0:1.5 0/0:37:0:0,0:18,19:0:2,0:25.3:1:30.2:1:1:0:60:74:1:0:0.2 -7 50738265 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAGTTTTGTTGTCCTGGGTG;RSEQ=GTGCTCATCTCAGGCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:42:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:30:1:1:0:60:4:1:0:1 -7 50739151 . G A 88 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=GATCCAGCTAACTATCCCAC;RSEQ=TAGACCAGCAAATGATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:7,0:10,0:0.4118:0,0:23.3:1:31.4:1:1:0:60:14:0.4375:0:1.1 0/0:2:0:0,0:2,0:0:0,0:18:1:29:1:1:0:60:4:1:0:0 -7 50739320 . T G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCATAACAGCTTCAGCCT;RSEQ=GGCAAGGCGTCCAACTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:185,11:0.0101:2,2:22.5:1:30.5:1:0.11783:16.14892:60:4:0.0104:0:1 0/0:61:0:0,0:56,5:0:2,0:24.5:1:30.1:1:1:0:60:122:1:0:0.1 -7 50739383 . G T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07958;SOR=4.45963;LSEQ=AGGAGATGGATAAAACGGGT;RSEQ=GCCAGTGCCACTTTCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:2:0,2:363,151:0.0039:2,0:34:1:15:1:0.08751:0:60:0:0:0:4 0/1:234:4:1,3:161,69:0.0171:2,2:5.3:1:27.5:1:0.08781:6.93598:60:8:0.0175:0:1.8 -7 50739455 . T C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.33991;LSEQ=AAGATAATCTGACGTTTTAG;RSEQ=GTCCACAAAAGCTTCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1032:403:197,206:297,327:0.3905:2,2:26.2:1:30.9:1:0.70149:1.05:60:402:0.393:0:1.3 1/0:565:339:176,163:117,105:0.6:2,2:25.5:1:30.5:1:0.86321:1.03194:60:66.8:0.5996:0:1.4 -7 50739472 . C T 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TAGTGTCCACAAAAGCTTCT;RSEQ=TATTTATTGGGTTGTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1038:0:0,0:464,574:0:2,0:26.8:1:31.6:1:1:0:60:128.75:1:0:0.6 0/1:563:26:13,13:253,284:0.0462:2,2:25.5:1:28.5:1:0.8419:1.12:60:12:0.0432:0:2.5 -7 50739526 . G A 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00036;SOR=1.71671;LSEQ=TCCTGTGTTGACTTTAAAGC;RSEQ=GCTCAGAGACATCGCCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:216:65,151:89,215:0.4138:2,2:24.1:1:31.1:1:0.84605:1.04:60:432:0.4186:0:1.6 1/0:281:154:46,108:38,89:0.548:2,2:21.9:1:30.2:1:1:1.00243:60:153:0.5543:0:1.8 -7 50739588 . C G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00972;SOR=2.35664;LSEQ=CAAAGACAAAAAATCCCCAC;RSEQ=AAAGAGGCTCACAATAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:56:0,56:4,83:0.3916:1,1:26.9:1:31.2:1:0.15526:0:60:55:0.3873:0:1.6 1/0:53:32:1,31:2,19:0.6038:2,1:22.8:1:31.5:1:0.55537:3.1891:60:64:0.6154:0:1.7 -7 50741391 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACCACTGCCCCCACGAC;RSEQ=CCTGGCAACCAGAATGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:19:1:29:1:1:1.73:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 50825947 . C A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00783;SOR=Inf;LSEQ=CCAACACCCCGAGAGTAGAC;RSEQ=AGCACACTTCACACGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:4,3:7,4:0.3889:2,2:31.6:1:30.4:1:1:1.29262:60:14:0.3889:0:1.4 1/1:7:7:4,3:0,0:1:0,2:19.7:1:30.3:1:1:0:60:14:1:0:1.1 -7 50825976 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACACGCTGACCCGGACCA;RSEQ=TGGACAGAAGTTACAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:20:0:31.5:1:1:1.13389:60:4:0.1176:0:2.5 0/0:7:0:0,0:4,3:0:2,0:39.1:1:31.6:1:1:0:60:14:1:0:1.1 -7 50826694 . C CA 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTCAAGACCAGTTATGG;RSEQ=ATATAGCGTGACCCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35:0:31.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 50826889 . C CA 29 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAGACTCTGCCT;RSEQ=AAAAAAAAAAAAAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39.5:1:29.5:1:1:0:60:4:1:0:0.5 -7 51449823 . T G 26 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04329;SOR=Inf;LSEQ=TGCACTCCAGCCTGCCAAAC;RSEQ=GCATCTCAAAACAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:0:1,0:18.4:1:30.4:1:1:0:60:16:1:0:0 0/1:5:2:1,1:3,0:0.4:0,2:24:0:26.5:1:0.4:0:60:4:0.4:0:1 -7 51449830 . C CAAAACAAAAAACAA 27 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=29;MSI=6.000;MSILEN=1;SSF=0.03968;SOR=Inf;LSEQ=CAGCCTGCCAAACTGCATCT;RSEQ=AAAACAAAAAACAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:20,2:0:2,0:18.9:1:31.8:1:1:0:60:44:1:0:0 0/1:6:2:1,1:4,0:0.3333:0,2:32:0:27.6:1:0.33333:0:60:4:0.3333:0:1 -7 51450020 . A G 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGATGTCTGCGTCCAGC;RSEQ=AGGCCTCTGGTGGTGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:219,186:0:2,0:22.3:1:29.6:1:1:0:59.2:49.625:1:0:0.1 0/1:195:17:10,7:103,75:0.0872:2,2:29.4:1:31:1:1:1.04:54.2:34:0.0876:0:1.1 -7 51450037 . C A 38 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04687;SOR=Inf;LSEQ=AGCAAGGCCTCTGGTGGTGT;RSEQ=AGCATGTTTGTGTGGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:0:0,0:246,224:0:2,0:27:1:31.4:1:1:0:59.3:77.333:1:0:0.1 0/1:266:3:1,2:144,118:0.0113:2,2:7.3:1:24:1:0.59147:2.43265:54.7:2:0.0076:0:1.7 -7 51450101 . C A 45 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0702;SOR=6.6646;LSEQ=TGTTCTCCTGGTACTCTGTC;RSEQ=CCTTCCTGACCCCTCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:1:1,0:177,239:0.0024:2,0:1:0:25:0:0.42686:0:60:2:0.0024:0:1 0/1:253:4:2,2:107,142:0.0158:2,2:22.3:1:22.8:1:1:1.33:60:3:0.0122:0:1.3 -7 51450119 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15814;SOR=Inf;LSEQ=TCCCCTTCCTGACCCCTCCC;RSEQ=GCAGCCGCGTGAGGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:111,172:0:2,0:21.8:1:29.8:1:1:0:47.7:27.3:0.9964:0:0.1 0/1:188:2:1,1:72,114:0.0106:2,2:7:0:32:0:1:1.58:47:4:0.0108:0:1.5 -7 51450153 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13009;SOR=Inf;LSEQ=GCCCAGCAACCTGCCAGTCA;RSEQ=TCAGTGGCCTCCAACCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:40,108:0:2,0:26.3:1:32.1:1:1:0:43.3:48.333:1:0:0.1 0/1:84:2:1,1:18,64:0.0238:2,2:8:1:29.5:1:0.40333:3.49:49:4:0.0238:0:1 -7 51450249 . GC G 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGTGCTGACCCTGGGCG;RSEQ=CCCCTGCAGCCACCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:49,62:0.0175:2,2:23:0:34:0:1:1.26:60:4:0.0175:0:0 0/0:51:0:0,0:22,29:0:2,0:25.7:1:31:1:1:0:57.9:102:1:0:0.2 -7 51450279 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10295;SOR=Inf;LSEQ=GCCACCTGCCCTGAAAGCCC;RSEQ=GGGCCCGGAACCCCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:50,59:0:2,0:28.7:1:30.7:1:1:0:54.6:218:1:0:0.1 0/1:52:2:1,1:21,29:0.0385:2,2:41:1:29.5:1:1:1.37:60:4:0.0392:0:1 -7 51450282 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.09877;SOR=Inf;LSEQ=ACCTGCCCTGAAAGCCCAGG;RSEQ=CCCGGAACCCCACACACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:49,59:0:2,0:28.7:1:31.5:1:1:0:54.5:53:1:0:0.1 0/1:50:2:1,1:20,28:0.04:2,2:15.5:1:26.5:1:1:1.39:48:4:0.0408:0:1.5 -7 51450358 . G GC 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.07929;SOR=0.25613;LSEQ=CCATGGAGGAGGAGCCCTGG;RSEQ=CCCTCAGGGGAGTCCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:52:23,29:2,1:0.9286:2,2:25.8:1:31:1:0.58548:2.48027:38.5:104:0.963:0.1607:0.1 1/0:17:13:9,4:2,2:0.7647:2,2:26.3:1:33.2:1:0.58403:2.14:39.5:26:0.8125:0:0 -7 51450416 . C A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGACCACGATGATGCTTTC;RSEQ=TCTCCGTCATGTCTCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:64,35:0.0198:2,2:12:0:32:1:1:1.81693:60:4:0.02:0:1.5 0/0:37:0:0,0:27,10:0:2,0:24:1:29.8:1:1:0:53.6:36:1:0:0.1 -7 51450458 . A T 30 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82355;LSEQ=CCCAGTTGCCTCTACGATTC;RSEQ=GATGATGTCAGGCCCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:71,59:0.0152:2,2:25:0:30.5:1:1:1.20169:60:4:0.0155:0:1.5 0/1:80:1:0,1:47,32:0.0125:2,0:1:0:24:0:0.4125:0:45:2:0.0127:0:1 -7 51450476 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.53332;SOR=0;LSEQ=TCAGATGATGTCAGGCCCAG;RSEQ=CCCTCAGTGCCCTGTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:86,84:0.0116:2,2:40:1:32:1:1:1.02367:60:4:0.0119:0:1 0/0:100:0:0,0:56,44:0:2,0:24.5:1:28.5:1:1:0:53.4:24:1:0:0.1 -7 51450572 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.5363;SOR=0;LSEQ=ACCACATCTGGTGGCCCATG;RSEQ=GTGGCGGTCACGATCTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:56,59:0.0171:2,2:9:0:32:0:1:1.05:60:4:0.0175:0:2 0/0:66:0:0,0:30,36:0:2,0:23.8:1:29.8:1:1:0:57.2:65:1:0:0.3 -7 51450578 . G A 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0022;SOR=Inf;LSEQ=TCTGGTGGCCCATGAGTGGC;RSEQ=GTCACGATCTTCAGCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:56,52:0:2,0:26.8:1:30.4:1:1:0:58.5:53:1:0:0.2 0/1:64:6:2,4:25,33:0.0938:2,2:42.5:1:30.2:1:1:1.50567:56.5:12:0.0938:0:1.2 -7 51450625 . G C 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05631;SOR=0.37216;LSEQ=GGCCCTGGCAGGGCGCACCA;RSEQ=GGTCACCCCTACCAGGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:27:13,14:60,38:0.216:2,2:21.6:1:30.7:1:0.27196:1.69295:56.7:54:0.216:0:1.4 0/1:54:5:3,2:26,23:0.0926:2,2:27.6:1:29.2:1:1:1.32:57.6:4:0.0769:0:1.6 -7 51450658 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12987;SOR=Inf;LSEQ=CAGGATAACTGGACCATCAG;RSEQ=CAGATCCTGAGCGAGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:81,53:0:2,0:26.5:1:31.5:1:1:0:55.9:133:1:0:0.5 0/1:76:2:1,1:47,27:0.0263:2,2:25.5:1:28:1:1:1.72738:60:4:0.0278:0:1 -7 51450675 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52736;SOR=0;LSEQ=CAGCCAGATCCTGAGCGAGC;RSEQ=GTGGTACACCCTGGGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:98,54:0.013:2,2:24.5:1:30:1:1:1.80729:47.5:4:0.0134:0:1.5 0/0:94:0:0,0:62,32:0:2,0:25.5:1:28.9:1:1:0:53.2:46:1:0:0.6 -7 51450682 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14148;SOR=Inf;LSEQ=ATCCTGAGCGAGCGGTGGTA;RSEQ=ACCCTGGGGCCCAATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:107,63:0:2,0:23.8:1:31.9:1:1:0:51.5:55.667:1:0:0.5 0/1:103:2:1,1:64,37:0.0194:2,2:13.5:1:27:1:1:1.72002:48:4:0.02:0:1.5 -7 51450702 . TG CA 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06128;SOR=0.49434;LSEQ=CACCCTGGGGCCCAATGAGA;RSEQ=CAGAAGTACCACGACCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:29:19,10:104,64:0.1436:2,2:23.8:1:30.7:1:0.83635:1.17:43.8:58:0.151:0.0099:1.2 0/1:144:11:6,5:77,56:0.0764:2,2:23.4:1:30.3:1:1:1.14474:45.4:22:0.0803:0.0139:1.4 -7 51450715 . C T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5749;SOR=2.7716;LSEQ=AATGAGATGCAGAAGTACCA;RSEQ=GACCTGGCCTTCCAGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:1:1,0:130,84:0.0047:2,0:41:0:14:0:1:0:40:0:0:0:5 0/1:156:2:1,1:87,67:0.0128:2,2:16:1:26.5:1:1:1.2963:50:4:0.013:0:2 -7 51450736 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16019;SOR=Inf;LSEQ=GACCTGGCCTTCCAGGTGAA;RSEQ=GTGGCCCACTTGCAACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:139,112:0:2,0:26.6:1:31.5:1:1:0:45.5:82.667:1:0:0.2 0/1:168:2:1,1:92,74:0.0119:2,2:16:1:28:1:1:1.24161:50:4:0.0122:0:2 -7 51450740 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15832;SOR=Inf;LSEQ=TGGCCTTCCAGGTGAAGGTG;RSEQ=CCCACTTGCAACAAGGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:142,116:0:2,0:26.7:1:31.3:1:1:0:45.9:63.5:1:0:0.2 0/1:171:2:1,1:93,76:0.0117:2,2:22.5:1:31.5:1:1:1.22223:42.5:4:0.0118:0:1 -7 51450799 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1162;SOR=Inf;LSEQ=GGCCAAGCCCACAAGCCAGG;RSEQ=GCTAGCAGGAGTGTACAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:109,152:0:2,0:27.9:1:30.9:1:1:0:53.4:64.25:1:0:0.1 0/1:136:2:1,1:57,77:0.0147:2,2:17:1:29:1:1:1.35:52.5:4:0.0147:0:1 -7 51450917 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.50066;LSEQ=GCCCAGACACTCCTGAGCTC;RSEQ=GATACCAAGGAGCAGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:4:2,2:112,104:0.0182:2,2:29.5:1:29.3:1:1:1.07654:60:8:0.0183:0:1.3 0/1:125:37:16,21:48,40:0.296:2,2:27.1:1:30.7:1:0.32727:1.56922:59.4:74:0.296:0:1.1 -7 51450947 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54053;SOR=0;LSEQ=GAGCAGCTTCTGTGGGGGCA;RSEQ=AACAGCTGCACACAGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:103,93:0.0101:2,2:8:1:30.5:1:1:1.10695:60:4:0.0103:0:1 0/0:109:0:0,0:57,52:0:2,0:25.4:1:31:1:1:0:59.9:218:1:0:0.5 -7 51450951 . A G 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=AGCTTCTGTGGGGGCAGAAC;RSEQ=GCTGCACACAGTCAGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:101,97:0:2,0:24.2:1:30.5:1:1:0:59.9:197:1:0:0.1 0/1:112:8:4,4:54,48:0.0714:2,2:27.8:1:28.4:1:1:1.12379:59.9:16:0.0721:0:1.4 -7 51451045 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53175;SOR=0;LSEQ=TGGCAGGGAAATAGACCGTC;RSEQ=GGCACTACAGGAACTGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:62,69:0.015:2,2:28:1:29.5:1:1:1.11:56:4:0.0155:0:1 0/0:78:0:0,0:36,42:0:2,0:26.1:1:30.1:1:1:0:51.2:77:1:0:0.3 -7 51451068 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=9.23644;LSEQ=CACTACAGGAACTGACACAG;RSEQ=TGGTGTCTGGCACTGCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:4:1,3:61,57:0.0328:2,2:33:1:29:1:0.36058:3.18234:45:8:0.0342:0:1 0/1:79:19:11,8:23,37:0.2405:2,2:28.8:1:28:1:0.18454:2.19:39.9:38:0.2468:0:1.1 -7 51451083 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5288;SOR=0;LSEQ=CACAGGTGGTGTCTGGCACT;RSEQ=CATCATACTCTGGCCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:57,61:0.0167:2,2:34:1:30.5:1:1:1.07:47:4:0.0169:0:1 0/0:72:0:0,0:26,46:0:2,0:28.9:1:31.5:1:1:0:44.4:144:1:0:0.4 -7 51451275 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=10.85011;LSEQ=ATGAGGAGGAGGGGGTGATG;RSEQ=TGTCATTGCTGATGACGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:4:2,2:71,78:0.0261:2,2:27.5:1:30.3:1:1:1.10:26.5:8:0.027:0:1 0/1:57:13:6,7:26,18:0.2281:2,2:22.2:1:30.3:1:0.52827:1.66949:35.8:26:0.2321:0:1 -7 51451287 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGATGGTGTCATTGCTG;RSEQ=TGACGGCTTTAGCACCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:80,82:0.0122:2,2:7.5:1:31:1:1:1.02:53:4:0.0124:0:1 0/0:67:0:0,0:40,27:0:2,0:19.2:1:29:1:1:0:48:66:1:0:0.4 -7 51451376 . A G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14684;SOR=1.76208;LSEQ=AACTCTGGGGAGGAGCCAGA;RSEQ=AGCAACAAGGGCTTTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:25:7,18:28,52:0.2381:2,2:24.8:1:31:1:0.62989:1.38045:39.4:24:0.2376:0:1 0/1:59:21:8,13:14,24:0.3559:2,2:25.2:1:30.3:1:1:1.05:39.7:42:0.3559:0:1 -7 51451379 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13419;SOR=Inf;LSEQ=TCTGGGGAGGAGCCAGAAAG;RSEQ=AACAAGGGCTTTGGTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:29,67:0:2,0:23.8:1:31.7:1:1:0:54.1:31:1:0:0.4 0/1:56:2:1,1:20,34:0.0357:2,2:35.5:1:28:1:1:1.68:60:4:0.0357:0:1 -7 51451564 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56049;SOR=0;LSEQ=TCCTCCTCAACCTTGGCACC;RSEQ=ACCTCCTTCTTACTGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:1,2:68,38:0.0275:2,2:14.3:1:24.7:1:0.553:3.53526:47:2:0.0187:0:1.7 0/0:42:0:0,0:26,16:0:2,0:27.2:1:30.5:1:1:0:41.4:41:1:0:0.2 -7 51451610 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCAAAGCCCAGGAGTCT;RSEQ=GTCAGGGCAGCAGAGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:71,77:0.0133:2,2:39:1:30.5:1:1:1.08:53.5:4:0.0136:0:1 0/0:53:0:0,0:24,29:0:2,0:26.5:1:30.6:1:1:0:49.8:106:1:0:0.3 -7 51451627 . A G 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01785;SOR=0.18827;LSEQ=TCTGGTCAGGGCAGCAGAGC;RSEQ=GGCCCCCTACGGCCCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:25:11,14:55,68:0.1678:2,2:26.6:1:29.5:1:1:1.02922:42.4:50:0.1701:0:1.1 0/1:55:2:0,2:24,27:0.0364:2,0:24:1:26:1:0.49492:0:44:4:0.0364:0:1 -7 51451636 . AC GT 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30766;SOR=2.65166;LSEQ=GGCAGCAGAGCAGGCCCCCT;RSEQ=GGCCCCTACCCCTGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:68,76:0.0137:2,2:15:1:30.5:1:1:1.12:42:4:0.0138:0.0068:1.5 0/1:56:2:0,2:22,32:0.0357:2,0:17.5:1:31.5:1:0.51429:0:33.5:4:0.0364:0:2 -7 51451729 . T C 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCTTCTGGTGCAAGAGA;RSEQ=CTGAAAGTGTGGGCGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:116:116:61,55:0,0:1:0,2:28.1:1:30.4:1:1:0:37.4:15.571:1:0:1.3 1/1:41:41:21,20:0,0:1:0,2:27.1:1:30.4:1:1:0:33:40:1:0:1 -7 51451784 . C T 160 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCAGTCATCGTGGTCCCTC;RSEQ=CAACACTAAGGCTTTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:41:10,31:12,32:0.4824:2,2:25:1:29.9:1:0.80832:1.16044:43.1:82:0.4881:0:1.5 0/0:29:0:0,0:13,16:0:2,0:24.1:1:30.1:1:1:0:38.8:58:1:0:0.6 -7 51451925 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCACTGGAGGACCCCACCA;RSEQ=GCTCAAATGCAAGATGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:25:1:29:0:1:1.13389:30.5:4:0.1176:0:3 0/0:3:0:0,0:1,2:0:2,0:32:1:31:1:1:0:37:6:1:0:0.3 -7 51451928 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGAGGACCCCACCACGC;RSEQ=CAAATGCAAGATGAGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:22:1:30:1:1:1.26772:30.5:4:0.1176:0:3 0/0:4:0:0,0:1,3:0:2,0:23.5:1:26:1:1:0:34:3:1:0:0.3 -7 51452002 . A G 52 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01081;SOR=Inf;LSEQ=AGTGTGCCATGTGTGATGGG;RSEQ=ACAGCTTCCCCTTTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:0:2,0:27.6:1:28.8:1:1:0:49.9:13:1:0:0.1 0/1:9:3:2,1:3,3:0.3333:2,2:15.7:1:33:0:1:1.85:60:6:0.3333:0:1 -7 51452216 . C T 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00842;SOR=Inf;LSEQ=CCCCTCCAAGGTTTGTTCTG;RSEQ=CCCTGCCCTGATTCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:22,17:0:2,0:21.2:1:31.7:1:1:0:55.5:78:1:0:0.3 0/1:11:3:1,2:6,2:0.2727:2,2:30.7:1:29.3:1:0.49091:4.9538:60:6:0.3:0:1 -7 51452312 . CAT C 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11595;SOR=8.21865;LSEQ=CTGCCTCTGCCCGAGAGTCA;RSEQ=GAGGCTGAGAGTAGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:1,0:23,8:0.0313:2,0:11:0:32:0:1:0:49:2:0.0323:0:0 0/1:9:2:1,1:4,3:0.2222:2,2:25:1:32.5:1:1:1.29098:43.5:4:0.25:0:0 -7 51452395 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52882;SOR=0;LSEQ=GAGCCTCAGCCTCGCGGGCT;RSEQ=CTCTGTGGGACTGATGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:53,34:0.0225:2,2:39.5:1:26:1:1:1.55077:54.5:4:0.0238:0:1 0/0:53:0:0,0:32,20:0:2,0:23.5:1:31.6:1:1:0:55:51:0.9808:0:0.2 -7 51452404 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13327;SOR=Inf;LSEQ=CCTCGCGGGCTGCTCTGTGG;RSEQ=ACTGATGACTGCATGATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:55,45:0:2,0:25.1:1:30.5:1:1:0:55.7:32.333:1:0:0.1 0/1:58:2:1,1:34,22:0.0345:2,2:30.5:1:29:1:1:1.53351:60:4:0.0345:0:1 -7 51452450 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13675;SOR=Inf;LSEQ=CACCTCACGGATCTTCCACT;RSEQ=CAGGTGAAACGGATGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:75,69:0:2,0:25.7:1:32.1:1:1:0:59.4:143:1:0:0.2 0/1:85:2:1,1:50,33:0.0235:2,2:25:1:29.5:1:1:1.50752:60:4:0.0244:0:1 -7 51452504 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52758;SOR=0;LSEQ=CTGCTGGGAGCCGCTGCATG;RSEQ=GTCCCAGAGGCTGGACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:57,63:0.0164:2,2:43:1:31:1:1:1.10:48.5:4:0.0167:0:1 0/0:74:0:0,0:34,39:0:2,0:25.4:1:29.4:1:1:0:56.2:35.5:1:0:0.3 -7 51452581 . C T 116 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=15.17371;LSEQ=AGGATGTTCTGCACACAAAC;RSEQ=TTGAAGAAGAAGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:16,42:0.0333:2,2:36:1:32.5:1:0.48983:2.58:36:4:0.0345:0:1 0/1:40:14:5,9:6,20:0.35:2,2:27.4:1:30.7:1:0.46919:1.82:46.5:28:0.35:0:1 -7 52528708 . C T 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGCAGTGAGCCGAGATCG;RSEQ=GTCACTGCACTCTGGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:16.5:1:30.8:1:1:0:60:8:0.4:0:1 0/0:1:0:0,0:1,0:0:0,0:16:0:31:0:1:0:60:2:1:0:1 -7 52528757 . C CA 62 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.28268;SOR=0;LSEQ=ACGACTCCATCCCCCGCCCA;RSEQ=AAAAAAAAAAAGAAATTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:4,0:18,0:0.1818:1,0:12.8:1:31.2:1:1:0:60:8:0.1905:0.1364:0.3 0/0:10:0:0,0:10,0:0:0,0:17.8:1:31.7:1:1:0:60:20:1:0:0.1 -7 52528898 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.67415;LSEQ=AATCAGATTTTCAGGTGGGT;RSEQ=TCTTTAGTCTAGTGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:270:145:110,35:85,40:0.537:2,2:27.5:1:31:1:0.17357:1.48:60:23.167:0.5346:0:1.2 1/0:189:143:96,47:26,20:0.7566:2,2:26.9:1:31:1:0.21657:1.57:60:142:0.7676:0:1.3 -7 52528952 . A AT 177 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.91;SOR=1.03421;LSEQ=AACTCTGAAATATAATTTTG;RSEQ=TTTTTTTTTTTCTGGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:55:37,18:255,173:0.1129:2,2:26.6:1:30.7:1:0.30698:1.39:60:54:0.1151:0:0.8 0/1:318:37:25,12:146,129:0.1164:2,2:29.7:1:30.9:1:0.1142:1.84:60:74:0.1201:0:0.8 -7 52528964 . C T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41069;SOR=1.42714;LSEQ=TAATTTTGATTTTTTTTTTT;RSEQ=TGGAGACAGTGTAATCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:13:9,4:320,241:0.0226:2,2:12.1:1:24.2:1:0.57227:1.69:58.5:3.333:0.0189:0:2.2 0/1:376:12:6,6:189,175:0.0319:2,2:30:1:25:1:1:1.07976:60:3:0.0255:0:2.4 -7 52528967 . G T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12307;SOR=3.7801;LSEQ=TTTTGATTTTTTTTTTTCTG;RSEQ=AGACAGTGTAATCCGACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:2:0,2:335,256:0.0034:2,0:1:0:25:1:0.18888:0:60:4:0.0035:0:1.5 0/1:396:5:1,4:206,185:0.0126:2,2:8.6:1:25.4:1:0.19693:4.43875:60:10:0.013:0:1.6 -7 52528988 . A C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=2.90774;LSEQ=AGACAGTGTAATCCGACCAT;RSEQ=TTTAAAAACAACGTTCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:710:367:200,167:173,169:0.5169:2,2:26.8:1:30.7:1:0.32792:1.17:60:13.68:0.5089:0:1.3 1/0:469:355:186,169:57,56:0.7569:2,2:26.2:1:30.9:1:0.7464:1.08:60:28.583:0.7522:0:1.2 -7 52529160 . G A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGAATGTATGGGAGATAC;RSEQ=TGGAATAAATGGGAACTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:1,54:0:1,0:23.6:1:31.7:1:1:0:60:54:1:0:0.7 0/1:33:12:0,12:1,19:0.3636:1,0:18.7:1:29.5:1:1:0:60:11:0.3548:0:1.8 -7 52529181 . C T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26531;SOR=0;LSEQ=TGGAATAAATGGGAACTTCG;RSEQ=TGAGGCCTGAAGATGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:1,35:0,0:1:0,1:28:1:29.4:1:1:0:60:17:1:0:1.1 1/1:13:12:1,11:0,1:0.9231:0,2:25.4:1:30.3:1:1:0:60:24:0.9231:0:1.4 -7 53722738 . A G 140 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=54.83213;LSEQ=TTAATCAGAATAAAAATATA;RSEQ=AATATCAATACTTATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:65,7:0.027:2,0:15.5:1:33.5:1:1:0:60:4:0.027:0:1 1/0:34:21:19,2:11,2:0.6176:2,2:21.3:1:32.1:1:0.62718:1.70:60:42:0.6176:0:1 -7 53722820 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5562;SOR=0;LSEQ=ACAAATTCAAATATAGTCTA;RSEQ=AAATAGACTGGCATATTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:0,3:160,90:0.0119:2,0:17:1:25.7:1:0.04865:0:60:6:0.0121:0:1 0/0:143:0:0,0:81,62:0:2,0:26.1:1:30.9:1:1:0:60:46.667:1:0:0.4 -7 53722880 . T A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=69.25689;LSEQ=AAAACAATTCAAAAAATTCT;RSEQ=TAATTTTCTAGACTTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:5:3,2:132,156:0.0171:2,2:19.4:1:28.4:1:0.66451:1.77:60:10:0.0174:0:1 1/0:164:90:40,50:33,41:0.5488:2,2:24.3:1:29.2:1:1:1.00606:60:180:0.5488:0:1 -7 53722906 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12318;SOR=Inf;LSEQ=TTCTAGACTTACTTTAGGGA;RSEQ=ACTGAGCAATACAGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:119,163:0:2,0:26.2:1:31.1:1:1:0:60:39.286:1:0:0.1 0/1:153:2:1,1:64,86:0.0131:2,2:36:1:29:1:1:1.34:60:4:0.0132:0:2 -7 53854866 . G A 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0;LSEQ=TTAACTCAGTTAGGGATTTG;RSEQ=ATCCTGCTCCTAATCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:724:21:15,6:435,267:0.029:2,2:16.6:1:30.2:1:0.49506:1.53:60:42:0.0295:0:1.2 0/0:439:0:0,0:277,161:0:2,0:27:1:30.8:1:1:0:60:86.6:0.9977:0:0.1 -7 53855035 . T TA 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.30567;SOR=0;LSEQ=AGCATTCCTTCTTTTTTAGG;RSEQ=AAAAAAAATCTTTGTAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:4:1,3:35,258:0.0135:2,2:20.3:1:30.5:1:0.40528:2.45:60:8:0.0137:0.0067:1.3 0/0:150:0:0,0:26,122:0:2,0:23.8:1:27.9:1:1:0:59.8:36:0.9931:0:0.1 -7 54022754 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTTATCTGGCCCCACCC;RSEQ=CATCCTGCTGATTGGTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:31:1:1:0:41.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 54023350 . A G 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32394;SOR=0;LSEQ=AAGATACAGAGCCCAAAGGC;RSEQ=AGTAACAGCAAGATGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:28,20:0,0:1:0,2:19.5:1:29.4:1:1:0:44.2:47:1:0:1.1 1/1:23:22:16,6:0,0:0.9565:0,2:27.8:1:30.2:1:1:0:45.6:21:0.9545:0:1 -7 54023409 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52458;SOR=0;LSEQ=GAGAAGCCATGTTGCCCAAC;RSEQ=CCAGAGGTTGGTATAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:34,31:0.0299:2,2:18:1:29.5:1:1:1.09526:43:4:0.0299:0:1.5 0/0:41:0:0,0:23,18:0:2,0:28.2:1:29:1:1:0:43.3:40:1:0:0.4 -7 54023644 . C T 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGAGTAAGGATAGATTT;RSEQ=GTTATTTCTTGCAAACTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:15.3:1:31:1:1:0:53.3:6:1:0:1 1/1:4:4:1,3:0,0:1:0,2:6.5:1:30.3:1:1:0:46.8:8:1:0:1.3 -7 54024192 . A G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGAATTTTGGATTCTCA;RSEQ=CAAGGCCATGGGCAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:1:31:1:1:0:27:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 54024198 . C T 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTGGATTCTCAACAAGG;RSEQ=CATGGGCAAAAGAGTAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:1:28.5:1:1:0:27:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55086755 . G T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCGCGGCCGCAGCAGCCTCC;RSEQ=CCCCCCGCACGGTGTGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13:0:32.5:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:8:0:31:1:1:0:60:4:1:0:1.5 -7 55086780 . A C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCACGGTGTGAGCGCCCG;RSEQ=CGCGGCCGAGGCGGCCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55086848 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCAGACCGGACGACAGG;RSEQ=CACCTCGTCGGCGTCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:67,2:0.0282:1,2:14.5:1:27:1:0.0833:27.55605:60:4:0.029:0:1 0/0:19:0:0,0:19,0:0:1,0:19.5:1:32.1:1:1:0:60:18:1:0:0.2 -7 55086908 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23986;SOR=4.30156;LSEQ=AACGCCACAACCACCGCGCA;RSEQ=GGCCCCCTGACTCCGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:1,0:238,47:0.0035:2,0:18:0:33:0:1:0:60:2:0.0036:0:1 0/1:134:2:1,1:97,35:0.0149:2,2:22.5:1:27:1:0.46661:2.74672:60:4:0.0149:0:1 -7 55086974 . C T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19171;SOR=3.73612;LSEQ=CTCTTCGGGGAGCAGCGATG;RSEQ=GACCCTCCGGGACGGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:2:1,1:379,327:0.0028:2,2:13.5:1:32:0:1:1.15878:60:4:0.0029:0:1 0/1:382:4:2,2:206,172:0.0105:2,2:25.5:1:30.3:1:1:1.1971:60:8:0.0107:0:1 -7 55087083 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14268;SOR=Inf;LSEQ=GGGCGTGTCTCGCCGGCTCC;RSEQ=GCGCCGCCCCCGGATCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:78,247:0:2,0:20.4:1:30.4:1:1:0:60:80.25:0.9969:0:0.2 0/1:199:2:1,1:66,130:0.0101:2,2:42:1:29:1:1:1.96:60:4:0.0104:0:1 -7 55087092 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15649;SOR=Inf;LSEQ=TCGCCGGCTCCCGCGCCGCC;RSEQ=CCGGATCGCGCCCCGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:54,178:0:2,0:19:1:31.3:1:1:0:60:45.4:0.9956:0:0.2 0/1:153:2:1,1:47,104:0.0131:2,2:24.5:1:29:1:0.53044:2.20:60:4:0.0133:0:1 -7 55087102 . GC G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14196;SOR=Inf;LSEQ=CCGCGCCGCCCCCGGATCGC;RSEQ=CCCGGACCCCGCAGCCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:30,123:0:2,0:15.4:1:31.3:1:1:0:60:29.6:1:0:0.2 0/1:93:2:1,1:24,66:0.0215:2,2:43:0:32:1:0.47181:2.71:60:4:0.0222:0:1 -7 55087139 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.2;SOR=Inf;LSEQ=CCGCCCAACCGCGCACCGGC;RSEQ=CACCGGCTCGGCGCCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:6.1:1:32:1:1:0:60:14:1:0:0.1 0/1:8:3:1,2:2,3:0.375:2,2:9:1:28.7:1:1:1.28664:60:6:0.375:0:1 -7 55088415 . T C 62 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GGAAGGTTTAATTGCACAAT;RSEQ=CCAACCTTGAGCTGCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:0.5:2,2:33.8:1:31.3:1:1:1:60:8:0.5:0:1.3 1/1:2:2:1,1:0,0:1:0,2:3:0:31.5:1:1:0:60:4:1:0:1.5 -7 55209637 . C A 48 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.36364;SOR=Inf;LSEQ=ATTTTCATCTACCACCCACC;RSEQ=CTTTAAATTTCAACATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:25.3:1:30.7:1:1:0:60:6:0.3:0:1 1/1:1:1:0,1:0,0:1:0,0:20:0:30:0:1:0:60:2:1:0:1 -7 55209936 . G T 50 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03074;SOR=9.38629;LSEQ=TGTTTTATTTTAGTTTTTCT;RSEQ=CATTTCTCAGTATTTCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:1:0,1:606,102:0.0014:2,0:29:0:13:0:0.14528:0:60:0:0:0:2 0/1:305:4:1,3:236,65:0.0131:2,2:11:1:25.3:1:0.0359:10.77779:60:8:0.0132:0:1 -7 55210188 . G A 85 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00079;SOR=18.41142;LSEQ=AGAAAATCTAAGTGGAGAAA;RSEQ=GCCTGGGCAGAATTCCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:1:1,0:55,410:0.0021:2,0:1:0:25:0:0.12017:0:60:2:0.0022:0:1 0/1:183:7:1,6:26,150:0.0383:2,2:24:1:30.3:1:1:1.03979:60:14:0.0387:0:1 -7 55210733 . G C 113 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGAGTGTTGAACCCCGT;RSEQ=AGGCATGAGAGCACAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:12,0:9,1:0.5455:2,0:20.2:1:31.7:1:0.45455:0:60:24:0.5455:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55213918 . A C 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54747;SOR=0.36853;LSEQ=CAGGGCTGTAGCACTCAGGA;RSEQ=CTGCCTCCCTGCCCTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:2,0:0.75:0,2:27.2:1:30:1:1:0:60:12:0.75:0:1 1/0:4:2:1,1:1,1:0.5:2,2:15:1:29.5:1:1:1:60:4:0.5:0:1 -7 55214348 . C T 307 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33758;LSEQ=AACAACCCTGCCCTGTGCAA;RSEQ=GTGGAGAGCATCCAGTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1626:1144:648,496:258,222:0.7036:2,2:25.3:1:30.3:1:0.29833:1.12:60:53.476:0.7036:0:1.1 0/1:850:378:214,164:261,211:0.4447:2,2:23.9:1:29.7:1:0.72837:1.05:60:188:0.4487:0:1.2 -7 55214443 . G A 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23605;LSEQ=CCTGGGCAGCTGTAAGTGTC;RSEQ=CATACACACTATCTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1283:158:50,108:419,706:0.1231:2,2:24.1:1:29.6:1:0.18616:1.28168:60:51.667:0.1226:0:1.1 0/1:686:22:7,15:270,394:0.0321:2,2:25.1:1:30.7:1:0.50993:1.46767:60:44:0.0326:0:1.1 -7 55214535 . A T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00625;SOR=Inf;LSEQ=ATGTTTAGTAAGTCACATTA;RSEQ=TCAGAAACAAAAAGTAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:8,277:0:1,0:22.3:1:31:1:1:0:60:94:1:0:0.1 0/1:113:4:0,4:6,103:0.0354:2,0:25:1:30.3:1:1:0:60:8:0.0364:0:1 -7 55214647 . G T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.53807;LSEQ=CAGCCCAGCTGGTTGGCAGT;RSEQ=CAGGCCACCGGAGGCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:18:0,18:0,14:0.5625:1,1:25.1:1:29.9:1:1:0:60:17:0.5484:0:1.1 1/0:6:4:0,4:0,2:0.6667:0,0:8:1:26.3:1:1:0:60:3:0.6:0:1 -7 55215018 . A C 85 d7;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTCAGCGTGGCGCCCTG;RSEQ=CTCAGGCCAGCACTGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:29.8:1:33:1:1:0:60:12:1:0:1.3 1/1:1:1:0,1:0,0:1:0,0:29:0:32:0:1:0:60:2:1:0:4 -7 55217047 . C G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCACTCTCACTGT;RSEQ=TCTCTTTCTGTCACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:32.5:1:30.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55218903 . T C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.33285;LSEQ=GATTGTCTTCATTTATTGAA;RSEQ=GTGCTTAACTCAGGCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:271:237,34:100,24:0.6826:2,2:23.5:1:31.5:1:0.09167:1.67:60:44.167:0.683:0:1.1 0/1:144:60:44,16:65,19:0.4167:2,2:21.2:1:30.3:1:0.69393:1.2421:60:120:0.4196:0:1.1 -7 55218915 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07809;SOR=Inf;LSEQ=TTATTGAATGTGCTTAACTC;RSEQ=GGCCCGGGAAAGGGCGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:517:0:0,0:404,113:0:2,0:23.6:1:30.1:1:1:0:60:50.7:1:0:0.6 0/1:201:2:1,1:139,58:0.01:2,2:21.5:1:28:1:0.50612:2.38471:60:4:0.0102:0:1 -7 55219159 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.26178;LSEQ=CTGAAGACTCCAAAGAGTTA;RSEQ=TTTATTACAGGGTCAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:351:247:20,227:11,92:0.7037:2,2:21.4:1:30.3:1:0.41802:1.35585:60:48.4:0.7076:0:1.1 0/1:115:44:4,40:6,65:0.3826:2,2:19.3:1:29.9:1:1:1.08:60:88:0.3894:0:1 -7 55219290 . T C 137 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00106;SOR=0.03869;LSEQ=AAGTGAACATCAGCAGGGGC;RSEQ=GGGCGCGGTGGCTCACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:29:0,29:0,6:0.8286:0,1:23.9:1:28.3:1:1:0:60:28:0.8235:0:1.8 0/1:7:1:0,1:0,6:0.1429:0,0:17:0:25:0:1:0:60:2:0.1429:0:1 -7 55219307 . C G 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00769;SOR=0;LSEQ=GGCTGGGCGCGGTGGCTCAC;RSEQ=CCTATAATCCCAGCACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:20:0,20:0,3:0.8696:0,1:26.8:1:32.5:1:1:0:60:40:0.8696:0:2 0/0:3:0:0,0:0,3:0:0,0:16.7:1:32.7:1:1:0:60:6:1:0:0 -7 55219568 . AAAC A 28 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=CAGAGCGAGACTCCGTCTCA;RSEQ=AACAACAACAACAACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28:1:29.5:1:1:0:54.5:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28.9:1:1:0:60:4:1:0.5:0 -7 55220177 . A G 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32328;LSEQ=GTCTGCAAGTGCTCTGCGAC;RSEQ=TCCCTGGGAAATGATCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1182:855:576,279:224,102:0.7234:2,2:23:1:30.3:1:0.67666:1.06369:60:84.5:0.7241:0:1.1 0/1:570:261:174,87:197,112:0.4579:2,2:23:1:29.8:1:0.48162:1.14:60:522:0.4611:0:1.1 -7 55220349 . G A 64 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01535;SOR=10.53806;LSEQ=GCACAGGCCCCCGGGAGAGC;RSEQ=ACTGCCTGGTAAGATGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:926:1:1,0:307,615:0.0011:2,0:1:0:25:0:0.33369:0:60:2:0.0011:0:1 0/1:443:5:3,2:157,281:0.0113:2,2:13.8:1:27.8:1:0.35679:2.68:60:4:0.0092:0:1.2 -7 55220905 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTGAGCTGCACCCTGC;RSEQ=CTCAAGGGGTCCTGAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:32:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55221447 . C G 139 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCTATACGTTAGTAAA;RSEQ=AGACGTATTTTTATCATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:21:21,0:6,0:0.7778:0,1:28:1:31.8:1:1:0:60:20:0.7692:0:1.5 1/1:1:1:1,0:0,0:1:0,0:6:0:34:0:1:0:60:2:1:0:1 -7 55221469 . C T 93 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.54148;LSEQ=GACGTATTTTTATCATAATC;RSEQ=ATAAATTATGATAGGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:8:8,0:25,0:0.2424:1,0:26.8:1:31.3:1:1:0:60:16:0.25:0:1.8 0/1:3:1:1,0:2,0:0.3333:0,0:9:0:32:0:1:0:60:2:0.3333:0:1 -7 55221550 . C A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00799;SOR=Inf;LSEQ=CTTTCTGACTCTGCAGAGGG;RSEQ=GCCAGCTGGGTTTTCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:132,0:0:1,0:24.4:1:32:1:1:0:60:43:1:0:0.2 0/1:34:3:2,1:31,0:0.0882:1,2:17:1:29.7:1:0.08824:0:60:6:0.0938:0:1 -7 55221619 . G T 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17216;SOR=5.61427;LSEQ=TAACTTGGGCTTTCTGACGG;RSEQ=AGTCAACACCGTGCTGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:1:0,1:320,24:0.0029:2,0:1:0:26:0:0.07246:0:60:2:0.003:0:4 0/1:124:2:1,1:107,15:0.0161:2,2:10:0:30.5:1:0.24233:6.93899:60:4:0.0165:0:1.5 -7 55221627 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07167;SOR=Inf;LSEQ=GCTTTCTGACGGGAGTCAAC;RSEQ=CCGTGCTGCGCTTCCTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:358,38:0:2,0:22.4:1:30.2:1:1:0:60:98:0.9949:0:0.3 0/1:146:2:1,1:124,20:0.0137:2,2:8.5:1:29:1:0.26783:6.07495:60:4:0.0138:0:1 -7 55221643 . T C 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28673;SOR=2.79005;LSEQ=CAACACCGTGCTGCGCTTCC;RSEQ=CCGTGTGTGGCGCTGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:2:1,1:451,80:0.0038:2,2:30:1:29.5:1:0.28109:5.60887:60:4:0.0038:0:1 0/1:192:2:1,1:154,36:0.0104:2,2:33:0:32:0:0.34909:4.23325:60:4:0.0105:0:1 -7 55221655 . G A 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00744;SOR=1.54275;LSEQ=GCGCTTCCTCCGTGTGTGGC;RSEQ=CTGAGTGTACTTACCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:652:170:147,23:388,94:0.2607:2,2:24.5:1:30.4:1:0.08267:1.55:60:169:0.2649:0:1.1 0/1:261:92:76,16:126,40:0.3525:2,2:23.3:1:29.6:1:0.26974:1.51:60:184:0.3525:0:1.1 -7 55222033 . G T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02509;SOR=Inf;LSEQ=CTGGCTTGCTACCGAGGAGC;RSEQ=GGCAGGTGGTGGCCATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:0:0,0:230,374:0:2,0:24.6:1:30:1:1:0:60:32.556:1:0:0.1 0/1:251:3:1,2:96,152:0.012:2,2:16:1:29.7:1:1:1.262:60:6:0.0121:0:1.3 -7 55222094 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17037;SOR=5.64573;LSEQ=GCACAGGGCAGATCTGGGTG;RSEQ=CCAGGCCACCTCACAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:1:0,1:268,284:0.0018:2,0:41:0:31:0:1:0:60:2:0.0018:0:1 0/1:197:2:1,1:99,95:0.0102:2,2:8.5:1:27.5:1:1:1.0419:60:4:0.0103:0:1 -7 55222433 . G T 80 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00298;SOR=13.61712;LSEQ=CCAGGGTTTAGGGAAATTGT;RSEQ=ACATAAAATAATTCCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1335:1:1,0:649,681:7e-04:2,0:6:0:13:0:0.48835:0:60:0:0:0:1 0/1:692:7:3,4:335,350:0.0101:2,2:23.9:1:28.7:1:1:1.27574:60:14:0.0103:0:1.7 -7 55222593 . A C 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=4.000;MSILEN=1;SSF=0.00054;SOR=0;LSEQ=CAGATTTGTGTACATGAAAA;RSEQ=TTTTACATTCCGTATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:21:12,9:301,373:0.0301:2,2:20.3:1:30.9:1:0.27375:1.65:59.6:9.5:0.0278:0:1.2 0/0:308:0:0,0:135,172:0:2,0:23.2:1:29.9:1:1:0:60:75.75:1:0:0.2 -7 55222610 . G GA 248 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.3235;LSEQ=AAAATTTTACATTCCGTATG;RSEQ=AAAAAAAAAACACAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:303:141,162:150,159:0.4516:2,2:26.3:1:30.2:1:0.62805:1.08376:59.9:302:0.4646:0.0671:0.3 0/1:276:58:30,28:93,108:0.2101:2,2:23.7:1:29.2:1:0.55079:1.24:60:57:0.2135:0.0181:0.3 -7 55222755 . G A 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21576;LSEQ=TAGGAAAACACTTCGAGCCT;RSEQ=AGATACCAAGAGCAGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1139:663:368,295:271,205:0.5821:2,2:25.1:1:28.9:1:0.67181:1.05963:60:330.5:0.5855:0:1.1 0/1:537:124:68,56:225,187:0.2309:2,2:21.3:1:28.7:1:1:1.01:60:123:0.2316:0:1.1 -7 55222954 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15942;LSEQ=GGACCAGCCTGGCCAACAGG;RSEQ=TGAAACCTCGTCTCTACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:127:13,114:8,64:0.6382:2,2:27.1:1:31.3:1:0.81568:1.09564:60:62.5:0.6345:0:1 0/1:55:12:1,11:2,41:0.2182:1,2:28:1:30.5:1:0.5296:1.84:60:24:0.2222:0:1 -7 55223101 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08711;SOR=Inf;LSEQ=GCTGAGATCACACCACTGCA;RSEQ=TCCAGCCTGGGTGACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:226,57:0:2,0:23.7:1:31.7:1:1:0:59.2:55.6:1:0:0.4 0/1:119:2:1,1:83,34:0.0168:2,2:20.5:1:29:1:0.50349:2.42052:54.5:4:0.0171:0:3.5 -7 55223176 . G A 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34558;LSEQ=ATAGAGCTCCTAAAAATAAC;RSEQ=CAGAAGTCTGCTATTAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:925:644:395,249:160,120:0.6962:2,2:26.1:1:30.1:1:0.2427:1.19:60:213.667:0.699:0:1.1 0/1:498:220:126,94:159,119:0.4418:2,2:26.3:1:29.9:1:1:1.00:60:440:0.4462:0:1.2 -7 55223790 . T C 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21558;SOR=0.44702;LSEQ=AGAAGATAAAGCTGTAAAGC;RSEQ=AGGTTAGGCAATGGGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:43:5,38:3,16:0.6935:2,2:24.2:1:32.3:1:0.69167:1.41651:60:86:0.7049:0:1 1/0:14:7:0,7:0,7:0.5:0,0:32:1:31.9:1:1:0:60:14:0.5:0:1 -7 55224143 . C T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1507;SOR=3.6859;LSEQ=TCCGGTGACCGGAATTCCTT;RSEQ=CTGCTTCCCTCTGCCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:2:1,1:404,64:0.0043:2,2:17:1:19.5:1:0.25772:6.27151:60:1:0.0022:0:1.5 0/1:193:3:1,2:157,33:0.0155:2,2:14:1:28.3:1:0.08524:9.34854:60:6:0.0159:0:1 -7 55224152 . C T 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02833;SOR=Inf;LSEQ=CGGAATTCCTTCCTGCTTCC;RSEQ=TCTGCCTGTGGATCCCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:0:0,0:438,107:0:2,0:22.5:1:31:1:1:0:60:108:1:0:0.1 0/1:240:3:1,2:184,52:0.0125:2,2:10:1:27:1:0.12887:7.00083:60:6:0.0128:0:1 -7 55225140 . G C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.61126;LSEQ=GGCGGGAGACATGCGGAATC;RSEQ=CAGCGGAAGGCGGGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:11:10,1:18,0:0.3793:1,2:12.5:1:31.4:1:0.37931:0:60:22:0.3793:0:2 1/0:4:2:2,0:2,0:0.5:0,0:7.5:1:28:1:1:0:60:4:0.5:0:1.5 -7 55225170 . G C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGGAGGCAGCTGTGAACT;RSEQ=TGGCTCGGCCTGCGTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:45,2:0,0:1:0,1:24.5:1:31.8:1:1:0:60:94:1:0:1.3 1/1:4:4:4,0:0,0:1:0,0:30:1:31.8:1:1:0:60:8:1:0:1.5 -7 55227781 . A T 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02945;SOR=Inf;LSEQ=GAAACAAAGTTTTCAGGGAT;RSEQ=CATTGTTTTTATAATTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:311,65:0:2,0:22.9:1:28.6:1:1:0:60:375:1:0:0.1 0/1:169:3:1,2:132,34:0.0178:2,2:15.7:1:25.7:1:0.11507:7.63666:60:6:0.0178:0:1 -7 55228053 . A T 289 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08816;LSEQ=TAAGTCACCGCTTTCTGTTT;RSEQ=GTTTATGGAGTTGGTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:804:779:247,532:9,14:0.9689:2,2:25.8:1:30.1:1:0.49762:1.38406:60:154.8:0.9687:0:1.1 1/0:389:285:94,191:37,66:0.7326:2,2:24.1:1:29.9:1:0.62735:1.13871:60:284:0.7339:0:1.1 -7 55228085 . T A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19167;SOR=5.15509;LSEQ=TGGTTCTAATGGGTCCTTTA;RSEQ=TTGTATTTAGAATATTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:1:0,1:105,398:0.002:2,0:13:0:19:0:1:0:60:0:0:0:3 0/1:197:2:1,1:57,138:0.0102:2,2:6.5:1:29:1:0.50321:2.41:60:4:0.0103:0:2 -7 55228160 . T G 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00126;SOR=0;LSEQ=TTAAGAAGCAAATTAAAATC;RSEQ=TAAGATTCCTAACTGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:31:2,29:1,88:0.2583:1,2:22.2:1:32.2:1:0.16337:5.96:60:62:0.2583:0:1.7 0/0:28:0:0,0:2,26:0:2,0:22.9:1:30.9:1:1:0:60:56:1:0:0.5 -7 55228173 . C T 193 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.04358;LSEQ=TAAAATCTTAAGATTCCTAA;RSEQ=TGTGAAATTACCATGTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:92:90:3,87:0,2:0.9783:0,1:25:1:29.8:1:1:0:60:21.5:0.9773:0:1.3 1/0:23:15:0,15:1,7:0.6522:2,1:18.6:1:30.8:1:0.34783:0:60:30:0.6522:0:1 -7 55228217 . A T 25 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04407;SOR=Inf;LSEQ=ATTAAAACTTTTTCCAGATC;RSEQ=TTACCATTCAATGGGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:2,44:0:1,0:23.1:1:30.7:1:1:0:60:45:0.9783:0:0.7 0/1:13:2:1,1:0,11:0.1538:0,2:26:1:25.5:1:0.15385:0:60:4:0.1538:0:1 -7 55229015 . A G 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14922;SOR=3.33076;LSEQ=CACAACTACTTTGTCCTTCC;RSEQ=GTCACGGTCGGCCTCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:7:7,0:40,0:0.1489:1,0:9.1:1:30:1:1:0:60:14:0.1489:0:1 0/1:8:3:2,1:5,0:0.375:0,2:36.3:1:30.3:1:0.375:0:60:6:0.375:0:1 -7 55229255 . G A 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00263;SOR=1.46962;LSEQ=CTGCTGGGGCCCGGAGCCCA;RSEQ=GGACTGCGTCTCTTGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1667:166:98,68:839,657:0.0996:2,2:26:1:30:1:0.50954:1.13:60:40.5:0.0985:0:1.1 0/1:894:125:74,51:428,340:0.1398:2,2:24.3:1:29.9:1:0.49712:1.15:60:61.5:0.1393:0:1.2 -7 55229414 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08821;SOR=Inf;LSEQ=ACAGGCATTCTGTTTGATTT;RSEQ=CTCTTCCTTTTATTCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:458:0:0,0:25,433:0:2,0:22.9:1:30.2:1:1:0:60:113.5:1:0:0.1 0/1:194:2:1,1:13,178:0.0103:2,2:9:0:32:1:0.14017:13.23:60:4:0.0104:0:1 -7 55229543 . T C 119 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.16833;LSEQ=AATAAGCAAGTATTATTGCC;RSEQ=AATATAATCCAATAATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:14:0,14:0,41:0.2545:1,1:13.4:1:31.5:1:1:0:60:28:0.2545:0:1.1 0/1:7:2:0,2:0,5:0.2857:0,0:31:1:22.5:1:1:0:60:1:0.1667:0:1 -7 55230840 . A G 39 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTGCTGGAGGGTAGAACT;RSEQ=TGCTTGACTACTAGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29.3:1:24.7:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55231357 . A T 48 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03293;SOR=9.13831;LSEQ=CAAGTTATTTGGAATTTTGA;RSEQ=GAGGTGATTTGTGTTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:1:0,1:520,165:0.0015:2,0:1:0:25:0:0.24198:0:60:2:0.0015:0:1 0/1:304:4:1,3:218,82:0.0132:2,2:8.5:1:24:1:0.0678:7.91242:60:3:0.0101:0:1 -7 55231575 . G A 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34325;SOR=2.92855;LSEQ=GAAGGGCCTTCACAGAAGCC;RSEQ=AACAGTGATGATGGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:2:2,0:57,262:0.0062:2,0:1:0:27.5:1:0.03331:0:60:4:0.0063:0:1 0/1:166:3:3,0:39,124:0.0181:2,0:8:1:25:1:0.01533:0:60:6:0.0186:0:1 -7 55232333 . A G 36 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGAGTGGACAAAACCAAC;RSEQ=TGAGAGAACTTAGCCAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:23:1:23.3:1:1:0:60:2:0.6667:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55232726 . G T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33705;SOR=0.34481;LSEQ=GCAGAATGCAATAATGTAGA;RSEQ=AATATCATTTCTTTCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:20:20,0:10,0:0.6667:0,1:25:1:30.5:1:1:0:60:19:0.6552:0:1 0/1:5:2:2,0:3,0:0.4:0,0:19.5:1:30.5:1:1:0:60:4:0.4:0:1 -7 55233159 . AT A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.04714;SOR=Inf;LSEQ=AAAGTGAAGGAGAACAGAAC;RSEQ=TTCCTCTCTTGCAAATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:95,340:0:2,0:22.8:1:30.1:1:1:0:60:61.143:1:0:0.1 0/1:247:3:2,1:69,175:0.0121:2,2:27.3:1:30:1:0.19931:5.03:60:6:0.0122:0.004:0.7 -7 55235215 . G A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGTGGTGGTGGTGATGGTG;RSEQ=TGAGGAGGTGGGAGTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:0:31:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55235345 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTCACAATGGTAGTGG;RSEQ=GATGATGGTGTTGGTGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:27.5:1:1:0:60:4:1:0:1 -7 55235804 . C A 61 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTCGCCTTTGGGTATA;RSEQ=CAACATGCCAGCTCTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:28:1:30.5:1:1:0:60:8:0.5:0:2.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55236020 . T C 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00176;SOR=Inf;LSEQ=TCTCTGCATCAATATCTCTA;RSEQ=ATCAGTATCTCTGTGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:94,1:0:1,0:26.2:1:31.3:1:1:0:60:94:1:0:0.1 0/1:26:4:4,0:21,1:0.1538:1,0:34.8:1:32.8:1:1:0:60:8:0.1538:0:1 -7 55236175 . G A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAAGATTTAAATTAAAAAT;RSEQ=TTAGTGGTCATTTTTCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1269:0:0,0:753,516:0:2,0:25.7:1:32.1:1:1:0:60:125.9:1:0:0.1 0/1:666:18:11,7:361,284:0.027:2,2:23.6:1:28:1:0.81104:1.24:60:36:0.0274:0:1.2 -7 55236774 . A G 51 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCCAGACGAGGGGGAGG;RSEQ=ACCCTGGAGGAATAGCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:39:1:32.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55236796 . C T 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGAGGAATAGCTATTT;RSEQ=TTTTTTTTTTTTGTCGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:8:1:29.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55237913 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05367;SOR=Inf;LSEQ=GAGACCTGGAGAGCAGAGAT;RSEQ=GAAACTGTTAGGATCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:427,29:0:2,0:22.7:1:28.6:1:1:0:60:151:1:0:0.1 0/1:138:2:1,1:127,9:0.0145:2,2:33.5:1:31:1:0.14017:13.4396:60:4:0.0145:0:1 -7 55237977 . T C 139 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=56.41443;LSEQ=AGGCCTCTCACATATTGAAA;RSEQ=GTACTTGTCCATCTTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1418:1:1,0:910,507:7e-04:2,0:15:0:34:0:1:0:60:2:7e-04:0:1 0/1:652:25:15,10:414,213:0.0383:2,2:23.5:1:30:1:0.526:1.2952:60:50:0.0388:0:1.1 -7 55238087 . C T 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30172;LSEQ=AATGATGGCAGCGTGTCCCA;RSEQ=CAGAGCGGGAGCCCAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2221:300:143,157:1000,918:0.1351:2,2:25.2:1:30.2:1:0.15352:1.19587:60:36.5:0.1335:0:1.2 0/1:1067:48:20,28:500,518:0.045:2,2:24.4:1:28.9:1:0.37573:1.35097:60:96:0.0457:0:1.1 -7 55238253 . G T 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTGAGCCTCATGCCTTCAC;RSEQ=TGTCTGTTCCCCCCGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1384:0:0,0:478,902:0:2,0:26.5:1:31.1:1:1:0:60:64.714:0.9971:0:0.2 0/1:732:53:21,32:271,408:0.0724:2,2:23.7:1:30.1:1:1:1.01212:60:52:0.0721:0:1.8 -7 55238268 . G A 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00202;SOR=1.59622;LSEQ=TTCACGTGTCTGTTCCCCCC;RSEQ=CTTTTCCTTTCTGCCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1165:124:43,81:331,710:0.1064:2,2:23.4:1:29.8:1:0.54188:1.14:60:248:0.1084:0:1.1 0/1:582:93:31,62:186,303:0.1598:2,2:24.5:1:28.9:1:0.4149:1.2273:60:92:0.16:0:1.5 -7 55238464 . T G 91 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03482;LSEQ=TGTCAGAAACCTGCAGGGAC;RSEQ=CCATGCTGCCAGCCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:2,27:0.1944:2,0:18.1:1:32.7:1:1:0:60:14:0.1944:0:1 0/1:5:1:0,1:0,4:0.2:0,0:4:0:31:0:1:0:60:2:0.2:0:1 -7 55238874 . T A 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.92385;LSEQ=TTCACTTCCTACAGATGCAC;RSEQ=GGGCCAGGTCTTGAAGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1298:136:74,62:694,467:0.1048:2,2:25.8:1:30.6:1:0.23196:1.24487:60:135:0.1052:0:1.1 0/1:631:116:66,50:275,240:0.1838:2,2:25.6:1:30:1:0.53664:1.15:60:57:0.183:0:1.1 -7 55238941 . G A 113 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=8.78828;LSEQ=CTCTGTGTCACATGGACCTC;RSEQ=TCAAGAATGACCACACTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1098:4:4,0:421,673:0.0036:2,0:2.3:1:23.8:1:0.02225:0:60:3:0.0028:0:1 0/1:449:14:6,8:182,253:0.0312:2,2:28.5:1:29.8:1:1:1.04:60:28:0.0315:0:1.5 -7 55238990 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=AGATGCTTTCCTGCATTTCT;RSEQ=ACTGTCCTCTGTCCTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:0:0,0:46,384:0:2,0:24.2:1:31.4:1:1:0:60:85:1:0:0.1 0/1:175:2:1,1:33,140:0.0114:2,2:30.5:1:27:1:0.35172:4.19:60:4:0.0114:0:1 -7 55240461 . G C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0354;SOR=0.2332;LSEQ=ATTTTAAAAAATGAGGAAAA;RSEQ=TGTGCCTGGTAGGGGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:83:47:46,1:33,3:0.5663:2,1:25.2:1:32.4:1:0.31173:4.11:60:94:0.5663:0:1.1 0/1:13:3:3,0:10,0:0.2308:0,0:27.3:1:31.7:1:1:0:60:6:0.2308:0:1 -7 55241755 . G A 124 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=45.29505;LSEQ=AGGTAAGGTCCCTGGCACAG;RSEQ=CCTCTGGGCTGGGCCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:832:1:1,0:292,538:0.0012:2,0:1:0:30:0:0.35259:0:60:2:0.0012:0:1 0/1:386:20:7,13:126,238:0.0518:2,2:25.7:1:28.7:1:1:1.02:60:40:0.0525:0:1.1 -7 55242609 . A G 228 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16645;LSEQ=CTCTGCTCTAGACCCTGCTC;RSEQ=TCTCCACATCCTAAATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:229:136:4,132:3,90:0.5939:1,1:26:1:32.2:1:1:1.09954:60:44.333:0.5938:0:1.1 0/1:118:23:1,22:5,90:0.1949:2,1:22.8:1:30.6:1:1:1.22026:60:22:0.1913:0:1 -7 55242782 . T C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TAGTTTCTTGACACGCATGA;RSEQ=GAGTGAGTGCTCTTGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:2,12:0,0:1:0,2:18.6:1:30:1:1:0:60:28:1:0:1.3 1/1:2:2:1,1:0,0:1:0,2:13:1:30:1:1:0:60:4:1:0:1 -7 55248231 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATAGGGAGCCTGGGGGC;RSEQ=CAGCACAGAGAGACCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55248787 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00805;SOR=0.11498;LSEQ=GATGCACCCAGGAGGGGCCC;RSEQ=CTCCCACTGCATCTGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:28:28,0:3,0:0.9032:0,1:21.9:1:29.7:1:1:0:60:13:0.8966:0:1.1 1/0:12:6:6,0:6,0:0.5:0,0:22.2:1:32:0:1:0:60:12:0.5:0:1 -7 55248893 . C A 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTATTTTGAAACTCAAGAT;RSEQ=GCATTCATGCGTCTTCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:307,14:0:1,0:23.6:1:31.4:1:1:0:60:106:1:0:0.4 0/1:88:11:11,0:70,7:0.125:2,0:29.3:1:27.2:1:0.58918:0:60:22:0.131:0:1.1 -7 55248926 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14381;LSEQ=CTTCACCTGGAAGGGGTCCA;RSEQ=GTGCCCCTCCTTCTGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:254:205,49:270,57:0.4364:2,2:24:1:31.5:1:0.58918:1.13198:60:253:0.437:0:1.1 0/1:220:22:18,4:147,50:0.1:2,2:21.5:1:30.6:1:0.60511:1.53:60:44:0.1009:0:1.5 -7 55249063 . G A 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18596;LSEQ=TGCCTCACCTCCACCGTGCA;RSEQ=CTCATCACGCAGCTCATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1527:1295:656,639:119,111:0.8481:2,2:24.8:1:29.8:1:0.77508:1.04428:60:70.944:0.8496:0:1.1 1/0:823:419:225,194:193,208:0.5091:2,2:24.8:1:29.5:1:0.12422:1.25:60:138.667:0.5111:0:1.1 -7 55249208 . G A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00356;SOR=Inf;LSEQ=GATACGGGGAGGGGAGATAA;RSEQ=GAGCCAGGATCCTCACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:973:0:0,0:322,651:0:2,0:22.9:1:30.8:1:1:0:60:59.813:1:0:0.1 0/1:468:5:4,1:157,306:0.0107:2,2:9.8:1:25.8:1:0.04983:7.76:60:10:0.0108:0:1 -7 55249229 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07875;SOR=7.25731;LSEQ=GAGCCAGGATCCTCACATGC;RSEQ=GTCTGCGCTCCTGGGATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:1:0,1:138,524:0.0015:2,0:50:0:16:0:1:0:60:0:0:0:3 0/1:276:3:2,1:59,213:0.0109:2,2:11.3:1:25.3:1:0.12472:7.15:60:6:0.011:0:1 -7 55251103 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTGCATTTAGGACCCAC;RSEQ=CTAAATCCAGGATGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55259622 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10485;SOR=Inf;LSEQ=CTGACACCAGGGACCAGGCT;RSEQ=CCTTCCCACTAGCTGTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:83,319:0:2,0:22.8:1:31.9:1:1:0:60:66:1:0:0.1 0/1:193:2:1,1:49,142:0.0104:2,2:23:1:25:1:0.45202:2.88:60:4:0.0104:0:1 -7 55259763 . A G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24482;SOR=3.57184;LSEQ=GCCAGAGCTGCTTTGGGAAC;RSEQ=GTACTTGCTGGGACAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:18:2,16:0,22:0.45:1,2:25.7:1:31.4:1:0.19615:0:60:36:0.4615:0:1.2 1/0:8:6:0,6:0,2:0.75:0,0:20.5:1:30:1:1:0:60:12:0.75:0:1.2 -7 55260334 . A G 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57618;SOR=0;LSEQ=GGAGGCGCCGGGCCTGGGGG;RSEQ=CGGGTCCTGGGGTGATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:3,0:264,6:0.011:1,0:12:1:26.3:1:1:0:60:2:0.0077:0:2.3 0/0:91:0:0,0:88,3:0:1,0:25.4:1:28.7:1:1:0:60:29.333:1:0:0 -7 55265940 . G C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATCAAATGGAACTTAA;RSEQ=CTTTTTCATTTCCAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:13.7:1:31.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55266336 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07622;SOR=Inf;LSEQ=CAAGAAACAGTAACCAGTAA;RSEQ=GATGACTAAAGCAAGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:0:0,0:448,62:0:2,0:23.5:1:30.9:1:1:0:60:84:1:0:0.4 0/1:195:2:2,0:166,27:0.0103:2,0:18.5:1:32:1:1:0:60:4:0.0104:0:1.5 -7 55266417 . T C 320 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30134;LSEQ=TTCATCCTCTCAGGGGTGAC;RSEQ=GTTTGGGAGTTGATGACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1625:1572:881,691:29,20:0.9674:2,2:25.6:1:30.2:1:0.77038:1.13718:60:86.333:0.9688:0:1.1 1/1:894:804:463,341:44,43:0.8993:2,2:26:1:29.6:1:0.21239:1.33:60:60.846:0.8978:0:1.1 -7 55266757 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69421;SOR=0.61348;LSEQ=CATTGGGCAGTATGACCTGA;RSEQ=ATTTGCCCATGTTTGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:0,11:1,19:0.3548:1,0:22.4:1:25.2:1:1:0:60:4.5:0.3214:0:1.3 0/1:8:2:0,2:0,6:0.25:0,0:10:1:29:0:1:0:60:4:0.25:0:1 -7 55268916 . C T 201 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=243.95239;LSEQ=CATTTGCCAAGTCCTACAGA;RSEQ=TCCAACTTCTACCGTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1539:1:0,1:849,689:6e-04:2,0:1:0:28:0:0.44834:0:60:2:7e-04:0:1 0/1:890:122:64,58:421,345:0.1371:2,2:26:1:29.1:1:0.62538:1.10576:60:29.5:0.1345:0:1.1 -7 55269675 . C CAG 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07497;SOR=0.12687;LSEQ=CCAGTAGTAGCATCGCCTGG;RSEQ=CTTGTTAGAAACGCCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:84:82:4,78:0,2:0.9762:0,1:23.1:1:31.6:1:1:0:60:164:0.988:0.2976:0.2 1/1:12:10:0,10:0,2:0.8333:0,0:23.8:1:31.9:1:1:0:60:20:0.8333:0.25:0 -7 55270119 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAACCTACTAATCAGAAC;RSEQ=AGCATCTCAAGGAGATCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:157,7:0.012:1,2:7.5:1:28.5:1:0.09434:21.04679:60:4:0.0121:0:1 0/0:63:0:0,0:61,2:0:1,0:20.9:1:31:1:1:0:60:126:1:0:0.1 -7 55270463 . C T 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCAGACACAGTGAAGGG;RSEQ=GTAAGGAGCAGATAAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:910:0:0,0:263,646:0:2,0:24.2:1:30.1:1:1:0:60:33.962:0.9989:0:0.1 0/1:455:19:5,14:145,291:0.0418:2,2:27.4:1:29.8:1:0.62481:1.39423:60:38:0.042:0:1.1 -7 55272334 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CCACAGACACACACCACACA;RSEQ=ACATACACATACACACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:28:0:33:1:1:0:23:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55272339 . A G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GACACACACCACACATACAT;RSEQ=CACATACACACACCACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:23:0:32.5:1:1:0:23:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55272357 . C T 27 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATACACATACACACACCACA;RSEQ=ACACGTACACACACCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:5:0:27.5:1:1:0:23:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55272496 . TAC T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACCATACATACACACGTA;RSEQ=ACACACCACATATACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:26:1:31.3:1:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 55272826 . G A 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56906;SOR=0.71374;LSEQ=AACAGCAAGAGGGCCCTCCC;RSEQ=AGGCTCCTGCTCCCTGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:118:117,1:4,0:0.9672:0,1:22.1:1:30.4:1:1:0:60:117:0.9669:0:1.1 1/1:22:21:21,0:1,0:0.9545:0,1:21.4:1:31:1:1:0:60:42:0.9545:0:1 -7 55804335 . CA C 51 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.0415;SOR=Inf;LSEQ=CAGCCTGCCAAACTGCATCT;RSEQ=AAAAAAAAAAAACAAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:0:1,0:17.5:1:30.3:1:1:0:57.5:30:1:0:1.1 0/1:9:3:3,0:6,0:0.3333:0,0:28.7:1:32.3:1:1:0:60:6:0.3333:0:2 -7 55804456 . AC A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGAGCCCCTGCCAGGA;RSEQ=CCCCTGCCCAGACCATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:97,60:0.0126:2,2:38:1:32.5:1:1:1.61154:47.5:4:0.0127:0:0 0/0:79:0:0,0:49,26:0:2,0:27:1:30.8:1:1:0:51.6:74:0.9487:0:0.2 -7 55804511 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13909;SOR=Inf;LSEQ=CCCTGATGTCTGCGTCCAGC;RSEQ=AGGCGTCCGGTGGCGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:139,108:0:2,0:20.5:1:30.1:1:1:0:54.1:60.75:0.9959:0:0.4 0/1:148:2:1,1:72,74:0.0135:2,2:14.5:1:27.5:1:1:1.03:56.5:4:0.0139:0:1.5 -7 55804543 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.17079;SOR=Inf;LSEQ=GGCGTCAGCATGTTTGTGTG;RSEQ=AGGAATGTGGAACCTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:134,117:0:2,0:27.5:1:30.8:1:1:0:54.1:49.2:0.996:0:0.4 0/1:178:2:1,1:80,96:0.0112:2,2:38.5:1:28:1:1:1.20:49:4:0.0115:0:2 -7 55804561 . T C 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51711;SOR=1.16105;LSEQ=TGGAGGAATGTGGAACCTTG;RSEQ=TCTGTGGCTGTGTTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:75:34,41:87,81:0.3086:2,2:33.9:1:32.4:1:0.40523:1.29382:46.1:74:0.3083:0:1.2 0/1:164:56:23,33:48,60:0.3415:2,2:29.8:1:31.4:1:0.74086:1.14686:45:55:0.3416:0:1.2 -7 55804619 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.49691;LSEQ=TGACCCCTCCCTGCAGCCGC;RSEQ=TGAGGCCCAGCAACCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:59,100:0.0124:2,2:25:1:29:1:1:1.69:49:4:0.0126:0:1 0/1:54:1:0,1:16,37:0.0185:2,0:35:0:27:0:1:0:44:2:0.0185:0:1 -7 55804717 . A T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAGTGTCCACCAGGTGGG;RSEQ=CAGGGAGTGCTGACCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:31,55:0.0227:2,2:17:0:32:0:1:1.76:21:4:0.0233:0:1.5 0/0:39:0:0,0:22,17:0:2,0:24.2:1:29.4:1:1:0:48.7:78:1:0:0.4 -7 55804738 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07037;SOR=Inf;LSEQ=CAGGGAGTGCTGACCCTGGG;RSEQ=GGCCCCCTGAAGCCACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:34,56:0:2,0:24.9:1:30.1:1:1:0:53.7:89:1:0:0.2 0/1:33:2:1,1:18,13:0.0606:2,2:40.5:1:31:1:1:1.37079:30:4:0.0606:0:1.5 -7 55804747 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07185;SOR=Inf;LSEQ=CTGACCCTGGGCGGCCCCCT;RSEQ=AAGCCACCTGCCCTGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:33,53:0:2,0:23.8:1:31.4:1:1:0:54.7:172:1:0:0.2 0/1:32:2:1,1:16,14:0.0625:2,2:15.5:1:29.5:1:1:1.13808:31:4:0.0645:0:1.5 -7 55804758 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08807;SOR=Inf;LSEQ=CGGCCCCCTGAAGCCACCTG;RSEQ=CCTGAAAGCCCAGGGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:31,46:0:2,0:23.8:1:31.6:1:1:0:54.7:76:1:0:0.2 0/1:33:2:1,1:17,14:0.0606:2,2:21:1:31.5:1:1:1.20712:60:4:0.0645:0:1 -7 55804827 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07792;SOR=Inf;LSEQ=CCTGGTAAAAGCCCACCTCC;RSEQ=ACCATGGAGGAGGAGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:16,24:0:2,0:19.3:1:29.1:1:1:0:58.4:39:1:0:0 0/1:16:2:2,0:5,9:0.125:2,0:12.5:1:32:0:0.175:0:40:4:0.1333:0:2.5 -7 55804863 . T C 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55263;SOR=3.3251;LSEQ=CCCTGGGCCCCTCAGGGGAG;RSEQ=CCCTGCTGGACAGTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:1,0:19,15:0.0286:2,0:9:0:33:0:1:0:53:2:0.0294:0:2 0/1:22:2:2,0:9,11:0.0909:2,0:45:1:33:1:0.47619:0:40:4:0.0909:0:2.5 -7 55804913 . T C 26 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63791;SOR=1.61995;LSEQ=CACAATGTTGCTTTCCTCTC;RSEQ=GTCATGTCTCCTGACACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:44,13:0.0339:2,2:43.5:1:31:1:0.42139:3.29831:56.5:4:0.0345:0:1.5 0/1:37:2:1,1:24,11:0.0541:2,2:26.5:1:26:1:1:2.13205:43.5:4:0.0541:0:2 -7 55804944 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17888;SOR=Inf;LSEQ=CTGACACCCAGTTGCCTCCA;RSEQ=CACTCAGATGATGTCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:60,28:0:2,0:23:1:31.8:1:1:0:58.5:87:1:0:0.2 0/1:65:2:1,1:38,25:0.0308:2,2:20.5:1:28:1:1:1.50993:60:4:0.0323:0:1 -7 55804945 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.57409;SOR=2.76311;LSEQ=TGACACCCAGTTGCCTCCAC;RSEQ=ACTCAGATGATGTCAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:0,1:62,27:0.0111:2,0:23:0:26:0:0.31111:0:60:2:0.0114:0:1 0/1:66:2:1,1:38,26:0.0303:2,2:7.5:1:28:1:1:1.45294:48:4:0.0313:0:1.5 -7 55805070 . G A 149 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03384;SOR=0.4252;LSEQ=TCCGGTGGCCCATGAGTGGC;RSEQ=TTCATGATCTTCAGCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:30:13,17:74,72:0.1695:2,2:28.4:1:30.4:1:0.54907:1.34176:60:29:0.1667:0:1.1 0/1:113:9:3,6:54,50:0.0796:2,2:20.2:1:28.9:1:0.32117:2.14571:60:18:0.0796:0:1.2 -7 55805089 . C T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78835;SOR=1.28376;LSEQ=CGTTCATGATCTTCAGCAAG;RSEQ=GGCACTAGGCCCTGGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:8:4,4:81,82:0.0468:2,2:25:1:30.6:1:1:1.01:60:16:0.0476:0:1.1 0/1:118:7:3,4:54,57:0.0593:2,2:22.1:1:31.6:1:1:1.26067:60:14:0.0603:0:1.1 -7 55805107 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05124;SOR=Inf;LSEQ=AGCGGCACTAGGCCCTGGCA;RSEQ=GGCGCACCAGGGTCACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:90,86:0:2,0:25.7:1:31.4:1:1:0:58.1:175:1:0:0.3 0/1:105:3:2,1:51,51:0.0286:2,2:38:1:27:1:1:1.99:60:6:0.0291:0:1.7 -7 55805114 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14259;SOR=Inf;LSEQ=CTAGGCCCTGGCAGGGCGCA;RSEQ=CAGGGTCACCCCAACCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:89,75:0:2,0:26.8:1:31.5:1:1:0:57.8:81:1:0:0.3 0/1:100:2:1,1:51,47:0.02:2,2:31.5:1:28.5:1:1:1.0842:60:4:0.0211:0:2 -7 55805125 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5274;SOR=0;LSEQ=CAGGGCGCACCAGGGTCACC;RSEQ=CAACCAGGATAACCGGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:0,2:91,82:0.0114:2,0:17:1:28.5:1:0.22897:0:52:4:0.0117:0:1 0/0:107:0:0,0:55,52:0:2,0:24.8:1:30.4:1:1:0:58.4:106:1:0:0.3 -7 55805138 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14569;SOR=Inf;LSEQ=GGTCACCCCAACCAGGATAA;RSEQ=CGGACCGTCAGCCAGATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:89,90:0:2,0:22.1:1:31.6:1:1:0:57.7:178:1:0:0.2 0/1:111:2:1,1:56,53:0.018:2,2:33.5:1:28.5:1:1:1.0561:54.5:4:0.0189:0:1 -7 55805166 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52921;SOR=0;LSEQ=TCAGCCAGATCCTGAGCGAG;RSEQ=GGTGGTACACCCTGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:88,73:0.0123:2,2:15:0:31.5:1:1:1.20409:49.5:4:0.0123:0:1.5 0/0:98:0:0,0:50,48:0:2,0:25.9:1:30.4:1:1:0:57.3:48:1:0:0.2 -7 55805301 . G C 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02741;SOR=0.34391;LSEQ=CAAGCCAGGGGCTAGCAGGA;RSEQ=TGTACAAGGGCTCATGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:25:7,18:71,96:0.1295:2,2:31.4:1:32.8:1:0.19524:1.89577:44:50:0.1323:0:1.2 0/1:103:5:1,4:39,59:0.0485:2,2:25.8:1:32.8:1:0.64617:2.62262:40.4:10:0.0495:0:1 -7 55805408 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCAGACATTCCAGAGCTC;RSEQ=GATACCAAGGAGCAGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:64,45:0.018:2,2:11.5:1:32.5:1:1:1.4176:37:4:0.0182:0:1.5 0/0:47:0:0,0:27,20:0:2,0:23.1:1:29.9:1:1:0:51.7:46:1:0:0.1 -7 55805495 . C G 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.93506;LSEQ=GCCCAAGCCTTCTCCCACAG;RSEQ=GGGGTACTCAGCCTGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:13:2,11:29,52:0.1383:2,2:22.8:1:31.5:1:0.20835:3.03664:38.4:26:0.1398:0:1.9 0/1:46:6:1,5:15,25:0.1304:2,2:23.8:1:29.8:1:0.64891:2.93965:39:12:0.1304:0:2.3 -7 55805503 . T G 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTCCCACAGCGGGGTAC;RSEQ=CAGCCTGGACGGCAGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:85:30,55:0,0:1:0,2:26.1:1:30.4:1:1:0:38.4:20.25:1:0:1.2 1/1:38:38:11,27:0,0:1:0,2:26.2:1:31.2:1:1:0:38.9:76:1:0:1.3 -7 55805703 . A G 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56106;SOR=0;LSEQ=CTCATTCCCAGCACATGGCC;RSEQ=GTGAGGACACAGCGAGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:3:3,0:53,44:0.03:2,0:21.3:1:27.7:1:0.25333:0:34.7:6:0.03:0:1.7 0/0:38:0:0,0:26,12:0:2,0:19.5:1:29.6:1:1:0:44.8:76:1:0:0.1 -7 55805716 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2637;SOR=4.00053;LSEQ=CATGGCCAGTGAGGACACAG;RSEQ=GAGTGACGAGGAGCCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:1,0:56,43:0.01:2,0:17:0:32:0:1:0:40:2:0.0101:0:1 0/1:51:2:2,0:30,19:0.0392:2,0:21:1:28.5:1:0.52314:0:33.5:4:0.04:0:1.5 -7 55805756 . G C 109 Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05346;SOR=0.14902;LSEQ=GTCATCCATGAGGAGGAGGG;RSEQ=GTGATGATGTCATTGCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:10:10,0:57,54:0.0826:2,0:19.8:1:33:1:0.00215:0:38.3:20:0.0833:0:1.1 0/1:76:1:1,0:44,31:0.0132:2,0:7:0:33:0:1:0:40:2:0.0133:0:1 -7 55805779 . C T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31369;SOR=0.3988;LSEQ=GATGATGTCATTGCTGATGA;RSEQ=GGCTTTAGCACCACTGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:7:7,0:60,54:0.0579:2,0:8.1:1:31.6:1:0.01658:0:24.7:14:0.0579:0:1 0/1:84:2:2,0:46,36:0.0238:2,0:25:1:30.5:1:0.5043:0:23:4:0.0244:0:1 -7 55805928 . A G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.48197;SOR=0.46695;LSEQ=CTTCTTCCTTTACTCCTGCC;RSEQ=CCCCTTGCTCGATCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:11:2,9:8,24:0.25:2,2:22.7:1:31.5:1:1:1.48669:38.6:22:0.2619:0:1.7 0/1:15:2:1,1:3,10:0.1333:2,2:40:1:31:1:0.47619:3.03:26:4:0.1333:0:2 -7 55805938 . C G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70869;SOR=0.64266;LSEQ=TACTCCTGCCACCCCTTGCT;RSEQ=GATCCTGAGCCCCCAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:1,6:9,20:0.1944:2,2:30.6:1:31.1:1:0.6454:2.63711:36.3:14:0.2059:0:2.1 0/1:15:2:1,1:3,10:0.1333:2,2:30:1:30:1:0.47619:3.03:26:4:0.1333:0:2 -7 55806087 . G T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09227;SOR=0.25578;LSEQ=CAGGAGCCTTCAAAGCCCAG;RSEQ=AATCTGGTCAGGGCAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:16:13,3:42,29:0.1839:2,2:29.3:1:29.7:1:0.15083:2.96:56.8:32:0.1882:0:1 0/1:37:2:2,0:20,15:0.0541:2,0:36.5:1:30:1:0.5045:0:60:4:0.0556:0:1 -7 55806109 . C T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63875;SOR=1.55573;LSEQ=ATCTGGTCAGGGCAGCAGAG;RSEQ=GGGCCCCCTATGGCCCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:3:1,2:56,40:0.0303:2,2:19.7:1:30.3:1:0.57263:2.77104:31.3:6:0.0303:0:2.3 0/1:43:2:1,1:24,17:0.0465:2,2:43:0:30:1:1:1.40026:21:4:0.0476:0:2.5 -7 55806116 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09804;SOR=Inf;LSEQ=CAGGGCAGCAGAGCGGGCCC;RSEQ=CTATGGCCCCTACCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:56,46:0:2,0:24.4:1:30.6:1:1:0:57.7:50:1:0:0.3 0/1:47:2:1,1:26,19:0.0426:2,2:43:1:27:1:1:1.35916:60:4:0.0426:0:2.5 -7 55806127 . T C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60515;SOR=1.97169;LSEQ=AGCGGGCCCCCTATGGCCCC;RSEQ=ACCCCTGGGGATGGGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:60,43:0.019:2,2:6.5:1:30.5:1:1:1.39083:27:4:0.019:0:2.5 0/1:54:2:1,1:35,17:0.037:2,2:25:0:33:1:1:2.02925:21:4:0.0377:0:2.5 -7 55806150 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53231;SOR=0;LSEQ=CCCTGGGGATGGGGGCCCAG;RSEQ=GATGCCTTCCAAGGCGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:54,49:0.019:2,2:11:1:28:1:1:1.10102:60:4:0.0196:0:1 0/0:61:0:0,0:35,26:0:2,0:26.2:1:30.5:1:1:0:50.5:60:1:0:0.3 -7 55806357 . G A 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.70324;LSEQ=CTGACTGGGCTTTGGGGGTC;RSEQ=GGGCAGAGGGAACCCCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:3,0:13,10:0.1154:2,0:16.7:1:31.3:1:0.26154:0:30.3:6:0.12:0:1.7 0/1:12:1:1,0:4,7:0.0833:2,0:25:0:30:0:0.41667:0:40:2:0.0833:0:1 -7 55806420 . A G 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01893;SOR=Inf;LSEQ=CCCCACCACGCTCAAATGCA;RSEQ=GATGAGAAGATGCTCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:45,21:0:2,0:25.3:1:30.1:1:1:0:36.3:65:1:0:0.1 0/1:25:3:1,2:14,8:0.12:2,2:13:1:29.3:1:0.54348:3.3216:24.7:6:0.125:0:1 -7 55806460 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07513;SOR=Inf;LSEQ=TGCAGCCCAAAGCCCAACAC;RSEQ=CCCAAGTGTGCCATGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:44,50:0:2,0:27.9:1:30.2:1:1:0:44:93:1:0:0.1 0/1:36:2:1,1:16,18:0.0556:2,2:11.5:1:26.5:1:1:1.12:60:4:0.0556:0:2 -7 55806527 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07568;SOR=Inf;LSEQ=CAGGTGGGAGAAGCCGAGGA;RSEQ=GGGCTCAGGGAACCGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:17,37:0:2,0:20.3:1:30.8:1:1:0:57.3:53:1:0:0.2 0/1:21:2:1,1:5,14:0.0952:2,2:22.5:1:31:1:0.5:2.65:60:4:0.0952:0:2 -7 55806542 . G A 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.8655;LSEQ=GAGGACGGGCTCAGGGAACC;RSEQ=GAGACCGAGAAGGCGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:4:1,3:16,22:0.0952:2,2:9.5:1:31.5:1:0.63549:2.14496:33.5:8:0.0976:0:1 0/1:24:2:0,2:9,13:0.0833:2,0:20:1:33:0:0.51087:0:24:4:0.0833:0:2 -7 55806557 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08386;SOR=Inf;LSEQ=GAACCGGAGACCGAGAAGGC;RSEQ=GTGTCCTCTTCACTGCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:15,23:0:2,0:23.1:1:29.6:1:1:0:53.5:18:1:0:0.2 0/1:16:2:0,2:6,8:0.125:2,0:5:1:32:0:0.5:0:24:4:0.125:0:2 -7 55806766 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.70115;SOR=0.62491;LSEQ=TCACCTGGCTAGACTCTGAC;RSEQ=CTGCCCTGGCTGCCCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:6:3,3:17,9:0.1875:2,2:22:1:30.3:1:0.64713:1.84998:55.5:12:0.1875:0:1 0/1:16:2:1,1:10,4:0.125:2,2:9.5:1:28.5:1:1:2.34522:57.5:4:0.1333:0:1 -7 55806821 . T TAGGGGC 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=3.000;MSILEN=6;SSF=0.52863;SOR=1.49398;LSEQ=GAGTCACGTGAGGCTGAGAG;RSEQ=AGGGGCAGGGGCAGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:7:5,2:43,19:0.1:2,2:28.7:1:29.7:1:1:1.10:41:14:0.1014:0.0286:0.1 0/1:35:5:4,1:19,11:0.1429:2,2:9.8:1:31.3:1:0.63994:2.27:44.4:10:0.1429:0.1143:0.4 -7 55806849 . TG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGCAGCAGTGGTGCCAGT;RSEQ=GGGGGCGGTCCAGTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:65,35:0.0196:2,2:42:1:31.5:1:1:1.84527:43:4:0.02:0:0 0/0:50:0:0,0:33,17:0:2,0:27.8:1:32:1:1:0:43.5:100:1:0:0.2 -7 55806855 . GC G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.09199;SOR=0.25774;LSEQ=GCAGTGGTGCCAGTTGGGGG;RSEQ=GGTCCAGTGGGAGGAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:14:10,4:62,33:0.1284:2,2:29.9:1:31.1:1:0.7686:1.33:43.7:28:0.1308:0.0092:0.3 0/1:55:2:1,1:34,19:0.0364:2,2:27.5:1:31.5:1:1:1.76954:42.5:4:0.037:0:0 -7 55806859 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGCCAGTTGGGGGGCGG;RSEQ=CCAGTGGGAGGAGCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:75,38:0.0174:2,2:34.5:1:29.5:1:1:1.96122:43.5:4:0.0177:0:1 0/0:56:0:0,0:35,21:0:2,0:27.2:1:29.7:1:1:0:42.8:55:1:0:0.2 -7 55806957 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8305;LSEQ=CTTCAACTGCAGGTGAAACG;RSEQ=ATGCTGGTGGTGGGTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:84,77:0.0123:2,2:29.5:1:29.5:1:1:1.09032:41.5:4:0.0123:0:1 0/1:98:1:0,1:53,43:0.0102:2,0:1:0:23:0:0.45361:0:49:2:0.0103:0:1 -7 55806991 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5228;SOR=0;LSEQ=GTGCAGGGCCGCTGGGAGCC;RSEQ=CTGCATGGGTCCCAGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:63,89:0.013:2,2:32.5:1:30.5:1:1:1.41:60:4:0.0131:0:1 0/0:98:0:0,0:45,53:0:2,0:28.6:1:30.4:1:1:0:45.4:97:1:0:0.2 -7 55807008 . G A 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00048;SOR=0.11424;LSEQ=GCCGCTGCATGGGTCCCAGA;RSEQ=GCTGGACTGCGGCAGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:25:10,15:46,76:0.1701:2,2:31.9:1:30.6:1:0.82501:1.10:53.8:50:0.1712:0:1.1 0/1:88:2:1,1:39,47:0.0227:2,2:30:1:26.5:1:1:1.20:48.5:4:0.0227:0:1 -7 55807012 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14205;SOR=Inf;LSEQ=CTGCATGGGTCCCAGAGGCT;RSEQ=GACTGCGGCAGGTGCCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:56,87:0:2,0:28.4:1:31:1:1:0:53.3:34.75:1:0:0.3 0/1:87:2:1,1:37,48:0.023:2,2:28:1:28.5:1:1:1.29:28:4:0.023:0:2 -7 55807018 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13748;SOR=Inf;LSEQ=GGGTCCCAGAGGCTGGACTG;RSEQ=GGCAGGTGCCAACTGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:52,88:0:2,0:27:1:30.2:1:1:0:54.1:45.667:1:0:0.3 0/1:83:2:1,1:35,46:0.0241:2,2:28:1:29.5:1:1:1.31:28:4:0.0241:0:2 -7 55807087 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17505;SOR=Inf;LSEQ=CACACAAACCTTGGAGAAGA;RSEQ=GTGTGCATAGCGGGTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:7,33:0:2,0:24.6:1:30.9:1:1:0:58.1:80:0.9756:0:0 0/1:30:2:0,2:7,21:0.0667:2,0:28:1:32:0:1:0:54.5:4:0.0667:0:1 -7 55809054 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGAAGTTGTGGGCCTAC;RSEQ=AGGGCCACTGGGAGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:28:1:1:0:50:4:1:0:1.5 -7 55865547 . A G 59 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=0.20333;LSEQ=GTGGCAGCTGCTGAGATTGC;RSEQ=CCACTGCACTCCAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:20.3:1:29.8:1:1:0:60:8:0.6667:0:1 0/1:4:1:1,0:2,1:0.25:2,0:16:0:25:0:1:0:60:2:0.25:0:2 -7 55865699 . G C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52679;SOR=0;LSEQ=AGGGGGCTGAGGAAGTGTGA;RSEQ=CCCCTGCCAGGAACCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:97,35:0.0149:2,2:7:0:33:0:0.46661:2.74672:60:4:0.0156:0:1.5 0/0:82:0:0,0:58,24:0:2,0:21.6:1:30.5:1:1:0:60:12.667:1:0:0 -7 55865719 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16348;SOR=Inf;LSEQ=GCCCCTGCCAGGAACCCCTG;RSEQ=CCAGACCATGTACTCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:116,63:0:2,0:25.6:1:30.9:1:1:0:60:24.571:1:0:0.2 0/1:122:2:1,1:78,42:0.0164:2,2:16:0:31.5:1:1:1.84722:60:4:0.0167:0:1 -7 55865734 . C T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00226;SOR=Inf;LSEQ=CCCTGCCCAGACCATGTACT;RSEQ=GGCCCACAGGCCCCTGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:130,83:0:2,0:26.3:1:30.4:1:1:0:60:70:0.9906:0:0.2 0/1:158:7:4,3:89,62:0.0443:2,2:16:1:27.7:1:1:1.07611:60:6:0.0387:0:1.1 -7 55865867 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12767;SOR=Inf;LSEQ=TCCTTCCTGACCCCTCCCTG;RSEQ=AGCCACGCAAAGCCCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:52,82:0:2,0:25.6:1:31.7:1:1:0:60:66:1:0:0.1 0/1:75:2:1,1:37,36:0.0267:2,2:17.5:1:28:1:1:1.02741:60:4:0.027:0:1.5 -7 55865896 . A T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17879;SOR=2.19199;LSEQ=AAAGCCCAGCAACCTGCCAG;RSEQ=CACTCAGTGGCCTCCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:7:2,5:42,71:0.0583:2,2:23.4:1:30.3:1:1:1.47431:60:14:0.0593:0:1 0/1:75:9:3,6:29,37:0.12:2,2:32.1:1:29.9:1:0.72439:1.55849:60:18:0.12:0:1.1 -7 55865957 . C A 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27258;SOR=0;LSEQ=TGGCAGCTGTTGCTCATGAG;RSEQ=GTCCACCAGGTGGGACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:3:1,2:48,63:0.0263:2,2:26:1:32.3:1:1:1.51841:60:6:0.0265:0:1 0/0:78:0:0,0:33,45:0:2,0:24.7:1:30.8:1:1:0:59:156:1:0:0.2 -7 55865970 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16368;SOR=Inf;LSEQ=TCATGAGCGTCCACCAGGTG;RSEQ=GACAGGGAGTGCTGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:55,62:0:2,0:25.5:1:30.8:1:1:0:56.6:38:1:0:0.3 0/1:80:2:1,1:33,44:0.025:2,2:33:1:29.5:1:1:1.33:60:4:0.0263:0:1 -7 55865979 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52008;SOR=0;LSEQ=TCCACCAGGTGGGACAGGGA;RSEQ=TGCTGACCCTGGGCGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:52,60:0.0175:2,2:41.5:1:30.5:1:1:1.15:60:4:0.0179:0:1 0/0:74:0:0,0:32,42:0:2,0:24:1:31:1:1:0:55.7:148:1:0:0.1 -7 55866109 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19616;SOR=Inf;LSEQ=GAGGAGGAGCCCTGGGCCCC;RSEQ=CAGGGGAGCCCCTGCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:0:2,0:26.5:1:30.7:1:1:0:57.1:122:1:0:0.1 0/1:49:2:1,1:26,21:0.0408:2,2:7.5:1:27:1:1:1.23267:48:4:0.0417:0:2 -7 55866151 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17388;SOR=Inf;LSEQ=GTGAGACAGAGAATGACCAC;RSEQ=ATGATGCTTTCCTCTCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:46,26:0:2,0:23.9:1:29.9:1:1:0:53.7:23:1:0:0.6 0/1:52:2:1,1:28,22:0.0385:2,2:17.5:1:32:0:1:1.26678:48:4:0.0392:0:1 -7 55866158 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01444;SOR=Inf;LSEQ=AGAGAATGACCACAATGATG;RSEQ=TTTCCTCTCCGTCATGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:48,24:0:2,0:23.8:1:32.2:1:1:0:53.2:71:1:0:0.6 0/1:56:5:3,2:31,20:0.0893:2,2:17.8:1:28.8:1:1:1.03275:53.6:10:0.0893:0:1.8 -7 55866192 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2405;SOR=Inf;LSEQ=ATGTCTCCTGACACCCAGTT;RSEQ=CCTCTACCACCCAAATGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:65,28:0:2,0:23.6:1:32:1:1:0:48.9:92:1:0:1.2 0/1:90:2:1,1:53,35:0.0222:2,2:7:1:29:1:1:1.50709:60:4:0.0225:0:1 -7 55866203 . C T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00032;SOR=0.34028;LSEQ=CACCCAGTTGCCTCTACCAC;RSEQ=CAAATGATGTCAGGCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:101:67:46,21:22,12:0.6634:2,2:24.3:1:30.5:1:0.8227:1.19:42.8:66:0.66:0:2 0/1:95:38:23,15:32,25:0.4:2,2:29.3:1:30.3:1:0.83223:1.20:42.5:76:0.413:0:2.2 -7 55866206 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00016;SOR=0.33793;LSEQ=CCAGTTGCCTCTACCACCCA;RSEQ=ATGATGTCAGGCCCAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:70:47,23:23,12:0.6667:2,2:24.6:1:31.5:1:1:1.07:43.9:34:0.6602:0:2.1 0/1:102:41:24,17:34,27:0.402:2,2:28.1:1:31.7:1:0.84001:1.12:43.8:82:0.41:0:2.1 -7 55866274 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00365;SOR=Inf;LSEQ=CATCTTCTGAGAAGGATGGA;RSEQ=GCAGCCCCAACAAATGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:95,82:0:2,0:26.5:1:30.8:1:1:0:57.2:176:1:0:1 0/1:147:7:4,3:68,72:0.0476:2,2:32.3:1:30:1:0.71525:1.41:60:14:0.0479:0:1 -7 55866295 . AAGG A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00897;SOR=Inf;LSEQ=GCAGCCCCAACAAATGGGAC;RSEQ=ACCACATCCGGCAGCCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:103,85:0:2,0:21.8:1:30.1:1:1:0:59.3:93:1:0:1 0/1:122:5:1,4:63,54:0.041:2,2:36.2:1:29.8:1:0.18988:4.61473:60:10:0.0417:0:0 -7 55866297 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18636;LSEQ=AGCCCCAACAAATGGGACAA;RSEQ=GACCACATCCGGCAGCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:187:142:79,63:23,22:0.7594:2,2:21.5:1:30.3:1:0.61055:1.20:59.2:70:0.7568:0:1.2 0/1:122:45:25,20:38,34:0.3689:2,2:25.8:1:29.8:1:0.8496:1.12:59.7:21.5:0.3805:0:1.2 -7 55866300 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51874;SOR=0;LSEQ=CCCAACAAATGGGACAAGGA;RSEQ=CACATCCGGCAGCCCGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:99,89:0.0105:2,2:8:0:31.5:1:1:1.11173:46:4:0.0106:0:2.5 0/0:127:0:0,0:69,58:0:2,0:25.5:1:30.9:1:1:0:60:126:1:0:0.5 -7 55866313 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1556;SOR=Inf;LSEQ=ACAAGGACCACATCCGGCAG;RSEQ=CCGTGAGTGGCACTCATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:108,100:0:2,0:21.3:1:30.8:1:1:0:60:33.667:1:0:0.7 0/1:136:2:1,1:70,64:0.0147:2,2:18:1:27.5:1:1:1.09302:60:4:0.0152:0:1.5 -7 55866443 . A G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00098;SOR=Inf;LSEQ=GTGGTACACTCTGGGGCCCA;RSEQ=TGAGAGGCAGAAGTACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:67,107:0:2,0:26.3:1:30.5:1:1:0:60:57:1:0:0.1 0/1:106:7:3,4:40,59:0.066:2,2:25.3:1:31:1:1:1.11:60:14:0.0673:0:1.3 -7 55866455 . A T 76 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0156;SOR=9.75702;LSEQ=GGGGCCCAATGAGAGGCAGA;RSEQ=GTACCATGACCTGACCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:1:0,1:58,101:0.0063:2,0:37:0:32:0:1:0:60:2:0.0063:0:1 0/1:103:6:2,4:39,58:0.0583:2,2:14.8:1:29.7:1:1:1.34108:60:12:0.0588:0:1.2 -7 56430016 . C CA 65 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.17356;SOR=3.67888;LSEQ=AAAAACAAAAAACAAAACAA;RSEQ=AAAAAAAAAACAAAACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:5,0:23,1:0.1724:1,0:24.2:1:28.2:1:1:0:56.2:4:0.1429:0:0.6 0/1:9:4:3,1:5,0:0.4444:0,2:24.8:1:30:1:0.44444:0:56.3:8:0.4444:0.1111:0 -7 56430156 . G T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1161;SOR=Inf;LSEQ=CCTGCCCAGACCAAGTACTT;RSEQ=GCCCACAGGCCTGCGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:215,82:0:2,0:22.8:1:31.4:1:1:0:59.8:58.4:1:0:0.1 0/1:154:2:1,1:103,48:0.013:2,2:7:0:27.5:1:0.53939:2.13416:60:4:0.0133:0:1 -7 56430192 . C T 55 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47667;SOR=1.714;LSEQ=TCCAGCGAGGCCTCCCGTGG;RSEQ=GTCAGCATGTTCATGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:570:4:0,4:329,237:0.007:2,0:1:0:23.3:1:0.0315:0:50.3:3:0.0053:0:1 0/1:334:4:1,3:186,144:0.012:2,2:10.5:1:27.5:1:0.32398:3.8602:60:8:0.0122:0:1 -7 56430244 . C A 57 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04178;SOR=7.4727;LSEQ=CTCGCTCTGTGGCTGTGTTC;RSEQ=CCTGGTACTCTGTCCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:742:1:1,0:331,410:0.0013:2,0:1:0:29:0:0.44744:0:60:2:0.0014:0:1 0/1:500:5:4,1:233,261:0.01:2,2:9.2:1:24.8:1:0.19569:4.47:60:4:0.0081:0:1.2 -7 56430396 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTGGGACAGGGAGTGTT;RSEQ=ACCCTGGGCGGCCCCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:35,73:0.0182:2,2:18.5:1:28:1:0.54946:2.07:43:4:0.0187:0:1 0/0:44:0:0,0:14,30:0:2,0:24:1:30.4:1:1:0:39.1:43:1:0:0.3 -7 56430441 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54409;SOR=0;LSEQ=CCTGCCCTGAAAGCCCAGGG;RSEQ=CCGGAACCCCACACACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:31,54:0.023:2,2:23:1:29.5:1:1:1.73:27:4:0.023:0:1 0/0:46:0:0,0:19,27:0:2,0:26:1:31.3:1:1:0:37.7:92:1:0:0.2 -7 56430522 . A C 76 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66242;SOR=0.45177;LSEQ=AGGAGGAGCCCTGGGCCCCT;RSEQ=AGGGGAGTCCCTGCTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:0,5:21,26:0.0962:2,0:20.6:1:32.8:1:0.07321:0:34.4:10:0.0962:0:1.8 0/1:22:1:1,0:11,10:0.0455:2,0:42:0:33:0:1:0:27:2:0.0455:0:3 -7 56430530 . T C 51 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81886;LSEQ=CCCTGGGCCCCTAAGGGGAG;RSEQ=CCCTGCTGGACAGTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:0,3:21,28:0.0577:2,0:12.3:1:32.3:1:0.26357:0:39.7:6:0.0577:0:2.3 0/1:21:1:1,0:10,10:0.0476:2,0:34:0:34:0:1:0:27:2:0.0476:0:3 -7 56430560 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTGAGACAGAGAATGAC;RSEQ=ACGATGATGCTTTCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:22,28:0.0385:2,2:20.5:1:28.5:1:1:1.27:60:4:0.0385:0:1 0/0:21:0:0,0:13,8:0:2,0:24.2:1:30.5:1:1:0:48:42:1:0:0.2 -7 56430650 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00857;SOR=0.25866;LSEQ=CCCAGTCCCTCAGTGCACTG;RSEQ=GCAAGGAACAGGACTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:56:26,30:4,5:0.8615:2,2:27.2:1:29.3:1:1:1.08:56.7:27:0.8571:0:1.1 1/0:31:19:8,11:6,6:0.6129:2,2:23.9:1:29.2:1:0.7241:1.36082:57.4:18:0.6:0:1.2 -7 56430693 . C A 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17241;SOR=0;LSEQ=TAAGAAGGATGGACACAGCC;RSEQ=CAACAAATGGGACAAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:4,2:35,26:0.0896:2,2:34.3:1:30.5:1:1:1.48:60:12:0.0896:0:1 0/0:31:0:0,0:17,14:0:2,0:18.9:1:30.1:1:1:0:59.6:62:1:0:0.6 -7 56430775 . A G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04275;LSEQ=GCGGCACCAGGCTCTGGCAG;RSEQ=GCGCACCAGGGTCACCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:41:24,17:6,2:0.8367:2,2:23.5:1:30.6:1:0.45827:2.09474:39.6:82:0.8367:0:1 0/1:35:6:5,1:19,10:0.1714:2,2:26.3:1:30.5:1:0.63994:2.57:41.2:12:0.1714:0:1 -7 56430843 . C T 91 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05125;SOR=0;LSEQ=CCTGAGCAAGCGGTGGTACA;RSEQ=CCTGGGGCCCAATGAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:7:7,0:91,41:0.0504:2,0:32.3:1:32.6:1:0.10468:0:60:14:0.0511:0:1.1 0/0:78:0:0,0:50,28:0:2,0:21.1:1:30.5:1:1:0:58.7:38:1:0:0.3 -7 56430879 . T A 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACACAGAAGTACCACGACC;RSEQ=GGCCTTCCAAGTGAAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:138,91:0:2,0:23.9:1:30.5:1:1:0:57.3:75.333:1:0:0.2 0/1:127:24:16,8:60,43:0.189:2,2:23.2:1:29.6:1:0.4963:1.43:55:23:0.1855:0:1.1 -7 56430940 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14388;SOR=Inf;LSEQ=AAAGAAGTCCAGCTCAGAGG;RSEQ=CAAGCCCACAAGCCAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:111,150:0:2,0:27.1:1:31.1:1:1:0:51.6:36.286:1:0:0.2 0/1:160:2:1,1:73,85:0.0125:2,2:23.5:1:31:1:1:1.16:49:4:0.0129:0:1 -7 56431041 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10412;SOR=Inf;LSEQ=CCCCTGGGGTGTCCTCTGAA;RSEQ=TCCTGTCAGTTGCAGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:40,66:0:2,0:27.7:1:32.1:1:1:0:58.2:34.333:1:0:0.2 0/1:51:2:1,1:18,31:0.0392:2,2:38.5:1:28:1:1:1.70:54.5:4:0.0392:0:1 -7 56431109 . A G 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11373;SOR=3.66946;LSEQ=CAGCTTCTGTGGGGCAGGAC;RSEQ=GCTGCACACAGTCAGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:3:1,2:44,34:0.037:2,2:45:1:32:1:0.58228:2.55838:40:6:0.037:0:1 0/1:40:5:2,3:16,19:0.125:2,2:21.2:1:30.4:1:1:1.25588:52.8:10:0.1282:0:1 -7 56431160 . C CA 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02944;LSEQ=CTGGCCCAAGCCTTCTCCCA;RSEQ=GGGGGGTACACAGCCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:86:84:47,37:2,0:0.9767:0,2:23.7:1:30.4:1:0.50397:0:41.4:168:0.9767:0.2209:0.2 1/0:35:19:14,5:8,7:0.5429:2,2:22.8:1:29:1:0.28827:2.38:43.1:38:0.5588:0.1429:0.5 -7 56431170 . A G 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1308;SOR=3.07644;LSEQ=CCTTCTCCCACGGGGGGTAC;RSEQ=CAGCCTGGACGGCAGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:4:3,1:44,43:0.044:2,2:12.8:1:31:1:0.61738:2.90:54.8:8:0.044:0:1.3 0/1:40:5:3,2:22,13:0.125:2,2:15.4:1:29.4:1:1:1.12477:47.2:10:0.1282:0:1.2 -7 56431180 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10811;SOR=Inf;LSEQ=CGGGGGGTACACAGCCTGGA;RSEQ=GGCAGGGAAATAGACCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:48,51:0:2,0:22.5:1:30.5:1:1:0:46.9:48.5:1:0:0.1 0/1:49:2:1,1:24,23:0.0408:2,2:26:1:28.5:1:1:1.04259:29:4:0.0426:0:1.5 -7 56431197 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14189;SOR=Inf;LSEQ=GGACGGCAGGGAAATAGACC;RSEQ=TCAGGCACTACAGGAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:60,55:0:2,0:24:1:30.2:1:1:0:52.5:56.5:1:0:0.2 0/1:70:2:0,2:37,31:0.0286:2,0:36:1:31.5:1:0.21863:0:35.5:4:0.0294:0:1 -7 56431233 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52325;SOR=0;LSEQ=ACTGACACAAGTGGTGTCTG;RSEQ=CACTGCATCATACTCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:75,73:0.0133:2,2:20.5:1:28.5:1:1:1.02722:25:4:0.0136:0:1 0/0:95:0:0,0:46,49:0:2,0:31.6:1:31.3:1:1:0:49.4:94:1:0:0.3 -7 56431383 . C T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03544;LSEQ=CATGGCCAGTGAGGACACAG;RSEQ=GAGTGACGAGGAGCCCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:59:35,24:11,4:0.7973:2,2:27.6:1:30.2:1:0.38342:1.8704:44.6:58:0.8169:0:1.1 0/1:34:4:2,2:21,9:0.1176:2,2:15.3:1:28.5:1:0.57993:2.27026:40.5:8:0.1176:0:1 -7 56431439 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGGTGACGATGTCATTG;RSEQ=TGATGATGGCTTTAGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:98,65:0.0121:2,2:22.5:1:31.5:1:1:1.5038:60:4:0.0125:0:1 0/0:55:0:0,0:32,23:0:2,0:21:1:31.9:1:1:0:49.8:54:1:0:0.1 -7 56431560 . CT TG 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=0.07939;LSEQ=GGGCTTTGGTGGGAAGGTAT;RSEQ=GCACCTGTCATTCCTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:25:8,17:2,4:0.8065:2,2:24.8:1:31.1:1:1:1.06041:33.3:50:0.8065:0.129:1 0/1:17:4:1,3:3,10:0.2353:2,2:35:1:30:1:1:1.10:33:8:0.25:0:1 -7 56431671 . G A 51 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63089;SOR=0.45302;LSEQ=AAAGTCTATGGTCCCACCCC;RSEQ=TCCTCCTCCTACACACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:16,4:0.1304:2,0:22.7:1:32.3:1:0.01976:0:37:6:0.1304:0:1 0/1:16:1:0,1:10,5:0.0625:2,0:5:0:30:0:0.375:0:27:2:0.0625:0:1 -7 56431756 . G A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0488;LSEQ=GGAGCCTTCAAAGCCCAGGA;RSEQ=TCTGGTCAGGGCAGCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:42:30,12:8,9:0.7119:2,2:31.3:1:30.3:1:0.13177:2.76:46.5:41:0.7193:0:1.2 0/1:48:5:5,0:20,23:0.1042:2,0:26.4:1:29.6:1:0.05068:0:45.6:10:0.1042:0:1 -7 56431767 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17746;SOR=Inf;LSEQ=AGCCCAGGAGTCTGGTCAGG;RSEQ=CAGCAGAGCCGGCCCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:42,26:0:2,0:26.5:1:31:1:1:0:52.2:21.667:1:0:0.9 0/1:50:2:1,1:27,21:0.04:2,2:36:1:27.5:1:1:1.2792:60:4:0.0408:0:1 -7 56431789 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53535;SOR=0;LSEQ=AGCAGAGCCGGCCCCCTGTG;RSEQ=CCCCTACCCCTGGGGACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:2,0:57,33:0.0217:2,0:18.5:1:28.5:1:0.53488:0:46.5:4:0.0222:0:2 0/0:52:0:0,0:31,21:0:2,0:22.8:1:31.2:1:1:0:55.8:25:1:0:0.6 -7 56431805 . AC GT 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00301;SOR=Inf;LSEQ=TGTGGCCCCTACCCCTGGGG;RSEQ=GGGGGCCCAGGGATGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:61,42:0:2,0:24.2:1:29.9:1:1:0:51.7:102:1:0:0.5 0/1:49:5:3,2:26,18:0.102:2,2:20.6:1:30.4:1:1:1.04:37:10:0.1042:0:1.4 -7 56431807 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11182;SOR=2.02829;LSEQ=TGGCCCCTACCCCTGGGGAC;RSEQ=GGGGCCCAGGGATGCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:14:8,6:54,34:0.1373:2,2:30.4:1:30.4:1:0.77549:1.1891:59.8:28:0.14:0:1 0/1:49:12:8,4:21,16:0.2449:2,2:27.4:1:31.4:1:0.73773:1.51:55.1:24:0.2449:0:1.1 -7 56431826 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGGGCCCAGGGATGCCTT;RSEQ=CAAGGCGACCTGTTTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:61,48:0.018:2,2:33:1:28.5:1:1:1.26806:54.5:4:0.0185:0:1 0/0:46:0:0,0:26,20:0:2,0:25.6:1:30.2:1:1:0:47.2:45:1:0:0.4 -7 56431835 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07627;SOR=Inf;LSEQ=AGGGATGCCTTCCAAGGCGA;RSEQ=CTGTTTCCTCCCAATGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:61,53:0:2,0:28.3:1:31.3:1:1:0:45.4:56:1:0:0.3 0/1:44:2:0,2:24,18:0.0455:2,0:19:1:29.5:1:0.20085:0:26:4:0.0455:0:1.5 -7 56432215 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07422;SOR=Inf;LSEQ=GGGCTCAGGGAACTGGAGAC;RSEQ=GAGAAGGCGGTGTCCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:0:2,0:21:1:28.9:1:1:0:56:13:1:0:0.2 0/1:11:2:1,1:2,7:0.1818:2,2:16.5:1:28.5:1:0.49091:3.06:50:4:0.1818:0:1.5 -7 56432558 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13498;SOR=Inf;LSEQ=GAGCCTCAGCCTCGCAGGCT;RSEQ=CTCCGTGGGACTGATGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:63,36:0:2,0:28.6:1:32.2:1:1:0:38.2:198:1:0:0.1 0/1:58:2:1,1:40,16:0.0345:2,2:24:1:28.5:1:0.50393:2.4555:21:4:0.0351:0:1 -7 56432646 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52922;SOR=0;LSEQ=ATGCTGGTGGTGGGTGCAGG;RSEQ=CCGCTGGGAGCCGCTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:70,73:0.0138:2,2:46:1:27:1:1:1.04:49.5:4:0.0139:0:1.5 0/0:87:0:0,0:37,50:0:2,0:29.7:1:31.1:1:1:0:47.3:86:1:0:0.3 -7 56432659 . G A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14041;SOR=Inf;LSEQ=GTGCAGGGCCGCTGGGAGCC;RSEQ=CTGCATGGGTCCCAGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:63,78:0:2,0:26.8:1:30.2:1:1:0:46.5:34.25:1:0:0.8 0/1:85:2:1,1:34,49:0.0235:2,2:33:0:29.5:1:1:1.43:47.5:4:0.0235:0:1.5 -7 56432708 . T C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02875;LSEQ=GCAGGGGCCAACTGAAGCTG;RSEQ=TGGGGCAGCATGAGCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:80:19,61:2,3:0.9412:2,2:26:1:32.5:1:0.59322:2.11831:49.7:79:0.9405:0:2.1 0/1:49:15:5,10:10,24:0.3061:2,2:16.3:1:31.7:1:1:1.20:46.7:30:0.3061:0:2 -7 56432714 . C A 189 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.02627;LSEQ=GCCAACTGAAGCTGTTGGGG;RSEQ=AGCATGAGCAGGATGTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:77:15,62:1,3:0.9506:2,2:24.7:1:30.2:1:1:1.37186:49.8:37.5:0.9494:0:2.1 0/1:40:13:3,10:7,20:0.325:2,2:14.8:1:27.2:1:1:1.16222:46.3:5.5:0.2895:0:2.2 -7 56432875 . G T 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=CTGCCACTGCCTCTGCCCCA;RSEQ=AGTTGGGACCTTGACAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:3,8:0.2667:2,0:15:1:29.3:1:0.51648:0:52.5:8:0.2667:0:1 0/0:5:0:0,0:1,4:0:2,0:22.6:1:30.2:1:1:0:57:10:1:0:0.2 -7 56434776 . A C 48 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=0;LSEQ=GCGGGAGCTGAGTCCAAAGA;RSEQ=GTTGTTGGGAGGCCGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:32.3:1:30.3:1:1:1.7321:60:6:0.6:0:1 0/0:2:0:0,0:1,1:0:2,0:33.5:1:31:1:1:0:60:4:1:0:0.5 -7 56438193 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGGCCGGTGTGAGGCAA;RSEQ=GGGCTCACGCTGACCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33:1:29:1:1:0:27:4:1:0:1 -7 56439421 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53613;SOR=0;LSEQ=CGCTGACCTCTCTCGGCGTG;RSEQ=GAGGGGCCGGTGTGAGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:19,2:0.087:2,2:12.5:1:31.5:1:0.24901:7.95767:46:4:0.087:0:1 0/0:12:0:0,0:10,2:0:2,0:25.3:1:30.3:1:1:0:24.6:11:1:0:0.2 -7 56439453 . T C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.04216;LSEQ=GTGAGGCAAGGGGCTCACGC;RSEQ=GACCTCTCTCGGCGTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:21:14,7:5,1:0.7778:2,2:33:1:30.3:1:0.63336:2.42585:26.3:42:0.7778:0:1.1 0/1:17:2:1,1:9,6:0.1176:2,2:15.5:1:27.5:1:1:1.46382:25:4:0.125:0:1 -7 56439610 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=CTCTCAGCGTGGGAGGAGCC;RSEQ=GTGTGAGGCAGGGACTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,5:0.25:2,0:31.5:1:32.5:1:1:0:32.5:4:0.25:0:1 0/0:6:0:0,0:3,3:0:2,0:29.7:1:31:1:1:0:28.8:12:1:0:0 -7 56441233 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTGCTGGGAGGCAGGGC;RSEQ=GGGAGACGCTGACTTCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:36,22:0.0333:2,2:10.5:1:28.5:1:1:1.62241:36.5:4:0.0345:0:1.5 0/0:23:0:0,0:15,8:0:2,0:22.2:1:29.4:1:1:0:42.7:22:1:0:0.5 -7 56441286 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGGTCGCCAGGAGGCC;RSEQ=AAGCTGGGCGCGGAGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:22,28:0.0385:2,2:32.5:1:31:1:1:1.27:25:4:0.0408:0:1.5 0/0:21:0:0,0:8,13:0:2,0:30.3:1:30.5:1:1:0:38.8:20:1:0:0.4 -7 56442996 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGCCTGCGGAAGTGGC;RSEQ=GAGAGGCAGGAGTTTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:29:1:1:0:60:4:1:0:2.5 -7 56443001 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGCGGAAGTGGCGGAGA;RSEQ=GCAGGAGTTTTGGACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:31:0:1:0:60:4:1:0:2.5 -7 56747708 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTTAATATTAACCATTA;RSEQ=GGCCAGCCCCCTCTCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 56748760 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGTGATTACAATATTAATA;RSEQ=CATCATCTAGATAGAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:36.5:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 56748814 . T C 67 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGAAATTGCTTCAACTTA;RSEQ=AATAATTTAGAAACTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:35.8:1:33.5:1:1:0:60:8:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:15:0:33:0:1:0:60:2:1:0:2 -7 56748878 . T C 71 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0.2582;LSEQ=AAAAATGTATCAATGCATTT;RSEQ=CCTCAGTTTTTCTGTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:22.8:1:30.6:1:1:0:57.8:10:0.8333:0:1.4 1/0:2:1:1,0:1,0:0.5:0,0:22:0:26:0:1:0:60:2:0.5:0:2 -7 56748970 . A G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37479;SOR=0.37236;LSEQ=TATTCTGGGTCCAGCAGCAC;RSEQ=TGGGAGGAGCCAATATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:14,0:4,0:0.7778:0,1:27.2:1:30.4:1:1:0:60:28:0.7778:0:1.1 1/0:9:5:5,0:4,0:0.5556:0,0:21.6:1:29.4:1:1:0:60:10:0.5556:0:1 -7 56749207 . T C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33876;LSEQ=AATGACCAAAATGTTGGCTA;RSEQ=GCTTAGGTGACTAAGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:563:459:219,240:44,60:0.8153:2,2:26.2:1:30.6:1:0.32946:1.24:57.9:113.75:0.8154:0:1.1 1/0:369:221:101,120:69,78:0.5989:2,2:25.9:1:29.8:1:0.8316:1.05086:58.2:72.667:0.5956:0:1.1 -7 56749239 . T A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05783;SOR=Inf;LSEQ=TAAGAGTGAAAACTGTAGAC;RSEQ=GTGAATCTCACCCAGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:0:0,0:157,313:0:2,0:25:1:30.3:1:1:0:59.9:93:1:0:0.8 0/1:298:3:1,2:108,187:0.0101:2,2:30.7:1:29:1:1:1.15456:60:6:0.0103:0:1.3 -7 56749338 . C T 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15932;SOR=0.50315;LSEQ=TATTATTCCAAATTTTAAAT;RSEQ=CACAGAACTCATTTTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:80:65:2,63:2,13:0.8125:2,1:21.8:1:30.6:1:0.15765:4.71263:59.4:130:0.8125:0:1.6 1/0:38:26:0,26:2,10:0.6842:2,1:20.8:1:28.7:1:0.09388:0:60:52:0.7027:0:1.6 -7 56749362 . T C 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.69262;SOR=0.70166;LSEQ=AGAACTCATTTTATTTGCAA;RSEQ=ATTTAACATTCACACTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:43:1,42:0,6:0.8776:0,1:21.5:1:32.1:1:1:0:58.3:86:0.8776:0:1.9 1/1:18:15:1,14:0,3:0.8333:0,1:23.3:1:31.8:1:1:0:60:30:0.8333:0:2 -7 56749612 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGTGGACAGTGTATGCCTC;RSEQ=TATCTCAATTAACTGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26:1:31.5:1:1:0:38:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 56750181 . C G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACATGGCTGGGGAGGCCT;RSEQ=AAGAACCTTACAATAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:25:0:33.5:1:1:0:53:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 56872279 . G T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCCCGCGAGCGGCCCA;RSEQ=CTCCTCCCTCACGGTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:22:0:31.5:1:1:1:60:4:0.5:0:1 -7 56873050 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11348;SOR=Inf;LSEQ=AGTACTCGGCCCACAGGACT;RSEQ=TGTCCAGCGAGGCCTCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:34,28:0:2,0:26.7:1:31.7:1:1:0:42.5:30:1:0:0.1 0/1:32:2:1,1:14,16:0.0625:2,2:19:1:29:0:1:1.14:27:4:0.0625:0:1 -7 56873337 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.21514;SOR=Inf;LSEQ=CAGGGCCCAGAACCCCACAC;RSEQ=CTTTGGGGGTGGTGGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:20,6:0:2,0:25.9:1:30:1:1:0:38.4:52:1:0:0.1 0/1:23:2:1,1:13,8:0.087:2,2:20:1:30:1:1:1.58984:27:4:0.087:0:1 -7 56873374 . C T 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08811;SOR=0;LSEQ=ACCTGGTAAGGGCCCACCTC;RSEQ=CACCATGGAGGAGGAGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:4,2:28,14:0.125:2,2:6.8:1:29.7:1:1:1:34.3:12:0.125:0:1.3 0/0:25:0:0,0:12,13:0:2,0:31.4:1:29.8:1:1:0:43.7:50:1:0:0.1 -7 56873424 . G A 99 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05363;SOR=0;LSEQ=AGGGGAGTCCCTGCTGGACA;RSEQ=TGAGACAGAGAATGACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:9:7,2:29,23:0.1475:2,2:25.8:1:31.4:1:0.2862:2.73:30.7:18:0.1475:0:1 0/0:25:0:0,0:11,14:0:2,0:25.1:1:31.6:1:1:0:47.1:50:1:0:0.1 -7 56873469 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11744;SOR=Inf;LSEQ=TGCTTTCCTCTCCGTCATGT;RSEQ=TCCTGACACCCAGTTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:44,26:0:2,0:21.9:1:31.3:1:1:0:38.4:69:1:0:0.2 0/1:37:2:1,1:22,13:0.0541:2,2:18:1:28:1:1:1.66733:33:4:0.0541:0:1 -7 56873470 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54162;SOR=0;LSEQ=GCTTTCCTCTCCGTCATGTC;RSEQ=CCTGACACCCAGTTGCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:0,2:45,24:0.0282:2,0:16:1:31.5:1:0.13078:0:26:4:0.0282:0:1 0/0:38:0:0,0:24,14:0:2,0:23.4:1:29.9:1:1:0:37:76:1:0:0.2 -7 56873600 . C T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07014;LSEQ=AATGGGACAAGGACCACATC;RSEQ=GGTGGCCCATGAGTGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:17:11,6:47,30:0.1809:2,2:21.7:1:31.4:1:1:1.17:36.7:34:0.1828:0:1.4 0/1:68:13:9,4:35,20:0.1912:2,2:25.7:1:28.5:1:1:1.28:34.3:5.5:0.1692:0:1.5 -7 56873638 . G A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04868;SOR=Inf;LSEQ=GGTCATGATCTTCAGCAAGC;RSEQ=GCACCAGGCCCTGGCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:83,70:0:2,0:26.2:1:30.2:1:1:0:44.2:75.5:1:0:0.3 0/1:89:3:2,1:41,45:0.0337:2,2:22.3:1:30.3:1:0.60811:2.18:36.3:6:0.0337:0:2 -7 56873693 . G A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99288;LSEQ=CCAACCAGGACAACCGGACC;RSEQ=TCAGCCAGATCCTGAGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:28:13,15:65,74:0.1677:2,2:25:1:29:1:1:1.01343:47.9:13:0.1585:0:1.5 0/1:96:16:7,9:29,51:0.1667:2,2:22.4:1:29.8:1:0.58317:1.36:43.1:32:0.1667:0:1.5 -7 56873733 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53112;SOR=0;LSEQ=GCGGTGGTACACCCTGGGGC;RSEQ=CAATGAGACGCAGAAGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:40,71:0.0175:2,2:28:1:30:1:1:1.77:41.5:4:0.0192:0:1.5 0/0:67:0:0,0:25,42:0:2,0:25.7:1:29.6:1:1:0:50.1:32.5:1:0:0.4 -7 56873755 . T C 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04558;SOR=0.48278;LSEQ=AATGAGACGCAGAAGTACCA;RSEQ=GACCTGGCCTTCCAGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:48:15,33:20,37:0.4571:2,2:22.5:1:30.4:1:0.8356:1.18723:45.8:96:0.4615:0:1.4 0/1:59:17:8,9:16,26:0.2881:2,2:26.4:1:30.6:1:0.56868:1.44:38.4:34:0.2881:0:1.4 -7 56873781 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53059;SOR=0;LSEQ=GGCCTTCCAGGTGAAGGTGG;RSEQ=CCACTTGCAACAGGGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:25,55:0.0244:2,2:35:1:29.5:1:0.53628:2.18:53.5:4:0.0253:0:2 0/0:48:0:0,0:19,29:0:2,0:23.8:1:30.6:1:1:0:52.4:23:1:0:0.5 -7 56873822 . T C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62091;SOR=0.73312;LSEQ=AAGAAGTCCAGCTCAGAGGC;RSEQ=AAGCCCACAAACCAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:17:5,12:24,34:0.2267:2,2:21.4:1:30.5:1:0.41267:1.68264:52.9:16:0.2192:0:1.5 0/1:34:6:3,3:11,17:0.1765:2,2:24:1:30.3:1:0.67217:1.53:54:12:0.1818:0:1.2 -7 56874003 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49976;SOR=0;LSEQ=GCAGAACGGCTGCATACAGG;RSEQ=AACCTGGCTCAGCCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:32,36:0.0286:2,2:27:1:28.5:1:1:1.12:27:4:0.0286:0:1 0/0:59:0:0,0:29,30:0:2,0:27.9:1:30.4:1:1:0:34:58:1:0:0.1 -7 56874006 . C G 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=GAACGGCTGCATACAGGGAA;RSEQ=CTGGCTCAGCCTGGCCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:13:4,9:30,28:0.1831:2,2:29.5:1:32.9:1:0.22536:2.38166:37.2:26:0.1831:0:1 0/0:62:0:0,0:31,31:0:2,0:27:1:30.3:1:1:0:34.4:61:1:0:0.1 -7 56874075 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07683;SOR=Inf;LSEQ=TGACGGCAGGGAAATAGACC;RSEQ=TCAGGCACTACAGGAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:58,38:0:2,0:24.3:1:30.2:1:1:0:39.1:95:1:0:0.1 0/1:72:3:1,2:38,31:0.0417:2,2:25.7:1:29.7:1:0.58999:2.42182:34.3:6:0.0435:0:1 -7 56874096 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16872;SOR=Inf;LSEQ=TCAGGCACTACAGGAACTGA;RSEQ=AGAAGTGGTGTCTGGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:66,38:0:2,0:27.3:1:31.9:1:1:0:37.4:51:1:0:0 0/1:73:2:1,1:42,29:0.0274:2,2:43.5:1:28.5:1:1:1.44076:49:4:0.0294:0:1 -7 56874271 . G A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00807;SOR=Inf;LSEQ=GATGACATAGTGAGTGATGA;RSEQ=GAGCACATGGTCATCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:64,56:0:2,0:27.6:1:31.4:1:1:0:57:29:1:0:0.2 0/1:76:5:3,2:40,31:0.0658:2,2:23.4:1:31.2:1:1:1.16:55.6:10:0.0667:0:1 -7 56874297 . AG A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.51765;SOR=0;LSEQ=CATGGTCATCCATGAGGAGG;RSEQ=GGGGTGACAATGTCATTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:73,48:0.0163:2,2:26:1:30.5:1:1:1.51547:60:4:0.0165:0:0 0/0:82:0:0,0:44,38:0:2,0:23:1:31.4:1:1:0:53.5:164:1:0:0.2 -7 56874325 . G A 131 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04808;SOR=0.39376;LSEQ=ACAATGTCATTGCTGATGAT;RSEQ=GCTTTAGCACCACTGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:23:11,12:74,64:0.1429:2,2:18:1:29.1:1:0.65632:1.25953:51.6:46:0.1447:0:1 0/1:114:7:3,4:55,52:0.0614:2,2:17.4:1:29.4:1:0.71418:1.40602:53.1:14:0.0625:0:1.6 -7 56874400 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52111;SOR=0;LSEQ=AGTGGTGACAGCTCTGGGGA;RSEQ=GAGACAGAGGGCAACAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:47,98:0.0136:2,2:21.5:1:29.5:1:0.54795:2.07:54.5:4:0.0138:0:1 0/0:95:0:0,0:38,57:0:2,0:23.1:1:30:1:1:0:52.1:30.667:1:0:0.3 -7 56874425 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12659;SOR=Inf;LSEQ=CAGAGGGCAACAAGGGCTTT;RSEQ=GTGGGAAGGTATTTGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:22,64:0:2,0:21:1:31.1:1:1:0:45.7:172:1:0:0.2 0/1:48:2:1,1:11,35:0.0417:2,2:32:0:31.5:1:0.44149:3.09:50.5:4:0.0417:0:1.5 -7 56874457 . C T 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09175;SOR=0;LSEQ=TTTGCACCTGTCATTCCTTC;RSEQ=TCCTTTACTCCTGCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:0,8:7,26:0.1951:2,0:27.6:1:31:1:0.31029:0:37.8:16:0.2:0:1.5 0/0:18:0:0,0:3,15:0:2,0:22.2:1:31.8:1:1:0:40.7:36:1:0:0 -7 56874473 . G A 62 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.52603;LSEQ=CTTCCTCCTTTACTCCTGCC;RSEQ=CCCCTTGCTGGATCCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:0,4:5,22:0.129:2,0:33.5:1:31.3:1:1:0:33.5:8:0.1379:0:2 0/1:14:1:0,1:4,9:0.0714:2,0:12:0:25:0:1:0:27:2:0.0769:0:1 -7 56874631 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49254;SOR=0;LSEQ=TGGGCCCAGGAGCCTTCAAA;RSEQ=CCTAGGAGTCTGGTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:22,10:0.0588:2,2:28.5:1:32:1:1:2.1448:47:4:0.0606:0:1 0/0:34:0:0,0:20,14:0:2,0:28.6:1:31.6:1:1:0:53.2:68:1:0:0.1 -7 56874659 . CC TG 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73996;SOR=1.34981;LSEQ=GTCTGGTCAGGGCAGCAGAG;RSEQ=GGCCCCCTACGGCCCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:5:3,2:18,24:0.1064:2,2:9.8:1:31.6:1:0.64405:1.97:40:10:0.1064:0.0426:0.6 0/1:36:5:3,2:14,17:0.1389:2,2:16.2:1:28.9:1:0.65043:1.79:35.4:10:0.1389:0.0278:0.8 -7 56874694 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11373;SOR=Inf;LSEQ=CCCTACCCCTGGGGATGGGG;RSEQ=CCCAGGGACGCCTTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:24,32:0:2,0:23.9:1:32.2:1:1:0:54.4:112:1:0:0.2 0/1:29:2:1,1:13,14:0.069:2,2:34.5:1:28.5:1:1:1.07:60:4:0.069:0:1 -7 56875198 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CCTGTCCACTAGGCCACAGC;RSEQ=GCTCTCCAGGCCCACTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:1,3:0.3333:2,0:8:1:32.5:1:0.4:0:27:4:0.3333:0:1 0/0:5:0:0,0:3,2:0:2,0:9.4:1:26.4:1:1:0:29.6:10:1:0:0 -7 56875368 . A AG 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21406;SOR=Inf;LSEQ=AGTCACGTGAGGCTGAGAGT;RSEQ=GGGGCAGGGGCAGCAATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:37,16:0:2,0:22.6:1:29:1:1:0:33.9:106:0.9815:0:0.1 0/1:47:2:1,1:30,15:0.0426:2,2:28:1:32.5:1:1:1.96856:45:4:0.0435:0:0 -7 56875460 . A G 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.004;LSEQ=CGTGGGACTGATGACTGCAT;RSEQ=ATCTTCTGGGCACCTCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:3:0,3:80,45:0.0234:2,0:14.7:1:31.7:1:0.05067:0:20.3:6:0.0234:0:1 0/1:85:2:0,2:47,36:0.0235:2,0:20:0:33:0:0.19692:0:21:4:0.0238:0:1 -7 56875512 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.51591;SOR=0;LSEQ=CAGGTGAAACGGATGCTGGT;RSEQ=GTGGGTGCAGGGCCGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:38,65:0.019:2,2:8.5:1:29.5:1:1:1.70:40:4:0.0194:0:1.5 0/0:71:0:0,0:26,45:0:2,0:24.9:1:30.3:1:1:0:35.2:70:1:0:0.1 -7 56877516 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAGAGGCAGGAGCTGACCCC;RSEQ=GAGGGGCCCTCGTTGACGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44:1:31:1:1:0:60:4:1:0:1 0/0:2:0:0,0:0,2:0:0,0:28:1:30.5:1:1:0:60:4:1:0:0 -7 57227889 . G A 47 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.55233;LSEQ=GCAATAGCAATAGAAACTCT;RSEQ=CATATTGTGGGTCCAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:0.2727:0,0:37.3:1:30:0:1:0:60:6:0.2727:0:1 0/1:6:1:1,0:5,0:0.1667:0,0:34:0:25:0:1:0:60:2:0.1667:0:1 -7 57228051 . C T 224 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGGTTGTGAACACAATAAA;RSEQ=GTCTTTGCATGAAAAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:163:163:117,46:0,0:1:0,2:27.1:1:30.6:1:1:0:60:326:1:0:1.1 1/0:188:101:61,40:57,30:0.5372:2,2:21:1:29.6:1:0.54548:1.24444:59.8:202:0.543:0:1.2 -7 57228283 . G T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28118;SOR=0;LSEQ=CCAAATTGTAAATCCACAGA;RSEQ=CTCATTTTATTTGCAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:0,4:1,23:0.1429:1,0:22.5:1:29.8:1:1:0:60:8:0.1481:0:1.3 0/0:17:0:0,0:0,17:0:1,0:30.1:1:31.5:1:1:0:60:16:1:0:0.2 -7 57536431 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50499;SOR=0;LSEQ=ATGATTATTTTTGAGTGGGT;RSEQ=AAGTTCACAGTCTACAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:64,17:0.0241:2,2:19.5:1:29.5:1:0.38877:3.68736:60:4:0.0241:0:1 0/0:64:0:0,0:39,25:0:2,0:21.5:1:28.6:1:1:0:60:128:1:0:0 -7 57536496 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51113;SOR=0;LSEQ=CAACATTTTGGTCATTTTCT;RSEQ=TGAGCAAATTTTGGAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:65,65:0.0152:2,2:25:1:29:1:1:1:60:4:0.0153:0:1 0/0:95:0:0,0:49,46:0:2,0:25.7:1:31.5:1:1:0:60:190:1:0:0.1 -7 57536632 . C T 72 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36226;SOR=0.27085;LSEQ=CCCTGATTTTTAGTGTCTTC;RSEQ=GTTACATTGCCATCAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:0,5:0,13:0.2778:1,0:18.4:1:31.4:1:1:0:60:10:0.2941:0:1 0/1:11:1:0,1:0,10:0.0909:0,0:8:0:31:0:1:0:60:2:0.0909:0:1 -7 57658797 . T C 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACCACGTTGGCCAGGCTGG;RSEQ=CTCGAACTCCTGACCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:33.5:1:1:0:33:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 57658808 . T C 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCTGGTCTCGAACTCC;RSEQ=GACCTCAAGTGATCCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:1:32:0:1:0:33:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 57658823 . CA TT 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ACTCCTGACCTCAAGTGATC;RSEQ=CCAGCCTCAGCCTCCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:1:31.3:1:1:0:33:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 57658827 . A C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACCTCAAGTGATCCACC;RSEQ=GCCTCAGCCTCCCAGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:48:1:31.5:1:1:0:33:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 57658836 . C A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=AGTGATCCACCAGCCTCAGC;RSEQ=TCCCAGAGTGCTGGGATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:44:1:31:1:1:0:33:4:0.6667:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 57659196 . T G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTGTTTTTTATATACTG;RSEQ=TTTTACTTTATATAGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:12:1:32.5:1:1:0:47:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 57659408 . A AT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.5457;SOR=0;LSEQ=TTTTAGTTCTTATTAATTCT;RSEQ=TTTTTTTCCCATCCTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:2,0:165,5:0.0116:1,0:26.5:1:31.2:1:1:0:30.5:4:0.0118:0.0058:2.5 0/0:91:0:0,0:85,6:0:2,0:24.6:1:27.9:1:1:0:52:44.5:1:0:0.6 -7 57659427 . G T 157 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45298;SOR=1.25937;LSEQ=TATTTTTTTCCCATCCTGTT;RSEQ=AGATGGTTTCCTAGAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:39:35,4:190,9:0.1566:1,2:25.8:1:29.8:1:0.23659:2.40133:31.3:38:0.1577:0:3.4 0/1:116:22:22,0:79,12:0.1897:2,1:33.9:1:29.3:1:0.11883:0:30:10:0.1754:0:2.8 -7 57659430 . A G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56278;SOR=0.54844;LSEQ=TTTTTTCCCATCCTGTTGAG;RSEQ=TGGTTTCCTAGAAACATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:11:10,1:229,18:0.0426:2,2:19.9:1:32.4:1:0.57637:1.27092:26.8:22:0.0431:0:2.5 0/1:126:3:3,0:110,13:0.0238:2,0:29.3:1:31.7:1:1:0:28.7:6:0.0238:0:2 -7 57659469 . TTA T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.91928;LSEQ=ATTGTTTATTGGCGTTGATC;RSEQ=CAGTCTGGTGAGGACTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:19:10,9:311,115:0.0369:2,2:34.7:1:31.6:1:0.06652:2.42834:27:38:0.0375:0:1.9 0/1:294:10:5,5:156,87:0.034:2,2:26.2:1:30.9:1:0.50373:1.78865:35.6:20:0.0348:0:1.2 -7 57659470 . TA CG 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99255;LSEQ=TTGTTTATTGGCGTTGATCT;RSEQ=CAGTCTGGTGAGGACTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:67:38,29:311,115:0.1301:2,2:31.7:1:30.8:1:0.00896:2.06053:30.8:134:0.1324:0.0019:3.1 0/1:294:38:17,21:156,87:0.1293:2,2:27:1:29.2:1:0.03051:2.20843:29:18:0.1254:0.0068:3 -7 57659484 . G A 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.91557;SOR=0.96362;LSEQ=TGATCTTACAGTCTGGTGAG;RSEQ=ACTTCTTTACTGATAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:605:67:36,31:355,183:0.1107:2,2:34.9:1:29.7:1:0.05751:1.66904:31.1:66:0.1119:0:3.2 0/1:364:39:17,22:188,136:0.1071:2,2:33.2:1:28.9:1:0.09048:1.78597:28.4:78:0.1096:0:3.3 -7 57659513 . G T 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71937;SOR=0.89536;LSEQ=ACTGATAATGTCAAGTTCAG;RSEQ=TTATCCTCCCAACCAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:827:50:20,30:450,327:0.0605:2,2:24.3:1:30.4:1:0.01772:2.06241:31.8:100:0.0617:0:3.3 0/1:514:28:6,22:266,220:0.0545:2,2:28.9:1:31.5:1:7e-04:4.42155:29.8:56:0.0549:0:3.3 -7 57659517 . T C 111 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61423;SOR=0.71519;LSEQ=ATAATGTCAAGTTCAGGTTA;RSEQ=CCTCCCAACCAAGGAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:840:11:2,9:464,365:0.0131:2,2:21.5:1:32.1:1:0.0146:5.70924:27:22:0.0133:0:1.7 0/0:532:5:1,4:278,249:0.0094:2,2:15.4:1:32.2:1:0.19627:4.4543:34.4:10:0.0095:0:1.2 -7 57659596 . TG CA 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02122;SOR=Inf;LSEQ=AGTATACATTTCCCAGCACC;RSEQ=CCACCAGCAGGTAAGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:597:0:0,0:210,385:0:2,0:24.5:1:30.2:1:1:0:59.9:84:0.9966:0:0.1 0/1:370:4:4,0:147,218:0.0108:2,0:7.5:1:30:1:0.02738:0:34.5:8:0.011:0.0054:1.8 -7 57659636 . T C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01582;LSEQ=CAAATACTATGCAAATTGCA;RSEQ=GTTTTTTGTGTTTTTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:20:3,17:62,275:0.0559:2,2:26.7:1:30.9:1:1:1.27675:34.6:40:0.0565:0:2 0/1:194:11:6,5:40,143:0.0567:2,2:33.3:1:29.6:1:0.02311:4.25:32.1:22:0.057:0:1.7 -7 57659643 . TG T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.85086;SOR=1.07101;LSEQ=TATGCAAATTGCATGTTTTT;RSEQ=TGTTTTTCTTTACTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:20:3,17:52,239:0.0643:2,2:34.7:1:31:1:1:1.23213:34.6:40:0.0647:0:2 0/1:175:12:6,6:31,132:0.0686:2,2:30.8:1:29.5:1:0.02099:4.21:31.5:24:0.0694:0.0057:1.9 -7 57659700 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78104;SOR=0.78292;LSEQ=TGGTAGAAACCACCAAATTT;RSEQ=CCTTTTTTTAAAGTGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:13:1,12:6,87:0.1215:2,1:9.7:1:32.8:1:1:1.21:37.5:26:0.1238:0:2.4 0/1:41:4:0,4:2,35:0.0976:2,0:19.5:1:33.3:1:1:0:29.5:8:0.0976:0:2.5 -7 57659702 . C CT 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.57598;SOR=0;LSEQ=GTAGAAACCACCAAATTTAC;RSEQ=TTTTTTTAAAGTGGCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:4:0,4:6,93:0.0385:2,0:15.3:1:30.8:1:1:0:33.3:8:0.0388:0.0096:3.3 0/0:40:0:0,0:2,37:0:2,0:26.7:1:32.8:1:1:0:57.8:78:0.975:0:0.2 -7 57659710 . A T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49926;SOR=1.5295;LSEQ=CACCAAATTTACCTTTTTTT;RSEQ=AAGTGGCAAGAGCTATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:0,6:4,72:0.0732:2,0:6.5:1:28.2:1:1:0:32.2:12:0.0741:0:3.2 0/1:37:4:1,3:2,31:0.1081:2,2:18.3:1:26:1:0.29781:4.80:31.5:3:0.0857:0:2.8 -7 57659737 . G A 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0075;SOR=6.04936;LSEQ=CAAGAGCTATTTACAAAGAC;RSEQ=AGGAACCAAAGGTTGGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:0,4:3,44:0.0784:2,0:27.8:1:29.8:1:1:0:33.5:8:0.08:0:2.5 0/1:26:9:2,7:1,16:0.3462:1,2:20.7:1:25.8:1:0.26769:4.28:39.2:8:0.32:0:2.7 -7 57659793 . A G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=14.84237;LSEQ=TCTTACTGTGGCTTTATGCC;RSEQ=ATTTCAGGAGTTGAACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:0,4:0,22:0.1538:1,0:15.3:1:32.5:1:1:0:33.5:8:0.1538:0:2.5 1/0:12:9:2,7:1,2:0.75:2,2:25.4:1:30.7:1:1:1.66417:39.9:8:0.7273:0:2.6 -7 57659818 . GC G 74 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0027;SOR=30.44931;LSEQ=CAGGAGTTGAACTTGTCTTT;RSEQ=TTTTGATGATAGGAGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:0,16:0.0588:1,0:18:0:27:0:1:0:30:2:0.0588:0:1 1/0:7:5:0,5:1,1:0.7143:2,0:9.6:1:31.9:1:0.28571:0:38.2:10:0.7143:0.4286:2.4 -7 57659928 . C T 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=TGGTTGAGTTTTAAGCTGGC;RSEQ=AGATAACTTGGCATGTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:7.7:1:27.3:1:1:0:29:6:0.75:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:34:1:30.5:1:1:0:31:4:0.6667:0:1 -7 57669663 . A G 80 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52754;SOR=1.73054;LSEQ=ACTCCATCCTCTCCAATTTC;RSEQ=GGGCAACCATGTGGAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:4:4,0:285,201:0.0082:2,0:7.8:1:29.3:1:0.14779:0:40:8:0.0083:0:4.3 0/1:427:6:6,0:241,180:0.0141:2,0:17:1:31.2:1:0.04185:0:32.3:12:0.0143:0:4.5 -7 57669695 . C T 98 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10341;SOR=2.80965;LSEQ=TGGAGATGATCAAAATGCTT;RSEQ=ACCTTCAAAACTTTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:508:4:4,0:253,248:0.0079:2,0:38.3:1:31.5:1:0.12375:0:36:8:0.008:0:5.5 0/1:458:10:8,2:232,216:0.0218:2,2:40.6:1:29.7:1:0.10959:3.71:31.6:20:0.0219:0:4.1 -7 57669714 . G C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1278;SOR=2.45579;LSEQ=TCACCTTCAAAACTTTCAAA;RSEQ=GAAGAGTTAATACAGAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:5:5,0:207,250:0.0108:2,0:41.6:1:32.6:1:0.01983:0:36.8:10:0.0109:0:5.8 0/1:420:11:8,3:188,219:0.0262:2,2:32.5:1:28.4:1:0.12386:3.10:34.2:10:0.0242:0:3.8 -7 57669729 . G A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19384;SOR=2.17763;LSEQ=TCAAAGGAAGAGTTAATACA;RSEQ=AGTATGGATCGTGTAAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:5:5,0:186,251:0.0113:2,0:27.8:1:28.6:1:0.01462:0:36.8:10:0.0114:0:5.8 0/1:411:10:8,2:177,223:0.0243:2,2:16.6:1:26.8:1:0.04802:5.02:31.6:9:0.0222:0:4.1 -7 57669748 . C T 51 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37492;SOR=0.26667;LSEQ=AGAGTATGGATCGTGTAAAT;RSEQ=GAGAAATTGCAAAAGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:4:3,1:157,234:0.0101:2,2:13:1:25.5:1:0.30789:4.45:41:8:0.0102:0:5.5 0/0:370:1:1,0:162,207:0.0027:2,0:3:0:27:0:0.44054:0:40:2:0.0027:0:6 -7 57669804 . T A 100 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0759;SOR=3.48126;LSEQ=CTGAAAAAGAAACAAGTAAA;RSEQ=GTCTTTGCTTAATATATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:3:3,0:97,203:0.0099:2,0:27.3:1:29.3:1:0.03522:0:27:6:0.0101:0:4.3 0/1:267:9:8,1:94,164:0.0337:2,2:23.3:1:31.6:1:0.00232:13.84:25.3:18:0.034:0:4.4 -7 57669813 . T C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05494;SOR=3.19377;LSEQ=AAACAAGTAAATGTCTTTGC;RSEQ=TAATATATTCTAAGAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:4:3,1:83,191:0.0144:2,2:28.5:1:27.3:1:0.0894:6.85:26.3:3:0.0109:0:4.5 0/1:224:10:8,2:77,137:0.0446:2,2:29.6:1:31.6:1:0.0073:7.06:25.3:20:0.0448:0:4.4 -7 57669833 . G A 109 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0028;SOR=4.98323;LSEQ=TTAATATATTCTAAGAATGT;RSEQ=TGTTTTTCTCCCTACAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:4:3,1:53,160:0.0184:2,2:39.8:1:27.5:1:0.05375:8.94:26.3:8:0.019:0:4.5 0/1:163:14:10,4:47,102:0.0859:2,2:30.8:1:28.7:1:0.00596:5.36:27.6:28:0.0864:0:4.4 -7 57669848 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1735;SOR=Inf;LSEQ=AATGTGTGTTTTTCTCCCTA;RSEQ=AGAAGATATTTTTGAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:46,148:0:2,0:22.3:1:31.7:1:1:0:56.1:37.8:1:0:0.6 0/1:139:2:1,1:40,96:0.0144:2,2:12.5:1:29.5:1:0.50746:2.38:21:4:0.0144:0:5 -7 57669857 . T A 144 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01446;SOR=2.03484;LSEQ=TTTTCTCCCTACAGAAGATA;RSEQ=TTTTGAGTTTTCCATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:26:6,20:30,120:0.1477:2,2:15.5:1:28.7:1:0.79253:1.20:30.3:12:0.1404:0:4.1 0/1:134:35:15,20:22,77:0.2612:2,2:17.9:1:28.1:1:0.02723:2.60:31.2:34:0.2595:0:3.9 -7 57669864 . G A 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.58919;SOR=2.47221;LSEQ=CCTACAGAAGATATTTTTGA;RSEQ=TTTTCCATATTTTGAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:1:0,1:27,128:0.0064:2,0:4:0:18:0:1:0:60:0:0:0:6 0/1:127:2:1,1:33,92:0.0157:2,2:13.5:1:28.5:1:0.46532:2.76:27:4:0.016:0:4.5 -7 57669868 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20208;SOR=Inf;LSEQ=CAGAAGATATTTTTGAGTTT;RSEQ=CCATATTTTGAAACTTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:23,127:0:2,0:22:1:29.7:1:1:0:51.2:49:1:0:1 0/1:123:2:1,1:30,91:0.0163:2,2:22:1:29.5:1:0.44209:3.00:60:4:0.0167:0:1 -7 57669876 . T C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4418;SOR=0.69154;LSEQ=ATTTTTGAGTTTTCCATATT;RSEQ=TGAAACTTTACATAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:21:3,18:12,104:0.1533:2,2:27:1:30.9:1:0.70234:1.44:33.2:20:0.1515:0:3.9 0/1:99:11:3,8:15,73:0.1111:2,2:23.5:1:30.2:1:0.4151:1.81:26.9:22:0.1111:0:4.3 -7 57669906 . T C 115 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.02688;SOR=0.19969;LSEQ=ACATAAAAGGAATCATGCCT;RSEQ=ATATATTCTGACTTGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:13:1,12:5,80:0.1327:2,1:37.6:1:31.2:1:0.58451:1.33:25.7:12:0.125:0:3.6 0/1:68:2:1,1:11,55:0.0294:2,2:26:1:33.5:1:0.32397:4.83:27:4:0.0294:0:4.5 -7 57669908 . TA CG 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.02732;SOR=2.05267;LSEQ=ATAAAAGGAATCATGCCTTA;RSEQ=TATTCTGACTTGCTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:44:5,39:1,51:0.449:1,2:36.2:1:31.1:1:0.09049:6.42:30.9:43:0.4526:0:2.3 1/0:67:42:10,32:2,23:0.6269:2,2:35.4:1:30.5:1:0.18608:3.53:35.6:84:0.6269:0.0149:2.1 -7 57669994 . T GC 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=CACTGTCTGATTATATGATT;RSEQ=AGAGAGTGAAATTTTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:1,19:0.0909:1,0:12:1:33:0:1:0:39.5:4:0.0909:0:1 0/0:10:0:0,0:2,8:0:2,0:33.3:1:29.7:1:1:0:59.6:20:1:0:0 -7 57670051 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13725;SOR=Inf;LSEQ=TTTTTTTTCTATTCCATACA;RSEQ=TGGTGCTGGTTTTTGGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:0:0,0:17.8:1:31.5:1:1:0:54.5:22:1:0:0.4 0/1:7:2:1,1:0,5:0.2857:0,2:26.5:1:29.5:1:0.28571:0:41.5:4:0.2857:0:1 -7 61967178 . G T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAATTCTCAGTAACTTCTTT;RSEQ=TGTTGTGTGTATTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:32:0:1:0:29:4:1:0:2 -7 61967182 . T G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCAGTAACTTCTTTGTGT;RSEQ=GTGTGTATTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:32.5:1:1:0:29:4:1:0:2 -7 61967399 . C G 34 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTTCTTTTCATAGAGGA;RSEQ=TTTGGAAACACACTGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:38.5:1:34:0:1:0:24.5:4:1:0:4 -7 61967523 . T G 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGTAAATTCTTTGTGTT;RSEQ=TGTGCATTCAACTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:12:0:34:0:1:0:31:2:1:0:3 1/1:5:4:4,0:0,1:0.8:0,0:14.8:1:33.5:1:0.2:0:25:8:0.8:0:1.8 -7 61967546 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51567;SOR=Inf;LSEQ=TGCATTCAACTCACAGAGTG;RSEQ=AACGTCCCTTTAGACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:19.5:1:31.4:1:1:0:35.2:20:1:0:0.9 0/1:17:2:1,1:8,7:0.1176:2,2:29:1:32.5:1:1:1.13389:25:4:0.125:0:3 -7 61967553 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15726;SOR=0;LSEQ=AACTCACAGAGTGGAACGTC;RSEQ=CTTTAGACAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:0.1538:2,2:24:0:32.5:1:1:1.18321:47:4:0.1538:0:1 0/0:19:0:0,0:10,9:0:2,0:28.8:1:31.1:1:1:0:37.2:38:1:0:0.9 -7 61967555 . T C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16221;SOR=0;LSEQ=CTCACAGAGTGGAACGTCCC;RSEQ=TTAGACAGAGCAGATTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:5:0:33.5:1:1:1:43:4:0.1429:0:1.5 0/0:20:0:0,0:10,10:0:2,0:29.4:1:31.1:1:1:0:36.7:40:1:0:0.9 -7 61967562 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49231;SOR=Inf;LSEQ=AGTGGAACGTCCCTTTAGAC;RSEQ=GAGCAGATTTGAAACACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:22.7:1:31.3:1:1:0:38.3:36:1:0:1 0/1:22:2:1,1:10,10:0.0909:2,2:43.5:1:31:1:1:1:25:4:0.0909:0:3 -7 61967590 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=TTTGAAACACTCTTTTTGCG;RSEQ=AATTTGCAAGTGGAGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:32.3:1:31.7:1:1:0:38.3:36:1:0:1 0/1:26:2:1,1:11,13:0.0769:2,2:29:1:28:1:1:1.17:23:4:0.0769:0:5.5 -7 61967597 . C G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=CACTCTTTTTGCGGAATTTG;RSEQ=AAGTGGAGATTTCTAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:27.2:1:32.3:1:1:0:38.3:36:1:0:1 0/1:26:2:1,1:11,13:0.0769:2,2:29:1:30:1:1:1.17:23:4:0.0769:0:5.5 -7 61967600 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=TCTTTTTGCGGAATTTGCAA;RSEQ=TGGAGATTTCTAGCCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:24.8:1:32.6:1:1:0:38.3:36:1:0:1 0/1:26:2:1,1:11,13:0.0769:2,2:29:1:28:1:1:1.17:23:4:0.0769:0:5.5 -7 61967602 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16173;SOR=0;LSEQ=TTTTTGCGGAATTTGCAAGT;RSEQ=GAGATTTCTAGCCATTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:16.5:1:31:1:1:1:49.5:4:0.1111:0:1.5 0/0:26:0:0,0:12,14:0:2,0:20.9:1:30:1:1:0:37.4:52:1:0:1.1 -7 61967611 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48791;SOR=Inf;LSEQ=AATTTGCAAGTGGAGATTTC;RSEQ=AGCCATTTGATGCCAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:14.6:1:29.6:1:1:0:38.3:36:1:0:1 0/1:20:2:1,1:6,12:0.1:2,2:29:1:28.5:1:1:1.93:23:4:0.1:0:5.5 -7 61967632 . G A 69 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCATTTGATGCCAACAGT;RSEQ=GAAAGGGAAATATCTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:12.5:1:32.3:1:1:0:29.5:8:1:0:1.3 1/1:5:5:1,4:0,0:1:0,2:20.6:1:29.8:1:1:0:32:10:1:0:2 -7 61967993 . T C 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GAAAAGGAAATATCTGCAAA;RSEQ=AAAAACAAGACAGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:32:1:1:0:23:4:1:0:3.5 0/0:6:0:0,0:4,2:0:2,0:23:1:29:1:1:0:30.3:12:1:0:2.3 -7 61968000 . A T 54 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=AAATATCTGCAAATAAAAAC;RSEQ=AGACAGAATCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30:1:1:0:23:4:1:0:3.5 1/0:7:4:2,2:1,0:0.5714:0,2:25.3:1:27.3:1:1:0:26:8:0.5714:0:1 -7 61968014 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAACAAGACAGAATCATT;RSEQ=TCAGAAAGTGCTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:10:0:32:0:1:0:25:2:0.5:0:0 0/1:8:2:1,1:3,3:0.25:2,2:15.5:1:27:1:1:1:38:4:0.25:0:7.5 -7 61968022 . G C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAGAATCATTCTCAGAAA;RSEQ=TGCTTTGTGATGTGTGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:33.5:1:1:0:24:4:1:0:2.5 0/1:8:2:1,1:3,3:0.25:2,2:23.5:1:29.5:1:1:1:38:4:0.25:0:7.5 -7 61968040 . G A 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.86336;LSEQ=AAGTGCTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:18:0:33:0:1:0:23:2:0.2:0:5 0/1:17:3:1,2:6,8:0.1765:2,2:31.3:1:27.7:1:1:1.46561:41:6:0.1765:0:6 -7 61968054 . G C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGTGCGTTCAACTCACAGA;RSEQ=TTTAACCTTTCTTTTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:20.3:1:32.6:1:1:0:34.4:14:1:0:1.4 0/1:20:2:1,1:9,9:0.1:2,2:17:0:33.5:1:1:1:48.5:4:0.1:0:1 -7 61968059 . A C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTTCAACTCACAGAGTTTA;RSEQ=CCTTTCTTTTCATAGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:26.5:1:30.3:1:1:0:36.3:12:1:0:0.8 0/1:26:2:1,1:11,12:0.0769:2,2:6:0:33:0:1:1.09:28:4:0.0769:0:3 -7 61968061 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCTTTTCATAGAGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:27.8:1:32.2:1:1:0:36.3:12:1:0:0.8 0/1:27:2:1,1:12,13:0.0741:2,2:31.5:1:30.5:1:1:1.08:31:4:0.0741:0:1 -7 61968065 . C G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCACAGAGTTTAACCTTT;RSEQ=TTTTCATAGAGGAGTTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:30.5:1:31.8:1:1:0:36.3:12:1:0:0.8 0/1:29:2:1,1:13,14:0.069:2,2:31:1:32:1:1:1.07:38:4:0.069:0:7.5 -7 61968071 . A C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGTTTAACCTTTCTTTTC;RSEQ=TAGAGGAGTTTGGAAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:34.5:1:30.7:1:1:0:36.3:12:1:0:0.8 0/1:29:2:1,1:13,14:0.069:2,2:25:1:32:0:1:1.07:38:4:0.069:0:7.5 -7 61968077 . GA CC 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAACCTTTCTTTTCATAGAG;RSEQ=GTTTGGAAACACACTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:37.3:1:31.3:1:1:0:36.3:12:1:0:0.8 0/1:31:2:1,1:14,15:0.0645:2,2:18:1:32:1:1:1.07:38:4:0.0645:0:6.5 -7 61968092 . C A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGAGGAGTTTGGAAACACA;RSEQ=TGTTTGTAAAGTCTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:32:1:31.8:1:1:0:36.3:12:1:0:0.8 0/1:30:2:1,1:13,15:0.0667:2,2:26.5:1:28.5:1:1:1.15:25:4:0.0667:0:1 -7 61968100 . A G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGGAAACACACTGTTTGT;RSEQ=AAGTCTGCAAGTGGATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:24:1:29:1:1:0:36.3:12:1:0:0.8 0/1:28:2:1,1:13,13:0.0714:2,2:19:0:32:1:1:1:28:4:0.0714:0:3 -7 61968102 . A G 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAACACACTGTTTGTAA;RSEQ=GTCTGCAAGTGGATATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:22:1:30.7:1:1:0:36.3:12:1:0:0.8 0/1:28:2:1,1:13,13:0.0714:2,2:28:0:33:1:1:1:47:4:0.0714:0:2.5 -7 61968104 . T A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACACACTGTTTGTAAAG;RSEQ=CTGCAAGTGGATATATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:20:1:30.2:1:1:0:36.3:12:1:0:0.8 0/1:28:2:1,1:13,13:0.0714:2,2:26:0:31.5:1:1:1:47:4:0.0714:0:2.5 -7 61968108 . C A 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.02151;SOR=0;LSEQ=CACACTGTTTGTAAAGTCTG;RSEQ=AAGTGGATATATGGACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:18:0:32:0:1:1.73:47:4:0.4:0:1.5 0/0:26:0:0,0:11,13:0:2,0:17.3:1:32.7:1:1:0:38.3:48:0.9231:0:0.9 -7 61968110 . A C 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTGTTTGTAAAGTCTGCA;RSEQ=GTGGATATATGGACCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:17.8:1:31.2:1:1:0:38.6:10:1:0:1 0/1:26:2:1,1:11,13:0.0769:2,2:9:0:30.5:1:1:1.17:28:4:0.0769:0:3 -7 61968254 . A G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTCATAGAGCAGTTTGG;RSEQ=AACACTCTGTTGGTAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:30:1:1:1:48.5:4:0.6667:0:3 0/0:1:0:0,0:1,0:0:0,0:48:0:28:0:1:0:21:2:1:0:2 -7 61968286 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=GGTAATGTCTGCAAGTGGAT;RSEQ=TATGGACCGCTTGGAGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28.5:1:31:1:1:1:44.5:4:0.5:0:7 0/0:2:0:0,0:1,1:0:2,0:16.5:1:27.5:1:1:0:21:4:1:0:2.5 -7 61968294 . C G 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CTGCAAGTGGATATATGGAC;RSEQ=GCTTGGAGGCTTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:20.5:1:28:1:1:1:44.5:4:0.5:0:7 0/0:2:0:0,0:1,1:0:2,0:16.5:1:28:1:1:0:21:4:1:0:2.5 -7 61968299 . G T 58 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGATATATGGACCGCTT;RSEQ=GAGGCTTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:17.3:1:29.3:1:1:0:46.5:8:1:0:5 1/1:2:2:1,1:0,0:1:0,2:16.5:1:29.5:1:1:0:21:4:1:0:2.5 -7 61968305 . T C 48 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATGGACCGCTTGGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:16:1:30.7:1:1:0:45:6:1:0:5.7 1/1:1:1:0,1:0,0:1:0,0:36:0:34:0:1:0:21:2:1:0:3 -7 61968328 . C A 44 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CGTTGGAAACGGGATTTCTT;RSEQ=ATTTCATGCTAGACAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:6:0:35:0:1:0:46:2:1:0:3 1/0:4:3:2,1:0,1:0.75:0,2:9.7:1:28:1:1:0:35.7:6:0.75:0:6.3 -7 61968386 . C G 64 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTTGTGTGTATTCAACT;RSEQ=ACAGACTGGAACGTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:32.8:1:32:1:1:0:36.8:8:1:0:6 -7 61968390 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTGTGTATTCAACTCACA;RSEQ=ACTGGAACGTCCCTTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:24:0:33.5:1:1:1:31:4:0.5:0:6.5 -7 61968392 . C T 61 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTATTCAACTCACAGA;RSEQ=TGGAACGTCCCTTTACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:28.8:1:30.5:1:1:0:36.8:8:1:0:6 -7 61968398 . C T 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCAACTCACAGACTGGAA;RSEQ=GTCCCTTTACACAGAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:22.8:1:30.3:1:1:0:36.8:8:1:0:6 -7 61968404 . T A 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACAGACTGGAACGTCCC;RSEQ=TTACACAGAGCAGATTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:0,1:0.8:0,2:16.8:1:30.3:1:1:0:36.8:8:0.8:0:6 -7 61968616 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ACACACTGTTTGTAAAGTCT;RSEQ=CAATTGGATATATGGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:31.7:1:32:1:1:0:38.3:6:1:0:0.7 1/1:2:2:1,1:0,0:1:0,2:24:1:28:1:1:0:44.5:4:1:0:4.5 -7 61968635 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGCAATTGGATATATGGACC;RSEQ=GTTTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:28.5:1:31.5:1:1:0:41:8:1:0:1 1/0:4:2:1,1:2,0:0.5:0,2:24:1:29:1:1:0:44.5:4:0.5:0:4.5 -7 61968657 . C A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=TTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTTATCATATAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:20.4:1:30.8:1:1:0:40:10:1:0:1 0/1:7:2:1,1:3,2:0.2857:2,2:10:0:32.5:1:1:1.41418:46.5:4:0.2857:0:3 -7 61968707 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GAATTCTCAGTAAATTCTTT;RSEQ=TGTTGTGTGCATTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:24.7:1:32.7:1:1:0:40.8:12:1:0:1.3 0/1:16:2:1,1:10,4:0.125:2,2:38:1:30.5:1:1:2.34522:27:4:0.125:0:1.5 -7 61968708 . T G 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AATTCTCAGTAAATTCTTTG;RSEQ=GTTGTGTGCATTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:24.7:1:30.8:1:1:0:40.8:12:1:0:1.3 0/1:16:2:1,1:10,4:0.125:2,2:30:1:31.5:1:1:2.34522:49:4:0.125:0:1.5 -7 61968717 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAATTCTTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:19.9:1:33:1:1:0:39.5:16:1:0:1.3 0/1:17:2:1,1:11,4:0.1176:2,2:25:1:28:1:0.51471:2.56905:46.5:4:0.1176:0:3 -7 61968728 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13547;SOR=0;LSEQ=TGTTGTGTGCATTCAACTCA;RSEQ=AGAGTGGAACGTCCCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:9,0:0.1818:0,2:11:1:31.5:1:0.18182:0:49:4:0.1818:0:1.5 0/0:18:0:0,0:13,5:0:2,0:24.8:1:31.1:1:1:0:36.2:36:1:0:1.4 -7 61968752 . G C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.7753;LSEQ=GTGGAACGTCCCTTTAGACA;RSEQ=AGCAGATTTGAAACACTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:17,1:0.0526:1,0:14:0:33:0:1:0:27:2:0.0526:0:2 0/1:22:2:2,0:16,4:0.0909:2,0:18:1:31.5:1:1:0:24:4:0.0909:0:2.5 -7 61968755 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23171;SOR=0;LSEQ=GAACGTCCCTTTAGACAGAG;RSEQ=AGATTTGAAACACTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:18,0:0.1:1,2:5.5:1:30.5:1:0.1:0:27:4:0.1:0:2.5 0/0:21:0:0,0:18,3:0:2,0:24.5:1:31.8:1:1:0:31.8:20:1:0:1.6 -7 61968770 . G C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.3736;SOR=0.30151;LSEQ=CAGAGCAGATTTGAAACACT;RSEQ=TTTTTGCGGAATTTGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:22:21,1:0,0:0.9565:0,1:27.7:1:31.9:1:1:0:37.5:44:0.9565:0:1.4 1/1:30:26:24,2:0,0:0.8667:0,2:20.9:1:31.2:1:1:0:34.6:25:0.8621:0:1.4 -7 61968795 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16341;SOR=0;LSEQ=TGCGGAATTTGCAAGTGGAG;RSEQ=TTTCTAGCCATTTGATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:39,7:0.0417:2,2:35:1:31:1:0.30851:5.27809:27:4:0.0417:0:2.5 0/0:70:0:0,0:48,22:0:2,0:21.4:1:28.6:1:1:0:36.3:22.333:1:0:0.8 -7 61968805 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51169;SOR=Inf;LSEQ=GCAAGTGGAGATTTCTAGCC;RSEQ=TTTGATGCCAACAGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:45,9:0:2,0:25.7:1:30.5:1:1:0:40.1:108:1:0:0.7 0/1:77:2:1,1:54,21:0.026:2,2:37.5:1:29.5:1:0.49248:2.53547:27:4:0.0267:0:2 -7 61968812 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50734;SOR=Inf;LSEQ=GAGATTTCTAGCCATTTGAT;RSEQ=CCAACAGTAGAAAGGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:51,10:0:2,0:25.6:1:32.3:1:1:0:40.1:60:1:0:0.6 0/1:82:2:1,1:58,22:0.0244:2,2:29.5:1:28.5:1:0.48479:2.60055:24:4:0.0244:0:4.5 -7 61968813 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07385;SOR=0;LSEQ=AGATTTCTAGCCATTTGATG;RSEQ=CAACAGTAGAAAGGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:2,1:49,9:0.0492:2,2:36:1:28.7:1:0.42137:2.66395:31.3:6:0.0508:0:2 0/0:83:0:0,0:60,23:0:2,0:28.2:1:31.7:1:1:0:37.2:82:1:0:0.7 -7 61968826 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56739;SOR=0.33809;LSEQ=TTTGATGCCAACAGTAGAAA;RSEQ=GGAAATATCTTCAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:2,0:61,17:0.025:2,0:13:1:29:1:1:0:48.5:4:0.0253:0:3.5 0/0:117:1:1,0:72,43:0.0085:2,0:2:0:30:0:1:0:60:2:0.0088:0:2 -7 61968832 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40156;SOR=0.45479;LSEQ=GCCAACAGTAGAAAGGGAAA;RSEQ=ATCTTCAAATAAAAACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:2,1:65,22:0.0333:2,2:27.7:1:32:1:1:1.47033:51.7:6:0.0341:0:1 0/1:130:2:1,1:76,52:0.0154:2,2:16:0:30:1:1:1.45715:33:4:0.0155:0:2 -7 61968834 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51012;SOR=Inf;LSEQ=CAACAGTAGAAAGGGAAATA;RSEQ=CTTCAAATAAAAACCAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:70,24:0:2,0:23.1:1:30.5:1:1:0:45.8:46:1:0:0.6 0/1:129:2:1,1:76,51:0.0155:2,2:49.5:1:31.5:1:1:1.48544:24:4:0.0155:0:4.5 -7 61968838 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.52407;LSEQ=AGTAGAAAGGGAAATATCTT;RSEQ=AAATAAAAACCAGACAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:1:1,0:71,29:0.0099:2,0:18:0:13:0:1:0:57:0:0:0:5 0/1:133:2:1,1:77,53:0.015:2,2:11.5:1:28:1:1:1.4486:60:4:0.0152:0:1 -7 61968842 . T G 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14358;SOR=Inf;LSEQ=GAAAGGGAAATATCTTCAAA;RSEQ=AAAAACCAGACAGAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:73,30:0:2,0:23.4:1:30.2:1:1:0:47.8:102:1:0:0.5 0/1:145:4:3,1:85,56:0.0276:2,2:20:1:31.8:1:1:1.97:51:8:0.0282:0:1.3 -7 61968843 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51066;SOR=Inf;LSEQ=AAAGGGAAATATCTTCAAAT;RSEQ=AAAACCAGACAGAATCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:75,31:0:2,0:23.1:1:28.6:1:1:0:48.2:52:1:0:0.5 0/1:146:2:1,1:86,56:0.0137:2,2:40.5:1:32.5:1:1:1.53096:24:4:0.0137:0:4.5 -7 61968847 . A T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.26748;SOR=Inf;LSEQ=GGAAATATCTTCAAATAAAA;RSEQ=CCAGACAGAATCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:77,35:0:2,0:23.3:1:29.8:1:1:0:49.1:55:1:0:0.5 0/1:156:3:1,2:90,63:0.0192:2,2:16.7:1:27:1:0.57111:2.83793:40:6:0.0194:0:1.3 -7 61968849 . C T 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4449;SOR=0.49821;LSEQ=AAATATCTTCAAATAAAAAC;RSEQ=AGACAGAATCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:4:4,0:72,36:0.0357:2,0:30.3:1:33.3:1:0.30343:0:39.8:8:0.0367:0:2 0/1:166:3:2,1:94,68:0.0181:2,2:22.3:1:29.3:1:1:1.44:30:6:0.0183:0:2.7 -7 61968853 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51514;SOR=Inf;LSEQ=ATCTTCAAATAAAAACCAGA;RSEQ=AGAATCATTCTCAGAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:80,38:0:2,0:24.3:1:32.4:1:1:0:49.6:236:1:0:0.5 0/1:171:2:1,1:96,73:0.0117:2,2:44.5:1:32:1:1:1.31293:33:4:0.0118:0:1 -7 61968862 . T C 33 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.40418;LSEQ=TAAAAACCAGACAGAATCAT;RSEQ=CTCAGAAAATTCTTTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:1:1,0:82,41:0.0081:2,0:39:0:32:0:1:0:39:2:0.0081:0:2 0/1:177:2:1,1:99,76:0.0113:2,2:21.5:1:33:0:1:1.30065:24:4:0.0116:0:4.5 -7 61968868 . A C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.95608;LSEQ=CCAGACAGAATCATTCTCAG;RSEQ=AAATTCTTTGTGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:3,2:81,46:0.0379:2,2:20:1:33.4:1:1:1.17245:50.4:10:0.0385:0:1.4 0/1:193:7:3,4:105,81:0.0363:2,2:28.3:1:30.4:1:0.70143:1.72342:47:14:0.0366:0:1 -7 61968874 . C A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57097;SOR=0.34804;LSEQ=AGAATCATTCTCAGAAAATT;RSEQ=TTTGTGATGTGTGCGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:87,49:0.0145:2,2:48:1:28:1:1:1.76765:51.5:4:0.0147:0:1 0/0:197:1:1,0:105,90:0.0051:2,0:1:0:26:0:1:0:50:2:0.0051:0:1 -7 61968887 . G T 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64725;SOR=2.09312;LSEQ=GAAAATTCTTTGTGATGTGT;RSEQ=CGTTCAACTCACATAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:1:0,1:86,58:0.0069:2,0:1:0:26:0:0.4069:0:60:2:0.0071:0:1 0/1:209:3:2,1:104,102:0.0144:2,2:26.3:1:30:1:1:1.96:60:6:0.0148:0:1.3 -7 61968889 . G C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2638;SOR=Inf;LSEQ=AAATTCTTTGTGATGTGTGC;RSEQ=TTCAACTCACATAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:90,65:0:2,0:26.6:1:30.3:1:1:0:54.9:50.667:0.9935:0:0.4 0/1:209:3:1,2:102,101:0.0144:2,2:28:1:32:1:1:2.01316:36.3:6:0.0144:0:3.3 -7 61968890 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18169;SOR=0;LSEQ=AATTCTTTGTGATGTGTGCG;RSEQ=TCAACTCACATAGTTTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:90,66:0.0127:2,2:31.5:1:31:1:1:1.3609:50:4:0.0128:0:2 0/0:212:0:0,0:105,107:0:2,0:26.8:1:29.6:1:1:0:52.2:424:1:0:0.6 -7 61968894 . A G 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24702;SOR=0.36232;LSEQ=CTTTGTGATGTGTGCGTTCA;RSEQ=CTCACATAGTTTAACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:4:2,2:92,66:0.0245:2,2:29.3:1:31.5:1:1:1.39101:57:8:0.025:0:2.3 0/0:222:2:1,1:109,111:0.009:2,2:35:1:30.5:1:1:1.02:51:4:0.009:0:4.5 -7 61968901 . T G 95 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08497;SOR=6.05152;LSEQ=ATGTGTGCGTTCAACTCACA;RSEQ=AGTTTAACCTTTCTTTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:1,0:98,72:0.0058:2,0:6:0:34:0:1:0:60:2:0.0059:0:2 0/1:232:8:4,4:111,111:0.0345:2,2:22.9:1:31.9:1:1:1:48.6:16:0.0348:0:2.4 -7 61968903 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17472;SOR=0;LSEQ=GTGTGCGTTCAACTCACATA;RSEQ=TTTAACCTTTCTTTTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:97,71:0.0118:2,2:29:1:31.5:1:1:1.36363:60:4:0.0119:0:2.5 0/0:236:0:0,0:118,118:0:2,0:25.2:1:31.5:1:1:0:53.6:235:1:0:0.6 -7 61968907 . A C 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14282;SOR=Inf;LSEQ=GCGTTCAACTCACATAGTTT;RSEQ=ACCTTTCTTTTCATAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:99,74:0:2,0:25.3:1:28.9:1:1:0:57:172:0.9942:0:0.4 0/1:241:4:1,3:118,119:0.0166:2,2:27.8:1:30.3:1:0.62197:2.96271:49.5:8:0.0166:0:1.8 -7 61968910 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57423;SOR=0.35832;LSEQ=TTCAACTCACATAGTTTAAC;RSEQ=TTTCTTTTCATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:99,74:0.0114:2,2:40:1:31:1:1:1.33557:56:4:0.0117:0:1 0/0:243:1:0,1:117,125:0.0041:2,0:2:0:27:0:1:0:60:2:0.0041:0:1 -7 61968915 . T C 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57207;SOR=0.35107;LSEQ=CTCACATAGTTTAACCTTTC;RSEQ=TTTCATAGAGCAGTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:95,78:0.0114:2,2:23:1:30:1:1:1.21656:43.5:4:0.0117:0:6 0/0:248:1:0,1:119,128:0.004:2,0:1:0:30:0:1:0:60:2:0.004:0:1 -7 61968926 . C G 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47102;LSEQ=TAACCTTTCTTTTCATAGAG;RSEQ=AGTTTGGAAACACTCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:2,0:88,85:0.0114:2,0:20.5:1:33:0:0.49754:0:60:4:0.0116:0:2 0/1:239:4:2,2:115,119:0.0167:2,2:29.3:1:31.8:1:1:1.03:54.8:8:0.017:0:1.5 -7 61968931 . T A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2681;SOR=Inf;LSEQ=TTTCTTTTCATAGAGCAGTT;RSEQ=GGAAACACTCTGTTTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:91,84:0:2,0:25.8:1:30:1:1:0:58.7:174:1:0:0.5 0/1:243:3:1,2:123,117:0.0123:2,2:13.3:1:29.3:1:0.6158:2.09635:37:6:0.0123:0:1.3 -7 61968932 . G C 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.73249;LSEQ=TTCTTTTCATAGAGCAGTTT;RSEQ=GAAACACTCTGTTTGTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:88,81:0.0115:2,2:25:1:32:1:1:1.08588:54:4:0.0117:0:3.5 0/0:237:2:1,1:119,112:0.0084:2,2:28:1:31.5:1:1:1.06225:51:4:0.0085:0:4.5 -7 61968940 . T A 41 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6536;SOR=0.47665;LSEQ=ATAGAGCAGTTTGGAAACAC;RSEQ=CTGTTTGTAAAGTCTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:2,1:89,83:0.0171:2,2:22.3:1:26:1:1:1.86:56:2:0.0116:0:3 0/0:243:2:1,1:121,118:0.0082:2,2:20:1:31.5:1:1:1.02532:51:4:0.0083:0:4.5 -7 61968942 . T A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.26761;SOR=Inf;LSEQ=AGAGCAGTTTGGAAACACTC;RSEQ=GTTTGTAAAGTCTGCAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:89,84:0:2,0:25.6:1:30.7:1:1:0:58.9:85.5:0.9884:0:0.5 0/1:242:3:2,1:121,117:0.0124:2,2:19.7:1:31:1:1:1.93:37.3:6:0.0125:0:3 -7 61968944 . T C 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64512;SOR=2.132;LSEQ=AGCAGTTTGGAAACACTCTG;RSEQ=TTGTAAAGTCTGCAAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:1:1,0:83,84:0.0059:2,0:42:0:34:0:1:0:60:2:0.0061:0:3 0/1:239:3:1,2:119,115:0.0126:2,2:6.7:1:31.7:1:0.61866:2.06343:49.7:6:0.0127:0:2 -7 61968946 . T G 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40408;SOR=0.45922;LSEQ=CAGTTTGGAAACACTCTGTT;RSEQ=GTAAAGTCTGCAAGTGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:3:1,2:83,82:0.0179:2,2:22.3:1:31:1:1:2.0162:53:6:0.0183:0:1.7 0/0:242:2:1,1:122,118:0.0083:2,2:27.5:1:32.5:1:1:1.03376:35:4:0.0083:0:4 -7 61968951 . A C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18305;SOR=0;LSEQ=TGGAAACACTCTGTTTGTAA;RSEQ=GTCTGCAAGTGGATATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:84,80:0.0119:2,2:29:1:32.5:1:1:1.04971:60:4:0.012:0:1.5 0/0:224:0:0,0:110,110:0:2,0:25.1:1:30.5:1:1:0:58.5:440:0.9821:0:0.5 -7 61968955 . T A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26208;SOR=Inf;LSEQ=AACACTCTGTTTGTAAAGTC;RSEQ=GCAAGTGGATATATGGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:87,84:0:2,0:25.2:1:30.5:1:1:0:59.4:56:1:0:0.5 0/1:225:3:2,1:111,111:0.0133:2,2:15.3:1:31.3:1:1:1.99:37.3:6:0.0135:0:3 -7 61968960 . G C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25619;SOR=Inf;LSEQ=TCTGTTTGTAAAGTCTGCAA;RSEQ=TGGATATATGGACCGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:90,91:0:2,0:23.5:1:32.1:1:1:0:59.4:180:0.9945:0:0.5 0/1:224:3:2,1:109,112:0.0134:2,2:13.7:1:31.3:1:0.61996:2.05:37.3:6:0.0135:0:3 -7 61968962 . G A 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32225;SOR=0.25564;LSEQ=TGTTTGTAAAGTCTGCAAGT;RSEQ=GATATATGGACCGCATTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:2,1:86,86:0.0171:2,2:31.7:1:30.7:1:1:1.99:60:6:0.0175:0:2.3 0/0:226:1:1,0:110,114:0.0044:2,0:28:0:30:0:0.49333:0:60:2:0.0045:0:3 -7 61968966 . A C 81 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.04595;SOR=0.12372;LSEQ=TGTAAAGTCTGCAAGTGGAT;RSEQ=TATGGACCGCATTGAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:6:3,3:84,83:0.0347:2,2:19.7:1:31.5:1:1:1.01198:60:12:0.0353:0:1.5 0/0:227:1:1,0:110,116:0.0044:2,0:4:0:32:0:0.48899:0:60:2:0.0044:0:1 -7 61968968 . A T 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.06986;SOR=Inf;LSEQ=TAAAGTCTGCAAGTGGATAT;RSEQ=TGGACCGCATTGAGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:86,82:0:2,0:24.5:1:29.5:1:1:0:59.3:167:0.994:0:0.5 0/1:215:5:3,2:103,107:0.0233:2,2:20.4:1:30.8:1:0.6802:1.56:53.2:10:0.0234:0:1.4 -7 61968975 . G A 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01504;SOR=0;LSEQ=TGCAAGTGGATATATGGACC;RSEQ=CATTGAGGCCTTCGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:5:3,2:79,78:0.0305:2,2:17.6:1:29:1:1:1.48:60:10:0.0314:0:1.2 0/0:213:0:0,0:107,105:0:2,0:24.8:1:30.7:1:1:0:59.6:69.667:0.9952:0:0.5 -7 61968976 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19148;SOR=0;LSEQ=GCAAGTGGATATATGGACCG;RSEQ=ATTGAGGCCTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:82,82:0.012:2,2:22:1:29.5:1:1:1:60:4:0.0123:0:1 0/0:214:0:0,0:106,105:0:2,0:24.9:1:31.7:1:1:0:59.6:69.333:0.9858:0:0.5 -7 61968977 . A T 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29855;SOR=0.44812;LSEQ=CAAGTGGATATATGGACCGC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:5:2,3:78,78:0.0307:2,2:27.8:1:31:1:1:1.49627:51.8:10:0.0313:0:4.2 0/1:215:3:2,1:106,106:0.014:2,2:29:1:26.7:1:1:1.99:59.7:2:0.0095:0:2 -7 61968983 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.72135;LSEQ=GATATATGGACCGCATTGAG;RSEQ=CCTTCGTTGGAAACGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:78,82:0.0123:2,0:28:1:32:0:0.24231:0:60:4:0.0127:0:2 0/0:224:2:1,1:118,104:0.0089:2,2:35.5:1:30.5:1:1:1.13397:60:4:0.009:0:1.5 -7 61968984 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26553;SOR=Inf;LSEQ=ATATATGGACCGCATTGAGG;RSEQ=CTTCGTTGGAAACGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:81,82:0:2,0:24.4:1:31.1:1:1:0:59.1:26.167:0.9937:0:0.5 0/1:223:3:2,1:117,103:0.0135:2,2:28.3:1:28.3:1:1:1.76:60:6:0.0136:0:1.7 -7 61968989 . G A 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65352;SOR=0.47847;LSEQ=TGGACCGCATTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:75,79:0.0191:2,2:23.7:1:31.3:1:0.61543:2.10:60:6:0.0192:0:2.3 0/0:217:2:2,0:113,100:0.0092:2,0:12.5:1:31:1:0.50011:0:60:4:0.0093:0:1 -7 61968997 . C T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31103;SOR=0.23283;LSEQ=ATTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCATTTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:1,2:70,81:0.0195:2,2:19.7:1:31:1:1:1.72251:60:6:0.0197:0:1 0/0:218:1:0,1:112,101:0.0046:2,0:50:0:29:0:0.47664:0:60:2:0.0046:0:3 -7 61968999 . G A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57248;SOR=0.35284;LSEQ=TGAGGCCTTCGTTGGAAACG;RSEQ=GATTTCTTCATTTCATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:69,83:0.013:2,2:36:1:31.5:1:1:1.20:60:4:0.0131:0:2 0/0:217:1:0,1:111,105:0.0046:2,0:48:0:30:0:0.48848:0:60:2:0.0047:0:3 -7 61969011 . T G 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26364;SOR=Inf;LSEQ=TGGAAACGGGATTTCTTCAT;RSEQ=TCATGCTAGACAGAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:71,85:0:2,0:24.8:1:29.8:1:1:0:59.4:51:0.9935:0:0.6 0/1:210:3:1,2:106,99:0.0143:2,2:12.3:1:32:1:0.61254:2.13383:52.3:6:0.0144:0:6 -7 61969013 . C A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77395;LSEQ=GAAACGGGATTTCTTCATTT;RSEQ=ATGCTAGACAGAAGAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:3:2,1:74,83:0.0188:2,2:15:1:28.7:1:0.60453:2.23:51:6:0.019:0:4.7 0/1:206:3:2,1:102,94:0.0146:2,2:21:1:30:1:1:1.84:45.7:6:0.0147:0:7.7 -7 61969014 . A G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.25636;SOR=Inf;LSEQ=AAACGGGATTTCTTCATTTC;RSEQ=TGCTAGACAGAAGAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:78,87:0:2,0:23.4:1:30.4:1:1:0:59.2:330:1:0:0.7 0/1:204:3:1,2:103,96:0.0147:2,2:18.7:1:31.7:1:0.61217:2.13799:57.7:6:0.0149:0:1.3 -7 61969016 . G A 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47108;SOR=1.99898;LSEQ=ACGGGATTTCTTCATTTCAT;RSEQ=CTAGACAGAAGAATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:76,88:0.012:2,2:30:1:28:1:1:1.16:60:4:0.0123:0:1.5 0/1:211:5:2,3:106,98:0.0237:2,2:17.8:1:27.4:1:0.67444:1.61872:60:10:0.0238:0:2.2 -7 61969017 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18064;LSEQ=CGGGATTTCTTCATTTCATG;RSEQ=TAGACAGAAGAATTCTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:2,0:75,88:0.0121:2,0:37.5:1:30.5:1:0.21626:0:46.5:4:0.0125:0:4.5 0/1:210:3:2,1:105,102:0.0143:2,2:25:1:30:1:1:1.94:45.7:6:0.0145:0:7.7 -7 61969018 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19607;SOR=0;LSEQ=GGGATTTCTTCATTTCATGC;RSEQ=AGACAGAAGAATTCTCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:76,86:0.0121:2,2:19:1:30.5:1:1:1.13:60:4:0.0125:0:1.5 0/0:207:0:0,0:106,100:0:2,0:24.5:1:29.5:1:1:0:57.6:205:0.9951:0:1 -7 61969030 . T G 51 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65185;SOR=2.02296;LSEQ=TTTCATGCTAGACAGAAGAA;RSEQ=TCTCAGTAACTTCTTTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:1,0:77,77:0.0065:2,0:38:0:31:0:1:0:33:2:0.0066:0:8 0/1:231:3:2,1:117,111:0.013:2,2:16.7:1:32.7:1:1:1.89:40.7:6:0.0132:0:4 -7 61969032 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27569;SOR=Inf;LSEQ=TCATGCTAGACAGAAGAATT;RSEQ=TCAGTAACTTCTTTGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:79,77:0:2,0:25.2:1:31.6:1:1:0:58.2:38:1:0:0.8 0/1:230:3:1,2:117,110:0.013:2,2:19:1:28:1:0.61371:2.12052:56.3:6:0.013:0:3.3 -7 61969040 . C A 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14978;SOR=Inf;LSEQ=GACAGAAGAATTCTCAGTAA;RSEQ=TTCTTTGTGCTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:81,81:0:2,0:24.7:1:32:1:1:0:56.9:80:1:0:1 0/1:237:4:3,1:121,112:0.0169:2,2:32.8:1:25:1:0.62344:2.77:36.3:3:0.0129:0:4.8 -7 61969042 . T C 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90053;LSEQ=CAGAAGAATTCTCAGTAACT;RSEQ=CTTTGTGCTGTGTGTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:3:1,2:81,77:0.0186:2,2:39.7:1:33:1:0.61567:2.09451:53.3:6:0.019:0:2.3 0/1:238:4:3,1:122,111:0.0168:2,2:32.8:1:26.8:1:0.62409:2.72:36.3:3:0.0129:0:4.8 -7 61969043 . CT C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16219;SOR=0;LSEQ=AGAAGAATTCTCAGTAACTT;RSEQ=TTGTGCTGTGTGTATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:81,77:0.0123:2,2:31.5:1:31:1:1:1.05164:60:4:0.0127:0:0.5 0/0:241:0:0,0:125,112:0:2,0:24.8:1:30.6:1:1:0:54.2:78:0.9873:0:1.3 -7 61969044 . T C 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.39688;SOR=0.44722;LSEQ=GAAGAATTCTCAGTAACTTC;RSEQ=TTGTGCTGTGTGTATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:3:2,1:81,77:0.0184:2,2:12.3:1:30.3:1:1:1.89:46.7:6:0.019:0:2.3 0/0:241:2:1,1:125,112:0.0083:2,2:35:1:30:1:1:1.11556:60:4:0.0084:0:1.5 -7 61969045 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.275;SOR=Inf;LSEQ=AAGAATTCTCAGTAACTTCT;RSEQ=TGTGCTGTGTGTATTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:84,79:0:2,0:24.9:1:30:1:1:0:56.3:53.333:1:0:1 0/1:239:3:1,2:125,111:0.0126:2,2:22:1:30.7:1:0.60394:2.24484:52.3:6:0.0126:0:1.3 -7 61969050 . C T 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01894;LSEQ=TTCTCAGTAACTTCTTTGTG;RSEQ=TGTGTGTATTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:4:2,2:84,77:0.0242:2,2:10.8:1:30:1:1:1.09033:48.3:8:0.0248:0:2.8 0/1:243:6:3,3:126,108:0.0247:2,2:23.8:1:29.2:1:1:1.16591:40.5:12:0.0252:0:4 -7 61969051 . T C 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.15335;SOR=Inf;LSEQ=TCTCAGTAACTTCTTTGTGC;RSEQ=GTGTGTATTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:83,79:0:2,0:25.2:1:30.6:1:1:0:54.8:53:1:0:1.1 0/1:243:4:2,2:127,111:0.0165:2,2:30.3:1:30.3:1:1:1.1435:60:8:0.0165:0:1.5 -7 61969063 . A T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.27687;SOR=Inf;LSEQ=CTTTGTGCTGTGTGTATTCA;RSEQ=CTCACAGAGTGGAACGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:73,80:0:2,0:26.2:1:30.2:1:1:0:52.6:306:0.9935:0:1.3 0/1:229:3:1,2:121,105:0.0131:2,2:31.3:1:27:1:0.60019:2.29661:53.3:6:0.0132:0:2.7 -7 61969064 . C G 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.56745;SOR=0.33505;LSEQ=TTTGTGCTGTGTGTATTCAA;RSEQ=TCACAGAGTGGAACGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:71,80:0.0131:2,2:37:1:29:0:1:1.13:53:4:0.0131:0:3 0/0:227:1:1,0:120,106:0.0044:2,0:6:0:33:0:1:0:40:2:0.0044:0:5 -7 61969068 . CAG C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.1615;SOR=0;LSEQ=TGCTGTGTGTATTCAACTCA;RSEQ=AGTGGAACGTCCCTTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:0,2:71,78:0.0132:2,0:13.5:1:33:1:0.49845:0:43:4:0.0132:0.0066:2.5 0/0:224:0:0,0:116,106:0:2,0:25.2:1:30.2:1:1:0:51:54.5:0.9909:0:1.6 -7 61969074 . G T 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1509;SOR=Inf;LSEQ=GTGTATTCAACTCACAGAGT;RSEQ=GAACGTCCCTTTACACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:70,79:0:2,0:25.4:1:31.7:1:1:0:51.4:148:1:0:1.4 0/1:220:4:3,1:109,107:0.0182:2,2:15.5:1:31:1:0.6218:2.93:41.8:8:0.0186:0:4.3 -7 61969079 . G C 24 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70461;LSEQ=TTCAACTCACAGAGTGGAAC;RSEQ=TCCCTTTACACAGAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:69,74:0.0136:2,2:24:0:33.5:1:1:1.07:60:4:0.0137:0:1 0/0:208:2:2,0:100,98:0.0096:2,0:11:1:24:1:0.49769:0:32:1:0.005:0:5.5 -7 61969081 . C T 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26653;SOR=Inf;LSEQ=CAACTCACAGAGTGGAACGT;RSEQ=CCTTTACACAGAGCAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:72,75:0:2,0:24.9:1:31.2:1:1:0:49.4:72.5:1:0:1.5 0/1:202:3:2,1:98,100:0.0149:2,2:24.3:1:31.7:1:0.62124:2.03:42:6:0.0152:0:6.3 -7 61969082 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5095;SOR=Inf;LSEQ=AACTCACAGAGTGGAACGTC;RSEQ=CTTTACACAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:72,75:0:2,0:24.9:1:31.1:1:1:0:49.3:72.5:1:0:1.5 0/1:198:2:1,1:97,99:0.0101:2,2:42:0:31:1:1:1.02:49:4:0.0105:0:2.5 -7 61969083 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50806;SOR=Inf;LSEQ=ACTCACAGAGTGGAACGTCC;RSEQ=TTTACACAGAGCAGATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:72,75:0:2,0:24.8:1:31.7:1:1:0:49.3:72.5:1:0:1.5 0/1:194:2:1,1:96,96:0.0103:2,2:33.5:1:30.5:1:1:1:49:4:0.0105:0:2.5 -7 61969087 . A G 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1844;SOR=0.707;LSEQ=ACAGAGTGGAACGTCCCTTT;RSEQ=CACAGAGCAGATTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:146:109:54,55:16,18:0.7466:2,2:25.1:1:32.1:1:0.846:1.10:48.1:108:0.75:0:1.9 1/0:191:129:63,66:33,28:0.6754:2,2:26.2:1:31.3:1:0.53644:1.23332:49:42:0.6738:0:1.8 -7 61969088 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50668;SOR=Inf;LSEQ=CAGAGTGGAACGTCCCTTTA;RSEQ=ACAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:73,73:0:2,0:24.3:1:32.2:1:1:0:48.2:292:1:0:1.6 0/1:190:2:1,1:95,91:0.0105:2,2:17:1:31:1:1:1.04373:41:4:0.0109:0:1.5 -7 61969090 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18546;SOR=0;LSEQ=GAGTGGAACGTCCCTTTACA;RSEQ=AGAGCAGATTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:72,74:0.0135:2,2:37.5:1:31:1:1:1.03:21:4:0.0138:0:3 0/0:195:0:0,0:98,96:0:2,0:24.7:1:30.5:1:1:0:47.2:37.8:0.9947:0:1.6 -7 61969095 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5065;SOR=Inf;LSEQ=GAACGTCCCTTTACACAGAG;RSEQ=AGATTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:72,76:0:2,0:23.6:1:31.9:1:1:0:46.6:73:0.9932:0:1.6 0/1:192:2:1,1:98,91:0.0104:2,2:22.5:1:27.5:1:1:1.07648:33:4:0.0106:0:2 -7 61969098 . A T 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26324;SOR=Inf;LSEQ=CGTCCCTTTACACAGAGCAG;RSEQ=TTTGAAACACTCTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:71,69:0:2,0:24.6:1:30.3:1:1:0:45.8:139:1:0:1.6 0/1:187:3:1,2:96,88:0.016:2,2:28:1:29.3:1:0.60927:2.17303:25.7:6:0.0162:0:4.7 -7 61969102 . G T 57 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13816;SOR=Inf;LSEQ=CCTTTACACAGAGCAGATTT;RSEQ=AAACACTCTTTTTGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:68,66:0:2,0:25.2:1:31.4:1:1:0:44.6:133:1:0:1.7 0/1:179:4:2,2:89,86:0.0223:2,2:27.5:1:28.8:1:1:1.0347:47.5:8:0.0234:0:4 -7 61969107 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51112;SOR=Inf;LSEQ=ACACAGAGCAGATTTGAAAC;RSEQ=CTCTTTTTGTGGAATTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:64,68:0:2,0:25.3:1:29.8:1:1:0:43.3:131:1:0:1.7 0/1:182:2:1,1:90,89:0.011:2,2:31.5:1:30:1:1:1.01117:27:4:0.0112:0:2.5 -7 61969109 . T C 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26255;SOR=Inf;LSEQ=ACAGAGCAGATTTGAAACAC;RSEQ=CTTTTTGTGGAATTTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:65,69:0:2,0:24.7:1:30.1:1:1:0:43.2:66:1:0:1.7 0/1:178:3:2,1:87,87:0.0169:2,2:8.7:1:29.7:1:1:1.99:46.7:6:0.0174:0:4.3 -7 61969116 . G C 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57498;SOR=0.36189;LSEQ=AGATTTGAAACACTCTTTTT;RSEQ=TGGAATTTGCAAGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:57,62:0.0165:2,2:37.5:1:33.5:1:1:1.09:40.5:4:0.0165:0:3.5 0/0:166:1:1,0:81,82:0.006:2,0:50:0:30:0:1:0:40:2:0.0061:0:4 -7 61969117 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50893;SOR=Inf;LSEQ=GATTTGAAACACTCTTTTTG;RSEQ=GGAATTTGCAAGTGGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:60,63:0:2,0:26.1:1:30:1:1:0:41.4:246:1:0:1.7 0/1:165:2:1,1:83,80:0.0121:2,2:21.5:1:29.5:1:1:1.03728:44.5:4:0.0125:0:2.5 -7 61969118 . G C 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26427;SOR=Inf;LSEQ=ATTTGAAACACTCTTTTTGT;RSEQ=GAATTTGCAAGTGGAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:59,63:0:2,0:26.2:1:31.7:1:1:0:41.2:244:1:0:1.7 0/1:165:3:1,2:84,78:0.0182:2,2:29.3:1:23:1:0.6115:2.14419:47.7:2:0.0124:0:2 -7 61969120 . AA GG 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57808;SOR=0.37165;LSEQ=TTGAAACACTCTTTTTGTGG;RSEQ=TTTGCAAGTGGAGATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:59,61:0.0164:2,2:18:1:31.5:1:1:1.03:42.5:4:0.0164:0.0082:1.5 0/0:163:1:1,0:81,81:0.0061:2,0:46:0:29:0:1:0:40:2:0.0064:0:3 -7 61969121 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.24772;LSEQ=TGAAACACTCTTTTTGTGGA;RSEQ=TTTGCAAGTGGAGATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:107:51,56:7,5:0.877:2,2:26.1:1:32.1:1:0.55247:1.53171:40.9:106:0.8833:0:1.8 1/0:160:102:54,48:27,30:0.6375:2,2:24.8:1:30.5:1:0.51327:1.25:41.9:50:0.6452:0:1.8 -7 61969126 . C T 27 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58582;SOR=0.39484;LSEQ=CACTCTTTTTGTGGAATTTG;RSEQ=AAGTGGAGATTTCAAGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:58,64:0.0161:2,2:21:1:27.5:1:1:1.10:27:4:0.0163:0:4 0/0:156:1:0,1:78,77:0.0064:2,0:3:0:27:0:1:0:49:2:0.0068:0:2 -7 61969129 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20514;SOR=0;LSEQ=TCTTTTTGTGGAATTTGCAA;RSEQ=TGGAGATTTCAAGCGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:59,67:0.0156:2,2:18:1:29:1:1:1.13:27:4:0.0157:0:4 0/0:154:0:0,0:77,77:0:2,0:24.6:1:30.6:1:1:0:42.1:37.5:1:0:1.6 -7 61969132 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.50045;SOR=Inf;LSEQ=TTTTGTGGAATTTGCAAGTG;RSEQ=AGATTTCAAGCGATTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:61,73:0:2,0:23.6:1:31:1:1:0:42.9:268:1:0:1.5 0/1:153:2:1,1:74,77:0.0131:2,2:5.5:1:29:1:1:1.04:48.5:4:0.0132:0:3 -7 61969142 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22053;SOR=0;LSEQ=TTTGCAAGTGGAGATTTCAA;RSEQ=CGATTTGATGCCAACAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:58,68:0.0156:2,2:24.5:1:31.5:1:1:1.17:40:4:0.0157:0:2.5 0/0:144:0:0,0:64,80:0:2,0:25.4:1:31.3:1:1:0:42.7:27.8:1:0:1.4 -7 61969149 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21935;SOR=0;LSEQ=GTGGAGATTTCAAGCGATTT;RSEQ=ATGCCAACAGTAGAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:59,68:0.0154:2,2:30.5:1:31:1:1:1.15:44.5:4:0.0155:0:1.5 0/0:147:0:0,0:67,80:0:2,0:24.7:1:31.1:1:1:0:42.5:48:1:0:1.3 -7 61969155 . A T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34422;SOR=0.29116;LSEQ=ATTTCAAGCGATTTGATGCC;RSEQ=ACAGTAGAAAAGGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:3:2,1:62,65:0.0231:2,2:18.3:1:31.3:1:0.61628:2.09:48.3:6:0.0233:0:2.7 0/0:147:1:0,1:70,76:0.0068:2,0:32:0:30:0:1:0:60:2:0.0069:0:2 -7 61969162 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22591;SOR=0;LSEQ=GCGATTTGATGCCAACAGTA;RSEQ=AAAAGGAAATATCTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:71,67:0.0143:2,2:36.5:1:30:1:1:1.05929:46:4:0.0145:0:2 0/0:154:0:0,0:74,80:0:2,0:23.4:1:31.2:1:1:0:43.7:76:1:0:1.1 -7 61969165 . A G 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12437;SOR=Inf;LSEQ=ATTTGATGCCAACAGTAGAA;RSEQ=AGGAAATATCTTCAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:76,67:0:2,0:23.5:1:30.2:1:1:0:44.8:286:1:0:1 0/1:158:4:2,2:78,76:0.0253:2,2:27.3:1:30:1:1:1.02615:49:8:0.0256:0:1.3 -7 61969167 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49913;SOR=Inf;LSEQ=TTGATGCCAACAGTAGAAAA;RSEQ=GAAATATCTTCAAATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:76,70:0:2,0:23.5:1:31.4:1:1:0:45:145:1:0:0.9 0/1:158:2:1,1:79,76:0.0127:2,2:39:1:29.5:1:1:1.03923:27:4:0.0127:0:4 -7 61969171 . A G 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.36005;SOR=0.31331;LSEQ=TGCCAACAGTAGAAAAGGAA;RSEQ=TATCTTCAAATAAAAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:3,0:75,73:0.0199:2,0:13:1:31.7:1:0.24583:0:37.3:6:0.0199:0:2.7 0/0:159:1:1,0:79,79:0.0063:2,0:19:0:34:0:1:0:40:2:0.0063:0:3 -7 61969177 . T G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.97023;LSEQ=CAGTAGAAAAGGAAATATCT;RSEQ=CAAATAAAAACTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:1,0:77,77:0.0065:2,0:20:0:34:0:1:0:40:2:0.0065:0:5 0/1:158:2:1,1:80,76:0.0127:2,2:29:1:30.5:1:1:1.05231:45.5:4:0.0131:0:2 -7 61969179 . AA GT 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24821;SOR=Inf;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=ATAAAAACTAGACAGAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:75,76:0:2,0:25.1:1:30.2:1:1:0:46.2:302:1:0:0.8 0/1:160:3:2,1:79,77:0.0188:2,2:10:1:28.3:1:1:1.94:27.3:6:0.0192:0.0125:0.3 -7 61969181 . A C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=AGAAAAGGAAATATCTTCAA;RSEQ=TAAAAACTAGACAGAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:74,76:0:2,0:25.7:1:30.4:1:1:0:46.4:149:1:0:0.8 0/1:163:2:1,1:82,79:0.0123:2,2:41.5:1:31:1:1:1.03775:50.5:4:0.0124:0:1.5 -7 61969184 . A G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52508;SOR=0.58586;LSEQ=AAAGGAAATATCTTCAAATA;RSEQ=AAACTAGACAGAATCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:6:3,3:72,71:0.0403:2,2:19.2:1:31.3:1:1:1.01399:48.7:12:0.0405:0:1.7 0/1:167:4:2,2:80,80:0.024:2,2:29.8:1:31.8:1:1:1:46.3:8:0.0241:0:1.5 -7 61969189 . TA CT 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25073;SOR=Inf;LSEQ=AAATATCTTCAAATAAAAAC;RSEQ=GACAGAATCATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:79,77:0:2,0:25.8:1:29.8:1:1:0:47.8:312:1:0:0.7 0/1:177:3:1,2:88,86:0.0169:2,2:11:1:28.2:1:0.62073:2.03853:27:6:0.017:0.0056:2.7 -7 61969198 . T G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5019;SOR=Inf;LSEQ=CAAATAAAAACTAGACAGAA;RSEQ=CATTCTCAGAAACTACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:84,80:0:2,0:26.3:1:30.5:1:1:0:48.9:81:1:0:0.7 0/1:193:2:0,2:95,96:0.0104:2,0:16.5:1:33.5:1:0.49752:0:50:4:0.0104:0:2.5 -7 61969200 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21034;SOR=0;LSEQ=AATAAAAACTAGACAGAATC;RSEQ=TTCTCAGAAACTACTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:83,79:0.0122:2,2:29:1:31.5:1:1:1.05034:52.5:4:0.0122:0:2.5 0/0:193:0:0,0:95,98:0:2,0:24.4:1:29.7:1:1:0:49.7:63.333:1:0:0.7 -7 61969202 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50172;SOR=Inf;LSEQ=TAAAAACTAGACAGAATCAT;RSEQ=CTCAGAAACTACTTTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:84,79:0:2,0:27:1:30.2:1:1:0:49.3:162:1:0:0.6 0/1:191:2:1,1:96,93:0.0105:2,2:34:1:29.5:1:1:1.03209:49:4:0.0107:0:2 -7 61969204 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21131;SOR=0;LSEQ=AAAACTAGACAGAATCATTC;RSEQ=CAGAAACTACTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:83,78:0.0123:2,2:36.5:1:30:1:1:1.06373:48:4:0.0123:0:1.5 0/0:191:0:0,0:96,94:0:2,0:25.7:1:29.8:1:1:0:50.4:94:1:0:0.7 -7 61969207 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5048;SOR=Inf;LSEQ=ACTAGACAGAATCATTCTCA;RSEQ=AAACTACTTTGTGATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:83,77:0:2,0:28.2:1:32.1:1:1:0:49.9:320:1:0:0.6 0/1:200:2:1,1:99,99:0.01:2,2:24:1:28.5:1:1:1:54.5:4:0.0101:0:1 -7 61969208 . A G 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63171;SOR=2.43107;LSEQ=CTAGACAGAATCATTCTCAG;RSEQ=AACTACTTTGTGATGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:1:0,1:84,76:0.0062:2,0:29:0:33:0:0.47826:0:47:2:0.0063:0:1 0/1:200:3:2,1:98,99:0.015:2,2:25.7:1:26.7:1:1:2.01:53.3:2:0.0102:0:1.3 -7 61969211 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.19631;SOR=0;LSEQ=GACAGAATCATTCTCAGAAA;RSEQ=TACTTTGTGATGTGTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:83,76:0.0123:2,2:33:1:31:1:1:1.0915:45.5:4:0.0124:0:3.5 0/0:203:0:0,0:99,100:0:2,0:25.9:1:31.5:1:1:0:50.9:198:0.9802:0:0.7 -7 61969213 . A T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65999;SOR=0.53557;LSEQ=CAGAATCATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:1,2:84,76:0.0182:2,2:36.3:1:29.7:1:0.60701:2.20013:46:6:0.0185:0:2.7 0/0:204:2:1,1:98,100:0.0098:2,2:29.5:1:27:0:1:1.02:48:4:0.0099:0:2.5 -7 61969214 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19792;SOR=0;LSEQ=AGAATCATTCTCAGAAACTA;RSEQ=TTTGTGATGTGTGCCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:86,79:0.0119:2,2:38.5:1:31:1:1:1.08804:45.5:4:0.012:0:1 0/0:209:0:0,0:106,103:0:2,0:25.7:1:31.4:1:1:0:51.3:103.5:1:0:0.7 -7 61969225 . G C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.25374;SOR=Inf;LSEQ=CAGAAACTACTTTGTGATGT;RSEQ=TGCCTTCAACTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:91,88:0:2,0:25:1:32.3:1:1:0:50.3:178:1:0:0.6 0/1:213:3:1,2:107,103:0.0141:2,2:38.3:1:32.7:1:0.61795:2.07078:48.3:6:0.0142:0:2 -7 61969228 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20429;SOR=0;LSEQ=AAACTACTTTGTGATGTGTG;RSEQ=CTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:86,89:0.0113:2,2:19.5:1:28.5:1:1:1.03:53.5:4:0.0114:0:1 0/0:214:0:0,0:105,106:0:2,0:27:1:31.5:1:1:0:51.8:51.75:0.9857:0:0.7 -7 61969229 . C G 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1345;SOR=5.01691;LSEQ=AACTACTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:1:0,1:87,90:0.0056:2,0:34:0:34:0:1:0:45:2:0.0057:0:4 0/1:217:6:3,3:102,103:0.0276:2,2:28.5:1:30.8:1:1:1.01:32.7:12:0.0279:0:3.3 -7 61969232 . C T 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08079;SOR=0.24751;LSEQ=TACTTTGTGATGTGTGCCTT;RSEQ=AACTCACAGAGTTTAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:6:3,3:84,84:0.0345:2,2:26.2:1:27.5:1:1:1:46.2:12:0.0345:0:1.2 0/0:229:2:2,0:111,114:0.0087:2,0:22:1:31.5:1:0.2467:0:60:4:0.0087:0:1.5 -7 61969234 . A G 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.26366;SOR=Inf;LSEQ=CTTTGTGATGTGTGCCTTCA;RSEQ=CTCACAGAGTTTAACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:87,89:0:2,0:24.8:1:30.1:1:1:0:49.9:352:1:0:0.8 0/1:235:3:1,2:116,115:0.0128:2,2:5.3:1:26.3:1:1:2.01156:45.7:2:0.0085:0:1.7 -7 61969240 . A C 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00098;SOR=0;LSEQ=GATGTGTGCCTTCAACTCAC;RSEQ=GAGTTTAACCTTTCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:8:4,4:81,84:0.046:2,2:23:1:28.3:1:1:1.04:39.6:7:0.0405:0:3.4 0/0:235:0:0,0:119,114:0:2,0:25.2:1:30.5:1:1:0:50.8:115.5:0.9914:0:0.9 -7 61969243 . G C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26567;SOR=Inf;LSEQ=GTGTGCCTTCAACTCACAGA;RSEQ=TTTAACCTTTCTTTTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:85,89:0:2,0:24.1:1:32.3:1:1:0:49.7:348:0.9943:0:0.9 0/1:238:3:2,1:122,113:0.0126:2,2:30:1:30.3:1:1:1.85:55.7:6:0.0126:0:2 -7 61969246 . T C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74341;SOR=0.87966;LSEQ=TGCCTTCAACTCACAGAGTT;RSEQ=AACCTTTCTTTTCTTAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:19:11,8:78,84:0.105:2,2:20:1:31.4:1:0.47355:1.48:49.8:38:0.1056:0:1.4 0/1:246:23:15,8:113,110:0.0935:2,2:19.7:1:30.7:1:0.19715:1.82:51.4:22:0.0905:0:1.6 -7 61969248 . A T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07081;SOR=0;LSEQ=CCTTCAACTCACAGAGTTTA;RSEQ=CCTTTCTTTTCTTAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:3:2,1:85,88:0.017:2,2:20.3:1:28.3:1:0.61857:2.06:48.3:6:0.0171:0:1 0/0:248:0:0,0:127,121:0:2,0:23.3:1:29.9:1:1:0:50.6:247:1:0:0.9 -7 61969261 . T G 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05716;SOR=0.25345;LSEQ=GAGTTTAACCTTTCTTTTCT;RSEQ=AGAGCAGTTTAGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:8:3,5:78,83:0.0473:2,2:22.4:1:27.4:1:0.72186:1.56219:41.5:3:0.0361:0:3.8 0/1:242:3:2,1:116,122:0.0124:2,2:27.3:1:30.7:1:0.61573:2.10:34:6:0.0124:0:4.7 -7 61969266 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1602;SOR=0;LSEQ=TAACCTTTCTTTTCTTAGAG;RSEQ=AGTTTAGAAACACTCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:76,80:0.0127:2,2:16:1:28.5:1:1:1.05:34.5:4:0.0127:0:4 0/0:236:0:0,0:115,119:0:2,0:23.9:1:31.8:1:1:0:52.4:116:0.9915:0:1.1 -7 61969269 . T C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08737;SOR=0.42234;LSEQ=CCTTTCTTTTCTTAGAGCAG;RSEQ=TTAGAAACACTCTGCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:11:4,7:73,73:0.0696:2,2:22.9:1:32.3:1:0.53468:1.74389:47.8:22:0.0701:0:2.7 0/1:229:7:3,4:106,114:0.0306:2,2:20.6:1:31:1:1:1.2386:48.9:14:0.0307:0:4.1 -7 61969270 . T A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.27206;SOR=Inf;LSEQ=CTTTCTTTTCTTAGAGCAGT;RSEQ=TAGAAACACTCTGCTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:80,81:0:2,0:25:1:30.4:1:1:0:52.6:322:1:0:1.2 0/1:231:3:1,2:110,118:0.013:2,2:24:1:29.7:1:1:1.85958:53:6:0.0131:0:3 -7 61969272 . A G 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14633;SOR=Inf;LSEQ=TTCTTTTCTTAGAGCAGTTT;RSEQ=GAAACACTCTGCTTGTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:83,79:0:2,0:25:1:29.9:1:1:0:52.9:324:1:0:1.2 0/1:231:4:1,3:110,116:0.0173:2,2:24:1:30.5:1:0.62263:2.83333:46.8:8:0.0174:0:3 -7 61969276 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1787;SOR=0;LSEQ=TTTCTTAGAGCAGTTTAGAA;RSEQ=CACTCTGCTTGTTATGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:83,81:0.012:2,2:33.5:1:30.5:1:1:1.02455:54.5:4:0.0123:0:1.5 0/0:226:0:0,0:111,115:0:2,0:24.9:1:29.6:1:1:0:53.1:225:1:0:1.3 -7 61969279 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.26503;SOR=Inf;LSEQ=CTTAGAGCAGTTTAGAAACA;RSEQ=TCTGCTTGTTATGTCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:84,83:0:2,0:24.7:1:32.2:1:1:0:53.7:166:1:0:1.3 0/1:226:3:1,2:108,113:0.0133:2,2:24.7:1:28.3:1:1:1.90619:53.7:6:0.0133:0:1.7 -7 61969287 . G C 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18064;LSEQ=AGTTTAGAAACACTCTGCTT;RSEQ=TTATGTCTGCAAGTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:78,85:0.0121:2,2:13.5:1:33:0:1:1.09:23:4:0.0123:0:2.5 0/1:210:3:2,1:99,104:0.0143:2,2:29.3:1:30:1:0.61593:2.09:40.7:6:0.0146:0:2.3 -7 61969288 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19237;SOR=0;LSEQ=GTTTAGAAACACTCTGCTTG;RSEQ=TATGTCTGCAAGTGGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:77,84:0.0123:2,2:22.5:1:30.5:1:1:1.09:60:4:0.0123:0:3 0/0:208:0:0,0:103,104:0:2,0:25.3:1:29.6:1:1:0:53.1:102.5:0.9951:0:1.4 -7 61969289 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19369;SOR=0;LSEQ=TTTAGAAACACTCTGCTTGT;RSEQ=ATGTCTGCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:77,85:0.0122:2,2:19:1:28:1:1:1.10:45.5:4:0.0123:0:2.5 0/0:208:0:0,0:103,104:0:2,0:25.1:1:28.9:1:1:0:53.1:414:1:0:1.4 -7 61969291 . T C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20034;SOR=0.47973;LSEQ=TAGAAACACTCTGCTTGTTA;RSEQ=GTCTGCAAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:10:7,3:72,83:0.0595:2,2:21.3:1:29.6:1:0.19689:2.67:50.2:9:0.0542:0:1.8 0/1:204:6:2,4:100,94:0.0294:2,2:24.5:1:30.7:1:0.43801:2.11988:60:12:0.0294:0:1.3 -7 61969293 . T A 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46477;SOR=2.073;LSEQ=GAAACACTCTGCTTGTTATG;RSEQ=CTGCAAGTGGATATTTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:0,2:78,84:0.0122:2,0:26.5:1:29:1:0.49813:0:60:4:0.0124:0:1.5 0/1:200:5:3,2:100,95:0.025:2,2:17.8:1:28.2:1:1:1.42:56.4:10:0.025:0:2.2 -7 61969295 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5025;SOR=Inf;LSEQ=AACACTCTGCTTGTTATGTC;RSEQ=GCAAGTGGATATTTGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:81,85:0:2,0:25:1:30.9:1:1:0:54.2:332:1:0:1.6 0/1:198:2:0,2:101,95:0.0101:2,0:25.5:1:31:0:0.23873:0:50:4:0.0102:0:5 -7 61969299 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19898;SOR=0;LSEQ=CTCTGCTTGTTATGTCTGCA;RSEQ=GTGGATATTTGGACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:83,83:0.0119:2,2:11.5:1:33.5:1:1:1:60:4:0.012:0:3 0/0:208:0:0,0:105,101:0:2,0:23.9:1:30.1:1:1:0:53.3:102:0.9903:0:1.6 -7 61969302 . G T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93468;LSEQ=TGCTTGTTATGTCTGCAAGT;RSEQ=GATATTTGGACCTCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:6:3,3:82,78:0.0359:2,2:22.3:1:31.8:1:1:1.05099:48.5:12:0.0361:0:4 0/1:208:7:3,4:102,99:0.0337:2,2:28.9:1:30.1:1:0.71987:1.37165:48.9:14:0.0338:0:4.1 -7 61969310 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18989;SOR=0;LSEQ=ATGTCTGCAAGTGGATATTT;RSEQ=GACCTCTTTGAGGGCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:81,81:0.0121:2,2:6.5:1:29:1:1:1:60:4:0.0123:0:2 0/0:213:0:0,0:110,100:0:2,0:22.7:1:30.3:1:1:0:53.9:41:0.9951:0:1.8 -7 61969323 . GG AC 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.65218;LSEQ=GATATTTGGACCTCTTTGAG;RSEQ=CTTCGTTGCAAACGGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:0,1:85,73:0.0063:2,0:29:0:31.5:0:0.46541:0:60:2:0.0064:0:1 0/1:193:2:2,0:96,94:0.0104:2,0:27.5:1:31:1:0.4976:0:60:4:0.0107:0:4 -7 61969324 . G C 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73653;SOR=0.62659;LSEQ=ATATTTGGACCTCTTTGAGG;RSEQ=CTTCGTTGCAAACGGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:158:155:81,74:1,0:0.981:0,2:25.4:1:31.7:1:1:0:54.6:76.5:0.9935:0:2.1 1/1:200:194:96,98:0,0:0.97:0,2:23.6:1:30.9:1:1:0:54.1:47.5:0.9896:0:2.1 -7 61969331 . T G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19224;SOR=0;LSEQ=GACCTCTTTGAGGGCTTCGT;RSEQ=GCAAACGGGGTTTCTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:85,72:0.0126:2,2:38:1:31.5:1:1:1.17932:27:4:0.0127:0:5 0/0:203:0:0,0:102,101:0:2,0:23.2:1:29.7:1:1:0:55.4:100.5:1:0:2.2 -7 61969334 . A T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50348;SOR=Inf;LSEQ=CTCTTTGAGGGCTTCGTTGC;RSEQ=AACGGGGTTTCTTCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:89,74:0:2,0:24.5:1:30.2:1:1:0:55.9:326:0.9879:0:2.1 0/1:201:2:1,1:100,99:0.01:2,2:19.5:1:27.5:1:1:1.01005:42.5:4:0.0101:0:6.5 -7 61969338 . G A 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.58647;SOR=0.3961;LSEQ=TTGAGGGCTTCGTTGCAAAC;RSEQ=GGGTTTCTTCCTTTCATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:88,74:0.0122:2,2:28.5:1:32:0:1:1.18792:60:4:0.0122:0:3 0/0:206:1:0,1:102,103:0.0049:2,0:6:0:33:0:1:0:21:2:0.005:0:2 -7 61969341 . G A 73 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24837;SOR=0.31055;LSEQ=AGGGCTTCGTTGCAAACGGG;RSEQ=TTTCTTCCTTTCATGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:5:3,2:87,73:0.0301:2,2:28.8:1:31.8:1:1:1.26:32.2:10:0.0305:0:5.2 0/0:210:2:0,2:105,102:0.0095:2,0:13.5:1:29.5:1:0.24641:0:33.5:4:0.0096:0:3 -7 61969349 . C A 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.6313;SOR=2.4451;LSEQ=GTTGCAAACGGGGTTTCTTC;RSEQ=TTTCATGCTAGACTAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:1:0,1:91,74:0.006:2,0:17:0:33:0:0.45181:0:40:2:0.006:0:8 0/1:205:3:1,2:101,101:0.0146:2,2:17.7:1:29.7:1:1:1.99349:41.3:6:0.0149:0:5.7 -7 61969353 . C A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22103;SOR=0.73651;LSEQ=CAAACGGGGTTTCTTCCTTT;RSEQ=ATGCTAGACTAAGAAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:44:29,15:63,62:0.2604:2,2:23.4:1:28.6:1:0.08155:1.90:52.9:43:0.256:0:3 0/1:209:43:20,23:85,78:0.2057:2,2:25:1:29.1:1:0.60744:1.25182:57:86:0.2129:0:3.1 -7 61969369 . G T 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.66183;SOR=0.54689;LSEQ=CTTTCATGCTAGACTAAGAA;RSEQ=AGTTCTCAGGAACTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:2,1:89,82:0.0171:2,2:25.7:1:30.7:1:1:1.84:45.3:6:0.0171:0:3 0/0:212:2:1,1:108,102:0.0094:2,2:29:0:28:1:1:1.05856:60:4:0.0096:0:3.5 -7 61969370 . A T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.84725;LSEQ=TTTCATGCTAGACTAAGAAG;RSEQ=GTTCTCAGGAACTTTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:3:1,2:92,85:0.0167:2,2:27.3:1:30:1:0.61063:2.15574:60:6:0.0168:0:2.7 0/1:212:3:1,2:107,100:0.0142:2,2:41.7:1:28.3:1:0.61265:2.1325:60:6:0.0144:0:4.7 -7 61969371 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62857;SOR=2.54592;LSEQ=TTCATGCTAGACTAAGAAGA;RSEQ=TTCTCAGGAACTTTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:1:1,0:92,90:0.0055:2,0:3:0:30:0:1:0:49:2:0.0055:0:2 0/1:217:3:3,0:110,102:0.0138:2,0:5:1:28.7:1:0.24847:0:40:6:0.0139:0:3.3 -7 61969372 . T A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12797;SOR=Inf;LSEQ=TCATGCTAGACTAAGAAGAG;RSEQ=TCTCAGGAACTTTTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:91,91:0:2,0:23.7:1:29.7:1:1:0:55.3:59.667:1:0:2 0/1:215:4:3,1:111,100:0.0186:2,2:12:1:23.5:1:0.62426:2.69:60:3:0.0144:0:4 -7 61969374 . C T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25206;SOR=Inf;LSEQ=ATGCTAGACTAAGAAGAGTT;RSEQ=TCAGGAACTTTTTTGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:94,92:0:2,0:23.6:1:31.6:1:1:0:55.2:61:1:0:2 0/1:215:3:1,2:112,100:0.014:2,2:30.3:1:30.7:1:0.60483:2.23187:54.7:6:0.0143:0:4.7 -7 61969376 . C G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21746;SOR=0;LSEQ=GCTAGACTAAGAAGAGTTCT;RSEQ=AGGAACTTTTTTGTGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:93,89:0.0109:2,2:43.5:1:32.5:1:1:1.04471:60:4:0.0109:0:3.5 0/0:210:0:0,0:112,98:0:2,0:24.7:1:31.5:1:1:0:57.2:104:1:0:2 -7 61969379 . G T 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07372;SOR=0.16206;LSEQ=AGACTAAGAAGAGTTCTCAG;RSEQ=AACTTTTTTGTGTTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:185:184:93,91:0,0:0.9946:0,2:24.4:1:29.1:1:1:0:55:91:0.9945:0:1.9 1/1:215:208:111,97:0,0:0.9674:0,2:24.2:1:28.8:1:1:0:57.1:103:0.9671:0:1.9 -7 61969382 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.217;SOR=0;LSEQ=CTAAGAAGAGTTCTCAGGAA;RSEQ=TTTTTTGTGTTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:93,92:0.0106:2,2:25:1:30.5:1:1:1.01081:27:4:0.0107:0:4.5 0/0:215:0:0,0:113,100:0:2,0:23.9:1:31.5:1:1:0:56.8:212:1:0:1.9 -7 61969385 . T C 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.37593;SOR=3.61083;LSEQ=AGAAGAGTTCTCAGGAACTT;RSEQ=TTTGTGTTGTGTGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:1:1,0:98,93:0.0052:2,0:14:0:32:0:1:0:45:2:0.0053:0:4 0/1:215:4:1,3:114,95:0.0186:2,2:5:1:31.3:1:0.33606:3.57985:39.3:8:0.0192:0:3 -7 61969387 . T C 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.69031;SOR=1.73727;LSEQ=AAGAGTTCTCAGGAACTTTT;RSEQ=TGTGTTGTGTGTATTCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:0,2:100,87:0.0106:2,0:13.5:1:32.5:1:0.22042:0:60:4:0.0106:0:3.5 0/1:219:4:2,2:118,97:0.0183:2,2:18.3:1:32.3:1:1:1.2154:54.5:8:0.0188:0:2.5 -7 61969389 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21293;SOR=0;LSEQ=GAGTTCTCAGGAACTTTTTT;RSEQ=TGTTGTGTGTATTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:99,88:0.0106:2,2:13.5:1:27.5:1:1:1.1243:51:4:0.0106:0:2.5 0/0:220:0:0,0:122,98:0:2,0:23.7:1:31.3:1:1:0:56.6:72.333:1:0:1.8 -7 61969397 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.21041;SOR=0;LSEQ=AGGAACTTTTTTGTGTTGTG;RSEQ=GTATTCAACTCACAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:92,87:0.011:2,2:33:1:29:1:1:1.05717:51:4:0.0111:0:2 0/0:213:0:0,0:115,98:0:2,0:24.6:1:29.7:1:1:0:56.4:212:1:0:1.7 -7 61969399 . T C 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31793;LSEQ=GAACTTTTTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:94,88:0.0109:2,2:35:1:30.5:1:1:1.06777:35.5:4:0.0109:0:5.5 0/1:210:3:1,2:113,94:0.0143:2,2:24.3:1:34:0:0.59361:2.39446:46.3:6:0.0144:0:4.7 -7 61969408 . C A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62662;SOR=2.63344;LSEQ=TGTGTTGTGTGTATTCAACT;RSEQ=ACAGAGTTGAACCTTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:1,0:92,91:0.0054:2,0:1:0:27:0:1:0:53:2:0.0055:0:2 0/1:211:3:1,2:108,99:0.0142:2,2:28.3:1:28.3:1:0.60928:2.17399:59.7:6:0.0144:0:2 -7 61969413 . A T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.22296;SOR=0;LSEQ=TGTGTGTATTCAACTCACAG;RSEQ=GTTGAACCTTGCTTTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:0,2:89,91:0.0109:2,0:14:1:28.5:1:0.49748:0:50:4:0.0111:0:5 0/0:204:0:0,0:106,97:0:2,0:25.7:1:29.3:1:1:0:55.9:66.667:0.995:0:1.3 -7 61969415 . T A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24919;SOR=Inf;LSEQ=TGTGTATTCAACTCACAGAG;RSEQ=TGAACCTTGCTTTAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:90,93:0:2,0:26.7:1:30.3:1:1:0:54.3:366:1:0:1.3 0/1:198:3:2,1:101,93:0.0152:2,2:25:1:29.7:1:1:1.84:48:6:0.0155:0:4.7 -7 61969416 . T G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.91564;LSEQ=GTGTATTCAACTCACAGAGT;RSEQ=GAACCTTGCTTTAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:90,94:0.0108:2,2:18:1:29.5:1:1:1.04:35.5:4:0.0108:0:5.5 0/0:203:2:1,1:101,100:0.0099:2,2:5:0:32.5:1:1:1.00995:47.5:4:0.0101:0:3.5 -7 61969422 . T C 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00214;SOR=0;LSEQ=TCAACTCACAGAGTTGAACC;RSEQ=TGCTTTAGAGAGAGCAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:8:3,5:80,92:0.0444:2,2:30.4:1:30.9:1:0.72723:1.44635:52.8:16:0.0447:0:1.9 0/0:204:0:0,0:101,103:0:2,0:43:0:16:0:1:0:60:0:0:0:2 -7 61969424 . G T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99312;LSEQ=AACTCACAGAGTTGAACCTT;RSEQ=CTTTAGAGAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:5:2,3:79,88:0.0289:2,2:30.2:1:31:1:1:1.34429:49.4:10:0.0291:0:3.8 0/1:209:6:3,3:98,103:0.0287:2,2:23:1:31:1:1:1.05:43.5:12:0.029:0:2.3 -7 61969428 . T C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25509;SOR=Inf;LSEQ=CACAGAGTTGAACCTTGCTT;RSEQ=AGAGAGAGCAGATTTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:81,97:0:2,0:25.5:1:29.1:1:1:0:53.9:177:1:0:1.1 0/1:216:3:1,2:105,108:0.0139:2,2:36:1:31.3:1:1:1.93869:45:6:0.014:0:5 -7 61969441 . T G 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72797;SOR=0.73876;LSEQ=CTTGCTTTAGAGAGAGCAGA;RSEQ=TTGAAACACTCTTGCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:4:2,2:77,95:0.0227:2,2:26.8:1:32.5:1:1:1.23:51.8:8:0.0229:0:2.8 0/1:237:4:2,2:114,118:0.0169:2,2:13:0:32.5:1:1:1.03:35.3:8:0.0174:0:2.8 -7 61969450 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.17841;SOR=0;LSEQ=GAGAGAGCAGATTTGAAACA;RSEQ=TCTTGCTGTGGCATTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:77,97:0.0114:2,2:40.5:1:30:1:1:1.26:60:4:0.0116:0:2 0/0:240:0:0,0:119,121:0:2,0:23.4:1:30.9:1:1:0:56.3:79:1:0:0.8 -7 61969454 . T C 110 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00262;SOR=0.16701;LSEQ=GAGCAGATTTGAAACACTCT;RSEQ=GCTGTGGCATTTTCAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:12:4,8:72,83:0.0719:2,2:20.6:1:30.9:1:0.54954:1.72942:45.8:24:0.0723:0:2.4 0/1:236:3:2,1:114,115:0.0127:2,2:23.7:1:30.3:1:1:2.01:46:6:0.0129:0:2 -7 61969455 . G A 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06795;SOR=0;LSEQ=AGCAGATTTGAAACACTCTT;RSEQ=CTGTGGCATTTTCAGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:3:2,1:74,86:0.0184:2,2:29.7:1:26.7:1:0.59874:2.31:54.3:6:0.0186:0:2 0/0:235:0:0,0:116,117:0:2,0:24.5:1:31.4:1:1:0:56.6:76.667:0.9914:0:0.7 -7 61969456 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69428;LSEQ=GCAGATTTGAAACACTCTTG;RSEQ=TGTGGCATTTTCAGGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:78,85:0.0121:2,2:6.5:1:29.5:1:1:1.09:59.5:4:0.0123:0:1.5 0/0:237:2:0,2:117,116:0.0084:2,0:39:1:29.5:1:0.49787:0:42.5:4:0.0087:0:1 -7 61969458 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27336;SOR=Inf;LSEQ=AGATTTGAAACACTCTTGCT;RSEQ=TGGCATTTTCAGGTGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:80,85:0:2,0:24:1:31.8:1:1:0:54.4:81.5:1:0:0.8 0/1:239:3:1,2:119,117:0.0126:2,2:30.7:1:30:1:0.62184:2.02836:60:6:0.0128:0:1 -7 61969462 . C A 108 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01456;SOR=0.29064;LSEQ=TTGAAACACTCTTGCTGTGG;RSEQ=ATTTTCAGGTGGAGATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:13:5,8:70,72:0.0823:2,2:22.8:1:29.2:1:0.56679:1.55118:41.6:12:0.0784:0:2.2 0/1:237:6:5,1:115,115:0.0253:2,2:22.3:1:28.5:1:0.21315:4.97:42:12:0.0259:0:2.7 -7 61969468 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29047;SOR=Inf;LSEQ=CACTCTTGCTGTGGCATTTT;RSEQ=AGGTGGAGATTTCAAGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:72,79:0:2,0:25.7:1:31.4:1:1:0:54.5:74.5:1:0:0.6 0/1:245:3:1,2:120,120:0.0122:2,2:33.7:1:29:1:1:1.9945:60:6:0.0127:0:2 -7 61969471 . G C 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63471;SOR=0.60423;LSEQ=TCTTGCTGTGGCATTTTCAG;RSEQ=TGGAGATTTCAAGCGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:71,72:0.0138:2,2:6:0:34:0:1:1.01:48:4:0.014:0:2.5 0/0:239:2:1,1:115,119:0.0084:2,2:33:0:33.5:1:1:1.03:60:4:0.0087:0:2.5 -7 61969478 . T A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02088;SOR=0;LSEQ=GTGGCATTTTCAGGTGGAGA;RSEQ=TTCAAGCGATTTGAGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:4:2,2:69,72:0.0276:2,2:37:1:25.5:1:1:1.04:60:3:0.021:0:1 0/0:234:0:0,0:109,124:0:2,0:25.5:1:29.8:1:1:0:56.1:57.25:1:0:0.5 -7 61969484 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15467;SOR=0;LSEQ=TTTTCAGGTGGAGATTTCAA;RSEQ=CGATTTGAGGACAATTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:69,75:0.0136:2,2:29:0:32:1:1:1.09:60:4:0.0139:0:2 0/0:226:0:0,0:104,122:0:2,0:26.4:1:32:1:1:0:55.5:112:1:0:0.6 -7 61969487 . A T 26 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.64707;SOR=0.64397;LSEQ=TCAGGTGGAGATTTCAAGCG;RSEQ=TTTGAGGACAATTGCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:70,76:0.0135:2,2:26:0:32:0:1:1.09:60:4:0.0136:0:2 0/0:229:2:0,2:104,122:0.0087:2,0:24:1:26.5:1:0.50166:0:43:4:0.009:0:2.5 -7 61969488 . T C 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6431;SOR=0.63125;LSEQ=CAGGTGGAGATTTCAAGCGA;RSEQ=TTGAGGACAATTGCAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:69,76:0.0136:2,2:23:0:33.5:1:1:1.10:48:4:0.0138:0:2.5 0/0:232:2:1,1:105,125:0.0086:2,2:16:0:33.5:1:1:1.19:60:4:0.0088:0:2.5 -7 61969501 . G A 73 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08619;SOR=Inf;LSEQ=CAAGCGATTTGAGGACAATT;RSEQ=CAGAAAAGGAAATATCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:70,82:0:2,0:23.3:1:32.1:1:1:0:54.9:75:1:0:0.5 0/1:244:6:2,4:115,120:0.0246:2,2:18.2:1:28.5:1:0.68436:1.91169:50.5:12:0.0248:0:1.2 -7 61969502 . C T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.95461;LSEQ=AAGCGATTTGAGGACAATTG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:0,1:72,82:0.0065:2,0:1:0:28:0:1:0:55:2:0.0066:0:1 0/1:239:3:1,2:116,120:0.0126:2,2:10.7:1:25.7:1:1:1.92821:52.7:6:0.0126:0:3 -7 61969504 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56428;SOR=0.32251;LSEQ=GCGATTTGAGGACAATTGCA;RSEQ=AAAAGGAAATATCTTCGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:74,81:0.0127:2,2:20:1:28.5:1:1:1.09:54:4:0.0128:0:2 0/0:242:1:1,0:121,119:0.0041:2,0:1:0:25:0:1:0:60:2:0.0041:0:2 -7 61969513 . A C 67 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21337;SOR=0.31361;LSEQ=GGACAATTGCAGAAAAGGAA;RSEQ=TATCTTCGTATAATAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:4:2,2:82,80:0.0241:2,2:25.3:1:33.5:1:1:1.02485:57.3:8:0.0242:0:1 0/0:261:2:1,1:128,131:0.0077:2,2:1:0:31.5:1:1:1.02:60:4:0.0077:0:1.5 -7 61969515 . A T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.05917;SOR=0;LSEQ=ACAATTGCAGAAAAGGAAAT;RSEQ=TCTTCGTATAATAACCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:3:1,2:84,80:0.018:2,2:17.3:1:32:0:0.61601:2.09099:60:6:0.0182:0:1.3 0/0:260:0:0,0:130,130:0:2,0:22.3:1:29:1:1:0:55:259:1:0:0.6 -7 61969527 . T C 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.6523;SOR=2.69934;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACCAGACAGAATCATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:1:1,0:86,78:0.006:2,0:41:0:33:0:1:0:37:2:0.0061:0:1 0/1:248:4:2,2:125,117:0.0161:2,2:11.3:1:31.3:1:1:1.06806:41.5:8:0.0163:0:3 -7 61969531 . C G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15388;SOR=0;LSEQ=AAATATCTTCGTATAATAAC;RSEQ=AGACAGAATCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:81,74:0.0127:2,2:32:0:32.5:1:1:1.09396:50:4:0.0129:0:1 0/0:244:0:0,0:124,119:0:2,0:23.9:1:30.6:1:1:0:54:59.75:0.9958:0:0.6 -7 61969557 . T G 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07273;SOR=0;LSEQ=GAATCATTCTCAGAAAGTGC;RSEQ=TTGTGATGTGTGCGTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:1,2:57,79:0.0214:2,2:32.3:1:33:1:1:1.43938:52:6:0.0217:0:1 0/0:194:0:0,0:85,109:0:2,0:27.5:1:29.9:1:1:0:51.4:63.667:1:0:0.7 -7 61969560 . G C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5104;SOR=Inf;LSEQ=TCATTCTCAGAAAGTGCTTT;RSEQ=TGATGTGTGCGTTCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:57,80:0:2,0:28.2:1:31.7:1:1:0:51.5:44.667:1:0:0.4 0/1:187:2:1,1:78,105:0.0107:2,2:42:0:32:0:1:1.34:60:4:0.0108:0:1.5 -7 61969561 . T A 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57639;SOR=0.366;LSEQ=CATTCTCAGAAAGTGCTTTG;RSEQ=GATGTGTGCGTTCAACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:55,80:0.0146:2,2:41:1:31:1:1:1.45:60:4:0.0148:0:1 0/0:186:1:1,0:78,105:0.0054:2,0:1:0:26:0:0.42935:0:52:2:0.0054:0:1 -7 61969568 . T C 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13513;SOR=Inf;LSEQ=AGAAAGTGCTTTGTGATGTG;RSEQ=GCGTTCAACTCACAGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:52,79:0:2,0:27.3:1:29.7:1:1:0:51.1:130:1:0:0.5 0/1:170:4:1,3:67,98:0.0235:2,2:15:1:31:1:0.64922:2.04314:54.5:8:0.024:0:1 -7 61969569 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50736;SOR=Inf;LSEQ=GAAAGTGCTTTGTGATGTGT;RSEQ=CGTTCAACTCACAGAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:51,78:0:2,0:27.4:1:31.9:1:1:0:51.1:258:1:0:0.5 0/1:169:2:1,1:67,99:0.0118:2,2:43:1:30.5:1:1:1.47:47:4:0.0122:0:3.5 -7 61969570 . C T 41 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15398;LSEQ=AAAGTGCTTTGTGATGTGTG;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:49,78:0.0155:2,2:32:1:31:1:1:1.59:31:4:0.0156:0:3 0/1:168:3:1,2:67,98:0.0179:2,2:18:1:26.3:1:1:1.36489:49:2:0.0121:0:1.7 -7 61969571 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50718;SOR=Inf;LSEQ=AAGTGCTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:48,79:0:2,0:27:1:30.9:1:1:0:51:254:1:0:0.5 0/1:166:2:1,1:65,96:0.012:2,2:16:0:32:1:1:1.47:60:4:0.0123:0:3 -7 61969572 . T C 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13532;SOR=Inf;LSEQ=AGTGCTTTGTGATGTGTGCG;RSEQ=TCAACTCACAGAGTTTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:48,78:0:2,0:26.9:1:29.5:1:1:0:51:125:1:0:0.5 0/1:164:4:2,2:63,96:0.0244:2,2:24:1:32.3:1:1:1.52:55:8:0.0247:0:1.3 -7 61969575 . A C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.28634;SOR=0.51579;LSEQ=GCTTTGTGATGTGTGCGTTC;RSEQ=ACTCACAGAGTTTAACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:9:4,5:42,73:0.0726:2,2:28.1:1:31.7:1:0.72522:1.39:55.8:18:0.0726:0:1 0/1:155:6:3,3:59,90:0.0387:2,2:18.7:1:33:1:0.68384:1.52:52.3:12:0.0387:0:2.5 -7 61969584 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19087;SOR=0;LSEQ=TGTGTGCGTTCAACTCACAG;RSEQ=GTTTAACCTTTCTTTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:39,72:0.0177:2,2:32:1:30:1:1:1.84:50:4:0.0182:0:1.5 0/0:145:0:0,0:56,89:0:2,0:22.5:1:29.9:1:1:0:50.8:290:1:0:0.8 -7 61969586 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19063;SOR=0;LSEQ=TGTGCGTTCAACTCACAGAG;RSEQ=TTAACCTTTCTTTTCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:37,70:0.0183:2,2:32.5:1:31.5:1:1:1.88:31:4:0.0185:0:3 0/0:140:0:0,0:54,86:0:2,0:22.1:1:29.3:1:1:0:50.6:45.667:1:0:0.8 -7 61969588 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50126;SOR=Inf;LSEQ=TGCGTTCAACTCACAGAGTT;RSEQ=AACCTTTCTTTTCATAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:35,70:0:2,0:24.8:1:28.6:1:1:0:49.7:210:1:0:0.7 0/1:124:2:1,1:44,78:0.0161:2,2:15:1:29.5:1:1:1.76:60:4:0.0161:0:2 -7 61969590 . A C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50002;SOR=Inf;LSEQ=CGTTCAACTCACAGAGTTTA;RSEQ=CCTTTCTTTTCATAGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:35,69:0:2,0:24.1:1:29.7:1:1:0:49.4:208:1:0:0.7 0/1:119:2:1,1:41,76:0.0168:2,2:40:1:31:1:1:1.84:47:4:0.0168:0:1 -7 61969593 . T A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22579;SOR=0;LSEQ=TCAACTCACAGAGTTTAACC;RSEQ=TTCTTTTCATAGAGGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:34,65:0.0198:2,2:22:1:32:1:1:1.90:39.5:4:0.0202:0:1.5 0/0:111:0:0,0:37,74:0:2,0:23.4:1:30:1:1:0:49.3:222:1:0:0.9 -7 61969602 . A T 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.82399;LSEQ=AGAGTTTAACCTTTCTTTTC;RSEQ=TAGAGGAGTTTGGAAACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:1:0,1:27,59:0.0115:2,0:28:0:32:0:1:0:40:2:0.0116:0:3 0/1:96:2:1,1:25,69:0.0208:2,2:12:1:32.5:1:0.47039:2.73:52.5:4:0.0211:0:3.5 -7 61969608 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49743;SOR=Inf;LSEQ=TAACCTTTCTTTTCATAGAG;RSEQ=AGTTTGGAAACACACTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:15,56:0:2,0:23.5:1:31.2:1:1:0:45.9:142:1:0:0.9 0/1:77:2:1,1:13,62:0.026:2,2:6:1:31.5:1:0.33254:4.63:52.5:4:0.026:0:3.5 -7 61969611 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.3046;LSEQ=CCTTTCTTTTCATAGAGGAG;RSEQ=TTGGAAACACACTGTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:0,2:11,50:0.0317:2,0:17:1:33.5:1:1:0:44.5:4:0.0323:0:2 0/1:73:3:1,2:11,59:0.0411:2,2:18:1:31.7:1:0.42135:2.63:34:6:0.0411:0:1.7 -7 61969633 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49333;SOR=0;LSEQ=TGGAAACACACTGTTTGTAA;RSEQ=GTCTGCAAGTGGAAATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:0,2:0,36:0.0526:1,0:5:1:31:0:1:0:40:4:0.0526:0:1.5 0/0:37:0:0,0:1,32:0:1,0:24:1:31.2:1:1:0:40:32:0.8889:0:1.4 -7 61969635 . T A 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1148;SOR=Inf;LSEQ=GAAACACACTGTTTGTAAAG;RSEQ=CTGCAAGTGGAAATATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:0:1,0:22.7:1:30.9:1:1:0:38.9:72:1:0:1.4 0/1:37:4:0,4:1,32:0.1081:1,0:27.8:1:30.3:1:1:0:40:8:0.1081:0:3 -7 61969642 . G T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72004;SOR=0.62407;LSEQ=ACTGTTTGTAAAGTCTGCAA;RSEQ=TGGAAATATGGACCTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:0,5:0,24:0.1724:1,0:16.2:1:31.2:1:1:0:37.4:10:0.1724:0:2.2 0/1:35:4:0,4:1,30:0.1143:1,0:19:1:31.8:1:1:0:35.3:8:0.1143:0:1.8 -7 61969646 . AA CT 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49336;SOR=Inf;LSEQ=TTTGTAAAGTCTGCAAGTGG;RSEQ=ATATGGACCTGTTTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:0,25:0:1,0:20.4:1:31.6:1:1:0:38.5:50:1:0:1.8 0/1:29:2:0,2:1,26:0.069:1,0:23:1:29:1:1:0:40:4:0.069:0.0345:1.5 -7 61969647 . A T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23959;SOR=0;LSEQ=TTGTAAAGTCTGCAAGTGGA;RSEQ=ATATGGACCTGTTTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:0,23:0,0:1:0,1:21.2:1:29.5:1:1:0:38.4:46:1:0:1.9 1/1:27:24:0,24:1,1:0.8889:2,1:24.1:1:28.8:1:0.07692:0:39.2:48:0.9231:0:1.9 -7 61969649 . T C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34727;SOR=0.46401;LSEQ=GTAAAGTCTGCAAGTGGAAA;RSEQ=ATGGACCTGTTTGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:0,9:0,13:0.4091:1,0:27.1:1:33.7:1:1:0:39:18:0.4286:0:2.6 0/1:25:6:0,6:1,18:0.24:1,0:25.5:1:32.5:1:1:0:40:12:0.24:0:2.5 -7 61969663 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49677;SOR=Inf;LSEQ=TGGAAATATGGACCTGTTTG;RSEQ=GGCCTTCGTTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:0:1,0:17.6:1:32.5:1:1:0:38.6:26:1:0:2 0/1:18:2:1,1:0,16:0.1111:1,2:37:1:29:1:0.11111:0:54:4:0.1111:0:4.5 -7 61969704 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTTCTTCATTGAATGCTAGA;RSEQ=GGAAGAATTCTCAGCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:24:1:29.5:1:1:0:30.5:4:1:0:2.5 1/0:4:2:1,1:0,2:0.5:0,2:23:1:30.5:1:1:0:54:4:0.5:0:4.5 -7 61969848 . G A 28 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTTGATGCCAACAGTAGAAA;RSEQ=GGAAATATCTTCAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:28.5:1:1:0:49:4:1:0:1 0/0:2:0:0,0:2,0:0:0,0:23:1:31.5:1:1:0:38:4:1:0:1 -7 61969889 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ACTAGACAGAATCATCCTCA;RSEQ=AAAATTCTTTGTGATGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:45:0:32.5:1:1:0:49:4:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:40:1:30:0:1:1:49:4:0.5:0:1.5 -7 61970199 . G T 47 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATAGAAAAGGAAATATCT;RSEQ=CAAATAAAAACTAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:10.3:1:29.7:1:1:0:45.3:6:0.75:0:2 -7 61970265 . GT G 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07715;SOR=0;LSEQ=GTGTGCGTTCAACTCACAGA;RSEQ=TTAACCTTTCTTTTCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:2,1:18,3:0.125:2,2:26:1:33.7:1:0.43676:2.82726:44.7:6:0.125:0:2 0/0:31:0:0,0:23,8:0:2,0:22.2:1:29.5:1:1:0:39.7:62:1:0:0.9 -7 61970277 . T C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.67981;LSEQ=CTCACAGAGTTTAACCTTTC;RSEQ=TTTCATAGAGGAGTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:20,5:0.0741:2,2:15.5:1:29.5:1:0.40171:3.74166:42.5:4:0.0741:0:1.5 0/1:39:2:1,1:28,9:0.0513:2,2:16:0:33:1:0.45209:3.00366:30:4:0.0513:0:1.5 -7 61970285 . G A 50 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08368;SOR=0;LSEQ=GTTTAACCTTTCTTTTCATA;RSEQ=AGGAGTTTGGAAACACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:2,1:26,7:0.0833:2,2:32:0:31.7:1:0.54118:1.82091:44.7:6:0.0882:0:2 0/0:45:0:0,0:33,12:0:2,0:24.8:1:32.1:1:1:0:40.6:90:1:0:1.5 -7 61970291 . T C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69117;SOR=0.70282;LSEQ=CCTTTCTTTTCATAGAGGAG;RSEQ=TTGGAAACACACTGTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:1,2:28,7:0.0789:2,2:24.7:1:31.7:1:0.13371:7.43027:50.3:6:0.0811:0:2 0/1:53:3:2,1:38,12:0.0566:2,2:10.7:1:30.7:1:1:1.56828:49:6:0.0577:0:4 -7 61970302 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50338;SOR=Inf;LSEQ=ATAGAGGAGTTTGGAAACAC;RSEQ=CTGTTTGTAAAGTCTGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:38,10:0:2,0:25.3:1:29.7:1:1:0:43.1:23:1:0:1.5 0/1:63:2:1,1:43,18:0.0317:2,2:7:1:28:1:0.51562:2.35208:43.5:4:0.0317:0:3 -7 61970313 . A G 51 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31303;SOR=0.24141;LSEQ=TGGAAACACACTGTTTGTAA;RSEQ=GTCTGCAATTGGATATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:3:3,0:46,15:0.0469:2,0:27.7:1:32.7:1:1:0:35.7:6:0.0508:0:3 0/1:86:1:1,0:51,24:0.0116:2,0:47:0:34:0:1:0:25:2:0.0116:0:3 -7 61970314 . G C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47864;LSEQ=GGAAACACACTGTTTGTAAA;RSEQ=TCTGCAATTGGATATATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:1:1,0:48,15:0.0156:2,0:5:0:33:0:1:0:49:2:0.0161:0:2 0/1:87:2:1,1:57,28:0.023:2,2:17.5:1:29.5:1:1:2.01784:27:4:0.023:0:3.5 -7 61970315 . T A 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30855;SOR=0.23173;LSEQ=GAAACACACTGTTTGTAAAG;RSEQ=CTGCAATTGGATATATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:3,0:46,15:0.0462:2,0:29.7:1:30.7:1:1:0:35.7:6:0.0476:0:3 0/1:91:1:1,0:59,31:0.011:2,0:49:0:31:0:1:0:25:2:0.011:0:3 -7 61970321 . A T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17146;SOR=0;LSEQ=CACTGTTTGTAAAGTCTGCA;RSEQ=TTGGATATATGGACCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:54,18:0.027:2,2:6:0:32.5:1:0.4502:2.94684:60:4:0.0278:0:1.5 0/0:104:0:0,0:64,36:0:2,0:21.2:1:29.7:1:1:0:46.1:200:0.9615:0:1.5 -7 61970322 . T G 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96314;LSEQ=ACTGTTTGTAAAGTCTGCAA;RSEQ=TGGATATATGGACCTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:38:32,6:25,13:0.5:2,2:21.1:1:31.6:1:0.11062:2.74:38.2:37:0.5:0:1.9 0/1:106:52:40,12:24,25:0.4906:2,2:20.3:1:31.2:1:0.00417:3.43:40.8:104:0.5098:0:1.8 -7 61970329 . T C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08281;SOR=0.44837;LSEQ=GTAAAGTCTGCAATTGGATA;RSEQ=ATGGACCTGTTTGAGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:15:12,3:52,19:0.1744:2,2:20.5:1:31.9:1:0.7503:1.46:40.1:30:0.1786:0:1.9 0/1:116:10:8,2:65,41:0.0862:2,2:30.4:1:29.8:1:0.31871:2.51:40.2:20:0.0862:0:2.5 -7 61970330 . A T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.26261;SOR=Inf;LSEQ=TAAAGTCTGCAATTGGATAT;RSEQ=TGGACCTGTTTGAGGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:64,23:0:2,0:22.7:1:28.8:1:1:0:46.1:20.75:1:0:1.4 0/1:117:3:2,1:71,42:0.0256:2,2:35.3:1:30.7:1:1:1.18:40.3:6:0.0261:0:6 -7 61970335 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50378;SOR=Inf;LSEQ=TCTGCAATTGGATATATGGA;RSEQ=CTGTTTGAGGCCTTCGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:70,27:0:2,0:22.5:1:31.3:1:1:0:47.1:23.25:1:0:1.4 0/1:121:2:1,1:74,44:0.0165:2,2:10.5:1:29:1:1:1.67415:33:4:0.0165:0:2 -7 61970337 . TGT GCA 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25595;SOR=Inf;LSEQ=TGCAATTGGATATATGGACC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:71,29:0:2,0:22.6:1:30.5:1:1:0:47.4:32.333:1:0:1.3 0/1:125:3:2,1:75,46:0.024:2,2:28.7:1:28.9:1:1:1.22:56:6:0.0244:0.008:2.3 -7 61970338 . G C 52 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.62535;SOR=2.64267;LSEQ=GCAATTGGATATATGGACCT;RSEQ=TTTGAGGCCTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:1:1,0:74,32:0.0093:2,0:49:0:29:0:1:0:40:2:0.0093:0:3 0/1:124:3:2,1:73,45:0.0242:2,2:32.7:1:33:0:1:1.23:40.3:6:0.025:0:6 -7 61970339 . T C 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.72634;LSEQ=CAATTGGATATATGGACCTG;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:1:1,0:75,34:0.0091:2,0:40:0:15:0:1:0:60:0:0:0:4 0/1:128:2:1,1:75,48:0.0156:2,2:14.5:1:33.5:1:1:1.5567:21:4:0.016:0:2.5 -7 61970341 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20222;SOR=0;LSEQ=ATTGGATATATGGACCTGTT;RSEQ=GAGGCCTTCGTTGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:72,35:0.0182:2,2:17:1:32:0:1:2.04246:43:4:0.0187:0:2.5 0/0:134:0:0,0:84,50:0:2,0:24.6:1:29.8:1:1:0:48.6:133:1:0:1.3 -7 61970342 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81273;LSEQ=TTGGATATATGGACCTGTTT;RSEQ=AGGCCTTCGTTGGAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:72,36:0.0182:2,2:10:0:30.5:1:1:1.9865:50:4:0.0192:0:1 0/1:135:2:1,1:83,49:0.0148:2,2:26:0:31:1:1:1.68685:49:4:0.015:0:2 -7 61970343 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50405;SOR=Inf;LSEQ=TGGATATATGGACCTGTTTG;RSEQ=GGCCTTCGTTGGAAACGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:72,37:0:2,0:23.7:1:30.3:1:1:0:48.7:53.5:1:0:1.2 0/1:136:2:1,1:83,51:0.0147:2,2:23:0:31:1:1:1.62134:60:4:0.0148:0:1 -7 61970349 . T C 128 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01317;SOR=0.34427;LSEQ=TATGGACCTGTTTGAGGCCT;RSEQ=CGTTGGAAACGGGATTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:18:9,9:66,30:0.1579:2,2:25.7:1:30.8:1:0.17483:2.18366:55.4:36:0.1607:0:1.8 0/1:149:9:4,5:84,53:0.0604:2,2:21.6:1:31.7:1:0.4838:1.97157:51.8:18:0.0604:0:1.8 -7 61970351 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57956;SOR=0.37632;LSEQ=TGGACCTGTTTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:77,39:0.0168:2,2:21:1:29.5:1:1:1.9622:60:4:0.0172:0:3 0/0:157:1:0,1:92,60:0.0064:2,0:46:0:32:0:0.39869:0:60:2:0.0064:0:2 -7 61970353 . T A 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.54203;LSEQ=GACCTGTTTGAGGCCTTCGT;RSEQ=GGAAACGGGATTTCTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:1,0:79,42:0.0081:2,0:30:0:11:0:1:0:40:0:0:0:6 0/1:160:2:1,1:94,64:0.0125:2,2:18:1:31:1:1:1.46511:38:4:0.0126:0:6.5 -7 61970355 . G T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50699;SOR=Inf;LSEQ=CCTGTTTGAGGCCTTCGTTG;RSEQ=AAACGGGATTTCTTCATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:82,43:0:2,0:25.9:1:31.1:1:1:0:50.4:40.667:1:0:1.1 0/1:163:2:1,1:96,65:0.0123:2,2:16:1:31:1:1:1.47327:38:4:0.0127:0:6.5 -7 61970360 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50902;SOR=Inf;LSEQ=TTGAGGCCTTCGTTGGAAAC;RSEQ=GGATTTCTTCATTGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:84,48:0:2,0:26.8:1:30.4:1:1:0:51.3:65:1:0:1.1 0/1:177:2:1,1:107,68:0.0113:2,2:21:1:29.5:1:1:1.56932:48.5:4:0.0113:0:2.5 -7 61970368 . T A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08248;SOR=0;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TCATTGAATGCTAGACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:2,1:93,52:0.0201:2,2:33:1:31.7:1:1:1.12:50.3:6:0.0205:0:2 0/0:192:0:0,0:116,75:0:2,0:24.4:1:30.3:1:1:0:52.8:62.667:0.9947:0:1 -7 61970371 . A G 21 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75573;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TTGAATGCTAGACGGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:94,54:0.0133:2,2:44.5:1:31.5:1:1:1.73391:43:4:0.0136:0:2.5 0/1:198:2:0,2:116,80:0.0101:2,0:15:1:21.5:1:0.17028:0:44.5:1:0.0052:0:4 -7 61970372 . T C 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13562;SOR=Inf;LSEQ=TTGGAAACGGGATTTCTTCA;RSEQ=TGAATGCTAGACGGAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:95,55:0:2,0:27.1:1:30.2:1:1:0:51.9:24:1:0:1 0/1:195:4:2,2:112,77:0.0205:2,2:18.5:1:33.5:1:1:1.45163:60:8:0.0208:0:1.8 -7 61970374 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1879;SOR=0;LSEQ=GGAAACGGGATTTCTTCATT;RSEQ=AATGCTAGACGGAAGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:93,56:0.0132:2,2:26.5:1:27.5:1:1:1.65484:50:4:0.0135:0:2 0/0:198:0:0,0:117,80:0:2,0:24.8:1:31.4:1:1:0:52.5:196:0.9949:0:0.9 -7 61970378 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08505;SOR=0;LSEQ=ACGGGATTTCTTCATTGAAT;RSEQ=CTAGACGGAAGAATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:3:2,1:93,62:0.019:2,2:43.7:1:24.7:1:1:1.33:44.7:2:0.0131:0:2.7 0/0:200:0:0,0:115,85:0:2,0:25.2:1:31.7:1:1:0:52.4:99:1:0:0.8 -7 61970381 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50474;SOR=Inf;LSEQ=GGATTTCTTCATTGAATGCT;RSEQ=GACGGAAGAATTCTCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:95,64:0:2,0:26.4:1:28.7:1:1:0:51.3:38.75:0.9936:0:0.8 0/1:201:2:1,1:112,86:0.01:2,2:39.5:1:31:1:1:1.30058:60:4:0.01:0:2 -7 61970383 . A G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13129;SOR=Inf;LSEQ=ATTTCTTCATTGAATGCTAG;RSEQ=CGGAAGAATTCTCAGTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:93,68:0:2,0:26.7:1:29.2:1:1:0:51.3:25.833:1:0:0.9 0/1:199:4:2,2:108,87:0.0201:2,2:38:1:31:1:1:1.24002:57:8:0.0206:0:1.8 -7 61970384 . C G 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63045;SOR=2.47123;LSEQ=TTTCTTCATTGAATGCTAGA;RSEQ=GGAAGAATTCTCAGTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:0,1:93,68:0.0062:2,0:47:0:33:0:0.42593:0:39:2:0.0064:0:3 0/1:198:3:1,2:108,87:0.0152:2,2:14.7:1:32.3:1:0.58887:2.4716:54:6:0.0153:0:1 -7 61970385 . G A 66 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06695;SOR=Inf;LSEQ=TTCTTCATTGAATGCTAGAC;RSEQ=GAAGAATTCTCAGTAAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:91,72:0:2,0:26.6:1:29.9:1:1:0:51.4:162:1:0:0.8 0/1:199:5:3,2:107,87:0.0251:2,2:25.8:1:28.6:1:1:1.22:48.4:10:0.0253:0:2.2 -7 61970390 . A G 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.86189;LSEQ=CATTGAATGCTAGACGGAAG;RSEQ=ATTCTCAGTAAATTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:4:3,1:88,80:0.0233:2,2:31.3:1:30:1:0.62317:2.71:52.8:8:0.0241:0:1.8 0/1:199:4:2,2:102,93:0.0201:2,2:15.8:1:31:1:1:1.09626:55.5:8:0.0203:0:1.5 -7 61970392 . T A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21426;SOR=0;LSEQ=TTGAATGCTAGACGGAAGAA;RSEQ=TCTCAGTAAATTCTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:89,79:0.0116:2,2:11.5:1:32:1:1:1.12579:47:4:0.0118:0:1 0/0:199:0:0,0:104,95:0:2,0:27.5:1:29.9:1:1:0:50.9:198:1:0:0.8 -7 61970399 . T G 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09376;SOR=0;LSEQ=CTAGACGGAAGAATTCTCAG;RSEQ=AAATTCTTTGTGTTGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:1,2:83,78:0.0182:2,2:34.7:1:24.7:1:0.61361:2.11873:43:2:0.0122:0:3.3 0/0:197:0:0,0:99,98:0:2,0:27.7:1:28.8:1:1:0:50.5:394:1:0:0.8 -7 61970400 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50308;SOR=Inf;LSEQ=TAGACGGAAGAATTCTCAGT;RSEQ=AATTCTTTGTGTTGTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:84,79:0:2,0:27.3:1:28.6:1:1:0:51.6:80.5:1:0:0.8 0/1:197:2:1,1:98,97:0.0102:2,2:23.5:1:33:1:1:1.01026:54.5:4:0.0104:0:1.5 -7 61970402 . A C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25543;SOR=Inf;LSEQ=GACGGAAGAATTCTCAGTAA;RSEQ=TTCTTTGTGTTGTGTGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:82,80:0:2,0:27.3:1:29.7:1:1:0:51.4:26:1:0:0.8 0/1:198:3:2,1:97,98:0.0152:2,2:31:1:31:1:1:2.01:30.3:6:0.0152:0:3.7 -7 61970404 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50557;SOR=Inf;LSEQ=CGGAAGAATTCTCAGTAAAT;RSEQ=CTTTGTGTTGTGTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:77,80:0:2,0:28:1:29.8:1:1:0:51.5:77.5:1:0:0.8 0/1:199:2:1,1:96,101:0.0101:2,2:36:1:29.5:1:1:1.05:50:4:0.0102:0:2.5 -7 61970408 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19422;SOR=0;LSEQ=AGAATTCTCAGTAAATTCTT;RSEQ=GTGTTGTGTGCATTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:0,2:73,76:0.0132:2,0:24.5:1:32:0:0.49722:0:53.5:4:0.0133:0:1 0/0:191:0:0,0:92,99:0:2,0:27.5:1:29.7:1:1:0:50:382:1:0:0.8 -7 61970411 . G A 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03428;SOR=0;LSEQ=ATTCTCAGTAAATTCTTTGT;RSEQ=TTGTGTGCATTCAACTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:4:2,2:65,74:0.0276:2,2:20.5:1:28.8:1:1:1.14:47.3:8:0.0284:0:1.3 0/0:190:0:0,0:90,100:0:2,0:27:1:30.8:1:1:0:50:46.5:1:0:0.8 -7 61970412 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50585;SOR=Inf;LSEQ=TTCTCAGTAAATTCTTTGTG;RSEQ=TGTGTGCATTCAACTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:67,78:0:2,0:28.8:1:29.7:1:1:0:51.3:144:1:0:0.8 0/1:185:2:1,1:87,96:0.0108:2,2:28:1:30.5:1:1:1.10:33:4:0.0109:0:4 -7 61970413 . T G 66 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17316;SOR=0.19254;LSEQ=TCTCAGTAAATTCTTTGTGT;RSEQ=GTGTGCATTCAACTCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:4:2,2:63,75:0.0282:2,2:31.8:1:33:1:1:1.19:60:8:0.0288:0:1 0/0:181:1:0,1:85,94:0.0055:2,0:2:0:31:0:1:0:60:2:0.0056:0:1 -7 61970415 . T A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.2567;SOR=Inf;LSEQ=TCAGTAAATTCTTTGTGTTG;RSEQ=GTGCATTCAACTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:65,77:0:2,0:28.7:1:29.6:1:1:0:51.4:141:1:0:0.8 0/1:177:3:1,2:82,92:0.0169:2,2:32:1:29.3:1:1:1.77703:47.3:6:0.0169:0:2 -7 61970419 . C T 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06534;SOR=Inf;LSEQ=TAAATTCTTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:63,76:0:2,0:28:1:31.7:1:1:0:51.3:138:1:0:0.8 0/1:166:5:2,3:74,87:0.0301:2,2:12.4:1:27.2:1:1:1.27401:45.2:10:0.0303:0:2.8 -7 61970421 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50304;SOR=Inf;LSEQ=AATTCTTTGTGTTGTGTGCA;RSEQ=TCAACTCACAGAGTGGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:57,78:0:2,0:28.1:1:29.9:1:1:0:51.4:44:1:0:0.7 0/1:164:2:1,1:72,90:0.0122:2,2:40:1:31.5:1:1:1.25:25:4:0.0123:0:1.5 -7 61970423 . C G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30868;SOR=0.40828;LSEQ=TTCTTTGTGTTGTGTGCATT;RSEQ=AACTCACAGAGTGGAACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:6:2,4:53,74:0.0451:2,2:19.2:1:32.2:1:1:1.4287:51:12:0.0455:0:2 0/1:159:3:2,1:69,87:0.0189:2,2:22.3:1:31.3:1:0.58655:2.51:53.3:6:0.019:0:1.3 -7 61970424 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.2035;SOR=0;LSEQ=TCTTTGTGTTGTGTGCATTC;RSEQ=ACTCACAGAGTGGAACGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:53,77:0.0152:2,2:43:1:30:0:1:1.45:48:4:0.0153:0:2 0/0:160:0:0,0:71,88:0:2,0:27.6:1:29:1:1:0:49.5:52:0.9936:0:0.7 -7 61970425 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.19872;SOR=0;LSEQ=CTTTGTGTTGTGTGCATTCA;RSEQ=CTCACAGAGTGGAACGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:50,78:0.0154:2,2:18.5:1:31:1:1:1.55:50:4:0.0156:0:3 0/0:161:0:0,0:71,90:0:2,0:27.2:1:28.4:1:1:0:49.3:39.25:1:0:0.7 -7 61970428 . C G 90 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.042;SOR=7.03867;LSEQ=TGTGTTGTGTGCATTCAACT;RSEQ=ACAGAGTGGAACGTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:1:0,1:50,80:0.0076:2,0:21:0:33:0:1:0:60:2:0.0078:0:4 0/1:155:8:4,4:63,84:0.0516:2,2:26.1:1:30:1:0.72709:1.33:51.8:16:0.0516:0:2 -7 61970430 . C G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09431;SOR=0;LSEQ=TGTTGTGTGCATTCAACTCA;RSEQ=AGAGTGGAACGTCCCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:3:1,2:46,77:0.0234:2,2:29.3:1:31.7:1:1:1.1932:53.3:6:0.0234:0:1.3 0/0:152:0:0,0:64,88:0:2,0:26.8:1:30.9:1:1:0:49.3:151:1:0:0.7 -7 61970435 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50309;SOR=Inf;LSEQ=TGTGCATTCAACTCACAGAG;RSEQ=GGAACGTCCCTTTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:40,77:0:2,0:26.7:1:29.5:1:1:0:50.2:38:1:0:0.7 0/1:143:2:1,1:56,85:0.014:2,2:15:1:31:1:1:1.51:60:4:0.0141:0:2 -7 61970436 . G T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.82795;LSEQ=GTGCATTCAACTCACAGAGT;RSEQ=GAACGTCCCTTTAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:39,76:0.0171:2,2:31:1:30.5:1:1:1.94:51:4:0.0174:0:2.5 0/1:141:2:1,1:56,83:0.0142:2,2:5:1:27.5:1:1:1.48:60:4:0.0145:0:1 -7 61970449 . AG GC 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50116;SOR=Inf;LSEQ=ACAGAGTGGAACGTCCCTTT;RSEQ=ACAGAGCAGATTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:29,70:0:2,0:22:1:29.6:1:1:0:48:32:1:0:0.7 0/1:117:2:0,2:41,74:0.0171:2,0:16:1:32:1:0.54082:0:39.5:4:0.0174:0.0085:3 -7 61970451 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20826;SOR=0;LSEQ=AGAGTGGAACGTCCCTTTAG;RSEQ=CAGAGCAGATTTGAAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:22,68:0.0217:2,2:16.5:1:29:1:0.43956:3.05:48:4:0.0225:0:2 0/0:109:0:0,0:36,73:0:2,0:23.2:1:28.9:1:1:0:44.5:218:1:0:0.7 -7 61970454 . G C 85 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04809;SOR=0.13167;LSEQ=GTGGAACGTCCCTTTAGACA;RSEQ=AGCAGATTTGAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:6:0,6:21,62:0.0674:2,0:21.3:1:33.2:1:0.32899:0:51.3:12:0.0682:0:1.2 0/0:107:1:0,1:35,71:0.0093:2,0:33:0:33:0:1:0:25:2:0.0094:0:1 -7 61970459 . GA G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21626;SOR=0;LSEQ=ACGTCCCTTTAGACAGAGCA;RSEQ=TTTGAAACACTCTTTTTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:14,61:0.026:2,2:11.5:1:30.6:1:0.35373:4.24:48:4:0.0267:0.013:2 0/0:88:0:0,0:19,69:0:2,0:22.3:1:29.8:1:1:0:41:176:1:0:0.8 -7 61970479 . C T 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05685;SOR=Inf;LSEQ=GATTTGAAACACTCTTTTTG;RSEQ=GGAATTTCCAAGTGGAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:4,48:0:2,0:21:1:29.6:1:1:0:41.2:51:1:0:1 0/1:54:5:0,5:5,44:0.0926:2,0:8.4:1:30.4:1:1:0:40:10:0.0943:0:2.2 -7 61970487 . C G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTCTTTTTGCGGAATTT;RSEQ=CAAGTGGAGATTTCTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:0,35:0,0:1:0,1:27.1:1:32.1:1:1:0:39.3:70:1:0:1.3 1/1:38:38:0,38:0,0:1:0,1:24.8:1:32.7:1:1:0:37.7:76:1:0:1.4 -7 61970608 . T TA 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGCGTTCAACTCACATAGTT;RSEQ=ACCTTTCTTTTCATAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:1:0:30.5:1:1:0:32.5:4:1:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:9:1:28.5:1:1:0:36.5:4:0.6667:0.3333:1.5 -7 61970796 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCTTTAGACAGAGCAGA;RSEQ=TTGAAACACTCTTTTTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:32.5:1:1:0:39:4:1:0:2.5 -7 61971096 . T A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAACTTTTTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23:1:30.8:1:1:0:37.8:8:1:0:1.5 0/1:15:2:1,1:6,7:0.1333:2,2:23.5:1:31:0:1:1.15:21:4:0.1333:0:2.5 -7 61971098 . T A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTTTTTGTGTTGTGTGTA;RSEQ=TCAACTCACAGAGTTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21:1:27.5:1:1:0:37.8:3:1:0:1.5 0/1:15:2:1,1:6,7:0.1333:2,2:32.5:1:31:0:1:1.15:51.5:4:0.1333:0:1.5 -7 61971121 . G C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTCACAGAGTTGAACCTT;RSEQ=CTTTAGAGAGAGCAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:7:0:34:0:1:0:33:2:1:0:0 0/1:8:2:1,1:3,3:0.25:2,2:6:0:32.5:1:1:1:21:4:0.25:0:2.5 -7 61971733 . A C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACGTGATTTCTTCATTTA;RSEQ=TGCTAGACAGAAGAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:32:1:1:0:26:4:1:0:3 -7 61971759 . C A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAAGAATTCTCAGTAA;RSEQ=TTCTTTGTGTTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:32:0:1:0:26:4:1:0:3 -7 61971761 . T C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGAATTCTCAGTAACT;RSEQ=CTTTGTGTTGTGTGTATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:33:0:1:0:26:4:1:0:3 -7 62803003 . A G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.46429;SOR=5.78427;LSEQ=CATTATATATTATGTCTGAC;RSEQ=TATATTATGTCACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:4,0:0.2:0,0:28:0:24:0:1:0:21:2:0.2:0:3 1/0:3:2:2,0:1,0:0.6667:0,0:8.5:1:28.5:1:1:0:48.5:4:0.6667:0:1.5 -7 62865378 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGGAACATGAGGCAGTCAGA;RSEQ=AGCAGGCACCACATGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15:1:32.5:1:1:0:27:4:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:14:0:33:0:1:0:21:2:1:0:0 -7 62865668 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53224;SOR=Inf;LSEQ=AGACGAGAGTCACTCATCTT;RSEQ=GTGTTGAAAAATGTTATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:7,16:0:2,0:27.4:1:29.2:1:1:0:29.7:22:1:0:0.3 0/1:41:2:1,1:15,24:0.0488:2,2:30.5:1:29.5:1:1:1.58:48:4:0.0488:0:1 -7 62865826 . A ATT 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.4;SOR=Inf;LSEQ=AATATAATATAATATAATAT;RSEQ=ATATAATATAATATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:18:1:27:0:1:0:21:4:1:0:1 1/0:3:2:0,2:0,1:0.6667:0,0:20:1:30.5:1:1:0:39:4:0.6667:0:0.5 -7 62865859 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTATATAATATAATATA;RSEQ=TGTGACATAATATATGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:30:1:32:0:1:0:24:4:0.6667:0:2 0/0:1:0:0,0:0,1:0:0,0:43:0:32:0:1:0:39:2:1:0:0 -7 62865874 . T C 47 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATATACTGTGACATAATATA;RSEQ=GTCAGACATAATATATAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:31:1:30:1:1:0:23:6:0.75:0:1.7 0/0:1:0:0,0:0,1:0:0,0:28:0:32:0:1:0:39:2:1:0:0 -7 63229060 . C G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAGCCCGCGAGGCTGAG;RSEQ=CTCCTCCCACTGGACCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:4,10:0.125:2,0:42.5:1:33:1:1:0:20:4:0.1333:0:1 0/0:1:0:0,0:0,1:0:0,0:22:0:33:0:1:0:43:2:1:0:0 -7 63229377 . C T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33484;SOR=4.00619;LSEQ=GCGTGCAGTGAAGAGGACAG;RSEQ=GCCTTCTCGGTCTCCGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:4,1:0.4444:2,2:35.5:1:30.5:1:0.52381:3.38757:42.8:8:0.4444:0:1 1/0:9:7:5,2:2,0:0.7778:0,2:33.4:1:30.6:1:1:0:45:14:0.7778:0:1.1 -7 63229524 . T C 55 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20635;SOR=10.9072;LSEQ=CTTCTCATCTTGCATTTGGG;RSEQ=GTGGTGGGGTCGTCCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:1,3:0.2:2,0:31:0:32:0:1:0:40:2:0.3333:0:1 1/1:5:4:1,3:0,1:0.8:0,2:30.3:1:27.8:1:1:0:33.5:3:0.75:0:2.5 -7 63229802 . T A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.87212;LSEQ=GGGCCCCCATCCCCAGGGGT;RSEQ=GGGGCCGTAGGGGGCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:10:6,4:27,29:0.1515:2,2:10.1:1:29.5:1:0.73302:1.60:44.8:20:0.1515:0:1.1 0/1:52:7:4,3:20,24:0.1346:2,2:10.4:1:28.7:1:0.69319:1.59:40.9:14:0.1346:0:1.4 -7 63229816 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23696;SOR=Inf;LSEQ=AGGGGTTGGGGCCGTAGGGG;RSEQ=CCCACTCTGCTGCCCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:34,34:0:2,0:24.4:1:31.3:1:1:0:56.1:67:1:0:0.2 0/1:65:2:1,1:31,32:0.0308:2,2:29.5:1:30:1:1:1.03:47.5:4:0.0308:0:2.5 -7 63230061 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5352;SOR=0;LSEQ=AATACCTTCCCACCAAAGCC;RSEQ=TTGTTGCCCTCTGGCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:61,22:0.0235:2,2:17:1:32.5:1:0.47031:2.73392:47:4:0.0238:0:1 0/0:48:0:0,0:33,15:0:2,0:18.5:1:30.2:1:1:0:44.9:47:1:0:0.2 -7 63230088 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06168;SOR=Inf;LSEQ=CCCTCTGGCTCCTCCCCAGA;RSEQ=CTGTCACCACTCTCAGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:73,51:0:2,0:27.1:1:31.6:1:1:0:46.5:23.8:1:0:0.2 0/1:82:3:2,1:45,34:0.0366:2,2:33.3:1:30:1:1:1.50:47:6:0.037:0:1.3 -7 63230102 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51747;SOR=0;LSEQ=CCCAGAGCTGTCACCACTCT;RSEQ=AGTCGGTCACCCACTCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:73,58:0.015:2,2:20:0:31:1:1:1.25642:47:4:0.0153:0:1.5 0/0:89:0:0,0:51,38:0:2,0:29.7:1:30.9:1:1:0:46.5:43.5:1:0:0.2 -7 63230106 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1625;SOR=Inf;LSEQ=GAGCTGTCACCACTCTCAGT;RSEQ=GGTCACCCACTCCTTGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:74,60:0:2,0:29:1:30.1:1:1:0:46.8:66:1:0:0.2 0/1:91:2:2,0:49,40:0.022:2,0:32:1:31:1:0.50183:0:49:4:0.0235:0:1 -7 63230155 . G A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70044;SOR=0.6528;LSEQ=GTGTCAGTGGTGCTAAAGCC;RSEQ=TCATCAGCAATGACATTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:4:3,1:41,58:0.0388:2,2:10.5:1:29.8:1:0.31038:4.19:41.3:8:0.0392:0:1 0/1:78:2:1,1:31,45:0.0256:2,2:14:1:28:1:1:1.44:28:4:0.0256:0:1 -7 63230226 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17448;SOR=Inf;LSEQ=TCCTCATCACTCACTATGTC;RSEQ=TCACTGGCCATGTGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:34,35:0:2,0:26.4:1:30.8:1:1:0:58.1:33.5:1:0:0.3 0/1:50:2:2,0:26,22:0.04:2,0:13.5:1:27.5:1:0.49714:0:37:4:0.0408:0:1 -7 63230324 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18891;SOR=Inf;LSEQ=GGCTGCAAAGTGGCCTGGAG;RSEQ=TCCATACTGAGTAGAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:52,41:0:2,0:27:1:31.5:1:1:0:37.7:92:1:0:0.1 0/1:72:2:1,1:39,31:0.0278:2,2:31.5:1:30:1:1:1.25402:27:4:0.0282:0:1 -7 63230363 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49944;SOR=0;LSEQ=CTTTGGGCCAGAGTATGATG;RSEQ=AGTGCCAGACACCACTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:43,51:0.0208:2,2:23.5:1:30:1:1:1.18:27:4:0.0215:0:1 0/0:84:0:0,0:44,40:0:2,0:28.6:1:31.8:1:1:0:33.8:168:1:0:0.1 -7 63230653 . G A 102 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00388;SOR=0.0882;LSEQ=TGCTAGCCCCTGGCTTGTGG;RSEQ=CTTGGCCTCTGAGCTGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:13:7,6:43,41:0.134:2,2:28.4:1:27.8:1:1:1.11:60:5.5:0.1196:0:1.2 0/1:75:1:0,1:41,33:0.0133:2,0:2:0:29:0:0.45333:0:60:2:0.0141:0:1 -7 63230670 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50812;SOR=0;LSEQ=TGGGCTTGGCCTCTGAGCTG;RSEQ=ACTTCTTTCGGTCCCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:51,47:0.0198:2,2:28.5:1:31.5:1:1:1.0842:54.5:4:0.02:0:2 0/0:75:0:0,0:40,35:0:2,0:30.1:1:28.2:1:1:0:59.5:150:1:0:0.2 -7 63230698 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=TCGGTCCCTGTTGCAAGTGG;RSEQ=CCACCTTCACCTGGAAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:46,46:0.0213:2,2:24:1:28.5:1:1:1:54.5:4:0.022:0:2 0/0:84:0:0,0:44,40:0:2,0:19.7:1:30.4:1:1:0:56.6:20:1:0:0.4 -7 63230769 . G A 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.7191;LSEQ=CCCAGGGTGTACCACCGCTC;RSEQ=CTCAGGATCTGGCAGACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:39:25,14:35,29:0.375:2,2:26.7:1:30.2:1:0.41238:1.47:54.7:38:0.3762:0:1.6 1/0:81:60:30,30:13,8:0.7407:2,2:22.8:1:29.3:1:0.44803:1.61531:54.4:120:0.7407:0:1.4 -7 63230786 . C A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88062;SOR=0.92909;LSEQ=CTCGCTCAGGATCTGGCAGA;RSEQ=GGTCCGGTTGTCCTGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:37:22,15:43,38:0.3058:2,2:24.2:1:30.1:1:0.55489:1.29:55.6:74:0.3109:0:1.7 0/1:93:27:15,12:34,32:0.2903:2,2:24.3:1:30.4:1:0.82037:1.17:56.1:54:0.2935:0:2 -7 63230820 . C T 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=TGGTTGGGGTGACCCTGGTG;RSEQ=GCCCTGCCAGGGCCTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:65,67:0:2,0:27.6:1:30.5:1:1:0:57.8:32:1:0:0.6 0/1:93:10:5,5:44,39:0.1075:2,2:26.8:1:30.8:1:1:1.12674:58.8:20:0.1099:0:2.2 -7 63230832 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51181;SOR=0;LSEQ=CCCTGGTGCGCCCTGCCAGG;RSEQ=CCTGGTGCCGCTTGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:68,59:0.0155:2,2:20.5:1:29:1:1:1.15127:54:4:0.0157:0:2 0/0:92:0:0,0:52,40:0:2,0:28.5:1:30.7:1:1:0:58.4:29.667:1:0:0.7 -7 63230932 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16511;SOR=Inf;LSEQ=ATCCATCCTTCTCAGAAGAT;RSEQ=AGTCCTGTTCCTTGCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:51,52:0:2,0:23.2:1:31.2:1:1:0:44.8:102:1:0:0.1 0/1:71:2:1,1:32,37:0.0282:2,2:39.5:1:28:1:1:1.15:47.5:4:0.0286:0:1 -7 63231073 . T C 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CATTGTCCAGCAGGGACTCC;RSEQ=CTGAGGGGCCCAGGGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1:0,1:22.5:1:32.1:1:1:0:28:26:1:0:1.1 1/1:10:10:0,10:0,0:1:0,0:28:1:31.9:1:1:0:30.7:20:1:0:1.2 -7 63231360 . C T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95554;LSEQ=GACGGAGTACCAGGGGAACA;RSEQ=GGCCACAGAGTGAGGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:6,2:20,1:0.2759:1,2:27.9:1:31.4:1:0.17625:6.14271:30.3:16:0.2759:0:1 0/1:15:4:4,0:10,1:0.2667:2,0:23.8:1:30.8:1:1:0:33.5:8:0.2667:0:1 -7 63231411 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.71756;LSEQ=CACGAACACGCTGACGCCAC;RSEQ=GGAGGCCTCGCTGGACACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:21,19:0.0476:2,0:29:1:30:1:0.49245:0:30:4:0.0476:0:1 0/1:29:1:0,1:15,13:0.0345:2,0:45:0:33:0:0.48276:0:27:2:0.0345:0:1 -7 63317423 . C CA 32 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACAAGAATGAAACTCTGCCT;RSEQ=AAAAAAAAAAAAAAATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28.5:1:32:0:1:0:60:4:1:0:0 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 63317573 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49531;SOR=0;LSEQ=CTGCCAGGCTCAGTGGAGGA;RSEQ=GCAGATGACAACAGGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:21,14:0.0541:2,2:48:0:31.5:1:1:1.4832:60:4:0.0541:0:3 0/0:32:0:0,0:19,13:0:2,0:29.8:1:30.6:1:1:0:60:31:1:0:0.8 -7 63317590 . GT CG 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46006;SOR=1.51532;LSEQ=GGAGGCAGATGACAACAGGG;RSEQ=CAGCATGGGTGGCGACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:12:6,6:19,13:0.2727:2,2:29:1:31.7:1:0.73497:1.44877:60:24:0.2727:0.0227:1.1 0/1:33:12:8,4:11,10:0.3636:2,2:26.9:1:30.1:1:0.48606:1.79:60:11:0.3548:0.0303:1.2 -7 63318062 . A T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAATCCCAGCACTTTGGG;RSEQ=GGCCGAGGTGGGCAGATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:1:31.5:1:1:0:60:4:1:0:2 -7 63398593 . GT G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1805;SOR=Inf;LSEQ=AAGCAGTGAGCCATTCATGA;RSEQ=TTTTAGAGCACAGCTACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:37,206:0:2,0:25.3:1:30.4:1:1:0:60:120.5:1:0:0.1 0/1:180:2:1,1:34,144:0.0111:2,2:6.5:1:27.5:1:0.35196:4.19:60:4:0.0112:0.0056:0.5 -7 63398616 . G A 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13656;SOR=0;LSEQ=TTTAGAGCACAGCTACACTG;RSEQ=CATAGACGTCCAACTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:4:3,1:34,146:0.0217:2,2:26:1:30.3:1:0.02614:12.63:60:8:0.0221:0:1 0/0:140:0:0,0:30,110:0:2,0:22.4:1:31.3:1:1:0:60:45.667:1:0:0.2 -7 63398887 . C CAATAT 43 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=45;MSI=10.000;MSILEN=5;SSF=0.50549;SOR=0;LSEQ=GGCCATGTCAATTAGCTGGA;RSEQ=AATATAATATAATATAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:0,7:0.3:0,2:21.7:1:27.6:1:0.3:0:60:6:0.3333:0.1:0.3 0/0:4:0:0,0:1,3:0:2,0:19:1:31.3:1:1:0:60:8:1:0:0 -7 63733693 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGGAGAGTTAATATTAA;RSEQ=GGATAATTATTAAATGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:35.5:1:31.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 63734030 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23313;SOR=Inf;LSEQ=TGGAGATTATGGCAGATTTA;RSEQ=ATTAAAACAATTACTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:38,74:0:2,0:28.2:1:31.3:1:1:0:60:36.333:0.9909:0:0.1 0/1:106:2:1,1:44,60:0.0189:2,2:18:1:29.5:1:1:1.36:60:4:0.0192:0:1 -7 63734057 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49983;SOR=0;LSEQ=ACAATTACTCAGTTATTTTT;RSEQ=ATGCAAAGATGTTTATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:25,55:0.0244:2,2:7:0:31:1:0.53628:2.18:60:4:0.0247:0:2.5 0/0:70:0:0,0:24,46:0:2,0:21:1:31.8:1:1:0:60:140:1:0:0 -7 63734095 . CAT C 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08099;SOR=3.87888;LSEQ=GTGTTCACAGAGTGACCAAT;RSEQ=GTGACAGGTGGCAACACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:0,3:0,34:0.0811:1,0:21:1:31.5:1:1:0:60:6:0.0811:0.027:0 0/1:27:7:0,7:4,16:0.2593:2,0:34:1:31.7:1:0.5453:0:60:14:0.2593:0:0 -7 64721312 . GA G 104 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.68928;SOR=1.74976;LSEQ=CACAGCAAGACTCTGTCTCA;RSEQ=AAAAAAAAAAAGAACCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:9,0:18,0:0.3103:1,0:19.1:1:32.9:1:1:0:60:18:0.3103:0.1034:0.4 0/1:9:4:4,0:5,0:0.4444:0,0:22.3:1:33.3:1:1:0:60:8:0.4444:0.1111:0.5 -7 64721546 . A G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.84458;LSEQ=CCAGGCCCCTTTTCTCCCCA;RSEQ=CTAGGAGCTCCCCAGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:636:189:77,112:187,258:0.2972:2,2:23.4:1:31.8:1:0.79203:1.0542:60:36.8:0.2997:0:1.1 1/0:443:242:109,133:89,112:0.5463:2,2:24.8:1:31.2:1:0.9236:1.03:60:25.889:0.5431:0:1.2 -7 64721622 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11878;SOR=Inf;LSEQ=TGCTATAGCCAGAGTATTCA;RSEQ=GATGCCAACCCTAAGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:25,168:0:2,0:23:1:31.3:1:1:0:60:192:1:0:0.2 0/1:102:2:1,1:22,78:0.0196:2,2:16.5:1:28.5:1:0.40186:3.49:60:4:0.0196:0:1.5 -7 64721626 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10614;SOR=Inf;LSEQ=ATAGCCAGAGTATTCAGGAT;RSEQ=CCAACCCTAAGGTCCCTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:22,157:0:2,0:22.6:1:32.2:1:1:0:60:178:1:0:0.2 0/1:87:2:1,1:15,70:0.023:2,2:7.5:1:26:1:0.33574:4.55:60:4:0.023:0:2.5 -7 65969262 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACGTGAGCTCCAGTGGGGT;RSEQ=CACTCCAGCCGGGACAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42:1:31.5:1:1:0:60:4:1:0:1 -7 65970002 . T TA 66 v4;MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.01343;SOR=7.10034;LSEQ=AAACCATTTGTTAAAAATAT;RSEQ=AAAAAAAAAAAAAAATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:3,0:29,0:0.0909:1,0:10.3:1:30.6:1:1:0:60:6:0.0909:0.0606:0.3 0/1:14:6:5,1:7,0:0.4286:0,2:17.3:1:25.6:1:0.46154:0:56.7:5:0.3846:0.1429:1 -7 65970113 . T C 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17879;SOR=Inf;LSEQ=GGTTTGTCCCGGCCCTTGTC;RSEQ=CCGTCCCGTCTCCCTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:169,61:0:2,0:18.9:1:30.3:1:1:0:60:56.5:1:0:0.1 0/1:169:2:1,1:122,45:0.0118:2,2:25:0:29.5:1:0.47147:2.69245:60:4:0.012:0:1.5 -7 65970295 . G A 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGTCCACTAACATCTTCA;RSEQ=GATGAACTCCCGCGCCGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:0:0,0:382,344:0:2,0:25.5:1:31.3:1:1:0:60:71.6:1:0:0.2 0/1:585:32:16,16:286,267:0.0547:2,2:27.8:1:29.6:1:0.85798:1.07101:60:31:0.0538:0:1.1 -7 65970528 . A C 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=7.52805;LSEQ=GGACTTGGTCGTATTCACTG;RSEQ=GGGCGACGAGAAACGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:668:23:9,14:267,377:0.0344:2,2:19.5:1:29.5:1:1:1.10155:60:22:0.0338:0:1 0/1:538:114:57,57:198,224:0.2119:2,2:22.5:1:30.6:1:0.59776:1.13:60:113:0.2128:0:1.1 -7 65970570 . T G 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00108;SOR=Inf;LSEQ=ACGTCAGGTTCTCAAAGCAG;RSEQ=GGATCCACTTCCTCTGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:0:0,0:242,293:0:2,0:25.6:1:30:1:1:0:60:88.167:1:0:0.1 0/1:475:9:2,7:204,262:0.0189:2,2:27.6:1:29.8:1:0.3108:2.72008:60:18:0.0191:0:1 -7 65970698 . A G 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCTGCTGGGTGGGCAGGT;RSEQ=GCTCGAGGTGGCGATGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:278,213:0:2,0:26.3:1:29.4:1:1:0:60:97.2:1:0:0.1 0/1:432:42:25,17:225,163:0.0972:2,2:28:1:31:1:0.87104:1.07:60:84:0.0993:0:1.2 -7 65970787 . T A 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCTGCGGTCGTAGCACTCG;RSEQ=GGATGCCGGGGTCGTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:823:40:23,17:426,357:0.0486:2,2:22.6:1:30.6:1:0.74686:1.13:60:39:0.0479:0:1.2 0/0:716:0:0,0:384,332:0:2,0:25.7:1:29.6:1:1:0:60:118.333:1:0:0.2 -7 65971009 . T G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.29134;LSEQ=AGCCCCTTTTGTCCTCCTCC;RSEQ=AGTACCCGGCGCCATGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:842:44:23,21:375,423:0.0523:2,2:27.5:1:29.9:1:0.53695:1.24:60:21:0.0509:0:1.1 0/1:621:274:134,140:164,182:0.4412:2,2:23.9:1:30.4:1:0.7463:1.06:60:90.333:0.4479:0:1.2 -7 65971238 . G C 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03065;SOR=Inf;LSEQ=GCCACGGCCGCCACCCACCG;RSEQ=CCCCCGGCCCGACTTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:458:0:0,0:109,347:0:2,0:24.9:1:31.4:1:1:0:60:23:0.9954:0:0.2 0/1:331:4:2,2:93,231:0.0121:2,2:10.8:1:30.3:1:0.58244:2.48:60:8:0.0125:0:1.3 -7 65971260 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.26181;LSEQ=CCCCGGCCCGACTTTGGCCG;RSEQ=AGCCGCCTCGGTCGCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:14:1,13:26,214:0.0551:2,1:9.9:1:31.5:1:1:1.57702:60:28:0.0556:0:1.1 0/1:160:67:10,57:19,74:0.4188:2,2:16.9:1:31.2:1:0.41203:1.4601:60:134:0.4241:0:1.3 -7 65971276 . C G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.11884;SOR=Inf;LSEQ=GCCGAAGCCGCCTCGGTCGC;RSEQ=GCCCGCCTCGGCCCTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:7,127:0:2,0:14.6:1:29.9:1:1:0:60:25.8:1:0:0.2 0/1:71:2:1,1:7,62:0.0282:2,2:5.5:1:28:1:0.21408:8.35:60:4:0.0294:0:3 -7 66224040 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50345;SOR=Inf;LSEQ=ATTTGTGCAATGTATGTGTA;RSEQ=AGTGTCATGCACATTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:16.2:1:29.9:1:1:0:60:24:1:0:0 0/1:18:2:1,1:9,7:0.1111:2,2:27.5:1:27.5:1:1:1.26772:60:4:0.1111:0:1 -7 66760511 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00684;SOR=0.11612;LSEQ=CATGTCTCAATAGATTATGG;RSEQ=AAGAGAATCAACTGAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:20:19,1:11,0:0.6452:0,1:26:1:32.9:1:1:0:33.5:40:0.6452:0:1.1 0/1:12:2:2,0:8,2:0.1667:2,0:40.5:1:31:1:1:0:32.5:4:0.1667:0:1 -7 66760853 . T C 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.99086;LSEQ=GATGTTGAGCATTGACTATG;RSEQ=TTTTCTTCACTTGCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:48:1,47:9,73:0.3692:2,1:22.8:1:32.6:1:0.09055:5.73768:29.5:96:0.375:0:1 0/1:158:58:0,58:16,84:0.3671:2,1:23.5:1:32:1:0.00058:0:34.9:57:0.3631:0:1 -7 66760969 . G A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.78405;LSEQ=TCTAAGGTTTGGCATCTAAA;RSEQ=GACAGCGAGACAGAGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:2,12:0.1765:2,0:28.3:1:32:1:1:0:29.7:6:0.1875:0:1.3 0/1:14:2:0,2:0,12:0.1429:0,0:20:1:29.5:1:1:0:39.5:4:0.1538:0:1 -7 66761667 . A T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18182;SOR=0;LSEQ=AACTATCATTTATTACCTAT;RSEQ=TGTTATGTTAAAATTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:18.2:1:30.8:1:1:0:46.6:10:0.625:0:1 0/0:3:0:0,0:2,1:0:2,0:13.7:1:29:1:1:0:55.3:6:1:0:0 -7 66761773 . T C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59132;SOR=0.70944;LSEQ=TTTCCCACATTTCAGAAGTA;RSEQ=TAGGACTTAGATTGGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:17:17,0:27,3:0.3617:2,1:12.1:1:31.3:1:0.29232:0:34.1:16:0.3478:0:1.2 0/1:21:6:6,0:13,2:0.2857:2,0:15.7:1:30.8:1:1:0:32.5:12:0.2857:0:1 -7 66761852 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50827;SOR=0;LSEQ=GAGATAGAAAATTGTAAATA;RSEQ=TAACGATTCCAATTAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:172,18:0.0104:2,2:29:1:33:1:0.18859:9.3277:49:4:0.0105:0:1 0/0:145:0:0,0:123,22:0:2,0:22.5:1:30.3:1:1:0:54.2:290:1:0:0.1 -7 66762039 . G A 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21778;SOR=Inf;LSEQ=TTTCAGAGCTGAAAGAGACT;RSEQ=TAAAGTAAGGACTAAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:46,181:0:2,0:23.6:1:31.9:1:1:0:48.5:74.667:1:0:0.5 0/1:200:2:1,1:36,162:0.01:2,2:5:0:26.5:1:0.33653:4.45:49:4:0.0102:0:1 -7 66762050 . A T 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=0.44115;LSEQ=AAAGAGACTGTAAAGTAAGG;RSEQ=CTAAGATACCTCAAGTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:198:107:27,80:18,73:0.5404:2,2:28.3:1:29.9:1:0.39816:1.37:46.2:106:0.5408:0:1 0/1:173:59:15,44:21,93:0.341:2,2:27:1:29.3:1:0.32483:1.51:49.1:58:0.3412:0:1.1 -7 66762277 . C T 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29367;SOR=0.73773;LSEQ=ATGAGATCCACTCCATAGTC;RSEQ=TTAAGCTTTAGATCTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:136:77:64,13:52,7:0.5662:2,2:30.5:1:30.8:1:0.47124:1.50447:28.7:76:0.5714:0:1.1 0/1:102:50:42,8:43,9:0.4902:2,2:30.1:1:30.3:1:1:1.10:28:49:0.4851:0:1.2 -7 66762340 . A C 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00752;SOR=Inf;LSEQ=TAAAAATGGACCCATGCTAG;RSEQ=ATGGCATGAACCCGGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:17,107:0:2,0:20.3:1:28.9:1:1:0:27.4:40.333:1:0:0.1 0/1:101:6:1,5:26,69:0.0594:2,2:21.7:1:32:1:1:1.87388:27.3:12:0.0606:0:1 -7 66762461 . T A 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.96966;LSEQ=AAAAAAAAATGGACCCATGC;RSEQ=ATAAGCTTTTATATTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:26:2,24:1,20:0.5532:1,2:22:1:31:1:1:1.65:45.9:52:0.5532:0:2.3 1/0:22:12:0,12:0,9:0.5455:0,0:27.4:1:30.1:1:1:0:47.2:24:0.5455:0:2.6 -7 66762473 . T C 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54017;SOR=0;LSEQ=ACCCATGCTATAAGCTTTTA;RSEQ=ATTGATATTATTTATAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:3,24:0.1:2,0:26.3:1:33.7:1:1:0:43.3:6:0.1071:0:2.7 0/0:15:0:0,0:0,15:0:1,0:25.5:1:28.5:1:1:0:47.5:30:1:0:1.5 -7 66763611 . G A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATTGAGACGGAGTCTT;RSEQ=CTCTGTCCCAGGCTGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:17:0:31:1:1:0:50.5:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 66764110 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33621;SOR=0.36464;LSEQ=TGTCGTTATTATTATTACTA;RSEQ=CTAGCTAAGTACTAGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:14:14,0:48,0:0.2258:1,1:23.9:1:31.1:1:1:0:34.8:28:0.2295:0:1 0/1:21:2:2,0:19,0:0.0952:1,0:23.5:1:31:0:1:0:40:4:0.0952:0:1 -7 66764127 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.78666;SOR=0.80816;LSEQ=CTACCTAGCTAAGTACTAGG;RSEQ=ACATAATAGGTGCTAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:11:11,0:71,0:0.1341:1,0:27:1:31.5:1:1:0:35.6:22:0.1392:0:1 0/1:45:5:5,0:40,0:0.1111:1,0:27.6:1:32:0:1:0:36:10:0.1111:0:1 -7 66764136 . G A 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00193;SOR=Inf;LSEQ=TAAGTACTAGGCACATAATA;RSEQ=GTGCTAACTTTAACTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:98,0:0:1,0:25.1:1:31.8:1:1:0:36.8:31.667:1:0:0.4 0/1:56:6:6,0:50,0:0.1071:1,0:14.3:1:31.5:1:1:0:30:12:0.1071:0:1 -7 66764392 . T C 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCGATCGATAGGTTTGA;RSEQ=GGCCTTAGCAGGTTCTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:67,374:0:2,0:23.4:1:30.2:1:1:0:53:54.125:1:0:0.1 0/1:373:34:8,26:77,262:0.0912:2,2:23.4:1:30.2:1:1:1.05:53.6:68:0.0929:0:1 -7 66764438 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19098;SOR=Inf;LSEQ=AAATGTTACAAGAAACAAAG;RSEQ=AAGTATTCAGCTATATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:10,171:0:2,0:23.2:1:32:1:1:0:46.2:35.2:1:0:0.1 0/1:141:2:1,1:15,124:0.0142:2,2:19.5:1:26:1:0.21479:8.04:45:4:0.0143:0:1 -7 66767267 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21022;SOR=Inf;LSEQ=GGGGCCTCCACGCCTCGCCA;RSEQ=GCCCCTCGGCCATGTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:56,6:0:2,0:24.7:1:31.4:1:1:0:60:30:1:0:0.1 0/1:53:2:1,1:43,8:0.0377:2,2:16:1:27.5:1:0.3135:5.12631:60:4:0.0385:0:1 -7 66767335 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49875;SOR=0;LSEQ=GGTTCTCAAGGAGGACGCGC;RSEQ=AGAAGGGAGACCGCGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:135,61:0.0101:2,2:16.5:1:27:0:0.5293:2.20335:60:4:0.0102:0:2 0/0:195:0:0,0:123,72:0:2,0:23.8:1:29.4:1:1:0:60:64:1:0:0.2 -7 66767460 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07024;SOR=Inf;LSEQ=ACAGGCGCCCCGCCTCCTGG;RSEQ=CTCCCATTGGCTGCTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:58,147:0:2,0:24.7:1:31.5:1:1:0:59.9:101.5:1:0:0.2 0/1:145:3:2,1:37,105:0.0207:2,2:26.7:1:28:1:0.1762:5.59:60:6:0.021:0:1 -7 66767476 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53588;SOR=0;LSEQ=CTGGGCTCCCATTGGCTGCT;RSEQ=TTGACGTTGTGCTCCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:29,122:0.0131:2,2:28.5:1:31:1:0.35475:4.15:60:4:0.0133:0:1 0/0:87:0:0,0:18,69:0:2,0:20.6:1:29.7:1:1:0:60:86:1:0:0.1 -7 66767579 . G A 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03676;SOR=Inf;LSEQ=GTCGAGTCCGTGACGTCAAA;RSEQ=AGCATGGGCCAATCAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:3,19:0:2,0:26:1:30.8:1:1:0:60:21:1:0:0.5 0/1:12:3:0,3:1,8:0.25:2,0:11:1:31.7:1:1:0:60:6:0.3:0:2.3 -7 66767611 . T G 37 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0.08333;SOR=9.27984;LSEQ=ATCAGAGCACACCGGACTGC;RSEQ=TTTTTTTTTTTTCCCGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:1,10:0.2143:2,2:18:1:31.7:1:0.3956:4.28:60:6:0.2143:0:1 1/0:4:3:1,2:0,1:0.75:0,2:8.7:1:23.7:1:1:0:60:2:0.6667:0:2.7 -7 66767624 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=3.05504;LSEQ=GGACTGCTTTTTTTTTTTTT;RSEQ=CCGAACGACCGCAGCAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:1,5:0.2222:2,0:30.5:1:30.5:1:1:0:60:4:0.2222:0:2 1/0:2:1:0,1:0,1:0.5:0,0:27:0:31:0:1:0:60:2:0.5:0:4 -7 67073834 . T TAAAACAAAAC 108 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=33;MSI=8.000;MSILEN=5;SSF=0.72752;SOR=1.35291;LSEQ=TACAGAGTGAGACTCTGTCT;RSEQ=AAAACAAAACAAAACAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:11:11,0:18,0:0.3793:1,0:22.1:1:31.4:1:1:0:60:22:0.3793:0.1379:0 0/1:11:5:5,0:6,0:0.4545:0,0:28.6:1:30.1:1:1:0:58:10:0.4545:0.0909:0.2 -7 67073876 . C CA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAAAACAAACAAACAAA;RSEQ=AAAAAAACCCACCATGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:2,0:72,10:0.0235:2,0:31.5:1:30:1:1:0:60:4:0.0238:0:0.5 0/0:40:0:0,0:37,3:0:2,0:24.7:1:31:1:1:0:59.8:39:1:0:0.2 -7 67073935 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21629;SOR=Inf;LSEQ=AAAATCTGTTTTGGACCTTC;RSEQ=AATCAGGATATCAGAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:107,50:0:2,0:25.6:1:30.9:1:1:0:60:77.5:1:0:0.6 0/1:137:2:1,1:87,48:0.0146:2,2:41:1:31:1:1:1.80409:60:4:0.0148:0:1 -7 67073968 . G A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35663;LSEQ=AGAAGAAAATGTCCCTTGTG;RSEQ=CATATGAAGGCATAGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:117:71,46:49,33:0.5879:2,2:24.2:1:29.9:1:1:1.04:60:57.5:0.5897:0:1.6 0/1:202:68:46,22:71,63:0.3366:2,2:25.3:1:28.6:1:0.05103:1.85:60:136:0.3383:0:1.8 -7 67074004 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.11927;SOR=0;LSEQ=CACAGAGCGGTAGCCAGCCA;RSEQ=CCAGCAAGGGGAGGGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:2,1:131,121:0.0118:2,2:32:1:29.3:1:1:1.84:60:6:0.0121:0:2.3 0/0:262:0:0,0:132,130:0:2,0:25.2:1:31.5:1:1:0:60:42.667:1:0:0.8 -7 67074017 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.44318;LSEQ=CCAGCCAGCCAGCAAGGGGA;RSEQ=GGTTTTACACCAAGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:279:162:83,79:59,58:0.5806:2,2:25.7:1:30.2:1:0.90402:1.03:60:53:0.5846:0:1.6 0/1:279:106:50,56:88,85:0.3799:2,2:26:1:29.8:1:0.62188:1.15891:60:105:0.3846:0:1.6 -7 67074055 . A G 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10137;SOR=Inf;LSEQ=AAAGCCACTCCTGCAGAAAA;RSEQ=GTGATGAGTAGAGGGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:107,162:0:2,0:26.6:1:30.6:1:1:0:60:66.25:1:0:0.6 0/1:236:3:2,1:99,134:0.0127:2,2:20.7:1:26.7:1:0.57764:2.70:60:2:0.0087:0:2 -7 67074069 . G A 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.59837;SOR=2.32889;LSEQ=AGAAAAAGTGATGAGTAGAG;RSEQ=GCATTTCTCAGACTGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:0,1:78,153:0.0043:2,0:32:0:19:0:1:0:60:0:0:0:2 0/1:200:2:1,1:78,119:0.01:2,2:10:1:24:1:1:1.52:60:4:0.0109:0:1.5 -7 67074094 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51379;SOR=0;LSEQ=TTCTCAGACTGCTTTGGGCA;RSEQ=AAGCAGTTTTCTTAGCAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:45,120:0.012:2,2:28.5:1:28.5:1:0.47623:2.65:60:4:0.0122:0:1.5 0/0:117:0:0,0:36,81:0:2,0:25.2:1:31.1:1:1:0:60:234:1:0:0.3 -7 67074170 . A G 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95102;LSEQ=GAGCCCAGAGGTCAGAAAAG;RSEQ=GGTGAGATGATTCTGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:0,12:0,19:0.3871:1,0:23.8:1:31.9:1:1:0:60:24:0.4:0:1 0/1:16:6:0,6:0,10:0.375:0,0:22.8:1:30.3:1:1:0:60:12:0.4:0:1 -7 68105734 . A C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16471;SOR=0;LSEQ=AACATAAAAACTCCCAGAAA;RSEQ=CTAGAAATAGCCTTTCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:14,5:0.0952:2,2:18:1:30:1:0.5:2.64575:60:4:0.0952:0:1 0/0:30:0:0,0:17,13:0:2,0:24.9:1:28.5:1:1:0:60:29:1:0:0.1 -7 68105743 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51429;SOR=Inf;LSEQ=ACTCCCAGAAAACTAGAAAT;RSEQ=GCCTTTCGGCCAGAACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,6:0:2,0:26.2:1:28.5:1:1:0:60:42:1:0:0.1 0/1:34:2:1,1:17,15:0.0588:2,2:31:1:30.5:1:1:1.12916:60:4:0.0588:0:1 -7 68105811 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18363;SOR=Inf;LSEQ=AAAGCAAAGGGAAAGAGGAG;RSEQ=AGCACCCGATATATGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:16,22:0:2,0:23.3:1:30.2:1:1:0:60:76:1:0:0.2 0/1:29:2:1,1:14,13:0.069:2,2:33:1:32.5:1:1:1.07415:60:4:0.069:0:1 -7 68105921 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13178;SOR=0;LSEQ=GTAGACATCAAGGGAATGGG;RSEQ=ACTGTTCAAAAAAGAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:28:1:28.5:1:1:1.07415:60:4:0.069:0:1 0/0:50:0:0,0:28,22:0:2,0:17:1:27.6:1:1:0:60:15.667:1:0:0.2 -7 69180637 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12422;SOR=Inf;LSEQ=GTCAAAATGGAGAGATGAAG;RSEQ=ATTGGTGTTGGGTAATGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,26:0:2,0:23.9:1:30.9:1:1:0:60:44:1:0:0.2 0/1:25:2:1,1:9,14:0.08:2,2:7:0:31:1:1:1.53:60:4:0.08:0:1 -7 69180656 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50909;SOR=0;LSEQ=GGATTGGTGTTGGGTAATGA;RSEQ=AGCAAGGGATGGTCATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:11,14:0.0741:2,2:24.5:1:28:1:1:1.26:60:4:0.0741:0:1 0/0:18:0:0,0:6,12:0:2,0:20.5:1:30.3:1:1:0:60:36:1:0:0 -7 69180681 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48571;SOR=0;LSEQ=AGGGATGGTCATAGAACTCA;RSEQ=AGATGATAATGTGACCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:1,9:0.1667:2,2:20.5:1:30.5:1:0.31818:6.71:60:4:0.1667:0:1 0/0:9:0:0,0:1,8:0:2,0:27.2:1:29.4:1:1:0:60:18:1:0:0 -7 70231200 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49614;SOR=Inf;LSEQ=CCGCCCTACCTGCGGACCGA;RSEQ=TTCCATCAGCACCAGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:27,27:0:2,0:25.8:1:31.7:1:1:0:60:108:1:0:0.2 0/1:58:2:1,1:30,26:0.0345:2,2:11.5:1:28:1:1:1.15099:60:4:0.0351:0:4.5 -7 70231291 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13564;SOR=0;LSEQ=CCCACGCCATCCCACCCACC;RSEQ=CCATCATGCCGACGCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:3,13:0.1111:2,2:25:1:28:1:0.40523:3.89:60:4:0.1111:0:1.5 0/0:30:0:0,0:11,19:0:2,0:20.5:1:29.7:1:1:0:60:14:1:0:0.3 -7 70859491 . C T 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01122;SOR=1.50163;LSEQ=TCTGCTCCACTTTATGTGTT;RSEQ=TGACAGTTTCCCATTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:337:186:100,86:73,78:0.5519:2,2:25.7:1:30:1:0.32674:1.24:60:61:0.5512:0:1.1 1/0:325:211:103,108:57,57:0.6492:2,2:24.7:1:29.8:1:0.90752:1.04842:60:210:0.6502:0:1.1 -7 70859603 . A G 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00172;SOR=Inf;LSEQ=TCCTGGGTCTTTGTAGCTCC;RSEQ=TTGGTCCAATGATGAACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:27,102:0:2,0:20.1:1:30.3:1:1:0:60:42:1:0:0.1 0/1:90:7:2,5:26,57:0.0778:2,2:28:1:29.1:1:1:1.13871:60:14:0.0787:0:1 -7 70859670 . C T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02797;SOR=0;LSEQ=GTGACCAGGATGGAGGAATT;RSEQ=GGGTGCACAGAGGTATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:1,5:0,33:0.1538:1,2:19.7:1:31.5:1:0.15385:0:60:12:0.1538:0:1 0/0:33:0:0,0:0,33:0:1,0:24.1:1:29.7:1:1:0:60:66:1:0:0.1 -7 71296782 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTACTCGGGAAGCTGAGT;RSEQ=AGAAGAATCGCATGAGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:29:1:1:0:60:4:1:0:1 -7 71297418 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22833;SOR=0;LSEQ=TTGCTTGTGCTTAGCAAATG;RSEQ=ATGAAGTGTGGATTTACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:141,57:0.01:2,2:9:1:27.5:1:0.49693:2.46096:60:4:0.0102:0:1 0/0:218:0:0,0:155,63:0:2,0:23.6:1:28.6:1:1:0:60:42.6:1:0:0.1 -7 71297516 . T C 224 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.48218;SOR=0.90262;LSEQ=TTCCCAGATGCCAAGGTGAC;RSEQ=GCTGAAAACCCTTCAATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:170:79,91:126,141:0.3881:2,2:24.7:1:30.3:1:0.92181:1.0293:60:340:0.3917:0:1.1 0/1:423:154:74,80:119,150:0.3641:2,2:26.9:1:29.6:1:0.47831:1.17:60:76:0.3645:0:1.1 -7 71297752 . AT A 54 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACTATCACGCCAGGCTA;RSEQ=TTTTTTTTTTTTTTTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:0,4:0,8:0.2857:0,0:25.3:1:27.1:1:1:0:60:3:0.2727:0.0714:1.5 0/0:2:0:0,0:0,2:0:0,0:17:1:32:0:1:0:60:4:1:0:0 -7 71679909 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCACCGTCTCCCATCAC;RSEQ=CCCAGATAGGACTATCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:25:1:29.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 71681409 . C A 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTATGTCTTTAAAAAAAAA;RSEQ=ATTAAAGATAAATAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:5:1:31.3:1:1:0:60:6:0.75:0:2 1/1:1:1:1,0:0,0:1:0,0:35:0:30:0:1:0:60:2:1:0:1 -7 71681489 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTGGAGAAGCCATAATTCTG;RSEQ=GTATCATAGGGTGCATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:7,4:1,0:0.9167:0,2:17.7:1:30.5:1:1:0:60:22:0.9167:0:1.4 1/1:11:11:8,3:0,0:1:0,2:18.7:1:31.4:1:1:0:60:22:1:0:1 -7 71681620 . T G 72 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.79176;LSEQ=CCTGCCTTCTCACTCCTGAG;RSEQ=TCTAGACATAGAGAACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:25.5:1:31.5:1:1:0:60:4:0.4:0:1 1/0:9:5:1,4:2,2:0.5556:2,2:27.8:1:31.2:1:0.52381:3.38757:60:10:0.5556:0:1 -7 71682465 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTCTATAGCAACCAGTT;RSEQ=CTCTTCAAAGAGCAAAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:30.5:1:1:0:60:4:1:0:1 -7 72483668 . A G 299 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.24672;LSEQ=ATCGGCGAAGGTTGGGACTC;RSEQ=ACTGGTGTTTTTGATCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:966:960:569,391:1,0:0.9938:0,2:26.8:1:30.2:1:1:0:33.5:52.333:0.9937:0:1.1 1/1:802:798:447,351:0,0:0.995:0,2:27.8:1:30.1:1:1:0:35.5:87.667:0.9975:0:1.2 -7 73260381 . TTC T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACGCTGACGTATGCTGCC;RSEQ=TCTCTCTCTGTTTCGGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:20,12:0.0588:2,2:28:1:30.5:1:1:1.64076:56.5:4:0.0588:0:0 0/0:15:0:0,0:10,5:0:2,0:20.7:1:28.7:1:1:0:60:30:1:0:0.4 -7 73260400 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09661;SOR=Inf;LSEQ=CTTCTCTCTCTCTGTTTCGG;RSEQ=TACCTAAGAGGGAAGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:0:2,0:24.3:1:31.1:1:1:0:59.7:40:1:0:0 0/1:19:2:1,1:9,8:0.1053:2,2:19.5:1:27.5:1:1:1.11803:60:4:0.1111:0:1 -7 73260415 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11392;SOR=Inf;LSEQ=TTCGGCTACCTAAGAGGGAA;RSEQ=GGCCCCCTGTCCTACGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:27,25:0:2,0:25.6:1:31.5:1:1:0:59.2:51:1:0:0.1 0/1:27:2:1,1:15,10:0.0741:2,2:41:0:27:1:1:1.47706:60:4:0.0741:0:1.5 -7 73260509 . T A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.42942;LSEQ=CCCCCTTGTCTCCTATGCAA;RSEQ=AAATATCAGCACTTCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:4,9:0.0714:2,0:1:0:26:0:0.35714:0:60:2:0.0714:0:1 0/1:20:2:1,1:7,11:0.1:2,2:22:1:27.5:1:1:1.54:60:4:0.1053:0:1.5 -7 74306708 . G GA 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.06061;SOR=0;LSEQ=GACCCTGCTGCGGGCGTTCG;RSEQ=AAAAAAAACGCAGTCCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:5,1:2,0:0.75:0,2:12.8:1:29.9:1:1:0:29.7:12:0.75:0.375:0.3 0/0:4:0:0,0:1,3:0:2,0:28.5:1:31.3:1:1:0:25:8:1:0:0 -7 74306884 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18943;SOR=Inf;LSEQ=GGAGCCCAGGAGGCGGGGCG;RSEQ=CTGTGGGAACCGTGGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:103,30:0:2,0:22.3:1:30.7:1:1:0:36.4:21.167:1:0:1.1 0/1:103:2:1,1:81,19:0.0194:2,2:14.5:1:29:1:0.35527:4.18079:25:4:0.0196:0:2 -7 74306893 . A G 233 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.52801;LSEQ=GAGGCGGGGCGCCTGTGGGA;RSEQ=CCGTGGAGGGCACTTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:168:166:121,45:0,0:0.9881:0,2:20.7:1:31.6:1:1:0:38.8:54.333:0.9879:0:1.1 1/1:128:127:95,32:0,0:0.9922:0,2:19.8:1:30.8:1:1:0:40.5:24.4:1:0:1.2 -7 74306962 . G C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0799;SOR=0.52303;LSEQ=CTTGGAGAGAGCTGAGAGCT;RSEQ=GAGGTGAGCTGGGCTCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:22:13,9:132,163:0.0692:2,2:21.5:1:30.2:1:0.26716:1.78:33.8:44:0.0701:0:1 0/1:321:12:6,6:150,159:0.0374:2,2:28.6:1:29.8:1:1:1.06:33:24:0.0379:0:1 -7 74307015 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49883;SOR=Inf;LSEQ=CGCGCCCTCTTTGAGAACCA;RSEQ=GGCTTCCAACCTCCCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:67,125:0:2,0:25.5:1:30.2:1:1:0:57:63:1:0:0.2 0/1:198:2:1,1:69,127:0.0101:2,2:41.5:1:30.5:1:1:1.83:60:4:0.0103:0:1 -7 74307022 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49863;SOR=Inf;LSEQ=TCTTTGAGAACCACGGCTTC;RSEQ=AACCTCCCTGGAAATGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:54,129:0:2,0:23.6:1:31.4:1:1:0:57.5:29.5:1:0:0.2 0/1:183:2:1,1:55,126:0.0109:2,2:31:1:30:1:0.51955:2.28:60:4:0.0109:0:1 -7 74307057 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23547;SOR=Inf;LSEQ=TGGGGGGAACATGGCCGAGG;RSEQ=GCGTGGCGAGGTCACCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:20,76:0:2,0:23.3:1:29:1:1:0:59.3:31:1:0:0.2 0/1:91:2:1,1:21,68:0.022:2,2:20:1:28.5:1:0.42711:3.19:60:4:0.0225:0:1 -7 74310260 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51762;SOR=Inf;LSEQ=CCTGCTAAGGCCATCAAACC;RSEQ=ATTGATCGGAAGTCAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:96,12:0:2,0:23:1:31.3:1:1:0:49.2:107:1:0:0.1 0/1:161:2:1,1:139,20:0.0124:2,2:19:1:30.5:1:0.24457:6.80611:50:4:0.0125:0:1 -7 74310274 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55524;SOR=Inf;LSEQ=CAAACCTATTGATCGGAAGT;RSEQ=AGTCCATCAGATTTGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:103,36:0:2,0:24.8:1:31.3:1:1:0:52.2:138:1:0:0.1 0/1:253:3:1,2:186,64:0.0119:2,2:7:1:26.3:1:0.16755:5.76336:60:6:0.0119:0:1 -7 74310282 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11893;SOR=0;LSEQ=TTGATCGGAAGTCAGTCCAT;RSEQ=AGATTTGCTCTGGGCCGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:111,45:0.0125:2,2:26.5:1:28.5:1:0.49883:2.45069:52:4:0.0127:0:1 0/0:303:0:0,0:214,89:0:2,0:32:0:14:0:1:0:60:0:0:0:1 -7 74310420 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.52376;SOR=Inf;LSEQ=AGAAATGATCAGTGAATGTT;RSEQ=TTGTAGTCAAGAAACATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:19,107:0:2,0:22.2:1:31.7:1:1:0:41.1:62:1:0:0.1 0/1:199:2:1,1:33,164:0.0101:2,2:17.5:1:29.5:1:0.31323:4.91:45:4:0.0101:0:1 -7 74312339 . CG TA 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.09344;LSEQ=GGGGTAGAAGAAGAAAACTT;RSEQ=AAGGCTTAAGTAAGTTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:26:22,4:14,8:0.5417:2,2:20.4:1:28.5:1:0.11066:3.07:23.3:25:0.5319:0.0625:0.9 0/1:31:3:3,0:26,2:0.0968:2,0:13.7:1:28:1:1:0:20:6:0.0968:0:1.7 -7 74312430 . CA C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50755;SOR=0;LSEQ=TAACACTGTCTTGGGAAACA;RSEQ=AAAACAGTTTTCTAAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:79,58:0.0143:2,2:30.5:1:34:0:1:1.35898:34:4:0.0146:0:0 0/0:106:0:0,0:61,45:0:2,0:25.1:1:29.6:1:1:0:43.7:25.5:1:0:0.1 -7 74312504 . C A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACTTGAGATGTCTTAGTC;RSEQ=TTACTTTACAGTCTCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:222,54:0:2,0:25.8:1:31.2:1:1:0:41.3:68:1:0:0 0/1:226:15:10,5:173,38:0.0664:2,2:20.3:1:29.9:1:0.1703:2.26622:39.7:14:0.0625:0:1.3 -7 74711828 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATGTATATATATGTATATA;RSEQ=ATGTATATATATGTATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:29.5:1:33.5:1:1:0:41.5:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 74712316 . C T 232 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02606;LSEQ=AGTTTCAACCCGAGTTAGGT;RSEQ=GGCAAACTCTCGAATCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1398:221:109,112:534,643:0.1581:2,2:27.3:1:29.8:1:0.30325:1.17:29.6:109.5:0.1585:0:1.1 0/0:1232:6:2,4:549,677:0.0049:2,2:27.5:1:29.7:1:0.69712:1.62125:32.3:12:0.0049:0:1.5 -7 74712329 . A C 214 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTAGGTCGGCAAACTCTCG;RSEQ=ATCTTAGATGTGTGATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1347:0:0,0:549,797:0:2,0:23.7:1:29.7:1:1:0:29.4:63.095:1:0:0.2 0/1:1183:113:43,70:423,647:0.0955:2,2:25.5:1:31.5:1:0.83967:1.06426:28.5:55.5:0.0948:0:1.1 -7 75140221 . T TA 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04831;SOR=Inf;LSEQ=TGCTCATGTGCATTAACCAA;RSEQ=ACTCTTGAAAACCAAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:82,14:0:2,0:24.1:1:30.8:1:1:0:43.1:192:1:0:0.1 0/1:56:3:3,0:45,8:0.0536:2,0:10.3:1:30.6:1:1:0:42:6:0.0536:0.0357:0 -7 75140295 . C T 96 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01841;SOR=5.41511;LSEQ=TCCTTATGGCGCACAGGTAG;RSEQ=GTAGAAAATAACTGCTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:2:1,1:218,60:0.0071:2,2:25:1:28:1:0.38886:3.61133:32:4:0.0073:0:1 0/1:266:10:8,2:197,59:0.0376:2,2:26.9:1:29.1:1:1:1.20:29.6:20:0.0376:0:1 -7 75140436 . G A 37 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66377;SOR=0.55512;LSEQ=CAGGTAGAAATGGTGACATC;RSEQ=CTGTGAGAGAATACCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:70,222:0.0102:2,2:17:1:23.7:1:0.14866:6.29:53.7:2:0.0069:0:1 0/0:353:2:2,0:103,248:0.0057:2,0:1:0:25.5:1:0.08788:0:60:4:0.0058:0:1 -7 75140455 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59699;SOR=0.42562;LSEQ=CGCTGTGAGAGAATACCAGG;RSEQ=GTGGTGTGTTCAGTGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:2,0:22,170:0.0103:2,0:12.5:1:31:0:0.01474:0:24:4:0.0105:0:1 0/0:227:1:1,0:40,186:0.0044:2,0:26:0:31:0:0.18062:0:24:2:0.0046:0:1 -7 75141838 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14404;SOR=Inf;LSEQ=AAAACTGTTTTTGCGTTTCC;RSEQ=AAGACAGTGTTACTCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:43,51:0:2,0:19.5:1:31.7:1:1:0:37.4:93:1:0:0 0/1:58:2:1,1:29,27:0.0345:2,2:23.5:1:25.5:1:1:1.07272:45.5:4:0.0357:0:1 -7 75142045 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21189;SOR=Inf;LSEQ=TTATTAAAAATGGACCCATG;RSEQ=TAGAATGGCATGAACCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:33,85:0:2,0:16.3:1:30.6:1:1:0:27.1:58:1:0:0.1 0/1:102:2:1,1:33,67:0.0196:2,2:29:0:29:1:1:2.02:25:4:0.0204:0:1 -7 75142062 . CG C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1.2486;LSEQ=ATGCTAGAATGGCATGAACC;RSEQ=GGGGGCGGAGCTTGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:17,93:0.0179:2,2:41:1:31.5:1:0.29681:5.35:47:4:0.018:0:0 0/1:90:2:1,1:13,74:0.0222:2,2:27.5:1:29.5:1:0.29137:5.52:25:4:0.0227:0:0 -7 75142141 . GA G 130 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0.95557;LSEQ=GTGAGACTCCGTCTCAAAAA;RSEQ=AAAAAAAAAAAAATGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:19:1,18:2,43:0.2794:1,1:24.8:1:30.8:1:1:1.19:30.8:38:0.2879:0.0294:0.4 0/1:37:10:1,9:2,22:0.2703:2,2:28.8:1:31.2:1:1:1.21:33.2:20:0.2703:0.027:0.4 -7 75143737 . T C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.56044;SOR=2.88294;LSEQ=TTAAATGAGATATTTCTGTG;RSEQ=AATTCTTAGCATAACACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:13,2:0.0625:2,0:43:0:32:0:1:0:25:2:0.0625:0:1 0/1:12:2:2,0:8,2:0.1667:2,0:31.5:1:32:1:1:0:24:4:0.1667:0:1 -7 76093469 . G T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTACCCACATCCAGAAAGGG;RSEQ=ACGGTTAGAGGGAAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:0.3:0,0:19.7:1:31.3:1:1:0:45.3:6:0.3:0:1.3 0/1:10:3:3,0:6,1:0.3:2,0:32.3:1:28.7:1:1:0:41.7:6:0.3:0:1 -7 76093553 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5335;SOR=0;LSEQ=GAGTAGGACTTAGAAAGTGG;RSEQ=GCACAGTCACCTGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:42,28:0.0278:2,2:31:1:31.5:1:1:1.49132:48.5:4:0.029:0:1.5 0/0:41:0:0,0:22,19:0:2,0:26.6:1:30.1:1:1:0:50.4:19.5:1:0:0.3 -7 76093562 . A G 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.06505;LSEQ=TTAGAAAGTGGGGCACAGTC;RSEQ=CCTGGGAGAGGAGTCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:7:6,1:40,29:0.0921:2,2:12.6:1:28.1:1:0.23391:4.28:26.1:14:0.0946:0:1 0/1:41:4:4,0:18,19:0.0976:2,0:17:1:31.3:1:0.11051:0:32:8:0.0976:0:1 -7 76093565 . TG T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00409;SOR=0.3038;LSEQ=GAAAGTGGGGCACAGTCACC;RSEQ=GGAGAGGAGTCAGCGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:41:23,18:23,14:0.5256:2,2:25.3:1:31.3:1:0.64881:1.28156:51.8:82:0.5256:0.0897:0.7 0/1:44:11:5,6:19,14:0.25:2,2:31:1:31.1:1:0.50926:1.61033:49.9:22:0.25:0.0455:0.5 -7 76093627 . G C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.04314;SOR=0.3086;LSEQ=ACACAGCTGGGCTACTGTAA;RSEQ=TAGCTTAGTATGTAATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:17:7,10:9,20:0.3617:2,2:17.6:1:31.4:1:0.53406:1.54:48.6:34:0.3617:0:1.2 0/1:34:5:2,3:13,16:0.1471:2,2:21:1:30.2:1:1:1.21174:52.6:10:0.1471:0:1.4 -7 76093686 . G C 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.03004;LSEQ=AGAGGGCTCTGAGCGAGGAG;RSEQ=GTTATGTGGGCCATGCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:1,10:0.2667:2,0:31:1:30:1:1:0:32.5:8:0.2667:0:1.8 0/1:11:3:0,3:0,8:0.2727:0,0:29.7:1:31.3:1:1:0:47.3:6:0.2727:0:1.7 -7 76093738 . T C 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GAAGGATTTTAGGAGATTTC;RSEQ=ATGAGGGTCATTTTATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:17.5:1:32.5:1:1:0:27:4:0.5:0:2 0/0:3:0:0,0:0,3:0:0,0:20:1:29:1:1:0:50:6:1:0:0 -7 76151377 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18953;SOR=Inf;LSEQ=AGTAGAAAACAGTCTGGATG;RSEQ=TGGTGCCACTAATATTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:74,163:0:2,0:21:1:31.4:1:1:0:33.2:28.625:0.9957:0:0.1 0/1:184:2:1,1:58,124:0.0109:2,2:7:1:28.5:1:0.53968:2.13:25:4:0.0111:0:1 -7 76151378 . T C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58333;SOR=2.58631;LSEQ=GTAGAAAACAGTCTGGATGC;RSEQ=GGTGCCACTAATATTGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:71,161:0.0043:2,0:1:0:31:0:1:0:48:2:0.0043:0:1 0/1:181:2:1,1:55,122:0.011:2,2:25.5:1:29:1:0.52903:2.21:31:4:0.0112:0:1.5 -7 76153809 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51676;SOR=0;LSEQ=CACGGGTCTCTCACTGAACA;RSEQ=ACCACGCCTGGTATTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:135,24:0.0124:2,0:30:1:30:1:1:0:44.5:4:0.0126:0:1.5 0/0:109:0:0,0:91,17:0:2,0:23.4:1:31.2:1:1:0:44:216:0.9908:0:0.1 -7 76153815 . G A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31015;SOR=0.37824;LSEQ=TCTCTCACTGAACACACCAC;RSEQ=CCTGGTATTCTCTCACAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:7:7,0:138,27:0.0407:2,0:34.4:1:30.3:1:0.59805:0:24.4:14:0.0414:0:1.1 0/1:127:2:2,0:102,23:0.0157:2,0:38:1:32:0:1:0:25:4:0.0163:0:1 -7 76154001 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49724;SOR=0;LSEQ=TGTGCGCCATAAGGAATTTC;RSEQ=AAGGAATGTTAAGAAGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:7,79:0.0227:2,2:17.5:1:29:1:0.1745:10.62:47:4:0.0233:0:1 0/0:85:0:0,0:13,72:0:2,0:21.7:1:29.2:1:1:0:50.3:16:1:0:0.2 -7 76154037 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50747;SOR=0;LSEQ=GGTACAGTAAATTAATCTTG;RSEQ=TTTTCAAGAGTATTGGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:7,50:0.0339:2,2:20.5:1:28.5:1:0.25482:6.75:54.5:4:0.0345:0:1 0/0:43:0:0,0:8,35:0:2,0:22:1:30.8:1:1:0:53.3:86:1:0:0.1 -7 76591609 . T C 96 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23603;LSEQ=GAGGGAAGGTCAGGAAGGCT;RSEQ=CTGGAAGGTGGTAGTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:7,1:9,1:0.4444:2,2:12.4:1:32.1:1:1:1.26772:26.3:16:0.4444:0:1 1/0:2:1:1,0:1,0:0.5:0,0:17:0:33:0:1:0:27:2:0.5:0:1 -7 76591745 . G T 27 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.67309;LSEQ=CTGGGCTACTGTAAGTAGCT;RSEQ=AGTATGTAATAGAGGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:3,9:0.1429:2,2:19.5:1:28:1:0.50549:2.74:27:4:0.1429:0:1 0/1:9:2:1,1:2,5:0.2222:2,2:1.5:1:27:1:1:2.24:39:4:0.2222:0:1 -7 76641232 . G A 189 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCATCAAACCTATTGATC;RSEQ=GAAGTCAGTCCATCAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:87:85:64,21:2,0:0.977:0,2:24.2:1:29.5:1:1:0:36:84:0.9767:0:1 0/0:44:0:0,0:27,17:0:2,0:24.4:1:28.8:1:1:0:39.3:88:1:0:0.1 -7 76641333 . A G 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=TGGATGCTGGTGCCACTAAT;RSEQ=TTGGTAAGTTTGGGAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:2,45:0:1,0:19.3:1:31.2:1:1:0:38.5:94:1:0:0.3 0/1:18:6:1,5:0,12:0.3333:0,2:23.8:1:30:1:0.33333:0:36.8:12:0.3333:0:1 -7 76643751 . C G 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09365;SOR=7.23725;LSEQ=CAATCTAAGTCCTAGTACTT;RSEQ=TGAAATGTGAGCAATAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:0,1:0,28:0.0345:1,0:43:0:31:0:1:0:21:2:0.0357:0:2 0/1:14:3:0,3:0,11:0.2143:0,0:22.3:1:32:1:1:0:20:6:0.2143:0:1 -7 76669157 . T C 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22003;SOR=5.07055;LSEQ=TTGTTAATATAATAAATGAA;RSEQ=AGATTAGACCCATAAACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:1,0:19,0:0.05:1,0:2:0:32:0:1:0:40:2:0.05:0:2 0/1:9:2:2,0:7,0:0.2222:0,0:6.5:1:28.5:1:1:0:30:4:0.2222:0:2.5 -7 76669180 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97024;LSEQ=ATTAGACCCATAAACTATTT;RSEQ=CAGTGTTGAGTCATTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:11,0:32,0:0.2558:1,0:13.5:1:29.5:1:1:0:36.5:22:0.2558:0:1.2 0/1:12:3:3,0:9,0:0.25:0,0:15.3:1:28.7:1:1:0:21:6:0.2727:0:1.7 -7 76669333 . A C 242 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19121;SOR=0.86448;LSEQ=CCATCAGATTTGCTCTGGGC;RSEQ=GGTGGTACTGAGTCTAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:953:280:181,99:354,200:0.2938:2,2:22.6:1:29.8:1:0.87854:1.03:55:24.455:0.2874:0:1.1 0/1:741:196:128,68:253,154:0.2645:2,2:24.2:1:29.6:1:0.47195:1.15:56.6:64.333:0.264:0:1.1 -7 76669341 . C T 161 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=52.97247;LSEQ=TTTGCTCTGGGCAGGTGGTA;RSEQ=TGAGTCTAAGCACTGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1039:1:0,1:643,393:0.001:2,0:1:0:25:0:0.37994:0:60:2:0.001:0:1 0/1:884:43:26,17:517,324:0.0486:2,2:25.7:1:29.8:1:0.87409:1.04325:59.6:86:0.0491:0:1.1 -7 76669571 . GTAA G 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.33033;SOR=0.41315;LSEQ=GCCTAGTACTTAGCTAGGTA;RSEQ=TAATAATAACGACAGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:11:0,11:0,45:0.1964:1,0:34.2:1:32.7:1:1:0:42.5:22:0.2037:0:0 0/1:22:2:0,2:2,18:0.0909:2,0:17.5:1:31.5:1:1:0:54:4:0.0952:0.0455:0 -7 77857327 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09804;SOR=Inf;LSEQ=ACATGATCTCTGTTGCAACT;RSEQ=CTCAACTCTGCCCTCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:23:1:28.1:1:1:0:60:22:1:0:0 0/1:11:2:1,1:3,6:0.1818:2,2:46.5:1:30.5:1:1:1.87:60:4:0.1818:0:1 -7 78021432 . C T 123 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=GATACGATCCTTGCCTCAAA;RSEQ=ACTTTACCATCTACTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:15,1:0,0:1:0,1:23.3:1:30.9:1:1:0:60:32:1:0:1.3 1/0:5:3:3,0:2,0:0.6:0,0:38.7:1:30.7:1:1:0:60:6:0.6:0:1.3 -7 78021500 . A G 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00469;SOR=Inf;LSEQ=GAAATGGATCTGTAAGGGGT;RSEQ=TTTATGCATGAAGGTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:68,5:0:2,0:24:1:28.6:1:1:0:60:72:1:0:0.2 0/1:40:5:5,0:34,1:0.125:1,0:27.6:1:33:1:1:0:60:10:0.125:0:1.2 -7 78021636 . A T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00068;SOR=0.5572;LSEQ=TGAAGAAGGCAAAAAATAGA;RSEQ=GTGGGGGCTGTTAGGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:113:57,56:287,241:0.1763:2,2:28.2:1:30.4:1:0.46811:1.16969:60:112:0.1767:0:1.1 0/1:554:59:26,33:258,237:0.1065:2,2:29.3:1:29.7:1:0.2714:1.38088:60:118:0.1081:0:1.1 -7 78319485 . T C 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13122;SOR=0.14271;LSEQ=GTTTTTATTTTCCTATCTTT;RSEQ=AATTCTTGACAAAATTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:0.8889:0,0:24:1:32.5:1:1:0:60:16:0.8889:0:1 1/0:8:4:4,0:4,0:0.5:0,0:9.5:1:30.8:1:1:0:60:8:0.5:0:2 -7 78319656 . C T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35096;SOR=3.32753;LSEQ=GCATATGAGTTTCCATAATA;RSEQ=CATGTATGTTTCACAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:176,93:0.0037:2,0:1:0:25:0:0.34815:0:60:2:0.0037:0:3 0/1:245:3:1,2:144,98:0.0122:2,2:23:1:26.3:1:0.56879:2.92578:60:6:0.0125:0:2.3 -7 78319710 . C A 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03517;SOR=Inf;LSEQ=TTTGCTAAATTCCCATTCCT;RSEQ=TCTGACCGCTGCTCCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:192,204:0:2,0:27.3:1:31.7:1:1:0:60:197:1:0:1.5 0/1:304:4:3,1:144,156:0.0132:2,2:12.5:1:27.3:1:0.35674:3.24:60:8:0.0134:0:1.5 -7 78319728 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17582;LSEQ=CTCTCTGACCGCTGCTCCCT;RSEQ=CTTAACTGTCATCATAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:345:289:118,171:25,30:0.8377:2,2:26.7:1:29:1:0.55249:1.20695:60:71.25:0.8407:0:2.1 0/1:259:123:54,69:56,80:0.4749:2,2:25.7:1:28.1:1:0.70631:1.12:60:29.75:0.4722:0:2.1 -7 78319731 . T C 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTGACCGCTGCTCCCTGCT;RSEQ=AACTGTCATCATAGCATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:340:340:140,200:0,0:1:0,2:26.2:1:31.7:1:1:0:60:55.667:1:0:1.9 1/0:249:173:74,99:31,45:0.6948:2,2:26.3:1:31.1:1:0.78252:1.08:60:85.5:0.6951:0:1.8 -7 78319761 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17232;SOR=Inf;LSEQ=CATAGCATTAAGAAGCAAAA;RSEQ=TATTTATAAAATTTGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:71,165:0:2,0:22.7:1:30.7:1:1:0:60:472:1:0:1.5 0/1:168:2:1,1:57,109:0.0119:2,2:8.5:1:27:1:1:1.90:60:4:0.0121:0:1 -7 78319797 . T C 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06577;SOR=Inf;LSEQ=AAGAACTGTAGACATTAGCT;RSEQ=GAGAATGTGAGCCACTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:24,106:0:2,0:24.9:1:30.3:1:1:0:60:260:1:0:0.8 0/1:89:3:1,2:21,65:0.0337:2,2:18:1:21.3:1:1:1.54:60:2:0.0227:0:2.3 -7 78319926 . G A 104 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTGTTGTATAAGAGAGA;RSEQ=CACACAAAAGATACTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1:0,0:19.2:1:30.2:1:1:0:60:22:1:0:1 1/1:1:1:0,1:0,0:1:0,0:46:0:30:0:1:0:60:2:1:0:1 -7 78867410 . T C 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28272;SOR=0.84251;LSEQ=ACAAATCTAAGCATTCCATT;RSEQ=GATTCTACTGGGAAATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:413:227:108,119:95,90:0.5496:2,2:25.5:1:30.3:1:0.4883:1.16264:60:226:0.5512:0:1.1 1/0:290:147:75,72:70,71:0.5069:2,2:26.8:1:29.6:1:0.90619:1.06:59.9:35.75:0.5:0:1.2 -7 78902550 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15182;SOR=Inf;LSEQ=AATCACCCTTAAGATGGTAG;RSEQ=CCAAAAAAAAATAGTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:103,9:0:2,0:26:1:30.7:1:1:0:60:27:1:0:0.2 0/1:72:2:1,1:61,9:0.0278:2,2:25.5:1:27.5:1:0.26017:6.48246:60:4:0.0278:0:1 -7 78902552 . C CA 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.24087;SOR=0.68731;LSEQ=TCACCCTTAAGATGGTAGGC;RSEQ=AAAAAAAAATAGTTTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:62:56,6:56,10:0.4844:2,2:25.4:1:29.8:1:0.42768:1.66:60:61:0.4959:0.0781:0.1 0/1:74:29:26,3:35,8:0.3919:2,2:25.9:1:29.8:1:0.50721:1.96:60:58:0.3919:0.0135:0.2 -7 78902615 . G T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.31301;SOR=4.23257;LSEQ=CACTTAGCCAATTAGCCACA;RSEQ=AAAATTAGTACTGAATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:1:0,1:213,124:0.0029:2,0:1:0:24:0:0.36982:0:60:2:0.003:0:2 0/1:242:3:1,2:148,90:0.0124:2,2:16:1:26.7:1:0.55972:3.27219:60:6:0.0128:0:1.7 -7 78902684 . G A 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77825;SOR=0.95873;LSEQ=CTTAGTATGAGGCTCCCCAT;RSEQ=TTCCAGGAAACAATTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:461:255:105,150:99,107:0.5531:2,2:27.1:1:29.7:1:0.15729:1.32094:60:84:0.5538:0:1.1 1/0:363:197:89,108:78,86:0.5427:2,2:24.3:1:28.6:1:0.67254:1.10031:60:48.25:0.5406:0:1.1 -7 78924617 . G T 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTTTAAGACCAGAGTTCA;RSEQ=ATAGTGAAGGAATAGACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:181,123:0:2,0:26:1:31.5:1:1:0:60:100.333:0.9967:0:0.3 0/1:240:16:10,6:132,92:0.0667:2,2:20.8:1:29.4:1:1:1.16:60:32:0.0675:0:1.4 -7 78924689 . C T 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0018;SOR=0.59596;LSEQ=AAAATCAAGACAAAAAGTGA;RSEQ=TTCAGTATAAAATAATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:322:173:69,104:67,82:0.5373:2,2:26.5:1:30.3:1:0.36767:1.23072:60:172:0.5375:0:1.2 0/1:274:112:42,70:77,83:0.4088:2,2:27.5:1:29.7:1:0.10626:1.54367:60:111:0.4081:0:1.1 -7 78924696 . A G 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAAAAAGTGACTTCAGT;RSEQ=TAAAATAATCAGTGCTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:125,181:0:2,0:25.4:1:29.7:1:1:0:60:101:0.9967:0:0.7 0/1:259:29:14,15:97,133:0.112:2,2:28:1:30.9:1:0.55534:1.28:60:58:0.1124:0:1.2 -7 78924711 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0965;SOR=Inf;LSEQ=TCAGTATAAAATAATCAGTG;RSEQ=TATCACCTGCAGTATATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:96,164:0:2,0:24.5:1:32.2:1:1:0:60:259:0.9923:0:0.6 0/1:223:3:1,2:87,132:0.0135:2,2:10:1:27:1:1:1.3166:60:6:0.0135:0:1.7 -7 78924870 . G T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGGCACGGTCGAGTCAA;RSEQ=GGAAAATGGTTAATATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:23.7:1:28.8:1:1:0:60:8:1:0:1.4 1/1:7:7:1,6:0,0:1:0,2:19.6:1:30.7:1:1:0:60:14:1:0:1.1 -7 79764514 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=CGCCGAGGACAAGGCGGCGG;RSEQ=GGAGCGGAGTAAGATGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:30:1:31.5:1:1:1.36624:60:4:0.1429:0:1 0/0:8:0:0,0:5,3:0:2,0:15.3:1:28.4:1:1:0:60:16:1:0:0 -7 80802042 . GA G 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.21067;SOR=Inf;LSEQ=AAAAAAGAAACTGGTTCTGG;RSEQ=AAACCAGCCATAACTTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:126,62:0:2,0:15.9:1:29.5:1:1:0:55:30.333:1:0:0.8 0/1:160:2:0,2:96,62:0.0125:2,0:32:0:27:0:0.15849:0:60:4:0.0127:0:1 -7 80802077 . C G 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=CTTAGGGGTTCTTCTTTCAC;RSEQ=CAATCCCATTGGAATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:205,147:0:2,0:28.5:1:30.9:1:1:0:57.2:49.286:1:0:0.8 0/1:287:12:8,4:160,114:0.0418:2,2:18:1:29.8:1:0.76654:1.42:55:24:0.0424:0:2.1 -7 80802110 . A C 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.88312;SOR=1.02499;LSEQ=AATTCTGCTTTGCTATAGAA;RSEQ=CATGCTCAAACCAAGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:426:278:147,131:70,76:0.6526:2,2:26.7:1:31.4:1:0.35829:1.22:57.5:68.5:0.6539:0:1.1 1/0:392:258:136,122:64,70:0.6582:2,2:26.9:1:30.8:1:0.39441:1.22:58.7:257:0.6573:0:1.1 -7 80802406 . C T 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATGAAACCTATGAATTC;RSEQ=TTGTATCATATATATTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:33:1:31:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 81061369 . CTGGAGGG TGGGGGT 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15408;SOR=Inf;LSEQ=AGATGGAGGTCATTGTATCA;RSEQ=GGTTCCCCCTTGCTGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:1,40:0:1,0:25.5:1:31.9:1:1:0:60:40:1:0:0.1 0/1:27:2:1,1:0,25:0.0741:1,2:39:0:31.9:1:0.07407:0:49.5:4:0.0741:0:2 -7 81061381 . CCCCCT ACCTCCA 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.11104;SOR=Inf;LSEQ=TTGTATCACTGGAGGGGGTT;RSEQ=TGCTGTTCTCATGATAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:2,35:0:2,0:23.5:1:30.2:1:1:0:60:74:1:0:0.1 0/1:19:2:1,1:0,17:0.1053:1,2:28:0:32.4:1:0.10526:0:49.5:4:0.1053:0:4 -7 81061460 . T C 81 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCTCTTCCCCCCTTCGCT;RSEQ=GGCACTTCTCCTTCCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:5,5:0.375:2,2:20.7:1:31.7:1:1:1:60:12:0.4:0:1.5 0/0:1:0:0,0:0,1:0:0,0:41:0:32:0:1:0:60:2:1:0:0 -7 81061523 . C T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85124;LSEQ=TTCCTTGTTACCTTCCGCCA;RSEQ=GATTGTAAGTTTCCTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:13,0:7,4:0.5417:2,1:19.5:1:31.5:1:0.03106:0:55:26:0.5417:0:1.2 1/0:4:2:2,0:2,0:0.5:0,0:29:1:30:1:1:0:56:4:0.5:0:3 -7 81061668 . A G 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=TATTCTTGTAGATCCTATGT;RSEQ=CCACCTGCAACAGTGGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:156,112:0:2,0:28.1:1:28.4:1:1:0:60:43.667:0.9924:0:0.3 0/1:162:8:4,4:97,57:0.0494:2,2:35.4:1:31.6:1:0.47624:1.69586:60:16:0.0497:0:1 -7 81061732 . G A 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14572;SOR=1.39037;LSEQ=TTAACCTATAAGTATGGCCT;RSEQ=AGCTCCACTCAAAGATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:72:26,46:43,69:0.3913:2,2:20.2:1:28.5:1:0.87611:1.10198:60:23:0.3855:0:1.2 0/1:144:68:28,40:31,45:0.4722:2,2:26.4:1:28.3:1:1:1.02:60:33:0.4748:0:1.1 -7 81061754 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19905;SOR=Inf;LSEQ=GCTCCACTCAAAGATTTTCA;RSEQ=ACCTGAAACTGTGGCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:26,99:0:2,0:21.3:1:31.7:1:1:0:60:250:0.9921:0:0.4 0/1:102:2:1,1:29,71:0.0196:2,2:16:1:25.5:1:0.50379:2.42:60:4:0.0198:0:1 -7 81061893 . C G 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.48822;LSEQ=GGGATGCTCAGAGCATGGTT;RSEQ=ACAGGGAACAGCTGAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:1,6:0.4167:2,2:30.2:1:32.2:1:1:1.45:60:10:0.4167:0:1.2 0/1:4:1:1,0:0,3:0.25:0,0:1:0:29:0:0.25:0:60:2:0.3333:0:1 -7 81062013 . C A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71617;SOR=0.63912;LSEQ=GGGCAGGATTCTCCTTCAGG;RSEQ=ATTCAATCAACTGTCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:19:14,5:5,1:0.76:2,2:24.1:1:30.6:1:1:1.74814:60:38:0.76:0:1.8 1/0:15:10:9,1:4,1:0.6667:2,2:20.5:1:29.4:1:1:2.12:60:20:0.6667:0:1.8 -7 81062046 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.49648;SOR=0;LSEQ=GTCATCCCACCTGAGCAAAA;RSEQ=CAGCAGCAGAAACAGCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:25,11:0.0526:2,2:36:1:30:0:0.5377:2.2191:60:4:0.0526:0:2.5 0/0:32:0:0,0:19,13:0:2,0:24.5:1:30.7:1:1:0:60:64:1:0:1.1 -7 81062065 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36727;SOR=1.59344;LSEQ=AGCAGCAGCAGAAACAGCAG;RSEQ=AGCAGGACCACATCTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:26:14,12:14,5:0.5652:2,2:25.2:1:31.8:1:0.22239:2.35358:60:52:0.5909:0:1.6 1/0:37:25:15,10:5,7:0.6757:2,2:29.6:1:30.6:1:0.48211:2.06:60:50:0.6757:0:1.4 -7 81076550 . A G 99 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38462;SOR=0;LSEQ=ATTTAATCAAACATTTTAAT;RSEQ=CTGTGAAAATTCTTAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:0.6667:0,0:26.6:1:33:1:1:0:60:16:0.6667:0:1.8 0/0:1:0:0,0:1,0:0:0,0:27:0:28:0:1:0:60:2:1:0:0 -7 81076607 . C T 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02667;SOR=0;LSEQ=AAAACAAACTCAAAAATATA;RSEQ=GTGCCCTATGAACATAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:9,0:9,0:0.5:0,0:17.6:1:30:1:1:0:60:18:0.5:0:1.7 0/0:7:0:0,0:7,0:0:0,0:28.4:1:31.9:1:1:0:60:14:1:0:0 -7 81076682 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54801;SOR=0;LSEQ=AAAAATTGCTTTTGGATTTT;RSEQ=CTTCTTTTTTCCTGTACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:57,0:0.0339:1,0:33:1:30:0:1:0:60:4:0.0345:0:1 0/0:30:0:0,0:30,0:0:1,0:24.2:1:32.2:1:1:0:60:60:1:0:0.3 -7 81076719 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52446;SOR=0;LSEQ=CATCAAAAAAATCATGCAGT;RSEQ=CCCTTCTAATAATAAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:101,22:0.016:2,2:25.5:1:28:1:0.33535:4.51219:60:4:0.0164:0:2 0/0:78:0:0,0:65,13:0:2,0:21.3:1:31.7:1:1:0:60:156:1:0:0.5 -7 81076743 . A C 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16623;SOR=1.3706;LSEQ=TTCTAATAATAAATATAAAC;RSEQ=TTTTAACTATTTTTGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:76:57,19:100,39:0.3519:2,2:22.4:1:31.4:1:0.74812:1.17:60:152:0.3585:0:1.3 0/1:164:70:49,21:71,23:0.4268:2,2:21.5:1:30.5:1:0.47808:1.32068:60:140:0.4321:0:1.3 -7 81076832 . G A 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69721;SOR=0.94341;LSEQ=GAAACTGACAGCAGAACTAC;RSEQ=TGCAATGTCCCTGATAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:220:116,104:144,138:0.4374:2,2:25.2:1:30.6:1:0.71972:1.07:60:219:0.4415:0:1.2 0/1:468:198:98,100:137,132:0.4231:2,2:26.9:1:29.4:1:0.77931:1.05891:60:197:0.4264:0:1.2 -7 81076924 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50985;SOR=0;LSEQ=CTACTCCCTGTGAGGGATTC;RSEQ=TATTTACCTTCATCTGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:30,151:0.0109:2,2:6.5:1:29:1:0.31087:4.97:60:4:0.0112:0:1.5 0/0:135:0:0,0:35,100:0:2,0:21.6:1:30.2:1:1:0:60:134:1:0:0.5 -7 81076933 . T A 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01582;LSEQ=GTGAGGGATTCGTATTTACC;RSEQ=TCATCTGCTATGTGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:65:8,57:10,79:0.4221:2,2:22.3:1:30.8:1:1:1.11:60:130:0.4248:0:1.1 0/1:108:46:9,37:11,51:0.4259:2,2:18.2:1:29.4:1:0.80798:1.13:60:45:0.4286:0:1.1 -7 81076943 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.51807;SOR=0;LSEQ=CGTATTTACCTTCATCTGCT;RSEQ=TGTGATGGTGGTGGGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:11,112:0.016:2,2:23.5:1:31:1:0.18348:9.79:60:4:0.0161:0:2 0/0:83:0:0,0:10,73:0:2,0:20.3:1:29.7:1:1:0:60:166:1:0:0.4 -7 81331847 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16017;SOR=Inf;LSEQ=TCCACATTCTCTGAAATCTT;RSEQ=ATGTAAAAGACAGTTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:223,55:0:2,0:23.4:1:31.4:1:1:0:60:138:1:0:0 0/1:186:2:1,1:133,50:0.0108:2,2:17.5:1:27.5:1:0.47644:2.64368:60:4:0.0108:0:1 -7 81332000 . C T 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=50.60787;LSEQ=GATTTGGAATGGCACATCCA;RSEQ=GACCAGGAACAATGACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1349:2:0,2:687,657:0.0015:2,0:1:0:26:0:0.23952:0:60:4:0.0015:0:1 0/1:1028:72:35,37:504,452:0.07:2,2:23.1:1:29.3:1:0.54159:1.17857:60:71:0.0697:0:1.1 -7 81332114 . T TA 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.07545;SOR=Inf;LSEQ=AACAAAGTATTATTAGGAAT;RSEQ=AAAAAAAAGCTCATTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:46,297:0:2,0:24.3:1:28.3:1:1:0:60:84.75:1:0:0.1 0/1:252:3:1,2:48,201:0.0119:2,2:28.7:1:27.7:1:0.47877:2.09:60:6:0.012:0:0 -7 81335460 . C T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.13481;LSEQ=CACAGAGAGACCCAAACGCA;RSEQ=GCATATATACATATATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:50:48,2:31,1:0.6098:1,1:25.7:1:30.7:1:1:1.28776:60:49:0.6049:0:1.1 0/1:35:6:6,0:27,1:0.1714:1,0:14.2:1:31.3:1:1:0:60:12:0.1765:0:1 -7 81336265 . C T 79 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAAAGAAGTAGTGAGGA;RSEQ=TGAAAAAAGCCTATTGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:2,0:0.75:0,2:25.3:1:30.8:1:1:0:60:12:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 81336535 . C A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14271;LSEQ=AAAATGAATACATATTATAA;RSEQ=CTTAAGAGCAAAGTGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:110:93,17:249,61:0.2613:2,2:25.7:1:30.4:1:0.39238:1.34:60:220:0.2619:0:1 0/1:292:14:11,3:217,60:0.0479:2,2:18.4:1:30.2:1:1:1.01:60:28:0.0486:0:1 -7 81336744 . C T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28224;SOR=0;LSEQ=AGAGTGACTGCCAATTAATG;RSEQ=AAAGCCTGTGGCTCCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:0,3:20,219:0.0124:2,0:22.7:1:23.3:1:1:0:60:2:0.0084:0:1 0/0:157:0:0,0:15,142:0:2,0:24.3:1:31.9:1:1:0:60:77.5:1:0:0.1 -7 81338269 . T A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTGAGAAAAGGGTATAC;RSEQ=AAAAAAAGAACTTTAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 81339005 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTCTAGAATTTAAAATT;RSEQ=CCATTTTTCATTTGATTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 81339304 . A C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01641;SOR=4.52957;LSEQ=AATTATAGTCCAGAGCTTAC;RSEQ=GTCTGGCAAGCAGATGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:57:56,1:27,0:0.6786:1,1:25.7:1:31.3:1:1:0:60:56:0.6829:0:1.1 1/1:32:29:29,0:3,0:0.9063:0,1:21.7:1:31:1:1:0:60:58:0.9063:0:1.1 -7 81339357 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5487;SOR=0;LSEQ=TTACTGCCTCACCCAGGTGC;RSEQ=CTGTGGAGGGTACAACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:186,1:0.0106:1,0:25:1:30.5:1:1:0:60:4:0.0108:0:1 0/0:98:0:0,0:97,1:0:1,0:23.8:1:29.3:1:1:0:60:23.5:1:0:0.3 -7 81340916 . C A 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00216;SOR=0;LSEQ=AACCAAATATATATTAAAAT;RSEQ=CAAGTATCAATGAATTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:12:1,11:16,163:0.0628:2,2:21.3:1:30.2:1:1:1.07934:60:24:0.0638:0:1 0/0:127:0:0,0:17,110:0:2,0:22:1:31.1:1:1:0:60:126:1:0:0.1 -7 81340934 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51924;SOR=0;LSEQ=ATCCAAGTATCAATGAATTC;RSEQ=GTAATTTACTAAAATTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:2,118:0.0164:1,2:21.5:1:29.5:1:0.04877:48.38:60:4:0.0164:0:2 0/0:80:0:0,0:6,74:0:2,0:22.8:1:31.1:1:1:0:60:160:1:0:0.1 -7 81346292 . A G 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATGCTTTCGGAATCCCA;RSEQ=TGGAAATCTTCTGAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:14,0:0.125:1,0:7:1:32:1:1:0:60:4:0.125:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 81346393 . CTG C 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.31283;SOR=0;LSEQ=AGAGAGACCATGTGGTGTGT;RSEQ=TGTGTGTGTTGTGTACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:4:4,0:84,1:0.0449:1,0:23.8:1:31:1:1:0:60:8:0.046:0.0112:0.3 0/0:39:0:0,0:38,1:0:1,0:23.4:1:30.8:1:1:0:60:38:1:0:0.1 -7 81346685 . T C 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.03573;LSEQ=GTTCCCAGAAGATATGACTG;RSEQ=GGAAACAACAGGCCTTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:689:456:129,327:68,159:0.6618:2,2:25.4:1:30.2:1:0.65489:1.08397:60:455:0.6633:0:1.1 1/1:449:414:137,277:11,24:0.922:2,2:24.4:1:29.9:1:1:1.08:60:58.143:0.9208:0:1.1 -7 81346925 . G A 92 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCATAATTGGCATATTAG;RSEQ=TTTTGTGATTTTGCCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:0,2:0.8:0,0:26.5:1:30.8:1:1:0:60:16:0.8:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 81350208 . A G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.44016;LSEQ=AGTCCAATGAATATCAAGGC;RSEQ=GATAAAACAAAAAGGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:247:34,213:19,138:0.6114:2,2:22.2:1:30.8:1:0.65385:1.16:60:246:0.6165:0:1.7 1/1:288:252:40,212:5,31:0.875:2,2:23.2:1:30:1:1:1.17:60:62:0.8732:0:1.7 -7 81350223 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=3.84794;LSEQ=AAGGCAGATAAAACAAAAAG;RSEQ=TTTTTTACAAGTATATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:270:160:7,153:4,106:0.5926:1,1:25.4:1:31.3:1:1:1.21:60:159:0.6046:0:2.1 1/1:205:174:11,163:2,28:0.8488:2,2:22.5:1:30.3:1:1:1.05815:60:348:0.8488:0:2 -7 81350445 . C T 71 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGGTGGGCGCCTGTAGT;RSEQ=CCAGCTACTCGAGAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:23.8:1:30.8:1:1:0:57:10:1:0:1 1/1:2:2:0,2:0,0:1:0,0:19:1:30:1:1:0:48.5:4:1:0:1 -7 81355066 . G A 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14017;SOR=2.56122;LSEQ=ATAAACATAAGAAAAATCCA;RSEQ=CTTCAAACTTGGTGATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:63:61,2:25,0:0.7159:1,1:22.6:1:29.7:1:1:0:60:30.5:0.7093:0:1.1 1/1:30:26:26,0:4,0:0.8667:0,1:22.5:1:30.8:1:1:0:60:52:0.8667:0:1.1 -7 81355069 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACATAAGAAAAATCCAGCT;RSEQ=CAAACTTGGTGATTTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:90,2:0.0213:1,2:17.5:1:30:1:0.06314:36.93876:60:4:0.0222:0:2 0/0:34:0:0,0:34,0:0:1,0:20.3:1:30.4:1:1:0:60:68:1:0:0.9 -7 81355449 . T A 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=TTTATAAATAGAGTTCTAAC;RSEQ=TTTTGGACTCAGAATAGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:0,97:0:1,0:26:1:30.2:1:1:0:60:194:1:0:0.1 0/1:52:8:0,8:1,43:0.1538:1,0:21.4:1:30.9:1:1:0:60:16:0.1569:0:1 -7 81358266 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACACATGGCATTGTGT;RSEQ=TGTGCCTGTCTGCAAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:40:1:33:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 81358712 . G A 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.94223;LSEQ=TCTGGATCTGAACCACCTAG;RSEQ=GTCCTTAATGAAATGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:10,0:10,0:0.5:0,0:26.9:1:28.3:1:1:0:60:9:0.4737:0:1 1/0:3:2:2,0:1,0:0.6667:0,0:6.5:1:29.5:1:1:0:60:4:0.6667:0:1 -7 81359051 . C T 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=37.11326;LSEQ=TCCTTGACCTTGGATGCATT;RSEQ=AGTTGTTTCCAAAGGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1383:2:1,1:576,803:0.0014:2,2:25:1:20:1:1:1.39:60:1:7e-04:0:2 0/1:1058:54:19,35:452,550:0.051:2,2:26.3:1:28.3:1:0.16245:1.51329:60:53:0.0506:0:1.1 -7 81359116 . CA C 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=2.07142;LSEQ=CTATTGGCAAAAAACAACAA;RSEQ=AAAAAAAACTTATATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:220:21,199:56,187:0.4752:2,2:26:1:32.2:1:1e-04:2.83163:60:219:0.4792:0.041:0.2 1/0:351:229:37,192:41,78:0.6524:2,2:26.5:1:31.5:1:0.00022:2.71883:60:228:0.6533:0.0285:0.2 -7 81359189 . A AT 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.44542;SOR=2.03975;LSEQ=ATTGGCATTTGTATTAGCAG;RSEQ=TTTTTTTTTCTGTTACTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:4:0,4:0,129:0.0301:1,0:29.5:1:30.9:1:1:0:60:8:0.0303:0.0075:0 0/1:67:4:0,4:1,62:0.0597:1,0:15:1:30:1:1:0:60:8:0.0615:0.0299:0.3 -7 81372047 . A G 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11215;SOR=3.72316;LSEQ=ATTGTAAATTCAGAAAAGCT;RSEQ=GGTAAGGGCCAGCATGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:29:29,0:20,0:0.5918:1,1:25.2:1:32.5:1:1:0:60:28:0.5833:0:1.2 1/1:13:11:10,1:2,0:0.8462:0,2:20:1:33:1:1:0:60:22:0.8462:0:1 -7 81372114 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.08744;SOR=Inf;LSEQ=ACAGATCGAAACAGAATGCA;RSEQ=GCTGGGTACAAAGACAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:154,2:0:1,0:22.5:1:32:1:1:0:60:38:1:0:0.6 0/1:66:2:2,0:60,4:0.0303:2,0:26.5:1:32:0:1:0:60:4:0.0308:0:2 -7 81372156 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.39494;LSEQ=AGAGGTAGGGATCAGCTATA;RSEQ=AGATTAGAGACATCTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:189:181,8:120,5:0.6:1,1:23.4:1:32.3:1:1:1.06058:60:93.5:0.6013:0:1.1 1/1:170:154:143,11:15,1:0.9059:1,2:21.9:1:32.1:1:1:1.15289:60:76:0.9048:0:1.1 -7 81372375 . T A 40 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.02094;SOR=Inf;LSEQ=GCACACATTTCCGATCTTTT;RSEQ=CTCTCTCTGTGGTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:0:0,0:61,417:0:2,0:22.7:1:30.1:1:1:0:60:52.111:1:0:0.1 0/1:295:4:3,1:55,236:0.0136:2,2:10:1:20:1:0.02502:12.72:60:3:0.0103:0:1.5 -7 81372452 . A G 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01725;SOR=2.47035;LSEQ=CATAAGTAAAAATGTTTTCT;RSEQ=TGGATGTGTGTATTTGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:147:94:28,66:18,35:0.6395:2,2:22.6:1:32.3:1:0.71132:1.21063:60:93:0.6414:0:1.1 1/1:54:44:7,37:2,8:0.8148:2,2:20:1:31.8:1:0.66673:1.31422:60:88:0.8148:0:1 -7 81372893 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1202;SOR=Inf;LSEQ=GGTTGTCTACACCTAGCTGG;RSEQ=GAAAGAGGACGTTTTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:1,112:0:1,0:26.5:1:31.1:1:1:0:60:27.25:1:0:0.2 0/1:61:2:1,1:0,59:0.0328:1,2:13:1:30:1:0.03279:0:60:4:0.0333:0:1 -7 81374247 . G C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13409;SOR=Inf;LSEQ=ATATAAAGAGAATTTCCACA;RSEQ=CAGTGTGTCATAGAGTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:198,40:0:2,0:23.5:1:32.1:1:1:0:60:118:1:0:0.1 0/1:138:2:1,1:112,24:0.0145:2,2:17.5:1:27:1:0.33058:4.59277:60:4:0.0147:0:1 -7 81374500 . G C 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCAAAAACACCACTGTT;RSEQ=CATTTAAAGAACAGCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:240:240:41,199:0,0:1:0,2:22.5:1:30.9:1:1:0:60:47:1:0:1.1 1/1:168:168:30,138:0,0:1:0,2:21.9:1:30.5:1:1:0:60:55:1:0:1.1 -7 81374551 . A T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29823;SOR=0;LSEQ=AGATTTTTAAAAAATCCTAC;RSEQ=CATCATTCTAACTTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:4:0,4:1,86:0.044:1,0:27:1:29.5:1:1:0:60:8:0.0444:0:1.5 0/0:48:0:0,0:1,47:0:1,0:22.3:1:30:1:1:0:60:96:1:0:0.9 -7 81375051 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCAGGTTTACATTCCT;RSEQ=TCTGGCTTAGGATAGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 81381326 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.07585;LSEQ=TATTTGTAGTTGCATTTGCA;RSEQ=GAACAACATATTTGTTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:125:125,0:96,3:0.558:1,1:26.5:1:31.8:1:0.08486:0:60:250:0.558:0:1.1 1/1:119:103:100,3:16,0:0.8655:1,1:24.1:1:30.4:1:1:0:60:206:0.8655:0:1 -7 81381621 . C CT 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.59296;SOR=1.3748;LSEQ=TACAGTATAAGAGCATGCAA;RSEQ=TTTTTTTTGCCTATTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:7:2,5:74,382:0.0151:2,2:32.6:1:30:1:0.32306:2.06:60:14:0.0151:0:0 0/1:340:7:1,6:62,270:0.0206:2,2:17.1:1:29.6:1:1:1.37659:60:14:0.0208:0.0029:0 -7 81381731 . T C 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02209;SOR=3.93406;LSEQ=ACCTTAAAATTCTGTCATTT;RSEQ=CATCTGTCCTTAAAACGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:30:0,30:0,24:0.5556:1,1:20.7:1:31.6:1:1:0:60:60:0.5556:0:1 1/1:24:20:0,20:1,3:0.8333:2,1:21.9:1:31.9:1:0.16667:0:60:40:0.8333:0:1 -7 81386418 . TG T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1635;SOR=Inf;LSEQ=TGGCTAAGTTATTTTAGGAT;RSEQ=TAGAATTATTCTGAAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:224,36:0:2,0:22.5:1:32.2:1:1:0:60:129:1:0:0 0/1:177:2:1,1:153,22:0.0113:2,2:21:1:29.3:1:0.24364:6.82324:60:4:0.0114:0.0056:0 -7 81387856 . GT G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06383;SOR=Inf;LSEQ=TAAAAATAGTCAAGATACTA;RSEQ=TTCAACTGTCTTAATGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:105,0:0:1,0:22.7:1:30.2:1:1:0:60:104:1:0:0 0/1:36:2:1,1:34,0:0.0556:1,2:44.5:1:31.5:1:0.05556:0:60:4:0.0571:0:0 -7 81388001 . C A 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCAATATTTAGGGAGAAGT;RSEQ=AGTTACCTTTGTTTTCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1085:58:41,17:600,425:0.0535:2,2:22.3:1:29:1:0.07451:1.71:60:116:0.0538:0:1 0/0:849:0:0,0:502,345:0:2,0:47:0:11:0:1:0:60:0:0:0:7 -7 82274286 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20657;SOR=Inf;LSEQ=AATGCCTTTCAAACTCTATA;RSEQ=CAAACTCTGGAGTTGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:22,17:0:2,0:30.4:1:30.1:1:1:0:60:12:1:0:0.3 0/1:33:2:2,0:18,13:0.0606:2,0:13.5:1:31:1:0.50758:0:60:4:0.0606:0:1 -7 82948338 . C T 94 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.51811;LSEQ=TGTGAGGAAAAACATTATTC;RSEQ=AACTTCATGCTCACTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:7,1:8,0:0.5:0,2:27.4:1:31.6:1:1:0:60:16:0.5333:0:2 0/1:3:1:1,0:2,0:0.3333:0,0:22:0:33:0:1:0:60:2:0.3333:0:2 -7 82948362 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91231;LSEQ=TTCATGCTCACTTTTTTTAA;RSEQ=CCTTTTTTTTGCACTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:10,1:9,0:0.5238:0,2:27.3:1:31.4:1:1:0:60:22:0.5238:0:2.2 1/0:6:3:3,0:3,0:0.5:0,0:23.3:1:31:1:1:0:60:6:0.5:0:2 -7 82948434 . T G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00567;SOR=0.15666;LSEQ=TGCAACTCCACAGAATTGAG;RSEQ=ACTCTGTCTGTGTAAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:25:24,1:9,0:0.7353:0,1:27:1:31.6:1:1:0:60:50:0.7353:0:1.3 0/1:17:5:4,1:12,0:0.2941:0,2:25.2:1:30:1:0.29412:0:60:10:0.2941:0:1.4 -7 82948537 . C T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38049;LSEQ=TCCCTGCTCTCTTCTTGTCA;RSEQ=TCAGGCAAAGAATTTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:244:137:102,35:77,30:0.5615:2,2:27.3:1:30.3:1:0.6648:1.13:60:67.5:0.5649:0:1.9 0/1:214:70:51,19:97,47:0.3271:2,2:25.8:1:30.2:1:0.43527:1.30:60:34:0.3269:0:1.9 -7 82948594 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.35849;LSEQ=GATTTACAAACTTTTGCCAA;RSEQ=GGAAGAAAATAATGAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:455:260:136,124:110,85:0.5714:2,2:26.2:1:30.3:1:0.39394:1.1795:59.9:25:0.5643:0:2.2 0/1:458:148:80,68:169,141:0.3231:2,2:25.4:1:29.7:1:1:1.01876:60:73:0.3259:0:2.2 -7 82948627 . G T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.36916;LSEQ=TGAGGTTGCTTGGAGGTAGA;RSEQ=AAGAGGTGGGATTTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:481:269:118,151:95,116:0.5593:2,2:26.7:1:28.6:1:0.85322:1.04786:59.9:28.889:0.5579:0:1.9 0/1:480:153:69,84:149,177:0.3188:2,2:28.2:1:28.2:1:0.92186:1.02476:60:29.6:0.3136:0:1.9 -7 82948699 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51082;SOR=0;LSEQ=GAGGGCAGTAAGCAATCCTC;RSEQ=TAGAAAGAGACTATGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:27,154:0.0109:2,2:20:1:30:1:0.28331:5.62:60:4:0.0112:0:1.5 0/0:134:0:0,0:27,107:0:2,0:20.6:1:29.9:1:1:0:60:66:1:0:0.3 -7 82948727 . C CTGTT 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=6.000;MSILEN=4;SSF=0.00043;SOR=0.24835;LSEQ=AGACTATGTCTGTTTTTTCC;RSEQ=TGTTTGTTTGTTTGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:44:1,43:0,58:0.4272:1,1:29.5:1:30:1:0.43137:0:59.8:88:0.4356:0.0583:0.2 0/1:58:9:0,9:2,47:0.1552:1,0:30.9:1:31.3:1:1:0:59.4:18:0.1579:0.0172:0.3 -7 82948848 . G A 47 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TAAAGTAACTGAAATTGTAA;RSEQ=CAGGTAGACTGAGACAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:25:1:30:1:1:0:60:6:0.75:0:1 0/0:1:0:0,0:0,1:0:0,0:10:0:33:0:1:0:60:2:1:0:0 -7 82949154 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCAATTTAATATTTG;RSEQ=TATTTTTCAAAATCTTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:31.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 82949179 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAAAATCTTCAAGGATA;RSEQ=ATCATCTCTGGAAAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:32.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 82956889 . C T 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.46966;LSEQ=AATAATGCCTCCTGTGATTG;RSEQ=CTGGCTTGTGGTAGAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:587:380:207,173:112,95:0.6474:2,2:26.4:1:29.6:1:0.93117:1.01:60:41.222:0.6475:0:1.1 0/1:538:249:133,116:154,135:0.4628:2,2:27:1:28.8:1:1:1.01:60:123.5:0.4643:0:1.1 -7 83192801 . ACAGCAGCAG A 32 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=3;SSF=0.50529;SOR=0;LSEQ=AGGTGGTCTCTGGACCAGCA;RSEQ=CAGCAGCAGCAGCTAGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:14,10:0.0769:2,2:27:1:32.7:1:1:1.38168:60:4:0.0769:0.0385:0 0/0:18:0:0,0:9,7:0:2,0:25:1:31:1:1:0:60:32:0.8889:0:0.1 -7 83194444 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCCTAGACACATACACC;RSEQ=TCCCAAGACTAAACCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:1:33.5:1:1:0:52:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 83542173 . G A 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.1803;LSEQ=ATGTCTTTCAGAGATGACAT;RSEQ=TCTCCCATTTGTCTTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:594:90:37,53:256,246:0.1515:2,2:26:1:29.4:1:0.08727:1.48965:60:44:0.1512:0:1.1 0/1:403:113:59,54:142,147:0.2804:2,2:25.7:1:28.9:1:0.6573:1.13:60:226:0.2839:0:1.2 -7 83542230 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06135;SOR=Inf;LSEQ=TATTTCTGTAAGCAGAATGG;RSEQ=CTTTTCTGTTTCCTTATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:138,252:0:2,0:23.5:1:31.3:1:1:0:60:54.714:1:0:0.2 0/1:255:3:2,1:98,154:0.0118:2,2:32:1:26.7:1:0.563:3.13:60:6:0.0119:0:1 -7 83542648 . C A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTCACTTAGGTTAATGA;RSEQ=CTTCAGTTCCATCCATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:28:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:44.5:1:30.5:1:1:0:60:4:1:0:1.5 -7 84354805 . T C 25 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATTGAACAACCTGCTCC;RSEQ=GAATGACTCCTGGGTAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:25:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 85244212 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51652;SOR=0;LSEQ=GAGCAGTGGAAAGTTCCAGG;RSEQ=AGCCAGTCCCTGTGACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:0.087:2,2:19.5:1:27.5:1:1:1.09544:60:4:0.0909:0:1 0/0:14:0:0,0:7,7:0:2,0:28.1:1:32.1:1:1:0:60:28:1:0:0.2 -7 85244362 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACAGGAGTGCAGTTTG;RSEQ=CCCCATTTCCCCACTGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 85607920 . A G 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00151;SOR=Inf;LSEQ=AAGGGTGAATAGGAAGTCAA;RSEQ=TTAGTAAATTAAGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:0:1,0:26.5:1:30.4:1:1:0:60:58:1:0:0 0/1:13:5:5,0:8,0:0.3846:0,0:17:1:33.2:1:1:0:60:10:0.3846:0:1 -7 85608016 . TTGTC T 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AAAAACTAAGCTAAAGGATA;RSEQ=TATTATCTTTGTAATATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:115,21:0:2,0:21.2:1:30.1:1:1:0:60:272:1:0:0.3 0/1:102:18:13,5:70,14:0.1765:2,2:27.4:1:28.5:1:0.31845:1.90917:60:17:0.1683:0.0098:1 -7 85608081 . A T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.00701;LSEQ=TGATTCACATATATGAAATG;RSEQ=GGAATTAAATGAGCAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:150:88,62:140,100:0.3846:2,2:27.7:1:30:1:1:1.01:60:149:0.387:0:1.7 1/0:343:224:125,99:66,53:0.6531:2,2:27.3:1:29.5:1:1:1.01:60:73.667:0.6558:0:1.8 -7 85608107 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.07899;LSEQ=TAAATGAGCAAAAAATTAAT;RSEQ=GTTTTTCAGGGGTCATGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:98:52,46:173,165:0.2248:2,2:26.6:1:29.8:1:0.81854:1.08:60:196:0.2279:0:2.2 1/0:378:205:102,103:83,90:0.5423:2,2:26.2:1:29:1:0.75732:1.07:60:410:0.5467:0:2 -7 85608162 . G A 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01908;SOR=1.62513;LSEQ=GTTATATTATGAGGTTTCTC;RSEQ=AAATAGTGCTGTCTTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:65:21,44:68,142:0.2364:2,2:24.7:1:29.8:1:1:1.00334:60:130:0.2372:0:1.9 0/1:212:71:27,44:43,98:0.3349:2,2:22.9:1:30:1:0.28252:1.40:60:142:0.3381:0:2 -7 85608189 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1768;SOR=Inf;LSEQ=TGCTGTCTTGGGTAGAAAGA;RSEQ=GTCCCCAAAGGACAATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:41,143:0:2,0:23.6:1:31.1:1:1:0:60:60.333:1:0:0.3 0/1:134:2:1,1:32,100:0.0149:2,2:46.5:1:30:1:0.43328:3.09:60:4:0.015:0:1 -7 86544591 . C T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08155;SOR=Inf;LSEQ=TTCAAATTTTTTATCTTTTT;RSEQ=CTTCAGAGATTCTGATAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:248,102:0:2,0:23.5:1:31:1:1:0:60:57.333:1:0:0.3 0/1:269:3:0,3:185,81:0.0112:2,0:8:1:21.7:1:0.0297:0:60:2:0.0076:0:2.7 -7 86544667 . G T 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49296;LSEQ=ATACTTGCAAGTTCCAGGGT;RSEQ=ACTTTATCCAAGTGCATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:618:384:176,208:108,124:0.6214:2,2:25.5:1:29.2:1:0.86791:1.02929:60:191:0.6211:0:1.1 0/1:472:211:96,115:115,146:0.447:2,2:24.4:1:28.3:1:0.78042:1.06:60:69.333:0.4454:0:1.2 -7 87600830 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24696;SOR=Inf;LSEQ=CAATATTATTCTGTAATACC;RSEQ=GAAGTACCTGTTTAATAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:95,29:0:2,0:22.5:1:30.8:1:1:0:60:123:1:0:0.1 0/1:123:2:1,1:92,28:0.0163:2,2:40.5:1:29.5:1:0.4204:3.24605:60:4:0.0165:0:1 -7 87600844 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24341;SOR=0;LSEQ=AATACCTGAAGTACCTGTTT;RSEQ=ATAGTTTTTAAAATCACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:123,43:0.0119:2,2:24.5:1:27.5:1:0.45637:2.83924:60:4:0.012:0:1.5 0/0:172:0:0,0:122,50:0:2,0:23.6:1:27.8:1:1:0:60:42:1:0:0.3 -7 87600926 . G C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10667;LSEQ=ATTACGTTTTTCCAGTATCT;RSEQ=TGAGGGGTATTACTACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:362:317:156,161:20,24:0.8757:2,2:26.7:1:31.8:1:0.74794:1.16:60:104.667:0.8771:0:2 0/1:327:140:65,75:98,89:0.4281:2,2:28.2:1:31.5:1:0.31504:1.26958:60:139:0.429:0:2 -7 87600931 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.10601;LSEQ=GTTTTTCCAGTATCTGTGAG;RSEQ=GGTATTACTACTTTTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:359:313:151,162:22,23:0.8719:2,2:26.5:1:30.4:1:1:1.02613:60:77.25:0.8754:0:2 0/1:330:138:62,76:98,94:0.4182:2,2:27.9:1:29.4:1:0.31507:1.27701:60:137:0.419:0:2 -7 91077042 . A T 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54118;SOR=0;LSEQ=CCATTTGTAAGACCATCTGT;RSEQ=GCTTCATGGCCTTGATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:9,1:0.2308:2,0:8.3:1:30.3:1:1:0:40:6:0.2308:0:7 0/0:4:0:0,0:2,2:0:2,0:38.5:1:30:1:1:0:60:8:1:0:0 -7 91077047 . C G 52 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54118;SOR=0;LSEQ=TGTAAGACCATCTGTAGCTT;RSEQ=ATGGCCTTGATTCTAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:9,1:0.2308:2,0:13.3:1:33.3:1:1:0:40:6:0.2308:0:7 0/0:4:0:0,0:2,2:0:2,0:40.3:1:32.3:1:1:0:60:8:1:0:0 -7 91077051 . G A 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52206;SOR=0;LSEQ=AGACCATCTGTAGCTTCATG;RSEQ=CCTTGATTCTAGAGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:9,1:0.2308:2,0:17.3:1:31.3:1:1:0:40:6:0.2308:0:7 0/0:5:0:0,0:3,2:0:2,0:33:1:31.8:1:1:0:60:10:1:0:0 -7 91077075 . T C 65 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26382;SOR=0;LSEQ=TGATTCTAGAGGAAACAAAT;RSEQ=TGACAAGGAGGTTAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:12,1:0.2353:1,0:37:1:32.8:1:1:0:40:8:0.2353:0:6.3 0/0:10:0:0,0:7,3:0:2,0:16.6:1:27.6:1:1:0:60:9:1:0:0.2 -7 91077096 . C T 63 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27203;SOR=0;LSEQ=TGACAAGGAGGTTAAAAATA;RSEQ=AGAGCCCGAAGGCGAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:12,4:0.2:2,0:36.5:1:31.8:1:0.53767:0:40:8:0.2:0:6.3 0/0:10:0:0,0:8,2:0:2,0:22.9:1:31.6:1:1:0:60:20:1:0:0.2 -7 91077099 . A G 64 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27203;SOR=0;LSEQ=CAAGGAGGTTAAAAATACAG;RSEQ=GCCCGAAGGCGAGTAATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:12,4:0.2:2,0:33.5:1:32:1:0.53767:0:40:8:0.2:0:6.3 0/0:10:0:0,0:8,2:0:2,0:24.4:1:29.5:1:1:0:60:20:1:0:0.2 -7 91077127 . C A 60 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11355;SOR=0;LSEQ=GGCGAGTAATAGCAAGATGG;RSEQ=TGCCAAGAGACCTAGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:4,0:17,12:0.1212:2,0:5.5:1:30:1:0.27126:0:40:8:0.1212:0:6.3 0/0:32:0:0,0:15,13:0:2,0:18.6:1:31.9:1:1:0:59.9:56:0.875:0:0.2 -7 91077168 . C A 45 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11643;SOR=0;LSEQ=GGAGAAGCCATGTTGCCCAA;RSEQ=TCCAGAGGTTGGTATAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:0,3:19,21:0.0698:2,0:22:1:28.7:1:0.24252:0:40:6:0.0714:0:5.3 0/0:44:0:0,0:21,23:0:2,0:30.3:1:31.1:1:1:0:57.9:88:1:0:0.2 -7 91077180 . G A 57 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11785;SOR=0;LSEQ=TTGCCCAACTCCAGAGGTTG;RSEQ=TATAAGAGTTTGAAAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:0,4:18,23:0.0889:2,0:28.5:1:28.8:1:0.13833:0:40:8:0.0909:0:5.5 0/0:41:0:0,0:18,23:0:2,0:28:1:30.8:1:1:0:57.7:82:1:0:0.2 -7 91077199 . G T 59 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12546;SOR=0;LSEQ=GGTATAAGAGTTTGAAAGGT;RSEQ=TTGTCTGATTTCAGAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:4:0,4:15,24:0.093:2,0:41:1:29.5:1:0.2802:0:40:8:0.0952:0:5.5 0/0:34:0:0,0:13,21:0:2,0:21.8:1:31.2:1:1:0:57.9:33:1:0:0.1 -7 91077210 . T C 63 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11991;SOR=0;LSEQ=TTGAAAGGTGTTGTCTGATT;RSEQ=CAGAAGCCTTTTCCTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:0,4:9,20:0.1212:2,0:36.3:1:31.8:1:0.55484:0:40:8:0.129:0:5.5 0/0:27:0:0,0:9,18:0:2,0:20.8:1:29.3:1:1:0:58.2:54:1:0:0.1 -7 91077235 . A G 51 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53613;SOR=0;LSEQ=AGCCTTTTCCTGTAAATGCC;RSEQ=GGCGGCATCTCATACTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:0,3:4,17:0.125:2,0:20.3:1:32.3:1:1:0:40:6:0.1364:0:6 0/0:12:0:0,0:4,8:0:2,0:21.3:1:30.3:1:1:0:57:24:1:0:0.1 -7 91077238 . C T 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53281;SOR=0;LSEQ=CTTTTCCTGTAAATGCCAGG;RSEQ=GGCATCTCATACTATCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:3,15:0.1429:2,0:17.3:1:31:0:1:0:40:6:0.15:0:6 0/0:10:0:0,0:2,8:0:2,0:22.7:1:29.8:1:1:0:59.3:20:1:0:0.1 -7 91177925 . G A 29 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATATATATATTTATGGTGC;RSEQ=TGTGTGTGTGTGTAATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36:1:29:1:1:0:60:4:1:0:3 -7 91179796 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.74445;LSEQ=ACACTTTCAGTGTAATAGAC;RSEQ=TCTGCACCCAGTTGAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:1,2:146,84:0.0128:2,2:26:1:28.3:1:0.55656:3.45685:60:6:0.013:0:1 0/0:209:2:1,1:134,73:0.0096:2,2:7.5:1:16:1:1:1.83003:60:0:0:0:2 -7 91179891 . A G 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00151;SOR=0.5779;LSEQ=TACTTCTCTGAAGTATGCAC;RSEQ=AGTACAAAATGACATATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:314:212:99,113:45,57:0.6752:2,2:23.9:1:30.4:1:0.71733:1.11:60:105:0.6731:0:1.1 1/0:264:144:67,77:52,68:0.5455:2,2:20.8:1:29.8:1:0.62124:1.14:60:71:0.5441:0:1.1 -7 91179983 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50325;SOR=0;LSEQ=TAATGCTATTTAGAATGTTT;RSEQ=TATTAGCATATTTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:32,87:0.0165:2,2:24:1:29.5:1:0.47273:2.69:60:4:0.0168:0:1.5 0/0:98:0:0,0:22,76:0:2,0:24:1:31.2:1:1:0:60:97:1:0:0.3 -7 91180001 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51134;SOR=0;LSEQ=TTGTATTAGCATATTTTTTC;RSEQ=TTTCTTGCTCCTATTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:19,72:0.0215:2,2:6.5:1:30.5:1:0.38569:3.72:60:4:0.0217:0:1 0/0:66:0:0,0:12,54:0:2,0:22.1:1:32:1:1:0:60:132:1:0:0.2 -7 91180056 . T C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19115;SOR=0.40365;LSEQ=GTAAAAACTAGGTTTTGGCC;RSEQ=CTGGCATCCATTCATCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:26:1,25:0,9:0.7429:0,1:31.5:1:31.7:1:1:0:60:52:0.7429:0:1 1/0:15:8:0,8:0,7:0.5333:0,0:19.8:1:29.4:1:1:0:60:7:0.5:0:1.3 -7 91180083 . T C 97 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30855;SOR=0;LSEQ=TCCATTCATCCTACTTCCTT;RSEQ=ACTAATTCTCCTTTCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:0,8:1,20:0.2759:1,0:23.9:1:32.6:1:1:0:60:16:0.2759:0:1 0/0:5:0:0,0:0,5:0:0,0:30:1:27.4:1:1:0:60:10:1:0:0.4 -7 92242414 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCTCCTTTATTATCTT;RSEQ=CTCTAGAAAACAATGTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:27.5:1:31:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 92244368 . C T 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.27837;SOR=0;LSEQ=GCCTCCAGATAGCAATCCTC;RSEQ=ACAGCTCTGTAGGGCTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:1,2:115,14:0.0227:2,2:7.7:1:20.3:1:0.03865:15.74956:60:2:0.0156:0:1 0/0:87:0:0,0:77,10:0:2,0:23.5:1:29.8:1:1:0:60:28:1:0:0.3 -7 92244422 . C T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.84841;LSEQ=AAGCCACCAAGGGTGTTCTC;RSEQ=GCAGGATCAGCTTAAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:353:8:5,3:251,94:0.0227:2,2:21.3:1:31:1:0.68918:1.59979:60:16:0.023:0:1 0/1:316:77:50,27:169,70:0.2437:2,2:23.6:1:29.5:1:0.39409:1.30255:60:18.25:0.237:0:1.2 -7 92244630 . TATACA T 159 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=22.74587;LSEQ=AGAAAAAAATAATTGGTTGA;RSEQ=ATACATCAATGTAAATAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:42,199:0.0123:2,2:28:1:33:0:0.44247:2.36:60:6:0.0128:0:0.3 0/1:194:43:8,35:29,122:0.2216:2,2:24.1:1:29.4:1:1:1.03975:60:42:0.2188:0.0361:0.2 -7 92244650 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.506;SOR=0;LSEQ=TATACAATACATCAATGTAA;RSEQ=TAATGTACTTACAGAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:13,148:0.0123:2,2:14:1:31:1:0.16489:11.01:60:4:0.0123:0:1 0/0:127:0:0,0:13,114:0:2,0:23.2:1:29.9:1:1:0:60:62.5:1:0:0.1 -7 92247112 . C T 60 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATATGTCAAAGTGAAT;RSEQ=GAGAGGCTTCTAAACCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:29.8:1:30:1:1:0:60:8:0.4:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 92247333 . A G 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=10.34641;LSEQ=CCACCACCCAGTCTGGGTAG;RSEQ=GCAGGTGTCTCACTGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:452:12:10,2:349,90:0.0265:2,2:17.2:1:31.4:1:1:1.29:60:24:0.027:0:1.1 0/1:331:73:56,17:199,59:0.2205:2,2:21:1:30.9:1:1:1.02386:60:146:0.2246:0:1.1 -7 92247539 . A G 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGCTACAAAAGAACCACAC;RSEQ=TGGACATAAGCATTAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:696:0:0,0:199,497:0:2,0:24.5:1:30.5:1:1:0:60:52.538:1:0:0.1 0/1:559:57:16,41:161,339:0.102:2,2:26.1:1:30.3:1:0.65258:1.21662:60:27.5:0.1007:0:1.1 -7 92252191 . AC A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CTGCATAAAACGGCACTTCT;RSEQ=CATGTCTCCACTCACCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:2,0:56,1:0.0333:1,0:30:1:29.5:1:1:0:60:4:0.0339:0:0.5 0/0:45:0:0,0:43,2:0:1,0:22.6:1:31:1:1:0:60:44:1:0:0.2 -7 92252203 . C G 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20574;LSEQ=GCACTTCTACCATGTCTCCA;RSEQ=TCACCACACAAATAGTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:5,0:63,1:0.0725:1,0:14.4:1:30.2:1:1:0:60:10:0.0725:0:1 0/1:58:5:5,0:51,2:0.0862:1,0:20.6:1:28.4:1:1:0:60:4:0.0702:0:1.4 -7 92252239 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18929;SOR=Inf;LSEQ=TAACACTGTCTGCAGCAGCT;RSEQ=CTTGAAGTAAGAAAGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:105,19:0:2,0:23.5:1:31.8:1:1:0:60:61:1:0:0.1 0/1:96:2:2,0:79,15:0.0208:2,0:25.5:1:29:1:1:0:60:4:0.0211:0:1 -7 92300587 . G A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00111;SOR=Inf;LSEQ=ACTGTAAGCACTGAGAAGGC;RSEQ=GTTTCAGGACAGGCTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:0:1,0:24.9:1:29.9:1:1:0:60:30:1:0:0.1 0/1:22:7:7,0:14,1:0.3182:1,0:15:1:31.6:1:1:0:60:14:0.3182:0:1 -7 92300798 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04711;SOR=Inf;LSEQ=CCAGAGATCCACGGGGGTGG;RSEQ=GTAGCTGGACTGGAGCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:237,213:0:2,0:26.4:1:30.6:1:1:0:60:63.286:1:0:0.2 0/1:394:4:2,2:196,193:0.0102:2,2:29.8:1:30:1:1:1.01551:60:8:0.0104:0:1 -7 92300858 . G A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04664;SOR=Inf;LSEQ=CAGCGTGACGACCTGCAATG;RSEQ=CAAGCGGATCCAAGTGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:125,205:0:2,0:26.2:1:31.3:1:1:0:60:40.25:1:0:0.1 0/1:288:4:3,1:99,185:0.0139:2,2:20.8:1:28.3:1:0.1289:5.57:60:8:0.0141:0:1 -7 92300880 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31709;SOR=4.07389;LSEQ=AAGCGGATCCAAGTGTTACT;RSEQ=AGAAGGTGGCTGTTGGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:1:1,0:80,190:0.0037:2,0:1:0:24:0:0.29889:0:60:2:0.0038:0:1 0/1:202:3:2,1:58,141:0.0149:2,2:29.7:1:25.7:1:0.21099:4.82:60:6:0.015:0:1 -7 92354913 . A T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08104;SOR=Inf;LSEQ=AAATAGGAAAAATAAGTTTA;RSEQ=TAAAAGGACAGCACTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:294,93:0:2,0:23.3:1:30.2:1:1:0:60:54.286:0.9974:0:0.1 0/1:297:3:1,2:205,89:0.0101:2,2:11.3:1:22:1:0.22327:4.58014:60:2:0.0068:0:2.3 -7 92355225 . C T 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=Inf;LSEQ=GGCATGCGGCAGGCATTTGA;RSEQ=AGGTATTGGCTGAATGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:2,33:0:2,0:24.8:1:32.1:1:1:0:60:34:1:0:0.1 0/1:20:7:0,7:0,13:0.35:1,0:16.6:1:29:1:1:0:60:14:0.35:0:1 -7 92404120 . G A 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00325;SOR=Inf;LSEQ=TTTGGTTTCTCTGTCTGTTC;RSEQ=TGACACTGTGCACACATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:848:0:0,0:340,508:0:2,0:25.3:1:31:1:1:0:60:76.091:1:0:0.1 0/1:533:6:5,1:200,327:0.0113:2,2:13.8:1:25.8:1:0.03353:8.14:60:5:0.0094:0:1.3 -7 92404179 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10527;SOR=Inf;LSEQ=CAAAGAGGTTAAGTAGGTGG;RSEQ=AATAAGCAAAGAAGTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:73,282:0:2,0:23.6:1:32.1:1:1:0:60:58.167:1:0:0.1 0/1:171:2:1,1:29,140:0.0117:2,2:8:1:29.5:1:0.32095:4.76:60:4:0.0119:0:1 -7 92404285 . A G 82 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17683;SOR=0;LSEQ=TCTTGTGATCATATGTAAAG;RSEQ=TATCAAATGAGATCTGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:0,6:0,45:0.1154:1,0:19.8:1:32:1:1:0:60:12:0.1176:0:1 0/0:20:0:0,0:0,20:0:1,0:21.3:1:30.3:1:1:0:60:19:1:0:0 -7 92462641 . G A 44 v4;q23;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24194;SOR=2.80876;LSEQ=AGGCCGTCCTTCTCCATGCC;RSEQ=CCTGGACGCCGCCCGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:2:1,1:80,367:0.0044:2,2:9.5:1:28.5:1:0.32859:4.57:60:4:0.0045:0:1 0/1:324:4:4,0:74,246:0.0123:2,0:8.3:1:22.3:1:0.00316:0:60:3:0.0095:0:1.8 -7 92462690 . T C 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56215;SOR=3.06964;LSEQ=GGGGCGGGCGGGGGGTGCGC;RSEQ=CAACTAGCTGGCGGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:1:0,1:2,57:0.0167:1,0:3:0:19:0:1:0:60:0:0:0:1 0/1:40:2:1,1:1,37:0.05:1,2:7:1:31.5:1:0.09872:26.51:60:4:0.0513:0:1 -7 92462938 . A T 27 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12;SOR=0;LSEQ=CCTCTTCCCTCCTCGAAGCG;RSEQ=AGTCCTCAACACAGACACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:33.5:1:27.5:1:1:2.24:60:4:0.2222:0:1 0/0:16:0:0,0:7,9:0:2,0:27.3:1:29.1:1:1:0:60:32:1:0:0 -7 95912679 . CA C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=TCACCAAAATGGGATGAACA;RSEQ=AAGGGAAAGAGGAGAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:0.125:2,2:15:1:30:1:1:1.30929:60:4:0.125:0:0 0/0:12:0:0,0:8,4:0:2,0:21.6:1:27.1:1:1:0:60:5:1:0:0.2 -7 95912778 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49315;SOR=0;LSEQ=TATGCAAATCTATAAGAAAG;RSEQ=TGATATTGTAGACATTAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:23,12:0.0541:2,2:17.5:1:28.5:1:1:1.88115:60:4:0.0556:0:1 0/0:36:0:0,0:20,16:0:2,0:27.1:1:31.2:1:1:0:60:72:1:0:0.2 -7 95912847 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22169;SOR=Inf;LSEQ=TTACAAGTGTTACCATGGCA;RSEQ=AAGTAGAGGAGTCTACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:29,30:0:2,0:30.7:1:29.8:1:1:0:60:58:1:0:0.1 0/1:53:2:1,1:29,22:0.0377:2,2:44.5:1:31:1:1:1.31123:60:4:0.0377:0:1 -7 95913083 . T C 75 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAACTCACGGGAAGGAGC;RSEQ=TGCATTGCTGGAAGCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:24.2:1:32.6:1:1:0:60:10:1:0:1.8 1/1:3:3:0,3:0,0:1:0,0:16.7:1:32.7:1:1:0:60:6:1:0:1 -7 96635355 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49758;SOR=0;LSEQ=TCGTCCAAATCCGCCTTCAT;RSEQ=GAGTTCGGGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:9,15:0.0769:2,2:8.5:1:28:1:1:1.63:60:4:0.087:0:1.5 0/0:20:0:0,0:12,8:0:2,0:26.5:1:28.2:1:1:0:60:5.667:1:0:0.6 -7 96635388 . ACAG A 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.23684;SOR=Inf;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:8,21:0:2,0:27.4:1:31.6:1:1:0:60:28:1:0:0.4 0/1:28:2:1,1:10,15:0.0714:2,2:29.5:1:30:1:1:1.48:60:4:0.0741:0:0 -7 96635543 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGCGGCAGCGGCCGGCT;RSEQ=GCACCACCACCACCACCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:15.5:1:28:1:1:1.22474:60:4:0.1818:0:1.5 0/0:4:0:0,0:2,2:0:2,0:19.3:1:28.8:1:1:0:60:8:1:0:0.3 -7 96636627 . C A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCGCTCCGCCCGGACAG;RSEQ=TGCCGCCTTGCTGCGCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 97096756 . AT A 33 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATAAGGAAAACCATCACT;RSEQ=TTTTTTTTTTTAAGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:35:1:33:0:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 97097087 . A G 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00249;SOR=2.01396;LSEQ=CTTTACAGTTAAAAAAGGAG;RSEQ=GTAGGTTATCTGTTAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:33:16,17:174,162:0.0894:2,2:25.8:1:30.5:1:0.71999:1.14079:60:66:0.0904:0:1.1 0/1:357:59:31,28:137,160:0.1653:2,2:24.7:1:30.7:1:0.39389:1.29:60:118:0.1667:0:1.1 -7 97097173 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13927;SOR=Inf;LSEQ=TCATGAGGTTAACCAGGAAT;RSEQ=AAAACACCCAAAGCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:37,115:0:2,0:24.3:1:31.2:1:1:0:60:49.667:1:0:0.1 0/1:91:2:1,1:24,65:0.022:2,2:21.5:1:27:1:0.47619:2.67:60:4:0.022:0:1 -7 97793130 . GC G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.5046;SOR=0;LSEQ=CATAACCCAAGGCAGGACCT;RSEQ=CCCCTGGCCGCAATACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:103,53:0.0127:2,2:27:1:31:1:1:1.93471:60:4:0.013:0:0 0/0:126:0:0,0:84,42:0:2,0:21.8:1:30.9:1:1:0:60:62:1:0:0.3 -7 97793182 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1085;SOR=Inf;LSEQ=GCACAGAGGGCAGCGGTCTG;RSEQ=GCTCTGTAAAAAGCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:137,123:0:2,0:27.5:1:30.2:1:1:0:60:17.571:1:0:0.4 0/1:239:3:1,2:130,106:0.0126:2,2:18.3:1:27:1:0.5907:2.44383:60:6:0.0128:0:1.7 -7 97793209 . G T 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.92256;SOR=0.96985;LSEQ=TAAAAAGCTGCTGTGGCCAC;RSEQ=GTGAAGGACCGGCTATCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:77:36,41:83,86:0.313:2,2:26.5:1:29.4:1:0.78386:1.09874:60:18.25:0.3067:0:1.2 0/1:248:76:38,38:87,85:0.3065:2,2:26.7:1:30.4:1:1:1.02344:60:75:0.3099:0:1.2 -7 97793227 . G A 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.05541;SOR=0;LSEQ=ACGGTGAAGGACCGGCTATC;RSEQ=CTGCCTGTCTTAGCAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:4:3,1:87,114:0.0194:2,2:17.3:1:28:1:0.32159:3.91:60:8:0.0198:0:1.5 0/0:217:0:0,0:100,117:0:2,0:25.3:1:30.7:1:1:0:60:107.5:1:0:0.4 -7 97793237 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22765;SOR=0;LSEQ=ACCGGCTATCGCTGCCTGTC;RSEQ=TAGCAGGTCAAGAGCGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:72,109:0.0109:2,2:33.5:1:31:1:1:1.51:60:4:0.0111:0:2.5 0/0:200:0:0,0:88,111:0:2,0:24.7:1:30.1:1:1:0:60:398:0.995:0:0.4 -7 97826105 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53387;SOR=0;LSEQ=AGGTACAGAGATCAAATACC;RSEQ=GACATGCTTAATGGACGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:2,0:85,20:0.0185:2,0:24:1:31.5:1:1:0:60:4:0.0187:0:1 0/0:62:0:0,0:50,12:0:2,0:22.2:1:30.3:1:1:0:60:124:1:0:0 -7 97826123 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.57136;SOR=2.85359;LSEQ=CCAGACATGCTTAATGGACG;RSEQ=GAGGCTTTGACAAGGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:1:0,1:110,39:0.0067:2,0:1:0:25:0:0.26667:0:60:2:0.0067:0:1 0/1:106:2:1,1:74,30:0.0189:2,2:12.5:1:28:1:0.50135:2.44291:60:4:0.019:0:1.5 -7 97826220 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07556;SOR=Inf;LSEQ=TTTCTGATGATCTGAAATTC;RSEQ=TTTGCTTATGCGTCTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:180,175:0:2,0:24.1:1:30.6:1:1:0:60:117.333:1:0:0.4 0/1:261:3:2,1:138,119:0.0115:2,2:7:1:24:1:1:1.72:60:6:0.0116:0:1 -7 97826232 . G A 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21104;SOR=1.23996;LSEQ=TGAAATTCGTTTGCTTATGC;RSEQ=TCTCATGCAGCATGCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:129:65,64:102,120:0.3675:2,2:26:1:30.5:1:0.43943:1.19:60:128:0.3668:0:1.1 0/1:265:111:62,49:76,78:0.4189:2,2:27:1:29.2:1:0.32021:1.30:60:26.75:0.4131:0:1.1 -7 97826289 . G T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25504;SOR=0;LSEQ=CGTTCAGGCCGAGGACTGAG;RSEQ=GTTTCCTCCCACTCCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:88,165:0.0117:2,2:33.7:1:30.3:1:1:1.06641:60:6:0.012:0:2 0/0:212:0:0,0:86,126:0:2,0:25.2:1:30.4:1:1:0:60:105:1:0:0.6 -7 97826331 . T G 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73544;SOR=0.64762;LSEQ=CTTTTTTAATGAGCTGGTTT;RSEQ=GAAGTTGTGTAGTTTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:6:2,4:29,99:0.0448:2,2:28.8:1:30.3:1:0.62193:1.70:60:12:0.0451:0:1.2 0/1:102:3:0,3:24,75:0.0294:2,0:25.7:1:30.3:1:1:0:60:6:0.0297:0:1 -7 97826340 . G A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2521;SOR=0.70233;LSEQ=TGAGCTGGTTTTGAAGTTGT;RSEQ=TAGTTTTTAAGCAGTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:111:57:13,44:10,44:0.5135:2,2:20.5:1:30.2:1:0.64371:1.30:60:114:0.5229:0:1.1 0/1:87:37:6,31:9,41:0.4253:2,2:22:1:29.7:1:1:1.13251:60:74:0.4458:0:1.1 -7 97826359 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50484;SOR=0;LSEQ=TGTAGTTTTTAAGCAGTTGA;RSEQ=GTATCTTGGCTCCAAACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:7,64:0.0274:2,2:26.5:1:29.5:1:0.20852:8.62:60:4:0.0278:0:1.5 0/0:56:0:0,0:6,49:0:2,0:23.4:1:30.6:1:1:0:60:54:1:0:0.6 -7 97872172 . ACATATACCCACCTATCCATCTACC A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATACCTTCCATTCATCCAC;RSEQ=CATACACCCACCCACCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:32:0:1:0:25:4:1:0:0.5 -7 99926442 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.57346;SOR=2.79608;LSEQ=ACCAATATTCTTGAAAACCA;RSEQ=GATTAATTTACTGTACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:1:0,1:125,14:0.0071:2,0:1:0:27:0:0.10714:0:60:2:0.0072:0:1 0/1:101:2:1,1:86,13:0.0198:2,2:7.5:1:27.5:1:0.25921:6.4117:60:4:0.02:0:1 -7 99926522 . A G 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=119.67785;LSEQ=GTAGAAAATAACTGCTTCAC;RSEQ=CTGACTGTCATCCCTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:1:0,1:413,207:0.0016:2,0:33:0:15:0:0.33494:0:40:0:0:0:1 0/1:450:73:46,27:246,131:0.1622:2,2:27.2:1:29.5:1:0.78891:1.10198:46:23.333:0.1584:0:1.2 -7 99926612 . C T 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTCGAGTCCCAACCTTCGC;RSEQ=GATACATGGCAGGTAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:744:0:0,0:299,445:0:2,0:24.7:1:30:1:1:0:54.4:92:1:0:0.1 0/1:670:31:13,18:267,371:0.0463:2,2:27.7:1:29.9:1:1:1.00:52.4:62:0.0466:0:1.2 -7 99926684 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1663;SOR=Inf;LSEQ=GGTGTGTTCAGTGAGAGATC;RSEQ=GTGATGTTGGGCACTGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:18,202:0:2,0:23.3:1:29.6:1:1:0:41:35.667:1:0:0 0/1:152:2:1,1:7,143:0.0132:1,2:6.5:1:28.5:1:0.10282:19.19:44:4:0.0132:0:1 -7 99926811 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11106;SOR=Inf;LSEQ=GTCATCATAAAATCTAAGGT;RSEQ=TGGCATCTAAAAGACAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:5,38:0:2,0:21.9:1:32.1:1:1:0:40.2:86:1:0:0.1 0/1:22:2:1,1:4,16:0.0909:2,2:34.5:1:30:1:0.41126:3.69:30:4:0.0909:0:1 -7 99927803 . A T 67 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06256;SOR=4.09579;LSEQ=ATGGATAAAAATATTTTATC;RSEQ=CCTCAGTGCACAAAGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:786:2:0,2:498,285:0.0025:2,0:1:0:25.5:1:0.13337:0:50.5:4:0.0026:0:1 0/1:773:8:2,6:483,282:0.0103:2,2:5.4:1:22.6:1:0.05762:5.12737:53.3:7:0.0091:0:1.1 -7 99928236 . G A 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01099;SOR=Inf;LSEQ=ATGCTATCAGTTTTTATATT;RSEQ=ATATTATTTATAACGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:20,235:0:2,0:21.7:1:31.3:1:1:0:51.9:62.75:1:0:0.1 0/1:230:6:0,6:34,190:0.0261:2,0:31.7:1:30.5:1:0.59564:0:46.8:12:0.0265:0:1.2 -7 99929849 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAACTCTTAGCATAACA;RSEQ=CTGCCTGGCGCACCATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:34,0:0.0556:1,2:28.5:1:31:1:0.05556:0:60:4:0.0556:0:1.5 0/0:11:0:0,0:10,1:0:2,0:26.6:1:30.4:1:1:0:59.9:10:1:0:0.1 -7 99933398 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20435;SOR=Inf;LSEQ=ATGTTCCCCCCATTTCCAGG;RSEQ=AGGTTGGACGCCGTGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:112,27:0:2,0:22.2:1:31.3:1:1:0:59.7:138:1:0:0.1 0/1:116:2:1,1:95,19:0.0172:2,2:19.5:1:29:0:0.31634:4.89908:60:4:0.0175:0:1.5 -7 99933418 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49936;SOR=0;LSEQ=GAGGTTGGACGCCGTGGTTC;RSEQ=TAAAGAGGGCGCGCGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:144,50:0.0102:2,2:25.5:1:30.5:1:0.45369:2.86151:60:4:0.0103:0:1 0/0:183:0:0,0:129,54:0:2,0:22.9:1:30.1:1:1:0:60:29.5:1:0:0.2 -7 100401825 . T G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGATGGGGTTTTGCTAT;RSEQ=TTGGCCAGGCTGCTCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:44.5:1:32:1:1:0:60:4:1:0:1 -7 100403213 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50695;SOR=0;LSEQ=CCTGGGGGAAGCGGGGCCGG;RSEQ=CATTCCGGTCTTTCTGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:38,25:0.0308:2,2:14.5:1:28.5:1:1:1.50993:60:4:0.0328:0:1 0/0:48:0:0,0:29,19:0:2,0:24.4:1:31.4:1:1:0:60:96:1:0:0.2 -7 100403250 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51256;SOR=0;LSEQ=CCAACAGTCCAGCATGAGCT;RSEQ=GTGGAGGGAGGTGGGACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:36,37:0.0267:2,2:27.5:1:28:1:1:1.03:60:4:0.027:0:1 0/0:52:0:0,0:30,22:0:2,0:28.9:1:30.5:1:1:0:60:104:1:0:0.2 -7 100403280 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.53512;SOR=0;LSEQ=GGTGGGACAGTCTGGGGGCG;RSEQ=GGGCAGCCGGTAGTCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:26,38:0.0303:2,2:45:1:31:1:1:1.45:60:4:0.0308:0:1 0/0:37:0:0,0:20,17:0:2,0:21.5:1:30.2:1:1:0:60:74:1:0:0.2 -7 100404135 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10989;SOR=Inf;LSEQ=CAGGCATCACTGGCGGAAGT;RSEQ=AACTTCCGGAAGGCAATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:25.7:1:30.2:1:1:0:60:18:1:0:0.1 0/1:5:2:1,1:1,2:0.4:2,2:29.5:1:27:1:1:1.73:60:4:0.4:0:1 -7 100405060 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22711;SOR=0;LSEQ=GGCCAAAGTCAGACACTTTG;RSEQ=AGACGAGGTTGCTGTTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:13,11:0.0769:2,2:32.5:1:29.5:1:1:1.17422:60:4:0.0769:0:1 0/0:28:0:0,0:16,12:0:2,0:26:1:31.5:1:1:0:60:27:1:0:0.2 -7 100405072 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49176;SOR=Inf;LSEQ=ACACTTTGCAGACGAGGTTG;RSEQ=TGTTGACTAGGATGTTGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:28.3:1:31:1:1:0:60:11:1:0:0.2 0/1:27:2:1,1:14,11:0.0741:2,2:10:0:29.5:1:1:1.2613:60:4:0.0769:0:1.5 -7 100411278 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAGGGCAACCCACCATG;RSEQ=CCGATGAGATACTGTCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45.5:1:32:1:1:0:60:4:1:0:1 -7 101977547 . A G 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01753;SOR=0;LSEQ=ATGTTATAAATAATATCAAT;RSEQ=TAAAAGCTTATAGCATGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:8,0:18,1:0.2963:1,0:27.1:1:32.5:1:1:0:31.4:16:0.2963:0:1.6 0/0:16:0:0,0:15,1:0:1,0:20.6:1:29.2:1:1:0:32.1:32:1:0:0.6 -7 101977585 . C T 34 v4;q23;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.54897;SOR=0;LSEQ=GGTCCATTTTTTTTTTTTTT;RSEQ=TTTTTGAGACGGAGTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:3,0:54,3:0.05:2,0:13.3:1:22:1:1:0:33.7:2:0.05:0:4 0/0:32:0:0,0:31,1:0:1,0:9:0:9:0:1:0:40:0:0:0:1 -7 101977597 . G A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06104;SOR=2.23211;LSEQ=TTTTTTTTCTTTTTGAGACG;RSEQ=AGTCTCACTGTCTCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:16:16,0:88,4:0.1481:1,1:18.4:1:29.9:1:1:0:29.4:32:0.1524:0:1.3 0/1:57:16:16,0:40,1:0.2807:1,1:23.8:1:29:1:1:0:31.9:32:0.2807:0:1.3 -7 101977641 . G T 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AGTACAGTGGCGCGATCTCG;RSEQ=CTCACTGCAAGCTCCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:133,4:0:1,0:34.7:1:30.6:1:1:0:33.5:18.571:1:0:0.4 0/1:87:11:11,0:75,1:0.1264:1,0:27.3:1:30.4:1:1:0:28:22:0.1341:0:1.4 -7 101977657 . GC G 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.56781;SOR=2.95748;LSEQ=CTCGGCTCACTGCAAGCTCC;RSEQ=CCCCCGGGTTCATGCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:1,0:141,9:0.0066:2,0:44:0:31:0:1:0:49:2:0.0068:0:0 0/1:103:2:1,1:89,12:0.0194:2,2:22.5:1:29.5:1:0.23758:7.16504:25:4:0.0202:0.0097:0 -7 101977945 . C T 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.42049;LSEQ=ATATCATGTATATCTGTTGT;RSEQ=TTAGCACTTGAGGTATCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:245:142:90,52:65,38:0.5796:2,2:25.7:1:30.3:1:1:1.01:46.8:46.333:0.5816:0:1.1 0/1:161:59:39,20:70,32:0.3665:2,2:23.7:1:30.1:1:0.86129:1.12099:46.8:118:0.3734:0:1.1 -7 101978188 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1041;SOR=Inf;LSEQ=TTTACAATTTTCTATCTCGG;RSEQ=ATCTCAGCTTCTAGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:13,135:0:2,0:24:1:28.4:1:1:0:53.5:73:1:0:0.1 0/1:71:2:1,1:5,64:0.0282:2,2:8:1:28.5:1:0.16298:11.78:60:4:0.0286:0:1 -7 101978488 . GTA G 33 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATATATACATATATATGT;RSEQ=TATATATATATACACATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:36.5:1:33.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 101979280 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22293;SOR=Inf;LSEQ=GGGATCATCAGCTTTTTAAG;RSEQ=AAGTTTTGAGAGAAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:100,9:0:2,0:24.2:1:30.1:1:1:0:46.7:108:1:0:0 0/1:98:2:1,1:82,14:0.0204:2,2:35:1:32:1:0.28403:5.69299:44.5:4:0.0204:0:1 -7 103122556 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.08476;SOR=Inf;LSEQ=TTAATCACTTAAATTTGCTT;RSEQ=CAAATTGACTGAAATCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:167,50:0:2,0:23.2:1:32.3:1:1:0:60:434:1:0:0.1 0/1:171:3:2,1:130,38:0.0175:2,2:30:1:29:1:0.54243:1.70444:60:6:0.0176:0:2 -7 103122561 . T A 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTTAAATTTGCTTGCAAA;RSEQ=TGACTGAAATCAGCCAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:188,59:0:2,0:22.8:1:30.5:1:1:0:60:60.75:1:0:0.1 0/1:187:21:15,6:127,39:0.1123:2,2:21.3:1:29.6:1:0.59475:1.30063:60:20:0.1081:0:1.6 -7 103122645 . A G 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.24891;LSEQ=CCTATCTACCGAGAAGATTC;RSEQ=CCTCTCCTTGCCAACCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:73:37,36:246,263:0.1254:2,2:26.3:1:31.5:1:0.70948:1.10:60:146:0.1263:0:1.1 0/1:503:160:80,80:163,177:0.3181:2,2:25.3:1:30.2:1:0.70166:1.09:60:79:0.3192:0:1.2 -7 103122715 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07872;SOR=Inf;LSEQ=TAAGCATTCCAGTTCTACAG;RSEQ=AACTAGATCATTAGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:76,208:0:2,0:24.1:1:31:1:1:0:60:93.667:1:0:0.1 0/1:214:3:2,1:54,157:0.014:2,2:5:1:29.7:1:0.16829:5.76:60:6:0.0143:0:1.7 -7 103122754 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51478;SOR=0;LSEQ=AAAGCAAGTCATCTCTCTGT;RSEQ=AGGGAACAGTCAACCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:0,2:12,111:0.016:2,0:40:1:30:0:1:0:60:4:0.0164:0:1 0/0:86:0:0,0:7,79:0:2,0:23.8:1:31.9:1:1:0:60:172:1:0:0.1 -7 103214940 . T C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25584;LSEQ=ATCAAAAACACTATTCTGCC;RSEQ=CTGTAAATTTTTATTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:517:407:137,270:42,66:0.7872:2,2:23.2:1:30.9:1:0.30916:1.25356:60:80.4:0.7898:0:1.1 0/1:389:189:71,118:76,123:0.4859:2,2:23.7:1:30.6:1:0.91693:1.02685:60:93.5:0.4895:0:1.1 -7 103215120 . T A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=1;SOR=1.47399;LSEQ=GGGGCAGTCAGTCTCAAATT;RSEQ=AAAAAAAATCCTTGAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:0,12:0,5:0.6667:0,0:18.3:1:30.5:1:1:0:60:24:0.7059:0:1.2 1/0:4:3:0,3:0,1:0.75:0,0:14.3:1:32:0:1:0:60:6:0.75:0:1 -7 103275803 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.33086;LSEQ=ATATCTAGAATTTTATACCA;RSEQ=TTGAATTATGATTTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:224:115,109:64,57:0.6493:2,2:26.9:1:31.8:1:0.82177:1.06401:60:36.333:0.6488:0:1.1 0/1:311:118:63,55:106,87:0.3794:2,2:28.3:1:30.9:1:0.81525:1.06345:60:117:0.3799:0:1.1 -7 103275875 . G A 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0429;SOR=Inf;LSEQ=AATGCTTTCCAACATACCTG;RSEQ=GCTCATGATAGCTGAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:90,174:0:2,0:26:1:30.4:1:1:0:60:32:1:0:0.4 0/1:222:4:3,1:86,132:0.018:2,2:19.5:1:27.3:1:0.30462:4.57:60:8:0.0183:0:1 -7 103275910 . G T 39 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2636;SOR=0;LSEQ=AGATATGAATAATGCTCCAG;RSEQ=AGTTTCCAAGTTATCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:1,2:23,116:0.021:2,2:25:0:24.7:1:0.42867:2.50:60:2:0.0144:0:1.3 0/0:106:0:0,0:19,87:0:2,0:23.8:1:31.3:1:1:0:60:212:1:0:0 -7 103275947 . A C 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.04013;SOR=0;LSEQ=CATTATCATAAGAATAATGC;RSEQ=ACAAAACTCCTTCACCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:0,7:0,53:0.1167:1,0:13.7:1:32.4:1:1:0:60:14:0.1273:0:1.1 0/0:39:0:0,0:3,36:0:2,0:23.9:1:30.9:1:1:0:60:78:1:0:0 -7 104414109 . C T 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=GCAGTCACACTGCAGTAGGG;RSEQ=AGGCCCCTGGCCCAGTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:29.8:1:29.3:1:1:0:60:5:1:0:0.2 1/0:3:2:2,0:1,0:0.6667:0,0:9:1:29.5:1:1:0:60:4:1:0:1 -7 104414278 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49538;SOR=Inf;LSEQ=AGGGGAGAGGCCTGGGACAG;RSEQ=TGTTCCCTTGCAGCCCTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:15,28:0:2,0:25:1:30.4:1:1:0:60:86:1:0:0 0/1:47:2:1,1:19,26:0.0426:2,2:25:1:29.5:1:1:1.36:60:4:0.0435:0:1 -7 104414284 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49367;SOR=Inf;LSEQ=GAGGCCTGGGACAGATGTTC;RSEQ=CTTGCAGCCCTAAGGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:14,26:0:2,0:23.9:1:30.9:1:1:0:60:80:1:0:0.1 0/1:40:2:1,1:15,23:0.05:2,2:26.5:1:28.5:1:1:1.52:60:4:0.05:0:1 -7 104414291 . GC G 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.46573;SOR=0.51407;LSEQ=GGGACAGATGTTCCCTTGCA;RSEQ=CCTAAGGAGGAACCAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:7,21:0.1515:2,2:35.4:1:31.6:1:0.59705:1.95:60:10:0.1515:0:0 0/1:36:3:0,3:13,19:0.0833:2,0:33.3:1:32:1:0.27899:0:60:6:0.0857:0:0.3 -7 105280862 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGACTGTGGACAGCTTGTG;RSEQ=GGAGGTTACTTCTAAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:43:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 106507968 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17634;SOR=Inf;LSEQ=GGAAAGTGCCTTTCTTGTGA;RSEQ=AAATCCCTGTGTCCCTCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:179,80:0:2,0:23.3:1:32:1:1:0:60:258:1:0:0.1 0/1:188:2:1,1:122,64:0.0106:2,2:11:1:28.5:1:1:1.89933:60:4:0.0108:0:1.5 -7 106508385 . G T 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62404;SOR=2.87284;LSEQ=ACTGCCTGCGCTACTGGAAG;RSEQ=CCACGCACCGGAGCCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:0,1:112,146:0.0038:2,0:1:0:29:0:1:0:60:2:0.004:0:1 0/1:273:3:1,2:143,127:0.011:2,2:7.7:1:25:1:0.60399:2.24549:60:6:0.0113:0:1.7 -7 106508397 . A G 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=ACTGGAAGGCCACGCACCGG;RSEQ=GCCCGGGCCAGATCCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:120,143:0:2,0:25.4:1:30.6:1:1:0:60:51.6:0.9961:0:0.1 0/1:277:13:4,9:135,129:0.0469:2,2:25.6:1:30.5:1:0.16842:2.3477:60:26:0.048:0:1.2 -7 106508462 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4987;SOR=0;LSEQ=GAGTCCCAAGCCTTCCAGCG;RSEQ=CAGCTCACGGCGCTGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:87,103:0.0104:2,2:22:1:29.5:1:1:1.18:60:4:0.0106:0:1 0/0:190:0:0,0:81,109:0:2,0:25.7:1:31.4:1:1:0:60:46.5:1:0:0.3 -7 106508516 . C T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.59205;LSEQ=GACGTCAGCAACGTGCACGA;RSEQ=GATGAGCTGGAGTTCACGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:128,60:0.0105:2,2:12.5:1:27.5:1:0.54018:2.12407:60:4:0.0108:0:1 0/0:160:1:0,1:96,63:0.0063:2,0:1:0:26:0:0.4:0:60:2:0.0063:0:1 -7 106508978 . A G 279 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.73109;LSEQ=GTGAGGAAGGAAGAGTGGCC;RSEQ=CTGGTGGATGACTGCACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:563:561:335,226:1,1:0.9964:2,2:24.8:1:30.6:1:1:1.48:60:92.5:0.9964:0:2 1/1:412:410:243,167:1,0:0.9951:0,2:24.8:1:30.3:1:1:0:60:81:0.9951:0:2.1 -7 106508987 . T C 286 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.49518;LSEQ=GAAGAGTGGCCACTGGTGGA;RSEQ=GACTGCACGGGAGTCACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:589:587:356,231:0,2:0.9966:0,2:25.6:1:31.1:1:0.15608:0:60:82.857:0.9966:0:2 1/1:440:439:263,176:0,0:0.9977:0,2:25.4:1:30.3:1:1:0:60:72.167:1:0:2 -7 106509082 . G A 145 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.33745;LSEQ=GTCCCTGTGGGACTGCGACC;RSEQ=CAAGTTCAGGGTCAAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:999:1:1,0:532,465:0.001:2,0:44:0:32:0:1:0:60:2:0.001:0:1 0/1:1016:30:18,12:537,445:0.0295:2,2:30.4:1:29.6:1:0.58339:1.24:60:29:0.0291:0:1.1 -7 106509331 . C A 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=3.07336;LSEQ=CGGTAAAGCTCCAGCACTGT;RSEQ=CAGCAAGGCCTCTGCAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1014:66:42,24:497,451:0.0651:2,2:22.7:1:29.1:1:0.09669:1.59:60:132:0.0657:0:1.1 0/1:896:158:79,79:381,356:0.1763:2,2:26.1:1:28.8:1:0.72614:1.07012:60:316:0.1791:0:1 -7 106509933 . A G 168 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGATGAAAATGTAAGAGCC;RSEQ=TTGCAGTTCAGAAACTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1119:0:0,0:473,645:0:2,0:23.8:1:30.6:1:1:0:60:185.333:0.9991:0:0.1 0/1:1006:47:20,27:439,519:0.0467:2,2:22.3:1:30.3:1:0.76462:1.14176:60:94:0.0472:0:1.1 -7 106510076 . A G 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.45647;SOR=1.18008;LSEQ=TATGCACAGGCACTCCATTC;RSEQ=GTTGTCATCAAATGCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:78:9,69:13,154:0.3184:2,2:23.1:1:30:1:0.3453:1.54:60:25:0.3125:0:1.1 0/1:166:59:9,50:20,87:0.3554:2,2:20.6:1:30:1:0.67199:1.2753:60:58:0.3537:0:1.1 -7 106512878 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21654;SOR=Inf;LSEQ=AGATTTTCATCTTTCTAGCC;RSEQ=TGAAGACCCAGTAAAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:129,6:0:1,0:22:1:29.7:1:1:0:60:44:1:0:0 0/1:118:2:2,0:107,9:0.0169:2,0:36.5:1:30.5:1:1:0:60:4:0.0169:0:1.5 -7 106513011 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19705;LSEQ=TTTGAACCATACCATGATAG;RSEQ=GCCCTTGCCAGATTTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:683:413:202,211:140,130:0.6047:2,2:28.8:1:29.8:1:0.48145:1.12471:60:67.833:0.6039:0:1.1 0/1:644:149:78,71:255,240:0.2314:2,2:27.7:1:29.8:1:0.92554:1.03:60:148:0.2313:0:1.2 -7 106519943 . T C 286 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50086;SOR=Inf;LSEQ=TATTCATTGTGTGTGGGGAA;RSEQ=ATGTGACTGCTTCCTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:513:511:363,148:0,2:0.9961:0,2:23.8:1:31.8:1:0.08509:0:60:72:0.996:0:1.1 1/1:462:462:306,156:0,0:1:0,2:23.5:1:31.1:1:1:0:60:114.5:1:0:1.1 -7 106520111 . G T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02344;SOR=Inf;LSEQ=AAGACATGCTTATTTTACAG;RSEQ=TATGCTAATTTTAAGATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:116,324:0:2,0:26.3:1:31.8:1:1:0:60:87:0.9977:0:0.1 0/1:285:4:0,4:81,200:0.014:2,0:38.3:1:30.8:1:0.58041:0:60:8:0.0141:0:1 -7 106522307 . A AAAAAC 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCTACAAAACAAAAAC;RSEQ=AAAACAAAACAAAACAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:10,1:0.2143:2,0:27:1:31.3:1:1:0:60:6:0.2143:0.0714:0 0/0:1:0:0,0:1,0:0:0,0:47:0:28:0:1:0:60:2:1:0:0 -7 106522411 . T C 33 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03613;SOR=Inf;LSEQ=AGAAACTTTAGAGTACCAGA;RSEQ=TGACCAATAAACGTACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:65,1:0:1,0:23.2:1:31.3:1:1:0:60:132:1:0:0 0/1:16:2:2,0:14,0:0.125:1,0:8.5:1:33:0:1:0:60:4:0.125:0:0.5 -7 106522520 . A AAT 69 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.24874;SOR=0.23016;LSEQ=GAAGAAAAATATATTAAGTT;RSEQ=ATATATATATAATATAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:6:4,2:342,73:0.0143:2,2:15.7:1:26.8:1:0.29075:2.33648:60:5:0.012:0.0071:1.7 0/0:302:1:1,0:226,75:0.0033:2,0:17:0:31.5:0:1:0:60:2:0.0033:0:0 -7 106522592 . A G 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATGGAGTCTATTTGGGAG;RSEQ=CTGAATCTTTGGATCTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1090:0:0,0:603,485:0:2,0:27.2:1:29.6:1:1:0:60:44.333:1:0:0.1 0/1:901:41:21,20:479,380:0.0455:2,2:29.4:1:29.7:1:0.63042:1.20025:60:12.667:0.0427:0:1.2 -7 106522693 . G A 227 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01599;LSEQ=ATGAATAGACCTCTCAGCTC;RSEQ=TTTGAAAAGATTATAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:636:176:46,130:128,332:0.2767:2,2:23.7:1:30.5:1:0.6921:1.08945:60:57.667:0.2746:0:1.1 0/0:495:3:1,2:167,323:0.0061:2,2:4:1:25.7:1:1:1.03399:60:2:0.0041:0:1 -7 106522738 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.17939;SOR=Inf;LSEQ=GTGTAGACATTTAATAACTG;RSEQ=AAAATCATAATCTTAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:20,242:0:2,0:23.3:1:30.4:1:1:0:60:86.333:1:0:0.2 0/1:193:2:1,1:23,168:0.0104:2,2:29.5:1:28:1:0.23381:7.17:60:4:0.0106:0:1 -7 106523440 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07751;SOR=Inf;LSEQ=TCCTCTGGGCCAGGTACTGG;RSEQ=CCCCAATCTCCATCAGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:195,66:0:2,0:25.4:1:31.6:1:1:0:59.9:129.5:1:0:0.3 0/1:195:3:2,1:148,44:0.0154:2,2:36.7:1:28.3:1:0.54695:1.67676:60:6:0.0157:0:1.3 -7 106523446 . A G 162 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCAGGTACTGGCCCCCA;RSEQ=TCTCCATCAGACTCTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:201,72:0:2,0:26.5:1:29.6:1:1:0:59.9:26.3:1:0:0.3 0/1:214:35:27,8:135,44:0.1636:2,2:26.8:1:31.7:1:1:1.10:60:70:0.1691:0:1.3 -7 106523620 . CT C 76 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.45121;SOR=0.39851;LSEQ=GAAGAAAAGGTGAGCTCATG;RSEQ=TTTTCCCAGTCTAATGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:5:2,3:157,269:0.0116:2,2:34.6:1:33:1:1:1.14:60:10:0.0119:0:0.2 0/0:430:2:1,1:166,259:0.0047:2,2:27:1:34:0:1:1.56:60:4:0.0047:0:0 -7 106523670 . G C 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01876;SOR=2.45042;LSEQ=TTGTCATTTATATAGCAGTA;RSEQ=TGGCTTCAAGTTTTCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:13:1,12:34,175:0.0586:2,1:30.3:1:31.8:1:0.69755:2.32468:60:26:0.061:0:1 0/1:166:22:5,17:33,111:0.1325:2,2:31.1:1:32:1:1:1.01075:60:44:0.135:0:1.1 -7 106523673 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17181;SOR=Inf;LSEQ=TCATTTATATAGCAGTAGTG;RSEQ=CTTCAAGTTTTCAGAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:32,182:0:2,0:24.3:1:31.7:1:1:0:60:70.333:1:0:0.2 0/1:152:2:1,1:30,120:0.0132:2,2:12.5:1:25.5:1:0.36738:3.95:60:4:0.0135:0:1 -7 106524542 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17592;SOR=Inf;LSEQ=CTTTTTAGAAGTCATTTGTA;RSEQ=ATTCATGATGCTTTTTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:195,41:0:2,0:22.2:1:31.9:1:1:0:60:77.667:1:0:0.1 0/1:171:2:1,1:139,30:0.0117:2,2:20:1:27.5:1:0.33058:4.57438:60:4:0.0118:0:1 -7 106524644 . CTG C 173 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GTTTATTCCTGTGCAGGCTA;RSEQ=TGTGGCAACCTTTGTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:44:21,23:319,323:0.064:2,2:29.3:1:31.8:1:0.87659:1.08153:60:88:0.0651:0.0029:0.8 0/0:593:0:0,0:289,304:0:2,0:25.6:1:30.1:1:1:0:60:83.714:1:0:0.2 -7 106524689 . C T 168 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=2.34567;LSEQ=ATAGGCGACAGACACAATGA;RSEQ=AATATTATGATCACCGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:40:13,27:200,327:0.0705:2,2:24.7:1:29:1:0.61193:1.26977:60:80:0.0716:0:1 0/1:443:67:21,46:154,221:0.1512:2,2:25.5:1:27.7:1:0.13878:1.52498:60:21.333:0.1478:0:1.1 -7 106524745 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17565;SOR=Inf;LSEQ=GTGCAGAATAAACTTTTATT;RSEQ=TGGTAAAATATATATAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:38,189:0:2,0:21.7:1:32:1:1:0:60:226:0.9956:0:0.1 0/1:165:2:1,1:36,127:0.0121:2,2:7.5:1:30.5:1:0.39926:3.49:60:4:0.0121:0:1 -7 106526802 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5641;SOR=3.08197;LSEQ=GATGGTTCCTGCAGCACTCC;RSEQ=CAGCCTTCACCTCTCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:1:1,0:15,129:0.0069:2,0:1:0:29:0:0.11034:0:60:2:0.007:0:1 0/1:95:2:0,2:9,84:0.0211:2,0:29.5:1:27.5:1:1:0:60:4:0.0213:0:1 -7 106546087 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCATTGGAGAATATTCT;RSEQ=GGTTTAAACAGACTAATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:21.7:1:29.7:1:1:0:60:6:0.375:0:1 0/0:2:0:0,0:1,1:0:2,0:22.5:1:32.5:1:1:0:60:4:1:0:0 -7 107730490 . T A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTACTAGATGTATGACTT;RSEQ=GAGTGACTTACCTAACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:3,0:14,0:0.1765:1,0:20.3:1:27.7:1:1:0:60:6:0.1765:0:1 0/0:4:0:0,0:4,0:0:0,0:15.8:1:30.5:1:1:0:60:8:1:0:0 -7 107730650 . G A 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAACAGTAACAGCATAGCAA;RSEQ=CATACCATGAAATTTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:156,46:0:2,0:24.8:1:32:1:1:0:60:201:1:0:0 0/1:162:17:14,3:99,46:0.1049:2,2:23:1:29.5:1:0.27788:2.16:60:34:0.1056:0:1.1 -7 107730749 . C A 200 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCATACCCTCAGCAGAGAA;RSEQ=GAAAATTATTCACATTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:0:0,0:264,276:0:2,0:26.5:1:30.7:1:1:0:60:89:0.9944:0:0.1 0/1:466:101:52,49:189,176:0.2167:2,2:24.3:1:30.1:1:1:1.01189:60:100:0.2169:0:1.1 -7 107730838 . C T 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19008;LSEQ=TCATAGGTATTATTTTCTAA;RSEQ=TTGTTAAGAAAAATTCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:57:17,40:39,136:0.2446:2,2:19:1:30.6:1:0.28544:1.48:60:114:0.2468:0:1.1 0/1:173:10:2,8:37,126:0.0578:2,2:28:1:30.7:1:1:1.17355:60:20:0.0578:0:1.3 -7 107730846 . GA G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50482;SOR=0;LSEQ=ATTATTTTCTAACTTGTTAA;RSEQ=AAAATTCACCTGCCCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:35,146:0.0109:2,2:29.5:1:31:1:0.35561:4.13:60:4:0.011:0:0 0/0:146:0:0,0:26,120:0:2,0:23.9:1:29.9:1:1:0:60:72:1:0:0.2 -7 108943980 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=AAAAGGCTTCTGAAATCAGA;RSEQ=AACGCCTTTCAAGCTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:21.4:1:29.8:1:1:0:60:18:1:0:0.1 0/1:13:2:1,1:8,3:0.1538:2,2:6.5:1:26.5:1:1:2.4495:60:4:0.1538:0:2 -7 108943982 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=AAGGCTTCTGAAATCAGACA;RSEQ=CGCCTTTCAAGCTCTTATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:21.9:1:27.2:1:1:0:60:8.5:1:0:0.1 0/1:13:2:1,1:8,3:0.1538:2,2:8.5:1:29:1:1:2.4495:60:4:0.1538:0:2 -7 111819870 . A G 60 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.63089;SOR=0.32501;LSEQ=AAAATCAGAAATACACAGTG;RSEQ=AACACACACCTCAAAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:4,0:18,1:0.1739:1,0:22:1:30.3:1:1:0:60:8:0.1739:0:1.8 0/1:16:1:1,0:15,0:0.0625:1,0:49:0:30:0:1:0:60:2:0.0625:0:2 -7 111819901 . T A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.79298;SOR=0.74197;LSEQ=TCAAAGGTATGATGAATATT;RSEQ=AACTGGGGCTCGTATCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:17:17,0:43,0:0.2787:1,1:19.3:1:28.6:1:1:0:60:34:0.2881:0:1.4 0/1:27:6:6,0:21,0:0.2222:1,0:14.2:1:28.3:1:1:0:60:12:0.2222:0:1.3 -7 111820090 . G A 262 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.53628;LSEQ=ACTAAGTCCAAAAGTCTAAA;RSEQ=TAGAACATAAATGGAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:517:394:172,222:49,72:0.7621:2,2:23.8:1:30.4:1:0.5998:1.14:60:48.25:0.7583:0:1.1 1/0:470:297:132,165:73,99:0.6319:2,2:24.3:1:29.5:1:0.6999:1.08:60:48.5:0.6326:0:1.1 -7 111820157 . C CG 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.83181;SOR=0.94093;LSEQ=AATAGCTTCAAAGTCAACTA;RSEQ=GGTTTAGCTGTCAGTACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:76:22,54:61,154:0.2603:2,2:30.7:1:30.6:1:1:1.03:60:75:0.2622:0.024:0.4 0/1:193:48:16,32:43,102:0.2487:2,2:25.8:1:29.9:1:0.71809:1.18:60:96:0.25:0.0363:0.6 -7 111820439 . T C 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTCACTTCTGCAGACAAC;RSEQ=TTTACCCCGACAGGTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:29.5:1:31:1:1:0:60:4:0.5:0:1 1/1:1:1:0,1:0,0:1:0,0:19:0:34:0:1:0:60:2:1:0:1 -7 112160713 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07753;SOR=Inf;LSEQ=GCTGGTGCGAAGGATGAACT;RSEQ=CACATTGTTGAAGCAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:125,140:0:2,0:27.6:1:32.2:1:1:0:59.9:131.5:1:0:0.1 0/1:198:3:2,1:97,98:0.0152:2,2:14:1:28.7:1:1:2.01:60:6:0.0154:0:1.3 -7 112160813 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50405;SOR=0;LSEQ=AGGCAACAGTTTCCCTTGGG;RSEQ=GCTTTGAAATACCACTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:69,59:0.0154:2,2:23.5:1:31:0:1:1.16808:60:4:0.0157:0:1 0/0:104:0:0,0:53,51:0:2,0:21.9:1:30.2:1:1:0:59.9:33.667:1:0:0.1 -7 112160841 . T A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52308;SOR=0;LSEQ=AATACCACTACCTGTGGTCT;RSEQ=ACAATCGAAGTGTGGTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:112,75:0.0105:2,2:16:0:31:1:1:1.49005:60:4:0.0106:0:1 0/0:121:0:0,0:69,52:0:2,0:25.2:1:28.8:1:1:0:60:120:1:0:0.1 -7 112160911 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12571;SOR=Inf;LSEQ=GTAGCTGTGGAGGAAGATGC;RSEQ=GAATCAGAAGATGAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:96,127:0:2,0:25.3:1:30.4:1:1:0:60:446:1:0:0.3 0/1:123:2:1,1:52,69:0.0163:2,2:18:1:32:0:1:1.32:60:4:0.0163:0:1 -7 112160927 . G A 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14153;SOR=0.54144;LSEQ=ATGCAGAATCAGAAGATGAG;RSEQ=TGGGGGACGTGAAACTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:27:8,19:53,101:0.1492:2,2:26.2:1:30.3:1:0.82563:1.2448:60:54:0.1517:0:1.1 0/1:104:9:3,6:36,59:0.0865:2,2:17.7:1:29.9:1:1:1.21804:60:18:0.0874:0:1.1 -7 112160973 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18275;SOR=Inf;LSEQ=ATCTGGAAAGTGATCTGCTC;RSEQ=TGCAGGTGGTAGCAGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:10,67:0:2,0:22.2:1:31.9:1:1:0:60:37.5:1:0:0.2 0/1:58:2:1,1:13,43:0.0345:2,2:18.5:1:27.5:1:0.42771:3.22:60:4:0.0345:0:2 -7 112161076 . C T 51 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22619;SOR=0;LSEQ=ACGAGGAAACTGAAGAAAAA;RSEQ=TCCGGTGAAAAAATCTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:1,2:4,8:0.2:2,2:14.7:1:32.3:1:1:1:56.7:6:0.2:0:2.7 0/0:13:0:0,0:7,6:0:2,0:22.4:1:30.3:1:1:0:57.8:26:1:0:0.5 -7 112161080 . G A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.77084;LSEQ=GGAAACTGAAGAAAAACTCC;RSEQ=GTGAAAAAATCTATATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:4,7:3,4:0.6111:2,2:17:1:31.5:1:1:1.29262:59.1:22:0.6111:0:1.5 1/0:11:6:4,2:1,4:0.5455:2,2:31.5:1:30.8:1:0.24242:6.44:55.3:12:0.5455:0:1 -7 112161717 . T C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=ATCTCTGGCAGTGGAGGGAG;RSEQ=CACTTTAAGAAAAGAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:28.3:1:29.3:1:1:0:60:12:1:0:0.3 0/1:7:2:1,1:2,3:0.2857:2,2:26.5:1:29:1:1:1.41:60:4:0.2857:0:1 -7 112286315 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21429;SOR=Inf;LSEQ=AGTCTTTAAGGCTGCTGACC;RSEQ=TTGGATGGGGATTTTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:23.6:1:31.5:1:1:0:60:22:1:0:0.1 0/1:10:2:1,1:6,2:0.2:2,2:48.5:1:30.5:1:1:2.64575:60:4:0.2:0:1.5 -7 112287067 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCTTTCCCCTCCCAGGGA;RSEQ=CTGAGCGTGTTAGGCAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35:1:32.5:1:1:0:60:4:1:0:1 0/1:7:2:1,1:3,2:0.2857:2,2:33.5:1:30.5:1:1:1.41418:60:4:0.2857:0:2 -7 112287096 . G A 67 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAGGCAGTTGTGAGTCCC;RSEQ=GTGCTGGCTGTTGCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29.5:1:1:0:60:4:1:0:1 1/0:7:5:3,2:1,1:0.7143:2,2:24.8:1:29.2:1:1:1.41:60:10:0.7143:0:1.6 -7 112724525 . A G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCATAAGTCCAGGTAGA;RSEQ=CCATTTTTGACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:32.7:1:32.7:1:1:0:60:6:1:0:1 1/1:2:2:2,0:0,0:1:0,0:32:1:33.5:1:1:0:60:4:1:0:1 -7 112724644 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16844;SOR=Inf;LSEQ=CAAGGTCTTATCTTTCACTA;RSEQ=CAAAATGGAGATCAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:19,9:0:2,0:16.9:1:31.4:1:1:0:60:13:1:0:0.1 0/1:20:2:1,1:12,6:0.1:2,2:31:1:28.5:1:1:1.92731:60:4:0.1:0:1 -7 112724654 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11389;SOR=Inf;LSEQ=TCTTTCACTAGCAAAATGGA;RSEQ=ATCAGGAGGTTGCCCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:21,13:0:2,0:20.5:1:32:1:1:0:60:68:1:0:0.1 0/1:33:3:1,2:17,13:0.0909:2,2:5.7:1:26.3:1:0.57936:2.54081:60:6:0.0909:0:1 -7 112724704 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49591;SOR=0;LSEQ=TATTATGAAACCCAAGGAAG;RSEQ=CAGTTTCAGAAAGGCTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:25,20:0.0426:2,2:11.5:1:30.5:1:1:1.24403:60:4:0.0444:0:1 0/0:42:0:0,0:20,22:0:2,0:28.4:1:29.5:1:1:0:60:84:1:0:0.2 -7 112724795 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06536;SOR=Inf;LSEQ=ATAGATGGATGGAGGATAAG;RSEQ=ATACAGCCTCAGTCAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:0:1,0:27:1:31.5:1:1:0:60:26:1:0:0 0/1:5:2:0,2:0,3:0.4:0,0:18.5:1:28.5:1:1:0:60:4:0.4:0:1 -7 112726624 . CGCG C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.50549;SOR=Inf;LSEQ=TCCCCCAGTAACGCAGGGGC;RSEQ=GCGGCGGCGGCTGCGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:32.2:1:31:1:1:0:60:10:1:0:0.4 0/1:9:2:1,1:4,3:0.2222:2,2:31:0:33:1:1:1.29098:60:4:0.2222:0:0 -7 112726660 . G C 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=GCGGTGGCGAGGGCGGCGGC;RSEQ=GGGCTGCTTCAGCCTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:30:1:31:0:1:0:60:4:0.6667:0:1 0/0:9:0:0,0:5,4:0:2,0:30.4:1:29.3:1:1:0:60:18:1:0:0.7 -7 114268637 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50427;SOR=0;LSEQ=TGACTCCCCAGGTGATCACC;RSEQ=CTCAGCAAATGCAGCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:44,47:0.0215:2,2:27.5:1:31:1:1:1.07:60:4:0.0222:0:1.5 0/0:73:0:0,0:38,35:0:2,0:23.2:1:29.2:1:1:0:60:35.5:1:0:0.1 -7 114268667 . C T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07463;SOR=Inf;LSEQ=TGCAGCAGATCCTTCAGCAA;RSEQ=AAGTCCTGTCTCCTCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:35,53:0:2,0:26:1:31.9:1:1:0:60:87:1:0:0.1 0/1:65:3:1,2:20,42:0.0462:2,2:16.7:1:22:1:1:1.05:60:2:0.0313:0:2 -7 114269859 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14901;SOR=Inf;LSEQ=AAGTCAAAATGGTTTATTCA;RSEQ=CAACAACTACAAGAGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:61,5:0:2,0:24.7:1:32.4:1:1:0:60:65:1:0:0.1 0/1:42:2:1,1:37,3:0.0476:2,2:20.5:1:32:0:0.18351:10.82458:60:4:0.05:0:1 -7 114269915 . TGCA T 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.05561;SOR=Inf;LSEQ=GCAGTTACATCTTCAGCTTT;RSEQ=GCAGCAGCAGCAACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:112,58:0:2,0:29.2:1:31.7:1:1:0:60:55.667:1:0:0.1 0/1:162:4:1,3:109,49:0.0247:2,2:33.5:1:30.5:1:0.09772:6.58912:60:8:0.0253:0.0062:0.3 -7 114269932 . C CAGCAGCAGCAACAATAAGAGCAGCAACAACAGCAACAGT 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=1.000;MSILEN=1;SSF=0.05781;SOR=Inf;LSEQ=TTTTGCAGCAGCAGCAGCAA;RSEQ=AGCAGCAGCAGCAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:116,81:0:2,0:26.7:1:31.8:1:1:0:60:64.667:0.9949:0:0.2 0/1:192:4:0,4:118,68:0.0208:2,0:24.3:1:27.9:1:0.01956:0:32.8:8:0.0212:0.0208:0 -7 114269956 . C T 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24837;SOR=Inf;LSEQ=AGCAGCAGCAACAACAGCAG;RSEQ=AACAACAGCAGCAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:118,108:0:2,0:22.7:1:31.1:1:1:0:59.4:17.833:1:0.0044:0.2 0/1:229:3:1,2:125,101:0.0131:2,2:11.7:1:21:1:0.58938:2.46566:60:2:0.0089:0:1.3 -7 114269970 . GCAA G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.19688;SOR=0.34845;LSEQ=CAGCAGCAACAACAGCAGCA;RSEQ=CAACAACAACAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:7:2,5:103,100:0.0335:2,2:25.3:1:29.9:1:0.44516:2.56412:56.3:6:0.0297:0.0096:0.3 0/1:252:3:2,1:136,110:0.0119:2,2:39:1:30.7:1:1:1.61:60:6:0.0127:0:0 -7 114269979 . A G 41 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.09482;SOR=0;LSEQ=CAACAGCAGCAGCAACAACA;RSEQ=CAACAACAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:3:2,1:109,116:0.0131:2,2:24.3:1:26.3:1:0.61362:2.12:42.7:2:0.0093:0:4.3 0/0:272:0:0,0:146,125:0:2,0:21.5:1:27.9:1:1:0:60:21.583:0.9962:0:0.3 -7 114269997 . ACAG A 100 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.24088;SOR=2.49257;LSEQ=CAACAACAACAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:110,127:0.0124:2,2:15:1:31:1:0.5999:2.30:60:6:0.0131:0.0041:0.3 0/1:295:9:5,4:140,144:0.0305:2,2:24.4:1:31.7:1:0.74796:1.28:60:18:0.0318:0:0.2 -7 114270000 . G A 77 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.00303;SOR=0;LSEQ=CAACAACAGCAGCAACAACA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:7:4,3:101,120:0.0303:2,2:34.1:1:27.7:1:0.7061:1.58:60:6:0.0275:0:1.4 0/0:294:0:0,0:135,142:0:2,0:24.7:1:31.2:1:1:0:60:26.7:0.9963:0:0.3 -7 114270001 . C A 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.23661;SOR=3.96412;LSEQ=AACAACAGCAGCAACAACAG;RSEQ=AGCAGCAGCAGCAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:106,123:0.0043:2,0:31:0:13:0:1:0:60:0:0:0:6 0/1:297:5:3,2:141,149:0.0168:2,2:20.8:1:27.4:1:0.67816:1.58:60:4:0.014:0:1.2 -7 114270009 . G A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.0817;SOR=0;LSEQ=CAGCAACAACAGCAGCAGCA;RSEQ=CAGCAACAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:96,122:0.0136:2,2:20.3:1:31:1:0.58566:2.53:51.3:6:0.0139:0:2.7 0/0:287:0:0,0:134,153:0:2,0:22:0:13:0:1:0:60:0:0:0:1 -7 114270015 . ACAG A 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.57237;SOR=0.64499;LSEQ=CAACAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:7:4,3:85,121:0.0324:2,2:25.6:1:31:1:0.45498:1.89:57.1:14:0.033:0.0046:0.7 0/1:284:6:2,4:126,152:0.0211:2,2:31:1:31.8:1:0.6934:1.65506:60:12:0.0216:0:0.2 -7 114270027 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.26159;SOR=Inf;LSEQ=CAGCAGCAACAGCAGCAGCA;RSEQ=CAGCAACAGCATCCTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:81,119:0:2,0:29.9:1:32.2:1:1:0:59.8:99:0.9851:0:0.5 0/1:265:3:2,1:115,146:0.0113:2,2:5.7:1:29:1:0.58589:2.53:60:6:0.0115:0.0075:1.3 -7 114270065 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50361;SOR=Inf;LSEQ=AAAGCAAGCGAAAGAGGTAG;RSEQ=ATCCGGTTATCTCATTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:42,99:0:2,0:21.5:1:30.4:1:1:0:60:22.5:1:0:0.6 0/1:173:2:1,1:59,112:0.0116:2,2:21:1:27.5:1:1:1.89:60:4:0.0118:0:1 -7 114270077 . T G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.11687;LSEQ=AGAGGTAGGATCCGGTTATC;RSEQ=CATTGATACATAACAGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:48:11,37:12,43:0.466:2,2:22.4:1:31.4:1:1:1.06:60:96:0.4752:0:1.1 0/1:120:11:3,8:28,81:0.0917:2,2:15.6:1:30.8:1:1:1.08:60:22:0.0957:0:1 -7 114302159 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15797;SOR=Inf;LSEQ=TTAGCCTGCACAAGTGTTTT;RSEQ=TTCGAGTAGAAAATGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:97,69:0:2,0:26.4:1:32:1:1:0:60:165:1:0:0.1 0/1:110:2:1,1:54,54:0.0182:2,2:36:1:31:1:1:1:60:4:0.0183:0:1 -7 114302194 . T C 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51369;SOR=0;LSEQ=GTTAAAGGAGCAGTATGGAC;RSEQ=GTGGATGAAGTAGAATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:82,94:0.0112:2,2:30:0:30.5:1:1:1.15:60:4:0.0114:0:1 0/0:125:0:0,0:53,71:0:2,0:28.2:1:30.3:1:1:0:60:123:0.9919:0:0.1 -7 114302265 . T C 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54914;SOR=0;LSEQ=TGTTTGTGATAGTTTTGTAA;RSEQ=CCTGTATCCTGCATCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:0,3:4,50:0.0526:2,0:24.7:1:33.3:1:1:0:60:6:0.0588:0:1 0/0:31:0:0,0:3,28:0:2,0:25.3:1:29.3:1:1:0:60:62:1:0:0 -7 114302267 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53109;SOR=0;LSEQ=TTTGTGATAGTTTTGTAATC;RSEQ=TGTATCCTGCATCCACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:2,50:0.037:1,2:6:1:26.5:1:0.10901:20.61:60:4:0.0377:0:1 0/0:31:0:0,0:3,28:0:2,0:23.9:1:32.2:1:1:0:60:62:1:0:0 -7 116187033 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=CCTTGTCTCTCCTAGTTTCT;RSEQ=GTGGTTTGCTGGCAATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:43,31:0:2,0:27.4:1:31.8:1:1:0:60:73:1:0:0.3 0/1:65:2:1,1:33,30:0.0308:2,2:20:1:29:1:1:1.09839:60:4:0.0308:0:1 -7 116187106 . G A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.08852;LSEQ=CTCTGCCTCCATCATTAATG;RSEQ=CCTTCTGCCTGAGTGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:25:6,19:6,10:0.6098:2,2:28.3:1:29.8:1:0.48495:1.86941:60:50:0.6098:0:1 0/1:34:4:1,3:9,21:0.1176:2,2:20.5:1:30:1:1:1.27668:60:8:0.1176:0:1 -7 116339672 . C T 119 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.05451;LSEQ=TGTCCTGACTGTGTGGTGAG;RSEQ=GCCCTGGGAGCCAAAGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:19:11,8:306,211:0.0354:2,2:24:1:28.2:1:1:1.05459:60:8.5:0.0323:0:1.4 0/0:501:1:0,1:280,220:0.002:2,0:1:0:25:0:0.44112:0:60:2:0.002:0:1 -7 116340269 . C T 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACGACTTCTTCAACAAGAT;RSEQ=GTCAACAAAAACAATGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:661:0:0,0:278,383:0:2,0:25.8:1:30.4:1:1:0:60:109.167:1:0:0.1 0/1:599:19:5,14:256,324:0.0317:2,2:21.3:1:27.4:1:0.15934:2.20961:60:8.5:0.0287:0:1 -7 116340401 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19728;SOR=Inf;LSEQ=ATTAGAAATAAGTATCAGTC;RSEQ=CAAAAAGAATATCCAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:6,106:0:2,0:24.7:1:30.2:1:1:0:60:36.333:1:0:0.1 0/1:90:2:1,1:10,78:0.0222:2,2:12.5:1:28:1:0.23071:7.48:60:4:0.0227:0:1 -7 116340531 . A AT 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08669;SOR=0;LSEQ=AATTATATCTTTAAAATGTA;RSEQ=ATGGTAACTAAAAGAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:0,9:0,6:0.6:0,0:21.1:1:29.1:1:1:0:60:18:0.6:0.2:0.4 0/0:4:0:0,0:0,4:0:0,0:20:1:31.5:1:1:0:60:8:1:0:0 -7 116340582 . A C 88 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=TTCAGATTTGCATGTTCGTG;RSEQ=CATTTCAGATTATATTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:27.4:1:31.6:1:1:0:60:14:0.875:0:1 0/0:1:0:0,0:0,1:0:0,0:33:0:32:0:1:0:60:2:1:0:0 -7 116371650 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20771;SOR=Inf;LSEQ=CCTCCAGGCTCTGAAAATAC;RSEQ=CACTGAAAGGTTTCTTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:140,23:0:2,0:23.9:1:30.3:1:1:0:60:162:1:0:0.1 0/1:137:2:1,1:110,25:0.0146:2,2:16:1:28:1:0.34468:4.33413:60:4:0.0146:0:1 -7 116395257 . C T 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAATTTGTGACCCTTTT;RSEQ=CCTTTAGTGAAAATTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:39,0:0,0:1:0,1:26.7:1:30.7:1:1:0:60:78:1:0:1 1/1:26:26:26,0:0,0:1:0,1:25.4:1:29.5:1:1:0:60:25:1:0:1 -7 116397478 . G GT 82 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.5885;SOR=1.37585;LSEQ=TGTCATGTATTAAACTTTGG;RSEQ=TTTTTTTTCCAGATTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:643:6:4,2:392,245:0.0093:2,2:33.2:1:28.7:1:1:1.25:60:12:0.0095:0:0.2 0/1:547:7:3,4:334,206:0.0128:2,2:31.1:1:29.3:1:0.43705:2.15867:60:14:0.013:0:0 -7 116397572 . A G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04763;LSEQ=AATGGCCACGGGACAACACA;RSEQ=TACAGTACATTCTCCTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:336:176,160:339,333:0.3333:2,2:27.1:1:32:1:0.59302:1.08:60:111:0.3343:0:1.1 0/1:990:23:11,12:468,499:0.0232:2,2:23.8:1:30.8:1:1:1.02312:60:46:0.0235:0:1.2 -7 116397724 . C T 86 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07701;SOR=3.51975;LSEQ=ACAAGTATTTCGCCGAAATA;RSEQ=GGTCCTATGGCTGGTGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:961:3:1,2:539,417:0.0031:2,2:17:1:29:1:0.58388:2.58262:60:6:0.0032:0:1 0/1:825:9:5,4:472,344:0.0109:2,2:13.2:1:27.2:1:1:1.09755:60:8:0.0098:0:1.7 -7 116397904 . TTG T 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.80099;SOR=1.15836;LSEQ=TAAAAATTAAGCAGATTGTT;RSEQ=TGTGTGTGTGTGGAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:7:0,7:128,315:0.0156:2,0:25:1:30.6:1:0.19932:0:60:14:0.0158:0.0022:0 0/1:445:8:2,6:119,315:0.018:2,2:34.6:1:29.4:1:1:1.13302:60:16:0.0181:0:0 -7 116398498 . A AT 92 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28153;SOR=0.47635;LSEQ=AGCTAAAATTCACTTCCTTA;RSEQ=TTTTTTTTGTTCAGTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:10:4,6:390,186:0.0171:2,2:20:1:27.9:1:0.08735:3.13838:60:20:0.0174:0.0085:0.4 0/0:488:4:3,1:318,166:0.0082:2,2:16.3:1:29.1:1:1:1.56:60:8:0.0085:0.0041:0.3 -7 116399131 . G A 94 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36022;SOR=0.29661;LSEQ=GTTCAATCTGCCTTGTTTCC;RSEQ=TTAATTCTATCAGTCTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:7,1:6,3:0.4706:2,2:20:1:31.5:1:0.57647:3.26:60:16:0.5:0:1 0/1:5:1:1,0:2,2:0.2:2,0:18:0:32:0:1:0:60:2:0.2:0:1 -7 116399719 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50764;SOR=0;LSEQ=TGAAATTATCTAGAGTCTTG;RSEQ=GCTAACCATGTGGAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:0,2:8,161:0.0117:1,0:18.5:1:30.5:1:1:0:60:4:0.0118:0:1 0/0:130:0:0,0:16,114:0:2,0:22.4:1:30.4:1:1:0:60:260:1:0:0 -7 116400378 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGCTAACAAAGAAAGA;RSEQ=CATTAGAATATTTATGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:28.5:1:1:0:60:4:1:0:1 -7 116403052 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22123;SOR=Inf;LSEQ=TAAATTATAAAGTTGCTATG;RSEQ=ATGTTGCCAAGCTGTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:161,40:0:2,0:24.3:1:30.9:1:1:0:60:49.25:1:0:0.1 0/1:179:2:1,1:129,47:0.0112:2,2:20.5:1:27.5:1:0.46772:2.72645:60:4:0.0114:0:1 -7 116403127 . A G 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00058;SOR=0;LSEQ=TGTCAACATCGCTCTAATTC;RSEQ=GAGATAATCTGTTGTACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:12:9,3:253,184:0.0267:2,2:21.9:1:29.9:1:0.37428:2.18:60:24:0.0272:0:1.2 0/0:395:0:0,0:223,171:0:2,0:23.3:1:30:1:1:0:60:77.8:0.9974:0:0.1 -7 116409675 . CT C 198 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.82917;SOR=1.05619;LSEQ=AACTGTGAAGTGTTAACAAC;RSEQ=TTTTTTTTTTTTTTCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:77:72,5:94,20:0.3516:2,2:25.3:1:31.6:1:0.02929:3.05:59:76:0.3551:0.0274:1.1 0/1:162:59:48,11:69,14:0.3642:2,2:20.7:1:30:1:0.82537:1.12849:59.2:13.75:0.3526:0.1296:0.9 -7 116409950 . T C 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19291;LSEQ=GCTCATTTATGTGTGGGTTT;RSEQ=GGCTCATCAACTCAGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:48:9,39:47,162:0.1868:2,2:24.2:1:30:1:0.69919:1.25609:60:96:0.1875:0:1 0/1:260:11:3,8:74,175:0.0423:2,2:29.5:1:30.1:1:1:1.12711:60:22:0.0425:0:1 -7 116409970 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24802;SOR=Inf;LSEQ=TGGCTCATCAACTCAGCCTG;RSEQ=ATTCCTAGTTGTTATTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:30,160:0:2,0:23:1:32.3:1:1:0:60:380:1:0:0.2 0/1:189:2:1,1:40,147:0.0106:2,2:7.5:1:29:1:0.38771:3.64:60:4:0.0106:0:1 -7 116411441 . T C 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00108;SOR=Inf;LSEQ=CCTGAAGGCAGTTATGCCAT;RSEQ=TGTAGAATGGTAATAACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:88,0:0:1,0:24:1:30.9:1:1:0:60:176:1:0:0.1 0/1:44:6:6,0:37,1:0.1364:1,0:20:1:31.3:1:1:0:60:12:0.1395:0:1 -7 116411824 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11239;SOR=Inf;LSEQ=GTAGTCCATAAAACCCATGA;RSEQ=TTCTGGGCACTGGGTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:146,85:0:2,0:26.8:1:32.3:1:1:0:59.9:45.2:1:0:0 0/1:117:2:0,2:73,42:0.0171:2,0:14:1:30.5:1:0.1394:0:60:4:0.0172:0:1 -7 116411832 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12382;SOR=Inf;LSEQ=TAAAACCCATGAGTTCTGGG;RSEQ=ACTGGGTCAAAGTCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:155,78:0:2,0:26.7:1:32.1:1:1:0:59.9:45.6:1:0:0 0/1:127:2:1,1:88,37:0.0157:2,2:23:1:29.5:1:0.51056:2.36019:60:4:0.0159:0:1 -7 116411923 . C T 195 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02139;LSEQ=ATCTGGGCAGTGAATTAGTT;RSEQ=GCTACGATGCAAGAGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:88:53,35:329,238:0.1344:2,2:27.7:1:30.2:1:0.72857:1.10:60:87:0.1343:0:1 0/0:606:2:0,2:348,256:0.0033:2,0:1:0:27.5:1:0.18085:0:60:4:0.0033:0:1 -7 116415226 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10253;SOR=Inf;LSEQ=CAGTAAGCATTTTATCTTTG;RSEQ=CCTTTGCAGATTAGGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:30,203:0:2,0:22.1:1:31.7:1:1:0:60:57.25:1:0:0.1 0/1:206:3:1,2:44,157:0.0146:2,2:28.3:1:29:1:0.52851:1.78:60:6:0.0149:0:2 -7 116416327 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTCAAACACCCCAGAG;RSEQ=GTAATCCTTTGTGTGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 116417606 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15907;SOR=Inf;LSEQ=TATAATAAAACGTTGATTTA;RSEQ=ACTTTCCCCTTGTGGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:12,144:0:2,0:22.7:1:32.4:1:1:0:60:312:1:0:0.1 0/1:104:2:1,1:17,85:0.0192:2,2:27:1:27.5:1:0.31759:4.89:60:4:0.0196:0:1 -7 116417848 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTATTGGAAGCATGTTG;RSEQ=CACCTACAGTAGTAATGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:45.5:1:30.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 116421967 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=0;SOR=0.08246;LSEQ=GATAATTTTTTATAAATAAA;RSEQ=ATTTCAGAATTCTAAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:167:156:138,18:11,0:0.9341:0,2:21.9:1:32.1:1:0.6103:0:60:155:0.9337:0:1.1 1/0:123:66:56,10:52,5:0.5366:2,2:20.9:1:30.9:1:0.40837:1.84807:60:65:0.5328:0:1.1 -7 116422185 . T A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11828;SOR=0;LSEQ=TCTCTGTGCCACAATCCAAA;RSEQ=TAAGTGACAAGGAGGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:84,209:0.0101:2,2:18:1:28.3:1:0.20331:4.95:60:6:0.0104:0:1.3 0/0:307:0:0,0:88,217:0:2,0:23.7:1:29.4:1:1:0:60:37.125:0.9966:0:0.1 -7 116423161 . G A 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00628;SOR=0;LSEQ=TTTCCTCAGCCTGTTGAATT;RSEQ=GCAATGTCAATGTCAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:9,0:19,0:0.3214:1,0:23:1:28.6:1:1:0:58.7:18:0.3214:0:1.8 0/0:21:0:0,0:18,3:0:2,0:26:1:31.4:1:1:0:60:42:1:0:0 -7 116435768 . C T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.62654;LSEQ=GGAGCCCCACCTTATCCTGA;RSEQ=GTAAACACCTTTGATATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:70:39,31:505,419:0.0704:2,2:22.7:1:30.8:1:0.90137:1.04:60:140:0.0708:0:1.1 0/1:910:445:230,215:237,227:0.489:2,2:24.4:1:29.7:1:0.89441:1.02:60:221.5:0.489:0:1.1 -7 116436022 . G A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.87259;LSEQ=CTGGTGTCCCGGATATCAGC;RSEQ=ATCTTCTCTACTTTCATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:89:48,41:443,475:0.0883:2,2:28.1:1:29.7:1:0.31936:1.26:60:28.667:0.0865:0:1.3 1/0:882:472:221,251:213,193:0.5351:2,2:25.7:1:29.7:1:0.1043:1.25311:60:156.333:0.5391:0:1.3 -7 116436097 . G A 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.05841;LSEQ=AACGTAAAATGTGTCGCTCC;RSEQ=TATCCTTCTCTGTTGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:709:70:33,37:265,373:0.0987:2,2:23.1:1:30.6:1:0.37481:1.25:60:69:0.0986:0:1.4 0/1:684:341:146,195:142,199:0.4985:2,2:24.7:1:30.1:1:0.81611:1.05:60:340:0.5:0:1.4 -7 116436233 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55828;SOR=3.38169;LSEQ=TGTCCAATGGTTTTTTCACT;RSEQ=CCTGACCTTTAAAAGGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:1,0:37,165:0.0049:2,0:1:0:23:0:0.18719:0:60:2:0.005:0:1 0/1:121:2:1,1:23,96:0.0165:2,2:5:1:28:1:0.35868:4.11:60:4:0.0167:0:1.5 -7 116436249 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54113;SOR=0;LSEQ=CACTGCCTGACCTTTAAAAG;RSEQ=CCATCGATATTCTTTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:24,135:0.0124:2,2:11.5:1:28.5:1:0.28727:5.53:60:4:0.0126:0:1 0/0:88:0:0,0:15,73:0:2,0:22:1:31.7:1:1:0:60:176:1:0:0 -7 121088614 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCGTGGTGGTGCACGC;RSEQ=TGTAATCCCACTACTAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 121090859 . T G 279 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28942;LSEQ=GACAGCAAGAAAACCTTGGG;RSEQ=TACCCTAGATGGTGACTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:547:494:244,250:25,27:0.9031:2,2:25.9:1:31.2:1:0.88495:1.05:60:60.75:0.905:0:1.1 1/0:447:326:162,164:52,66:0.7293:2,2:27.7:1:30.9:1:0.33349:1.25:60:162:0.733:0:1.1 -7 121943574 . A G 32 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=18;MSI=12.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGGAAGGAAGGAAGGAAGGA;RSEQ=GGAAGGAAGGAAGGAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:32.5:1:1:0:52.5:4:1:0:4.5 -7 121943578 . A G 32 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=14;MSI=11.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGGAAGGAAGGAAGGAAGGA;RSEQ=GGAAGGAAGGAAGGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:32.5:1:1:0:52.5:4:1:0:4.5 -7 121943582 . A G 32 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=10;MSI=10.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGGAAGGAAGGAAGGAAGGA;RSEQ=GGAAGGAAGGAGGGAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:32.5:1:1:0:52.5:4:1:0:4.5 -7 121943586 . A G 32 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=9.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGGAAGGAAGGAAGGAAGGA;RSEQ=GGAAGGAGGGAGGGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:32:1:1:0:52.5:4:1:0:4.5 -7 123382152 . A C 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15087;SOR=0.62506;LSEQ=CAGAACTTGGTGAAAGAGAC;RSEQ=CTGTTCAAAAGGCCCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:53:49,4:39,2:0.5638:1,2:25.3:1:31.4:1:0.6933:1.58427:60:106:0.5699:0:1 0/1:65:29:28,1:33,3:0.4462:2,1:19.4:1:29.8:1:0.62221:2.51:60:28:0.4444:0:1 -7 123382290 . C T 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00795;SOR=0.72148;LSEQ=TTTGCATCTTAAAAGCATGC;RSEQ=TAATTTTGGCATTCATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:579:303:166,137:143,133:0.5233:2,2:26.8:1:30.3:1:0.50494:1.13:60:49.5:0.522:0:1.1 0/1:525:232:124,108:148,145:0.4419:2,2:25:1:30.2:1:0.53847:1.12:60:231:0.4434:0:1.2 -7 123382412 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15076;SOR=Inf;LSEQ=CATAATTTCAGCATGTTGTC;RSEQ=AGTGCATTACAAAAAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:9,132:0:2,0:20.9:1:32.1:1:1:0:60:69.5:1:0:0.1 0/1:90:2:1,1:8,80:0.0222:2,2:35.5:1:30:1:0.19101:9.49:60:4:0.0227:0:1.5 -7 123382509 . C T 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61419;LSEQ=TGAATCAGTCTCTAAAGTAA;RSEQ=CAAGTCAATTCACTATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:0.1304:1,0:11:1:31:0:1:0:60:6:0.1304:0:1 0/1:12:1:0,1:0,11:0.0833:0,0:30:0:31:0:1:0:60:2:0.0909:0:1 -7 123522765 . G A 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08235;SOR=Inf;LSEQ=AGACTCAGACACAGACTGAA;RSEQ=TTATGCCATCAGCCCACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:17.9:1:32.3:1:1:0:60:16:1:0:0.1 0/1:9:4:2,2:5,0:0.4444:0,2:15:1:30.8:1:0.16667:0:60:8:0.4444:0:1 -7 124270259 . T C 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTCTCAATTGAATTCCA;RSEQ=AATTCTGGATAAAAATAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:37.8:1:32.3:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 124270348 . G T 132 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06274;SOR=0.10484;LSEQ=CATATTCTTATCACTTCCAG;RSEQ=TTTAATTACTTCAATAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:21:21,0:1,0:0.9545:0,1:18.2:1:30.1:1:1:0:60:42:0.9545:0:1.1 1/0:9:6:6,0:3,0:0.6667:0,0:15.2:1:27.8:1:1:0:60:5:0.625:0:1.2 -7 124270427 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54201;SOR=0;LSEQ=TGCTAATTTAGAAAATAACT;RSEQ=ATTGAGCTTTTATCTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:88,3:0.0215:1,2:21:1:27:1:0.08462:25.54759:60:4:0.022:0:1 0/0:50:0:0,0:47,3:0:2,0:22.7:1:30.5:1:1:0:60:15.667:1:0:0.1 -7 124270508 . G T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12643;SOR=Inf;LSEQ=TGAAAGAGTTGGTTGGCAGG;RSEQ=CTGAGTGACACCCAAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:168,95:0:2,0:26.4:1:31.5:1:1:0:59.9:86.667:1:0:0.4 0/1:297:4:1,3:182,110:0.0135:2,2:19.8:1:28:1:0.15725:4.93699:60:8:0.0136:0:1.3 -7 124270574 . A C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.31226;LSEQ=GAGTCTTCATGTAAAGAATT;RSEQ=ATTTATGGCTATTTTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:368:300:144,156:27,40:0.8152:2,2:25.6:1:31.6:1:0.28005:1.37:60:149:0.8209:0:1.1 1/0:449:260:126,134:94,94:0.5791:2,2:25.7:1:31.3:1:0.77437:1.06333:60:129:0.585:0:1.2 -7 124270654 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1061;SOR=Inf;LSEQ=TGTTTTAGTGCTTCTGGGAG;RSEQ=CATACTGCAAATTAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:58,150:0:2,0:22.3:1:31.5:1:1:0:60:40.6:1:0:0.5 0/1:188:3:1,2:57,127:0.016:2,2:27:1:30.7:1:1:1.11:60:6:0.0163:0:1 -7 124270668 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2242;SOR=Inf;LSEQ=TGGGAGGCATACTGCAAATT;RSEQ=AGATGACAGATGGGAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:33,121:0:2,0:22.3:1:29.4:1:1:0:60:76:1:0:0.3 0/1:139:2:1,1:32,105:0.0144:2,2:26.5:1:28:1:0.41977:3.25:60:4:0.0145:0:1.5 -7 124270732 . A G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00054;SOR=0.13999;LSEQ=GAGAAGGTTGCCAAGAGCCC;RSEQ=TTAATTTTGTGTTTCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:41:0,41:0,8:0.8367:0,1:23.9:1:32.1:1:1:0:60:82:0.8367:0:1 0/1:22:9:0,9:0,13:0.4091:1,0:31:1:31.1:1:1:0:60:18:0.4091:0:1 -7 124271606 . G A 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAATGCATCATTAGCAC;RSEQ=ATACTTTTTAATACCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:32:0:1:0:60:4:1:0:1 -7 124954610 . C T 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.2984;LSEQ=ACCTTGCTATTACTTACCTT;RSEQ=CAGCCCTGTATTTTTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:0,4:4,13:0.1905:2,0:14.5:1:30.3:1:0.54553:0:60:8:0.1905:0:1 0/1:17:4:2,2:3,10:0.2353:2,2:19.3:1:30.8:1:0.53782:3.07:60:8:0.2353:0:1.5 -7 124954625 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49206;SOR=Inf;LSEQ=ACCTTCCAGCCCTGTATTTT;RSEQ=AACTTCCTTGTCAAATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:1,11:0:2,0:25.1:1:29.7:1:1:0:60:24:1:0:0.1 0/1:16:2:1,1:4,10:0.125:2,2:6.5:1:28.5:1:1:2.35:60:4:0.125:0:1.5 -7 124954746 . A C 50 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGACCCCTGGACTGACCC;RSEQ=CTGGCCCTTTCACTGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:1,0:0.75:0,2:36.3:1:32:1:1:0:60:6:0.75:0:1.3 -7 125932788 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=ACACACCAGCGGTGGCAGTC;RSEQ=GCGGCCAGAGTGCTTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:29.3:1:30.3:1:1:0:60:18:1:0:0.2 0/1:11:2:1,1:2,7:0.1818:2,2:31:0:32:1:0.49091:3.06:60:4:0.1818:0:1.5 -7 127153538 . C T 94 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00223;SOR=0.05425;LSEQ=TAGCCCTGTTGTGCAAAGAA;RSEQ=AGTACCGCTGCTGCTGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:4,5:0.5:2,2:33:1:29.9:1:0.63719:2.37:60:18:0.5:0:1.2 0/1:21:1:0,1:11,9:0.0476:2,0:47:0:27:0:0.47619:0:60:2:0.0476:0:1 -7 127153540 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21764;SOR=0;LSEQ=GCCCTGTTGTGCAAAGAACA;RSEQ=TACCGCTGCTGCTGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:43.5:1:31:1:1:1.26772:60:4:0.1111:0:2 0/0:20:0:0,0:10,10:0:2,0:30.8:1:31.3:1:1:0:60:40:1:0:0.2 -7 127668967 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23333;SOR=Inf;LSEQ=CTGCTGCGGATGTTGCTGCT;RSEQ=GGATGTCTTCGTCCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:0:2,0:26:1:31.6:1:1:0:60:46:1:0:0.2 0/1:22:2:1,1:7,12:0.0909:2,2:35.5:1:29.5:1:1:1.67:60:4:0.0952:0:1 -7 128102411 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49805;SOR=0;LSEQ=TAACAAGCATTTTCTGAAAT;RSEQ=GAAATTTGTTTTTTTATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:68,5:0.0267:2,2:5:0:31:1:0.15459:12.50609:60:4:0.0267:0:1 0/0:67:0:0,0:63,4:0:2,0:24.6:1:32:1:1:0:52.2:66:1:0:0 -7 128102508 . C CTCTT 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.0156;SOR=0.57537;LSEQ=TTAAAATACCACATATGGTG;RSEQ=TCTTGTGAGCTTGCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:78:44,34:51,34:0.4756:2,2:24.3:1:30.2:1:0.75064:1.15804:34.9:156:0.4756:0.1463:0.1 0/1:181:62:35,27:62,52:0.3425:2,2:22.6:1:30.2:1:0.87426:1.09:34.7:124:0.3444:0.1105:0 -7 128102522 . C A 88 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0402;SOR=7.25729;LSEQ=ATGGTGCTCTTGTGAGCTTG;RSEQ=TTTTCTCCACAATTTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:1,0:84,70:0.0065:2,0:29:0:13:0:1:0:21:0:0:0:3 0/1:177:8:6,2:89,79:0.0452:2,2:8.1:1:29.5:1:0.29047:2.65:45.1:16:0.0452:0:1.4 -7 128102618 . T C 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00371;SOR=Inf;LSEQ=TCAGAGCCATGCTAATGATG;RSEQ=GTTGTATTAAAGAATGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:27,96:0:2,0:23.9:1:30:1:1:0:49.7:60.5:1:0:0.1 0/1:136:9:4,5:36,90:0.0662:2,2:29.9:1:29.8:1:0.4495:1.99:56.7:18:0.0682:0:1.3 -7 128102625 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22608;SOR=0;LSEQ=CATGCTAATGATGTGTTGTA;RSEQ=TAAAGAATGTTGATGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:21,89:0.0179:2,2:37.5:1:33:1:0.35569:4.16:33:4:0.0185:0:1 0/0:123:0:0,0:33,90:0:2,0:25.7:1:29.5:1:1:0:52.1:60.5:1:0:0.1 -7 128296052 . T G 84 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAGACCCCCCAGGTGTT;RSEQ=AGGCAGGGCTGGGGTGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:31.2:1:32.8:1:1:0:28.3:12:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 128296224 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52833;LSEQ=TGGACCCGCTATGCACACAT;RSEQ=GTCTTCTCCAAGGTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:17,7:0.0769:2,2:24:1:29:1:0.52923:2.3376:22:4:0.0769:0:1 0/1:24:1:1,0:18,5:0.0417:2,0:30:0:32:0:1:0:40:2:0.0417:0:1 -7 128296778 . C G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25134;SOR=Inf;LSEQ=GCCTTCTCGGTCTCCGGTTC;RSEQ=CTGAGCCTGTCCTTGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,5:0:2,0:18.9:1:31.4:1:1:0:37.7:28:1:0:0.1 0/1:20:3:1,2:10,7:0.15:2,2:33:1:31:1:0.56579:2.70974:21.3:6:0.1579:0:1.3 -7 128297096 . A T 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39104;SOR=0.35877;LSEQ=TCCAGGTCGCCCACACTTTC;RSEQ=GGTCTCTTGCACCAGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:3,1:18,6:0.1429:2,2:11:1:29:1:1:1:25.8:8:0.1481:0:1 0/1:36:2:2,0:23,11:0.0556:2,0:31:1:33:0:1:0:22:4:0.0556:0:1 -7 128297306 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.23124;SOR=Inf;LSEQ=CATCCGAGTATGTGTAGGAG;RSEQ=AGGACAAGGTGGGACCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:12,22:0:2,0:24.4:1:30.2:1:1:0:45.2:33:1:0:0.1 0/1:32:2:1,1:12,18:0.0625:2,2:35:1:30.5:1:1:1.48:46.5:4:0.0625:0:1 -7 128297567 . C A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.49231;SOR=Inf;LSEQ=TGACATCATCACCCCCTCCT;RSEQ=CTCATGGATGACCGTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:21,12:0:2,0:26.1:1:31.4:1:1:0:34:66:1:0:0.1 0/1:33:2:1,1:18,13:0.0606:2,2:36:0:27.5:1:1:1.37079:45:4:0.0625:0:1 -7 128297785 . C T 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGTTCCCGTAGTGCCTGA;RSEQ=GGTCTATTTCCCTGCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:44,43:0:2,0:18.4:1:30.7:1:1:0:44.4:86:1:0:0.1 0/1:74:23:13,10:25,25:0.3108:2,2:17:1:29:1:0.62469:1.30:42.5:46:0.3151:0:1.1 -7 128297916 . G A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02251;SOR=0.24069;LSEQ=TCCTTGGTATCCGAGCTCTG;RSEQ=AGTGTTTGGGCTGCAACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:5,6:15,11:0.2973:2,2:16.8:1:30.5:1:0.71947:1.6144:40.4:22:0.2973:0:1.1 0/1:44:4:3,1:21,19:0.0909:2,2:9:1:29.5:1:0.6137:2.66:44:8:0.093:0:1 -7 128298001 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49743;SOR=0;LSEQ=CTGATATTCTCCGCTCCCAC;RSEQ=AGCCCTTGTTACACTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:51,24:0.026:2,2:36.5:1:30:0:0.54682:2.10243:41.5:4:0.0263:0:1 0/0:71:0:0,0:42,29:0:2,0:27.3:1:28.5:1:1:0:41.2:13.2:1:0:0.2 -7 128298272 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22097;SOR=Inf;LSEQ=CTCATGGGCCACCGGATGTG;RSEQ=TCCTTGTCCCATTTGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:49,44:0:2,0:23.1:1:31.5:1:1:0:34.4:186:1:0:0 0/1:83:2:1,1:39,42:0.0241:2,2:31:1:28:1:1:1.08:25:4:0.0241:0:1 -7 128298370 . C G 134 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.13085;LSEQ=CTGGGCCTGACATCATCTGG;RSEQ=TGGTAGAGGCAACTGGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:18:1,17:34,46:0.1837:2,1:25.3:1:32.3:1:0.00243:12.33898:33.5:36:0.1837:0:1.1 0/1:141:4:0,4:67,70:0.0284:2,0:44.3:1:30:1:0.12151:0:37:8:0.0288:0:1 -7 128298600 . T A 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.31348;SOR=0.51777;LSEQ=CCCAGGGTCAGCACTCCCTG;RSEQ=CCCACCTGGTGGACACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:24:15,9:18,19:0.3934:2,2:24.8:1:29.9:1:0.30862:1.74:59.2:48:0.4:0:1.3 0/1:24:6:3,3:9,9:0.25:2,2:20.5:1:29.3:1:1:1:53.5:12:0.25:0:1 -7 128298668 . A T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25252;SOR=4.19082;LSEQ=CTTTGCTCTGGTTGGAGGCC;RSEQ=CTGAGTGACTGGCAGGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:1:1,0:46,20:0.0149:2,0:31:0:33:0:1:0:60:2:0.0154:0:1 0/1:33:2:0,2:23,8:0.0606:2,0:25.5:1:27:1:0.08523:0:60:4:0.0625:0:1 -7 128298741 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20599;SOR=Inf;LSEQ=AAGGGGACAGAGTACCAGGA;RSEQ=AACACAGCCACAGAGCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:84,61:0:2,0:26.4:1:31.7:1:1:0:53.6:144:1:0:0.2 0/1:121:2:1,1:68,51:0.0165:2,2:41:1:27.5:1:1:1.33011:60:4:0.0168:0:2 -7 128298749 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20721;SOR=Inf;LSEQ=AGAGTACCAGGAGAACACAG;RSEQ=CACAGAGCAAGGTTCCACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:84,65:0:2,0:26.5:1:30.9:1:1:0:53.1:20.286:1:0:0.2 0/1:125:2:1,1:70,53:0.016:2,2:33:1:26:1:1:1.31777:60:4:0.016:0:2 -7 128298881 . C A 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01937;SOR=Inf;LSEQ=TTCCTGGCAGGGGCTCACAC;RSEQ=TCCTCAGCCCCCTCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:17,43:0:2,0:22.5:1:31:1:1:0:45.8:29:1:0:0.3 0/1:52:5:2,3:9,38:0.0962:2,2:14.8:1:28.6:1:0.28303:2.75:33.8:10:0.0962:0:1.4 -7 128298889 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49949;SOR=0;LSEQ=AGGGGCTCACACCTCCTCAG;RSEQ=CCCCTCCTCAGCCAAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:10,36:0.0408:2,2:19:1:29:1:0.40957:3.48:52:4:0.0426:0:1.5 0/0:40:0:0,0:7,33:0:2,0:23.3:1:30.5:1:1:0:44.8:80:1:0:0.2 -7 128298920 . C T 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20026;SOR=0.37322;LSEQ=GCCAAGGCAGCTTGGACCCA;RSEQ=GGAAGTGGGGATGGAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:9:1,8:2,19:0.2903:2,2:33.1:1:30.6:1:1:1.18:56.6:18:0.3:0:1 0/1:23:3:0,3:0,20:0.1304:1,0:30.3:1:29.3:1:1:0:54:6:0.1304:0:1 -7 128299031 . C T 27 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAGTGGTGCGATCTCAG;RSEQ=TCACTGAAACCTCCACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:0,7:0.2222:0,2:18.5:1:27.5:1:0.22222:0:49:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 128431032 . TG T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49126;SOR=Inf;LSEQ=AGTCAGCGCGGACTGCTAGG;RSEQ=GGGGCGCCGGCCGGGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:17,9:0:2,0:29.5:1:31.5:1:1:0:60:25:1:0:0.7 0/1:28:2:1,1:15,11:0.0714:2,2:31.5:1:30.5:1:1:1.34838:60:4:0.0714:0:0.5 -7 128431054 . GA G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=GGGGCGCCGGCCGGGCGGGG;RSEQ=GGGAGGGAAGGAGGGGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:14,8:0.0833:2,2:47:0:32:1:1:1.70775:60:4:0.1053:0:0.5 0/0:23:0:0,0:12,11:0:2,0:24:1:28:1:1:0:60:10.5:1:0:0.4 -7 128519723 . G A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGTGATGTCGAGGCACAT;RSEQ=GGTGGACAGCACAGGATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:11:1:33:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:30.5:1:1:0:60:4:1:0:1 -7 128766528 . G C 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62555;SOR=1.19439;LSEQ=CTCCCGGCCCGCCCACTACG;RSEQ=GCCCAGGCTAGAGGCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:53:46,7:26,3:0.6463:2,2:10.4:1:31.2:1:1:1.31454:47.6:25.5:0.6375:0:3 1/0:86:59:52,7:20,7:0.686:2,2:9.8:1:32.6:1:0.12192:2.57:46.7:118:0.6941:0:3.1 -7 128766533 . A C 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9887;LSEQ=GGCCCGCCCACTACGGGCCC;RSEQ=GGCTAGAGGCGCCGCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:71:62,9:28,4:0.6893:2,2:12.3:1:30.6:1:1:1.01597:46:22.667:0.6869:0:2.8 1/0:99:68:57,11:22,8:0.6869:2,2:13.3:1:31:1:0.27075:1.87:45.8:136:0.701:0:2.9 -7 128766550 . GCCA G 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.05861;SOR=Inf;LSEQ=CCCAGGCTAGAGGCGCCGCC;RSEQ=CCGGCCCGCGGAGCCCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:191,48:0:2,0:19.6:1:32.1:1:1:0:52.6:38.833:1:0:1.5 0/1:233:4:3,1:165,64:0.0172:2,2:19.5:1:32.3:1:1:1.16:54.3:8:0.0174:0:0.5 -7 128766553 . A G 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1367;SOR=1.43713;LSEQ=AGGCTAGAGGCGCCGCCGCC;RSEQ=CCGGCCCGCGGAGCCCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:257:202:156,46:46,9:0.786:2,2:18.4:1:30.5:1:0.35736:1.50488:51.3:49.5:0.7888:0:1.7 1/1:245:206:150,56:22,13:0.8408:2,2:20.3:1:30.8:1:0.23121:1.58:52.1:205:0.8542:0:1.8 -7 128766773 . GACGATGACTTCGAAAGGACCT AGAACCC 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAGGTCGGCGAACTCAAA;RSEQ=CAGAGCTGGACGCGGGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1057:0:0,0:505,550:0:2,0:23.8:1:30.1:1:1:0:59.8:74.357:0.999:0:0.1 0/1:1051:53:27,26:476,513:0.0504:2,2:29.1:1:30.7:1:0.77816:1.12:54.8:106:0.0508:0.001:1 -7 128766796 . AGAGCTGGA GC 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGACTTCGAAAGGACCTC;RSEQ=CGCGGGCAACGGCGGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1035:0:0,0:495,539:0:2,0:25.6:1:30.7:1:1:0:59.8:113.889:1:0:0.1 0/1:1014:72:40,32:440,494:0.071:2,2:21.8:1:31:1:0.17925:1.40:55.7:35:0.0708:0.0217:2.3 -7 128766971 . G A 142 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.03281;LSEQ=CGTACATCGTGGGCTTCTAC;RSEQ=GGGCCTTCTACTGTGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:595:26:11,15:303,265:0.0437:2,2:20.4:1:30.3:1:0.31741:1.55799:60:52:0.0446:0:1 0/0:669:1:1,0:335,333:0.0015:2,0:1:0:23:0:1:0:60:2:0.0015:0:1 -7 128767157 . C T 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATGCACCGAAATGTGAAG;RSEQ=CCTCCAACATCCTCGTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:949:0:0,0:505,444:0:2,0:24.5:1:31.5:1:1:0:56.7:66.786:1:0:0.1 0/1:993:65:31,34:457,471:0.0655:2,2:23:1:29.2:1:0.89802:1.06414:57.2:31.5:0.0644:0:1.4 -7 128767250 . G A 227 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTCCATGGCCAACTCCTTC;RSEQ=TGGGCACGCGCTCCTACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:182:77,105:357,377:0.1985:2,2:24.6:1:30.3:1:0.13581:1.29093:53:90:0.1985:0:1.1 0/0:810:0:0,0:384,423:0:2,0:27:1:30.2:1:1:0:54.1:114.286:0.9963:0:0.2 -7 128767410 . A G 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04158;SOR=1.35136;LSEQ=GCTGGAGGCCATCTTTGGCC;RSEQ=GCCCGTGGTCGACAGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:714:587:264,323:51,73:0.8221:2,2:26.6:1:30:1:0.48637:1.17:59.7:38.133:0.8218:0:1.3 1/1:703:606:283,323:45,51:0.862:2,2:25.8:1:29.6:1:1:1.00706:58.9:59.6:0.8625:0:1.3 -7 128767490 . T C 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00454;SOR=1.82386;LSEQ=CCGGGCGCCCCAACAGCGGT;RSEQ=ACGGGATGGACAGCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:412:340:153,187:34,38:0.8252:2,2:25.1:1:31.3:1:0.79473:1.09333:60:29.909:0.8266:0:2.1 1/1:404:362:180,182:18,24:0.896:2,2:22.3:1:30.8:1:0.41961:1.32:60:59.333:0.8967:0:2.1 -7 128767506 . T G 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=1.99815;LSEQ=CGGTTACGGGATGGACAGCC;RSEQ=GCCCGCCATGGCCATCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:400:318:156,162:45,35:0.795:2,2:24.9:1:29.9:1:0.26261:1.33419:60:30.8:0.7979:0:2 1/1:394:349:176,173:22,21:0.8858:2,2:23.4:1:29.2:1:1:1.02969:60:86.25:0.8846:0:1.9 -7 128767825 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49872;SOR=Inf;LSEQ=CTGCCCACCGTCCCTGTCCA;RSEQ=GCCCCGCCCTTCCAGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:38,147:0:2,0:25:1:29.9:1:1:0:58.2:36:1:0:0.1 0/1:189:2:1,1:42,144:0.0106:2,2:21:0:32:0:0.40608:3.40:60:4:0.0106:0:1.5 -7 128767848 . C G 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00579;SOR=Inf;LSEQ=CCCGCCCTTCCAGCTGAGGA;RSEQ=AGGCTGGCGCCTCCACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:21,117:0:2,0:25.1:1:32.2:1:1:0:57.3:68:1:0:0.2 0/1:104:6:1,5:18,80:0.0577:2,2:20.8:1:30.8:1:1:1.12377:58.2:12:0.0583:0:1 -7 128767969 . A G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27203;SOR=Inf;LSEQ=GTCCCTGCCGGCGTGCCTCT;RSEQ=GGGACGGGCGACGCTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:16:0,16:1,3:0.8:2,1:23.4:1:32.1:1:0.2:0:60:32:0.8:0:1 1/1:10:10:1,9:0,0:1:0,2:23.2:1:30.2:1:1:0:60:20:1:0:1 -7 128828953 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.49922;SOR=Inf;LSEQ=GGGGGGCTCCGAGGAGCAGG;RSEQ=GGGGGCGCCGGGGCTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:0:2,0:23.1:1:31.4:1:1:0:60:86:1:0:0.4 0/1:52:2:1,1:27,23:0.0385:2,2:26:1:31:1:1:1.17028:60:4:0.0392:0:1 -7 128828973 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.25552;SOR=Inf;LSEQ=CGGGGGCGCCGGGGCTTTTG;RSEQ=TGAGTTGGCGGGGTTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:48,45:0:2,0:18.7:1:31.8:1:1:0:60:30:1:0:0.4 0/1:116:3:1,2:57,56:0.0259:2,2:16:1:27.3:1:1:2.0237:60:6:0.0261:0:1.3 -7 128828981 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51427;SOR=Inf;LSEQ=CCGGGGCTTTTGCTGAGTTG;RSEQ=CGGGGTTGGCCATGGCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:51,49:0:2,0:21.5:1:31.3:1:1:0:60:19:1:0:0.4 0/1:144:2:1,1:72,70:0.0139:2,2:6:1:27.5:1:1:1.02838:60:4:0.0139:0:1 -7 128829002 . G A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50913;SOR=Inf;LSEQ=CGGGGTTGGCCATGGCCGCT;RSEQ=CCCGCCCAGCGCGGGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:56,56:0:2,0:25:1:32.1:1:1:0:60:55:1:0:0.4 0/1:151:2:1,1:74,75:0.0132:2,2:33:1:24.5:1:1:1.01:60:4:0.0136:0:1.5 -7 128829011 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=2;SSF=0.25968;SOR=Inf;LSEQ=CCATGGCCGCTGCCCGCCCA;RSEQ=CGCGGGGGCCGGAGCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:54,53:0:2,0:26.5:1:32.1:1:1:0:60:52.5:1:0:0.5 0/1:139:3:3,0:65,71:0.0216:2,0:11.3:1:22.7:1:0.11442:0:60:2:0.015:0:2 -7 128829014 . C A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.25863;SOR=Inf;LSEQ=TGGCCGCTGCCCGCCCAGCG;RSEQ=GGGGGCCGGAGCTCCCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:53,52:0:2,0:26.5:1:31:1:1:0:60:104:1:0:0.5 0/1:135:3:2,1:63,67:0.0222:2,2:9.7:1:22.3:1:0.6137:2.12:60:2:0.0153:0:1.3 -7 128829020 . C T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3151;SOR=0.24336;LSEQ=CTGCCCGCCCAGCGCGGGGG;RSEQ=CGGAGCTCCCGCTCCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:3:1,2:50,48:0.0297:2,2:12:1:23:1:0.61746:2.06874:60:2:0.0202:0:1.3 0/0:136:1:0,1:67,68:0.0074:2,0:1:0:22:0:1:0:60:2:0.0075:0:1 -7 128829039 . GGCT G 66 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.29435;SOR=0.44124;LSEQ=GCCGGAGCTCCCGCTCCTGG;RSEQ=GCTGCTGCTGCTGCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:5:2,3:51,44:0.0495:2,2:37.4:1:28.6:1:0.66364:1.72906:60:4:0.0417:0:1 0/1:134:3:2,1:63,67:0.0224:2,2:9:1:31:1:0.6137:2.12:60:6:0.0224:0.0075:0.3 -7 128829052 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.51758;SOR=Inf;LSEQ=CTCCTGGGGCTGCTGCTGCT;RSEQ=CTGCTGCTGGGGGACCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:47,46:0:2,0:20.5:1:31.6:1:1:0:60:30:1:0:0.5 0/1:139:2:1,1:66,69:0.0144:2,2:16:1:27.5:1:1:1.05:60:4:0.015:0:1 -7 128829066 . A G 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00024;SOR=0;LSEQ=GCTGCTGCTGCTGCTGGGGG;RSEQ=CCCGGGCCGGGGGGCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:9:4,5:39,39:0.1034:2,2:21.7:1:32.4:1:1:1.2468:60:18:0.1084:0:1.3 0/0:126:0:0,0:61,64:0:2,0:21.1:1:27.7:1:1:0:60:14.625:1:0:0.4 -7 128829069 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0.77872;LSEQ=GCTGCTGCTGCTGGGGGACC;RSEQ=GGGCCGGGGGGCGGCCTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:44,46:0.0215:2,0:1:0:25:0:0.49546:0:60:4:0.0222:0:1 0/1:119:2:1,1:55,61:0.0168:2,2:38.5:1:31:1:1:1.11:60:4:0.0172:0:1 -7 128829098 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.44077;LSEQ=GGGCGGCCTCGAGCGGGAAC;RSEQ=CGACCGGGCCTGGGCCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:1,0:51,50:0.0098:2,0:1:0:29:0:1:0:60:2:0.0104:0:1 0/1:142:2:1,1:68,70:0.0141:2,2:12.5:1:30.5:1:1:1.03:60:4:0.0146:0:1 -7 128829105 . G T 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64328;SOR=2.1521;LSEQ=CTCGAGCGGGAACGCGACCG;RSEQ=GCCTGGGCCTCGGAGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:1:0,1:49,51:0.0099:2,0:1:0:28:0:1:0:60:2:0.0102:0:1 0/1:142:3:0,3:70,69:0.0211:2,0:17.3:1:23.7:1:0.24483:0:60:2:0.0145:0:1.3 -7 128829150 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25606;SOR=Inf;LSEQ=GAGCGCGAGGAGGAGCGCGG;RSEQ=GGTGACTGGCCCTCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:151,48:0:2,0:16.6:1:31.6:1:1:0:60:65.333:1:0:0.2 0/1:244:3:1,2:169,72:0.0123:2,2:6:1:28:1:0.21911:4.66087:60:6:0.0124:0:1 -7 128829169 . G A 58 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.19409;SOR=0.22183;LSEQ=GCGGTGACTGGCCCTCCGCC;RSEQ=CCGCTGAGCCACTGCGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:4:4,0:245,72:0.0125:2,0:17:1:29:1:0.57843:0:60:8:0.0128:0:1 0/0:359:1:1,0:245,110:0.0028:2,0:39:0:32:0:1:0:60:2:0.0029:0:1 -7 128829172 . G T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.12727;SOR=Inf;LSEQ=GTGACTGGCCCTCCGCCGCC;RSEQ=CTGAGCCACTGCGGCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:267,79:0:2,0:22.1:1:30.6:1:1:0:60:68.2:1:0:0.2 0/1:395:4:1,3:270,120:0.0101:2,2:21:1:27:1:0.09211:6.71435:60:8:0.0103:0:1 -7 128829694 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGATTCAAGGAGGTGTT;RSEQ=AAGACCCTGGGGAAATTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:27.5:1:33:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 128843151 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19836;SOR=Inf;LSEQ=GCAGTGTGGCAAAGGCCTGG;RSEQ=GGACAGGGGTGAAGCTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:197,34:0:2,0:24.9:1:29.5:1:1:0:60:24.667:1:0:0.5 0/1:186:2:1,1:145,38:0.0108:2,2:13:1:29:1:0.37808:3.77952:60:4:0.0112:0:1 -7 128843169 . C T 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00174;SOR=1.69377;LSEQ=GGAGGACAGGGGTGAAGCTG;RSEQ=GTCTGTGGGTCAGAGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:318:159:120,39:117,41:0.5:2,2:22.3:1:29.3:1:0.79698:1.08:60:38.75:0.5016:0:1.1 1/0:283:178:132,46:75,29:0.629:2,2:22.4:1:29.6:1:0.78019:1.11:60:88:0.6286:0:1.1 -7 128843436 . T C 126 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.05735;LSEQ=CCTGAAGGCTGCACGGTGAG;RSEQ=GCTCTGTGAGACAAGGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:1:0,1:127,266:0.0025:2,0:30:0:9:0:1:0:60:0:0:0:6 0/1:357:23:8,15:122,210:0.0644:2,2:21.4:1:27.9:1:1:1.08904:60:6.667:0.0575:0:1.6 -7 128843490 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50452;SOR=0;LSEQ=GGGCAGGACCGGGTATAGGG;RSEQ=AGGGTCCAGTGGGGAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:19,121:0.0141:2,2:7.5:1:27:1:0.26271:6.23:60:4:0.0143:0:1.5 0/0:113:0:0,0:21,92:0:2,0:24.3:1:31.7:1:1:0:60:226:1:0:0.1 -7 128843757 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGGGAGTTAAGGCGCGAGC;RSEQ=TGTGAAACAGCTAGAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:28.5:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 128844857 . A AAAAG 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00132;SOR=Inf;LSEQ=TGTCTAAAAAAAGAAAGAAA;RSEQ=AAAGAAAGAAAGAAGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:12,0:21,0:0.3636:1,0:23.4:1:31.9:1:1:0:60:24:0.3871:0.0606:0 1/1:9:9:8,1:0,0:1:0,2:20.4:1:29.6:1:1:0:59.4:8:1:0.4444:0.4 -7 128844953 . C A 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00124;SOR=Inf;LSEQ=CCTGGAAGTGTATCTCCAGC;RSEQ=ACCCTGCCATGCTACCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:139,5:0:1,0:22.6:1:31.2:1:1:0:60:71:1:0:0.4 0/1:93:7:6,1:82,4:0.0753:1,2:18.1:1:28.9:1:0.32989:3.34656:60:14:0.0769:0:1.1 -7 128845018 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.19788;LSEQ=GTCCCTGAGCTGCCTTGACA;RSEQ=CGTCTTTTCCCATCCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:224:168,56:160,73:0.488:2,2:24:1:30.6:1:0.14608:1.37:60:43.8:0.4867:0:1.1 1/1:477:423:300,123:36,18:0.8868:2,2:25.3:1:29.3:1:0.52863:1.22:60:59.429:0.887:0:1.1 -7 128845223 . C T 192 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACATCGCGGCCTTCGGGGC;RSEQ=GTCACGGGCCTCTGCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:81:27,54:98,250:0.1888:2,2:27.1:1:30.4:1:0.4153:1.27:60:80:0.1891:0:1.4 0/0:379:0:0,0:124,255:0:2,0:23.6:1:29.4:1:1:0:60:74.8:1:0:0.4 -7 128845275 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18799;SOR=Inf;LSEQ=TCAGCCGCGGGAGGGCAGGC;RSEQ=CGGGGGGCCCTCAGCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:52,142:0:2,0:24:1:30.9:1:1:0:60:47.5:1:0:0.9 0/1:149:2:1,1:38,109:0.0134:2,2:10:1:27.5:1:0.45629:2.84:60:4:0.0136:0:1.5 -7 128845277 . G C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=5.88524;LSEQ=AGCCGCGGGAGGGCAGGCCC;RSEQ=GGGGGCCCTCAGCCTGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:99:30,69:26,73:0.4975:2,2:21.8:1:29.7:1:0.63616:1.22:60:32:0.4898:0:1.8 1/1:144:123:33,90:5,15:0.8542:2,2:20.5:1:29.7:1:1:1.10:60:122:0.8531:0:1.5 -7 128845299 . T C 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCCCTCAGCCTGGAACG;RSEQ=GGGAAGAGAGCCAGAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:59,98:0:2,0:23.5:1:29.9:1:1:0:60:38.25:1:0:0.9 0/1:94:12:4,8:25,57:0.1277:2,2:21.7:1:30.1:1:1:1.14:60:24:0.129:0:1 -7 128845325 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=8.32248;LSEQ=GAGAGCCAGAGGGAAGGGGG;RSEQ=CAAAGAGGTCTTGGTGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:78:47,31:47,38:0.4785:2,2:22.5:1:30.3:1:0.53063:1.22:60:156:0.4845:0:1.6 1/1:87:77:35,42:4,6:0.8851:2,2:25:1:29.6:1:1:1.25:60:154:0.8953:0:1.6 -7 128845378 . G A 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00124;SOR=Inf;LSEQ=GGTCATGATCAGAAGGGTCT;RSEQ=GGGCTCAGTTAAGGGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:183,30:0:2,0:24.6:1:32.2:1:1:0:60:212:1:0:0.4 0/1:136:7:7,0:112,17:0.0515:2,0:14.3:1:29.7:1:0.59579:0:60:14:0.0519:0:1.3 -7 128845398 . T C 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25677;SOR=0;LSEQ=GGGGCTCAGTTAAGGGTGTC;RSEQ=GTGTCAGCAGAATAACCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:241,41:0.0105:2,2:25:1:24.3:1:0.38129:2.92358:60:2:0.0071:0:3.7 0/0:231:0:0,0:193,38:0:2,0:20.7:1:30.9:1:1:0:60:76:1:0:0.2 -7 128845702 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.95276;LSEQ=TACCCCAAAGGGAGCAGGTG;RSEQ=GTGTAAAACCGAGATCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:147:85:12,73:8,54:0.5782:2,2:24.2:1:30.1:1:1:1.11:60:84:0.5793:0:1.1 1/1:94:82:11,71:3,9:0.8723:2,2:21.5:1:30:1:0.37907:2.13042:60:164:0.8723:0:1.1 -7 128845907 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.89961;LSEQ=AACCTCCAGACCTCAGCAGC;RSEQ=GAGGGTCTGGGCACAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:92:90,2:81,11:0.5:2,1:20.5:1:31:1:0.01808:6.06:60:45:0.4972:0:1.1 1/1:140:130:116,14:10,0:0.9286:0,2:22:1:30.1:1:0.59814:0:60:129:0.9281:0:1.1 -7 128846207 . G A 152 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=13.46952;LSEQ=GTGGCAATCCTTGCTGTGGC;RSEQ=CAGGTATAGTGACTGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:855:3:2,1:374,478:0.0035:2,2:16.3:1:21.3:1:0.58533:2.55:60:2:0.0024:0:1 0/1:816:37:17,20:346,433:0.0453:2,2:20.5:1:29.3:1:0.86708:1.06:60:74:0.0461:0:1.1 -7 128846223 . G A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCGCAGGTATAGTGACTG;RSEQ=TAGGAACGGGAGACCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:783:0:0,0:348,434:0:2,0:23.1:1:31.5:1:1:0:60:64.167:1:0:0.1 0/1:680:33:18,15:300,347:0.0485:2,2:18.7:1:29.1:1:0.37657:1.39:60:15.5:0.0463:0:1.1 -7 128846328 . G C 316 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.43564;LSEQ=GATGGGGACTCTGTGAGTGG;RSEQ=ATTTGTTTTGTGGGCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1057:498:249,249:290,268:0.4711:2,2:25.7:1:32.1:1:0.53783:1.08201:60:98.6:0.4736:0:1.1 1/1:1186:1010:519,491:90,81:0.8516:2,2:25.6:1:31.7:1:0.80414:1.05114:60:76.692:0.8543:0:1.2 -7 128846444 . G A 53 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38818;SOR=0.30963;LSEQ=CCGAGGTGAGTGAAGACCAG;RSEQ=CCAGGACCAGTTGGGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:4:3,1:88,309:0.01:2,2:7.8:1:26.8:1:0.038:10.45:60:8:0.0102:0:1.3 0/0:322:1:1,0:83,237:0.0031:2,0:1:0:24:0:0.26168:0:60:2:0.0031:0:1 -7 128846469 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=5.31549;LSEQ=GACCAGTTGGGCAACAAAAT;RSEQ=TACTGGGCACTTGCTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:120:16,104:13,110:0.4938:2,2:23.2:1:31.9:1:0.55642:1.30:59.9:59:0.4937:0:1.1 1/1:180:151:25,126:2,27:0.8389:2,2:23.3:1:31.3:1:0.25894:2.67:60:150:0.8427:0:1.1 -7 128846485 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51728;SOR=0;LSEQ=AAATATACTGGGCACTTGCT;RSEQ=CCAGTACTGGGAGCTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:10,163:0.0114:2,2:22:1:26.5:1:0.1221:15.59:60:4:0.0116:0:2 0/0:118:0:0,0:10,108:0:2,0:25:1:32.3:1:1:0:60:58:1:0:0.9 -7 128846557 . C CAG 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03467;SOR=3.90597;LSEQ=GCTCCTATAGGGCCTTCACA;RSEQ=AGTAGAAGGTGACCCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:16:0,16:1,31:0.3333:1,1:17.5:1:31.3:1:1:0:59.4:32:0.3404:0.125:0.6 1/0:15:10:0,10:0,5:0.6667:0,0:31.6:1:31.7:1:1:0:60:20:0.6667:0:0.2 -7 128846679 . GT G 74 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCCAGGGCTCACAGCTT;RSEQ=TTTTTTTGTTTGTTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:0.4545:0,0:36.4:1:32:1:1:0:60:10:0.4545:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 128846716 . A G 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTTTGAGACAGAGTCT;RSEQ=GCTCTGTTGCCCAGGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:18.3:1:32.5:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 128847732 . TC T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACAGAGTGAGACCCTGTC;RSEQ=CAAAGAAAACAAGACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:46.5:1:31.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 128848301 . A AT 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCTCAAAAAAAAAATTAT;RSEQ=TGGATAGCGCTGTTCTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:0.4286:0,0:7.3:1:30.3:1:1:0:60:6:0.4286:0.2857:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 128848756 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18367;SOR=Inf;LSEQ=CAACACTGCACCCTCCTGGG;RSEQ=CTATGCGACCGGCAGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:36,190:0:2,0:23.4:1:31.5:1:1:0:60:31.286:1:0:0.1 0/1:170:2:1,1:27,141:0.0118:2,2:18.5:1:26.5:1:0.3031:5.15:60:4:0.0121:0:1 -7 128849078 . C A 183 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=AGACTCTCTCCTCCCCACTG;RSEQ=TGCTGCGGGACTGGGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:607:70:50,20:352,183:0.1153:2,2:27.4:1:30:1:0.41954:1.30:60:69:0.1168:0:1.1 0/0:606:0:0,0:382,223:0:2,0:23.7:1:31.5:1:1:0:60:150.25:0.9983:0:0.1 -7 128849281 . C A 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90766;LSEQ=GCAGTGCTGGGAGCTGGAGC;RSEQ=AAGGCCATAAAGACACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:4:3,1:97,265:0.0109:2,2:12.8:1:28.3:1:0.06381:8.14:60:8:0.0111:0:1 0/0:303:3:2,1:91,209:0.0099:2,2:17:1:28:1:0.22397:4.57:60:6:0.0104:0:1 -7 128850084 . T G 153 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01786;LSEQ=TGAGCCCAGGAGTTGGAAGC;RSEQ=GCAGTGGGTTGTGATCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:39:39,0:36,0:0.52:1,1:26.4:1:29:1:1:0:60:12:0.5:0:1 0/1:54:1:1,0:53,0:0.0185:1,0:8:0:31:0:1:0:60:2:0.0185:0:1 -7 128850103 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21547;SOR=Inf;LSEQ=CTGCAGTGGGTTGTGATCAC;RSEQ=CCACCGCACTCTAGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:97,4:0:1,0:24.2:1:29.6:1:1:0:60:49.5:1:0:0.5 0/1:88:2:2,0:79,7:0.0227:2,0:20:1:30:1:1:0:60:4:0.0227:0:1 -7 128850108 . C T 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22437;SOR=Inf;LSEQ=GTGGGTTGTGATCACGCCAC;RSEQ=GCACTCTAGCCTGGGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:106,9:0:2,0:23.2:1:30.9:1:1:0:60:114:1:0:0.4 0/1:104:2:1,1:90,12:0.0192:2,2:6:0:32.5:1:0.23544:7.2445:52:4:0.0194:0:5 -7 128850115 . T C 33 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59372;SOR=2.39542;LSEQ=GTGATCACGCCACCGCACTC;RSEQ=AGCCTGGGTGACAGAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:0,1:122,15:0.0072:2,0:8:0:14:0:0.11594:0:60:0:0:0:1 0/1:116:2:1,1:99,15:0.0172:2,2:13:0:33:1:0.25787:6.42262:52:4:0.0172:0:5 -7 128850137 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=Inf;LSEQ=GCCTGGGTGACAGAGCAAGA;RSEQ=CCTATCTCAAAAAAAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:172,44:0:2,0:23.4:1:30.7:1:1:0:60:432:1:0:0.3 0/1:228:3:2,1:172,53:0.0132:2,2:30.3:1:30.7:1:0.55736:1.61879:54.7:6:0.0134:0:3.7 -7 128850167 . A G 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00105;SOR=Inf;LSEQ=AAAAAAGAGAGAGGAAAAGA;RSEQ=AGGAAAGCCTCACCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:276,110:0:2,0:24.1:1:30:1:1:0:60:47.25:1:0:0.2 0/1:428:11:5,6:285,132:0.0257:2,2:20.8:1:29.9:1:0.18685:2.58454:60:10:0.0235:0:1.3 -7 128850377 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44146;SOR=2.10251;LSEQ=CACGCTGCTCATCTGGAGGC;RSEQ=TACCTGGTGCAGGTGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:2:1,1:105,257:0.0055:2,2:3:1:28.5:1:0.49818:2.44:60:4:0.0056:0:1 0/1:348:4:3,1:117,227:0.0115:2,2:19.8:1:30:1:0.12029:5.79:60:8:0.0117:0:1.3 -7 128850744 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=GAATGGCATCGCTGGCCCTT;RSEQ=CCAAGATTTGATGGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:162,25:0.0106:2,2:27.5:1:27:1:0.25684:6.37375:60:4:0.0107:0:1 0/0:174:0:0,0:142,31:0:2,0:21.3:1:30.8:1:1:0:59.9:85.5:1:0:0.1 -7 128850798 . G T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01047;SOR=0;LSEQ=GCTCCTTCCCTATCCCTTCT;RSEQ=CTCTCAGGTTGACTGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:6:3,3:309,184:0.012:2,2:9.5:1:29.3:1:0.67627:1.67745:60:12:0.0123:0:1 0/0:565:0:0,0:343,221:0:2,0:24.2:1:31.8:1:1:0:60:187:1:0:0.2 -7 128850875 . T C 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=ATGATTGCCAAGGCCTTCTC;RSEQ=AAGCGGCACGAGCTCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:0:0,0:314,332:0:2,0:23.9:1:29.3:1:1:0:60:70.778:0.9984:0:0.1 0/1:763:15:7,8:348,398:0.0197:2,2:22.7:1:30.6:1:1:1.00:60:30:0.0198:0:1.1 -7 128850984 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62122;SOR=0.4908;LSEQ=ACCCCTCCTCTACCGGAGCC;RSEQ=CCTGGCCCCGCGCTGCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:39,156:0.0102:2,2:23.5:1:28.5:1:0.36569:3.96:60:4:0.0103:0:1 0/0:200:1:0,1:57,142:0.005:2,0:9:0:32:0:1:0:60:2:0.0051:0:1 -7 128850990 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.49868;SOR=0;LSEQ=CCTCTACCGGAGCCGCCTGG;RSEQ=CCCGCGCTGCCCATGTGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:31,151:0.0109:2,2:38.5:1:30.5:1:0.31837:4.81:60:4:0.0109:0:1 0/0:180:0:0,0:45,134:0:2,0:22.2:1:30.9:1:1:0:60:58.667:0.9944:0:0.1 -7 128851072 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14119;SOR=Inf;LSEQ=ACCGACTGTGAGGAGCAAGG;RSEQ=GCTCCCTCCATCGCTCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:2,47:0:1,0:22.7:1:30.7:1:1:0:60:98:1:0:0.1 0/1:30:2:0,2:1,27:0.0667:1,0:36:1:28:0:1:0:60:4:0.0667:0:1 -7 128851669 . T C 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.33678;SOR=3.57754;LSEQ=GCACAGAGGCTGGGGGCTTC;RSEQ=GGGACTGGAGTACAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:1:0,1:80,214:0.0034:2,0:44:0:9:0:1:0:60:0:0:0:7 0/1:249:3:1,2:77,169:0.012:2,2:32:1:28.3:1:1:1.10:60:6:0.0123:0:1 -7 128851674 . C G 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00147;SOR=0;LSEQ=GAGGCTGGGGGCTTCTGGGA;RSEQ=TGGAGTACAGGGGCTGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:11:5,6:71,201:0.0389:2,2:13.6:1:32.9:1:0.17202:2.35:60:22:0.04:0:1 0/0:229:0:0,0:67,161:0:2,0:23.8:1:30.8:1:1:0:60:24.333:0.9955:0:0.1 -7 128851816 . C T 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02749;SOR=Inf;LSEQ=TCCCAGGGGAGCGGGGGTGG;RSEQ=ATGGACAGAGCCAGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:331,155:0:2,0:24.9:1:31.8:1:1:0:60:43.182:1:0:0.1 0/1:464:5:2,3:300,159:0.0108:2,2:17.2:1:27.2:1:0.34826:2.82338:60:10:0.0111:0:1.2 -7 128851980 . G A 182 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.25135;LSEQ=AGGAAGAAGGAGGTGTGCCC;RSEQ=CTGGCGCCGCCCCCTGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:893:3:2,1:460,425:0.0034:2,2:3:1:28.7:1:1:1.85:60:6:0.0034:0:1.3 0/1:842:78:45,33:396,365:0.0926:2,2:22.1:1:29:1:0.4048:1.26:60:38:0.0919:0:1.6 -7 128852381 . C T 153 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02664;LSEQ=AGCATGCTTCCCTAGGATCC;RSEQ=GTCTTCCAGAGAACCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:34:0,34:2,46:0.4146:1,1:24.3:1:30.1:1:0.50858:0:60:68:0.4198:0:1.1 0/1:55:1:0,1:2,52:0.0182:1,0:40:0:32:0:1:0:60:2:0.0185:0:1 -7 128852511 . G A 48 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26667;SOR=Inf;LSEQ=ACCCCAGGGACAGGGCCCTG;RSEQ=AGCTCAGGGTCCTTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:0.2143:0,0:22.7:1:30.3:1:1:0:60:6:0.2308:0:1.3 1/1:1:1:0,1:0,0:1:0,0:12:0:32:0:1:0:60:2:1:0:1 -7 131819962 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGGCTTTATTTGTAAAAAG;RSEQ=GTGAACAAATAACCTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38:1:30:1:1:0:60:4:1:0:1.5 -7 131820939 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52767;SOR=0;LSEQ=GCGGCACTACCTCTGCCGGG;RSEQ=GAACCTTGCTTCCTTCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:10,13:0.08:2,2:32.5:1:30:1:1:1.29:60:4:0.08:0:1 0/0:14:0:0,0:6,8:0:2,0:24.5:1:30.2:1:1:0:60:28:1:0:0.1 -7 131936098 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15873;SOR=Inf;LSEQ=GCCCCTTCTGAACTGGGACC;RSEQ=GGAACCTACTGTTGTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:24,90:0:2,0:17.2:1:29.9:1:1:0:60:27.5:1:0:0.2 0/1:76:2:1,1:12,62:0.0263:2,2:5:1:29.5:1:0.31474:5.00:60:4:0.0267:0:1 -7 134247635 . T C 29 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=9.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTTCTTTCTTTCTTTCTTTC;RSEQ=TTCTTTCCTTCTTTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 134249263 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17874;SOR=Inf;LSEQ=TGGGCGACATGGCTTCTCCC;RSEQ=TTTCTAGGTCCCATGAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,23:0:2,0:28.7:1:31:1:1:0:59.5:42:1:0:0.1 0/1:32:2:1,1:14,16:0.0625:2,2:26:0:30.5:1:1:1.14:60:4:0.0625:0:1.5 -7 134806700 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=CCCACGCCACCAGGGCCTAG;RSEQ=GTCCCAACCCCAGAGCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:0:2,0:32.6:1:31.6:1:1:0:60:22:1:0:0.1 0/1:17:2:1,1:8,7:0.1176:2,2:12:1:28:1:1:1.13389:60:4:0.1176:0:1 -7 134807084 . T C 32 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTCCTCATTGGGTGGGGCTT;RSEQ=CCTGCAGGAACTTCAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18.5:1:30.5:1:1:0:60:4:0.6667:0:1.5 1/0:3:2:1,1:1,0:0.6667:0,2:2:0:32.5:1:1:0:60:4:0.6667:0:1.5 -7 134807552 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGCAGCAGCCCTATAGAAAA;RSEQ=GGACCTGACCAATGAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:16.3:1:30.5:1:1:0:60:8:1:0:0.8 0/1:6:2:1,1:3,1:0.3333:2,2:14.5:1:29.5:1:1:2.44949:60:4:0.3333:0:1.5 -7 135127927 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCACCATGGCGAAACCC;RSEQ=ATCTCTACCAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:30.5:1:1:0:60:4:1:0:1 -7 135127936 . CAA C 26 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCGAAACCCTATCTCTAC;RSEQ=AAAAAAAAAAAAAAAATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22.5:1:26.9:1:1:0:60:4:1:0.5:1 -7 135128789 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTAGCTACTCAGGAGGCC;RSEQ=AGGTAGGAGGATCACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:34:1:31:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 135129053 . A G 67 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28003;SOR=0;LSEQ=CTGAAAGGACTTGAACAGAT;RSEQ=CTTGTGCACCAGTGTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:14,2:0.2:2,0:29.5:1:33.8:1:1:0:60:8:0.2:0:1 0/0:9:0:0,0:9,0:0:0,0:29:1:28.7:1:1:0:60:18:1:0:0 -7 135129250 . G A 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.73746;LSEQ=TTGCAGTGCCCAAGGAGGTC;RSEQ=AGCTCTGTTGCTGTGAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:1:1,0:281,206:0.002:2,0:1:0:25:0:1:0:60:2:0.0021:0:1 0/1:556:33:18,15:302,220:0.0594:2,2:19.9:1:29.7:1:0.71981:1.14366:60:66:0.0601:0:1.2 -7 135129443 . G A 185 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=68.72441;LSEQ=TTGCTCCTGGGTCTGCTTCC;RSEQ=GCTGCTTGTTTGAATCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:897:1:1,0:478,417:0.0011:2,0:1:0:26:0:1:0:60:2:0.0011:0:1 0/1:1108:79:42,37:527,502:0.0713:2,2:24.1:1:29.5:1:0.8155:1.08:60:38.5:0.0703:0:1.2 -7 135129586 . T C 181 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTGCCAAGGCAGGGCTTT;RSEQ=GGCACTTTCAGCTTTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:0:0,0:190,385:0:2,0:24.5:1:30:1:1:0:45.4:114:1:0:0.1 0/1:631:72:27,45:202,357:0.1141:2,2:26:1:29.4:1:0.89648:1.06:44.5:71:0.1141:0:1.1 -7 135129641 . G A 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50426;SOR=0;LSEQ=TATTTCAACTATCACGATGT;RSEQ=GGCATCTGCAAAGCTGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:0,2:5,179:0.0108:1,0:28:1:33:0:1:0:33:4:0.0109:0:1 0/0:150:0:0,0:4,146:0:1,0:23.8:1:30.5:1:1:0:39.9:300:1:0:0.2 -7 135129731 . C CT 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.96202;LSEQ=TGTAAGCCTCTTTGCCTCTG;RSEQ=TTGTCATGCCATTAAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:52:4,48:0,5:0.9123:0,2:24.1:1:30.2:1:1:0:43.1:25:0.9091:0.1404:0.1 1/1:22:20:1,19:0,2:0.9091:0,1:22.5:1:30.5:1:1:0:45.5:40:0.9091:0.1818:0.2 -7 135129961 . A G 42 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGCTAAACATGATATATG;RSEQ=GCTTTTGCCTTTTAATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:0.6:0,0:19.3:1:27:1:1:0:31.7:2:0.5:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 135335678 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20753;LSEQ=CCTCTATCCCTCCGCCTCCC;RSEQ=GACTACTGCTGCTGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:16,1:0.1053:1,0:16.5:1:31.5:1:1:0:60:4:0.1053:0:1 0/1:16:2:1,1:14,0:0.125:1,2:19:0:31.5:1:0.125:0:60:4:0.125:0:1 -7 135335767 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22687;SOR=Inf;LSEQ=GAGAGTGACAAGCAACAACA;RSEQ=AGATTTCAATCTGCGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:81,24:0:2,0:24.2:1:31.8:1:1:0:60:104:1:0:0.2 0/1:96:2:1,1:61,33:0.0208:2,2:35:1:29:1:1:1.83604:60:4:0.0211:0:1.5 -7 135335822 . C T 157 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10655;LSEQ=ATAATGCACTGGAATGAAAT;RSEQ=GTAGGGACCACATCAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:40:22,18:80,65:0.2162:2,2:30.2:1:29.6:1:1:1.00696:60:39:0.2155:0:1.2 0/1:176:5:2,3:89,82:0.0284:2,2:20:1:28.8:1:0.67364:1.62357:60:10:0.0289:0:1.2 -7 135335825 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49971;SOR=0;LSEQ=ATGCACTGGAATGAAATCGT;RSEQ=GGGACCACATCAAAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:105,86:0.0104:2,2:10:0:33:0:1:1.21966:60:4:0.0107:0:1.5 0/0:176:0:0,0:91,85:0:2,0:26.7:1:29.2:1:1:0:60:57.667:1:0:0.2 -7 135335842 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21778;SOR=Inf;LSEQ=CGTAGGGACCACATCAAAGG;RSEQ=AGCCTCCAGTTTGTGGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:95,93:0:2,0:26.6:1:31.7:1:1:0:60:46:1:0:0.4 0/1:165:2:1,1:83,80:0.0121:2,2:42:1:29.5:1:1:1.03728:60:4:0.0123:0:1 -7 135335861 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=GCAGCCTCCAGTTTGTGGGA;RSEQ=GCAGTCCCAACACTCCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:81,87:0.0118:2,2:37:1:30.5:1:1:1.07:60:4:0.0119:0:1 0/0:157:0:0,0:86,71:0:2,0:24.2:1:30.3:1:1:0:60:77.5:1:0:0.3 -7 135335862 . G A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00209;SOR=Inf;LSEQ=CAGCCTCCAGTTTGTGGGAC;RSEQ=CAGTCCCAACACTCCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:86,89:0:2,0:24.6:1:30.5:1:1:0:60:86.5:1:0:0.3 0/1:154:8:4,4:79,67:0.0519:2,2:37:1:29.5:1:1:1.17784:60:16:0.0533:0:1.1 -7 135335900 . T G 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00023;SOR=Inf;LSEQ=GGAGAGAAGGCCATAGAGTA;RSEQ=ATCCAGCATATGCGAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:83,93:0:2,0:22.8:1:29.4:1:1:0:60:28.333:1:0:0.1 0/1:159:11:6,5:81,67:0.0692:2,2:27.3:1:31.2:1:1:1.00742:60:22:0.0705:0:1.1 -7 135335907 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23224;SOR=Inf;LSEQ=AGGCCATAGAGTATATCCAG;RSEQ=ATATGCGAAGGGAAAAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:90,89:0:2,0:24.1:1:32.4:1:1:0:60:88.5:1:0:0.1 0/1:167:2:1,1:95,70:0.012:2,2:28.5:1:28:1:1:1.35461:60:4:0.0123:0:1 -7 135335913 . C T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49873;SOR=0;LSEQ=TAGAGTATATCCAGCATATG;RSEQ=GAAGGGAAAAACCACACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:93,85:0.0111:2,2:7.5:1:25.5:1:1:1.09357:60:4:0.0112:0:1.5 0/0:174:0:0,0:104,70:0:2,0:23.6:1:30.3:1:1:0:60:57:1:0:0.2 -7 135336211 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.60233;SOR=2.26017;LSEQ=TAAACACTGTCTCCATCATC;RSEQ=TCCTTTCCGTTTCCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:18,57:0.0132:2,0:1:0:28:0:0.25:0:60:2:0.0132:0:1 0/1:68:2:1,1:15,51:0.0294:2,2:6.5:1:28.5:1:0.41791:3.32:60:4:0.0308:0:1 -7 135336264 . T G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25996;SOR=0.31033;LSEQ=CTATTTTTCTCTTTCTCCCT;RSEQ=AAAAATTGTTTTTTAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:0,7:0,18:0.28:1,0:21.9:1:32.4:1:1:0:60:14:0.2917:0:1 0/1:19:2:0,2:1,16:0.1053:1,0:18:1:30:1:1:0:60:4:0.1111:0:2.5 -7 135336556 . G GCCTGGGCAACAGAGCAAGAGTCTGT 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGCACCACTGCACTCCA;RSEQ=CCCCCTCCCTACCCCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:31:1:31.2:1:1:0:60:4:1:1:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 135681518 . T C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.62445;LSEQ=AAATCGTAAGATTGTTCTTA;RSEQ=GAGAAAATGTGATATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:31:19,12:65,87:0.1694:2,2:22.7:1:31:1:0.07516:2.11:60:62:0.1722:0:1.1 0/1:209:89:44,45:63,56:0.4258:2,2:26.8:1:30.2:1:0.67472:1.14979:60:178:0.4279:0:1.1 -7 135681586 . T A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24684;SOR=Inf;LSEQ=GGCACTGTATAGTAAAAATT;RSEQ=GGAACCACATATATGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:31,88:0:2,0:24:1:30.4:1:1:0:60:238:1:0:0.2 0/1:119:3:2,1:29,87:0.0252:2,2:15.7:1:26.7:1:0.16586:5.89:60:6:0.0254:0:1.7 -7 135878184 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATTGGAGTGATGCGTCT;RSEQ=CAAGCCAAGGGACACCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:0.1538:2,2:33.5:1:31:1:1:1.67325:60:4:0.1538:0:1 0/0:2:0:0,0:2,0:0:0,0:27.5:1:28.5:1:1:0:60:4:1:0:0 -7 136219193 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00162;SOR=0.12294;LSEQ=AAGTGCTTCGTTAAATGGGT;RSEQ=CTGCTCCCCGTGCCAACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:9,6:10,6:0.4839:2,2:24.9:1:30.1:1:1:1.10734:60:30:0.4839:0:1.3 0/1:30:3:2,1:14,13:0.1:2,2:31:1:31.7:1:1:1.82:60:6:0.1:0:1.3 -7 136219237 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=GGTGAGAACCTCCAACAGTG;RSEQ=CTGTCAGACAGCCTAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:28.5:1:29:1:1:1:60:4:0.1:0:1 0/0:20:0:0,0:8,12:0:2,0:16.5:1:31.2:1:1:0:60:19:1:0:0.3 -7 136220339 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAGGAGCAACGCCAAGAC;RSEQ=CATAATCATCAGATTTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 136299225 . CTTG C 32 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.25519;SOR=0.23633;LSEQ=GATGGGGGTTTTGTGGGGGC;RSEQ=TTGTTGTTGTTGTTGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:0.1053:2,2:40:1:32:1:1:1.11803:60:4:0.1053:0:0.5 0/1:38:1:1,0:18,18:0.0263:2,0:42:0:31:0:1:0:60:2:0.0286:0:1 -7 136299244 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.14154;SOR=0;LSEQ=CCTTGTTGTTGTTGTTGTTG;RSEQ=TGATGCTGTTGTTATCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:34:1:29:1:1:1:60:4:0.1111:0:1 0/0:29:0:0,0:15,14:0:2,0:22.1:1:29.7:1:1:0:60:58:1:0:0.6 -7 136299286 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04103;SOR=Inf;LSEQ=CTTTGTTTTTCTTTCAAACA;RSEQ=TCAGTCCCTCTTCTGTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:4,3:1,2:0.7:2,2:21.9:1:31.3:1:1:2.41:60:14:0.7:0:1 1/1:17:17:7,10:0,0:1:0,2:22.5:1:29.8:1:1:0:60:34:1:0:1.2 -7 136299366 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5328;SOR=Inf;LSEQ=ATCTGATTCGCTCCCATGCC;RSEQ=GGAAATGTCATTCAAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:0:2,0:33.9:1:31.2:1:1:0:60:34:1:0:0.1 0/1:31:2:1,1:12,17:0.0645:2,2:46:0:31:1:1:1.40:60:4:0.0645:0:1.5 -7 136299405 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52962;SOR=Inf;LSEQ=GGCTGGAGAGCAGCAAAAAT;RSEQ=GGTGCCTGCTCCTTCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:12.3:1:30.5:1:1:0:60:30:1:0:0.1 0/1:27:2:1,1:11,14:0.0741:2,2:13:0:32:0:1:1.26:60:4:0.0741:0:1 -7 136299515 . A G 83 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTTGGAGATTCTCACCC;RSEQ=GTTGGGTGGCATGGGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:39.5:1:31:1:1:0:60:4:1:0:1 1/1:7:7:2,5:0,0:1:0,2:28.7:1:29.9:1:1:0:60:14:1:0:1.3 -7 138883381 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTACGTGATAGGAACTCCC;RSEQ=GAATCTTACAGATTCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:11:0:15:0:1:0:60:0:0:0:1 1/1:2:2:2,0:0,0:1:0,0:9.5:1:30:1:1:0:60:4:1:0:1 -7 138883596 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23331;SOR=Inf;LSEQ=ATTACACAATCAGTTATATA;RSEQ=GGGATACACGTGGCCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:47,52:0:2,0:23:1:30:1:1:0:59.8:98:1:0:0.1 0/1:93:2:1,1:38,53:0.0215:2,2:13.5:1:29:1:1:1.39:60:4:0.0215:0:1.5 -7 138883637 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49553;SOR=Inf;LSEQ=ACAGTCCGTCATTGACTGCA;RSEQ=TAAGTCTGGTTTGGCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:11,39:0:2,0:26.1:1:32.6:1:1:0:60:100:1:0:0.1 0/1:53:2:1,1:15,36:0.0377:2,2:25:1:28.5:1:0.51669:2.36:60:4:0.0377:0:1 -7 139210235 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=TGCGTCACCAAGGAGAAGAG;RSEQ=TGTAGCAGAGCTGTGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:10,2:0:2,0:21.1:1:31.3:1:1:0:60:24:1:0:0 0/1:13:2:1,1:10,1:0.1538:2,2:9:1:27.5:1:0.29487:7.41607:60:4:0.1667:0:1.5 -7 139210321 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50918;SOR=Inf;LSEQ=TGACGCTGTCTCCGGCTTTA;RSEQ=TGTTGGAGTGGCCCTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:0:2,0:26.1:1:31.9:1:1:0:60:66:1:0:0.1 0/1:47:2:1,1:21,24:0.0426:2,2:37:1:29:1:1:1.14:60:4:0.0426:0:1 -7 139337849 . CT C 31 d7;v4;MAF0.05;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCCGAGATCACGCCACTG;RSEQ=ACTCCAGCCTGGGTGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:17:0:31.5:1:1:0:40:4:0.6667:0:1 1/1:1:1:1,0:0,0:1:0,0:46:0:32:0:1:0:54:2:1:0:0 -7 139338077 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49908;SOR=0;LSEQ=CTTTGATTTCTTCAGAGAGC;RSEQ=ACTACAGACAAAGAGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:118,67:0.0107:2,2:7.5:1:30.5:1:1:1.7555:60:4:0.0109:0:1.5 0/0:176:0:0,0:121,55:0:2,0:22:1:30.1:1:1:0:60:352:1:0:0.6 -7 139338133 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.79711;LSEQ=GTAACTGGAAAATGCAGTGC;RSEQ=GAGGACTATCAACTGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:170:88,82:67,75:0.5449:2,2:27.5:1:29.9:1:0.42866:1.20:60:33:0.5464:0:1.1 1/1:350:287:140,147:32,31:0.82:2,2:29.4:1:29.8:1:0.78265:1.08361:60:286:0.8195:0:1.1 -7 139338197 . CT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50118;SOR=0;LSEQ=TCTTATGGGACAAATCACAC;RSEQ=CCCACACCGCCATCTCGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:69,124:0.0103:2,2:17:1:30.6:1:1:1.79:60:4:0.0105:0.0051:0.5 0/0:169:0:0,0:54,115:0:2,0:23.1:1:29.3:1:1:0:60:83.5:1:0:0.6 -7 139338235 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50456;SOR=0;LSEQ=GTATGGTAAAACTCTGACCC;RSEQ=TGGACCTCGGGAAGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:11,78:0.022:2,2:28.5:1:32:0:0.24762:6.83:60:4:0.0233:0:1.5 0/0:71:0:0,0:13,57:0:2,0:23.6:1:30.2:1:1:0:60:140:1:0:0.4 -7 139338270 . C G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00312;SOR=12.79783;LSEQ=GAGGCCTCTGCCTCCTGTTA;RSEQ=AGACATGCCATTGAGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:32:0,32:0,15:0.6809:1,1:23:1:31.5:1:1:0:60:64:0.6809:0:1 1/1:29:28:2,26:0,1:0.9655:0,2:20.5:1:31.1:1:1:0:60:56:0.9655:0:1 -7 139435814 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2297;SOR=0;LSEQ=GGGTCTGGAAAGGCTGGAGT;RSEQ=AGCGTGGCAGGTCTTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:77,66:0.0138:2,2:12.5:1:29:0:1:1.16542:60:4:0.0139:0:1.5 0/0:157:0:0,0:80,77:0:2,0:24.5:1:31.1:1:1:0:60:156:1:0:0.2 -7 140111486 . A T 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=AGATGGTCGTTCCCCAACCA;RSEQ=GGAGGATATCCAAGTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:0.4286:2,0:30.3:1:32.3:1:1:0:60:6:0.4286:0:2 1/0:4:2:2,0:2,0:0.5:0,0:20:1:31:1:1:0:60:4:0.5:0:2 -7 140111509 . G C 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34694;SOR=0.32347;LSEQ=AGGATATCCAAGTCATCCAG;RSEQ=GAGCAACTGAAAGAATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:29.2:1:33.2:1:1:0:60:10:0.625:0:1.6 0/1:9:3:3,0:6,0:0.3333:0,0:17:1:33.7:1:1:0:60:6:0.3333:0:1.7 -7 140111635 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20687;SOR=Inf;LSEQ=GGAGTTCCCATTACCTGTGG;RSEQ=AACCCCTGATTTGGACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:138,34:0:2,0:21.8:1:31.1:1:1:0:60:85:1:0:0.1 0/1:144:2:1,1:105,37:0.0139:2,2:11:1:29.5:1:0.4595:2.81355:60:4:0.0139:0:1 -7 140434294 . TA T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14175;SOR=0;LSEQ=AAGTGTTCTTTGGTTCACCT;RSEQ=AAAAAAAAGAGAGTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:4:4,0:100,1:0.0381:1,0:19.8:1:30.3:1:1:0:60:8:0.0392:0:0 0/0:75:0:0,0:75,0:0:1,0:24.4:1:28.5:1:1:0:60:150:1:0:0.2 -7 140434572 . T TA 54 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0504;SOR=7.35818;LSEQ=GCTCAATAGAGGCGAGAATC;RSEQ=ACAAAAAAAAAAAGAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:0,1:55,194:0.0039:2,0:27:0:12:0:1:0:60:0:0:0:2 0/1:214:6:1,5:53,151:0.028:2,2:40.7:1:21.1:1:1:1.75096:55.8:2:0.0253:0.0047:3.8 -7 140434574 . CA C 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.50834;SOR=0.71339;LSEQ=TCAATAGAGGCGAGAATCTA;RSEQ=AAAAAAAAAAGAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:13:3,10:44,189:0.0526:2,2:23.2:1:32.2:1:0.71811:1.29:59.9:26:0.0537:0:0.8 0/1:210:8:2,6:47,153:0.0381:2,2:22:1:30.9:1:1:1.08:60:16:0.0388:0:1.1 -7 140434580 . A ATTTT 28 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.21231;SOR=Inf;LSEQ=GAGGCGAGAATCTACAAAAA;RSEQ=AAAAAGAAAAAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:31,158:0:2,0:18.2:1:30.4:1:1:0:56.7:378:1:0:1.4 0/1:162:2:1,1:35,125:0.0123:2,2:27:1:28.9:1:0.39614:3.54:50:4:0.0125:0:5 -7 140434586 . G GA 66 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.73763;SOR=1.46555;LSEQ=AGAATCTACAAAAAAAAAAA;RSEQ=AAAAAAAAAAGAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:4:0,4:19,106:0.0241:2,0:24:1:30.8:1:1:0:55:8:0.0449:0:2 0/1:143:5:0,5:22,80:0.035:2,0:14.2:1:28.5:1:0.58098:0:48.8:10:0.0538:0.007:1.8 -7 140434587 . AAAAAAAAAAG A 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.41652;SOR=2.42905;LSEQ=GAATCTACAAAAAAAAAAAG;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:0,2:20,142:0.0122:2,0:6.6:1:26.2:1:1:0:60:8:4e-04:0.0107:0 0/1:137:4:0,4:25,107:0.0292:2,0:21:1:28:1:1:0:50:8:0.0301:0.0146:3 -7 140434596 . AG GA 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50118;SOR=0;LSEQ=AAAAAAAAAAGAAAAAAAAA;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:0,2:13,108:0.0159:2,0:16:1:28.3:1:1:0:50:4:0.0171:0:1.5 0/0:107:0:0,0:16,81:0:2,0:19.7:1:28.6:1:1:0:55.8:11.125:0.957:0:2.1 -7 140434597 . G GA 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.59539;SOR=0.85771;LSEQ=AAAAAAAAAGAAAAAAAAAA;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:56:2,54:4,40:0.4375:2,1:25.9:1:30.1:1:0.40055:2.6734:55.3:112:0.4956:0.0156:2.2 0/1:105:42:1,41:6,29:0.4:2,1:25.9:1:29.8:1:0.04236:8.27475:56:84:0.4828:0:1.8 -7 140434604 . A G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00978;SOR=Inf;LSEQ=AAGAAAAAAAAAAGAAAAAA;RSEQ=AAGAAAAAAGAAAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:6,98:0:2,0:20:1:30.2:1:1:0:54:51:1:0:2 0/1:92:6:2,4:10,76:0.0652:2,2:25.2:1:24.5:1:0.17402:3.72:58.7:2:0.0471:0:2.7 -7 140434607 . G A 58 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.05896;SOR=0;LSEQ=AAAAAAAAAAGAAAAAAAAA;RSEQ=AAAAAAGAAAAAAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:5:3,2:1,81:0.0575:1,2:12.8:1:25.4:1:0.00037:92.94:60:4:0.0506:0:2.8 0/0:85:0:0,0:1,75:0:1,0:22.8:1:29.3:1:1:0:55:8.5:1:0:2.2 -7 140434614 . G GA 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.24522;SOR=0;LSEQ=AAAGAAAAAAAAAGAAAAAA;RSEQ=AAAAAAAAAGAAAGAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:3:0,3:2,71:0.038:1,0:25:1:29.5:1:1:0:53.3:6:0.0423:0.0127:1 0/0:78:0:0,0:3,71:0:1,0:23.1:1:29.8:1:1:0:55.1:13.8:0.9857:0:2.1 -7 140434620 . A AAAAG 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.29715;SOR=0.54614;LSEQ=AAAAAAAGAAAAAAGAAAAA;RSEQ=AAAGAAAGAAAGAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:10:0,10:3,53:0.1471:2,0:33.5:1:31:1:1:0:56:20:0.1471:0:1.7 0/1:70:6:0,6:3,58:0.0857:1,0:27.7:1:28.8:1:1:0:60:12:0.0909:0.0143:0.8 -7 140439319 . TG T 75 MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAAACAAAAGCTCTTTG;RSEQ=GGGGGGGGGGTCTTCGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:23.4:1:32.7:1:1:0:60:10:0.7143:0.1429:0.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 140439756 . G GA 154 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=8.63374;LSEQ=ATAAAAATTATCTGGAGAGA;RSEQ=AAAAAAAAGGGAAATAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:5:4,1:140,319:0.0108:2,2:11.8:1:26.8:1:0.03408:9.07:60:10:0.0109:0.0065:0.6 0/1:418:36:9,27:134,246:0.0861:2,2:28.3:1:29.9:1:0.27144:1.63235:60:72:0.0867:0.0072:0.3 -7 140449071 . C G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26899;LSEQ=CGGTAAAATAAACACCAAGA;RSEQ=GTGGTAAATATTTACCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:709:221:134,87:286,199:0.3117:2,2:25:1:31.4:1:0.74096:1.07:60:54.25:0.3096:0:1.4 0/1:765:83:48,35:400,280:0.1085:2,2:25:1:30.9:1:0.90618:1.04164:60:166:0.1094:0:1.4 -7 140449150 . T C 239 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27465;LSEQ=ATCAATTCATACAGAACAAT;RSEQ=CCAAATGCATATACATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:752:228:107,121:226,297:0.3032:2,2:25.8:1:30.6:1:0.37967:1.16:54.6:44.6:0.3014:0:1.3 0/1:750:80:36,44:287,380:0.1067:2,2:23.9:1:31.1:1:0.81139:1.08:55.3:160:0.1078:0:1.4 -7 140453009 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50194;SOR=0;LSEQ=GTTGAGACCTTCAATGACTT;RSEQ=CTAGTAACTCAGCAGCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:166,32:0.01:2,2:19:1:32:1:0.30347:5.12379:60:4:0.0103:0:1 0/0:170:0:0,0:131,39:0:2,0:23.3:1:29:1:1:0:60:23.286:1:0:0.1 -7 140453136 . A T 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCACTCCATCGAGATTTC;RSEQ=CTGTAGCTAGACCAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:537:78:42,36:211,248:0.1453:2,2:26.2:1:30.5:1:0.22052:1.37:59.8:77:0.1442:0:1.1 0/0:640:0:0,0:303,337:0:2,0:25.8:1:29.5:1:1:0:60:63:1:0:0.1 -7 140453896 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49819;SOR=Inf;LSEQ=ACAGTATATCGAACTTAGCA;RSEQ=GAAAACTGTTTTTACATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:115,23:0:2,0:21.1:1:30.7:1:1:0:60:137:1:0:0.1 0/1:139:2:1,1:113,24:0.0144:2,2:14:1:28:1:0.32843:4.6336:60:4:0.0145:0:1 -7 140476936 . G A 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00076;SOR=Inf;LSEQ=TTAAATGTCGACAAACTTTA;RSEQ=CAATTCTTACAAAAGAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:31,195:0:2,0:27.6:1:31.8:1:1:0:60:36.667:1:0:0.1 0/1:189:9:3,6:33,147:0.0476:2,2:24.9:1:30.9:1:0.3761:2.22:60:18:0.0484:0:1 -7 140476958 . A G 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.57544;SOR=2.75081;LSEQ=AATTCTTACAAAAGAGAACC;RSEQ=AAGTAGTCTGTCGGTAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:0,1:8,148:0.0064:2,0:26:0:15:0:1:0:60:0:0:0:1 0/1:115:2:1,1:15,98:0.0174:2,2:16.5:1:26.5:1:0.25995:6.36:60:4:0.0183:0:2 -7 140476993 . CT C 74 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.86964;LSEQ=TAAAATGTTGTCAGAAAAAG;RSEQ=TTTTTTTTTTTAAAAAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:0,5:0,55:0.0833:1,0:34.4:1:32:1:1:0:60:10:0.0877:0:0 0/1:41:3:0,3:2,36:0.0732:2,0:29.3:1:32.3:1:1:0:60:6:0.0732:0:1 -7 140477006 . A T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.00932;SOR=Inf;LSEQ=GAAAAAGCTTTTTTTTTTTT;RSEQ=AAAAAGGCAACAAAAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:0,51:0:1,0:21.9:1:29.6:1:1:0:60:50:1:0:0.3 0/1:35:5:0,5:1,28:0.1429:1,0:12.2:1:26.4:1:1:0:60:4:0.1176:0:1.4 -7 140477727 . T C 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=AAGCTAATAGTTGCTACCAC;RSEQ=GGGAACCAGGAGCTAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:235,44:0:2,0:24.4:1:30.9:1:1:0:60:68.75:1:0:0.1 0/1:223:10:8,2:167,46:0.0448:2,2:20.9:1:30.2:1:1:1.10:60:20:0.0455:0:1 -7 140477756 . C G 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGAGCTAATAAAAATAACTT;RSEQ=TTTCTCTGGAAAAGAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:0:0,0:341,129:0:2,0:23.6:1:31.3:1:1:0:60:57.75:1:0:0.1 0/1:460:17:12,5:297,146:0.037:2,2:22.9:1:31.6:1:1:1.18:60:34:0.0371:0:1.2 -7 140481964 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18111;SOR=Inf;LSEQ=GTGAGAACATGTGGTGTTTG;RSEQ=TTTTCTGTCCTTGTGATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:143,20:0:2,0:22.1:1:31.1:1:1:0:59.7:31.6:0.9937:0:0.1 0/1:122:2:1,1:104,16:0.0164:2,2:15.5:1:28.5:1:0.26026:6.33618:60:4:0.0165:0:1 -7 140481972 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2071;SOR=Inf;LSEQ=ATGTGGTGTTTGGTTTTCTG;RSEQ=CCTTGTGATACTTTGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:160,25:0:2,0:23.3:1:30:1:1:0:59.8:60.667:1:0:0.1 0/1:155:2:1,1:129,24:0.0129:2,2:19:0:33.5:1:0.29744:5.28689:60:4:0.013:0:1 -7 140482427 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07306;LSEQ=GAATGTGCAGGTTTGTTACA;RSEQ=ACGTATACATGTGCCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:171:85,86:171,198:0.3167:2,2:26.5:1:32.2:1:0.51679:1.14:59.9:342:0.3184:0:1.1 0/1:459:15:4,11:193,251:0.0327:2,2:24.1:1:30.9:1:0.28923:2.11134:57.9:30:0.0328:0:1.1 -7 140482430 . G A 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00891;SOR=Inf;LSEQ=TGTGCAGGTTTGTTACATAC;RSEQ=TATACATGTGCCATGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:0:0,0:272,279:0:2,0:26.4:1:31.2:1:1:0:59.9:136.75:0.9982:0:0.4 0/1:464:6:3,3:203,253:0.0129:2,2:9.2:1:31.2:1:1:1.25:60:12:0.013:0:1.3 -7 140482612 . G A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04859;SOR=Inf;LSEQ=ACTGTTACTCTTCCAAAACT;RSEQ=CCTTTTACTAAATTATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:174,274:0:2,0:24.1:1:32:1:1:0:60:48.778:1:0:0.1 0/1:398:4:3,1:168,226:0.0101:2,2:12.5:1:26.8:1:0.3185:4.02:60:8:0.0101:0:1.3 -7 140483224 . G T 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTACTGGTGCAAAATCTAG;RSEQ=AGAAAAACAATCTCTCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:727:0:0,0:330,397:0:2,0:26.7:1:31.2:1:1:0:60:120.167:1:0:0.1 0/1:754:43:17,26:347,364:0.057:2,2:24.6:1:28.8:1:0.27269:1.45726:60:42:0.0563:0:1.1 -7 140483231 . A T 168 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.28897;LSEQ=GTGCAAAATCTAGGAGAAAA;RSEQ=CAATCTCTCTAAAACAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:733:2:1,1:327,404:0.0027:2,2:1:0:23:1:1:1.24:60:1:0.0014:0:1.5 0/1:757:58:29,29:326,371:0.0766:2,2:26:1:28.8:1:0.68228:1.14:60:18.333:0.0734:0:1.2 -7 140483386 . T TA 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.79661;SOR=1.24863;LSEQ=CCTCAACAGCCAATCAATAT;RSEQ=AAAAAAAAGGAAATCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:7:4,3:355,291:0.0107:2,2:31:1:29.6:1:1:1.09:60:14:0.0108:0:1 0/1:601:8:5,3:315,277:0.0133:2,2:18:1:29.4:1:0.72963:1.46:60:16:0.0135:0.005:0.8 -7 140483400 . T C 241 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.35972;LSEQ=CAATATTAAAAAAAAGGAAA;RSEQ=CCCCAGATGGAAACATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:185:107,78:248,226:0.2807:2,2:28.1:1:32:1:0.22363:1.25:60:184:0.2853:0:2.1 0/1:634:78:42,36:296,257:0.123:2,2:26.6:1:30.5:1:1:1.01:60:38:0.1248:0:1.2 -7 140483403 . C T 232 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0.00391;LSEQ=TATTAAAAAAAAGGAAATCC;RSEQ=CAGATGGAAACATTTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:192:111,81:253,230:0.2844:2,2:26.7:1:30.6:1:0.23084:1.25:60:63:0.2868:0:2.1 0/0:646:1:0,1:337,307:0.0015:2,0:1:0:26:0:0.47752:0:60:2:0.0016:0:1 -7 140483605 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.09489;LSEQ=AAAGTTAATGTAAATAAAGC;RSEQ=GGGCATATTTCTCAAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:157:72,85:187,216:0.2804:2,2:24.6:1:30.4:1:0.92507:1.02202:60:38.25:0.2777:0:1.1 0/1:534:19:8,11:242,271:0.0356:2,2:24.4:1:30.3:1:0.81589:1.22739:60:38:0.0359:0:1.1 -7 140484450 . CT C 144 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11023;SOR=1.7337;LSEQ=GACATCTGTCCCAATTTTTA;RSEQ=TTTTTTTTTTTGAGATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:16:2,14:86,221:0.0483:2,2:31.9:1:31.3:1:0.25158:2.71735:60:32:0.0521:0.003:0.1 0/1:321:26:6,20:85,205:0.081:2,2:21.8:1:30.7:1:0.65241:1.3808:60:52:0.0861:0.0125:0.2 -7 140484483 . CA TG 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21661;SOR=Inf;LSEQ=GAGATGGAGTCTTGCTCTGT;RSEQ=CCCAGGCTGGAGTACAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:27,116:0:2,0:23.4:1:30.7:1:1:0:59:13.3:1:0:0.6 0/1:125:2:1,1:14,109:0.016:2,2:8:1:28.3:1:0.22645:7.56:60:4:0.0164:0.008:0.5 -7 140484528 . T A 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53006;SOR=0;LSEQ=GATCTCGGCTCACTGCAACC;RSEQ=CCGCCTCCTGGGTTCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:0,2:8,69:0.025:2,0:11:1:24:0:1:0:60:4:0.026:0:2.5 0/0:47:0:0,0:0,47:0:1,0:22.4:1:28.1:1:1:0:59.4:14.667:1:0:0.3 -7 140484637 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09208;SOR=Inf;LSEQ=TTTGTATTTTTGTAGAGACG;RSEQ=GGTTTCACCACATTGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:58,9:0:2,0:21.7:1:31.5:1:1:0:59.9:66:1:0:0.1 0/1:57:3:3,0:50,4:0.0526:2,0:13:1:31.3:1:1:0:53.3:6:0.0526:0:3 -7 140485297 . C T 162 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=54.17925;LSEQ=TAAAAATTTATGACAGACAG;RSEQ=ATACAGAAAGCTTGTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:1:0,1:284,252:0.0019:2,0:1:0:24:0:0.47114:0:60:2:0.0019:0:2 0/1:587:54:31,23:264,269:0.092:2,2:24.2:1:28.2:1:0.31786:1.37:60:53:0.0915:0:1.8 -7 140485335 . T C 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41375;LSEQ=CAGTGAGTACGTGTGAGACG;RSEQ=ACATTCAAAGCATTCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:220:124,96:221,209:0.3369:2,2:24.8:1:32:1:0.24542:1.22:60:72.333:0.3385:0:1.1 0/1:720:125:70,55:308,287:0.1736:2,2:24.3:1:31.6:1:0.43088:1.19:60:124:0.1744:0:1.4 -7 140485690 . C T 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.48381;LSEQ=AAGAAGTCATGGGGAATAAA;RSEQ=AAGATGAATTGAAGCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:871:247:117,130:283,341:0.2836:2,2:25.4:1:29.3:1:0.59829:1.08:60:246:0.286:0:1.1 0/1:890:143:66,77:346,401:0.1607:2,2:25.3:1:28.6:1:1:1.00664:60:142:0.1606:0:1.2 -7 140485985 . G GA 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.13002;SOR=0.57642;LSEQ=GTTCATGAAATAACAAACAG;RSEQ=AAAAAAAAAGCTTGTGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:860:23:10,13:411,426:0.0267:2,2:26.2:1:29.7:1:0.67505:1.25389:59.3:22:0.026:0.0058:0.6 0/1:834:13:7,6:387,426:0.0156:2,2:23.4:1:28.9:1:0.78196:1.28:60:12:0.0146:0.0048:0.1 -7 140486118 . C T 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGTTTATAACAATGTTTA;RSEQ=TCAATGTAAAATATTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:707:0:0,0:343,362:0:2,0:24.5:1:32:1:1:0:60:63.091:0.9971:0:0.1 0/1:691:51:24,27:317,321:0.0738:2,2:27.1:1:29.4:1:0.77195:1.11081:60:50:0.0737:0:1.1 -7 140486288 . C T 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34676;LSEQ=CCTGGAAGAACACTTCAAGA;RSEQ=AGTCTCAAATATCACCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:196:90,106:203,254:0.3002:2,2:25:1:29.3:1:0.73208:1.06:60:64.333:0.2988:0:1.1 0/1:572:74:35,39:231,266:0.1294:2,2:22.9:1:28:1:0.9013:1.03:60:36:0.127:0:1.1 -7 140486513 . A G 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACATTTAAAACACTTCCAG;RSEQ=AAGTTGAAGGAAGTGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:876:0:0,0:465,410:0:2,0:25.7:1:29.7:1:1:0:60:42.75:0.9988:0:0.1 0/1:860:38:23,15:433,385:0.0442:2,2:21:1:31.2:1:0.40782:1.36:60:76:0.0448:0:1.1 -7 140486743 . T C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08294;LSEQ=TGTAGTCTACGGCCATACCA;RSEQ=CCTGAACGTGTCCGATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1040:275:117,158:355,409:0.2644:2,2:25.2:1:31.6:1:0.2895:1.17195:60:136.5:0.2679:0:1.1 0/1:1348:39:19,20:635,670:0.0289:2,2:24.5:1:30.8:1:1:1.00:60:38:0.0287:0:1.1 -7 140486825 . G A 45 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12482;SOR=Inf;LSEQ=TTAAGACTTCCTTTTGGCCG;RSEQ=GCGCGGTGGCTCACGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:103,267:0:2,0:23:1:30.5:1:1:0:57.8:32.636:1:0:0.2 0/1:396:4:3,1:105,286:0.0101:2,2:11.3:1:22.5:1:0.06402:8.12:60:3:0.0078:0:1 -7 140486867 . C A 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5839;SOR=2.57213;LSEQ=ATCCCAGCACTTTGGGAGGC;RSEQ=GAGGCGGGCGGATCACGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:15,172:0.0053:2,0:26:0:16:0:1:0:52:0:0:0:4 0/1:147:2:1,1:2,143:0.0136:1,2:16.5:1:29:1:0.04054:58.51:50:4:0.014:0:4 -7 140486874 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50481;SOR=0;LSEQ=CACTTTGGGAGGCCGAGGCG;RSEQ=GCGGATCACGAGGTCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:9,150:0.0124:2,0:25.5:1:30:1:1:0:50:4:0.0127:0:1 0/0:128:0:0,0:1,127:0:1,0:21.6:1:30.4:1:1:0:49.4:41.667:1:0:0.2 -7 140487072 . A G 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16969;SOR=0;LSEQ=GATCGCGCCACTGCACTCCA;RSEQ=CCTGGGCGACAGAGCGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:123,17:0.0141:2,0:30:1:34:0:1:0:33.5:4:0.0144:0:2 0/0:202:0:0,0:170,32:0:2,0:21.4:1:28.6:1:1:0:45.7:24.25:1:0:0.9 -7 140487202 . C T 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39397;LSEQ=TATTAGAGGTAAATGACAAA;RSEQ=ACTACAGAAAAACAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:756:257:142,115:262,234:0.3399:2,2:21.9:1:29.2:1:0.53835:1.10:60:63.25:0.3401:0:1.1 0/1:1032:174:88,86:417,438:0.1686:2,2:24.4:1:28.4:1:0.6782:1.07:60:20.75:0.165:0:1.2 -7 140487494 . C T 201 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00792;LSEQ=AATTATTTTATTAATTAAAA;RSEQ=AATACATCTTATAACTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:111:51,60:293,365:0.1442:2,2:24.9:1:29.6:1:0.83663:1.06:60:110:0.1444:0:1.2 0/0:752:1:0,1:349,401:0.0013:2,0:1:0:22:0:1:0:60:2:0.0013:0:1 -7 140487927 . G A 43 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04612;SOR=Inf;LSEQ=ACCCTGCACATCCTGCACAT;RSEQ=TACCCCTGAACTTTGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:0:0,0:165,264:0:2,0:22:1:31.9:1:1:0:60:84.8:1:0:0.1 0/1:372:4:4,0:149,219:0.0108:2,0:5:1:21.5:1:0.02795:0:60:3:0.0082:0:2 -7 140487982 . T TA 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.4966;SOR=1.75292;LSEQ=AAAATGGCTTCATCAATCCT;RSEQ=AAAAAAAATTATACTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:3:1,2:238,163:0.0074:2,2:27.7:1:29:1:0.5698:2.91246:60:6:0.0076:0:0 0/1:386:5:2,3:201,180:0.013:2,2:27:1:29.2:1:0.67121:1.67276:60:10:0.0131:0:0.4 -7 140488156 . T G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11033;LSEQ=AAAAAGTTATAAATAATTAT;RSEQ=TCTCTATTATAGGCATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:172:84,88:196,196:0.305:2,2:25.5:1:32:1:0.85492:1.04756:60:56.333:0.3056:0:1.1 0/1:564:26:13,13:271,266:0.0461:2,2:21.2:1:30.9:1:1:1.01877:60:52:0.0468:0:1 -7 140488495 . CC TT 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1702;SOR=Inf;LSEQ=GCCTCTTGGGTTCAAGTGAT;RSEQ=TCCTGCCTCAGCCTCCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:24,196:0:2,0:23.6:1:31.3:1:1:0:60:109:1:0:0.1 0/1:155:2:0,2:11,142:0.0129:2,0:17:0:32:0:1:0:36.5:4:0.013:0:2.5 -7 140488595 . G A 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23817;SOR=Inf;LSEQ=GACGGGGTTTCACCATGTTG;RSEQ=CCAGGCTGGTCTTGAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:117,22:0:2,0:26.4:1:31.2:1:1:0:56.6:45.333:1:0:0.1 0/1:133:2:1,1:105,26:0.015:2,2:6:0:26:1:0.36603:3.9818:60:4:0.0152:0:1 -7 140488655 . C T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23053;SOR=4.1378;LSEQ=CACCTCAGCCTCCCAAAGTG;RSEQ=TGGGATTACATGCATAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:1:0,1:178,209:0.0026:2,0:1:0:27:0:1:0:60:2:0.0026:0:1 0/1:472:5:0,5:238,229:0.0106:2,0:7.4:1:26.8:1:0.0293:0:60:10:0.0107:0:1 -7 140488738 . C A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0668;SOR=Inf;LSEQ=AGCTCTTTATGCGCCGGGTG;RSEQ=GGTGGCTCAAGCCTGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:178,177:0:2,0:24.8:1:30.2:1:1:0:60:34.5:0.9971:0:0.2 0/1:429:5:4,1:207,216:0.0117:2,2:7.6:1:23.4:1:0.21014:4.16:60:4:0.0095:0:1.2 -7 140488743 . G A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69289;SOR=1.69468;LSEQ=TTTATGCGCCGGGTGCGGTG;RSEQ=CTCAAGCCTGTAATACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:2:2,0:168,161:0.006:2,0:1:0:27:0:0.49886:0:60:4:0.0062:0:1 0/1:392:4:3,1:196,192:0.0102:2,2:5.8:1:25.3:1:0.62325:2.93:60:8:0.0105:0:1 -7 140488751 . C A 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69034;SOR=1.75373;LSEQ=CCGGGTGCGGTGGCTCAAGC;RSEQ=TGTAATACCAGCACTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:2:2,0:146,148:0.0068:2,0:1:0:27.5:1:0.49831:0:60:4:0.0069:0:1 0/1:339:4:3,1:159,176:0.0118:2,2:25.3:1:25.3:1:0.35198:3.31:60:3:0.009:0:1.5 -7 140488783 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22873;SOR=0;LSEQ=CACTTTGGGAGGCTGAGGCT;RSEQ=GTGGATCACGAGGTTAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:39,108:0.0134:2,2:11.5:1:29.5:1:0.46617:2.75:60:4:0.0135:0:1 0/0:162:0:0,0:33,129:0:2,0:22.9:1:30.1:1:1:0:59.9:161:1:0:0.1 -7 140489019 . C CA 215 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.21511;LSEQ=ACTCCATCACAGAAAAAAAA;RSEQ=AAAAAAAAAACTATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:154:120,34:272,60:0.295:2,2:19.1:1:29.7:1:0.32398:1.28372:59.8:29.8:0.2927:0.1073:0.2 0/1:485:40:30,10:337,86:0.0825:2,2:24.4:1:29.5:1:0.53989:1.3054:60:39:0.0826:0.0021:0.1 -7 140489030 . CTA C 89 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.02122;SOR=8.77528;LSEQ=GAAAAAAAACAAAAAAAAAA;RSEQ=TATATATATTTAGCTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:657:1:1,0:493,163:0.0015:2,0:20:0:33:0:1:0:60:2:0.0016:0:0 0/1:681:9:4,5:470,200:0.0132:2,2:12.3:1:28.1:1:0.13818:2.93221:60:18:0.0135:0.0088:0.4 -7 140489173 . A G 189 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GAGGGATTGAATGGCCCCAA;RSEQ=TATCTCTGAATAGTCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1276:62:27,35:508,706:0.0486:2,2:25.6:1:31.9:1:0.79335:1.07:60:61:0.0485:0:1.1 0/0:1334:0:0,0:604,727:0:2,0:26:1:29.8:1:1:0:60:82.188:0.9985:0:0.1 -7 140489562 . C T 173 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GATTTTGAGATGAAGTCTTG;RSEQ=TCTTGTCACCCAGGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:181,303:0:2,0:23.5:1:31.9:1:1:0:60:120:0.9979:0:0.1 0/1:505:57:25,32:165,280:0.1129:2,2:21.9:1:29.7:1:0.38423:1.32:60:114:0.1135:0:1.2 -7 140490074 . A C 167 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CTTACAAGTTACTGCTAGTA;RSEQ=CAACATAAACTTAGATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:910:0:0,0:436,473:0:2,0:23.3:1:30.1:1:1:0:60:112.625:0.9989:0:0.1 0/1:943:40:21,19:461,441:0.0424:2,2:28.3:1:31.5:1:0.87333:1.06:60:80:0.0426:0:1.1 -7 140490207 . T C 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03303;SOR=1.41127;LSEQ=CAACTTTTTTCCCACTCTTT;RSEQ=GTAGTTCCTTCTCTTACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:933:73:28,45:395,464:0.0782:2,2:25.9:1:29.7:1:0.22267:1.36769:60:35.5:0.0771:0:1.1 0/1:972:104:51,53:384,483:0.107:2,2:25.4:1:30.1:1:0.404:1.21:60:103:0.1068:0:1.1 -7 140490382 . C T 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41756;LSEQ=ATTCAAACCACTATGGAAGG;RSEQ=AAACACTACTAGCCCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:137:69,68:169,142:0.3058:2,2:23.3:1:28.7:1:0.4725:1.17247:60:136:0.3063:0:1.1 0/1:496:77:44,33:233,186:0.1552:2,2:26.1:1:29.2:1:0.90073:1.06:60:154:0.1565:0:1.1 -7 140490645 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25027;SOR=0;LSEQ=GGCTGGGTGCAGTGGCTCAC;RSEQ=CCTGTAATCCCAACACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:2,1:48,224:0.0109:2,2:20.7:1:25.7:1:0.08611:9.22:60:2:0.0074:0:3.3 0/0:250:0:0,0:32,217:0:2,0:21.2:1:31.8:1:1:0:60:123.5:0.996:0:0.1 -7 140490658 . A G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25775;SOR=0;LSEQ=GGCTCACGCCTGTAATCCCA;RSEQ=CACTCTGGGAGGCGGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:1,2:34,195:0.0129:2,2:10.3:1:32:1:0.38916:2.85:53.3:6:0.0132:0:2.7 0/0:185:0:0,0:10,175:0:2,0:22:1:30:1:1:0:60:184:1:0:0.1 -7 140490765 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50537;SOR=0;LSEQ=ACAAAAATTAGCTGGGCATG;RSEQ=TGGCGGGAGCCTGTAATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:82,23:0.0187:2,2:12:1:33:0:0.39993:3.51117:41.5:4:0.0189:0:0.5 0/0:83:0:0,0:70,13:0:2,0:19.7:1:29.8:1:1:0:60:82:1:0:0.1 -7 140490928 . C A 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.48504;LSEQ=AAAACAAAACAAAAACAAAA;RSEQ=CCGAAAAACCAAAAAAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1629:513:297,216:651,459:0.3149:2,2:25.5:1:29.8:1:0.78669:1.03149:60:63.125:0.3131:0:1.2 0/1:2145:391:215,176:971,777:0.1823:2,2:25.7:1:29.2:1:0.86597:1.02299:60:64.167:0.1811:0:1.2 -7 140490938 . CA C 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.10724;SOR=1.48568;LSEQ=AAAAACAAAACCCGAAAAAC;RSEQ=AAAAAAATTGTCCCTCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1918:27:15,12:1050,839:0.0141:2,2:28.9:1:31.7:1:1:1.00119:60:54:0.0143:0.0016:0.5 0/1:2455:51:26,25:1269,1128:0.0208:2,2:23.9:1:30.8:1:0.7792:1.08168:60:102:0.021:0.0037:0.4 -7 140491101 . A G 206 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTAAAGATGACATTTCA;RSEQ=TTGCCAAAATTGATAGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1163:0:0,0:527,635:0:2,0:23.6:1:30.5:1:1:0:60:76.467:1:0:0.1 0/1:1287:98:41,57:550,637:0.0761:2,2:21.3:1:31.2:1:0.40117:1.2002:60:196:0.0773:0:1 -7 140491258 . C T 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACTTAGGAAGAGCCAGCC;RSEQ=ATAAAGGAGACAGAGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:698:0:0,0:299,398:0:2,0:25.2:1:31.5:1:1:0:60:68.7:1:0:0.1 0/1:715:26:14,12:326,363:0.0364:2,2:25.7:1:29.4:1:0.55297:1.30:60:52:0.0365:0:1.1 -7 140491331 . T TCAATTTACATATGCTCTTTGAG 136 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTACATTTTCTCCCCTTT;RSEQ=CAATTTACATATGCTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:785:0:0,0:378,406:0:2,0:25.2:1:30:1:1:0:60:111:1:0:0.1 0/1:837:23:11,12:404,410:0.0275:2,2:25.9:1:30.1:1:1:1.07482:60:46:0.0277:0.0096:0.1 -7 140491678 . G A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.30225;LSEQ=AAACAGTATAGTGGTTAAGT;RSEQ=TAAGAGAGAAAGGCCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1003:342:176,166:346,315:0.341:2,2:23.4:1:29.5:1:0.8415:1.03598:60:56:0.3387:0:1.1 0/1:984:133:70,63:460,386:0.1352:2,2:20.3:1:28.9:1:0.70929:1.07245:60:132:0.1354:0:1.2 -7 140492039 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06146;LSEQ=ATACTGTAAAAACCACATTA;RSEQ=TGACAGTCCTGCCTCTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:680:206:92,114:202,272:0.3029:2,2:25.8:1:32.2:1:0.67372:1.09:60:205:0.3042:0:1.1 0/1:616:16:5,11:272,328:0.026:2,2:26.3:1:32.3:1:0.31556:1.8227:60:32:0.0263:0:1.1 -7 140492411 . T C 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTGTCCCTTCTCTGCTCAA;RSEQ=GTTCCTAGATCCAACCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1122:0:0,0:480,642:0:2,0:25.6:1:30.4:1:1:0:60:123.667:1:0:0.1 0/1:1000:29:11,18:442,528:0.029:2,2:25.3:1:30.8:1:0.4543:1.36941:60:58:0.0293:0:1 -7 140493029 . A G 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAAAAGGATGATAGTTTTC;RSEQ=AAGTAAAGATGAAGGTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1113:0:0,0:582,528:0:2,0:24.4:1:30.1:1:1:0:60:110:0.9973:0:0.1 0/1:1083:49:24,25:515,518:0.0452:2,2:28:1:29.7:1:1:1.03561:60:48:0.0447:0:1.1 -7 140493455 . T C 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.13344;SOR=Inf;LSEQ=TTTTCTTTTGAGACAGGGTC;RSEQ=CACTCTGTTGCTCAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:74,183:0:2,0:23.4:1:30:1:1:0:60:41.833:1:0:0.1 0/1:323:4:2,2:91,228:0.0124:2,2:26.5:1:31.3:1:0.3267:2.50:60:8:0.0126:0:1.3 -7 140493462 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26154;SOR=Inf;LSEQ=TTGAGACAGGGTCTCACTCT;RSEQ=TTGCTCAGGCTGGAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:59,162:0:2,0:23.6:1:31.6:1:1:0:60:43.2:1:0:0 0/1:288:3:2,1:76,209:0.0104:2,2:11.3:1:25.3:1:0.17937:5.46:56.7:6:0.0106:0:3 -7 140494073 . G GT 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17679;SOR=0.59912;LSEQ=AAAATAAAGATACATACTTG;RSEQ=TTTTTTTTTAGTTCTAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:806:22:13,9:450,333:0.0273:2,2:30.2:1:29.4:1:1:1.07:60:21:0.0264:0:0.1 0/1:847:14:5,9:473,359:0.0165:2,2:34.7:1:29.3:1:0.1722:2.36919:60:28:0.0167:0:0.1 -7 140494413 . A C 205 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAGCAGTAATGACTTTTAA;RSEQ=AGTATTAATTTAAAAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:86:46,40:286,276:0.1325:2,2:25:1:32:1:0.72844:1.11:60:172:0.1337:0:1.1 0/0:763:0:0,0:378,384:0:2,0:23.7:1:29.9:1:1:0:60:761:0.9987:0:0.1 -7 140495349 . GA G 93 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.13293;SOR=0.34705;LSEQ=TTGTGAGACGTGAGGAATGG;RSEQ=AAAAAATATAGTAGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:759:8:5,3:400,347:0.0105:2,2:21.6:1:31.3:1:0.73094:1.45:60:16:0.0107:0:0.1 0/0:815:3:1,2:423,386:0.0037:2,2:20.7:1:21.3:1:0.60862:2.18967:60:0.5:0.0012:0:1 -7 140495542 . C T 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.0307;SOR=Inf;LSEQ=TTATATTAATGAAATGAATC;RSEQ=ACTTAGAATTGATATGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:169,231:0:2,0:24.9:1:31.7:1:1:0:60:43.444:1:0:0.7 0/1:406:6:2,4:169,229:0.0148:2,2:21.5:1:29.3:1:1:1.47461:60:12:0.015:0:2.3 -7 140495573 . T C 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01823;LSEQ=GATATGCAAATAATAAAATA;RSEQ=TATGTACTAAAAAAAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:373:372:209,163:0,1:0.9973:0,2:23:1:32:1:0.43968:0:60:45.5:1:0:1.1 1/1:380:331:168,163:28,21:0.8711:2,2:22.2:1:31:1:0.44581:1.29277:60:54.167:0.869:0:1.2 -7 140495581 . TA T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16157;SOR=0.52556;LSEQ=AATAATAAAATATTATGTAC;RSEQ=AAAAAAAATTGGTATCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:17:13,4:208,160:0.0442:2,2:18:1:29.7:1:0.13376:2.49:60:16:0.0426:0.0234:0.9 0/1:380:9:5,4:203,167:0.0237:2,2:20.4:1:29.9:1:1:1.03:60:18:0.0241:0.0079:1 -7 140495583 . A C 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.02846;SOR=Inf;LSEQ=TAATAAAATATTATGTACTA;RSEQ=AAAAAAATTGGTATCGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:222,163:0:2,0:22.9:1:30:1:1:0:60:63.167:1:0:1 0/1:373:5:3,2:203,165:0.0134:2,2:19:1:33.4:1:1:1.22:60:10:0.0136:0:2.6 -7 140495598 . C T 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTAAAAAAAAATTGGTAT;RSEQ=GGCTCAATGAGAATTATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:246,160:0:2,0:24.3:1:30.5:1:1:0:60:66.667:1:0:0.8 0/1:410:19:9,10:225,166:0.0463:2,2:16.3:1:30.6:1:0.47787:1.50447:60:38:0.0467:0:1.7 -7 140496563 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07216;LSEQ=GTGATCATAATCTGATGTCA;RSEQ=TGAATATCTCAGCCATGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:228:86,142:222,278:0.3128:2,2:24.8:1:32.2:1:0.10566:1.31805:60:227:0.314:0:1.1 0/1:630:20:12,8:266,344:0.0317:2,2:24.6:1:31:1:0.17237:1.94:60:40:0.0318:0:1.1 -7 140496743 . A AT 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.11341;SOR=5.35454;LSEQ=TTACCTGGTATCCTGATTCA;RSEQ=TTTTTTTTCTGATTTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:1:1,0:302,215:0.0019:2,0:49:0:30:0:1:0:60:2:0.0019:0:0 0/1:488:5:2,3:269,214:0.0102:2,2:24.4:1:30.2:1:0.65973:1.88303:60:10:0.0104:0:0 -7 140496901 . TC T 255 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGTCGGCAAACTGGCTTTC;RSEQ=CCAATGATACCTGTACCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:288:142,146:288,301:0.3265:2,2:26.6:1:31.3:1:0.9427:1.02:60:287:0.3269:0.0385:0.1 0/0:848:0:0,0:415,432:0:2,0:25.1:1:31:1:1:0:60:120:0.9988:0:0.1 -7 140497586 . A T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=0.08833;LSEQ=GGACCTGCCATTAGAAAGGC;RSEQ=TCATGGTCTACAGAATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:205:103,102:209,219:0.3239:2,2:25.6:1:30.6:1:0.79889:1.06:60:40:0.319:0:1.1 0/1:543:22:14,8:278,242:0.0405:2,2:22.2:1:29.1:1:0.3894:1.52:60:21:0.0393:0:1.1 -7 140497677 . T TA 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.95426;LSEQ=AACATTTTGATTTGACCATC;RSEQ=AAAAAAAACACAGCTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:741:11:8,3:390,340:0.0148:2,2:33.4:1:27.7:1:0.23732:2.32:60:10:0.014:0.0013:0.2 0/1:776:11:7,4:406,354:0.0142:2,2:32.3:1:28.4:1:0.55743:1.53:60:22:0.0146:0:0 -7 140498062 . C CT 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.82406;SOR=0.87605;LSEQ=GACAGAATGCTGTATGGGGA;RSEQ=TTTTTTTTTCTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:10:7,3:359,415:0.0126:2,2:18.2:1:30.1:1:0.20212:2.69:60:20:0.0137:0:0 0/1:905:10:5,5:433,454:0.011:2,2:16.6:1:25.5:1:1:1.05:56.8:4:0.0095:0.0011:1.1 -7 140498071 . T C 117 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=16.87109;LSEQ=CTGTATGGGGACTTTTTTTT;RSEQ=CTTTTTTTTGAGACGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:1:0,1:283,343:0.0016:2,0:10:0:12:0:1:0:60:0:0:0:3 0/1:766:20:12,8:362,381:0.0261:2,2:9.3:1:27.3:1:0.36937:1.58:58.5:5.667:0.0228:0:1.4 -7 140498072 . C T 155 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.40621;SOR=0.86817;LSEQ=TGTATGGGGACTTTTTTTTT;RSEQ=TTTTTTTTGAGACGGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:617:80:5,75:258,246:0.1297:2,2:9.9:1:24.7:1:0:15.67518:50.6:2.2:0.1089:0:2.7 0/1:751:86:3,83:350,286:0.1145:2,1:10.4:1:24.2:1:0:33.74928:47.3:2.071:0.0906:0:2.4 -7 140498081 . G T 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-04;SOR=0.28702;LSEQ=ACTTTTTTTTTCTTTTTTTT;RSEQ=AGACGGAGTCTTGCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:28:13,15:18,73:0.2353:2,2:1.1:1:29.8:1:0.00724:3.47:60:56:0.2667:0:1.1 0/1:235:19:10,9:59,156:0.0809:2,2:5.7:1:27.1:1:0.03307:2.92:58.9:8.5:0.0794:0:1.6 -7 140498106 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52383;SOR=Inf;LSEQ=GGAGTCTTGCTCTGTCACCC;RSEQ=GGCTGGAATGCAGTGACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:13,77:0:2,0:27.1:1:29.8:1:1:0:51.8:7.182:1:0:1.1 0/1:143:2:1,1:29,112:0.014:2,2:28:1:27:1:0.37674:3.81:49.5:4:0.0159:0:2.5 -7 140498381 . A T 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01595;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=AAGCATGTGCTTCCAGACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:8:4,4:229,133:0.0212:2,2:19.3:1:25.9:1:0.47502:1.71907:55:7:0.0203:0:2.8 0/1:464:10:3,7:286,166:0.0216:2,2:13.2:1:25:1:0.04512:4.00756:58:20:0.0238:0:1.5 -7 140498658 . T C 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGCCTTTGCATTATTTTTA;RSEQ=TTTTTTGAGACAGAATCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:998:0:0,0:424,571:0:2,0:23.4:1:30.5:1:1:0:60:198:0.997:0:0.1 0/1:1220:42:15,27:491,681:0.0344:2,2:21.3:1:31.4:1:0.52457:1.29752:60:84:0.0347:0:1.1 -7 140498739 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24321;SOR=Inf;LSEQ=CACTGCAACCTCCACCTCCC;RSEQ=GGTTCAAGTGATTCTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:15,189:0:2,0:25:1:31:1:1:0:56.3:33:1:0:0.2 0/1:199:2:0,2:4,192:0.0101:1,0:8.5:1:31.5:1:1:0:40:4:0.0103:0:6 -7 140498800 . C T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0376;SOR=Inf;LSEQ=GGATTACAGGTGTGTGCCAT;RSEQ=ATGCCCAGCTAATTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:28,87:0:2,0:20.2:1:31.7:1:1:0:58.5:37.333:1:0:0.4 0/1:92:4:2,2:28,60:0.0435:2,2:23.3:1:30.5:1:0.59394:2.12:60:8:0.046:0:1 -7 140498929 . T G 74 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21795;SOR=4.80982;LSEQ=CCCAAAGTGCTGGGATTACA;RSEQ=GCGTGAACCACCGCACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:1:0,1:320,127:0.0022:2,0:31:0:27:0:0.28571:0:33:2:0.0023:0:6 0/1:469:5:3,2:322,141:0.0107:2,2:28:1:32:1:0.64365:1.52099:54.8:10:0.0108:0:4.4 -7 140499107 . C T 284 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.7427;LSEQ=CCTCTCTCAGTTTTCACTAC;RSEQ=AACAACATCCTAGGTTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1552:565:259,306:461,523:0.364:2,2:26.4:1:29.4:1:0.71133:1.0414:60:93.167:0.3632:0:1.1 0/1:1770:884:415,469:415,466:0.4994:2,2:25.3:1:29.1:1:0.96198:1.00643:60:109.5:0.5011:0:1.1 -7 140500135 . C T 178 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=61.85077;LSEQ=AAGCGGTTCAAGTAGCATGT;RSEQ=GCCCAAGAGCAGAAGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1506:1:1,0:794,710:7e-04:2,0:50:0:30:0:1:0:60:2:7e-04:0:1 0/1:1671:66:35,31:787,817:0.0395:2,2:25.1:1:29.6:1:0.53322:1.17:60:65:0.0394:0:1.2 -7 140500384 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11664;SOR=Inf;LSEQ=TGAGATCAAATTCCATTCTC;RSEQ=GAAACAACTGTTAAAATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:0,107:0:1,0:23.8:1:31.5:1:1:0:60:214:1:0:0.2 0/1:56:2:1,1:2,52:0.0357:1,2:25.5:1:29:1:0.10519:21.43:60:4:0.0357:0:1 -7 140501405 . A T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22994;SOR=Inf;LSEQ=TTTCAAAAACTCACAAGAAA;RSEQ=CTTTCTAGAAACTGACGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:34,163:0:2,0:25.1:1:29.3:1:1:0:60:23.625:1:0:0.1 0/1:182:2:1,1:32,148:0.011:2,2:20.5:1:26.5:1:0.33058:4.57:60:4:0.0112:0:1 -7 140507735 . CA C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.91555;LSEQ=TCTAAACATTTTTGACATTT;RSEQ=AAAAAAAATGTAAAGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:11:8,3:297,88:0.0277:2,2:24:1:31.5:1:0.72022:1.26483:60:22:0.0278:0.0025:0 0/1:354:9:7,2:239,103:0.0254:2,2:19:1:30.6:1:0.72997:1.51:60:18:0.0255:0.0085:0.1 -7 140507901 . C T 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCCTTTCTTGGTTATTACA;RSEQ=CTAAAAATATTCATATACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:27:6,21:71,239:0.0799:2,2:23.1:1:30.6:1:1:1.03966:60:54:0.0811:0:1.1 0/0:338:0:0,0:92,245:0:2,0:23:1:30.8:1:1:0:60:66.4:0.997:0:0.1 -7 140508842 . C A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25288;SOR=0;LSEQ=GAGGTAAAGGGAGCAAATTA;RSEQ=ATTTTTTCATATCATTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:2,1:31,200:0.0128:2,2:11:1:23:1:0.05293:12.66:60:2:0.0086:0:3.3 0/0:200:0:0,0:35,165:0:2,0:22.1:1:31.4:1:1:0:60:65.667:1:0:0 -7 140534267 . C T 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45158;SOR=0.59054;LSEQ=ACTTTGCCACCAAATAATTA;RSEQ=ATATTTTTCATTCCTGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:16:15,1:45,2:0.254:1,1:20.8:1:30.3:1:1:1.48954:60:32:0.254:0:1.1 0/1:36:6:6,0:30,0:0.1667:1,0:24.8:1:30.8:1:1:0:60:12:0.1714:0:1 -7 140534563 . A C 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAAGATGTAACGGTATCC;RSEQ=TTGATGCAGAGCTAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:694:0:0,0:370,323:0:2,0:25.8:1:30.5:1:1:0:59.8:137.6:0.9985:0:0.1 0/1:752:52:24,28:353,347:0.0691:2,2:23.1:1:31.3:1:0.56864:1.18657:59.7:104:0.0698:0:1.1 -7 140549900 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00714;SOR=Inf;LSEQ=AAATTACTAGATATGATACT;RSEQ=AAAAGCTTACCTCCAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:476,234:0:2,0:24.8:1:31.6:1:1:0:60:100.429:1:0:0.1 0/1:695:7:3,4:413,275:0.0101:2,2:18:1:23.7:1:0.44719:2.0004:60:6:0.0088:0:1.6 -7 140624311 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09231;SOR=Inf;LSEQ=CCTCTTTCCAAAATAAACAC;RSEQ=AGCCAGCCGCCGAGCCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:93,61:0:2,0:22.5:1:30.9:1:1:0:60:50.333:1:0:0.2 0/1:128:3:1,2:81,44:0.0234:2,2:11.3:1:26.7:1:0.29308:3.64239:60:6:0.0238:0:1 -7 140624380 . C T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70425;SOR=1.51429;LSEQ=ACTCACCTCCTCCGGAATGG;RSEQ=AGGGTCCGCAGCCGAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:2:0,2:121,178:0.0066:2,0:1:0:24:0:0.51761:0:60:4:0.0068:0:1 0/1:400:4:2,2:189,206:0.01:2,2:12.5:1:27.3:1:1:1.09:60:8:0.0101:0:1 -7 140624431 . G T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41025;SOR=3.36847;LSEQ=GGCGCCGGCGCCGGCCTCGG;RSEQ=CTCCATGTCCCCGTTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:1:0,1:139,143:0.0035:2,0:1:0:25:0:1:0:60:2:0.0035:0:1 0/1:423:5:1,4:197,221:0.0118:2,2:5:1:26:1:0.37716:3.55624:60:10:0.012:0:1 -7 140624459 . G A 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2409;SOR=3.87099;LSEQ=TCCCCGTTGAACAGAGCCTG;RSEQ=CCCGGCTCCGCGCCGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:1:1,0:167,154:0.0031:2,0:1:0:27:0:1:0:60:2:0.0032:0:1 0/1:419:5:4,1:202,211:0.0119:2,2:9.4:1:27.4:1:0.20993:4.17:60:10:0.0122:0:1.2 -7 140624460 . C T 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07326;SOR=Inf;LSEQ=CCCCGTTGAACAGAGCCTGG;RSEQ=CCGGCTCCGCGCCGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:165,152:0:2,0:25.4:1:31.7:1:1:0:60:51.833:0.9968:0:0.2 0/1:418:5:2,3:202,211:0.012:2,2:22.2:1:29.4:1:1:1.43479:60:10:0.0122:0:1.4 -7 140624524 . C G 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24805;SOR=Inf;LSEQ=CTTATAACCGAGAGCCGGGG;RSEQ=CCGAGCGGCCGCTGTCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:72,116:0:2,0:23.7:1:30.3:1:1:0:60:16.091:0.9944:0:0.2 0/1:192:3:1,2:82,106:0.0156:2,2:14:1:25:1:1:1.54378:60:2:0.0109:0:3.7 -7 140624526 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24525;SOR=0;LSEQ=TATAACCGAGAGCCGGGGCC;RSEQ=GAGCGGCCGCTGTCGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:67,111:0.011:2,2:36.5:1:31:1:1:1.65:60:4:0.0116:0:1 0/0:185:0:0,0:80,105:0:2,0:23.2:1:28.4:1:1:0:60:25.429:1:0:0.3 -7 140624530 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49856;SOR=Inf;LSEQ=ACCGAGAGCCGGGGCCCGAG;RSEQ=GGCCGCTGTCGGGCGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:59,105:0:2,0:23.8:1:29.2:1:1:0:60:17.222:1:0:0.2 0/1:168:2:0,2:69,96:0.0119:2,0:14.5:1:26.5:1:0.51216:0:60:4:0.0122:0:1 -7 144115822 . G C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45849;SOR=0.51051;LSEQ=GAAACAAATTTGACAAGAAG;RSEQ=TTAAAAATACAGGGCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:5,1:11,1:0.3333:2,2:23.5:1:33.2:1:1:2.09766:58.2:12:0.3333:0:1.5 0/1:15:3:2,1:9,3:0.2:2,2:34.3:1:33:1:1:1.45761:52.3:6:0.2:0:3 -7 144115845 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=AAAAATACAGGGCCCAAAGG;RSEQ=GAGTAACAGCAAGATGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:21,7:0:2,0:24.8:1:31.2:1:1:0:59.7:13:1:0:0.4 0/1:28:3:2,1:19,6:0.1071:2,2:26.7:1:29.7:1:1:1.55524:45.7:6:0.1071:0:2.3 -7 144115885 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.06212;LSEQ=GCCATGGGACCTAGAAATGG;RSEQ=AGAAGCCATGTTGCCCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:13:9,4:16,9:0.3421:2,2:29:1:29.1:1:1:1.26:59.4:12:0.3243:0:1.3 0/1:59:21:12,9:21,17:0.3559:2,2:23:1:28.4:1:1:1.08:54.9:20:0.3509:0:1.5 -7 144662618 . TA T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1208;SOR=0;LSEQ=TAGCCTTTGCCTAATTCAAA;RSEQ=ATACCATATTCCCTGATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:1,2:168,92:0.0114:2,2:22.7:1:28.7:1:0.29117:3.63323:60:6:0.0116:0.0038:1.3 0/0:268:0:0,0:169,99:0:2,0:25.7:1:28.8:1:1:0:60:88.333:1:0:0.4 -7 144662674 . T G 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40777;SOR=1.14251;LSEQ=CCTCTGCTTTTAAGCAGGTG;RSEQ=TTATCCCATATAAAGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:135:75,60:102,109:0.389:2,2:26.8:1:31.2:1:0.22524:1.33:60:66.5:0.3935:0:1.1 0/1:387:163:79,84:115,109:0.4212:2,2:27.3:1:30.8:1:0.60742:1.12149:60:39.75:0.4173:0:1.1 -7 144662746 . A G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11432;SOR=Inf;LSEQ=ATCGGTACACTTTTCTATGA;RSEQ=GATTTTGTGAATCTGGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:68,125:0:2,0:25.8:1:30.5:1:1:0:60:47.25:1:0:0.3 0/1:183:3:1,2:57,123:0.0164:2,2:22.3:1:30:1:1:1.08:60:6:0.0167:0:1.3 -7 144662974 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAAGTGTGATATAAGAC;RSEQ=ACTACTATGGTGTCAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 144663029 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGCATTTCATAAAGTTA;RSEQ=TTAAAGGGAACTTTAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 144799690 . GCAA G 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.08656;SOR=0.25309;LSEQ=GACCCTATCTCAAAACAACA;RSEQ=CAACAACAACAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:7,4:4,3:0.5789:2,2:27.8:1:32.5:1:1:1.29:60:22:0.5789:0.0526:0.2 0/1:16:4:3,1:6,6:0.25:2,2:43:1:32.5:1:0.58462:2.81:60:8:0.25:0:0.5 -7 144799697 . C TAGCAGCAGT 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.08061;SOR=Inf;LSEQ=TCTCAAAACAACAGCAACAA;RSEQ=AACAACAACAACAACAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,7:0:2,0:26.8:1:29.9:1:1:0:60:40:1:0:0.2 0/1:17:3:1,2:9,5:0.1765:2,2:14:1:28.2:1:0.53676:3.32592:44:6:0.1765:0.1765:3 -7 144799705 . A G 33 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.49854;SOR=Inf;LSEQ=CAACAGCAACAACAACAACA;RSEQ=CAACAACAGCAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:17,9:0:2,0:25.5:1:29.1:1:1:0:60:25:1:0:0.2 0/1:33:2:1,1:18,13:0.0606:2,2:8:0:33.5:1:1:1.37079:36:4:0.0606:0:4 -7 144799707 . A C 33 v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.50446;SOR=Inf;LSEQ=ACAGCAACAACAACAACAAC;RSEQ=ACAACAGCAACAACAACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:17,10:0:2,0:25.6:1:29.3:1:1:0:60:26:1:0:0.3 0/1:37:2:1,1:21,14:0.0541:2,2:6:0:33:1:1:1.4832:52:4:0.0541:0:2 -7 144799717 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.51129;SOR=Inf;LSEQ=CAACAACAACAACAACAGCA;RSEQ=CAACAACAACAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:19,11:0:2,0:26.8:1:30.2:1:1:0:60:60:1:0:0.2 0/1:44:2:1,1:26,16:0.0455:2,2:20:0:33:1:1:1.60645:36:4:0.0455:0:4 -7 144799718 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51129;SOR=Inf;LSEQ=AACAACAACAACAACAGCAA;RSEQ=AACAACAACAGCAACAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:19,11:0:2,0:27.1:1:30.9:1:1:0:60:14:1:0:0.2 0/1:44:2:1,1:26,16:0.0455:2,2:30:1:30.5:1:1:1.60645:60:4:0.0455:0:1 -7 144799720 . AC TT 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51579;SOR=Inf;LSEQ=CAACAACAACAACAGCAACA;RSEQ=AACAACAGCAACAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:19,11:0:2,0:27.7:1:29:1:1:0:60:14:1:0:0.2 0/1:46:2:1,1:27,17:0.0435:2,2:24:0:30:1:1:1.57176:36:4:0.0435:0:3 -7 144799735 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.51704;SOR=Inf;LSEQ=CAACAACAACAACAGCAACA;RSEQ=CAGCAGCAACAACAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:0:2,0:26.9:1:32.4:1:1:0:60:62:1:0:0.2 0/1:48:2:1,1:26,20:0.0417:2,2:17.5:1:29.5:1:1:1.29283:52:4:0.0417:0:2 -7 148504716 . AG A 301 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=2.69117;LSEQ=TAAGGCAGCTGTTTCAGAGG;RSEQ=GGGGGAGGAGGTAGCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1107:634:313,321:247,222:0.5727:2,2:28.7:1:31.7:1:0.30047:1.14091:60:316:0.5745:0.0497:0.2 1/0:1037:812:417,395:119,104:0.783:2,2:27.1:1:31.2:1:0.59751:1.08377:60:161.4:0.7873:0.0887:0.2 -7 148504854 . A AGACTT 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.02305;SOR=1.5522;LSEQ=CACCCATCCAACATGTGCTG;RSEQ=GACTTAACACAACAAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:244:132:7,125:17,92:0.541:2,2:31.1:1:30.1:1:0.0094:3.28355:59.2:43:0.5584:0.0451:0.5 1/0:218:141:26,115:18,56:0.6468:2,2:26.9:1:29.6:1:0.37388:1.41936:59.3:140:0.6542:0.133:0.3 -7 148505788 . T C 75 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAGATATGCATAGTATA;RSEQ=TGTCAAGTAAAACCATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:36.8:1:32.6:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 148505864 . G A 80 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGAAAACGCTCCACGAGT;RSEQ=AGCATGCAGCATGCGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:0.7:0,0:24.1:1:28.7:1:1:0:60:14:0.7:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 148506064 . A G 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=2.84921;LSEQ=TGCTCATGGCAAAGTGACCC;RSEQ=TCAAAAGAAGCAAAGAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:186:117:106,11:66,3:0.629:1,2:24.9:1:30.3:1:0.25937:2.27404:60:116:0.6339:0:1.1 1/1:152:126:118,8:26,0:0.8289:1,2:24.2:1:30.1:1:0.35221:0:60:252:0.8289:0:1.1 -7 148506274 . G A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01109;SOR=Inf;LSEQ=AGAGACACACTGGTGTCAGT;RSEQ=AGCATGAAGACGGGCCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:499:0:0,0:215,284:0:2,0:24:1:31.5:1:1:0:60:54.444:1:0:0.1 0/1:449:6:5,1:178,264:0.0134:2,2:14.3:1:25:1:0.04393:7.38:60:12:0.0135:0:1 -7 148506363 . T G 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGTCCATCATCACAGGAC;RSEQ=GAAAAGGGAGTTCCAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:622:0:0,0:346,276:0:2,0:26:1:30.5:1:1:0:60:61.2:1:0:0.1 0/1:567:35:21,14:305,227:0.0617:2,2:20.1:1:28.8:1:0.86048:1.12:60:34:0.0608:0:1.1 -7 148506754 . CA C 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTACTGAGCAAAACATAG;RSEQ=AAAAAAAAAAAAAATCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:39:1:32.5:1:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 148507365 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24944;SOR=0;LSEQ=CCTCGTTTCTGAACACTCGG;RSEQ=CGGCAGAAGGCTGCCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:210,71:0.0106:2,2:29.3:1:30.3:1:1:1.47665:60:6:0.0106:0:1 0/0:266:0:0,0:194,72:0:2,0:26.2:1:31.2:1:1:0:60:52.2:1:0:0.1 -7 148507534 . C CT 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGACACAGGAGAAAATT;RSEQ=TTTTGGATAAAGGTGATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:88,200:0:2,0:24.7:1:31.6:1:1:0:60:40.143:1:0:0.1 0/1:265:17:6,11:71,177:0.0642:2,2:23.8:1:30.4:1:0.58493:1.36:60:34:0.0644:0.0075:0.2 -7 148507556 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1809;SOR=Inf;LSEQ=TTTGGATAAAGGTGATCAAG;RSEQ=CTGACAGAACACACAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:44,157:0:2,0:23.4:1:31.4:1:1:0:60:99.5:1:0:0.1 0/1:150:2:1,1:29,118:0.0133:2,2:19.5:1:28.5:1:0.36323:4.02:60:4:0.0137:0:1 -7 148508481 . A G 69 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCAACTCCTGAGCTCAAGC;RSEQ=ATCCACCTGCCTCGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:31.6:1:30:1:1:0:60:10:0.5556:0:1 1/1:1:1:1,0:0,0:1:0,0:42:0:32:0:1:0:60:2:1:0:2 -7 148508656 . CTAAAA C 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTTACCTAATAAAATCAAT;RSEQ=TAAAGTAAAGTTAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:287,99:0:2,0:23.8:1:30:1:1:0:60:54.143:1:0:0.1 0/1:435:22:17,5:293,120:0.0506:2,2:22.7:1:31.2:1:0.63382:1.39:60:44:0.0515:0.0092:0.3 -7 148508821 . T C 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCAATAGATGCTAGAGAA;RSEQ=AAAACACAATCACATCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:476:0:0,0:153,322:0:2,0:25.1:1:28.8:1:1:0:60:78.167:0.9979:0:0.6 0/1:498:24:7,17:166,308:0.0482:2,2:23.3:1:30.7:1:0.66346:1.30823:60:23:0.0468:0:1.8 -7 148508833 . A G 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=1.90915;LSEQ=CTAGAGAATAAAACACAATC;RSEQ=CATCATCAAAAAAGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:393:245:72,173:33,115:0.6234:2,2:25.1:1:31.2:1:0.12823:1.45:60:80.667:0.6205:0:1.1 1/0:383:291:86,205:26,65:0.7598:2,2:24.7:1:30.6:1:0.89575:1.05:60:40.571:0.7594:0:1.1 -7 148512455 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23317;SOR=Inf;LSEQ=ACTGGGGATTCATCAGTAGA;RSEQ=GTCCTCCATTCAAATTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:65,3:0:1,0:22.6:1:32.1:1:1:0:60:67:1:0:0 0/1:64:2:1,1:60,2:0.0313:1,2:8:1:28.5:1:0.09226:24.69852:60:4:0.0317:0:1 -7 148512722 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24696;SOR=0;LSEQ=TGCTTAACTGGATCTATCTG;RSEQ=GCCATGAATACAGGAATGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:10,111:0.0163:2,2:16.5:1:31:1:0.17153:10.63:60:4:0.0163:0:1 0/0:124:0:0,0:20,104:0:2,0:21.4:1:29.9:1:1:0:60:123:1:0:0.1 -7 148513943 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23941;SOR=0;LSEQ=CATTCTTATACTCATGCATA;RSEQ=CAGAAAAATGTCTTTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:15,155:0.0116:2,2:35:1:31:1:0.17789:10.04:60:4:0.012:0:1 0/0:179:0:0,0:25,154:0:2,0:22.4:1:31.1:1:1:0:60:178:1:0:0.1 -7 148515269 . G GA 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.84708;LSEQ=AAACTCATTTTGATGGAAGA;RSEQ=AAAAAAAAATACTATATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:4:0,4:7,140:0.0261:1,0:28:1:31.3:1:1:0:60:8:0.0272:0:0 0/1:135:3:0,3:11,121:0.0222:2,0:15.7:1:31.7:1:1:0:60:6:0.0229:0:0.3 -7 148516878 . C T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01207;SOR=Inf;LSEQ=GTCAATTAATGGATTATAAT;RSEQ=TTGCTAATATGTGGTTTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:0:1,0:18.4:1:31.9:1:1:0:60:88:1:0:0 0/1:43:6:0,6:1,36:0.1395:1,0:14.8:1:31.2:1:1:0:60:12:0.1395:0:1 -7 148523604 . C T 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28772;SOR=2.9424;LSEQ=AAACATCGCCTACAGAAAAG;RSEQ=GTATGAAAGGAGTGTAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:2:0,2:309,276:0.0034:2,0:1:0:26.5:1:0.22387:0:60:4:0.0034:0:1 0/1:602:6:2,4:314,281:0.01:2,2:18:1:27.3:1:0.43001:2.23199:60:12:0.01:0:1.2 -7 148523709 . G A 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01991;SOR=Inf;LSEQ=GCGCCTGGGAGCTGCTGTTC;RSEQ=GTGAGTTCTTTATATCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:170,307:0:2,0:25.4:1:30.1:1:1:0:60:42.364:0.9957:0:0.1 0/1:405:5:2,3:153,247:0.0123:2,2:15.4:1:28.6:1:1:1.08:60:10:0.0124:0:1.2 -7 148523777 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50309;SOR=0;LSEQ=TGAAACAAAAATCACTTTTT;RSEQ=GAAAACAGTTTCTAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:18,123:0.014:2,2:8.5:1:29:1:0.24889:6.68:60:4:0.014:0:1 0/0:117:0:0,0:20,97:0:2,0:21.9:1:29.8:1:1:0:60:116:1:0:0 -7 148524380 . G GA 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.2522;SOR=Inf;LSEQ=TAAACAGGAGAATATGAAAG;RSEQ=AAAAAAAGAATGGAAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:53,187:0:2,0:22.5:1:31.2:1:1:0:60:79:1:0:0.1 0/1:276:3:2,1:82,191:0.0109:2,2:16.7:1:26:1:0.22059:4.63:60:6:0.0109:0.0036:0.7 -7 148525760 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2071;SOR=Inf;LSEQ=AGAAAGAAGAAACTAAGCCC;RSEQ=ATTTCTACTCTTTCTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:159,26:0:2,0:21.9:1:31:1:1:0:60:91.5:1:0:0.1 0/1:155:2:2,0:135,18:0.0129:2,0:10.5:1:31.5:1:1:0:60:4:0.0129:0:1 -7 148525904 . C G 254 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTCTCCATCATCATCATCGT;RSEQ=ATCATCATTATATTGACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:922:0:0,0:465,457:0:2,0:26.5:1:31.4:1:1:0:60:60.467:1:0:0.1 0/1:1011:292:155,137:369,349:0.2888:2,2:24.6:1:31.1:1:0.67691:1.07:60:145:0.2883:0:1.1 -7 148526807 . G A 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTTTTTCCAAGAGAAGAA;RSEQ=CATATGGCTCACCTCTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:0:0,0:397,249:0:2,0:26:1:32.2:1:1:0:60:70.778:1:0:0.1 0/1:613:38:22,16:337,237:0.062:2,2:28.2:1:29.6:1:1:1.0341:60:76:0.0629:0:1.1 -7 148527012 . C CT 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.5003;SOR=0;LSEQ=TGAAATAACTAAAATACAAC;RSEQ=TTTTTTTCATGTGTACATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:5,101:0.0185:1,2:34.5:1:30:1:0.10852:18.53:60:4:0.0187:0:0 0/0:93:0:0,0:0,93:0:1,0:19.8:1:32.5:1:1:0:60:92:1:0:0.1 -7 148529918 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49898;SOR=0;LSEQ=TAGCCATCATATTGTAAAGA;RSEQ=ATGCTGCCTACCCAAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:2,107:0.018:1,2:23.5:1:31:1:0.05356:43.88:60:4:0.0182:0:1 0/0:100:0:0,0:2,98:0:1,0:24:1:31.1:1:1:0:60:99:1:0:0.1 -7 148529946 . GA G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19948;SOR=Inf;LSEQ=CTACCCAAATATTTAATTTT;RSEQ=AAAAAAAGTCCTTACCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:1,69:0:1,0:23.5:1:30.7:1:1:0:60:140:1:0:0 0/1:57:2:0,2:1,54:0.0351:1,0:40.5:1:32:1:1:0:60:4:0.0357:0:0 -7 148543525 . A G 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=2.41788;LSEQ=CCAATAGCATAAACCAAAAG;RSEQ=TGATGATAATTACTACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:329:197:145,52:98,33:0.5988:2,2:24.7:1:31.1:1:0.89773:1.06481:60:48.25:0.5957:0:1.1 1/0:346:271:194,77:52,23:0.7832:2,2:23.4:1:30.7:1:0.77361:1.11:60:134.5:0.7843:0:1.1 -7 148543693 . TA T 229 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00102;SOR=1.71204;LSEQ=ATTGGAACTAAACATACTCT;RSEQ=AAAAAAAAAATGAAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:305:158:39,119:43,93:0.518:2,2:29:1:30.3:1:0.19474:1.40912:60:316:0.5215:0.023:0.1 1/0:341:221:63,158:37,69:0.6481:2,2:27.9:1:29.5:1:0.25061:1.34355:60:109.5:0.646:0.0499:0.3 -7 148543753 . C T 147 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTTAGAAAATGTATAACA;RSEQ=CTGTAAAGCAGGTTAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:6,100:0:2,0:25.5:1:31.7:1:1:0:60:212:1:0:0.1 0/1:92:34:1,33:0,58:0.3696:1,1:24.4:1:29:1:0.36957:0:60:33:0.3626:0:1 -7 149018755 . G A 79 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47773;SOR=1.86912;LSEQ=CAGTGCTTACTTAGCTCACT;RSEQ=ACAGTGCTGCTGTTGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:10,8:0.1429:2,2:18:1:28.7:1:1:1.57:60:6:0.1429:0:1 0/1:25:6:3,3:10,9:0.24:2,2:22:1:30.8:1:1:1.10643:60:12:0.24:0:1.3 -7 149031030 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24489;SOR=0;LSEQ=CTGCTGTCATTCTCTCCTGT;RSEQ=CGGCTGTTCTCTTGCGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:74,45:0.0165:2,2:20:1:28:1:1:1.63736:60:4:0.0165:0:1 0/0:123:0:0,0:77,46:0:2,0:21.4:1:30.5:1:1:0:60:19.5:1:0:0.1 -7 149031035 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2321;SOR=0;LSEQ=GTCATTCTCTCCTGTGCGGC;RSEQ=GTTCTCTTGCGCAGTGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:77,47:0.0159:2,2:19.5:1:31.5:1:1:1.63157:60:4:0.0159:0:1 0/0:135:0:0,0:83,52:0:2,0:22.5:1:30.1:1:1:0:60:270:1:0:0.1 -7 149031303 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10699;SOR=Inf;LSEQ=GAAGCAGAGGCAATGAATTA;RSEQ=GAAGGCAGTCCAATTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:72,32:0:2,0:24.3:1:31.1:1:1:0:59.6:51:1:0:0.1 0/1:95:3:1,2:65,26:0.0316:2,2:12.7:1:26:1:0.21056:4.90227:60:6:0.0319:0:1 -7 149031307 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49852;SOR=0;LSEQ=CAGAGGCAATGAATTACGAA;RSEQ=GCAGTCCAATTAAAGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:74,32:0.0185:2,2:5.5:1:28.5:1:0.51973:2.29256:60:4:0.019:0:1 0/0:99:0:0,0:69,30:0:2,0:21.1:1:30.5:1:1:0:59.3:32:1:0:0.2 -7 149031386 . C T 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00078;SOR=0.40962;LSEQ=CCTTGGGGGCTTTGAAATAA;RSEQ=ACCACCAGTGGTCTTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:46:25,21:98,105:0.1847:2,2:23.7:1:29.7:1:0.515:1.27:60:92:0.1862:0:1.1 0/1:283:24:11,13:135,124:0.0848:2,2:32.2:1:29:1:0.67052:1.2855:60:48:0.0854:0:1 -7 149031536 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24043;SOR=Inf;LSEQ=ATCTGGAAAGCAGTCTGCCC;RSEQ=TGGCGGTGGTAGCAAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:25,41:0:2,0:24.8:1:31.4:1:1:0:59.9:32:1:0:0.1 0/1:64:2:1,1:20,42:0.0313:2,2:22.5:1:30:1:1:2.07:60:4:0.0317:0:1 -7 149031681 . A G 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=CTCCAAGCCAAAAATGCACA;RSEQ=AAGTCAAATCAGAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:44,45:0:2,0:25.1:1:30.4:1:1:0:60:178:1:0:0.1 0/1:74:10:3,7:30,33:0.1351:2,2:27.1:1:31.6:1:0.49586:2.10038:60:20:0.1389:0:1.2 -7 149031692 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2051;SOR=Inf;LSEQ=AAATGCACAAAAGTCAAATC;RSEQ=GAATGGAAAAGACTCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:43,47:0:2,0:24.9:1:30.2:1:1:0:60:44:1:0:0.1 0/1:75:2:1,1:33,40:0.0267:2,2:15:0:32:0:1:1.21:60:4:0.0267:0:2 -7 149031853 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18928;SOR=Inf;LSEQ=AAAAAGGTGGTTCTATTCCC;RSEQ=CAGTGGAAGCCAAGTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:15,22:0:2,0:21.2:1:29.1:1:1:0:59.9:36:1:0:0 0/1:29:2:1,1:13,14:0.069:2,2:32:1:29.5:1:1:1.07:60:4:0.069:0:1 -7 149031988 . C CTCATT 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=ATTTATTAAAAAATTTTCAT;RSEQ=TCATTTCTGTAACAGTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:1,6:0.3:2,2:20.3:1:31.7:1:1:2.65:60:6:0.3:0.1:0.3 0/0:4:0:0,0:1,3:0:2,0:19.3:1:30.5:1:1:0:60:8:1:0:0.3 -7 150485659 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTCTCCCTGTGTCCTCA;RSEQ=GTGGCCTTCCCTCTGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 150485701 . A G 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGCATTCTGATTGCCTCT;RSEQ=ATATGACATCAGACATATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:19.3:1:32.5:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 150485864 . G A 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02544;SOR=0.23182;LSEQ=ACAAAAATTCAGCCTCTCAC;RSEQ=CCCACCACCTCCCACCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:16:16,0:19,0:0.4571:1,1:16.8:1:30.3:1:1:0:60:32:0.4848:0:1.1 0/1:25:4:4,0:21,0:0.16:1,0:18.3:1:30.3:1:1:0:60:8:0.1667:0:1 -7 150486019 . C T 50 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11979;SOR=5.15453;LSEQ=CTGAATATCAACATCTGTGA;RSEQ=AACTAAAAGACAACCCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:1:0,1:257,187:0.0022:2,0:1:0:23:0:0.42247:0:60:2:0.0023:0:1 0/1:435:5:1,4:239,191:0.0115:2,2:5:1:21.6:1:0.17828:4.98924:60:4:0.0093:0:1.8 -7 150486083 . G A 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.09992;SOR=0.81317;LSEQ=TGGAGTCAGGGTGGTGAGTG;RSEQ=GCAAGTAACTCAGTCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:242:111,131:116,139:0.4859:2,2:27.1:1:30.4:1:1:1.02:60:39.333:0.4807:0:1.1 0/1:596:259:116,143:160,177:0.4346:2,2:25.8:1:29.7:1:0.56196:1.11415:60:128.5:0.4349:0:1.1 -7 150486169 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24508;LSEQ=GCGTTCTCATGGCTGTTCAC;RSEQ=ACATGAGCAACGGCAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:63:13,50:10,82:0.4038:2,2:24.5:1:29.4:1:0.11002:2.12:60:30.5:0.3987:0:1 0/1:134:19:3,16:17,98:0.1418:2,2:27:1:30.3:1:1:1.08:60:38:0.1429:0:1.1 -7 150486191 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15469;SOR=Inf;LSEQ=CATGAGCAACGGCAAGCTCA;RSEQ=GGTGCTCTGCCCCTGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:6,112:0:2,0:25:1:31.2:1:1:0:60:117:1:0:0.4 0/1:77:2:1,1:3,72:0.026:1,2:15:0:32.5:1:0.10185:20.93:60:4:0.026:0:1.5 -7 150794726 . G C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTCAGGGAGCTTTTTAC;RSEQ=GGTGGCAGAAAGCAAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 150904933 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49629;SOR=0;LSEQ=AGGGCACAGAAACAGTTCAC;RSEQ=CTTTATTTTTGTCAGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:33,19:0.037:2,2:22:1:30.5:1:1:1.71824:60:4:0.0377:0:1 0/0:49:0:0,0:31,17:0:2,0:19.2:1:30.2:1:1:0:60:96:0.9796:0:0.1 -7 151164348 . G A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.45031;LSEQ=TTAGTGTGAAGCCGAACTCC;RSEQ=AGAGTATTTTACGGACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:578:341:86,255:55,181:0.59:2,2:22.5:1:30.1:1:0.6233:1.11:60:67.2:0.5905:0:1.1 0/1:514:202:55,147:87,225:0.393:2,2:21.6:1:29.5:1:0.91969:1.0334:60:201:0.3941:0:1.2 -7 151164378 . C T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.32112;SOR=3.95086;LSEQ=TACGGACTGAGGAGGGCGTG;RSEQ=CGCCTGCCCTGCCCTCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:0,1:32,268:0.0033:2,0:35:0:32:0:1:0:60:2:0.0034:0:1 0/1:231:3:1,2:23,205:0.013:2,2:14:1:28:1:0.28152:4.41:60:6:0.0133:0:1.3 -7 151164470 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCAGTAAGGCCACTGTC;RSEQ=ACCCCTCCTGACCCAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:0,58:0.0333:1,2:21.5:1:27:1:0.03333:0:60:4:0.0345:0:1 0/0:26:0:0,0:0,26:0:1,0:27.9:1:32.7:1:1:0:60:52:1:0:0 -7 151164622 . T TG 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCACCCCAGTGTCCTC;RSEQ=GACCTCAGGGTCCCTCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:18.3:1:33:0:1:0:60:6:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 151164844 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=GCCCTCCCTATCTCCTGGCC;RSEQ=CTCCTCTCCTGCCCGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:19.7:1:29.7:1:1:0:60:6:1:0:0.7 1/1:2:2:1,1:0,0:1:0,2:10:1:31:1:1:0:60:4:1:0:1 -7 151167575 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59918;SOR=2.31673;LSEQ=ACACAGGAGTGATCAAGACA;RSEQ=AGGTCAAATGCCAACTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:1:0,1:191,33:0.0044:2,0:1:0:23:0:0.15111:0:60:2:0.0045:0:1 0/1:195:2:1,1:156,37:0.0103:2,2:20.5:1:27:1:0.35258:4.17369:60:4:0.0104:0:1 -7 151168415 . CAAT C 270 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.00141;SOR=0.69208;LSEQ=AAATATTCTTGACATCAGAA;RSEQ=AATTAAAATGATACTTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:654:341:235,106:222,92:0.5214:2,2:25.3:1:32.1:1:0.67037:1.0883:60:682:0.523:0.0474:0.2 0/1:584:251:164,87:238,92:0.4298:2,2:23.1:1:30.9:1:0.08524:1.37157:60:250:0.431:0.0976:0.2 -7 151168534 . G A 275 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.48766;LSEQ=ACATAATAGGTATTCTATTT;RSEQ=TAAGAAAAAAAAGACAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1183:650:342,308:263,263:0.5495:2,2:25.7:1:29.5:1:0.37933:1.11:60:80.25:0.5487:0:1.1 0/1:1164:434:217,217:352,374:0.3729:2,2:23.8:1:28.7:1:0.62772:1.06:60:85.8:0.3718:0:1.1 -7 151168756 . G A 200 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02179;LSEQ=AGTTTTTAAATGTATGTTAT;RSEQ=TTGCCAGCTGGAAAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:93:19,74:92,322:0.1831:2,2:23.5:1:30.6:1:0.78221:1.11256:60:186:0.1849:0:1.2 0/0:413:2:1,1:98,312:0.0048:2,2:22:1:26.5:1:0.42329:3.17:60:4:0.0049:0:1 -7 151168830 . C T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10617;SOR=0.60368;LSEQ=AAAATGAACACAAAGAACTC;RSEQ=TGTTTTTTCCTAGCAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:74:0,74:2,61:0.5401:1,1:23:1:30.4:1:0.20964:0:60:73:0.5407:0:1.3 0/1:70:29:1,28:0,41:0.4143:1,1:23.4:1:30.3:1:0.41429:0:60:58:0.4203:0:1.1 -7 151174049 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATTCAAAGGATAAGATA;RSEQ=TGAACAAACCCAAACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:18.5:1:30:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 151174286 . C A 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05918;SOR=0.56474;LSEQ=CCAGCAATCCAGTTGCTCCA;RSEQ=GAGAAAATCACTAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:112:61:61,0:51,0:0.5446:1,1:24:1:30.7:1:1:0:60:122:0.5495:0:1.1 0/1:82:33:33,0:47,2:0.4024:1,1:22.1:1:30.8:1:0.5131:0:60:66:0.4024:0:1 -7 151174509 . GA G 105 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.34678;SOR=1.66646;LSEQ=TAGAATATTCATCCTGTGGG;RSEQ=AAAAAAATTATCTTTGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:897:7:3,4:335,554:0.0078:2,2:33.3:1:30.9:1:1:1.24:60:14:0.008:0:0 0/1:850:11:4,7:362,477:0.0129:2,2:28.4:1:30.5:1:0.76541:1.32766:60:22:0.0131:0.0024:0.3 -7 151175458 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGAATTACTGCCCTATG;RSEQ=TAAAGTTCTTTAAAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:20.7:1:29.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 151187851 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGATGGCAGGGGATGCAG;RSEQ=CATGGAAGGAAAAATCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:2,0:92,1:0.0208:1,0:29:0:33:0:1:0:60:4:0.0213:0:1 0/0:40:0:0,0:37,3:0:2,0:23:1:30:1:1:0:60:80:1:0:0.1 -7 151216510 . C T 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03062;SOR=Inf;LSEQ=GCTCCCAGGCGAGGCCCCGG;RSEQ=GGCGCGAGGAGGCCGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:208,82:0:2,0:17.7:1:31.5:1:1:0:60:71.5:1:0:0.2 0/1:301:6:2,4:200,94:0.0199:2,2:17.3:1:28.8:1:0.09151:4.23275:60:12:0.0203:0:1 -7 151216513 . C T 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.74736;SOR=0.76317;LSEQ=CCCAGGCGAGGCCCCGGCGG;RSEQ=GCGAGGAGGCCGCGCGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:5:2,3:220,88:0.016:2,2:17.6:1:28.2:1:0.14932:3.73178:60:10:0.0161:0:1.4 0/1:327:4:2,2:212,111:0.0122:2,2:12:1:27.5:1:0.61089:1.90594:60:8:0.0125:0:1.5 -7 151216692 . G T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12401;SOR=Inf;LSEQ=CGGCCGCGCCGGGAGAGAGC;RSEQ=GCATACAGAGCAGGGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:59,239:0:2,0:23.5:1:30.6:1:1:0:45.1:36.25:1:0:0.2 0/1:309:4:2,2:67,237:0.0129:2,2:15.5:1:29:1:0.21786:3.52:47:8:0.0132:0:1 -7 151216693 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24882;SOR=Inf;LSEQ=GGCCGCGCCGGGAGAGAGCG;RSEQ=CATACAGAGCAGGGGCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:53,235:0:2,0:23.5:1:31.8:1:1:0:45:40.143:0.9965:0:0.2 0/1:296:3:2,1:62,231:0.0101:2,2:14:1:24:0:0.11905:7.38:47.7:6:0.0102:0:1 -7 151216793 . C T 30 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GCGCGGCGGCGCCCCTCCCC;RSEQ=CCACAACACGCCCACGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:0:32:1:1:0:47:4:1:0:1 0/1:6:2:1,1:2,2:0.3333:2,2:15:1:30.5:1:1:1:47:4:0.3333:0:1 -7 151430709 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08773;LSEQ=AAAAGTCATCTTTTTAGACC;RSEQ=TGTTAGTGAGTCTCCCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:337:295:149,146:23,17:0.8754:2,2:26.2:1:29.9:1:0.50063:1.32459:60:41.143:0.8754:0:1.2 0/1:334:127:63,64:105,102:0.3802:2,2:25.6:1:29.6:1:0.91031:1.04564:60:62.5:0.3811:0:1.2 -7 151430890 . T C 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.12958;LSEQ=CTCCCAGGCTCAAGCGATCT;RSEQ=CCCACTTCAGCTTTCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:0,5:0,17:0.2273:1,0:36.4:1:31.2:1:1:0:60:10:0.2273:0:1 0/1:16:4:0,4:0,12:0.25:0,0:14.3:1:32.3:1:1:0:60:8:0.25:0:1 -7 151478602 . T C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.6567;SOR=1.95517;LSEQ=TATGAAACTTATCATTGTCC;RSEQ=CTCTCACATGCGGGCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:4,8:1,3:0.75:2,2:21.1:1:31.7:1:1:1.46:60:24:0.75:0:1.8 1/1:14:12:4,8:1,1:0.8571:2,2:19.1:1:29.4:1:1:1.89743:60:24:0.8571:0:1.5 -7 151478613 . C T 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19681;SOR=0.25669;LSEQ=TCATTGTCCTCTCTCACATG;RSEQ=GGGCCCCCCATAGTACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:3,4:0,5:0.5833:0,2:19.4:1:29.4:1:0.20455:0:60:14:0.5833:0:2.1 0/1:8:2:0,2:1,5:0.25:2,0:16.5:1:29.5:1:1:0:60:4:0.25:0:3 -7 151828793 . T C 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=CTGGAACGCTGTTCCCACCA;RSEQ=GTTGGGTTACGTTGTAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:15:9,6:30,18:0.2381:2,2:25.1:1:30.3:1:1:1.10924:60:30:0.2459:0:1.1 0/0:54:0:0,0:27,27:0:2,0:24.2:1:29:1:1:0:60:108:1:0:0.1 -7 151828824 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22786;SOR=Inf;LSEQ=GTTGTAGGTTTGGCCGAAGT;RSEQ=AGCGTGGCGAGAGCAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:38,37:0:2,0:29.5:1:31.9:1:1:0:60:150:1:0:0.4 0/1:69:2:1,1:31,36:0.029:2,2:14.5:1:31:1:1:1.16:60:4:0.029:0:2 -7 151828951 . A AG 76 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCAGGGCTGGAGTGAGGG;RSEQ=GGGTAGTGGGAGGAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:19.5:1:29.6:1:1:0:60:12:1:0.1667:0 1/1:2:2:0,2:0,0:1:0,0:27.5:1:28.5:1:1:0:60:4:1:0:0 -7 151830436 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCAGGCTCAAGTGATCC;RSEQ=CCTGCCTCAGCCTCCCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 151830890 . G C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCACGTGACATGGGGCCAAA;RSEQ=GAGGATAGGAGAAGCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:19.3:1:24.3:1:1:0:60:2:1:0:1 1/0:4:2:1,1:1,1:0.5:2,2:34.5:1:29.5:1:1:1:60:4:0.5:0:1 -7 151833641 . CA C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACAAAACAAAAAACAAA;RSEQ=AAAAAAAAAGAAAAGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:14.5:1:31.6:1:1:0:60:4:0.1667:0.0833:0 0/0:2:0:0,0:2,0:0:0,0:27.5:1:31:1:1:0:60:4:1:0:0 -7 151833826 . A G 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01759;SOR=Inf;LSEQ=AAGTCATAAAACAGAAAACA;RSEQ=AAATCTCTTTCTGTCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:118,11:0:2,0:20.6:1:30.4:1:1:0:60:63.5:1:0:0.1 0/1:157:7:7,0:130,20:0.0446:2,0:32.7:1:32.9:1:0.59648:0:60:14:0.0458:0:1 -7 151836188 . CT C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49861;SOR=0;LSEQ=CGCCAGGCTGCCGTGAGAGC;RSEQ=TTCCCTTGGCTTCAGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:121,32:0.0129:2,2:36:1:32:1:0.38157:3.739:60:4:0.0129:0:0 0/0:148:0:0,0:112,36:0:2,0:21.1:1:30.3:1:1:0:60:296:1:0:0.1 -7 151836228 . C T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTCTCCACCAGCACTGGCC;RSEQ=CACAAGCAAAAGCACTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:161,89:0:2,0:24.6:1:30.6:1:1:0:60:61.5:1:0:0.1 0/1:260:17:10,7:153,90:0.0654:2,2:20.4:1:29.3:1:0.79742:1.18918:60:16:0.0635:0:1.3 -7 151836397 . T C 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00736;SOR=0;LSEQ=GTCGACCTGAAACTCCCCTC;RSEQ=GTGTTCCTATCCACACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:8:3,5:66,146:0.0362:2,2:24.9:1:26.1:1:0.7081:1.33:60:7:0.0323:0:1 0/0:215:0:0,0:60,154:0:2,0:21.6:1:29.9:1:1:0:60:41.8:0.9952:0:0.1 -7 151836659 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25257;SOR=0;LSEQ=TTTGTTTAAAGCTGAATGCA;RSEQ=CATGACAGATTTCATTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:1,2:189,8:0.015:1,2:8.7:1:28:1:0.0066:43.8613:60:6:0.0152:0:1 0/0:171:0:0,0:155,16:0:2,0:23.6:1:32.2:1:1:0:60:170:1:0:0.1 -7 151836878 . T TA 125 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02228;SOR=2.38854;LSEQ=CAGCATACAGGCCCAGCCCC;RSEQ=AAAAAAAAGTGTGTACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:666:11:5,6:227,425:0.0165:2,2:29.6:1:28.6:1:0.52856:1.56:60:22:0.0168:0:0 0/1:596:23:13,10:228,343:0.0386:2,2:21.6:1:27.7:1:0.13111:1.95:60:46:0.0387:0.0084:0.3 -7 151836945 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23953;SOR=Inf;LSEQ=TTTTCTGTTTTTCATACAAA;RSEQ=GTTTCACCCTCGGGTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:12,168:0:2,0:23.3:1:30.9:1:1:0:60:44:0.9944:0:0.1 0/1:174:2:1,1:32,140:0.0115:2,2:14.5:1:28.5:1:0.34423:4.32:60:4:0.0116:0:1.5 -7 151841593 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=GGATTCCACTGGTCTGCTTT;RSEQ=CCTTTGGGGAAGCCAATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:17,0:0:1,0:25.9:1:30.8:1:1:0:60:34:1:0:0.1 0/1:13:2:1,1:11,0:0.1538:0,2:30.5:1:28:1:0.15385:0:60:4:0.1538:0:1 -7 151842217 . T C 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=AGAAACCCTGGGCTGTACTA;RSEQ=GTGAAGTTAAAACAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:461:0:0,0:306,155:0:2,0:24.5:1:30.5:1:1:0:60:75.833:1:0:0.1 0/1:423:14:10,4:274,135:0.0331:2,2:26.2:1:30.1:1:1:1.23:60:28:0.0336:0:1.2 -7 151842397 . C T 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.00021;SOR=Inf;LSEQ=GAAGCTGAAAAGAAGCAAAG;RSEQ=AGACACAAAGTCACCCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:113,289:0:2,0:24:1:31.9:1:1:0:60:56.429:0.9975:0:0.1 0/1:353:11:5,6:103,239:0.0312:2,2:24.2:1:27.6:1:0.3221:1.93:60:22:0.0318:0:1.2 -7 151843635 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50027;SOR=0;LSEQ=CATGTGTTCAAGTGGTCACA;RSEQ=TGAATCAGGAAAGCAATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:160,33:0.0103:2,2:18.5:1:32.5:1:0.31906:4.79162:60:4:0.0103:0:1 0/0:174:0:0,0:131,43:0:2,0:49:0:16:0:1:0:60:0:0:0:7 -7 151843648 . G T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69272;LSEQ=GGTCACACTGAATCAGGAAA;RSEQ=CAATTCCAATCTCAAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:3:1,2:181,63:0.0121:2,2:17:1:28.7:1:0.17018:5.69682:60:6:0.0123:0:1 0/0:237:2:0,2:170,65:0.0084:2,0:1:0:24:1:0.07906:0:60:4:0.0085:0:1 -7 151844858 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCAATGCAAATGACAGGC;RSEQ=ACCTTTATCTACAAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:9,1:0.1667:2,2:21:1:29:1:0.31818:6.70817:60:4:0.1667:0:1 0/0:2:0:0,0:2,0:0:0,0:32:1:32:0:1:0:60:4:1:0:0 -7 151846291 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=ATAATTCACAAGCCCGGAAA;RSEQ=CAATTCTTGTTAAGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:27,144:0:2,0:23.9:1:31.9:1:1:0:60:56:1:0:0 0/1:143:2:1,1:19,122:0.014:2,2:18.5:1:28.5:1:0.26101:6.28:60:4:0.0141:0:1 -7 151847840 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13664;SOR=Inf;LSEQ=AAGGCTCCCTACACCCTCTC;RSEQ=TCCTCTGCCGGGTCAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:50,2:0:1,0:21.1:1:31:1:1:0:60:104:1:0:0 0/1:31:2:1,1:29,0:0.0645:1,2:18:1:28.5:1:0.06452:0:60:4:0.0667:0:1 -7 151847946 . G T 46 Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05763;SOR=0;LSEQ=CCAGAACACAGAAGTCACTC;RSEQ=TTACACATTGTTATCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:4:0,4:201,77:0.0142:2,0:5.8:1:23:1:0.00645:0:60:3:0.0108:0:1 0/0:292:0:0,0:196,96:0:2,0:23.9:1:30:1:1:0:60:291:1:0:0.1 -7 151849692 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22688;SOR=Inf;LSEQ=GGACTATACGCCAGCATGTT;RSEQ=CCTGTCCGTTGTTAAAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:89,5:0:2,0:22.2:1:28.5:1:1:0:60:188:1:0:0.1 0/1:86:2:1,1:77,7:0.0233:2,2:27.5:1:31.5:1:0.17839:10.35624:60:4:0.0235:0:1 -7 151851197 . C T 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAAAATATAAAGTGCCTGG;RSEQ=TCAGTTTTGATGTCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:816:0:0,0:353,460:0:2,0:26.4:1:31.8:1:1:0:60:41.789:0.9962:0:0.1 0/1:748:35:17,18:320,392:0.0468:2,2:28.4:1:29.6:1:0.72933:1.16:60:70:0.0471:0:1.1 -7 151851275 . T A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06427;SOR=Inf;LSEQ=AGGAAAATAGTGTTAATGGA;RSEQ=TTTCAAAATCAAAATATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:217,211:0:2,0:24.5:1:30.6:1:1:0:60:84.6:1:0:0.1 0/1:287:3:2,1:123,161:0.0105:2,2:16.3:1:25.7:1:0.5819:2.61:60:2:0.007:0:2.3 -7 151851663 . G C 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12013;SOR=3.90972;LSEQ=CTATACGATGAGCAGCAAAT;RSEQ=AATCAGCTCAGAGCCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:0,2:2,40:0.0444:1,0:33:1:33:1:1:0:60:4:0.0465:0:1 0/1:32:5:0,5:2,25:0.1563:2,0:22.4:1:31.4:1:1:0:60:10:0.1563:0:1 -7 151852951 . AG A 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01603;SOR=Inf;LSEQ=ATACATTTATTTTTTTTAAA;RSEQ=AAGAAATAACTAAGAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:117,18:0:2,0:24.8:1:32.5:1:1:0:60:134:1:0:0.1 0/1:155:7:5,2:121,27:0.0452:2,2:29.9:1:30.1:1:0.61576:1.78472:60:14:0.0455:0.0065:0.6 -7 151853470 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50223;SOR=0;LSEQ=TTTAAATTATATGCTACTGA;RSEQ=CGAATATGCAATGACCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:32,118:0.0132:2,2:40.5:1:29.5:1:0.3882:3.65:60:4:0.0132:0:1 0/0:127:0:0,0:33,94:0:2,0:22.5:1:31.8:1:1:0:60:126:1:0:0.1 -7 151854778 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11064;SOR=Inf;LSEQ=AACTAAATACAAAAATAAGA;RSEQ=AAGCTCTATCAATTCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:241,59:0:2,0:22.2:1:32.2:1:1:0:60:600:1:0:0.1 0/1:278:3:1,2:209,66:0.0108:2,2:17.3:1:26.3:1:0.1492:6.28048:60:6:0.0109:0:2 -7 151855878 . G T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59255;SOR=2.41933;LSEQ=CCAAAGTGCTGGGATTACAG;RSEQ=CATGAGCCACTGCCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:0,1:198,18:0.0046:2,0:1:0:25:0:0.08756:0:60:2:0.0047:0:1 0/1:181:2:1,1:168,11:0.011:2,2:23:1:24.5:1:0.12855:14.6648:60:4:0.0112:0:1 -7 151859061 . T TAGAAATG 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=2.000;MSILEN=7;SSF=0.01309;SOR=0;LSEQ=AAACATGGGTTCCAGAGAGG;RSEQ=AGAAATGACAAAATAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:10:10,0:63,1:0.1333:1,0:22.5:1:31.1:1:1:0:60:20:0.137:0.0533:0 0/0:43:0:0,0:41,2:0:1,0:20.6:1:29.9:1:1:0:60:20.5:1:0:0 -7 151859129 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10413;SOR=Inf;LSEQ=AATAATGTGGAAATACAGTT;RSEQ=CTGGTACTAATCTGCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:221,30:0:2,0:23.7:1:32.1:1:1:0:60:49.2:1:0:0.1 0/1:224:3:1,2:190,31:0.0134:2,2:11:1:26.3:1:0.05752:12.02486:60:6:0.0135:0:1 -7 151859670 . G T 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATTGGGAGTGGATGGGCC;RSEQ=ACTGGTTCCACCGACTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:675:0:0,0:343,331:0:2,0:24.5:1:30.5:1:1:0:60:83.25:0.9985:0:0.1 0/1:620:31:14,17:306,282:0.05:2,2:19.1:1:29:1:0.46771:1.31704:60:30:0.0492:0:1.1 -7 151859683 . G A 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGGCCGACTGGTTCCACC;RSEQ=ACTCTTGGTCGGCTTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:0:0,0:347,298:0:2,0:25.3:1:30.3:1:1:0:60:63.5:0.9984:0:0.1 0/1:637:46:26,20:315,276:0.0722:2,2:24:1:29.7:1:0.75951:1.14:60:92:0.073:0:1.1 -7 151866412 . GA G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50441;SOR=0;LSEQ=AAAACTTTAAAAGAAAGAAA;RSEQ=AAAAAAGAAATGGAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:6,101:0.0183:2,2:34.5:1:30:1:0.12487:15.66:60:4:0.0183:0:3.5 0/0:86:0:0,0:9,77:0:2,0:23.3:1:29.7:1:1:0:60:172:1:0:0.1 -7 151868207 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51564;SOR=0;LSEQ=AATTGCGGTTTTTGCCACTG;RSEQ=CAAATGGCATATGGTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:106,1:0.0183:1,0:20.5:1:31.5:1:1:0:60:4:0.0189:0:1 0/0:74:0:0,0:74,0:0:1,0:23.2:1:31.4:1:1:0:60:73:1:0:0 -7 151871381 . T C 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58956;SOR=2.46892;LSEQ=GTAATTAGTTCAACGTACAC;RSEQ=AAGAAGTAATTCAAATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:1:0,1:26,172:0.005:2,0:50:0:14:0:1:0:60:0:0:0:2 0/1:162:2:1,1:27,133:0.0123:2,2:11:1:29:1:0.31669:4.86:60:4:0.0126:0:1 -7 151873255 . G C 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TACCCATAGTAATATACGTT;RSEQ=AGACTCAAGAAAACTCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:0:0,0:477,244:0:2,0:26:1:31.9:1:1:0:60:64.545:1:0:0.1 0/1:584:21:15,6:336,226:0.036:2,2:20.2:1:31.5:1:0.36616:1.68:60:42:0.0366:0:1.4 -7 151873853 . C T 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.74854;LSEQ=GCAGGTAGTTGAGTGGATGC;RSEQ=TGAATGACATTTGCACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1014:342:175,167:346,325:0.3373:2,2:24.2:1:30.5:1:0.94702:1.01593:60:84.5:0.3404:0:1.1 0/1:1032:486:251,235:260,285:0.4709:2,2:26.3:1:30.1:1:0.21258:1.17:60:43.182:0.4689:0:1.2 -7 151874060 . T C 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTTAGAATTTGGAGACAG;RSEQ=ACTTCCGTTTTTACCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1245:0:0,0:632,613:0:2,0:25.6:1:29:1:1:0:60:112.182:1:0:0.1 0/1:1238:57:26,31:612,568:0.046:2,2:22.6:1:31.7:1:0.41595:1.2844:60:56:0.0456:0:1.2 -7 151874147 . CT C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.79835;SOR=0.92955;LSEQ=AGAGTTTTGTTTTCTTGTTC;RSEQ=TTTTTTTTGGTTCAACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:33:12,21:316,456:0.0408:2,2:27.3:1:31.9:1:0.71834:1.21243:60:66:0.0414:0.005:0.4 0/1:788:30:13,17:311,446:0.0381:2,2:28.6:1:31:1:0.85108:1.10:60:60:0.0385:0:0.1 -7 151874498 . C T 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00253;SOR=5.50756;LSEQ=TCCTCTAGACCATCAGAAGG;RSEQ=TGGGTGGTTATCTGTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:616:3:1,2:278,334:0.0049:2,2:23.3:1:26:1:1:1.66335:60:6:0.005:0:1.3 0/1:647:17:6,11:301,329:0.0263:2,2:29.9:1:29.8:1:0.33681:1.676:60:34:0.0266:0:1.2 -7 151874581 . G C 217 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTGAAAATTCACCACCTA;RSEQ=TGGATGGTTCAGAGTCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:114:60,54:282,254:0.1746:2,2:23.6:1:31.8:1:1:1.00:60:56:0.1742:0:1.1 0/0:670:0:0,0:357,312:0:2,0:24.8:1:31.5:1:1:0:60:166.25:0.9985:0:0.1 -7 151875047 . G A 192 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02849;LSEQ=TGCTGAGGAGGCACAAGGAA;RSEQ=CGCTCTTGACTCGGCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:86:28,58:158,211:0.189:2,2:29:1:30:1:0.0889:1.54965:60:172:0.1982:0:1.2 0/0:456:3:0,3:190,262:0.0066:2,0:13:1:15.3:1:0.26877:0:60:0:0:0:6.3 -7 151875091 . C A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25837;SOR=0;LSEQ=ATGACTACCTCCTGGAAATC;RSEQ=AAATCTTTTAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:2,1:66,180:0.012:2,2:16:1:22.7:1:0.18191:5.41:60:2:0.0102:0:3 0/0:199:0:0,0:74,125:0:2,0:29:0:16:0:1:0:60:0:0:0:3 -7 151876744 . TGGG T 67 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=15.000;MSILEN=1;SSF=0.34372;SOR=2.60131;LSEQ=TTTAAATTTGTTGAAGAGGT;RSEQ=GGGGGGGGGGGGTGGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:4,0:15,0:0.1379:1,0:20.8:1:33.5:1:1:0:60:8:0.1429:0:1.5 0/1:10:3:3,0:4,1:0.3:2,0:12.7:1:33:1:1:0:60:6:0.3333:0:0 -7 151878923 . T C 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCCTAGGAGATGGTTTAG;RSEQ=AAAGTGATCACTGGTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:735:0:0,0:370,365:0:2,0:26.1:1:28.7:1:1:0:60:65.818:1:0:0.1 0/1:546:19:10,9:273,254:0.0348:2,2:29.2:1:31.7:1:1:1.03:60:38:0.0353:0:1.1 -7 151879433 . G A 181 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=67.82519;LSEQ=ATCTGAAGATGTAGACGTAG;RSEQ=GGTACTGGGTGGCTGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1170:1:1,0:561,607:9e-04:2,0:1:0:25:0:0.48075:0:60:2:9e-04:0:1 0/1:1184:65:30,35:551,568:0.0549:2,2:27.9:1:30.1:1:0.70225:1.13163:60:31.5:0.0541:0:1.2 -7 151879937 . A G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18087;SOR=Inf;LSEQ=ATTTTACTGAAAAGAGAAAC;RSEQ=AGTCTATCCTAAATCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:174,1:0:1,0:25.8:1:30.5:1:1:0:60:174:1:0:0.1 0/1:130:2:2,0:127,1:0.0154:1,0:17.5:1:26:1:1:0:60:4:0.0157:0:1 -7 151882411 . C T 87 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTCCTTCCCCCCTAAAA;RSEQ=AGCTGATTTTCAATCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:24.5:1:32.3:1:1:0:60:12:1:0:1.2 1/1:7:7:6,1:0,0:1:0,2:23.6:1:31:1:1:0:60:14:1:0:1.1 -7 151882564 . G GT 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.68972;SOR=0.58148;LSEQ=ATTTTCTGAAATGGAAATTT;RSEQ=TTTTTTATTAACCTAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:4:4,0:101,22:0.0315:2,0:24.5:1:30.8:1:1:0:36.5:8:0.0317:0.0157:0 0/1:108:2:1,1:91,15:0.0185:2,2:23.5:1:28:1:0.27553:5.90624:40.5:4:0.0185:0.0093:0.5 -7 151882622 . TAG T 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.93105;SOR=1.02735;LSEQ=GTATTTAAATATTTAAAAGA;RSEQ=AGGAGTTTCTTAAAATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:87:53,34:206,100:0.2214:2,2:24.4:1:30.4:1:0.30532:1.32051:51.4:174:0.2237:0.0814:0.2 0/1:376:85:56,29:178,115:0.2261:2,2:23.3:1:30.1:1:0.44713:1.25:50.9:170:0.2285:0.0479:0.3 -7 151882672 . C A 131 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCTTTCTTGTGAGCTTG;RSEQ=TTTTCTCCACAATTTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:0:0,0:289,257:0:2,0:27.8:1:31.9:1:1:0:56.1:77:1:0:0.2 0/1:641:21:10,11:313,303:0.0328:2,2:29.4:1:30:1:0.82697:1.13607:52.8:42:0.033:0:1.2 -7 151882735 . G A 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06924;SOR=1.50157;LSEQ=ATCTGCAACAAAAGAACAGA;RSEQ=TATAACACTTTCTCAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:42:12,30:110,190:0.1228:2,2:13.7:1:30.5:1:0.39017:1.44587:41.6:84:0.1235:0:1.2 0/1:351:61:11,50:114,176:0.1738:2,2:14.3:1:29.8:1:0.00181:2.93607:44.5:29.5:0.17:0:1.2 -7 151882775 . A T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46958;SOR=1.44021;LSEQ=CATGCTAATGATGTGTTGTA;RSEQ=TAAAGAATGTTGATGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:9:0,9:43,143:0.0462:2,0:30.1:1:30.2:1:0.21074:0:23.7:18:0.0471:0:2.1 0/1:138:9:0,9:26,103:0.0652:2,0:19.9:1:30.9:1:0.20785:0:28.6:18:0.0657:0:2 -7 151882841 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5461;SOR=0;LSEQ=TATTCTCATGAGGTCATAGA;RSEQ=CTATATTAAGTTTTTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:0,2:0,59:0.0323:1,0:14:1:31:0:1:0:21:4:0.0328:0:2 0/0:32:0:0,0:0,32:0:1,0:4:0:18:0:1:0:27:0:0:0:2 -7 151884270 . T C 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03206;SOR=Inf;LSEQ=AATTAGTTAAGCTACCTTTC;RSEQ=ATTGCAGTTAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:114,8:0:2,0:22.8:1:31.1:1:1:0:60:121:1:0:0.5 0/1:91:4:4,0:80,7:0.044:2,0:20.5:1:31.3:1:1:0:58.8:8:0.0455:0:2.5 -7 151884272 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50745;SOR=0;LSEQ=TTAGTTAAGCTACCTTTCTA;RSEQ=TGCAGTTAAAAAAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:118,7:0.0157:2,2:27:1:29:1:0.12248:15.82823:60:4:0.016:0:1.5 0/0:96:0:0,0:87,9:0:2,0:20.8:1:29.3:1:1:0:59.9:47:1:0:0.4 -7 151884279 . TA T 153 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.17093;SOR=0.64108;LSEQ=AGCTACCTTTCTATTGCAGT;RSEQ=AAAAAAAAAAAGGTATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:34:34,0:110,9:0.2125:2,1:24.6:1:30.2:1:0.2084:0:60:33:0.2089:0.0313:0.6 0/1:129:19:17,2:87,18:0.1473:2,2:22.1:1:30.3:1:0.73576:1.75:60:38:0.1496:0.0388:0.1 -7 151884607 . C T 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=TTATGAACATAAAATAACTT;RSEQ=TTAATATATGTTCAAGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:62,219:0:2,0:22.4:1:31.9:1:1:0:60:139.5:1:0:0.1 0/1:230:10:3,7:44,175:0.0435:2,2:22.5:1:29.3:1:0.43241:1.70:60:20:0.0437:0:1 -7 151884963 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25177;SOR=0;LSEQ=AAAAATAATTCCGTTGGCAT;RSEQ=ATATTCACAAGTAACAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:1,2:25,167:0.0154:2,2:34.7:1:23.3:1:0.35059:3.31:60:2:0.0106:0:1.3 0/0:169:0:0,0:28,141:0:2,0:24.1:1:31.1:1:1:0:60:83.5:1:0:0.1 -7 151891018 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0777;SOR=Inf;LSEQ=TAAAGAATAGGGCAAAACTT;RSEQ=CTTGTGTGTGTATATGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:124,9:0:2,0:21:1:32.2:1:1:0:60:132:1:0:0.1 0/1:100:3:2,1:87,10:0.03:2,2:23.7:1:23:1:0.29769:4.24719:60:2:0.0202:0:1 -7 151891255 . G A 209 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00684;LSEQ=GTAACAAGATTAAAAGACTA;RSEQ=TAGGGTCCTGGTATGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:121:68,53:327,265:0.1685:2,2:26.6:1:30.3:1:0.92011:1.04:60:39.333:0.1676:0:1.1 0/0:724:1:1,0:391,329:0.0014:2,0:1:0:26:0:1:0:60:2:0.0014:0:1 -7 151891358 . TA T 177 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.36562;SOR=1.20863;LSEQ=GAATTGCTCCTAGAATAAAT;RSEQ=AAAAAAAAAAAGAAACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:49:11,38:131,236:0.1161:2,2:30.8:1:29.9:1:0.0777:1.91482:60:98:0.1192:0.0095:0.2 0/1:467:64:21,43:145,251:0.137:2,2:28.1:1:29.6:1:0.57858:1.18244:60:63:0.1376:0.0107:0.2 -7 151896573 . G GGTTA 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.12314;SOR=Inf;LSEQ=AGATAAGCACATACAAAAAT;RSEQ=GTTAGAAAATTCTAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:40,138:0:2,0:24.9:1:31.5:1:1:0:60:177:1:0:0.1 0/1:185:4:2,2:47,134:0.0216:2,2:26.5:1:28.3:1:0.28606:2.83:60:8:0.0216:0:0 -7 151896582 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49843;SOR=0;LSEQ=CATACAAAAATGGTTAGAAA;RSEQ=TTCTAAAAAGACAATAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:31,126:0.0126:2,2:21.5:1:31:1:0.36303:4.02:60:4:0.0129:0:1 0/0:157:0:0,0:41,116:0:2,0:23.2:1:29.4:1:1:0:60:77.5:1:0:0.1 -7 151899878 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16491;SOR=Inf;LSEQ=TTTTATGGACCCCTGAAAGG;RSEQ=AAAAATGGCATTTATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:68,0:0:1,0:23:1:30.1:1:1:0:60:67:1:0:0 0/1:47:2:2,0:45,0:0.0426:1,0:23:1:30.5:1:1:0:60:4:0.0426:0:1 -7 151900186 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49891;SOR=0;LSEQ=ATTTATAAATATGTGACATT;RSEQ=AAAATTTCTAGACAAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:22,136:0.0124:2,0:15.5:1:33.5:1:1:0:60:4:0.0127:0:1 0/0:151:0:0,0:28,123:0:2,0:22.3:1:28.7:1:1:0:60:302:1:0:0.1 -7 151900951 . T A 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCTAGCCAGAACATAAGGAA;RSEQ=CCATGAAAAACAAAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:50:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:30.5:1:1:0:60:4:1:0:0 -7 151902156 . TA T 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39424;SOR=1.56685;LSEQ=TCAAGACCAAAGGGTTACAT;RSEQ=AAAAAAAAATTTTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:9:7,2:215,33:0.035:2,2:23.3:1:29.1:1:0.35286:1.85591:60:18:0.0359:0.0039:0.1 0/1:260:14:12,2:203,43:0.0538:2,2:22.4:1:28.7:1:1:1.27:60:28:0.0543:0.0231:0.4 -7 151902166 . A AT 55 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.44769;SOR=0.48966;LSEQ=AGGGTTACATTAAAAAAAAA;RSEQ=TTTTTTTTTAAGTCAGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:4:4,0:256,53:0.0125:2,0:25:1:27.8:1:1:0:57.5:3:0.0097:0:0.5 0/0:324:2:1,1:252,66:0.0062:2,2:12:1:28:1:0.37543:3.79709:60:4:0.0063:0.0031:0.5 -7 151902343 . G A 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAATTAGGTAAACTGATAA;RSEQ=TAATTTCTCCCTACATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:158,390:0:2,0:22.3:1:31.8:1:1:0:59.5:90.333:0.9963:0:0.1 0/1:525:18:7,11:151,356:0.0343:2,2:28.9:1:29.6:1:0.43647:1.50:47.8:36:0.0346:0:1.1 -7 151919159 . GA G 155 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.58992;SOR=0.84392;LSEQ=TCTGAGGAAGGCACTGAAAC;RSEQ=AAAAAAAAAATCCAGGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:423:32:8,24:113,274:0.0757:2,2:27.8:1:31.1:1:0.6894:1.23659:59.8:64:0.0766:0.0024:0.3 0/1:418:27:6,21:135,253:0.0646:2,2:26.7:1:30.6:1:0.21235:1.86506:60:54:0.0652:0.0048:0 -7 151919756 . G A 83 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0044;SOR=11.1427;LSEQ=TATTTAAGTTCTGACAAACT;RSEQ=CATGCATCCATCTAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:929:1:0,1:371,557:0.0011:2,0:1:0:31:0:1:0:60:2:0.0011:0:1 0/1:842:10:8,2:366,466:0.0119:2,2:7.5:1:25.1:1:0.02712:5.08:57.8:20:0.012:0:1.1 -7 151919797 . T A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATATTTGTACATTTTTTT;RSEQ=AAAAAATGGAATATACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:114,336:0:2,0:24:1:28.5:1:1:0:44.9:55.25:1:0:0.1 0/1:417:25:9,16:123,269:0.06:2,2:19.2:1:28.6:1:0.65978:1.23:41.7:50:0.061:0:1 -7 151920970 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18242;SOR=Inf;LSEQ=TCTGTAAGTTTCTAGGTGAC;RSEQ=AAAAATCTACAAGGCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:106,6:0:2,0:28:1:31:1:1:0:57.9:36.333:1:0:0.1 0/1:84:2:2,0:71,11:0.0238:2,0:10:1:32:0:1:0:24:4:0.0241:0:3 -7 151920992 . T C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20276;SOR=Inf;LSEQ=AAAATCTACAAGGCAAAAAG;RSEQ=TCTGTACCTAAAACTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:132,8:0:2,0:26.6:1:30.1:1:1:0:56.9:139:1:0:0.2 0/1:116:2:2,0:101,13:0.0172:2,0:32:1:34:0:1:0:24:4:0.0175:0:3 -7 151921037 . G GT 170 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00949;SOR=1.78894;LSEQ=GGAAAAGCTATTTTCCATTT;RSEQ=TTTTTTTTTTTGCTACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:42:34,8:211,53:0.1308:2,2:21.1:1:29.4:1:1:1.07:45.8:20:0.132:0.0312:0.3 0/1:292:62:46,16:171,42:0.2123:2,2:21.5:1:28.7:1:0.29473:1.41426:43.1:30:0.2198:0.0548:0.2 -7 151921880 . A G 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05236;SOR=0.23793;LSEQ=ATGTTCATACACGCTTTTAG;RSEQ=AGCCTACTGAGCAGAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:14:0,14:1,60:0.1867:1,1:35.8:1:32.4:1:1:0:23:28:0.1944:0:1.2 0/1:39:2:0,2:3,34:0.0513:2,0:35.5:1:33:0:1:0:23:4:0.0513:0:1 -7 151926935 . G A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07142;SOR=1.95839;LSEQ=AATACTTAATTGTGAGAACT;RSEQ=GGAGCTCATGTTACTACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:14:14,0:100,5:0.1176:1,1:11.6:1:28.5:1:1:0:34.5:13:0.1102:0:3.7 0/1:106:22:20,2:79,5:0.2075:2,2:23.4:1:29.1:1:0.63305:1.57241:35:44:0.2095:0:3.5 -7 151926945 . G A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08273;SOR=1.77901;LSEQ=TGTGAGAACTGGGAGCTCAT;RSEQ=TTACTACTAAAACCAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:18:18,0:117,6:0.1277:1,1:15.7:1:28.7:1:1:0:37.4:36:0.1286:0:3.7 0/1:145:30:27,3:108,7:0.2069:2,2:23:1:28.7:1:0.43194:1.70706:36.2:60:0.2113:0:3.4 -7 151926956 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49873;SOR=Inf;LSEQ=GGAGCTCATGTTACTACTAA;RSEQ=ACCAAATAAAAATTCAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:179,7:0:1,0:25:1:30.5:1:1:0:36.8:61:0.9946:0:1 0/1:191:2:1,1:176,13:0.0105:2,2:38:1:31:1:0.14158:13.08304:40:4:0.0105:0:1 -7 151926977 . A G 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01489;SOR=1.53788;LSEQ=ACCAAATAAAAATTCAATAC;RSEQ=TATTTGTTAACTCAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:73:67,6:214,25:0.2332:2,2:21.6:1:30.5:1:0.66095:1.30:37.5:146:0.234:0:2.2 0/1:345:110:97,13:205,29:0.3188:2,2:18.3:1:29.9:1:1:1.06:39.2:54:0.3176:0:2.3 -7 151927016 . T C 138 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01562;SOR=0.38258;LSEQ=AAGGATGTTTACCTTAATAC;RSEQ=GACACAGTATGGATGGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:21:18,3:465,154:0.0328:2,2:34.4:1:31.6:1:0.43769:1.99:34.8:42:0.033:0:1.6 0/1:704:9:5,4:517,178:0.0128:2,2:31.8:1:25.6:1:0.24724:2.32037:30.6:3.5:0.0101:0:1.4 -7 151927021 . C A 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00884;SOR=0.75808;LSEQ=TGTTTACCTTAATACTGACA;RSEQ=AGTATGGATGGTAACACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:713:335:238,97:282,96:0.4698:2,2:24.5:1:30:1:0.31112:1.19691:31.2:82.75:0.4682:0:2 0/1:774:311:218,93:331,132:0.4018:2,2:23:1:29.7:1:0.68704:1.06965:31.4:310:0.4021:0:2.1 -7 151927025 . A G 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.34997;LSEQ=TACCTTAATACTGACACAGT;RSEQ=TGGATGGTAACACTGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:759:119:87,32:449,191:0.1568:2,2:23.8:1:32.1:1:0.58404:1.16:35.8:238:0.1576:0:1.6 0/1:835:254:175,79:398,181:0.3042:2,2:26.3:1:31.2:1:1:1.01:36.9:126:0.3051:0:1.4 -7 151927026 . T C 264 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00517;SOR=0.75425;LSEQ=ACCTTAATACTGACACAGTA;RSEQ=GGATGGTAACACTGACCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:788:364:246,118:304,120:0.4619:2,2:24.7:1:31.1:1:0.21411:1.21487:31.5:181:0.4635:0:1.9 0/1:855:336:226,110:356,161:0.393:2,2:23.8:1:30.1:1:0.65182:1.07614:32.1:83:0.392:0:2 -7 151927127 . A G 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00034;SOR=0.68691;LSEQ=CATATCCTGAAGTTAAGAAA;RSEQ=CAGAACATATTTTAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:756:334:76,258:139,283:0.4418:2,2:23.1:1:31.8:1:0.00206:1.66624:32.3:82.5:0.4418:0:1.1 0/1:798:281:69,212:168,349:0.3521:2,2:22.2:1:31.8:1:0.01893:1.47829:34.2:139.5:0.3541:0:1.1 -7 151932292 . G GTA 30 d7;v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTGGTATCGTTTTCAAGGGT;RSEQ=TATATATATATATATATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:35:1:30.3:1:1:0:60:4:0.6667:0:0 1/1:1:1:1,0:0,0:1:0,0:11:0:28.5:0:1:0:42:2:1:0:0 -7 151932560 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTTAGCAAATATATTTG;RSEQ=AATACACATATAAATAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:5:1:31:0:1:0:40:4:0.25:0:5 0/0:2:0:0,0:2,0:0:0,0:37.5:1:31:1:1:0:60:4:1:0:0 -7 151932581 . C T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATACACATATAAATAAAGC;RSEQ=TCATAACATGATAGTAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:26:1:32:0:1:0:40:4:0.25:0:5 0/0:3:0:0,0:2,1:0:2,0:17.3:1:30.3:1:1:0:56.3:6:1:0:0 -7 151932651 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1957;SOR=Inf;LSEQ=TAAAAGAGCAACTATATTAC;RSEQ=TACTGACTTTTTAGAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:17,0:0:1,0:15.2:1:31.2:1:1:0:34.2:34:1:0:1.2 0/1:14:2:2,0:8,4:0.1429:2,0:16:1:32:0:1:0:32.5:4:0.1429:0:2.5 -7 151932654 . C A 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36494;SOR=3.08205;LSEQ=AAGAGCAACTATATTACATA;RSEQ=TGACTTTTTAGAGAGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:16,0:0.1111:1,0:8:1:31:0:1:0:36.5:4:0.1111:0:4.5 0/1:14:4:3,1:7,3:0.2857:2,2:30:1:31.5:1:1:1.26:24:8:0.2857:0:1.8 -7 151932667 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.16474;LSEQ=TTACATACTGACTTTTTAGA;RSEQ=AGGGTTGGCATAGAAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:5,0:19,0:0.2083:1,0:17.4:1:31:1:1:0:30.4:10:0.2083:0:1.2 0/1:17:4:4,0:9,4:0.2353:2,0:30.8:1:31.5:1:0.51933:0:28.8:8:0.2353:0:2 -7 151932694 . C CAAAGAGGAAGGTAAGA 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=4.000;MSILEN=1;SSF=0.03848;SOR=0;LSEQ=GGCATAGAAAGATAAGGAGT;RSEQ=AAAGAGGAAGGTAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:7:7,0:34,1:0.1667:1,0:26.1:1:30.6:1:1:0:35.6:14:0.1795:0.0952:2.7 0/0:26:0:0,0:19,6:0:2,0:24.6:1:29.7:1:1:0:45.2:11.5:0.9583:0:0.7 -7 151932714 . G A 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.69716;SOR=0.64695;LSEQ=CAAAGAGGAAGGTAAGAAAA;RSEQ=AGAAAGGATGAGAAAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:4:4,0:53,5:0.0645:2,0:16.5:1:30.3:1:1:0:24:8:0.0656:0:4.8 0/1:47:2:2,0:35,10:0.0426:2,0:12:1:27.5:1:1:0:33.5:4:0.0435:0:4 -7 151932717 . A G 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94856;LSEQ=AGAGGAAGGTAAGAAAAGAG;RSEQ=AAGGATGAGAAAGTAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:6:6,0:57,7:0.0857:2,0:14.7:1:31.7:1:1:0:31.3:12:0.087:0:3.7 0/1:49:4:4,0:33,12:0.0816:2,0:5:0:30:1:0.55993:0:28.8:8:0.0816:0:2 -7 151932720 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5106;SOR=0;LSEQ=GGAAGGTAAGAAAAGAGAAA;RSEQ=GATGAGAAAGTAAATATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:64,6:0.0278:2,2:25:1:31:1:0.18623:9.9523:50:4:0.0278:0:2 0/0:51:0:0,0:39,12:0:2,0:20.1:1:30.7:1:1:0:50.4:24.5:1:0:1 -7 151932722 . A G 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70853;SOR=0.53745;LSEQ=AAGGTAAGAAAAGAGAAAGG;RSEQ=TGAGAAAGTAAATATACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:6:6,0:61,8:0.08:2,0:16.3:1:31.5:1:1:0:24:12:0.0811:0:4.7 0/1:45:2:2,0:32,11:0.0444:2,0:12:1:26:1:1:0:33.5:4:0.0465:0:4 -7 151932747 . CA TG 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03596;LSEQ=AAAGTAAATATACAAGAAAA;RSEQ=TAACCAGAGGCTCAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:52:48,4:70,12:0.3852:2,2:17.1:1:31.7:1:0.28211:2.05:38.1:104:0.3969:0.0889:3.4 0/1:94:37:34,3:48,9:0.3936:2,2:17.8:1:31.2:1:0.35348:2.11:40.9:74:0.3936:0.0957:3.5 -7 151932748 . A G 76 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08358;SOR=0;LSEQ=AAGTAAATATACAAGAAAAC;RSEQ=TAACCAGAGGCTCAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:6:5,1:72,11:0.0465:2,2:26.8:1:29.5:1:1:1.30479:37:12:0.0674:0:2.8 0/0:89:0:0,0:49,9:0:2,0:25:1:30.3:1:1:0:58.9:116:1:0:0.1 -7 151932756 . A T 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19944;SOR=1.46526;LSEQ=ATACAAGAAAACATAACCAG;RSEQ=GGCTCAAAAAAAAAAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:35:30,5:117,12:0.2121:2,2:20.3:1:30.1:1:0.36468:1.61967:39.5:70:0.2188:0:3.6 0/1:113:32:30,2:70,11:0.2832:2,2:14.2:1:30.5:1:0.34427:2.34:39.1:64:0.2909:0:3.5 -7 151932761 . CAA C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=1;SOR=1.03525;LSEQ=AGAAAACATAACCAGAGGCT;RSEQ=AAAAAAAAGCAAAGTAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:35:33,2:112,17:0.1862:2,2:15.8:1:31.3:1:0.37048:2.49:41:70:0.1862:0.0745:2.8 0/1:141:27:25,2:86,14:0.1915:2,2:12.1:1:30.8:1:0.51964:2.03:41.9:54:0.1915:0.1135:3 -7 151932765 . AAAAAAAGC A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.26007;SOR=0;LSEQ=AACATAACCAGAGGCTCAAA;RSEQ=AAAGTAGGACAGTAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:3:3,0:177,24:0.0147:2,0:9.7:1:31.2:1:1:0:41:6:0.0149:0.0098:1.7 0/0:158:0:0,0:137,21:0:2,0:20.2:1:30.5:1:1:0:49.9:316:1:0:1.7 -7 151932773 . C A 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.99422;LSEQ=CAGAGGCTCAAAAAAAAAAG;RSEQ=AAAGTAGGACAGTAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:68:63,5:135,22:0.2996:2,2:17.2:1:30.6:1:0.18559:2.05:41.1:67:0.316:0:3.3 0/1:181:54:47,7:108,19:0.2983:2,2:15.5:1:30.1:1:0.81989:1.18:43.3:108:0.3176:0:3.1 -7 151932774 . A G 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06037;SOR=1.57478;LSEQ=AGAGGCTCAAAAAAAAAAGC;RSEQ=AAGTAGGACAGTAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:44:35,9:178,19:0.1826:2,2:26.8:1:29.8:1:0.06458:2.39832:39.5:88:0.1849:0:3.4 0/1:192:50:41,9:122,20:0.2604:2,2:22:1:30.1:1:0.49818:1.3369:38.9:100:0.266:0:3 -7 151932808 . TTA T 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=10.08839;LSEQ=AAATAAACATTTTGACCTAT;RSEQ=TATGACTCTTAAGATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:8:6,2:435,85:0.0152:2,2:28.5:1:30.2:1:0.62419:1.70385:45.9:16:0.0155:0.0019:3.4 0/1:483:65:45,20:350,69:0.1346:2,2:27.2:1:30:1:0.00917:2.24992:40:130:0.1363:0.0248:2.7 -7 151932819 . T A 239 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.39851;SOR=1.11306;LSEQ=TTGACCTATTTATATGACTC;RSEQ=TAAGATCAAAATAACTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:578:238:191,47:276,64:0.4118:2,2:28.8:1:30.6:1:0.83028:1.06107:38.9:118:0.417:0:2.3 0/1:548:240:183,57:249,59:0.438:2,2:27.6:1:30.3:1:0.20669:1.31385:40.2:480:0.4404:0:2 -7 151932822 . A T 132 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=6.31225;LSEQ=ACCTATTTATATGACTCTTA;RSEQ=GATCAAAATAACTTGCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:4:3,1:479,119:0.0066:2,2:29.3:1:30.3:1:1:1.34102:38:8:0.0068:0:2.8 0/1:567:23:13,10:427,117:0.0406:2,2:28.4:1:29.2:1:0.02021:2.80084:47.6:46:0.0411:0:2.5 -7 151932823 . G A 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTATTTATATGACTCTTAA;RSEQ=ATCAAAATAACTTGCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:614:0:0,0:488,126:0:2,0:26.1:1:32:1:1:0:47.9:46.231:1:0:1.3 0/1:575:21:10,11:431,123:0.0365:2,2:29.1:1:29.5:1:0.00303:3.84327:44:42:0.0369:0:2.8 -7 151932824 . A T 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28474;SOR=1.18908;LSEQ=CTATTTATATGACTCTTAAG;RSEQ=TCAAAATAACTTGCTATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:99:66,33:424,96:0.1599:2,2:27.1:1:29.5:1:0.00171:2.20506:38.9:48.5:0.1614:0:2.4 0/1:585:108:74,34:372,104:0.1846:2,2:28.4:1:28.9:1:0.04408:1.6419:38.5:53:0.185:0:2.6 -7 151932830 . A T 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.46681;LSEQ=ATATGACTCTTAAGATCAAA;RSEQ=TAACTTGCTATGAGATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:102:75,27:446,131:0.1502:2,2:31:1:30.9:1:0.44559:1.2253:37.4:101:0.151:0:3.4 0/1:630:48:39,9:426,156:0.0762:2,2:31.6:1:29.8:1:0.30472:1.59:36.8:96:0.0766:0:3.4 -7 151932846 . T C 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=8e-05;SOR=0.50545;LSEQ=CAAAATAACTTGCTATGAGA;RSEQ=TTTCATCATTAACTGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:810:106:72,34:497,206:0.1309:2,2:30.3:1:31.6:1:0.5695:1.1391:37:52:0.1321:0:3.3 0/1:778:55:38,17:485,237:0.0707:2,2:29.2:1:30:1:0.88171:1.09:35.7:54:0.0707:0:3.1 -7 151932876 . G T 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56388;SOR=1.11944;LSEQ=TAACTGACATTTAGATTAGA;RSEQ=AAAATATACATGAAGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1094:54:26,28:593,446:0.0494:2,2:20.5:1:28.8:1:0.20732:1.43137:38.3:53:0.0493:0:2.1 0/1:1074:59:26,33:592,422:0.0549:2,2:22.5:1:28.1:1:0.04126:1.77951:36.4:58:0.0545:0:2.3 -7 151932897 . C A 250 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.61508;LSEQ=AAAATATACATGAAGCAAGC;RSEQ=TCACCCCAGGTAATACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1236:304:168,136:453,478:0.246:2,2:28.3:1:30.4:1:0.04765:1.30:45:151:0.2465:0:1.2 0/1:1233:206:112,94:514,512:0.1671:2,2:26.7:1:30:1:0.28522:1.19:45.9:102:0.1669:0:1.2 -7 151932923 . G A 145 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23008;SOR=1.47289;LSEQ=CCAGGTAATACAACAGCTCC;RSEQ=ATTCCACTTTTCAGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1224:18:0,18:557,648:0.0147:2,1:27.9:1:29.9:1:3e-05:0:31.3:36:0.0148:0:2.7 0/1:1255:27:3,24:606,622:0.0215:2,2:25.6:1:30.6:1:5e-05:7.78452:32.9:54:0.0218:0:2.4 -7 151932945 . C T 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01028;SOR=1.43446;LSEQ=TTCCACTTTTCAGCTTTGAC;RSEQ=TGCCTCGGCCACCTCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1114:93:38,55:445,575:0.0835:2,2:17.8:1:30.1:1:0.6625:1.12:36.2:92:0.0832:0:2.7 0/1:1194:138:58,80:485,571:0.1156:2,2:18.3:1:30:1:0.41398:1.17141:37.9:137:0.1166:0:2.6 -7 151932965 . C T 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05835;SOR=1.27868;LSEQ=CTGCCTCGGCCACCTCGCCC;RSEQ=GACAGTCCTGCACCTCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1010:123:47,76:387,500:0.1218:2,2:29.3:1:30.3:1:0.28531:1.2513:36.6:122:0.122:0:2.7 0/1:1122:169:70,99:413,539:0.1506:2,2:31:1:30.1:1:0.67377:1.08363:38.5:83.5:0.1513:0:2.5 -7 151932985 . G A 103 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.38187;SOR=0.64798;LSEQ=CGACAGTCCTGCACCTCGAG;RSEQ=TCTCCGCTTTCCTGGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:906:12:1,11:390,504:0.0132:2,2:15.6:1:28.9:1:0.01632:8.5005:31.1:11:0.0123:0:3.7 0/0:1044:9:3,6:453,582:0.0086:2,2:14.2:1:27:1:0.73897:1.55607:36.6:3.5:0.0069:0:3.3 -7 151932990 . C T 181 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04692;SOR=0.66996;LSEQ=GTCCTGCACCTCGAGGTCTC;RSEQ=GCTTTCCTGGAAATCCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:878:60:25,35:349,469:0.0683:2,2:31:1:30.8:1:1:1.04175:40.1:59:0.0681:0:2.8 0/1:1025:48:20,28:418,558:0.0468:2,2:32.5:1:30.1:1:1:1.04871:35.8:47:0.0464:0:3.2 -7 151932991 . G A 94 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.81357;SOR=0.83972;LSEQ=TCCTGCACCTCGAGGTCTCC;RSEQ=CTTTCCTGGAAATCCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:852:9:1,8:372,469:0.0106:2,2:14.1:1:30:1:0.08579:6.33532:28.4:18:0.0107:0:3.9 0/0:1013:9:1,8:433,566:0.0089:2,2:12.2:1:29.8:1:0.08633:6.11212:32:18:0.009:0:3.9 -7 151933033 . G A 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25197;SOR=0.73713;LSEQ=ACGGCCCTATGTAACAGATT;RSEQ=GGAAAAGTCAACATTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:36:5,31:199,338:0.0628:2,2:12.9:1:31.3:1:0.00386:3.64375:28.4:35:0.0619:0:3.2 0/1:616:29:4,25:221,366:0.0471:2,2:13.7:1:31.2:1:0.00931:3.76752:28.6:58:0.0475:0:3 -7 151933145 . G A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.34968;LSEQ=TCCTTAGATAAGTATTAAGA;RSEQ=ACCTGGCTTATTATTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:0,2:4,92:0.0204:1,0:7:1:31.5:1:1:0:35.5:4:0.0208:0:5 0/1:73:2:1,1:5,66:0.0274:2,2:3.5:1:28.5:1:0.15868:12.14:29:4:0.0278:0:4 -7 151933152 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51187;SOR=0;LSEQ=ATAAGTATTAAGAGACCTGG;RSEQ=TTATTATTTTTATCTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:0,2:4,78:0.0238:1,0:14:1:31.5:1:1:0:35.5:4:0.0241:0:5 0/0:59:0:0,0:6,53:0:2,0:22.2:1:31.8:1:1:0:57.7:28.5:1:0:0.3 -7 151933173 . C A 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.79602;LSEQ=TTATTATTTTTATCTTTAAA;RSEQ=GTATACTCCACAACTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:4:0,4:3,51:0.069:2,0:25:1:30:1:1:0:31.3:8:0.069:0:4.3 0/1:36:2:1,1:2,32:0.0556:2,2:31.5:1:32:1:0.1619:13.27:29:4:0.0588:0:4 -7 151933181 . C G 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09876;LSEQ=TTTATCTTTAAACGTATACT;RSEQ=CACAACTTAAAAATCTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:0,5:2,42:0.102:1,0:28:1:30.2:1:1:0:31.6:10:0.1042:0:4 0/1:36:4:2,2:2,30:0.1111:2,2:21.5:1:31.5:1:0.05271:12.86:32.3:8:0.1176:0:3.5 -7 151933217 . C A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06418;SOR=3.30869;LSEQ=TAAATATAAAATGCTTACAA;RSEQ=CTTAGAATCATACCTTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:1,6:1,28:0.1944:1,2:32.6:1:27.9:1:0.35556:4.40:30.9:6:0.1765:0:3.4 0/1:20:9:5,4:1,10:0.45:2,2:21.3:1:30.2:1:0.04985:10.80:39.3:18:0.4737:0:2.9 -7 151933251 . T C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00968;SOR=7.85655;LSEQ=CTTAGGCCTGTCACTGTGAA;RSEQ=GCTATCAGCAAGCCTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:2,4:0,19:0.24:1,2:29.3:1:30.8:1:0.05:0:36.7:12:0.24:0:2.2 1/0:11:8:4,4:0,3:0.7273:0,2:32.8:1:30:1:0.23636:0:40.9:16:0.8:0:2.6 -7 151935279 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTTTGAGTTAATACTTT;RSEQ=TCAAATTAATTTTTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:32:1:1:0:24:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 151935567 . A C 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88488;LSEQ=AGGACTTCTCCCTCATAAAA;RSEQ=CAGTAGTAATCACAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:9,2:0.3125:2,0:29.2:1:32:1:1:0:33.2:10:0.3125:0:1.2 0/1:7:2:2,0:5,0:0.2857:0,0:15:1:33:0:1:0:31.5:4:0.3333:0:1 -7 151935619 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAAGAGGTATTAAAAAT;RSEQ=TATACTTGATTTTTAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:37,2:0.0488:2,0:20:1:30:1:1:0:34.5:4:0.0488:0:1.5 0/0:18:0:0,0:18,0:0:1,0:28.3:1:32.7:1:1:0:44.7:36:1:0:0.2 -7 151935688 . CT C 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3081;SOR=1.34569;LSEQ=TTTAGATTTAAAAAGTGTTT;RSEQ=TGGAAGCTCAATCTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:40:38,2:99,7:0.274:2,2:16.1:1:31:1:1:1.34:36.6:39:0.269:0.137:0.4 0/1:89:30:30,0:55,4:0.3371:2,1:23.6:1:30.7:1:0.29573:0:37:60:0.3371:0.1124:0.3 -7 151935695 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50718;SOR=0;LSEQ=TTAAAAAGTGTTTCTTGGAA;RSEQ=CTCAATCTAGAAAAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:150,14:0.012:2,2:6:0:31.5:1:0.17306:10.38551:31:4:0.0123:0:2 0/0:127:0:0,0:120,7:0:2,0:18.6:1:32.1:1:1:0:49.4:126:1:0:0.1 -7 151935768 . G T 89 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02322;SOR=0.12401;LSEQ=ATCAGACAGAAATGATATAT;RSEQ=AATGTAAATGCAATTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:660:9:6,3:422,229:0.0136:2,2:35:1:28.2:1:1:1.09:35.4:18:0.0138:0:1.1 0/0:585:1:0,1:376,208:0.0017:2,0:1:0:27:0:0.35726:0:50:2:0.0017:0:1 -7 151935992 . A G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09264;SOR=0.38001;LSEQ=CAGCAACTAAGGAATTTTAG;RSEQ=ACAGCAAAAACAAATGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:14:0,14:18,105:0.1022:2,1:39:1:31.6:1:0.21467:0:31.9:28:0.1029:0:1.1 0/1:121:5:0,5:21,95:0.0413:2,0:32.6:1:30.6:1:0.58577:0:27.2:10:0.042:0:1.4 -7 151936009 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21251;SOR=Inf;LSEQ=TAGAACAGCAAAAACAAATG;RSEQ=AAACGTATGGAAATTTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:16,98:0:2,0:25.7:1:31.9:1:1:0:45.9:56:1:0:0.3 0/1:98:2:1,1:14,82:0.0204:2,2:9:1:28.5:1:0.28403:5.69:25:4:0.0204:0:1 -7 151944649 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=2.60168;LSEQ=AATAGATGTTAGTTACTGTA;RSEQ=ACCCAAAACTATACTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:32:1:31:1:1:0:49:4:0.4:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:25:1:29.5:1:1:0:60:4:0.6667:0:1 -7 151944702 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=TTTACTGCAGCACAGAACTA;RSEQ=AAGAATTTTTAAAGTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:31.5:1:29:1:1:0:34.9:7:1:0:1.1 1/0:4:2:1,1:1,1:0.5:2,2:49:0:32:1:1:1:60:4:0.5:0:1 -7 151944707 . AT A 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=1.30524;LSEQ=TGCAGCACAGAACTAAAAGA;RSEQ=TTTTAAAGTTCTTTCTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:38:1:31.5:1:1:0:52.5:4:0.2:0:1.5 0/1:4:1:1,0:1,2:0.25:2,0:25:0:28:0:1:0:27:2:0.25:0:2 -7 151944717 . T C 32 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.88511;LSEQ=AACTAAAAGAATTTTTAAAG;RSEQ=TCTTTCTATTAGAAACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:42.5:1:32:1:1:0:52.5:4:0.2:0:1.5 0/1:3:1:1,0:1,1:0.3333:2,0:33:0:31:0:1:0:27:2:0.3333:0:2 -7 151944720 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAGAATTTTTAAAGTTC;RSEQ=TTCTATTAGAAACTATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:23.5:1:32:0:1:0:33.5:4:0.2:0:4 0/0:3:0:0,0:2,1:0:2,0:32.7:1:28.7:1:1:0:49:6:1:0:1.3 -7 151944745 . G A 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53924;SOR=0;LSEQ=ATTAGAAACTATTATCAATA;RSEQ=GTTGCATCTTTATGGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:14,0:0.1765:1,2:34.3:1:31:1:0.17647:0:31.3:6:0.1765:0:4.3 0/0:6:0:0,0:5,1:0:2,0:18.3:1:32:1:1:0:54:12:1:0:1 -7 151944765 . A G 86 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3645;SOR=0.25626;LSEQ=GGTTGCATCTTTATGGCCCA;RSEQ=CTGAGTTGAAATTCCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:6,1:12,0:0.3684:0,2:28:1:30.7:1:0.36842:0:32.9:14:0.3684:0:2.9 0/1:8:1:1,0:6,1:0.125:2,0:20:0:34:0:1:0:27:2:0.1429:0:2 -7 151944791 . A C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90238;LSEQ=TTGAAATTCCAAATAAGATC;RSEQ=CTTCAAATTTAATAAATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:7,1:18,0:0.3077:1,2:22.3:1:31.1:1:0.30769:0:35.6:16:0.32:0:2.8 0/1:14:4:4,0:9,1:0.2857:2,0:14:1:26.8:1:1:0:40.8:3:0.2308:0:2 -7 151944808 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54204;SOR=0;LSEQ=ATCACTTCAAATTTAATAAA;RSEQ=GGCATTCTTCATTAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:31,0:0.0606:1,2:19.5:1:32.5:1:0.06061:0:33:4:0.0625:0:4.5 0/0:17:0:0,0:16,1:0:1,0:25.5:1:30.2:1:1:0:45.4:16:1:0:0.6 -7 151944819 . A T 62 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87686;LSEQ=TTTAATAAATGGCATTCTTC;RSEQ=TTAACAGCATTTAAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:4:3,1:35,0:0.1026:1,2:13.3:1:31.3:1:0.10256:0:36.5:8:0.1053:0:3.3 0/1:22:2:2,0:19,1:0.0909:1,0:3:1:30.5:1:1:0:30.5:4:0.0952:0:2 -7 151944852 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00052;SOR=4.6113;LSEQ=AAAAAATAATGGCTGAAACA;RSEQ=ATAATCAACATTACACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:13:13,0:57,1:0.1831:1,1:29.9:1:31.8:1:1:0:37.4:26:0.1857:0:1.2 1/0:41:21:20,1:20,0:0.5122:1,1:24.1:1:31.1:1:1:0:37.4:42:0.5122:0:1.1 -7 151944861 . C T 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16586;SOR=0.37991;LSEQ=TGGCTGAAACACATAATCAA;RSEQ=ATTACACTGAAGTTCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:12:12,0:73,1:0.1395:1,0:22.6:1:30.6:1:1:0:37.8:11:0.131:0:1.4 0/1:52:3:3,0:47,2:0.0577:1,0:37.7:1:31:1:1:0:33.7:6:0.0577:0:1.7 -7 151944908 . C A 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0188;SOR=0;LSEQ=AGAAAAAGTTGCCATCCACA;RSEQ=CAAAGCTACACATATACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:7:7,0:159,5:0.0409:1,0:26.7:1:31:1:1:0:26.1:14:0.0412:0:1.4 0/0:136:0:0,0:133,3:0:1,0:23.3:1:31.3:1:1:0:36.8:272:1:0:0.3 -7 151944961 . T A 160 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00256;SOR=2.23017;LSEQ=AATTGTTCCAATATCTTTTC;RSEQ=GTCAATATCATTAAAATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:22:20,2:361,38:0.0523:2,2:24.9:1:29:1:1:1.05:37.1:10:0.0487:0:2 0/1:438:48:42,6:342,47:0.1096:2,2:24:1:28.7:1:1:1.03943:38.6:23:0.106:0:1.7 -7 151945007 . C T 267 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35519;SOR=1.08713;LSEQ=CTGTTTGGACCGAGGTCTAC;RSEQ=AGGAGAAAATTTTCTCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:446:297,149:358,166:0.4598:2,2:26.1:1:29.8:1:0.58251:1.08186:51.7:110.5:0.4623:0:1.1 0/1:1109:533:341,192:372,204:0.4806:2,2:25.4:1:29.5:1:0.85088:1.02672:53:176.667:0.4831:0:1.1 -7 151945060 . G A 134 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11094;SOR=1.85313;LSEQ=TACCCATGCCAATTTTTGGA;RSEQ=TGACTGAGATGTAAGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1374:10:7,3:714,649:0.0073:2,2:5.1:1:30.4:1:0.34819:2.12:32.6:20:0.0074:0:2 0/1:1641:22:14,8:828,789:0.0134:2,2:5.3:1:30.1:1:0.28706:1.67:36.1:44:0.0135:0:2.1 -7 151945071 . G GT 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05253;SOR=1.21589;LSEQ=ATTTTTGGAGTGACTGAGAT;RSEQ=TAAGTTGTTGGCATGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1422:200:86,114:640,580:0.1406:2,2:24:1:29.4:1:0.01454:1.4623:53.9:39:0.1394:0.0331:0.1 0/1:1699:282:150,132:701,715:0.166:2,2:27.5:1:28.9:1:0.26804:1.16:57.3:27.2:0.1624:0.0129:0.2 -7 151945101 . G C 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02018;SOR=0.79751;LSEQ=GGCATGATGTTTCCAGCAGA;RSEQ=GAACTAAGAGCTGAAGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1470:261:137,124:545,664:0.1776:2,2:26.6:1:31.3:1:0.03377:1.35:40.1:522:0.1814:0:1.2 0/1:1709:251:137,114:665,789:0.1469:2,2:28.2:1:30.3:1:0.01119:1.43:41.8:82.667:0.1466:0:1.2 -7 151945140 . C T 256 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.54487;LSEQ=TAATTATGCAGCATGTCATG;RSEQ=GAAGGCAAGTCTGAAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1389:259:82,177:495,633:0.1865:2,2:25.8:1:30.3:1:0.00035:1.68733:44.4:518:0.1886:0:1.9 0/1:1518:397:134,263:516,603:0.2615:2,2:26.6:1:29.7:1:2e-05:1.67893:45.6:197.5:0.263:0:1.9 -7 151945167 . G T 243 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.14009;SOR=1.15946;LSEQ=AAGTCTGAAGAAGGTGTTGG;RSEQ=GAGGAAGACACATCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1100:250:60,190:358,491:0.2273:2,2:24.1:1:29.9:1:0:2.30724:42:61.5:0.2271:0:2.1 0/1:1160:295:80,215:369,493:0.2543:2,2:23.7:1:29.7:1:0:2.01038:42.6:58:0.2531:0:2.2 -7 151945204 . G A 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.31991;SOR=1.13483;LSEQ=CCTTGCTTATGTCTGCTGAT;RSEQ=ATGAAAATGATGACTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:663:161:1,160:239,262:0.2428:2,1:18.1:1:30.5:1:0:145.36879:34.8:79.5:0.2427:0:2.1 0/1:697:186:5,181:234,277:0.2669:2,1:17.4:1:30.5:1:0:30.48076:34.1:372:0.2676:0:2 -7 151945225 . T C 138 Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03258;SOR=0.43259;LSEQ=ATGAAAATGATGACTCTGTC;RSEQ=CAGATGATAACTTTATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:23:0,23:211,304:0.0427:2,1:25.5:1:30.6:1:1e-05:0:37.5:22:0.0414:0:3 0/1:529:10:0,10:210,309:0.0189:2,0:20.3:1:29.9:1:0.00744:0:37.7:20:0.0191:0:2.5 -7 151945252 . C T 107 Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00051;SOR=0;LSEQ=ATAACTTTATAGATTTGCCT;RSEQ=CTTGGTATGAAACATCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:12:0,12:204,268:0.0248:2,0:26.1:1:30.1:1:0.00175:0:37:24:0.0253:0:3 0/0:444:0:0,0:180,263:0:2,0:23.1:1:30.8:1:1:0:42.3:39.273:0.9977:0:0.2 -7 151945313 . A G 98 Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0083;SOR=0;LSEQ=AGTCATTTCAGAGTCCATCA;RSEQ=TCCAGTAGAAAGTTCAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:8:0,8:254,268:0.0151:2,0:21.5:1:32.9:1:0.00777:0:35:16:0.0153:0:2.5 0/0:473:0:0,0:237,235:0:2,0:23.6:1:29.8:1:1:0:45.8:77.667:0.9979:0:0.1 -7 151945672 . T A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.44753;LSEQ=CTTCATTAGAAATCTGTTTT;RSEQ=CCAATTCAGTATTCACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:2:1,1:105,176:0.0071:2,2:13.5:1:24.5:1:1:1.67:60:4:0.0072:0:1 0/1:294:3:2,1:114,176:0.0102:2,2:18:1:27:1:0.56457:3.08:60:6:0.0103:0:1 -7 151946883 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11413;SOR=Inf;LSEQ=CGTAATGTATATACATACAG;RSEQ=AATCGCAAAAATGTCTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:172,34:0:2,0:22:1:32:1:1:0:59.1:67.667:0.9951:0:0.1 0/1:196:3:2,1:156,37:0.0153:2,2:23.7:1:29:1:0.4781:2.0984:60:6:0.0154:0:1 -7 151946914 . T C 90 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10752;SOR=3.9162;LSEQ=ATGTCTTTGGGATAAAGACA;RSEQ=TATCTTGTAACTCAATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:2:1,1:254,102:0.0056:2,2:13.5:1:32:1:0.49322:2.48296:45:4:0.0056:0:3 0/1:371:8:4,4:255,107:0.0216:2,2:19.4:1:30:1:0.24764:2.37691:49.8:7:0.0192:0:2.9 -7 151946921 . G A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.45881;SOR=1.37628;LSEQ=TGGGATAAAGACATTATCTT;RSEQ=TAACTCAATCAAATTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:12:6,6:268,112:0.0306:2,2:22.5:1:31:1:0.19659:2.38689:47.2:24:0.0311:0:1.9 0/1:432:18:9,9:281,132:0.0417:2,2:17.8:1:29.8:1:0.12641:2.12476:49.1:36:0.0427:0:2.2 -7 151946985 . C G 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATAAGAAGACTATCTGTGT;RSEQ=AAGACTTTCTGAGGGATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:24:13,11:333,312:0.0358:2,2:26:1:31:1:0.83824:1.11:60:48:0.036:0:1 0/0:797:0:0,0:414,383:0:2,0:25.8:1:31.2:1:1:0:59.9:131.833:1:0:0.1 -7 151948998 . TA T 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=9e-04;SOR=0;LSEQ=CATTACAAAAACAAAAAATT;RSEQ=AAAAAAAATCATTCTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:11:4,7:248,85:0.032:2,2:16.5:1:28:1:0.01006:5.07646:60:22:0.0324:0.0145:0.7 0/0:339:0:0,0:248,90:0:2,0:23:1:28.1:1:1:0:60:111.667:0.997:0:0.1 -7 151949068 . C G 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCTCACCTGGCTGTAAA;RSEQ=GATCCATCTCAGCTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:0:0,0:440,321:0:2,0:26.8:1:31:1:1:0:60:94.125:0.9987:0:0.1 0/1:747:25:11,14:392,329:0.0335:2,2:26.8:1:31:1:0.31624:1.51557:60:50:0.0338:0:1.1 -7 151949735 . T C 262 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTTGGTAACAATTGTCACA;RSEQ=ATCAGGCAATTGTGGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:829:308:129,179:206,314:0.3715:2,2:24.9:1:31.8:1:0.55796:1.10:60:76:0.3712:0:1.1 0/0:835:0:0,0:354,478:0:2,0:24:1:28.4:1:1:0:60:137.667:0.9964:0:0.1 -7 151949832 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08318;SOR=Inf;LSEQ=GAAAAATAAAAACAAAAACA;RSEQ=TTTGTTATGCATTTGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:50,203:0:2,0:21.4:1:32:1:1:0:60:506:1:0:0.1 0/1:197:3:1,2:44,150:0.0152:2,2:12:1:24:1:0.54275:1.70:60:2:0.0104:0:3 -7 151949944 . C CT 50 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.53902;SOR=0;LSEQ=ACACTAATTTAGGGTACATG;RSEQ=TTTTTTTTTTTGAGATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:0,3:0,25:0.1071:1,0:29.7:1:32:0:1:0:60:6:0.1154:0:0 0/0:14:0:0,0:0,14:0:1,0:20.2:1:31.4:1:1:0:60:13:1:0:0.1 -7 151960128 . T A 95 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00624;SOR=10.86521;LSEQ=TTCCAGCCATTGGTTGGTAC;RSEQ=GATTTCATAACTGGTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1057:1:1,0:586,470:9e-04:2,0:1:0:30:0:1:0:51:2:0.001:0:1 0/1:1079:11:6,5:559,509:0.0102:2,2:13.5:1:27.6:1:1:1.09:52.4:4.5:0.0085:0:2 -7 151961997 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2029;SOR=Inf;LSEQ=AGTAATTTTTTTAAGTATGA;RSEQ=GAAGTCACTGAATGAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:0:1,0:25.2:1:31.5:1:1:0:60:50:1:0:0 0/1:21:2:2,0:17,2:0.0952:2,0:20:0:33:0:1:0:60:4:0.0952:0:1 -7 151962055 . C T 111 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00176;SOR=13.60534;LSEQ=CTCTATTATATTACACAAAC;RSEQ=TTTAGCACCTAGTAATAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:1:1,0:62,12:0.0133:2,0:32:0:32:0:1:0:27:2:0.0137:0:4 0/1:70:11:11,0:51,8:0.1571:2,0:15.5:1:32.1:1:0.33998:0:29.7:22:0.1594:0:3.7 -7 151962068 . T C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32172;SOR=1.34577;LSEQ=CACAAACCTTTAGCACCTAG;RSEQ=AATAGGGTCCCTCTTAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:36:35,1:83,24:0.2517:2,1:6:1:32.5:1:0.00506:10.02:26.3:72:0.2517:0:2.1 0/1:109:34:34,0:62,13:0.3119:2,1:12.8:1:32:1:0.00856:0:28.2:33:0.3084:0:2.7 -7 151962077 . C G 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41862;SOR=1.21253;LSEQ=TTAGCACCTAGTAATAGGGT;RSEQ=CCTCTTAAACCCAATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:56:55,1:97,29:0.3077:2,1:10.8:1:32.9:1:0.00014:16.30:26.8:112:0.3094:0:1.8 0/1:157:55:55,0:82,19:0.3503:2,1:15.2:1:32.5:1:0.00018:0:27.6:110:0.3503:0:2.1 -7 151962113 . G T 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=26.53781;LSEQ=ACACAGCTTTGAATTGAAAT;RSEQ=AAAACTTACTTGCAGTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:1:1,0:343,108:0.0022:2,0:41:0:32:0:1:0:27:2:0.0022:0:2 0/1:504:28:19,9:357,119:0.0556:2,2:22.3:1:29.5:1:0.37962:1.41999:35.3:56:0.0559:0:1.8 -7 151962134 . G T 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06476;SOR=0.60703;LSEQ=AAAACTTACTTGCAGTTCTG;RSEQ=CACACTTTGCACTCAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:690:35:25,10:445,208:0.0507:2,2:26.7:1:30.3:1:0.85229:1.17:39.5:70:0.0516:0:2 0/1:796:25:16,9:509,260:0.0314:2,2:23.9:1:28:1:0.83183:1.10106:38.6:24:0.0307:0:1.9 -7 151962168 . C A 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00558;SOR=0.53881;LSEQ=CAGGACATTGCCAACCTGCA;RSEQ=GTTTTAATGGAGTAACCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1007:51:32,19:532,423:0.0506:2,2:27.2:1:29.9:1:0.3855:1.34:40.8:102:0.0515:0:1.7 0/1:1253:35:18,17:672,542:0.0279:2,2:27.4:1:30.1:1:0.73096:1.17082:43.1:70:0.0282:0:1.7 -7 151962176 . T A 259 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06739;SOR=0.84813;LSEQ=TGCCAACCTGCACGTTTTAA;RSEQ=GGAGTAACCGCTATATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1075:348:187,161:389,338:0.3237:2,2:26.9:1:30.2:1:0.948:1.01:41.8:57:0.3245:0:1.2 0/1:1323:382:203,179:502,439:0.2887:2,2:26.4:1:30.2:1:0.95159:1.00831:42.4:764:0.2909:0:1.2 -7 151962257 . C T 164 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00986;SOR=2.02344;LSEQ=AACTGATCTAAGAGGTCTCC;RSEQ=GGGCTGTCGCACACTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:20:5,15:152,379:0.0363:2,2:21.7:1:29.6:1:1:1.20276:43.5:19:0.0349:0:1.9 0/1:621:44:12,32:193,383:0.0709:2,2:24.3:1:30.1:1:0.50631:1.34317:37.8:88:0.0714:0:2 -7 151962265 . C T 155 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01046;SOR=2.19067;LSEQ=TAAGAGGTCTCCCGGGCTGT;RSEQ=GCACACTGCACAGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:16:4,12:123,333:0.0339:2,2:18.4:1:30.1:1:1:1.10787:42.6:32:0.0343:0:2.1 0/1:518:37:10,27:149,331:0.0714:2,2:20:1:29.8:1:0.71322:1.21494:36.1:36:0.0699:0:2.2 -7 151962269 . C T 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.12528;SOR=0.5707;LSEQ=AGGTCTCCCGGGCTGTCGCA;RSEQ=ACTGCACAGTTTGCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:22:3,19:110,296:0.0514:2,2:19.6:1:29.8:1:0.21664:2.34978:35.3:44:0.0523:0:1.6 0/1:467:14:5,9:132,321:0.03:2,2:12.1:1:29.1:1:0.56353:1.35:38.2:28:0.0304:0:1.1 -7 151962290 . C G 64 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12843;SOR=Inf;LSEQ=ACTGCACAGTTTGCATCTTC;RSEQ=TTCGCTATAATTAACAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:42,191:0:2,0:21.1:1:32.1:1:1:0:37.2:232:1:0:0.3 0/1:274:4:0,4:63,207:0.0146:2,0:19:1:32.3:1:0.57675:0:24:8:0.0147:0:1.5 -7 151962294 . G A 97 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00081;SOR=0;LSEQ=CACAGTTTGCATCTTCCTTC;RSEQ=CTATAATTAACAGTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:9:1,8:40,160:0.0431:2,2:13.7:1:30.9:1:1:1.99454:31.4:18:0.0446:0:2.4 0/0:247:0:0,0:61,186:0:2,0:9:0:14:0:1:0:40:0:0:0:1 -7 151962296 . T C 77 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01862;SOR=0;LSEQ=CAGTTTGCATCTTCCTTCGC;RSEQ=ATAATTAACAGTGAAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:5:0,5:41,153:0.0251:2,0:8.4:1:33.4:1:0.58553:0:25.8:10:0.0255:0:3 0/0:240:0:0,0:59,181:0:2,0:22.8:1:28.8:1:1:0:41.5:119:1:0:0.2 -7 151962307 . G T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16779;SOR=0;LSEQ=TTCCTTCGCTATAATTAACA;RSEQ=TGAAACAATGAAATTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:30,92:0.0161:2,2:19:0:29:1:0.43902:3.03:49:4:0.0165:0:1 0/0:178:0:0,0:49,129:0:2,0:23.4:1:31.1:1:1:0:47.5:58.333:1:0:0.2 -7 151970640 . G A 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79471;SOR=1.2003;LSEQ=TGATAACATTTCCCTCCCCA;RSEQ=CGATCCCTGGCAACGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:12:12,0:25,1:0.3158:1,0:13.5:1:31.2:1:1:0:27.5:24:0.3158:0:4.6 0/1:28:10:10,0:17,1:0.3571:1,0:15.5:1:31.9:1:1:0:27.6:20:0.3571:0:4.3 -7 151970642 . G A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47298;SOR=1.43707;LSEQ=ATAACATTTCCCTCCCCAGC;RSEQ=ATCCCTGGCAACGATCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:14:14,0:27,1:0.3333:1,1:13.6:1:31.4:1:1:0:26.6:28:0.3333:0:4.5 0/1:31:13:13,0:17,1:0.4194:1,1:13.9:1:31.8:1:1:0:29:26:0.4194:0:4 -7 151970646 . C T 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6643;SOR=1.27581;LSEQ=CATTTCCCTCCCCAGCGATC;RSEQ=CTGGCAACGATCCCTCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:24:24,0:28,1:0.4528:1,1:11.2:1:31.8:1:1:0:32.4:48:0.4528:0:3.6 1/0:35:18:18,0:16,1:0.5143:1,1:13.6:1:32.2:1:0.48571:0:33.1:36:0.5143:0:3.7 -7 151970671 . AA GT 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.97769;LSEQ=CAACGATCCCTCAGATTTTA;RSEQ=GATTATGTATTATTACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:7:7,0:127,4:0.0507:1,0:27.1:1:32:1:1:0:39:14:0.0507:0:3 0/1:141:7:7,0:133,1:0.0496:1,0:21.3:1:32.2:1:1:0:43.3:14:0.05:0:2.7 -7 151970672 . A T 206 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06008;SOR=1.62333;LSEQ=AACGATCCCTCAGATTTTAA;RSEQ=GATTATGTATTATTACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:142:88:86,2:45,2:0.6197:1,1:17.1:1:31.4:1:0.61024:1.90:41.4:87:0.6493:0:1.9 1/0:146:106:106,0:32,1:0.726:1,1:16.9:1:30.7:1:0.23741:0:41.8:105:0.7609:0:1.8 -7 151970687 . A C 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.85499;SOR=1.12771;LSEQ=TTTAAAGATTATGTATTATT;RSEQ=CCTTTTAATACAAGTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:15:15,0:202,9:0.0661:1,1:27.7:1:32.3:1:1:0:45.5:30:0.0673:0:3.5 0/1:230:17:17,0:206,7:0.0739:1,1:20.6:1:32.4:1:1:0:49:34:0.0739:0:2.8 -7 151970688 . C T 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01498;SOR=Inf;LSEQ=TTAAAGATTATGTATTATTA;RSEQ=CTTTTAATACAAGTAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:221,9:0:1,0:22.3:1:32.6:1:1:0:47.7:460:1:0:1 0/1:236:7:7,0:221,8:0.0297:1,0:22.7:1:31.7:1:1:0:47.4:14:0.0303:0:1.6 -7 151970690 . T C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24862;SOR=Inf;LSEQ=AAAGATTATGTATTATTACC;RSEQ=TTTAATACAAGTAGAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:240,9:0:1,0:22.1:1:31.9:1:1:0:48.5:248:1:0:1 0/1:255:3:3,0:240,12:0.0118:1,0:26.7:1:32:0:1:0:49:6:0.0118:0:2 -7 151970695 . A T 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45743;SOR=0.78872;LSEQ=TTATGTATTATTACCTTTTA;RSEQ=TACAAGTAGAATAACACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:26:25,1:244,10:0.0929:1,1:19.8:1:31.3:1:1:1.02:52.3:52:0.0932:0:1.6 0/1:308:23:21,2:262,23:0.0747:2,2:21.7:1:30:1:1:1.08462:52.2:46:0.0749:0:1.7 -7 151970705 . A C 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35259;SOR=0.77141;LSEQ=TTACCTTTTAATACAAGTAG;RSEQ=ATAACACTCAGGGAATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:33:33,0:320,29:0.0864:2,1:22.1:1:32.8:1:0.15751:0:52.7:66:0.0871:0:2.8 0/1:412:28:25,3:344,40:0.068:2,2:23.9:1:32:1:1:1.03192:50.6:27:0.066:0:2.7 -7 151970714 . C A 143 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00444;SOR=2.71284;LSEQ=AATACAAGTAGAATAACACT;RSEQ=AGGGAATTTACAACATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:11:9,2:406,56:0.0233:2,2:34.3:1:29.5:1:0.63251:1.60918:33.4:22:0.0235:0:2.1 0/1:527:32:28,4:413,81:0.0607:2,2:28.1:1:28.6:1:0.80388:1.37:30.9:64:0.0615:0:1.9 -7 151970758 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.91237;SOR=1.04832;LSEQ=TTTCAGTAAATACATTGGTT;RSEQ=AAGTTTAAAAGTCTATCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1082:39:28,11:730,313:0.036:2,2:29.5:1:28.4:1:1:1.09:56.6:38:0.0357:0:1.1 0/1:1246:47:32,15:794,404:0.0377:2,2:28.7:1:28.8:1:0.87576:1.09:54:94:0.0383:0:1.2 -7 151970775 . C G 210 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00857;SOR=1.52213;LSEQ=GTTGAAGTTTAAAAGTCTAT;RSEQ=CGTAGTAAACTTACATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1321:69:52,17:798,453:0.0522:2,2:25:1:31.8:1:0.05316:1.74:28.1:68:0.0523:0:1.4 0/1:1434:111:78,33:800,522:0.0774:2,2:27.7:1:31:1:0.043:1.54:27.5:36:0.0764:0:1.4 -7 151970777 . G A 211 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06852;SOR=0.777;LSEQ=TGAAGTTTAAAAGTCTATCC;RSEQ=TAGTAAACTTACATCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1346:129:79,50:779,438:0.0958:2,2:28:1:30.2:1:0.56368:1.12555:53.1:63.5:0.0953:0:1.6 0/1:1472:112:69,43:817,541:0.0761:2,2:25.9:1:29.6:1:0.84088:1.06:53.7:111:0.0763:0:1.6 -7 151970797 . A T 147 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00189;SOR=2.91459;LSEQ=GTAGTAAACTTACATCTTTC;RSEQ=GGAGCTTGGTCAATGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1512:10:7,3:842,659:0.0066:2,2:25.3:1:31:1:0.5273:1.83:53.4:20:0.0067:0:1.4 0/1:1733:33:19,14:918,782:0.019:2,2:28.3:1:29.3:1:0.72722:1.16:52.4:15.5:0.0181:0:1.4 -7 151970856 . T A 304 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24877;SOR=1.12789;LSEQ=GTGACTGAAATCCTGAAAGG;RSEQ=GCCGGCTCCTGCAGCACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1305:1063:388,675:113,126:0.8146:2,2:26:1:30.6:1:0.00251:1.55958:45.2:61.529:0.8146:0:1.4 1/1:1441:1199:447,752:106,136:0.8321:2,2:26.5:1:29.8:1:0.0598:1.31095:44.8:46.96:0.8309:0:1.4 -7 151970859 . C T 195 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00047;SOR=0.52894;LSEQ=ACTGAAATCCTGAAAGGTGC;RSEQ=GGCTCCTGCAGCACAAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1271:82:30,52:453,736:0.0645:2,2:30.1:1:30.7:1:0.81513:1.0668:47.5:164:0.0653:0:2.1 0/1:1421:50:16,34:518,853:0.0352:2,2:30.3:1:30.1:1:0.45936:1.29021:45:49:0.0349:0:2.1 -7 151970877 . G A 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39927;LSEQ=GCCGGCTCCTGCAGCACAAG;RSEQ=ATAATGATACATCTGGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:97:29,68:296,615:0.0962:2,2:25.4:1:30:1:0.64884:1.12845:39.5:47.5:0.0963:0:2.2 0/1:1153:47:16,31:372,734:0.0408:2,2:20.8:1:29.3:1:1:1.02:39.5:94:0.0413:0:2.3 -7 151970931 . G A 237 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.32347;SOR=1.17189;LSEQ=GCATTTGATAGTGGCTCCAA;RSEQ=GTGCTTACAAAATGCACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:182:15,167:68,122:0.4866:2,2:18.7:1:31.6:1:0:6.17572:31.3:364:0.4959:0:1.9 1/0:323:170:11,159:59,94:0.5263:2,2:16.2:1:31.1:1:0:9.01013:30.6:84:0.5283:0:1.9 -7 151970945 . G T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03626;SOR=Inf;LSEQ=CTCCAAGGTGCTTACAAAAT;RSEQ=CACATCGCTGAAAGGGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:63,236:0:2,0:20.8:1:32:1:1:0:42.3:98.667:1:0:0.7 0/1:233:4:1,3:52,177:0.0172:2,2:29.3:1:28.5:1:1:1.13:28.5:8:0.0173:0:2 -7 151970951 . C T 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0012;SOR=Inf;LSEQ=GGTGCTTACAAAATGCACAT;RSEQ=GCTGAAAGGGGTAAAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:56,203:0:2,0:21.7:1:29.7:1:1:0:42.2:42.167:1:0:0.6 0/1:200:8:0,8:44,148:0.04:2,0:22.8:1:30.8:1:0.20393:0:27:16:0.0406:0:2 -7 151970969 . A C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25194;SOR=0.44691;LSEQ=ATCGCTGAAAGGGGTAAAGG;RSEQ=GAGAAATCTCTTTATAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:9:0,9:37,157:0.0443:2,0:16.8:1:26.4:1:0.36959:0:35:8:0.0404:0:2 0/1:148:3:0,3:30,115:0.0203:2,0:25.3:1:29:1:1:0:29.3:6:0.0204:0:2 -7 151970977 . C A 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08286;SOR=2.47079;LSEQ=AAGGGGTAAAGGAGAGAAAT;RSEQ=TCTTTATAAAACCTTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:6:1,5:30,143:0.0335:2,2:25.5:1:31:1:1:1.04869:49:12:0.0341:0:1 0/1:139:11:4,7:26,102:0.0791:2,2:18.6:1:28:1:0.25146:2.23:47.8:22:0.0797:0:1.3 -7 151970982 . T C 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.11386;LSEQ=GTAAAGGAGAGAAATCTCTT;RSEQ=ATAAAACCTTGAAAAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:8:2,6:27,136:0.0468:2,2:26.1:1:30:1:0.62461:1.67:37.4:16:0.0482:0:1.8 0/1:135:7:1,6:23,104:0.0519:2,2:23:1:31.1:1:1:1.32434:38.1:14:0.053:0:1.9 -7 151971015 . G A 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01126;SOR=0;LSEQ=AAAGGAATATTCAAATATAA;RSEQ=CTGGGAAGGTATAAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:9:0,9:13,109:0.0687:2,0:29.8:1:30.3:1:0.59774:0:42.8:18:0.0709:0:2.1 0/0:98:0:0,0:18,80:0:2,0:28.4:1:32.3:1:1:0:43.6:97:1:0:0.9 -7 151971043 . T C 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.74105;SOR=0.88745;LSEQ=GGTATAAAAAACTCTCTGTA;RSEQ=ATCACAAGTAAAACAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:67:6,61:2,29:0.6837:2,2:24.7:1:32.5:1:1:1.42:42.4:134:0.6837:0:1.8 1/0:70:46:11,35:2,21:0.6571:2,2:22.8:1:31.3:1:0.19385:3.25:39.1:22:0.6471:0:1.7 -7 151971052 . TA T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0.96429;LSEQ=AACTCTCTGTATATCACAAG;RSEQ=AAACAAATTGAACCTGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:49:0,49:2,29:0.6125:2,1:27.2:1:30.4:1:0.14715:0:42.1:48:0.6154:0.075:1.9 1/0:53:32:7,25:3,18:0.6038:2,2:23:1:30.3:1:0.72186:1.66:36.5:64:0.6038:0.0566:1.8 -7 151971075 . T C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.79392;SOR=1.18593;LSEQ=AACAAATTGAACCTGCAAAA;RSEQ=ATTAAACAAAGGATTCGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:12:0,12:0,41:0.2264:1,0:27.3:1:31.8:1:1:0:41.8:11:0.2157:0:3.3 0/1:31:8:0,8:4,19:0.2581:2,0:9.9:1:30.1:1:0.54972:0:40.1:7:0.2333:0:2.1 -7 151971078 . TAAAC T 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17278;SOR=0;LSEQ=AAATTGAACCTGCAAAATAT;RSEQ=AAAGGATTCGTTAAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:5:0,5:0,45:0.1:1,0:28:1:31.7:1:1:0:45.2:10:0.102:0.02:2 0/0:23:0:0,0:3,20:0:2,0:24:1:30.1:1:1:0:46.4:46:1:0:1.7 -7 151971092 . G A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.11587;LSEQ=AAATATTAAACAAAGGATTC;RSEQ=TTAAAAATAATAAAATCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:23:0,23:0,18:0.561:1,1:20:1:31:1:1:0:42.8:22:0.55:0:3 1/0:17:10:2,8:1,6:0.5882:2,2:25.1:1:30.7:1:1:1.47:38.4:20:0.5882:0:2.9 -7 151971125 . A T 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13356;SOR=5.66049;LSEQ=AAATCTACATTACTCAATTT;RSEQ=GCGCTTCGTGTGCTACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:1,13:0.1765:1,0:14.7:1:31.3:1:1:0:40.3:6:0.1765:0:3.7 1/0:7:4:0,4:0,3:0.5714:0,0:12.8:1:31:1:1:0:34.5:8:0.5714:0:3.5 -7 151971127 . C T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.27101;LSEQ=ATCTACATTACTCAATTTAG;RSEQ=GCTTCGTGTGCTACCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:0,7:1,8:0.4375:2,0:23.4:1:31.4:1:1:0:32.9:14:0.4375:0:4.1 1/0:6:3:0,3:0,3:0.5:0,0:14.3:1:31:1:1:0:31:6:0.5:0:3.7 -7 151971132 . C T 62 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53216;SOR=0;LSEQ=CATTACTCAATTTAGCGCTT;RSEQ=GTGTGCTACCAACTCATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:0,4:1,11:0.25:2,0:31.5:1:31.3:1:1:0:27.3:8:0.25:0:4.5 0/0:5:0:0,0:0,5:0:0,0:24.8:1:29.4:1:1:0:42.6:10:1:0:2.4 -7 151971591 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATCTTGCAAGTGGTAAAA;RSEQ=GCACAGAAATAAGCCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29.5:1:1:0:51:4:1:0:2 -7 151971607 . C T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACGCACAGAAATAAGCC;RSEQ=CAAACAAGAGGGGCAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30.5:1:31.5:1:1:0:51:4:1:0:2 -7 151983386 . G C 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTGAAAAATATCAACTTACA;RSEQ=TTTCAAGAAGCTCAGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:2,0:0.8:0,0:20.9:1:33.4:1:1:0:34.9:16:0.8:0:1.4 1/1:10:8:8,0:1,1:0.8:2,0:30.5:1:30.8:1:0.2:0:35:16:0.8889:0:1.8 -7 151983389 . T G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59627;SOR=2.87331;LSEQ=AAAAATATCAACTTACAGTT;RSEQ=CAAGAAGCTCAGCAACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:10,0:0.0909:0,0:8:0:34:0:1:0:40:2:0.0909:0:2 0/1:13:3:3,0:7,3:0.2308:2,0:24.3:1:31.3:1:0.52797:0:38.7:6:0.2308:0:2.7 -7 151983422 . T C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01511;SOR=4.05622;LSEQ=CAACCCCCAAGCAGGATGAA;RSEQ=ACAAAGAAAACCACACCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:6,1:10,4:0.3333:2,2:21:1:34:0:0.62436:2.31:42.7:14:0.3333:0:1.1 1/0:37:25:17,8:7,5:0.6757:2,2:19.9:1:31.4:1:0.71613:1.50:46.5:50:0.6757:0:1.4 -7 151983478 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52757;SOR=Inf;LSEQ=ACTGCTGAAAACCAAAGATA;RSEQ=AGAGAAAATCCTGAAAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,19:0:2,0:31.2:1:30.1:1:1:0:50.2:70:1:0:0.3 0/1:59:2:1,1:25,32:0.0339:2,2:25:1:31.5:1:1:1.27:54.5:4:0.0339:0:1 -7 151983505 . AAT A 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.45242;SOR=2.29393;LSEQ=AATCCTGAAAGCAGCCAGAG;RSEQ=ATCAAAACATTATTATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:7,17:0.0769:2,0:28:1:31:1:1:0:43.5:4:0.0769:0:0 0/1:37:6:3,3:9,22:0.1622:2,2:18.3:1:29.2:1:0.36663:2.38:54.8:12:0.1622:0.0541:0.8 -7 151983551 . A G 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29323;SOR=4.39103;LSEQ=GGAATAATGATACTACTGAC;RSEQ=CCACACCTGACTTCTCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:0,11:0.0833:0,0:10:0:32:0:1:0:60:2:0.0833:0:1 0/1:10:3:0,3:0,7:0.3:0,0:20:1:33.7:1:1:0:59:6:0.3:0:1 -7 152006398 . AT A 31 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=21.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAATGGCTTACACAAATTA;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:31:1:1:0:60:4:1:0:1 -7 152011990 . G A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52206;SOR=0;LSEQ=TTTAGTTTTGTGATCACACC;RSEQ=CTTTCATATACAATTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:10,0:0.2308:0,0:11:1:29.7:1:1:0:60:6:0.2308:0:1.3 0/0:5:0:0,0:5,0:0:0,0:23.2:1:30.2:1:1:0:60:10:1:0:0 -7 152012477 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=AAAAGTAGCTTTATTCAACT;RSEQ=CTTTAAGCGATAACTATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:17,142:0:2,0:22.5:1:31.9:1:1:0:60:38.75:1:0:0.1 0/1:162:2:1,1:21,139:0.0123:2,2:18.5:1:26:1:0.25389:6.49:60:4:0.0124:0:1 -7 152027452 . T C 26 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01;SOR=Inf;LSEQ=GGTAATATTCTGTACTGGCC;RSEQ=GAGGTGACTAGAGTAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:0:1,0:16:1:30.8:1:1:0:60:44:1:0:0 1/0:3:2:2,0:1,0:0.6667:0,0:29:1:26.5:1:1:0:60:4:0.6667:0:1 -7 152055618 . C A 106 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=CAAATGCTACATGCAGTGTA;RSEQ=AAACATATGCAAAGCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:397,133:0:2,0:22.7:1:32:1:1:0:60:264:1:0:0.1 0/1:509:13:10,3:359,136:0.0255:2,2:20.5:1:28.8:1:1:1.26:60:26:0.0259:0:1 -7 152055741 . T C 153 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=31.40406;LSEQ=GTCCTCATCTTCCACTGCAG;RSEQ=TTTCCCCCTACTTCGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:941:1:1,0:353,587:0.0011:2,0:27:0:26:0:0.3762:0:60:2:0.0011:0:1 0/1:958:31:10,21:347,577:0.0324:2,2:23:1:30.9:1:0.70635:1.26259:60:14.5:0.0309:0:1.3 -7 152055764 . C CA 67 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10802;SOR=0.25198;LSEQ=TCCCCCTACTTCGAGGTCTA;RSEQ=AGAAAAAAAAAAAAATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:8:1,7:162,416:0.0134:2,2:26:1:22.5:1:0.45405:2.7222:60:1.667:0.01:0.0017:2.8 0/0:589:2:0,2:172,396:0.0034:2,0:28:1:26:0:1:0:60:4:0.004:0:3 -7 152055780 . T A 74 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=TCTACAGAAAAAAAAAAAAA;RSEQ=AATAAGTACATAGAGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:0:0,0:81,347:0:2,0:22.9:1:27.8:1:1:0:59.7:17.609:1:0:0.5 0/1:420:10:8,2:94,314:0.0238:2,2:6.2:1:22.3:1:0.00029:13.26:56.5:1.5:0.0157:0:1.8 -7 152132473 . G T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGACTGAAAAGTAAAGTGT;RSEQ=CGGAGCCGGGCGCCGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:28.5:1:1:0:60:4:1:0:1 -7 152132651 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26949;SOR=Inf;LSEQ=CCGCGGGGCGGGCGCCCGGT;RSEQ=ACAGCTCCGGCCCGGCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:95,26:0:2,0:10.7:1:32:1:1:0:53.6:59.5:1:0:0.2 0/1:171:3:1,2:126,42:0.0175:2,2:5:1:29:1:0.1629:5.92295:42:6:0.0175:0:1.3 -7 152132661 . G A 29 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0.7042;LSEQ=GGCGCCCGGTGACAGCTCCG;RSEQ=CCCGGCGCCGCCGCTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:125,34:0.0124:2,2:14:0:31.5:1:0.38859:3.63842:50:4:0.0126:0:1 0/0:228:2:1,1:164,62:0.0088:2,2:22:0:29.5:1:0.47716:2.63208:51:4:0.0089:0:1.5 -7 152132667 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26507;SOR=Inf;LSEQ=CGGTGACAGCTCCGGCCCGG;RSEQ=GCCGCCGCTGGCTCCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:154,46:0:2,0:19:1:31.8:1:1:0:56:199:1:0:0.2 0/1:270:3:1,2:197,70:0.0111:2,2:12:1:27:1:0.17438:5.58529:53:6:0.0112:0:1 -7 152132812 . C T 176 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCCGGGGCTCCAGGCTC;RSEQ=TCGGGGGGTGGTGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:790:0:0,0:378,412:0:2,0:24.8:1:31:1:1:0:59.9:40.579:1:0:0.2 0/1:1055:58:21,37:447,549:0.055:2,2:21.7:1:30.2:1:0.22214:1.43407:59.7:57:0.055:0:1.2 -7 152132933 . GGCC G 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.52172;SOR=1.86327;LSEQ=TGGGGGGCTCCCGCCGCCGC;RSEQ=GCCGCCGCCGCCGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:0,3:25,115:0.021:2,0:33:1:32:1:1:0:57:6:0.0216:0:0 0/1:182:7:1,6:48,127:0.0385:2,2:26.6:1:31.1:1:0.67633:2.25939:58.6:14:0.0389:0.0165:0.4 -7 152132942 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.07928;SOR=0;LSEQ=CCCGCCGCCGCGGCCGCCGC;RSEQ=GCCGCCGCTGCTGCTCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:3:1,2:17,100:0.025:2,2:13.7:1:25:1:0.38862:2.90:60:2:0.0175:0:2.7 0/0:158:0:0,0:37,120:0:2,0:22.5:1:28.7:1:1:0:59.8:30.4:1:0:0.2 -7 152132948 . C T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=0.86206;LSEQ=GCCGCGGCCGCCGCCGCCGC;RSEQ=GCTGCTGCTCGGGTTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:3:0,3:14,98:0.0261:2,0:17:1:29.3:1:1:0:58:6:0.0268:0:1.3 0/1:133:3:0,3:23,107:0.0226:2,0:8.4:1:30.7:1:1:0:57.3:6:0.0228:0:1 -7 152133893 . G T 25 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=AGCTGTGGACCCAGAGATCC;RSEQ=GGATCGGGATCGGGGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:34.5:1:31.5:1:1:0:60:12:1:0:0.3 0/1:6:2:1,1:0,4:0.3333:0,2:18:1:25:0:0.33333:0:60:4:0.3333:0:1 -7 152345228 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACTTTAGGGCTGGGCAC;RSEQ=GGCCTGTAATCCTAGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:14.5:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 152345498 . GAA G 29 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=0.21891;SOR=4.83234;LSEQ=GAGTAAGACTGTTTCAAAAA;RSEQ=AAAAAAAAAAAAAGAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:7,0:0.1538:0,0:15:1:32.9:1:1:0:60:4:0.1667:0.0769:0 1/0:4:2:1,1:0,1:0.5:0,2:25.5:1:29.3:1:1:0:60:4:0.6667:0.25:0 -7 152346007 . C T 212 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0;SOR=16.6857;LSEQ=TCGTTGCAAAAAGAACCAGG;RSEQ=GATAGTCATTTACAAGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1286:9:0,9:630,645:0.007:2,0:1.3:1:27.2:1:0.00385:0:60:18:0.0071:0:1 0/1:1425:150:79,71:627,648:0.1053:2,2:25.5:1:29.4:1:0.43797:1.15:60:300:0.1066:0:1.1 -7 152346219 . CA C 120 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.70403;SOR=0.85934;LSEQ=GTGCTACTACTGCAGTACAC;RSEQ=AAAAAAATCTTCCCAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1304:14:5,9:664,626:0.0107:2,2:28.2:1:31.6:1:0.28866:1.90833:60:28:0.0108:0.0015:0.1 0/0:1407:13:8,5:713,681:0.0092:2,2:23.9:1:30.6:1:0.58083:1.53:60:26:0.0093:0.0014:0.2 -7 152357711 . G C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22694;SOR=Inf;LSEQ=AACTCTTGTGAGGAGTATGT;RSEQ=TATACATGTGAGCTTATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:182,12:0:2,0:25.3:1:32.4:1:1:0:60:193:1:0:0.1 0/1:177:2:1,1:160,15:0.0113:2,2:13.5:1:27:1:0.17309:10.36026:60:4:0.0115:0:1 -7 152357777 . A AT 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTATTTATATAAAGGTTGT;RSEQ=TTTTTTACCATGCACAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:51:28,23:420,214:0.0745:2,2:26.9:1:30.3:1:0.12526:1.61102:60:102:0.0752:0.0117:0.2 0/0:782:0:0,0:483,294:0:2,0:25.4:1:28.5:1:1:0:60:76.7:0.9935:0:0.1 -7 152357922 . C A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12806;SOR=Inf;LSEQ=TAAAAATATAAAATCCTAGA;RSEQ=ATCTATATTTATACCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:62,270:0:2,0:21.4:1:32.2:1:1:0:60:109.667:1:0:0.1 0/1:385:4:3,1:90,291:0.0104:2,2:6.8:1:23.8:1:0.04528:9.63:60:3:0.0079:0:1.8 -7 152357935 . A G 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09512;SOR=0;LSEQ=TCCTAGACATCTATATTTAT;RSEQ=CCATTTTCCGAAAGTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:27,207:0.0127:2,2:26.3:1:30.7:1:0.31538:3.80:60:6:0.0127:0:1 0/0:281:0:0,0:56,224:0:2,0:19.9:1:29.5:1:1:0:60:139:1:0:0.1 -7 152357945 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23282;SOR=0;LSEQ=CTATATTTATACCATTTTCC;RSEQ=AAAGTCTGTAAGATTTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:13,158:0.0116:2,2:25.5:1:29:0:0.15573:11.75:60:4:0.0117:0:1 0/0:185:0:0,0:22,163:0:2,0:21.7:1:31.1:1:1:0:60:184:1:0:0.1 -7 152372816 . C G 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=GGGGTTTTTAGACCATAACT;RSEQ=TTGGGAGGAGAGACCTCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:11,1:0:2,0:25.8:1:32.2:1:1:0:60:24:1:0:0 1/0:4:2:2,0:2,0:0.5:0,0:29.5:1:32:1:1:0:60:4:0.5:0:1 -7 152372924 . G A 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83267;SOR=1.1211;LSEQ=CCCACCTCGGAGGACTCCAG;RSEQ=CTGCCCAGGGGCGGACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:35:35,0:25,0:0.5833:1,1:27.7:1:30.2:1:1:0:60:70:0.5833:0:1.1 1/0:36:22:21,1:14,0:0.6111:1,1:28.2:1:29.4:1:1:0:60:44:0.6111:0:1.1 -7 152372982 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50133;SOR=0;LSEQ=TGGCAGAGGGTGCCAGCATC;RSEQ=CGGGCGTCTAGGCCGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:135,3:0.0142:1,2:10:1:26.5:1:0.05653:39.09288:60:4:0.0146:0:1.5 0/0:120:0:0,0:117,3:0:1,0:22.3:1:30:1:1:0:60:119:1:0:0.2 -7 152373233 . A C 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCATTCACCAACTGCGCAG;RSEQ=CTCTACGGCCAGTCAAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:0:0,0:216,464:0:2,0:24.7:1:29.3:1:1:0:60:39:1:0:0.3 0/1:916:65:24,41:324,524:0.071:2,2:25:1:29.7:1:0.89507:1.05624:60:15.25:0.0682:0:1.2 -7 152373252 . C G 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=7e-05;SOR=1.75136;LSEQ=GACTCTACGGCCAGTCAAAC;RSEQ=CGCCCACCCGCGCGCGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:101:23,78:104,279:0.2087:2,2:24:1:30.8:1:0.44572:1.26352:60:32.667:0.2068:0:1.2 0/1:617:195:63,132:141,278:0.316:2,2:24.6:1:30.4:1:0.78281:1.06261:60:31.5:0.315:0:1.2 -7 152373367 . C T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03816;SOR=0;LSEQ=GTTCCTGTGACGTCAGACTT;RSEQ=CGCGTCCCCCGCGGCGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:4:0,4:2,28:0.1176:2,0:21.5:1:29.8:1:1:0:60:8:0.1212:0:1.3 0/0:41:0:0,0:0,41:0:1,0:15.4:1:31:1:1:0:60:40:1:0:0.1 -7 153621334 . T C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCCCGAGTAGCTGGGATTA;RSEQ=AGGCACATGTCACCACGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:33.5:1:1:0:60:4:1:0:1 -7 153622067 . T C 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCACCTACCTAGCTACAC;RSEQ=TGGTCTGGTTGTTGACATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:16:1:30:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 153622306 . G T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.78795;LSEQ=AGACCATCCGCATAGTAGAA;RSEQ=GTCCCCAAGATTCTGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:110:74,36:208,94:0.2657:2,2:24.9:1:30.3:1:0.81077:1.07629:60:35.667:0.2642:0:1.6 1/0:356:206:134,72:98,51:0.5787:2,2:22.7:1:29.6:1:0.91042:1.0324:60:205:0.5824:0:1.5 -7 153622382 . C G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.31646;LSEQ=TCTGATGAAGGGAGATCATC;RSEQ=CGCATGGTGGAGGGTCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:190:95,95:206,207:0.3146:2,2:27:1:30.2:1:1:1.00:60:26.143:0.3091:0:1.4 1/0:641:387:193,194:120,133:0.6037:2,2:25.5:1:30.3:1:0.57175:1.10:59.9:54.286:0.6061:0:1.5 -7 153622403 . A G 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=19.4912;LSEQ=CGCATGGTGGAGGGTCCCCG;RSEQ=GGTTCTGATGAAGAGAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:2:1,1:275,288:0.0035:2,2:8:1:21.5:1:1:1.05:60:1:0.0018:0:3 0/1:586:38:15,23:262,286:0.0648:2,2:26.3:1:30.5:1:0.40128:1.40385:60:76:0.066:0:1.2 -7 153622450 . G A 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03439;SOR=1.45362;LSEQ=CATGGTTGAGGGTCCCTGCA;RSEQ=TTCTGATGAAGGGAGATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:75:34,41:180,229:0.1546:2,2:24.4:1:29.5:1:0.89949:1.05:60:36.5:0.1527:0:1.1 0/1:395:83:37,46:135,177:0.2101:2,2:27:1:29.6:1:0.90098:1.05:60:26.667:0.2067:0:1.2 -7 153622472 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.40942;LSEQ=TCTGATGAAGGGAGATCATC;RSEQ=CGCATCGTGGAGGGTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:131:54,77:145,196:0.2775:2,2:26.3:1:29.9:1:0.83548:1.0548:60:25.2:0.2745:0:2.5 1/0:383:241:98,143:67,74:0.6292:2,2:22.5:1:28.8:1:0.20057:1.32016:60:25.778:0.6237:0:1.4 -7 153622478 . CG AA 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGGGAGATCATCCCGCAT;RSEQ=TGGAGGGTCCCTGAGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:41:17,24:186,241:0.0874:2,2:27.5:1:29.8:1:0.8697:1.08941:60:40:0.0895:0.0064:2.1 0/0:371:0:0,0:160,210:0:2,0:22.9:1:29.5:1:1:0:60:51.857:1:0:1 -7 153622479 . G A 200 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25743;LSEQ=AAGGGAGATCATCCCGCATC;RSEQ=TGGAGGGTCCCTGAGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:99:42,57:145,186:0.2115:2,2:24:1:30.2:1:0.81845:1.05787:59.9:32:0.2264:0:2.3 0/1:372:24:12,12:149,198:0.0645:2,2:21.9:1:29.4:1:0.52859:1.33:60:48:0.0652:0:2.5 -7 153622556 . A G 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.28962;LSEQ=CGAGGTTCTGATGAAGGGAT;RSEQ=TCCTGCATGATCGAGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:104:44,60:110,150:0.2857:2,2:24:1:30.5:1:1:1:59.9:16.333:0.2808:0:1.7 0/1:328:34:18,16:137,157:0.1037:2,2:22.7:1:30.2:1:0.58687:1.29:60:16:0.0988:0:1.7 -7 153622591 . A G 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.41769;SOR=2.43609;LSEQ=GGGTCCCTGTGGTTCTGATG;RSEQ=GGGGAGATCATCCTGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:2:1,1:137,196:0.006:2,2:20:1:13.5:1:1:1.43:60:0:0:0:3.5 0/1:277:4:2,2:125,148:0.0144:2,2:23.3:1:31:1:1:1.18:60:8:0.0148:0:1 -7 153622662 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14456;LSEQ=GACCACTCCATATGGTGGAG;RSEQ=GTCTCTGCAGTTCTGATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:78:32,46:68,85:0.3362:2,2:21.2:1:30.6:1:0.67454:1.1493:60:77:0.3438:0:1.8 0/1:206:14:9,5:92,100:0.068:2,2:31.1:1:29.6:1:0.27708:1.95:60:28:0.0697:0:1.9 -7 153622682 . T A 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00352;SOR=2.64687;LSEQ=GGTCTCTGCAGTTCTGATAA;RSEQ=GGGAGATCATCCTGCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:215:180:77,103:16,19:0.8372:2,2:23.1:1:30.6:1:0.85243:1.12582:60:89:0.8357:0:1.4 1/1:205:191:93,98:9,5:0.9317:2,2:25.5:1:30.4:1:0.28334:1.89096:60:190:0.936:0:1.1 -7 153622714 . G T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11836;SOR=Inf;LSEQ=CTGCATGGTAGAAGGTCCCT;RSEQ=AGGTTCTGATAAAGGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:105,121:0:2,0:25.8:1:31.8:1:1:0:60:112:1:0:0.8 0/1:219:3:1,2:104,112:0.0137:2,2:12:1:20.3:1:1:1.8521:60:2:0.0093:0:1.3 -7 153622715 . A T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62341;SOR=0.33858;LSEQ=TGCATGGTAGAAGGTCCCTG;RSEQ=GGTTCTGATAAAGGGAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:3:1,2:104,120:0.0132:2,2:14.7:1:27.7:1:1:1.72931:60:6:0.0135:0:1.7 0/0:222:1:0,1:107,113:0.0045:2,0:1:0:27:0:1:0:60:2:0.0046:0:1 -7 153622749 . G T 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0;LSEQ=GGAGATCATCCCACATGGTG;RSEQ=AGGGTCCCTGAGGTTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:14:5,9:96,123:0.0601:2,2:22.8:1:27.2:1:0.59265:1.40288:60:6:0.0522:0:1.6 0/0:230:0:0,0:112,118:0:2,0:23.6:1:30.6:1:1:0:60:56.5:1:0:0.5 -7 153622819 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23365;SOR=Inf;LSEQ=TCCCCAAGGTTTGGATGAAC;RSEQ=GAGATCATCCCACATGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:23,78:0:2,0:24.7:1:30.4:1:1:0:60:49.5:1:0:0.2 0/1:95:2:1,1:29,64:0.0211:2,2:9:0:32.5:1:0.53415:2.19:60:4:0.0211:0:1.5 -7 153749753 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.37975;SOR=3.19953;LSEQ=TGGCGCGCGGGAGGAGCGGC;RSEQ=GCCGGCGCTGGGCTTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:5,7:5,3:0.6:2,2:20.2:1:29:1:0.64992:2.2341:58.4:11:0.6111:0:1.4 1/1:6:5:2,3:0,1:0.8333:0,2:42.8:1:30.2:1:1:0:59.6:10:0.8333:0:1 -7 153749772 . TTGC T 65 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.64241;SOR=1.74629;LSEQ=CCGCCGGCGCTGGGCTTGCC;RSEQ=TGCTGCTGCTGCTGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:4,5:0.3571:2,2:28:1:28.4:1:1:1.18452:59.4:10:0.3571:0:1.6 1/0:6:3:1,2:1,2:0.5:2,2:37.3:1:30.7:1:1:1:59.3:6:0.5:0:1 -7 153749805 . CT C 66 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=1.55528;LSEQ=TGCTGCTGCCTCCCCACCGC;RSEQ=TTTTTTTTTTTTAATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:1,4:1,7:0.3846:2,2:34.2:1:28.6:1:1:1.67:57:4:0.4444:0:1.8 1/0:4:2:0,2:0,2:0.5:0,0:22:1:32.5:1:1:0:60:4:0.6667:0:0.5 -7 153750177 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCTCGGGGGCGGGGGGCGG;RSEQ=GGCGGGTTCTCCGGGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 154594008 . G T 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00061;SOR=0;LSEQ=CCTCAAAGGCAATTTCAAAA;RSEQ=AAAATCCAAGAACATCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:12:8,4:91,50:0.0784:2,2:29.5:1:30.1:1:1:1.10:60:24:0.0789:0:1.5 0/0:128:0:0,0:70,58:0:2,0:27.1:1:31.2:1:1:0:60:256:1:0:0.3 -7 154594042 . TGATGGAATCAGGGTGGGGGCTGCGGGACCCCTGG T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=0.2467;SOR=0.4336;LSEQ=ATCCGCACTAAGAGCAGCTC;RSEQ=GATGGAATCGGGGTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:9:1,8:112,84:0.0439:2,2:12.4:1:30.8:1:0.01177:10.56666:48.2:18:0.0441:0.0439:1.4 0/1:154:3:0,3:80,70:0.0195:2,0:9:1:29.9:1:0.10627:0:60:6:0.0196:0.0195:1 -7 154594052 . AGGGTGGGGGCTGCGGGACCCCTGGGATGGAATCG A 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=4.000;MSILEN=1;SSF=0.24162;SOR=0.77303;LSEQ=AGAGCAGCTCTGATGGAATC;RSEQ=GGGTGGGGGCTGCGGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:212:123:62,61:44,37:0.5802:2,2:23.7:1:31.7:1:0.66772:1.1691:58.7:246:0.6029:0.1792:0.6 1/0:153:79:46,33:31,39:0.5163:2,2:22.7:1:31.2:1:0.10214:1.75:59.4:78:0.5235:0.2353:0.5 -7 154594095 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5134;SOR=0;LSEQ=GGGATGGAATCGGGGTGGGG;RSEQ=CTGCGGGACTCCTGGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:83,91:0.0114:2,2:25:1:29:1:1:1.10:57.5:4:0.0115:0:1.5 0/0:124:0:0,0:70,54:0:2,0:24.6:1:31.5:1:1:0:59.9:123:1:0:0.2 -7 154594099 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57939;SOR=2.66335;LSEQ=TGGAATCGGGGTGGGGGCTG;RSEQ=GGGACTCCTGGGATGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:1:0,1:82,93:0.0057:2,0:42:0:29:0:1:0:60:2:0.0058:0:2 0/1:133:2:1,1:71,60:0.015:2,2:27.5:1:28:1:1:1.18183:60:4:0.0152:0:1 -7 154594112 . A G 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08504;SOR=Inf;LSEQ=GGGGCTGCGGGACTCCTGGG;RSEQ=TGGAAATGGCGTCTCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:82,104:0:2,0:29.7:1:30.3:1:1:0:59.2:61:1:0:0.4 0/1:147:3:2,1:73,71:0.0204:2,2:23.3:1:24.3:1:1:1.94:60:2:0.0141:0:1.3 -7 154594127 . C T 150 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGATGGAAATGGCGTCT;RSEQ=TTGGAGGTTCAGGTGCAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:35:12,23:60,87:0.1923:2,2:27.7:1:29.3:1:0.56563:1.31985:57.8:16.5:0.1864:0:1.2 0/0:149:0:0,0:71,78:0:2,0:28.6:1:31.2:1:1:0:59.9:73.5:1:0:0.2 -7 154594141 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50299;SOR=0;LSEQ=GCGTCTCTTGGAGGTTCAGG;RSEQ=GCAATTTTTTCTCAGTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:58,104:0.0121:2,2:28:1:30.5:1:1:1.79:57.5:4:0.0123:0:1 0/0:136:0:0,0:63,73:0:2,0:29.3:1:28.7:1:1:0:59.9:44.333:1:0:0.2 -7 154594230 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01115;SOR=Inf;LSEQ=TCCTGCGGTCTTCATTCTAC;RSEQ=ATCCAAATTCTTTTGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:0:1,0:25.4:1:32.8:1:1:0:60:60:1:0:0 0/1:16:4:0,4:0,12:0.25:0,0:25.8:1:29.5:1:1:0:60:8:0.25:0:1 -7 154760119 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48897;SOR=Inf;LSEQ=TCTCCATTACTAACTCTCCA;RSEQ=TGCTGGATCATGTCCAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:14,6:0:2,0:26:1:31.9:1:1:0:60:40:1:0:0.1 0/1:22:2:1,1:12,8:0.0909:2,2:5:0:28:1:1:1.47192:60:4:0.0909:0:0 -7 154760182 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.4965;SOR=0;LSEQ=TGGTGGCTGCTGTTGCTGCT;RSEQ=CTGCTGCGGGGGCTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:0.0556:2,2:21:1:28.5:1:1:1.26:60:4:0.0571:0:1 0/0:30:0:0,0:12,18:0:2,0:24.6:1:31:1:1:0:60:14:1:0:0.1 -7 154760266 . TCTG T 31 v4;MAF0.05;pSTD;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=0.88734;LSEQ=TGGCGCTGTCTGACTTTGCA;RSEQ=CTGCTGCTGCTGCTGCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:7,14:0.08:2,2:36:0:31.5:1:1:1.94:60:4:0.087:0:0 0/1:14:1:0,1:5,7:0.0714:2,0:36:0:29:0:1:0:60:2:0.0769:0:0 -7 154760267 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52767;SOR=0;LSEQ=GGCGCTGTCTGACTTTGCAT;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:7,14:0.08:2,2:28:1:28.5:1:1:1.94:60:4:0.087:0:1 0/0:14:0:0,0:5,7:0:2,0:18.6:1:29.7:1:1:0:60:11:0.8462:0:0.3 -7 154760369 . A G 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26354;SOR=0.33116;LSEQ=TGCTGCTGCTGGAGCTGGGC;RSEQ=AGCTGCTGCTGCTGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:7,4:5,2:0.6111:2,2:19.4:1:30.5:1:1:1.40086:60:22:0.6111:0:1 0/1:12:4:2,2:4,4:0.3333:2,2:25.5:1:29.3:1:1:1:60:8:0.3333:0:1 -7 154760495 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49198;SOR=Inf;LSEQ=TGTGGAGGATGCAACTGTTG;RSEQ=TGTGGAAACTGTAGCTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:17.2:1:31.7:1:1:0:60:30:1:0:0.2 0/1:19:2:1,1:10,7:0.1053:2,2:7:0:30.5:1:1:1.40151:60:4:0.1053:0:1.5 -7 154760608 . TCTG T 50 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=1.04248;LSEQ=GGGGTAAGGTTGCTGAGAGA;RSEQ=CTGCTGCTGCTGCTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:1.1:1:30.5:1:1:1.62:60:6:0.1175:0.1136:1.5 0/1:26:3:1,2:11,12:0.1154:2,2:35.3:1:32:1:1:1.79243:60:6:0.12:0:0 -7 154760666 . C T 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0419;SOR=Inf;LSEQ=TGGGGCTGAAGGTGTAAAAC;RSEQ=GGGTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:25.1:1:30:1:1:0:60:16:1:0:0.1 1/0:12:6:2,4:1,5:0.5:2,2:33.3:1:29.2:1:1:2.32:60:12:0.5:0:1.7 -7 154762322 . T G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAATCCAGAAAAGAAGA;RSEQ=GGGACAATTCACCCCACAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:0:32.5:1:1:0:60:4:1:0:1 -7 154798939 . G GA 48 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.11196;SOR=Inf;LSEQ=CTAGGAAAAATAAAAAATTA;RSEQ=AAAAAAAAAAGTAGATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:28,1:0:1,0:23.1:1:32.2:1:1:0:59.3:58:1:0:0.4 0/1:28:3:3,0:24,1:0.1071:1,0:14.7:1:30.3:1:1:0:60:6:0.1071:0.0357:0 -7 154799030 . T C 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.50601;SOR=0;LSEQ=TAGATTATTTCCAAATGGCT;RSEQ=TTTTTAAATGTATTTCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:120,61:0.0109:2,2:33:0:31.5:1:1:1.95946:60:4:0.011:0:1.5 0/0:143:0:0,0:93,50:0:2,0:24:1:30:1:1:0:60:286:1:0:0.8 -7 154799035 . T A 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08109;SOR=0.67175;LSEQ=TATTTCCAAATGGCTTTTTT;RSEQ=AAATGTATTTCTATATTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:93:58,35:71,33:0.4721:2,2:24.8:1:28.6:1:0.45328:1.29659:60:92:0.4718:0:1.8 0/1:152:57:35,22:63,32:0.375:2,2:26.1:1:28.8:1:0.60079:1.23574:60:114:0.3775:0:1.6 -7 154799093 . T G 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04;SOR=1.4342;LSEQ=TCATCTCTCCTGTTCAGCTA;RSEQ=CCATACATCCCTTAAAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:131:62,69:71,72:0.4746:2,2:25.5:1:31.8:1:0.71805:1.09707:60:64.5:0.4813:0:1.6 1/0:271:153:74,79:64,54:0.5646:2,2:27.6:1:31.8:1:0.39118:1.26415:60:152:0.5651:0:1.3 -7 155569538 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGTCACTGCCCACTCATT;RSEQ=CCACAGTTAGATACGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 155571603 . A G 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01679;SOR=Inf;LSEQ=TCAGCGTGTGTGATGGCAGC;RSEQ=TGCTGTGCCGGCACATCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:9,12:0:2,0:26.5:1:30.2:1:1:0:60:42:1:0:0 0/1:29:7:4,3:10,12:0.2414:2,2:30.7:1:31.9:1:0.68166:1.57:60:14:0.2414:0:1.4 -7 155713471 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGCTGGGAGGAGGGGCA;RSEQ=CTGTTCTCCGAGAAAAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:30.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 155714824 . T C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACCAGCGTCTCCCTGGC;RSEQ=CTGTGTGAAGCAGCCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:24,11:0,0:1:0,2:24.5:1:31:1:1:0:60:34:1:0:1.1 1/1:26:26:15,11:0,0:1:0,2:24.2:1:30.5:1:1:0:60:52:1:0:1.1 -7 155714920 . C A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12192;SOR=Inf;LSEQ=CGGGGGCCCTCCCTGGCCAG;RSEQ=TCAGCCCTCCTGCAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:11,19:0:2,0:26.8:1:30.3:1:1:0:60:14:1:0:0.2 0/1:37:4:2,2:14,19:0.1081:2,2:35.3:1:23.8:1:1:1.35:60:3:0.0833:0:1 -7 155716465 . T A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACGGACATCGAGACCAA;RSEQ=CCCTGAGCTCCTCCTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30.5:1:1:0:60:4:1:0:1.5 -7 155835193 . A G 34 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAACTGGGGGTCTCAGCA;RSEQ=TGCTGGGACTAGGGAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:0.2222:2,0:18:1:34:0:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 155835521 . C T 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=32.11638;LSEQ=GGGATGGCCACTGGTCTCAC;RSEQ=GTAATTATTTGAGAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:1:0,1:277,220:0.002:2,0:1:0:24:0:0.44378:0:60:2:0.0021:0:3 0/1:378:23:12,11:192,162:0.0608:2,2:21.7:1:27:1:1:1.08618:58.7:4.75:0.0523:0:2.3 -7 155835541 . T TA 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.90042;LSEQ=CGTAATTATTTGAGAAGAAT;RSEQ=AATCCCCCCCCCCCAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:6:0,6:270,251:0.0113:2,0:22:1:24.5:1:0.01305:0:60:5:0.01:0:2 0/1:392:4:0,4:206,180:0.0102:2,0:35:1:23.5:1:0.04869:0:60:3:0.008:0:3.8 -7 155835544 . TC T 232 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05172;SOR=0.75894;LSEQ=AATTATTTGAGAAGAATTAA;RSEQ=CCCCCCCCCCAGGAAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:192:95,97:173,178:0.3368:2,2:29.3:1:30.7:1:1:1.01:59.8:31:0.3438:0.0246:0.3 0/1:417:116:58,58:141,144:0.2782:2,2:26.1:1:30.7:1:1:1.02:59.9:232:0.3037:0.1007:0.4 -7 155835549 . C A 126 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGAGAAGAATTAATCCCC;RSEQ=CCCCCCAGGAAAGCCTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:579:0:0,0:278,300:0:2,0:24.1:1:30:1:1:0:59.6:20.407:0.9982:0:1 0/1:376:21:11,10:170,182:0.0559:2,2:26.1:1:28.9:1:0.82335:1.18:60:20:0.0557:0:2 -7 155835556 . A G 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.11248;LSEQ=AGAATTAATCCCCCCCCCCC;RSEQ=GGAAAGCCTTATCCAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:151:69,82:168,221:0.274:2,2:24.6:1:27.8:1:0.62955:1.11:59.2:7.882:0.2769:0:2 0/1:383:170:80,90:90,112:0.4439:2,2:24:1:27.2:1:0.67633:1.11:59.6:10.333:0.4669:0:1.9 -7 155835626 . C G 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01213;SOR=0;LSEQ=GCTGAACAATGATATTTTGC;RSEQ=CAAAGCCTTCTTTCTGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:9:0,9:78,200:0.0314:2,0:22.8:1:32.4:1:0.1197:0:59.4:18:0.0321:0:1.1 0/0:209:0:0,0:69,139:0:2,0:26.6:1:30.7:1:1:0:60:68.333:1:0:0.3 -7 155835631 . G T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01169;SOR=Inf;LSEQ=ACAATGATATTTTGCCCAAA;RSEQ=CCTTCTTTCTGTGAATTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:69,204:0:2,0:22.4:1:31.3:1:1:0:59.9:20:1:0:0.3 0/1:193:5:1,4:60,128:0.0259:2,2:27.6:1:30:1:1:1.86965:60:10:0.0262:0:1.4 -7 155836562 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCATCGATCAACTCCATC;RSEQ=GTCCTTACACCCACCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 155973830 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=TTGCTCTGCACCAAGACATC;RSEQ=TCAAGCCTGCAGCCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:1,3:0.375:2,0:16:1:29:1:1:0:60:6:0.375:0:1 0/0:4:0:0,0:0,4:0:0,0:30.3:1:33.8:1:1:0:60:8:1:0:0 -7 156713290 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24778;SOR=Inf;LSEQ=GGGCAGGGTAAGGAGGGTGA;RSEQ=TCGTCCAAGTGATTGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:41,21:0:2,0:25.1:1:32.7:1:1:0:60:124:1:0:0.2 0/1:71:3:2,1:39,29:0.0423:2,2:31:1:30.3:1:1:1.48:60:6:0.0423:0:1 -7 157081587 . T C 31 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCTCCTGAGCCCCAGCTCC;RSEQ=GTGGGGGGATGTGAAGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:49:1:31.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:1:0:25:0:1:0:60:2:1:0:2 -7 157083569 . C T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25237;SOR=Inf;LSEQ=GAGTCAGCGTTTCATGGGGA;RSEQ=AGAGATTCAGCTTGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:14,21:0:2,0:24.8:1:31.2:1:1:0:60:34:1:0:0.1 0/1:45:3:2,1:20,22:0.0667:2,2:35:1:24:1:0.60775:2.16:60:2:0.0465:0:1.3 -7 157083598 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49899;SOR=Inf;LSEQ=AGCTTGGGAAGATGGAAAGT;RSEQ=CTGCGGACGATGGAGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:0:2,0:29.3:1:29.8:1:1:0:60:48:1:0:0 0/1:31:2:1,1:10,19:0.0645:2,2:23.5:1:28:1:1:1.86:60:4:0.0645:0:1 -7 157745058 . G A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=CACGAAGGGAGACAGGCGAG;RSEQ=GTGGGACAGGCAAGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:25:1:25:1:1:0:60:2:0.5:0:1.7 0/0:10:0:0,0:10,0:0:0,0:21.3:1:29.9:1:1:0:58.5:9:1:0:0.5 -7 157745070 . AAGGGTGGGTAGTGTGCATCCCTGAGACGGGGTGGGGGACACGGGGGGAGACAGGCG A 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00224;SOR=Inf;LSEQ=CAGGCGAGGGTGGGACAGGC;RSEQ=AGGGTGGGTAGTGTGCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:21:1:29.3:1:1:0:60:24:1:0:2.7 1/0:14:8:5,3:7,0:0.5714:0,2:26:1:29:1:0.2:0:54.4:7:0.5:0.4286:1.9 -7 157745089 . C G 123 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=CAAGGGTGGGTAGTGTGCAT;RSEQ=CCTGAGACGGGGTGGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:15:15,0:7,0:0.6818:0,1:19.1:1:31.5:1:1:0:60:14:0.6667:0:2.3 0/0:15:0:0,0:7,0:0:0,0:28.6:1:29.1:1:1:0:60:6:1:0:0.1 -7 157745114 . GGGGAGACAGGCGAGGGTGGGTAGTGTGCATGCCTGAGACGGGGTGGGGGACACA G 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.00111;SOR=Inf;LSEQ=AGACGGGGTGGGGGACACGG;RSEQ=GGGAGACAGGCGAGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:35,3:0:2,0:22.6:1:29.6:1:1:0:60:11.667:1:0:1.4 0/1:32:8:5,3:18,4:0.25:2,2:31.8:1:30.5:1:0.3446:2.60027:54.4:16:0.2667:0.0313:1.8 -7 157745220 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49836;SOR=Inf;LSEQ=TGACTCCGTGGTGGAACGTG;RSEQ=GTAGGTGATAGGCTGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:61,76:0:2,0:27.1:1:30.8:1:1:0:60:67.5:1:0:0.5 0/1:142:2:1,1:69,71:0.0141:2,2:24.5:1:31:1:1:1.03:60:4:0.0143:0:1 -7 157745232 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61701;SOR=2.08215;LSEQ=GGAACGTGGGTAGGTGATAG;RSEQ=CTGGCTCCCTGAGCAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:1,0:50,68:0.0084:2,0:1:0:26:0:0.42857:0:60:2:0.0088:0:1 0/1:115:2:1,1:50,63:0.0174:2,2:36.5:1:28:1:1:1.26:60:4:0.0179:0:1.5 -7 157745271 . T C 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05629;LSEQ=CCTCCCCTGTGGTGCAGAGC;RSEQ=GTGGGTCTAGGGGTGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:51:16,35:3,6:0.85:2,2:19.7:1:29.5:1:1:1.0921:60:50:0.8475:0:1 0/1:51:12:2,10:5,34:0.2353:2,2:22.2:1:29.6:1:0.66183:1.35:60:24:0.2353:0:1.3 -7 158387885 . G T 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATGGTGGTGGAGGTGGA;RSEQ=CTGGTGATGATGGAGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:41:0:31.5:1:1:1.7321:60:4:0.4:0:2 0/0:2:0:0,0:1,1:0:2,0:4.5:1:29.5:1:1:0:60:4:1:0:2 -7 158387904 . G C 44 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGGTGATGATGGAGGTG;RSEQ=AGGTGTTAGTGGTGGTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:3,2:0.375:2,2:5:0:28:1:1:1.29:25.7:2:0.2857:0:2 0/0:2:0:0,0:1,1:0:2,0:23.5:1:31.5:1:1:0:60:4:1:0:2 -7 158387913 . G C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=TGATGGAGGTGGAGGTGTTA;RSEQ=TGGTGGTGACGCTGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:20:1:32.4:1:1:0:39.4:10:1:0:2 1/0:3:2:1,1:1,0:0.6667:0,2:32:0:32.5:1:1:0:60:4:0.6667:0:2 -7 158387921 . G A 44 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=GTGGAGGTGTTAGTGGTGGT;RSEQ=ACGCTGGTGGTGGTGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:22:0:28.3:1:1:1.73:25.7:6:0.6:0:2 0/0:3:0:0,0:1,1:0:2,0:24:0:33:1:1:0:60:4:0.6667:0:2 -7 158387923 . C A 47 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=GGAGGTGTTAGTGGTGGTGA;RSEQ=GCTGGTGGTGGTGGAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:22:0:30:1:1:1.73:25.7:6:0.6:0:2 0/0:3:0:0,0:2,1:0:2,0:18.3:1:32:1:1:0:52.7:6:1:0:2.7 -7 158387928 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.28307;SOR=Inf;LSEQ=TGTTAGTGGTGGTGACGCTG;RSEQ=TGGTGGTGGAGGTGGTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:7.4:1:30.9:1:1:0:47.6:28:1:0:1.4 0/1:24:3:2,1:10,11:0.125:2,2:6:1:28.3:1:1:2.13:52.7:6:0.125:0:2.7 -7 158387936 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.60258;SOR=0.50557;LSEQ=GTGGTGACGCTGGTGGTGGT;RSEQ=GAGGTGGTGGTAGAGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:8,12:0.087:2,2:6:0:28:1:1:1.47:60:4:0.087:0:2 0/1:44:2:1,1:21,21:0.0455:2,2:9:0:31:1:1:1:60:4:0.0455:0:2 -7 158387945 . G A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22648;SOR=4.68413;LSEQ=CTGGTGGTGGTGGAGGTGGT;RSEQ=GTAGAGGTGGTGATGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:17:6,11:1,1:0.8947:2,2:17.2:1:28.9:1:1:1.77272:48.3:16:0.8889:0:1.6 1/1:42:41:20,21:1,0:0.9762:0,2:18.5:1:29:1:1:0:46.4:40:1:0:1.7 -7 158387955 . GTGA G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.09135;SOR=0;LSEQ=TGGAGGTGGTGGTAGAGGTG;RSEQ=TGGTGGTTATGGTGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:0.1:2,2:21:0:33:0:1:1.54:60:4:0.1053:0:0 0/0:45:0:0,0:22,23:0:2,0:21:1:28.2:1:1:0:45.6:44:1:0:1.6 -7 158387973 . A G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05234;SOR=3.4255;LSEQ=TGGTGATGGTGGTTATGGTG;RSEQ=TGGTGGCGAAGTTGTAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:3,2:6,9:0.25:2,2:7:0:33.2:1:0.61687:2.16:51.6:10:0.2632:0:2.4 1/0:39:21:11,10:8,10:0.5385:2,2:5.9:1:28.6:1:0.75119:1.36:44.3:9.5:0.5429:0:2 -7 158387981 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTTATGGTGATGGTGGC;RSEQ=AAGTTGTAACAGAGGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:11:1:29:1:1:0:60:4:0.6667:0:1 -7 158449534 . T C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTAGCACTTCCATGCTC;RSEQ=CCAATGCAGGAATAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:31.5:1:1:0:60:4:1:0:1 -7 158450965 . A T 227 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.70611;SOR=0.92272;LSEQ=TGGTCTGCTGACATGAATTA;RSEQ=TAATTCAGCACAACAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:264:183:94,89:40,41:0.6932:2,2:23.7:1:30.3:1:0.79069:1.08:60:90.5:0.6935:0:1.1 1/0:256:173:85,88:43,39:0.6758:2,2:23.9:1:29.9:1:0.68793:1.14088:60:346:0.6758:0:1.1 -7 158451054 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6139;SOR=2.11838;LSEQ=ATGGGGGGACAGCAGAGGCC;RSEQ=GCATAAAGGACATTAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:1:0,1:26,93:0.0083:2,0:2:0:17:0:1:0:60:0:0:0:2 0/1:114:2:1,1:33,78:0.0175:2,2:21:1:27.5:1:0.51312:2.34:60:4:0.018:0:1 -7 158451102 . T C 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01229;SOR=0;LSEQ=GGATCTTGCAGCGATCATCC;RSEQ=AAAAGCGAAAAAAGAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:9:0,9:2,48:0.1525:1,0:18.8:1:33.3:1:1:0:60:18:0.1579:0:1.1 0/0:36:0:0,0:2,34:0:2,0:25.1:1:27.7:1:1:0:60:72:1:0:0.1 -7 158451830 . T C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGGAGTTCGAGAGCAGCC;RSEQ=GATCAACATGGTGAAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:29:1:1:0:60:4:1:0:1 -7 158511431 . C T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAAGTGAAAGAAGCCAAT;RSEQ=TGAAAAGGCCGTATACTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:23.5:1:30:1:1:0:60:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 158512319 . T C 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTAAGTTAAAATATTCA;RSEQ=CTAGAGATGGACATGGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:7.5:1:32:1:1:0:60:8:1:0:1 1/1:3:3:3,0:0,0:1:0,0:13.7:1:32:1:1:0:60:6:1:0:1 -7 158512355 . AG A 74 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22474;LSEQ=GTAATGCACAACTAGAGTTC;RSEQ=CCACGCTTCCTTTCGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:35.5:1:33.5:1:1:0:60:8:0.8:0:1 1/1:6:5:5,0:1,0:0.8333:0,0:31.4:1:31.9:1:1:0:60:10:0.8333:0.1667:0.6 -7 158512451 . T TGGC 33 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.06388;SOR=0;LSEQ=GGCTCCCGATGGATGTTCTC;RSEQ=GGCCTTTTAGAAAACGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:5,4:0.1818:2,0:28.5:1:33:1:0.49091:0:60:4:0.1818:0:0.5 0/0:31:0:0,0:18,12:0:2,0:27.7:1:30.3:1:1:0:60:60:1:0:0.6 -7 158512485 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54902;SOR=Inf;LSEQ=ACGTGGAGTTGTTCCTTTGG;RSEQ=CACGTATATGCGAGTCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:25.9:1:31.1:1:1:0:59.4:46:1:0:0.6 0/1:46:2:1,1:25,19:0.0435:2,2:8:0:30.5:1:1:1.30786:60:4:0.0465:0:1.5 -7 158512522 . A G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01602;SOR=3.94396;LSEQ=TATAAGAAAGGTGATACTGT;RSEQ=GACATCAAGGGAATAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:5,8:6,8:0.4815:2,2:27.2:1:31.7:1:1:1.19191:60:26:0.4815:0:1.1 1/0:38:30:12,18:3,5:0.7895:2,2:26.9:1:30.6:1:1:1.11:60:60:0.8108:0:1.2 -7 158512748 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCCGCAGAGAAAGGTAC;RSEQ=TGCTTCAACTAAAGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -7 158512836 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTGAGCTGCTGGAAGCTA;RSEQ=TCCCTGTGAATTCATGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:31:0:34:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:20:1:30.5:1:1:0:60:4:1:0:3 -7 158512856 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTGTGAATTCATGACA;RSEQ=CATAGGTGTTCAAATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:11:0:32:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:20:1:29.5:1:1:0:60:4:1:0:3 -7 158604837 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCACCCTGGAGAGGGCA;RSEQ=CCTGTGCCCACTCTGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39.5:1:28:1:1:0:60:4:1:0:1 -7 158628009 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04443;LSEQ=CCTTCTTACCCTGCCCCCTT;RSEQ=TCTTGTATGCAATAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:20:10,10:6,11:0.5405:2,2:22.2:1:31.3:1:0.50847:1.80:60:40:0.5556:0:1.1 0/1:42:2:1,1:16,24:0.0476:2,2:5:0:28:1:1:1.49:60:4:0.0476:0:0.5 -7 158628016 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49344;SOR=Inf;LSEQ=ACCCTGCCCCCTTATCTTGT;RSEQ=TGCAATAAATATCAGCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:12,20:0:2,0:22.7:1:29.9:1:1:0:60:64:1:0:0.6 0/1:35:2:1,1:11,22:0.0571:2,2:12.5:1:29:1:1:1.96:60:4:0.0588:0:1 -7 158951489 . A AC 74 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACTGCTGAGGCTGAAGG;RSEQ=CCACCTCCCACCGGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:23.2:1:32.3:1:1:0:60:10:1:0.4:0 1/1:1:1:1,0:0,0:1:0,0:38:0:33:0:1:0:60:2:1:0:0 -7 158951622 . C T 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29551;SOR=3.86387;LSEQ=GGCCTCTCTCTGTCTCTCCA;RSEQ=GTGGGCTCTCTGTGTGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:0.0952:2,2:14:0:32:0:1:1.10554:60:4:0.0952:0:1.5 0/1:10:3:2,1:6,1:0.3:2,2:21.3:1:31.7:1:1:2.64575:60:6:0.3:0:1 -7 158951648 . G GC 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTGTGTGGCTGGGGCT;RSEQ=CCACGTGTGTGGAGTCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:13,13:0,0:1:0,2:29.9:1:31.5:1:1:0:60:52:1:0.0385:0.7 1/1:14:14:8,6:0,0:1:0,2:30.3:1:30.8:1:1:0:60:28:1:0.0714:1.1 -7 158951696 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCACATGGAGTGGCTTCC;RSEQ=GAAGGCAGGTGACATCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:6,13:0,0:1:0,2:29.3:1:30.4:1:1:0:60:38:1:0:1.1 1/1:14:14:6,8:0,0:1:0,2:27.4:1:30.7:1:1:0:60:28:1:0:1.2 -8 564840 . T A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACTGATCTGAAAAAGCA;RSEQ=CCTTCGTGACAGGTGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:35:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 564944 . G C 85 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TCTGGGAAATGCACTTATTA;RSEQ=GAGAGGGACAAACTGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:28.2:1:33:1:1:0:60:12:1:0:2 1/0:2:1:1,0:1,0:0.5:0,0:26:0:27:0:1:0:60:2:0.5:0:2 -8 564957 . C G 78 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41667;SOR=0.21822;LSEQ=CTTATTAGGAGAGGGACAAA;RSEQ=TGTGACTGAGCCACAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:31:1:30.5:1:1:0:60:5:0.8333:0:2 1/0:2:1:1,0:1,0:0.5:0,0:13:0:27:0:1:0:60:2:0.5:0:2 -8 565200 . G T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06571;SOR=0;LSEQ=GTTCCTCTTGACCTGGAATT;RSEQ=TCCAAGTCAGCACCACAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:152,120:0.0109:2,2:6:1:26:0:0.58622:2.52493:60:6:0.0111:0:1 0/0:405:0:0,0:212,188:0:2,0:27.1:1:31.2:1:1:0:60:132.333:0.9876:0:0.6 -8 565219 . C G 103 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00702;SOR=Inf;LSEQ=TGTCCAAGTCAGCACCACAG;RSEQ=TGGTTAAGGCAGCCCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:150,144:0:2,0:26.3:1:31.9:1:1:0:60:72.5:1:0:0.2 0/1:430:10:5,5:216,204:0.0233:2,2:35.3:1:31.3:1:1:1.05871:60:20:0.0236:0:2.1 -8 565232 . C G 241 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCACAGCTGGTTAAGGCAG;RSEQ=CCCTCTCTCTTTCCTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:142,154:0:2,0:25:1:31.2:1:1:0:60:36:1:0:0.2 1/0:424:219:112,107:102,103:0.5165:2,2:26.7:1:31.1:1:0.84592:1.06:60:53.75:0.5193:0:1.2 -8 565280 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17694;SOR=0;LSEQ=TTGGCTTTAAGTCTGCTTAG;RSEQ=ACTCCTGGAAAATCAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:71,117:0.0105:2,2:19.5:1:28:1:1:1.64:60:4:0.0108:0:1 0/0:261:0:0,0:99,161:0:2,0:25.2:1:30.8:1:1:0:60:129:1:0:0.5 -8 565303 . G T 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01154;SOR=Inf;LSEQ=TCCTGGAAAATCAGGTTAAG;RSEQ=GAGATCAGTTGTGTTCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:39,101:0:2,0:22.4:1:31.1:1:1:0:60:280:1:0:0.1 0/1:186:8:2,6:57,121:0.043:2,2:19.4:1:27:1:1:1.41076:60:7:0.0387:0:1.6 -8 566375 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTCGGCCAGGTGTGGGCGGC;RSEQ=GCCGTCCAGAGAGAAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:29.5:1:1:0:60:4:1:0:1.5 -8 566417 . C T 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACGTGTGTGAGGCTGAC;RSEQ=GAACCCCGCACACCCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:13.3:1:30.7:1:1:0:60:6:1:0:2.7 -8 566429 . A C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTGACCGAACCCCGCAC;RSEQ=CCCCATGCTCTCCTGGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:32:0:1:0:60:4:1:0:3 -8 566432 . C G 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACCGAACCCCGCACACC;RSEQ=CATGCTCTCCTGGCTAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:30.5:1:1:0:60:4:1:0:3 -8 2387881 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14289;SOR=0;LSEQ=ATTTAAATATCTGGCTCTAG;RSEQ=TGTTTTCACCATAATCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:52,17:0.0282:2,2:34.5:1:30:1:0.44547:3.00108:60:4:0.0282:0:1 0/0:116:0:0,0:85,31:0:2,0:21.8:1:29.1:1:1:0:60:115:1:0:0.1 -8 2387959 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14435;SOR=0;LSEQ=ACTCTCTCGTCCACGCTGGA;RSEQ=CCAAATAAATGCACTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:94,92:0.0106:2,2:9.5:1:29.5:1:1:1.02163:60:4:0.0109:0:1 0/0:306:0:0,0:151,153:0:2,0:26.8:1:32:1:1:0:60:100.333:0.9967:0:0.7 -8 2387976 . A G 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.85124;SOR=0.95222;LSEQ=GGAGCCAAATAAATGCACTC;RSEQ=TCCTATTTGCTGAAGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:190:112:49,63:40,37:0.5895:2,2:28.4:1:30.9:1:0.30063:1.3875:60:224:0.6022:0:1.6 1/0:303:175:80,95:62,63:0.5776:2,2:25.3:1:30.3:1:0.55799:1.16804:60:174:0.58:0:1.1 -8 2387994 . T C 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TCATCCTATTTGCTGAAGAG;RSEQ=GTGATTAATGCTCTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:49:20,29:57,70:0.2784:2,2:23.9:1:29.6:1:0.73494:1.1796:60:48:0.2775:0:2.1 0/0:278:0:0,0:123,155:0:2,0:24.1:1:29.6:1:1:0:60:277:1:0:0.7 -8 2388081 . A C 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58289;SOR=0.80381;LSEQ=TCAATGTCAGATTATTATGC;RSEQ=TGAGACCATAACTTCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:23:4,19:3,26:0.4423:2,2:17.6:1:32.1:1:0.68559:1.80:60:46:0.4423:0:1.2 0/1:72:28:9,19:11,33:0.3889:2,2:26.3:1:31:1:0.59294:1.41:60:56:0.3889:0:1.3 -8 2388159 . G C 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68817;SOR=0.59617;LSEQ=GAGAGTGTCGTGTGTGTGTG;RSEQ=GTTGGTGTGTGCAAGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:18.8:1:30.8:1:1:0:60:12:0.6667:0:2.2 0/1:15:7:0,7:0,8:0.4667:0,0:26.4:1:31:1:1:0:60:14:0.4667:0:2.1 -8 2388179 . G C 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68659;LSEQ=GGTTGGTGTGTGCAAGTGTT;RSEQ=ACCTGCCAACACTGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:16.5:1:34:0:1:0:60:4:0.5:0:2.5 0/1:10:4:0,4:0,6:0.4:0,0:15.3:1:32.8:1:1:0:60:8:0.4:0:2.5 -8 3174523 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGAGGCAAGAGTGTGTGC;RSEQ=TGGATGAAGCATGCACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 3176240 . G A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTGGGTGGTGGTCACA;RSEQ=GAGTTCCCTAGCTGGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:31.5:1:27:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 3176263 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCCTAGCTGGAGTGTCA;RSEQ=GGTTCCTTCTGCAGGGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:8.5:1:27.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 3176512 . A T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.42365;LSEQ=TTATACAAAGGGAGACCCAG;RSEQ=AACACAACAACACAGATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:1:0,1:71,11:0.012:2,0:1:0:24:0:0.14458:0:60:2:0.0122:0:1 0/1:117:2:1,1:105,10:0.0171:2,2:8:1:28.5:1:0.17993:10.05896:60:4:0.0175:0:1 -8 3176527 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15845;SOR=0;LSEQ=CCCAGAAACACAACAACACA;RSEQ=ATTCAGCCATTCCTATGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:82,19:0.0194:2,2:25:1:29:0:0.35218:4.23209:60:4:0.0198:0:1 0/0:155:0:0,0:124,31:0:2,0:24.8:1:31.6:1:1:0:60:76.5:1:0:0.1 -8 3176558 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11833;SOR=0;LSEQ=TCCTATGGATCACTCCCTTA;RSEQ=ACAGAATGGAATTTGATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:101,48:0.0132:2,2:30.5:1:30:1:0.54517:2.09292:60:4:0.0132:0:1.5 0/0:287:0:0,0:185,102:0:2,0:23.9:1:30.7:1:1:0:60:56.4:1:0:0.3 -8 3176639 . C T 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20374;SOR=0.80758;LSEQ=GTCTTGCATCCAGATAATAA;RSEQ=TGAAGAAGTAACTTCCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:243:144:57,87:46,53:0.5926:2,2:28.2:1:30.3:1:0.29405:1.32316:60:47:0.5875:0:1.3 1/0:474:256:118,138:104,113:0.5401:2,2:24.6:1:29.5:1:0.71214:1.07618:60:84.333:0.5406:0:1.2 -8 3176670 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12227;SOR=0;LSEQ=ACTTCCTTGCTGAAAAGGCC;RSEQ=AGCTTTTAAAAAAAATCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:65,119:0.0108:2,2:40.5:1:32:1:1:1.82:60:4:0.0108:0:1 0/0:345:0:0,0:141,202:0:2,0:25.3:1:28.8:1:1:0:60:56.167:0.9941:0:0.7 -8 3176677 . TAA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=8.000;MSILEN=1;SSF=0.12141;SOR=0;LSEQ=TGCTGAAAAGGCCTAGCTTT;RSEQ=AAAAAATCTAGGAATAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:56,103:0.0123:2,2:8:1:31.6:1:1:1.83:60:4:0.0123:0.0062:0.5 0/0:302:0:0,0:123,177:0:2,0:26.7:1:28.9:1:1:0:60:600:0.9934:0:0.6 -8 3176692 . A G 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19724;LSEQ=GCTTTTAAAAAAAATCTAGG;RSEQ=ATAAATGGTCAAAAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:32:11,21:29,66:0.252:2,2:23.4:1:30.5:1:0.66759:1.19:60:31:0.248:0:1.8 0/1:258:16:6,10:80,162:0.062:2,2:25.1:1:29.7:1:0.78588:1.21:60:15:0.0588:0:1.9 -8 3176717 . C G 75 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.32706;SOR=Inf;LSEQ=ATGGTCAAAAAAATGAAACT;RSEQ=ACATATTTCTGTTTTTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:20,57:0:2,0:20.6:1:32:1:1:0:60:154:1:0:0.6 0/1:175:5:1,4:42,128:0.0286:2,2:36:1:32.6:1:1:1.31058:60:10:0.0289:0:1.2 -8 3489660 . T C 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29901;SOR=Inf;LSEQ=AACATTTTCTTTAACATTCC;RSEQ=GCTAGAGAAAAGGGATTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:57,11:0:2,0:23.2:1:30.8:1:1:0:60:67:1:0:0.7 0/1:111:4:2,2:85,22:0.036:2,2:25.5:1:28.3:1:0.20358:3.80255:60:8:0.036:0:1 -8 3489668 . A C 123 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00066;SOR=Inf;LSEQ=CTTTAACATTCCTGCTAGAG;RSEQ=AAAGGGATTTATTTTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:69,18:0:2,0:20.7:1:29.1:1:1:0:60:20.75:1:0:0.7 0/1:142:15:12,3:90,37:0.1056:2,2:26.8:1:31.7:1:0.55717:1.64:60:30:0.1064:0:1.1 -8 3489674 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11554;LSEQ=CATTCCTGCTAGAGAAAAGG;RSEQ=ATTTATTTTAAAAAATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:27:23,4:60,21:0.2477:2,2:20.4:1:29.7:1:0.29868:2.00:60:54:0.25:0:2 0/1:165:6:5,1:109,50:0.0364:2,2:22:1:29.5:1:0.6672:2.28:60:12:0.0368:0:2 -8 3489677 . T C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.09725;LSEQ=TCCTGCTAGAGAAAAGGGAT;RSEQ=TATTTTAAAAAATTCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:30:25,5:60,21:0.2703:2,2:19.4:1:31.3:1:0.44943:1.74:60:60:0.2778:0:2 0/1:174:6:5,1:113,55:0.0345:2,2:25:1:31.8:1:0.66549:2.42:60:12:0.0347:0:2 -8 3489756 . G C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.28946;LSEQ=GAAAATGCAATCATTTCTAG;RSEQ=GCTGGGCTTTAACCATTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:18:10,8:101,104:0.0804:2,2:19.8:1:29.7:1:0.63257:1.29:60:36:0.0807:0:1.1 0/1:390:152:79,73:113,124:0.3897:2,2:25.6:1:30.7:1:0.467:1.19:60:151:0.3974:0:1.1 -8 3489816 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15678;SOR=0;LSEQ=AGTGTTGGTTGGAGGCATTC;RSEQ=TCCATCTCATAGGTAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:60,105:0.012:2,2:6.5:1:31.5:1:1:1.74:60:4:0.012:0:1.5 0/0:254:0:0,0:98,156:0:2,0:24:1:30.3:1:1:0:60:126:1:0:0.4 -8 3489842 . C T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0476;LSEQ=CTCATAGGTAAAGCCCCGTT;RSEQ=GCCTTCTTGGACCTTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:43:15,28:24,54:0.3554:2,2:24.6:1:28.6:1:0.68711:1.20:60:9.75:0.3362:0:1.3 0/1:158:4:0,4:54,100:0.0253:2,0:10.3:1:28:1:0.29986:0:60:8:0.026:0:1.5 -8 3489935 . G T 94 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00439;SOR=0.07133;LSEQ=AAAGACTACCCCTGGGATAT;RSEQ=TCCATGTTATAGGAGATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:0.3913:1,0:15.3:1:29.8:1:1:0:60:18:0.4091:0:1.3 0/1:24:1:0,1:2,21:0.0417:2,0:6:0:31:0:1:0:60:2:0.0417:0:2 -8 4166193 . C T 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=ACAGTTTATAAGAGGCTTTA;RSEQ=GCAAATATCTGGGTGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:0.3636:0,0:34.8:1:31.8:1:1:0:60:8:0.3636:0:1.5 0/0:3:0:0,0:3,0:0:0,0:16.3:1:33:0:1:0:60:6:1:0:0 -8 4166304 . A C 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57595;SOR=0.62318;LSEQ=ATGACTAAAGATTATTTACA;RSEQ=AACTAATTCACAGATGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:43:40,3:6,0:0.8776:0,2:26.4:1:32.9:1:1:0:60:86:0.8776:0:2 1/1:49:40:33,7:7,2:0.8163:2,2:23.1:1:31.9:1:0.6631:1.34:60:80:0.8163:0:2 -8 4166317 . G A 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03474;SOR=0.32491;LSEQ=ATTTACAAAACTAATTCACA;RSEQ=ATGAGTTATTATGCTATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:62:53,9:5,0:0.9254:0,2:23.4:1:30.5:1:1:0:60:124:0.9254:0:1.7 1/1:80:64:46,18:13,3:0.8:2,2:20.7:1:29.6:1:0.54021:1.68536:60:63:0.7975:0:1.6 -8 4166426 . A G 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0093;SOR=0.5478;LSEQ=ACATGGTTTAAAATACTCAG;RSEQ=AAATATCAAAGGTCCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:193:158:75,83:20,15:0.8187:2,2:27.5:1:31.1:1:0.35203:1.47256:60:38.5:0.8148:0:2.2 1/0:288:205:104,101:41,42:0.7118:2,2:25.8:1:30.7:1:0.89669:1.05:60:67.333:0.7113:0:2.2 -8 4166452 . C G 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00096;SOR=Inf;LSEQ=TCAAAGGTCCATTTATTTCT;RSEQ=CTTTTTTAAAGACTCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:85,106:0:2,0:25:1:31.2:1:1:0:60:190:1:0:2.1 0/1:266:13:7,6:114,139:0.0489:2,2:24:1:29.4:1:0.57813:1.42:60:5.5:0.0418:0:1 -8 4166465 . C A 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14588;SOR=0.68435;LSEQ=TATTTCTCCTTTTTTAAAGA;RSEQ=TCTCAAATACTCCCTGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:164:133:55,78:15,16:0.811:2,2:26.2:1:30.6:1:0.54693:1.32719:60:132:0.8098:0:3 1/0:236:176:76,100:27,33:0.7458:2,2:25.5:1:29.9:1:0.88042:1.07622:60:175:0.7479:0:2.9 -8 4166475 . C T 213 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39057;SOR=0.79484;LSEQ=TTTTTAAAGACTCTCAAATA;RSEQ=TCCCTGTAACCTTCTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:120:44,76:14,20:0.7792:2,2:26.2:1:30.1:1:0.69016:1.20757:60:59:0.7763:0:3.2 1/0:213:157:61,96:24,31:0.7371:2,2:24.6:1:29.3:1:0.63176:1.21725:60:38.25:0.7356:0:3 -8 4166496 . A G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50343;SOR=Inf;LSEQ=TCCCTGTAACCTTCTGACAT;RSEQ=ATGTTGAACTAATTCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:41,87:0:2,0:23.9:1:28.9:1:1:0:60:127:1:0:2.5 0/1:157:2:1,1:53,102:0.0127:2,2:18:1:26.5:1:1:1.92:60:4:0.0129:0:3.5 -8 4166516 . A T 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATGTTGAACTAATTCCTAA;RSEQ=ACTAGGTGAGAAAATGCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:16:4,12:17,62:0.1684:2,2:26.1:1:28.9:1:0.74778:1.21:60:32:0.1702:0:3.7 0/0:114:0:0,0:31,83:0:2,0:23.2:1:29:1:1:0:60:56:1:0:2.1 -8 4166522 . G A 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50376;SOR=0.76036;LSEQ=GAACTAATTCCTAAAACTAG;RSEQ=TGAGAAAATGCATAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:83:62:10,52:6,15:0.747:2,2:24.7:1:31:1:0.21811:2.05968:60:124:0.747:0:3.1 1/0:94:65:14,51:8,20:0.6915:2,2:26.4:1:29:1:0.59533:1.45105:60:64:0.6957:0:2.9 -8 4166565 . C T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.92948;LSEQ=TGATTATTGATGTCATTCTT;RSEQ=ACACCTATATTACTTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:28:0,28:0,11:0.7179:0,1:25.4:1:28.5:1:1:0:60:56:0.7179:0:2.5 1/0:37:26:1,25:0,11:0.7027:0,1:19.5:1:28.4:1:1:0:60:52:0.7027:0:2.5 -8 4166691 . G C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TTCAACAACTTTCTGAAGAT;RSEQ=TGTGGAGATTCTGAAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:36:0:33:0:1:0:60:2:1:0:0 1/1:2:2:0,2:0,0:1:0,0:34:1:31.5:1:1:0:60:4:1:0:3 -8 4166712 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGGAGATTCTGAAGGTTA;RSEQ=TTTCAATTCCTAGGGTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:4:0:26:0:1:0:60:2:0.5:0:5 1/1:2:2:0,2:0,0:1:0,0:23.5:1:30.5:1:1:0:60:4:1:0:3 -8 5498148 . CT C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=3.38757;LSEQ=TGGGAGAACGGACTAACTCA;RSEQ=GGGATACAGAAATGTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:29.5:1:33:1:1:0:60:4:0.3333:0:0.5 1/0:3:2:2,0:1,0:0.6667:0,0:12.5:1:32.5:1:1:0:60:4:0.6667:0:0 -8 5498230 . TTC T 110 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=12.000;MSILEN=2;SSF=0.03235;SOR=4.34851;LSEQ=CTTTCTCTCTCTCTTTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:4,0:17,0:0.1818:1,0:22.3:1:31.5:1:1:0:60:8:0.1905:0:0.5 1/0:24:12:12,0:9,0:0.5:0,0:27.7:1:30.9:1:1:0:60:24:0.5455:0.0417:1.3 -8 5498260 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=8.43667;LSEQ=CTCTCTCTCTCTCTCTGTCT;RSEQ=TCTCTCTCTCTCATACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:4,0:22,2:0.129:2,0:35:1:33:1:1:0:60:8:0.1538:0:1 1/0:48:27:25,2:20,0:0.5625:1,2:23.1:1:30.7:1:0.50046:0:59.6:26:0.5652:0:1.2 -8 5498335 . T C 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0452;SOR=Inf;LSEQ=AAGTGCAATCTTCTTTCTCT;RSEQ=ATTAGGAATTCTAAATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:131,50:0:2,0:24:1:29.4:1:1:0:60:59.333:1:0:0.7 0/1:271:7:7,0:177,87:0.0258:2,0:20.7:1:32:1:0.10067:0:60:14:0.026:0:2.9 -8 5498364 . G C 249 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7496;SOR=1.06348;LSEQ=TTCTAAATTACTTGGCATCG;RSEQ=TCTTACACCTTTACAAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:157:100,57:70,42:0.5836:2,2:25.7:1:31.8:1:0.89814:1.05:60:51.333:0.5811:0:1.6 1/0:411:246:144,102:96,69:0.5985:2,2:25.6:1:31.4:1:1:1.01:60:48.2:0.5951:0:2 -8 5498411 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.14416;LSEQ=AATCTCACTCCTTCTTGGCT;RSEQ=CCAGTTTCTCGATGGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:93:45,48:125,125:0.2711:2,2:26.2:1:30.9:1:0.80907:1.06644:60:45.5:0.2692:0:2.5 1/0:486:295:127,168:92,98:0.607:2,2:27:1:30.8:1:0.26272:1.24128:60:72.75:0.6088:0:2.4 -8 5498446 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.03145;LSEQ=GGCTCTGCTCTCTCCACCCC;RSEQ=GAGGCCTTACATACGGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:72:29,43:73,116:0.2759:2,2:26.1:1:30.5:1:0.88725:1.07:60:71:0.2763:0:2.5 1/0:353:214:74,140:50,88:0.6062:2,2:24.3:1:30:1:0.81931:1.07472:60:41.8:0.6023:0:2.6 -8 5498487 . C T 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.64143;LSEQ=CATATTCCTGAATGCCCACG;RSEQ=CTCACCTGACTCATTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:35:7,28:18,82:0.2593:2,2:19.8:1:28.8:1:0.80331:1.14:60:34:0.2556:0:2.2 1/0:137:85:20,65:10,42:0.6204:2,2:22.5:1:29.3:1:0.67163:1.29:60:170:0.6204:0:2.3 -8 5498584 . C A 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.53281;SOR=0;LSEQ=GGACCGAGGCCCTGTGTGAC;RSEQ=CCAATAAGAGCAGTTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:0,18:0.1429:1,0:36:1:29:1:1:0:60:6:0.1429:0:1 0/0:10:0:0,0:0,10:0:0,0:24.6:1:31.4:1:1:0:60:20:1:0:0.2 -8 6327065 . A G 72 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.36252;SOR=0.27848;LSEQ=TATATGATTCTGATAGTACC;RSEQ=TATATATTTAGATGGGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:5,0:12,0:0.2941:0,0:22.2:1:31.4:1:1:0:60:10:0.3125:0:1 0/1:10:1:1,0:9,0:0.1:0,0:11:0:25:0:1:0:60:2:0.1:0:1 -8 6327147 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18227;SOR=0;LSEQ=GGTTATCTCCTTATTTTACT;RSEQ=ATTCTTAAGGAAAATTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:61,12:0.0267:2,2:14:1:31.5:1:0.31856:4.92389:60:4:0.027:0:1 0/0:100:0:0,0:82,18:0:2,0:23.5:1:29.9:1:1:0:60:200:1:0:0.1 -8 6327177 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1684;SOR=0;LSEQ=GAAAATTAATTTCACTGTTT;RSEQ=CCAAAGAACTGATAGCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:101,35:0.0144:2,2:10:1:30:1:0.45509:2.8594:60:4:0.0145:0:1.5 0/0:199:0:0,0:134,65:0:2,0:23.2:1:28.3:1:1:0:60:198:1:0:0.2 -8 6327194 . TA T 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07203;SOR=0;LSEQ=TTTACCAAAGAACTGATAGC;RSEQ=AACCCAAAAGATTTCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:1,2:123,51:0.0169:2,2:21.7:1:29.3:1:0.21384:4.77481:60:6:0.0171:0.0056:0.3 0/0:247:0:0,0:161,86:0:2,0:25.4:1:28.4:1:1:0:60:494:1:0:0.3 -8 6327274 . C G 272 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.32984;LSEQ=AAACGGGTATATCTGTTTAA;RSEQ=TTGACCTATCTTTGGTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:352:234:128,106:62,55:0.6648:2,2:26.2:1:32:1:0.82041:1.07:60:233:0.6638:0:1.1 1/1:495:407:226,181:43,42:0.8222:2,2:25.7:1:31.4:1:0.47248:1.22:60:134.667:0.8211:0:1.1 -8 6327350 . TTC T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.02609;SOR=0;LSEQ=TCATGCATTCAATACTCTTT;RSEQ=TCTCTCTCTCCCTGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:4:1,3:65,167:0.0169:2,2:35.8:1:30.5:1:1:1.16692:60:8:0.0174:0:0.3 0/0:349:0:0,0:125,224:0:2,0:23.2:1:29:1:1:0:60:115.333:1:0:0.4 -8 6710087 . TC T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAGTCTCTGTTTGTTCT;RSEQ=CCCACTATTCTCAAATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:8.5:1:32.1:1:1:0:60:4:1:0.5:0 1/1:2:2:2,0:0,0:1:0,0:23:1:30:1:1:0:60:4:1:0:0 -8 6710305 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13509;SOR=0;LSEQ=TTATCAGCTGCTAAGTCTTT;RSEQ=CACACAGCCTGTCAAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:81,50:0.015:2,2:16:0:32:0:1:1.61385:60:4:0.0155:0:1.5 0/0:228:0:0,0:130,98:0:2,0:22:0:14:0:1:0:60:0:0:0:2 -8 6710324 . G T 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16234;SOR=Inf;LSEQ=TCCACACAGCCTGTCAAAGG;RSEQ=AGAAAGACATGTTTCTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:98,69:0:2,0:25.4:1:31:1:1:0:60:82.5:1:0:0.5 0/1:280:5:2,3:144,131:0.0179:2,2:20.6:1:26.8:1:0.67278:1.64592:60:10:0.0185:0:1.4 -8 6710326 . G T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30224;SOR=Inf;LSEQ=CACACAGCCTGTCAAAGGGA;RSEQ=AAAGACATGTTTCTAACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:100,73:0:2,0:25:1:31.5:1:1:0:60:85.5:1:0:0.5 0/1:285:4:1,3:144,137:0.014:2,2:17.3:1:26.8:1:0.36372:3.14173:60:8:0.0143:0:1.5 -8 6710357 . T C 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03007;SOR=1.4822;LSEQ=TTCTAACTGCCCGCATTCTG;RSEQ=TCTGCTGCATTTCTCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:197:101:53,48:49,47:0.5127:2,2:26.8:1:31.5:1:0.88703:1.06:60:32.667:0.5078:0:1.1 1/0:338:206:101,105:57,73:0.6095:2,2:26.8:1:32.1:1:0.37107:1.23:60:102:0.6108:0:1.3 -8 6710414 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19336;SOR=0;LSEQ=CTGGGCCCCATCCCAGGGAG;RSEQ=CAGAGAAGCTGGCTTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:46,82:0.0154:2,2:22:1:31.5:1:1:1.77:60:4:0.0157:0:2 0/0:165:0:0,0:57,108:0:2,0:23.4:1:31.1:1:1:0:60:164:1:0:0.7 -8 6710415 . C T 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGCCCCATCCCAGGGAGC;RSEQ=AGAGAAGCTGGCTTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:42,83:0:2,0:24.1:1:31.7:1:1:0:60:250:0.9921:0:0.5 0/1:162:22:9,13:48,92:0.1358:2,2:23.1:1:28:1:0.63237:1.32:60:44:0.1366:0:1.8 -8 6710502 . A C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77459;SOR=0.82681;LSEQ=TGTTCCAGGAAACTTTCCCC;RSEQ=AGGGGAGACCACAAGTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:0,17:2,12:0.5484:2,1:24.1:1:31.9:1:0.1957:0:60:34:0.5667:0:1.1 1/0:18:9:0,9:1,8:0.5:2,0:28.2:1:33.2:1:1:0:60:18:0.5294:0:1 -8 7717592 . A G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05447;LSEQ=TGTTTAAAGTCATCGTACGT;RSEQ=GCATTTGCAGATCTGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:3,4:9,10:0.2692:2,2:22:1:32.4:1:1:1.19164:57.1:14:0.28:0:1 0/1:25:7:2,5:7,11:0.28:2,2:19.1:1:28.6:1:1:1.56245:60:6:0.2609:0:1.1 -8 10335775 . T C 58 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACCCTAATCCAGTGACC;RSEQ=AGCAGAAGTAATTCCTCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:20.8:1:25.4:1:1:0:57.8:1.5:1:0:1.4 1/1:2:2:2,0:0,0:1:0,0:15:1:32:0:1:0:60:4:1:0:1.5 -8 10335888 . AGGCTGCAGTGGTTGT A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=1.133;MSILEN=1;SSF=0.08034;SOR=Inf;LSEQ=GCCTGGCTGCAGTGGTTGTC;RSEQ=GGCTGCAGTGGTTGTGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:24,1:0:1,0:25.4:1:30.7:1:1:0:60:7.333:1:0:0.3 0/1:20:3:3,0:16,1:0.15:1,0:39.7:1:34:0:1:0:60:6:0.1579:0:0 -8 10336140 . A G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.63159;LSEQ=TAAAAAGCTTAAAAGCTTTT;RSEQ=AAACAGCTCCCAGGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:0,9:0,3:0.75:0,0:27.1:1:30.6:1:1:0:60:18:0.75:0:1.1 1/1:12:10:0,10:0,2:0.8333:0,0:24.5:1:31.5:1:1:0:60:20:0.8333:0:1.1 -8 10470068 . C T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCCGCCTTGCTCTGGGC;RSEQ=GCCCAGCCCTGCTCCATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:41:1:31.5:1:1:1:60:4:0.3333:0:1 -8 10470069 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCCGCCTTGCTCTGGGCC;RSEQ=CCCAGCCCTGCTCCATCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:17.5:1:28.5:1:1:1:60:4:0.3333:0:1 -8 10470758 . G C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.21169;SOR=Inf;LSEQ=GCCAGGAGCAGGGCCCACCG;RSEQ=GGGGTTGCTAGGACCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:17,0:0:1,0:26.4:1:31.4:1:1:0:60:34:1:0:0.2 0/1:15:2:2,0:13,0:0.1333:1,0:32:1:34:0:1:0:60:4:0.1333:0:1.5 -8 10470801 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49808;SOR=Inf;LSEQ=TCTGGCAGCCGTGGCGTGCT;RSEQ=CCTGGCGGAGACCGCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:27,2:0:2,0:21.6:1:32.9:1:1:0:60:58:1:0:0.1 0/1:36:2:1,1:31,3:0.0556:2,2:40:1:29:1:0.2127:9.09212:60:4:0.0556:0:1.5 -8 10470915 . A G 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.84102;SOR=1.0524;LSEQ=CTGTGAGCCATGGGGGCAGC;RSEQ=TCAGGATAAAGGAATAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:159:90:51,39:33,36:0.566:2,2:26.5:1:30.6:1:0.33633:1.42:60:180:0.566:0:2 1/0:280:162:83,79:65,53:0.5786:2,2:26.3:1:30.3:1:0.54618:1.16666:60:80:0.5861:0:2 -8 10470933 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12935;SOR=0;LSEQ=GCATCAGGATAAAGGAATAA;RSEQ=ACAGTCACGAGCCTCCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:81,86:0.0118:2,2:15.5:1:30.5:1:1:1.06:60:4:0.012:0:2.5 0/0:300:0:0,0:157,142:0:2,0:26.8:1:29.6:1:1:0:60:73.75:0.9966:0:1.6 -8 10470940 . AC GT 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13216;SOR=0;LSEQ=GATAAAGGAATAAAACAGTC;RSEQ=GAGCCTCCCACGACCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:80,87:0.0118:2,2:42.5:1:30.3:1:1:1.09:60:4:0.012:0:1.5 0/0:295:0:0,0:148,147:0:2,0:26.6:1:29.5:1:1:0:60:58:1:0:1.6 -8 10470941 . C T 242 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13506;SOR=Inf;LSEQ=ATAAAGGAATAAAACAGTCA;RSEQ=GAGCCTCCCACGACCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:169:167:80,87:0,0:0.9882:0,2:27.5:1:30.3:1:1:0:60:82.5:1:0:1.6 1/1:290:290:145,145:0,0:1:0,2:27:1:29.6:1:1:0:60:71.5:1:0:1.7 -8 10470985 . C T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30052;SOR=Inf;LSEQ=ACCACTGCCTCCAAAATGCA;RSEQ=GGTGACAGCTGTGCGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:37,65:0:2,0:22.7:1:30.8:1:1:0:60:204:1:0:1.2 0/1:183:4:2,2:68,111:0.0219:2,2:23.3:1:27.8:1:0.6375:1.63:60:8:0.0222:0:2 -8 10471002 . G A 94 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1025;SOR=5.14433;LSEQ=GCACGGTGACAGCTGTGCGC;RSEQ=GTGGCTCAGGCCTGTAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:1:0,1:18,51:0.0143:2,0:29:0:32:0:1:0:60:2:0.0145:0:2 0/1:129:9:3,6:38,82:0.0698:2,2:16.6:1:29.7:1:1:1.08:60:18:0.0703:0:1.9 -8 10471109 . C A 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTAGTGAGACACCATCTCT;RSEQ=CAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:0,11:0,1:0.9167:0,0:5.2:1:30.5:1:1:0:60:22:1:0:1 1/1:5:5:0,5:0,0:1:0,0:5.4:1:30:1:1:0:60:10:1:0:1 -8 10584029 . A T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1827;SOR=0;LSEQ=TCAGAAGGAAGCCCGGGTCC;RSEQ=CGCGCTTGCACAGCCGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:36,17:0.0364:2,2:10.5:1:28.5:1:1:2.08642:60:4:0.0364:0:1 0/0:73:0:0,0:53,20:0:2,0:22:1:28.7:1:1:0:60:72:1:0:0 -8 10584048 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50779;SOR=Inf;LSEQ=CACGCGCTTGCACAGCCGCT;RSEQ=GGCCTGCTTCTTCCTGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:47,33:0:2,0:23:1:29.5:1:1:0:60:39:1:0:0.1 0/1:107:2:1,1:62,43:0.0187:2,2:5:0:30.5:1:1:1.4368:60:4:0.0187:0:1 -8 10584117 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17948;SOR=0;LSEQ=CATGTGCTGCAGGCGCAGCC;RSEQ=CTCCGCCTCGTCCACGTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:2,0:42,55:0.0202:2,0:22:1:27.5:1:0.19501:0:60:4:0.0204:0:1 0/0:134:0:0,0:57,77:0:2,0:25.7:1:30.8:1:1:0:60:66:1:0:0.2 -8 10584160 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4989;SOR=Inf;LSEQ=CTCTTCTGGGACAGCGTCAG;RSEQ=GCCTTCCACGACTTTCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:16,32:0:2,0:26.2:1:30.1:1:1:0:60:47:1:0:0.4 0/1:57:2:1,1:17,38:0.0351:2,2:10:0:32:0:0.53571:2.20:60:4:0.0351:0:1 -8 10584212 . C T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07363;SOR=0.28543;LSEQ=AGAGGAGGCCATGCTCAGTG;RSEQ=TGTGCCCCGCAGGCATCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:2,16:0,5:0.7826:0,2:21.2:1:30.4:1:1:0:60:36:0.8182:0:1.2 1/0:26:13:2,11:2,11:0.5:2,2:13.5:1:30.2:1:1:1:60:26:0.5:0:1.2 -8 10584288 . C T 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACACCTCCCTTCCCCCTC;RSEQ=CAGCCACAGAGGACACGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:19.8:1:30.4:1:1:0:60:10:0.8333:0:2 1/1:5:5:0,5:0,0:1:0,0:29.8:1:26.2:1:1:0:60:4:1:0:1.6 -8 10634248 . T C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02271;SOR=0.15384;LSEQ=GAGGAAGGGGAAGCAAGGGA;RSEQ=GGGATGGTGCTGCCCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:10,8:1,1:0.9:2,2:24.3:1:30.5:1:1:1.24:60:36:0.9:0:1 1/0:28:16:10,6:6,6:0.5714:2,2:24.1:1:30.8:1:0.70217:1.64:60:32:0.5926:0:1.4 -8 10634261 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50192;SOR=Inf;LSEQ=CAAGGGATGGGATGGTGCTG;RSEQ=CCAGACCTGTCACCAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:0:2,0:24:1:30.9:1:1:0:60:27:1:0:0.6 0/1:37:2:1,1:20,15:0.0541:2,2:43:0:30.5:1:1:1.32286:60:4:0.0556:0:2 -8 10634324 . C T 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00087;SOR=Inf;LSEQ=ACGGCTGGAGACGCTGGAGA;RSEQ=GCAGAGCTTTGCCTTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:0:2,0:21.1:1:31.2:1:1:0:60:46:1:0:0.4 0/1:37:13:6,7:11,13:0.3514:2,2:22.5:1:29.4:1:1:1.01:60:26:0.3514:0:1.4 -8 11096045 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17286;SOR=0;LSEQ=GGAGGAAGGAAGGTGAGTAT;RSEQ=AGATATATTATCCAGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:113,20:0.0148:2,2:27:1:27.5:1:0.28789:5.53825:60:4:0.0148:0:2 0/0:189:0:0,0:150,39:0:2,0:22.9:1:31.4:1:1:0:60:62:1:0:0.6 -8 11096054 . T C 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.43045;SOR=1.21254;LSEQ=AAGGTGAGTATGAGATATAT;RSEQ=ATCCAGGCAGTGTGTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:43:34,9:88,17:0.2905:2,2:27:1:32:1:0.4849:1.36723:60:86:0.2925:0:1 0/1:235:78:59,19:116,41:0.3319:2,2:25.5:1:31.3:1:0.87406:1.10:60:156:0.3333:0:1.2 -8 11096085 . C T 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.40351;LSEQ=TGTGTTCTTTTAAAAATTTC;RSEQ=TCCTAAGAACCAGAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:82:53,29:123,60:0.3094:2,2:24:1:30.1:1:0.67592:1.1212:60:40:0.3077:0:1.7 0/1:425:65:36,29:224,136:0.1529:2,2:26.7:1:29.7:1:0.33367:1.32587:60:130:0.1551:0:1.4 -8 11096119 . A G 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00855;SOR=0;LSEQ=AAAAAGATGGAAAAGCAAAA;RSEQ=GGCGAGGAGGGGTGGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:5:2,3:211,172:0.0129:2,2:17.2:1:24.8:1:0.66142:1.8372:60:10:0.0132:0:2 0/0:616:0:0,0:317,298:0:2,0:26.3:1:30.3:1:1:0:60:152.75:1:0:0.7 -8 11096153 . G C 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49387;LSEQ=GGGATTCAAGAAGAAACTCA;RSEQ=TACATATGCTAATGTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:418:261:113,148:73,84:0.6244:2,2:26:1:31.9:1:0.54314:1.13787:60:86:0.6262:0:1.3 0/1:588:265:116,149:149,173:0.4507:2,2:23.6:1:31.5:1:0.56045:1.1061:60:264:0.4513:0:1.3 -8 11096235 . G T 127 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00136;SOR=0.21506;LSEQ=GTGAAGATATATTTCCAGCC;RSEQ=AAAAGAATAATTTTTAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:20:2,18:19,105:0.1379:2,2:25.5:1:29.4:1:0.73842:1.62368:60:40:0.1418:0:1.4 0/1:151:5:2,3:34,111:0.0331:2,2:28.2:1:29:1:0.59394:2.16:60:10:0.0331:0:1.4 -8 11096240 . G A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2498;SOR=Inf;LSEQ=GATATATTTCCAGCCGAAAA;RSEQ=AATAATTTTTAAAACATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:16,113:0:2,0:24.6:1:31.4:1:1:0:60:42:1:0:0.4 0/1:146:3:1,2:32,111:0.0205:2,2:16.3:1:25:1:0.53917:1.73:60:2:0.0142:0:1.7 -8 11096295 . CA C 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.61239;SOR=2.11706;LSEQ=GCACATGAAACCGTGTTGTC;RSEQ=AAAAAAAAACCCCAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:0,30:0.0323:1,0:22:0:33:0:1:0:60:2:0.0323:0:0 0/1:30:2:0,2:0,28:0.0667:1,0:23:1:31:1:1:0:60:4:0.0667:0.0333:0.5 -8 11267777 . A G 32 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.66417;LSEQ=ACCTGAGTTAATATTAAGCT;RSEQ=AGAAATCCTTTTTAAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:0.2222:2,0:17:1:32.5:1:1:0:60:4:0.25:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:5:0:32:0:1:0:60:2:0.3333:0:1 -8 11268077 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=15.08621;LSEQ=TTTATATTATAAGGAACAGA;RSEQ=GGCCTTTTGTGATTGTAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:34:11,23:82,110:0.1504:2,2:26.9:1:30:1:0.34467:1.55571:60:33:0.1467:0:1.1 1/0:387:282:124,158:43,62:0.7287:2,2:24.3:1:30.3:1:0.64488:1.13:60:281:0.7337:0:1.1 -8 11268155 . T C 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=GAGATGGGCACCAGGAAGAC;RSEQ=GAAGAGGCAAACCGGAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:17,71:0:2,0:24.7:1:30.5:1:1:0:60:43:1:0:0.1 0/1:125:16:5,11:22,87:0.128:2,2:17:1:28.3:1:0.33526:1.79:60:15:0.122:0:1.7 -8 11268305 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=TGAAATCTGAAGTCTGGGGG;RSEQ=TTTTAATATATGAAAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:16.6:1:32.4:1:1:0:60:16:1:0:0.1 0/1:6:2:0,2:0,4:0.3333:0,0:29.5:1:31:1:1:0:60:4:0.3333:0:1.5 -8 11268344 . G A 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AATGATAGAAAGATGTAAGG;RSEQ=TTTCTTGCTTTTCAGTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:30:1:25.5:1:1:0:60:1:1:0:0 1/1:3:3:0,3:0,0:1:0,0:16:1:28.7:1:1:0:60:6:1:0:1.3 -8 11414237 . T C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCATGTCTCCAGAAGCCTT;RSEQ=CTGGGTGAGGCCAACGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:10,1:0,0:1:0,2:26.9:1:32:1:1:0:60:22:1:0:1 1/1:6:6:6,0:0,0:1:0,0:24.5:1:30.7:1:1:0:60:12:1:0:1 -8 11414294 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4898;SOR=Inf;LSEQ=GAGCGGCTGGTCCGACTCTA;RSEQ=GCAGTGGTCACCAAGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:0:2,0:29.6:1:31:1:1:0:60:50:1:0:0.3 0/1:25:2:1,1:11,12:0.08:2,2:30:0:32.5:1:1:1.09:60:4:0.0833:0:1 -8 11414440 . CA C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTGCGGTGGGTTCACCAGGC;RSEQ=GGGGGTCCTGCAGATCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:23.5:1:31.8:1:1:0:60:8:1:0:0.3 1/0:4:2:0,2:0,2:0.5:0,0:37.5:1:31:0:1:0:60:4:0.5:0:0 -8 11421358 . C A 47 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.4;SOR=0;LSEQ=GCGGGACGCTCAGGGCCCCC;RSEQ=ACCCACCGAGGACCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:35.3:1:29.7:1:1:0:60:6:1:0:2.3 1/0:2:1:1,0:1,0:0.5:0,0:12:0:32:0:1:0:60:2:0.5:0:2 -8 11421384 . C T 82 d7;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.01515;SOR=0;LSEQ=CCGAGGACCCCAGCCCCTCA;RSEQ=CCCCGCTTGCGGTCTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:19.3:1:31.8:1:1:0:60:12:1:0:1.7 0/1:5:1:1,0:4,0:0.2:0,0:38:0:31:0:1:0:60:2:0.2:0:2 -8 11421626 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49317;SOR=0;LSEQ=CTGCAGCCCTAGCCGGCCGC;RSEQ=CCCGCCTGCGCCCCGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:7,27:0.0556:2,2:19.5:1:28:1:0.4:3.67:60:4:0.0556:0:1 0/0:34:0:0,0:6,28:0:2,0:24.1:1:30.6:1:1:0:60:68:1:0:0.1 -8 11587064 . C CAA 99 v4;MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.02707;SOR=9.67594;LSEQ=AACAGTGCGAGACTGTGTCT;RSEQ=AAAAAAAAAAAAAATGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:14,0:0.0526:1,0:10:0:31:0:1:0:60:2:0.0526:0:2 0/1:25:9:9,0:13,0:0.36:1,0:28.4:1:31.3:1:1:0:60:18:0.36:0:1.2 -8 11587138 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.51508;SOR=Inf;LSEQ=ACTGTGTAGTTCAGTAGTGT;RSEQ=TGTTCTGAGAAAGCCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:92,31:0:2,0:25.8:1:31.9:1:1:0:60:60.5:1:0:0.1 0/1:178:2:1,1:119,57:0.0112:2,2:23.5:1:28.5:1:0.54675:2.07837:60:4:0.0116:0:1.5 -8 11587234 . G T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06944;LSEQ=CATGATGCAAAATTGTGTTC;RSEQ=CTGAAAAGCAGGGGTTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:56:25,31:47,64:0.3353:2,2:24:1:30.2:1:0.86877:1.10:60:27:0.3313:0:1.1 0/1:327:11:5,6:144,171:0.0336:2,2:24.7:1:29.2:1:1:1.01049:60:22:0.0342:0:1 -8 11587313 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17444;SOR=0;LSEQ=CCCATGGTGGTTGCTCAATT;RSEQ=TGAGTGAGTTTGGAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:22,64:0.0227:2,2:15.5:1:28.5:1:0.45664:2.87:60:4:0.0227:0:1 0/0:122:0:0,0:31,91:0:2,0:21.8:1:31.1:1:1:0:60:29.5:1:0:0.1 -8 11587396 . A G 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10399;SOR=0.27514;LSEQ=TTGGTTTTTAAACCCAATAT;RSEQ=TAATTCCTGGATATTCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:0,10:0,12:0.4545:0,0:26.8:1:33.1:1:1:0:60:20:0.4545:0:1 0/1:22:4:0,4:0,18:0.1818:1,0:12.5:1:32.3:1:1:0:60:8:0.1818:0:1.3 -8 11587455 . G GAGA 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=GTTGTTTCTATTGTTTTTGA;RSEQ=AGAAGGTCTTGCTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:26.5:1:32.5:1:1:0:60:4:0.5:0:0 1/1:2:2:0,2:0,0:1:0,0:24.5:1:29.5:1:1:0:60:4:1:0:0 -8 11606312 . T C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCCGAGGTGGTCTTCTC;RSEQ=TTCCAAGGAAAGGGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:24.3:1:30.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 11606451 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5251;SOR=Inf;LSEQ=TGTTTGACGACTTCTCAGAA;RSEQ=GCAGAGAGTGTGTCAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:0:1,0:22.5:1:32.5:1:1:0:60:50:1:0:0 0/1:42:2:1,1:36,4:0.0476:2,2:25:1:27:1:0.22648:8.16006:60:4:0.0488:0:1 -8 11606537 . C T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28085;SOR=Inf;LSEQ=TATCTGTGCAACGCCTGCGG;RSEQ=CTCTACCACAAGATGAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:38,33:0:2,0:25.6:1:31.2:1:1:0:60:34.5:1:0:0.2 0/1:110:3:1,2:55,52:0.0273:2,2:31:1:22:1:0.61468:2.10148:60:2:0.0183:0:1.7 -8 11606567 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1259;SOR=0;LSEQ=AAGATGAACGGCATCAACCG;RSEQ=CCGCTCATCAAGCCTCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:22,26:0.04:2,2:17:1:28.5:1:1:1.18:60:4:0.0408:0:1 0/0:90:0:0,0:35,55:0:2,0:26.1:1:30.9:1:1:0:60:44:1:0:0.1 -8 11606591 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1293;SOR=0;LSEQ=CTCATCAAGCCTCAGCGCCG;RSEQ=CTGGTAAGCACGTGCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:13,22:0.0541:2,2:25.5:1:29:1:1:1.67:60:4:0.0588:0:1 0/0:65:0:0,0:19,46:0:2,0:22:1:31.4:1:1:0:60:64:1:0:0.1 -8 11607682 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54902;SOR=Inf;LSEQ=ACCACCACCACCACGCTGTG;RSEQ=CGCCGCAATGCGGAGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:30,16:0:2,0:30.3:1:30.8:1:1:0:60:45:1:0:0.1 0/1:90:2:1,1:49,39:0.0222:2,2:32.5:1:30:1:1:1.25319:60:4:0.0227:0:1 -8 12586219 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15262;SOR=0;LSEQ=GAATCTATGTTCTAGTCTTC;RSEQ=AAGTTCTCTTAGAATGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:109,78:0.0106:2,2:32:1:30.5:1:1:1.3949:60:4:0.0107:0:2 0/0:294:0:0,0:165,129:0:2,0:24.6:1:30.5:1:1:0:60:146:1:0:0.7 -8 12586261 . A G 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00112;SOR=1.777;LSEQ=CAGTTTCAGAGCAAGATACG;RSEQ=AAAAGGTAACTTGGAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:212:112:57,55:51,49:0.5283:2,2:24:1:31:1:1:1.00428:60:111:0.5311:0:1.1 1/0:383:255:120,135:63,63:0.6658:2,2:25.5:1:30.7:1:0.66299:1.12465:60:30.875:0.664:0:1.1 -8 12586264 . A C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.22017;LSEQ=TTTCAGAGCAAGATACGAAA;RSEQ=AGGTAACTTGGAGCACATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:60:35,25:75,80:0.2791:2,2:23.8:1:31.5:1:0.22442:1.49:60:59:0.277:0:1 0/1:383:30:15,15:171,182:0.0783:2,2:26.6:1:31.1:1:1:1.06:60:29:0.0763:0:1.3 -8 12586296 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05001;SOR=0;LSEQ=AGCACATTCTCATCACAGTG;RSEQ=TAAGGCTGTCTGATAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:3:1,2:78,102:0.0164:2,2:19:1:25.3:1:1:1.52601:60:2:0.011:0:1.3 0/0:312:0:0,0:139,172:0:2,0:25.8:1:30.7:1:1:0:60:61.2:1:0:0.8 -8 13443158 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50076;SOR=Inf;LSEQ=GGTTTGTTCCTTGTGAGGGC;RSEQ=GTGAGGGAGAATCTGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:20,12:0:2,0:23.8:1:30.8:1:1:0:60:64:1:0:0.1 0/1:41:2:1,1:24,15:0.0488:2,2:18:1:28.5:1:1:1.58108:60:4:0.05:0:1 -8 13443286 . T C 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08492;SOR=0;LSEQ=TTCATATTTTATTCTACCCA;RSEQ=GCTCATATCCCTATCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:7.5:1:29.8:1:1:0:60:8:0.5:0:1 0/0:6:0:0,0:0,6:0:0,0:26.8:1:26.5:1:1:0:60:5:1:0:0.2 -8 13465795 . C A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=AAAGTCTTAAAGTCTTTGAT;RSEQ=TTTCTTATAAGTGCATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:31.3:1:31.4:1:1:0:60:14:1:0:0 0/1:8:3:2,1:3,2:0.375:2,2:26.7:1:30.3:1:1:1.29:60:6:0.375:0:2.3 -8 13465836 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22462;SOR=Inf;LSEQ=GAAAACGCTGATGTATGCCG;RSEQ=CTTCCCTCTCTGCTTCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:11,1:0:2,0:17.5:1:29.3:1:1:0:60:24:1:0:0 0/1:14:3:2,1:8,3:0.2143:2,2:32.3:1:30.3:1:1:1.30524:60:6:0.2143:0:2.3 -8 13466001 . C A 49 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=CAGCCATTCTGGGCTACTAC;RSEQ=GGTCTCCGCGTCTTGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:31.4:1:30:1:1:0:60:10:1:0:0 0/1:12:3:0,3:0,9:0.25:0,0:16.7:1:31.3:1:1:0:60:6:0.25:0:2.7 -8 13745451 . A G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTGAATCTATTTATTATATG;RSEQ=ATTTGTAAGACGTCTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:11,0:12,0:0.4783:0,0:26.4:1:30.9:1:1:0:60:22:0.4783:0:2.7 0/1:23:11:11,0:12,0:0.4783:0,0:22.7:1:32.2:1:1:0:60:22:0.4783:0:3 -8 13745462 . C T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97818;LSEQ=TATTATATGAATTTGTAAGA;RSEQ=GTCTCTTTTACTTAAATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:15:15,0:11,0:0.5769:0,1:22.9:1:30.9:1:1:0:60:30:0.5769:0:2.6 1/0:28:16:15,1:12,0:0.5714:0,1:23.6:1:30.6:1:1:0:60:32:0.5714:0:2.7 -8 13745472 . A G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1157;LSEQ=ATTTGTAAGACGTCTCTTTT;RSEQ=CTTAAATACTACTTTCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:16,1:14,0:0.5484:1,1:22.8:1:32.1:1:1:0:60:34:0.5484:0:2.4 1/0:33:19:17,2:13,1:0.5758:1,2:25.9:1:32.2:1:1:1.51052:60:38:0.5758:0:2.5 -8 13745495 . G T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26653;SOR=Inf;LSEQ=TAAATACTACTTTCATAACT;RSEQ=AAATGTGCCATTTATTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:41,9:0:2,0:21.1:1:31.6:1:1:0:60:49:1:0:0.8 0/1:71:3:1,2:56,12:0.0423:2,2:6:1:24.7:1:0.09712:8.91114:60:6:0.0423:0:2 -8 13745588 . G A 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53371;SOR=1.16001;LSEQ=TATGGAGCTGTGTAATACTT;RSEQ=TATCTAAAAGCCAAAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:60:27,33:45,44:0.4027:2,2:27.8:1:29.6:1:0.61627:1.24812:60:59:0.3986:0:1.1 0/1:262:115:60,55:72,75:0.4389:2,2:29.1:1:28.8:1:0.62068:1.14:60:114:0.4402:0:1.2 -8 13745647 . AT A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5219;SOR=Inf;LSEQ=ATGACAGAAATAGAGCAGTA;RSEQ=TTCAAGAATTATGTTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:37,71:0:2,0:23.5:1:30.1:1:1:0:60:107:1:0:0.4 0/1:168:2:2,0:58,108:0.0119:2,0:7.5:1:26.5:1:0.12618:0:60:4:0.012:0.006:2 -8 13745701 . A G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.82837;SOR=1.15517;LSEQ=AACAGTTGCTATGTCCTGAT;RSEQ=TAAATGAAGAGCCACGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:20:1,19:2,16:0.5263:2,1:27.8:1:30.4:1:0.59459:2.32256:60:9:0.5:0:1 1/0:48:27:4,23:2,19:0.5625:2,2:22.9:1:30.9:1:0.68299:1.64:60:54:0.5625:0:1 -8 14166427 . G C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24291;SOR=0;LSEQ=GAAATACATTTTCTTAATTT;RSEQ=AAATCCAGTAGACTAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:3,0:19,0:0.1364:1,0:38.3:1:31.3:1:1:0:60:6:0.1364:0:1 0/0:17:0:0,0:17,0:0:1,0:23.4:1:32.3:1:1:0:60:34:1:0:0 -8 14166528 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30213;SOR=Inf;LSEQ=CGGCCTCAGCCTCACTTTTA;RSEQ=CAGAAAATGAAACCGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:97,17:0:2,0:19.7:1:31.8:1:1:0:60:228:1:0:0.2 0/1:198:3:1,2:152,42:0.0152:2,2:15:1:27:1:0.12589:7.1419:60:6:0.0154:0:1 -8 14166550 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12359;SOR=0;LSEQ=AGAAAATGAAACCGGAAGCC;RSEQ=CCCCTACTCTTAATTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:143,42:0.0107:2,2:8:0:32.5:1:0.40797:3.37662:60:4:0.0107:0:1.5 0/0:344:0:0,0:235,109:0:2,0:23.4:1:30.3:1:1:0:60:85:1:0:0.2 -8 14166825 . G A 218 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CTTTTTAAGGATGGTATTGA;RSEQ=ACTATGTGGGAAGATGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:162:95,67:167,126:0.356:2,2:23.3:1:29.8:1:0.76681:1.07:57.9:53:0.3549:0:1.1 0/0:713:0:0,0:410,302:0:2,0:22.7:1:31.2:1:1:0:58.9:46.467:0.9986:0:0.1 -8 14166895 . C T 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTGAACAGTCAGCAGAGA;RSEQ=GAAGTGACCTCGATCGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:765:0:0,0:387,378:0:2,0:26:1:31:1:1:0:59.6:108.286:1:0:0.2 0/1:1333:47:21,26:656,630:0.0353:2,2:26.2:1:30:1:0.45837:1.28894:59:94:0.0355:0:1.1 -8 14167023 . G T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14291;SOR=Inf;LSEQ=AATTGTGATAAGAGAGCAGT;RSEQ=TGGACTACTGAATGTGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:71,182:0:2,0:24.1:1:31.9:1:1:0:60:125.5:1:0:0.1 0/1:349:4:2,2:93,251:0.0115:2,2:11.5:1:27.8:1:0.30059:2.69:60:8:0.0115:0:1 -8 14167065 . A C 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24739;SOR=0;LSEQ=AAAGAAGCTGTTACACATAC;RSEQ=GGGACGGTATAACAAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:1,2:27,113:0.0208:2,2:8.3:1:25:1:0.48259:2.08:55.7:2:0.0141:0:3.7 0/0:144:0:0,0:25,119:0:2,0:24.1:1:31.1:1:1:0:60:143:1:0:0.3 -8 14167113 . C T 192 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTTCATCCAAAGATAGTGA;RSEQ=TGGTTATCAGTCCCACGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:84:84:14,70:0,0:1:0,2:26:1:30.1:1:1:0:54.4:41:1:0:1.2 1/0:67:45:11,34:4,18:0.6716:2,2:23.1:1:30:1:0.75704:1.45:53.8:90:0.6716:0:1.1 -8 14167258 . T G 95 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCTGAACCAAAGCCTCT;RSEQ=CAAAAAGCAGAGTGGACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:19.4:1:33.9:1:1:0:51.6:14:1:0:1.3 1/1:1:1:0,1:0,0:1:0,0:40:0:34:0:1:0:60:2:1:0:2 -8 14167289 . C G 50 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGACTGCATTTAAATTT;RSEQ=ATTTCCATCTAAATGTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:17.3:1:31.7:1:1:0:36.3:6:1:0:1.3 1/1:1:1:0,1:0,0:1:0,0:9:0:32:0:1:0:60:2:1:0:2 -8 16703980 . A T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46578;SOR=1.38783;LSEQ=GTTCCAAACAGGAAAAATGA;RSEQ=TGGGAAATTCCACCTACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:18:15,3:32,4:0.3333:2,2:23.4:1:31.1:1:0.67431:1.58542:60:36:0.3396:0:1.2 0/1:78:32:26,6:37,9:0.4103:2,2:24.3:1:29.3:1:1:1.05:60:31:0.4079:0:1.5 -8 16704010 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14906;SOR=0;LSEQ=CCACCTACAGCTACTAGCGT;RSEQ=TGCCTGCTCAGTTCCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:57,22:0.0247:2,2:27.5:1:28.5:1:0.48981:2.5561:60:4:0.0247:0:1 0/0:128:0:0,0:93,35:0:2,0:24:1:31.2:1:1:0:60:127:1:0:0.9 -8 16704073 . C A 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01554;SOR=1.60067;LSEQ=TAAAGGGAGAGACATGGGGA;RSEQ=AGAGAATTAGGAGACAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:59:33,26:84,70:0.2744:2,2:31.9:1:29.3:1:0.87887:1.06:60:18.667:0.2679:0:3.1 0/1:326:123:65,58:108,95:0.3773:2,2:26.4:1:29.8:1:1:1.01437:60:246:0.3808:0:2.9 -8 16704077 . G A 206 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03353;SOR=1.50866;LSEQ=GGGAGAGACATGGGGACAGA;RSEQ=AATTAGGAGACAGGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:62:33,29:83,71:0.287:2,2:30.4:1:29.7:1:1:1.0272:60:61:0.2877:0:3 0/1:328:124:64,60:109,95:0.378:2,2:26.6:1:29.7:1:0.81967:1.07542:60:123:0.3808:0:2.9 -8 16704099 . G C 221 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06327;SOR=1.40542;LSEQ=ATTAGGAGACAGGCAATGGA;RSEQ=AGAATCAGAAGGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:71:33,38:76,81:0.3114:2,2:23.4:1:31.5:1:0.88626:1.08006:60:70:0.3084:0:2.7 0/1:355:138:66,72:102,114:0.3887:2,2:25.7:1:31.2:1:0.91362:1.02:60:137:0.3892:0:2.6 -8 17522020 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.175;SOR=Inf;LSEQ=GATGGAGAAGAGCAGCCTGC;RSEQ=TCCAGCTCTGCCTGCAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:25.4:1:30:1:1:0:60:8:1:0:0.1 0/1:7:2:0,2:2,3:0.2857:2,0:20.5:1:26.5:1:1:0:60:4:0.2857:0:1 -8 17945818 . A G 187 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02449;SOR=0.54195;LSEQ=TTACCTGTATTACTGCAAGT;RSEQ=GCTCAACCTAGTAAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:55:51,4:52,4:0.4955:2,2:21.8:1:32.4:1:1:1.01943:60:110:0.4955:0:1 0/1:124:43:40,3:75,5:0.3468:2,2:20.8:1:32.3:1:1:1.1239:60:86:0.3496:0:1.1 -8 17945990 . T G 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.04623;SOR=0.71912;LSEQ=CTGCTCATTTTGGATGCTTT;RSEQ=TTATTGGTTACTACTATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:80:23,57:108,185:0.2145:2,2:26.4:1:31.6:1:0.18903:1.44538:60:79:0.2153:0:1.1 0/1:707:116:47,69:228,362:0.1641:2,2:24.7:1:30.3:1:0.75488:1.08:59.9:28:0.1626:0:1.2 -8 17946435 . G T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16761;LSEQ=ATCTCCTGACCTCGTGATCC;RSEQ=TCCGCCGTCATCTCTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:40:35,5:71,21:0.303:2,2:24.4:1:30.7:1:0.23467:2.06:60:80:0.3053:0:1.1 0/1:222:15:13,2:159,46:0.0676:2,2:26.6:1:31.1:1:0.53219:1.88:60:30:0.0676:0:1 -8 17946458 . C T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30265;SOR=Inf;LSEQ=CGCCGTCATCTCTTGAACTG;RSEQ=CATCTGTCAGCTAAGTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:157,59:0:2,0:24.2:1:31.9:1:1:0:60:215:1:0:0.3 0/1:358:4:1,3:238,116:0.0112:2,2:14.8:1:25.3:1:0.10904:6.1222:60:8:0.0113:0:1 -8 17946658 . G GA 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.28425;SOR=Inf;LSEQ=CATGAAGAATTCAGAATCTG;RSEQ=AAAAAAGGTCCATAATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:94,94:0:2,0:25.1:1:31.3:1:1:0:60:61.667:1:0:0.1 0/1:293:3:1,2:119,171:0.0102:2,2:20.7:1:28.3:1:1:1.3903:60:6:0.0105:0.0034:0 -8 17946946 . C T 177 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTGTGTGTTTGTACTGCT;RSEQ=GGCTAAAACCAGTGGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:0:0,0:277,246:0:2,0:27:1:30.3:1:1:0:59.5:64.375:0.9981:0:0.1 0/1:736:68:39,29:333,333:0.0924:2,2:25.4:1:29.1:1:0.25504:1.34:59.6:33:0.0905:0:1.1 -8 17947063 . T C 222 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00278;SOR=0.6331;LSEQ=AAAGTCCTTTTCGAGGTTTA;RSEQ=ATAAGGCATGTTCCAGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:119:47,72:115,145:0.314:2,2:22.9:1:32.2:1:0.43395:1.21434:60:238:0.3173:0:1.1 0/1:521:117:47,70:168,236:0.2246:2,2:22.1:1:31.3:1:0.83146:1.06012:60:234:0.2276:0:1.1 -8 17947318 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53048;SOR=Inf;LSEQ=ATTATAAAAACTAAAAAACT;RSEQ=ATAGCATGGAATATATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:47,59:0:2,0:24.6:1:31:1:1:0:60:25.5:1:0:0.2 0/1:178:2:0,2:91,85:0.0112:2,0:9.5:1:26:1:0.23748:0:60:4:0.0114:0:2 -8 17947327 . G C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53117;SOR=Inf;LSEQ=ACTAAAAAACTGATAGCATG;RSEQ=AATATATTTCTGAATGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:54,63:0:2,0:24.5:1:30.6:1:1:0:59.5:22.4:1:0:0.4 0/1:199:2:1,1:101,96:0.0101:2,2:12:0:33.5:1:1:1.05184:60:4:0.0102:0:1.5 -8 17947391 . G A 151 LongAT STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=5.11149;LSEQ=TCTATTTGGGAATCAGTAAT;RSEQ=CTATTCTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:8:4,4:27,35:0.1127:2,2:13.1:1:25:1:1:1.29:60:7:0.1167:0:1.5 0/1:162:64:34,30:40,56:0.3951:2,2:18.9:1:25.3:1:0.19549:1.58:58:8.143:0.413:0:1.5 -8 17947440 . A G 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04354;SOR=0;LSEQ=GAGTCTAGCTCTGTCACCCA;RSEQ=GTTGGAGTGAGGTGGCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:2,21:0,0:1:0,2:30.6:1:30:1:1:0:58.9:22:1:0:1.9 1/1:44:36:7,29:1,7:0.8182:2,2:23.4:1:29.3:1:1:1.67:54.1:35:0.814:0:2 -8 17948372 . G T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGATCTGCCTCCCCACAGTA;RSEQ=TAGATATGCCTGCCCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:31.5:1:1:0:60:4:1:0:1 -8 17996495 . A G 28 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGAGCATAAAATATTGC;RSEQ=TAGGTTTTAGCATGTCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:28.5:1:1:0:60:4:1:0:1 1/0:2:1:1,0:1,0:0.5:0,0:25:0:30:0:1:0:60:2:0.5:0:1 -8 17996542 . C A 29 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24176;SOR=0.19209;LSEQ=CATTCCAATGTCTTCCTTTG;RSEQ=CTAACATTCAGAAGTAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:23.5:1:29:1:1:1.7321:60:4:0.4:0:1 0/1:10:1:1,0:8,1:0.1:2,0:24:0:31:0:1:0:60:2:0.1:0:1 -8 18040824 . A G 71 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=AATTTCAACATCAGTTGGGG;RSEQ=AGGGGACAAACATTCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:35.6:1:30.6:1:1:0:60:10:1:0:1 1/0:2:1:0,1:0,1:0.5:0,0:22:0:31:0:1:0:60:2:0.5:0:1 -8 18100654 . C T 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60033;SOR=1.1822;LSEQ=AAAAGGGTCACATGTGTATG;RSEQ=CTGTAATATCTGTTTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:30:24,6:80,34:0.2083:2,2:23.7:1:29.7:1:0.36263:1.69:60:60:0.2113:0:1.1 0/1:198:47:30,17:103,45:0.2374:2,2:23.1:1:28.6:1:0.47599:1.29522:60:94:0.2423:0:1.1 -8 18100721 . T C 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.06695;SOR=0;LSEQ=ATTTCACTGTGAGTAGTAAG;RSEQ=ACAGTCATGGGGACTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:137,115:0.0117:2,2:29.3:1:25.7:1:0.59504:2.37471:60:2:0.0079:0:1.7 0/0:373:0:0,0:192,180:0:2,0:24.8:1:28.6:1:1:0:60:123:1:0:0.7 -8 18100755 . T G 250 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAAATTACTGTGTACAGTA;RSEQ=TAGGGCTCTTCAACGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:231:231:111,120:0,0:1:0,2:24.7:1:31.8:1:1:0:60:230:1:0:1.1 1/0:345:262:121,141:43,40:0.7594:2,2:24.5:1:31.2:1:0.38043:1.25186:60:51.4:0.7649:0:1.1 -8 18100778 . T A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06773;SOR=0;LSEQ=GGGCTCTTCAACGGAAAAGC;RSEQ=TCCAAGGCTGTCAGGACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:3:2,1:77,124:0.0147:2,2:11:1:30.3:1:0.56086:3.20:60:6:0.015:0:2 0/0:295:0:0,0:133,162:0:2,0:1:0:17:0:1:0:60:0:0:0:3 -8 18100789 . T A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27951;SOR=Inf;LSEQ=CGGAAAAGCTTCCAAGGCTG;RSEQ=CAGGACACGATGCAAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:69,123:0:2,0:23.8:1:29.7:1:1:0:60:95:1:0:0.8 0/1:290:3:2,1:119,168:0.0103:2,2:6.7:1:22.7:1:0.57301:2.81:60:2:0.007:0:3.3 -8 18100870 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49927;SOR=Inf;LSEQ=ATGGGCAACAGGGCCTCATC;RSEQ=CCTTTAAGGGCATTGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:13,60:0:2,0:20:1:32.1:1:1:0:60:146:1:0:0.2 0/1:84:2:1,1:10,71:0.0238:2,2:16.5:1:30:1:0.2489:6.82:60:4:0.0244:0:1 -8 18100881 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22732;SOR=0;LSEQ=GGCCTCATCGCCTTTAAGGG;RSEQ=ATTGAAATAAAACTTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:10,45:0.0351:2,2:35.5:1:27:0:0.3515:4.34:60:4:0.0351:0:1 0/0:62:0:0,0:9,53:0:2,0:18.4:1:30.9:1:1:0:60:19.667:1:0:0.1 -8 18100994 . G A 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22078;SOR=0;LSEQ=CTGTTTTTTTTCTTTCAGAA;RSEQ=GACACATGTGATTGTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:0.4444:0,0:38:1:31.8:1:1:0:60:8:0.5:0:1.3 0/0:5:0:0,0:0,5:0:0,0:27:1:30.6:1:1:0:60:10:1:0:0 -8 18464688 . C A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.17741;LSEQ=CTTTCTCTAATCTCACTCAA;RSEQ=TATAGGACCTTCAAAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:0.6364:0,0:18.6:1:31.7:1:1:0:60:14:0.6364:0:1.1 1/1:5:4:4,0:1,0:0.8:0,0:35:1:31.5:1:1:0:60:8:0.8:0:1.3 -8 18464759 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.26488;SOR=Inf;LSEQ=AGGCACAGTCTCTGTGCCTG;RSEQ=CCCCTCAGGTGCTCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:26,0:0:1,0:25.1:1:32.2:1:1:0:60:52:1:0:0.9 0/1:38:3:3,0:35,0:0.0789:1,0:12:1:30:1:1:0:60:6:0.0789:0:2.7 -8 18464798 . G A 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99845;LSEQ=CTCCACATTTCTGCAGAATA;RSEQ=TTATCTAATATTACTAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:40:35,5:8,1:0.8163:2,2:20.8:1:30.2:1:1:1.13985:60:80:0.8163:0:1 1/1:87:71:65,6:15,1:0.8161:1,2:21.8:1:29.7:1:1:1.37988:60:142:0.8161:0:1.1 -8 18464826 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.50799;SOR=Inf;LSEQ=ATATTACTAATAATTACAGA;RSEQ=GTAGTAATAGCACAGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:102,25:0:2,0:20.2:1:30.5:1:1:0:60:126:1:0:0.4 0/1:168:2:1,1:123,43:0.0119:2,2:38.5:1:31:1:0.45637:2.83924:60:4:0.012:0:2.5 -8 18464842 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27589;SOR=Inf;LSEQ=CAGAAGTAGTAATAGCACAG;RSEQ=AAATGATTGCTGAACACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:130,45:0:2,0:24:1:32.2:1:1:0:60:174:1:0:0.4 0/1:258:3:1,2:166,89:0.0116:2,2:16.7:1:26.3:1:0.28467:3.71027:60:6:0.0117:0:1.3 -8 18464910 . G A 156 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.41869;LSEQ=ACCTGTATAAACAAAAGCCC;RSEQ=TAAGTCTATGAGGGATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:1,0:192,169:0.0028:2,0:1:0:26:0:1:0:60:2:0.0028:0:1 0/1:527:36:16,20:242,248:0.0683:2,2:29.8:1:30.2:1:0.60752:1.2193:60:35:0.0672:0:1.1 -8 18464930 . C T 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01248;SOR=1.50359;LSEQ=GTAAGTCTATGAGGGATCCA;RSEQ=GGTTATAACCTCCATCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:81:36,45:123,136:0.2375:2,2:25.1:1:29.9:1:0.70225:1.13011:60:39.5:0.2358:0:1.1 0/1:492:157:77,80:160,173:0.3191:2,2:25.6:1:30:1:0.84696:1.04:60:314:0.3211:0:1.1 -8 18464950 . C T 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=CGGTTATAACCTCCATCTCA;RSEQ=AGATGTGGAACCTATGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:109,175:0:2,0:25.2:1:31.8:1:1:0:60:55.8:1:0:0.4 0/1:442:21:8,13:196,225:0.0475:2,2:23.6:1:29.1:1:0.50681:1.41446:60:42:0.0476:0:1 -8 18916823 . C T 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5182;SOR=1.65716;LSEQ=CCTTAGACCCCCTTTACCTG;RSEQ=GTAGGAAGATGTCCCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:6,0:0.5714:0,0:20.4:1:28.8:1:1:0:60:16:0.5714:0:1 1/0:42:29:29,0:12,1:0.6905:1,1:20.9:1:28.2:1:0.30952:0:60:28:0.6829:0:1 -8 18916911 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10795;SOR=0;LSEQ=AAAAGGAGAGCTCATGAGAA;RSEQ=CACAAGGAAAGCAGGGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:102,34:0.0145:2,2:43:0:31:1:0.4443:2.97127:60:4:0.0146:0:2.5 0/0:281:0:0,0:170,111:0:2,0:26.1:1:31.6:1:1:0:60:39.143:1:0:0.3 -8 18916918 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10266;SOR=0;LSEQ=GAGCTCATGAGAAGCACAAG;RSEQ=AAAGCAGGGTACACCAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:103,36:0.0142:2,2:40.5:1:30:0:0.45735:2.83585:60:4:0.0145:0:2.5 0/0:298:0:0,0:177,121:0:2,0:26.3:1:30.8:1:1:0:60:73.5:1:0:0.3 -8 18916990 . A C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.24799;LSEQ=GCAGCTGGTGCAGAACAAGA;RSEQ=ACTAGCCCCAGCAATCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:200:142:74,68:24,33:0.71:2,2:25.1:1:32.1:1:0.21361:1.49:60:141:0.7121:0:1.1 0/1:350:132:68,64:95,121:0.3771:2,2:22.8:1:31.2:1:0.18508:1.35:60:65:0.379:0:1.2 -8 18917036 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14632;SOR=0;LSEQ=AGAAAAGTCTAAGATTTAAG;RSEQ=CAGTATCAGGTGGGACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:63,104:0.0118:2,2:20:1:31.5:1:1:1.65:60:4:0.0121:0:2 0/0:272:0:0,0:104,168:0:2,0:29:0:14:0:1:0:60:0:0:0:1 -8 18917043 . C A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2863;SOR=Inf;LSEQ=TCTAAGATTTAAGCCAGTAT;RSEQ=AGGTGGGACCAAAGTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:57,103:0:2,0:24.8:1:31.7:1:1:0:60:159:1:0:0.5 0/1:253:3:2,1:95,154:0.0119:2,2:19:1:25.7:1:0.56073:3.23:60:6:0.0119:0:1 -8 18917162 . A C 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.06846;SOR=0;LSEQ=GTTAGTCAAGAAATTTAAAA;RSEQ=ATTTCTACGTCTGTAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:0,21:0.1923:1,0:17.6:1:32.6:1:1:0:60:10:0.1923:0:1.2 0/0:18:0:0,0:0,18:0:1,0:20.4:1:30.3:1:1:0:60:36:1:0:0.2 -8 18917215 . A G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAATCATTCCCACAAGA;RSEQ=AAAGAAGAAAGGTTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:27.7:1:30.5:1:1:0:60:9:1:0:1.5 1/1:3:3:0,3:0,0:1:0,0:14.7:1:32.3:1:1:0:60:6:1:0:1 -8 19097201 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48949;SOR=0;LSEQ=GCCTTCTGTCTTCTGTATTT;RSEQ=TGTGTCCAAATTTCTATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:4,14:0.1:2,2:15:1:32:0:0.44737:3.24:60:4:0.1:0:1 0/0:17:0:0,0:4,13:0:2,0:24.2:1:30.5:1:1:0:60:16:1:0:0.1 -8 21417475 . C T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.67307;SOR=1.56399;LSEQ=GGACAGCACTTTCCAGATGA;RSEQ=CCCCATCTGTTCCTCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:2,3:7,1:0.3846:2,2:16.8:1:30.4:1:0.21678:8.36696:60:10:0.3846:0:1.4 1/0:8:4:3,1:3,1:0.5:2,2:24:1:29.8:1:1:1:60:8:0.5:0:1 -8 21417519 . CGAT C 85 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=0.54403;SOR=0.66407;LSEQ=GATGATGATGAAGATGATGA;RSEQ=GATGATGATGATGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:2,5:11,9:0.2593:2,2:34.1:1:30.4:1:0.38454:2.93201:60:14:0.2593:0:1 0/1:32:6:3,3:13,10:0.1875:2,2:32.2:1:31.7:1:1:1.28819:60:12:0.1875:0:0.3 -8 21419585 . GC G 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTTTTTTTTTTCAGTAGA;RSEQ=ACGGGGTTTCACCATGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:0:30:0:1:0:33:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 22248197 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49708;SOR=Inf;LSEQ=ATTGCTGGAAGATGGTGGTT;RSEQ=CAGCTGAAAGGCTTTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:32,54:0:2,0:27.5:1:30.5:1:1:0:60:20.5:1:0:0.1 0/1:86:2:1,1:35,49:0.0233:2,2:7:0:31.5:1:1:1.39:60:4:0.0238:0:1.5 -8 22248226 . C CT 63 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.01836;LSEQ=AGGCTTTTTAAAATTTTTAA;RSEQ=TTTTTTTTTTTAACAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:4:0,4:18,37:0.0678:2,0:23.8:1:31.8:1:0.30274:0:60:8:0.0678:0:0 0/1:58:4:0,4:21,33:0.069:2,0:26:1:31.5:1:0.28576:0:60:8:0.0702:0:0 -8 22438859 . C G 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00152;SOR=0;LSEQ=TCCCTTCTCCAGCTGGGCCA;RSEQ=GGTCTGAGCATGCCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:5,1:9,2:0.3529:2,2:28:1:32.5:1:1:1.10:60:12:0.3529:0:1 0/0:28:0:0,0:14,13:0:2,0:14.9:1:29.6:1:1:0:60:54:0.9643:0:0.2 -8 22440434 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGCCCACCCCCCCCCCC;RSEQ=CCCCCATCTCCCGCCTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,2:0.5:0,0:6.5:1:30:1:0.33333:0:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 22458349 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=CAGCCTTCAGGAATGCTGGG;RSEQ=GTGTTGGGGGTGGCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:0.1053:2,2:13.5:1:29.5:1:1:1.77272:60:4:0.1053:0:1.5 0/0:11:0:0,0:6,5:0:2,0:16.9:1:30.2:1:1:0:60:22:1:0:0.2 -8 22458401 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GACTCTCCATGCAGATGGGG;RSEQ=TGGCGAGGGCCTGGCACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:0:2,0:21.8:1:32.2:1:1:0:60:42:1:0:0.4 0/1:15:2:1,1:5,8:0.1333:2,2:40.5:1:31:1:1:1.55:60:4:0.1429:0:2 -8 22994522 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGACTGCTGATTTGTAT;RSEQ=CAGGCAACCCATGTAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 22995745 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.543;SOR=Inf;LSEQ=CTGGAACCAGCAGCCTCCTC;RSEQ=TCTGACACCCTTCAGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:16,32:0:2,0:23.1:1:31.8:1:1:0:60:96:1:0:0.1 0/1:90:2:1,1:36,51:0.0222:2,2:44:1:29.5:1:1:1.41:60:4:0.0225:0:1 -8 23531306 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49927;SOR=Inf;LSEQ=TTGGAGATGGGTAATAAATG;RSEQ=TTCTGGATGACCAGGTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:179,8:0:1,0:22:1:32.3:1:1:0:60:186:1:0:0.1 0/1:200:2:1,1:189,9:0.01:1,2:5.5:1:27:1:0.09774:19.975:60:4:0.0101:0:1.5 -8 23531563 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.5119;SOR=Inf;LSEQ=AACTCCTCCCTTCCTGGTGG;RSEQ=CACCTCCAGGTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:4,104:0:1,0:23.6:1:32.1:1:1:0:60:53:1:0:0 0/1:151:2:0,2:12,135:0.0132:2,0:39.5:1:30:1:1:0:60:4:0.0133:0:1 -8 23535883 . C T 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01073;SOR=Inf;LSEQ=TGATGGTTGCGTATGTATTC;RSEQ=ATGGTATATATGCACATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:117,0:0:1,0:26.2:1:31.2:1:1:0:60:38:1:0:0 0/1:107:6:6,0:100,1:0.0561:1,0:26.8:1:32.7:1:1:0:60:12:0.0571:0:1.3 -8 23536098 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.35529;LSEQ=GCTGAGGCTTTTGATCACCA;RSEQ=AGGTTGCAATTGGTGTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:630:83:30,53:216,330:0.1317:2,2:24.5:1:31.9:1:0.62951:1.15608:60:82:0.1338:0:1.1 0/1:791:267:111,156:226,297:0.3375:2,2:25.7:1:31:1:0.70389:1.06931:60:43.5:0.3376:0:1.1 -8 23538533 . A G 107 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09341;SOR=0.07274;LSEQ=TGACCTACAGTATGCACTGG;RSEQ=GGAATGACTTAGGTATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:10,0:1,0:0.9091:0,0:30:1:32.5:1:1:0:60:20:0.9091:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:45:0:31:0:1:0:60:2:0.3333:0:1 -8 23540036 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21074;SOR=0;LSEQ=GGAAGGTCCCTCTGCCTGTC;RSEQ=CCGCGGAGCCCCGCGTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:48,15:0.0308:2,2:19:1:31.5:1:0.43462:3.13049:60:4:0.0323:0:1 0/0:76:0:0,0:59,16:0:2,0:20.8:1:29.7:1:1:0:60:74:1:0:0.1 -8 23540054 . C T 21 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50115;SOR=Inf;LSEQ=TCGCCGCGGAGCCCCGCGTC;RSEQ=CTGCACCCCGAGCTCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:66,42:0:2,0:20:1:30.6:1:1:0:60:53:1:0:0.3 0/1:127:2:1,1:83,42:0.0157:2,2:19.5:1:21.5:1:1:1.96487:60:4:0.0161:0:1 -8 23540090 . C T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.30903;SOR=0.22693;LSEQ=TGGGGGTCCGCCTTGGGCTG;RSEQ=CCCCCTTCCCCGGCCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:1,2:108,80:0.0157:2,2:17.3:1:29:1:0.57778:2.68609:60:6:0.0161:0:1 0/0:278:1:0,1:172,105:0.0036:2,0:1:0:27:0:0.38129:0:60:2:0.0037:0:1 -8 23540338 . G T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13222;SOR=Inf;LSEQ=AGGACGTGAGCGGCTTGGAC;RSEQ=GGGTCGGCGGCGCGGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:97,145:0:2,0:25.4:1:30.1:1:1:0:60:79.667:1:0:0.3 0/1:300:4:2,2:119,177:0.0133:2,2:20.8:1:28:1:1:1.49:60:3:0.0102:0:1 -8 23540370 . C A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.66274;LSEQ=GCGGCCCCCTCCGCTTTCGC;RSEQ=TCCCCGGGCCGCGGCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:1,0:56,108:0.0061:2,0:1:0:26:0:0.34545:0:60:2:0.0061:0:1 0/1:199:2:1,1:69,128:0.0101:2,2:23.5:1:28.5:1:1:1.85:60:4:0.0102:0:1 -8 23540375 . C G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25487;SOR=Inf;LSEQ=CCCCTCCGCTTTCGCCTCCC;RSEQ=GGGCCGCGGCTCCGGAACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:47,101:0:2,0:25.1:1:29.8:1:1:0:60:147:1:0:0.6 0/1:180:3:0,3:62,115:0.0167:2,0:16.7:1:31.7:1:0.55225:0:60:6:0.0173:0:1 -8 23540377 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50462;SOR=Inf;LSEQ=CCTCCGCTTTCGCCTCCCCG;RSEQ=GCCGCGGCTCCGGAACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:41,94:0:2,0:26.6:1:30.5:1:1:0:60:44:1:0:0.6 0/1:169:2:1,1:57,110:0.0118:2,2:27.5:1:29:1:1:1.92:60:4:0.0121:0:2 -8 23540382 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20574;SOR=0;LSEQ=GCTTTCGCCTCCCCGGGCCG;RSEQ=GGCTCCGGAACCCTGAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:39,88:0.0154:2,2:39:1:30.5:1:0.52568:2.24:60:4:0.0157:0:1.5 0/0:156:0:0,0:55,101:0:2,0:23.8:1:29.1:1:1:0:60:25:1:0:0.5 -8 23540408 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49701;SOR=Inf;LSEQ=CGGAACCCTGAGCATCCCGG;RSEQ=GGCCCCGCCTTGGCCTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:14,64:0:2,0:23:1:29.8:1:1:0:60:25:1:0:1.1 0/1:81:2:1,1:20,59:0.0247:2,2:19.5:1:29:1:0.4537:2.90:60:4:0.025:0:2 -8 23540417 . C T 183 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00028;SOR=0;LSEQ=GAGCATCCCGGCGGCCCCGC;RSEQ=TTGGCCTGAATGCACCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:66:9,57:0,0:1:0,2:21.1:1:30.3:1:1:0:60:32:1:0:1.2 1/1:66:54:14,40:2,10:0.8182:2,2:23:1:29.5:1:0.715:1.74:60:108:0.8182:0:1.1 -8 23548231 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08867;SOR=Inf;LSEQ=TTGCTCATACCCATTCATGC;RSEQ=TCCTATCTCATACCTGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:0:1,0:26.4:1:32:1:1:0:60:40:1:0:0.2 0/1:9:2:1,1:7,0:0.2222:0,2:11.5:1:31.5:1:0.22222:0:60:4:0.2222:0:3 -8 23548345 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20568;SOR=Inf;LSEQ=CTCTCCCTGCAGGCCTTTCT;RSEQ=TAAGGCCAAGGCATGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:97,0:0:1,0:23.7:1:32.3:1:1:0:60:47.5:1:0:0.1 0/1:81:2:2,0:76,3:0.0247:1,0:17:1:31.5:1:1:0:60:4:0.0247:0:1 -8 23548490 . GC G 200 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAGTATTTTGCTAACAGT;RSEQ=CCTGGTCACCTTTCCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1063:0:0,0:608,453:0:2,0:24.8:1:31.3:1:1:0:60:38.296:0.9981:0:0.2 0/1:1451:81:44,37:747,621:0.0558:2,2:24.4:1:31.7:1:1:1.01152:60:162:0.0564:0.0048:0.3 -8 23548530 . T C 209 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCTCCATGGCTGCCGGCT;RSEQ=CTGGAGAGCCCCAGGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1168:111:62,49:542,513:0.095:2,2:24.8:1:30.8:1:0.42452:1.20:60:36:0.0938:0:1.1 0/0:1629:0:0,0:833,794:0:2,0:25.4:1:29.2:1:1:0:60:59.259:0.9988:0:0.2 -8 23548749 . T C 207 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42949;SOR=0;LSEQ=CTCTGCCACTCCCTGCCGCA;RSEQ=AGTGCCCACCATAAAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:89:89:2,87:0,0:1:0,1:25.5:1:32:1:1:0:60:28.667:1:0:1.2 1/1:67:66:3,63:0,1:0.9851:0,1:23.5:1:32.1:1:1:0:60:132:0.9851:0:1.1 -8 23548805 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17143;SOR=Inf;LSEQ=CTCCTGGCGCCCCAACATGA;RSEQ=GCCTTCCCAGGTGGATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:0:1,0:25:1:28.9:1:1:0:60:13.5:1:0:0.7 0/1:21:2:0,2:3,16:0.0952:2,0:8.5:1:30:1:1:0:60:4:0.0952:0:2 -8 23560366 . C A 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12427;SOR=Inf;LSEQ=TGCGTGGACGTGAGCTGCAG;RSEQ=GCGCTGGCCAGGTGCTCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:90,152:0:2,0:26.5:1:30.4:1:1:0:60:79.667:1:0:0.1 0/1:258:4:2,2:107,147:0.0155:2,2:14.3:1:28.3:1:1:1.37:60:8:0.0158:0:1.3 -8 23560375 . C A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24843;SOR=Inf;LSEQ=GTGAGCTGCAGCGCGCTGGC;RSEQ=AGGTGCTCGCGCTCGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:80,143:0:2,0:24.4:1:31.3:1:1:0:60:54.75:1:0:0.1 0/1:228:3:2,1:88,137:0.0132:2,2:16.3:1:22:1:0.56359:3.10:60:2:0.009:0:2.3 -8 23560437 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50323;SOR=0;LSEQ=GAAGCGCCGCTCCAGGGCCA;RSEQ=CACCTGCGCCTGCGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:5,63:0.0286:2,2:40.5:1:30:1:0.16522:11.59:60:4:0.0286:0:1 0/0:55:0:0,0:8,47:0:2,0:26:1:31.8:1:1:0:60:54:1:0:0.2 -8 23560449 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56788;SOR=2.89655;LSEQ=CAGGGCCAGCACCTGCGCCT;RSEQ=CGAAAAGAGCACGCGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:6,54:0.0164:2,0:26:0:27:0:1:0:60:2:0.0167:0:1 0/1:43:2:1,1:7,34:0.0465:2,2:42:1:27.5:1:0.34109:4.61:60:4:0.0465:0:1 -8 23561168 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGAGCCGAGATCGTGC;RSEQ=ACTGCACTCCAGCCTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:1:30:1:1:0:43.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 24533193 . C T 263 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0099;LSEQ=ATTTGCTTGAAAATAAATTA;RSEQ=GATTCACAACACAAAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:436:434:193,241:0,0:0.9954:0,2:24.5:1:30.1:1:1:0:60:85.8:1:0:1.1 1/0:600:409:205,204:86,105:0.6817:2,2:25.1:1:29.7:1:0.25532:1.23:60:408:0.6823:0:1.1 -8 25057387 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.23881;SOR=Inf;LSEQ=TGCTGAGCTTTGAACTTCCT;RSEQ=CAGAACAAAAGTAAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:14,20:0:2,0:21.5:1:29.4:1:1:0:60:33:1:0:0.1 0/1:33:2:1,1:14,17:0.0606:2,2:41.5:1:29:0:1:1.21:60:4:0.0606:0:1.5 -8 25057479 . AT A 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.46249;LSEQ=GACTGCATGATTTGTTTTAG;RSEQ=TTGTTAATTTACATTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,1:0.9:0,0:21.6:1:31.4:1:1:0:60:18:0.9:0.4:0.1 1/1:10:8:0,8:0,2:0.8:0,0:37.1:1:29.4:1:1:0:60:16:0.8:0:0 -8 25058491 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGTGCAGTGGTGCAATCT;RSEQ=GGCTCACTGCAACCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29.5:1:1:0:51:4:1:0:2.5 -8 26148748 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGAGCACGTAAACTGGA;RSEQ=TCCTAAGCCCGCCCCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:32:1:29:1:1:0:60:4:1:0:1 -8 28157847 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GAACAAGATGAAGATGCTTA;RSEQ=AAGAAACAGTTCTCTCAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:4,1:0.1667:2,0:31:0:32:0:1:0:60:2:0.1667:0:1 1/1:2:2:1,1:0,0:1:0,2:28.5:1:30.5:1:1:0:60:4:1:0:1.5 -8 28157994 . C G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=0.12258;LSEQ=TTAAAAAGAAGAGGTGGAAC;RSEQ=ATCCCAAAATGTCCCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:14:8,6:16,13:0.3256:2,2:25.7:1:30.4:1:1:1.08:60:28:0.3256:0:1.1 0/1:73:4:3,1:40,29:0.0548:2,2:25.5:1:29.8:1:0.63911:2.15:60:8:0.0548:0:1 -8 28158029 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5292;SOR=Inf;LSEQ=CTCACTCAGAAGAAAGATCA;RSEQ=GTAGCTCAAAAGAAGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:27,24:0:2,0:30.7:1:31.9:1:1:0:60:50:1:0:0.4 0/1:86:2:1,1:42,42:0.0233:2,2:31:0:31.5:1:1:1:60:4:0.0235:0:1.5 -8 28158138 . A G 64 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.62785;SOR=0.41915;LSEQ=AGACAATAAACTTATGGACA;RSEQ=CAACTAAAAAAAAAGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:0,4:0,13:0.2353:1,0:21.5:1:32.3:1:1:0:60:8:0.2353:0:1 0/1:9:1:0,1:1,7:0.1111:2,0:23:0:34:0:1:0:60:2:0.1111:0:1 -8 29168492 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTTCTAGGTCCCGTGGCA;RSEQ=CCATCTTGCTGTTACTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,12:0:2,0:25.2:1:29.3:1:1:0:57.2:8:0.9412:0:0.3 0/1:46:2:1,1:20,23:0.0435:2,2:13:1:27.5:1:1:1.15:57:4:0.0444:0:1 -8 29496423 . C T 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACAAATACCTAATGCATG;RSEQ=GGGGCTTAAAACCTAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:17:1:31:1:1:0:58.7:6:0.5:0:1 0/0:1:0:0,0:1,0:0:0,0:3:0:31:0:1:0:52:2:1:0:1 -8 29496424 . G A 49 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAAATACCTAATGCATGC;RSEQ=GGGCTTAAAACCTAGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:0.5:0,0:30.7:1:31:1:1:0:49.7:6:0.5:0:1 1/1:1:1:1,0:0,0:1:0,0:4:0:32:0:1:0:52:2:1:0:1 -8 29496672 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20681;SOR=0;LSEQ=AAAAATAGAACTTAATTGAA;RSEQ=GTGATTTTGAAAGAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:154,33:0.0106:2,2:23.5:1:32:0:0.32821:4.61246:60:4:0.0106:0:1 0/0:226:0:0,0:176,50:0:2,0:21.7:1:31.4:1:1:0:60:225:1:0:0.2 -8 29496762 . T G 292 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.70994;LSEQ=TGGGTCAGGCTGAGTTGGAC;RSEQ=CTTGGCAATTCTGAGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:637:454:228,226:91,90:0.7127:2,2:28:1:30.7:1:1:1.00224:60:89.8:0.7138:0:1.1 1/1:817:737:348,389:37,39:0.9021:2,2:27.3:1:30.7:1:0.81067:1.06038:60:80.889:0.9043:0:1.2 -8 29496868 . T C 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TGATGGTTAAGAACATAGTC;RSEQ=ATGGGGTCAGACATGCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:17:2,15:11,117:0.1172:2,2:16.1:1:31.6:1:0.65101:1.41:60:34:0.1172:0:1 0/0:129:0:0,0:13,116:0:2,0:23.1:1:28.7:1:1:0:60:258:1:0:0 -8 29497050 . TA T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTTGGCTCAGTCAGCAC;RSEQ=AAAAAATGGTGGCGATGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:24.9:1:28.8:1:1:0:60:14:1:0.2857:0.1 1/1:2:2:0,2:0,0:1:0,0:38.5:1:30.5:1:1:0:60:4:1:0:0 -8 29885106 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21445;SOR=0;LSEQ=GGCTCACCCTCCGAAGGCAG;RSEQ=CTCGCCGAAGGCAGACGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:2,0:97,5:0.0192:1,0:17:1:31:0:1:0:60:4:0.0192:0:1.5 0/0:120:0:0,0:113,7:0:2,0:24.2:1:31.7:1:1:0:60:59:1:0:0.5 -8 29885149 . A G 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00162;SOR=0.57611;LSEQ=CGGACTTGGTCCTGCACAGC;RSEQ=GGCGCGGAGCAGCGCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:101:74,27:107,31:0.4226:2,2:23.6:1:29.8:1:0.45006:1.25813:60:49.5:0.4231:0:1.1 0/1:361:107:75,32:177,76:0.2964:2,2:22.8:1:29.2:1:1:1.01:60:52.5:0.2983:0:1.2 -8 29885245 . C A 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00338;SOR=0.72263;LSEQ=CAAAATGCCCAAGAAGACGC;RSEQ=GACGCCCATCCAGCTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:631:213:102,111:214,204:0.3376:2,2:25.2:1:30.5:1:0.44939:1.14134:60:70:0.3382:0:1.2 0/1:1048:282:141,141:395,368:0.2691:2,2:24.9:1:30:1:0.62601:1.07329:60:55.4:0.2687:0:1.3 -8 29885635 . A G 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07356;SOR=0.74104;LSEQ=GCTTCTGTGGTGCATTCTAC;RSEQ=GCGAGAGGCGAGATCAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:98:52,46:108,97:0.3234:2,2:26.9:1:29.9:1:1:1.02:60:48:0.3232:0:1.3 0/1:478:125:63,62:176,176:0.2615:2,2:23.1:1:29.2:1:1:1.02:60:40.667:0.2607:0:1.3 -8 29885706 . C T 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00319;SOR=0.58692;LSEQ=GGATCAAGTCCTGAAGAAAG;RSEQ=GGGAAGAATTCCTGAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:83:44,39:122,122:0.2538:2,2:25.6:1:30.2:1:0.70333:1.13:60:82:0.2531:0:1.3 0/1:487:81:36,45:198,208:0.1663:2,2:25.7:1:29.8:1:0.54287:1.18948:60:80:0.166:0:1.4 -8 29885884 . G A 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15268;SOR=1.33256;LSEQ=GGGTCAGTGGGCAGCTCATC;RSEQ=ACTCCATGGCCAACTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:44:25,19:261,268:0.0767:2,2:26.5:1:30.2:1:0.35162:1.35:60:88:0.0784:0:1.8 0/1:803:80:44,36:379,344:0.0996:2,2:24.8:1:29.4:1:0.72374:1.11:60:39:0.0977:0:1.7 -8 29885928 . C G 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.43767;LSEQ=GGCCCAAGGTCCTACATGTC;RSEQ=CCAGAAAGATTCCAGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:212:107,105:158,180:0.3841:2,2:24.6:1:30.5:1:0.43028:1.16:60:34.333:0.385:0:1.3 0/1:784:168:83,85:260,289:0.2143:2,2:22.7:1:30.7:1:0.65974:1.09:60:167:0.2174:0:1.2 -8 29886141 . G C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=0.57203;LSEQ=CCTCTTAGCTCATATGGAAT;RSEQ=GACAGCCGACCTCCCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:112:49,63:160,182:0.2462:2,2:25.5:1:30.5:1:0.58701:1.12999:59.8:111:0.2467:0:1.9 0/1:642:101:48,53:257,281:0.1573:2,2:25.7:1:30:1:1:1.00985:60:32.667:0.1558:0:2 -8 29886157 . G A 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.53984;LSEQ=GAATGGACAGCCGACCTCCC;RSEQ=TGGCAATTTTTGAGTTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:116:52,64:160,174:0.2578:2,2:23.3:1:30.5:1:0.59062:1.13143:59.9:57:0.2573:0:1.9 0/1:659:104:51,53:269,284:0.1578:2,2:25.1:1:29.9:1:1:1.02:60:208:0.16:0:2 -8 29886263 . TA T 238 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00041;SOR=0.62081;LSEQ=TTTTGTGAATAAATGCCTAA;RSEQ=AAAACCCCGTAGAGAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:210:100,110:68,83:0.5817:2,2:24:1:30.5:1:0.66924:1.11:60:104:0.581:0.1136:0.2 0/1:598:277:142,135:158,163:0.4632:2,2:25.4:1:29.4:1:0.62372:1.08:60:91.333:0.4636:0.0736:0.2 -8 29886372 . G A 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02792;SOR=0;LSEQ=GTTGGCTCTGCTCCACCATC;RSEQ=GGCTTAACCAGCCCAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:4:4,0:182,211:0.0101:2,0:5.8:1:27.3:1:0.04736:0:60:8:0.0102:0:1 0/0:572:0:0,0:251,321:0:2,0:25.1:1:29.5:1:1:0:59.6:51:1:0:0.5 -8 29886373 . G A 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.78273;SOR=0.96084;LSEQ=TTGGCTCTGCTCCACCATCG;RSEQ=GCTTAACCAGCCCAGCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:140:63,77:119,134:0.3562:2,2:26.8:1:30.5:1:0.75157:1.08518:60:34:0.3542:0:1.1 0/1:556:193:88,105:157,206:0.3471:2,2:25:1:29.3:1:0.65378:1.10:59.8:26.571:0.3432:0:1.2 -8 29886439 . C A 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62429;SOR=2.8054;LSEQ=GTTTGGGAAGCAGCAAAGAG;RSEQ=AAGTCCCCTGCCCAGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:1,0:57,151:0.0048:2,0:1:0:15:0:0.27751:0:60:0:0:0:1 0/1:226:3:2,1:66,157:0.0133:2,2:20.3:1:27:1:0.21599:4.72:60:6:0.0135:0:1.3 -8 29886452 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50031;SOR=Inf;LSEQ=CAAAGAGCAAGTCCCCTGCC;RSEQ=AGTGGTTTGCCATGTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:41,129:0:2,0:22.1:1:31.6:1:1:0:59.9:84:1:0:0.3 0/1:191:2:1,1:49,140:0.0105:2,2:12:1:27:1:0.45605:2.84:60:4:0.0106:0:1 -8 29886463 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.85617;LSEQ=TCCCCTGCCCAGTGGTTTGC;RSEQ=ATGTCACTTTTGGGCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:1:0,1:23,110:0.0075:2,0:22:0:11:0:1:0:60:0:0:0:1 0/1:145:2:1,1:31,112:0.0138:2,2:21:1:30:1:0.39387:3.57:60:4:0.0142:0:1 -8 29886613 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTATTACTATTATTGTTCC;RSEQ=CTAAGTGGATTGGCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:18.5:1:32.5:1:1:0:40:4:0.25:0:1 0/0:3:0:0,0:0,3:0:0,0:25.3:1:28.3:1:1:0:59:6:1:0:0 -8 30349808 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.52512;SOR=Inf;LSEQ=ATAAAGCACTTTCACACATG;RSEQ=ATGCATCCATTGTCTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:64,11:0:2,0:23.1:1:31.7:1:1:0:60:36.5:1:0:0.1 0/1:121:2:1,1:92,27:0.0165:2,2:24:1:27:1:0.41074:3.36408:60:4:0.0168:0:1 -8 30349837 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52752;SOR=Inf;LSEQ=ATTGTCTCATTTTGCCTGAT;RSEQ=AGTGCATAATATGTATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:81,42:0:2,0:23.8:1:28.3:1:1:0:60:60.5:1:0:0.1 0/1:201:2:1,1:126,73:0.01:2,2:30.5:1:30.5:1:1:1.72103:60:4:0.0101:0:1 -8 30349914 . A G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29229;SOR=1.2352;LSEQ=AGATTAATGTGTAATTATGT;RSEQ=TAATTAGTCCTTTCTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:62:27,35:56,73:0.3246:2,2:27.1:1:30.9:1:1:1.01:60:14.5:0.3118:0:1.1 0/1:314:117:55,62:82,113:0.3726:2,2:26:1:30.9:1:0.41129:1.22:60:116:0.3742:0:1.1 -8 30349928 . C T 37 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05647;SOR=0;LSEQ=TTATGTATAATTAGTCCTTT;RSEQ=TTTAAAGAGCTGACACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:0,3:79,102:0.0163:2,0:8:1:23.7:1:0.26096:0:60:2:0.0111:0:2.7 0/0:294:0:0,0:125,169:0:2,0:25.3:1:31:1:1:0:60:97:1:0:0.5 -8 30349976 . T TA 163 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.03265;SOR=1.92698;LSEQ=ACACCAGTAACCCTTTGACT;RSEQ=AAAAAAAAAATACCCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:20:7,13:18,53:0.2041:2,2:33.4:1:29.8:1:0.40636:1.58:60:40:0.2083:0:0.2 0/1:160:53:18,35:36,68:0.3313:2,2:27.9:1:28.6:1:1:1.02923:59.9:106:0.3376:0.025:0.3 -8 31397667 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3021;SOR=0.2858;LSEQ=TTAGTGACCACGTGTGTTGA;RSEQ=GACAGGTAAATGTTTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:113,46:0.0124:2,2:31:1:29.5:1:0.49992:2.44099:60:4:0.0125:0:1 0/0:280:1:1,0:171,108:0.0036:2,0:4:0:30:0:1:0:60:2:0.0036:0:2 -8 31397748 . G A 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01085;LSEQ=GTTAATAATAATTAACACTA;RSEQ=GGAGGCAGCTGACAACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:261:159:72,87:52,50:0.6092:2,2:24.5:1:30.6:1:0.37717:1.25555:60:158:0.61:0:1.1 1/0:340:208:93,115:63,69:0.6118:2,2:24.3:1:30.2:1:0.65524:1.12863:60:103:0.6113:0:1.1 -8 31398144 . T C 31 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTTTATTGTGAGGCACC;RSEQ=GTATGGTTTAGACTTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33:1:31.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:4:0:25:0:1:0:60:2:1:0:2 -8 34731644 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51652;SOR=Inf;LSEQ=AAACTAAGATACAGCCTTTT;RSEQ=GCTGGAACCGCCATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,5:0:2,0:26.3:1:31.8:1:1:0:60:28:1:0:0.1 0/1:23:2:1,1:13,8:0.087:2,2:13.5:1:29:1:1:1.58984:60:4:0.087:0:1.5 -8 34731853 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.11178;SOR=0;LSEQ=GCCCCACAAGTGTTACCACG;RSEQ=CAAAACTGGAAGAGTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:58,52:0.0179:2,2:25:1:28.5:1:1:1.11429:60:4:0.0187:0:1 0/0:222:0:0,0:117,105:0:2,0:28.6:1:30.7:1:1:0:60:36:1:0:0.1 -8 34731913 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53773;SOR=Inf;LSEQ=GTTGTAAACAAACAAGTTAA;RSEQ=GGCAAGATTCTTGCCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:25,38:0:2,0:18.7:1:31.3:1:1:0:55.6:126:1:0:0 0/1:113:2:1,1:34,77:0.0177:2,2:19:1:29:1:0.52544:2.25:60:4:0.018:0:1 -8 35982376 . TT C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.53635;SOR=Inf;LSEQ=GGTCTATCCGTTTTGTTAAT;RSEQ=TTTTCAGAAAACCTGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:26,21:0:2,0:22.1:1:29.9:1:1:0:60:94:1:0:0.2 0/1:84:2:1,1:49,32:0.0238:2,2:6:1:28.7:1:1:1.52314:60:4:0.0247:0.0119:0.5 -8 35982438 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54594;SOR=Inf;LSEQ=AGGGTTTTTTGTGTTTATAT;RSEQ=TCCTTCAATTCTTCTCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:0:2,0:26.2:1:31.4:1:1:0:60:46:1:0:0.4 0/1:90:2:1,1:47,41:0.0222:2,2:21.5:1:30:1:1:1.1446:60:4:0.0233:0:3.5 -8 35982446 . A G 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29719;SOR=Inf;LSEQ=TTGTGTTTATATCTCCTTCA;RSEQ=TTCTTCTCTGATCTTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,18:0:2,0:23.4:1:29.8:1:1:0:60:38:1:0:0.4 0/1:75:4:2,2:36,33:0.0533:2,2:10:1:30:1:1:1.0896:60:8:0.0541:0:2.8 -8 35982447 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54393;SOR=Inf;LSEQ=TGTGTTTATATCTCCTTCAA;RSEQ=TCTTCTCTGATCTTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,18:0:2,0:22.4:1:30.4:1:1:0:60:78:1:0:0.4 0/1:74:2:1,1:37,35:0.027:2,2:7:0:33:0:1:1.05637:60:4:0.0286:0:1 -8 35982451 . T G 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29315;SOR=Inf;LSEQ=TTTATATCTCCTTCAATTCT;RSEQ=CTCTGATCTTAATTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:21,13:0:2,0:21.3:1:29.7:1:1:0:60:68:1:0:0.5 0/1:61:4:2,2:32,25:0.0656:2,2:5:1:30.3:1:1:1.27477:60:8:0.0667:0:2.8 -8 36091703 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTTTACTTACAAAACA;RSEQ=AAATTCAGAGATACAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:27.5:1:1:0:60:4:1:0:1 -8 36092310 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20119;SOR=0;LSEQ=TTTCCTTTTTTCCCCTTTCT;RSEQ=TGCTGTCAAATCGACTATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:82,32:0.0172:2,2:23.5:1:31:1:0.48981:2.53872:60:4:0.0177:0:1 0/0:142:0:0,0:96,46:0:2,0:23.5:1:29.6:1:1:0:60:141:1:0:0.1 -8 36092421 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.94105;LSEQ=TACGCAGAACTCTCTCTGGG;RSEQ=GCCCAATGCTCCGTGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:95:46,49:54,62:0.4481:2,2:23.4:1:29.9:1:0.88984:1.08:60:94:0.4541:0:1.2 1/1:263:218:105,113:24,21:0.8289:2,2:26.8:1:29.7:1:0.62366:1.22896:60:108:0.8276:0:1.2 -8 36092439 . T A 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.26057;SOR=Inf;LSEQ=GGCGCCCAATGCTCCGTGAT;RSEQ=GACTGATCTGTGAAGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:87,104:0:2,0:26.2:1:30.1:1:1:0:60:94.5:1:0:0.6 0/1:247:3:3,0:108,136:0.0121:2,0:8.3:1:20:1:0.0894:0:60:2:0.0082:0:1.7 -8 36092461 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17296;SOR=0;LSEQ=ACTGATCTGTGAAGCCAGAA;RSEQ=CCTCTCTGCTTTTGAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:60,93:0.0129:2,2:15.5:1:30.5:1:1:1.55:60:4:0.0133:0:1 0/0:217:0:0,0:91,126:0:2,0:24.1:1:28.8:1:1:0:60:107.5:1:0:0.7 -8 37136808 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47368;SOR=0;LSEQ=CACGAACCCATGCTACCGGG;RSEQ=CCTAGCGTCCCAACCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:1,7:0.2:2,2:5.5:1:30:1:0.37778:5.29:60:4:0.2:0:1.5 0/0:10:0:0,0:4,6:0:2,0:23.1:1:31.5:1:1:0:60:20:1:0:0 -8 37137291 . C T 41 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AGGGGTGGCTACAGTATCTG;RSEQ=GGACCAGCAGACTTAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:28:0:31:0:1:0:60:2:1:0:0 1/1:3:3:2,1:0,0:1:0,2:33.3:1:26.3:1:1:0:60:6:1:0:1.7 -8 37137809 . GA G 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.08399;SOR=3.15455;LSEQ=GGAGATGGGAAAGAGTCAAT;RSEQ=AAAAAATGCTGAAAACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:2,4:8,10:0.25:2,2:23.7:1:32.5:1:1:1.56956:60:12:0.25:0:0.5 1/0:27:14:5,9:7,6:0.5185:2,2:20.5:1:31.2:1:0.44948:2.04175:59.6:28:0.5185:0.037:0.3 -8 37137887 . G C 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1451;SOR=6.57383;LSEQ=ACATCTCTCCATCAGGGGCA;RSEQ=AGAACTGGGTGGAGGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:1,5:0.1429:2,0:20:0:28:0:1:0:60:2:0.1429:0:1 1/0:9:5:1,4:0,4:0.5556:0,2:34.6:1:32:1:1:0:60:10:0.5556:0:1.2 -8 38271057 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5008;SOR=Inf;LSEQ=TCCTGCCAGCAGGAAAGGGG;RSEQ=CAGGGACGGACAGGTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:130,19:0:2,0:21.7:1:29.1:1:1:0:60:15.556:1:0:0.2 0/1:171:2:1,1:130,39:0.0117:2,2:12.5:1:32:0:0.41417:3.30401:60:4:0.0119:0:2 -8 38271106 . C T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08232;SOR=Inf;LSEQ=GGGGCTGTGGGTGAGGGTTA;RSEQ=AGCTGACGGTGGAGTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:221,111:0:2,0:27.7:1:31.6:1:1:0:60:40.5:1:0:0.1 0/1:478:5:1,4:287,186:0.0105:2,2:23:1:23.4:1:0.08401:6.15001:60:4:0.0084:0:1 -8 38271547 . G A 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCATCATCATGTACCTGCG;RSEQ=CAGGACTGTAAGGTCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:205,342:0:2,0:22.5:1:31.7:1:1:0:60:90.167:0.9963:0:0.1 0/1:607:26:11,15:222,359:0.0428:2,2:25.6:1:28.3:1:0.68438:1.19:60:52:0.0436:0:1 -8 38271986 . A T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19398;SOR=Inf;LSEQ=TTTCTCTCTGGGGCAGAAAG;RSEQ=GGACTCCTCAGTCCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:173,36:0:2,0:24.5:1:30.6:1:1:0:60:208:1:0:0 0/1:165:2:1,1:131,31:0.0121:2,2:12.5:1:25.5:1:0.35313:4.1751:60:4:0.0123:0:1 -8 38272046 . A T 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.13584;SOR=4.98457;LSEQ=CTAGAAGCTCTCTATCCCAC;RSEQ=CCTCCCTGGCAATTGCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:1:0,1:284,171:0.0022:2,0:1:0:27:0:0.37719:0:60:2:0.0022:0:1 0/1:553:6:1,5:322,224:0.0108:2,2:14.8:1:25.8:1:0.0867:7.16356:60:12:0.0111:0:1 -8 38272417 . G A 50 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13586;SOR=0.28476;LSEQ=GCTGCCAGGTCTCGGTGTAT;RSEQ=CACTGAGGAAGGAGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:5:3,2:171,314:0.0102:2,2:21.8:1:21.6:1:0.3525:2.75:60:1.5:0.0063:0:1.4 0/0:684:2:2,0:246,436:0.0029:2,0:1:0:21:0:0.13112:0:60:4:0.003:0:1.5 -8 38272447 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13113;SOR=Inf;LSEQ=AGGAGGAAGGGAGAGCGGGA;RSEQ=GCGGGGAGGTGAGGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:78,235:0:2,0:22.5:1:31:1:1:0:60:155.5:1:0:0.1 0/1:381:4:3,1:94,283:0.0105:2,2:14:1:29:1:0.05246:8.97:60:8:0.0107:0:1 -8 38272475 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49895;SOR=0;LSEQ=GGTGAGGGAGCTGGAAGGCT;RSEQ=TGGGCGGCCGCCACCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:26,164:0.0104:2,2:24:1:29:1:0.26211:6.21:60:4:0.0106:0:1 0/0:183:0:0,0:24,158:0:2,0:22.8:1:31.7:1:1:0:60:90:1:0:0.2 -8 38272485 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49831;SOR=Inf;LSEQ=CTGGAAGGCTCTGGGCGGCC;RSEQ=CCACCCATGCAACTAGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:14,133:0:2,0:25.8:1:31.8:1:1:0:60:72.5:1:0:0.1 0/1:148:2:1,1:12,134:0.0135:2,2:17.5:1:27.5:1:0.16851:10.77:60:4:0.014:0:1 -8 38272542 . C G 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTGCCACACTGCTCTGCCC;RSEQ=CCGAACCTTTGCTTTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:2,64:0:1,0:24.3:1:30.5:1:1:0:60:21:1:0:0.2 0/1:51:13:0,13:3,35:0.2549:2,1:24.9:1:30.5:1:0.56115:0:60:5.5:0.234:0:1.2 -8 38273261 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50267;SOR=0;LSEQ=GAGAGCCTAAGACAACACAC;RSEQ=GGGCACACAGGGCCAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:2,0:102,4:0.0185:1,0:17.5:1:30.5:1:1:0:60:4:0.0189:0:2.5 0/0:88:0:0,0:86,2:0:1,0:22:1:30.3:1:1:0:60:87:1:0:0.1 -8 38273278 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20924;SOR=Inf;LSEQ=CACAGGGCACACAGGGCCAG;RSEQ=GCTCAGTGCATCCACAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:132,5:0:1,0:25.6:1:30.2:1:1:0:60:67.5:1:0:0.1 0/1:116:2:1,1:109,5:0.0172:1,2:15.5:1:28:1:0.1012:19.99168:60:4:0.0172:0:1 -8 38273613 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.21886;SOR=Inf;LSEQ=GAAGAGGCCATGGGGCCAGC;RSEQ=GCAGGTGAGCAGGTTTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:22,131:0:2,0:22:1:30.6:1:1:0:60:37.25:1:0:0.1 0/1:135:2:1,1:26,107:0.0148:2,2:27.5:1:29.5:1:0.36119:4.06:60:4:0.015:0:1.5 -8 38274799 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09107;SOR=0;LSEQ=TCTTCTCCCCGCTGGGCAGG;RSEQ=AAAGCCAGTCTGGCCGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:205,67:0.0109:2,2:23:1:27.3:1:0.15624:6.06942:60:6:0.0111:0:1 0/0:335:0:0,0:235,100:0:2,0:23.6:1:30.4:1:1:0:60:29.455:1:0:0.1 -8 38275547 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0951;SOR=0;LSEQ=GAGTGGCATAAGTTGGGGCT;RSEQ=GTGAAGTTCAAACCTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:0,3:63,197:0.0114:2,0:39:1:24.7:1:1:0:60:2:0.0078:0:1 0/0:312:0:0,0:78,233:0:2,0:25.3:1:30.2:1:1:0:60:50.833:0.9967:0:0.1 -8 38275607 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20902;SOR=Inf;LSEQ=TCTGTATTTCACCCAACTGC;RSEQ=AGCAGAAAGTGGAATGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:57,92:0:2,0:24.1:1:30.9:1:1:0:60:73.5:1:0:0.1 0/1:126:2:1,1:52,71:0.0159:2,2:37.5:1:29.5:1:1:1.36:60:4:0.016:0:1 -8 38275637 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61942;SOR=2.05572;LSEQ=TGGAATGAATGTTTCTGCAG;RSEQ=CATTTCATGAACCTTCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:0,1:81,54:0.0074:2,0:30:0:32:0:0.40441:0:60:2:0.0075:0:1 0/1:133:2:1,1:88,43:0.015:2,2:10.5:1:28:1:1:2.03464:60:4:0.0153:0:1 -8 38275661 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2442;SOR=Inf;LSEQ=TTCATGAACCTTCACCGCCC;RSEQ=GAAGGTGTTAGTATACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:124,71:0:2,0:21.6:1:30.4:1:1:0:60:64:1:0:0.1 0/1:191:2:1,1:131,58:0.0105:2,2:32.5:1:28.5:1:0.52351:2.24796:60:4:0.0106:0:1 -8 38275681 . C T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.33664;SOR=0.27928;LSEQ=AGAAGGTGTTAGTATACACA;RSEQ=CTTCCACCACTAGAATAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:163,92:0.0116:2,2:6.3:1:27.3:1:0.30077:3.52532:60:6:0.0118:0:1 0/0:306:1:0,1:202,103:0.0033:2,0:1:0:22:0:0.33987:0:60:2:0.0033:0:1 -8 38275935 . G A 25 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.92985;LSEQ=CTAGAGCAAGGAGGGGGGAC;RSEQ=GGGTGACTCCTTCCCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:42,143:0.0107:2,2:6:1:23.5:1:0.40797:3.38:60:4:0.0107:0:1 0/1:201:2:0,2:45,154:0.01:2,0:5:1:25:1:1:0:60:1:0.0051:0:1 -8 38279065 . G A 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00254;SOR=0;LSEQ=CCAGATCCCGGGCATGCATT;RSEQ=CAATGGCCAGGGGGAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:13:13,0:30,0:0.3023:1,1:18.2:1:28.1:1:1:0:60:26:0.3023:0:1.2 0/0:23:0:0,0:22,1:0:1,0:24.3:1:32.8:1:1:0:60:46:1:0:0 -8 38279120 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50587;SOR=0;LSEQ=GGTGGGAGGCCTCCGTGCGC;RSEQ=TGCAAAACTAGGGAAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:121,11:0.0149:2,2:11:1:27.5:1:0.1717:10.57526:60:4:0.0152:0:1 0/0:104:0:0,0:79,25:0:2,0:20.7:1:30:1:1:0:60:33.667:1:0:0.2 -8 38279133 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23871;SOR=Inf;LSEQ=CGTGCGCCTGCAAAACTAGG;RSEQ=AAGCTCTTCTCTGAGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:147,21:0:2,0:23.9:1:31.5:1:1:0:60:55:1:0:0.1 0/1:161:2:1,1:113,46:0.0124:2,2:19.5:1:28:1:0.49992:2.44099:60:4:0.0127:0:1.5 -8 38279138 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24511;SOR=Inf;LSEQ=GCCTGCAAAACTAGGGAAGC;RSEQ=CTTCTCTGAGCTGAGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:157,23:0:2,0:24.6:1:31.1:1:1:0:60:89:1:0:0.1 0/1:177:2:1,1:125,50:0.0113:2,2:18:0:32.5:1:0.49441:2.48526:60:4:0.0117:0:1.5 -8 38279177 . G A 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12569;SOR=Inf;LSEQ=ATTCAGCCCTCAAAGCTGGG;RSEQ=CAGGATGTGGCACCAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:229,91:0:2,0:25.9:1:31.1:1:1:0:60:79:1:0:0.1 0/1:353:4:3,1:230,117:0.0113:2,2:11:1:27.5:1:1:1.52:60:8:0.0116:0:1.3 -8 38279518 . G A 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00975;SOR=Inf;LSEQ=ACATGAGACCTCTAAGAGAC;RSEQ=CAGAGCAAGGGAAGGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:10,136:0:2,0:22.7:1:32:1:1:0:60:47.667:1:0:0.1 0/1:128:6:0,6:16,106:0.0469:2,0:34.2:1:27.8:1:1:0:60:5:0.04:0:1 -8 38281658 . G A 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=AAAGATCGTACGTAACTCAG;RSEQ=ACACAGGGCTAAGACTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:50,0:0:1,0:24.5:1:30.8:1:1:0:60:24:1:0:0 0/1:30:9:8,1:21,0:0.3:1,2:26.8:1:28.2:1:0.3:0:60:8:0.2759:0:1 -8 38281729 . A T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58802;SOR=2.4912;LSEQ=CAATGAAAAGGCAGGGGTCC;RSEQ=AATGCCTTCCTTGTGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:122,18:0.0071:2,0:1:0:24:0:0.13475:0:60:2:0.0071:0:1 0/1:114:2:1,1:99,13:0.0175:2,2:24:1:28:1:0.23149:7.37604:60:4:0.018:0:1 -8 38281742 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23395;SOR=Inf;LSEQ=GGGGTCCAAATGCCTTCCTT;RSEQ=TGTAGCTGACCCCAAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:148,34:0:2,0:22.4:1:32:1:1:0:60:59.667:1:0:0.1 0/1:171:2:1,1:137,32:0.0117:2,2:5.5:1:28.5:1:0.34964:4.23125:60:4:0.0117:0:1 -8 38283759 . C T 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGATGCTCCAGGTGGCATAA;RSEQ=GGACCTGAGGGGAAATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:45:13,32:165,272:0.093:2,2:25.9:1:30.4:1:0.26071:1.49203:60:90:0.0943:0:1 0/0:648:0:0,0:228,420:0:2,0:23.9:1:29.7:1:1:0:60:91.571:1:0:0.2 -8 38285614 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14192;SOR=Inf;LSEQ=TCCAATATGGAGCTACGGCT;RSEQ=CCCGGGGAAAGCCAAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:77,156:0:2,0:23.7:1:32:1:1:0:60:37.833:1:0:0.1 0/1:319:4:3,1:109,206:0.0125:2,2:6:1:25.3:1:0.1261:5.64:60:8:0.0128:0:1 -8 38285623 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17125;SOR=0;LSEQ=GAGCTACGGCTGCCCGGGGA;RSEQ=AGCCAAGAGAGACAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:66,133:0.01:2,2:22.5:1:33:1:1:2.01:60:4:0.0101:0:1 0/0:284:0:0,0:94,190:0:2,0:23.9:1:29.8:1:1:0:60:93.667:1:0:0.1 -8 38285645 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50276;SOR=Inf;LSEQ=GCCAAGAGAGACAGGCAGGG;RSEQ=GGAGAGGAGCAGCTGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:55,97:0:2,0:24.8:1:29.9:1:1:0:60:49.667:1:0:0.1 0/1:184:2:1,1:48,134:0.0109:2,2:14:1:28.5:1:0.46276:2.77:60:4:0.0111:0:1.5 -8 38285913 . GTCA G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=1.04336;LSEQ=TCTTTCTCCTCTGAAGAGGA;RSEQ=TCATCATCATCATCATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:656:15:8,7:261,380:0.0229:2,2:20.3:1:31.9:1:0.42688:1.66:59.7:30:0.0233:0.0091:0.3 0/1:965:23:9,14:410,529:0.0238:2,2:24.2:1:31:1:0.83204:1.2054:60:22:0.0232:0.0062:0.2 -8 38285926 . T G 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AAGAGGAGTCATCATCATCA;RSEQ=CATCATCCTCCGAGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:0:0,0:234,378:0:2,0:24.3:1:29.9:1:1:0:60:35:0.9966:0:0.1 0/1:829:48:20,28:334,445:0.0579:2,2:25.7:1:32.1:1:1:1.05073:60:96:0.0585:0:1.1 -8 38285934 . C A 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00266;SOR=0;LSEQ=TCATCATCATCATCATCATC;RSEQ=TCCGAGGAGGGGAGAGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:578:7:2,5:208,362:0.0121:2,2:32.7:1:27.6:1:1:1.43561:59.3:6:0.0106:0:1.6 0/0:766:0:0,0:313,451:0:2,0:22.6:1:30.6:1:1:0:60:75.4:1:0:0.2 -8 38286225 . G A 52 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTATTTAACTTAATTCC;RSEQ=TCCTACATTCAAAGGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:17:1:26:1:1:0:60:3:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 38287114 . A G 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33391;SOR=3.63369;LSEQ=GGGGCAGATCACGGAGGGGG;RSEQ=GGAGGTTCACCTTCCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:1,0:214,18:0.0043:2,0:39:0:11:0:1:0:60:0:0:0:7 0/1:194:3:3,0:169,22:0.0155:2,0:31.3:1:23.7:1:1:0:60:2:0.0113:0:3.3 -8 38287486 . G A 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04578;SOR=0.1198;LSEQ=GCTGCAGCCACCACGGGGCC;RSEQ=GGAAGGGAAGCCAAGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:6:4,2:102,202:0.0194:2,2:23:1:27.3:1:0.18583:3.94:60:5:0.0162:0:1.2 0/0:425:1:1,0:157,267:0.0024:2,0:1:0:25:0:0.37176:0:60:2:0.0024:0:1 -8 38297776 . G C 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCGGGGGCCCTCTGCAGA;RSEQ=GTTTTTTTATTACGTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:29:18,11:167,90:0.1003:2,2:25.8:1:31.7:1:0.8381:1.13344:60:58:0.101:0:1 0/0:507:0:0,0:302,202:0:2,0:26.2:1:30.9:1:1:0:60:83:0.994:0:0.2 -8 38314796 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23814;SOR=0;LSEQ=CCCTGTTGACCACATCACCT;RSEQ=CAACCATATCACCTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:79,11:0.0217:2,2:27.5:1:29:1:0.2451:6.9194:60:4:0.022:0:1 0/0:96:0:0,0:77,19:0:2,0:20:1:31.6:1:1:0:60:47:1:0:0.1 -8 38314813 . C T 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05651;SOR=0;LSEQ=CCTGCAACCATATCACCTCC;RSEQ=TCCCAGCCCATCCTGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:4:3,1:99,25:0.031:2,2:27:1:27:1:1:1.31692:60:3:0.024:0:2.8 0/0:134:0:0,0:102,32:0:2,0:23.9:1:30.7:1:1:0:60:66:1:0:0.1 -8 38314814 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49913;SOR=Inf;LSEQ=CTGCAACCATATCACCTCCC;RSEQ=CCCAGCCCATCCTGTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:103,26:0:2,0:25.9:1:29.7:1:1:0:60:15.125:1:0:0.3 0/1:141:2:1,1:104,35:0.0142:2,2:31.5:1:31:1:0.44681:2.94382:60:4:0.0146:0:1.5 -8 38315105 . GA G 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0478;SOR=0;LSEQ=AGGGTCTAGGTAGGGGAGGG;RSEQ=AAGGAAAAACAGAAGGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:4:2,2:36,167:0.0193:2,2:13:1:30.3:1:0.15449:4.59:60:8:0.0194:0.0048:0.3 0/0:234:0:0,0:54,180:0:2,0:22.9:1:29:1:1:0:60:57.5:1:0:0.2 -8 38315123 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2279;SOR=0;LSEQ=GGGAAAGGAAAAACAGAAGG;RSEQ=AAAGTATGCCATGTGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:13,128:0.014:2,2:11.5:1:30:1:0.18684:9.52:60:4:0.0143:0:1 0/0:156:0:0,0:16,140:0:2,0:22.6:1:28.1:1:1:0:60:155:1:0:0.1 -8 38316852 . G C 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCGCAAGTGAGTCAGTGCTG;RSEQ=CTGGCAGAAAAGCCCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:34:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 38736031 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20295;SOR=0;LSEQ=CTGAGAATGCATCTCTCTGA;RSEQ=GGATAGAAGGGACATTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:65,45:0.0179:2,2:15.5:1:30:1:1:1.43958:60:4:0.0182:0:1 0/0:136:0:0,0:79,57:0:2,0:26.6:1:30.9:1:1:0:60:67:1:0:0.4 -8 38736051 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20061;SOR=0;LSEQ=GGGATAGAAGGGACATTGAG;RSEQ=TGCAGGGACCTGCCAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:63,58:0.0163:2,2:22.5:1:29:1:1:1.08546:60:4:0.0164:0:1 0/0:151:0:0,0:79,72:0:2,0:24.7:1:31.7:1:1:0:60:302:1:0:0.5 -8 38736089 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49851;SOR=0;LSEQ=CTTCCCCGTGCCTCCTAGGC;RSEQ=TGGTTTGCTCCCAGGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:68,60:0.0154:2,2:16:0:32:0:1:1.13224:60:4:0.0155:0:1.5 0/0:122:0:0,0:18,26:0:2,0:31.7:1:30.4:1:1:0:60:88:0.3636:0:0.1 -8 38736105 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24493;SOR=Inf;LSEQ=AGGCGTGGTTTGCTCCCAGG;RSEQ=TGACTAGATGAGAACCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:57,67:0:2,0:25.1:1:31.6:1:1:0:60:30:1:0:0.1 0/1:122:2:1,1:46,74:0.0164:2,2:39.5:1:29.5:1:1:1.60:60:4:0.0168:0:1 -8 38858277 . CA TG 145 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.03388;LSEQ=ATTACAGGTGTGAACCACCA;RSEQ=CCTGGCCTTAAATCACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:27:26,1:0,0:0.9643:0,1:21.8:1:30.7:1:1:0:60:54:1:0.2143:0.8 0/1:47:22:20,2:24,1:0.4681:1,2:24:1:31:1:0.59297:2.35655:60:44:0.4681:0.0426:1 -8 38858278 . A G 106 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19385;SOR=3.25109;LSEQ=TTACAGGTGTGAACCACCAC;RSEQ=CCTGGCCTTAAATCACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:0,0:0.087:0,0:25.5:1:22:1:1:0:60:1:1:0:1.5 0/1:46:11:10,1:15,0:0.2391:1,2:19.9:1:30.9:1:0.42308:0:60:22:0.4231:0:1.1 -8 38858336 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53036;SOR=Inf;LSEQ=GAACCTTAGAAATTAACTTG;RSEQ=TCCGTTTTAAAATATGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:72,19:0:2,0:26.2:1:31.6:1:1:0:60:90:1:0:0.3 0/1:153:2:1,1:112,39:0.0131:2,2:28:1:29:1:0.4558:2.8483:60:4:0.0132:0:1 -8 38858353 . C T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29702;SOR=0.28091;LSEQ=TTGGTCCGTTTTAAAATATG;RSEQ=AGTTCTGTTTGTATTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:85,37:0.0161:2,2:8.5:1:27.5:1:0.52072:2.28019:60:4:0.0164:0:1.5 0/0:219:1:0,1:146,72:0.0046:2,0:1:0:22:0:0.33333:0:60:2:0.0046:0:1 -8 38858431 . A T 155 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TACTGGAAGAAAAGAAAATG;RSEQ=TATCACCCCCAGACATGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:108,133:0:2,0:27.4:1:30.6:1:1:0:60:119.5:1:0:0.2 0/1:389:40:16,24:163,186:0.1028:2,2:26.6:1:29.2:1:0.50371:1.3136:60:39:0.1018:0:1.5 -8 38858484 . G A 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACTCAAAGGGAATGGGAC;RSEQ=TTCCCTTTGATGAATTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:40,100:0:2,0:23.2:1:31.3:1:1:0:60:139:1:0:0.2 0/1:203:24:7,17:56,123:0.1182:2,2:18.9:1:29.4:1:1:1.10516:60:23:0.1156:0:1.8 -8 38858496 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16743;SOR=0;LSEQ=AATGGGACGTTCCCTTTGAT;RSEQ=AATTGTTCTTTTAATGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:20,80:0.0194:2,2:18.5:1:31:1:0.371:3.93:60:4:0.0198:0:1.5 0/0:148:0:0,0:42,105:0:2,0:24.8:1:31.3:1:1:0:60:146:1:0:0.2 -8 41790412 . C A 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTGCATAGGAAGTCACAG;RSEQ=AGGAGAATGGCTATAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:10:0:34:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:22:0:31.5:1:1:0:60:4:0.6667:0:1 -8 41790674 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGGGGTGGGGGTGGAGGCTG;RSEQ=TGGGGCTGAGGCTGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:21:1:33.2:1:1:0:60:12:1:0:0 0/1:32:2:1,1:19,11:0.0625:2,2:18.5:1:27.5:1:1:1.69662:60:4:0.0645:0:1 -8 41790704 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGCTGCGGCTGCTGTTGCGG;RSEQ=TGCTGCTGGGGTGGTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:13,4:0:2,0:21:1:32.5:1:1:0:60:34:1:0:0 0/1:52:2:1,1:28,21:0.0385:2,2:31.5:1:28:1:1:1.32572:60:4:0.04:0:1 -8 41790787 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50376;SOR=Inf;LSEQ=CTGTGGAGGCGGTGGTGGCG;RSEQ=CTGCTGCTGCTGGTTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,13:0:2,0:22.9:1:31.2:1:1:0:60:46:0.9583:0:0 0/1:33:2:1,1:13,17:0.0606:2,2:23:1:26:1:1:1.30:60:4:0.0606:0:1 -8 41790866 . G C 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CTGCAGTTGGCAGCAGGCTG;RSEQ=ACGCTGCTCTGCTGCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:23.3:1:31.7:1:1:0:60:14:1:0:0.1 0/1:7:3:0,3:0,4:0.4286:0,0:37.7:1:33.7:1:1:0:60:6:0.4286:0:1 -8 42199219 . A AT 32 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=GCTGAACTGCAGTGGGAACA;RSEQ=TTTTTTTTTTCTGTCCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:23.8:1:29.3:1:1:0:60:8:1:0:0.5 0/1:8:2:2,0:6,0:0.25:0,0:20.5:1:32:0:1:0:60:4:0.25:0:1 -8 42199294 . T A 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGTTTGGTTTAGCTCTC;RSEQ=GCAGCCCCCTCCTGAGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:11,5:0,0:1:0,2:27.7:1:28.3:1:1:0:60:7:1:0:1.4 1/1:33:33:24,9:0,0:1:0,2:19.5:1:29.3:1:1:0:60:32:1:0:1.1 -8 43092757 . T C 56 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTACTTCCTTTGGTATTT;RSEQ=AGGTAGAGTATATAATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:5:0:28:0:1:0:51:2:1:0:5 1/1:5:4:2,2:1,0:0.8:0,2:9:1:28.3:1:1:0:48:3:0.75:0:6.5 -8 43092759 . G T 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTTCCTTTGGTATTTTA;RSEQ=GTAGAGTATATAATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:7:0:25:0:1:0:51:2:1:0:5 1/1:5:5:3,2:0,0:1:0,2:10.4:1:29.8:1:1:0:47:10:1:0:6 -8 43092774 . A C 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTTAGGTAGAGTATATAAT;RSEQ=TATATTTCGTGTACTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:16.8:1:29.3:1:1:0:43:8:1:0:3.8 0/1:19:2:1,1:10,7:0.1053:2,2:16:1:33:1:1:1.40151:33.5:4:0.1111:0:3.5 -8 43092782 . C G 119 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTATATAATATATATTT;RSEQ=GTGTACTTTGATATTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:24.8:1:32.5:1:1:0:43:8:1:0:3.8 1/0:19:15:8,7:1,1:0.7895:2,2:25:1:30.7:1:1:1.13:43.5:30:0.7895:0:4.3 -8 43092783 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GAGTATATAATATATATTTC;RSEQ=TGTACTTTGATATTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:25.8:1:31.8:1:1:0:43:8:1:0:3.8 0/1:19:2:1,1:9,7:0.1053:2,2:20.5:1:31:1:1:1.26772:33.5:4:0.1111:0:3.5 -8 43092784 . T G 114 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23744;LSEQ=AGTATATAATATATATTTCG;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:27.3:1:31.3:1:1:0:43.3:6:0.75:0:4 1/0:19:15:8,7:3,1:0.7895:2,2:25.1:1:29.3:1:0.60268:2.50209:43.5:14:0.7778:0:4.3 -8 43092787 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATAATATATATTTCGTGT;RSEQ=CTTTGATATTTTATGTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:28.3:1:28.8:1:1:0:43:8:1:0:3.8 0/1:21:2:1,1:10,7:0.0952:2,2:27.5:1:29.5:1:1:1.40151:51:4:0.1:0:5 -8 43092792 . G C 41 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10093;SOR=0.18201;LSEQ=ATATATATTTCGTGTACTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:0.5:2,2:9:1:30:1:1:1:50.3:6:0.5:0:4.7 0/1:21:3:2,1:10,8:0.1429:2,2:17.3:1:26.3:1:1:1.57:29.3:2:0.1053:0:3.3 -8 43092793 . A G 81 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28425;SOR=Inf;LSEQ=TATATATTTCGTGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:16.2:1:30.8:1:1:0:48.7:12:1:0:4.2 0/1:21:6:3,3:7,5:0.2857:2,2:20.5:1:31.5:1:1:1.3738:45:12:0.2857:0:4.7 -8 43092799 . T A 74 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28425;SOR=Inf;LSEQ=TTTCGTGTACTTTGATATTT;RSEQ=ATGTACAGTATATAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:14.2:1:29.7:1:1:0:48.7:12:1:0:4.2 0/1:21:6:3,3:8,6:0.2857:2,2:14.5:1:28.7:1:1:1.31413:45:12:0.3:0:4.7 -8 43092800 . A T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21839;SOR=0.23946;LSEQ=TTCGTGTACTTTGATATTTT;RSEQ=TGTACAGTATATAATATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:16:0:30.5:1:1:2.44949:49.5:4:0.3333:0:4 0/1:20:2:1,1:11,7:0.1:2,2:16:0:28:1:1:1.53525:50:4:0.1:0:6 -8 43092801 . T C 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCGTGTACTTTGATATTTTA;RSEQ=GTACAGTATATAATATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:13.5:1:30.8:1:1:0:48.7:12:1:0:4.2 0/1:19:2:1,1:10,7:0.1053:2,2:15:0:29.5:1:1:1.40151:27:4:0.1053:0:3 -8 43092807 . G C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTTGATATTTTATGTACA;RSEQ=TATATAATATGTAATTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:11.5:1:33:1:1:0:48.7:12:1:0:4.2 0/1:15:2:1,1:7,5:0.1333:2,2:21.5:1:33:0:1:1.36624:51:4:0.1333:0:6 -8 43092808 . T A 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.07143;SOR=0;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAATATGTAATTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:17.5:1:30.5:1:1:2.44949:60:4:0.4:0:5 0/0:15:0:0,0:9,6:0:2,0:8.7:1:27:1:1:0:40.9:14:1:0:4.9 -8 43092812 . T G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATATGTAATTGGTGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:9.8:1:30.5:1:1:0:48.7:12:1:0:4.2 0/1:13:2:1,1:7,4:0.1538:2,2:26.5:1:32.5:1:1:1.67325:51:4:0.1818:0:6 -8 43092816 . ATGTAATTGGTGTAATTTGATATTTTATGTTCAGT CTATATTTGATGTGCTTTCATATTTTATGTACCTA 85 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01818;SOR=Inf;LSEQ=TTTTATGTACAGTATATAAT;RSEQ=ATATAATATGTATTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25.5:1:30.5:1:1:0:60:4:1:0:5 1/1:3:9:6,3:0,0:1:0,2:15.3:1:27:1:1:0:39.9:18:1:1:5.2 -8 43092818 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTACAGTATATAATAT;RSEQ=TAATTGGTGTAATTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30.5:1:1:0:60:4:1:0:5 1/1:2:2:1,1:0,0:1:0,2:26:0:31:1:1:0:51:4:1:0:6 -8 43092821 . AT TC 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGTACAGTATATAATATGTA;RSEQ=TGGTGTAATTTGATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:30.5:1:32:0:1:0:60:4:1:0:5 1/1:2:2:1,1:0,0:1:0,2:22:0:32.5:0:1:0:51:4:1:0:5 -8 43092824 . G T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACAGTATATAATATGTAATT;RSEQ=GTGTAATTTGATATTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31.5:1:1:0:60:4:1:0:5 0/0:2:0:0,0:1,1:0:2,0:20:0:32:0:1:0:51:4:1:0:5 -8 43092846 . T A 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAATTTGATATTTTATGT;RSEQ=CAGTATATAATATGTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:11:1:28.7:1:1:0:49.7:6:1:0:6 1/1:3:3:1,2:0,0:1:0,2:12.3:1:28.7:1:1:0:31.3:6:1:0:4.7 -8 43092853 . A G 33 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13333;SOR=0;LSEQ=TGATATTTTATGTTCAGTAT;RSEQ=TAATATGTATTTGGTGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:5:0:33.5:1:1:0:60:4:0.5:0:5 0/0:6:0:0,0:4,2:0:2,0:9:1:27:1:1:0:35.8:5:1:0:6 -8 43092860 . G A 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=Inf;LSEQ=TTATGTTCAGTATATAATAT;RSEQ=TATTTGGTGTACTTTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,0:0.6667:0,0:6.5:1:30.5:1:1:0:37.5:4:1:0:8 1/1:10:10:6,4:0,0:1:0,2:10.1:1:27.8:1:1:0:41.3:20:1:0:7.5 -8 43092867 . G A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.64646;SOR=1.83088;LSEQ=CAGTATATAATATGTATTTG;RSEQ=TGTACTTTTTGATATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:1,1:0.5714:2,2:7.5:1:30.5:1:1:1:46:8:0.5714:0:7.8 1/0:21:15:10,5:3,2:0.7143:2,2:8.2:1:29.7:1:1:1.31:46.1:30:0.7143:0:7.7 -8 43092868 . T G 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17625;SOR=0.16279;LSEQ=AGTATATAATATGTATTTGG;RSEQ=GTACTTTTTGATATTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,2:0.25:2,2:16:1:29:1:1:1:34.5:4:0.2857:0:7.5 0/1:21:1:0,1:12,5:0.0476:2,0:34:0:32:0:0.33333:0:46:2:0.05:0:6 -8 43092876 . TTG C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.68816;SOR=1.83396;LSEQ=ATAATATGTATTTGGTGTAC;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:1,1:0.4444:2,2:8:1:31.5:1:1:2.44949:46.5:8:0.5714:0.2222:7.3 1/0:20:12:8,4:1,3:0.6:2,2:14.1:1:31.6:1:0.26154:5.32:47.1:24:0.7059:0:6.6 -8 43092883 . T A 70 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21685;SOR=0.4296;LSEQ=TTTGGTGTACTTTTTGATAT;RSEQ=TTATGTACAGTATATAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:1,2:80,67:0.0199:2,2:9:0:31.7:1:0.59449:2.37456:44.7:6:0.0199:0:6 0/0:580:5:3,2:306,263:0.0086:2,2:7.4:1:30.4:1:1:1.29:39.4:10:0.0087:0:4.6 -8 43092885 . T C 94 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04549;LSEQ=TGGTGTACTTTTTGATATTT;RSEQ=ATGTACAGTATATAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:82,71:0.0127:2,2:11:0:31.5:1:1:1.15385:33.5:4:0.0127:0:7 0/1:601:8:4,4:315,271:0.0133:2,2:4.1:1:31.4:1:1:1.16206:39.9:16:0.0134:0:6.6 -8 43092886 . A T 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48235;SOR=1.28738;LSEQ=GGTGTACTTTTTGATATTTT;RSEQ=TGTACAGTATATAATATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:15:8,7:77,65:0.0949:2,2:11.5:1:30.3:1:1:1.03632:36.3:30:0.0955:0:5.8 0/1:605:72:40,32:280,245:0.119:2,2:11.3:1:30.3:1:0.80129:1.09:37.6:144:0.12:0:5.6 -8 43092887 . T C 100 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.69642;SOR=2.35236;LSEQ=GTGTACTTTTTGATATTTTA;RSEQ=GTACAGTATATAATATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:0,1:85,73:0.0063:2,0:12:0:32:0:0.46541:0:29:2:0.0063:0:6 0/1:613:9:5,4:323,279:0.0147:2,2:11.7:1:31.8:1:1:1.08:38.2:18:0.0149:0:5 -8 43092888 . G A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09899;LSEQ=TGTACTTTTTGATATTTTAT;RSEQ=TACAGTATATAATATGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:7:3,4:84,71:0.0429:2,2:10:1:30.9:1:0.70497:1.573:45.4:14:0.0435:0:5.9 0/1:617:29:15,14:311,266:0.047:2,2:11.3:1:29:1:0.85044:1.09107:39.1:58:0.0475:0:6 -8 43092889 . T A 45 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27604;SOR=0.38823;LSEQ=GTACTTTTTGATATTTTATG;RSEQ=ACAGTATATAATATGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:87,74:0.0123:2,2:11:0:32:0:1:1.1745:21:4:0.0123:0:6 0/0:626:3:1,2:335,287:0.0048:2,2:10:1:29:1:0.59835:2.33142:22.3:6:0.0048:0:5.7 -8 43092890 . A G 99 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00467;SOR=0.24857;LSEQ=TACTTTTTGATATTTTATGT;RSEQ=CAGTATATAATATGTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:9:3,6:85,68:0.0552:2,2:14.8:1:32.3:1:0.30272:2.48609:48.6:18:0.0556:0:4.8 0/1:630:9:3,6:333,284:0.0143:2,2:11:1:31.4:1:0.31517:2.34197:32.6:18:0.0144:0:6 -8 43092891 . C G 106 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.42502;LSEQ=ACTTTTTGATATTTTATGTA;RSEQ=AGTATATAATATGTATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:0,2:86,73:0.0122:2,0:17:0:31.5:1:0.21545:0:29:4:0.0123:0:7 0/1:636:11:4,7:325,281:0.0173:2,2:14.6:1:30.7:1:0.36234:2.02172:48.4:22:0.0174:0:5.5 -8 43092892 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1761;SOR=0.45339;LSEQ=CTTTTTGATATTTTATGTAC;RSEQ=GTATATAATATGTATTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:5:2,3:85,72:0.0305:2,2:17.2:1:31:1:0.66332:1.76459:41.6:10:0.0311:0:6 0/1:641:9:5,4:332,288:0.014:2,2:15.7:1:30.8:1:1:1.08:45.9:18:0.0142:0:6.2 -8 43092893 . G T 63 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01789;SOR=0.12604;LSEQ=TTTTTGATATTTTATGTACA;RSEQ=TATATAATATGTATTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:4:2,2:85,75:0.0242:2,2:13.5:1:31.5:1:1:1.13247:45:8:0.0244:0:6 0/0:643:2:2,0:339,295:0.0031:2,0:17:1:31.5:1:0.50183:0:43.5:4:0.0031:0:7 -8 43092894 . T C 111 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.73584;SOR=0.85714;LSEQ=TTTTGATATTTTATGTACAG;RSEQ=ATATAATATGTATTTTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:3:2,1:87,76:0.0181:2,2:15.3:1:34.3:1:1:1.74:31.3:6:0.0181:0:6.3 0/1:644:10:6,4:335,293:0.0155:2,2:18.4:1:33.5:1:0.75787:1.31:46.4:20:0.0157:0:6.2 -8 43092895 . A G 34 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10818;SOR=0.12778;LSEQ=TTTGATATTTTATGTACAGT;RSEQ=TATAATATGTATTTTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:87,76:0.012:2,2:17:0:34:0:1:1.1438:34.5:4:0.012:0:5 0/0:645:1:0,1:333,289:0.0016:2,0:16:0:33:0:0.46549:0:31:2:0.0016:0:5 -8 43092896 . T C 80 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.1275;SOR=0.38027;LSEQ=TTGATATTTTATGTACAGTA;RSEQ=ATAATATGTATTTTGGGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:4:2,2:86,75:0.0241:2,2:20:1:32.3:1:1:1.14571:30.5:8:0.0244:0:5 0/0:646:6:2,4:342,296:0.0093:2,2:20.5:1:31.2:1:0.42477:2.3079:31.8:12:0.0093:0:6.2 -8 43092897 . A G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.77205;SOR=0.89443;LSEQ=TGATATTTTATGTACAGTAT;RSEQ=TAATATGTATTTTGGGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:4:3,1:85,74:0.0241:2,2:20.5:1:33:1:0.6252:2.60:34:8:0.0248:0:6.8 0/1:648:14:7,7:337,294:0.0216:2,2:20:1:30.4:1:1:1.14601:37.9:13:0.0203:0:6.1 -8 43092898 . T G 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.67553;SOR=1.1838;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATATGTATTTTGGGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:16:8,8:76,63:0.0964:2,2:23.5:1:32.2:1:0.79433:1.20488:35.8:32:0.0994:0:5.9 0/1:651:73:40,33:285,248:0.1121:2,2:23.4:1:31.8:1:0.90061:1.05:37.6:72:0.1116:0:5.6 -8 43092902 . A G 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11748;SOR=0.72263;LSEQ=TTTTATGTACAGTATATAAT;RSEQ=TGTATTTTGGGTACTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:45:30,15:59,61:0.2663:2,2:24.3:1:31.6:1:0.05414:2.06:39.9:21.5:0.259:0:5.1 0/1:650:135:79,56:254,242:0.2077:2,2:23.1:1:31.5:1:0.14503:1.34:41.1:270:0.2103:0:5.2 -8 43092903 . TG CA 251 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33425;SOR=1.20533;LSEQ=TTTATGTACAGTATATAATA;RSEQ=TATTTTGGGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:63:28,35:57,38:0.3728:2,2:26.5:1:32.2:1:0.07284:1.86743:42.5:126:0.3841:0:4.7 0/1:654:273:133,140:177,139:0.4174:2,2:25.6:1:31.1:1:0.08261:1.33971:44.7:546:0.432:0.0031:4.4 -8 43092904 . G A 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54461;SOR=0.8969;LSEQ=TTATGTACAGTATATAATAT;RSEQ=TATTTTGGGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:80:50,30:3,5:0.4734:2,2:25.8:1:29.6:1:0.25675:2.74:38.5:79:0.8316:0:5.2 0/1:652:291:161,130:13,9:0.4463:2,2:25.9:1:28.7:1:0.82576:1.16575:40.5:47.5:0.8824:0:5.3 -8 43092906 . AT GC 234 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.76143;SOR=0.9288;LSEQ=ATGTACAGTATATAATATGT;RSEQ=TTTGGGTACTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:42:19,23:70,52:0.2456:2,2:29:1:33.1:1:0.20964:1.6246:45.3:84:0.2545:0:4.2 0/1:659:153:78,75:261,224:0.2322:2,2:28.3:1:32.3:1:0.57755:1.12016:47.6:306:0.2372:0:4 -8 43092907 . T G 244 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.52352;SOR=0.87937;LSEQ=TGTACAGTATATAATATGTA;RSEQ=TTTGGGTACTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:61:36,25:10,10:0.3609:2,2:27.6:1:32.2:1:0.60427:1.43:40.4:60:0.4878:0:5.2 0/1:660:219:122,97:49,46:0.3318:2,2:26.4:1:31.4:1:0.53831:1.18:40.8:108.5:0.4429:0:5 -8 43092909 . T A 79 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24881;SOR=0.44327;LSEQ=TACAGTATATAATATGTATT;RSEQ=TGGGTACTTTGATATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:4:2,2:98,90:0.0208:2,2:31.5:1:29:1:1:1.0884:35.5:8:0.0216:0:2.5 0/0:750:7:4,3:386,354:0.0093:2,2:27:1:28.4:1:1:1.22:43:14:0.0095:0:4.7 -8 43092910 . T G 74 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20991;SOR=0.42216;LSEQ=ACAGTATATAATATGTATTT;RSEQ=GGGTACTTTGATATTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:2,1:98,91:0.0156:2,2:28.3:1:33.7:1:1:1.85:30:6:0.016:0:3.3 0/0:752:5:4,1:385,355:0.0066:2,2:16.8:1:32.2:1:0.37578:3.68:28.4:10:0.0067:0:7 -8 43092911 . G T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57591;SOR=0.75529;LSEQ=CAGTATATAATATGTATTTT;RSEQ=GGTACTTTGATATTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:5:1,4:97,88:0.026:2,2:30.6:1:31:1:0.19977:4.37823:40.8:10:0.0267:0:5.2 0/1:758:15:8,7:380,348:0.0198:2,2:29.5:1:29.7:1:1:1.05:38.1:30:0.02:0:5.3 -8 43092912 . G A 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2694;SOR=0.38095;LSEQ=AGTATATAATATGTATTTTG;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:100,92:0.0103:2,2:17:1:32.5:1:1:1.08648:43.5:4:0.0105:0:5.5 0/0:760:3:2,1:395,361:0.0039:2,2:7:1:29.3:1:1:1.83:23.3:4:0.0018:0:8 -8 43092914 . T A 22 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18434;SOR=0.25246;LSEQ=TATATAATATGTATTTTGGG;RSEQ=ACTTTGATATTTTATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:0,2:101,90:0.0103:2,0:31:0:32:0:0.22593:0:29.5:4:0.0108:0:4 0/0:764:2:1,1:390,357:0.0026:2,2:31:0:22.5:1:1:1.0923:51:1:0.0013:0:4.5 -8 43092924 . T C 75 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.66732;SOR=0.76113;LSEQ=GTATTTTGGGTACTTTGATA;RSEQ=TTTATGTACAGTATATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:100,92:0.0103:2,2:20:1:33:1:1:1.08648:27.5:4:0.0106:0:5 0/0:763:6:2,4:395,359:0.0079:2,2:24:1:29.2:1:0.43288:2.19836:29.5:5:0.0066:0:5.7 -8 43092927 . T A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77281;SOR=0.89765;LSEQ=TTTTGGGTACTTTGATATTT;RSEQ=ATGTACAGTATATAATAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:4:3,1:97,92:0.0207:2,2:18:1:30.5:1:0.62207:2.83:31.5:8:0.0209:0:5.3 0/1:751:14:10,4:380,355:0.0186:2,2:16.6:1:28.6:1:0.18074:2.33:54.8:28:0.0187:0:3 -8 43092928 . A T 230 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32081;SOR=0.83561;LSEQ=TTTGGGTACTTTGATATTTT;RSEQ=TGTACAGTATATAATAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:59:25,34:75,57:0.3057:2,2:19.2:1:30.5:1:0.08434:1.78399:44.6:58:0.3053:0:3.4 0/1:740:199:99,100:278,252:0.2689:2,2:19.7:1:30.2:1:0.56046:1.11415:46.8:398:0.2734:0:3.6 -8 43092929 . T A 65 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09558;SOR=0.32421;LSEQ=TTGGGTACTTTGATATTTTA;RSEQ=GTACAGTATATAATAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:4:2,2:98,89:0.0208:2,2:13:1:31.8:1:1:1.10057:60:8:0.0212:0:1.8 0/0:731:5:4,1:369,347:0.0068:2,2:10.2:1:28.4:1:0.37477:3.76:45.8:10:0.0069:0:5 -8 43092930 . G A 44 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28006;SOR=0.39316;LSEQ=TGGGTACTTTGATATTTTAT;RSEQ=TACAGTATATAATAAGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:99,89:0.0105:2,0:19:1:32.5:1:0.22807:0:40:4:0.0106:0:6 0/0:725:3:2,1:354,336:0.0041:2,2:25.7:1:28:1:1:1.90:41:6:0.0042:0:5 -8 43092931 . T G 128 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14389;SOR=4.52382;LSEQ=GGGTACTTTGATATTTTATG;RSEQ=ACAGTATATAATAAGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:1,0:95,90:0.0053:2,0:14:0:31:0:1:0:40:2:0.0054:0:5 0/1:719:17:7,10:361,334:0.0236:2,2:18:1:31.5:1:0.46443:1.54311:50.5:34:0.0238:0:4.8 -8 43092932 . A G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37356;SOR=0.66486;LSEQ=GGTACTTTGATATTTTATGT;RSEQ=CAGTATATAATAAGTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:9:5,4:88,84:0.0489:2,2:22.8:1:31.6:1:1:1.19:44.6:18:0.0495:0:5.2 0/1:696:23:14,9:345,324:0.033:2,2:19.9:1:31.1:1:0.40478:1.46:40.7:22:0.0319:0:4.8 -8 43092933 . C G 76 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00536;SOR=0.10259;LSEQ=GTACTTTGATATTTTATGTA;RSEQ=AGTATATAATAAGTATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:5:3,2:88,85:0.0281:2,2:14.8:1:33:1:1:1.45:37:10:0.0284:0:5 0/0:679:2:1,1:341,322:0.0029:2,2:24:1:30:1:1:1.05894:24:4:0.003:0:5 -8 43092934 . A T 63 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61184;SOR=0.5326;LSEQ=TACTTTGATATTTTATGTAC;RSEQ=GTATATAATAAGTATTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:88,85:0.0114:2,2:29:1:30:1:1:1.0351:40:4:0.0114:0:6.5 0/0:658:4:2,2:332,307:0.0061:2,2:11:0:31.8:1:1:1.08128:22.5:8:0.0061:0:2.8 -8 43092935 . G C 205 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23784;SOR=0.76273;LSEQ=ACTTTGATATTTTATGTACA;RSEQ=TATATAATAAGTATTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:32:23,9:63,74:0.185:2,2:15.9:1:31.8:1:0.01039:2.98:39.2:64:0.1871:0:5.9 0/1:644:95:50,45:267,252:0.1475:2,2:21.3:1:31.3:1:0.91116:1.05:39.6:190:0.148:0:6.2 -8 43092936 . T C 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.09971;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAATAAGTATTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:85,82:0.0118:2,2:27.5:1:34:0:1:1.03638:36.5:4:0.0119:0:4 0/1:619:8:4,4:313,293:0.0129:2,2:17.9:1:32.9:1:1:1.06811:34.5:16:0.013:0:5.8 -8 43092939 . A G 116 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54445;SOR=1.86527;LSEQ=TGATATTTTATGTACAGTAT;RSEQ=TAATAAGTATTTGGTGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:72,75:0.0133:2,2:6:0:31.5:1:1:1.04:38:4:0.0134:0:5 0/1:569:14:6,8:283,270:0.0246:2,2:9.9:1:30.7:1:0.59657:1.3967:34.8:28:0.0249:0:4.9 -8 43092940 . T G 186 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATAAGTATTTGGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:61:33,28:27,32:0.4519:2,2:10.6:1:31.5:1:0.46531:1.39:44.3:122:0.4552:0:4.4 0/0:530:0:0,0:135,133:0:2,0:13:1:29:1:1:0:39.6:267:0.8266:0:4.6 -8 43092941 . A T 78 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.51664;LSEQ=ATATTTTATGTACAGTATAT;RSEQ=ATAAGTATTTGGTGTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:1:1,0:61,61:0.0076:2,0:43:0:30:0:1:0:57:2:0.0083:0:8 0/1:520:6:4,2:241,235:0.0115:2,2:35.7:1:30.2:1:0.6858:1.95:25.2:12:0.0125:0:7.7 -8 43092944 . AAG CTA 106 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13216;SOR=Inf;LSEQ=TTTTATGTACAGTATATAAT;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:54,54:0:2,0:8.4:1:29.3:1:1:0:42.8:216:0.9818:0:4.5 0/1:468:11:6,5:210,209:0.0235:2,2:26.5:1:30.9:1:1:1.19:37.6:22:0.0258:0.0021:5.1 -8 43092945 . AG TA 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42784;SOR=1.32372;LSEQ=TTTATGTACAGTATATAATA;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:20:14,6:4,1:0.4:2,2:22.2:1:29:1:1:1.68048:42.6:40:0.5128:0:6.4 0/1:194:91:42,49:12,6:0.4691:2,2:25.4:1:29.6:1:0.12874:2.31544:41.8:182:0.6276:0:6.2 -8 43092946 . G A 89 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70413;SOR=0.69489;LSEQ=TTATGTACAGTATATAATAA;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:2,1:0,0:0.0698:0,2:13.3:1:25.7:1:1:0:54.7:2:1:0:7 0/1:182:9:5,4:1,1:0.0495:2,2:31.6:1:28.2:1:1:1.22:31.2:8:0.6667:0:7.3 -8 43092948 . A G 74 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=1.13826;LSEQ=ATGTACAGTATATAATAAGT;RSEQ=TTTGGTGTACTTTGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:1:1,0:18,11:0.0238:2,0:36:0:31:0:1:0:57:2:0.0333:0:8 0/1:185:5:3,2:63,68:0.027:2,2:36:0:32.2:1:0.67378:1.61:23.8:10:0.0365:0:7.6 -8 43092949 . T G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5113;SOR=0.67759;LSEQ=TGTACAGTATATAATAAGTA;RSEQ=TTGGTGTACTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:4:2,2:17,9:0.093:2,2:25.3:1:31.5:1:0.61106:1.84719:45.3:8:0.1379:0:6.5 0/1:185:12:6,6:53,57:0.0649:2,2:29:1:31.4:1:1:1.07:40.3:24:0.0882:0:6.5 -8 43092950 . T C 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.85026;SOR=1.1267;LSEQ=GTACAGTATATAATAAGTAT;RSEQ=TGGTGTACTTTGATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:11:9,2:10,10:0.2619:2,2:17.3:1:31.4:1:0.12837:4.29:41.3:22:0.3548:0:6.5 0/1:182:52:23,29:43,42:0.2857:2,2:20.5:1:31.8:1:0.48671:1.28847:42.7:104:0.3796:0:6.8 -8 43092952 . G T 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09934;LSEQ=ACAGTATATAATAAGTATTT;RSEQ=GTGTACTTTGATATTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:6:2,4:17,9:0.1395:2,2:24:1:30.2:1:0.19374:3.61419:41.3:12:0.1875:0:6.2 0/1:185:28:14,14:49,60:0.1514:2,2:27.1:1:30.1:1:0.6747:1.22:39.6:56:0.2014:0:6.4 -8 43092953 . G A 129 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26416;SOR=2.63262;LSEQ=CAGTATATAATAAGTATTTG;RSEQ=TGTACTTTGATATTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:18,12:0.0465:2,2:18.5:1:27.5:1:1:1.48061:48.5:4:0.0625:0:6.5 0/1:184:21:10,11:49,61:0.1141:2,2:18.3:1:29.5:1:0.81509:1.13:39.9:20:0.146:0:4.9 -8 43092954 . T G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98329;LSEQ=AGTATATAATAAGTATTTGG;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:6:2,4:17,9:0.1818:2,2:22:1:31.2:1:0.19374:3.61419:41.3:12:0.1935:0:6.2 0/1:145:26:14,12:49,63:0.1793:2,2:26.4:1:30.4:1:0.38783:1.50:38.2:52:0.1884:0:6.4 -8 43092956 . T A 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59853;SOR=Inf;LSEQ=TATATAATAAGTATTTGGTG;RSEQ=ACTTTGATATTTTATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:22,21:0:2,0:16.5:1:29:1:1:0:41.6:86:1:0:6.3 0/1:181:6:2,4:79,93:0.0331:2,2:24.7:1:28.2:1:0.68993:1.69407:43.7:5:0.0282:0:6.7 -8 43092958 . C G 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATAATAAGTATTTGGTGTA;RSEQ=TTTGATATTTTATGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:21,20:0:2,0:15.6:1:30.8:1:1:0:41.3:12.667:0.9744:0:6.3 0/1:183:3:2,1:78,99:0.0164:2,2:22:1:29.7:1:0.58571:2.53:35.3:6:0.0168:0:6.3 -8 43092959 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAATAAGTATTTGGTGTAC;RSEQ=TTGATATTTTATGTACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:20,21:0:2,0:15.2:1:30:1:1:0:41.8:19.5:1:0:6.3 0/1:179:2:1,1:76,100:0.0112:2,2:15:1:32:0:1:1.31:42:4:0.0114:0:7.5 -8 43092962 . G C 143 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2642;SOR=2.60028;LSEQ=ATAAGTATTTGGTGTACTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:18,18:0.0513:2,2:18.5:1:31:1:1:1:47:4:0.0526:0:7.5 0/1:178:22:10,12:61,87:0.1236:2,2:17:1:32.1:1:0.8176:1.19:37.2:44:0.1236:0:5.2 -8 43092963 . A G 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TAAGTATTTGGTGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:18,20:0:2,0:12.3:1:30.5:1:1:0:42.6:76:0.9744:0:6.3 0/1:178:4:2,2:72,98:0.0225:2,2:14.5:1:32.5:1:1:1.36:51.3:8:0.0225:0:5.3 -8 43092964 . T C 50 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGTATTTGGTGTACTTTGA;RSEQ=ATTTTATGTACAGTATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:12.2:1:29.4:1:1:0:42:74:1:0:6.2 0/1:175:3:2,1:70,98:0.0171:2,2:21:0:32:1:0.57344:2.78:26.7:6:0.0172:0:6.7 -8 43092965 . A G 60 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTATTTGGTGTACTTTGAT;RSEQ=TTTTATGTACAGTATATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:11.4:1:29.5:1:1:0:42:74:1:0:6.2 0/1:173:4:1,3:69,99:0.0231:2,2:16.8:1:30:1:0.64669:2.0828:36.8:8:0.0231:0:6.8 -8 43092967 . T A 109 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47214;SOR=3.00138;LSEQ=TATTTGGTGTACTTTGATAT;RSEQ=TTATGTACAGTATATAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:1,0:15,19:0.0278:2,0:18:0:24:0:0.45714:0:36:2:0.0278:0:6 0/1:164:13:6,7:62,89:0.0793:2,2:14.1:1:29.5:1:0.7741:1.23:42.3:26:0.0798:0:5.5 -8 43092969 . T C 110 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69579;SOR=2.47954;LSEQ=TTTGGTGTACTTTGATATTT;RSEQ=ATGTACAGTATATAACATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:1,0:12,19:0.0313:2,0:13:0:33:0:0.40625:0:40:2:0.0323:0:6 0/1:148:11:3,8:59,78:0.0743:2,2:13.1:1:31.8:1:0.35965:2.00818:42.5:22:0.0753:0:6.5 -8 43092970 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGGTGTACTTTGATATTTT;RSEQ=TGTACAGTATATAACATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:9,18:0:2,0:9.7:1:29.9:1:1:0:42.1:54:0.9643:0:6.3 0/1:144:2:0,2:60,81:0.0139:2,0:17.5:1:29.5:1:0.5095:0:25:4:0.014:0:6 -8 43092974 . A G 101 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.828;LSEQ=TGTACTTTGATATTTTATGT;RSEQ=CAGTATATAACATGTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:9,12:0.0455:2,0:4:0:32:0:1:0:52:2:0.0455:0:8 0/1:112:9:5,4:39,64:0.0804:2,2:11.3:1:32:1:0.31172:2.04:51.3:18:0.0811:0:6.8 -8 43092975 . C G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49765;SOR=0.546;LSEQ=GTACTTTGATATTTTATGTA;RSEQ=AGTATATAACATGTATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:1,0:6,12:0.05:2,0:7:0:34:0:0.36842:0:40:2:0.05:0:6 0/1:108:3:1,2:43,61:0.0278:2,2:13:1:31.3:1:1:1.40548:47.3:6:0.028:0:7.3 -8 43092978 . T A 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.31524;SOR=0.51873;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAACATGTATTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:6,3:0.3571:2,2:19:1:29.4:1:0.58042:2.76:41:10:0.3571:0:6.2 0/1:72:16:6,10:17,19:0.2222:2,2:19.4:1:29:1:0.56001:1.47986:41.7:32:0.2222:0:6.1 -8 43092980 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTGATATTTTATGTACAGTA;RSEQ=ATAACATGTATTTGGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:11.5:1:27.5:1:1:0:36.2:10:1:0:6.2 0/1:58:2:1,1:20,35:0.0345:2,2:5:0:33:0:1:1.73:30:4:0.0345:0:6 -8 43092982 . T A 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.34585;SOR=0.3838;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AACATGTATTTGGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:3,1:0.4286:2,2:34.3:1:28.7:1:0.48571:4.4496:39:6:0.4286:0:6.3 0/1:50:11:2,9:15,21:0.22:2,2:28.4:1:28.6:1:0.28235:3.14285:34.6:10:0.2083:0:6.4 -8 43092983 . AACATGTATTTGGTGTACTTTG CATATATATTTGGGGTTCCTTT 55 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATATTTTATGTACAGTATAT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:16.7:1:27:1:1:0:39:14:1:0:6 0/1:49:4:0,4:18,27:0.0816:2,0:26.3:1:27.7:1:0.28234:0:36.8:8:0.0833:0.0816:7 -8 43092985 . C T 83 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61254;SOR=0.54654;LSEQ=ATTTTATGTACAGTATATAA;RSEQ=ATGTATTTGGTGTACTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:19:1:29:1:1:1:31.5:4:0.6667:0:6.5 0/1:23:8:1,7:4,10:0.3478:2,2:24:1:27.8:1:0.61297:2.68275:31.1:16:0.3636:0:7.1 -8 43092988 . G A 115 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTACAGTATATAACAT;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:39.7:1:25.7:1:1:0:39:2:1:0:6.3 1/1:20:16:4,12:1,1:0.8:2,2:25.7:1:28.9:1:0.4902:2.79285:36.3:32:0.8:0:6.6 -8 43092991 . TTTGGTGT GTTGTGA 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTACAGTATATAACATGTA;RSEQ=ACTTTGATATTTTATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:38:0:30.7:1:1:0:39:6:1:0:6.3 0/1:21:2:1,1:6,13:0.0952:2,2:20:1:30.7:1:1:2.08:36.5:4:0.0952:0.0476:5.5 -8 43092995 . G A 102 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.60435;SOR=0.38068;LSEQ=CAGTATATAACATGTATTTG;RSEQ=TGTACTTTGATATTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:34:0:25.3:1:1:0:39:2:0.6667:0:6.3 1/0:21:11:2,9:4,5:0.5238:2,2:29.9:1:29.5:1:0.33591:3.36357:32.4:22:0.55:0:6.3 -8 43092996 . T G 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTATATAACATGTATTTGG;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:25.5:1:30.8:1:1:0:35.3:8:1:0:6.3 0/1:21:3:1,2:5,12:0.1429:2,2:18.3:1:28.7:1:1:1.19:38:6:0.15:0:7 -8 43093004 . G C 105 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65879;SOR=0.59813;LSEQ=ACATGTATTTGGTGTACTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:1,2:0.5:2,2:25:0:32.7:1:1:1:39:6:0.5:0:6.3 0/1:27:10:2,8:8,8:0.3704:2,2:23.2:1:31.8:1:0.21773:3.79236:31.2:20:0.3846:0:6.2 -8 43093005 . A G 59 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CATGTATTTGGTGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:16.8:1:30.3:1:1:0:30.7:12:1:0:6.5 0/1:29:4:2,2:8,17:0.1379:2,2:13.5:1:29.8:1:0.59202:2.07:39.5:8:0.1379:0:5.8 -8 43093009 . T A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTGGTGTACTTTGATAT;RSEQ=TTATGTACAGTATATAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:16.8:1:30.3:1:1:0:30.7:12:1:0:6.5 0/1:29:2:0,2:10,17:0.069:2,0:14:1:32:0:0.53202:0:25:4:0.069:0:4.5 -8 43093015 . T A 30 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02521;SOR=0;LSEQ=GTGTACTTTGATATTTTATG;RSEQ=ACAGTATATAATATGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:14:0:30.5:1:1:2.45:47:4:0.3333:0:6.5 0/0:29:0:0,0:10,19:0:2,0:18.1:1:28.3:1:1:0:31.6:58:1:0:5.8 -8 43093017 . CA TG 23 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACTTTGATATTTTATGTA;RSEQ=GTATATAATATGTATTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:16.8:1:31.7:1:1:0:30.7:12:1:0:6.5 0/1:29:2:0,2:10,17:0.069:2,0:14:0:23.8:1:0.53202:0:31.5:4:0.069:0:5 -8 43093020 . T A 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13654;SOR=0.24051;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAATATGTATTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:1,2:0.5:2,2:24.7:1:30:1:1:1:22.3:6:0.5:0:6.7 0/1:27:5:2,3:7,13:0.1852:2,2:26.2:1:28.6:1:1:1.23:34.2:10:0.1923:0:5.8 -8 43093024 . T A 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.30923;SOR=0.29892;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATATGTATTTGGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:1,2:0.5:2,2:28.7:1:30:1:1:1:22.3:6:0.5:0:6.7 0/1:27:6:2,4:7,14:0.2222:2,2:30.3:1:29.3:1:1:1:33.5:12:0.2222:0:5.7 -8 43093028 . A C 93 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=2.06366;LSEQ=TTTTATGTACAGTATATAAT;RSEQ=TGTATTTGGTGTACTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:1,4:0.1667:2,0:32:0:32:0:0.33333:0:20:2:0.1667:0:8 0/1:27:8:3,5:6,13:0.2963:2,2:28.8:1:31.1:1:1:1.29:34.9:16:0.2963:0:5.8 -8 43093029 . TGTATTTGGTGTACTTTAATATTTTACATACAGTATATAATATGTATTTTGTGTAT CATGCTTTGGGTAC 116 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22222;SOR=Inf;LSEQ=TTTATGTACAGTATATAATA;RSEQ=TTTGATATTTTGTGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:33.7:1:29:1:1:0:22.3:6:1:0:6.7 1/0:25:14:3,11:7,4:0.56:2,2:19.1:1:30.6:1:0.04862:5.88717:27.9:28:0.5833:0.56:6.1 -8 43093030 . G A 119 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTACAGTATATAATAT;RSEQ=TATTTGGTGTACTTTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:34.7:1:30:1:1:0:22.3:6:1:0:6.7 1/1:19:18:7,11:1,0:0.9474:0,2:28.2:1:28.7:1:0.42105:0:32.2:36:0.9474:0:5.4 -8 43093037 . G A 111 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGTATATAATATGTATTTG;RSEQ=TGTACTTTAATATTTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:34:0:31:1:1:0:22.3:6:1:0:6.7 1/0:19:14:5,9:3,2:0.7368:2,2:25.6:1:29.3:1:0.60268:2.5556:34.3:28:0.7368:0:5.7 -8 43093046 . A C 120 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGTATTTGGTGTACTTT;RSEQ=ATATTTTACATACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:25:0:32:1:1:0:22.3:6:1:0:6.7 1/1:17:14:5,9:2,0:0.8235:0,2:16.6:1:31.7:1:0.175:0:34.3:28:0.8235:0:5.7 -8 43093055 . C T 48 d7;v4;pSTD;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.03571;SOR=0;LSEQ=TGGTGTACTTTAATATTTTA;RSEQ=ATACAGTATATAATATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:16:0:29.3:1:1:0:22.3:6:1:0:6.7 0/1:13:3:2,1:4,6:0.2308:2,2:16:0:30.7:1:0.55944:2.75:23:6:0.2308:0:6.3 -8 43093062 . T TATATAATATGTATTCGTAAGGTATATAATCTATATTTGATGTACTTTCATATTTTATGTACCTA 43 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=2.000;MSILEN=1;SSF=0.51648;SOR=Inf;LSEQ=CTTTAATATTTTACATACAG;RSEQ=ATATAATATGTATTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:8.3:1:27.5:1:1:0:24.5:8:1:0:6.8 0/1:11:3:2,1:3,5:0.2727:2,2:33.3:1:27.5:1:0.54545:2.97:40.7:6:0.2727:0.2727:5.3 -8 43093072 . G A 42 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACATACAGTATATAATAT;RSEQ=TATTTTGTGTATTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:13:1:26.5:1:1:0:37:4:1:0:6.5 1/0:5:3:1,2:1,1:0.6:2,2:11.3:1:26.7:1:1:1.7321:45.7:6:0.6:0:7.3 -8 43093077 . T C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACAGTATATAATATGTATT;RSEQ=TGTGTATTTTGATATTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:18:1:26:1:1:0:37:4:1:0:6.5 0/1:10:2:1,1:3,4:0.2:2,2:13:1:29.5:1:1:1.29:24:4:0.2:0:5.5 -8 43093078 . TG GA 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACAGTATATAATATGTATTT;RSEQ=TGTATTTTGATATTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:19:1:26.5:1:1:0:37:4:1:0:6.5 0/1:10:2:1,1:3,5:0.2:2,2:17:0:29.3:1:1:1.58:48.5:4:0.2:0:6 -8 43093080 . T G 27 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01282;SOR=0;LSEQ=AGTATATAATATGTATTTTG;RSEQ=GTATTTTGATATTTTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21:1:27.5:1:1:0:37:4:1:0:6.5 0/0:11:0:0,0:4,7:0:2,0:10.1:1:27.5:1:1:0:31.5:22:1:0:5.5 -8 43093084 . T C 70 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TATAATATGTATTTTGTGTA;RSEQ=TTTGATATTTTGTGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:25:1:27:1:1:0:37:4:1:0:6.5 0/1:12:5:1,4:2,3:0.4167:2,2:15.8:1:30.2:1:1:2.41422:29.6:10:0.4167:0:6.2 -8 43093088 . G C 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATGTATTTTGTGTATTTT;RSEQ=ATATTTTGTGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:29:1:28.5:1:1:0:37:4:1:0:6.5 0/1:20:2:1,1:6,12:0.1:2,2:26:0:30.5:1:1:1.93:48.5:4:0.1:0:6 -8 43093096 . G A 92 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59316;SOR=0.48573;LSEQ=TTTGTGTATTTTGATATTTT;RSEQ=TGTACAGTATATAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,0:0.5:0,0:37:1:29:1:1:0:37:4:0.6667:0:6.5 0/1:28:9:4,5:1,5:0.3214:2,2:15.6:1:29.2:1:0.58042:3.66:31.7:18:0.3214:0:5.4 -8 43093108 . T G 103 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.30721;SOR=Inf;LSEQ=GATATTTTGTGTACAGTATA;RSEQ=AATATATATTTTGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:20.7:1:27.7:1:1:0:40.7:12:1:0:4.2 0/1:35:10:3,7:10,15:0.2857:2,2:27:1:31.3:1:0.7094:1.53648:35.3:20:0.2941:0:5.4 -8 43093112 . A G 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTTGTGTACAGTATATAAT;RSEQ=TATATTTTGTGTACTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:20.7:1:27.7:1:1:0:40.7:5:1:0:4.2 0/1:35:3:1,2:11,18:0.0857:2,2:27.3:1:32.7:1:1:1.21473:39.7:6:0.0882:0:5.3 -8 43093113 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTGTGTACAGTATATAATA;RSEQ=ATATTTTGTGTACTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:20.7:1:28:1:1:0:40.7:12:1:0:4.2 0/1:35:2:1,1:12,21:0.0571:2,2:36:0:32.5:1:1:1.72:25:4:0.0588:0:5 -8 43093115 . T C 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTGTACAGTATATAATATA;RSEQ=ATTTTGTGTACTTTGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:20.7:1:25.8:1:1:0:40.7:5:1:0:4.2 0/1:36:3:1,2:13,19:0.0833:2,2:29:1:32.7:1:1:1.35659:30:6:0.0882:0:5 -8 43093116 . AT GG 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGTACAGTATATAATATAT;RSEQ=TTTGTGTACTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:20.7:1:30.3:1:1:0:40.7:12:1:0:4.2 0/1:36:2:1,1:13,20:0.0556:2,2:21.5:1:29.8:1:1:1.52:41:4:0.0571:0:4.5 -8 43093117 . T G 112 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGTACAGTATATAATATATA;RSEQ=TTTGTGTACTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:14:1:28.5:1:1:0:35.5:4:0.3333:0:3 0/1:36:12:5,7:4,6:0.3333:2,2:24.3:1:31.5:1:1:1.07:40.5:24:0.3636:0:5 -8 43093120 . TG GA 67 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACAGTATATAATATATATTT;RSEQ=TGTACTTTGATATTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:20.7:1:27.3:1:1:0:40.7:5:1:0:4.2 0/1:39:5:2,3:12,20:0.1282:2,2:7.2:1:29.2:1:1:1.11:51.8:10:0.1389:0.0769:3.2 -8 43093122 . T G 117 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.65812;SOR=0.56757;LSEQ=AGTATATAATATATATTTTG;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:0.5:0,2:26.3:1:32.7:1:1:0:42:6:0.75:0:5 0/1:39:14:5,9:9,14:0.359:2,2:24.4:1:30.9:1:1:1.1526:29.6:13:0.3514:0:4.3 -8 43093124 . T A 79 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09162;LSEQ=TATATAATATATATTTTGTG;RSEQ=ACTTTGATATTTTATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:1,4:0.1667:2,0:26:0:27:0:1:0:31:2:0.1667:0:3 0/1:39:7:3,4:12,20:0.1795:2,2:26.6:1:28.4:1:1:1.24:38.3:14:0.1795:0:5 -8 43093125 . A C 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01943;SOR=0;LSEQ=ATATAATATATATTTTGTGT;RSEQ=CTTTGATATTTTATGTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:2,3:0.2857:2,0:23.5:1:32.5:1:1:0:37:4:0.2857:0:6.5 0/0:40:0:0,0:15,25:0:2,0:19.5:1:29.7:1:1:0:37.8:80:1:0:4.2 -8 43093126 . C T 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.86005;LSEQ=TATAATATATATTTTGTGTA;RSEQ=TTTGATATTTTATGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:1,5:0.1429:2,0:23:0:33:0:0.28571:0:52:2:0.1429:0:2 0/1:40:5:2,3:13,21:0.125:2,2:23.2:1:28.2:1:1:1.07:32:4:0.1053:0:3 -8 43093130 . G C 82 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58498;SOR=0.45047;LSEQ=ATATATATTTTGTGTACTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:6.5:1:32.5:1:1:3.16:59:4:0.2857:0:1 0/1:40:6:2,4:13,21:0.15:2,2:10:1:31.8:1:1:1.23163:50.3:12:0.15:0:4 -8 43093137 . T C 73 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56681;SOR=Inf;LSEQ=TTTTGTGTACTTTGATATTT;RSEQ=ATGTACAGTATATTATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,4:0:2,0:15.7:1:29.8:1:1:0:48.5:12:0.8571:0:3.5 0/1:35:6:2,4:10,19:0.1714:2,2:15.8:1:28.3:1:1:1.0511:37.2:5:0.1515:0:5.2 -8 43093139 . T A 80 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56681;SOR=Inf;LSEQ=TTGTGTACTTTGATATTTTA;RSEQ=GTACAGTATATTATATGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:15:1:31.4:1:1:0:46:14:1:0:3.4 0/1:34:6:2,4:9,18:0.1765:2,2:11.7:1:31.3:1:1:1:31.7:12:0.1875:0:3.3 -8 43093143 . C G 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55991;SOR=Inf;LSEQ=GTACTTTGATATTTTATGTA;RSEQ=AGTATATTATATGTGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:12.3:1:33.1:1:1:0:46:14:1:0:3.4 0/1:30:5:2,3:8,17:0.1667:2,2:9.2:1:30.8:1:1:1.40:38.6:10:0.1667:0:5.2 -8 43093151 . T C 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52797;SOR=Inf;LSEQ=ATATTTTATGTACAGTATAT;RSEQ=ATATGTGTTTTCTGTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:15.3:1:29.7:1:1:0:55:6:1:0:2 0/1:10:3:1,2:3,3:0.3:2,2:5.3:1:30.3:1:1:1.8525:33.7:6:0.3333:0:5.7 -8 43093155 . TG CA 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTATGTACAGTATATTATA;RSEQ=TGTTTTCTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:34:0:28:0:1:0:47:2:1:0:4 0/1:7:3:0,3:1,3:0.4286:2,0:22.7:1:31.5:1:1:0:47:6:0.4286:0.1429:7 -8 43093159 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGTACAGTATATTATATGTG;RSEQ=TTTCTGTACTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:30:0:32:0:1:0:47:2:1:0:4 1/1:2:2:0,2:0,0:1:0,0:33:0:33.5:1:1:0:50:4:1:0:7 -8 43093162 . T TCTGTACTTTGATAGTATAGTTTGGGTACTTTGCTATTTTATGTACCCTATAGAATATATATCTG 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGTATATTATATGTGTTT;RSEQ=CTGTACTTTGATATTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:27:0:32:0:1:0:47:2:1:0:4 1/0:3:2:1,1:0,2:0.6667:0,2:38:1:28.6:1:1:0:36:4:0.6667:0.6667:0 -8 43093163 . CT TG 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTATATTATATGTGTTTT;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:26:0:35:0:1:0:47:2:1:0:4 1/0:3:2:0,2:0,1:0.6667:0,0:28:0:32:0:1:0:50:4:0.6667:0:6 -8 43093173 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATGTGTTTTCTGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:19:0:32:0:1:0:47:2:1:0:4 0/1:5:2:0,2:2,1:0.4:2,0:19:0:31.5:1:0.4:0:50:4:0.4:0:6 -8 43093180 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCTGTACTTTGATATTTT;RSEQ=TGTACAGTATATAAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:12:0:32:0:1:0:47:2:1:0:4 0/1:5:2:0,2:2,1:0.4:2,0:12:0:31:1:0.4:0:50:4:0.4:0:6 -8 43093201 . TTTGGT AATGTATAGTTTGG 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTACAGTATATAAAATGTA;RSEQ=GTACTTTGATATTTTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:0.5:2,0:17:1:30.2:1:1:0:40:4:0.5:0.25:6 -8 43093221 . T C 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGTGTACTTTGATATTT;RSEQ=ATGCACAGTATATAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:13:0:33:0:1:0:60:2:1:0:8 0/1:13:6:4,2:5,2:0.4615:2,2:10.3:1:32:1:1:1.22862:52.7:12:0.4615:0:7.5 -8 43093225 . C T 88 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTACTTTGATATTTTATG;RSEQ=ACAGTATATAATATGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:17:0:32:0:1:0:60:2:1:0:8 1/0:13:9:6,3:2,1:0.6923:2,2:13.8:1:28:1:1:1:52.9:8:0.7273:0:7.2 -8 43093227 . C G 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTACTTTGATATTTTATGCA;RSEQ=AGTATATAATATGTATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:19:0:34:0:1:0:60:2:1:0:8 0/1:15:7:5,2:6,2:0.4667:2,2:14.3:1:32.1:1:1:1.18545:53.7:14:0.4667:0:7.6 -8 43093229 . G C 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTTGATATTTTATGCACA;RSEQ=TATATAATATGTATTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:21:0:34:0:1:0:60:2:1:0:8 0/1:21:4:3,1:11,6:0.1905:2,2:22.3:1:32:1:1:1.60:50:8:0.1905:0:6.3 -8 43093234 . T A 120 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATATTTTATGCACAGTATA;RSEQ=AATATGTATTTGGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:26:0:32:0:1:0:60:2:1:0:8 1/0:31:17:10,7:5,3:0.5484:2,2:11.3:1:29.5:1:1:1.15953:54.4:16:0.5333:0:7.1 -8 43093240 . G A 148 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGCACAGTATATAATAT;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:32:0:30:0:1:0:60:2:1:0:8 1/1:38:37:21,16:0,1:0.9737:0,2:14.1:1:28.6:1:0.44737:0:51.3:36:0.973:0:6.7 -8 43093244 . T C 83 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACAGTATATAATATGTAT;RSEQ=TGGTGTACTTTGATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:36:0:32:0:1:0:60:2:1:0:8 0/1:48:6:4,2:20,22:0.125:2,2:23.2:1:32.3:1:0.66617:2.16:52.3:12:0.1277:0:6.5 -8 43093246 . G T 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGTATATAATATGTATTT;RSEQ=GTGTACTTTGATATTATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:38:0:34:0:1:0:60:2:1:0:8 0/1:49:3:1,2:23,22:0.0612:2,2:23.7:1:30.3:1:1:2.05999:36:6:0.0625:0:7.3 -8 43093248 . T G 160 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTATATAATATGTATTTGG;RSEQ=GTACTTTGATATTATATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:37:0:33:0:1:0:60:2:1:0:8 1/0:51:38:19,19:6,6:0.7451:2,2:16.1:1:30.6:1:1:1:53.3:76:0.76:0:6.2 -8 43093250 . T A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATATAATATGTATTTGGTG;RSEQ=ACTTTGATATTATATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:10.3:1:28.5:1:1:0:58.3:8:1:0:4.3 0/1:62:2:1,1:29,31:0.0323:2,2:15.5:1:27.5:1:1:1.07:38.5:4:0.0328:0:8 -8 43093252 . C CTTTGATATTCATGCTTTGGGTACTTTGATATTTTTTGTACAGTATAGAATATATACCTTGGGTAT 65 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATAATATGTATTTGGTGTA;RSEQ=TTTGATATTATATGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:11.3:1:32.3:1:1:0:58.3:8:1:0:4.3 0/1:69:5:1,4:31,32:0.0725:2,2:37.6:1:28.3:1:0.3605:3.80794:37.2:10:0.0725:0.0725:3 -8 43093253 . T A 161 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.28988;SOR=0;LSEQ=ATAATATGTATTTGGTGTAC;RSEQ=TTGATATTATATGTACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:11.8:1:30.5:1:1:0:58.3:8:1:0:4.3 1/0:69:43:20,23:12,14:0.6232:2,2:17.5:1:29.7:1:1:1.01:55.1:42:0.6364:0:5.8 -8 43093256 . G T 39 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATGTATTTGGTGTACTTT;RSEQ=ATATTATATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:13.3:1:32:1:1:0:58.3:8:1:0:4.3 0/1:71:3:1,2:30,38:0.0423:2,2:18:1:24.7:1:1:1.56921:52.7:2:0.0286:0:7.7 -8 43093260 . T A 70 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTATTTGGTGTACTTTGATA;RSEQ=TATATGTACAGTATATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15.3:1:31:1:1:0:58.3:8:1:0:4.3 0/1:73:5:2,3:29,39:0.0685:2,2:17.2:1:30.4:1:1:1.11369:43.4:10:0.0685:0:5 -8 43093262 . A ATATGTACAGTATATAATATATATTTGGATATACTTTCATATTTTATGTACCTAATATATATTTGATGTAATTTCATATTTTATGTACAGTATAAAATGTATACATGGGCAACTTTAATATAT 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATTTGGTGTACTTTGATATT;RSEQ=TATGTACAGTATATAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:16.3:1:30:1:1:0:58.3:8:1:0:4.3 0/1:75:5:3,2:26,37:0.0667:2,2:38.8:1:27.6:1:0.64405:2.11:45.6:10:0.0704:0.0667:4.6 -8 43093269 . C G 80 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACTTTGATATTATATGTA;RSEQ=AGTATATAATATATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:19.8:1:32.8:1:1:0:58.3:8:1:0:4.3 0/1:76:6:3,3:29,41:0.0789:2,2:21:1:31:1:0.69201:1.41:40.2:12:0.0811:0:3.5 -8 43093272 . T A 70 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTTTGATATTATATGTACAG;RSEQ=ATATAATATATATTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21.3:1:29.8:1:1:0:58.3:8:1:0:4.3 0/1:76:5:2,3:29,40:0.0658:2,2:21.8:1:30.4:1:1:1.0863:58.8:10:0.0676:0:6.4 -8 43093276 . T A 97 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GATATTATATGTACAGTATA;RSEQ=AATATATATTTGGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23.3:1:30.5:1:1:0:58.3:8:1:0:4.3 0/1:75:9:4,5:27,37:0.12:2,2:14.3:1:30.7:1:1:1.09:52.2:18:0.1216:0:5.4 -8 43093280 . A C 171 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.15205;SOR=0;LSEQ=TTATATGTACAGTATATAAT;RSEQ=TATATTTGGTGTACTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:25.3:1:31.8:1:1:0:58.3:8:1:0:4.3 1/0:73:43:18,25:13,17:0.589:2,2:23.4:1:31.6:1:1:1.0612:54.9:42:0.5833:0:5.7 -8 43093285 . T G 50 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTACAGTATATAATATATA;RSEQ=TTGGTGTACTTTTTGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:27:0:31.3:1:1:0:57.7:6:1:0:3 0/1:64:3:2,1:26,34:0.0469:2,2:13:1:32:1:0.58047:2.58:35.3:6:0.0476:0:2.3 -8 43093288 . G T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGTATATAATATATATTT;RSEQ=GTGTACTTTTTGATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:24:0:32.3:1:1:0:57.7:6:1:0:3 0/1:61:2:1,1:24,35:0.0328:2,2:16:1:31.5:1:1:1.45:23:4:0.0328:0:2.5 -8 43093289 . G A 160 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGTATATAATATATATTTG;RSEQ=TGTACTTTTTGATATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:23:0:31.7:1:1:0:57.7:6:1:0:3 1/0:57:43:16,27:7,7:0.7544:2,2:17.2:1:29.6:1:0.53243:1.67157:54.3:86:0.7544:0:5.5 -8 43093290 . TGTACTT GGTTC 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTATATAATATATATTTGG;RSEQ=TTTGATATTTTATGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:22:0:31.7:1:1:0:57.7:6:1:0:3 0/1:54:2:1,1:18,30:0.037:2,2:23:0:32.5:1:1:1.65:40:4:0.0377:0:2 -8 43093295 . TT ATTCATATTTTATGTACCCAAAATATA 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=ATAATATATATTTGGTGTAC;RSEQ=TTTGATATTTTATGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:18:0:33.3:1:1:0:57.7:6:1:0:3 0/1:44:2:1,1:14,25:0.0455:2,2:33.5:1:28.4:1:1:1.76:60:4:0.0488:0.0455:4 -8 43093298 . TTG C 149 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.54204;SOR=0;LSEQ=ATAATATATATTTGGTGTAC;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:17:0:32.2:1:1:0:57.7:6:1:0:2 1/0:47:31:11,20:3,5:0.6596:2,2:14.7:1:30.2:1:1:1.08846:54.2:62:0.7561:0.1702:5 -8 43093300 . G GATATTTTATGTACCTAATATATATTTGATGTAATTTC 126 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATATTTGGTGTACTTTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:11:20:6,14:0,0:1:0,2:23.9:1:29.3:1:1:0:53.8:40:0.9091:1:5.8 -8 43093317 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGATATTTTATGTACAGT;RSEQ=TATAATAAGTAGTTGGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:13:2:1,1:3,8:0.1538:2,2:7:0:31:1:1:2.45:22:4:0.1538:0:4 -8 43093412 . ATGTATTTGGTGTACTTTTTGATATTTTATGTACAGTACATAATATGTATTTGGTGTACTTTGA GTATAGTTTGGGTAATTTCATATTTTTTGTACACTATAAAATATATATCTGGTGTACTTGTT 68 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=TTTTATGTACAGTATGTAAT;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14:1:31:1:1:0:33:4:1:0:7.5 1/1:2:5:2,3:0,0:1:0,2:44.6:1:29.6:1:1:0:36.2:10:1:1:1.2 -8 43093426 . C A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAATATGTATTTGGTGTA;RSEQ=TTTTTGATATTTTATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:32:1:1:0:33:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 43093437 . T A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=TTTGGTGTACTTTTTGATAT;RSEQ=TTATGTACAGTACATAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:1.5:1:29.5:1:1:1:40:4:0.5:0:6 0/1:6:2:2,0:2,2:0.3333:2,0:5:0:27.5:1:0.46667:0:26:4:0.3333:0:5 -8 43093442 . G A 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TGTACTTTTTGATATTTTAT;RSEQ=TACAGTACATAATATGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:44:1:30.5:1:1:1:33:4:0.6667:0:7.5 0/0:6:0:0,0:4,2:0:2,0:11.3:1:31.3:1:1:0:33.5:12:1:0:6.3 -8 43093450 . C T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0.53707;LSEQ=TTGATATTTTATGTACAGTA;RSEQ=ATAATATGTATTTGGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:49:1:30:0:1:1:33:4:0.5:0:7.5 0/1:6:2:1,1:3,1:0.3333:2,2:18:1:29:1:1:2.44949:43.5:4:0.3333:0:7 -8 43093452 . T C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=GATATTTTATGTACAGTACA;RSEQ=AATATGTATTTGGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:16.5:1:33:1:1:0:40:4:0.5:0:6 0/1:6:2:2,0:2,2:0.3333:2,0:20:0:30.5:1:0.46667:0:26:4:0.3333:0:5 -8 43093458 . G C 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TTATGTACAGTACATAATAT;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22.5:1:31.5:1:1:1:40:4:0.5:0:6 0/0:6:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 43093461 . T G 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TGTACAGTACATAATATGTA;RSEQ=TTGGTGTACTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,1:0:2,0:38:1:30.5:1:1:0:33:4:0.6667:0:7.5 0/1:10:3:2,1:2,3:0.3:2,2:30.3:1:32.7:1:1:2.60:39.7:6:0.3:0:7.3 -8 43093462 . T TTGGTGTACTTTGATATTTTAGCTTTGGATACTTTGATATTTTTTGTACAGTATAGAATATATATC 100 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0063;SOR=Inf;LSEQ=GTACAGTACATAATATGTAT;RSEQ=TGGTGTACTTTGATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:31.8:1:29.5:1:1:0:36.5:8:1:0:6.8 1/1:13:11:6,5:2,0:0.8462:0,2:15.8:1:29:1:0.48718:0:44.2:10:0.8333:0.8462:5 -8 43093463 . T A 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19706;SOR=0.19028;LSEQ=TACAGTACATAATATGTATT;RSEQ=GGTGTACTTTGATATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:27.5:1:30.5:1:1:1:40:4:0.5:0:6 0/1:14:2:2,0:7,5:0.1429:2,0:23.5:1:26:1:0.50549:0:26:4:0.1429:0:5 -8 43093464 . G T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGTACATAATATGTATTT;RSEQ=GTGTACTTTGATATTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:31.8:1:28:1:1:0:36.5:3:1:0:6.8 0/1:15:2:1,1:9,4:0.1333:2,2:36:0:30.5:1:1:2.12136:31:4:0.1333:0:7 -8 43093466 . T A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTACATAATATGTATTTGG;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:31:1:29.8:1:1:0:36.5:8:1:0:6.8 0/1:17:2:2,0:8,6:0.1176:2,0:20.5:1:27:1:0.5:0:26:4:0.1176:0:5 -8 43093467 . G A 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01846;SOR=0;LSEQ=GTACATAATATGTATTTGGT;RSEQ=TACTTTGATATTTTATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:32:1:29:1:1:1:33:4:0.5:0:7.5 0/0:22:0:0,0:14,8:0:2,0:11:1:30.9:1:1:0:39.2:21:1:0:6.4 -8 43093468 . T A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACATAATATGTATTTGGTG;RSEQ=ACTTTGATATTTTATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:29:1:29.5:1:1:0:36.5:8:1:0:6.8 0/1:25:2:1,1:14,9:0.08:2,2:34:0:30:1:1:1.52748:31:4:0.08:0:7 -8 43093470 . C CAT 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0121;SOR=0;LSEQ=CATAATATGTATTTGGTGTA;RSEQ=TTTGATATTTTATGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:1:30:1:1:1:33:4:0.5:0:7.5 0/0:28:0:0,0:16,12:0:2,0:10.4:1:31.3:1:1:0:42.2:56:1:0:6.4 -8 43093471 . T C 73 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAATATGTATTTGGTGTAC;RSEQ=TTGATATTTTATGTACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:25:1:31:1:1:0:36.5:8:1:0:6.8 0/1:28:5:2,3:14,8:0.1786:2,2:10.6:1:31.8:1:0.37049:2.52834:53.6:10:0.1852:0:6.4 -8 43093474 . G C 87 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5585;SOR=Inf;LSEQ=ATATGTATTTGGTGTACTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:18:1:32:1:1:0:41.2:10:1:0:6.6 0/1:30:7:4,3:12,9:0.2333:2,2:11.7:1:31:1:1:1:37:14:0.2333:0:6.1 -8 43093475 . A T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATGTATTTGGTGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:17.4:1:30.2:1:1:0:41.2:10:1:0:6.6 0/1:31:2:0,2:17,12:0.0645:2,0:9:1:28.5:1:0.1957:0:60:4:0.0667:0:7 -8 43093477 . A G 61 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTATTTGGTGTACTTTGAT;RSEQ=TTTTATGTACAGTATATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:16.2:1:29.8:1:1:0:41.2:10:1:0:6.6 0/1:36:4:2,2:17,14:0.1111:2,2:14:1:30.8:1:1:1.20753:51:8:0.1111:0:6.8 -8 43093481 . T A 27 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01276;SOR=0;LSEQ=TTTGGTGTACTTTGATATTT;RSEQ=ATGTACAGTATATAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:16:1:27.5:1:1:2.44949:33:4:0.3333:0:7.5 0/0:43:0:0,0:22,19:0:2,0:12.5:1:29.1:1:1:0:43.8:82:0.9535:0:5.8 -8 43093484 . G A 27 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02542;SOR=0;LSEQ=GGTGTACTTTGATATTTTAT;RSEQ=TACAGTATATAGTATATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:13:1:27.5:1:1:1.58108:33:4:0.2:0:7.5 0/0:50:0:0,0:27,23:0:2,0:13.4:1:31.6:1:1:0:42.9:100:1:0:5.8 -8 43093487 . C G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACTTTGATATTTTATGTA;RSEQ=AGTATATAGTATATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:7.3:1:31.5:1:1:0:40:22:1:0:5.8 0/1:51:2:1,1:26,23:0.0392:2,2:15:0:30.5:1:1:1.12771:31:4:0.0392:0:7 -8 43093488 . AGT CTA 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTTTGATATTTTATGTAC;RSEQ=ATATAGTATATATTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:7.5:1:30.5:1:1:0:40:22:1:0:5.8 0/1:50:2:1,1:25,23:0.04:2,2:15:0:31.3:1:1:1.08513:37:4:0.04:0:5 -8 43093490 . T A 155 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.48114;SOR=1.61257;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAGTATATATTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:4,3:1,1:0.6364:2,2:9.3:1:30.6:1:1:1.29:42:14:0.6364:0:5.3 1/0:50:37:19,18:6,5:0.74:2,2:17.6:1:29.9:1:1:1.13381:46.8:74:0.7708:0:5.7 -8 43093494 . T A 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.71698;SOR=1.4597;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AGTATATATTTGGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:4,3:2,2:0.6364:2,2:13.3:1:31:1:1:1.30:42:14:0.6364:0:5.3 1/0:50:36:19,17:7,6:0.72:2,2:21.2:1:30.4:1:1:1.04296:46.5:72:0.7347:0:5.6 -8 43093496 . G A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58292;SOR=0;LSEQ=TATTTTATGTACAGTATATA;RSEQ=TATATATTTGGTGTACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:13.6:1:31.5:1:1:0:40.9:16:1:0:5.6 1/1:51:45:24,21:2,3:0.8824:2,2:22.4:1:30.4:1:0.66131:1.70:45.1:90:0.8824:0:5.8 -8 43093499 . T C 74 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.5779;SOR=Inf;LSEQ=TTTATGTACAGTATATAGTA;RSEQ=ATATTTGGTGTACTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:10.1:1:30:1:1:0:46.2:30:1:0:3.5 0/1:54:5:3,2:24,25:0.0926:2,2:33:0:32:1:1:1.55:28.6:10:0.0926:0:7 -8 43093503 . T C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTACAGTATATAGTATATA;RSEQ=TTGGTGTACTTTTTGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:14.1:1:31.1:1:1:0:46.2:30:1:0:3.5 0/1:56:2:1,1:28,26:0.0357:2,2:37:0:32:1:1:1.07547:24:4:0.0357:0:7 -8 43093506 . G T 71 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57731;SOR=Inf;LSEQ=ACAGTATATAGTATATATTT;RSEQ=GTGTACTTTTTGATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:17.1:1:32.2:1:1:0:46.2:30:1:0:3.5 0/1:55:5:3,2:26,24:0.0909:2,2:36:0:30.6:1:1:1.38:28.6:10:0.0909:0:7 -8 43093507 . G A 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.90513;LSEQ=CAGTATATAGTATATATTTG;RSEQ=TGTACTTTTTGATATTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:6,7:0,0:0.8667:0,2:17.1:1:31.3:1:1:0:49.6:26:0.8667:0:3.3 1/1:55:47:24,23:3,2:0.8545:2,2:26.4:1:29.5:1:1:1.42761:47.1:46:0.8519:0:4.9 -8 43093508 . TGTACTTTTTGA GGAACTTTGC 50 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTATATAGTATATATTTGG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,7:0:2,0:18.1:1:31.2:1:1:0:49.6:26:1:0:3.3 0/1:55:3:2,1:24,23:0.0545:2,2:30:0:31.6:1:1:1.89:31.7:6:0.0577:0:6 -8 43093511 . ACTTTTTG GCTTTC 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATAGTATATATTTGGTGT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,7:0:2,0:20.4:1:29.8:1:1:0:49.6:26:1:0:3.3 0/1:55:2:1,1:23,22:0.0364:2,2:30:0:31.5:1:1:1.04448:37:4:0.0435:0:4 -8 43093516 . TTG C 163 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.10386;SOR=0;LSEQ=ATAGTATATATTTGGTGTAC;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:6,7:0,0:1:0,2:21.6:1:31.7:1:1:0:49.6:26:1:0:2.3 1/0:52:40:20,20:1,1:0.7692:2,2:25.7:1:30.8:1:1:1:47.1:80:0.8889:0:3.8 -8 43093518 . G C 57 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56125;SOR=Inf;LSEQ=ATATATTTGGTGTACTTTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,2:0:2,0:3.7:1:31:1:1:0:42.3:6:1:0:1.3 0/1:22:4:2,2:5,4:0.1818:2,2:9:1:28.5:1:1:1.22862:43.8:3:0.25:0:2 -8 43093521 . A G 32 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03489;SOR=0;LSEQ=TATTTGGTGTACTTTTTGAT;RSEQ=TTTTATGTACAGTATATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:0.0769:2,2:7:0:32:1:1:1:39:4:0.0769:0:1.5 0/0:111:0:0,0:53,57:0:2,0:12.5:1:29.7:1:1:0:44.8:220:0.991:0:2.7 -8 43093522 . T G 66 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGGTGTACTTTTTGATA;RSEQ=TTTATGTACAGTATATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:15:1:31.4:1:1:0:43.3:52:1:0:2.3 0/1:112:4:2,2:51,55:0.0357:2,2:8:0:33:1:1:1.08:40:8:0.0357:0:1 -8 43093544 . G A 116 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59595;SOR=1.9419;LSEQ=TTATGTACAGTATATAATAC;RSEQ=TATTTAGTGTACTATTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:4.8:1:30.3:1:1:1:33:8:0.6667:0:1.3 1/1:20:16:8,8:2,2:0.8:2,2:7.4:1:29.1:1:1:1:55.3:15:0.7895:0:2.9 -8 43093547 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTACAGTATATAATACGTA;RSEQ=TTAGTGTACTATTTGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:3:0:30.3:1:1:0:31:6:1:0:1 0/1:12:2:1,1:5,5:0.1667:2,2:28:0:33:1:1:1:42:4:0.1667:0:5 -8 43093550 . AGTGTAC TGTG 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTATATAATACGTATTT;RSEQ=TATTTGATATTATATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:31.5:1:1:0:42:4:1:0:5 -8 43093566 . T G 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTAGTGTACTATTTGATA;RSEQ=TATATGTACAGTATATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:31.5:1:1:0:42:4:1:0:5 -8 43093568 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTAGTGTACTATTTGATATT;RSEQ=TATGTACAGTATATAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:30:1:1:0:42:4:1:0:5 -8 43093789 . C A 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18452;LSEQ=GTACTTTGATATTTTATGGA;RSEQ=AGTATATAATAGGTATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,1:0.4:2,0:14:1:30:1:0.4:0:34.5:4:0.4:0:3.5 0/1:9:4:2,2:3,2:0.4444:2,2:18.5:1:30:1:1:1.43328:35.5:8:0.4444:0:4.3 -8 43093800 . AGGTAT GTATGG 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.45539;LSEQ=TTTTATGGACAGTATATAAT;RSEQ=TTTGTGTAGTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,1:0.25:2,0:28:0:26.6:0:1:0:42:2:0.25:0:6 0/1:9:3:2,1:3,2:0.3333:2,2:23:1:29:1:1:1.29:38.3:6:0.3333:0.1111:3.7 -8 43093801 . G T 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TTTATGGACAGTATATAATA;RSEQ=GTATTTTGTGTAGTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:0.5:0,2:21.5:1:32:1:1:0:60:4:0.6667:0:6 0/0:5:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 43093805 . T G 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACAGTATATAATAGGTA;RSEQ=TTTGTGTAGTTTGATATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:25.5:1:33.5:1:1:0:60:4:0.6667:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 43093812 . T A 45 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=TATATAATAGGTATTTTGTG;RSEQ=AGTTTGATATTTTATGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:33:1:30.7:1:1:0:54:6:1:0:6 0/1:7:3:2,1:1,3:0.4286:2,2:28:1:28.7:1:0.48571:4.45:38:6:0.4286:0:5.7 -8 43093814 . G C 52 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TATAATAGGTATTTTGTGTA;RSEQ=TTTGATATTTTATGTACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:31:1:33:1:1:0:54:6:1:0:6 0/1:7:2:1,1:2,2:0.2857:2,2:24.5:1:30:1:1:1:44:4:0.2857:0:5 -8 43093825 . T C 61 d7;v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0307;SOR=0;LSEQ=TTTTGTGTAGTTTGATATTT;RSEQ=ATGTACAGTATAAAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:20:1:33.7:1:1:0:54:6:1:0:6 0/1:17:4:2,2:4,7:0.2353:2,2:21.8:1:30.5:1:1:1.68:35.3:8:0.2353:0:5.8 -8 43093831 . C G 48 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01754;SOR=0;LSEQ=GTAGTTTGATATTTTATGTA;RSEQ=AGTATAAAATATGTATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:14:1:29:1:1:0:54:6:1:0:6 0/1:17:3:1,2:5,8:0.1765:2,2:8.3:1:30.7:1:1:1.23302:38.3:6:0.1875:0:5.3 -8 43093833 . G C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTTGATATTTTATGTACA;RSEQ=TATAAAATATGTATTTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:12:1:33.3:1:1:0:54:6:1:0:6 0/1:16:2:1,1:6,8:0.125:2,2:23:0:31:1:1:1.31:26:4:0.125:0:4 -8 43093834 . T A 84 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52105;SOR=Inf;LSEQ=GTTTGATATTTTATGTACAG;RSEQ=ATAAAATATGTATTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:11:1:30:1:1:0:54:6:1:0:6 0/1:17:7:3,4:3,5:0.4118:2,2:19.9:1:30:1:1:1.23:42.4:14:0.4118:0:4.7 -8 43093838 . A G 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATATGTATTTGGTGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:7:1:31.7:1:1:0:54:6:1:0:6 0/1:17:2:1,1:6,8:0.1176:2,2:28:0:31.5:1:1:1.31:26:4:0.1176:0:4 -8 43093843 . TG CA 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTATGTACAGTATAAAATA;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:8:0:27:0:1:0:42:2:1:0:6 0/1:17:2:1,1:7,8:0.1176:2,2:25.5:1:31.5:1:1:1.13:45:4:0.1176:0:4.5 -8 43093844 . G A 114 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTACAGTATAAAATAT;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:7:0:31:0:1:0:42:2:1:0:6 1/1:17:15:7,8:0,0:0.8824:0,2:25.1:1:29.3:1:1:0:35.2:30:1:0:5.1 -8 43093848 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACAGTATAAAATATGTAT;RSEQ=TGGTGTACTTTGATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:3:0:30:0:1:0:42:2:1:0:6 0/1:17:2:1,1:7,8:0.1176:2,2:7:0:33.5:1:1:1.13:30:4:0.1176:0:7 -8 43093851 . G A 96 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGTATAAAATATGTATTTG;RSEQ=TGTACTTTGATATTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:17:9:4,5:4,4:0.5294:2,2:32.4:1:30.3:1:1:1.23365:43:18:0.5294:0:4.7 -8 43093852 . T G 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTATAAAATATGTATTTGG;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:3:2,1:6,7:0.1765:2,2:22.3:1:31.7:1:1:2.21:30.7:6:0.1765:0:4.7 -8 43093860 . G C 102 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGTATTTGGTGTACTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:8:0:32:0:1:0:30:2:1:0:1 1/0:17:9:4,5:4,4:0.5294:2,2:23.4:1:32.4:1:1:1.23365:43:18:0.5294:0:4.7 -8 43093861 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATGTATTTGGTGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:9:0:32:0:1:0:30:2:1:0:1 0/1:17:2:1,1:7,8:0.1176:2,2:24:0:33:0:1:1.13:33:4:0.1176:0:4 -8 43093869 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGTGTACTTTGATATTTTA;RSEQ=GTACAGTATATAATATGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:16:0:32:0:1:0:30:2:1:0:1 0/1:17:2:1,1:7,8:0.1176:2,2:16:0:33:1:1:1.13:46:4:0.1176:0:5 -8 43093875 . G C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTTGATATTTTATGTACA;RSEQ=TATATAATATGCATTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:10:0:34:0:1:0:30:2:1:0:1 0/1:17:2:1,1:7,8:0.1176:2,2:10:0:31:1:1:1.13:46:4:0.1176:0:5 -8 43093876 . T A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAATATGCATTTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:9:0:30:0:1:0:30:2:1:0:1 0/1:15:2:1,1:6,7:0.1333:2,2:35:0:30.5:1:1:1.15:30:4:0.1333:0:7 -8 43093880 . T A 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATATGCATTTGATGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:5:0:25:0:1:0:30:2:1:0:1 0/1:15:3:1,2:6,6:0.2:2,2:23.3:1:31:1:1:1.91151:29:6:0.2:0:7 -8 43093886 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTACAGTATATAATAT;RSEQ=CATTTGATGTAGTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:30:1:1:0:30:4:1:0:7 -8 43093898 . G C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAATATGCATTTGATGTA;RSEQ=TTTGATATTTTATGTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:31.5:1:1:0:30:4:1:0:7 -8 43093902 . G C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGCATTTGATGTAGTTT;RSEQ=ATATTTTATGTACTCTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:31:1:1:0:30:4:1:0:7 -8 43093916 . T A 26 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTTGATATTTTATGTAC;RSEQ=CTATATAATATGTATTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:7.5:1:26:1:1:1:36:4:0.5:0:4 -8 43093922 . T G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATATTTTATGTACTCTATA;RSEQ=AATATGTATTTGGTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:29.5:1:1:1:36:4:0.5:0:4 -8 43093928 . G A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTACTCTATATAATAT;RSEQ=TATTTGGTGTATTTTGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:19.5:1:28:1:1:0:36:4:0.6667:0:4 -8 43093932 . T C 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACTCTATATAATATGTAT;RSEQ=TGGTGTATTTTGATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:23:0:29:1:1:0:36:4:0.6667:0:4 -8 43094017 . A G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATATCAAAGTACACCAA;RSEQ=TGCATTTTATATACTGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:1:28:1:1:0:60:4:1:0:1 -8 43094095 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACATAGTTTGAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:11:0:30:1:1:0:44:4:0.6667:0:6 -8 43094102 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:18:0:30:1:1:0:44:4:0.6667:0:6 -8 43094108 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTGTACATAAAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:24:0:31.5:1:1:0:44:4:0.6667:0:6 -8 43094112 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCAAATACATATTATAT;RSEQ=CTGTACATAAAATGTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:28:0:30.5:1:1:0:44:4:0.6667:0:6 -8 43094128 . CAA C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATACTGTACATAAAATGT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:33.5:1:1:0:44:4:1:0:6 -8 43094142 . A G 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGTCAAAAAGTACACCA;RSEQ=ATACATATTATATACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6.5:1:33:0:1:0:44:4:1:0:6 -8 43094400 . C T 27 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACACAAAATATCAAAGTAC;RSEQ=CAAAATACATATGATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:27.5:1:1:0:52:4:1:0:2.5 -8 43094406 . TACATATG T 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATATCAAAGTACCCAAAA;RSEQ=ATATACTGTACATAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:29.5:1:1:0:52:4:1:0:2.5 -8 43094431 . A C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGATATACTGTACATAAAA;RSEQ=ATCAAAGTACAAAAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:31:0:1:0:52:4:1:0:2.5 -8 43094662 . C T 46 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACTTAATA;RSEQ=ATATTATATACTATACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:5:0:29.3:1:1:0:50.3:6:1:0:6.7 -8 43094668 . A T 48 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACACTTAATACATATT;RSEQ=TATACTATACATAATATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:15:3:2,1:6,6:0.2:2,2:11:0:30.3:1:1:1.91:50.3:6:0.2:0:6.7 -8 43094675 . A G 122 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAATACATATTATATACT;RSEQ=TACATAATATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:15:14:7,7:0,0:0.9333:0,2:13.3:1:32.3:1:1:0:51.1:28:1:0:5.6 -8 43094681 . A G 51 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATATTATATACTATACAT;RSEQ=ATATATCAAAGTACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:6:0:30:1:1:0:35.7:6:1:0:2 0/1:22:3:2,1:10,9:0.1364:2,2:24:0:32.3:1:1:1.75:50.3:6:0.1364:0:6.7 -8 43094683 . T A 48 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATATTATATACTATACATAA;RSEQ=ATATCAAAGTACACAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:8:0:30:1:1:0:35.7:6:1:0:2 0/1:22:3:2,1:10,9:0.1364:2,2:26:0:30.7:1:1:1.75:50.3:6:0.1364:0:6.7 -8 43094692 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTATACATAATATATCAAA;RSEQ=TACACAAAATATATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:17:0:33.3:1:1:0:35.7:6:1:0:2 0/1:28:2:1,1:15,11:0.0714:2,2:35:0:31:1:1:1.34838:56:4:0.0714:0:7 -8 43094694 . A T 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATACATAATATATCAAAGT;RSEQ=CACAAAATATATATTATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:18:1:30.3:1:1:0:35.7:6:1:0:2 0/1:28:5:3,2:13,10:0.1786:2,2:24.6:1:27:1:1:1.15:50.6:4:0.1481:0:5.2 -8 43094696 . A C 119 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22759;SOR=Inf;LSEQ=TACATAATATATCAAAGTAC;RSEQ=CAAAATATATATTATATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:16.7:1:31.7:1:1:0:35.7:6:1:0:2 1/0:27:14:7,7:7,5:0.5185:2,2:23.9:1:31.4:1:0.71269:1.38191:48:28:0.5185:0:5.4 -8 43094697 . CA TC 32 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03693;SOR=0.0487;LSEQ=ACATAATATATCAAAGTACA;RSEQ=AAATATATATTATATGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:16:0:32.3:1:1:0:43:4:0.6667:0:1 0/1:28:2:1,1:14,10:0.0714:2,2:23:0:32:1:1:1.38168:44:4:0.0741:0:4.5 -8 43094698 . A C 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.67614;LSEQ=CATAATATATCAAAGTACAC;RSEQ=AAATATATATTATATGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,0:0.3333:0,0:12:0:32:0:1:0:21:2:1:0:2 0/1:28:7:5,2:10,9:0.25:2,2:17.3:1:30.3:1:0.65761:2.18:42.6:14:0.2692:0:4.7 -8 43094699 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAATATATCAAAGTACACA;RSEQ=AATATATATTATATGCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:13.7:1:30:1:1:0:35.7:6:1:0:1.3 0/1:31:2:1,1:16,13:0.0645:2,2:35:0:33:0:1:1.22249:44:4:0.0645:0:6 -8 43094700 . A G 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.45254;SOR=0.39858;LSEQ=TAATATATCAAAGTACACAA;RSEQ=ATATATATTATATGCTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:10:0:34:0:1:0:21:2:0.5:0:2 0/1:31:5:3,2:14,12:0.1613:2,2:22:1:30.8:1:1:1.28:43.4:10:0.1613:0:6 -8 43094701 . A G 90 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AATATATCAAAGTACACAAA;RSEQ=TATATATTATATGCTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:11.7:1:31.3:1:1:0:35.7:6:1:0:1.3 0/1:31:7:3,4:8,6:0.2258:2,2:19.6:1:32.1:1:0.65944:1.72912:57.3:14:0.2333:0:5.6 -8 43094705 . A G 88 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATCAAAGTACACAAAATAT;RSEQ=TATTATATGCTGTACATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:7.7:1:30.7:1:1:0:35.7:6:1:0:1.3 0/1:31:8:3,5:15,8:0.2581:2,2:18.9:1:29.6:1:0.22848:3.00549:51.6:7:0.2414:0:5.5 -8 43094708 . TTATATG GCATA 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CAAAGTACACAAAATATATA;RSEQ=CTGTACATATAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:4.7:1:31.7:1:1:0:35.7:6:1:0:1.3 0/1:31:2:1,1:17,12:0.0645:2,2:23:0:31.2:1:1:1.40053:44:4:0.0645:0:5 -8 43094710 . A C 63 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGTACACAAAATATATATT;RSEQ=TATGCTGTACATATAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:4:0:31:1:1:0:43:4:1:0:1 0/1:30:4:2,2:14,10:0.1333:2,2:26:1:31.8:1:1:1.38301:43:8:0.1538:0:7 -8 43094714 . G A 101 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAAAATATATATTATAT;RSEQ=CTGTACATATAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:28:11:6,5:8,5:0.3929:2,2:12:1:29.3:1:1:1.31735:46.2:22:0.4231:0:5.2 -8 43094716 . T G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAAATATATATTATATGC;RSEQ=GTACATATAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:30:2:1,1:15,11:0.0667:2,2:13.5:1:32:0:1:1.34838:44:4:0.069:0:4.5 -8 43094724 . T A 116 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATTATATGCTGTACATA;RSEQ=AATATCAAAGTATACATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:21:15:7,8:4,2:0.7143:2,2:12.3:1:29.7:1:0.63512:2.19746:44.3:30:0.7143:0:5.7 -8 43094729 . T A 69 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATGCTGTACATATAATA;RSEQ=CAAAGTATACATAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:18:5:3,2:7,6:0.2778:2,2:5.8:1:29.8:1:1:1.27:43.2:10:0.2778:0:5.8 -8 43094730 . C G 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGCTGTACATATAATAT;RSEQ=AAAGTATACATAATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:2:1,1:8,6:0.1176:2,2:7:0:30:1:1:1.30929:59:4:0.1176:0:4 -8 43094737 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTACATATAATATCAAAGTA;RSEQ=ACATAATATATATTATACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:0:31.5:1:1:0:27:4:1:0:6 -8 43094741 . T A 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAATATCAAAGTATACA;RSEQ=AATATATATTATACACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36:0:29.5:1:1:0:27:4:1:0:6 -8 43094747 . A T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATCAAAGTATACATAATAT;RSEQ=TATTATACACTGTACTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:6:0:29.5:1:1:0:24:4:1:0:6.5 0/1:7:2:1,1:4,1:0.2857:2,2:30:0:29.5:1:1:3.1622:27:4:0.2857:0:6 -8 43094752 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AAGTATACATAATATATATT;RSEQ=TACACTGTACTTAAAATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,0:0:0,0:8:1:28.5:1:1:0:25:4:0.6667:0:6.5 0/1:7:2:2,0:3,2:0.2857:2,0:10:1:32.5:1:1:0:38.5:4:0.2857:0:6 -8 43094755 . C T 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22183;LSEQ=TATACATAATATATATTATA;RSEQ=ACTGTACTTAAAATACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:11:1:32:0:1:0:27:4:0.6667:0:8 1/0:7:5:3,2:0,0:0.7143:0,2:16.8:1:30:1:1:0:29.8:10:0.7143:0:6.8 -8 43094759 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATAATATATATTATACACT;RSEQ=TACTTAAAATACCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:16:1:33.7:1:1:0:25.3:6:1:0:7 0/1:18:2:2,0:10,6:0.1111:2,0:18:0:33:0:0.52941:0:37:4:0.1111:0:8 -8 43094762 . CT GA 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATATATATTATACACTGTA;RSEQ=TAAAATACCAAAGTACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:19:1:33.3:1:1:0:25.3:6:1:0:7 0/1:19:2:2,0:11,6:0.1053:2,0:21:1:32:1:1:0:38.5:4:0.1053:0:5 -8 43094763 . T A 113 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07935;LSEQ=ATATATATTATACACTGTAC;RSEQ=TAAAATACCAAAGTACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:22:0:31:1:1:0:24:4:0.6667:0:6.5 1/0:19:13:9,4:1,1:0.6842:2,2:8.5:1:30.8:1:1:2.12:32.9:26:0.7647:0:7.3 -8 43094765 . A G 34 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.38217;SOR=0.29107;LSEQ=ATATATTATACACTGTACTT;RSEQ=AAATACCAAAGTACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,0:0.25:0,0:24:0:34:0:1:0:22:2:0.25:0:5 0/1:24:2:2,0:15,7:0.0833:2,0:24:0:34:0:1:0:37:4:0.0833:0:8 -8 43094767 . A T 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATTATACACTGTACTTAA;RSEQ=ATACCAAAGTACACAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:11.6:1:31.7:1:1:0:29.1:14:1:0:6.9 0/1:34:2:1,1:22,9:0.0588:2,2:9:0:27.5:1:0.52083:2.37114:43.5:4:0.0588:0:6 -8 43094770 . AC TA 31 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01468;SOR=0;LSEQ=TTATACACTGTACTTAAAAT;RSEQ=CAAAGTACACAAAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:5,0:0.2857:0,2:6:0:31:0:0.28571:0:36:4:0.2857:0:6.5 0/0:47:0:0,0:29,18:0:2,0:9:1:28.4:1:1:0:33.3:46:1:0:6.2 -8 43094771 . C T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.08539;LSEQ=TATACACTGTACTTAAAATA;RSEQ=CAAAGTACACAAAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:0,0:0.5:0,0:19.4:1:32:1:1:0:26.4:10:0.5556:0:6.6 1/0:48:25:16,9:7,7:0.5208:2,2:11.2:1:28.8:1:0.50307:1.75:30.4:24:0.5217:0:5.8 -8 43094777 . T G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTACTTAAAATACCAAAG;RSEQ=ACACAAAATATATATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:10.4:1:28.4:1:1:0:28.4:40:1:0:6.5 0/1:76:2:2,0:40,34:0.0263:2,0:19.5:1:31.5:1:0.49895:0:37.5:4:0.0263:0:7.5 -8 43094778 . A T 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.76329;SOR=0.80191;LSEQ=TGTACTTAAAATACCAAAGT;RSEQ=CACAAAATATATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:7,8:0.25:2,2:19.2:1:31:1:0.31889:4.25:27.2:10:0.25:0:5.4 0/1:76:16:7,9:35,25:0.2105:2,2:12.4:1:27.9:1:0.39791:1.78592:28.8:15:0.2027:0:4.8 -8 43094780 . A C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.79695;SOR=1.27991;LSEQ=TACTTAAAATACCAAAGTAC;RSEQ=CAAAATATATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:4,2:9,8:0.2609:2,2:9.7:1:31.3:1:0.66002:1.73:26.5:12:0.2609:0:7 0/1:77:24:16,8:25,23:0.3117:2,2:16.5:1:30.8:1:0.31469:1.82:39.3:48:0.3117:0:6.6 -8 43094781 . CA TC 116 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55945;SOR=1.62324;LSEQ=ACTTAAAATACCAAAGTACA;RSEQ=AAATATATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:0,3:11,8:0.12:2,0:6.7:1:26.7:1:0.21429:0:25.7:6:0.12:0:6.3 0/1:88:16:7,9:33,31:0.1818:2,2:7.6:1:29:1:0.78061:1.3633:29.8:32:0.186:0:6.6 -8 43094782 . A C 127 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.4039;SOR=1.89151;LSEQ=CTTAAAATACCAAAGTACAC;RSEQ=AAATATATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:12,8:0.1111:2,2:6.7:1:30:1:0.55957:2.85795:31:6:0.1304:0:6.7 0/1:99:19:8,11:35,25:0.1919:2,2:5.3:1:30.1:1:0.29178:1.90884:35:38:0.2289:0:7.1 -8 43094784 . AA GG 29 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55496;SOR=0.61342;LSEQ=TAAAATACCAAAGTACACAA;RSEQ=TATATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:1:1,0:29,27:0.0175:2,0:22:0:33.5:0:1:0:28:2:0.0175:0:7 0/1:185:2:1,1:95,87:0.0108:2,2:22:0:29.8:1:1:1.09142:30:4:0.0109:0:6 -8 43094785 . A C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.56795;SOR=1.37712;LSEQ=AAAATACCAAAGTACACAAA;RSEQ=TATATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:9:5,4:22,24:0.1552:2,2:17.9:1:32.3:1:0.72873:1.36:30.7:18:0.1607:0:5.8 0/1:193:39:20,19:76,71:0.2021:2,2:19.5:1:31.9:1:1:1.01681:30.6:78:0.2063:0:5.5 -8 43094786 . T TATATATTGAAGGCACATCAAAG 85 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=2;SSF=0.20658;SOR=Inf;LSEQ=AAATACCAAAGTACACAAAA;RSEQ=ATATATTATATACTGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:30,28:0:2,0:8.8:1:29:1:1:0:31.8:57:0.9661:0:6.2 0/1:213:8:5,3:104,100:0.0376:2,2:16.8:1:28.5:1:0.72218:1.60:34.9:16:0.0379:0.0376:4.8 -8 43094787 . A G 66 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.5797;SOR=Inf;LSEQ=AATACCAAAGTACACAAAAT;RSEQ=TATATTATATACTGTACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:32,30:0:2,0:9.5:1:29:1:1:0:31.5:61:1:0:6.2 0/1:222:4:2,2:112,104:0.018:2,2:27.3:1:33:1:1:1.07654:31:8:0.0183:0:6.8 -8 43094789 . A ATATTATATACTGTACATAAAATATCAAAGTACCCCAAGGTATATATTCAATACTGTACAAAAAATATCAAAGTACCCAAAGCATG 90 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1e-05;SOR=0;LSEQ=TACCAAAGTACACAAAATAT;RSEQ=TATTATATACTGTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:8:3,5:29,29:0.1159:2,2:28.1:1:30.3:1:0.70964:1.65399:33.6:16:0.1159:0.1159:5.3 0/0:224:0:0,0:115,106:0:2,0:11.6:1:28.6:1:1:0:33.8:109.5:0.9865:0:6.4 -8 43094790 . T A 108 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0.91349;LSEQ=ACCAAAGTACACAAAATATA;RSEQ=ATTATATACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:1,2:32,31:0.0429:2,2:23:1:30.7:1:1:2.04269:38:6:0.0429:0:7 0/1:280:11:7,4:134,119:0.0393:2,2:24.8:1:31.5:1:0.55097:1.55:28.5:22:0.0393:0:6.5 -8 43094791 . A ATTATATACTGTACATAAAATATCAAAGTTACCCAAACTATACT 56 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=28;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAAAGTACACAAAATATAT;RSEQ=TTATATACTGTACATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:34,35:0:2,0:11.9:1:29.1:1:1:0:32:68:0.9855:0:6.2 0/1:286:4:3,1:149,129:0.014:2,2:17:1:28.2:1:0.62693:2.59:33:8:0.0142:0.014:7.3 -8 43094792 . T C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26329;SOR=0.37104;LSEQ=CAAAGTACACAAAATATATA;RSEQ=TATATACTGTACATAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:34,34:0.0278:2,2:12:0:33.5:1:1:1:45.5:4:0.0282:0:6 0/1:287:3:2,1:152,132:0.0105:2,2:19:1:31.3:1:1:1.73:55:6:0.0105:0:7 -8 43094794 . A T 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.88149;SOR=1.0932;LSEQ=AAGTACACAAAATATATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:18:8,10:24,24:0.25:2,2:12.4:1:28.8:1:0.78519:1.24578:31.9:36:0.25:0:6.6 0/1:292:78:37,41:112,89:0.2671:2,2:13.6:1:29.3:1:0.23058:1.39278:33.9:38:0.2639:0:6.8 -8 43094798 . A T 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55936;SOR=0.83958;LSEQ=ACACAAAATATATATTATAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:22:11,11:22,19:0.3014:2,2:16.4:1:29.4:1:0.79782:1.1552:32.4:44:0.3014:0:6.1 0/1:301:80:39,41:108,87:0.2658:2,2:16.9:1:29:1:0.35244:1.30376:34.4:39:0.2635:0:6.4 -8 43094800 . T A 59 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAAAATATATATTATATAC;RSEQ=GTACATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:33,32:0:2,0:18.9:1:30.6:1:1:0:31.7:130:0.9848:0:5.9 0/1:302:4:3,1:148,129:0.0132:2,2:10.5:1:29.8:1:0.62654:2.61:29:8:0.0142:0:7.5 -8 43094802 . T C 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.31058;SOR=0.45245;LSEQ=AAAATATATATTATATACTG;RSEQ=ACATAAAATATCAAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:0,2:40,39:0.0247:2,0:23:1:30:1:0.49383:0:20:4:0.0247:0:6.5 0/1:354:4:1,3:179,169:0.0113:2,2:21.8:1:31.8:1:0.36179:3.16803:33.3:8:0.0114:0:6.5 -8 43094803 . A G 32 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0337;SOR=0;LSEQ=AAATATATATTATATACTGT;RSEQ=CATAAAATATCAAAGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:39,40:0.0247:2,2:20:0:32:1:1:1.03:44:4:0.0247:0:4 0/0:358:0:0,0:184,172:0:2,0:17.1:1:28.9:1:1:0:33.9:177:0.9944:0:6.3 -8 43094804 . C T 79 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59822;SOR=Inf;LSEQ=AATATATATTATATACTGTA;RSEQ=ATAAAATATCAAAGTACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:40,41:0:2,0:20.1:1:32.3:1:1:0:32:162:1:0:5.9 0/1:358:6:5,1:180,172:0.0168:2,2:19.3:1:30.7:1:0.21639:4.76:26.2:12:0.0168:0:6.7 -8 43094805 . A G 29 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0334;SOR=0;LSEQ=ATATATATTATATACTGTAC;RSEQ=TAAAATATCAAAGTACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:39,40:0.0247:2,2:22:0:29.5:1:1:1.03:45:4:0.025:0:7 0/0:360:0:0,0:180,169:0:2,0:18.7:1:30:1:1:0:33.8:173.5:0.9693:0:6.3 -8 43094806 . T A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05543;SOR=0.33881;LSEQ=TATATATTATATACTGTACA;RSEQ=AAAATATCAAAGTACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:7:4,3:36,39:0.0854:2,2:23:1:29.6:1:0.70912:1.44:27.9:14:0.0864:0:5.3 0/1:360:11:7,4:176,169:0.0306:2,2:22.8:1:30.1:1:0.54421:1.68:31.3:22:0.0311:0:6.1 -8 43094807 . A G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62585;SOR=1.45409;LSEQ=ATATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:4:3,1:37,41:0.0488:2,2:25.3:1:32:1:0.35349:3.28:42:8:0.0488:0:6.5 0/1:360:25:12,13:170,161:0.0694:2,2:27.1:1:31.2:1:0.83671:1.14346:29.6:24:0.0674:0:6.6 -8 43094809 . A T 81 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.69645;SOR=2.07416;LSEQ=ATATTATATACTGTACATAA;RSEQ=ATATCAAAGTACACCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:1:0,1:40,41:0.0122:2,0:27:0:28:0:1:0:20:2:0.0122:0:7 0/1:360:9:5,4:180,170:0.025:2,2:25.1:1:25.7:1:1:1.18:40.1:3.5:0.0197:0:6.8 -8 43094813 . T C 93 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.21952;SOR=Inf;LSEQ=TATATACTGTACATAAAATA;RSEQ=CAAAGTACACCAAATACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:40,42:0:2,0:26.5:1:30.6:1:1:0:32.1:81:1:0:5.9 0/1:356:9:5,4:176,168:0.0253:2,2:32.2:1:29.4:1:1:1.19:34.7:8:0.0231:0:6.3 -8 43094814 . C G 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13981;SOR=1.46189;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:34:15,19:24,20:0.4198:2,2:24.5:1:32.2:1:0.49364:1.51177:33.9:68:0.4198:0:6 1/0:352:181:92,89:79,81:0.5142:2,2:21.6:1:31.8:1:0.82851:1.06:35.1:180:0.5202:0:6.4 -8 43094817 . A G 107 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73225;SOR=0.84067;LSEQ=TACTGTACATAAAATATCAA;RSEQ=GTACACCAAATACATATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:3:2,1:37,38:0.0375:2,2:30.3:1:33.3:1:1:2.04:39:6:0.0375:0:5.3 0/1:347:11:4,7:170,163:0.0317:2,2:36.3:1:31.2:1:0.37509:1.82202:44.5:22:0.0323:0:7 -8 43094818 . G T 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03204;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACCAAATACATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:4:2,2:37,38:0.0506:2,2:21:1:30.8:1:1:1.03:34.5:8:0.0513:0:7.3 0/1:345:18:12,6:160,161:0.0522:2,2:21:1:30.4:1:0.22605:2.01:30.7:36:0.0531:0:7 -8 43094819 . T A 30 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0342;SOR=0;LSEQ=CTGTACATAAAATATCAAAG;RSEQ=ACACCAAATACATATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:38,39:0.0253:2,2:37:0:30:1:1:1.03:23:4:0.0253:0:7 0/0:346:0:0,0:174,168:0:2,0:29.9:1:28.9:1:1:0:33.8:67.4:0.9883:0:6.3 -8 43094820 . A T 129 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59216;SOR=1.61377;LSEQ=TGTACATAAAATATCAAAGT;RSEQ=CACCAAATACATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:2,1:35,39:0.0385:2,2:39.7:1:30:1:0.60547:2.21:47.7:6:0.0385:0:6.7 0/1:346:21:11,10:162,157:0.0607:2,2:38.8:1:29.5:1:1:1.07:31.3:42:0.0616:0:6.8 -8 43094821 . CACCAAAT C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09435;SOR=0.33089;LSEQ=GTACATAAAATATCAAAGTA;RSEQ=ACATATTATATACTGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:4:2,2:30,33:0.0533:2,2:39.3:1:31.5:1:1:1.10:28:8:0.0556:0:5.5 0/1:329:6:4,2:146,141:0.0182:2,2:38.5:1:32.2:1:0.6848:1.93:30:12:0.0186:0:6.3 -8 43094822 . A C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62577;SOR=1.52166;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:4:2,2:30,33:0.0533:2,2:37.3:1:31.8:1:1:1.10:23:8:0.0556:0:6.5 0/1:329:26:15,11:146,141:0.079:2,2:36.9:1:29.2:1:0.54444:1.32:32.2:25:0.0776:0:6.7 -8 43094823 . C T 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09798;SOR=1.55955;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:32:14,18:18,17:0.4211:2,2:29.1:1:30.3:1:0.6267:1.35505:33.9:31:0.4559:0:5.9 1/0:331:176:93,83:72,69:0.5317:2,2:29.7:1:29.5:1:0.82112:1.07:35.6:57.667:0.5457:0:6.4 -8 43094824 . C A 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.83742;SOR=1.2357;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:7:5,2:27,34:0.0921:2,2:37.4:1:30.3:1:0.24089:3.10:36.3:14:0.1029:0:6.6 0/1:332:37:21,16:142,135:0.1114:2,2:37.9:1:29.5:1:0.60081:1.25:32.2:36:0.115:0:7 -8 43094826 . A G 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74144;SOR=0.87918;LSEQ=TAAAATATCAAAGTACACCA;RSEQ=ATACATATTATATACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:15:7,8:25,28:0.1974:2,2:38.4:1:31.8:1:1:1.02011:33:30:0.2174:0:6.7 0/1:332:59:29,30:133,119:0.1777:2,2:36.3:1:31.2:1:0.66519:1.15564:33.4:58:0.1841:0:6.7 -8 43094827 . A C 145 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44652;SOR=1.95167;LSEQ=AAAATATCAAAGTACACCAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:3:2,1:30,34:0.04:2,2:37:0:32:1:0.60255:2.24:47.7:6:0.0448:0:6.7 0/1:332:25:12,13:145,133:0.0753:2,2:36.4:1:31.3:1:0.83498:1.18043:30:24:0.0772:0:6.8 -8 43094829 . ACA CCAAAGCATG 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16126;SOR=0.36018;LSEQ=AATATCAAAGTACACCAAAT;RSEQ=TATTATATACTGTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:2,1:29,34:0.0411:2,2:38:1:30.5:1:0.59692:2.32:29.3:6:0.0435:0:6 0/1:330:5:3,2:163,149:0.0152:2,2:38.8:1:31.1:1:1:1.37:29.4:10:0.0157:0:6.2 -8 43094830 . C T 236 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11127;SOR=1.79025;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:59:27,32:2,1:0.8194:2,2:31:1:29.7:1:0.59513:2.3383:32.7:118:0.9219:0:6.1 1/1:329:293:153,140:7,8:0.8906:2,2:32.8:1:28.9:1:0.7931:1.25:34.6:72.25:0.9383:0:6.5 -8 43094832 . T G 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.86995;SOR=1.12749;LSEQ=ATCAAAGTACACCAAATACA;RSEQ=ATTATATACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:13:5,8:28,31:0.1781:2,2:29:1:31.9:1:0.75975:1.43786:32.5:26:0.1806:0:5.5 0/1:331:65:28,37:140,122:0.1964:2,2:31.1:1:32:1:0.16553:1.51444:34.2:130:0.1982:0:6 -8 43094834 . T G 83 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29155;LSEQ=CAAAGTACACCAAATACATA;RSEQ=TATATACTGTACATAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:1:0,1:32,38:0.0141:2,0:30:0:32:0:1:0:30:2:0.0145:0:8 0/1:331:6:2,4:167,157:0.0181:2,2:29.3:1:32.3:1:0.43868:2.12267:42.3:12:0.0184:0:7.3 -8 43094836 . A C 194 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.64284;SOR=0.86297;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:18:8,10:17,23:0.2535:2,2:28.2:1:31.2:1:1:1.08:31.5:17:0.2429:0:6.4 0/1:331:75:37,38:79,85:0.2266:2,2:27:1:31.2:1:0.88982:1.05:33.7:74:0.2305:0:6.6 -8 43094837 . TATACT G 66 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06693;LSEQ=AGTACACCAAATACATATTA;RSEQ=GTACATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:1:0,1:31,39:0.0141:2,0:18:0:33.5:0:1:0:42:2:0.0143:0:7 0/1:333:5:3,2:162,161:0.015:2,2:14.6:1:28.7:1:1:1.49:26.4:10:0.0153:0.015:7.4 -8 43094840 . A T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12014;SOR=1.77263;LSEQ=ACACCAAATACATATTATAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:11:5,6:22,30:0.1549:2,2:24.9:1:31:1:1:1.13:34.2:22:0.1571:0:5.8 0/1:334:82:47,35:106,117:0.2455:2,2:30.2:1:29.6:1:0.15544:1.48:36:164:0.2531:0:6.4 -8 43094841 . C G 187 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99119;LSEQ=CACCAAATACATATTATATA;RSEQ=TGTACATAAAATATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:14:6,8:24,30:0.1972:2,2:23.3:1:32.2:1:1:1.06568:33.4:28:0.2029:0:6.6 0/1:332:65:32,33:130,126:0.1958:2,2:21.8:1:31.2:1:0.88978:1.06375:33.4:64:0.1994:0:6.6 -8 43094842 . T G 67 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59126;SOR=Inf;LSEQ=ACCAAATACATATTATATAC;RSEQ=GTACATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:31,39:0:2,0:22.7:1:30.6:1:1:0:32.5:69:1:0:5.8 0/1:326:5:3,2:157,156:0.0153:2,2:20.6:1:29.2:1:1:1.49:43.6:10:0.0157:0:7 -8 43094843 . G C 76 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0867;LSEQ=CCAAATACATATTATATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:1:0,1:31,39:0.0141:2,0:18:0:33:0:1:0:41:2:0.0143:0:6 0/1:327:5:2,3:163,159:0.0153:2,2:21:1:33:1:0.68271:1.53573:28.2:10:0.0155:0:6.8 -8 43094844 . T C 115 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.70123;SOR=2.425;LSEQ=CAAATACATATTATATACTG;RSEQ=ACATAAAATATCAAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:1:0,1:31,39:0.0141:2,0:20:0:33:0:1:0:30:2:0.0143:0:8 0/1:328:11:4,7:160,154:0.0335:2,2:17.4:1:33.5:1:0.37573:1.8149:40.6:22:0.0337:0:7 -8 43094846 . C G 33 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0313;SOR=0;LSEQ=AATACATATTATATACTGTA;RSEQ=ATAAAATATCAAAGTACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:29,38:0.0282:2,2:18:0:33:1:1:1.31:58.5:4:0.0286:0:6.5 0/0:328:0:0,0:163,161:0:2,0:21:1:31.6:1:1:0:34.4:648:0.9878:0:6.3 -8 43094848 . T A 118 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.75197;SOR=1.78419;LSEQ=TACATATTATATACTGTACA;RSEQ=AAAATATCAAAGTACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:30,39:0.0282:2,2:16:0:29.5:1:1:1.30:23.5:4:0.0282:0:6.5 0/1:325:16:6,10:157,152:0.0492:2,2:18.3:1:29.5:1:0.31922:1.71865:35.3:32:0.0498:0:6.9 -8 43094849 . A G 114 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13724;SOR=Inf;LSEQ=ACATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:30,39:0:2,0:16:1:29.7:1:1:0:32.9:138:0.9718:0:5.9 0/1:324:13:8,5:151,155:0.0401:2,2:15.3:1:31:1:0.41338:1.64:26.5:26:0.0405:0:6.3 -8 43094855 . T C 113 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92976;LSEQ=TATATACTGTACATAAAATA;RSEQ=CAAAGTACACCAAATACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:3:1,2:28,34:0.0441:2,2:5.7:1:32:1:1:1.63495:30.7:6:0.0441:0:5.7 0/1:316:13:8,5:144,149:0.0411:2,2:10.3:1:30.6:1:0.4114:1.65:30.5:26:0.0421:0:6.3 -8 43094856 . C G 105 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00734;SOR=0.25712;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:8:4,4:23,32:0.125:2,2:10.6:1:32.3:1:0.71528:1.38:29.8:16:0.125:0:6 0/1:312:11:6,5:147,152:0.0353:2,2:14.4:1:30.5:1:0.76783:1.24:31.5:10:0.0325:0:6.5 -8 43094859 . A T 102 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37932;SOR=Inf;LSEQ=TACTGTACATAAAATATCAA;RSEQ=GTACACCAAATACATATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:23,35:0:2,0:7.9:1:30.1:1:1:0:33.5:57:0.9828:0:6 0/1:297:10:2,8:142,145:0.0337:2,2:17.5:1:30.9:1:0.10506:3.90119:34.3:20:0.0338:0:7.2 -8 43094862 . A T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTACATAAAATATCAAAGT;RSEQ=CACCAAATACATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:22,28:0:2,0:5.9:1:29:1:1:0:33.2:100:1:0:6.1 0/1:253:3:2,1:117,131:0.0119:2,2:20:1:29:1:0.60491:2.23:25.7:6:0.012:0:7.3 -8 43094864 . A C 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61819;SOR=1.51498;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:2,3:5,11:0.2273:2,2:12.4:1:32:1:1:1.44:33.6:10:0.2273:0:6.2 0/1:149:46:17,29:58,43:0.3087:2,2:11.9:1:30.6:1:0.03219:2.28771:35.5:45:0.3061:0:6.5 -8 43094865 . C T 67 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22932;SOR=0.36418;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:5,11:0.1111:2,0:10.5:1:31.5:1:1:0:28:4:0.1111:0:6 0/1:139:6:3,3:67,65:0.0432:2,2:13.3:1:26.3:1:1:1.03055:32.7:5:0.0373:0:6.7 -8 43094866 . C A 94 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.05842;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:4,9:0.0667:2,0:7:0:31:0:1:0:24:2:0.0667:0:7 0/1:128:9:5,4:59,59:0.0703:2,2:19.9:1:29.9:1:1:1.25:36.3:18:0.072:0:6.7 -8 43094868 . A G 151 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1777;SOR=4.24496;LSEQ=TAAAATATCAAAGTACACCA;RSEQ=ATACATATTATATACTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:2,8:0.0909:2,0:12:0:33:0:1:0:43:2:0.0909:0:8 0/1:100:30:18,12:31,37:0.3:2,2:8.3:1:30.8:1:0.27304:1.78:36:60:0.3061:0:7.4 -8 43094871 . ACA GTG 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATATCAAAGTACACCAAAT;RSEQ=TATTATATACTGTTCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,7:0:2,0:10.5:1:31.6:1:1:0:34.9:16:0.8889:0:6.1 0/1:87:3:1,2:41,39:0.0345:2,2:27.3:1:32.1:1:0.6158:2.08441:47.3:6:0.0361:0:3 -8 43094872 . C T 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34652;SOR=2.01055;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ATATTATATACTGTTCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:1,6:1,1:0.7778:2,2:6.7:1:29.9:1:0.41667:4.58262:34:14:0.7778:0:6.4 1/1:73:64:34,30:1,2:0.8767:2,2:7.5:1:28.8:1:0.60255:2.24:35.5:128:0.9412:0:7.1 -8 43094879 . TA AG 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGTACACCAAATACATATTA;RSEQ=TACTGTTCATAAAATATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:8.1:1:30.3:1:1:0:39.4:14:1:0:4.1 0/1:42:2:1,1:18,21:0.0476:2,2:19:1:29.5:1:1:1.16:34:4:0.0476:0:6 -8 43094887 . T A 77 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.52085;LSEQ=AAATACATATTATATACTGT;RSEQ=CATAAAATATCAAAGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:14:0:31:0:1:0:41:2:0.3333:0:4 0/1:16:7:4,3:5,4:0.4375:2,2:11.3:1:27.6:1:1:1.06:34.6:14:0.4375:0:7 -8 43094899 . AAAGTACACAAATTACATGTTATATACTGTACATAAAATATCAATGTGCACCAAATACATATTAT GAACTCCCCAAAGTATGTTTTACCTACTGTACATGAAATATCAAACTCCCCAAAGTATGTTTTAC 94 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.25;SOR=Inf;LSEQ=TATACTGTTCATAAAATATC;RSEQ=ATACTGTACATAAAATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:2:0:31:0:1:0:41:2:1:0:4 1/1:11:9:4,5:0,0:0.8182:0,2:28.2:1:29.9:1:1:0:39.1:18:0.8182:0.8182:3.8 -8 43094904 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTTCATAAAATATCAAAGT;RSEQ=CACAAATTACATGTTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:31:0:33:0:1:1:47:4:0.3333:0:7 -8 43094906 . A C 57 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCATAAAATATCAAAGTAC;RSEQ=CAAATTACATGTTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:3,1:0,1:0.8:0,2:17.8:1:28.8:1:0.4:0:35:8:0.8:0:5.8 -8 43094914 . CA TG 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACAAATTA;RSEQ=TGTTATATACTGTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:28:0:32.8:1:1:0:47:4:1:0:6 -8 43094946 . G A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTACATAAAATATCAATGT;RSEQ=CACCAAATACATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:22:0:30:0:1:0:33:2:1:0:8 1/0:3:2:2,0:0,0:0.6667:0,0:24:1:28.5:1:1:0:21:4:0.6667:0:7 -8 43094948 . A C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACATAAAATATCAATGTGC;RSEQ=CCAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:31:0:1:0:33:2:1:0:8 1/0:3:2:2,0:0,1:0.6667:0,0:26:1:31.5:1:0.33333:0:21:4:0.6667:0:7 -8 43094956 . C T 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAATGTGCACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:32:0:31:0:1:0:33:2:1:0:8 1/1:5:5:3,2:0,0:1:0,2:21.2:1:30.6:1:1:0:38.2:10:1:0:6.8 -8 43094958 . T TATTATATACTGTACATAAAATATCAAAGTACCCCAAACTATGC 92 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.27273;SOR=Inf;LSEQ=ATCAATGTGCACCAAATACA;RSEQ=ATTATATACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:31:0:1:0:33:2:1:0:8 1/1:10:8:3,5:2,0:0.8:0,2:7.9:1:30.8:1:0.44444:0:27.8:16:0.8:0.8:5.5 -8 43094962 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATGTGCACCAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:38:0:28:0:1:0:33:2:1:0:8 0/1:10:2:2,0:2,4:0.2:2,0:33:0:30.5:1:0.42857:0:21:4:0.2:0:7 -8 43094968 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCAAATACATATTATATAC;RSEQ=GTACATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:31:0:1:0:33:2:1:0:8 0/1:14:2:0,2:7,5:0.1429:2,0:12:0:32:0:0.46154:0:27:4:0.1538:0:7 -8 43094969 . G C 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81093;LSEQ=CCAAATACATATTATATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:33:0:31:0:1:0:33:2:0.3333:0:8 0/1:14:4:3,1:4,6:0.2857:2,2:20:1:31.8:1:0.55944:4.03:40.5:8:0.3077:0:6.5 -8 43094974 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACATATTATATACTGTACA;RSEQ=AAAATATCAAAGTACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:13.3:1:28.3:1:1:0:40.3:6:1:0:7.3 0/1:21:2:0,2:11,8:0.0952:2,0:18:0:31.5:1:0.21429:0:27:4:0.1:0:7 -8 43094975 . A G 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52125;SOR=0.48821;LSEQ=ACATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:27:0:32:0:1:0:33:2:0.3333:0:8 0/1:21:4:3,1:8,9:0.1905:2,2:20:0:32:1:0.58647:3.19:40.5:8:0.2:0:6.5 -8 43094978 . A C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATTATATACTGTACATAAA;RSEQ=TATCAAAGTACACAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:14.7:1:30.3:1:1:0:40.3:6:1:0:7.3 0/1:21:2:1,1:10,9:0.0952:2,2:8:0:32:1:1:1.10554:60:4:0.0952:0:5 -8 43094982 . C G 33 d7;v4;pSTD;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03162;SOR=0.03705;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAAGTACACAAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:14:0:33:1:1:0:44:4:0.6667:0:7 0/1:21:1:0,1:11,9:0.0476:2,0:24:0:33:0:0.47619:0:22:2:0.0476:0:4 -8 43094984 . A G 33 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01087;SOR=0;LSEQ=ATACTGTACATAAAATATCA;RSEQ=AGTACACAAAATACATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:16:0:33:0:1:0:44:4:0.6667:0:7 0/0:21:0:0,0:11,10:0:2,0:19.2:1:30.7:1:1:0:35.2:42:1:0:5.3 -8 43094988 . A T 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52125;SOR=0.48821;LSEQ=TGTACATAAAATATCAAAGT;RSEQ=CACAAAATACATATTATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:14:0:28:0:1:0:33:2:0.3333:0:8 0/1:21:4:3,1:8,9:0.1905:2,2:20:1:29:1:0.58647:3.19:40.5:8:0.1905:0:6.5 -8 43094989 . CA GC 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTACATAAAATATCAAAGTA;RSEQ=CAAAATACATATTATACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:18.3:1:32:1:1:0:40.3:6:1:0:7.3 0/1:21:2:0,2:11,8:0.0952:2,0:34:0:32.3:1:0.21429:0:27:4:0.1:0:6 -8 43094990 . A C 92 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2663;SOR=Inf;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CAAAATACATATTATACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:18.7:1:30.3:1:1:0:40.3:6:1:0:7.3 0/1:21:9:5,4:4,3:0.4286:2,2:25.4:1:29.3:1:1:1.06235:35.6:8:0.4444:0:4.8 -8 43094991 . CA TC 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01087;SOR=0;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=AAATACATATTATACACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:24:0:32.5:1:1:0:44:4:0.6667:0:6 0/0:21:0:0,0:11,9:0:2,0:23.7:1:31.7:1:1:0:35.9:40:0.9524:0:5.3 -8 43094995 . A C 77 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80777;LSEQ=AAAATATCAAAGTACACAAA;RSEQ=TACATATTATACACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:7:0:30:0:1:0:33:2:0.3333:0:8 0/1:21:6:3,3:1,3:0.2857:2,2:29.3:1:29.8:1:0.57143:2.69:43.3:5:0.25:0:5.2 -8 43094997 . ACA GTG 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATATCAAAGTACACAAAAT;RSEQ=TATTATACACTGTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:21:1:27.7:1:1:0:40.3:6:1:0:6.7 0/1:18:2:1,1:7,8:0.1111:2,2:30:0:31.5:1:1:1.13:36:4:0.125:0:4 -8 43094998 . C T 99 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=ATATCAAAGTACACAAAATA;RSEQ=ATATTATACACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:21.3:1:29.3:1:1:0:40.3:6:1:0:6.7 1/0:18:11:6,5:0,0:0.6111:0,2:26.4:1:28.8:1:1:0:35.5:10:0.7143:0:4.5 -8 43095000 . T G 33 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01186;SOR=0;LSEQ=ATCAAAGTACACAAAATACA;RSEQ=ATTATACACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:29:0:33:1:1:0:44:4:0.6667:0:6 0/0:20:0:0,0:7,9:0:2,0:23.6:1:29.8:1:1:0:38.5:32:0.8421:0:4 -8 43095017 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATATTATACACTGTACAT;RSEQ=AAATATCAAAGTATGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:12:0:22.5:1:1:0:44:1:1:0:6 0/1:22:2:1,1:10,10:0.0909:2,2:14:0:30:1:1:1:36:4:0.0909:0:4 -8 43095019 . A T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATTATACACTGTACATAA;RSEQ=ATATCAAAGTATGCAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10:0:29:1:1:0:44:4:1:0:6 0/1:22:2:0,2:11,9:0.0909:2,0:8.5:1:28.5:1:0.47619:0:27:4:0.0909:0:5 -8 43095023 . T C 30 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00362;SOR=0;LSEQ=TATACACTGTACATAAAATA;RSEQ=CAAAGTATGCAAAACATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:30.5:1:1:0:44:4:1:0:6 0/0:22:0:0,0:11,11:0:2,0:5.4:1:29.4:1:1:0:37.7:44:1:0:3.4 -8 43095064 . CT AA 29 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TACTGCACATAAAATATCAA;RSEQ=TACACGAAGTATATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:0:30.8:1:1:0:51:4:1:0:6 1/0:4:2:1,1:1,0:0.5:0,2:24:0:29.5:1:1:0:50:4:0.5:0:6 -8 43095069 . A C 48 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACATAAAATATCAACTTAC;RSEQ=CGAAGTATATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:0:32:1:1:0:51:4:1:0:6 1/0:4:3:2,1:0,0:0.75:0,2:28.7:1:30.7:1:1:0:52.7:6:0.75:0:6.3 -8 43095071 . G A 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAATATCAACTTACAC;RSEQ=AAGTATATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30:0:31:1:1:0:51:4:1:0:6 1/1:4:4:2,2:0,0:1:0,2:28.5:1:30:1:1:0:46.5:8:1:0:5.8 -8 43095073 . A G 48 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATATCAACTTACACGA;RSEQ=GTATATATTATATACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:0:32.5:1:1:0:51:4:1:0:6 1/0:4:3:2,1:0,1:0.75:0,2:32:1:30.7:1:1:0:52.7:6:0.75:0:6.3 -8 43095079 . T G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATCAACTTACACGAAGTATA;RSEQ=ATTATATACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:32:0:31:1:1:0:51:4:1:0:6 0/1:9:2:1,1:3,4:0.2222:2,2:5:0:32:0:1:1.29:22:4:0.2222:0:1.5 -8 43095083 . A C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09091;SOR=0;LSEQ=ACTTACACGAAGTATATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:0:33:0:1:0:51:4:1:0:6 0/1:10:2:1,1:2,3:0.2:2,2:23.5:1:30:1:1:1.41:50:4:0.2:0:6 -8 43095087 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACGAAGTATATATTATAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24:0:30.5:1:1:0:51:4:1:0:6 0/1:10:2:1,1:4,4:0.2:2,2:13:0:30.5:1:1:1:60:4:0.2:0:5 -8 43095095 . T A 59 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=TATATATTATATACTGTACA;RSEQ=AAAATATCAAAGTACACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:32:0:1:0:51:4:1:0:6 0/1:10:4:3,1:2,4:0.4:2,2:13.8:1:29.8:1:0.52381:4.92:45.5:8:0.4:0:5.3 -8 43095111 . A C 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCGAATATATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:2,1:1,1:0.5:2,2:22:1:30.3:1:1:1.73:22.7:6:0.5:0:2 -8 43095114 . G A 46 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAATATCAAAGTACACC;RSEQ=AATATATATTATATACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:3:2,1:2,3:0.375:2,2:8.7:1:29.3:1:1:2.60:32.3:6:0.375:0:6 -8 43095115 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATATCAAAGTACACCG;RSEQ=ATATATATTATATACTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:3,4:0.2222:2,2:17:0:33:0:1:1.29:60:4:0.2222:0:5 -8 43095125 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACACCGAATATATATT;RSEQ=TATACTGAACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:2:1,1:2,2:0.25:2,2:7:0:33.5:1:1:1:60:4:0.2857:0:5 -8 43095133 . A T 38 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATATATATTATATACTG;RSEQ=ACATAAAATATCAAATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:0.6:2,2:17:1:24:1:1:1.7321:40:2:0.5:0:6.3 -8 43095138 . A G 47 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATATTATATACTGAACAT;RSEQ=AAATATCAAATCACACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,1:0.75:0,2:25.3:1:29.7:1:1:0:40.7:6:0.75:0:7.3 -8 43095144 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATACTGAACATAAAATA;RSEQ=CAAATCACACATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:30.5:1:29.5:1:1:0:49:4:0.5:0:7.5 -8 43095149 . TC GT 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGAACATAAAATATCAAA;RSEQ=ACACATATTATATATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:36.5:1:29.3:1:1:0:49:4:0.6667:0:6.5 -8 43095167 . A C 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13267;SOR=0.27479;LSEQ=AATCACACATATTATATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:11,9:0.1304:2,2:8:1:33:0:1:1.60:45.7:6:0.1304:0:6 0/1:77:3:3,0:43,29:0.039:2,0:6.3:1:31.3:1:0.27892:0:47.7:6:0.039:0:5 -8 43095171 . A G 96 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19761;SOR=Inf;LSEQ=ACACATATTATATATTATAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:9.7:1:29.3:1:1:0:48.2:27:1:0:5.4 0/1:98:8:4,4:49,39:0.0816:2,2:11.8:1:32.3:1:1:1.2534:55.3:16:0.0825:0:4.9 -8 43095172 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACATATTATATATTATATA;RSEQ=TGTACATAAAATATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:10.7:1:32.9:1:1:0:48.2:56:1:0:5.4 0/1:102:2:1,1:55,44:0.0196:2,2:8.5:1:29.5:1:1:1.24721:47:4:0.0198:0:6.5 -8 43095174 . G C 74 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58302;SOR=Inf;LSEQ=CATATTATATATTATATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:12.7:1:32.9:1:1:0:48.2:56:1:0:5.4 0/1:109:5:3,2:58,45:0.0459:2,2:12.2:1:32:1:1:1.16:50:10:0.0459:0:7.2 -8 43095175 . T C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18076;SOR=0.24189;LSEQ=ATATTATATATTATATACTG;RSEQ=ACATAAAATATCAAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:14,12:0.0714:2,2:17:0:34.5:1:1:1.16024:39:4:0.0714:0:5 0/1:111:2:1,1:59,49:0.018:2,2:17:0:31.5:1:1:1.20204:60:4:0.0182:0:7 -8 43095177 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16411;SOR=0.22542;LSEQ=ATTATATATTATATACTGTA;RSEQ=ATAAAATATCAAAGTACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:14,12:0.0714:2,2:19:0:29.5:1:1:1.16024:46:4:0.0714:0:7.5 0/1:119:2:1,1:64,53:0.0168:2,2:10:1:29:1:1:1.20562:44.5:4:0.0169:0:7 -8 43095178 . A G 52 v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02074;SOR=0.07074;LSEQ=TTATATATTATATACTGTAC;RSEQ=TAAAATATCAAAGTACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:1,2:14,11:0.1071:2,2:15.7:1:33.3:1:0.58333:2.46268:55.3:6:0.1071:0:7.3 0/0:122:1:0,1:67,54:0.0082:2,0:11:0:28:0:0.45082:0:51:2:0.0082:0:4 -8 43095179 . T A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2339;SOR=0.33093;LSEQ=TATATATTATATACTGTACA;RSEQ=AAAATATCAAAGTACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:14,12:0.0714:2,2:21:0:22:1:1:1.16024:39:1:0.037:0:5 0/1:122:3:3,0:62,53:0.0246:2,0:17.7:1:28.7:1:0.25141:0:46:6:0.0246:0:5.3 -8 43095180 . A T 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.81917;SOR=0.84995;LSEQ=ATATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:4,5:11,8:0.3214:2,2:20.2:1:29.9:1:0.68913:1.6853:58.8:18:0.3214:0:5.7 0/1:129:37:20,17:48,41:0.2868:2,2:18.1:1:29.3:1:1:1.00:53.8:74:0.2868:0:6.1 -8 43095181 . A T 26 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.43189;SOR=0.4059;LSEQ=TATATTATATACTGTACATA;RSEQ=AATATCAAAGTACACCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:1,0:14,13:0.0357:2,0:23:0:30:0:1:0:23:2:0.037:0:6 0/1:136:2:1,1:70,64:0.0147:2,2:9.5:1:26:1:1:1.09302:26.5:4:0.0148:0:7 -8 43095186 . T C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83547;SOR=0.86266;LSEQ=TATATACTGTACATAAAATA;RSEQ=CAAAGTACACCAAATACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:13:6,7:9,6:0.4643:2,2:26.8:1:32.3:1:0.70508:1.71491:54.1:26:0.4643:0:6.2 0/1:145:62:35,27:39,36:0.4276:2,2:20.5:1:30.7:1:0.61075:1.20:51:30:0.4196:0:5.8 -8 43095187 . C G 98 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.35801;SOR=Inf;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:25.7:1:32.5:1:1:0:48.2:56:1:0:5.4 0/1:145:9:5,4:69,60:0.0621:2,2:13:1:31:1:1:1.09:37.7:18:0.0657:0:6.2 -8 43095190 . A C 32 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02295;SOR=0;LSEQ=TACTGTACATAAAATATCAA;RSEQ=GTACACCAAATACATATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:11,11:0.0714:2,2:32:0:32:1:1:1:46:4:0.0741:0:7.5 0/0:154:0:0,0:78,70:0:2,0:21.2:1:30.2:1:1:0:47.6:36:0.96:0:5.4 -8 43095191 . G TC 27 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.02295;SOR=0;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACCAAATACATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:11,11:0.0714:2,2:21:0:27.8:1:1:1:57:4:0.0741:0:5 0/0:154:0:0,0:78,70:0:2,0:21.2:1:30.2:1:1:0:47.6:36:0.96:0:5.4 -8 43095192 . T C 33 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0227;SOR=0;LSEQ=CTGTACATAAAATATCAAAG;RSEQ=ACACCAAATACATATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:14,12:0.0714:2,2:34:0:33.5:1:1:1.16024:46:4:0.0714:0:7.5 0/0:155:0:0,0:80,68:0:2,0:23.3:1:29:1:1:0:47.3:296:0.9548:0:5.6 -8 43095193 . A T 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTACATAAAATATCAAAGT;RSEQ=CACCAAATACATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:31.8:1:29.5:1:1:0:48.2:56:1:0:5.4 0/1:157:2:1,1:82,72:0.0127:2,2:35:0:30:1:1:1.13794:47:4:0.0128:0:8 -8 43095194 . CA C 117 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.21753;LSEQ=GTACATAAAATATCAAAGTA;RSEQ=CCAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:1,1:0.069:2,2:25:0:33.5:1:1:1:46:4:0.069:0:3 0/1:157:13:7,6:8,4:0.0828:2,2:27.7:1:31.8:1:0.68817:1.67739:44.7:26:0.0844:0.0127:4.4 -8 43095195 . A C 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45294;SOR=1.40164;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:22:12,10:1,1:0.7586:2,2:33.2:1:31.7:1:1:1.19:47.4:44:0.7586:0:5.7 1/1:157:128:67,61:8,4:0.8153:2,2:26:1:30.4:1:0.38197:1.81337:48.5:63:0.8182:0:5.4 -8 43095196 . C T 70 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,12:0:2,0:32.7:1:31.5:1:1:0:48:52:1:0:5.5 0/1:157:5:4,1:79,72:0.0318:2,2:17:1:30.4:1:0.37212:3.62:45:10:0.0325:0:6.2 -8 43095197 . C A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,13:0:2,0:33.2:1:32:1:1:0:48.1:54:1:0:5.5 0/1:159:2:1,1:83,73:0.0126:2,2:38:0:29.5:1:1:1.13606:47:4:0.0127:0:8 -8 43095199 . A T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAAATATCAAAGTACACCA;RSEQ=ATACATATTATATACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,13:0:2,0:33.2:1:30.3:1:1:0:48.1:54:1:0:5.5 0/1:163:3:2,1:84,76:0.0184:2,2:26:1:30.3:1:1:1.80:46:6:0.0186:0:6.3 -8 43095200 . A G 51 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAATATCAAAGTACACCAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,13:0:2,0:33:1:30.7:1:1:0:48.1:54:1:0:5.5 0/1:163:3:2,1:83,75:0.0184:2,2:32.7:1:32.7:1:1:1.80:48:6:0.0185:0:5.7 -8 43095202 . ACA CCAAAGCATG 30 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02214;SOR=0;LSEQ=AATATCAAAGTACACCAAAT;RSEQ=TATTATATACTGTACATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:37:0:30.1:1:1:1.07415:39:4:0.069:0:5 0/0:163:0:0,0:85,77:0:2,0:27.2:1:29:1:1:0:47.4:80:0.9938:0:5.5 -8 43095203 . C T 215 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06073;SOR=11.66747;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:27:14,13:0,0:0.931:0,2:32.1:1:29.7:1:1:0:48.1:54:1:0:5.5 1/1:162:161:84,77:0,0:0.9938:0,2:27.4:1:29.4:1:1:0:47.5:322:1:0:5.5 -8 43095205 . T G 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAAAGTACACCAAATACA;RSEQ=ATTATATACTGTACATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:0:2,0:31.3:1:28.8:1:1:0:47.4:28:1:0:5.4 0/1:169:4:3,1:86,79:0.0237:2,2:24:1:31.8:1:0.62267:2.74:46.5:8:0.0238:0:7.3 -8 43095206 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAAGTACACCAAATACAT;RSEQ=TTATATACTGTACATGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:0:2,0:30.7:1:29.2:1:1:0:47.4:58:1:0:5.4 0/1:169:2:1,1:88,79:0.0118:2,2:29:0:33:1:1:1.11321:58.5:4:0.0119:0:6.5 -8 43095208 . T C 112 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.93428;LSEQ=AAAGTACACCAAATACATAT;RSEQ=ATATACTGTACATGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:29.5:1:33:1:1:1.07415:46:4:0.069:0:3 0/1:170:11:5,6:82,73:0.0647:2,2:30.5:1:32.5:1:0.75836:1.34551:41.9:22:0.0655:0:4.5 -8 43095209 . A T 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55302;SOR=0.77614;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTGTACATGAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:16:8,8:7,6:0.5517:2,2:26.4:1:29.6:1:1:1.16047:49:32:0.5517:0:6.2 0/1:170:83:45,38:44,40:0.4882:2,2:23.7:1:29.8:1:0.87712:1.08:51:40.5:0.485:0:5.8 -8 43095213 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACCAAATACATATTATAT;RSEQ=CTGTACATGAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:24.5:1:28.8:1:1:0:45.7:62:1:0:5.4 0/1:170:2:1,1:89,79:0.0118:2,2:28:1:30:1:1:1.12579:44.5:4:0.0118:0:6.5 -8 43095215 . T G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCAAATACATATTATATAC;RSEQ=GTACATGAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:23.3:1:30.2:1:1:0:45.7:62:1:0:5.4 0/1:170:2:1,1:88,79:0.0118:2,2:22:1:29:1:1:1.11321:60:4:0.0118:0:7.5 -8 43095216 . G C 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11839;SOR=0.43516;LSEQ=CCAAATACATATTATATACT;RSEQ=TACATGAAATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:4,2:12,13:0.1935:2,2:17:1:30:1:0.65394:2.11:35.3:12:0.1935:0:4 0/1:170:16:10,6:80,74:0.0941:2,2:27.9:1:30.6:1:0.44566:1.54:39.4:32:0.0958:0:5.4 -8 43095221 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACATATTATATACTGTACA;RSEQ=GAAATATCAAAGTACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:19:1:30:1:1:0:45.7:62:1:0:5.4 0/1:169:2:1,1:88,79:0.0118:2,2:14:0:32.5:1:1:1.11321:38:4:0.0118:0:4.5 -8 43095223 . A T 26 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATATTATATACTGTACATG;RSEQ=AATATCAAAGTACACCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:17.4:1:29.3:1:1:0:45.7:62:1:0:5.4 0/1:169:2:1,1:87,79:0.0118:2,2:12:0:26.5:1:1:1.10063:47:4:0.012:0:8 -8 43095224 . A T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATTATATACTGTACATGA;RSEQ=ATATCAAAGTACACCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:16.5:1:29:1:1:0:45.7:30:1:0:5.4 0/1:168:2:1,1:87,78:0.0119:2,2:27.5:1:27.5:1:1:1.11465:44.5:4:0.012:0:6.5 -8 43095227 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTATATACTGTACATGAAAT;RSEQ=TCAAAGTACACCAAATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:14.1:1:28.5:1:1:0:45.7:62:1:0:5.4 0/1:168:2:1,1:87,79:0.0119:2,2:8:0:32:1:1:1.10063:43:4:0.012:0:3 -8 43095229 . C G 89 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.63783;SOR=0.65228;LSEQ=ATATACTGTACATGAAATAT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:15,13:0.0645:2,2:8.5:1:30.5:1:1:1.14834:39:4:0.0645:0:5 0/1:163:7:4,3:78,74:0.0429:2,2:21.7:1:32:1:1:1.26:50.9:14:0.0432:0:6.4 -8 43095230 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATACTGTACATGAAATATC;RSEQ=AAGTACACCAAATACATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:11.7:1:29.1:1:1:0:45.7:62:1:0:5.4 0/1:160:2:1,1:82,76:0.0125:2,2:25.5:1:32:1:1:1.07841:28:4:0.0127:0:7 -8 43095234 . T A 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05236;SOR=0.07744;LSEQ=CTGTACATGAAATATCAAAG;RSEQ=ACACCAAATACATATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,10:0.0909:2,2:17:0:32:0:1:1:21:4:0.0909:0:4 0/0:134:1:1,0:68,65:0.0075:2,0:1:0:26:0:1:0:60:2:0.0075:0:5 -8 43095235 . A T 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12462;SOR=2.47983;LSEQ=TGTACATGAAATATCAAAGT;RSEQ=CACCAAATACATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:5,5:3,4:0.5882:2,2:12.8:1:28.5:1:1:1.31:46.6:20:0.5882:0:5.7 1/0:87:68:32,36:8,6:0.7816:2,2:21.3:1:29.7:1:0.56518:1.49257:46.3:136:0.7816:0:6.7 -8 43095237 . A C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1469;SOR=0.22347;LSEQ=TACATGAAATATCAAAGTAC;RSEQ=CCAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:14:0:32.5:1:1:1:21:4:0.1667:0:4 0/1:72:3:2,1:29,34:0.0417:2,2:22.7:1:30.7:1:0.59692:2.32:51.3:6:0.0448:0:8 -8 43095238 . C T 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATGAAATATCAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:18.5:1:31.3:1:1:0:43.2:20:1:0:6.3 0/1:67:3:2,1:29,35:0.0448:2,2:8.7:1:31.3:1:0.59232:2.38:60:6:0.0455:0:5.7 -8 43095239 . C A 168 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18573;SOR=0;LSEQ=CATGAAATATCAAAGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:21.9:1:29.4:1:1:0:39:16:1:0:6.4 1/0:64:48:22,26:4,4:0.75:2,2:22.7:1:30.2:1:1:1.17828:43.3:96:0.8:0:6.9 -8 43095242 . A C 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68634;SOR=1.49093;LSEQ=GAAATATCAAAGTACACCAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:0.625:2,2:21.8:1:30.8:1:1:2.60168:47.4:10:0.625:0:7.6 1/0:63:45:19,26:7,6:0.7143:2,2:20.5:1:32.2:1:0.53517:1.58344:43.2:90:0.7627:0:7 -8 43095245 . C T 169 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:15.9:1:28.5:1:1:0:39:16:1:0:6.4 1/1:62:57:26,31:0,0:0.9194:0,2:16.8:1:29:1:1:0:45.4:114:1:0:6.9 -8 43095249 . T G 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAAGTACACCAAATACATA;RSEQ=TATATACTGTACATAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:11.9:1:29.6:1:1:0:39:16:1:0:6.4 0/1:59:4:2,2:24,31:0.0678:2,2:17:1:31.5:1:1:1.29:54.5:8:0.069:0:6.5 -8 43095261 . C G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31642;SOR=0.23481;LSEQ=AATACATATTATATACTGTA;RSEQ=ATAAAAAGCAACGTACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:0.2:2,0:7:0:33:0:1:0:60:2:0.2:0:7 0/1:38:2:1,1:15,21:0.0526:2,2:7:0:33.5:1:1:1.39:36.5:4:0.0526:0:7 -8 43095262 . A C 48 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATACATATTATATACTGTAC;RSEQ=TAAAAAGCAACGTACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:5:1:30.8:1:1:0:44.5:8:1:0:6.8 0/1:37:3:2,1:13,21:0.0811:2,2:6:0:30.7:1:0.55405:3.13:55:6:0.0811:0:6.7 -8 43095283 . A C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAAAAAGCAACGTACACAAA;RSEQ=TATATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:0,2:0,1:0.5:0,0:20:1:32:1:1:0:27:4:0.6667:0:5 -8 43095885 . C T 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAAAATTACAGAAAATA;RSEQ=ATATTATATACTGTATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:6:0:30:0:1:0:40:2:1:0:2 1/0:10:6:5,1:2,2:0.6:2,2:5.2:1:26.8:1:0.5:4.17:34.2:5:0.5556:0:4.7 -8 43095890 . T TATATACTGTATATAAAATATCAAAGTAGCCCAAAGTATGTATC 98 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.35747;SOR=Inf;LSEQ=AAATTACAGAAAATACATAT;RSEQ=ATATACTGTATATAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:3.8:1:29.4:1:1:0:46.8:38:1:0:4.4 0/1:106:10:6,4:54,42:0.0943:2,2:22.5:1:29.8:1:1:1.16:39.4:20:0.0962:0.0943:3.1 -8 43095891 . A T 85 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35384;SOR=Inf;LSEQ=AATTACAGAAAATACATATT;RSEQ=TATACTGTATATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,9:0:2,0:4.2:1:29.9:1:1:0:45.9:38:0.95:0:4.3 0/1:106:8:5,3:52,40:0.0755:2,2:8.3:1:28.4:1:1:1.28:37.3:16:0.0769:0:6.9 -8 43095895 . A G 34 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGAAAATACATATTATAT;RSEQ=CTGTATATAAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:8:1:29.8:1:1:0:45.8:44:1:0:4.5 0/1:110:2:1,1:61,46:0.0182:2,2:9:0:34:0:1:1.3226:54:4:0.0189:0:8 -8 43095897 . T A 29 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43161;SOR=0.40353;LSEQ=AGAAAATACATATTATATAC;RSEQ=GTATATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:11,11:0.0435:2,0:10:0:31:0:1:0:24:2:0.0435:0:6 0/1:112:2:1,1:62,47:0.0179:2,2:15:0:29:1:1:1.31581:40.5:4:0.0182:0:6 -8 43095898 . G C 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAAATACATATTATATACT;RSEQ=TATATAAAATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:10.4:1:32.7:1:1:0:45.1:46:1:0:4.6 0/1:113:4:2,2:62,46:0.0354:2,2:15.3:1:31:1:1:1.34417:34:8:0.0357:0:7.5 -8 43095899 . T G 50 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAAATACATATTATATACTG;RSEQ=ATATAAAATATCAAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:11.3:1:29.3:1:1:0:45.1:46:1:0:4.6 0/1:115:3:1,2:64,46:0.0261:2,2:14:0:31.7:1:0.57358:2.75756:48:6:0.0265:0:7 -8 43095901 . T C 154 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.16582;SOR=3.33003;LSEQ=AATACATATTATATACTGTA;RSEQ=ATAAAATATCAAAGTACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:0,2:12,9:0.087:2,0:13.5:1:31.5:1:0.21739:0:24.5:4:0.087:0:6 0/1:124:30:17,13:42,31:0.2419:2,2:13.8:1:31.4:1:1:1.03572:38.7:60:0.2439:0:6.2 -8 43095903 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACATATTATATACTGTATA;RSEQ=AAAATATCAAAGTACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:13.6:1:30.1:1:1:0:43.2:50:1:0:4.7 0/1:128:2:1,1:71,55:0.0156:2,2:18:0:30.5:1:1:1.2883:29:4:0.0157:0:6.5 -8 43095904 . A G 86 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59817;SOR=Inf;LSEQ=ACATATTATATACTGTATAT;RSEQ=AAATATCAAAGTACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:14.1:1:29.6:1:1:0:43.2:50:1:0:4.7 0/1:132:7:4,3:72,53:0.053:2,2:15.7:1:30.9:1:1:1.01873:30.3:14:0.053:0:6.7 -8 43095906 . A T 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATTATATACTGTATATAA;RSEQ=ATATCAAAGTACACAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:15.2:1:30.8:1:1:0:43.2:50:1:0:4.7 0/1:138:2:0,2:79,57:0.0145:2,0:20:0:27:1:0.181:0:32:4:0.0146:0:8 -8 43095910 . TC AG 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATATACTGTATATAAAATA;RSEQ=AAAGTACACAAAATATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:16.9:1:31.1:1:1:0:43.2:50:1:0:4.7 0/1:139:2:1,1:78,59:0.0144:2,2:26:0:32:1:1:1.31933:51:4:0.0146:0:6 -8 43095911 . C G 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.36972;SOR=1.59173;LSEQ=ATATACTGTATATAAAATAT;RSEQ=AAAGTACACAAAATATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:4,4:7,6:0.3478:2,2:17.9:1:31.9:1:1:1.15812:55.5:16:0.3478:0:4 0/1:137:63:32,31:45,27:0.4599:2,2:18.8:1:31.1:1:0.22254:1.60875:45.3:30.5:0.4586:0:5.2 -8 43095914 . A G 64 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTGTATATAAAATATCAA;RSEQ=GTACACAAAATATGTATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,11:0:2,0:20.5:1:30.8:1:1:0:43.7:44:0.9565:0:4.9 0/1:138:4:2,2:75,57:0.029:2,2:27.8:1:32:1:1:1.31309:48:8:0.0294:0:7.5 -8 43095915 . G T 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGTATATAAAATATCAAA;RSEQ=TACACAAAATATGTATTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:22:1:32.6:1:1:0:43.5:44:1:0:5.2 0/1:137:4:2,2:74,58:0.0292:2,2:28.8:1:29.3:1:1:1.27355:44:8:0.0292:0:7.3 -8 43095917 . A G 32 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01886;SOR=0;LSEQ=TGTATATAAAATATCAAAGT;RSEQ=CACAAAATATGTATTGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,10:0.0909:2,2:28:0:32.5:1:1:1:48:4:0.0909:0:4.5 0/0:135:0:0,0:69,54:0:2,0:22.3:1:28.8:1:1:0:42.8:246:0.9111:0:5.3 -8 43095919 . A C 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59613;SOR=1.55708;LSEQ=TATATAAAATATCAAAGTAC;RSEQ=CAAAATATGTATTGTATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:2,2:6,6:0.1818:2,2:29:1:31.5:1:1:1:38:8:0.1818:0:6.3 0/1:132:34:21,13:38,37:0.2576:2,2:25.8:1:30.2:1:0.30667:1.57:38:68:0.2615:0:5.2 -8 43095920 . CA TC 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16766;SOR=0.47057;LSEQ=ATATAAAATATCAAAGTACA;RSEQ=AAATATGTATTGTATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:4,4:4,5:0.4:2,2:23.5:1:31.1:1:1:1.23:55.6:16:0.4706:0.05:4.4 0/1:122:29:12,17:30,24:0.2377:2,2:29.3:1:31:1:0.25476:1.75858:44.6:58:0.2566:0:5.8 -8 43095921 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATAAAATATCAAAGTACAC;RSEQ=AAATATGTATTGTATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:4,5:0:2,0:28.6:1:31.2:1:1:0:31.3:18:1:0:5.9 0/1:116:2:1,1:40,26:0.0172:2,2:19:1:29.5:1:1:1.52841:42:4:0.029:0:5 -8 43095923 . AA GG 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAAATATCAAAGTACACAA;RSEQ=TATGTATTGTATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:24.3:1:30.6:1:1:0:42.6:46:1:0:5.4 0/1:118:2:2,0:59,53:0.0169:2,0:37:0:33.5:0:0.49806:0:30:4:0.0171:0:6 -8 43095924 . A C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.77335;SOR=0.82615;LSEQ=AAAATATCAAAGTACACAAA;RSEQ=TATGTATTGTATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:3,2:7,7:0.2174:2,2:29.2:1:33.6:1:1:1.47:24.2:10:0.2174:0:5.8 0/1:118:22:13,9:27,33:0.1864:2,2:26.9:1:30.1:1:0.32184:1.75:38.5:10:0.1802:0:5.1 -8 43095925 . T G 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATATCAAAGTACACAAAA;RSEQ=ATGTATTGTATACTGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,11:0:2,0:24.3:1:30:1:1:0:42.7:44:1:0:5.4 0/1:120:4:1,3:52,49:0.0333:2,2:33:1:32.5:1:0.36292:3.15145:47.8:8:0.0381:0:7.3 -8 43095926 . A G 62 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57467;SOR=0.72596;LSEQ=AATATCAAAGTACACAAAAT;RSEQ=TGTATTGTATACTGTACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:1,0:10,10:0.0455:2,0:35:0:33:0:1:0:24:2:0.0476:0:6 0/1:120:4:2,2:61,55:0.0333:2,2:32:1:31.3:1:1:1.10813:44.3:8:0.0345:0:5.5 -8 43095928 . G A 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62602;SOR=0.68199;LSEQ=TATCAAAGTACACAAAATAT;RSEQ=TATTGTATACTGTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:9,7:1,3:0.7273:2,2:22.2:1:29.8:1:0.58204:3.61:43.9:32:0.7619:0:5.4 1/0:121:78:37,41:25,14:0.6446:2,2:28.2:1:29.7:1:0.11625:1.96722:42:156:0.6555:0:5.8 -8 43095930 . A G 49 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50547;SOR=0.56202;LSEQ=TCAAAGTACACAAAATATGT;RSEQ=TTGTATACTGTACATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:12,9:0.0435:2,0:31:0:34:0:0.45455:0:24:2:0.0455:0:4 0/1:121:3:3,0:60,56:0.0248:2,0:29:1:31:1:0.24626:0:26.7:6:0.0254:0:4 -8 43095932 . T G 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGTACACAAAATATGTAT;RSEQ=GTATACTGTACATAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,10:0:2,0:22.8:1:30.2:1:1:0:42.7:44:1:0:5.4 0/1:124:5:3,2:62,54:0.0403:2,2:19.8:1:29.4:1:1:1.30:48:10:0.0417:0:3.6 -8 43095933 . G A 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37611;SOR=0.57763;LSEQ=AAGTACACAAAATATGTATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:3,3:6,5:0.2727:2,2:26.3:1:30.2:1:1:1.18716:36.5:12:0.2727:0:5.8 0/1:124:22:16,6:26,23:0.1774:2,2:27.1:1:28.7:1:0.19123:2.33:33:44:0.1864:0:5.5 -8 43095935 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GTACACAAAATATGTATTGT;RSEQ=TACTGTACATAAAATATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,10:0:2,0:21.4:1:29.9:1:1:0:42.3:46:0.9583:0:5.2 0/1:124:2:0,2:64,55:0.0161:2,0:23.5:1:32.5:1:0.21983:0:40:4:0.0164:0:7 -8 43095937 . A T 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47933;SOR=1.6246;LSEQ=ACACAAAATATGTATTGTAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:3,3:10,7:0.25:2,2:14.3:1:29.7:1:1:1.40628:54.3:12:0.25:0:5.2 0/1:125:44:18,26:45,34:0.352:2,2:22.7:1:30:1:0.09474:1.90159:44.7:88:0.3607:0:6 -8 43095945 . T A 81 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5911;SOR=Inf;LSEQ=TATGTATTGTATACTGTACA;RSEQ=AAAATATCAAAGTACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:17.3:1:29.8:1:1:0:39.2:54:1:0:5.4 0/1:127:6:4,2:58,62:0.0472:2,2:19.7:1:31.7:1:0.43611:2.13:45.7:12:0.0472:0:5.7 -8 43095948 . A T 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60749;SOR=0.51918;LSEQ=GTATTGTATACTGTACATAA;RSEQ=ATATCAAAGTACACCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:11:1:27.5:1:1:1.0801:27:4:0.0769:0:6 0/1:126:5:2,3:60,61:0.0397:2,2:12.6:1:30.4:1:1:1.47091:39.4:10:0.0403:0:6 -8 43095949 . A G 57 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATTGTATACTGTACATAAA;RSEQ=TATCAAAGTACACCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:16.4:1:30.4:1:1:0:39.2:54:1:0:5.4 0/1:124:4:2,2:58,60:0.0323:2,2:16.5:1:28.5:1:1:1.03:52:8:0.0325:0:5.8 -8 43095950 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGTATACTGTACATAAAA;RSEQ=ATCAAAGTACACCAAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:16:1:29.1:1:1:0:39.2:26:1:0:5.4 0/1:122:2:2,0:58,62:0.0164:2,0:10.5:1:29.5:1:0.2398:0:31.5:4:0.0165:0:4 -8 43095953 . C G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01442;SOR=0.30001;LSEQ=GTATACTGTACATAAAATAT;RSEQ=AAAGTACACCAAATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:5,5:6,6:0.4348:2,2:22.3:1:31.3:1:1:1:39.4:20:0.4348:0:6 0/1:113:21:11,10:42,45:0.1858:2,2:18.2:1:31.4:1:0.81033:1.18:37.7:42:0.1892:0:5 -8 43095956 . A G 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05777;SOR=0.24592;LSEQ=TACTGTACATAAAATATCAA;RSEQ=GTACACCAAATATATATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:2,2:8,8:0.1818:2,2:30:1:31.8:1:1:1:50:8:0.1818:0:6.8 0/1:98:5:1,4:47,44:0.051:2,2:23.2:1:32.2:1:0.36163:4.21632:46:10:0.051:0:6 -8 43095957 . G C 32 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03463;SOR=0;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACCAAATATATATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:8,10:0.0909:2,2:13:1:32.5:1:1:1.24:21:4:0.0909:0:5.5 0/0:94:0:0,0:44,43:0:2,0:12.5:1:31.1:1:1:0:38.7:86:0.9247:0:5.3 -8 43095961 . ACCAAA CAATAC 31 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03921;SOR=0;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=TATATATTATTTACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:10,9:0.0952:2,0:16.5:1:31.7:1:0.47619:0:36:4:0.1:0.0476:5 0/0:83:0:0,0:42,41:0:2,0:12.4:1:28.2:1:1:0:38.8:40.5:1:0:5.4 -8 43095962 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05314;SOR=0.28267;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=CAAATATATATTATTTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:4,4:3,1:0.5333:2,2:21.8:1:30.6:1:0.57576:2.74155:38.6:16:0.5714:0:6 0/1:50:12:6,6:13,24:0.24:2,2:18.3:1:29:1:0.49755:1.82:36.7:11:0.2245:0:5.8 -8 43095963 . C A 99 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.49121;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATATATATTATTTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,4:0.1429:2,2:21.5:1:29:1:1:1.22474:38:4:0.1818:0:6.5 0/1:50:10:4,6:15,24:0.2:2,2:24.3:1:29.9:1:1:1.07:41.3:20:0.2041:0:5.7 -8 43095965 . A G 124 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02727;SOR=Inf;LSEQ=TAAAATATCAAAGTACACCA;RSEQ=ATATATATTATTTACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:21.8:1:29.9:1:1:0:37.7:26:1:0:5.6 0/1:50:16:5,11:14,20:0.32:2,2:11.7:1:31.1:1:0.54928:1.52695:37.3:32:0.32:0:6.2 -8 43095966 . A G 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=1.08939;LSEQ=AAAATATCAAAGTACACCAA;RSEQ=TATATATTATTTACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:7,5:0.0769:2,0:11:0:33:0:0.46154:0:21:2:0.0769:0:7 0/1:48:4:2,2:15,28:0.0833:2,2:23:1:30:1:0.61304:1.84:35:8:0.0833:0:7 -8 43095967 . T G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.32242;SOR=0.41631;LSEQ=AAATATCAAAGTACACCAAA;RSEQ=ATATATTATTTACTGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:21:0:33:1:1:1:57.5:4:0.1429:0:7.5 0/1:47:3:1,2:16,28:0.0638:2,2:16.3:1:32.7:1:1:1.1397:50:6:0.0638:0:6.7 -8 43095970 . A G 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=1.2339;LSEQ=TATCAAAGTACACCAAATAT;RSEQ=TATTATTTACTGTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:7,6:0.0714:2,0:7:0:33:0:1:0:21:2:0.0714:0:7 0/1:46:4:2,2:14,28:0.087:2,2:19:1:29.8:1:0.60192:1.97:35:8:0.087:0:7 -8 43095971 . T G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.04508;SOR=0.18134;LSEQ=ATCAAAGTACACCAAATATA;RSEQ=ATTATTTACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:6,4:0.2857:2,2:25.8:1:32.5:1:0.55944:4.03195:25.8:8:0.2857:0:5.8 0/1:46:3:0,3:16,27:0.0652:2,0:17.3:1:31.7:1:0.5415:0:35.7:6:0.0667:0:5.3 -8 43095973 . T C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.67203;LSEQ=CAAAGTACACCAAATATATA;RSEQ=TATTTACTGTACATAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:6,7:0.0714:2,0:19:0:28:0:1:0:55:2:0.0714:0:6 0/1:41:2:0,2:15,24:0.0488:2,0:15:1:32.5:1:0.52439:0:42.5:4:0.0488:0:5.5 -8 43095975 . A C 98 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03962;SOR=Inf;LSEQ=AAGTACACCAAATATATATT;RSEQ=TTTACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:0:2,0:13.9:1:29.1:1:1:0:37.7:26:0.9286:0:5.6 0/1:30:9:3,6:6,13:0.3:2,2:13.1:1:31:1:1:1.08:38.8:18:0.3:0:5.4 -8 43095977 . T A 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53281;SOR=0;LSEQ=GTACACCAAATATATATTAT;RSEQ=TACTGTACATAAAATATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:4,6:0,0:1:0,2:16.9:1:28.7:1:1:0:37.8:9:1:0:5.9 1/1:21:18:5,13:1,1:0.8571:2,2:16.1:1:29.8:1:0.52105:2.46307:37.3:36:0.8571:0:6.1 -8 43095979 . A T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35783;SOR=0.40221;LSEQ=ACACCAAATATATATTATTT;RSEQ=CTGTACATAAAATATCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:3,4:0.3:2,2:10.7:1:31.7:1:1:1.44135:53.3:6:0.3:0:7 0/1:21:3:1,2:5,13:0.1429:2,2:10.7:1:30.7:1:1:1.28:41:6:0.1429:0:7.3 -8 43095980 . C G 80 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14107;SOR=Inf;LSEQ=CACCAAATATATATTATTTA;RSEQ=TGTACATAAAATATCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:13.9:1:32.7:1:1:0:37.8:20:1:0:5.9 0/1:21:6:2,4:4,11:0.2857:2,2:14:1:31:1:1:1.35:36.7:12:0.2857:0:4.8 -8 43095989 . A T 29 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11067;SOR=0;LSEQ=TATATTATTTACTGTACATA;RSEQ=AATATCAAACATACCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:3,3:0.25:2,0:9:0:29.5:1:0.46429:0:27:4:0.25:0:6 0/0:15:0:0,0:5,10:0:2,0:7.7:1:30.2:1:1:0:41.6:30:1:0:5.4 -8 43095990 . A T 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27273;SOR=Inf;LSEQ=ATATTATTTACTGTACATAA;RSEQ=ATATCAAACATACCAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:5.4:1:30.5:1:1:0:32.9:16:1:0:5.5 0/1:14:3:2,1:3,8:0.2143:2,2:6.7:1:29:1:0.50549:4.65:33:6:0.2143:0:5.7 -8 43096077 . C T 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TATATACTGTACATAAAATA;RSEQ=CTAAGTACACCAAATACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:21:0:33:0:1:0:49:2:1:0:7 1/0:6:4:4,0:1,1:0.6667:2,0:10:1:30:1:0.33333:0:49.8:8:0.6667:0:8 -8 43096079 . T A 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATACTGTACATAAAATACC;RSEQ=AAGTACACCAAATACATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:30:0:1:0:49:2:1:0:7 1/1:8:8:6,2:0,0:1:0,2:12.1:1:29.3:1:1:0:46.9:16:1:0:8 -8 43096086 . A C 139 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATAAAATACCTAAGTAC;RSEQ=CCAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:9.3:1:30.8:1:1:0:48.8:12:1:0:7.2 1/1:30:30:15,15:0,0:1:0,2:8.9:1:28.5:1:1:0:48.8:14:1:0:6.9 -8 43096094 . C T 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACCTAAGTACACCAAATA;RSEQ=ATATTATATACTCTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:6,9:0,0:1:0,2:10.1:1:28.8:1:1:0:42.7:30:1:0:6.5 1/1:58:58:27,31:0,0:1:0,2:10.9:1:28.5:1:1:0:48.7:116:1:0:6.4 -8 43096095 . A ATATTATATACTCCCAAGGTATATATTCTATACTGTACAAAAAATATCAAAGTACCCAAAGTATG 185 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCTAAGTACACCAAATAC;RSEQ=TATTATATACTCTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:0:2,0:9.9:1:29.3:1:1:0:41.4:34:1:0:6.4 1/1:69:83:32,51:0,0:1:0,2:16.4:1:29.1:1:1:0:45.3:166:1:1:5.6 -8 43096100 . A T 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.80703;SOR=1.18329;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTCTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:3,4:6,10:0.3043:2,2:13.6:1:29.7:1:1:1.24:42.3:14:0.3043:0:6.9 0/1:82:28:9,19:26,27:0.3415:2,2:14.9:1:29.3:1:0.16422:2.01526:45.2:56:0.3415:0:6.5 -8 43096104 . A T 29 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04062;SOR=0;LSEQ=ACACCAAATACATATTATAT;RSEQ=CTCTACATAAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:9,15:0.0769:2,2:16.5:1:29.5:1:1:1.63:33:4:0.0769:0:7.5 0/0:101:0:0,0:44,57:0:2,0:14.4:1:28.7:1:1:0:46.4:202:1:0:5.9 -8 43096106 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCAAATACATATTATATAC;RSEQ=CTACATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:10,16:0:2,0:15.3:1:29.9:1:1:0:40.9:52:1:0:6 0/1:104:2:1,1:44,58:0.0192:2,2:24:1:28.5:1:1:1.31:52:4:0.0192:0:7 -8 43096107 . C A 28 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03939;SOR=0;LSEQ=CCAAATACATATTATATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:19:1:28:1:1:1.74:26:4:0.0741:0:7.5 0/0:107:0:0,0:44,59:0:2,0:16.6:1:31.4:1:1:0:46.2:102:0.9623:0:5.8 -8 43096110 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATACATATTATATACTCTA;RSEQ=ATAAAATATCAAAGTACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:18.4:1:31.7:1:1:0:41.1:54:1:0:6 0/1:108:2:1,1:45,60:0.0185:2,2:13:0:31:1:1:1.33:48:4:0.0187:0:5 -8 43096112 . TA GG 62 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.58344;SOR=Inf;LSEQ=TACATATTATATACTCTACA;RSEQ=AAATATCAAAGTACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:20.3:1:29.3:1:1:0:41.1:26:1:0:6 0/1:108:4:2,2:44,60:0.037:2,2:20:1:31.4:1:1:1.36:56.5:8:0.0377:0:5.5 -8 43096113 . A G 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02542;SOR=3.06827;LSEQ=ACATATTATATACTCTACAT;RSEQ=AAATATCAAAGTACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:18:7,11:3,6:0.6667:2,2:22.7:1:30.5:1:1:1.26:42.3:17:0.68:0:6 1/1:108:93:40,53:4,7:0.8611:2,2:23.2:1:31.3:1:0.75624:1.32:46:92:0.8932:0:5.8 -8 43096116 . A T 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATTATATACTCTACATAAA;RSEQ=TATCAAAGTACACAAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:24:1:30.4:1:1:0:41.1:54:1:0:6 0/1:108:2:0,2:46,60:0.0185:2,0:21:0:28.5:1:0.5064:0:28.5:4:0.0187:0:6 -8 43096119 . T C 32 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.03881;SOR=0;LSEQ=TATATACTCTACATAAAATA;RSEQ=CAAAGTACACAAAATACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:23.5:1:32:1:1:1.74:47.5:4:0.0769:0:6 0/0:108:0:0,0:45,61:0:2,0:27.6:1:29.2:1:1:0:46.2:105:0.9813:0:5.8 -8 43096124 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17846;SOR=0.23931;LSEQ=ACTCTACATAAAATATCAAA;RSEQ=TACACAAAATACATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:8,15:0.0741:2,2:30:0:30.5:1:1:1.83:33:4:0.0741:0:7.5 0/1:108:2:1,1:44,59:0.0185:2,2:22.5:1:29:1:1:1.34:35:4:0.0192:0:5.5 -8 43096125 . T A 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10183;SOR=0.11951;LSEQ=CTCTACATAAAATATCAAAG;RSEQ=ACACAAAATACATATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:29:1:29:1:1:1.74:53.5:4:0.0741:0:4.5 0/0:108:1:0,1:46,61:0.0093:2,0:16:0:25:0:1:0:30:2:0.0093:0:7 -8 43096126 . A T 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00205;SOR=5.40431;LSEQ=TCTACATAAAATATCAAAGT;RSEQ=CACAAAATACATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:18:7,11:3,6:0.6667:2,2:33.9:1:30.1:1:1:1.26:42.3:36:0.6667:0:6 1/1:108:99:43,56:3,6:0.9167:2,2:34:1:29.3:1:0.73003:1.53:46.4:198:0.9167:0:5.8 -8 43096127 . CA GC 32 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49088;SOR=0.49367;LSEQ=CTACATAAAATATCAAAGTA;RSEQ=CAAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:10,16:0.037:2,0:25:0:33.5:0:1:0:21:2:0.037:0:6 0/1:108:2:1,1:45,61:0.0185:2,2:20.5:1:32.3:1:1:1.35:57:4:0.0187:0:2.5 -8 43096128 . A C 85 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02338;SOR=0.24601;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CAAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:2,4:8,12:0.2222:2,2:32.3:1:30.5:1:1:1.31893:43.7:12:0.24:0:5.2 0/1:108:7:3,4:41,56:0.0648:2,2:30.4:1:30.6:1:1:1.02:44:14:0.0667:0:7.1 -8 43096130 . A C 33 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10325;SOR=0.12063;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:24:0:33:1:1:1.74:33:4:0.0741:0:7.5 0/0:107:1:0,1:46,60:0.0093:2,0:26:0:28:0:1:0:24:2:0.0093:0:7 -8 43096131 . A C 83 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.34395;SOR=Inf;LSEQ=ATAAAATATCAAAGTACACA;RSEQ=AATACATATTATATACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:33.4:1:30.3:1:1:0:41.1:54:1:0:5.9 0/1:107:7:3,4:43,57:0.0654:2,2:35:1:29.7:1:1:1.00579:49.9:6:0.0571:0:6.3 -8 43096132 . AA GG 43 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.75174;LSEQ=TAAAATATCAAAGTACACAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:10,16:0.037:2,0:37:0:33:0:1:0:40:2:0.037:0:7 0/1:107:3:1,2:45,58:0.028:2,2:30.3:1:27.7:1:1:1.54556:38.7:6:0.0286:0:6.3 -8 43096133 . A C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13204;SOR=1.99352;LSEQ=AAAATATCAAAGTACACAAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:11:4,7:3,4:0.4074:2,2:36.7:1:32.1:1:1:1.29262:42:22:0.4231:0:5.9 1/0:107:62:31,31:2,3:0.5794:2,2:34.7:1:31.8:1:1:1.49:47.4:61:0.5922:0:5.5 -8 43096136 . C T 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30187;SOR=0.29115;LSEQ=ATATCAAAGTACACAAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:25:9,16:0,1:0.9615:0,2:32.2:1:29.6:1:1:0:41.6:50:0.9615:0:5.6 1/1:107:94:40,54:2,1:0.8785:2,2:32.5:1:28.7:1:0.57698:2.67266:46:93:0.93:0:5.6 -8 43096142 . A C 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1325;SOR=0.29845;LSEQ=AAGTACACAAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:1,2:8,14:0.1154:2,2:17.3:1:33.7:1:1:1.13689:35.3:6:0.1154:0:7.3 0/1:108:4:1,3:44,57:0.037:2,2:28.5:1:29.8:1:0.63343:2.29903:35:8:0.0377:0:6.5 -8 43096144 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTACACAAAATACATATTAT;RSEQ=TACTGTACATAAAATATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,16:0:2,0:25.2:1:30.6:1:1:0:40.6:50:0.9615:0:5.6 0/1:108:2:1,1:44,60:0.0185:2,2:26:0:32.5:1:1:1.36:44:4:0.0187:0:5 -8 43096147 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACAAAATACATATTATATA;RSEQ=TGTACATAAAATATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,17:0:2,0:22.1:1:32.1:1:1:0:40.8:25:1:0:5.6 0/1:108:2:1,1:45,60:0.0185:2,2:23.5:1:29.5:1:1:1.33:56:4:0.0185:0:7 -8 43096148 . T C 29 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03702;SOR=0;LSEQ=ACAAAATACATATTATATAC;RSEQ=GTACATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:8,16:0.0769:2,2:19:1:29.5:1:1:1.94:47.5:4:0.0769:0:6 0/0:107:0:0,0:45,61:0:2,0:20.8:1:30.3:1:1:0:45.6:52:0.9905:0:5.5 -8 43096154 . T A 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07929;SOR=0.21156;LSEQ=TACATATTATATACTGTACA;RSEQ=AAAATATCAAAGTACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:1,2:7,14:0.125:2,2:14:1:29:1:1:1:45:6:0.125:0:6.3 0/1:104:3:1,2:43,58:0.0288:2,2:16:0:29:1:1:1.47737:38.7:6:0.03:0:6.3 -8 43096157 . A T 30 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03396;SOR=0;LSEQ=ATATTATATACTGTACATAA;RSEQ=ATATCAAAGTACACCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:7,15:0.0833:2,2:13:0:30.5:1:1:2.07:53.5:4:0.087:0:4.5 0/0:104:0:0,0:44,60:0:2,0:12.2:1:29.8:1:1:0:45.9:103:1:0:5.4 -8 43096161 . T A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATATACTGTACATAAAATA;RSEQ=CAAAGTACACCAAATTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,16:0:2,0:9.3:1:31:1:1:0:41.5:48:1:0:5.5 0/1:100:3:1,2:41,56:0.03:2,2:9.7:1:30:1:1:1.45892:36.7:6:0.0303:0:6.7 -8 43096162 . C A 45 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.7284;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAAGTACACCAAATTCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:8,15:0.0417:2,0:23:0:32:0:1:0:21:2:0.0417:0:6 0/1:98:3:1,2:39,55:0.0306:2,2:8:0:28.7:1:1:1.41327:40:6:0.0306:0:5.7 -8 43096170 . A C 66 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.44461;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCAAATTCATATTACATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:5.7:1:31:1:1:0:45.7:6:0.75:0:6.7 1/0:9:5:1,4:2,2:0.5556:2,2:1.2:1:28.8:1:0.52381:3.38757:46.6:10:0.5556:0:5.8 -8 43096216 . T G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAAAATTTCAAAGTACACCA;RSEQ=ATACATATTATATGCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:31.5:1:1:0:45.5:4:1:0:2 -8 43096220 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCAAAGTACACCATATA;RSEQ=ATATTATATGCTGTGCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:30.5:1:1:0:45.5:4:1:0:2 -8 43096249 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TGCTGTGCATAAAATATCAA;RSEQ=GTACACAAAGTACATATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:10.5:1:32:1:1:1:33:4:0.5:0:4.5 0/0:2:0:0,0:0,2:0:0,0:16.5:1:30:1:1:0:25.5:4:1:0:5 -8 43096254 . A C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=TGCATAAAATATCAAAGTAC;RSEQ=CAAAGTACATATTATATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:15.5:1:32.5:1:1:1:33:4:0.5:0:4.5 1/1:2:2:0,2:0,0:1:0,0:21.5:1:30.5:1:1:0:25.5:4:1:0:5 -8 43096259 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AAAATATCAAAGTACACAAA;RSEQ=TACATATTATATACCATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:18:0:33.5:1:1:0:33:4:0.5:0:4 0/0:2:0:0,0:0,2:0:0,0:26.5:1:31:1:1:0:25.5:4:1:0:5 -8 43096262 . CA TG 33 d7;v4;MAF0.05;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATATCAAAGTACACAAAGTA;RSEQ=TATTATATACCATACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22:0:33:0:1:1:33:4:0.5:0:3 1/0:2:1:0,1:0,0:0.5:0,0:33:0:29.5:0:1:0:27:2:0.5:0:3 -8 43096274 . C T 31 d7;v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=ACAAAGTACATATTATATAC;RSEQ=ATACATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22:0:31:1:1:1:33:4:0.5:0:3 0/1:4:1:0,1:1,2:0.25:2,0:21:0:30:0:1:0:24:2:0.25:0:6 -8 43096284 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16667;SOR=0;LSEQ=TATTATATACCATACATAAA;RSEQ=TATCAAAGTACACTAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:12:0:31:1:1:1:33:4:0.5:0:4.5 0/0:5:0:0,0:2,3:0:2,0:8.2:1:31.6:1:1:0:31.4:10:1:0:1.8 -8 43096414 . T G 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATACTGTATGTAAAATAT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:11:1:33.5:1:1:0:21:4:0.5:0:5.5 -8 43096423 . C T 61 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTAAAATATTAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:10.5:1:30.8:1:1:1:40.5:8:0.6667:0:4.8 -8 43096426 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATATTAAAGTACACCA;RSEQ=ATACATATTATATACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:2:1,1:3,3:0.25:2,2:18:0:33:1:1:1:31:4:0.2857:0:5 -8 43096430 . C T 91 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:8:8:4,4:0,0:1:0,2:15.8:1:30.6:1:1:0:38.8:16:1:0:4.9 -8 43096436 . A T 80 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:6:3,3:1,1:0.6:2,2:19.2:1:31.2:1:1:1:41.3:12:0.6:0:4.8 -8 43096440 . A T 79 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCAAATACATATTATAT;RSEQ=CTGTACATAAAATATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:6:3,3:2,2:0.6:2,2:20.7:1:30.8:1:1:1:41.3:12:0.6:0:4.8 -8 43096441 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCAAATACATATTATATA;RSEQ=TGTACATAAAATATCAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:3,3:0.2:2,2:22:0:33.5:1:1:1:31:4:0.2:0:5 -8 43096472 . C T 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAATTACACCAAATA;RSEQ=ATATAATATACTATACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:27.5:1:1:0:43:4:1:0:5 -8 43096477 . A TTC 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AAATTACACCAAATACATAT;RSEQ=ATATACTATACATAAAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:1:27.5:1:1:0:43:4:1:0.5:5 -8 43096556 . C T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCAAAGTACACCAGATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:12:0:32:0:1:0:26:2:1:0:8 1/0:5:3:2,1:1,1:0.6:2,2:19.3:1:29.7:1:1:1.73:41.3:6:0.6:0:6 -8 43096562 . A C 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.68606;LSEQ=AAGTACACCAGATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:18:0:33:0:1:0:26:2:0.3333:0:8 0/1:12:3:2,1:3,4:0.25:2,2:22.7:1:28.3:1:1:2.41:41.3:2:0.1818:0:6 -8 43096565 . T C 33 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.07353;SOR=0;LSEQ=TACACCAGATACATATTATA;RSEQ=ACTGTACATAAAATATCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:9:0:33.5:1:1:1.7321:50:4:0.4:0:8 0/0:12:0:0,0:6,6:0:2,0:14.2:1:28.8:1:1:0:42.9:11:1:0:5.8 -8 43096566 . AC CG 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=ACACCAGATACATATTATAT;RSEQ=TGTACATAAAATATCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:7.4:1:29.9:1:1:0:40.9:14:1:0:6.4 0/1:12:2:1,1:5,5:0.1667:2,2:22:0:30.3:1:1:1:60:4:0.1667:0:2 -8 43096567 . C G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.75091;LSEQ=CACCAGATACATATTATATA;RSEQ=TGTACATAAAATATCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:3,3:0.1429:2,0:23:0:34:0:1:0:26:2:0.1429:0:8 0/1:13:3:2,1:4,4:0.2308:2,2:24.3:1:33:1:1:1.88:41.3:6:0.2727:0:6 -8 43096576 . A T 44 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.52923;SOR=Inf;LSEQ=CATATTATATACTGTACATA;RSEQ=AATATCAATGTACACAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:15.1:1:29.9:1:1:0:40.2:8:1:0:6.4 0/1:17:3:1,2:8,6:0.1765:2,2:18:0:28.3:1:0.57647:2.51691:28.7:6:0.1765:0:7.3 -8 43096585 . T G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13689;LSEQ=TACTGTACATAAAATATCAA;RSEQ=GTACACAAAATACATATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:3,4:0.1111:2,0:17:0:34:0:1:0:36:2:0.1111:0:7 0/1:16:2:1,1:6,6:0.125:2,2:26:0:33:1:1:1:42.5:4:0.1333:0:5 -8 43096590 . A C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.90412;LSEQ=TACATAAAATATCAATGTAC;RSEQ=CAAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,0:0.6667:0,2:27.7:1:32:1:1:0:45.5:12:0.6667:0:7 1/0:14:9:5,4:3,1:0.6429:2,2:26.4:1:31.9:1:1:2.24915:42:18:0.6429:0:6.8 -8 43096592 . A C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.5977;LSEQ=CATAAAATATCAATGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:30:0:30:1:1:1.29098:48.5:4:0.2222:0:6.5 0/1:14:2:1,1:6,3:0.1429:2,2:23:0:33:1:1:1.87089:57:4:0.1538:0:6 -8 43096593 . AAA TGG 32 v4;pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14229;SOR=0;LSEQ=ATAAAATATCAATGTACACA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:37:0:32.5:1:1:1.29098:50:4:0.25:0:6 0/0:14:0:0,0:8,6:0:2,0:29.4:1:30.7:1:1:0:39.5:28:1:0:6.6 -8 43096594 . AA GG 68 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11566;SOR=Inf;LSEQ=TAAAATATCAATGTACACAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,2:0:2,0:23.7:1:30.2:1:1:0:35.8:12:1:0:5.8 0/1:14:5:3,2:4,3:0.3571:2,2:30.6:1:29.3:1:1:1.11:40.8:10:0.3571:0:6 -8 43096595 . A C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30888;SOR=0.29632;LSEQ=AAAATATCAATGTACACAAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:1,1:0.375:2,2:28:1:32.7:1:1:1.73:29.7:6:0.6:0:7 0/1:14:2:2,0:3,4:0.1429:2,0:24.5:1:30.5:1:0.44444:0:32:4:0.2222:0:7.5 -8 43096598 . C T 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34783;SOR=Inf;LSEQ=ATATCAATGTACACAAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:4,3:0,0:0.875:0,2:31:1:27.6:1:1:0:40.9:6:0.8571:0:6.6 1/1:15:15:9,6:0,0:1:0,2:26.9:1:29.8:1:1:0:39.3:30:1:0:6.3 -8 43096600 . T A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATCAATGTACACAAAATACA;RSEQ=ATTATATACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:4,2:0.125:2,0:24:0:29:0:1:0:26:2:0.1429:0:8 0/1:16:2:2,0:7,7:0.125:2,0:19.5:1:29.5:1:0.475:0:32:4:0.125:0:7.5 -8 43096604 . A C 89 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66076;SOR=2.04058;LSEQ=ATGTACACAAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,1:0.25:2,2:28:0:32.5:1:1:2.44949:50:4:0.25:0:6 0/1:17:7:4,3:4,1:0.4118:2,2:25:1:31.9:1:0.57576:2.74155:41.3:14:0.4118:0:5.7 -8 43096611 . G C 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.14757;LSEQ=CAAAATACATATTATATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:19:0:25:1:1:1.8258:48.5:1:0.1429:0:6.5 0/1:18:5:2,3:9,4:0.2778:2,2:19:0:32.2:1:0.32598:3.13525:40:10:0.2778:0:6.4 -8 43096612 . T C 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.95205;LSEQ=AAAATACATATTATATACTG;RSEQ=ACATAAAATATCAAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:5,2:0.125:2,0:12:0:34:0:0.375:0:40:2:0.125:0:6 0/1:18:4:2,2:9,5:0.2222:2,2:20:0:31.8:1:1:1.74002:44:8:0.2222:0:6 -8 43096616 . T G 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02435;SOR=0;LSEQ=TACATATTATATACTGTACA;RSEQ=AAAATATCAAAGTACACCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:4,1:0.375:2,2:13.3:1:32:1:0.46429:5.78427:46.7:6:0.375:0:6 0/0:17:0:0,0:6,4:0:2,0:13.7:1:28.1:1:1:0:33.4:9:0.5625:0:6.1 -8 43096617 . A G 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.23909;LSEQ=ACATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:13:0:33.5:1:1:1.8258:48.5:4:0.25:0:6.5 0/1:17:5:2,3:8,4:0.2941:2,2:13:0:31.4:1:0.59276:2.80013:40:10:0.3125:0:6.4 -8 43096637 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATATCAAAGTACACCAA;RSEQ=TACATATTATATACTCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:0.5:2,0:32:1:30:1:1:0:30.5:4:0.5:0:7 -8 43096640 . C T 54 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ATATTATATACTCTATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:3,1:0,0:1:0,2:28.3:1:27:1:1:0:28.3:3:1:0:5.5 -8 43096688 . A C 86 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTGTGCATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:6:4,2:2,2:0.6:2,2:6:0:33.3:1:1:1.86:52.3:12:0.6:0:7 -8 43096697 . G A 69 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACATATTATATACTGT;RSEQ=CATAAAATATCAAAGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:12:5:4,1:4,3:0.4167:2,2:12.8:1:29.8:1:0.57576:2.74:45.2:10:0.4167:0:7 -8 43096700 . T A 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACATATTATATACTGTGCA;RSEQ=AAAATATCAAAGTACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:3:0:28:0:1:0:42:2:1:0:6 0/1:14:4:3,1:6,4:0.2857:2,2:15.5:1:31.3:1:1:1.91:44.8:8:0.2857:0:7.5 -8 43096716 . A C 97 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGCATAAAATATCAAAGTAC;RSEQ=CAAAGTACATATTATATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:17:9:5,4:4,3:0.5294:2,2:29.3:1:30.8:1:1:1.06235:47.3:18:0.5294:0:5.6 -8 43096718 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAGTACATATTATATAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:21:0:30:0:1:0:42:2:1:0:6 0/1:17:2:1,1:8,6:0.1176:2,2:12:0:33:1:1:1.30929:47:4:0.125:0:5 -8 43096720 . A G 47 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAAATATCAAAGTACACAA;RSEQ=GTACATATTATATAGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:23:0:26:0:1:0:42:2:1:0:6 0/1:17:3:1,2:7,4:0.1765:2,2:38:0:30:1:0.53846:3.18702:41.7:6:0.1875:0:6 -8 43096722 . T C 74 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATATCAAAGTACACAAAG;RSEQ=ACATATTATATAGTGTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:25:0:31:0:1:0:42:2:1:0:6 0/1:18:5:3,2:7,5:0.2778:2,2:29:1:32:1:1:1.07:43.8:10:0.2941:0:7 -8 43096724 . CA TG 98 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=ATATCAAAGTACACAAAGTA;RSEQ=TATTATATAGTGTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:18:9:6,3:0,0:0.5:0,2:31.1:1:31.2:1:1:0:47.3:18:0.5294:0:5.4 -8 43096730 . A C 101 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29402;SOR=0.22686;LSEQ=AAGTACACAAAGTACATATT;RSEQ=TATAGTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:5:1:32.7:1:1:0:39:6:0.75:0:1.3 0/1:23:9:5,4:9,4:0.3913:2,2:17.6:1:32.1:1:0.66192:1.75137:37.4:18:0.4091:0:3.7 -8 43096732 . AT GC 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTACACAAAGTACATATTAT;RSEQ=AGTGTACATAAAATATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:11.3:1:30:1:1:0:39.8:8:1:0:2.5 0/1:25:2:1,1:15,7:0.08:2,2:28:1:31.8:1:1:2.07024:60:4:0.087:0:5 -8 43096733 . T C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TACACAAAGTACATATTATA;RSEQ=AGTGTACATAAAATATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:11.8:1:31:1:1:0:39.8:8:1:0:2.5 0/1:25:2:2,0:13,7:0.08:2,0:25:0:32:1:1:0:43.5:4:0.0952:0:3.5 -8 43096735 . G C 92 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5641;SOR=Inf;LSEQ=CACAAAGTACATATTATATA;RSEQ=TGTACATAAAATATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:8:1:32.3:1:1:0:39.3:8:0.8:0:1 0/1:32:8:4,4:17,7:0.25:2,2:21.1:1:30.9:1:0.39704:2.35688:43:16:0.2581:0:6 -8 43096738 . T TACATAAAATATCAAAGTACTCTAAACTATATTCTGTACATAAAATATCAATTAATGAAATCTATGTATTTTATACTGG 73 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGTACATATTATATAGTG;RSEQ=ACATAAAATATCAAAGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:12.4:1:29.4:1:1:0:39.8:10:1:0:2 0/1:35:6:4,2:18,11:0.1714:2,2:26:1:28.5:1:1:1.22:42.5:12:0.1714:0.1714:1.5 -8 43096742 . T A 47 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACATATTATATAGTGTACA;RSEQ=AAAATATCAAAGTACTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:13:1:27.4:1:1:0:39.8:4:1:0:2 0/1:35:3:1,2:21,11:0.0857:2,2:16:0:29.7:1:0.54118:3.66543:41.7:6:0.0882:0:6 -8 43096750 . C G 60 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATAGTGTACATAAAATAT;RSEQ=AAAGTACTCTAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:7:1:32.8:1:1:0:39.3:8:0.8:0:1 0/1:34:4:3,1:17,11:0.1176:2,2:8:0:30:1:1:1.90:44.3:8:0.1212:0:4.5 -8 43096752 . A T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAGTGTACATAAAATATCA;RSEQ=AGTACTCTAAATACATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:4.8:1:30.8:1:1:0:39.8:10:1:0:2 0/1:33:2:1,1:20,11:0.0606:2,2:6:0:31:1:1:1.78367:33:4:0.0606:0:2.5 -8 43096760 . T A 71 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAATATCAAAGTACTC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:1:0,2:15.4:1:30.6:1:1:0:48.2:10:1:0:5.6 -8 43096763 . A C 66 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATATCAAAGTACTCTAA;RSEQ=TACATATTATATACTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:1,3:1,0:0.8:0,2:18.3:1:33:1:0.4:0:45.3:8:0.8:0:5.5 -8 43096766 . C T 48 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACTCTAAATA;RSEQ=ATATTATATACTGTATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:24.3:1:30.7:1:1:0:43.7:6:1:0:6.7 -8 43096772 . A G 52 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACTCTAAATACATATT;RSEQ=TATACTGTATTCAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:21.3:1:33:0:1:0:43.7:6:1:0:6.7 -8 43096782 . TTC CAT 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATACATATTATATACTGTA;RSEQ=AAAATATCAAAGTACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30.8:1:1:0:41.5:4:1:0:6 -8 43096786 . A C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATTATATACTGTATTCA;RSEQ=AATATCAAAGTACACAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:32:1:1:0:41.5:4:1:0:6 -8 43096846 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CTAAATATTAAACTACACCA;RSEQ=ATACATATTATATACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:1.3:1:30.3:1:1:0:44:6:1:0:4.7 0/1:6:2:2,0:3,1:0.3333:2,0:6.5:1:32.5:1:1:0:50:4:0.3333:0:8 -8 43096850 . C T 72 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07537;SOR=Inf;LSEQ=ATATTAAACTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:4.2:1:32.4:1:1:0:42.4:10:1:0:4.4 1/0:8:5:4,1:2,1:0.625:2,2:6.6:1:31.2:1:1:1.83:41.4:10:0.625:0:6.6 -8 43096856 . A C 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14396;SOR=Inf;LSEQ=AACTACACCAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:7.9:1:29.2:1:1:0:36.4:18:1:0:5.2 0/1:19:5:4,1:8,5:0.2632:2,2:8.6:1:30.6:1:0.61485:2.38:49.6:10:0.2632:0:7.6 -8 43096859 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TACACCAAATACATATTATA;RSEQ=ACTGTACATAAAATATCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:10.9:1:29.9:1:1:0:36.4:18:1:0:5.2 0/1:24:2:1,1:15,7:0.0833:2,2:6:0:33.5:1:1:2.07024:45:4:0.0833:0:6 -8 43096861 . C G 96 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07602;SOR=Inf;LSEQ=CACCAAATACATATTATATA;RSEQ=TGTACATAAAATATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:12.9:1:32.4:1:1:0:36.4:18:1:0:5.2 0/1:27:9:7,2:11,7:0.3333:2,2:8.9:1:30.3:1:0.66729:2.16:45.6:8:0.3077:0:6.9 -8 43096865 . A C 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08418;SOR=0;LSEQ=AAATACATATTATATACTGT;RSEQ=CATAAAATATCAAAGTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:14:0:30.5:1:1:1:21:4:0.1429:0:6 0/0:33:0:0,0:18,15:0:2,0:11.8:1:29.5:1:1:0:42:66:1:0:6 -8 43096867 . A G 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.84552;LSEQ=ATACATATTATATACTGTAC;RSEQ=TAAAATATCAAAGTACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:8,6:0.0667:2,0:16:0:30:0:0.46667:0:45:2:0.0667:0:6 0/1:34:4:3,1:16,14:0.1176:2,2:16:0:32.3:1:0.61284:2.56:47.5:8:0.1176:0:6.8 -8 43096870 . A T 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATATTATATACTGTACATA;RSEQ=AATATCAAAGTACACCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:15.7:1:30.7:1:1:0:40.3:30:1:0:5.4 0/1:38:2:1,1:19,17:0.0526:2,2:17:0:30.5:1:1:1.11437:45:4:0.0526:0:6 -8 43096875 . T A 103 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.05519;SOR=Inf;LSEQ=TATATACTGTACATAAAATA;RSEQ=CAAAGTACACCAAATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:19.7:1:30.4:1:1:0:41.4:15:1:0:5.6 0/1:52:11:6,5:21,19:0.2115:2,2:12.5:1:29.8:1:1:1.08:57.5:22:0.2115:0:7.9 -8 43096876 . C G 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.37993;SOR=0.46709;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAAGTACACCAAATACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:8,5:0.1875:2,2:17.7:1:31.3:1:0.55:2.96927:29.7:6:0.1875:0:5.7 0/1:52:5:0,5:28,19:0.0962:2,0:14.2:1:32.4:1:0.01635:0:28:10:0.0962:0:4.4 -8 43096878 . A G 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.2046;LSEQ=ATACTGTACATAAAATATCA;RSEQ=AGTACACCAAATACACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:9,7:0.0588:2,0:27:0:31:0:0.47059:0:45:2:0.0588:0:6 0/1:57:4:3,1:28,25:0.0702:2,2:27:0:32.8:1:0.61741:2.64:47.5:8:0.0702:0:6.8 -8 43096880 . G A 49 v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03313;SOR=0.08422;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACCAAATACACATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:7,7:0.1765:2,2:25:1:31.3:1:1:1.92:33:6:0.1765:0:6.7 0/1:59:1:0,1:30,25:0.0169:2,0:30:0:30:0:0.46429:0:48:2:0.0175:0:8 -8 43096881 . T G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03257;SOR=0.22977;LSEQ=CTGTACATAAAATATCAAAG;RSEQ=ACACCAAATACACATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:4,3:5,5:0.4118:2,2:30:1:32.6:1:1:1.31:47.4:14:0.4118:0:4.3 0/1:59:8:4,4:27,23:0.1356:2,2:31.5:1:32.4:1:1:1.17066:36:16:0.1379:0:4.4 -8 43096883 . CA AC 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACATAAAATATCAAAGTA;RSEQ=CCAAATACACATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:26:1:32.4:1:1:0:42.2:34:1:0:5.7 0/1:59:2:1,1:29,25:0.0339:2,2:33:0:30.8:1:1:1.15692:60:4:0.0345:0:6 -8 43096884 . A C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16841;SOR=0.40752;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCAAATACACATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:7,5:1,2:0.7059:2,2:25.5:1:31.8:1:0.56923:2.61:48.9:24:0.7059:0:5.7 0/1:59:29:18,11:9,13:0.4915:2,2:22.9:1:31.2:1:0.16432:2.32:43:58:0.537:0:6.5 -8 43096885 . C T 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36745;SOR=0.43777;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=CAAATACACATTATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:8,6:0.1765:2,2:26.7:1:30.7:1:0.57647:2.51691:29.7:6:0.1765:0:5.7 0/1:59:5:0,5:30,22:0.0847:2,0:23.2:1:30.6:1:0.01928:0:28:10:0.0877:0:4.4 -8 43096886 . C A 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.70433;SOR=1.33378;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATACACATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:14:8,6:1,2:0.8235:2,2:26.5:1:30.7:1:0.57647:2.52:44.9:28:0.8235:0:5.7 1/1:58:50:29,21:1,6:0.8621:2,2:21.7:1:30.5:1:0.04465:8.02:47.2:100:0.8772:0:6.6 -8 43096889 . A C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02843;SOR=3.41425;LSEQ=AAAATATCAAAGTACACCAA;RSEQ=TACACATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:5,2:5,6:0.3889:2,2:20.1:1:32.3:1:0.36652:2.82:44.6:14:0.3889:0:7.1 1/0:61:42:24,18:7,10:0.6885:2,2:19.9:1:31.8:1:0.38863:1.88:50.5:84:0.7119:0:7.1 -8 43096892 . C T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07623;SOR=2.72821;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ACATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:6,5:0,0:0.5789:0,2:22.1:1:30.1:1:1:0:41.9:22:0.5789:0:6.5 1/0:72:57:30,27:1,1:0.7917:2,2:18.2:1:29.2:1:1:1.11:48.8:114:0.8028:0:6.4 -8 43096893 . A ACATTATAGATACCCAAAGTATG 76 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.59291;SOR=Inf;LSEQ=TATCAAAGTACACCAAATAC;RSEQ=CATTATATACTGTACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:16,15:0:2,0:13.7:1:29.6:1:1:0:46.4:62:1:0:4.9 0/1:147:6:3,3:66,70:0.0408:2,2:17.7:1:29.6:1:1:1.06:48.3:12:0.042:0.0408:2.3 -8 43096894 . C G 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.61339;SOR=0.54633;LSEQ=ATCAAAGTACACCAAATACA;RSEQ=ATTATATACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:0,2:16,15:0.0588:2,0:24:1:33:0:0.48485:0:30:4:0.0588:0:5 0/1:152:5:0,5:74,72:0.0329:2,0:18.6:1:32.8:1:0.05862:0:28:10:0.0333:0:4.4 -8 43096902 . A T 25 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15528;SOR=0.21817;LSEQ=ACACCAAATACACATTATAT;RSEQ=CTGTACATAAAATATCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:2,0:16,17:0.0571:2,0:18:1:29.5:1:0.48571:0:44.5:4:0.0588:0:5 0/1:155:2:0,2:75,76:0.0129:2,0:7:1:25.5:1:0.4969:0:46:4:0.0129:0:3.5 -8 43096913 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATTATATACTGTACATAA;RSEQ=ATATCAAACTACACCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:0:2,0:16:1:30.9:1:1:0:46.8:66:1:0:4.9 0/1:150:2:1,1:74,74:0.0133:2,2:24:0:33:1:1:1:26:4:0.0136:0:6 -8 43096918 . C G 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10803;SOR=2.46267;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAACTACACCAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:19:10,9:4,2:0.76:2,2:24.2:1:32.9:1:0.66087:1.75892:54.7:38:0.76:0:5.4 1/1:124:110:55,55:6,8:0.8871:2,2:22.8:1:31.6:1:0.7781:1.33:51.3:109:0.8862:0:5.2 -8 43096920 . A G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATACTGTACATAAAATATCA;RSEQ=ACTACACCAAATACATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:22.3:1:30.8:1:1:0:53.7:42:1:0:5.3 0/1:118:2:0,2:58,58:0.0169:2,0:24:0:30.5:1:0.49587:0:26:4:0.0169:0:5 -8 43096921 . AC GA 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTGTACATAAAATATCAA;RSEQ=TACACCAAATACATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,8:0:2,0:20.8:1:31.4:1:1:0:55.2:38:0.95:0:5.1 0/1:115:2:1,1:55,58:0.0174:2,2:29:0:31.5:1:1:1.05:25:4:0.0175:0:6 -8 43096922 . C T 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12014;SOR=2.71864;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACCAAATACATATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:9,8:1,0:0.8095:0,2:20.1:1:31.8:1:1:0:56.4:34:0.85:0:5.1 1/1:114:105:51,54:3,2:0.9211:2,2:19.2:1:30.3:1:0.6759:1.58162:51.8:210:0.9375:0:5.2 -8 43096925 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACATAAAATATCAAACTA;RSEQ=ACCAAATACATATTATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:18.6:1:32.8:1:1:0:53.7:42:1:0:5.3 0/1:113:2:1,1:54,57:0.0177:2,2:19:0:31.5:1:1:1.06:20:4:0.0177:0:5 -8 43096926 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACATAAAATATCAAACTAC;RSEQ=CCAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:17.6:1:30.7:1:1:0:53.7:20:1:0:5.3 0/1:113:2:1,1:52,55:0.0177:2,2:31:0:32:0:1:1.06:25:4:0.0179:0:6 -8 43096927 . C T 195 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71677;SOR=1.27952;LSEQ=ACATAAAATATCAAACTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:18:9,9:2,0:0.8571:0,2:16.7:1:29.8:1:0.47895:0:55.5:8:0.8421:0:5.2 1/1:113:100:50,50:2,3:0.885:2,2:14.4:1:29.4:1:1:1.49:51.8:49:0.8991:0:5.2 -8 43096928 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATAAAATATCAAACTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:15.6:1:32.6:1:1:0:53.7:42:1:0:5.3 0/1:113:2:1,1:54,57:0.0177:2,2:29:0:31.5:1:1:1.06:25:4:0.0179:0:6 -8 43096931 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAATATCAAACTACACCAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:13.3:1:30.8:1:1:0:55:19:1:0:5.2 0/1:111:2:1,1:53,56:0.018:2,2:26:0:33:1:1:1.06:25:4:0.0183:0:6 -8 43096934 . C T 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAACTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:10,8:0,0:1:0,2:11.4:1:29.9:1:1:0:56.3:17:1:0:5.2 1/1:95:90:42,48:1,2:0.9474:2,2:9.4:1:29.2:1:1:1.74:52.2:180:0.9474:0.0211:5.3 -8 43096940 . A G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AACTACACCAAATACATATT;RSEQ=TATACTGTACATAAAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:5.4:1:30.2:1:1:0:56.3:36:1:0:5.2 0/1:89:2:1,1:39,47:0.0225:2,2:8:1:33:1:1:1.20:56:4:0.0225:0.0225:1.5 -8 43096944 . A G 50 d7;v4;MAF0.05;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01818;SOR=0;LSEQ=ACACCAAATACATATTATAT;RSEQ=CTGTACATAAAAAATCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:12.3:1:32:1:1:0:46.7:6:1:0:6 0/1:9:1:0,1:2,3:0.1111:2,0:11:0:34:0:1:0:60:2:0.1111:0:3 -8 43096948 . T C 32 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=CAAATACATATTATATACTG;RSEQ=ACATAAAAAATCAAACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:9:0:32.5:1:1:0:40:4:0.6667:0:7.5 0/0:7:0:0,0:3,4:0:2,0:9.6:1:28.7:1:1:0:40.1:14:1:0:5.3 -8 43096976 . C T 31 d7;v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCAAACTACACCAAATA;RSEQ=ATATTATAAACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:0:31:1:1:0:48:4:1:0:2 1/0:2:1:0,1:0,0:0.5:0,0:1:0:24:0:1:0:21:2:1:0:6 -8 43096983 . T TAAACGCCCAAACTATGTATTATATACTGTACATAAAATATGAAAGCACCCAAACATTTATAAA 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.01429;SOR=Inf;LSEQ=ACTACACCAAATACATATTA;RSEQ=AAACTGTACATAAAATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:5:1:29.8:1:1:0:37.9:28:1:0:4.1 0/1:24:9:5,4:6,9:0.375:2,2:30.1:1:28:1:0.67517:1.83:36.3:18:0.375:0.375:3.4 -8 43096984 . A T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53333;SOR=Inf;LSEQ=CTACACCAAATACATATTAT;RSEQ=AACTGTACATAAAATATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:6:1:29.4:1:1:0:37.9:28:1:0:4.1 0/1:26:2:1,1:11,13:0.0769:2,2:6:0:30:1:1:1.17:37:4:0.08:0:2.5 -8 43096995 . A C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53412;SOR=Inf;LSEQ=ACATATTATAAACTGTACAT;RSEQ=AAATATCAAAGTACACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,7:0:2,0:15.1:1:29.2:1:1:0:37.8:34:0.9444:0:4.4 0/1:33:2:1,1:11,17:0.0606:2,2:12:0:33:0:1:1.52:26:4:0.0606:0:5 -8 43097002 . C G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.72521;LSEQ=ATAAACTGTACATAAAATAT;RSEQ=AAAGTACACAAAATACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:10,8:0.0526:2,0:14:0:34:0:1:0:26:2:0.0526:0:7 0/1:34:3:1,2:13,18:0.0882:2,2:9.7:1:30.7:1:1:1.42942:47.3:6:0.0882:0:5.3 -8 43097008 . A T 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.63934;SOR=2.47722;LSEQ=TGTACATAAAATATCAAAGT;RSEQ=CACAAAATACATATTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:11,6:0.0556:2,0:21:0:32:0:0.38889:0:26:2:0.0556:0:4 0/1:31:4:2,2:11,16:0.129:2,2:24:1:29.5:1:1:1.44:25.8:8:0.129:0:5.5 -8 43097010 . A T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1221;SOR=0.35599;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CAAAATACATATTATATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:1,1:0.5:2,2:28.3:1:31.1:1:1:1.87:41.1:18:0.5:0:5 0/1:31:8:3,5:3,4:0.2581:2,2:26:1:29.4:1:1:1.23147:41.4:16:0.2581:0:4.5 -8 43097011 . CA TC 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52551;SOR=Inf;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=AAATACATATTATATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,6:0:2,0:28.3:1:32.3:1:1:0:38.8:30:0.9375:0:4.9 0/1:31:2:1,1:7,12:0.0645:2,2:20:1:29.3:1:1:1.67:47:4:0.0952:0:6.5 -8 43097014 . AA GG 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61813;SOR=0.55879;LSEQ=TAAAATATCAAAGTACACAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,5:0.1111:2,2:36:0:33:1:1:1.54914:30:4:0.125:0:5.5 0/1:31:2:1,1:7,12:0.0645:2,2:37:0:30.5:1:1:1.67:43.5:4:0.0952:0:6 -8 43097015 . A C 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87089;LSEQ=AAAATATCAAAGTACACAAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:5,3:3,3:0.4211:2,2:32.5:1:32.4:1:1:1.61:39:16:0.5714:0:4.5 0/1:31:12:4,8:2,3:0.3871:2,2:30.5:1:32.3:1:1:1.31049:35.8:24:0.6316:0:5.4 -8 43097018 . C T 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84663;LSEQ=ATATCAAAGTACACAAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:5,5:2,0:0.5263:0,2:32.1:1:28.4:1:0.4697:0:37.3:9:0.6:0:5.2 0/1:31:15:4,11:2,1:0.4839:2,2:29:1:28.7:1:0.2451:4.92608:34.2:30:0.7143:0:5.9 -8 43097020 . T C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23256;SOR=Inf;LSEQ=ATCAAAGTACACAAAATACA;RSEQ=ATTATATACTGTACATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:9,9:0:2,0:22.4:1:29.5:1:1:0:34.3:36:0.9474:0:5.3 0/1:22:3:1,2:7,12:0.1364:2,2:9.7:1:31:1:1:1.15862:25.3:6:0.1364:0:7 -8 43097023 . T C 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13662;SOR=0.28086;LSEQ=AAAGTACACAAAATACATAT;RSEQ=ATATACTGTACATAAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:3,3:8,7:0.2609:2,2:25:1:28.8:1:1:1.1356:41.8:5:0.25:0:4.5 0/1:34:3:0,3:11,17:0.0882:2,0:29.3:1:33:1:0.53504:0:33.3:6:0.1:0:5 -8 43097024 . A C 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.66127;LSEQ=AAGTACACAAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:0.087:2,2:27:0:33.5:1:1:1.09544:30:4:0.0909:0:5.5 0/1:34:2:1,1:9,17:0.0588:2,2:28:0:30.5:1:1:1.84:43.5:4:0.0645:0:6 -8 43097028 . A T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26951;SOR=Inf;LSEQ=ACACAAAATACATATTATAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:19.7:1:28.9:1:1:0:34.3:46:1:0:4.8 0/1:35:3:1,2:12,18:0.0857:2,2:35:1:30:1:1:1.32209:42.7:6:0.0882:0:7 -8 43097029 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51301;SOR=Inf;LSEQ=CACAAAATACATATTATATA;RSEQ=TGTACATAAAATATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:19.3:1:32.1:1:1:0:34.3:46:1:0:4.8 0/1:35:2:1,1:13,20:0.0571:2,2:23.5:1:29:1:1:1.52:36:4:0.0571:0:4.5 -8 43097030 . T A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98464;LSEQ=ACAAAATACATATTATATAC;RSEQ=GTACATAAAATATCAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:10,11:0.087:2,0:19:1:30:1:0.47826:0:44:4:0.0952:0:4.5 0/1:35:3:2,1:12,20:0.0857:2,2:22:0:32:0:0.5508:3.22:54.7:6:0.0882:0:4.7 -8 43097031 . G A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51301;SOR=Inf;LSEQ=CAAAATACATATTATATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:18.6:1:31.8:1:1:0:34.3:22:1:0:4.8 0/1:35:2:1,1:12,20:0.0571:2,2:21:0:28:1:1:1.64:43.5:4:0.0571:0:6 -8 43097034 . C T 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86248;LSEQ=AATACATATTATATACTGTA;RSEQ=ATAAAATATCAAAGTACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:10,10:0.1304:2,2:15:1:30.3:1:1:1.94:37.3:6:0.1364:0:5 0/1:35:4:2,2:12,19:0.1143:2,2:18:0:26.3:1:1:1.56:48:3:0.0882:0:4.3 -8 43097036 . T A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.63352;SOR=0.60536;LSEQ=TACATATTATATACTGTACA;RSEQ=AAAATATCAAAGTACACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:0.087:2,2:15:0:31:0:1:1.09544:30:4:0.0909:0:5.5 0/1:37:2:1,1:14,21:0.0541:2,2:16:0:27.5:1:1:1.48:43.5:4:0.0541:0:6 -8 43097042 . A G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62041;SOR=0.56488;LSEQ=TTATATACTGTACATAAAAT;RSEQ=TCAAAGTACACGAAATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:9,10:0.0952:2,0:10:0:29:0:0.47619:0:42:4:0.0952:0:5 0/1:36:2:1,1:13,21:0.0556:2,2:10:0:33.5:1:1:1.59:58:4:0.0556:0:5 -8 43097044 . C G 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.54545;SOR=Inf;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAAGTACACGAAATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:14.8:1:31.4:1:1:0:33.4:40:1:0:5.1 0/1:36:3:1,2:13,20:0.0833:2,2:8.3:1:30.7:1:1:1.29082:37.7:6:0.0833:0:4 -8 43097045 . A C 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.28443;LSEQ=TATACTGTACATAAAATATC;RSEQ=AAGTACACGAAATATATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:39.5:1:31:1:1:1.26772:30:4:0.1111:0:7 0/1:36:5:1,4:12,17:0.1389:2,2:23.6:1:30.4:1:0.62718:2.74789:31.4:10:0.1429:0:6 -8 43097048 . G A 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16324;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACGAAATATATATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:8,6:0.1765:2,2:36.3:1:31:1:0.57647:2.51691:28:6:0.1875:0:6.7 0/1:35:7:2,5:12,16:0.2:2,2:27.1:1:28.6:1:0.67603:1.84301:28.7:14:0.2:0:6 -8 43097052 . A T 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66871;SOR=1.71075;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CGAAATATATATTACATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,0:0.2857:0,2:40:1:30.5:1:1:0:30:4:0.3333:0:7 0/1:17:7:2,5:3,3:0.4118:2,2:30:1:29:1:0.59207:2.32357:28.7:14:0.4375:0:6 -8 43097054 . G A 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.18839;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATATATATTACATACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,1:0.6:0,2:38.7:1:29.3:1:1:0:28.7:6:0.6:0:7.3 1/0:14:9:2,7:2,2:0.6429:2,2:31.9:1:28.8:1:0.53007:3.13792:29.9:8:0.6667:0:6.4 -8 43097056 . A G 64 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27273;SOR=Inf;LSEQ=TAAAATATCAAAGTACACGA;RSEQ=ATATATATTACATACTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,2:0:2,0:31.2:1:27.6:1:1:0:27.2:4:0.8:0:6.2 0/1:16:4:2,2:3,8:0.25:2,2:15:1:32:1:0.56044:2.48:46:8:0.2667:0:6.3 -8 43097057 . A G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAAATATCAAAGTACACGAA;RSEQ=TATATATTACATACTGTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,2:0:2,0:28.8:1:31.8:1:1:0:27.5:8:0.8:0:6.5 0/1:16:2:0,2:5,8:0.125:2,0:31:1:32.5:1:0.52381:0:34:4:0.1538:0:8 -8 43097066 . AC CT 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53333;SOR=Inf;LSEQ=AAGTACACGAAATATATATT;RSEQ=ATACTGTACCTAAAATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,2:0:2,0:24.8:1:30.4:1:1:0:27.6:10:0.7143:0:6.2 0/1:14:2:1,1:3,8:0.1429:2,2:28:0:31.5:0:1:2.45:45:4:0.1429:0:5 -8 43097071 . C G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53333;SOR=Inf;LSEQ=CACGAAATATATATTACATA;RSEQ=TGTACCTAAAATATCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:20.3:1:32.2:1:1:0:27.3:12:0.8571:0:6.3 0/1:14:2:1,1:3,9:0.1429:2,2:24:0:32:1:0.50549:2.74:45:4:0.1429:0:5 -8 43097077 . C A 105 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=ATATATATTACATACTGTAC;RSEQ=TAAAATATCAAAGTACACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,0:0.6667:0,2:17:0:31.3:1:1:0:28:8:0.6667:0:6 1/1:11:11:3,8:0,0:1:0,2:15:1:30.4:1:1:0:32.9:22:1:0:6.1 -8 43097085 . T A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TACATACTGTACCTAAAATA;RSEQ=CAAAGTACACGAAATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:9:0:27.6:1:1:0:27.6:4:1:0:6 0/1:10:3:1,2:2,5:0.3:2,2:9.7:1:29.7:1:1:1.22:42.3:6:0.3:0:5.3 -8 43097119 . C A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACACATTAAATACTGTAC;RSEQ=TAAAATATCAAAATACACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7:0:31:1:1:0:30:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 43097144 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAATACACGAAATA;RSEQ=ATATTATATACTGTACCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:31.5:1:1:0:30:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 43097150 . A C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATACACGAAATACATATT;RSEQ=TATACTGTACCTAAAATATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:33.5:1:1:0:30:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 43830863 . C A 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAAGTCACAGAGTTGAAC;RSEQ=TTCCGTTTCATAGAGTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:1:31.5:1:1:0:40:4:1:0:5 -8 43830868 . G C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACAGAGTTGAACCTTCC;RSEQ=TTTCATAGAGTAGGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:1:32:1:1:0:40:4:1:0:5 -8 43830870 . T A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGAGTTGAACCTTCCGT;RSEQ=TCATAGAGTAGGTTGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:1:30:1:1:0:40:4:1:0:5 -8 43830889 . A T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTCATAGAGTAGGTTGGAA;RSEQ=CACTCATTTTGTAGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:29:1:1:0:40:4:1:0:5 -8 43830895 . A C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTAGGTTGGAAACACTC;RSEQ=TTTTGTAGTATCTGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36.5:1:30:1:1:0:40:4:1:0:5 -8 43831538 . A T 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTCAAGTCACAGAACTGAAC;RSEQ=TCCCCTCACATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:9:1:32:1:1:0:36.3:6:0.75:0:2.3 0/0:2:0:0,0:2,0:0:0,0:11.5:1:32:0:1:0:31.5:4:1:0:1.5 -8 43831564 . G A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68134;LSEQ=TCACATAGAGCAGTTGTGCA;RSEQ=CACTCTATTTGTAGTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:2:0:32:0:1:1:43:4:0.25:0:3 0/1:11:2:1,1:5,4:0.1818:2,2:13.5:1:30:1:1:1.22474:31.5:4:0.1818:0:2 -8 43831571 . A T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72824;SOR=0.67477;LSEQ=GAGCAGTTGTGCAGCACTCT;RSEQ=TTTGTAGTATCTGGAAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:5,2:4,4:0.4667:2,2:7.1:1:30.4:1:0.60839:2.35:41.6:14:0.4667:0:2 0/1:19:7:3,4:7,5:0.3684:2,2:6.3:1:30.1:1:0.64992:1.80535:43.9:14:0.3684:0:1.1 -8 43831601 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17421;SOR=0;LSEQ=TCTGGAAGTGGACATTTGGA;RSEQ=GGCTTTGTAGCCTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,10:0.0909:2,2:28.5:1:29:1:1:1:21:4:0.0909:0:3 0/0:30:0:0,0:15,15:0:2,0:30.1:1:31:1:1:0:37.4:60:1:0:0.7 -8 43831606 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17421;SOR=0;LSEQ=AAGTGGACATTTGGAGGGCT;RSEQ=TGTAGCCTATCTGGAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,10:0.0909:2,2:28.5:1:28:1:1:1:21:4:0.0909:0:3 0/0:30:0:0,0:15,15:0:2,0:29.8:1:30.2:1:1:0:37.4:60:1:0:0.7 -8 43831617 . C G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00852;SOR=0.1572;LSEQ=TGGAGGGCTTTGTAGCCTAT;RSEQ=TGGAAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:5,5:4,5:0.5263:2,2:31:1:32.2:1:1:1.24:40.9:20:0.5263:0:1.9 0/1:28:4:2,2:12,12:0.1429:2,2:19.3:1:30.5:1:1:1:31.8:8:0.1429:0:1.3 -8 43831635 . T G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50337;SOR=Inf;LSEQ=ATCTGGAAAAAGGAAATATC;RSEQ=TCCCATGAATGCGAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:20.3:1:30.9:1:1:0:40.4:32:1:0:1.4 0/1:23:2:1,1:9,12:0.087:2,2:27:1:29:1:1:1.32:20:4:0.087:0:1.5 -8 48101793 . T G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGGGCCTCTCCTTATTT;RSEQ=TGCATTGGTCTCTGTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:32:1:1:0:60:4:1:0:1 -8 48649959 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22064;SOR=Inf;LSEQ=CCGGAGGCCGGCCAGGTCCC;RSEQ=CGTGAGCTGCTCCACGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:124,3:0:1,0:24.9:1:30:1:1:0:60:126:1:0:0.1 0/1:113:2:1,1:106,5:0.0177:1,2:13.5:1:32:0:0.10382:19.45094:60:4:0.0179:0:1 -8 48649975 . G C 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.24808;SOR=Inf;LSEQ=TCCCGCGTGAGCTGCTCCAC;RSEQ=CGCTGGTGCAGCTTCTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:145,19:0:2,0:23.6:1:29.7:1:1:0:60:163:1:0:0.1 0/1:171:3:2,1:139,29:0.0175:2,2:15:1:26.7:1:0.44149:2.38097:60:2:0.0119:0:1.7 -8 48649992 . C A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25044;SOR=Inf;LSEQ=CACGCGCTGGTGCAGCTTCT;RSEQ=GTTCTCAGCCGACAGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:173,57:0:2,0:23:1:30.3:1:1:0:60:45:0.9956:0:0.1 0/1:256:3:1,2:179,72:0.0117:2,2:21.7:1:24.7:1:0.20415:4.93611:60:2:0.0079:0:1.3 -8 48650123 . G A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13077;SOR=Inf;LSEQ=ACTCGGGGCTGCCGCGGTCC;RSEQ=GGCCCCTCTTGCCGGCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:56,189:0:2,0:25.7:1:31.1:1:1:0:60:244:1:0:0.2 0/1:298:4:3,1:85,209:0.0134:2,2:8.5:1:28.5:1:0.07881:7.32:60:8:0.0138:0:1 -8 48650173 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5328;SOR=0;LSEQ=GCGGGGCCGGGCGCGGGGGT;RSEQ=TGCCTGGGGCTGCTGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:0,2:0,29:0.0645:1,0:12.5:1:31.5:1:1:0:60:4:0.0645:0:1.5 0/0:17:0:0,0:1,16:0:1,0:7.6:1:32:1:1:0:60:34:1:0:0.1 -8 48650427 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24226;SOR=Inf;LSEQ=CGCCTTGTGATTGCTGTTGA;RSEQ=GAGGTCGGCGAAGAGCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:82,32:0:2,0:21.6:1:30.1:1:1:0:60:113:1:0:0.1 0/1:111:2:1,1:81,28:0.018:2,2:14:1:30:1:0.45602:2.86004:60:4:0.018:0:1 -8 48650451 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24527;SOR=Inf;LSEQ=GTCGGCGAAGAGCTCGTCGT;RSEQ=GCACAGCTCCAGGGTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:102,84:0:2,0:22.1:1:31.1:1:1:0:60:61:1:0:0.2 0/1:183:2:1,1:106,75:0.0109:2,2:20:1:29:1:1:1.41059:60:4:0.0112:0:1 -8 48650452 . G T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36904;SOR=3.07324;LSEQ=TCGGCGAAGAGCTCGTCGTG;RSEQ=CACAGCTCCAGGGTGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:105,84:0.0053:2,0:1:0:27:0:0.44737:0:60:2:0.0053:0:1 0/1:187:3:1,2:108,76:0.016:2,2:5.3:1:26:1:0.57191:2.82625:60:6:0.0162:0:1 -8 48650457 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22474;SOR=0;LSEQ=GAAGAGCTCGTCGTGGCACA;RSEQ=CTCCAGGGTGGGCACGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:107,88:0.0102:2,2:25.5:1:30.5:1:1:1.21469:60:4:0.0102:0:1 0/0:218:0:0,0:125,93:0:2,0:25.1:1:31.3:1:1:0:60:71.667:1:0:0.2 -8 48650482 . G T 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12924;SOR=Inf;LSEQ=AGGGTGGGCACGGCGGCCAT;RSEQ=GAGTCGATGTAGGCGCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:113,135:0:2,0:28.8:1:31.5:1:1:0:60:496:1:0:0.2 0/1:295:4:2,2:142,149:0.0136:2,2:19.8:1:31.8:1:1:1.05:60:8:0.0137:0:1.5 -8 48650526 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49909;SOR=Inf;LSEQ=GATGGCGCTCTCGTCGTCGT;RSEQ=CATGGCGGGGGCGGCGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:63,117:0:2,0:24.1:1:29.1:1:1:0:60:89:1:0:0.3 0/1:191:2:1,1:68,121:0.0105:2,2:15:1:31:0:1:1.77:60:4:0.0106:0:1 -8 48650534 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.1021;SOR=Inf;LSEQ=TCTCGTCGTCGTACATGGCG;RSEQ=GGGCGGCGGCGCCTGGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:51,96:0:2,0:23.4:1:30.5:1:1:0:60:23.5:1:0:0.2 0/1:130:3:2,1:39,88:0.0231:2,2:11.3:1:29.7:1:0.23379:4.45:60:6:0.0233:0:1 -8 50347199 . CTT C 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02574;SOR=Inf;LSEQ=CAGACAATGCCTTTCAAACT;RSEQ=ATACCAACCTCTGGAGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:29,26:0:2,0:27.8:1:30.1:1:1:0:51.4:54:1:0:0.1 0/1:53:5:2,3:28,20:0.0943:2,2:31.8:1:30.2:1:0.64206:2.07035:43:10:0.0962:0:0 -8 50562306 . G C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTGGGTTCGTGGTCTCA;RSEQ=TGGCCTCAGGAGTGAAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:33.5:1:1:0:60:4:1:0:1.5 -8 50563145 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53939;SOR=Inf;LSEQ=TCTGATTTCAGAAGACTTTT;RSEQ=CTGTAAATGCCGGGCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:18.2:1:31.7:1:1:0:54.6:38:1:0:0.3 0/1:36:2:1,1:14,20:0.0556:2,2:14:1:27.5:1:1:1.41:53:4:0.0556:0:1 -8 51786608 . G A 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=TTGGAAGATCCCACTCATGA;RSEQ=CCCATGCCTCCAGGGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:0:2,0:28.4:1:32.3:1:1:0:60:72:1:0:0.1 0/1:44:13:7,6:14,17:0.2955:2,2:20.7:1:29.6:1:0.74375:1.41:59.2:26:0.2955:0:1.5 -8 51786658 . C A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=CACAGAGCCAAGCGGATTCT;RSEQ=AACAGCCACTAAGCTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:4,11:0:2,0:24.1:1:32.3:1:1:0:60:30:1:0:0 1/0:15:10:5,5:2,3:0.6667:2,2:15.3:1:28.1:1:1:1.46:60:20:0.6667:0:1.2 -8 53901153 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24599;SOR=Inf;LSEQ=ATTTGTCAAAGGCTCACTCA;RSEQ=TCAGAGCAAAAATAACTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:82,12:0:2,0:24:1:31.3:1:1:0:60:188:1:0:0 0/1:93:2:1,1:76,15:0.0215:2,2:11.5:1:29:1:0.31604:4.93807:60:4:0.0215:0:1 -8 53901222 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10057;SOR=0;LSEQ=GCCAGCCCTTAATCAGGTAA;RSEQ=CAGTCTCACATATACTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:1,2:169,115:0.0105:2,2:22.7:1:28.7:1:0.56893:2.92803:60:6:0.0105:0:1.3 0/0:329:0:0,0:190,138:0:2,0:27.7:1:31.7:1:1:0:60:81:0.9969:0:0.3 -8 53901248 . G T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04217;SOR=0;LSEQ=TCACATATACTTGGCTGACA;RSEQ=CACTGGGTATACATTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:4:1,3:173,150:0.0122:2,2:8:1:24.8:1:0.34353:3.44784:60:3:0.0092:0:1.3 0/0:394:0:0,0:210,184:0:2,0:25:1:31.5:1:1:0:60:64.667:1:0:0.4 -8 53901283 . G T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13216;SOR=Inf;LSEQ=TTGAATCTTCCACTTTGTGA;RSEQ=TAGTTCGTCTCCTATGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:141,148:0:2,0:24.5:1:31.9:1:1:0:60:95.333:1:0:0.7 0/1:357:4:3,1:164,189:0.0112:2,2:17.5:1:28:1:0.34367:3.45:60:3:0.0085:0:2 -8 53901286 . G A 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.47363;LSEQ=AATCTTCCACTTTGTGAGTA;RSEQ=TTCGTCTCCTATGGCTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:292:172:77,95:59,61:0.589:2,2:22.9:1:30.3:1:0.47634:1.19259:60:85:0.5923:0:1.1 0/1:344:139:62,77:95,110:0.4041:2,2:26.3:1:30:1:0.82548:1.07235:60:278:0.4076:0:1.2 -8 53901341 . G A 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.49046;LSEQ=TGAAAGAAAAATATCTCACA;RSEQ=TCTGCCAAAACTTGGAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:60,127:0.0106:2,0:1:0:25.5:1:0.10644:0:60:4:0.0107:0:1.5 0/1:191:3:2,1:62,126:0.0157:2,2:12.7:1:23.7:1:0.26042:4.03:60:2:0.0106:0:2.7 -8 53901365 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=GCCAAAACTTGGAATTGGTT;RSEQ=GCACAGAAATGCATGATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:38,104:0.0138:2,2:46:1:31:1:0.4697:2.71:60:4:0.0142:0:1 0/0:125:0:0,0:32,93:0:2,0:23.3:1:30.4:1:1:0:60:124:1:0:0.3 -8 53901381 . A C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03992;SOR=Inf;LSEQ=GGTTGGCACAGAAATGCATG;RSEQ=TTAAAACATCAAAGTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:18,89:0:2,0:22.1:1:31.1:1:1:0:60:214:1:0:0.2 0/1:88:4:0,4:17,67:0.0455:2,0:19.3:1:32.3:1:1:0:60:8:0.0455:0:1 -8 54049779 . A T 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.77661;LSEQ=GTAATAGCAAGATGGCTGTC;RSEQ=TGGGACCTAGAAAGGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:0,1:30,20:0.0196:2,0:1:0:25:0:0.41176:0:60:2:0.0208:0:1 0/1:58:2:0,2:31,25:0.0345:2,0:13:1:24.5:1:0.21234:0:60:4:0.0345:0:1 -8 54049807 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5064;SOR=Inf;LSEQ=TAGAAAGGGGTGAAGCCATG;RSEQ=CGCCCAACTCCAGAGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:36,29:0:2,0:31.7:1:31.4:1:1:0:60:31.5:1:0:0.5 0/1:86:2:1,1:41,43:0.0233:2,2:41.5:1:30:1:1:1.05:53:4:0.0238:0:1 -8 54049868 . T A 109 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0.03761;LSEQ=TGTCTGATTTCAGAAGCCTT;RSEQ=TCCTGTAAATGCTGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:14:7,7:8,18:0.35:2,2:20.3:1:28.8:1:0.31011:2.20:60:28:0.35:0:1.9 0/1:52:1:0,1:18,33:0.0192:2,0:27:0:32:0:1:0:60:2:0.0196:0:3 -8 54049884 . G A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03152;SOR=0.25965;LSEQ=CCTTTTCCTGTAAATGCTGG;RSEQ=TGGAGTCTTATACTATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:22:6,16:0,5:0.8148:0,2:23.5:1:30.2:1:0.55518:0:60:44:0.8148:0:2.2 1/0:36:19:4,15:6,11:0.5278:2,2:18.5:1:29.5:1:0.46288:2.00454:60:38:0.5278:0:1.8 -8 54049893 . T C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49057;SOR=0;LSEQ=GTAAATGCTGGGTGGAGTCT;RSEQ=ATACTATCCCTGACTGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:5,22:0,0:1:0,2:23.1:1:31.2:1:1:0:60:26:1:0:2 1/1:26:25:5,20:0,1:0.9615:0,2:19.2:1:31.8:1:1:0:59.2:50:0.9615:0:1.6 -8 54378749 . G A 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGAGGAACCTGTGGGGCC;RSEQ=TCAGCTCAGGAGTCCCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:30:1:1:0:47.5:4:1:0:2.5 -8 54380628 . T C 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74902;SOR=1.42992;LSEQ=AGGCTTCTGAAATGGGACAA;RSEQ=GCCTTTCAAACTCTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:3,1:15,8:0.1481:2,2:25.8:1:31.8:1:1:1.57:45:8:0.1481:0:1 0/1:40:8:5,3:18,14:0.2:2,2:10.6:1:29.9:1:1:1.29:41.3:16:0.2:0:1.1 -8 54445348 . C T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06839;SOR=Inf;LSEQ=TCAGTCCAGCAGTTCGAGGC;RSEQ=GCACTGAGCCGCGATGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:39,0:0:1,0:27.8:1:31.3:1:1:0:60:78:1:0:0 0/1:28:3:3,0:25,0:0.1071:1,0:31.7:1:32.3:1:1:0:60:6:0.1111:0:1 -8 54445414 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22032;SOR=Inf;LSEQ=AGCAAGACTTTGTCTAATTA;RSEQ=AAGCAAAAACTGGCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:100,68:0:2,0:21.8:1:29.4:1:1:0:60:32.6:0.9939:0:0.1 0/1:150:2:1,1:93,54:0.0133:2,2:21:1:29.5:1:1:1.71556:60:4:0.0135:0:1 -8 54445438 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10039;SOR=Inf;LSEQ=CAAAAACTGGCCTTTCAGCT;RSEQ=GAACCACCATCTTCCAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:132,111:0:2,0:26.4:1:31.1:1:1:0:60:59.75:1:0:0.2 0/1:212:3:0,3:116,93:0.0142:2,0:7.3:1:22.7:1:0.09126:0:60:2:0.0096:0:1.3 -8 54445482 . G A 127 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCAAAATGACGAACACAAA;RSEQ=GGAAAGAGGAGAGACACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:95,135:0:2,0:25.1:1:31.2:1:1:0:60:75.667:1:0:0.2 0/1:212:20:8,12:82,110:0.0943:2,2:20.7:1:29.5:1:1:1.11757:60:40:0.098:0:1.3 -8 54445600 . T C 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03778;SOR=0;LSEQ=GAGAGGCCGAGGCAGGAGGA;RSEQ=TGCCTGAGCTCAGGAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:0,7:0,17:0.2917:1,0:33:1:33:1:1:0:60:14:0.2917:0:1 0/0:13:0:0,0:0,13:0:1,0:29.8:1:29.2:1:1:0:60:26:1:0:0.1 -8 54445817 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11667;SOR=Inf;LSEQ=GGGTGACAGAGTGAGACTCC;RSEQ=TCTCAAAAATACAAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:22,4:0:2,0:29.4:1:31.6:1:1:0:60:52:1:0:0.1 0/1:14:2:2,0:11,1:0.1429:2,0:12:1:30:1:1:0:60:4:0.1429:0:1 -8 54445839 . CA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.13825;SOR=Inf;LSEQ=CTCAAAAATACAAACAACAA;RSEQ=AAAAAAAACATGGAGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:33,5:0:2,0:22.1:1:30.4:1:1:0:60:76:1:0:0.1 0/1:23:2:2,0:20,1:0.087:1,0:25.5:1:30:1:1:0:60:4:0.087:0:0 -8 54445879 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21426;SOR=Inf;LSEQ=TTCCTTTGGCCATGTTTATG;RSEQ=AAATCTGTAAGAGAGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:60,16:0:2,0:22.9:1:32.3:1:1:0:60:152:1:0:0.1 0/1:66:2:1,1:56,8:0.0303:2,2:8.5:1:27.5:1:0.25594:6.65902:60:4:0.0317:0:1 -8 54445919 . G T 25 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.8221;LSEQ=TATTATAGATATCAAGGGAA;RSEQ=GGGTACTGTTCAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:101,51:0.013:2,2:37.5:1:30:1:1:1.97101:60:4:0.0131:0:1 0/1:187:2:0,2:129,56:0.0107:2,0:1:0:25:0:0.09505:0:60:4:0.0108:0:2 -8 54446056 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49655;SOR=Inf;LSEQ=TTGCCAAGAGAATTAATGTG;RSEQ=GTATTGAGCACATTAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:1,69:0:1,0:25.9:1:30.1:1:1:0:59.5:140:1:0:0 0/1:72:2:1,1:4,66:0.0278:2,2:40:1:30:1:0.13498:14.87:60:4:0.0286:0:1 -8 54446265 . T C 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTATGGATTCATGGCATAT;RSEQ=AACTGTTTAAATGAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:25:1:30:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:1:0,0:12:0:33:0:1:0:60:2:1:0:1 -8 55364337 . C A 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.58251;LSEQ=GTCTTTATTTTGTCCCTGCG;RSEQ=TTTCCATTAGGTTCTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:0.375:0,0:18.3:1:31:1:1:0:60:6:0.375:0:1 0/1:4:1:0,1:0,3:0.25:0,0:11:0:32:0:1:0:60:2:0.25:0:1 -8 55367444 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2676;SOR=2.76072;LSEQ=ATCTCTTGTGTTGAGAAAAG;RSEQ=AAGGCTTGCAGGAAGCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:2:0,2:278,108:0.0051:2,0:11.5:1:18:1:0.07985:0:60:1:0.0026:0:1 0/1:355:5:1,4:241,108:0.0141:2,2:7.8:1:24.6:1:0.03636:8.86808:60:10:0.0142:0:1.2 -8 55367460 . C T 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12284;SOR=0.19734;LSEQ=AAAGCAAGGCTTGCAGGAAG;RSEQ=CACTCCGGATGTTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:5:2,3:307,161:0.0106:2,2:31:1:30.8:1:0.34674:2.85341:60:10:0.0109:0:1.2 0/0:476:1:0,1:309,164:0.0021:2,0:1:0:24:0:0.3481:0:60:2:0.0021:0:1 -8 55370619 . C T 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGGCATCTCAGTGCCTCA;RSEQ=TCCCCACCCCCTCCCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:86,10:0:2,0:23.7:1:31.9:1:1:0:60:95:1:0:0.1 0/1:46:17:15,2:26,3:0.3696:2,2:26.8:1:30.8:1:1:1.15187:60:34:0.3696:0:1 -8 55370660 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07743;SOR=Inf;LSEQ=TCGGGGGAGGCGGCGCGTCC;RSEQ=GCGGAGGGTTGAGGGGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:144,66:0:2,0:22.3:1:29.5:1:1:0:60:51.5:1:0:0.1 0/1:157:3:2,1:110,44:0.0191:2,2:22.7:1:30.3:1:1:1.24819:60:6:0.0194:0:1 -8 55370898 . G A 81 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07751;SOR=5.93756;LSEQ=CCGAGCCAAGGGCGAGTCCC;RSEQ=TATCCGGCGGCCGATGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:536:1:0,1:301,234:0.0019:2,0:19:0:32:0:0.43843:0:60:2:0.0019:0:1 0/1:637:7:4,3:334,294:0.011:2,2:15.4:1:28.9:1:1:1.17:60:14:0.0111:0:1.3 -8 55370946 . G A 85 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07327;SOR=6.2672;LSEQ=GGTGTGGGCTAAGGACGAGC;RSEQ=CAAGCGGCTGGCGCAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:606:1:1,0:301,304:0.0017:2,0:1:0:25:0:0.49835:0:60:2:0.0017:0:1 0/1:682:7:4,3:329,345:0.0103:2,2:23.4:1:30.6:1:0.71966:1.40:60:14:0.0104:0:1.3 -8 55371061 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.79325;LSEQ=GCTGGCGCGAATCGCTAGGC;RSEQ=GATTTCTTAAACCCCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:0,1:23,127:0.0066:2,0:18:0:31:0:1:0:60:2:0.0068:0:1 0/1:169:2:1,1:29,138:0.0118:2,2:7.5:1:29:1:0.32439:4.70:60:4:0.012:0:1.5 -8 55371080 . C CAG 167 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=79.87495;LSEQ=CCGATTTCTTAAACCCCAAA;RSEQ=TGTTCTTTGCGAGCCTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:1:0,1:10,97:0.0093:2,0:37:0:33:0:1:0:60:2:0.0093:0:0 0/1:102:44:6,38:11,47:0.4314:2,2:25.9:1:30.6:1:0.59491:1.47667:60:43:0.4257:0.098:0.1 -8 55371154 . C T 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01552;SOR=Inf;LSEQ=TTCTTAAGGCTCTGGGTTCC;RSEQ=TTCCCGCTTCCCGCCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:0:1,0:22.2:1:32.7:1:1:0:60:72:1:0:0.1 0/1:13:3:0,3:1,9:0.2308:2,0:23.3:1:30.3:1:1:0:60:6:0.2308:0:1 -8 55371472 . C A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.7914;SOR=0.75303;LSEQ=AAGGGCTCGGACTCAGGAGT;RSEQ=CCAGATCTCCCTCTTTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:12:12,0:26,1:0.3077:1,0:22.9:1:28.6:1:1:0:60:24:0.3077:0:2.6 0/1:32:8:8,0:24,0:0.25:1,0:23.1:1:28.5:1:1:0:60:16:0.2581:0:2.4 -8 55371474 . C A 68 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0628;SOR=0;LSEQ=GGGCTCGGACTCAGGAGTCC;RSEQ=AGATCTCCCTCTTTAACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:5:5,0:37,1:0.1163:1,0:20.2:1:29.4:1:1:0:60:10:0.1163:0:2 0/0:34:0:0,0:34,0:0:1,0:21.1:1:30.7:1:1:0:60:33:1:0:1.4 -8 55371478 . T C 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08842;SOR=2.14031;LSEQ=TCGGACTCAGGAGTCCCAGA;RSEQ=CTCCCTCTTTAACTTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:20:20,0:23,1:0.4545:1,1:20.8:1:32.4:1:1:0:60:40:0.4545:0:2.4 1/0:42:27:27,0:15,0:0.6429:1,1:21.7:1:31.7:1:1:0:60:54:0.6429:0:2 -8 55371499 . C T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11947;SOR=Inf;LSEQ=CTCCCTCTTTAACTTCACCC;RSEQ=GGTTGCGCAATTCAAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:63,4:0:2,0:23:1:30.5:1:1:0:60:32.5:1:0:0.9 0/1:68:4:3,1:63,1:0.0588:1,2:16.5:1:30:1:0.11501:18.32472:60:8:0.0615:0:2.5 -8 55371538 . A G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.12495;LSEQ=CTGAGGGGGGAGGTGCGTCC;RSEQ=GGTGGGGCCAGGTGGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:36:28,8:109,13:0.2264:2,2:24.6:1:28.6:1:0.09297:2.38011:60:17:0.2237:0:1.6 1/0:133:80:71,9:43,10:0.6015:2,2:27.3:1:29.3:1:0.31129:1.83:60:79:0.6077:0:1.4 -8 55371548 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20059;SOR=Inf;LSEQ=AGGTGCGTCCAGGTGGGGCC;RSEQ=GGTGGGGCCTGGAGCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:151,37:0:2,0:23.9:1:29.8:1:1:0:60:25.857:1:0:0.4 0/1:153:2:1,1:125,26:0.0131:2,2:15:1:27.5:1:0.32276:4.7367:60:4:0.0133:0:1 -8 55371724 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01436;SOR=Inf;LSEQ=CACCCCAACTACAAGTACCG;RSEQ=CCGCGGCGGCGCAAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:562:0:0,0:184,378:0:2,0:24.3:1:31.3:1:1:0:59.9:50.091:1:0:0.1 0/1:549:6:5,1:205,336:0.0109:2,2:7.7:1:23.3:1:0.03327:8.16:60:5:0.0094:0:1.2 -8 55371789 . C T 121 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=18.00242;LSEQ=CGGCTTCCTGCACGGCCTGG;RSEQ=TGAGCCGCAGGCGGCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:28,141:0.0059:2,0:11:0:31:0:1:0:60:2:0.006:0:2 0/1:155:15:2,13:38,102:0.0968:2,2:23.3:1:31.1:1:0.35674:2.41024:60:30:0.098:0:1 -8 55371820 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49708;SOR=0;LSEQ=GCGGCCGCGCTGGGCCCCGA;RSEQ=GGCGGCCGCGTGGCCATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:33,48:0.0241:2,2:5.5:1:30:1:1:1.45:60:4:0.0241:0:1.5 0/0:80:0:0,0:29,51:0:2,0:14.7:1:30.8:1:1:0:60:160:1:0:0.2 -8 55371888 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11421;SOR=0;LSEQ=GGGCTTCCCCGCCGGCCCGC;RSEQ=GCTGCTGCCTCCGCACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:1,2:95,34:0.0227:2,2:25.3:1:29:1:0.18048:5.50151:60:6:0.0229:0:1 0/0:139:0:0,0:89,50:0:2,0:24.2:1:29.8:1:1:0:60:68.5:1:0:0.2 -8 55372088 . G A 53 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05011;SOR=0;LSEQ=ACGCGCAGGTCTCGGACTAC;RSEQ=CTGGCCCCCCGGAGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:4:4,0:126,193:0.0124:2,0:7.8:1:26.8:1:0.02552:0:60:8:0.0127:0:1 0/0:358:0:0,0:154,203:0:2,0:23.5:1:29.8:1:1:0:60:21.313:1:0:0.2 -8 55372109 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=0;LSEQ=CTGGCCCCCCGGAGCCTCCC;RSEQ=CCGGTCCCATGCACCCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:2,1:108,162:0.011:2,2:13.3:1:22:1:0.56697:2.99:60:2:0.0075:0:1 0/0:263:0:0,0:116,147:0:2,0:22.9:1:30.5:1:1:0:60:64.75:1:0:0.2 -8 55372224 . C T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38097;SOR=3.4394;LSEQ=CGCGATGGGCTCGCCCGGGG;RSEQ=GGGCGGCGGGCGCGGCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:1:0,1:184,155:0.0029:2,0:1:0:29:0:0.45882:0:60:2:0.0029:0:1 0/1:400:4:1,3:209,187:0.01:2,2:24.3:1:28:1:0.34988:3.34359:60:8:0.0103:0:1 -8 55372258 . ACACCAG A 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=4.000;MSILEN=6;SSF=0.00421;SOR=Inf;LSEQ=GGCTTCCAGATGCAGCCGCA;RSEQ=CACCAGCACCAGCACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:291,208:0:2,0:26:1:32.2:1:1:0:60:165.333:0.996:0:0.2 0/1:560:9:4,5:293,256:0.0161:2,2:25:1:30.9:1:0.74032:1.42973:60:18:0.0164:0.0054:0.1 -8 55372516 . C G 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCGGTGGTGTCCGACGC;RSEQ=AGCTCCGCGGTATATTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:0:0,0:270,447:0:2,0:24.1:1:31.6:1:1:0:60:88.625:1:0:0.2 0/1:804:68:28,40:308,426:0.0846:2,2:25.9:1:30.3:1:1:1.03283:60:136:0.0859:0:1.2 -8 55374911 . T TCTAA 122 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.01887;SOR=2.55911;LSEQ=AAATACTAGGTCTTATTCCT;RSEQ=CTATGTTTTTTTTTTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:12:11,1:140,6:0.0759:1,2:24.3:1:28.6:1:0.43117:2.1078:58.3:11:0.0719:0.019:0.3 0/1:109:19:17,2:87,3:0.1743:1,2:22.5:1:28.9:1:0.20826:3.35975:59.6:18:0.1682:0.0642:1 -8 55374915 . TG ACTATGT 169 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=0;SOR=4.53779;LSEQ=AATACTAGGTCTTATTCCTT;RSEQ=TTTTTTTTTTTTTGGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:20:20,0:128,6:0.1242:1,1:33.6:1:31.3:1:1:0:60:40:0.1274:0:0.2 0/1:140:55:50,5:77,4:0.3929:1,2:19.5:1:29.4:1:0.48453:1.91549:59:54:0.3971:0.2143:0.7 -8 55374948 . A G 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGGTAGTTTTAAATTACCA;RSEQ=AACATTTGGTATCCTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:26:20,6:238,75:0.0767:2,2:23.3:1:29.5:1:1:1.05:60:7.667:0.0695:0:1.1 0/0:330:0:0,0:251,79:0:2,0:18.6:1:29.5:1:1:0:59.8:81.5:1:0:0.3 -8 55379760 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49887;SOR=0;LSEQ=TCGGCGCGCGGGGCAGGCCT;RSEQ=GAGCGCCGTGAGCAGGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:97,53:0.0132:2,2:42:1:30:0:1:1.82238:60:4:0.0135:0:1 0/0:142:0:0,0:89,53:0:2,0:25.1:1:30.9:1:1:0:60:141:1:0:0.2 -8 55379765 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22596;SOR=Inf;LSEQ=GCGCGGGGCAGGCCTGGAGC;RSEQ=CCGTGAGCAGGCCGGATGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:104,61:0:2,0:27.3:1:30.1:1:1:0:60:40.25:1:0:0.2 0/1:150:2:1,1:91,57:0.0133:2,2:36.5:1:29:1:1:1.59128:60:4:0.0135:0:2 -8 55379777 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2309;SOR=Inf;LSEQ=CCTGGAGCGCCGTGAGCAGG;RSEQ=CGGATGCGGGATACGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:108,72:0:2,0:28.6:1:31.3:1:1:0:60:21.5:1:0:0.2 0/1:167:2:1,1:96,69:0.012:2,2:24.5:1:28:1:1:1.38849:60:4:0.0122:0:2 -8 55379808 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20617;SOR=Inf;LSEQ=ATACGCCAGTGACTACCAGA;RSEQ=CCAGACCCGGAGCGCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:109,96:0:2,0:24.8:1:31.7:1:1:0:60:40:1:0:0.2 0/1:171:2:1,1:84,85:0.0117:2,2:17.5:1:28:1:1:1.01:60:4:0.0118:0:1.5 -8 55379824 . G A 98 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00661;SOR=6.69144;LSEQ=CAGAGCCAGACCCGGAGCGC;RSEQ=CTGCCGGCGGTGACGGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:2,0:89,102:0.0104:2,0:1:0:28:1:0.22102:0:60:4:0.0109:0:1 0/1:152:10:4,6:64,78:0.0658:2,2:26.3:1:29.8:1:1:1.22911:60:20:0.0667:0:1.2 -8 55379825 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63687;LSEQ=AGAGCCAGACCCGGAGCGCG;RSEQ=TGCCGGCGGTGACGGCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:85,102:0.0106:2,2:5.5:1:29:1:1:1.20:60:4:0.0109:0:1.5 0/0:148:1:1,0:65,82:0.0068:2,0:1:0:23:0:0.44595:0:60:2:0.0069:0:2 -8 55379838 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18488;SOR=Inf;LSEQ=GAGCGCGCTGCCGGCGGTGA;RSEQ=GGCTAGGCTGGGCCCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:77,95:0:2,0:24.8:1:29.9:1:1:0:60:27.667:0.994:0:0.2 0/1:131:2:1,1:51,78:0.0153:2,2:26.5:1:29.5:1:1:1.52:60:4:0.0156:0:1 -8 55379851 . C A 37 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.9421;LSEQ=GCGGTGACGGCTAGGCTGGG;RSEQ=CCCTGTCCTTGGGCCGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:63,91:0.0191:2,2:17.3:1:23.7:1:0.56996:2.87:60:2:0.0135:0:1 0/1:111:2:1,1:40,69:0.018:2,2:1.5:1:20:1:1:1.72:60:1:0.0095:0:1.5 -8 55379865 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13885;SOR=Inf;LSEQ=GCTGGGCCCCTGTCCTTGGG;RSEQ=CGAGTTGCCGAGCTCCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:54,95:0:2,0:26.2:1:30.7:1:1:0:60:28.8:1:0:0.1 0/1:89:2:1,1:29,58:0.0225:2,2:11.5:1:26:1:1:1.98:60:4:0.023:0:2 -8 55379903 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51218;SOR=0;LSEQ=TCGGGGACTTGAAGGTGAAG;RSEQ=GCGAGGCGCCGGCCGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:27,80:0.0183:2,2:13.5:1:29:1:0.44954:2.93:60:4:0.0192:0:1 0/0:77:0:0,0:24,53:0:2,0:24.3:1:29.6:1:1:0:60:37.5:1:0:0.3 -8 55379916 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.20554;SOR=Inf;LSEQ=GGTGAAGGGCGAGGCGCCGG;RSEQ=CGGGGCCGCGGGCCGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:21,64:0:2,0:22.8:1:29.8:1:1:0:60:9.625:1:0:0.2 0/1:71:2:1,1:21,48:0.0282:2,2:18:1:31.5:1:0.52676:2.26:60:4:0.0286:0:1 -8 56063806 . T C 193 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00438;SOR=0.56834;LSEQ=AGAATTTATACTTTCATTTC;RSEQ=GGCCTGCCAAGCAAACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:95:41,54:50,60:0.4634:2,2:25.8:1:29.5:1:0.77906:1.09706:60:46.5:0.4581:0:1.8 0/1:228:75:35,40:63,88:0.3289:2,2:26.2:1:29.6:1:0.56876:1.22:60:150:0.3319:0:2 -8 56063814 . C A 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36113;SOR=0.8145;LSEQ=TACTTTCATTTCTGGCCTGC;RSEQ=AAGCAAACTTCACAGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:78:33,45:53,74:0.3805:2,2:25.9:1:29.7:1:1:1.02:60:156:0.3842:0:2 0/1:219:73:35,38:59,87:0.3333:2,2:27.1:1:29.7:1:0.3128:1.36:60:72:0.3349:0:2 -8 56063856 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23799;SOR=Inf;LSEQ=ATCTGACCTTAACAATTATC;RSEQ=GATCTAACACTGACAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:57,101:0:2,0:24.5:1:30.4:1:1:0:60:78:1:0:0.6 0/1:151:2:1,1:47,102:0.0132:2,2:42.5:1:31:1:0.53616:2.16:60:4:0.0136:0:1 -8 56265933 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=ACACACACACAGGGAGAATG;RSEQ=CCTGTGAAGAAGACAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:19,5:0.0769:2,2:14:1:30.5:1:0.41538:3.55868:60:4:0.08:0:1 0/0:14:0:0,0:12,2:0:2,0:21.4:1:30.8:1:1:0:60:28:1:0:0.1 -8 56265985 . CA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49803;SOR=Inf;LSEQ=CTCTACAAGCTGAGGAATGC;RSEQ=AAGATTGCCAGCAAACCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:0:2,0:27.4:1:29.8:1:1:0:60:60:1:0:0.1 0/1:69:2:1,1:40,27:0.029:2,2:32:1:30.5:1:1:1.47282:60:4:0.029:0:0 -8 56266019 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51194;SOR=Inf;LSEQ=AAACCACCAGAAACTACTGA;RSEQ=GGGTGGCATGCAACAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:21,27:0:2,0:28.3:1:30.5:1:1:0:60:23:1:0:0.1 0/1:69:2:1,1:33,34:0.029:2,2:46:0:32:1:1:1.03:60:4:0.0294:0:1.5 -8 56319983 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTATCCCACTTGAGAATTAC;RSEQ=GACTTAGAAGAGCTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:25.4:1:29.4:1:1:0:60:22:1:0:0 0/1:51:2:1,1:30,19:0.0392:2,2:35.5:1:29.5:1:1:1.56436:60:4:0.0392:0:1 -8 56319986 . CT C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCCACTTGAGAATTACGGA;RSEQ=TAGAAGAGCTGCAGTGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:26.3:1:29.3:1:1:0:60:11.5:1:0:0 0/1:56:2:1,1:32,22:0.0357:2,2:23.5:1:28.9:1:1:1.4446:60:4:0.0357:0.0179:0 -8 56320018 . C A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5474;SOR=Inf;LSEQ=GCAGTGTCACCTACAGGGTC;RSEQ=CGCTGTCCACGCTGCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:19,18:0:2,0:26.2:1:32:1:1:0:60:74:1:0:0.2 0/1:72:2:1,1:35,35:0.0278:2,2:10:0:32:0:1:1:60:4:0.0278:0:1 -8 56320041 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53393;SOR=Inf;LSEQ=CTGTCCACGCTGCCTCCGCC;RSEQ=GAGTGATGAACCTGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:17,18:0:2,0:25.9:1:31.3:1:1:0:60:70:1:0:0.2 0/1:62:2:1,1:25,35:0.0323:2,2:43.5:1:31.5:1:1:1.39:60:4:0.0323:0:1 -8 56320062 . G A 24 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12033;SOR=0;LSEQ=GAGTGATGAACCTGTCTGTT;RSEQ=CACATTCACGGGCCTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:11,13:0.0769:2,2:7.5:1:24:1:1:1.17:60:4:0.0769:0:2 0/0:48:0:0,0:19,29:0:2,0:22.2:1:32:1:1:0:60:96:1:0:0.2 -8 56320071 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14132;SOR=0;LSEQ=ACCTGTCTGTTGCACATTCA;RSEQ=GGGCCTGATGAACTGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:10,12:0.0833:2,2:40.5:1:30.5:1:1:1.19:60:4:0.0833:0:2 0/0:39:0:0,0:16,23:0:2,0:20.9:1:30.1:1:1:0:60:78:1:0:0.2 -8 56879449 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53324;SOR=Inf;LSEQ=TACATCATCACCGAGTACAT;RSEQ=GCCAAGGGTGAGTTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:0:2,0:33.8:1:32:1:1:0:60:48:1:0:0 0/1:43:2:1,1:17,24:0.0465:2,2:34.5:1:30:1:1:1.40:60:4:0.0476:0:1 -8 56879965 . C T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTGCAACCCCTGCCTC;RSEQ=CGGGTTCAAGCGATTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:1:31:0:1:0:60:4:1:0:2 -8 56880021 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCTGGGACTACAGGCAC;RSEQ=TGCCACCATGCCCAGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:1:27.5:1:1:0:60:4:1:0:2 -8 57013717 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5043;SOR=Inf;LSEQ=TCCTTTCTCCCCATCTTTGG;RSEQ=CTTAATTTACCAGTAGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:47,40:0:2,0:27.9:1:31.8:1:1:0:59.5:174:1:0:0.1 0/1:110:2:1,1:64,44:0.0182:2,2:23:0:28:0:1:1.44946:60:4:0.0185:0:2 -8 57013846 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19918;SOR=Inf;LSEQ=GTTTTTCCTGTTTTTTGAAG;RSEQ=AGTCTTGTCCTTTTGATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:56,60:0:2,0:24.8:1:31.1:1:1:0:60:57:1:0:0.2 0/1:94:2:1,1:46,46:0.0213:2,2:14.5:1:27.5:1:1:1:60:4:0.0213:0:1.5 -8 57013974 . CTCA C 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.02741;SOR=Inf;LSEQ=GGTGCTTTCTCTTCAGTTCC;RSEQ=TCATCAAAATCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:40,19:0:2,0:25.4:1:30.5:1:1:0:60:58:1:0:0.1 0/1:42:4:3,1:24,14:0.0952:2,2:37.3:1:27.8:1:1:1.73:60:3:0.0732:0.0238:1.3 -8 57013992 . ATCATCT A 56 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.03757;SOR=Inf;LSEQ=CCCTCATCATCAAAATCATC;RSEQ=TCATCATCATCATTATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:43,25:0:2,0:26.4:1:29.8:1:1:0:60:21.667:1:0:0.1 0/1:55:4:2,2:38,13:0.0727:2,2:31:1:28:1:0.2975:2.85655:60:8:0.0769:0.0182:0.3 -8 57014012 . TATC T 32 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=1.10779;LSEQ=ATCATCTTCATCATCATCAT;RSEQ=ATCATCATCATCATCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:0,2:57,35:0.0213:2,0:20.5:1:27:1:0.15237:0:60:4:0.0217:0:0 0/1:85:2:1,1:53,30:0.0235:2,2:17:0:32:0:1:1.75417:43:4:0.0241:0:0.5 -8 57014031 . A T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.68027;SOR=1.55454;LSEQ=TTATCATCATCATCATCATC;RSEQ=TCTTCATCAGCAGCAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:60,48:0.0182:2,2:34:0:31.5:1:1:1.24744:60:4:0.0182:0:1 0/1:107:3:2,1:63,41:0.028:2,2:26.7:1:29.7:1:1:1.30:60:6:0.0283:0:1 -8 57014062 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49834;SOR=Inf;LSEQ=CAGCAAGTTTTACTTTTTTC;RSEQ=GTGGAACCTTGCTACCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:77,58:0:2,0:23.8:1:30.4:1:1:0:59.6:134:1:0:0.2 0/1:140:2:1,1:79,59:0.0143:2,2:33.5:1:28.5:1:1:1.33614:60:4:0.0145:0:1 -8 57014065 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49838;SOR=Inf;LSEQ=CAAGTTTTACTTTTTTCTGT;RSEQ=GAACCTTGCTACCACCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:79,59:0:2,0:23.8:1:31.3:1:1:0:59.6:45:0.9926:0:0.2 0/1:144:2:1,1:83,59:0.0139:2,2:25.5:1:26.5:1:1:1.40336:60:4:0.0141:0:1 -8 57014075 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23582;SOR=0;LSEQ=TTTTTTCTGTGGAACCTTGC;RSEQ=ACCACCTCCAGTAGCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:80,62:0.0139:2,2:15.5:1:30:1:1:1.28801:60:4:0.0141:0:1 0/0:152:0:0,0:91,61:0:2,0:25.8:1:30:1:1:0:59.9:304:1:0:0.2 -8 57014148 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22193;SOR=0;LSEQ=TCCTCCTCTTCATCTTCTGA;RSEQ=TCTGCATCTTCTACCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:110,80:0.0104:2,2:30.5:1:30.5:1:1:1.37266:60:4:0.0106:0:1 0/0:215:0:0,0:107,108:0:2,0:25.1:1:30.9:1:1:0:60:214:1:0:0.1 -8 57014156 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19764;SOR=0;LSEQ=TTCATCTTCTGACTCTGCAT;RSEQ=TTCTACCACAGCTACTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:111,82:0.0103:2,2:32:1:30.5:1:1:1.35151:60:4:0.0105:0:1 0/0:243:0:0,0:121,122:0:2,0:25:1:31:1:1:0:60:120.5:1:0:0.1 -8 57014164 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.188;SOR=0;LSEQ=CTGACTCTGCATCTTCTACC;RSEQ=CAGCTACTAAGTGCTGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:111,85:0.0101:2,2:28.5:1:30:1:1:1.30409:60:4:0.0103:0:1 0/0:258:0:0,0:124,134:0:2,0:26:1:29.2:1:1:0:59.7:85:1:0:0.1 -8 57014350 . A G 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCTGCTTCAACAATGTGC;RSEQ=ATTCATCCTTTGCACCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:256,195:0:2,0:27.1:1:29.2:1:1:0:56.6:13.094:1:0:0.5 0/1:515:30:20,10:276,203:0.0583:2,2:27:1:29.6:1:0.34881:1.47:54.5:29:0.0594:0:1.2 -8 57014412 . G A 35 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62587;SOR=2.70273;LSEQ=TTTTTTTTAGACAGAGTTTC;RSEQ=CTTTGTCGCCCAGGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:1,0:91,167:0.0038:2,0:1:0:26:0:0.35521:0:60:2:0.0045:0:1 0/1:290:3:2,1:107,177:0.0103:2,2:22.7:1:22.7:1:0.5596:3.29:55:2:0.0079:0:3.3 -8 57014644 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48943;SOR=Inf;LSEQ=CCACCTCAGCCTCCCAAAGT;RSEQ=CTGGGATTACAAGCATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:25.5:1:32.3:1:1:0:59.2:42:1:0:0.1 0/1:23:2:1,1:15,6:0.087:2,2:28:1:32.5:1:0.52569:2.39047:56:4:0.087:0:1 -8 57014659 . A G 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02347;SOR=Inf;LSEQ=AAAGTGCTGGGATTACAAGC;RSEQ=TGAGCCACCGCGCCCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:17,11:0:2,0:19.9:1:30.3:1:1:0:60:56:1:0:0.1 0/1:29:6:4,2:17,6:0.2069:2,2:22.3:1:27.7:1:1:1.39897:60:12:0.2143:0:1.2 -8 57014752 . G A 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAAAGTGATAATCTTTGTT;RSEQ=GCCTTCAGTTCACAACCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:61,19:0:2,0:22.7:1:31.2:1:1:0:60:39:1:0:0.1 0/1:101:21:12,9:47,33:0.2079:2,2:27:1:28.8:1:1:1.06748:60:42:0.2121:0:1 -8 57014805 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50082;SOR=Inf;LSEQ=GGGCCTCAGGAGGCTCATGT;RSEQ=CATGTCCATCAAATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:76,51:0:2,0:24.3:1:30.9:1:1:0:60:62.5:1:0:0.1 0/1:148:2:1,1:83,61:0.0135:2,2:34:1:28.5:1:1:1.35773:60:4:0.0137:0:1 -8 57014840 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23503;SOR=0;LSEQ=CTTCCATCGGGTGGCAGCAC;RSEQ=CACTTAGGTGGCAGAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:80,86:0.0119:2,2:31:1:31:1:1:1.07:60:4:0.0122:0:1 0/0:178:0:0,0:92,85:0:2,0:28.8:1:30.4:1:1:0:60:43.25:0.9943:0:0.2 -8 59337107 . G T 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20752;SOR=0.23748;LSEQ=CTTTTTAGGGAGAGAGTGAA;RSEQ=TCCACATCTATTTTTGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:4:1,3:182,71:0.0156:2,2:11:1:28.5:1:0.07329:7.62052:60:8:0.016:0:1 0/0:268:1:0,1:185,80:0.0037:2,0:1:0:27:0:0.30451:0:60:2:0.0038:0:1 -8 59337246 . CG C 178 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.28517;SOR=0.78941;LSEQ=CGTGGAGTTGGAGTACAAGG;RSEQ=GGGGGGGGGGCTCTGATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:51:24,27:191,214:0.1099:2,2:30:1:31.5:1:1:1.00408:59.6:50:0.1121:0.0065:0.5 0/1:518:46:19,27:231,232:0.0888:2,2:31.4:1:30:1:0.28288:1.41396:60:22:0.0894:0:0.3 -8 59337251 . G C 213 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.2891;SOR=0.85798;LSEQ=AGTTGGAGTACAAGGCGGGG;RSEQ=GGGGGGCTCTGATCTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:136:64,72:158,176:0.2887:2,2:25.8:1:30.2:1:1:1.00992:60:26.2:0.2892:0:1.2 0/1:542:140:67,73:188,212:0.2583:2,2:25.3:1:29.9:1:0.9217:1.03:59.7:27:0.2576:0:1.1 -8 59337488 . CTCTCTGTTGATGTCAG C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0;SOR=4.46343;LSEQ=ATGTTGCAGTCAACACCTTT;RSEQ=TCAGAATATCAATCACAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:35:14,21:112,147:0.1182:2,2:20.1:1:31.4:1:0.8559:1.14234:59.9:70:0.1224:0.027:0.1 0/1:320:120:54,66:84,116:0.375:2,2:25.2:1:31.4:1:0.64158:1.13:59.9:240:0.3822:0.0688:0.1 -8 59337497 . G C 203 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAACACCTTTCTCTCTGTT;RSEQ=ATGTCAGTCAGAATATCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:85:40,45:70,105:0.2962:2,2:22.8:1:31.7:1:0.2878:1.33:60:84:0.3281:0:1.2 0/0:278:0:0,0:73,107:0:2,0:23.7:1:31:1:1:0:60:89:1:0:0.1 -8 59338272 . C A 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=5.48052;LSEQ=TCAGCAACATTTATACGAGT;RSEQ=GTGTTAAGGGGCTACGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:1:1,0:215,255:0.0021:2,0:1:0:23:0:0.4586:0:60:2:0.0022:0:1 0/1:434:5:4,1:204,223:0.0115:2,2:6.4:1:27:1:0.20044:4.36:60:10:0.0117:0:1 -8 59338663 . A C 221 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00089;SOR=0.61157;LSEQ=CATCTCCATTCTTCTCTTTT;RSEQ=ATTGCCCGTGATGTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:126:64,62:174,195:0.2545:2,2:25.9:1:31.7:1:0.5357:1.16:60:252:0.2587:0:1.1 0/1:637:110:40,70:252,274:0.1727:2,2:20.8:1:31.2:1:0.02764:1.60829:60:220:0.1741:0:1.1 -8 59338856 . G C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52741;SOR=1.72161;LSEQ=GCTCACTGTAAGCTCCGCCT;RSEQ=CTGGGTTCATGCCATTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:23:1,22:0,10:0.697:0,1:22.6:1:28.1:1:1:0:44.8:4.75:0.6786:0:1.6 1/1:20:16:2,14:0,4:0.8:0,2:15.9:1:27:1:1:0:44.8:4.333:0.7647:0:1.1 -8 59339186 . A G 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTCAGCTCCTCTTATCAAC;RSEQ=GTGGGTTTTCTGCCTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:109:63,46:234,218:0.194:2,2:26.4:1:29.5:1:0.28558:1.28:60:26.25:0.1909:0:1.2 0/0:592:0:0,0:313,277:0:2,0:25.8:1:30.1:1:1:0:60:72.75:1:0:0.2 -8 59339279 . T C 285 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=1.8559;LSEQ=CCGGCTCCGTGACAGACCCG;RSEQ=TCCTTGCTCAGGCTCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:503:387:175,212:45,68:0.7694:2,2:28:1:32:1:0.3334:1.25:60:95.75:0.7753:0:1.2 1/1:590:508:216,292:37,45:0.861:2,2:26.9:1:31.8:1:0.71859:1.11132:60:71.571:0.8623:0:1.1 -8 59339351 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50022;SOR=0;LSEQ=GCCCGCTCGGGACCAGATGC;RSEQ=GGGCGGAGCCAGCCGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:0,2:33,148:0.0109:2,0:26.5:1:31.5:1:1:0:60:4:0.0112:0:1 0/0:164:0:0,0:31,133:0:2,0:20.6:1:29.7:1:1:0:60:163:1:0:0.7 -8 59339364 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49882;SOR=0;LSEQ=CAGATGCGGGGCGGAGCCAG;RSEQ=CGACTGTGCACAGACCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:0,2:12,123:0.0146:2,0:18.5:1:28.5:1:1:0:60:4:0.015:0:1 0/0:127:0:0,0:15,111:0:2,0:20.3:1:31:1:1:0:60:125:0.9921:0:0.6 -8 59339451 . AT A 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.68923;SOR=0.62975;LSEQ=GCTTGCTCCTCCTCCCTGTA;RSEQ=TTTTTTTTTCTCTGTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:4:0,4:1,29:0.1176:1,0:34.3:1:32:1:1:0:60:8:0.1176:0:0 0/1:26:2:0,2:1,23:0.0769:1,0:30.5:1:31:1:1:0:60:4:0.08:0:0 -8 59339914 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGCCTGTAGTCCCAACTGCT;RSEQ=GGGAGGCTGAAGTGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:49:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:32:1:30:1:1:0:60:4:1:0:2 -8 59339925 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAACTGCTCGGGAGGCTGA;RSEQ=GTGGCAGGATAGCTTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:38:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:32:1:30.5:1:1:0:60:4:1:0:2 -8 59790108 . G A 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50757;SOR=0;LSEQ=ATAACCCTCCAACCTTGCCT;RSEQ=CTGTTTGCACACATGGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:133,22:0.0127:2,2:32:0:29:1:0.27233:5.93479:60:4:0.0127:0:1 0/0:120:0:0,0:90,30:0:2,0:23:1:31.3:1:1:0:60:59:1:0:0 -8 59790110 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50668;SOR=0;LSEQ=AACCCTCCAACCTTGCCTGC;RSEQ=GTTTGCACACATGGTTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:138,26:0.012:2,2:9:0:32:0:0.29967:5.22743:60:4:0.012:0:1 0/0:128:0:0,0:94,34:0:2,0:22.7:1:30.1:1:1:0:60:63:1:0:0 -8 59790210 . G C 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01832;SOR=0.65779;LSEQ=GGGATCTGAAAGAACATCCT;RSEQ=TAGGTTATATGCAGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:99:42,57:126,151:0.2626:2,2:24.5:1:31.3:1:0.63851:1.13208:60:98:0.2613:0:1 0/1:369:70:35,35:149,149:0.1897:2,2:27.2:1:31.7:1:1:1:60:69:0.1885:0:1.1 -8 59790308 . A G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24306;SOR=0;LSEQ=GTCATCCAAAGCAAATATGC;RSEQ=GTCGTGCAGTGTACTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:20,101:0.0161:2,2:17.5:1:28:0:0.31347:4.95:60:4:0.0161:0:1 0/0:127:0:0,0:28,99:0:2,0:22.1:1:30.8:1:1:0:60:254:1:0:0.1 -8 59790418 . A T 68 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=13.000;MSILEN=1;SSF=0.25654;SOR=0;LSEQ=TTGGAGAAAGCCTACATATT;RSEQ=AAAAAAAAAAAAGCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,6:0.3571:0,0:22.6:1:29.4:1:1:0:60:10:0.3571:0:1 0/0:5:0:0,0:0,2:0:0,0:11:1:26.5:1:1:0:60:4:0.4:0:0.5 -8 61207343 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTTTCATGTGCCTCCCATA;RSEQ=TCCTGGTTCCTCTTTGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:29.5:1:1:0:60:4:1:0:1 -8 61207461 . CT C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22222;SOR=Inf;LSEQ=GCTGACATATGCTGCCTTCT;RSEQ=CTCTGCTTCGGCTACCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:11,3:0:2,0:16.6:1:30.5:1:1:0:57.1:28:1:0:0.1 0/1:13:2:1,1:8,3:0.1538:2,2:23:1:29.5:1:1:2.4495:27:4:0.1538:0.0769:2 -8 61207464 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.48148;SOR=Inf;LSEQ=GACATATGCTGCCTTCTCTC;RSEQ=CTGCTTCGGCTACCTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:11,3:0:2,0:17.7:1:30.6:1:1:0:57.1:28:1:0:0.1 0/1:14:2:2,0:7,5:0.1429:2,0:20.5:1:29:1:0.50549:0:60:4:0.1429:0:1 -8 61207470 . TC T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=TGCTGCCTTCTCTCTCTGCT;RSEQ=GGCTACCTAAAAGGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:0.1111:2,2:6:1:29.5:1:1:1.61828:54.5:4:0.1176:0.0556:1 0/0:17:0:0,0:10,7:0:2,0:18.1:1:29.5:1:1:0:53.6:34:1:0:0.4 -8 61207493 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.49336;SOR=0;LSEQ=GCTACCTAAAAGGGAAGGGC;RSEQ=CCCTGTCCTATGATCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:16,11:0.069:2,2:6.5:1:29.5:1:1:1.43545:60:4:0.069:0:1 0/0:25:0:0,0:16,9:0:2,0:26.2:1:29.1:1:1:0:55.6:11.5:1:0:0.3 -8 61207576 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.20854;SOR=Inf;LSEQ=TACCCTGACCCCCTTGTCTT;RSEQ=TATGCAATAAATAGCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:0:2,0:20.2:1:30.7:1:1:0:60:21:1:0:0.1 0/1:19:2:1,1:7,10:0.1053:2,2:24:1:30.5:1:1:1.40:60:4:0.1111:0:1.5 -8 62114798 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61181;SOR=0.4661;LSEQ=TTTCTTTATCATGGCTAGCA;RSEQ=ATATTTAAGAATGTCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:133,13:0.0135:2,2:23.5:1:29.5:1:0.18082:9.89563:60:4:0.0135:0:1 0/0:158:1:0,1:134,23:0.0063:2,0:1:0:21:0:0.1519:0:60:2:0.0063:0:2 -8 62114818 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25183;SOR=Inf;LSEQ=GATATTTAAGAATGTCCCCT;RSEQ=GTGTGATTCCATCCTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:188,61:0:2,0:22.3:1:31.9:1:1:0:60:248:1:0:0.1 0/1:284:3:2,1:191,90:0.0106:2,2:14.3:1:30:1:1:1.06089:60:6:0.0106:0:1.3 -8 62114861 . G A 239 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=187.44912;LSEQ=TGTTCTCTGGAGCAGCATTC;RSEQ=TTTATCTTCGTCCGCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:2:1,1:276,203:0.0042:2,2:30.5:1:29.5:1:1:1.35871:60:4:0.0042:0:1 0/1:591:260:138,122:180,150:0.4399:2,2:27.1:1:29.8:1:0.73984:1.06075:60:520:0.4422:0:1.2 -8 62114982 . G T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62648;SOR=2.66328;LSEQ=TTTTTGGTTGTGAACTAAAG;RSEQ=CTGACAAAGATTGTCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:0,1:127,122:0.004:2,0:1:0:15:0:0.492:0:60:0:0:0:1 0/1:283:3:3,0:154,126:0.0106:2,0:25.7:1:27.7:1:0.25637:0:60:2:0.0072:0:1.3 -8 62115211 . G C 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACACCACCAGTAGTCTTAA;RSEQ=GTTGAAGTGTGGTTCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:110,119:0:2,0:27.7:1:31.3:1:1:0:56.4:75.333:1:0:0.1 0/1:253:79:41,38:88,85:0.3123:2,2:27.6:1:30.3:1:0.89279:1.04:55.5:158:0.3185:0:1.2 -8 62115263 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2225;SOR=0;LSEQ=AGTGGACAGCACTTAGTAGC;RSEQ=GTGGAGGAAGATGCAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:81,105:0.0106:2,2:15:1:29:1:1:1.29:60:4:0.0108:0:1 0/0:210:0:0,0:87,121:0:2,0:25.6:1:29.7:1:1:0:48.6:68.333:0.9903:0:0.2 -8 62115359 . G A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00334;SOR=Inf;LSEQ=GCCCTCGGAGGTAGTAGCAA;RSEQ=CTTCCACAGAAAAAAGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:46,73:0:2,0:24.1:1:32.2:1:1:0:59.9:238:1:0:0.1 0/1:119:9:4,5:54,56:0.0756:2,2:19.3:1:30.2:1:1:1.20347:60:18:0.0769:0:1.1 -8 62115395 . AGAT A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.68384;SOR=0.50543;LSEQ=GTAAAACTTGCTGCTGATGA;RSEQ=GATGATGATGATGAAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:4:1,3:59,64:0.0315:2,2:34.5:1:29.8:1:0.62132:2.74533:57.5:8:0.0315:0:0.5 0/1:124:2:1,1:60,62:0.0161:2,2:42.5:1:31:1:1:1.03:60:4:0.0164:0:0 -8 62115413 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24069;SOR=0;LSEQ=GAAGATGATGATGATGATGA;RSEQ=GAAGATGATGATGATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:55,60:0.0169:2,0:29.5:1:29.5:1:0.49749:0:55:4:0.0171:0:1.5 0/0:122:0:0,0:60,62:0:2,0:24.4:1:30:1:1:0:59.9:60:1:0:0.2 -8 62115416 . AGAT A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.49877;SOR=Inf;LSEQ=GATGATGATGATGATGAAGA;RSEQ=GATGATGATGAAGATGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:52,58:0:2,0:27:1:32.2:1:1:0:59.5:220:1:0:0.2 0/1:120:2:1,1:59,59:0.0167:2,2:13.5:1:30:1:1:1:60:4:0.0169:0:0 -8 62115431 . AGAT A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GAAGAAGATGATGATGATGA;RSEQ=GATGATGATGATTTTAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:23:11,12:37,34:0.2447:2,2:28.9:1:31.2:1:0.81207:1.18499:58.2:22:0.2418:0.0213:0.3 0/0:107:0:0,0:51,56:0:2,0:22.6:1:31:1:1:0:59.9:34.667:1:0:0.2 -8 62115450 . A AATG 199 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0.40098;SOR=0.71928;LSEQ=AAGATGATGATGATGATTTT;RSEQ=ATGAGGAAGCTGAAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:91:75:38,37:8,7:0.8242:2,2:22.8:1:30.8:1:1:1.11146:59.3:150:0.8242:0.1538:0.1 1/0:131:101:53,48:14,16:0.771:2,2:21.4:1:29.9:1:0.67849:1.26:59.9:202:0.7829:0.2137:0.2 -8 62115677 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26498;SOR=Inf;LSEQ=AGCAAGTATAGAAAAAGGTG;RSEQ=TTCTCTTCCCAAAGTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:75,59:0:2,0:24:1:31.7:1:1:0:57.4:268:1:0:0.1 0/1:182:3:1,2:106,73:0.0165:2,2:6.7:1:27:1:0.56962:2.88706:60:6:0.0167:0:1 -8 62136814 . T C 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.554;SOR=0.31144;LSEQ=AGGAAAGAGGCACTCTGGCC;RSEQ=TTTGGGTTTTCAGCATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:24:0:33.5:1:1:1.12:60:4:0.1053:0:1.5 0/1:29:1:1,0:17,11:0.0345:2,0:2:0:29:0:1:0:60:2:0.037:0:1 -8 62136991 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATAGTCAGGCCTCTCTTCT;RSEQ=TAGGGCTGCTGCAGTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:26:1:32:1:1:0:60:10:1:0:0 0/1:12:2:1,1:3,6:0.1667:2,2:22:1:27.5:1:1:1.87:60:4:0.2:0:1 -8 62137199 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17787;SOR=Inf;LSEQ=CAACCCCTGTTGGGGGGTCT;RSEQ=ACCCCGTTGGGTGGCATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:0:2,0:30.2:1:31.5:1:1:0:60:26:1:0:0.2 0/1:10:2:1,1:5,3:0.2:2,2:23.5:1:29:1:1:1.58108:60:4:0.2:0:1 -8 62137222 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16923;SOR=Inf;LSEQ=CCCGTTGGGTGGCATAGGGA;RSEQ=CAGGACCCATTTAACAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:30.8:1:32.2:1:1:0:60:30:1:0:0.1 0/1:11:2:1,1:5,4:0.1818:2,2:31:0:31:0:1:1.22474:60:4:0.1818:0:1.5 -8 65193106 . C T 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCTGGTCACTTATGTTTTCA;RSEQ=TACTCAATCACTTCGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:220,201:0:2,0:26:1:31.9:1:1:0:60:139.333:1:0:0.2 0/1:423:26:10,16:215,182:0.0615:2,2:21.2:1:29.9:1:0.15533:1.88725:60:52:0.0618:0:1.1 -8 65193137 . T C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55491;SOR=0.87541;LSEQ=CTTCGCTTTTGTACGGATTG;RSEQ=TAGATAACTATGTCCAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:59:27,32:160,174:0.1501:2,2:27.2:1:32:1:0.77924:1.08957:60:118:0.1513:0:1.1 0/1:463:62:28,34:194,205:0.1339:2,2:26.3:1:31.9:1:0.68247:1.14878:60:61:0.1332:0:1.1 -8 65193242 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20338;SOR=Inf;LSEQ=TAGTAAGCAGCACCTTGAAG;RSEQ=TAGACACTGTGGCCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:20,106:0:2,0:22.8:1:32.2:1:1:0:60:252:1:0:0.1 0/1:104:2:1,1:17,85:0.0192:2,2:35:1:28:1:0.31759:4.89:60:4:0.0192:0:1 -8 65193342 . A G 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCTCCTCAAAATTTGAAGA;RSEQ=GTAAGTATTTTGTGAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:0,4:0,17:0.1905:1,0:28:1:31.8:1:1:0:60:8:0.2:0:1 0/0:4:0:0,0:0,4:0:0,0:18:1:31:1:1:0:60:8:1:0:0 -8 65193545 . C CA 27 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTTTTAAAGATGGGTAA;RSEQ=AAAAAAAAAAAAAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:26.5:1:27:0:0.33333:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 65193903 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATGTATTCTTTCTTTTC;RSEQ=AAATGTTAAAGGACATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:30:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 66183802 . T C 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11559;SOR=Inf;LSEQ=AGAGGAGGTCACCTACAGTG;RSEQ=CCTGTTTGAGAGGCTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:148,111:0:2,0:27.2:1:29.7:1:1:0:60:128.5:1:0:0.5 0/1:247:3:2,1:138,106:0.0121:2,2:21.3:1:24.7:1:1:1.53:60:2:0.0083:0:1.7 -8 66183815 . G T 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11891;SOR=Inf;LSEQ=TACAGTGTCCTGTTTGAGAG;RSEQ=CTGGAGCCCACGGCTGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:155,121:0:2,0:27.8:1:31.3:1:1:0:60:54.2:1:0:0.6 0/1:269:3:2,1:141,125:0.0112:2,2:20.3:1:22.7:1:1:1.77:60:2:0.0076:0:3.3 -8 66183866 . G A 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATTTGGTATGTTTTGCCAGC;RSEQ=CAGCATTGCCTGCCCGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:255:255:116,139:0,0:1:0,2:24.7:1:29.4:1:1:0:60:50:1:0:1.1 1/1:246:204:93,111:20,21:0.8293:2,2:26:1:29.8:1:0.73391:1.13611:60:203:0.832:0:1.1 -8 66184044 . T C 123 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05037;SOR=0;LSEQ=TGTGCTCCCCAGAGCCTTTG;RSEQ=GTCCACATTTCAGAATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:0,17:0,0:1:0,1:30.4:1:30.1:1:1:0:60:34:1:0:1.1 1/0:11:8:0,8:1,2:0.7273:2,0:32.6:1:30.1:1:0.27273:0:60:16:0.7273:0:1 -8 66631972 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.70947;LSEQ=GAACTGACAAATATATCTAA;RSEQ=CTTTTCTGGTTATCCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:17:7,10:135,163:0.054:2,2:23.2:1:29.6:1:0.80635:1.18255:60:16:0.0516:0:1.1 0/1:421:140:67,73:137,144:0.3325:2,2:25.7:1:28.8:1:0.91764:1.03651:60:69:0.3325:0:1.1 -8 66632039 . T A 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37184;SOR=3.94352;LSEQ=AAGCAAAAATACACTGCCCA;RSEQ=CTAAACTCTGAGGATACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:1:0,1:61,121:0.0055:2,0:2:0:30:0:1:0:60:2:0.0057:0:1 0/1:188:4:3,1:54,130:0.0213:2,2:10.5:1:28:1:0.08388:7.14:60:8:0.0219:0:1 -8 66632041 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=GCAAAAATACACTGCCCATC;RSEQ=AAACTCTGAGGATACTCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:57,117:0:2,0:23.9:1:29:1:1:0:60:86:1:0:0.1 0/1:178:2:1,1:51,125:0.0112:2,2:29.5:1:29.5:1:0.5001:2.44:60:4:0.0115:0:1 -8 66632048 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22987;SOR=0;LSEQ=TACACTGCCCATCTAAACTC;RSEQ=GAGGATACTCGGGCATAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:44,112:0.0127:2,2:16:0:32:0:0.4898:2.53:60:4:0.0135:0:1 0/0:171:0:0,0:49,122:0:2,0:23.5:1:29.9:1:1:0:60:56:1:0:0.2 -8 66632081 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49677;SOR=Inf;LSEQ=GCATAGCCCAATTCGAGGCA;RSEQ=AGTTGCAGTGCAACAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:10,68:0:2,0:25.7:1:31.3:1:1:0:60:38:1:0:0.1 0/1:78:2:1,1:8,68:0.0256:2,2:15.5:1:29.5:1:0.21878:8.07:60:4:0.0256:0:1 -8 67249953 . C T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24571;SOR=0;LSEQ=ATTTTAATCAATCTCCTGAA;RSEQ=CTTCCCCTAGGCCCAACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:2,1:14,11:0.1071:2,2:15.3:1:31.7:1:1:1.55:60:6:0.1111:0:1 0/0:22:0:0,0:12,10:0:2,0:27.5:1:31:1:1:0:60:44:1:0:0.1 -8 67249986 . A T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18586;SOR=Inf;LSEQ=CCAACTGTGCACTTCCTTGT;RSEQ=AAATCCAGTTTTAGCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:29.7:1:29:1:1:0:60:62:1:0:0.1 0/1:24:2:1,1:8,14:0.0833:2,2:21:1:26:1:1:1.71:60:4:0.0833:0:2 -8 67251732 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGAAGAGCCAAGGTAG;RSEQ=GTTCTGTGTAATATGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:31.5:1:1:0:60:4:1:0:1.5 -8 68097716 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50003;SOR=Inf;LSEQ=TCCAATTAAAGTAACACTGG;RSEQ=AACTTTGAAAATGTACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:68,50:0:2,0:23.6:1:32.2:1:1:0:59.7:117:1:0:0.1 0/1:134:2:1,1:76,56:0.0149:2,2:28:1:28.5:1:1:1.35399:60:4:0.0152:0:1 -8 68097772 . C G 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06147;SOR=Inf;LSEQ=GGGCTTTGAAATAACATCAC;RSEQ=AGTGGTCTGTCGGTTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:96,83:0:2,0:25.3:1:31.4:1:1:0:60:88.5:1:0:0.1 0/1:191:5:3,2:100,86:0.0262:2,2:35.2:1:25.4:1:1:1.29:60:4:0.0214:0:1.2 -8 68097816 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.23545;SOR=0;LSEQ=CTTCAGGGCCAGTGCATATT;RSEQ=GTTGACAGCAATTAGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:83,88:0.0116:2,2:26.5:1:30:1:1:1.06:60:4:0.0119:0:1 0/0:183:0:0,0:92,91:0:2,0:25.4:1:29.2:1:1:0:60:90.5:1:0:0.1 -8 68097836 . T C 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5019;SOR=Inf;LSEQ=AGTTGACAGCAATTAGTAGC;RSEQ=GTGGAGGAAGATGCAGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:66,91:0:2,0:25.6:1:30.4:1:1:0:60:38.25:1:0:0.1 0/1:185:2:1,1:80,103:0.0108:2,2:23.5:1:25:0:1:1.29:60:4:0.011:0:1 -8 68097913 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50611;SOR=Inf;LSEQ=TATCTGGAAAGCAGTCTACC;RSEQ=CTGGAGGTGGTAGCAAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:43,59:0:2,0:23.3:1:30.9:1:1:0:60:33:1:0:0.1 0/1:132:2:1,1:56,74:0.0152:2,2:6.5:1:27:1:1:1.32:60:4:0.0155:0:1 -8 68097955 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22437;SOR=0;LSEQ=CAAAGAAAAAAGTAAAACTT;RSEQ=CTGCTGCTGAAGATGATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:63,57:0.0164:2,2:13:1:32:0:1:1.10435:60:4:0.0164:0:1 0/0:135:0:0,0:66,69:0:2,0:24.5:1:31.8:1:1:0:60:66.5:1:0:0.1 -8 68097975 . AGAT A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.49847;SOR=Inf;LSEQ=GCTGCTGCTGAAGATGATGA;RSEQ=GATGATGATGAGTTTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:74,57:0:2,0:26:1:31.8:1:1:0:60:42.667:1:0:0.2 0/1:138:2:1,1:67,69:0.0145:2,2:41.5:1:31:1:1:1.03:60:4:0.0147:0:0 -8 68098012 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5048;SOR=Inf;LSEQ=TTGATGATGAGGAAGCTGAA;RSEQ=AAAAAGCACCAGTGAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:73,46:0:2,0:26.2:1:31.9:1:1:0:60:118:1:0:0.1 0/1:150:2:1,1:85,63:0.0133:2,2:6:0:27:1:1:1.34646:60:4:0.0135:0:1 -8 68098042 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5053;SOR=Inf;LSEQ=CAGTGAAGAAATCTATACAA;RSEQ=ATACTCCAGCCAGAAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:84,51:0:2,0:21.4:1:31.7:1:1:0:60:134:1:0:0.1 0/1:171:2:1,1:108,61:0.0117:2,2:22.5:1:28:1:1:1.76418:60:4:0.012:0:1 -8 68098051 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50814;SOR=Inf;LSEQ=AATCTATACAAGATACTCCA;RSEQ=CCAGAAATGCATAAAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:89,47:0:2,0:23.2:1:32.2:1:1:0:60:135:1:0:0.1 0/1:180:2:1,1:117,61:0.0111:2,2:6.5:1:27:1:1:1.91068:60:4:0.0112:0:2 -8 68098207 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18422;SOR=0;LSEQ=CCTTTGCACTTAAAGCAAAA;RSEQ=TGCAAGCAAGTATAGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:21,72:0.0208:2,2:12.5:1:30:1:0.41142:3.37:60:4:0.0211:0:2 0/0:127:0:0,0:35,92:0:2,0:21.9:1:29.6:1:1:0:60:254:1:0:0.1 -8 69707655 . A C 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01818;SOR=Inf;LSEQ=TGTTGAAAACTGGACATGTA;RSEQ=TATAACATAATGTGGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:22.5:1:30.4:1:1:0:60:16:1:0:0 1/0:4:3:3,0:1,0:0.75:0,0:23:1:32:1:1:0:60:6:0.75:0:1 -8 70250304 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16771;SOR=Inf;LSEQ=TCTGCAGAAAGTGAATCCAG;RSEQ=CTGCAGAGCTGAGGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:118,37:0:2,0:23.9:1:31.5:1:1:0:60:50.667:1:0:0 0/1:108:2:1,1:76,29:0.0185:2,2:29.5:1:27.5:1:0.48404:2.59354:60:4:0.0187:0:1 -8 70250326 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19713;SOR=Inf;LSEQ=TGCAGAGCTGAGGCTGCTCT;RSEQ=ATGCAGCAAAACTTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:141,65:0:2,0:26:1:31.4:1:1:0:60:28.429:1:0:0.2 0/1:165:2:1,1:102,60:0.0121:2,2:19:1:29.5:1:1:1.69418:60:4:0.0125:0:1.5 -8 70250399 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.103;SOR=Inf;LSEQ=ACCCAAGAGGCCCTTCCCCA;RSEQ=TTGGACCACAGCCAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:145,161:0:2,0:25.3:1:31.7:1:1:0:60:101:1:0:0.5 0/1:271:3:2,1:129,139:0.0111:2,2:6.7:1:24.3:1:0.61145:2.15:60:6:0.0112:0:1.3 -8 70250407 . A G 220 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43973;SOR=0.86626;LSEQ=GGCCCTTCCCCACTTGGACC;RSEQ=CAGCCAGCAGTTTGCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:137:60,77:75,88:0.4567:2,2:26.2:1:31.1:1:0.7277:1.09342:60:274:0.4582:0:1.1 0/1:254:107:53,54:68,78:0.4213:2,2:27.9:1:31:1:0.70271:1.13:60:106:0.4257:0:1.2 -8 70250462 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22345;SOR=Inf;LSEQ=GCTGAAGGGACATCTGTGTC;RSEQ=ATGCAACCCACGTACAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:56,142:0:2,0:24.8:1:28.8:1:1:0:60:65:1:0:0.4 0/1:178:2:1,1:74,102:0.0112:2,2:9:1:29.5:1:1:1.38:60:4:0.0115:0:1.5 -8 70250559 . G A 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05839;SOR=0;LSEQ=GGGAGAGCTCAGTGGGAATC;RSEQ=ATGGAGAGGAGGACTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:0,5:2,24:0.1613:2,0:30:1:30.6:1:1:0:60:10:0.1613:0:1.2 0/0:25:0:0,0:0,25:0:1,0:21.8:1:31.8:1:1:0:60:50:1:0:0.3 -8 70250609 . G T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.65702;SOR=1.89033;LSEQ=CCAGAACCGGCTGACCATGT;RSEQ=CTGGCCACTCTCTGCCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:1,8:0,5:0.6429:0,2:28.6:1:29.4:1:1:0:60:18:0.6429:0:1.1 1/0:9:7:0,7:0,2:0.7778:0,0:23.1:1:28.6:1:1:0:60:14:0.7778:0:1.3 -8 72265404 . C T 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.58159;SOR=0.38276;LSEQ=GGTCACCTACGGGCCTTCTG;RSEQ=AGCTCCTGTCAGTGGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:62,44:0.0185:2,2:7.5:1:27.5:1:1:1.40451:60:4:0.0187:0:1.5 0/0:140:1:0,1:80,59:0.0071:2,0:1:0:24:0:0.42857:0:60:2:0.0072:0:1 -8 72265468 . C A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6268;SOR=2.57574;LSEQ=CCTGCCGGCGCAGGGACCTG;RSEQ=GGCAGTCTGGGTGACTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:1:1,0:42,64:0.0093:2,0:1:0:26:0:0.40187:0:60:2:0.0093:0:1 0/1:126:3:2,1:58,65:0.0238:2,2:18.3:1:29:1:0.60461:2.23:60:6:0.024:0:1.3 -8 72265495 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49645;SOR=0;LSEQ=CTGGGTGACTATATCCACAC;RSEQ=CAGTCTGTACTCTGCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:21,48:0.0282:2,2:30:1:30:1:0.52676:2.26:60:4:0.0282:0:1 0/0:70:0:0,0:21,49:0:2,0:20.6:1:30.3:1:1:0:60:34:1:0:0.1 -8 72265510 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09591;SOR=Inf;LSEQ=CACACCCAGTCTGTACTCTG;RSEQ=AGTAGGCATGCTTTACCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:10,35:0:2,0:22.9:1:31.8:1:1:0:60:44:1:0:0.1 0/1:39:3:1,2:5,31:0.0769:2,2:30.7:1:29.3:1:0.403:2.98:60:6:0.0789:0:1 -8 73306731 . T C 115 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01491;SOR=0;LSEQ=CAGTCAGGGATAGTACAAGA;RSEQ=GCTGCCTGGGATTTATAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:10,3:0,0:1:0,2:21.9:1:31.1:1:1:0:60:26:1:0:1.5 1/0:12:7:5,2:4,1:0.5833:2,2:15.4:1:30.9:1:1:1.53983:60:14:0.5833:0:1 -8 73307007 . A G 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GAGGACCCCTGGCCCAACCC;RSEQ=CTGGCCCTTTGACTGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:11:1:32.5:1:1:0:60:4:0.5:0:1 0/0:2:0:0,0:0,2:0:0,0:35.5:1:31:1:1:0:60:4:1:0:0 -8 73408209 . CT C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2182;SOR=0;LSEQ=CATCTCAGGGATGGGCCTGC;RSEQ=TAGTATTTCTGCCACATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:27,39:0.0294:2,2:45:1:32:1:1:1.44:60:4:0.0299:0:0 0/0:77:0:0,0:29,48:0:2,0:31.8:1:30.3:1:1:0:60:76:1:0:0.1 -8 73408246 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49438;SOR=Inf;LSEQ=ATTCCATCATTGAGCAGCCC;RSEQ=TGGAAAGGATGGCCTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:16,29:0:2,0:21.8:1:30:1:1:0:60:44:1:0:0.1 0/1:45:2:0,2:14,29:0.0444:2,0:20:1:32.5:1:1:0:60:4:0.0444:0:1 -8 74502130 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.20913;SOR=0;LSEQ=GGATGACAAAGATGAGGATG;RSEQ=GGATGAGGAAGGAAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:9,19:0.0667:2,2:35:1:30:1:1:2.05:60:4:0.0769:0:1 0/0:35:0:0,0:14,21:0:2,0:29.5:1:28.7:1:1:0:60:16.5:1:0:0.1 -8 74825468 . T A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50263;SOR=Inf;LSEQ=TTCAAACTCTTATACCAACC;RSEQ=CTGGAGTTGGGCAACATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:22,20:0:2,0:27.8:1:29.5:1:1:0:55.4:13:1:0:0.1 0/1:54:2:1,1:24,28:0.037:2,2:21.5:1:24.5:1:1:1.16:50:4:0.0385:0:1.5 -8 74825478 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21711;SOR=0;LSEQ=TATACCAACCTCTGGAGTTG;RSEQ=GCAACATGGCTTCTCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:20,23:0.0444:2,2:10.5:1:29:1:1:1.15:22:4:0.0455:0:4 0/0:51:0:0,0:21,30:0:2,0:28.9:1:29.3:1:1:0:55.1:16:1:0:0.1 -8 74859123 . T G 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAATTCATATGTTGAAGTC;RSEQ=TAACCCCTTGTACCACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:1,52:0:1,0:23.9:1:30.4:1:1:0:60:52:1:0:0 1/0:21:11:0,11:0,10:0.5238:0,0:17.3:1:31.6:1:1:0:60:22:0.5238:0:1.1 -8 74859253 . G A 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=TGTTTGTTTGAGACAGAGTC;RSEQ=CGCTCTGTCACCCAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:43:1:32:0:1:0:60:6:0.75:0:1 0/0:2:0:0,0:1,1:0:2,0:13:1:31.5:1:1:0:60:4:1:0:0.5 -8 74859292 . C G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GAAGTGCAATGGCGGGATCT;RSEQ=AGCTCACTGCAACCTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:8.5:1:31.8:1:1:0:57.8:8:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:39:1:30.5:1:1:0:60:4:1:0:1 -8 74868305 . T C 226 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TCCATCTAAAGTAAAGTAAG;RSEQ=AGTGAAACAATTTTTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:531:0:0,0:209,322:0:2,0:26.3:1:28.6:1:1:0:60:264.5:1:0:0.1 0/1:732:139:57,82:237,354:0.1899:2,2:26.3:1:31.8:1:0.84813:1.04:60:68.5:0.1908:0:1.1 -8 74868355 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24044;SOR=0;LSEQ=ACTAAAACTAAACAGGTTTG;RSEQ=CTGGGCGCAGTGGCTCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:27,161:0.0105:2,0:31.5:1:29.5:1:1:0:60:4:0.0108:0:1.5 0/0:198:0:0,0:30,167:0:2,0:21.1:1:31.7:1:1:0:60:64.667:0.9949:0:0.4 -8 74868359 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.61742;SOR=2.07953;LSEQ=AAACTAAACAGGTTTGGCTG;RSEQ=GCGCAGTGGCTCACGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:0,1:18,156:0.0057:2,0:12:0:15:0:1:0:60:0:0:0:7 0/1:169:2:1,1:21,146:0.0118:2,2:24:1:27.5:1:0.24408:6.82:60:4:0.0119:0:1 -8 74868374 . G A 141 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=37.68944;LSEQ=GGCTGGGCGCAGTGGCTCAC;RSEQ=CCTGTAATCCCAGCACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:1:1,0:3,123:0.0079:1,0:1:0:26:0:0.0315:0:60:2:0.0079:0:1 0/1:112:26:0,26:2,84:0.2321:1,1:23.2:1:30.1:1:1:0:60:52:0.2321:0:1 -8 74868478 . T C 116 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.71398;SOR=1.59456;LSEQ=AAAAATACAAAAATTAGCTG;RSEQ=GTGTGGTGGCGCACACATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:0,13:0,14:0.4815:1,1:23.6:1:31.4:1:1:0:60:26:0.4815:0:1 1/0:10:6:0,6:0,4:0.6:0,0:23:1:29.3:1:1:0:60:12:0.6:0:1 -8 74872101 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.23477;SOR=Inf;LSEQ=ATTAATGTTGCAAGAGACAA;RSEQ=TTTTCATTCACTGTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:1,124:0:1,0:22.9:1:32.2:1:1:0:60:61.5:1:0:0.1 0/1:118:2:0,2:3,113:0.0169:1,0:14.5:1:24.5:1:1:0:60:4:0.0169:0:1 -8 74874810 . CA C 123 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01172;LSEQ=TACTCTTTTAAAAAACAAAA;RSEQ=AAAAAAAAAACAAAACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:14:13,1:32,1:0.2917:1,1:22.8:1:32.5:1:0.51156:2.40879:60:28:0.2979:0.0625:0.3 0/1:17:5:5,0:12,0:0.2941:0,0:25.2:1:32.2:1:1:0:60:10:0.2941:0:0 -8 74884451 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTTCCGCTGGGTCAGAGCC;RSEQ=CTTTCGGCGACGCGCGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:42:1:31:1:1:0:60:4:1:0:1 -8 74884999 . T C 169 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=33.16985;LSEQ=CACAGCAACGACTAGCGCAA;RSEQ=CGGCTGGCCTCATTTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1169:1:0,1:637,531:9e-04:2,0:27:0:11:0:0.45509:0:60:0:0:0:1 0/1:1520:42:25,17:821,656:0.0276:2,2:26.1:1:31.4:1:0.64025:1.17:60:84:0.028:0:1.2 -8 74885157 . A AC 303 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.04245;LSEQ=GAAAATCCAGGCGCCTGCCA;RSEQ=ACCGTTACTCAGTTTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:749:741:199,542:5,3:0.9893:2,2:24:1:31.8:1:0.03823:4.5283:60:147.2:0.9919:0.2336:0.1 1/0:808:644:161,483:67,94:0.797:2,2:26.8:1:31.5:1:5e-05:2.13609:60:57.545:0.7952:0.0495:0.2 -8 74885209 . AC A 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.09751;SOR=Inf;LSEQ=CATTCCACGCCCCGCTTCCC;RSEQ=CCCCCCGCGTTTCCTATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:12,219:0:2,0:24.7:1:30.9:1:1:0:60:27.875:1:0:0.1 0/1:198:3:1,2:7,188:0.0152:1,2:19.3:1:33:0:0.11695:12.89:60:6:0.0155:0:0 -8 74885277 . G A 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03794;SOR=0;LSEQ=GGCTGAAACAGCTAAATAAA;RSEQ=TTCACCTTCTACTGTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:6:0,6:1,43:0.12:1,0:15.8:1:31.2:1:1:0:60:12:0.1224:0:1 0/0:36:0:0,0:2,34:0:2,0:21.4:1:31.5:1:1:0:60:72:1:0:0 -8 74951823 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54338;SOR=Inf;LSEQ=ACAAGCGGGGCAGGGTAAGG;RSEQ=GGGTGGATCTTCTAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:23.2:1:30:1:1:0:58.6:50:1:0:0.2 0/1:48:2:1,1:27,19:0.0417:2,2:31.5:1:30.5:1:1:1.41046:60:4:0.0417:0:1 -8 74951835 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.52048;SOR=Inf;LSEQ=GGGTAAGGAGGGTGGATCTT;RSEQ=TAAGTGATTGATAAGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:0:2,0:27.5:1:31.5:1:1:0:58.1:60:1:0:0.3 0/1:48:2:1,1:26,20:0.0417:2,2:26.5:1:26.5:1:1:1.29283:60:4:0.0417:0:1 -8 74951878 . AG A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49531;SOR=Inf;LSEQ=AAGTCATGTGATCATAGGAC;RSEQ=GGGGCCCTTCCCTTTTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:14,17:0:2,0:25.4:1:31.3:1:1:0:58.1:62:0.9688:0:0.2 0/1:37:2:1,1:17,18:0.0541:2,2:26.5:1:31:1:1:1.06:49:4:0.0541:0:0 -8 77617027 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.18721;SOR=Inf;LSEQ=TGTCTATGATCTCCGACACA;RSEQ=GAGAGAGAAAGACTATCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:141,17:0:2,0:20.8:1:30.2:1:1:0:60:38.5:1:0:0.1 0/1:121:2:1,1:103,16:0.0165:2,2:6.5:1:29:1:0.26226:6.27554:60:4:0.0171:0:1 -8 77618304 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20487;SOR=Inf;LSEQ=AATATCAGCAGACCCTGGAG;RSEQ=CCCATATGAAGGAGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:103,27:0:2,0:27.2:1:31:1:1:0:60:42.333:1:0:0.1 0/1:108:2:1,1:67,39:0.0185:2,2:37.5:1:28.5:1:1:1.70887:60:4:0.0187:0:1 -8 77618681 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08282;SOR=Inf;LSEQ=AGGAACCTCCGAATTCATAT;RSEQ=ACCAGCGAAAAGCACATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:105,159:0:2,0:25:1:31.4:1:1:0:60:263:1:0:0.1 0/1:205:3:2,1:91,111:0.0146:2,2:24:1:24:1:0.59143:2.43:60:6:0.0149:0:1 -8 77618940 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCCTGCTTTTCTGCACT;RSEQ=TTGTTAGTTTCTAATCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:26.5:1:29:1:1:0:60:4:0.4:0:3.5 0/0:1:0:0,0:0,1:0:0,0:14:0:32:0:1:0:60:2:1:0:0 -8 77619945 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5162;SOR=0;LSEQ=TCACCTCTGACAGCCTGGAG;RSEQ=CCCTAAGTGTGCATGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:134,1:0.0146:1,2:46.5:1:30.5:1:0.02909:95.10689:60:4:0.0152:0:1 0/0:93:0:0,0:91,2:0:1,0:23.8:1:31.6:1:1:0:60:186:1:0:0.1 -8 77620114 . C A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37316;SOR=3.95486;LSEQ=GCAGAAATATCAACTGGTGG;RSEQ=TCACATTAAAGAAGGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:1:1,0:68,249:0.0031:2,0:1:0:24:0:0.21698:0:60:2:0.0032:0:1 0/1:324:4:2,2:89,231:0.0123:2,2:21:1:29:1:0.3143:2.59:60:8:0.0126:0:1.3 -8 77764531 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=AACATCACGTTGGTCAAACT;RSEQ=AACTCCAGATACTACAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:14,0:0.125:1,0:47:1:31.5:1:1:0:60:4:0.125:0:1 0/0:24:0:0,0:22,2:0:2,0:23.4:1:32:1:1:0:60:48:1:0:0 -8 77764658 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22483;SOR=Inf;LSEQ=ACAGCAGGCAAGCAAATTAT;RSEQ=GAAACAAGAGCAAAGTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:22,34:0:2,0:30.4:1:30.2:1:1:0:60:55:1:0:0.1 0/1:51:2:1,1:18,31:0.0392:2,2:23.5:1:27:1:1:1.70:60:4:0.0392:0:1.5 -8 77767089 . GA G 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=1.5344;LSEQ=ATTGCCCGCGAAGTCGGGCT;RSEQ=AAAAAAGGGTCGTGCAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:1,0:29,8:0.0263:2,0:24:0:34:0:1:0:60:2:0.0278:0:0 0/1:50:2:2,0:26,22:0.04:2,0:10.5:1:33:1:0.49714:0:60:4:0.04:0:0 -8 77767130 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49712;SOR=Inf;LSEQ=CTGGTTCCAGAATACACGAG;RSEQ=GCGGGAGAGGAAAGGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:35,24:0:2,0:29.8:1:30.7:1:1:0:60:58:1:0:0.2 0/1:65:2:1,1:25,38:0.0308:2,2:20:0:28.5:1:1:1.51:60:4:0.0317:0:1 -8 77776848 . TA T 113 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.23529;SOR=0;LSEQ=AAAAATAAAAAATAAAAAAA;RSEQ=AAAAAAAAATAAGACTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:0,13:0,3:0.8125:0,1:30.6:1:30.7:1:1:0:60:26:0.8125:0:0 0/0:1:0:0,0:0,1:0:0,0:23:0:31:0:1:0:60:2:1:0:0 -8 81288634 . A G 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.09375;LSEQ=GGTCACACATTTAAAAACTC;RSEQ=TTGAATTATACACTGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:0.5714:0,0:35.8:1:31.3:1:1:0:60:8:0.5714:0:1 1/0:4:3:3,0:1,0:0.75:0,0:22.3:1:29.3:1:1:0:60:6:0.75:0:1 -8 81288734 . A T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48003;SOR=0.69561;LSEQ=TACCACAGGTGAGGCTGGAA;RSEQ=GGTGGGCAGGGACAGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:32:31,1:18,0:0.64:1,1:22.4:1:30.6:1:1:0:60:31:0.6327:0:1.1 1/0:29:16:15,1:12,1:0.5517:1,1:29.9:1:30.4:1:1:1.24:60:32:0.5714:0:1.1 -8 81288806 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.20691;SOR=0;LSEQ=AAAGAGGCTGAACTTGGCTC;RSEQ=AAAAGCATTAGGGAGCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:91,31:0.0161:2,2:13.5:1:28:1:0.45109:2.90529:60:4:0.0161:0:1.5 0/0:148:0:0,0:114,34:0:2,0:21.9:1:30.2:1:1:0:60:296:1:0:0.1 -8 81288812 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2555;SOR=Inf;LSEQ=GCTGAACTTGGCTCTAAAAG;RSEQ=ATTAGGGAGCTATTGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:100,40:0:2,0:22.3:1:31.5:1:1:0:60:139:1:0:0.2 0/1:172:3:2,1:121,48:0.0174:2,2:19.3:1:28.3:1:1:1.25868:60:6:0.0175:0:1 -8 81288925 . G T 232 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.81571;SOR=0.95834;LSEQ=TGCCTTTCCTAGTATTCATT;RSEQ=TTTTATGTCAACATCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:308:187:91,96:62,59:0.6071:2,2:27.3:1:30.3:1:0.72648:1.10821:60:374:0.6071:0:1.2 1/0:392:234:114,120:75,82:0.5969:2,2:25.7:1:29.6:1:0.91783:1.04:60:77:0.5954:0:1.1 -8 81289045 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22195;SOR=Inf;LSEQ=TTATCCCAAGAGATCTCTTT;RSEQ=ATTTCTTATGACCTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:10,77:0:2,0:24.7:1:27.9:1:1:0:60:42.5:1:0:0.1 0/1:78:2:1,1:7,69:0.0256:2,2:30:1:30:1:0.1958:9.29:60:4:0.026:0:1 -8 81289060 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50236;SOR=0;LSEQ=TCTTTTATTTCTTATGACCT;RSEQ=GTTTTATAGAAATCTGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:4,63:0.029:2,2:6.5:1:28.5:1:0.14066:14.19:60:4:0.0299:0:1 0/0:55:0:0,0:4,51:0:2,0:23.1:1:30:1:1:0:60:54:1:0:0.1 -8 81291019 . G A 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGGATGCCAAGAACAGCTGT;RSEQ=GAAATGTGCTGATGACAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:21.5:1:30.5:1:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:20:0:30:1:1:0:60:4:0.6667:0:1.5 -8 83004063 . C G 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77227;LSEQ=ACTCTCTAGGCCAGCCAAAG;RSEQ=GTCAGCGGGTCAGTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:6,1:6,2:0.4667:2,2:24.3:1:28:1:1:1.91:60:6:0.4286:0:1 0/1:5:2:2,0:2,1:0.4:2,0:23.5:1:30.5:1:1:0:60:4:0.4:0:1 -8 83004237 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24708;SOR=0;LSEQ=TAGCAATATGGCTGTCACGG;RSEQ=ACCTAGAAAGGGGAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:72,54:0.0156:2,2:24.5:1:31:1:1:1.33029:60:4:0.0157:0:1 0/0:129:0:0,0:72,57:0:2,0:24.7:1:30.5:1:1:0:59.1:63.5:1:0:0.4 -8 83004264 . C T 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00088;SOR=Inf;LSEQ=AAAGGGGAGAAGCCATGTCG;RSEQ=CCAACTCCAGAGGTTGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:68,75:0:2,0:28.9:1:31.3:1:1:0:59:34.75:1:0:0.4 0/1:155:11:5,6:78,66:0.071:2,2:32.7:1:28.9:1:0.75569:1.41496:56.4:22:0.071:0:2.2 -8 83004303 . G C 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01345;SOR=0.49987;LSEQ=ATAAGAGTTTGAAAGGCATT;RSEQ=TCTGATTTCAGAAAACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:46:16,30:23,42:0.4107:2,2:24.3:1:31:1:1:1.02655:58:22:0.4037:0:1.2 0/1:128:33:15,18:41,54:0.2578:2,2:21.9:1:30.5:1:0.841:1.10:59.2:32:0.256:0:1.5 -8 83004383 . T C 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23792;SOR=3.08004;LSEQ=GGTTAGTGTAAAAACAACAC;RSEQ=CTTCCCCTAAGAAGGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:3,16:0.0952:2,0:31.5:1:33:0:1:0:60:4:0.1:0:1.5 0/1:20:5:0,5:2,13:0.25:2,0:23.6:1:31.6:1:1:0:60:10:0.25:0:1.4 -8 84050892 . T C 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23843;SOR=1.20008;LSEQ=AGATTTAACTACTTCCTCAT;RSEQ=TCCCAGAGCTTAAAGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:432:265:127,138:76,90:0.6134:2,2:26.2:1:31.6:1:0.69231:1.09:60:264:0.6125:0:1.1 1/0:366:240:120,120:57,68:0.6557:2,2:25.3:1:31:1:0.44157:1.19:60:79:0.6565:0:1.1 -8 86484883 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCAGAGCTTGGACACACA;RSEQ=AACTTCAGTTTCCTCAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:13:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 86485227 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49959;SOR=0;LSEQ=AATCAGCACCCAAATACTTA;RSEQ=GGATACTGCACTGTGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:124,66:0.0104:2,2:20.5:1:27:1:1:1.87229:60:4:0.0105:0:1 0/0:176:0:0,0:119,57:0:2,0:25.1:1:30.3:1:1:0:60:175:1:0:0.3 -8 86485232 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22206;SOR=Inf;LSEQ=GCACCCAAATACTTACGGAT;RSEQ=CTGCACTGTGAGGGGCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:143,73:0:2,0:24.9:1:28.5:1:1:0:60:215:1:0:0.3 0/1:193:2:1,1:125,66:0.0104:2,2:22.5:1:31:0:1:1.88733:60:4:0.0105:0:1.5 -8 86485245 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.102;SOR=Inf;LSEQ=TACGGATACTGCACTGTGAG;RSEQ=GGCTGTCACTAACCCTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:158,94:0:2,0:26.2:1:30.2:1:1:0:60:21.909:1:0:0.4 0/1:222:3:1,2:134,85:0.0135:2,2:13.7:1:29:1:0.56257:3.13633:60:6:0.0138:0:1.3 -8 86485306 . G C 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01214;SOR=1.53365;LSEQ=CTCATCGTGTTGCTCTGGGA;RSEQ=TTGAGCTCAGGCTACCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:285:150:66,84:67,67:0.5263:2,2:26.4:1:31.7:1:0.34155:1.27163:60:74:0.5267:0:1.1 1/0:303:191:91,100:56,56:0.6304:2,2:24.4:1:30.9:1:0.72187:1.09856:60:37.2:0.6284:0:1.2 -8 86485358 . T C 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGTGATCTGCTCACTCTC;RSEQ=GGCTTAAAATCACCCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:57,123:0:2,0:21.1:1:30.1:1:1:0:60:44:1:0:0.4 0/1:186:33:11,22:48,102:0.1774:2,2:24.2:1:29.5:1:1:1.06:60:32:0.1778:0:1.1 -8 87557789 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAATTTCTAATACTCAA;RSEQ=AATTAATACTTATGATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:24.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 87558138 . A G 173 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00044;SOR=0.29593;LSEQ=TAAATTTCATATAGTTGTAG;RSEQ=AATTTAAAGAGGTAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:44:42,2:132,6:0.2418:1,1:25.3:1:31.7:1:1:1.04735:60:88:0.2431:0:1 0/1:128:11:11,0:112,5:0.0859:1,0:19.1:1:32:1:1:0:60:22:0.0859:0:1.2 -8 87558142 . T G 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.002;SOR=0.49765;LSEQ=TTTCATATAGTTGTAGAAAT;RSEQ=TAAAGAGGTAGATAGAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:194:115:107,8:74,5:0.5928:2,2:25.2:1:32.6:1:1:1.106:60:230:0.599:0:1 0/1:143:60:56,4:77,5:0.4196:2,2:25.3:1:32.1:1:1:1.09926:60:120:0.4225:0:1.1 -8 87558210 . G T 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACAGAGGAGAACAACTTGA;RSEQ=CCAAGCCCTAAAGATGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:0:0,0:343,257:0:2,0:27.2:1:31.7:1:1:0:60:53.545:1:0:0.4 0/1:599:25:14,11:332,242:0.0417:2,2:20.5:1:29.2:1:0.83979:1.07779:60:50:0.042:0:1.9 -8 87558283 . C A 246 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=0.64405;LSEQ=TTGGGGGAAGGAAATATAAA;RSEQ=AAGAGGAGGTGTTAGATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:576:318:124,194:110,145:0.5521:2,2:25.1:1:29.9:1:0.34704:1.18651:60:158:0.5544:0:1.1 0/1:721:319:147,172:173,228:0.4424:2,2:24.3:1:29.6:1:0.45071:1.13:60:105.333:0.442:0:1.2 -8 87558346 . C T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGAGAAGATCTTTGATG;RSEQ=ATATTTTACCATAGAGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:54,214:0:2,0:25.6:1:31.8:1:1:0:60:43.667:1:0:0.4 0/1:249:17:7,10:57,174:0.0683:2,2:23.6:1:29.2:1:0.1531:2.13:60:34:0.0694:0:1.6 -8 87558392 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=ATATATTTGTTTTATGATGT;RSEQ=ATTTTTTTTTCTTTTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:5,100:0:1,0:25.9:1:28.6:1:1:0:60:104:1:0:0.1 0/1:88:2:1,1:7,79:0.0227:2,2:12:1:32:1:0.1745:10.62:60:4:0.0227:0:1.5 -8 87558393 . A AT 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08188;SOR=4.43014;LSEQ=TATATTTGTTTTATGATGTT;RSEQ=TTTTTTTTTCTTTTCTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:5,96:0.0192:1,0:27:1:31:1:1:0:60:4:0.0192:0:0 0/1:87:7:0,7:8,72:0.0805:2,0:32.6:1:30.4:1:1:0:60:14:0.0805:0:0.1 -8 87558415 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1537;SOR=Inf;LSEQ=TTTTTTTTCTTTTCTTTGCA;RSEQ=CATATTTTCGTTCTTTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:0,69:0:1,0:23.4:1:32.5:1:1:0:60:33.5:1:0:0.1 0/1:45:2:1,1:1,42:0.0444:1,2:5:1:28.5:1:0.08788:30.05:60:4:0.0455:0:1 -8 87938650 . C T 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00699;SOR=Inf;LSEQ=AGTTGTAAGACCATCTGTAG;RSEQ=TTGATGGCCTTGATCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:20.5:1:31.5:1:1:0:60:16:1:0:0.1 1/0:8:6:3,3:1,1:0.75:2,2:35.8:1:28.5:1:1:1:60:12:0.75:0:1.3 -8 87938708 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11084;SOR=Inf;LSEQ=GGAGGTTAAAAATACAGGGC;RSEQ=TAAAGGCAAGTAATACCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:14,5:0:2,0:16.9:1:31.8:1:1:0:60:38:1:0:0.1 0/1:10:2:1,1:4,4:0.2:2,2:26:1:30.5:1:1:1:60:4:0.2:0:1.5 -8 87938783 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20054;SOR=Inf;LSEQ=ATGTCACCCAACTCCAGAGG;RSEQ=TGGTGTCAGAGTTTGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,26:0:2,0:27.9:1:29.7:1:1:0:60:44:1:0:0.1 0/1:37:2:1,1:19,16:0.0541:2,2:23:1:30.5:1:1:1.18197:60:4:0.0541:0:1.5 -8 87938824 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.52715;SOR=Inf;LSEQ=CATTGTCTGATTTCAGAAGC;RSEQ=TTTCCTGTAAACACCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:22.3:1:31.2:1:1:0:60:38:1:0:0.2 0/1:33:2:1,1:15,16:0.0606:2,2:12.5:1:30:1:1:1.06:60:4:0.0625:0:0 -8 88515609 . T C 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTATATATATACTTAATTCC;RSEQ=GTAACAGGAAGAAGATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:7:1:32.5:1:1:0:60:4:0.3333:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:25:0:27:0:1:0:60:2:0.3333:0:1 -8 88515743 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4964;SOR=Inf;LSEQ=AGCATCAGATCTTGGGGAAA;RSEQ=GTTTTTATTCAAGGCTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:43,27:0:2,0:26.8:1:31.7:1:1:0:60:140:1:0:0.1 0/1:70:2:1,1:48,20:0.0286:2,2:13.5:1:28.5:1:0.51304:2.36645:60:4:0.029:0:1 -8 88515744 . G T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24468;SOR=0;LSEQ=GCATCAGATCTTGGGGAAAG;RSEQ=TTTTTATTCAAGGCTATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:3:1,2:42,26:0.0423:2,2:19.7:1:26.3:1:0.55762:3.17645:60:6:0.0423:0:1 0/0:70:0:0,0:49,21:0:2,0:21.9:1:31.3:1:1:0:60:140:1:0:0.2 -8 88515764 . GGTT G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.2074;SOR=0;LSEQ=GTTTTTATTCAAGGCTATGT;RSEQ=GTTGTTGTTGTTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:48,45:0.0211:2,2:41:1:33:1:1:1.06598:60:4:0.0215:0:0 0/0:113:0:0,0:64,49:0:2,0:23.8:1:30.7:1:1:0:59.4:55.5:1:0:0.2 -8 88515778 . TTGC T 31 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.58597;SOR=0.39593;LSEQ=CTATGTGGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:50,47:0.0202:2,2:49:0:31.5:1:1:1.0632:60:4:0.0202:0:0 0/0:124:1:1,0:65,58:0.0081:2,0:23:0:32:0:1:0:60:2:0.0081:0:0 -8 88515792 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5073;SOR=Inf;LSEQ=TTGTTGTTGCTGCTGCTGCT;RSEQ=TTGCTGCTGCTTTGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:44,53:0:2,0:27.8:1:31.9:1:1:0:60:31.333:1:0:0.1 0/1:128:2:1,1:63,63:0.0156:2,2:32:1:27.5:1:1:1:60:4:0.0157:0:1 -8 88515868 . G C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.83585;LSEQ=AGGAAGACAGTAGTGTTAGA;RSEQ=AGTGAAAGAAAGAAAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:2,4:1,19:0.2308:1,2:31.2:1:27.7:1:0.12308:8.40:60:5:0.2:0:1 0/1:35:7:0,7:5,23:0.2:2,0:20.3:1:31.4:1:0.5585:0:60:14:0.2:0:1 -8 90282757 . A T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19335;SOR=4.52592;LSEQ=TTGTTACATCCAATAATATG;RSEQ=TACATGTTTTGAGATACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:0,1:147,97:0.0041:2,0:1:0:30:0:0.4:0:60:2:0.0041:0:1 0/1:219:4:4,0:133,82:0.0183:2,0:17.5:1:30.8:1:0.2995:0:60:8:0.0184:0:1 -8 90282811 . T A 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57826;SOR=0.88853;LSEQ=AGATACTCCCTACTATCTTT;RSEQ=AACATTAAATTCCAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:81:42,39:100,114:0.2746:2,2:24.9:1:29.4:1:0.43721:1.23:60:162:0.2774:0:1.1 0/1:306:77:39,38:122,107:0.2516:2,2:27.4:1:28.6:1:0.69472:1.11057:60:37.5:0.2483:0:1.1 -8 90282866 . AT A 56 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.12346;SOR=0;LSEQ=TTTTTCTGGGTGTCATGGCC;RSEQ=TTTTAGCTGGCATTTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:4:3,1:83,141:0.0175:2,2:17.8:1:28.3:1:0.15189:5.06:60:8:0.0177:0.0088:0.5 0/0:222:0:0,0:94,128:0:2,0:25:1:29.7:1:1:0:60:110:1:0:0.2 -8 90947537 . C T 63 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=TTTAGTCTTTACCTTACGTA;RSEQ=ATTTAGAATTTTGAACTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:33:1:31.5:1:1:0:60:8:0.4:0:1 1/1:1:1:1,0:0,0:1:0,0:10:0:31:0:1:0:60:2:1:0:1 -8 90948042 . CA C 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54177;SOR=0;LSEQ=TGATGAAAATATGGTAAAAA;RSEQ=AAAAAAAAATCAACAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:1,26:0.1:1,0:31.7:1:33.3:1:1:0:60:6:0.1034:0:0 0/0:13:0:0,0:1,12:0:1,0:25.8:1:28.3:1:1:0:60:12:1:0:0.1 -8 90949097 . T C 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02586;SOR=0;LSEQ=GCTATAGCCAATAAACCCAA;RSEQ=TGAGAGGTGCTTAAGTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:10:10,0:31,0:0.2439:1,0:24.9:1:32.7:1:1:0:60:20:0.25:0:1.1 0/0:17:0:0,0:16,1:0:1,0:21.9:1:30.9:1:1:0:60:34:1:0:0 -8 90949166 . G C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00256;SOR=Inf;LSEQ=ACTAGGTGTCTATGAGGACA;RSEQ=AAGAAACAAATTCTTAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:109,19:0:2,0:23.9:1:32.2:1:1:0:60:256:1:0:0.1 0/1:119:8:5,3:93,17:0.0672:2,2:12.1:1:31.3:1:0.13324:3.23805:60:16:0.0678:0:1 -8 90949174 . A T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.49786;LSEQ=TCTATGAGGACAGAAGAAAC;RSEQ=AATTCTTAATTTCTATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:123,32:0.0127:2,2:28:1:30:0:0.37727:3.80042:60:4:0.0127:0:1 0/0:157:1:0,1:121,35:0.0064:2,0:1:0:25:0:0.2293:0:60:2:0.0064:0:1 -8 90955170 . G C 59 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TACATTTAAGTGATATATTT;RSEQ=TAATATCCTCCACATTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:18.3:1:29.8:1:1:0:60:8:0.6667:0:1.5 0/0:2:0:0,0:2,0:0:0,0:9.5:1:32.5:1:1:0:60:4:1:0:0.5 -8 90955253 . T G 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06218;SOR=0;LSEQ=ATTAGGATGTAAACTGAATT;RSEQ=CTTAGGTCTCACCTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:11,0:0.4211:0,0:20.1:1:31.3:1:1:0:60:16:0.4211:0:2.9 0/0:7:0:0,0:7,0:0:0,0:15.7:1:30.7:1:1:0:60:14:1:0:1 -8 90955358 . C T 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06515;SOR=0.57798;LSEQ=TGCTCTGTAACTCAGGAATG;RSEQ=TCCTGAATGAATGACTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:61:60,1:85,0:0.4178:1,1:28.3:1:30:1:0.41781:0:60:60:0.4196:0:1 0/1:82:24:23,1:58,0:0.2927:1,1:27.5:1:29.2:1:0.29268:0:60:23:0.2875:0:1 -8 90955397 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15604;SOR=Inf;LSEQ=ATGTCACTTATTTTAATTTG;RSEQ=TTTTAAGAAGAATTTGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:266,38:0:2,0:22.7:1:31.3:1:1:0:60:59.8:1:0:0.2 0/1:199:2:1,1:160,36:0.0101:2,2:18.5:1:27:1:0.33959:4.39766:60:4:0.0102:0:1 -8 90955561 . T A 69 v4;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00218;SOR=Inf;LSEQ=TAGATCTGATCCTCCAATGA;RSEQ=GTGTGGAAGTTTTCCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:828:0:0,0:321,507:0:2,0:24.9:1:30.1:1:1:0:60:62.692:1:0:0.2 0/1:723:8:8,0:316,399:0.0111:2,0:6.6:1:23:1:0.00155:0:60:3:0.0084:0:1.3 -8 90955583 . A C 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGGAAGTTTTCCTGCTCC;RSEQ=GGATATGTGACCTATTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:0:0,0:237,472:0:2,0:25.9:1:30.6:1:1:0:60:40.706:1:0:0.3 0/1:554:26:10,16:209,319:0.0469:2,2:29.2:1:30.4:1:1:1.04819:60:52:0.0476:0:1.7 -8 90955624 . T A 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.46071;LSEQ=AATAAAAGTAGTACAGTAAA;RSEQ=CATATTAACAAACAAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:159:42,117:55,168:0.413:2,2:22.7:1:29.8:1:0.72153:1.10:60:158:0.4169:0:1.1 0/1:323:79:27,52:70,174:0.2446:2,2:23.2:1:29.3:1:0.39727:1.29:60:78:0.2461:0:1.4 -8 90955655 . T A 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AACAAAAATGACCATTTTTT;RSEQ=AAAAAGATTAAAAAGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:25,162:0:2,0:22.2:1:28.5:1:1:0:60:186:1:0:0.5 0/1:148:13:2,11:12,123:0.0878:2,2:27.1:1:30:1:0.35428:1.85:60:26:0.0878:0:2 -8 90958341 . C A 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAAACATTTCAAACACTGAC;RSEQ=TCTTGTGATACAGTTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:31:24,7:246,114:0.0791:2,2:26.3:1:28.9:1:0.41782:1.59:60:9.333:0.0727:0:1 0/0:346:0:0,0:236,110:0:2,0:24.3:1:30.4:1:1:0:60:114.333:1:0:0.2 -8 90958422 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32738;LSEQ=TAATCATCATTTATGCCAGA;RSEQ=GGATTTCTGGAAGTAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:264:144,120:241,197:0.375:2,2:26.4:1:30.8:1:0.93764:1.01944:60:131:0.3792:0:1.1 0/1:640:105:63,42:279,256:0.1641:2,2:26.1:1:30.5:1:0.16417:1.38:60:210:0.1667:0:1.1 -8 90958530 . T C 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.45201;LSEQ=AGTTTGTCATTGTTCTTAAA;RSEQ=GGGGTTAAGATGGATAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:169:55,114:78,174:0.4014:2,2:23.3:1:30.2:1:0.74912:1.08:60:41.25:0.4024:0:1.1 0/1:413:96:33,63:109,207:0.2324:2,2:25.1:1:29.8:1:1:1.00526:60:95:0.2363:0:1 -8 90959884 . A AAAT 43 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.27419;SOR=0;LSEQ=AATAAATAAACAAATAAATA;RSEQ=AATAATAATAATAATAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:3:3,0:72,0:0.04:1,0:24.7:1:27.2:1:1:0:60:2:0.027:0:2.7 0/0:50:0:0,0:50,0:0:1,0:21.8:1:30.8:1:1:0:60:100:1:0:0.1 -8 90959969 . T C 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12502;SOR=Inf;LSEQ=TTAGGAAAGAGAAATAATCC;RSEQ=AAGAATGTAAAATCACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:218,54:0:2,0:24.5:1:30.5:1:1:0:60:271:1:0:0.1 0/1:296:4:2,2:231,61:0.0135:2,2:33.8:1:30.5:1:0.19984:3.7646:60:8:0.0137:0:1 -8 90965928 . T TA 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22639;SOR=0.40051;LSEQ=TCATCCCTTTCCCTTAGATT;RSEQ=AAAAAAAAAGAAGAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:8:2,6:69,236:0.0256:2,2:29.8:1:28.5:1:1:1.14:60:16:0.0261:0:0.1 0/1:289:3:2,1:89,197:0.0104:2,2:22.3:1:25.7:1:0.23417:4.40:60:6:0.0104:0.0035:0.3 -8 90967464 . CT C 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTCTACAACAGTATAAAAAA;RSEQ=TTCATTTTTTTTTCAGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:249,69:0:2,0:23.2:1:31:1:1:0:60:62.6:1:0:0.1 0/1:275:15:12,3:190,70:0.0545:2,2:20.6:1:30.8:1:0.76586:1.47:60:30:0.0547:0.0109:0 -8 90967469 . A AT 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.87132;LSEQ=CAACAGTATAAAAAACTTTC;RSEQ=TTTTTTTTTCAGAGACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:8:6,2:255,80:0.0231:2,2:20.4:1:28:1:1:1.06232:60:7:0.0206:0.0029:0.1 0/1:297:6:3,3:210,80:0.0202:2,2:13:1:27.6:1:0.35458:2.61512:60:12:0.0205:0.0101:0.5 -8 90967711 . A G 245 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82751;SOR=1.02902;LSEQ=GACTCCTTTACAGTGGGTGC;RSEQ=TCTTGTGAAAGCATTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:281:122,159:178,229:0.4084:2,2:25.1:1:31.2:1:0.93785:1.01301:60:69.25:0.4092:0:1.1 0/1:703:292:134,158:186,223:0.4154:2,2:26:1:30:1:0.93877:1.02:60:72:0.4162:0:1.2 -8 90967862 . G T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06365;SOR=0.50724;LSEQ=GAAACAAAGATCGTTAAATA;RSEQ=TTCTAACGTAATATAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:39:1,38:0,67:0.3679:1,1:28.9:1:30.2:1:0.36792:0:60:78:0.3679:0:1.1 0/1:66:15:0,15:0,50:0.2273:1,1:17.1:1:30.5:1:1:0:60:30:0.2308:0:1.2 -8 90967869 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12668;SOR=Inf;LSEQ=AGATCGTTAAATAGTTCTAA;RSEQ=GTAATATAACCTTAGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:1,94:0:1,0:26.1:1:30.5:1:1:0:60:190:1:0:0.4 0/1:53:2:0,2:0,51:0.0377:1,0:8:1:30.5:1:1:0:60:4:0.0377:0:2 -8 90970862 . G T 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58994;SOR=0.84378;LSEQ=TTCCATGCTTTCTCTCTCAA;RSEQ=AGACAACCTGATAAAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:55:53,2:97,3:0.3548:1,1:25.5:1:31:1:1:1.2185:60:54:0.3553:0:1.5 0/1:101:32:32,0:66,3:0.3168:1,1:24.5:1:30.8:1:0.54952:0:60:64:0.3168:0:1.4 -8 90970935 . G A 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.55064;LSEQ=AGAATAATAACAATAGTACG;RSEQ=TAATGAAGAAGCTTTACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:696:253:170,83:292,150:0.3635:2,2:23.2:1:30.1:1:0.80238:1.05:60:83.333:0.3634:0:1.2 0/1:669:160:101,59:321,185:0.2392:2,2:26.3:1:28.9:1:1:1.01358:60:159:0.2405:0:1.2 -8 90976405 . C T 81 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63559;LSEQ=CTAAATCTTGATCTTCAGAA;RSEQ=ATAAAGTTTATAATAACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:6,0:15,0:0.2857:1,0:12:1:31.7:1:1:0:60:12:0.3:0:1.2 0/1:5:1:1,0:4,0:0.2:0,0:3:0:28:0:1:0:60:2:0.2:0:2 -8 90976753 . T A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00497;SOR=Inf;LSEQ=TGCCTATTAGAATAAAATAG;RSEQ=TTAAGTATGATAATATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:145,406:0:2,0:24.3:1:29.9:1:1:0:60:109.2:1:0:0.1 0/1:489:7:5,2:145,336:0.0143:2,2:5.4:1:24:1:0.031:5.77:60:6:0.0124:0:1 -8 90976799 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07852;SOR=Inf;LSEQ=AGCAACTTTTATTCAGATAA;RSEQ=GTCAAGATAAAGCAACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:8,223:0:1,0:22:1:30.4:1:1:0:60:56.75:1:0:0.1 0/1:174:3:0,3:8,163:0.0172:1,0:12.7:1:30.7:1:1:0:60:6:0.0172:0:1 -8 90976818 . CT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50995;SOR=0;LSEQ=ATGTCAAGATAAAGCAACCT;RSEQ=TTTTTTTCCTCCCAAATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:0,2:0,147:0.0133:1,0:32.5:1:33:1:1:0:60:4:0.0137:0:0 0/0:110:0:0,0:2,108:0:1,0:21.9:1:30.5:1:1:0:60:109:1:0:0.1 -8 90976866 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54534;SOR=0;LSEQ=GTATAGACAGAATTTCAAAT;RSEQ=CAGAGTACTATAATAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:0,2:0,69:0.0282:1,0:24.5:1:29:1:1:0:60:4:0.029:0:1 0/0:37:0:0,0:0,37:0:1,0:24.8:1:32.8:1:1:0:60:74:1:0:0.2 -8 90976906 . G A 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28545;SOR=0;LSEQ=ACTCGCTGGGGCACTGTTAC;RSEQ=TTGACAAGTCTACCATCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:0,4:0,29:0.1212:1,0:6:1:30.3:1:1:0:60:8:0.1212:0:1 0/0:17:0:0,0:0,17:0:1,0:20.8:1:30.6:1:1:0:60:16:1:0:0.3 -8 90982425 . C T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0063;SOR=Inf;LSEQ=AGGCAGAAGTTGCAGTGAGC;RSEQ=GAGATCGTGCCACTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:0:1,0:24.7:1:30.5:1:1:0:60:23:1:0:0.2 0/1:11:4:4,0:7,0:0.3636:0,0:17:1:32.5:1:1:0:55:8:0.3636:0:1 -8 90982477 . CA C 64 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.09791;LSEQ=ACAAGAGCAAGACTCCGTCT;RSEQ=AAAAAAAAAAATTCTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:4:4,0:60,1:0.0597:1,0:32.8:1:32:1:1:0:60:8:0.0597:0:0 0/1:46:3:3,0:43,0:0.0652:1,0:30.3:1:32:1:1:0:60:6:0.0652:0:0 -8 90982556 . C T 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=GTTAAACATAAAATCTCCTA;RSEQ=TTGCAGTTTTTTACTAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:225,62:0:2,0:23.7:1:31.7:1:1:0:60:34.875:1:0:0.1 0/1:303:15:13,2:217,71:0.0495:2,2:25.3:1:30.1:1:0.53523:2.12:60:30:0.0507:0:1.1 -8 90982803 . C T 129 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGCTAAAAATGGAAGGAAA;RSEQ=ATTTTTTAAAGTAAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:81,318:0:2,0:21.6:1:32.1:1:1:0:60:78.8:1:0:0.1 0/1:328:23:5,18:65,240:0.0701:2,2:23.3:1:28.6:1:1:1.03:60:46:0.0708:0:1 -8 90982814 . G A 102 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00169;SOR=13.75855;LSEQ=GGAAGGAAACATTTTTTAAA;RSEQ=TAAAATGTAGTAATTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:1:1,0:46,244:0.0034:2,0:1:0:25:0:0.16151:0:60:2:0.0035:0:1 0/1:242:11:2,9:45,186:0.0455:2,2:21.1:1:29.5:1:1:1.08833:60:22:0.0462:0:1 -8 90983251 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06604;SOR=Inf;LSEQ=TCACAGCCATGATCACTGGG;RSEQ=AGGTCTGGTGCCTGGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:37,2:0:2,0:23.9:1:32.5:1:1:0:60:78:1:0:0.1 0/1:14:2:1,1:11,1:0.1429:2,2:27:0:30.5:1:0.27473:8.12278:60:4:0.1429:0:1.5 -8 90983317 . C G 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00139;SOR=Inf;LSEQ=CAAAATCCCAAAATGAAATA;RSEQ=GTTAACAACTACTGATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:109,14:0:2,0:24.9:1:31.8:1:1:0:60:60.5:1:0:0.1 0/1:100:8:7,1:80,10:0.08:2,2:19.1:1:32.5:1:1:1.1412:60:16:0.0816:0:1.1 -8 90990479 . C G 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.49214;LSEQ=TGGAGGCTGCTTCTTGGACT;RSEQ=AACTGCTTTCAGGAATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:301:148,153:255,232:0.3815:2,2:26.9:1:31.6:1:0.41987:1.13608:60:59.2:0.3805:0:1.1 0/1:726:169:89,80:285,270:0.2328:2,2:25.7:1:31.1:1:0.79235:1.05:60:168:0.2337:0:1.2 -8 90992670 . G C 51 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTTAAGACTGAAAACACAAA;RSEQ=TATGCACTGTCATAACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:24:1:32.7:1:1:0:60:6:0.75:0:1 0/0:1:0:0,0:1,0:0:0,0:21:0:34:0:1:0:60:2:1:0:0 -8 90992882 . TA T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.75096;LSEQ=TCTGATAGTTTTAAAGTAAT;RSEQ=AAAAAAAATCTGTGTATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:2,0:117,12:0.0153:2,0:32:1:28.5:1:1:0:60:4:0.0153:0:0 0/1:87:1:1,0:82,4:0.0115:1,0:34:0:32:0:1:0:60:2:0.0115:0:0 -8 90993138 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50997;SOR=0;LSEQ=TATTCTGTAAATGAGAATAA;RSEQ=TTAAATAAAGTCATAGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:27,141:0.0118:2,2:21:1:31:0:0.3031:5.15:60:4:0.012:0:1 0/0:125:0:0,0:21,104:0:2,0:23.5:1:31.4:1:1:0:60:250:1:0:0.1 -8 90993150 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16663;SOR=Inf;LSEQ=GAGAATAAGTTAAATAAAGT;RSEQ=ATAGTATCAGAGTTGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:14,123:0:2,0:22.3:1:32.2:1:1:0:60:67.5:1:0:0.1 0/1:95:2:0,2:12,81:0.0211:2,0:19.5:1:29.5:1:1:0:60:4:0.0217:0:1 -8 90993395 . C T 88 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2451;SOR=0;LSEQ=GAGGAATCGAAGAAATGTAA;RSEQ=TTCCCATGAAGTCCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:0.4667:0,0:23.1:1:31.7:1:1:0:60:14:0.4667:0:1 0/0:3:0:0,0:3,0:0:0,0:17:1:29:1:1:0:60:6:1:0:0 -8 90993883 . C T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16504;SOR=0.29145;LSEQ=GCAGACAACAATTACTGCTT;RSEQ=GGTTGCCTTGAGAGGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:0,10:0,17:0.3704:1,0:21:1:30.9:1:1:0:60:20:0.3704:0:1.2 0/1:14:2:0,2:0,12:0.1429:0,0:26:1:31:1:1:0:60:4:0.1429:0:1 -8 90995019 . C T 240 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.4893;LSEQ=ATCGACTGATCATTTTCAAT;RSEQ=AGAATGGCACAGTTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:803:315:148,167:223,265:0.3923:2,2:25.6:1:29:1:0.77189:1.05:60:314:0.3935:0:1.1 0/1:721:173:87,86:258,290:0.2399:2,2:28.7:1:28.7:1:0.48554:1.14:60:346:0.242:0:1.1 -8 90995093 . AT A 59 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.71536;SOR=1.45104;LSEQ=GTATGGTTCTCCTGAGATAA;RSEQ=TTTTTTTTAAAAAAAGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:3:0,3:69,237:0.0097:2,0:23.3:1:29.8:1:1:0:60:6:0.0098:0.0032:0 0/1:285:4:1,3:75,206:0.014:2,2:26.5:1:29.8:1:1:1.0919:60:8:0.0142:0.0035:0.3 -8 90995102 . T A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.35983;SOR=3.19595;LSEQ=TCCTGAGATAAATTTTTTTT;RSEQ=AAAAAAAGATAAGTTGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:51,218:0.0037:2,0:18:0:31:0:1:0:40:2:0.0038:0:6 0/1:255:3:1,2:59,193:0.0118:2,2:13.3:1:28.3:1:0.55445:1.63:60:6:0.012:0:1.3 -8 90996258 . A G 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAAAAATCGACTTTTCCC;RSEQ=TTGTTCTGATGACATTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:15.5:1:30.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:11:0:32:0:1:0:60:2:1:0:1 -8 91433917 . T C 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.01823;LSEQ=TGGTTCTGCTTTCCTCATTC;RSEQ=AACTCATTTCACTTGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:282:142,140:171,171:0.4519:2,2:26.4:1:31.2:1:0.93607:1.01:60:46:0.4495:0:1.8 1/0:581:363:174,189:114,104:0.6248:2,2:28:1:30.3:1:0.34594:1.19029:60:89.75:0.6233:0:1.7 -8 91433947 . C T 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06124;SOR=1.27021;LSEQ=CACTTGAGGTCGGGTTCTGA;RSEQ=GTTGTATCTTTGTCAATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:233:95,138:129,159:0.4472:2,2:25.8:1:30.1:1:0.37435:1.17817:60:57.25:0.4464:0:1.9 1/0:509:258:105,153:111,137:0.5069:2,2:24.3:1:29.4:1:0.36973:1.18021:60:35.857:0.5:0:1.9 -8 91434011 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18677;SOR=Inf;LSEQ=AAACATGTCATACTCAGCTG;RSEQ=ATTCAGCCAGAAAGACTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:45,158:0:2,0:23.5:1:31:1:1:0:60:100.5:1:0:0.6 0/1:155:2:1,1:33,120:0.0129:2,2:21:1:29:1:0.39171:3.60:60:4:0.0131:0:3 -8 91434018 . C T 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38424;SOR=0.30305;LSEQ=TCATACTCAGCTGGATTCAG;RSEQ=CAGAAAGACTATGGGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:4:2,2:31,142:0.0225:2,2:25.5:1:30.3:1:0.15846:4.53:60:8:0.0231:0:2.3 0/0:145:1:0,1:28,116:0.0069:2,0:34:0:26:0:1:0:60:2:0.0071:0:1 -8 91434037 . C A 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0435;SOR=0;LSEQ=GCCAGAAAGACTATGGGATC;RSEQ=CAGGAGTTTGTTCTAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:7:1,6:12,115:0.0522:2,2:24.1:1:30:1:0.51895:1.59:60:14:0.0534:0:2 0/0:90:0:0,0:6,84:0:2,0:22.3:1:31.1:1:1:0:60:180:1:0:0.6 -8 91434040 . G A 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47526;SOR=1.24996;LSEQ=AGAAAGACTATGGGATCCCA;RSEQ=GAGTTTGTTCTAGCATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:51:4,47:6,66:0.4146:2,2:20.4:1:30.4:1:1:1.06763:60:50:0.4167:0:1.4 0/1:83:39:1,38:2,42:0.4699:1,1:22.9:1:31.8:1:1:1.79714:60:78:0.4756:0:1.2 -8 92236662 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13462;SOR=Inf;LSEQ=TGTTTTCTTTCAATAGTCAG;RSEQ=ACCCTCTTCTGTAGGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:0:2,0:23.9:1:29.8:1:1:0:60:24:1:0:0.2 0/1:15:2:1,1:11,2:0.1333:2,2:37.5:1:30:0:0.37143:4.69047:60:4:0.1333:0:1.5 -8 92236730 . C T 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0284;SOR=Inf;LSEQ=CCTTATTCATCTGATTTGCT;RSEQ=CCATGCCTGGAGATGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:30,31:0:2,0:26:1:30.7:1:1:0:59.7:19.333:1:0:0.2 0/1:44:4:2,2:20,20:0.0909:2,2:25.3:1:30.5:1:1:1:60:8:0.0952:0:1.5 -8 92236869 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11077;SOR=Inf;LSEQ=TGTATAGGGTGTCTGACAAA;RSEQ=CCTGTTGGAAGGTCTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:21.6:1:31.3:1:1:0:60:16:1:0:0.2 0/1:9:2:1,1:3,4:0.2222:2,2:5.5:1:26.5:1:1:1.29:60:4:0.2222:0:1.5 -8 92236962 . TG T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.51648;SOR=Inf;LSEQ=GTGGAGAGGGTGTGTTGTGC;RSEQ=GGGGGAAACCCACTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:3,4:1,3:0.6364:2,2:30.7:1:31.1:1:1:2.09:60:14:0.6364:0:0 1/1:4:4:2,2:0,0:1:0,2:24.8:1:30.5:1:1:0:60:8:1:0.25:0.3 -8 92297537 . T TTCA 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TCATGTGGCATTCACATGCC;RSEQ=TCATCACATGTGTTTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:8:0:30:0:1:0:60:2:1:0:0 1/0:3:2:0,2:0,1:0.6667:0,0:26:1:31.8:1:1:0:60:4:0.6667:0:0 -8 92833865 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1922;SOR=0;LSEQ=AGACCAGAAATAACTAAAAT;RSEQ=AGAGTAGAACTGAAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:21,22:0.0444:2,2:10.5:1:30:1:1:1.05:60:4:0.0444:0:1 0/0:57:0:0,0:31,26:0:2,0:27.8:1:27.9:1:1:0:59.8:27.5:1:0:0.2 -8 93284530 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21587;SOR=0;LSEQ=CTCATGTATTGTTTTCTCCT;RSEQ=CCAAGGAGAGAAAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:2,13:0.1176:2,2:14.5:1:28:1:0.33088:5.51:60:4:0.1176:0:1 0/0:19:0:0,0:4,15:0:2,0:19.8:1:31.1:1:1:0:60:38:1:0:0.1 -8 93406621 . G A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1301;SOR=Inf;LSEQ=AATACAGGGCCCAAAGGCGA;RSEQ=TAATGCAAGACGGCTGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:22,9:0:2,0:18.6:1:31.8:1:1:0:58.9:62:1:0:0.3 0/1:18:2:1,1:13,3:0.1111:2,2:15:0:28.5:1:0.40523:3.89444:60:4:0.1111:0:1 -8 93406768 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATCTCATACTATCCCTGA;RSEQ=TGGTTAGTGTAAAAACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:3,17:0.0909:2,2:28.5:1:29.5:1:0.33766:5.05:60:4:0.0952:0:1 0/0:8:0:0,0:1,7:0:2,0:24.9:1:33.4:1:1:0:60:16:1:0:0 -8 93407601 . T C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACAAGGTGGTATAGGGTTA;RSEQ=AGAGAAGACCTTCAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:36:0:34:0:1:0:54:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1.5 -8 93408721 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGGGGCCTGGCTATCTC;RSEQ=CTGTATCTGGGGATCCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:29:1:1:0:60:4:1:0:1 -8 97963297 . A T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGTTATAGAGTTAAAAC;RSEQ=GATGAAATAATGCTTCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:33:1:32.5:1:1:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 97963715 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.56592;SOR=3.04319;LSEQ=TCAGTTCAAACACCTGAATT;RSEQ=ATTTTCACCAATGCTACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:1:1,0:192,78:0.0037:2,0:15:0:11:0:1:0:60:0:0:0:4 0/1:179:2:1,1:119,58:0.0112:2,2:15:1:27:1:0.55182:2.04285:60:4:0.0115:0:1 -8 97963811 . T C 285 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61082;SOR=0.92122;LSEQ=TATAGCTTTTTCCCTTTTTG;RSEQ=AAGCTATTATTGAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:646:480:248,232:79,85:0.743:2,2:24.9:1:32:1:0.46969:1.15:60:79:0.7418:0:1.1 1/0:392:285:143,142:51,56:0.727:2,2:25.7:1:31.6:1:0.73386:1.11:60:141.5:0.7256:0:1.2 -8 97964081 . G GT 62 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.51471;SOR=2.56905;LSEQ=AATCTTTCCTAGAGAGAATT;RSEQ=TTTTTTTTTTGAATGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:0,10:0.2667:0,0:38.3:1:31:1:1:0:60:8:0.2667:0:0.8 1/0:2:1:0,1:0,1:0.5:0,0:47:0:30:0:1:0:60:2:0.5:0:7 -8 98179766 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12381;SOR=Inf;LSEQ=TAAGCTGAGGGAGTTACAGT;RSEQ=ATTCCCAGTGAGAGGCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:0:2,0:35.1:1:32:1:1:0:60:46:1:0:0.1 0/1:13:2:1,1:8,3:0.1538:2,2:23:0:31:1:1:2.4495:60:4:0.1538:0:1.5 -8 98381926 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09756;SOR=Inf;LSEQ=TTAGGATGTCTGAACTTTCT;RSEQ=CTTTATGTTTTCAACTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:193,52:0:2,0:23.6:1:32:1:1:0:60:121.5:1:0:0.1 0/1:210:3:2,1:149,58:0.0143:2,2:14.7:1:29:1:1:1.2829:60:6:0.0146:0:1 -8 98381945 . C CT 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.57518;SOR=1.3005;LSEQ=TGCTTTATGTTTTCAACTAT;RSEQ=TTTTTTTTTAATGGCATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:14:8,6:248,77:0.0408:2,2:21.9:1:30:1:0.11614:2.40816:60:28:0.0412:0.0058:0.6 0/1:305:16:10,6:191,98:0.0525:2,2:26.4:1:29.4:1:0.78995:1.16876:60:15:0.0502:0.0098:0.7 -8 98382025 . G A 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01042;SOR=1.35346;LSEQ=TTCTTAAACTCTGATGCTCT;RSEQ=GGGCTAAGAACAACAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:674:388:204,184:142,141:0.5757:2,2:24.4:1:29.3:1:0.58411:1.10:60:193:0.5761:0:1.1 1/0:573:371:182,189:103,99:0.6475:2,2:26.1:1:29:1:0.66308:1.08027:60:73.2:0.6466:0:1.1 -8 98382120 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15869;SOR=Inf;LSEQ=GAATCGCTTTCCAGAAAGGC;RSEQ=GTTACTGGAAACAGCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:51,205:0:2,0:23:1:30.6:1:1:0:60:50.2:1:0:0.1 0/1:170:2:1,1:37,131:0.0118:2,2:18.5:1:31:0:0.39812:3.51:60:4:0.0119:0:1 -8 98382175 . C CCTAT 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.68321;SOR=0.83124;LSEQ=AGGGCTGCTCAACAATGCCT;RSEQ=CTCCCCCAACACCCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:72:1,71:0,20:0.7742:1,1:24.8:1:30.3:1:1:0:59.9:71:0.7802:0.1935:0.1 1/0:50:37:1,36:0,13:0.74:1,1:27.2:1:29.9:1:1:0:60:74:0.74:0.1:0.2 -8 98382341 . C G 104 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGTCCTGCTACGTCCA;RSEQ=TGTTGTCTTAGATCTAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:0.9091:0,0:35.5:1:31.6:1:1:0:60:20:0.9091:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 98696129 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGGTGGATCACCTGAGGT;RSEQ=GGAAGTTTGAGACCACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:31.5:1:1:0:60:4:1:0:2.5 -8 98696815 . A G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48837;SOR=0;LSEQ=TTGCAAAGCCTAACATATTT;RSEQ=CTATTTGATCCTTTGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:12,8:0.0909:2,2:10:0:31:1:1:1.47192:60:4:0.0909:0:1 0/0:22:0:0,0:11,11:0:2,0:30.5:1:27.2:1:1:0:60:10:1:0:0.1 -8 98924613 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.50474;LSEQ=CCCTAACATAGGGCGTTAAG;RSEQ=TTAACGGAGTCAGCGAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:20,14:0.0556:2,2:10:1:28.5:1:1:1.41419:60:4:0.0556:0:1 0/1:35:1:1,0:18,16:0.0286:2,0:25:0:32:0:1:0:60:2:0.0286:0:1 -8 98924637 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20448;SOR=Inf;LSEQ=ACGGAGTCAGCGAGAGCAGC;RSEQ=GGAGCCGGGCATTGAAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:0:2,0:31.6:1:30:1:1:0:60:42:1:0:0.2 0/1:36:2:1,1:15,19:0.0556:2,2:13.5:1:32:0:1:1.26:60:4:0.0556:0:1 -8 98924642 . C G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01598;SOR=Inf;LSEQ=GTCAGCGAGAGCAGCTGGAG;RSEQ=CGGGCATTGAAGCGCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:23,22:0:2,0:30.6:1:30.9:1:1:0:60:44:1:0:0.2 0/1:37:5:3,2:12,20:0.1351:2,2:30.6:1:26.2:1:0.37732:2.44:60:4:0.1111:0:1.6 -8 98924702 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53202;SOR=0;LSEQ=TTGGCTCAATAGTTTTCCTT;RSEQ=TGTGTAATATACTGTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:2,15:0.1053:2,0:33.5:1:32:1:1:0:60:4:0.1053:0:1 0/0:10:0:0,0:1,9:0:2,0:21.8:1:30.5:1:1:0:60:20:1:0:0.1 -8 99812821 . A G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGAAGGTGTGGAGGGAGA;RSEQ=GCGTGGGCAGGAACCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:42:0:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 100176569 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23973;SOR=Inf;LSEQ=TTGGTATAAGTATTTGAAAG;RSEQ=CATTGTCTGATTTCAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:14,23:0:2,0:25.3:1:31.9:1:1:0:60:74:1:0:0.1 0/1:36:2:1,1:13,21:0.0556:2,2:24:1:27.5:1:1:1.59:60:4:0.0571:0:1 -8 100176596 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15796;SOR=Inf;LSEQ=CTGATTTCAGAAGCCTTTTC;RSEQ=TGTAAACGCCGGGCAGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:9,16:0:2,0:19.8:1:31.8:1:1:0:60:50:1:0:0 0/1:17:2:0,2:4,11:0.1176:2,0:14:1:32:0:1:0:56:4:0.1176:0:1 -8 101822347 . C A 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TGGCGACCACTTCCCCCACC;RSEQ=CCCACCCCGGTTCTCATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18:1:31.5:1:1:0:60:4:1:0:1 0/0:3:0:0,0:1,2:0:2,0:44.3:1:29.3:1:1:0:60:6:1:0:1 -8 101822736 . ACAG A 100 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=10.000;MSILEN=3;SSF=0.35498;SOR=1.96851;LSEQ=CCAGACCTTGTCTCAAAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:10,7:0.3333:2,2:20.3:1:31.9:1:0.68284:1.74571:60:18:0.3462:0.037:0.3 1/0:18:9:6,3:5,6:0.5:2,2:23.9:1:31.6:1:0.40586:2.29:60:18:0.5:0.1111:0.1 -8 101981199 . T A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTAACACCAGTGCCTTGG;RSEQ=AGGCACCCGTACTTAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 101981658 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=ATAAATATCAGTGTGCCCAG;RSEQ=CATTCAGGGCCACTGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:26.4:1:32.2:1:1:0:60:10:1:0:0 0/1:7:2:1,1:1,4:0.2857:2,2:33.5:1:30:0:1:3.16:60:4:0.3333:0:1.5 -8 102983797 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTCTCTCATCTTCCACC;RSEQ=TGACTGGAAGTTTCCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 102983996 . C A 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTTCTGTTGATGGCTGA;RSEQ=ATGGCTTAATAAAAGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:3,0:19,0:0.1364:1,0:18:1:31.3:1:1:0:60:6:0.1364:0:1 0/0:3:0:0,0:3,0:0:0,0:23.3:1:31.3:1:1:0:60:6:1:0:0 -8 102984091 . C T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0194;SOR=2.77091;LSEQ=GCCCACCTAACCCCAGTTAT;RSEQ=CTCCCCTTTCCCTTCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:21:20,1:62,0:0.253:1,1:21.7:1:30.6:1:0.25301:0:60:42:0.253:0:1.1 0/1:37:18:17,1:17,1:0.4865:1,1:23.9:1:30.6:1:1:1:60:36:0.4865:0:1.1 -8 102984149 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12618;SOR=Inf;LSEQ=GAAATCTGGAAAAGACATGA;RSEQ=AAAATATGTAATGACTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:232,43:0:2,0:22.7:1:31.8:1:1:0:60:54:1:0:0.1 0/1:152:2:1,1:127,23:0.0132:2,2:25.5:1:28:1:0.29174:5.42681:60:4:0.0134:0:1 -8 102984279 . A G 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04341;SOR=1.34642;LSEQ=GTATTCTCACAAAACCTCTC;RSEQ=CAGGAATCCACGGATTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:602:409:166,243:77,116:0.6794:2,2:24.5:1:30.9:1:0.92912:1.03:60:80.8:0.679:0:1.5 1/0:370:274:113,161:38,56:0.7405:2,2:23.6:1:30.5:1:0.90397:1.03:60:90.333:0.7404:0:1.9 -8 102984312 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0;SOR=3.95526;LSEQ=GATTCACTAGAGGTATGTGA;RSEQ=GAGGAGGAGGATGTTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:180:53,127:93,193:0.3838:2,2:25.2:1:31:1:0.53857:1.1543:60:89:0.3853:0:2.3 1/0:274:195:70,125:32,45:0.7117:2,2:26.3:1:30.4:1:0.40633:1.26869:60:64:0.7138:0:2.4 -8 102984352 . T A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.97943;LSEQ=AGGATGAAAACTGACATGCA;RSEQ=ATTTAAACTTCTACCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:108:23,85:44,135:0.3763:2,2:25.4:1:30.3:1:0.56668:1.20374:60:216:0.3803:0:2.3 1/0:150:106:28,78:17,27:0.7067:2,2:20.7:1:30:1:0.17099:1.74712:60:105:0.7047:0:2.5 -8 103647027 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48986;SOR=Inf;LSEQ=GCGTTTGTAGTTCACGGGAG;RSEQ=CAGCGTTGGTGGATGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:29.6:1:30.3:1:1:0:60:21:1:0:0.2 0/1:24:2:1,1:11,11:0.0833:2,2:25.5:1:31:1:1:1:60:4:0.087:0:1.5 -8 103647073 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GGAGGCTATGGTCAGATCAT;RSEQ=AAAATCTTCTGAATGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:22.7:1:31.6:1:1:0:60:38:1:0:0.1 0/1:13:2:1,1:3,8:0.1538:2,2:26.5:1:29:1:1:2.45:60:4:0.1538:0:1.5 -8 103648670 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCACAGGCCTTTGAGCA;RSEQ=GGATGGCAGCCAGGACTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 103805097 . T C 86 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACACTTTTCTATAGAAGTCA;RSEQ=TGCAGATTGAATTGTGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:39.8:1:33.3:1:1:0:60:12:1:0:1.2 1/0:3:2:2,0:1,0:0.6667:0,0:24.5:1:32:0:1:0:60:4:0.6667:0:1.5 -8 103805165 . T G 107 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00591;SOR=0;LSEQ=TAACCCTCAGGATCAGAATG;RSEQ=GACCTCTTTTGGAAATAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:1:0,2:24.1:1:31:1:1:0:60:22:1:0:1.1 0/1:13:6:3,3:4,3:0.4615:2,2:13.3:1:29.3:1:1:1.30401:60:5:0.4167:0:1.3 -8 103805792 . A G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTGCCTGCCAGTGCCCC;RSEQ=ACAGACATCCACAGAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:47:1:31:1:1:0:60:4:1:0:1.5 -8 103858199 . G T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56452;SOR=3.06333;LSEQ=TCTATGTCTTTTTGCTTAAA;RSEQ=TCGCAGTTTCCAAGAACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:0,1:115,22:0.0072:2,0:1:0:27:0:0.16667:0:60:2:0.0073:0:1 0/1:91:2:1,1:67,22:0.022:2,2:18:1:26:1:0.44371:3.00065:60:4:0.022:0:1 -8 103858308 . C T 216 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10694;SOR=0.76747;LSEQ=TATATATGTAGTATTTAGTA;RSEQ=TTAGTTGAAAACCTTTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:147:71,76:147,143:0.3364:2,2:22.3:1:30.1:1:0.68573:1.10012:60:72.5:0.3349:0:1.1 0/1:300:84:48,36:118,98:0.28:2,2:23.5:1:30:1:0.79601:1.11:60:168:0.2819:0:1.2 -8 103858488 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27768;SOR=2.25963;LSEQ=GTACTTATAAAAACATCAGG;RSEQ=CCACTGGATCAAGTCTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:0,29:0.1944:1,0:24.7:1:31:1:1:0:60:14:0.1944:0:1 0/1:14:5:1,4:0,9:0.3571:0,2:11.4:1:27.4:1:0.35714:0:60:10:0.3571:0:1 -8 104028894 . TC T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53146;SOR=0;LSEQ=TGGTTGCTGGTATGATTCCA;RSEQ=CTGCACAGCTGTTCTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:92,32:0.0159:2,2:14:1:27.9:1:0.45676:2.84645:60:4:0.016:0.0079:1.5 0/0:74:0:0,0:55,19:0:2,0:20.6:1:30.8:1:1:0:60:73:1:0:0.1 -8 104028971 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5061;SOR=0;LSEQ=CCTAAGTGCTTGCCGCCACC;RSEQ=ATGGAAGATTTGACGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:74,111:0.0107:2,2:41.5:1:28.5:1:1:1.50:60:4:0.0108:0:1 0/0:146:0:0,0:63,83:0:2,0:25.5:1:30.8:1:1:0:60:145:1:0:0.1 -8 104028978 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50435;SOR=0;LSEQ=GCTTGCCGCCACCCATGGAA;RSEQ=ATTTGACGGACATGGACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:58,111:0.0116:2,2:8:1:25.5:1:1:1.91:60:4:0.0117:0:1 0/0:139:0:0,0:57,82:0:2,0:25.2:1:31.4:1:1:0:60:138:1:0:0.1 -8 104029480 . C G 88 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=0.10236;LSEQ=ATGATGATGAAGAGGAAGAA;RSEQ=ATTTTGATGAAGGGAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:3,4:1,0:0.875:0,2:26.6:1:31.6:1:1:0:60:14:0.875:0:1 0/1:3:1:0,1:1,1:0.3333:2,0:41:0:29:0:1:0:60:2:0.3333:0:1 -8 104029679 . T G 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGGACCTAGTTTTGTAGAA;RSEQ=ATATTAAAAGCAAAAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:6,3:1,0:0.9:0,2:31:1:31.9:1:1:0:60:18:0.9:0:1.3 1/1:9:9:4,5:0,0:1:0,2:9.8:1:31.7:1:1:0:60:18:1:0:1.1 -8 104088015 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12204;SOR=Inf;LSEQ=TTACCTCCTACCGTTAGCTG;RSEQ=CCACCCTCTGCATTCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:193,78:0:2,0:22.7:1:31.1:1:1:0:60:44.167:1:0:0.1 0/1:146:2:1,1:101,43:0.0137:2,2:9.5:1:31.5:1:0.51337:2.33348:60:4:0.0139:0:1 -8 104088053 . GC G 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.43344;SOR=2.27073;LSEQ=GCTTGTGAAGCATTCTGGAG;RSEQ=CCCCCCGCCCCATCCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:3:2,1:240,185:0.007:2,2:10:1:30.2:1:1:1.54:60:6:0.0071:0.0023:0.3 0/1:255:4:2,2:143,107:0.0157:2,2:33.5:1:31.3:1:1:1.33489:60:8:0.0158:0:1 -8 104088071 . C G 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGCCCCCCCGCCCCATCCT;RSEQ=CACTCCCGGCTCTTCCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:274,226:0:2,0:25.8:1:30.9:1:1:0:60:54.556:1:0:0.6 0/1:284:50:25,25:130,102:0.1761:2,2:24.4:1:32:1:0.43898:1.2734:60:49:0.1763:0:1.9 -8 104088119 . T C 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.40405;LSEQ=CACTGGCCATATTTCTTTCC;RSEQ=AGTCTGTTCTGACAGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:479:336:153,183:63,80:0.7015:2,2:26.2:1:31.8:1:0.84102:1.06:60:335:0.7053:0:1.2 0/1:263:128:58,70:64,71:0.4867:2,2:24:1:30.9:1:0.80476:1.08756:60:256:0.4904:0:1.4 -8 104088194 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54336;SOR=0;LSEQ=TCAGCTCACCCCAGTTCTGG;RSEQ=ACCAGAGGACTGGCAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:45,146:0.0104:2,2:15.5:1:28:1:0.42082:3.22:60:4:0.0106:0:1.5 0/0:104:0:0,0:27,77:0:2,0:24.8:1:30.3:1:1:0:60:33.667:1:0:0.2 -8 107805455 . G A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13036;SOR=0;LSEQ=ATTTACAGGAAAAGGCTTCT;RSEQ=AAATCAGACAATGCCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:4:4,0:50,26:0.05:2,0:18:1:29.5:1:0.29818:0:36.3:8:0.0506:0:3 0/0:63:0:0,0:38,25:0:2,0:1:0:17:0:1:0:42:0:0:0:3 -8 107805490 . C A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4383;SOR=1.37338;LSEQ=CTTTCAAACTCTTATACCAA;RSEQ=CTCTGGAGTTGGGCGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:18:9,9:55,49:0.1475:2,2:29.7:1:28.6:1:1:1.12138:38.9:36:0.1488:0:2.8 0/1:78:15:10,5:31,32:0.1923:2,2:28.1:1:27:1:0.26154:2.05:43.5:6.5:0.1733:0:2.5 -8 107805500 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14039;SOR=Inf;LSEQ=CTTATACCAACCTCTGGAGT;RSEQ=GGGCGACATGGCTTCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:60,66:0:2,0:30.4:1:29.9:1:1:0:48.8:125:1:0:0.7 0/1:76:2:1,1:35,39:0.0263:2,2:30.5:1:29.5:1:1:1.11:48.5:4:0.0263:0:1 -8 107805505 . G A 25 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52643;SOR=0;LSEQ=ACCAACCTCTGGAGTTGGGC;RSEQ=ACATGGCTTCTCCCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:0,2:56,65:0.0161:2,0:15:0:25:0:0.49993:0:45:4:0.0163:0:3 0/0:76:0:0,0:35,41:0:2,0:27.7:1:29.6:1:1:0:49.3:75:1:0:1 -8 107805509 . T C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06578;SOR=1.98099;LSEQ=ACCTCTGGAGTTGGGCGACA;RSEQ=GGCTTCTCCCCTTTCTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:19:11,8:43,59:0.157:2,2:32.6:1:31.4:1:0.22026:1.88:48.7:38:0.157:0:1 0/1:74:20:9,11:23,31:0.2703:2,2:23.3:1:28.8:1:1:1.10:50.6:19:0.2603:0:1.1 -8 107805532 . T C 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54482;SOR=0;LSEQ=CTTCTCCCCTTTCTAGGTCC;RSEQ=GTGACAGCCATCTTGCTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:0,2:44,60:0.0189:2,0:42:0:29:0:0.50979:0:45:4:0.0194:0:3 0/0:56:0:0,0:20,36:0:2,0:25.8:1:30.4:1:1:0:49.4:112:1:0:1.1 -8 107805536 . A G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5442;SOR=0;LSEQ=TCCCCTTTCTAGGTCCTGTG;RSEQ=CAGCCATCTTGCTATTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:0,2:40,58:0.02:2,0:46:0:31:0:0.51515:0:45:4:0.0202:0:3 0/0:53:0:0,0:21,32:0:2,0:25.4:1:28.7:1:1:0:50.4:25.5:1:0:1.1 -8 107805547 . G A 114 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00932;SOR=3.08216;LSEQ=GGTCCTGTGACAGCCATCTT;RSEQ=CTATTACTCGCCTTCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:12:3,9:27,52:0.1319:2,2:21.6:1:29.3:1:0.74421:1.55057:41:24:0.1348:0:3.3 0/1:53:17:7,10:13,23:0.3208:2,2:23.7:1:27.9:1:0.76782:1.23:44.3:34:0.3269:0:2.8 -8 107805562 . C T 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18503;SOR=2.16029;LSEQ=ATCTTGCTATTACTCGCCTT;RSEQ=GGGCCCTGTATTTTTAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:8:1,7:8,46:0.129:2,2:13.5:1:30.9:1:1:1.21373:45.4:16:0.1333:0:3.6 0/1:41:10:1,9:11,19:0.2439:2,2:22.4:1:30.3:1:0.23069:5.03832:42.6:20:0.2632:0:3.3 -8 107805573 . T G 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.5048;SOR=1.61383;LSEQ=ACTCGCCTTCGGGCCCTGTA;RSEQ=TTTTAACCTCCTTGTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:0,5:3,36:0.1136:2,0:10:1:32.6:1:1:0:40:10:0.1136:0:4 0/1:29:5:0,5:7,17:0.1724:2,0:26.8:1:32.4:1:0.29649:0:41.2:10:0.1724:0:3.6 -8 107805600 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18857;SOR=Inf;LSEQ=CCTCCTTGTCAAATTTGTTT;RSEQ=CTCTAGGATTGAGGCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:5,23:0:2,0:30:1:31.9:1:1:0:57.6:56:1:0:0.1 0/1:22:2:0,2:6,14:0.0909:2,0:6.5:1:30:1:1:0:40:4:0.0909:0:4 -8 109141918 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAAGAAAGAAAGAAAG;RSEQ=AAAGGAAGAAAGAAAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 109143183 . GA G 104 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.16747;SOR=0.21906;LSEQ=ACACTTATTTACCAAAAAAA;RSEQ=AAAAAAAAAAGCTTCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:9,0:3,0:0.75:0,0:30.3:1:33:1:1:0:60:18:0.75:0.0833:0 0/1:8:3:2,1:4,0:0.375:0,2:17:1:33:1:0.42857:0:60:6:0.375:0.125:0 -8 109143310 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22832;SOR=Inf;LSEQ=AGACGCCCCCGAGTGAATGT;RSEQ=AGGGACCACCAGGGGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:136,23:0:2,0:23:1:31.1:1:1:0:60:52:1:0:0.2 0/1:146:2:1,1:116,28:0.0137:2,2:20:1:27.5:1:0.3589:4.08831:60:4:0.014:0:1 -8 109143785 . C A 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14202;SOR=Inf;LSEQ=GCAGTACATCAGAGCATCTG;RSEQ=CACCTCCCCCGTGATGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:11,51:0:2,0:24.8:1:30.8:1:1:0:60:30:1:0:0.1 0/1:38:2:1,1:6,30:0.0526:2,2:6:0:26.5:1:0.33855:4.71:60:4:0.0526:0:1 -8 109143994 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21737;SOR=Inf;LSEQ=TCTGCCTGCGCATCTGGTGC;RSEQ=CCCCACGCCCTCCTCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:49,34:0:2,0:24.2:1:30:1:1:0:60:19.75:1:0:0.2 0/1:73:2:1,1:44,27:0.0274:2,2:7:1:30:1:1:1.61829:60:4:0.0274:0:1 -8 109144063 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49693;SOR=Inf;LSEQ=GAAATGGCTTGTCTTCTTTC;RSEQ=AGCCAAGTACACATGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:31,51:0:2,0:25.3:1:30.2:1:1:0:60:81:1:0:0.2 0/1:82:2:1,1:35,45:0.0244:2,2:14.5:1:27.5:1:1:1.28:60:4:0.0244:0:1 -8 109144095 . CCCAGGGGACGC T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01494;SOR=0;LSEQ=CATGTACAAACTTGTCTTTG;RSEQ=CCAGTCTCAAGGTCGTCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:2,5:10,36:0.1296:2,2:19.4:1:28.9:1:0.64996:1.43:60:14:0.1346:0.0556:0.6 0/0:45:0:0,0:13,32:0:2,0:21.4:1:32.1:1:1:0:60:90:1:0:0.2 -8 109235569 . G A 94 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=AAACACAGGTAGGACACTAA;RSEQ=TAGACCTCCAGATGAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1:0,0:31.6:1:29.8:1:1:0:60:18:1:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:12:0:31:0:1:0:60:2:0.3333:0:1 -8 109235785 . G T 229 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAATTCAGATTATTTTTATT;RSEQ=AGAAAACAAAATACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:237:237:153,84:0,0:1:0,2:25.3:1:29.1:1:1:0:60:58.25:1:0:1.5 0/1:294:91:60,31:128,75:0.3095:2,2:25.5:1:28.9:1:0.69421:1.13:60:182:0.3095:0:1.7 -8 109235849 . T C 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05985;SOR=1.59897;LSEQ=TTTCTACAAGTGGAGAGTAA;RSEQ=AGGGCATTGTATTACAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:28:14,14:176,168:0.0753:2,2:22.3:1:32.1:1:1:1.04751:60:56:0.0759:0:2.5 0/1:460:53:24,29:197,208:0.1152:2,2:26:1:31.1:1:0.66394:1.14409:60:106:0.1165:0:2.5 -8 109235858 . G C 268 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00237;LSEQ=GTGGAGAGTAATAGGGCATT;RSEQ=TATTACAAATGGATTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:365:363:177,186:0,0:0.9945:0,2:25.7:1:31.6:1:1:0:60:71.6:0.9972:0:1.6 0/1:426:127:61,66:140,159:0.2981:2,2:26.1:1:31.2:1:0.83266:1.05:60:62.5:0.2955:0:1.9 -8 109235929 . G A 229 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTCATCTCCGATAGCCTAC;RSEQ=AACACTGCTCTATCTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:192:192:44,148:0,0:1:0,2:26.6:1:30.3:1:1:0:60:95:1:0:1.5 0/1:162:46:12,34:36,80:0.284:2,2:27.2:1:29.3:1:0.57293:1.27313:60:45:0.2813:0:1.5 -8 109236119 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CTTTCATTTTAAGGACAAAC;RSEQ=TATACATGATCTCTAACGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:41.3:1:31.7:1:1:0:60:6:1:0:1 0/0:3:0:0,0:0,3:0:0,0:22:1:32.3:1:1:0:60:6:1:0:0 -8 109735675 . ATG A 99 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.31728;SOR=1.67466;LSEQ=GAAATCTATTTTTCGTGTGT;RSEQ=TGTGTGTGTGTGCATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:9:9,0:49,1:0.1525:1,0:21.9:1:30.2:1:1:0:60:18:0.1552:0.0339:0.1 0/1:43:10:9,1:32,1:0.2326:1,2:20.2:1:30.1:1:0.41528:3.42527:60:20:0.2381:0.0233:0.1 -8 109735688 . TGC CAT 29 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.17987;SOR=Inf;LSEQ=CGTGTGTATGTGTGTGTGTG;RSEQ=ATATATATATATATGAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:65,8:0:2,0:21.4:1:30.5:1:1:0:60:146:0.9865:0:0.2 0/1:55:2:2,0:47,6:0.0364:2,0:12.5:1:29.8:1:1:0:60:4:0.037:0.0182:0.5 -8 109735690 . CAT C 65 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.68929;LSEQ=TGTGTATGTGTGTGTGTGTG;RSEQ=ATATATATATATGAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:4:4,0:67,9:0.0494:2,0:13:1:32.9:1:1:0:58.8:8:0.0506:0.0123:0.3 0/1:58:2:2,0:50,6:0.0345:2,0:26.5:1:33.5:1:1:0:60:4:0.0351:0:0 -8 109735723 . T C 165 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.134;LSEQ=ATGAATATGTTTCACTAAAA;RSEQ=AGGCAAGGCAGCAATCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:34:28,6:92,23:0.2282:2,2:21.6:1:32.6:1:1:1.17:59.9:68:0.2313:0:1 0/1:132:5:3,2:96,31:0.0379:2,2:25.6:1:30.8:1:0.59839:2.05154:60:10:0.0382:0:1 -8 109735830 . C T 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11215;SOR=1.36281;LSEQ=TCAACTATAAATGGCTTTCA;RSEQ=GGAAACAAGTCCAAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:64:30,34:178,178:0.1524:2,2:23.5:1:30.3:1:0.68504:1.13299:60:63:0.1518:0:1.1 0/1:381:75:40,35:158,148:0.1969:2,2:25.1:1:29.5:1:0.79819:1.07:60:74:0.1963:0:1.1 -8 110539105 . GGCA G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.49206;SOR=0;LSEQ=CAGAGTCTGTCTCTAGCAGT;RSEQ=GCAGCAGCAGCAGCAACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:0.1:2,2:33.5:1:33:1:1:1.23603:60:4:0.1:0:0 0/0:16:0:0,0:10,5:0:2,0:25.9:1:32.1:1:1:0:60:30:0.9375:0:0.3 -8 110595268 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50046;SOR=Inf;LSEQ=CTATGGTACTGGGTTATGCA;RSEQ=CCCTAGCAGACTAATATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:18,2:0:2,0:21.3:1:32.9:1:1:0:60:40:1:0:0.1 0/1:27:2:1,1:20,5:0.0741:2,2:22.5:1:29:1:0.40171:3.74166:60:4:0.08:0:1 -8 110595321 . CCAG C 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=1.50228;LSEQ=GATTACCATCATAACCACCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:36,22:0.0333:2,2:18.5:1:31:1:1:1.62241:60:4:0.0333:0:0 0/1:81:4:2,2:43,34:0.0494:2,2:32.5:1:31.5:1:1:1.26101:60:8:0.0506:0:0.5 -8 111298431 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19557;SOR=Inf;LSEQ=ACTTTCATTTCTTTATTTTA;RSEQ=TTTTGGTTTTAAAACTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:161,49:0:2,0:22.6:1:31.9:1:1:0:60:69:1:0:0.1 0/1:167:2:1,1:126,39:0.012:2,2:13:1:28:1:0.42277:3.20275:60:4:0.012:0:1 -8 111298543 . G A 253 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.96657;LSEQ=TGGTTTATTGACTCCACCGA;RSEQ=TGAAATAGTGTCTATGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:282:132,150:139,151:0.4921:2,2:25.5:1:30.4:1:0.80208:1.046:60:140:0.4912:0:1.1 1/0:593:389:180,209:100,104:0.656:2,2:26.9:1:29.5:1:0.54514:1.11624:60:63.833:0.6558:0:1.1 -8 115984457 . T C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TCGAGTGTTGATGGTTTTTA;RSEQ=AAAAGGTAGTGACGAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:30:1:33.7:1:1:0:60:6:0.75:0:1 0/0:4:0:0,0:4,0:0:0,0:39:1:32:0:1:0:60:8:1:0:0 -8 115984546 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.13986;SOR=Inf;LSEQ=GATGCTTTCGTGTTGTTGTT;RSEQ=TTATTGTTGTTGTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:21,20:0:2,0:26.4:1:32:1:1:0:60:82:1:0:0.1 0/1:25:2:1,1:12,11:0.08:2,2:40.5:1:28.5:1:1:1.0871:60:4:0.08:0:1.5 -8 115984574 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.17306;SOR=Inf;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGTTGCTGTTATTTTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:17,23:0:2,0:27.4:1:32.3:1:1:0:60:80:1:0:0.1 0/1:29:2:1,1:14,13:0.069:2,2:19:0:31.5:1:1:1.07415:60:4:0.069:0:1 -8 117352461 . G A 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06769;SOR=0;LSEQ=GCGCTCTTGGCATGGATAGG;RSEQ=CCCTCGGTGTTCACATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:4,5:7,7:0.3913:2,2:34:1:30.1:1:1:1.23792:60:18:0.4091:0:1 0/0:8:0:0,0:3,5:0:2,0:22.3:1:31.1:1:1:0:60:16:1:0:0.3 -8 117860152 . T C 127 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06399;SOR=0.13691;LSEQ=CTGTGGCAATCAGTGAATTC;RSEQ=TGCTCGTTAGTTAACACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:16:1,15:0,19:0.4571:1,1:23.9:1:31.8:1:0.45714:0:60:32:0.4706:0:1.4 0/1:10:1:0,1:0,9:0.1:0,0:35:0:33:0:1:0:60:2:0.1:0:1 -8 117860257 . A T 31 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22183;LSEQ=CTCCCCCTTTGCCTTCCACC;RSEQ=TGACTATAAGCTTTCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:20.5:1:31:1:1:0:60:4:0.2857:0:1.5 0/1:3:1:0,1:1,1:0.3333:2,0:8:0:31:0:1:0:60:2:0.3333:0:1 -8 117861000 . TA T 123 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.43088;SOR=0.54;LSEQ=AATTAAAACTTAAACTATAA;RSEQ=AAAAAAAAAAAGAAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:18:16,2:70,2:0.1935:1,2:24.2:1:29.6:1:0.17724:4.27811:60:17:0.1868:0.043:0.7 0/1:35:4:4,0:28,3:0.1143:2,0:20.3:1:31.3:1:1:0:60:8:0.1212:0.0571:0 -8 117861112 . C CT 185 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.24445;SOR=0.74042;LSEQ=TTTCTGTTTCCAGCATCTAA;RSEQ=TTTTTTTTTTTCAGGGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:61:56,5:419,77:0.1087:2,2:29.7:1:31.3:1:0.17801:2.06:59.7:122:0.1117:0.0018:0.5 0/1:326:27:22,5:238,58:0.0828:2,2:29:1:30.4:1:1:1.07:59.1:54:0.0852:0:0.4 -8 117861516 . T C 123 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19868;SOR=0.1743;LSEQ=GCTGAAAGTATGCTTCTATA;RSEQ=TGCGCTATAAGGATGCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:0,14:0,14:0.5:1,1:21.4:1:32.5:1:1:0:60:28:0.5:0:1.1 0/1:7:1:0,1:1,5:0.1429:2,0:11:0:33:0:1:0:60:2:0.1667:0:1 -8 117862569 . T C 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGTCCACTGACCACAAGA;RSEQ=AGTAAAAGCAGCTACACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:0.1053:1,0:32:1:32:1:1:0:60:4:0.1111:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 117863365 . A AAAT 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTTGAATGTCTCACGGCAGC;RSEQ=AATAATAGGAGTGAGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:0.5:2,0:21.7:1:29.7:1:1:0:60:6:0.5:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 117864217 . A G 298 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32276;LSEQ=GGCTCTGGGTCAATTTGTCC;RSEQ=GCTTTTCGCTTAACTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2492:946:481,465:773,770:0.3796:2,2:25.6:1:30.2:1:0.74115:1.03:60:62.067:0.3794:0:1.1 0/1:1783:294:146,148:770,714:0.1649:2,2:27.1:1:29.7:1:0.52309:1.09315:60:146:0.1655:0:1.1 -8 117864369 . C G 205 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATGAAGAGAAAACATAGGT;RSEQ=ATACAGTTTTGAACAGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:774:93:16,77:161,520:0.1202:2,2:25.9:1:31.4:1:0.18888:1.48935:60:45.5:0.1185:0:1.1 0/0:480:0:0,0:121,358:0:2,0:24.8:1:31.5:1:1:0:60:94.8:0.9979:0:0.2 -8 117864436 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.075;SOR=Inf;LSEQ=TACACTAAGACATACATAAT;RSEQ=CTTTCTTTAATGAAGAAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:18,214:0:2,0:23.9:1:32.1:1:1:0:60:37.667:1:0:0.1 0/1:88:2:0,2:0,86:0.0227:1,0:14:1:30.5:1:1:0:60:4:0.0227:0:1 -8 117866426 . CT C 184 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.05918;SOR=0.61136;LSEQ=TGATTCAAAGGTTTTAGAAT;RSEQ=TTTTTTTTTAGATGCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:63:55,8:557,104:0.0865:2,2:19.9:1:30.9:1:0.71479:1.28:60:126:0.087:0.022:0.1 0/1:402:22:18,4:316,62:0.0547:2,2:25:1:30.9:1:0.77045:1.13228:60:44:0.0547:0.01:0.2 -8 117866817 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08107;SOR=Inf;LSEQ=CTTTTCTACACACAGACTCT;RSEQ=GCAGAGAAGTTAAACTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:4,256:0:1,0:24.5:1:31.4:1:1:0:60:64:1:0:0.1 0/1:104:2:0,2:1,101:0.0192:1,0:16.5:1:31.5:1:1:0:60:4:0.0198:0:1 -8 117868278 . C CA 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0719;SOR=7.68354;LSEQ=TAGCAGATCAGTAGACAGGC;RSEQ=AAAAAAACAGAAAAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:1:1,0:198,6:0.0049:1,0:13:0:25:0:1:0:60:2:0.005:0:0 0/1:82:3:3,0:71,8:0.0366:2,0:13.7:1:29.3:1:1:0:60:6:0.037:0.0122:0.7 -8 117868703 . CA C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.0632;SOR=Inf;LSEQ=CAGACTTGAACCCAATTGGC;RSEQ=AAAAAATGGGGAGGGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:30,34:0:2,0:28.9:1:30:1:1:0:60:63:1:0:0.2 0/1:22:2:2,0:11,9:0.0909:2,0:35:1:31:0:0.49351:0:60:4:0.0952:0:0 -8 117868714 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.05928;SOR=Inf;LSEQ=CCAATTGGCCAAAAAAATGG;RSEQ=GAGGGGTGCAAGATTAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:43,30:0:2,0:27.5:1:31.3:1:1:0:60:146:1:0:0.2 0/1:24:2:1,1:15,7:0.0833:2,2:34:1:28:1:1:2.07024:60:4:0.0833:0:1 -8 117869181 . T TA 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTATAAAACACTTGGTATA;RSEQ=AAAAAAAAATTCTCATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:0,2:18,71:0.022:2,0:18:1:29:1:1:0:60:4:0.023:0:0 0/0:38:0:0,0:3,35:0:2,0:25:1:28.9:1:1:0:60:76:1:0:0 -8 117869241 . AT A 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.06368;SOR=0.26795;LSEQ=ATTTATCTATTTTAAAAAAT;RSEQ=TTTACTTAACACAGCTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:49:25,24:7,4:0.8167:2,2:23.3:1:30.7:1:0.51874:1.66572:59.8:98:0.8167:0.1667:0.3 1/0:13:7:3,4:2,4:0.5385:2,2:20.4:1:30.9:1:1:1.45:60:14:0.5385:0.0769:0 -8 117869460 . A G 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.67149;LSEQ=TTCCAAAACTTTACAACTTA;RSEQ=TAAAGAAATTCTGTTTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1028:246:160,86:534,247:0.2393:2,2:25:1:32.2:1:0.34889:1.16186:60:245:0.2407:0:1.1 0/1:676:233:155,78:295,146:0.3447:2,2:22.4:1:31.6:1:0.93166:1.01677:60:466:0.3493:0:1.1 -8 117869851 . AAACTTT A 116 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATGTTAAAATATCTAGTTT;RSEQ=AATTCTTTAGCATCTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:0,156:0:1,0:21.1:1:30.8:1:1:0:60:312:1:0:0 0/1:58:15:0,15:0,43:0.2586:1,1:22.7:1:29.9:1:1:0:60:30:0.2586:0.0517:0.1 -8 117870036 . TATA T 106 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGCTGAAACTTTCCCGT;RSEQ=ATGTGTTTCATCAAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:1:0,2:27.5:1:32:1:1:0:60:20:1:0.2:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 117870196 . A C 84 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGCCACGGCACTCCAGC;RSEQ=TGGATAACACAGCAGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:5,4:1,1:0.8182:2,2:27.6:1:26.6:1:1:1.22:60:3.5:0.7778:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 117870375 . A G 154 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17767;SOR=0.20185;LSEQ=GAAATCAATATATAGGTTCT;RSEQ=TGATTGCATATAGGGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:28:27,1:21,1:0.56:1,1:21.4:1:32.1:1:1:1.28:60:56:0.5714:0:1.1 0/1:5:1:1,0:4,0:0.2:0,0:28:0:34:0:1:0:60:2:0.2:0:1 -8 117870446 . T A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31516;SOR=0;LSEQ=AATAATGCTTAATCTACTGG;RSEQ=AGAAAGCCAAATTCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:4:4,0:137,4:0.0276:1,0:26.5:1:29.8:1:1:0:60:8:0.0276:0:1 0/0:64:0:0,0:64,0:0:1,0:22.8:1:30.4:1:1:0:60:128:1:0:0 -8 117874055 . A AT 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01364;SOR=0;LSEQ=TATTGCAGACCAAGTCAACA;RSEQ=TTTTTTTTAAAAGAAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:896:9:5,4:634,253:0.01:2,2:19.2:1:29.1:1:0.2869:2.00308:60:18:0.0102:0.0045:0.4 0/0:597:0:0,0:400,196:0:2,0:24.1:1:29.4:1:1:0:60:58.6:0.9983:0:0.1 -8 117878493 . G GT 60 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TTTACAGCACTTCCACGTCG;RSEQ=TTTTTTTTTTTTTTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:2,0:0.5714:0,0:29.8:1:30:1:1:0:60:8:0.6667:0.1429:2 0/0:2:0:0,0:1,0:0:0,0:15:0:13:0:1:0:60:0:0:0:0 -8 117878691 . C T 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.88399;SOR=1.06237;LSEQ=TAGAGGTGATAAGGACTTCA;RSEQ=ATAATAAAGAAACATTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:55:55,0:153,2:0.2619:1,1:26.3:1:31.6:1:1:0:60:110:0.2619:0:1 0/1:84:23:22,1:59,2:0.2738:1,1:19.8:1:30.1:1:1:1.33596:60:46:0.2771:0:1 -8 117879010 . G GA 66 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03661;SOR=7.84521;LSEQ=CAGAAGAAAACCTAAGAGGG;RSEQ=AAAAAAAAGTTAATGTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:757:1:0,1:169,585:0.0013:2,0:16:0:32:0:1:0:60:2:0.0013:0:0 0/1:486:5:2,3:135,346:0.0103:2,2:8.6:1:28.6:1:0.62392:1.71:60:10:0.0105:0.0062:1.2 -8 117879369 . G C 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTATGAAGAAAGATACTCAG;RSEQ=CACAGATAAAAATCTGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:18.3:1:31.3:1:1:0:60:6:0.75:0:1 1/1:1:1:1,0:0,0:1:0,0:39:0:34:0:1:0:60:2:1:0:1 -8 120071761 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15849;SOR=Inf;LSEQ=AATGAACCATTAATGTGAGA;RSEQ=TGTATTTCTGGGCTTACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:88,8:0:2,0:23.6:1:29.9:1:1:0:60:47:1:0:0 0/1:64:2:1,1:52,9:0.0313:2,2:13:1:28.5:1:0.29442:5.5338:60:4:0.0313:0:1 -8 120071898 . C T 207 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.41248;LSEQ=GCTGATAAAACTGCAATTCT;RSEQ=ACCAACTGCCATGAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:102:50,52:190,177:0.2175:2,2:25.8:1:28.9:1:0.65511:1.11612:60:101:0.2167:0:1.7 0/1:366:147:70,77:105,113:0.4016:2,2:28.8:1:28.8:1:1:1.02207:60:146:0.4056:0:1.7 -8 120071906 . G A 51 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03859;SOR=Inf;LSEQ=AACTGCAATTCTCACCAACT;RSEQ=CCATGAGGAGAGAGGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:0:0,0:230,248:0:2,0:25:1:31.9:1:1:0:60:78.667:1:0:0.5 0/1:382:4:2,2:176,202:0.0105:2,2:24.3:1:25.8:1:1:1.15:60:3:0.0079:0:3.3 -8 120071939 . A G 204 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=1.87892;LSEQ=AGGTGGAGTTTTTTCCATAC;RSEQ=TGAAGGCCTCATACTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:92:35,57:130,183:0.2272:2,2:26.6:1:31:1:0.62948:1.15649:60:184:0.23:0:1.8 0/1:309:110:39,71:85,114:0.356:2,2:24.3:1:30.2:1:0.22732:1.35606:60:54:0.3529:0:2 -8 120072087 . C T 55 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07668;SOR=5.15847;LSEQ=TACTCAATCCATTCATGTAT;RSEQ=AAAATTGCAAATGTACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:0,2:0,27:0.069:1,0:31:1:28:1:1:0:60:4:0.069:0:1.5 0/1:14:4:0,4:0,10:0.2857:0,0:7.5:1:27.8:1:1:0:60:8:0.2857:0:2.3 -8 120072214 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTGACTTCTTCACATAG;RSEQ=CATGGCTGAAACTTCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:28:1:32.5:1:1:0:60:4:0.25:0:1 0/0:1:0:0,0:1,0:0:0,0:22:0:31:0:1:0:60:2:1:0:0 -8 120428447 . G A 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00191;SOR=0.03302;LSEQ=GAGCCCTGGGTCCTGGCCTC;RSEQ=GAACTCCACCCAGCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:6,2:1,0:0.8889:0,2:19.5:1:29.8:1:1:0:60:16:1:0:1.1 0/1:12:2:1,1:6,4:0.1667:2,2:22.5:1:30:1:1:1.4491:60:4:0.1667:0:1 -8 120994394 . A G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.53481;LSEQ=AGGGAGAGATTGGTTTCTAC;RSEQ=TATTTATTACTTTCACTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:82:42,40:100,122:0.2689:2,2:23.3:1:31:1:0.36606:1.28:60:164:0.2742:0:1.1 0/1:176:85:45,40:41,49:0.483:2,2:26.2:1:30.5:1:0.36574:1.34:60:170:0.4857:0:1.1 -8 121504119 . A G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.3405;LSEQ=AGGAGAAGACTTAACCCCAA;RSEQ=AGGGCCATCCCTCCTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:861:666:356,310:111,82:0.7735:2,2:27.7:1:31.6:1:0.32602:1.17852:60:54.5:0.7767:0:1.2 1/0:454:244:120,124:104,106:0.5374:2,2:26.1:1:31.2:1:1:1.01381:60:80.333:0.5367:0:1.1 -8 121504249 . TA T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.29036;SOR=2.78316;LSEQ=GAGTACAGAAATGCTAAAAA;RSEQ=AAAAAAATTAAAAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:0,2:10,168:0.011:2,0:22.5:1:31:0:1:0:60:4:0.0111:0:0 0/1:66:2:0,2:5,59:0.0303:2,0:19.5:1:32:0:1:0:60:4:0.0303:0:0 -8 121519850 . T TG 147 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58426;SOR=0.46721;LSEQ=GCTTAATCGGAATTATACTG;RSEQ=ATAAATATTGCCTTTAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:22:22,0:5,0:0.8148:0,1:27.9:1:33:1:1:0:60:44:0.8148:0.1481:0 1/0:6:4:4,0:2,0:0.6667:0,0:15.8:1:31.4:1:1:0:60:8:0.6667:0.1667:0 -8 121520055 . CT TG 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.61328;SOR=1.87944;LSEQ=GAGTAATTTTTTTCCCATAA;RSEQ=TTGAAAGATTGATAACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:2:0,2:181,169:0.0057:2,0:2.1:1:26.9:1:0.23529:0:60:4:0.0041:0.0074:0 0/1:188:2:1,1:91,95:0.0106:2,2:24.5:1:30.3:1:1:1.04:60:4:0.0109:0:1 -8 121520056 . T G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25557;LSEQ=AGTAATTTTTTTCCCATAAC;RSEQ=TTGAAAGATTGATAACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:355:295:154,141:33,27:0.831:2,2:26.6:1:30.8:1:0.77701:1.11869:60:97.333:0.8319:0:1.1 1/0:187:104:52,52:37,43:0.5561:2,2:25.2:1:29.7:1:0.65679:1.16:60:103:0.5659:0:1.1 -8 121520095 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09777;SOR=Inf;LSEQ=TTTGTTGTGGGAATCAAGAA;RSEQ=GTAAAGAAATATACATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:149,195:0:2,0:26.2:1:30.5:1:1:0:60:67.8:1:0:0.7 0/1:157:2:1,1:60,95:0.0127:2,2:25.5:1:29.5:1:1:1.58:60:4:0.0128:0:1.5 -8 121520098 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09762;SOR=Inf;LSEQ=GTTGTGGGAATCAAGAAAGT;RSEQ=AAGAAATATACATGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:147,193:0:2,0:25.5:1:29.1:1:1:0:60:112.333:1:0:0.7 0/1:155:2:1,1:58,95:0.0129:2,2:16:0:33.5:1:1:1.63:60:4:0.0131:0:2.5 -8 121520223 . T TG 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.36194;SOR=0.42316;LSEQ=TATGTAAGTTGTACTCTTTT;RSEQ=ACAGAATGTCTTTCTAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:29:1,28:0,9:0.7632:0,1:25.6:1:31.6:1:1:0:60:58:0.7838:0.2105:0 1/0:7:4:0,4:0,3:0.5714:0,0:11.3:1:30.3:1:1:0:60:8:0.5714:0.2857:0.3 -8 121520238 . T C 32 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00605;SOR=Inf;LSEQ=CTTTTTACAGAATGTCTTTC;RSEQ=AGATGCATTGTAGGGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:1,28:0:1,0:29.8:1:29.1:1:1:0:60:58:1:0:0.1 1/0:3:2:0,2:0,1:0.6667:0,0:32:1:32:1:1:0:60:4:0.6667:0:1 -8 124660447 . A C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCATCTTTCAGTTTAGA;RSEQ=CATTGAGGCTCTGAGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 124664130 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGTGACTGACCAGACTC;RSEQ=TCCCTGAGCTGACAGCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:29:1:1:0:60:4:1:0:2 -8 125182561 . CAAA C 31 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=22.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:0:31.5:1:1:0:53:4:1:0:4 -8 125184039 . A T 28 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTAAGGTGCAGGGTAAA;RSEQ=GCCCCTGAGAGTAATAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:19.5:1:30:1:1:0:60:4:1:0:1 1/0:3:2:2,0:1,0:0.6667:0,0:31:1:28.5:1:1:0:60:4:0.6667:0:3 -8 125184142 . A G 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11537;SOR=0.15059;LSEQ=AATCCAGGAGTGGCCAACCC;RSEQ=GAGATTCATTCCTTGTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:13,6:1,0:0.95:0,2:23.6:1:30.6:1:1:0:60:38:0.95:0:1 1/0:11:8:4,4:2,1:0.7273:2,2:25.9:1:27.9:1:1:1.87936:59.4:16:0.7273:0:1.3 -8 125184178 . C CCCCGT 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=6.000;MSILEN=5;SSF=0.40685;SOR=0.57191;LSEQ=TTTATGAGAAACATCTGAGT;RSEQ=CCCGTCCCGTCCCGTCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:27:17,10:7,2:0.75:2,2:27.1:1:30.5:1:0.68547:2.02045:59.3:54:0.75:0.1944:0.7 1/0:27:17:7,10:2,1:0.6296:2,2:18.7:1:29.9:1:0.56579:2.70974:59.7:34:0.6538:0.1111:0.6 -8 125184316 . C A 107 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=TGGAGGTCGTTAAGGGGAAG;RSEQ=TGTTAACTGAAAATGCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:23.8:1:32.4:1:1:0:60:20:1:0:1.3 1/0:3:2:0,2:0,1:0.6667:0,0:25:1:28:1:1:0:60:4:0.6667:0:1 -8 125313532 . A T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01893;SOR=Inf;LSEQ=TGATATAGGTCTGATGGACA;RSEQ=GATGTGTCATGTGGCAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:160,24:0:2,0:25.1:1:29.9:1:1:0:60:35.8:1:0:0.1 0/1:110:4:4,0:90,16:0.0364:2,0:24.8:1:30:1:1:0:60:8:0.0364:0:1.3 -8 125313560 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06711;SOR=Inf;LSEQ=CATGTGGCAACTTAAAAGTT;RSEQ=GCTCAACAGGGTCGGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:200,79:0:2,0:25.6:1:31.2:1:1:0:60:38.857:1:0:0.1 0/1:192:3:1,2:136,53:0.0156:2,2:19.7:1:28:1:0.19778:5.08135:60:6:0.0158:0:1 -8 125313780 . T C 313 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.37378;LSEQ=CAGTACAACTCCATGACCAG;RSEQ=TCGCAGACCTGCGAGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:898:862:491,371:21,15:0.9599:2,2:26.4:1:32.2:1:1:1.05779:60:85.2:0.9616:0:1.1 1/1:527:474:263,211:28,20:0.8994:2,2:25.8:1:31.7:1:0.76168:1.12293:59.9:157:0.9023:0:1.2 -8 125314015 . G A 96 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00211;SOR=13.07476;LSEQ=GCAGCCCGGTGCCCGCCACG;RSEQ=CCATTAACGACACACTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:1:1,0:119,273:0.0025:2,0:1:0:26:0:0.30534:0:60:2:0.0026:0:1 0/1:278:9:2,7:99,170:0.0324:2,2:19.9:1:30.4:1:0.49468:2.0336:60:18:0.033:0:1.4 -8 125873537 . A G 34 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAAGCAGGAAGGACTGGA;RSEQ=CAGATCCTTTCCTCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:34:0:1:0:60:4:1:0:1.5 -8 125874959 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.41929;LSEQ=GAGGTAAAGTCTGTATTTAC;RSEQ=AATGGTTAGAGACATGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1034:162:71,91:410,461:0.1567:2,2:27.2:1:31.3:1:0.49277:1.13975:60:53:0.1556:0:1.1 0/1:583:263:119,144:146,174:0.4511:2,2:25.3:1:30.7:1:0.9336:1.01533:60:86.667:0.4506:0:1.1 -8 125875063 . G A 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAGACCCAAATACTAGTAAT;RSEQ=AGATGCCAAAGTGAACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:60:11,49:39,190:0.2076:2,2:21:1:30.3:1:0.84836:1.09:60:120:0.2091:0:1.1 0/0:121:0:0,0:22,99:0:2,0:22.7:1:30.8:1:1:0:60:120:1:0:0 -8 125875306 . A C 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACATTTCTTCAAACTTT;RSEQ=TTGCTCAGAACGTCAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:26.3:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 126458554 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49949;SOR=0;LSEQ=CCAACCAGTTCCTGGGTGAG;RSEQ=CCGATGCTGCTGGCGTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:19,28:0.0408:2,2:29.5:1:29:1:1:1.46:60:4:0.0426:0:1.5 0/0:40:0:0,0:20,20:0:2,0:25:1:30.2:1:1:0:60:39:1:0:0.1 -8 128306327 . C A 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ACCCAGAGTGACTTCCCATT;RSEQ=CTCATTGTCTCTTGCAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:35:1:29.5:1:1:0:60:4:0.6667:0:1 0/0:4:0:0,0:4,0:0:0,0:23.3:1:29.8:1:1:0:60:8:1:0:0 -8 128306459 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13725;SOR=Inf;LSEQ=TCACTGCTATTTGTGCAGTT;RSEQ=CCATGTGCCAGTGAATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:25.1:1:31.5:1:1:0:60:22:1:0:0.1 0/1:7:2:1,1:1,4:0.2857:2,2:36.5:1:28:1:1:3.16:60:4:0.2857:0:1 -8 128343601 . G GT 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTAGAGCAAGAACTTTTA;RSEQ=TTTTTTGAGAAAGGCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:4,0:22,1:0.1481:1,0:23.5:1:31.1:1:1:0:60:8:0.1481:0.037:0 0/0:2:0:0,0:2,0:0:0,0:25.5:1:34:0:1:0:60:4:1:0:0.5 -8 128343879 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.39688;LSEQ=CTAATTGTAAGTAATTCCAT;RSEQ=TATTTGTAGAATGCTTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:158:67,91:344,445:0.1667:2,2:26.4:1:29.7:1:0.79271:1.0499:60:316:0.1683:0:1.1 0/1:546:221:96,125:151,174:0.4048:2,2:25.5:1:28.8:1:0.53986:1.12971:60:109.5:0.4093:0:1.1 -8 128343948 . T C 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00917;SOR=0.6025;LSEQ=ACATGTACTATTATACAATA;RSEQ=GCAAAATAATTTTAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:211:41,170:33,94:0.6243:2,2:22.5:1:30.1:1:0.17536:1.45392:60:69.333:0.6209:0:1 1/0:164:82:19,63:15,65:0.5:2,2:25.1:1:30:1:0.56444:1.30:60:164:0.5031:0:1.1 -8 128343983 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGATATATTGACTATT;RSEQ=CACCCAAGACTTATATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:18,149:0.0118:2,2:25:1:31.5:1:0.21281:8.08:60:4:0.012:0:2 0/0:77:0:0,0:6,71:0:2,0:25.4:1:29.1:1:1:0:60:76:1:0:0.6 -8 128747953 . G T 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGGCGCGCAGTGCGTTCTC;RSEQ=GTGTGGAGGGCAGCTGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:43:40,3:237,46:0.1319:2,2:28:1:31.3:1:0.16671:2.58:60:42:0.1304:0:1 0/0:181:0:0,0:142,39:0:2,0:24.2:1:29.4:1:1:0:60:44.25:1:0:0.1 -8 128748494 . C G 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAACTCGCTGTAGTAATT;RSEQ=CAGCGAGAGGCAGAGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:15,1:0.1579:1,2:42.3:1:33.7:1:0.05057:20.38237:60:6:0.1579:0:1 0/0:1:0:0,0:1,0:0:0,0:31:0:33:0:1:0:60:2:1:0:0 -8 128748671 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAACCCTTGCCGCATCCAC;RSEQ=AAACTTTGCCCATAGCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:126,4:0.0152:1,2:25:1:28:1:0.0746:28.29628:60:4:0.0156:0:1 0/0:39:0:0,0:36,3:0:2,0:23.1:1:30:1:1:0:60:78:1:0:0.1 -8 128749165 . A C 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59965;SOR=2.28617;LSEQ=GCTGACTCCCGGCCGGTCGG;RSEQ=CATTCCTGCTTTATTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:0,1:19,26:0.0217:2,0:47:0:13:0:1:0:60:0:0:0:2 0/1:41:2:1,1:18,21:0.0488:2,2:5:0:32:1:1:1.16:60:4:0.0488:0:0 -8 128750212 . C T 65 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TTCCTCTGCCGCTGCGGGGC;RSEQ=GACTCCCGGGCTTTGCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:38.5:1:32.5:1:1:0:60:8:0.6667:0:1 0/0:1:0:0,0:1,0:0:0,0:34:0:27:0:1:0:60:2:1:0:0 -8 128750260 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGGGAGCGGGGGCTCGG;RSEQ=GGGCACCAAGCCGCTGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:0.1667:0,0:24.5:1:31.5:1:1:0:60:4:0.1667:0:1 0/0:5:0:0,0:5,0:0:0,0:20.2:1:32.8:1:1:0:60:10:1:0:0 -8 128750413 . C G 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00044;SOR=0.3786;LSEQ=AGAGGTTCGGGACTGTGGCG;RSEQ=GCACTGCGCGCTGCGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:90:89,1:156,5:0.3586:1,1:23.7:1:31.2:1:0.42452:2.84:60:44:0.3592:0:1.1 0/1:109:19:19,0:87,3:0.1743:1,1:19.9:1:31.6:1:1:0:60:38:0.1792:0:1.1 -8 128750439 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11153;SOR=Inf;LSEQ=GCGCGCTGCGCCAGGTTTCC;RSEQ=CACCAAGACCCCTTTAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:334,21:0:2,0:24.4:1:29.9:1:1:0:60:49.714:0.9971:0:0.3 0/1:179:2:1,1:153,24:0.0112:2,2:13:0:28:1:0.2605:6.26659:60:4:0.0116:0:1 -8 128750604 . CCAG C 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.55107;SOR=1.21679;LSEQ=GACGAGGAGGAGAACTTCTA;RSEQ=CAGCAGCAGCAGAGCGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1529:27:14,13:720,778:0.0177:2,2:25.6:1:31.3:1:0.70313:1.16:60:54:0.0178:0.0026:0.1 0/1:981:21:10,11:465,489:0.0214:2,2:27.3:1:31.2:1:1:1.04598:60:42:0.0217:0.0031:0.2 -8 128751016 . G A 140 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=58.661;LSEQ=ACCCCGCCCGCGGCCACAGC;RSEQ=TCTGCTCCACCTCCAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:884:1:1,0:469,414:0.0011:2,0:14:0:20:0:1:0:60:2:0.0012:0:1 0/1:465:29:18,11:220,216:0.0624:2,2:18.9:1:29:1:0.25365:1.60:60:28:0.0614:0:1.3 -8 128751201 . G A 196 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03363;LSEQ=TCCTCGACGGAGTCCTCCCC;RSEQ=CAGGGCAGCCCCGAGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:108:37,71:221,374:0.1534:2,2:26.9:1:29.1:1:0.58932:1.13367:60:53:0.153:0:1.1 0/0:496:3:3,0:185,308:0.006:2,0:13.7:1:22.3:1:0.05391:0:60:2:0.0041:0:1 -8 128751278 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12029;SOR=Inf;LSEQ=CGACTCTGGTAAGCGAAGCC;RSEQ=GCCCAGGCCTGTCAAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:31,210:0:2,0:23.4:1:29.8:1:1:0:60:47.2:0.9958:0:0.2 0/1:129:2:1,1:26,101:0.0155:2,2:30.5:1:31:1:0.37609:3.83:60:4:0.0159:0:1.5 -8 128751285 . G C 40 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03891;SOR=Inf;LSEQ=GGTAAGCGAAGCCCGCCCAG;RSEQ=CCTGTCAAAAGTGGGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:19,179:0:2,0:25.5:1:32.1:1:1:0:60:98:0.9949:0:0.1 0/1:103:3:1,2:18,81:0.0291:2,2:18.7:1:25.7:1:0.46487:2.23:60:2:0.0196:0:0.7 -8 128752552 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11911;SOR=Inf;LSEQ=AGAGACCTTTCTAACGTATT;RSEQ=ATGCCTTGTATTTGTACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:173,12:0:2,0:22.7:1:31.5:1:1:0:60:91.5:1:0:0.1 0/1:98:2:1,1:87,9:0.0204:2,2:13.5:1:30:0:0.19461:9.22316:60:4:0.0208:0:1 -8 128752745 . C A 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCACCTTCTGCTGGAGGCCA;RSEQ=AGCAAACCTCCTCACAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:852:0:0,0:386,466:0:2,0:25.1:1:31.9:1:1:0:60:105.5:1:0:0.1 0/1:543:16:8,8:235,291:0.0295:2,2:21.6:1:29.4:1:0.79995:1.24:60:32:0.0296:0:1.1 -8 128753298 . A G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09683;SOR=Inf;LSEQ=TGATCAAATGCAACCTCACA;RSEQ=CCTTGGCTGAGTCTTGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:0,82:0:1,0:24.8:1:29:1:1:0:60:26.333:1:0:0 0/1:38:2:0,2:2,34:0.0526:2,0:40:1:34:0:1:0:60:4:0.0556:0:1 -8 128755075 . A C 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTGATTATATAGGTAAATG;RSEQ=AGGATGCTATTGCTGTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:973:0:0,0:646,327:0:2,0:23.9:1:29.8:1:1:0:60:68.5:1:0:0.2 0/1:597:23:16,7:366,205:0.0385:2,2:23.2:1:31.4:1:0.66302:1.28:60:46:0.039:0:1.1 -8 128755087 . G A 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.90784;LSEQ=GGTAAATGAAGGATGCTATT;RSEQ=CTGTTCTAATTACCTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1113:94:60,34:642,376:0.0845:2,2:22.7:1:28.3:1:0.91154:1.03:60:93:0.0847:0:1.1 0/1:728:193:118,75:318,212:0.2651:2,2:24.8:1:28.8:1:0.7972:1.05:60:192:0.2656:0:1.1 -8 128755332 . A T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09863;SOR=Inf;LSEQ=CAAAGGGAGATGCAATCCAC;RSEQ=GAAGTATAGTAGTTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:1,94:0:1,0:22.8:1:31.6:1:1:0:60:94:1:0:0.1 0/1:44:2:0,2:0,42:0.0455:1,0:11:1:31.5:1:1:0:60:4:0.0455:0:1 -8 129385621 . A G 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11002;SOR=4.68932;LSEQ=TTGGTGCTGGTGCTGCTGGT;RSEQ=CAGATTATGGTGCTGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:4,3:6,4:0.4118:2,2:23.7:1:32.9:1:1:1.11721:60:14:0.4375:0:1.3 1/0:9:7:5,2:1,1:0.7778:2,2:12.4:1:32.9:1:1:2.24:60:14:0.7778:0:1.1 -8 129385897 . G T 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70756;SOR=1.4733;LSEQ=CTAGTGATGCAGGTGCTGGT;RSEQ=GTGCTGATGCTGCTGGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:3,2:13,13:0.1613:2,2:28.8:1:29.4:1:1:1.48:60:10:0.1613:0:1 0/1:18:4:2,2:6,8:0.2222:2,2:22.5:1:28.8:1:1:1.31:60:8:0.2222:0:1 -8 129386059 . T G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68879;SOR=1.82594;LSEQ=TTGCTGGTGCTGGTGCTGGT;RSEQ=CAGGCACTGGTGCTGCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:3,7:3,5:0.5556:2,2:33.6:1:31.5:1:1:1.3738:60:20:0.5556:0:1.8 1/0:10:7:3,4:1,2:0.7:2,2:27.4:1:33:1:1:1.44:60:14:0.7:0:1 -8 129386118 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GGTGCTGGCGCTGGTGCTAC;RSEQ=TGTGTTAGTACTGGTGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:16.6:1:30.6:1:1:0:60:18:1:0:1.1 0/1:9:2:1,1:3,4:0.2222:2,2:10:1:32:0:1:1.29:60:4:0.2222:0:1 -8 129389172 . G A 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1009;SOR=Inf;LSEQ=CTGAGAAAGGAGGACTTTGC;RSEQ=CCTTCTTAGGGGAAGAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:3,2:0.5:2,2:26.2:1:28.8:1:1:2.41:48:10:0.5:0:1.2 1/1:5:5:2,3:0,0:1:0,2:27.4:1:28.6:1:1:0:49.8:10:1:0:2.2 -8 129389233 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08772;SOR=8.53453;LSEQ=AGGGATAGTACGAGATGCCG;RSEQ=CTGGCATTTACAGGAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:6,7:0.0714:2,0:39:0:33:0:1:0:60:2:0.0714:0:1 0/1:7:3:1,2:3,1:0.4286:2,2:37:1:32:1:0.48571:4.4496:47.7:6:0.4286:0:2.3 -8 129389271 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08867;SOR=Inf;LSEQ=AGGCTTCTGAAATCAGACAA;RSEQ=GCCTTTCAAACTCTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:0:2,0:20.5:1:30.7:1:1:0:60:40:1:0:0.3 0/1:9:2:1,1:4,3:0.2222:2,2:5.5:1:27:1:1:1.29098:47:4:0.2222:0:2.5 -8 130841905 . C A 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.40479;SOR=2.37144;LSEQ=CAGTTTAGCCAGAACCCCCA;RSEQ=CCTCATTATCTGCGCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:7,10:0.1053:2,2:37.5:1:30:1:1:1.40:60:4:0.1111:0:1 0/1:18:4:2,2:7,7:0.2222:2,2:34.3:1:28.8:1:1:1:60:8:0.2222:0:1 -8 131097984 . G A 93 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=1;SSF=1;SOR=0.91854;LSEQ=GAACAAGACGTTGTCTTTAA;RSEQ=AAAAAAAAAAAAAAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:9:9,0:20,0:0.2903:1,0:12.6:1:29.4:1:1:0:48.9:8:0.2857:0:2.6 0/1:11:3:3,0:8,0:0.2727:0,0:17.7:1:25.3:1:1:0:30:2:0.2:0:3 -8 131098084 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06162;SOR=Inf;LSEQ=TCCACAGGACTATTTGTTTT;RSEQ=CTATCAAAAGCCTGCCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:142,51:0:2,0:24:1:31.8:1:1:0:60:95.5:1:0:0.2 0/1:127:3:0,3:87,37:0.0236:2,0:12:1:26:1:0.02964:0:60:6:0.024:0:1 -8 131098162 . T C 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.24348;SOR=0.82415;LSEQ=GCAGGACTTCAGTAATGTAA;RSEQ=GCTGGGGCTATTTTGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:157:75,82:140,140:0.3576:2,2:26.7:1:30.6:1:0.69045:1.09311:60:77.5:0.3555:0:1.2 0/1:318:100:54,46:104,113:0.3145:2,2:23.8:1:29.5:1:0.33525:1.27:60:32.333:0.3099:0:1.2 -8 131098227 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16496;SOR=Inf;LSEQ=GAAAAAGCCTGGGGTGGCCC;RSEQ=CCCAGCCTGGGCAGCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:99,181:0:2,0:24.1:1:30:1:1:0:60:45.667:1:0:0.3 0/1:192:2:1,1:75,115:0.0104:2,2:30:0:32.5:1:1:1.53:60:4:0.0106:0:1 -8 131098238 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20429;SOR=Inf;LSEQ=GGGTGGCCCTCCCAGCCTGG;RSEQ=CAGCGCAGGAGCTGCATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:68,146:0:2,0:25.6:1:31.4:1:1:0:60:41.8:1:0:0.2 0/1:177:2:1,1:65,110:0.0113:2,2:21.5:1:28:1:1:1.69:60:4:0.0115:0:1.5 -8 131098264 . G T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51031;SOR=0;LSEQ=CAGGAGCTGCATACCAGGGT;RSEQ=CCATGCTGCAGATGGATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:26,108:0.0147:2,2:8:0:28:1:0.35882:4.10:60:4:0.0149:0:1 0/0:99:0:0,0:21,76:0:2,0:21.3:1:31.7:1:1:0:60:194:0.9898:0:0.1 -8 131098341 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACCATGCTAAGTTGATC;RSEQ=CCTTCTCCACACTTCAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:0,2:0,35:0.0541:1,0:26.5:1:28:1:1:0:60:4:0.0556:0:1 0/0:12:0:0,0:0,12:0:0,0:20.3:1:33.4:1:1:0:60:24:1:0:0 -8 131759339 . C T 110 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0596;SOR=0.13609;LSEQ=AATAGTGAAAGTCTTAAAGT;RSEQ=TTTGATCTTTCTTACAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:12,0:13,1:0.4615:1,0:24.8:1:30.7:1:1:0:60:24:0.4615:0:1.6 0/1:10:1:1,0:8,1:0.1:2,0:16:0:32:0:1:0:60:2:0.1:0:2 -8 131759411 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13243;SOR=Inf;LSEQ=CCCTCTCTGCTTTGGCTACC;RSEQ=AGAAGGGAAGGGCCACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:65,39:0:2,0:23.2:1:29.5:1:1:0:59.8:51:1:0:0.4 0/1:60:2:1,1:35,23:0.0333:2,2:30.5:1:31.5:1:1:1.51079:60:4:0.0339:0:1.5 -8 131759413 . G T 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09836;SOR=0.50694;LSEQ=CTCTCTGCTTTGGCTACCTA;RSEQ=AAGGGAAGGGCCACCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:31:19,12:46,28:0.2952:2,2:22.5:1:28.7:1:1:1.03726:60:30:0.2885:0:1.3 0/1:63:11:7,4:31,21:0.1746:2,2:14.9:1:28.2:1:1:1.18:60:22:0.1774:0:1.2 -8 131759529 . G A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03137;SOR=0.23334;LSEQ=TTTGCAATAAATGTCAGCGC;RSEQ=CCCAGCCATTCTGGGCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:23:6,17:0,13:0.6389:1,2:21.6:1:29.3:1:0.0679:0:60:22:0.6471:0:1 0/1:14:4:0,4:2,8:0.2857:2,0:14.3:1:27.5:1:1:0:60:8:0.2857:0:1 -8 131862420 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTTCAAGGTGGGTTTT;RSEQ=TGAAGATTTCCCCCTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:13:1:33.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 131862601 . C T 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00429;SOR=0.14299;LSEQ=TCACTCTCGAGTTTACATCT;RSEQ=GAGTTTCAAACTCTCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:26:26,0:18,0:0.5909:1,1:28:1:29.8:1:1:0:60:25:0.5814:0:1.1 0/1:18:3:3,0:15,0:0.1667:1,0:15:1:29.7:1:1:0:60:6:0.1667:0:1 -8 131862736 . C G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.16633;LSEQ=CATCTTTAACTCCTGTCTCC;RSEQ=CTATCAACCTATTTATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:223:137,86:137,87:0.4967:2,2:25.5:1:30.9:1:1:1.01:60:110.5:0.4955:0:1.3 0/1:263:37:22,15:129,97:0.1407:2,2:25.5:1:30.6:1:0.85869:1.10:60:74:0.1407:0:1.3 -8 131862819 . T C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38996;LSEQ=CTCTGTGTAGCCATTCATGT;RSEQ=CTACACTGGCAGCTCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:559:343:151,192:99,117:0.6136:2,2:22.9:1:30.9:1:0.72686:1.07576:60:56.167:0.6116:0:1.2 0/1:314:120:49,71:86,108:0.3822:2,2:24.4:1:31:1:0.55957:1.15329:60:240:0.3846:0:1.2 -8 131862896 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11507;SOR=Inf;LSEQ=TGTTAAAGGGTACCTTGATA;RSEQ=AAGTGGAGGGAAATTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:68,194:0:2,0:24.7:1:31.3:1:1:0:60:51.4:1:0:0.4 0/1:135:2:1,1:45,87:0.0148:2,2:6.5:1:26.5:1:1:1.92:60:4:0.015:0:1.5 -8 131907452 . G A 58 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATATTTAAAGTGCTATAC;RSEQ=TTTATTGGGTCTTGTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:0.5:0,0:15.5:1:29.3:1:1:0:60:8:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 131907569 . C A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00683;SOR=0.11906;LSEQ=AGTTTTAGCAGGTTATCAGC;RSEQ=ATGGGAGTAACCGTGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:53:53,0:5,0:0.9138:0,1:23.6:1:30.5:1:1:0:60:106:0.9138:0:1.7 1/0:11:6:6,0:5,0:0.5455:0,0:26.5:1:28.7:1:1:0:60:12:0.5455:0:1 -8 131907638 . A C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17207;LSEQ=TATTTTTCATGTCTGTGGTT;RSEQ=TACATAAGCCTCAGTCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:227:202:184,18:25,0:0.8899:1,2:23.2:1:31.4:1:0.23223:0:60:66.333:0.8924:0:1.2 1/0:69:40:38,2:27,2:0.5797:2,2:23.9:1:31.2:1:1:1.40:60:39:0.5821:0:1 -8 131907776 . C G 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21463;LSEQ=CATTCAATGTTCTCTGGAAG;RSEQ=CTTCAAATCCACTTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:735:608:282,326:61,64:0.8272:2,2:26.5:1:31.4:1:0.62431:1.10169:60:49.667:0.8266:0:1.1 1/0:391:198:92,106:93,100:0.5064:2,2:26.9:1:31.4:1:0.76173:1.07133:60:65:0.5078:0:1.2 -8 132408439 . C A 31 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03011;SOR=Inf;LSEQ=GATAGAAATCAGGAGACATT;RSEQ=CTTTCAGGGCTGATTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:0:0,0:377,211:0:2,0:26.6:1:31:1:1:0:60:64.333:0.9983:0:0.1 0/1:267:3:1,2:162,102:0.0112:2,2:17:1:20:1:0.56226:3.16244:60:2:0.0077:0:3.3 -8 132408509 . A G 229 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=867.20366;LSEQ=TATTTGACTATAAAACCATC;RSEQ=TTTCCAACCATAGAACCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:821:1:0,1:392,428:0.0012:2,0:15:0:31:0:1:0:60:2:0.0012:0:1 1/0:388:200:97,103:93,94:0.5155:2,2:27.3:1:30:1:0.83911:1.05039:60:39:0.5145:0:1.1 -8 132506242 . ATAACCCCAGCTTCTGCCCCCACTATATCTACATTAATTAAT A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAAAGCATAGGTGATTG;RSEQ=TAGTACAGATTCACTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:22.5:1:31.9:1:1:0:60:4:0.2857:0.2857:0 0/0:2:0:0,0:2,0:0:0,0:22:1:32:0:1:0:60:4:1:0:0 -8 132506286 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=ATATCTACATTAATTAATTA;RSEQ=TACAGATTCACTACTGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:0.1818:2,2:13:1:30:1:1:1.87089:60:4:0.1818:0:1.5 0/0:6:0:0,0:4,2:0:2,0:28.2:1:30.5:1:1:0:60:12:1:0:0 -8 132506457 . G C 64 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CATTGCTCTGGAGAGATGAT;RSEQ=AAGGTAGGGCAAGATAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:0.6667:0,0:13.3:1:32.3:1:1:0:60:8:0.6667:0:1 0/0:2:0:0,0:0,2:0:0,0:37:1:33:0:1:0:60:4:1:0:0 -8 134015166 . T G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01771;SOR=5.88811;LSEQ=GCCATGGTAACACCTGTGGG;RSEQ=TATACCTTTTTGAACAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:34:18,16:23,11:0.5:2,2:28.6:1:30.8:1:0.32159:1.84152:60:33:0.5:0:1.1 1/1:14:12:6,6:1,1:0.8571:2,2:19.2:1:31.1:1:1:1:60:24:0.8571:0:1 -8 134015236 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTACAGATTCACATGTA;RSEQ=CTGGCCAAACGAACAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:57,28:0.023:2,2:28.5:1:30.5:1:1:2.01784:60:4:0.023:0:2 0/0:36:0:0,0:24,12:0:2,0:26.2:1:31.6:1:1:0:60:72:1:0:0.2 -8 134015264 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGAACAACTCCATGTTTT;RSEQ=CAAAAGGCTTGGAGAACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:78,35:0.0174:2,0:16.5:1:26.5:1:1:0:60:4:0.0179:0:1.5 0/0:51:0:0,0:34,16:0:2,0:25.2:1:30.5:1:1:0:60:100:0.9804:0:0.1 -8 134015351 . AG A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11624;SOR=Inf;LSEQ=TACTGGAAGATGGTGGTTCC;RSEQ=CTGAAAGGCTTTTTGGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:86,116:0:2,0:25.8:1:32.2:1:1:0:59.7:404:1:0:0.1 0/1:105:2:1,1:47,56:0.019:2,2:26.5:1:30:1:1:1.19:60:4:0.019:0:0 -8 134015367 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10935;SOR=Inf;LSEQ=TTCCAGCTGAAAGGCTTTTT;RSEQ=GCAATTTTTAACAGCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:64,104:0:2,0:23.9:1:30.9:1:1:0:60:83:0.994:0:0.1 0/1:84:2:1,1:35,45:0.0238:2,2:41:1:30.5:1:1:1.28:60:4:0.0238:0:1 -8 134015382 . C A 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55228;SOR=0;LSEQ=TTTTTGGCAATTTTTAACAG;RSEQ=TGAAAATAAACCTTGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:3:2,1:43,88:0.0224:2,2:16.7:1:28:1:0.26091:4.05:60:6:0.0224:0:1 0/0:68:0:0,0:28,40:0:2,0:21.3:1:31.6:1:1:0:60:136:1:0:0.1 -8 134015507 . A G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.57576;SOR=2.74155;LSEQ=AGAGTGAAGGAGGGAAGAAA;RSEQ=GAGAATTAAACACGATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:20.5:1:31.5:1:1:0:60:8:0.5:0:1 1/0:4:3:0,3:0,1:0.75:0,0:17.7:1:31.7:1:1:0:60:6:0.75:0:1 -8 134042069 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4918;SOR=0;LSEQ=TTTCCTCTTTTCTGAAGGGT;RSEQ=CGGAGAGGTGAGTGGCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:20,9:0.0645:2,2:38:0:31.5:1:1:2.16029:60:4:0.0645:0:1.5 0/0:31:0:0,0:13,18:0:2,0:27.8:1:30.6:1:1:0:60:62:1:0:0.2 -8 134042158 . C T 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03153;SOR=Inf;LSEQ=TCCGAGGATTTGGCGGGGAC;RSEQ=CTCGGCGCGTGTCCCTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:10,20:0:2,0:21.5:1:30.5:1:1:0:60:29:1:0:0.3 0/1:7:2:1,1:3,2:0.2857:2,2:35.5:1:31.5:1:1:1.41418:60:4:0.2857:0:1.5 -8 136801602 . C T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATCTCAGTGGTGTTCTCTG;RSEQ=ATTTCCTGAATTTGAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:35:0:32:0:1:0:60:2:0.5:0:2 1/1:2:2:2,0:0,0:1:0,0:20.5:1:32:0:1:0:60:4:1:0:2 -8 139766211 . G C 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=0;LSEQ=ATACTCCGTGGTGAAAACAG;RSEQ=AGAGGCTGCACAGTCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:21.9:1:31.7:1:1:0:60:13:1:0:1.6 0/0:1:0:0,0:1,0:0:0,0:15:0:33:0:1:0:60:2:1:0:0 -8 139766407 . G C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0996;SOR=Inf;LSEQ=AGTATAGACCTTCAATACTT;RSEQ=CCAATAATAGATCTGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:201,81:0:2,0:23.3:1:32.1:1:1:0:60:140:0.9964:0:0.4 0/1:131:2:1,1:89,39:0.0153:2,2:11:0:33:0:0.52236:2.266:60:4:0.016:0:1 -8 139766478 . T C 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00677;SOR=0.66563;LSEQ=TTGGAACACACTGCATTCTC;RSEQ=GCATTATCTAGTTTAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:603:396:213,183:104,103:0.6567:2,2:25:1:30.3:1:0.4398:1.15:60:131:0.655:0:1.1 1/0:275:154:82,72:59,62:0.56:2,2:24:1:29.5:1:0.46875:1.20:60:50.333:0.5613:0:1.2 -8 139766508 . T TACA 258 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.13993;SOR=0.78925;LSEQ=AGTTTAAATCTCTCAACAGT;RSEQ=ACAATTGTGGGCAGCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:573:367:171,196:31,36:0.6405:2,2:26.8:1:30.4:1:1:1.01:59.9:366:0.6421:0.1257:0.8 1/0:255:149:74,75:29,40:0.5843:2,2:27.4:1:29.4:1:0.31069:1.36:60:298:0.5936:0.1059:0.9 -8 139766879 . A G 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAACTCACATCATAAGAT;RSEQ=ATCACAAGGGCCCTTTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:22.7:1:30.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 141608898 . T C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATGGCACAAGACAATTG;RSEQ=ACAGCAGACCCACCTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:36.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 141609046 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATCTGCTCAATGACAGAAA;RSEQ=GCGACAACAGAGGCCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 141610497 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=GGTCTACAGATCCAAAACAC;RSEQ=GGCCGGGCGCGGTGGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:20.6:1:30.9:1:1:0:60:32:1:0:0.1 0/1:22:2:1,1:9,11:0.0909:2,2:33:1:31:1:1:1.21:60:4:0.0909:0:1 -8 141611030 . CA C 32 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGTGAGGCTCCGTCT;RSEQ=AAAAAAAAAAACCCGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:32.5:1:1:0:60:4:1:0:1.5 -8 141611064 . A C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGAATTCGAATTGTGTCTA;RSEQ=ATCTGTCCACTTCACCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40.5:1:31:1:1:0:60:4:1:0:1.5 -8 141611909 . C T 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATATTTTTTATTGCTTTT;RSEQ=TCCCCCCAAATATTTTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:44.5:1:30.5:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:33:0:27:0:1:0:60:2:1:0:1 -8 141840645 . G A 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44834;SOR=1.87771;LSEQ=TCTGAAATATAAAAAGAAGC;RSEQ=TATTAACAAATAACACCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:8,0:38,0:0.1739:1,0:15:1:30.5:1:1:0:60:16:0.1739:0:1.3 0/1:14:4:4,0:10,0:0.2857:0,0:35:1:28.8:1:1:0:60:8:0.2857:0:1 -8 141840739 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.55787;LSEQ=ATCCTTCCATATATTATTTA;RSEQ=GAAGGAAACAAGTATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:43:39,4:187,20:0.172:2,2:22.5:1:30.5:1:1:1.04:60:42:0.1694:0:1.1 1/0:80:43:40,3:34,2:0.5375:2,2:23.9:1:29:1:1:1.27113:60:9.75:0.52:0:1.1 -8 141840767 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08289;SOR=Inf;LSEQ=ACAAGTATAATAATGCTTTA;RSEQ=TTTACCAGTATATTCACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:320,119:0:2,0:23.2:1:30.1:1:1:0:60:86.8:1:0:0.1 0/1:178:2:1,1:127,49:0.0112:2,2:8:0:33:0:0.48403:2.57588:60:4:0.0114:0:1.5 -8 141840816 . T C 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACAAATCATTTTCTAGATA;RSEQ=GTACTGGAAACATGAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:834:0:0,0:459,375:0:2,0:27.9:1:30.5:1:1:0:60:74.818:1:0:0.2 0/1:371:15:9,6:197,159:0.0404:2,2:28.5:1:30.9:1:0.79581:1.21:60:30:0.0408:0:1.5 -8 141840881 . T C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.19583;LSEQ=TGGTTTTTTCTTTTTTTACC;RSEQ=TTATTGTTGAAAACTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:91:38,53:216,337:0.1409:2,2:23.2:1:31.1:1:0.64447:1.12:60:44.5:0.1393:0:1.2 1/0:333:168:82,86:65,100:0.5045:2,2:24.3:1:30.3:1:0.0979:1.47:60:83:0.503:0:1.2 -8 141840944 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11775;SOR=Inf;LSEQ=TATAGTGTATTAAAAACTGT;RSEQ=CTTTTTCAGATATTTCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:99,257:0:2,0:24.4:1:31.2:1:1:0:60:117.667:1:0:0.1 0/1:187:2:1,1:60,124:0.0107:2,2:41.5:1:30.5:1:0.54955:2.06:60:4:0.0109:0:1 -8 142097729 . G A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCAGGAAAGGGGGCGTGA;RSEQ=GTTGTGTGGCAGCAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:32.5:1:1:0:60:4:1:0:2.5 -8 142098849 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09117;SOR=Inf;LSEQ=TTCTGGCAGCCACTGCACTT;RSEQ=CATTCAGAGTGGCAGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:78,11:0:2,0:28:1:32.2:1:1:0:60:43.5:1:0:0.2 0/1:39:2:1,1:32,5:0.0513:2,2:21:1:27.5:1:0.28745:5.93298:60:4:0.0526:0:1 -8 142098892 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.07763;SOR=Inf;LSEQ=GGTGCCTCGGGACCCCTCCC;RSEQ=TCCAAAGTAGCAGGAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:163,48:0:2,0:23.4:1:31.2:1:1:0:60:69.333:1:0:0.1 0/1:82:2:1,1:60,20:0.0244:2,2:27:0:30.5:1:0.44896:2.95195:60:4:0.025:0:1 -8 142098977 . A G 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=42.6312;LSEQ=AGGCCAGGCCCTGGGGAACC;RSEQ=GTTTGAGAAGCTCCTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:2:1,1:252,257:0.0039:2,2:11:0:14.5:1:1:1.02:60:0:0:0:1 0/1:250:36:18,18:109,105:0.144:2,2:21.8:1:28.3:1:1:1.03795:60:72:0.1457:0:1.3 -8 142099013 . G A 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02742;SOR=Inf;LSEQ=CCTCTTCTGGGTACATGTGG;RSEQ=GTGGATGGGCTGGGAGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:183,263:0:2,0:26.9:1:30.8:1:1:0:60:62.714:0.9977:0:0.2 0/1:194:3:2,1:83,107:0.0155:2,2:5.7:1:29:1:0.58365:2.57:60:6:0.0157:0:2.3 -8 142099035 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.19878;SOR=5.01682;LSEQ=TGGATGGGCTGGGAGGGTCT;RSEQ=CTCTGCGGCAGGGGGTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:1:1,0:115,235:0.0028:2,0:45:0:13:0:0.33048:0:60:0:0:0:1 0/1:141:2:1,1:52,87:0.0142:2,2:24:1:27.5:1:1:1.67:60:4:0.0143:0:1 -8 142099052 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56214;SOR=0;LSEQ=TCTGCTCTGCGGCAGGGGGT;RSEQ=CATCCTTCTCTCTTGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:2,1:71,193:0.0112:2,2:18:1:24:1:0.18236:5.40:60:2:0.0078:0:1.3 0/0:105:0:0,0:34,70:0:2,0:23.9:1:31.3:1:1:0:60:33.667:1:0:0.2 -8 142591787 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52821;SOR=0;LSEQ=GGAGGCGGAGCAGGAGTCAG;RSEQ=GCTGAGGAGGGCACAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:10,18:0.0667:2,2:31:1:31.5:1:1:1.76:60:4:0.0667:0:2.5 0/0:17:0:0,0:8,9:0:2,0:29.1:1:31.9:1:1:0:60:34:1:0:0.9 -8 142591816 . A G 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCACAGGGGACATGCCTG;RSEQ=CTCCGTCTGGGTGCCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:7,12:0,0:1:0,2:20.3:1:30.7:1:1:0:60:8.5:1:0:1.3 1/1:12:12:5,7:0,0:1:0,2:20.8:1:31.4:1:1:0:60:24:1:0:1.2 -8 142592872 . C T 61 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGAGCAGCAGCGGGCTC;RSEQ=GCAGGGCCTCCAGGCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:22.8:1:30.8:1:1:0:60:8:1:0:2.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 142592961 . G T 56 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAGGCTGAGGGGCACAG;RSEQ=CTGGGGCAGGAATCTCGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:18.3:1:28.3:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 142593546 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGAGCATTTCTGAGGGA;RSEQ=CCGTGAGTGTCGGGAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:30.5:1:1:0:60:4:1:0:1.5 -8 142938133 . G A 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGGGAGGGGCAGACTGA;RSEQ=GACAAGAGGTGGGGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:23:1:32:1:1:1:60:4:0.3333:0:1 0/0:2:0:0,0:1,1:0:2,0:9:0:33:1:1:0:60:4:1:0:0 -8 142938272 . A T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAGGGCCCTGGGGAGAA;RSEQ=GGGGCTGGGCTCTCAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:29:1:28.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 142939269 . G A 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.62671;LSEQ=TTGTTACCATCACCATCATC;RSEQ=CCATTCCCGTCATCATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,1:0.7143:2,2:10.6:1:29.8:1:1:1.41418:60:10:0.7143:0:1 1/0:5:3:1,2:1,1:0.6:2,2:14.7:1:29:1:1:1.7321:60:6:0.6:0:1.3 -8 143164976 . G A 89 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGGGCTCTCCCAGGGTCA;RSEQ=TGTGGAATACAACAAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:2,5:3,3:0.5385:2,2:37.6:1:31.9:1:0.59207:2.32357:60:14:0.5385:0:1.1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 143283778 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCCACCTCTGAGCGGGG;RSEQ=CCCTGTCCTGGTCTGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:29.5:1:32.5:1:1:1:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 143284844 . T C 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGAGCAGTGGGCCCCCTC;RSEQ=CTGCCTGCACACTCACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:26:0:1:1:43.5:4:0.5:0:1.5 -8 143284867 . T G 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGCACACTCACTGCCTC;RSEQ=GAGCGGCCCAGCCCCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:31:1:30.3:1:1:0:49:6:1:0:1.7 -8 143285674 . C G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCTGGAAGCCTGGGGG;RSEQ=TGACTCCGGCACCAGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:17,12:0.0645:2,2:8:0:33:1:1:1.40053:60:4:0.0645:0:1 0/0:11:0:0,0:7,4:0:2,0:28.9:1:32.7:1:1:0:60:22:1:0:0.4 -8 143285754 . T C 26 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01579;SOR=Inf;LSEQ=ATTGATTCTCCTTTTCATGA;RSEQ=CGTGGCACCCACGATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,12:0:2,0:24:1:28.9:1:1:0:60:16:1:0:0.6 1/0:3:2:1,1:0,1:0.6667:0,2:22:1:26.5:1:1:0:60:4:0.6667:0:1 -8 143285765 . A G 89 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57842;LSEQ=TTTTCATGATCGTGGCACCC;RSEQ=CGATGGAAATGGCATCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:2,6:2,7:0.4706:2,2:16.8:1:29.9:1:1:1.16:60:16:0.4706:0:1 0/1:3:1:0,1:1,1:0.3333:2,0:31:0:33:0:1:0:60:2:0.3333:0:1 -8 143285848 . A G 32 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGTGCGAGAATGCTTCAG;RSEQ=CAGAGGCATGCGGGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26:1:32.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:5:0:31:0:1:0:60:2:1:0:1 -8 143287465 . A AAGGGGC 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=28;MSI=5.000;MSILEN=6;SSF=1;SOR=0;LSEQ=GAGCAGCCACGAGACAGCGG;RSEQ=AGGGGCAGGGGCAGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:34:0:32.4:1:1:0:60:4:1:0:0 -8 143349510 . A G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCTGCCCTCCCTGCGTGCC;RSEQ=CCTGCCATTCCATGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:20:10,10:1,0:0.9524:0,2:30.3:1:29.6:1:1:0:60:19:0.95:0:1.5 1/1:5:5:2,3:0,0:1:0,2:33.6:1:32.2:1:1:0:60:10:1:0:1.2 -8 143350750 . T C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGAAGGTTGGGGCTCAGC;RSEQ=AGCACCAGAGTAGAGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:31:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:14.5:1:29:1:1:0:60:4:1:0:0 -8 143445733 . A G 78 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30769;SOR=0;LSEQ=TTTTTAAGATGCACAGAGAA;RSEQ=TACAGATATAGATGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:2,3:15,16:0.1389:2,2:25.2:1:34:1:1:1.39312:60:10:0.1389:0:1.4 0/0:16:0:0,0:6,10:0:2,0:25.8:1:28.3:1:1:0:60:15:1:0:0 -8 143486125 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGGACCAATGCCTGTCTGA;RSEQ=AGCTGTCAGTCTGGACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11.5:1:29.5:1:1:0:60:4:1:0:1.5 -8 143486688 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.28202;SOR=3.72692;LSEQ=AGCTCTGGGCTCCCTCCTTC;RSEQ=TCCAGAGAAGCAGGACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:0,1:193,133:0.003:2,0:1:0:27:0:0.40979:0:60:2:0.0031:0:2 0/1:177:2:1,1:97,77:0.0113:2,2:8.5:1:28.5:1:1:1.25807:60:4:0.0114:0:3.5 -8 143486698 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=5.20369;LSEQ=TCCCTCCTTCCTCCAGAGAA;RSEQ=CAGGACTCCCTGGGAAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:55:27,28:174,126:0.1541:2,2:27.6:1:29.9:1:0.23853:1.4306:60:54:0.1525:0:1.7 0/1:199:97:54,43:50,52:0.4874:2,2:22.7:1:29.4:1:0.3951:1.30:60:194:0.4924:0:1.9 -8 143486745 . T C 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00091;SOR=1.79017;LSEQ=CCCACCCCTTGGCCAACCAG;RSEQ=GAGACCAACAGGGTGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:194:92,102:94,105:0.4936:2,2:28.2:1:31:1:1:1.01:60:96:0.4948:0:1.3 1/0:217:138:63,75:31,46:0.6359:2,2:26.4:1:30.8:1:0.47577:1.25:60:137:0.6372:0:1.7 -8 143498097 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07433;SOR=Inf;LSEQ=TCCCCAGACCACCTGCATGG;RSEQ=CGGAGTCAGGTTCAGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:31,21:0:2,0:26.8:1:31.8:1:1:0:60:51:1:0:0.2 0/1:20:2:1,1:10,8:0.1:2,2:12:0:31.5:1:1:1.23603:60:4:0.1053:0:1.5 -8 143498115 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCGGAGTCAGGTTCAGCA;RSEQ=GGTCCCGGGCCACCTGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:28,26:0.0357:2,2:22:1:29:1:1:1.07547:60:4:0.0357:0:1 0/0:21:0:0,0:11,10:0:2,0:26.7:1:32.2:1:1:0:58.8:42:1:0:0.4 -8 143498175 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTCCCCGGCCACCTGCGT;RSEQ=ACCGGAGTCAGGTTCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:15,22:0.0513:2,2:30.5:1:30:0:1:1.45:60:4:0.0541:0:1.5 0/0:14:0:0,0:6,8:0:2,0:19.6:1:30.5:1:1:0:60:28:1:0:0.5 -8 143500243 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTCCCCATGTCTTATGGA;RSEQ=GGGGAGACTGAGGCTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 143714120 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=GCAGTGGCCACTCTCTGGGG;RSEQ=CATGGCCCTGCAGGCGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:24.8:1:29.4:1:1:0:60:7:1:0:0 0/1:6:2:2,0:3,1:0.3333:2,0:25.5:1:25:1:1:0:60:4:0.3333:0:1 -8 143714467 . A G 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATGCAGGGGCTGTCTGA;RSEQ=TGGGTACAGGGCAAGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,2:0.4:0,2:5.5:1:29.5:1:1:0:60:4:0.5:0:1.5 0/0:2:0:0,0:1,1:0:2,0:40.5:1:29.5:1:1:0:60:4:1:0:0 -8 143716030 . G T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTTCCAGAGGCCCTCT;RSEQ=GGATCCTCTGGCCCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 143719962 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08365;SOR=Inf;LSEQ=GGTGAGTCGCTTCACAGGAA;RSEQ=CGTCCCCCGGTGGCCATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:0:0,0:172,305:0:2,0:22.1:1:31.4:1:1:0:60:42.364:0.9979:0:0.5 0/1:195:2:1,1:74,118:0.0103:2,2:17:1:27:1:1:1.59:60:4:0.0104:0:1 -8 143719983 . G C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12867;LSEQ=CGTCCCCCGGTGGCCATGAC;RSEQ=CCAGTGGCCATGTGGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:297:209:51,158:20,67:0.7037:2,2:22.6:1:30.4:1:0.88161:1.08:60:51.25:0.6997:0:1.1 0/1:103:24:6,18:21,58:0.233:2,2:18.4:1:29.7:1:1:1.08536:60:11:0.22:0:1.2 -8 143720876 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGGCAGATGGGTGGAC;RSEQ=GATGGACAGCCGGATGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 143855670 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGGCCCCAGGCTGCTCCCAA;RSEQ=CCCCAGCCTGTGCGCGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:30:0:1:0:60:2:1:0:0 1/1:2:2:2,0:0,0:1:0,0:28.5:1:29:1:1:0:60:4:1:0:1 -8 143855749 . A C 98 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTGTGGTTGGGGACCAGG;RSEQ=CTCGGGGGACCACCTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:7,1:2,1:0.7273:2,2:24.5:1:32.9:1:0.49091:3.06:60:16:0.7273:0:2.1 1/1:1:1:0,1:0,0:1:0,0:26:0:33:0:1:0:60:2:1:0:2 -8 143855755 . G C 103 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTGGGGACCAGGACTCGG;RSEQ=GGACCACCTGCTCTGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:8,1:4,2:0.6:2,2:26.9:1:32.6:1:0.52527:3.62:60:18:0.6:0:2 1/1:1:1:0,1:0,0:1:0,0:32:0:24:0:1:0:60:2:1:0:2 -8 143856488 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCATGGCTGAGGAGGTC;RSEQ=CAGGGAGTGTGGAGGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:0.1538:2,2:28:1:30:1:1:1.67325:60:4:0.1538:0:1 0/0:1:0:0,0:1,0:0:0,0:39:0:25:0:1:0:60:2:1:0:0 -8 144225187 . AGATG A 27 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=7.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GGGTGGGCGGGCAGGCGGGC;RSEQ=GATGGATGGATGGATGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:1:2:0,2:0,0:2:0,0:30.5:1:27.5:1:1:0:60:4:1:1:1 -8 144226165 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07589;SOR=Inf;LSEQ=CTTGTGTACTTGGCTCAGCG;RSEQ=TGCCCGCACATGCCCACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:25,21:0:2,0:23.1:1:32:1:1:0:60:45:1:0:0.2 0/1:18:2:1,1:9,7:0.1111:2,2:31:0:31.5:1:1:1.26772:60:4:0.1111:0:1 -8 144227057 . G C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTCAATTAGCTGGACAA;RSEQ=GTGGCTCACATTTGTAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:43.5:1:28:1:1:0:60:4:1:0:1 -8 144227433 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGATTTATTCTGTGGGTG;RSEQ=GGGTGGTGTGCGATGAGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29.5:1:1:0:60:4:1:0:2 -8 144227728 . A G 78 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGCCCCCTCCCCTTTCCA;RSEQ=CTGCGGAACCTGGAGCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:25:1:34:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144342581 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTCCGGTGAGGTCACCC;RSEQ=GGAGGGGAGTCCCAGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,1:0.4:2,0:6:1:28:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144342831 . G A 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCAGCCTCTCTTGGCCACCC;RSEQ=GACCAGCGGGCACCACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:32:0:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:0:0,0:49:0:29:0:1:0:60:2:1:0:0 -8 144343973 . C G 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.38489;SOR=1.92615;LSEQ=GTCTCCAGCAGCCCCTGCCC;RSEQ=CACCCGCACCCCTGCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:23:11,12:7,7:0.6216:2,2:28.4:1:27.9:1:1:1.08834:57.7:6.667:0.6452:0:1.7 1/0:21:16:9,7:3,2:0.7619:2,2:26.2:1:27.9:1:1:1.15818:57.7:7:0.7778:0:1.3 -8 144343986 . TGCACCTGCCACGCCTGTCTCCGGCAGCCCCTGCCCGCACCCGCACCCCTGCACCTGCCACGCCCGTCTCCGGCAGCACCTGCCACGCCCGTCTCCGGCA T 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=2.000;MSILEN=3;SSF=0.15237;SOR=0;LSEQ=CCTGCCCCCACCCGCACCCC;RSEQ=GCACCTGCCACGCCCGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:2,3:19,21:0.1111:2,2:15.4:1:27.5:1:1:1.34807:51.6:10:0.1316:0.1111:1.4 0/0:25:0:0,0:13,12:0:2,0:25.2:1:29.5:1:1:0:58.5:11.5:1:0:1.1 -8 144344008 . G A 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54608;SOR=0;LSEQ=CACCTGCCACGCCTGTCTCC;RSEQ=GCAGCCCCTGCCCGCACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:3:2,1:18,21:0.0638:2,2:10.3:1:31.7:1:0.59756:2.29:33.7:6:0.0811:0:5 0/0:24:0:0,0:11,13:0:2,0:24.9:1:28.1:1:1:0:58.5:11:1:0:1.2 -8 144344022 . G C 51 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54499;SOR=0;LSEQ=GTCTCCGGCAGCCCCTGCCC;RSEQ=CACCCGCACCCCTGCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:2,1:10,18:0.0882:2,2:24.3:1:32.7:1:0.54349:3.45:33.7:6:0.1034:0:5 0/0:19:0:0,0:9,10:0:2,0:25.9:1:28.4:1:1:0:58.1:8.5:1:0:1.2 -8 144344035 . TGCACCTGCCACGCCCGTCTCCGGCAGCACCTGCCACGCCCGTCTCCGGCA T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=52;MSI=2.000;MSILEN=3;SSF=0.06591;SOR=Inf;LSEQ=CCTGCCCGCACCCGCACCCC;RSEQ=GCACCTGCCACGCCCGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:9,15:0:2,0:24.4:1:31.7:1:1:0:55.5:48:1:0:1.8 0/1:20:3:1,2:9,8:0.15:2,2:11:1:28.7:1:1:2.16219:60:6:0.1579:0.15:1 -8 144344050 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50968;SOR=0;LSEQ=ACCCCTGCACCTGCCACGCC;RSEQ=GTCTCCGGCAGCACCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:6,8:0.1053:2,2:44.5:1:30.5:1:1:1.31:32:4:0.1333:0:5 0/0:12:0:0,0:5,4:0:2,0:29.7:1:29.8:1:1:0:57:18:1:0:1 -8 144344088 . A C 51 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26008;SOR=0;LSEQ=CCACGCCCGTCTCCGGCAGC;RSEQ=CCTGCCACGCCCGTCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:2,2:4,8:0.25:2,2:5.3:1:25.8:1:0.6044:1.91:39.3:3:0.2143:0:4.3 0/0:9:0:0,0:4,4:0:2,0:19.3:1:30:1:1:0:46.3:16:1:0:0.5 -8 144344100 . C T 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0095;SOR=0;LSEQ=CCGGCAGCACCTGCCACGCC;RSEQ=GTCTCCGGCAGCACCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:5,5:3,5:0.5556:2,2:12.8:1:28.2:1:0.66406:1.62:55.4:4:0.5714:0:1.6 0/0:8:0:0,0:4,4:0:2,0:19.3:1:26.8:1:1:0:46.3:7:1:0:0.5 -8 144344194 . T C 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=1;SOR=1.42516;LSEQ=CGTCTCCGGCAGCCCCTGCC;RSEQ=GCACCCGCACCCCTCACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:0,2:12,11:0.08:2,0:15:0:31:0:0.48:0:40.5:4:0.087:0:2 0/1:18:2:1,1:10,5:0.1111:2,2:12.5:1:28:1:1:1.91491:60:4:0.1111:0:1.5 -8 144344213 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51923;SOR=0;LSEQ=CTGCACCCGCACCCCTCACG;RSEQ=CTGTCTCCGGCAGCCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,10:0.08:2,2:37:1:26:1:1:1.19087:60:4:0.087:0:3 0/0:15:0:0,0:8,7:0:2,0:27.5:1:30.3:1:1:0:60:30:1:0:0.6 -8 144344261 . G T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05268;SOR=Inf;LSEQ=CGCACCTCTGCACCTCCCAC;RSEQ=CCCCTCTCCGGCAGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:23.7:1:25.6:1:1:0:60:4.5:1:0:0.1 0/1:15:5:2,3:4,6:0.3333:2,2:23.6:1:23.6:1:1:1:60:1.5:0.2308:0:1.2 -8 144344387 . A G 34 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGGCCACCGCTCAGCCAA;RSEQ=TGGATTCAGCGAGGGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19:1:34:0:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:1:0,0:40:0:32:0:1:0:60:2:1:0:1 -8 144344456 . T C 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TGTTTCCTGGTGAGGCTGGA;RSEQ=GCCTGGCATGTCTGAACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:14.7:1:31.3:1:1:0:60:6:0.75:0:1.3 0/0:1:0:0,0:1,0:0:0,0:39:0:26:0:1:0:60:2:1:0:0 -8 144346229 . C T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCCCTTCTGCTGCCTCC;RSEQ=CTCCCTCCTTCCTGCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:36:0:32:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144350854 . A G 34 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTTCTGGAAGACTCCCT;RSEQ=TGCCTTTCTCTGGGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:18.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144351029 . C CTGCTGCTGCTGCTGT 113 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.02718;SOR=0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGTTTGAGTCTTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:5,9:1,0:0.5:0,2:25.1:1:29.8:1:0.4:0:57.8:28:0.5185:0.3214:0.9 0/0:7:0:0,0:2,0:0:0,0:3:0:28.5:1:1:0:60:4:0.2857:0:0 -8 144351109 . T G 83 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAACCTCCACCTCCTGA;RSEQ=TTCAAGCTGTTCTCCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:24.5:1:32.3:1:1:0:60:12:1:0:1.3 1/1:5:5:0,5:0,0:1:0,0:26.4:1:32:1:1:0:60:10:1:0:1 -8 144351632 . A G 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTCAGTCTCTCATCACC;RSEQ=GGGACACCTGGAACCCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:29.5:1:1:0:60:4:1:0:1 1/1:3:3:1,2:0,0:1:0,2:20:0:29.7:1:1:0:60:6:1:0:1 -8 144352953 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGCACCCCCCCAGGCC;RSEQ=GATGAGGTGTGACTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144405960 . GCAC A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACACACAGGCACACCACAC;RSEQ=AAGTGCACACACACCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17.5:1:31:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144406043 . C A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTGTGCACATGCACACAC;RSEQ=CCCCCCATCAGAATGAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:2,1:0.5714:2,2:22.3:1:31:1:1:1.41:60:8:0.5714:0:1 0/0:1:0:0,0:1,0:0:0,0:20:0:32:0:1:0:60:2:1:0:0 -8 144406627 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGGGACCTCCTGGGGAG;RSEQ=AAACACCCTGCCAAGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144579523 . C G 70 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.0013;SOR=47.98972;LSEQ=CACCGCCTTCCCAATCCCCC;RSEQ=CAACCCCGCCACCAGTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:8,7:0.0625:2,0:17:0:32:0:1:0:60:2:0.0625:0:1 1/1:6:5:2,3:0,1:0.8333:0,2:31.8:1:30.2:1:1:0:60:10:0.8333:0:1 -8 144595042 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACTGAGAGTGCTCAGTGGC;RSEQ=CGGGGAGGTACACGCAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144766011 . G CC 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.71085;SOR=0.70175;LSEQ=GATTCACCCTCCTTACCCTG;RSEQ=CCCCTTGTCTTGTATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:23:5,18:3,4:0.7419:2,2:21.7:1:30.3:1:0.3446:2.60027:48.7:46:0.7419:0.1935:1 1/0:12:8:3,5:1,1:0.6667:2,2:27.4:1:30.4:1:1:1.58108:36.5:16:0.6667:0:1 -8 144894702 . C CT 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGACCCTACCTACCTTGC;RSEQ=CCACAAGCCTGACCCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32:1:31:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144896157 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACCCCACCCAGCCCCTG;RSEQ=CCAGGCTCCCCACCGTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:0.0556:2,2:9:0:31.5:1:1:1:60:4:0.0556:0:1.5 0/0:13:0:0,0:7,6:0:2,0:22.1:1:27.6:1:1:0:60:3.333:1:0:0.4 -8 144905927 . T C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCTCCACCTCTGAGAGGACC;RSEQ=GCTCCCAAGGCTGGGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:31:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:0:0,0:36:0:32:0:1:0:60:2:1:0:0 -8 144907814 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCATGCGCCGCCACACCT;RSEQ=GCTAATTTTTGTATTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144996408 . T G 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.23584;LSEQ=TGCTCCTCACGCAGCTGCTG;RSEQ=GCCTTGGCCACCTCGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:3,7:0.2857:2,2:31.3:1:30:1:1:1.2634:60:8:0.3077:0:1 0/1:6:2:1,1:1,3:0.3333:2,2:38:1:29.5:1:1:2.45:60:4:0.3333:0:1 -8 144997656 . C T 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02451;SOR=Inf;LSEQ=TGCTCCGCCTGTGCCCGCCG;RSEQ=GCCGCCTCTTGCTCGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:30.9:1:31.1:1:1:0:60:24:1:0:0 1/0:6:3:2,1:1,2:0.5:2,2:34.7:1:29.7:1:1:3.11:60:6:0.5:0:1 -8 144997927 . G A 49 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCTCCTTCTGCTGCACC;RSEQ=CGAAGGCGTGTGCCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:0.6:0,2:7.7:1:31:1:1:0:60:6:0.6:0:1 0/0:1:0:0,0:0,1:0:0,0:34:0:33:0:1:0:60:2:1:0:0 -8 144998146 . C T 29 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACGCGCTCCTCAGCCTCA;RSEQ=GGCGCCGCCGCTCCTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:0.1818:2,2:32:1:29:1:1:1.87089:60:4:0.1818:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 144998266 . A G 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.42857;SOR=Inf;LSEQ=TGCGTCCCAGCTCCAGCTCC;RSEQ=GCTCCGCCTTGCCAGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:30.5:1:31.5:1:1:0:60:8:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:46:0:31:1:1:1:60:4:0.6667:0:1.5 -8 144999065 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGGCCTGCTCCTCCGCCT;RSEQ=GCCGCGCCGCCGCGCCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:15:1:28.5:1:1:1.21106:60:4:0.0909:0:1 0/0:8:0:0,0:4,4:0:2,0:33.4:1:29.5:1:1:0:60:16:1:0:0.3 -8 144999077 . G A 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.15284;SOR=0;LSEQ=CTCCGCCTTGCCGCGCCGCC;RSEQ=CGCCTCGCGCTCCGCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:2,3:8,7:0.25:2,2:33.6:1:28.4:1:1:1.66859:60:10:0.25:0:1 0/0:9:0:0,0:5,4:0:2,0:29.6:1:29.3:1:1:0:60:8:1:0:0.2 -8 144999417 . C T 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGGGCCACCTGTACCTGCCG;RSEQ=GCTCGCTCCACCTCGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35:1:31:1:1:0:60:4:1:0:0 0/1:7:2:1,1:3,2:0.2857:2,2:46:0:28:1:1:1.41418:60:4:0.2857:0:1 -8 145002359 . A T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGTTGGGAGCCTCTGTAAC;RSEQ=CAAGGACACTCAGGACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:19:0:32:0:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 145002431 . C G 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACCCCAAGGCCCCGAGA;RSEQ=AGGACGAGCCCACTGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:40:1:33:1:1:1.73:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 145004255 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14154;SOR=Inf;LSEQ=CAGGTCAGGGCTACAGTCAG;RSEQ=GTCACCAGCGCCCCACCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:0:2,0:31.7:1:31:1:1:0:60:28:1:0:0.2 0/1:18:2:1,1:9,7:0.1111:2,2:20:0:29.5:1:1:1.26772:60:4:0.1111:0:1.5 -8 145004345 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGCCTCCTGGTTGGGC;RSEQ=GGGGCACCAGGAAGCACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:0,11:0.1538:0,2:25.5:1:27.5:1:0.15385:0:60:4:0.1538:0:1 0/0:4:0:0,0:0,4:0:0,0:17.3:1:28:1:1:0:60:8:1:0:0.3 -8 145004546 . G A 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGTGGACCCCCGGCCTGC;RSEQ=CTCACCTCCACCTGCTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:27.7:1:29.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 145005450 . T C 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATCCTGCCTCATTCCCCCCT;RSEQ=GGCTGACCTCTACACCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:30.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:0,2:0:0,0:12:1:30.5:1:1:0:60:4:1:0:0 -8 145005688 . A AC 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTCCTGACACGCCCCTGCAC;RSEQ=CCCCCTCCCTCACCTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:24.5:1:33:0:1:1.73:60:4:0.4:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31:1:1:0:60:4:1:0:0 -8 145005851 . G A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCAGCGGGAGGGGGTCAC;RSEQ=CCAGGCTACCTGGGACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:8:0:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 145589672 . G T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=Inf;LSEQ=CTGCCTTCTCTCTCTGCTTC;RSEQ=GCTACCTAAGAGGGAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:48,23:0:2,0:20.6:1:29.6:1:1:0:58.9:70:0.9859:0:0.2 0/1:21:5:3,2:11,5:0.2381:2,2:29:1:31.2:1:1:1.43927:60:10:0.2381:0:1.2 -8 145589703 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07498;SOR=Inf;LSEQ=AGGGAAGGGCCCCCTGTCCT;RSEQ=TGATCATGTGACTTGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:66,52:0:2,0:28.5:1:29.4:1:1:0:57.8:117:1:0:0.2 0/1:45:2:1,1:24,19:0.0444:2,2:28:0:33.5:1:1:1.25655:33:4:0.0444:0:2 -8 145589705 . G A 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31362;SOR=2.61329;LSEQ=GGAAGGGCCCCCTGTCCTAT;RSEQ=ATCATGTGACTTGCTTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:68,53:0.0163:2,2:2:0:25:1:1:1.28039:39:1:0.0083:0:1.5 0/1:48:2:1,1:26,20:0.0417:2,2:30:0:31:1:1:1.29283:33:4:0.0417:0:2 -8 145589753 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACTTAGAAGATTCACCCT;RSEQ=CTTACCCTGCCCCCCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:2,0:38,55:0.0211:2,0:17:1:27:1:0.17469:0:55.5:4:0.0211:0:1 0/0:41:0:0,0:20,21:0:2,0:33.1:1:30.6:1:1:0:57.6:82:1:0:0.2 -8 145589762 . GC G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.53481;SOR=0;LSEQ=AGATTCACCCTCCTTACCCT;RSEQ=CCCCCCTTGTCTTGTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:23,46:0.0282:2,2:29.5:1:32:1:1:1.98:39:4:0.0282:0:1.5 0/0:40:0:0,0:20,20:0:2,0:25.9:1:31:1:1:0:57.5:80:1:0:0.2 -8 145589765 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.52742;SOR=0;LSEQ=TTCACCCTCCTTACCCTGCC;RSEQ=CCCCTTGTCTTGTATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:21,44:0.0299:2,2:31.5:1:29.5:1:1:2.07:60:4:0.0299:0:1 0/0:40:0:0,0:20,20:0:2,0:24:1:29.9:1:1:0:57.5:80:1:0:0.2 -8 145736791 . C T 279 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGACAACCCCAGCTCTACC;RSEQ=GACATCCCCCAATGCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1275:575:381,194:442,253:0.451:2,2:24.5:1:30.5:1:0.34507:1.12:60:51.273:0.4498:0:1.1 0/0:472:0:0,0:291,181:0:2,0:23.2:1:29.5:1:1:0:60:66.429:1:0:0.2 -8 145737013 . G T 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00219;SOR=Inf;LSEQ=GAGCCTCCCAGGCCTCACCT;RSEQ=CCCCAGCCCCCAGCCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:871:0:0,0:444,426:0:2,0:24.7:1:31.9:1:1:0:60:42.5:1:0:0.4 0/1:242:4:0,4:126,111:0.0165:2,0:8.5:1:23.3:1:0.05043:0:60:3:0.0127:0:1.8 -8 145737040 . C T 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04536;SOR=0.74963;LSEQ=CCCCCAGCCCCAGCCTGCAG;RSEQ=GGGTGGGGCCTCCCAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:993:358:193,165:360,274:0.3605:2,2:24.2:1:29.4:1:0.38769:1.12312:60:34.8:0.3595:0:1.1 0/1:303:90:55,35:129,84:0.297:2,2:21.9:1:29.5:1:1:1.02:60:89:0.3007:0:1.2 -8 145737086 . C T 157 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=64.79635;LSEQ=ATGCCGTGGAAGATGCGGGC;RSEQ=ACAGCCCTGCTGGAGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1575:2:0,2:873,697:0.0013:2,0:1:0:24.5:1:0.19756:0:60:4:0.0013:0:1 0/1:564:43:21,22:290,231:0.0762:2,2:20.6:1:29.1:1:0.42691:1.31454:60:86:0.0772:0:1.1 -8 145737123 . G A 174 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=37.4588;LSEQ=ACTTCTCCTCTGGCCTCAGG;RSEQ=ACAGGAACTGGCGGATGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1901:5:3,2:975,918:0.0026:2,2:17.6:1:23:1:1:1.41:60:1.5:0.0016:0:2.2 0/1:711:64:35,29:325,321:0.09:2,2:21.8:1:29.1:1:0.51553:1.19:60:128:0.0905:0:1.3 -8 145737285 . TG CA 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGAGCTGCCTGGCCTTAC;RSEQ=CACTCACTCTGGCCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2267:0:0,0:1202,1064:0:2,0:24.7:1:30.2:1:1:0:60:112.3:1:0:0.5 0/1:787:94:52,42:360,330:0.1194:2,2:27.1:1:30.5:1:0.58377:1.13:60:188:0.1219:0.0025:1.1 -8 145737286 . G A 273 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43752;LSEQ=ATGAGCTGCCTGGCCTTACT;RSEQ=CACTCACTCTGGCCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2283:753:414,339:792,732:0.3298:2,2:24.6:1:28.6:1:0.18084:1.13:60:74.3:0.3307:0:1.2 0/1:796:141:74,67:289,273:0.1771:2,2:25.5:1:28.5:1:0.85082:1.04:60:282:0.2046:0:1.2 -8 145737514 . G A 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00376;SOR=1.44844;LSEQ=GATGGTCCCAGGCCCCGCCC;RSEQ=CCTCCTCCCAACCTGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1112:366:234,132:469,275:0.3291:2,2:23.3:1:30:1:0.79126:1.04:60:182:0.333:0:1.1 0/1:349:145:90,55:124,80:0.4155:2,2:22.6:1:29.5:1:0.82436:1.06:60:144:0.4198:0:1.1 -8 145737636 . A G 345 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01196;SOR=0.17403;LSEQ=GTCCTTCTCCTCAGCGGTCA;RSEQ=GTCCCCCGGGCTGCGAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2099:2096:1008,1088:1,0:0.9986:0,2:25.8:1:31.3:1:0.48116:0:60:66.613:0.9985:0:1.1 1/1:735:729:352,377:2,0:0.9918:0,2:24.9:1:30.5:1:0.23417:0:60:59.75:0.9931:0:1.2 -8 145737816 . C T 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00338;SOR=0.69979;LSEQ=ACTGCAGCTGGCAGAGAGCC;RSEQ=GCCGCACAGAGGCCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1255:445:217,228:421,387:0.3546:2,2:25.1:1:30.5:1:0.26251:1.14288:60:48.444:0.3539:0:1.1 0/1:443:123:64,59:159,159:0.2777:2,2:24.2:1:30.2:1:0.75035:1.08:60:122:0.2805:0:1.2 -8 145738410 . T TGGTGCA 169 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=4.000;MSILEN=6;SSF=0;SOR=Inf;LSEQ=TTCCTGCTCCGAGGGCGGCC;RSEQ=GGTGCAGGTGCAGGTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1678:0:0,0:713,963:0:2,0:24:1:30.3:1:1:0:60:53.065:0.9994:0:0.5 0/1:639:48:21,27:263,326:0.0751:2,2:29.5:1:30.3:1:1:1.0372:59.8:47:0.0754:0.0141:0.3 -8 145738441 . G A 277 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CAGGTGCAGGCTGGGAACAC;RSEQ=CGCTGTACCAGCCTCTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1342:675:264,411:250,415:0.503:2,2:24.8:1:29.5:1:0.57469:1.07:60:47.214:0.5015:0:1.2 0/0:492:0:0,0:201,291:0:2,0:23.5:1:30.3:1:1:0:60:36.846:1:0:0.2 -8 145738442 . C T 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00149;SOR=Inf;LSEQ=AGGTGCAGGCTGGGAACACG;RSEQ=GCTGTACCAGCCTCTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1319:0:0,0:502,817:0:2,0:25:1:30.4:1:1:0:60:49.731:1:0:0.7 0/1:495:5:2,3:199,291:0.0101:2,2:19.4:1:28.6:1:1:1.02572:60:10:0.0104:0:1.2 -8 145738575 . GCA G 70 Bias;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68919;SOR=0.47599;LSEQ=CACTGGGGGCTCGAGCACTG;RSEQ=GTGTGGGGGGGGGGGGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:7:0,7:354,87:0.0155:2,0:29.1:1:25.1:1:1e-05:0:60:14:0.0168:0:3.7 0/0:135:1:0,1:98,28:0.0074:2,0:30:0:23:0:0.22835:0:60:2:0.0083:0:5 -8 145738581 . TG T 196 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.68215;SOR=0.84443;LSEQ=GGGCTCGAGCACTGGCAGTG;RSEQ=GGGGGGGGGGGTGCCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:77:71,6:183,247:0.1242:2,2:26:1:31.3:1:0:15.90:59.9:18.25:0.1313:0.0113:0.6 0/1:159:17:15,2:38,54:0.1069:2,2:28.3:1:31:1:0.00039:10.45:58.5:34:0.1206:0:1.4 -8 145738592 . GGT G 49 MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.49707;SOR=1.59406;LSEQ=CTGGCAGTGTGGGGGGGGGG;RSEQ=GCCAACCTGGGGCTGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:9:9,0:345,295:0.0137:2,0:23.8:1:15.7:1:0.00485:0:60:0.286:0.0036:0:1.7 0/1:184:4:4,0:99,80:0.0217:2,0:18.8:1:23.3:1:0.13277:0:60:3:0.0186:0:2.5 -8 145738604 . G A 95 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=34.10269;LSEQ=GGGGGGGGGGTGCCAACCTG;RSEQ=GGCTGCAGGAAGAGGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:1:1,0:369,315:0.0015:2,0:1:0:27:0:1:0:60:2:0.0015:0:1 0/1:210:10:6,4:112,88:0.0476:2,2:29.9:1:28.6:1:1:1.18:60:9:0.0443:0:1.2 -8 145738622 . G A 36 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01322;SOR=Inf;LSEQ=TGGGGCTGCAGGAAGAGGTG;RSEQ=CAGTGGGCAGGCTGCCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:775:0:0,0:421,350:0:2,0:24.4:1:30.3:1:1:0:60:11.639:0.9986:0:0.5 0/1:241:3:2,1:138,100:0.0124:2,2:26:1:23.3:1:1:1.45:60:2:0.0089:0:2.7 -8 145738767 . CG C 335 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40343;SOR=0.70137;LSEQ=CCACCGTGGCCACCACCACC;RSEQ=GCAACTGGCCCTGCATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1695:1674:783,891:7,7:0.9876:2,2:26.3:1:31.3:1:1:1.13784:60:208.25:0.9887:0.1392:0.2 1/1:569:559:282,277:5,3:0.9824:2,2:26.6:1:30.7:1:0.72478:1.63571:60:278.5:0.9841:0.109:0.3 -8 145738827 . C T 132 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=69.39081;LSEQ=CGTTCCCGGCTGCACATGCC;RSEQ=GCGTGGTAGGCCTCGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1078:1:0,1:431,646:9e-04:2,0:31:0:14:0:1:0:60:0:0:0:1 0/1:346:21:6,15:118,207:0.0607:2,2:27.3:1:30.1:1:0.63964:1.42373:60:42:0.0616:0:1.3 -8 145738911 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.05044;SOR=Inf;LSEQ=GTGGGATGGGACCATGTGTG;RSEQ=CCAAGGTGGGTCCACGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:339,260:0:2,0:24.4:1:31.6:1:1:0:60:53.455:1:0:0.1 0/1:174:2:1,1:112,60:0.0115:2,2:23:1:27:1:1:1.85962:60:4:0.0118:0:1 -8 145739073 . G A 101 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=14.39565;LSEQ=TCGAGGTTTTGAAAACGTTT;RSEQ=CCTTGCAGCAGCGTCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1304:2:2,0:564,738:0.0015:2,0:1:0:23.5:1:0.18821:0:60:4:0.0016:0:1 0/1:554:12:6,6:227,315:0.0217:2,2:26:1:28.2:1:0.57099:1.39:60:24:0.0219:0:1.3 -8 145739115 . CGTGGGCA C 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTGATGAGGAGCGGTTGG;RSEQ=GTGGGGAGTGAGGAGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:727:0:0,0:208,514:0:2,0:25.5:1:30.9:1:1:0:59.6:59.167:0.993:0:0.3 0/1:258:23:8,15:67,168:0.0891:2,2:23.6:1:30.4:1:0.6306:1.34:59.3:46:0.0891:0.0194:0.6 -8 145739134 . G T 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGTGGGCAGTGGGGAGTGA;RSEQ=GAGGGGTCGGCGTGTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:0:0,0:111,446:0:2,0:23.5:1:30.8:1:1:0:59.6:54.7:0.9982:0:0.5 0/1:167:11:2,9:32,123:0.0659:2,2:18.5:1:31.3:1:1:1.16966:60:22:0.0671:0:1 -8 145739175 . C G 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01004;SOR=0;LSEQ=GGGGAGTGAGGAGGGGTCGG;RSEQ=GTGGGGAGTGAGGAGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:20:16,4:13,193:0.0826:2,2:5.6:1:27.4:1:0:56.63:54.3:5.667:0.0885:0:3.9 0/0:71:0:0,0:2,43:0:1,0:16.9:1:26.6:1:1:0:59.2:5.429:0.6129:0.0141:0.6 -8 145739186 . A G 67 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.79371;LSEQ=AGGGGTCGGCGTGGGGAGTG;RSEQ=GGAGGGGTCGGCGTGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:19:0,19:221,181:0.0446:2,1:13.1:1:16:1:0:0:52.2:0.118:0.0055:0:4.1 0/1:84:3:1,2:48,33:0.0357:2,2:12:1:29.3:1:0.56803:2.87211:60:6:0.0395:0:4 -8 145739199 . G C 69 v4;NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=34.34775;LSEQ=GGGAGTGAGGAGGGGTCGGC;RSEQ=TGGGCGGTGGGGAGTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:1:0,1:327,173:0.002:2,0:24:0:27:0:0.34731:0:25:2:0.0021:0:6 0/1:93:6:3,3:64,23:0.0645:2,2:20.7:1:26.8:1:0.34377:2.74723:50.5:5:0.0562:0:4.3 -8 145739204 . C T 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06641;SOR=10.80559;LSEQ=TGAGGAGGGGTCGGCGTGGG;RSEQ=GGTGGGGAGTGAGAAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:1:0,1:358,163:0.0019:2,0:22:0:15:0:0.31418:0:55:0:0:0:7 0/1:98:2:2,0:73,22:0.0204:2,0:29.5:1:26.5:1:1:0:60:4:0.0227:0:3 -8 145739205 . G A 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03564;LSEQ=GAGGAGGGGTCGGCGTGGGC;RSEQ=GTGGGGAGTGAGAAGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:534:31:3,28:374,129:0.0581:2,2:23.6:1:29.5:1:0:26.88654:55.9:5.2:0.0544:0:3.1 0/1:100:6:1,5:75,18:0.06:2,2:15:1:26.7:1:0.00237:19.99099:59.2:2:0.0435:0:2.2 -8 145739218 . A G 275 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00853;SOR=0.58511;LSEQ=CGTGGGCGGTGGGGAGTGAG;RSEQ=AGGGGTCGGCGTGGGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:599:417:281,136:1,0:0.6962:0,2:29.3:1:31.6:1:1:0:54.6:33.75:0.7068:0:2.6 1/0:124:71:53,18:0,1:0.5726:0,2:30.6:1:30.5:1:0.26389:0:52.8:22.667:0.5862:0:3.1 -8 145739235 . G A 83 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.81629;LSEQ=GAGAAGGGGTCGGCGTGGGC;RSEQ=GTGGGGAGTGAGGAGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:769:10:4,6:597,162:0.013:2,2:15.1:1:25.1:1:0.00957:5.51135:51.8:1.5:0.0087:0:4.5 0/1:188:2:1,1:141,45:0.0106:2,2:31.5:1:24:1:0.43048:3.11029:49:1:0.006:0:5 -8 145739248 . G T 41 q23 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04643;SOR=3.45333;LSEQ=CGTGGGCGGTGGGGAGTGAG;RSEQ=AGGGGTCGGCGTGGGCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:919:6:6,0:701,207:0.0065:2,0:17:1:16.2:1:0.34654:0:47:0.5:0.0023:0:3 0/1:225:5:3,2:162,57:0.0222:2,2:14:1:20.6:1:0.60904:1.88854:46.6:1.5:0.0144:0:2.6 -8 145739289 . G T 50 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01166;SOR=13.34891;LSEQ=AGCAGCCAGGGCCCTGCAGG;RSEQ=TCCCCAGAGCACACACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1275:1:0,1:826,448:8e-04:2,0:1:0:25:0:0.35216:0:60:2:8e-04:0:1 0/1:385:4:1,3:231,150:0.0104:2,2:15.5:1:25:1:0.30552:4.60209:60:3:0.008:0:1.8 -8 145739817 . G A 183 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=99.69523;LSEQ=CCTCACCCCTAGGCCCATGA;RSEQ=GCCCCCACCTTCTGCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2150:2:2,0:1158,987:9e-04:2,0:1:0:27:1:0.50301:0:60:4:0.001:0:1 0/1:790:67:38,29:404,318:0.0848:2,2:26.8:1:30.3:1:1:1.03:60:21.333:0.0828:0:1.1 -8 145739924 . G A 260 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=0.65649;LSEQ=AGACACCTGCAAATGCAGGA;RSEQ=CGACAGCCGTCATACGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1297:450:139,311:265,582:0.347:2,2:23.9:1:29.6:1:0.89989:1.01874:60:149:0.3484:0:1.1 0/1:468:121:37,84:114,233:0.2585:2,2:23.8:1:29.2:1:0.73489:1.11049:60:59.5:0.2565:0:1.2 -8 145740238 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00046;SOR=Inf;LSEQ=CCCAGGGGAGGGGGTGGTTA;RSEQ=GGGACAAGCAGCAGTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:0:0,0:317,47:0:2,0:23.9:1:32.2:1:1:0:60:120.333:1:0:0.1 0/1:102:5:5,0:77,20:0.049:2,0:26.2:1:29.6:1:0.58002:0:60:10:0.0495:0:1.6 -8 145740375 . C T 152 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=52.85653;LSEQ=CCAACGTGAGGCAGGGGCTG;RSEQ=GCCGGCTGTAGAGCAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1404:2:1,1:716,685:0.0014:2,2:30:1:29.5:1:1:1.04524:60:4:0.0015:0:1 0/1:484:34:16,18:230,220:0.0702:2,2:31:1:30:1:0.72328:1.17574:60:68:0.0716:0:1.1 -8 145740443 . C A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACCTGTAGGCAGCACCAG;RSEQ=AGCGTGGAGATGCCTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1100:0:0,0:551,547:0:2,0:25.1:1:32:1:1:0:60:90.5:0.9991:0:0.1 0/1:377:31:14,17:171,175:0.0822:2,2:18.7:1:29.5:1:0.70989:1.18599:60:62:0.0833:0:1.3 -8 145740956 . G A 31 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03119;SOR=Inf;LSEQ=AGGCAGTGCCCTTCCTCTGG;RSEQ=CTACTTTTTCCAAAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:70,268:0:2,0:24.6:1:32:1:1:0:60:41.25:1:0:0.1 0/1:73:2:0,2:10,61:0.0274:2,0:19.5:1:31:0:1:0:60:4:0.0278:0:1 -8 145741073 . TA T 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04504;SOR=Inf;LSEQ=AAGGCCTGTTGCTTGGAACA;RSEQ=AGTGTCCCCCAAAAGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:618:0:0,0:518,99:0:2,0:22.9:1:28.4:1:1:0:60:76.125:1:0:0.4 0/1:167:2:1,1:136,29:0.012:2,2:13.5:1:30.5:1:0.3279:4.62778:60:4:0.012:0:2.5 -8 145741097 . C T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05487;SOR=4.44729;LSEQ=TGTCCCCCAAAAGAGCACTG;RSEQ=GCCCTCTCCACAGTGTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:955:3:1,2:712,240:0.0031:2,2:6.3:1:23.3:1:0.1598:5.91972:60:2:0.0021:0:2.7 0/1:289:4:1,3:221,64:0.0138:2,2:23.5:1:27:1:0.04005:10.24982:60:8:0.014:0:2 -8 145741130 . C T 271 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03088;SOR=0.79176;LSEQ=GTGTTGGCCGGACCCACCCT;RSEQ=CAGGGCAGATGTCTCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1557:562:367,195:680,313:0.361:2,2:26.6:1:29.7:1:0.21568:1.15422:60:36.467:0.3596:0:1.1 0/1:534:165:104,61:243,126:0.309:2,2:24.5:1:29:1:0.55635:1.13091:60:330:0.3096:0:1.2 -8 145741702 . C G 288 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.5873;LSEQ=TGTGCGGGGCTCTCCCAGGG;RSEQ=TCCTCGTTCCATCTCCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1881:567:253,314:614,696:0.3014:2,2:23.8:1:31.5:1:0.39144:1.09483:60:55.7:0.3008:0:1.4 0/1:642:261:133,128:182,199:0.4065:2,2:24.5:1:30.7:1:0.46956:1.14:60:64.25:0.4086:0:1.3 -8 145741765 . G A 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.66854;LSEQ=TGGGGGCTCCCCACACGGAT;RSEQ=CTGACTTCTTGGAAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1802:552:295,257:646,600:0.3063:2,2:24.4:1:28.7:1:0.53944:1.07:60:68:0.3063:0:1.5 0/1:645:147:78,69:253,245:0.2279:2,2:24.5:1:28.1:1:0.63997:1.09:60:72.5:0.2273:0:1.5 -8 145742005 . C T 74 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0259;SOR=4.19233;LSEQ=TGGAGCCGGCCTGGCCTTGG;RSEQ=TGGGGCTCAGGGAGCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1590:4:0,4:774,811:0.0025:2,0:1:0:27.3:1:0.12503:0:60:8:0.0026:0:1 0/1:573:6:2,4:285,282:0.0105:2,2:26.3:1:28.8:1:0.45025:2.01887:60:12:0.0107:0:1 -8 145742138 . G A 30 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04991;SOR=Inf;LSEQ=GCCACGGTCTGCGGCCCAGG;RSEQ=CTGGTCCGGCCTGGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:697:0:0,0:214,483:0:2,0:23.1:1:31.4:1:1:0:60:48.786:1:0:0.1 0/1:201:2:1,1:55,144:0.01:2,2:21:0:30:0:0.4806:2.60:60:4:0.0101:0:1.5 -8 145742172 . C G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GGAGGGGAACAACAGAACAG;RSEQ=AGGAGGAACTCAGGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:95,331:0:2,0:26.5:1:32.1:1:1:0:60:41.6:0.9952:0:0.1 0/1:118:7:1,6:24,87:0.0593:2,2:25.4:1:30.7:1:1:1.64896:60:14:0.0619:0:1 -8 145742514 . A G 336 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19984;LSEQ=GCGGCTCCGCCCTGGCGTAG;RSEQ=CTGTGGACTCTTGGTCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1655:1648:732,916:1,1:0.9958:2,2:26.3:1:31.5:1:1:1.25119:60:48.939:0.9969:0:1.2 1/1:567:565:249,316:1,0:0.9965:0,2:24.4:1:31.3:1:0.4417:0:60:50.364:0.9982:0:1.2 -8 145742653 . T C 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04301;SOR=Inf;LSEQ=CCAGCCACCCCTCCCGCACC;RSEQ=GGAGCGAGGCCCGGCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:65,235:0:2,0:23.3:1:30.1:1:1:0:60:22.077:1:0:0.5 0/1:79:2:1,1:22,55:0.0253:2,2:5:1:29:1:0.50016:2.47:60:4:0.0253:0:1 -8 145742716 . C A 226 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.49819;LSEQ=CCAAGTTCTGTGCCCCACGG;RSEQ=GGCCTGGCCGCGACTCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:245:238:143,95:1,0:0.9714:0,2:22.7:1:28.7:1:1:0:60:7.815:0.9953:0:1.3 1/1:52:51:40,11:1,0:0.9808:0,2:21.1:1:28.3:1:1:0:60:16:1:0:1.1 -8 145742850 . T C 150 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=59.33534;LSEQ=TGCGGAGCCCGCCGCCGGCC;RSEQ=GGCCCGTGGTACGCTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1012:2:1,1:478,531:0.002:2,2:8:1:21.5:1:1:1.11:60:1:0.001:0:1.5 0/1:370:39:20,19:158,172:0.1054:2,2:26.4:1:28.4:1:0.73641:1.15:60:18.5:0.1022:0:1.4 -8 145742879 . T C 264 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1379;SOR=1.21609;LSEQ=GTACGCTTCAGAGTGCGGTA;RSEQ=TCCCGGTAGAGCGCTGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1039:306:121,185:292,440:0.2945:2,2:27.8:1:32:1:0.94461:1.01464:60:75.5:0.2952:0:1.2 0/1:389:131:60,71:107,150:0.3368:2,2:24.1:1:31.1:1:0.44943:1.18:60:42.667:0.3333:0:1.2 -8 145743000 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.003;SOR=Inf;LSEQ=GCTCACCGCGGGTCTCCTCC;RSEQ=GCGCCGCCTCCACGTCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1054:0:0,0:524,528:0:2,0:26:1:30.1:1:1:0:60:51.6:0.9981:0:0.2 0/1:482:5:3,2:236,241:0.0104:2,2:24.8:1:29.4:1:0.68361:1.53:60:10:0.0105:0:1.2 -8 145743004 . C T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00285;SOR=Inf;LSEQ=ACCGCGGGTCTCCTCCGGCG;RSEQ=CGCCTCCACGTCGTCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1045:0:0,0:513,530:0:2,0:26:1:31.4:1:1:0:60:51.15:0.998:0:0.2 0/1:471:5:1,4:230,236:0.0106:2,2:11:1:25.8:1:0.37279:3.8883:60:10:0.0107:0:1.4 -8 145743077 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.6343;SOR=1.60199;LSEQ=AGCCCCTCGGCCCCTGGGCA;RSEQ=CCCGCACCTGGCTCGGTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:3:3,0:143,213:0.0084:2,0:1:0:25.7:1:0.06644:0:60:6:0.0085:0:1 0/1:150:2:1,1:61,87:0.0133:2,2:34:1:29:1:1:1.42:60:4:0.0133:0:1 -8 145743081 . G A 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18843;SOR=0;LSEQ=CCTCGGCCCCTGGGCAGCCC;RSEQ=CACCTGGCTCGGTCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:6:5,1:129,188:0.0186:2,2:9.7:1:27.7:1:0.08551:7.25:60:12:0.0189:0:1.3 0/0:131:0:0,0:53,78:0:2,0:16.5:1:30.9:1:1:0:60:130:1:0:0.3 -8 145743087 . G A 37 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63096;SOR=1.63261;LSEQ=CCCCTGGGCAGCCCGCACCT;RSEQ=GCTCGGTCGCCGCCCGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:3,0:109,173:0.0105:2,0:1:0:23.7:1:0.0597:0:60:6:0.0108:0:1 0/1:117:2:1,1:46,69:0.0171:2,2:10:0:25:1:1:1.49:60:4:0.0172:0:1.5 -8 145743096 . G A 43 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61449;SOR=1.81633;LSEQ=AGCCCGCACCTGGCTCGGTC;RSEQ=CCGCCCGCGCTGCCGTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:86,127:0.0139:2,2:3.7:1:27.7:1:0.56817:2.94:60:6:0.014:0:1 0/1:80:2:1,1:33,45:0.025:2,2:31:0:30:1:1:1.36:60:4:0.0256:0:1 -8 145743121 . G A 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.56283;SOR=0;LSEQ=CCGCGCTGCCGTCGGAACGC;RSEQ=CGCTCCCACGCCTGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:2,1:67,68:0.0214:2,2:12.7:1:24.3:1:1:2.02:60:2:0.0149:0:2 0/0:53:0:0,0:26,27:0:2,0:24.8:1:30.9:1:1:0:60:52:1:0:0.4 -8 145743128 . C A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.56002;SOR=0;LSEQ=GCCGTCGGAACGCGCGCTCC;RSEQ=ACGCCTGCAGCCGCTCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:3,0:71,68:0.0211:2,0:10.7:1:22.3:1:0.24603:0:60:2:0.0145:0:2 0/0:56:0:0,0:29,27:0:2,0:20.6:1:30.8:1:1:0:60:112:1:0:0.4 -8 145743136 . C A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13636;LSEQ=AACGCGCGCTCCCACGCCTG;RSEQ=AGCCGCTCCCGCACGTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:72,68:0.014:2,2:26.5:1:30.5:1:1:1.05842:60:4:0.0142:0:1.5 0/1:63:1:1,0:32,30:0.0159:2,0:1:0:23:0:1:0:60:2:0.0164:0:1 -8 145743160 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTCCCGCACGTCCCGCAG;RSEQ=CGCTCCATGGCGCGCGCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:64,66:0.0152:2,2:8:1:31.5:1:1:1.03:60:4:0.0155:0:1 0/0:49:0:0,0:24,25:0:2,0:19.6:1:31.6:1:1:0:60:98:1:0:0.3 -8 145743227 . C G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52193;SOR=0;LSEQ=CCAGCGAATCTCCCGCGCAG;RSEQ=CGTCGCGGGGGCCGACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:19,23:0.0455:2,2:5.5:1:30:1:1:1.21:60:4:0.0455:0:1.5 0/0:27:0:0,0:12,14:0:2,0:18.5:1:31.3:1:1:0:60:52:0.963:0:0.3 -8 145743657 . C A 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCCCTGGTGGGAGACG;RSEQ=ATCCGACCTGGAGGAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:23:1:27.5:1:0.33333:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 145745182 . T C 74 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTGCCAGGCCCTGCCC;RSEQ=TGCTGCCACGCGAACTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:29.8:1:32:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 145892218 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCTCCAGTTCTCACAGC;RSEQ=AAGCCCCAATACAGTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:48,9:0.0339:2,2:25:1:31:1:0.31268:5.1122:60:4:0.0339:0:1 0/0:29:0:0,0:24,5:0:2,0:31.9:1:30.4:1:1:0:60:58:1:0:0.1 -8 146187396 . GT G 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGGGATATTGGTCTGTA;RSEQ=TTTTTTTTTTTGTTTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 146259250 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATTGATTTAAAACCACAAT;RSEQ=AGATACCATCTCACACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:31:1:1:0:33:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -8 146260665 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TCTCAAAGGATTTCTCAGTT;RSEQ=GCAATAAATAACAAAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:15:1:31.5:1:1:1:60:4:0.5:0:2 1/1:2:2:2,0:0,0:1:0,0:22.5:1:31:0:1:0:59.5:4:1:0:2 -8 146260670 . T G 34 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AAGGATTTCTCAGTTCGCAA;RSEQ=AAATAACAAAATCTATCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:20:1:33:0:1:3.1622:60:4:0.2857:0:2 1/1:2:2:2,0:0,0:1:0,0:27.5:1:34:0:1:0:59.5:4:1:0:2 -8 146261019 . T C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64098;SOR=1.95182;LSEQ=CCTTGCCAAATTTGTTTCCT;RSEQ=CAGGATTGAGGCCATCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:1,7:5,11:0.3333:2,2:29.6:1:32.1:1:0.62139:3.04782:60:16:0.3333:0:1.9 1/0:6:3:0,3:1,2:0.5:2,0:17.3:1:28:1:1:0:60:6:0.5:0:1.7 -8 146261031 . C T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87916;LSEQ=TGTTTCCTTCAGGATTGAGG;RSEQ=CATCAAGCTACAGATGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:1,7:4,10:0.3636:2,2:22.6:1:31.5:1:0.61297:2.68275:60:16:0.3636:0:1.9 0/1:6:2:0,2:1,3:0.3333:2,0:24:1:26.5:1:1:0:60:4:0.3333:0:2 -8 146261151 . G A 31 d7;v4;MAF0.05;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTAGAGAGTTCCCTTCTGA;RSEQ=GACACTACCACTGGAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:42:0:31.5:1:1:1.73:60:4:0.4:0:1.5 1/1:1:1:0,1:0,0:1:0,0:28:0:33:0:1:0:60:2:1:0:1 -8 146278052 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGCGGAGCCCGGCTTCC;RSEQ=GGCCCAGTTTCCAGCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:19,7:0.0714:2,2:30:1:32:0:0.49735:2.60494:60:4:0.0714:0:1 0/0:11:0:0,0:10,1:0:2,0:13.5:1:29.3:1:1:0:60:22:1:0:0.1 -8 146278107 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51097;SOR=0;LSEQ=TCTGTCTCTGCCCAGAGCAA;RSEQ=CTACGTGCAGTAACGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:27,23:0.0385:2,2:36:1:29.5:1:1:1.17028:60:4:0.0385:0:1 0/0:36:0:0,0:20,16:0:2,0:29.4:1:30.7:1:1:0:60:35:1:0:0.1 -8 146278188 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=CGAAAAAACAAAAGAATAAG;RSEQ=AGAAAACGCGGAACAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:0.1:2,2:21:1:27.5:1:1:1.54:60:4:0.1:0:1 0/0:14:0:0,0:2,12:0:2,0:20.7:1:29.9:1:1:0:60:28:1:0:0.1 -9 117428 . G C 66 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GGGCAGGGGCCCCAAGCAGA;RSEQ=GGCCTGGGCGGGGGTTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:23:1:33:1:1:0:46.8:8:1:0:1 0/1:3:1:1,0:2,0:0.3333:0,0:40:0:31:0:1:0:34:2:0.3333:0:3 -9 117667 . G A 23 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11089;SOR=0;LSEQ=AGCGAGAGGTTGTGGCGGAT;RSEQ=CTGTTCTGCCAGGCGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:0.1818:2,2:8.5:1:23.5:1:1:1.22:23.5:4:0.1818:0:2 0/0:21:0:0,0:8,13:0:2,0:23.6:1:31.5:1:1:0:52.7:42:1:0:0.1 -9 117696 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02451;SOR=0;LSEQ=CCAGGCGGGGAACTTGCGGC;RSEQ=GTAGTAGGGGAAGCGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:2,1:0.5:2,0:22:1:27.3:1:0.4:0:23.3:6:0.5:0:2.3 0/0:12:0:0,0:4,8:0:2,0:14.5:1:29.9:1:1:0:46.8:24:1:0:0.3 -9 117713 . T C 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33484;SOR=0.28941;LSEQ=GGCGGTAGTAGGGGAAGCGG;RSEQ=CACTAATGAAGGCGCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:2,4:2,2:0.6:2,2:20:1:29.8:1:1:1.86195:27.7:12:0.6:0:1.7 0/1:7:2:0,2:2,3:0.2857:2,0:22.5:1:32.5:1:1:0:33.5:4:0.2857:0:1 -9 117784 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.19615;SOR=Inf;LSEQ=TGCAGGATGGCCATGGTGAT;RSEQ=AGCGCGATGTACGAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:31.1:1:31.2:1:1:0:46:21:1:0:0.3 0/1:18:2:1,1:9,7:0.1111:2,2:33.5:1:27:1:1:1.26772:46.5:4:0.1111:0:1 -9 117877 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.44444;SOR=0;LSEQ=GCCCTGAACTCGGTGCCAAA;RSEQ=TCTGAGGGGTCGCTCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:39:1:29:1:1:1.73:47:4:0.4:0:1 0/0:4:0:0,0:0,4:0:0,0:31:1:33.8:1:1:0:44.3:8:1:0:0 -9 421860 . A G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1286;LSEQ=TTCTTCTTATATTCTAGTCT;RSEQ=TCAATCAAAGAGCGGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:40:35,5:41,7:0.4545:2,2:28.2:1:32.9:1:1:1.19:60:80:0.4545:0:1 0/1:94:9:9,0:72,13:0.0957:2,0:23.8:1:32.7:1:0.35191:0:60:18:0.0978:0:1.1 -9 421980 . T A 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2165;SOR=0.81925;LSEQ=CTTCTCAGTTGAGCTTGTTA;RSEQ=GAACTTCTGGTTATCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:153:75,78:85,83:0.4752:2,2:27:1:30.3:1:0.82343:1.06484:60:75.5:0.4719:0:1.1 0/1:357:152:71,81:94,111:0.4258:2,2:27.3:1:30.4:1:0.91466:1.03:60:151:0.4266:0:1.1 -9 422157 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66225;SOR=0.58813;LSEQ=TGAGTCACTCGGCAACTTTC;RSEQ=GCTACTTTTACCTAAAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:23:0,23:0,4:0.8519:0,1:27.8:1:31:1:1:0:60:46:0.8519:0:1 1/0:13:10:1,9:0,3:0.7692:0,2:26.9:1:30.5:1:1:0:60:20:0.7692:0:1 -9 1011564 . A AT 82 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TGCGCCATCACACCAGGCTA;RSEQ=TTTTTTTTTTTTGTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:1,0:0.75:0,0:21.5:1:32:1:1:0:53.3:12:0.75:0:1.2 0/0:2:0:0,0:1,0:0:0,0:32:1:31:1:1:0:60:2:0.5:0:5 -9 1011653 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13356;SOR=0;LSEQ=GACCTCAAGTAATCTACCCG;RSEQ=CTCGGCCTCCCAAAGTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:22,3:0.0741:2,2:20:1:27:0:0.2792:6.49359:60:4:0.0769:0:1 0/0:46:0:0,0:41,5:0:2,0:23.8:1:31.9:1:1:0:60:92:1:0:0 -9 1011681 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14351;SOR=0;LSEQ=TCCCAAAGTACTGGGATTAC;RSEQ=GGCGTGAGCCACTGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:36,18:0.0357:2,2:23:0:32.5:1:1:1.97357:60:4:0.0364:0:1.5 0/0:91:0:0,0:68,23:0:2,0:21.7:1:29.9:1:1:0:60:90:1:0:0.1 -9 1011695 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17837;SOR=0;LSEQ=GATTACAGGCGTGAGCCACT;RSEQ=CAGCTGGCCTGGTTGGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:47,29:0.0256:2,2:6.5:1:25.5:1:1:1.61025:60:4:0.026:0:1 0/0:106:0:0,0:74,32:0:2,0:25.3:1:31.9:1:1:0:60:212:1:0:0.1 -9 1011710 . G C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50566;SOR=Inf;LSEQ=CCACTGCAGCTGGCCTGGTT;RSEQ=GCCTTTTTTAAGATACCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:68,41:0:2,0:24.4:1:31.4:1:1:0:60:26.25:0.9906:0:0.2 0/1:141:2:1,1:86,51:0.0142:2,2:15:0:31:1:1:1.67959:60:4:0.0143:0:1.5 -9 1011738 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20638;SOR=0;LSEQ=TTAAGATACCAACCTGTGTG;RSEQ=CATCCATGCCAGACATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:87,73:0.0123:2,2:7:1:28.5:1:1:1.19048:60:4:0.0123:0:1 0/0:194:0:0,0:100,94:0:2,0:25.6:1:31.2:1:1:0:60:63.667:1:0:0.2 -9 1011775 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49838;SOR=Inf;LSEQ=GTAACAATTATGCCAAAAGG;RSEQ=ATCCAGCTAGCACGTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:71,80:0:2,0:28.8:1:31.5:1:1:0:60:49.333:0.9933:0:0.1 0/1:154:2:1,1:62,88:0.013:2,2:23:1:29.5:1:1:1.42:60:4:0.0131:0:1 -9 1011900 . C T 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.2381;SOR=0;LSEQ=GAACAATAGACATTTTTTTT;RSEQ=GTGGGGCCAAAAGGTACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:0.1875:1,0:31.3:1:31.3:1:1:0:60:6:0.1875:0:1 0/0:12:0:0,0:1,11:0:2,0:26.2:1:29.9:1:1:0:60:24:1:0:0.1 -9 2039699 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50508;SOR=0;LSEQ=AAATGCTGGCCCGAGGCCAG;RSEQ=CCCTCCCCGAAACGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:19,10:0.0645:2,2:30:1:31:1:1:1.85871:60:4:0.0667:0:1 0/0:22:0:0,0:18,4:0:2,0:19.7:1:31.4:1:1:0:60:21:1:0:0.2 -9 2039827 . G A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCAGCAGCAACAGCAGCC;RSEQ=CAGCAGCAGCCGCCGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:11,13:9,13:0.5217:2,2:22.8:1:30.9:1:0.77386:1.22:60:48:0.5333:0:1 0/0:37:0:0,0:17,20:0:2,0:25.5:1:31.1:1:1:0:60:36:1:0:0.4 -9 2039860 . A G 66 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03146;SOR=Inf;LSEQ=CCGCAACCACAGACGCAGCA;RSEQ=CAACAGCAGCCGGCCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:9,26:0:2,0:26.3:1:29.6:1:1:0:60:70:1:0:0.5 0/1:27:4:2,2:8,15:0.1481:2,2:38.8:1:33.3:1:0.61254:1.83:60:8:0.1481:0:1.3 -9 2039945 . G A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.005;SOR=0;LSEQ=ATAATGCCATGGTCCAACTC;RSEQ=GATAACAAAGACTGCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:0.8:0,0:12:1:31.5:1:1:0:60:8:0.8:0:1 0/0:9:0:0,0:1,8:0:2,0:24.1:1:29.6:1:1:0:60:18:1:0:0 -9 2047439 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14079;SOR=0;LSEQ=CATCAGCCCCATCCAGAAAC;RSEQ=GCAAGGCCTGGACCCCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:55,51:0.0185:2,2:31:0:31.5:1:1:1.07765:60:4:0.0187:0:1.5 0/0:179:0:0,0:92,87:0:2,0:28.3:1:29.4:1:1:0:60:178:1:0:0.2 -9 2047444 . G A 28 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55889;SOR=0.30018;LSEQ=GCCCCATCCAGAAACCGCAA;RSEQ=GCCTGGACCCCGTGGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:54,50:0.0189:2,2:37:0:28.5:1:1:1.07919:60:4:0.019:0:1 0/0:175:1:1,0:86,86:0.0057:2,0:1:0:25:0:1:0:60:2:0.0058:0:1 -9 2056861 . G GT 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00274;SOR=Inf;LSEQ=ACCAGGTTCTTAGACCCTGG;RSEQ=CTTTGCTCACCCTCACTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:11,24:0:2,0:22.3:1:31.6:1:1:0:60:70:1:0:0 0/1:40:9:2,7:12,19:0.225:2,2:27.7:1:30:1:0.45271:2.17012:60:18:0.225:0.025:0 -9 2086803 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22691;SOR=Inf;LSEQ=ATTTTCCCTTGCTTACTACA;RSEQ=GTCCGTCCTTCCTCTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:61,11:0:2,0:20.1:1:31.5:1:1:0:60:144:1:0:0.1 0/1:66:2:1,1:53,11:0.0303:2,2:29:1:29:1:0.33287:4.65641:60:4:0.0313:0:1 -9 2115851 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17849;SOR=0;LSEQ=GCCCAAGACCGAGCTCACCG;RSEQ=ATCGGGCAGCAGAACGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:45,23:0.0286:2,2:17:1:28.5:1:1:1.93656:60:4:0.0286:0:1 0/0:95:0:0,0:58,37:0:2,0:25.8:1:31.5:1:1:0:60:46.5:1:0:0.2 -9 2115881 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18019;SOR=0;LSEQ=CAGAACGAGGTCCGGGTACT;RSEQ=AGGCTCTGTACCGTGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:42,31:0.0267:2,2:20.5:1:28.5:1:1:1.34927:60:4:0.0274:0:1 0/0:101:0:0,0:56,44:0:2,0:26.8:1:31.6:1:1:0:60:99:0.99:0:0.1 -9 2116002 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2321;SOR=Inf;LSEQ=AAAAGTCTTCAAGCCACGAG;RSEQ=GGAGGGCATTCCTGCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:15,49:0:2,0:23.5:1:30.8:1:1:0:60:128:1:0:0.1 0/1:60:2:1,1:18,40:0.0333:2,2:26:1:26.5:1:0.53672:2.19:60:4:0.0333:0:1 -9 2116037 . G A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02395;SOR=Inf;LSEQ=CAGGCCATCTTGGAGCATGA;RSEQ=GAGGAAAATGAGGTATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:1,30:0:1,0:26:1:31.4:1:1:0:60:62:1:0:0 0/1:30:5:0,5:3,22:0.1667:2,0:23:1:32.2:1:1:0:60:10:0.1667:0:1 -9 2875494 . A G 286 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=903.41216;LSEQ=GTTGGATGAAGGGGAGCCAA;RSEQ=GGCCAGGTTGGCTTGTAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1153:1:0,1:576,575:9e-04:2,0:15:0:26:0:1:0:60:2:9e-04:0:1 0/1:1362:602:312,290:362,398:0.442:2,2:24.2:1:31:1:0.1269:1.18:60:119.4:0.4435:0:1.1 -9 2876109 . C G 270 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=248.99312;LSEQ=ATGTCAGGGTGGTCAGGTCA;RSEQ=TCTGTTCCTTTCGCCTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1029:2:1,1:522,505:0.0019:2,2:22.5:1:30.5:1:1:1.03364:60:4:0.002:0:1 0/1:1184:387:191,196:413,381:0.3269:2,2:24.3:1:31.5:1:0.42019:1.11226:59.9:192.5:0.3277:0:1.1 -9 2876160 . T C 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGTAAAACTTCCTTGAGC;RSEQ=GCAGGAAAAGCTGGTGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1064:0:0,0:581,483:0:2,0:25.1:1:30.7:1:1:0:59.8:117.222:1:0:0.1 0/1:1224:71:38,33:604,547:0.058:2,2:26.8:1:29.7:1:0.90295:1.04:59.4:34.5:0.0571:0:1.2 -9 2876417 . C G 256 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCTTGGGGTGCTCCAAGA;RSEQ=TGCGGGCATGGTGCTGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:815:0:0,0:345,469:0:2,0:26:1:32.1:1:1:0:60:202.5:0.9988:0:0.1 0/1:949:298:133,165:285,364:0.314:2,2:24.7:1:31.2:1:0.88795:1.03:59.9:58.6:0.3117:0:1.2 -9 2876506 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60588;SOR=2.22265;LSEQ=AAACAGGGACCGCCTTCTCT;RSEQ=TGCTTTCTCCGTGTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:0,1:17,189:0.0048:2,0:44:0:13:0:1:0:60:0:0:0:1 0/1:187:2:1,1:26,159:0.0107:2,2:23.5:1:28.5:1:0.26859:6.02:60:4:0.0108:0:1 -9 2876508 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10244;SOR=Inf;LSEQ=ACAGGGACCGCCTTCTCTGT;RSEQ=CTTTCTCCGTGTCTCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:17,182:0:2,0:24.5:1:31.9:1:1:0:60:38.8:1:0:0.2 0/1:176:3:0,3:24,149:0.017:2,0:17:1:26.3:1:1:0:60:2:0.0116:0:1.7 -9 3206158 . A G 205 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTAAGAAATGGGGTAGGC;RSEQ=GTATTCATTTGTGATCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:246,205:0:2,0:26.7:1:30.4:1:1:0:60:55.375:1:0:0.1 0/1:506:124:64,60:202,180:0.2451:2,2:27.3:1:29.6:1:0.8364:1.05201:60:248:0.247:0:1.1 -9 3253549 . AT A 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.86692;SOR=1.12002;LSEQ=TCTGCCCAAGAAAGGCAGTG;RSEQ=TTTTTTTTTCTGCCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:190:168:128,40:17,1:0.8842:1,2:22.8:1:31.1:1:0.12972:5.28204:59.9:336:0.8889:0.1842:0.8 1/1:172:154:117,37:12,4:0.8953:2,2:21.8:1:30.2:1:1:1.05:60:308:0.8953:0.186:0.8 -9 3253559 . TC T 43 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.11652;SOR=Inf;LSEQ=AAAGGCAGTGATTTTTTTTT;RSEQ=TGCCTCCCAGGGAACCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:159,60:0:2,0:22.7:1:31.2:1:1:0:59.9:42.8:0.9907:0:0.8 0/1:212:3:1,2:148,60:0.0142:2,2:19.3:1:27.3:1:0.20705:4.89057:60:6:0.0144:0.0047:1.7 -9 3253564 . C T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24874;SOR=0;LSEQ=CAGTGATTTTTTTTTTCTGC;RSEQ=TCCCAGGGAACCACAATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:3:1,2:173,78:0.0118:2,2:16:1:22.7:1:0.23416:4.40698:60:2:0.008:0:3 0/0:245:0:0,0:164,81:0:2,0:21.2:1:30:1:1:0:60:34:1:0:0.8 -9 3253613 . G A 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.01524;LSEQ=AGCCAGGTTAGGCAAGGAGA;RSEQ=AGCCCCCATTCAGAGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:472:471:249,222:0,0:0.9979:0,2:27.3:1:30:1:1:0:60:66.286:0.9978:0:1.1 1/1:473:415:219,196:29,28:0.8774:2,2:26.1:1:29.4:1:0.88765:1.08:60:58.286:0.8774:0:1.2 -9 3253649 . G A 146 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.08233;LSEQ=CAGAACCTCTTTGTAGCGCT;RSEQ=TATCAACTGCTATTATGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:1:1,0:180,253:0.0023:2,0:1:0:24:0:0.41705:0:60:2:0.0023:0:2 0/1:464:33:16,17:190,241:0.0711:2,2:22:1:29.1:1:0.71692:1.19:60:66:0.0717:0:1.2 -9 3776575 . A G 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTTAATGGAATTAAAGG;RSEQ=AGGAAAATTTCTGGGCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1:0,2:19.3:1:31.2:1:1:0:60:20:1:0:1.5 1/1:9:9:9,0:0,0:1:0,0:27.8:1:31.9:1:1:0:60:18:1:0:1.2 -9 3776612 . C G 121 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00492;SOR=0.06465;LSEQ=TTTAGGGCTTTAGGGCAAGG;RSEQ=TCACTCACTCGCATTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:11,2:11,0:0.5417:0,2:27.7:1:32.8:1:0.48188:0:60:26:0.5417:0:1.4 0/1:15:1:1,0:14,0:0.0667:1,0:41:0:28:0:1:0:60:2:0.0667:0:2 -9 4099378 . G A 85 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01465;SOR=9.10194;LSEQ=AATCTTTGGCTTGCAGATGC;RSEQ=TCACTCCAATCCTTGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:6,11:0.1053:2,0:22:1:30:1:1:0:60:4:0.1053:0:1 1/0:13:7:2,5:1,5:0.5385:2,2:32:1:30.4:1:1:1.90:60:14:0.5385:0:1 -9 4099422 . C T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2451;SOR=0;LSEQ=TTCACTTGGAGTTGCCCCCC;RSEQ=GAGCCTCTGTCTTTGCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:1,3:1,7:0.3333:2,2:22.5:1:30:1:1:2.16:60:8:0.3333:0:1.3 0/0:6:0:0,0:2,4:0:2,0:12.2:1:29.5:1:1:0:60:12:1:0:0.8 -9 4110692 . C T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54747;SOR=2.71347;LSEQ=TTCCCTACTCAGGCTCTGGG;RSEQ=TAGCCAACCACAGATCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:19:1:28.5:1:1:0:60:4:0.25:0:2.5 1/0:4:2:2,0:2,0:0.5:0,0:26:1:32:0:1:0:60:4:0.5:0:1.5 -9 4110798 . GA G 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.66534;LSEQ=GAAACTAATAAATCTACCTG;RSEQ=AAAAAAAATAAACATCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:51,6:0.0339:2,0:8.5:1:32:1:1:0:60:4:0.0345:0.0169:0 0/1:44:1:1,0:40,2:0.0227:1,0:34:0:33:0:1:0:60:2:0.0227:0:0 -9 4110947 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06368;LSEQ=ACACATTCAAATTCTATCTG;RSEQ=ACCCTAAAATGACAACACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:305:238:117,121:28,37:0.7803:2,2:28.9:1:29.9:1:0.40376:1.28:60:46.6:0.7819:0:1.1 0/1:479:88:46,42:190,201:0.1837:2,2:26.3:1:29.3:1:0.55672:1.16:60:87:0.1839:0:1.1 -9 4111006 . T A 40 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90795;LSEQ=ATCAAGAAATATTCCAAAGG;RSEQ=CACAAAGGGTGTTTCTAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:58,129:0.0106:2,2:12:1:29:1:0.52803:2.21:60:4:0.0109:0:2 0/0:312:3:3,0:110,199:0.0096:2,0:1:0:25.3:1:0.0467:0:60:6:0.0097:0:1 -9 4111100 . A G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02037;SOR=4.651;LSEQ=ACATTTTAGAATCTATATAC;RSEQ=AACAAATCTCCAAAGGTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:0,4:0,25:0.1379:1,0:25.8:1:31.3:1:1:0:60:8:0.1481:0:1 0/1:30:13:0,13:0,17:0.4333:1,1:24.8:1:30.6:1:1:0:60:12:0.4286:0:1.2 -9 4803726 . TA T 69 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.22848;SOR=0.33272;LSEQ=TGGGGAGGCAGTGTGAAAGG;RSEQ=AAAAAAAAAAAGCTACTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:3,2:5,3:0.3846:2,2:21.4:1:29.8:1:1:1.10211:60:10:0.4167:0:0.2 0/1:18:3:2,1:9,1:0.1667:2,2:16:1:29.7:1:0.42308:3.87298:60:6:0.1667:0:1 -9 4804389 . G A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACTGCTGAGTGGGTGCC;RSEQ=GCACGGCTGCCTTTGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:15:1:31.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:1:0,0:6:0:32:0:1:0:60:2:1:0:1 -9 4804708 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21336;SOR=Inf;LSEQ=AAAGCGGCCGGTGGCCGGTG;RSEQ=GCTGGTGGGGAGGACGATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:38,15:0:2,0:21.7:1:30.3:1:1:0:60:16.667:1:0:0.1 0/1:46:2:1,1:29,15:0.0435:2,2:36:1:29:1:1:1.90401:60:4:0.0435:0:1 -9 4804709 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.21776;SOR=Inf;LSEQ=AAGCGGCCGGTGGCCGGTGC;RSEQ=CTGGTGGGGAGGACGATCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:37,15:0:2,0:22.8:1:29.9:1:1:0:60:25:1:0:0.1 0/1:46:2:1,1:29,15:0.0435:2,2:21.5:1:32:0:1:1.90401:60:4:0.0435:0:1 -9 4804762 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50359;SOR=Inf;LSEQ=AGGACACGGTGGCGGCCACT;RSEQ=ACTCCTGCCGGAGCAGCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:32,31:0:2,0:27.8:1:30.2:1:1:0:60:14.75:1:0:0.1 0/1:80:2:1,1:36,42:0.025:2,2:33.5:1:29:1:1:1.16:60:4:0.026:0:1 -9 4804901 . A G 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03509;SOR=0;LSEQ=CAAGTCTGTCACCAGGTCAT;RSEQ=GGGTGGCTGGGAAGCACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:1,5:0.4545:2,0:37.4:1:32.2:1:1:0:60:10:0.4545:0:1.2 0/0:10:0:0,0:2,8:0:2,0:24:1:31.8:1:1:0:60:20:1:0:0.3 -9 4804950 . T C 66 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTATGTGGAGAGCACCT;RSEQ=CAACTGCCGGACGGTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:10.8:1:28.8:1:1:0:60:4:1:0:1.2 1/1:2:2:1,1:0,0:1:0,2:35:1:33:0:1:0:60:4:1:0:1 -9 4805110 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCGAAGCAGCAGGGGTAT;RSEQ=TCAAAGCCAATGAAGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:21.5:1:31.7:1:1:0:60:26:1:0:0.1 0/1:27:2:1,1:9,16:0.0741:2,2:34:1:28.5:1:1:1.74:60:4:0.0741:0:1 -9 5021924 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.80918;LSEQ=ATTACAGGTGTGAGACACTG;RSEQ=GCCCAGCCCATTTGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:0,1:137,27:0.0061:2,0:1:0:26:0:0.1697:0:60:2:0.0062:0:1 0/1:183:2:1,1:145,36:0.0109:2,2:22:1:28.5:1:0.36438:3.98665:60:4:0.011:0:1 -9 5029986 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22897;SOR=Inf;LSEQ=AAATATTTTTTAATTGCAAG;RSEQ=TACTTAATACCAGATACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:4,87:0:1,0:22.8:1:31.7:1:1:0:60:29.333:1:0:0.1 0/1:84:2:0,2:4,78:0.0238:1,0:24:1:29:1:1:0:57:4:0.0238:0:3.5 -9 5042708 . G A 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGAGGGGTGCTGTGGG;RSEQ=CCATCTTGCCCAGGCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:27.5:1:1:0:60:4:1:0:1 -9 5050369 . G C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGGTGTGATCATAGCT;RSEQ=AAGAGATCCTCCTACCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:39.5:1:31:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 5050706 . C T 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.08921;LSEQ=TGGCGGCATGATTTTGTGCA;RSEQ=GGATGGATAAAAGTACCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:433:69:46,23:235,128:0.1594:2,2:29.2:1:30.5:1:0.78496:1.09:60:16.25:0.1529:0:1.1 0/1:532:151:87,64:215,166:0.2838:2,2:24.2:1:29.7:1:0.84631:1.05:60:150:0.2857:0:1.1 -9 5050860 . T A 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24863;SOR=Inf;LSEQ=CTTTTGCAAATCCTTACACA;RSEQ=AAGTGTGAGTAGAGATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:67,205:0:2,0:24.5:1:28.6:1:1:0:60:89.667:1:0:0.1 0/1:274:3:2,1:79,192:0.0109:2,2:14.3:1:21.7:1:0.20957:4.83:60:2:0.0075:0:2 -9 5050864 . T C 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00652;SOR=Inf;LSEQ=TGCAAATCCTTACACATAAG;RSEQ=GTGAGTAGAGATTTTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:61,200:0:2,0:23.9:1:29.7:1:1:0:60:42.5:1:0:0.1 0/1:252:7:0,7:69,175:0.0278:2,0:13.6:1:29.1:1:0.19485:0:60:14:0.0281:0:1.1 -9 5050895 . A AT 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50422;SOR=0;LSEQ=ATTTTATATAATTCGTATAT;RSEQ=TTTTCTGTGTTTACCCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:10,122:0.0149:2,2:37.5:1:31.5:1:0.15801:11.68:60:4:0.0149:0:0 0/0:107:0:0,0:13,94:0:2,0:23.1:1:30.1:1:1:0:60:214:1:0:0.1 -9 5050910 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06623;SOR=Inf;LSEQ=TATATATTTTCTGTGTTTAC;RSEQ=CATGCCTTTTGATTTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:2,101:0:1,0:21.4:1:31.7:1:1:0:60:206:1:0:0.1 0/1:71:3:0,3:2,66:0.0423:1,0:26.7:1:30:1:1:0:60:6:0.0423:0:1 -9 5054548 . CT C 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.6082;SOR=2.19148;LSEQ=GTTTTGTTTTTCTGTATGTG;RSEQ=TTTTTATCCCTAGCTACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:1:1,0:146,32:0.0056:2,0:10:0:33:0:1:0:60:2:0.0056:0:0 0/1:165:2:1,1:134,29:0.0121:2,2:22.5:1:28.5:1:0.33149:4.55997:60:4:0.0122:0:0 -9 5055015 . C T 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.56921;LSEQ=GAAGTGGAAGTTTTTAATAG;RSEQ=GTGAACCTATCAAGGTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:38:0,38:0,1:0.95:0,1:23.4:1:30.1:1:1:0:60:37:0.9737:0:1 1/1:31:30:0,30:0,1:0.9677:0,1:21.9:1:30.3:1:1:0:60:60:0.9677:0:1 -9 5065149 . GT G 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.21917;SOR=Inf;LSEQ=AGAAAAAAATAATTTGACAA;RSEQ=TTTTTTTAAACAAAAGGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:0,71:0:1,0:22:1:30.5:1:1:0:60:70:1:0:0.1 0/1:63:2:0,2:1,60:0.0317:1,0:40:0:29.5:1:1:0:60:4:0.0328:0:0 -9 5066572 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.15014;SOR=Inf;LSEQ=AACATATAAAGTAGAGGAGA;RSEQ=AATTCTGACAGTTTTAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:175,6:0:1,0:25.1:1:32.2:1:1:0:60:362:1:0:0.1 0/1:115:2:1,1:111,2:0.0174:1,2:20.5:1:29.5:1:0.05172:45.51972:60:4:0.0179:0:1 -9 5066795 . T A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0859;SOR=Inf;LSEQ=ACTTTTGCTGTCGAGGTTAG;RSEQ=ATGTCACACTTATTAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:33,257:0:2,0:24.4:1:28.5:1:1:0:60:289:1:0:0 0/1:230:3:2,1:40,187:0.013:2,2:19:1:27.7:1:0.08661:9.21:60:6:0.0131:0:1 -9 5068944 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50357;SOR=0;LSEQ=ATTCTGTTGCTTGTTCTTGT;RSEQ=ATATCATTTTGTCAGAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:2,0:119,15:0.0147:2,0:11.5:1:29.5:1:1:0:60:4:0.0148:0:1 0/0:110:0:0,0:99,11:0:2,0:23.5:1:31.7:1:1:0:60:220:1:0:0 -9 5069836 . C T 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=GTTATTAAGCATTTCTTATA;RSEQ=GTAGAACACATTTCATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:89,0:0:1,0:23.9:1:32.6:1:1:0:60:178:1:0:0.2 0/1:69:8:8,0:61,0:0.1159:1,0:21.9:1:30.5:1:1:0:60:16:0.1194:0:1.1 -9 5069837 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=3.41919;LSEQ=TTATTAAGCATTTCTTATAC;RSEQ=TAGAACACATTTCATTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:20:20,0:73,0:0.2151:1,1:23.9:1:30.5:1:1:0:60:40:0.2174:0:1 0/1:70:34:34,0:36,0:0.4857:1,1:23.5:1:30.8:1:1:0:60:68:0.4857:0:1 -9 5070129 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51071;SOR=0;LSEQ=TTCTTGATTTACATTCATGT;RSEQ=ACATTGGAATTATTTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:8,124:0.0149:2,2:17.5:1:27:1:0.13029:14.67:60:4:0.0149:0:1.5 0/0:97:0:0,0:5,92:0:2,0:20.5:1:31.3:1:1:0:60:96:1:0:0 -9 5070227 . ATTATC A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52696;SOR=0;LSEQ=GTTAGATGTTAGCAAAATTA;RSEQ=TTAATTATCCTAAGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:0,14:0.1765:1,0:28.7:1:31.7:1:1:0:60:6:0.1765:0:0.3 0/0:8:0:0,0:0,8:0:0,0:23.3:1:31.4:1:1:0:60:16:1:0:0 -9 5072798 . T C 75 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2908;SOR=0;LSEQ=AGAATTACAGGGTTTGAAAA;RSEQ=TACCGGATTAAAAAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:0.2083:1,0:21.2:1:32.4:1:1:0:60:10:0.2083:0:1 0/0:10:0:0,0:2,8:0:2,0:25.6:1:30.4:1:1:0:60:20:1:0:0.4 -9 5072846 . G A 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00303;SOR=Inf;LSEQ=CTAATTATGTTTAGCATTAT;RSEQ=TTAGGAGTGTTATTACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:21.3:1:33.6:1:1:0:60:14:1:0:0.1 1/1:4:4:1,3:0,0:1:0,2:16.3:1:28.8:1:1:0:60:8:1:0:1 -9 5073681 . CT C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.98905;LSEQ=TCAAACAACAATTCTTTGTA;RSEQ=TTTTTTTTTCCTTAGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:11:7,4:176,57:0.0451:2,2:19.3:1:31.5:1:0.47439:1.75978:60:22:0.0451:0.0123:0.2 0/1:269:12:8,4:190,66:0.0446:2,2:19.5:1:30.6:1:0.51805:1.43729:60:24:0.0449:0.0149:0.2 -9 5073875 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50281;SOR=Inf;LSEQ=TTTCAGGATCACAGCTAGGT;RSEQ=TCAGTGTAAACTATAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:0,69:0:1,0:21.1:1:31.7:1:1:0:60:33.5:1:0:0 0/1:86:2:0,2:2,82:0.0233:1,0:41:1:31.5:1:1:0:60:4:0.0233:0:1 -9 5077508 . G T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.37916;SOR=3.50133;LSEQ=CTAGATACATATCTGAAAAA;RSEQ=AATAAAAATTGTATAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:1:0,1:146,153:0.0033:2,0:1:0:27:0:1:0:60:2:0.0034:0:1 0/1:345:4:2,2:174,167:0.0116:2,2:22.3:1:29:1:1:1.04181:60:8:0.0117:0:1.3 -9 5077517 . T C 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03272;SOR=Inf;LSEQ=TATCTGAAAAAGAATAAAAA;RSEQ=TGTATAAATATATTATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:143,156:0:2,0:23.5:1:30.2:1:1:0:60:58.8:1:0:0.1 0/1:343:6:4,2:163,173:0.0175:2,2:12.5:1:29.8:1:0.43917:2.12:60:12:0.0175:0:1 -9 5077560 . G A 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10111;SOR=0;LSEQ=TTGAAGTTGCTAAACAGTTG;RSEQ=CATGGGCCATGCATTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:113,158:0.0109:2,2:24.7:1:26:1:0.57402:2.79:60:2:0.0074:0:1.3 0/0:313:0:0,0:126,187:0:2,0:26.9:1:31.2:1:1:0:60:77.25:1:0:0.1 -9 5077615 . T C 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=CTTTTTATCAAAAGATACTA;RSEQ=TTTATTTTATAAAACAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:46,95:0:2,0:24.6:1:30.5:1:1:0:60:140:1:0:0 0/1:150:13:5,8:37,100:0.0867:2,2:24.2:1:31.8:1:0.51793:1.68:60:26:0.0872:0:1 -9 5078117 . T C 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52632;SOR=0;LSEQ=TTCATCACAAGCATAGATTA;RSEQ=TGTGTTATTTAAAATGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:12,0:0.2:0,0:12.7:1:33:1:1:0:60:6:0.2:0:1 0/0:6:0:0,0:6,0:0:0,0:19.8:1:30.2:1:1:0:60:12:1:0:0.2 -9 5080382 . T A 57 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37547;SOR=0.2703;LSEQ=TGCTCTGGATTCTCAAAGAG;RSEQ=AAGTTTATATAGACTAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:4:3,1:140,227:0.0108:2,2:15.5:1:28.5:1:0.16159:4.84:60:8:0.0109:0:1 0/0:341:1:1,0:135,205:0.0029:2,0:1:0:24:0:0.39883:0:60:2:0.003:0:1 -9 5080448 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22681;SOR=Inf;LSEQ=ATATTTCTTTCACATGATTT;RSEQ=TATTTTTTAGCCCATCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:109,106:0:2,0:22.2:1:32.3:1:1:0:60:214:1:0:0.1 0/1:196:2:1,1:114,80:0.0102:2,2:10.5:1:25:0:1:1.42235:60:4:0.0103:0:1 -9 5080484 . G T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10275;SOR=Inf;LSEQ=CTAATTTTAAAAAGAAGGTT;RSEQ=GTGTGGCATTACACAATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:211,100:0:2,0:22.4:1:32:1:1:0:60:622:1:0:0.1 0/1:275:3:0,3:181,90:0.0109:2,0:13:1:21.7:1:0.03827:0:60:2:0.0074:0:1 -9 5080718 . T C 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00403;SOR=Inf;LSEQ=GATCTTATTGATTTTCCAGC;RSEQ=TTCTATCTTTATTGTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:78,302:0:2,0:24.1:1:30.4:1:1:0:60:94:1:0:0.1 0/1:418:9:2,7:114,294:0.0215:2,2:12.3:1:31.2:1:1:1.35618:60:18:0.0218:0:1.3 -9 5081585 . A G 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00283;SOR=Inf;LSEQ=GATTAAAGGCTCCCATTAAT;RSEQ=TAATTGAAACTATTTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:0:1,0:20.5:1:28.3:1:1:0:59.6:98:1:0:0.1 0/1:24:5:5,0:19,0:0.2083:1,0:26.6:1:31.6:1:1:0:60:10:0.2083:0:1.2 -9 5081678 . G T 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60323;SOR=2.25877;LSEQ=GTATATCAGTTTAGTCCAGA;RSEQ=AATGTTATTTGCTAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:1,0:178,37:0.0046:2,0:5:0:32:0:1:0:60:2:0.0048:0:1 0/1:192:2:1,1:158,32:0.0104:2,2:10:0:30:1:0.31495:4.87757:60:4:0.0105:0:1 -9 5081780 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.67921;LSEQ=AATATGAGGATAGGTGCCCT;RSEQ=GGGTTTTCTGGTGCCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:693:124:69,55:294,275:0.1789:2,2:24.7:1:28.6:1:0.42938:1.17:60:23.8:0.175:0:1.3 0/1:876:390:210,180:258,227:0.4452:2,2:25.3:1:29.2:1:0.89156:1.03:60:129:0.4464:0:1.1 -9 5081966 . TAG T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11475;SOR=Inf;LSEQ=AACATTTTAAGGAGTGCTTG;RSEQ=AAAAAAAAGGTTTGGTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:0,55:0:1,0:25.6:1:32.1:1:1:0:60:110:1:0:0.1 0/1:53:3:0,3:1,49:0.0566:1,0:8:1:27.7:1:1:0:60:6:0.0566:0.0377:0.7 -9 5090641 . G A 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACATTAGGAAATCATCTA;RSEQ=ACGTTTTCATAGATAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:110,119:0:2,0:22.7:1:31.5:1:1:0:60:44.8:1:0:0.1 0/1:156:48:20,28:60,47:0.3077:2,2:24.8:1:29.2:1:0.1184:1.78051:60:47:0.3052:0:1.1 -9 5090934 . A T 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38372;SOR=0.75909;LSEQ=GAGTATATTTCAGTATGATA;RSEQ=ATGAAATTTTAGAGCACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:34:9,25:31,117:0.1868:2,2:20.2:1:27.6:1:0.49519:1.36:60:16:0.1818:0:1.1 0/1:155:23:7,16:31,100:0.1484:2,2:22.8:1:27.7:1:0.59996:1.41:60:46:0.1503:0:1 -9 5090966 . ATTG A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0.71235;SOR=0.86523;LSEQ=GAGCACAGACTTCAAACTTT;RSEQ=TTGTTATTTAATAGTTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:19:1,18:10,67:0.1979:2,1:33:1:30.9:1:0.68719:2.66505:60:38:0.1979:0.0104:1 0/1:91:16:3,13:13,63:0.1758:2,2:24.1:1:29.5:1:1:1.12:60:32:0.1758:0.033:0.7 -9 5091045 . C CT 31 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=CTTTTAAGTCTTACATTTAA;RSEQ=TTTTTTTTTTTAGGTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:0,16:0.1111:1,0:36:1:31:0:1:0:60:4:0.1176:0:0 0/0:12:0:0,0:1,10:0:2,0:19.4:1:30.6:1:1:0:60:10:0.9091:0:0.6 -9 5110427 . C G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAATTGGCATTAATCAG;RSEQ=CACATCTAGCATTCCTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:5.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 5110841 . TG T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.69274;SOR=1.44888;LSEQ=GCCCGTTTGTTCGGGGAAGG;RSEQ=GGGGGGACGCTTCATGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:3:2,1:289,72:0.0082:2,2:31.7:1:30:1:0.49011:2.00243:60:6:0.0084:0.0027:0.3 0/1:252:3:2,1:196,52:0.0119:2,2:28:1:30.3:1:0.5107:1.87897:60:6:0.0122:0.004:0.7 -9 5110899 . T C 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02776;SOR=0.75987;LSEQ=TCCATGTCTGAGATGCCCGC;RSEQ=CTGGCCCCAAGAGAATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:181:104,77:408,287:0.2066:2,2:26.1:1:31.1:1:0.79962:1.05245:60:362:0.2124:0:1.1 0/1:896:148:92,56:427,321:0.1652:2,2:25.6:1:30.3:1:0.2747:1.23:59.7:73:0.1655:0:1.2 -9 5111224 . GC G 214 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.7382;LSEQ=CGGAGGCAAGAGCAGCTAGC;RSEQ=GGGCCTATTCCTCCTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:57:28,29:261,269:0.0969:2,2:23.7:1:30.3:1:1:1.0049:60:27.5:0.0948:0.0136:0.3 0/1:471:135:63,72:154,180:0.2866:2,2:24.9:1:30.3:1:0.91891:1.02:60:270:0.2916:0.0297:0.2 -9 5111358 . AC A 219 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.73588;SOR=1.04707;LSEQ=GAAGGGGACCTCCCGGTACT;RSEQ=CCCTCCTACGCCAGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:844:135:63,72:341,368:0.16:2,2:23.7:1:31:1:0.77865:1.05896:60:270:0.1613:0.0403:0.1 0/1:764:127:73,54:315,319:0.1662:2,2:26.4:1:31.2:1:0.11997:1.37:60:254:0.1675:0.0183:0.2 -9 5111380 . TGGCGGACAGA T 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCCTCCTACGCCAGCAGCTC;RSEQ=GGCGGACAGCGGCCTGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:783:0:0,0:382,399:0:2,0:24.5:1:31.5:1:1:0:60:85.778:0.9974:0:0.1 0/1:747:71:31,40:360,314:0.095:2,2:23.9:1:30.4:1:0.13403:1.47855:59.9:70:0.0954:0.0228:0.2 -9 5112054 . G T 202 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTATCACCCAGCTACGACG;RSEQ=GGGTCTCCACGGCCTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1191:0:0,0:578,613:0:2,0:25.8:1:30.9:1:1:0:60:61.684:1:0:0.2 0/1:1079:118:57,61:470,491:0.1094:2,2:25.1:1:29.4:1:0.92252:1.02439:60:117:0.1096:0:1.2 -9 5112171 . C A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07979;SOR=Inf;LSEQ=TGCACACGCTGCTACCCGGC;RSEQ=ACCGGGCGCTGGCCTTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:120,257:0:2,0:23:1:31.2:1:1:0:60:25.929:1:0:0.1 0/1:286:3:2,1:82,201:0.0105:2,2:18.3:1:26:1:0.20721:4.87:60:6:0.0106:0:1.7 -9 5112266 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06382;SOR=Inf;LSEQ=ACACCCTGAGGACGGCCCTG;RSEQ=GGGCAGCGCCAGCCTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:184,136:0:2,0:26.1:1:30.9:1:1:0:60:44.714:1:0:0.3 0/1:214:3:1,2:114,97:0.014:2,2:10.3:1:27.7:1:0.59707:2.34139:60:6:0.0142:0:1.3 -9 5112288 . C T 191 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=2.24844;LSEQ=GGCAGCGCCAGCCTCATGCA;RSEQ=ATCCATGTTGCCCTCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:65:42,23:171,113:0.1862:2,2:26.7:1:30.1:1:0.57385:1.21:60:64:0.185:0:1.1 0/1:247:84:58,26:96,67:0.3401:2,2:24.8:1:30:1:0.12917:1.55:60:168:0.3457:0:1.1 -9 5112447 . A G 207 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACCACTCAAGAGGAGAAG;RSEQ=AGGAGCTGAAGGACCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1537:0:0,0:758,779:0:2,0:26.4:1:30:1:1:0:60:63.042:1:0:0.2 0/1:1635:105:53,52:768,760:0.0642:2,2:23.4:1:30.9:1:1:1.01:60:104:0.0644:0:1.2 -9 5112519 . G A 227 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGATGACCTTTTCCCCCCA;RSEQ=AGCAGAAGGCCGAGTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1183:0:0,0:614,569:0:2,0:24.3:1:31.4:1:1:0:60:33.794:1:0:0.2 0/1:1227:214:114,100:506,504:0.1744:2,2:24.8:1:29.4:1:0.40865:1.14:60:52.5:0.1754:0:1.1 -9 5112675 . C G 222 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTATCCTGCACCAGGCCGT;RSEQ=TCGGTCATCCTGAATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1526:0:0,0:722,803:0:2,0:24.1:1:31.5:1:1:0:60:79.263:0.9993:0:0.2 0/1:1719:139:74,65:770,808:0.0809:2,2:23.5:1:31.3:1:0.33116:1.19:60:138:0.0811:0:1.2 -9 5112844 . G A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.94603;LSEQ=CCCACAACCCCGCTGGGCAC;RSEQ=TGTGAAAGGTACGCCTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:132:54,78:156,288:0.2292:2,2:22.7:1:29.9:1:0.25725:1.28:60:32:0.2257:0:1.1 1/0:628:374:145,229:90,163:0.5955:2,2:23.9:1:29.9:1:0.44949:1.15:60:186:0.601:0:1.1 -9 5112918 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2338;SOR=0;LSEQ=GGGCCCAGAACGCCCACTTG;RSEQ=GGCCCTGGGCTTCATCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:26,156:0.0109:2,2:33:1:29.5:1:0.27263:5.91:60:4:0.011:0:1.5 0/0:196:0:0,0:48,148:0:2,0:23:1:30.2:1:1:0:60:64.333:1:0:0.4 -9 5112921 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22758;SOR=0;LSEQ=CCCAGAACGCCCACTTGAGG;RSEQ=CCTGGGCTTCATCCACATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:19,151:0.0116:2,2:10.5:1:27.5:1:0.21964:7.77:60:4:0.0118:0:1 0/0:188:0:0,0:43,143:0:2,0:22.7:1:30.5:1:1:0:60:25.571:0.989:0:0.4 -9 5113087 . C G 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.23646;SOR=3.00706;LSEQ=CCCCGGCTCACCCCTCACTG;RSEQ=CCTCGCTCCCCCTGCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:0,7:0,11:0.3889:0,0:23.6:1:33.3:1:1:0:60:14:0.3889:0:1.1 1/0:9:6:2,4:0,3:0.6667:0,2:27.7:1:28.8:1:0.5:0:60:12:0.6667:0:1 -9 5122854 . AG A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.01115;SOR=Inf;LSEQ=TTCACAGGTGCCAGGCAAAA;RSEQ=GCCCTTTTAATCATAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:0:1,0:21.5:1:32.5:1:1:0:60:60:1:0:0 0/1:16:4:4,0:12,0:0.25:0,0:36.8:1:31.8:1:1:0:60:8:0.2667:0:0.3 -9 5122910 . GT G 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.00167;LSEQ=GATAACTCTTTTCTCTACAT;RSEQ=TTTTTTTTTTAATTTATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:11:11,0:83,2:0.1146:1,0:23.2:1:32.1:1:1:0:60:22:0.1146:0.0313:0 0/1:61:7:7,0:52,2:0.1148:1,0:15.7:1:31:1:1:0:60:14:0.1148:0.0492:0.6 -9 5126281 . ATT A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.21534;SOR=0;LSEQ=CTGGAGGAAATTGAGAAAGA;RSEQ=TTGCTACAAATTAAATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:139,37:0.0112:2,2:26.5:1:30.3:1:0.38234:3.7205:60:4:0.0114:0.0056:0 0/0:205:0:0,0:159,46:0:2,0:22.9:1:29.8:1:1:0:60:204:1:0:0.1 -9 5126453 . AT A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.78156;SOR=0.77883;LSEQ=GATGCCCAGATGAGGTAACA;RSEQ=TTTTTTTTAATCCAGGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:7:4,3:100,207:0.0223:2,2:24.4:1:30.4:1:0.22542:2.75:60:14:0.0225:0.0032:0.1 0/1:344:6:2,4:122,215:0.0174:2,2:21.2:1:29.2:1:1:1.13449:60:12:0.0176:0.0058:0.5 -9 5126632 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18586;SOR=Inf;LSEQ=ATTAATGTCTTCCACCAATT;RSEQ=AAAGATGGCCCTTAGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:145,47:0:2,0:21.3:1:28.8:1:1:0:60:191:1:0:0 0/1:146:2:1,1:112,32:0.0137:2,2:29.5:1:30:1:0.40217:3.46178:60:4:0.0138:0:1 -9 5126742 . G T 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATCAACGCCCCTCCTTTA;RSEQ=GGATCTAGCTCTTCGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:57:30,27:242,247:0.1044:2,2:30.3:1:30.5:1:0.67672:1.13:60:56:0.1047:0:1.2 0/0:670:0:0,0:355,315:0:2,0:26.1:1:30.7:1:1:0:60:50.538:1:0:0.2 -9 5126860 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=TTTATATTTCACATTGCTGT;RSEQ=GACTATTATTACATATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:7,117:0:2,0:22.5:1:31:1:1:0:60:61:1:0:0 0/1:134:2:0,2:13,118:0.0149:2,0:15.5:1:31:1:1:0:60:4:0.0153:0:1 -9 5455732 . T G 65 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCTCCTTGCTCTGAAAT;RSEQ=TTGTACAGGGCAGGTTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:30.3:1:32.5:1:1:0:60:8:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 5456029 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24812;SOR=Inf;LSEQ=ATTTCAGTTAGAACCACCAA;RSEQ=TCCCATATTGTCATATTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:153,41:0:2,0:24.3:1:32:1:1:0:60:96:1:0:0.1 0/1:197:3:2,1:151,43:0.0152:2,2:14.7:1:28.3:1:0.5336:1.75007:60:6:0.0152:0:1 -9 5456083 . G A 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGTGAAGCAGTCTTCTTTTC;RSEQ=TGTTTTCCATAATTAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:30:18,12:232,156:0.0716:2,2:24.7:1:30.8:1:1:1.01:60:60:0.0719:0:1.1 0/0:529:0:0,0:321,207:0:2,0:24.9:1:30:1:1:0:60:131:0.9981:0:0.1 -9 5456523 . T C 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=TTTCAGTCTTGGTTGCTCTG;RSEQ=GACATGCCTTTCCTGATGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:31.3:1:31.7:1:1:0:60:6:0.75:0:1.7 0/0:1:0:0,0:0,1:0:0,0:35:0:32:0:1:0:60:2:1:0:0 -9 5456550 . T C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCCTGATGAGGATACT;RSEQ=TAAGGAAGAATTGTAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:25:1:31:1:1:0:60:4:0.6667:0:2 0/0:1:0:0,0:0,1:0:0,0:8:0:31:0:1:0:60:2:1:0:0 -9 5456775 . C G 71 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGATGTCTACATGAAACCAA;RSEQ=TCTCCCTGGTTGTAAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:15.4:1:31:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 5457032 . T G 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11642;SOR=Inf;LSEQ=TGTGCCAATTTTGTAAATGT;RSEQ=TCGAGGAATTTTCCCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:122,31:0:2,0:23:1:30:1:1:0:60:152:1:0:0.1 0/1:147:3:1,2:112,32:0.0204:2,2:27.3:1:29:1:0.13376:6.87964:60:6:0.0204:0:2 -9 5457049 . T C 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00367;SOR=Inf;LSEQ=TGTTTCGAGGAATTTTCCCT;RSEQ=TTCTGAAGATTGTCCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:152,55:0:2,0:23.2:1:30:1:1:0:60:206:1:0:0.1 0/1:218:9:5,4:154,55:0.0413:2,2:19.1:1:30.8:1:0.2571:2.23055:60:18:0.0417:0:1.6 -9 5457364 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13686;SOR=Inf;LSEQ=GCAGGATGCAGGGGTGTACC;RSEQ=CTGCATGATCAGCTATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:104,173:0:2,0:26:1:31:1:1:0:60:68.25:1:0:0.1 0/1:361:4:2,2:148,208:0.0111:2,2:13.5:1:29.5:1:1:1.40:60:8:0.0112:0:1 -9 5457443 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=AAGAATTATTATAGATGAGA;RSEQ=GCCTGATCTTTATTGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:33,115:0.0133:2,2:27:1:28:1:0.40313:3.45:60:4:0.0136:0:1 0/0:141:0:0,0:42,99:0:2,0:24.1:1:29.8:1:1:0:60:27.2:1:0:0.1 -9 5462746 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23579;SOR=Inf;LSEQ=TCTGAGAACCAGCCTGCATT;RSEQ=ATACTCTTTCTAATGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:95,21:0:2,0:22.8:1:31.8:1:1:0:60:57:1:0:0.1 0/1:110:2:1,1:88,20:0.0182:2,2:24.5:1:26.5:1:0.34679:4.31829:60:4:0.0187:0:1 -9 5462767 . A G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10618;SOR=Inf;LSEQ=ATACTCTTTCTAATGTGGAC;RSEQ=GCATCAAGCTATGTACGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:135,54:0:2,0:22.9:1:30.4:1:1:0:60:378:1:0:0.1 0/1:171:3:2,1:121,46:0.0175:2,2:34:1:31.3:1:1:1.31299:60:6:0.018:0:1 -9 5462876 . C G 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=AAGAATTTTGGTTGTGGATC;RSEQ=AGTCACCTCTGAACATGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:0:0,0:262,175:0:2,0:25.5:1:31.3:1:1:0:60:71.833:0.9977:0:0.1 0/1:596:17:12,5:348,228:0.0285:2,2:27.8:1:28.7:1:0.45962:1.57:60:16:0.0273:0:1 -9 5463135 . T A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.24827;SOR=Inf;LSEQ=ATCCCAGGTAATATTCTGAA;RSEQ=GTGTCCATTAAAATATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:47,155:0:2,0:25:1:30.3:1:1:0:60:201:1:0:0.1 0/1:207:3:2,1:50,154:0.0145:2,2:18.7:1:28:1:0.15624:6.09:60:6:0.0146:0:1 -9 5463243 . G A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01615;SOR=0.1591;LSEQ=GAATGAATGAATAACACTAT;RSEQ=TTTACAAAATATATCCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:17:0,17:0,20:0.4474:1,1:22.5:1:32:1:1:0:60:34:0.4474:0:1 0/1:18:2:0,2:0,16:0.1111:1,0:20:1:31:0:1:0:60:4:0.1111:0:1 -9 5465732 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15241;LSEQ=AGGCATTCCACTGTTCAACA;RSEQ=CAATTATATTGAAGCTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:59:0,59:1,33:0.6344:1,1:21.7:1:30.4:1:0.36559:0:60:118:0.6344:0:1 0/1:58:12:0,12:1,45:0.2069:1,0:18.8:1:28.6:1:1:0:60:24:0.2069:0:1 -9 5466739 . A G 157 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=26.22621;LSEQ=GGGATGTAGAGCTGTGCTAT;RSEQ=TGGAAATAAAAATGATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:1:1,0:177,96:0.0036:2,0:49:0:14:0:1:0:60:0:0:0:5 0/1:387:34:20,14:224,129:0.0879:2,2:24.7:1:30.9:1:0.58281:1.21486:60:33:0.0862:0:1.1 -9 5467801 . C T 111 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00514;SOR=10.2385;LSEQ=TTGTTACTTTTTCCCCAGAC;RSEQ=ACTTCCCATGAAATTAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:1:0,1:209,146:0.0028:2,0:1:0:23:0:0.41292:0:60:2:0.0029:0:1 0/1:463:13:8,5:266,184:0.0281:2,2:16.8:1:30.1:1:1:1.11:60:26:0.0283:0:1 -9 5467807 . C T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01762;SOR=0;LSEQ=CTTTTTCCCCAGACCACTTC;RSEQ=CATGAAATTAATATACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:5:1,4:215,164:0.013:2,2:11.4:1:27.2:1:0.1727:5.22396:60:10:0.0132:0:1.2 0/0:476:0:0,0:276,200:0:2,0:25:1:30.2:1:1:0:60:118:1:0:0.2 -9 5467955 . G A 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30199;SOR=1.28902;LSEQ=GTGACAAGAGGAAGGAATGG;RSEQ=CCCGTGGGATGCAGGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:152:95:14,81:10,47:0.625:2,2:22.3:1:30.3:1:0.65244:1.22928:60:190:0.6333:0:1.1 1/0:189:129:28,101:8,52:0.6825:2,2:20.1:1:28.7:1:0.23248:1.80:60:258:0.6898:0:1 -9 5468257 . G C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACTCAATGCCTCAATTT;RSEQ=TTTTCTGCATGACTGAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:34:0:33:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 5670073 . G A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49446;SOR=1.83738;LSEQ=TGAGGCACATCAGGTCTCCA;RSEQ=TTAGTATGGATACCTGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:0,5:0,16:0.2381:1,0:31.2:1:30.8:1:1:0:60:10:0.25:0:1 0/1:19:7:0,7:0,12:0.3684:0,0:24:1:29.4:1:1:0:60:14:0.3684:0:1 -9 5754903 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17625;SOR=0;LSEQ=GATTTTATGGTCCTTGCGTG;RSEQ=TATAACATAAATGACCGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:65,50:0.0171:2,2:43.5:1:32.5:1:1:1.29705:60:4:0.0172:0:1.5 0/0:161:0:0,0:90,71:0:2,0:27.5:1:29.4:1:1:0:60:160:1:0:0.2 -9 5754944 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16075;SOR=0;LSEQ=AGAAGAGGTAAGTTTTTTCT;RSEQ=TCAGAAATAACAGATTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:61,66:0.0155:2,2:6.5:1:30:0:1:1.08:60:4:0.0155:0:2 0/0:192:0:0,0:91,101:0:2,0:24.3:1:31.3:1:1:0:60:384:1:0:0.3 -9 5754976 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5005;SOR=Inf;LSEQ=AGATTTTTATATTTTAAAGC;RSEQ=ATTAAGCATGAATTAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:51,69:0:2,0:25.9:1:29.1:1:1:0:60:119:1:0:0.6 0/1:138:2:1,1:56,80:0.0145:2,2:6:0:33:1:1:1.42:60:4:0.0148:0:1.5 -9 5754988 . A T 170 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10221;SOR=1.60101;LSEQ=TTTAAAGCTATTAAGCATGA;RSEQ=TTAATTTTATATAGAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:37:15,22:29,39:0.3524:2,2:30.1:1:30.4:1:1:1.08969:60:74:0.3524:0:1.7 0/1:118:55:21,34:27,36:0.4661:2,2:26.1:1:29.5:1:0.70772:1.21228:60:110:0.4783:0:1.3 -9 5755022 . T A 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21045;SOR=0.62493;LSEQ=GAAAATAGTCGATTGAAAAC;RSEQ=GAACAAAACATTTTATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:24:6,18:16,32:0.3333:2,2:24.3:1:31.6:1:0.59072:1.49178:60:48:0.338:0:2 0/1:80:19:5,14:17,44:0.2375:2,2:20.1:1:31.2:1:1:1.08078:60:38:0.2375:0:1.8 -9 7549605 . C G 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=TGTCCCCCACCATTCAAACA;RSEQ=ACGGGCTGTGGCAGACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22.5:1:30.5:1:1:1:60:4:0.5:0:1 0/0:4:0:0,0:2,2:0:2,0:15.8:1:31.3:1:1:0:60:8:1:0:0 -9 7903859 . T A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTCTACTGATTAAAAAAT;RSEQ=TTGAAGACCACTGAATTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:30.5:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 8317796 . A G 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11183;SOR=Inf;LSEQ=AAGTTAAGAAGGACTTCTCA;RSEQ=GTGCCCTGTATGGCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:240,73:0:2,0:24.3:1:30:1:1:0:60:77.25:1:0:0.1 0/1:292:3:2,1:215,73:0.0103:2,2:7:1:29.3:1:1:1.47047:60:6:0.0105:0:1 -9 8317999 . T TAGAAAAATAA 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=3.000;MSILEN=1;SSF=0.13768;SOR=0.44687;LSEQ=GGACCATGAGCATATTTTAA;RSEQ=AGAAAAATAAAAATCAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:11:1,10:35,158:0.0539:2,2:21.1:1:30.2:1:0.69305:2.20837:60:22:0.0545:0.0147:0 0/1:242:6:1,5:51,185:0.0248:2,2:26.3:1:29.4:1:1:1.3767:60:12:0.0252:0.0083:0.2 -9 8319732 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24551;SOR=Inf;LSEQ=AGTTTGATGCTTTCCCCACA;RSEQ=TATTTTGTGTCTGGTGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:187,9:0:1,0:23.4:1:32.4:1:1:0:60:97:1:0:0.1 0/1:193:2:1,1:176,15:0.0104:2,2:7:1:30:1:0.15933:11.39325:60:4:0.0106:0:1 -9 8319806 . C T 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.22346;LSEQ=AAACGTAGGCTCTTGAGATG;RSEQ=GAAAAATGCAATGGATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:57:38,19:341,243:0.0889:2,2:22.5:1:29.6:1:0.25977:1.42:60:56:0.0889:0:1.2 0/1:689:165:96,69:299,225:0.2395:2,2:24:1:29:1:0.85685:1.05:60:54:0.2372:0:1.1 -9 8320065 . G A 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56731;SOR=1.40676;LSEQ=TCTACCAGCTTCCACACTCC;RSEQ=TATCTCTTTATAGCCATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:8:0,8:3,91:0.0784:1,0:22.1:1:31.9:1:1:0:60:16:0.08:0:1.1 0/1:56:6:0,6:2,48:0.1071:1,0:13.8:1:29.5:1:1:0:60:12:0.1091:0:1 -9 8331207 . G T 32 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGATAGCTATTCATGAG;RSEQ=TTTTCACAAACAGAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:37.5:1:32:0:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 8331406 . ATTATTTTCAC A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=1.200;MSILEN=1;SSF=0.00271;SOR=0.12216;LSEQ=GGGCTAAACATTTTCCTCTG;RSEQ=TTATTTTCACTTTATGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:23,0:26,0:0.4694:1,1:22.9:1:31.7:1:1:0:60:46:0.4694:0.0816:0 0/1:21:2:2,0:19,0:0.0952:1,0:27:1:31:1:1:0:60:4:0.0952:0:0 -9 8331498 . A C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24897;SOR=Inf;LSEQ=CCAAGAATAAAATTTCAAAT;RSEQ=AGCAAACTTACTACAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:200,24:0:2,0:22.2:1:28.2:1:1:0:60:36.333:0.9954:0:0.1 0/1:238:3:3,0:199,36:0.0126:2,0:29.3:1:32.7:1:1:0:60:6:0.0127:0:1 -9 8331507 . T TA 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03234;SOR=Inf;LSEQ=AAATTTCAAATAAGCAAACT;RSEQ=ACTACAAAAAGTGTATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:223,39:0:2,0:22.7:1:30:1:1:0:60:130:1:0:0.1 0/1:298:6:6,0:232,60:0.0201:2,0:18.7:1:29.5:1:0.60416:0:60:12:0.0204:0.0101:0.5 -9 8331548 . C T 167 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01759;LSEQ=ACAATGAAGAAACACCACCA;RSEQ=TTATCACTGCTTTATTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:41:32,9:350,180:0.0718:2,2:22.3:1:31.2:1:0.12444:1.83:59.8:82:0.0722:0:1.1 0/0:738:1:0,1:455,282:0.0014:2,0:1:0:25:0:0.38347:0:60:2:0.0014:0:1 -9 8331574 . A AAACTTACCATTCTTGAACTGT 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.10866;LSEQ=ACTGCTTTATTCACAAATGG;RSEQ=AACTTACCTGCAATGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:215:128,87:288,195:0.2894:2,2:30.7:1:30.5:1:1:1.00384:59.8:430:0.2925:0.0175:0.1 0/1:1087:46:28,18:444,374:0.0423:2,2:31.9:1:29.7:1:0.44757:1.31:59.8:92:0.0428:0:0 -9 8331761 . G A 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37403;SOR=3.81341;LSEQ=AGAAGGAAAGCCACATACCC;RSEQ=GCCGCAAAGGAAGACGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:1,0:68,251:0.0031:2,0:1:0:26:0:0.21563:0:60:2:0.0032:0:1 0/1:338:4:2,2:87,247:0.0118:2,2:21.3:1:30:1:0.28383:2.83:60:8:0.012:0:1 -9 8331841 . A G 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49882;SOR=0;LSEQ=TTCATTTCCCGAAAACAAAA;RSEQ=GGGTAGAAAAAGTTAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:0,2:1,82:0.0235:1,0:18.5:1:26.5:1:1:0:60:4:0.0238:0:1 0/0:75:0:0,0:0,75:0:1,0:24.1:1:31.7:1:1:0:60:150:1:0:0.2 -9 8331863 . T A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15495;SOR=Inf;LSEQ=GGTAGAAAAAGTTAGGAACA;RSEQ=GTTTAAATAGAAACTTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:1,66:0:1,0:27.1:1:30:1:1:0:60:66:1:0:0.2 0/1:44:2:0,2:0,42:0.0455:1,0:18.5:1:32.5:1:1:0:60:4:0.0455:0:1 -9 8331926 . TAAATCCTAAATTTATTTACTCTTG T 69 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.8083;LSEQ=TGTCCACACTCACATACCTT;RSEQ=AAATCCTAAATTTATTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:0,5:0,12:0.2941:0,0:34:1:30:1:1:0:60:10:0.2941:0:0.2 0/1:4:1:0,1:0,3:0.25:0,0:40:1:32:1:1:0:60:2:0.25:0.25:0 -9 8332033 . A G 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TCCACATAGTTCCCCCATTA;RSEQ=CAAATGTTTCTGAGACCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:17.3:1:31:1:1:0:60:12:0.75:0:1 0/0:2:0:0,0:1,1:0:2,0:8:0:31.5:1:1:0:60:4:1:0:0 -9 8338690 . G T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06536;SOR=Inf;LSEQ=TGCATCCCCAAGGTTGAGCT;RSEQ=CCAGATGTTATGTTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:0:1,0:26.6:1:32.4:1:1:0:60:26:1:0:0.1 0/1:5:2:2,0:3,0:0.4:0,0:27:1:32:0:1:0:60:4:0.4:0:1 -9 8338778 . T TA 131 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=33.56196;LSEQ=TTACTCTTACATATTAAACA;RSEQ=AAAAAAAAACGTTCTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:72,0:0.027:1,0:22.5:1:27:1:1:0:60:4:0.0278:0:1.5 0/1:51:25:25,0:19,2:0.4902:2,1:26.8:1:28.4:1:0.2029:0:60:50:0.5:0.0196:0.2 -9 8338878 . A C 165 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGAGAGGTATCTTAGACT;RSEQ=CTTTTCAGCTAATGGTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:0:0,0:309,128:0:2,0:23.4:1:28.4:1:1:0:60:108.25:1:0:0.1 0/1:467:43:29,14:284,137:0.0921:2,2:23.3:1:30.5:1:1:1.00075:60:42:0.0923:0:1.3 -9 8339203 . A T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATATGACTCATTTCCTCTT;RSEQ=GAAACCATGAGCTCCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:0:1,0:22.9:1:30.3:1:1:0:60:28:1:0:0.2 1/0:12:9:1,8:0,3:0.75:0,2:19:1:28.1:1:1:0:60:8:0.7273:0:2 -9 8339233 . C G 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=AGCTCCCTTCATAGGGAAAC;RSEQ=CTTTGGTTCAGTATTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:0,18:0:1,0:28.3:1:29.2:1:1:0:60:8:1:0:0.2 1/1:4:4:1,3:0,0:1:0,2:37:1:30.5:1:1:0:60:8:1:0:1.8 -9 8340155 . A C 109 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTAGATCTTTCTTTAAAAC;RSEQ=CATAAATTTAAACACTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:31,1:0:1,0:23.8:1:30.1:1:1:0:60:31:1:0:0.1 1/0:20:14:14,0:5,1:0.7:2,1:15.4:1:28.7:1:0.3:0:60:6:0.6667:0:1.9 -9 8340168 . C A 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAAAACACATAAATTTAAA;RSEQ=ACTTGATGTGGCTTTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:40,1:0:1,0:24.9:1:32.4:1:1:0:60:82:1:0:0.2 1/0:23:14:14,0:8,1:0.6087:2,1:23.3:1:31.2:1:0.3913:0:60:28:0.6364:0:1.9 -9 8340226 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11894;SOR=Inf;LSEQ=AATGATGGTCCGGATTATGT;RSEQ=CAGAGTGCACTGCATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:92,1:0:1,0:22.9:1:31.2:1:1:0:60:30:1:0:0.1 0/1:91:3:3,0:86,2:0.033:1,0:20:1:31.3:1:1:0:60:6:0.0337:0:1 -9 8341018 . TA T 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTGAATGGAGATGAAATT;RSEQ=TTCTGGTTATTAAACTAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:175,26:0:2,0:25.3:1:28.4:1:1:0:60:99.5:1:0:0.1 0/1:168:38:31,7:103,27:0.2262:2,2:27.7:1:29.2:1:0.82265:1.16:60:76:0.2262:0.0119:0.2 -9 8341280 . GA G 162 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30278;SOR=0.7585;LSEQ=GGCTAGACGCTGTTGAATAG;RSEQ=AAAAAAAAAAAGGAAAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:37:10,27:60,150:0.148:2,2:28.3:1:31.2:1:1:1.07967:60:74:0.151:0.004:0.4 0/1:275:32:8,24:78,150:0.1164:2,2:28.4:1:31.1:1:0.42227:1.55749:60:64:0.1221:0:0.4 -9 8341445 . T C 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TAATCACTCTCTATAGCCTA;RSEQ=TGGATTTCTATATATTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:18,8:0:2,0:21.9:1:29.6:1:1:0:60:12:1:0:0.3 1/1:4:4:3,1:0,0:1:0,2:25.3:1:31:1:1:0:60:8:1:0:2.5 -9 8375569 . G T 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATAAATAGTAAAAAGGTT;RSEQ=TATCAGTCCAGCCCACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:0.8:0,0:21.3:1:30.3:1:1:0:60:8:0.8:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 8375861 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=TTACTATTCCAGAATGTCAA;RSEQ=AAGTTGCAGAAACATCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:177,9:0.0106:1,2:12.5:1:29.5:1:0.10382:18.7021:60:4:0.0107:0:1 0/0:175:0:0,0:171,4:0:1,0:23.5:1:32.3:1:1:0:60:86.5:1:0:0.1 -9 8376049 . G A 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17902;SOR=3.38477;LSEQ=CCATGATCAGGCCAGGCGGT;RSEQ=AACTGGAATTGTCTCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:666:2:2,0:263,400:0.003:2,0:1:0:23.5:1:0.15844:0:60:4:0.003:0:1 0/1:693:7:6,1:285,401:0.0101:2,2:9.7:1:24.1:1:0.04561:8.42:60:14:0.0102:0:1 -9 8376147 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21338;SOR=Inf;LSEQ=CAAGCCTCAGGTGGTAATGA;RSEQ=GAATAACAGGGAAGAGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:16,143:0:2,0:24.1:1:30.5:1:1:0:59.9:78.5:1:0:0.1 0/1:137:2:1,1:20,115:0.0146:2,2:27.5:1:28.5:1:0.28403:5.64:60:4:0.0152:0:1 -9 8376287 . A G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.52206;SOR=0;LSEQ=ATATTTGCGCAGGAAGACAA;RSEQ=ATTCTTAGGTGAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:4,6:0.2308:2,0:26:1:31.3:1:0.4965:0:60:6:0.2308:0:1 0/0:5:0:0,0:1,4:0:2,0:24.8:1:32:0:1:0:60:10:1:0:0 -9 8376477 . C T 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11733;SOR=0.52752;LSEQ=GCTGAGTGATAATGGAAGAT;RSEQ=TATTTCATTCTTCACTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:30:29,1:24,0:0.5556:1,1:25.6:1:30.8:1:1:0:60:60:0.566:0:1 0/1:48:19:19,0:29,0:0.3958:1,1:22.9:1:30.2:1:1:0:60:18:0.3913:0:1 -9 8376530 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49844;SOR=Inf;LSEQ=AGATTTAAGTAAAGCCTTAA;RSEQ=AGATTTCATTTCTCAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:142,19:0:2,0:24:1:31.9:1:1:0:60:52.667:1:0:0.2 0/1:161:2:1,1:138,21:0.0124:2,2:10:0:30:1:0.25536:6.44356:60:4:0.0126:0:1.5 -9 8376785 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24265;SOR=Inf;LSEQ=TCAATTTCTCTATTAACTTT;RSEQ=CTTTGAGTTGCTGTTGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:9,111:0:2,0:24.8:1:32.4:1:1:0:60:119:1:0:0 0/1:117:2:1,1:12,103:0.0171:2,2:5:0:31.5:1:0.21073:8.29:60:4:0.0174:0:0.5 -9 8376899 . T C 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1032;SOR=0;LSEQ=AATTACTGCTCTGATGCCAA;RSEQ=ATAAACCACATTTTTCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:0,7:0.5333:0,0:25.9:1:33.5:1:1:0:60:16:0.5333:0:1 0/0:4:0:0,0:0,4:0:0,0:11:1:29.3:1:1:0:60:8:1:0:0.3 -9 8389364 . C G 306 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00771;LSEQ=TAGGCATTTTGCTTCCTATA;RSEQ=CCATCTATGTAGTTGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:763:758:315,443:0,0:0.9934:0,2:24.9:1:32:1:1:0:60:93.75:0.9934:0:1.1 1/0:809:435:159,276:154,220:0.5377:2,2:24.1:1:31.7:1:0.19269:1.21479:60:53.375:0.5364:0:1.1 -9 8389592 . A T 134 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04615;SOR=0;LSEQ=GAACCGTCATGTTAAAAAAA;RSEQ=GTATGCAAAAAAGTGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:1:0,1:18.2:1:31.2:1:1:0:60:40:1:0:1.1 1/0:6:4:0,4:0,2:0.6667:0,0:26.8:1:29.8:1:1:0:60:8:0.6667:0:1 -9 8404607 . G A 151 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=15.6692;LSEQ=GCGTATCTATTCTTTGGTTT;RSEQ=TTTACTTCCAAGTTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:2:2,0:374,406:0.0026:2,0:1:0:26.5:1:0.23087:0:60:4:0.0026:0:1 0/1:983:38:18,20:456,488:0.0387:2,2:26.2:1:28.8:1:1:1.03822:60:76:0.039:0:1.2 -9 8404720 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49973;SOR=0;LSEQ=TGAAAACCACCAGATTATAG;RSEQ=CATTTATCACATGTAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:13,146:0.0124:2,0:32:1:31.5:1:1:0:60:4:0.0127:0:1 0/0:145:0:0,0:16,129:0:2,0:21.7:1:31.6:1:1:0:60:47.333:1:0:0.1 -9 8436531 . G T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62352;SOR=3.01805;LSEQ=AAGTTAATTTTCAAGAATAT;RSEQ=GTCAAAAAAAGAGAAGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:210,43:0.0039:2,0:47:0:29:0:1:0:60:2:0.004:0:1 0/1:254:3:0,3:195,56:0.0118:2,0:6.3:1:21.3:1:0.01204:0:60:2:0.008:0:1.7 -9 8436534 . C CA 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05814;SOR=0;LSEQ=TTAATTTTCAAGAATATGGT;RSEQ=AAAAAAAGAGAAGAGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:4:2,2:215,43:0.0153:2,2:18:1:30.5:1:0.13775:4.95508:60:8:0.0154:0.0038:0.8 0/0:270:0:0,0:204,64:0:2,0:22.7:1:31:1:1:0:60:88.333:0.9962:0:0.3 -9 8436560 . A T 198 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAGAAGAGTAACTCTTGA;RSEQ=ATTACTGTAAAGAATAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:286,129:0:2,0:24.8:1:30:1:1:0:60:206.5:1:0:0.1 0/1:447:112:74,38:219,116:0.2506:2,2:22.2:1:29.1:1:0.90918:1.03:60:224:0.2506:0:1.1 -9 8436703 . C G 235 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=541.07565;LSEQ=GCCATACCTATTGAAAAAAG;RSEQ=AAAGAAGAAACACATTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:1:0,1:118,299:0.0024:2,0:35:0:33:0:1:0:60:2:0.0024:0:1 1/0:341:193:56,137:48,97:0.566:2,2:22.5:1:31:1:0.47521:1.20991:60:192:0.5731:0:1.1 -9 8437015 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14423;SOR=Inf;LSEQ=GCTTGATGTCAACTTCTGCT;RSEQ=TGAGTAATGACTTTTATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:37,3:0:2,0:25:1:30:1:1:0:60:39:1:0:0.2 0/1:25:2:2,0:23,0:0.08:1,0:32:1:31:0:1:0:60:4:0.0833:0:1 -9 8437092 . T A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22152;SOR=0;LSEQ=AATTGTGTGGAATTAAATGG;RSEQ=GTAAAGTGAAATAAGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:2,0:167,12:0.011:2,0:21:1:25.5:1:1:0:60:4:0.0114:0:1 0/0:203:0:0,0:185,15:0:2,0:50:0:16:0:1:0:60:0:0:0:3 -9 8437288 . C CA 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.0242;LSEQ=ATAAAATAGAACAAATTCTT;RSEQ=AAAAAAAAATGAAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:6:1,5:24,160:0.0311:2,2:22.3:1:30.6:1:0.57628:1.33:60:12:0.0321:0.0104:0 0/1:220:7:2,5:45,168:0.0318:2,2:23:1:27.7:1:0.64328:1.49:60:14:0.0327:0.0045:0.1 -9 8449502 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=AGTTCTTCCAAAATTTGAAG;RSEQ=ATACCCATATTTCTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:10,0:0:0,0:19.5:1:31.6:1:1:0:60:20:1:0:0.1 0/1:10:2:2,0:7,1:0.2:2,0:27.5:1:33.5:1:1:0:60:4:0.2222:0:1 -9 8449665 . A G 159 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTTCAACTCTTAATATCA;RSEQ=TTGAGCTGTACAACTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:213,31:0:2,0:24:1:30.1:1:1:0:60:33.857:1:0:0 0/1:249:31:25,6:176,42:0.1245:2,2:23.6:1:32.2:1:1:1.00569:60:62:0.126:0:1 -9 8449993 . C A 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.02019;SOR=0;LSEQ=ACCCAGTTCGGGTTGCTTTT;RSEQ=CCCCCTGGCCTAATTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:1,9:0,8:0.5556:0,2:21.3:1:29.5:1:1:0:60:20:0.5556:0:1.1 0/0:7:0:0,0:0,7:0:0,0:20.1:1:31.7:1:1:0:60:14:1:0:0 -9 8454073 . C A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTAGCTATTATTATTGCT;RSEQ=TTATTATTCAAGACTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28.5:1:28:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 8454265 . G T 102 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTATGAGACACCTCACAT;RSEQ=TCTGCTCTGTAAACACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1:0,0:19.9:1:29.7:1:1:0:60:10:1:0:1.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 8454413 . A G 213 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAATATTTATTTTCCCCAG;RSEQ=ATCATCTTAATGAAGTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:107:107,0:0,0:1:0,1:21.9:1:31.6:1:1:0:60:34.667:1:0:1 1/0:78:50:50,0:26,2:0.641:2,1:20.6:1:30.9:1:0.12587:0:60:49:0.6364:0:1 -9 8454491 . C T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1241;SOR=Inf;LSEQ=GTATTATCTTTTGTGTGCAG;RSEQ=CCCGCCCTCCCCTCTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:0:0,0:291,102:0:2,0:23.6:1:31.5:1:1:0:60:55.143:1:0:0.2 0/1:399:4:1,3:264,131:0.01:2,2:18.8:1:27.3:1:0.11223:6.01718:60:8:0.0102:0:1.5 -9 8454495 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TATCTTTTGTGTGCAGCCCC;RSEQ=CCCTCCCCTCTTCAACAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:0:0,0:308,121:0:2,0:23.1:1:30.1:1:1:0:60:70.5:1:0:0.2 0/1:445:17:11,6:278,147:0.0382:2,2:23.6:1:28.1:1:1:1.03149:60:34:0.0393:0:1.4 -9 8454566 . T C 240 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGAACATTAAAGGGGTTTGT;RSEQ=CTCTATTCCTCACCTGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:819:0:0,0:394,424:0:2,0:26.9:1:29.9:1:1:0:60:61.923:0.9988:0:0.1 0/1:847:222:112,110:306,316:0.2621:2,2:25.5:1:30.9:1:0.7551:1.05:60:110:0.2619:0:1.2 -9 8460277 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11281;SOR=Inf;LSEQ=TCTTACTGTAATGTAAACAC;RSEQ=TTTCCAAAAATAATTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:0:1,0:25.1:1:31.9:1:1:0:60:62:1:0:0 0/1:30:3:3,0:26,1:0.1:1,0:31.3:1:30.7:1:1:0:60:6:0.1:0:1 -9 8460591 . A G 170 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGAGGAAAAGCAGAGTCT;RSEQ=TTTCAGTTATAAAATAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:78,234:0:2,0:24.8:1:30.3:1:1:0:60:77:1:0:0.1 0/1:399:42:12,30:123,233:0.1053:2,2:22.3:1:31.6:1:0.49414:1.31885:60:41:0.1035:0:1.1 -9 8470930 . AG A 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00028;SOR=Inf;LSEQ=TCCTGAAAGGCCTCCAAGGG;RSEQ=GGGGGCGGAAATGCAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:207,79:0:2,0:21.6:1:31.6:1:1:0:60:70.5:0.993:0:0.1 0/1:325:13:11,2:216,95:0.04:2,2:23.7:1:31.1:1:0.3579:2.41:60:26:0.041:0.0031:1.4 -9 8470932 . G T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.37896;SOR=3.50745;LSEQ=CTGAAAGGCCTCCAAGGGAG;RSEQ=GGGGCGGAAATGCAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:1,0:208,81:0.0034:2,0:17:0:31:0:1:0:60:2:0.0035:0:1 0/1:333:4:1,3:231,98:0.012:2,2:19.3:1:28.3:1:0.08495:7.02544:60:8:0.0121:0:1 -9 8470974 . G A 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATAACGAATAAAAGACAT;RSEQ=GCCAACAATGACACAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:556:0:0,0:340,216:0:2,0:26.9:1:31.6:1:1:0:60:68.5:1:0:0.1 0/1:704:42:27,15:395,267:0.0597:2,2:22.6:1:29.1:1:0.62778:1.22:60:84:0.0606:0:1.4 -9 8471481 . A G 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATGTTTTTAAAAGGAGGAT;RSEQ=TAGATGAAAAATTTCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 8484039 . C T 143 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.93256;LSEQ=TTAAGCAGTATCTTCTTTTA;RSEQ=GACCTCTATAATTTTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:0,1:121,15:0.0073:2,0:1:0:25:0:0.11679:0:60:2:0.0073:0:1 0/1:134:25:22,3:98,11:0.1866:2,2:19.3:1:30.9:1:0.72491:1.21303:60:50:0.1866:0:1.1 -9 8484047 . A G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49878;SOR=Inf;LSEQ=TATCTTCTTTTACGACCTCT;RSEQ=TAATTTTGAGATATAATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:139,23:0:2,0:22.5:1:28.6:1:1:0:60:161:1:0:0 0/1:170:2:2,0:141,27:0.0118:2,0:33.5:1:34:0:1:0:60:4:0.0118:0:2 -9 8484240 . T G 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCAGTCTTTGCCGTGACCC;RSEQ=GTGCTGCAGCCCACCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:760:0:0,0:368,392:0:2,0:24.7:1:30.4:1:1:0:60:68.091:1:0:0.1 0/1:941:54:25,29:423,462:0.0574:2,2:25.6:1:29.9:1:0.88884:1.06203:60:108:0.058:0:1.2 -9 8484397 . T TA 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.85333;SOR=1.08254;LSEQ=ATCTAAAGAGATAAAACCAA;RSEQ=AAAAAAAAAATCTGGTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:15:3,12:66,218:0.0495:2,2:24.7:1:29.4:1:1:1.21026:60:14:0.0488:0.0066:0.1 0/1:281:15:4,11:72,191:0.0534:2,2:28.7:1:28.8:1:1:1.03648:60:30:0.0551:0.0036:0.1 -9 8485099 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49746;SOR=0;LSEQ=ACTGTCTCCCATGTGAAAGT;RSEQ=ACAAATGAAAATAGCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:44,1:0.0426:1,2:19.5:1:28.5:1:0.08418:31.46141:60:4:0.0426:0:1 0/0:40:0:0,0:40,0:0:1,0:20.8:1:30.8:1:1:0:60:80:1:0:0.1 -9 8485125 . G A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10672;SOR=Inf;LSEQ=TGAAAATAGCAAGGACACGT;RSEQ=GCCAAAACAAAGTGGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:78,4:0:1,0:23.2:1:32.1:1:1:0:60:40:1:0:0.1 0/1:75:3:3,0:72,0:0.04:1,0:10.3:1:29.3:1:1:0:60:6:0.04:0:2 -9 8485128 . C A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11821;SOR=Inf;LSEQ=AAATAGCAAGGACACGTGGC;RSEQ=AAAACAAAGTGGTCTGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:79,4:0:1,0:24.7:1:31.6:1:1:0:60:166:1:0:0.1 0/1:81:3:3,0:78,0:0.037:1,0:11.3:1:31:1:1:0:60:6:0.037:0:2 -9 8485201 . T C 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCTACTTTTATCTGTGAT;RSEQ=TCTTACAAATTAGAAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:254,97:0:2,0:23.6:1:30.3:1:1:0:60:174.5:1:0:0.1 0/1:480:115:76,39:236,129:0.2396:2,2:23.7:1:31:1:0.82314:1.07:60:114:0.239:0:1.1 -9 8485380 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50001;SOR=Inf;LSEQ=TCTTAAAACAGATGACCTGT;RSEQ=CTTTCCACCATGGACCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:18,134:0:2,0:23.3:1:31:1:1:0:60:49.667:1:0:0.1 0/1:170:2:1,1:31,137:0.0118:2,2:26:1:28:1:0.34194:4.37:60:4:0.012:0:1 -9 8485435 . G C 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.0027;SOR=Inf;LSEQ=TGCTGTCTACTTTGATCAGA;RSEQ=AGAGAAGTATGATTTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:3,62:0:1,0:26.4:1:31.1:1:1:0:60:31.5:1:0:0.1 0/1:52:7:0,7:2,43:0.1346:1,0:23.3:1:30.4:1:1:0:60:14:0.1346:0:1 -9 8485686 . T C 161 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGAATGGGCTGATCAGTTA;RSEQ=TATAGCTTCAAAATACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:143,27:0:2,0:22.8:1:30.4:1:1:0:60:23.286:1:0:0.1 0/1:159:36:31,5:102,21:0.2264:2,2:21.9:1:31.2:1:0.80012:1.27:60:35:0.2229:0:1.2 -9 8485834 . G A 219 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=184.86999;LSEQ=CCCTTTGCTCGTATGAGCAC;RSEQ=TACTTTTACATCGTATGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:700:1:1,0:379,319:0.0014:2,0:45:0:13:0:1:0:60:0:0:0:2 0/1:740:155:82,73:323,261:0.2095:2,2:21.8:1:30.1:1:0.65001:1.10157:60:310:0.2117:0:1.2 -9 8486420 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18045;SOR=Inf;LSEQ=TTTCAGTCATTGCCAAATGA;RSEQ=GGAGTTCCACTCTACTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:0:1,0:25.7:1:31:1:1:0:60:43:1:0:0 0/1:33:2:1,1:0,31:0.0606:1,2:10:0:32.5:1:0.06061:0:60:4:0.0606:0:1.5 -9 8486482 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13547;SOR=Inf;LSEQ=AAACAAAACAAAACAGGCAA;RSEQ=GTTTGACCTACATACCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:0,18:0:1,0:22.1:1:28.8:1:1:0:60:5:1:0:0.1 0/1:11:2:0,2:0,9:0.1818:0,0:15:1:32:0:1:0:60:4:0.2:0:1 -9 8492614 . CA C 50 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGACACACAGAAGGTGCT;RSEQ=AAAAAAAAAAAAAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,0:0.5:0,0:12.7:1:31.8:1:1:0:60:6:0.6:0.3333:0.7 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:60:2:1:0:0 -9 8492703 . AT A 93 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.12295;SOR=2.71387;LSEQ=ACTATTTTTTTCCCTGATCT;RSEQ=TTTTTTTTTTTTACCCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:6:6,0:24,0:0.1818:1,0:19.8:1:31.2:1:1:0:60:12:0.1818:0.0303:0 0/1:21:8:8,0:9,0:0.381:0,0:26.1:1:31.2:1:1:0:60:16:0.381:0.0952:0 -9 8492902 . A T 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTTTGGGCTTGCTGCGAGC;RSEQ=CCATCTCCTTTGGTTGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:819:0:0,0:413,405:0:2,0:25.5:1:29.8:1:1:0:60:115.857:1:0:0.1 0/1:1007:51:24,27:475,481:0.0506:2,2:25.1:1:29.4:1:0.77456:1.11085:60:102:0.0508:0:1.2 -9 8499578 . C T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50355;SOR=0;LSEQ=TCGAAAAACTAAAATAAGAG;RSEQ=AATTTCAGGATATGAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:2,0:122,6:0.0154:1,0:20:1:25.5:1:1:0:60:4:0.0157:0:1 0/0:105:0:0,0:90,15:0:2,0:22.5:1:31.7:1:1:0:60:210:1:0:0.1 -9 8499906 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22788;SOR=Inf;LSEQ=ACCCTATCAGAGCATTTTCT;RSEQ=CATTTTCTTTACTTAGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:20,159:0:2,0:23.3:1:31.6:1:1:0:60:28.833:1:0:0.1 0/1:164:2:1,1:17,145:0.0122:2,2:12:1:26.5:1:0.20807:8.32:60:4:0.0125:0:1 -9 8499960 . T C 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=TGGGTAAACCCACTATGTTT;RSEQ=CTTTGAAGAATACAAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:1,67:0:1,0:22.3:1:30.4:1:1:0:60:136:1:0:0 0/1:38:8:0,8:0,30:0.2105:1,0:18.3:1:31:1:1:0:60:16:0.2105:0:1 -9 8500029 . G A 35 v4;q23;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCTACCTTTTAAGAAAA;RSEQ=ATCAAAAAACATGACCGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:1,16:0.15:1,0:36.7:1:22.7:1:1:0:60:2:0.1111:0:4.3 0/0:6:0:0,0:0,6:0:0,0:31:0:10:0:1:0:54:0:0:0:7 -9 8501113 . G GA 96 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.46382;SOR=1.44977;LSEQ=GTGAAAGGACAGGAGTGGTT;RSEQ=AAAAAAAAAATGATAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:8:0,8:10,147:0.0476:2,0:25.1:1:30.3:1:1:0:60:16:0.0485:0:0.6 0/1:133:9:0,9:13,111:0.0677:2,0:32.4:1:30.3:1:0.59858:0:60:18:0.0703:0:0.7 -9 8504101 . G T 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00914;SOR=Inf;LSEQ=ATCAAGTGATGAGACCAAAA;RSEQ=AAGTCACAGTTACACTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:38,1:0:1,0:27.6:1:32.6:1:1:0:60:38:1:0:0.2 0/1:19:4:4,0:15,0:0.2105:1,0:27:1:29.5:1:1:0:60:8:0.2105:0:1 -9 8504209 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2487;SOR=0;LSEQ=GTGAAGGTGAAAGCTAGCAA;RSEQ=ATCTCCCCGAGGAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:2,1:180,47:0.013:2,2:41.7:1:29:1:0.50623:1.90844:60:6:0.0133:0:1 0/0:220:0:0,0:168,52:0:2,0:23.8:1:31.1:1:1:0:60:440:1:0:0.1 -9 8504387 . G A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01803;SOR=0;LSEQ=CAGCCTATATGATGTCCCTG;RSEQ=CTCAATGGTAATTCGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:5:4,1:153,287:0.0112:2,2:12.8:1:28.4:1:0.05459:7.47:60:10:0.0113:0:1 0/0:546:0:0,0:221,324:0:2,0:26:1:31.2:1:1:0:60:59.556:0.9981:0:0.1 -9 8518143 . T C 171 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=39.45545;LSEQ=TCCCTCGGGGCACTGGATGG;RSEQ=GCTTGCTCTGAGGTTTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:577:1:1,0:278,296:0.0017:2,0:36:0:13:0:0.48522:0:60:0:0:0:3 0/1:701:45:25,20:335,320:0.0642:2,2:24:1:31.3:1:0.64453:1.19:60:90:0.0653:0:1.1 -9 8518395 . G A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00325;SOR=Inf;LSEQ=ATGCTTGTAGCTGTGCTCTC;RSEQ=GTCACTACAGGAGTTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:73,162:0:2,0:27.8:1:30.5:1:1:0:60:116.5:1:0:0.1 0/1:315:11:5,6:116,188:0.0349:2,2:20.2:1:30.4:1:0.75439:1.35:60:22:0.0353:0:1.5 -9 8521244 . C T 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCACTTGGCTTGAGTGTAC;RSEQ=CAGATCCTCAAAGCATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:158,64:0:2,0:27.9:1:30.7:1:1:0:60:26.75:1:0:0.1 0/1:268:29:19,10:162,76:0.1082:2,2:21:1:29.2:1:0.83412:1.12139:60:28:0.1069:0:1.1 -9 8523421 . A G 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00194;SOR=Inf;LSEQ=CCATTAACCAAAAGAAGAAC;RSEQ=CAATGCAGCTACATTCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:180,67:0:2,0:23.4:1:29.8:1:1:0:60:60.75:1:0:0.1 0/1:269:10:5,5:180,79:0.0372:2,2:24.3:1:30.1:1:0.29428:2.27078:60:20:0.0379:0:1.2 -9 8524875 . T C 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.6278;SOR=2.5965;LSEQ=GGACCCTGCGGCGTCTCAAC;RSEQ=CCCCCTGAGCCTGAATGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:1,0:187,67:0.0039:2,0:28:0:31:0:1:0:60:2:0.004:0:1 0/1:296:3:1,2:213,80:0.0101:2,2:23.7:1:24:1:0.1868:5.28955:60:2:0.0068:0:1.3 -9 8526505 . G GA 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.66622;SOR=1.2628;LSEQ=TCATAACCAAACAGTACAAA;RSEQ=AAAAAAAAAAAGTTGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:11:9,2:80,10:0.1068:2,2:32.4:1:29.8:1:0.61608:1.76581:60:22:0.11:0:0.1 0/1:99:13:11,2:70,12:0.1313:2,2:14.7:1:27.8:1:1:1.05995:59.6:12:0.1263:0.0606:0.4 -9 8526566 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.12684;SOR=Inf;LSEQ=AAACAGGACAAAGATGAGAG;RSEQ=GATGAAAGGACAGAAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:172,95:0:2,0:27.3:1:31:1:1:0:60:65.75:1:0:0.1 0/1:304:4:2,2:170,130:0.0132:2,2:38:1:29.5:1:1:1.30651:60:8:0.0136:0:1.3 -9 8526697 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26326;SOR=Inf;LSEQ=GAAAGAAGAAGCATTAGTAC;RSEQ=AGAAGAAGGAGGCTAGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:64,154:0:2,0:26.2:1:30.8:1:1:0:60:71.667:1:0:0.1 0/1:289:3:2,1:105,179:0.0104:2,2:41.7:1:30.3:1:0.55788:3.39:60:6:0.0105:0:1 -9 8526718 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21778;SOR=0;LSEQ=AGAAGAAGGAGGCTAGGGCT;RSEQ=GGGAGAAGAATTAAATTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:37,132:0.0116:2,2:6.5:1:27:1:0.39608:3.53:60:4:0.0118:0:1 0/0:196:0:0,0:65,131:0:2,0:23.3:1:30.5:1:1:0:60:195:1:0:0.1 -9 8526744 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24151;SOR=0;LSEQ=AAGAATTAAATTAGATTTAC;RSEQ=GAATTAAATAAGGTCTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:13,86:0.0198:2,2:27.5:1:29:1:0.25921:6.41:60:4:0.0206:0:1 0/0:104:0:0,0:25,79:0:2,0:20.4:1:30.7:1:1:0:60:208:1:0:0.1 -9 8527273 . TTAA T 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.00011;SOR=Inf;LSEQ=AATGCATGCCATGCATTTTA;RSEQ=TAATAATAATAATATTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:114,33:0:2,0:24.1:1:30:1:1:0:60:294:1:0:0.1 0/1:162:14:8,6:107,41:0.0864:2,2:27.7:1:29.8:1:0.23366:1.94843:60:28:0.0875:0.0062:0.1 -9 8527408 . C A 22 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21204;SOR=Inf;LSEQ=ATAAAAATATTATTATATTC;RSEQ=TTATAATTTGGTACAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:62,153:0:2,0:23.8:1:31.7:1:1:0:60:430:1:0:0.1 0/1:184:2:1,1:54,127:0.0109:2,2:11:1:22:1:0.51192:2.34:60:4:0.011:0:2.5 -9 8528541 . TA T 183 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.02959;SOR=1.56983;LSEQ=AAATAAGGAGAGAGAAAAAT;RSEQ=AAAAAAAAAATTCTCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:41:29,12:333,110:0.0847:2,2:24.3:1:29.9:1:0.57312:1.25208:60:82:0.0858:0.0207:0.1 0/1:591:75:51,24:352,156:0.1269:2,2:23.7:1:29.4:1:0.89355:1.06173:59.7:74:0.1265:0.0305:0.3 -9 8528811 . T A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24904;SOR=Inf;LSEQ=AAGGTGATAGAAACATTCAG;RSEQ=TAATAAGTCAGATGCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:61,228:0:2,0:20.7:1:30:1:1:0:60:95.333:1:0:0.1 0/1:301:3:3,0:80,218:0.01:2,0:7.3:1:20.3:1:0.02042:0:60:2:0.0068:0:2.3 -9 8632149 . C G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTGTGTGTGTGTGTGT;RSEQ=TGTGTGTGTGTGTGTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:31:1:1:0:60:4:1:0:1.5 -9 8632223 . A G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATTACTGCTGGCCTCCA;RSEQ=ATAAATAAGTTCTTGACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:1:28:0:1:0:60:4:1:0:1.5 -9 8632768 . C T 27 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGAAAGGGATTTGTCAG;RSEQ=CCAGTTATTTAGATCAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:34:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 8633210 . G T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25704;SOR=0;LSEQ=TCTTACAAACATTTAACTGA;RSEQ=TTTCCCATTTAAGCACCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:3:2,1:206,4:0.0141:1,2:22.7:1:25.3:1:0.0691:24.02334:60:2:0.0094:0:1 0/0:171:0:0,0:166,5:0:1,0:25:1:32.5:1:1:0:60:170:1:0:0 -9 10093976 . T G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGTGGGCTAAAAAATCCC;RSEQ=ATAGGGTACTATGCTCACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:32.5:1:1:0:60:4:1:0:1 -9 10094898 . A T 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.12224;LSEQ=TAATCGTGGACTACTTCAAA;RSEQ=GCAAGAATATTAGCATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:547:55:30,25:213,279:0.1005:2,2:27.2:1:30.3:1:0.11756:1.57:60:110:0.102:0:1.1 0/1:589:113:53,60:227,249:0.1919:2,2:27.2:1:29.5:1:0.91676:1.03201:60:55.5:0.1924:0:1.1 -9 10633805 . T C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=TTTTTATTTTTTATTTATTT;RSEQ=TTGAGGGGGCATGAAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:23.2:1:29.8:1:1:0:60:12:1:0:0.2 1/0:4:2:2,0:2,0:0.5:0,0:9:1:32.5:1:1:0:60:4:0.5:0:1 -9 10633964 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50441;SOR=Inf;LSEQ=TCCTAGCCAATGGCTGAGCA;RSEQ=CAGGAAATACAAAGGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:38,34:0:2,0:29.9:1:32.1:1:1:0:60:71:1:0:0.1 0/1:92:2:1,1:46,44:0.0217:2,2:29.5:1:28.5:1:1:1.04497:60:4:0.0222:0:1 -9 10634079 . A G 101 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05366;SOR=0;LSEQ=ATCCTGTAACTATTTACTTG;RSEQ=GAGTATTAGACTCTTCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1:0,0:26:1:32.1:1:1:0:60:18:1:0:1 1/0:13:8:0,8:0,5:0.6154:0,0:24.1:1:30.3:1:1:0:60:16:0.6154:0:1 -9 12036108 . T G 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCTATAGCTCCAGGCT;RSEQ=TGCTTTTCTGCTGCTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:15.5:1:30:1:1:0:60:16:1:0:1 1/1:12:12:5,7:0,0:1:0,2:28:1:31.6:1:1:0:60:24:1:0:1.1 -9 12036280 . G C 74 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTCCAGCCAGAGGCTCAGA;RSEQ=ACAGAATTCGGATCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:23.8:1:33.8:1:1:0:60:8:1:0:1 1/1:5:5:2,3:0,0:1:0,2:22.6:1:32:1:1:0:60:10:1:0:1 -9 12036394 . T C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGAGGAATCTGGGCAGTC;RSEQ=AGACAAGTGGGTTTGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:9,8:0,0:1:0,2:32.8:1:31.2:1:1:0:60:16:1:0:1.8 1/1:12:12:6,6:0,0:1:0,2:33.5:1:30:1:1:0:60:24:1:0:1.6 -9 12036418 . G T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.25064;LSEQ=CAAGTGGGTTTGCCCCCAGC;RSEQ=AAACACACCCTCTCAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:5,5:3,6:0.5263:2,2:27.6:1:29.6:1:0.64992:1.93:60:20:0.5263:0:2.3 1/0:12:7:3,4:2,3:0.5833:2,2:17.6:1:29.1:1:1:1.11:60:14:0.5833:0:2 -9 12036736 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02564;SOR=0;LSEQ=ACTATTGAAAGAAAAACAAG;RSEQ=AGAAAGCAACAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:2,1:0.5714:2,2:15.8:1:29.3:1:1:1.81007:60:8:0.5714:0:1.8 0/0:8:0:0,0:4,4:0:2,0:24.5:1:32:1:1:0:60:16:1:0:1.1 -9 12036767 . CAAC T 85 d7;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AACAACAACAGCATCATCAT;RSEQ=AACAACAACAACAACAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:19.7:1:28.4:1:1:0:60:12:1:0.5:1.2 1/1:7:7:3,4:0,0:1:0,2:37.4:1:30.5:1:1:0:60:14:1:0.1429:0.4 -9 12518558 . C CT 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.73;SOR=1.10407;LSEQ=TCGTTTTCCTCTTTTACTGC;RSEQ=TTTTACCACACTTACTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:748:32:13,19:348,368:0.0428:2,2:27.6:1:30.6:1:0.47026:1.38151:60:64:0.0431:0.0053:0.1 0/1:1042:49:27,22:485,508:0.047:2,2:28.4:1:30.7:1:0.46472:1.29:60:98:0.0474:0.0029:0.2 -9 12518586 . A T 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.39589;LSEQ=ACACTTACTGTTCATATTTT;RSEQ=TTTGTCCATTGAACTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:681:55:22,33:272,350:0.0808:2,2:29.1:1:30.4:1:0.67097:1.16545:60:110:0.0821:0:1.2 0/1:909:209:96,113:325,370:0.2299:2,2:24.8:1:29.8:1:0.87442:1.0339:60:103.5:0.2315:0:1.2 -9 12518676 . C A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=TGTTCCCATGTGCATTATTG;RSEQ=ATTATTTATCTTTCTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:47,174:0:2,0:22:1:31.9:1:1:0:60:109.5:1:0:0.1 0/1:229:12:3,9:41,176:0.0524:2,2:20.9:1:29.5:1:0.70489:1.43:60:24:0.0533:0:1.1 -9 12519087 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGATATTAGGGTTGAAC;RSEQ=TGTAAATACCAACACTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 12746316 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59773;SOR=0.43382;LSEQ=ATATCCTGAAGTATGTTTTC;RSEQ=AGTTTGTTTCCATTTTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:18,12:0.0625:2,2:45:1:30:0:1:1.48061:60:4:0.0625:0:2 0/1:36:1:0,1:21,14:0.0278:2,0:1:0:22:0:0.41667:0:60:2:0.0286:0:2 -9 12746337 . G A 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.08768;LSEQ=AGTTTGTTTCCATTTTCCCC;RSEQ=TCTCCTTCTGGTACACCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:31:18,13:4,2:0.8378:2,2:27.7:1:30.6:1:1:1.43053:59.7:62:0.8378:0:1.2 1/1:53:45:24,21:5,3:0.8491:2,2:24.4:1:30.4:1:0.71525:1.44814:60:90:0.8491:0:1.2 -9 12746343 . T A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50818;SOR=Inf;LSEQ=TTTCCATTTTCCCCGTCTCC;RSEQ=TCTGGTACACCAATCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:21,17:0:2,0:27.6:1:30.7:1:1:0:59.7:76:1:0:1 0/1:53:2:1,1:28,23:0.0377:2,2:35:0:31.5:1:1:1.21285:60:4:0.0377:0:1 -9 12746401 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52715;SOR=Inf;LSEQ=TGAAGTCCCATATTTCTTGG;RSEQ=GGCTTTGTTCATTCCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:21:1:30.5:1:1:0:60:38:1:0:0.5 0/1:33:2:1,1:16,15:0.0606:2,2:16.5:1:28.5:1:1:1.06462:60:4:0.0606:0:2.5 -9 12746899 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49376;SOR=0;LSEQ=TTGTCTAGTTTTGGTCTTTG;RSEQ=GGCTGCTGACCCTTGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:16,18:0.0541:2,2:37:1:31:1:1:1.12:60:4:0.0541:0:1 0/0:34:0:0,0:20,14:0:2,0:23.6:1:29.5:1:1:0:58.3:68:1:0:0.2 -9 13731155 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.23184;LSEQ=CTGGGCATTAACTGAAAAAA;RSEQ=CTCTGCATCTTGCTCACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:101:59,42:73,47:0.457:2,2:26.3:1:31.5:1:0.78337:1.10516:60:100:0.4566:0:1.7 1/1:271:221:131,90:24,26:0.8155:2,2:26.3:1:30.8:1:0.15695:1.57:60:109.5:0.8172:0:1.7 -9 13731201 . C G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.25099;LSEQ=ATCATGGTCCCATCCTGGCC;RSEQ=TGTTTAAGCCCCAGGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:117:56,61:71,79:0.4382:2,2:25.8:1:30.3:1:1:1.02:60:38:0.4351:0:1.7 1/1:281:226:112,114:25,29:0.8043:2,2:25.5:1:29.8:1:0.76218:1.14:60:55.5:0.8043:0:1.7 -9 13731294 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49836;SOR=Inf;LSEQ=AGGATTCTCCAAAGCATCTC;RSEQ=ACTCATGTTTCTTGCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:25,79:0:2,0:23.7:1:32:1:1:0:60:103:1:0:0.2 0/1:112:2:1,1:28,81:0.0179:2,2:19.5:1:31:1:0.45602:2.86:60:4:0.018:0:1 -9 13731367 . G C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00274;SOR=6.07592;LSEQ=GCTCCCCACCCAGCTTCTAG;RSEQ=CCACCACTCTGACCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:0,12:1,20:0.3636:1,0:27.4:1:32.1:1:1:0:60:24:0.3636:0:2.3 1/0:23:18:0,18:0,5:0.7826:0,1:18.3:1:30.1:1:1:0:60:8:0.7619:0:1.6 -9 13731412 . G C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.66686;LSEQ=TAATATCCATTTCAATGCAG;RSEQ=TTTTTGGCTTGAGGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:0.5385:0,0:25.7:1:29.7:1:1:0:60:6:0.5:0:3.7 1/0:6:4:0,4:0,2:0.6667:0,0:31.3:1:33:1:1:0:60:8:0.6667:0:3.8 -9 13731416 . T A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.06713;LSEQ=ATCCATTTCAATGCAGGTTT;RSEQ=TGGCTTGAGGTCTCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:0.5833:0,0:24:1:30.3:1:1:0:60:14:0.5833:0:3.7 1/0:5:3:0,3:0,2:0.6:0,0:37:1:30.7:1:1:0:60:6:0.6:0:4.3 -9 13731425 . G C 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68659;LSEQ=AATGCAGGTTTTTGGCTTGA;RSEQ=GTCTCTTTCCAAATTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:24.2:1:26.3:1:1:0:60:5:0.5556:0:3.7 1/0:4:2:0,2:0,1:0.5:0,0:27:1:28.5:1:1:0:60:4:0.5:0:4.5 -9 16181267 . G C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.1071;LSEQ=TTTGGAGGGCAAGAGTTTCA;RSEQ=AAAGACACTAGAAAGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:23,0:26,0:0.4694:1,1:24.2:1:32.5:1:1:0:60:46:0.4694:0:1.1 0/1:59:5:5,0:54,0:0.0847:1,0:26.6:1:32.2:1:1:0:60:10:0.0877:0:1 -9 16181342 . ACTG A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=1;SOR=0.75839;LSEQ=AGCAGATTATTGCTGCTACT;RSEQ=CTGCTGCTGTTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:164,117:0.0105:2,2:25.7:1:32:1:1:1.43:60:6:0.0107:0:0.3 0/0:375:3:1,2:215,157:0.008:2,2:29.3:1:29:1:0.57655:2.73154:60:6:0.008:0.0027:0.3 -9 16181428 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18946;LSEQ=TAACTGAAGAAGAACACGTT;RSEQ=CTGATGACTGTGAGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:75:24,51:30,63:0.4464:2,2:23.3:1:29.3:1:1:1.01183:60:150:0.4518:0:1.1 0/1:197:26:7,19:56,115:0.132:2,2:23.3:1:28:1:0.65526:1.31993:60:52:0.1333:0:1 -9 16181703 . A G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCATGTGCCGGTCACTGT;RSEQ=CTGAGTACTTCATAGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 16206644 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23751;SOR=Inf;LSEQ=ATGGAAATGATTTATTCGGA;RSEQ=AACCTTGTCAGTACTGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:60,11:0:2,0:23.3:1:32.2:1:1:0:60:142:1:0:0.1 0/1:68:2:1,1:59,7:0.0294:2,2:5.5:1:26:1:0.223:7.95036:60:4:0.0303:0:1 -9 16206695 . A G 130 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTATTTCATTATGGGCCATG;RSEQ=GTGGGCTAGACTACATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:128,60:0:2,0:24.8:1:30.4:1:1:0:60:93:1:0:0.6 0/1:201:20:10,10:119,61:0.0995:2,2:29:1:30.2:1:0.21687:1.94395:60:40:0.102:0:1.6 -9 16206756 . T G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02041;LSEQ=CATTTCCACAACTGGTTATT;RSEQ=CAGTTGACAATTAACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:108:53,55:73,75:0.4202:2,2:26.7:1:31.6:1:1:1.01002:60:26:0.416:0:2.2 0/1:345:5:3,2:175,164:0.0145:2,2:10.6:1:30.4:1:1:1.40:60:10:0.0147:0:2.2 -9 16206760 . T G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28415;LSEQ=TCCACAACTGGTTATTTCAG;RSEQ=TGACAATTAACAGGAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:110:54,56:73,74:0.4264:2,2:26:1:31:1:1:1.02294:60:26.5:0.4223:0:2.2 0/1:339:59:29,30:145,135:0.174:2,2:25.9:1:30.5:1:0.77501:1.11076:60:28.5:0.1696:0:1.5 -9 16206766 . A G 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01221;SOR=Inf;LSEQ=ACTGGTTATTTCAGTTGACA;RSEQ=TTAACAGGAAATGATGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:120,131:0:2,0:26.2:1:30:1:1:0:60:40.833:1:0:1 0/1:339:9:3,6:168,162:0.0265:2,2:23:1:30.7:1:0.33357:2.06975:60:18:0.0269:0:1.8 -9 16243162 . T A 27 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGGGTGTCTATAAAATT;RSEQ=TTTTTTTTATTACTCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:4:1:29:1:1:0:60:4:1:0:2 1/1:2:2:2,0:0,0:1:0,0:26:1:27:1:1:0:60:4:1:0:1.5 -9 16243229 . G C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCTGAGTCCTACCAGATT;RSEQ=TTCTGCCCTCACACCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1:0,2:25.8:1:31.7:1:1:0:60:20:1:0:1.2 1/1:5:5:4,1:0,0:1:0,2:28:1:30.6:1:1:0:60:10:1:0:1.2 -9 16243286 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48889;SOR=0;LSEQ=AGGCACGGCCCCCTCCACTG;RSEQ=CAGCCACTGTCTGGACGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:0.087:2,2:34.5:1:31:1:1:1.09544:60:4:0.087:0:1 0/0:23:0:0,0:12,11:0:2,0:32.3:1:32.1:1:1:0:60:46:1:0:0.4 -9 16243289 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=CACGGCCCCCTCCACTGCCA;RSEQ=CCACTGTCTGGACGCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:29.5:1:32.5:1:1:0:60:44:1:0:0.4 0/1:23:2:1,1:11,10:0.087:2,2:30.5:1:30:1:1:1.09544:60:4:0.087:0:1.5 -9 16243361 . A C 75 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00137;SOR=Inf;LSEQ=GACATCACAGCCCAGGCTCA;RSEQ=TTCAAAAGTGGCAGGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:0:2,0:24.3:1:31.9:1:1:0:60:20:1:0:0.1 1/1:6:5:1,4:0,1:0.8333:0,2:21.2:1:32.4:1:1:0:60:10:0.8333:0:1 -9 16245046 . A C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCAACCTAACAGCATTC;RSEQ=ACAGACAAAGAACAAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:28.5:1:1:0:60:4:1:0:2 -9 18994588 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCGGCAGGGAAGTATGTT;RSEQ=AATGTTTTGAAGGTGCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24:1:29:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 18994973 . T C 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.78441;SOR=1.29408;LSEQ=TGTGCAATGTTTAACTTTAT;RSEQ=AAATATGTCAAGGTTGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:17:17,0:9,0:0.6538:0,1:20.5:1:31.6:1:1:0:60:34:0.6538:0:1.1 1/0:38:27:27,0:11,0:0.7105:0,1:20.9:1:31.9:1:1:0:60:54:0.7105:0:1 -9 18995032 . T A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03266;SOR=Inf;LSEQ=AAGAGACTGAGTTTTTCTTT;RSEQ=TGAAATGCACAAAATAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:86,5:0:2,0:24.1:1:30.7:1:1:0:60:182:1:0:0.2 0/1:109:6:6,0:96,7:0.055:2,0:18.2:1:27.3:1:1:0:60:12:0.055:0:1 -9 18995150 . C A 231 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.00173;SOR=0.67616;LSEQ=TCTCCCTCCCTTTTCTCCCC;RSEQ=CAAAAATACCTTTGGGGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:466:245:117,128:111,110:0.5258:2,2:26.8:1:29.7:1:0.64282:1.10373:60:490:0.5258:0:1.1 0/1:621:266:127,139:171,184:0.4283:2,2:24.9:1:28.8:1:0.93543:1.01714:60:52.2:0.4293:0:1.1 -9 18995323 . C T 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09801;LSEQ=GCTGGCATCAGCCAGTCTCA;RSEQ=TTGTGGGATAATTAATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:14:1,13:1,21:0.3889:1,1:25.3:1:31.1:1:1:1.59:60:28:0.3889:0:1 0/1:17:7:0,7:0,10:0.4118:0,0:19:1:30:1:1:0:60:14:0.4118:0:1.1 -9 20776649 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50016;SOR=Inf;LSEQ=TTTTCATTTTTGCCTTCATA;RSEQ=TTTAAGTTCCATCCACTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:110,29:0:2,0:23.4:1:31:1:1:0:60:278:1:0:0.1 0/1:157:2:1,1:114,41:0.0127:2,2:38.5:1:30.5:1:0.46472:2.75921:60:4:0.0128:0:0 -9 20776658 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50109;SOR=Inf;LSEQ=TTGCCTTCATACTTTTAAGT;RSEQ=CCATCCACTTAAAAATACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:118,37:0:2,0:25.1:1:30.1:1:1:0:60:76.5:1:0:0.1 0/1:179:2:1,1:128,49:0.0112:2,2:8.5:1:26:1:0.48177:2.59608:60:4:0.0112:0:2 -9 20776743 . A C 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00243;SOR=1.90157;LSEQ=AGTAATAGCTTGTGTGAAAA;RSEQ=GGCTTTCCAATAATAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:36:20,16:181,163:0.0942:2,2:25.5:1:31:1:0.86101:1.13:60:72:0.0945:0:1.1 0/1:478:79:42,37:209,189:0.1653:2,2:26.5:1:29.6:1:1:1.03:60:38.5:0.1628:0:1.2 -9 20776791 . T C 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13465;SOR=Inf;LSEQ=AGCAGTGCTTTTCTTTGTTG;RSEQ=TGATCGTTTTGGAATCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:112,190:0:2,0:26.1:1:30.2:1:1:0:60:150:1:0:0.2 0/1:384:4:2,2:158,221:0.0104:2,2:23.3:1:31.5:1:1:1.40:60:8:0.0104:0:1.3 -9 20777008 . A G 75 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGACTGTATTTCAAAACA;RSEQ=TGAACACATATATTCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:13.2:1:32.4:1:1:0:60:10:0.8333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 20781865 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25396;SOR=Inf;LSEQ=GAAGAAGGTCCCTCTAGGCA;RSEQ=CAGTTGGCTCTAAACCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:101,30:0:2,0:22.2:1:31.9:1:1:0:60:130:1:0:0.1 0/1:158:3:1,2:121,34:0.019:2,2:7.3:1:27:1:0.13024:7.00189:60:6:0.0192:0:1 -9 20781866 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50378;SOR=Inf;LSEQ=AAGAAGGTCCCTCTAGGCAG;RSEQ=AGTTGGCTCTAAACCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:103,30:0:2,0:22.3:1:31.7:1:1:0:60:65.5:1:0:0.1 0/1:164:2:0,2:123,39:0.0122:2,0:14.5:1:26.5:1:0.06135:0:60:4:0.0123:0:1 -9 20781872 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20809;SOR=0;LSEQ=GTCCCTCTAGGCAGCAGTTG;RSEQ=CTCTAAACCTTTTGGAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:112,38:0.013:2,2:22:1:28.5:1:0.44859:2.92209:60:4:0.0132:0:1 0/0:183:0:0,0:135,47:0:2,0:20.7:1:30.9:1:1:0:60:59.667:0.9944:0:0.1 -9 20781979 . C A 163 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=17.48096;LSEQ=AAAGTGTCGATGTGGGATTT;RSEQ=GGTCTTTACGGATAATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:2:2,0:211,216:0.0047:2,0:1:0:23:0:0.24593:0:60:4:0.0047:0:1 0/1:673:51:24,27:312,306:0.0758:2,2:26.1:1:28.8:1:0.66438:1.14682:60:24.5:0.0749:0:1.1 -9 20782100 . T C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.97689;LSEQ=TGGACTATAAGAAGGGATAG;RSEQ=AGTCCTGTTGTGAAATAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:4:0,4:5,84:0.043:2,0:31.8:1:30.8:1:1:0:60:8:0.043:0:1 1/0:89:50:2,48:1,38:0.5618:1,1:25.6:1:32.6:1:1:1.58:60:100:0.5618:0:1.1 -9 20782260 . G A 74 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTTTTAAAATTATACT;RSEQ=TTAGTTAAGTACAGCATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:26.2:1:32.2:1:1:0:60:10:1:0:1 1/1:1:1:0,1:0,0:1:0,0:45:0:30:0:1:0:60:2:1:0:1 -9 21636636 . T TAC 26 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=38;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGCCAGAAAGTAAAGAAT;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:25:1:26.5:1:1:1.73:60:4:0.5:0.2:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 21638439 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49891;SOR=Inf;LSEQ=GCCGGACCCTTCGTCATTAC;RSEQ=AGAAACTGACTGAGCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:144,30:0:2,0:23.2:1:30.8:1:1:0:60:23.857:1:0:0.1 0/1:183:2:1,1:145,36:0.0109:2,2:27.5:1:28.5:1:0.36438:3.98665:60:4:0.011:0:1 -9 21638592 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.93786;LSEQ=TGGTGGGTTTGTTTGAAGGT;RSEQ=CTAACGTGTGTGCCATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:300:151:78,73:86,63:0.5033:2,2:22:1:29.1:1:0.29923:1.27652:60:302:0.5067:0:1 1/1:335:268:133,135:31,34:0.8:2,2:25.3:1:28.5:1:0.78424:1.08:60:267:0.8042:0:1.1 -9 21638732 . T G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79829;SOR=0.79807;LSEQ=AGTGAAGGCAGATTTTATGG;RSEQ=ATTTTGTAATAAAGTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:10:2,8:1,73:0.119:1,2:27.5:1:28.8:1:0.03621:16.99:60:9:0.1169:0:1.7 0/1:72:7:1,6:3,61:0.0972:1,2:20.6:1:29.3:1:0.34608:3.30:60:6:0.0909:0:2.1 -9 21968199 . C G 245 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACTGATGATCTAAGTTTCC;RSEQ=GAGGTTTCTCAGAGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:232:232:115,117:0,0:1:0,2:27.5:1:27.7:1:1:0:60:7:1:0:1.4 1/1:623:505:244,261:61,52:0.8106:2,2:25.1:1:27.3:1:0.29872:1.25434:60:7.559:0.7964:0:1.4 -9 21968225 . C T 41 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.16002;SOR=0.2813;LSEQ=TTCTCAGAGCCTCTCTGGTT;RSEQ=TTTCAATCGGGGATGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:2,1:110,144:0.0117:2,2:8.3:1:26:1:0.58183:2.61:60:2:0.0085:0:1.7 0/0:605:2:2,0:275,328:0.0033:2,0:7:1:13.5:1:0.20922:0:60:0:0:0:4.5 -9 21968318 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09651;SOR=0;LSEQ=ACATCCCGCCCTCCTCTCTT;RSEQ=CCGTCCCTACCGGCATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:23,74:0.0198:2,2:24.5:1:29:1:0.42795:3.17:60:4:0.0208:0:1 0/0:223:0:0,0:54,169:0:2,0:24.5:1:31.3:1:1:0:60:36.167:1:0:0.2 -9 21968335 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTGCCGTCCCTACCGGCAT;RSEQ=GAAATACTTATGGATAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:14,57:0:2,0:28.1:1:30.3:1:1:0:60:70:0.9859:0:0.2 0/1:149:2:1,1:27,120:0.0134:2,2:12.5:1:32:0:0.34156:4.38:60:4:0.0139:0:1 -9 21968646 . C T 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23321;SOR=0.22686;LSEQ=GGCATCTTTTGCACCTGGTG;RSEQ=GGAGTGAGCCAGCCAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:90,26:0.0168:2,2:36.5:1:30:1:0.40678:3.41555:60:4:0.0169:0:1 0/0:260:1:0,1:188,71:0.0038:2,0:1:0:26:0:0.27692:0:60:2:0.0039:0:1 -9 21968658 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09431;SOR=0;LSEQ=ACCTGGTGCGGAGTGAGCCA;RSEQ=CCAGCTTGCGATAACCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:2,0:101,38:0.0142:2,0:11:1:32:0:1:0:60:4:0.0145:0:1 0/0:317:0:0,0:217,100:0:2,0:25.2:1:31.4:1:1:0:60:34.222:1:0:0.1 -9 21968877 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GTTCGGTTCTCCCGAGGCAG;RSEQ=ATTTACACTTGAGAGTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:5,78:0:2,0:25:1:31.8:1:1:0:60:82:1:0:0.1 0/1:180:2:1,1:15,163:0.0111:2,2:19.5:1:27.5:1:0.17033:10.55:60:4:0.0111:0:1 -9 21970916 . C T 149 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=19.71604;LSEQ=CTCACCTGAGGGACCTTCCG;RSEQ=GGCATCTATGCGGGCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:1:0,1:251,231:0.0021:2,0:1:0:29:0:0.48033:0:60:2:0.0021:0:1 0/1:968:38:22,16:498,432:0.0393:2,2:28.4:1:28.4:1:0.62287:1.19:60:18:0.0377:0:1.1 -9 21971125 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09515;SOR=0;LSEQ=CGTCGTGCACGGGTCGGGTG;RSEQ=GAGTGGCGGGGTCGGCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:81,115:0.0101:2,2:23.5:1:29.5:1:1:1.42:60:4:0.0104:0:1 0/0:445:0:0,0:194,251:0:2,0:23.4:1:29.6:1:1:0:60:48.444:1:0:0.3 -9 21971145 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10364;SOR=0;LSEQ=AGAGTGGCGGGGTCGGCGCA;RSEQ=TTGGGCTCCGCGCCGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:72,96:0.0118:2,2:5.5:1:28.5:1:1:1.33:60:4:0.0128:0:1.5 0/0:357:0:0,0:154,202:0:2,0:23.5:1:29.6:1:1:0:60:11.714:1:0:0.3 -9 21971227 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11446;SOR=0;LSEQ=CCTGCCAGAGAGAACAGAAT;RSEQ=GTCAGAGCCAGGGTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:31,58:0.022:2,2:24.5:1:30:1:1:1.86:60:4:0.0227:0:1.5 0/0:177:0:0,0:61,116:0:2,0:24.4:1:30.4:1:1:0:60:58:1:0:0.1 -9 21974218 . A G 34 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=AATAATTTCGATCAAAATTT;RSEQ=TATTCGATATTTATTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:28:1:28.3:1:1:0:60:6:1:0:0.3 1/1:2:2:2,0:0,0:1:0,0:18.5:1:34:0:1:0:60:4:1:0:1 -9 21974374 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51412;SOR=Inf;LSEQ=CCTTTTTATCCCAAACGTTC;RSEQ=TAAATTTTGTATCTGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:108,0:0:1,0:22.7:1:29.8:1:1:0:60:26:1:0:0.1 0/1:155:2:2,0:152,1:0.0129:1,0:27.5:1:30:1:1:0:60:4:0.0131:0:1.5 -9 21974855 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54831;SOR=Inf;LSEQ=CCGCCGCCCGCTGCCTGCTC;RSEQ=CCCCCTCTCCGCAGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:47,56:0:2,0:23.9:1:29.8:1:1:0:60:16.167:1:0:0.1 0/1:198:2:1,1:83,113:0.0101:2,2:14.5:1:29:1:1:1.36:60:4:0.0105:0:1.5 -9 21975017 . C T 71 d7;v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00794;SOR=Inf;LSEQ=CTTTCCAGGCAAGGGGACGC;RSEQ=GTGAGCGAGTGCTCGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:0:0,0:21.8:1:31.5:1:1:0:60:8:1:0:0 1/1:5:5:0,5:0,0:1:0,0:24.2:1:31:1:1:0:60:10:1:0:1 -9 21993964 . T C 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGGGAGGTCCAGGTTCAA;RSEQ=GGTACTGCGAGAACCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:39:39,0:39,0:0.5:1,1:21.8:1:31.2:1:1:0:60:12:0.48:0:1.2 0/0:65:0:0,0:65,0:0:1,0:18.3:1:30.3:1:1:0:60:64:1:0:0.1 -9 21994030 . TCTC T 69 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.06386;SOR=Inf;LSEQ=GAAGCCTCCACCGGCGGTTA;RSEQ=CTCCTCCTCCTAGCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:257,41:0:2,0:24.7:1:31.4:1:1:0:60:98.333:1:0:0.1 0/1:338:5:4,1:289,43:0.0148:2,2:27.2:1:29.8:1:0.50542:1.67713:60:10:0.0149:0.0059:0 -9 21994368 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24927;SOR=Inf;LSEQ=GGCCGAGCTCGGCAGCCGCT;RSEQ=CGCCGCCCTTTGGCACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:60,173:0:2,0:26.5:1:31.9:1:1:0:60:45.6:0.9956:0:0.1 0/1:250:3:2,1:63,184:0.012:2,2:10.7:1:23:1:0.16653:5.79:60:2:0.0082:0:3.7 -9 22003223 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTGATAAGTTACTATTT;RSEQ=AATACAACCAGGTGGTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:31.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 22003367 . G A 40 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGTTTCCCTTAATATCA;RSEQ=GTTGTCATTAGGAAAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:30.3:1:25.3:1:1:0:60:2:0.6667:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 22003749 . TG T 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.17879;SOR=1.79562;LSEQ=TTGGGTTTTTATAGGTGTGT;RSEQ=GGGGGGGTTATTCTCCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:8:3,5:191,311:0.0157:2,2:33.4:1:31.9:1:1:1.02353:60:16:0.0159:0:0.3 0/1:720:20:7,13:292,406:0.0278:2,2:30.9:1:31.1:1:0.64853:1.33515:60:40:0.0282:0.0014:0.2 -9 22003803 . C A 61 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05232;SOR=0;LSEQ=AAAATAGTTTTCAAACAAAC;RSEQ=GTTTATATTTACTAGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:4:1,3:37,153:0.0206:2,2:23:1:30.8:1:0.58507:1.38:60:8:0.0211:0:1 0/0:210:0:0,0:42,168:0:2,0:23.3:1:29.7:1:1:0:60:209:1:0:0.1 -9 22003878 . C CT 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.21026;SOR=Inf;LSEQ=GAGATCATTGTGTATTTCTG;RSEQ=TTTTTTTTAAAAAAAGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:1,48:0:1,0:19.9:1:32.5:1:1:0:60:98:1:0:0.1 0/1:42:2:0,2:1,39:0.0476:1,0:34.5:1:27:1:1:0:60:4:0.0513:0:0 -9 22005882 . G A 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2483;SOR=Inf;LSEQ=ACAGGCTTGCAGGCTTACAG;RSEQ=CTTTCCGCCGCTCCCCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:176,13:0:2,0:27.8:1:30.9:1:1:0:60:36.8:1:0:0.1 0/1:196:3:3,0:184,9:0.0153:1,0:29.7:1:25.3:1:1:0:60:2:0.0107:0:1.3 -9 22006266 . G A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24853;SOR=0;LSEQ=CCTGCCAGAGAGAGCAGAGT;RSEQ=GTCAGAGCCAGGGTGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:1,2:56,196:0.0118:2,2:30:1:25.3:1:0.53346:1.75:60:2:0.008:0:1 0/0:254:0:0,0:71,183:0:2,0:24.3:1:30.4:1:1:0:60:253:1:0:0.2 -9 22006273 . G T 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGAGAGCAGAGTGGTCAGA;RSEQ=CCAGGGTGGGGGCAGGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:49,183:0:2,0:28.4:1:32.2:1:1:0:60:76.333:1:0:0.1 0/1:220:25:6,19:54,141:0.1136:2,2:31.3:1:28.6:1:0.81426:1.21172:60:24:0.1111:0:1 -9 22006348 . C T 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05264;SOR=Inf;LSEQ=TTTAAAGAAACACCTAATTG;RSEQ=AAAGTTTTCACCCAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:0,56:0:1,0:25.3:1:32.2:1:1:0:60:17.667:1:0:0.2 0/1:53:4:0,4:1,48:0.0755:1,0:24:1:29:1:1:0:60:8:0.0769:0:1.3 -9 22008026 . G T 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4958;SOR=0;LSEQ=AAAGTACAAAAGAGTTGTCC;RSEQ=AGATTGTAAAAGAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:15,0:0,0:1:0,1:14.9:1:30.9:1:1:0:60:30:1:0:1.1 1/1:20:18:17,1:2,0:0.9:0,1:26.7:1:31.6:1:1:0:60:36:0.9:0:1.1 -9 22008143 . G T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2507;SOR=Inf;LSEQ=ATTATTTATGAAGATCCTTT;RSEQ=CCATTCAAAAAGGACCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:155,67:0:2,0:23.1:1:31.8:1:1:0:60:54.5:1:0:0.1 0/1:248:3:1,2:176,69:0.0121:2,2:9.7:1:24.3:1:0.19789:5.06257:60:2:0.0082:0:1.7 -9 22008380 . TA T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24321;SOR=0;LSEQ=CATATAGTAGCTTAGAAGTT;RSEQ=CATTGATTTTTTCCATGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:31,166:0.0101:2,2:23.5:1:30.5:1:0.29643:5.29:60:4:0.0101:0:0 0/0:204:0:0,0:39,165:0:2,0:24.1:1:29.3:1:1:0:60:203:1:0:0.1 -9 22008660 . C T 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.63273;SOR=2.41173;LSEQ=GGGTAAAAGCCTGTTTTACG;RSEQ=GTGGAATGCACACCTCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:0,1:146,69:0.0046:2,0:1:0:25:0:0.32407:0:60:2:0.0047:0:1 0/1:270:3:1,2:167,99:0.0111:2,2:28.3:1:24:1:0.55836:3.35797:60:2:0.0077:0:1.7 -9 22009031 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50259;SOR=Inf;LSEQ=GACACTCTTCCCTTCTTTCC;RSEQ=ACGCTGCTCCGGCGCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:6,77:0:2,0:21.4:1:32.5:1:1:0:60:166:1:0:0.1 0/1:102:2:1,1:10,90:0.0196:2,2:32.5:1:29:1:0.20501:8.63:60:4:0.02:0:1 -9 22011642 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTATAATTATTTTTCA;RSEQ=TCTACACTGTGTTTTCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:30:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 22012051 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10719;LSEQ=CTAGTAATAATATTTTTATA;RSEQ=TCTAGTTGGTGAAATTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:166:73,93:142,169:0.348:2,2:24:1:31.6:1:0.77219:1.07026:60:82:0.346:0:1.1 0/1:611:33:15,18:264,313:0.054:2,2:24.9:1:31.9:1:1:1.01212:60:66:0.0545:0:1.1 -9 22012135 . C A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11047;SOR=0;LSEQ=CTTTTTCTTCAGCGAGGCAG;RSEQ=CGAGCTGCAGACACAGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:3:3,0:60,163:0.0132:2,0:6.3:1:22.7:1:0.02092:0:60:2:0.009:0:1.3 0/0:245:0:0,0:82,163:0:2,0:23.4:1:30.6:1:1:0:60:39.833:1:0:0.1 -9 22012151 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4995;SOR=Inf;LSEQ=GCAGCCGAGCTGCAGACACA;RSEQ=AGATGCAGATCTTTGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:30,132:0:2,0:23.2:1:31.3:1:1:0:60:80:1:0:0.1 0/1:177:2:1,1:41,133:0.0113:2,2:11:1:26:1:0.42136:3.22:60:4:0.0115:0:1 -9 22440456 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19087;SOR=0;LSEQ=ATCAGGTTTCCTACAGGAAA;RSEQ=GCTTCTCAAATCAGACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:43,23:0.0294:2,2:14:0:33:0:1:1.85143:60:4:0.0299:0:1.5 0/0:87:0:0,0:55,32:0:2,0:29.3:1:30.1:1:1:0:60:174:1:0:0.1 -9 22440462 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49878;SOR=Inf;LSEQ=TTTCCTACAGGAAAAGCTTC;RSEQ=CAAATCAGACAATGCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:51,29:0:2,0:25.7:1:29.7:1:1:0:59.2:19:1:0:0.4 0/1:90:2:1,1:54,34:0.0222:2,2:28:1:29:1:1:1.57976:60:4:0.0227:0:1 -9 22440463 . CA GG 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66524;SOR=0.57527;LSEQ=TTCCTACAGGAAAAGCTTCT;RSEQ=AATCAGACAATGCCTTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:3:2,1:50,30:0.0361:2,2:8:1:32.9:1:1:1.20:29:6:0.037:0.012:6 0/1:95:2:1,1:56,37:0.0211:2,2:4.5:1:27.9:1:1:1.5067:47:6:0.016:0.0241:6.5 -9 22440475 . TG AA 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.58669;SOR=0.69404;LSEQ=AAGCTTCTCAAATCAGACAA;RSEQ=CCTTTCAAACTCTTATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:8:4,4:59,38:0.0762:2,2:13.5:1:30.6:1:0.7106:1.5459:37.3:16:0.0769:0:4.4 0/1:111:6:3,3:60,45:0.0541:2,2:7.3:1:29.7:1:1:1.32982:48.3:12:0.0545:0.018:4.5 -9 22440494 . C T 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.35223;SOR=0.60069;LSEQ=ATGCCTTTCAAACTCTTATA;RSEQ=CAACCTCTGGATTTGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:12:6,6:56,51:0.1008:2,2:25.9:1:31:1:1:1.09717:39:24:0.1043:0:4.4 0/1:127:8:4,4:61,58:0.063:2,2:20.9:1:29.4:1:1:1.05133:51.3:16:0.063:0:4.5 -9 22440533 . T C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.91318;LSEQ=AACATGGCTTCTCCCCTTTC;RSEQ=AGGTCCTGTGGCAGCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:10:5,5:29,52:0.1099:2,2:21.3:1:31.8:1:0.49198:1.78:36.8:20:0.1111:0:4.9 0/1:79:8:4,4:29,42:0.1013:2,2:20:1:31.1:1:0.71333:1.44:51.3:16:0.1026:0:4.5 -9 22440535 . G A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95481;LSEQ=CATGGCTTCTCCCCTTTCTA;RSEQ=GTCCTGTGGCAGCCATCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:11:6,5:28,49:0.125:2,2:17.6:1:30.3:1:0.32432:2.08:38.9:22:0.125:0:4.6 0/1:75:9:5,4:26,40:0.12:2,2:16.1:1:30.7:1:0.47529:1.91:49.8:18:0.1216:0:4.1 -9 22440547 . G T 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90582;LSEQ=CCTTTCTAGGTCCTGTGGCA;RSEQ=CCATCTTGCTGTTGCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:8:4,4:24,46:0.1026:2,2:9.3:1:30.9:1:0.44778:1.90:37.8:16:0.1026:0:4.9 0/1:64:6:2,4:20,38:0.0938:2,2:8:1:30:1:1:1.0518:51.8:12:0.0938:0:4.8 -9 23917339 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.48791;SOR=0;LSEQ=CCACGGGACCTAGAAAGGGG;RSEQ=GAAGCCATGTTGCCCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,7:0.1:2,2:33:1:30:1:1:1.53525:53:4:0.1:0:1 0/0:18:0:0,0:10,8:0:2,0:26.8:1:28.3:1:1:0:54.1:17:1:0:0 -9 23917489 . C A 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ACTCTTCCCCTAAGAAGGTG;RSEQ=AGAGTCCTCCTGTCTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:28.5:1:31.5:1:1:0:60:4:1:0:1.5 0/1:5:1:0,1:1,3:0.2:2,0:38:0:26:0:1:0:60:2:0.2:0:1 -9 24646774 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCTTCCAATCCATGGGTT;RSEQ=CACAGTCCCTTGGTAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:27.4:1:32.4:1:1:0:60:40:1:0:0.1 0/1:48:2:1,1:24,22:0.0417:2,2:42.5:1:28:1:1:1.08892:60:4:0.0417:0:1 -9 25247018 . C T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55304;SOR=0.31382;LSEQ=TAGGGGAAGAGTGTTGTTTT;RSEQ=ACACTAACCAGTCAGGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:23:21,2:0,0:0.9583:0,2:18.1:1:30.5:1:1:0:51.4:46:0.9583:0:1.3 1/1:16:14:12,2:1,1:0.875:2,2:28.1:1:30.1:1:0.35:5.10:51.6:28:0.9333:0:1.4 -9 25247090 . T C 158 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03437;SOR=2.20438;LSEQ=AGGCTTCTGAAATCAGACAA;RSEQ=GCCTTTCAAACTCTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:19:14,5:24,17:0.3167:2,2:23.5:1:31.6:1:0.38842:1.96:50.4:38:0.3276:0:1.4 1/0:73:37:20,17:19,17:0.5068:2,2:22.5:1:30.4:1:1:1.05:48.2:74:0.5068:0:1.3 -9 25247125 . G A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07992;SOR=0.55097;LSEQ=TATACCAACCTCTGGAGTTG;RSEQ=GCAACATGGCTTTTCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:37:18,19:14,16:0.5441:2,2:31.2:1:29.7:1:1:1.08:58.9:17.5:0.5303:0:1.1 0/1:96:38:17,21:30,28:0.3958:2,2:28.7:1:29.8:1:0.53704:1.31965:59:76:0.3958:0:1.1 -9 25247133 . G A 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.04215;SOR=Inf;LSEQ=CCTCTGGAGTTGGGCAACAT;RSEQ=GCTTTTCCCCTTTCTAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:28,37:0:2,0:30.2:1:31.2:1:1:0:57.1:130:1:0:0.9 0/1:96:7:3,4:44,45:0.0729:2,2:26.4:1:30.3:1:1:1.30012:51.6:14:0.0737:0:2 -9 25247160 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50323;SOR=Inf;LSEQ=CCCCTTTCTAGGTACCATGG;RSEQ=AGCCATCTTGCTGTTACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:22,33:0:2,0:23.6:1:30.3:1:1:0:57.6:12.75:1:0:0.8 0/1:70:2:1,1:27,41:0.0286:2,2:11:1:27:1:1:1.51:46.5:4:0.0286:0:2 -9 25247195 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49499;SOR=Inf;LSEQ=TACTCACCTTTGGGCCCTGT;RSEQ=TTTTTAACCTTCTTGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:1,25:0:1,0:23.6:1:31.8:1:1:0:55.6:52:1:0:0.6 0/1:31:2:1,1:8,21:0.0645:2,2:25:1:30:1:0.50323:2.53:54.5:4:0.0645:0:1.5 -9 25247234 . G A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22;SOR=0;LSEQ=AATTTGTTTCCTCTAGAATC;RSEQ=AGGCCATCAAGCTACAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1:0,1:23.5:1:30.8:1:1:0:49:26:1:0:1 1/1:12:10:1,9:0,2:0.8333:0,2:25.1:1:31.1:1:1:0:43.8:20:0.8333:0:1.1 -9 26077141 . G T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TTCAGTCAATTTGTCCACCT;RSEQ=ATACACCATTCAGTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:42.3:1:32.7:1:1:0:60:6:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:10.5:1:28.5:1:1:1:60:4:0.5:0:1 -9 26077209 . T C 62 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TTGAAGGAGAAGAGGCACTC;RSEQ=GGCCTTTTGGGTTTTCCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14:1:26.5:1:1:0:60:4:1:0:0 1/0:7:4:2,2:2,1:0.5714:2,2:10.5:1:31.3:1:1:1.81007:60:8:0.5714:0:1.5 -9 26077466 . G C 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0394;SOR=Inf;LSEQ=CTGATTTGCTCCCGTGCCTG;RSEQ=AAATGTTACTCAAGGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:17,25:0:2,0:27.8:1:31.2:1:1:0:60:84:1:0:0.1 0/1:59:7:4,3:24,27:0.1186:2,2:43.7:1:32.4:1:0.70141:1.49:60:14:0.1207:0:1.4 -9 26077627 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1567;SOR=0;LSEQ=CTTACCCAGTTGGGTGGCAC;RSEQ=GGGAGCAGGACGCATTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:0.1818:2,2:43.5:1:31.5:1:1:1.87:60:4:0.1818:0:1 0/0:16:0:0,0:6,10:0:2,0:30.6:1:30.3:1:1:0:60:32:1:0:0.3 -9 26078320 . A G 96 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27273;SOR=0;LSEQ=GGAAAAAGCACAGTTTCCCC;RSEQ=GCTGGGTAGCGTGCTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:31.1:1:30.6:1:1:0:60:14:1:0:1.4 1/0:16:12:5,7:2,2:0.75:2,2:22.8:1:27:1:1:1.3705:60:11:0.7333:0:1.7 -9 26078375 . C T 71 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTCGGGGAATAGGGTTCTCC;RSEQ=TCCCTTTGTGTCTCGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:31:1:29.6:1:1:0:60:10:1:0:1.6 1/1:7:6:0,6:0,1:0.8571:0,0:27.2:1:27.7:1:1:0:60:5:0.8333:0:2.2 -9 27687049 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18367;SOR=0;LSEQ=AAGATCTGTAACTCAGGATG;RSEQ=TATTCCAGAACTTGAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:60,9:0.0282:2,2:21.5:1:32:1:0.26358:6.37705:60:4:0.0286:0:2 0/0:94:0:0,0:73,21:0:2,0:23.2:1:29.8:1:1:0:60:93:1:0:0 -9 27687125 . TA T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25658;SOR=Inf;LSEQ=CTTACATTATTTCAGATTTT;RSEQ=AAATGAGAAGAGGGAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:133,87:0:2,0:25.4:1:28.8:1:1:0:60:109:1:0:0.6 0/1:271:3:2,1:160,108:0.0111:2,2:16:1:27.7:1:1:1.35:60:6:0.0112:0.0074:2 -9 27687133 . G T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09868;SOR=0;LSEQ=ATTTCAGATTTTTAAAATGA;RSEQ=AAGAGGGAAAATAGAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:2,1:149,99:0.012:2,2:18.7:1:30.3:1:1:1.33:60:6:0.0123:0:1.3 0/0:291:0:0,0:164,127:0:2,0:24.9:1:31.1:1:1:0:60:96:1:0:0.8 -9 27687159 . A G 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00152;SOR=1.68112;LSEQ=GGAAAATAGAGGATGAAACT;RSEQ=TTGGGACTGATGCTTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:322:194:101,93:72,55:0.6025:2,2:25.1:1:32:1:0.42541:1.20469:60:96:0.6019:0:1.1 1/0:355:255:139,116:49,50:0.7183:2,2:25.5:1:31.1:1:0.40856:1.22:60:62.75:0.7213:0:1.2 -9 27687197 . A C 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00114;SOR=Inf;LSEQ=GGATTTTCCCATGCTTTCGT;RSEQ=TTTATGAAGCCAAGTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:137,164:0:2,0:26.6:1:29.5:1:1:0:60:74.25:1:0:0.6 0/1:345:11:5,6:148,186:0.0319:2,2:24.8:1:32.3:1:1:1.05:60:22:0.0321:0:2 -9 28385381 . A G 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTTGAAAAGCAAATTCAC;RSEQ=TACAGGTTGATTTTATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:34.5:1:31:1:1:0:60:4:0.4:0:1 1/1:1:1:1,0:0,0:1:0,0:15:0:25:0:1:0:60:2:1:0:2 -9 28385515 . C G 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05743;LSEQ=ATACTGTTATGCTTCATAAT;RSEQ=CTATTTTCTTCTTTCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:44:41,3:32,0:0.5789:1,2:23:1:32.1:1:0.25895:0:60:43:0.5733:0:1.2 1/0:54:32:29,3:21,1:0.5926:1,2:17.8:1:32.6:1:0.63771:2.14409:60:64:0.5926:0:1.2 -9 28385583 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08915;SOR=0;LSEQ=AGAAGGTATATGCAGCTTAG;RSEQ=GAAAATTATGAAGCAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:141,75:0.0137:2,2:23.7:1:24.7:1:0.283:3.73614:60:2:0.0093:0:1.3 0/0:270:0:0,0:160,110:0:2,0:25.8:1:30.4:1:1:0:60:269:1:0:0.7 -9 28385612 . C T 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42646;SOR=1.14894;LSEQ=TGAAGCAGAAGGAAATGGAG;RSEQ=GAACAAAAGATAAATATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:124:65,59:92,67:0.4366:2,2:26.4:1:29.6:1:0.39943:1.2454:60:61:0.4342:0:1.5 0/1:363:171:96,75:99,92:0.4711:2,2:26.6:1:28.6:1:0.45999:1.19:60:84.5:0.4708:0:1.5 -9 28385636 . C T 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAAAGATAAATATTCAAAA;RSEQ=ATAAACTTGCCCTGGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:146,161:0:2,0:25.8:1:32:1:1:0:60:306:1:0:0.7 0/1:405:26:13,13:191,188:0.0642:2,2:23.3:1:28.4:1:1:1.01592:60:52:0.0645:0:1.4 -9 28385672 . A C 229 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01578;SOR=1.48928;LSEQ=AAGTCTCAAATGTACTAAAT;RSEQ=CTCTATGAATTGTGTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:116:52,64:63,95:0.4234:2,2:23.9:1:31.1:1:0.45783:1.22:60:115:0.4212:0:1.8 1/0:356:186:83,103:75,95:0.5225:2,2:25.9:1:30.5:1:1:1.02:60:36.2:0.5216:0:1.7 -9 28385738 . C G 224 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00532;SOR=0;LSEQ=GGAAAAATATATGTGCATGT;RSEQ=CTTCATTAGCATACCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:115:115:36,79:0,0:1:0,2:23:1:32.3:1:1:0:60:230:1:0:1.3 1/1:146:137:35,102:4,4:0.9384:2,2:24.3:1:31.6:1:0.21124:2.8889:60:67.5:0.9375:0:1.4 -9 28966193 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21752;SOR=0;LSEQ=TCATCCTGAGAAATTAAGAG;RSEQ=CTGAAAAAACTGGCTAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:92,21:0.0174:2,2:37.5:1:29.5:1:0.34737:4.30343:60:4:0.0179:0:1 0/0:131:0:0,0:100,31:0:2,0:23.4:1:30.7:1:1:0:60:42.667:1:0:1.3 -9 28966206 . G A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=5.20131;LSEQ=TTAAGAGGCTGAAAAAACTG;RSEQ=CTAATGTCTGAAAAGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:56:39,17:76,18:0.3733:2,2:26.1:1:30.3:1:0.16176:1.8327:60:112:0.3836:0:2 1/0:177:134:98,36:29,14:0.7571:2,2:22.5:1:29.1:1:0.55951:1.31:60:133:0.7557:0:1.9 -9 28966263 . G A 249 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04617;LSEQ=AAGAGAGGTTGAGAAGCAGG;RSEQ=TAAGAATCGAGGCCTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:347:344:192,152:1,2:0.9914:2,2:26.3:1:30.3:1:0.58669:2.52:60:171:0.9942:0:1.4 1/1:446:375:206,169:38,33:0.8408:2,2:27.2:1:29.2:1:0.8967:1.06:60:124:0.8416:0:1.9 -9 28966298 . T G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.98409;LSEQ=TCTTTACCTTTGAAGAACTA;RSEQ=GAACAAACGGTTAGAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:89:46,43:120,133:0.2602:2,2:24.4:1:31.2:1:0.53818:1.19:60:88:0.2619:0:1.9 1/0:476:278:133,145:93,105:0.584:2,2:25.2:1:30.5:1:0.85292:1.04:60:91.667:0.5839:0:1.8 -9 28966306 . C T 180 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGAAGAACTATGAACAAA;RSEQ=GGTTAGAGAATCACACAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:152,168:0:2,0:25.1:1:30.6:1:1:0:60:63:1:0:1.1 0/1:467:68:32,36:182,216:0.1456:2,2:27.4:1:29.7:1:0.89549:1.05:60:33:0.1438:0:1.1 -9 28966324 . GTAA G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=3.44325;LSEQ=AACGGTTAGAGAATCACACA;RSEQ=TAATTAGTAGCACTATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:68:29,39:80,116:0.2556:2,2:27.4:1:31.8:1:0.88643:1.08:60:136:0.2595:0.0263:1.3 1/0:378:205:77,128:68,104:0.5423:2,2:26:1:30.6:1:0.75004:1.08667:60:204:0.544:0.0688:1.4 -9 28966416 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18765;SOR=Inf;LSEQ=TTTATCTATTATAAACTGTA;RSEQ=GTCAACTTTGTCAGGTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:2,68:0:1,0:21.1:1:29.8:1:1:0:60:140:1:0:0.3 0/1:54:2:1,1:4,48:0.037:2,2:27.5:1:27:1:0.1782:10.84:60:4:0.04:0:1.5 -9 28966455 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=12.98123;LSEQ=GCAGTGGATATTTTTTTTCC;RSEQ=GATAAAGCAAGGTTGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:17:0,17:0,23:0.425:1,1:28.9:1:32.6:1:1:0:60:34:0.425:0:1 1/1:22:20:2,18:0,2:0.9091:0,2:31.4:1:30.1:1:1:0:60:40:0.9091:0:1.2 -9 28966554 . C T 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=ATTATGTGAAATATGTAGTA;RSEQ=TATTACTCCTATCTTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:23.7:1:28:1:1:0:60:6:0.5:0:1 1/1:2:2:0,2:0,0:1:0,0:27:1:31.5:1:1:0:60:4:1:0:1.5 -9 28966575 . T A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTACTCCTATCTTATGCA;RSEQ=GAACACACAAGTATATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:30:1:31:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:0,1:0:0,0:13:0:32:0:1:0:60:2:1:0:1 -9 31112822 . T C 242 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.72246;LSEQ=TTTGCATTAATATTCTGCTA;RSEQ=AGATATTATACTTATGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:152:151:94,57:0,0:0.9934:0,2:25.3:1:31.9:1:1:0:60:150:1:0:1.8 1/1:220:218:140,78:1,1:0.9909:2,2:24:1:31.2:1:1:1.79:59.9:217:0.9909:0:1.4 -9 31112836 . A T 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.66475;LSEQ=CTGCTATAGATATTATACTT;RSEQ=TGTCCAAGGCAAAAATCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:102,70:0.0115:2,2:39:1:30.5:1:1:1.45389:60:4:0.0118:0:3 0/0:261:2:0,2:151,108:0.0077:2,0:1:0:26.5:1:0.17669:0:60:4:0.0077:0:1.5 -9 31112857 . A G 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=TGTCCAAGGCAAAAATCATC;RSEQ=TAAAGATGCAATAAATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:214:214:113,101:0,0:1:0,2:24.9:1:30.3:1:1:0:60:41.8:1:0:1.6 0/1:301:120:66,54:102,77:0.3987:2,2:27.1:1:30.3:1:0.81212:1.08353:60:240:0.4013:0:1.6 -9 31114520 . T G 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGCAATTTCACACCTTG;RSEQ=CATTTACCCAAATGAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46:0:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 32890348 . G A 75 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00365;SOR=34.68841;LSEQ=AGTGTTGAAAGTGACGGTAG;RSEQ=AAAATTATAATGTCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:9,0:0.1:0,0:9:0:31:0:1:0:60:2:0.1:0:1 1/1:7:6:6,0:1,0:0.8571:0,0:29:1:29.2:1:1:0:60:12:0.8571:0:1 -9 32890471 . A TTTT 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=59.5315;LSEQ=GAGCATGGTGCTTGACAGTC;RSEQ=TACATTGGTACTCTCTAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:16:10,6:82,22:0.1333:2,2:20.3:1:30:1:0.2015:2.2191:60:32:0.1345:0.0417:1 1/1:84:76:55,21:10,0:0.9048:0,2:20.4:1:29.7:1:0.10996:0:59.9:152:0.9048:0.2619:1 -9 32890555 . G T 94 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=GGAATAATGTGCTATTCTTT;RSEQ=TACACTAAGATGGTGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:155,142:0:2,0:25.9:1:32:1:1:0:60:73.25:1:0:0.2 0/1:284:10:3,7:144,129:0.0352:2,2:25.3:1:28.5:1:0.20371:2.59623:60:9:0.0318:0:1 -9 32890588 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=17.40406;LSEQ=GTGCTACTAATCTTATATGC;RSEQ=TTTAGCCATATATAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:28:15,13:106,119:0.1107:2,2:30.8:1:30.4:1:0.55246:1.29:60:27:0.108:0:1.1 1/0:264:181:84,97:41,42:0.6856:2,2:25.2:1:29.9:1:0.69144:1.12675:60:362:0.6856:0:1.1 -9 32890699 . T G 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00095;SOR=Inf;LSEQ=CTAAATGGTAGCAAATTACT;RSEQ=CCTTGATGTGGTACAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:9,68:0:2,0:28.3:1:29.3:1:1:0:60:14.4:1:0:0.1 0/1:70:9:3,6:13,48:0.1286:2,2:21.2:1:30.1:1:0.41723:1.83:60:8:0.1194:0:1.2 -9 32890733 . C T 109 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=21.46761;LSEQ=CAGGAATATTCACTGCATAG;RSEQ=ACAGTTGAGGAAAAAGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:0,39:0.0488:1,0:5:1:28.5:1:1:0:60:4:0.05:0:1 1/0:26:14:0,14:0,12:0.5385:0,1:23.6:1:28.7:1:1:0:60:28:0.5385:0:1.1 -9 32890815 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=TGACAGCCATCAGGAATCCA;RSEQ=TGATACAGTCTTTCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:16.7:1:28:1:1:0:60:6:1:0:0 0/1:5:2:0,2:0,3:0.4:0,0:11.5:1:31.5:1:1:0:60:4:0.4:0:1.5 -9 33675364 . TA T 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.34331;SOR=0.4666;LSEQ=ACACAATGTCCTATTGCCAT;RSEQ=AAAAAAAAGGTCCCTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:7:7,0:165,11:0.0383:2,0:24.3:1:31.5:1:1:0:59.6:14:0.0391:0.0109:0.1 0/1:165:3:3,0:142,20:0.0182:2,0:22.7:1:32:0:1:0:60:6:0.0185:0:0 -9 33675427 . T TA 152 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=7.49717;LSEQ=TGGTGTTTTATCCCTCTTGA;RSEQ=AAAAAAAAATTCAGACTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:6:2,4:280,160:0.0134:2,2:34.3:1:28.9:1:0.1987:3.48974:48.3:12:0.0138:0.0022:0 0/1:453:42:24,18:248,163:0.0927:2,2:31.5:1:28.3:1:0.74172:1.14076:41.6:84:0.0938:0.0044:0.1 -9 33675629 . A C 221 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=159.20946;LSEQ=GAAGTACAGCTTCACCTTAA;RSEQ=ATTTGGAGAAAAGTATCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1090:1:1,0:477,606:9e-04:2,0:36:0:13:0:0.44096:0:60:0:0:0:2 0/1:1073:137:64,73:419,516:0.1277:2,2:24.6:1:31.2:1:0.71335:1.08:57.1:274:0.1295:0:1.1 -9 33676027 . C A 193 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGAGGATTGCAAGTTCCG;RSEQ=CACTGAACATTGGAATAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:209,233:0:2,0:24.2:1:31.2:1:1:0:59.7:43.2:1:0:0.1 0/1:427:103:52,51:156,168:0.2412:2,2:23:1:29:1:0.73456:1.10:59.5:102:0.2506:0:1.1 -9 33676094 . C G 196 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCCACTGGTCTATAATCCA;RSEQ=ATGATTCTTTACCAGGTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:245,246:0:2,0:28.1:1:31.9:1:1:0:59.6:48.1:1:0:0.1 0/1:516:77:40,37:226,213:0.1492:2,2:29.2:1:31.4:1:1:1.02:50.7:76:0.1493:0:1.1 -9 33676157 . C A 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02818;SOR=Inf;LSEQ=CTGACTGGGAATAGTTACTC;RSEQ=CTTTTTGTCTCTGGTCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:219,230:0:2,0:23.8:1:30.8:1:1:0:59.6:43.9:1:0:0.1 0/1:433:5:3,2:205,223:0.0115:2,2:18.4:1:29.8:1:0.67462:1.63:60:10:0.0116:0:1 -9 33676618 . C T 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTGATATCTCCTTTTGTTT;RSEQ=TGCTAACGATCTCTTTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:28:11,17:164,245:0.0639:2,2:27.8:1:30.2:1:1:1.03443:53.6:56:0.0648:0:1 0/0:543:0:0,0:244,298:0:2,0:18:0:18:0:1:0:49:0:0:0:1 -9 33676700 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18877;SOR=0;LSEQ=GGAGAGAGATGGCAGAAGCT;RSEQ=CTGGTGGCGGGGCTCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:39,117:0.0127:2,2:26:1:27.5:1:0.44344:2.97:54.5:4:0.0128:0:1 0/0:205:0:0,0:49,156:0:2,0:25:1:31.7:1:1:0:56.7:204:1:0:0.1 -9 33677007 . TGCC T 52 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=9.000;MSILEN=3;SSF=0.14286;SOR=0;LSEQ=CCGGCCCGGGTCCCTCCATG;RSEQ=GCCGCCGCCGCCGCCGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,1:0.75:0,0:20.7:1:33.3:1:0.25:0:60:6:0.75:0:0 0/0:4:0:0,0:2,2:0:2,0:14.5:1:30.8:1:1:0:60:8:1:0:1 -9 35207997 . G A 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTTAATTTTTGTATGTCAT;RSEQ=TGAGGTTTTTGGTTTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:85,2:0:1,0:26:1:32.3:1:1:0:60:174:1:0:0 0/1:94:23:22,1:69,2:0.2447:1,1:22.7:1:26.7:1:1:1.55992:60:10.5:0.2308:0:1.1 -9 35208096 . G A 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGATAACTGTCATTTTTAA;RSEQ=TCTGTGGATAAAAGAGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:0:0,0:250,188:0:2,0:27:1:32:1:1:0:60:218:1:0:0.7 0/1:505:23:13,10:267,214:0.0455:2,2:36:1:30:1:1:1.04:60:46:0.0461:0:1.7 -9 35208145 . T C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24827;LSEQ=CCAACTTGTAAACTCCCCTT;RSEQ=CTGGAACGATACCTCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:569:507:247,260:32,30:0.891:2,2:25.4:1:30.9:1:0.68835:1.12258:60:38:0.8901:0:1.1 1/0:651:436:205,231:99,115:0.6697:2,2:25.5:1:30.9:1:0.86751:1.03:60:108:0.675:0:1.2 -9 36839398 . G T 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCCAGCTGCCTGCTAA;RSEQ=CTCCACGAGGACGGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:38.5:1:26.5:1:1:0:60:4:1:0:2.5 -9 36840623 . G A 283 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00688;LSEQ=CGGGCGGCAGCGCTATAATA;RSEQ=TAGGGGGAGCCTGGAAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:612:611:225,386:0,0:0.9984:0,2:25.6:1:30.6:1:1:0:60:75.375:1:0:1.1 1/1:618:499:189,310:50,68:0.8074:2,2:25:1:29.5:1:0.4009:1.20566:60:98.8:0.8059:0:1.2 -9 36840665 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11095;SOR=Inf;LSEQ=GGGAGAGAGCACCGAGGTCA;RSEQ=ATCCGGGGTCCCCTTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:63,257:0:2,0:24.3:1:31.5:1:1:0:60:79:1:0:0.9 0/1:297:3:1,2:66,227:0.0101:2,2:7.3:1:23:1:0.53833:1.72:60:2:0.0069:0:3 -9 36840727 . C G 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05817;SOR=Inf;LSEQ=TTTCCTCCCCTCACTCAGTC;RSEQ=GGGCCACCATCCTCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:1,97:0:1,0:22.4:1:29.9:1:1:0:60:97:1:0:0.1 0/1:63:3:0,3:3,57:0.0476:2,0:15.7:1:29:1:1:0:60:6:0.0492:0:1 -9 36841160 . A G 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTGAATTCATTTCCCTC;RSEQ=GGGAAGGCCCCTCCTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:27.5:1:29:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:0,1:0:0,0:29:0:32:0:1:0:60:2:1:0:0 -9 36846990 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18423;SOR=Inf;LSEQ=ATCCAGTTCAGAAAAGGCCC;RSEQ=GGGTCCCAGCCAGCCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:46,205:0:2,0:22.3:1:30.1:1:1:0:60:82.667:0.996:0:0.1 0/1:190:2:1,1:38,149:0.0105:2,2:24.5:1:27.5:1:0.37099:3.88:60:4:0.0108:0:1 -9 36847139 . G A 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCCCCTCCTTATCAGTG;RSEQ=GAGTGAATGGCAGACTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:1:0,1:22.4:1:31.2:1:1:0:60:13:1:0:1 1/1:3:3:0,3:0,0:1:0,0:25:1:26:1:1:0:60:2:1:0:2 -9 36848347 . C CCACACACACACA 26 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=22.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAACCACAGGCAGAGCGTGT;RSEQ=CACACACACACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:26.7:1:1:0:60:4:1:1:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 36848386 . C T 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACACACACACACATGCTCG;RSEQ=GCTCCTCCTCGGGCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 36880489 . A T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCATGGGAGAGTGGGCA;RSEQ=GGCTTCAGCAGGGCTAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:31:0:1:0:60:4:1:0:1.5 -9 36881866 . T C 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00261;SOR=Inf;LSEQ=GCAGGCCCAGCTGCAGAGAG;RSEQ=GCAGACCTCTGCCTGATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:56,1:0:1,0:20.9:1:29.9:1:1:0:60:114:1:0:0.1 0/1:27:5:5,0:22,0:0.1852:1,0:17.2:1:31.8:1:1:0:60:10:0.1852:0:1.2 -9 36881930 . T TG 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.08325;SOR=0;LSEQ=TAGAGGTCACCCAGGCTGTT;RSEQ=GGGGGGGGATGTCCCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:5:4,1:159,20:0.027:2,2:20:1:30:1:0.45831:1.97811:60:10:0.0278:0:0 0/0:126:0:0,0:103,23:0:2,0:23.6:1:29.7:1:1:0:60:62:1:0:0.1 -9 36881956 . C T 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25758;SOR=0;LSEQ=GGGATGTCCCCCCACCGAAA;RSEQ=CCCGTCCGCTGCCTGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:1,2:241,50:0.0102:2,2:7:1:21.3:1:0.08182:9.52714:60:2:0.0069:0:3 0/0:236:0:0,0:179,57:0:2,0:22.9:1:31.1:1:1:0:60:235:1:0:0.1 -9 36881985 . G T 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02232;SOR=Inf;LSEQ=CTGCCTGCTGTGGAGACGCC;RSEQ=ACAGTGCAAACTCACCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:499:0:0,0:356,143:0:2,0:22.7:1:29.5:1:1:0:60:37.385:1:0:0.2 0/1:440:5:2,3:295,140:0.0114:2,2:7.8:1:23.2:1:0.33512:3.15159:60:4:0.0092:0:1.2 -9 36882141 . T C 130 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=20.44526;LSEQ=AAATCACAGGGTGAGCATCT;RSEQ=CGCGGCCAGCCGCTCATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:622:1:0,1:220,401:0.0016:2,0:43:0:30:0:1:0:60:2:0.0016:0:2 0/1:658:21:10,11:240,395:0.0319:2,2:26.2:1:29.6:1:0.36966:1.50:60:20:0.0309:0:1.4 -9 36882292 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13732;SOR=Inf;LSEQ=CACACACACACACACACACA;RSEQ=TCATGCACACACATCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:0,45:0:1,0:23.3:1:32.2:1:1:0:60:21.5:1:0:0.4 0/1:27:2:1,1:2,22:0.0741:2,2:37.5:1:31:1:0.22154:9.18:60:4:0.0741:0:1 -9 36922960 . T A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGATTCTGCCTGCCAACA;RSEQ=CAATCTGCAAGGAATCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9.5:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 36923303 . ATC A 110 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.07563;SOR=0.34744;LSEQ=TCTTCCCACCACACACTCCT;RSEQ=TCTCTCTCTCTCCCTCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:12:8,4:254,77:0.035:2,2:17.5:1:30.9:1:0.48783:1.64666:60:24:0.0351:0.0087:0.3 0/1:322:4:3,1:234,83:0.0124:2,2:24.5:1:30.4:1:1:1.06:60:8:0.0125:0.0031:0 -9 36923529 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23529;SOR=Inf;LSEQ=CACCAAGACTCCACAGTACC;RSEQ=TAGTCAAATGCCAACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:23,158:0:2,0:22.7:1:29.6:1:1:0:60:35.2:1:0:0.1 0/1:171:2:1,1:22,147:0.0117:2,2:30:1:30:1:0.2516:6.56:60:4:0.0118:0:1 -9 36923608 . G A 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11507;SOR=Inf;LSEQ=TGTGCCAAGGCCCACAAGGG;RSEQ=CTCATGAACACTTCCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:0,38:0:1,0:25.8:1:32.5:1:1:0:60:76:1:0:0.1 0/1:38:4:1,3:1,33:0.1053:1,2:25.5:1:28.8:1:0.20199:9.67:60:8:0.1081:0:1 -9 36924719 . A AAAAG 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGAGCAAGACTCTGTCAAAA;RSEQ=AAAGAAAGAGGTGGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:31:0:32:0:1:0:60:2:1:0:1 1/1:2:2:2,0:0,0:1:0,0:26.5:1:29.4:1:1:0:60:4:1:0.5:0 -9 36930460 . T G 94 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGAACTGCTGAGCTCAA;RSEQ=TGATCCACCCACCCCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1:0,0:25.3:1:31.6:1:1:0:58.8:16:1:0:1.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 36930536 . T G 68 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGCCCTTAGTTCATTT;RSEQ=TATCTGCATCATTGATAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:22.5:1:34:0:1:0:60:8:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 36930973 . G C 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.069;SOR=0.65076;LSEQ=TGGAGGAGAAAAGAAACACA;RSEQ=ACACGTGAGAAGGAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:535:50:17,33:149,335:0.0935:2,2:25.4:1:32.1:1:0.63313:1.16:60:49:0.0937:0:1.1 0/1:541:34:13,21:177,330:0.0628:2,2:21.2:1:30.1:1:0.71273:1.15:58.9:33:0.0627:0:1.3 -9 36931239 . A G 64 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGGGTGAGAGGTGTCTCCAG;RSEQ=GCCTGGCTCCAGCGACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,0:0.8:0,0:14.5:1:32.3:1:1:0:60:8:0.8:0:1 1/1:1:1:0,1:0,0:1:0,0:22:0:32:0:1:0:60:2:1:0:1 -9 36966379 . A G 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09365;SOR=2.25285;LSEQ=AGACAAGCCCTCCCGACCTT;RSEQ=TAGGATGTAGCGACTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:37:36,1:27,1:0.5692:1,1:20.9:1:31.9:1:1:1.33:60:36:0.5625:0:1 1/0:40:30:26,4:10,0:0.75:0,2:26.2:1:32.3:1:0.55575:0:60:60:0.75:0:1.1 -9 36966501 . G A 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00219;SOR=Inf;LSEQ=TTCAGGAACCTGGCTGGGCC;RSEQ=GTGTGGCGGTGGCAGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:512:0:0,0:340,172:0:2,0:23.5:1:29.7:1:1:0:60:55.889:1:0:0.2 0/1:578:10:6,4:369,199:0.0173:2,2:28.8:1:29.5:1:0.74666:1.23569:60:20:0.0176:0:1 -9 37001471 . T A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACAGCACCGCAGCCTAC;RSEQ=GAGTTAAAGACGTCTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:48:0:31:1:1:1.7321:60:4:0.4:0:1 -9 37002439 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47826;SOR=Inf;LSEQ=GGGGAGGCCAGCAAGAATGC;RSEQ=ACAGTCTCACCCTGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:0:0,0:28.8:1:30.3:1:1:0:60:11:1:0:0.3 0/1:12:2:2,0:9,1:0.1667:2,0:34.5:1:32.5:1:1:0:60:4:0.1818:0:1 -9 37002556 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22064;SOR=Inf;LSEQ=TGCAGGTAAGGGGGGTGTTC;RSEQ=CGGGCACCTCTGCTGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:122,5:0:1,0:26.3:1:29.7:1:1:0:60:41.333:1:0:0.1 0/1:113:2:2,0:106,5:0.0177:1,0:24.5:1:28.5:1:1:0:60:4:0.018:0:1 -9 37002577 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49947;SOR=0;LSEQ=CGGGCACCTCTGCTGCCACC;RSEQ=GCGACCGAGCGCCGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:157,33:0.0104:2,2:20:1:31.5:1:0.32357:4.70203:60:4:0.0105:0:1 0/0:177:0:0,0:146,31:0:2,0:23.9:1:29.5:1:1:0:60:58:1:0:0.1 -9 37002596 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10428;SOR=Inf;LSEQ=CCGCGACCGAGCGCCGGAAA;RSEQ=AGACCCCGTGGAGCGCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:218,80:0:2,0:22.1:1:31.6:1:1:0:60:73.5:1:0:0.1 0/1:266:3:2,1:195,68:0.0113:2,2:19:1:29:1:1:1.43173:60:6:0.0114:0:1 -9 37006208 . A AT 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTATAGACCCCCATTAGTGG;RSEQ=TTTTTTTTTGGCTTAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:38:1:30.5:1:1:0:60:4:1:0:0.5 1/0:4:2:2,0:2,0:0.5:0,0:23:1:31.5:1:1:0:60:4:0.5:0:0 -9 37006359 . G A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16452;SOR=Inf;LSEQ=CAAAGAAGGCGCATTAGTAC;RSEQ=TGTGCTGAAGTGTTTTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:73,1:0:1,0:22.6:1:29.6:1:1:0:60:36:1:0:0.3 0/1:51:2:2,0:47,2:0.0392:1,0:10.5:1:32:0:1:0:60:4:0.0392:0:1 -9 37006455 . A T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06546;SOR=Inf;LSEQ=TAGATTTTTAAATTTTTTTT;RSEQ=AAAGTTCCTCTTACCTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:253,142:0:2,0:22.1:1:28.6:1:1:0:60:64.833:0.9949:0:0.1 0/1:463:5:1,4:287,171:0.0108:2,2:6.8:1:24.8:1:0.07011:6.68699:60:10:0.0109:0:1.6 -9 37006544 . G A 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12535;SOR=5.64556;LSEQ=TCCGGATGATCCTGTGGGCA;RSEQ=TTGAAAAACAAAATTGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:1:0,1:212,325:0.0019:2,0:42:0:16:0:1:0:60:0:0:0:1 0/1:576:6:5,1:236,333:0.0104:2,2:6.7:1:27.2:1:0.0873:7.03:60:12:0.0105:0:1.2 -9 37015450 . G A 88 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATAATTTTGATATTAGTT;RSEQ=TATGTTGAAATAACAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:21.5:1:29.4:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 37020622 . A C 223 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59334;SOR=0.92133;LSEQ=ATCAAGGGAAGCCTCGAGCT;RSEQ=CTGCCTTTACCTGCCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:142:109,33:128,53:0.4396:2,2:25.8:1:31.2:1:0.25431:1.37:60:46.333:0.4344:0:1.1 0/1:379:159:113,46:148,71:0.4195:2,2:25.7:1:30.5:1:0.50011:1.18:60:38.75:0.4167:0:1.1 -9 37020950 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14413;SOR=Inf;LSEQ=GTCCAATCGTGCAAACTACA;RSEQ=GAAGTCCCCAGATTGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:0,58:0:1,0:18.9:1:28.7:1:1:0:60:13.5:1:0:0.2 0/1:36:2:0,2:0,34:0.0556:1,0:30.5:1:27.5:1:1:0:60:4:0.0556:0:1 -9 37033693 . A G 75 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATACATATACTGTAATGA;RSEQ=CACACTGAGTCCCTTATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:21.6:1:32.4:1:1:0:60:10:1:0:1.4 1/1:1:1:1,0:0,0:1:0,0:10:0:33:0:1:0:60:2:1:0:1 -9 37034085 . CT C 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.2192;SOR=0;LSEQ=AAGTTTCCACTTTTTTGTGC;RSEQ=TTTTTTTTCTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:23,118:0.0139:2,2:14:0:29.5:1:0.30848:5.04:60:4:0.0149:0:0 0/0:163:0:0,0:49,113:0:2,0:15.4:1:28.1:1:1:0:57:11.462:1:0:0.8 -9 37034095 . C T 130 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=28.000;MSILEN=1;SSF=0.17609;SOR=1.57128;LSEQ=TTTTTTGTGCCTTTTTTTTT;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:23:1,22:19,60:0.2212:2,1:14.4:1:22.9:1:0.03889:6.87973:46:1.556:0.1842:0:2.4 0/1:123:38:0,38:37,46:0.3089:2,1:14.8:1:24.8:1:0:0:44.7:2.8:0.2887:0:3.1 -9 37205328 . CA C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.48908;SOR=Inf;LSEQ=TAGCTTCACGTGTATGTGGC;RSEQ=AAAGAACAACTCTTTTCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:27.4:1:29:1:1:0:60:15:1:0:0.3 0/1:19:2:1,1:8,9:0.1053:2,2:15:1:28:1:1:1.12:60:4:0.1111:0:0.5 -9 37206287 . T C 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGGCTTTCTCCCTCCCT;RSEQ=CCCCCTTCCCCCTCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:17.5:1:28:1:1:0:60:4:0.6667:0:1.5 -9 37490422 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTTAAACACCTGTCAC;RSEQ=CCATGAATTCATAGGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 37490577 . C G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54545;SOR=0.28445;LSEQ=TTCTAATCATCTTTCTTCAC;RSEQ=CGTTTCATGAAGCTTTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:7.7:1:29.3:1:1:0:60:6:0.75:0:2 0/1:7:3:2,1:3,1:0.4286:2,2:15:1:30.3:1:1:1.41418:60:6:0.4286:0:1 -9 37490620 . T A 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13725;SOR=0;LSEQ=TCTTAGAGTGCTTAATGTGC;RSEQ=CAATACGCACACTAATTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:41:0:31.5:1:1:3.1622:60:4:0.2857:0:2.5 0/0:11:0:0,0:7,4:0:2,0:27.4:1:30:1:1:0:60:22:1:0:0.4 -9 37490814 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49231;SOR=Inf;LSEQ=TTCACATATATGTGGCCAAA;RSEQ=GAACAACTCCATGTTTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:14,18:0:2,0:27.8:1:32.1:1:1:0:60:64:1:0:0.4 0/1:33:2:1,1:16,15:0.0606:2,2:25:1:28.5:1:1:1.06462:60:4:0.0625:0:1 -9 37490859 . G A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09046;SOR=0.28788;LSEQ=GTCTAGAGAACATATATTGG;RSEQ=TGCCTCTCCTCTTTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:2,6:2,6:0.5:2,2:23.1:1:30.9:1:1:1:60:16:0.5:0:2.5 0/1:23:5:2,3:7,10:0.2174:2,2:21:1:28.2:1:1:1.04769:60:10:0.2381:0:2 -9 37490862 . C A 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08148;SOR=0.26063;LSEQ=TAGAGAACATATATTGGGTG;RSEQ=CTCTCCTCTTTCCCTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:2,6:2,6:0.5:2,2:23.1:1:30.3:1:1:1:60:16:0.5:0:2.5 0/1:20:4:2,2:6,10:0.2:2,2:24.3:1:27.8:1:1:1.62:60:8:0.2105:0:2.3 -9 37490930 . G T 77 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08788;SOR=0.08176;LSEQ=ATGGCAGTTCTGGCCGAAAG;RSEQ=GTTCTTTCTTAATTCTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:2,4:0,1:0.8571:0,2:18.8:1:30:1:1:0:60:12:0.8571:0:2.3 0/1:4:1:0,1:1,2:0.25:2,0:4:0:30:0:1:0:60:2:0.25:0:3 -9 66455952 . T C 72 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCACCCCGGAGCCGCTTGCC;RSEQ=GTGGCCGGGCTGCTCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:0,0:0.8571:0,2:19.3:1:28.2:1:1:0:40.7:12:0.8571:0:2.8 1/1:1:1:1,0:0,0:1:0,0:1:0:31:0:1:0:46:2:1:0:7 -9 66455961 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCGCTTGCCTGTGGCCGG;RSEQ=CTGCTCTCCCCCTCTACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:5.5:1:30.5:1:1:1.29098:36:4:0.25:0:5 0/0:3:0:0,0:3,0:0:0,0:5.7:1:31.7:1:1:0:44.3:6:1:0:6 -9 66455978 . C G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.66417;LSEQ=CGGGCTGCTCTCCCCCTCTA;RSEQ=GCCCAAGCACCACCATCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:30.5:1:32.5:1:1:1.29098:25:4:0.2222:0:4 0/1:3:1:1,0:2,0:0.3333:0,0:27:0:34:0:1:0:46:2:0.3333:0:7 -9 66455985 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCCCCTCTACGCCCAA;RSEQ=CACCACCATCGCCGCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:36:0:31.5:1:1:1:25:4:0.2857:0:4 0/0:3:0:0,0:3,0:0:0,0:29.7:1:33.7:1:1:0:44.3:6:1:0:6 -9 66455993 . A AG 100 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01818;SOR=0;LSEQ=CTCTACGCCCAAGCACCACC;RSEQ=TCGCCGCGCTGCGCTTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1:0,2:28.8:1:33.4:1:1:0:36.1:16:1:0.125:4.8 0/1:4:1:1,0:0,0:0.25:0,0:43:0:32:0:1:0:46:2:0.25:0:7 -9 66456006 . G T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=0;LSEQ=CACCACCATCGCCGCGCTGC;RSEQ=CTTTCCGCCGACCTCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:38.5:1:32.5:1:1:1.29:36:4:0.25:0:5 0/0:5:0:0,0:4,1:0:2,0:30.2:1:30:1:1:0:40.6:10:1:0:5.6 -9 66456015 . C T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.48718;SOR=0;LSEQ=CGCCGCGCTGCGCTTTCCGC;RSEQ=GACCTCCCAGAGCGTCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:31:1:32.5:1:1:1.83:36:4:0.25:0:5 0/0:5:0:0,0:4,1:0:2,0:29:1:29.8:1:1:0:40.6:10:1:0:5.6 -9 66456016 . G A 63 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1049;SOR=0;LSEQ=GCCGCGCTGCGCTTTCCGCC;RSEQ=ACCTCCCAGAGCGTCCCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:1,3:0.5:2,2:11.8:1:31.5:1:1:2.60:26:8:0.5:0:5 0/0:5:0:0,0:3,1:0:2,0:29.8:1:29.5:1:1:0:44:8:0.8:0:5 -9 66456029 . G A 47 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=0.28445;LSEQ=TTCCGCCGACCTCCCAGAGC;RSEQ=TCCCGATGTCGCCGGCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:1,2:0.5:2,2:14.7:1:30:1:1:1:33:6:0.5:0:6 0/1:5:1:1,0:3,1:0.2:2,0:22:0:25:0:1:0:46:2:0.2:0:7 -9 66456035 . A C 74 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8165;LSEQ=CGACCTCCCAGAGCGTCCCG;RSEQ=TGTCGCCGGCGGCCAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:0,1:0.8333:0,2:24.2:1:32:1:1:0:31.6:10:0.8333:0:6 1/1:5:4:3,1:1,0:0.8:0,2:21.3:1:31.3:1:1:0:44:8:0.8:0:6.5 -9 66456056 . T C 59 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=TGTCGCCGGCGGCCAGACCA;RSEQ=GCGCGAGACAGCCCAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:28.8:1:29.8:1:1:0:27:8:0.8:0:6.5 1/0:4:2:1,1:1,1:0.5:2,2:19:1:29:1:1:1:51.5:4:0.5:0:5.5 -9 66456061 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10714;SOR=Inf;LSEQ=CCGGCGGCCAGACCATGCGC;RSEQ=AGACAGCCCAGGCGCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:28:1:29.4:1:1:0:29.6:10:1:0:4.4 1/0:3:2:1,1:0,1:0.6667:0,2:26.5:1:30.5:1:1:0:27:4:0.6667:0:2.5 -9 66456066 . A C 46 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=GGCCAGACCATGCGCGAGAC;RSEQ=GCCCAGGCGCCAGAGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:34.3:1:29.3:1:1:1.7321:27:6:0.6:0:6.7 0/1:3:1:0,1:1,1:0.3333:2,0:26:0:32:0:1:0:43:2:0.3333:0:7 -9 66456070 . C G 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=AGACCATGCGCGAGACAGCC;RSEQ=AGGCGCCAGAGACCTCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:24:1:29.5:1:1:1:27:4:0.4:0:6 0/0:3:0:0,0:1,1:0:2,0:26.5:1:30:1:1:0:27:4:0.6667:0:2.5 -9 66456082 . A G 73 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGCCCAGGCGCCAGAG;RSEQ=CCTCCATCCCCTGCCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:27:1:31.8:1:1:0:29.6:10:1:0:4.4 1/1:3:3:1,2:0,0:1:0,2:21:1:31.3:1:1:0:32.3:6:1:0:4 -9 66456199 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACCTGGGGCCCGCTTAGGA;RSEQ=GGGGTGTGCTCCGAGGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:39:1:31:1:1:0:37.5:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:8:0:32:1:1:0:47:4:1:0:6.5 -9 66456217 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GACGGGGTGTGCTCCGAGGC;RSEQ=TCAGGGCCCAGGGCCCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27.5:1:31.3:1:1:0:44.3:8:1:0:0.8 1/1:2:2:1,1:0,0:1:0,2:26:0:32:0:1:0:47:4:1:0:6.5 -9 66456236 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CGTCAGGGCCCAGGGCCCAC;RSEQ=GTCCTGGGGTCCCCTCCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27.8:1:26:1:1:0:44.3:3:1:0:0.8 1/1:2:2:1,1:0,0:1:0,2:45:0:31.5:1:1:0:47:4:1:0:6.5 -9 66456271 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCGGTCCTCCGCCTTGCCG;RSEQ=GGAAAAATTATTTTGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:18:0:33.5:1:1:0:51:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:27.5:1:1:0:47:4:1:0:6.5 -9 66456276 . A C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCTCCGCCTTGCCGCGGAA;RSEQ=AATTATTTTGGATTCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13:0:31.5:1:1:0:51:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:29.5:1:1:0:47:4:1:0:6.5 -9 66456426 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCATCGTCGCTTGTTCTGA;RSEQ=GAGGACCCGCCATGGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14.5:1:30:1:1:0:60:4:1:0:0 1/1:2:2:2,0:0,0:1:0,0:24.5:1:31:1:1:0:46.5:4:1:0:4 -9 66456474 . CC TG 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGCTCTGCTTTGCCCCG;RSEQ=CTGGCACTAGAGCCCCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:16:0:32.8:1:1:1:48:4:0.3333:0:2.5 0/0:1:0:0,0:1,0:0:0,0:49:0:31:0:1:0:60:2:1:0:1 -9 66456478 . G A 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTGCTTTGCCCCGCCCT;RSEQ=GCACTAGAGCCCCGGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:19:0:31:1:1:1:48:4:0.3333:0:2.5 0/0:2:0:0,0:1,1:0:2,0:23:1:28.5:1:1:0:46.5:4:1:0:3.5 -9 66456565 . C A 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACTACCACGAGCAAACCCAC;RSEQ=CTGACACACCCACGGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:42.5:1:31:1:1:0:39:4:0.6667:0:4.5 0/0:2:0:0,0:0,2:0:0,0:28:1:32.5:1:1:0:36.5:4:1:0:4.5 -9 66456575 . C A 48 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAACCCACCCTGACACAC;RSEQ=CACGGATACACACGGGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:23.7:1:30.7:1:1:0:42.3:6:1:0:3.3 1/1:1:1:0,1:0,0:1:0,0:36:0:32:0:1:0:40:2:1:0:4 -9 66456589 . G A 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACACCCACGGATACACAC;RSEQ=GGTGCATGCGCGCAGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18.5:1:32.5:1:1:0:39:4:0.6667:0:4.5 0/0:1:0:0,0:0,1:0:0,0:22:0:32:0:1:0:40:2:1:0:4 -9 66456594 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACGGATACACACGGGTG;RSEQ=ATGCGCGCAGACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:13.5:1:31:1:1:0:39:4:0.6667:0:4.5 0/0:1:0:0,0:0,1:0:0,0:17:0:34:0:1:0:40:2:1:0:4 -9 66456775 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATCCACAGGCAGACAGCCC;RSEQ=GCGCCACACCCTGGGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29.5:1:1:0:25:4:1:0:1.5 -9 66457019 . G A 49 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACAGGAATTGCTCACTC;RSEQ=GAGAGCTTGGTTTTTGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:3,0:1,1:0.6:2,0:22.7:1:31:1:0.4:0:54:6:0.6:0:3 -9 66457063 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTCTGCGGATGCTCCCAG;RSEQ=TGAATAAAGCCCTTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:17:0:34:0:1:0:60:2:1:0:7 0/1:6:2:1,1:3,1:0.3333:2,2:29.5:1:30.5:1:1:2.44949:60:4:0.3333:0:1 -9 66457076 . T C 48 d7;v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03333;SOR=0;LSEQ=CTCCCAGCTGAATAAAGCCC;RSEQ=TCCTTCTACAACTCGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:14:1:30.7:1:1:0:60:6:1:0:6.7 0/1:7:1:1,0:4,2:0.1429:2,0:33:0:27:0:1:0:42:2:0.1429:0:7 -9 66457110 . C G 33 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=CGGTGTCTGAGGGGTTCTGT;RSEQ=TGCAGCTCCTCCTGCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:40.5:1:33:1:1:0:60:4:0.6667:0:7 0/0:5:0:0,0:3,2:0:2,0:23:1:33:1:1:0:53.4:10:1:0:0.8 -9 66457112 . G A 45 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01786;SOR=0;LSEQ=GTGTCTGAGGGGTTCTGTCT;RSEQ=CAGCTCCTCCTGCTGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:39.7:1:29:1:1:0:60:6:1:0:6.7 0/0:5:0:0,0:3,2:0:2,0:23.4:1:33.4:1:1:0:53.4:10:1:0:0.8 -9 66457127 . GCA ATG 49 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01786;SOR=0;LSEQ=TGTCTGCAGCTCCTCCTGCT;RSEQ=GAAGGAGAGCAAGGGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:32.7:1:31:1:1:0:60:6:1:0:4.7 0/0:5:0:0,0:3,0:0:0,0:27.7:1:32:1:1:0:59:6:0.6:0:0.3 -9 66457151 . G C 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05455;SOR=0;LSEQ=AAGGAGAGCAAGGGAGAGAG;RSEQ=GATGGAGAAATAGAACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:30.5:1:1:0:60:4:1:0:4.5 0/1:9:1:0,1:4,4:0.1111:2,0:4:0:21:0:1:0:40:2:0.125:0:6 -9 66457161 . A G 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGGAGAGAGGGATGGAGAA;RSEQ=TAGAACCAGAGGGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:8:1:29:1:1:0:60:4:1:0:4.5 0/1:9:2:1,1:3,4:0.2222:2,2:29.5:1:30:1:1:1.29:50:4:0.2222:0:1.5 -9 66457173 . GGAGAGAGAGAGACAGCGATAGAGAGA G 30 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGGAGAAATAGAACCAGAG;RSEQ=GAGAGAGAGAGACAGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:0,3:0.2857:0,2:41.5:1:30:1:0.4:0:50:4:0.2857:0:1.5 -9 66457231 . G GAC 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=5.000;MSILEN=2;SSF=0.01786;SOR=0;LSEQ=ACAGAAAAGGGGGGAGGAGA;RSEQ=AGAGAGGGGGGAAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:21.7:1:27.7:1:1:0:45:2:1:0.3333:3 0/0:5:0:0,0:1,4:0:2,0:17:1:32.2:1:1:0:45:10:1:0:2.4 -9 66457253 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=GAGAGGGGGGAAGAGAGAGC;RSEQ=CCACAGTAGAGCGCGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0.75:0,2:31:1:32:1:1:0:53:6:0.75:0:2 1/0:3:2:1,1:0,1:0.6667:0,2:19:0:33:1:1:0:51:4:0.6667:0:1 -9 66457310 . T G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=AAGGGAGAGGGTGAGGGAGT;RSEQ=GTGGAGCGACAGCGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:4.5:1:31:1:1:0:37.5:4:1:0:3.5 1/0:4:2:1,1:0,1:0.5:0,2:27:1:28.5:1:1:0:27:4:0.5:0:5.5 -9 66457313 . G A 42 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAGGGTGAGGGAGTTGT;RSEQ=GAGCGACAGCGACAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:4:0:32:0:1:0:48:2:1:0:3 1/0:4:3:2,1:0,1:0.75:0,2:33.7:1:26.7:1:1:0:27:6:0.75:0:5 -9 66457317 . C T 43 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGTGAGGGAGTTGTGGAG;RSEQ=GACAGCGACAGAGCCTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:0,1:0.75:0,2:34.7:1:27.3:1:1:0:27:6:0.75:0:5 -9 66457324 . G A 40 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGTTGTGGAGCGACAGC;RSEQ=ACAGAGCCTTGGAGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:2:0:28:0:1:0:27:2:1:0:6 1/0:4:3:2,1:0,1:0.75:0,2:32.3:1:25.7:1:1:0:27:6:0.75:0:5 -9 66457388 . T G 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCAGCAGGCCGGGGTG;RSEQ=GGTGGAGGGTTCTTGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:29.3:1:32.3:1:1:0:28.5:8:1:0:5.3 1/1:2:2:0,2:0,0:1:0,0:21:1:31:1:1:0:27:4:1:0:7 -9 66457399 . T G 66 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCCGGGGTGTGGTGGAGGGT;RSEQ=CTTGGGCCGGGCTAGAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:34.8:1:33.3:1:1:0:28.5:8:1:0:5.3 1/0:2:1:0,1:0,0:0.5:0,0:2:0:16:0:1:0:27:0:0:0:7 -9 66457404 . G A 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGGTGGAGGGTTCTTG;RSEQ=GCCGGGCTAGAACAGGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:40:1:32:1:1:1:30:4:0.5:0:6 0/0:1:0:0,0:0,1:0:0,0:45:0:32:0:1:0:27:2:1:0:6 -9 66457423 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCGGGCTAGAACAGGGG;RSEQ=TCAGGGCCCCCCACCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:35:1:28.5:1:1:0:30:4:0.6667:0:6 0/0:1:0:0,0:0,1:0:0,0:37:0:33:0:1:0:27:2:1:0:6 -9 66457440 . A G 28 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGGTCAGGGCCCCCCACCC;RSEQ=GGAAAACCAATGGAGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:18:1:28.5:1:1:0:30:4:0.6667:0:6 1/1:1:1:0,1:0,0:1:0,0:20:0:32:0:1:0:27:2:1:0:6 -9 66457451 . T C 45 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCACCCAGGAAAACCAA;RSEQ=GGAGCCCTGAGACTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:6:1:29:1:1:0:29:6:1:0:5 1/1:1:1:0,1:0,0:1:0,0:9:0:31:0:1:0:27:2:1:0:6 -9 66457513 . A T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTTTGGGGGTGCGTTTCATA;RSEQ=GGTCCTTCCTTTGTTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:27:0:33:0:1:0:59:2:0.5:0:6 1/1:3:3:2,1:0,0:1:0,2:27:1:29:1:1:0:37.3:6:1:0:5 -9 66457549 . A G 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTTCTTTCTGTCTCCTTG;RSEQ=TGCGGTGGGCCCCGAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:33.3:1:32:1:1:0:42:6:0.75:0:4.3 1/1:3:3:2,1:0,0:1:0,2:28.3:1:30:1:1:0:37.3:6:1:0:5 -9 66457553 . GG CA 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCTTTCTGTCTCCTTGATGC;RSEQ=TGGGCCCCGAGATTTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28:0:33:1:1:1:33.5:4:0.5:0:2.5 0/0:3:0:0,0:2,1:0:2,0:25.7:1:29:1:1:0:37.3:6:1:0:5 -9 66457572 . A T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=Inf;LSEQ=CGGTGGGCCCCGAGATTTGT;RSEQ=GAGTGTGCTCGTGTGTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,2:0.25:2,0:15:0:25:0:1:0:59:2:0.25:0:6 1/1:2:2:1,1:0,0:1:0,2:16:1:31.5:1:1:0:40.5:4:1:0:5 -9 66457581 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CCGAGATTTGTAGAGTGTGC;RSEQ=CGTGTGTCTGGCAGGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,2:0.25:2,0:6:0:27:0:1:0:59:2:0.25:0:6 1/1:2:2:1,1:0,0:1:0,2:7:1:31:1:1:0:40.5:4:1:0:5 -9 66457582 . CGTGTGTCTGGCAGGAGCCGTGGCGCCGAGCC GGTTTGCCTGCTGGGAGCAGTGGCACCGAGTG 48 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CGAGATTTGTAGAGTGTGCT;RSEQ=TGTCCACGGGGCGAGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:32.7:1:30.7:1:1:0:35.7:6:1:1:4 0/0:2:0:0,0:1,1:0:2,0:6:1:30.5:1:1:0:40.5:4:1:0:5 -9 66457585 . G T 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATTTGTAGAGTGTGCTCGT;RSEQ=TGTCTGGCAGGAGCCGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5:1:29.5:1:1:0:41.5:4:1:0:4 1/1:1:1:1,0:0,0:1:0,0:8:0:32:0:1:0:50:2:1:0:5 -9 66457646 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GAGGCCTGGGTCTCTCTCCT;RSEQ=TCCTCCGGACTGGAGTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:11.5:1:31.5:1:1:0:43.5:4:0.6667:0:6.5 0/0:2:0:0,0:1,1:0:2,0:14:1:33:0:1:0:47:4:1:0:4 -9 66457652 . C A 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTCTCTCTCCTGTCCTC;RSEQ=GGACTGGAGTTTACACGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:21:1:31.7:1:1:0:42.3:6:1:0:6 1/1:2:2:1,1:0,0:1:0,2:20:1:31:0:1:0:47:4:1:0:4 -9 66457664 . T C 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCCTCCGGACTGGAGTT;RSEQ=ACACGAAGTCGGTGGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:25:1:33.3:1:1:0:42.3:6:1:0:6 1/1:2:2:1,1:0,0:1:0,2:32:1:33:1:1:0:47:4:1:0:4 -9 66457680 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGTTTACACGAAGTCGGTGG;RSEQ=ATTGGGAAACAGGGTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:29:0:1:0:43.5:4:1:0:6.5 0/0:2:0:0,0:1,1:0:2,0:48:1:32:1:1:0:47:4:1:0:4 -9 66457691 . A C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCGGTGGCATTGGGAAAC;RSEQ=GGGTGCACAGGGACGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:1:30:1:1:0:43.5:4:1:0:6.5 1/1:2:2:1,1:0,0:1:0,2:42:1:29.5:1:1:0:47:4:1:0:4 -9 66457925 . A G 34 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48571;SOR=4.4496;LSEQ=CTCAGGGAACCCGCGCCTGC;RSEQ=CCCTCGGGGTCGGTCCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:21:0:32:0:1:0:45:2:0.3333:0:5 1/0:4:3:3,0:1,0:0.75:0,0:15.7:1:22:1:1:0:39.7:2:0.6667:0:5.3 -9 66457947 . C T 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.59207;SOR=3.04364;LSEQ=CCTCGGGGTCGGTCCCGTCC;RSEQ=GCCCGGGTTGGGTGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:2,2:0.3333:2,0:29:1:32.5:1:0.46667:0:39:4:0.3333:0:4 1/0:8:5:5,0:3,0:0.625:0,0:18.4:1:30:1:1:0:39:10:0.625:0:4.6 -9 66457957 . G GGAGCCGGGCTCCT 98 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06347;SOR=8.88906;LSEQ=GGTCCCGTCCCGCCCGGGTT;RSEQ=GGTGGGGCTGCCGCGAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:2,2:0.1667:2,0:26:0:31.4:0:1:0:33:2:0.1667:0:3 1/0:15:10:9,1:3,1:0.6667:2,2:24.3:1:29.6:1:0.50549:2.74:40:20:0.7143:0.4:2.6 -9 66457977 . G A 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05314;SOR=7.67145;LSEQ=GGGTGGGGCTGCCGCGAGTC;RSEQ=GAAGAGGTGGGATGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:11,4:0.0625:2,0:20:0:32:0:1:0:58:2:0.0625:0:4 0/1:20:7:6,1:9,4:0.35:2,2:29.4:1:27:1:0.61262:2.55:43.4:6:0.3158:0:3.9 -9 66457980 . A G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49403;SOR=1.82812;LSEQ=TGGGGCTGCCGCGAGTCGGA;RSEQ=GAGGTGGGATGCTGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:3,1:9,4:0.2353:2,2:17.5:1:32.8:1:1:1.31:44:8:0.25:0:3 0/1:22:8:7,1:9,5:0.3636:2,2:28.3:1:26.9:1:0.35116:3.68:43:7:0.3889:0:3.6 -9 66457986 . G A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3087;SOR=0.24358;LSEQ=TGCCGCGAGTCGGAAGAGGT;RSEQ=GGATGCTGCTGCCTGGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:2,1:11,6:0.15:2,2:16.3:1:29:0:1:1.09:42.7:6:0.15:0:3 0/1:25:1:0,1:17,7:0.04:2,0:29:0:33:0:0.32:0:39:2:0.0435:0:2 -9 66457999 . C A 79 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17473;SOR=0.37495;LSEQ=AAGAGGTGGGATGCTGCTGC;RSEQ=TGGCGGTGCTGCAGTGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:3,3:10,6:0.2727:2,2:28.2:1:30.8:1:0.65502:1.62737:44.2:12:0.2727:0:2 0/1:33:4:2,2:16,13:0.1212:2,2:31.3:1:28.5:1:1:1.223:34.8:8:0.1212:0:1.8 -9 66458013 . G T 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.69122;SOR=0.7139;LSEQ=TGCTGCCTGGCGGTGCTGCA;RSEQ=TGGCGGATCTTCAGGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:1,2:12,10:0.12:2,2:29.3:1:29:1:0.59304:2.31861:47.3:6:0.12:0:3.3 0/1:34:3:2,1:15,16:0.0882:2,2:19.7:1:27.7:1:1:2.09:40.3:6:0.0909:0:2.7 -9 66458014 . T C 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12969;SOR=Inf;LSEQ=GCTGCCTGGCGGTGCTGCAG;RSEQ=GGCGGATCTTCAGGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:25.8:1:29.1:1:1:0:46.9:50:1:0:2.7 0/1:34:4:2,2:15,15:0.1176:2,2:36.3:1:29.3:1:1:1:56.5:8:0.1212:0:2.3 -9 66458019 . G A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16131;SOR=0;LSEQ=CTGGCGGTGCTGCAGTGGCG;RSEQ=ATCTTCAGGAGGAGGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:0.0833:2,2:22:1:28:1:1:1:52.5:4:0.0833:0:5.5 0/0:35:0:0,0:18,17:0:2,0:27.4:1:30.1:1:1:0:47.5:34:1:0:2.9 -9 66458028 . G T 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.14618;SOR=Inf;LSEQ=CTGCAGTGGCGGATCTTCAG;RSEQ=AGGAGGTCCTGGGCTTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:29.9:1:31:1:1:0:47.3:44:1:0:2.9 0/1:34:4:2,2:14,16:0.1176:2,2:32:1:27.5:1:1:1.14:56.5:8:0.1212:0:2.3 -9 66458030 . G C 76 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.28525;SOR=3.02187;LSEQ=GCAGTGGCGGATCTTCAGGA;RSEQ=GAGGTCCTGGGCTTCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,10:0.0909:2,2:22:1:29.5:1:1:1:52.5:4:0.0909:0:5.5 0/1:34:8:3,5:13,13:0.2353:2,2:27.8:1:25.6:1:0.69326:1.64198:45.9:7:0.2188:0:4.8 -9 66458055 . A G 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10973;SOR=0.29351;LSEQ=TCCTGGGCTTCGGCTGGGGC;RSEQ=CGGGGGCGGTCAACGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:14:6,8:1,2:0.8235:2,2:25.8:1:30.9:1:1:1.47:44.1:28:0.8235:0:4.6 1/0:28:16:5,11:5,7:0.5714:2,2:28.4:1:30.4:1:0.69794:1.54582:44.1:15:0.5769:0:4.1 -9 66458058 . G A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.29616;LSEQ=TGGGCTTCGGCTGGGGCACG;RSEQ=GGGCGGTCAACGGGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:5,10:0.0625:2,0:28:0:31:0:0.375:0:33:2:0.0625:0:8 0/1:25:2:1,1:8,15:0.08:2,2:17:1:27.5:1:1:1.83:60:4:0.08:0:1.5 -9 66458061 . G T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63089;SOR=0.59928;LSEQ=GCTTCGGCTGGGGCACGGGG;RSEQ=CGGTCAACGGGGAGCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:4,9:0.1333:2,2:35:1:30.5:1:1:2.12:53:4:0.1333:0:6.5 0/1:24:2:1,1:8,14:0.0833:2,2:29.5:1:29.5:1:1:1.71:52:4:0.0909:0:6 -9 66458063 . G T 54 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68566;SOR=0.55883;LSEQ=TTCGGCTGGGGCACGGGGGC;RSEQ=GTCAACGGGGAGCAGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:2,2:3,8:0.2667:2,2:33:1:31.8:1:0.56044:2.48:44:8:0.2667:0:6.3 0/1:24:4:2,2:7,13:0.1667:2,2:30.8:1:27.3:1:0.61462:1.81:43.3:3:0.1364:0:5.8 -9 66458069 . C G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.46566;SOR=0.44714;LSEQ=TGGGGCACGGGGGCGGTCAA;RSEQ=GGGGAGCAGAGGCGGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:4,8:1,2:0.8:2,2:21:1:32:1:1:1:42.8:24:0.8:0:5.1 1/0:22:14:5,9:2,6:0.6364:2,2:20.7:1:31.3:1:1:1.63:44.1:28:0.6364:0:4.4 -9 66458072 . GGAGCAGAGGCGGGGC G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20168;SOR=0;LSEQ=GGCACGGGGGCGGTCAACGG;RSEQ=GCAGTTGGGAAGCACGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:3,10:0.125:2,0:29:1:31.7:1:1:0:48:4:0.125:0.125:2 0/0:19:0:0,0:6,13:0:2,0:20.8:1:31.7:1:1:0:48.3:38:1:0:3.7 -9 66458081 . G T 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15495;SOR=6.56883;LSEQ=GCGGTCAACGGGGAGCAGAG;RSEQ=CGGGGCGCAGTTGGGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:4,3:0.0909:2,0:26:0:31:0:1:0:47:2:0.1111:0:7 0/1:12:5:1,4:2,5:0.4167:2,2:15.6:1:29.4:1:1:1.53983:43.8:10:0.4167:0:5.2 -9 66458082 . C A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.64041;SOR=0.54823;LSEQ=CGGTCAACGGGGAGCAGAGG;RSEQ=GGGGCGCAGTTGGGAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:3,2:0.2727:2,2:10.3:1:30.3:1:1:2.60168:43.3:6:0.375:0:5.7 0/1:12:2:1,1:2,8:0.1667:2,2:24.5:1:29:1:0.45455:3.46:47:4:0.1667:0:7 -9 66458087 . C G 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32127;SOR=3.68059;LSEQ=AACGGGGAGCAGAGGCGGGG;RSEQ=GCAGTTGGGAAGCACGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:0,0:0.5:0,2:24.5:1:31.5:1:1:0:43:8:0.8:0:7.8 1/1:10:8:3,5:0,2:0.8:0,2:18.3:1:31.4:1:1:0:49.6:16:0.8:0:4.8 -9 66458090 . A G 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84422;LSEQ=GGGGAGCAGAGGCGGGGCGC;RSEQ=GTTGGGAAGCACGGAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:16.3:1:32.3:1:1:1.7321:46.3:6:0.6:0:7.7 1/0:9:5:2,3:1,3:0.5556:2,2:15.2:1:30:1:1:1.85:43.4:10:0.5556:0:6.4 -9 66458123 . A G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GGAGACAAAAGGGGGAAAGA;RSEQ=GGAGGGAGCGGGAAGCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:10:1:30.5:1:1:0:33:4:0.6667:0:7 1/0:3:2:0,2:0,1:0.6667:0,0:29:1:29.5:1:1:0:40:4:0.6667:0:4 -9 66458128 . G A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAAAAGGGGGAAAGAAGGAG;RSEQ=GAGCGGGAAGCCAAAAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:11:0:32:0:1:0:33:2:0.5:0:6 1/0:4:2:0,2:1,1:0.5:2,0:29:1:30.5:1:1:0:40:4:0.5:0:4 -9 66458150 . C T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGCGGGAAGCCAAAAGCCTA;RSEQ=GGTACCGCTATTACCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:18:0:33:0:1:0:27:2:0.3333:0:4 0/1:6:2:1,1:1,3:0.3333:2,2:22:1:27.5:1:1:2.45:43.5:4:0.3333:0:4.5 -9 66458152 . GTACCG TACCAT 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CGGGAAGCCAAAAGCCTACG;RSEQ=CTATTACCAGGCGGAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:21.3:1:32.3:1:1:0:43.7:6:1:0:1.3 0/1:6:2:1,1:1,1:0.3333:2,2:23:0:31.9:1:1:1:45:4:0.3333:0:3.5 -9 66458169 . C T 59 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06993;SOR=Inf;LSEQ=ACGGTACCGCTATTACCAGG;RSEQ=GGAATCCCATCCAAGTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:27.2:1:31.2:1:1:0:41.7:12:1:0:1.3 1/0:7:4:1,3:1,2:0.5714:2,2:33.3:1:29.5:1:1:1.41418:42.5:8:0.5714:0:4.3 -9 66458195 . T G 63 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.28205;SOR=0.18851;LSEQ=CCCATCCAAGTACTAACCAG;RSEQ=CCCGACCCTGCTTAGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:2,1:0.5:2,0:21.3:1:31.5:1:0.14286:0:40:8:0.5:0:1.5 0/1:7:1:1,0:1,1:0.1429:2,0:11:0:32:0:1:0:49:2:0.1429:0:4 -9 66458231 . GC G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21678;SOR=0.11952;LSEQ=CTTCAACAGATCAGAGGCGA;RSEQ=CGGGCGCGTTCAGGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:2,5:0,0:0.875:0,2:22.3:1:32.7:1:1:0:45.6:14:1:0.25:0.9 0/1:5:2:1,1:0,1:0.4:0,2:35:1:34:0:1:0:46.5:4:0.4:0:2.5 -9 66458266 . A G 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24242;SOR=6.06919;LSEQ=GGTGGTGTGGCCTAGACGCC;RSEQ=GCAGCGGCGCCTGGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:1,4:0.1667:2,0:4:0:29:0:0.33333:0:60:2:0.1667:0:4 1/0:5:3:2,1:1,1:0.6:2,2:34.3:1:28:1:1:1.73:48.7:6:0.6:0:3.3 -9 66458329 . T C 79 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCATGACTCCAGGCGTCA;RSEQ=CGCCACCCCGGGGCCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:18.5:1:30.8:1:1:0:55.5:12:1:0:2.8 1/1:5:5:2,3:0,0:1:0,2:24:1:30:1:1:0:51.8:10:1:0:3.8 -9 66458331 . GC CT 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28613;SOR=4.35427;LSEQ=GCATGACTCCAGGCGTCATC;RSEQ=CACCCCGGGGCCGCGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:33:1:30.3:1:1:1.41:60:4:0.2857:0:2.5 1/0:6:4:2,2:0,1:0.6667:0,2:26:1:28.8:1:1:0:58:8:0.6667:0:2.3 -9 66458336 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19231;SOR=0;LSEQ=ACTCCAGGCGTCATCGCCAC;RSEQ=CCGGGGCCGCGGGTCTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:8:1:28:1:1:1:33:4:0.3333:0:5.5 0/0:7:0:0,0:3,4:0:2,0:17.7:1:29.4:1:1:0:50.4:14:1:0:4 -9 66458347 . G T 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CATCGCCACCCCGGGGCCGC;RSEQ=GGTCTCGGATCCAGGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:29.2:1:29.5:1:1:0:51:12:1:0:3 0/1:7:3:1,2:2,2:0.4286:2,2:11.3:1:28.7:1:1:1.81007:44.7:6:0.4286:0:7 -9 66458360 . A G 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30401;LSEQ=GGGCCGCGGGTCTCGGATCC;RSEQ=GGACCCCCAGAGGCGCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:24:1:31.3:1:1:1.81007:31:6:0.4286:0:6 1/0:6:3:1,2:1,2:0.5:2,2:24.3:1:28.7:1:1:1:44.7:6:0.5:0:7 -9 66458375 . GC TG 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06061;SOR=Inf;LSEQ=GATCCAGGACCCCCAGAGGC;RSEQ=TCGCCCGTGCCCCCGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:35:1:32:1:1:0:45.5:12:1:0:3.7 1/0:5:3:1,2:0,2:0.6:0,2:33.3:1:30.5:1:1:0:44.7:6:0.6:0:6 -9 66458382 . C G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55808;SOR=3.3264;LSEQ=GACCCCCAGAGGCGCTCGCC;RSEQ=GTGCCCCCGGGCAGCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,2:0.2857:2,2:43:0:31.5:1:1:1:33:4:0.2857:0:5.5 1/0:5:3:1,2:0,2:0.6:0,2:31.3:1:30.3:1:1:0:44.7:6:0.6:0:6 -9 66458391 . G A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.88578;LSEQ=AGGCGCTCGCCCGTGCCCCC;RSEQ=GGCAGCTGTCTCCCTCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:35.7:1:32.7:1:1:1.81007:31:6:0.4286:0:6 1/0:5:3:1,2:0,2:0.6:0,2:28.3:1:31.3:1:1:0:44.7:6:0.6:0:6 -9 66458418 . G C 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=4.34109;LSEQ=TGTCTCCCTCTACACCCGAG;RSEQ=ACCGCCGGCCTCCCAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:2,1:0.5:2,2:15.3:1:33.7:1:1:3.10575:31:6:0.5:0:6 1/1:6:5:3,2:0,1:0.8333:0,2:17:1:31.6:1:1:0:51.4:10:0.8333:0:5.4 -9 66458423 . C T 60 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00699;SOR=Inf;LSEQ=CCCTCTACACCCGAGGACCG;RSEQ=CGGCCTCCCAGAGAGTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:13.5:1:31.8:1:1:0:49.1:16:1:0:2.6 1/1:5:4:3,1:0,1:0.8:0,2:19:1:30:1:0.4:0:54.3:8:0.8:0:5 -9 66458428 . C T 71 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=TACACCCGAGGACCGCCGGC;RSEQ=TCCCAGAGAGTCCCGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:23.4:1:28.6:1:1:0:53.4:4:1:0:1.8 1/1:6:5:3,2:0,1:0.8333:0,2:20.2:1:30.6:1:1:0:55.4:10:0.8333:0:4.4 -9 66458449 . T A 68 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=TCCCAGAGAGTCCCGCCGTC;RSEQ=CCGGCGGCCAGGCCTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:25.5:1:30.5:1:1:1.7321:43.5:4:0.4:0:4.5 1/1:5:5:3,2:0,0:1:0,2:33.4:1:29.4:1:1:0:55.4:10:1:0:4.4 -9 66458463 . C T 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GCCGTCTCCGGCGGCCAGGC;RSEQ=TGGCTCAGGACCAATGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:29.4:1:30.4:1:1:0:60:10:1:0:0.4 0/1:5:2:1,1:2,1:0.4:2,2:21:0:32.5:1:1:1.7321:60:4:0.4:0:3.5 -9 66458549 . A C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CTGCGCAGGCTTCCGGCTCT;RSEQ=GGGGCGGCCTCCTTTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:2,2:0.3333:2,0:13.5:1:31.5:1:0.46667:0:33:4:0.3333:0:7.5 0/0:3:0:0,0:3,0:0:0,0:15.3:1:29.3:1:1:0:45.7:6:1:0:0.7 -9 66458578 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=CTCCTTTCCGCCCACGCTCC;RSEQ=GTCCTTCCGGGAGCTCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:27:1:31:1:1:1:27:4:0.25:0:6 0/0:6:0:0,0:3,3:0:2,0:21.7:1:29.7:1:1:0:43.5:12:1:0:1.7 -9 66458586 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CGCCCACGCTCCAGTCCTTC;RSEQ=GGGAGCTCCGGAGCTCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:16.8:1:29.6:1:1:0:45.8:18:1:0:3.7 0/1:6:2:1,1:2,2:0.3333:2,2:33:1:29.5:1:1:1:27:4:0.3333:0:2 -9 66458588 . G C 70 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28671;SOR=0.18136;LSEQ=CCCACGCTCCAGTCCTTCCG;RSEQ=GAGCTCCGGAGCTCCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:1,3:0.5556:2,2:24.4:1:30.4:1:1:1.85:38.4:10:0.5556:0:6.6 0/1:6:1:0,1:3,2:0.1667:2,0:22:0:30:0:1:0:47:2:0.1667:0:6 -9 66458596 . G C 76 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1451;SOR=0.15212;LSEQ=CCAGTCCTTCCGGGAGCTCC;RSEQ=GAGCTCCGGGGCTTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:1,2:0.6:2,2:22.7:1:29.5:1:1:1.85:36.7:12:0.6667:0:6.7 0/1:6:1:0,1:2,3:0.1667:2,0:30:0:32:0:1:0:47:2:0.1667:0:6 -9 66458603 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=TTCCGGGAGCTCCGGAGCTC;RSEQ=GGGGCTTCCACCACATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:12.5:1:28.5:1:1:2.24:44:4:0.2222:0:7 0/0:6:0:0,0:2,4:0:2,0:37.2:1:29.3:1:1:0:41.7:12:1:0:1.8 -9 66458605 . GG AA 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.71643;LSEQ=CCGGGAGCTCCGGAGCTCCG;RSEQ=GCTTCCACCACATCTGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:38:1:29.8:1:1:2.24:39:4:0.2222:0:6 0/1:6:1:0,1:2,3:0.1667:2,0:40:0:31:0:1:0:47:2:0.1667:0:5 -9 66458606 . G A 69 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04396;SOR=0;LSEQ=CGGGAGCTCCGGAGCTCCGG;RSEQ=GCTTCCACCACATCTGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:0,2:0.5556:0,2:23.2:1:30:1:1:0:40.4:10:0.7143:0:6.4 0/0:6:0:0,0:2,3:0:2,0:36.6:1:29.6:1:1:0:40.6:10:1:0:1 -9 66458619 . T G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71643;LSEQ=GCTCCGGGGCTTCCACCACA;RSEQ=CTGCCGGCTCAGGACGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:38:1:32.5:1:1:2.24:39:4:0.2222:0:6 0/1:6:1:0,1:2,3:0.1667:2,0:48:0:33:0:1:0:47:2:0.1667:0:5 -9 66458621 . T G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=TCCGGGGCTTCCACCACATC;RSEQ=GCCGGCTCAGGACGGGTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:30.5:1:30:1:1:2.24:44:4:0.2222:0:7 0/0:6:0:0,0:2,4:0:2,0:32.2:1:27.8:1:1:0:41.7:5:1:0:1.7 -9 66458624 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=GGGGCTTCCACCACATCTGC;RSEQ=GGCTCAGGACGGGTCGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:33.5:1:30:1:0.46429:3.87:44:4:0.25:0:7 0/0:6:0:0,0:2,4:0:2,0:30.2:1:30.5:1:1:0:41.7:12:1:0:1.7 -9 66458635 . G T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CACATCTGCCGGCTCAGGAC;RSEQ=GGTCGTGCTCATCCCTTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:44.5:1:31:1:0.46429:3.87:44:4:0.25:0:7 0/0:8:0:0,0:3,5:0:2,0:19:1:30.5:1:1:0:43.3:16:1:0:2.3 -9 66458640 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTGCCGGCTCAGGACGGGTC;RSEQ=TGCTCATCCCTTAACTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:0:2,0:36.3:1:33:1:1:0:44.1:16:1:0:4.6 0/1:8:2:1,1:2,4:0.25:2,2:12.5:1:31.5:1:1:1.83:48:4:0.25:0:4 -9 66458642 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GCCGGCTCAGGACGGGTCGT;RSEQ=CTCATCCCTTAACTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:0:2,0:34.8:1:33.5:1:1:0:44.1:16:1:0:4.6 0/1:8:2:1,1:2,4:0.25:2,2:10:1:27.5:1:1:1.83:27:4:0.25:0:2 -9 66458645 . C T 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52315;LSEQ=GGCTCAGGACGGGTCGTGCT;RSEQ=ATCCCTTAACTTTTTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:16.5:1:28:1:0.46429:3.87:39:4:0.25:0:6 0/1:7:1:0,1:2,4:0.1429:2,0:22:0:30:0:1:0:47:2:0.1429:0:5 -9 66458659 . T G 67 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.19394;SOR=0;LSEQ=CGTGCTCATCCCTTAACTTT;RSEQ=TAACTTTTTGTTGTTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:0,3:0.5714:0,2:23:1:33.5:1:1:0:43.8:8:0.5714:0:6.3 0/0:4:0:0,0:1,3:0:2,0:27:1:30.8:1:1:0:48:8:1:0:3.5 -9 66458666 . TTTG T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCTTAACTTTTTAACTT;RSEQ=TTGTTTCTATTTATATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:0,5:0.2857:0,2:24.5:1:32:0:0.28571:0:44:4:0.2857:0:7 0/0:3:0:0,0:1,2:0:2,0:36:1:30.7:1:1:0:48.3:6:1:0:3 -9 66458714 . TG CA 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCTATGTCTTGAAATGTTGT;RSEQ=TAGCTATTACTTTTGATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:28.8:1:1:0:48:4:1:0:3 -9 66458719 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTGAAATGTTGTTGTAG;RSEQ=TATTACTTTTGATTGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:27:1:1:0:48:4:1:0:3 -9 66458868 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTAGGTGATCATTTATT;RSEQ=CTCATTAATGTCCTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:30.5:1:1:0:26:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 66833114 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGGAAAGGGAATATCTTCA;RSEQ=ATAAAATCTAGACAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:5:0:33:0:1:0:59:4:0.6667:0:5 -9 66833133 . A C 34 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAAAATCTAGACAGAAG;RSEQ=ATTCTCAGAAGCTTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:24:0:34:0:1:0:59:4:0.6667:0:5 -9 66833144 . G A 63 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGAAGAATTCTCAGAA;RSEQ=CTTCTTTGTGATGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:1,0:0.8:0,2:18.5:1:31.8:1:1:0:42:8:0.8:0:4.3 -9 66833153 . T G 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AATTCTCAGAAGCTTCTTTG;RSEQ=GATGTTTGCATTGAAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:9:0:31:0:1:0:40:2:1:0:5 0/1:5:2:1,1:2,1:0.4:2,2:40:0:31.5:1:1:1.7321:59:4:0.4:0:5 -9 66833179 . T A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGCATTGAAGTCACAGAGT;RSEQ=GAACATTCCCTTTCATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:32:0:1:0:40:2:1:0:5 0/1:7:2:1,1:3,2:0.2857:2,2:14:0:28.5:1:1:1.41418:59:4:0.2857:0:5 -9 66833193 . C G 65 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=CAGAGTTGAACATTCCCTTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:26:0:33:0:1:0:40:2:1:0:5 1/1:4:4:2,2:0,0:1:0,2:24:1:32.5:1:1:0:32.5:8:1:0:3 -9 66833195 . T G 65 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=GAGTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:33:0:1:0:40:2:1:0:5 1/1:4:4:2,2:0,0:1:0,2:22:1:32.5:1:1:0:32.5:8:1:0:3 -9 66833322 . T C 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACATTCTCAGAAACTTGTT;RSEQ=GTGATGTGTGTAATCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:32:0:1:0:38:4:1:0:1 -9 66833442 . T A 75 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAGGATTTCGTTGGAAA;RSEQ=GGGAATATATTCATATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:6:4,2:0,1:0.8571:0,2:10.8:1:29.2:1:0.42857:0:35.5:12:0.8571:0:5.8 -9 66833451 . AT CG 69 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCGTTGGAAATGGGAATAT;RSEQ=TCATATAAAATCTAGACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:5:3,2:0,1:0.7143:0,2:21.6:1:30.1:1:1:0:38.4:10:0.7143:0:5.2 -9 66833458 . T C 90 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATGGGAATATATTCATA;RSEQ=AAAATCTAGACAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:9:8:4,4:0,1:0.8889:0,2:20.6:1:30:1:1:0:34.3:16:0.8889:0:5.5 -9 66833490 . G C 82 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGCATTCTCACAAACTT;RSEQ=TTGGTGATGTGTGTACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:1:0,2:30.2:1:31.8:1:1:0:35.7:12:1:0:6.3 -9 66833493 . G T 71 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATTCTCACAAACTTGTT;RSEQ=GTGATGTGTGTACTCAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:1,4:0,0:1:0,2:35.2:1:30.8:1:1:0:35.4:10:1:0:6.8 -9 66833505 . A C 75 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTGTTGGTGATGTGTGT;RSEQ=CTCAACTAACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:1,4:0,0:1:0,2:32.2:1:32.4:1:1:0:35.4:10:1:0:6.8 -9 66833538 . AG GC 51 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTTGAACCTTTCTTTTGAT;RSEQ=AGCAGTTTTGAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:1:0,0:12.3:1:32.6:1:1:0:33.3:6:1:0.3333:6.7 -9 66833548 . T G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTTGATAGAGCAGTTT;RSEQ=GAAACACTCTTTTTGTAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:7.5:1:31.5:1:1:0:30.5:4:1:0:6.5 -9 66833774 . T A 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAACGCTTTGTGGCCTA;RSEQ=GGTGAAAAAGGAAATATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:6:1:31.5:1:1:0:42:4:1:0:7 1/1:1:1:1,0:0,0:1:0,0:6:0:32:0:1:0:28:2:1:0:8 -9 66833796 . G C 63 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GTGAAAAAGGAAATATCTTC;RSEQ=CATAAAAACTAGACAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:4:4,0:0,0:0.5714:0,0:16:1:31.8:1:1:0:22.5:8:0.5714:0:7.3 -9 66833804 . A G 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60804;SOR=0.55095;LSEQ=GGAAATATCTTCGCATAAAA;RSEQ=CTAGACAGAAGCATTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:5:0:34:0:0.4:0:41:4:0.4:0:6 0/1:19:5:4,1:11,3:0.2632:2,2:6.4:1:33.6:1:1:1.09:38.4:10:0.2632:0:4.8 -9 66833806 . T C 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28051;SOR=0.22393;LSEQ=AAATATCTTCGCATAAAAAC;RSEQ=AGACAGAAGCATTCTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:6.7:1:33:1:1:0:47:6:0.6:0:5.7 0/1:21:5:4,1:13,3:0.2381:2,2:8.4:1:31.8:1:1:1.07915:38.4:10:0.2381:0:4.8 -9 66833807 . A G 75 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56914;SOR=Inf;LSEQ=AATATCTTCGCATAAAAACT;RSEQ=GACAGAAGCATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:0:2,0:14.7:1:31:1:1:0:44:14:1:0:5.6 0/1:35:5:5,0:21,9:0.1429:2,0:23.8:1:32.4:1:0.2972:0:22.4:10:0.1429:0:7 -9 66833809 . A T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52269;SOR=0.55458;LSEQ=TATCTTCGCATAAAAACTAG;RSEQ=CAGAAGCATTCTCAGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:5,1:0.1429:2,0:42:0:32:0:1:0:40:2:0.1429:0:7 0/1:36:3:1,2:26,7:0.0833:2,2:21.7:1:29.7:1:0.1479:6.90592:26:6:0.0833:0:7.7 -9 66833813 . A C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTCGCATAAAAACTAGACAG;RSEQ=AGCATTCTCAGAAACTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:10,2:0.0714:2,0:46:0:34:0:1:0:40:2:0.0714:0:7 0/1:42:3:1,2:29,10:0.0714:2,2:25.7:1:32.7:1:0.19164:5.51539:26:6:0.0714:0:7.7 -9 66833821 . T C 29 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04969;SOR=0;LSEQ=AAAACTAGACAGAAGCATTC;RSEQ=CAGAAACTTGTTTGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:11,3:0.125:2,2:23:1:29.5:1:0.45:3.31654:44.5:4:0.125:0:5 0/0:54:0:0,0:37,17:0:2,0:16.8:1:29.8:1:1:0:36.3:26:1:0:4.9 -9 66833829 . T C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.85175;LSEQ=ACAGAAGCATTCTCAGAAAC;RSEQ=TGTTTGTGATGTGTGTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:12,5:0.0556:2,0:37:0:33:0:1:0:40:2:0.0588:0:7 0/1:63:3:1,2:38,22:0.0476:2,2:34.7:1:30.3:1:0.55216:3.38449:26:6:0.0484:0:7.7 -9 66833831 . G C 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60806;SOR=0.53808;LSEQ=AGAAGCATTCTCAGAAACTT;RSEQ=TTTGTGATGTGTGTACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:11,5:0.1111:2,0:28:1:33:0:1:0:31.5:4:0.1111:0:7.5 0/1:64:4:2,2:38,22:0.0625:2,2:31.8:1:30.8:1:0.6268:1.71184:26.8:8:0.0625:0:7.8 -9 66833834 . TG CT 75 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00028;SOR=0;LSEQ=AGCATTCTCAGAAACTTGTT;RSEQ=TGATGTGTGTACTCAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:3,2:8,1:0.2778:2,2:29:1:32.6:1:0.50549:4.64888:41.8:10:0.2778:0:4.8 0/0:66:0:0,0:27,17:0:2,0:23.9:1:29.4:1:1:0:36.2:88:0.6667:0:4.8 -9 66833835 . G A 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.71161;SOR=0.77831;LSEQ=GCATTCTCAGAAACTTGTTT;RSEQ=TGATGTGTGTACTCAACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:2,1:8,2:0.1667:2,2:23.7:1:29.3:1:1:1.88511:43.3:6:0.2308:0:6 0/1:67:9:7,2:34,23:0.1343:2,2:31.7:1:28.7:1:0.46449:2.34:30.8:18:0.1343:0:6.8 -9 66833838 . A C 102 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27612;SOR=3.71109;LSEQ=TTCTCAGAAACTTGTTTGTG;RSEQ=TGTGTGTACTCAACTAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:1,0:13,11:0.0385:2,0:28:0:33:0:1:0:41:2:0.04:0:8 0/1:69:9:7,2:33,25:0.1304:2,2:32.7:1:32.2:1:0.29479:2.62:30.8:18:0.1304:0:6.8 -9 66833840 . G A 90 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.27629;SOR=3.75963;LSEQ=CTCAGAAACTTGTTTGTGAT;RSEQ=TGTGTACTCAACTAACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:15,12:0.0357:2,0:17:0:26:0:0.46429:0:34:2:0.037:0:8 0/1:73:9:5,4:39,25:0.1233:2,2:26.9:1:28.7:1:1:1.24414:27.3:18:0.125:0:7.1 -9 66833842 . G A 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.72346;SOR=1.80431;LSEQ=CAGAAACTTGTTTGTGATGT;RSEQ=TGTACTCAACTAACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:18:1:28:1:1:1.07415:33:4:0.069:0:7 0/1:76:9:7,2:37,30:0.1184:2,2:33.2:1:28.4:1:0.28824:2.80:30.8:18:0.1216:0:6.8 -9 66833844 . G C 103 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.50651;SOR=1.97423;LSEQ=GAAACTTGTTTGTGATGTGT;RSEQ=TACTCAACTAACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:20:1:30.5:1:1:1.07415:33:4:0.0714:0:7 0/1:78:10:8,2:37,31:0.1282:2,2:30.3:1:31.1:1:0.17678:3.31:31.9:20:0.1282:0:6.8 -9 66833846 . A C 97 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28299;SOR=3.59401;LSEQ=AACTTGTTTGTGATGTGTGT;RSEQ=CTCAACTAACAGAGTTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:17,14:0.0313:2,0:23:0:28:0:0.46875:0:34:2:0.0323:0:8 0/1:86:9:5,4:42,35:0.1047:2,2:32.7:1:30.9:1:1:1.04:29:18:0.1047:0:7.2 -9 66833848 . T C 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5637;SOR=Inf;LSEQ=CTTGTTTGTGATGTGTGTAC;RSEQ=CAACTAACAGAGTTGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:0:2,0:21.9:1:30.3:1:1:0:38.2:68:1:0:4.9 0/1:93:3:3,0:45,45:0.0323:2,0:39.7:1:30:1:0.24264:0:29.3:6:0.0323:0:7 -9 66833849 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07513;SOR=0;LSEQ=TTGTTTGTGATGTGTGTACT;RSEQ=AACTAACAGAGTTGAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:16,18:0.0556:2,2:25:1:28:1:1:1.12:49.5:4:0.0556:0:6.5 0/0:94:0:0,0:48,46:0:2,0:27.1:1:30.6:1:1:0:35.4:188:1:0:5.1 -9 66833851 . AC TG 81 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44583;SOR=2.73624;LSEQ=GTTTGTGATGTGTGTACTCA;RSEQ=TAACAGAGTTGAACCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:1,0:16,19:0.0278:2,0:42:0:33.5:0:0.47222:0:23:2:0.0278:0:7 0/1:96:7:3,4:41,42:0.0729:2,2:16.4:1:29.1:1:1:1.2978:34.3:14:0.0729:0.0104:5.9 -9 66833856 . C A 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69847;SOR=0.83278;LSEQ=TGATGTGTGTACTCAACTAA;RSEQ=AGAGTTGAACCTTTCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:17:9,8:7,13:0.4595:2,2:30.6:1:30.4:1:0.33089:2.05:40.2:34:0.4595:0:4.6 0/1:99:41:22,19:23,31:0.4141:2,2:35.6:1:28.6:1:0.30691:1.55:40.4:19.5:0.4021:0:3.6 -9 66833858 . G A 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31126;SOR=2.05284;LSEQ=ATGTGTGTACTCAACTAACA;RSEQ=AGTTGAACCTTTCTTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:2,2:12,17:0.1081:2,2:21.8:1:29.8:1:1:1.40:42.3:8:0.1111:0:6.5 0/1:100:20:9,11:39,41:0.2:2,2:20.2:1:29.3:1:0.80694:1.16085:31.8:40:0.202:0:6.5 -9 66833859 . A T 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.72703;SOR=1.70602;LSEQ=TGTGTGTACTCAACTAACAG;RSEQ=GTTGAACCTTTCTTTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:15,20:0.0541:2,2:24:1:29:1:1:1.32:23:4:0.0541:0:5.5 0/1:101:9:4,5:44,48:0.0891:2,2:21:1:28.9:1:1:1.14429:36:18:0.0891:0:5.7 -9 66833860 . G T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGTGTACTCAACTAACAGA;RSEQ=TTGAACCTTTCTTTTGATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:16,21:0:2,0:27.2:1:31.5:1:1:0:37.4:74:1:0:5 0/1:101:2:1,1:47,52:0.0198:2,2:40.5:1:31:1:1:1.11:42:4:0.02:0:4 -9 66833862 . T C 26 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07045;SOR=0;LSEQ=GTGTACTCAACTAACAGAGT;RSEQ=GAACCTTTCTTTTGATAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:15,20:0.0541:2,2:45:0:26:1:1:1.32:41:4:0.0541:0:5.5 0/0:101:0:0,0:48,52:0:2,0:29.2:1:28.9:1:1:0:34.8:49:0.9899:0:5.1 -9 66833865 . A C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTCAACTAACAGAGTTGA;RSEQ=CCTTTCTTTTGATAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:16,21:0:2,0:28.4:1:29.4:1:1:0:37.4:74:1:0:5 0/1:101:2:1,1:47,52:0.0198:2,2:36.5:1:31:1:1:1.11:47:4:0.0198:0:2 -9 66833867 . C T 98 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28755;SOR=3.81851;LSEQ=CTCAACTAACAGAGTTGAAC;RSEQ=TTTCTTTTGATAGAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:0,1:15,20:0.0278:2,0:44:0:28:0:1:0:34:2:0.0286:0:8 0/1:101:10:5,5:40,46:0.099:2,2:35:1:29.8:1:1:1.15:28.2:20:0.099:0:7.1 -9 66833868 . T A 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72744;SOR=1.65753;LSEQ=TCAACTAACAGAGTTGAACC;RSEQ=TTCTTTTGATAGAGCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:14,20:0.0556:2,2:24:1:29:1:1:1.41:23:4:0.0556:0:5.5 0/1:101:9:4,5:44,48:0.0891:2,2:28.3:1:28.9:1:1:1.14429:36:18:0.0891:0:5.7 -9 66833869 . T A 76 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02152;SOR=0.21133;LSEQ=CAACTAACAGAGTTGAACCT;RSEQ=TCTTTTGATAGAGCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:1,5:14,16:0.1667:2,2:32:0:29.5:1:0.36668:4.22155:29.3:12:0.1667:0:3.2 0/1:100:4:1,3:46,48:0.04:2,2:26.8:1:24:1:0.61845:2.847:27:3:0.0309:0:4.3 -9 66833870 . T C 112 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55794;SOR=1.65712;LSEQ=AACTAACAGAGTTGAACCTT;RSEQ=CTTTTGATAGAGCAGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:1,2:14,18:0.0833:2,2:23.7:1:29:1:1:1.53673:28.7:6:0.0857:0:6 0/1:99:13:5,8:36,40:0.1313:2,2:27.5:1:30.5:1:0.76454:1.43418:32.6:26:0.1327:0:6 -9 66833872 . TT CA 99 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.28721;SOR=3.9035;LSEQ=CTAACAGAGTTGAACCTTTC;RSEQ=TTGATAGAGCAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:0,1:15,20:0.0278:2,0:50:0:31:0:1:0:34:2:0.0278:0:7 0/1:99:10:5,5:41,48:0.101:2,2:33.1:1:30.1:1:1:1.17:28.2:20:0.101:0:6.1 -9 66833873 . T A 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.84495;SOR=1.13962;LSEQ=TAACAGAGTTGAACCTTTCT;RSEQ=TTGATAGAGCAGTTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:15:8,7:7,13:0.4167:2,2:28.5:1:29:1:0.32078:2.08:39.3:30:0.4286:0:4.5 0/1:98:44:23,21:15,26:0.449:2,2:30.4:1:27.6:1:0.19123:1.88:39:21:0.4884:0:3.8 -9 66833876 . G C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29579;SOR=0.36116;LSEQ=CAGAGTTGAACCTTTCTTTT;RSEQ=ATAGAGCAGTTTTGAAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:15,19:0.0556:2,0:31.5:1:31:1:0.5:0:42.5:4:0.0556:0:5.5 0/1:97:2:0,2:44,51:0.0206:2,0:14:0:32:1:0.49914:0:25:4:0.0211:0:8 -9 66833878 . T C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06202;LSEQ=GAGTTGAACCTTTCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:1,5:14,15:0.1667:2,2:33.7:1:30.7:1:0.20724:4.48961:31:12:0.1667:0:4.7 0/1:97:17:6,11:33,37:0.1753:2,2:31.6:1:30.9:1:0.42643:1.62607:31.3:34:0.1753:0:5.6 -9 66833879 . AG GC 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56359;SOR=Inf;LSEQ=AGTTGAACCTTTCTTTTGAT;RSEQ=AGCAGTTTTGAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:0:2,0:31.8:1:29.6:1:1:0:37.3:72:1:0:4.9 0/1:98:3:1,2:43,52:0.0306:2,2:38.7:1:33.3:1:1:1.64572:36.7:6:0.0309:0:5.7 -9 66833880 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0707;SOR=0;LSEQ=GTTGAACCTTTCTTTTGATA;RSEQ=AGCAGTTTTGAAACACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:14,20:0.0556:2,2:26.5:1:28.5:1:1:1.41:49.5:4:0.0556:0:6.5 0/0:98:0:0,0:42,51:0:2,0:28.1:1:31.1:1:1:0:35.1:186:0.9789:0:5 -9 66833883 . C G 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56359;SOR=Inf;LSEQ=GAACCTTTCTTTTGATAGAG;RSEQ=AGTTTTGAAACACTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:0:2,0:31.2:1:32:1:1:0:37.3:72:1:0:4.9 0/1:98:3:1,2:43,52:0.0306:2,2:43:1:29.3:1:1:1.64572:32.7:6:0.0309:0:6.7 -9 66833884 . A T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06778;SOR=0;LSEQ=AACCTTTCTTTTGATAGAGC;RSEQ=GTTTTGAAACACTCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:14,19:0.0571:2,2:39.5:1:31.5:1:1:1.35:47:4:0.0571:0:6 0/0:98:0:0,0:44,54:0:2,0:27.4:1:29.9:1:1:0:34.9:97:1:0:5 -9 66833888 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.06795;SOR=0;LSEQ=TTTCTTTTGATAGAGCAGTT;RSEQ=TGAAACACTCTTTTTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:13,19:0.0588:2,2:35.5:1:32:1:1:1.44:47:4:0.0606:0:6 0/0:95:0:0,0:41,52:0:2,0:27:1:29.4:1:1:0:35.1:92:0.9787:0:4.9 -9 66833889 . T G 71 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86702;LSEQ=TTCTTTTGATAGAGCAGTTT;RSEQ=GAAACACTCTTTTTGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:14,19:0.0294:2,0:42:0:30:0:1:0:40:2:0.0294:0:7 0/1:93:5:1,4:39,49:0.0538:2,2:26:1:30.8:1:0.38645:3.14943:32:10:0.0538:0:6.6 -9 66833894 . CA TG 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0354;LSEQ=TTGATAGAGCAGTTTTGAAA;RSEQ=CTCTTTTTGTAGAATCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:2,2:10,17:0.1212:2,2:27.8:1:31.1:1:0.63045:1.67:33.3:8:0.1212:0:5.3 0/1:80:10:3,7:29,38:0.125:2,2:39.1:1:31.8:1:0.50872:1.768:35.9:20:0.125:0:5.1 -9 66833896 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GATAGAGCAGTTTTGAAACA;RSEQ=TCTTTTTGTAGAATCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:11,18:0:2,0:28.3:1:31.1:1:1:0:35.9:28:1:0:4.9 0/1:80:2:1,1:31,44:0.025:2,2:43.5:1:29:1:1:1.41:25:4:0.0263:0:5.5 -9 66833906 . A G 161 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13751;SOR=0.42601;LSEQ=TTTTGAAACACTCTTTTTGT;RSEQ=GAATCTGCAAGTGGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:22:7,15:1,4:0.8148:2,2:24.2:1:32.1:1:1:1.83:34.7:44:0.8148:0:4.9 1/0:60:39:9,30:8,12:0.65:2,2:25.7:1:30.6:1:0.22801:2.19036:34.1:38:0.6552:0:5 -9 66833907 . G C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08403;SOR=0;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=AATCTGCAAGTGGATATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:5,17:0.08:2,2:16.5:1:31.5:1:0.44565:3.19:47:4:0.0833:0:6 0/0:60:0:0,0:17,43:0:2,0:25.7:1:31.3:1:1:0:34.4:59:1:0:5 -9 66833909 . A T 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79119;SOR=1.27805;LSEQ=TGAAACACTCTTTTTGTAGA;RSEQ=TCTGCAAGTGGATATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:1,5:5,14:0.24:2,2:29:1:31.2:1:1:1.74814:34.7:12:0.25:0:5.5 0/1:59:17:5,12:11,31:0.2881:2,2:17.6:1:30.1:1:1:1.17:37.9:34:0.2881:0:4.7 -9 66833910 . T A 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22916;LSEQ=GAAACACTCTTTTTGTAGAA;RSEQ=CTGCAAGTGGATATTTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:6,17:0.0417:2,0:39:0:32:0:1:0:40:2:0.0417:0:8 0/1:59:3:1,2:15,40:0.0508:2,2:31.3:1:30:1:1:1.33:36.7:6:0.0517:0:5.7 -9 66833914 . C T 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.54762;SOR=Inf;LSEQ=CACTCTTTTTGTAGAATCTG;RSEQ=AAGTGGATATTTGGATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:5,18:0:2,0:20.3:1:32.2:1:1:0:34.5:22:1:0:5.1 0/1:51:3:1,2:12,36:0.0588:2,2:27.3:1:28.3:1:1:1.49:36.7:6:0.06:0:5.7 -9 66833917 . G A 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08949;SOR=0.14029;LSEQ=TCTTTTTGTAGAATCTGCAA;RSEQ=TGGATATTTGGATAGCTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:1,2:4,16:0.1304:2,2:7.7:1:31.7:1:0.53924:1.93:25.3:6:0.1304:0:3 0/1:50:1:0,1:12,36:0.02:2,0:6:0:31:0:1:0:34:2:0.0204:0:7 -9 66833918 . T A 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21228;SOR=0.20328;LSEQ=CTTTTTGTAGAATCTGCAAG;RSEQ=GGATATTTGGATAGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:3,16:0.0952:2,2:22.5:1:31.5:1:0.35238:4.76:24:4:0.0952:0:6 0/1:49:1:0,1:12,36:0.0204:2,0:20:0:33:0:1:0:36:2:0.0204:0:6 -9 66833929 . A C 105 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31261;LSEQ=ATCTGCAAGTGGATATTTGG;RSEQ=TAGCTTTGAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:0,11:0.2143:0,2:11.3:1:33.7:1:0.21429:0:42.7:6:0.2143:0:5.7 0/1:34:9:1,8:5,20:0.2647:2,2:15.7:1:33.3:1:1:1.96412:32.3:18:0.2647:0:5.3 -9 66833931 . A T 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23657;SOR=0.3969;LSEQ=CTGCAAGTGGATATTTGGAT;RSEQ=GCTTTGAGGATTTCGTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:1,8:0.3077:2,0:15.3:1:31.5:1:1:0:36:8:0.3077:0:5.5 0/1:34:5:0,5:6,23:0.1471:2,0:12.6:1:31.8:1:0.5585:0:33.4:10:0.1471:0:5 -9 66833933 . C G 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17608;SOR=0.16974;LSEQ=GCAAGTGGATATTTGGATAG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:0,9:0.1667:0,2:9.5:1:31:1:0.18182:0:43:4:0.1667:0:6 0/1:32:1:0,1:5,18:0.0313:2,0:7:0:33:0:1:0:24:2:0.0313:0:4 -9 66833936 . T G 70 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5628;SOR=Inf;LSEQ=AGTGGATATTTGGATAGCTT;RSEQ=GAGGATTTCGTTGGAAACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:12.3:1:31.3:1:1:0:36.4:16:1:0:5.8 0/1:31:5:1,4:5,19:0.1613:2,2:10.6:1:30.4:1:1:1.05078:27.4:10:0.1613:0:4.6 -9 66834493 . G A 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCTTAAAAACTACACAGAA;RSEQ=CATTCTCAGAAACTTGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:13:0:35:0:1:0:22:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:13:0:29:1:1:0:30:4:1:0:1 -9 66834726 . A T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTGAACCTTCCCTTTCAT;RSEQ=GAGCAGGTTTGAAACATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:1:28.5:1:1:0:47:4:1:0:5.5 -9 66834739 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCATAGAGCAGGTTTGA;RSEQ=ACATTCTTTTTGTAGTATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:31:1:1:0:47:4:1:0:5.5 -9 66834743 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGAGCAGGTTTGAAACA;RSEQ=TCTTTTTGTAGTATCCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31:1:31:1:1:0:47:4:1:0:5.5 -9 66834752 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGTTTGAAACATTCTTTTTG;RSEQ=AGTATCCGGAAGTGGAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:1:29.5:1:1:0:47:4:1:0:5.5 -9 66834785 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAATTTGGAGCGCTTTG;RSEQ=GGCCTGTGGTGAATGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:32:0:1:0:47:4:1:0:5.5 -9 66834791 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGAGCGCTTTGAGGCCT;RSEQ=TGGTGAATGAGGAAACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:31:1:1:0:47:4:1:0:5.5 -9 66835094 . A C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGAAACACTCTTTTTGT;RSEQ=GTATCTGGAAGTGGACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:31.5:1:1:0:33:4:1:0:2 -9 66835127 . G C 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACATTTGGAGCACTTTGA;RSEQ=GCCTATTTTGAAAAAGGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:27.5:1:1:0:33:4:1:0:2 -9 66835506 . G C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAAATATCTTCCCATAAAAA;RSEQ=TTGACAGAAGCATTCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:18:0:33.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:1.5 -9 66835613 . TT CG 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AACACTCTTTTTGTAGAATC;RSEQ=CATGTGGATATTTGCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25:0:32.5:1:1:0:31:4:1:0:4 1/1:2:2:1,1:0,0:1:0,2:27.5:1:30:1:1:0:48:4:1:0:5 -9 66835614 . T G 34 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTCTTTTTGTAGAATCT;RSEQ=CATGTGGATATTTGCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:34:0:1:0:31:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 66835617 . T A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTTTTTGTAGAATCTTCA;RSEQ=GTGGATATTTGCATAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:0:32:1:1:0:31:4:1:0:4 1/1:2:2:1,1:0,0:1:0,2:30.5:1:30.5:1:1:0:48:4:1:0:5 -9 66835619 . T A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTGTAGAATCTTCATG;RSEQ=GGATATTTGCATAGCTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:0:32:1:1:0:31:4:1:0:4 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30:0:1:0:48:4:1:0:5 -9 66835649 . T G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGCTTTGAGGATTTCGT;RSEQ=GGAAACGGGAATAGCTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:0:31.5:1:1:0:31:4:1:0:4 1/1:2:2:1,1:0,0:1:0,2:13:0:32.5:1:1:0:48:4:1:0:5 -9 67320748 . CA GT 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=GACAGAAGCATTCTCAGAAA;RSEQ=TCTCTGTGATGTTTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:13.5:1:32.3:1:1:0:29:4:0.6667:0:6 0/1:4:1:1,0:1,1:0.25:2,0:12:0:33:0:1:0:40:2:0.25:0:6 -9 67320749 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=ACAGAAGCATTCTCAGAAAC;RSEQ=TCTCTGTGATGTTTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,0:0.3333:0,0:41:0:33:0:1:0:25:2:1:0:6 1/0:4:2:1,1:0,0:0.5:0,2:18:1:29:1:1:0:32.5:4:1:0:6.5 -9 67320753 . C T 89 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGCATTCTCAGAAACATCT;RSEQ=TGTGATGTTTGCATTCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:25.7:1:31.7:1:1:0:27.7:6:1:0:6 1/1:8:8:7,1:0,0:1:0,2:11.3:1:29.9:1:1:0:33.8:16:1:0:6.9 -9 67320761 . T A 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68213;SOR=0.59346;LSEQ=TCAGAAACATCTCTGTGATG;RSEQ=TTGCATTCAAGTCACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:11.2:1:31.3:1:1:0:30.5:12:0.75:0:5.7 1/0:22:14:11,3:7,1:0.6364:2,2:7.5:1:29.9:1:1:1.85732:34.7:28:0.6364:0:6.4 -9 67320769 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCTCTGTGATGTTTGCATT;RSEQ=AAGTCACAGAGTTGAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:19.6:1:32.8:1:1:0:30.5:16:1:0:5.8 0/1:32:2:2,0:24,5:0.0625:2,0:6:1:31:1:1:0:31.5:4:0.0625:0:2.5 -9 67320779 . A T 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTTTGCATTCAAGTCACAG;RSEQ=GTTGAACATTCCCTTTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:0:2,0:23:1:30.7:1:1:0:30.9:20:1:0:6.2 0/1:40:3:2,1:29,8:0.075:2,2:27.3:1:29.3:1:0.54504:1.78205:29.3:6:0.075:0:4 -9 67320780 . G A 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3464;SOR=2.56653;LSEQ=GTTTGCATTCAAGTCACAGA;RSEQ=TTGAACATTCCCTTTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:2,1:0.7273:2,0:27.3:1:31.4:1:0.27273:0:32.4:16:0.7273:0:6 1/1:40:35:27,8:4,1:0.875:2,2:21.3:1:31.3:1:1:1.18034:35.5:70:0.875:0:6.2 -9 67320782 . T G 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56242;SOR=Inf;LSEQ=TTGCATTCAAGTCACAGAGT;RSEQ=GAACATTCCCTTTCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:11,1:0:2,0:20.3:1:31.1:1:1:0:33.3:24:0.9231:0:6.6 0/1:42:4:4,0:29,9:0.0952:2,0:24:1:32.5:1:0.5613:0:27.8:8:0.0952:0:5.8 -9 67320788 . T C 66 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.21387;LSEQ=TCAAGTCACAGAGTTGAACA;RSEQ=TCCCTTTCACAGAGCAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:12,2:0.0667:2,0:35:0:32:0:1:0:36:2:0.0667:0:6 0/1:50:4:4,0:35,11:0.08:2,0:37.8:1:33:0:0.56349:0:40:8:0.08:0:4.8 -9 67320790 . C G 63 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56488;SOR=Inf;LSEQ=AAGTCACAGAGTTGAACATT;RSEQ=CCTTTCACAGAGCAGGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:13,3:0:2,0:21.4:1:31.5:1:1:0:33.8:32:1:0:6.7 0/1:50:4:2,2:36,9:0.08:2,2:28.3:1:31.5:1:0.21364:3.85617:42.8:8:0.0833:0:6.3 -9 67320802 . G A 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAACATTCCCTTTCACAGA;RSEQ=CAGGTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:13,5:0:2,0:25.7:1:30.6:1:1:0:35.1:8:1:0:6.8 0/1:59:3:2,1:40,16:0.0508:2,2:31:1:29.3:1:1:1.24513:42:6:0.0536:0:6.3 -9 67320815 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCACAGAGCAGGTTTGAAAC;RSEQ=CTCTTTTTGTAGTATCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:24.1:1:28.8:1:1:0:33.5:48:1:0:7 0/1:73:2:1,1:44,26:0.0274:2,2:16.5:1:29:1:1:1.67936:41:4:0.0282:0:7.5 -9 67320817 . T C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05928;SOR=0;LSEQ=ACAGAGCAGGTTTGAAACAC;RSEQ=CTTTTTGTAGTATCTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:13,9:0.0833:2,2:6.5:1:29.5:1:1:1.42202:24:4:0.087:0:8 0/0:73:0:0,0:45,28:0:2,0:26.8:1:28.7:1:1:0:36.2:17.25:1:0:6.7 -9 67320819 . T C 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.14759;SOR=0.15445;LSEQ=AGAGCAGGTTTGAAACACTC;RSEQ=TTTTGTAGTATCTGGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:13,9:0.0833:2,2:8.5:1:31:1:1:1.42202:24:4:0.0833:0:8 0/1:74:1:1,0:44,29:0.0135:2,0:38:0:26:0:1:0:27:2:0.0141:0:8 -9 67320823 . T G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGTTTGAAACACTCTTTT;RSEQ=GTAGTATCTGGAAGTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:15,10:0:2,0:26.3:1:29:1:1:0:33.9:24:1:0:6.9 0/1:79:2:2,0:47,30:0.0253:2,0:11:0:30:1:0.52288:0:31:4:0.026:0:5 -9 67320826 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTGAAACACTCTTTTTGT;RSEQ=GTATCTGGAAGTGCACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,11:0:2,0:27.1:1:28.8:1:1:0:33.2:50:0.9615:0:7 0/1:82:2:2,0:48,32:0.0244:2,0:39:1:28.5:1:0.51822:0:33.5:4:0.0253:0:8 -9 67320829 . A G 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11544;LSEQ=TGAAACACTCTTTTTGTAGT;RSEQ=TCTGGAAGTGCACATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:11,9:2,2:0.8333:2,2:32.7:1:30.7:1:1:1.21:34.2:19:0.8636:0:7.3 1/1:79:67:39,28:8,4:0.8481:2,2:27.2:1:30.7:1:0.75269:1.42951:36.4:134:0.8481:0:7 -9 67320831 . C G 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63392;SOR=0.72104;LSEQ=AAACACTCTTTTTGTAGTAT;RSEQ=TGGAAGTGCACATTTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:10,6:3,5:0.6667:2,2:36.1:1:32.1:1:0.39045:2.66:35.1:32:0.6667:0:7.3 1/0:78:46:26,20:21,11:0.5897:2,2:31.3:1:30.2:1:0.48505:1.46131:37.2:45:0.5844:0:7.2 -9 67320833 . GG AT 96 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72679;SOR=1.61079;LSEQ=ACACTCTTTTTGTAGTATCT;RSEQ=AAGTGCACATTTGGAGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:13,9:0.0833:2,0:27.5:1:26:1:0.19928:0:25:4:0.087:0:7 0/1:78:10:6,4:41,27:0.1282:2,2:29.4:1:28.9:1:1:1.01219:32.2:20:0.1316:0:7 -9 67320834 . G T 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.7972;SOR=0.75571;LSEQ=CACTCTTTTTGTAGTATCTG;RSEQ=AAGTGCACATTTGGAGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:18:11,7:2,2:0.75:2,2:33.6:1:28.8:1:1:1.54:35.2:36:0.8182:0:7.2 1/0:75:52:29,23:9,4:0.6933:2,2:28.9:1:27.8:1:0.53208:1.76915:37.8:104:0.8125:0:7 -9 67320837 . G C 93 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88994;LSEQ=TCTTTTTGTAGTATCTGGAA;RSEQ=TGCACATTTGGAGCGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:1,2:12,11:0.1154:2,2:22:1:32.7:1:1:2.11883:24.7:6:0.12:0:7.3 0/1:77:8:6,2:37,32:0.1039:2,2:18.5:1:31.3:1:0.29107:2.57:30.5:16:0.1053:0:6.5 -9 67320840 . C G 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.60297;SOR=0.70236;LSEQ=TTTTGTAGTATCTGGAAGTG;RSEQ=ACATTTGGAGCGCATTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:20:10,10:0,0:0.8:0,2:31:1:30.4:1:1:0:33.6:19:0.7917:0:7.1 1/0:76:56:31,25:0,0:0.7368:0,2:26.6:1:29.6:1:1:0:36.9:17.667:0.7361:0:6.9 -9 67320842 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05601;SOR=0;LSEQ=TTGTAGTATCTGGAAGTGCA;RSEQ=ATTTGGAGCGCATTCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:11,12:0.08:2,2:23.5:1:31.5:1:1:1.09:26:4:0.08:0:7 0/0:79:0:0,0:41,38:0:2,0:24.9:1:29.8:1:1:0:36.2:25.333:1:0:6.6 -9 67320843 . A T 92 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.446;SOR=2.79531;LSEQ=TGTAGTATCTGGAAGTGCAC;RSEQ=TTTGGAGCGCATTCAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:12,13:0.0385:2,0:35:0:29:0:1:0:22:2:0.0385:0:8 0/1:79:8:6,2:35,36:0.1013:2,2:23:1:30.8:1:0.26605:3.04:30.5:16:0.1053:0:6.5 -9 67320845 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06307;SOR=0;LSEQ=TAGTATCTGGAAGTGCACAT;RSEQ=TGGAGCGCATTCAGGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:11,14:0.0741:2,2:16.5:1:29.5:1:1:1.26:36:4:0.0769:0:6.5 0/0:79:0:0,0:39,40:0:2,0:24.9:1:28.3:1:1:0:36.1:18.75:1:0:6.5 -9 67320849 . A C 112 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34751;SOR=2.68789;LSEQ=ATCTGGAAGTGCACATTTGG;RSEQ=GCGCATTCAGGCCTAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:11,13:0.0769:2,0:42.5:1:28:1:0.49231:0:25:4:0.0769:0:7 0/1:76:14:6,8:31,31:0.1842:2,2:32.9:1:29.6:1:0.76959:1.3283:32.6:28:0.1918:0:6.4 -9 67320850 . GC TT 42 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.05576;LSEQ=TCTGGAAGTGCACATTTGGA;RSEQ=GCATTCAGGCCTAAGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:11,14:0.0385:2,0:37:0:32:0:1:0:36:2:0.04:0:6 0/1:74:3:0,3:35,35:0.0405:2,0:37.7:1:26.7:1:0.24087:0:40:6:0.0429:0:5 -9 67320851 . C T 109 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54766;SOR=1.7795;LSEQ=CTGGAAGTGCACATTTGGAG;RSEQ=GCATTCAGGCCTAAGGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:1,2:10,12:0.1154:2,2:40.3:1:27.3:1:1:1.63407:31:6:0.125:0:6.3 0/1:74:14:6,8:30,27:0.1892:2,2:34.1:1:28.7:1:0.56276:1.47328:32.6:28:0.209:0:6.4 -9 67320852 . G A 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00448;SOR=0.23939;LSEQ=TGGAAGTGCACATTTGGAGC;RSEQ=CATTCAGGCCTAAGGTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:5,8:4,7:0.5417:2,2:28.4:1:30.1:1:1:1.09:37.2:26:0.5652:0:6.7 0/1:69:15:6,9:25,29:0.2174:2,2:32.7:1:27.9:1:0.77315:1.28833:39.5:14:0.2059:0:7.7 -9 67320853 . CA AT 60 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.38935;LSEQ=GGAAGTGCACATTTGGAGCG;RSEQ=TTCAGGCCTAAGGTGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:9,14:0.0417:2,0:44:0:30.5:0:1:0:22:2:0.0417:0:7 0/1:70:4:3,1:28,38:0.0571:2,2:34.5:1:30:1:0.31522:3.99:31:8:0.0588:0:5.5 -9 67320854 . A T 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55959;LSEQ=GAAGTGCACATTTGGAGCGC;RSEQ=TTCAGGCCTAAGGTGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:23:9,14:0,0:0.9583:0,2:30.2:1:30:1:1:0:34.1:22:1:0:6.7 1/1:69:64:26,38:1,0:0.9275:0,2:28:1:29.3:1:0.41538:0:36.3:128:0.9846:0:6.4 -9 67320856 . T A 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21943;SOR=0.3741;LSEQ=AGTGCACATTTGGAGCGCAT;RSEQ=CAGGCCTAAGGTGAAAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:7,14:0.16:2,2:23.3:1:29.5:1:0.60158:1.94:37.8:8:0.16:0:7 0/1:76:5:2,3:29,42:0.0658:2,2:33.6:1:30:1:1:1.03524:44:10:0.0676:0:8 -9 67320858 . A C 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16922;SOR=0.4719;LSEQ=TGCACATTTGGAGCGCATTC;RSEQ=GGCCTAAGGTGAAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:18:7,11:2,6:0.6923:2,2:23.6:1:29.4:1:0.66729:1.86:34.9:17:0.7083:0:6.4 1/0:76:39:16,23:13,21:0.5132:2,2:25:1:28.4:1:1:1.12:38.4:18.5:0.5068:0:6.5 -9 67320861 . C G 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45778;SOR=0.53097;LSEQ=ACATTTGGAGCGCATTCAGG;RSEQ=CTAAGGTGAAAAAGGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:2,2:6,16:0.1538:2,2:39.8:1:31.5:1:0.56334:2.56:29.3:8:0.16:0:6.5 0/1:80:7:5,2:25,48:0.0875:2,2:38.7:1:32:1:0.09638:4.70:28.6:14:0.0897:0:5.7 -9 67320862 . C G 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTTGGAGCGCATTCAGGC;RSEQ=TAAGGTGAAAAAGGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:8,18:0:2,0:27.1:1:30.7:1:1:0:34.3:12:1:0:5.9 0/1:79:2:0,2:29,48:0.0253:2,0:21:0:29.5:1:0.52937:0:30.5:4:0.0256:0:5 -9 67320866 . G C 132 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11326;SOR=2.98478;LSEQ=TGGAGCGCATTCAGGCCTAA;RSEQ=GTGAAAAAGGAAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:0,3:8,15:0.1154:2,0:31.7:1:29:1:0.52923:0:30:6:0.1154:0:5 0/1:78:22:7,15:18,38:0.2821:2,2:26.6:1:29.7:1:1:1.01484:32.8:44:0.2857:0:4.6 -9 67320872 . A C 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.57096;SOR=Inf;LSEQ=GCATTCAGGCCTAAGGTGAA;RSEQ=AAGGAAATATCTTCCCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:7,18:0:2,0:24.6:1:29.6:1:1:0:34.1:24:1:0:5.8 0/1:75:3:0,3:22,50:0.04:2,0:31:1:33:1:0.55104:0:38.7:6:0.04:0:6.3 -9 67320878 . A C 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.35064;LSEQ=AGGCCTAAGGTGAAAAAGGA;RSEQ=ATATCTTCCCATAAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:5,16:0.087:2,2:11.5:1:33.5:1:0.46245:3.01:40.5:4:0.087:0:7 0/1:70:8:2,6:16,46:0.1143:2,2:21.4:1:30.4:1:1:1.04283:36.6:16:0.1143:0:5 -9 67320898 . A G 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0229;LSEQ=AATATCTTCCCATAAAAACT;RSEQ=GACAGAAGCATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:0,11:0.1538:0,2:21.5:1:30.5:1:0.15385:0:26:4:0.1538:0:7 0/1:51:8:4,4:4,39:0.1569:2,2:20.5:1:29.1:1:0.01469:9.07:22:16:0.16:0:6.4 -9 67320911 . C G 51 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAACTAGACAGAAGCATT;RSEQ=TCAGAAACTTGTTTAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:0:2,0:10.1:1:33:1:1:0:32.5:20:1:0:3.9 0/1:37:3:0,3:3,31:0.0811:2,0:11:0:32.3:1:1:0:28:6:0.0811:0:3.3 -9 67320927 . G T 49 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCTCAGAAACTTGTTTA;RSEQ=GATGTGTGTACTCAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:0,3:0,0:0.6:0,0:43.3:1:31:1:1:0:20:6:1:0:7 -9 67320929 . A C 52 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCAGAAACTTGTTTAGG;RSEQ=TGTGTGTACTCAACTAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:0,3:0,2:0.6:0,0:41.3:1:33.3:1:1:0:20:6:0.6:0:7 -9 67320933 . G A 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAAACTTGTTTAGGATGT;RSEQ=TGTACTCAACTAACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:0,3:0,2:0.6:0,0:37.3:1:31.7:1:1:0:20:6:0.6:0:7 -9 67320935 . G C 53 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAACTTGTTTAGGATGTGT;RSEQ=TACTCAACTAACAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:0,3:0,2:0.6:0,0:35.3:1:33.7:1:1:0:20:6:0.6:0:7 -9 67320949 . G A 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGTGTACTCAACTAACA;RSEQ=AGTTGAAACTTTCTTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:0,3:0,2:0.6:0,0:21.3:1:32:0:1:0:20:6:0.6:0:7 -9 67320957 . A C 51 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCAACTAACAGAGTTGAA;RSEQ=CTTTCTTTTGATAGAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:1:0,0:13.3:1:32.7:1:1:0:20:6:1:0:7 -9 67322275 . A G 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGGCTCACTGCAACCTCC;RSEQ=CCTCCCGGGTTCACACCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:30:1:1:0:22:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 67322281 . C T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACTGCAACCTCCACCTCC;RSEQ=GGGTTCACACCATTCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26.5:1:30:1:1:0:22:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68412219 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAAGGAGAGCACCGACA;RSEQ=GATGCTGGTCTTCCACGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:42:0:31:0:1:0:21:2:1:0:4 1/0:3:2:1,1:1,0:0.6667:0,2:7:0:32:0:1:0:60:4:0.6667:0:7.5 -9 68412248 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TCTTCCACGCATTCCTGGAA;RSEQ=TTTCTGGGGCCCCACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14:1:25.5:1:1:0:23.5:4:1:0:5.5 1/0:4:2:1,1:1,1:0.5:2,2:36:0:33:1:1:1:60:4:0.5:0:7.5 -9 68412255 . G C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CGCATTCCTGGAAGTTTCTG;RSEQ=GGCCCCACAGAGCTCGCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:14:1:29:1:1:0:23.5:4:1:0:5.5 1/0:4:2:1,1:1,1:0.5:2,2:43:0:32:0:1:1:60:4:0.5:0:7.5 -9 68412268 . C G 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTCTGGGGCCCCACAGAG;RSEQ=TCGCGAAACAAACAGTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:35:0:31:0:1:0:26:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:14.5:1:27:1:1:1:45.5:4:0.5:0:4.5 -9 68412270 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTCTGGGGCCCCACAGAGCT;RSEQ=GCGAAACAAACAGTCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:37:0:29:0:1:0:26:2:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:37.5:1:30:1:1:1:60:4:0.5:0:7.5 -9 68412272 . C G 45 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGGGGCCCCACAGAGCTCG;RSEQ=GAAACAAACAGTCAACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:33.7:1:29:1:1:0:57:6:1:0:6.7 -9 68412283 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAGCTCGCGAAACAAACA;RSEQ=TCAACATGGTCACGCTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:50:0:13:0:1:0:26:0:0:0:5 1/0:3:2:1,1:0,1:0.6667:0,2:24.5:1:30.5:1:1:0:60:4:0.6667:0:7.5 -9 68412293 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACAAACAGTCAACATGG;RSEQ=CACGCTTTCGGGGGGCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:41:0:29:0:1:0:26:2:1:0:5 1/0:3:2:1,1:0,1:0.6667:0,2:14.5:1:30:1:1:0:60:4:0.6667:0:7.5 -9 68412485 . A G 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATGTGGATGAAAAACAGACA;RSEQ=CTACCTGAGTCTCGGCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:20:1:31.5:1:1:0:35.5:4:1:0:4 1/1:3:3:2,1:0,0:1:0,2:13.7:1:31.3:1:1:0:44.7:6:1:0:5.7 -9 68412487 . T C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGATGAAAAACAGACAAC;RSEQ=ACCTGAGTCTCGGCTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:20:1:32.5:1:1:0:35.5:4:1:0:4 1/1:3:3:2,1:0,0:1:0,2:14.3:1:30.3:1:1:0:44.7:6:1:0:5.7 -9 68412507 . G T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACCTGAGTCTCGGCTCATT;RSEQ=CTCTCTGGGGAATTCGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:50:0:31:0:1:0:40:2:1:0:2 1/0:3:2:1,1:1,0:0.6667:0,2:34.5:1:31:0:1:0:48.5:4:0.6667:0:5.5 -9 68412510 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTGAGTCTCGGCTCATTGCT;RSEQ=TCTGGGGAATTCGCTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:47:0:30:0:1:0:40:2:1:0:2 1/0:3:2:2,0:0,1:0.6667:0,0:25:1:31:1:0.33333:0:50:4:0.6667:0:6 -9 68412517 . G A 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCGGCTCATTGCTCTCTGGG;RSEQ=AATTCGCTCATTCCTTCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:1:31:1:1:0:50:4:1:0:2 1/0:4:3:1,2:1,0:0.75:0,2:30:1:29:1:1:0:52.3:6:0.75:0:5.3 -9 68412522 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATTGCTCTCTGGGGAATT;RSEQ=GCTCATTCCTTCGGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:22:1:30.5:1:1:0:50:4:1:0:2 0/1:5:2:1,1:1,2:0.4:2,2:17.5:1:29:1:1:1.73:49.5:4:0.4:0:7 -9 68412534 . C T 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=GGGGAATTCGCTCATTCCTT;RSEQ=GGAAACGGAATTGGTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:12:0:31:0:1:0:50:2:0.3333:0:5 1/0:5:3:1,2:1,1:0.6:2,2:33.3:1:30.3:1:1:1.7321:52.3:6:0.6:0:5.3 -9 68412540 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TTCGCTCATTCCTTCGGAAA;RSEQ=GGAATTGGTCTGAATTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:20.7:1:31.3:1:1:0:50:6:1:0:3 0/1:6:2:1,1:2,2:0.3333:2,2:35.5:1:29:1:1:1:49.5:4:0.3333:0:7 -9 68412547 . G C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ATTCCTTCGGAAACGGAATT;RSEQ=GTCTGAATTGCTCCGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.8:1:30.3:1:1:0:51.5:8:1:0:2.8 0/1:6:2:1,1:2,2:0.3333:2,2:36:1:29.5:1:1:1:49.5:4:0.3333:0:7 -9 68412584 . T C 47 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGAAGTAACCCAGGCTGG;RSEQ=GATCCAGAGGGCCGCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:36.3:1:30.3:1:1:0:55.3:6:1:0:3 1/0:4:3:1,2:1,0:0.75:0,2:24.3:1:29.7:1:1:0:53:6:0.75:0:6.3 -9 68412707 . AT CG 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTTCTGGAGGCATAAGAC;RSEQ=TTTTTGTCTCTGCCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:44:0:32.5:0:1:0:40:2:1:0:4 1/1:3:3:2,1:0,0:1:0,2:16:1:30.4:1:1:0:52.7:6:1:0.3333:5.7 -9 68412726 . T C 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTTTTGTCTCTGCCTTC;RSEQ=GTTCTCTGTTTCTTGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:27:0:33:0:1:0:40:2:1:0:4 1/1:4:4:2,2:0,0:1:0,2:26:1:30.3:1:1:0:54.5:8:1:0:5.5 -9 68412753 . T C 61 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTTTCTTGCTCCTTTTGTC;RSEQ=CTCCGTCCATCCTTCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:39.3:1:30.8:1:1:0:54.5:8:1:0:5.5 -9 68412756 . CC TG 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTGCTCCTTTTGTCTCT;RSEQ=GTCCATCCTTCCATCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:39:1:30.4:1:1:0:54.5:8:1:0:4.5 -9 68412779 . A T 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCCTTCCATCTGTTCT;RSEQ=CCCTCCCTCCCCTGGCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:11:1:29.7:1:1:0:60:6:1:0:5.3 1/1:4:4:2,2:0,0:1:0,2:22.5:1:29.3:1:1:0:58.8:8:1:0:5 -9 68412792 . T C 48 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CTGTTCTACCCTCCCTCCCC;RSEQ=GGCTTTTTCCTCCCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24:1:30.7:1:1:0:60:6:1:0:5.3 0/1:4:1:1,0:1,2:0.25:2,0:22:0:32:0:1:0:57:2:0.25:0:7 -9 68412795 . C G 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TTCTACCCTCCCTCCCCTGG;RSEQ=TTTTTCCTCCCTTTCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0.75:0,2:27:1:32:1:1:0:60:6:0.75:0:5.3 0/0:4:0:0,0:1,2:0:2,0:11:1:31:1:1:0:59.3:6:0.75:0:4.3 -9 68412801 . C T 29 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53981;LSEQ=CCTCCCTCCCCTGGCTTTTT;RSEQ=CTCCCTTTCTCCCTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:7:1:29.5:1:1:1.73:60:4:0.4:0:2.5 0/1:4:1:1,0:1,2:0.25:2,0:31:0:28:0:1:0:57:2:0.25:0:7 -9 68412809 . TCTCC T 51 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCTGGCTTTTTCCTCCCTT;RSEQ=CTCCCTCCCTCTTTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:2,1:0.5:2,2:40.3:1:32.3:1:1:3.10575:60:6:0.5:0:5.3 1/1:1:1:1,0:0,0:1:0,0:40:0:31:0:1:0:57:2:1:0:7 -9 68412820 . C T 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=TCCTCCCTTTCTCCCTCCCT;RSEQ=CCTCTTTCTCTCCCTTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:3,2:0.375:2,2:37.3:1:30.7:1:1:2.60168:60:6:0.375:0:5.3 0/0:3:0:0,0:2,1:0:2,0:22:1:32:1:1:0:59:6:1:0:3.3 -9 68412840 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=CCCTCTTTCTCTCCCTTCCG;RSEQ=GGTCCCTCCTTCCACCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:17:0:32.5:1:1:1.29098:60:4:0.2222:0:2.5 0/0:8:0:0,0:4,4:0:2,0:20.6:1:30:1:1:0:54:16:1:0:3.9 -9 68412841 . G T 25 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=4.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=CCTCTTTCTCTCCCTTCCGG;RSEQ=GTCCCTCCTTCCACCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:19:1:31.9:1:1:0:56:18:1:0:3.2 0/1:9:2:1,1:4,3:0.2222:2,2:19:1:25.5:1:1:1.29098:57.5:4:0.2222:0:6.5 -9 68412864 . G T 89 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07692;SOR=10.6592;LSEQ=CCCTCCTTCCACCCATCCTT;RSEQ=CCTAGCTCCATCCTTCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,0:0.4:0,2:27.5:1:31.5:1:1:0:42:4:0.5:0:3 1/1:10:9:4,5:1,0:0.9:0,2:27.2:1:28.2:1:1:0:52.9:18:0.9:0:4 -9 68412896 . CT TC 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.30472;LSEQ=CCTTCCATCTCACTCTGTCT;RSEQ=GTTCCTGTCCTCATCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:0.3333:0,0:42:0:32.5:0:1:0:24:2:0.3333:0:3 0/1:10:4:2,2:3,3:0.4:2,2:27.3:1:29.3:1:1:1:49.3:8:0.4:0:2.8 -9 68412897 . T C 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51049;SOR=0.24443;LSEQ=CTTCCATCTCACTCTGTCTC;RSEQ=GTTCCTGTCCTCATCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:15.5:1:20.5:1:1:0:60:1:1:0:1 0/1:10:3:1,2:2,1:0.3:2,2:36.7:1:30:1:1:3.10575:49.3:6:0.5:0:5 -9 68412922 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTCCTCATCTCTGCCTGC;RSEQ=TTCCCTCTTGCCTGGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:17:0:33:0:1:0:24:2:1:0:3 0/1:10:2:1,1:3,5:0.2:2,2:28:0:32:0:1:1.58:45:4:0.2:0:4.5 -9 68412929 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCTCTGCCTGCCTTCCCT;RSEQ=TTGCCTGGAAAGGGCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:10:0:33:0:1:0:24:2:1:0:3 0/1:8:2:1,1:3,3:0.25:2,2:21:0:32:0:1:1:45:4:0.25:0:4.5 -9 68412940 . A T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTCCCTCTTGCCTGGAA;RSEQ=GGGCAGCACCCTGGTTTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:3,2:0.2857:2,2:10:0:32:0:1:1.41418:45:4:0.3333:0:4.5 -9 68412969 . C G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGTTTGCGCGAGGTCT;RSEQ=GGGTCTTTATTTAGTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:29:1:28.5:1:1:1.73:60:4:0.4:0:2.5 -9 68412987 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGGGTCTTTATTTAGTTG;RSEQ=AAGGCGCTCTATGGTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:10:0:27:0:1:0:23:2:1:0:8 1/0:3:2:1,1:0,1:0.6667:0,2:29:1:31.5:1:1:0:60:4:0.6667:0:2.5 -9 68413038 . G C 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20455;SOR=Inf;LSEQ=GGCGGGACACGGGTTGGCAA;RSEQ=TGATGGTGAGCGAAGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:2,3:0.4444:2,2:13.8:1:33.5:1:1:1.43:60:8:0.5:0:2 1/1:3:3:1,2:0,0:1:0,2:27.7:1:31.7:1:1:0:60:6:1:0:3.7 -9 68413045 . T A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGGGTTGGCAAGTGATGG;RSEQ=GAGCGAAGAGGCGGAGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:27:1:32:0:1:1.41:30:4:0.3333:0:7 0/0:3:0:0,0:1,2:0:2,0:30:1:30:1:1:0:60:6:1:0:3.7 -9 68413058 . G A 63 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GTGATGGTGAGCGAAGAGGC;RSEQ=GAGGAGTTGAGCCACAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:1,2:0.5714:2,2:26.5:1:31.5:1:1:1.81:38.5:8:0.5714:0:5.8 0/0:2:0:0,0:1,1:0:2,0:44.5:1:30.5:1:1:0:60:4:1:0:4 -9 68413066 . T C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCGAAGAGGCGGAGGAGT;RSEQ=GAGCCACAGAAAGGAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:20.3:1:30.9:1:1:0:47.6:14:1:0:4.7 1/1:2:2:1,1:0,0:1:0,2:37:1:31.5:1:1:0:60:4:1:0:4 -9 68413072 . A G 61 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGGCGGAGGAGTTGAGCC;RSEQ=CAGAAAGGAGAACTGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,0:0.6667:0,2:15.3:1:30.5:1:1:0:42.3:8:0.8:0:5.5 1/1:2:2:1,1:0,0:1:0,2:31:1:32.5:1:1:0:60:4:1:0:4 -9 68413094 . A C 65 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AGAAAGGAGAACTGGCCTGG;RSEQ=TTCTGCCCCGGCCCAGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:24.3:1:32.5:1:1:0:44:8:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:9:1:31:1:1:0:60:4:0.6667:0:4 -9 68413106 . C G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCTGGATTCTGCCCCGG;RSEQ=CCAGTGTTTCGCGGACTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:0.4:2,0:34.5:1:32.5:1:0.4:0:40:4:0.4:0:4.5 0/0:2:0:0,0:1,1:0:2,0:15:1:31.5:1:1:0:60:4:1:0:2 -9 68413143 . T C 53 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGTCTCCGCCAACCCGA;RSEQ=TGAAGAACGCGGGGGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:32:1:34:0:1:0:43:6:0.6:0:6.7 0/0:1:0:0,0:1,0:0:0,0:37:0:26:0:1:0:60:2:1:0:0 -9 68413159 . GG AA 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCGATTGAAGAACGCGGGGG;RSEQ=AAAGGGAGGAGAGCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:38:0:31.3:1:1:0:47:4:0.5:0:5.5 0/0:2:0:0,0:1,1:0:2,0:18.5:1:29:1:1:0:60:4:1:0:0 -9 68413160 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CGATTGAAGAACGCGGGGGG;RSEQ=AAAGGGAGGAGAGCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,0:0.5:0,0:12.5:1:28:1:1:0:40:4:1:0:4.5 0/0:2:0:0,0:1,1:0:2,0:18.5:1:29.5:1:1:0:60:4:1:0:0 -9 68413168 . G T 75 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GAACGCGGGGGGGAAAGGGA;RSEQ=GAGAGCTCCGCCTGGGCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:23.3:1:29.3:1:1:0:44.8:12:1:0:5.2 0/0:2:0:0,0:1,1:0:2,0:18.5:1:29:1:1:0:60:4:1:0:0 -9 68413195 . G A 60 d7;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2;SOR=0;LSEQ=TCCGCCTGGGCTAGTTAGAA;RSEQ=ACTAGGCTGCTGCCTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:21.5:1:30.3:1:1:0:47.3:8:1:0:5.5 0/0:1:0:0,0:0,1:0:0,0:49:0:33:0:1:0:60:2:1:0:0 -9 68413290 . G T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCGGGATGCTCAGGAAT;RSEQ=CTTTCTTTTCATTGTTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:39:1:31.5:1:1:0:49:4:0.6667:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68413298 . T G 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTCAGGAATGCTTTCTT;RSEQ=TCATTGTTGACAGCCCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:31:1:33.5:1:1:0:49:4:0.6667:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68413304 . G C 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAATGCTTTCTTTTCATT;RSEQ=TTGACAGCCCTACTCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:25:1:33.5:1:1:0:49:4:0.6667:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68413316 . A C 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTCATTGTTGACAGCCCT;RSEQ=CTCTGTGTGGAGTCTCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:13:1:32.5:1:1:0:49:4:0.6667:0:7 1/1:1:1:0,1:0,0:1:0,0:2:0:28:0:1:0:60:2:1:0:4 -9 68413363 . G C 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TGGAACTCAGGGATCCTAGG;RSEQ=AGGTCAGCTGGAAGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:25.7:1:33.3:1:1:0:46:6:0.75:0:6.7 1/1:5:5:2,3:0,0:1:0,2:27.4:1:31.6:1:1:0:54.8:10:1:0:4.8 -9 68413383 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=2.41422;LSEQ=GAGGTCAGCTGGAAGGGAAG;RSEQ=CACGCCTCTCCATACCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:2,2:0.2:2,0:4:0:15:0:1:0:42:0:0:0:5 0/1:5:2:1,1:1,2:0.4:2,2:37.5:1:31.5:1:1:1.73:60:4:0.4:0:5 -9 68413386 . C G 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GTCAGCTGGAAGGGAAGACA;RSEQ=GCCTCTCCATACCAAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:41:1:32:1:1:1.7321:39:4:0.4:0:8 0/0:5:0:0,0:2,3:0:2,0:38:1:30.8:1:1:0:54.8:10:1:0:4.8 -9 68413396 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=AGGGAAGACACGCCTCTCCA;RSEQ=ACCAAGCCTGAGGTTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:19.5:1:31.5:1:1:1:54.5:4:0.3333:0:3.5 0/1:5:2:1,1:1,2:0.4:2,2:46.5:1:32:1:1:1.73:47:4:0.4:0:5 -9 68413413 . A G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CCATACCAAGCCTGAGGTTC;RSEQ=CTGCAAAAGAGAGGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:31.5:1:30:1:1:1:39:4:0.3333:0:8 0/0:5:0:0,0:2,3:0:2,0:23:1:29.8:1:1:0:54.8:10:1:0:4.8 -9 68413415 . T C 67 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATACCAAGCCTGAGGTTCAC;RSEQ=GCAAAAGAGAGGCCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:0.8333:0,2:26.8:1:29.2:1:1:0:45.8:10:0.8333:0:5.6 1/1:4:4:2,2:0,0:1:0,2:26.3:1:30:1:1:0:53.5:8:1:0:5 -9 68413418 . A G 57 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=CCAAGCCTGAGGTTCACTGC;RSEQ=AAAGAGAGGCCGCCGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:23:1:28.8:1:1:1:46.8:8:0.6667:0:5.8 1/0:4:2:1,1:1,1:0.5:2,2:24.5:1:32.5:1:1:1:47:4:0.5:0:5 -9 68413430 . GCCGCCCTGCCCCCACCCTGCCC G 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=TTCACTGCAAAAGAGAGGCC;RSEQ=CCACCCTGCCCCAAACCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:21.3:1:31.4:1:1:1:45:8:0.6667:0.5:5.8 1/0:4:2:1,1:1,1:0.5:2,2:12.5:1:30.5:1:1:1:53.5:4:0.5:0.5:3 -9 68413467 . A C 30 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.77001;LSEQ=CTGCCCCCACCCTGCCCCAA;RSEQ=CCCGCCCCAACCTGCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:0,2:0.4:0,0:13:1:32.5:1:0.33333:0:41.5:4:0.4:0:6 0/1:6:2:2,0:2,1:0.3333:2,0:1.5:1:30.5:1:1:0:50:4:0.3333:0:6 -9 68413485 . C A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=AAACCCGCCCCAACCTGCTC;RSEQ=TCCAGCAGAGCCCTGTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:25.8:1:32.6:1:1:0:48.8:10:1:0:4.2 0/1:6:2:2,0:3,1:0.3333:2,0:23:1:31.5:1:1:0:58.5:4:0.3333:0:3.5 -9 68413499 . T A 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51049;SOR=0.24443;LSEQ=CTGCTCCTCCAGCAGAGCCC;RSEQ=GTGTTCTTCCTGTCTGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:19:1:29:1:1:1.73:42:4:0.4:0:5.5 0/1:8:1:1,0:4,3:0.125:2,0:33:0:32:0:1:0:43:2:0.125:0:7 -9 68413505 . C A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=CTCCAGCAGAGCCCTGTGTT;RSEQ=TTCCTGTCTGAGGAGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:19:1:29.8:1:1:0:48.7:12:1:0:4.3 0/1:9:2:1,1:4,3:0.2222:2,2:30:1:30:1:1:1.29098:52:4:0.2222:0:3.5 -9 68413506 . T G 47 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04396;SOR=0;LSEQ=TCCAGCAGAGCCCTGTGTTC;RSEQ=TCCTGTCTGAGGAGTGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:1,2:0.5:2,2:19:1:29.7:1:1:1:43.7:6:0.5:0:5.7 0/0:9:0:0,0:4,4:0:2,0:31.6:1:29.8:1:1:0:54.5:16:0.8889:0:2.8 -9 68413508 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.175;SOR=0;LSEQ=CAGCAGAGCCCTGTGTTCTT;RSEQ=CTGTCTGAGGAGTGGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:25:1:30.5:1:1:1.41:44:4:0.2857:0:6.5 0/0:9:0:0,0:5,4:0:2,0:33.2:1:31:1:1:0:53.2:18:1:0:3.1 -9 68413512 . T G 98 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCCCTGTGTTCTTCCTG;RSEQ=CTGAGGAGTGGTTCCAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:20.3:1:31.2:1:1:0:48:12:1:0:4.8 1/1:9:9:5,4:0,0:1:0,2:34:1:31.2:1:1:0:53.2:18:1:0:3.1 -9 68413535 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.25853;LSEQ=GAGGAGTGGTTCCAGCAAAG;RSEQ=GGGCTCTTCCACGTCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:2,5:0.125:2,0:20:0:32:0:0.375:0:34:2:0.125:0:3 0/1:13:2:1,1:6,5:0.1538:2,2:12:0:31.5:1:1:1.18321:60:4:0.1538:0:3 -9 68413537 . G T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14617;SOR=0.19966;LSEQ=GGAGTGGTTCCAGCAAAGCG;RSEQ=GCTCTTCCACGTCCTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:2,2:0.5:2,2:19.5:1:31.5:1:1:2.60168:47.3:8:0.5:0:5.3 0/1:13:2:1,1:6,5:0.1538:2,2:25:1:29.5:1:1:1.18321:52.5:4:0.1538:0:5 -9 68413547 . C G 52 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03231;SOR=0;LSEQ=CAGCAAAGCGGGCTCTTCCA;RSEQ=GTCCTTCAGCTCCCCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:3,3:0.3333:2,2:34:1:33:0:1:1.8525:43:6:0.3333:0:6.7 0/0:17:0:0,0:8,7:0:2,0:18.6:1:30.3:1:1:0:53.7:30:0.8824:0:2.8 -9 68413562 . C A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.36723;LSEQ=TTCCACGTCCTTCAGCTCCC;RSEQ=CAGTGGCGCCGGATCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:3,6:0.1:2,0:47:0:32:0:0.4:0:34:2:0.1:0:3 0/1:15:2:1,1:6,7:0.1333:2,2:25.5:1:27.5:1:1:1.15:51.5:4:0.1333:0:4 -9 68413563 . C G 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04615;SOR=0;LSEQ=TCCACGTCCTTCAGCTCCCC;RSEQ=AGTGGCGCCGGATCTAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:3,4:0.3:2,2:45.7:1:32:1:1:1.44135:43:6:0.3:0:6.7 0/0:16:0:0,0:8,8:0:2,0:24.3:1:30.7:1:1:0:53.4:32:1:0:2.6 -9 68413565 . G A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26154;SOR=Inf;LSEQ=CACGTCCTTCAGCTCCCCCA;RSEQ=TGGCGCCGGATCTAGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:32.2:1:33:1:1:0:46.5:20:1:0:4.5 0/1:16:3:2,1:6,7:0.1875:2,2:22.7:1:30.7:1:1:2.21:40:6:0.1875:0:2.7 -9 68413566 . TG T 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.3172;LSEQ=ACGTCCTTCAGCTCCCCCAG;RSEQ=GCGCCGGATCTAGGAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:3,5:0.1111:2,0:29:0:33:0:1:0:43:2:0.1111:0:4 0/1:14:2:1,1:5,7:0.1429:2,2:28.5:1:33.5:1:1:1.37:60:4:0.1429:0:1 -9 68413569 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25296;SOR=Inf;LSEQ=TCCTTCAGCTCCCCCAGTGG;RSEQ=GCCGGATCTAGGAAAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:35.4:1:31.9:1:1:0:47.1:18:1:0:4.2 0/1:14:3:2,1:4,7:0.2143:2,2:24:1:30.7:1:0.53846:3.19:40:6:0.2143:0:2.7 -9 68413570 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51087;SOR=Inf;LSEQ=CCTTCAGCTCCCCCAGTGGC;RSEQ=CCGGATCTAGGAAAGGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:35.2:1:32.6:1:1:0:47.1:18:1:0:4.2 0/1:15:2:1,1:5,8:0.1333:2,2:42:0:30:1:1:1.55:60:4:0.1333:0:3 -9 68413581 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52;SOR=Inf;LSEQ=CCCAGTGGCGCCGGATCTAG;RSEQ=AAAGGTTGTGCCTTTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:31:1:32.3:1:1:0:47.1:18:1:0:4.2 0/1:16:2:1,1:6,8:0.125:2,2:36:1:32:1:1:1.31:60:4:0.125:0:1 -9 68413585 . G T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63491;SOR=0.51539;LSEQ=GTGGCGCCGGATCTAGGAAA;RSEQ=GTTGTGCCTTTTGCTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:1,3:0.3333:2,2:20:1:31.7:1:1:1.41:41.3:6:0.3333:0:4.3 0/1:15:3:1,2:6,6:0.2:2,2:40.7:1:30.7:1:1:1.91151:60:6:0.2:0:1.3 -9 68413586 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32559;SOR=0.32462;LSEQ=TGGCGCCGGATCTAGGAAAG;RSEQ=TTGTGCCTTTTGCTGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:2,4:0.3333:2,2:28:1:30.7:1:1:1:43:6:0.3333:0:6.7 0/1:15:2:1,1:6,7:0.1333:2,2:45:1:27:1:1:1.15:60:4:0.1333:0:4 -9 68413590 . T A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.62319;SOR=0.45948;LSEQ=GCCGGATCTAGGAAAGGTTG;RSEQ=GCCTTTTGCTGAAACTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:3,5:0.2727:2,2:24:1:30.7:1:1:1.18052:43:6:0.2727:0:6.7 0/1:14:2:1,1:6,6:0.1429:2,2:48.5:1:29:1:1:1:60:4:0.1429:0:4 -9 68413594 . T G 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48148;SOR=Inf;LSEQ=GATCTAGGAAAGGTTGTGCC;RSEQ=TTTGCTGAAACTCTGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:14.5:1:31.2:1:1:0:49.2:26:1:0:3.8 0/1:14:2:1,1:6,6:0.1429:2,2:48:1:27:1:1:1:60:4:0.1429:0:4 -9 68413602 . A G 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=AAAGGTTGTGCCTTTTGCTG;RSEQ=AACTCTGGGGTTGACAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:0.1538:2,2:13:0:31:1:1:1.18:55.5:4:0.1538:0:2 0/0:14:0:0,0:7,7:0:2,0:28.7:1:28.8:1:1:0:55:28:1:0:2.1 -9 68413604 . ACT A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32593;SOR=3.7142;LSEQ=AGGTTGTGCCTTTTGCTGAA;RSEQ=CTGGGGTTGACAGGAGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:6,6:0.0714:2,0:27:0:34:0:1:0:60:2:0.0714:0:1 0/1:13:3:2,1:5,5:0.2308:2,2:38:1:30.7:1:1:1.90:41.7:6:0.2308:0:1.3 -9 68413607 . C T 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.64831;SOR=0.42986;LSEQ=TTGTGCCTTTTGCTGAAACT;RSEQ=TGGGGTTGACAGGAGCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:5,5:0.2857:2,2:9.3:1:31.3:1:0.58042:2.77987:51:8:0.2857:0:6 0/1:14:2:1,1:7,5:0.1429:2,2:35:1:30.5:1:1:1.36624:60:4:0.1429:0:4 -9 68413612 . G A 62 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10007;SOR=0;LSEQ=CCTTTTGCTGAAACTCTGGG;RSEQ=TTGACAGGAGCTCATCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:5,5:0.2857:2,2:9.3:1:31.3:1:0.58042:2.77987:51:8:0.2857:0:6 0/0:12:0:0,0:7,5:0:2,0:27.5:1:30.8:1:1:0:55.4:24:1:0:1.7 -9 68413635 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15584;SOR=0;LSEQ=GACAGGAGCTCATCTAACAG;RSEQ=CTGGAGGTGAGTGCAGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:44:0:31:1:1:1.29098:47.5:4:0.2222:0:5.5 0/0:13:0:0,0:7,6:0:2,0:15.1:1:30:1:1:0:55.8:12:1:0:1.8 -9 68413638 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15584;SOR=0;LSEQ=AGGAGCTCATCTAACAGGCT;RSEQ=GAGGTGAGTGCAGACGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:39:0:31:1:1:1.29098:60:4:0.2222:0:5 0/0:13:0:0,0:7,6:0:2,0:14.4:1:29.7:1:1:0:55.8:12:1:0:1.8 -9 68413653 . C T 61 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0915;SOR=0;LSEQ=AGGCTGGAGGTGAGTGCAGA;RSEQ=GAGAGCCCCGGCTCCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:3,3:0.4:2,2:31.3:1:30.8:1:1:1:53.8:8:0.4:0:5.3 0/0:8:0:0,0:3,2:0:2,0:15.6:1:28:1:1:0:55.8:4:0.5714:0:1.4 -9 68413657 . AG CA 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48529;SOR=0;LSEQ=TGGAGGTGAGTGCAGACGAG;RSEQ=CCCCGGCTCCTGGAGCGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:26.5:1:30.8:1:1:1:47.5:4:0.2:0:4.5 0/0:7:0:0,0:5,2:0:2,0:28.1:1:28.7:1:1:0:60:14:1:0:1.6 -9 68413660 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=AGGTGAGTGCAGACGAGAGC;RSEQ=CCGGCTCCTGGAGCGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:24.5:1:30.5:1:1:1:47.5:4:0.2:0:4.5 0/0:7:0:0,0:5,2:0:2,0:29.4:1:30.1:1:1:0:60:14:1:0:1.6 -9 68413664 . GC G 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GAGTGCAGACGAGAGCCCCG;RSEQ=TCCTGGAGCGGTTGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:19:0:31.5:1:1:1:60:4:0.25:0:5 0/0:8:0:0,0:5,3:0:2,0:28.1:1:29.5:1:1:0:60:7:1:0:1.6 -9 68413675 . G T 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20588;SOR=0;LSEQ=AGAGCCCCGGCTCCTGGAGC;RSEQ=GTTGGGAGGTGCCCGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:10:0:29.5:1:1:1:60:4:0.25:0:5 0/0:9:0:0,0:5,4:0:2,0:27.4:1:28.6:1:1:0:60:18:1:0:1.8 -9 68413706 . C T 87 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCGGTTGGCTGGCATCTG;RSEQ=GCTTGACGCGGAGGCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31:1:1:0:60:4:1:0:1.5 1/1:9:8:3,5:1,0:0.8889:0,2:24.6:1:29.3:1:0.44444:0:60:16:0.8889:0:2 -9 68413740 . G C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GCCTCCGGGGTCACGAGCTC;RSEQ=GGAGGTGAAGGTGCCCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:8:1:31.5:1:1:0:60:4:0.6667:0:2.5 1/0:6:4:1,3:1,0:0.6667:0,2:29.5:1:25:1:0.4:0:60:3:0.6:0:2.3 -9 68413748 . A G 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0.23975;LSEQ=GGTCACGAGCTCGGGAGGTG;RSEQ=AGGTGCCCCGTCTTCGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:11.5:1:30:1:1:1:41.5:4:0.5:0:6 0/1:6:1:1,0:2,3:0.1667:2,0:41:0:33:0:1:0:25:2:0.1667:0:5 -9 68413775 . CC AA 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CCCGTCTTCGGGTTCCCATG;RSEQ=GCCCTGGCGACCTGGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:39.5:1:29.5:1:1:3.1622:41.5:4:0.2857:0:5 0/1:7:2:1,1:2,3:0.2857:2,2:22.5:1:28.5:1:1:1.41:37:4:0.2857:0:6 -9 68413791 . G C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CATGCCGCCCTGGCGACCTG;RSEQ=GGCTCCAGCCCCACCACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:4,3:0.3:2,2:25.3:1:31:1:1:1.44:60:6:0.3:0:3 0/0:5:0:0,0:2,3:0:2,0:29.8:1:30.6:1:1:0:36.8:10:1:0:4.2 -9 68413801 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.52381;SOR=0;LSEQ=TGGCGACCTGGGGCTCCAGC;RSEQ=CCACCACGGACTCCGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:17:1:31.5:1:1:1.58108:42:4:0.2:0:1.5 0/0:5:0:0,0:2,3:0:2,0:35.6:1:30.6:1:1:0:36.8:10:1:0:4.2 -9 68413832 . T C 75 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4697;SOR=0;LSEQ=CTCCGGTGGGACGTGGGTGG;RSEQ=GCAAGCACACCTTTCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:28:1:31.6:1:1:0:56:10:1:0:3 1/0:7:5:4,1:0,1:0.7143:0,2:21.8:1:32.6:1:0.33333:0:38.2:10:0.7143:0:4.2 -9 68413838 . CA TG 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.18052;LSEQ=TGGGACGTGGGTGGTGCAAG;RSEQ=CACCTTTCCCCTGTGACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:7:0:30.5:0:1:0:40:2:0.25:0:4 0/1:7:2:1,1:3,2:0.2857:2,2:15.5:1:33:0:1:1.41418:37:4:0.2857:0:5 -9 68413846 . T G 66 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=GGGTGGTGCAAGCACACCTT;RSEQ=CCCCTGTGACTCAGCTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:28.3:1:31.7:1:1:0:60:6:1:0:2.3 1/0:7:4:2,2:2,1:0.5714:2,2:16:1:33.3:1:1:1.81007:31:8:0.5714:0:4.8 -9 68413849 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGTGCAAGCACACCTTTCC;RSEQ=CTGTGACTCAGCTTGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:25.3:1:32:1:1:0:60:6:1:0:2.3 0/1:7:2:1,1:3,2:0.2857:2,2:5.5:1:30.5:1:1:1.41418:37:4:0.2857:0:5 -9 68413870 . C G 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTGTGACTCAGCTTGAGGGG;RSEQ=CCCAAGCTGTCCCACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:2:1:30:1:1:1:40.5:4:0.5:0:6 1/0:6:3:2,1:2,1:0.5:2,2:17.7:1:28.3:1:1:1:36.3:6:0.5:0:6.3 -9 68413893 . G A 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.5321;LSEQ=CAAGCTGTCCCACTGAGCAC;RSEQ=CGCCCAGCAGGCCGTCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:23.5:1:30:1:1:2.44949:60:4:0.3333:0:4.5 0/1:5:1:1,0:3,1:0.2:2,0:12:0:25:0:1:0:25:2:0.2:0:6 -9 68413901 . C A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CCCACTGAGCACGCGCCCAG;RSEQ=AGGCCGTCGCGCTGTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:22.5:1:29:1:1:2.44949:40.5:4:0.3333:0:7 0/0:5:0:0,0:4,1:0:2,0:20.8:1:27:1:1:0:40.2:4:1:0:4.4 -9 68413905 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=CTGAGCACGCGCCCAGCAGG;RSEQ=CGTCGCGCTGTGGGTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:26.5:1:29.5:1:1:1.41418:40.5:4:0.2857:0:7 0/0:4:0:0,0:3,1:0:2,0:25:1:31:1:1:0:44:8:1:0:4 -9 68413909 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=0;LSEQ=GCACGCGCCCAGCAGGCCGT;RSEQ=GCGCTGTGGGTTCTGGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:39.5:1:31:1:1:1.8258:60:4:0.25:0:4.5 0/0:4:0:0,0:3,1:0:2,0:25:1:29:1:1:0:44:8:1:0:4 -9 68413916 . T C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.1321;LSEQ=CCCAGCAGGCCGTCGCGCTG;RSEQ=GGGTTCTGGTCTTCCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:4,3:1,0:0.7778:0,2:29.6:1:31.4:1:1:0:54.4:14:0.875:0:5 1/1:5:4:2,2:0,0:0.8:0,2:15.3:1:28.5:1:1:0:56.3:8:1:0:4.3 -9 68413918 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=CAGCAGGCCGTCGCGCTGTG;RSEQ=GTTCTGGTCTTCCTGTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:4,3:0.2222:2,0:20.5:1:33:0:0.5:0:60:4:0.2222:0:5 0/0:6:0:0,0:1,4:0:2,0:22.2:1:25.2:1:1:0:51:4:0.8:0:4.8 -9 68413927 . C T 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25296;SOR=0;LSEQ=GTCGCGCTGTGGGTTCTGGT;RSEQ=TTCCTGTCATTTGTTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:7,4:0.2143:2,2:22.7:1:31.3:1:1:1.13:60:6:0.2143:0:4.3 0/0:9:0:0,0:3,6:0:2,0:16.7:1:31.7:1:1:0:55:18:1:0:5.1 -9 68413948 . T G 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.67063;SOR=2.19053;LSEQ=TTCCTGTCATTTGTTGGGGT;RSEQ=CGGAGGCCACCAGGGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:7,5:1,3:0.6667:2,2:26:1:31.3:1:0.56923:3.84:56.8:11:0.6471:0:4.8 1/1:11:9:3,6:0,2:0.8182:0,2:22.9:1:33:1:1:0:54:18:0.8182:0:5.3 -9 68413950 . G A 48 v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97062;LSEQ=CCTGTCATTTGTTGGGGTTC;RSEQ=GAGGCCACCAGGGAGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:2,1:8,8:0.1579:2,2:37.3:1:30.3:1:1:1.93:60:6:0.1579:0:4.3 0/1:13:2:1,1:3,8:0.1538:2,2:28:1:24:1:1:2.45:60:1:0.0909:0:6 -9 68413954 . G A 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12084;LSEQ=TCATTTGTTGGGGTTCGGAG;RSEQ=CCACCAGGGAGTCTGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:2,2:8,7:0.2105:2,2:25.3:1:30:1:1:1.13484:50.3:8:0.2222:0:6.8 0/1:13:3:1,2:3,7:0.2308:2,2:28.3:1:28.3:1:1:1.15:57:6:0.25:0:7 -9 68413955 . C A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97062;LSEQ=CATTTGTTGGGGTTCGGAGG;RSEQ=CACCAGGGAGTCTGAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:9,7:0.1579:2,2:25:1:28.3:1:0.58204:2.44724:60:6:0.1579:0:2.7 0/1:13:2:0,2:4,7:0.1538:2,0:40:1:26.5:1:1:0:60:4:0.1538:0:3 -9 68413956 . C T 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.02204;LSEQ=ATTTGTTGGGGTTCGGAGGC;RSEQ=ACCAGGGAGTCTGAGGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:2,2:8,7:0.2105:2,2:25.3:1:29.5:1:1:1.13484:50.3:8:0.2222:0:6.8 0/1:14:3:1,2:4,7:0.2143:2,2:30.3:1:28:1:1:1.1321:57:6:0.2308:0:7 -9 68413958 . C G 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07339;SOR=Inf;LSEQ=TTGTTGGGGTTCGGAGGCCA;RSEQ=CAGGGAGTCTGAGGATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:25.7:1:31.2:1:1:0:57.8:36:1:0:3.7 0/1:14:3:1,2:4,7:0.2143:2,2:28:1:33.3:1:1:1.1321:57:6:0.2143:0:5.3 -9 68413969 . G A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=CGGAGGCCACCAGGGAGTCT;RSEQ=AGGATGGGAGAGCCCCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:20.5:1:28.5:1:1:1.26772:60:4:0.1111:0:4 0/0:12:0:0,0:4,8:0:2,0:32.8:1:31.6:1:1:0:58.5:24:1:0:4.4 -9 68413971 . G A 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15172;SOR=Inf;LSEQ=GAGGCCACCAGGGAGTCTGA;RSEQ=GATGGGAGAGCCCCAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:23.2:1:31.3:1:1:0:60:36:1:0:3.5 0/1:12:2:0,2:4,6:0.1667:2,0:25:0:33:0:0.51515:0:55.5:4:0.1667:0:5 -9 68413990 . TCGGAGGGAGGG CCGGAGGA 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42831;SOR=2.25359;LSEQ=AGGATGGGAGAGCCCCAGTT;RSEQ=GCCAGGACAGTGAACACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:2,4:1,2:0.4286:2,2:21:1:31.3:1:1:1:60:12:0.4615:0.2143:5.5 1/0:11:7:2,5:0,2:0.6364:0,2:18.6:1:31.2:1:1:0:57.4:14:0.6364:0.3636:4.3 -9 68413991 . CGGAG C 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0.36146;SOR=0.3518;LSEQ=GGATGGGAGAGCCCCAGTTT;RSEQ=GGAGGGGCCAGGACAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:1,2:0.4:2,2:32.3:1:32.3:1:1:1.81:60:8:0.5714:0:2.8 0/1:11:2:0,2:1,3:0.1818:2,0:24:1:32:0:1:0:60:4:0.3333:0:3 -9 68414008 . A G 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1698;SOR=0.21947;LSEQ=TTTCGGAGGGAGGGGCCAGG;RSEQ=CAGTGAACACAAAGCCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:4,4:1,1:0.6667:2,2:25.4:1:32.1:1:1:1:60:16:0.6667:0:4.4 0/1:7:2:0,2:0,0:0.2857:0,0:12:1:34:0:1:0:60:4:0.3333:0:3 -9 68414012 . T C 51 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GGAGGGAGGGGCCAGGACAG;RSEQ=GAACACAAAGCCCCGCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:5,4:0.2308:2,2:21:1:32.3:1:1:2.31595:60:6:0.25:0:6.7 0/0:7:0:0,0:1,4:0:2,0:14.4:1:30:1:1:0:58.2:10:0.8333:0:5.4 -9 68414027 . G A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21429;SOR=5.76413;LSEQ=GACAGTGAACACAAAGCCCC;RSEQ=CATGCTCGGGCAGGTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:4,6:0.2308:2,0:18.7:1:32:0:0.19231:0:60:6:0.2308:0:6.3 1/0:3:2:2,0:0,1:0.6667:0,0:18:1:29.5:1:0.33333:0:60:4:0.6667:0:6.5 -9 68414033 . T C 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAACACAAAGCCCCGCATGC;RSEQ=CGGGCAGGTTGGGAGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:5,6:0,1:0.8462:0,2:23:1:31.1:1:1:0:60:22:0.8462:0:4.5 1/1:2:2:1,1:0,0:1:0,2:20.5:1:32:0:1:0:55.5:4:1:0:7.5 -9 68414040 . G T 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCCGCATGCTCGGGCA;RSEQ=GTTGGGAGAGTCCTTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:7,6:0.1875:2,2:25.3:1:31.7:1:1:1.66:60:6:0.1875:0:6.3 0/0:2:0:0,0:1,1:0:2,0:13.5:1:32.5:1:1:0:55.5:4:1:0:7.5 -9 68414052 . C A 27 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGGGCAGGTTGGGAGAGT;RSEQ=CTTCTGCCTGTGCAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:10,4:0.125:2,2:7:0:27:1:1:2.34522:33:4:0.125:0:6 0/0:2:0:0,0:1,1:0:2,0:9:1:29:1:1:0:60:4:1:0:6 -9 68414063 . T C 122 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGGGAGAGTCCTTCTGCCTG;RSEQ=GCAGCCTGGCTGGGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:10,6:0,0:0.8889:0,2:21.3:1:30.6:1:1:0:54.3:32:1:0:5.2 1/1:1:1:0,1:0,0:1:0,0:21:0:25:0:1:0:60:2:1:0:4 -9 68414078 . C T 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07143;SOR=Inf;LSEQ=GCCTGTGCAGCCTGGCTGGG;RSEQ=TGGAGCAGGGGGATGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:28.6:1:32.4:1:1:0:53.9:30:1:0:5.3 0/1:6:2:1,1:2,2:0.3333:2,2:6:0:28.5:1:1:1:60:4:0.3333:0:6.5 -9 68414085 . AG A 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52569;SOR=0;LSEQ=CAGCCTGGCTGGGCTGGAGC;RSEQ=GGGGATGACCCTTGCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:0.1333:2,2:41:0:32:1:1:1.1547:33:4:0.1333:0:6 0/0:8:0:0,0:4,4:0:2,0:16.5:1:31.4:1:1:0:57.5:16:1:0:4.9 -9 68414087 . G C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11067;SOR=Inf;LSEQ=GCCTGGCTGGGCTGGAGCAG;RSEQ=GGGATGACCCTTGCTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:29.8:1:30.9:1:1:0:53.9:30:1:0:5.3 0/1:8:2:1,1:3,3:0.25:2,2:15:0:32:1:1:1:60:4:0.25:0:6.5 -9 68414089 . G A 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11067;SOR=Inf;LSEQ=CTGGCTGGGCTGGAGCAGGG;RSEQ=GATGACCCTTGCTTCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:29.9:1:30.8:1:1:0:53.9:30:1:0:5.3 0/1:8:2:1,1:3,3:0.25:2,2:17:0:32:1:1:1:59:4:0.25:0:4.5 -9 68414094 . A G 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCTGGAGCAGGGGGATG;RSEQ=CCCTTGCTTCCTGGCTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:10,6:0,0:1:0,2:28.3:1:31:1:1:0:51.9:32:1:0:5.3 1/1:8:8:4,4:0,0:1:0,2:24.1:1:32.9:1:1:0:57.5:16:1:0:4.9 -9 68414103 . T G 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.36898;SOR=3.33265;LSEQ=GCAGGGGGATGACCCTTGCT;RSEQ=CCTGGCTCACGAAAGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:5,5:0,0:0.6667:0,2:29.2:1:32:1:1:0:54.6:20:0.6667:0:4.8 1/1:8:7:3,4:0,0:0.875:0,2:30:1:32.9:1:1:0:57.1:14:0.875:0:4.6 -9 68414110 . T C 47 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.51364;LSEQ=GATGACCCTTGCTTCCTGGC;RSEQ=CACGAAAGCCCCCTGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:5,7:0.2:2,2:40.3:1:30:1:0.56923:2.61:47.7:6:0.2:0:6.3 0/1:9:1:1,0:3,5:0.1111:2,0:44:0:32:0:0.44444:0:60:2:0.1111:0:7 -9 68414113 . C T 32 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87959;LSEQ=GACCCTTGCTTCCTGGCTCA;RSEQ=GAAAGCCCCCTGTGGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,7:0.125:2,2:28:0:32:1:1:1.15:33:4:0.125:0:6 0/1:9:1:0,1:3,3:0.1111:2,0:10:0:24:0:1:0:40:2:0.1111:0:5 -9 68414124 . TG AC 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52923;SOR=0;LSEQ=CCTGGCTCACGAAAGCCCCC;RSEQ=TGGGAGAGCCCCAGGAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:18.5:1:29.8:1:1:1.46:50:4:0.1176:0:6 0/0:9:0:0,0:4,5:0:2,0:31.2:1:29.6:1:1:0:55.6:18:1:0:4.9 -9 68414128 . G T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51087;SOR=0;LSEQ=GCTCACGAAAGCCCCCTGTG;RSEQ=GAGAGCCCCAGGAGCGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:13:0:32:0:1:1.15:33:4:0.1333:0:6 0/0:9:0:0,0:4,5:0:2,0:28.1:1:30:1:1:0:55.6:18:1:0:4.9 -9 68414141 . A C 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.64992;SOR=1.80535;LSEQ=CCCTGTGGGAGAGCCCCAGG;RSEQ=GCGCAGGGCATGTGGGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:2,4:0.4167:2,2:23:1:30.2:1:1:1.87936:44.6:10:0.4167:0:6 1/0:7:4:2,2:0,0:0.5714:0,2:21.3:1:29.5:1:1:0:60:8:0.5714:0:6 -9 68414143 . C T 44 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61637;LSEQ=CTGTGGGAGAGCCCCAGGAG;RSEQ=GCAGGGCATGTGGGGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:3,5:0.25:2,2:17:1:28:1:1:1.18052:41:6:0.2727:0:5.7 0/1:6:1:1,0:2,2:0.1667:2,0:24:0:32:0:1:0:60:2:0.2:0:7 -9 68414149 . G A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=GAGAGCCCCAGGAGCGCAGG;RSEQ=CATGTGGGGTGCAGGAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:24.6:1:31.6:1:1:0:46.5:22:1:0:5 0/1:6:2:1,1:2,2:0.3333:2,2:20.5:1:26.5:1:1:1:60:4:0.3333:0:6.5 -9 68414161 . CAGGAAGCGACGTTCCCCACGCCCCGGTGTAGGTGAACCCG TGGGAAGCGCAATTCCCGGGCGAACTCA 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23077;SOR=0;LSEQ=AGCGCAGGGCATGTGGGGTG;RSEQ=ATAGAGGAGGGAGGAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:1,4:2,3:0.4545:2,2:25.8:1:28:1:1:2.41422:52.6:10:0.4545:0.4545:3.8 0/0:4:0:0,0:1,2:0:2,0:8.3:1:28.7:1:1:0:53.3:6:0.75:0:5.3 -9 68414162 . A G 48 v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.58251;LSEQ=GCGCAGGGCATGTGGGGTGC;RSEQ=GGAAGCGACGTTCCCCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:1,3:0.375:2,2:15:1:30.3:1:1:1.41:23:6:0.4286:0:5 0/1:4:1:0,1:1,1:0.25:2,0:7:0:29:0:1:0:40:2:0.3333:0:3 -9 68414170 . A C 72 NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGTGGGGTGCAGGAAGCG;RSEQ=CGTTCCCCACGCCCCGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:1,1:0.7143:2,2:26.4:1:31.2:1:1:3.1622:40.4:10:0.7143:0:5.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68414172 . G T 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGGTGCAGGAAGCGAC;RSEQ=TTCCCCACGCCCCGGTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,1:0.5714:2,2:26.3:1:29.5:1:1:2.44949:60:8:0.5714:0:3.8 0/0:1:0:0,0:0,1:0:0,0:1:0:33:0:1:0:60:2:1:0:4 -9 68414186 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGACGTTCCCCACGCCCC;RSEQ=GTGTAGGTGAACCCGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:18:1:30:1:1:1.41418:21:4:0.2857:0:6 0/0:1:0:0,0:0,1:0:0,0:15:0:32:0:1:0:60:2:1:0:4 -9 68414191 . A G 50 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTTCCCCACGCCCCGGTGT;RSEQ=GGTGAACCCGATAGAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:0.5:2,2:12.7:1:32:1:1:3.11:34:6:0.5:0:6.7 1/1:1:1:0,1:0,0:1:0,0:20:0:32:0:1:0:60:2:1:0:4 -9 68414199 . C T 74 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCCCGGTGTAGGTGAAC;RSEQ=CGATAGAGGAGGGAGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:22.2:1:32:1:1:0:52.2:10:1:0:4.6 1/1:1:1:0,1:0,0:1:0,0:28:0:31:0:1:0:60:2:1:0:4 -9 68414203 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGGTGTAGGTGAACCCGA;RSEQ=AGAGGAGGGAGGAGGGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:12.5:1:32.5:1:1:3.16:60:4:0.2857:0:7 0/0:1:0:0,0:0,1:0:0,0:32:0:30:0:1:0:60:2:1:0:4 -9 68414208 . G T 29 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGGTGAACCCGATAGAG;RSEQ=AGGGAGGAGGGTGACACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:2,5:0.2222:2,0:15:1:29.5:1:1:0:60:4:0.2222:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68414231 . A G 62 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGGAGGGTGACACCCACC;RSEQ=GGGGTGCTAATTAGTAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,2:0.5714:2,2:32.5:1:31.3:1:1:1.41418:60:8:0.5714:0:4.5 1/1:1:1:0,1:0,0:1:0,0:25:0:32:0:1:0:60:2:1:0:4 -9 68414235 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGTGACACCCACCAGGG;RSEQ=TGCTAATTAGTAACCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:39:1:30:1:1:2.45:60:4:0.3333:0:7 0/0:1:0:0,0:0,1:0:0,0:21:0:33:0:1:0:60:2:1:0:4 -9 68414259 . C T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTAGTAACCACAGTGGC;RSEQ=TCAAAGAACTCAAATGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:32.5:1:31.5:1:1:1.73:60:4:0.4:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68414262 . A T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGTAACCACAGTGGCCTC;RSEQ=AAGAACTCAAATGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:29.5:1:31:1:1:2.45:60:4:0.3333:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68414291 . A C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGAAAGGAAGACTTGCA;RSEQ=GTCTCTCACTTTAAGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:19.5:1:31.5:1:1:0:60:4:0.5:0:4 0/0:1:0:0,0:0,1:0:0,0:17:0:26:0:1:0:60:2:1:0:2 -9 68414479 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACTCTGAAAATCTCAGG;RSEQ=CCCTTAAGAATTATGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:21:1:31.5:1:1:0:50:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 68414626 . C A 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.7321;LSEQ=GCTCAGAAAAAAAAAAAAAA;RSEQ=GATTCTTTTAAAAAGATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:42:0:31:0:1:0:60:2:1:0:7 1/0:3:2:1,1:1,0:0.6667:0,2:21.5:1:29:1:1:0:60:4:0.6667:0:4.5 -9 68414632 . T C 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAAAAAACGATTC;RSEQ=TTTAAAAAGATTGTTGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:21:1:33.5:1:1:0:60:4:1:0:5.5 1/1:3:3:2,1:0,0:1:0,2:20.3:1:28.7:1:1:0:53.3:6:1:0:4.3 -9 68414641 . G T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AAAAACGATTCTTTTAAAAA;RSEQ=ATTGTTGGTTGGCCAGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:35:1:30:0:1:0:60:4:0.6667:0:6.5 0/0:2:0:0,0:1,0:0:0,0:21:0:27:0:1:0:40:2:0.5:0:4 -9 68414643 . T C 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.57733;LSEQ=AAACGATTCTTTTAAAAAGA;RSEQ=TGTTGGTTGGCCAGGCATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:35:1:32.5:1:1:0:60:4:0.6667:0:6.5 1/0:2:1:0,1:1,0:0.5:0,0:11:0:33:0:1:0:60:2:0.5:0:6 -9 68414649 . G C 51 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTTAAAAAGATTGTTG;RSEQ=TTGGCCAGGCATAGTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:30.7:1:32.7:1:1:0:60:6:1:0:5.7 1/0:3:2:1,1:1,0:0.6667:0,2:9:1:29:1:1:0:50:4:0.6667:0:5 -9 68414671 . T C 50 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TGGCCAGGCATAGTGGCTCA;RSEQ=ACTTGTAATCCCTGCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:31:1:32:1:1:0:60:6:1:0:4.3 1/0:2:1:0,1:1,0:0.5:0,0:13:0:34:0:1:0:60:2:0.5:0:3 -9 68414674 . T C 50 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CCAGGCATAGTGGCTCATAC;RSEQ=TGTAATCCCTGCACTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:32:1:31.7:1:1:0:60:6:1:0:4.3 1/0:2:1:0,1:1,0:0.5:0,0:16:0:34:0:1:0:60:2:0.5:0:3 -9 68414916 . T C 47 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.40825;LSEQ=TCCAGCCTGGGCAACAAGAG;RSEQ=GAAACTACGTCAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:42:1:29.7:1:1:0:39.3:6:1:0:5.7 1/0:2:1:1,0:1,0:0.5:0,0:35:0:33:0:1:0:58:2:0.5:0:4 -9 68414947 . A G 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=39.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAAAAAAAAAAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:14.5:1:30:1:1:1:45:4:0.5:0:6 0/0:3:0:0,0:2,1:0:2,0:16.3:1:24.7:1:1:0:46:2:1:0:3.3 -9 72744848 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19843;SOR=0;LSEQ=ATCTGCCCTATGCCTCTCTC;RSEQ=CATTTCTGGTGGTGTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:12,9:0.087:2,2:29.5:1:30.5:1:1:1.31655:60:4:0.087:0:1 0/0:28:0:0,0:19,9:0:2,0:19.9:1:29.9:1:1:0:60:13:1:0:0.2 -9 73641667 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51111;SOR=0;LSEQ=GGACTCCCCTGCACCCTAAG;RSEQ=GGCCACCACTGCCAGTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:8,12:0.0909:2,2:8:1:29.5:1:1:1.47:60:4:0.0909:0:1 0/0:14:0:0,0:1,13:0:1,0:18.7:1:30.3:1:1:0:60:28:1:0:0 -9 75046971 . T C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22872;SOR=Inf;LSEQ=CCAGTTTGAGAAATTTTTTT;RSEQ=CCTAAAGAAAATAGAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:54,12:0:2,0:26.2:1:29.8:1:1:0:60:65:1:0:0.2 0/1:61:2:1,1:51,8:0.0328:2,2:31:1:26.5:1:0.27541:6.06906:60:4:0.0328:0:1 -9 75047061 . C G 212 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42458;SOR=1.19093;LSEQ=ATATATTGCTTGCTGAGGAA;RSEQ=ACATTTAACTCAGAACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:105:55,50:58,51:0.4907:2,2:26.9:1:31.6:1:1:1.03372:60:104:0.4906:0:1.2 1/0:189:101:56,45:52,36:0.5344:2,2:22.7:1:30.8:1:0.65978:1.1598:60:49.5:0.5294:0:1 -9 75047282 . C T 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59207;SOR=0.32855;LSEQ=TTGGCTTACTGCAACCTCTG;RSEQ=CTCCTGGGTTCAGTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:18.2:1:29.6:1:1:0:60:10:0.625:0:1 0/1:6:2:0,2:0,4:0.3333:0,0:17:1:31:0:1:0:60:4:0.3333:0:1 -9 75154200 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGGTGGCATGTGCTTG;RSEQ=AGTCCCAGTTACTCGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:30.5:1:1:0:60:4:1:0:1 -9 75155834 . G A 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00049;SOR=0;LSEQ=GGATGTTGTGAAGCTTCAGT;RSEQ=AGTTAATACAGATATAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:14,1:14,0:0.5172:1,1:22.8:1:27.7:1:1:0:60:14:0.5:0:1 0/0:15:0:0,0:15,0:0:1,0:23.1:1:31.1:1:1:0:60:30:1:0:0.1 -9 75155897 . A G 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00241;SOR=Inf;LSEQ=TCCAATCATCAATACTACCC;RSEQ=GCTTTATTAAAACTTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:85,1:0:1,0:26.9:1:30.2:1:1:0:60:85:1:0:0.2 0/1:66:7:7,0:59,0:0.1061:1,0:29.4:1:29.4:1:1:0:60:14:0.1077:0:1 -9 75156057 . C T 234 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00237;SOR=1.50271;LSEQ=ATAATCTTTGATTTCTCTTG;RSEQ=CCACATGGATGGTTACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:236:98,138:103,143:0.4886:2,2:25.1:1:29.8:1:1:1.01424:60:235:0.4947:0:1.1 1/0:441:260:108,152:82,99:0.5896:2,2:25.6:1:29.2:1:0.43624:1.16532:60:259:0.5927:0:1.1 -9 75794689 . T A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.22209;LSEQ=GTGCCTTCTTACAATTATTA;RSEQ=CATTGCTTACTTTTTTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:48:20,28:171,223:0.1086:2,2:21.6:1:30.1:1:0.87808:1.07339:60:47:0.1085:0:1.1 0/1:397:135:57,78:121,141:0.3401:2,2:25.9:1:29.2:1:0.45837:1.17384:60:66.5:0.3419:0:1.1 -9 75794764 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50747;SOR=0;LSEQ=CAACCCTAACTCAGAATTAG;RSEQ=CTATGTGATTCAAATCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:35,131:0.0119:2,2:7:0:31.5:1:0.38366:3.70:60:4:0.012:0:1 0/0:128:0:0,0:33,95:0:2,0:23.7:1:31.3:1:1:0:60:31:1:0:0.2 -9 75794996 . A T 70 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGAAACTTTCCTTTAACA;RSEQ=GATAATGCATTATGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:20.4:1:30.4:1:1:0:60:10:0.8333:0:1.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 79104807 . T C 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGGCCAGTCAAAAGGCCAG;RSEQ=GGGTCAGTCCAGGGGTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:6:1:30:1:1:0:51:4:0.6667:0:1.5 1/1:1:1:1,0:0,0:1:0,0:4:0:30:0:1:0:40:2:1:0:2 -9 79104873 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1;LSEQ=TTGGGGTTCCATTTGTAAGA;RSEQ=CATCTGTAGCTTGATGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:0.6667:0,0:37:1:32.5:1:0.33333:0:41:4:0.6667:0:2 1/0:3:2:2,0:0,1:0.6667:0,0:35.5:1:32:1:0.33333:0:40:4:0.6667:0:1.5 -9 79104883 . C A 43 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=ATTTGTAAGATCATCTGTAG;RSEQ=TTGATGGCCTCAATCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:33.3:1:27.3:1:1:0:40.7:2:1:0:1.3 1/0:5:3:1,2:2,0:0.6:0,2:12.3:1:27.7:1:0.4:0:38.3:6:0.6:0:7 -9 79104888 . T C 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=TAAGATCATCTGTAGCTTGA;RSEQ=GGCCTCAATCCTAGAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21.8:1:27:1:1:0:43:3:1:0:1 1/0:5:3:1,2:2,0:0.6:0,2:17.3:1:29.7:1:0.4:0:38.3:6:0.6:0:7 -9 79104893 . T C 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TCATCTGTAGCTTGATGGCC;RSEQ=CAATCCTAGAGGAAACAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:19.3:1:31.5:1:1:0:43:8:1:0:1 1/0:6:3:1,2:3,0:0.5:0,2:22.3:1:30.3:1:0.4:0:38.3:6:0.5:0:7 -9 79104924 . G A 50 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=GGAAACAAATTTGACAAGGA;RSEQ=GTTAAAAATACAGGGCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:20.5:1:31:1:1:0:51.3:8:1:0:0.5 0/1:8:3:1,2:5,0:0.375:0,2:43:1:31.7:1:0.10714:0:38.3:6:0.375:0:7 -9 79104951 . G C 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25714;SOR=Inf;LSEQ=AATACAGGGCCCGAAGGCAA;RSEQ=TAATAGCAAGATGGCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:19.6:1:31.6:1:1:0:58.1:16:1:0:0.3 0/1:13:3:1,2:5,4:0.2308:2,2:18.7:1:33.3:1:1:2.31595:38.3:6:0.2308:0:7 -9 79104957 . G T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2663;SOR=Inf;LSEQ=GGGCCCGAAGGCAAGTAATA;RSEQ=CAAGATGGCTGTCATGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:20.7:1:31.3:1:1:0:58.3:18:1:0:0.2 0/1:15:3:1,2:7,5:0.2:2,2:12.7:1:30.7:1:0.56923:2.61246:38.3:6:0.2:0:7 -9 79105108 . A G 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21891;SOR=4.83234;LSEQ=ACTATCCCTGACTGGTTAGT;RSEQ=TAAAAGCAACACTCTTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:5,6:0.1538:2,0:39:1:33:1:0.48718:0:60:4:0.1538:0:1 1/0:4:2:1,1:0,2:0.5:0,2:26:1:29.5:1:1:0:60:4:0.5:0:1 -9 79231007 . C A 48 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTGTTTTTTTGAAATGAG;RSEQ=AAATAGCTCTTCGCTTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:21:1:30.7:1:1:0:60:6:0.6:0:1.3 1/1:1:1:1,0:0,0:1:0,0:4:0:31:0:1:0:60:2:1:0:1 -9 79231247 . G A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02635;SOR=Inf;LSEQ=AAAAGGTCCTTCCTGTTCCC;RSEQ=GAAATCTGTAGTAAGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:241,97:0:2,0:23.2:1:30.1:1:1:0:60:111.667:0.997:0:0.2 0/1:319:5:2,3:199,114:0.0157:2,2:22.8:1:29:1:0.36131:2.61007:60:10:0.0158:0:1.8 -9 79231317 . T C 148 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=30.02448;LSEQ=TCACGGTGTTGGTTGACTTT;RSEQ=TCCCATAGATGAAGAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:1:0,1:231,243:0.0021:2,0:37:0:30:0:1:0:60:2:0.0021:0:1 0/1:471:28:13,15:221,222:0.0594:2,2:25.9:1:30.8:1:0.846:1.14831:60:27:0.0577:0:1.5 -9 79231339 . T G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.29557;LSEQ=CCCATAGATGAAGAGAATAT;RSEQ=TACTAAACCAAAATTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:409:237:100,137:63,109:0.5795:2,2:23.6:1:31.9:1:0.26258:1.26:60:58.25:0.5753:0:1.9 1/1:405:332:139,193:31,42:0.8198:2,2:25.6:1:30.9:1:1:1.02479:60:109.667:0.8184:0:1.9 -9 79231357 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=8.82507;LSEQ=ATTTACTAAACCAAAATTTG;RSEQ=GGCACATCGTCTAAAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:351:206:76,130:46,98:0.5869:2,2:25.5:1:30.4:1:0.36322:1.24:60:40.2:0.5843:0:2 1/1:353:327:132,195:14,12:0.9263:2,2:26.1:1:29.5:1:0.21553:1.72071:60:31.7:0.9242:0:2 -9 79231549 . C T 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72593;LSEQ=TAATTCATCCCTTCAGCTTT;RSEQ=GTTAACTCAAAAGCTAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:0,14:0,2:0.875:0,1:17.6:1:29.5:1:1:0:60:13:0.8667:0:1 1/1:6:5:0,5:0,1:0.8333:0,0:23.6:1:29:1:1:0:60:10:0.8333:0:1.2 -9 79634764 . T A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22319;SOR=Inf;LSEQ=GAACAGCCTGCGCCACAACC;RSEQ=CTCCTTCAACGACTGCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:27.6:1:30.7:1:1:0:60:48:1:0:0 0/1:22:2:1,1:13,7:0.0909:2,2:19:0:30.5:1:1:1.80284:60:4:0.0909:0:1.5 -9 79634815 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21647;SOR=Inf;LSEQ=GCGGAGGCCCGACCAGCCTG;RSEQ=CAAGGGTAGCTTCTGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:25.1:1:30.7:1:1:0:60:12.5:1:0:0.1 0/1:24:2:1,1:12,10:0.0833:2,2:8:0:31:0:1:1.19087:60:4:0.087:0:1.5 -9 79635080 . CCCG C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=CAGCCGCCGCCGCCGCCGCC;RSEQ=CCGCCGCCGCACATGGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:21.5:1:30:1:1:1.13389:60:4:0.1176:0:0 0/0:11:0:0,0:6,5:0:2,0:22.3:1:29.1:1:1:0:60:22:1:0:1 -9 80144099 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.96404;LSEQ=GTGAACCCCTTTCTGTCTTC;RSEQ=TCGCTGTAACCAGACCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:8,9:0.0556:2,0:14:0:32:0:1:0:60:2:0.0588:0:1 0/1:19:2:1,1:7,10:0.1053:2,2:9.5:1:29:1:1:1.40:60:4:0.1111:0:1 -9 80336195 . A G 117 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00109;SOR=13.74139;LSEQ=GTCCCTCTTGTGTATCTTCA;RSEQ=TAGCCCACCAGGGAAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:1,0:172,33:0.0048:2,0:28:0:14:0:1:0:60:0:0:0:4 0/1:191:12:11,1:141,37:0.0628:2,2:18.1:1:32.7:1:0.46519:2.87:60:24:0.0628:0:1.2 -9 80336405 . G A 57 v4;q23;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50675;SOR=1.93574;LSEQ=TCTTCAGAATGAATTCTCGG;RSEQ=CTGCCTGGGCATCTCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:3:3,0:203,348:0.0054:2,0:16.7:1:17.3:1:0.05094:0:60:0.5:0.0019:0:3.3 0/1:576:6:6,0:211,359:0.0104:2,0:9:1:22.2:1:0.00274:0:60:5:0.0089:0:1 -9 80343336 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21416;SOR=Inf;LSEQ=GGCTGCACAGGGCAAGGGCA;RSEQ=CAATGGTGCACTGTAGTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:78,5:0:2,0:22.9:1:32.3:1:1:0:60:166:1:0:0 0/1:72:2:2,0:68,2:0.0278:1,0:32:1:31:1:1:0:60:4:0.029:0:1.5 -9 80343349 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21463;SOR=Inf;LSEQ=AAGGGCAGCAATGGTGCACT;RSEQ=TAGTGCGTTAACTCCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:98,8:0:2,0:23.7:1:32.2:1:1:0:60:52:1:0:0.1 0/1:92:2:1,1:81,9:0.0217:2,2:15.5:1:27.5:1:0.20664:8.58847:60:4:0.0222:0:1 -9 80343383 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4987;SOR=0;LSEQ=CCCACACTGGGGTTTGGAGA;RSEQ=AAAACCTATTCACAGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:146,44:0.0104:2,2:26:1:31.5:1:0.41476:3.29229:60:4:0.0106:0:1 0/0:192:0:0,0:141,51:0:2,0:21.6:1:30.8:1:1:0:60:95:1:0:0.1 -9 80343586 . G A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21963;SOR=4.60916;LSEQ=GCTTTCCTCCATTCGGTTCT;RSEQ=GAAAAAAAAAAAAAATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:1:1,0:97,238:0.0029:2,0:1:0:24:0:0.29167:0:60:2:0.0032:0:1 0/1:371:5:4,1:130,235:0.0135:2,2:5.6:1:23.2:1:0.05982:7.19:60:4:0.0119:0:1.6 -9 80409138 . C G 67 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.54771;LSEQ=TGTTATTTTCATTTTCAGAA;RSEQ=CTCTGCATAGTGTTAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:0.6667:0,0:25.5:1:33.8:1:1:0:60:8:0.6667:0:1.3 1/0:2:1:1,0:1,0:0.5:0,0:33:0:34:0:1:0:60:2:0.5:0:1 -9 80409345 . A G 243 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=1.66337;LSEQ=TACTTGTATCAGATAATAAA;RSEQ=TGATAATCCATTGCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:163:124,39:177,54:0.4127:2,2:24.7:1:31.9:1:0.90469:1.03085:60:39.75:0.4098:0:1.2 1/0:397:214:157,57:118,64:0.539:2,2:21.7:1:31.4:1:0.07978:1.49:60:106:0.5381:0:1.1 -9 80409358 . G T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02892;SOR=0;LSEQ=TAATAAAATGATAATCCATT;RSEQ=CCTGTCTAAAGAACACTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:5:3,2:356,121:0.0104:2,2:23.8:1:25.6:1:0.60575:1.9584:60:4:0.0085:0:1.8 0/0:496:0:0,0:325,168:0:2,0:24.4:1:31.4:1:1:0:60:48.3:0.9938:0:0.5 -9 80412372 . G T 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20247;SOR=0.23183;LSEQ=ACATGATTCCAGTATTTATA;RSEQ=AGTTTACCAAATGTACTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:4:2,2:281,80:0.011:2,2:15.3:1:29.5:1:0.21903:3.4969:60:8:0.0111:0:1 0/0:391:1:0,1:285,105:0.0026:2,0:1:0:23:0:0.2711:0:60:2:0.0026:0:1 -9 80430741 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.22809;SOR=Inf;LSEQ=ATTACTTTCCAAATTTTCTT;RSEQ=GCTTTGCATATTACATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:16,153:0:2,0:22.3:1:30.3:1:1:0:60:83.5:1:0:0.2 0/1:155:2:1,1:18,135:0.0129:2,2:13:1:28:1:0.23083:7.33:60:4:0.0129:0:1 -9 80430802 . C A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01655;SOR=3.64577;LSEQ=CCTTCATATACTGGTCTTTA;RSEQ=ACTGGTTTACAATAAAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:27:1,26:0,30:0.4737:1,1:24.6:1:31.1:1:0.47368:0:60:54:0.4737:0:1 1/0:26:20:0,20:0,6:0.7692:0,1:25.4:1:29.9:1:1:0:60:19:0.76:0:1.2 -9 80537016 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49858;SOR=0;LSEQ=TCAAGAGGCTACTCGTGTTG;RSEQ=CACATTATTGTGAACACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:155,13:0.0118:2,2:21:1:30:1:0.15837:11.52661:60:4:0.0118:0:1 0/0:166:0:0,0:143,23:0:2,0:23.9:1:29.7:1:1:0:60:165:1:0:0.2 -9 80537095 . G T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29052;SOR=0.65554;LSEQ=ACCTTATTGTGCTCATACTT;RSEQ=TATGGGATCTTGAGTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:636:20:14,6:392,224:0.0314:2,2:8:1:30.8:1:0.64257:1.33:41.9:40:0.0317:0:2.2 0/1:624:13:11,2:359,252:0.0208:2,2:8.7:1:30.1:1:0.08515:3.85:46:26:0.021:0:2.1 -9 80537112 . T A 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.37551;SOR=1.27795;LSEQ=CTTGTATGGGATCTTGAGTG;RSEQ=GTCCATGGCTCTGATCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:737:28:17,11:417,292:0.038:2,2:20.3:1:31.4:1:1:1.08:43.1:56:0.0383:0:1.9 0/1:770:37:22,15:413,320:0.0481:2,2:15.1:1:29.7:1:0.73746:1.14:47.6:74:0.0485:0:1.6 -9 80537223 . T G 97 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15847;LSEQ=TGACCCATGGATGATTCTCA;RSEQ=CTGCTTGATAAACGTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:6:1,5:248,415:0.009:2,2:4.7:1:32.3:1:0.41987:2.98397:29:12:0.0091:0:1 0/1:771:8:1,7:344,419:0.0104:2,2:7.8:1:32.5:1:0.081:5.73712:25.5:16:0.0105:0:1.1 -9 80537237 . G A 93 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01493;SOR=8.43869;LSEQ=TTCTCATCTGCTTGATAAAC;RSEQ=TACTCTTGCCACTCTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:1:1,0:221,372:0.0017:2,0:1:0:27:0:0.37374:0:60:2:0.0017:0:1 0/1:713:10:5,5:302,398:0.014:2,2:27.4:1:28.1:1:0.75288:1.32:59.5:20:0.0142:0:1.1 -9 80645803 . CTG C 25 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=31;MSI=16.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TGTGCTGCGTGTGTGTGTCG;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:33:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:22.5:1:25.5:1:1:0:60:4:1:0.5:0 -9 80645940 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5004;SOR=0;LSEQ=GCCGGGGGGCGGGGGCGCCG;RSEQ=AGGCAGCTGCCCCGCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:101,14:0.0171:2,2:15.5:1:27.5:1:0.24094:7.00406:60:4:0.0175:0:1 0/0:101:0:0,0:84,17:0:2,0:11.8:1:29.5:1:1:0:60:100:1:0:0.2 -9 80646091 . T A 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCGCTCGATCTCGTCGTTGA;RSEQ=CCGCCGGGCTTCCTTGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:893:52:27,25:423,418:0.0582:2,2:26.6:1:29.2:1:0.88672:1.07:45.9:51:0.0582:0:1.1 0/0:1043:0:0,0:531,511:0:2,0:25.2:1:28.9:1:1:0:48.6:79.154:1:0:0.1 -9 80646212 . A G 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.40742;SOR=0.5868;LSEQ=TGCTCACAGCGCGCACACAC;RSEQ=CCCTCCCGCCCTCGCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:8:1,7:21,189:0.0365:2,2:12:1:29.9:1:0.57929:1.28:38.9:7:0.0327:0:2 0/1:230:5:0,5:39,186:0.0217:2,0:8.4:1:29:1:0.59186:0:45.4:4:0.0182:0:1.6 -9 80646215 . C T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33532;SOR=0.48605;LSEQ=TCACAGCGCGCACACACACC;RSEQ=TCCCGCCCTCGCTCCCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:6:1,5:19,178:0.0296:2,2:10.7:1:28.2:1:0.4677:1.87:38.5:5:0.0254:0:2.7 0/1:206:3:0,3:29,174:0.0146:2,0:5.3:1:30.3:1:1:0:37.7:6:0.0151:0:2 -9 80646504 . AGCC A 34 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GCGGCCCGCCTCGCCCCCCG;RSEQ=GCCGCCGCCGCCGCCGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28.5:1:33.5:1:1:0:60:4:1:0:0.5 0/1:6:2:1,1:2,2:0.3333:2,2:14:0:34:0:1:1:60:4:0.3333:0:0.5 -9 80795402 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5096;SOR=Inf;LSEQ=GTTTATAACAATGCCAACAG;RSEQ=ATGCTGGGGAACATTGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:86,54:0:2,0:27.7:1:32.1:1:1:0:58.1:69:1:0:0.5 0/1:189:2:1,1:103,84:0.0106:2,2:34:1:30.5:1:1:1.22485:60:4:0.0108:0:1.5 -9 80795406 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.49824;LSEQ=ATAACAATGCCAACAGCATG;RSEQ=TGGGGAACATTGTAGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:1,0:86,55:0.007:2,0:11:0:12:0:1:0:59:0:0:0:6 0/1:190:2:1,1:100,88:0.0105:2,2:23:1:29.5:1:1:1.1356:60:4:0.0109:0:1 -9 80795416 . T C 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22419;LSEQ=CAACAGCATGCTGGGGAACA;RSEQ=TGTAGACTCTTCCAGTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:53:32,21:57,41:0.351:2,2:31.2:1:32.2:1:0.8631:1.10:55.8:106:0.3533:0:1.1 0/1:195:21:12,9:83,91:0.1077:2,2:35:1:31:1:0.49121:1.46:52.9:42:0.1088:0:1 -9 80795435 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50442;SOR=Inf;LSEQ=ATTGTAGACTCTTCCAGTTT;RSEQ=GCCATGGTGACACTTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:81,76:0:2,0:28.8:1:29.3:1:1:0:58.3:51.333:1:0:0.5 0/1:195:2:1,1:81,112:0.0103:2,2:37.5:1:30.5:1:1:1.38:43:4:0.0104:0:1.5 -9 80795441 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5033;SOR=Inf;LSEQ=GACTCTTCCAGTTTAGCCAT;RSEQ=GTGACACTTGTGGGGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:77,81:0:2,0:27.1:1:31:1:1:0:58.3:30.6:1:0:0.5 0/1:192:2:1,1:77,112:0.0104:2,2:32.5:1:30:1:1:1.45:60:4:0.0106:0:1 -9 80795452 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20661;SOR=0;LSEQ=TTTAGCCATGGTGACACTTG;RSEQ=GGGGCATTCCTTTTTGAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:0,2:64,82:0.0135:2,0:29:1:32:0:0.50579:0:60:4:0.0138:0:1 0/0:177:0:0,0:66,110:0:2,0:25.2:1:29.3:1:1:0:58.8:57.667:0.9943:0:0.2 -9 80795467 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50082;SOR=Inf;LSEQ=ACTTGTGGGGCATTCCTTTT;RSEQ=GAACAGTACCCATTCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:46,72:0:2,0:24.3:1:29.3:1:1:0:58:38.333:1:0:0.4 0/1:137:2:1,1:48,87:0.0146:2,2:13.5:1:27.5:1:1:1.80:60:4:0.0147:0:1 -9 80795476 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49857;SOR=Inf;LSEQ=GCATTCCTTTTTGAACAGTA;RSEQ=CCATTCCCTTGATGTCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:38,69:0:2,0:22.6:1:30.8:1:1:0:58.1:52.5:1:0:0.4 0/1:116:2:1,1:32,82:0.0172:2,2:19:1:26.5:1:0.48981:2.54:60:4:0.018:0:1 -9 80795495 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49673;SOR=0;LSEQ=ACCCATTCCCTTGATGTCAA;RSEQ=GATATCACCTTTCTCGTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:21,54:0.026:2,2:20.5:1:30:1:0.49248:2.54:60:4:0.0267:0:1 0/0:76:0:0,0:15,61:0:2,0:20.3:1:30.3:1:1:0:59.7:75:1:0:0.2 -9 80795501 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24085;SOR=0;LSEQ=TCCCTTGATGTCAACGATAT;RSEQ=ACCTTTCTCGTAGATTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:16,49:0.0299:2,2:19.5:1:27.5:1:0.44595:3.00:60:4:0.0303:0:1 0/0:69:0:0,0:14,55:0:2,0:21.6:1:31.8:1:1:0:60:68:1:0:0.2 -9 80801556 . G A 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24451;SOR=0;LSEQ=CCCCACTCCTGCCCGCCAGA;RSEQ=AACAATACCCCTTTGACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:20.2:1:31.6:1:1:0:60:10:0.4167:0:1.6 0/0:5:0:0,0:4,1:0:2,0:17.2:1:32.2:1:1:0:60:10:1:0:0.6 -9 80801741 . G A 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03243;SOR=Inf;LSEQ=CATGGATGCGCATGAAGTTC;RSEQ=TCATTTTGGCGAATTACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:166,143:0:2,0:29.5:1:30.8:1:1:0:60:76.25:1:0:0.2 0/1:351:6:3,3:180,165:0.0171:2,2:25.5:1:30.3:1:1:1.09063:60:12:0.0174:0:1.5 -9 80801786 . C A 49 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.20062;SOR=0.22965;LSEQ=TGGTGGTTCTGGCTGAAAGG;RSEQ=AAAAAAAACAAAAACATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:4:3,1:103,159:0.015:2,2:10.8:1:24.8:1:0.30466:4.61:60:3:0.0115:0:1 0/0:288:1:1,0:113,174:0.0035:2,0:1:0:24:0:0.39583:0:60:2:0.0036:0:1 -9 82832611 . C A 113 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=15.94135;LSEQ=AGTTGTTCTTAGTATAGGTC;RSEQ=CTACTTGGTAAAGAGGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:41,0:0.0465:1,0:7:1:30:1:1:0:60:4:0.0476:0:1 0/1:29:13:12,1:15,0:0.4483:1,1:23.8:1:30.8:1:0.46429:0:60:26:0.4643:0:1.1 -9 82832653 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20801;SOR=Inf;LSEQ=CACAGCCAGAGCAAAGATTT;RSEQ=GACTAACTAAAGCTATTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:79,17:0:2,0:24.5:1:32.3:1:1:0:60:192:1:0:0.1 0/1:81:2:1,1:64,14:0.0247:2,2:21.5:1:29.5:1:0.34177:4.4508:60:4:0.025:0:1 -9 82832717 . T A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12365;SOR=Inf;LSEQ=ACAGAATGCCTTTTCTCCAT;RSEQ=TCTTGGCAGAGACTGGTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:163,85:0:2,0:23.6:1:30.1:1:1:0:60:48.6:1:0:0.1 0/1:255:4:3,1:157,94:0.0157:2,2:28.3:1:23.5:1:1:1.79:60:3:0.0119:0:1.5 -9 82832769 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.07644;LSEQ=GTAGGGATATAAAAATGCTT;RSEQ=CCATTTCAACACAGTGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:20:12,8:174,177:0.0539:2,2:26.9:1:30.5:1:0.49141:1.52:60:40:0.0551:0:1 0/1:374:160:84,76:109,105:0.4278:2,2:26:1:30.8:1:0.8344:1.06:60:79:0.4305:0:1.1 -9 82832848 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49857;SOR=Inf;LSEQ=ACAAATCACAGTGCTAATTA;RSEQ=AATTAAGCAAGTACGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:38,134:0:2,0:22.4:1:29.9:1:1:0:60:171:1:0:0.1 0/1:174:2:1,1:55,117:0.0115:2,2:15:1:30:1:0.54136:2.12:60:4:0.0116:0:1.5 -9 82929082 . T C 80 d7;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=CCATAACTGACCCCCATTAT;RSEQ=CTTAATTTACTAATGTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:17:1:31.3:1:1:0:60:12:1:0:2.2 1/0:5:3:3,0:2,0:0.6:0,0:41.7:1:32:1:1:0:60:6:0.6:0:1.3 -9 82929142 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02479;SOR=0.1573;LSEQ=AGTCTCCCACTGCTGCTATC;RSEQ=TCTCTTTCTCTGCATATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:16,1:3,1:0.8095:2,1:26.3:1:30:1:0.35238:4.76:60:34:0.8095:0:2.1 0/1:13:5:5,0:8,0:0.3846:0,0:18.6:1:29.6:1:1:0:60:10:0.3846:0:2 -9 82929174 . C T 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25599;SOR=0.45508;LSEQ=GCATATCCCTCTTCACCCAC;RSEQ=AGGGTTCTAACACTCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:32:23,9:3,3:0.8421:2,2:21.3:1:29.7:1:0.35666:2.49:60:64:0.8421:0:1.5 1/0:34:24:17,7:7,3:0.7059:2,2:23.7:1:30.5:1:1:1.04:60:48:0.7059:0:1.2 -9 82929206 . C T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5098;SOR=Inf;LSEQ=ACTCTGGCCTTGGCTTCCAC;RSEQ=CTCTCACCTCACCTGTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:0:2,0:29.3:1:30:1:1:0:60:14.667:1:0:0.8 0/1:66:2:1,1:36,28:0.0303:2,2:15.5:1:23.5:1:1:1.28077:60:4:0.0313:0:1.5 -9 82929232 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50942;SOR=Inf;LSEQ=ACCTCACCTGTGCGCTGACA;RSEQ=CGGCATGAGGATATTCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:21,30:0:2,0:26.1:1:31.2:1:1:0:60:50:1:0:0.8 0/1:71:2:1,1:32,37:0.0282:2,2:37:1:28:0:1:1.15:60:4:0.0286:0:1 -9 82929301 . C G 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CCAACACTTCATGACAGGCA;RSEQ=CTTACCTACACAGCCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:3,12:0,0:1:0,2:21.9:1:32.9:1:1:0:60:30:1:0:1.1 1/1:21:19:3,16:0,2:0.9048:0,2:21.8:1:32.8:1:1:0:60:38:0.9048:0:1.1 -9 82929397 . T C 86 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCCTTGTCCTGCTAAGG;RSEQ=TTTGCCACTCTACACTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1:0,0:26.8:1:33.3:1:1:0:60:12:1:0:1.2 1/1:1:1:0,1:0,0:1:0,0:19:0:34:0:1:0:60:2:1:0:1 -9 84386538 . A AT 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.65152;SOR=0.45024;LSEQ=GTTCTTGAGTTGCCTCCACT;RSEQ=TTTTTTTTTCTGTGTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:4,0:41,0:0.0889:1,0:15.3:1:31.2:1:1:0:60:8:0.0889:0.0444:0.5 0/1:24:1:1,0:23,0:0.0417:1,0:16:0:30:0:1:0:60:2:0.0417:0:0 -9 84386587 . G A 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02802;SOR=Inf;LSEQ=ATTGGCTAAATCATAGAAAA;RSEQ=CAAATTAAATTTGCAATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:86,9:0:2,0:23.9:1:31.6:1:1:0:60:22.75:1:0:0.1 0/1:93:5:5,0:76,12:0.0538:2,0:21.2:1:30.2:1:1:0:60:10:0.0556:0:1.6 -9 84386609 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49875;SOR=Inf;LSEQ=AAATTAAATTTGCAATCTAG;RSEQ=CAATTTCTGTAAACAAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:110,29:0:2,0:23.2:1:31.3:1:1:0:60:45.333:1:0:0.1 0/1:148:2:1,1:108,38:0.0135:2,2:13.5:1:27:1:0.45891:2.81839:60:4:0.0139:0:1 -9 84386667 . A G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGGTTGTAGCTACGACA;RSEQ=CAGCTGCCTAGAATGAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:177,125:0:2,0:26.4:1:29.8:1:1:0:60:99.667:1:0:0.1 0/1:286:19:11,8:154,113:0.0664:2,2:19.4:1:31.5:1:1:1.01:60:38:0.0667:0:2.8 -9 84386700 . A T 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGAAGTGGAATCTGTTTAG;RSEQ=GGGCTCATGTAAGAAGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:183,167:0:2,0:24.1:1:30.1:1:1:0:60:37.889:1:0:0.1 0/1:331:25:11,14:150,156:0.0755:2,2:26.7:1:29.9:1:0.68122:1.22303:60:50:0.0765:0:3 -9 84386712 . A G 233 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=508.94013;LSEQ=CTGTTTAGAGGGCTCATGTA;RSEQ=GAAGTGAGTCATACATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:1:1,0:178,172:0.0028:2,0:35:0:30:0:1:0:60:2:0.0029:0:1 1/0:328:195:97,98:60,72:0.5945:2,2:26.2:1:30.7:1:0.49878:1.19:60:47.75:0.5895:0:1.4 -9 84386759 . C T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34785;SOR=3.37811;LSEQ=TAAAGATGACCAGGAGGATA;RSEQ=AGACAGGGAAGGGGATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:0,1:126,182:0.0032:2,0:31:0:29:0:1:0:60:2:0.0033:0:1 0/1:276:3:1,2:106,167:0.0109:2,2:17:1:29:1:1:1.26838:60:6:0.0109:0:1 -9 84386769 . A G 113 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CAGGAGGATACAGACAGGGA;RSEQ=GGGGATATCACAGAACTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:108,176:0:2,0:26.3:1:30.5:1:1:0:60:93.667:1:0:0.1 0/1:236:13:4,9:86,137:0.0551:2,2:27.5:1:30.6:1:0.77088:1.41043:60:26:0.0553:0:2.2 -9 87285552 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52221;SOR=0;LSEQ=CTCGGCACGCCCGCAACAAG;RSEQ=ACCGAGGAGTTAAGAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:75,4:0.0247:2,2:42.5:1:30:0:0.12037:16.88119:60:4:0.025:0:2 0/0:51:0:0,0:49,2:0:1,0:28.4:1:31.8:1:1:0:60:50:1:0:0.5 -9 87285595 . C G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2349;LSEQ=AAGCGCAGGGAAGGCCTCCC;RSEQ=GCACGGGTGGGGGAAAGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:185:145:131,14:35,5:0.7838:2,2:21.5:1:30:1:0.56596:1.33:60:71.5:0.7901:0:1.2 0/1:133:61:53,8:56,14:0.4586:2,2:19.4:1:29.4:1:0.35282:1.65:60:60:0.458:0:1.1 -9 87285607 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17911;SOR=Inf;LSEQ=GGCCTCCCCGCACGGGTGGG;RSEQ=GAAAGCGGCCGGTGCAGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:193,37:0:2,0:23.3:1:30.9:1:1:0:60:56.5:1:0:0.7 0/1:170:2:1,1:134,33:0.0118:2,2:28:1:28.5:1:0.36285:4.01535:60:4:0.012:0:1 -9 87285616 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17875;SOR=Inf;LSEQ=GCACGGGTGGGGGAAAGCGG;RSEQ=CGGTGCAGCGCGGGGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:222,49:0:2,0:23.8:1:31.5:1:1:0:60:66.75:1:0:0.6 0/1:199:2:1,1:151,46:0.0101:2,2:15.5:1:28:1:0.41749:3.25822:60:4:0.0102:0:1 -9 87285915 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10947;LSEQ=CCTCCTTTTTCTCCTTGCCC;RSEQ=TAGGGCCCGAGCTGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:250:237:47,190:1,12:0.948:1,2:22.5:1:29.9:1:0.47235:2.96:60:32.857:0.9465:0:1.2 1/0:227:151:27,124:12,64:0.6652:2,2:22.3:1:29.6:1:0.85231:1.16:60:49.333:0.6607:0:1.2 -9 87285923 . C G 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59974;SOR=2.30801;LSEQ=TTCTCCTTGCCCCTAGGGCC;RSEQ=GAGCTGGCCAGGTGGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:1:0,1:28,179:0.0048:2,0:26:0:15:0:1:0:60:0:0:0:4 0/1:181:2:1,1:22,157:0.011:2,2:11.5:1:29.5:1:0.23861:7.00:60:4:0.0114:0:1 -9 87285992 . G A 177 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.06079;LSEQ=GGGGAGAAGTCAAAGACAAG;RSEQ=GATGCAGGACAGGGTCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:53:1,52:0,2:0.9636:0,1:21.4:1:31:1:1:0:60:52:0.963:0:1.6 1/0:41:25:0,25:0,16:0.6098:1,1:16.5:1:31.6:1:1:0:60:50:0.6098:0:1.9 -9 87314676 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTATTTTTAAATTGT;RSEQ=TTTTTTCTTTTTTTTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:14.5:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 87315023 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49941;SOR=0;LSEQ=CTTACACAGCTGGTAGGAGG;RSEQ=GACAGGCTTGCCTGGAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:110,49:0.0124:2,2:9:1:29:1:0.52601:2.23245:60:4:0.0127:0:1 0/0:147:0:0,0:99,48:0:2,0:24.2:1:30.3:1:1:0:60:48:1:0:0.2 -9 87315033 . G T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.90724;LSEQ=TGGTAGGAGGGGACAGGCTT;RSEQ=CCTGGAAGTCTGGATTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:111,60:0.0058:2,0:20:0:26:0:1:0:60:2:0.006:0:1 0/1:181:2:1,1:119,60:0.011:2,2:40:1:29.5:1:1:1.97532:60:4:0.0114:0:1 -9 87315117 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17207;LSEQ=CAGTTGCATGAGAAAAAGTA;RSEQ=TAAAATTCAGGGCTCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:280:220:108,112:28,31:0.7857:2,2:25.8:1:32.2:1:0.88381:1.07:60:440:0.7885:0:1.1 0/1:316:122:65,57:97,97:0.3861:2,2:26:1:30.8:1:0.64394:1.14:60:121:0.3878:0:1.1 -9 87315204 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49876;SOR=Inf;LSEQ=GGTCTCTATTGAAAATGTTG;RSEQ=TGAAAAATCTTGCAAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:28,112:0:2,0:22.3:1:31.7:1:1:0:60:139:0.9929:0:0.2 0/1:150:2:1,1:45,103:0.0133:2,2:10:1:24.5:1:0.52072:2.27:60:4:0.0133:0:1.5 -9 87315206 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22542;SOR=0;LSEQ=TCTCTATTGAAAATGTTGGT;RSEQ=AAAAATCTTGCAAAAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:25,110:0.0146:2,2:34:1:30:1:0.34468:4.33:60:4:0.0146:0:1 0/0:151:0:0,0:44,107:0:2,0:22.3:1:31.2:1:1:0:60:302:1:0:0.1 -9 87315356 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTCCTGCACATTTATTA;RSEQ=GTGTGCCAGGCCCTGGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:0,7:0.2222:0,2:21.5:1:30.5:1:0.22222:0:60:4:0.25:0:1 0/0:2:0:0,0:0,2:0:0,0:29.5:1:30:1:1:0:60:4:1:0:0 -9 87316868 . A T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.27793;SOR=0.43843;LSEQ=GAGAAATGAAACCCAGTGCA;RSEQ=GGGTTATTGACCATGAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:21:21,0:9,0:0.7:0,1:23.5:1:31.4:1:1:0:60:42:0.7:0:1 1/0:10:5:5,0:5,0:0.5:0,0:29.6:1:29.8:1:1:0:60:10:0.5:0:1.2 -9 87317391 . C A 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.2487;SOR=0;LSEQ=ATTTTATTCAATATTTCCCC;RSEQ=CTCTGTTTATTTTCCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:2,1:55,199:0.0117:2,2:24:1:23:1:0.12462:7.16:60:2:0.0079:0:1 0/0:249:0:0,0:72,177:0:2,0:23.6:1:30.4:1:1:0:60:61.25:1:0:0.1 -9 87317412 . TT CC 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22763;SOR=Inf;LSEQ=CTCTGTTTATTTTCCTTCTT;RSEQ=CCAACTTGAAACCTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:23,154:0:2,0:23.5:1:30.1:1:1:0:60:176:1:0:0.2 0/1:162:2:1,1:32,128:0.0123:2,2:5.5:1:30:1:0.36692:3.95:60:4:0.0124:0.0062:0.5 -9 87322376 . A C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTTTAGTTTTAAGGCAT;RSEQ=TTTTTTCCCTACTGGGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:26:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 87322540 . T C 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.58856;LSEQ=GACATTAAAAATACACAATA;RSEQ=ATTTATGCTACCCCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:14,0:2,0:0.875:0,1:30.4:1:33:1:1:0:60:28:0.875:0:1 1/1:5:4:3,1:1,0:0.8:0,2:26.3:1:32.5:1:1:0:60:8:0.8:0:1 -9 87322719 . A T 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12453;SOR=Inf;LSEQ=TACTGTGTTCCTAAAATGTA;RSEQ=CATTTTAAATTCATGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:262,116:0:2,0:25.9:1:30.1:1:1:0:60:377:1:0:0.1 0/1:398:4:1,3:262,132:0.0101:2,2:10:1:26.3:1:0.11526:5.92666:60:8:0.0101:0:1.3 -9 87325451 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18912;SOR=Inf;LSEQ=TGGTATGACTTCCAAGCATT;RSEQ=CTGGCTAGAAAGAATTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:123,5:0:1,0:26:1:31.8:1:1:0:60:20.333:1:0:0.1 0/1:99:2:1,1:84,13:0.0202:2,2:19:1:27:1:0.26407:6.26345:60:4:0.0204:0:1 -9 87325763 . G T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19132;SOR=Inf;LSEQ=TTAATTATTCTCATTGCCTT;RSEQ=GTGCGGTAGTCTGGGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:26,154:0:2,0:21.8:1:31.2:1:1:0:60:179:0.989:0:0.1 0/1:142:2:1,1:16,123:0.0141:2,2:6:1:23.5:1:0.22736:7.49:60:4:0.0142:0:1 -9 87325994 . A G 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTTTTTCCATCTATCCATCC;RSEQ=TCCATTTATCCACCCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:19.3:1:31.8:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 87338267 . T A 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03571;SOR=0.07141;LSEQ=GGCAATAATGCTTTAAGTAA;RSEQ=GTGCATAATTTATTTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:0.9:0,0:23.7:1:29.3:1:1:0:60:8:0.8889:0:1 0/1:6:2:2,0:3,1:0.3333:2,0:29.5:1:28:1:1:0:60:4:0.3333:0:1 -9 87339327 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24851;SOR=Inf;LSEQ=AATGATCATGGACGTACCTA;RSEQ=GTTTGTTGCTGGGGCACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:31,178:0:2,0:24.4:1:30:1:1:0:60:40.8:1:0:0.1 0/1:218:3:1,2:40,175:0.0138:2,2:20.3:1:29:1:0.46648:2.18:60:6:0.0138:0:1 -9 87339329 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23734;SOR=0;LSEQ=TGATCATGGACGTACCTACG;RSEQ=TTGTTGCTGGGGCACTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:28,169:0.01:2,2:8:1:33.5:1:0.27085:5.95:60:4:0.0103:0:1 0/0:210:0:0,0:39,171:0:2,0:23.1:1:29.8:1:1:0:60:209:1:0:0.1 -9 87342854 . G A 72 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0624;SOR=0;LSEQ=GATTTCTGCTCACTTCATGG;RSEQ=CTGGCCTGGAATTGACGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:5:3,2:143,286:0.0115:2,2:15:1:31.2:1:0.34049:2.99:60:10:0.012:0:1.2 0/0:407:0:0,0:156,251:0:2,0:25.1:1:31.2:1:1:0:60:57.143:1:0:0.1 -9 87356684 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51054;SOR=0;LSEQ=GTTTTGTTTACCTGTCCTGT;RSEQ=AAAGCAGTCTATTAAATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:170,14:0.0108:2,2:11:1:27:1:0.15519:11.76578:60:4:0.0112:0:1 0/0:136:0:0,0:132,4:0:1,0:23.6:1:31.9:1:1:0:60:135:1:0:0 -9 87359808 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5028;SOR=0;LSEQ=ATTTGTCTTGCTTCATTCTG;RSEQ=CTCTTACTGTGGCCCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:164,17:0.0109:2,2:6:1:30.5:1:0.18753:9.4038:60:4:0.0113:0:1 0/0:152:0:0,0:137,14:0:2,0:22.1:1:30.8:1:1:0:60:20.571:1:0:0.1 -9 87360021 . C A 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12522;SOR=Inf;LSEQ=AATAGGTGTCTGAATTGGTT;RSEQ=TGAGCATTTTGGATGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:97,258:0:2,0:24.1:1:31.5:1:1:0:60:49.714:1:0:0.1 0/1:385:4:2,2:120,261:0.0104:2,2:11:1:26:1:0.59425:2.17:60:8:0.0105:0:1 -9 87360102 . GTTAACACCT ATTAA 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00257;SOR=Inf;LSEQ=TGTTCAGATATAAATAGGGT;RSEQ=AGGTTGGAAGAATTAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:0,94:0:1,0:24.6:1:32.2:1:1:0:60:93:1:0:0.4 0/1:73:7:2,5:1,64:0.0959:1,2:24.4:1:30.5:1:0.02347:22.91:60:14:0.0986:0:1.4 -9 87360106 . ACACCT A 196 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00529;SOR=0.29205;LSEQ=CAGATATAAATAGGGTGTTA;RSEQ=AGGTTGGAAGAATTAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:76:0,76:0,9:0.8941:0,1:25.2:1:31.5:1:1:0:60:152:0.8941:0.1529:0.4 1/0:62:44:1,43:0,11:0.7097:0,1:20.4:1:31.1:1:1:0:59.7:88:0.8:0.1935:0.4 -9 87360153 . G A 153 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05862;SOR=0.12635;LSEQ=GGCTTAACAAAAGTGATAAA;RSEQ=GTGTTATATGGCCTTTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:29:0,29:0,1:0.9667:0,1:20.6:1:31.6:1:1:0:60:58:0.9667:0:1 1/0:18:14:2,12:0,4:0.7778:0,2:24.9:1:31.5:1:1:0:60:28:0.7778:0:1.6 -9 87475806 . GTTTATTTA G 156 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=10.000;MSILEN=4;SSF=0.71434;SOR=0.83036;LSEQ=GCTTTCATCCCAAGTGGTTT;RSEQ=TTTATTTATTTATTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:28:28,0:37,0:0.3333:1,1:24.1:1:32.5:1:1:0:60:56:0.3415:0.1071:0.1 0/1:58:17:17,0:16,0:0.2931:1,1:21.9:1:32.3:1:1:0:60:34:0.2982:0.0345:0.1 -9 87482409 . T A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30975;SOR=4.3717;LSEQ=GCTGTATCAACCAGAGTGTT;RSEQ=ATCAGAGCCCCTGATAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:1,0:40,245:0.0035:2,0:1:0:23:0:0.14336:0:60:2:0.0035:0:1 0/1:198:3:2,1:24,171:0.0152:2,2:18:1:28:1:0.04591:13.90:60:6:0.0155:0:1 -9 87482418 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.173;SOR=Inf;LSEQ=ACCAGAGTGTTTATCAGAGC;RSEQ=CCTGATAGGGATGACTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:20,211:0:2,0:22.2:1:31.1:1:1:0:60:37.5:1:0:0.1 0/1:165:2:1,1:17,146:0.0121:2,2:21:1:28:0:0.20687:8.37:60:4:0.0125:0:1 -9 87549000 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50095;SOR=0;LSEQ=GGGCCTGGAAGCTCAGGTAC;RSEQ=GGCCACCAACTCTTCACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:142,31:0.0114:2,2:28:1:31.5:1:0.33314:4.52437:60:4:0.0116:0:1 0/0:152:0:0,0:122,30:0:2,0:21.7:1:29.8:1:1:0:60:151:1:0:0.1 -9 87549003 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=0;LSEQ=CCTGGAAGCTCAGGTACAGG;RSEQ=CACCAACTCTTCACCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:146,35:0.0109:2,2:22:1:28.5:1:0.35561:4.12715:60:4:0.0112:0:1 0/0:167:0:0,0:131,36:0:2,0:21.2:1:31.5:1:1:0:60:334:1:0:0.1 -9 87549007 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23893;SOR=Inf;LSEQ=GAAGCTCAGGTACAGGCCAC;RSEQ=AACTCTTCACCCGCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:153,41:0:2,0:24.7:1:30.8:1:1:0:60:31.333:1:0:0.1 0/1:186:2:1,1:141,43:0.0108:2,2:24:1:29.5:1:0.41813:3.25305:60:4:0.0109:0:1 -9 87549019 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11893;SOR=Inf;LSEQ=CAGGCCACCAACTCTTCACC;RSEQ=GCTGCCTTCACCTCCACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:187,60:0:2,0:24.1:1:30.6:1:1:0:60:122.5:1:0:0.1 0/1:240:3:1,2:177,60:0.0125:2,2:16.3:1:29.7:1:0.16456:5.84669:60:6:0.0125:0:1 -9 87562375 . A C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACCTTCCATGCCAGTGACC;RSEQ=CACCCAATATAGCATTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:31.5:1:1:0:60:4:1:0:2 -9 87563252 . T C 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=TCCTCAGTTATTAGCACAAA;RSEQ=GTTATTTCCTTAGGAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:66:65,1:0,0:1:0,1:25.6:1:32.2:1:1:0:60:132:1:0:1.1 1/0:36:27:27,0:9,0:0.75:0,1:25:1:31.7:1:1:0:60:26:0.7429:0:1.2 -9 87563274 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=Inf;LSEQ=TTATTTCCTTAGGAACTAGG;RSEQ=TGTTTTCTCATCTTTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:116,6:0:1,0:20.1:1:31.8:1:1:0:60:23.4:1:0:0.6 0/1:61:2:2,0:56,3:0.0328:2,0:23.5:1:29.5:1:1:0:60:4:0.0333:0:1.5 -9 87563370 . T C 135 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTCTCTTTTAACACCCA;RSEQ=CCCCAGACCCTGAAGGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:0:0,0:261,176:0:2,0:24.6:1:29.8:1:1:0:60:32.615:1:0:0.1 0/1:445:22:10,12:254,168:0.0494:2,2:27.3:1:30.3:1:0.18642:1.81172:60:21:0.0482:0:1.2 -9 87563460 . C A 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCTCCAGCATGAGCACAT;RSEQ=GTCAAGTTCTATGGCGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:560:0:0,0:256,304:0:2,0:25.3:1:30.2:1:1:0:60:61.222:1:0:0.1 0/1:563:26:13,13:263,274:0.0462:2,2:17:1:29.5:1:1:1.04:60:52:0.047:0:1.1 -9 87563562 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.28107;LSEQ=TTCCTCAGGTACAGTGAGGC;RSEQ=GGGAGGTGGGCTCCAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:167:55,112:83,123:0.4453:2,2:24.1:1:30.5:1:0.1613:1.37295:60:166:0.4486:0:1.1 0/1:359:66:26,40:126,167:0.1838:2,2:22.9:1:30:1:0.67947:1.16028:60:32:0.1813:0:1.1 -9 87563984 . G T 27 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCCAGACTGTGGAATGAACA;RSEQ=TAAGGAAGGGAAGCAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:44.7:1:26:1:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:23:0:27.5:1:1:0:60:4:1:0:1 -9 87570089 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13648;SOR=Inf;LSEQ=CTTTTAGCACCAGCAGCTAC;RSEQ=GGGTGGGGGTGAGGAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:58,6:0:2,0:23.6:1:30.3:1:1:0:60:63:1:0:0 0/1:38:2:1,1:33,3:0.0526:2,2:13.5:1:29:1:0.20199:9.66955:60:4:0.0541:0:1.5 -9 87570143 . C T 84 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01009;SOR=9.62143;LSEQ=GGAGGGGCAGGGGCAAAGGG;RSEQ=CCCTGGAGTGAAAATGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:1,0:103,24:0.0078:2,0:2:0:30:0:1:0:60:2:0.0079:0:1 0/1:127:9:5,4:84,34:0.0709:2,2:28.4:1:26.7:1:0.45007:1.96488:60:8:0.0645:0:1 -9 87570173 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23798;SOR=Inf;LSEQ=GAAAATGCTGAGGCCCCCAG;RSEQ=TTCATTCTCCATGTCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:143,57:0:2,0:24.5:1:32.1:1:1:0:60:49:1:0:0.2 0/1:191:2:1,1:125,63:0.0105:2,2:16.5:1:26.5:1:1:1.97649:60:4:0.0108:0:2 -9 87570204 . C T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04012;SOR=Inf;LSEQ=ATGTCCTTCCCCAGGGCACA;RSEQ=GGCCCTGATGCCGTGCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:190,97:0:2,0:26.4:1:31.4:1:1:0:60:94.667:1:0:0.2 0/1:234:4:2,2:156,74:0.0171:2,2:19.3:1:28.8:1:0.59739:2.10083:60:8:0.0172:0:1 -9 87570478 . C A 198 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02723;LSEQ=CCCAGGGACCTCTTTCCCTG;RSEQ=GGGACCCCTGCTGTATTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:84:28,56:167,367:0.1357:2,2:26.2:1:31.1:1:0.70615:1.10:60:168:0.1375:0:1.1 0/0:706:3:2,1:273,428:0.0042:2,2:32.3:1:27.7:1:0.564:3.13:60:6:0.0043:0:1.3 -9 87570601 . G A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01488;SOR=Inf;LSEQ=AGTCCAAGCTCAAGGTGTGA;RSEQ=TGGGATTGGTTCCTCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:0,62:0:1,0:24.8:1:32.3:1:1:0:60:61:1:0:0.2 0/1:49:5:0,5:1,43:0.102:1,0:28:1:27.6:1:1:0:60:4:0.0833:0:1 -9 87636058 . G A 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=CTGAGAAAACAAAACCAAGA;RSEQ=TGGGCTTCTTTTGTAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:87,4:0:1,0:27.5:1:31.7:1:1:0:60:29.333:1:0:0.1 0/1:76:10:10,0:57,8:0.1316:2,0:26:1:31.5:1:0.58735:0:60:20:0.1351:0:1 -9 87636107 . C T 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25127;SOR=Inf;LSEQ=CTGCTGTTTTTTTGCACTGA;RSEQ=ATTTCTTCGATGTGCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:156,43:0:2,0:22.6:1:32:1:1:0:60:98.5:1:0:0.1 0/1:226:3:1,2:163,60:0.0133:2,2:25:1:20:1:0.18328:5.38512:60:2:0.009:0:2 -9 87636619 . T TC 88 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=0.41176;SOR=Inf;LSEQ=TTTTTAAATTTTCTTTTTCT;RSEQ=TTTTTTTTCGTCTTCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:0.375:0,0:39.8:1:34.2:1:1:0:60:12:0.375:0:0.2 1/1:1:1:0,1:0,0:1:0,0:36:0:34:0:1:0:60:2:1:0:0 -9 88763008 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTTAGCTAGACACAGAA;RSEQ=GCTGATTGGTGCATTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:1:29:1:1:0:60:4:1:0:1 -9 88763628 . G A 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14395;SOR=6.24534;LSEQ=GAAACAAATTTGACAAGGAG;RSEQ=TTAAAAATACAGGGCCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:11,4:0.0625:2,0:6:0:32:0:1:0:52:2:0.0625:0:1 0/1:13:4:2,2:7,2:0.3077:2,2:29.3:1:30:1:0.53007:3.13792:60:8:0.3077:0:1.5 -9 88763699 . A G 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49399;SOR=Inf;LSEQ=ACCTAGAAAGGGGAGAAGCC;RSEQ=TGTTGCCCAACTCCAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:23,16:0:2,0:27.8:1:29.9:1:1:0:48.9:38:1:0:0.1 0/1:41:2:1,1:21,18:0.0488:2,2:9:0:28.5:1:1:1.16227:60:4:0.05:0:1 -9 88763925 . G T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAAGAGTCTATTTGGGATT;RSEQ=TAGAGTAAGGATAGATTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:17.3:1:33.3:1:1:0:56.7:6:1:0:0 0/1:7:2:1,1:1,4:0.2857:2,2:35:0:31.5:1:1:3.16:58.5:4:0.2857:0:1 -9 91100046 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18018;SOR=0;LSEQ=ATACCAACAGCATGTGGGTA;RSEQ=CATTATAGACTGCTCCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:0.125:2,2:32:1:33.5:1:1:1.73197:60:4:0.125:0:1 0/0:21:0:0,0:12,9:0:2,0:28.8:1:30.5:1:1:0:60:42:1:0:0.1 -9 92494768 . A G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCTGTGAGGGTCAGGGA;RSEQ=GGCCTCTGGATTCACCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:0.4:0,0:12:1:33:0:1:0:60:4:0.4:0:1 0/0:2:0:0,0:2,0:0:0,0:9:1:32:0:1:0:60:4:1:0:0.5 -9 92494807 . C T 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.2634;LSEQ=GAAATGGCTCGTTAAAGCAG;RSEQ=GTGGACCCCTTCCACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:0.7:0,0:23.4:1:29.3:1:1:0:60:14:0.7:0:1 1/0:4:3:3,0:1,0:0.75:0,0:33.7:1:31:1:1:0:60:6:0.75:0:1 -9 92494972 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49816;SOR=Inf;LSEQ=AGGCTTGTAGCATTTACAGT;RSEQ=ACAAAAGCAAACACTTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:88,38:0:2,0:25.4:1:29.4:1:1:0:60:125:1:0:0.1 0/1:130:2:1,1:91,37:0.0154:2,2:25:0:30.5:1:0.50078:2.44019:60:4:0.0159:0:1 -9 92495076 . C T 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.42774;LSEQ=ACAGATGAGTCATATGTAGG;RSEQ=ACTCGGTGTCAGCTGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:212:155:68,87:30,26:0.7311:2,2:24.1:1:28.8:1:0.27382:1.47347:60:154:0.7404:0:2.1 1/0:255:137:61,76:57,61:0.5373:2,2:23.9:1:28.2:1:0.61463:1.1635:60:274:0.5373:0:2.1 -9 92495109 . C T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.38078;LSEQ=CTGCAGAGAGGCCGCAGTCC;RSEQ=ACTGTGTGCTTGGGTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:161:117:45,72:18,26:0.7267:2,2:24.4:1:28.8:1:0.85664:1.10698:60:57.5:0.7278:0:2.6 1/0:205:103:41,62:44,58:0.5024:2,2:26.3:1:28.2:1:0.67179:1.14641:60:102:0.5:0:2.8 -9 92495123 . G C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00014;SOR=0.41063;LSEQ=CAGTCCCACTGTGTGCTTGG;RSEQ=TGTCTTGAGCTGGCAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:105:32,73:13,30:0.7095:2,2:25.1:1:31.7:1:1:1.01:60:51.5:0.7153:0:2.6 1/0:188:94:32,62:40,54:0.5:2,2:25:1:31.4:1:0.2936:1.43239:60:46:0.5:0:2.8 -9 92495136 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50323;SOR=Inf;LSEQ=TGCTTGGGTGTCTTGAGCTG;RSEQ=CAGGGCCGGACCTCGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:34,92:0:2,0:26.6:1:31.3:1:1:0:60:30.5:1:0:1.7 0/1:154:2:1,1:50,102:0.013:2,2:23:1:31:0:1:2.03:60:4:0.0131:0:3 -9 92495150 . C T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=GAGCTGGCAGGGCCGGACCT;RSEQ=GGCTTTGAACCCTGGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:29,83:0:2,0:26.5:1:29.9:1:1:0:60:224:1:0:1.5 0/1:125:16:5,11:31,78:0.128:2,2:23.3:1:28.5:1:0.77563:1.14:60:7:0.1148:0:3.1 -9 92496042 . C A 25 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTCAGGTTATTCACCTG;RSEQ=CTGGGCCTCCCAAAGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5.5:1:25.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 92802411 . A T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22375;SOR=0;LSEQ=TGGGGTTCCTGGCTAAACTG;RSEQ=CTTAGCAGGTTTCTTGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:18,20:0.05:2,2:26.5:1:25.5:1:1:1.11:60:4:0.0526:0:1 0/0:44:0:0,0:19,25:0:2,0:28.9:1:28.7:1:1:0:60:43:1:0:0.1 -9 92803759 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGGTTTACTGTGAAGAC;RSEQ=GCAAGGACAAAGCTTCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:31.5:1:1:0:60:4:1:0:1 -9 93606103 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=0.33951;LSEQ=AAACGTTCCCTGCCACGTGG;RSEQ=GTCCTCACCAAAGTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:84:82,2:77,4:0.5091:1,1:25.4:1:30.5:1:0.43746:2.12:60:83:0.5155:0:1.2 0/1:104:27:25,2:70,7:0.2596:2,2:22.1:1:29:1:1:1.25:60:54:0.2621:0:1.1 -9 93606151 . C T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0802;SOR=Inf;LSEQ=CTTGCCCAGGTGGACACCTG;RSEQ=GCAGGTGTGTGCCCTCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:0:0,0:293,71:0:2,0:24.7:1:31.4:1:1:0:60:51:1:0:0.3 0/1:277:3:1,2:206,68:0.0108:2,2:12.7:1:24.7:1:0.15829:6.01014:60:6:0.0109:0:1 -9 93606309 . G A 228 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.95221;LSEQ=GGGCTTTATTTGCTGCGCCA;RSEQ=AGCCGCAACTACCTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:852:55:29,26:373,421:0.0646:2,2:22.5:1:29.1:1:0.48541:1.26:60:26.5:0.0629:0:1.1 0/1:820:209:100,109:292,319:0.2549:2,2:24.3:1:29.7:1:1:1.00:60:103.5:0.2556:0:1.2 -9 93606505 . C T 89 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00302;SOR=Inf;LSEQ=TCCTCAAGAAGCCCTTCAAC;RSEQ=GGCCCCAAGGGGTGCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:0:0,0:311,384:0:2,0:26.8:1:30.3:1:1:0:60:138:1:0:0.1 0/1:656:8:5,3:294,352:0.0122:2,2:16.9:1:29.8:1:0.47957:1.99:60:7:0.0108:0:1.3 -9 93606676 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=5.16912;LSEQ=TTCCTGGCTACATGCAACAC;RSEQ=TGTGCCTATGTGCCCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:11:1,10:2,72:0.1294:1,2:29.1:1:32:1:0.34369:3.52:60:22:0.1294:0:1.3 0/1:64:28:1,27:1,34:0.4375:1,1:23.4:1:30.2:1:1:1.25:60:27:0.4355:0:1.1 -9 93607520 . G A 41 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03529;SOR=14.21149;LSEQ=GAGCCACCGTGCCCGGCCAT;RSEQ=TTATTTTTATTTATACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:16,1:0.0556:1,0:16:0:30:0:1:0:60:2:0.0556:0:1 1/0:6:3:3,0:3,0:0.5:0,0:17:1:26.3:1:1:0:60:6:0.5:0:1 -9 93607623 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53295;SOR=0;LSEQ=AAGTTTTGATCCTGTTTTAC;RSEQ=ATGCCAGGACTCGAGATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:2,0:88,2:0.0217:1,0:25.5:1:31.5:1:1:0:60:4:0.0222:0:3 0/0:53:0:0,0:49,4:0:2,0:22.6:1:30.6:1:1:0:60:52:1:0:0.1 -9 93607642 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.60322;LSEQ=CCATGCCAGGACTCGAGATA;RSEQ=ATTGGAAATGCCTTCTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:118,6:0.0159:1,2:37:1:29:1:0.10844:18.27967:60:4:0.0161:0:1 0/0:104:1:1,0:84,19:0.0096:2,0:14:0:32:0:1:0:60:2:0.0096:0:1 -9 93607915 . G A 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCTCACCTCCTGCCACCAG;RSEQ=CCTGTGTGGACAATTGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:63:19,44:126,242:0.1462:2,2:25.5:1:29.8:1:0.56667:1.2052:60:62:0.1473:0:1.1 0/0:346:0:0,0:112,233:0:2,0:23.1:1:31.3:1:1:0:60:56.5:1:0:0.1 -9 93608130 . G A 92 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=CGAGGGATGTAATATTTAAA;RSEQ=AAAATGTGATTCAGCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:0.5:0,0:18.8:1:30.9:1:1:0:60:16:0.5333:0:1.3 0/0:2:0:0,0:0,2:0:0,0:22.5:1:32.5:1:1:0:60:4:1:0:0 -9 93624407 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=0;LSEQ=AGAGAGCGGCTGCTGACCAT;RSEQ=CAGGCCAGGGTGCTTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:137,30:0.0118:2,2:13:0:32.5:1:0.33411:4.50879:60:4:0.012:0:1.5 0/0:164:0:0,0:125,39:0:2,0:23.9:1:29.3:1:1:0:60:53.667:1:0:0.1 -9 93624419 . G T 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35267;SOR=0.30299;LSEQ=CTGACCATTCAGGCCAGGGT;RSEQ=CTTCCTCCCAGGGTCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:2,1:161,52:0.0138:2,2:12:1:30:1:0.57222:1.54462:60:6:0.014:0:1 0/0:237:1:0,1:163,73:0.0042:2,0:1:0:25:0:0.31224:0:60:2:0.0043:0:1 -9 93624755 . T C 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00108;SOR=0;LSEQ=TGTGGTCCCCAGGCCAGCAG;RSEQ=AGCTCTGGAGCTCATGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:66:0,66:0,0:1:0,1:25.5:1:32.7:1:1:0:60:65:1:0:1.1 1/1:43:36:1,35:0,6:0.8372:0,1:22.7:1:32.6:1:1:0:60:72:0.8372:0:1 -9 93626609 . C T 103 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0.38925;LSEQ=ATAAACAAAGGACACAGATA;RSEQ=GGTATGAGGCCCACAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:11,0:4,0:0.7333:0,0:26.2:1:29.8:1:1:0:60:10:0.7143:0:1.1 1/0:2:1:1,0:1,0:0.5:0,0:27:0:32:0:1:0:60:2:0.5:0:1 -9 93627226 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17579;SOR=Inf;LSEQ=CAGAAAGCGTGCTCACTTCT;RSEQ=AAGCAGCAGCACATCCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:224,26:0:2,0:25.3:1:31.5:1:1:0:60:82.333:1:0:0.1 0/1:181:2:1,1:150,29:0.011:2,2:24:1:30:0:0.30479:5.10254:60:4:0.011:0:1 -9 93627484 . C T 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09144;SOR=0.63759;LSEQ=AGGCATTGATATTTTGATTG;RSEQ=GCTTCAAAACATACTCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:80:3,77:0,50:0.6154:1,1:24.5:1:30:1:0.28444:0:60:79:0.6124:0:1.1 1/0:111:56:4,52:0,54:0.5045:1,2:26.8:1:30.3:1:0.1184:0:60:55:0.5189:0:1.1 -9 93629347 . G A 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01416;LSEQ=GCAAATTTAAGTAGCATGTC;RSEQ=TGGAAGGGATCCTGTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:306:305:209,96:0,0:0.9967:0,2:24.4:1:30.1:1:1:0:59.9:42.571:0.9967:0:1.1 1/1:318:258:192,66:41,17:0.8113:2,2:22.1:1:29.2:1:0.62061:1.21:60:35.857:0.8123:0:1.1 -9 93629530 . G A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24899;SOR=Inf;LSEQ=AACTAAGTGGTAGGACCAAC;RSEQ=CGCACTCAGCTCCCGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:74,195:0:2,0:23.1:1:30.9:1:1:0:60:37.429:1:0:0.2 0/1:281:3:1,2:78,200:0.0107:2,2:19:1:28.3:1:1:1.28:60:6:0.0109:0:1.3 -9 93629630 . T C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=9e-05;SOR=0.11018;LSEQ=TTGCCCTTGCTCACACCTGC;RSEQ=GTTCCTGGGCAGCCGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:25:1,24:1,17:0.5814:1,1:21.3:1:29.5:1:1:1.40026:60:24:0.5854:0:1.1 0/1:31:4:0,4:0,27:0.129:1,0:18:1:27.3:1:1:0:60:8:0.1333:0:1 -9 93629789 . C G 48 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATAGCTAATTATCATGTC;RSEQ=GAAAATCTTTTCAAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:41.3:1:30.7:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:1:0,0:49:0:32:0:1:0:60:2:1:0:1 -9 93636257 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02747;SOR=0.20026;LSEQ=ACCCTCTGAACACCTCACAG;RSEQ=GTCCCTTGAGTTGTAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:17:17,0:12,0:0.5862:0,1:28.4:1:32.5:1:1:0:60:34:0.5862:0:1.9 0/1:14:3:3,0:11,0:0.2143:0,0:40.3:1:31.7:1:1:0:60:6:0.2143:0:2.3 -9 93636270 . G C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00538;SOR=0.13018;LSEQ=CTCACAGAGTCCCTTGAGTT;RSEQ=TAGCAGCACAAGCTTGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:19:19,0:11,0:0.6333:0,1:32.7:1:31.7:1:1:0:60:38:0.6333:0:1.8 0/1:17:3:3,0:14,0:0.1765:1,0:40.7:1:30.7:1:1:0:60:6:0.1765:0:2.3 -9 93636357 . G A 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00738;SOR=Inf;LSEQ=TATTTTCTTCCCTGTTTTTC;RSEQ=TAATTCTTTCCTTTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:179,3:0:1,0:25.4:1:30.2:1:1:0:60:90:0.9945:0:0.3 0/1:147:6:6,0:139,2:0.0408:1,0:29.5:1:31.3:1:1:0:60:12:0.0414:0:1 -9 93636424 . C T 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07056;SOR=6.62596;LSEQ=GGAAAATAAAAATAATTATG;RSEQ=AGATCAACTTAACAGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:1:0,1:442,208:0.0015:2,0:1:0:25:0:0.32104:0:60:2:0.0016:0:2 0/1:694:7:2,5:429,258:0.0101:2,2:17.9:1:25:1:0.11124:4.14829:60:14:0.0102:0:1 -9 93636431 . A G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08092;LSEQ=AAAAATAATTATGCAGATCA;RSEQ=CTTAACAGTTTTGTGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:731:315:207,108:275,140:0.4309:2,2:24.3:1:31.9:1:0.87502:1.02482:60:77.75:0.4302:0:1.1 0/1:798:46:25,21:454,295:0.0576:2,2:27.8:1:31.8:1:0.43891:1.2923:60:92:0.0582:0:1.3 -9 93636664 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=0.30037;LSEQ=GGTTCACGAATCCACACCAC;RSEQ=TCCGTGATTGCAATACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:100:50:2,48:3,47:0.5:2,1:22.4:1:30.1:1:1:1.52546:60:24:0.4948:0:1.2 0/1:74:17:0,17:1,56:0.2297:1,1:24.5:1:29.9:1:1:0:60:34:0.2297:0:1.6 -9 93636671 . A G 86 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00171;SOR=Inf;LSEQ=GAATCCACACCACGTCCGTG;RSEQ=TTGCAATACAGCCACAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:5,81:0:2,0:23.6:1:31.1:1:1:0:60:85:1:0:0.6 0/1:61:7:0,7:1,53:0.1148:1,0:21.6:1:30.9:1:1:0:60:14:0.1167:0:2.3 -9 93636875 . A G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00162;SOR=Inf;LSEQ=TACTCTGAGTTCATATTCCC;RSEQ=TGAAGATCATGTTCTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:137,25:0:2,0:22.7:1:29.7:1:1:0:60:22.143:1:0:0.1 0/1:135:8:7,1:113,14:0.0593:2,2:14.8:1:29:1:1:1.15176:60:16:0.0606:0:1 -9 93636923 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04648;SOR=0;LSEQ=TCCTGGTGTGGGGTCCAGCC;RSEQ=CAGGTCGTATGTTTCTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:4:2,2:216,123:0.0117:2,2:13.3:1:25.8:1:0.62435:1.75298:60:3:0.009:0:2.3 0/0:394:0:0,0:255,139:0:2,0:25.3:1:30.1:1:1:0:60:130.333:1:0:0.1 -9 93637015 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1527;LSEQ=GAGAGCCCCTACGCGGACCC;RSEQ=GAGGAGATCAGGCCCAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:299:161,138:184,120:0.495:2,2:24:1:30.3:1:0.10049:1.31367:60:41.714:0.4924:0:1.1 0/1:746:97:52,45:369,278:0.13:2,2:23.4:1:29.8:1:0.58308:1.14844:60:31.333:0.1282:0:1.1 -9 93637282 . G T 110 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00185;SOR=0.06592;LSEQ=GGTACTATTATAATGAAAGC;RSEQ=TCCATTACCTTTAATGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:0,15:0,17:0.4688:1,1:20.1:1:28.3:1:1:0:60:6.5:0.4483:0:1.3 0/1:19:1:0,1:0,18:0.0526:1,0:15:0:32:0:1:0:60:2:0.0526:0:1 -9 93637525 . AT A 31 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTGTCTCTACAAAAAAA;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:20:1:31.5:1:1:0:54:4:0.6667:0.3333:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 93639489 . A G 43 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACAGGCTTGCACTGTCAC;RSEQ=CCTGGGTGATTTTTTTTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:29:1:27.7:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 93639590 . A G 83 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTCAACCTCCCAAAGT;RSEQ=TGGGGATTGTCAGCATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1:0,0:32.5:1:32.2:1:1:0:60:12:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 93639640 . T C 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CAGCCCCCACCATTCTTTTT;RSEQ=AGTAATGGAGTATTACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:21:1:31.6:1:1:0:60:10:0.4167:0:2 0/0:3:0:0,0:3,0:0:0,0:27:1:32:0:1:0:60:6:1:0:0 -9 93639679 . G A 118 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02041;SOR=0.08518;LSEQ=TCATTGTCTATAAAATAAGG;RSEQ=AATATAGGTTGGAAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:14,0:10,0:0.5833:0,1:23.5:1:31.1:1:1:0:60:28:0.6087:0:1.2 0/1:10:1:1,0:9,0:0.1:0,0:33:0:15:0:1:0:60:0:0:0:1 -9 93639789 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25238;SOR=Inf;LSEQ=AGGGGGATTATGCTTCACAG;RSEQ=ATAAGATTATCTAAAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:133,35:0:2,0:23.5:1:31.2:1:1:0:60:55:1:0:1.3 0/1:196:3:1,2:150,43:0.0153:2,2:16:1:25.7:1:0.13245:6.88667:60:6:0.0155:0:2 -9 93639793 . A T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13175;SOR=Inf;LSEQ=GGATTATGCTTCACAGGATA;RSEQ=GATTATCTAAAAGTGAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:140,44:0:2,0:23.4:1:30.3:1:1:0:60:91:1:0:1.4 0/1:228:4:2,2:166,58:0.0175:2,2:13.8:1:25.3:1:0.2833:2.84642:60:3:0.0136:0:3 -9 93639803 . A G 257 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.58219;SOR=2.61203;LSEQ=TCACAGGATAAGATTATCTA;RSEQ=AAGTGAGGCATTTTGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:229:227:160,67:0,0:0.9913:0,2:23.9:1:31.7:1:1:0:60:55.75:0.9911:0:1.4 1/1:298:297:207,90:1,0:0.9966:0,2:21.4:1:31.4:1:1:0:60:98:1:0:1.3 -9 93639846 . C G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14773;LSEQ=TCTTGTGTGTTATGATTTCT;RSEQ=TTGCAGAGTTGTGAAAACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:209:114,95:137,85:0.4849:2,2:26.5:1:31.9:1:0.14324:1.34219:60:103.5:0.4894:0:1.5 0/1:558:68:33,35:281,209:0.1219:2,2:27.8:1:31.6:1:0.19247:1.42504:60:136:0.123:0:1.6 -9 93639849 . G A 178 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTGTTATGATTTCTCTT;RSEQ=CAGAGTTGTGAAAACCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:0:0,0:254,188:0:2,0:26.2:1:31.9:1:1:0:60:62.143:0.9977:0:1 0/1:567:76:44,32:272,218:0.134:2,2:26.6:1:28.6:1:0.71168:1.10:60:75:0.1335:0:1.6 -9 93639973 . G C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15733;LSEQ=GACAACCCGTACATCGTGCG;RSEQ=ATGATCGGGATATGCGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:550:281:142,139:140,125:0.5109:2,2:26.4:1:31.7:1:0.60797:1.09615:60:45.833:0.5121:0:1.8 0/1:518:73:32,41:222,222:0.1409:2,2:18.6:1:31:1:0.37698:1.28063:60:72:0.1404:0:1.8 -9 93640009 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17755;LSEQ=GAGGCCGAGTCCTGGATGCT;RSEQ=GTTATGGAGATGGCAGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:598:306:140,166:144,148:0.5117:2,2:24.8:1:29.7:1:0.41293:1.15339:60:152:0.5144:0:1.8 0/1:600:94:46,48:251,254:0.1567:2,2:23.7:1:29.2:1:0.91096:1.03111:60:93:0.1563:0:1.7 -9 93640072 . G A 56 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20351;SOR=0.23303;LSEQ=CAGCAGAACAGGTATTGTCA;RSEQ=GTGCCCCCACACATCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:4:3,1:134,241:0.0106:2,2:16.3:1:28:1:0.13649:5.37:60:8:0.0106:0:1 0/0:404:1:1,0:162,241:0.0025:2,0:1:0:24:0:0.40347:0:60:2:0.0025:0:1 -9 93640120 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.14137;LSEQ=CCTAAGGGACAGGGCCCACC;RSEQ=CTGGATGGGCCGAGCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:159:86:14,72:13,60:0.5409:2,2:28:1:30.1:1:0.8345:1.11352:60:27.667:0.539:0:1.8 0/1:155:22:3,19:27,106:0.1419:2,2:21.4:1:28.9:1:0.57189:1.60879:60:21:0.1409:0:1.7 -9 93640131 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12512;LSEQ=GGGCCCACCCCTGGATGGGC;RSEQ=GAGCAGCCTGATTTCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:71:7,64:10,54:0.5259:2,2:28.9:1:30.7:1:0.43675:1.68649:60:70:0.5224:0:2 0/1:124:15:2,13:19,90:0.121:2,2:22.7:1:30.9:1:1:1.36898:60:30:0.121:0:2 -9 93640226 . T C 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01193;SOR=0.12599;LSEQ=GACAGAGGGACAGGGAGACA;RSEQ=AGTCTTTGGATTCAGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:21:0,21:0,10:0.6774:0,1:23.2:1:30:1:1:0:60:6:0.6429:0:1.5 0/1:10:2:0,2:0,8:0.2:0,0:30:1:32.5:1:1:0:60:4:0.2:0:1.5 -9 93640294 . T C 83 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0.53451;LSEQ=CATTTGACAGTTTTGTCTTT;RSEQ=TTTTCTTCCTGTAGTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:0.6667:0,0:6.8:1:32.3:1:1:0:60:12:0.6667:0:1.8 1/0:2:1:0,1:0,1:0.5:0,0:5:0:32:0:1:0:60:2:0.5:0:2 -9 93640832 . G A 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTTGCAATTCCAAGCAT;RSEQ=CCAGGAAACTCAATCCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:30.3:1:30:0:1:0:60:8:0.4444:0:2.5 0/0:1:0:0,0:1,0:0:0,0:19:0:34:0:1:0:60:2:1:0:0 -9 93640872 . C A 100 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61462;SOR=0.319;LSEQ=TGAACACCAGGAGAATATGG;RSEQ=ATTGAGTCCTGAAGAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:9,0:11,0:0.45:0,0:22.8:1:31.6:1:1:0:60:18:0.45:0:2.2 0/1:5:1:1,0:4,0:0.2:0,0:16:0:31:0:1:0:60:2:0.2:0:2 -9 93640895 . G A 114 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00387;SOR=0.07411;LSEQ=TGAGTCCTGAAGAGCTATAT;RSEQ=CTAACAAAGTTATTTGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:15,0:17,0:0.4688:1,1:21.5:1:29.3:1:1:0:60:30:0.4688:0:1.6 0/1:17:1:1,0:16,0:0.0588:1,0:39:0:30:0:1:0:60:2:0.0588:0:2 -9 93641175 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13136;LSEQ=TTGCTAGTTACCCAACATTA;RSEQ=GCCAAGATCAGTGATTTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:637:327:148,179:143,163:0.5133:2,2:24.6:1:30.4:1:0.74971:1.06094:60:162.5:0.5151:0:1.6 0/1:683:83:41,42:273,327:0.1215:2,2:26.7:1:29.6:1:0.55728:1.17:60:40.5:0.1202:0:1.3 -9 93641193 . C T 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACGCCAAGATCAGTGATTT;RSEQ=GGACTTTCCAAAGCACTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:610:38:14,24:252,319:0.0623:2,2:20.6:1:29.5:1:0.40394:1.35357:60:37:0.0615:0:1.1 0/0:617:0:0,0:270,346:0:2,0:24.7:1:29.8:1:1:0:60:40.067:0.9983:0:0.3 -9 93641199 . T C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08109;LSEQ=AAGATCAGTGATTTCGGACT;RSEQ=TCCAAAGCACTGCGTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:221:92,129:165,199:0.3778:2,2:24.7:1:31.5:1:0.39154:1.16231:60:72.667:0.3759:0:2 0/1:598:28:11,17:241,328:0.0468:2,2:21:1:31.2:1:0.84575:1.13526:60:56:0.0469:0:1.9 -9 93641282 . G A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16645;LSEQ=AGCAGCAGGTGGTAAAAAAT;RSEQ=CAAGATAAATGTACGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:110:13,97:19,94:0.4933:2,2:24.3:1:30.1:1:0.34131:1.50541:60:109:0.4955:0:1.3 0/1:180:25:5,20:25,130:0.1389:2,2:21.7:1:29.7:1:0.57431:1.30:60:50:0.1397:0:1.2 -9 93641296 . C T 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAATGCAAGATAAATGTA;RSEQ=GTTTTCTTTATTTTATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:13,158:0:2,0:22.7:1:30.3:1:1:0:60:170:1:0:0.5 0/1:134:29:2,27:13,92:0.2164:2,2:19.8:1:29.1:1:0.52271:1.89974:60:28:0.2121:0:1 -9 93649829 . A C 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22414;SOR=Inf;LSEQ=TCCCAAGTAGCTGGAATTAC;RSEQ=GGCACCCGCCACCACACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:0:1,0:22.5:1:30:1:1:0:60:30:1:0:0 0/1:15:3:3,0:12,0:0.2:0,0:22:1:29:1:1:0:60:6:0.2:0:1 -9 93649968 . A T 48 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1276;SOR=0;LSEQ=GTGCTGGGATTACAGGCATG;RSEQ=ACCAATGTGCCCGGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:4:1,3:251,58:0.0128:2,2:18.3:1:24:1:0.02445:12.83552:60:8:0.0132:0:1 0/0:271:0:0,0:207,64:0:2,0:20.2:1:28.8:1:1:0:59.9:89.333:1:0:0.3 -9 93650015 . T A 211 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=92.41128;LSEQ=TTCTTAATGGAATTTCTCCC;RSEQ=CTGCTTTGCTTTTAGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:2:0,2:433,279:0.0028:2,0:44.5:1:17.5:1:0.15455:0:60:1:0.0014:0:1 0/1:699:144:84,60:330,225:0.206:2,2:25.6:1:29.5:1:0.84918:1.04752:60:71:0.2085:0:1.2 -9 93650231 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16955;SOR=Inf;LSEQ=TAGAACAGATAAGCACCAGA;RSEQ=TGTCTTTACAACAACCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:18,187:0:2,0:23.2:1:30:1:1:0:60:101.5:1:0:0.1 0/1:144:2:1,1:15,127:0.0139:2,2:35:1:32:1:0.21057:8.23:60:4:0.0142:0:1 -9 93650245 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51614;SOR=0;LSEQ=ACCAGATTGTCTTTACAACA;RSEQ=CCTGAAAATCCTAATCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:6,139:0.0136:1,2:23:1:30.5:1:0.09328:21.52:60:4:0.014:0:1 0/0:100:0:0,0:10,90:0:2,0:23:1:29.7:1:1:0:60:200:1:0:0.1 -9 93650322 . G A 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00965;SOR=0;LSEQ=CCCTCAGTCTATTCCAAACT;RSEQ=AGAATGAAATATCTGATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:13:0,13:3,18:0.3824:2,1:20.3:1:28.8:1:0.27005:0:60:12:0.3636:0:1 0/0:14:0:0,0:0,14:0:1,0:29.7:1:30.5:1:1:0:60:28:1:0:0.2 -9 93650755 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25348;SOR=Inf;LSEQ=TTGTTTTGTTTGACTAACAC;RSEQ=TTTAAAAAAAAAAAAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:164,54:0:2,0:20.5:1:30.3:1:1:0:60:20.8:1:0:0.5 0/1:257:3:1,2:185,69:0.0117:2,2:16.7:1:30.7:1:0.18574:5.32096:60:6:0.0119:0:1 -9 93650758 . TA T 144 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.88901;SOR=0.92726;LSEQ=TTTTGTTTGACTAACACCTT;RSEQ=AAAAAAAAAAAGCTTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:28:17,11:147,49:0.1167:2,2:21.1:1:30.3:1:0.11604:1.93486:60:56:0.1212:0.0208:0.1 0/1:275:30:21,9:167,66:0.1091:2,2:30.6:1:29.4:1:0.83235:1.08407:60:60:0.1128:0:0.4 -9 93650759 . A T 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.58867;SOR=1.58883;LSEQ=TTTGTTTGACTAACACCTTT;RSEQ=AAAAAAAAAAAGCTTATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:5:3,2:147,49:0.0208:2,2:10.4:1:29:1:0.60264:1.99219:60:10:0.0216:0:1 0/1:275:9:5,4:167,66:0.0327:2,2:8.4:1:27.8:1:0.28642:2.01773:60:18:0.0338:0:1 -9 93650771 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1276;SOR=Inf;LSEQ=ACACCTTTAAAAAAAAAAAA;RSEQ=CTTATGCATATCTTGCATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:201,99:0:2,0:21.9:1:30.9:1:1:0:60:15.667:1:0:0.4 0/1:348:4:1,3:225,119:0.0115:2,2:15:1:24.5:1:0.12572:5.64316:60:8:0.0121:0:1 -9 93650950 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50087;SOR=0;LSEQ=GTGATGTATTCAGATGCTCT;RSEQ=GAAACAGGTGAAATGGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:35,153:0.0105:2,2:19:1:27.5:1:0.34386:4.32:60:4:0.0105:0:1 0/0:166:0:0,0:39,127:0:2,0:25.5:1:30.4:1:1:0:60:165:1:0:0 -9 93650976 . TA T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.78882;LSEQ=AGGTGAAATGGTTGGGCGTC;RSEQ=AAAAAAAGGATAAAGTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:1,2:6,98:0.028:2,2:21:1:30.3:1:0.18533:7.81:60:6:0.0286:0:0 0/1:90:2:0,2:15,73:0.0222:2,0:39.5:1:32:0:1:0:60:4:0.0222:0:0 -9 93657740 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21253;SOR=Inf;LSEQ=CACTGGTACTCAGCCTGCAG;RSEQ=GGCCCTGCTTGTGATCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:160,37:0:2,0:22.7:1:30.1:1:1:0:60:48.25:1:0:1 0/1:169:2:1,1:131,36:0.0118:2,2:24:1:30:1:0.39096:3.60271:60:4:0.0119:0:1 -9 93657745 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22271;SOR=Inf;LSEQ=GTACTCAGCCTGCAGAGGCC;RSEQ=TGCTTGTGATCAGCAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:174,47:0:2,0:22.3:1:31.3:1:1:0:60:442:1:0:1 0/1:198:2:1,1:146,50:0.0101:2,2:8.5:1:29.5:1:0.44978:2.90126:60:4:0.0102:0:2.5 -9 93657761 . A T 252 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCCTGCTTGTGATCAGCA;RSEQ=TTTTTCACAAGCACATTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:296:296:214,82:0,0:1:0,2:23.3:1:30.8:1:1:0:60:295:1:0:1.1 1/0:293:189:133,56:73,31:0.6451:2,2:22.7:1:29.9:1:1:1.01:60:378:0.6517:0:1.1 -9 93657832 . G A 84 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01331;SOR=8.85028;LSEQ=TGGAAAACAGGCCCGGATTC;RSEQ=CAGCAGTGGAACTGCGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:616:1:1,0:311,303:0.0016:2,0:1:0:29:0:1:0:60:2:0.0016:0:3 0/1:704:10:6,4:369,323:0.0142:2,2:23.7:1:25.5:1:0.75794:1.31:60:4:0.0116:0:1.6 -9 93657958 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=TGTATCCAGAGGAATTGATT;RSEQ=TCAGCCACCTCCCTCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:20,128:0:2,0:21.7:1:32:1:1:0:60:147:1:0:0.1 0/1:155:2:1,1:28,125:0.0129:2,2:17:1:28.5:1:0.34018:4.40:60:4:0.0131:0:1 -9 93659079 . C A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACTTTAGGAGGCCGAGG;RSEQ=GGGTGGATCACTTGAGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 94661354 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57328;SOR=0.35629;LSEQ=CGTGTGTCAGGACAAACAGC;RSEQ=GCCAAGAGCTGCCTGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:80,40:0.0164:2,2:8.5:1:29.5:1:1:1.98783:60:4:0.0167:0:1 0/0:170:1:0,1:100,69:0.0059:2,0:1:0:26:0:0.41176:0:60:2:0.0061:0:1 -9 94661448 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26342;SOR=Inf;LSEQ=AAACACATGGACCGGAAAGG;RSEQ=CCCCCAGGGGGTGCGGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:51,88:0:2,0:23.6:1:31.5:1:1:0:60:138:1:0:0 0/1:186:3:2,1:75,108:0.0161:2,2:19.3:1:26.7:1:0.5705:2.86:60:6:0.0164:0:1 -9 94661537 . G A 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05066;SOR=Inf;LSEQ=GCAAATAGGTGGCATTATCT;RSEQ=CTGGGAGCCTCTGCAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:0,19:0:1,0:19.7:1:31.9:1:1:0:60:18:1:0:0.2 0/1:22:5:0,5:0,17:0.2273:1,0:11.2:1:30.6:1:1:0:60:10:0.2273:0:1 -9 94768173 . A T 109 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=16.000;MSILEN=1;SSF=0.06724;SOR=0.17429;LSEQ=CCATCTCAAAAAAAAAAAAA;RSEQ=AATAATAATAATAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:10,1:10,0:0.5238:0,2:11.2:1:31.7:1:1:0:60:22:0.5238:0:1 0/1:13:2:2,0:10,0:0.1538:0,0:35:1:28.5:1:1:0:60:4:0.1538:0:1 -9 94768176 . T A 73 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.14402;SOR=0;LSEQ=TCTCAAAAAAAAAAAAAAAA;RSEQ=AATAATAATAAATAAATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:18,1:0.2:1,0:17.2:1:31.6:1:1:0:52:10:0.2:0:2.8 0/0:13:0:0,0:13,0:0:1,0:20:0:12:0:1:0:60:0:0:0:5 -9 94768377 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12315;SOR=Inf;LSEQ=AGGGAAAGGGGAGAGGCACC;RSEQ=GATATGTGTTCTCTAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:73,130:0:2,0:23.5:1:29.9:1:1:0:60:66.667:1:0:0.1 0/1:202:3:1,2:73,125:0.0149:2,2:24:1:27.7:1:1:1.16715:60:6:0.015:0:1 -9 94768388 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50116;SOR=0;LSEQ=AGAGGCACCCGATATGTGTT;RSEQ=TCTAGGCCTTTTGGAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:0,2:54,109:0.012:2,0:14.5:1:27.5:1:1:0:60:4:0.0123:0:1 0/0:143:0:0,0:52,91:0:2,0:20.5:1:31.2:1:1:0:60:286:1:0:0.1 -9 94768402 . GA G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.17287;SOR=Inf;LSEQ=TGTGTTCTCTAGGCCTTTTG;RSEQ=AAACATGGAGTTGTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:41,96:0:2,0:23.5:1:29.8:1:1:0:60:44.667:1:0:0.1 0/1:98:2:1,1:27,69:0.0204:2,2:24.5:1:28.7:1:0.4919:2.53:60:4:0.0206:0.0102:0 -9 94768542 . A G 156 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACTGGAAGAGTCTACAAT;RSEQ=TTACCCAGCATGCTCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:20,40:0:2,0:27.8:1:29.1:1:1:0:60:19:1:0:0.2 1/0:61:35:16,19:11,15:0.5738:2,2:28.6:1:30.5:1:1:1.15:60:34:0.5763:0:1.1 -9 95232038 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16944;SOR=0;LSEQ=CAGAGTCAGCGAGGCAGGAG;RSEQ=TGTGCTGAGGGGAGGCGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:0.1111:2,2:28.5:1:28:1:1:1.62:60:4:0.1111:0:1 0/0:25:0:0,0:12,13:0:2,0:26.9:1:31.4:1:1:0:60:11.5:1:0:0.3 -9 95439427 . A G 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0515;SOR=0;LSEQ=GAGCTTAATGTGCTCAATAC;RSEQ=CACGTTAATTCTCTTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:4,2:6,1:0.4615:2,2:28.2:1:31.7:1:0.55944:2.75172:60:12:0.4615:0:1.3 0/0:7:0:0,0:6,1:0:2,0:25.1:1:31.4:1:1:0:60:14:1:0:0.1 -9 95439439 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48308;SOR=0;LSEQ=CTCAATACACACGTTAATTC;RSEQ=CTTGGCAAGAATCTTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:10,2:0.1429:2,2:32.5:1:31.5:1:0.3956:4.28175:60:4:0.1429:0:2 0/0:12:0:0,0:10,2:0:2,0:20.7:1:31.7:1:1:0:60:24:1:0:0.1 -9 95439555 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54902;SOR=Inf;LSEQ=CATTCCTTTTTGAACAGTAC;RSEQ=TATTCTTTTGATGTCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:0:2,0:25:1:31.3:1:1:0:60:46:1:0:0 0/1:46:2:1,1:24,20:0.0435:2,2:18:1:28.5:1:1:1.19523:60:4:0.0435:0:1.5 -9 95439677 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50445;SOR=Inf;LSEQ=GGGCCCCTCTTCTCTTCCCT;RSEQ=TGTGTTCATCATTTTGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:85,43:0:2,0:25:1:30.2:1:1:0:60:127:1:0:0.2 0/1:160:2:1,1:98,60:0.0125:2,2:28.5:1:29.5:1:1:1.62807:60:4:0.0129:0:1 -9 95439693 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17621;SOR=0;LSEQ=CCCTTTGTGTTCATCATTTT;RSEQ=GCAAATTACTGGAAGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:75,53:0.0154:2,2:34.5:1:31.5:1:1:1.41122:60:4:0.0155:0:1 0/0:179:0:0,0:95,84:0:2,0:29.1:1:30.6:1:1:0:59.8:178:1:0:0.2 -9 95439721 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16835;SOR=0;LSEQ=ACTGGAAGATGGCGCTTCCA;RSEQ=CCAAAAGGCAGAACTTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:53,61:0.0172:2,2:16.5:1:29.5:1:1:1.15:60:4:0.0172:0:1 0/0:166:0:0,0:74,92:0:2,0:26.7:1:30.5:1:1:0:60:17.444:1:0:0.2 -9 95439722 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16662;SOR=0;LSEQ=CTGGAAGATGGCGCTTCCAG;RSEQ=CAAAAGGCAGAACTTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:51,62:0.0174:2,0:15.5:1:30:1:0.21022:0:60:4:0.0175:0:1 0/0:166:0:0,0:73,93:0:2,0:26.2:1:30.5:1:1:0:60:82:1:0:0.2 -9 95439768 . T A 25 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86183;LSEQ=GATGGCATTAATCCCACCTA;RSEQ=GAGGACAGAGCCCTTATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:1,0:11,47:0.0169:2,0:1:0:26:0:0.20339:0:60:2:0.0182:0:1 0/1:64:2:1,1:5,57:0.0313:2,2:9:1:25.5:1:0.18006:10.50:54.5:4:0.0345:0:4.5 -9 95439897 . G A 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAACCTCTGCCTTGCAG;RSEQ=TTCAAGTGATTCTCCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:0.5:0,0:20.3:1:30.3:1:1:0:60:6:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 95625972 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAGTGTCATATACTGAAG;RSEQ=AGAGATTGATGAATGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41.5:1:31:1:1:0:60:4:1:0:1 -9 95626730 . A C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=10.000;MSILEN=1;SSF=1;SOR=1.87936;LSEQ=GACATAGAGAACAACAACAA;RSEQ=AAAAAAAGGTGTATAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:0.2:0,0:15:0:33:0:1:0:60:2:0.2:0:1 0/1:6:2:1,1:0,4:0.3333:0,2:10.5:1:29.5:1:0.33333:0:60:4:0.3333:0:1 -9 97401653 . C T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49499;SOR=0;LSEQ=CAGGTGCGGGGCTGCAGGTG;RSEQ=GGGCGGCAAGAGAGGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:0.0645:2,2:11:1:26.5:1:1:1.22249:60:4:0.0645:0:1 0/0:26:0:0,0:12,14:0:2,0:21.5:1:28.4:1:1:0:60:12:1:0:0.1 -9 97401786 . G A 33 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTCCGCAGCGCTCGTG;RSEQ=TGCAACTGGGCCAGGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:0.2857:0,0:31.5:1:33:0:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 97408513 . G A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGGCAGTTCCAAAGAC;RSEQ=GATGACAGCTGAGCACCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 97409370 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49231;SOR=Inf;LSEQ=ACAAAATAGCATGAGAAAGC;RSEQ=GAAGTGAGTGTGTAACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:26.9:1:30.1:1:1:0:60:22:1:0:0.3 0/1:15:2:1,1:7,6:0.1333:2,2:33:1:28.5:1:1:1.1547:60:4:0.1333:0:1 -9 97409419 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.23636;SOR=Inf;LSEQ=AGTGGAGCGTGTTAGTGAGA;RSEQ=AGGAGTCAGCGTGCCCCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:0:2,0:17:1:31.5:1:1:0:60:27:1:0:0.3 0/1:27:2:1,1:13,12:0.0741:2,2:6.5:1:26.5:1:1:1.0801:60:4:0.0741:0:1.5 -9 97409437 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19831;SOR=0;LSEQ=GAGAGGAGTCAGCGTGCCCC;RSEQ=AGAGCCGGTGGGCGAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:18:0:32:0:1:1.0801:60:4:0.0769:0:1.5 0/0:33:0:0,0:17,16:0:2,0:19.9:1:30.6:1:1:0:60:66:1:0:0.4 -9 97409450 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.23469;SOR=Inf;LSEQ=GTGCCCCGAGAGCCGGTGGG;RSEQ=GAGGCCACGGAGGGAGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:25.8:1:31.1:1:1:0:60:50:1:0:0.4 0/1:24:2:1,1:12,10:0.0833:2,2:40.5:1:30.5:1:1:1.19087:60:4:0.087:0:1 -9 97409454 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=CCCGAGAGCCGGTGGGCGAG;RSEQ=CCACGGAGGGAGGGCGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:0.0833:2,2:26:1:30.5:1:1:1:60:4:0.0909:0:1 0/0:24:0:0,0:13,11:0:2,0:31.5:1:31.8:1:1:0:60:48:1:0:0.4 -9 97863896 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50875;SOR=0;LSEQ=CAGCCCAGCGAGGGCACTTA;RSEQ=TCCACAAATGCGTGGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:126,0:0.0156:1,0:35.5:1:32:1:1:0:60:4:0.0159:0:1 0/0:95:0:0,0:91,4:0:1,0:23.6:1:31:1:1:0:60:46.5:1:0:0.1 -9 97869591 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07824;SOR=Inf;LSEQ=AGGGGAGAGGTTAGGAAGAG;RSEQ=CAGGACAGACATACTTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:94,286:0:2,0:24:1:32:1:1:0:60:62.333:1:0:0.1 0/1:285:3:2,1:83,199:0.0105:2,2:8.3:1:26:1:0.2129:4.77:60:6:0.0105:0:1 -9 97869692 . A G 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19294;SOR=2.3392;LSEQ=GGGAGCTAGGCAGCGGCCGA;RSEQ=TTTACACTCGATTTCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:0,6:1,44:0.1176:1,0:24:1:31.8:1:1:0:60:12:0.1176:0:1 0/1:25:6:0,6:0,19:0.24:1,0:26.3:1:31.5:1:1:0:60:12:0.25:0:1.2 -9 97873339 . G A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00074;SOR=5.33268;LSEQ=GATGGAAGCAAGCCCTGGCC;RSEQ=GGCTGCTGGGGAGCGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:6:6,0:73,0:0.0759:1,0:25.5:1:30.2:1:1:0:60:12:0.0769:0:1 0/1:52:16:14,2:34,2:0.3077:2,2:31:1:29.8:1:0.57802:2.38266:60:32:0.3137:0:1.3 -9 97873432 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0746;SOR=Inf;LSEQ=GCCTCTGCAGGGCACGCCTT;RSEQ=GAGGACGCGACCCTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:0:0,0:273,97:0:2,0:22.8:1:31.4:1:1:0:60:51.857:1:0:0.3 0/1:270:3:1,2:183,84:0.0111:2,2:9:1:28:1:0.23885:4.33088:60:6:0.0112:0:1 -9 97873435 . G A 180 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01898;SOR=1.6118;LSEQ=TCTGCAGGGCACGCCTTGGA;RSEQ=GACGCGACCCTGGGGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:56:41,15:245,92:0.1421:2,2:21.8:1:30.6:1:1:1.03:60:112:0.1455:0:1.1 0/1:294:62:47,15:152,80:0.2109:2,2:23.4:1:30.3:1:0.12998:1.65:60:61:0.2096:0:1.1 -9 97873553 . G A 105 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00161;SOR=12.40077;LSEQ=GTCTCGTCTCTGGCCACCTC;RSEQ=GTGGGGACAGGAGAACGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:882:1:0,1:420,461:0.0011:2,0:22:0:33:0:1:0:60:2:0.0011:0:1 0/1:864:12:8,4:399,453:0.0139:2,2:27.3:1:29.4:1:0.24472:2.27:60:24:0.0141:0:1.1 -9 97873698 . C T 59 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.12676;LSEQ=TCTCTGCAAGCTCCTCTCAG;RSEQ=CCCCCAGAGCCCACCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:5:4,1:236,218:0.0109:2,2:18.8:1:25.6:1:0.3749:3.69:60:4:0.009:0:1.6 0/1:327:4:1,3:172,151:0.0122:2,2:9.8:1:22:1:0.34602:3.40535:60:1:0.0063:0:2.5 -9 97873931 . G A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11964;SOR=0.19385;LSEQ=CCGCAGGACCTGGAACAGAG;RSEQ=CAGAACACATGGCAGTTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:5:4,1:123,327:0.011:2,2:8.6:1:27:1:0.02292:10.57:60:4:0.0089:0:1.2 0/0:466:1:1,0:148,317:0.0021:2,0:1:0:24:0:0.31974:0:60:2:0.0022:0:1 -9 97873957 . A G 198 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00082;SOR=1.99846;LSEQ=CACATGGCAGTTGACAACCT;RSEQ=AATTCTTCTTCCTTTGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:48:10,38:30,201:0.172:2,2:25.2:1:31.7:1:0.17513:1.76:60:96:0.1752:0:1.1 0/1:269:79:14,65:33,157:0.2937:2,2:23.2:1:31.5:1:1:1.02:60:78:0.2932:0:1.1 -9 97873995 . G A 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04423;SOR=Inf;LSEQ=GTTTTTAAAGCAACTTTAAC;RSEQ=TTTGCCAACGGTTGGCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:3,118:0:1,0:23.8:1:32.3:1:1:0:60:242:1:0:0.3 0/1:104:4:0,4:4,96:0.0385:1,0:23:1:31:1:1:0:60:8:0.0385:0:2 -9 97879887 . A AAAATAAT 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04817;SOR=0.09834;LSEQ=AAGTCACCTTCTGGGACTTA;RSEQ=AAATTTATGCTCTTGATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:0,16:0,2:0.8889:0,1:25:1:30.5:1:1:0:60:32:0.8889:0.2778:0.1 0/1:5:2:0,2:0,3:0.4:0,0:31:1:31.4:0:1:0:60:4:0.4:0:0 -9 97887335 . G T 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2174;SOR=4.86443;LSEQ=CAACAGCGTCTTATTCTCTG;RSEQ=GATGAATGAGTAATATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:1:1,0:266,116:0.0026:2,0:48:0:14:0:1:0:60:0:0:0:3 0/1:398:5:2,3:270,123:0.0126:2,2:17:1:27.8:1:0.33174:3.28168:60:10:0.0128:0:1 -9 97888730 . C T 119 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCCCATGATACAGCCAGAGA;RSEQ=TACCACAACATTTTCTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:263,60:0:2,0:24.2:1:32.1:1:1:0:60:63.6:1:0:0.1 0/1:337:17:13,4:248,71:0.0504:2,2:22:1:29.2:1:1:1.07453:60:16:0.048:0:1.1 -9 97888955 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1735;SOR=Inf;LSEQ=AAAGGAGTTACTGGGAACTG;RSEQ=TGATGTCCAGAAAACTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:10,170:0:2,0:25.2:1:32:1:1:0:60:44:1:0:0.1 0/1:129:2:0,2:8,119:0.0155:2,0:25:1:29.5:1:1:0:60:4:0.0156:0:1 -9 97897840 . G A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0.23487;SOR=0;LSEQ=ATGGCTCACTGAAAAAAGAA;RSEQ=ATTAAAAAAAGTTCAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:7,94:0.0194:2,2:14.5:1:27:1:0.15001:12.63:60:4:0.0194:0:4.5 0/0:109:0:0,0:11,98:0:2,0:24:1:31.1:1:1:0:60:108:1:0:0.1 -9 97912036 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11103;SOR=Inf;LSEQ=CTCCCAAAGTGCTGGGATTA;RSEQ=AGGTGTGAGCCACCACACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:35,0:0:1,0:22.5:1:31.8:1:1:0:55.4:34:1:0:0.1 0/1:18:2:1,1:15,1:0.1111:1,2:6.5:1:28.5:1:0.21569:10.95468:50:4:0.1111:0:1 -9 97931108 . G A 26 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCATGTGCCACCGCACCTG;RSEQ=CCTAAATTGTGTACTGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:33:1:26.5:1:1:0:60:4:1:0:1 -9 97933252 . T C 167 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=2.94321;LSEQ=AATAATCTTTCTATATAAAA;RSEQ=ACAACCATAACTGAACATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:20:17,3:115,16:0.1325:2,2:21.7:1:31.4:1:0.71948:1.26625:60:40:0.1333:0:1.2 0/1:148:46:34,12:84,18:0.3108:2,2:20.5:1:30.4:1:0.27179:1.64113:60:45:0.3061:0:1.1 -9 97933268 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2482;SOR=Inf;LSEQ=AAAATACAACCATAACTGAA;RSEQ=ATCCATTTCCTATGAATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:161,37:0:2,0:22.3:1:32.2:1:1:0:60:197:1:0:0.2 0/1:202:3:1,2:148,51:0.0149:2,2:11.3:1:25.7:1:0.16902:5.74266:60:6:0.0151:0:2.3 -9 98002436 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAGTGAGCAGCAGAGGC;RSEQ=GCGCAGCACCAAGATCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:26.5:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 98009492 . CGCGTGT C 29 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=12.000;MSILEN=2;SSF=0.03695;SOR=Inf;LSEQ=GATCTGCATGGGTGCGTGCA;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:22,1:0:1,0:31.3:1:28.4:1:1:0:60:22:1:0:0.1 0/1:6:2:2,0:4,0:0.3333:0,0:12:1:29.5:1:1:0:60:4:0.3333:0.1667:1 -9 98009494 . CGT C 96 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=12.000;MSILEN=2;SSF=0.40439;SOR=0.31313;LSEQ=TCTGCATGGGTGCGTGCACG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:8:8,0:20,1:0.2667:1,0:22.8:1:32.3:1:1:0:60:16:0.2667:0.1:0.6 0/1:10:1:1,0:8,0:0.1:0,0:42:0:31:0:1:0:60:2:0.1111:0:0 -9 98009613 . TA T 140 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.03616;SOR=0.45594;LSEQ=CATTTGATAAGTTGTTCCAT;RSEQ=AAAAAAAAAAACTAGGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:25:23,2:139,5:0.1471:1,2:24.8:1:30.3:1:0.27664:2.40097:59:50:0.1497:0.0353:0.6 0/1:165:12:12,0:138,12:0.0727:2,0:28.2:1:30.9:1:0.60247:0:60:24:0.0736:0.0061:0.1 -9 98009794 . G C 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTTTCAATGACTGTATTA;RSEQ=AATCCTGTGAAAGAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:28:11,17:215,361:0.0461:2,2:26.2:1:32.2:1:0.84344:1.09:60:56:0.0467:0:1.1 0/0:603:0:0,0:221,380:0:2,0:23.7:1:31:1:1:0:60:199.333:0.9967:0:0.1 -9 98011320 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24099;SOR=Inf;LSEQ=CTTCAGTCAATACCACAAGT;RSEQ=CCGATTCTGGGTGGCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:119,7:0:2,0:25.1:1:31.1:1:1:0:60:62:1:0:0.1 0/1:122:2:1,1:110,10:0.0164:2,2:15:1:27.5:1:0.17288:10.53577:60:4:0.0165:0:1.5 -9 98011608 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12146;SOR=Inf;LSEQ=AAAGGTGATGTCCCTTCACA;RSEQ=CAGCCTGTCCAGCACTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:58,207:0:2,0:25.5:1:32:1:1:0:60:87.333:1:0:0.1 0/1:261:3:2,1:74,184:0.0115:2,2:20.3:1:29:1:0.20399:4.94:60:6:0.0115:0:1 -9 98209594 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.74434;LSEQ=CGTCTCTGCGCGGTCTGTAG;RSEQ=GGGGTGGCCACAAGCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:27:15,12:160,140:0.0826:2,2:23.7:1:30.2:1:0.84362:1.09:60:54:0.0846:0:1 0/1:337:101:62,39:119,117:0.2997:2,2:24.1:1:29.6:1:0.07391:1.56:60:49.5:0.3028:0:1.1 -9 98209693 . G A 180 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=52.65984;LSEQ=CCAGGTGGGGCTGCTGTCTC;RSEQ=GGTTCGAGGGTGGGTGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:1:1,0:293,301:0.0017:2,0:1:0:28:0:0.49412:0:60:2:0.0017:0:1 0/1:699:57:28,29:312,328:0.0815:2,2:26.9:1:30.9:1:1:1.02:60:114:0.0827:0:1.3 -9 98209764 . G T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=0;LSEQ=TGAGGGTGGGTTAGAAGGGT;RSEQ=GTATCCCAGGCTGGGCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:2,1:83,212:0.01:2,2:30.3:1:30.7:1:0.19678:5.08:60:6:0.0102:0:1 0/0:291:0:0,0:91,200:0:2,0:20.7:1:30:1:1:0:60:40.571:1:0:0.2 -9 98209777 . G A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25038;SOR=0;LSEQ=GAAGGGTGGTATCCCAGGCT;RSEQ=GGCATGGTCCCCGCAGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:2,1:43,166:0.0142:2,2:20:1:21.3:1:0.11466:7.62:60:2:0.0096:0:1 0/0:190:0:0,0:50,140:0:2,0:20.7:1:30.4:1:1:0:60:62.333:1:0:0.1 -9 98209907 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13937;SOR=Inf;LSEQ=TCTAATAACCTCCAGGACCT;RSEQ=GCGGAGGAGCGTGTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:0:1,0:19.8:1:31.7:1:1:0:60:52:1:0:0.1 0/1:16:2:1,1:2,12:0.125:2,2:9.5:1:27:1:0.35:5.10:60:4:0.125:0:1.5 -9 98211012 . G GA 49 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGACATGCACCTTAAGAG;RSEQ=AAAAAAAAAAAAAAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:18:1:31.3:1:1:0:60:6:0.375:0.125:2.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 98211572 . T A 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTGGCTCAGGGGAGGGTG;RSEQ=GGGCAGGCGGTTCAAGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:650:0:0,0:271,379:0:2,0:25.3:1:29.7:1:1:0:60:64:1:0:0.2 0/1:661:34:15,19:288,339:0.0514:2,2:22.3:1:29.7:1:0.86177:1.07601:60:68:0.0518:0:1.2 -9 98211643 . C A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24874;SOR=0;LSEQ=ATGTTAAAAGTGTTCTTGTC;RSEQ=ATTTACCTGCTGGCCACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:84,205:0.0103:2,2:8:1:27.7:1:0.20825:4.85:60:6:0.0105:0:1 0/0:288:0:0,0:100,188:0:2,0:23.5:1:30.7:1:1:0:60:56.6:1:0:0.1 -9 98212282 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=GGGTGGATCGCGCCACCCTC;RSEQ=GTGTGCCCGACACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:21,159:0:2,0:22.7:1:29.4:1:1:0:60:35:1:0:0.1 0/1:184:2:1,1:26,156:0.0109:2,2:7.5:1:31:1:0.27263:5.91:60:4:0.0111:0:1 -9 98215421 . A AT 30 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACCTGAGCTAATAACAAT;RSEQ=TTTTTTTTTTTGAGACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:36.5:1:30:1:1:0:60:4:0.5:0:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 98215631 . T C 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02711;SOR=Inf;LSEQ=CCATCTTGGCCAGGCTGGTC;RSEQ=TGAACTCCTTGACCTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:71,0:0:1,0:26.4:1:31.1:1:1:0:60:70:1:0:0.2 0/1:50:4:4,0:46,0:0.08:1,0:47:1:29.5:1:1:0:60:8:0.0816:0:1 -9 98215968 . C G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03215;SOR=Inf;LSEQ=TGGTAAATGCTCAGCTCTGT;RSEQ=CTAAATGTTACAAGCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:16,129:0:2,0:22.1:1:31.4:1:1:0:60:71.5:1:0:0.1 0/1:108:4:0,4:20,84:0.037:2,0:14.5:1:30.3:1:1:0:60:8:0.0374:0:1 -9 98218474 . G GC 191 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13222;SOR=0.66452;LSEQ=CTGCCACGCACAGGGAGAAT;RSEQ=CAAGGTTCCCACTTGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:64:54,10:68,10:0.4476:2,2:23.8:1:31.9:1:0.6377:1.25719:60:128:0.4539:0.0839:0 0/1:123:43:37,6:71,9:0.3496:2,2:22.5:1:31.3:1:0.77397:1.27662:59.7:42:0.3471:0.0813:0.3 -9 98218744 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49832;SOR=Inf;LSEQ=GCGGGCAGGTCACCCTCTGG;RSEQ=GCTGCCCACAAGGGAGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:23,126:0:2,0:24.8:1:31.1:1:1:0:60:148:1:0:0.1 0/1:149:2:1,1:36,111:0.0134:2,2:30:1:30:1:0.43624:3.05:60:4:0.0139:0:1 -9 98220237 . A T 33 v4;q23;Bias;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24841;SOR=0;LSEQ=AAACAAAACTTCCCGGCTGC;RSEQ=GAAAGAGCTATGCTGAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:0,3:179,44:0.0133:2,0:7:1:21.3:1:0.00854:0:60:2:0.0089:0:1 0/0:221:0:0,0:170,51:0:2,0:22.1:1:29.9:1:1:0:59.9:72.667:1:0:0.2 -9 98220322 . A C 171 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGCCGTCCAGGGGTTCAG;RSEQ=AGGAAGACAGCGCACACGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:0:0,0:387,243:0:2,0:24.7:1:29.8:1:1:0:60:47.462:0.9984:0:0.1 0/1:624:45:23,22:339,240:0.0721:2,2:23.2:1:31.2:1:0.3497:1.3504:60:44:0.0717:0:1.4 -9 98220556 . G A 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06208;SOR=Inf;LSEQ=AAAGGGAACTGGGCATACTC;RSEQ=ATGGGCTCTGCTGCCGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:0:0,0:154,257:0:2,0:24.3:1:30.2:1:1:0:60:67.5:0.9975:0:0.1 0/1:431:5:3,2:158,268:0.0116:2,2:10:1:28.4:1:0.36699:2.54:60:10:0.0118:0:1 -9 98220603 . G T 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.67298;SOR=0.60595;LSEQ=GAGAAGGGCACAGGTTAGGA;RSEQ=CAGCCCAGGGTAGAAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:1,2:41,156:0.015:2,2:18.3:1:30.3:1:0.50894:1.90:60:6:0.015:0:1 0/0:219:2:1,1:52,165:0.0091:2,2:19.5:1:29.5:1:0.42629:3.15:60:4:0.0095:0:1.5 -9 98221780 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17206;SOR=Inf;LSEQ=ATTGTTCTGTTTACACTTCT;RSEQ=AACCCTGGGTAGCGTCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:158,12:0:2,0:22.3:1:32.3:1:1:0:60:84:1:0:0.2 0/1:121:2:1,1:108,11:0.0165:2,2:24.5:1:26.5:1:0.18926:9.44362:60:4:0.0168:0:1 -9 98221861 . T C 229 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07853;SOR=0.79644;LSEQ=CCTCTGTAAGTTCCCAGACC;RSEQ=CCCGATAAAACGCTACTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:200:125,75:192,117:0.3929:2,2:25.8:1:30.6:1:1:1.02:60:49:0.3912:0:1.2 0/1:591:201:124,77:230,160:0.3401:2,2:24.6:1:30:1:0.53641:1.12:60:99.5:0.3413:0:1.2 -9 98222104 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24715;SOR=Inf;LSEQ=CAGAGGCCTTTGAGAATGGG;RSEQ=TTGGGGGTAAACACACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:26,106:0:2,0:23:1:31.6:1:1:0:60:43:1:0:0.1 0/1:131:2:1,1:34,95:0.0153:2,2:32:1:29:1:0.46447:2.77:60:4:0.0155:0:1 -9 98224087 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61734;SOR=2.08049;LSEQ=TCAAGCAGCCTCCACCAGGG;RSEQ=AGCGGCCCCGCAGCCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:0,1:142,30:0.0058:2,0:1:0:25:0:0.17919:0:60:2:0.0058:0:1 0/1:167:2:1,1:143,22:0.012:2,2:13:1:27:1:0.2572:6.37932:60:4:0.012:0:1 -9 98224090 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24385;SOR=Inf;LSEQ=AGCAGCCTCCACCAGGGCAG;RSEQ=GGCCCCGCAGCCCTGGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:151,33:0:2,0:21.9:1:31.7:1:1:0:60:368:1:0:0.1 0/1:180:2:1,1:152,26:0.0111:2,2:11:1:27:1:0.27821:5.75576:60:4:0.0114:0:1.5 -9 98224360 . C G 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8638;SOR=0.89353;LSEQ=AGCGGGGTGGGCTGAGGAGA;RSEQ=TGAGCAGGGCAGGGGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:28:1,27:2,48:0.359:1,1:20.9:1:30.9:1:1:1.12335:60:13:0.3421:0:1 0/1:72:24:3,21:1,47:0.3333:1,2:25.8:1:31:1:0.10476:6.52:60:48:0.3333:0:1 -9 98229297 . G A 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08891;SOR=0.62264;LSEQ=AGTCCATGAAACACGTCAGT;RSEQ=TTACATTCTAATCTAACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:59:58,1:92,5:0.3782:2,1:23.2:1:28.6:1:0.40967:3.13:60:58:0.3742:0:1.4 0/1:113:31:29,2:78,4:0.2743:1,2:19.8:1:28.6:1:0.66522:1.3411:60:62:0.2743:0:1.3 -9 98229389 . C G 251 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00242;SOR=0.70292;LSEQ=AAGGACGAGAGCCTCCCACG;RSEQ=CGTCTTACCCTGAAGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:684:265:176,89:261,155:0.3874:2,2:23.2:1:31.3:1:0.36736:1.17:60:131.5:0.3879:0:1.2 0/1:663:204:122,82:276,183:0.3077:2,2:23.2:1:30.7:1:1:1.01369:60:28.143:0.3017:0:1.2 -9 98229707 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24953;SOR=Inf;LSEQ=AAAAAGGAAGATCACCACTA;RSEQ=CTGGAACAGAAGAGGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:60,206:0:2,0:24.7:1:31.3:1:1:0:60:65.5:1:0:0.1 0/1:285:3:1,2:87,195:0.0105:2,2:37:1:30.7:1:1:1.12:60:6:0.0107:0:1.3 -9 98229745 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21824;SOR=Inf;LSEQ=CAAGGTCAGACCCCAGGGAG;RSEQ=ACCACTGACTCTTCCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:18,124:0:2,0:24.5:1:31.5:1:1:0:60:19.286:1:0:0.1 0/1:125:2:1,1:26,97:0.016:2,2:14:1:27.5:1:0.38671:3.68:60:4:0.0161:0:1 -9 98229754 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21806;SOR=Inf;LSEQ=ACCCCAGGGAGCACCACTGA;RSEQ=TCTTCCTGGACAAAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:11,106:0:2,0:24.6:1:32.2:1:1:0:60:57.5:1:0:0.1 0/1:103:2:1,1:17,84:0.0194:2,2:18:1:28.5:1:0.32039:4.83:60:4:0.0196:0:1 -9 98230924 . AT A 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.57455;SOR=0.69721;LSEQ=ATGTATCATACTTAAACGAA;RSEQ=TTTTTTTTTTTTAAGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:13,1:16,0:0.4375:1,1:24.4:1:31.4:1:0.46667:0:60:28:0.4375:0:0.5 0/1:20:7:7,0:11,0:0.35:0,0:24:1:30.1:1:1:0:60:14:0.35:0:0.3 -9 98230982 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18307;SOR=Inf;LSEQ=CAATCTGATGAACTCCAAAG;RSEQ=TTCTGTTATTTTTTTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:92,25:0:2,0:21.7:1:30.9:1:1:0:60:22.4:1:0:0.1 0/1:88:2:1,1:63,23:0.0227:2,2:5.5:1:26:1:0.47335:2.70266:60:4:0.0235:0:1.5 -9 98231008 . A G 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07271;SOR=Inf;LSEQ=TTATTTTTTTGAAGACAGGA;RSEQ=GAGCCTTAAGTTGTGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:146,55:0:2,0:24.3:1:30.3:1:1:0:60:49.25:1:0:0.1 0/1:145:3:2,1:94,48:0.0207:2,2:20.7:1:31.7:1:1:1.02:60:6:0.0208:0:1 -9 98231043 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25102;SOR=0;LSEQ=GGCAGATTACCTTGGCTTTT;RSEQ=GTTTCAAGAGGAAAGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:183,92:0.0108:2,2:21:1:29.7:1:1:1.01:60:6:0.0109:0:1 0/0:248:0:0,0:154,94:0:2,0:24.6:1:31.1:1:1:0:60:81.667:1:0:0.2 -9 98231419 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21941;SOR=Inf;LSEQ=CTGAGGTTCAACCTGAATCA;RSEQ=TCTGCTGACGCAGGGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:55,168:0:2,0:25.7:1:31.8:1:1:0:60:54.75:1:0:0.2 0/1:197:2:1,1:57,138:0.0102:2,2:18:1:28.5:1:0.50321:2.41:60:4:0.0104:0:1 -9 98231424 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19715;SOR=Inf;LSEQ=GTTCAACCTGAATCACTCTG;RSEQ=TGACGCAGGGGCTGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:46,169:0:2,0:24.3:1:32:1:1:0:60:106.5:1:0:0.1 0/1:173:2:1,1:46,125:0.0116:2,2:36.5:1:29:0:0.47069:2.70:60:4:0.0116:0:1.5 -9 98231908 . G A 80 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.63781;SOR=0.39178;LSEQ=ACTGTTCAGCTGCGGCAGGG;RSEQ=AGAAGGAAGCCCAGGGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:6,0:15,1:0.2727:1,0:26.3:1:31.2:1:1:0:60:12:0.2727:0:1 0/1:8:1:1,0:7,0:0.125:0,0:24:0:25:0:1:0:60:2:0.125:0:1 -9 98232223 . G GA 47 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.1261;SOR=0;LSEQ=ACTACCGCTGCCTGGGAGCA;RSEQ=AAAAAAAATTCAGAGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:4:0,4:143,252:0.01:2,0:18.5:1:23.5:1:0.30152:0:60:3:0.0076:0.0025:0.8 0/0:359:0:0,0:132,227:0:2,0:26.1:1:31:1:1:0:60:88.75:1:0:0.1 -9 98232255 . C A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09331;SOR=Inf;LSEQ=AGAGGTCACCAACATGCCTC;RSEQ=GCCCAATCAGAGGACTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:46,207:0:2,0:24.4:1:30.3:1:1:0:60:125.5:1:0:0.1 0/1:211:3:2,1:49,159:0.0142:2,2:13:1:30:1:0.14566:6.42:60:6:0.0142:0:1 -9 98238244 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19133;SOR=Inf;LSEQ=ACTGAAGTGCCTTAGCAGAG;RSEQ=CCGCAGACATGGGATGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:167,33:0:2,0:25:1:29.5:1:1:0:60:24:1:0:0.1 0/1:156:2:1,1:127,27:0.0128:2,2:26:1:31.5:1:0.32771:4.63712:60:4:0.0128:0:1 -9 98238358 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29876;LSEQ=GCGGGAATTGGGATTAACGC;RSEQ=GCCATGAAGAAGGCTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:617:251:130,121:174,192:0.4068:2,2:26:1:30.5:1:0.32553:1.19:60:49.2:0.4046:0:1.2 0/1:771:131:73,58:335,304:0.1699:2,2:27.8:1:30.2:1:0.50278:1.14:60:262:0.1708:0:1.2 -9 98238379 . A G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCATGAAGAAGGCTGTGAC;RSEQ=TTGCTGATGGACGTGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:0:0,0:296,332:0:2,0:26.1:1:30.3:1:1:0:60:47.308:1:0:0.5 0/1:791:27:14,13:377,387:0.0341:2,2:18.2:1:28.1:1:0.84652:1.11:60:12.5:0.0323:0:1.2 -9 98238466 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26451;SOR=Inf;LSEQ=GAATAAAAAAACACAGCGCT;RSEQ=AGAGCTGCACTGGACATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:43,152:0:2,0:24.3:1:31.1:1:1:0:60:194:1:0:0.1 0/1:262:3:2,1:61,198:0.0115:2,2:18.3:1:26.7:1:0.14456:6.43:60:6:0.0118:0:1 -9 98238473 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2602;SOR=Inf;LSEQ=AAAACACAGCGCTGAGAGCT;RSEQ=CACTGGACATGGTCCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:32,140:0:2,0:24.1:1:31.8:1:1:0:60:42:1:0:0.1 0/1:222:3:1,2:39,180:0.0135:2,2:18:1:31:1:0.45064:2.30:60:6:0.014:0:1 -9 98239147 . A G 163 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAATGGCAAAACCTACAGC;RSEQ=AAAACAGAGGATGGTGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:168,287:0:2,0:25.8:1:29.8:1:1:0:60:74.833:1:0:0.3 0/1:420:49:19,30:134,236:0.1167:2,2:24.1:1:29.2:1:0.75343:1.12:60:11.25:0.1095:0:1.1 -9 98239190 . G C 210 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09662;SOR=0.69372;LSEQ=GACATGCGAGATGCAATTCA;RSEQ=ATGATTCTAAAGCTAGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:95:18,77:19,100:0.4419:2,2:22.2:1:32:1:0.58942:1.23:60:94:0.4476:0:1.2 0/1:175:62:15,47:22,90:0.3543:2,2:22.9:1:30.8:1:0.56238:1.30:60:30:0.3529:0:1.2 -9 98239200 . AAGCTAGTTA GCTAGTT 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18483;SOR=Inf;LSEQ=ATGCAATTCAGATGATTCTA;RSEQ=GGACTCTGCCACCAGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:24,157:0:2,0:23.1:1:30.3:1:1:0:60:362:1:0:0.6 0/1:137:2:1,1:23,112:0.0146:2,2:9.5:1:27.5:1:0.32074:4.79:60:4:0.0146:0.0073:0 -9 98239730 . G A 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00256;SOR=Inf;LSEQ=AAAGGCTGCAAGACCCTTCC;RSEQ=GTGAGAAGGACACACAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:195,23:0:2,0:22.1:1:29.8:1:1:0:60:108:1:0:0.1 0/1:165:7:5,2:137,21:0.0424:2,2:21.9:1:27.6:1:0.25246:2.58911:60:6:0.0366:0:1 -9 98240028 . A T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.19661;SOR=Inf;LSEQ=CAGAACAAAAGCCGAACATT;RSEQ=GAATGTGTTGTGATTCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:25,125:0:2,0:26.9:1:31.1:1:1:0:60:300:1:0:0.1 0/1:120:2:1,1:20,98:0.0167:2,2:30:1:28:1:0.32059:4.81:60:4:0.0168:0:1 -9 98240120 . G A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75306;SOR=0.73123;LSEQ=AACAAAACTTTACATCAAGG;RSEQ=CGTCACATAAAATGACAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:11:3,8:9,19:0.2821:2,2:26.1:1:30.8:1:1:1.25576:60:22:0.2821:0:1 0/1:18:4:2,2:2,12:0.2222:2,2:25.8:1:29.5:1:0.19706:5.26:60:8:0.2222:0:1 -9 98240230 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24013;SOR=Inf;LSEQ=CGCTCTCTCTGTCCTGGATG;RSEQ=ACATCGATGTTAAGAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:61,3:0:1,0:26.2:1:31.9:1:1:0:60:31:1:0:0.1 0/1:62:2:1,1:55,5:0.0323:2,2:14.5:1:27.5:1:0.18562:10.1325:60:4:0.0339:0:1.5 -9 98240535 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56273;SOR=3.1456;LSEQ=CCACAAGCCTCGACAGCACA;RSEQ=ATCTCAGGTGACACAGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:19,150:0.0059:2,0:20:0:11:0:1:0:53:0:0:0:4 0/1:109:2:1,1:12,95:0.0183:2,2:23.5:1:28.5:1:0.22528:7.65:60:4:0.0185:0:1 -9 98240879 . C A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGCCACTTTTAAAAGGTCA;RSEQ=ATGCAGCTCAGTAGAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:21.5:1:29:1:1:2.44949:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 98241185 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19829;SOR=Inf;LSEQ=TCCCAGAATTGCAATGTTTT;RSEQ=AAAATAAAGCGAATGGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:162,18:0:2,0:23.1:1:32:1:1:0:60:89:1:0:0.1 0/1:145:2:1,1:129,14:0.0138:2,2:7.5:1:25:0:0.19684:8.93663:60:4:0.0138:0:1 -9 98242112 . A G 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40691;SOR=0.65508;LSEQ=GTCTGCTACTATTTCTTAAT;RSEQ=TTCTATGACGCCACCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:29:29,0:40,1:0.4143:1,1:17.1:1:32.2:1:1:0:60:58:0.4203:0:1.2 0/1:38:12:12,0:26,0:0.3158:1,0:22.8:1:33.1:1:1:0:60:24:0.3158:0:1 -9 98242151 . A G 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18319;SOR=Inf;LSEQ=CTAGCGAGGATAACGGTTTA;RSEQ=GTATTAATACAAATACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:143,2:0:1,0:21.2:1:30.3:1:1:0:60:47.333:1:0:0.2 0/1:109:2:1,1:102,5:0.0183:1,2:5:0:28:1:0.10754:18.70551:60:4:0.0185:0:0.5 -9 98242177 . T C 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=AATACAAATACACTTGCCGA;RSEQ=GTCAGGAGGGAAGTGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:194,27:0:2,0:23.8:1:31:1:1:0:60:109.5:1:0:0.1 0/1:215:13:10,3:165,37:0.0605:2,2:20:1:31.2:1:0.7127:1.33588:60:26:0.0613:0:1 -9 98242443 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22987;SOR=Inf;LSEQ=ATGCCTTGTTAAAATCCAGT;RSEQ=CATTAAGGGCTTGTGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:20,113:0:2,0:24.6:1:31.8:1:1:0:60:43.333:1:0:0.1 0/1:123:2:1,1:14,106:0.0163:2,2:25:1:25.5:1:0.23168:7.35:60:4:0.0168:0:1 -9 98242593 . TA T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19393;SOR=Inf;LSEQ=TGAAATGTTAAAAATGAAAA;RSEQ=ATAAAGTGAACGATGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:204,33:0:2,0:23.5:1:28.6:1:1:0:60:236:1:0:0.1 0/1:187:2:1,1:154,31:0.0107:2,2:12:1:28.8:1:0.31373:4.90546:60:4:0.0109:0.0053:0 -9 98242625 . G T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04777;SOR=Inf;LSEQ=CGATGAATGGACACAAAAAA;RSEQ=TGTTTTGCTCTCCACCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:308,114:0:2,0:24.6:1:32:1:1:0:60:69.333:1:0:0.1 0/1:372:4:1,3:266,102:0.0108:2,2:14.8:1:27:1:0.06984:7.77362:60:8:0.0109:0:1 -9 98242925 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.30407;LSEQ=GAGCCTTCTAAACGCATCGT;RSEQ=AAGTAACACGGCTGCGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:63:5,58:11,93:0.3772:2,2:26.9:1:31.2:1:0.7871:1.36954:60:62:0.3735:0:1.3 0/1:187:29:4,25:28,130:0.1551:2,2:21.3:1:30.6:1:0.79032:1.34413:60:58:0.1551:0:1.4 -9 98242984 . G A 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56051;SOR=0.78131;LSEQ=AGGTTCCTGGCAATGCTGCA;RSEQ=TTCTGGGACTCTGGCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:30:0,30:0,32:0.4839:1,1:25.7:1:31.1:1:1:0:60:29:0.4754:0:1.6 0/1:45:19:0,19:1,25:0.4222:1,1:26.7:1:30.6:1:1:0:60:38:0.4318:0:1.4 -9 98244096 . CA C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCCCCGACTATTCACT;RSEQ=AAAAATGCACATGGAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:2,0:76,1:0.0253:1,0:35.5:1:33:0:1:0:60:4:0.0253:0:0 0/0:30:0:0,0:29,1:0:1,0:25:1:30.3:1:1:0:60:60:1:0:0 -9 98244157 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20047;SOR=Inf;LSEQ=CAAAACTGAAATGGAACAAA;RSEQ=AATGATAAGCAACATTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:196,18:0:2,0:23.5:1:32.3:1:1:0:60:428:1:0:0 0/1:174:2:2,0:150,22:0.0115:2,0:17:1:29.5:1:1:0:60:4:0.0115:0:1 -9 98244563 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.22023;SOR=Inf;LSEQ=AATTCGAAATGATAGAACAT;RSEQ=AAAAAGAACTGCAATTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:5,103:0:1,0:23.4:1:28.3:1:1:0:60:216:1:0:0.1 0/1:96:2:1,1:16,78:0.0208:2,2:10.5:1:28:1:0.32434:4.76:60:4:0.0213:0:0.5 -9 98244575 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21928;SOR=Inf;LSEQ=TAGAACATATAAAAAGAACT;RSEQ=CAATTTCGATCACTTTTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:1,87:0:1,0:24.2:1:32:1:1:0:60:43:1:0:0.1 0/1:78:2:1,1:9,67:0.0256:2,2:23:1:27.5:1:0.24143:7.11:60:4:0.0278:0:1 -9 98247897 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21914;SOR=Inf;LSEQ=TCATTTACTAAAATAACGGG;RSEQ=CCTAAACCAGCAGCCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:130,16:0:2,0:24.2:1:30.8:1:1:0:60:28.2:1:0:0.1 0/1:129:2:1,1:107,20:0.0155:2,2:14:0:30.5:1:0.30015:5.24552:60:4:0.0163:0:1 -9 98268595 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5314;SOR=0;LSEQ=GGCAGGGGGTTTCGCCGGCC;RSEQ=CAGCCAGGCTCTAGGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:157,2:0.0124:1,0:38.5:1:31.5:1:1:0:60:4:0.0126:0:1 0/0:95:0:0,0:95,0:0:1,0:26.5:1:29.6:1:1:0:60:46.5:1:0:0.2 -9 98268765 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13423;LSEQ=GCGAAGGCCCCAAATATGAG;RSEQ=AGGCCCACAACCAAGAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1156:474:219,255:326,355:0.41:2,2:25.4:1:29.9:1:0.59007:1.06919:60:35.462:0.4101:0:1.1 0/1:1431:122:59,63:642,662:0.0853:2,2:24.3:1:28.4:1:0.92461:1.03552:60:23.4:0.0853:0:1.2 -9 98268923 . G A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24816;SOR=0;LSEQ=GGAGTGAGCGCCGGGGAGTC;RSEQ=CGGCCCGCGCGCCCACGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:3:1,2:5,114:0.0246:1,2:34.7:1:30:1:0.14151:10.80:60:6:0.025:0:1 0/0:112:0:0,0:14,98:0:2,0:22.6:1:31.6:1:1:0:60:27:1:0:0.2 -9 98270316 . TGTGA T 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0.00877;SOR=Inf;LSEQ=TGCTGCTTTTCCTGGAGAGG;RSEQ=GTGAGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:133,1:0:1,0:25.9:1:32.7:1:1:0:59.9:133:1:0:0.2 0/1:114:6:6,0:105,3:0.0526:1,0:30.3:1:29.7:1:1:0:60:12:0.0536:0.0088:0.2 -9 98270320 . AGTGAGTGT A 187 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=8.000;MSILEN=2;SSF=0.01283;SOR=0.50131;LSEQ=GCTTTTCCTGGAGAGGTGTG;RSEQ=GTGTGTGTGTGTGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:60:59,1:86,1:0.4082:1,1:25.3:1:31.8:1:1:1.45378:59.3:59:0.4041:0.0816:0.3 0/1:117:30:30,0:82,3:0.2564:1,1:25.6:1:32.2:1:0.56623:0:59.8:60:0.2632:0.0342:0.2 -9 98270369 . T G 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.21362;SOR=4.09413;LSEQ=GAGGAAGAGAGTGTGTGTGT;RSEQ=TGTGTGTGGCGGGGGCGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:1:1,0:276,88:0.0027:2,0:46:0:32:0:1:0:60:2:0.0028:0:6 0/1:359:4:3,1:258,97:0.0111:2,2:10.5:1:25.5:1:1:1.13:60:3:0.0085:0:2.3 -9 98270385 . C T 74 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34475;SOR=2.17821;LSEQ=GTGTTTGTGTGTGGCGGGGG;RSEQ=GATCCCAAAGAGTTAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:3:0,3:321,148:0.0064:2,0:1:0:26.7:1:0.0323:0:60:6:0.0066:0:1 0/1:509:7:2,5:316,185:0.0138:2,2:5.3:1:26.7:1:0.10859:4.25778:60:14:0.0143:0:1.3 -9 98270568 . G A 46 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62472;SOR=2.78024;LSEQ=CCTCCCGCCTCCAGCCGGCC;RSEQ=TCCCGGGGCACCGATACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:1:1,0:60,173:0.0043:2,0:1:0:22:0:0.26068:0:60:2:0.0043:0:1 0/1:255:3:2,1:82,170:0.0118:2,2:25.7:1:29.3:1:0.25315:4.12:60:6:0.0122:0:1.3 -9 98270569 . T A 31 v4;q23;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.24889;SOR=Inf;LSEQ=CTCCCGCCTCCAGCCGGCCG;RSEQ=CCCGGGGCACCGATACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:59,171:0:2,0:20.2:1:30.3:1:1:0:60:56.5:1:0:0.3 0/1:242:3:1,2:80,159:0.0124:2,2:17.3:1:20:1:1:1.00626:60:2:0.0086:0:4.3 -9 98270588 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21607;SOR=0;LSEQ=GTCCCGGGGCACCGATACAG;RSEQ=CGCTGCCGCCGCCGCCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:45,89:0.0147:2,2:5:0:32:0:1:1.97:60:4:0.015:0:1 0/0:156:0:0,0:61,95:0:2,0:20.9:1:31.5:1:1:0:60:77:1:0:0.4 -9 98270592 . TGCC T 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.69226;SOR=1.66845;LSEQ=CGGGGCACCGATACAGCCGC;RSEQ=GCCGCCGCCGCGGTCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:42,65:0.0183:2,2:39.5:1:32:1:1:1.54:60:4:0.0183:0:0 0/1:132:4:2,2:52,75:0.0303:2,2:38.3:1:32.5:1:1:1.44:60:8:0.0317:0:0.3 -9 98270596 . G A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.12423;SOR=Inf;LSEQ=GCACCGATACAGCCGCTGCC;RSEQ=CCGCCGCCGCGGTCCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:44,58:0:2,0:22.6:1:30.7:1:1:0:60:50:1:0:0.4 0/1:115:4:3,1:49,62:0.0348:2,2:21.8:1:27:1:0.32671:3.75:60:8:0.0357:0:1 -9 98278644 . C A 30 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCGCTCGGGGCTCGCTCCT;RSEQ=CGTCCGCCGCGCGGGGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:0:30.5:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:0:2,0:31:0:32.5:1:1:0:60:4:1:0:0.5 -9 98278729 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25207;SOR=Inf;LSEQ=AGGCGAGGTGGCGTCGGCGG;RSEQ=CGCCGCGCTGGCTGCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:164,56:0:2,0:21.2:1:32:1:1:0:60:43:1:0:0.2 0/1:253:3:2,1:173,77:0.0119:2,2:11:1:29:1:1:1.12284:60:6:0.012:0:1 -9 98278828 . C CT 117 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00794;SOR=0.24076;LSEQ=CTTGGATTTCACATCAATTC;RSEQ=TTTTTTTTCCCTGGCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:830:14:11,3:570,241:0.0169:2,2:18.6:1:30.8:1:0.76825:1.55:60:28:0.0173:0.006:0.6 0/0:973:4:3,1:608,356:0.0041:2,2:21:1:27:1:1:1.76:60:3:0.0031:0:0.3 -9 98278958 . TTTC T 117 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.5638;SOR=1.30927;LSEQ=GTCTTTTTCTTCTCCTCCGT;RSEQ=TTCTTCTTCTTCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1265:11:1,10:525,726:0.0087:2,2:29.9:1:29.5:1:0.03103:7.22234:59.1:22:0.0088:0.0016:0.3 0/1:1409:16:7,9:590,799:0.0114:2,2:29.9:1:29.3:1:1:1.05:59.1:32:0.0116:0.0014:0.3 -9 98278972 . TCTC T 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CTCCGTTTTCTTCTTCTTCT;RSEQ=CTCCTCCTCCGTCTTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1066:19:7,12:413,635:0.0178:2,2:19.9:1:30.6:1:1:1.11487:58.4:38:0.0179:0.0084:0.6 0/0:1169:0:0,0:496,669:0:2,0:23.1:1:31.2:1:1:0:60:96.083:0.9965:0:0.2 -9 98279102 . T A 112 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=GTTTCTATTAAGCAGTTCCA;RSEQ=GGCCCTCGGCGTGGGTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:150,300:0:2,0:23.6:1:30:1:1:0:60:39.909:1:0:0.1 0/1:485:13:4,9:170,301:0.0268:2,2:17.5:1:30.5:1:0.77813:1.27018:60:26:0.0274:0:1.4 -9 98279188 . T A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=7e-04;SOR=0.24497;LSEQ=AAAACTTTACCCCTTTACAA;RSEQ=AAACTCAAGGAAAGCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:29:1,28:0,59:0.3295:1,1:22.2:1:29.3:1:0.32955:0:60:13.5:0.3176:0:1.3 0/1:75:8:0,8:1,66:0.1067:1,0:19.3:1:27.6:1:1:0:60:7:0.0946:0:1 -9 98851044 . C CGAT 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.46074;SOR=0.46187;LSEQ=TGATGAGATGACAATGATAA;RSEQ=GATGATGATGATATGATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:6,4:2,2:0.7143:2,2:25.4:1:29.8:1:1:1.46:60:9:0.6923:0.1429:1.2 1/0:17:9:5,4:5,3:0.5294:2,2:16.1:1:28.5:1:1:1.31092:60:18:0.5294:0.2353:0.9 -9 98851075 . C G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0114;SOR=0.15632;LSEQ=ATATGATGACAATGAGATTT;RSEQ=ATGATAATGATGATGACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:9,8:1,2:0.85:2,2:26.1:1:29.8:1:1:2.16:60:16:0.8421:0:1.1 0/1:24:11:5,6:7,6:0.4583:2,2:26.3:1:31.6:1:1:1.3804:60:22:0.4583:0:1.2 -9 98852303 . A G 47 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTGCTGGTGCCAGCTAC;RSEQ=GATGCCCTTGCCGAAGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:11:1:30:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 98981273 . C A 87 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01446;SOR=13.14064;LSEQ=GTTAGATTTTAACCCAAACA;RSEQ=TGTCCCTTCTAATGTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:9,2:0.0833:2,0:2:0:32:0:1:0:60:2:0.0833:0:1 1/0:14:8:4,4:3,3:0.5714:2,2:24.4:1:29.3:1:1:1:60:7:0.5385:0:1.3 -9 98981308 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5328;SOR=0;LSEQ=TTCTCCGCTGCCGCCCAGTG;RSEQ=AGCTCCCAACGCTGACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:0.0645:2,2:25.5:1:30:1:1:1.22249:60:4:0.0645:0:1 0/0:17:0:0,0:9,8:0:2,0:32.2:1:32.4:1:1:0:60:34:1:0:0.6 -9 98981387 . C T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12782;SOR=8.54954;LSEQ=ACTCCCGCGCTCCACCGAGC;RSEQ=GGAGGGCAGCCCAGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:5,10:0.0625:2,0:19:0:32:0:1:0:60:2:0.0625:0:1 0/1:5:2:1,1:1,2:0.4:2,2:10.5:1:27.5:1:1:1.73:60:4:0.4:0:1 -9 100615914 . A G 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGAGTCCAGTCCCGGTC;RSEQ=CGAGGCCACCGCCGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:36:0:30:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:1:0,2:35.5:1:28.5:1:1:0:60:4:1:0:1.5 -9 100616396 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCTCATCGCCATGGCCATCG;RSEQ=GCACGCGCCCGAGCGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:19.1:1:33.1:1:1:0:60:16:1:0:0 0/1:17:2:1,1:15,0:0.1176:1,2:24:0:31.5:1:0.11765:0:60:4:0.1176:0:1.5 -9 100616453 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50456;SOR=Inf;LSEQ=CTACAAGTTCATCACCGAGC;RSEQ=CTTCCCCTTCTACCGCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:37,7:0:2,0:25.1:1:30.3:1:1:0:60:88:1:0:0 0/1:58:2:1,1:38,18:0.0345:2,2:5.5:1:27:1:1:2.08172:60:4:0.0351:0:1.5 -9 100616468 . G C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19636;SOR=0;LSEQ=CGAGCGCTTCCCCTTCTACC;RSEQ=CGACAACCCCAAAAAGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:43,12:0.0351:2,2:23:0:33:0:0.40727:3.48238:60:4:0.0357:0:1 0/0:71:0:0,0:43,28:0:2,0:23.7:1:29.8:1:1:0:60:34.5:1:0:0.3 -9 100616583 . T C 160 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18555;SOR=1.85488;LSEQ=AAGGGCAACTACTGGGCGCT;RSEQ=GACCCCAACGCGGAGGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:30:7,23:2,14:0.6522:2,2:21.4:1:30:1:0.46277:2.10:60:60:0.6522:0:1.1 1/0:54:42:11,31:3,9:0.7778:2,2:19.5:1:29.8:1:1:1.06:60:84:0.7778:0:1.1 -9 100968289 . C T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGTAACTTTCTCTTTTTT;RSEQ=GAGATGGAGTCTTGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:16.3:1:31.3:1:1:0:54.7:6:0.75:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 100968490 . A G 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10185;SOR=2.87185;LSEQ=CCTCGTGATCTGCCTGCCTC;RSEQ=GCCTCCCAAAGTGCTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:24,1:0.1667:1,0:26.6:1:29.8:1:1:0:56.2:10:0.1667:0:1.2 0/1:38:14:10,4:18,6:0.3684:2,2:17.5:1:30.1:1:1:1.19418:59.1:28:0.3784:0:1.4 -9 100968566 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22025;LSEQ=GTAACTTTCTGTTTTAAGCA;RSEQ=TAAATATTTACATGAATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:0,1:74,41:0.0085:2,0:1:0:26:0:0.36207:0:60:2:0.0088:0:1 0/1:192:2:1,1:110,80:0.0104:2,2:26.5:1:30:1:1:1.37266:60:4:0.0105:0:1 -9 100968598 . T C 216 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0.45259;LSEQ=ATGAATACCAATTATCTGCA;RSEQ=TTGCATATCAAATTTAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:175:112:63,49:34,28:0.64:2,2:25.5:1:31.8:1:0.87459:1.06:60:111:0.6453:0:1.1 0/1:238:106:59,47:72,60:0.4454:2,2:26.4:1:31.3:1:0.89618:1.05:60:212:0.4454:0:1.1 -9 100968820 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=TCTGCCCCTTCAGCACAGGT;RSEQ=GAACTCCAAAAGCAGGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:0:0,0:24:1:31.4:1:1:0:60:14:1:0:0 0/1:7:2:0,2:0,5:0.2857:0,0:42:1:29.5:1:1:0:60:4:0.2857:0:1 -9 101866715 . C A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCAGGATCTGGGTCTGA;RSEQ=GCTGGGATCTGAGGACTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 101867396 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50529;SOR=Inf;LSEQ=GCCGGAGCGAGGCCGCCGCG;RSEQ=CGGCTAGGGAGGTGGGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:19.3:1:32.1:1:1:0:60:22:1:0:0.2 0/1:17:2:1,1:8,7:0.1176:2,2:38.5:1:28:1:1:1.13389:60:4:0.1176:0:1 -9 101867411 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29153;SOR=Inf;LSEQ=CCGCGGCGGCTAGGGAGGTG;RSEQ=GGCGAGGCGAGGTTTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:17.1:1:30.5:1:1:0:60:44:1:0:0.2 0/1:38:3:1,2:18,17:0.0789:2,2:7.7:1:27:1:1:2.0774:60:6:0.0789:0:1 -9 101867454 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.52697;SOR=Inf;LSEQ=TGAGGCAGCGGCGCGGCCGG;RSEQ=CCGGGCCGGGCCACAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:24,23:0:2,0:25.6:1:31.1:1:1:0:60:22.5:1:0:0.3 0/1:78:2:1,1:36,39:0.0256:2,2:32:1:28:1:1:1.08:60:4:0.0278:0:1 -9 101867464 . G T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.28385;SOR=Inf;LSEQ=GCGCGGCCGGGCCGGGCCGG;RSEQ=CCACAGGCGGTGGCGGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:34,35:0:2,0:19.9:1:31.2:1:1:0:60:22:1:0:0.4 0/1:109:3:1,2:52,53:0.0275:2,2:31.7:1:27.3:1:1:1.9505:60:6:0.028:0:1 -9 101867506 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53761;SOR=Inf;LSEQ=CCATGGAGGCGGCGGTCGCT;RSEQ=CTCCGCGTCCCCGGCTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:39,40:0:2,0:26.4:1:32.1:1:1:0:60:18.75:1:0:0.5 0/1:141:2:1,1:68,69:0.0142:2,2:14.5:1:28:1:1:1.01:60:4:0.0146:0:1.5 -9 101891409 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12006;SOR=Inf;LSEQ=TGTATAAAATTTTTTTCCTA;RSEQ=ATACTACAAGAAAAACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:30,198:0:2,0:24:1:31.1:1:1:0:60:56:1:0:0.1 0/1:223:3:3,0:48,172:0.0135:2,0:9.7:1:22.3:1:0.01142:0:60:2:0.0091:0:2.3 -9 101900151 . G T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01628;SOR=Inf;LSEQ=TTACCTTTAGGTTTACCATT;RSEQ=CTTGTTCAGAGAACAATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:360,126:0:2,0:24.4:1:32.2:1:1:0:60:80:1:0:0.1 0/1:542:7:2,5:382,153:0.0129:2,2:12.3:1:25.7:1:0.02462:6.21706:60:14:0.0132:0:1 -9 101904795 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.04733;SOR=0;LSEQ=AAATGGTCTGCAGCCCAACC;RSEQ=AAATGTTAATTCTGTTTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:4:1,3:272,118:0.0102:2,2:8:1:25.8:1:0.08809:6.87794:60:8:0.0102:0:1 0/0:449:0:0,0:302,147:0:2,0:23.9:1:29.7:1:1:0:60:111.25:1:0:0.1 -9 101905005 . T A 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30723;SOR=0.22088;LSEQ=GGTAATTCTATAAGCAGTTC;RSEQ=ATTATTTAAGCTTTAAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:43,189:0.0128:2,2:13:1:26.7:1:0.09473:8.67:60:6:0.0128:0:1 0/0:352:1:1,0:93,257:0.0028:2,0:1:0:23:0:0.26781:0:60:2:0.0029:0:1 -9 101907193 . T A 33 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10192;SOR=Inf;LSEQ=ATACTTTTGAACAACTATAT;RSEQ=TAATATCTTCTGAAATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:48,187:0:2,0:24.6:1:30.3:1:1:0:60:57.75:1:0:0.1 0/1:207:3:1,2:57,147:0.0145:2,2:19:1:21.3:1:1:1.29:60:2:0.0099:0:1.7 -9 101907243 . T C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06785;SOR=Inf;LSEQ=TTCTCTTTCATATATACATA;RSEQ=CATTGCTGAAACTCAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:2,88:0:1,0:22.1:1:30.3:1:1:0:60:180:1:0:0.1 0/1:63:3:0,3:2,58:0.0476:1,0:17:1:32.7:1:1:0:60:6:0.0517:0:1.3 -9 101908756 . AT A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.93049;LSEQ=TTTCAAAGTTCTTTTTGCAA;RSEQ=TTTTTTTAGGTACATGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:701:9:3,6:370,321:0.0128:2,2:36.3:1:31.4:1:0.31713:2.30263:60:18:0.0129:0:0.9 0/1:920:11:6,5:500,409:0.012:2,2:28.8:1:29.5:1:1:1.01873:60:22:0.012:0.0011:0.2 -9 101908915 . G A 192 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=89.02998;LSEQ=AATTGCTCTCCTCTCCCCCA;RSEQ=TAGTTTGTCATGAGCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:1:1,0:155,318:0.0021:2,0:1:0:25:0:0.32911:0:60:2:0.0021:0:1 0/1:586:93:33,60:177,315:0.1587:2,2:25.2:1:29.5:1:1:1.02161:60:45.5:0.1583:0:1.1 -9 101910151 . ACTTTT A 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=GCTACTTTTCTTTAAGGAAA;RSEQ=CTTTAAGAATTTTCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:0,118:0:1,0:23.3:1:32:1:1:0:59.9:15.857:1:0:0.2 0/1:110:13:0,13:1,95:0.1182:1,1:28.6:1:32.6:1:1:0:60:26:0.1193:0.0091:0 -9 101911436 . A AT 135 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.15346;SOR=0.58767;LSEQ=GGAAAATGGTGCATGCATTA;RSEQ=TTTTTTTTTTTATATTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:20:18,2:137,28:0.1075:2,2:21.7:1:31.3:1:0.53824:1.83:60:40:0.1087:0.0161:0.4 0/1:212:14:13,1:157,40:0.066:2,1:24.3:1:30.2:1:0.31321:3.30:60:28:0.068:0.0189:0.1 -9 101911448 . A T 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.62832;SOR=2.56681;LSEQ=ATGCATTAATTTTTTTTTTT;RSEQ=TATTTTCTTGTAGGCCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:1:1,0:177,45:0.0045:2,0:17:0:9:0:1:0:60:0:0:0:3 0/1:262:3:1,2:196,63:0.0115:2,2:13.7:1:20.3:1:0.15302:6.16805:60:2:0.0081:0:2.3 -9 101911656 . A G 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTTTAATTTGGGAGGTCA;RSEQ=TTGTTCTACCTCACTGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:17,133:0:2,0:24.1:1:31.2:1:1:0:60:149:1:0:0 0/1:180:40:4,36:18,122:0.2222:2,2:22.3:1:31:1:0.7874:1.32587:60:39:0.2203:0:1.1 -9 102136067 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23662;SOR=0;LSEQ=TATTTCAACCCAATTCTCCT;RSEQ=CCTCCCAACCCAGGTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:101,32:0.0148:2,2:17:1:27.5:1:0.43051:3.12354:60:4:0.0154:0:1 0/0:142:0:0,0:104,38:0:2,0:22.9:1:30.9:1:1:0:60:27.4:1:0:0.1 -9 102136177 . T G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=5.35264;LSEQ=CCACTCCCCACAAATTCAAT;RSEQ=TTCCCCCTCTTCCTAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:129:50,79:67,94:0.4448:2,2:25:1:31.2:1:0.63223:1.12571:60:42:0.4452:0:1.2 1/1:334:271:111,160:30,32:0.8114:2,2:25.5:1:31.4:1:0.31958:1.35009:60:134.5:0.8127:0:1.1 -9 102136212 . CG C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=AGAAGCACAGGCCCTGGGGT;RSEQ=GGGGGTCCTGGCTGTGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:44,127:0:2,0:23:1:30:1:1:0:60:33.2:1:0:0.7 0/1:177:2:1,1:43,131:0.0113:2,2:10:1:28:1:0.43857:3.02:60:4:0.0114:0:1 -9 102136227 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49955;SOR=0;LSEQ=GGGGTCGGGGGGTCCTGGCT;RSEQ=TGCCCAGTATGCAGGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:0,2:27,105:0.0149:2,0:24.5:1:27:1:1:0:60:4:0.0153:0:2.5 0/0:120:0:0,0:27,93:0:2,0:22.4:1:31.1:1:1:0:60:240:1:0:0.8 -9 102136291 . A G 163 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAAGCCGCTACTTGCCAC;RSEQ=GTTGGAAACCCACTGCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:0,41:0,0:1:0,1:23.1:1:30.6:1:1:0:60:19.5:1:0:1.2 1/1:21:21:0,21:0,0:1:0,1:20.1:1:29.8:1:1:0:60:20:1:0:1 -9 102159548 . G A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31202;SOR=0.45489;LSEQ=AGGGCTGCAAGCCCTGGAGA;RSEQ=CAACATTAAGGTGATGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:10,1:10,1:0.5:2,2:18.5:1:30.8:1:1:1:60:22:0.5:0:1 0/1:13:4:4,0:8,1:0.3077:2,0:27:1:28.3:1:1:0:60:8:0.3077:0:1 -9 102159610 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07797;SOR=Inf;LSEQ=TGTGAATTCCAAGCCATCCT;RSEQ=TTACCTTCACTTTGGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:37,26:0:2,0:26:1:31.6:1:1:0:60:62:1:0:0.3 0/1:48:3:2,1:26,19:0.0625:2,2:21.7:1:28.7:1:1:1.45:60:6:0.0625:0:1 -9 102159777 . C A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTTGCCATTTCAGTGCA;RSEQ=GCAGCCAGACTTCCAGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:18.5:1:29.5:1:1:0:60:4:0.3333:0:1 0/0:2:0:0,0:0,2:0:0,0:39.5:1:29.5:1:1:0:60:4:1:0:0 -9 102160116 . C T 27 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTATCATTGTTCAGCTCC;RSEQ=ACTTATGAGTGAGAACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:27.5:1:1:0:60:4:1:0:1.5 -9 102585044 . G A 27 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.51711;SOR=Inf;LSEQ=CTCTCGGCGGCGGCGGCGGC;RSEQ=GCGGCAGCGGCAGCGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:30.3:1:30:1:1:0:60:17:1:0:0.1 0/1:29:2:1,1:16,11:0.069:2,2:39:1:27:1:1:1.43545:60:4:0.069:0:1 -9 106905519 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAACTCTTAATCTGGAGTCA;RSEQ=CGTTTCCCTCAGGTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:9,12:0:2,0:23.9:1:31.4:1:1:0:60:42:1:0:0 0/1:54:2:1,1:23,29:0.037:2,2:44:0:28.5:1:1:1.26:60:4:0.0377:0:1.5 -9 107040713 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.53244;LSEQ=AATTTTTGGCACACCTTTTA;RSEQ=GATCACCCTCTCTTAAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:568:73:29,44:243,251:0.1285:2,2:25.2:1:30.7:1:0.13452:1.46789:60:146:0.129:0:1.1 0/1:646:259:126,133:185,201:0.4009:2,2:28.4:1:29.6:1:0.87255:1.03:60:258:0.4038:0:1.2 -9 107040779 . AT A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28557;SOR=2.53217;LSEQ=AGATGCCTTTATTAGATGCC;RSEQ=TTTTTTTTCTTTTAGATAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:2:0,2:85,197:0.007:2,0:30:1:31.5:1:1:0:60:4:0.0071:0:0 0/1:283:5:1,4:85,193:0.0177:2,2:27.4:1:29.8:1:1:1.75855:60:10:0.0179:0.0035:0.4 -9 107040789 . C T 48 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02898;SOR=Inf;LSEQ=ATTAGATGCCATTTTTTTTT;RSEQ=TTTTAGATAACTCTGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:58,179:0:2,0:21.6:1:31.8:1:1:0:60:78:1:0:0.2 0/1:232:5:4,1:56,171:0.0216:2,2:10.2:1:21:1:0.01666:12.06:60:1.5:0.0132:0:2 -9 107068085 . G C 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00444;SOR=0.03977;LSEQ=GCAAAAGCCCTACAGAAGAG;RSEQ=GACTGGACTATTGAAAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:25.2:1:28:1:1:0:60:5:0.8333:0:1.2 0/1:13:2:2,0:8,3:0.1538:2,0:34.5:1:29.5:1:1:0:60:4:0.1538:0:1.5 -9 107068102 . G GA 46 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=2.11388;LSEQ=GAGGGACTGGACTATTGAAA;RSEQ=AAAAAAAAAACAAGTGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:6,2:0.1111:2,0:15:0:31:0:1:0:60:2:0.1111:0:0 0/1:14:3:2,1:9,2:0.2143:2,2:24:1:29.3:1:1:2.10574:60:6:0.2143:0:1 -9 107068143 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=GTGACAACAGCATCAACAAA;RSEQ=ACAACAAAAAGGCCCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:21.3:1:29.7:1:1:0:60:40:1:0:0.3 0/1:25:2:1,1:13,10:0.08:2,2:7.5:1:29.5:1:1:1.28628:60:4:0.0833:0:1.5 -9 109484504 . A G 149 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAAAAATGAGAATTACAGT;RSEQ=AAATTCAGCTTGTCTAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:24:24,0:16,0:0.6:1,1:23.1:1:32.5:1:1:0:60:48:0.6:0:1 0/0:24:0:0,0:23,1:0:1,0:22.1:1:28.6:1:1:0:60:48:1:0:0 -9 109485116 . C T 213 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGATGATACAAATGAATA;RSEQ=GTTAGTGCTGTGTGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:0:0,0:271,272:0:2,0:23.8:1:31:1:1:0:60:89.5:1:0:0.1 0/1:460:136:67,69:151,171:0.2957:2,2:22.9:1:30.1:1:0.68254:1.10:60:135:0.2961:0:1.1 -9 109485318 . C A 25 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.25323;LSEQ=ATGTCTCTCCCTAAAGTCAT;RSEQ=AGGGTTTTGGGTTTGTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:2:0,2:26,216:0.0082:2,0:23.5:1:30:1:1:0:60:4:0.0083:0:1 0/1:195:2:1,1:29,164:0.0103:2,2:23:1:25:1:0.28469:5.58:60:4:0.0103:0:1 -9 109485333 . G A 166 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCATCAGGGTTTTGGGTTT;RSEQ=TTTTGAATATTTTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:9,174:0:1,0:22.8:1:32.3:1:1:0:60:90.5:1:0:0 0/1:132:46:3,43:4,82:0.3485:1,2:21.4:1:30.2:1:0.69414:1.43:59.9:92:0.3594:0:1.1 -9 110246982 . G GT 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.82797;SOR=1.12468;LSEQ=ATTTATGGTAAAACTAAATA;RSEQ=TTTTTTTTTAATAAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:9:6,3:228,85:0.028:2,2:21.9:1:29.8:1:0.70909:1.33988:58.3:18:0.0281:0:0.9 0/1:383:12:9,3:262,106:0.0313:2,2:29.5:1:28.6:1:1:1.21:60:24:0.0314:0.0026:0.3 -9 110246994 . TA T 85 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.36226;SOR=0.48263;LSEQ=ACTAAATAGTTTTTTTTTAA;RSEQ=AAAAAAGGTATTTTAATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:7:3,4:281,130:0.0167:2,2:28.3:1:30.6:1:0.21763:2.87395:60:14:0.017:0.0024:0.4 0/0:491:4:2,2:324,163:0.0081:2,2:16.8:1:26.8:1:0.60538:1.98479:60:8:0.0082:0.0041:0.5 -9 110247041 . C T 93 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07697;SOR=4.07253;LSEQ=ATAAAGTTGGCTTTTTTGTG;RSEQ=GTGCTTCTTACATGCCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:804:2:0,2:425,377:0.0025:2,0:1:0:26.5:1:0.2219:0:60:4:0.0025:0:1 0/1:994:10:4,6:524,459:0.0101:2,2:24.4:1:28:1:0.5285:1.71148:60:20:0.0102:0:1.2 -9 110247965 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19198;SOR=0;LSEQ=CTCCTTCCCTCATCGGGAAG;RSEQ=CAGTGTGAAAAGTAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:88,15:0.019:2,2:34:1:29.5:1:0.28278:5.71261:60:4:0.019:0:1 0/0:134:0:0,0:102,32:0:2,0:21.2:1:28.6:1:1:0:60:66:1:0:0.1 -9 110248129 . C T 77 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08698;SOR=Inf;LSEQ=GGCGGTGCCCCGTGTGTTTA;RSEQ=GGTAGTGCCTGGTCAGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:187,205:0:2,0:23.9:1:30.5:1:1:0:60:64.333:1:0:0.2 0/1:564:6:3,3:263,295:0.0106:2,2:18.2:1:30:1:1:1.12:60:12:0.0107:0:1.2 -9 110248177 . C T 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08752;SOR=0.14164;LSEQ=GGGCGAATTTCCATCCACAG;RSEQ=CGTCCCAGTCACAGTGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:5:2,3:124,217:0.0144:2,2:22.2:1:30.8:1:1:1.17:60:10:0.0146:0:1.2 0/0:485:1:0,1:195,289:0.0021:2,0:1:0:26:0:1:0:60:2:0.0021:0:1 -9 110248222 . G GA 127 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.08148;SOR=0.50109;LSEQ=TCTCACCTGTAAAGGTAAAA;RSEQ=AAAAAAAAAATTGACGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:17:2,15:34,128:0.0944:2,2:24.5:1:31.2:1:0.53036:1.98586:58.8:34:0.0977:0.0111:0.4 0/1:242:12:4,8:66,162:0.0496:2,2:22.3:1:27.8:1:0.74983:1.23:59.6:24:0.0517:0.0083:0.5 -9 110248233 . T A 68 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07889;SOR=Inf;LSEQ=AAGGTAAAAGAAAAAAAAAA;RSEQ=TGACGCTATTGCTATATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:20,117:0:2,0:24.4:1:30.6:1:1:0:60:274:1:0:0.1 0/1:196:5:1,4:48,143:0.0255:2,2:15.2:1:29.4:1:1:1.34076:59:10:0.0259:0:1.4 -9 110249505 . C T 258 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.77094;LSEQ=GAAGGTGGGGTGAGCATCAT;RSEQ=CCGTGTGTCCCGAAGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1280:170:83,87:530,578:0.1328:2,2:25.3:1:30.2:1:0.86909:1.04:60:169:0.1342:0:1.1 0/1:1510:450:211,239:513,545:0.298:2,2:23.6:1:29.3:1:0.57381:1.06612:60:149:0.2988:0:1.1 -9 110249840 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12428;SOR=Inf;LSEQ=GCACGAAGAGACCGCCTCCT;RSEQ=CTTGATCTTGGGGCACGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:131,164:0:2,0:24.7:1:32.1:1:1:0:60:146.5:1:0:0.1 0/1:311:4:3,1:136,170:0.0129:2,2:16.3:1:24.8:1:0.32904:3.73:60:8:0.0132:0:1 -9 110249872 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25066;SOR=Inf;LSEQ=GGCACGTGCGCGGCGGCCCG;RSEQ=CGTTGTAGGGCGCCACCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:108,144:0:2,0:25.6:1:31.3:1:1:0:60:62:0.996:0:0.1 0/1:281:3:1,2:121,157:0.0107:2,2:12:1:29:1:1:1.53912:60:6:0.0108:0:1.7 -9 110249994 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24992;SOR=0;LSEQ=GACGCCTTCAGCACGAACTT;RSEQ=CCCATCAGCCCGCCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:1,2:126,113:0.0124:2,2:19.7:1:29.7:1:0.60559:2.22294:60:6:0.0125:0:1 0/0:221:0:0,0:136,84:0:2,0:24.5:1:31.7:1:1:0:60:54:1:0:0.2 -9 110250003 . C T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20638;SOR=4.23392;LSEQ=AGCACGAACTTGCCCATCAG;RSEQ=CCGCCACCTGGCGGCTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:1:1,0:133,108:0.0041:2,0:20:0:25:0:1:0:60:2:0.0042:0:1 0/1:232:4:2,2:142,86:0.0172:2,2:29.5:1:30.5:1:0.63536:1.64738:60:8:0.0176:0:1 -9 110250554 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1713;SOR=Inf;LSEQ=CTCCTCCCGCCAGCGCTGCG;RSEQ=GGACAGGGCGGGAGAGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:9,88:0:2,0:22.7:1:31.4:1:1:0:60:194:1:0:0.1 0/1:69:2:1,1:6,61:0.029:2,2:38:1:29.5:1:0.19395:9.49:60:4:0.0294:0:1 -9 110251860 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAACTGGTCGGCGGCGCA;RSEQ=GGCGCGGACTCCGGTGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:33:1:1:0:60:4:1:0:1.5 -9 112787105 . GTT G 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GCCAGTGTCTTGGGTTTTTT;RSEQ=TTTTTTTTTTAACAGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:31:1:30.5:1:1:0:60:4:1:0:1 1/0:3:2:1,1:1,0:0.6667:0,2:37:1:31:1:1:0:60:4:0.6667:0:0 -9 112787369 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49673;SOR=0;LSEQ=TGCTTAATGTGCTCAATATG;RSEQ=ACATTAATTCTCTTGGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:2,0:68,7:0.026:2,0:22.5:1:31:0:1:0:60:4:0.027:0:1 0/0:76:0:0,0:68,8:0:2,0:23.6:1:32.4:1:1:0:59.7:75:1:0:0.1 -9 112787398 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49829;SOR=Inf;LSEQ=TCTCTTGGCAAGAATCTTGC;RSEQ=CTTAACTTGTTTGTTTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:99,46:0:2,0:21.1:1:30.9:1:1:0:59.7:144:0.9863:0:0.2 0/1:147:2:1,1:93,52:0.0136:2,2:19.5:1:28.5:1:1:1.78091:60:4:0.0138:0:1.5 -9 112787597 . C T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06382;SOR=Inf;LSEQ=TTTCTAAAAGGCCTAGAGAA;RSEQ=ATATGTCGGGAGCCTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:44,57:0:2,0:21.9:1:31.4:1:1:0:56:32.667:1:0:0.3 0/1:119:5:2,3:61,53:0.042:2,2:20:1:24.8:1:0.66516:1.71853:60:4:0.0354:0:1.2 -9 112787668 . C T 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31611;LSEQ=TTACTGGAAGATGGAGGTTC;RSEQ=GCCCGAAAGGCTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:1:1,0:40,70:0.009:2,0:5:0:16:0:0.36937:0:42:0:0:0:1 0/1:169:2:1,1:86,81:0.0118:2,2:36.5:1:31.5:1:1:1.06138:60:4:0.0127:0:1 -9 112787669 . G A 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15801;SOR=Inf;LSEQ=TACTGGAAGATGGAGGTTCC;RSEQ=CCCGAAAGGCTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:41,64:0:2,0:23.2:1:27.3:1:1:0:59.8:4.526:1:0:0.6 0/1:168:4:3,1:84,78:0.0238:2,2:22.3:1:27.8:1:0.6222:2.77:52.3:8:0.0265:0:1.5 -9 113137239 . G GT 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.53184;SOR=1.55268;LSEQ=AATGGTAGACTGGATAAAGT;RSEQ=TTTTTTTTTTCATTTTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:10,0:9,0:0.4762:0,0:28.1:1:29.9:1:1:0:60:20:0.4762:0.0476:0 1/0:17:10:10,0:7,0:0.5882:0,0:19.3:1:30.9:1:1:0:60:20:0.5882:0.1765:0 -9 113137380 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50022;SOR=Inf;LSEQ=GTGTAATGTCTTCTCTATGC;RSEQ=CTGCAAAATGAAGCAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:78,57:0:2,0:24.7:1:30.3:1:1:0:60:26:1:0:0.6 0/1:153:2:1,1:89,62:0.0131:2,2:22.5:1:28.5:1:1:1.432:60:4:0.0133:0:1 -9 113137400 . A T 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73642;SOR=1.08418;LSEQ=TCTGCAAAATGAAGCAGATG;RSEQ=CATAAAGAAGACAGATAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:151:90:50,40:30,31:0.596:2,2:27.5:1:29.8:1:0.50723:1.29:60:89:0.5933:0:1.1 1/0:182:112:64,48:40,30:0.6154:2,2:25.4:1:28.4:1:1:1:60:36.333:0.6124:0:1.1 -9 113560061 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11442;SOR=0;LSEQ=CTTATTTACTTTCTCAAATA;RSEQ=TATACATTTAGTCATTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:1,2:140,91:0.0128:2,2:21.7:1:29:1:0.5646:3.06194:60:6:0.0129:0:2 0/0:248:0:0,0:144,104:0:2,0:25.3:1:30.6:1:1:0:60:34.429:1:0:0.8 -9 113560071 . A C 192 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64743;SOR=0.91195;LSEQ=TTCTCAAATAGTATACATTT;RSEQ=GTCATTAAACAAACATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:88:52,36:96,77:0.3359:2,2:25.1:1:30.1:1:0.59952:1.16:60:87:0.3346:0:1.7 0/1:282:89:42,47:111,81:0.3156:2,2:24.7:1:29.8:1:0.12212:1.53111:60:88:0.3154:0:2 -9 113560119 . A G 235 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.18783;LSEQ=TATTTTCAAGATTATCAAGC;RSEQ=ATTCCTGTTTCAACTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:147:65,82:55,70:0.5404:2,2:26.5:1:30.3:1:1:1.01:60:48:0.5373:0:2 1/0:304:219:96,123:43,42:0.7204:2,2:26.9:1:30.3:1:0.30681:1.31056:60:72:0.7248:0:1.9 -9 113560161 . G A 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAATGTTGACTCTGTATTC;RSEQ=TATACAGTTTATAACATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:193:193:62,131:0,0:1:0,2:25.5:1:30.7:1:1:0:60:192:1:0:1.5 1/1:207:168:62,106:16,23:0.8116:2,2:23.9:1:29.7:1:0.71435:1.18832:60:83:0.8098:0:1.8 -9 113560217 . C A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23676;SOR=Inf;LSEQ=ATTCAAACAGAAACTATGTA;RSEQ=AGTTTTCCAATTTAACCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:8,59:0:2,0:19.7:1:32.9:1:1:0:60:134:1:0:0.9 0/1:64:2:1,1:9,53:0.0313:2,2:6:0:27.5:1:0.29018:5.64:60:4:0.0317:0:2 -9 114910765 . G A 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTGTGAGCCAACAGCCG;RSEQ=GTGCCAGCCCCCAGATTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:0:30.5:1:1:0:60:4:1:0:1.5 -9 114912617 . A C 225 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02847;SOR=0.73236;LSEQ=TCCTTTTAGAGCTGATCTAC;RSEQ=CAGTTAGCTTTTTTTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:165:90,75:109,96:0.4459:2,2:27.8:1:30.9:1:0.8341:1.06:60:81.5:0.4454:0:1.1 0/1:472:175:90,85:153,143:0.3708:2,2:25.3:1:30.3:1:1:1.01047:60:86.5:0.3704:0:1.1 -9 114912625 . C CT 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.03765;SOR=0;LSEQ=GAGCTGATCTACACAGTTAG;RSEQ=TTTTTTTGGGAGAAAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:4:1,3:199,178:0.0105:2,2:16.3:1:28.5:1:0.34983:3.34411:60:8:0.0106:0.0052:1 0/0:482:0:0,0:245,237:0:2,0:26.5:1:31.6:1:1:0:60:79.333:1:0:0.5 -9 114912713 . GT G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.05572;SOR=Inf;LSEQ=CCAGTGGGCCCCTCATATCC;RSEQ=TTAATGGCCTCTCACAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:48,142:0:2,0:24.8:1:29.2:1:1:0:60:22.75:1:0:0.1 0/1:182:4:1,3:48,130:0.022:2,2:27.8:1:31.3:1:1:1.10708:60:8:0.0223:0.0055:0 -9 114912752 . A C 143 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGCACTCAATTCTTATTCA;RSEQ=CCAAAAGTACCCTCCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:4,83:0:1,0:23.1:1:29.9:1:1:0:60:42.5:1:0:0.1 0/1:77:23:0,23:6,48:0.2987:2,1:24.7:1:31.7:1:0.17047:0:60:46:0.2987:0:1.1 -9 116790592 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATCAGGCCCCTCTGCCTC;RSEQ=CCCCCAGCCCCGGCATGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 116791055 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50431;SOR=0;LSEQ=ACCGGATGATCCAGACACGG;RSEQ=CTCTGAGTGTTCACATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:101,30:0.015:2,2:37.5:1:30.5:1:0.41319:3.32823:60:4:0.0156:0:1 0/0:106:0:0,0:79,25:0:2,0:23.8:1:30.9:1:1:0:60:33.667:0.9806:0:0.1 -9 116791095 . C T 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24877;SOR=0;LSEQ=GAGGTCTCCCCATCTCCACG;RSEQ=TTCGTGGCAGCGAAGACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:3:1,2:179,80:0.0115:2,2:17:1:25.3:1:0.23162:4.44653:60:6:0.0118:0:2 0/0:253:0:0,0:161,92:0:2,0:23.6:1:31.7:1:1:0:60:506:1:0:0.5 -9 116791143 . G T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05032;SOR=Inf;LSEQ=CAGTCGGGGAAAAAAGCTCC;RSEQ=GCCTCCGTGGTCCGATGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:252,190:0:2,0:25.4:1:29.9:1:1:0:60:48.111:0.9977:0:0.9 0/1:401:4:1,3:213,183:0.01:2,2:15.8:1:29.5:1:0.34172:3.48169:60:8:0.0102:0:2 -9 116791161 . T C 266 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.34322;LSEQ=CCGGCCTCCGTGGTCCGATG;RSEQ=GCCACCCTCTTACACCGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:470:400:218,182:36,34:0.8511:2,2:27.3:1:30.8:1:0.69698:1.13:60:65.667:0.851:0:1.1 1/0:432:286:146,140:78,67:0.662:2,2:24.3:1:30.6:1:0.61103:1.11605:60:142:0.6636:0:1.2 -9 117485190 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCACTGCACGTCTGCAAG;RSEQ=TCACTGGATGAAAACGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:23.6:1:32:1:1:0:60:28:1:0:0 0/1:39:2:1,1:21,15:0.0513:2,2:13.5:1:28:1:1:1.38742:60:4:0.0513:0:1 -9 117485255 . C T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.56614;SOR=Inf;LSEQ=GTGCTTGGGTACAGTTCCTC;RSEQ=AAATGCCTCTTGCTAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:21.3:1:30.6:1:1:0:60:17:1:0:0 0/1:55:4:2,2:22,29:0.0727:2,2:24.8:1:30.3:1:1:1.31:60:8:0.0727:0:1.3 -9 118486252 . G T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTACGGAGCTCCCATGGGGA;RSEQ=GGGCAACCAGCATCACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:28:0:29:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:7.5:1:28.5:1:1:0:60:4:1:0:1.5 -9 118486817 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50101;SOR=Inf;LSEQ=CCCAACTGGGTGAGACCCTC;RSEQ=AACAGGGGATGTCAGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:24.2:1:31.2:1:1:0:60:38:1:0:0.1 0/1:26:2:1,1:11,13:0.0769:2,2:37.5:1:30.5:1:1:1.17:60:4:0.08:0:1 -9 118486836 . C T 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01419;SOR=Inf;LSEQ=CCAACAGGGGATGTCAGACA;RSEQ=CCTATACAGGAGCGATCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:0:2,0:18.2:1:31.2:1:1:0:60:34:1:0:0.1 0/1:23:7:3,4:7,9:0.3043:2,2:15.9:1:24.6:1:1:1.03541:60:2.5:0.2381:0:2 -9 118486938 . G C 51 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TTTGCTGTCCTCCAGCCTCC;RSEQ=TGAGTGACATCTCCAGGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:29:1:32.3:1:1:0:60:6:1:0:1 0/1:5:1:1,0:2,2:0.2:2,0:37:0:31:0:1:0:60:2:0.2:0:1 -9 119904284 . G C 48 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGGTGAGGTTGGACAGA;RSEQ=CAGAGAAGACAGCGTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:18:1:30.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 119905188 . C G 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20458;SOR=0.35481;LSEQ=TTCTTCTTCAGTTTGAGCTA;RSEQ=CTGCTGTCTGATGCCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:18:17,1:23,0:0.439:1,1:21.8:1:32.2:1:0.43902:0:60:36:0.439:0:1.1 0/1:14:3:3,0:10,1:0.2143:2,0:31:1:33.7:1:1:0:60:6:0.2143:0:1 -9 119905254 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5177;SOR=0;LSEQ=TCTTTGAAGGGGCTTCATCA;RSEQ=ACTAGACAAAGAAGGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:105,18:0.0159:2,2:14:1:28.5:1:0.28194:5.70477:60:4:0.0161:0:1 0/0:84:0:0,0:67,17:0:2,0:21.8:1:31.6:1:1:0:60:83:1:0:0.2 -9 119905342 . G T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37487;SOR=3.74928;LSEQ=GCTTATCAGGTTAGACAGAT;RSEQ=TGTCTGCAGAGTAAGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:1:0,1:197,156:0.0028:2,0:1:0:26:0:0.4435:0:60:2:0.0028:0:2 0/1:380:4:2,2:212,164:0.0105:2,2:29.5:1:27.5:1:1:1.29179:60:8:0.0106:0:1.8 -9 119905369 . G C 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.26224;SOR=0.85016;LSEQ=CAGAGTAAGTCAGACCTAGA;RSEQ=GGCTTGTTCTGGTATTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:161:77,84:135,145:0.3643:2,2:24.8:1:30.7:1:1:1.01564:60:160:0.3628:0:1.2 0/1:458:150:78,72:159,148:0.3275:2,2:26.2:1:30.1:1:1:1.01:60:74:0.326:0:1.2 -9 119905437 . C T 100 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00071;SOR=Inf;LSEQ=ATAGGGAAAAGGTATGATTG;RSEQ=TAAGGTAAAAAGACAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:117,184:0:2,0:25.4:1:32:1:1:0:60:74.25:1:0:0.3 0/1:287:10:2,8:99,177:0.0348:2,2:30.2:1:30.3:1:0.50257:2.23184:60:20:0.0352:0:1 -9 119905583 . T C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15556;SOR=6.88885;LSEQ=TCCAGACATGGGGTCCCTTC;RSEQ=TCAAGCCTGGGATGAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:1,18:0.05:1,0:30:0:34:0:1:0:60:2:0.05:0:1 0/1:7:2:0,2:0,5:0.2857:0,0:38:1:31:1:1:0:60:4:0.3333:0:1 -9 119965718 . AT A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=TGCTCTTTTGGGTTTTTAGC;RSEQ=TTTTTCATTGATTATTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:24.4:1:29.4:1:1:0:60:18:1:0:0 0/1:13:2:1,1:7,4:0.1538:2,2:24.5:1:31.5:1:1:1.67325:60:4:0.1538:0:0 -9 119965809 . TTTG T 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.53131;SOR=Inf;LSEQ=ATGGGGTTTTTGTGGGGGCC;RSEQ=TTGTTGTTGTTGTTGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:25.8:1:29.5:1:1:0:60:15:1:0:0.1 0/1:29:2:1,1:14,13:0.069:2,2:42.5:1:31.5:1:1:1.07415:60:4:0.0741:0:0 -9 119966410 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=TACACCTGAACAGGCACTGT;RSEQ=GCCGCCTACTGCCATTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:35.5:1:29.5:1:1:1:60:4:0.125:0:1 0/0:16:0:0,0:6,10:0:2,0:25.5:1:30.6:1:1:0:60:32:1:0:0.1 -9 119966491 . A G 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCCTCCCTGGCTCCACA;RSEQ=AAATTTTTGTGTATTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:18.3:1:31.3:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:1:0,0:27:0:33:0:1:0:60:2:1:0:1 -9 122204648 . A AG 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.6662;SOR=0.77632;LSEQ=GAAGTCAAAATTCAAATCTC;RSEQ=CAGGCTGACTCCAAAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:30:30,0:19,0:0.6122:1,1:25.6:1:31.4:1:1:0:60:29:0.6042:0.0816:0.1 1/0:40:22:22,0:18,0:0.55:1,1:21.3:1:31.6:1:1:0:59.5:44:0.55:0.175:0.1 -9 122204709 . A T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59814;SOR=0.4293;LSEQ=CTTCCTCTGCTGCATCCCAC;RSEQ=CTGCTCCCCATCCACAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:107,30:0.0144:2,2:19:1:28.5:1:0.39756:3.52481:60:4:0.0145:0:1 0/0:161:1:0,1:115,45:0.0062:2,0:1:0:24:0:0.28571:0:60:2:0.0064:0:1 -9 122204804 . A C 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00323;SOR=1.55358;LSEQ=AAGACAGGATGTGTTCTGCC;RSEQ=AGTGGCACCTTAAACGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:375:211:101,110:82,80:0.5627:2,2:27.6:1:31.5:1:0.60327:1.11601:60:69.333:0.5606:0:1.1 1/0:408:272:142,130:56,80:0.6667:2,2:25.4:1:30.6:1:0.03643:1.56:60:67:0.6634:0:1.1 -9 122204884 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23764;SOR=Inf;LSEQ=GTTCCTGCCTCTGCCCCAGT;RSEQ=TAAGAAGGGGGCAGGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:42,132:0:2,0:24.3:1:32.1:1:1:0:60:348:1:0:0.3 0/1:166:2:1,1:48,116:0.012:2,2:33.5:1:28:1:0.50449:2.40:60:4:0.0123:0:1 -9 122204917 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2314;SOR=Inf;LSEQ=AGGCAGATACTGAGGCCCTG;RSEQ=CTTTATTTCTGTGTCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:11,78:0:2,0:24.6:1:30:1:1:0:60:43.5:1:0:0.1 0/1:83:2:1,1:9,72:0.0241:2,2:29:1:32.5:1:0.22774:7.64:60:4:0.025:0:1 -9 122623982 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20479;SOR=0;LSEQ=TTACAGGGCCCTAGCAAACC;RSEQ=ATACACTGGATAACCTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:0.0909:2,2:24:1:31:1:1:1.21:60:4:0.0952:0:1 0/0:26:0:0,0:12,14:0:2,0:29.8:1:29.5:1:1:0:60:52:1:0:0.5 -9 122623999 . T C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13631;SOR=2.73434;LSEQ=ACCAATACACTGGATAACCT;RSEQ=GAGCAATATATTAAACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:3,7:6,8:0.4167:2,2:27.5:1:30:1:0.67846:1.70978:60:20:0.4167:0:1.1 1/0:21:14:6,8:3,4:0.6667:2,2:26.3:1:29.5:1:1:1:60:28:0.6667:0:1 -9 124037184 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52087;SOR=Inf;LSEQ=TGGATTTTACAAGGAAGTGC;RSEQ=CAGGTAGGCCTAGGAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:32.3:1:30.2:1:1:0:60:44:1:0:0.2 0/1:36:2:1,1:18,16:0.0556:2,2:41.5:1:32:0:1:1.12132:60:4:0.0556:0:1.5 -9 125532953 . G A 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.53112;SOR=0;LSEQ=GATGGGAAATAACCAAGATC;RSEQ=GGGGGAACTGAAGGAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:12,13:0,0:1:0,2:23.7:1:29.9:1:1:0:60:24:1:0:1.1 1/1:44:42:25,17:1,1:0.9545:2,2:25.4:1:29.5:1:1:1.46:60:41:0.9535:0:1.2 -9 125767291 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58204;SOR=3.22054;LSEQ=GTTGCAGTGAGCCGAGATCG;RSEQ=GCCATTGCACTCCAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:8,0:0.1111:0,0:30:0:31:0:1:0:41:2:0.1667:0:1 0/1:10:3:3,0:7,0:0.3:0,0:29.7:1:28.7:1:1:0:52:6:0.3:0:1 -9 125767432 . G T 35 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33122;SOR=0.27057;LSEQ=GGAACTTCTTTTTGTCCTTT;RSEQ=AATATGTTTCAGTAAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:2,1:228,45:0.0109:2,2:5.3:1:22.3:1:0.42256:2.52213:60:2:0.0074:0:3 0/0:338:1:0,1:263,74:0.003:2,0:1:0:22:0:0.22189:0:60:2:0.003:0:1 -9 125767540 . C G 233 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.02159;LSEQ=ATAGTTAGGTTCATTTGTTT;RSEQ=CATTTATTTTAGCTTAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:49:20,29:308,373:0.0666:2,2:26:1:30.1:1:0.65597:1.19703:60:6:0.0632:0:1.3 0/1:964:215:107,108:319,425:0.223:2,2:26.7:1:30.2:1:0.08635:1.32:60:10.316:0.2175:0:1.3 -9 125767567 . AT A 257 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.49837;LSEQ=TTTTAGCTTAGGGGCTTGGG;RSEQ=TTTTTTTTTTCCTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:540:349:116,233:77,106:0.6463:2,2:28.7:1:30.5:1:0.0467:1.45798:60:68.8:0.6503:0.0167:0.4 0/1:680:324:104,220:137,188:0.4765:2,2:29.9:1:30.1:1:0.00929:1.54046:60:107:0.482:0:0.3 -9 125767578 . T C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1745;SOR=1.42971;LSEQ=GGGCTTGGGATTTTTTTTTT;RSEQ=CCTTTTTTTTTTGAATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:26:12,14:133,282:0.0566:2,2:18.5:1:28:1:0.19506:1.81:60:5.5:0.0497:0:2.4 0/1:569:45:19,26:154,349:0.0791:2,2:16.5:1:28.6:1:0.13127:1.65:60:14:0.0757:0:2 -9 125767580 . C T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=0.65713;SOR=1.16834;LSEQ=GCTTGGGATTTTTTTTTTTC;RSEQ=TTTTTTTTTTGAATATATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:20:7,13:130,281:0.0456:2,2:25.2:1:28:1:0.80694:1.16:60:4:0.0392:0:2.9 0/1:530:28:11,17:149,344:0.0528:2,2:24.4:1:29.4:1:0.30138:1.49:60:27:0.0536:0:2.7 -9 125767591 . G T 57 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51631;SOR=1.73154;LSEQ=TTTTTTTTCCTTTTTTTTTT;RSEQ=AATATATAAAATACTTATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:3:3,0:89,270:0.0082:2,0:12.3:1:19:1:0.01602:0:60:2:0.006:0:2 0/1:425:6:3,3:107,309:0.0141:2,2:11.7:1:22.3:1:0.18528:2.88:60:2:0.0103:0:3.8 -9 126974713 . AT A 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.66086;SOR=0.53979;LSEQ=TCCGGCTTTCTTTTCTAATC;RSEQ=TTTTTTTGTTGCTCCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:2,1:139,51:0.0155:2,2:40:1:31.3:1:1:1.36042:60:6:0.0155:0:1.3 0/0:237:2:2,0:179,56:0.0084:2,0:48.5:1:32:0:1:0:60:4:0.0085:0:1.5 -9 126974738 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.12145;LSEQ=TTTTGTTGCTCCTTTTCTCC;RSEQ=TTTGACATAACAAACCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:272:240:158,82:23,9:0.8824:2,2:26.4:1:30.6:1:0.55508:1.32497:60:119:0.8848:0:1.1 0/1:351:167:114,53:119,63:0.4758:2,2:25.3:1:30.4:1:0.57214:1.14:60:166:0.477:0:2.1 -9 126974767 . G T 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAAACCAGTTTGTTTTCC;RSEQ=ATCTGATTGTTCTCAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:202,146:0:2,0:26.8:1:30.2:1:1:0:60:68.6:1:0:0.7 0/1:484:160:93,67:179,144:0.3306:2,2:26.4:1:29:1:0.62623:1.12:60:31:0.3263:0:2.5 -9 126974804 . C G 225 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGAATGTCCTTTCCTTCTC;RSEQ=GTTACTCTCGGTTTAATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:181,215:0:2,0:25.9:1:30.3:1:1:0:60:98:1:0:0.4 0/1:530:207:98,109:151,172:0.3906:2,2:27.1:1:29.3:1:0.92901:1.02:60:102.5:0.3905:0:2 -9 126974902 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23002;SOR=0;LSEQ=CCCACAAACGCTGTCCTGTG;RSEQ=GTCCCCTTCCTCATCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:17,105:0.0161:2,2:15:1:30:1:0.27026:6.03:60:4:0.0168:0:1 0/0:134:0:0,0:25,109:0:2,0:21.8:1:30.4:1:1:0:60:66:1:0:0.2 -9 126975022 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.05848;SOR=Inf;LSEQ=TGAGACCTTCTCCCATGTGT;RSEQ=TGTCCTGTGATTGTGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:1,13:0:1,0:21.1:1:31.1:1:1:0:60:13:1:0:0.5 0/1:5:2:0,2:0,3:0.4:0,0:40.5:1:29.5:1:1:0:60:4:0.4:0:1 -9 127180842 . T TA 29 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CAACAGAGAAAGACTCTGTC;RSEQ=AAAAAAAAAAAAAAAAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:9.5:1:29:1:1:0:60:4:0.6667:0.3333:1.5 0/0:3:0:0,0:1,0:0:0,0:26:1:28.5:1:1:0:60:2:0.3333:0:5 -9 127181726 . C T 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCTGGGAGGCGGAGGTTG;RSEQ=AGTGAGCTGAGATCACACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:0:28.5:1:1:0:60:4:1:0:1 -9 127911821 . TA T 113 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.83041;SOR=1.12767;LSEQ=AATTTAGATAATTTAAAATT;RSEQ=AAAAAAAAAAGGCAAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:13:13,0:129,2:0.0897:1,1:20.5:1:30.6:1:1:0:60:26:0.0909:0.0345:0.2 0/1:110:11:10,1:97,2:0.1:1,2:24.5:1:30:1:0.27324:4.73152:60:22:0.1:0.0364:0.2 -9 127912316 . G A 173 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.041;SOR=1.86749;LSEQ=AGGCATCAAGATTATAGAAC;RSEQ=CACTCTATAATTATCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:33:0,33:2,51:0.3837:1,1:21.2:1:29.8:1:0.52148:0:60:32:0.3902:0:1.1 1/0:104:56:3,53:1,47:0.5385:1,2:23:1:29.8:1:0.62221:2.64:60:112:0.5437:0:1 -9 127915872 . A G 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGGACTGATAGCCCAGGT;RSEQ=TCCACATCTTCAGGATCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1233:0:0,0:665,567:0:2,0:24.4:1:29.3:1:1:0:60:122.2:0.9992:0:0.1 0/1:1509:59:31,28:783,664:0.0391:2,2:25.3:1:31.4:1:0.89415:1.06503:60:58:0.0387:0:1.2 -9 127916095 . A C 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTCATCAGTGAATACTAAAG;RSEQ=TATCAATATAATTGAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:0:0,0:222,220:0:2,0:24.3:1:30.7:1:1:0:60:146.333:1:0:0.1 0/1:432:43:23,20:183,206:0.0995:2,2:24:1:32.1:1:0.42715:1.29:60:86:0.1005:0:1 -9 127916233 . A G 157 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGTACAGTATCTCCAGGC;RSEQ=TTAGCATTTCCATATTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1065:0:0,0:499,565:0:2,0:24.9:1:30.5:1:1:0:60:132:0.9991:0:0.2 0/1:1245:37:19,18:585,622:0.0297:2,2:20.5:1:30.2:1:0.74172:1.12:60:74:0.0299:0:1.2 -9 127916457 . G A 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60095;SOR=1.39531;LSEQ=GTGACTAACTACATACAGTT;RSEQ=TATGTCCCTTAACCATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:16:0,16:0,19:0.4571:1,1:23.7:1:30.6:1:1:0:60:32:0.4571:0:1.1 1/0:24:13:0,13:0,11:0.5417:0,1:19.8:1:29.2:1:1:0:60:26:0.5417:0:1.1 -9 127920158 . A C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTATTTTTAGAAGAGA;RSEQ=GGGGTTTCACCATATTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:11:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 127920934 . A AT 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGAAAAAAAAAACCACC;RSEQ=TTTTTTTTTCTTTTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:0,12:0.1429:0,0:7.5:1:30:1:1:0:60:4:0.1429:0.0714:1.5 0/0:2:0:0,0:0,2:0:0,0:13.5:1:30:1:1:0:60:4:1:0:0 -9 127923013 . TG CT 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01057;SOR=0.49482;LSEQ=ATACACATCTTTTAATATAC;RSEQ=AAATAGGGACTGTCACATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:53:51,2:62,0:0.4609:1,1:21.1:1:31.2:1:0.21022:0:60:106:0.469:0.0609:0.9 0/1:118:35:35,0:79,3:0.2966:1,1:19.5:1:31:1:0.55317:0:60:70:0.2966:0.0678:0.9 -9 127923255 . G A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=AAAGCAACAAAACTGAGAGT;RSEQ=AAATGTGTAAAGAAGCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:47,245:0:2,0:25.4:1:31.5:1:1:0:60:291:1:0:0.1 0/1:297:3:1,2:70,224:0.0101:2,2:19.3:1:23:1:0.56079:1.60:60:2:0.0069:0:2.7 -9 127933739 . TAC T 29 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCAAACACACACACACATA;RSEQ=ACACACACACACACACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:21:1:29.5:1:1:0:60:4:0.25:0.125:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 127933747 . C TAT 60 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=CACACACACATATACACACA;RSEQ=ACACACACACATATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:0.5:0,0:13.8:1:30.1:1:1:0:51.5:8:0.5:0.375:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 127951072 . C CAATAAT 175 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=11.000;MSILEN=3;SSF=0.1005;SOR=0.65342;LSEQ=GACTCTATCTCAGTTAAAAA;RSEQ=AATAATAATAATAATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:49:49,0:104,9:0.2816:2,1:28.8:1:31.2:1:0.05826:0:59.9:98:0.2816:0:0 0/1:162:33:28,5:109,5:0.2037:1,2:20.5:1:29.5:1:0.04566:3.84667:60:66:0.2037:0.0617:0.4 -9 127951429 . G C 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09621;SOR=Inf;LSEQ=CCGCCAGTACCAAACCACTC;RSEQ=GGCCCACCGCCTTCCCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:2,37:0:2,0:19.3:1:30.7:1:1:0:60:38:1:0:0.1 0/1:34:3:0,3:0,31:0.0882:1,0:16:1:28:1:1:0:60:6:0.0882:0:1 -9 127951582 . GC CT 88 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.65753;LSEQ=GGCACTGCCGCGGGGGCTCG;RSEQ=TCCGACTGCGGGAGACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:4,3:6,3:0.4375:2,2:26.7:1:31.6:1:1:1.46198:60:14:0.4375:0:1 0/1:3:1:1,0:1,1:0.3333:2,0:20:0:33.5:0:1:0:60:2:0.3333:0:1 -9 127951863 . G A 263 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00408;SOR=1.30287;LSEQ=GGCGGGGGTCCTGGAGAAAG;RSEQ=AAGGGCCGGCCGGCGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:885:410:223,187:258,215:0.4633:2,2:26.3:1:29.9:1:1:1.00627:60:67.333:0.4649:0:1.1 1/0:1056:559:318,241:262,233:0.5294:2,2:24.6:1:28.9:1:0.21476:1.17:60:45.583:0.5285:0:1.2 -9 127952023 . AGCG A 162 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.0889;SOR=1.68406;LSEQ=GAATAACAAGCCGCGGCAAC;RSEQ=GCGGCGGCGGCTGTAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:645:18:8,10:232,395:0.0279:2,2:31.7:1:31.8:1:0.62205:1.36:60:36:0.0283:0:0.1 0/1:737:34:11,23:275,425:0.0461:2,2:29.1:1:32:1:0.47492:1.3524:59.9:68:0.0466:0.0041:0.2 -9 127952210 . G T 88 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CGACTGCAGGCCCCAAGAGA;RSEQ=CCCGCTTCGGTCCACCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:0.6154:0,0:27.1:1:29.4:1:1:0:60:16:0.6154:0:1 0/0:1:0:0,0:0,1:0:0,0:2:0:33:0:1:0:60:2:1:0:0 -9 127952430 . A ACTCT 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTTCCAACCCTTTTAAGC;RSEQ=CTCTCCAGAATATCTTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:35:1:31.6:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 128736041 . T C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00162;SOR=4.70464;LSEQ=GAGGTGCCGGCTGGAGTAGG;RSEQ=CTCTGCATCGGGGCTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:24:10,14:11,12:0.5106:2,2:26.3:1:32.1:1:0.77248:1.27651:60:48:0.5333:0:1.2 1/1:42:35:16,19:3,4:0.8333:2,2:24.1:1:30.1:1:1:1.12:60:34:0.8293:0:1.1 -9 128736150 . C T 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=GAAACACACACGCATCACCC;RSEQ=AGCTGCTTGAGAGTGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:45.5:1:30:0:1:0:60:4:0.5:0:2 1/1:7:7:1,6:0,0:1:0,2:22.6:1:28.1:1:1:0:60:14:1:0:1.9 -9 128736180 . G A 79 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGTGCAATCTGAATGC;RSEQ=TCTCAGTTTTTTGGTTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23:1:33:0:1:0:60:4:1:0:2 1/1:6:6:1,5:0,0:1:0,2:29.3:1:30.8:1:1:0:60:12:1:0:2 -9 129467722 . G T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTCAGGCCACGAGGTGGC;RSEQ=ATCCGGAGTCAGTCAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:27:0:30.5:1:1:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 129467746 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CGGAGTCAGTCAGGTGTAGC;RSEQ=CACGTGGCCGGCGGAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:33:1:30.3:1:1:0:60:6:1:0:2 0/0:2:0:0,0:1,1:0:2,0:16.5:1:29.5:1:1:0:60:4:1:0:0.5 -9 129469433 . G A 174 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04315;SOR=0.41823;LSEQ=TTTTTGATGTAAGATACGCA;RSEQ=TGGACAACATATATCATCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:67:53:38,15:12,2:0.791:2,2:23:1:30.5:1:0.49063:2.34201:60:106:0.791:0:1.2 1/0:54:33:22,11:15,6:0.6111:2,2:22.2:1:29.5:1:0.77174:1.24489:60:66:0.6111:0:1.2 -9 129469523 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19828;SOR=Inf;LSEQ=CTGGTGTGGGGTCTCCTCTG;RSEQ=TCCCCCTCACACACAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:53,56:0:2,0:22.5:1:31.3:1:1:0:60:218:1:0:0.8 0/1:88:2:1,1:44,42:0.0227:2,2:20:1:29:1:1:1.04708:60:4:0.023:0:2 -9 129469533 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.50029;SOR=0;LSEQ=GTCTCCTCTGGTCCCCCTCA;RSEQ=ACACAGAGAGCAGGGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:39,55:0.0208:2,2:37:1:29:1:1:1.41:60:4:0.0213:0:2.5 0/0:82:0:0,0:37,45:0:2,0:24:1:31.5:1:1:0:60:164:1:0:0.5 -9 129469539 . G C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21927;LSEQ=TCTGGTCCCCCTCACACACA;RSEQ=AGAGCAGGGACAGCTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:72:31,41:8,12:0.7742:2,2:24.8:1:32.2:1:1:1.13:60:71:0.7802:0:1.1 0/1:82:35:14,21:21,26:0.4268:2,2:25:1:31.5:1:0.82174:1.2087:60:70:0.4268:0:1.1 -9 129470630 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCAGCCAGCAGGTTGGTT;RSEQ=AGACATGACAAGAAGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 131041700 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49661;SOR=Inf;LSEQ=TGCATACAAAACAAGGGGGG;RSEQ=AGGGTAAGGAAGGTGAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,12:0:2,0:18.4:1:32.2:1:1:0:60:52:0.963:0:0.2 0/1:33:2:1,1:20,11:0.0606:2,2:5:0:31.5:1:1:1.78367:60:4:0.0645:0:1 -9 131041752 . A G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03615;SOR=Inf;LSEQ=GATAAGATCAAGCAAGTCAC;RSEQ=TGATCGTGGGCCAGTGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:18,24:0:2,0:27.8:1:30.1:1:1:0:60:41:1:0:0.2 0/1:34:4:2,2:13,17:0.1176:2,2:32.5:1:31.8:1:1:1.30:60:8:0.1176:0:1.3 -9 131482467 . T C 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGCCCTAAGTGAGCGCC;RSEQ=GTCCTATTGCCCAGCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:1:0,0:4:0:32:0:1:0:60:2:1:0:1 -9 133710740 . G GC 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=CGGCTGGCGGGGCCGGGGGC;RSEQ=CCGGGGGGGCGCGCGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:0,0:0.6667:0,2:9.5:1:32.4:1:1:0:56.3:8:0.6667:0.5:1.8 1/0:4:3:2,1:0,0:0.75:0,2:5.1:1:28:1:1:0:60:8:0.7444:0.7333:0.3 -9 133710760 . G T 28 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.34927;LSEQ=GCCGGGGGGGCGCGCGGGCC;RSEQ=AGCCGGGCCTGAGCCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:0,1:63,12:0.0132:2,0:1:0:23:0:0.17105:0:60:2:0.0135:0:2 0/1:113:2:1,1:87,24:0.0177:2,2:6:0:28.5:1:0.39507:3.57182:60:4:0.0179:0:2.5 -9 133710768 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.4678;LSEQ=GGCGCGCGGGCCGAGCCGGG;RSEQ=CTGAGCCGGGCCCGCGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:1:0,1:118,26:0.0069:2,0:1:0:26:0:0.18621:0:60:2:0.0071:0:2 0/1:198:2:1,1:147,49:0.0101:2,2:10.5:1:27.5:1:0.44224:2.97992:60:4:0.0104:0:2 -9 133710774 . C T 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.7055;SOR=1.74094;LSEQ=CGGGCCGAGCCGGGCCTGAG;RSEQ=CGGGCCCGCGGACCGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:139,36:0.0113:2,2:17.5:1:28.5:1:0.37532:3.82225:60:4:0.0116:0:2 0/1:256:5:1,4:190,61:0.0195:2,2:5:1:24.8:1:0.01562:12.31215:60:10:0.0198:0:2 -9 133710785 . G T 32 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07611;SOR=0;LSEQ=GGGCCTGAGCCGGGCCCGCG;RSEQ=ACCGAGCTGGGAGAGGGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:205,71:0.0108:2,2:15.3:1:20.3:1:0.16856:5.73062:60:2:0.0073:0:2.3 0/0:378:0:0,0:274,104:0:2,0:18.7:1:31.2:1:1:0:60:125:1:0:1.2 -9 133710804 . T C 298 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=1.38951;LSEQ=GGACCGAGCTGGGAGAGGGG;RSEQ=TCCGGCCCCCGACGTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:478:477:334,143:0,1:0.9979:0,2:23.8:1:32:1:0.30126:0:59.9:33.071:0.9978:0:1.3 1/1:664:663:436,227:0,1:0.9985:0,2:23.2:1:31.9:1:0.34337:0:60:54.25:0.9985:0:1.2 -9 133710819 . T TC 293 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02469;SOR=0.2593;LSEQ=AGGGGTTCCGGCCCCCGACG;RSEQ=GCTGGCGCGGGAAAATGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:720:717:480,237:0,0:0.9958:0,2:23.8:1:30.6:1:1:0:59.9:58.75:1:0.2153:0.9 1/1:818:805:513,292:6,7:0.9841:2,2:27.8:1:30.4:1:0.2461:2.05:60:46.353:0.9838:0.0244:1 -9 133711028 . C CT 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.63294;SOR=0.41656;LSEQ=GCGCCCTCCCCGGGTCTTGT;RSEQ=TTTTTTTTCTTTCTTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:0,3:12,220:0.0128:2,0:11.3:1:31.3:1:1:0:60:6:0.013:0.0043:0.3 0/0:187:1:0,1:7,178:0.0053:1,0:45:0:28:0:1:0:60:2:0.0054:0:0 -9 133711045 . CCTCTT C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=4.000;MSILEN=5;SSF=0;SOR=4.03907;LSEQ=TGTCTTTTTTTTCTTTCTTC;RSEQ=CTCTTCTCTTCTCTTCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:51:0,51:5,112:0.3036:1,1:30.9:1:33:1:0.32418:0:59.9:102:0.3036:0.0238:0.1 1/0:144:92:4,88:1,50:0.6389:1,1:28.8:1:32:1:0.65515:2.26:59.8:184:0.6434:0.0556:0.3 -9 133711062 . T A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=5;SSF=0.05043;SOR=Inf;LSEQ=TTCCCTCTTCTCTTCTCTTC;RSEQ=CTTCAGTTCTCTTATATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:0,124:0:1,0:25.9:1:30.1:1:1:0:60:40.333:1:0:0.1 0/1:115:4:1,3:4,107:0.0348:1,2:10.3:1:23.3:1:0.16492:8.51:60:3:0.027:0:2.8 -9 133711138 . T TTTTCTC 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.07461;SOR=3.24017;LSEQ=CTCTTCTCTTGTCTCTCTCT;RSEQ=TTTCTCTCTCTCTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:0,14:0.3333:1,0:27:1:32.2:1:1:0:58.6:14:0.3333:0.0476:0.4 1/0:24:15:2,13:0,9:0.625:0,2:19.1:1:29.3:1:0.51087:0:58.7:14:0.6087:0.2917:0.5 -9 133711140 . TTCTC T 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=5.000;MSILEN=2;SSF=0.04784;SOR=0;LSEQ=CTTCTCTTGTCTCTCTCTTT;RSEQ=TCTCTCTGTCTCTTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:0,5:0,16:0.2381:1,0:26.6:1:30.4:1:1:0:60:10:0.25:0.0476:0 0/0:20:0:0,0:2,18:0:2,0:20.2:1:28.8:1:1:0:59:19:1:0:0.4 -9 133729466 . C T 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12799;SOR=5.39755;LSEQ=TCCAGAAGCCCTTCAGCGGC;RSEQ=AGTAGCATCTGACTTTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:1:0,1:358,159:0.0019:2,0:1:0:24:0:0.30888:0:60:2:0.0019:0:1 0/1:580:6:1,5:376,196:0.0103:2,2:8.8:1:25:1:0.02111:9.55725:60:12:0.0105:0:1 -9 133730139 . A T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24808;SOR=Inf;LSEQ=AGAATCAATGAAAAAGAACG;RSEQ=AGCTGGTTTCCAAAGCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:159,34:0:2,0:23.8:1:30.2:1:1:0:60:95.5:1:0:0.1 0/1:195:3:1,2:143,49:0.0154:2,2:10.7:1:27:1:0.16799:5.7726:60:6:0.0155:0:1 -9 133730543 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19938;SOR=Inf;LSEQ=CAGGGGAACCAGAGGTCCTG;RSEQ=TGTCGGATTGATAAATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:18,145:0:2,0:22.6:1:32.7:1:1:0:60:326:1:0:0 0/1:132:2:0,2:26,103:0.0152:2,0:18:1:32:0:1:0:60:4:0.0153:0:1 -9 133730792 . TA T 24 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAATAAGATTCTTCCTT;RSEQ=AAAAAAATATTTTATAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:21:1:24.5:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 133732029 . G T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCCCAGAGGCAAGCACT;RSEQ=GTACTAGTTCCTTCTAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:31.5:1:1:0:60:4:1:0:1.5 -9 133738320 . G A 147 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=26.4382;LSEQ=AAGTGGGAGATGGAACGCAC;RSEQ=GACATCACCATGAAGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:1:1,0:231,315:0.0018:2,0:1:0:26:0:0.42413:0:60:2:0.0019:0:1 0/1:627:29:13,16:257,341:0.0463:2,2:16.9:1:30.4:1:0.85006:1.08:60:58:0.0472:0:1.1 -9 133738401 . G T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04395;SOR=0;LSEQ=TGGAAGAAATACAGCCTGAC;RSEQ=GTGGCCGTGAAGACCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:4:2,2:91,181:0.0145:2,2:16.3:1:31.5:1:0.60501:1.98:60:8:0.0148:0:1 0/0:325:0:0,0:120,205:0:2,0:24.6:1:29.6:1:1:0:60:53.167:1:0:0.2 -9 133747414 . C T 81 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0817;SOR=4.0393;LSEQ=TCACAAAACGCAGCCCAGGA;RSEQ=GAGTATGCGCTGAAGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:119,11:0.0152:2,2:24:1:20:1:0.17418:10.40114:60:1:0.0078:0:4.5 0/1:102:6:6,0:81,15:0.0588:2,0:19:1:31.5:1:0.58839:0:60:12:0.06:0:2 -9 133747425 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=AGCCCAGGACGAGTATGCGC;RSEQ=GAAGCTCCATTTTGCATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:131,20:0.0131:2,2:16.5:1:32.5:1:0.25645:6.4165:60:4:0.0132:0:1 0/0:136:0:0,0:108,28:0:2,0:21.8:1:30.3:1:1:0:60:33:1:0:0.3 -9 133747457 . C T 117 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TTGCATTAACTAGTCAAGTA;RSEQ=TTACCCACTGAAAAGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:179,91:0:2,0:24.4:1:31.5:1:1:0:60:37.571:1:0:0.1 0/1:284:15:10,5:190,79:0.0528:2,2:27.2:1:30:1:0.77398:1.2017:60:30:0.0536:0:1.6 -9 133747640 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.62721;SOR=2.62586;LSEQ=TGAAGAGAGGGTCTCGCGCC;RSEQ=CACCCCCAGGGTGACACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:1,0:64,192:0.0039:2,0:1:0:26:0:0.25292:0:60:2:0.004:0:1 0/1:295:3:2,1:83,208:0.0102:2,2:10.3:1:29:1:0.20154:4.98:60:6:0.0103:0:1 -9 133747734 . C T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00547;SOR=0.24216;LSEQ=GTGCTCTGCCGACGTTCAGC;RSEQ=GCGGGTAAAATGAGGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:22:1,21:0,18:0.55:1,1:28.6:1:28.8:1:1:0:60:10:0.5263:0:1.3 0/1:40:9:1,8:0,30:0.225:1,2:23.2:1:30.4:1:0.23077:0:60:18:0.2308:0:1.3 -9 133748083 . A G 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06083;SOR=0.24164;LSEQ=AGCCTGGCCATGTCCCTCCC;RSEQ=CACGAGCACAGTCTCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:11:11,0:18,1:0.3667:1,0:25.3:1:30.1:1:1:0:60:22:0.3667:0:1 0/1:25:3:2,1:22,0:0.12:1,2:26.3:1:30:1:0.12:0:60:6:0.12:0:1 -9 133748150 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24308;SOR=0;LSEQ=TTGGGCCCAGGACTGAGGAG;RSEQ=AGAGTCAGAATCCTTCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:85,2:0.0225:1,2:24.5:1:28:1:0.06665:34.90295:60:4:0.0227:0:1 0/0:91:0:0,0:85,6:0:2,0:23.3:1:31.8:1:1:0:60:90:1:0:0.1 -9 133748468 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60004;SOR=2.30107;LSEQ=GCGCCATGGAGTCACAGGGC;RSEQ=TGGAGCCGGGCAGCCTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:1,0:31,119:0.0066:2,0:1:0:27:0:0.21192:0:60:2:0.0066:0:1 0/1:132:2:0,2:27,103:0.0152:2,0:25:1:30:1:1:0:60:4:0.0154:0:1 -9 133748475 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21201;SOR=Inf;LSEQ=GGAGTCACAGGGCGTGGAGC;RSEQ=GGGCAGCCTTTTACAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:21,112:0:2,0:21.9:1:30:1:1:0:60:266:1:0:0.1 0/1:114:2:1,1:18,94:0.0175:2,2:14:1:27:1:0.30678:5.11:60:4:0.0177:0:1 -9 133750539 . G GT 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00242;SOR=Inf;LSEQ=TCTTTTCTTCCTTTCTTTTT;RSEQ=TTTTTTTGAGACGGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:0,160:0:1,0:20.7:1:32.4:1:1:0:60:159:1:0:0.3 0/1:146:8:0,8:1,137:0.0548:1,0:25.9:1:24.8:1:1:0:60:3:0.0423:0.0068:0.4 -9 133750550 . A G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03651;LSEQ=TTTCTTTTTGTTTTTTTGAG;RSEQ=CGGAGTCTCACTCTGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:39:0,39:0,80:0.325:1,1:20.3:1:32.2:1:1:0:60:78:0.3305:0:1.1 0/1:117:2:0,2:0,115:0.0171:1,0:36.5:1:31:1:1:0:60:4:0.0179:0:1 -9 133750552 . G A 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01347;SOR=Inf;LSEQ=TCTTTTTGTTTTTTTGAGAC;RSEQ=GAGTCTCACTCTGTCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:0,116:0:1,0:22.2:1:31.1:1:1:0:60:57:1:0:0.4 0/1:113:6:0,6:0,107:0.0531:1,0:15.5:1:31.5:1:1:0:60:12:0.0545:0:1.2 -9 133750838 . TT C 33 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGCACAGCCACCCTTTT;RSEQ=TTTTTTTTTTAACTGTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:16.5:1:33.3:1:1:0:60:4:0.6667:0.3333:0.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 133753901 . G A 80 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4229;SOR=0.57312;LSEQ=GCTGCTAGAGAAGGACTACC;RSEQ=CATGGAGCGCCCAGAAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:801:9:7,2:333,458:0.0112:2,2:8.3:1:25.3:1:0.04162:4.80:60:8:0.0102:0:1 0/0:773:5:4,1:332,435:0.0065:2,2:5.8:1:25.8:1:0.17307:5.23:60:10:0.0065:0:1.2 -9 133754032 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.21313;LSEQ=TGTGCAGGAGTGTGTACACA;RSEQ=AGTTGAAAGTTTTTCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:70:9,61:6,69:0.4828:2,2:23.8:1:30.9:1:0.41756:1.69:60:69:0.4825:0:1.2 0/1:103:17:4,13:15,71:0.165:2,2:20.6:1:29.9:1:0.51201:1.45:60:16:0.16:0:1.2 -9 133754099 . C A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.07063;LSEQ=GCAGCTAATGTAGCCATTTG;RSEQ=TACCTATTGACCTTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:28:0,28:0,22:0.56:1,1:26.9:1:32.1:1:1:0:60:56:0.5714:0:1.6 0/1:25:2:0,2:1,22:0.08:1,0:10.5:1:29.5:1:1:0:60:4:0.08:0:2 -9 133754220 . T C 110 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGATTCCTGGGCCCTGC;RSEQ=TTCACAGACATTCTGCTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:0,13:0,2:0.8667:0,1:27.5:1:29.9:1:1:0:60:12:0.8571:0:1.4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 133754261 . AT A 48 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCTAAGCTCATGAGGTG;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,3:0.375:0,0:35.3:1:30.7:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 133754326 . G A 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTACAATGGC;RSEQ=CAATGTTGGCTCACTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:10.5:1:28:1:1:0:48.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 133755282 . T G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.05681;LSEQ=CATCTAACGTCTTTTCAAAT;RSEQ=CTTAATGTCTATAACAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:25:24,1:17,0:0.5952:1,1:23.7:1:32.8:1:1:0:60:50:0.5952:0:1.2 0/1:27:2:2,0:22,3:0.0741:2,0:6:1:29:1:1:0:60:4:0.0741:0:1 -9 133755293 . A G 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05571;SOR=Inf;LSEQ=TTTTCAAATTCTTAATGTCT;RSEQ=TAACAGGACATGATGACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:54,1:0:1,0:20.6:1:28.6:1:1:0:60:54:1:0:0.6 0/1:35:3:2,1:30,2:0.0857:2,2:29.7:1:26.3:1:0.24217:6.73144:60:2:0.0588:0:1.7 -9 133755528 . A G 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21267;LSEQ=TTTGAAACAATGTTCCAGGA;RSEQ=TCCAGTATCTCAGACGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:850:428:182,246:168,254:0.5035:2,2:24.7:1:32.1:1:0.44356:1.12:60:84.6:0.5078:0:1.2 0/1:801:142:61,81:283,376:0.1773:2,2:22.8:1:31.1:1:1:1.00:60:34.5:0.1765:0:1.2 -9 133755573 . G T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02272;SOR=Inf;LSEQ=CCCATCCCGGGGTACCTGCA;RSEQ=TGGGGTGAAAGGGCAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:132,270:0:2,0:24.7:1:31.7:1:1:0:60:79.4:0.9975:0:0.5 0/1:359:5:2,3:116,238:0.0139:2,2:33.8:1:26.8:1:0.66524:1.37:60:4:0.0112:0:1.2 -9 133755636 . A C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06277;SOR=Inf;LSEQ=TCGGTTCACTTCCTGGTGAA;RSEQ=GTTCACAGACCAGCCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:13,128:0:2,0:24.1:1:31:1:1:0:60:46:1:0:0.1 0/1:94:3:0,3:3,88:0.0319:1,0:27.3:1:31.7:1:1:0:60:6:0.0333:0:1 -9 133755748 . C A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53996;SOR=0;LSEQ=AGAAATGCTAAGGGCTGTTT;RSEQ=TCCGGTATCCACGTGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:69,26:0.0206:2,2:23:1:26:1:0.48131:2.62304:60:4:0.0211:0:2 0/0:53:0:0,0:46,7:0:2,0:19.9:1:31.3:1:1:0:60:52:1:0:0.5 -9 133755754 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06957;LSEQ=GCTAAGGGCTGTTTCTCCGG;RSEQ=ATCCACGTGCCTTTTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:96:87:66,21:8,1:0.9063:2,2:25.1:1:32.3:1:0.67938:2.52583:60:174:0.9158:0:1.1 0/1:58:23:19,4:32,3:0.3966:2,2:19.4:1:32:1:0.41844:2.21314:60:46:0.3966:0:1 -9 133758838 . C T 64 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTGCAGTGAGCTGAGAT;RSEQ=GTGCCACTGCACTCCAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:23.3:1:32:0:1:0:56.3:8:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 133759201 . TTTTG T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.11009;SOR=Inf;LSEQ=GGGATGACCTTTGACAATTT;RSEQ=TTTGTTTGTTTGTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:88,0:0:1,0:22.3:1:30.6:1:1:0:60:28.333:1:0:0.3 0/1:82:3:3,0:78,1:0.0366:1,0:20.3:1:30.3:1:1:0:60:6:0.037:0.0122:0.3 -9 133759283 . C T 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17955;SOR=4.95035;LSEQ=AGCAGTGGCACTCTGCCTCC;RSEQ=GGGTTCAAGCGATTCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:1:1,0:336,62:0.0025:2,0:45:0:33:0:1:0:60:2:0.0025:0:1 0/1:325:4:2,2:253,68:0.0123:2,2:16.5:1:28.8:1:0.20399:3.70123:60:8:0.0124:0:1 -9 133759489 . CAAG C 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.00044;SOR=1.87341;LSEQ=AACTTGTTCAGCGCCTTGAT;RSEQ=AAGAAGAAGAAGACAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1291:53:23,30:638,599:0.0411:2,2:27.1:1:31.7:1:0.26359:1.38891:60:106:0.0414:0.0031:0.1 0/1:1158:86:42,44:527,545:0.0743:2,2:25.8:1:31.6:1:1:1.01301:59.9:172:0.0749:0.0078:0.3 -9 133759745 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18056;SOR=Inf;LSEQ=CTCCCCACCTGTGGAAGAAG;RSEQ=CCAGCACGCTGACCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:86,184:0:2,0:26:1:29.7:1:1:0:60:26:1:0:0.1 0/1:200:2:1,1:83,115:0.01:2,2:37.5:1:32:1:1:1.38:60:4:0.0103:0:1.5 -9 133759957 . G T 173 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01724;LSEQ=GGGCACAAAAGTGAGAAGCC;RSEQ=GCTCTGCCTCGGAAGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:924:54:23,31:424,444:0.0584:2,2:27.7:1:30.2:1:0.40206:1.28676:60:53:0.0582:0:1.3 0/0:937:1:0,1:472,463:0.0011:2,0:1:0:31:0:0.49573:0:60:2:0.0011:0:1 -9 133760029 . C G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20046;LSEQ=GGCACAGTAACGCCTCCCCC;RSEQ=AGGCTGGTGAAAAAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:658:312:142,170:154,191:0.4742:2,2:24.7:1:30.7:1:0.87525:1.04:60:311:0.4755:0:1.1 0/1:667:102:41,61:241,323:0.1529:2,2:25.6:1:30.3:1:0.6643:1.1099:60:204:0.1548:0:1.2 -9 133760038 . GA G 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00746;SOR=Inf;LSEQ=ACGCCTCCCCCCAGGCTGGT;RSEQ=AAAAGAATGAGGAAGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:0:0,0:283,333:0:2,0:23.9:1:29.9:1:1:0:60:87:0.9984:0:0.6 0/1:614:7:3,4:260,347:0.0114:2,2:27:1:31.1:1:1:1.00:60:14:0.0116:0:0.4 -9 133760617 . C T 140 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.19528;LSEQ=ACCCCCATCAGCCCAGCCCC;RSEQ=GTTCCCTCCACGTTGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1245:1:0,1:605,637:8e-04:2,0:1:0:15:0:1:0:60:0:0:0:2 0/1:1121:24:13,11:532,562:0.0214:2,2:22.2:1:30.7:1:0.68151:1.25:60:48:0.0217:0:1.4 -9 133761001 . A G 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2505;LSEQ=GCGACAGCAGGCAGTGGTCC;RSEQ=GCGGCCACTCAGGACTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1012:842:381,461:78,91:0.832:2,2:25.7:1:30.3:1:0.86568:1.0371:60:92.556:0.8313:0:1.1 1/0:990:548:255,293:201,240:0.5535:2,2:24.2:1:29.8:1:0.7975:1.04:60:181.667:0.5567:0:1.2 -9 133761115 . G A 42 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17025;SOR=5.36744;LSEQ=GCCCGTCGGAGCTGCCTGCA;RSEQ=CACATGCGGGCTCGCCCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:1:1,0:42,246:0.0035:2,0:1:0:25:0:0.14879:0:60:2:0.0035:0:1 0/1:218:4:3,1:40,174:0.0183:2,2:19.5:1:21.3:1:0.02494:12.84:60:3:0.014:0:1.3 -9 133761139 . G A 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=Inf;LSEQ=ATGCGGGCTCGCCCATACCC;RSEQ=TGACAGTGGCTGACAAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:5,158:0:1,0:24.3:1:32.2:1:1:0:60:162:0.9939:0:0.1 0/1:122:9:1,8:5,108:0.0738:1,2:9.9:1:30.2:1:0.37494:2.67:60:18:0.0744:0:1 -9 133762433 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCCGGAGCCCAGATAC;RSEQ=GGGGCTGTGACTCTGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:14:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 133762590 . G A 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGCCAGCAGCCTCGCACA;RSEQ=GCCCTAGCTTTACGCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28:1:29.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 133797274 . T C 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.29755;SOR=1.6903;LSEQ=CTTGAAGACAGGTTTAGAGA;RSEQ=GTGTCTGTCTTTGGGGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:33:21,12:17,10:0.55:2,2:26.5:1:31.2:1:1:1.03:60:66:0.55:0:1.1 1/0:40:27:18,9:8,5:0.675:2,2:26.1:1:29.7:1:1:1.24:60:26:0.7027:0:1.1 -9 133797332 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51851;SOR=Inf;LSEQ=CGCACGCTGACTCCTAACAT;RSEQ=GCAGGCTCTGCCTTGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:28,35:0:2,0:26.1:1:29.5:1:1:0:60:30.5:1:0:0.3 0/1:96:2:1,1:46,48:0.0208:2,2:47:1:30:1:1:1.04:60:4:0.0215:0:1 -9 133887735 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCAGCCTCAGTTTCCTTA;RSEQ=CTGTACCGTACGGATAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:19.8:1:31.5:1:1:0:60:30:1:0:0 0/1:35:2:1,1:18,15:0.0571:2,2:28.5:1:27:1:1:1.19373:60:4:0.0571:0:1 -9 133887746 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54498;SOR=Inf;LSEQ=GTTTCCTTACCTGTACCGTA;RSEQ=GGATAAGAGTCGCCACTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:20.6:1:31.7:1:1:0:60:36:1:0:0 0/1:40:3:1,2:17,20:0.075:2,2:25.7:1:29.7:1:1:1.67842:60:6:0.075:0:1 -9 133887901 . C T 32 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TGCTCGTCCCGGCCGCCCTG;RSEQ=CTCCTCAAAGACATCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:38:1:32:0:1:0:60:4:0.6667:0:1.5 0/0:3:0:0,0:1,2:0:2,0:13.3:1:30.3:1:1:0:60:6:1:0:0 -9 135771515 . A G 158 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02251;LSEQ=CCTCCGTCCCATTTCCACAC;RSEQ=TGAACTTGCACTCAGACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:39:39,0:50,0:0.4382:1,1:24:1:29.9:1:1:0:60:78:0.4382:0:1.1 0/1:59:1:1,0:54,4:0.0169:2,0:11:0:31:0:1:0:60:2:0.0169:0:1 -9 135771524 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51716;SOR=0;LSEQ=CATTTCCACACATGAACTTG;RSEQ=ACTCAGACCCTGGAAACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:98,2:0.0196:1,2:13:1:27.5:1:0.05824:40.17587:60:4:0.0202:0:1 0/0:68:0:0,0:65,3:0:1,0:24.3:1:32.3:1:1:0:60:67:1:0:0.1 -9 135771987 . CGCT C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=0.86112;LSEQ=TTTCTCTGGGGTAGAAAGCT;RSEQ=GCTGCTGCTGCTGCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:8:3,5:97,198:0.0264:2,2:36.9:1:31.6:1:0.72183:1.22:60:16:0.0268:0:0 0/1:263:6:2,4:96,160:0.0228:2,2:32.8:1:31.5:1:1:1.19914:60:12:0.0233:0:0 -9 135772144 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49983;SOR=Inf;LSEQ=TCATTACAACAGTCAAGCCT;RSEQ=TAAGAAAGCCGGGGAGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:45,108:0:2,0:26.4:1:32.2:1:1:0:60:75.5:1:0:0.2 0/1:171:2:1,1:68,101:0.0117:2,2:29.5:1:30.5:1:1:1.48:60:4:0.0118:0:1 -9 135772530 . C T 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21936;SOR=4.64317;LSEQ=AGTCCTTATGCTGGAATTGG;RSEQ=AGCTTAGTCCCAAGGTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:1:1,0:290,96:0.0026:2,0:46:0:30:0:1:0:60:2:0.0027:0:1 0/1:420:5:2,3:298,117:0.0119:2,2:22.8:1:26:1:0.14342:3.80628:60:10:0.012:0:1.2 -9 135772717 . G A 210 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=67.29488;LSEQ=GCCTCATACCTGCTCTCTGC;RSEQ=GCCTGCAGCTGTCCTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:925:2:2,0:403,520:0.0022:2,0:1:0:25.5:1:0.19144:0:60:4:0.0022:0:1 0/1:973:124:51,73:368,481:0.1274:2,2:25:1:30.3:1:0.69803:1.09497:60:123:0.1288:0:1.1 -9 135772977 . G A 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTAGCTCTTTCCGATAGGC;RSEQ=GCTTTCATCATTTCTACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:0:0,0:151,322:0:2,0:23.2:1:29.5:1:1:0:59.6:15.31:1:0:0.6 0/1:514:35:11,24:172,306:0.0681:2,2:22.7:1:29.8:1:0.71537:1.22587:60:34:0.0711:0:1.4 -9 135773022 . T C 43 v4;q23;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68552;SOR=1.92188;LSEQ=AAAAAAAAAAAAAAAAAGAC;RSEQ=GGAATTAGTACTTATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:2,0:11,158:0.011:2,0:23:1:20:1:0.00537:0:60:1:0.0063:0:2 0/1:191:4:4,0:10,171:0.0209:2,0:16:1:21.8:1:2e-05:0:60:3:0.0168:0:1.5 -9 135773114 . C T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04153;SOR=0.24121;LSEQ=GCATTTTAGTATACTGATAA;RSEQ=AGAAATATAAACTAGTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:14:1,13:1,21:0.3889:1,1:20.1:1:28.4:1:1:1.59:60:28:0.4:0:1.8 0/1:23:3:0,3:1,19:0.1304:1,0:40.3:1:28.3:1:1:0:60:6:0.1304:0:1 -9 135773164 . C T 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13116;SOR=0;LSEQ=AAGTAAGCTGGTAGTATTAT;RSEQ=CTAGTAACCCTTCCTTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:0,8:0,9:0.4706:0,0:26.5:1:29.3:1:1:0:60:16:0.4706:0:2.4 0/0:4:0:0,0:0,4:0:0,0:25.5:1:31.8:1:1:0:60:8:1:0:0 -9 135776034 . C T 193 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21389;SOR=1.28188;LSEQ=AAGCCATTCTCTATGCCATG;RSEQ=GGGAGACATACTGTCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:91:76,15:125,24:0.3792:2,2:25:1:30.4:1:1:1.02786:60:182:0.3808:0:1.1 0/1:214:94:75,19:100,20:0.4393:2,2:24.2:1:29.5:1:0.59312:1.26524:60:93:0.4387:0:1 -9 135776341 . C A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00163;SOR=0.24023;LSEQ=AATGTTAAGGCAAAATAAAC;RSEQ=AGTCCCATGGGTTCACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:30:0,30:0,51:0.3659:1,1:21.3:1:30.7:1:1:0:60:60:0.375:0:1 0/1:58:7:0,7:2,49:0.1207:1,0:33.7:1:30.6:1:1:0:60:14:0.125:0:1 -9 135776845 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15472;SOR=Inf;LSEQ=AAATGTCAGGGACTATGGGG;RSEQ=CAGCAGAACCACTTCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:62,2:0:1,0:25.2:1:31.1:1:1:0:60:31:1:0:0 0/1:42:2:2,0:40,0:0.0476:1,0:26.5:1:30:1:1:0:60:4:0.0476:0:1 -9 135776925 . T C 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAACCTGTCTGAAGGAAGAA;RSEQ=GTTAGCAAATGGTGTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:218,34:0:2,0:23.6:1:31.3:1:1:0:60:125:1:0:0.1 0/1:303:30:23,7:209,63:0.099:2,2:27.3:1:30.9:1:1:1.00963:60:60:0.1007:0:1.3 -9 135777121 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18907;LSEQ=GTGGACATGAAGTTTGAGGA;RSEQ=CACCAACAGGCCAGATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:185:58,127:70,175:0.4302:2,2:25.3:1:32.1:1:0.59445:1.14:60:370:0.4312:0:1.1 0/1:441:55:16,39:102,284:0.1247:2,2:22.8:1:31.8:1:0.74483:1.14:60:110:0.125:0:1.1 -9 135777755 . G GA 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTTTCCTTTTGGCTGCA;RSEQ=AAAAAAAAATGACTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:0.1053:1,0:21.5:1:32:0:1:0:60:4:0.1111:0:0 0/0:5:0:0,0:4,1:0:2,0:28:1:31.8:1:1:0:60:10:1:0:0 -9 135778210 . C A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12291;SOR=0;LSEQ=AATGTCATCATTTTAGCTGT;RSEQ=TTCCAACACAGGCAATTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:2,1:47,217:0.0112:2,2:10:1:22.7:1:0.0876:9.12:60:2:0.0076:0:1.7 0/0:269:0:0,0:55,214:0:2,0:24.9:1:31.5:1:1:0:60:37.429:1:0:0.1 -9 135778867 . T C 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01637;SOR=0;LSEQ=CCCACGGTTTCTGAGAATTA;RSEQ=GAGGGAATTCCGAGGTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:8,1:19,0:0.3214:1,2:21.9:1:32.9:1:0.32143:0:60:18:0.3333:0:1 0/0:16:0:0,0:16,0:0:1,0:26.1:1:30.8:1:1:0:60:32:1:0:0.1 -9 135779251 . G A 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3579;SOR=3.2232;LSEQ=CAGAAATGCCTTTTACAGAT;RSEQ=GTTCAATCAAGCCCCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:1,0:41,224:0.0037:2,0:1:0:24:0:0.15789:0:60:2:0.0038:0:1 0/1:251:3:2,1:57,190:0.012:2,2:9:1:21:1:0.13965:6.60:60:2:0.0081:0:1.7 -9 135779530 . T C 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86239;LSEQ=TGTGTTCTCCCCCAGGAAGA;RSEQ=GCTTCACTCTGGTCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:5,2:7,5:0.3684:2,2:23.6:1:31.9:1:0.65617:1.73:60:14:0.4118:0:1.1 0/1:6:2:1,1:4,0:0.3333:0,2:9.5:1:31:0:0.33333:0:60:4:0.3333:0:1.5 -9 135780006 . TACACTGG T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.70027;SOR=0.5747;LSEQ=AGAGAGTTAGAGGAGAAGCC;RSEQ=ACACAATGGGAGGCGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:11:0,11:0,25:0.3056:1,0:23.9:1:30.9:1:1:0:60:22:0.3056:0:0 0/1:10:2:0,2:0,8:0.2:0,0:33:1:31.5:1:1:0:60:4:0.2:0:0 -9 135780288 . A G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAGTAGGTAATTTACCT;RSEQ=AGCCTATCATACCAAATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:20:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 135781563 . G A 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14267;LSEQ=AAACAAAAGAAATGGCAGTC;RSEQ=GTATTCCACCTGGGAAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1548:554:258,296:478,516:0.3579:2,2:24.6:1:30.4:1:0.59557:1.06273:60:78.143:0.3585:0:1.1 0/1:1861:137:63,74:810,914:0.0736:2,2:21.8:1:30.7:1:0.85904:1.04094:60:274:0.0745:0:1.2 -9 135781709 . G C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.10164;LSEQ=TTGGGAGGCTGAGGAGGGAG;RSEQ=ATCACTTGAGCCCAGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:80:0,80:1,102:0.4348:1,1:25.3:1:31.8:1:1:0:59.8:39:0.4333:0:1.1 0/1:111:8:0,8:2,100:0.0721:1,0:27.4:1:33.4:1:1:0:60:16:0.0727:0:1 -9 135781735 . C G 126 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGAGCCCAGGAGTTAGAGA;RSEQ=CAGCCTGGACAACATAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:1,124:0:1,0:26.4:1:31.4:1:1:0:59.8:124:1:0:0.5 0/1:66:14:0,14:0,52:0.2121:1,1:24.4:1:33.1:1:1:0:60:28:0.2188:0:1 -9 135782026 . C A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07535;LSEQ=ACCTCAAGAGAAGAAAAATC;RSEQ=AGCAAGCCTGTGAGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:94:84,10:113,22:0.4069:2,2:21.5:1:30.3:1:0.25038:1.63:60:93:0.4097:0:1.1 0/1:225:11:9,2:184,30:0.0489:2,2:11.5:1:29:1:0.65881:1.36089:60:22:0.0502:0:1.8 -9 135782221 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0824;LSEQ=CCTTTGCTGCCAGGTGGCTC;RSEQ=TCTGAAGAGAAACAAAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:239:83,156:94,187:0.4587:2,2:22.9:1:31.6:1:0.78106:1.06:60:118.5:0.4584:0:1.1 0/1:476:31:9,22:146,299:0.0651:2,2:20.7:1:31:1:0.84313:1.19321:60:30:0.0638:0:1.1 -9 135782396 . A G 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07054;SOR=0;LSEQ=ACTGAAATATTAAAAATAAT;RSEQ=TAACTAAAAGTACCAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:4,10:7,12:0.4242:2,2:21.6:1:31.2:1:0.71934:1.44185:60:13:0.4063:0:1.1 0/0:6:0:0,0:1,5:0:2,0:30.3:1:30.3:1:1:0:60:12:1:0:0.2 -9 135782479 . G A 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19082;SOR=0.3348;LSEQ=AAAGAGATATAGTCAAGTCA;RSEQ=AATACAGGTACTTCACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:15:9,6:12,6:0.4545:2,2:17.9:1:29.5:1:0.73066:1.32167:60:14:0.4375:0:1.1 0/1:14:3:3,0:9,2:0.2143:2,0:27.3:1:29.3:1:1:0:60:6:0.2143:0:1 -9 135782869 . G T 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25474;SOR=0;LSEQ=GCAGTGATTCTCAAATTGTT;RSEQ=GGATGTTTTCTTTTCTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:3:1,2:1,92:0.0313:1,2:13.3:1:23.3:1:0.06184:37.75:54.7:2:0.0213:0:2.7 0/0:77:0:0,0:1,76:0:1,0:22:1:30.7:1:1:0:60:154:1:0:0.1 -9 135782947 . G GC 74 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15712;SOR=0.16469;LSEQ=AGTGCAATGGCACAATCTCG;RSEQ=CTCACTGCAACCTCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:0.4545:0,0:22.6:1:32.2:1:1:0:53.8:10:0.4545:0:0 0/1:9:1:0,1:0,8:0.1111:0,0:18:0:26:0:1:0:60:2:0.1111:0:0 -9 135785688 . CA C 56 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=22.000;MSILEN=1;SSF=0.23739;SOR=0;LSEQ=ACAGAGCAAGACCCTGTCTC;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:5,0:0.3636:0,0:10.3:1:28.2:1:1:0:60:3:0.2727:0.2727:1.3 0/0:6:0:0,0:5,0:0:0,0:12:1:28.2:1:1:0:57.6:10:0.8333:0:0 -9 135785789 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56071;SOR=3.20204;LSEQ=TTGGAACCACCCAGGGGTCG;RSEQ=CAGATCACACCTTGAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:0,1:104,12:0.0085:2,0:1:0:26:0:0.11111:0:60:2:0.0088:0:1 0/1:74:2:1,1:64,8:0.027:2,2:14.5:1:27.5:1:0.22991:7.60108:60:4:0.0282:0:1 -9 135785790 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14852;SOR=Inf;LSEQ=TGGAACCACCCAGGGGTCGG;RSEQ=AGATCACACCTTGAGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:109,13:0:2,0:21.1:1:31.6:1:1:0:60:29.5:1:0:0 0/1:77:2:1,1:66,9:0.026:2,2:21:1:27.5:1:0.24436:7.00947:60:4:0.026:0:1 -9 135786112 . T C 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12691;LSEQ=GGCAGAACATATATGAACAC;RSEQ=GAGCCCAACTATTAGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:195:58,137:98,228:0.3743:2,2:23:1:29.8:1:1:1.01525:60:96.5:0.3755:0:1.1 0/1:426:30:11,19:146,250:0.0704:2,2:23.4:1:29.6:1:1:1.00871:60:60:0.0709:0:1.1 -9 135786139 . A AT 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14692;SOR=3.87388;LSEQ=AACTATTAGAAAAACTGCCG;RSEQ=TTTTTTTTCAGCCTATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:2:0,2:60,237:0.0066:2,0:21:1:29.3:1:1:0:60:4:0.0069:0.0033:0.5 0/1:237:6:2,4:56,175:0.0253:2,2:16.7:1:30.9:1:0.63643:1.56:60:12:0.0255:0.0042:0 -9 135786557 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15303;SOR=Inf;LSEQ=GAATGCTAAGTCATCCACGA;RSEQ=GTTTATATCCATGGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:28,200:0:2,0:25.6:1:31.6:1:1:0:60:227:1:0:0.1 0/1:147:2:1,1:17,128:0.0136:2,2:20:1:29:1:0.23064:7.35:60:4:0.0137:0:1 -9 135786727 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25336;SOR=Inf;LSEQ=TATCATGGATCCTTAAAAGT;RSEQ=ACTCCTGAAATGAGCAGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:192,57:0:2,0:25:1:31.7:1:1:0:60:30.125:1:0:0.1 0/1:292:3:1,2:221,67:0.0103:2,2:12:1:25.3:1:0.14102:6.54235:60:6:0.0104:0:1 -9 135786904 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.16848;LSEQ=TCTGAGGTAGCTGCCCTGGC;RSEQ=TATTTAACAACATCAGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:652:235:97,138:181,234:0.3604:2,2:25.9:1:31.1:1:0.62062:1.10029:60:77.333:0.3614:0:1.2 0/1:739:64:25,39:292,381:0.0866:2,2:24:1:30.6:1:0.59749:1.1953:60:128:0.0876:0:1.2 -9 135786975 . C A 55 q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56128;SOR=0.61726;LSEQ=CCTAAAATGGAAGAGAAGAA;RSEQ=ACAGGGGGTTAGTGTGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:7:1,6:88,203:0.0235:2,2:13.7:1:19.7:1:0.67848:2.59433:57.7:0.75:0.0106:0:5.9 0/1:342:5:3,2:117,220:0.0146:2,2:8.6:1:20.8:1:0.34858:2.81:56:1.5:0.0091:0:3.4 -9 135787591 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20738;SOR=Inf;LSEQ=GAACTAAGTCTTACTCCAGA;RSEQ=AAGAAAATCAACAAAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:199,36:0:2,0:24.3:1:29.9:1:1:0:60:38.167:1:0:0.1 0/1:197:2:1,1:159,36:0.0102:2,2:17.5:1:28:1:0.34114:4.37026:60:4:0.0103:0:1 -9 135796608 . A C 152 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03184;LSEQ=TTTAAACTCACACAAATTTT;RSEQ=GCTGTATGAGTGCTTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:28:28,0:40,1:0.4058:1,1:26.3:1:31.7:1:1:0:60:56:0.4058:0:1 0/1:48:1:1,0:46,1:0.0208:1,0:9:0:33:0:1:0:60:2:0.0208:0:1 -9 135798707 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08084;SOR=0;LSEQ=AAAGCATTCACCTCACAGGG;RSEQ=CCAACAGGTATATGAGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:177,64:0.0123:2,2:14:1:25:1:0.17879:5.48499:60:2:0.0084:0:1.3 0/0:319:0:0,0:204,115:0:2,0:24:1:30.9:1:1:0:60:34.444:1:0:0.1 -9 135798868 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20675;LSEQ=CCTGTTGTGAGGACAACGAC;RSEQ=TCAGTGTCCATCTGCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:3:3,0:106,200:0.0097:2,0:1:0:27:1:0.04311:0:60:6:0.0099:0:1 0/1:342:4:3,1:126,212:0.0117:2,2:13.3:1:27:1:0.15257:5.02:60:8:0.0118:0:1 -9 135798898 . A T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12641;SOR=Inf;LSEQ=ATCTGCAGGAGAAAAGGTCA;RSEQ=ACAGGAAACGTCTGTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:39,143:0:2,0:23.2:1:29.7:1:1:0:60:25:1:0:0.1 0/1:208:4:2,2:62,142:0.0192:2,2:27.8:1:28.5:1:0.58831:2.28:60:8:0.0192:0:1.3 -9 135800897 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19474;SOR=Inf;LSEQ=TAAAAGTTAAAATCTAGCTT;RSEQ=CTTGCTTTAAGTTGCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:176,31:0:2,0:20.6:1:31:1:1:0:60:50.75:1:0:0.1 0/1:164:2:1,1:131,31:0.0122:2,2:11.5:1:29:1:0.35313:4.1751:60:4:0.0123:0:1 -9 135800911 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10295;SOR=Inf;LSEQ=TAGCTTCCTTGCTTTAAGTT;RSEQ=CCTAAAATTTCAGAAACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:200,46:0:2,0:25.4:1:31.8:1:1:0:60:34.143:1:0:0.1 0/1:218:3:1,2:156,59:0.0138:2,2:17.3:1:26.3:1:0.18984:5.24073:60:6:0.0139:0:1 -9 135802549 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2484;SOR=0;LSEQ=ACAGAAGCTGTTGTACTCAT;RSEQ=AAGAACATATGAAATGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:171,45:0.0137:2,2:23.7:1:28.3:1:0.11707:7.50481:60:6:0.014:0:1 0/0:213:0:0,0:163,50:0:2,0:21.2:1:31.4:1:1:0:60:105.5:1:0:0.1 -9 135804327 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49917;SOR=Inf;LSEQ=TTCTGAAGGTTCTTCATTGG;RSEQ=GCCACTACCAAACTGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:27,151:0:2,0:24:1:30.2:1:1:0:60:24.429:1:0:0.1 0/1:190:2:1,1:34,154:0.0105:2,2:13.5:1:26.5:1:0.33528:4.48:60:4:0.0108:0:1 -9 136205738 . T C 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.41667;SOR=0;LSEQ=TCCTGTTTTAGATTTTAAGA;RSEQ=TCCAAAATAACAACCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1:0,1:24.3:1:31.9:1:1:0:60:28:1:0:1.7 1/1:10:9:9,0:1,0:0.9:0,0:28:1:30.2:1:1:0:60:18:0.9:0:1.7 -9 136205775 . T C 166 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATGCAACACACAATAAAAA;RSEQ=AGGCATAAAAGCCTTTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:34:22,12:0,0:1:0,2:22.2:1:32.8:1:1:0:60:68:1:0:1.4 1/0:27:14:7,7:7,6:0.5185:2,2:24.6:1:30.6:1:1:1.16002:60:28:0.5185:0:1.5 -9 136205813 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50588;SOR=0;LSEQ=AGCTGGAACCGCCACCTTCC;RSEQ=GTAATTCGCCAAAATGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:25,22:0.0408:2,2:31:1:30.5:1:1:1.13339:60:4:0.0408:0:1.5 0/0:36:0:0,0:18,18:0:2,0:27.9:1:30.5:1:1:0:59.5:72:1:0:0.6 -9 136206057 . CAAGT C 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00164;SOR=0;LSEQ=GCTGTTGGCACTGTTGTAAA;RSEQ=AAGGGCAAGATTCTTGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:5,7:5,4:0.5714:2,2:19.9:1:31.8:1:0.66992:1.70337:60:24:0.6:0.0952:0.1 0/0:11:0:0,0:5,6:0:2,0:17.5:1:29.9:1:1:0:60:22:1:0:0 -9 136546924 . A G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=CGGTGCGCGGCGTGTTTCCC;RSEQ=GCAGCTGGGCCTCCTTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:21:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:29:1:28.5:1:1:0:60:4:1:0:1.5 -9 136548625 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTGGAGCTGGAGTCGGG;RSEQ=CATCTGAAGGCCGTGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:14,0:0.125:1,0:27.5:1:29.5:1:1:0:60:4:0.125:0:1.5 0/0:3:0:0,0:3,0:0:0,0:24.7:1:33:1:1:0:60:6:1:0:0.3 -9 136548767 . C T 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00271;SOR=Inf;LSEQ=TGCTTCCTGCCCCTGTGCAG;RSEQ=CTCTGGAGAGGGGAGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:62,50:0:2,0:24.8:1:31.4:1:1:0:60:111:1:0:0.2 0/1:106:8:4,4:57,41:0.0755:2,2:21.6:1:30.3:1:0.72008:1.38584:60:16:0.0769:0:2.6 -9 136548777 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49842;SOR=Inf;LSEQ=CCCTGTGCAGCCTCTGGAGA;RSEQ=GGGAGGTGAGAGCAGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:65,60:0:2,0:26.3:1:31.3:1:1:0:60:124:1:0:0.2 0/1:132:2:1,1:75,55:0.0152:2,2:35:0:31.5:1:1:1.36037:60:4:0.0154:0:3.5 -9 136548790 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49841;SOR=Inf;LSEQ=CTGGAGAGGGGAGGTGAGAG;RSEQ=AGAGCCGCTGGGATCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:73,74:0:2,0:26.8:1:31.6:1:1:0:60:72.5:1:0:0.2 0/1:151:2:1,1:84,65:0.0132:2,2:10.5:1:25:1:1:1.29008:60:4:0.0132:0:2 -9 136548799 . T C 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGTGAGAGCAGAGCCGC;RSEQ=GGGATCTCCCTAGTTTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:85,81:0:2,0:25.5:1:30.1:1:1:0:60:26.667:1:0:0.2 1/0:155:103:56,47:28,24:0.6645:2,2:28.6:1:29.9:1:1:1.02:60:206:0.6645:0:1.3 -9 136548809 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=GCAGAGCCGCTGGGATCTCC;RSEQ=TAGTTTCTGGCCGCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:84,85:0:2,0:26.2:1:31.4:1:1:0:60:41.25:1:0:0.2 0/1:174:2:1,1:92,80:0.0115:2,2:38:1:30:1:1:1.14907:60:4:0.0116:0:1 -9 136548873 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23282;SOR=Inf;LSEQ=TTATCTGCTAACAGAACCCA;RSEQ=ATTTGTCCCCCAGGACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:43,68:0:2,0:22.4:1:31:1:1:0:60:54.5:1:0:0.2 0/1:104:2:1,1:37,65:0.0192:2,2:12:1:30:1:1:1.75:60:4:0.0196:0:1 -9 136548879 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49931;SOR=0;LSEQ=GCTAACAGAACCCAGATTTG;RSEQ=CCCCCAGGACCTCCAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:41,62:0.019:2,2:40.5:1:32.5:1:1:1.51:60:4:0.0192:0:1.5 0/0:93:0:0,0:30,63:0:2,0:25.9:1:29.1:1:1:0:60:92:1:0:0.3 -9 136548920 . T A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.18792;SOR=Inf;LSEQ=TCTGCAGGCCAGGACCTCGC;RSEQ=CCTCCCCAACCTTCCTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:7,42:0:2,0:25:1:30.1:1:1:0:60:98:1:0:0.1 0/1:38:2:1,1:5,31:0.0526:2,2:17.5:1:24:1:0.29445:5.75:60:4:0.0526:0:1 -9 136549171 . G A 24 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGGCGACATCTCCTCCA;RSEQ=CATGAGCGCTGGAGGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:24:1:1:0:60:4:1:0:1.5 -9 136901221 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50653;SOR=Inf;LSEQ=TCCAGTTCCCGCAAAGTGGT;RSEQ=GGTTTCAGAGTCTCAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:50,22:0:2,0:24.2:1:31.7:1:1:0:60:35:1:0:0.1 0/1:95:2:1,1:60,33:0.0211:2,2:17:1:28:1:1:1.80601:60:4:0.0215:0:1 -9 136901317 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55191;SOR=Inf;LSEQ=ATGTGCACTACCCGGCCCAG;RSEQ=TTCTCCCCGGGCAGCCGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:13,38:0:2,0:26.6:1:32.3:1:1:0:60:50:1:0:0.2 0/1:109:3:2,1:41,65:0.0275:2,2:24:1:27:1:0.56065:3.14:60:6:0.0275:0:1 -9 136902522 . G A 26 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCAAATGGTGAAACCCT;RSEQ=TCTCTACTAAAAATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:26:1:1:0:57.5:4:1:0:2 -9 136913123 . C G 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=CCCTGCTCCCCGACAGCCCC;RSEQ=ACTCAGCCGGCACAAGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:21:1:30.5:1:1:0:60:4:0.3333:0:1 1/0:4:2:2,0:2,0:0.5:0,0:46:1:27.5:1:1:0:60:4:0.5:0:1 -9 136913355 . T C 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00553;SOR=0.35294;LSEQ=AGGATGCTGTCGCAGTAGCG;RSEQ=AGGTGCTCCGACAGCTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:96:24,72:3,8:0.8972:2,2:23:1:31.8:1:1:1.12372:60:47:0.8952:0:1.1 1/0:122:92:26,66:7,23:0.7541:2,2:22.2:1:30.9:1:0.64532:1.29:60:22:0.7521:0:1.1 -9 136913369 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.78216;LSEQ=GTAGCGTAGGTGCTCCGACA;RSEQ=CTTGCCCTTCTTGCCTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:1,0:12,64:0.013:2,0:1:0:26:0:0.16883:0:60:2:0.013:0:2 0/1:87:2:1,1:18,67:0.023:2,2:24:1:28.5:1:0.39107:3.65:60:4:0.0238:0:2.5 -9 136917487 . C A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25378;SOR=0;LSEQ=GTCCTGCATACATTCGCTTG;RSEQ=ACTCCAATAATAATTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:3:2,1:26,19:0.0625:2,2:12:1:29.7:1:1:1.45:60:6:0.0638:0:1 0/0:37:0:0,0:15,22:0:2,0:23:1:30.9:1:1:0:60:36:1:0:0.1 -9 136918260 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGACTTCCTGAGGCAC;RSEQ=GGCTGTCCCCAGCTTAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:14.5:1:30:1:1:0:60:4:0.6667:0:1 -9 138041494 . G A 59 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=AAGAAATAAAGACACAAGAC;RSEQ=AAGAGACAAAGAGAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:40.5:1:32.5:1:1:0:60:4:1:0:0 1/1:5:4:3,1:1,0:0.8:0,2:23.5:1:29.5:1:1:0:60:8:0.8:0:1 -9 138041654 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50571;LSEQ=TAAGTGATTGATAAGGTCAA;RSEQ=CAAGTCAAGTGATCATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:16,12:0.0667:2,2:22.5:1:28.5:1:1:1.32044:60:4:0.069:0:1 0/1:29:1:0,1:16,12:0.0345:2,0:43:0:30:0:0.44828:0:60:2:0.0345:0:1 -9 138041726 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=CAGAGAGAGAAGGCAGCATA;RSEQ=GTCAGCGTTTTCTTCTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:0:2,0:22.3:1:29.9:1:1:0:60:18:1:0:0.6 0/1:9:2:1,1:1,6:0.2222:2,2:45:0:31:1:0.41667:4.58:60:4:0.2222:0:1 -9 138263531 . A G 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=0;LSEQ=CTGCAGCCGCCGTCAGCGTC;RSEQ=GCAGCCGCCCTTCTTCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:0:32:0:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:33:0:32:1:1:0:60:4:1:0:1.5 -9 138263555 . G T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GCCGCCCTTCTTCGCCAGGT;RSEQ=TGCTGATTGCAAGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:15:0:33.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:15.5:1:30:1:1:0:60:4:1:0:1.5 -9 138265191 . A G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50435;SOR=0;LSEQ=CCAGTGCCTGGAATCCTGCA;RSEQ=CCTGGAGGCAGCCTTGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:29:0:33.5:1:1:1.74:60:4:0.0741:0:1.5 0/0:19:0:0,0:8,11:0:2,0:28.6:1:29.8:1:1:0:60:38:1:0:0.1 -9 138265212 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=CCTGGAGGCAGCCTTGCGAT;RSEQ=AGCTCTGCTGCAGGCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:3,9:0.1429:2,2:39.5:1:28:1:0.50549:2.74:60:4:0.1429:0:1 0/0:14:0:0,0:5,9:0:2,0:30.6:1:30.9:1:1:0:60:28:1:0:0.1 -9 138517853 . G C 77 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCTTTGGAGGTTAAAG;RSEQ=CTCGTGAATGCTGATCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:22:1:33.2:1:1:0:60:10:1:0:1.2 1/1:1:1:1,0:0,0:1:0,0:9:0:34:0:1:0:60:2:1:0:1 -9 138517935 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=0;LSEQ=CTGCCAGTAGCAAAGACGGC;RSEQ=AGGCCCACAGTGATATTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:14,10:0.0769:2,2:28:1:30:1:1:1.38168:60:4:0.0769:0:1.5 0/0:23:0:0,0:14,9:0:2,0:30.1:1:29.8:1:1:0:60:46:1:0:0.3 -9 138518010 . A G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGTCCCTTCCCATAGGAC;RSEQ=GGAGCGAGCCAGTCTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,0:0.9:0,0:24.8:1:32:1:1:0:60:18:1:0:1.1 1/1:7:7:1,6:0,0:1:0,2:25.6:1:30.6:1:1:0:60:14:1:0:1 -9 138570258 . G A 85 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02098;SOR=0;LSEQ=GTGGTCACAGCCATGGCTGT;RSEQ=GTTGCAGTGACCGTGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1:0,2:26.9:1:30.6:1:1:0:60:14:1:0:1 0/1:6:2:1,1:1,3:0.3333:2,2:43.5:1:30:1:1:2.45:60:4:0.3333:0:1 -9 138663730 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20408;SOR=Inf;LSEQ=GCCACCTCCGTACAGTGGCC;RSEQ=AGGCAGAGGCTGACCCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:38,16:0:2,0:23.7:1:31.6:1:1:0:60:108:1:0:0.4 0/1:45:2:1,1:28,15:0.0444:2,2:45.5:1:30:0:1:1.83945:60:4:0.0444:0:1.5 -9 138663773 . TG T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50803;SOR=0;LSEQ=GCACCCCAGCACGCCCACCC;RSEQ=GGGTGTTGTTACACGGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:53,42:0.0206:2,2:35:1:31.5:1:1:1.25885:60:4:0.0208:0:0 0/0:72:0:0,0:33,39:0:2,0:23.4:1:30.2:1:1:0:60:71:1:0:0.6 -9 138663796 . G T 167 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64209;SOR=1.19698;LSEQ=GGTGTTGTTACACGGTGGCT;RSEQ=CTGGGGCACCAGGTGGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:48:24,24:35,26:0.4404:2,2:25.3:1:30:1:0.56161:1.34245:60:96:0.4404:0:1.2 0/1:68:33:16,17:17,18:0.4853:2,2:27.4:1:29.5:1:1:1.00342:60:66:0.4853:0:1.2 -9 138829472 . A G 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAAATGAGAGATTGTTT;RSEQ=AGGAGACACAAATACGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1:0,2:21.8:1:33:1:1:0:60:20:1:0:1.2 1/1:5:5:5,0:0,0:1:0,0:17:1:32.6:1:1:0:60:10:1:0:1 -9 138829545 . G A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00814;SOR=4.97828;LSEQ=GCCACGGCGACGGCCACACC;RSEQ=GAGGGAGGGATGAGGTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:5,0:42,2:0.102:1,0:27.2:1:29.2:1:1:0:60:10:0.102:0:1.2 0/1:30:11:11,0:19,0:0.3667:1,0:19.4:1:29.6:1:1:0:60:22:0.3793:0:1.1 -9 138829610 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50166;SOR=0;LSEQ=AGCTGAATAGTAGATACATG;RSEQ=CTATTAGTTTTATTCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:107,32:0.0142:2,2:22.5:1:28.5:1:0.41459:3.30801:60:4:0.0146:0:1 0/0:119:0:0,0:94,25:0:2,0:23.5:1:30.5:1:1:0:60:38.667:1:0:0.2 -9 138829709 . C T 232 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00169;SOR=0.63602;LSEQ=ATTGCCATCGAAGACCCTGA;RSEQ=GAGTAGTAAGAGCAAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:389:206:103,103:94,89:0.5296:2,2:27.2:1:30.3:1:0.83913:1.05601:60:102:0.5285:0:1.2 0/1:398:166:82,84:112,120:0.4171:2,2:24.8:1:29.5:1:0.83943:1.05:60:165:0.4177:0:1.2 -9 138829775 . G T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22005;SOR=Inf;LSEQ=GTTCCTAAGCTGCTGGCGCA;RSEQ=TCTCCACCCCGCTGGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:63,156:0:2,0:25.7:1:32.1:1:1:0:60:108.5:1:0:0.4 0/1:194:2:1,1:59,133:0.0103:2,2:16:0:28.5:1:0.52401:2.24:60:4:0.0104:0:2 -9 138829787 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20613;SOR=Inf;LSEQ=CTGGCGCAGTCTCCACCCCG;RSEQ=TGGCCCTCGGAAAGCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:44,143:0:2,0:24.3:1:32.3:1:1:0:60:186:1:0:0.3 0/1:156:2:1,1:43,111:0.0128:2,2:39.5:1:27:1:0.48586:2.56:60:4:0.0132:0:1 -9 138980116 . C T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGAACTGTACCACTGCCCA;RSEQ=ATCAGGCCCAGATGGAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 138981325 . AC A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCCTGAGCCTCCATGTC;RSEQ=CCCCCACAACCCCACCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30.5:1:1:0:60:4:1:0:0 -9 138982093 . G T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10493;SOR=4.88092;LSEQ=TGGGGGCCCTGGCCAGAGGG;RSEQ=ATGCCTCAGGGGTCCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:5,2:0.4615:2,0:26.5:1:30.8:1:0.46154:0:60:12:0.4615:0:1 1/1:11:9:7,2:1,1:0.8182:2,2:17.8:1:28.6:1:0.49091:3.06:60:18:0.8182:0:1.1 -9 138982177 . CT C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.49429;SOR=0;LSEQ=GCAGGGCCAACGCTGACTCC;RSEQ=CCAAGACCGCCGCAGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:19,15:0.0556:2,2:45.5:1:32:1:1:1.2583:60:4:0.0606:0:0 0/0:32:0:0,0:16,16:0:2,0:24.9:1:29.2:1:1:0:60:31:1:0:0.4 -9 138982193 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49508;SOR=0;LSEQ=CTCCCTCCAAGACCGCCGCA;RSEQ=AAGAACCAAGGAAGGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:15,16:0.0606:2,2:32:1:30.5:1:1:1.06:60:4:0.0625:0:1 0/0:28:0:0,0:13,15:0:2,0:32.9:1:31.2:1:1:0:60:56:1:0:0.2 -9 139121812 . C T 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACAGTCTGGGCCCAGGC;RSEQ=AGGTGGTGCTGCTCTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:31.5:1:1:0:60:4:1:0:1.5 -9 139141535 . T G 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGGGTGCCTGGAGGCT;RSEQ=TGCTTCCCAGGAAAGTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:31:1:1:0:60:4:1:0:1.5 -9 139143513 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14376;SOR=Inf;LSEQ=CCCTTCCTGGCATAGGCGCT;RSEQ=CTCCGCCCCGTCCTCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:28.7:1:31.3:1:1:0:60:26:1:0:0 0/1:17:2:1,1:8,7:0.1176:2,2:9.5:1:25:1:1:1.13389:60:4:0.1176:0:1 -9 139270366 . T A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGCGCCGGCCACGCCCAGTC;RSEQ=GCTTGGTAAACCTGACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:11:1:26:1:1:0:60:4:1:0:1 -9 139271664 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11475;SOR=0;LSEQ=AGCACACGTGTGTGTGGCGT;RSEQ=TGCGGCTCAGAGCCGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:0.0952:2,2:26:1:31:1:1:1.66897:60:4:0.0952:0:1 0/0:40:0:0,0:20,20:0:2,0:31:1:31.2:1:1:0:60:39:1:0:0.3 -9 139271747 . G A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGGCAGCATCAGGATGGCC;RSEQ=GAGGCTCCTGCACGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:2,4:1,5:0.5:2,2:24.2:1:32.2:1:1:2.32:60:12:0.5:0:1.2 1/0:8:4:2,2:2,2:0.5:2,2:19.8:1:31:1:1:1:60:8:0.5:0:1 -9 139271850 . A G 78 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=CGCAACTGGGCAGGCCAGGA;RSEQ=CCAGCTTCCTCCTCCTAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:20.6:1:33.8:1:1:0:60:10:1:0:1.6 1/0:2:1:0,1:0,1:0.5:0,0:6:0:34:0:1:0:60:2:0.5:0:1 -9 139271919 . C T 45 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ACTTCCACCAGCCCCCACCC;RSEQ=ACTGCTCCAGGCAGGCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:10.7:1:29:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139390348 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53297;SOR=0;LSEQ=AAATAAAAAGGCAGTGTTTC;RSEQ=GTGTAAAATAAAAGTACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:46,0:0.0417:1,2:19.5:1:29.5:1:0.04167:0:60:4:0.0426:0:2.5 0/0:27:0:0,0:25,2:0:2,0:19.6:1:30.3:1:1:0:60:12.5:1:0:0.7 -9 139390378 . TA T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.52385;SOR=0;LSEQ=AAAAGTACATAAATAAATAC;RSEQ=AAAAAAATTAAAATCCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:2,0:86,1:0.0222:1,0:26.5:1:32.5:1:1:0:60:4:0.0227:0:1 0/0:56:0:0,0:54,2:0:1,0:25.1:1:28.6:1:1:0:60:55:1:0:0.5 -9 139390397 . C T 215 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAAAAAAAATTAAAATCCT;RSEQ=GTTCTTATTTTGTATAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:131:128,3:0,0:1:0,1:22:1:30.6:1:1:0:60:262:1:0:1.1 0/1:87:40:37,3:44,3:0.4598:2,2:23.5:1:30.4:1:1:1.18681:60:80:0.4598:0:1.1 -9 139390944 . TGTG T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=1;SOR=1.0097;LSEQ=AGCTCACGCCAAGGTGCGGC;RSEQ=GTGGTGGTGGTGGCGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:665:15:8,7:320,330:0.0226:2,2:29.4:1:32.9:1:0.79904:1.18:60:30:0.0228:0:0.7 0/1:527:12:8,4:253,262:0.0228:2,2:25.8:1:31.5:1:0.25733:2.07:59.6:24:0.023:0.0038:0.2 -9 139391461 . T C 186 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGCCACGTTCAGGTGCCCGA;RSEQ=GCCCAGGTGGGTGTCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:62:31,31:393,339:0.0781:2,2:22.2:1:31.3:1:0.59792:1.15907:59.9:61:0.078:0:1.1 0/0:643:0:0,0:336,306:0:2,0:22.6:1:29.4:1:1:0:60:57.364:0.9984:0:0.2 -9 139391636 . G A 287 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00219;LSEQ=TCCAGCAGGCAGCCCTTGCC;RSEQ=TCCTGGGACTTCTTCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:662:661:311,350:0,0:0.9985:0,2:24.8:1:30.7:1:1:0:60:219.333:1:0:1.1 1/0:576:341:174,167:107,127:0.592:2,2:23.3:1:29.8:1:0.23465:1.24:60:169.5:0.5947:0:1.2 -9 139392025 . CG C 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.08358;SOR=6.14141;LSEQ=CTCCTCCTGGGGGATGAGGG;RSEQ=GGGGCCGGTGAGGGGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:544:1:0,1:133,410:0.0018:2,0:33:0:32:0:1:0:60:2:0.0019:0:1 0/1:357:4:1,3:93,260:0.0112:2,2:17.8:1:30.5:1:1:1.07287:60:8:0.0115:0.0028:0.3 -9 139392062 . C A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3021;SOR=3.499;LSEQ=GGCCAGGCCAGGCGTGGGGA;RSEQ=CCTCCCCAAGGTTCCATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:1:1,0:23,256:0.0036:2,0:1:0:25:0:0.08571:0:60:2:0.0036:0:1 0/1:161:2:1,1:17,142:0.0124:2,2:16.5:1:30.5:1:0.21172:8.15:60:4:0.0128:0:1 -9 139392076 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10668;SOR=Inf;LSEQ=TGGGGACCCTCCCCAAGGTT;RSEQ=CATCACCAGAGGAAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:7,227:0:1,0:24.6:1:31:1:1:0:60:22.4:1:0:0.3 0/1:114:2:1,1:7,105:0.0175:2,2:20:1:31:1:0.136:14.10:60:4:0.0183:0:1 -9 139393067 . C T 117 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGCCAGGCTGTGTGCCC;RSEQ=GCCATGACTGCCGCCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:12,2:0,0:1:0,2:26.3:1:30.8:1:1:0:60:28:1:0:1.1 1/1:1:1:0,1:0,0:1:0,0:6:0:23:0:1:0:60:2:1:0:1 -9 139393162 . G A 175 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTGGAAGGGCTCCATAAAC;RSEQ=GGGGCTGAAGGAAGGCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:49,3:0,0:1:0,2:25.3:1:30.8:1:1:0:60:51:1:0:2 0/1:9:2:2,0:7,0:0.2222:0,0:20.5:1:23.5:1:1:0:60:1:0.125:0:2.5 -9 139393175 . A G 190 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00678;LSEQ=CATAAACGGGGGCTGAAGGA;RSEQ=GGCAGGAGCACTAACGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:64:60,4:0,0:0.9846:0,2:24.7:1:31.8:1:1:0:60:15:0.9836:0:1.9 0/1:15:4:4,0:11,0:0.2667:0,0:20:1:28.3:1:1:0:60:3:0.2143:0:1.8 -9 139393307 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17982;LSEQ=TGGCCCTCACTTCTCTGTGG;RSEQ=TTCAGCCCTCACGTCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:235:154,81:246,132:0.3827:2,2:25.3:1:31:1:0.93066:1.02:60:46:0.3853:0:1.1 0/1:549:55:37,18:305,188:0.1002:2,2:21.2:1:30.7:1:0.4664:1.27:60:54:0.1007:0:1.1 -9 139393520 . C T 72 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04226;SOR=4.76818;LSEQ=AGTCCCACCCGTCCCTGTGG;RSEQ=GGTCCCGCCCCACGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:590:2:2,0:313,275:0.0034:2,0:37.5:1:28:1:0.50145:0:60:4:0.0034:0:1 0/1:438:7:2,5:234,196:0.016:2,2:6.6:1:25.7:1:0.25575:2.97757:60:14:0.0163:0:1.1 -9 139393743 . T A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07508;SOR=Inf;LSEQ=GGAGAGGCTCAGGCGGGTGC;RSEQ=GGGCAGACGTACACCGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:84,246:0:2,0:23.7:1:30.2:1:1:0:60:65:0.9939:0:0.2 0/1:244:3:3,0:81,160:0.0123:2,0:9:1:24:1:0.03984:0:60:6:0.0123:0:2.3 -9 139393790 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13174;SOR=Inf;LSEQ=CCCAGAACGAACGCCTGGAC;RSEQ=GGAAGCCCCACTGTCTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:11,118:0:2,0:25.3:1:30.7:1:1:0:60:42:1:0:0 0/1:74:2:1,1:8,64:0.027:2,2:8.5:1:27.5:1:0.22991:7.60:60:4:0.0278:0:1.5 -9 139394573 . T G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCACCGGCAAGCTGAGCCC;RSEQ=AGGTCTGCAGGCACCGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:12:0:25:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:1:0,2:37:1:31.5:1:1:0:60:4:1:0:1 -9 139394979 . G T 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.26673;SOR=0;LSEQ=CGGCCCTGAGGAGGGCAGGT;RSEQ=GGCACACAGGCAGCCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:1,2:201,70:0.0109:2,2:5.3:1:22.3:1:0.16985:5.69851:60:2:0.0075:0:1.7 0/0:200:0:0,0:135,64:0:2,0:23.9:1:30.7:1:1:0:60:48.75:0.9949:0:0.2 -9 139395161 . C T 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03869;SOR=0.20876;LSEQ=GCAAGGCGGTCTCGCCCGTG;RSEQ=GGTCTGTCTGGTTGTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:955:10:2,8:450,495:0.0105:2,2:16.5:1:27.7:1:0.11255:3.63194:60:20:0.0106:0:1 0/0:908:2:0,2:445,461:0.0022:2,0:22.5:1:29:1:0.49965:0:60:4:0.0022:0:1 -9 139395259 . G A 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25633;SOR=2.99204;LSEQ=CTGTTGCCCGTCTCCAGGCC;RSEQ=CCCCCGCTGCAGGAGGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:2:2,0:171,343:0.0039:2,0:1:0:26:1:0.11197:0:60:4:0.004:0:1 0/1:434:5:3,2:169,260:0.0115:2,2:24.4:1:29.2:1:0.38923:2.30:60:10:0.0117:0:1 -9 139395311 . G A 114 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=20.12136;LSEQ=TGAAGCCATCTGCAGAGGCA;RSEQ=AGACGGGTGCTCAGTCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:1,0:56,193:0.004:2,0:1:0:28:0:0.228:0:60:2:0.0041:0:1 0/1:173:13:3,10:39,121:0.0751:2,2:29.2:1:31:1:1:1.07394:60:26:0.0751:0:1.1 -9 139395337 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18415;SOR=Inf;LSEQ=GGTGCTCAGTCTGGAGGGCC;RSEQ=GTCCCCAGCTGCAGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:15,132:0:2,0:22:1:30.3:1:1:0:60:28.4:1:0:0.1 0/1:111:2:1,1:18,91:0.018:2,2:14.5:1:29:1:0.31433:4.95:60:4:0.018:0:1 -9 139395473 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66002;SOR=0.57652;LSEQ=TGAAGTCCGCCTGGGCTGCT;RSEQ=AGTGGACAGAGCCGAATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:0,8:0,9:0.4706:0,0:33.1:1:29.1:1:1:0:60:16:0.5:0:2.1 0/1:6:2:0,2:0,4:0.3333:0,0:16.5:1:26.5:1:1:0:60:4:0.3333:0:1 -9 139395891 . CA C 52 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAGACTCCATCTCAAAAA;RSEQ=AAAAAAAAAGAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:0.375:0,0:13.7:1:32.9:1:1:0:60:6:0.375:0.125:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139395901 . AG GAA 49 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=ATCTCAAAAACAAAAAAAAA;RSEQ=AAAAAAAAAAAGAAAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,0:0.3:0,0:29.7:1:31.1:1:1:0:60:6:0.3:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139396113 . T A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08135;LSEQ=CCAATTCTAAGTTTCCAGAG;RSEQ=ATCAACTGTACCCCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:90:83,7:98,10:0.4545:2,2:22.3:1:29.7:1:0.80211:1.21:60:29:0.4531:0:1.1 0/1:111:7:7,0:88,16:0.0631:2,0:24:1:27.9:1:0.59057:0:60:14:0.0631:0:1.3 -9 139396159 . G T 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02659;SOR=Inf;LSEQ=TTAGGGGAGAGAGGCAGGTG;RSEQ=GCCACGGGGCTAGGGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:338,147:0:2,0:26.4:1:31:1:1:0:60:59.625:1:0:0.3 0/1:330:4:1,3:215,111:0.0121:2,2:5.8:1:27.3:1:0.1208:5.7787:60:8:0.0125:0:1 -9 139396408 . A G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.08728;LSEQ=GCCTGTCAGGGCAGCCCGGC;RSEQ=GCAGGTGCCCGGGAGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:780:722:419,303:32,24:0.9256:2,2:24.2:1:30.1:1:0.88934:1.04:60:71.2:0.9271:0:1.1 1/0:644:335:185,150:165,143:0.5202:2,2:22.3:1:29.5:1:0.69238:1.07:60:82.75:0.5213:0:1.2 -9 139396632 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12953;SOR=Inf;LSEQ=GCCTGGCGTGGGAGGTGGGC;RSEQ=CTGGGTCGGGAGGGGCAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:112,160:0:2,0:24:1:31:1:1:0:60:29.222:0.9962:0:0.1 0/1:154:2:1,1:57,95:0.013:2,2:27:1:28:1:1:1.66:60:4:0.0132:0:1 -9 139396690 . C T 193 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCAGGTCCCACCTCCCAC;RSEQ=GGGGACCCAGAAGCAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:206,160:0:2,0:25.2:1:30.1:1:1:0:60:35.6:1:0:0.1 0/1:257:81:49,32:101,75:0.3152:2,2:24.4:1:30.6:1:0.68404:1.14:60:162:0.3176:0:1.1 -9 139396772 . C T 69 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04977;SOR=7.46539;LSEQ=GCTCCCGCCGCTTCTTCTTG;RSEQ=TGGCCTCAGACACTTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:1:1,0:350,288:0.0016:2,0:24:0:31:0:1:0:60:2:0.0016:0:1 0/1:518:6:2,4:272,240:0.0116:2,2:16.8:1:27:1:0.42753:2.2632:60:5:0.0098:0:1.2 -9 139396843 . C T 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.15015;SOR=3.69997;LSEQ=CGCCGGCGCTTGCGGGACAG;RSEQ=AGCACCCCGCAGCCCACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:644:2:1,1:270,371:0.0031:2,2:34.5:1:27.5:1:1:1.37:60:4:0.0031:0:1 0/1:526:6:2,4:236,283:0.0114:2,2:20.3:1:29.2:1:0.6939:1.66628:60:12:0.0116:0:1.5 -9 139396881 . C T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09811;SOR=6.02258;LSEQ=GAAGAACAGAAGCACAAAGG;RSEQ=GGCCGCCGCCACGTACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:1:0,1:182,331:0.0019:2,0:1:0:30:0:1:0:60:2:0.002:0:1 0/1:431:5:1,4:179,247:0.0116:2,2:17:1:27.2:1:0.40585:2.89264:60:10:0.0117:0:1.4 -9 139396925 . G A 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16426;SOR=5.85134;LSEQ=GCAGCTGCGCCGGCGGGGGC;RSEQ=GCTCCACGGTCTCACCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:1:1,0:107,207:0.0032:2,0:1:0:25:0:0.34286:0:60:2:0.0032:0:1 0/1:218:4:2,2:73,141:0.0183:2,2:17.5:1:29.3:1:0.60902:1.93:60:8:0.0186:0:1 -9 139396959 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55068;SOR=0;LSEQ=ACCTGCGGGCACGGGGGCCA;RSEQ=GGGCAGGTGCCCGGACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:38,139:0.0111:2,2:29.5:1:30.5:1:0.38924:3.62:60:4:0.0112:0:1 0/0:92:0:0,0:21,69:0:2,0:25.7:1:30.5:1:1:0:60:89:0.978:0:0.2 -9 139396983 . A G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00365;SOR=0.2184;LSEQ=CAGGTGCCCGGACATCAGGC;RSEQ=GCGGCTACGCAGCAGGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:32:3,29:19,59:0.2909:2,2:20.9:1:31.9:1:0.11376:3.08577:60:64:0.2963:0:1 0/1:49:4:0,4:7,38:0.0816:2,0:30.5:1:30.5:1:1:0:60:8:0.0816:0:1 -9 139397312 . C CT 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.43315;SOR=0.68788;LSEQ=ATCAATTCTTCTCTCTCTCT;RSEQ=TTTTTTTTTCTTTAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:16:14,2:250,77:0.0462:2,2:32.6:1:31.6:1:0.54171:2.15:60:32:0.0466:0:0 0/1:341:11:9,2:234,95:0.0323:2,2:19.3:1:31:1:0.73499:1.82:60:22:0.0327:0:0.3 -9 139397426 . G A 135 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=9.18238;LSEQ=ACTTTCCCGTGGCTGGACTC;RSEQ=TTCCCAGGTGGCTCCACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1065:3:2,1:550,510:0.0028:2,2:5:1:24.7:1:1:1.85:60:2:0.0019:0:1 0/1:988:25:12,13:483,479:0.0253:2,2:20.4:1:29.2:1:0.84263:1.09227:60:50:0.0257:0:1 -9 139397551 . C T 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00156;SOR=Inf;LSEQ=CACCCGTGGGTAGCAACTGG;RSEQ=ACAAACAGCCAGCGTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:992:0:0,0:502,490:0:2,0:24.9:1:31.7:1:1:0:60:44.091:1:0:0.5 0/1:801:8:2,6:391,398:0.01:2,2:17.1:1:26.6:1:0.28696:2.94379:60:16:0.0102:0:1.3 -9 139397557 . C G 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09575;LSEQ=TGGGTAGCAACTGGCACAAA;RSEQ=AGCCAGCGTGTCTGGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:417:209,208:300,288:0.4145:2,2:24.6:1:31.3:1:0.79803:1.03666:60:40.7:0.4136:0:1.1 0/1:820:52:26,26:377,390:0.0634:2,2:27.6:1:30.7:1:1:1.03:60:104:0.0644:0:1.1 -9 139397587 . G A 84 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01331;SOR=9.94957;LSEQ=GTCTGGGGCACGGGGGGATG;RSEQ=CACCCCCTGCAGGCAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:941:1:1,0:441,499:0.0011:2,0:1:0:26:0:0.46971:0:60:2:0.0011:0:1 0/1:763:8:4,4:363,391:0.0105:2,2:19:1:28.3:1:1:1.08:60:16:0.0107:0:1.1 -9 139397590 . CC A 148 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGCACGGGGGGATGGCA;RSEQ=CCCTGCAGGCAGAGCCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:941:0:0,0:439,498:0:2,0:25.7:1:31.4:1:1:0:60:77.083:0.9968:0:0.4 0/1:757:29:15,14:345,381:0.0383:2,2:23.9:1:30.5:1:0.70712:1.18:59.8:58:0.0388:0.0106:0.4 -9 139397707 . G A 248 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.56754;LSEQ=GCTCCCAGGAATGCGGCCAC;RSEQ=TCGGTGGCACTCTGGAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:603:316:142,174:131,156:0.524:2,2:26:1:29.9:1:0.87022:1.02895:60:23.308:0.5179:0:1.1 0/1:463:178:84,94:133,152:0.3844:2,2:23.4:1:29.4:1:0.924:1.02:60:88:0.3834:0:1.2 -9 139399070 . G A 186 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGGGGCAGGGAGGCCGTC;RSEQ=GGGAGGGCCCAGGAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:236,100:0:2,0:24.2:1:30.1:1:1:0:60:111:0.994:0:0.2 0/1:256:78:49,29:114,62:0.3047:2,2:26.2:1:29.6:1:0.77811:1.08785:60:25:0.3:0:1.1 -9 139399641 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07538;LSEQ=CTCCAGCCCACTGGCCAGCC;RSEQ=CGGGGGACGTCCCTGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:77:30,47:47,59:0.4208:2,2:22.5:1:30.7:1:0.54449:1.24651:60:154:0.4254:0:1.1 0/1:97:5:2,3:51,41:0.0515:2,2:37.2:1:30.6:1:0.65613:1.85383:60:10:0.0521:0:1 -9 139399711 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07612;SOR=Inf;LSEQ=GCCTCCGGGCCCAAGCCAGG;RSEQ=CACATCCAAGTTCAGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:253,109:0:2,0:23.5:1:31.6:1:1:0:60:50.714:1:0:0.1 0/1:268:3:1,2:184,81:0.0112:2,2:17:1:26:1:0.22742:4.51453:60:6:0.0115:0:1.3 -9 139399714 . C T 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31844;SOR=4.03818;LSEQ=TCCGGGCCCAAGCCAGGCCA;RSEQ=ATCCAAGTTCAGGTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:1:1,0:262,117:0.0026:2,0:23:0:27:0:1:0:60:2:0.0027:0:2 0/1:284:3:1,2:189,92:0.0106:2,2:17:1:25.7:1:0.25534:4.08646:60:6:0.0109:0:1 -9 139400271 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12421;SOR=Inf;LSEQ=CCGGAGATGCATGTGCCGCC;RSEQ=TTGAGGCAGCGCAGGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:90,249:0:2,0:25.4:1:31.3:1:1:0:60:55.5:1:0:0.1 0/1:185:2:1,1:56,127:0.0108:2,2:19:1:28.5:1:0.52244:2.26:60:4:0.0109:0:1 -9 139400406 . C T 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.73284;SOR=0.80003;LSEQ=CCGCCACCTCACACCCAGCC;RSEQ=TCGGCCAGCAGTGCCACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:32:0,32:0,16:0.6531:1,1:22.4:1:30.4:1:1:0:60:64:0.6667:0:1 1/0:10:6:1,5:0,4:0.6:0,2:20.8:1:30.5:1:1:0:60:12:0.6:0:1.2 -9 139400835 . TA T 105 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.11429;SOR=2.33892;LSEQ=CTAAAATCATTTATTGAAAC;RSEQ=AAAAAAAAAAAAAGACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:10:10,0:49,4:0.1449:2,0:20.2:1:31.6:1:1:0:58.5:20:0.1493:0.0145:1.4 0/1:35:10:9,1:24,0:0.2857:1,2:18.1:1:31.7:1:0.29412:0:59.5:20:0.2941:0.0857:1.7 -9 139400887 . T C 46 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69611;SOR=1.43383;LSEQ=GAGGATGAAGGCCGGGAGGA;RSEQ=CACTGCCCGGTCTGCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:4:4,0:203,19:0.0177:2,0:17:1:23:1:1:0:60:3:0.0141:0:6.3 0/1:119:3:3,0:111,5:0.0252:1,0:27.3:1:12.7:1:1:0:60:0:0:0:5.7 -9 139400904 . C T 217 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.43783;SOR=0.85711;LSEQ=GGATCACTGCCCGGTCTGCG;RSEQ=CCCGAGGCCCCCACGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:285:156:138,18:112,17:0.5474:2,2:28.5:1:29.8:1:0.71902:1.16:60:77:0.55:0:1.2 1/0:169:86:75,11:76,7:0.5089:2,2:21.9:1:28.9:1:0.45675:1.58804:59.9:27.667:0.5123:0:1.2 -9 139401456 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2563;SOR=0;LSEQ=AGGTTTCGTCAGTGGCCCAA;RSEQ=CCCGCCACACCCCGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:69,184:0.0116:2,2:33.3:1:29.3:1:1:1.33:60:6:0.0123:0:3 0/0:210:0:0,0:64,146:0:2,0:24.3:1:30.7:1:1:0:60:18.091:1:0:0.3 -9 139401467 . C A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19964;SOR=Inf;LSEQ=GTGGCCCAAGCCCGCCACAC;RSEQ=CCGGCCCTGCCGTGCCGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:53,168:0:2,0:22.5:1:30.7:1:1:0:60:30.571:1:0:0.7 0/1:179:2:2,0:48,128:0.0112:2,0:5:1:25:1:0.07776:0:60:4:0.0114:0:2.5 -9 139401504 . G A 207 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06009;LSEQ=GCGTGTCCGTCCCGGAAGAC;RSEQ=AGCGCTCAGGTCTGGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:123:118:24,94:0,5:0.9593:0,2:24.1:1:30.1:1:0.58187:0:60:58:0.9587:0:1.5 1/0:67:39:8,31:3,25:0.5821:2,2:23.6:1:30.9:1:0.33662:2.13:60:78:0.5821:0:1.3 -9 139401565 . A G 156 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=0.06112;LSEQ=AGGTGTCAAGGGTGCCGTGG;RSEQ=GACGCCCTTCCCACTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:32:17,15:24,26:0.3902:2,2:18.6:1:31.3:1:0.82113:1.22:60:64:0.3902:0:1.7 0/1:27:1:0,1:15,11:0.037:2,0:40:0:32:0:0.44444:0:60:2:0.0385:0:1 -9 139401577 . C G 166 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39673;SOR=0.64314;LSEQ=TGCCGTGGAGACGCCCTTCC;RSEQ=ACTGGGACCCCCGCTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:45:23,22:23,12:0.5625:2,2:20.3:1:30.4:1:0.2551:1.81942:60:44:0.5641:0:1.5 0/1:31:14:10,4:10,7:0.4516:2,2:22.2:1:29.9:1:0.70738:1.72:60:28:0.4667:0:1.4 -9 139401646 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.06763;LSEQ=CTTGGCCTCACACAGGAAAA;RSEQ=GGGAGTTTCTGGCTGGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:69:66,3:100,10:0.3855:2,1:24.7:1:32.2:1:0.37542:2.19:60:138:0.3855:0:1.1 0/1:99:4:4,0:89,6:0.0404:2,0:21.8:1:32.3:1:1:0:60:8:0.0408:0:1 -9 139401658 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12295;SOR=Inf;LSEQ=CAGGAAAATGGGAGTTTCTG;RSEQ=CTGGTTCCTGGATGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:209,16:0:2,0:24.3:1:31.1:1:1:0:60:44:1:0:0.5 0/1:122:2:1,1:108,12:0.0164:2,2:25.5:1:30.5:1:0.20255:8.68875:60:4:0.0165:0:1 -9 139401686 . C T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05651;SOR=Inf;LSEQ=CTGGATGCCTCTGGCCGGTC;RSEQ=CGGGGTGCCTGCCCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:305,74:0:2,0:22.8:1:30.6:1:1:0:60:93.75:1:0:0.3 0/1:237:3:1,2:175,59:0.0127:2,2:9.7:1:23.3:1:0.16345:5.87765:60:2:0.0087:0:1.7 -9 139401725 . C T 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08848;SOR=6.91044;LSEQ=CCTGCCCTGGCCATGGATGG;RSEQ=CAACACCAGCCCTCCGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:671:1:0,1:426,242:0.0015:2,0:25:0:26:0:0.36323:0:60:2:0.0015:0:1 0/1:489:5:1,4:291,193:0.0102:2,2:14.6:1:26.8:1:0.16302:6.01051:60:10:0.0104:0:1 -9 139401920 . G A 62 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23634;SOR=0.25154;LSEQ=GACAGAACGAGGGGCCCTTC;RSEQ=GCTCAGCCGGCGCCAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:5:3,2:98,290:0.0127:2,2:10.6:1:27:1:0.10967:4.42:60:4:0.0104:0:2.4 0/0:310:1:1,0:90,219:0.0032:2,0:1:0:25:0:0.29355:0:60:2:0.0033:0:1 -9 139401947 . TC T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14604;SOR=Inf;LSEQ=CCGGCGCCAGGATGCAGTGC;RSEQ=CCACACCCCACTGTGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:31,201:0:2,0:23.2:1:31:1:1:0:60:32.143:1:0:0.2 0/1:144:2:1,1:14,128:0.0139:2,2:8:1:29.8:1:0.19814:8.87:60:4:0.0141:0.0069:0 -9 139401969 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52707;SOR=0;LSEQ=CCACACCCCACTGTGAGGGC;RSEQ=GACAGGGCCACATGAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:13,137:0.0132:2,2:25.5:1:31.5:1:0.17628:10.19:60:4:0.0134:0:1 0/0:93:0:0,0:5,88:0:2,0:22.4:1:30:1:1:0:60:92:1:0:0.1 -9 139402218 . CT C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06314;SOR=Inf;LSEQ=TTCTCAGTATAGGTACCCTC;RSEQ=TCAGGCTTTCCACAGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:64,6:0:2,0:23.1:1:31.3:1:1:0:60:140:1:0:0 0/1:24:2:1,1:22,0:0.0833:1,2:12.5:1:26.6:1:0.08333:0:60:4:0.0833:0.0417:0 -9 139402663 . T C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1159;LSEQ=TGATGGGCTGGGACCCGAGC;RSEQ=GGGTGGGCACAGCAGGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:620:574:277,297:21,24:0.9258:2,2:25.5:1:29.8:1:0.8778:1.07:60:37.267:0.927:0:1.1 1/0:425:251:128,123:91,83:0.5906:2,2:25.1:1:29.3:1:0.84364:1.0534:60:40.833:0.5889:0:1.2 -9 139402880 . AT A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12211;SOR=Inf;LSEQ=TGGGTGCCCGCGCCCCGGCC;RSEQ=TTCCCCGGTAGCTCAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:62,198:0:2,0:21.6:1:30.2:1:1:0:60:85.667:1:0:0.6 0/1:257:3:2,1:73,181:0.0117:2,2:19.3:1:27.3:1:0.20477:4.92:60:6:0.0119:0.0039:0.7 -9 139402908 . T C 205 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02313;LSEQ=GGTAGCTCAGAACGCACATC;RSEQ=GCCAAGGGGCCTACTCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:125:123:16,107:0,2:0.984:0,2:22.2:1:29.6:1:1:0:60:40:0.9836:0:1.3 1/0:142:83:16,67:12,47:0.5845:2,2:22.5:1:28.7:1:1:1.06864:60:40.5:0.5827:0:1.3 -9 139402959 . A G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.0202;LSEQ=ACCCATTCTACAGAAGTGGA;RSEQ=ACTGCCGCCCCTGGACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:28:1,27:0,25:0.5283:1,1:24.9:1:30.4:1:1:0:60:13:0.5098:0:1.8 1/0:45:24:3,21:1,20:0.5333:1,2:23.1:1:31.6:1:0.61099:2.80:60:48:0.5333:0:1.8 -9 139403102 . T C 135 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=TTCCCCAATTCCTGAGCTCC;RSEQ=GCCCCGGCTCCAGAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:15,5:0,0:1:0,2:18.2:1:31.4:1:1:0:60:40:1:0:1 1/0:2:1:0,1:1,0:0.5:0,0:1:0:29:0:1:0:60:2:0.5:0:1 -9 139403235 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54576;SOR=0;LSEQ=GACCCCGAGCCGACACAGTG;RSEQ=GACCTGGGGTGACCGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:139,18:0.0126:2,2:12.5:1:29:1:0.22538:7.54319:60:4:0.0129:0:2 0/0:84:0:0,0:76,8:0:2,0:23.5:1:30.8:1:1:0:60:27:1:0:0.7 -9 139403240 . T TG 200 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.90213;SOR=0.96494;LSEQ=CGAGCCGACACAGTGGGACC;RSEQ=GGGGTGACCGTTCCCACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:80:68,12:87,12:0.4469:2,2:22.2:1:31.7:1:0.66086:1.27763:60:79:0.4489:0.0782:1.1 0/1:105:46:38,8:49,10:0.4381:2,2:22.9:1:31.8:1:1:1.03129:60:92:0.46:0.0952:1.1 -9 139403268 . T C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1169;LSEQ=CCGTTCCCACCTCCCGCAGG;RSEQ=AGGCACCCACCCAGGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:266:242:191,51:17,7:0.9098:2,2:25.9:1:32:1:0.43538:1.54:60:79.667:0.9122:0:1.6 1/0:189:102:75,27:61,26:0.5397:2,2:23.7:1:31.7:1:0.62888:1.18:60:101:0.5372:0:1.3 -9 139403280 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0;SOR=0.144;LSEQ=CCCGCAGGTAGGCACCCACC;RSEQ=AGGGCCCCTCCTTCGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:145:113,32:135,64:0.4203:2,2:25.6:1:30.3:1:0.05115:1.67:60:47.333:0.4226:0:1.9 0/1:244:23:16,7:146,75:0.0943:2,2:22.1:1:29.5:1:0.82001:1.17:60:22:0.0913:0:2 -9 139403554 . T C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07178;LSEQ=GTGGGCAGGCGGGGGCTGAG;RSEQ=GGAGGGCATTGGTGGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:382:360:68,292:4,16:0.9424:2,2:23.6:1:30.2:1:1:1.07334:60:179:0.9471:0:1.1 1/0:282:152:32,120:30,100:0.539:2,2:21.1:1:30.2:1:0.77321:1.12453:60:151:0.5393:0:1.1 -9 139403591 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11771;SOR=Inf;LSEQ=TCCCCGCTCCAGCAGATTCT;RSEQ=CCTCGCCAGCACCTCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:10,192:0:1,0:22.5:1:32.1:1:1:0:60:49.5:1:0:0.9 0/1:106:2:0,2:8,96:0.0189:2,0:16:1:27:1:1:0:60:4:0.0192:0:1.5 -9 139403661 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.08006;SOR=Inf;LSEQ=GACAGGCCCAGGGCAGCCTG;RSEQ=CTGACCCAGGGAGGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:1,56:0:1,0:26.3:1:32.4:1:1:0:60:56:1:0:0.1 0/1:23:2:1,1:1,20:0.087:1,2:29.5:1:27.5:1:0.16996:14.49:60:4:0.0952:0:1 -9 139404118 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17003;SOR=Inf;LSEQ=CGCCTGCATGGTGTGCCAGG;RSEQ=TGCCAGCTACTGCGTGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:152,24:0:2,0:26:1:32.4:1:1:0:60:352:1:0:0.1 0/1:124:2:1,1:101,21:0.0161:2,2:23.5:1:29:1:0.32455:4.7222:60:4:0.0161:0:1.5 -9 139404479 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11317;SOR=Inf;LSEQ=ACACCTGCGGGAGGGGGCCG;RSEQ=GAAGGCTGCATGGCTGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:29,187:0:2,0:23.9:1:30.7:1:1:0:60:42.2:1:0:0.1 0/1:110:2:1,1:12,95:0.0182:2,2:15:1:28.5:1:0.22528:7.65:60:4:0.0187:0:1 -9 139404895 . C T 108 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06786;SOR=0.13788;LSEQ=GGGCTCTCGTGACTCTTCCG;RSEQ=GAAGTGCAGGGAGGAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:12,1:19,0:0.4063:1,1:28:1:29.4:1:0.40625:0:60:12:0.4:0:1 0/1:12:1:1,0:10,1:0.0833:2,0:4:0:27:0:1:0:60:2:0.0833:0:3 -9 139404988 . C T 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=ACACCTGACCCAACCCTCCC;RSEQ=GGCCACACTCCGGCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:152,7:0:1,0:24.7:1:31.1:1:1:0:60:78.5:1:0:0.1 0/1:93:9:9,0:80,4:0.0968:1,0:19.9:1:31.4:1:1:0:60:18:0.0968:0:1.2 -9 139405093 . G A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.08571;LSEQ=CTGGAGGAGGCCAGAGCCGC;RSEQ=GGGCTACTCACTGGGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:876:478:282,196:226,168:0.5457:2,2:27.3:1:30.5:1:0.62985:1.07:60:118.5:0.5499:0:1.1 0/1:719:67:39,28:361,290:0.0932:2,2:27.9:1:29.2:1:0.69997:1.12:60:15.75:0.0894:0:1.1 -9 139405261 . C T 242 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03005;SOR=1.3099;LSEQ=GACCTCACAGGTCTGCCCTG;RSEQ=GGGGCAGGAGGAGGCCGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:264:90,174:121,216:0.4393:2,2:25.7:1:30.1:1:0.6674:1.08287:60:65:0.4384:0:1.1 1/0:460:233:85,148:94,133:0.5065:2,2:25.2:1:29.4:1:0.29375:1.23004:60:28.125:0.5:0:1.1 -9 139405307 . A G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26695;SOR=0;LSEQ=CCAGCGGCCCCTGGCCCTCC;RSEQ=GGCCCTTCCCAGGCTGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:55,226:0.0106:2,2:31:1:32:1:0.48392:2.05:60:6:0.0106:0:1.7 0/0:207:0:0,0:54,153:0:2,0:22.5:1:30.2:1:1:0:60:102.5:1:0:0.7 -9 139405361 . A G 215 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01448;LSEQ=GCCTCTCCCGACCCAGGAGT;RSEQ=GGCTTCCGTGACCCCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:114:113:12,101:0,0:0.9912:0,2:25.9:1:31.6:1:1:0:60:55.5:0.9911:0:1.1 1/0:65:40:2,38:2,23:0.6154:2,2:25.3:1:30.9:1:0.63518:1.63891:60:80:0.6154:0:1.2 -9 139405475 . C T 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=TCCTGATTCCAGAACTTCTC;RSEQ=GACCAGGGCCTCCTCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:128,20:0:2,0:24.9:1:31.2:1:1:0:60:48.333:1:0:1 0/1:56:7:6,1:46,3:0.125:2,2:17:1:30.6:1:0.42314:2.49898:60:14:0.1273:0:1.7 -9 139405501 . A G 233 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00969;LSEQ=GGGCCTCCTCAGCACCCACC;RSEQ=GCTCCTCTTCAAAGACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:225:224:202,22:0,0:0.9956:0,2:23:1:29.9:1:1:0:60:111:0.9955:0:1.1 1/0:91:62:57,5:29,0:0.6813:1,2:25.1:1:29.7:1:0.17337:0:60:61:0.6854:0:1.2 -9 139405530 . C T 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00167;SOR=Inf;LSEQ=TCAAAGACTCATCTAGCCTG;RSEQ=CTGGGAGCTGCCTGTGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:312,64:0:2,0:22.8:1:31.6:1:1:0:60:52.714:1:0:0.6 0/1:200:6:4,2:160,34:0.03:2,2:23.2:1:29.7:1:0.29495:2.3403:60:12:0.0308:0:1.3 -9 139406334 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCTGGCAAAGGCTATGT;RSEQ=GGAACCACGTGCACAGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:25:1:32:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139407359 . G GC 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTCACGGCTTCCCAGGCC;RSEQ=CCCCCACCCCTGGCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:106,3:0.018:1,2:16:1:34:0:0.07109:30.75138:60:4:0.0198:0:0 0/0:33:0:0,0:30,3:0:2,0:24.8:1:28.2:1:1:0:60:15.5:1:0:1.8 -9 139407438 . C T 41 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18053;LSEQ=CGCCCCTCCCACATAGGCCC;RSEQ=GCCCCCTCCAGCACAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:3:0,3:241,92:0.0089:2,0:9.7:1:25.7:1:0.02209:0:60:6:0.0092:0:2 0/1:285:3:1,2:195,87:0.0105:2,2:15:1:26.3:1:0.2308:4.45649:60:6:0.0107:0:1.3 -9 139407447 . C T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48118;SOR=1.95892;LSEQ=CACATAGGCCCCGCCCCCTC;RSEQ=AGCACAGGCCCCACCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:3:0,3:248,131:0.0078:2,0:8:1:19.3:1:0.04254:0:56:2:0.0053:0:3.7 0/1:328:5:2,3:201,122:0.0152:2,2:6.8:1:24.2:1:0.37319:2.46422:60:4:0.0124:0:2.4 -9 139407452 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.12294;LSEQ=AGGCCCCGCCCCCTCCAGCA;RSEQ=AGGCCCCACCCACCCCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:435:375:243,132:33,23:0.8621:2,2:21.7:1:27.4:1:0.45563:1.28:60:6.813:0.8651:0:1.6 0/1:362:157:95,62:127,77:0.4337:2,2:21.5:1:27.7:1:0.74465:1.0762:60:11.077:0.4235:0:1.5 -9 139407610 . G A 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00595;SOR=Inf;LSEQ=GAGGGAAGGGGACAGCACTC;RSEQ=GCATGTCCAGCACTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:690:0:0,0:274,415:0:2,0:23.8:1:30.1:1:1:0:60:42.063:1:0:0.1 0/1:514:6:5,1:190,317:0.0117:2,2:5.3:1:26.5:1:0.03174:8.31:60:12:0.0118:0:1.2 -9 139407932 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.06165;LSEQ=CAAGGGTTGGATTCACACTC;RSEQ=TTGTTGTTGATGTCACAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1067:62:29,33:479,525:0.0581:2,2:22.8:1:31.2:1:0.89668:1.0382:60:124:0.0592:0:1.1 0/1:1062:407:194,213:308,347:0.3832:2,2:26.5:1:30.2:1:0.84978:1.03:60:57.143:0.3817:0:1.2 -9 139408016 . G A 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32228;SOR=3.92105;LSEQ=GGGGGACCACACTGCAGGTC;RSEQ=AGGGAGGCCCGAGCAGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:1,0:73,295:0.0027:2,0:1:0:25:0:0.20054:0:60:2:0.0028:0:2 0/1:284:3:1,2:75,206:0.0106:2,2:11.7:1:29:1:1:1.37:60:6:0.0108:0:1.3 -9 139408756 . A G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCATGCAGCCCACAAGGAC;RSEQ=CGCAGCACACAGCTGCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:18,0:0,0:1:0,1:23.8:1:30.8:1:1:0:60:36:1:0:1.3 1/1:2:2:2,0:0,0:1:0,0:32:1:30.5:1:1:0:60:4:1:0:1 -9 139408840 . C A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGAGGGGAGCTCCCTGCCA;RSEQ=CCAGCCCCGTCCGAGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:59,0:0.0328:1,2:19:1:28.5:1:0.03279:0:60:4:0.0328:0:1.5 0/0:21:0:0,0:21,0:0:1,0:24:1:31.2:1:1:0:60:20:1:0:0.1 -9 139408892 . C T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00379;LSEQ=TCTCAAGCTCTGTGCAGGTG;RSEQ=CACCCTCCTGGCAGCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:150:139:124,15:11,0:0.9267:0,2:24.8:1:29.8:1:0.60315:0:60:45.333:0.9252:0:1.1 0/1:70:3:2,1:55,12:0.0429:2,2:16.7:1:29.7:1:0.46547:2.25824:60:6:0.0429:0:1 -9 139409648 . G A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15464;SOR=2.08261;LSEQ=CCCAGGTGGGCAGCACCAAA;RSEQ=CCCTCACCCAACCCCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:9:8,1:86,5:0.09:2,2:25.6:1:29:1:0.44083:2.12854:60:18:0.0918:0:1 0/1:70:12:9,3:48,10:0.1714:2,2:21:1:29.8:1:0.6834:1.58823:60:24:0.1739:0:1.1 -9 139409676 . G T 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07782;SOR=0;LSEQ=CCAACCCCTCAGCAGCCCCA;RSEQ=GGCAGAGTGGCTGACCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:5:3,2:134,29:0.0298:2,2:15:1:26:1:0.22975:3.05342:60:4:0.0247:0:2.4 0/0:120:0:0,0:92,28:0:2,0:23.9:1:31.3:1:1:0:60:119:1:0:0.2 -9 139409694 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16213;SOR=Inf;LSEQ=CAGGGCAGAGTGGCTGACCT;RSEQ=GACCTCTGAGCACAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:178,68:0:2,0:22.8:1:29.7:1:1:0:60:60.5:1:0:0.2 0/1:167:2:1,1:118,47:0.012:2,2:30:1:27.5:1:0.49347:2.49486:60:4:0.012:0:1 -9 139409943 . C A 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0101;SOR=Inf;LSEQ=CTGGCCGGCCACCTGTGGTC;RSEQ=CCTTCAGGCAGAAGCAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:0:0,0:378,305:0:2,0:25.3:1:30.7:1:1:0:60:28.696:1:0:0.2 0/1:596:6:3,3:318,268:0.0101:2,2:33.3:1:25:1:1:1.18622:60:2:0.0069:0:1 -9 139410177 . T C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=9.73557;LSEQ=TCCCCGTGTACCCTGGACCG;RSEQ=GGGAGGGGCGGGCACAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:28:11,17:78,188:0.0946:2,2:21.6:1:30.3:1:0.28489:1.56:60:56:0.0976:0:1.1 1/0:174:88:24,64:18,68:0.5057:2,2:24.4:1:29.2:1:0.37762:1.41:60:21:0.5:0:1.1 -9 139410211 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54734;SOR=0;LSEQ=ACAGGAAGACTTAGGACTGG;RSEQ=GGCCCCCGGGACACCCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:50,122:0.0115:2,2:15.5:1:28.5:1:0.50149:2.43:60:4:0.0118:0:1 0/0:91:0:0,0:20,71:0:2,0:23.1:1:29.1:1:1:0:60:17.2:1:0:0.6 -9 139410218 . C G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.55269;SOR=0;LSEQ=GACTTAGGACTGGCGGCCCC;RSEQ=GGGACACCCATGACCAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:1,2:43,109:0.0194:2,2:12.7:1:31.3:1:1:1.27:60:6:0.0196:0:1 0/0:76:0:0,0:17,58:0:2,0:22.9:1:29.6:1:1:0:60:150:0.9868:0:0.6 -9 139410300 . TGGGGCTGA T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.34444;LSEQ=CATTCCCACCTACTCAGGAT;RSEQ=GCTGTGCTCTCGGCCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:7:4,3:99,31:0.0511:2,2:17.1:1:31.3:1:0.36461:2.37724:60:14:0.0515:0.0146:0 0/1:67:27:26,1:34,6:0.403:2,1:23.9:1:31.6:1:0.22765:4.50:59.8:54:0.4091:0.0896:0.2 -9 139410424 . A G 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=426.25485;LSEQ=CCTCCCCGCTGGTGGGCGCC;RSEQ=GCCCGCACCTTCCGTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:869:384:232,152:295,185:0.4419:2,2:24.2:1:29.5:1:0.77909:1.04471:60:37.4:0.441:0:1.1 1/1:679:677:390,287:0,0:0.9971:0,2:25.9:1:29.3:1:1:0:60:51.077:0.9985:0:1.2 -9 139410437 . C T 125 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCGCCAGCCCGCACCTTC;RSEQ=GTGCACACACAGGTGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1009:0:0,0:588,421:0:2,0:24.7:1:30.3:1:1:0:60:111.111:1:0:0.5 0/1:787:20:9,11:423,343:0.0254:2,2:25:1:29.1:1:0.37379:1.50648:60:19:0.0245:0:1.8 -9 139410467 . G A 152 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=50.09952;LSEQ=CAGGTGTAAGTGTTGGGTCC;RSEQ=TCCAGGCACTTGGCACCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1262:1:1,0:656,604:8e-04:2,0:1:0:26:0:1:0:60:2:8e-04:0:1 0/1:1045:40:21,19:517,488:0.0383:2,2:23.2:1:28.7:1:1:1.04:60:39:0.0378:0:1.7 -9 139410589 . A G 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.09802;LSEQ=AGGGAGTCATGTGCAACAGC;RSEQ=CTATGGCCCTTCAGGGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:113:17,96:21,152:0.3951:2,2:22.2:1:31.7:1:0.4819:1.28:60:55.5:0.3964:0:1 1/1:170:136:18,118:4,30:0.8:2,2:21.3:1:31.1:1:1:1.14:60:44.333:0.8012:0:1.2 -9 139410595 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13603;SOR=Inf;LSEQ=TCATGTGCAACAGCACTATG;RSEQ=CCCTTCAGGGACCCCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:17,232:0:2,0:22.4:1:32.1:1:1:0:60:61.25:1:0:0.4 0/1:146:2:1,1:16,127:0.0137:2,2:31.5:1:28:1:0.22146:7.73:60:4:0.0142:0:2 -9 139410679 . T C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=8e-04;SOR=10.70733;LSEQ=TCAGCCTGAGCTCAGCCAGC;RSEQ=CCAGCTCTCCCTGCCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:4:0,4:0,64:0.0588:1,0:25.5:1:27.3:1:1:0:60:3:0.0476:0:1 0/1:17:7:0,7:0,10:0.4118:0,0:29.9:1:32.3:1:1:0:60:14:0.4118:0:1.1 -9 139411479 . G A 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00075;SOR=Inf;LSEQ=GGGCAGGGGACACAATCCAC;RSEQ=GCCAGGCCCCCCTCAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:15,3:0:2,0:35.9:1:29.8:1:1:0:59.8:36:1:0:0.4 1/1:3:3:2,1:0,0:1:0,2:28.7:1:31.3:1:1:0:60:6:1:0:1.3 -9 139411619 . G A 41 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02902;SOR=Inf;LSEQ=CCCTCACCCCTCAGGAGGCC;RSEQ=GGGTGCAGATGGCCCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:136,6:0:1,0:24.3:1:30.1:1:1:0:60:70:1:0:0.1 0/1:64:3:3,0:61,0:0.0469:1,0:42:1:26:1:1:0:60:2:0.0328:0:2.7 -9 139411622 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=21.74701;LSEQ=TCACCCCTCAGGAGGCCGGG;RSEQ=TGCAGATGGCCCGGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:7:7,0:137,5:0.047:1,0:27.7:1:29.9:1:1:0:60:14:0.0476:0:1.1 1/0:67:35:35,0:32,0:0.5224:1,1:28.2:1:28.1:1:1:0:60:16.5:0.5156:0:1.3 -9 139411714 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.01073;LSEQ=CCGGGGGCAGGGGGCGGGGG;RSEQ=GGCCCTCACCCGTGGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:47:34,13:470,240:0.062:2,2:23.4:1:31:1:0.42856:1.34:60:22.5:0.0608:0:1.3 0/1:514:238:145,93:166,109:0.463:2,2:23.6:1:30.8:1:0.92792:1.02:60:118:0.4673:0:1.3 -9 139411880 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=14.4961;LSEQ=GGGGGGCACGCGCGGCCCCA;RSEQ=TGCCCCACTGGGCACAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:27:9,18:140,329:0.0544:2,2:22:1:29.1:1:0.67166:1.17:60:26:0.0535:0:1.1 0/1:373:170:52,118:62,140:0.4558:2,2:23.5:1:29.7:1:1:1.00493:60:84:0.4553:0:1.2 -9 139412073 . T C 165 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.98966;LSEQ=GCCTCAGTTTCCCCATGCCC;RSEQ=GTGCAGGCTGTGGGCCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:44:34,10:42,13:0.4444:2,2:24.8:1:30.3:1:1:1.05:60:43:0.4574:0:1.2 0/1:43:19:16,3:23,1:0.4419:1,2:28.4:1:31.1:1:0.30596:4.17195:60:38:0.4419:0:1.1 -9 139412105 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCAGAAGGCATGGAGG;RSEQ=TGGGGAAAGCGGAAGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:125,16:0.014:2,2:27:1:29.5:1:0.22437:7.60942:60:4:0.0145:0:1 0/0:67:0:0,0:62,5:0:2,0:26:1:31.9:1:1:0:60:66:1:0:0.3 -9 139412142 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18208;SOR=Inf;LSEQ=AACCCACAGATGTTCCCGGG;RSEQ=CTGCCCCTCCAAGGCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:227,37:0:2,0:22.1:1:31.3:1:1:0:60:43:1:0:0.8 0/1:197:2:0,2:159,36:0.0102:2,0:14.5:1:25:1:0.03641:0:60:4:0.0102:0:1.5 -9 139412182 . G A 233 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCCTCGACTCGGTTTCCC;RSEQ=CCCTGGCCCCGGCCGACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:228:163,65:219,106:0.4116:2,2:23.7:1:29.8:1:0.35002:1.21:60:56:0.4118:0:2 0/0:447:0:0,0:293,154:0:2,0:26.1:1:30.2:1:1:0:60:48.667:1:0:0.6 -9 139412197 . G A 250 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49633;SOR=0.92017;LSEQ=TTCCCGCCCTGGCCCCGGCC;RSEQ=ACGCACCGGGCATGCAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:329:217,112:235,144:0.4647:2,2:24.7:1:30:1:0.30801:1.19:60:163.5:0.4665:0:1.7 0/1:563:250:154,96:190,120:0.444:2,2:25.9:1:30:1:1:1.01:60:249:0.4462:0:1.2 -9 139412593 . C T 69 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73858;SOR=0.63478;LSEQ=CTGTGCTGGCACCTACCCAG;RSEQ=GAGCACTCATCCACGTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:6:2,4:320,166:0.0122:2,2:9.5:1:27:1:0.18856:3.84393:60:12:0.0123:0:1 0/0:386:3:2,1:241,141:0.0078:2,2:31.7:1:30.3:1:1:1.17:60:6:0.0079:0:1 -9 139412753 . G A 50 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0164;SOR=Inf;LSEQ=GGCACAGCAGACCTGGGCAG;RSEQ=CAGCGGCGGTCAGTGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:570:0:0,0:200,370:0:2,0:24.6:1:31.4:1:1:0:60:80.429:1:0:0.1 0/1:449:5:5,0:175,269:0.0111:2,0:13.8:1:21.6:1:0.01001:0:60:1.5:0.0068:0:2.2 -9 139412761 . G A 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03368;SOR=Inf;LSEQ=AGACCTGGGCAGGCAGCGGC;RSEQ=GTCAGTGGGCACGGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:0:0,0:168,329:0:2,0:25.1:1:30.3:1:1:0:60:70:1:0:0.1 0/1:374:4:2,2:139,231:0.0107:2,2:20.8:1:27.3:1:0.63421:1.66:60:8:0.0108:0:1.3 -9 139412777 . C A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06543;SOR=Inf;LSEQ=CGGCGGTCAGTGGGCACGGC;RSEQ=CCTGGGCCAGGCATGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:125,278:0:2,0:24.5:1:30.7:1:1:0:60:43.778:1:0:0.1 0/1:273:3:2,1:90,180:0.011:2,2:12.3:1:22.3:1:0.26335:3.98:60:2:0.0076:0:3 -9 139412853 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGGAGCTGCCCGCCGT;RSEQ=ACCCCGTCGGGCATCCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:2,0:24,111:0.0146:2,0:16.5:1:31.5:1:0.03489:0:60:4:0.0147:0:1 0/0:65:0:0,0:15,50:0:2,0:24.8:1:31:1:1:0:60:31.5:1:0:0.4 -9 139412884 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.94948;LSEQ=GCATCCCGTGACACTTGGGA;RSEQ=GTTCCGGGGGACTCACAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:6:5,1:46,64:0.0517:2,2:24:1:29.3:1:0.08537:6.85:60:5:0.0442:0:1 1/0:60:30:15,15:11,19:0.5:2,2:22.4:1:30.6:1:0.43482:1.71:60:60:0.5:0:1 -9 139413358 . C A 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55582;SOR=0;LSEQ=AAGACGCAGGGTGGCAATGC;RSEQ=GCCCCCTCCAGGAAGCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:3:1,2:14,235:0.0119:2,2:24.3:1:31.7:1:0.16878:8.23:60:6:0.012:0:1 0/0:141:0:0,0:11,130:0:2,0:7:0:19:0:1:0:60:0:0:0:2 -9 139413400 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCTGACTCCTCCACCCA;RSEQ=CGCCAGCCTAAATCACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:4,115:0.0165:1,2:26:1:31:1:0.08127:25.83:60:4:0.0167:0:1 0/0:55:0:0,0:2,53:0:1,0:22.8:1:31.7:1:1:0:60:110:1:0:0.1 -9 139413539 . C T 85 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAATTCCCGAACACAGGGC;RSEQ=TGTCTGTTCATCCAGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:1,6:0.4667:2,2:30.9:1:30.3:1:1:2.26:60:14:0.5833:0:1.1 0/0:1:0:0,0:0,1:0:0,0:19:0:34:0:1:0:60:2:1:0:0 -9 139413908 . C T 257 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01123;LSEQ=TACGCGCCTGTCCACTCTGG;RSEQ=GGGCAGCGGCAGTTGTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:996:412:248,164:336,247:0.4137:2,2:25.9:1:29.6:1:0.43331:1.11:60:136.333:0.4148:0:1.1 0/0:766:6:2,4:437,323:0.0078:2,2:9.7:1:25.8:1:0.41032:2.7024:60:5:0.0066:0:1.3 -9 139414065 . G A 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCCTGAGGTCCAGTCCG;RSEQ=CTCCTGCCTGGACCCCCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:89,274:0:2,0:23.1:1:31.3:1:1:0:60:35.3:1:0:0.1 0/1:253:22:7,15:56,175:0.087:2,2:18.8:1:29.8:1:0.44349:1.46:60:44:0.0891:0:1.1 -9 139414099 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12477;SOR=Inf;LSEQ=CCCCGACACACTGCTCTGGA;RSEQ=ACAAGAGCCTGGCCTCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:12,183:0:2,0:23.5:1:31.8:1:1:0:60:64:1:0:0.1 0/1:107:2:1,1:11,94:0.0187:2,2:22:1:27.5:1:0.21266:8.22:60:4:0.0189:0:1 -9 139415262 . G T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCTGCACCCCGGCTCC;RSEQ=AGGCAGATGGGGCCCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:0:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139417208 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCCCGCCATGGGCCCTC;RSEQ=CAGGGCTGCCCCTACACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:2,0:69,1:0.0278:1,0:35.5:1:30.5:1:1:0:60:4:0.0278:0:1 0/0:35:0:0,0:33,2:0:2,0:27.2:1:29.5:1:1:0:60:70:1:0:0 -9 139417277 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13699;SOR=Inf;LSEQ=CAGCCGGGGAGGGGCTCGTG;RSEQ=ACCCCGGCCAGCGGGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:234,97:0:2,0:25.5:1:31.8:1:1:0:60:40.375:1:0:0.2 0/1:195:2:1,1:129,63:0.0103:2,2:18:1:27:1:0.55211:2.03947:60:4:0.0104:0:1 -9 139417309 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.02563;SOR=Inf;LSEQ=CGGGCAGCACTACCTGGCAG;RSEQ=CAGGCACACTCGTGGGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:0:0,0:360,177:0:2,0:25.6:1:31.1:1:1:0:60:34.8:0.9962:0:0.2 0/1:361:4:2,2:230,126:0.0111:2,2:18.8:1:29.3:1:0.61792:1.82206:60:8:0.0111:0:1.3 -9 139418124 . C T 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65886;SOR=1.91507;LSEQ=GTTGCCTGGGCAGCTGGCGG;RSEQ=GGGCCTGGGTCTGCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:2:0,2:284,93:0.0053:2,0:1:0:26:0:0.06233:0:60:4:0.0054:0:1.5 0/1:298:3:1,2:212,82:0.0101:2,2:15.3:1:27:1:0.19383:5.13737:60:6:0.0103:0:1 -9 139418138 . C T 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.167;SOR=5.62853;LSEQ=TGGCGGCGGGCCTGGGTCTG;RSEQ=CCACCCCTCAGGCTGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:1:0,1:378,159:0.0019:2,0:1:0:26:0:0.2974:0:60:2:0.0019:0:1 0/1:385:4:2,2:256,124:0.0104:2,2:22.3:1:27.5:1:0.60033:2.06033:60:8:0.0105:0:1.3 -9 139418260 . A G 280 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06883;SOR=0.85733;LSEQ=CAGGGGTTGGTGAGGCAGGC;RSEQ=TTGTCCAGGGGTGTCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1327:585:297,288:376,365:0.4408:2,2:26.1:1:30.5:1:1:1.00:60:52.182:0.4409:0:1.2 0/1:1091:440:225,215:329,321:0.4033:2,2:24.2:1:30.1:1:0.90174:1.02:60:87:0.402:0:1.2 -9 139418466 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12586;SOR=Inf;LSEQ=GCCAGGGCAGTTAGTTCCCA;RSEQ=CTGCTTCCCCAGCGCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:54,247:0:2,0:20.4:1:30.6:1:1:0:60:26.364:1:0:0.3 0/1:166:2:1,1:31,133:0.012:2,2:44.5:1:28.5:1:0.34932:4.24:60:4:0.0125:0:1.5 -9 139418642 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=AACTTTGGGAATGTACTGAA;RSEQ=GCCACTGAATGAGGCTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:0:2,0:25:1:29.3:1:1:0:55.7:20:1:0:1 0/1:6:2:1,1:1,3:0.3333:2,2:32.5:1:31:1:1:2.45:60:4:0.3333:0:2 -9 139418661 . A G 81 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATGCCACTGAATGAGGCTGA;RSEQ=GCAGGAGAATCACTTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:0.6:0,2:19.2:1:31.5:1:1:0:49.5:12:0.6:0:1.8 1/0:5:3:1,2:1,1:0.6:2,2:37.3:1:30.3:1:1:1.7321:54.3:6:0.6:0:1.7 -9 139419951 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGCGGCCCGGGAAGGCAGC;RSEQ=GCCTCACGGCTCAGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29.5:1:1:0:60:4:1:0:1.5 -9 139420026 . G A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAACCGTCCCGCCTTCC;RSEQ=GAGCCCACCTGGGTGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:29:1:1:0:60:4:1:0:1 -9 139438653 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52661;SOR=0;LSEQ=GACCTGCACCCAGCCAAGGG;RSEQ=CATCGTCCGCCCCCTACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:13,154:0.0118:2,2:19:1:29.5:1:0.15927:11.45:60:4:0.012:0:1 0/0:104:0:0,0:11,93:0:2,0:18.9:1:31.9:1:1:0:60:103:1:0:0.1 -9 139440075 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2465;SOR=0;LSEQ=CTTTTCCCTCTCCATGCTGG;RSEQ=CTCCCCGCCGCCCGCTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:3:1,2:49,22:0.0405:2,2:11.7:1:27.3:1:0.24411:4.35573:60:6:0.0429:0:1 0/0:67:0:0,0:45,22:0:2,0:18:1:31:1:1:0:60:134:1:0:0.1 -9 139440112 . G A 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.35479;SOR=0.30603;LSEQ=CCCAGCCGTGGGGCGCGCGC;RSEQ=CCGGGCGCCGCCAAAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:3:1,2:92,80:0.017:2,2:23.7:1:27.7:1:0.60045:2.28938:60:2:0.0118:0:1.3 0/0:190:1:0,1:100,89:0.0053:2,0:38:0:31:0:0.47368:0:60:2:0.0054:0:1 -9 139440119 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59916;SOR=0.43155;LSEQ=GTGGGGCGCGCGCGCCGGGC;RSEQ=CCGCCAAAGTTTCCAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:106,93:0.01:2,2:5.5:1:29:1:1:1.13904:60:4:0.0101:0:1.5 0/0:232:1:0,1:121,110:0.0043:2,0:1:0:23:0:0.47845:0:60:2:0.0043:0:1 -9 139440142 . C T 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37883;SOR=3.51687;LSEQ=GCCAAAGTTTCCAAAGGGCG;RSEQ=GGAAAGTGGGGGCTCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:1:0,1:154,156:0.0032:2,0:1:0:25:0:1:0:60:2:0.0033:0:1 0/1:356:4:1,3:179,172:0.0112:2,2:24:1:27:1:0.36593:3.11304:60:8:0.0116:0:1.3 -9 139440144 . G T 56 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08437;LSEQ=CAAAGTTTCCAAAGGGCGCG;RSEQ=AAAGTGGGGGCTCGCGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:4:1,3:160,161:0.0123:2,2:9.8:1:19.5:1:0.62274:2.97242:60:1:0.0063:0:1 0/1:375:5:1,4:185,185:0.0133:2,2:12.2:1:24.2:1:0.37173:3.98686:60:10:0.0137:0:1 -9 139440203 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0904;SOR=0;LSEQ=GCGGCGAGCGCGGGCAGCAG;RSEQ=GCCAGGCAGAGCAGGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:2,1:118,143:0.0114:2,2:37.3:1:24.7:1:0.59249:2.42:60:2:0.0077:0:2 0/0:323:0:0,0:146,176:0:2,0:26.3:1:30.2:1:1:0:60:52.667:0.9968:0:0.3 -9 139440261 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19831;SOR=0;LSEQ=CTCCCCACCGGCTGCCCTCT;RSEQ=CGCCCGGGCGGCGGCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:8,17:0.0741:2,2:39.5:1:31.5:1:1:2.06:60:4:0.0833:0:1.5 0/0:33:0:0,0:12,21:0:2,0:6:0:13:0:1:0:60:0:0:0:1 -9 139561715 . G C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTTACCCCAGCCTCTGCCCC;RSEQ=ACCCGAAGCCTGGCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1 -9 139562148 . T C 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTAGAATGTGTGCACCC;RSEQ=CCGCACGGTTCCTGCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:31:1:31:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139562460 . G C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=CACCAAGAGCTCTGGACAGC;RSEQ=TCACCCCCCCTGTGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:0.2222:0,0:37.5:1:30.5:1:1:0:60:4:0.2222:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:12:0:33:1:1:0:60:4:0.6667:0:1.5 -9 139562993 . C T 217 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=1.73539;LSEQ=GGGACTCCTGGGCTGACCCC;RSEQ=TCTCCACCCCCGCAGCCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1097:122:69,53:543,431:0.1112:2,2:25.4:1:30.3:1:0.92305:1.03:60:121:0.1118:0:1.1 0/1:891:159:95,64:403,329:0.1785:2,2:25.8:1:29.8:1:0.2915:1.21:60:158:0.1795:0:1.1 -9 139563144 . C A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39096;LSEQ=CGGTGAGTGCCCCACCACAC;RSEQ=GAGCTCACCCAGCCCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:244:70,174:91,219:0.4404:2,2:25:1:30.8:1:0.92495:1.03283:60:80.333:0.4422:0:1.1 0/1:353:83:23,60:78,191:0.2351:2,2:25.1:1:30.6:1:0.89004:1.06515:60:166:0.2392:0:1.1 -9 139563893 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCACCGGAAGGCCCAGG;RSEQ=AGGGAAACGGCTGTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:2,0:102,0:0.0192:1,0:32:1:31.5:1:1:0:60:4:0.0196:0:1 0/0:44:0:0,0:43,1:0:1,0:22.3:1:31.5:1:1:0:60:21:1:0:0.1 -9 139564192 . G A 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14962;SOR=3.74225;LSEQ=AGGTGAGGGCTATGTCCCTC;RSEQ=GCGCCCGGTGTTAGGAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:2:2,0:267,426:0.0029:2,0:1:0:25.5:1:0.14947:0:60:4:0.0029:0:1 0/1:561:6:5,1:223,331:0.0107:2,2:14.3:1:23.8:1:0.04349:7.40:60:5:0.0091:0:1 -9 139564321 . G A 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.036;SOR=Inf;LSEQ=AGCAGCTGCCCCCACAGGGT;RSEQ=CTGGGGACCCAACTGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:0:0,0:240,196:0:2,0:25.8:1:31.8:1:1:0:60:47.444:1:0:0.1 0/1:338:4:2,2:193,141:0.0118:2,2:17.3:1:29:1:1:1.36748:60:8:0.0121:0:1.3 -9 139564474 . C G 194 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.44317;LSEQ=CCAGTCAGGTGAGGCTGGCT;RSEQ=TACCCTGGGGGGCCCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:27:12,15:180,218:0.0635:2,2:22.9:1:31.9:1:1:1.03204:60:54:0.0646:0:1.3 0/1:319:74:32,42:109,136:0.232:2,2:22.8:1:31.4:1:0.89422:1.05178:60:148:0.2349:0:1.1 -9 139564668 . G A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28999;LSEQ=GCGGCTGTCCCCAGCGCTGC;RSEQ=TCAACACCGCCGGCAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:871:349:184,165:275,247:0.4007:2,2:26.2:1:30.6:1:1:1.00:60:86.25:0.4012:0:1.1 0/1:764:124:61,63:327,312:0.1623:2,2:25.8:1:29.6:1:0.69582:1.08232:60:61:0.1631:0:1.2 -9 139564818 . G A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57023;SOR=2.90337;LSEQ=TGTGCCTGGCCTGGGGAGGC;RSEQ=GGCAGGCAGTGGACATTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:1:1,0:60,215:0.0036:2,0:1:0:25:0:0.22101:0:60:2:0.0036:0:1 0/1:191:2:1,1:47,142:0.0105:2,2:24.5:1:28:1:0.44045:3.00:60:4:0.0106:0:1 -9 139565150 . A G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69439;SOR=1.62423;LSEQ=TCCACGGCACCGCATCGAAA;RSEQ=CGCCGCTGAGACCTCAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:14:14,0:20,3:0.3784:2,1:21.3:1:32.1:1:0.27477:0:60:28:0.3889:0:1 1/0:8:4:3,1:4,0:0.5:0,2:12:1:30.5:1:1:0:60:8:0.5:0:1 -9 139565285 . C T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11518;SOR=1.50879;LSEQ=CGCCAGGCAGGCAGCGGGGG;RSEQ=GGCAGAGGCCTGGGCCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:38:35,3:214,23:0.1377:2,2:27.6:1:30.3:1:1:1.25:60:76:0.1418:0:1.1 0/1:175:34:31,3:127,12:0.1943:2,2:26.7:1:30.1:1:1:1.02405:60:68:0.1965:0:1.1 -9 139565475 . TTGG T 132 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08784;LSEQ=CTGCTGGAGGAGGTGAGGCA;RSEQ=TGGGGGGGGGGGGGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:939:32:5,27:468,388:0.0341:2,2:31.3:1:26.5:1:1e-05:6.50104:59:5.4:0.0372:0:3.7 0/0:972:3:1,2:461,474:0.0031:2,2:38.3:1:23.3:1:1:1.94381:60:2:0.0025:0:3.3 -9 139565582 . CG C 94 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00385;SOR=11.71646;LSEQ=TGCTGGAGGAGGTGAGGCAT;RSEQ=GGGGGGTAGGCAGGCAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:596:1:0,1:246,347:0.0017:2,0:26:0:27:0:1:0:57:2:0.0018:0:2 0/1:517:10:4,6:230,276:0.0193:2,2:17.4:1:28.3:1:1:1.24947:48.3:20:0.0202:0.0077:0.4 -9 139565644 . G A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21398;SOR=1.51502;LSEQ=GGTGAGGCGTCGGGGGGGCA;RSEQ=GCAGTCCAGGGTGGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:413:19:10,9:185,207:0.046:2,2:34.2:1:25.7:1:0.64784:1.24:40.3:2.167:0.0346:0:2.1 0/1:367:25:11,14:151,188:0.0681:2,2:35.4:1:26:1:1:1.02218:49.8:2.571:0.0525:0:2 -9 139565682 . C T 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.34007;SOR=3.51493;LSEQ=TGCTGGAGGAGGTGAGGCGT;RSEQ=GGGGGGGCAGGCAGTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:1:0,1:174,146:0.0031:2,0:6:0:14:0:0.45794:0:60:0:0:0:5 0/1:279:3:0,3:136,135:0.0108:2,0:15:1:23.3:1:0.24729:0:39:2:0.0082:0:2.3 -9 139565683 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=7.000;MSILEN=1;SSF=0;SOR=0.06219;LSEQ=GCTGGAGGAGGTGAGGCGTC;RSEQ=GGGGGGCAGGCAGTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:323:246:136,110:35,36:0.7616:2,2:23.9:1:28.3:1:0.41814:1.27:52.4:6.235:0.7794:0:1.7 0/1:285:47:26,21:115,123:0.1649:2,2:23.2:1:27.5:1:0.42648:1.32:52.3:4.875:0.1489:0:1.9 -9 139565692 . G A 142 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=3.62479;LSEQ=GGTGAGGCGTCGGGGGGGCA;RSEQ=GCAGTCCAGGGTGGACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:13:8,5:147,138:0.0435:2,2:14.5:1:25.3:1:0.57666:1.50:39.6:3.333:0.0355:0:1.9 0/1:254:36:19,17:108,110:0.1417:2,2:20.6:1:27.6:1:0.85747:1.14:50.9:11:0.1392:0:1.4 -9 139565694 . C T 43 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0.78605;LSEQ=TGAGGCGTCGGGGGGGCAGG;RSEQ=AGTCCAGGGTGGACCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:156,140:0.01:2,2:6.3:1:27.7:1:0.60573:2.2228:60:6:0.0112:0:2 0/0:254:2:0,2:124,127:0.0079:2,0:1:0:25.5:1:0.49821:0:41.5:4:0.0089:0:1 -9 139565711 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08428;SOR=Inf;LSEQ=AGGCAGTCCAGGGTGGACCT;RSEQ=CTGGAGGAGATGAGGCGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:153,142:0:2,0:22.1:1:30:1:1:0:54.6:8.833:0.9962:0:1.7 0/1:236:3:2,1:110,123:0.0127:2,2:17.7:1:22.3:1:0.60512:2.23:60:2:0.0093:0:2.3 -9 139565721 . A G 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21818;SOR=1.58003;LSEQ=GGGTGGACCTGCTGGAGGAG;RSEQ=TGAGGCGTCGGGGGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:16:5,11:144,134:0.0539:2,2:18.3:1:23.2:1:0.12819:2.35753:38.8:1.286:0.0391:0:3.4 0/1:230:19:6,13:105,101:0.0826:2,2:17.5:1:24.3:1:0.14948:2.24465:45.3:2.167:0.0688:0:2.9 -9 139565730 . C CG 145 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=7.18243;LSEQ=TGCTGGAGGAGATGAGGCGT;RSEQ=GGGGGGGGAGGCAGGCAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:6:5,1:148,137:0.02:2,2:32.5:1:27.3:1:0.21766:4.61:56.5:12:0.0241:0:1.2 0/1:234:30:18,12:101,96:0.1282:2,2:28.1:1:29.6:1:0.435:1.42:58.1:60:0.1493:0:1.1 -9 139565735 . GGGGA G 110 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.0368;SOR=2.50383;LSEQ=GAGGAGATGAGGCGTCGGGG;RSEQ=GGCAGGCAGTCCAGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:9:4,5:163,152:0.0277:2,2:18.3:1:29.7:1:0.74393:1.33924:46.4:8:0.0263:0.0062:1.9 0/1:240:16:10,6:120,104:0.0667:2,2:13.4:1:27.6:1:0.60674:1.44:55.5:7:0.0633:0.0417:2 -9 139565738 . G T 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45681;SOR=1.89153;LSEQ=GAGATGAGGCGTCGGGGGGG;RSEQ=AGGCAGGCAGTCCAGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:3:1,2:164,149:0.0093:2,2:6.7:1:17.7:1:0.60781:2.19603:56.7:0.5:0.0035:0:2 0/1:230:4:3,1:118,101:0.0174:2,2:8.3:1:25.8:1:0.62712:2.56:60:3:0.0145:0:3 -9 139565742 . C T 31 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.08503;SOR=Inf;LSEQ=TGAGGCGTCGGGGGGGGAGG;RSEQ=AGGCAGTCCAGGGTGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:164,160:0:2,0:23.9:1:30.3:1:1:0:56.3:11:0.9933:0:1.7 0/1:260:3:1,2:136,120:0.0115:2,2:14.3:1:20:1:0.60291:2.25973:49.7:2:0.0086:0:1.7 -9 139565778 . A G 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACCTGCTGGAGGAGGTGAG;RSEQ=CGTCGGCAGGGGGCAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:310:130,180:0,0:1:0,2:27:1:31.1:1:1:0:57.6:22.846:1:0:1.6 1/1:246:212:89,123:16,17:0.8618:2,2:28.1:1:30.6:1:0.5713:1.2993:57.8:29.286:0.8613:0:1.6 -9 139565815 . C A 23 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.38005;LSEQ=GTCTTCACAACAGCAGAGGC;RSEQ=CAGGCCCGGGTACAGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:2:2,0:67,153:0.009:2,0:1:0:26:1:0.09563:0:60:4:0.0097:0:2 0/1:162:2:1,1:59,101:0.0123:2,2:28.5:1:23:1:1:1.71:60:4:0.0132:0:2 -9 139565820 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50831;SOR=0;LSEQ=CACAACAGCAGAGGCCCAGG;RSEQ=CCGGGTACAGGCTCCGTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:53,141:0.0102:2,2:13.5:1:31:1:0.47614:2.64:60:4:0.0106:0:2 0/0:148:0:0,0:52,96:0:2,0:23.5:1:29.5:1:1:0:59.8:15.444:1:0:1.1 -9 139565987 . A AC 93 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.27273;SOR=0;LSEQ=GCAGCTGGACACTGACCAGG;RSEQ=CCCCCCAGGGCCGGAGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:1,1:0.8:2,0:29.6:1:31.3:1:0.2:0:60:16:0.8:0.1:0 0/0:1:0:0,0:0,1:0:0,0:28:0:32:0:1:0:60:2:1:0:0 -9 139566232 . C A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAAGCTTTTCTGCCACGG;RSEQ=AGCCCCCTCTAGTGGACACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:31,0:0.0606:1,2:17:0:30.5:1:0.06061:0:60:4:0.0606:0:1.5 0/0:12:0:0,0:12,0:0:0,0:31.7:1:32.3:1:1:0:60:24:1:0:0.3 -9 139566288 . G A 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.12047;LSEQ=GAGGCGGGGGCTGGAGGCTT;RSEQ=TGGAGCCCTTCCCAGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:50:47,3:43,3:0.5208:2,2:23.8:1:28.8:1:1:1.09:60:100:0.5208:0:1.1 0/1:35:4:4,0:26,5:0.1143:2,0:24.3:1:25.5:1:1:0:60:8:0.1176:0:1 -9 139566362 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11818;SOR=Inf;LSEQ=GGCCGGCCCAGGGTCACTGC;RSEQ=CTTCTGCACCCACAGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:237,97:0:2,0:25.6:1:30.9:1:1:0:60:46.714:1:0:0.2 0/1:176:2:1,1:114,60:0.0114:2,2:16:1:32:0:1:1.89268:60:4:0.0114:0:1 -9 139566421 . A G 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17447;SOR=5.1655;LSEQ=ACTGCACAGCCTGGCCTCGC;RSEQ=GGCACTGGAGCATGGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:1:1,0:285,191:0.0021:2,0:39:0:28:0:1:0:60:2:0.0021:0:1 0/1:372:4:2,2:223,144:0.0108:2,2:36.5:1:31:1:0.64787:1.54668:60:8:0.0109:0:1.3 -9 139566548 . C A 105 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.00162;SOR=8.08854;LSEQ=CAGCTGGGGTCCTGTGAGTG;RSEQ=CCCCACCCTCCAGAGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:789:2:1,1:380,407:0.0025:2,2:27.5:1:13.5:1:1:1.07:60:0:0:0:5 0/1:595:12:5,7:286,297:0.0202:2,2:22.5:1:29.4:1:0.77277:1.34747:60:24:0.0206:0:1 -9 139566748 . G A 159 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=24.65275;LSEQ=AAGACTCGTGACTGCCCAGC;RSEQ=CCCCAGGCTGGACTGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1092:2:2,0:514,573:0.0018:2,0:23:1:19.5:1:0.22428:0:60:1:9e-04:0:2 0/1:1039:45:20,25:478,514:0.0433:2,2:25.4:1:29:1:0.65018:1.16228:60:21.5:0.0425:0:1.2 -9 139566823 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.45842;LSEQ=AACATGCTGGGGGTCCAGAA;RSEQ=CCACCTCGGGGTGACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:452:282:71,211:39,128:0.6239:2,2:23.9:1:31.9:1:0.73369:1.10:60:55.4:0.6211:0:1.2 1/1:371:316:87,229:15,40:0.8518:2,2:23.5:1:31.5:1:1:1.01:60:315:0.8537:0:1.1 -9 139566889 . G A 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.03072;LSEQ=TCTTCCTCCTCCCCTTCCTC;RSEQ=GGAGGCTCCCCAGACCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:8:0,8:1,126:0.0593:1,0:27.9:1:31.6:1:1:0:60:16:0.0611:0:1.8 0/1:82:5:0,5:0,77:0.061:1,0:14.4:1:32.4:1:1:0:60:10:0.0625:0:1.6 -9 139566996 . G A 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01129;SOR=0;LSEQ=GGCATCCCAAGGCCAGGTGG;RSEQ=CCCTCAGCTGAGGGAAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:0,3:0.85:0,1:22.9:1:28.8:1:1:0:60:16:0.8889:0:1.1 0/0:3:0:0,0:0,3:0:0,0:6:1:32:1:1:0:60:6:1:0:0 -9 139587610 . CA C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1918;SOR=Inf;LSEQ=CTGACTCCGTAGAACAAAAT;RSEQ=AATGGAAACACATCAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,19:0:2,0:27.3:1:29.8:1:1:0:60:68:1:0:0.8 0/1:27:2:1,1:13,12:0.0741:2,2:18.5:1:30.5:1:1:1.0801:60:4:0.0741:0.037:1.5 -9 139587632 . A G 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGAAACACATCAGCTAC;RSEQ=ACAGGAAATAACCTCTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:9,15:0,0:1:0,2:24.6:1:30.8:1:1:0:60:48:1:0:1.1 1/1:16:16:8,8:0,0:1:0,2:25.6:1:29.6:1:1:0:60:32:1:0:1.1 -9 139588349 . A C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TTGCCTCTGGGTAAGAGGTG;RSEQ=GGGTTAAGGTCCAGCAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:29:1:32:1:1:0:60:4:1:0:0.5 1/0:3:2:1,1:1,0:0.6667:0,2:9:0:33:1:1:0:60:4:0.6667:0:1.5 -9 139637087 . T C 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTGCGGGGCCCCTGTGC;RSEQ=GGAGGCTGCAGTGGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139637329 . C G 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03275;SOR=0;LSEQ=AGCACCAGCACCAGCACCAG;RSEQ=GCCAGCACCAGCAGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:4:2,2:28,28:0.0667:2,2:26.8:1:32.8:1:1:1:60:8:0.0667:0:1 0/0:79:0:0,0:35,44:0:2,0:27.4:1:30.5:1:1:0:58.4:158:1:0:0.1 -9 139637341 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.50103;SOR=Inf;LSEQ=AGCACCAGCGCCAGCACCAG;RSEQ=AGCCCCTGCCTCATCTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:29,31:0:2,0:29:1:32.2:1:1:0:60:59:1:0:0.4 0/1:73:2:1,1:29,42:0.0274:2,2:23.5:1:30:1:1:1.44:60:4:0.0278:0:1 -9 139637383 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49508;SOR=Inf;LSEQ=CTCCTCCCTCAGCCGCCAAG;RSEQ=CCAGTGTTTAAACCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:7,21:0:2,0:18.2:1:30.4:1:1:0:60:27:1:0:0.3 0/1:33:2:1,1:9,22:0.0606:2,2:9:1:27.5:1:0.52083:2.37:60:4:0.0606:0:1 -9 139792926 . T C 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63287;SOR=1.91506;LSEQ=CTGTGGGTTGGTTGTGTGGA;RSEQ=GCCAGCTGTGTGGTCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:27.4:1:33:1:1:0:60:10:0.5:0:2 1/0:6:4:4,0:1,1:0.6667:2,0:33.5:1:29.5:1:0.33333:0:60:8:0.6667:0:1 -9 139793211 . AC A 109 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.52476;SOR=1.37327;LSEQ=TCATGGCTGCAGCTAGCGTG;RSEQ=CCCCCCTGGCTCCCTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1112:9:3,6:631,469:0.0081:2,2:27.3:1:29.2:1:0.18319:2.68846:60:8:0.0073:0.0027:0.4 0/1:1173:13:7,6:626,531:0.0111:2,2:18.2:1:29.6:1:1:1.01048:60:26:0.0112:0.0026:0.3 -9 139793425 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.1009;SOR=Inf;LSEQ=GGAGGGGCAGGCAGGCTAGG;RSEQ=TGGTTTTAGAGCCACGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:52,265:0:2,0:21.8:1:31.8:1:1:0:60:44.286:0.9968:0:0.1 0/1:278:3:1,2:60,215:0.0108:2,2:5:1:31:1:0.52585:1.79:60:6:0.0109:0:1 -9 139793845 . C A 139 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07952;SOR=2.70742;LSEQ=GTTCAGGCGTGCCTTCCTCA;RSEQ=AAACGGAGTGATAAAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:20,3:24,2:0.4694:2,2:27:1:30.9:1:0.65504:1.7785:60:46:0.4694:0:1.1 1/0:24:17:17,0:7,0:0.7083:0,1:27.2:1:30.6:1:1:0:60:34:0.7083:0:1.1 -9 139794209 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23869;SOR=0;LSEQ=GGGTGGGGCTGGGCACAGTG;RSEQ=CTCACACCTGTAATCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:0,2:15,165:0.011:2,0:32:1:31:1:1:0:60:4:0.0112:0:1 0/0:190:0:0,0:22,168:0:2,0:23.7:1:31.8:1:1:0:59.9:46.5:1:0:0.1 -9 139794225 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22873;SOR=Inf;LSEQ=AGTGGCTCACACCTGTAATC;RSEQ=CAGCACTTTGGGAGGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:3,147:0:1,0:26.5:1:31.4:1:1:0:60:49:1:0:0.1 0/1:138:2:1,1:2,134:0.0145:1,2:6:0:31:1:0.04316:54.95:60:4:0.0147:0:1 -9 139794331 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93535;LSEQ=TACAAAAAGCAAAAAACTTA;RSEQ=CAGGGGCCGGGCTCAGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:0,12:0,7:0.6316:0,0:19.6:1:30.4:1:1:0:60:24:0.6316:0:1.1 1/0:13:8:0,8:1,4:0.6154:2,0:14.1:1:29.9:1:0.38462:0:60:16:0.6154:0:1 -9 139794565 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCGGAGGTTGCAGTGA;RSEQ=CCAAGATCGCATGCCACTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:27.3:1:31.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139794635 . G A 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTTTAAAAAAAAAAAAA;RSEQ=AATAAAGGGCCGCCAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:6,0:0.2727:0,0:15.7:1:30.7:1:1:0:53.3:6:0.375:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139794638 . T A 72 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAAAAAAAAAAAAAGAA;RSEQ=AAAGGGCCGCCAGAAGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:10:1:31.2:1:1:0:56:10:0.4167:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139802949 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGGAGGCTGAGGCGGG;RSEQ=GGATCACGAGGTCCGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:0.3333:0,0:23:1:30.7:1:1:0:54.7:6:0.3333:0:1 0/0:1:0:0,0:0,1:0:0,0:41:0:30:0:1:0:60:2:1:0:0 -9 139803958 . G A 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTGACCATAGCACATCT;RSEQ=GGGTGCCAAGCCCTCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:0.6:0,0:26:1:28.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139804274 . G A 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01922;SOR=1.6048;LSEQ=GGGTGACCACGTGCTCCTGC;RSEQ=GCCCCTCGGCGCTGCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:115:113,2:114,4:0.4936:1,1:24.5:1:30.5:1:0.68357:1.98:60:114:0.5:0:1.5 1/0:195:119:116,3:71,5:0.6103:2,1:23.5:1:29.8:1:0.26576:2.71:60:238:0.6166:0:1.6 -9 139804346 . C T 261 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=1.79873;LSEQ=CTGGCATTGGCGTCCACCCT;RSEQ=ACACTCCTGATCCCTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:949:452:259,193:296,201:0.4763:2,2:25.2:1:29:1:0.50968:1.09726:60:112:0.4751:0:1.2 1/0:928:576:329,247:196,155:0.6207:2,2:24.9:1:28.5:1:0.73278:1.05:60:71:0.6208:0:1.3 -9 139804679 . T C 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28466;SOR=2.59793;LSEQ=TCCTCATCCTCCAGTGTACA;RSEQ=AGCTGCTTACTTTTCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:0,13:0,11:0.5:0,1:26.2:1:32.8:1:1:0:60:26:0.52:0:1 1/0:11:8:0,8:0,3:0.7273:0,0:28.6:1:32.6:1:1:0:60:16:0.7273:0:1.1 -9 139810595 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTACGTTTTGCTTCATGT;RSEQ=GTGTCTGTGTCATCCTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:35.5:1:29.5:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:0,1:0:0,0:32:0:32:0:1:0:60:2:1:0:0 -9 139810652 . G A 65 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGTGGGCGTTTGATTCT;RSEQ=GGTTTTGAACCCAGGCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:32.4:1:28.2:1:1:0:60:10:0.5556:0:1.2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139811482 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTGAGCCCTCCGCCACCA;RSEQ=CAGGCACTCGGGCCCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139811585 . A G 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCCGTCACTGCCCTGTCCAC;RSEQ=TCATCCTCATCTCTCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24.7:1:31:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139812710 . TTTATTTAA T 29 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=15.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATATATATATATATATA;RSEQ=TTAATTAATTTATTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29.8:1:1:0:60:4:1:0.5:0.5 -9 139814584 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51435;SOR=0;LSEQ=ATCCCTATCTATGACCCTGG;RSEQ=CTGTCTCCTCAGCTCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:150,2:0.013:1,2:19.5:1:28:1:0.03871:61.4348:60:4:0.0132:0:1 0/0:107:0:0,0:102,5:0:1,0:23.5:1:32:1:1:0:60:106:1:0:0.2 -9 139814629 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09624;SOR=Inf;LSEQ=CCACGTCTTGGTGGCCGTCC;RSEQ=CGGGTGGGAGCCGAATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:261,70:0:2,0:22.3:1:30.8:1:1:0:60:109.333:1:0:0.1 0/1:281:3:1,2:216,62:0.0107:2,2:13.7:1:28:1:0.13096:6.90484:60:6:0.0108:0:1 -9 139814631 . G T 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33089;SOR=3.70376;LSEQ=ACGTCTTGGTGGCCGTCCCC;RSEQ=GGTGGGAGCCGAATGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:1:1,0:277,78:0.0028:2,0:44:0:30:0:1:0:60:2:0.0029:0:1 0/1:290:3:2,1:221,66:0.0103:2,2:12.3:1:24.7:1:0.54672:1.67088:60:2:0.0069:0:1.3 -9 139815053 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.89848;LSEQ=AGCAGGTTCTAGCAGGTCCT;RSEQ=GAGCTTTAGAGCCCGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:46:2,44:27,241:0.1465:2,1:21.9:1:31:1:0.27894:2.45941:60:45:0.1461:0:1.1 1/0:267:145:27,118:10,112:0.5431:2,2:21:1:30.3:1:0.01989:2.55:60:144:0.5455:0:1.1 -9 139815159 . GG AA 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.07809;SOR=Inf;LSEQ=CTGAGTCCTGTCATCTAAGG;RSEQ=CCCAAACCCTGGAAGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:6,52:0:2,0:27.7:1:31.4:1:1:0:60:57:1:0:1.1 0/1:23:2:0,2:3,18:0.087:2,0:41.5:1:31:1:1:0:60:4:0.087:0:1 -9 139815160 . G A 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08006;SOR=0;LSEQ=TGAGTCCTGTCATCTAAGGG;RSEQ=CCCAAACCCTGGAAGGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:57:5,52:0,0:1:0,2:27.7:1:29.8:1:1:0:60:56:1:0:1.1 1/1:23:21:3,18:0,0:0.913:0,2:23.8:1:29.9:1:1:0:60:20:1:0:1.1 -9 139815354 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55155;SOR=0;LSEQ=GGGGTTGGGTTCTTGTGTGC;RSEQ=GGGAGTGGACATGAGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:102,7:0.018:2,2:25:1:29:1:0.13956:13.69699:60:4:0.018:0:1 0/0:56:0:0,0:54,2:0:1,0:20.4:1:30:1:1:0:60:112:1:0:0.2 -9 139815417 . G A 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00069;SOR=Inf;LSEQ=GCACTGTCCTGCTGGAGATC;RSEQ=GTGGGTGTGGGAGGCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:270,20:0:2,0:24.2:1:30.1:1:1:0:60:95.667:1:0:0.2 0/1:199:8:8,0:178,13:0.0402:2,0:19.1:1:29.3:1:1:0:60:16:0.0402:0:1 -9 139815960 . A G 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01515;SOR=0;LSEQ=AGCCTGGTCCTCTGGCACAC;RSEQ=GCCCTAAAGCAGACATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1:0,0:23.1:1:30.4:1:1:0:60:20:1:0:1.4 0/0:2:0:0,0:1,1:0:2,0:3:0:24:1:1:0:60:1:1:0:2 -9 139817331 . A C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATGGGCCTGGGGGCACG;RSEQ=GGTGGAGAGGACTAGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26.5:1:31:1:1:0:60:4:1:0:1 -9 139818169 . CTT C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=3.68622;LSEQ=ATAGTTTGAGGGAAAAAAAA;RSEQ=TTCTTTGCACCCCAGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:54:54,0:62,1:0.4576:1,1:24.2:1:32.3:1:1:0:60:108:0.4696:0.1102:0.1 1/0:62:47:47,0:15,0:0.7581:1,1:24.4:1:31.3:1:1:0:60:94:0.7705:0.2097:0.1 -9 139818263 . G T 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09761;SOR=6.0533;LSEQ=AAGAGCCCTGCCCCGCCCTT;RSEQ=CTGAGTGTCAGCTCACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:560:1:1,0:403,156:0.0018:2,0:37:0:31:0:1:0:60:2:0.0018:0:1 0/1:466:5:2,3:319,141:0.0107:2,2:19.4:1:27.2:1:0.17499:3.38337:60:10:0.0109:0:1 -9 139818485 . G A 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06176;SOR=Inf;LSEQ=CTGCAGGCTTCGCTAGGGCC;RSEQ=CACCTGGGAGTCCCTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:100,304:0:2,0:25.7:1:31.7:1:1:0:60:201:1:0:0.1 0/1:409:5:4,1:122,282:0.0122:2,2:7:1:25:1:0.03306:9.19:60:4:0.0098:0:1.2 -9 139818543 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50176;SOR=0;LSEQ=TGCAGGGTTGTGCGGGACAA;RSEQ=GTGGCTTGGGCTCGCTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:6,139:0.0136:1,2:36:1:30:1:0.09328:21.52:60:4:0.0139:0:1 0/0:124:0:0,0:8,116:0:2,0:23.8:1:30.6:1:1:0:60:123:1:0:0.1 -9 139818848 . C CA 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTGAGAACCCATGTCTA;RSEQ=AAAAAAAATAGAAAAATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:30:1:32.5:1:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -9 139819984 . C T 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCTGTGGCAGGAGCAAGGC;RSEQ=GCCCACCACGTGGTCTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:91,1:0:1,0:27.5:1:31.2:1:1:0:60:91:1:0:0.3 0/1:39:19:19,0:20,0:0.4872:1,1:26.1:1:31.6:1:1:0:60:38:0.4872:0:1.1 -9 139820048 . G A 186 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.004;SOR=0.54305;LSEQ=TCCTGGGATGGCCTCCTGCT;RSEQ=GTGGCCCTGCCAGTGTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:99:92,7:97,6:0.4877:2,2:23.1:1:28.1:1:0.78003:1.22881:60:48.5:0.485:0:1.2 0/1:188:64:60,4:116,8:0.3404:2,2:19.2:1:28.6:1:1:1.03:60:63:0.3387:0:1.1 -9 139820363 . A G 213 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=134.64719;LSEQ=CAGGGCTCTAACTGCCCCCT;RSEQ=CTGGTGTCTGGGGGTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1028:1:0,1:434,593:0.001:2,0:49:0:17:0:1:0:60:0:0:0:4 0/1:922:107:43,64:352,461:0.1161:2,2:23.1:1:31.6:1:0.60372:1.13629:60:214:0.1172:0:1.1 -9 139820421 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.87426;LSEQ=GCTCACGGAGGGGCCACCAC;RSEQ=CTGGGCCAGGGTCTCACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:45:4,41:40,282:0.1226:2,2:25.1:1:29.7:1:0.62842:1.45256:60:44:0.1232:0:1 1/0:282:148:24,124:23,111:0.5248:2,2:22.9:1:29.3:1:0.87369:1.07029:60:73:0.5252:0:1 -9 139820621 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGTCTTCGGGTGCTTCC;RSEQ=AGCACAAGCTGCCCTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:0.2222:0,0:20:1:27:1:1:0:60:4:0.2222:0:1 0/0:2:0:0,0:0,2:0:0,0:12.5:1:31.5:1:1:0:60:4:1:0:0 -GL000199.1 34091 . A C 29 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTACAAAAAGAGTGTTTC;RSEQ=AACCTGCTCCATGAAAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:31.5:1:1:0:31:4:1:0:8 1/0:3:2:1,1:1,0:0.6667:0,2:15:0:29.5:1:1:0:30:4:0.6667:0:8 -GL000199.1 34101 . C T 28 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AGAGTGTTTCAAACCTGCTC;RSEQ=ATGAAAGGCAATAATCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:0:30:1:1:0:31:4:1:0:8 1/0:4:2:1,1:1,1:0.5:2,2:25:0:28.5:1:1:1:30:4:0.5:0:8 -GL000199.1 34109 . G A 31 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=TCAAACCTGCTCCATGAAAG;RSEQ=CAATAATCAACTCCGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:0:31:1:1:0:31:4:1:0:8 0/0:4:0:0,0:1,1:0:2,0:21.5:1:30:1:1:0:60:4:0.5:0:1 -GL000199.1 34114 . AA GT 30 d7;v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCTGCTCCATGAAAGGCAAT;RSEQ=TCAACTCCGTGACTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:39:0:32.5:1:1:0:31:4:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:39:0:30.3:1:1:1:30:4:0.5:0:7 -GL000199.1 34115 . A T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGCTCCATGAAAGGCAATA;RSEQ=TCAACTCCGTGACTTGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:27.5:1:28.5:1:1:0:60:4:1:0:1 -GL000199.1 34139 . A C 32 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ACTCCGTGACTTGAATGCAA;RSEQ=CATCACAAAGACGTTTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:33.5:1:1:0:31:4:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:26:1:32.5:1:1:1:30:4:0.5:0:7 -GL000199.1 34148 . A G 33 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CTTGAATGCAAACATCACAA;RSEQ=GACGTTTCTGAGAATGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7:0:33:1:1:0:31:4:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:17:1:33:1:1:1:30:4:0.5:0:7 -GL000199.1 34151 . C A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GAATGCAAACATCACAAAGA;RSEQ=GTTTCTGAGAATGCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:4:0:32:0:1:0:31:4:1:0:7 1/0:4:2:1,1:1,1:0.5:2,2:14:1:32.5:1:1:1:30:4:0.5:0:7 -GL000199.1 34355 . T C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTTCTGTCTAGTTTTTATT;RSEQ=GAAGATATTTCCTTTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:25:0:32:0:1:0:20:2:1:0:7 1/0:3:2:2,0:1,0:0.6667:0,0:23.5:1:33:0:1:0:30.5:4:0.6667:0:6 -GL000199.1 34374 . A T 51 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02757;SOR=0.05703;LSEQ=TTGAAGATATTTCCTTTCTC;RSEQ=CCATAGGCCTGAAAGCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,0:0.75:0,0:18.3:1:32.3:1:1:0:35.3:6:0.75:0:6.3 0/1:17:2:2,0:9,0:0.1176:0,0:10.5:1:32.5:1:1:0:39.5:4:0.1176:0:6 -GL000199.1 34377 . A G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAGATATTTCCTTTCTCACC;RSEQ=TAGGCCTGAAAGCGCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:5,1:0.1429:2,0:10:0:31:0:1:0:40:2:0.1429:0:8 0/1:21:3:3,0:17,1:0.1429:1,0:17.7:1:30.3:1:1:0:28:6:0.1429:0:7.3 -GL000199.1 34395 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATAGGCCTGAAAGCGCTT;RSEQ=AAACGTCCGCTTGCAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:11,4:0:2,0:17.3:1:32.2:1:1:0:34.7:30:1:0:6.2 0/1:40:2:2,0:30,8:0.05:2,0:12.5:1:29.5:1:1:0:34:4:0.0513:0:6.5 -GL000199.1 34398 . AC TT 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGGCCTGAAAGCGCTTGAA;RSEQ=GTCCGCTTGCAGATACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:12,4:0:2,0:18.9:1:31.2:1:1:0:35:32:1:0:6.1 0/1:42:2:2,0:31,9:0.0476:2,0:20.5:1:32:0:1:0:35:4:0.0488:0:6.5 -GL000199.1 34399 . C T 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30851;SOR=0;LSEQ=AGGCCTGAAAGCGCTTGAAA;RSEQ=GTCCGCTTGCAGATACTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:12,4:0,0:1:0,2:19.8:1:31.6:1:1:0:35:32:1:0:6.1 1/1:42:37:28,9:2,0:0.881:0,2:24.9:1:30.6:1:1:0:34.9:74:0.925:0:6.2 -GL000199.1 34401 . T C 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52039;SOR=0.59704;LSEQ=GCCTGAAAGCGCTTGAAACG;RSEQ=CCGCTTGCAGATACTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:8,2:0.375:2,2:27:1:32.3:1:0.6044:1.91107:35.3:12:0.375:0:5.8 0/1:42:11:8,3:25,6:0.2619:2,2:25.2:1:32.7:1:0.67565:1.54496:38:22:0.2619:0:5.5 -GL000199.1 34404 . G A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66088;SOR=0.3802;LSEQ=TGAAAGCGCTTGAAACGTCC;RSEQ=CTTGCAGATACTACAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:12,4:1,0:0.9412:0,2:23.5:1:30.8:1:1:0:35.9:32:0.9412:0:5.8 1/1:42:36:28,8:3,0:0.8571:0,2:28.8:1:30.6:1:1:0:34.9:72:0.878:0:6.1 -GL000199.1 34408 . G C 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65875;SOR=0.43628;LSEQ=AGCGCTTGAAACGTCCGCTT;RSEQ=CAGATACTACAGAAAGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:14,5:0,0:0.95:0,2:23.8:1:31.7:1:1:0:35.1:38:0.95:0:5.6 1/1:46:41:32,9:2,1:0.8913:2,2:31:1:31.5:1:0.54817:1.75:34.9:82:0.8913:0:6.1 -GL000199.1 34413 . T C 63 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.28676;LSEQ=TTGAAACGTCCGCTTGCAGA;RSEQ=ACTACAGAAAGAGTGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:0,1:14,6:0.0476:2,0:7:0:34:0:0.33333:0:60:2:0.0476:0:8 0/1:66:4:2,2:41,21:0.0606:2,2:17.5:1:31.8:1:0.60617:1.9314:30.5:8:0.0606:0:5.5 -GL000199.1 34417 . A C 84 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.33024;SOR=Inf;LSEQ=AACGTCCGCTTGCAGATACT;RSEQ=CAGAAAGAGTGTTTCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:15,8:0:2,0:27.3:1:29.8:1:1:0:36.8:46:1:0:5.2 0/1:72:6:3,3:44,22:0.0833:2,2:6:1:32.5:1:0.41207:1.97954:28.7:12:0.0833:0:6.5 -GL000199.1 34418 . C G 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62213;SOR=0.7217;LSEQ=ACGTCCGCTTGCAGATACTA;RSEQ=AGAAAGAGTGTTTCAAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:6,4:9,4:0.4348:2,2:28.9:1:32.4:1:0.68502:1.47341:37.2:20:0.4348:0:4.5 0/1:73:26:14,12:33,14:0.3562:2,2:22.1:1:31.7:1:0.20479:2.00022:39.5:52:0.3562:0:3.4 -GL000199.1 34419 . A C 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTCCGCTTGCAGATACTAC;RSEQ=GAAAGAGTGTTTCAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,8:0:2,0:29:1:31.4:1:1:0:37.4:44:0.9565:0:5.1 0/1:74:3:2,1:43,26:0.0405:2,2:23.3:1:29.7:1:1:1.21:23:6:0.0411:0:6.3 -GL000199.1 34420 . G A 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59336;SOR=0.46902;LSEQ=GTCCGCTTGCAGATACTACA;RSEQ=AAAGAGTGTTTCAAACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:14,7:0.0833:2,2:7.5:1:31.5:1:1:1.93655:50:4:0.087:0:7.5 0/1:74:3:2,1:43,26:0.0405:2,2:29.3:1:29.7:1:1:1.21:36:6:0.0435:0:5.7 -GL000199.1 34423 . A T 135 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01851;SOR=5.58784;LSEQ=CGCTTGCAGATACTACAGAA;RSEQ=GAGTGTTTCAAACCTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:15,9:0.0769:2,0:36.5:1:33:0:0.52923:0:29:4:0.0769:0:8 0/1:78:25:18,7:30,23:0.3205:2,2:29.3:1:29.1:1:0.22132:1.95:31.6:24:0.3117:0:6 -GL000199.1 34427 . T G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCAGATACTACAGAAAGAG;RSEQ=GTTTCAAACCTGCTCTATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:17,10:0:2,0:29.3:1:30.3:1:1:0:37.6:54:1:0:5.1 0/1:84:2:1,1:44,35:0.0238:2,2:23.5:1:31:0:1:1.25356:41.5:4:0.0244:0:5 -GL000199.1 34432 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05869;SOR=0;LSEQ=ATACTACAGAAAGAGTGTTT;RSEQ=AAACCTGCTCTATGAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:15,11:0.0714:2,2:12.5:1:31:1:1:1.34838:40:4:0.0714:0:6.5 0/0:86:0:0,0:49,35:0:2,0:27.8:1:31.2:1:1:0:35.8:168:0.9767:0:5 -GL000199.1 34436 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05798;SOR=0;LSEQ=TACAGAAAGAGTGTTTCAAA;RSEQ=CTGCTCTATGAAAGGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:0.0667:2,2:24.5:1:29:1:1:1.14834:25:4:0.0667:0:6.5 0/0:93:0:0,0:51,40:0:2,0:27.1:1:30.8:1:1:0:35.2:182:0.9785:0:4.9 -GL000199.1 34439 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05721;SOR=0;LSEQ=AGAAAGAGTGTTTCAAACCT;RSEQ=CTCTATGAAAGGGAATGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:15,14:0.0645:2,2:27.5:1:28.5:1:1:1.06901:25:4:0.0645:0:6.5 0/0:97:0:0,0:54,43:0:2,0:26.7:1:30.9:1:1:0:35.5:31.333:1:0:4.8 -GL000199.1 34440 . C T 57 v4;pSTD;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.26101;LSEQ=GAAAGAGTGTTTCAAACCTG;RSEQ=TCTATGAAAGGGAATGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:16,14:0.0323:2,0:34:0:31:0:0.48387:0:60:2:0.0323:0:8 0/1:99:4:1,3:53,42:0.0404:2,2:17:0:28.5:1:0.32715:3.73795:56:8:0.0417:0:5 -GL000199.1 34441 . T A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01484;SOR=0.32019;LSEQ=AAAGAGTGTTTCAAACCTGC;RSEQ=CTATGAAAGGGAATGTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:7,6:9,9:0.4194:2,2:27.6:1:29.8:1:1:1.16:34.8:26:0.4194:0:5.3 0/1:102:19:11,8:43,39:0.1863:2,2:25.7:1:28:1:0.79995:1.24:37.2:18:0.18:0:5.4 -GL000199.1 34444 . A G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35555;SOR=0.59824;LSEQ=GAGTGTTTCAAACCTGCTCT;RSEQ=TGAAAGGGAATGTTCAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:13,11:0.1515:2,2:19.8:1:32:1:0.65134:1.738:37.6:10:0.1515:0:3.2 0/1:104:10:4,6:49,38:0.0962:2,2:23.9:1:30.6:1:0.50439:1.92103:46.6:20:0.0971:0:4.8 -GL000199.1 34445 . TG CC 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05668;SOR=0;LSEQ=AGTGTTTCAAACCTGCTCTA;RSEQ=AAAGGGAATGTTCAATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:0.0606:2,2:26.5:1:31.8:1:1:1.06462:40:4:0.0606:0:5.5 0/0:104:0:0,0:56,48:0:2,0:26.3:1:28.9:1:1:0:36.4:25:1:0:4.7 -GL000199.1 34446 . G C 158 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00137;SOR=7.77663;LSEQ=GTGTTTCAAACCTGCTCTAT;RSEQ=AAAGGGAATGTTCAATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:14,14:0.0606:2,2:29.5:1:30:1:1:1:25:4:0.0645:0:6.5 0/1:104:35:19,16:34,30:0.3365:2,2:22.8:1:30.9:1:1:1.05:31.7:34:0.3301:0:4.9 -GL000199.1 34448 . A T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTCAAACCTGCTCTATGA;RSEQ=AGGGAATGTTCAATTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:18,17:0:2,0:26.4:1:30.2:1:1:0:36.5:70:1:0:4.6 0/1:106:2:2,0:54,50:0.0189:2,0:26:1:32:0:0.49686:0:25:4:0.0192:0:7.5 -GL000199.1 34450 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00358;SOR=0.26971;LSEQ=TTCAAACCTGCTCTATGAAA;RSEQ=GGAATGTTCAATTCTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:14:8,6:10,11:0.4:2,2:26.1:1:30.2:1:0.73322:1.45:35.2:28:0.4:0:5.1 0/1:106:16:9,7:46,42:0.1509:2,2:28.9:1:29.7:1:0.79309:1.17:36.8:32:0.1509:0:5.3 -GL000199.1 34451 . G T 160 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00034;SOR=7.13876;LSEQ=TCAAACCTGCTCTATGAAAG;RSEQ=GAATGTTCAATTCTGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:2,1:16,17:0.0833:2,2:30:1:30:1:1:2.08:27.7:6:0.0833:0:7 0/1:106:42:22,20:33,29:0.3962:2,2:22.2:1:29.7:1:1:1.03416:33.1:84:0.4118:0:5 -GL000199.1 34452 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAACCTGCTCTATGAAAGG;RSEQ=AATGTTCAATTCTGTGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:0:2,0:25.7:1:31.3:1:1:0:36.6:72:1:0:4.5 0/1:107:2:1,1:55,49:0.0187:2,2:35.5:1:33.5:1:1:1.12122:46:4:0.019:0:2 -GL000199.1 34455 . T C 78 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33631;SOR=Inf;LSEQ=ACCTGCTCTATGAAAGGGAA;RSEQ=GTTCAATTCTGTGACTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:0:2,0:25.3:1:30.5:1:1:0:36.6:72:1:0:4.5 0/1:112:6:2,4:55,51:0.0536:2,2:25.3:1:30.5:1:0.43395:2.14254:57.3:12:0.055:0:4.3 -GL000199.1 34456 . G C 82 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33639;SOR=Inf;LSEQ=CCTGCTCTATGAAAGGGAAT;RSEQ=TTCAATTCTGTGACTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:0:2,0:25.2:1:32.1:1:1:0:36.6:72:1:0:4.5 0/1:111:6:3,3:53,52:0.0541:2,2:31.2:1:31.8:1:1:1.01906:28.7:12:0.0556:0:6.5 -GL000199.1 34459 . C G 34 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.65686;LSEQ=GCTCTATGAAAGGGAATGTT;RSEQ=AATTCTGTGACTTGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:0,1:19,18:0.0263:2,0:38:0:33:0:1:0:60:2:0.0263:0:8 0/1:115:2:2,0:55,58:0.0174:2,0:26:1:34:0:0.24348:0:25:4:0.0179:0:7.5 -GL000199.1 34460 . A T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.06046;SOR=0;LSEQ=CTCTATGAAAGGGAATGTTC;RSEQ=ATTCTGTGACTTGAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:18,18:0.0526:2,2:38:0:31:1:1:1:40:4:0.0526:0:5.5 0/0:115:0:0,0:55,54:0:2,0:24.8:1:29.3:1:1:0:35.3:108:0.9474:0:4.4 -GL000199.1 34462 . T C 82 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33747;SOR=Inf;LSEQ=CTATGAAAGGGAATGTTCAA;RSEQ=TCTGTGACTTGAATGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:19,19:0:2,0:22.7:1:30.2:1:1:0:36.8:76:1:0:4.4 0/1:114:6:3,3:51,55:0.0526:2,2:25.2:1:31.8:1:1:1.08:28.7:12:0.0526:0:6.5 -GL000199.1 34466 . G A 85 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11157;SOR=Inf;LSEQ=GAAAGGGAATGTTCAATTCT;RSEQ=TGACTTGAATGCAAACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:19,20:0:2,0:21.1:1:32:1:1:0:36.8:78:1:0:4.5 0/1:110:8:5,3:46,56:0.0727:2,2:22.4:1:28.5:1:0.46793:2.02:27.8:16:0.0727:0:6.5 -GL000199.1 34470 . C G 95 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11074;SOR=Inf;LSEQ=GGGAATGTTCAATTCTGTGA;RSEQ=TTGAATGCAAACATCACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:0:2,0:21.4:1:32.2:1:1:0:36.6:74:1:0:4.4 0/1:104:8:5,3:40,55:0.0769:2,2:19.4:1:31.8:1:0.29213:2.27:27.8:16:0.0777:0:6.5 -GL000199.1 34473 . G C 167 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00059;SOR=6.75643;LSEQ=AATGTTCAATTCTGTGACTT;RSEQ=AATGCAAACATCACAAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:2,1:13,18:0.0882:2,2:22.7:1:32.3:1:0.57136:2.69:27.7:6:0.0882:0:7 0/1:103:41:16,25:29,33:0.3981:2,2:28.9:1:31.3:1:0.54329:1.36887:32.6:40:0.396:0:4.3 -GL000199.1 34475 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTTCAATTCTGTGACTTGA;RSEQ=TGCAAACATCACAAAGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:0:2,0:23.9:1:31.1:1:1:0:35.8:62:1:0:4.4 0/1:100:2:1,1:42,56:0.02:2,2:40.5:1:31.5:1:1:1.33:38.5:4:0.0202:0:5 -GL000199.1 34480 . A G 76 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33372;SOR=Inf;LSEQ=AATTCTGTGACTTGAATGCA;RSEQ=ACATCACAAAGAAGTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:12,17:0:2,0:24.3:1:29.4:1:1:0:35.4:13.5:1:0:4.3 0/1:91:6:3,3:35,50:0.0659:2,2:7.2:1:29.7:1:0.69117:1.42:28.7:12:0.0659:0:6.5 -GL000199.1 34481 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05983;SOR=0;LSEQ=ATTCTGTGACTTGAATGCAA;RSEQ=CATCACAAAGAAGTTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:11,16:0.069:2,2:5.5:1:30.5:1:1:1.44:40:4:0.069:0:2 0/0:88:0:0,0:36,52:0:2,0:26.1:1:29.2:1:1:0:37:87:1:0:4 -GL000199.1 34484 . T G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTGACTTGAATGCAAACA;RSEQ=CACAAAGAAGTTCCTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:24.7:1:30.7:1:1:0:35.5:54:1:0:4.1 0/1:80:2:1,1:29,48:0.025:2,2:18.5:1:34:0:1:1.64:59.5:4:0.025:0:3 -GL000199.1 34486 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06436;SOR=0;LSEQ=GTGACTTGAATGCAAACATC;RSEQ=CAAAGAAGTTCCTGAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:9,15:0.0769:2,2:12:0:32.5:1:1:1.63:40:4:0.0769:0:5.5 0/0:75:0:0,0:27,48:0:2,0:28:1:30:1:1:0:36.1:74:1:0:3.7 -GL000199.1 34487 . C G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02544;SOR=0.32897;LSEQ=TGACTTGAATGCAAACATCA;RSEQ=AAAGAAGTTCCTGAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:5,8:4,8:0.52:2,2:30.6:1:31.7:1:1:1.24:35.2:26:0.52:0:4.3 0/1:73:19:6,13:20,34:0.2603:2,2:27.1:1:31.8:1:0.78408:1.27035:34.7:38:0.2714:0:4.7 -GL000199.1 34492 . A T 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33077;SOR=Inf;LSEQ=TGAATGCAAACATCACAAAG;RSEQ=AGTTCCTGAGAATGCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:0:2,0:24.6:1:30.3:1:1:0:36.3:44:1:0:4 0/1:69:5:1,4:24,40:0.0725:2,2:31.4:1:28.2:1:0.64647:2.37363:41:10:0.0758:0:4.8 -GL000199.1 34520 . T A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24822;SOR=0.29492;LSEQ=GAGAATGCTTCTCTCTAGAT;RSEQ=TTATATGTAATCCCGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:2,8:0.1667:2,0:21.5:1:32:0:1:0:41.5:4:0.1667:0:2 0/1:37:2:0,2:10,25:0.0541:2,0:35.5:1:31.5:1:1:0:40:4:0.0541:0:2 -GL000199.1 34524 . T A 42 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58907;SOR=0.47504;LSEQ=ATGCTTCTCTCTAGATTTTA;RSEQ=ATGTAATCCCGTTTCCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:1,8:0.1818:2,0:10:1:31:0:1:0:31.5:4:0.1818:0:5.5 0/1:32:3:1,2:8,21:0.0938:2,2:17.3:1:27:1:1:1.30:40:6:0.0938:0:5 -GL000199.1 34526 . T C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03674;SOR=0.19672;LSEQ=GCTTCTCTCTAGATTTTATA;RSEQ=GTAATCCCGTTTCCAACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:1,7:0,3:0.7273:0,2:16.9:1:30.6:1:1:0:35.4:16:0.7273:0:5.1 0/1:27:9:2,7:5,13:0.3333:2,2:19.2:1:30.9:1:1:1.33177:38.9:18:0.3333:0:4.7 -GL000199.1 34529 . A C 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04471;SOR=0.1866;LSEQ=TCTCTCTAGATTTTATATGT;RSEQ=ATCCCGTTTCCAACGAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:0.6:0,2:17:1:32.5:1:1:0:37.7:12:0.6:0:3.8 0/1:24:5:0,5:6,13:0.2083:2,0:20.4:1:33.4:1:0.28007:0:38.6:10:0.2083:0:3.6 -GL000199.1 34536 . T C 110 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04644;SOR=11.86207;LSEQ=AGATTTTATATGTAATCCCG;RSEQ=TTCCAACGAAATCCTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:1,4:0.1667:2,0:39:0:30:0:1:0:33:2:0.1667:0:7 1/0:15:11:2,9:0,4:0.7333:0,2:11.4:1:31.8:1:1:0:37.3:22:0.7333:0:4.3 -GL000199.1 34551 . T A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCCGTTTCCAACGAAATCC;RSEQ=CAAAGCTATCCAAATATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,1:0:0,0:47:0:30:0:1:0:33:2:0.5:0:7 0/1:8:2:0,2:0,6:0.25:0,0:23.5:1:31:1:1:0:36.5:4:0.25:0:4.5 -GL000199.1 34685 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGAATGCTTCTGTCTGG;RSEQ=TTTTATGGGAAGATATTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:33.5:1:1:0:51:4:1:0:4.5 -GL000199.1 34692 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTCTGTCTGGTTTTTAT;RSEQ=GGAAGATATTTCCTTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:31:1:1:0:51:4:1:0:4.5 -GL000199.1 34699 . TA CG 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGGTTTTTATGGGAAGA;RSEQ=TTTCCTTTTTCAACGTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:32.5:0:1:0:51:4:1:0:3.5 -GL000199.1 57075 . T C 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAGGGAAGTGTTCAACTC;RSEQ=ATGAGTTGAATGCAAACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:11:0:33:0:1:0:25:2:1:0:3 1/0:8:4:4,0:3,1:0.5:2,0:7.5:1:31:1:1:0:38:8:0.5:0:4.5 -GL000199.1 57076 . A AC 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GAAGGGAAGTGTTCAACTCT;RSEQ=TGAGTTGAATGCAAACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:13:0:33:0:1:0:25:2:1:0:3 0/1:11:2:2,0:6,1:0.1818:2,0:13.5:1:31.7:1:1:0:30:4:0.1818:0.0909:2 -GL000199.1 57081 . T C 52 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAGTGTTCAACTCTATGAG;RSEQ=TGAATGCAAACATCACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:7:1:29.3:1:1:0:23.3:6:1:0:3.7 0/1:15:3:3,0:10,1:0.2:2,0:10.7:1:33.3:1:1:0:40:6:0.2143:0:4.3 -GL000199.1 57082 . T G 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGTGTTCAACTCTATGAGT;RSEQ=GAATGCAAACATCACAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:8:1:29.7:1:1:0:23.3:6:1:0:3.7 0/1:16:3:3,0:11,2:0.1875:2,0:10.3:1:32.3:1:1:0:45:6:0.1875:0:8 -GL000199.1 57098 . A T 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42149;SOR=0.35817;LSEQ=GAGTTGAATGCAAACATCAC;RSEQ=GAGAAGTTTCTGAGAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:3,2:0.1667:2,0:1:0:29:0:1:0:20:2:0.1667:0:4 0/1:31:2:2,0:19,10:0.0645:2,0:34:1:33:0:1:0:36:4:0.0645:0:4.5 -GL000199.1 57099 . G A 48 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGTTGAATGCAAACATCACA;RSEQ=AGAAGTTTCTGAGAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:16.3:1:30.7:1:1:0:28.3:12:1:0:2.7 0/1:31:3:2,1:19,9:0.0968:2,2:18.7:1:30.3:1:1:1.0537:51.3:6:0.0968:0:3.7 -GL000199.1 57101 . G C 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGAATGCAAACATCACAGA;RSEQ=AAGTTTCTGAGAATGCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:18.3:1:30.5:1:1:0:28.3:12:1:0:2.7 0/1:32:2:1,1:19,11:0.0625:2,2:28.5:1:28.5:1:1:1.69662:60:4:0.0625:0:8 -GL000199.1 57103 . A T 106 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68566;SOR=0.70511;LSEQ=GAATGCAAACATCACAGAGA;RSEQ=GTTTCTGAGAATGCTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:2,2:0.4286:2,2:29:1:30.7:1:1:1.81:23.3:6:0.4286:0:3.7 0/1:32:11:8,3:11,9:0.3438:2,2:19.8:1:30.7:1:0.45164:2.13:36.5:22:0.3438:0:3.9 -GL000199.1 57109 . T C 116 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.72584;SOR=1.44749;LSEQ=AAACATCACAGAGAAGTTTC;RSEQ=GAGAATGCTTCTGTCTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:4,3:0.3:2,2:35:1:30:1:1:1.44:23.3:6:0.3:0:3.7 0/1:39:15:10,5:14,10:0.3846:2,2:18.5:1:29.9:1:0.7397:1.42:39.2:30:0.3846:0:3.3 -GL000199.1 57118 . T A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5193;SOR=0.65865;LSEQ=AGAGAAGTTTCTGAGAATGC;RSEQ=TCTGTCTTGATTTTATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:7,4:0.3125:2,2:9.4:1:30.4:1:1:1.15538:39:10:0.3125:0:7 0/1:48:11:8,3:21,16:0.2292:2,2:32.3:1:30.7:1:0.48781:2.00:37.2:22:0.234:0:6.7 -GL000199.1 57120 . CTGTC GTGT 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAAGTTTCTGAGAATGCTT;RSEQ=TTGATTTTATATGAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:19.1:1:31.4:1:1:0:33.3:32:1:0:4.1 0/1:49:2:1,1:28,19:0.0408:2,2:46:1:30.5:1:1:1.46176:40:4:0.0408:0:4.5 -GL000199.1 57123 . TC T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.77789;SOR=0.80929;LSEQ=AGTTTCTGAGAATGCTTCTG;RSEQ=TTGATTTTATATGAAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:4,3:7,5:0.3684:2,2:11.7:1:30:1:1:1.04727:38.7:14:0.3684:0.1053:3.7 0/1:50:16:9,7:20,14:0.32:2,2:25.3:1:30:1:1:1.10876:43.3:32:0.32:0.04:3.3 -GL000199.1 57129 . T G 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.95668;LSEQ=TGAGAATGCTTCTGTCTTGA;RSEQ=TTTATATGAAGATATTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:3,2:8,6:0.2632:2,2:20.4:1:33:1:1:1.12:39:10:0.2632:0:7 0/1:55:14:8,6:21,19:0.2545:2,2:30.5:1:31.7:1:1:1.20:38.6:28:0.2545:0:6.1 -GL000199.1 57133 . A C 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.39563;SOR=0.49221;LSEQ=AATGCTTCTGTCTTGATTTT;RSEQ=TATGAAGATATTCCCGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:2,1:10,9:0.1364:2,2:22.3:1:33:1:1:1.75:38.3:6:0.1364:0:7 0/1:56:4:3,1:27,25:0.0714:2,2:43.5:1:32.5:1:0.61509:2.73:44.5:8:0.0714:0:7.8 -GL000199.1 57135 . A G 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57247;SOR=Inf;LSEQ=TGCTTCTGTCTTGATTTTAT;RSEQ=TGAAGATATTCCCGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:24.1:1:29.5:1:1:0:35.5:44:1:0:4.2 0/1:56:4:2,2:28,24:0.0714:2,2:37.3:1:30.5:1:1:1.16345:34.5:8:0.0727:0:7 -GL000199.1 57138 . A C 33 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76638;LSEQ=TTCTGTCTTGATTTTATATG;RSEQ=AGATATTCCCGTTTCCAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:1,0:11,10:0.0455:2,0:36:0:33:0:1:0:20:2:0.0455:0:8 0/1:57:2:1,1:28,26:0.0351:2,2:35.5:1:33:1:1:1.07547:60:4:0.0351:0:8 -GL000199.1 57139 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGTCTTGATTTTATATGA;RSEQ=GATATTCCCGTTTCCAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:26.3:1:30.9:1:1:0:35.5:44:1:0:4.2 0/1:59:2:1,1:30,27:0.0339:2,2:21.5:1:30:1:1:1.10912:40:4:0.0339:0:5.5 -GL000199.1 57142 . T A 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62329;SOR=1.33201;LSEQ=GTCTTGATTTTATATGAAGA;RSEQ=ATTCCCGTTTCCAACGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:7,5:5,6:0.5217:2,2:30.3:1:30.8:1:0.68427:1.64:38.8:24:0.5217:0:5.1 1/0:59:35:19,16:12,12:0.5932:2,2:29.7:1:29.5:1:0.79525:1.18:40.4:34:0.5862:0:4.8 -GL000199.1 57144 . T C 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18055;SOR=0.17943;LSEQ=CTTGATTTTATATGAAGATA;RSEQ=TCCCGTTTCCAACGAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,9:0.087:2,2:38.5:1:32.5:1:1:1.21106:40:4:0.087:0:7 0/1:61:1:1,0:30,30:0.0164:2,0:40:0:33:0:1:0:20:2:0.0167:0:8 -GL000199.1 57146 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06627;SOR=0;LSEQ=TGATTTTATATGAAGATATT;RSEQ=CCGTTTCCAACGAAATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:40.5:1:30:0:1:1.21106:40:4:0.0909:0:7 0/0:62:0:0,0:30,30:0:2,0:28.6:1:30.8:1:1:0:39.4:120:0.9677:0:4.2 -GL000199.1 57148 . C G 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03167;LSEQ=ATTTTATATGAAGATATTCC;RSEQ=GTTTCCAACGAAATCTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:4,4:8,6:0.3636:2,2:21.9:1:29.9:1:1:1.31588:27:16:0.3636:0:3.5 0/1:62:23:11,12:20,19:0.371:2,2:30.7:1:29.5:1:1:1.14576:38.3:46:0.371:0:3.1 -GL000199.1 57154 . C T 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGAAGATATTCCCGTTTC;RSEQ=AACGAAATCTTCAAAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:31.1:1:31.8:1:1:0:34.5:48:1:0:4.3 0/1:62:2:1,1:30,30:0.0323:2,2:12:0:28.5:1:1:1:31:4:0.0333:0:4 -GL000199.1 57164 . T C 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76128;LSEQ=TTCCCGTTTCCAACGAAATC;RSEQ=TCAAAGCTATCCAAATATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:11,11:0.0435:2,0:43:0:31:0:1:0:40:2:0.0435:0:6 0/1:60:2:1,1:28,30:0.0333:2,2:13.5:1:29:1:1:1.07:34:4:0.0333:0:7.5 -GL000199.1 57166 . C A 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.0395;LSEQ=CCCGTTTCCAACGAAATCTT;RSEQ=AAAGCTATCCAAATATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:3,2:8,10:0.2174:2,2:29.8:1:29.2:1:0.64041:1.82:39:10:0.2174:0:7 0/1:58:13:7,6:21,24:0.2241:2,2:22.2:1:28.8:1:0.75695:1.33:36.9:26:0.2241:0:6.5 -GL000199.1 57168 . A G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31645;SOR=0.51903;LSEQ=CGTTTCCAACGAAATCTTCA;RSEQ=AGCTATCCAAATATCCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:2,3:9,9:0.2174:2,2:37.2:1:31.6:1:1:1.47392:34.8:10:0.2174:0:4.8 0/1:56:7:3,4:24,25:0.125:2,2:29.4:1:31.3:1:1:1.2744:38.9:14:0.1273:0:3.7 -GL000199.1 57170 . G T 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11279;LSEQ=TTTCCAACGAAATCTTCAAA;RSEQ=CTATCCAAATATCCACCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:3,2:8,10:0.2174:2,2:25.8:1:31:1:0.64041:1.82:39:10:0.2174:0:7 0/1:55:13:7,6:20,22:0.2364:2,2:19.4:1:29.1:1:0.75848:1.28:36.9:12:0.2222:0:6.5 -GL000199.1 57171 . C T 46 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02623;SOR=0;LSEQ=TTCCAACGAAATCTTCAAAG;RSEQ=TATCCAAATATCCACCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:1,2:10,10:0.1304:2,2:19.7:1:29.3:1:1:1.94223:21.7:6:0.1304:0:4.3 0/0:52:0:0,0:24,28:0:2,0:23.7:1:32.1:1:1:0:38.8:104:1:0:4.2 -GL000199.1 57173 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAACGAAATCTTCAAAGCT;RSEQ=TCCAAATATCCACCTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:28.3:1:29.8:1:1:0:34.9:46:1:0:4.3 0/1:52:2:1,1:23,27:0.0385:2,2:7.5:1:30:1:1:1.17:37:4:0.0385:0:7.5 -GL000199.1 57178 . A C 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.7807;SOR=0.78752;LSEQ=GAAATCTTCAAAGCTATCCA;RSEQ=ATATCCACCTGCAGATTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:4,4:6,7:0.381:2,2:29.3:1:32.8:1:1:1.16:37:16:0.381:0:4.1 0/1:43:14:5,9:11,18:0.3256:2,2:23.6:1:32:1:1:1.09755:41.5:28:0.3333:0:3.6 -GL000199.1 57198 . A T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.26509;LSEQ=AATATCCACCTGCAGATTCT;RSEQ=CAAAAAGAGTGTTTCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:6,8:0.0667:2,0:12:0:32:0:0.46667:0:40:2:0.0667:0:4 0/1:24:2:1,1:6,15:0.0833:2,2:30.5:1:28:1:0.52569:2.39:44.5:4:0.0833:0:5 -GL000199.1 57204 . A G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=CACCTGCAGATTCTACAAAA;RSEQ=GAGTGTTTCCAAAATGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:5,5:0,1:0.9091:0,2:18.4:1:32.1:1:1:0:34:20:0.9091:0:4.1 1/1:22:20:6,14:0,0:0.9091:0,2:15.6:1:29.5:1:1:0:32.7:19:0.9048:0:4.2 -GL000199.1 57216 . A T 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=CTACAAAAAGAGTGTTTCCA;RSEQ=AATGTTGTATCCAAACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,4:0.3333:0,2:5:0:32:1:0.33333:0:42:4:0.3333:0:3 0/0:10:0:0,0:0,10:0:0,0:16.5:1:31.4:1:1:0:30.6:20:1:0:4.9 -GL000199.1 57221 . T C 105 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGAGTGTTTCCAAAATG;RSEQ=TGTATCCAAACAAAGGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:18:1:33.7:1:1:0:22:6:1:0:5.3 1/1:9:9:0,9:0,0:1:0,0:12.8:1:33.2:1:1:0:30.4:18:1:0:5 -GL000199.1 57228 . C A 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTCCAAAATGTTGTATC;RSEQ=AAACAAAGGTTCAACTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:11:1:31.3:1:1:0:22:6:1:0:5.3 1/1:5:4:0,4:0,1:0.8:0,0:11:1:31:1:1:0:26.3:8:0.8:0:5.3 -GL000199.1 57245 . A G 85 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=ATCCAAACAAAGGTTCAACT;RSEQ=TGTTAGTTGAGGACACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:7:4,3:0,0:0.7778:0,2:7.1:1:30.6:1:1:0:51.4:14:0.7778:0:5.6 -GL000199.1 57250 . A C 84 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.66417;LSEQ=AACAAAGGTTCAACTATGTT;RSEQ=GTTGAGGACACACATCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:3:0:31:1:1:0:41:4:0.6667:0:3.5 1/0:9:7:4,3:1,1:0.7778:2,2:12.1:1:30:1:1:1.29:51.4:14:0.7778:0:5.6 -GL000199.1 57251 . G A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6009;LSEQ=ACAAAGGTTCAACTATGTTA;RSEQ=TTGAGGACACACATCGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:19:0:32:0:1:0:21:2:0.3333:0:5 0/1:9:2:1,1:4,3:0.2222:2,2:16.5:1:31.5:1:1:1.29098:28:4:0.2222:0:5.5 -GL000199.1 57254 . G T 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.66417;LSEQ=AAGGTTCAACTATGTTAGTT;RSEQ=AGGACACACATCGCAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:7:0:30.5:1:1:0:41:4:0.6667:0:3.5 1/0:9:7:4,3:1,1:0.7778:2,2:16.1:1:28.7:1:1:1.29:51.4:14:0.7778:0:5.6 -GL000199.1 57257 . G C 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53047;LSEQ=GTTCAACTATGTTAGTTGAG;RSEQ=ACACACATCGCAAATAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:25:0:34:0:1:0:21:2:0.3333:0:5 0/1:10:2:1,1:4,4:0.2:2,2:22.5:1:33:1:1:1:28:4:0.2:0:5.5 -GL000199.1 57267 . G A 90 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56044;SOR=2.48238;LSEQ=GTTAGTTGAGGACACACATC;RSEQ=CAAATAAGTTTCTGAGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,0:0.6:0,2:15.7:1:31.7:1:1:0:34:6:0.6:0:3.7 1/1:10:8:4,4:0,0:0.8:0,2:27.1:1:30.1:1:1:0:50:16:0.8:0:5.1 -GL000199.1 57269 . A C 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4965;SOR=Inf;LSEQ=TAGTTGAGGACACACATCGC;RSEQ=AATAAGTTTCTGAGAATCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:17.7:1:32:0:1:0:34:6:1:0:3.7 0/1:10:4:2,2:3,3:0.4:2,2:26.5:1:32:1:1:1:50:8:0.4:0:4.8 -GL000199.1 57308 . G C 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24451;SOR=Inf;LSEQ=CTTCTGTCTAGTTTTTATTT;RSEQ=AAGATATTTCCTTTCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:20.8:1:31.8:1:1:0:28.8:10:1:0:3.2 0/1:11:4:2,2:3,4:0.3636:2,2:12.3:1:31.3:1:1:1.30:60:8:0.3636:0:5.8 -GL000199.1 57326 . A C 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAGATATTTCCTTTCTC;RSEQ=CCATAGGCCTGAAATCGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:16:1:32.5:1:1:0:30.5:4:1:0:4 1/1:4:4:1,3:0,0:1:0,2:15.8:1:30.5:1:1:0:35.3:8:1:0:3.3 -GL000199.1 57329 . A G 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATATTTCCTTTCTCACC;RSEQ=TAGGCCTGAAATCGCTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:27:0:34:0:1:0:20:2:1:0:4 1/0:4:3:1,2:0,1:0.75:0,2:8:1:28.3:1:1:0:40:6:0.75:0:3.7 -GL000199.1 72807 . G T 48 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTATATGAAGATATCCCGT;RSEQ=TCCAACGAAATCCTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:5.5:1:30.5:1:1:0:40:4:1:0:6 1/0:4:3:3,0:1,0:0.75:0,0:33.3:1:30.3:1:1:0:23.7:6:0.75:0:5.3 -GL000199.1 72827 . G C 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCAACGAAATCCTCAAAG;RSEQ=TATCAAAATATCCACTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:21.7:1:34:0:1:0:40:6:1:0:6 1/1:10:8:8,0:2,0:0.8:0,0:19.3:1:32.1:1:1:0:29.6:16:0.8:0:5.8 -GL000199.1 72832 . A C 102 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54118;SOR=0;LSEQ=ACGAAATCCTCAAAGGTATC;RSEQ=AAATATCCACTTGCAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:21:1:31.3:1:1:0:40:8:1:0:5.5 1/0:13:10:10,0:3,0:0.7692:0,0:18:1:30.8:1:1:0:28.2:20:0.7692:0:5.6 -GL000199.1 72856 . A C 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.29123;SOR=Inf;LSEQ=TATCCACTTGCAGATTCTAC;RSEQ=AAAAGAGTGCTTCAAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:26.8:1:31.1:1:1:0:36.9:16:1:0:5.3 0/1:23:5:5,0:18,0:0.2174:1,0:23.2:1:31.4:1:1:0:36.2:10:0.2174:0:5.8 -GL000199.1 72863 . G T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23783;SOR=0.35382;LSEQ=TTGCAGATTCTACAAAAAGA;RSEQ=TGCTTCAAAACTGCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:5,1:0.4545:2,0:33:1:32:1:1:0:40:10:0.4545:0:5.8 0/1:27:6:6,0:20,0:0.2222:1,0:27.8:1:31:1:1:0:27:12:0.2308:0:6 -GL000199.1 72866 . C T 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64856;SOR=0.37475;LSEQ=CAGATTCTACAAAAAGAGTG;RSEQ=TTCAAAACTGCTCTGTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:9,1:1,0:0.9091:0,2:25.2:1:31.3:1:1:0:37.1:20:0.9091:0:6 1/0:28:22:22,0:6,0:0.7857:0,1:22.7:1:31:1:1:0:33.3:44:0.7857:0:6.1 -GL000199.1 72876 . G A 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65953;SOR=2.68633;LSEQ=AAAAAGAGTGCTTCAAAACT;RSEQ=CTCTGTCAAAAGGAAGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:12,3:0.0625:2,0:17:0:29:0:1:0:40:2:0.0625:0:6 0/1:39:6:5,1:27,6:0.1538:2,2:16.8:1:29.3:1:1:1.11:34.3:12:0.1579:0:5.5 -GL000199.1 72879 . C G 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56135;SOR=0.65308;LSEQ=AAGAGTGCTTCAAAACTGCT;RSEQ=TGTCAAAAGGAAGGTTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:7,1:6,4:0.4444:2,2:25.1:1:32.3:1:0.31373:4.30:40.1:16:0.4444:0:5.8 0/1:41:14:10,4:23,4:0.3415:2,2:21.4:1:32.1:1:0.41053:2.25003:26.6:28:0.3415:0:5.9 -GL000199.1 72891 . A T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57274;SOR=0.69438;LSEQ=AAACTGCTCTGTCAAAAGGA;RSEQ=GGTTCAACTCTGTTACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:4,3:12,4:0.3043:2,2:22:1:30.3:1:0.62584:2.16624:46.9:14:0.3182:0:6.9 0/1:56:13:8,5:27,16:0.2321:2,2:23.9:1:28.9:1:1:1.05367:41.7:26:0.2321:0:6.6 -GL000199.1 72892 . G T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTGCTCTGTCAAAAGGAA;RSEQ=GTTCAACTCTGTTACTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:0:2,0:21.6:1:31.4:1:1:0:39:50:1:0:5.7 0/1:58:2:1,1:35,21:0.0345:2,2:28.5:1:31.5:1:1:1.65138:23:4:0.0345:0:6.5 -GL000199.1 72900 . T A 149 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63845;SOR=0.76564;LSEQ=TGTCAAAAGGAAGGTTCAAC;RSEQ=CTGTTACTTGAGTACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:7,9:8,1:0.64:2,2:25.9:1:29.9:1:0.04045:9.38442:38:32:0.6667:0:5.9 1/0:66:38:21,17:19,9:0.5758:2,2:23.4:1:28.5:1:0.32236:1.69514:39.3:37:0.5692:0:5.9 -GL000199.1 72904 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08119;SOR=0;LSEQ=AAAAGGAAGGTTCAACTCTG;RSEQ=TACTTGAGTACACACATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:14,12:0.0714:2,2:19:1:30:1:1:1.16024:50:4:0.0714:0:7 0/0:69:0:0,0:41,28:0:2,0:25.1:1:28.9:1:1:0:36.3:138:1:0:5.3 -GL000199.1 72907 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07091;SOR=0;LSEQ=AGGAAGGTTCAACTCTGTTA;RSEQ=TTGAGTACACACATCACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:22:1:29.5:1:1:1.0801:50:4:0.08:0:7 0/0:73:0:0,0:43,30:0:2,0:25:1:30.3:1:1:0:36.2:72:1:0:5.4 -GL000199.1 72908 . T A 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.80928;SOR=0.85394;LSEQ=GGAAGGTTCAACTCTGTTAC;RSEQ=TGAGTACACACATCACAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:4,5:11,8:0.3214:2,2:28.7:1:30.9:1:0.68913:1.6853:41.3:18:0.3214:0:6.9 0/1:73:21:12,9:31,21:0.2877:2,2:23.3:1:29.5:1:1:1.10559:42.8:42:0.2877:0:6.7 -GL000199.1 72921 . T A 156 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.67885;SOR=1.22058;LSEQ=CTGTTACTTGAGTACACACA;RSEQ=CACAAGGAAGTTTCTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:6,9:9,8:0.4688:2,2:39.5:1:30.1:1:0.50226:1.65989:37.9:30:0.4839:0:5.9 1/0:79:41:21,20:21,17:0.519:2,2:32.9:1:29.3:1:0.82242:1.17405:39.8:82:0.519:0:5.9 -GL000199.1 72924 . C A 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08163;SOR=0.46547;LSEQ=TTACTTGAGTACACACATCA;RSEQ=AAGGAAGTTTCTGAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:7,8:7,9:0.4839:2,2:21.7:1:28.7:1:1:1.12:44.9:30:0.4839:0:5.9 0/1:86:26:15,11:27,30:0.3023:2,2:26.1:1:29.1:1:0.47935:1.51:33.6:52:0.3059:0:5.5 -GL000199.1 72927 . G A 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.28379;SOR=0.25552;LSEQ=CTTGAGTACACACATCACAA;RSEQ=GAAGTTTCTGAGAATGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:30:13,17:1,0:0.9677:0,2:31.6:1:30.1:1:0.45161:0:41.4:60:0.9677:0:5.9 1/1:86:76:37,39:5,5:0.8837:2,2:29.5:1:29.8:1:1:1.05343:37.9:75:0.8824:0:5.7 -GL000199.1 72929 . A C 82 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00947;SOR=0.15011;LSEQ=TGAGTACACACATCACAAGG;RSEQ=AGTTTCTGAGAATGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:3,3:11,14:0.1935:2,2:25.2:1:31.8:1:1:1.26:40.7:12:0.1935:0:6.3 0/1:88:3:2,1:40,43:0.0341:2,2:32.3:1:27:1:0.61176:2.13:42.3:2:0.023:0:6 -GL000199.1 72942 . T C 53 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.42459;LSEQ=CACAAGGAAGTTTCTGAGAA;RSEQ=GCTTCTGTCTGGTTTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:12,18:0.0323:2,0:35:0:31:0:1:0:60:2:0.0323:0:7 0/1:88:4:2,2:37,47:0.0455:2,2:25.3:1:26.8:1:1:1.27:38.3:3:0.0345:0:7.5 -GL000199.1 72947 . C G 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83513;SOR=0.85692;LSEQ=GGAAGTTTCTGAGAATGCTT;RSEQ=TGTCTGGTTTTTATGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:5,10:7,10:0.4688:2,2:32.7:1:30.7:1:0.72567:1.38533:44.9:30:0.4688:0:5.4 0/1:86:37:19,18:18,31:0.4302:2,2:29.6:1:30.6:1:0.19392:1.81:36.5:36:0.4286:0:5.1 -GL000199.1 72949 . G T 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44394;SOR=0.36446;LSEQ=AAGTTTCTGAGAATGCTTCT;RSEQ=TCTGGTTTTTATGAGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:30:11,19:0,1:0.9677:0,2:29.4:1:29.9:1:1:0:41.4:60:0.9677:0:5.7 1/1:83:76:34,42:0,7:0.9157:0,2:30.8:1:29.4:1:0.03786:0:38.9:37:0.9136:0:5.5 -GL000199.1 72958 . T C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18947;SOR=0.34138;LSEQ=AGAATGCTTCTGTCTGGTTT;RSEQ=TATGAGAAGATATTTCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:2,1:8,19:0.1:2,2:19.3:1:31.7:1:0.25123:4.48:53.3:6:0.1:0:7 0/1:83:3:1,2:28,52:0.0361:2,2:34:1:32.3:1:1:1.07598:48.3:6:0.037:0:7.3 -GL000199.1 72961 . T G 87 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67648;SOR=2.41083;LSEQ=ATGCTTCTGTCTGGTTTTTA;RSEQ=GAGAAGATATTTCCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:8,18:0.037:2,0:22:0:27:0:1:0:21:2:0.037:0:1 0/1:82:7:0,7:27,48:0.0854:2,0:41.3:1:31:1:0.08943:0:22:14:0.0864:0:1 -GL000199.1 72983 . A C 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67553;SOR=0.43339;LSEQ=AGAAGATATTTCCTTTTTCA;RSEQ=CATAGGCCTCAAAGCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:3,13:0,1:0.9412:0,2:22.6:1:32.2:1:1:0:41.1:32:0.9412:0:5.5 1/1:63:55:19,36:0,7:0.873:0,2:23:1:29.9:1:0.08935:0:39.6:12.75:0.8644:0:4.8 -GL000199.1 72989 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTCCTTTTTCAACATAG;RSEQ=CCTCAAAGCGCTGCAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:2,13:0:2,0:23:1:32.3:1:1:0:39.6:30:1:0:5.2 0/1:55:2:1,1:17,36:0.0364:2,2:43:1:30:1:1:2.09:40:4:0.037:0:3 -GL000199.1 72990 . C A 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29528;LSEQ=ATTTCCTTTTTCAACATAGG;RSEQ=CTCAAAGCGCTGCAAATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:0,2:2,11:0.1333:2,0:2:0:30:0:1:0:22:4:0.1333:0:7 0/1:54:9:3,6:15,30:0.1667:2,2:13.6:1:28.9:1:1:1:45.9:18:0.1698:0:7 -GL000199.1 72999 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTCAACATAGGCCTCAAAGC;RSEQ=CTGCAAATGTCCACTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:2,10:0:2,0:18.6:1:31.5:1:1:0:42.5:11:1:0:4.8 0/1:42:2:1,1:11,29:0.0476:2,2:43:0:31:1:0.49477:2.57:40:4:0.0476:0:2 -GL000199.1 73002 . GC CG 87 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32208;SOR=Inf;LSEQ=AACATAGGCCTCAAAGCGCT;RSEQ=AAATGTCCACTTCCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:20.9:1:33.3:1:1:0:43.3:18:1:0:4.3 0/1:40:7:0,7:11,22:0.175:2,0:11.3:1:31.3:1:0.15919:0:36:14:0.1795:0.05:5.7 -GL000199.1 73012 . A G 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAAGCGCTGCAAATGTCC;RSEQ=CTTCCAAATATTACAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:1,7:0:2,0:12.8:1:30.1:1:1:0:43.8:16:1:0:4.1 0/1:28:3:0,3:6,17:0.1071:2,0:8.7:1:33:0:1:0:35.7:6:0.1071:0:5 -GL000199.1 73026 . CA C 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTCCACTTCCAAATATTA;RSEQ=AAAAGAGTGTTTCAAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:14.3:1:31:1:1:0:33.7:6:1:0:2.3 0/1:9:2:1,1:1,6:0.2222:2,2:20:1:30:1:0.41667:4.58:40:4:0.2222:0:3 -GL000199.1 73784 . C A 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACATCACAAAGCAGTTT;RSEQ=TGAGAATGCTTCCGTCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:15:0:29:1:1:1.7321:43:4:0.5:0:1 -GL000199.1 73940 . A C 27 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTTAATTGAGGACATAC;RSEQ=GCACAAAGAAGTTTCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:6:0:27.5:1:1:0:40:4:0.6667:0:1 -GL000199.1 74003 . A C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAAGATATCCCGTTTCCAA;RSEQ=GAAATCCTCAAATGTATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:34:0:31:0:1:0:20:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:29:1:30.5:1:1:1:21:4:0.5:0:4 -GL000199.1 74017 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCAAAGAAATCCTCAAAT;RSEQ=TATCCAAATATCTACTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:48:0:32:0:1:0:20:2:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:23.5:1:30:1:1:1:21:4:0.5:0:4 -GL000204.1 15437 . G A 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6044;SOR=0.42404;LSEQ=TCAACCTGTGTGTATCATAC;RSEQ=ACTGTCATACAACTGTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:0.4545:0,0:39.4:1:27.8:1:1:0:27:4:0.4:0:1.4 0/1:4:1:1,0:3,0:0.25:0,0:2:0:32:0:1:0:27:2:0.25:0:1 -GL000204.1 15649 . G A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01746;SOR=Inf;LSEQ=AGTCTGACGCTGACTCCGGC;RSEQ=GTTAGTGTCAGAGCTGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:175,229:0:2,0:26.7:1:30.1:1:1:0:37.8:56.714:1:0:0.3 0/1:326:5:4,1:130,191:0.0153:2,2:11.6:1:26.6:1:0.16343:5.85:41.2:10:0.0154:0:1 -GL000204.1 15656 . G A 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03168;SOR=Inf;LSEQ=CGCTGACTCCGGCGGTTAGT;RSEQ=TCAGAGCTGAACGGCAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:159,224:0:2,0:24.2:1:31.7:1:1:0:37.3:75.6:1:0:0.4 0/1:281:4:3,1:109,168:0.0142:2,2:23:1:24:1:0.30489:4.60:50:3:0.0108:0:2 -GL000204.1 15663 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0682;SOR=Inf;LSEQ=TCCGGCGGTTAGTGTCAGAG;RSEQ=TGAACGGCAGTCACCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:140,219:0:2,0:21.6:1:31.7:1:1:0:36.6:70.8:1:0:0.4 0/1:249:3:1,2:95,151:0.012:2,2:32:1:24:1:1:1.25713:41.7:2:0.0082:0:2.3 -GL000204.1 15683 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.25364;LSEQ=CTGAACGGCAGTCACCCTCT;RSEQ=GGGGTGGGAACAGAGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:98:27,71:29,82:0.4689:2,2:22:1:29.6:1:0.87611:1.07:32.2:97:0.4732:0:1.1 0/1:159:29:8,21:41,88:0.1824:2,2:20.7:1:29.4:1:0.82471:1.22147:35.3:13.5:0.1753:0:1.1 -GL000204.1 15694 . C G 121 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=12.79565;LSEQ=TCACCCTCTCGGGGTGGGAA;RSEQ=AGAGGCATCATGCCGTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:29,131:0.0123:2,2:10.5:1:29:1:0.33701:4.46:48:4:0.0126:0:1 0/1:108:15:4,11:23,70:0.1389:2,2:26.1:1:31.1:1:1:1.11:27.8:30:0.1415:0:1.2 -GL000204.1 56386 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.0873;SOR=Inf;LSEQ=CCGCCACAGCCACCACCACC;RSEQ=CCACCGCCACCGCCACTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:15,10:0:2,0:25.6:1:31.6:1:1:0:60:50:1:0:0.2 0/1:11:2:1,1:5,4:0.1818:2,2:27:0:31:1:1:1.22474:60:4:0.1818:0:1.5 -GL000204.1 56431 . T C 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00401;SOR=Inf;LSEQ=CCACGCAGCGCGCGGGACTC;RSEQ=CTGGCGTCTCCATGGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:21.6:1:30.1:1:1:0:60:24:1:0:0.2 0/1:10:4:2,2:3,3:0.4:2,2:33.5:1:31.8:1:1:1:60:8:0.4:0:1.5 -GL000204.1 56622 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTCAGCCCCGGCCGCGCTCA;RSEQ=CAGCCCGCCTCCCACTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41.5:1:28.5:1:1:0:60:4:1:0:1.5 -GL000212.1 55 . ATT A 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48768;SOR=0;LSEQ=CTACACAGAAGTGATCCAAT;RSEQ=TAGCTATAGAGCTATATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:14,0:0.125:1,0:30:1:33:0:1:0:29.5:4:0.125:0:0.5 0/0:13:0:0,0:13,0:0:1,0:25.6:1:31.3:1:1:0:36.5:26:1:0:0.2 -GL000212.1 145 . T C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10326;SOR=0;LSEQ=TCCATTTAAAATATGTTCTG;RSEQ=TTTCTTAACTTCAGGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:2,0:51,19:0.0278:2,0:26.5:1:34:0:1:0:23:4:0.0278:0:2 0/0:151:0:0,0:110,41:0:2,0:21.7:1:28.8:1:1:0:41.8:29.2:1:0:0.1 -GL000212.1 203 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11714;SOR=0;LSEQ=TTTTGGCCAAGGAGCAGAAG;RSEQ=AGGATTACTTGCCTGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:72,67:0.0142:2,2:42.5:1:29.5:1:1:1.07405:49.5:4:0.0144:0:1.5 0/0:270:0:0,0:129,141:0:2,0:26.8:1:30.6:1:1:0:51.4:134:1:0:0.1 -GL000212.1 205 . G A 97 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02821;SOR=0.30095;LSEQ=TTGGCCAAGGAGCAGAAGGA;RSEQ=GATTACTTGCCTGTTCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:10:9,1:64,67:0.0704:2,2:24.7:1:29.2:1:0.018:9.31:27.5:20:0.0719:0:1.8 0/1:270:6:6,0:121,143:0.0222:2,0:27.7:1:30.5:1:0.01016:0:40:12:0.0226:0:1.2 -GL000212.1 246 . A G 84 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.01539;SOR=0.15011;LSEQ=TGTGGTCAGTGTTACCATCC;RSEQ=TAGTTTGTCAGTATTAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:8:3,5:30,57:0.0842:2,2:32.1:1:28:1:1:1.14:29.8:7:0.0761:0:2.4 0/1:148:2:1,1:45,101:0.0135:2,2:32:1:30.5:1:0.52648:2.23:23:4:0.0135:0:2 -GL000212.1 249 . G C 96 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03537;SOR=0.2565;LSEQ=GGTCAGTGTTACCATCCATA;RSEQ=TTTGTCAGTATTAAGGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:9:3,6:24,54:0.1034:2,2:34.1:1:30.6:1:1:1.12:29.1:18:0.1071:0:2.2 0/1:140:4:3,1:42,93:0.0286:2,2:28.5:1:32.3:1:0.09958:6.55:26:8:0.0292:0:2.5 -GL000212.1 295 . T C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16376;SOR=0.43131;LSEQ=TTAAATTGAGTTAACAAATA;RSEQ=GTATTGAATTTTTATTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:9:4,5:3,30:0.2143:2,2:29.9:1:30.4:1:0.02805:7.45:41.2:18:0.2195:0:1.7 0/1:67:7:3,4:12,48:0.1045:2,2:26.1:1:28.7:1:0.18122:2.94:40.4:14:0.1045:0:2.3 -GL000212.1 327 . C T 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59486;SOR=0.73463;LSEQ=TTATTTGGTTTTAGTAGTAA;RSEQ=ATGAGCTCCTAGTTCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:3,5:4,16:0.2857:2,2:27.3:1:28.4:1:0.37148:2.32:40.5:16:0.2857:0:1.8 0/1:53:12:4,8:10,31:0.2264:2,2:26.1:1:27.9:1:0.71086:1.54:48.1:24:0.2264:0:1.5 -GL000212.1 337 . T C 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54715;SOR=Inf;LSEQ=TTAGTAGTAACATGAGCTCC;RSEQ=AGTTCTCACAATTAAGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:7,20:0:2,0:24.5:1:28.9:1:1:0:49:54:1:0:0.6 0/1:53:3:2,1:13,37:0.0566:2,2:15.7:1:28:1:0.18975:5.47:26.7:6:0.0577:0:1.3 -GL000212.1 628 . G A 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATTATTGGCCCATTCT;RSEQ=TTCTTTCCCGCATTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:36.5:1:31.3:1:1:0:31:8:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:43.5:1:30:1:1:0:60:4:1:0:2 -GL000212.1 664 . G A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTCCTCTGTGCTCACTC;RSEQ=TATACAAAATGACATTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:16:1:31.5:1:1:0:25:4:1:0:2 1/1:2:2:1,1:0,0:1:0,2:7.5:1:28:1:1:0:60:4:1:0:2 -GL000212.1 1048 . TA AT 28 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTATAGAGGATTCAGATT;RSEQ=AATTCAGAAGTTAGAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:28.3:1:1:0:50:4:1:0:4 1/1:1:1:0,1:0,0:1:0,0:19:0:31:0:1:0:60:2:1:0:3 -GL000212.1 1065 . A G 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTAAATTCAGAAGTTAGA;RSEQ=TGAAAAAGAATTATATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:32:1:1:0:50:4:1:0:4 1/1:1:1:0,1:0,0:1:0,0:3:0:30:0:1:0:60:2:1:0:3 -GL000212.1 40527 . C G 64 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATAATGTGTGGGCTTGG;RSEQ=ATTCAGTTTTTGAAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:3,1:0,0:1:0,2:13.3:1:32.3:1:1:0:31.5:8:1:0:2.8 -GL000212.1 40532 . A T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTGTGGGCTTGGCATTC;RSEQ=GTTTTTGAAACAAAACACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:0.5:2,0:24:0:32.5:1:1:0:35.5:4:0.5:0:2 -GL000212.1 40536 . T C 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGCTTGGCATTCAGTT;RSEQ=TTGAAACAAAACACTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:16.5:1:33:0:1:0:27.5:4:0.5:0:3.5 -GL000212.1 40549 . A T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCAGTTTTTGAAACAAAAC;RSEQ=CTGAGCCTTCAATGACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:0.5:0,2:18:0:32:1:1:0:27.5:4:0.5:0:3.5 -GL000212.1 40569 . CCTGTACATGTAAAAGCACACCTGTCTGCA TCGGTCTCTGTAGAAGCGCTCCTGTCTTCC 81 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGAGCCTTCAATGACCTT;RSEQ=TGGCAGCAGTTGGACCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:7:6,1:0,0:1:0,2:21.3:1:29:1:1:0:37.6:14:1:1:3.7 -GL000212.1 40596 . G T 49 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTAAAAGCACACCTGTCT;RSEQ=CATGGCAGCAGTTGGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:1:0,2:10.3:1:31:1:1:0:27.7:6:1:0:6 -GL000212.1 40598 . A C 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAAAAGCACACCTGTCTGC;RSEQ=TGGCAGCAGTTGGACCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:1:0:31:0:1:0:40:2:1:0:2 1/0:5:3:2,1:0,0:0.6:0,2:12.3:1:32.7:1:1:0:27.7:6:0.6:0:6 -GL000212.1 40628 . T A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTGGACCTCACAATGTGGAT;RSEQ=GTGCCTTCACCCTGGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:23.4:1:31:1:1:0:33.4:14:1:0:3.9 0/1:24:2:1,1:13,9:0.0833:2,2:30:0:29:0:1:1.42202:40:4:0.087:0:6 -GL000212.1 40634 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6417;SOR=1.49828;LSEQ=CTCACAATGTGGATTGTGCC;RSEQ=TCACCCTGGAATGTTTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:1,0:0.7143:0,2:24.8:1:32.4:1:1:0:33.8:10:0.7143:0:4.6 1/0:24:19:11,8:0,0:0.7917:0,2:28.9:1:30.6:1:1:0:33.9:38:0.7917:0:6.6 -GL000212.1 40641 . T A 105 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20146;SOR=4.85038;LSEQ=TGTGGATTGTGCCTTCACCC;RSEQ=GGAATGTTTATGCCCTATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:4,2:0.1429:2,0:41:0:33:0:0.42857:0:26:2:0.1429:0:8 0/1:24:11:6,5:8,5:0.4583:2,2:34:1:30.5:1:1:1.31735:31.3:22:0.4583:0:6.9 -GL000212.1 40643 . G C 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22581;SOR=Inf;LSEQ=TGGATTGTGCCTTCACCCTG;RSEQ=AATGTTTATGCCCTATCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:1,0:0.8571:0,2:29.2:1:32.8:1:1:0:32.3:12:0.8571:0:4.2 1/1:24:24:14,10:0,0:1:0,2:33.4:1:31.8:1:1:0:33.9:48:1:0:6 -GL000212.1 40645 . A G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTGTGCCTTCACCCTGGA;RSEQ=TGTTTATGCCCTATCGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:32.4:1:31.1:1:1:0:33.4:14:1:0:3.9 0/1:25:2:1,1:14,9:0.08:2,2:19.5:1:31.5:1:1:1.52748:24:4:0.0833:0:6 -GL000212.1 40650 . T G 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55228;SOR=Inf;LSEQ=TGCCTTCACCCTGGAATGTT;RSEQ=ATGCCCTATCGCCATGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:32.9:1:29.6:1:1:0:33.4:14:1:0:3.9 0/1:25:4:3,1:12,9:0.16:2,2:28.8:1:32.8:1:0.62648:2.18:32.3:8:0.1667:0:6.8 -GL000212.1 40656 . C T 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACCCTGGAATGTTTATGCC;RSEQ=TATCGCCATGGTGATGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:25.9:1:31.1:1:1:0:32:16:1:0:4.3 0/1:29:2:1,1:16,11:0.069:2,2:36:0:32:1:1:1.43545:48:4:0.0714:0:5.5 -GL000212.1 40671 . T C 142 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19355;SOR=Inf;LSEQ=ATGCCCTATCGCCATGGTGA;RSEQ=GGGATTAGGGATCTCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:1,0:0.8333:0,2:24.4:1:30.8:1:1:0:30.2:10:0.8333:0:5.4 1/1:25:25:13,12:0,0:1:0,2:27.4:1:30.6:1:1:0:34.5:50:1:0:6.8 -GL000212.1 40673 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCTATCGCCATGGTGATG;RSEQ=GATTAGGGATCTCCTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:23.5:1:30.2:1:1:0:31.8:12:1:0:4.8 0/1:25:2:1,1:12,11:0.08:2,2:24:1:28.5:1:1:1.0871:32:4:0.0833:0:6.5 -GL000212.1 40674 . G A 96 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37409;SOR=3.85381;LSEQ=CCCTATCGCCATGGTGATGG;RSEQ=ATTAGGGATCTCCTGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:4,2:0.1429:2,0:27:0:32:0:0.42857:0:26:2:0.1429:0:8 0/1:25:10:6,4:7,8:0.4:2,2:20.1:1:29:1:0.68817:1.68:33.8:20:0.4167:0:7.4 -GL000212.1 40682 . A G 97 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37409;SOR=3.85381;LSEQ=CCATGGTGATGGGATTAGGG;RSEQ=TCTCCTGCCCTTGGTCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:4,2:0.1429:2,0:19:0:34:0:0.42857:0:26:2:0.1429:0:8 0/1:25:10:6,4:7,8:0.4:2,2:19.6:1:29.4:1:0.68817:1.68:32.6:9:0.3913:0:7.7 -GL000212.1 40691 . C T 139 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17241;SOR=Inf;LSEQ=TGGGATTAGGGATCTCCTGC;RSEQ=CTTGGTCCTAAGTGCCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:0.8:0,2:23.3:1:31.3:1:1:0:31.8:8:0.8:0:6.8 1/1:24:24:12,12:0,0:1:0,2:18.3:1:30.5:1:1:0:33.8:48:1:0:7 -GL000212.1 40695 . G C 94 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63612;SOR=2.22344;LSEQ=ATTAGGGATCTCCTGCCCTT;RSEQ=GTCCTAAGTGCCACTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:3,1:0.2:2,0:6:0:32:0:0.4:0:26:2:0.2:0:8 0/1:22:8:4,4:7,7:0.3636:2,2:10:1:31.5:1:1:1:30.5:16:0.3636:0:8 -GL000212.1 40699 . C G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGATCTCCTGCCCTTGGTC;RSEQ=TAAGTGCCACTGTCTGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23.3:1:32.3:1:1:0:31.8:8:1:0:6.8 0/1:20:2:2,0:9,9:0.1:2,0:12:0:32:0:0.47895:0:38.5:4:0.1053:0:8 -GL000212.1 40703 . GT AG 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20984;SOR=0.22009;LSEQ=TCTCCTGCCCTTGGTCCTAA;RSEQ=GCCACTGTCTGTGATGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:0.4:2,0:5.6:1:30.9:1:1:0:50:4:0.246:0.2139:8 0/1:17:2:1,1:9,6:0.1176:2,2:8:1:27.7:1:1:1.46382:32.5:4:0.1176:0.0588:5 -GL000212.1 40704 . T G 102 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51703;SOR=0;LSEQ=CTCCTGCCCTTGGTCCTAAG;RSEQ=GCCACTGTCTGTGATGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:29.7:1:32.3:1:1:0:33.7:6:1:0:6.3 1/0:16:10:5,5:0,0:0.625:0,2:25.2:1:30.9:1:1:0:34.1:20:0.6667:0:7.1 -GL000212.1 40713 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=TTGGTCCTAAGTGCCACTGT;RSEQ=TGTGATGAGTTTTTCAAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:15.6:1:30.9:1:1:0:42.3:14:1:0:7.3 0/1:12:2:1,1:6,4:0.1667:2,2:22.5:1:28.5:1:1:1.4491:34:4:0.1818:0:7.5 -GL000212.1 40718 . A C 93 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTAAGTGCCACTGTCTGTG;RSEQ=TGAGTTTTTCAAAGGTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:1:0,2:21.2:1:32.5:1:1:0:45.7:12:1:0:7.7 1/1:7:7:3,4:0,0:1:0,2:28:1:33.3:1:1:0:36.3:14:1:0:7.4 -GL000212.1 40721 . A T 87 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=AAGTGCCACTGTCTGTGATG;RSEQ=GTTTTTCAAAGGTCAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,0:0.8333:0,2:24.6:1:31:1:1:0:47.8:10:0.8333:0:7.6 1/1:7:7:3,4:0,0:1:0,2:26.7:1:31.3:1:1:0:36.3:14:1:0:7.4 -GL000212.1 40727 . T C 65 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1033;SOR=Inf;LSEQ=CACTGTCTGTGATGAGTTTT;RSEQ=CAAAGGTCAGAGCAGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:25.8:1:30.5:1:1:0:45.7:12:1:0:7.7 0/1:9:4:1,3:3,2:0.4444:2,2:29:1:32.8:1:0.52381:3.76419:29.5:8:0.4444:0:7 -GL000212.1 40738 . AG CA 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19231;SOR=0;LSEQ=ATGAGTTTTTCAAAGGTCAG;RSEQ=CAGATTGAACCTTTGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:1,2:0.3333:2,0:35:0:33:0:0.4:0:50:4:0.3333:0:7 0/0:7:0:0,0:3,4:0:2,0:21.6:1:31.4:1:1:0:35.9:14:1:0:7.3 -GL000212.1 40739 . G A 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59207;SOR=2.32357;LSEQ=TGAGTTTTTCAAAGGTCAGA;RSEQ=CAGATTGAACCTTTGTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,1:0.5:0,2:25:1:30.3:1:1:0:46.3:6:0.75:0:7.3 1/0:7:5:2,3:0,0:0.7143:0,2:23.6:1:31.6:1:1:0:35.2:10:0.7143:0:7 -GL000212.1 40744 . T G 84 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0101;SOR=0.0367;LSEQ=TTTTCAAAGGTCAGAGCAGA;RSEQ=TGAACCTTTGTGGTTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:0,1:0.8571:0,2:31.5:1:32.5:1:1:0:45.7:12:0.8571:0:7.3 0/1:8:1:1,0:3,4:0.125:2,0:32:0:34:0:1:0:60:2:0.125:0:7 -GL000212.1 40761 . C T 82 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AGATTGAACCTTTGTGGTTT;RSEQ=ATTTTCCCTGATTTTGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:0.8333:0,2:35.6:1:29.2:1:1:0:50.4:10:0.8333:0:7.4 1/1:8:8:5,3:0,0:1:0,2:23.4:1:27.4:1:1:0:38.6:7:1:0:6.5 -GL000212.1 40772 . AT TG 61 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23352;SOR=Inf;LSEQ=TTGTGGTTTCATTTTCCCTG;RSEQ=TTTGATTTTTCTTATGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:25.8:1:31.7:1:1:0:49.3:12:1:0:6.3 0/1:10:4:2,2:4,2:0.4:2,2:19:1:30.6:1:1:1.86195:41:8:0.4:0:5.3 -GL000212.1 40773 . T G 96 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61485;SOR=0.41937;LSEQ=TGTGGTTTCATTTTCCCTGA;RSEQ=TTTGATTTTTCTTATGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:29.5:1:33.5:1:1:0:48.8:8:0.8:0:7.5 1/0:13:8:5,3:0,0:0.6154:0,2:18.9:1:32:1:1:0:45.3:16:0.8889:0:7 -GL000212.1 40778 . A C 103 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.06478;SOR=7.87587;LSEQ=TTTCATTTTCCCTGATTTTG;RSEQ=TTTTTCTTATGGGGAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:3,3:0.3333:2,2:4:0:31.3:1:1:1.8525:60:6:0.3333:0:7.3 1/1:11:9:5,4:1,1:0.8182:2,2:20.1:1:32.7:1:1:1.22:44.8:18:0.8182:0:6.3 -GL000212.1 40786 . T C 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35714;SOR=Inf;LSEQ=TCCCTGATTTTGATTTTTCT;RSEQ=ATGGGGAACCTGTGTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:4,5:0,1:0.9:0,2:13.1:1:32.6:1:1:0:55:18:0.9:0:7.4 1/1:18:18:7,11:0,0:1:0,2:16.6:1:32:1:1:0:50.1:36:1:0:6.7 -GL000212.1 40798 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATTTTTCTTATGGGGAACCT;RSEQ=TGTTGCTGCATTCAAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:13.5:1:32.6:1:1:0:51.2:28:1:0:6.6 0/1:29:2:1,1:12,15:0.069:2,2:6.5:1:28.5:1:1:1.24:60:4:0.069:0:7 -GL000212.1 40801 . T G 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.6561;SOR=2.44345;LSEQ=TTTCTTATGGGGAACCTGTG;RSEQ=TGCTGCATTCAAGGTATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:4,8:0.0769:2,0:5:0:30:0:1:0:35:2:0.0769:0:8 0/1:35:6:3,3:14,15:0.1714:2,2:15.3:1:31.5:1:1:1.07:56.3:12:0.1714:0:7.3 -GL000212.1 40808 . A T 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91098;LSEQ=TGGGGAACCTGTGTTGCTGC;RSEQ=TTCAAGGTATGTTCATACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:5,6:0,1:0.9167:0,2:20.9:1:30.8:1:1:0:51.5:22:0.9167:0:7 1/1:33:30:15,15:2,1:0.9091:2,2:18.7:1:30.3:1:1:1.9597:55.4:60:0.9091:0:6.7 -GL000212.1 40811 . C G 157 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29363;SOR=2.91996;LSEQ=GGAACCTGTGTTGCTGCATT;RSEQ=AAGGTATGTTCATACTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:5,6:1,1:0.8462:2,2:23.9:1:32.2:1:1:1.18321:51.5:22:0.8462:0:7 1/1:35:33:18,15:1,1:0.9429:2,2:19.1:1:31.2:1:1:1.19:56.5:66:0.9429:0:6.5 -GL000212.1 40819 . G A 158 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05553;SOR=Inf;LSEQ=TGTTGCTGCATTCAAGGTAT;RSEQ=TTCATACTGGCCTGTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:7,6:1,1:0.8667:2,2:26.6:1:30.2:1:1:1.15:51.9:26:0.8667:0:6.8 1/1:47:47:23,24:0,0:1:0,2:19.5:1:28.6:1:1:0:56.2:94:1:0:6 -GL000212.1 40827 . T G 74 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00034;SOR=0;LSEQ=CATTCAAGGTATGTTCATAC;RSEQ=GGCCTGTCAAATGCGAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:6,5:0.3125:2,2:28.2:1:32:1:1:1.73457:47.6:10:0.3125:0:6.6 0/0:55:0:0,0:27,28:0:2,0:21.8:1:30.1:1:1:0:56.8:110:1:0:5.7 -GL000212.1 40833 . G T 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12689;SOR=7.32861;LSEQ=AGGTATGTTCATACTGGCCT;RSEQ=TCAAATGCGAACTCTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:15:7,8:1,1:0.8824:2,2:24.5:1:30.3:1:1:1.13389:53:30:0.8824:0:6.5 1/1:58:57:30,27:0,0:0.9828:0,2:24.1:1:29.7:1:1:0:56.4:56:0.9825:0:5.5 -GL000212.1 40842 . G C 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95365;LSEQ=CATACTGGCCTGTCAAATGC;RSEQ=AACTCTTCAAATTACTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:7,9:1,0:0.9412:0,2:21.6:1:31.4:1:0.47059:0:53.4:32:0.9412:0:6.3 1/1:65:61:30,31:1,1:0.9385:2,2:25.9:1:30.6:1:1:1.0328:57.1:29.5:0.9365:0:5.3 -GL000212.1 40844 . A G 92 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.79595;LSEQ=TACTGGCCTGTCAAATGCGA;RSEQ=CTCTTCAAATTACTAGTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:8,8:0.0588:2,0:6:0:33:0:1:0:60:2:0.0588:0:3 0/1:69:7:4,3:29,32:0.1014:2,2:26.1:1:33.1:1:0.70532:1.46:55.6:14:0.1029:0:5.6 -GL000212.1 40845 . C A 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACTGGCCTGTCAAATGCGAA;RSEQ=TCTTCAAATTACTAGTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:22:1:32.3:1:1:0:53.8:34:1:0:6.1 0/1:71:4:2,2:32,35:0.0563:2,2:32.5:1:30.8:1:1:1.09:57:8:0.0563:0:6.5 -GL000212.1 40852 . A T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48307;SOR=0.51191;LSEQ=TGTCAAATGCGAACTCTTCA;RSEQ=ATTACTAGTTAATGCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:5,7:0.0769:2,0:25:0:33:0:0.46154:0:60:2:0.0769:0:8 0/1:74:3:2,1:33,38:0.0405:2,2:20.3:1:29.3:1:0.59992:2.28:59.7:6:0.0411:0:4.7 -GL000212.1 40860 . G C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCGAACTCTTCAAATTACTA;RSEQ=TTAATGCTTTCAAAATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:30.3:1:32.6:1:1:0:54.8:24:1:0:5.8 0/1:79:2:1,1:37,40:0.0253:2,2:32.5:1:33:0:1:1.08:60:4:0.0256:0:7 -GL000212.1 40865 . T G 180 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00358;SOR=6.99994;LSEQ=CTCTTCAAATTACTAGTTAA;RSEQ=GCTTTCAAAATATGTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:5,4:0.25:2,0:23.3:1:32.3:1:0.20455:0:60:6:0.25:0:5.7 1/0:78:55:26,29:11,10:0.7051:2,2:30.4:1:31.3:1:0.79915:1.22361:53.4:110:0.7051:0:5 -GL000212.1 40875 . A G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00022;SOR=0.05777;LSEQ=TACTAGTTAATGCTTTCAAA;RSEQ=TATGTTATTTAAAAAATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:4,2:1,4:0.5455:2,2:40.2:1:33.2:1:0.24242:6.44:52.8:12:0.5455:0:5.2 0/1:82:5:2,3:37,40:0.061:2,2:22:1:31.6:1:1:1.38204:55.6:10:0.0625:0:6.8 -GL000212.1 40876 . T C 82 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59342;SOR=Inf;LSEQ=ACTAGTTAATGCTTTCAAAA;RSEQ=ATGTTATTTAAAAAATTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:29.4:1:29.8:1:1:0:54.3:22:1:0:5.6 0/1:82:7:4,3:35,40:0.0854:2,2:26.9:1:29.3:1:0.70334:1.52:32.6:6:0.0741:0:4 -GL000212.1 40880 . T G 87 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTAATGCTTTCAAAATATG;RSEQ=TATTTAAAAAATTATCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:30.6:1:30.8:1:1:0:53.7:20:1:0:5.4 0/1:81:7:4,3:35,38:0.0864:2,2:30.6:1:31.1:1:0.70866:1.44:40.9:14:0.0864:0:4.6 -GL000212.1 40884 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGCTTTCAAAATATGTTAT;RSEQ=TAAAAAATTATCCTCTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:28.6:1:30.5:1:1:0:51.7:20:1:0:5.2 0/1:80:2:1,1:38,40:0.025:2,2:11.5:1:31.5:1:1:1.05:29:4:0.0256:0:3.5 -GL000212.1 40886 . A C 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=6e-05;SOR=0.03884;LSEQ=GCTTTCAAAATATGTTATTT;RSEQ=AAAAATTATCCTCTGTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:1,3:0.6:2,2:28.2:1:31.7:1:0.57143:2.69:49.5:12:0.6:0:5.5 0/1:79:4:2,2:37,36:0.0506:2,2:14:1:30:1:1:1.02742:54.5:8:0.0506:0:6.5 -GL000212.1 40896 . C A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTTATTTAAAAAATTAT;RSEQ=CTCTGTATTTTCCATATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:21.4:1:31.4:1:1:0:51.7:20:1:0:5.2 0/1:76:2:1,1:33,41:0.0263:2,2:40:1:26.5:1:1:1.24:57:4:0.0263:0:6 -GL000212.1 40900 . T C 32 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01168;SOR=0;LSEQ=TTATTTAAAAAATTATCCTC;RSEQ=GTATTTTCCATATGCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,3:0.2222:2,2:26:1:32:1:1:1:54.5:4:0.2222:0:5.5 0/0:70:0:0,0:29,39:0:2,0:25.3:1:29.7:1:1:0:46.1:67:0.971:0:4.9 -GL000212.1 40906 . T G 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.43119;SOR=0.43706;LSEQ=AAAAAATTATCCTCTGTATT;RSEQ=TCCATATGCAGTTATAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:2,4:0.125:2,0:50:0:31:0:1:0:40:2:0.125:0:7 0/1:69:4:2,2:27,38:0.058:2,2:20.5:1:31.3:1:1:1.40:54.8:8:0.0588:0:5.3 -GL000212.1 40910 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AATTATCCTCTGTATTTTCC;RSEQ=TATGCAGTTATAAATATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:16:1:30.4:1:1:0:52.1:18:1:0:4.8 0/1:66:2:0,2:26,38:0.0303:2,0:10:1:28.5:1:0.51515:0:44:4:0.0308:0:6.5 -GL000212.1 40924 . A G 159 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00446;SOR=Inf;LSEQ=TTTTCCATATGCAGTTATAA;RSEQ=TATGTTTCATGGCTATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:20.4:1:30.2:1:1:0:44:10:1:0:5.6 1/0:50:35:11,24:3,7:0.7:2,2:24.6:1:31.1:1:1:1.07:40.9:70:0.7:0:5.5 -GL000212.1 40927 . T G 159 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=TCCATATGCAGTTATAAATA;RSEQ=GTTTCATGGCTATGTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,4:0:0,0:18.8:1:28:1:1:0:45:8:0.8:0:5.3 1/1:51:41:13,28:2,5:0.8039:2,2:24:1:29.8:1:1:1.16:40:40:0.8:0:5.5 -GL000212.1 40937 . C T 155 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTATAAATATGTTTCATGG;RSEQ=TATGTTTTATTCCTCAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:1:0,0:27.5:1:28.5:1:1:0:40:8:1:0:5.8 1/1:42:41:10,31:0,0:0.9762:0,2:26:1:29.1:1:1:0:37:82:0.9762:0:5.8 -GL000212.1 40945 . T C 30 d7;v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01929;SOR=0.03345;LSEQ=TATGTTTCATGGCTATGTTT;RSEQ=ATTCCTCAATTTATATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:30:1:30.5:1:1:0:40:4:0.5:0:5.5 0/1:39:1:0,1:10,28:0.0256:2,0:30:0:27:0:1:0:38:2:0.0256:0:7 -GL000212.1 40954 . A G 153 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10256;SOR=Inf;LSEQ=TGGCTATGTTTTATTCCTCA;RSEQ=TTTATATGTTTGATTATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:21:1:30.7:1:1:0:40:6:0.75:0:6 1/1:35:35:9,26:0,0:1:0,2:24.8:1:30:1:1:0:33.8:34:1:0:6.2 -GL000212.1 40958 . A C 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATGTTTTATTCCTCAATTT;RSEQ=TATGTTTGATTATTGTACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:36.7:1:31:1:1:0:40:6:1:0:5.3 0/1:34:3:1,2:7,24:0.0882:2,2:5:1:30:1:1:1.68:22:6:0.0882:0:5.7 -GL000212.1 40961 . TG CA 140 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01404;SOR=Inf;LSEQ=GTTTTATTCCTCAATTTATA;RSEQ=TTTGATTATTGTACCAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:35.7:1:28:1:1:0:40:6:1:0:5.3 1/1:31:25:6,19:0,6:0.8065:0,2:26.2:1:30.3:1:0.30933:0:33.8:50:0.8065:0.0323:5.4 -GL000212.1 40962 . G A 77 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0154;SOR=0;LSEQ=TTTTATTCCTCAATTTATAT;RSEQ=TTTGATTATTGTACCAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:35.3:1:30.7:1:1:0:40:6:1:0:5.3 0/1:30:6:0,6:0,0:0.2:0,0:21.8:1:30:1:1:0:31.3:12:1:0:6.5 -GL000212.1 40970 . A C 34 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCAATTTATATGTTTGATT;RSEQ=TTGTACCAAGCAGAGTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:32.7:1:30.7:1:1:0:40:6:1:0:5.3 0/1:27:2:0,2:4,21:0.0741:2,0:25.5:1:34:0:1:0:32.5:4:0.0741:0:6.5 -GL000212.1 40975 . A C 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTATATGTTTGATTATTGT;RSEQ=CCAAGCAGAGTACCTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:29.3:1:30.7:1:1:0:40:6:1:0:5.3 0/1:24:2:0,2:3,19:0.0833:2,0:20.5:1:33:0:1:0:32.5:4:0.0833:0:6.5 -GL000212.1 40988 . C G 33 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTATTGTACCAAGCAGAGTA;RSEQ=CTTTGAAATTTTTCTTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:27:1:32:0:1:0:40:4:1:0:5.5 0/1:20:2:0,2:1,17:0.1:1,0:7.5:1:33.5:1:1:0:32.5:4:0.1:0:6.5 -GL000212.1 41002 . C T 112 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=AGAGTACCTTTGAAATTTTT;RSEQ=TTCATTTAAAAAATATGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:0.5:0,0:20:0:32:0:1:0:40:2:0.5:0:6 1/1:13:13:1,12:0,0:1:0,1:25.4:1:30.4:1:1:0:32.6:12:1:0:6 -GL000212.1 41020 . T G 95 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TTCTTCATTTAAAAAATATG;RSEQ=ATCTTGGCTAAGGCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:2:0:30:0:1:0:40:2:1:0:6 1/1:9:8:1,7:0,1:0.8889:0,2:15.3:1:31.8:1:1:0:30.8:16:0.8889:0:5.9 -GL000212.1 41030 . A C 71 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAATATGTATCTTGGCT;RSEQ=AGGCCTGTAATCCCAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:1,4:0,0:1:0,2:17.6:1:30.6:1:1:0:27.2:4:1:0:5.4 -GL000212.1 41153 . T G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACAAAAAATTAGCCAG;RSEQ=CATGGTGGCAGCTGGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:10:1:31.5:1:1:0:33.5:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000212.1 41173 . C G 52 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TCATGGTGGCAGCTGGTGTA;RSEQ=TCCCAGTGTGGTGTAGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:26:1:33.3:1:1:0:35.7:6:1:0:6.3 1/0:5:3:3,0:0,0:0.6:0,0:13.7:1:33:1:1:0:38.7:6:0.6:0:5.3 -GL000212.1 41189 . G T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTACTCCCAGTGTGGTGTA;RSEQ=TCCCAGCTACCTGGGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:25:1:33:1:1:0:41.3:12:1:0:6.3 0/1:17:2:1,1:12,3:0.1176:2,2:22.5:1:30.5:1:0.42647:3.6058:49:4:0.1176:0:5 -GL000212.1 41212 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGCTACCTGGGAGGCTGA;RSEQ=GCAGGACTATCGCTTGAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:32.7:1:32:1:1:0:41.3:12:1:0:6.3 0/1:18:2:1,1:12,4:0.1111:2,2:22.5:1:29:1:0.4902:2.79285:46:4:0.1111:0:7 -GL000212.1 41214 . C G 119 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54644;SOR=0;LSEQ=AGCTACCTGGGAGGCTGAGG;RSEQ=AGGACTATCGCTTGAACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1:0,2:32.7:1:31:1:1:0:41.3:12:1:0:6.3 1/1:18:15:11,4:0,0:0.8333:0,2:35.1:1:30.7:1:1:0:45.3:30:0.8824:0:6.5 -GL000212.1 41220 . T A 102 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.62867;SOR=0.41394;LSEQ=CTGGGAGGCTGAGGCAGGAC;RSEQ=ATCGCTTGAACCCGTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:0,0:0.8333:0,2:34.2:1:29:1:1:0:41.6:10:0.8333:0:6.6 1/0:18:12:9,3:0,0:0.6667:0,2:38.2:1:28.7:1:1:0:40.8:24:0.6667:0:6.8 -GL000212.1 41222 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGAGGCTGAGGCAGGACTA;RSEQ=CGCTTGAACCCGTGAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:31.5:1:30.2:1:1:0:41.3:12:1:0:6.3 0/1:18:2:1,1:12,4:0.1111:2,2:43.5:1:32:1:0.4902:2.79285:60:4:0.1111:0:5.5 -GL000212.1 41229 . A G 99 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.35095;SOR=0.26336;LSEQ=TGAGGCAGGACTATCGCTTG;RSEQ=ACCCGTGAGGCAGAGGTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:0.8333:0,2:26.6:1:30.2:1:1:0:40.2:10:0.8333:0:6.4 1/0:18:10:8,2:5,3:0.5556:2,2:38:1:29.9:1:0.60784:2.28:39.7:20:0.5556:0:6.7 -GL000212.1 41238 . G T 25 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTATCGCTTGAACCCGTGA;RSEQ=GCAGAGGTTGCATTGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:19.2:1:30.7:1:1:0:43.5:12:1:0:6.5 0/1:19:2:2,0:11,6:0.1053:2,0:15:0:25:0:1:0:33.5:4:0.1053:0:7 -GL000212.1 41244 . G A 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61752;SOR=0.44089;LSEQ=GCTTGAACCCGTGAGGCAGA;RSEQ=GTTGCATTGAGCCAAGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:0,0:0.6:0,2:23:1:28.3:1:1:0:44.7:6:0.6:0:6.7 0/1:18:7:5,2:0,0:0.3889:0,2:26.1:1:28.1:1:1:0:40.6:14:0.3889:0:6.6 -GL000212.1 41251 . T G 127 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGTGAGGCAGAGGTTGCA;RSEQ=TGAGCCAAGATGGCGCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1:0,2:14.4:1:31:1:1:0:44.2:10:1:0:6.8 1/1:17:17:11,6:0,0:1:0,2:21.1:1:31.2:1:1:0:46.2:34:1:0:6.8 -GL000212.1 41257 . C A 110 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAGAGGTTGCATTGAGC;RSEQ=AAGATGGCGCCATTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:19.3:1:30:1:1:0:44.7:6:1:0:7 1/1:15:13:8,5:1,1:0.8667:2,2:20:1:29.8:1:1:1.55:46.1:26:0.8667:0:7 -GL000212.1 41273 . C T 81 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCCAAGATGGCGCCATTG;RSEQ=ACTCCAGCCTGTGCAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30.5:1:1:0:43.5:4:1:0:7.5 1/1:7:7:5,2:0,0:1:0,2:13:1:29:1:1:0:44.9:14:1:0:7.4 -GL000212.1 41277 . C T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGATGGCGCCATTGCACT;RSEQ=CAGCCTGTGCAACAGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:27:0:30:0:1:0:40:2:1:0:8 1/0:5:3:2,1:1,1:0.6:2,2:15.3:1:29:1:1:1.73:50:6:0.6:0:7.7 -GL000212.1 41280 . G C 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGCGCCATTGCACTCCA;RSEQ=CCTGTGCAACAGAACAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:24:0:32:0:1:0:40:2:1:0:8 1/0:4:3:2,1:0,1:0.75:0,2:12.3:1:28.3:1:1:0:50:6:0.75:0:7.7 -GL000212.1 41762 . T C 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.25;SOR=Inf;LSEQ=TAACTAGCACAGCATAATAA;RSEQ=GTGTGGGCTTCGGATTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:7:0:26:0:1:0:36:2:1:0:8 1/1:3:3:2,1:0,0:1:0,2:5.7:1:31.3:1:1:0:41.3:6:1:0:6.7 -GL000212.1 41773 . C G 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATAATAATGTGTGGGCTT;RSEQ=GGATTCAGTTTTTGAAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:18:0:28:0:1:0:36:2:1:0:8 1/1:4:4:2,2:0,0:1:0,2:15.3:1:31.8:1:1:0:42.8:8:1:0:6.8 -GL000212.1 41784 . T C 64 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TGTGGGCTTCGGATTCAGTT;RSEQ=TTGAAACAAAACACTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:29:0:28:0:1:0:36:2:1:0:8 1/1:4:4:2,2:0,0:1:0,2:26:1:32:1:1:0:42.8:8:1:0:6.8 -GL000212.1 41797 . A T 62 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2;SOR=Inf;LSEQ=TTCAGTTTTTGAAACAAAAC;RSEQ=CTGAGCCTTCAATGACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:42:0:30:0:1:0:36:2:1:0:8 1/1:4:4:2,2:0,0:1:0,2:32.5:1:31:1:1:0:42.8:8:1:0:6.8 -GL000212.1 41817 . C T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGAGCCTTCAATGACCTT;RSEQ=CTGTACATGTAAAAGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:29:0:31:0:1:0:36:2:1:0:8 1/1:3:3:1,2:0,0:1:0,2:26.3:1:29.7:1:1:0:46.7:6:1:0:7.7 -GL000212.1 41819 . T G 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCTTCAATGACCTTCC;RSEQ=GTACATGTAAAAGCACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:27:0:33:0:1:0:36:2:1:0:8 1/1:3:3:1,2:0,0:1:0,2:24.3:1:27.7:1:1:0:46.7:2:1:0:7.7 -GL000212.1 41822 . AC CT 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GCCTTCAATGACCTTCCTGT;RSEQ=ATGTAAAAGCACTCCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:20.3:1:29.5:1:1:0:46.7:6:1:0:6.7 -GL000212.1 42268 . T G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTCATTTAAAAAATATG;RSEQ=ATCTTGGCTAAGGCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:25:1:32:0:1:0:20:4:1:0:8 -GL000212.1 42278 . A C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAATATGTATCTTGGCT;RSEQ=AGGCCTGTAATCCCAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:0.5:2,0:33.5:1:33:0:1:0:20:4:0.5:0:8 -GL000212.1 42297 . TT AA 72 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGGCCTGTAATCCCAGCA;RSEQ=TTGGGAGGCCAAGGCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:5:5,0:1,1:0.7143:2,0:22:1:31.1:1:0.28571:0:28.2:10:0.7143:0:6.8 -GL000212.1 42301 . G T 78 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGTAATCCCAGCATTTT;RSEQ=GGAGGCCAAGGCAAGAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:8:6:6,0:1,1:0.75:2,0:20.3:1:30.3:1:0.25:0:28.2:12:0.75:0:6.8 -GL000212.1 42317 . A G 117 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGGGAGGCCAAGGCAAG;RSEQ=GGATCACAAGGTGAGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:18:16:8,8:1,1:0.8889:2,2:19.2:1:29.3:1:1:1:32:15:0.8824:0:6.1 -GL000212.1 42330 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAAGAGGATCACAAGGT;RSEQ=AGGAGATCAAGACCATCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:2:1,1:7,8:0.1176:2,2:29:0:30.5:1:1:1.13:42:4:0.1176:0:7 -GL000212.1 42332 . G A 116 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGAGGATCACAAGGTGA;RSEQ=GAGATCAAGACCATCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:17:15:7,8:1,1:0.8824:2,2:32.5:1:29.9:1:1:1.13389:32.8:30:0.8824:0:6.1 -GL000212.1 42367 . C G 117 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGCCAATACAGTGAAAC;RSEQ=CTGTCTCTACTAAAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:16:14:6,8:1,1:0.875:2,2:27.6:1:30.9:1:1:1.30929:33.7:28:0.875:0:6 -GL000212.1 42373 . T A 112 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAATACAGTGAAACCCTGTC;RSEQ=CTACTAAAAATACAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:15:14:6,8:0,1:0.9333:0,2:21.6:1:29.6:1:1:0:33.7:28:0.9333:0:6 -GL000212.1 42378 . T G 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGAAACCCTGTCTCTAC;RSEQ=AAAAATACAAAAAATTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:5,7:0.1429:2,2:18:0:29:1:1:1.37:42:4:0.1429:0:7 -GL000212.1 42385 . A C 107 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTGTCTCTACTAAAAAT;RSEQ=CAAAAAATTAGCCAGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:12:11:4,7:0,0:0.9167:0,2:11.9:1:31:1:1:0:33.5:22:0.9167:0:6 -GL000212.1 160620 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54821;SOR=Inf;LSEQ=CTGTTCTAAAATTCCTTAGT;RSEQ=GCTGGCTTTGACCGTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:37,4:0:2,0:24.7:1:30:1:1:0:57.6:19.5:1:0:0 0/1:80:2:1,1:61,17:0.025:2,2:24:1:30:1:0.40158:3.5154:60:4:0.0267:0:1 -GL000212.1 160659 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11375;SOR=0;LSEQ=TGTTGCTGAGTTTTACACAT;RSEQ=TATTTTCTCAACTGCCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:63,21:0.0233:2,2:37.5:1:29:1:0.44843:2.95415:60:4:0.0235:0:1 0/0:168:0:0,0:119,49:0:2,0:22.4:1:31.1:1:1:0:59.1:55:1:0:0.1 -GL000212.1 160695 . G T 33 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.73873;LSEQ=CATATCCTAGGAGGCCTGGA;RSEQ=TACCCATAATACTGTGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:0,1:109,61:0.0058:2,0:1:0:28:0:0.36257:0:60:2:0.006:0:1 0/1:296:3:1,2:180,113:0.0101:2,2:14.3:1:21.3:1:0.56217:3.1731:60:2:0.0069:0:1 -GL000212.1 160730 . T C 124 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83962;SOR=0.86863;LSEQ=TGAGCCCACCTTCCTTGTCC;RSEQ=CAGACATTTCAGAAGGTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:11:10,1:137,106:0.0433:2,2:5:1:29.4:1:0.02756:7.69:32.4:10:0.04:0:2 0/1:423:16:16,0:214,192:0.0378:2,1:5.9:1:31.1:1:5e-05:0:37:32:0.0384:0:1.9 -GL000212.1 160743 . A G 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.71991;SOR=0.90373;LSEQ=CTTGTCCTCAGACATTTCAG;RSEQ=AGGTCGGGAAATTTTTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:33:23,10:139,113:0.1158:2,2:10.7:1:31.6:1:0.13591:1.87:42.3:66:0.1191:0:1.4 0/1:482:51:39,12:227,204:0.1058:2,2:9.5:1:30.8:1:0.00155:2.91:46.1:102:0.1094:0:1.4 -GL000212.1 160866 . G A 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.72414;LSEQ=GATTTGTTTTGCCCTACTGG;RSEQ=TGTTAAGAATTAAATCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:2,0:22,114:0.0145:2,0:40.5:1:29:1:0.0292:0:29:4:0.0146:0:1 0/1:190:2:2,0:35,153:0.0105:2,0:29:1:31:0:0.03709:0:31.5:4:0.0108:0:1 -GL000212.1 161053 . A G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21429;SOR=Inf;LSEQ=ATGAGGGAGAAGTCCTTGAC;RSEQ=TGTAGACCAAAAGGTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:0:2,0:33.2:1:30.4:1:1:0:39.4:20:1:0:0.6 0/1:11:3:1,2:1,7:0.2727:2,2:16.3:1:32.7:1:0.49091:3.06:24.3:6:0.2727:0:2 -GL000212.1 161054 . T C 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31078;SOR=4.76886;LSEQ=TGAGGGAGAAGTCCTTGACA;RSEQ=GTAGACCAAAAGGTAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:1,8:0.1:2,0:40:0:28:0:1:0:27:2:0.1:0:1 0/1:11:4:0,4:2,5:0.3636:2,0:36.3:1:29.5:1:0.49091:0:29.8:8:0.4:0:1 -GL000212.1 161060 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=AGAAGTCCTTGACATGTAGA;RSEQ=CAAAAGGTAATTAAGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:0:2,0:36.1:1:31.4:1:1:0:39.3:18:1:0:0.7 0/1:11:2:1,1:1,8:0.1818:2,2:9:1:30:1:0.34545:6.00:24:4:0.2:0:2 -GL000212.1 161078 . C T 30 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.62174;LSEQ=GACCAAAAGGTAATTAAGGA;RSEQ=CTTTTCATTCATGATATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,5:0.25:2,0:40.5:1:30.5:1:1:0:42:4:0.25:0:1.5 0/1:6:1:0,1:0,5:0.1667:0,0:42:0:31:0:1:0:25:2:0.1667:0:2 -GL000212.1 163250 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AATACAATTTGTTGCACTTC;RSEQ=AAATATCTGGATCAGACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:20.7:1:29.7:1:1:0:40.7:6:1:0:0.7 1/0:4:2:1,1:1,1:0.5:2,2:26:0:32:0:1:1:48:4:0.5:0:2 -GL000212.1 163266 . A G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTTCGAAATATCTGGATCAG;RSEQ=CTATAGTTGTTGTCGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:26:1:19.7:1:1:0:40.7:0.5:1:0:0.7 1/0:4:2:1,1:2,0:0.5:0,2:40.5:1:32.5:1:1:0:48:4:0.5:0:2 -GL000212.1 163372 . G T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47144;LSEQ=CCCGAAAGTATGATTCTAAG;RSEQ=TTGTAAGCATTTTATATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:0.2:0,0:6:1:31:0:1:0:23:4:0.2:0:3 0/1:11:3:3,0:6,2:0.2727:2,0:10:1:29.7:1:1:0:30.7:6:0.2727:0:3 -GL000212.1 163408 . G C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17386;SOR=0.44814;LSEQ=ATTTAGATTTTTAAGTTGTG;RSEQ=AGTATACTTTTAAAGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:14:13,1:15,0:0.4828:1,1:26.1:1:33.3:1:0.48276:0:26.5:28:0.4828:0:2.2 0/1:24:7:6,1:12,4:0.2917:2,2:34.6:1:32:1:1:1.95:33:14:0.3182:0:2.6 -GL000212.1 163444 . C T 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20302;SOR=0.47432;LSEQ=ATAAAAATAATAAGCCAGGT;RSEQ=TCTTAATACTTATCTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:14:13,1:22,1:0.3784:1,1:37.5:1:30.4:1:1:1.66733:26.5:28:0.4:0:2.2 0/1:36:8:6,2:23,5:0.2222:2,2:23.5:1:28.8:1:0.63895:1.51389:34.3:16:0.2222:0:2.6 -GL000212.1 163453 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24074;SOR=Inf;LSEQ=ATAAGCCAGGTCTCTTAATA;RSEQ=TTATCTAAAGAAGTGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:39,2:0:1,0:27.6:1:31.4:1:1:0:37.1:40:1:0:0.8 0/1:40:2:2,0:32,5:0.05:2,0:23.5:1:30:1:1:0:40:4:0.05:0:1 -GL000212.1 163535 . T A 88 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01031;SOR=0.17632;LSEQ=TTAAAAATTATTTTGGGCTG;RSEQ=CACAGAATGTTGACTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:9:1,8:83,37:0.0698:2,2:24.6:1:28:1:0.00093:17.56221:25.6:18:0.0714:0:3.2 0/1:231:3:0,3:160,68:0.013:2,0:25.7:1:32:0:0.02819:0:23.3:6:0.013:0:3 -GL000212.1 163555 . T C 92 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00926;SOR=0.18583;LSEQ=TCACAGAATGTTGACTTTTC;RSEQ=TAATCTGTTACATAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:8:1,7:100,57:0.0485:2,2:37.9:1:30.9:1:0.00586:12.11486:25.6:16:0.0488:0:3.5 0/0:321:3:0,3:203,115:0.0093:2,0:45.7:1:34:0:0.04887:0:23.3:6:0.0095:0:3 -GL000212.1 163574 . T C 109 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00026;SOR=0.14484;LSEQ=CTTAATCTGTTACATAGGGC;RSEQ=GTGGGTCTGGATTTCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:13:4,9:124,74:0.0616:2,2:28.3:1:29.6:1:0.03681:3.74592:26.7:12:0.0585:0:3.2 0/0:426:4:1,3:253,169:0.0094:2,2:28.3:1:31.5:1:0.30764:4.47577:24.8:8:0.0096:0:3 -GL000212.1 163592 . G A 71 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16437;SOR=0.3887;LSEQ=GCTGTGGGTCTGGATTTCCA;RSEQ=GAAAGCGGAGACCTCGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:5:4,1:132,97:0.0214:2,2:24.2:1:30.6:1:0.40269:2.93:23.6:10:0.0216:0:2.2 0/0:476:4:4,0:261,208:0.0084:2,0:14:1:30.8:1:0.13433:0:26.8:8:0.0085:0:2.5 -GL000212.1 163599 . G A 39 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.39911;SOR=0.4841;LSEQ=GTCTGGATTTCCAGGAAAGC;RSEQ=GAGACCTCGAGGTGCAGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:3:0,3:145,106:0.0118:2,0:23:1:31.7:1:0.07778:0:23.3:6:0.012:0:4.3 0/0:522:3:3,0:282,236:0.0057:2,0:1.7:1:25:1:0.2552:0:60:6:0.0058:0:1 -GL000212.1 163628 . T C 52 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04571;SOR=0.12488;LSEQ=GAGGTGCAGGACTGTCGGGG;RSEQ=GAGGTGGCCGAGGCAGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:4:1,3:149,155:0.0129:2,2:35.3:1:26:1:0.62306:2.87509:27.3:3:0.0099:0:3.3 0/0:615:1:0,1:302,312:0.0016:2,0:48:0:26:0:1:0:23:2:0.0017:0:3 -GL000212.1 163644 . G A 97 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00108;SOR=0.10497;LSEQ=GGGGTGAGGTGGCCGAGGCA;RSEQ=GTCAAAGCTGAAAAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:9:6,3:138,148:0.0305:2,2:13.4:1:30.8:1:0.32613:2.14:33.1:18:0.0308:0:3.2 0/0:609:2:0,2:304,303:0.0033:2,0:34.5:1:24:1:0.49918:0:41.5:1:0.0017:0:2 -GL000212.1 163666 . C T 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24129;SOR=1.46956;LSEQ=TCAAAGCTGAAAAGTGGAAT;RSEQ=GGAGCTGTTGTATTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:14:6,8:125,144:0.0491:2,2:22.7:1:30.7:1:1:1.15681:30.7:28:0.0495:0:1.5 0/1:595:42:20,22:264,289:0.0706:2,2:20.1:1:30.5:1:1:1.00484:38.8:84:0.0716:0:1.5 -GL000212.1 163697 . C G 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09656;SOR=0.41303;LSEQ=TATTGCCTGGGGTGAGGCTT;RSEQ=CTTCATGTATATTTTCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:8:6,2:72,142:0.036:2,2:27.4:1:33.9:1:0.02367:5.87:30:16:0.037:0:3 0/1:461:7:0,7:185,268:0.0152:2,0:13.1:1:33.1:1:0.04512:0:26.6:14:0.0155:0:1.9 -GL000212.1 163713 . C A 238 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.55484;SOR=0;LSEQ=GCTTCCTTCATGTATATTTT;RSEQ=TCTAATCTAAATGTCAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:156:156:46,110:0,0:1:0,2:23.7:1:30:1:1:0:54.5:77:1:0:1.4 1/1:334:331:129,202:0,3:0.991:0,2:25.4:1:28.5:1:0.2867:0:55.1:65.2:0.9909:0:1.3 -GL000212.1 163741 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10335;SOR=0;LSEQ=TAAATGTCAGTTAATGATGA;RSEQ=AATCTCATAGCAAGTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:2,0:20,78:0.02:2,0:18.5:1:30.5:1:0.04667:0:26:4:0.02:0:4 0/0:210:0:0,0:61,149:0:2,0:12:0:13:0:1:0:40:0:0:0:4 -GL000212.1 163775 . T C 208 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTATTTTGAACTTAAGAGT;RSEQ=ATATAAATAGGTCAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:6,59:0,0:1:0,2:24.2:1:32:1:1:0:53.8:130:1:0:2.1 1/1:96:96:12,84:0,0:1:0,2:24.3:1:31.6:1:1:0:57.2:47:1:0:1.8 -GL000212.1 163808 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2178;SOR=0.51122;LSEQ=CAAAATGTTTATTTTACTGT;RSEQ=CTACTTTGCTTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:11:2,9:2,25:0.2895:2,2:38:1:31.4:1:0.56411:2.69:33.9:22:0.2895:0:4.5 0/1:70:12:6,6:11,47:0.1714:2,2:31.8:1:30.4:1:0.05775:4.16:36.3:11:0.1594:0:4.8 -GL000212.1 163815 . T C 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17525;SOR=0.46863;LSEQ=TTTATTTTACTGTTCTACTT;RSEQ=GCTTTTTTTTTGAGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:9:1,8:3,20:0.2813:2,2:40.1:1:30.6:1:1:1.19338:34.1:18:0.2903:0:4.9 0/1:65:10:5,5:12,43:0.1538:2,2:34.3:1:29.6:1:0.11122:3.50:36.2:9:0.1406:0:5 -GL000212.1 163816 . G T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60084;SOR=0.49577;LSEQ=TTATTTTACTGTTCTACTTT;RSEQ=CTTTTTTTTTGAGCCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:3,27:0.0625:2,2:16.5:1:31.5:1:0.2379:7.94:33:4:0.0645:0:3 0/1:63:2:1,1:16,45:0.0317:2,2:39.5:1:30.5:1:0.47005:2.76:37:4:0.0328:0:3.5 -GL000212.1 163817 . CT C 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.49399;LSEQ=TATTTTACTGTTCTACTTTG;RSEQ=TTTTTTTTGAGCCTCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:4,26:0.0323:2,0:15:0:34:0:1:0:60:2:0.0333:0:1 0/1:63:3:1,2:16,44:0.0476:2,2:36.7:1:33.3:1:1:1.37:60:6:0.0476:0:0.7 -GL000212.1 163832 . T A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27088;SOR=0.51758;LSEQ=CTTTGCTTTTTTTTTGAGCC;RSEQ=CTGGTTACGTTTTCTTGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:1,8:2,16:0.3333:2,2:25.7:1:30.8:1:1:1:34.1:18:0.3333:0:4.9 0/1:49:10:5,5:11,28:0.2041:2,2:30.4:1:26.7:1:0.26085:2.49:36.2:4:0.1702:0:5 -GL000212.1 163841 . G A 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05449;SOR=0.33669;LSEQ=TTTTTTGAGCCTCTGGTTAC;RSEQ=TTTTCTTGTATATTTACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:2,9:1,9:0.5238:2,2:16:1:31.7:1:1:1.94:33.9:22:0.5238:0:4.5 0/1:45:12:6,6:9,24:0.2667:2,2:21.8:1:28.5:1:0.1736:2.60:36.3:24:0.2667:0:4.8 -GL000212.1 163871 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52941;SOR=Inf;LSEQ=ATATTTACTTTCTCATCCTT;RSEQ=CTCTATTCTTACCTTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:2,10:0:2,0:21.3:1:29.6:1:1:0:56.4:24:1:0:0.5 0/1:22:2:0,2:4,16:0.0909:2,0:13:1:31:1:1:0:31.5:4:0.0909:0:5.5 -GL000212.1 173849 . A G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.99051;LSEQ=CAATGTAGACAATGTGATAG;RSEQ=TATTGTGCTATTTTTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:6:4,2:98,177:0.0214:2,2:15.5:1:27.3:1:0.19434:3.59:27.8:5:0.0187:0:2.8 0/1:520:11:10,1:197,312:0.0212:2,2:14.6:1:28.7:1:0.00062:15.77:34.9:4.5:0.0185:0:2.7 -GL000212.1 173859 . A G 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.73136;SOR=0.72203;LSEQ=AATGTGATAGATATTGTGCT;RSEQ=TTTTTTCATCTTTTTAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:4:2,2:95,170:0.0149:2,2:11.5:1:27.3:1:0.6211:1.79:27.5:3:0.0119:0:2.5 0/1:464:5:4,1:176,275:0.0108:2,2:18:1:28.6:1:0.0819:6.23:21:4:0.0096:0:2.2 -GL000212.1 173898 . G A 43 q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25236;SOR=0.40788;LSEQ=GCTTTTCTCTTTGAAATGTA;RSEQ=CAAAAAAAAAAAAAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:4:1,3:27,75:0.0374:2,2:20.8:1:21.5:1:1:1.07923:44.3:3:0.0366:0:3.5 0/1:193:3:0,3:63,126:0.0155:2,0:21.3:1:17.7:1:0.55211:0:47.7:0.5:0.0072:0:3.7 -GL000212.1 173956 . A G 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0.91041;LSEQ=TCACAAGTTTTAGGTACAGA;RSEQ=CTTTTTGCCTTGTAGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:1,3:0,24:0.1429:1,2:5.5:1:30.8:1:0.14286:0:42.5:8:0.1481:0:1.8 0/1:38:5:0,5:0,33:0.1316:1,0:16.4:1:33:1:1:0:35.6:10:0.1316:0:1.6 -GL000212.1 175100 . A T 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00057;SOR=0;LSEQ=CTTAGGGCTTTTAAGTTTGA;RSEQ=GACTCAGTGTTACAGGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:11:11,0:45,0:0.1964:1,0:23.9:1:32.3:1:1:0:23.9:22:0.2037:0:1 0/0:55:0:0,0:54,1:0:1,0:22.3:1:30.6:1:1:0:25.3:110:1:0:0.3 -GL000212.1 175161 . A G 184 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00134;SOR=0.47207;LSEQ=ATATTCCATTTTTTAAAAAA;RSEQ=ATGTACAAATATGGTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:60:42,18:114,69:0.2469:2,2:26.7:1:31.2:1:0.352:1.41:29.7:59:0.2458:0:1.1 0/1:254:34:26,8:147,73:0.1339:2,2:27.7:1:31.6:1:0.32482:1.61:31.4:68:0.1349:0:1.2 -GL000212.1 175166 . AC A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.56605;LSEQ=CCATTTTTTAAAAAAAATGT;RSEQ=AAATATGGTCTTTTTAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:115:73,42:76,53:0.4713:2,2:28:1:29.5:1:0.51171:1.21:30.5:56.5:0.4708:0.0615:0.6 1/0:268:204:130,74:36,23:0.7612:2,2:29.2:1:29.7:1:0.75988:1.12:30.4:203:0.7632:0.056:0.2 -GL000212.1 175709 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20126;SOR=0;LSEQ=ATTTATTTTAATAAAATGAG;RSEQ=ATAGAAACAGAAATTTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:34,6:0.0476:2,2:20:1:28.5:1:0.30894:5.323:25:4:0.05:0:1 0/0:51:0:0,0:43,8:0:2,0:24.3:1:29.2:1:1:0:35.1:50:1:0:0.3 -GL000212.1 175717 . CAG C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49744;SOR=Inf;LSEQ=TAATAAAATGAGTATAGAAA;RSEQ=AAATTTTAATCATATATAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:43,7:0:2,0:23.1:1:30.7:1:1:0:36.1:100:1:0:0.6 0/1:57:2:2,0:47,8:0.0351:2,0:38:1:32.5:1:1:0:27:4:0.0351:0:0 -GL000212.1 175724 . T G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00578;SOR=0.2506;LSEQ=ATGAGTATAGAAACAGAAAT;RSEQ=TTAATCATATATAAGTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:18:18,0:28,7:0.3396:2,1:27.5:1:32.9:1:0.08112:0:34.2:36:0.3396:0:1 0/1:62:7:6,1:46,9:0.1129:2,2:19:1:30.7:1:1:1.17:41.4:6:0.0984:0:1 -GL000212.1 175735 . A G 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.92367;LSEQ=AACAGAAATTTTAATCATAT;RSEQ=TAAGTATGTAAATACACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:5,0:43,7:0.0909:2,0:28.2:1:33.6:1:1:0:41.6:10:0.0926:0:1.8 0/1:71:6:5,1:55,10:0.0845:2,2:21.8:1:29.7:1:1:1.0985:38:5:0.0714:0:2.5 -GL000212.1 175752 . CTT C 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02421;SOR=0;LSEQ=TATATAAGTATGTAAATACA;RSEQ=TACCTTTTCTGAAAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:4:3,1:47,15:0.0606:2,2:24.3:1:31.6:1:1:1.04375:46.5:8:0.0635:0.0152:0.5 0/0:99:0:0,0:81,18:0:2,0:23.8:1:29.7:1:1:0:42.9:15.5:1:0:0.6 -GL000212.1 175754 . T C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63984;SOR=0.74296;LSEQ=TATAAGTATGTAAATACACT;RSEQ=TACCTTTTCTGAAAAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:10:10,0:37,13:0.1538:2,0:19.3:1:32.5:1:0.09931:0:41.4:20:0.1667:0:1.5 0/1:101:12:10,2:73,16:0.1188:2,2:19.2:1:28.8:1:1:1.09:44.3:5:0.1042:0:1.8 -GL000212.1 175863 . A G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.38202;SOR=0.57351;LSEQ=AAATTGTCACAAAAGTAAAA;RSEQ=AGCTAGGTAAAATTTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:7:1,6:17,47:0.0986:2,2:5:1:31:1:0.66985:2.15039:45.4:14:0.1014:0:2.1 0/1:85:5:1,4:13,67:0.0588:2,2:8.2:1:31.4:1:1:1.28:40.2:10:0.0588:0:2 -GL000212.1 175943 . C G 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ACATAATTGGCTTACCACTT;RSEQ=TAAAATCTGCTTCAATCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:0,3:0,16:0.1579:1,0:31.3:1:33.7:1:1:0:28:6:0.1579:0:1.7 0/1:19:3:0,3:0,15:0.1579:1,0:28.3:1:33:0:1:0:33.3:6:0.1667:0:1.7 -GL000212.1 177006 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18681;SOR=Inf;LSEQ=CATGAAGTTAATTATTCATG;RSEQ=ATTTCATAGATACATAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:43,1:0:1,0:21.9:1:33.2:1:1:0:29:88:1:0:0 0/1:34:2:2,0:30,2:0.0588:2,0:15:1:29.5:1:1:0:27:4:0.0588:0:1 -GL000212.1 177056 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51913;SOR=0;LSEQ=ACTACAGTCACATTCCCTTG;RSEQ=CATGGGTATTTTGGAACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:159,4:0.0121:1,2:24:1:29:1:0.05987:35.66214:33:4:0.0121:0:1 0/0:109:0:0,0:105,4:0:1,0:24.5:1:29.1:1:1:0:26.8:35.333:1:0:0.1 -GL000212.1 177081 . A G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27536;SOR=0;LSEQ=GGTATTTTGGAACAGTAATC;RSEQ=GTCAAATTTAAAATGAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:3,0:143,8:0.0195:2,0:40.7:1:31.7:1:1:0:24:6:0.0196:0:2 0/0:104:0:0,0:92,12:0:2,0:31.8:1:30:1:1:0:26.2:208:1:0:0.1 -GL000212.1 177088 . T C 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26655;SOR=0;LSEQ=TGGAACAGTAATCAGTCAAA;RSEQ=TTAAAATGAAAGTTTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:3,0:131,10:0.0208:2,0:43:1:33:1:1:0:24:6:0.0211:0:2 0/0:104:0:0,0:88,16:0:2,0:31.7:1:29.4:1:1:0:25.7:51:1:0:0.1 -GL000212.1 177250 . A G 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31553;SOR=0.54259;LSEQ=ACTGTCAAAACCAAAACTGA;RSEQ=ATTGAAGATTATAAATCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:16:0,16:0,57:0.2192:1,1:36.5:1:31.6:1:1:0:24:32:0.2254:0:1 0/1:38:5:0,5:0,33:0.1316:1,0:35.6:1:28.2:1:1:0:24:4:0.1111:0:1.8 -GL000214.1 127634 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCACCATTGAATTAGAAGAC;RSEQ=CACATATGTTGAGAATAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:19.5:1:29:1:1:0:22:4:0.6667:0:2 -GL000214.1 127637 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCATTGAATTAGAAGACACA;RSEQ=ATATGTTGAGAATAATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:16.5:1:28:1:1:0:22:4:0.6667:0:2 -GL000214.1 127945 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACCCATCACCTAGGTATTAG;RSEQ=CCCAGCATGCAGTAGCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:29:1:1:0:45:4:1:0:1 0/0:2:0:0,0:1,1:0:2,0:27.5:1:31.5:1:1:0:48:4:1:0:0 -GL000214.1 128098 . C T 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTCCCTGGATAAGTTTG;RSEQ=TGAGGGTAATGACCACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:28:1:1:0:25:4:1:0:2 -GL000214.1 128104 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGATAAGTTTGCTGAGG;RSEQ=TAATGACCACACATCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17.5:1:28:1:1:0:25:4:1:0:2 -GL000214.1 129007 . C T 49 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.58251;LSEQ=CGAATCTTGAAAATATTGTG;RSEQ=TACGTGTTATGTCAGTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:3,2:0.375:2,2:33:1:31:1:1:1.29:49:6:0.375:0:1 0/1:4:1:0,1:2,1:0.25:2,0:35:0:32:0:1:0:27:2:0.25:0:1 -GL000214.1 129129 . A C 75 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=0.2582;LSEQ=GTAGTTGCTACCTAGGGCTG;RSEQ=GGGTCAGGGAGAGGGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:1,0:0.8333:0,2:29.6:1:32.4:1:1:0:41:10:0.8333:0:1.6 1/0:2:1:0,1:1,0:0.5:0,0:44:0:32:0:1:0:33:2:0.5:0:1 -GL000214.1 129542 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16923;SOR=0;LSEQ=GTAGTTTGGCCCGCAGGGAC;RSEQ=CCGACCTGCTGGAGCGTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:0.1818:2,2:9.5:1:28:1:0.49091:3.05504:45:4:0.1818:0:2.5 0/0:15:0:0,0:10,5:0:2,0:16.2:1:30.5:1:1:0:31.9:30:1:0:0.2 -GL000214.1 129547 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48506;SOR=Inf;LSEQ=TTGGCCCGCAGGGACGCCGA;RSEQ=CTGCTGGAGCGTCGTGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,4:0:2,0:16.6:1:31.4:1:1:0:33.6:28:1:0:0.5 0/1:16:2:1,1:9,5:0.125:2,2:32:0:33.5:1:1:1.73197:30:4:0.125:0:1 -GL000214.1 129595 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19843;SOR=Inf;LSEQ=TGTGGCAGCCACGTGGGCCA;RSEQ=CAGGGGGTTCCCGCTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:15,13:0:2,0:32.4:1:31.3:1:1:0:30.5:27:1:0:0.7 0/1:23:2:1,1:12,9:0.087:2,2:36.5:1:30.5:1:1:1.31655:24:4:0.087:0:1 -GL000214.1 129603 . T G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49714;SOR=0;LSEQ=CCACGTGGGCCAGCAGGGGG;RSEQ=TCCCGCTGCACAGCTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:14,12:0.0714:2,2:30.5:1:33:0:1:1.16024:45:4:0.0714:0:2.5 0/0:22:0:0,0:12,10:0:2,0:30.1:1:29.5:1:1:0:30.2:44:1:0:0.2 -GL000214.1 129609 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49734;SOR=0;LSEQ=GGGCCAGCAGGGGGTTCCCG;RSEQ=TGCACAGCTGTGGGGTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:0.0741:2,2:22:1:28.5:1:1:1.0801:24:4:0.0769:0:1 0/0:21:0:0,0:11,10:0:2,0:27.2:1:32:1:1:0:30.5:42:1:0:0.2 -GL000214.1 129892 . G T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGGAGTGCCTGAGTGTAAGT;RSEQ=GAGATGGGTTTGGGGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:43.7:1:31.7:1:1:0:28.7:6:1:0:0.3 1/0:3:2:1,1:0,1:0.6667:0,2:41:1:29.5:1:1:0:26:4:0.6667:0:1.5 -GL000214.1 131391 . C T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GCTTGGTTAGGAAAGGGAAA;RSEQ=GTAAAGTTGTGGAATTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:19.4:1:29.8:1:1:0:39.4:10:1:0:1.6 1/0:3:2:1,1:1,0:0.6667:0,2:28.5:1:31.5:1:1:0:37:4:0.6667:0:4.5 -GL000214.1 131401 . T A 29 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GAAAGGGAAACGTAAAGTTG;RSEQ=GGAATTCTGTTGATGACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:24:0:29.5:1:1:1.7321:44.5:4:0.4:0:2.5 0/0:3:0:0,0:2,1:0:2,0:35:1:28.3:1:1:0:32:6:1:0:3.3 -GL000214.1 131403 . G A 29 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=AAGGGAAACGTAAAGTTGTG;RSEQ=AATTCTGTTGATGACGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:26:0:29:1:1:1.7321:44.5:4:0.4:0:2.5 0/0:3:0:0,0:2,1:0:2,0:37:1:25.3:1:1:0:32:2:1:0:3.3 -GL000214.1 131411 . TT CC 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=CGTAAAGTTGTGGAATTCTG;RSEQ=GATGACGGATGTGAGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:31.4:1:28.4:1:1:0:39.4:10:1:0:1.6 1/0:3:2:1,1:1,0:0.6667:0,2:48:1:31.3:1:1:0:37:4:1:0:3.5 -GL000214.1 131458 . G T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCCTGCGGGATGATGTAGAG;RSEQ=ACTTCCACATCCCTGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:18:1:32.4:1:1:0:40.4:10:1:0:1.4 0/1:5:2:1,1:1,0:0.4:0,2:5.5:1:28:1:1:0:37:4:0.4:0:3.5 -GL000214.1 131549 . A G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGAGGCAGACATGAATCTTG;RSEQ=GGAGTCAGGGCTGGGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:0.5:0,0:4:0:30:0:1:0:31:2:0.5:0:2 1/0:4:2:1,1:1,1:0.5:2,2:12:0:32:0:1:1:41:4:0.5:0:2.5 -GL000214.1 131569 . C A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGAGTCAGGGCTGGGGGAC;RSEQ=GCTCATAATCTCCCGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:33:0:1:0:31:2:1:0:2 0/1:7:2:1,1:4,1:0.2857:2,2:32:0:32:1:1:3.1622:41:4:0.2857:0:2.5 -GL000214.1 131608 . C T 107 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTGAGTCTCTGGGGGAC;RSEQ=CCTGGGCGCATGGGGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:25.5:1:29.8:1:1:0:34:8:1:0:1.3 1/1:12:12:7,5:0,0:1:0,2:27.7:1:30.1:1:1:0:25.8:24:1:0:1.8 -GL000214.1 131616 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52941;SOR=Inf;LSEQ=TCTCTGGGGGACCCCTGGGC;RSEQ=CATGGGGCTGACTCCCGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:20.7:1:29.2:1:1:0:32:12:1:0:1.5 0/1:12:2:1,1:6,4:0.1667:2,2:38:1:31.5:1:1:1.4491:24.5:4:0.1667:0:2.5 -GL000214.1 131678 . A G 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.58824;SOR=0.35335;LSEQ=GTAACTGGGAGCCACAGGAG;RSEQ=GTCCCTGAGGCCTGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:4,3:0.3:2,2:33.3:1:32:1:1:1.44:26.7:6:0.3:0:3.3 0/1:8:1:1,0:3,4:0.125:2,0:19:0:33:0:1:0:40:2:0.1429:0:5 -GL000216.1 79159 . T C 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGAGTCCATTCCATTCCAT;RSEQ=CCATTCCATTTGACTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29:0:30.5:1:1:0:28:4:1:0:5.5 -GL000216.1 80336 . T C 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGGAGTCCATTCCATTC;RSEQ=GTTCGAGTCCATTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:1:27.5:1:1:0:46:4:1:0:8 -GL000216.1 80353 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTTCGAGTCCATTCCA;RSEQ=TGCATTGCGTTCGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:30.5:1:1:0:46:4:1:0:8 -GL000216.1 80355 . G T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTGTTCGAGTCCATTCCATT;RSEQ=CATTGCGTTCGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:28.5:1:1:0:46:4:1:0:8 -GL000216.1 80359 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCGAGTCCATTCCATTGCAT;RSEQ=GCGTTCGATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:36:1:30:1:1:0:46:4:1:0:8 -GL000216.1 80362 . G A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCATTCCATTGCATTGC;RSEQ=TTCGATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:1:28:1:1:0:46:4:1:0:8 -GL000216.1 80368 . T G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTGCATTGCGTTCGA;RSEQ=TCCATTCCATTCCACTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45:1:31:1:1:0:46:4:1:0:8 -GL000216.1 80405 . G C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTCCATTTGAGTCCATT;RSEQ=CATTCCATTCCATTTGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:1:32.5:1:1:0:46:4:1:0:8 -GL000216.1 80407 . A T 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTTGAGTCCATTGC;RSEQ=TTCCATTCCATTTGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:1:32:0:1:0:46:4:1:0:8 -GL000216.1 80671 . C T 47 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.36381;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:12,14:0.037:2,0:46:0:33:0:0.48148:0:40:2:0.037:0:5 0/1:60:3:1,2:28,26:0.05:2,2:32.7:1:29.7:1:0.61148:2.12591:53:6:0.05:0:3 -GL000216.1 80672 . A G 48 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.54913;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCTTTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,13:0:2,0:29.6:1:30.6:1:1:0:31.7:52:0.963:0:3.5 0/1:60:3:3,0:28,28:0.05:2,0:35.3:1:30.7:1:0.23904:0:24.7:6:0.05:0:5 -GL000216.1 80676 . C T 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0.8977;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCTTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:13,13:0.037:2,0:13:0:30:0:1:0:21:2:0.0385:0:4 0/1:60:2:1,1:30,28:0.0333:2,2:32.5:1:28:1:1:1.07017:40:4:0.0339:0:6 -GL000216.1 80680 . C T 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0.8977;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CTTTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:12,14:0.037:2,0:41:0:31:0:0.48148:0:21:2:0.037:0:7 0/1:60:2:2,0:29,29:0.0333:2,0:30:1:28.5:1:0.49209:0:33:4:0.0333:0:4 -GL000216.1 80682 . T G 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36904;SOR=0.42574;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:12,11:0.1111:2,2:33.7:1:32:1:1:2.11883:22:6:0.1111:0:6.3 0/1:60:3:2,1:26,25:0.05:2,2:28.3:1:27.3:1:1:1.90:35.3:6:0.0508:0:5.3 -GL000216.1 80684 . T A 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67194;SOR=0.57544;LSEQ=TCCATTCCATTCCATTCCTT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:12,12:0.1111:2,2:31.7:1:29:1:1:1.95076:21.7:6:0.1154:0:5 0/1:60:4:2,2:29,26:0.0667:2,2:34:1:28.5:1:1:1.11332:44.5:8:0.0702:0:4.3 -GL000216.1 80685 . C T 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.8977;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:13,13:0.037:2,0:41:0:32:0:1:0:27:2:0.037:0:7 0/1:60:2:0,2:31,27:0.0333:2,0:40:1:31:0:0.22938:0:30:4:0.0333:0:6.5 -GL000216.1 80687 . A G 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0.91632;LSEQ=ATTCCATTCCATTCCTTTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:5,5:7,9:0.3704:2,2:34.4:1:28.8:1:1:1.27:23.9:9:0.3462:0:3.8 0/1:60:21:10,11:20,18:0.35:2,2:36.1:1:30.2:1:0.78917:1.21806:39.4:42:0.3559:0:2.7 -GL000216.1 80721 . C T 28 v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.54762;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCTTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,11:0:2,0:12.4:1:31.3:1:1:0:32.4:36:0.9474:0.1053:3.7 0/1:38:2:1,1:17,18:0.0526:2,2:5:0:28.5:1:1:1.06:22:4:0.0541:0:3 -GL000216.1 80723 . T A 28 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCTTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,12:0:2,0:12.7:1:30.3:1:1:0:30.4:16:1:0.1176:3.8 0/1:36:2:1,1:16,18:0.0556:2,2:13.5:1:28:1:1:1.12:21:4:0.0571:0:5 -GL000216.1 80727 . A G 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=1.07522;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCTTTCCATTCCATTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:5,9:0.125:2,0:14.5:1:33:1:1:0:23:4:0.125:0:6 0/1:30:4:1,3:13,13:0.1333:2,2:9.3:1:30:1:0.60153:2.89897:39.8:8:0.1429:0:3.3 -GL000216.1 80730 . C T 42 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.26667;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CTTTCCATTCCATTCGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:8.4:1:31.5:1:1:0:29.2:28:1:0.1429:3.9 0/1:22:3:2,1:8,10:0.1364:2,2:8.3:1:26.7:1:0.58647:2.39:31.3:6:0.1364:0:5 -GL000216.1 80732 . T A 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61079;SOR=0.41858;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCGAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:0,3:0.3333:0,2:5:1:27.7:1:0.4:0:31:6:0.375:0.1111:2.3 0/1:12:2:0,2:5,4:0.1667:2,0:13.5:1:30:1:0.45455:0:22.5:4:0.1667:0:5 -GL000216.1 80737 . A G 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=ATTCCATTCCATTCCTTTCC;RSEQ=TTCCATTCGAGTCCATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:13:1:31:1:1:0:26:10:1:0:4.6 0/1:10:2:1,1:4,4:0.2:2,2:8.5:1:27.5:1:1:1:27:4:0.2222:0:4 -GL000216.1 82260 . TG CA 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATACCTTT;RSEQ=TGTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41:1:28.8:1:1:0:46:4:1:0:2 -GL000216.1 82281 . CATTTGAGTC GAGTT 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCCATTCCATTCCATTC;RSEQ=CATTCCATTCCATTCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:1:30.3:1:1:0:46:4:1:0:2 -GL000216.1 143148 . CTTA C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCTATACAAGAGTTACAT;RSEQ=TCGGTGATCAGTGCAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:33:1:1:0:26:4:1:0:3 -GL000216.1 143198 . C G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGCCCCTGTAGGCAGAG;RSEQ=CTAGACAAGAGTTGCATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8.5:1:30:1:1:0:26:4:1:0:3 -GL000216.1 145146 . G C 31 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GGTGATCAGTGCAGAGATAT;RSEQ=TCACAGTACCCCCATAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:30:0:31.5:1:1:0:22:4:0.5:0:6 1/0:2:1:1,0:1,0:0.5:0,0:30:0:33:0:1:0:24:2:0.5:0:8 -GL000216.1 145152 . G A 62 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTGCAGAGATATGTCACA;RSEQ=TACCCCCATAGGCAGATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:0,0:0.8:0,0:20.8:1:31:1:1:0:21.8:8:0.8:0:6.5 1/1:2:2:2,0:0,0:1:0,0:31:1:32:0:1:0:23:4:1:0:8 -GL000216.1 145154 . A G 65 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.31624;LSEQ=GTGCAGAGATATGTCACAGT;RSEQ=CCCCCATAGGCAGATCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:0,0:0.8:0,0:22.8:1:32.5:1:1:0:21.8:8:0.8:0:6.5 1/0:2:1:1,0:1,0:0.5:0,0:28:0:32:0:1:0:22:2:0.5:0:8 -GL000216.1 145169 . T A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=ACAGTACCCCCATAGGCAGA;RSEQ=CCAAGACAAGAGTCCGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:7,2:0.25:2,2:20:1:30.3:1:1:1.66417:27:6:0.3:0:3.3 0/0:6:0:0,0:6,0:0:0,0:20.7:1:31.7:1:1:0:35.5:12:1:0:6 -GL000216.1 145172 . A G 62 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02073;SOR=15.47999;LSEQ=GTACCCCCATAGGCAGATCC;RSEQ=AGACAAGAGTCCGTCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:9,5:0.0667:2,0:17:0:32:0:1:0:33:2:0.0714:0:8 1/0:7:4:4,0:3,0:0.5714:0,0:18.3:1:31:1:1:0:36:8:0.5714:0:6.5 -GL000216.1 145176 . C G 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17183;SOR=4.6167;LSEQ=CCCCATAGGCAGATCCAAGA;RSEQ=AAGAGTCCGTCACCTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:4,1:6,4:0.3333:2,2:18.8:1:33.2:1:0.6004:2.51:31.6:10:0.3333:0:6.4 1/0:7:5:5,0:2,0:0.7143:0,0:17.4:1:33.6:1:1:0:40.2:10:0.7143:0:6 -GL000216.1 145183 . C T 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11532;SOR=4.12234;LSEQ=GGCAGATCCAAGACAAGAGT;RSEQ=CGTCACCTGGGTGATCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:4,1:6,5:0.3125:2,2:25.8:1:30.6:1:0.58791:3.10:31.6:10:0.3571:0:6.4 1/0:9:6:5,1:2,0:0.6667:0,2:15.7:1:29.7:1:1:0:43.7:12:0.6667:0:5 -GL000216.1 145184 . C T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59475;LSEQ=GCAGATCCAAGACAAGAGTC;RSEQ=GTCACCTGGGTGATCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:7,5:0.1765:2,2:28.7:1:31:1:1:1.40:27:6:0.1875:0:3.3 0/1:9:1:1,0:7,1:0.1111:2,0:43:0:33:0:1:0:22:2:0.1111:0:8 -GL000216.1 145186 . T C 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04607;SOR=6.76252;LSEQ=AGATCCAAGACAAGAGTCCG;RSEQ=CACCTGGGTGATCAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:4,2:6,5:0.3529:2,2:24.5:1:32.2:1:1:1.62:35:12:0.375:0:6.2 1/1:10:8:6,2:2,0:0.8:0,2:16.5:1:32:1:1:0:45.1:16:0.8:0:5.1 -GL000216.1 145195 . T G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6158;LSEQ=ACAAGAGTCCGTCACCTGGG;RSEQ=GATCAGTGCAGAAATATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:24.5:1:32.5:1:1:1.40151:33:4:0.1053:0:6 0/1:15:1:1,0:9,5:0.0667:2,0:7:0:33:0:1:0:24:2:0.0667:0:8 -GL000216.1 145196 . G A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48908;SOR=0;LSEQ=CAAGAGTCCGTCACCTGGGT;RSEQ=ATCAGTGCAGAAATATGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:33.5:1:28.5:1:1:1.40151:44:4:0.1111:0:7 0/0:16:0:0,0:10,6:0:2,0:19.3:1:32.1:1:1:0:42:32:1:0:4.7 -GL000216.1 145201 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01892;SOR=6.06429;LSEQ=GTCCGTCACCTGGGTGATCA;RSEQ=TGCAGAAATATGTCACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:5,3:5,4:0.4211:2,2:30.8:1:30.5:1:1:1.31:33.1:16:0.4444:0:5.9 1/1:17:14:8,6:2,1:0.8235:2,2:21.2:1:30.7:1:1:1.46561:43.1:28:0.8235:0:4.6 -GL000216.1 145228 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48949;SOR=0;LSEQ=AATATGTCACAATGCCCCCT;RSEQ=AGGCAGAGCCTAGACAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,7:0.1:2,2:33.5:1:30:1:1:1.26772:44:4:0.1:0:5 0/0:17:0:0,0:9,8:0:2,0:35.5:1:28.8:1:1:0:42.1:34:1:0:3.7 -GL000216.1 145241 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19861;SOR=Inf;LSEQ=GCCCCCTTAGGCAGAGCCTA;RSEQ=ACAAAAGCCCCATCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,11:0:2,0:23.2:1:31.8:1:1:0:33.3:44:1:0:4.9 0/1:19:2:1,1:9,8:0.1053:2,2:29:1:29:1:1:1.11803:43.5:4:0.1053:0:2.5 -GL000216.1 145243 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49245;SOR=0;LSEQ=CCCCTTAGGCAGAGCCTAGA;RSEQ=AAAAGCCCCATCACCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:10,11:0.087:2,2:18.5:1:31:0:1:1.10:44:4:0.087:0:5 0/0:19:0:0,0:10,9:0:2,0:28.1:1:30.9:1:1:0:40.2:38:1:0:3.7 -GL000216.1 145249 . CC TT 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48846;SOR=0;LSEQ=AGGCAGAGCCTAGACAAAAG;RSEQ=CCATCACCTGGATGATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:8,11:0.0952:2,2:14:1:28.8:1:1:1.35:33:4:0.0952:0:5 0/0:19:0:0,0:10,9:0:2,0:24.2:1:31.2:1:1:0:40.2:38:1:0:3.7 -GL000216.1 145250 . C T 81 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0027;SOR=Inf;LSEQ=GGCAGAGCCTAGACAAAAGC;RSEQ=CCATCACCTGGATGATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:8,11:0:2,0:22:1:30.2:1:1:0:33.9:18:1:0:4.6 0/1:19:7:4,3:5,6:0.3684:2,2:25.7:1:29.1:1:1:1.56:35.7:14:0.3684:0:5.7 -GL000216.1 145271 . G A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72651;LSEQ=CCATCACCTGGATGATCAGT;RSEQ=CAGACTTATGTCACAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:3,4:1,3:0.6364:2,2:31:1:30.4:1:1:2.09:32:14:0.6364:0:5.9 1/0:9:5:2,3:1,3:0.5556:2,2:17.4:1:29.8:1:1:1.85:33.2:10:0.5556:0:6.4 -GL000216.1 145275 . AC GG 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84139;LSEQ=CACCTGGATGATCAGTGCAG;RSEQ=TTATGTCACAAAGTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:1,2:0.6:2,2:32.3:1:32.4:1:1:1.85:33.8:12:0.6:0:5.3 1/0:9:5:2,3:1,3:0.5556:2,2:14.4:1:31:1:1:1.85:33.2:10:0.5556:0:5.4 -GL000216.1 145276 . C G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.31198;LSEQ=ACCTGGATGATCAGTGCAGA;RSEQ=TTATGTCACAAAGTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:0,0:0.2:0,2:15:1:30.5:1:1:0:30:4:0.6667:0:4 0/1:8:2:0,2:0,0:0.25:0,0:33.5:1:31:1:1:0:31:4:0.6667:0:4 -GL000216.1 145291 . CCC TAA 68 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3007;SOR=0.22461;LSEQ=GCAGACTTATGTCACAAAGT;RSEQ=TTTAGGCAGATCCTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:1,2:0.5556:2,2:22.8:1:29.7:1:1:1.29:29:10:0.5556:0.2222:4.2 0/1:5:1:1,0:2,2:0.2:2,0:41:0:31.3:0:1:0:24:2:0.2:0:4 -GL000216.1 145296 . T A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=0;LSEQ=CTTATGTCACAAAGTCCCTT;RSEQ=AGGCAGATCCTAGACAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:27.5:1:28:1:1:1.41:40:4:0.2857:0:4 0/0:10:0:0,0:3,7:0:2,0:15:1:27.7:1:1:0:26.4:20:1:0:3.9 -GL000216.1 145302 . G C 62 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0915;SOR=Inf;LSEQ=TCACAAAGTCCCTTTAGGCA;RSEQ=ATCCTAGACAAGGGTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:20.1:1:31.8:1:1:0:33:16:1:0:4.3 0/1:10:4:0,4:4,2:0.4:2,0:9:0:31:1:0.07619:0:24.3:8:0.4:0:4.5 -GL000216.1 145315 . G A 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31561;SOR=4.58929;LSEQ=TTAGGCAGATCCTAGACAAG;RSEQ=GTTACATCACTTGGATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:2,3:0.1429:2,0:24:0:33:0:1:0:48:2:0.1429:0:3 0/1:11:5:1,4:2,2:0.4545:2,2:21:1:30.4:1:0.52381:3.38757:25:10:0.5:0:4.4 -GL000216.1 145323 . C A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=ATCCTAGACAAGGGTTACAT;RSEQ=ACTTGGATGATCAGTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:14.6:1:31.4:1:1:0:30.4:8:1:0:4.2 0/1:12:2:1,1:3,6:0.1667:2,2:17:1:31:1:1:1.87:24:4:0.1667:0:7 -GL000216.1 145324 . A T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.60301;SOR=2.55208;LSEQ=TCCTAGACAAGGGTTACATC;RSEQ=CTTGGATGATCAGTGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:3,5:0.1111:2,0:15:0:31:0:1:0:48:2:0.125:0:3 0/1:12:3:1,2:3,6:0.25:2,2:17.3:1:28.7:1:1:1:25.3:6:0.25:0:4.3 -GL000216.1 145333 . A G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16374;SOR=0;LSEQ=AGGGTTACATCACTTGGATG;RSEQ=TCAGTGCAGAGATATGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,5:0.25:2,2:27.5:1:33:1:0.46429:3.87:25:4:0.25:0:7 0/0:11:0:0,0:4,7:0:2,0:29.4:1:30.4:1:1:0:26.4:22:1:0:4.7 -GL000216.1 145335 . C T 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61991;SOR=2.27808;LSEQ=GGTTACATCACTTGGATGAT;RSEQ=AGTGCAGAGATATGTCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:29.5:1:30.5:1:1:2.45:25:4:0.3333:0:7 1/0:11:6:1,5:3,2:0.5455:2,2:28.3:1:29.3:1:0.24242:6.06919:26.8:12:0.5455:0:4.8 -GL000216.1 145361 . CT TC 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46472;LSEQ=AGAGATATGTCACAATGCCA;RSEQ=GTAGGCAGAGCCTAGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:42:1:30.5:1:1:1.73:25:4:0.4:0:6 1/0:12:6:0,6:2,3:0.5:2,0:19.7:1:28.4:1:0.18182:0:26.7:12:0.5:0.0833:5 -GL000216.1 145362 . TG CA 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89556;LSEQ=GAGATATGTCACAATGCCAC;RSEQ=TAGGCAGAGCCTAGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:1,1:0.2:2,0:47:0:33.5:0:1:0:35:2:0.3333:0:4 0/1:11:2:1,1:1,3:0.1818:2,2:41.5:1:30:1:1:2.45:24:4:0.3333:0:6 -GL000216.1 145364 . T A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATATGTCACAATGCCACTG;RSEQ=AGGCAGAGCCTAGACAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,3:0:2,0:38:1:28.8:1:1:0:28:8:0.8:0:4.5 0/1:11:2:1,1:1,8:0.1818:2,2:25.5:1:28:1:0.34545:6.00:27:4:0.1818:0:2 -GL000216.1 145366 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TATGTCACAATGCCACTGTA;RSEQ=GCAGAGCCTAGACAAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:33.3:1:31.5:1:1:0:30.8:12:1:0:4.2 0/1:10:2:1,1:1,7:0.2:2,2:41:1:29.5:1:0.37778:5.29:24:4:0.2:0:6 -GL000216.1 145368 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=TGTCACAATGCCACTGTAGG;RSEQ=AGAGCCTAGACAAGAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,3:0:2,0:38:1:28.4:1:1:0:27.4:4:0.8:0:4 0/1:9:2:1,1:1,5:0.2222:2,2:39:1:28.5:1:0.46429:3.87:24:4:0.25:0:6 -GL000216.1 145374 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=AATGCCACTGTAGGCAGAGC;RSEQ=TAGACAAGAGTTACATGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:32.5:1:30:1:1:1.41:25:4:0.2857:0:6 0/0:8:0:0,0:2,6:0:2,0:30.8:1:30.4:1:1:0:27:16:1:0:4.8 -GL000216.1 145382 . G A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61927;SOR=0.47532;LSEQ=TGTAGGCAGAGCCTAGACAA;RSEQ=AGTTACATGACCTTGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:1,2:0.5714:2,2:20:1:29.8:1:1:1.81:36.8:8:0.5714:0:5.3 0/1:8:3:0,3:2,3:0.375:2,0:39:1:29.7:1:0.46429:0:29:6:0.375:0:5.7 -GL000216.1 145396 . T A 80 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=AGACAAGAGTTACATGACCT;RSEQ=GGTGATCAGTGCAGAGATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:15.5:1:29:1:1:1:27.5:8:0.6667:0:4.5 1/1:6:6:1,5:0,0:1:0,2:26.2:1:31:1:1:0:27:12:1:0:5.3 -GL000216.1 145416 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TGGTGATCAGTGCAGAGATA;RSEQ=ATTGCAATGTCCCTGTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:23:0:31:1:1:0:48.5:4:0.5:0:4.5 0/0:3:0:0,0:0,3:0:0,0:20:1:33.7:1:1:0:24.7:6:1:0:4.7 -GL000216.1 145419 . T C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATCAGTGCAGAGATACAT;RSEQ=GCAATGTCCCTGTAGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:20:0:32.5:1:1:0:48.5:4:0.6667:0:4.5 1/1:3:3:0,3:0,0:1:0,0:17:1:32:0:1:0:24.7:6:1:0:4.7 -GL000216.1 145427 . C G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GCAGAGATACATTGCAATGT;RSEQ=CCTGTAGGCAGAGCCTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:12:0:33.5:1:1:0:48.5:4:0.6667:0:4.5 1/0:3:2:0,2:0,1:0.6667:0,0:10.5:1:33.5:1:1:0:23.5:4:0.6667:0:5.5 -GL000216.1 146580 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGTCATCAGTTCAGGGA;RSEQ=ATGTGAAAACGCCCCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7:0:31:1:1:0:47:4:1:0:6.5 -GL000216.1 146582 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGTCATCAGTTCAGGGATA;RSEQ=GTGAAAACGCCCCTGTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:32:0:1:0:47:4:1:0:6.5 -GL000216.1 146615 . A C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTAGGCAGAGCCTAGAAA;RSEQ=TAGTTACATCACCTAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:42:0:31.5:1:1:1:47:4:0.5:0:6.5 -GL000216.1 146618 . G T 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGCAGAGCCTAGAAAATA;RSEQ=TTACATCACCTAGTTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:42.5:1:31:1:1:1:47:4:0.5:0:6.5 -GL000216.1 146624 . T A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCCTAGAAAATAGTTACA;RSEQ=CACCTAGTTGATCAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:36.5:1:28:1:1:1:47:4:0.5:0:6.5 -GL000216.1 146651 . T C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGATCAGTGCAGAGATAT;RSEQ=TCACAATACCCCCTGTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:9.5:1:29.5:1:1:1:47:4:0.5:0:6.5 -GL000216.1 146934 . CC AT 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGTATGCCACAAAGCCC;RSEQ=TGTAGGCAAAGCCTAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:10:0:31.8:1:1:1:40:4:0.5:0:5 -GL000216.1 146937 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTATGCCACAAAGCCCCCT;RSEQ=TAGGCAAAGCCTAGAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:12:0:31:1:1:1:40:4:0.5:0:5 -GL000216.1 146940 . G C 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCACAAAGCCCCCTGTA;RSEQ=GCAAAGCCTAGAAAATCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:14.5:1:32.5:1:1:1:41:4:0.5:0:7.5 -GL000216.1 146957 . C G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGGCAAAGCCTAGAAAAT;RSEQ=GTTACATCACTTGGGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:31.5:1:32:0:1:0:41:4:0.5:0:7.5 -GL000216.1 146986 . G C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTTGGGTGATCAGTGGCGA;RSEQ=ATCTCTCACAAATCCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:40.5:1:31:1:1:1:41:4:0.5:0:7.5 -GL000216.1 146998 . A T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGCGAGATCTCTCACAA;RSEQ=TCCCCTGTAGGCAGAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:24.5:1:29:1:1:0:40:4:0.5:0:5 -GL000216.1 147002 . C G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAGATCTCTCACAAATCC;RSEQ=CTGTAGGCAGAGCTTATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:20.5:1:29:1:1:1:40:4:0.5:0:5 -GL000216.1 147015 . C G 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATCCCCTGTAGGCAGAG;RSEQ=TTATACAACAGTTACTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:11.5:1:29:1:1:1:41:4:0.5:0:6.5 -GL000216.1 147019 . T C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCCCTGTAGGCAGAGCTTA;RSEQ=ACAACAGTTACTTCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:7.5:1:29.5:1:1:1:41:4:0.5:0:6.5 -GL000216.1 162372 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTTTGTGACATATCACTGCA;RSEQ=TGATCACCTAGGTGATGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:35:0:34:0:1:0:22:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:10.5:1:29.5:1:1:0:43.5:4:1:0:7 -GL000216.1 162536 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ACCCAGGTGATGGACTCTTG;RSEQ=CTTAGATCTGCCTACATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:37:1:31.7:1:1:0:22:6:1:0:6 1/1:2:2:1,1:0,0:1:0,2:31.5:1:31.5:1:1:0:41.5:4:1:0:3 -GL000216.1 163517 . A G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GTGCCTACTGGGGACATTGT;RSEQ=ACATATCTCTGCACTGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:28.5:1:33.5:1:1:0:23.5:4:0.6667:0:3 1/1:4:4:3,1:0,0:1:0,2:7.5:1:31.3:1:1:0:37.3:8:1:0:3.8 -GL000216.1 163524 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47619;SOR=Inf;LSEQ=CTGGGGACATTGTAACATAT;RSEQ=TCTGCACTGATCTCCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:0:2,0:11.9:1:31.9:1:1:0:39:20:1:0:2.7 0/1:11:2:1,1:5,4:0.1818:2,2:5.5:1:30.5:1:1:1.22474:47.5:4:0.1818:0:6 -GL000216.1 163527 . TG AC 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20308;SOR=Inf;LSEQ=GGGACATTGTAACATATCTC;RSEQ=CACTGATCTCCCAGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:10.6:1:29.9:1:1:0:38:28:1:0:3.1 0/1:12:2:1,1:5,5:0.1667:2,2:21.5:1:28.8:1:1:1:42:4:0.1667:0:3 -GL000216.1 163534 . A G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49024;SOR=0;LSEQ=TGTAACATATCTCTGCACTG;RSEQ=TCTCCCAGGTGCTGTAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:13,7:0.0909:2,2:18.5:1:33:1:1:1.80284:24:4:0.0952:0:4 0/0:19:0:0,0:10,8:0:2,0:13.7:1:29:1:1:0:40:36:0.9474:0:3.3 -GL000216.1 163536 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48889;SOR=0;LSEQ=TAACATATCTCTGCACTGAT;RSEQ=TCCCAGGTGCTGTAACTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:13,8:0.087:2,2:6:1:28:1:1:1.58984:45.5:4:0.087:0:5 0/0:23:0:0,0:10,9:0:2,0:11.4:1:30.3:1:1:0:40.4:38:0.8636:0:2.9 -GL000216.1 163541 . A T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=TATCTCTGCACTGATCTCCC;RSEQ=GGTGCTGTAACTTTAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:12,8:0.0833:2,2:11:0:32:0:1:1.47192:45:4:0.0833:0:3.5 0/0:23:0:0,0:12,11:0:2,0:17.1:1:28.7:1:1:0:41.2:22:1:0:3.1 -GL000216.1 163542 . G C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=ATCTCTGCACTGATCTCCCA;RSEQ=GTGCTGTAACTTTAGTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,7:0.0833:2,2:26.5:1:32.5:1:1:1.53525:24:4:0.0952:0:4 0/0:23:0:0,0:12,11:0:2,0:18:1:30.1:1:1:0:41.2:46:1:0:3.1 -GL000216.1 163543 . G T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0466;LSEQ=TCTCTGCACTGATCTCCCAG;RSEQ=TGCTGTAACTTTAGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:13,9:0.0833:2,2:12:1:32:0:1:1.42202:25:4:0.087:0:4 0/1:23:2:1,1:11,10:0.087:2,2:16.5:1:27:1:1:1.09544:31:4:0.0909:0:3 -GL000216.1 163545 . G A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09316;LSEQ=TCTGCACTGATCTCCCAGGT;RSEQ=CTGTAACTTTAGTCTAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:13,10:0.08:2,2:15:0:19.5:1:1:1.28628:45:1:0.0417:0:3.5 0/1:23:2:1,1:11,10:0.087:2,2:11.5:1:27:1:1:1.09544:48:4:0.087:0:2.5 -GL000216.1 163546 . CTGTAACTTTAG ATATAACACTTT 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=0;LSEQ=CTGCACTGATCTCCCAGGTG;RSEQ=TCTAGGCTCTGGCTACACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:13,11:0.0769:2,2:18:1:29.3:1:1:1.17422:25:4:0.0769:0.0385:3.5 0/0:23:0:0,0:12,11:0:2,0:21.7:1:31.8:1:1:0:41.2:46:1:0:3.1 -GL000216.1 163549 . T C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09316;LSEQ=CACTGATCTCCCAGGTGCTG;RSEQ=AACTTTAGTCTAGGCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,10:0.08:2,2:28:0:32:1:1:1.19087:45:4:0.087:0:5 0/1:23:2:1,1:11,10:0.087:2,2:30.5:1:33.5:1:1:1.09544:47.5:4:0.0952:0:6 -GL000216.1 163553 . T A 60 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11052;SOR=0;LSEQ=GATCTCCCAGGTGCTGTAAC;RSEQ=TTAGTCTAGGCTCTGGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:11,9:0.16:2,2:22.5:1:30:1:1:1.21199:35.5:8:0.1739:0:4.5 0/0:23:0:0,0:12,11:0:2,0:28.1:1:30.3:1:1:0:41.2:46:1:0:3.1 -GL000216.1 163558 . T G 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04179;SOR=Inf;LSEQ=CCCAGGTGCTGTAACTTTAG;RSEQ=CTAGGCTCTGGCTACACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:30.3:1:29:1:1:0:36.4:12:1:0:3.5 0/1:23:4:2,2:10,9:0.1739:2,2:40.3:1:31.8:1:1:1.10603:45:8:0.1818:0:3.8 -GL000216.1 163560 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22531;SOR=Inf;LSEQ=CAGGTGCTGTAACTTTAGTC;RSEQ=AGGCTCTGGCTACACGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:31.9:1:29.2:1:1:0:36.4:25:1:0:3.5 0/1:24:2:1,1:11,11:0.0833:2,2:41.5:1:32:1:1:1:47.5:4:0.087:0:6 -GL000216.1 163563 . G A 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25028;SOR=0.31001;LSEQ=GTGCTGTAACTTTAGTCTAG;RSEQ=CTCTGGCTACACGGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:3,3:11,8:0.2308:2,2:35.7:1:28.7:1:1:1.35739:39.7:12:0.24:0:3.8 0/1:24:2:1,1:11,11:0.0833:2,2:33:0:27.5:1:1:1:47:4:0.0909:0:2.5 -GL000216.1 163565 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49061;SOR=0;LSEQ=GCTGTAACTTTAGTCTAGGC;RSEQ=CTGGCTACACGGCATTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,11:0.0769:2,2:35:1:29.5:1:1:1.0871:45.5:4:0.0769:0:5 0/0:24:0:0,0:12,12:0:2,0:37.3:1:28.9:1:1:0:40.3:48:1:0:3 -GL000216.1 163567 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22531;SOR=Inf;LSEQ=TGTAACTTTAGTCTAGGCTC;RSEQ=GGCTACACGGCATTGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:36.3:1:29.8:1:1:0:36.4:25:1:0:3.5 0/1:24:2:1,1:11,11:0.0833:2,2:40.5:1:30:1:1:1:31:4:0.0833:0:3 -GL000216.1 163577 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49025;SOR=0;LSEQ=GTCTAGGCTCTGGCTACACG;RSEQ=CATTGTGACATATCACTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:0.08:2,2:29:0:31.5:1:1:1.0871:45:4:0.087:0:5 0/0:23:0:0,0:11,12:0:2,0:37.3:1:30.4:1:1:0:40.3:22:1:0:3 -GL000216.1 163580 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49025;SOR=0;LSEQ=TAGGCTCTGGCTACACGGCA;RSEQ=TGTGACATATCACTGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:0.08:2,2:30.5:1:31.5:1:1:1.0871:50:4:0.087:0:1.5 0/0:23:0:0,0:11,12:0:2,0:35:1:29.8:1:1:0:40.3:46:1:0:3 -GL000216.1 163584 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=0;LSEQ=CTCTGGCTACACGGCATTGT;RSEQ=ACATATCACTGCACTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,11:0.0769:2,2:22:0:31:1:1:1.0871:45:4:0.08:0:5 0/0:23:0:0,0:11,12:0:2,0:31.7:1:31.7:1:1:0:40.3:46:1:0:3 -GL000216.1 163590 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=0;LSEQ=CTACACGGCATTGTGACATA;RSEQ=CACTGCACTGATCACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,11:0.0769:2,2:30.5:1:31:1:1:1.0871:48:4:0.0833:0:2.5 0/0:23:0:0,0:11,12:0:2,0:26.3:1:28.7:1:1:0:40.3:22:1:0:3 -GL000216.1 163593 . C G 34 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=0;LSEQ=CACGGCATTGTGACATATCA;RSEQ=TGCACTGATCACCCAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,11:0.0769:2,2:13:0:34:0:1:1.0871:45:4:0.0833:0:5 0/0:23:0:0,0:11,12:0:2,0:23.6:1:30.7:1:1:0:40.3:10.5:1:0:3 -GL000216.1 163595 . G A 57 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04179;SOR=Inf;LSEQ=CGGCATTGTGACATATCACT;RSEQ=CACTGATCACCCAGGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,12:0:2,0:25.4:1:30.9:1:1:0:36.9:24:1:0:3.5 0/1:23:4:2,2:8,9:0.1739:2,2:19:1:28.5:1:1:1.12:45.8:8:0.1818:0:5.3 -GL000216.1 163597 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21514;SOR=Inf;LSEQ=GCATTGTGACATATCACTGC;RSEQ=CTGATCACCCAGGTGATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,12:0:2,0:23.6:1:29.4:1:1:0:36.9:50:1:0:3.5 0/1:23:2:1,1:10,11:0.087:2,2:20:1:29.5:1:1:1.10:47.5:4:0.087:0:6 -GL000216.1 163602 . T C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=GTGACATATCACTGCACTGA;RSEQ=CACCCAGGTGATATAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:10,10:0.0833:2,2:29:1:33:1:1:1:45.5:4:0.0909:0:5 0/0:23:0:0,0:11,12:0:2,0:14.9:1:28.7:1:1:0:40.3:22:1:0:3 -GL000216.1 163603 . C A 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=TGACATATCACTGCACTGAT;RSEQ=ACCCAGGTGATATAACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,11:0:2,0:20.7:1:31.5:1:1:0:36.5:44:1:0:3.5 0/1:23:2:1,1:10,11:0.087:2,2:16:0:26.5:1:1:1.10:48:4:0.0909:0:1 -GL000216.1 163604 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=GACATATCACTGCACTGATC;RSEQ=CCCAGGTGATATAACCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,11:0:2,0:19.8:1:29.5:1:1:0:36.5:44:1:0:3.5 0/1:23:2:1,1:10,11:0.087:2,2:7:0:32:1:1:1.10:31:4:0.0909:0:3 -GL000216.1 163605 . C A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ACATATCACTGCACTGATCA;RSEQ=CCAGGTGATATAACCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:5,4:6,7:0.3913:2,2:23.4:1:27.9:1:1:1.43:33.7:8:0.381:0:3.9 0/1:23:9:4,5:7,7:0.3913:2,2:10.1:1:28.2:1:1:1.23792:46:8:0.3636:0:3.1 -GL000216.1 163609 . G C 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4878;SOR=Inf;LSEQ=ATCACTGCACTGATCACCCA;RSEQ=GTGATATAACCCTTGTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:9,10:0:2,0:17.6:1:29.9:1:1:0:36.3:18:1:0:3.4 0/1:21:2:1,1:9,10:0.0952:2,2:7.5:1:25:0:1:1.11:30:4:0.1053:0:3 -GL000216.1 163610 . G C 34 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21923;SOR=0;LSEQ=TCACTGCACTGATCACCCAG;RSEQ=TGATATAACCCTTGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:7,8:0.1053:2,2:21:1:34:0:1:1.13:45.5:4:0.1176:0:5 0/0:21:0:0,0:10,11:0:2,0:8:1:29.4:1:1:0:39.9:20:1:0:3.1 -GL000216.1 163611 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22857;SOR=Inf;LSEQ=CACTGCACTGATCACCCAGG;RSEQ=GATATAACCCTTGTCTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,9:0:2,0:17.5:1:29.4:1:1:0:34.7:34:1:0:3.6 0/1:17:2:1,1:7,8:0.1176:2,2:13:1:30.5:1:1:1.13:35:4:0.125:0:4 -GL000216.1 163616 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52;SOR=0;LSEQ=CACTGATCACCCAGGTGATA;RSEQ=AACCCTTGTCTAGGCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,7:0.125:2,2:14:1:29.5:1:1:1.15:44.5:4:0.1333:0:3 0/0:9:0:0,0:2,7:0:2,0:8.3:1:27.1:1:1:0:37.4:8:1:0:2.9 -GL000216.1 163620 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCACCCAGGTGATATAAC;RSEQ=CTTGTCTAGGCTCTGCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:2,1:0.1538:2,2:11:1:31.5:1:1:1.7321:45.5:4:0.4:0:5 0/0:4:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000216.1 163624 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCAGGTGATATAACCCTT;RSEQ=TCTAGGCTCTGCCTACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,4:0.1667:2,2:16:1:29:1:1:1:25:4:0.1818:0:3.5 0/0:4:0:0,0:0,1:0:0,0:1:0:30:0:1:0:45:2:0.25:0:3 -GL000216.1 163626 . C A 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTGATATAACCCTTGT;RSEQ=TAGGCTCTGCCTACAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:4,4:0.25:2,2:9:1:30:1:1:1.87936:30:6:0.2727:0:4 0/0:3:0:0,0:1,2:0:2,0:7.7:1:31.7:1:1:0:25:6:1:0:2.7 -GL000216.1 163716 . C T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATCTGCCTACAGGGTGC;RSEQ=TTGTGACATATCCCTGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:26.5:1:32:0:1:0:25.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000216.1 164362 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=CGGATCACCTAGGTGATGTA;RSEQ=CTCTTGTCTACCCTCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:30:1:1:0:37:4:1:0:4.5 0/0:2:0:0,0:0,1:0:0,0:25:0:31:0:1:0:38:2:0.5:0:2 -GL000216.1 164409 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GGCATTGTGAAATATCTCTG;RSEQ=ACTGATCACCCAGGTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:36.5:1:30:1:0.4:0:37:4:0.4:0:4.5 0/0:4:0:0,0:3,1:0:2,0:27.3:1:33.3:1:1:0:29.8:8:1:0:3.8 -GL000216.1 164427 . T C 33 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TGCACTGATCACCCAGGTGA;RSEQ=TCAACTCTTGTCTAGGATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:18.5:1:33.5:1:0.4:0:37:4:0.4:0:4.5 0/0:4:0:0,0:3,1:0:2,0:27.3:1:30.8:1:1:0:29.8:8:1:0:3.8 -GL000216.1 164433 . T A 26 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GATCACCCAGGTGATTCAAC;RSEQ=CTTGTCTAGGATCTGCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:17.5:1:26:0:1:2.44949:23:4:0.3333:0:5.5 0/0:4:0:0,0:3,1:0:2,0:24.3:1:31.3:1:1:0:29.8:8:1:0:3.8 -GL000216.1 164438 . T A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=CCCAGGTGATTCAACTCTTG;RSEQ=CTAGGATCTGCCTACAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:0.4:2,0:41:1:30:1:0.4:0:32:4:0.4:0:6.5 1/0:3:2:2,0:1,0:0.6667:0,0:36.5:1:28.5:1:1:0:20.5:4:0.6667:0:5 -GL000216.1 164445 . T A 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77722;LSEQ=GATTCAACTCTTGTCTAGGA;RSEQ=CTGCCTACAGGGGGTATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:0.4:2,0:39.5:1:32:0:0.4:0:32:4:0.4:0:6.5 0/1:3:1:1,0:1,1:0.3333:2,0:29:0:32:0:1:0:21:2:0.3333:0:7 -GL000216.1 164452 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=CTCTTGTCTAGGATCTGCCT;RSEQ=CAGGGGGTATTGTGAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:17.5:1:29:1:1:1.7321:23:4:0.4:0:5.5 0/0:3:0:0,0:2,1:0:2,0:17.7:1:25.3:1:1:0:32:6:1:0:3.7 -GL000216.1 164456 . G A 43 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.48571;SOR=6.40831;LSEQ=TGTCTAGGATCTGCCTACAG;RSEQ=GGGTATTGTGAAATATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,1:0.25:2,0:19:0:31:0:1:0:39:2:0.3333:0:6 1/0:4:3:2,1:0,1:0.75:0,2:13.7:1:27.7:1:1:0:20.3:6:0.75:0:6 -GL000216.1 164457 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GTCTAGGATCTGCCTACAGG;RSEQ=GGTATTGTGAAATATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:0.5:0,2:17.5:1:28.5:1:1:0:23:4:0.6667:0:5.5 0/0:4:0:0,0:2,2:0:2,0:13.3:1:28.5:1:1:0:29:8:1:0:4.8 -GL000216.1 164459 . G T 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=CTAGGATCTGCCTACAGGGG;RSEQ=TATTGTGAAATATCTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:25.5:1:30.5:1:1:0:32:4:0.5:0:5.5 1/0:4:3:2,1:0,1:0.75:0,2:12.7:1:29.7:1:1:0:20.3:6:0.75:0:6 -GL000216.1 164485 . C A 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.57733;LSEQ=TGAAATATCTCTGCACTGAT;RSEQ=AACTAGGTGATGTAACACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:17.5:1:29.5:1:1:0:25:4:0.6667:0:6 1/0:2:1:0,1:0,1:0.5:0,0:33:0:32:0:1:0:20:2:0.5:0:8 -GL000220.1 6904 . C T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GGTGCGATGCTCTGGAAACC;RSEQ=CCCGCGGGTGTGTATGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:25:1:33:1:1:0:60:6:1:0:1.3 1/1:2:2:1,1:0,0:1:0,2:10:0:30.5:1:1:0:60:4:1:0:1.5 -GL000220.1 6908 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CGATGCTCTGGAAACCCCCC;RSEQ=CGGGTGTGTATGTGAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:16.5:1:31:0:1:0:60:4:0.6667:0:2 0/0:2:0:0,0:1,1:0:2,0:6:0:32.5:1:1:0:60:4:1:0:1.5 -GL000220.1 6910 . G T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATGCTCTGGAAACCCCCCGC;RSEQ=GGTGTGTATGTGAGAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:14.5:1:31.5:1:1:0:60:4:0.6667:0:2 0/0:2:0:0,0:1,1:0:2,0:4:0:30:1:1:0:60:4:1:0:1.5 -GL000220.1 7456 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CGCCCCCAAGCCCAACGCAT;RSEQ=CTGGGATTGTAGTCAGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:8.3:1:32.7:1:1:0:60:6:1:0:0.7 1/0:3:2:1,1:0,1:0.6667:0,2:42.5:1:27.5:1:1:0:60:4:0.6667:0:2 -GL000220.1 7476 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGATTGTAGTCAGGTA;RSEQ=TCCTGGGACCAACTGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:25:0:34:0:1:0:60:2:1:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:32:1:30.5:1:1:0:60:4:0.6667:0:2 -GL000220.1 7604 . T G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GCCCGGTGGCTGCTGGGATT;RSEQ=TAGTCTGCAGGCCGGGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:44:0:34:0:1:0:60:2:0.3333:0:2 1/1:2:2:1,1:0,0:1:0,2:29:1:30:1:1:0:60:4:1:0:1.5 -GL000220.1 8064 . G A 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51417;SOR=Inf;LSEQ=GGGGAGCCTATCTGTTCCCA;RSEQ=ACTTCTGCGTGCGAGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:10,12:1,1:0.9167:2,2:31.5:1:30.4:1:1:1.19087:60:44:0.9167:0:1.5 1/1:15:15:8,7:0,0:1:0,2:30.4:1:29.5:1:1:0:60:30:1:0:1.6 -GL000220.1 8087 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49758;SOR=0;LSEQ=TTCTGCGTGCGAGGAGACAG;RSEQ=GTGGCCAGGGCAGGTGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:10,14:0.0769:2,2:15.5:1:31.5:1:1:1.38:60:4:0.0769:0:2 0/0:20:0:0,0:10,10:0:2,0:27.6:1:30.9:1:1:0:60:40:1:0:1.6 -GL000220.1 8122 . G A 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1197;LSEQ=TGGTCTCACTTGTAATTGTG;RSEQ=CACAGTCTCCCCACGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:2,6:2,2:0.6667:2,2:20.8:1:29.6:1:0.54747:2.71347:60:16:0.6667:0:2.3 1/0:13:9:4,5:2,2:0.6923:2,2:27.9:1:28.3:1:1:1.22862:60:18:0.75:0:2.4 -GL000220.1 8143 . G C 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37423;SOR=2.76313;LSEQ=CACAGTCTCCCCACGTGCCA;RSEQ=TTGTACGACTATTTGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:2,5:0.2222:2,0:27.5:1:34:0:1:0:60:4:0.2222:0:3.5 0/1:11:5:2,3:3,3:0.4545:2,2:24.8:1:30.6:1:1:1.44544:60:10:0.4545:0:3.4 -GL000220.1 8160 . G C 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54545;SOR=2.97405;LSEQ=CCAGTTGTACGACTATTTGT;RSEQ=CCTGAAGTTTGATTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:36:0:33:0:1:0:60:2:0.3333:0:4 1/0:8:5:2,3:1,2:0.625:2,2:24.4:1:29.8:1:1:1.29:60:10:0.625:0:3.4 -GL000220.1 8193 . A G 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTCTCTGACAAGACAGA;RSEQ=CCCGGGAGCCTCCAACAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:9.3:1:30.3:1:1:0:60:6:1:0:2.7 1/1:4:4:1,3:0,0:1:0,2:26:1:31.5:1:1:0:60:8:1:0:3.5 -GL000220.1 8227 . C T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGCCTGCCCAGCGTTGC;RSEQ=GTAACGCTTGCTCTCGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:47:0:29:0:1:0:60:2:1:0:3 0/1:5:2:1,1:1,2:0.4:2,2:33:0:32:0:1:1.73:60:4:0.4:0:2.5 -GL000220.1 8232 . C A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTGCCCAGCGTTGCCGTAA;RSEQ=GCTTGCTCTCGGGGAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:49:0:30:0:1:0:60:2:1:0:3 1/0:4:2:0,2:1,1:0.5:2,0:26:1:29.5:1:1:0:60:4:0.5:0:3.5 -GL000220.1 8240 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCGTTGCCGTAACGCTTGCT;RSEQ=TCGGGGAGCTGGGCGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:41:0:31:0:1:0:60:2:1:0:3 1/0:3:2:1,1:0,1:0.6667:0,2:46:0:31:1:1:0:60:4:0.6667:0:2.5 -GL000220.1 9608 . T C 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGTCACTGGGACCGCAG;RSEQ=CTTGCACCACCATGCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:46.5:1:32:1:1:0:60:4:1:0:1 -GL000220.1 9666 . T C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTAGAGACAGGGTTTCAC;RSEQ=ATGTTGCCCAAACTGGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:33.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000220.1 9676 . A C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGTTTCACTATGTTGCCC;RSEQ=AACTGGCATGTCTGCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16:0:33.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000220.1 10143 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGATCAGGTCATGGTG;RSEQ=TTATAGAGAAAGGTAGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000220.1 118088 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17874;SOR=Inf;LSEQ=GGAACGATACGGCAGCGCCG;RSEQ=GGAGCCTCGGTTGGCCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:16,27:0:2,0:28.2:1:31.1:1:1:0:59.3:86:1:0:0.4 0/1:32:2:1,1:11,19:0.0625:2,2:11:0:30:1:1:1.70:57:4:0.0645:0:2.5 -GL000220.1 118094 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14962;SOR=Inf;LSEQ=ATACGGCAGCGCCGCGGAGC;RSEQ=TCGGTTGGCCTCGGATAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:16,26:0:2,0:28.2:1:32:1:1:0:59.3:84:1:0:0.5 0/1:27:2:1,1:8,17:0.0741:2,2:17:0:28.5:1:1:2.06:57:4:0.0769:0:2.5 -GL000220.1 118144 . GC G 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.65502;SOR=1.62737;LSEQ=CCTGTCCCCGCCGGCGGGCC;RSEQ=CCCCCCCCTCCACGCGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:2,4:3,7:0.375:2,2:27.2:1:30:1:1:1.16:60:5:0.3333:0:1.5 1/0:6:3:0,3:2,1:0.5:2,0:13:1:31.7:1:0.4:0:55:6:0.5:0.1667:0.7 -GL000220.1 118243 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52893;SOR=0;LSEQ=TGCCCTTCGTCCTGGGAAAC;RSEQ=GGGCGCGGCCGGAGAGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:25,13:0.05:2,2:11.5:1:29:1:1:1.88989:47:4:0.0513:0:2 0/0:23:0:0,0:14,9:0:2,0:25.3:1:30.1:1:1:0:55.5:46:1:0:1.6 -GL000220.1 118253 . C T 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05251;SOR=3.04496;LSEQ=CCTGGGAAACGGGGCGCGGC;RSEQ=GGAGAGGCGGCCGCCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:9:5,4:22,11:0.2143:2,2:19.2:1:30.2:1:0.69794:1.58156:55.2:18:0.2143:0:2 0/1:24:11:6,5:9,4:0.4583:2,2:28.5:1:30.7:1:0.67517:1.82559:58.5:22:0.4583:0:2.2 -GL000220.1 118257 . G A 164 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAAACGGGGCGCGGCCGGA;RSEQ=AGGCGGCCGCCCCCTCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:26,16:0,0:1:0,2:25.5:1:30.5:1:1:0:54.5:84:1:0:1.5 1/1:26:26:17,9:0,0:1:0,2:24.6:1:30.5:1:1:0:54.2:52:1:0:1.7 -GL000220.1 118283 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50982;SOR=0;LSEQ=GCCGCCCCCTCGCCCGTCAC;RSEQ=CACCGCACGTTCGTGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:26,18:0.0435:2,2:36:0:31.5:1:1:1.43267:47:4:0.0435:0:3 0/0:32:0:0,0:19,13:0:2,0:21.7:1:29.9:1:1:0:54.8:31:1:0:0.9 -GL000220.1 118387 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50918;SOR=Inf;LSEQ=GCTCCCTCGCTGCGATCTAT;RSEQ=GAAAGTCAGCCCTCGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:13,20:0:2,0:27.8:1:29.4:1:1:0:57.7:15.5:1:0:0.4 0/1:47:2:1,1:19,26:0.0426:2,2:49.5:1:29.5:1:1:1.36:60:4:0.0444:0:1.5 -GL000220.1 118436 . C T 124 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=11.000;MSILEN=2;SSF=0.26829;SOR=0;LSEQ=TCCGCGCGCGCGCGCGCGCG;RSEQ=GCGTGCGGGGGGCCCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:6,10:0,0:1:0,2:20.6:1:30.8:1:1:0:60:32:1:0:1.4 1/1:25:22:8,14:1,1:0.88:2,2:16.8:1:27.9:1:1:1.70775:60:6.333:0.8636:0:1.5 -GL000220.1 118442 . C CG 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.5122;SOR=Inf;LSEQ=CGCGCGCGCGCGCGCGCGTG;RSEQ=GGGGGGCCCGGCGGGGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:18.8:1:31.4:1:1:0:60:32:1:0:1.3 0/1:25:2:1,1:8,15:0.08:2,2:16:0:31.5:1:1:1.83:60:4:0.0833:0:0.5 -GL000220.1 118515 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17105;SOR=0;LSEQ=TTCCTCCCTCCCGGCCTCTC;RSEQ=CGCCGACCGCGGGCGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:21,17:0.05:2,2:21:0:31:0:1:1.22874:60:4:0.0526:0:1.5 0/0:56:0:0,0:32,24:0:2,0:27.6:1:29.9:1:1:0:59.6:27:1:0:0.8 -GL000220.1 118541 . GGT G 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52444;SOR=1.36431;LSEQ=ACCGCGGGCGTGGTGGTGGG;RSEQ=GTGGGGGGGAGGGCGCGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:15:10,5:12,11:0.3947:2,2:20:1:31.9:1:0.50608:1.80:60:30:0.4054:0:0.1 0/1:53:25:14,11:18,10:0.4717:2,2:24.5:1:31.4:1:0.5838:1.40498:59.8:50:0.4808:0.0189:0.3 -GL000220.1 118543 . T G 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.6329;SOR=2.29278;LSEQ=CGCGGGCGTGGTGGTGGGGG;RSEQ=GTGGGGGGGAGGGCGCGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:0,1:11,10:0.0263:2,0:13:0:32:0:1:0:60:2:0.0476:0:5 0/1:51:3:1,2:15,7:0.0588:2,2:18:1:23:1:0.53043:4.02111:53.3:2:0.0909:0:3.3 -GL000220.1 118545 . T G 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.3435;SOR=0.62143;LSEQ=CGGGCGTGGTGGTGGGGGTG;RSEQ=GGGGGGGAGGGCGCGCGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:13:6,7:10,5:0.3824:2,2:20.1:1:31.4:1:0.44545:2.26154:60:26:0.3939:0:1.6 0/1:47:13:7,6:16,13:0.2766:2,2:15.1:1:29.9:1:1:1.05357:58.5:26:0.3095:0:1.8 -GL000220.1 118552 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17647;SOR=0;LSEQ=GGTGGTGGGGGTGTGGGGGG;RSEQ=AGGGCGCGCGACCCCGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:0.0556:2,2:30.5:1:30.5:1:1:1:60:4:0.0606:0:2 0/0:49:0:0,0:27,21:0:2,0:19.4:1:29.4:1:1:0:59.2:11:1:0:0.8 -GL000220.1 118597 . G A 50 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10206;SOR=0;LSEQ=GCCCCGCTTCTTCGGTTCCC;RSEQ=CCTCCTCCCCGTTCACCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:1,2:18,23:0.0682:2,2:26:0:32:0:1:1.54994:60:6:0.0714:0:1.7 0/0:49:0:0,0:23,26:0:2,0:24.7:1:29.5:1:1:0:59.6:15.333:1:0:0.5 -GL000220.1 118607 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23679;SOR=Inf;LSEQ=TTCGGTTCCCGCCTCCTCCC;RSEQ=GTTCACCGCCGGGGCGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:21,26:0:2,0:23.6:1:30.1:1:1:0:60:46:0.9787:0:0.3 0/1:46:2:1,1:20,24:0.0435:2,2:21:1:27:1:1:1.20:60:4:0.0455:0:1.5 -GL000220.1 118655 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50906;SOR=0;LSEQ=CCGGGCCGGGACGGGGTCCG;RSEQ=GGAGCGTGGTTTGGGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:15,18:0.0571:2,2:13:0:32:1:1:1.19:60:4:0.0571:0:1.5 0/0:24:0:0,0:9,15:0:2,0:18.1:1:30.4:1:1:0:60:23:1:0:0.3 -GL000220.1 118796 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52742;SOR=Inf;LSEQ=TCGCGCGTCCTTCCTCCTCG;RSEQ=TCCTCCGCACGGGTCGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:21,18:0:2,0:26.7:1:32.3:1:1:0:60:78:0.975:0:0.7 0/1:67:2:1,1:33,32:0.0299:2,2:5.5:1:27.5:1:1:1.03078:60:4:0.0328:0:1.5 -GL000220.1 118807 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17584;SOR=0;LSEQ=TCCTCCTCGCTCCTCCGCAC;RSEQ=GGTCGACCAGCAGACCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:23,21:0.0435:2,2:36:1:30:1:1:1.09307:60:4:0.0444:0:1 0/0:63:0:0,0:32,31:0:2,0:24.5:1:29.1:1:1:0:60:62:1:0:0.7 -GL000220.1 118825 . C CGGGTGGT 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=2.000;MSILEN=3;SSF=0.08916;SOR=0;LSEQ=ACGGGTCGACCAGCAGACCG;RSEQ=GGGTGGTGGGCGGCGGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:2,1:19,21:0.0698:2,2:33.3:1:32:1:0.60692:2.17:60:6:0.0714:0:0.3 0/0:52:0:0,0:25,27:0:2,0:22.3:1:29.3:1:1:0:60:25:1:0:0.8 -GL000220.1 118829 . TGGTGGGC T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.04452;SOR=0;LSEQ=GTCGACCAGCAGACCGCGGG;RSEQ=GGCGGGCGGCGAGGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:4:2,2:19,21:0.0909:2,2:34.5:1:31.3:1:1:1.10:60:8:0.0909:0:0 0/0:50:0:0,0:24,26:0:2,0:21.2:1:30.3:1:1:0:60:49:1:0:0.9 -GL000220.1 118832 . T C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12945;SOR=0.50086;LSEQ=GACCAGCAGACCGCGGGTGG;RSEQ=GGGCGGCGGGCGGCGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:20:9,11:9,9:0.4762:2,2:25:1:31.3:1:1:1.21576:59.2:40:0.5405:0:1.6 0/1:45:14:6,8:15,16:0.3111:2,2:26.1:1:30.9:1:0.75883:1.24382:60:28:0.3256:0:1.6 -GL000220.1 118861 . C G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17019;SOR=0;LSEQ=GGCGGCGAGGCCCCACGGGG;RSEQ=GTCCCCGCACCCGGCCGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:13,15:0.0667:2,2:42.5:1:31.5:1:1:1.15:60:4:0.069:0:2 0/0:42:0:0,0:21,21:0:2,0:17.7:1:30.7:1:1:0:60:41:1:0:1.3 -GL000220.1 118878 . G T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47155;SOR=0.58576;LSEQ=GGGCGTCCCCGCACCCGGCC;RSEQ=ACCTCCGCTCGCGACCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:1,3:12,12:0.1379:2,2:12.5:1:29.8:1:0.6:2.89166:56:8:0.1379:0:2.5 0/1:47:4:3,1:23,20:0.0851:2,2:23.5:1:31.8:1:0.61736:2.56:60:8:0.0851:0:2.5 -GL000220.1 118882 . T G 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.25215;LSEQ=GTCCCCGCACCCGGCCGACC;RSEQ=CCGCTCGCGACCTCTCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:16:0:31.5:1:1:1.07415:60:4:0.0714:0:3 0/1:47:4:2,2:24,19:0.0851:2,2:15:1:29.8:1:1:1.25684:60:8:0.0851:0:2.3 -GL000220.1 118890 . C T 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46866;SOR=1.49137;LSEQ=ACCCGGCCGACCTCCGCTCG;RSEQ=GACCTCTCCTCGGTCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:12:7,5:7,8:0.4444:2,2:20.1:1:29.2:1:0.70357:1.57:60:11:0.4231:0:2 1/0:44:24:13,11:12,8:0.5455:2,2:21.2:1:29.9:1:0.76618:1.26236:60:48:0.5455:0:2.1 -GL000220.1 118908 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15543;SOR=0;LSEQ=CGCGACCTCTCCTCGGTCGG;RSEQ=CCTCCGGGGTCGACCGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:20,13:0.0571:2,2:38.5:1:31:0:1:1.51907:60:4:0.0606:0:2 0/0:53:0:0,0:31,22:0:2,0:26.9:1:31.3:1:1:0:59.9:52:1:0:1.8 -GL000220.1 118923 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16391;SOR=0;LSEQ=GTCGGGCCTCCGGGGTCGAC;RSEQ=GCCTGCCGCCCGCGGGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:25,15:0.0476:2,2:27.5:1:30.5:1:1:1.64563:60:4:0.0476:0:3 0/0:61:0:0,0:37,24:0:2,0:26.3:1:30.1:1:1:0:59.9:122:1:0:1.8 -GL000220.1 118944 . G A 175 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37381;SOR=1.79137;LSEQ=GCCTGCCGCCCGCGGGCGTG;RSEQ=GACTCAGCCGGCGTCTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:49:29,20:4,3:0.875:2,2:22.8:1:30:1:1:1.09:59.8:98:0.8909:0:2 1/1:68:63:35,28:2,2:0.9265:2,2:23.6:1:29.4:1:1:1.25:59.9:62:0.9254:0:2.1 -GL000220.1 118959 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49593;SOR=Inf;LSEQ=GCGTGGGACTCAGCCGGCGT;RSEQ=TCGCCGTGTCCCGGGTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:0:2,0:23.5:1:31.5:1:1:0:59.5:122:1:0:1.8 0/1:62:2:1,1:32,28:0.0323:2,2:13:1:28:1:1:1.14039:60:4:0.0323:0:3 -GL000220.1 118979 . A C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGCCGTGTCCCGGGTCGA;RSEQ=CGGCGGGCCTTCTCCACCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:62:34,28:0,0:1:0,2:26.4:1:30.6:1:1:0:59.5:30:1:0:1.7 1/1:61:61:33,28:0,0:1:0,2:23.7:1:30.7:1:1:0:59:122:1:0:1.8 -GL000220.1 119071 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53873;SOR=Inf;LSEQ=CTCGGTCGGCACCTCCGGGG;RSEQ=CGACCAGCTGCCGCCCGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:16,20:0:2,0:17.5:1:29.1:1:1:0:55.6:17:1:0:0.7 0/1:66:2:1,1:29,34:0.0303:2,2:33.5:1:28:1:1:1.17:60:4:0.0313:0:1.5 -GL000220.1 119082 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCCGGGGTCGACCAGCTG;RSEQ=CGCCCGCGAGCTCCGGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:28.3:1:32.4:1:1:0:53.3:48:1:0:0.7 0/1:60:2:1,1:24,33:0.0333:2,2:17:1:28:1:1:1.37:60:4:0.0333:0:1 -GL000220.1 119111 . C T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2252;SOR=0.51388;LSEQ=AGCTCCGGACTTAGCCGGCG;RSEQ=CTGCACGTGTCCCGGGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:7,5:10,15:0.3243:2,2:20.3:1:28.7:1:0.48211:2.06:48.7:24:0.3243:0:1.3 0/1:61:12:7,5:18,31:0.1967:2,2:19:1:28.4:1:0.20336:2.38:52.4:24:0.2034:0:1.3 -GL000220.1 119130 . G C 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86572;LSEQ=GCCTGCACGTGTCCCGGGTC;RSEQ=ACCAGCAGGCGGCCGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:0.0556:2,2:13:0:33:1:1:1:48:4:0.0556:0:4 0/1:62:3:1,2:26,33:0.0484:2,2:15.7:1:30.3:1:1:1.56468:60:6:0.0484:0:1 -GL000220.1 119152 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26554;SOR=Inf;LSEQ=CCAGCAGGCGGCCGCCGGAC;RSEQ=CTGCGGCGCACCGACGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:21,15:0:2,0:26.4:1:31:1:1:0:55.4:72:0.973:0:1.5 0/1:53:3:2,1:24,26:0.0566:2,2:21:1:28.7:1:0.61043:2.14:60:6:0.0577:0:1.3 -GL000220.1 119172 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19604;SOR=0;LSEQ=GCTGCGGCGCACCGACGCGA;RSEQ=GGCGCTGATTCCCGTTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:27,16:0.0444:2,2:40.5:1:31.5:1:1:1.66708:60:4:0.0444:0:1.5 0/0:56:0:0,0:30,26:0:2,0:20.5:1:31:1:1:0:54.6:55:1:0:1.9 -GL000220.1 119175 . C T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84459;LSEQ=GCGGCGCACCGACGCGAGGG;RSEQ=GCTGATTCCCGTTCACGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:2,1:27,16:0.0652:2,2:28:1:30.7:1:1:1.18:45.7:6:0.0652:0:3.3 0/1:54:3:2,1:27,24:0.0556:2,2:23.3:1:31.3:1:1:1.76:60:6:0.0566:0:2 -GL000220.1 119177 . CT TC 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21593;SOR=1.71902;LSEQ=GGCGCACCGACGCGAGGGCG;RSEQ=GATTCCCGTTCACGCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:14:9,5:21,12:0.2979:2,2:20.4:1:30.8:1:1:1.03:47.6:28:0.2979:0:2.6 0/1:52:22:12,10:17,13:0.4231:2,2:22.1:1:30.2:1:1:1.08794:49.5:21:0.4118:0.0192:2.5 -GL000220.1 119178 . T C 105 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00299;SOR=0.0761;LSEQ=GCGCACCGACGCGAGGGCGC;RSEQ=GATTCCCGTTCACGCGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:10:7,3:15,9:0.2083:2,2:23.5:1:31.9:1:1:1.39:53.7:20:0.2941:0:2.1 0/1:52:1:1,0:16,13:0.0192:2,0:8:0:31:0:1:0:24:2:0.0333:0:2 -GL000220.1 119190 . A G 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24256;SOR=1.63049;LSEQ=GAGGGCGCTGATTCCCGTTC;RSEQ=CGCGCCCGCGACCTCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:16:11,5:19,14:0.3265:2,2:17.8:1:30.9:1:0.54121:1.61:47.6:32:0.3265:0:3.1 0/1:61:27:18,9:20,13:0.4426:2,2:18.9:1:30.3:1:0.78852:1.29:51:54:0.4576:0:2.7 -GL000220.1 119223 . C G 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.6079;SOR=0.82126;LSEQ=CTCCACCGGCCTCGGCCCGC;RSEQ=GTGGAGCTGGGACCACGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:27:20,7:21,13:0.4355:2,2:28:1:30.4:1:0.41242:1.75:48.3:54:0.4355:0:2.7 0/1:80:31:20,11:28,21:0.3875:2,2:25:1:29.4:1:0.64041:1.36:47.2:30:0.3797:0:2.5 -GL000220.1 119251 . T C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21545;SOR=0;LSEQ=TGGGACCACGCGGAACTCCC;RSEQ=CTCCCACATTTTTTTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:49,24:0.0267:2,2:21.5:1:33:0:1:2.02078:36:4:0.029:0:4.5 0/0:86:0:0,0:50,36:0:2,0:24.4:1:29.4:1:1:0:49.4:42:1:0:1.6 -GL000220.1 119255 . C T 148 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61471;SOR=1.20628;LSEQ=ACCACGCGGAACTCCCTCTC;RSEQ=CACATTTTTTTCAGCCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:23:17,6:29,16:0.3151:2,2:25.7:1:31.4:1:0.5851:1.55:53.3:46:0.3194:0:2.2 0/1:84:30:19,11:29,22:0.3571:2,2:26.5:1:30.3:1:0.64326:1.31:51.8:60:0.3571:0:2.2 -GL000220.1 119256 . C T 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.74816;SOR=0.86747;LSEQ=CCACGCGGAACTCCCTCTCC;RSEQ=ACATTTTTTTCAGCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:36:23,13:26,10:0.5:2,2:26.4:1:29.9:1:0.61376:1.46168:49.6:17:0.4928:0:1.4 0/1:84:39:21,18:27,17:0.4643:2,2:24.1:1:28.8:1:0.51255:1.35625:44.9:18.5:0.4568:0:1.4 -GL000220.1 119276 . C T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.98691;LSEQ=CACATTTTTTTCAGCCCCAC;RSEQ=GCGAGTTTGCGTCCGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:4:2,2:46,29:0.0506:2,2:10.5:1:30.3:1:0.64314:1.57661:35.3:8:0.0526:0:3 0/1:100:5:2,3:55,40:0.05:2,2:13.8:1:29.8:1:0.64905:2.04744:34.2:10:0.051:0:2.4 -GL000220.1 119290 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50077;SOR=Inf;LSEQ=CCCCACCGCGAGTTTGCGTC;RSEQ=GCGGGACTTTTAAGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:51,30:0:2,0:21.1:1:30:1:1:0:53.3:39.5:1:0:1 0/1:96:2:1,1:56,38:0.0208:2,2:36.5:1:31.5:1:1:1.46757:60:4:0.0208:0:2.5 -GL000220.1 119333 . A C 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ACTGCTGCCGTCAGCCAGTA;RSEQ=TGCTTCCTCCTTTTTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:8:7,1:62,34:0.0769:2,2:32.9:1:33.3:1:0.26178:3.80:56.6:16:0.0833:0:1.6 0/1:156:12:7,5:98,46:0.0769:2,2:26.2:1:30.5:1:0.52936:1.51745:48.7:11:0.0753:0:1.9 -GL000220.1 119355 . TA GT 52 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07249;SOR=0;LSEQ=GCTTCCTCCTTTTTTGCTTT;RSEQ=GGTTTTGTCTTGCCTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:3:3,0:72,38:0.0263:2,0:28.7:1:33:0:0.54962:0:51.7:6:0.0273:0:3 0/0:158:0:0,0:106,51:0:2,0:27.7:1:28.2:1:1:0:55.8:38.25:1:0:1.3 -GL000220.1 119403 . TTC T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0.76567;LSEQ=TTTTTTCTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:1,2:44,46:0.0319:2,2:17:1:30:1:1:1.90024:60:6:0.0326:0:1.3 0/1:122:3:2,1:59,57:0.0246:2,2:17.3:1:29.6:1:1:1.92:60:6:0.0256:0.0082:1.3 -GL000220.1 119407 . TTC T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.1375;SOR=0.4532;LSEQ=TTCTTTCTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:11:4,7:41,39:0.1111:2,2:14.2:1:30.5:1:0.52227:1.82762:52.7:22:0.1134:0.0404:1.1 0/1:131:7:5,2:54,56:0.0534:2,2:24.6:1:29.5:1:0.43873:2.57:39.7:14:0.0565:0.0076:2.3 -GL000220.1 119411 . TTC T 74 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=4;SSF=0.73503;SOR=1.56159;LSEQ=TTCTTTCTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:3:3,0:41,40:0.03:2,0:27.3:1:28.3:1:0.24269:0:51:6:0.0345:0:0.7 0/1:130:6:3,3:56,54:0.0462:2,2:26.5:1:28.9:1:1:1.03672:49.5:12:0.0504:0.0077:2 -GL000220.1 119413 . CTT C 33 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=4;SSF=1;SOR=1.54273;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TCTTTCTTTCTTTCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:1,0:43,43:0.0097:2,0:33:0:33:0:1:0:34:2:0.0118:0:1 0/1:134:2:1,1:61,57:0.0149:2,2:22.5:1:33:1:1:1.06954:36.5:4:0.0171:0:2 -GL000220.1 119415 . TTC T 156 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=7.000;MSILEN=4;SSF=0.67903;SOR=0.89132;LSEQ=TTCTTTCTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:34:22,12:30,34:0.2982:2,2:14.1:1:28.6:1:0.13618:2.06:52.1:16:0.3299:0.1579:2.6 0/1:142:39:21,18:43,46:0.2746:2,2:15.2:1:29.7:1:0.70122:1.25:51.8:78:0.3145:0.0704:1.9 -GL000220.1 119444 . GCTCTCGCT G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=3.000;MSILEN=2;SSF=1;SOR=0.9639;LSEQ=TCTTTCTTTCTTTCTTTCTC;RSEQ=CTCTCGCTCTCTCCCTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:78,72:0.0131:2,2:41.5:1:32.5:1:1:1.08274:43:4:0.0144:0:2 0/1:238:3:2,1:111,122:0.0126:2,2:18:1:32.3:1:0.60802:2.19:45.3:6:0.0133:0.0042:1.7 -GL000220.1 119449 . C T 96 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11622;SOR=2.95118;LSEQ=CTTTCTTTCTTTCTCGCTCT;RSEQ=GCTCTCTCGCTCTCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:3:1,2:81,74:0.0188:2,2:7:1:26:1:0.60866:2.1787:34.7:2:0.0134:0:4.3 0/1:243:13:4,9:109,117:0.0535:2,2:11.1:1:26:1:0.26304:2.08997:40.1:5.5:0.0482:0:3.3 -GL000220.1 119452 . T C 92 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.05406;SOR=4.09823;LSEQ=TCTTTCTTTCTCGCTCTCGC;RSEQ=CTCTCGCTCTCTCCCTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:86,75:0.0121:2,2:13:0:31.5:1:1:1.1457:22:4:0.0128:0:6 0/1:250:12:4,8:114,119:0.048:2,2:14.8:1:25.8:1:0.37964:1.91106:38.9:5:0.0422:0:3.3 -GL000220.1 119454 . TCTCG T 115 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.0051;SOR=0.25716;LSEQ=TTTCTTTCTCGCTCTCGCTC;RSEQ=CTCTCTCCCTCGCTCGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:15:4,11:47,39:0.0872:2,2:21.5:1:29.6:1:0.05421:3.27614:43.1:30:0.0915:0.0233:4.4 0/1:251:6:3,3:74,80:0.0239:2,2:22.7:1:31.6:1:1:1.08:37:12:0.025:0.008:3.2 -GL000220.1 119458 . GCTCT C 201 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.35839;SOR=0.81496;LSEQ=TTCTTTCTCGCTCTCGCTCT;RSEQ=CTCCCTCGCTCGTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:70:40,30:47,39:0.407:2,2:24.2:1:31.2:1:0.87135:1.11:46.4:140:0.4268:0.064:2 0/1:251:90:44,46:74,80:0.3586:2,2:24.9:1:31:1:1:1.03:45.9:89:0.3708:0.0239:1.9 -GL000220.1 119477 . TTCTTTCTCTTTCTCTTTCTCTCTCTC T 190 NM4;MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=16.000;MSILEN=2;SSF=0;SOR=0.04223;LSEQ=CGCTCTCTCCCTCGCTCGTT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:77:37,40:58,50:0.3909:2,2:14:1:30.4:1:0.45993:1.25251:43.2:10:0.3627:0.3909:4.5 0/1:267:7:3,4:117,127:0.0262:2,2:29.7:1:30.4:1:1:1.22735:34:14:0.0266:0.0225:1.6 -GL000220.1 119479 . CTTTCTCTTTCTCTTTCTCTCTC ATCTCTCTCTCGCTCTTGCCCTCTCGCTCTCTCCCTCGCTCGTTT 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00097;SOR=0;LSEQ=CTCTCTCCCTCGCTCGTTTT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:8:3,5:58,50:0.0406:2,2:25.9:1:27.2:1:0.47417:1.92244:35.6:7:0.0363:0.0406:2.1 0/0:267:0:0,0:117,127:0:2,0:22.2:1:29.4:1:1:0:52.1:243:0.924:0:1.6 -GL000220.1 119481 . T C 197 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTCCCTCGCTCGTTTTCT;RSEQ=TCTCTTTCTCTTTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:57,47:0:2,0:26.4:1:29:1:1:0:57.5:12:1:0:0.6 0/1:263:95:45,50:71,76:0.3612:2,2:12.3:1:30:1:0.89601:1.03787:43.7:12.571:0.4:0:3.1 -GL000220.1 119488 . T TCGCTCTTGCC 93 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04812;SOR=4.25967;LSEQ=TCGCTCGTTTTCTTTCTCTT;RSEQ=CTCTTTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:2,0:62,53:0.0138:2,0:23:0:22.7:1:0.50015:0:34.5:4:0.0147:0:5 0/1:195:11:2,9:67,76:0.0564:2,2:25.3:1:27:1:0.11264:3.93646:31.3:22:0.0659:0.041:5.1 -GL000220.1 119489 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=6;SSF=0.07871;SOR=0;LSEQ=CGCTCGTTTTCTTTCTCTTT;RSEQ=TCTTTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:1,2:67,52:0.0207:2,2:5.7:1:25:1:0.58335:2.55727:52:2:0.0179:0:3.3 0/0:192:0:0,0:68,84:0:2,0:8:0:14:0:1:0:60:0:0:0:2 -GL000220.1 119490 . TCTTT GCTCTTGCCCTCTCG 137 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.0345;SOR=0.46698;LSEQ=CGCTCGTTTTCTTTCTCTTT;RSEQ=CTCTCTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:22:5,17:62,53:0.1517:2,2:27.2:1:30.8:1:0.00972:3.93935:35.4:44:0.1618:0.0276:4.9 0/1:195:15:8,7:67,76:0.0769:2,2:30.9:1:30.1:1:0.78708:1.29:32.5:30:0.0898:0.0103:5 -GL000220.1 119493 . T C 83 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00039;SOR=0;LSEQ=CGTTTTCTTTCTCTTTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:9:4,5:58,42:0.0643:2,2:11.3:1:26.4:1:0.49547:1.71737:29.4:3.5:0.0693:0:4.6 0/0:189:0:0,0:64,70:0:2,0:26.9:1:27.6:1:1:0:57.7:9.308:0.9528:0:0.7 -GL000220.1 119527 . G C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94297;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCGCTCTCGCCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:12:4,8:82,78:0.0694:2,2:18.4:1:28.4:1:0.37017:2.09377:35.8:3:0.0647:0:4.5 0/1:198:13:9,4:83,99:0.0657:2,2:16.1:1:28.5:1:0.14925:2.67:42.6:5.5:0.0675:0:4.1 -GL000220.1 119531 . C G 56 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.48037;SOR=0.5152;LSEQ=CTCTCTCTCTCTCTCTGTCT;RSEQ=TCGCTCTCGCCCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:5:3,2:80,86:0.0289:2,2:29.6:1:24.2:1:0.67489:1.61:33.4:1.5:0.0181:0:4.4 0/1:199:3:3,0:91,105:0.0151:2,0:32.7:1:31:1:0.10361:0:44.7:6:0.0154:0:5 -GL000220.1 119533 . C T 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=6;SSF=0.01633;SOR=Inf;LSEQ=CTCTCTCTCTCTCTGTCTCT;RSEQ=GCTCTCGCCCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:86,87:0:2,0:22.8:1:29.5:1:1:0:52.7:23.714:1:0:1.6 0/1:199:7:2,5:91,101:0.0352:2,2:21.3:1:29.9:1:0.45194:2.24379:57.4:14:0.0355:0:1.1 -GL000220.1 119548 . T G 56 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=7.000;MSILEN=2;SSF=0.31008;SOR=0.41137;LSEQ=TCTCTCGCTCTCGCCCTCTC;RSEQ=CTCTCTCTCTTTCTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:6:4,2:70,80:0.0382:2,2:22.7:1:21.8:1:0.42379:2.27:34.5:2:0.027:0:5 0/1:187:3:3,0:81,97:0.016:2,0:24:1:27:1:0.09803:0:44.7:6:0.0165:0:5 -GL000220.1 119553 . CTCTCTTTC A 28 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=7.000;MSILEN=2;SSF=0.20785;SOR=0;LSEQ=CGCTCTCGCCCTCTCTCTCT;RSEQ=TCTCTGTCTCTCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:2,0:69,79:0.0131:2,0:24.5:1:28.2:1:0.22237:0:50:4:0.0139:0.0065:4.5 0/0:182:0:0,0:84,93:0:2,0:23.2:1:29:1:1:0:51.3:18.667:1:0:1.5 -GL000220.1 119573 . C G 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=1;SOR=0.88278;LSEQ=CTCTCTTTCTCTCTGTCTCT;RSEQ=TCTGTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:55,65:0.0164:2,0:35:0:24:1:0.21623:0:40:1:0.0083:0:7.5 0/1:138:2:2,0:63,70:0.0145:2,0:28.5:1:28.5:1:0.22996:0:57:4:0.0152:0:4 -GL000220.1 119577 . G C 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=12;MSI=1.000;MSILEN=1;SSF=0.02747;SOR=0.52898;LSEQ=CTTTCTCTCTGTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:44:17,27:25,28:0.3729:2,2:18.6:1:29.6:1:0.41862:1.41293:48.5:5.286:0.3814:0:3.4 0/1:134:32:17,15:39,38:0.2388:2,2:21.8:1:30.9:1:0.83642:1.10:44.3:64:0.2783:0:3.3 -GL000220.1 119595 . CTC GTCGCTCTCGCCCTCTCGCTCTCTCTCTGTCTCTGTCTGTG 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00146;SOR=0;LSEQ=CTGTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTCCCTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:9:3,6:47,56:0.0804:2,2:25.3:1:29.9:1:0.72877:1.67109:35.9:18:0.0833:0.0804:2.6 0/0:115:0:0,0:54,60:0:2,0:18.4:1:28.4:1:1:0:52.1:11.667:0.9906:0:1.9 -GL000220.1 119610 . C T 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CTCCCCCTCCCTCCCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:14:9,5:35,48:0.1373:2,2:8.9:1:24.8:1:0.15282:2.45:57.6:1.8:0.1084:0:1.8 0/0:96:0:0,0:42,47:0:2,0:21.4:1:28.1:1:1:0:53.2:8.889:1:0:2.2 -GL000220.1 119612 . TCC T 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.1507;SOR=0.45834;LSEQ=TCTCTCTCTCTCTCTCTCCC;RSEQ=CCCTCCCTCCCTCTCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:13:4,9:41,54:0.1215:2,2:11.1:1:27.7:1:0.55139:1.70024:56.7:5.5:0.1048:0.0748:3.6 0/1:101:6:1,5:51,44:0.0594:2,2:14.7:1:28.8:1:0.10534:5.70809:47.2:12:0.06:0.0198:3 -GL000220.1 119614 . C CCT 133 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0298;SOR=2.30841;LSEQ=TCTCTCTCTCTCTCTCCCTC;RSEQ=CCCTCCCTCCCTCTCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:12:3,9:35,45:0.1188:2,2:21.4:1:29.8:1:0.34681:2.31339:37.3:24:0.1379:0:3.8 0/1:105:25:12,13:41,34:0.2381:2,2:15.8:1:28.8:1:0.64607:1.30286:51.6:24:0.2553:0.0952:4.2 -GL000220.1 119628 . T C 177 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.04096;SOR=1.74652;LSEQ=TCCCTCCCCCTCCCTCCCTC;RSEQ=CTCCCCTTCCTTGGTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:37:15,22:40,50:0.2913:2,2:21.3:1:31.4:1:0.84397:1.17186:50.9:74:0.319:0:3.7 0/1:141:59:29,30:41,40:0.4184:2,2:19.2:1:30.1:1:1:1.05988:55.9:28.5:0.4453:0:3.5 -GL000220.1 119656 . C A 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.186;SOR=0;LSEQ=TCCTTGGTGCCTTCTCGGCT;RSEQ=TTGACACTTAGCCGCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:54,80:0.0146:2,2:45:1:27:1:1:1.48:60:4:0.0157:0:6 0/0:180:0:0,0:83,97:0:2,0:27:1:29.7:1:1:0:58.6:9.588:1:0:2 -GL000220.1 119661 . C G 202 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14068;SOR=1.41869;LSEQ=GGTGCCTTCTCGGCTCTTGA;RSEQ=ACTTAGCCGCTGTCTCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:69:28,41:27,43:0.4964:2,2:28.1:1:30.7:1:0.86313:1.09:57.1:16.25:0.4815:0:2.9 1/0:180:105:49,56:33,40:0.5833:2,2:27.1:1:30.1:1:0.87937:1.06:57.8:14:0.5665:0:2.9 -GL000220.1 119665 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50921;SOR=Inf;LSEQ=CCTTCTCGGCTCTTGACACT;RSEQ=AGCCGCTGTCTCGCCGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:58,82:0:2,0:26.7:1:28.6:1:1:0:59.2:34:1:0:1.8 0/1:188:2:1,1:81,102:0.0106:2,2:36:0:33:1:1:1.26:60:4:0.0114:0:3.5 -GL000220.1 119680 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17933;SOR=0;LSEQ=ACACTTAGCCGCTGTCTCGC;RSEQ=GTGTCCCGGGTCGACCGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:63,78:0.014:2,2:29:1:30.5:1:1:1.24:60:4:0.0144:0:1 0/0:194:0:0,0:87,107:0:2,0:25.8:1:28.7:1:1:0:59.5:23.25:1:0:1.7 -GL000220.1 119683 . GT AC 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.07123;LSEQ=CTTAGCCGCTGTCTCGCCGT;RSEQ=CCCGGGTCGACCGGCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:9:4,5:62,73:0.0625:2,2:29.2:1:29.7:1:1:1.06122:60:18:0.0652:0:2.3 0/1:195:13:5,8:80,101:0.0667:2,2:25.5:1:30.2:1:0.778:1.2658:58.6:26:0.0734:0:2.5 -GL000220.1 119684 . T C 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.73857;SOR=1.08533;LSEQ=TTAGCCGCTGTCTCGCCGTG;RSEQ=CCCGGGTCGACCGGCGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:58:26,32:36,41:0.4028:2,2:27.6:1:31.5:1:0.86274:1.08005:59.5:57:0.4351:0:2.4 0/1:194:82:39,43:41,58:0.4227:2,2:24.8:1:29.6:1:0.45352:1.28:59.2:15.4:0.4583:0:2.6 -GL000220.1 119688 . G C 15 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76501;LSEQ=CCGCTGTCTCGCCGTGTCCC;RSEQ=GGTCGACCGGCGGGCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:69,77:0.0135:2,2:28.5:1:29:1:1:1.12:60:4:0.0139:0:1 0/1:193:2:2,0:83,107:0.0104:2,0:12.5:1:15:0:0.1947:0:60:0:0:0:2.5 -GL000220.1 119705 . T C 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.0957;SOR=0;LSEQ=CCCGGGTCGACCGGCGGGCC;RSEQ=TCTCCACCGAGCGGCGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:3:2,1:62,80:0.0205:2,2:39.7:1:31.3:1:0.58331:2.56:60:6:0.0208:0:2.7 0/0:172:0:0,0:75,97:0:2,0:24:1:29.4:1:1:0:60:23.571:1:0:1.2 -GL000220.1 119716 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21467;SOR=0;LSEQ=CGGCGGGCCTTCTCCACCGA;RSEQ=CGGCGTGTAAGAGTGCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:57,71:0.0154:2,2:19:0:32:1:1:1.24:60:4:0.0161:0:3 0/0:150:0:0,0:62,87:0:2,0:25.7:1:31.4:1:1:0:60:48.667:0.9932:0:0.9 -GL000220.1 119726 . A G 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33934;SOR=0.28398;LSEQ=TCTCCACCGAGCGGCGTGTA;RSEQ=GAGTGCCCGTCGGGACGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:3:1,2:52,71:0.0238:2,2:27.7:1:32:1:1:1.46053:60:6:0.0248:0:1 0/0:146:1:1,0:56,89:0.0068:2,0:2:0:33:0:0.39041:0:60:2:0.0072:0:2 -GL000220.1 119734 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19963;SOR=0;LSEQ=GAGCGGCGTGTAAGAGTGCC;RSEQ=GTCGGGACGAGCCGGACCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:53,61:0.0172:2,2:34.5:1:30.5:1:1:1.15:60:4:0.0175:0:1 0/0:143:0:0,0:59,84:0:2,0:23.5:1:28.3:1:1:0:60:14.889:1:0:0.8 -GL000220.1 119753 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25688;SOR=Inf;LSEQ=CCGTCGGGACGAGCCGGACC;RSEQ=GCCGCGTCCCCGTCTCGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:44,59:0:2,0:25.8:1:29.7:1:1:0:60:33.333:1:0:0.7 0/1:130:3:2,1:53,74:0.0231:2,2:17.3:1:27:1:0.57339:2.77:60:6:0.024:0:2 -GL000220.1 119756 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50397;SOR=Inf;LSEQ=TCGGGACGAGCCGGACCCGC;RSEQ=GCGTCCCCGTCTCGGTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:42,58:0:2,0:25.8:1:30:1:1:0:59.8:200:1:0:0.7 0/1:125:2:1,1:50,73:0.016:2,2:14:0:29:1:1:1.46:60:4:0.0165:0:2 -GL000220.1 119764 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20346;SOR=0;LSEQ=AGCCGGACCCGCCGCGTCCC;RSEQ=GTCTCGGTCGGCACCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:37,56:0.0211:2,2:23.5:1:30:1:1:1.51:60:4:0.0211:0:1.5 0/0:115:0:0,0:48,67:0:2,0:25.6:1:28.7:1:1:0:59:27.75:1:0:0.7 -GL000220.1 119775 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49849;SOR=Inf;LSEQ=CCGCGTCCCCGTCTCGGTCG;RSEQ=CACCTCCGGGGTCGACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:37,55:0:2,0:23.2:1:30.9:1:1:0:58.7:29.667:1:0:0.6 0/1:101:2:1,1:41,58:0.0198:2,2:19.5:1:27:1:1:1.41:60:4:0.0211:0:1 -GL000220.1 119822 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.06932;LSEQ=CCGCGAGCTCCGGACTTAGC;RSEQ=GGCGTCTGCACGTGTCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:22:5,17:15,19:0.3929:2,2:21.9:1:30.7:1:0.15407:2.6378:53.6:44:0.3929:0:1.3 0/1:66:27:9,18:18,21:0.4091:2,2:17.3:1:28.9:1:0.32197:1.70031:52.1:26:0.4063:0:1.4 -GL000220.1 119826 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50206;SOR=Inf;LSEQ=GAGCTCCGGACTTAGCTGGC;RSEQ=TCTGCACGTGTCCCGGGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:19,32:0:2,0:28.2:1:31.1:1:1:0:57.2:50:1:0:0.6 0/1:64:2:1,1:25,37:0.0313:2,2:19:1:31:0:1:1.47:50:4:0.0323:0:2 -GL000220.1 119827 . T C 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80484;LSEQ=AGCTCCGGACTTAGCTGGCG;RSEQ=CTGCACGTGTCCCGGGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:18,31:0.0392:2,2:20:1:33.5:1:1:1.70:50:4:0.0392:0:2 0/1:63:2:1,1:24,37:0.0317:2,2:4:1:30.5:1:1:1.53:60:4:0.0328:0:2.5 -GL000220.1 119851 . G A 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1589;LSEQ=CACGTGTCCCGGGTCGACCA;RSEQ=CAGGCGGCCGCCGGACGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:2,1:20,27:0.06:2,2:19.3:1:30.3:1:0.57571:2.65:60:6:0.0625:0:1 0/1:58:4:2,2:22,32:0.069:2,2:23.5:1:29.5:1:1:1.44:60:8:0.069:0:1.3 -GL000220.1 119855 . GCGGCCGC G 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.5052;SOR=Inf;LSEQ=TGTCCCGGGTCGACCAGCAG;RSEQ=CGGACGCTGCGGCGCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:21,25:0:2,0:21.7:1:30.5:1:1:0:57.2:45:1:0:0.5 0/1:61:2:1,1:25,34:0.0328:2,2:13:0:34:0:1:1.35:59:4:0.0339:0:1 -GL000220.1 119880 . T C 112 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15197;SOR=2.8907;LSEQ=CGCCGGACGCTGCGGCGCAC;RSEQ=GACGCGAGGGCGTCGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:1,2:15,14:0.0938:2,2:27.3:1:31:1:1:2.09377:49.7:6:0.1034:0:1.7 0/1:56:13:7,6:17,24:0.2321:2,2:27.1:1:30.3:1:0.52825:1.63:58.3:26:0.2407:0:1.2 -GL000220.1 119901 . G C 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59845;SOR=0.48743;LSEQ=GACGCGAGGGCGTCGATTCC;RSEQ=GTTCACGCGCCGGCGACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:17,12:0.0645:2,2:16.5:1:32:1:1:1.40053:21:4:0.0645:0:3.5 0/1:62:2:1,1:30,30:0.0323:2,2:5.5:1:27.5:1:1:1:52:4:0.0323:0:3 -GL000220.1 119906 . A G 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.60309;SOR=0.5041;LSEQ=GAGGGCGTCGATTCCGGTTC;RSEQ=CGCGCCGGCGACCTCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:17,12:0.0645:2,2:21.5:1:32.5:1:1:1.40053:21:4:0.0667:0:3.5 0/1:60:2:1,1:30,28:0.0333:2,2:10.5:1:28:1:1:1.07017:52:4:0.0333:0:3 -GL000220.1 119911 . C T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=0;LSEQ=CGTCGATTCCGGTTCACGCG;RSEQ=CGGCGACCTCCACCGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:8:5,3:14,10:0.25:2,2:16.1:1:27:1:1:1.18:60:7:0.2333:0:2.1 0/0:57:0:0,0:30,25:0:2,0:25.7:1:30.3:1:1:0:59.7:17.333:0.963:0:0.5 -GL000220.1 119913 . G C 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.64064;SOR=0.62607;LSEQ=TCGATTCCGGTTCACGCGCC;RSEQ=GCGACCTCCACCGGCCTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:21,12:0.0571:2,2:28.5:1:32:1:1:1.72083:21:4:0.0588:0:3.5 0/1:55:2:1,1:29,24:0.0364:2,2:17.5:1:27:1:1:1.20416:52:4:0.037:0:3 -GL000220.1 119967 . T C 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00832;SOR=0;LSEQ=TGGGACCACGCGGAACTCCC;RSEQ=CTCCTACATTTTTTTCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:3,2:23,17:0.1111:2,2:30.4:1:31.8:1:1:1.11:55.8:10:0.1111:0:1.6 0/0:69:0:0,0:37,32:0:2,0:6:0:16:0:1:0:60:0:0:0:1 -GL000220.1 119970 . C T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15907;SOR=0.41595;LSEQ=GACCACGCGGAACTCCCTCT;RSEQ=CTACATTTTTTTCAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:9:6,3:22,17:0.1875:2,2:32.1:1:29.6:1:0.71608:1.53:59.3:18:0.1915:0:1.4 0/1:69:6:3,3:34,28:0.087:2,2:9.2:1:28.5:1:1:1.2108:57.3:12:0.0896:0:1.3 -GL000220.1 119972 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51326;SOR=Inf;LSEQ=CCACGCGGAACTCCCTCTCC;RSEQ=ACATTTTTTTCAGCCCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:28,20:0:2,0:27.1:1:29.7:1:1:0:59:96:1:0:0.5 0/1:70:2:2,0:37,31:0.0286:2,0:32.5:1:30:1:0.49938:0:39.5:4:0.0299:0:2.5 -GL000220.1 119992 . T C 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50744;SOR=1.73865;LSEQ=TACATTTTTTTCAGCCCCAC;RSEQ=GCGAGTTTGCGTCCGCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:3:3,0:33,22:0.0517:2,0:28:1:32.3:1:0.28131:0:40:6:0.0517:0:1 0/1:69:6:5,1:36,27:0.087:2,2:27.8:1:29.3:1:0.38936:3.69:39.8:12:0.0882:0:1.7 -GL000220.1 120003 . G C 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03608;SOR=0;LSEQ=CAGCCCCACTGCGAGTTTGC;RSEQ=TCCGCGGGACTTTTAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:4:2,2:34,23:0.0656:2,2:31.5:1:31.8:1:1:1.46857:57:8:0.0656:0:2.3 0/0:77:0:0,0:44,33:0:2,0:24.6:1:30:1:1:0:57.1:154:1:0:0.3 -GL000220.1 120071 . T G 23 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.69176;LSEQ=GCTTCCTCCTTTTTTGCTTT;RSEQ=TGGTTTTGCCTTGCGTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:0,2:52,44:0.0204:2,0:18.5:1:33.5:1:0.21776:0:44:4:0.0204:0:3.5 0/1:141:2:1,1:75,64:0.0142:2,2:28:1:23:1:1:1.17055:57:1:0.0072:0:3.5 -GL000220.1 120080 . C T 40 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30747;SOR=0.22579;LSEQ=TTTTTTGCTTTTTGGTTTTG;RSEQ=CTTGCGTTTTCTTTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:3:0,3:52,47:0.0294:2,0:8.7:1:25.7:1:0.11415:0:42.7:2:0.0213:0:3.7 0/0:148:1:0,1:76,71:0.0068:2,0:2:0:29:0:0.48649:0:59:2:0.0074:0:2 -GL000220.1 120101 . TTC T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50452;SOR=Inf;LSEQ=CTTGCGTTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:48,50:0:2,0:25.9:1:30.4:1:1:0:56.6:196:0.9899:0:0.7 0/1:125:2:0,2:64,59:0.016:2,0:7.5:1:27:1:0.23613:0:58.5:4:0.0163:0.008:2.5 -GL000220.1 120111 . CTT C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=4;SSF=0.4998;SOR=Inf;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TCTTTCTTTCTTTCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:44,54:0:2,0:23.9:1:30.4:1:1:0:56.9:97:1:0:0.8 0/1:114:2:1,1:55,56:0.0175:2,2:8:1:28.8:1:1:1.02:60:4:0.0179:0.0088:0 -GL000220.1 120137 . T CTCTC 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.2454;SOR=Inf;LSEQ=TTCTTTCTTTCTTTCTTTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:25,35:0:2,0:26.5:1:28.9:1:1:0:56.1:19:1:0:0.8 0/1:81:2:0,2:28,30:0.0247:2,0:43.5:1:31.9:1:0.49379:0:42.5:4:0.0345:0:2.5 -GL000220.1 120161 . G C 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00784;SOR=0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCCCCTCCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:6:4,2:36,53:0.0632:2,2:9.5:1:29.2:1:0.23557:2.91:40.7:5:0.0581:0:2.7 0/0:115:0:0,0:52,54:0:2,0:20.6:1:28.7:1:1:0:58.3:6.067:1:0:0.8 -GL000220.1 120210 . TGCTGCCTCTGCCTCCACGGTTCAAGCAAA AAG 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.703;SOR=0.60597;LSEQ=TGCCTTCTCGGCTCGCTGCT;RSEQ=CAGCAAGTTTTCTATTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:4:3,1:35,48:0.046:2,2:13.8:1:29.7:1:0.31406:4.05:51.8:8:0.0488:0.0345:0.8 0/1:106:3:1,2:45,55:0.0283:2,2:31.3:1:31.4:1:1:1.62887:60:6:0.03:0.0094:0 -GL000220.1 120211 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.50799;SOR=Inf;LSEQ=CTTCTCGGCTCGCTGCTGCT;RSEQ=CTGCCTCTGCCTCCACGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:33,45:0:2,0:25.6:1:31.5:1:1:0:60:14.6:1:0:0.2 0/1:106:2:1,1:47,55:0.0189:2,2:22:0:27.5:1:1:1.17:60:4:0.0206:0:1 -GL000220.1 120319 . C T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64314;SOR=0.63427;LSEQ=GAACTCCCGACCTAGTGATC;RSEQ=GCCCGCCTCGGCCTCCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:0,2:9,19:0.0645:2,0:37:0:29:1:1:0:60:4:0.069:0:1 0/1:48:2:1,1:17,29:0.0417:2,2:44:0:30:1:1:1.69:60:4:0.0426:0:1.5 -GL000220.1 120436 . TACACATACACACACACACACACACACAC T 72 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=25.000;MSILEN=2;SSF=0.04796;SOR=Inf;LSEQ=GCCGTGTATGAACATACATC;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:26.1:1:27.7:1:1:0:60:17:1:0:0.3 0/1:20:5:2,3:8,7:0.25:2,2:12.6:1:31.2:1:1:1.66859:60:10:0.2632:0.25:1 -GL000220.1 120483 . ACACACACACC A 58 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=20.000;MSILEN=2;SSF=0.0404;SOR=0;LSEQ=ACACACACACACACACACAC;RSEQ=CCCCGTAGTGATAAAACTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:2,2:4,8:0.2353:2,2:24.3:1:29.3:1:0.6044:1.91:60:8:0.2667:0.1176:0.5 0/0:19:0:0,0:8,10:0:2,0:18.5:1:27.2:1:1:0:58.8:3.5:1:0:0.9 -GL000220.1 120724 . A T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50834;SOR=Inf;LSEQ=CTCTGCGCTCTGGTGACCTC;RSEQ=GCCTCCCAAATAGCTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:17,11:0:2,0:26.1:1:29.5:1:1:0:60:27:1:0:0.1 0/1:40:2:1,1:21,17:0.05:2,2:7:0:29:1:1:1.22874:60:4:0.05:0:1 -GL000220.1 120725 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51153;SOR=Inf;LSEQ=TCTGCGCTCTGGTGACCTCA;RSEQ=CCTCCCAAATAGCTGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:16,11:0:2,0:26.9:1:31.8:1:1:0:60:54:1:0:0.1 0/1:40:2:1,1:20,18:0.05:2,2:40:1:28:1:1:1.10818:60:4:0.05:0:1 -GL000220.1 120822 . CTGCGGTGGGG C 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=5;SSF=0.23913;SOR=0;LSEQ=TCCACTCCAGCTTACGTGGG;RSEQ=TGGGGTGGGGTGGGGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:18,13:0.0588:2,2:27:1:29:1:1:1.37079:60:4:0.069:0.0294:2.5 0/0:35:0:0,0:18,7:0:2,0:26:1:32:1:1:0:60:54:0.8182:0.0286:0.2 -GL000220.1 120825 . CGGTGGGGTGG C 93 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=7.000;MSILEN=5;SSF=0.34672;SOR=2.05202;LSEQ=ACTCCAGCTTACGTGGGCTG;RSEQ=GGTGGGGTGGGGTGGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:2,2:15,10:0.125:2,2:30.3:1:30.6:1:1:1.47868:60:8:0.129:0.0313:2 0/1:35:8:6,2:17,7:0.2286:2,2:30.3:1:31.3:1:1:1.23:60:16:0.2353:0.0286:0.8 -GL000220.1 120836 . G A 29 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.49317;SOR=Inf;LSEQ=CGTGGGCTGCGGTGGGGTGG;RSEQ=GTGGGGTGGGGTGGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:0:2,0:18.2:1:30:1:1:0:60:33:1:0:1.1 0/1:36:2:1,1:25,9:0.0556:2,2:19.5:1:29.5:1:0.48413:2.68742:60:4:0.0556:0:2 -GL000220.1 120843 . T G 48 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.2988;SOR=0.42362;LSEQ=TGCGGTGGGGTGGGGTGGGG;RSEQ=GGGGTGGGGTGGGGTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:6:0,6:21,10:0.1622:2,0:22.8:1:18.7:1:0.00344:0:60:1:0.0968:0:3.5 0/1:40:3:0,3:26,11:0.075:2,0:18.7:1:20:1:0.03684:0:60:2:0.0625:0:4.7 -GL000220.1 120848 . T G 38 v4;MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.7225;SOR=1.39923;LSEQ=TGGGGTGGGGTGGGGTGGGG;RSEQ=GGGGTGGGGTGGGGTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:18,9:0.1:2,0:14.3:1:25.7:1:0.05419:0:60:6:0.12:0:4 0/1:37:5:1,4:23,9:0.1351:2,2:14.8:1:16.4:1:0.04232:9.52741:56:0.667:0.0645:0:2.4 -GL000220.1 120865 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50341;SOR=Inf;LSEQ=GGGTGGGGTGGGGTGGGGTG;RSEQ=AGAGAAAACGATTGATTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:0:2,0:23:1:31.8:1:1:0:60:33:1:0:0.9 0/1:45:2:1,1:22,21:0.0444:2,2:34.5:1:28:1:1:1.04655:60:4:0.0465:0:1.5 -GL000220.1 120903 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4999;SOR=Inf;LSEQ=GCGATCTCAATTGCCTTTTA;RSEQ=CTTCATTCATACCCTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:23,23:0:2,0:23.3:1:31.8:1:1:0:60:45:1:0:0.6 0/1:56:2:0,2:25,29:0.0357:2,0:8:1:30:1:0.49675:0:60:4:0.0364:0:1 -GL000220.1 120929 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.57659;SOR=1.46194;LSEQ=TTCATACCCTGTTATTTGCT;RSEQ=GTTTATTCTCATGGGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:6:4,2:30,25:0.0984:2,2:24.8:1:27.2:1:0.68477:1.65:60:5:0.0833:0:1.3 0/1:58:8:3,5:23,27:0.1379:2,2:28.5:1:29.1:1:0.71953:1.41133:60:16:0.1379:0:1.4 -GL000220.1 120952 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50116;SOR=0;LSEQ=TTATTCTCATGGGTTCTTCT;RSEQ=TGTCATTGTCACGTTCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:33,28:0.0317:2,2:32:0:31.5:1:1:1.17549:60:4:0.0323:0:1.5 0/0:51:0:0,0:22,29:0:2,0:25.8:1:31.5:1:1:0:59.9:102:1:0:0.4 -GL000220.1 121026 . TTCCTTCCC T 121 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=4;SSF=0.0135;SOR=4.09692;LSEQ=TTCCTTCCTTCCTTCCTTCC;RSEQ=TCCTTCCTTCCTTCCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:5:3,2:23,25:0.0943:2,2:48.2:1:30.4:1:0.66874:1.62:60:10:0.098:0:0.6 0/1:53:16:8,8:16,14:0.3019:2,2:27.8:1:30.3:1:1:1.13954:60:32:0.3636:0.1509:0.9 -GL000220.1 121036 . C CA 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2344;SOR=Inf;LSEQ=CCTTCCTTCCTTCCTTCCCT;RSEQ=CTTCCTTCCTTCCTTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:28,29:0:2,0:25.9:1:30:1:1:0:59.8:18:1:0:0.7 0/1:54:2:1,1:25,27:0.037:2,2:14:1:28.4:1:1:1.08:54.5:4:0.0377:0.0185:0.5 -GL000220.1 121057 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49524;SOR=Inf;LSEQ=CTTCCTTCCTTCCTTCCCTC;RSEQ=CTTACTGGCAGGGTCTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:26,26:0:2,0:27.8:1:29.1:1:1:0:59.8:9.4:1:0:0.6 0/1:53:2:1,1:28,23:0.0377:2,2:35:1:27:1:1:1.21285:60:4:0.0377:0:2 -GL000220.1 121290 . C G 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80451;LSEQ=GTGTGTGTGTGTGTGTGTAT;RSEQ=TATGTATGTATGTATGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:23.5:1:33.5:1:1:1:50:4:0.125:0:5.5 0/1:22:2:2,0:7,12:0.0909:2,0:10.5:1:29.5:1:0.17143:0:50:4:0.1:0:3.5 -GL000220.1 121293 . T TGTATGTAC 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80746;LSEQ=TGTGTGTGTGTGTGTATCTA;RSEQ=GTATGTATGTATGTATGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:6,8:2,2:0.7368:2,2:33.4:1:29.1:1:1:1.31198:58.8:28:0.7778:0.0526:0.2 1/0:26:18:6,12:4,1:0.6923:2,2:21.1:1:29.2:1:0.12687:7.26989:57.1:36:0.6923:0.2692:1.1 -GL000220.1 121297 . T TGTAC 39 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.07317;SOR=0;LSEQ=TGTGTGTGTGTATCTATGTA;RSEQ=GTATGTATGTATGTGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:2,1:7,9:0.1579:2,2:41:1:24.8:1:0.58204:2.45:60:2:0.1111:0:0.7 0/0:25:0:0,0:9,15:0:2,0:21.5:1:28.7:1:1:0:57:23:0.9583:0:1.3 -GL000220.1 121453 . TTGCCTGCCTGCC T 86 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=37;MSI=12.000;MSILEN=4;SSF=0.0104;SOR=0;LSEQ=GCGCCTGGCTCCTTCTACAT;RSEQ=TGCCTGCCTGCCTGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:3,4:8,8:0.25:2,2:36:1:30.9:1:1:1.31677:60:14:0.2593:0:0.3 0/0:26:0:0,0:10,9:0:2,0:24.2:1:30.1:1:1:0:57.4:38:0.7308:0:0.5 -GL000220.1 121738 . T C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24891;SOR=Inf;LSEQ=TTTGTCGTGGGTCGGTTCTT;RSEQ=CCGTTTTTAATACGGGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:25.3:1:30.2:1:1:0:60:46:1:0:0.1 0/1:30:3:2,1:14,13:0.1:2,2:43:1:32:1:1:1.82:60:6:0.1:0:2.3 -GL000220.1 121776 . C T 84 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07985;SOR=Inf;LSEQ=ACTGCGAACGAAGAAAATTT;RSEQ=CAGACGCATCTCACCGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:26.7:1:30.7:1:1:0:60:30:1:0:0.1 0/1:32:7:4,3:13,12:0.2188:2,2:15.3:1:30.1:1:1:1.22:60:14:0.2258:0:1.7 -GL000220.1 121989 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17273;SOR=0;LSEQ=CGGCTAATTTTTCTATTTTT;RSEQ=CTACAGATGGGGTTTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:12,4:0.1053:2,2:23.5:1:31:0:0.4902:2.79285:60:4:0.1176:0:1 0/0:26:0:0,0:15,11:0:2,0:24:1:28.7:1:1:0:60:52:1:0:0.3 -GL000220.1 121990 . C G 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68228;SOR=1.90571;LSEQ=GGCTAATTTTTCTATTTTTA;RSEQ=TACAGATGGGGTTTCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:11,6:0.1053:2,0:42.5:1:32.5:1:1:0:60:4:0.1111:0:1 0/1:27:5:4,1:12,10:0.1852:2,2:27.4:1:31.6:1:0.61848:3.20:60:10:0.1852:0:1.4 -GL000220.1 122041 . G C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06157;SOR=0;LSEQ=CTGGTCTTCAACTTCCGACC;RSEQ=TTGGAGAATCTTAACTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:23:1:29.5:1:1:1:60:4:0.1111:0:1 0/0:53:0:0,0:28,25:0:2,0:25.1:1:30.1:1:1:0:60:106:1:0:0.3 -GL000220.1 122079 . C CT 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.16629;SOR=0;LSEQ=TCTTGGTGGTGGTTGTTTTC;RSEQ=TTTTTCTTTTTTTTCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:19,16:0.0541:2,2:19:1:28.3:1:1:1.18197:60:4:0.0541:0.027:0 0/0:53:0:0,0:27,26:0:2,0:26.3:1:30.3:1:1:0:60:52:1:0:0.5 -GL000220.1 122085 . C CT 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.34199;LSEQ=TGGTGGTTGTTTTCCTTTTT;RSEQ=TTTTTTTTCTTTTCTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:17,16:0.0541:2,2:29.5:1:30.5:1:1:1.06069:50:4:0.0556:0:4 0/1:56:4:1,3:27,25:0.0714:2,2:31:1:23.5:1:0.61098:3.17735:60:3:0.0545:0:1 -GL000220.1 122089 . TTTTTC T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.18733;SOR=0;LSEQ=GGTTGTTTTCCTTTTTCTTT;RSEQ=TTTTCTTTTCTTTCCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:20,22:0.0455:2,2:28.5:1:28.5:1:1:1.10:60:4:0.0455:0:1 0/0:57:0:0,0:27,30:0:2,0:22.9:1:29.4:1:1:0:60:114:1:0:0.5 -GL000220.1 122116 . T TC 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.66846;SOR=0.6053;LSEQ=TTTCTTTTCTTTCCTTCTCC;RSEQ=CCCCCCCCACCCCCCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:0,3:16,18:0.075:2,0:34:1:32.7:1:0.24324:0:60:6:0.0968:0:0 0/1:43:2:0,2:16,22:0.0465:2,0:8:1:27.8:1:0.50769:0:47.5:4:0.0526:0.0233:1 -GL000220.1 122141 . G C 38 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.60993;SOR=0.34047;LSEQ=CCCCACCCCCCCTTGTCGTC;RSEQ=TCCTCCTCCTCCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:1,2:3,19:0.12:2,2:6.3:1:24:1:0.42174:2.98:60:2:0.0909:0:3.7 0/1:23:1:0,1:4,18:0.0435:2,0:25:0:30:0:1:0:35:2:0.05:0:2 -GL000220.1 122221 . G T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.7225;SOR=0.71468;LSEQ=TTTCAGCTGGGCTCTCCTAC;RSEQ=TGTGTTGCTCTGTTGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:5:2,3:18,13:0.1351:2,2:31:1:31.4:1:0.63713:2.03455:38.8:10:0.1429:0:1 0/1:30:3:2,1:14,13:0.1:2,2:45.7:1:31:1:1:1.82:50.7:6:0.1034:0:1.3 -GL000220.1 122382 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24324;SOR=0;LSEQ=GGTGTGAACGTTTCTCTTGC;RSEQ=GTCTCCCGGGGTGTACCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:30,23:0.0364:2,2:31.5:1:30:1:1:1.29798:60:4:0.037:0:1.5 0/0:56:0:0,0:29,26:0:2,0:26.8:1:29.5:1:1:0:60:110:0.9821:0:0.1 -GL000220.1 122448 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49946;SOR=Inf;LSEQ=GCTGAGTGGGTTTTCGGTGC;RSEQ=GAAACCTCCCGAGGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:30,22:0:2,0:25.9:1:29.7:1:1:0:60:51:1:0:0.1 0/1:62:2:1,1:30,30:0.0323:2,2:23.5:1:28:1:1:1:60:4:0.0323:0:1.5 -GL000220.1 122511 . C G 53 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1193;SOR=0;LSEQ=CTTCTCCCCCAGCCGAGGCT;RSEQ=CCACCGCCGCCCTGGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:2,1:34,28:0.0462:2,2:10.7:1:33.7:1:1:1.63:60:6:0.0462:0:1.3 0/0:66:0:0,0:30,36:0:2,0:25.7:1:30.5:1:1:0:59.6:132:1:0:0.2 -GL000220.1 122550 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.77498;LSEQ=TTTCCATAGGAGAGGTATGG;RSEQ=AGAGGACTGACACGCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:41,41:0.0238:2,2:24:1:29:1:1:1:60:4:0.0241:0:1 0/1:54:1:0,1:26,27:0.0185:2,0:1:0:22:0:1:0:60:2:0.0189:0:1 -GL000220.1 122573 . A G 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0657;SOR=0.41778;LSEQ=AGGACTGACACGCCTTCCAG;RSEQ=TCTATATCCTGCCGGACGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:25:13,12:28,33:0.2907:2,2:24.4:1:30.8:1:0.64127:1.27:60:24:0.2892:0:1.2 0/1:55:8:4,4:24,23:0.1455:2,2:19:1:31.4:1:1:1.04269:60:16:0.1538:0:1 -GL000220.1 122625 . C T 118 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00023;SOR=8.02965;LSEQ=GTGCCCCACCGGCTACCTGC;RSEQ=ACCTTCCAGGGAGCTCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:1,2:44,42:0.0337:2,2:33.3:1:28.7:1:0.61643:2.07845:60:6:0.0337:0:1 0/1:77:17:9,8:33,27:0.2208:2,2:25.6:1:29:1:1:1.08525:60:16:0.2133:0:1.4 -GL000220.1 122661 . A AC 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.5005;SOR=0;LSEQ=CTGAGGCGGATGCGACCCCC;RSEQ=CCCCCCCGTCACGTCCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:50,39:0.022:2,2:24.5:1:33:0:1:1.27851:60:4:0.0244:0:0 0/0:77:0:0,0:42,35:0:2,0:22.9:1:26.8:1:1:0:60:6:1:0:0.4 -GL000220.1 122711 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2454;SOR=Inf;LSEQ=CGGCTGGCCTTTGCCGGGCG;RSEQ=CCCCAGGGGAACCGCGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:38,44:0:2,0:22.5:1:28.8:1:1:0:60:26.333:1:0:0.2 0/1:81:2:1,1:40,39:0.0247:2,2:32:0:33:0:1:1.02533:60:4:0.0267:0:1.5 -GL000220.1 122762 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49848;SOR=0;LSEQ=GGATCCTCCGGCGAAGACTT;RSEQ=CACCGGATGCCCCGGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:33,40:0.0267:2,2:32:1:30.5:1:1:1.21:50:4:0.0267:0:1 0/0:66:0:0,0:32,34:0:2,0:25:1:30.6:1:1:0:55.9:65:1:0:0.2 -GL000220.1 122817 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49853;SOR=Inf;LSEQ=ACTGGACCACCCCGGACCGT;RSEQ=CTGTTCTTGGGGGTGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:31,30:0:2,0:27.5:1:32:1:1:0:56.7:122:1:0:0.1 0/1:70:2:1,1:34,34:0.0286:2,2:24:0:31:1:1:1:60:4:0.0286:0:1.5 -GL000220.1 122869 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19168;SOR=Inf;LSEQ=GGACTGGCAGCCCCAGCATT;RSEQ=TAAAGGGTGCGTGGGTATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:24,28:0:2,0:21.1:1:32.2:1:1:0:59.8:104:1:0:0.2 0/1:41:2:1,1:18,21:0.0488:2,2:9:0:31:1:1:1.16:48:4:0.05:0:1.5 -GL000220.1 123174 . A T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28205;SOR=Inf;LSEQ=TCTCTCTCTCTCTCTCTCGC;RSEQ=CGCGCACGCGCGCACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,18:0:2,0:18.9:1:29.6:1:1:0:59.1:33:1:0:0.5 0/1:56:3:1,2:24,28:0.0536:2,2:9:1:27.7:1:1:1.69821:48.3:6:0.0652:0:3 -GL000220.1 123178 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51489;SOR=Inf;LSEQ=TCTCTCTCTCTCTCGCACGC;RSEQ=CACGCGCGCACACACACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:19,19:0:2,0:18.2:1:29.3:1:1:0:57.4:11.667:1:0:0.5 0/1:57:2:1,1:26,29:0.0351:2,2:5:1:26:1:1:1.11:52.5:4:0.0351:0:2 -GL000220.1 123186 . GCA G 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.51036;SOR=Inf;LSEQ=TCTCTCGCACGCGCACGCGC;RSEQ=CACACACACACAATTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:0:2,0:20:1:30.5:1:1:0:57.6:11.333:1:0:0.5 0/1:53:2:1,1:24,27:0.0377:2,2:16.5:1:30:1:1:1.12:60:4:0.0408:0:0.5 -GL000220.1 123188 . A ACG 26 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.51209;SOR=Inf;LSEQ=TCTCGCACGCGCACGCGCGC;RSEQ=CACACACACACAATTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:0:2,0:20.2:1:29.8:1:1:0:57.6:36:1:0:0.5 0/1:54:2:1,1:24,26:0.037:2,2:28.5:1:26.3:1:1:1.08:60:4:0.0385:0:0.5 -GL000220.1 123214 . G C 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01904;SOR=0.09556;LSEQ=ACACACAATTTCCATATCTA;RSEQ=TTCACAGAGCACACTCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:3,4:13,15:0.2:2,2:26.9:1:33:1:1:1.15081:60:14:0.2059:0:1 0/1:44:1:0,1:20,23:0.0227:2,0:43:0:34:0:1:0:60:2:0.0233:0:1 -GL000220.1 123219 . C G 37 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.61817;SOR=2.72267;LSEQ=CAATTTCCATATCTAGTTCA;RSEQ=AGAGCACACTCACTTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:1:0,1:16,18:0.0286:2,0:21:0:33:0:1:0:60:2:0.0294:0:2 0/1:40:3:3,0:16,21:0.075:2,0:11.3:1:23.7:1:0.09808:0:53.3:2:0.0513:0:2.3 -GL000220.1 123233 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49985;SOR=Inf;LSEQ=AGTTCACAGAGCACACTCAC;RSEQ=TCCCCTTTTCACAGTACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:0:2,0:27:1:30.9:1:1:0:60:74:1:0:0.5 0/1:46:2:1,1:19,25:0.0435:2,2:21:0:33:1:1:1.31:60:4:0.0444:0:1.5 -GL000220.1 123239 . T C 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.16022;LSEQ=CAGAGCACACTCACTTCCCC;RSEQ=TTTCACAGTACGCAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:1,2:15,19:0.0811:2,2:26:1:32.3:1:1:1.56027:60:6:0.0811:0:1.3 0/1:43:4:2,2:19,20:0.093:2,2:12.8:1:30:1:1:1.05:60:8:0.093:0:2.3 -GL000220.1 123261 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24096;SOR=Inf;LSEQ=TTCACAGTACGCAGGCTGAG;RSEQ=AAAACCCGCCCCACCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:20,22:0:2,0:24.8:1:28.3:1:1:0:60:20:1:0:0.5 0/1:41:2:1,1:17,22:0.0488:2,2:30:1:28:1:1:1.29:60:4:0.0488:0:1 -GL000220.1 123277 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49384;SOR=Inf;LSEQ=TGAGTAAAACCCGCCCCACC;RSEQ=TCCACCCGTTGGCTGACGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:17,21:0:2,0:26.6:1:31.2:1:1:0:60:37:1:0:0.5 0/1:40:2:1,1:17,21:0.05:2,2:33:0:31.5:1:1:1.23:60:4:0.0513:0:2.5 -GL000220.1 123315 . G T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.82269;LSEQ=GAAACCCCTTCTCTACAATT;RSEQ=ATGAAAAAGATGATCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:4,3:9,13:0.2414:2,2:22.1:1:25.7:1:0.6665:1.88:60:6:0.2143:0:1.4 0/1:29:6:2,4:12,11:0.2069:2,2:23:1:29.7:1:0.65134:2.12461:60:12:0.2069:0:1.2 -GL000220.1 123380 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54229;SOR=Inf;LSEQ=ACTCCGGCACTTTGGGAGGC;RSEQ=GAGGCGGGTGGATCGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:0:2,0:20.3:1:29.4:1:1:0:59.1:22:1:0:0.8 0/1:44:2:1,1:21,21:0.0455:2,2:31.5:1:29:1:1:1:60:4:0.0455:0:1 -GL000220.1 123444 . G A 76 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49613;SOR=1.80804;LSEQ=GGCCGACGTGGCGAAACCCC;RSEQ=TCTCTCTGAAAAATAGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:3,1:14,14:0.125:2,2:26.3:1:28.5:1:0.60289:2.91:60:8:0.129:0:1 0/1:29:6:3,3:15,8:0.2069:2,2:15.5:1:29.7:1:0.6457:1.83303:60:12:0.2069:0:1.2 -GL000220.1 123455 . A C 84 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05853;SOR=7.28173;LSEQ=CGAAACCCCGTCTCTCTGAA;RSEQ=AATAGAACGATTAGCCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:19,14:0.0294:2,0:18:0:34:0:0.44118:0:60:2:0.0313:0:1 0/1:38:7:5,2:17,14:0.1842:2,2:11.3:1:30.1:1:0.67541:2.02:60:14:0.2:0:1 -GL000220.1 123504 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51386;SOR=Inf;LSEQ=GTGGGCTTGGAATCACGACC;RSEQ=CTCGGGAGACTGGGGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:23,14:0:2,0:22.2:1:31.2:1:1:0:60:74:1:0:0.4 0/1:55:2:1,1:31,21:0.0364:2,2:30.5:1:27.5:1:1:1.46529:60:4:0.0364:0:1 -GL000220.1 123520 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16433;SOR=0;LSEQ=GACCGCTCGGGAGACTGGGG;RSEQ=GGGCGACTTGTTCCAACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:23,13:0.0526:2,2:14:1:32:0:1:1.74146:60:4:0.0526:0:1 0/0:55:0:0,0:29,26:0:2,0:25.2:1:30.6:1:1:0:60:110:1:0:0.3 -GL000220.1 123569 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50022;SOR=Inf;LSEQ=AGGTTGCGATGAGCTGAGAT;RSEQ=GTGCCGTGGCGATGCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:22,21:0:2,0:26.4:1:30.2:1:1:0:60:42:1:0:0.3 0/1:53:2:1,1:23,27:0.0377:2,2:39:1:29.5:1:1:1.17:60:4:0.0377:0:1 -GL000220.1 123612 . C G 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.07066;LSEQ=ATGACGGAGCGAGACCCCGT;RSEQ=TCGAGAGAATCATGATGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:2,4:21,24:0.1176:2,2:37.2:1:29:1:0.67785:1.7315:60:5:0.1042:0:1.3 0/1:48:6:2,4:18,24:0.125:2,2:22.3:1:31.3:1:1:1.48776:60:12:0.1304:0:1 -GL000220.1 123725 . T G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10753;SOR=Inf;LSEQ=ATCACTTGAGGCCCCACAGG;RSEQ=CGAGGCTTCGGTCGGCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:0:2,0:25.1:1:29.8:1:1:0:60:42:1:0:0.1 0/1:40:3:2,1:21,16:0.075:2,2:32.3:1:31:1:1:1.51:60:6:0.0769:0:1.3 -GL000220.1 123806 . C T 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24603;SOR=Inf;LSEQ=CCCCTTCCCCGTTTGCTTTT;RSEQ=TTTTCTTCCCTTCTCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:50,42:0:2,0:23.8:1:31.6:1:1:0:59.9:184:1:0:0.1 0/1:94:3:1,2:45,46:0.0319:2,2:8.3:1:32:0:1:1.9431:60:6:0.0323:0:3 -GL000220.1 123809 . T G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49752;SOR=Inf;LSEQ=CTTCCCCGTTTGCTTTTCTT;RSEQ=TCTTCCCTTCTCTTTTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:51,44:0:2,0:23.6:1:30.1:1:1:0:59.9:190:1:0:0.1 0/1:98:2:1,1:48,48:0.0204:2,2:13:0:33.5:1:1:1:60:4:0.0211:0:4.5 -GL000220.1 123816 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=GTTTGCTTTTCTTTTCTTCC;RSEQ=TTCTCTTTTCTTCTTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:49,46:0:2,0:24.4:1:31.5:1:1:0:59.9:190:1:0:0.1 0/1:105:2:1,1:50,53:0.019:2,2:40:1:30.5:1:1:1.06:60:4:0.019:0:1 -GL000220.1 123835 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25985;SOR=Inf;LSEQ=CCTTCTCTTTTCTTCTTTTT;RSEQ=CTTCTCTTTTCTTTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:40,47:0:2,0:26.9:1:32.5:1:1:0:59.9:174:1:0:0.1 0/1:114:3:1,2:57,54:0.0263:2,2:23:1:30.3:1:0.61504:2.09776:51:6:0.0268:0:3.3 -GL000220.1 123842 . T TTTTCTTTCTTTC 134 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=35;MSI=11.000;MSILEN=4;SSF=0.15329;SOR=0.58322;LSEQ=TTTTCTTCTTTTTGCTTCTC;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:22:10,12:22,26:0.2391:2,2:16.9:1:30.2:1:1:1.01517:59.3:44:0.2418:0.1522:0.1 0/1:110:17:7,10:38,35:0.1545:2,2:22.8:1:30.6:1:0.59116:1.54347:57.8:34:0.1545:0.0636:0.2 -GL000220.1 123893 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24181;SOR=Inf;LSEQ=TCTTTTTCTTTTTCTCTCTT;RSEQ=CCCTCTTTCTTTCCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:35,42:0:2,0:24:1:31.1:1:1:0:59.5:37.5:1:0:0.3 0/1:75:2:1,1:36,37:0.0267:2,2:40.5:1:29.5:1:1:1.03:60:4:0.0282:0:1 -GL000220.1 123919 . CTTTCTTCT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=1;SSF=0.20138;SOR=0;LSEQ=TTTCTTTCCTGCCTTCCTGC;RSEQ=TTTCTTCTTTCCTCCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:27,35:0.0313:2,2:39:1:33:1:1:1.29:60:4:0.0313:0:0 0/0:78:0:0,0:37,41:0:2,0:22.6:1:29.7:1:1:0:59.5:77:1:0:0.3 -GL000220.1 123938 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49925;SOR=Inf;LSEQ=CCTTTCTTCTTTTCTTCTTT;RSEQ=CTCCCTTCCTCCCTTCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:21,35:0:2,0:19.8:1:30.9:1:1:0:59.3:55:1:0:0.4 0/1:66:2:1,1:28,36:0.0303:2,2:8.5:1:27.5:1:1:1.28:60:4:0.0308:0:1.5 -GL000220.1 123943 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.503;SOR=Inf;LSEQ=CTTCTTTTCTTCTTTCCTCC;RSEQ=TTCCTCCCTTCCTTCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:21,30:0:2,0:20.7:1:30.7:1:1:0:59.2:24.5:1:0:0.3 0/1:65:2:1,1:27,35:0.0308:2,2:27:0:30:1:1:1.29:60:4:0.0317:0:1 -GL000220.1 124003 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49352;SOR=Inf;LSEQ=AGTGCTGGGATGACTGGCGG;RSEQ=AGGCACCATGCCTGCTTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:11,24:0:2,0:24.7:1:31.4:1:1:0:59.6:34:0.9714:0:0.3 0/1:38:2:1,1:14,22:0.0526:2,2:8.5:1:30:1:1:1.55:60:4:0.0541:0:1.5 -GL000220.1 124249 . T TG 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49649;SOR=Inf;LSEQ=GTGCCCACACCGTTTTTAAT;RSEQ=GTTTTTTTTTCCCCCGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:0:2,0:25.8:1:30.4:1:1:0:60:62:1:0:0.1 0/1:37:2:1,1:18,17:0.0541:2,2:34.5:1:31.5:1:1:1.05721:60:4:0.0556:0:0 -GL000220.1 124250 . G GT 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.62671;SOR=2.40481;LSEQ=TGCCCACACCGTTTTTAATT;RSEQ=TTTTTTTTTCCCCCGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:17,12:0.0323:2,0:31:0:32:0:0.43333:0:60:2:0.0323:0:0 0/1:40:3:2,1:19,18:0.075:2,2:23.7:1:28:1:1:1.87:60:6:0.0769:0:0.7 -GL000220.1 124381 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.48949;SOR=0;LSEQ=CATCGGCCTCCTGAGTAGCC;RSEQ=GGATTGCGGGCATGCGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:0.1:2,2:30:1:31.5:1:1:1.54:60:4:0.1:0:1 0/0:17:0:0,0:7,10:0:2,0:23.2:1:29.9:1:1:0:60:34:1:0:0 -GL000220.1 124599 . C A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.29551;SOR=Inf;LSEQ=CTCATCATTTCTTTGCAACC;RSEQ=TCCTGCCCGGCGTCTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:20,13:0:2,0:23.5:1:32.2:1:1:0:59.8:66:1:0:0.2 0/1:57:3:2,1:31,23:0.0526:2,2:7.3:1:27:1:1:1.47:60:6:0.0536:0:1.3 -GL000220.1 124609 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTGCAACCCTCCTGCCCG;RSEQ=CGTCTCAAAGTGCTGGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:20,9:0:2,0:27.3:1:31.9:1:1:0:59.8:58:1:0:0.2 0/1:61:2:1,1:35,24:0.0328:2,2:21.5:1:26.5:1:1:1.44911:60:4:0.0357:0:1 -GL000220.1 124621 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTGCCCGGCGTCTCAAAGT;RSEQ=CTGGCGTGACGGGCGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:23,10:0:2,0:25.5:1:31.3:1:1:0:59.8:15.5:1:0:0.2 0/1:69:2:1,1:35,32:0.029:2,2:13.5:1:28.5:1:1:1.09232:60:4:0.0299:0:1.5 -GL000220.1 124623 . T C 83 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.14668;LSEQ=TGCCCGGCGTCTCAAAGTGC;RSEQ=GGCGTGACGGGCGTGAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:3,0:21,10:0.0882:2,0:24.3:1:30.3:1:0.53877:0:60:6:0.0909:0:1 0/1:70:7:4,3:32,31:0.1:2,2:29.9:1:29.7:1:1:1.29:60:14:0.1014:0:1.4 -GL000220.1 124637 . TG CA 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52412;SOR=Inf;LSEQ=AAGTGCTGGCGTGACGGGCG;RSEQ=AGCCACTGCGCCTGGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:28,17:0:2,0:21.2:1:29.2:1:1:0:59.9:90:1:0:0.4 0/1:73:2:1,1:38,33:0.0274:2,2:22.5:1:32.8:1:1:1.14928:60:4:0.0278:0:2.5 -GL000220.1 124648 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28127;SOR=Inf;LSEQ=TGACGGGCGTGAGCCACTGC;RSEQ=CCTGGACTCCGGGGAATGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:0:2,0:21.3:1:30:1:1:0:58.2:102:1:0:0.5 0/1:80:3:2,1:39,38:0.0375:2,2:13.7:1:29:1:1:1.93:60:6:0.038:0:2 -GL000220.1 124658 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15361;SOR=0;LSEQ=GAGCCACTGCGCCTGGACTC;RSEQ=GGGGAATGACTCACGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:23,27:0.037:2,2:34.5:1:29.5:1:1:1.17:60:4:0.04:0:1 0/0:83:0:0,0:44,39:0:2,0:22.7:1:29.8:1:1:0:58:82:1:0:0.5 -GL000220.1 124668 . C T 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15423;LSEQ=GCCTGGACTCCGGGGAATGA;RSEQ=TCACGACCACCATCGCTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:4:1,3:27,30:0.0656:2,2:16.3:1:28.8:1:0.61755:2.65986:54.3:8:0.0656:0:1.5 0/1:80:6:4,2:38,36:0.075:2,2:35.3:1:29.3:1:0.67772:1.88:60:12:0.075:0:1.5 -GL000220.1 124732 . TTTC ATTTA 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=1.20276;LSEQ=TTTCTTTCTTTCTTTCTTTC;RSEQ=TTGATGAATTATCTTATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:21,32:0.0364:2,2:26:1:31.1:1:1:1.51:60:4:0.037:0:4 0/1:69:3:1,2:29,37:0.0435:2,2:20.7:1:28.3:1:1:1.55778:60:6:0.0435:0.0145:2.7 -GL000220.1 124792 . T TGGGCG 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=4.000;MSILEN=1;SSF=0.58875;SOR=0.73446;LSEQ=TTTCAGACGGAGTCTCGCTC;RSEQ=GGGCGGGGCGAGGCGAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:4,5:13,6:0.3214:2,2:25.6:1:31.4:1:0.4087:2.60758:60:18:0.3333:0.0714:0.9 0/1:35:9:5,4:11,15:0.2571:2,2:27.1:1:30.7:1:0.70027:1.68:60:18:0.2571:0.0571:0.7 -GL000220.1 124874 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50766;SOR=Inf;LSEQ=AAAGCCCCATTCGTATGCAC;RSEQ=GAGCCTTATTCCCTTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:0:2,0:27.6:1:31.1:1:1:0:60:58:1:0:0 0/1:41:2:1,1:20,19:0.0488:2,2:30.5:1:27:1:1:1.05134:60:4:0.05:0:1 -GL000220.1 124875 . G C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50766;SOR=Inf;LSEQ=AAGCCCCATTCGTATGCACA;RSEQ=AGCCTTATTCCCTTCCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:0:2,0:27.5:1:32.4:1:1:0:60:58:1:0:0 0/1:41:2:1,1:20,19:0.0488:2,2:29:0:33.5:1:1:1.05134:60:4:0.0488:0:1.5 -GL000220.1 124959 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16651;SOR=0;LSEQ=GGAAGCTTTGACAGGCGCAA;RSEQ=CCCACCCAGAGGCTGGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:18,26:0.0435:2,2:33:0:32:1:1:1.43:60:4:0.0435:0:1 0/0:66:0:0,0:36,30:0:2,0:24.3:1:30:1:1:0:59.8:32:1:0:0.3 -GL000220.1 124986 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51296;SOR=Inf;LSEQ=CAGAGGCTGGCTGCGGCTGA;RSEQ=GATTAGGGGGTGTGTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:19,27:0:2,0:22.6:1:31.8:1:1:0:60:92:1:0:0.2 0/1:67:2:1,1:34,31:0.0299:2,2:10:1:29.5:1:1:1.09526:60:4:0.0313:0:1 -GL000220.1 125098 . C G 73 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02061;SOR=0.09924;LSEQ=CTGAGATCCCCCGCCTCCAC;RSEQ=GCCTTGCAGGCTCACCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:2,3:20,14:0.1282:2,2:22.6:1:31.8:1:0.63624:2.10061:60:10:0.1351:0:1.2 0/1:71:1:0,1:33,37:0.0141:2,0:14:0:32:0:1:0:60:2:0.0143:0:1 -GL000220.1 125113 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51784;SOR=Inf;LSEQ=TCCACCGCCTTGCAGGCTCA;RSEQ=CTCTTACTTTCATTTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:0:2,0:22.5:1:30.4:1:1:0:60:13.333:1:0:0.4 0/1:66:2:1,1:28,36:0.0303:2,2:36.5:1:29.5:1:1:1.28:60:4:0.0313:0:1.5 -GL000220.1 125157 . G C 64 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.17242;LSEQ=CTTGCGTTTGAGGAGGGGGT;RSEQ=CGGGAATGAGGGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:3,0:15,22:0.075:2,0:26.3:1:25.3:1:0.08259:0:60:2:0.0541:0:1.7 0/1:46:4:2,2:19,23:0.087:2,2:21.3:1:32:1:1:1.21:60:8:0.0909:0:1 -GL000220.1 125243 . TCAC T 66 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.3866;SOR=0.35165;LSEQ=GATTTAGTGTCATGCCTCTT;RSEQ=CACCACCACCACCACCGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:1,3:9,11:0.1667:2,2:36.8:1:33:1:0.61462:2.37028:59.5:8:0.1667:0:1.3 0/1:31:2:1,1:13,16:0.0645:2,2:44:0:31:1:1:1.22:60:4:0.0645:0:1 -GL000220.1 125277 . G A 65 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38488;SOR=0.35366;LSEQ=ACCACCGAAGATGACAGCAA;RSEQ=GATCGGCTAAATACCGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:1,3:9,9:0.1818:2,2:23:1:32.5:1:0.59398:2.86158:59.5:8:0.1905:0:1.3 0/1:28:2:1,1:11,15:0.0714:2,2:14:0:28.5:1:1:1.35:60:4:0.0714:0:1 -GL000220.1 125359 . C A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16173;SOR=Inf;LSEQ=ATGGGCAGAACGAGGGGGAC;RSEQ=GGGGACGCGGAAGTCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:28.5:1:30.7:1:1:0:45.4:52:1:0:0.2 0/1:18:2:1,1:8,8:0.1111:2,2:9.5:1:32.5:1:1:1:60:4:0.1111:0:1 -GL000220.1 125373 . T C 66 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27792;SOR=0;LSEQ=GGGGACCGGGGACGCGGAAG;RSEQ=CTGCTTGAGGGAGGAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:1,3:13,9:0.1538:2,2:33:1:33:1:0.30609:4.09877:40:8:0.1538:0:1 0/0:15:0:0,0:8,7:0:2,0:27.9:1:29.3:1:1:0:47.5:30:1:0:0.2 -GL000220.1 125501 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24026;SOR=Inf;LSEQ=ACTGAACACCCCCGTCACAA;RSEQ=TTTACCTATGTCACAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:23,16:0:2,0:24.3:1:31.9:1:1:0:55.3:78:1:0:0.2 0/1:38:2:1,1:23,13:0.0526:2,2:6.5:1:30:1:1:1.74146:21:4:0.0526:0:3 -GL000220.1 125517 . A G 79 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05876;SOR=6.7796;LSEQ=ACAAGTTTACCTATGTCACA;RSEQ=TCTTGCACATGTATGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:0,1:24,22:0.0213:2,0:34:0:33:0:0.48936:0:60:2:0.0222:0:1 0/1:46:6:3,3:24,15:0.1304:2,2:26.2:1:30.7:1:0.67033:1.58283:58.2:12:0.1304:0:1.5 -GL000220.1 125524 . A T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00223;SOR=Inf;LSEQ=TACCTATGTCACAATCTTGC;RSEQ=CATGTATGCTTGAACGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,26:0:2,0:20.3:1:29.4:1:1:0:59.7:50:0.9804:0:0.3 0/1:49:8:4,4:26,15:0.1633:2,2:22.4:1:29.1:1:0.6938:1.71317:40.4:16:0.1633:0:2.4 -GL000220.1 125554 . A C 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01601;SOR=Inf;LSEQ=TTGAACGACAAATAAAAGTT;RSEQ=GGGGGGAGAAGAGAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:31,41:0:2,0:24.5:1:29.6:1:1:0:59.8:71:1:0:0.3 0/1:58:5:2,3:34,19:0.0862:2,2:29.2:1:31:1:0.35723:2.63629:36:10:0.0909:0:2.6 -GL000220.1 125555 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=TGAACGACAAATAAAAGTTA;RSEQ=GGGGGAGAAGAGAGGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:33,43:0:2,0:23.6:1:31.3:1:1:0:59.8:75:1:0:0.3 0/1:57:2:1,1:34,21:0.0351:2,2:31:0:30:1:1:1.60486:60:4:0.0357:0:1.5 -GL000220.1 125564 . AGAGAG GAGGA 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=1.22403;LSEQ=AAATAAAAGTTAGGGGGGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:36,40:0.0256:2,2:25.5:1:29.9:1:1:1.11:58.5:4:0.0267:0:0 0/1:64:2:1,1:33,25:0.0313:2,2:47:0:32.4:1:1:1.31382:60:4:0.0357:0:0.5 -GL000220.1 125592 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50915;SOR=0;LSEQ=GAGAGAGAGAGAGAGAGAGA;RSEQ=AGAGAGAGACAGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:38,40:0.025:2,2:35:1:27.5:1:1:1.05:60:4:0.0286:0:1 0/0:58:0:0,0:27,25:0:2,0:26.4:1:28.5:1:1:0:59.5:6.429:0.9184:0:0.5 -GL000220.1 125691 . C G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06363;LSEQ=TGGCCTTTTGGGAGAACGTT;RSEQ=AGCGACAATGCAGTATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:7:4,3:15,18:0.175:2,2:32.9:1:31.7:1:0.68893:1.58:43.6:14:0.175:0:1.7 0/1:38:7:2,5:14,17:0.1842:2,2:28.4:1:31.6:1:0.67541:2.02173:53.9:14:0.1842:0:1.4 -GL000220.1 125726 . T CTTC 49 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.68991;SOR=0.62473;LSEQ=GTATTTGGGCCCGTTCTTTT;RSEQ=TTCTTCTTCTTTTCTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:2,2:16,19:0.1:2,2:17.8:1:24.7:1:1:1.18:32:1:0.0526:0.075:2.3 0/1:31:2:0,2:15,14:0.0645:2,0:32:1:32.3:0:0.48387:0:40:4:0.069:0:2 -GL000220.1 125744 . C CTT 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=11.000;MSILEN=1;SSF=0.19989;SOR=Inf;LSEQ=TTTTTCTTCTTCTTTTCTTT;RSEQ=TTTTTTTTTGGACTGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,17:0:2,0:24.5:1:29.7:1:1:0:51.8:5.4:0.931:0:0.6 0/1:28:2:1,1:13,13:0.0714:2,2:12.5:1:30.8:1:1:1:40:4:0.0741:0.0357:2 -GL000220.1 125788 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57717;SOR=2.6095;LSEQ=TCGCTCTGTCACCCAGGCTG;RSEQ=GGTGCGGTGGCGCTCTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:11,12:0.04:2,0:44:0:32:0:1:0:40:2:0.0417:0:2 0/1:20:2:1,1:9,9:0.1:2,2:20.5:1:28.5:1:1:1:42.5:4:0.1:0:2 -GL000220.1 125972 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4902;SOR=0;LSEQ=CCTGACCTCAAATGATCCGC;RSEQ=TTCCTGGGCCTCCCAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:13,11:0.0769:2,2:14.5:1:29.5:1:1:1.17422:27:4:0.0769:0:1.5 0/0:25:0:0,0:16,9:0:2,0:23.3:1:30.2:1:1:0:58.7:50:1:0:0.2 -GL000220.1 126004 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49656;SOR=0;LSEQ=CCCAAAGTGCTGGAAACGAC;RSEQ=GGCCTGAGCCGCCGGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:16,16:0.0588:2,2:22.5:1:30:0:1:1:54.5:4:0.0588:0:1 0/0:28:0:0,0:15,13:0:2,0:24.5:1:29.5:1:1:0:55:56:1:0:0.3 -GL000220.1 126062 . T C 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47401;LSEQ=GGCCCTGCCACCTTTCGCTG;RSEQ=GGCCCTTACGCTCAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:12,11:0.0417:2,0:7:0:31:0:1:0:27:2:0.0417:0:2 0/1:33:2:2,0:14,17:0.0606:2,0:29:1:33.5:1:0.22727:0:27:4:0.0606:0:1 -GL000220.1 126086 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50508;SOR=Inf;LSEQ=CCTTACGCTCAGAATGACGT;RSEQ=TCCTCTCTGCCGTAGGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:25.5:1:31.5:1:1:0:53.8:44:1:0:0.1 0/1:31:2:1,1:13,16:0.0645:2,2:10.5:1:27:1:1:1.22:50:4:0.0645:0:1.5 -GL000220.1 126098 . G A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20814;SOR=0;LSEQ=AATGACGTGTCCTCTCTGCC;RSEQ=TAGGTTGACTCCTTGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:2,0:10,12:0.0833:2,0:17.5:1:32:1:0.47826:0:40:4:0.0833:0:1.5 0/0:28:0:0,0:13,15:0:2,0:26.4:1:30.1:1:1:0:50.8:56:1:0:0.3 -GL000220.1 126180 . C T 60 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37729;SOR=0.34257;LSEQ=TCCGTCCCCCCACCTCCCCG;RSEQ=GCACATAATAACTAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:6,8:0.2222:2,2:12:1:30.3:1:1:1.31:55:8:0.2222:0:1.5 0/1:23:2:1,1:10,11:0.087:2,2:41.5:1:20:1:1:1.10:50.5:1:0.0455:0:1 -GL000220.1 126188 . A ATAACTAAC 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=4;SSF=1;SOR=1.16262;LSEQ=CCCACCTCCCCGCGCACATA;RSEQ=TAACTAACTAACAAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,6:0.125:2,2:24:0:31.9:1:1:1.1547:60:4:0.125:0:1.5 0/1:28:4:2,2:12,12:0.1429:2,2:30.5:1:28.2:1:1:1:55.3:8:0.1429:0.0714:0.8 -GL000220.1 126229 . A C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.03238;SOR=0;LSEQ=TAACTAACTAAACTAACTAA;RSEQ=TAAATAAAATCTCTACACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:7,6:0.1875:2,2:29.3:1:31.7:1:1:1.66:60:6:0.1875:0:3 0/0:32:0:0,0:18,14:0:2,0:21.3:1:29.8:1:1:0:60:31:1:0:0.3 -GL000220.1 126233 . A C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.13564;SOR=0;LSEQ=TAACTAAACTAACTAAATAA;RSEQ=TAAAATCTCTACACGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:39.5:1:32.5:1:1:1.26772:60:4:0.1111:0:4 0/0:30:0:0,0:17,13:0:2,0:22.3:1:30:1:1:0:60:29:1:0:0.3 -GL000220.1 126254 . TC CA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19426;SOR=0;LSEQ=TAAAATCTCTACACGTCACC;RSEQ=TAAGTGTGTGTTCCCGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:0.0952:2,2:17.5:1:30:1:1:1.35399:60:4:0.0952:0:3 0/0:26:0:0,0:16,10:0:2,0:24.7:1:30.4:1:1:0:60:52:1:0:0.2 -GL000220.1 126307 . G A 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00248;SOR=0;LSEQ=AAGAAATGGCACTGTACACT;RSEQ=AACGCAGTGGCTCACGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:5,4:6,9:0.375:2,2:32.3:1:29.3:1:0.67517:1.83:52.7:18:0.375:0:1.2 0/0:19:0:0,0:9,10:0:2,0:21.3:1:31.1:1:1:0:52.8:38:1:0:0.2 -GL000220.1 126375 . AC A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.15152;SOR=0;LSEQ=AGCCCGGCCAACGTGGTGAA;RSEQ=CCCCGTCTCTACTGAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:0.4:0,0:29.5:1:28.5:1:1:0:33.5:4:0.4:0:1.5 0/0:7:0:0,0:0,7:0:0,0:19.9:1:30.1:1:1:0:41:14:1:0:0 -GL000220.1 126403 . G T 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CTCTACTGAAAATACGAAAT;RSEQ=GAGTCAGGCGCCGTGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:29.5:1:29.5:1:1:0:33.5:4:0.6667:0:1.5 0/0:4:0:0,0:0,4:0:0,0:33.8:1:29.5:1:1:0:36.8:8:1:0:0 -GL000220.1 126563 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15172;SOR=Inf;LSEQ=GACCCGGTCTCCAGATAAAT;RSEQ=CGTACATAAATAAATACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,5:0:2,0:21.5:1:28.7:1:1:0:49.8:34:0.9444:0:0.5 0/1:12:2:1,1:9,1:0.1667:2,2:28.5:1:31:1:0.31818:6.70817:27:4:0.1667:0:1 -GL000220.1 126582 . CACATACAT C 98 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=36;MSI=11.000;MSILEN=4;SSF=0.72858;SOR=0.62452;LSEQ=TACGTACATAAATAAATACA;RSEQ=ACATACATACATACATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:6,3:11,5:0.2571:2,2:15.4:1:31.2:1:1:1.09579:54.9:18:0.2571:0.1429:0.8 0/1:17:3:1,2:11,2:0.1765:2,2:34.3:1:29.3:1:0.13571:8.85639:38:6:0.2:0:0.7 -GL000220.1 126627 . C A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.33865;LSEQ=ACATACATACATACATACAT;RSEQ=CATGCATACAGATATACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:25,18:0.0444:2,2:36.5:1:28.5:1:1:1.3786:50:4:0.0444:0:2 0/1:34:2:1,1:17,15:0.0588:2,2:35:0:30:0:1:1.12916:60:4:0.0625:0:1.5 -GL000220.1 126760 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.20907;SOR=Inf;LSEQ=GTTCGTCTCTGTCTTTCTCT;RSEQ=TGTGTCTCTTTCTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:47,26:0:2,0:25.7:1:30.7:1:1:0:56.6:17.25:1:0:0.2 0/1:62:2:1,1:37,23:0.0323:2,2:13.5:1:30:1:1:1.59591:50:4:0.0323:0:2.5 -GL000220.1 126762 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20232;SOR=Inf;LSEQ=TCGTCTCTGTCTTTCTCTCT;RSEQ=TGTCTCTTTCTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:47,27:0:2,0:25.9:1:31.8:1:1:0:56.7:36:1:0:0.2 0/1:61:2:1,1:36,23:0.0328:2,2:15.5:1:30:1:1:1.55335:50:4:0.0328:0:2.5 -GL000220.1 126839 . T A 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58205;SOR=2.59691;LSEQ=TGTCTCTCTCTCTCCCTCTC;RSEQ=GCCTGTCTCACTGTGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:1:1,0:50,57:0.0093:2,0:11:0:14:0:0.47222:0:60:0:0:0:2 0/1:84:2:1,1:41,41:0.0238:2,2:18.5:1:28:1:1:1:60:4:0.0241:0:1 -GL000220.1 126840 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1947;SOR=Inf;LSEQ=GTCTCTCTCTCTCCCTCTCT;RSEQ=CCTGTCTCACTGTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:51,56:0:2,0:25:1:31.2:1:1:0:59.8:16.833:1:0:0.3 0/1:85:2:1,1:41,42:0.0235:2,2:16:0:30:0:1:1.02:51:4:0.0235:0:1.5 -GL000220.1 126865 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35099;SOR=3.32244;LSEQ=TCTCACTGTGTCTGTCTTCT;RSEQ=TCTTACTCTCTTTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:1,0:54,53:0.0092:2,0:1:0:23:0:1:0:60:2:0.0093:0:1 0/1:100:3:2,1:49,48:0.03:2,2:32.7:1:28.3:1:1:1.95:57.7:6:0.0309:0:2.7 -GL000220.1 126880 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49803;SOR=0;LSEQ=CTTCTGTCTTACTCTCTTTC;RSEQ=CTCCCCGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:58,56:0.0172:2,2:42:1:31.5:1:1:1.03541:60:4:0.0174:0:1 0/0:111:0:0,0:60,51:0:2,0:23.7:1:29.5:1:1:0:57.6:54.5:1:0:0.6 -GL000220.1 126883 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49782;SOR=Inf;LSEQ=CTGTCTTACTCTCTTTCTCT;RSEQ=CCCGTCTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:57,58:0:2,0:24.4:1:31.5:1:1:0:59.6:230:1:0:0.5 0/1:115:2:1,1:61,51:0.0174:2,2:9.5:1:31:1:1:1.19419:60:4:0.0175:0:2 -GL000220.1 126886 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.9251;LSEQ=TCTTACTCTCTTTCTCTCCC;RSEQ=GTCTGTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:1,0:56,55:0.0089:2,0:50:0:31:0:1:0:60:2:0.009:0:1 0/1:117:2:1,1:61,54:0.0171:2,2:12.5:1:30:1:1:1.12845:60:4:0.0174:0:2 -GL000220.1 126895 . CTCTCTCTCTCTCTCCCTCCCTGTTTGTT C 72 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.44679;SOR=2.4215;LSEQ=CTTTCTCTCCCCGTCTGTCT;RSEQ=TCTCTCTCTCCCTCCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:56,48:0.0187:2,2:27.5:1:30.1:1:1:1.16496:36:4:0.0187:0.0187:0 0/1:113:5:3,2:57,51:0.0442:2,2:17.4:1:31.4:1:1:1.34:58:10:0.045:0:0.4 -GL000220.1 126919 . T C 118 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54379;SOR=1.34652;LSEQ=CTCTCTCTCTCCCTCCCTGT;RSEQ=TGTTTCTCTCTCTCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:12:7,5:48,39:0.1188:2,2:27.8:1:30.5:1:1:1.14:58.1:11:0.117:0:2.2 0/1:104:16:11,5:42,41:0.1538:2,2:30.6:1:29.7:1:0.27384:2.13:55.5:7:0.1458:0:2.6 -GL000220.1 126923 . T C 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=0.41741;SOR=1.49277;LSEQ=CTCTCTCCCTCCCTGTTTGT;RSEQ=TCTCTCTCTCCCTCCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:11:5,6:49,39:0.1089:2,2:24.5:1:31.6:1:0.54033:1.50137:60:22:0.1134:0:1.8 0/1:110:17:10,7:46,42:0.1545:2,2:24.7:1:30.1:1:0.79156:1.30:59.8:16:0.16:0:2.2 -GL000220.1 126930 . T C 50 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=2;SSF=0.26395;SOR=Inf;LSEQ=CCTCCCTGTTTGTTTCTCTC;RSEQ=CTCCCTCCCTGTCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:51,41:0:2,0:23.7:1:29.7:1:1:0:59.2:17.4:1:0:0.6 0/1:125:3:2,1:66,54:0.024:2,2:7:0:32:0:1:1.63:54:6:0.0248:0:1.3 -GL000220.1 126934 . C T 40 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.07627;LSEQ=CCTGTTTGTTTCTCTCTCTC;RSEQ=CTCCCTGTCTGTTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:2,0:48,41:0.022:2,0:13:1:25.5:1:0.49939:0:46:1:0.0114:0:3.5 0/1:127:3:3,0:65,59:0.0236:2,0:27.7:1:25.7:1:0.24784:0:36:2:0.0167:0:4 -GL000220.1 126937 . CC TT 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.46744;LSEQ=GTTTGTTTCTCTCTCTCCCT;RSEQ=CTGTCTGTTTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:1:1,0:47,39:0.0115:2,0:8:0:31:0:1:0:37:2:0.0116:0:3 0/1:119:2:2,0:60,55:0.0168:2,0:12.5:1:28:1:0.49749:0:24:4:0.0168:0:3.5 -GL000220.1 126947 . TTC T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.02572;SOR=0;LSEQ=CTCTCTCCCTCCCTGTCTGT;RSEQ=TCTCTCTCTCTTTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:4:1,3:43,34:0.0494:2,2:27.5:1:28.8:1:0.32678:3.73549:60:8:0.0494:0.0123:2.3 0/0:119:0:0,0:63,56:0:2,0:22.6:1:28.8:1:1:0:58.9:38.667:1:0:0.6 -GL000220.1 126968 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.51485;SOR=Inf;LSEQ=TCTCTCTCTCTCTTTCTGTC;RSEQ=GTTTCTGTCTCTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:44,37:0:2,0:23.3:1:30.9:1:1:0:59.4:80:1:0:0.3 0/1:118:2:1,1:61,55:0.0169:2,2:40.5:1:28:1:1:1.10812:57.5:4:0.0171:0:1 -GL000220.1 126973 . CTG C 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=5.000;MSILEN=2;SSF=0.27761;SOR=Inf;LSEQ=CTCTCTCTTTCTGTCTGTTT;RSEQ=TCTCTCTCTGTCTGTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:43,37:0:2,0:24.1:1:30.8:1:1:0:59.4:79:1:0:0.4 0/1:121:3:1,2:65,53:0.0248:2,2:32:1:29.2:1:0.59034:2.43506:58.3:6:0.0254:0.0083:0.7 -GL000220.1 126975 . G GTCTC 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=6.000;MSILEN=2;SSF=0.51686;SOR=Inf;LSEQ=CTCTCTTTCTGTCTGTTTCT;RSEQ=TCTCTCTCTGTCTGTCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:43,38:0:2,0:23.4:1:32.3:1:1:0:59.4:162:1:0:0.2 0/1:122:2:2,0:65,53:0.0164:2,0:49.5:1:30:1:0.50266:0:60:4:0.0171:0:0 -GL000220.1 127030 . C T 76 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.14443;SOR=5.15855;LSEQ=TCTCTTTCTCTGTCTGTCTG;RSEQ=CTCTCTCTTTCTTTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:1:0,1:52,48:0.0099:2,0:3:0:27:0:0.48515:0:40:2:0.0103:0:7 0/1:142:7:3,4:64,71:0.0493:2,2:19.7:1:27.4:1:1:1.20033:59.3:14:0.0515:0:2 -GL000220.1 127035 . CTCTT C 126 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.1941;SOR=1.93402;LSEQ=TTCTCTGTCTGTCTGCCTCT;RSEQ=TCTTTTTCTGTGTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:7:2,5:52,48:0.066:2,2:8.9:1:31.3:1:0.27022:2.68444:44.4:14:0.0686:0.0472:3.7 0/1:141:17:8,9:59,65:0.1206:2,2:30.7:1:30.9:1:1:1.02101:57.1:34:0.1223:0.0071:1.6 -GL000220.1 127051 . G T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24977;SOR=Inf;LSEQ=CTCTCTCTTTCTTTTTCTGT;RSEQ=TCTCTCTGTCGGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:57,57:0:2,0:22.5:1:31.2:1:1:0:58.9:56:1:0:0.6 0/1:129:3:1,2:62,64:0.0233:2,2:31:1:29.7:1:1:1.92796:60:6:0.0233:0:1 -GL000220.1 127063 . GTC G 90 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.08407;SOR=6.01086;LSEQ=TTTTCTGTGTCTCTCTGTCG;RSEQ=TCTCTCTCTCTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:52,56:0.0089:2,0:10:0:34:0:1:0:60:2:0.0093:0:0 0/1:155:8:5,3:71,73:0.0516:2,2:35.8:1:30:1:0.7191:1.71:60:16:0.0526:0.0065:0.1 -GL000220.1 127071 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0.15848;SOR=0;LSEQ=GTCTCTCTGTCGGTCTCTCT;RSEQ=TCTCTGTCTGTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:50,53:0.019:2,2:37.5:1:31:1:1:1.06:59:4:0.02:0:5 0/0:158:0:0,0:78,77:0:2,0:22.8:1:31.4:1:1:0:58.6:76.5:1:0:0.7 -GL000220.1 127074 . T C 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.27415;SOR=Inf;LSEQ=TCTCTGTCGGTCTCTCTCTC;RSEQ=CTGTCTGTCTGTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:51,56:0:2,0:26.3:1:30:1:1:0:58.7:25.75:1:0:0.7 0/1:157:3:1,2:78,73:0.0191:2,2:35.7:1:22.7:1:0.61288:2.1268:60:2:0.0137:0:1.7 -GL000220.1 127077 . G C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=4;SSF=0.6848;SOR=1.28831;LSEQ=CTGTCGGTCTCTCTCTCTCT;RSEQ=TCTGTCTGTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:10:4,6:46,50:0.0943:2,2:34.3:1:27.5:1:0.74592:1.37586:46.7:2.333:0.0714:0:4.1 0/1:152:18:9,9:65,60:0.1184:2,2:19.2:1:30.6:1:1:1.08272:53.8:17:0.1181:0:2.8 -GL000220.1 127078 . T G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=4;SSF=0.16993;SOR=0;LSEQ=TGTCGGTCTCTCTCTCTCTG;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:48,55:0.019:2,2:33:0:33.5:1:1:1.14:59:4:0.0194:0:5 0/0:149:0:0,0:73,69:0:2,0:23.3:1:29.1:1:1:0:59:141:1:0:0.7 -GL000220.1 127079 . C T 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=4;SSF=1;SOR=0.92267;LSEQ=GTCGGTCTCTCTCTCTCTGT;RSEQ=TGTCTGTCTGTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:3:2,1:43,52:0.0288:2,2:15:1:23.7:1:0.5923:2.40:52:2:0.0202:0:4.7 0/1:150:4:3,1:67,64:0.0267:2,2:15.8:1:28.8:1:0.6204:2.85:46:8:0.0292:0:4 -GL000220.1 127081 . G CTCTTTC 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=1.16022;LSEQ=TCGGTCTCTCTCTCTCTGTC;RSEQ=TCTGTCTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:3:2,1:43,52:0.0288:2,2:45.3:1:31.7:1:0.5923:2.40:49:6:0.0303:0:3 0/1:150:5:3,2:67,64:0.0333:2,2:29.6:1:31.6:1:1:1.43:52.2:10:0.0365:0:2.8 -GL000220.1 127082 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=4;SSF=0.15968;SOR=0;LSEQ=GGTCTCTCTCTCTCTGTCTG;RSEQ=CTGTCTGTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:45,54:0.0198:2,2:29:0:31:1:1:1.20:59:4:0.0208:0:5 0/0:151:0:0,0:76,72:0:2,0:22.1:1:29.2:1:1:0:58.3:147:1:0:0.7 -GL000220.1 127086 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=4;SSF=0.16356;SOR=0;LSEQ=TCTCTCTCTCTGTCTGTCTG;RSEQ=CTGTCTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:44,55:0.0198:2,2:25:0:33.5:1:1:1.25:59:4:0.0211:0:5 0/0:148:0:0,0:73,70:0:2,0:22.1:1:29:1:1:0:58.2:142:0.9861:0:0.7 -GL000220.1 127128 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.39676;LSEQ=TGTGCCTATCTTCTGTCTTA;RSEQ=TCTCTTTCTCTGCCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:1:1,0:54,46:0.0099:2,0:10:0:32:0:1:0:21:2:0.01:0:8 0/1:145:2:1,1:77,66:0.0138:2,2:6.5:1:28:1:1:1.16542:60:4:0.0141:0:1 -GL000220.1 127139 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50867;SOR=Inf;LSEQ=TCTGTCTTACTCTCTTTCTC;RSEQ=GCCTGTCTGTCTGTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:53,49:0:2,0:23.9:1:30.3:1:1:0:58.9:33:1:0:0.5 0/1:137:2:1,1:74,61:0.0146:2,2:5.5:1:29:1:1:1.21139:40.5:4:0.0148:0:2 -GL000220.1 127141 . CCTGT C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=3.000;MSILEN=4;SSF=0.26331;SOR=Inf;LSEQ=TGTCTTACTCTCTTTCTCTG;RSEQ=CTGTCTGTCTCTCCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:55,48:0:2,0:24.2:1:31.1:1:1:0:59:24.75:0.99:0:0.5 0/1:140:3:1,2:74,64:0.0214:2,2:19:1:31.3:1:0.59951:2.29915:60:6:0.0219:0.0143:1 -GL000220.1 127164 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.50942;SOR=Inf;LSEQ=GTCTGTCTGTCTCTCCCTCC;RSEQ=TTTCTGTTTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:56,51:0:2,0:27.4:1:31:1:1:0:58.9:34.667:1:0:0.5 0/1:145:2:1,1:73,69:0.0138:2,2:39:0:31.5:1:1:1.05758:60:4:0.0141:0:1.5 -GL000220.1 127221 . C T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.58702;SOR=0.80846;LSEQ=TCTCCCTGTCTGTTTCTCTC;RSEQ=GTCTCTCTCTCTTTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:16:6,10:46,49:0.1441:2,2:16:1:29.6:1:0.58932:1.55841:54.9:15:0.1442:0:1.4 0/1:167:20:11,9:74,71:0.1198:2,2:25.4:1:29.4:1:0.81401:1.17:59.8:9:0.1139:0:1.5 -GL000220.1 127222 . GTC G 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.15427;SOR=Inf;LSEQ=CTCCCTGTCTGTTTCTCTCC;RSEQ=TCTCTCTCTTTCTGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:52,58:0:2,0:24.5:1:28.8:1:1:0:59.1:26.5:1:0:0.5 0/1:167:4:2,2:82,79:0.024:2,2:25.5:1:29.8:1:1:1.03775:60:8:0.0244:0:0 -GL000220.1 127232 . C A 29 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=1.33601;LSEQ=GTTTCTCTCCGTCTCTCTCT;RSEQ=TTTCTGTCTGTTTCTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:1,0:55,56:0.0089:2,0:11:0:25:0:1:0:60:2:0.009:0:2 0/1:168:2:1,1:78,88:0.0119:2,2:26:0:29.5:1:1:1.13:60:4:0.0122:0:1 -GL000220.1 127244 . T C 42 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63431;SOR=2.34804;LSEQ=CTCTCTCTCTTTCTGTCTGT;RSEQ=TCTCACTGTCTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:1,0:59,65:0.008:2,0:3:0:15:0:0.48:0:60:0:0:0:1 0/1:161:3:2,1:75,83:0.0186:2,2:5:0:27:1:0.60679:2.20:60:2:0.013:0:0.3 -GL000220.1 127266 . ATC A 94 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.15124;SOR=2.66742;LSEQ=CTCACTGTCTCTCTCTGTCC;RSEQ=TCTCTCTCTCTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:3:2,1:55,59:0.0252:2,2:31.7:1:31:1:0.61216:2.13:60:6:0.0275:0:0 0/1:139:9:4,5:65,63:0.0647:2,2:30.4:1:29.7:1:0.74451:1.28729:57.2:18:0.0672:0:0.7 -GL000220.1 127280 . C G 27 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.49882;SOR=Inf;LSEQ=CTGTCCATCTCTCTCTCTCT;RSEQ=TGTCTGTCTCTTTCGTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:63,64:0:2,0:26:1:31.9:1:1:0:59.7:254:1:0:0.6 0/1:137:2:2,0:68,65:0.0146:2,0:7.5:1:27:0:0.49696:0:47.5:4:0.0147:0:3 -GL000220.1 127304 . G C 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=4;SSF=0.21412;SOR=0.2062;LSEQ=CTGTCTCTTTCGTTCTCTCT;RSEQ=TCTGTCTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:5:1,4:62,57:0.0397:2,2:16.2:1:27.8:1:0.20366:4.30599:50.6:4:0.036:0:3.6 0/0:119:1:0,1:55,62:0.0084:2,0:8:0:34:0:1:0:60:2:0.01:0:3 -GL000220.1 127308 . G C 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=4;SSF=0.45379;SOR=0.44959;LSEQ=CTCTTTCGTTCTCTCTGTCT;RSEQ=TCTGTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:5:1,4:58,61:0.0397:2,2:10.4:1:30.4:1:0.36773:3.76743:53.6:10:0.041:0:3.4 0/1:110:2:0,2:51,54:0.0182:2,0:9:1:33.5:1:0.49639:0:60:4:0.0192:0:2.5 -GL000220.1 127312 . G C 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0;SOR=0;LSEQ=TTCGTTCTCTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:34:11,23:24,28:0.272:2,2:18.4:1:31.9:1:0.26305:1.78013:58.8:68:0.281:0:1.9 0/0:108:0:0,0:31,38:0:2,0:22.9:1:30:1:1:0:59.4:68:0.7083:0:0.6 -GL000220.1 127316 . CTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTGTCTCTCACTCTCTGTGTGTATCT C 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.09391;SOR=Inf;LSEQ=TTCTCTCTGTCTGTCTGTCT;RSEQ=TCTGTCTTACTCTCCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:62,62:0:2,0:21.3:1:30.1:1:1:0:58.5:23.8:1:0:1.1 0/1:106:3:1,2:43,57:0.0283:2,2:68:1:28.8:1:1:1.50299:60:6:0.0294:0.0283:0.7 -GL000220.1 127366 . G C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.24698;SOR=Inf;LSEQ=CTGTCTCTCACTCTCTGTGT;RSEQ=TATCTTCTGTCTTACTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:54,54:0:2,0:25.4:1:31.1:1:1:0:58.5:14.429:1:0:1.1 0/1:113:3:1,2:48,59:0.0265:2,2:20:1:30:1:1:1.62022:60:6:0.028:0:2.3 -GL000220.1 127368 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2472;SOR=Inf;LSEQ=GTCTCTCACTCTCTGTGTGT;RSEQ=TCTTCTGTCTTACTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:51,55:0:2,0:24.7:1:27.9:1:1:0:58.7:8.636:1:0:1 0/1:116:3:1,2:49,60:0.0259:2,2:19.3:1:30.7:1:1:1.62648:60:6:0.0283:0:2.3 -GL000220.1 127373 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50002;SOR=Inf;LSEQ=TCACTCTCTGTGTGTATCTT;RSEQ=TGTCTTACTCTCCTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:51,53:0:2,0:25.9:1:31.2:1:1:0:59.2:25:1:0:1 0/1:119:2:1,1:52,65:0.0168:2,2:5:0:32:0:1:1.25:52:4:0.0175:0:2 -GL000220.1 127378 . T C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42465;SOR=0.69062;LSEQ=CTCTGTGTGTATCTTCTGTC;RSEQ=TACTCTCCTTCTCTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:16:10,6:41,43:0.16:2,2:21.3:1:31.1:1:0.41572:1.74:59.4:15:0.1579:0:1.7 0/1:112:13:6,7:44,55:0.1161:2,2:20:1:29.5:1:1:1.07:52.8:12:0.1091:0:2.2 -GL000220.1 127386 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23722;SOR=0;LSEQ=GTATCTTCTGTCTTACTCTC;RSEQ=TTCTCTGCCTGTCCGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:48,51:0.0192:2,2:34:1:30.5:1:1:1.06:60:4:0.0211:0:1 0/0:109:0:0,0:49,60:0:2,0:24.1:1:29.9:1:1:0:58.9:12.625:1:0:0.7 -GL000220.1 127389 . CTCTGCCTGTCCGTCTG C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=4;SSF=0.24648;SOR=Inf;LSEQ=TCTTCTGTCTTACTCTCCTT;RSEQ=TCTGTCTGTCTGTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:53,54:0:2,0:23.3:1:30.6:1:1:0:59.9:214:1:0:0.8 0/1:106:2:1,1:50,54:0.0189:2,2:20.5:1:28.3:1:1:1.08:54.5:4:0.019:0.0189:0 -GL000220.1 127394 . CCTGTCCGTCTGTCTGT C 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=5.000;MSILEN=4;SSF=0.23593;SOR=0.57403;LSEQ=TGTCTTACTCTCCTTCTCTG;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:19:13,6:42,47:0.1759:2,2:22:1:31.3:1:0.12949:2.41:59.3:18:0.1714:0.0556:1.7 0/1:101:11:5,6:42,44:0.1089:2,2:24.7:1:30.5:1:1:1.14385:49.7:10:0.1064:0.0198:2.3 -GL000220.1 127400 . CGTCT C 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=6.000;MSILEN=4;SSF=0.61593;SOR=0.47762;LSEQ=ACTCTCCTTCTCTGCCTGTC;RSEQ=GTCTGTCTGTCTGTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:40,45:0.0198:2,2:7:1:28:1:1:1.12:60:4:0.0244:0.0099:0.5 0/0:105:1:1,0:44,47:0.0095:2,0:40:0:30:0:0.48913:0:60:2:0.0111:0:0 -GL000220.1 127439 . GTC G 72 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.24443;SOR=0.30157;LSEQ=CTGTCTCTCTCTCCCTTTCT;RSEQ=TCTCTCTCTCTCTGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:5:1,4:50,42:0.051:2,2:29.2:1:31.4:1:0.18686:4.69379:60:10:0.0521:0:0 0/1:126:2:2,0:63,61:0.0159:2,0:25:1:30.5:1:0.49651:0:60:4:0.0163:0.0079:0 -GL000220.1 127457 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.25139;SOR=Inf;LSEQ=CTGTCTCTCTCTCTCTCTGT;RSEQ=CCTCTCTCTTTCTGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:57,48:0:2,0:23.1:1:30.3:1:1:0:60:16.5:1:0:0.3 0/1:123:3:1,2:66,54:0.0244:2,2:28.7:1:27.3:1:0.59085:2.4271:60:6:0.0259:0:1.3 -GL000220.1 127458 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=1.67382;LSEQ=TGTCTCTCTCTCTCTCTGTC;RSEQ=CTCTCTCTTTCTGTCTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:1:1,0:57,47:0.0095:2,0:47:0:18:0:1:0:60:0:0:0:5 0/1:126:2:2,0:67,57:0.0159:2,0:7:1:30:1:0.50057:0:31:4:0.0172:0:3.5 -GL000220.1 127478 . CCT C 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.32898;SOR=0.57243;LSEQ=CCTCTCTCTTTCTGTCTGTT;RSEQ=CTCTCTCTCTCTGTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:11:8,3:50,54:0.0948:2,2:23.9:1:32.1:1:0.20355:2.85:60:22:0.0991:0.0172:0.2 0/1:124:7:4,3:60,57:0.0565:2,2:34.7:1:30.1:1:1:1.26:60:14:0.0579:0:0.9 -GL000220.1 127500 . T TCTGTCC 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.24941;SOR=Inf;LSEQ=TCTCTCTCTCTCTGTCTCTG;RSEQ=CTTTCTCTGTCTGTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:59,54:0:2,0:26.5:1:29.8:1:1:0:60:55.5:0.9911:0:0.2 0/1:128:3:2,1:62,63:0.0234:2,2:7:1:29.2:1:1:2.02:52.3:6:0.024:0.0234:0 -GL000220.1 127513 . GTCTGCCTCTCTCTTTCTTTCTCTT CTTTCTCTGTCTGTCTTTGTCTTTCCTTC 58 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.12199;SOR=Inf;LSEQ=GTCTCTGTCTTTCTCTGTCT;RSEQ=TCTGTGTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:61,60:0:2,0:26.3:1:30.4:1:1:0:60:59.5:1:0:0.2 0/1:124:4:2,2:60,60:0.0323:2,2:19.3:1:29:1:1:1:57.3:8:0.0325:0.0323:0.5 -GL000220.1 127531 . T C 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.62228;SOR=0.34284;LSEQ=CTGTCTGCCTCTCTCTTTCT;RSEQ=TCTCTTTCTGTGTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:3:1,2:61,64:0.0234:2,2:20.7:1:32:1:1:1.89703:60:6:0.0238:0:1.7 0/0:123:1:1,0:57,63:0.0081:2,0:38:0:28:0:0.47934:0:60:2:0.0083:0:1 -GL000220.1 127565 . GCCTATCTTCTGTCTTACTCTCTTTCTCTGCCTGCCTGCCTGTCTGTCTG C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=4;SSF=0.49787;SOR=Inf;LSEQ=CTCTCTGTCTCTCTCTCTGT;RSEQ=TCTGTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:60,58:0:2,0:25.5:1:32:1:1:0:59.8:38.333:1:0:0.3 0/1:118:2:1,1:57,59:0.0169:2,2:32.5:1:29.1:1:1:1.03:41.5:4:0.0172:0.0169:3 -GL000220.1 127601 . T C 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.61263;SOR=2.13376;LSEQ=ACTCTCTTTCTCTGCCTGCC;RSEQ=GCCTGTCTGTCTGTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:1,0:59,63:0.0081:2,0:6:0:33:0:0.4878:0:60:2:0.0083:0:2 0/1:116:2:1,1:56,57:0.0172:2,2:20.5:1:30:1:1:1.02:60:4:0.0175:0:2.5 -GL000220.1 127603 . C T 119 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.0044;SOR=4.64591;LSEQ=TCTCTTTCTCTGCCTGCCTG;RSEQ=CTGTCTGTCTGTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:4:1,3:58,59:0.0328:2,2:15.8:1:30.8:1:0.61915:2.9253:60:8:0.0339:0:1.5 0/1:117:16:8,8:50,50:0.1368:2,2:25.8:1:29.8:1:1:1:56.3:32:0.1391:0:1.5 -GL000220.1 127607 . T C 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=4;SSF=0.02407;SOR=Inf;LSEQ=TTTCTCTGCCTGCCTGCCTG;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:61,61:0:2,0:22.8:1:29.6:1:1:0:59.6:244:1:0:0.4 0/1:114:5:3,2:52,54:0.0439:2,2:16.2:1:31.2:1:0.67882:1.55:54.6:10:0.045:0:1.4 -GL000220.1 127628 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49788;SOR=Inf;LSEQ=CTGTCTGTCTGTCTCTCTCT;RSEQ=TCTCTCTCCCTGCCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:54,54:0:2,0:27:1:31.4:1:1:0:59.5:26:1:0:0.4 0/1:112:2:1,1:56,54:0.0179:2,2:5.5:1:29:1:1:1.03671:60:4:0.0185:0:2 -GL000220.1 127630 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.49767;SOR=Inf;LSEQ=GTCTGTCTGTCTCTCTCTGT;RSEQ=TCTCTCCCTGCCTTTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:53,54:0:2,0:27.3:1:31.4:1:1:0:59.5:52.5:1:0:0.4 0/1:108:2:1,1:54,52:0.0185:2,2:7.5:1:28.5:1:1:1.03811:60:4:0.019:0:2 -GL000220.1 127633 . T C 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.133;SOR=0.54812;LSEQ=TGTCTGTCTCTCTCTGTCTC;RSEQ=CTCCCTGCCTTTCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:21:11,10:43,44:0.1927:2,2:30:1:31.2:1:1:1.12:60:42:0.2:0:1.1 0/1:104:12:5,7:49,43:0.1154:2,2:24.6:1:27.8:1:0.5455:1.58818:60:5:0.098:0:1.6 -GL000220.1 127650 . TTC T 66 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.4928;SOR=0.56975;LSEQ=CTCTCTCCCTGCCTTTCTGT;RSEQ=TCTCTCTCTCTCCCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:5:1,4:43,46:0.0532:2,2:19:1:28.6:1:0.36665:3.69326:55.4:4:0.043:0.0213:2.2 0/1:97:3:3,0:51,43:0.0309:2,0:28.7:1:32:0:0.25193:0:51.7:6:0.0309:0:1.7 -GL000220.1 127653 . TCTCTCTCTCTCC T 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=6.000;MSILEN=2;SSF=1;SOR=0.92592;LSEQ=TCTCCCTGCCTTTCTGTTTC;RSEQ=CTCTCTCTCTCCCTCTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:5:1,4:42,45:0.0543:2,2:23:1:26.4:1:0.36658:3.6866:48.4:4:0.044:0.0326:1.6 0/1:99:5:1,4:52,41:0.0505:2,2:9.4:1:30.6:1:0.17653:4.99745:57:10:0.0515:0.0505:1.6 -GL000220.1 127667 . T C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.24722;SOR=Inf;LSEQ=TGTTTCTCTCTCTCTCTCCC;RSEQ=CTCTCTCTCCCTCTCTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:35,45:0:2,0:25.3:1:30.4:1:1:0:58.7:160:1:0:0.5 0/1:88:3:0,3:47,38:0.0341:2,0:5.7:1:31.3:1:0.09714:0:60:6:0.0353:0:2 -GL000220.1 127677 . C TT 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.49758;SOR=Inf;LSEQ=TCTCTCTCCCTCTCTCTCTC;RSEQ=CTCTCTCGCTCTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:36,42:0:2,0:22.1:1:30.7:1:1:0:58.7:38:1:0:0.5 0/1:84:2:1,1:45,37:0.0238:2,2:18:0:31.3:1:1:1.21336:60:4:0.0241:0:3 -GL000220.1 127685 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.5006;SOR=Inf;LSEQ=CCTCTCTCTCTCCCTCTCTC;RSEQ=CTCTCTCTGTCTTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:34,40:0:2,0:20.1:1:29.9:1:1:0:58.9:73:0.9865:0:0.4 0/1:89:2:1,1:46,40:0.0225:2,2:9:0:31:1:1:1.14817:60:4:0.0233:0:3 -GL000220.1 127687 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.19782;SOR=0;LSEQ=TCTCTCTCTCCCTCTCTCGC;RSEQ=CTCTCTGTCTTTCTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:34,39:0.0267:2,2:5.5:1:32:0:1:1.14:60:4:0.027:0:1 0/0:93:0:0,0:50,43:0:2,0:21.9:1:29.8:1:1:0:55.8:92:1:0:0.4 -GL000220.1 127728 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.52602;SOR=Inf;LSEQ=CTCTCTGTTTCTCTGTCTCT;RSEQ=TCTGTCCGTCTCTGTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:35,35:0:2,0:28.8:1:32.2:1:1:0:57.8:140:1:0:0.3 0/1:114:2:1,1:61,50:0.0175:2,2:37:0:33:1:1:1.21784:50:4:0.0179:0:1.5 -GL000220.1 127730 . C G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0.92243;LSEQ=CTCTGTTTCTCTGTCTCTCT;RSEQ=TGTCCGTCTCTGTCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:4:2,2:33,34:0.0563:2,2:16:1:33.3:1:1:1.03:35.3:8:0.058:0:2.3 0/1:115:6:4,2:57,51:0.0522:2,2:31.2:1:32.2:1:0.68387:1.78:43.2:12:0.0531:0:2.8 -GL000220.1 127738 . C CTGTCTGTCTGTCTGTCTG 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=6.000;MSILEN=4;SSF=0.28859;SOR=Inf;LSEQ=CTCTGTCTCTCTCTGTCCGT;RSEQ=TCTGTCTTTTTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:40,39:0:2,0:28.2:1:31.7:1:1:0:57.2:38.5:1:0:0.4 0/1:128:3:2,1:67,55:0.0234:2,2:27.3:1:25.2:1:1:1.64:60:2:0.0163:0.0234:1.3 -GL000220.1 127742 . GTCTTTT G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.52216;SOR=Inf;LSEQ=GTCTCTCTCTGTCCGTCTCT;RSEQ=TCTGTCTGTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:42,39:0:2,0:28.9:1:29.6:1:1:0:57.3:39.5:1:0:0.4 0/1:127:2:1,1:66,56:0.0157:2,2:25:0:32.5:1:1:1.177:45:4:0.0161:0:1 -GL000220.1 127748 . T TTCTG 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0.97202;LSEQ=CTCTGTCCGTCTCTGTCTTT;RSEQ=TCTGTCTGTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:5:3,2:43,40:0.0562:2,2:13.2:1:30.9:1:1:1.39:51:10:0.0581:0.0112:2 0/1:128:7:5,2:60,55:0.0547:2,2:28.3:1:30.4:1:0.44667:2.28:47.4:14:0.0583:0:1.9 -GL000220.1 127757 . T TCTGC 85 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03217;SOR=0.18106;LSEQ=TCTCTGTCTTTTTCTGTCTG;RSEQ=CTCTCTCTTTCTTTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:7:3,4:51,39:0.0722:2,2:28:1:30.4:1:0.69619:1.73348:41.3:6:0.0659:0.0103:1.9 0/1:145:2:1,1:69,62:0.0138:2,2:46:0:32:1:1:1.11201:37:4:0.0144:0:3 -GL000220.1 127770 . T C 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0.2636;SOR=Inf;LSEQ=CTGTCTGTCTCTCTCTTTCT;RSEQ=TCTGTCTGTCTCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:57,49:0:2,0:23.3:1:30:1:1:0:58.2:34.333:1:0:0.5 0/1:143:3:0,3:73,63:0.021:2,0:26:1:32.3:1:0.10448:0:45.3:6:0.0219:0:3.3 -GL000220.1 127774 . G GTC 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.25987;SOR=Inf;LSEQ=CTGTCTCTCTCTTTCTTTCT;RSEQ=TCTGTCTCTGTCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:58,47:0:2,0:23.5:1:31.6:1:1:0:58.1:20:1:0:0.5 0/1:138:3:1,2:69,60:0.0217:2,2:19:1:27.3:1:0.60036:2.28592:50.3:6:0.0229:0.0145:1.3 -GL000220.1 127778 . G C 33 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=1.63863;LSEQ=CTCTCTCTTTCTTTCTGTCT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:1:0,1:61,49:0.009:2,0:29:0:16:0:0.45045:0:60:0:0:0:5 0/1:136:2:0,2:69,60:0.0147:2,0:14.5:1:33.5:1:0.22208:0:42:4:0.0159:0:3 -GL000220.1 127790 . G CTCTCTCTGTC 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.00017;SOR=0;LSEQ=TTCTGTCTGTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTCTCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:11:5,6:58,42:0.0982:2,2:20.4:1:29.9:1:0.52667:1.64945:45.9:10:0.0935:0.0804:2.3 0/0:129:0:0,0:66,60:0:2,0:23.1:1:30.5:1:1:0:58:41:0.9919:0:0.4 -GL000220.1 127808 . G C 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15026;SOR=0.37402;LSEQ=CTGTCTCTCTCTCTCTCTCT;RSEQ=CTTGTCTCTCTCACTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:9:6,3:54,37:0.0882:2,2:22:1:32.6:1:0.73761:1.37:54.7:18:0.0928:0:1.9 0/1:115:4:2,2:56,55:0.0348:2,2:22:1:29:1:1:1.01802:51:8:0.0364:0:1.5 -GL000220.1 127833 . C T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68558;SOR=0.54602;LSEQ=TCTCTCTCACTGTGTCTGTC;RSEQ=TCTGTCTTACTCTCCTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:4:3,1:58,51:0.0351:2,2:13:1:30.3:1:0.62313:2.62:56.8:8:0.0374:0:2.5 0/1:103:2:1,1:49,52:0.0194:2,2:32:1:30.5:1:1:1.06:60:4:0.0202:0:2.5 -GL000220.1 127843 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23328;SOR=Inf;LSEQ=TGTGTCTGTCCTCTGTCTTA;RSEQ=TCTCCTTCTCTGCCTGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:61,53:0:2,0:24.3:1:31.7:1:1:0:59.4:37:1:0:0.4 0/1:107:2:1,1:46,59:0.0187:2,2:26:1:30.5:1:1:1.28:60:4:0.02:0:2.5 -GL000220.1 127848 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36314;SOR=3.14918;LSEQ=CTGTCCTCTGTCTTACTCTC;RSEQ=TTCTCTGCCTGTCCGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:1,0:59,57:0.0085:2,0:11:0:33:0:1:0:55:2:0.009:0:1 0/1:113:3:1,2:50,60:0.0265:2,2:23.7:1:30.7:1:1:1.65945:60:6:0.028:0:2.7 -GL000220.1 127871 . G A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.81977;SOR=0.84741;LSEQ=CTCTGCCTGTCCGTCTGTCT;RSEQ=TCTGTCTCTCTCTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:12:7,5:52,53:0.1026:2,2:24:1:29.2:1:0.76204:1.42:59.2:24:0.1081:0:1.4 0/1:102:9:4,5:42,50:0.0882:2,2:30.8:1:26.9:1:1:1.04951:53.8:8:0.0842:0:1.1 -GL000220.1 127875 . GTC G 48 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=1.18655;LSEQ=GCCTGTCCGTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCCCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:3:3,0:57,56:0.0256:2,0:37.3:1:33.7:1:0.24438:0:51.7:6:0.0259:0:1 0/1:99:3:2,1:43,53:0.0303:2,2:17.3:1:30.7:1:0.58945:2.44:60:6:0.0316:0:0 -GL000220.1 127891 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.501;SOR=0;LSEQ=GTCTGTCTCTCTCTCTCTCC;RSEQ=TCCCTTTCTGTTTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:59,59:0.0165:2,2:35:1:27.5:1:1:1:60:4:0.0169:0:1 0/0:103:0:0,0:47,56:0:2,0:23.7:1:30.4:1:1:0:59:206:1:0:0.4 -GL000220.1 127895 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50226;SOR=0;LSEQ=GTCTCTCTCTCTCTCCCTCC;RSEQ=TTTCTGTTTCTCTCTCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:58,60:0.0165:2,2:14.5:1:29:1:1:1.03:60:4:0.0169:0:1 0/0:100:0:0,0:48,51:0:2,0:24.9:1:30.7:1:1:0:58.6:48.5:1:0:0.4 -GL000220.1 127941 . G T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11818;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=CCTGTTTCTCTTTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:52,54:0:2,0:23.8:1:30.8:1:1:0:58.2:10.778:0.9798:0:0.4 0/1:107:3:2,1:50,51:0.028:2,2:24.7:1:23.7:1:1:2.03:55:2:0.0222:0:1.7 -GL000220.1 127944 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49765;SOR=0;LSEQ=TCTCTCTCTCTCTCTCTGCC;RSEQ=GTTTCTCTTTCTCTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:53,52:0.0187:2,2:30:1:28.5:1:1:1.01905:60:4:0.0202:0:1 0/0:107:0:0,0:53,54:0:2,0:24:1:30:1:1:0:56.8:214:1:0:0.5 -GL000220.1 127947 . T TTC 87 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.06579;SOR=7.01761;LSEQ=CTCTCTCTCTCTCTGCCTGT;RSEQ=TCTCTTTCTCTCTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:1:1,0:52,51:0.0096:2,0:36:0:29.5:0:1:0:40:2:0.0108:0:3 0/1:109:7:3,4:52,50:0.0642:2,2:30.1:1:31.3:1:0.71609:1.38253:34.3:14:0.0686:0:1.7 -GL000220.1 127960 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.2246;SOR=0;LSEQ=TGCCTGTTTCTCTTTCTCTC;RSEQ=CTGTCTGTCTCTGTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:53,50:0.019:2,2:26.5:1:29:1:1:1.05944:60:4:0.0202:0:1.5 0/0:116:0:0,0:60,56:0:2,0:23.5:1:29.7:1:1:0:57.3:115:1:0:0.5 -GL000220.1 127973 . GTCTTTCTCTGTCTGTCTCTT CTCTC 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.68379;SOR=1.94145;LSEQ=TTCTCTCTCTGTCTGTCTCT;RSEQ=TCTCTGTCTGTCTGTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:2,0:52,58:0.0179:2,0:22:1:21:1:0.23021:0:42:8:-0.0036:0.0142:5 0/1:117:4:2,2:54,56:0.0342:2,2:19.3:1:31.5:1:1:1.04:34.8:8:0.0348:0.0256:2 -GL000220.1 127985 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0.82469;LSEQ=CTGTCTCTGTCTTTCTCTGT;RSEQ=TGTCTCTTTCTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:46,56:0.019:2,2:20:1:20:1:1:1.22:60:1:0.0098:0:2.5 0/1:127:2:0,2:59,62:0.0157:2,0:7:1:28.5:1:0.49673:0:47.5:4:0.0169:0:1 -GL000220.1 127987 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=1;SOR=1.76822;LSEQ=GTCTCTGTCTTTCTCTGTCT;RSEQ=TCTCTTTCTCTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:1:0,1:50,59:0.0091:2,0:15:0:22:0:1:0:60:2:0.0096:0:2 0/1:125:2:1,1:56,61:0.016:2,2:12.5:1:28:1:1:1.09:60:4:0.0169:0:2 -GL000220.1 127993 . T C 50 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66588;SOR=0.57515;LSEQ=GTCTTTCTCTGTCTGTCTCT;RSEQ=TCTCTGTCTGTCTGTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:3:1,2:50,55:0.0278:2,2:5:0:32:1:1:1.80854:60:6:0.0286:0:2 0/1:124:2:1,1:60,62:0.0161:2,2:17:1:24:1:1:1.03:52:1:0.0084:0:4 -GL000220.1 128026 . C T 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.11788;SOR=0.38948;LSEQ=TGTCTCCTTCTCTCTGTCTC;RSEQ=GTCTCTGTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:11:7,4:44,55:0.1:2,2:20.9:1:28.5:1:0.3403:2.17:56.4:4.5:0.0849:0:2.1 0/1:121:5:4,1:54,62:0.0413:2,2:24.6:1:27.4:1:0.19286:4.54:52.2:4:0.0339:0:1.8 -GL000220.1 128033 . G GTC 49 v4;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.33576;SOR=0.27876;LSEQ=TTCTCTCTGTCTCCGTCTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:1,2:49,53:0.028:2,2:40:1:31.5:1:1:1.83868:46.7:6:0.0286:0:1.3 0/0:126:1:1,0:61,60:0.0079:2,0:44:0:27:0:1:0:60:2:0.0084:0:4 -GL000220.1 128047 . GTC G 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.03049;SOR=Inf;LSEQ=GTCTCTGTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTGCCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:52,55:0:2,0:24.7:1:29.6:1:1:0:58.9:25.75:1:0:0.4 0/1:120:6:3,3:57,57:0.05:2,2:29.2:1:31.7:1:1:1:59.8:12:0.0504:0:0.5 -GL000220.1 128059 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.21445;SOR=0;LSEQ=CTCTCTCTGTCTCTCTCTCT;RSEQ=TGCCTGTCTCACTGTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:49,53:0.0192:2,2:42.5:1:30:0:1:1.08:60:4:0.0196:0:1.5 0/0:120:0:0,0:58,61:0:2,0:23.4:1:31:1:1:0:58.4:38.667:0.9915:0:0.4 -GL000220.1 128063 . CTGTCTCACTG C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.50235;SOR=Inf;LSEQ=CTCTGTCTCTCTCTCTCTGC;RSEQ=TGTCTGTCTTCTGTCTTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:50,55:0:2,0:23.6:1:30.6:1:1:0:58.8:51.5:1:0:0.5 0/1:127:2:1,1:58,65:0.0157:2,2:9:1:28.6:1:1:1.12:60:4:0.0163:0.0157:1 -GL000220.1 128065 . G C 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12734;SOR=Inf;LSEQ=CTGTCTCTCTCTCTCTGCCT;RSEQ=TCTCACTGTGTCTGTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:50,55:0:2,0:23.6:1:32.1:1:1:0:58.8:104:0.9905:0:0.5 0/1:126:4:2,2:57,61:0.0317:2,2:15.3:1:28:1:1:1.07:41:3:0.025:0:1.8 -GL000220.1 128110 . C G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=1;SOR=0.94013;LSEQ=TATTCTCTTTCTCTGTCTGT;RSEQ=TGTCTCTCTCTCTCCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:13:8,5:45,39:0.134:2,2:19.8:1:31.9:1:0.76655:1.38:59.2:26:0.1354:0:2.5 0/1:126:16:9,7:62,47:0.127:2,2:25:1:31.4:1:1:1.0258:52.8:32:0.129:0:1.9 -GL000220.1 128112 . GTC G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.17718;SOR=0;LSEQ=TTCTCTTTCTCTGTCTGTCT;RSEQ=TCTCTCTCTCCCTTCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:2,0:50,43:0.0211:2,0:26.5:1:33.5:1:0.49922:0:60:4:0.0215:0:0.5 0/0:130:0:0,0:73,57:0:2,0:24.2:1:28.9:1:1:0:58:260:1:0:0.5 -GL000220.1 128138 . TTCTC T 179 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=10.000;MSILEN=2;SSF=0.77949;SOR=0.89422;LSEQ=CTCTCTCCCTTCCTGTCTCT;RSEQ=TCTCTCTCTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:45:25,20:16,17:0.5357:2,2:29.2:1:30.6:1:0.64737:1.32:60:90:0.5488:0.1071:0.3 1/0:130:66:37,29:19,26:0.5077:2,2:25.3:1:29.7:1:0.17852:1.74:59.4:132:0.5156:0.1077:0.4 -GL000220.1 128154 . CTCTCTTTCTG T 106 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.3491;SOR=0.63638;LSEQ=TGTCTCTTTCTCTCTCTCTC;RSEQ=TCTGTTTCTCTCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:10:4,6:38,31:0.1235:2,2:33.9:1:31.3:1:0.50214:1.82451:50.9:20:0.1299:0:2.4 0/1:134:11:5,6:64,55:0.0821:2,2:25.6:1:30.9:1:0.7546:1.39276:42.1:22:0.0846:0:0.9 -GL000220.1 128164 . G C 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.29882;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTTTCT;RSEQ=TCTGTTTCTCTCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:37,30:0:2,0:20.7:1:31.3:1:1:0:60:32.5:0.9848:0:0.2 0/1:114:4:2,2:58,48:0.0351:2,2:13.5:1:30.8:1:1:1.20624:53.8:8:0.0364:0:4 -GL000220.1 128188 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.51012;SOR=Inf;LSEQ=GTTTCTCTCTGCCTGTCTCC;RSEQ=TCTTTCTCTGTCTGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:45,43:0:2,0:22.3:1:29.6:1:1:0:57.8:28.333:1:0:0.8 0/1:121:2:1,1:60,58:0.0165:2,2:14:1:31.5:1:1:1.0342:60:4:0.0167:0:1 -GL000220.1 128194 . C CTCTG 91 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=4;SSF=0.04296;SOR=Inf;LSEQ=CTCTGCCTGTCTCCGTCTTT;RSEQ=TCTGTCTGCCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:42,43:0:2,0:24.7:1:31.3:1:1:0:57.7:170:1:0:0.8 0/1:122:7:5,2:55,58:0.0574:2,2:23.4:1:32.6:1:0.43898:2.62:44.6:14:0.0583:0:1 -GL000220.1 128203 . CCTCTCTCTT TCTGCCTC 118 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0261;SOR=0.35877;LSEQ=TCTCCGTCTTTCTCTGTCTG;RSEQ=TCTTTTTCTGCGTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:15:6,9:41,36:0.1596:2,2:19.3:1:30.3:1:0.40587:1.6984:49.5:30:0.1667:0.0638:1.3 0/1:126:8:3,5:59,56:0.0635:2,2:13.4:1:30.6:1:0.49119:1.74804:56.1:16:0.0667:0.0397:1 -GL000220.1 128206 . CTCTCTT C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.15792;SOR=0;LSEQ=CCGTCTTTCTCTGTCTGCCT;RSEQ=TCTTTTTCTGCGTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:2,0:38,37:0.026:2,0:11.5:1:32:0:0.49419:0:60:4:0.0274:0:1 0/0:116:0:0,0:59,57:0:2,0:24.3:1:30:1:1:0:59:115:1:0:0.3 -GL000220.1 128212 . T C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63158;SOR=0.59514;LSEQ=TTCTCTGTCTGCCTCTCTCT;RSEQ=TCTTTTTCTGCGTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:34,37:0.0267:2,2:22.5:1:32.5:1:1:1.09:57.5:4:0.0286:0:4 0/1:125:2:1,1:61,62:0.016:2,2:2.1:1:33.1:1:1:1.02:60:4:0.0126:0:1.5 -GL000220.1 128216 . T A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51391;SOR=Inf;LSEQ=CTGTCTGCCTCTCTCTTTCT;RSEQ=TTTCTGCGTCTCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:41,47:0:2,0:28.9:1:29.9:1:1:0:58.2:87:0.9886:0:0.6 0/1:128:2:1,1:60,66:0.0156:2,2:8:0:30.5:1:1:1.10:60:4:0.0156:0:1 -GL000220.1 128232 . GTC G 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=1.01234;LSEQ=TTCTTTTTCTGCGTCTCTCT;RSEQ=TCTCTCTCTCTGTGCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:20:12,8:44,44:0.1852:2,2:27:1:32.2:1:0.46558:1.49:52.9:40:0.1887:0.0093:1.4 0/1:139:26:13,13:55,59:0.1871:2,2:24.1:1:29.5:1:1:1.07:57.3:25:0.1838:0.0216:0.8 -GL000220.1 128282 . CCTGT C 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.01804;SOR=0;LSEQ=TTACTCTGTTTCTCTGCCTG;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:2,3:58,52:0.0439:2,2:26.2:1:30.4:1:0.6689:1.66564:59.2:10:0.0442:0.0175:1.2 0/0:138:0:0,0:68,69:0:2,0:23.9:1:30.3:1:1:0:59.6:21.833:1:0:0.3 -GL000220.1 128293 . GTCTGTC G 32 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=7.000;MSILEN=2;SSF=1;SOR=0.89272;LSEQ=CTCTGCCTGCCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:62,54:0.0169:2,2:39.5:1:31.5:1:1:1.1468:60:4:0.0172:0:0 0/1:132:2:1,1:63,65:0.0152:2,2:44:0:32.5:1:1:1.03:60:4:0.0156:0:0.5 -GL000220.1 128297 . GTC G 102 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0.90869;LSEQ=GCCTGCCTGTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:10:5,5:57,50:0.084:2,2:29.3:1:32.5:1:1:1.13872:60:20:0.0855:0:0.1 0/1:130:10:6,4:56,61:0.0769:2,2:28.5:1:31:1:0.52408:1.63:60:20:0.08:0:0.3 -GL000220.1 128305 . C CTT 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.22841;SOR=0;LSEQ=GTCTGTCTGTCTGTCTCTCT;RSEQ=TCTCTCTGTCTCTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:65,58:0.016:2,2:10.5:1:29:1:1:1.11967:60:4:0.0161:0.008:1 0/0:136:0:0,0:62,73:0:2,0:23.5:1:31.3:1:1:0:59.8:44:0.9925:0:0.3 -GL000220.1 128329 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.4987;SOR=0;LSEQ=CTCTGTCTCTCTCTCTTTCT;RSEQ=TCTGTTTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:69,67:0.0144:2,2:32:0:31:1:1:1.02964:25:4:0.0144:0:2.5 0/0:130:0:0,0:63,67:0:2,0:24.1:1:30.7:1:1:0:59.2:25:1:0:0.2 -GL000220.1 128351 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=8;SSF=0.49798;SOR=Inf;LSEQ=CTGTTTCTCTCTGTCTCTCT;RSEQ=TCCATCTCTGTCTTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:64,54:0:2,0:28.7:1:32.1:1:1:0:58.9:58:1:0:0.3 0/1:121:2:1,1:56,61:0.0165:2,2:29.5:1:30:1:1:1.09:60:4:0.0171:0:1 -GL000220.1 128355 . A G 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24728;SOR=0;LSEQ=TTCTCTCTGTCTCTCTGTCC;RSEQ=TCTCTGTCTTTCTCTGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:3:1,2:64,53:0.025:2,2:24.3:1:32:1:0.59265:2.39779:36.7:6:0.0254:0:2.3 0/0:114:0:0,0:55,59:0:2,0:25.2:1:29:1:1:0:58.9:21.8:1:0:0.2 -GL000220.1 128374 . C T 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.16629;SOR=0.38697;LSEQ=CATCTCTGTCTTTCTCTGTC;RSEQ=GTCTCTCTCTTTCTCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:10:5,5:53,53:0.0862:2,2:16.7:1:31.1:1:1:1:55.9:20:0.0885:0:1.7 0/1:114:4:1,3:53,57:0.0351:2,2:8.5:1:28:1:0.62042:2.76646:60:8:0.0354:0:2.3 -GL000220.1 128389 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0.49778;SOR=Inf;LSEQ=CTGTCCGTCTCTCTCTTTCT;RSEQ=CCTGTCTCTGTCTCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:54,56:0:2,0:23.4:1:31.3:1:1:0:58.9:220:1:0:0.4 0/1:112:2:1,1:53,57:0.0179:2,2:15.5:1:27.5:1:1:1.07:60:4:0.018:0:1.5 -GL000220.1 128412 . CCT C 83 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.35372;SOR=0.4812;LSEQ=TGTCTCTGTCTCTGCCTCTG;RSEQ=CTCTCTCTCTCTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:7:4,3:45,49:0.0693:2,2:29.6:1:29.9:1:0.71:1.45:60:6:0.0606:0:0.1 0/1:116:4:2,2:57,55:0.0345:2,2:31.3:1:28.8:1:1:1.03606:60:8:0.0351:0:0 -GL000220.1 128425 . C G 80 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.15649;SOR=0.29515;LSEQ=GCCTCTGCCTCTCTCTCTCT;RSEQ=TGTCTCTCTCTTTCTATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:6:1,5:49,45:0.0588:2,2:33.5:1:31.3:1:0.2044:5.36536:49.8:12:0.0612:0:3.2 0/1:111:2:2,0:53,56:0.018:2,0:39:1:32:0:0.24324:0:60:4:0.0185:0:3.5 -GL000220.1 128427 . G C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.36803;SOR=0.53589;LSEQ=CTCTGCCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTTTCTATCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:7:2,5:52,47:0.0648:2,2:30.1:1:31.4:1:0.26559:2.74075:48.4:14:0.0673:0:3 0/1:112:4:3,1:54,54:0.0357:2,2:28.5:1:27.3:1:0.6184:2.97:46:3:0.0283:0:3.3 -GL000220.1 128441 . A G 54 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42354;SOR=0.43541;LSEQ=CTCTCTGTCTCTCTCTTTCT;RSEQ=TCTGTTTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:4:2,2:50,54:0.0367:2,2:5.8:1:27.3:1:1:1.08:36.3:3:0.0297:0:2.5 0/1:123:2:2,0:61,60:0.0163:2,0:18.5:1:24:1:0.4962:0:37.5:1:0.0088:0:1 -GL000220.1 128467 . A G 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04471;LSEQ=TTCTCTCTGTCTCTCTGTCC;RSEQ=TCTCTGTCTTTCTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:14:4,10:59,59:0.1061:2,2:26.4:1:31.5:1:0.16235:2.48352:55.4:28:0.1085:0:2.1 0/1:136:15:7,8:68,52:0.1103:2,2:24.9:1:28.5:1:0.58371:1.48998:52.2:14:0.1094:0:2 -GL000220.1 128495 . CTT C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.49829;SOR=0;LSEQ=CTTTCTCTGTCTGTCTCTCT;RSEQ=TCTCCCTGTCTCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:69,69:0.0143:2,2:31.5:1:30.5:1:1:1:60:4:0.0144:0:0 0/0:136:0:0,0:72,64:0:2,0:25.6:1:30:1:1:0:56.5:44.333:1:0:0.5 -GL000220.1 128497 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.44198;SOR=0.60574;LSEQ=TTCTCTGTCTGTCTCTCTCT;RSEQ=TCTCCCTGTCTCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:10:6,4:62,66:0.0714:2,2:14.1:1:32.6:1:0.5288:1.59:60:20:0.0735:0:1.2 0/1:135:6:3,3:69,60:0.0444:2,2:36.3:1:31.7:1:1:1.1488:58.2:12:0.0455:0:1.7 -GL000220.1 128500 . TC T 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0972;SOR=2.1669;LSEQ=TCTGTCTGTCTCTCTCTTTC;RSEQ=CCTGTCTCTGTCTCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:9:3,6:67,63:0.0647:2,2:28:1:31.9:1:0.32552:2.1158:59.7:18:0.0657:0:1.4 0/1:130:17:7,10:61,51:0.1308:2,2:32.4:1:30.8:1:0.43505:1.70155:47.8:34:0.1339:0.0154:1.4 -GL000220.1 128502 . CCTGTCTCTGTCTCTGCCTCTCTCTCTCTCTCTCTGTCTGTCTCTCTCACTGTGTGTG C 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.12269;SOR=0;LSEQ=TGTCTGTCTCTCTCTTTCTC;RSEQ=TGTCTCTGTCTCTGCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:4:3,1:65,67:0.0294:2,2:28.5:1:32.3:1:0.61938:3.07:41.3:8:0.0305:0:0.3 0/0:129:0:0,0:64,63:0:2,0:26.5:1:30.6:1:1:0:56.5:41.333:0.992:0:0.5 -GL000220.1 128551 . CTG C 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.62187;SOR=2.96142;LSEQ=CTCTCTGTCTGTCTCTCTCA;RSEQ=TGTGTGTGTCTCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:1,0:52,58:0.0087:2,0:40:0:29:0:0.47748:0:60:2:0.0093:0:0 0/1:118:3:2,1:51,63:0.0254:2,2:29.3:1:32.3:1:0.58925:2.45:60:6:0.0268:0:0.7 -GL000220.1 128606 . TCTCACTGTGT ACC 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.49993;SOR=Inf;LSEQ=TCTCTCTCTCTGTCTGTCTC;RSEQ=GTGTCTGTCTTCTGTCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:39,41:0:2,0:27.9:1:30.3:1:1:0:51.8:25.667:1:0:0.4 0/1:93:2:0,2:43,48:0.0215:2,0:16.5:1:30:1:0.49743:0:60:4:0.0215:0.0108:1.5 -GL000220.1 128656 . G A 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55007;SOR=0.6142;LSEQ=CTCTCCTTCTCTGCCTGTCC;RSEQ=TCTGTCTGTCTGTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:7:4,3:30,34:0.0959:2,2:18.3:1:29.3:1:0.70282:1.50:43.4:14:0.1014:0:1.4 0/1:82:5:2,3:43,33:0.061:2,2:26.2:1:28.4:1:0.65109:1.93828:40.2:10:0.0625:0:1 -GL000220.1 128676 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.24932;SOR=Inf;LSEQ=GTCTGTCTGTCTGTCTCTCC;RSEQ=TCTCTCTCCCTCCCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:38,41:0:2,0:24.1:1:31.1:1:1:0:48.6:38.5:1:0:0.2 0/1:91:3:1,2:46,42:0.033:2,2:5.7:1:30.3:1:0.60848:2.17225:54.3:6:0.0337:0:1 -GL000220.1 128689 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50015;SOR=Inf;LSEQ=TCTCTCCCTCTCTCTCCCTC;RSEQ=CTTTCTGTTTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:44,42:0:2,0:24:1:30:1:1:0:51.9:20.5:1:0:0.2 0/1:100:2:1,1:52,46:0.02:2,2:27:0:33:1:1:1.12905:21:4:0.0202:0:1 -GL000220.1 128720 . T C 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25625;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTGTCTGTTTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:48,45:0:2,0:25.6:1:30.5:1:1:0:52.7:92:1:0:0.2 0/1:117:3:3,0:54,60:0.0256:2,0:15:1:23:1:0.11248:0:50:2:0.0179:0:3.3 -GL000220.1 128748 . G GTCTGTCTCTGTCTTTC 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=2.000;MSILEN=2;SSF=0.3102;SOR=0.56653;LSEQ=GTTTCTCTCTTTCTCTCTCT;RSEQ=TCTGTCTCTTTCTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:10:6,4:49,46:0.0935:2,2:25.7:1:31.6:1:0.7445:1.40:49.6:20:0.0962:0.028:0.1 0/1:109:6:4,2:49,54:0.055:2,2:14.5:1:31:1:0.42939:2.19:51.8:12:0.0571:0.0459:0.5 -GL000220.1 128760 . CTCTG C 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.05412;SOR=Inf;LSEQ=CTCTCTCTGTCTGTCTCTTT;RSEQ=TCTGTCTGTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:59,50:0:2,0:24.2:1:30:1:1:0:53.4:26.25:1:0:0.2 0/1:104:4:2,2:48,51:0.0385:2,2:32:1:31.8:1:1:1.06:51.8:8:0.0396:0:0.8 -GL000220.1 128762 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23501;SOR=Inf;LSEQ=CTCTCTGTCTGTCTCTTTCT;RSEQ=TGTCTGTCTGTCTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:59,51:0:2,0:24.4:1:31.1:1:1:0:53.4:26.5:1:0:0.2 0/1:104:2:1,1:47,51:0.0192:2,2:5.5:1:28:1:1:1.08:47.5:4:0.0202:0:2.5 -GL000220.1 128764 . G C 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=4;SSF=0.04909;SOR=Inf;LSEQ=CTCTGTCTGTCTCTTTCTCT;RSEQ=TCTGTCTGTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:60,53:0:2,0:23.8:1:31.6:1:1:0:53.7:55.5:1:0:0.2 0/1:102:4:2,2:44,50:0.0392:2,2:29.5:1:28.8:1:1:1.13:50.3:3:0.0326:0:1.5 -GL000220.1 128773 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=4.000;MSILEN=2;SSF=0.21497;SOR=Inf;LSEQ=TCTCTTTCTCTGTCTGTCTG;RSEQ=CTCTCTCTTTCTTTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:59,47:0:2,0:25.8:1:29.4:1:1:0:53.6:52:0.9905:0:0.2 0/1:93:2:1,1:44,47:0.0215:2,2:24.5:1:28.5:1:1:1.07:50:4:0.0217:0:2.5 -GL000220.1 128785 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.50161;SOR=0;LSEQ=TCTGTCTGTCTCTCTCTTTC;RSEQ=TTTTCTCTGTCTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:66,57:0.016:2,2:14:1:29.5:1:1:1.15653:50:4:0.0163:0:1 0/0:105:0:0,0:53,52:0:2,0:23.5:1:30.4:1:1:0:54.5:210:1:0:0.3 -GL000220.1 128802 . G GTCTC 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=6.000;MSILEN=2;SSF=0.50022;SOR=0;LSEQ=TTCTTTTTCTCTGTCTCTCT;RSEQ=TCTCTCTCTGTGCCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:70,52:0.0161:2,2:27.5:1:29.1:1:1:1.34287:42:4:0.0164:0:3.5 0/0:108:0:0,0:53,55:0:2,0:25:1:31.1:1:1:0:55.7:35:1:0:0.3 -GL000220.1 128823 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.24467;SOR=0;LSEQ=TCTCTCTCTGTGCCTGTCTC;RSEQ=CTGTCTGTGCCTATCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:60,54:0.0172:2,2:27.5:1:31:1:1:1.1101:42:4:0.018:0:3.5 0/0:118:0:0,0:58,60:0:2,0:24.2:1:29.3:1:1:0:58.3:38.333:1:0:0.3 -GL000220.1 128838 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49818;SOR=Inf;LSEQ=GTCTCTCTGTCTGTGCCTAT;RSEQ=TTCTGTCTTACTCTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:56,57:0:2,0:24.9:1:31.6:1:1:0:58.8:55.5:1:0:0.3 0/1:120:2:1,1:56,62:0.0167:2,2:20.5:1:30:1:1:1.11:60:4:0.0171:0:1 -GL000220.1 128855 . TTCTCTGGCTGACTGCCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCTGTCTCCGTCCCTCCCTCCCTGTCTGTCTGTTTCTC T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=0.4978;SOR=Inf;LSEQ=TATCTTCTGTCTTACTCTCT;RSEQ=TCTCTGTCCATTTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:55,59:0:2,0:23:1:29.9:1:1:0:57.9:228:1:0:0.4 0/1:114:2:1,1:56,56:0.0175:2,2:31.5:1:29.1:1:1:1:60:4:0.0177:0.0175:0 -GL000220.1 128866 . A T 40 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67655;SOR=0.62667;LSEQ=TTACTCTCTTTCTCTGGCTG;RSEQ=CTGCCTGTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:0,3:56,50:0.0275:2,0:13.7:1:25.3:1:0.11159:0:44.7:2:0.0206:0:3.7 0/1:115:2:0,2:57,54:0.0174:2,0:33.5:1:15:0:0.24336:0:60:0:0:0:4.5 -GL000220.1 128908 . C T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.73524;SOR=0.74178;LSEQ=TCTCTCTCTCTCTCTCTCTG;RSEQ=CTGTCTCCGTCCCTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:5:3,2:56,64:0.0397:2,2:21.2:1:29.8:1:0.66616:1.71:46.8:10:0.0442:0:1.8 0/1:101:3:2,1:45,51:0.0297:2,2:23.7:1:24.7:1:0.60266:2.25:50:2:0.0222:0:3.3 -GL000220.1 128917 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58825;SOR=2.48533;LSEQ=CTCTCTCTCTGCCTGTCTCC;RSEQ=TCCCTCCCTCCCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:1:1,0:63,62:0.0079:2,0:1:0:27:0:1:0:60:2:0.0086:0:1 0/1:103:2:1,1:48,50:0.0194:2,2:39:1:27.5:1:1:1.04:60:4:0.0225:0:1 -GL000220.1 128921 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.21164;SOR=Inf;LSEQ=CTCTCTGCCTGTCTCCGTCC;RSEQ=TCCCTCCCTGTCTGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:62,62:0:2,0:26.3:1:31.6:1:1:0:58.4:248:1:0:0.4 0/1:107:2:1,1:49,54:0.0187:2,2:22:0:28.5:1:1:1.10:60:4:0.0192:0:2.5 -GL000220.1 128924 . C T 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.29229;SOR=0.37839;LSEQ=TCTGCCTGTCTCCGTCCCTC;RSEQ=CTCCCTGTCTGTCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:6:3,3:59,61:0.0472:2,2:23.3:1:27.5:1:1:1.03:47.3:5:0.0417:0:2.2 0/1:109:2:1,1:50,55:0.0183:2,2:28:0:31:1:1:1.10:45:4:0.0198:0:2 -GL000220.1 128928 . C CCTGTCTCCTCTCTCTCTCA 69 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06257;SOR=0;LSEQ=CCTGTCTCCGTCCCTCCCTC;RSEQ=CTGTCTGTCTGTTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:2,3:60,63:0.0379:2,2:14:1:29.8:1:1:1.42464:46.8:10:0.041:0.0379:1.6 0/0:116:0:0,0:54,60:0:2,0:21.1:1:29.5:1:1:0:58.6:21.8:1:0:0.6 -GL000220.1 128940 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21777;SOR=Inf;LSEQ=CCTCCCTCCCTGTCTGTCTG;RSEQ=TTCTCTCTCTGTCCATTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:68,72:0:2,0:24.5:1:29.4:1:1:0:58.5:45.667:1:0:0.4 0/1:123:2:1,1:59,60:0.0163:2,2:34:0:33:1:1:1.02:60:4:0.0168:0:1.5 -GL000220.1 128957 . TTCTG T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.06031;SOR=0;LSEQ=CTGTTTCTCTCTCTGTCCAT;RSEQ=TCTGTCTCTTTCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:5:3,2:62,64:0.0382:2,2:19.6:1:31:0:0.68017:1.54:60:10:0.0388:0:0 0/0:126:0:0,0:63,63:0:2,0:24.5:1:29.2:1:1:0:59.1:41:1:0:0.7 -GL000220.1 128996 . T C 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.11592;SOR=Inf;LSEQ=TTTCTCTCTCTTTCTTTCTC;RSEQ=CTGTCTCTCTCTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:65,58:0:2,0:23.8:1:30.2:1:1:0:58.8:23.6:0.9916:0:0.5 0/1:119:3:1,2:67,49:0.0252:2,2:24.7:1:31:1:0.57571:2.71177:60:6:0.0263:0:1 -GL000220.1 129003 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=2;SSF=0.22373;SOR=Inf;LSEQ=CTCTTTCTTTCTCTCTGTCT;RSEQ=TCTCTGTCTCTCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:66,55:0:2,0:23.5:1:31.9:1:1:0:58.6:242:1:0:0.6 0/1:110:2:1,1:62,44:0.0182:2,2:11.5:1:30:1:1:1.40451:53.5:4:0.0183:0:3 -GL000220.1 129009 . G C 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTCTCTCTGTCTCTCTCT;RSEQ=TCTCTCTCTGTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:65,49:0:2,0:23.1:1:29.5:1:1:0:59:6.125:1:0:0.5 0/1:109:17:7,10:54,35:0.156:2,2:21.7:1:29.5:1:0.18177:2.18722:56.8:7.5:0.1531:0:2.1 -GL000220.1 129011 . C CTT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.22416;SOR=Inf;LSEQ=TTCTCTCTGTCTCTCTCTGT;RSEQ=TCTCTCTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:66,57:0:2,0:23.3:1:31.2:1:1:0:58.6:40:1:0:0.7 0/1:112:2:2,0:63,46:0.0179:2,0:12.5:1:31.9:1:0.51024:0:50:4:0.0182:0.0089:2.5 -GL000220.1 129017 . C G 33 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.60552;SOR=2.223;LSEQ=CTGTCTCTCTCTGTCTCTCT;RSEQ=TGTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:1,0:59,56:0.0085:2,0:8:0:33:0:1:0:60:2:0.009:0:3 0/1:106:2:2,0:60,43:0.0189:2,0:23:1:33.5:1:0.51172:0:59:4:0.0194:0:5 -GL000220.1 129019 . G C 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00164;SOR=0;LSEQ=GTCTCTCTCTGTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:10:3,7:56,44:0.0877:2,2:18.4:1:29.4:1:0.18288:2.94101:57.6:4:0.087:0:2.3 0/0:108:0:0,0:48,33:0:2,0:24.1:1:28:1:1:0:58.1:5.75:0.9324:0:0.6 -GL000220.1 129072 . TCTCTCACTGTGTCGGTCTTCTGTCTTACTCTCTTTCTCTGCCTGCCTCTCTG T 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.05598;SOR=Inf;LSEQ=TCTCTCTCTCTCTGCCTTTC;RSEQ=TCTGTCTGTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:60,63:0:2,0:23.5:1:32:1:1:0:59.1:122:1:0:0.7 0/1:118:4:1,3:56,58:0.0339:2,2:6.5:1:27.2:1:0.6194:2.87299:57.3:8:0.0342:0.0339:1 -GL000220.1 129090 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23338;SOR=Inf;LSEQ=TCTCTCTCACTGTGTCGGTC;RSEQ=TCTGTCTTACTCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:63,67:0:2,0:23.2:1:29.5:1:1:0:59.4:15.25:1:0:0.6 0/1:122:2:1,1:57,62:0.0164:2,2:31:1:30:1:1:1.09:60:4:0.0175:0:1 -GL000220.1 129104 . C G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2311;SOR=Inf;LSEQ=TCGGTCTTCTGTCTTACTCT;RSEQ=TTTCTCTGCCTGCCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:59,69:0:2,0:23.6:1:31.5:1:1:0:59.1:127:1:0:0.5 0/1:119:2:1,1:59,57:0.0168:2,2:41:0:32.5:1:1:1.03479:27:4:0.0172:0:6.5 -GL000220.1 129109 . TC CT 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2311;SOR=Inf;LSEQ=CTTCTGTCTTACTCTCTTTC;RSEQ=TGCCTGCCTCTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:60,68:0:2,0:23.6:1:29.8:1:1:0:59.1:31:1:0:0.5 0/1:119:2:1,1:58,58:0.0168:2,2:35:0:32.3:1:1:1:27:4:0.0172:0:5.5 -GL000220.1 129117 . CCTCT C 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.06018;SOR=Inf;LSEQ=TTACTCTCTTTCTCTGCCTG;RSEQ=CTGTCTGTCTGTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:56,62:0:2,0:26.1:1:30.8:1:1:0:59.2:38.333:1:0:0.4 0/1:123:5:2,3:61,56:0.0407:2,2:14:1:31.3:1:0.67222:1.6274:40.6:10:0.041:0.0163:1.2 -GL000220.1 129120 . C CTCTGTCTG 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=6.000;MSILEN=4;SSF=0.3123;SOR=0.56976;LSEQ=CTCTCTTTCTCTGCCTGCCT;RSEQ=TCTGTCTGTCTGTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:10:6,4:49,59:0.0847:2,2:28.9:1:30.5:1:0.51131:1.80:56.3:20:0.0862:0:1.1 0/1:120:6:3,3:55,51:0.05:2,2:29.5:1:32.1:1:1:1.07768:49.8:12:0.0526:0:1.2 -GL000220.1 129130 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.49864;SOR=Inf;LSEQ=CTGCCTGCCTCTCTGTCTGT;RSEQ=TGTCTGTCTCTCTCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:54,66:0:2,0:26.2:1:31.1:1:1:0:59.1:39:1:0:0.3 0/1:129:2:1,1:68,59:0.0155:2,2:15:0:33.5:1:1:1.15127:27:4:0.0159:0:4.5 -GL000220.1 129150 . A ACGTC 79 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28159;SOR=2.98804;LSEQ=CTGTCTGTCTCTCTCCCTCC;RSEQ=TGTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:59,61:0.0163:2,2:29.5:1:31.8:1:1:1.03:60:4:0.0177:0:1.5 0/1:127:6:3,3:66,54:0.0472:2,2:28.7:1:30.7:1:1:1.22026:39.8:12:0.0504:0:1.3 -GL000220.1 129180 . G C 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02214;SOR=2.5643;LSEQ=CTCTCTCTCTCTCACTCACT;RSEQ=TCTCTCCGTCTCTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:9:5,4:56,62:0.0698:2,2:23.3:1:32.8:1:0.73684:1.38:55.6:18:0.0709:0:1.9 0/1:136:22:12,10:61,53:0.1618:2,2:20.2:1:30.5:1:1:1.04:49.4:21:0.1654:0:2.3 -GL000220.1 129184 . C G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49833;SOR=Inf;LSEQ=CTCTCTCTCACTCACTGTCT;RSEQ=TCCGTCTCTCTCTCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:65,69:0:2,0:22.9:1:32:1:1:0:59.5:133:1:0:0.3 0/1:139:2:1,1:73,64:0.0144:2,2:35:0:33:1:1:1.13954:60:4:0.0152:0:1.5 -GL000220.1 129187 . C T 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=1.000;MSILEN=1;SSF=0.02649;SOR=Inf;LSEQ=TCTCTCACTCACTGTCTCTC;RSEQ=GTCTCTCTCTCTTTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:72,71:0:2,0:21.8:1:29.9:1:1:0:59.6:27.6:1:0:0.3 0/1:136:5:3,2:69,62:0.0368:2,2:21.6:1:26:1:1:1.34:57.2:4:0.032:0:2.6 -GL000220.1 129188 . GTC G 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.36174;SOR=3.16838;LSEQ=CTCTCACTCACTGTCTCTCC;RSEQ=TCTCTCTCTTTCTGTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:1,0:72,68:0.007:2,0:45:0:24:0:1:0:60:2:0.0071:0:7 0/1:136:3:1,2:71,62:0.0221:2,2:26:1:31.3:1:0.60105:2.27679:48.3:6:0.0224:0:1.3 -GL000220.1 129214 . CTCTG C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.23874;SOR=0;LSEQ=CTCTCTTTCTGTCTGTTTCT;RSEQ=TCTCTGTCTTTCTGTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:70,68:0.0143:2,2:27:0:33:1:1:1.02921:48.5:4:0.0144:0:4.5 0/0:146:0:0,0:71,75:0:2,0:24.2:1:29.3:1:1:0:58.8:47.667:1:0:0.7 -GL000220.1 129228 . T G 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23046;SOR=0;LSEQ=GTTTCTCTCTGTCTCTGTCT;RSEQ=TCTGTGTGTCTGTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:68,68:0.0144:2,2:36:0:33.5:1:1:1:48.5:4:0.0148:0:4.5 0/0:150:0:0,0:72,78:0:2,0:24.6:1:28.7:1:1:0:59.5:17.75:1:0:0.6 -GL000220.1 129230 . CTGTG C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.51141;SOR=1.38853;LSEQ=TTCTCTCTGTCTCTGTCTTT;RSEQ=TGTCTGTCTGTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:9:5,4:66,62:0.0657:2,2:30.1:1:31:1:1:1.17:60:18:0.0662:0.0146:1.4 0/1:146:13:6,7:63,69:0.089:2,2:27.3:1:30.5:1:1:1.06478:56.5:12:0.0851:0.0137:2.4 -GL000220.1 129240 . GTCTGTC G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=2;SSF=0.50055;SOR=Inf;LSEQ=CTCTGTCTTTCTGTGTGTCT;RSEQ=TCTCTCTCTATTTGTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:65,64:0:2,0:27.7:1:30.2:1:1:0:59.8:258:1:0:0.4 0/1:148:2:1,1:70,76:0.0135:2,2:35:1:31:1:1:1.09:60:4:0.0138:0:3.5 -GL000220.1 129256 . A G 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15133;SOR=1.90013;LSEQ=GTCTGTCTGTCTCTCTCTCT;RSEQ=TTTGTCTTTCTCCCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:9:4,5:57,61:0.0692:2,2:32.3:1:32.2:1:1:1.16661:60:18:0.0744:0:1.8 0/1:137:17:8,9:54,63:0.1241:2,2:23.4:1:30.4:1:1:1.04:58.5:34:0.1382:0:2.4 -GL000220.1 129258 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24153;SOR=0;LSEQ=CTGTCTGTCTCTCTCTCTAT;RSEQ=TGTCTTTCTCCCTCCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:61,66:0.0154:2,2:25:1:30.5:1:1:1.08:48.5:4:0.0167:0:4.5 0/0:134:0:0,0:59,74:0:2,0:25.5:1:28.8:1:1:0:59.4:32.25:1:0:0.7 -GL000220.1 129313 . C T 181 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0622;SOR=0.5694;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CTGTCTGTCTGTTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:62:27,35:10,20:0.5849:2,2:22.7:1:30.5:1:0.37479:1.54:55.3:61:0.6932:0:1.4 0/1:90:40:15,25:9,16:0.4444:2,2:19.6:1:28.8:1:1:1.07:54.8:39:0.629:0:1.6 -GL000220.1 129329 . T A 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.40668;SOR=1.44365;LSEQ=TCTCCCTGTCTGTCTGTTTC;RSEQ=CTCTATCTCTCGCTGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:13:6,7:36,54:0.1262:2,2:30.5:1:29.5:1:0.76597:1.28:54.3:26:0.1275:0:1.9 0/1:81:14:6,8:27,40:0.1728:2,2:24.9:1:26.4:1:1:1.11:52.6:13:0.1711:0:2.3 -GL000220.1 129334 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.17303;SOR=Inf;LSEQ=CTGTCTGTCTGTTTCTCTCT;RSEQ=TCTCTCGCTGTCCATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:42,62:0:2,0:23.8:1:28.2:1:1:0:53.2:9.4:1:0:1 0/1:76:2:1,1:32,42:0.0263:2,2:42.5:1:31:1:1:1.31:47:4:0.0308:0:2.5 -GL000220.1 129424 . T C 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.1397;SOR=2.59607;LSEQ=CCGGGTAGGGCCCTGCCCCT;RSEQ=CCACGAAAGTGAGAAGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:4:1,3:24,31:0.0678:2,2:38.8:1:32.3:1:0.63021:2.29249:46.5:8:0.0678:0:2 0/1:50:8:3,5:20,22:0.16:2,2:31.6:1:30.4:1:0.71054:1.50279:46.5:16:0.16:0:2.1 -GL000220.1 129428 . C T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14065;SOR=2.70681;LSEQ=GTAGGGCCCTGCCCCTTCCA;RSEQ=GAAAGTGAGAAGCGCGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:4:1,3:23,28:0.0727:2,2:37:1:31:1:0.6237:2.42757:46.5:8:0.0727:0:2 0/1:51:9:3,6:20,22:0.1765:2,2:26.3:1:28.6:1:0.48748:1.79749:48:8:0.16:0:2 -GL000220.1 129516 . T C 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22337;SOR=0;LSEQ=GGGCTTCCCCACTCGGTGTA;RSEQ=GATTTCGGGAGGTCGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:2,0:23,23:0.0417:2,0:20:1:27.5:1:0.49025:0:40:4:0.0426:0:1 0/0:53:0:0,0:27,26:0:2,0:23.1:1:29.4:1:1:0:48.8:25.5:1:0:0.2 -GL000220.1 129583 . T C 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53222;SOR=1.71466;LSEQ=TTTTCAGACTTTTCTCTCGG;RSEQ=CACGTGTGGCGTCCGTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:5:2,3:17,20:0.119:2,2:36.2:1:32.2:1:1:1.26772:38.4:10:0.119:0:1 0/1:37:7:4,3:14,16:0.1892:2,2:20.1:1:31.6:1:0.6928:1.51:40.7:14:0.1892:0:1.1 -GL000220.1 129667 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.50274;SOR=Inf;LSEQ=GTCCTAAGGGTCGATTTAGT;RSEQ=TCATGCCTCTTTCACCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:0:2,0:22:1:32.6:1:1:0:60:62:1:0:0.2 0/1:41:2:1,1:19,20:0.0488:2,2:42.5:1:28.5:1:1:1.05:60:4:0.0488:0:1 -GL000220.1 129701 . A C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08418;LSEQ=ACCGCCACCACCGAAGATGA;RSEQ=AGCAAAGATCGGCTAAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:1,0:7,12:0.05:2,0:14:0:33:0:0.4:0:27:2:0.05:0:1 0/1:37:2:1,1:18,17:0.0541:2,2:32:1:31.5:1:1:1.05721:60:4:0.0541:0:1 -GL000220.1 129707 . A G 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02268;SOR=0;LSEQ=ACCACCGAAGATGAAAGCAA;RSEQ=GATCGGCTAAATACCGCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:3,1:9,12:0.16:2,2:17.8:1:31.8:1:0.32174:3.79:40.5:8:0.16:0:1 0/0:37:0:0,0:19,18:0:2,0:24.1:1:30:1:1:0:57.1:74:1:0:0.3 -GL000220.1 129728 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49392;SOR=Inf;LSEQ=GATCGGCTAAATACCGCGTG;RSEQ=TCTCATCTAGAAGTGGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:0:2,0:18.7:1:30.3:1:1:0:52:58:1:0:0.3 0/1:33:2:1,1:18,13:0.0606:2,2:9.5:1:32:1:1:1.37079:60:4:0.0606:0:1 -GL000220.1 129768 . C T 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49298;SOR=Inf;LSEQ=CTTACAGATGACAGTTCTTG;RSEQ=ATGGGCAGAACGAGGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:0:2,0:28.2:1:31.4:1:1:0:45.5:32:1:0:0.3 0/1:35:2:1,1:19,14:0.0571:2,2:26:1:23:1:1:1.34517:54.5:4:0.0588:0:1.5 -GL000220.1 129790 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21698;SOR=Inf;LSEQ=TGGGCAGAACGAGGGGGACC;RSEQ=GGGACGCGGAAGCCTGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:0:2,0:23.9:1:30.2:1:1:0:44.6:86:1:0:0.2 0/1:38:2:1,1:22,14:0.0526:2,2:44.5:1:30.5:1:1:1.55221:49:4:0.0526:0:1 -GL000220.1 129795 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19937;SOR=Inf;LSEQ=AGAACGAGGGGGACCGGGGA;RSEQ=GCGGAAGCCTGCTTGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:25,19:0:2,0:23.8:1:31:1:1:0:44.2:43:1:0:0.2 0/1:36:2:1,1:21,13:0.0556:2,2:16:1:31.5:1:1:1.5932:49:4:0.0606:0:1 -GL000220.1 129915 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13995;SOR=Inf;LSEQ=ATGAAATCATCTGCACACTG;RSEQ=ACACCCCCGTCACAAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:23,23:0:2,0:27.9:1:29.4:1:1:0:53.5:45:1:0:0.1 0/1:28:2:1,1:10,16:0.0714:2,2:39.5:1:29.5:1:1:1.57:60:4:0.0714:0:1 -GL000220.1 129931 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20024;SOR=Inf;LSEQ=ACTGAACACCCCCGTCACAA;RSEQ=TTTACCTATGTCACAGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:25,25:0:2,0:27.2:1:31.1:1:1:0:56.4:24:1:0:0.2 0/1:41:2:1,1:18,21:0.0488:2,2:44:1:31.5:1:1:1.16:33:4:0.05:0:3 -GL000220.1 129947 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22051;SOR=Inf;LSEQ=ACAAGTTTACCTATGTCACA;RSEQ=TCTTGCTCATGTATGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:23,25:0:2,0:24.8:1:31.7:1:1:0:59:47:1:0:0.4 0/1:43:2:1,1:24,17:0.0465:2,2:41:1:31:1:1:1.40026:33:4:0.0476:0:3 -GL000220.1 129984 . CG C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16296;SOR=0;LSEQ=TTGAACGACAAATAAAAGTT;RSEQ=GGGGGGAGAAGAGAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:17,14:0.0606:2,0:12.5:1:32.3:1:0.49621:0:52.5:4:0.0625:0.0303:1 0/0:48:0:0,0:29,18:0:2,0:22.4:1:28.6:1:1:0:58:14.667:0.9778:0:1 -GL000220.1 129989 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.16709;SOR=0;LSEQ=CGACAAATAAAAGTTCGGGG;RSEQ=GGAGAAGAGAGGAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:20,11:0.0606:2,2:9.5:1:29.5:1:1:1.78367:60:4:0.0625:0:1.5 0/0:47:0:0,0:30,17:0:2,0:22.1:1:29.9:1:1:0:59.1:14.667:1:0:1 -GL000220.1 130016 . ACGGGGAGAGAGGGGGGA GGAGATGGG 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.52344;SOR=Inf;LSEQ=GAGAGGAGAGAGAGAGAGAG;RSEQ=GAGGGGGGGGGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,8:0:2,0:20.2:1:28.7:1:1:0:59.9:4.5:0.9:0:1.1 0/1:43:2:2,0:28,13:0.0465:2,0:13.5:1:30:1:1:0:40:4:0.0526:0.0233:2.5 -GL000220.1 130027 . GGGGGGA TGGG 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.00256;SOR=0;LSEQ=GAGAGAGAGACGGGGAGAGA;RSEQ=GAGGGGGGGGGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:2,4:13,7:0.2069:2,2:16.7:1:24.5:1:0.34783:3.52018:56.2:5:0.25:0.1379:1.2 0/0:45:0:0,0:28,16:0:2,0:19.3:1:30.4:1:1:0:56.7:88:1:0:1.5 -GL000220.1 130035 . A G 60 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=0.6556;SOR=2.71587;LSEQ=GACGGGGAGAGAGGGGGGAG;RSEQ=GGGGGGGGGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:13,6:0.0435:2,0:13:0:13:0:1:0:56:0:0:0:1 0/1:45:5:2,3:21,11:0.1111:2,2:16:1:26:1:0.34588:2.77792:56:4:0.125:0:3.2 -GL000220.1 130043 . G A 54 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.64731;SOR=2.30563;LSEQ=GAGAGGGGGGAGAGGGGGGG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:13,6:0.0455:2,0:39:0:16:0:0.35:0:60:0:0:0:3 0/1:40:4:2,2:21,13:0.1:2,2:26.8:1:27:1:1:1.59441:60:8:0.1212:0:2.5 -GL000220.1 130109 . C A 80 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.01014;SOR=0.08689;LSEQ=AGAAAGAGAAGTAAAACCAA;RSEQ=CACCACCTCCTTGACCTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:8:4,4:19,24:0.1569:2,2:29.1:1:26.9:1:1:1.26:56.4:3:0.1364:0:2.5 0/1:64:1:0,1:31,32:0.0156:2,0:2:0:25:0:1:0:40:2:0.0172:0:2 -GL000220.1 130126 . T G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50165;SOR=Inf;LSEQ=CAACCACCACCTCCTTGACC;RSEQ=GAGTCAGGGGGTTTCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:25,29:0:2,0:26.5:1:29.5:1:1:0:59.3:17:1:0:0.7 0/1:67:2:1,1:30,35:0.0299:2,2:29.5:1:28:1:1:1.16:60:4:0.0313:0:2 -GL000220.1 130131 . CA C 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42632;SOR=0.44957;LSEQ=ACCACCTCCTTGACCTGAGT;RSEQ=GGGGGTTTCTGGCCTTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:4:2,2:25,25:0.0741:2,2:33:1:31.5:1:1:1:57.8:8:0.0784:0:2.5 0/1:58:2:1,1:27,29:0.0345:2,2:22:1:25:1:1:1.07:30.5:4:0.0364:0:2.5 -GL000220.1 130162 . C G 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09888;LSEQ=TGGCCTTTTGGGAGAACGTT;RSEQ=AGCGACAATGCAGTATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:3,2:19,25:0.102:2,2:23:1:32.8:1:0.64567:1.95:49.6:10:0.1064:0:2 0/1:45:5:3,2:20,20:0.1111:2,2:28.8:1:26.2:1:1:1.49:28.4:4:0.0909:0:1.8 -GL000220.1 130174 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23217;SOR=0;LSEQ=AGAACGTTCAGCGACAATGC;RSEQ=GTATTTGGGCCCGTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:21,24:0.0426:2,2:26.5:1:29:1:1:1.14:60:4:0.0455:0:1 0/0:50:0:0,0:23,27:0:2,0:24.6:1:29.5:1:1:0:56.5:24:1:0:0.3 -GL000220.1 130190 . C CT 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.97699;LSEQ=ATGCAGTATTTGGGCCCGTT;RSEQ=TTTTTTTCTTCTTCTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:3:2,1:17,25:0.0667:2,2:26.3:1:30.7:1:0.56483:2.87:39:6:0.0667:0:0.3 0/1:46:3:1,2:19,24:0.0652:2,2:28.7:1:29.7:1:1:1.56818:27.3:6:0.0682:0:2 -GL000220.1 130195 . T TTC 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.59846;SOR=0.43452;LSEQ=GTATTTGGGCCCGTTCTTTT;RSEQ=TTCTTCTTCTTCTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:14,23:0.0513:2,2:20:1:30.5:1:1:1.62:48.5:4:0.0513:0:0.5 0/1:44:1:1,0:16,26:0.0227:2,0:37:0:31:0:0.39535:0:39:2:0.0233:0:1 -GL000220.1 130216 . CT C 82 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.80415;LSEQ=TTCTTCTTCTTCTTTTCTTT;RSEQ=TTTTTTTTGGACTGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:3,3:11,14:0.1935:2,2:31.5:1:31.8:1:1:1.26:44.7:12:0.2:0:0.2 0/1:31:5:0,5:13,13:0.1613:2,0:20.6:1:30.8:1:0.058:0:47.6:10:0.1613:0:0.2 -GL000220.1 130339 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49059;SOR=Inf;LSEQ=TTCTTCGGTAGCTGGGATTA;RSEQ=AGGTGCGCACCATGACGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:9,11:0:2,0:20.1:1:31.1:1:1:0:53.5:19:1:0:0.4 0/1:23:2:1,1:9,12:0.087:2,2:26.5:1:31.5:1:1:1.32:60:4:0.087:0:1 -GL000220.1 130356 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49754;SOR=Inf;LSEQ=TTACAGGTGCGCACCATGAC;RSEQ=GCCGGCTCATCGTTCTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:27.3:1:30.8:1:1:0:59.8:24:1:0:0 0/1:17:2:1,1:5,10:0.1176:2,2:12.5:1:30:1:1:1.91:60:4:0.1176:0:1 -GL000220.1 130521 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50639;SOR=0;LSEQ=CTTTAAAAGCGCGGGCCCTG;RSEQ=CACCTTTCGCTGCGGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:11,12:0.08:2,2:20:1:27.5:1:1:1.09:60:4:0.0833:0:1 0/0:17:0:0,0:9,8:0:2,0:19.9:1:30.8:1:1:0:55.8:34:1:0:0 -GL000220.1 130652 . C T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.52833;LSEQ=TCCGTCCCCCCACCTCCCCG;RSEQ=GCACATAATAACTAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:10,14:0.0769:2,2:13:1:29.5:1:1:1.38:39:4:0.08:0:1 0/1:24:1:0,1:12,11:0.0417:2,0:14:0:32:0:1:0:49:2:0.0435:0:1 -GL000220.1 130660 . ATAAC A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=6.000;MSILEN=4;SSF=0.1836;SOR=0;LSEQ=CCCACCTCCCCGCGCACATA;RSEQ=TAACTAACTAACTAACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,12:0.087:2,2:36.5:1:30:1:1:1.32:60:4:0.087:0:0 0/0:30:0:0,0:14,14:0:2,0:17.6:1:28.7:1:1:0:53.2:56:0.9333:0:0.1 -GL000220.1 130669 . T TA 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=4;SSF=0.20202;SOR=0;LSEQ=CCGCGCACATAATAACTAAC;RSEQ=AACTAACTAACTAACTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:11,12:0.08:2,2:9.5:1:29.7:1:1:1.09:60:4:0.08:0.04:0 0/0:30:0:0,0:17,13:0:2,0:17.9:1:29.4:1:1:0:54.7:60:1:0:0.2 -GL000220.1 131027 . A C 52 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21569;SOR=Inf;LSEQ=GATAAATACGTACATAAATA;RSEQ=ATACACACATACATACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:26.5:1:29:1:1:0:47.4:16:1:0:0.9 0/1:10:3:3,0:4,3:0.3:2,0:30.3:1:33:0:0.475:0:53.3:6:0.3:0:3 -GL000220.1 131033 . C T 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.31373;SOR=4.29556;LSEQ=TACGTACATAAATAAATACA;RSEQ=ACATACATACATACATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:4,3:0.125:2,0:10:0:33:0:1:0:40:2:0.125:0:3 0/1:10:4:2,2:5,1:0.4:2,2:15:1:28.8:1:0.5:4.17095:51.3:8:0.4:0:2.8 -GL000220.1 131070 . A C 75 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=9.000;MSILEN=4;SSF=0.68082;SOR=1.81546;LSEQ=ACATACATACATACATACAT;RSEQ=CATACAGATATACAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,4:0.125:2,2:38:1:32:1:1:1.89743:33:4:0.1333:0:1.5 0/1:24:5:3,2:11,8:0.2083:2,2:29.4:1:32.6:1:1:1.09:47.4:10:0.2083:0:1.6 -GL000220.1 131092 . AAAAAAG CA 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.26427;SOR=0.24079;LSEQ=ATACAGATATACAAGAAAGA;RSEQ=AAAAGAAAAGAAAGAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:0.1333:2,2:13.5:1:31:1:1:1.54914:40:4:0.1333:0.0667:3 0/1:29:1:0,1:16,12:0.0345:2,0:36:0:32:0:0.44828:0:45:2:0.0345:0:3 -GL000220.1 131154 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49514;SOR=0;LSEQ=TGTATTGCTACTGGGCTAGG;RSEQ=CCTTCTCTCTGTCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:20,12:0.0588:2,2:20:1:30.5:1:1:1.64076:33.5:4:0.0588:0:3 0/0:29:0:0,0:19,10:0:2,0:21.7:1:30.9:1:1:0:45.8:28:1:0:0.1 -GL000220.1 131167 . CTGTT C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.50834;SOR=0;LSEQ=GGCTAGGGCCTTCTCTCTGT;RSEQ=TCTCTCTGTTCGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:2,0:23,16:0.05:2,0:9:1:33:1:0.5122:0:39.5:4:0.0513:0.025:1.5 0/0:28:0:0,0:18,10:0:2,0:25.4:1:30.2:1:1:0:45.6:56:1:0:0.1 -GL000220.1 131171 . T TTCTCTCTGTC 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=4.000;MSILEN=2;SSF=0.51304;SOR=0;LSEQ=AGGGCCTTCTCTCTGTCTGT;RSEQ=TCTCTCTGTTCGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:22,16:0.0476:2,2:24:1:32:1:1:1.36391:33.5:4:0.05:0.0238:3 0/0:28:0:0,0:18,10:0:2,0:25.8:1:29.6:1:1:0:46.3:56:1:0:0.1 -GL000220.1 131183 . G A 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15551;SOR=0;LSEQ=CTGTCTGTTTCTCTCTGTTC;RSEQ=TCTCTGTCTTTCTCTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:4:3,1:29,21:0.0741:2,2:25.5:1:29.8:1:0.63771:2.14:36.3:8:0.0741:0:1.8 0/0:34:0:0,0:21,12:0:2,0:23.6:1:29.6:1:1:0:49.8:66:0.9706:0:0.1 -GL000220.1 131211 . C CTCTG 104 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=7.000;MSILEN=4;SSF=0.81499;SOR=1.18981;LSEQ=CTTTCTCTCTGTGTCTCTTT;RSEQ=TCTGTCTGTCTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:11:5,6:37,19:0.1642:2,2:28.1:1:32.6:1:0.3063:2.30554:60:22:0.1642:0.0299:0.4 0/1:58:11:6,5:26,21:0.1897:2,2:21.6:1:30.3:1:1:1.0312:60:22:0.1897:0.0517:0.4 -GL000220.1 131247 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23375;SOR=Inf;LSEQ=GTCTGTCTGTCTCTTTCTTT;RSEQ=TTTCTGTCTCTGTCTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:48,38:0:2,0:23.1:1:32.1:1:1:0:58.8:172:1:0:0.2 0/1:81:2:1,1:38,41:0.0247:2,2:5:0:32:0:1:1.08:60:4:0.025:0:0.5 -GL000220.1 131280 . TCTCTGCCTGTCTCACTGTGTCTGTCT CCTGTCTGTTTCTCTCTCTCTCTCTCTCTCTGTCTCCCTCTCTTGCTCTC 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.12354;SOR=Inf;LSEQ=TCTTTGTCCCTCTCTCTCCC;RSEQ=TCTATCTTACTCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:55,36:0:2,0:24.5:1:31.7:1:1:0:58.4:182:1:0:0.2 0/1:102:4:2,2:51,47:0.0392:2,2:23.5:1:28.4:1:1:1.08422:59.3:8:0.0392:0.0392:0.3 -GL000220.1 131285 . G A 26 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.9497;LSEQ=GTCCCTCTCTCTCCCTCTCT;RSEQ=CCTGTCTCACTGTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:1,0:50,40:0.011:2,0:1:0:26:0:1:0:60:2:0.0111:0:1 0/1:94:2:2,0:48,43:0.0213:2,0:25.5:1:26.5:1:0.49743:0:60:4:0.022:0:1 -GL000220.1 131292 . TCACTGTGTCTGTCTTCTATCTTACTCTCTTTCTCTCCCC T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49904;SOR=Inf;LSEQ=TCTCTCCCTCTCTGCCTGTC;RSEQ=GTCTGTCTCTCTCTCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:49,40:0:2,0:24.7:1:31.8:1:1:0:58.6:88:1:0:0.3 0/1:100:2:1,1:53,45:0.02:2,2:12.5:1:26.3:1:1:1.17584:56.5:4:0.0206:0.02:2 -GL000220.1 131305 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=GCCTGTCTCACTGTGTCTGT;RSEQ=TTCTATCTTACTCTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:47,43:0:2,0:25:1:31.8:1:1:0:58.2:180:1:0:0.3 0/1:99:2:1,1:50,45:0.0202:2,2:24:1:30.5:1:1:1.1099:56:4:0.0213:0:3 -GL000220.1 131310 . A G 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58564;SOR=0.69487;LSEQ=TCTCACTGTGTCTGTCTTCT;RSEQ=TCTTACTCTCTTTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:8:4,4:44,42:0.0851:2,2:23.8:1:32:1:1:1.04712:45.9:16:0.0851:0:2.4 0/1:99:6:4,2:48,43:0.0606:2,2:21.3:1:29.3:1:0.68265:1.78:52.8:12:0.0625:0:2.2 -GL000220.1 131327 . TC T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.20019;SOR=0;LSEQ=TCTATCTTACTCTCTTTCTC;RSEQ=CCCGTCTGTCTCTCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:46,44:0.0217:2,2:21.5:1:31.5:1:1:1.04497:60:4:0.0217:0:0 0/0:113:0:0,0:57,54:0:2,0:23.3:1:30.5:1:1:0:58.2:36:1:0:0.5 -GL000220.1 131331 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50571;SOR=Inf;LSEQ=TCTTACTCTCTTTCTCTCCC;RSEQ=GTCTGTCTCTCTCTCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:46,47:0:2,0:25.7:1:30.1:1:1:0:57.9:186:1:0:0.3 0/1:120:2:1,1:61,55:0.0167:2,2:22.5:1:29:1:1:1.10812:60:4:0.0171:0:1 -GL000220.1 131332 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50736;SOR=Inf;LSEQ=CTTACTCTCTTTCTCTCCCC;RSEQ=TCTGTCTCTCTCTCACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:46,47:0:2,0:25.8:1:30.6:1:1:0:57.9:186:1:0:0.3 0/1:123:2:1,1:63,57:0.0163:2,2:9.5:1:28:1:1:1.10435:60:4:0.0168:0:1 -GL000220.1 131347 . A T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.61956;SOR=0.75572;LSEQ=TCCCCGTCTGTCTCTCTCTC;RSEQ=CTCCCTCCCTGTCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:9:4,5:45,45:0.0909:2,2:30.3:1:30.9:1:1:1.24719:45.2:18:0.0947:0:2.3 0/1:114:8:4,4:55,51:0.0702:2,2:35.6:1:30:1:1:1.0777:49.1:16:0.0741:0:2.3 -GL000220.1 131358 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.49818;SOR=Inf;LSEQ=CTCTCTCTCACTCCCTCCCT;RSEQ=TCTGTTTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:49,54:0:2,0:24.3:1:32.2:1:1:0:59.1:206:1:0:0.2 0/1:110:2:1,1:54,54:0.0182:2,2:9:0:31:1:1:1:50.5:4:0.0187:0:3 -GL000220.1 131364 . TTC T 139 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.29934;SOR=1.47;LSEQ=CTCACTCCCTCCCTGTCTGT;RSEQ=TCTCTCTCTCTCTTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:16:7,9:39,42:0.1633:2,2:25.4:1:30.9:1:0.79049:1.1917:55.3:32:0.1649:0.0204:0.9 0/1:112:25:12,13:45,43:0.2232:2,2:27.3:1:30.1:1:0.82372:1.13246:56.2:50:0.2273:0.0446:1.2 -GL000220.1 131386 . CTGTT C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5007;SOR=Inf;LSEQ=CTCTCTCTCTCTCTTTCTGT;RSEQ=TCTGTCTCTCTCTGTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:46,46:0:2,0:26.5:1:30.8:1:1:0:59.2:184:1:0:0.2 0/1:108:2:1,1:53,53:0.0185:2,2:25.5:1:31:1:1:1:60:4:0.0187:0:2.5 -GL000220.1 131388 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20703;SOR=0;LSEQ=CTCTCTCTCTCTTTCTGTCT;RSEQ=TTTCTGTCTCTCTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:43,44:0.0225:2,2:25.5:1:29.5:1:1:1.02:60:4:0.0225:0:1 0/0:106:0:0,0:52,51:0:2,0:25.3:1:31.4:1:1:0:59.2:102:0.9903:0:0.4 -GL000220.1 131395 . TCTCTCTCTGTCTGC T 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=2.000;MSILEN=1;SSF=0.51626;SOR=1.68504;LSEQ=TCTCTTTCTGTCTGTTTCTG;RSEQ=CTCTCTCTTTCTCTATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:1,2:40,47:0.0333:2,2:21.7:1:31.3:1:1:1.6925:51.7:6:0.0333:0.0111:1 0/1:109:6:2,4:49,54:0.055:2,2:8.2:1:28.3:1:0.68268:1.80528:56.5:6:0.0516:0.0472:2.5 -GL000220.1 131398 . C T 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=2;SSF=1;SOR=1.79268;LSEQ=CTTTCTGTCTGTTTCTGTCT;RSEQ=TCTCTGTCTGCCTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:0,1:41,46:0.0111:2,0:1:0:25:0:1:0:60:2:0.0114:0:2 0/1:101:2:1,1:48,51:0.0198:2,2:18.5:1:29:1:1:1.06:60:4:0.02:0:2.5 -GL000220.1 131399 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=2;SSF=0.49874;SOR=Inf;LSEQ=TTTCTGTCTGTTTCTGTCTC;RSEQ=CTCTGTCTGCCTCTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:43,47:0:2,0:25.1:1:30.5:1:1:0:59.2:180:1:0:0.2 0/1:102:2:1,1:49,51:0.0196:2,2:10.5:1:27:1:1:1.04:60:4:0.0202:0:1.5 -GL000220.1 131401 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.4996;SOR=Inf;LSEQ=TCTGTCTGTTTCTGTCTCTC;RSEQ=CTGTCTGCCTCTCTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:44,48:0:2,0:24.5:1:30.5:1:1:0:59.2:184:1:0:0.2 0/1:107:2:1,1:51,54:0.0187:2,2:31.5:1:30.5:1:1:1.06:60:4:0.0192:0:1.5 -GL000220.1 131409 . C T 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03089;SOR=Inf;LSEQ=TTTCTGTCTCTCTCTGTCTG;RSEQ=CTCTCTCTTTCTCTATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:45,44:0:2,0:24.4:1:30.9:1:1:0:59.9:28.667:1:0:0.2 0/1:105:6:2,4:49,50:0.0571:2,2:8.2:1:28.3:1:0.67903:1.94789:56.5:12:0.0594:0:2.5 -GL000220.1 131414 . C G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.24619;SOR=Inf;LSEQ=GTCTCTCTCTGTCTGCCTCT;RSEQ=TCTTTCTCTATCTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:52,46:0:2,0:22.6:1:31.4:1:1:0:59.9:97:1:0:0.2 0/1:99:3:1,2:46,50:0.0303:2,2:8.7:1:30.7:1:1:1.82914:53.7:6:0.0303:0:2.3 -GL000220.1 131450 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.49746;SOR=0;LSEQ=CTCTTTCTCTGTCTGTCTGC;RSEQ=CCTCTCTTTCTTTTTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:49,47:0.0204:2,2:18.5:1:30.5:1:1:1.04212:60:4:0.0204:0:1.5 0/0:96:0:0,0:48,48:0:2,0:23.1:1:30:1:1:0:59.7:47:1:0:0.3 -GL000220.1 131474 . C G 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.62128;SOR=3.01533;LSEQ=CTCTTTCTTTTTCTGTGTCT;RSEQ=TCTGTCTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:1:0,1:51,49:0.0099:2,0:3:0:29:0:0.49505:0:60:2:0.01:0:3 0/1:102:3:1,2:49,49:0.0294:2,2:5:1:30:1:1:1.9868:60:6:0.0297:0:2.7 -GL000220.1 131478 . G C 38 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.6813;SOR=0.64824;LSEQ=TTCTTTTTCTGTGTCTCTCT;RSEQ=TCTGTCTCTCTCTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:3:1,2:49,49:0.0297:2,2:7.7:1:24:1:1:1.9868:47.3:2:0.0206:0:4.7 0/1:103:2:1,1:49,52:0.0194:2,2:10:0:33:1:1:1.06:60:4:0.02:0:3 -GL000220.1 131482 . GTC G 61 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.717;SOR=0.71333;LSEQ=TTTTCTGTGTCTCTCTGTCT;RSEQ=TCTCTCTCTCTCTGTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:4:1,3:46,46:0.0408:2,2:5.3:1:30.8:1:0.61732:2.96876:58.8:8:0.0417:0.0306:0.8 0/1:102:3:1,2:51,48:0.0294:2,2:35.7:1:32.3:1:0.61386:2.10984:60:6:0.03:0:0.3 -GL000220.1 131497 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49741;SOR=Inf;LSEQ=TGTCTGTCTCTCTCTCTCTC;RSEQ=GTGCCTATCTTCTGTCTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:48,49:0:2,0:22.2:1:30.2:1:1:0:58.7:96:1:0:0.4 0/1:97:2:1,1:46,48:0.0206:2,2:27.5:1:28:1:1:1.04:60:4:0.0208:0:1 -GL000220.1 131537 . G GTTTCTCTCTCTCTCTCTTTCTGTCTGTT 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0919;SOR=Inf;LSEQ=CTCTCTTTCTCTGCCTGTCT;RSEQ=TCTGTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:55,51:0:2,0:26.1:1:31.5:1:1:0:59.1:20.2:1:0:0.5 0/1:89:3:1,2:41,44:0.0337:2,2:14:1:27.5:1:1:1.851:60:6:0.0353:0.0337:0.3 -GL000220.1 131545 . C CTCTCCCTGTCTCTCTTTCTCTATATCTGTCTTTCTCTCTCTG 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=2;SSF=0.10076;SOR=Inf;LSEQ=CTCTGCCTGTCTGTCTGTCT;RSEQ=TCTCTGTCTCTCCCTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:54,52:0:2,0:26.6:1:31.9:1:1:0:59.1:34.333:1:0:0.4 0/1:95:3:2,1:44,46:0.0316:2,2:20:1:28.1:1:0.6168:2.07:60:6:0.0323:0.0316:0.3 -GL000220.1 131565 . T C 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.32614;SOR=3.79269;LSEQ=CTCTCTGTCTCTCCCTCCCT;RSEQ=TCTGCTTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:1:0,1:59,58:0.0085:2,0:49:0:29:0:1:0:60:2:0.0089:0:4 0/1:95:3:1,2:46,44:0.0316:2,2:30.7:1:24.7:1:0.6168:2.07492:60:2:0.0238:0:1.7 -GL000220.1 131594 . C T 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.69559;SOR=0.62235;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CCCCTCCCTGTCTGTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:4:1,3:61,57:0.0328:2,2:18.3:1:31.3:1:0.36058:3.18234:60:8:0.0333:0:2 0/1:97:2:1,1:47,45:0.0206:2,2:12.5:1:29.5:1:1:1.04398:60:4:0.0215:0:1 -GL000220.1 131614 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.2291;SOR=Inf;LSEQ=CCCCCTCCCTGTCTGTTTCT;RSEQ=CTGTCTCCCTCTCTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:59,57:0:2,0:23.3:1:30.1:1:1:0:59.8:22.2:1:0:0.4 0/1:107:2:1,1:56,48:0.0187:2,2:13.5:1:30:1:1:1.16496:60:4:0.0189:0:0.5 -GL000220.1 131616 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49856;SOR=0;LSEQ=CCCTCCCTGTCTGTTTCTCT;RSEQ=TGTCTCCCTCTCTTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:56,57:0.0174:2,2:21.5:1:30:1:1:1.02:57.5:4:0.0179:0:1 0/0:106:0:0,0:56,49:0:2,0:23.9:1:31.4:1:1:0:59.8:104:1:0:0.3 -GL000220.1 131654 . CTCTG C 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.24321;SOR=1.88742;LSEQ=GTCTGTTTCTCACTGTCTCT;RSEQ=TCTGTCTGTTTCATTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:7:2,5:56,50:0.0614:2,2:30.6:1:32.7:1:0.26311:2.77576:60:14:0.0625:0:0 0/1:118:13:6,7:56,49:0.1102:2,2:22.8:1:31.8:1:0.77047:1.33007:57.6:26:0.1111:0:0.2 -GL000220.1 131665 . T A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.23213;SOR=0;LSEQ=ACTGTCTCTCTCTGTCTGTC;RSEQ=GTTTCATTCTCTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:57,54:0.0177:2,2:5:0:32.5:1:1:1.05507:60:4:0.0182:0:1 0/0:121:0:0,0:66,55:0:2,0:24:1:30.5:1:1:0:59.4:242:1:0:0.3 -GL000220.1 131681 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=6;SSF=0.49843;SOR=Inf;LSEQ=TGTCTGTTTCATTCTCTCTG;RSEQ=CTCTGTCTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:60,51:0:2,0:24.7:1:29.6:1:1:0:60:54.5:0.9909:0:0.2 0/1:120:2:1,1:61,57:0.0167:2,2:5.5:1:30:1:1:1.06954:60:4:0.0167:0:1.5 -GL000220.1 131686 . GTCTCTGTC G 62 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=7.000;MSILEN=2;SSF=0.12164;SOR=Inf;LSEQ=GTTTCATTCTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:59,52:0:2,0:25.1:1:29.4:1:1:0:60:36:1:0:0.2 0/1:112:4:3,1:54,54:0.0357:2,2:30.3:1:31.3:1:0.6184:2.97:59.8:8:0.0357:0.0179:0.8 -GL000220.1 131692 . GTC G 121 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.10053;SOR=0.41408;LSEQ=TTCTCTCTGTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:14:10,4:54,47:0.1197:2,2:30.5:1:31.8:1:0.25816:2.16:60:28:0.1207:0.0171:0.4 0/1:113:6:2,4:55,50:0.0531:2,2:35.3:1:31.5:1:0.42982:2.18486:60:12:0.0545:0:0 -GL000220.1 131700 . C CACTGTGTCTGTCTCTCTCTTTCCT 27 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.24037;SOR=Inf;LSEQ=GTCTCTGTCTCTGTCTCTCT;RSEQ=TCTCTCTGTCTCTCCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:67,50:0:2,0:25.3:1:31.4:1:1:0:60:116:0.9915:0:0.2 0/1:114:2:1,1:55,56:0.0175:2,2:19.5:1:27.9:1:1:1.02:44.5:4:0.0182:0.0175:0.5 -GL000220.1 131726 . G C 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20451;SOR=Inf;LSEQ=CTGTCTCTCCCTCTCTGTGT;RSEQ=TATCTTTTGTCTTACTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:69,60:0:2,0:23:1:31.4:1:1:0:60:20.5:1:0:0.2 0/1:107:2:1,1:51,50:0.0187:2,2:7:0:33.5:1:1:1.01981:60:4:0.0192:0:4.5 -GL000220.1 131728 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.20553;SOR=Inf;LSEQ=GTCTCTCCCTCTCTGTGTGT;RSEQ=TCTTTTGTCTTACTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:68,58:0:2,0:23.5:1:28.3:1:1:0:60:20:1:0:0.2 0/1:105:2:1,1:51,50:0.019:2,2:9:0:33.5:1:1:1.01981:60:4:0.0198:0:4.5 -GL000220.1 131733 . T C 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04624;SOR=Inf;LSEQ=TCCCTCTCTGTGTGTATCTT;RSEQ=TGTCTTACTCTCCTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:65,57:0:2,0:24.4:1:30.1:1:1:0:60:60:1:0:0.2 0/1:107:4:2,2:48,53:0.0374:2,2:8.3:1:30.8:1:1:1.10:60:8:0.0381:0:2.8 -GL000220.1 131773 . GTC G 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.62442;SOR=2.70172;LSEQ=GCCTGTCCGTCTGTCTGTCT;RSEQ=TCTCTCTCTCCCTGTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:1:0,1:57,56:0.0088:2,0:39:0:28:0:1:0:60:2:0.0089:0:1 0/1:128:3:1,2:58,65:0.0234:2,2:20.3:1:30.7:1:1:1.77676:60:6:0.0238:0:0 -GL000220.1 131841 . G C 90 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.01437;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTGTCTTTCTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:58,61:0:2,0:27.1:1:29.9:1:1:0:59.5:6.933:0.9905:0:0.5 0/1:125:7:2,5:58,59:0.056:2,2:17.3:1:32.3:1:0.44126:2.44097:55.4:14:0.0583:0:3 -GL000220.1 131847 . G C 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=6;SSF=0.11319;SOR=Inf;LSEQ=CTCTCTCTCTCTCTGTCTCT;RSEQ=TCTTTCTCTGTCTGTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:64,63:0:2,0:25.7:1:30.9:1:1:0:59.6:13.111:1:0:0.5 0/1:120:3:1,2:57,58:0.025:2,2:19.3:1:31:1:1:1.9547:54.3:6:0.0259:0:4.7 -GL000220.1 131851 . T C 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.62199;SOR=3.03659;LSEQ=CTCTCTCTCTGTCTCTGTCT;RSEQ=TCTCTGTCTGTCCCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:1:1,0:60,64:0.0079:2,0:41:0:17:0:0.488:0:60:0:0:0:2 0/1:126:3:1,2:58,62:0.0238:2,2:16.3:1:30.7:1:1:1.86183:60:6:0.0254:0:3.7 -GL000220.1 131877 . G C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.4995;SOR=Inf;LSEQ=GTCTGTCCCTTTCTCTGTCT;RSEQ=TCTGCCTCTCTCTTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:67,60:0:2,0:24.3:1:31.1:1:1:0:59.5:14.875:1:0:0.4 0/1:141:2:1,1:70,68:0.0142:2,2:5:0:30.5:1:1:1.02921:60:4:0.0144:0:0 -GL000220.1 131882 . C T 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.44804;SOR=2.41687;LSEQ=TCCCTTTCTCTGTCTGTCTG;RSEQ=CTCTCTCTTTCTCTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:68,60:0.0154:2,2:5:0:30:1:1:1.13224:45:4:0.0169:0:0 0/1:137:5:4,1:68,64:0.0365:2,2:14.2:1:25.2:1:0.36906:3.73:56.4:4:0.0315:0:1.8 -GL000220.1 131891 . T C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24959;SOR=Inf;LSEQ=CTGTCTGTCTGCCTCTCTCT;RSEQ=TCTCTTTCTGTGTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:64,59:0:2,0:24.3:1:29.4:1:1:0:59.3:14.375:1:0:0.5 0/1:139:3:2,1:70,65:0.0216:2,2:8.3:1:25.3:1:1:1.85:48:2:0.0149:0:3 -GL000220.1 131893 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21397;SOR=0;LSEQ=GTCTGTCTGCCTCTCTCTTT;RSEQ=TCTTTCTGTGTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:62,57:0.0165:2,2:6:0:32:0:1:1.08695:60:4:0.0168:0:2.5 0/0:140:0:0,0:74,66:0:2,0:23:1:31.2:1:1:0:58.7:45.667:1:0:0.3 -GL000220.1 131939 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50332;SOR=Inf;LSEQ=CTCTGTGCCTATCTTCTGTC;RSEQ=TACTCTCTTTCTCTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:52,56:0:2,0:23.8:1:30.4:1:1:0:59.3:107:1:0:0.3 0/1:133:2:1,1:62,67:0.015:2,2:42.5:1:31.5:1:1:1.08:60:4:0.015:0:1 -GL000220.1 131962 . A G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63749;SOR=0.76645;LSEQ=CTCTCTTTCTCTGCCTGTCT;RSEQ=TCTGTCTGTCTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:10:6,4:53,61:0.0806:2,2:8.1:1:32.6:1:0.5162:1.72:42.4:20:0.0826:0:1.2 0/1:143:9:5,4:66,67:0.0629:2,2:8.2:1:31.3:1:1:1.27:42.9:18:0.0652:0:1 -GL000220.1 131966 . GTCTGTCTCTC G 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=4.000;MSILEN=2;SSF=0.85286;SOR=1.08728;LSEQ=CTTTCTCTGCCTGTCTATCT;RSEQ=TCTGTCTCTCTCCCTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:15:7,8:55,64:0.1119:2,2:22.4:1:31.1:1:1:1.02:59.4:30:0.1136:0.0373:0.1 0/1:141:17:7,10:64,60:0.1206:2,2:27.4:1:31.4:1:0.45008:1.51927:60:34:0.1232:0.0142:0.3 -GL000220.1 131969 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.22135;SOR=0;LSEQ=TCTCTGCCTGTCTATCTGTC;RSEQ=GTCTCTCTCTGTCTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:50,60:0.0161:2,2:33:1:30:1:1:1.20:60:4:0.0179:0:1 0/0:139:0:0,0:65,59:0:2,0:23.8:1:30.2:1:1:0:57.8:30:1:0:0.3 -GL000220.1 132002 . T TTC 98 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.79887;SOR=0.80807;LSEQ=CTCTCTCCCTGCCTTTCTGT;RSEQ=TCTCTCTCTCTCCCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:9:6,3:60,76:0.0621:2,2:31:1:31:1:0.30062:2.52:41.7:18:0.0625:0.0069:0.8 0/1:138:7:3,4:60,70:0.0507:2,2:27:1:29.4:1:1:1.14175:47:14:0.0515:0.0072:0.7 -GL000220.1 132003 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=6.000;MSILEN=2;SSF=0.24029;SOR=Inf;LSEQ=TCTCTCCCTGCCTTTCTGTT;RSEQ=CTCTCTCTCTCCCTCTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:65,78:0:2,0:27:1:30.3:1:1:0:57.6:70.5:1:0:0.3 0/1:138:2:1,1:63,73:0.0145:2,2:18:0:32:1:1:1.16:60:4:0.0146:0:1.5 -GL000220.1 132056 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.24003;SOR=Inf;LSEQ=TTCTCTCTTTCTCTCTGTTT;RSEQ=TCTGTCTCTCTCTGTCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:55,59:0:2,0:23.8:1:31:1:1:0:56.8:37:1:0:0.4 0/1:110:2:2,0:48,60:0.0182:2,0:20.5:1:26.5:1:0.20434:0:60:4:0.0182:0:1 -GL000220.1 132060 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49776;SOR=Inf;LSEQ=CTCTTTCTCTCTGTTTCTCT;RSEQ=TCTCTCTCTGTCCGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:55,56:0:2,0:23.8:1:31.7:1:1:0:57.1:222:0.9911:0:0.3 0/1:112:2:1,1:48,62:0.0179:2,2:6.5:1:29.5:1:1:1.29:36.5:4:0.0185:0:4 -GL000220.1 132062 . C G 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.24443;SOR=Inf;LSEQ=CTTTCTCTCTGTTTCTCTGT;RSEQ=TCTCTCTGTCCGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:56,57:0:2,0:23.3:1:30.7:1:1:0:57.2:17.833:1:0:0.3 0/1:111:2:2,0:47,62:0.018:2,0:5.5:1:31:1:0.19263:0:43:4:0.0185:0:4 -GL000220.1 132068 . C G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0.88084;LSEQ=CTCTGTTTCTCTGTCTCTCT;RSEQ=TGTCCGTCTCTGTCTTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:9:5,4:49,54:0.0804:2,2:28.9:1:31.2:1:0.73627:1.37:42.8:18:0.0811:0:1.9 0/1:112:8:2,6:47,54:0.0714:2,2:33:1:30.1:1:0.29142:2.58994:41.9:7:0.0642:0:1.9 -GL000220.1 132074 . G A 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16647;SOR=2.53878;LSEQ=TTCTCTGTCTCTCTCTGTCC;RSEQ=TCTCTGTCTTTTTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:4:0,4:51,53:0.037:2,0:30.5:1:31:1:0.12034:0:55.5:8:0.0374:0:1 0/1:112:10:6,4:46,55:0.0893:2,2:27.4:1:28.2:1:0.51088:1.78:53.7:9:0.0833:0:1.8 -GL000220.1 132081 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50135;SOR=Inf;LSEQ=TCTCTCTCTGTCCGTCTCTG;RSEQ=CTTTTTCTGTCTGTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:48,55:0:2,0:25:1:30.1:1:1:0:57.7:206:1:0:0.3 0/1:122:2:1,1:55,65:0.0164:2,2:10.5:1:32:1:1:1.18:60:4:0.0165:0:1 -GL000220.1 132084 . TTTTCTGTCTGTCTGTCTCTCTCTTTC A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50126;SOR=Inf;LSEQ=CTCTCTGTCCGTCTCTGTCT;RSEQ=TTTCTGTCGTCTGTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:46,59:0:2,0:24.6:1:30:1:1:0:57.7:104:1:0:0.3 0/1:124:2:1,1:56,66:0.0161:2,2:9.5:1:28.3:1:1:1.18:60:4:0.0165:0.0161:0 -GL000220.1 132086 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.50057;SOR=Inf;LSEQ=CTCTGTCCGTCTCTGTCTTT;RSEQ=TCTGTCTGTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:46,60:0:2,0:24.4:1:30:1:1:0:57.6:52:1:0:0.3 0/1:123:2:0,2:55,63:0.0163:2,0:9.5:1:30:1:0.4993:0:50:4:0.0177:0:2 -GL000220.1 132099 . T C 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.40566;SOR=0.56393;LSEQ=TGTCTTTTTCTGTCTGTCTG;RSEQ=CTCTCTCTTTCTTTCTGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:8:2,6:44,49:0.0792:2,2:25.1:1:29.3:1:0.28537:2.66987:41.1:7:0.0707:0:3 0/1:130:6:1,5:61,60:0.0462:2,2:21.2:1:32.5:1:0.2083:5.02828:37:12:0.0476:0:2.2 -GL000220.1 132108 . T C 63 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.702;SOR=1.85639;LSEQ=CTGTCTGTCTGTCTCTCTCT;RSEQ=TCTTTCTGTCGTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:0,2:46,53:0.0198:2,0:31:1:15.5:1:0.49901:0:60:0:0:0:2.5 0/1:138:5:2,3:63,68:0.0362:2,2:11.6:1:27.4:1:1:1.38639:60:4:0.0301:0:2.8 -GL000220.1 132112 . T C 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14128;SOR=Inf;LSEQ=CTGTCTGTCTCTCTCTTTCT;RSEQ=TCTGTCGTCTGTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:49,56:0:2,0:23.6:1:30.1:1:1:0:58.3:51.5:1:0:0.4 0/1:145:4:2,2:67,74:0.0276:2,2:17.8:1:31:1:1:1.10:60:8:0.0294:0:3.3 -GL000220.1 132115 . TGTC T 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=1;SOR=1.16208;LSEQ=TCTGTCTCTCTCTTTCTTTC;RSEQ=GTCTGTCTCTGTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:0,6:50,49:0.0566:2,0:23:1:33:1:0.02789:0:40.2:12:0.0588:0:2.7 0/1:138:9:2,7:63,65:0.0652:2,2:16.4:1:31.5:1:0.17034:3.36533:42.2:18:0.0692:0.029:1.9 -GL000220.1 132116 . GTCGTCTGTC G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=6;SSF=0.19524;SOR=0;LSEQ=CTGTCTCTCTCTTTCTTTCT;RSEQ=TCTGTCTCTGTCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:2,0:47,49:0.019:2,0:13:1:32.6:1:0.49485:0:35.5:4:0.0213:0.0095:0.5 0/0:132:0:0,0:60,67:0:2,0:23.2:1:28.7:1:1:0:58.4:41.333:1:0:0.6 -GL000220.1 132119 . GTCTGTC G 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=4.000;MSILEN=6;SSF=0.06145;SOR=2.37907;LSEQ=TCTCTCTCTTTCTTTCTGTC;RSEQ=TCTGTCTCTGTCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:7:3,4:45,48:0.0686:2,2:20.9:1:31.9:1:1:1.24723:49.6:14:0.0722:0.0392:2.1 0/1:127:19:9,10:51,57:0.1496:2,2:21.2:1:30.1:1:1:1.01:56.4:18:0.1463:0.0551:1.1 -GL000220.1 132161 . C G 33 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.34617;LSEQ=GTCTCTCTCTCTCTCTCTCT;RSEQ=CTTGTCTCTCTCACTGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:0,1:46,44:0.0106:2,0:27:0:13:0:0.49451:0:40:0:0:0:5 0/1:140:2:2,0:68,68:0.0143:2,0:21.5:1:33:1:0.49646:0:33.5:4:0.015:0:4 -GL000220.1 132162 . C A 39 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03319;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=TTGTCTCTCTCACTGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:45,46:0.0211:2,2:16.5:1:27:1:1:1.02:60:4:0.0233:0:1 0/1:138:3:2,1:67,66:0.0217:2,2:22.3:1:25:1:1:1.96:59.7:2:0.0155:0:2.3 -GL000220.1 132169 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.5197;SOR=Inf;LSEQ=CTCTCTCTCTCTCCTTGTCT;RSEQ=TCTCACTGTGTCTGTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:47,46:0:2,0:27:1:31.1:1:1:0:58.3:30:1:0:0.4 0/1:145:2:1,1:72,70:0.0138:2,2:38:1:27:1:1:1.02838:60:4:0.0141:0:1 -GL000220.1 132201 . C T 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23901;SOR=3.89179;LSEQ=CTGTCTTCTGTCTTACTCTC;RSEQ=TTCTCTGCCTGTCCATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:1:0,1:54,48:0.0095:2,0:20:0:15:0:0.47573:0:60:0:0:0:1 0/1:138:5:1,4:66,66:0.0362:2,2:17:1:28.6:1:0.36632:3.96436:56:10:0.0382:0:2.2 -GL000220.1 132213 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5094;SOR=Inf;LSEQ=TTACTCTCCTTCTCTGCCTG;RSEQ=CCATCTGTCTGTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:50,52:0:2,0:24.8:1:29.6:1:1:0:59:204:1:0:0.3 0/1:141:2:1,1:71,67:0.0142:2,2:12.5:1:32.5:1:1:1.05929:60:4:0.0145:0:1.5 -GL000220.1 132215 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76556;LSEQ=ACTCTCCTTCTCTGCCTGTC;RSEQ=ATCTGTCTGTCTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:0,2:50,52:0.0189:2,0:31.5:1:11:0:0.49589:0:51.5:0:0:0:4.5 0/1:138:2:1,1:69,66:0.0145:2,2:10.5:1:27.5:1:1:1.04513:60:4:0.0152:0:1.5 -GL000220.1 132216 . ATCTG A 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.81014;SOR=1.22715;LSEQ=CTCTCCTTCTCTGCCTGTCC;RSEQ=TCTGTCTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:7:3,4:46,50:0.068:2,2:23.7:1:30.3:1:1:1.22425:59.3:14:0.07:0:1.4 0/1:146:12:7,5:67,66:0.0822:2,2:29.5:1:30:1:0.76514:1.38:54.9:24:0.0839:0.0068:1.3 -GL000220.1 132224 . G A 40 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.26627;SOR=Inf;LSEQ=CTCTGCCTGTCCATCTGTCT;RSEQ=TCTGTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:47,57:0:2,0:25.5:1:31.3:1:1:0:58.8:33.667:0.9902:0:0.3 0/1:145:3:1,2:73,69:0.0207:2,2:12.3:1:25.7:1:0.61464:2.10538:29.7:6:0.0213:0:5.3 -GL000220.1 132238 . CTCTCTCCCTACCTTTCTGTTTCTCTCTCGCTAGCTCTCTCTCTCTCTGCCTGTTTCTCTCTTTCTCTCTCTGTCTTTCTCTGTCTGTCTCTTTCTCTGTCTGTCTGTC T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.50776;SOR=Inf;LSEQ=CTGTCTGTCTGTCTCTCTCT;RSEQ=TCTTTCTCTCTGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:51,63:0:2,0:24.1:1:31.9:1:1:0:58.6:113:0.9912:0:0.4 0/1:152:2:1,1:77,73:0.0132:2,2:73:1:24.6:1:1:1.05445:44:4:0.0132:0.0132:1 -GL000220.1 132248 . A C 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11608;SOR=1.80739;LSEQ=GTCTCTCTCTCTCTCTCCCT;RSEQ=CCTTTCTGTTTCTCTCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:12:4,8:51,56:0.1008:2,2:31.3:1:30.1:1:0.38012:1.81255:57.5:11:0.0973:0:1.6 0/1:154:26:14,12:69,57:0.1688:2,2:22.7:1:30.1:1:1:1.03736:53.7:25:0.1736:0:2.2 -GL000220.1 132262 . CTCTCGCTAG GTCT 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.50738;SOR=Inf;LSEQ=CTCCCTACCTTTCTGTTTCT;RSEQ=CTCTCTCTCTCTCTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:56,62:0:2,0:25:1:31.6:1:1:0:59.2:117:1:0:0.3 0/1:155:2:1,1:81,71:0.0129:2,2:36:0:31.5:1:1:1.13987:60:4:0.0132:0:3.5 -GL000220.1 132270 . AG CT 71 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.22822;SOR=4.15957;LSEQ=CTTTCTGTTTCTCTCTCGCT;RSEQ=CTCTCTCTCTCTCTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:1:0,1:56,55:0.0088:2,0:42:0:31:0:1:0:35:2:0.0094:0:4 0/1:139:5:2,3:68,60:0.036:2,2:25.2:1:30.8:1:0.66737:1.69325:45:10:0.0376:0:4.4 -GL000220.1 132271 . GCT G 106 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.00583;SOR=Inf;LSEQ=TTTCTGTTTCTCTCTCGCTA;RSEQ=CTCTCTCTCTCTGCCTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:54,53:0:2,0:26.8:1:31.6:1:1:0:59.1:25.75:0.9904:0:0.3 0/1:147:10:4,6:73,63:0.068:2,2:21.2:1:32.1:1:0.51745:1.73152:59.8:20:0.0699:0.0272:0.2 -GL000220.1 132282 . C T 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.51847;SOR=Inf;LSEQ=CTCTCGCTAGCTCTCTCTCT;RSEQ=TCTGCCTGTTTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:51,54:0:2,0:26.3:1:31.9:1:1:0:58.9:51.5:1:0:0.4 0/1:158:2:2,0:81,74:0.0127:2,0:25:1:31.5:1:0.49845:0:50:4:0.013:0:2.5 -GL000220.1 132310 . GTCTTTC G 95 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=4;SSF=0.32391;SOR=2.69319;LSEQ=GTTTCTCTCTTTCTCTCTCT;RSEQ=TCTGTCTGTCTCTTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:50,52:0.0192:2,2:28:1:33.5:1:1:1.04:50.5:4:0.0194:0:4 0/1:159:8:4,4:77,73:0.0503:2,2:36.8:1:31.8:1:1:1.05446:57.9:16:0.0513:0:4.1 -GL000220.1 132322 . C G 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.2712;SOR=Inf;LSEQ=CTCTCTCTGTCTTTCTCTGT;RSEQ=TGTCTCTTTCTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:50,52:0:2,0:23.3:1:31.3:1:1:0:59.4:19.4:1:0:0.3 0/1:148:3:2,1:73,71:0.0203:2,2:14.3:1:24.7:1:1:1.94:60:2:0.0138:0:1 -GL000220.1 132323 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.51425;SOR=Inf;LSEQ=TCTCTCTGTCTTTCTCTGTC;RSEQ=GTCTCTTTCTCTGTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:52,52:0:2,0:22.8:1:30.3:1:1:0:59.4:25:1:0:0.3 0/1:151:2:1,1:75,73:0.0132:2,2:8:1:27.5:1:1:1.02722:60:4:0.0135:0:1.5 -GL000220.1 132324 . G C 98 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0.20795;SOR=3.1443;LSEQ=CTCTCTGTCTTTCTCTGTCT;RSEQ=TCTCTTTCTCTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:52,48:0.0194:2,2:35:1:32.5:1:1:1.08246:50.5:4:0.0211:0:4 0/1:153:9:5,4:72,71:0.0588:2,2:35.3:1:31:1:1:1.23:55.9:18:0.06:0:4.1 -GL000220.1 132326 . CTCTTTCTCTG C 76 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=4;SSF=0.08497;SOR=Inf;LSEQ=CTCTGTCTTTCTCTGTCTGT;RSEQ=TCTGTCTGTCTCTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:53,47:0:2,0:23.7:1:30.1:1:1:0:59.4:15.667:1:0:0.3 0/1:161:6:3,3:81,73:0.0373:2,2:11.3:1:29.5:1:1:1.10887:60:12:0.038:0.0373:1 -GL000220.1 132330 . T C 94 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.329;SOR=2.46782;LSEQ=GTCTTTCTCTGTCTGTCTCT;RSEQ=TCTCTGTCTGTCTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:53,45:0.0198:2,2:41:1:32.5:1:1:1.17584:50.5:4:0.0208:0:4 0/1:168:8:4,4:79,74:0.0476:2,2:37:1:31.6:1:1:1.0671:57.9:16:0.0523:0:4.1 -GL000220.1 132344 . G C 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.06329;SOR=0;LSEQ=GTCTCTTTCTCTGTCTGTCT;RSEQ=TCTCTTTCTCTCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:1,2:54,50:0.0275:2,2:14.7:1:26:1:0.61095:2.145:60:2:0.0198:0:2 0/0:163:0:0,0:78,84:0:2,0:23.7:1:30.2:1:1:0:59:26:1:0:0.5 -GL000220.1 132349 . T C 91 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32448;SOR=2.77017;LSEQ=TTTCTCTGTCTGTCTGTCTC;RSEQ=TTCTCTCTGTCTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:57,50:0.0183:2,2:41:1:31:1:1:1.13863:50.5:4:0.0189:0:4 0/1:162:8:4,4:71,82:0.0494:2,2:21.4:1:30.6:1:1:1.15:57.9:16:0.05:0:4.1 -GL000220.1 132352 . CTCTCTG C 84 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=3.000;MSILEN=6;SSF=0.00957;SOR=0.09564;LSEQ=CTCTGTCTGTCTGTCTCTTT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:7:1,6:60,47:0.0614:2,2:17.6:1:30.1:1:0.04838:7.54265:60:6:0.0541:0.0439:1.1 0/0:162:1:0,1:76,85:0.0062:2,0:14:0:34:0:1:0:60:2:0.0062:0:0 -GL000220.1 132362 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.50883;SOR=Inf;LSEQ=CTGTCTCTTTCTCTCTGTCT;RSEQ=TGTCTCTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:58,56:0:2,0:23.1:1:31.4:1:1:0:59.4:113:1:0:0.4 0/1:153:2:1,1:70,81:0.0131:2,2:16.5:1:29.5:1:1:1.16:60:4:0.0132:0:2 -GL000220.1 132405 . A T 16 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77319;LSEQ=TCTCTCTCTCTGCCTCTCTC;RSEQ=CTGTGTCTGTCTTCTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:47,65:0.0175:2,2:12.5:1:26.5:1:1:1.38:60:4:0.0189:0:2 0/1:147:2:1,1:67,78:0.0136:2,2:20:1:16:1:1:1.16:60:0:0:0:1.5 -GL000220.1 132414 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50891;SOR=Inf;LSEQ=CTGCCTCTCTCACTGTGTCT;RSEQ=TCTTCTGTCTTATTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:48,59:0:2,0:26:1:31:1:1:0:59.5:14.286:1:0:0.5 0/1:144:2:1,1:65,77:0.0139:2,2:16:0:32:0:1:1.18:60:4:0.0147:0:1.5 -GL000220.1 132427 . T G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5007;SOR=Inf;LSEQ=TGTGTCTGTCTTCTGTCTTA;RSEQ=TCTCTTTCTCTCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:51,61:0:2,0:21.4:1:29.4:1:1:0:59.8:27:1:0:0.5 0/1:130:2:1,1:57,70:0.0154:2,2:16:0:33.5:1:1:1.23:33:4:0.0156:0:2.5 -GL000220.1 132433 . T C 33 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.92172;LSEQ=TGTCTTCTGTCTTATTCTCT;RSEQ=TCTCTCTCTGTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:1:0,1:45,61:0.0093:2,0:39:0:14:0:1:0:60:0:0:0:3 0/1:112:2:1,1:49,61:0.0179:2,2:10:0:33.5:1:1:1.24:33:4:0.0183:0:2.5 -GL000220.1 132461 . T C 132 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02895;SOR=2.65142;LSEQ=CTGTCTCTCTCTCTCTCTCC;RSEQ=TTCCTGTCTGTTTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:7:4,3:31,46:0.0833:2,2:20.3:1:29.9:1:0.44334:1.96:59.6:14:0.0843:0:2.1 0/1:118:23:11,12:49,46:0.1949:2,2:23.7:1:29.4:1:0.81836:1.16057:57.7:10.5:0.181:0:2.1 -GL000220.1 132467 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.17377;SOR=0;LSEQ=CTCTCTCTCTCTCCTTTCCT;RSEQ=TCTGTTTTTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:37,48:0.023:2,2:45:1:28.5:1:1:1.29:60:4:0.0238:0:4 0/0:121:0:0,0:62,59:0:2,0:21.6:1:30.7:1:1:0:59.6:39.333:1:0:0.8 -GL000220.1 132473 . T G 134 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00492;SOR=4.40595;LSEQ=CTCTCTCCTTTCCTGTCTGT;RSEQ=TTTCTCTCTCTCTCTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:4:2,2:34,42:0.0482:2,2:41.3:1:29:1:1:1.23:60:3:0.038:0:1.5 0/1:120:22:11,11:52,45:0.1833:2,2:20:1:30.1:1:0.81572:1.15415:59.1:10:0.1724:0:1.8 -GL000220.1 132475 . T C 80 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=15;MSI=5.000;MSILEN=1;SSF=0.03176;SOR=0.17978;LSEQ=CTCTCCTTTCCTGTCTGTTT;RSEQ=TCTCTCTCTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:7:2,5:32,37:0.0875:2,2:26:1:28.7:1:0.4501:2.14158:60:2.5:0.0667:0:2.3 0/1:119:2:1,1:52,45:0.0168:2,2:5:1:33.5:1:1:1.15386:24.5:4:0.02:0.0168:0.5 -GL000220.1 132494 . TCTGC T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14572;SOR=0;LSEQ=TTTCTCTCTCTCTCTCTCTT;RSEQ=CTGTTTCTCTCTGTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:34,41:0.0244:2,2:20:0:30:1:1:1.20:33:4:0.0253:0:3.5 0/0:132:0:0,0:58,52:0:2,0:24:1:31:1:1:0:59:35.667:0.8359:0:0.4 -GL000220.1 132495 . C A 126 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01567;SOR=3.67014;LSEQ=TTCTCTCTCTCTCTCTCTTT;RSEQ=TGCCTGTTTCTCTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:4:3,1:34,41:0.0488:2,2:21.8:1:27:1:0.33565:3.56:59.3:8:0.0506:0:1.8 0/1:132:21:10,11:58,52:0.1591:2,2:25.7:1:28.9:1:0.81233:1.225:59.7:42:0.1641:0:1.9 -GL000220.1 132507 . CTCTG C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.52557;SOR=Inf;LSEQ=CTCTCTTTCTGCCTGTTTCT;RSEQ=TCTGTCTCTGTCTTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:39,41:0:2,0:23:1:30:1:1:0:59.3:25.667:0.9872:0:0.6 0/1:131:2:1,1:66,61:0.0153:2,2:30:1:32.5:1:1:1.08129:60:4:0.0153:0:0 -GL000220.1 132512 . T C 33 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.55707;SOR=0.29343;LSEQ=TTTCTGCCTGTTTCTCTCTG;RSEQ=CTGTCTCTGTCTTTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:36,40:0.0253:2,2:33:0:33.5:1:1:1.11:33:4:0.026:0:3.5 0/0:133:1:0,1:71,61:0.0075:2,0:14:0:32:0:0.46617:0:43:2:0.0076:0:2 -GL000220.1 132520 . T C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.61725;SOR=0.54766;LSEQ=TGTTTCTCTCTGTCTGTCTC;RSEQ=GTCTTTCTCTGTCTGTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:37,40:0.0253:2,2:29.5:1:30:1:1:1.08:33:4:0.026:0:3.5 0/1:143:2:0,2:77,64:0.014:2,0:13:1:29.5:1:0.21127:0:51.5:4:0.014:0:2 -GL000220.1 132539 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.53533;SOR=Inf;LSEQ=CTGTCTTTCTCTGTCTGTCT;RSEQ=CCTCTCTCTTTCTTTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:46,35:0:2,0:24.3:1:31.6:1:1:0:59.3:80:1:0:0.3 0/1:142:2:1,1:76,64:0.0141:2,2:12:1:28:1:1:1.18605:60:4:0.015:0:1 -GL000220.1 132552 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.5221;SOR=Inf;LSEQ=TCTGTCTGCCTCTCTCTTTC;RSEQ=TTTTCTGCGTCTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:46,37:0:2,0:23.9:1:30.4:1:1:0:60:82:1:0:0.3 0/1:130:2:1,1:70,58:0.0154:2,2:24:1:28:1:1:1.20514:60:4:0.0154:0:1.5 -GL000220.1 132567 . C G 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.21693;LSEQ=CTTTCTTTTTCTGCGTCTCT;RSEQ=TGTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:1:1,0:47,34:0.0122:2,0:4:0:32:0:1:0:60:2:0.0125:0:3 0/1:135:2:0,2:71,59:0.0148:2,0:5.5:1:28.5:1:0.21166:0:60:4:0.0153:0:2 -GL000220.1 132590 . T A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17165;SOR=0;LSEQ=TCTCTCTCTCTCTCTCTCTG;RSEQ=TCCTATCTTCTGTCTTACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:53,41:0.0208:2,2:20.5:1:28.5:1:1:1.28918:60:4:0.0217:0:1 0/0:135:0:0,0:75,60:0:2,0:22.1:1:28.7:1:1:0:59.9:66.5:1:0:0.5 -GL000220.1 132591 . T A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26811;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTGT;RSEQ=CCTATCTTCTGTCTTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:57,42:0:2,0:23.9:1:28.2:1:1:0:59.8:8.9:1:0:0.8 0/1:139:3:2,1:75,59:0.0216:2,2:17.7:1:24.3:1:1:1.57:60:6:0.0231:0:1 -GL000220.1 132618 . T TTGCC 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.20785;SOR=0;LSEQ=TTCTGTCTTACTCTGTTTCC;RSEQ=TGCCTGCCTGCCTGTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:0,2:67,53:0.0164:2,0:11.5:1:28:1:0.20119:0:60:4:0.0174:0.0082:4.5 0/0:145:0:0,0:77,68:0:2,0:26:1:29:1:1:0:59.6:15.111:1:0:0.7 -GL000220.1 132633 . T C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47248;SOR=0.65779;LSEQ=TTTCCTTGCCTGCCTGCCTG;RSEQ=CTGTGTGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:10:8,2:56,52:0.0847:2,2:26.3:1:29.1:1:0.10707:3.68:57.8:9:0.0776:0:4 0/1:157:9:5,4:76,72:0.0573:2,2:29.4:1:31.8:1:1:1.18:56.4:18:0.0584:0:5.3 -GL000220.1 132638 . G C 117 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00078;SOR=Inf;LSEQ=TTGCCTGCCTGCCTGTCTGT;RSEQ=TGTCTGTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:54,51:0:2,0:25.3:1:31.8:1:1:0:59.9:25.25:1:0:0.6 0/1:155:13:7,6:74,68:0.0839:2,2:27.7:1:31.8:1:1:1.07:57.5:26:0.0855:0:4.8 -GL000220.1 132644 . GTCTC G 149 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=15.000;MSILEN=2;SSF=0.65676;SOR=0.85237;LSEQ=GCCTGCCTGTCTGTGTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:28:14,14:35,30:0.224:2,2:17.7:1:29.5:1:0.82219:1.16473:59.5:8.333:0.2016:0.12:1.2 0/1:152:30:17,13:44,41:0.1974:2,2:29.9:1:30.4:1:0.67591:1.22:59.3:29:0.1933:0.0395:0.6 -GL000220.1 132683 . T C 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.12393;SOR=0.46697;LSEQ=TCTCTCTCTCTCCCTCCCTT;RSEQ=CTCTTTCTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:15:7,8:53,50:0.1271:2,2:21:1:28.2:1:0.78733:1.20946:59.7:4:0.1053:0:3.7 0/1:126:8:5,3:61,56:0.0635:2,2:20.6:1:25.3:1:0.72111:1.52:56.3:1.667:0.0417:0:4.4 -GL000220.1 132690 . CTCTG C 62 v4;NM4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.37633;SOR=3.5336;LSEQ=CTCTCCCTCCCTTTCTCTTT;RSEQ=TCTCTCTCTCTCTTTCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:0,1:60,57:0.0084:2,0:49:0:34:0:0.49153:0:60:2:0.0086:0:5 0/1:137:4:3,1:66,66:0.0292:2,2:23.5:1:31:1:0.61955:2.98:52:8:0.0296:0:4.8 -GL000220.1 132694 . GTC G 78 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.50302;SOR=1.88153;LSEQ=CCCTCCCTTTCTCTTTCTCT;RSEQ=TCTCTCTCTCTTTCTGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:3:2,1:57,59:0.0252:2,2:11.3:1:31.7:1:0.61862:2.06:60:6:0.0256:0.0084:0.7 0/1:129:6:1,5:61,62:0.0465:2,2:19.2:1:30.3:1:0.20984:4.86821:57.5:12:0.0469:0.0078:0.8 -GL000220.1 132713 . G T 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00078;SOR=2.57502;LSEQ=TGTCTCTCTCTCTCTTTCTG;RSEQ=GTGTTTCTCTCTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:26:13,13:45,50:0.2131:2,2:23.9:1:28.6:1:0.8284:1.11:58.3:12:0.2105:0:1.9 0/1:136:56:28,28:38,42:0.4118:2,2:22.4:1:29.2:1:0.86197:1.10:58.1:55:0.4231:0:1.7 -GL000220.1 132782 . G C 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.63076;SOR=2.44308;LSEQ=CTCTCTTTCTCTCTGTCTCT;RSEQ=TCTCTGCCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:0,1:56,60:0.0085:2,0:29:0:14:0:1:0:60:0:0:0:1 0/1:145:3:0,3:67,74:0.0207:2,0:13.7:1:24.3:1:0.2484:0:53.3:2:0.0152:0:3 -GL000220.1 132887 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37007;SOR=3.66503;LSEQ=CTCTCCTTCTCTGCCTGTCC;RSEQ=TCTGTCTGTCTGTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:1:1,0:27,33:0.0161:2,0:40:0:28:0:0.45902:0:27:2:0.0167:0:3 0/1:70:4:2,2:28,34:0.0571:2,2:25.5:1:28.8:1:1:1.21:45:8:0.0588:0:1 -GL000220.1 132898 . TGTCTCTCC T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=1.37198;LSEQ=TGCCTGTCCGTCTGTCTGTC;RSEQ=CTCTCTCTCCCTCCCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:0,2:31,35:0.0294:2,0:5:1:31:1:0.49649:0:40:6:0.028:0.0299:1 0/1:75:3:0,3:31,39:0.04:2,0:17.7:1:30:1:0.25685:0:37.3:6:0.0405:0.0267:1 -GL000220.1 132899 . GTCTCTCCC G 60 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0.05162;SOR=0;LSEQ=GCCTGTCCGTCTGTCTGTCT;RSEQ=TCTCTCTCCCTCCCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:4:1,3:31,33:0.0588:2,2:10:1:30.1:1:0.6163:2.7793:33.5:8:0.0597:0.0441:1.8 0/0:73:0:0,0:31,41:0:2,0:23:1:28.7:1:1:0:48.8:144:1:0:0.3 -GL000220.1 132908 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.23389;SOR=0;LSEQ=TCTGTCTGTCTGTCTCTCCC;RSEQ=CTCTCTCCCTCCCTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:33,32:0.0299:2,2:28.5:1:32:1:1:1.03078:60:4:0.0303:0:1.5 0/0:71:0:0,0:33,38:0:2,0:26.2:1:28.9:1:1:0:50.5:22.667:1:0:0.3 -GL000220.1 132929 . TTC T 113 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.14345;SOR=2.25094;LSEQ=CTCTCTCCCTCCCTTTCTGT;RSEQ=TCTCTCTCTCTCTTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:6:3,3:38,33:0.0779:2,2:25.5:1:30.3:1:1:1.1494:44:12:0.0789:0:0.3 0/1:81:13:7,6:35,33:0.1605:2,2:27.2:1:30.7:1:1:1.10:42.6:26:0.1646:0.0247:0.4 -GL000220.1 132940 . T C 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=7.000;MSILEN=2;SSF=0.23356;SOR=0;LSEQ=CCTTTCTGTTTCTCTCTCTC;RSEQ=CTCTTTCTGTCTGTTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:43,35:0.025:2,2:11:1:29.5:1:1:1.22539:48.5:4:0.025:0:1 0/0:85:0:0,0:46,39:0:2,0:23.2:1:29.6:1:1:0:49.9:20.25:1:0:0.3 -GL000220.1 132942 . T C 63 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.71367;SOR=0.6973;LSEQ=TTTCTGTTTCTCTCTCTCTC;RSEQ=CTTTCTGTCTGTTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:4:4,0:40,37:0.0494:2,0:10:1:31.8:1:0.12129:0:40:8:0.0494:0:4 0/1:86:3:3,0:43,40:0.0349:2,0:8:0:31.7:1:0.24487:0:40:6:0.0353:0:3 -GL000220.1 132945 . T G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.89347;LSEQ=CTGTTTCTCTCTCTCTCTCT;RSEQ=TCTGTCTGTTTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:4:4,0:38,37:0.0506:2,0:13:1:33.8:1:0.11845:0:40:8:0.0513:0:4 0/1:88:4:4,0:44,40:0.0455:2,0:9:1:32.3:1:0.12263:0:40:8:0.0465:0:2.8 -GL000220.1 132955 . TTCTC T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.21777;SOR=0;LSEQ=CTCTCTCTCTTTCTGTCTGT;RSEQ=TCTTTCTCTCTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:0,2:43,36:0.0247:2,0:19:1:28.5:1:0.21698:0:38.5:4:0.0253:0.0123:2 0/0:92:0:0,0:50,42:0:2,0:20.4:1:29.1:1:1:0:48.9:29.667:1:0:0.4 -GL000220.1 132963 . T CTGCCTCTC 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.05214;SOR=0.22011;LSEQ=CTCTCTTTCTGTCTGTTTCT;RSEQ=TCTCTCTCTGTCTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:8:7,1:35,39:0.0952:2,2:19.4:1:31.5:1:0.05772:7.64:41.3:16:0.0988:0:2.5 0/1:89:2:2,0:46,39:0.0225:2,0:18.5:1:30.3:1:0.4996:0:40:4:0.0227:0:2 -GL000220.1 132969 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.10687;SOR=Inf;LSEQ=GTCTGTTTCTCTCTTTCTCT;RSEQ=TCTGTCTGTCTCTTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:45,47:0:2,0:23.6:1:31.5:1:1:0:47:91:0.9891:0:0.6 0/1:85:3:2,1:47,35:0.0353:2,2:12.7:1:24.3:1:1:1.48:42:6:0.0357:0:1.3 -GL000220.1 133026 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24347;SOR=Inf;LSEQ=TTTCTTTTTCTCTGTCTCTC;RSEQ=GTCTCTCTCTGTGTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:66,69:0:2,0:23.4:1:30.2:1:1:0:46.5:44:1:0:0.6 0/1:132:2:1,1:70,60:0.0152:2,2:30:0:32:0:1:1.1653:60:4:0.0152:0:1.5 -GL000220.1 133035 . C T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.37077;SOR=3.98302;LSEQ=CTCTGTCTCTCTGTCTCTCT;RSEQ=TGTGTCTGTCTCTCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:1:0,1:72,70:0.007:2,0:1:0:25:0:0.4965:0:60:2:0.007:0:3 0/1:146:4:3,1:72,70:0.0274:2,2:23:1:30.5:1:0.62035:2.90:47.3:8:0.0276:0:2 -GL000220.1 133040 . T C 39 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.62278;SOR=0.34356;LSEQ=TCTCTCTGTCTCTCTCTGTG;RSEQ=CTGTCTCTCTTTCTGTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:3:1,2:75,75:0.0196:2,2:12.7:1:25:1:1:1.99128:43.3:2:0.0132:0:2.7 0/0:147:1:1,0:74,72:0.0068:2,0:47:0:31:0:1:0:21:2:0.0068:0:3 -GL000220.1 133043 . G C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49835;SOR=Inf;LSEQ=CTCTGTCTCTCTCTGTGTCT;RSEQ=TCTCTCTTTCTGTGCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:76,74:0:2,0:24.5:1:32.1:1:1:0:48.5:149:1:0:0.7 0/1:152:2:1,1:74,75:0.0132:2,2:21.5:1:33:0:1:1.01:48.5:4:0.0132:0:2.5 -GL000220.1 133051 . T G 192 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03243;SOR=0.59334;LSEQ=CTCTCTGTGTCTGTCTCTCT;RSEQ=TCTGTGCCTATCTTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:64:33,31:46,43:0.4183:2,2:25.9:1:32:1:1:1.0049:40.5:63:0.4172:0:1.5 0/1:154:46:22,24:53,53:0.2987:2,2:23:1:31.5:1:0.86077:1.09028:39.4:92:0.3046:0:1.8 -GL000220.1 133076 . C G 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.23657;SOR=0;LSEQ=TGCCTATCTTCTGTCTTACT;RSEQ=TCTTTCTCTGGCTGTCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:106,80:0.0106:2,2:6:0:34:0:1:1.32298:50:4:0.0108:0:1 0/0:198:0:0,0:103,92:0:2,0:20.9:1:31.2:1:1:0:53.9:96.5:0.9897:0:1 -GL000220.1 133087 . G T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01583;LSEQ=TGTCTTACTCTCTTTCTCTG;RSEQ=CTGTCTGCCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:0,2:108,84:0.0103:2,0:15:1:18.5:1:0.19524:0:60:1:0.0054:0:2 0/1:191:2:1,1:99,90:0.0105:2,2:20:1:27.5:1:1:1.09945:60:4:0.0109:0:1 -GL000220.1 133088 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02639;LSEQ=GTCTTACTCTCTTTCTCTGG;RSEQ=TGTCTGCCTGTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:1,2:109,85:0.0152:2,2:19.3:1:24.7:1:0.58437:2.55265:60:2:0.0105:0:3.7 0/1:192:3:1,2:100,89:0.0156:2,2:29.3:1:28.7:1:0.60427:2.23802:60:6:0.0159:0:2.3 -GL000220.1 133091 . T A 65 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50175;SOR=1.6988;LSEQ=TTACTCTCTTTCTCTGGCTG;RSEQ=CTGCCTGTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:1,2:111,87:0.0149:2,2:35.7:1:31.3:1:0.58507:2.54004:43.3:6:0.015:0:2.3 0/1:199:5:2,3:101,91:0.0251:2,2:12:1:28.4:1:0.67096:1.66055:29:10:0.0253:0:2 -GL000220.1 133096 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=CTCTTTCTCTGGCTGTCTGC;RSEQ=TGTCTCTCTCTCTCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:105,88:0:2,0:26:1:31.3:1:1:0:54.9:47.25:1:0:1 0/1:197:2:1,1:98,97:0.0102:2,2:8:0:32.5:1:1:1.01026:31:4:0.0105:0:1.5 -GL000220.1 133098 . G GTCTC 170 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=8.000;MSILEN=2;SSF=0.07845;SOR=0.62117;LSEQ=CTTTCTCTGGCTGTCTGCCT;RSEQ=TCTCTCTCTCTCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:47:27,20:73,69:0.2338:2,2:29.5:1:30.7:1:0.50389:1.27:46.2:94:0.2362:0.0448:3 0/1:201:32:14,18:77,71:0.1592:2,2:34.6:1:30.4:1:0.43936:1.39178:45.7:31:0.1574:0.005:2.8 -GL000220.1 133113 . C T 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99497;LSEQ=TGCCTGTCTCTCTCTCTCTG;RSEQ=CTGTCTCCGTCCCTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:57:31,26:69,69:0.2923:2,2:29.8:1:29.6:1:0.63771:1.19:48.7:56:0.2979:0:3.3 0/1:206:60:28,32:66,77:0.2913:2,2:30.7:1:29.5:1:1:1.02:48.7:120:0.2985:0:3.5 -GL000220.1 133122 . G GTCCC 126 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=4.000;MSILEN=4;SSF=0.00902;SOR=0.34498;LSEQ=CTCTCTCTCTGCCTGTCTCC;RSEQ=TCCCTCCCTCCCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:23:11,12:92,82:0.1162:2,2:24.3:1:27.9:1:0.66413:1.22268:59.1:4.75:0.1011:0.0354:0.7 0/1:208:9:2,7:95,104:0.0433:2,2:25.2:1:30.2:1:0.17918:3.18155:60:18:0.0457:0.0096:0.7 -GL000220.1 133129 . C T 168 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.82082;SOR=1.05529;LSEQ=TCTGCCTGTCTCCGTCCCTC;RSEQ=CTCCCTGTCTGTCTGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:50:27,23:74,68:0.2604:2,2:24.4:1:29.9:1:0.87002:1.08:49.9:24:0.2553:0:3.4 0/1:203:55:27,28:67,80:0.2709:2,2:27.6:1:29.1:1:0.75159:1.15:50.3:17.333:0.264:0:3.6 -GL000220.1 133157 . T C 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.43952;SOR=1.28703;LSEQ=TCTGTCTGTTTCTCTCTCTG;RSEQ=CTCTGTCTCTCTGTCCATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:20:8,12:68,69:0.1266:2,2:22.6:1:28.9:1:0.47862:1.47461:45.8:5.667:0.1111:0:5.1 0/1:178:28:13,15:72,76:0.1573:2,2:21.9:1:28.8:1:0.84016:1.09255:50.1:8.333:0.1479:0:4.6 -GL000220.1 133162 . GTCTCTCTGTCCA CTCTC 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.61728;SOR=1.22414;LSEQ=CTGTTTCTCTCTCTGTCTCT;RSEQ=TCTCTGTCTGTCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:18:7,11:70,69:0.1146:2,2:17.3:1:30.9:1:0.45491:1.58951:44.2:17:0.1133:0.0637:5.1 0/1:168:23:9,14:67,75:0.1369:2,2:19.5:1:31:1:0.50739:1.38689:47.1:46:0.1411:0.0655:5 -GL000220.1 133168 . CTGTCCA C 69 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=5.000;MSILEN=2;SSF=0.06158;SOR=Inf;LSEQ=CTCTCTCTGTCTCTGTCTCT;RSEQ=TCTCTGTCTGTCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:70,73:0:2,0:24.8:1:30.9:1:1:0:59.5:142:1:0:0.4 0/1:164:5:4,1:74,73:0.0305:2,2:11.2:1:29.8:1:0.36753:3.91:48.4:10:0.0338:0.0122:4.4 -GL000220.1 133169 . TGTCCATCT T 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.21837;SOR=0;LSEQ=TCTCTCTGTCTCTGTCTCTC;RSEQ=CTGTCTGTCTCTTTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:0,2:69,68:0.0136:2,0:26.5:1:33.5:1:0.4964:0:22.5:4:0.0148:0:7 0/0:167:0:0,0:75,75:0:2,0:22.7:1:31.2:1:1:0:59.5:149:1:0:0.4 -GL000220.1 133196 . T G 99 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.58691;SOR=0.6754;LSEQ=CTCTGTCTGTCTCTTTCTCT;RSEQ=TCTCTCTCTCTGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:8:2,6:69,63:0.0563:2,2:6.5:1:33:1:0.16253:3.25983:36.8:16:0.0593:0:6.3 0/1:155:6:2,4:73,75:0.0387:2,2:9.7:1:30:1:0.68191:1.93856:43:12:0.0395:0:6.7 -GL000220.1 133200 . C G 82 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.52549;SOR=0.59117;LSEQ=GTCTGTCTCTTTCTCTTTCT;RSEQ=TCTCTCTGTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:6:0,6:70,59:0.0438:2,0:4.3:1:32:1:0.011:0:26.7:12:0.0458:0:6.5 0/1:152:4:2,2:73,74:0.0263:2,2:9:1:27:1:1:1.01:45:3:0.0204:0:7.5 -GL000220.1 133202 . C CTCTCTG 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.49913;SOR=Inf;LSEQ=CTGTCTCTTTCTCTTTCTCT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:72,63:0:2,0:22.5:1:31.4:1:1:0:59:44:1:0:0.5 0/1:149:2:1,1:75,70:0.0134:2,2:18.5:1:30.1:1:1:1.07089:60:4:0.0137:0.0067:0.5 -GL000220.1 133204 . C G 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=1.33538;LSEQ=GTCTCTTTCTCTTTCTCTCT;RSEQ=TCTGTCTCTGTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:0,2:71,60:0.015:2,0:5:1:32.5:1:0.21542:0:34:4:0.0157:0:7.5 0/1:150:3:1,2:77,70:0.02:2,2:7.3:1:29.3:1:0.60781:2.18883:46:6:0.0201:0:7.7 -GL000220.1 133208 . G C 63 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=6;SSF=1;SOR=1.21979;LSEQ=CTTTCTCTTTCTCTCTCTCT;RSEQ=TCTCTGTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:3:1,2:72,58:0.0226:2,2:21:1:26.7:1:0.58863:2.46615:49.3:2:0.016:0:5.7 0/1:146:4:1,3:77,64:0.0274:2,2:7.8:1:31.8:1:0.33564:3.57962:47.5:8:0.0284:0:5.3 -GL000220.1 133214 . GTC G 119 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.36454;SOR=1.64819;LSEQ=CTTTCTCTCTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:8:3,5:74,53:0.0597:2,2:16.1:1:29.5:1:0.28859:2.31236:60:7:0.0526:0.0373:0.6 0/1:137:13:7,6:68,56:0.0949:2,2:30.3:1:32.2:1:1:1.04053:59.1:26:0.0963:0:0.2 -GL000220.1 133216 . C T 40 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=7.000;MSILEN=2;SSF=0.24771;SOR=Inf;LSEQ=TTCTCTCTCTCTGTCTCTGT;RSEQ=TCTCTCTCTCTCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:74,53:0:2,0:22.8:1:30.7:1:1:0:59.4:17.143:1:0:0.4 0/1:138:3:2,1:66,56:0.0217:2,2:19.3:1:25.7:1:1:1.69:60:2:0.0164:0:0.7 -GL000220.1 133242 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.24524;SOR=0;LSEQ=CTCTCTCTGCCTGTCTCTCT;RSEQ=ACTGTGTCTGTCTTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:68,60:0.0154:2,2:33:1:27:0:1:1.13224:60:4:0.0154:0:1 0/0:132:0:0,0:69,61:0:2,0:22.2:1:30.8:1:1:0:58.9:64:1:0:0.3 -GL000220.1 133251 . T G 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.11017;SOR=Inf;LSEQ=CCTGTCTCTCTCACTGTGTC;RSEQ=GTCTTCTGTCTTACTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:73,66:0:2,0:23.2:1:30.6:1:1:0:58.4:138:1:0:0.5 0/1:129:3:1,2:67,59:0.0233:2,2:12.3:1:24.7:1:0.60241:2.25719:34:2:0.0156:0:1.3 -GL000220.1 133273 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49847;SOR=0;LSEQ=TCTTCTGTCTTACTCTCTTT;RSEQ=TCTGCCTGCCTCTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:72,64:0.0145:2,2:33.5:1:30.5:1:1:1.12404:44.5:4:0.0148:0:3.5 0/0:131:0:0,0:72,59:0:2,0:23.5:1:30.7:1:1:0:58.1:25.2:1:0:0.4 -GL000220.1 133281 . GCCTC G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49846;SOR=0;LSEQ=CTTACTCTCTTTCTCTGCCT;RSEQ=TCTGTCTGTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:69,64:0.0147:2,2:31:0:33.5:1:1:1.0775:44.5:4:0.015:0:3.5 0/0:129:0:0,0:70,57:0:2,0:25:1:31.2:1:1:0:58.1:254:0.9922:0:0.3 -GL000220.1 133285 . CTCTG C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.4983;SOR=0;LSEQ=CTCTCTTTCTCTGCCTGCCT;RSEQ=TCTGTCTGTCTCTCTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:70,64:0.0147:2,2:34.5:1:31:1:1:1.09302:60:4:0.0148:0:0 0/0:131:0:0,0:72,59:0:2,0:25:1:29.5:1:1:0:57.8:130:1:0:0.4 -GL000220.1 133311 . A ACGTC 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02974;SOR=0;LSEQ=CTGTCTGTCTCTCTCCCTCC;RSEQ=TGTCTCTCTCTCTCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:6:2,4:66,62:0.0438:2,2:14.8:1:29.5:1:0.43714:2.11743:55.3:12:0.0462:0.0219:2.3 0/0:131:0:0,0:62,62:0:2,0:24.5:1:29.3:1:1:0:57.9:40.333:0.9528:0:0.3 -GL000220.1 133345 . G GTC 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.49833;SOR=Inf;LSEQ=CTCTCACTCACTCTCTCTCC;RSEQ=TCTCTCTCTCTTTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:63,71:0:2,0:23.7:1:28.8:1:1:0:55.5:11.182:1:0:0.2 0/1:139:2:2,0:65,70:0.0144:2,0:10.5:1:29.3:1:0.23733:0:39:4:0.0161:0.0072:1 -GL000220.1 133373 . CTCTG C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.5022;SOR=Inf;LSEQ=CTCTTTCTGTCTGTTTCTCT;RSEQ=TCTGTCTCTCTCCCTCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:56,65:0:2,0:26.6:1:30.4:1:1:0:50.5:59.5:1:0:0.2 0/1:145:2:1,1:69,74:0.0138:2,2:32:1:33:0:1:1.07:30:4:0.014:0:1 -GL000220.1 133396 . TG CGTCTGTC 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.26115;SOR=Inf;LSEQ=TGTCTGTCTCTCTCCCTCCA;RSEQ=TCTCTCTCTCTCTCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:51,60:0:2,0:25.6:1:29:1:1:0:49.4:10.1:1:0:0.2 0/1:150:3:1,2:69,74:0.02:2,2:24:1:27.4:1:1:1.85723:42.7:6:0.0233:0:2 -GL000220.1 133397 . G A 97 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4365;SOR=1.73082;LSEQ=GTCTGTCTCTCTCCCTCCAT;RSEQ=TCTCTCTCTCTCTCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:5:2,3:49,53:0.0442:2,2:27.8:1:29.4:1:1:1.38261:28.6:10:0.0463:0:1.8 0/1:148:11:6,5:62,66:0.0743:2,2:25.5:1:28.3:1:0.76101:1.28:38:22:0.0791:0:1.9 -GL000220.1 133431 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=12;MSI=1.000;MSILEN=1;SSF=0.01118;SOR=0;LSEQ=CTCTCACTCACTCTCTCTCC;RSEQ=TCTCTCTCTCTCTTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:5:2,3:46,53:0.0476:2,2:13:1:26.8:1:1:1.29863:34.4:4:0.044:0:1.8 0/0:150:0:0,0:67,73:0:2,0:23.1:1:28.2:1:1:0:46.3:13:0.9848:0:0.4 -GL000220.1 133485 . G GTC 29 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.18246;SOR=0;LSEQ=GTCTGTCTCTCTCCCTCCAT;RSEQ=TCTCTCTCTCTCCCTCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:40,42:0.023:2,2:7.5:1:29.9:1:1:1.05:51:4:0.0244:0.0115:0 0/0:116:0:0,0:49,53:0:2,0:23.7:1:30.9:1:1:0:47.1:33:0.9083:0:0.4 -GL000220.1 133496 . TCC T 29 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=7.000;MSILEN=2;SSF=0.50435;SOR=Inf;LSEQ=TCCCTCCATGTCTCTCTCTC;RSEQ=CTCTCACTCACTCTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:47,49:0:2,0:21.7:1:31.2:1:1:0:51.2:95:1:0:0.4 0/1:121:2:1,1:59,58:0.0165:2,2:19.5:1:29.5:1:1:1.0171:43:4:0.0171:0:2 -GL000220.1 133498 . C T 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.63048;SOR=1.43148;LSEQ=CCTCCATGTCTCTCTCTCTC;RSEQ=CTCTCACTCACTCTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:7:4,3:45,47:0.0707:2,2:17.4:1:29.6:1:0.71498:1.39:39.7:14:0.0753:0:2 0/1:122:12:5,7:55,52:0.0984:2,2:15.9:1:28.3:1:0.5585:1.4759:36.7:11:0.0973:0:2.7 -GL000220.1 133504 . A C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.1798;SOR=0;LSEQ=TGTCTCTCTCTCTCCCTCTC;RSEQ=CTCACTCTCTCTCCGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:44,47:0.0213:2,2:16:0:33.5:1:1:1.07:51:4:0.0244:0:1.5 0/0:127:0:0,0:63,59:0:2,0:22.1:1:27.6:1:1:0:49.1:12.556:1:0:0.6 -GL000220.1 133519 . G GTC 126 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.3567;SOR=1.50711;LSEQ=CTCTCACTCACTCTCTCTCC;RSEQ=TCTCTCTCTCTCTTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:13:6,7:43,46:0.125:2,2:17.9:1:30.4:1:1:1.08964:55.5:26:0.1444:0.0577:0.7 0/1:124:22:11,11:48,47:0.1774:2,2:22.4:1:28.4:1:1:1.0211:51.3:21:0.1721:0.0242:1.3 -GL000220.1 133532 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50784;SOR=Inf;LSEQ=TCTCTCCGTCTCTCTCTCTC;RSEQ=TTCTGTCTGTTTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:50,54:0:2,0:26.2:1:30.4:1:1:0:53:33.667:1:0:0.7 0/1:138:2:1,1:69,66:0.0145:2,2:22:0:33:1:1:1.04513:55:4:0.0147:0:1.5 -GL000220.1 133549 . G C 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=4;SSF=0.00011;SOR=0;LSEQ=CTCTTTCTGTCTGTTTCTCT;RSEQ=TCTGTCTGTCTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:10:4,6:46,51:0.0926:2,2:27.3:1:28.6:1:0.74752:1.34917:50.9:4:0.0851:0:2.2 0/0:153:0:0,0:66,68:0:2,0:23.7:1:30:1:1:0:56.5:11.182:1:0:0.5 -GL000220.1 133555 . CTG C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.17297;SOR=0;LSEQ=CTGTCTGTTTCTCTGTCTGT;RSEQ=TCTGTCTGTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:52,58:0.0177:2,2:12.5:1:30:1:1:1.11:60:4:0.018:0:0 0/0:158:0:0,0:77,77:0:2,0:23.2:1:29.9:1:1:0:56.8:76:1:0:0.7 -GL000220.1 133565 . G C 36 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=6.000;MSILEN=4;SSF=0.07933;SOR=0;LSEQ=CTCTGTCTGTCTGTCTGTCT;RSEQ=TCTGTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:3:1,2:50,57:0.027:2,2:16.7:1:23:1:1:1.7458:57:2:0.0194:0:2.7 0/0:146:0:0,0:72,68:0:2,0:16:0:14:0:1:0:60:0:0:0:2 -GL000220.1 133613 . T A 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00034;SOR=0;LSEQ=CTCTCTCTCTCTGTTTGTCT;RSEQ=TCTCCCTCCCTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:9:4,5:44,47:0.0882:2,2:20.3:1:26.2:1:1:1.16838:60:8:0.0889:0:1 0/0:140:0:0,0:60,78:0:2,0:24:1:29.3:1:1:0:58.8:33.5:0.9853:0:0.5 -GL000220.1 133622 . CCTGT C 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.63699;SOR=2.27647;LSEQ=TCTGTTTGTCTTTCTCCCTC;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:1,0:51,51:0.0097:2,0:43:0:29:0:1:0:60:2:0.0101:0:1 0/1:137:3:1,2:59,74:0.0219:2,2:20.3:1:32:1:1:1.58935:60:6:0.0224:0.0073:0.3 -GL000220.1 133645 . CTCTCTG C 134 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=2;SSF=0.15955;SOR=1.85765;LSEQ=GTCTGTCTGTCTGTCTCTCT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:9:6,3:43,44:0.0909:2,2:26.3:1:31.2:1:0.487:2.03:56.8:18:0.0947:0.0303:1.1 0/1:121:19:11,8:43,58:0.157:2,2:30.1:1:31.6:1:0.31487:1.85:57.1:38:0.1583:0.0413:0.9 -GL000220.1 133647 . CTCTG C 33 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=7.000;MSILEN=2;SSF=0.20469;SOR=0;LSEQ=CTGTCTGTCTGTCTCTCTCT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:46,42:0.0204:2,2:33.5:1:33:1:1:1.09413:60:4:0.0225:0:0 0/0:118:0:0,0:46,58:0:2,0:22.6:1:29.9:1:1:0:59.2:103:1:0:0.5 -GL000220.1 133663 . G GTC 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.50046;SOR=Inf;LSEQ=CTCTCTCTGTCTCTGTCTCT;RSEQ=TCTCTCTCTCTTTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:48,48:0:2,0:24.3:1:31.1:1:1:0:59.8:23:1:0:0.3 0/1:115:2:1,1:48,59:0.0174:2,2:27:0:29.5:1:1:1.23:60:4:0.019:0:2 -GL000220.1 133675 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.50056;SOR=Inf;LSEQ=CTGTCTCTGTCTCTCTCTCT;RSEQ=TCTCTTTCTGTCTGTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:52,44:0:2,0:24.9:1:29.8:1:1:0:59.1:192:1:0:0.3 0/1:112:2:1,1:50,59:0.0179:2,2:40:0:31:1:1:1.18:60:4:0.0183:0:2 -GL000220.1 133681 . T G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50251;SOR=Inf;LSEQ=CTGTCTCTCTCTCTTTCTCT;RSEQ=TCTGTCTGTTTCTCTCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:49,41:0:2,0:26.1:1:29.7:1:1:0:59.2:44:1:0:0.2 0/1:110:2:1,1:48,60:0.0182:2,2:46:0:31.5:1:1:1.25:60:4:0.0187:0:2 -GL000220.1 133704 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.39509;LSEQ=TGTCTGTTTCTCTCTATCTC;RSEQ=CGCTGTCCATCTCTGTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:41,41:0.0238:2,2:29.5:1:31:1:1:1:60:4:0.0244:0:1 0/1:91:3:2,1:39,49:0.033:2,2:23.7:1:31.7:1:0.58657:2.49:49:6:0.0333:0:1.3 -GL000220.1 133794 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19;SOR=Inf;LSEQ=TAGGGCCCTGCCCCTTCCAC;RSEQ=AGAGTGAGAAGCGCGTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:30,47:0:2,0:24.3:1:30.4:1:1:0:49.1:37.5:1:0:0.1 0/1:60:2:1,1:23,35:0.0333:2,2:29:1:27.5:1:1:1.51:49:4:0.0345:0:1 -GL000220.1 133832 . GAGAGGAATCT G 115 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.44525;SOR=0.60268;LSEQ=CTTCGGTGCTTAGAGAGGCC;RSEQ=AGACAGGCGGGCCTTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:13:5,8:24,28:0.2:2,2:27.1:1:31.2:1:0.75852:1.36485:50.2:26:0.2:0.0308:0.1 0/1:46:6:2,4:16,24:0.1304:2,2:34.7:1:28:1:1:1.32523:47.7:5:0.1136:0:0.5 -GL000220.1 133874 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1411;SOR=Inf;LSEQ=CCTTGCTGGGCTTCCCCACT;RSEQ=GGTGTACGATTTCGGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:23,36:0:2,0:23.7:1:30.5:1:1:0:49.3:118:1:0:0.2 0/1:36:2:1,1:18,16:0.0556:2,2:36:0:31.5:1:1:1.12132:50:4:0.0606:0:1.5 -GL000220.1 133881 . C T 71 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03507;SOR=8.4074;LSEQ=GGGCTTCCCCACTCGGTGTA;RSEQ=GATTTCGGGAGGTCGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:0,1:22,33:0.0179:2,0:3:0:30:0:1:0:39:2:0.0179:0:1 0/1:37:5:2,3:17,15:0.1351:2,2:23.6:1:30.8:1:0.65988:1.67584:37.2:10:0.1471:0:1 -GL000220.1 133958 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49231;SOR=0;LSEQ=TTTCTCTCGGTCACGTGTGG;RSEQ=GTCCGTACTTCTCCTATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:0.0606:2,2:12.5:1:27.5:1:1:1.06462:27:4:0.0606:0:1 0/0:33:0:0,0:17,16:0:2,0:22:0:17:0:1:0:60:0:0:0:4 -GL000220.1 134012 . T G 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16126;SOR=3.44365;LSEQ=TCGACTTCAACATAAACTGT;RSEQ=AAGGCCGGACGCAACACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:13,18:0.0606:2,0:25:1:31.5:1:0.19886:0:60:4:0.0625:0:1 0/1:38:7:3,4:16,15:0.1842:2,2:20.6:1:31.4:1:1:1.40911:56.9:14:0.1892:0:1.3 -GL000220.1 134021 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50192;SOR=Inf;LSEQ=ACATAAACTGTTAAGGCCGG;RSEQ=CGCAACACGGCGAAACCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:11,17:0:2,0:30:1:29.3:1:1:0:60:27:1:0:0.1 0/1:37:2:1,1:16,19:0.0541:2,2:15.5:1:29.5:1:1:1.18:60:4:0.0556:0:1 -GL000220.1 134075 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50992;SOR=Inf;LSEQ=TACAAAGCTGAGTCGGGAGC;RSEQ=GTGGGGCAGGCCCCTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:11,15:0:2,0:23.6:1:30.5:1:1:0:60:52:1:0:0.2 0/1:38:2:1,1:18,18:0.0526:2,2:41.5:1:27:1:1:1:60:4:0.0526:0:1 -GL000220.1 134098 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53115;SOR=Inf;LSEQ=GGGGCAGGCCCCTGTAATGC;RSEQ=AGCTCCTCGGGAGGCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:0:2,0:28.4:1:31.5:1:1:0:59.5:44:1:0:0.3 0/1:39:2:1,1:18,19:0.0513:2,2:23.5:1:29:1:1:1.05:60:4:0.0526:0:2 -GL000220.1 134139 . G A 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.3136;SOR=0.25045;LSEQ=CGGGAGAATCGCTTGAACCA;RSEQ=GGAAGCGGAGGCTGCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:1,2:6,13:0.1364:2,2:27.3:1:30.7:1:1:1.08:60:6:0.1429:0:2 0/1:27:1:0,1:12,14:0.037:2,0:2:0:32:0:1:0:60:2:0.0385:0:2 -GL000220.1 134143 . A G 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08034;SOR=0;LSEQ=AGAATCGCTTGAACCAGGGA;RSEQ=GCGGAGGCTGCAGGGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:5,12:0.15:2,2:26:1:31:1:1:1.19:60:6:0.1579:0:2 0/0:25:0:0,0:11,14:0:2,0:23.1:1:30.6:1:1:0:60:50:1:0:0.3 -GL000220.1 134439 . C A 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50204;SOR=Inf;LSEQ=TCCCTCGTTGCCTAGGGAAC;RSEQ=TCGCCTAGGGAACCTCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,17:0:2,0:21.1:1:31.2:1:1:0:60:76:1:0:0.1 0/1:50:2:1,1:25,23:0.04:2,2:23:0:28.5:1:1:1.08513:60:4:0.04:0:1.5 -GL000220.1 134473 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49666;SOR=Inf;LSEQ=CTCCGCCCTGGCGGGGGCCC;RSEQ=ATTGTTCTTTGATCGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:0:2,0:24.7:1:29.5:1:1:0:59.5:42:1:0:0.1 0/1:49:2:1,1:21,26:0.0408:2,2:13.5:1:28:1:1:1.23:60:4:0.0408:0:1 -GL000220.1 134633 . T TC 23 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0.69881;LSEQ=GTGAGTCGGTTAGGTGGGTT;RSEQ=CCCCCAAACCGCCCCCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:17,14:0.0588:2,2:31:1:31:1:1:1.20712:60:4:0.0645:0:2.5 0/1:48:2:2,0:27,19:0.0417:2,0:25:0:23:1:0.51152:0:60:1:0.025:0:1 -GL000220.1 134643 . CG AC 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06842;SOR=0;LSEQ=TAGGTGGGTTTCCCCCAAAC;RSEQ=CCCCCCCCCCCCCGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:2,1:19,14:0.0811:2,2:9.3:1:32:1:1:1.46:60:6:0.1071:0:1.7 0/0:52:0:0,0:31,18:0:2,0:17.9:1:26.1:1:1:0:59.2:7.167:0.9773:0:1.1 -GL000220.1 134695 . C A 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49533;SOR=0;LSEQ=TTGGAAACCTTCCAGAGCCA;RSEQ=CCCGGTGTGCCTCCGTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:0,2:25,27:0.037:2,0:49:0:28:0:0.49336:0:43.5:4:0.0392:0:1.5 0/0:54:0:0,0:23,31:0:2,0:26.3:1:31:1:1:0:50.5:26:1:0:0.4 -GL000220.1 134744 . A T 26 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.67408;LSEQ=TCCCCCACCCCTTGCCGGCG;RSEQ=TCTCATTCTTGCCAGGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:1:0,1:37,26:0.0156:2,0:1:0:25:0:0.42188:0:60:2:0.0164:0:1 0/1:77:2:1,1:39,36:0.026:2,2:10:0:26:1:1:1.08219:47:4:0.0267:0:1 -GL000220.1 134763 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=GATCTCATTCTTGCCAGGCT;RSEQ=ACATTTGCATCGGTGGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:42,29:0:2,0:23.4:1:31.4:1:1:0:51.7:34.5:1:0:0.3 0/1:87:2:1,1:45,40:0.023:2,2:20:0:31:1:1:1.12347:60:4:0.0233:0:1.5 -GL000220.1 134779 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50748;SOR=Inf;LSEQ=GGCTGACATTTGCATCGGTG;RSEQ=GCGTCAGGCCTCACTCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:41,30:0:2,0:22.3:1:30.8:1:1:0:54.8:142:1:0:0.3 0/1:95:2:1,1:49,44:0.0211:2,2:23.5:1:30:1:1:1.11237:55:4:0.0213:0:1 -GL000220.1 134785 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.17381;SOR=0;LSEQ=CATTTGCATCGGTGGGCGTC;RSEQ=GGCCTCACTCGGGGGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:37,33:0.0278:2,2:28.5:1:31:1:1:1.11943:50:4:0.0282:0:1 0/0:100:0:0,0:52,48:0:2,0:24.8:1:30.2:1:1:0:56.9:49:1:0:0.5 -GL000220.1 134793 . C T 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65581;SOR=0.7609;LSEQ=TCGGTGGGCGTCAGGCCTCA;RSEQ=TCGGGGGCCACCGTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:11:5,6:32,31:0.1486:2,2:18.9:1:30.3:1:1:1.23513:51.2:22:0.1507:0:2.5 0/1:111:13:7,6:50,48:0.1171:2,2:27:1:29.2:1:1:1.12:49.5:12:0.1101:0:2.5 -GL000220.1 134796 . G A 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.96674;LSEQ=GTGGGCGTCAGGCCTCACTC;RSEQ=GGGGCCACCGTTTTTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:8:4,4:32,39:0.1013:2,2:21.9:1:30.6:1:1:1.22:48.6:16:0.1039:0:3 0/1:112:11:6,5:51,50:0.0982:2,2:29.8:1:30.2:1:1:1.17:54.6:22:0.0991:0:2.6 -GL000220.1 134800 . G T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5968;SOR=0.68105;LSEQ=GCGTCAGGCCTCACTCGGGG;RSEQ=CCACCGTTTTTGAAGATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:8:4,4:29,40:0.1026:2,2:23.5:1:30.4:1:0.71841:1.37:48.6:16:0.1096:0:3 0/1:111:8:4,4:52,51:0.0721:2,2:21.3:1:29.1:1:1:1.01943:44.9:16:0.0721:0:2.8 -GL000220.1 134831 . TC T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50408;SOR=Inf;LSEQ=TGAAGATGGGGGCGGCACGG;RSEQ=CCACTTCCCCGGAGGCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:40,49:0:2,0:25.8:1:31:1:1:0:59.5:88:1:0:0.4 0/1:112:2:1,1:56,54:0.0179:2,2:21.5:1:27.5:1:1:1.03671:60:4:0.018:0.0089:0.5 -GL000220.1 134851 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50216;SOR=Inf;LSEQ=TCCCACTTCCCCGGAGGCAG;RSEQ=TTGGGCCGATGGCATAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:38,44:0:2,0:26.9:1:32.5:1:1:0:59.4:164:1:0:0.4 0/1:100:2:1,1:48,49:0.02:2,2:38:0:32.5:1:1:1.02:60:4:0.0206:0:1 -GL000220.1 134868 . GC G 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51869;SOR=0.57219;LSEQ=CAGCTTGGGCCGATGGCATA;RSEQ=CCCTTGACCCGCGTGGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:6:3,3:34,43:0.0723:2,2:34:1:33.7:1:1:1.26:56.8:12:0.0732:0:0.8 0/1:94:4:1,3:44,46:0.0426:2,2:24.5:1:30.5:1:0.61822:2.84048:54.5:8:0.044:0:0 -GL000220.1 134919 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.22365;SOR=0;LSEQ=TCTGCAGTTGTGAGGCTTTT;RSEQ=CCCCCGCTGCTTCCCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:34,29:0.0303:2,2:22:0:32:1:1:1.16953:60:4:0.0313:0:1.5 0/0:73:0:0,0:29,43:0:2,0:26.1:1:31.4:1:1:0:60:144:0.9863:0:0.2 -GL000220.1 134999 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17326;SOR=Inf;LSEQ=TCGGTCACCTTTTATCACGA;RSEQ=GTTTTAGTTTCTCCGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:25,36:0:2,0:20.2:1:30.3:1:1:0:60:60:1:0:0.3 0/1:44:2:1,1:18,24:0.0455:2,2:33:0:30:1:1:1.32:60:4:0.0455:0:1.5 -GL000220.1 135180 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=TTTGTTGGCTTGTTTTGTTT;RSEQ=GTTCTGTTTTGTTTTGTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:0:2,0:22.8:1:30.3:1:1:0:60:20:1:0:0.3 0/1:14:2:1,1:7,5:0.1429:2,2:17:0:32:0:1:1.36624:60:4:0.1429:0:3.5 -GL000220.1 135183 . TC AT 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=GTTGGCTTGTTTTGTTTCGT;RSEQ=TGTTTTGTTTTGTTCGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:0:2,0:23.8:1:29.6:1:1:0:60:20:1:0:0.3 0/1:14:2:1,1:8,4:0.1429:2,2:13:0:31.5:1:1:1.89743:60:4:0.1429:0:2.5 -GL000220.1 135224 . T C 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23585;SOR=0;LSEQ=TTTTCCTTTCTCGTATGTCT;RSEQ=TCTTTTCAGGTGAAGTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:15,9:0.0769:2,2:19:0:29.5:1:1:1.63293:60:4:0.0833:0:1.5 0/0:27:0:0,0:13,14:0:2,0:26:1:29.6:1:1:0:60:26:1:0:0.3 -GL000220.1 135265 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=ATCCCCAGTTTTCAGGAAGA;RSEQ=GTCTATTTTCCCCAAGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,12:0:2,0:29.7:1:30.4:1:1:0:60:44:1:0:0.3 0/1:23:2:1,1:11,10:0.087:2,2:5.5:1:28.5:1:1:1.09544:60:4:0.0952:0:1 -GL000220.1 135295 . C T 46 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62567;SOR=0.43796;LSEQ=CCCCAAGACACGTTAGCTGC;RSEQ=GTTTTTTCCTGTTGTGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:1,2:8,10:0.1429:2,2:36.3:1:29.3:1:1:1.56568:60:6:0.1429:0:1 0/1:15:1:1,0:8,6:0.0667:2,0:48:0:33:0:1:0:60:2:0.0714:0:1 -GL000220.1 135366 . T C 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95327;LSEQ=GAGAGCCGGTTGATGTTTAC;RSEQ=ATCCTTCATCATGACATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:2,3:12,8:0.2:2,2:16.6:1:31:1:0.62319:2.17635:60:10:0.2083:0:1.4 0/1:26:5:3,2:11,10:0.1923:2,2:18.8:1:30.8:1:1:1.35:60:10:0.1923:0:1.2 -GL000220.1 135436 . G GCTTTTGTTATTGTTGCAGCTACTTTTGTTGCTCCTC 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.50314;SOR=Inf;LSEQ=CTGCTGCTCTTGTTGCTGTT;RSEQ=TTGTTGTTGTTGTTGTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:26,19:0:2,0:26.8:1:32.4:1:1:0:59.9:90:1:0:0.2 0/1:58:2:1,1:29,27:0.0345:2,2:43.5:1:26.7:1:1:1.07272:60:4:0.0364:0.0345:0 -GL000220.1 135437 . T C 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.49973;SOR=Inf;LSEQ=TGCTGCTCTTGTTGCTGTTG;RSEQ=TGTTGTTGTTGTTGTCGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:26,22:0:2,0:25.5:1:29.7:1:1:0:59.9:96:1:0:0.2 0/1:58:2:1,1:29,27:0.0345:2,2:10.5:1:34:0:1:1.07272:51.5:4:0.0357:0:2 -GL000220.1 135438 . T C 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.23897;SOR=0.30507;LSEQ=GCTGCTCTTGTTGCTGTTGT;RSEQ=GTTGTTGTTGTTGTCGTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:5:1,4:25,18:0.1042:2,2:15.6:1:29.2:1:0.16487:5.3721:60:10:0.1064:0:1.6 0/1:59:2:0,2:30,27:0.0339:2,0:21:1:31:1:0.23729:0:60:4:0.0345:0:1.5 -GL000220.1 135480 . T C 51 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.647;SOR=2.06203;LSEQ=GCTGTTGTCGTTGTCGTTGT;RSEQ=GTTGTCGTTGTCGTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:1:0,1:24,23:0.0208:2,0:44:0:28:0:1:0:60:2:0.0208:0:2 0/1:71:3:2,1:36,32:0.0423:2,2:25.3:1:32.3:1:1:1.76:60:6:0.0429:0:1 -GL000220.1 135486 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.51379;SOR=Inf;LSEQ=GTCGTTGTCGTTGTTGTTGT;RSEQ=GTTGTCGTTGTTTTCAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:22,25:0:2,0:25.2:1:29.8:1:1:0:60:46:1:0:0.1 0/1:69:2:1,1:33,34:0.029:2,2:15:0:31:1:1:1.03:50:4:0.029:0:1.5 -GL000220.1 135510 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49981;SOR=Inf;LSEQ=GTCGTTGTTTTCAAAGTATA;RSEQ=CCCGGCCACCGTTTATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:23,24:0:2,0:23.9:1:31.9:1:1:0:60:94:1:0:0.1 0/1:57:2:1,1:27,28:0.0351:2,2:7:0:31.5:1:1:1.04:60:4:0.0364:0:1 -GL000220.1 135621 . T C 45 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12018;SOR=0;LSEQ=GTCTGTCTCTGTCTCTCTCT;RSEQ=TCTCTGTCTGTCTTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:0,3:39,35:0.039:2,0:18.7:1:29:1:0.11532:0:53:6:0.0405:0:4.7 0/0:78:0:0,0:43,35:0:2,0:26.5:1:28.8:1:1:0:59.2:18.5:1:0:0.3 -GL000220.1 135654 . G C 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21127;SOR=5.07448;LSEQ=TTCTCTCTCTCTCTCTCTCT;RSEQ=TGTCTCTCTCTCTCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:0,1:48,41:0.0109:2,0:36:0:14:0:0.46667:0:60:0:0:0:5 0/1:94:5:3,2:48,40:0.0532:2,2:9.8:1:30.4:1:1:1.25:60:10:0.0549:0:2 -GL000220.1 135656 . GTC G 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.67892;SOR=0.63892;LSEQ=CTCTCTCTCTCTCTCTCTGT;RSEQ=TCTCTCTCTCTGCCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:1,2:46,41:0.0333:2,2:37:1:32.7:1:0.60433:2.2244:60:6:0.0337:0:0 0/1:93:2:1,1:49,42:0.0215:2,2:29:1:32.5:1:1:1.16473:60:4:0.022:0:0.5 -GL000220.1 135680 . TTC T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.24412;SOR=Inf;LSEQ=CTCTCTCTCTGCCTGTCTGT;RSEQ=TCTCTCTCTGCCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:59,47:0:2,0:22.5:1:30.2:1:1:0:58.9:105:1:0:0.5 0/1:105:2:1,1:53,49:0.019:2,2:24:1:27:1:1:1.0808:60:4:0.0192:0.0095:0 -GL000220.1 135693 . CCT C 170 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=12.000;MSILEN=2;SSF=0.77787;SOR=1.08669;LSEQ=TGTCTGTTTCTCTCTCTCTG;RSEQ=CTCTCTCTCTCTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:41:23,18:23,21:0.3445:2,2:25.1:1:31.8:1:0.82833:1.16:59.6:82:0.3628:0.0588:0.3 0/1:99:36:21,15:15,16:0.3636:2,2:29.8:1:30.9:1:0.46759:1.48:59.6:72:0.3789:0.0505:0.3 -GL000220.1 135747 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=TCTCACTGTGTCTGTCTTCT;RSEQ=TCTTACTCCCTTTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:65,51:0:2,0:25.2:1:31.1:1:1:0:59.8:28:0.9912:0:0.3 0/1:126:2:1,1:63,59:0.0159:2,2:17:1:28.5:1:1:1.0672:60:4:0.0163:0:2.5 -GL000220.1 135756 . C T 50 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68819;SOR=1.76172;LSEQ=GTCTGTCTTCTGTCTTACTC;RSEQ=CTTTCTCTGTCTGTCTGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:61,52:0.0174:2,0:16:1:16:1:0.50023:0:51:0:0:0:4.5 0/1:132:4:2,2:68,60:0.0303:2,2:6.8:1:25:1:1:1.13226:60:3:0.0233:0:2 -GL000220.1 135799 . GT CC 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50933;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCCCT;RSEQ=CTGTATGTTTCTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:60,56:0:2,0:23.7:1:31.4:1:1:0:59.3:22.2:0.9911:0:0.4 0/1:158:2:1,1:78,75:0.0127:2,2:15:0:29.8:1:1:1.03975:60:4:0.0134:0:2 -GL000220.1 135801 . CTGTA C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50505;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCCCTGT;RSEQ=TGTTTCTCTCTGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:67,58:0:2,0:22.8:1:30.3:1:1:0:59.4:40.667:1:0:0.3 0/1:158:2:1,1:78,77:0.0127:2,2:28:0:33:0:1:1.01291:60:4:0.0127:0:1.5 -GL000220.1 135805 . A C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5064;SOR=Inf;LSEQ=CTCTCTCTCTCCCTGTCTGT;RSEQ=TGTTTCTCTCTGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:67,56:0:2,0:23.9:1:28.6:1:1:0:59.4:16.571:1:0:0.3 0/1:159:2:1,1:74,80:0.0126:2,2:20:0:31:1:1:1.08:60:4:0.0132:0:2 -GL000220.1 135823 . GTC G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.25975;SOR=Inf;LSEQ=GTATGTTTCTCTCTGTCTCT;RSEQ=TCTCTCTCTCTTTCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:68,53:0:2,0:26.2:1:29.8:1:1:0:58.9:242:1:0:0.3 0/1:158:3:2,1:80,75:0.019:2,2:22:1:29.8:1:1:1.87:56.7:6:0.019:0.0063:0.7 -GL000220.1 135829 . C CTCTCTCTTTCTGTTTCTCTCTCTCCG 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.00302;SOR=Inf;LSEQ=TTCTCTCTGTCTCTGTCTCT;RSEQ=TCTCTCTTTCTGTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:68,53:0:2,0:26.9:1:31.7:1:1:0:58.9:59.5:1:0:0.3 0/1:163:11:5,6:76,74:0.0675:2,2:26.5:1:28.8:1:0.76559:1.23083:59.1:22:0.0683:0.0368:0.2 -GL000220.1 135832 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.50996;SOR=Inf;LSEQ=TCTCTGTCTCTGTCTCTCTC;RSEQ=CTCTTTCTGTTTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:66,53:0:2,0:27.2:1:30.6:1:1:0:58.9:58.5:1:0:0.3 0/1:162:2:1,1:81,79:0.0123:2,2:11.5:1:29:1:1:1.02516:60:4:0.0127:0:2.5 -GL000220.1 135837 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50733;SOR=Inf;LSEQ=GTCTCTGTCTCTCTCTCTCT;RSEQ=TCTGTTTCTCTCTCTCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:66,54:0:2,0:25.8:1:29.7:1:1:0:59.1:29:1:0:0.3 0/1:160:2:2,0:79,79:0.0125:2,0:22:1:33:0:0.49693:0:40:4:0.0127:0:5 -GL000220.1 135841 . G C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50788;SOR=Inf;LSEQ=CTGTCTCTCTCTCTCTTTCT;RSEQ=TTTCTCTCTCTCCGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:66,54:0:2,0:25.5:1:31.5:1:1:0:59.3:29:1:0:0.3 0/1:160:2:2,0:78,79:0.0125:2,0:26:1:32.5:1:0.49686:0:40:4:0.0129:0:5 -GL000220.1 135843 . T A 27 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.5809;SOR=0.38042;LSEQ=GTCTCTCTCTCTCTTTCTGT;RSEQ=TCTCTCTCTCCGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:63,53:0.0169:2,2:10.5:1:27:1:1:1.18693:60:4:0.0179:0:1.5 0/0:154:1:1,0:72,75:0.0065:2,0:1:0:24:0:0.49324:0:60:2:0.0067:0:3 -GL000220.1 135854 . C T 49 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.63303;SOR=2.38194;LSEQ=TCTTTCTGTTTCTCTCTCTC;RSEQ=GTCTCTGTCTTTCTCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:1:0,1:68,57:0.0079:2,0:24:0:32:0:0.46032:0:40:2:0.0083:0:3 0/1:160:3:2,1:76,81:0.0188:2,2:20:1:31.3:1:0.61333:2.12:60:6:0.0192:0:3 -GL000220.1 135872 . A ACTGT 138 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.48131;SOR=1.37505;LSEQ=TCCGTCTCTGTCTTTCTCTG;RSEQ=CTGTCTCTCTCTTTCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:14:7,7:54,52:0.1167:2,2:18.7:1:30.3:1:1:1.03815:58.6:28:0.125:0.05:0.4 0/1:156:24:12,12:69,63:0.1538:2,2:20.2:1:30.1:1:1:1.0946:58.1:48:0.1569:0.0513:0.8 -GL000220.1 135874 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=0.50663;SOR=Inf;LSEQ=CGTCTCTGTCTTTCTCTGAC;RSEQ=GTCTCTCTCTTTCCTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:59,58:0:2,0:23.7:1:30.2:1:1:0:59.8:38:1:0:0.2 0/1:152:2:1,1:77,73:0.0132:2,2:19:1:28.5:1:1:1.05445:60:4:0.0132:0:1 -GL000220.1 135887 . CCTTCTC TTCTGTCTG 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.51702;SOR=Inf;LSEQ=CTCTGACTGTCTCTCTCTTT;RSEQ=TCTGTCTCTCTCTGCCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:56,52:0:2,0:26.1:1:31.4:1:1:0:60:107:1:0:0.2 0/1:160:2:1,1:77,81:0.0125:2,2:24:1:29:1:1:1.05:60:4:0.0127:0.0063:1.5 -GL000220.1 135888 . C T 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.26518;SOR=Inf;LSEQ=TCTGACTGTCTCTCTCTTTC;RSEQ=TTCTCTCTGTCTCTCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:55,57:0:2,0:25.5:1:30.7:1:1:0:60:27:1:0:0.2 0/1:153:3:2,1:74,74:0.0196:2,2:11.3:1:24.7:1:1:1.99:53.3:2:0.0134:0:3.3 -GL000220.1 135891 . C CTGTCGTCTGTCTCTGTCTCTG 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=6;SSF=0.26937;SOR=Inf;LSEQ=GACTGTCTCTCTCTTTCCTT;RSEQ=TCTCTGTCTCTCTCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:52,59:0:2,0:26:1:31.3:1:1:0:60:54.5:1:0:0.2 0/1:157:3:1,2:77,75:0.0191:2,2:18.3:1:29.2:1:0.62011:2.04415:60:6:0.02:0.0191:0 -GL000220.1 135908 . CCTGT C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51199;SOR=Inf;LSEQ=CTTCTCTCTGTCTCTCTCTG;RSEQ=CTCTCTCACTCTGTCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:54,59:0:2,0:26.2:1:31.4:1:1:0:60:36.667:1:0:0.2 0/1:158:2:1,1:75,81:0.0127:2,2:9:1:28.9:1:1:1.08:60:4:0.013:0.0063:0 -GL000220.1 135937 . ACT A 75 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.23595;SOR=3.96022;LSEQ=CTCACTCTGTCTTCTGTCTT;RSEQ=CTCTCTCTCTGCCTGCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:1:0,1:51,58:0.0091:2,0:46:0:34:0:1:0:60:2:0.0092:0:0 0/1:142:5:1,4:66,71:0.0352:2,2:23.4:1:32.5:1:0.37011:3.6883:60:10:0.0368:0.0141:0.2 -GL000220.1 135960 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.50388;SOR=Inf;LSEQ=CTCTCTCTCTGCCTGCCTGT;RSEQ=TCTCTCACTCTCTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:44,61:0:2,0:22.2:1:31.5:1:1:0:59.8:34:0.9903:0:0.2 0/1:132:2:1,1:60,70:0.0152:2,2:16:1:31:1:1:1.17:60:4:0.0155:0:2 -GL000220.1 135967 . ACT A 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.50442;SOR=Inf;LSEQ=TCTGCCTGCCTGTCTCTCTC;RSEQ=CTCTCTCTCTGTGTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:43,55:0:2,0:23.3:1:31.9:1:1:0:60:48:0.9796:0:0.2 0/1:126:2:0,2:57,67:0.0159:2,0:21:1:34:0:0.50057:0:60:4:0.016:0:0 -GL000220.1 135976 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0.50029;SOR=Inf;LSEQ=CTGTCTCTCTCACTCTCTCT;RSEQ=TCTGTGTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:50,55:0:2,0:21.4:1:31.8:1:1:0:59.8:104:1:0:0.3 0/1:121:2:1,1:53,64:0.0165:2,2:21.5:1:32:0:1:1.21:60:4:0.0167:0:1 -GL000220.1 135980 . G C 67 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06279;SOR=Inf;LSEQ=CTCTCTCACTCTCTCTCTCT;RSEQ=TGTGTCTCTCTCTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:49,53:0:2,0:21.9:1:32:1:1:0:60:50:0.9901:0:0.2 0/1:123:5:1,4:56,62:0.0407:2,2:28:1:29:1:0.37152:3.58007:60:4:0.0336:0:2.4 -GL000220.1 135982 . G C 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.76246;LSEQ=CTCTCACTCTCTCTCTCTGT;RSEQ=TGTCTCTCTCTCTCTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:1:0,1:51,54:0.0093:2,0:9:0:34:0:1:0:40:2:0.0093:0:5 0/1:122:2:1,1:57,62:0.0164:2,2:6.5:1:30.5:1:1:1.09:60:4:0.0167:0:1.5 -GL000220.1 135984 . GTC G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.83935;LSEQ=CTCACTCTCTCTCTCTGTGT;RSEQ=TCTCTCTCTCTTTCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:48,55:0.0189:2,2:14:0:33.5:1:1:1.14:60:4:0.019:0:0.5 0/1:126:2:1,1:60,64:0.0159:2,2:21:1:30.3:1:1:1.07:60:4:0.016:0.0079:0 -GL000220.1 135998 . T TTCTG 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06568;SOR=0.40076;LSEQ=CTGTGTGTCTCTCTCTCTCT;RSEQ=TCTGTTTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:14:6,8:40,47:0.1386:2,2:21.7:1:30.9:1:1:1.13334:58.6:28:0.1386:0.0396:0.9 0/1:116:7:4,3:46,60:0.0603:2,2:35.4:1:31.1:1:0.6977:1.73:56.7:14:0.0614:0:0.9 -GL000220.1 136020 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=8;SSF=0.49899;SOR=Inf;LSEQ=CTGTTTCTCTCTGTCTCTCT;RSEQ=TCCGTCTCTGTCTTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:50,49:0:2,0:25.5:1:32:1:1:0:59.8:48.5:1:0:0.2 0/1:110:2:1,1:50,58:0.0182:2,2:39.5:1:29.5:1:1:1.16:60:4:0.0183:0:1 -GL000220.1 136036 . CTCTG C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0.49761;SOR=Inf;LSEQ=CTCTGTCCGTCTCTGTCTTT;RSEQ=TCTGTCTCTTTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:52,52:0:2,0:23:1:30.9:1:1:0:59.3:103:1:0:0.3 0/1:105:2:0,2:50,52:0.019:2,0:29:1:31:1:0.49589:0:60:4:0.0192:0:0 -GL000220.1 136039 . T C 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=2.000;MSILEN=4;SSF=0.0511;SOR=0.27144;LSEQ=TGTCCGTCTCTGTCTTTCTC;RSEQ=GTCTGTCTCTTTGTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:11:7,4:46,50:0.1028:2,2:29.7:1:30.5:1:0.35911:1.89:58.2:22:0.1028:0:1.4 0/1:100:3:1,2:46,49:0.03:2,2:19.3:1:29:1:1:1.86598:60:6:0.0309:0:1.7 -GL000220.1 136042 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.24406;SOR=0;LSEQ=CCGTCTCTGTCTTTCTCTGT;RSEQ=TGTCTCTTTGTCTGTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:51,51:0.0192:2,2:6.5:1:30:1:1:1:60:4:0.0194:0:1.5 0/0:106:0:0,0:49,57:0:2,0:23.3:1:30.8:1:1:0:59.6:52:1:0:0.3 -GL000220.1 136103 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49809;SOR=Inf;LSEQ=TCTCTGTCTCTCTCACTGTG;RSEQ=CTGTCTTCTGTCTTAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:62,53:0:2,0:24.1:1:29.5:1:1:0:59.8:37.333:1:0:0.4 0/1:120:2:1,1:58,60:0.0167:2,2:10.5:1:29.5:1:1:1.03:60:4:0.0167:0:2.5 -GL000220.1 136106 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.87643;LSEQ=CTGTCTCTCTCACTGTGTCT;RSEQ=TCTTCTGTCTTAGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:1,0:62,49:0.0089:2,0:1:0:25:0:1:0:60:2:0.0098:0:1 0/1:120:2:1,1:56,62:0.0167:2,2:7.5:1:27:1:1:1.11:60:4:0.0174:0:2.5 -GL000220.1 136164 . TC T 33 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.50037;SOR=0;LSEQ=TGTCTGTCTCTCTCTCTCTC;RSEQ=CCCCTGTCTGTTTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:54,62:0.0169:2,2:26:0:33:0:1:1.15:60:4:0.0169:0:1 0/0:102:0:0,0:53,49:0:2,0:24.7:1:30.7:1:1:0:59.4:101:1:0:0.4 -GL000220.1 136166 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.66895;SOR=1.69091;LSEQ=TCTGTCTCTCTCTCTCTCTC;RSEQ=CCCTGTCTGTTTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:51,62:0.0174:2,2:15:1:20:1:1:1.21:60:1:0.0094:0:1 0/1:103:3:2,1:51,48:0.0291:2,2:13.7:1:27.7:1:1:1.87:60:6:0.0303:0:2 -GL000220.1 136168 . CCTG TGCCTT 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.22623;SOR=Inf;LSEQ=TGTCTCTCTCTCTCTCTCCC;RSEQ=TCTGTTTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:51,62:0:2,0:25.3:1:30.8:1:1:0:59.5:112:1:0:0.5 0/1:103:2:0,2:54,47:0.0194:2,0:6:1:26.8:1:0.22387:0:60:4:0.0194:0.0097:1 -GL000220.1 136177 . TTCTCTCTCTCTC T 134 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=16.000;MSILEN=2;SSF=0.29221;SOR=1.49269;LSEQ=CTCTCTCTCCCCCTGTCTGT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:18:8,10:16,23:0.1622:2,2:25.6:1:29.7:1:1:1.15:59.4:17:0.1589:0.045:0.5 0/1:98:22:11,11:19,17:0.2245:2,2:26.6:1:30.2:1:1:1.1155:58.9:44:0.2292:0.051:0.5 -GL000220.1 136220 . T A 29 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.62152;SOR=0.4923;LSEQ=TCTCTCTCTCTGTCTTTGTC;RSEQ=TTCTTTCTGTCTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:42,64:0.0185:2,2:9:0:29:1:1:1.52:60:4:0.0189:0:2 0/0:109:1:1,0:59,49:0.0092:2,0:1:0:24:0:1:0:60:2:0.0093:0:1 -GL000220.1 136257 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=2;SSF=0.20745;SOR=0;LSEQ=CTCTCTCTCTCTCTCTGTGT;RSEQ=TCTGTCTTCTGTCTTACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:37,51:0.0222:2,2:42:0:31:1:1:1.37:60:4:0.0227:0:1 0/0:107:0:0,0:58,49:0:2,0:26:1:31.2:1:1:0:59.6:52.5:1:0:0.4 -GL000220.1 136289 . T C 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52661;SOR=Inf;LSEQ=TCTTACTGTCTTTCTCTGCC;RSEQ=GTCTGTCTGTCTGTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:40,43:0:2,0:23.6:1:30.3:1:1:0:60:26.667:1:0:0.3 0/1:137:2:1,1:71,64:0.0146:2,2:6:0:27:1:1:1.10853:26:4:0.015:0:1.5 -GL000220.1 136294 . GTCTGTCTGTCTCTC G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=4.000;MSILEN=2;SSF=0.52563;SOR=Inf;LSEQ=CTGTCTTTCTCTGCCTGTCT;RSEQ=TCTGTCTGTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:43,42:0:2,0:23.6:1:29.9:1:1:0:60:84:1:0:0.3 0/1:139:2:2,0:74,63:0.0144:2,0:11.5:1:30.5:1:0.50078:0:60:4:0.0145:0.0072:1 -GL000220.1 136313 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.53054;SOR=Inf;LSEQ=TGTCTGTCTGTCTCTCTCTG;RSEQ=CTGTCTCTCTCTCTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:43,37:0:2,0:24.5:1:29.6:1:1:0:60:39:1:0:0.3 0/1:135:2:1,1:68,63:0.0148:2,2:28.5:1:29.5:1:1:1.07872:60:4:0.0152:0:2.5 -GL000220.1 136316 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.53144;SOR=Inf;LSEQ=CTGTCTGTCTCTCTCTGTCT;RSEQ=TCTCTCTCTCTCTCTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:41,39:0:2,0:24.1:1:30.5:1:1:0:60:10.429:1:0:0.3 0/1:136:2:1,1:70,64:0.0147:2,2:28.5:1:30:1:1:1.09302:60:4:0.0155:0:2.5 -GL000220.1 136320 . C T 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.52932;SOR=Inf;LSEQ=CTGTCTCTCTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCCCCCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:40,39:0:2,0:23.7:1:31.2:1:1:0:60:25.333:1:0:0.3 0/1:132:2:1,1:66,64:0.0152:2,2:34.5:1:30:1:1:1.03102:60:4:0.0156:0:1.5 -GL000220.1 136326 . CTCTCT C 32 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.53146;SOR=Inf;LSEQ=CTCTCTGTCTGTCTCTCTCT;RSEQ=CCCCCCGTCGGCTGTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:38,36:0:2,0:23.6:1:30:1:1:0:60:23.667:1:0:0.3 0/1:126:2:1,1:62,58:0.0159:2,2:16:1:32.1:1:1:1.06835:60:4:0.0164:0.0159:0 -GL000220.1 136330 . CT C 107 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00925;SOR=Inf;LSEQ=CTGTCTGTCTCTCTCTCTCT;RSEQ=CCCCCCGTCGGCTGTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:32,34:0:2,0:23:1:30.1:1:1:0:60:65:0.9286:0:0.2 0/1:131:12:7,5:53,53:0.0916:2,2:13.3:1:30.1:1:0.76249:1.40:60:24:0.0984:0.0763:0.8 -GL000220.1 136333 . C CT 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.15968;SOR=Inf;LSEQ=TCTGTCTCTCTCTCTCTCTC;RSEQ=CCCCGTCGGCTGTTTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:36,37:0:2,0:22.5:1:30.5:1:1:0:60:35.5:1:0:0.3 0/1:124:5:2,3:56,51:0.0403:2,2:35.2:1:25.7:1:0.67086:1.63978:60:1.5:0.028:0.0161:2.2 -GL000220.1 136337 . C CT 188 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.21886;SOR=0.65262;LSEQ=TCTCTCTCTCTCTCTCCCCC;RSEQ=GTCGGCTGTTTCTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:50:26,24:4,7:0.6944:2,2:28:1:30.7:1:0.50773:1.88:60:100:0.7143:0:0.2 1/0:124:74:37,37:6,7:0.5968:2,2:28.7:1:30.4:1:1:1.16:59.6:148:0.6667:0:0.3 -GL000220.1 136340 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54437;SOR=Inf;LSEQ=CTCTCTCTCTCTCCCCCCGT;RSEQ=GGCTGTTTCTCTGTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:34,33:0:2,0:25.1:1:30.1:1:1:0:60:66:1:0:0.4 0/1:126:2:1,1:64,57:0.0159:2,2:9:0:31:1:1:1.12175:60:4:0.0174:0:1.5 -GL000220.1 136362 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16036;SOR=0;LSEQ=GCTGTTTCTCTGTCTCTGTC;RSEQ=GTGTCTCTCTTTCTGTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:43,43:0.0227:2,2:37.5:1:30.5:1:1:1:60:4:0.0233:0:1.5 0/0:131:0:0,0:67,62:0:2,0:22.8:1:29.6:1:1:0:59.7:42:1:0:0.5 -GL000220.1 136383 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51212;SOR=Inf;LSEQ=GTGTCTCTCTTTCTGTCTGT;RSEQ=TCTCTCTGTCTGTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:44,44:0:2,0:25.5:1:29.7:1:1:0:60:28.333:1:0:0.3 0/1:124:2:1,1:59,59:0.0161:2,2:27.5:1:30:1:1:1:60:4:0.0169:0:1 -GL000220.1 136399 . TTCTC T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=4.000;MSILEN=2;SSF=0.507;SOR=Inf;LSEQ=CTGTTTCTCTCTGTCTGTCT;RSEQ=TCTCTGTCTCTTTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:44,44:0:2,0:23.9:1:30.2:1:1:0:59.8:87:1:0:0.4 0/1:116:2:1,1:56,58:0.0172:2,2:20:1:32:1:1:1.04:60:4:0.0175:0.0086:0.5 -GL000220.1 136453 . GTC G 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=1.70894;LSEQ=CTGTCTCTGTCTCTCTCTCT;RSEQ=TCTCTCTCTCTGTGGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:1:0,1:28,28:0.0175:2,0:40:0:26:0:1:0:60:2:0.0175:0:0 0/1:101:3:2,1:51,47:0.0297:2,2:33:1:30.3:1:1:1.83:56.7:6:0.0306:0:0.7 -GL000220.1 136472 . G T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.00296;LSEQ=TGTCTCTCTCTCTCTGTGGG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:5:1,4:25,23:0.0943:2,2:25.8:1:27.6:1:0.35072:4.24085:51:10:0.0943:0:2.6 0/1:74:7:4,3:34,27:0.0946:2,2:31.4:1:25.7:1:1:1.06:58.6:6:0.0923:0:1.9 -GL000220.1 136491 . GTGTATG A 124 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=21.000;MSILEN=2;SSF=0.11465;SOR=0.52272;LSEQ=GGGGTGTGTGTGTGTGTGTG;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:20:9,11:10,13:0.4082:2,2:21:1:28.9:1:1:1.06:60:19:0.4524:0.1837:0.3 0/1:72:19:12,7:24,21:0.2639:2,2:23.4:1:26.7:1:0.58451:1.49:55.9:18:0.2727:0.1389:0.8 -GL000220.1 136526 . C T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52149;SOR=Inf;LSEQ=TGTGTGTGTGTGTGTGTCTG;RSEQ=CTTCTGTCTTACTCTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:22,30:0:2,0:24.2:1:31.5:1:1:0:59.3:51:1:0:0.6 0/1:82:2:1,1:36,43:0.0244:2,2:5:0:26.5:1:1:1.19:30:4:0.026:0:0 -GL000220.1 136528 . T TTCTGTCTTACTCTCCTGGGTCTCTGTCTCTGTCTCTCTCCGTGTCTCTGTCTCTCTGTCTCTGTCTCTGTC 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=4.000;MSILEN=6;SSF=0.15433;SOR=Inf;LSEQ=TGTGTGTGTGTGTGTCTGCC;RSEQ=TCTGTCTTACTCTCTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:24,31:0:2,0:23.4:1:30.9:1:1:0:59.4:54:1:0:0.6 0/1:85:4:3,1:36,45:0.0471:2,2:33:1:27.8:1:0.32884:3.70:48.8:8:0.0513:0.0471:0.5 -GL000220.1 136574 . GTC G 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.65576;SOR=1.25701;LSEQ=GTCTGTCTGCCTGTCTGTTT;RSEQ=TCTCTCTCTCTGCCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:10:5,5:47,39:0.1042:2,2:28.7:1:32.4:1:1:1.20277:60:20:0.1042:0.0104:0.1 0/1:94:12:7,5:43,40:0.1277:2,2:23.4:1:30.8:1:0.7632:1.30:60:24:0.129:0.0319:0.2 -GL000220.1 136576 . C G 34 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=2;SSF=0.49733;SOR=0;LSEQ=CTGTCTGCCTGTCTGTTTGT;RSEQ=TCTCTCTCTCTGCCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:45,38:0.0213:2,2:18:0:34:0:1:1.18184:60:4:0.0241:0:1.5 0/0:93:0:0,0:43,40:0:2,0:25:1:31.5:1:1:0:59.5:40.5:1:0:0.3 -GL000220.1 136637 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.49802;SOR=Inf;LSEQ=TCTCTCTTTCTGTTTCTCTC;RSEQ=GTCTCTGTCCATCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:57,45:0:2,0:25.7:1:30.5:1:1:0:60:101:1:0:0.2 0/1:108:2:1,1:58,48:0.0185:2,2:35:0:31.5:1:1:1.2062:60:4:0.0187:0:1.5 -GL000220.1 136658 . TTCTCCGTCTGTCTCTTTATCTGTCTC T 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=4.000;MSILEN=2;SSF=0.77668;SOR=1.2943;LSEQ=GTCTCTGTCCATCTCTGTCT;RSEQ=TCTCCGTCTGTCTCTTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:5:2,3:40,41:0.0581:2,2:21.6:1:27.7:1:1:1.45702:60:10:0.061:0.0581:1.2 0/1:108:8:5,3:48,52:0.0741:2,2:25.9:1:29.8:1:0.4848:1.80:50.8:16:0.0755:0.0185:0.1 -GL000220.1 136680 . G A 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.17234;SOR=0;LSEQ=CTCCGTCTGTCTCTTTATCT;RSEQ=TCTCTCTCCGTCTGTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:2,0:40,35:0.025:2,0:25.5:1:26:1:0.49761:0:60:4:0.0263:0:1 0/0:112:0:0,0:51,52:0:2,0:23.2:1:31.1:1:1:0:59.3:102:0.9714:0:0.2 -GL000220.1 136706 . GTC G 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.02838;SOR=0;LSEQ=CTCCGTCTGTCTCTTTATCT;RSEQ=TCTCTCTCTCTTTCTGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:3,1:31,41:0.0526:2,2:31:1:33.5:1:0.31928:3.90:60:8:0.0541:0:0.3 0/0:107:0:0,0:55,52:0:2,0:26.1:1:29:1:1:0:60:106:1:0:0.2 -GL000220.1 136736 . C T 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.79375;SOR=0.78672;LSEQ=CTCTTTCTGTCTTTCTCTCT;RSEQ=TGTGTATCGTTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:8:3,5:34,43:0.0941:2,2:20.5:1:26.5:1:1:1.31363:56.1:3:0.075:0:1.8 0/1:106:8:5,3:49,48:0.0755:2,2:29.6:1:30.1:1:0.71655:1.63:56.3:16:0.0769:0:1.8 -GL000220.1 136737 . T C 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20191;SOR=0;LSEQ=TCTTTCTGTCTTTCTCTCTC;RSEQ=GTGTATCGTTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:36,49:0.023:2,2:23:1:28.5:1:1:1.36:60:4:0.023:0:1 0/0:106:0:0,0:54,52:0:2,0:22.2:1:30:1:1:0:59.5:105:1:0:0.5 -GL000220.1 136740 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50114;SOR=Inf;LSEQ=TTCTGTCTTTCTCTCTCTGT;RSEQ=TATCGTTGTCTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:39,52:0:2,0:25.3:1:31.7:1:1:0:59.7:44.5:1:0:0.4 0/1:108:2:2,0:52,54:0.0185:2,0:24:0:32:0:0.49533:0:60:4:0.0187:0:3 -GL000220.1 136782 . GTC G 139 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=13.000;MSILEN=2;SSF=0.72224;SOR=0.84594;LSEQ=GTCTCTGTCTCTGTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:20:7,13:14,23:0.2857:2,2:34.7:1:32.5:1:1:1.12802:60:40:0.2857:0.0143:0.1 0/1:95:24:10,14:24,18:0.2526:2,2:29.6:1:30.5:1:0.30701:1.84886:59.3:48:0.2581:0.0316:0.8 -GL000220.1 136815 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.5352;SOR=Inf;LSEQ=TCTCTCTCTCTCTCTGTCTG;RSEQ=CTGTCCGTCTGTCTGTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:20,28:0:2,0:21.2:1:30.1:1:1:0:60:96:1:0:0.2 0/1:85:2:1,1:36,47:0.0235:2,2:6.5:1:30.5:1:1:1.30:58:4:0.0241:0:3.5 -GL000220.1 136821 . C T 65 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16531;SOR=Inf;LSEQ=TCTCTCTCTGTCTGTCTGTC;RSEQ=GTCTGTCTGTCTCGGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:21,24:0:2,0:21.9:1:29.7:1:1:0:60:44:1:0:0.2 0/1:87:5:2,3:34,47:0.0575:2,2:10.8:1:28.2:1:1:1.0841:52.8:10:0.0602:0:3 -GL000220.1 136825 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=0.547;SOR=Inf;LSEQ=TCTCTGTCTGTCTGTCCGTC;RSEQ=GTCTGTCTCGGTCTCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:21,23:0:2,0:22.1:1:30.9:1:1:0:60:88:1:0:0.2 0/1:85:2:1,1:36,47:0.0235:2,2:43.5:1:31:1:1:1.30:60:4:0.0244:0:1.5 -GL000220.1 136875 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51482;SOR=Inf;LSEQ=TCCCGCCCTCTCTTTTTTTG;RSEQ=AAAAGAAGCTCAAGTACATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:14,17:0:2,0:25:1:32:1:1:0:60:62:1:0:0.2 0/1:47:2:1,1:18,27:0.0426:2,2:15:1:31:1:1:1.49:60:4:0.0426:0:1 -GL000220.1 136901 . T G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10182;LSEQ=AAGCTCAAGTACATCTAATC;RSEQ=AATCCCTTACCAAGGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:1,5:11,13:0.2:2,2:8.7:1:28.8:1:0.35753:4.05493:60:5:0.1724:0:1 0/1:37:8:2,6:14,15:0.2162:2,2:17.1:1:31.9:1:0.42271:2.72671:60:16:0.2162:0:1.1 -GL000220.1 137170 . C T 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25399;SOR=0.48554;LSEQ=TGTGACCGAGCCCTGTCCGT;RSEQ=CTGTCTCAAATATGTACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:4,5:8,13:0.3:2,2:24.2:1:29.4:1:1:1.29:60:18:0.3214:0:1.1 0/1:41:7:3,4:18,16:0.1707:2,2:27.6:1:29.7:1:0.69652:1.48521:60:14:0.175:0:1.1 -GL000220.1 137224 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50909;SOR=Inf;LSEQ=CCATTTCCACAACTACCCAC;RSEQ=GCCCCTTGTGGAACCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:0:2,0:25.8:1:29.9:1:1:0:60:17:1:0:0.4 0/1:27:2:1,1:11,14:0.0741:2,2:25:0:32.5:1:1:1.26:60:4:0.0741:0:1.5 -GL000220.1 137458 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2106;SOR=0;LSEQ=CACCGAGGTCAAATGGATAC;RSEQ=TCTGCATTGGCCCGAGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:26,20:0.0417:2,2:26.5:1:30.5:1:1:1.29283:60:4:0.0426:0:2.5 0/0:56:0:0,0:33,23:0:2,0:23.5:1:30.4:1:1:0:59.8:55:1:0:0.3 -GL000220.1 137494 . G A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12274;SOR=Inf;LSEQ=GGCCTCCGAAGTACATCACC;RSEQ=TCACCAACCGTCACCGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:33,31:0:2,0:23.8:1:29.7:1:1:0:59.7:11.8:1:0:0.4 0/1:73:4:2,2:34,35:0.0548:2,2:20.8:1:27.3:1:1:1.03:60:3:0.0423:0:1.8 -GL000220.1 137543 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18787;SOR=0;LSEQ=TGAGCCTGCCCAAGGCCCCG;RSEQ=CTCCGGGGAGACTCTTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:33,29:0.0313:2,2:36.5:1:30:1:1:1.13563:51.5:4:0.0333:0:3.5 0/0:83:0:0,0:39,43:0:2,0:25.2:1:31:1:1:0:60:26.333:0.9875:0:0.3 -GL000220.1 137567 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.19523;SOR=0;LSEQ=CGGGGAGACTCTTGGGAGCC;RSEQ=GGCCTTCGTCGGCTAAAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:31,34:0.0299:2,2:11.5:1:28:1:1:1.10:51.5:4:0.0308:0:5 0/0:84:0:0,0:42,42:0:2,0:24.5:1:29.3:1:1:0:59.8:41:1:0:0.2 -GL000220.1 137577 . C A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5999;SOR=0.4354;LSEQ=CTTGGGAGCCCGGCCTTCGT;RSEQ=GGCTAAAGTCCAAAGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:40,38:0.025:2,2:11.5:1:28:1:1:1.05198:51.5:4:0.0253:0:5 0/1:91:1:1,0:46,44:0.011:2,0:1:0:25:0:1:0:60:2:0.011:0:1 -GL000220.1 137666 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50096;SOR=Inf;LSEQ=TAGGTCAGAGAGGGGACCAG;RSEQ=AGGGGAGACGTCCCGACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:51,44:0:2,0:22.4:1:30.7:1:1:0:60:190:1:0:0.2 0/1:112:2:1,1:56,54:0.0179:2,2:37.5:1:28.5:1:1:1.03671:60:4:0.018:0:1 -GL000220.1 137690 . C T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.06261;LSEQ=GGAGACGTCCCGACAGGCGA;RSEQ=GAGTTCCCAAGGCTCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:6:3,3:51,50:0.0561:2,2:19.5:1:30:1:1:1.01981:60:12:0.0571:0:2.2 0/1:111:33:17,16:42,36:0.2973:2,2:17.4:1:30.3:1:0.83815:1.09711:60:66:0.3028:0:1.5 -GL000220.1 137741 . G A 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00631;SOR=0;LSEQ=CGCCCCACGCCCCACGTCCC;RSEQ=GGCACCCGCGGGACACCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:7:4,3:55,54:0.0603:2,2:18.3:1:29.6:1:1:1.31:60:6:0.0561:0:1.6 0/0:120:0:0,0:60,60:0:2,0:23.3:1:28:1:1:0:60:16.143:1:0:0.7 -GL000220.1 137748 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49969;SOR=Inf;LSEQ=CGCCCCACGTCCCGGGCACC;RSEQ=GCGGGACACCGCCGCTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:58,49:0:2,0:26.5:1:30:1:1:0:60:52.5:1:0:0.6 0/1:121:2:1,1:59,60:0.0165:2,2:20.5:1:32.5:1:1:1.02:60:4:0.0171:0:1 -GL000220.1 137762 . G C 145 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.63837;SOR=1.1778;LSEQ=GGCACCCGCGGGACACCGCC;RSEQ=CTTTATCCCCTCCTCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:23:13,10:47,39:0.211:2,2:25.3:1:29.6:1:1:1.08:60:22:0.2037:0:2 0/1:121:29:15,14:44,47:0.2397:2,2:23.2:1:30:1:0.83237:1.14:60:58:0.2458:0:1.5 -GL000220.1 137766 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24012;SOR=0;LSEQ=CCCGCGGGACACCGCCGCTT;RSEQ=ATCCCCTCCTCTGTCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:58,51:0.018:2,2:37:1:31:1:1:1.13593:60:4:0.0182:0:2 0/0:115:0:0,0:55,60:0:2,0:25.5:1:28:1:1:0:60:37.333:1:0:0.6 -GL000220.1 137786 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24638;SOR=0;LSEQ=TATCCCCTCCTCTGTCCACA;RSEQ=CCGGCCCCACCCCACCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:47,53:0.0194:2,2:15:1:28:1:1:1.13:60:4:0.0202:0:1.5 0/0:104:0:0,0:46,57:0:2,0:25.2:1:31.1:1:1:0:60:33.333:0.9901:0:0.3 -GL000220.1 137788 . C T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49761;SOR=0;LSEQ=TCCCCTCCTCTGTCCACAGC;RSEQ=GGCCCCACCCCACCACGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:48,54:0.0192:2,2:27.5:1:32:1:1:1.12:60:4:0.02:0:1.5 0/0:102:0:0,0:45,57:0:2,0:25:1:29.3:1:1:0:60:101:1:0:0.4 -GL000220.1 137843 . C T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20404;SOR=Inf;LSEQ=CTGGAGGTTCCAAAACCACA;RSEQ=GGTGTGACTAGAGCCTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:41,46:0:2,0:27.7:1:30.8:1:1:0:60:86:1:0:0.3 0/1:73:2:1,1:34,37:0.0274:2,2:25:0:32:0:1:1.09:60:4:0.0278:0:1 -GL000220.1 137901 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.49803;SOR=Inf;LSEQ=ACGAGGTGGGAGGGGTGGGG;RSEQ=TGGGGTGGGTTGGGGGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:29,31:0:2,0:21.6:1:28.9:1:1:0:58.1:9:1:0:0.9 0/1:68:2:0,2:33,33:0.0294:2,0:21:1:31.5:1:0.49298:0:60:4:0.0323:0:1 -GL000220.1 137902 . T G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.63932;SOR=0.78303;LSEQ=CGAGGTGGGAGGGGTGGGGG;RSEQ=GGGGTGGGTTGGGGGTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:11:0,11:29,19:0.1833:2,0:10.6:1:18.6:1:0.00032:0:51.1:1.2:0.1176:0:2.5 0/1:67:10:0,10:32,25:0.1493:2,0:10.6:1:20.8:1:0.001:0:56.9:2.333:0.1207:0:2.1 -GL000220.1 137912 . T TG 24 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1.68051;LSEQ=GGGGTGGGGGTGGGGTGGGT;RSEQ=GGGGGTTGTGGGGTCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:1:0,1:26,23:0.0182:2,0:21:0:9:0:0.48:0:60:0:0:0:3 0/1:66:2:0,2:30,31:0.0303:2,0:19:1:24:1:0.49309:0:60:4:0.04:0:2 -GL000220.1 137933 . C A 68 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23699;SOR=3.9059;LSEQ=GGGGGTTGTGGGGTCTGTGG;RSEQ=GAGCCCGATTCTCCCTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:1,0:17,28:0.0217:2,0:1:0:25:0:0.3913:0:60:2:0.0222:0:1 0/1:62:5:3,2:22,34:0.0806:2,2:26.4:1:29.4:1:0.39241:2.29:55.2:10:0.0847:0:2.2 -GL000220.1 137987 . T C 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.25926;SOR=2.65617;LSEQ=TAGAAATGAATATCGCTTCT;RSEQ=GGGCGGAGGGGCTTCCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:3:1,2:22,20:0.0667:2,2:23:1:23:1:0.60775:2.16282:60:2:0.0476:0:1.7 0/1:31:5:3,2:9,17:0.1613:2,2:15.2:1:30.4:1:0.34986:2.73:60:10:0.1613:0:1.2 -GL000220.1 138028 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATCACCGCTTGCGGGAC;RSEQ=ACCTCTCAAACCCTCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:24,30:0.0357:2,2:30:1:30.5:1:1:1.24:60:4:0.0364:0:1 0/0:25:0:0,0:11,14:0:2,0:22.4:1:29.8:1:1:0:60:50:1:0:0.4 -GL000220.1 138752 . A T 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13725;SOR=0;LSEQ=GATACACATTTAAAAAAATA;RSEQ=CAACACAAGGATCAACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:0.2857:2,2:27.5:1:31:1:1:3.16:60:4:0.2857:0:1 0/0:11:0:0,0:6,5:0:2,0:27.1:1:30.5:1:1:0:60:22:1:0:0.4 -GL000220.1 138786 . C A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AACCAGACTTGGGAAAAAAT;RSEQ=GAAAACCACACAAGTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:0:2,0:23.5:1:30:1:1:0:60:12:1:0:0.2 0/1:10:2:1,1:4,4:0.2:2,2:11:1:31.5:1:1:1:60:4:0.2:0:1 -GL000220.1 139010 . G T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AAGTGTTTCAGTAATATAAT;RSEQ=CTTCAGATTTAGAAGCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:18:1:29.3:1:1:0:60:6:1:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:41.5:1:29:1:1:2.44949:60:4:0.3333:0:1 -GL000220.1 139128 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49351;SOR=Inf;LSEQ=TGACTTCAGAATCATACTTT;RSEQ=TCTTGATATTTACTTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:28.4:1:32.4:1:1:0:60:18:1:0:0.2 0/1:13:2:1,1:5,6:0.1538:2,2:40:0:30:0:1:1.18:60:4:0.1538:0:1.5 -GL000220.1 139156 . AT A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.22414;SOR=0;LSEQ=ATTTACTTATGTATGTATTT;RSEQ=TTTTTTTAATTTATTTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:0.1429:2,2:20.5:1:31:1:1:1.36624:60:4:0.1538:0:0.5 0/0:15:0:0,0:7,8:0:2,0:17.6:1:30.9:1:1:0:60:30:1:0:0.3 -GL000220.1 139311 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTGGGACTACAGGTGCCC;RSEQ=CCACCACGCCCAGCTAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:23.5:1:31.6:1:1:0:60:22:1:0:0.1 0/1:32:2:1,1:14,16:0.0625:2,2:36:1:30.5:1:1:1.14:60:4:0.0625:0:1 -GL000220.1 139403 . G A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCTCTTGACCTCGTGACCC;RSEQ=CCCGCCTCGGCCTCCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:22.7:1:30:1:1:0:55:12:1:0:0.7 0/1:20:2:1,1:9,9:0.1:2,2:24.5:1:30:1:1:1:60:4:0.1053:0:1 -GL000220.1 139433 . G T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19368;SOR=0.2067;LSEQ=GCCTCCCAAAGTGCTGGGAT;RSEQ=ACAGGCGTGAGCCACTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:17.5:1:28.5:1:1:1.73:45:4:0.4:0:1.5 0/1:18:2:1,1:7,9:0.1111:2,2:29.5:1:27.5:1:1:1.27:59:4:0.1176:0:4 -GL000220.1 139440 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGTGCTGGGATGACAGGC;RSEQ=TGAGCCACTGAGCCCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:15.4:1:30.1:1:1:0:54.9:14:1:0:1.4 0/1:19:2:1,1:7,10:0.1053:2,2:32:1:29.5:1:1:1.40:59:4:0.1053:0:4 -GL000220.1 139635 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=ATACACGAGTACAAAAGAGT;RSEQ=AAACAGAGAGACTGCTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:25.1:1:26.9:1:1:0:59.9:6:1:0:0.1 0/1:12:2:1,1:4,6:0.1667:2,2:25:1:29.5:1:1:1.45:60:4:0.1667:0:1 -GL000220.1 139749 . T G 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80856;LSEQ=GTTTCCATGTATTTTTCTAT;RSEQ=ATCCAATAAGTGAACTATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:3,3:0.4545:2,2:24.2:1:33.4:1:0.54545:3.52:60:10:0.4545:0:1 0/1:10:4:2,2:2,4:0.4:2,2:22.5:1:31.3:1:1:1.86:60:8:0.4:0:1 -GL000220.1 139949 . C CGAT 47 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.58204;SOR=0.31051;LSEQ=TATAAGGATCTGGTATTCTA;RSEQ=GATCATGAGTTCACTTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:3,4:0.3:2,2:34.7:1:30.1:1:1:2.41:60:6:0.3:0:0 0/1:9:1:0,1:4,4:0.1111:2,0:30:0:32.3:0:1:0:60:2:0.1111:0:0 -GL000220.1 140156 . C T 93 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATTAGCACTTACCATGCCT;RSEQ=ACAATGTCTAGGATTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:31.4:1:29.4:1:1:0:60:10:1:0:1.2 1/1:9:9:5,4:0,0:1:0,2:30.7:1:29.6:1:1:0:60:18:1:0:1.4 -GL000220.1 140190 . A G 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.54545;SOR=3.51553;LSEQ=TTGACCCTGATAGCATTTCG;RSEQ=AAACAAGCTAATGCTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:6:0:33:0:1:0:60:2:0.25:0:2 1/0:7:4:2,2:1,2:0.5714:2,2:24.3:1:30.3:1:1:1.81:60:8:0.5714:0:2 -GL000220.1 140243 . A C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=GAAGACAAGCTCACGCCCTA;RSEQ=TGCGCTATAGGCATAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:17.2:1:31.5:1:1:0:60:12:1:0:0 1/0:4:2:1,1:0,2:0.5:0,2:13:0:33:1:1:0:60:4:0.5:0:2.5 -GL000220.1 140251 . T C 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14286;SOR=Inf;LSEQ=GCTCACGCCCTAATGCGCTA;RSEQ=AGGCATAAGCATCATTTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:0:2,0:15:1:30.1:1:1:0:60:18:1:0:0.1 0/1:6:2:1,1:1,3:0.3333:2,2:21:0:31.5:1:1:2.45:60:4:0.3333:0:2.5 -GL000220.1 140679 . T G 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5671;SOR=0.3704;LSEQ=CCTTTCACGAAGAAGGCTCA;RSEQ=CAAGCCTTCCGCTGCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:8.3:1:33:1:1:1.7321:60:6:0.6:0:1.3 0/1:6:2:1,1:2,2:0.3333:2,2:38.5:1:31.5:1:1:1:60:4:0.3333:0:1 -GL000220.1 140745 . C T 98 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=AGGCGCGATTGCGGCTATTT;RSEQ=CCCTTCTGAAATGACGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:5,5:0,0:1:0,2:16.6:1:29.8:1:1:0:60:9:1:0:1.3 1/0:6:4:2,2:1,1:0.6667:2,2:26:1:30.3:1:1:1:60:8:0.6667:0:1.8 -GL000220.1 140759 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=CTATTTCCCCTTCTGAAATG;RSEQ=CGGAAGAGTCCAATTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:16.9:1:30.5:1:1:0:60:22:1:0:1.1 0/1:6:2:1,1:2,2:0.3333:2,2:44.5:1:32:1:1:1:60:4:0.3333:0:2.5 -GL000220.1 140832 . T C 73 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36226;SOR=3.69214;LSEQ=TATTGCTCCTTTATTAGTTT;RSEQ=ACTTTTGGTTCTTCTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:5,5:0.0909:2,0:43:0:33:0:1:0:60:2:0.0909:0:2 0/1:18:5:3,2:8,5:0.2778:2,2:18.4:1:31.8:1:1:1.06284:60:10:0.2778:0:1 -GL000220.1 140869 . C T 29 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08523;SOR=0;LSEQ=TTTGGGATTTTAGGTGGAAA;RSEQ=TTCATTTTTAATTTTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:20:1:29:1:1:1:60:4:0.2:0:1.5 0/0:23:0:0,0:13,10:0:2,0:26.7:1:31.7:1:1:0:60:46:1:0:0.2 -GL000220.1 140934 . T G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25134;SOR=Inf;LSEQ=ACTAGTCAAGAGTCGTGAAT;RSEQ=TCTTCGAGGCGGTGCATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:24.9:1:29.6:1:1:0:60:13:1:0:0.1 0/1:20:3:1,2:10,7:0.15:2,2:27:1:31:1:0.56579:2.70974:60:6:0.1579:0:1.7 -GL000220.1 140964 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0812;LSEQ=CGGTGCATTTGGGGGAGATG;RSEQ=CATAGTGGGGCTCAATACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:8,5:0.0714:2,0:18:0:32:0:1:0:60:2:0.0769:0:1 0/1:26:2:1,1:13,11:0.0769:2,2:25:0:31.5:1:1:1.17422:60:4:0.08:0:1.5 -GL000220.1 140975 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54017;SOR=Inf;LSEQ=GGGGAGATGCCATAGTGGGG;RSEQ=TCAATACCTGAGGTGTTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:0:2,0:29.1:1:32.3:1:1:0:60:30:1:0:0.1 0/1:29:2:1,1:16,11:0.069:2,2:28:1:30:1:1:1.43545:60:4:0.08:0:2 -GL000220.1 141112 . T C 53 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.67393;SOR=0.64629;LSEQ=CCGATTCTGGCAACAGGCTT;RSEQ=TTTGAAGGGGCTCCGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:2,1:8,8:0.1579:2,2:23.7:1:31.3:1:1:1.93:60:6:0.1579:0:1 0/1:28:3:1,2:10,15:0.1071:2,2:16.3:1:33.7:1:1:1.32008:60:6:0.1071:0:1 -GL000220.1 141114 . T C 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.36716;SOR=1.90379;LSEQ=GATTCTGGCAACAGGCTTTT;RSEQ=TGAAGGGGCTCCGGTGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:4,4:5,5:0.4444:2,2:16.5:1:31:1:1:1:60:16:0.4444:0:1.6 1/0:28:17:7,10:4,7:0.6071:2,2:30.2:1:32:1:1:1.22:60:34:0.6071:0:1.6 -GL000220.1 141143 . A G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09144;SOR=0.27138;LSEQ=CTCCGGTGGATGGCACGTCA;RSEQ=TGACAGACGGTGTCTCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:5,4:1,4:0.6429:2,2:23.7:1:30.7:1:0.3007:4.45:60:18:0.6429:0:1.9 0/1:25:8:4,4:7,10:0.32:2,2:22.9:1:32:1:1:1.41:60:16:0.32:0:2.3 -GL000220.1 141152 . G T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.19386;LSEQ=ATGGCACGTCAATGACAGAC;RSEQ=GTGTCTCATACCAGTGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:6,6:0.0769:2,0:1:0:29:0:1:0:60:2:0.0769:0:1 0/1:22:2:1,1:10,10:0.0909:2,2:19.5:1:32.5:1:1:1:60:4:0.0909:0:2.5 -GL000220.1 141228 . G A 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAATGGCAAAATGCCAAC;RSEQ=CTTGGGGTTAATGGACTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:6,9:0,0:1:0,2:17.9:1:29.4:1:1:0:60:30:1:0:1.7 1/1:11:11:5,6:0,0:1:0,2:30.2:1:30.4:1:1:0:60:22:1:0:1.4 -GL000220.1 141281 . T G 57 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.64472;SOR=2.15287;LSEQ=TCCTAATAAACTTCGACCAG;RSEQ=TTTTGGTTTATGTTGAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:0.1667:2,2:16.5:1:30.5:1:1:1.45:60:4:0.1667:0:1.5 0/1:13:4:2,2:5,4:0.3077:2,2:10.3:1:28.5:1:1:1.22862:60:8:0.3077:0:1.5 -GL000220.1 141440 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TAAATTCCATCCGTTTCATT;RSEQ=GACGGTGTCCTGGGGTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:21.9:1:30.8:1:1:0:60:16:1:0:0.3 0/1:14:2:1,1:7,5:0.1429:2,2:30:1:31:1:1:1.36624:60:4:0.1429:0:1.5 -GL000220.1 141518 . T C 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75898;LSEQ=AGGACGAGGTCCAAGTGTTG;RSEQ=GGCGCAACACTTGGACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:3,3:6,3:0.4:2,2:28.7:1:32.2:1:0.62238:1.90694:60:12:0.4:0:1.2 0/1:9:3:0,3:3,3:0.3333:2,0:31:1:30.3:1:0.46429:0:60:6:0.3333:0:1.3 -GL000220.1 142014 . C CGGTA 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=1;SOR=0.97892;LSEQ=CTGCGGGGGAAACCGCATCT;RSEQ=GGTAGGCATAGTGGTTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:4,2:26,20:0.1154:2,2:23.3:1:30.4:1:1:1.53:60:12:0.1154:0.0385:0 0/1:53:6:3,3:30,17:0.1132:2,2:20.8:1:29:1:0.66134:1.74497:60:12:0.1132:0.0377:0.5 -GL000220.1 142091 . G C 51 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62121;SOR=0.36773;LSEQ=ACCGCCATCCTCGAGGCTCA;RSEQ=GCCCACTTTCTGCAGTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:2,1:32,26:0.0492:2,2:29.3:1:32.7:1:1:1.61:60:6:0.0517:0:2 0/1:54:1:1,0:31,22:0.0185:2,0:21:0:33:0:1:0:31:2:0.0204:0:2 -GL000220.1 142111 . A T 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93402;LSEQ=GGCCCACTTTCTGCAGTGCC;RSEQ=CAGGCACCCCCCCCCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:5:2,3:25,15:0.1064:2,2:25:1:25.6:1:0.37514:2.44745:60:4:0.1026:0:2 0/1:50:5:4,1:25,18:0.1:2,2:16.2:1:29.2:1:0.63509:2.82:46.6:4:0.093:0:3.4 -GL000220.1 142155 . C T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3422;SOR=0.46612;LSEQ=CGGCTCCGGCCCGGCCAGCC;RSEQ=CGGCTCATTTAAAGGCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:3,4:20,27:0.1296:2,2:27.7:1:28.7:1:1:1.01:60:6:0.1176:0:1.6 0/1:62:4:2,2:25,33:0.0645:2,2:11.8:1:31:1:1:1.31:60:8:0.0678:0:1 -GL000220.1 142201 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5133;SOR=Inf;LSEQ=CGTTACCGGGGGATGGGGGA;RSEQ=TCCGAGACAGAATGACTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:24,29:0:2,0:23.7:1:31.7:1:1:0:60:25.5:1:0:0.5 0/1:77:2:1,1:35,39:0.026:2,2:16:0:30:1:1:1.11:60:4:0.0274:0:1.5 -GL000220.1 142271 . G C 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGTGATCCATTGCAAAC;RSEQ=GAGAGTCACCTCGTGTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:28,19:0,0:1:0,2:28.7:1:30.4:1:1:0:60:46:1:0:1.1 1/1:66:66:32,34:0,0:1:0,2:21.7:1:29.4:1:1:0:60:65:1:0:1.3 -GL000220.1 142363 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22996;SOR=Inf;LSEQ=TAGGACGAAGGACTCTCTTC;RSEQ=TTCTGATTCGGTCTGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:39,31:0:2,0:23:1:31.2:1:1:0:58.8:69:1:0:0.4 0/1:65:2:1,1:28,35:0.0308:2,2:25.5:1:31.5:1:1:1.25:59:4:0.0308:0:4.5 -GL000220.1 142367 . T G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49907;SOR=0;LSEQ=ACGAAGGACTCTCTTCCTTC;RSEQ=GATTCGGTCTGCACAGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:38,31:0.0282:2,2:9.5:1:31:0:1:1.22227:27:4:0.0294:0:3 0/0:61:0:0,0:27,34:0:2,0:25.7:1:30.2:1:1:0:60:122:1:0:0.3 -GL000220.1 142373 . G A 30 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58478;SOR=2.53433;LSEQ=GACTCTCTTCCTTCTGATTC;RSEQ=GTCTGCACAGTGGGGCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:1:1,0:39,35:0.0133:2,0:39:0:28:0:1:0:40:2:0.0135:0:3 0/1:60:2:1,1:26,32:0.0333:2,2:35.5:1:30.5:1:1:1.23:59:4:0.0333:0:4.5 -GL000220.1 142378 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50787;SOR=0;LSEQ=TCTTCCTTCTGATTCGGTCT;RSEQ=CACAGTGGGGCCTAGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:42,36:0.025:2,2:30:0:30:1:1:1.16441:60:4:0.0256:0:1.5 0/0:59:0:0,0:28,31:0:2,0:27.1:1:31.5:1:1:0:60:58:1:0:0.4 -GL000220.1 142392 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4992;SOR=0;LSEQ=CGGTCTGCACAGTGGGGCCT;RSEQ=GGGCTGGAGCTCTCTCCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:45,39:0.023:2,2:20:1:30:1:1:1.15192:60:4:0.0241:0:2 0/0:76:0:0,0:37,39:0:2,0:21.3:1:28.5:1:1:0:60:24.333:1:0:0.4 -GL000220.1 142393 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4992;SOR=0;LSEQ=GGTCTGCACAGTGGGGCCTA;RSEQ=GGCTGGAGCTCTCTCCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:46,39:0.023:2,2:18:0:32.5:1:1:1.17724:27:4:0.0238:0:3 0/0:76:0:0,0:37,39:0:2,0:21.4:1:30.3:1:1:0:60:37:1:0:0.4 -GL000220.1 142410 . G A 28 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59613;SOR=2.35206;LSEQ=CTAGGGCTGGAGCTCTCTCC;RSEQ=TGCGGACCGCTGACTCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:1,0:51,40:0.0109:2,0:2:0:28:0:1:0:40:2:0.011:0:3 0/1:79:2:1,1:42,35:0.0253:2,2:21:1:28:1:1:1.19722:59:4:0.026:0:4.5 -GL000220.1 142413 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4988;SOR=0;LSEQ=GGGCTGGAGCTCTCTCCGTG;RSEQ=GGACCGCTGACTCCCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:48,37:0.023:2,2:12.5:1:29:1:1:1.29337:60:4:0.0238:0:1 0/0:77:0:0,0:42,35:0:2,0:22.6:1:30.3:1:1:0:60:76:1:0:0.4 -GL000220.1 142419 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18519;SOR=Inf;LSEQ=GAGCTCTCTCCGTGCGGACC;RSEQ=CTGACTCCCTCTACCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:53,38:0:2,0:24.9:1:30.5:1:1:0:60:44.5:0.9889:0:0.3 0/1:70:2:1,1:36,30:0.0286:2,2:18.5:1:32:1:1:1.19677:60:4:0.029:0:1.5 -GL000220.1 142483 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22289;SOR=Inf;LSEQ=GCCGGGCCTTGGCAGATTCT;RSEQ=GCCCTTCCTGGCCCTTCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:35,36:0:2,0:25.7:1:30.6:1:1:0:60:22.667:1:0:0.1 0/1:64:2:1,1:33,29:0.0313:2,2:19.5:1:30.5:1:1:1.13563:60:4:0.0317:0:1.5 -GL000220.1 142579 . TCTCTCCTCTACGCGCGGC T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.496;SOR=0;LSEQ=CTCTCCGGAAACATTGGAAA;RSEQ=CACCTGAAACCACAGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:23,37:0.0323:2,2:16:1:30:1:1:1.60:58:4:0.0328:0.0161:3 0/0:60:0:0,0:26,34:0:2,0:24.1:1:31.4:1:1:0:59.7:59:1:0:0.3 -GL000220.1 142627 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49503;SOR=Inf;LSEQ=CCACAGGAGCTCGGGACACA;RSEQ=GTGCTTTCGGGAGAGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:13,26:0:2,0:26.5:1:31:1:1:0:59.9:78:1:0:0.4 0/1:43:2:1,1:19,22:0.0465:2,2:41.5:1:30:1:1:1.15:60:4:0.0465:0:1 -GL000220.1 142636 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4965;SOR=Inf;LSEQ=CTCGGGACACACGTGCTTTC;RSEQ=GGAGAGAATGCTGAGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:13,23:0:2,0:27.8:1:31.3:1:1:0:60:72:1:0:0.1 0/1:42:2:1,1:18,22:0.0476:2,2:11:0:32.5:1:1:1.22:60:4:0.0476:0:1.5 -GL000220.1 142799 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22199;SOR=0;LSEQ=GCCGAGGCCGTAGGATCCCT;RSEQ=GAGGAATCGCCTAACCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:0.0952:2,2:20:1:29:1:1:1.11:47.5:4:0.1:0:3.5 0/0:23:0:0,0:11,12:0:2,0:26.2:1:30.5:1:1:0:60:46:1:0:0.2 -GL000220.1 142900 . ACAGG A 100 MSI6 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=7.000;MSILEN=4;SSF=0.0298;SOR=0.23709;LSEQ=AGACAGAATGAGGCCCTGCC;RSEQ=CAGGCAGGCAGGCAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:4,6:3,3:0.625:2,2:22.9:1:30.4:1:1:1.46198:60:20:0.625:0.25:0.4 0/1:29:8:5,3:9,12:0.2759:2,2:25.6:1:31.1:1:0.42699:2.16:60:16:0.2759:0:0.3 -GL000220.1 143001 . AT A 64 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.4029;SOR=0.4131;LSEQ=CAGAATACAGCACTTAATTA;RSEQ=TTTTTTTTTTCCCTTCGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:2,2:10,7:0.1905:2,2:26:1:32:1:1:1.40412:60:8:0.1905:0:0.8 0/1:23:2:1,1:11,10:0.087:2,2:11:0:32:0:1:1.09544:60:4:0.087:0:0.5 -GL000220.1 143111 . C T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24808;SOR=Inf;LSEQ=CCCGCGTTCAAGCGATTCTC;RSEQ=TGCCTCAGCCTCCTGAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:28.7:1:31.6:1:1:0:60:34:1:0:0.5 0/1:23:3:1,2:10,10:0.1304:2,2:10.3:1:30.7:1:1:1.94223:60:6:0.1304:0:1.3 -GL000220.1 143162 . G A 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0.77049;LSEQ=AGGGAGGAGCCACCACACCC;RSEQ=GCTGATTTTGTATTGTTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:8,12:1,3:0.8333:2,2:21.9:1:28.1:1:1:1.95:60:5.667:0.8095:0:1.4 1/0:29:23:11,12:5,1:0.7931:2,2:22.5:1:29:1:0.18336:5.17111:59.7:10.5:0.8077:0:1.4 -GL000220.1 143164 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20479;SOR=0;LSEQ=GGAGGAGCCACCACACCCGG;RSEQ=TGATTTTGTATTGTTAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:8,12:0.0909:2,2:36.5:1:31:1:1:1.47:60:4:0.0909:0:2 0/0:26:0:0,0:14,12:0:2,0:22.4:1:31.2:1:1:0:59.8:25:1:0:1.2 -GL000220.1 143376 . C CATTT 30 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=7.000;MSILEN=4;SSF=1;SOR=1.44805;LSEQ=TTAATCTATTTATTTATTTA;RSEQ=ATTTATTTATTTATTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:5,6:0.0833:2,0:45:0:28.8:0:1:0:60:2:0.0833:0:0 0/1:17:2:1,1:6,8:0.1176:2,2:40:0:30.8:1:1:1.31:60:4:0.125:0:0 -GL000220.1 143398 . T C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=4;SSF=0.48276;SOR=0;LSEQ=TTTATTTATTTATTTATTTA;RSEQ=TTACTTATTTATTTATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:14.5:1:32.5:1:1:1.15:60:4:0.1333:0:1 0/0:15:0:0,0:8,7:0:2,0:20.3:1:30.2:1:1:0:60:30:1:0:0.1 -GL000220.1 144015 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=GGCCTCACGGACTCTGAGCC;RSEQ=AGGAGTCCCCTGGTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:19.7:1:30:1:1:0:60:20:1:0:0.3 0/1:16:2:1,1:6,8:0.125:2,2:41:1:28:1:1:1.31:60:4:0.125:0:1 -GL000220.1 144120 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51111;SOR=Inf;LSEQ=ACAGAAATACACGGATTCAC;RSEQ=CAAAACACAGAAAGCAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,4:0:2,0:22.2:1:28.9:1:1:0:60:12:1:0:0.5 0/1:22:2:1,1:13,7:0.0909:2,2:11:0:30:0:1:1.80284:60:4:0.0909:0:1.5 -GL000220.1 144134 . G C 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63994;SOR=0.65149;LSEQ=ATTCACCCAAAACACAGAAA;RSEQ=CAGTCTTTTAGAAATGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:0.1818:2,2:9.5:1:28.5:1:0.49091:3.05504:60:4:0.1818:0:2 0/1:24:3:1,2:13,8:0.125:2,2:18.7:1:32.3:1:0.5504:3.08979:60:6:0.125:0:1 -GL000220.1 144208 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18857;SOR=0;LSEQ=GTTTGGACCTTGACTGAGAG;RSEQ=ATTCCCAGTCGGTCTCTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:13,7:0.0909:2,2:6:0:32:0:1:1.80284:60:4:0.0909:0:1.5 0/0:28:0:0,0:14,14:0:2,0:28.6:1:31.3:1:1:0:60:56:1:0:0.2 -GL000220.1 144421 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56537;SOR=1.50415;LSEQ=GGGCTGACACGCTCACTGGC;RSEQ=GGCGTCGGGCATCACCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:2,3:22,28:0.0909:2,2:26.4:1:31.2:1:1:1.17509:60:10:0.0909:0:1.2 0/1:61:8:4,4:21,31:0.1311:2,2:23.1:1:30.4:1:0.70818:1.47:60:16:0.1356:0:1 -GL000220.1 144457 . GA G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.20829;SOR=Inf;LSEQ=CTAGCGGTCACTGTTACTCT;RSEQ=AAACGGAGGCCTCACAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:22,31:0:2,0:21.7:1:29.9:1:1:0:59.9:52:1:0:0.2 0/1:45:2:1,1:20,23:0.0444:2,2:10:0:33.5:1:1:1.15:51:4:0.0455:0:0.5 -GL000220.1 144510 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21187;SOR=Inf;LSEQ=AGGCCGCCTGCGCACAGCCT;RSEQ=GGGCAACTGTGTCTTCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:0:2,0:23.7:1:31.5:1:1:0:59.9:50:1:0:0.7 0/1:44:2:1,1:18,24:0.0455:2,2:34:0:31.5:1:1:1.32:60:4:0.0465:0:1.5 -GL000220.1 144597 . T C 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05563;SOR=0;LSEQ=GAAATCGCCACTTTGACGAC;RSEQ=GGGTCTGATTGACCTTTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:15,18:0,0:1:0,2:28.6:1:30.4:1:1:0:60:32:1:0:1.7 1/1:37:32:16,16:2,3:0.8649:2,2:30.2:1:29.7:1:1:1.48:60:64:0.8649:0:1.8 -GL000220.1 144635 . A G 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2427;SOR=Inf;LSEQ=GATCAGGCAAAAACGAACAA;RSEQ=CAGATAAATCAATAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:13,16:0:2,0:22:1:30.4:1:1:0:60:58:1:0:1.5 0/1:34:3:2,1:14,17:0.0882:2,2:22.7:1:32.7:1:0.59091:2.37:60:6:0.0882:0:2 -GL000220.1 144645 . C A 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACGAACAAACAGATAAAT;RSEQ=AATAAAATAACACAAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:16,15:0,0:1:0,2:21.5:1:29:1:1:0:60:62:1:0:1.5 1/1:35:35:16,19:0,0:1:0,2:20.9:1:29.3:1:1:0:60:70:1:0:1.6 -GL000220.1 144739 . T A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=TACGATAGGATGCGATAGGA;RSEQ=ACGATAGGATACAATACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:0:2,0:23.8:1:29.6:1:1:0:60:32:1:0:0.5 0/1:22:2:1,1:11,9:0.0909:2,2:5:0:32:0:1:1.21106:60:4:0.0952:0:0.5 -GL000220.1 144761 . C G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.34783;SOR=0.28408;LSEQ=CGATAGGATACAATACAATA;RSEQ=GATACGATACAATACAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:3,4:0.3636:2,0:21:1:32:1:0.23636:0:60:8:0.3636:0:1 0/1:15:2:2,0:6,6:0.1333:2,0:34:1:29:1:0.47253:0:60:4:0.1333:0:1 -GL000220.1 144792 . A G 56 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=5;SSF=0.25497;SOR=Inf;LSEQ=AATACAATACAATACAATAC;RSEQ=ATACAATACAATACAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:16.6:1:31.3:1:1:0:51.4:14:1:0:0.9 0/1:14:4:2,2:7,3:0.2857:2,2:6.5:1:28.3:1:0.58042:2.18727:59.3:8:0.3077:0:1.8 -GL000220.1 144797 . A G 59 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=5;SSF=0.27273;SOR=Inf;LSEQ=AATACAATACAATACAATAC;RSEQ=ATACAATACAATACAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:14.4:1:31.1:1:1:0:51.4:14:1:0:0.9 0/1:16:4:2,2:7,5:0.25:2,2:9.8:1:29.8:1:1:1.3705:59.3:8:0.2667:0:2 -GL000220.1 144802 . A G 44 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=5;SSF=0.34262;SOR=0.29124;LSEQ=AATACAATACAATACAATAC;RSEQ=ATACAATACAATACAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:1,3:0.5:2,2:9.3:1:22.3:1:1:2.60:42.8:1:0.3333:0:3 0/1:14:3:2,1:6,5:0.2143:2,2:14.7:1:32.3:1:1:1.61:56.7:6:0.2143:0:2.7 -GL000220.1 144807 . A G 54 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=5;SSF=0.36304;SOR=0.35851;LSEQ=AATACAATACAATACAATAC;RSEQ=ATACAATACAATACAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:3,2:0.4444:2,2:12.8:1:27.3:1:0.52381:3.76419:42.8:3:0.375:0:3 0/1:14:3:2,1:6,5:0.2143:2,2:19.7:1:32.3:1:1:1.61:56.7:6:0.2143:0:2.7 -GL000220.1 144861 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50925;SOR=Inf;LSEQ=CAATACAATACAATACAATA;RSEQ=GCCGGGCGCGGTGGCTCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:25.1:1:28.8:1:1:0:55.4:14:1:0:1.1 0/1:23:2:0,2:9,12:0.087:2,0:41.5:1:32:0:0.50198:0:60:4:0.087:0:1.5 -GL000220.1 145162 . A AATAC 88 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=31;MSI=8.000;MSILEN=4;SSF=0.72808;SOR=0.68864;LSEQ=CAAAAATAAATACATAAATA;RSEQ=ATACATACATACATACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:2,6:6,5:0.3478:2,2:28.3:1:29.5:1:0.35207:3.35771:57.5:16:0.4706:0.087:0.8 0/1:15:4:1,3:2,9:0.2667:2,2:22.3:1:29.4:1:1:1.46:57.5:8:0.2667:0.1333:0.8 -GL000220.1 145237 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22;SOR=0;LSEQ=AAATAAATAAATGGGCCCTG;RSEQ=GCGGTGGCTCAAGCCTGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:11.5:1:29:0:1:1:60:4:0.1667:0:2.5 0/0:13:0:0,0:6,7:0:2,0:32.8:1:31.7:1:1:0:59.2:26:1:0:0.5 -GL000220.1 145257 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=CGCGGTGGCTCAAGCCTGTC;RSEQ=TCCCCTCACTTTGGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:23.6:1:29.7:1:1:0:60:20:1:0:0.7 0/1:16:2:1,1:6,8:0.125:2,2:23:1:32:1:1:1.31:60:4:0.125:0:1.5 -GL000220.1 145368 . T C 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.27126;SOR=0;LSEQ=ACACAACATTAGCCGGGCGC;RSEQ=GTGCTGTGCTGTACTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:1,2:10,11:0.125:2,2:18.7:1:30.3:1:1:1.77484:60:6:0.125:0:1.3 0/0:15:0:0,0:8,7:0:2,0:30.9:1:30.6:1:1:0:60:30:1:0:0.2 -GL000220.1 145381 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50639;SOR=0;LSEQ=CGGGCGCTGTGCTGTGCTGT;RSEQ=CTGTCTGTAATCCCAGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:11,12:0.08:2,2:29.5:1:29:0:1:1.09:60:4:0.08:0:1.5 0/0:17:0:0,0:9,8:0:2,0:25.8:1:28.5:1:1:0:60:34:1:0:0.2 -GL000220.1 145421 . C T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74106;LSEQ=CTCGGGAGGCCGAGCTGAGG;RSEQ=AGGAGAATCGCTTGAACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:5,6:0.1538:2,0:20:1:26.5:1:0.48718:0:60:4:0.1538:0:1.5 0/1:17:2:2,0:8,7:0.1176:2,0:20:1:32:0:0.48529:0:60:4:0.1176:0:1.5 -GL000220.1 145454 . T G 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26314;SOR=Inf;LSEQ=TGAACCTGGGAGGCGGAGGT;RSEQ=GCAGTGAGCCGAGATCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:0:2,0:26:1:27.7:1:1:0:59.6:8:1:0:0.2 0/1:17:4:2,2:7,6:0.2353:2,2:27.5:1:31:1:1:1.15611:60:8:0.2353:0:1.5 -GL000220.1 145725 . G T 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TTTATGTTATTATCGTGATT;RSEQ=ATGTTTCGAGACGGAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:47.5:1:30:0:1:1.73:49:4:0.4:0:1.5 0/0:4:0:0,0:3,1:0:2,0:31.5:1:30.8:1:1:0:38.5:8:1:0:0 -GL000220.1 146096 . TTC T 64 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=22.000;MSILEN=3;SSF=1;SOR=1.26339;LSEQ=TCTTCTTCTTCTTCTTCTTC;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:8,6:0.2222:2,2:17.3:1:29.6:1:1:1.31198:43.5:8:0.2222:0.0556:0 0/1:15:4:3,1:6,5:0.2667:2,2:32.5:1:32.3:1:0.6044:2.36:38:8:0.2667:0:0.5 -GL000220.1 146098 . CTT C 90 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=23.000;MSILEN=3;SSF=0.00213;SOR=0;LSEQ=TTCTTCTTCTTCTTCTTCTT;RSEQ=TTTTTTTTGAGACAGAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:4,3:5,4:0.4375:2,2:31.4:1:32.4:1:1:1.06:33.1:14:0.4375:0:0.1 0/0:18:0:0,0:8,7:0:2,0:25.8:1:29.3:1:1:0:41.3:30:0.8333:0:0.5 -GL000224.1 3404 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=TGAAAGAGAGAGGGCAGAAG;RSEQ=AGTAAGAGAGAAATAGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:26.3:1:31:1:1:0:48.4:20:1:0:0.9 0/1:10:2:1,1:5,3:0.2:2,2:26:0:31:1:1:1.58108:47:4:0.2:0:1 -GL000224.1 3435 . GGAAGCAAGGAAGACAGGAAGG A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=AAATAGGAGGAAGGAAGGAA;RSEQ=AAGGAAAGAAGGAAGGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:28.8:1:28.6:1:1:0:51.1:7:1:0:1 0/1:18:2:1,1:9,7:0.1111:2,2:18.5:1:31.4:1:1:1.26772:21:4:0.1111:0.1111:2 -GL000224.1 3445 . AAGAC A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=AAGGAAGGAAGGAAGCAAGG;RSEQ=AGGAAGGAAGGAAAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:20.5:1:29.6:1:1:0:51.1:16:1:0:1 0/1:17:2:1,1:7,6:0.1176:2,2:34:0:32:1:1:1.1547:43:4:0.1333:0:1 -GL000224.1 3449 . C A 108 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28327;SOR=0;LSEQ=AAGGAAGGAAGCAAGGAAGA;RSEQ=AGGAAGGAAGGAAAGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:1:0,2:20.7:1:26.7:1:1:0:50.3:6:1:0:1.1 1/0:17:13:7,6:0,0:0.7647:0,2:21.8:1:29.2:1:1:0:45.4:26:1:0:1.6 -GL000224.1 3472 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=Inf;LSEQ=GAAGGAAGGAAAGAAGGAAG;RSEQ=TAGGACGGAAGGAAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:12.9:1:32:1:1:0:45.4:14:1:0:2.4 0/1:13:2:1,1:7,4:0.1538:2,2:16:0:31.5:1:1:1.67325:21:4:0.1818:0:2 -GL000224.1 3473 . T A 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.64241;SOR=0.48456;LSEQ=AAGGAAGGAAAGAAGGAAGG;RSEQ=AGGACGGAAGGAAGGAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:0,2:0.7143:0,2:14.6:1:31:1:1:0:39.6:10:0.7143:0:3 1/0:13:7:4,3:4,2:0.5385:2,2:27.9:1:26.6:1:1:1.45385:44.6:6:0.6:0:2 -GL000224.1 3478 . C A 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0307;SOR=0.07512;LSEQ=AGGAAAGAAGGAAGGTAGGA;RSEQ=GGAAGGAAGGAAGGAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:0,3:0.5714:0,2:16.8:1:32.3:1:0.42857:0:42.8:8:0.5714:0:3.3 0/1:13:1:1,0:6,5:0.0769:2,0:47:0:31:0:1:0:60:2:0.0909:0:4 -GL000224.1 3497 . A AAGGG 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=4;SSF=0.03727;SOR=Inf;LSEQ=ACGGAAGGAAGGAAGGAAGG;RSEQ=AGGAAAGAAGGATGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:17.5:1:29.8:1:1:0:47.5:22:1:0:2.3 0/1:12:5:3,2:3,4:0.4167:2,2:21.4:1:31.6:1:1:1.89:36.8:10:0.4545:0.25:2.6 -GL000224.1 3510 . T C 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04247;SOR=Inf;LSEQ=AGGAAGGAAGGAAAGAAGGA;RSEQ=GAAAGGAAGGAGAAAACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:25.8:1:30.2:1:1:0:51.3:24:1:0:2.1 0/1:14:5:3,2:4,5:0.3571:2,2:23:1:30.2:1:1:1.79:36.8:10:0.3846:0:2.6 -GL000224.1 3528 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48768;SOR=Inf;LSEQ=GATGAAAGGAAGGAGAAAAC;RSEQ=CCGGTGTTACTAAAACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:31.8:1:29.6:1:1:0:49.3:26:1:0:1.9 0/1:16:2:1,1:7,7:0.125:2,2:26.5:1:30.5:1:1:1:60:4:0.1429:0:1.5 -GL000224.1 3549 . C CA 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.18333;SOR=Inf;LSEQ=CCGGTGTTACTAAAACCCCC;RSEQ=AAAAAATGGTTTCCCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:29.2:1:30.9:1:1:0:47.6:28:1:0:1.8 0/1:11:2:1,1:5,4:0.1818:2,2:24:1:27:1:1:1.22474:48.5:4:0.2:0:0 -GL000224.1 3550 . A C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.48667;SOR=0;LSEQ=CGGTGTTACTAAAACCCCCC;RSEQ=AAAAATGGTTTCCCCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:46.5:1:32:1:1:1:60:4:0.1538:0:1 0/0:11:0:0,0:6,5:0:2,0:25.5:1:28.1:1:1:0:49.9:10:1:0:1.3 -GL000224.1 3554 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=GTTACTAAAACCCCCCAAAA;RSEQ=ATGGTTTCCCCCTGTGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:34.4:1:28.9:1:1:0:49.5:10:1:0:1.3 0/1:11:2:1,1:5,4:0.1818:2,2:36.5:1:29.5:1:1:1.22474:45.5:4:0.2222:0:2.5 -GL000224.1 3577 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=GGTTTCCCCCTGTGGGTAAG;RSEQ=CTACAATGTGGATGAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:5:0:32:0:1:1:60:4:0.2:0:1.5 0/0:7:0:0,0:3,4:0:2,0:19.3:1:30.9:1:1:0:47.1:14:1:0:1.1 -GL000224.1 3744 . A G 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGGGCTGAGGGTCAGGGAG;RSEQ=GGGTTTGAGACAGAATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:15:0:31:0:1:0:60:2:1:0:0 0/1:14:2:1,1:8,4:0.1429:2,2:21.5:1:28.5:1:1:1.89743:43.5:4:0.1538:0:1 -GL000224.1 4030 . G A 27 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAGGGAGAGCGAAAAGG;RSEQ=AAAATGGTCCTATTTACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:14:1:29.4:1:1:0:38.8:4:1:0:0.8 0/1:18:2:1,1:12,4:0.1111:2,2:13:0:27.5:1:0.4902:2.79285:44:4:0.1111:0:2.5 -GL000224.1 4035 . T C 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGAGAGCGAAAAGGGAAAA;RSEQ=GGTCCTATTTACAAATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:17:1:32:1:1:0:38.8:10:1:0:0.8 0/1:20:2:1,1:13,5:0.1:2,2:27.5:1:32.5:1:0.52105:2.46307:41:4:0.1:0:2 -GL000224.1 4041 . T C 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCGAAAAGGGAAAATGGTCC;RSEQ=ATTTACAAATGACAGATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:0:0,0:22:1:32.6:1:1:0:40.8:10:1:0:0.8 0/1:20:2:1,1:13,5:0.1:2,2:24:0:30:1:0.52105:2.46307:44:4:0.1053:0:2.5 -GL000224.1 4080 . A G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56357;SOR=0.37622;LSEQ=TGAAACTGGGGTTCACATCA;RSEQ=CAGTGTCACTGCCAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:5,3:0.2:2,0:35:1:33.5:1:1:0:32.5:4:0.2:0:4.5 0/1:24:2:1,1:12,10:0.0833:2,2:31:1:30:1:1:1.19087:45.5:4:0.0833:0:2.5 -GL000224.1 4129 . T C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21429;SOR=0;LSEQ=GCTAGCCATGTCACCGGTAG;RSEQ=GTGGCCCGCAGGGACGCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:0.2:2,2:9.5:1:29:1:1:1.58:20:4:0.2:0:5 0/0:11:0:0,0:2,9:0:2,0:22.9:1:30.8:1:1:0:36.5:22:1:0:0.6 -GL000224.1 4144 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48538;SOR=Inf;LSEQ=GGTAGTGTGGCCCGCAGGGA;RSEQ=GCCGACCTGCTGGAGCGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:0:2,0:26.1:1:31.3:1:1:0:30.4:16:1:0:1.8 0/1:11:2:1,1:1,8:0.1818:2,2:21.5:1:29.5:1:0.34545:6.00:31:4:0.1818:0:1 -GL000224.1 4147 . C T 31 v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52315;LSEQ=AGTGTGGCCCGCAGGGACGC;RSEQ=GACCTGCTGGAGCGTCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:2,4:0.25:2,0:24:1:31:1:1:0:43:4:0.25:0:4 0/1:7:1:0,1:0,6:0.1429:0,0:34:0:32:0:1:0:40:2:0.1429:0:1 -GL000224.1 4151 . C A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=TGGCCCGCAGGGACGCCGAC;RSEQ=TGCTGGAGCGTCGTGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:2,3:0.2857:2,0:34:1:32.5:1:1:0:30:4:0.2857:0:5.5 0/0:7:0:0,0:0,7:0:0,0:24.4:1:32.6:1:1:0:37.9:14:1:0:0.3 -GL000224.1 4186 . C G 34 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.41421;LSEQ=GCCAGCATGGGCTGTGGCAA;RSEQ=CACGTGGGCCAGCAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:28:1:34:0:0.4:0:32.5:4:0.4:0:1 0/1:5:1:1,0:0,4:0.2:0,0:31:0:32:0:0.2:0:25:2:0.2:0:1 -GL000224.1 4391 . G A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.64625;LSEQ=ACGGGAACCGTGGAGAAATG;RSEQ=CCAGGTAACTGCGTCATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:5,2:0.125:2,0:1:0:26:0:1:0:49:2:0.125:0:1 0/1:24:2:1,1:10,12:0.0833:2,2:27.5:1:27:1:1:1.19:47:4:0.087:0:1.5 -GL000224.1 4417 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53281;SOR=Inf;LSEQ=TAACTGCGTCATGTGGGCTA;RSEQ=TAGATTGGCCAGGGCTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:22.7:1:31.4:1:1:0:37.7:20:1:0:0.5 0/1:21:3:2,1:8,10:0.1429:2,2:26.7:1:24:1:0.58647:2.39:47:2:0.1:0:1.7 -GL000224.1 4453 . T C 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.64472;SOR=0.4645;LSEQ=TTCGAACTGAAGGACGATAA;RSEQ=GGGGAGTAGCTGTCAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:6,3:0.3077:2,0:23.5:1:31.3:1:0.4965:0:24:8:0.3077:0:1.5 0/1:12:2:2,0:5,5:0.1667:2,0:31.5:1:33:0:0.4697:0:21:4:0.1667:0:1.5 -GL000224.1 4472 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=ATGGGGAGTAGCTGTCAGGC;RSEQ=CTGGGAGTGCCTGAGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:13:1:30:1:1:1.26772:20:4:0.1176:0:1.5 0/0:12:0:0,0:5,7:0:2,0:25.2:1:30:1:1:0:35.8:24:1:0:0.4 -GL000224.1 4495 . G T 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05683;SOR=0;LSEQ=GGGAGTGCCTGAGTGTAAGT;RSEQ=GAGATGGGTTTGGGGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:3,3:5,7:0.3333:2,2:25:1:30.5:1:1:1.37:42.2:12:0.3333:0:1.3 0/0:12:0:0,0:7,5:0:2,0:29.3:1:30.4:1:1:0:32.5:24:1:0:0.5 -GL000224.1 4500 . T A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.26136;SOR=0;LSEQ=TGCCTGAGTGTAAGTGGAGA;RSEQ=GGGTTTGGGGTCACTGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:2,1:7,10:0.15:2,2:12.7:1:30.7:1:0.56579:2.71:21.3:6:0.1667:0:1.7 0/0:13:0:0,0:8,5:0:2,0:27.9:1:29.8:1:1:0:31.5:26:1:0:0.5 -GL000224.1 4576 . G A 28 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TAGGGAGATAGTCTCGTGAG;RSEQ=CCTGTGAGTGTCTAGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:0,5:0.2857:0,2:15.5:1:28.5:1:0.28571:0:20:4:0.3333:0:1.5 0/0:14:0:0,0:6,8:0:2,0:23.9:1:30.7:1:1:0:23.1:28:1:0:0.1 -GL000224.1 4580 . G T 31 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GAGATAGTCTCGTGAGGCCT;RSEQ=TGAGTGTCTAGGGTTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:0.2857:2,0:17:1:31:0:1:0:31:4:0.3333:0:1.5 0/0:14:0:0,0:6,8:0:2,0:24.3:1:30.6:1:1:0:23.1:28:1:0:0.1 -GL000224.1 4958 . A C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52941;SOR=Inf;LSEQ=AGAGTAGCTGAAGGAGACAC;RSEQ=AGAGTCCCTGTGGGCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,1:0:2,0:26.2:1:30.4:1:1:0:34.8:10:1:0:0.2 0/1:12:2:1,1:5,5:0.1667:2,2:15.5:1:29.5:1:1:1:47.5:4:0.1667:0:1 -GL000224.1 4997 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGCAAAGACCTGAGACAGA;RSEQ=CAGGGAGGACCTCAGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:30.4:1:30.7:1:1:0:37.4:14:1:0:1.3 0/1:16:2:1,1:8,5:0.125:2,2:25:1:26:1:1:1.54914:27:4:0.125:0:1 -GL000224.1 5041 . G T 25 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGAGTCTGTAGGTGATTCC;RSEQ=GAGTGTGGGAGGCTGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:28:1:32.2:1:1:0:32.6:10:1:0:1.4 0/1:11:2:1,1:4,5:0.1818:2,2:18.5:1:25:0:1:1.22:27:4:0.1818:0:2 -GL000224.1 5092 . C G 33 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCGTGGTGGGAGAGTAG;RSEQ=TGGGACAGACAGGAGAGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13.5:1:32.5:1:1:0:24:4:1:0:1.5 1/0:3:2:0,2:0,1:0.6667:0,0:41.5:1:33:0:1:0:27:4:0.6667:0:2.5 -GL000224.1 5122 . C G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGAGTCCCAGGGGGCT;RSEQ=GGGGTGACGACGTGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:46:0:31:0:1:0:25:2:1:0:2 1/1:3:3:1,2:0,0:1:0,2:23.7:1:30.3:1:1:0:34.3:6:1:0:2 -GL000225.1 42673 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGCCTTTATATGAGCC;RSEQ=GTGGCTGGTAGTCCGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:3 -GL000225.1 42712 . C T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTCCTGGCTGCACCTG;RSEQ=GGCAGTGCACAGGCCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:17:0:31:0:1:0:60:2:1:0:4 1/1:2:2:1,1:0,0:1:0,2:29:0:32:0:1:0:60:4:1:0:3 -GL000225.1 43001 . T A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCAGGGTCCAGATTTGG;RSEQ=TTCAGAATGAGAGGTCACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:27:0:31:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 43014 . G T 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGGTTTCAGAATGAGA;RSEQ=GTCACGCCAGCTGAGGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:14:0:30.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 43197 . CC AG 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAGCTGGCCAGAGAGACGGG;RSEQ=TCCCGGAGTCCAGGATTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13.5:1:31:1:1:0:50.5:4:1:0:1.5 1/0:3:2:1,1:0,1:0.6667:0,2:19:1:29.5:1:1:0:27:4:0.6667:0.3333:5 -GL000225.1 43203 . G A 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GCCAGAGAGACGGGCCTCCC;RSEQ=GAGTCCAGGATTCAGATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19.5:1:31:1:1:0:50.5:4:1:0:1.5 0/0:3:0:0,0:1,2:0:2,0:21.3:1:29.3:1:1:0:38:6:1:0:6 -GL000225.1 43234 . A C 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TTCAGATCTGGTTTCAGAAT;RSEQ=GAAGGGCCAGGCACCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:6:0:30.5:1:1:0:50.5:4:1:0:1.5 1/1:3:3:1,2:0,0:1:0,2:34.7:1:30.3:1:1:0:38:6:1:0:6 -GL000225.1 43237 . A T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGATCTGGTTTCAGAATAGA;RSEQ=GGGCCAGGCACCCAGGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:0:32.5:1:1:0:50.5:4:1:0:1.5 1/0:3:2:1,1:0,1:0.6667:0,2:31:1:30:1:1:0:27:4:0.6667:0:5 -GL000225.1 43248 . C G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAATAGAAGGGCCAGGCA;RSEQ=CCAGGACAGGCTGGCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:20:1:32.5:1:1:0:27:4:0.6667:0:5 -GL000225.1 43298 . TG CA 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAAGCAGCCTATGCAACG;RSEQ=GCCCCCGGCCTTTGTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:32.8:1:1:0:60:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 43309 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGCAACGTGGCCCCCGGC;RSEQ=TTTGTCACCCTGCTCCCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:0:33:1:1:0:60:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 43311 . T G 34 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAACGTGGCCCCCGGCCT;RSEQ=TGTCACCCTGCTCCCTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:0:34:0:1:0:60:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 43318 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCCCCGGCCTTTGTCAC;RSEQ=CTGCTCCCTCGTGGGTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:0:32.5:1:1:0:60:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 43326 . C T 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGCCTTTGTCACCCTGCTCC;RSEQ=TCGTGGGTCGCCTTCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35:0:33:1:1:0:60:4:1:0:6 1/1:2:2:1,1:0,0:1:0,2:5:0:32:0:1:0:60:4:1:0:3 -GL000225.1 43333 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTCACCCTGCTCCCTCGTGG;RSEQ=TCGCCTTCACCCACACTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:0:33:1:1:0:60:4:1:0:6 0/0:2:0:0,0:1,1:0:2,0:12:0:33:0:1:0:60:4:1:0:3 -GL000225.1 43356 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCCTTCACCCACACTGGCAC;RSEQ=TGGGGGACGGGGCTTCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:6:0:30.5:1:1:0:60:4:0.6667:0:6 0/0:2:0:0,0:1,1:0:2,0:35:0:32:1:1:0:60:4:1:0:3 -GL000225.1 43362 . G A 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCCACACTGGCACGTGGGG;RSEQ=ACGGGGCTTCCCGCACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:29:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:41:0:30:1:1:0:60:4:1:0:3 -GL000225.1 43364 . C T 31 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCACACTGGCACGTGGGGGA;RSEQ=GGGGCTTCCCGCACCCCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:31:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:43:0:31:1:1:0:60:4:1:0:3 -GL000225.1 43395 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=GCACCCCACGTTCCCTGCGC;RSEQ=CCTGTGGCTCTCCCACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:13.5:1:30.5:1:1:0:60:4:0.6667:0:5.5 0/0:2:0:0,0:1,1:0:2,0:15.5:1:30:1:1:0:60:4:1:0:3 -GL000225.1 43412 . AG A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCGCCTGTGGCTCTCCCAC;RSEQ=GGGGCTTTCGTGAGGCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:31.5:1:32:0:1:0:60:4:0.6667:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 43450 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAGCGAGGGCCGTCCCC;RSEQ=TGCTCCAGCGCAGCCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:33.5:1:28.5:1:1:0:60:4:0.6667:0:5.5 0/0:1:0:0,0:1,0:0:0,0:2:0:27:0:1:0:60:2:1:0:3 -GL000225.1 43460 . G C 29 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GGCCGTCCCCGTGCTCCAGC;RSEQ=CAGCCAGGCCGGGCTGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:23.5:1:29:1:1:0:60:4:0.6667:0:5.5 1/1:1:1:1,0:0,0:1:0,0:12:0:31:0:1:0:60:2:1:0:3 -GL000225.1 43471 . G A 28 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTCCAGCGCAGCCAGGCC;RSEQ=GGCTGGCAGATGGGATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:12.5:1:28.5:1:1:0:60:4:0.6667:0:5.5 1/1:1:1:1,0:0,0:1:0,0:23:0:29:0:1:0:60:2:1:0:3 -GL000225.1 43532 . C T 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TGATATTGCCTACGAGGCCC;RSEQ=GGCTACTCCAGAAGGGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:16.7:1:30.3:1:1:0:53.3:6:1:0:0 1/1:2:2:1,1:0,0:1:0,2:33:1:26:1:1:0:60:4:1:0:2.5 -GL000225.1 43622 . GC AG 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=GGAGGACTGGGACCCACAGC;RSEQ=GACAGCCTGCCGGGCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:0.5:0,2:43.5:1:31.5:1:1:0:60:4:0.5:0:2 0/0:4:0:0,0:2,2:0:2,0:13:1:30.3:1:1:0:42.5:8:1:0:2.3 -GL000225.1 43634 . C T 43 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=CCCACAGCGCGACAGCCTGC;RSEQ=GGGCCCTTGCACGTTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:27.3:1:30.7:1:1:0:57:6:1:0:3.7 1/0:5:3:2,1:1,1:0.6:2,2:10:1:27.3:1:1:1.73:60:6:0.6:0:3.3 -GL000225.1 43685 . G A 43 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGAAGCAGGGCCACAGG;RSEQ=CCAAGGTGTGCCTGCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:34.7:1:27.7:1:1:0:60:6:1:0:3.7 -GL000225.1 43701 . A G 48 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCAAGGTGTGCCTGC;RSEQ=CCACCCGTGTCCCAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:29.3:1:30.3:1:1:0:60:6:1:0:3.7 -GL000225.1 43707 . C T 45 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGTGTGCCTGCACCACC;RSEQ=GTGTCCCAGGGGAGCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:1:0,2:25:1:29:1:1:0:60:6:1:0:3.7 -GL000225.1 43827 . G C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCCCCGGAGGACTCCGC;RSEQ=TGGCAGGTGCAGATGCACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23.5:1:29:1:1:0:60:4:1:0:4.5 -GL000225.1 43853 . T C 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGCAGATGCACGGCATCC;RSEQ=GGCGCCCTCCCAGGATCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:27:1:1:0:60:4:1:0:4.5 -GL000225.1 43859 . C A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGCACGGCATCCTGGCGC;RSEQ=CTCCCAGGATCTCCAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:28:1:1:0:60:4:1:0:4.5 -GL000225.1 43869 . T G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCCTGGCGCCCTCCCAGGA;RSEQ=CTCCAGGAGCCGGAACGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:30.5:1:1:0:60:4:1:0:4.5 -GL000225.1 44281 . C G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGCATCCCAGGGATCCCA;RSEQ=AGTCGGCACAGGTACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:16.5:1:30:1:1:0:46.5:4:1:0:6 -GL000225.1 44303 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GTCGGCACAGGTACCAGCAG;RSEQ=TGGGCCGCCTACTGCGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:9.5:1:28:1:1:1.7321:60:4:0.4:0:6.5 0/0:4:0:0,0:2,2:0:2,0:22.8:1:32.8:1:1:0:47.3:8:1:0:5.5 -GL000225.1 44308 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=CACAGGTACCAGCAGGTGGG;RSEQ=CGCCTACTGCGCACGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:14.5:1:28:1:1:1.7321:60:4:0.4:0:6.5 0/0:4:0:0,0:2,2:0:2,0:27.8:1:32.8:1:1:0:47.3:8:1:0:5.5 -GL000225.1 44318 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.59615;SOR=0.40576;LSEQ=AGCAGGTGGGCCGCCTACTG;RSEQ=GCACGCGCGGGTTTGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:3,1:0.4286:2,2:19.7:1:29:1:1:1.41418:54.7:6:0.4286:0:6 0/1:9:2:1,1:3,4:0.2222:2,2:28:1:32:0:1:1.29:58:4:0.2222:0:5.5 -GL000225.1 44319 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.48529;SOR=Inf;LSEQ=GCAGGTGGGCCGCCTACTGC;RSEQ=CACGCGCGGGTTTGCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:19.9:1:27.1:1:1:0:47.4:6:1:0:4.9 0/1:10:2:1,1:4,4:0.2:2,2:25.5:1:29.5:1:1:1:33:4:0.2:0:7 -GL000225.1 44323 . G A 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11928;SOR=Inf;LSEQ=GTGGGCCGCCTACTGCGCAC;RSEQ=CGCGGGTTTGCGGGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:23.9:1:26.9:1:1:0:47.4:6:1:0:4.9 0/1:11:4:2,2:3,4:0.3636:2,2:21.8:1:30.5:1:1:1.30:54:8:0.3636:0:5.5 -GL000225.1 44324 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49673;SOR=Inf;LSEQ=TGGGCCGCCTACTGCGCACG;RSEQ=GCGGGTTTGCGGGCAGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:24.9:1:29.1:1:1:0:47.4:6:1:0:4.9 0/1:11:2:1,1:4,5:0.1818:2,2:25.5:1:29.5:1:1:1.22:33:4:0.1818:0:7 -GL000225.1 44326 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.3127;LSEQ=GGCCGCCTACTGCGCACGCG;RSEQ=GGGTTTGCGGGCAGCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:0.1429:2,0:24:0:32:0:1:0:40:2:0.1667:0:5 0/1:11:2:1,1:4,5:0.1818:2,2:25.5:1:29.5:1:1:1.22:33:4:0.1818:0:7 -GL000225.1 44327 . G T 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=GCCGCCTACTGCGCACGCGC;RSEQ=GGTTTGCGGGCAGCTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:27.9:1:30.1:1:1:0:47.4:14:1:0:4.9 0/1:11:2:1,1:4,5:0.1818:2,2:15:0:29:1:1:1.22:31:4:0.1818:0:6 -GL000225.1 44328 . G T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=CCGCCTACTGCGCACGCGCG;RSEQ=GTTTGCGGGCAGCTGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:28.9:1:29.4:1:1:0:47.4:6:1:0:4.9 0/1:11:2:1,1:4,5:0.1818:2,2:38:1:31.5:1:1:1.22:58:4:0.1818:0:5.5 -GL000225.1 44333 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=TACTGCGCACGCGCGGGTTT;RSEQ=CGGGCAGCTGCCTGGGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:33.9:1:32.4:1:1:0:47.4:14:1:0:4.9 0/1:11:2:1,1:4,5:0.1818:2,2:43:1:30:1:1:1.22:58:4:0.1818:0:5.5 -GL000225.1 44334 . C T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94088;LSEQ=ACTGCGCACGCGCGGGTTTG;RSEQ=GGGCAGCTGCCTGGGCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:0.2857:2,2:42.5:1:21.5:1:1:3.1622:39:1:0.1667:0:3 0/1:11:3:1,2:4,4:0.2727:2,2:26:1:30.3:1:1:1.87936:43.7:6:0.2727:0:4 -GL000225.1 44335 . G T 48 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03612;SOR=0;LSEQ=CTGCGCACGCGCGGGTTTGC;RSEQ=GGCAGCTGCCTGGGCTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:3,1:0.4286:2,2:36.7:1:30.7:1:1:1.41418:54.7:6:0.4286:0:6 0/0:12:0:0,0:2,4:0:2,0:21:1:29:1:1:0:35.7:12:0.5:0:4.7 -GL000225.1 44342 . T C 73 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05573;SOR=0.10246;LSEQ=CGCGCGGGTTTGCGGGCAGC;RSEQ=GCCTGGGCTGTGGGAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:3,2:3,2:0.5:2,2:27.4:1:31.6:1:1:1:47.6:10:0.5:0:3.6 0/1:12:1:0,1:3,3:0.0833:2,0:42:0:32:0:1:0:40:2:0.0833:0:3 -GL000225.1 44344 . C A 70 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00957;SOR=0;LSEQ=CGCGGGTTTGCGGGCAGCTG;RSEQ=CTGGGCTGTGGGAGCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:3,2:3,2:0.5:2,2:44.2:1:30.2:1:1:1:48.4:10:0.5:0:4.8 0/0:12:0:0,0:5,7:0:2,0:30.8:1:30.8:1:1:0:41.3:24:1:0:5 -GL000225.1 44349 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19481;SOR=0;LSEQ=GTTTGCGGGCAGCTGCCTGG;RSEQ=CTGTGGGAGCAGCCCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:9:0:31:0:1:1.58108:60:4:0.2:0:3.5 0/0:12:0:0,0:5,7:0:2,0:32.4:1:31.2:1:1:0:41.3:24:1:0:5 -GL000225.1 44355 . GG AC 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19481;SOR=0;LSEQ=GGGCAGCTGCCTGGGCTGTG;RSEQ=AGCAGCCCGGGCAGAGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:26:1:32:1:1:1.58108:46:4:0.2:0:3 0/0:12:0:0,0:5,7:0:2,0:32.8:1:30:1:1:0:41.3:24:1:0:5 -GL000225.1 44358 . G A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.48052;SOR=Inf;LSEQ=CAGCTGCCTGGGCTGTGGGA;RSEQ=CAGCCCGGGCAGAGCTCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,4:0:2,0:28.6:1:32.7:1:1:0:50:18:1:0:4.1 0/1:12:2:1,1:4,6:0.1667:2,2:40:0:30.5:1:1:1.45:31:4:0.1667:0:5 -GL000225.1 44359 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=AGCTGCCTGGGCTGTGGGAG;RSEQ=AGCCCGGGCAGAGCTCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,4:0:2,0:27.2:1:31.7:1:1:0:50.4:18:0.9:0:4.1 0/1:11:2:1,1:3,6:0.1818:2,2:39:1:28:1:1:1.87:50:4:0.1818:0:5.5 -GL000225.1 44361 . G C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47619;SOR=Inf;LSEQ=CTGCCTGGGCTGTGGGAGCA;RSEQ=CCCGGGCAGAGCTCTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:27.6:1:30.9:1:1:0:49.4:9:1:0:4.2 0/1:11:2:1,1:3,6:0.1818:2,2:37:0:31.5:1:1:1.87:31:4:0.1818:0:5 -GL000225.1 44364 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=CCTGGGCTGTGGGAGCAGCC;RSEQ=GGGCAGAGCTCTCATGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:24:0:32:1:1:1.58108:60:4:0.2:0:3.5 0/0:11:0:0,0:4,7:0:2,0:30.2:1:30.3:1:1:0:42.1:22:1:0:4.7 -GL000225.1 44365 . G A 31 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.58647;SOR=0.41768;LSEQ=CTGGGCTGTGGGAGCAGCCC;RSEQ=GGCAGAGCTCTCATGCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,3:0.2:2,2:24:0:31:1:1:1.29098:46:4:0.2:0:3 0/1:11:1:0,1:4,6:0.0909:2,0:24:0:33:0:1:0:33:2:0.0909:0:6 -GL000225.1 44366 . G T 39 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07792;SOR=0;LSEQ=TGGGCTGTGGGAGCAGCCCG;RSEQ=GCAGAGCTCTCATGCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:4,3:0.3:2,2:25:1:25:1:1:1.44:54.7:2:0.2222:0:6 0/0:12:0:0,0:5,7:0:2,0:26.3:1:30.6:1:1:0:43.6:24:1:0:4.6 -GL000225.1 44367 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48052;SOR=Inf;LSEQ=GGGCTGTGGGAGCAGCCCGG;RSEQ=CAGAGCTCTCATGCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:24.4:1:30.6:1:1:0:49.4:9:1:0:4.2 0/1:12:2:1,1:4,6:0.1667:2,2:31:0:31:0:1:1.45:45.5:4:0.1667:0:3.5 -GL000225.1 44377 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48052;SOR=Inf;LSEQ=AGCAGCCCGGGCAGAGCTCT;RSEQ=ATGCCTTTCCACAACCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:18.4:1:30:1:1:0:49.4:9:1:0:4.2 0/1:12:2:1,1:4,6:0.1667:2,2:9.5:1:32.5:1:1:1.45:50:4:0.1667:0:3 -GL000225.1 44390 . A C 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.59564;LSEQ=GAGCTCTCATGCCTTTCCAC;RSEQ=ACCCCACACCCACCTGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:6:1:32:0:1:1:50:4:0.5:0:6 1/0:8:5:2,3:2,1:0.625:2,2:9:1:30:1:1:2.60168:38.8:10:0.625:0:5.6 -GL000225.1 44474 . C A 59 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCTGGGTGGAGACCCA;RSEQ=GTCCCTCAAAACACTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:4:2,2:1,0:0.5714:0,2:20:1:29.5:1:1:0:55:8:0.5714:0:7.8 -GL000225.1 44480 . T G 80 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTGGAGACCCACGTCCC;RSEQ=CAAAACACTGGGACCGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:6:3,3:1,0:0.8571:0,2:23.2:1:31.2:1:1:0:56.7:12:0.8571:0:6.5 -GL000225.1 44487 . A C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGACCCACGTCCCTCAAAAC;RSEQ=CTGGGACCGTGCAGCATCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:16:0:31.5:1:1:1:60:4:0.3333:0:4 -GL000225.1 44489 . T C 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCACGTCCCTCAAAACAC;RSEQ=GGGACCGTGCAGCATCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:27.8:1:30.3:1:1:1:55:8:0.6667:0:7.8 -GL000225.1 44494 . C G 65 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTCCCTCAAAACACTGGGA;RSEQ=CGTGCAGCATCCGGGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:0.6667:2,2:30.3:1:32.8:1:1:1:55:8:0.6667:0:7.8 -GL000225.1 44496 . G A 79 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTCAAAACACTGGGACC;RSEQ=TGCAGCATCCGGGCCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:1:0,2:23.2:1:30.8:1:1:0:56.7:12:1:0:6.5 -GL000225.1 44503 . A G 63 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACTGGGACCGTGCAGC;RSEQ=TCCGGGCCTGACACCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:34.8:1:31.8:1:1:0:55:8:1:0:7.8 -GL000225.1 44517 . C A 72 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11859;SOR=Inf;LSEQ=TGCAGCATCCGGGCCTGACA;RSEQ=CCCTCCGGCGGCTCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:8.8:1:30.8:1:1:0:38.6:10:1:0:4.4 0/1:11:5:2,3:5,1:0.4545:2,2:24:1:31.4:1:0.24242:6.06919:56:10:0.4545:0:7.4 -GL000225.1 44523 . CG C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCCGGGCCTGACACCCCTC;RSEQ=GCGGCTCGCCTCCTCTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:13.3:1:29.3:1:1:0:38.8:12:1:0:5 0/1:13:2:1,1:7,4:0.1538:2,2:11.5:1:29.4:1:1:1.67325:27:4:0.1538:0.0769:7.5 -GL000225.1 44525 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52941;SOR=Inf;LSEQ=CCGGGCCTGACACCCCTCCG;RSEQ=CGGCTCGCCTCCTCTGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:14.3:1:30.8:1:1:0:38.8:12:1:0:5 0/1:12:2:1,1:7,3:0.1667:2,2:13:1:30:1:1:2.16028:48:4:0.1667:0:5 -GL000225.1 44527 . G A 51 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34727;SOR=0.35351;LSEQ=GGGCCTGACACCCCTCCGGC;RSEQ=GCTCGCCTCCTCTGTGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:2,3:0.375:2,2:7.3:1:32.3:1:1:2.60:41:6:0.375:0:7.3 0/1:12:2:2,0:6,4:0.1667:2,0:20:0:32:0:0.51515:0:43:4:0.1667:0:6.5 -GL000225.1 44531 . C T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52569;SOR=Inf;LSEQ=CTGACACCCCTCCGGCGGCT;RSEQ=GCCTCCTCTGTGCCACCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,3:0:2,0:15:1:31.3:1:1:0:39.3:14:0.875:0:5.7 0/1:16:3:2,1:8,5:0.1875:2,2:5.7:1:30.3:1:1:1.23:39.7:6:0.1875:0:5.7 -GL000225.1 44537 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCCCTCCGGCGGCTCGCCTC;RSEQ=TCTGTGCCACCACGCCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:19.9:1:31.5:1:1:0:40.8:16:1:0:5.8 0/1:17:2:1,1:10,5:0.1176:2,2:21:1:31:1:1:1.91491:27:4:0.1176:0:7.5 -GL000225.1 44542 . T C 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29686;SOR=0.27416;LSEQ=CCGGCGGCTCGCCTCCTCTG;RSEQ=GCCACCACGCCACCGTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:3,2:0.375:2,2:29:1:29.3:1:1:2.60168:48.7:6:0.375:0:6.3 0/1:15:2:1,1:7,2:0.1333:2,2:14:0:31:0:0.49091:3.05504:45:4:0.1333:0:7.5 -GL000225.1 44546 . A T 95 NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12065;SOR=0;LSEQ=CGGCTCGCCTCCTCTGTGCC;RSEQ=CCACGCCACCGTCGCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:1:0,2:30.9:1:30.3:1:1:0:43:14:1:0:6.6 1/0:15:9:6,3:3,2:0.6:2,2:28.4:1:30:1:1:1.31:40.3:18:0.6:0:6.4 -GL000225.1 44548 . CA TG 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GCTCGCCTCCTCTGTGCCAC;RSEQ=CGCCACCGTCGCCGGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:32.9:1:28.1:1:1:0:43:6:1:0:6.6 0/1:16:2:1,1:9,5:0.125:2,2:22:0:32.3:1:1:1.73197:60:4:0.1333:0:2 -GL000225.1 44549 . A G 78 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=7e-05;SOR=0;LSEQ=CTCGCCTCCTCTGTGCCACC;RSEQ=CGCCACCGTCGCCGGCCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:2,4:1,0:0.8571:0,2:32.8:1:30.3:1:0.42857:0:45.2:12:0.8571:0:6.7 0/0:16:0:0,0:9,5:0:2,0:23.5:1:28.9:1:1:0:44.3:13:1:0:6.6 -GL000225.1 44551 . G A 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34575;SOR=0.31937;LSEQ=CGCCTCCTCTGTGCCACCAC;RSEQ=CCACCGTCGCCGGCCCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:1,2:0.5714:2,2:33:1:26.8:1:1:1.81:43.5:3:0.5:0:7 0/1:14:4:3,1:5,5:0.2857:2,2:34:1:30.5:1:0.58042:2.78:51.5:8:0.2857:0:4.3 -GL000225.1 44553 . C T 26 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=CCTCCTCTGTGCCACCACGC;RSEQ=ACCGTCGCCGGCCCGCCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:33.1:1:29.8:1:1:0:40.4:7:1:0:6.6 0/1:14:2:1,1:7,5:0.1429:2,2:25:0:26:1:1:1.36624:45:4:0.1429:0:7.5 -GL000225.1 44556 . C T 70 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35116;SOR=3.67665;LSEQ=CCTCTGTGCCACCACGCCAC;RSEQ=GTCGCCGGCCCGCCCGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:3,4:0.125:2,0:5:0:32:0:1:0:22:2:0.125:0:7 0/1:14:5:2,3:6,3:0.3571:2,2:19.4:1:30.4:1:0.58042:2.76:41:10:0.3571:0:6.4 -GL000225.1 44562 . C T 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.69565;SOR=1.47778;LSEQ=TGCCACCACGCCACCGTCGC;RSEQ=GGCCCGCCCGTGCCCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:3,5:0.25:2,2:39:1:31.3:1:0.54545:2.97:41:6:0.25:0:7.3 0/1:15:5:4,1:4,6:0.3333:2,2:35.8:1:31.2:1:0.28205:5.30:44:10:0.3333:0:6.2 -GL000225.1 44563 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18803;SOR=0;LSEQ=GCCACCACGCCACCGTCGCC;RSEQ=GCCCGCCCGTGCCCCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:6,4:0.1667:2,0:38:1:31:1:0.45455:0:41.5:4:0.1667:0:5.5 0/0:15:0:0,0:8,7:0:2,0:32.6:1:29.3:1:1:0:43.3:30:1:0:5.3 -GL000225.1 44564 . G A 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=CCACCACGCCACCGTCGCCG;RSEQ=CCCGCCCGTGCCCCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:25.7:1:31.3:1:1:0:40.4:24:1:0:5.9 0/1:15:2:1,1:6,6:0.1333:2,2:36:0:28:1:1:1:45:4:0.1333:0:7.5 -GL000225.1 44568 . GC TT 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62802;SOR=0.47523;LSEQ=CACGCCACCGTCGCCGGCCC;RSEQ=CCGTGCCCCTGCAGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:3,4:0.25:2,2:36.7:1:30.5:1:1:2.41:41:6:0.2727:0:6.3 0/1:15:2:2,0:5,6:0.1333:2,0:36.5:1:32.5:0:0.46154:0:43:4:0.1429:0:5.5 -GL000225.1 44572 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18803;SOR=0;LSEQ=CCACCGTCGCCGGCCCGCCC;RSEQ=TGCCCCTGCAGCCTCCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:34:0:31.5:1:1:1:46.5:4:0.1667:0:7 0/0:15:0:0,0:7,5:0:2,0:30.8:1:28.8:1:1:0:45.6:11:0.7857:0:5.5 -GL000225.1 44573 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=CACCGTCGCCGGCCCGCCCG;RSEQ=GCCCCTGCAGCCTCCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:26.2:1:29.4:1:1:0:40.4:24:1:0:5.7 0/1:15:2:1,1:7,6:0.1333:2,2:22.5:1:28.5:1:1:1.1547:27:4:0.1333:0:6.5 -GL000225.1 44574 . G A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=ACCGTCGCCGGCCCGCCCGT;RSEQ=CCCCTGCAGCCTCCCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:26.1:1:31.7:1:1:0:40.4:24:1:0:5.7 0/1:15:2:1,1:7,5:0.1333:2,2:28.5:1:26.5:1:1:1.36624:45:4:0.1333:0:7.5 -GL000225.1 44582 . A C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=CGGCCCGCCCGTGCCCCTGC;RSEQ=GCCTCCCAGCTGCCACCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:24.8:1:30.2:1:1:0:40.4:24:1:0:5.7 0/1:15:2:1,1:7,6:0.1333:2,2:24:0:31:1:1:1.1547:37:4:0.1538:0:5.5 -GL000225.1 44583 . G A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=GGCCCGCCCGTGCCCCTGCA;RSEQ=CCTCCCAGCTGCCACCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:24.6:1:31.2:1:1:0:40.4:24:1:0:5.7 0/1:15:2:1,1:7,6:0.1333:2,2:12.5:1:29.5:1:1:1.1547:27:4:0.1429:0:6.5 -GL000225.1 44606 . G C 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.53981;LSEQ=TCCCAGCTGCCACCATGGAG;RSEQ=GCCTTGCTGTGGAACGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,0:0.4:0,2:28:1:30.5:1:1:0:35.5:4:0.4:0:7 0/1:4:1:0,1:0,0:0.25:0,0:1:0:29:0:1:0:41:2:0.25:0:5 -GL000225.1 44611 . T G 63 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCCACCATGGAGGGCCT;RSEQ=GCTGTGGAACGCAGACCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,0:0.8:0,2:35.5:1:31.8:1:1:0:38.3:8:0.8:0:6.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 44614 . T G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCACCATGGAGGGCCTTGC;RSEQ=GTGGAACGCAGACCTCTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,0:0.4:0,0:29:1:31.5:1:0.33333:0:35.5:4:0.4:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 45812 . T C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTAGGCAAAGTCCATA;RSEQ=AAGGCTTACAACACCTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 46016 . C G 33 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCATAGACAGAGCCTAGA;RSEQ=AAGACTTCCATCACCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:14:1:33:0:1:0:42:4:0.6667:0:1 -GL000225.1 46103 . G C 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGAAGAGTCCCATCACCTG;RSEQ=GTGATCAGTGCAGAGATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:15:0:32:0:1:0:25:2:1:0:4 1/0:4:2:1,1:1,1:0.5:2,2:16:1:29.5:1:1:1:43:4:0.5:0:2 -GL000225.1 46104 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAAGAGTCCCATCACCTGG;RSEQ=TGATCAGTGCAGAGATATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:16:0:33:0:1:0:25:2:1:0:4 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:28.5:1:1:1:22:4:0.5:0:5 -GL000225.1 46112 . T G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCATCACCTGGGTGATCAG;RSEQ=GCAGAGATATTTCACAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:32:0:1:0:25:2:1:0:4 0/1:5:2:1,1:1,2:0.4:2,2:13.5:1:29:1:1:1.73:22:4:0.4:0:5 -GL000225.1 46161 . T A 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GGCAGAGAGTGGACAAGAGT;RSEQ=ACATAACCTAGGTGATCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:28.5:1:30.5:1:1:1:29:4:0.5:0:1.5 0/0:5:0:0,0:1,4:0:2,0:37.4:1:30:1:1:0:42:10:1:0:3.4 -GL000225.1 46165 . T A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GAGAGTGGACAAGAGTTACA;RSEQ=AACCTAGGTGATCTGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:35:1:29:1:1:1:25:4:0.5:0:3 0/0:5:0:0,0:1,4:0:2,0:33.4:1:29.4:1:1:0:42:10:1:0:3.4 -GL000225.1 46171 . A T 49 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GGACAAGAGTTACATAACCT;RSEQ=GGTGATCTGTGCAGAGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:24.5:1:29.5:1:1:0:27:8:1:0:2.3 1/0:5:3:1,2:0,2:0.6:0,2:33.7:1:31.3:1:1:0:47.3:6:0.6:0:3 -GL000225.1 46369 . C A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTAAACAAGAGTTACAT;RSEQ=ACCTGGGTTATCAGTGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:1:27:1:1:0:40:4:1:0:5 -GL000225.1 46492 . G T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCCCTGTAGACAAATCCCA;RSEQ=AAAATTGTTACATTACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:23:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:39:1:28.5:1:1:0:60:4:1:0:1.5 -GL000225.1 49252 . A G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATGTCACAATGTCCCTGT;RSEQ=GCCATATCCTTGACAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:1:31.5:1:1:0:31:4:1:0:7.5 -GL000225.1 49277 . T A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCCTTGACAAAAGTGACA;RSEQ=CACCTGGGTGATCAGTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29:1:1:0:31:4:1:0:7.5 -GL000225.1 49281 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGACAAAAGTGACATCAC;RSEQ=TGGGTGATCAGTGCGGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29:1:1:0:31:4:1:0:7.5 -GL000225.1 49285 . GT AG 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACAAAAGTGACATCACCTGG;RSEQ=GATCAGTGCGGAGATATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:1:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29:1:1:0:31:4:1:0:6.5 -GL000225.1 49288 . A G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAAGTGACATCACCTGGGTG;RSEQ=TCAGTGCGGAGATATGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:4:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29:1:1:0:31:4:1:0:6.5 -GL000225.1 49483 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCCTAGACAGTTTTACA;RSEQ=CACCTCAGCGATCAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:7.5:1:31:1:1:0:45.5:4:1:0:3 -GL000225.1 49504 . A G 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACCTCAGCGATCAGTGCAG;RSEQ=GATATGTCCCAATGTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:32:1:1:0:45.5:4:1:0:3 -GL000225.1 49525 . T A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATGTCCCAATGTTCCTC;RSEQ=AGGCAGAGCTTAGGAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10:0:32:0:1:0:45.5:4:1:0:3 -GL000225.1 49786 . CA C 66 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTAGTGCAGATATATGT;RSEQ=CAATGTCCCCTGTAGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:18:1:33:1:1:0:33.5:8:1:0:1.3 -GL000225.1 49794 . C T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGATATATGTCACAATGT;RSEQ=CCCTGTAGGCAAAGCCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:24:1:31:1:1:1:27:4:0.5:0:1.5 -GL000225.1 49955 . AT GG 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGCAGATCCTAGACAAG;RSEQ=TTGAATCACCTGGGTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:1:30.8:1:1:0:23:4:1:0.5:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 50171 . G A 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGATGAGTTACATCACCTT;RSEQ=GTGATCAGTGCAAAGGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:28:1:1:0:50:4:1:0:2.5 -GL000225.1 50340 . T C 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGATATGTCACAATGCCC;RSEQ=CATAGGCAGATCCAAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:30:1:1:0:49:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 50352 . C A 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATGCCCTCATAGGCAGAT;RSEQ=CAAGACAAGAGTCCGTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:0:30:1:1:0:49:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 50484 . G C 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAAAGTCCCTTTAGGCA;RSEQ=ATCCTAGACAAGAGTTAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:9:0:29:1:1:0:51:4:0.6667:0:4 -GL000225.1 50497 . A T 27 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTAGGCAGATCCTAGACAAG;RSEQ=GTTAAATCACTTGGATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:22:0:27:1:1:0:51:4:0.6667:0:4 -GL000225.1 50502 . A C 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGATCCTAGACAAGAGTTA;RSEQ=ATCACTTGGATGATCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:27:0:30.5:1:1:0:51:4:0.6667:0:4 -GL000225.1 50517 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTAAATCACTTGGATGAT;RSEQ=AGTGCAGAGATATGTCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:26:0:29:1:1:0:51:4:0.6667:0:4 -GL000225.1 50610 . CT C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGATACATCACAATGTC;RSEQ=TGTAGGCAGAGCCTTGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:33.5:1:1:0:45.5:4:1:0:4.5 -GL000225.1 50636 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCAGAGCCTTGACAAGTGG;RSEQ=ACATCACCTGGGTGATCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:18:0:31:0:1:0:40:2:1:0:7 1/0:3:2:1,1:1,0:0.6667:0,2:33.5:1:32.5:1:1:0:45.5:4:0.6667:0:4.5 -GL000225.1 50651 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGGTACATCACCTGGGTG;RSEQ=TCATTGCAGGGATATGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:33:0:30:0:1:0:40:2:1:0:7 1/0:3:2:1,1:1,0:0.6667:0,2:18.5:1:29.5:1:1:0:45.5:4:0.6667:0:4.5 -GL000225.1 50655 . T G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACATCACCTGGGTGATCA;RSEQ=TGCAGGGATATGTCACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:37:0:33:0:1:0:40:2:1:0:7 1/0:3:2:1,1:1,0:0.6667:0,2:14.5:1:31:1:1:0:45.5:4:0.6667:0:4.5 -GL000225.1 50661 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACCTGGGTGATCATTGCAG;RSEQ=GATATGTCACAAAGCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:40:0:33:0:1:0:40:2:1:0:7 1/0:3:2:1,1:1,0:0.6667:0,2:8.5:1:28.5:1:1:0:45.5:4:0.6667:0:4.5 -GL000225.1 50711 . A T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCCTAGAAAACAGTTACATC;RSEQ=TCTGGGTGATCATTGCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29:1:1:0:60:4:1:0:2.5 -GL000225.1 50724 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACATCATCTGGGTGATCA;RSEQ=TGCAAAGATATGTCACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:30:1:1:0:60:4:1:0:2.5 -GL000225.1 50806 . C T 48 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATCAGTGCAGAGATACAT;RSEQ=GCAATGCCCCTGTAGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:0.75:0,0:14:1:30.7:1:1:0:30.3:6:0.75:0:4.3 1/1:2:2:2,0:0,0:1:0,0:3.5:1:28:0:1:0:45:4:1:0:4 -GL000225.1 50821 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21053;SOR=0;LSEQ=TACATCGCAATGCCCCTGTA;RSEQ=GCAGAGTCTTGGCAAGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:5,2:0.2222:2,0:13:1:30.5:1:1:0:40:4:0.2222:0:6.5 0/0:10:0:0,0:6,4:0:2,0:11.3:1:29.6:1:1:0:45.8:20:1:0:4 -GL000225.1 50828 . T C 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.56343;LSEQ=CAATGCCCCTGTAGGCAGAG;RSEQ=CTTGGCAAGTGGTATATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:8,2:0,0:0.9091:0,2:19.6:1:30.6:1:1:0:34.7:9:0.9:0:4.6 1/1:13:11:7,4:1,1:0.8462:2,2:14.6:1:31.3:1:1:1.67:40.6:22:0.8462:0:4.6 -GL000225.1 50830 . T A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49206;SOR=Inf;LSEQ=ATGCCCCTGTAGGCAGAGTC;RSEQ=TGGCAAGTGGTATATCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:18.8:1:30.8:1:1:0:35.5:24:1:0:4.6 0/1:16:2:1,1:8,6:0.125:2,2:16.5:1:32:0:1:1.30929:41:4:0.125:0:6 -GL000225.1 50853 . T G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGTGGTATATCACCTGG;RSEQ=TGATCATTGCAGGGATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:9,9:0,0:1:0,2:26.3:1:29.6:1:1:0:34.2:17:1:0:4.3 1/1:21:21:12,9:0,0:1:0,2:31.7:1:31:1:1:0:41.7:42:1:0:4.1 -GL000225.1 50862 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21041;SOR=0;LSEQ=ATATCACCTGGTTGATCATT;RSEQ=CAGGGATATGTCACAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:0.1:2,2:26.5:1:29:1:1:1:49:4:0.1:0:4.5 0/0:23:0:0,0:12,11:0:2,0:34.6:1:31.8:1:1:0:40.6:46:1:0:4 -GL000225.1 50869 . T A 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13956;LSEQ=CTGGTTGATCATTGCAGGGA;RSEQ=ATGTCACAAAGCACCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:9,9:0.1429:2,2:18.3:1:31:1:1:1.94:41.3:6:0.1429:0:4 0/1:25:4:2,2:11,10:0.16:2,2:38.3:1:29.5:1:1:1.09581:39:8:0.16:0:4 -GL000225.1 50873 . T C 53 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39459;SOR=0.38741;LSEQ=TTGATCATTGCAGGGATATG;RSEQ=CACAAAGCACCCTGTGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:2,2:9,10:0.1739:2,2:13.8:1:26.8:1:1:1.11:41:3:0.1364:0:4.8 0/1:27:2:1,1:13,12:0.0741:2,2:42:1:30:1:1:1.0801:23:4:0.0741:0:4.5 -GL000225.1 50878 . A C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4949;SOR=Inf;LSEQ=CATTGCAGGGATATGTCACA;RSEQ=AGCACCCTGTGGGCAGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:0:2,0:26.7:1:29.4:1:1:0:38.2:22:1:0:4.2 0/1:28:2:1,1:14,12:0.0714:2,2:9:0:32:0:1:1.16024:58:4:0.0714:0:4 -GL000225.1 50882 . A T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.82439;LSEQ=GCAGGGATATGTCACAAAGC;RSEQ=CCCTGTGGGCAGATCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:0.08:2,2:36.5:1:30.5:1:1:1.0871:41.5:4:0.0833:0:5 0/1:30:2:1,1:15,13:0.0667:2,2:44.5:1:30:1:1:1.14834:36:4:0.0714:0:5.5 -GL000225.1 50886 . T C 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.73769;SOR=0.67156;LSEQ=GGATATGTCACAAAGCACCC;RSEQ=GTGGGCAGATCCTAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:3,3:10,10:0.2308:2,2:17.8:1:29.2:1:1:1:42.5:12:0.2308:0:4.8 0/1:30:5:3,2:13,12:0.1667:2,2:17.6:1:27.4:1:1:1.37:45.4:10:0.1724:0:5.4 -GL000225.1 50891 . G T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49899;SOR=0;LSEQ=TGTCACAAAGCACCCTGTGG;RSEQ=CAGATCCTAGAGAAGAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:12,12:0,0:1:0,2:27.3:1:29.1:1:1:0:38.1:23:1:0:4.5 1/1:31:29:16,13:0,0:0.9355:0,2:24.1:1:29.2:1:1:0:42.4:28:0.9333:0:4.1 -GL000225.1 50896 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50376;SOR=Inf;LSEQ=CAAAGCACCCTGTGGGCAGA;RSEQ=CCTAGAGAAGAGTTATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:27.3:1:30.7:1:1:0:38.1:48:1:0:4.5 0/1:33:2:1,1:17,14:0.0606:2,2:18:0:31:1:1:1.20712:44:4:0.0625:0:5 -GL000225.1 50897 . C G 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50376;SOR=Inf;LSEQ=AAAGCACCCTGTGGGCAGAT;RSEQ=CTAGAGAAGAGTTATATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:27.1:1:29.8:1:1:0:38.1:7:1:0:4.5 0/1:33:2:1,1:17,14:0.0606:2,2:10:0:34:0:1:1.20712:54:4:0.0625:0:3.5 -GL000225.1 50900 . A G 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.5013;SOR=Inf;LSEQ=GCACCCTGTGGGCAGATCCT;RSEQ=GAGAAGAGTTATATCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:0:2,0:26.1:1:28.3:1:1:0:38.1:11:1:0:4.5 0/1:32:2:2,0:15,15:0.0625:2,0:18.5:1:33.5:1:0.48589:0:30:4:0.0625:0:6 -GL000225.1 50906 . G T 72 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.44509;SOR=2.36322;LSEQ=TGTGGGCAGATCCTAGAGAA;RSEQ=AGTTATATCACCTGGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:8,11:0.0909:2,2:15:1:27.5:1:1:1.35:41.5:4:0.0952:0:5 0/1:31:6:3,3:11,12:0.1935:2,2:20.8:1:28.2:1:1:1.09:45.7:12:0.2:0:4.2 -GL000225.1 50907 . A T 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5;SOR=Inf;LSEQ=GTGGGCAGATCCTAGAGAAG;RSEQ=GTTATATCACCTGGGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:9,11:0:2,0:27.6:1:29.4:1:1:0:39.1:5.667:1:0:4.4 0/1:28:2:1,1:13,13:0.0714:2,2:7:0:30:0:1:1:44:4:0.0714:0:5 -GL000225.1 50912 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48986;SOR=Inf;LSEQ=CAGATCCTAGAGAAGAGTTA;RSEQ=ATCACCTGGGTGATCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:0:2,0:23.2:1:28.9:1:1:0:39.5:44:1:0:4.4 0/1:24:2:1,1:10,11:0.0833:2,2:40:0:30:1:1:1.10:58:4:0.087:0:4 -GL000225.1 50916 . A G 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72453;SOR=1.50069;LSEQ=TCCTAGAGAAGAGTTATATC;RSEQ=CCTGGGTGATCAGTGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:1,3:5,8:0.2353:2,2:22:1:32.3:1:1:1.81053:33.3:8:0.2353:0:5 0/1:22:7:3,4:8,7:0.3182:2,2:25.3:1:31.4:1:1:1.49477:35.6:14:0.3182:0:3.9 -GL000225.1 50933 . A C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22973;SOR=0;LSEQ=ATCACCTGGGTGATCAGTGC;RSEQ=GAGATATGTCACAAGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:5,11:0.1111:2,2:21.5:1:29:1:1:2.10:47.5:4:0.1176:0:8 0/0:19:0:0,0:9,10:0:2,0:24.1:1:30.2:1:1:0:40.7:18:1:0:4.2 -GL000225.1 50935 . A T 74 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.4054;SOR=2.61693;LSEQ=CACCTGGGTGATCAGTGCAG;RSEQ=GATATGTCACAAGACCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:6,8:0.125:2,0:12:1:31:0:0.5:0:33.5:4:0.125:0:4 0/1:18:5:2,3:7,6:0.2778:2,2:11.8:1:32:0:1:1.69618:33.2:10:0.3125:0:3.4 -GL000225.1 50945 . CAAGACCCCTGTAGGCAGAGCCTAGACAAGAGTTATATCAACTGGGTGATCAGTGCAGTGAAATGTCAA C 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.27086;SOR=Inf;LSEQ=ATCAGTGCAGAGATATGTCA;RSEQ=AATGCCGTGTGGCCAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:23:1:29.3:1:1:0:45:11:1:0:5.3 0/1:20:4:1,3:8,8:0.2:2,2:78:1:30.9:1:0.59133:2.84745:35.8:8:0.2105:0.2:3.3 -GL000225.1 50952 . CC AT 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.89326;LSEQ=CAGAGATATGTCACAAGACC;RSEQ=TGTAGGCAGAGCCTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:1,1:0.6:2,2:24.7:1:28.8:1:1:1:45:5:0.625:0.1:5.2 1/0:14:8:5,3:0,0:0.5714:0,2:24.9:1:29.6:1:1:0:43.6:16:0.8889:0:3.3 -GL000225.1 50962 . G C 31 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14229;SOR=0;LSEQ=TCACAAGACCCCTGTAGGCA;RSEQ=AGCCTAGACAAGAGTTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:21.5:1:31:0:1:1.29:47.5:4:0.2222:0:7 0/0:14:0:0,0:6,4:0:2,0:18.7:1:30.9:1:1:0:43.3:20:1:0:3.7 -GL000225.1 50970 . A G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.75091;LSEQ=CCCCTGTAGGCAGAGCCTAG;RSEQ=CAAGAGTTATATCAACTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:2,4:0.1429:2,0:11:0:32:0:0.42857:0:20:2:0.1429:0:6 0/1:13:3:2,1:3,3:0.2308:2,2:9:1:31:1:1:1.85:46.3:6:0.3333:0:4 -GL000225.1 50979 . A G 36 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.81204;LSEQ=GCAGAGCCTAGACAAGAGTT;RSEQ=TATCAACTGGGTGATCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:0.4286:2,2:11:1:31.7:1:1:1.81007:47:6:0.4286:0:4 0/1:8:3:1,2:1,0:0.375:0,2:12.7:1:23.3:1:1:0:43.3:2:0.6667:0:4.7 -GL000225.1 50985 . A C 50 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20635;SOR=0.11969;LSEQ=CCTAGACAAGAGTTATATCA;RSEQ=CTGGGTGATCAGTGCAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0.75:0,2:33.7:1:32:1:1:0:46.7:6:1:0:4.3 0/1:5:1:0,1:0,0:0.2:0,0:28:0:33:0:1:0:40:2:1:0:5 -GL000225.1 51218 . A T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAGTGCAGAGATATGTCAAA;RSEQ=TGCCCCTGTAGGCAGAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35:0:21.5:1:1:0:50:1:1:0:7.5 1/1:2:2:1,1:0,0:1:0,2:32:1:28.5:1:1:0:60:4:1:0:1 -GL000225.1 51220 . G T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTGCAGAGATATGTCAAAAT;RSEQ=CCCCTGTAGGCAGAGCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:0:29.5:1:1:0:50:4:1:0:7.5 0/0:2:0:0,0:1,1:0:2,0:34:1:31:1:1:0:60:4:1:0:1 -GL000225.1 51232 . A C 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=GTCAAAATGCCCCTGTAGGC;RSEQ=GAGCCTACAAAATTGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:49:0:28.5:1:1:0:50:4:1:0:7.5 0/0:2:0:0,0:1,1:0:2,0:39.5:1:30:1:1:0:60:4:1:0:1 -GL000225.1 51241 . A C 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCCCTGTAGGCAGAGCCTAC;RSEQ=AAATTGTTACATCACTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40:0:30.5:1:1:0:50:4:1:0:7.5 0/0:2:0:0,0:1,1:0:2,0:39.5:1:30:1:1:0:60:4:1:0:1 -GL000225.1 51248 . T G 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGGCAGAGCCTACAAAATTG;RSEQ=TACATCACTTAGGTGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:0:30:0:1:0:50:4:1:0:7.5 0/0:2:0:0,0:1,1:0:2,0:37:1:30.5:1:1:0:60:4:1:0:1 -GL000225.1 51258 . T A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TACAAAATTGTTACATCACT;RSEQ=AGGTGATCAGTGCAGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23:0:29:0:1:0:50:4:1:0:7.5 0/0:2:0:0,0:1,1:0:2,0:27:1:30.5:1:1:0:60:4:1:0:1 -GL000225.1 51273 . G T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=TCACTTAGGTGATCAGTGCA;RSEQ=AGATATGTCACAGTACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:30:1:1:0:50:4:1:0:7.5 0/0:2:0:0,0:1,1:0:2,0:12:1:32:1:1:0:60:4:1:0:1 -GL000225.1 51916 . A G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATGCCCCCATAGGCAGAG;RSEQ=CTACACAAAAGTCCCATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:32.5:1:1:0:22:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 51920 . C G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCCCCATAGGCAGAGACTA;RSEQ=ACAAAAGTCCCATCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:32.5:1:1:0:22:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 51948 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TCCCATCACCTGGGTGATCA;RSEQ=TGCAGAGATATGTCACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:31.5:1:1:0:22:4:0.6667:0:4.5 0/0:2:0:0,0:1,1:0:2,0:19:1:29.5:1:1:0:36:4:1:0:3.5 -GL000225.1 51971 . CT GA 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CAGAGATATGTCACAAAGCC;RSEQ=TGTAGGCAGAGCCTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:23.8:1:31.3:1:1:0:39.8:8:1:0:2.8 1/1:2:2:1,1:0,0:1:0,2:32.5:1:29.5:1:1:0:36:4:1:0:2.5 -GL000225.1 51972 . T C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGATATGTCACAAAGCCC;RSEQ=TGTAGGCAGAGCCTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:13.5:1:31.5:1:1:1:22:4:0.5:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 52049 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGCTCACTGTTTGCTCC;RSEQ=GGAGCTCTGCGGGCACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 52213 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CCGGGGAGGCATCTTCTCTC;RSEQ=GGGGTCTCACTCTGGTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:25.6:1:31.4:1:1:0:40.1:14:1:0:3.6 1/0:3:2:1,1:0,1:0.6667:0,2:19:1:29.5:1:1:0:42.5:4:0.6667:0:5.5 -GL000225.1 52217 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCATCTTCTCTCTGGG;RSEQ=TCTCACTCTGGTCTCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:0.2857:2,0:32:1:29:0:1:0:29:4:0.2857:0:6.5 0/0:3:0:0,0:1,2:0:2,0:24.3:1:31:1:1:0:44:6:1:0:5.7 -GL000225.1 52221 . CA TG 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GCATCTTCTCTCTGGGGTCT;RSEQ=CTCTGGTCTCCTACATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:28:1:31.7:1:1:0:40.1:14:1:0:3.6 1/0:3:2:1,1:0,1:0.6667:0,2:19:1:30:1:1:0:42.5:4:0.6667:0:4.5 -GL000225.1 52265 . CAT GGC 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGAGAGCCACAAGCCTG;RSEQ=GTGTGAGACTGTCCCGGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:19:1:33.3:0:1:0:38.5:4:0.5:0:2.5 0/0:1:0:0,0:0,1:0:0,0:21:0:32:0:1:0:40:2:1:0:7 -GL000225.1 52495 . C T 26 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGAAACGCACACCCCT;RSEQ=ACCCCTTCCCCCTCGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:26:1:1:0:39:4:1:0:4 -GL000225.1 52510 . G T 26 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTCACCCCTTCCCCCTC;RSEQ=CCCCCTTCCTCTTCGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:26:1:1:0:39:4:1:0:4 -GL000225.1 52518 . C T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTCCCCCTCGCCCCCTT;RSEQ=CTCTTCGTCTCTCTGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:28:1:1:0:39:4:1:0:4 -GL000225.1 52524 . C T 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTCGCCCCCTTCCTCTT;RSEQ=GTCTCTCTGGCCCCACCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:1:28.5:1:1:0:39:4:1:0:4 -GL000225.1 52594 . T C 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGCCCCCGGCCGCAGGCC;RSEQ=CGACGCCCTGGGACCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:0:29:1:1:0:33:4:1:0:5 0/1:6:2:1,1:3,1:0.3333:2,2:14:1:28.5:1:1:2.44949:41:4:0.3333:0:7.5 -GL000225.1 52598 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCCCGGCCGCAGGCCTCGA;RSEQ=GCCCTGGGACCCTTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:7:0:30:1:1:0:33:4:1:0:5 0/1:6:2:1,1:3,1:0.3333:2,2:18:1:27.5:1:1:2.44949:41:4:0.3333:0:7.5 -GL000225.1 52601 . CCTGGGACCCTTCCAGGGCGGGGCA TCTTAGAACCTTCCAGGGTGAGACG 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCGGCCGCAGGCCTCGACGC;RSEQ=GGCTGTCCCAGGGCTCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10:0:30.5:1:1:0:33:4:1:0:5 0/1:6:2:1,1:2,2:0.3333:2,2:41:1:29:1:1:1:41.5:4:0.3333:0.3333:5 -GL000225.1 52615 . A G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=CGACGCCCTGGGACCCTTCC;RSEQ=GGGCGGGGCAGGCTGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:2:0:26:0:1:0:58:2:0.3333:0:4 0/1:5:2:1,1:2,1:0.4:2,2:35:1:29:1:1:1.7321:41:4:0.4:0:7.5 -GL000225.1 52617 . G A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=ACGCCCTGGGACCCTTCCAG;RSEQ=GCGGGGCAGGCTGTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:24:1:29.5:1:1:0:33:4:0.6667:0:5 0/1:5:2:1,1:1,0:0.4:0,2:26:0:28.5:1:1:0:24:4:0.4:0:4.5 -GL000225.1 52619 . C T 57 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=GCCCTGGGACCCTTCCAGGG;RSEQ=GGGGCAGGCTGTCCCAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:24:1:30:1:1:0:33:4:0.6667:0:5 1/1:5:4:2,2:1,0:0.8:0,2:31.8:1:28.8:1:1:0:40.8:8:1:0:5.8 -GL000225.1 52623 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TGGGACCCTTCCAGGGCGGG;RSEQ=CAGGCTGTCCCAGGGCTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:19.3:1:32.3:1:1:0:41.3:6:1:0:4.7 0/1:6:2:1,1:2,2:0.3333:2,2:43:1:30:1:1:1:41:4:0.3333:0:7.5 -GL000225.1 52624 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GGGACCCTTCCAGGGCGGGG;RSEQ=AGGCTGTCCCAGGGCTCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:19.7:1:32:1:1:0:41.3:6:1:0:4.7 0/1:6:2:1,1:2,2:0.3333:2,2:9:1:28.5:1:1:1:48.5:4:0.3333:0:4 -GL000225.1 52625 . A G 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=GGACCCTTCCAGGGCGGGGC;RSEQ=GGCTGTCCCAGGGCTCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:24:1:31:1:1:0:33:4:0.6667:0:5 0/1:6:2:1,1:2,2:0.3333:2,2:25.5:1:27.5:1:1:1:24:4:0.3333:0:4.5 -GL000225.1 52629 . T A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0.23975;LSEQ=CCTTCCAGGGCGGGGCAGGC;RSEQ=GTCCCAGGGCTCACCGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:24:1:31:0:1:0:33:4:1:0:5 0/1:7:2:1,1:2,3:0.2857:2,2:21.5:1:27:1:1:1.41:24:4:0.2857:0:4.5 -GL000225.1 52644 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.54771;LSEQ=CAGGCTGTCCCAGGGCTCAC;RSEQ=GCCATTCATGAAGGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:31:0:31:0:1:0:33:2:0.5:0:6 0/1:6:2:1,1:1,3:0.3333:2,2:6.5:1:28:1:1:2.45:24:4:0.3333:0:4.5 -GL000225.1 52661 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CACCGCCATTCATGAAGGGG;RSEQ=GGAGCCTGCCTGCCTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:31:1:30.5:1:1:0:45.5:4:1:0:5 1/0:4:2:1,1:0,2:0.5:0,2:15:0:31:1:1:0:41:4:0.5:0:7.5 -GL000225.1 52690 . G A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCTGCCTGTGGGCCTTTATA;RSEQ=GAGCCGCTGGCTGGCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:15:1:31:1:1:0:59:4:1:0:2.5 1/1:2:2:0,2:0,0:1:0,0:11.5:1:32:0:1:0:40:4:1:0:4.5 -GL000225.1 52797 . CA TG 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCTCTCTGCCCGTGTCCTTC;RSEQ=TGAAATTCTGGCCGGGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:33:1:1:0:45:4:1:0:1.5 0/0:1:0:0,0:1,0:0:0,0:23:0:32:0:1:0:27:2:1:0:5 -GL000225.1 52819 . C T 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATTCTGGCCGGGGCTC;RSEQ=CTGCGATGGCCCTCACGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:27:1:1:0:27:4:1:0:4 -GL000225.1 52824 . G C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGGCCGGGGCTCCCTGC;RSEQ=ATGGCCCTCACGACACCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:29.5:1:1:0:27:4:1:0:4 -GL000225.1 52834 . A C 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCCCTGCGATGGCCCTC;RSEQ=CGACACCTTCGGACGGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:29.5:1:1:0:27:4:1:0:4 -GL000225.1 52943 . A G 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCGAGCTTGCTTTGAGC;RSEQ=GAACCCGTACCCGGGCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12.5:1:28:1:1:0:60:4:1:0:5 -GL000225.1 62992 . G A 29 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=TGTCGGAAGGTGTTGGGAGA;RSEQ=CCTCAGCTGGAATTTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:31:0:29.5:1:1:0:43.5:4:0.6667:0:5.5 0/0:8:0:0,0:4,4:0:2,0:25.8:1:32.9:1:1:0:50.6:16:1:0:4 -GL000225.1 62994 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TCGGAAGGTGTTGGGAGAGC;RSEQ=TCAGCTGGAATTTCACAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:36.3:1:30.8:1:1:0:41.8:8:1:0:6.5 0/1:8:2:1,1:3,3:0.25:2,2:21:1:30:1:1:1:30:4:0.25:0:5.5 -GL000225.1 63000 . T C 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=GGTGTTGGGAGAGCCTCAGC;RSEQ=GGAATTTCACAGACGGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,1:0:2,0:31:1:30.5:1:1:0:43.5:4:0.5:0:5.5 0/1:7:3:1,2:2,2:0.4286:2,2:37.7:1:29:1:1:1.81007:49:6:0.4286:0:6 -GL000225.1 63011 . A G 45 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=AGCCTCAGCTGGAATTTCAC;RSEQ=GACGGACAAGGGCACCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:35.7:1:28.7:1:1:0:36:6:0.75:0:6 0/0:5:0:0,0:2,3:0:2,0:21.8:1:30.6:1:1:0:51:10:1:0:5.2 -GL000225.1 63022 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GAATTTCACAGACGGACAAG;RSEQ=GCACCGAGAGGCCAGCGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:23.3:1:30:1:1:0:48.7:6:1:0:6 1/0:3:2:1,1:0,1:0.6667:0,2:13.5:1:28.5:1:1:0:58.5:4:0.6667:0:6.5 -GL000225.1 63027 . C A 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAGACGGACAAGGGCAC;RSEQ=GAGAGGCCAGCGGGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:29.3:1:24.7:1:1:0:42.3:2:1:0:6.7 1/1:3:3:1,2:0,0:1:0,2:16.3:1:29.3:1:1:0:49:6:1:0:6 -GL000225.1 63067 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCACGTCAGCAGGTGTGC;RSEQ=CAATAAGCGCAGGTCTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:32:1:1:0:60:4:1:0:2.5 -GL000225.1 63093 . T G 52 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07619;SOR=0;LSEQ=AGCGCAGGTCTAGCCAGGAG;RSEQ=CCGGCAAAGAGAGCTAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:16.8:1:26:1:1:1:31:3:0.6:0:4.5 0/0:4:0:0,0:2,2:0:2,0:21.5:1:28.3:1:1:0:60:8:1:0:3.5 -GL000225.1 63095 . C G 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CGCAGGTCTAGCCAGGAGTC;RSEQ=GGCAAAGAGAGCTAGAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,2:0.3333:2,2:17.5:1:29:1:1:1.73:33:4:0.3333:0:4 0/0:4:0:0,0:1,1:0:2,0:29.5:1:30:1:1:0:60:4:0.5:0:2.5 -GL000225.1 63096 . G C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=GCAGGTCTAGCCAGGAGTCC;RSEQ=GCAAAGAGAGCTAGAGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:25.5:1:31:1:1:1:60:4:0.3333:0:2 1/0:4:2:1,1:1,1:0.5:2,2:28.5:1:29:1:1:1:60:4:0.5:0:2.5 -GL000225.1 63124 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GAGCTAGAGGTCTGCGTTCC;RSEQ=CCACCAGGCCCTCCATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:29:1:31.5:1:1:1:33:4:0.4:0:4 0/0:3:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63127 . A G 33 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGAGGTCTGCGTTCCGCC;RSEQ=CCAGGCCCTCCATGGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:24:0:33:1:1:1.7321:60:4:0.4:0:2 0/0:2:0:0,0:1,1:0:2,0:23:0:31:1:1:0:60:4:1:0:3.5 -GL000225.1 63134 . C G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGCGTTCCGCCACCAGGC;RSEQ=CTCCATGGTGGCAGCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:23:1:30.7:1:1:1.73:34.3:6:0.6:0:4.7 1/1:2:2:1,1:0,0:1:0,2:16:0:33:1:1:0:60:4:1:0:3.5 -GL000225.1 63191 . C G 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGGCTGGCGATGGTGGCG;RSEQ=GGTGGCGCAGAGGAGGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:33:0:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63194 . T A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGCGATGGTGGCGCGG;RSEQ=GGCGCAGAGGAGGCGAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:0:32:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63204 . G A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGCGCGGTGGCGCAGAG;RSEQ=AGGCGAGCCGCCGGAAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:10:0:31.5:1:1:0:60:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63342 . G A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTATGGGTTGGTCAGGCG;RSEQ=GGGTGGGGTGGTAGAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:30.5:1:32:1:1:0:60:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63355 . A G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCGGGGGTGGGGTGGT;RSEQ=GAAAAGCATGAGAGCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:42:1:32:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63360 . A G 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGGGTGGGGTGGTAGAAA;RSEQ=GCATGAGAGCTCTGCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:43.7:1:32:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63398 . G A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGCTGCTCCCACTGCCCAG;RSEQ=CGGCTGCCCACAAACCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:13:1:29:1:1:1.73:60:4:0.4:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63416 . G C 33 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGCGGCTGCCCACAAACCC;RSEQ=CGCATGCGCAGTAGGCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:25.5:1:33:0:1:0:60:4:0.4:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63418 . G A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCGGCTGCCCACAAACCCGC;RSEQ=CATGCGCAGTAGGCGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,2:0.4:0,2:24:1:31.5:1:1:0:60:4:0.5:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63426 . A T 40 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACAAACCCGCGCATGCGC;RSEQ=GTAGGCGTCCCATCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:28.7:1:25.7:1:1:0:60:2:0.6667:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63433 . G T 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCGCATGCGCAGTAGGC;RSEQ=TCCCATCTGCTGGTACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:35.7:1:31:1:1:0:60:6:0.75:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63439 . T C 64 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCGCAGTAGGCGTCCCA;RSEQ=CTGCTGGTACCTGGGCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:36.8:1:32.3:1:1:0:60:8:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63494 . A C 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGCCCAGGAAAGAATGGC;RSEQ=GTTCTCCACTGTGTGGAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:1:30.5:1:1:0:60:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63581 . A G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGTGTAGGGGGCGGGGG;RSEQ=AAGACACGCCCCTCCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:33:0:1:0:47:4:1:0:7.5 1/1:2:2:1,1:0,0:1:0,2:10.5:1:32.5:1:1:0:50:4:1:0:7 -GL000225.1 63585 . A T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=GTGTAGGGGGCGGGGGAAAG;RSEQ=CACGCCCCTCCATAGCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:8:1:31.7:1:1:0:50.3:6:1:0:6.7 1/0:4:2:1,1:1,1:0.5:2,2:14.5:1:30.5:1:1:1:50:4:0.5:0:7 -GL000225.1 63588 . C T 31 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TAGGGGGCGGGGGAAAGACA;RSEQ=GCCCCTCCATAGCCAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:13:0:31:0:1:0:47:4:0.6667:0:7.5 0/0:4:0:0,0:2,2:0:2,0:11.3:1:30.8:1:1:0:37:8:1:0:6.8 -GL000225.1 63589 . G A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AGGGGGCGGGGGAAAGACAC;RSEQ=CCCCTCCATAGCCAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:12:1:32.3:1:1:0:50.3:6:1:0:6.7 1/0:4:2:1,1:1,1:0.5:2,2:6:0:28.5:1:1:1:24:4:0.5:0:6.5 -GL000225.1 63598 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GGGAAAGACACGCCCCTCCA;RSEQ=AGCCAGCCAGGTGTTCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:23:0:33.5:1:1:1.7321:47:4:0.4:0:7.5 0/0:4:0:0,0:2,2:0:2,0:21.3:1:28.8:1:1:0:37:8:1:0:6.8 -GL000225.1 63611 . G T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=CCCTCCATAGCCAGCCAGGT;RSEQ=TTCCCCGCGAAAAAGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:36:0:32:0:1:1.7321:47:4:0.4:0:7.5 1/0:4:2:1,1:1,1:0.5:2,2:40.5:1:30:0:1:1:50:4:0.5:0:7 -GL000225.1 63618 . G A 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=TAGCCAGCCAGGTGTTCCCC;RSEQ=CGAAAAAGAGGCCACCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:29.5:1:31.2:1:1:0:55.2:12:1:0:4.7 1/0:4:2:1,1:1,1:0.5:2,2:35:0:29.5:1:1:1:24:4:0.5:0:6.5 -GL000225.1 63624 . A T 68 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5;SOR=0.23975;LSEQ=GCCAGGTGTTCCCCGCGAAA;RSEQ=AGAGGCCACCGCCCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:1,0:0.8333:0,2:34.8:1:29.6:1:1:0:54.2:10:0.8333:0:5.4 1/0:4:2:1,1:1,1:0.5:2,2:36:1:30:1:1:1:24:4:0.5:0:6.5 -GL000225.1 63625 . A G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13333;SOR=Inf;LSEQ=CCAGGTGTTCCCCGCGAAAA;RSEQ=GAGGCCACCGCCCTGCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:30.7:1:29.8:1:1:0:55.2:12:1:0:4.7 1/0:4:2:1,1:1,1:0.5:2,2:42:1:30.5:1:1:1:50:4:0.5:0:7 -GL000225.1 63633 . CC AT 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=TCCCCGCGAAAAAGAGGCCA;RSEQ=GCCCTGCCCCGACCCGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:26.2:1:32.3:1:1:0:55.2:12:1:0:4.7 1/0:4:2:1,1:1,1:0.5:2,2:27.5:1:31.3:1:1:1:24:4:0.5:0:5.5 -GL000225.1 63634 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCCCGCGAAAAAGAGGCCAC;RSEQ=GCCCTGCCCCGACCCGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:26.5:1:30:0:1:2.44949:47:4:0.3333:0:7.5 0/0:4:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63641 . C T 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AAAAAGAGGCCACCGCCCTG;RSEQ=CCCGACCCGACACCGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:19:0:31.5:1:1:2.44949:60:4:0.3333:0:3.5 0/0:4:0:0,0:2,2:0:2,0:23.3:1:30.3:1:1:0:37:8:1:0:6.3 -GL000225.1 63649 . C T 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GCCACCGCCCTGCCCCGACC;RSEQ=GACACCGTCCCAACCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:11:0:32:1:1:2.44949:60:4:0.3333:0:3.5 0/0:4:0:0,0:2,2:0:2,0:15.3:1:30:1:1:0:37:8:1:0:6.3 -GL000225.1 63653 . A C 58 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00476;SOR=Inf;LSEQ=CCGCCCTGCCCCGACCCGAC;RSEQ=CCGTCCCAACCCTGTGTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:12.8:1:29.7:1:1:0:55.2:12:1:0:4.7 1/1:4:4:2,2:0,0:1:0,2:11.3:1:29.3:1:1:0:37:8:1:0:6.3 -GL000225.1 63706 . T G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAGCCTGGTATTCTTGC;RSEQ=CACTGAGGGGGGTGCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63814 . G C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAGAAACTCCGGGCTCA;RSEQ=CAGGAGCTTATCCAGTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33:0:33:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 63917 . T C 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGCATCTGCCAGTGCCA;RSEQ=GCAGAGGCCTCTGGGTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:1:28:1:1:0:60:4:1:0:6.5 -GL000225.1 63920 . A G 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCATCTGCCAGTGCCATGC;RSEQ=GAGGCCTCTGGGTGCGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:40:1:28.5:1:1:0:60:4:1:0:6.5 -GL000225.1 63936 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=ATGCAGAGGCCTCTGGGTGC;RSEQ=CGGGCTGGCAAGGTGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:9:0:31.5:1:1:0:60:4:0.6667:0:4.5 0/0:2:0:0,0:1,1:0:2,0:43.5:1:27:1:1:0:60:4:1:0:6.5 -GL000225.1 63937 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TGCAGAGGCCTCTGGGTGCG;RSEQ=GGGCTGGCAAGGTGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:11:1:33:1:1:0:60:6:1:0:4.7 1/1:2:2:1,1:0,0:1:0,2:42.5:1:27.5:1:1:0:60:4:1:0:6.5 -GL000225.1 63946 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGGGTGCGCGGGCTGGC;RSEQ=AGGTGGAGCTGCCCCGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:20:1:32:1:1:0:60:6:1:0:4.7 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29.5:1:1:0:60:4:1:0:6.5 -GL000225.1 63948 . G C 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGTGCGCGGGCTGGCAA;RSEQ=GTGGAGCTGCCCCGCCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:22:1:33:1:1:0:60:6:1:0:4.7 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29:1:1:0:60:4:1:0:6.5 -GL000225.1 63980 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCTTGGGGTTCCCACGC;RSEQ=GCCCGGGCGACCTGGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:15.5:1:30.5:1:1:0:60:4:0.6667:0:4.5 0/0:1:0:0,0:0,1:0:0,0:5:0:31:0:1:0:60:2:1:0:7 -GL000225.1 64027 . T C 62 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCAGCCCCACCACGGACTCC;RSEQ=CTGGGACGCGGGTTGCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:14.3:1:31:1:1:0:60:8:1:0:4.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64036 . C T 43 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGGACTCCTCTGGGACG;RSEQ=GGGTTGCGCAAACACACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:23.3:1:27.7:1:1:0:60:6:0.75:0:4.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64070 . T C 60 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCTTGGCCCTGTTGCCC;RSEQ=GCTTGAGCAGGCCCAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:41.3:1:30:1:1:0:60:8:1:0:4.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64098 . A G 51 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4;SOR=0;LSEQ=CAGGCCCAGGATGTCCCACC;RSEQ=CTCAAGGGCCTGGCAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0.75:0,2:22.3:1:32.7:1:1:0:60:6:1:0:4.7 0/0:2:0:0,0:2,0:0:0,0:10:0:31.5:1:1:0:40.5:4:1:0:5 -GL000225.1 64100 . T G 66 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=GGCCCAGGATGTCCCACCAC;RSEQ=CAAGGGCCTGGCAGGCCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:19.8:1:33:1:1:0:60:8:1:0:4.8 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64109 . TG CA 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TGTCCCACCACTCAAGGGCC;RSEQ=GCAGGCCATCGTGCTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:15.3:1:31.3:1:1:0:60:8:1:0:4.8 1/0:3:2:2,0:1,0:0.6667:0,0:22:0:30:1:1:0:40.5:4:0.6667:0:4 -GL000225.1 64122 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AAGGGCCTGGCAGGCCATCG;RSEQ=GCTGTGGGTCCCAGTCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25:1:31.5:1:1:0:60:4:1:0:4.5 1/0:3:2:2,0:1,0:0.6667:0,0:21:0:31.5:1:1:0:40.5:4:0.6667:0:4 -GL000225.1 64132 . C A 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGCCATCGTGCTGTGGGT;RSEQ=CCAGTCCTCCCAGCTTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:42:0:33:0:1:0:60:2:1:0:4 1/0:3:2:2,0:1,0:0.6667:0,0:11:0:27:1:1:0:40.5:4:0.6667:0:4 -GL000225.1 64190 . G A 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CGAGGAGCCTGAGGGTGGGA;RSEQ=AGCGCCCATTCCGGAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:17:1:29:1:1:0:55.5:4:1:0:3.5 1/1:2:2:1,1:0,0:1:0,2:14.5:1:28:1:1:0:60:4:1:0:3.5 -GL000225.1 64237 . A G 30 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGTATGCAAAATCCCCAC;RSEQ=TCCTGGGGCAGGTTGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:30:1:1:0:60:4:1:0:3 1/1:1:1:0,1:0,0:1:0,0:33:0:33:0:1:0:60:2:1:0:2 -GL000225.1 64295 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCCTTGCTGGGCTGGAGCAC;RSEQ=GGGACGGCCCTCACTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:21:0:32:0:1:0:60:2:1:0:4 1/1:2:2:1,1:0,0:1:0,2:7:0:32.5:1:1:0:53.5:4:1:0:3 -GL000225.1 64325 . AG A 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTCCCTGGCTCACGAA;RSEQ=CCCCCTGTGGTAGAGCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:32:0:1:0:53.5:4:1:0:3 -GL000225.1 64402 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCCACGCGCCGTTGTGGG;RSEQ=GAAGGCGACCCATGAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:6:0:30.5:1:1:1:31:4:0.5:0:5 -GL000225.1 64415 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTGGGCGAAGGCGACCCA;RSEQ=GAGGGAGCAGGGTGACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:19:0:31:1:1:1:31:4:0.5:0:5 -GL000225.1 64434 . AA CC 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATGAGGGAGCAGGGTGACAC;RSEQ=GCCGGGGGCTGTGTTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:19:0:31.5:1:1:0:40:4:1:0:1 1/1:2:2:1,1:0,0:1:0,2:24:0:29.8:1:1:0:31:4:1:0:4 -GL000225.1 64435 . A C 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGGAGCAGGGTGACACA;RSEQ=GCCGGGGGCTGTGTTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:20:0:30.5:1:1:0:40:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64496 . G A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGCCAGCCTGTCCCGG;RSEQ=TGCCTGGCCCTGAGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:31:1:1:0:60:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64520 . AG CC 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCCTGAGATTCTGAAA;RSEQ=ATTTCTGAATTCTGGACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:30.5:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64532 . T C 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGAAAAGATTTCTGAAT;RSEQ=CTGGACTCCGGGAAGCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:29.5:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64649 . CT TC 26 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGGGATCCAGTGACGGCGGT;RSEQ=GCTTTCGCCTGCCTTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7.5:1:26.6:1:1:0:45:4:1:0.5:5.5 0/0:2:0:0,0:1,1:0:2,0:24:0:32:1:1:0:60:4:1:0:8 -GL000225.1 64650 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATCCAGTGACGGCGGTC;RSEQ=GCTTTCGCCTGCCTTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25:0:31:1:1:0:60:4:1:0:8 -GL000225.1 64653 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATCCAGTGACGGCGGTCTGC;RSEQ=TTCGCCTGCCTTCTTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:8.5:1:31:0:1:0:45:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:28:0:32:0:1:0:60:4:1:0:8 -GL000225.1 64656 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAGTGACGGCGGTCTGCTTT;RSEQ=GCCTGCCTTCTTGCGGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:11.5:1:28.5:1:1:0:45:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:31:0:31.5:1:1:0:60:4:1:0:8 -GL000225.1 64662 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGGCGGTCTGCTTTCGCCTG;RSEQ=CTTCTTGCGGGCCGCGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:17.5:1:31.5:1:1:0:45:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:31:0:31:1:1:0:60:4:1:0:8 -GL000225.1 64676 . G T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CGCCTGCCTTCTTGCGGGCC;RSEQ=CGTCTCCCGGGCCAGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:30.5:1:1:0:45:4:1:0:5.5 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64682 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCTTCTTGCGGGCCGCGTCT;RSEQ=CCGGGCCAGGGCCCAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:37.5:1:32.5:1:1:0:45:4:1:0:5.5 1/1:2:2:1,1:0,0:1:0,2:11:0:31.5:1:1:0:60:4:1:0:7 -GL000225.1 64695 . CC TG 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCGTCTCCCGGGCCAGGGC;RSEQ=AGATTCCCGCCATTGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:1:31.3:1:1:0:45:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64709 . T G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCCAGATTCCCGCCA;RSEQ=TGCTGCCTCATCTTGCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34.5:1:31.5:1:1:0:45:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64720 . T G 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCGCCATTGCTGCCTCA;RSEQ=CTTGCGTGACCTCTCATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30:1:1:0:45:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64899 . A G 51 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCCGTCCCCGTCCCCGG;RSEQ=CTTCCGCGGGGAGGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:11.7:1:32.7:1:1:0:39:6:1:0:6.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64924 . A G 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCGGGGAGGGTGCTGTCCG;RSEQ=AGGTGTCGGGAGGGCCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:27:1:33:0:1:1:49.5:4:0.3333:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64926 . G A 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGGAGGGTGCTGTCCGAA;RSEQ=GTGTCGGGAGGGCCATCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:29:1:32:1:1:1:49.5:4:0.3333:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64927 . G T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGAGGGTGCTGTCCGAAG;RSEQ=TGTCGGGAGGGCCATCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:29.5:1:30.5:1:1:1:34.5:4:0.3333:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64929 . G A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAGGGTGCTGTCCGAAGGT;RSEQ=TCGGGAGGGCCATCGCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:32:1:31:1:1:1:49.5:4:0.3333:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64932 . G A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGCTGTCCGAAGGTGTC;RSEQ=GGAGGGCCATCGCGGGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:35:1:31.5:1:1:1:49.5:4:0.3333:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64946 . G C 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTCGGGAGGGCCATCGC;RSEQ=GGGAGCCCTGGGCAGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:33:1:30:1:1:1:34.5:4:0.3333:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 64955 . T C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCCATCGCGGGGAGCCC;RSEQ=GGGCAGAATTTCACGGACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:37:1:30.5:1:1:1.73:49.5:4:0.4:0:7.5 0/0:1:0:0,0:0,1:0:0,0:3:0:27:0:1:0:40:2:1:0:6 -GL000225.1 64958 . G C 61 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCATCGCGGGGAGCCCTGG;RSEQ=CAGAATTTCACGGACGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:33.3:1:30.8:1:1:0:42:8:0.8:0:6.8 1/1:1:1:0,1:0,0:1:0,0:6:0:26:0:1:0:40:2:1:0:6 -GL000225.1 64964 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGGGAGCCCTGGGCAGAA;RSEQ=TTCACGGACGGACATGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:26.5:1:29:1:1:1.41418:34.5:4:0.2857:0:6 0/0:2:0:0,0:1,0:0:0,0:4:0:32:0:1:0:40:2:0.5:0:6 -GL000225.1 64973 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGCAGAATTTCACGGA;RSEQ=GGACATGGGCAGAGAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:19:1:29:1:1:1.41418:49.5:4:0.2857:0:7.5 0/0:3:0:0,0:2,1:0:2,0:14.3:1:29.7:1:1:0:37:6:1:0:6.3 -GL000225.1 64979 . T C 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.6871;LSEQ=CAGAATTTCACGGACGGACA;RSEQ=GGGCAGAGAGAGGCCGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:3,2:0.3333:2,2:15:1:30.3:1:1:2.60168:60:6:0.3333:0:2 0/1:4:1:1,0:1,1:0.25:2,0:3:0:30:0:1:0:60:2:0.25:0:2 -GL000225.1 64997 . T C 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=CATGGGCAGAGAGAGGCCGG;RSEQ=GGGCTCCCGTGCACCTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1:0,2:20.3:1:30.3:1:1:0:45.1:14:1:0:4.1 1/1:6:5:3,2:0,0:0.8333:0,2:18.4:1:31:1:1:0:44.4:10:1:0:4.4 -GL000225.1 65016 . AA GC 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GTGGGCTCCCGTGCACCTCA;RSEQ=CGGCCTGTGCACTGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,1:0:2,0:44:1:30.5:1:1:0:60:4:0.6667:0:2 0/1:6:2:2,0:1,1:0.3333:2,0:13:1:32.9:1:1:0:45.5:4:0.4:0.1667:6.5 -GL000225.1 65019 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GGCTCCCGTGCACCTCAAAC;RSEQ=GCCTGTGCACTGCAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,2:0:2,0:22.8:1:31.2:1:1:0:50.5:12:1:0:3.8 0/1:8:2:2,0:5,1:0.25:2,0:14:1:28.5:1:1:0:49:4:0.25:0:6 -GL000225.1 65026 . G T 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09317;SOR=Inf;LSEQ=GTGCACCTCAAACGGCCTGT;RSEQ=CACTGCAGCAGGTGCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,4:0:2,0:16:1:32.6:1:1:0:46:22:1:0:4.8 0/1:11:3:2,1:6,2:0.2727:2,2:17:1:28.3:1:1:1.44322:43:6:0.2727:0:6 -GL000225.1 65033 . A G 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1;LSEQ=TCAAACGGCCTGTGCACTGC;RSEQ=GCAGGTGCAGCCAGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:3,1:6,3:0.2857:2,2:8.8:1:30.3:1:1:1.46:47.3:8:0.3077:0:6 0/1:14:4:3,1:5,4:0.2857:2,2:11.3:1:32:0:1:2.25:46.5:8:0.2857:0:5.8 -GL000225.1 65038 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.48506;SOR=0;LSEQ=CGGCCTGTGCACTGCAGCAG;RSEQ=TGCAGCCAGGAGGCCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,4:0.125:2,2:13.5:1:33:0:1:2.12136:53.5:4:0.125:0:7.5 0/0:14:0:0,0:8,4:0:2,0:21.1:1:30.6:1:1:0:41.3:24:0.8571:0:5.4 -GL000225.1 65045 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=TGCACTGCAGCAGGTGCAGC;RSEQ=AGGAGGCCTGCCCGGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:0.125:2,2:20.5:1:31:1:1:1.73197:53.5:4:0.125:0:7.5 0/0:15:0:0,0:9,6:0:2,0:21.8:1:31.1:1:1:0:44:30:1:0:5.4 -GL000225.1 65057 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GGTGCAGCCAGGAGGCCTGC;RSEQ=CGGACAGCCAGCCAGCGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,6:0.0952:2,2:32.5:1:30.5:1:1:1.92731:53.5:4:0.0952:0:7.5 0/0:15:0:0,0:8,7:0:2,0:26.8:1:30.5:1:1:0:44.3:30:1:0:5.3 -GL000225.1 65058 . C T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69403;SOR=1.52644;LSEQ=GTGCAGCCAGGAGGCCTGCC;RSEQ=GGACAGCCAGCCAGCGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:2,2:10,5:0.1905:2,2:25:1:32:0:0.60268:1.92451:34:8:0.1905:0:5.5 0/1:15:4:3,1:5,6:0.2667:2,2:38.5:1:31.8:1:0.56923:3.31:51.8:8:0.2667:0:6 -GL000225.1 65062 . C G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=AGCCAGGAGGCCTGCCCGGA;RSEQ=AGCCAGCCAGCGGCTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,7:0.1:2,2:14.5:1:33.5:1:1:1.26772:41:4:0.1:0:7.5 0/0:16:0:0,0:7,5:0:2,0:25.6:1:30.4:1:1:0:45:24:0.75:0:5 -GL000225.1 65065 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49198;SOR=0;LSEQ=CAGGAGGCCTGCCCGGACAG;RSEQ=CAGCCAGCGGCTCTTATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,6:0.1053:2,2:17.5:1:31.5:1:1:1.61828:41:4:0.1111:0:7.5 0/0:15:0:0,0:7,8:0:2,0:30.8:1:30.7:1:1:0:43.7:30:1:0:5.4 -GL000225.1 65069 . CC TG 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4958;SOR=0;LSEQ=AGGCCTGCCCGGACAGCCAG;RSEQ=AGCGGCTCTTATAAAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,6:0.1:2,2:22.5:1:32.8:1:1:1.61828:41:4:0.1053:0:6.5 0/0:15:0:0,0:7,8:0:2,0:32.4:1:30.8:1:1:0:43.7:30:1:0:5.4 -GL000225.1 65072 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.18018;SOR=Inf;LSEQ=CCTGCCCGGACAGCCAGCCA;RSEQ=CGGCTCTTATAAAGGCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:30.8:1:31.5:1:1:0:42.9:20:1:0:4.9 0/1:16:2:1,1:6,8:0.125:2,2:47.5:1:29.5:1:1:1.31:59:4:0.125:0:6.5 -GL000225.1 65073 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.37231;LSEQ=CTGCCCGGACAGCCAGCCAG;RSEQ=GGCTCTTATAAAGGCCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:10,8:0.1429:2,2:39.3:1:31:1:1:1.57:38.3:6:0.1429:0:5.3 0/1:16:3:0,3:7,6:0.1875:2,0:32.7:1:29.7:1:0.2125:0:50:6:0.1875:0:5 -GL000225.1 65074 . G A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07207;SOR=Inf;LSEQ=TGCCCGGACAGCCAGCCAGC;RSEQ=GCTCTTATAAAGGCCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:30.9:1:29:1:1:0:42.9:9.5:1:0:4.9 0/1:16:3:1,2:6,6:0.1875:2,2:35.3:1:30:1:1:1.91151:29.7:6:0.1875:0:7 -GL000225.1 65078 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50925;SOR=0;LSEQ=CGGACAGCCAGCCAGCGGCT;RSEQ=TTATAAAGGCCCACAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:12,9:0.087:2,2:44:1:30:1:1:1.31655:53.5:4:0.087:0:7.5 0/0:15:0:0,0:7,8:0:2,0:33.3:1:31.3:1:1:0:42.7:30:1:0:5.5 -GL000225.1 65080 . T C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49872;SOR=0;LSEQ=GACAGCCAGCCAGCGGCTCT;RSEQ=ATAAAGGCCCACAGGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:12,9:0.087:2,2:20.5:1:32.5:1:1:1.31655:39:4:0.087:0:7.5 0/0:17:0:0,0:8,9:0:2,0:29.4:1:28.9:1:1:0:43:34:1:0:5.4 -GL000225.1 65081 . A C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49872;SOR=0;LSEQ=ACAGCCAGCCAGCGGCTCTT;RSEQ=TAAAGGCCCACAGGCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:11,10:0.087:2,0:24.5:1:29.5:1:0.48617:0:52.5:4:0.087:0:4.5 0/0:17:0:0,0:7,8:0:2,0:30.3:1:29.1:1:1:0:40.7:30:0.8824:0:5.5 -GL000225.1 65083 . A G 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17436;SOR=Inf;LSEQ=AGCCAGCCAGCGGCTCTTAT;RSEQ=AAGGCCCACAGGCAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:0:2,0:28.9:1:28.8:1:1:0:43.4:46:1:0:5.2 0/1:17:2:1,1:7,8:0.1176:2,2:39:1:30.5:1:1:1.13:59:4:0.1176:0:6.5 -GL000225.1 65085 . A G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.49512;SOR=0;LSEQ=CCAGCCAGCGGCTCTTATAA;RSEQ=GGCCCACAGGCAGGCAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:12,9:0.087:2,2:25.5:1:33:0:1:1.31655:39:4:0.087:0:7.5 0/0:18:0:0,0:8,10:0:2,0:26.6:1:30.4:1:1:0:42.7:36:1:0:5.4 -GL000225.1 65087 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1777;SOR=Inf;LSEQ=AGCCAGCGGCTCTTATAAAG;RSEQ=CCCACAGGCAGGCAGGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:27.2:1:31.6:1:1:0:44.1:48:1:0:5.2 0/1:18:2:1,1:7,8:0.1111:2,2:21.5:1:28.5:1:1:1.13:60:4:0.1111:0:5 -GL000225.1 65089 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18659;SOR=Inf;LSEQ=CCAGCGGCTCTTATAAAGGC;RSEQ=CACAGGCAGGCAGGCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:0:2,0:28.2:1:30.6:1:1:0:44.9:22:1:0:5.2 0/1:18:2:1,1:7,9:0.1111:2,2:33:1:29:1:1:1.27:59:4:0.1111:0:6.5 -GL000225.1 65090 . CA AG 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17436;SOR=Inf;LSEQ=CAGCGGCTCTTATAAAGGCC;RSEQ=CAGGCAGGCAGGCTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:0:2,0:28.2:1:31.2:1:1:0:44.9:46:1:0:5.2 0/1:17:2:0,2:7,8:0.1176:2,0:39:0:31.5:1:0.48529:0:29:4:0.1176:0:6.5 -GL000225.1 65091 . A G 102 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00203;SOR=0;LSEQ=AGCGGCTCTTATAAAGGCCC;RSEQ=CAGGCAGGCAGGCTCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:6,4:4,5:0.4348:2,2:26:1:30.8:1:0.65628:1.81:42.4:20:0.4348:0:4 0/0:17:0:0,0:7,8:0:2,0:25.2:1:29.7:1:1:0:45.3:30:1:0:5.1 -GL000225.1 65093 . A G 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16585;SOR=Inf;LSEQ=CGGCTCTTATAAAGGCCCAC;RSEQ=GGCAGGCAGGCTCCACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:0:2,0:27:1:30.6:1:1:0:44:48:1:0:5.1 0/1:17:2:0,2:7,8:0.1176:2,0:37:0:30.5:1:0.48529:0:29:4:0.1176:0:6.5 -GL000225.1 65095 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.16585;SOR=Inf;LSEQ=GCTCTTATAAAGGCCCACAG;RSEQ=CAGGCAGGCTCCACCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:0:2,0:27:1:31.2:1:1:0:44:48:1:0:5.1 0/1:17:2:0,2:7,8:0.1176:2,0:35:0:31:0:0.48529:0:29:4:0.1176:0:6.5 -GL000225.1 65096 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49502;SOR=0;LSEQ=CTCTTATAAAGGCCCACAGG;RSEQ=AGGCAGGCTCCACCACTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:12,9:0.0833:2,2:21:0:31.5:1:1:1.31655:60:4:0.0833:0:5.5 0/0:19:0:0,0:8,11:0:2,0:23.3:1:31.7:1:1:0:41.7:38:1:0:4.9 -GL000225.1 65102 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.49024;SOR=0;LSEQ=TAAAGGCCCACAGGCAGGCA;RSEQ=GCTCCACCACTTCATGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,8:0.0909:2,2:36:1:31:1:1:1.23603:39:4:0.0909:0:7.5 0/0:19:0:0,0:8,9:0:2,0:21.9:1:30.7:1:1:0:41.9:34:0.8947:0:4.6 -GL000225.1 65103 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.20854;SOR=Inf;LSEQ=AAAGGCCCACAGGCAGGCAG;RSEQ=CTCCACCACTTCATGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:27.2:1:31.7:1:1:0:42.5:44:1:0:5 0/1:19:2:1,1:7,10:0.1053:2,2:22.5:1:28.5:1:1:1.40:37:4:0.1053:0:6.5 -GL000225.1 65104 . C T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1718;LSEQ=AAGGCCCACAGGCAGGCAGG;RSEQ=TCCACCACTTCATGAATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:36:1:30.5:1:1:1.21106:39:4:0.0909:0:7.5 0/1:19:2:1,1:7,10:0.1053:2,2:26:0:32:0:1:1.40:45:4:0.1053:0:4.5 -GL000225.1 65106 . CCAC GCA 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49024;SOR=0;LSEQ=GGCCCACAGGCAGGCAGGCT;RSEQ=CACTTCATGAATGGCGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:40.5:1:31.3:1:1:1.21106:41:4:0.0909:0:6.5 0/0:19:0:0,0:8,11:0:2,0:22.5:1:30.7:1:1:0:41.7:38:1:0:4.9 -GL000225.1 65109 . C T 44 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22973;SOR=Inf;LSEQ=CCACAGGCAGGCAGGCTCCA;RSEQ=CACTTCATGAATGGCGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:24.8:1:31.2:1:1:0:43.7:38:1:0:5.1 0/1:19:3:1,2:7,9:0.1579:2,2:22:1:28.3:1:1:1.52085:33.7:6:0.1579:0:6.7 -GL000225.1 65110 . CA AC 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21923;SOR=Inf;LSEQ=CACAGGCAGGCAGGCTCCAC;RSEQ=CTTCATGAATGGCGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:26:1:30.3:1:1:0:43.4:20:1:0:5.3 0/1:19:2:1,1:7,10:0.1053:2,2:23.5:1:32:1:1:1.40:45:4:0.1053:0:3.5 -GL000225.1 65111 . A C 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.17688;LSEQ=ACAGGCAGGCAGGCTCCACC;RSEQ=CTTCATGAATGGCGGTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:5,3:7,6:0.381:2,2:16.4:1:28.4:1:1:1.40:38.5:16:0.381:0:5.4 0/1:19:8:1,7:5,2:0.4211:2,2:24.6:1:31.5:1:0.04056:13.59412:38:16:0.4706:0:6.1 -GL000225.1 65124 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=CTCCACCACTTCATGAATGG;RSEQ=GGTGAGCCCTGGGACAGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,7:0.125:2,2:33.5:1:29:1:1:1.15:39:4:0.125:0:7.5 0/0:16:0:0,0:4,12:0:2,0:18.2:1:30.4:1:1:0:39.9:32:1:0:4.5 -GL000225.1 65125 . G A 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07433;LSEQ=TCCACCACTTCATGAATGGC;RSEQ=GTGAGCCCTGGGACAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:42.5:1:31.5:1:1:1:60:4:0.125:0:5.5 0/1:15:2:1,1:3,10:0.1333:2,2:23:1:29:1:0.47619:3.03:28:4:0.1333:0:1.5 -GL000225.1 65127 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2092;SOR=Inf;LSEQ=CACCACTTCATGAATGGCGG;RSEQ=GAGCCCTGGGACAGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:24.4:1:29.5:1:1:0:44.4:32:1:0:5.3 0/1:14:2:1,1:3,9:0.1429:2,2:7.5:1:30.5:1:0.50549:2.74:45:4:0.1429:0:3.5 -GL000225.1 65132 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=CTTCATGAATGGCGGTGAGC;RSEQ=CTGGGACAGCCTGCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:0.1667:2,2:35.5:1:30.5:1:1:1:60:4:0.1667:0:5.5 0/0:11:0:0,0:3,8:0:2,0:20.5:1:30.7:1:1:0:38.7:22:1:0:3.5 -GL000225.1 65144 . T C 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18903;LSEQ=CGGTGAGCCCTGGGACAGCC;RSEQ=GCCCCACCCCGGAAGGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:3,2:2,4:0.3846:2,2:16.2:1:30.4:1:0.5671:2.70:44:10:0.3846:0:7 0/1:7:3:0,3:0,2:0.4286:0,0:13.3:1:32:0:1:0:34.7:6:0.4286:0:6.3 -GL000225.1 65152 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCTGGGACAGCCTGCCCCAC;RSEQ=CCGGAAGGGTCCCAGGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,3:0.25:2,2:14:0:32.5:1:1:1.41:52:4:0.25:0:3 0/0:7:0:0,0:1,5:0:2,0:15.3:1:31.8:1:1:0:42.5:12:0.8571:0:3.8 -GL000225.1 65235 . A C 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TGGTGATGGTGGTGGTGGGG;RSEQ=CAGAGGCACGAACAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:18.5:1:33.5:1:1:0:32.5:4:0.6667:0:2 0/0:2:0:0,0:1,1:0:2,0:23.5:1:30.5:1:1:0:60:4:1:0:1.5 -GL000225.1 65248 . C A 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTGGGGACAGAGGCACGAA;RSEQ=AGGAAGGGGGCGAGGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0.5:0,0:29:0:31:0:1:0:60:2:0.5:0:4 1/1:2:2:1,1:0,0:1:0,2:10.5:1:30:1:1:0:60:4:1:0:1.5 -GL000225.1 65363 . A T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGGGCTCCCACGCATCT;RSEQ=CAGCAGGGAGAAACCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:0:32:0:1:0:31:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 65376 . A G 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCATCTACAGCAGGGAGAA;RSEQ=CCGGCCTGGGAGGGTGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:34:0:1:0:31:4:1:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 65485 . T C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGTGGGTGTTGCTGTTG;RSEQ=CTGGAAAGTCTCACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:31:1:1:0:60:4:1:0:3.5 -GL000225.1 65510 . C G 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTCTCACACACACAGGC;RSEQ=TGTGGCTCTCGTTCGTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:3:0:27:0:1:0:40:2:1:0:7 1/1:2:2:1,1:0,0:1:0,2:34:1:29.5:1:1:0:60:4:1:0:3.5 -GL000225.1 65522 . T C 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACAGGCCTGTGGCTCTCG;RSEQ=TCGTTTCCACGTAGGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:15:0:31:0:1:0:40:2:1:0:7 1/0:3:2:1,1:1,0:0.6667:0,2:34:1:31.5:1:1:0:60:4:0.6667:0:3.5 -GL000225.1 65570 . C T 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCCAGAGAGAAGATGCC;RSEQ=CCCCGGCGTGATGGTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:25:1:30.5:1:1:0:33.5:4:1:0:5 1/1:5:4:3,1:0,1:0.8:0,2:23.8:1:30.5:1:0.4:0:50.5:8:0.8:0:5.8 -GL000225.1 65585 . T C 72 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=ATGCCCCCCCGGCGTGATGG;RSEQ=CTGACGATGGATTCCCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,0:0:0,0:25:1:29:1:1:0:33.5:4:0.6667:0:5 1/0:7:5:3,2:1,1:0.7143:2,2:20.4:1:31.2:1:1:1.41:44.8:10:0.7143:0:5.6 -GL000225.1 65590 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.53983;LSEQ=CCCCCGGCGTGATGGTCTGA;RSEQ=GATGGATTCCCGTTTGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:3,1:0.2:2,0:18:0:27:0:1:0:40:2:0.2:0:7 0/1:7:2:1,1:3,2:0.2857:2,2:25.5:1:30.5:1:1:1.41418:22:4:0.2857:0:7 -GL000225.1 65591 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55808;SOR=0.30063;LSEQ=CCCCGGCGTGATGGTCTGAC;RSEQ=ATGGATTCCCGTTTGCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:0.6:0,2:13.7:1:30.3:1:1:0:25.7:6:0.6:0:2.3 0/1:7:2:1,1:3,2:0.2857:2,2:24.5:1:28.5:1:1:1.41418:60:4:0.2857:0:3.5 -GL000225.1 65594 . GG TT 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CGGCGTGATGGTCTGACGAT;RSEQ=ATTCCCGTTTGCGGCAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:13.1:1:30.9:1:1:0:36.1:14:1:0:4.9 0/1:8:2:1,1:3,3:0.25:2,2:35:1:28.5:1:1:1:60:4:0.25:0:5 -GL000225.1 65604 . T G 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31469;SOR=0.22353;LSEQ=GTCTGACGATGGATTCCCGT;RSEQ=TGCGGCAAAATGGGGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:2,1:0.625:2,2:20.2:1:33.2:1:1:1.28664:33.6:10:0.625:0:4.2 0/1:8:2:1,1:3,3:0.25:2,2:24.5:1:30:1:1:1:60:4:0.25:0:3.5 -GL000225.1 65613 . A C 66 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02564;SOR=0;LSEQ=TGGATTCCCGTTTGCGGCAA;RSEQ=ATGGGGAGTCTGCAGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:2,1:0.5714:2,2:25.5:1:33.3:1:1:1.81007:45.8:8:0.5714:0:6.3 0/0:8:0:0,0:3,3:0:2,0:33.2:1:30.5:1:1:0:60:12:0.75:0:3.3 -GL000225.1 65615 . T C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18947;SOR=Inf;LSEQ=GATTCCCGTTTGCGGCAAAA;RSEQ=GGGGAGTCTGCAGTGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:0:2,0:19.6:1:31.4:1:1:0:39.6:22:1:0:4.3 0/1:9:2:1,1:4,3:0.2222:2,2:45.5:1:31:1:1:1.29098:60:4:0.2222:0:5 -GL000225.1 65627 . A C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=CGGCAAAATGGGGAGTCTGC;RSEQ=GTGTGGCCGGTTTGGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:0:2,0:23.9:1:30.7:1:1:0:42.8:26:1:0:4.3 0/1:8:2:1,1:3,3:0.25:2,2:41:1:30.5:1:1:1:60:4:0.25:0:1.5 -GL000225.1 65628 . G A 64 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13116;SOR=0;LSEQ=GGCAAAATGGGGAGTCTGCA;RSEQ=TGTGGCCGGTTTGGAAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:5,4:0.3077:2,2:24.3:1:32.3:1:1:1.22862:46.8:8:0.3077:0:4.8 0/0:8:0:0,0:4,4:0:2,0:33.6:1:31.5:1:1:0:47.1:16:1:0:4.1 -GL000225.1 65648 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51567;SOR=0;LSEQ=GTGTGGCCGGTTTGGAAACT;RSEQ=GCAAGGAGAGCGAAGGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:17.5:1:29:1:1:1.13389:33:4:0.1176:0:5 0/0:10:0:0,0:4,6:0:2,0:22.8:1:31:1:1:0:48.9:20:1:0:5.1 -GL000225.1 65650 . C A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=GTGGCCGGTTTGGAAACTGG;RSEQ=AAGGAGAGCGAAGGCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:0:2,0:27.6:1:32.2:1:1:0:42.1:34:1:0:4.1 0/1:10:2:1,1:3,5:0.2:2,2:11:1:31:1:1:1.58:60:4:0.2:0:5 -GL000225.1 65656 . G C 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52923;SOR=0;LSEQ=GGTTTGGAAACTGGCAAGGA;RSEQ=AGCGAAGGCACCATACCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:7,7:0.1765:2,2:40:1:31.7:1:1:1.92:43.7:6:0.1765:0:7.3 0/0:9:0:0,0:3,6:0:2,0:23.6:1:31.2:1:1:0:47.7:18:1:0:5.1 -GL000225.1 65659 . C T 59 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26008;SOR=0;LSEQ=TTGGAAACTGGCAAGGAGAG;RSEQ=GAAGGCACCATACCGGTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:2,2:6,6:0.25:2,2:34.5:1:29.5:1:1:1:52.8:8:0.25:0:5.8 0/0:9:0:0,0:3,6:0:2,0:23.2:1:30.2:1:1:0:47.7:18:1:0:5.1 -GL000225.1 65663 . G A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12;SOR=Inf;LSEQ=AAACTGGCAAGGAGAGCGAA;RSEQ=GCACCATACCGGTCTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:29.1:1:31.8:1:1:0:43.1:32:1:0:4.1 0/1:9:2:1,1:2,5:0.2222:2,2:23.5:1:30.5:1:1:2.24:44:4:0.2222:0:8 -GL000225.1 65668 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52569;SOR=0;LSEQ=GGCAAGGAGAGCGAAGGCAC;RSEQ=ATACCGGTCTTCCACCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:26.5:1:29:1:1:1.15:45.5:4:0.1333:0:7 0/0:8:0:0,0:3,5:0:2,0:23.9:1:30.4:1:1:0:46.1:16:1:0:5.1 -GL000225.1 65669 . ATA CCG 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11067;SOR=Inf;LSEQ=GCAAGGAGAGCGAAGGCACC;RSEQ=CCGGTCTTCCACCCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:0:2,0:28.1:1:30.6:1:1:0:43.7:30:1:0:4.1 0/1:8:2:1,1:2,4:0.25:2,2:31.5:1:30.8:1:1:1.83:44:4:0.25:0:6 -GL000225.1 65671 . A G 103 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2031;SOR=0.28554;LSEQ=AAGGAGAGCGAAGGCACCAT;RSEQ=CCGGTCTTCCACCCTTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:5,4:1,2:0.6923:2,2:34.6:1:32.7:1:1:2.32:46.2:18:0.6923:0:3.9 0/1:8:3:1,2:1,1:0.375:2,2:18.7:1:32.7:1:1:1.7321:38.3:6:0.5:0:4.7 -GL000225.1 65684 . C A 43 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51703;SOR=0;LSEQ=GCACCATACCGGTCTTCCAC;RSEQ=CTTCCCTGCATGTTTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:4,6:0.2308:2,2:17:1:27.7:1:0.55944:2.75:43.7:6:0.2308:0:7.3 0/0:6:0:0,0:2,4:0:2,0:26.7:1:31.3:1:1:0:41.5:12:1:0:5 -GL000225.1 65685 . C A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06536;SOR=Inf;LSEQ=CACCATACCGGTCTTCCACC;RSEQ=TTCCCTGCATGTTTCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:19.5:1:31.5:1:1:0:46.5:26:1:0:4.2 0/1:5:2:1,1:1,2:0.4:2,2:38:0:31.5:1:1:1.73:44:4:0.4:0:6 -GL000225.1 65702 . A C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=ACCCTTCCCTGCATGTTTCC;RSEQ=GGTGCCCGCAGAGCTCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,0:0.4:0,2:18:0:32.5:1:1:0:60:4:0.4:0:4.5 1/0:4:2:1,1:0,0:0.5:0,2:21:0:32:0:1:0:44:4:0.5:0:6 -GL000225.1 65709 . C G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CCTGCATGTTTCCAGGTGCC;RSEQ=GCAGAGCTCCGGGAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:12:1:32:1:1:0:46.5:8:0.8:0:4.8 1/0:4:2:1,1:1,1:0.5:2,2:14:0:32:0:1:1:44:4:0.5:0:6 -GL000225.1 65711 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TGCATGTTTCCAGGTGCCCG;RSEQ=AGAGCTCCGGGAGCAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:11:0:30.5:1:1:1.7321:33:4:0.4:0:5 0/0:4:0:0,0:2,2:0:2,0:10.3:1:33.3:1:1:0:41.8:8:1:0:5.8 -GL000225.1 65719 . C T 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=TCCAGGTGCCCGCAGAGCTC;RSEQ=GGGAGCAACATTCAGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:1:0:32:1:1:1.73:60:4:0.4:0:4.5 1/1:3:3:1,2:0,0:1:0,2:5.3:1:32.3:1:1:0:44.7:6:1:0:6 -GL000225.1 66219 . A G 33 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=CTGCAGGGGCATTGTGAAAT;RSEQ=TCTCTGCACTGATCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:1:33.5:1:1:0:47.5:4:1:0:5 0/0:1:0:0,0:1,0:0:0,0:27:0:30:0:1:0:24:2:1:0:2 -GL000225.1 66244 . T A 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TGCACTGATCACCCAGGTGA;RSEQ=GGGACTCTTCTCTAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:30:1:32:1:1:0:40.3:6:1:0:4.7 0/0:2:0:0,0:2,0:0:0,0:29.5:1:30:1:1:0:30.5:4:1:0:1.5 -GL000225.1 66255 . T A 49 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1;SOR=0;LSEQ=CCCAGGTGATGGGACTCTTC;RSEQ=CTAGGCTCTGCCTACTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:41:1:31:1:1:0:40.3:6:1:0:4.7 0/0:2:0:0,0:2,0:0:0,0:29.5:1:30.5:1:1:0:30.5:4:1:0:1.5 -GL000225.1 66278 . A T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=AGGCTCTGCCTACTGGGGGC;RSEQ=TTGTCACATATTTCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:37:1:29.7:1:1:0:40.3:6:1:0:4.7 0/1:5:2:1,1:2,1:0.4:2,2:18.5:1:29:1:1:1.7321:24:4:0.4:0:4 -GL000225.1 66289 . T A 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=ACTGGGGGCATTGTCACATA;RSEQ=TTCTGCACTGATCACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:26:1:29:1:1:0:40.3:6:1:0:4.7 1/1:5:4:2,2:1,0:0.8:0,2:17.8:1:30.3:1:1:0:33.5:8:0.8:0:4.3 -GL000225.1 66297 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CATTGTCACATATTTCTGCA;RSEQ=TGATCACCCAGGTGATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:18:1:29.7:1:1:0:40.3:6:1:0:4.7 1/0:4:2:1,1:1,1:0.5:2,2:25:0:31.5:1:1:1:43:4:0.5:0:4.5 -GL000225.1 66304 . CC AA 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=ACATATTTCTGCACTGATCA;RSEQ=CAGGTGATGGACTCTTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:10:1:27.5:1:1:0:40.3:6:1:0:3.7 0/0:4:0:0,0:2,2:0:2,0:35.8:1:32.8:1:1:0:36.8:8:1:0:4 -GL000225.1 66313 . T C 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGCACTGATCACCCAGGTGA;RSEQ=GGACTCTTGTCTTGGATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:8:0:26:0:1:0:26:2:1:0:3 1/0:4:3:1,2:1,0:0.75:0,2:42:1:31:1:1:0:36.7:6:0.75:0:5 -GL000225.1 66333 . G T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCTTGTCTTGGATTT;RSEQ=CCTATGGGGGCATTGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:35.5:1:29:1:1:1:43:4:0.5:0:4.5 -GL000225.1 72073 . A T 61 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCGTTTCTAGGAAATTT;RSEQ=GCGCCTGCTGCAGAAACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:15.3:1:30.5:1:1:0:60:8:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72075 . C A 48 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTTTCTAGGAAATTTAG;RSEQ=GCCTGCTGCAGAAACTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:19.7:1:30.7:1:1:0:60:6:0.75:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72104 . A G 66 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAAACTCCAGGCTCGCCA;RSEQ=GAGCTCATCCAGCAGCAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:35.5:1:33.3:1:1:0:60:8:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72110 . C T 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAGGCTCGCCAAGAGCT;RSEQ=ATCCAGCAGCAAGCCGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:32.3:1:31.3:1:1:1.73:60:6:0.6:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72141 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCGGAGGGAAGTGCAGA;RSEQ=GAGCGCCCCAGCTCCTGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:30:1:29.5:1:1:0:60:4:0.6667:0:4 0/0:1:0:0,0:1,0:0:0,0:11:0:33:0:1:0:60:2:1:0:2 -GL000225.1 72151 . A G 58 d7;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTGCAGACGAGCGCCCC;RSEQ=GCTCCTGTAGCGCCTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:21:1:29:1:1:0:60:8:1:0:3.8 1/1:1:1:1,0:0,0:1:0,0:21:0:32:0:1:0:60:2:1:0:2 -GL000225.1 72315 . C G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCGCACCACGGACTCCA;RSEQ=TGGGACGTGGGTGGTGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:31:1:1:0:60:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72323 . T C 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGGACTCCACTGGGACG;RSEQ=GGGTGGTGCAAGCACACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:25.3:1:31:1:1:0:60:6:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72330 . T C 50 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCCACTGGGACGTGGGTGG;RSEQ=GCAAGCACACCTTGACCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:27.7:1:31.7:1:1:0:60:6:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72365 . C T 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTGTGGCCCCGCTTGAA;RSEQ=GGGACCAGGCTGTTCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:25:1:31:1:1:0:60:6:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72384 . C T 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACGGGACCAGGCTGTTCCTC;RSEQ=GCGCAGGGCCCGGCAGGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:32:1:1:0:60:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72417 . C T 27 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGCCGTCGTGCTGTGGG;RSEQ=CCCGATCCTCCCGGCTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:27.5:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72582 . A G 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTGCTGGGCTGGAGCAC;RSEQ=GGGACCGCCCTCGCTCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14.5:1:29:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72638 . CG TA 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CTGTGGGAGAGCACCAGGTG;RSEQ=CAGGGCACATGGGTTGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:45:0:30:1:1:0:60:4:0.6667:0:4.5 0/0:2:0:0,0:1,1:0:2,0:5.5:1:27.5:1:1:0:55.5:4:1:0:7 -GL000225.1 72645 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=AGAGCACCAGGTGCGCAGGG;RSEQ=ACATGGGTTGCGGGAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:35.7:1:33.3:1:1:0:60:6:1:0:4 1/1:2:2:1,1:0,0:1:0,2:12.5:1:28:1:1:0:55.5:4:1:0:7 -GL000225.1 72657 . G A 49 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GCGCAGGGCACATGGGTTGC;RSEQ=GGAAGCCCCGTTCCCCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:23.7:1:31.3:1:1:0:60:6:1:0:4 0/0:2:0:0,0:1,1:0:2,0:24.5:1:27:1:1:0:55.5:4:1:0:7 -GL000225.1 72676 . GA AC 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CGGGAAGCCCCGTTCCCCAC;RSEQ=GCCAGTGTGGGCGAAGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:8.3:1:32:1:1:0:60:6:1:0:3 1/1:2:2:1,1:0,0:1:0,2:44.5:1:29.8:1:1:0:55.5:4:1:0:6 -GL000225.1 72677 . A C 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAAGCCCCGTTCCCCACG;RSEQ=GCCAGTGTGGGCGAAGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:7:0:32.5:1:1:0:60:4:0.6667:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 72700 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAGTGTGGGCGAAGGCGACC;RSEQ=ACGAGGGAGGAGGGTGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:24:1:32.5:1:1:0:48.5:4:1:0:4 1/1:2:2:1,1:0,0:1:0,2:25:0:31:0:1:0:55.5:4:1:0:6 -GL000225.1 72710 . G C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4;SOR=Inf;LSEQ=GAAGGCGACCCACGAGGGAG;RSEQ=AGGGTGACACCCGCCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:25:0:34:0:1:0:37:2:0.3333:0:8 1/1:2:2:1,1:0,0:1:0,2:15:0:32:0:1:0:55.5:4:1:0:6 -GL000225.1 72755 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.4;SOR=Inf;LSEQ=TTGCCCCGACTGCCTGCCTG;RSEQ=GCGGGCGCCCTGCCAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:30:1:31:1:1:0:60:4:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:10:0:31.5:1:1:0:49.5:4:0.6667:0:4.5 -GL000225.1 72777 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGCGCCCTGCCAGCCTGT;RSEQ=CCGGGTGCCTTGCCCTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:16.5:1:33:0:1:0:48.5:4:1:0:3.5 0/1:6:2:1,1:3,1:0.3333:2,2:20.5:1:29:1:1:2.44949:39:4:0.3333:0:1.5 -GL000225.1 72782 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCTGCCAGCCTGTCCCGG;RSEQ=TGCCTTGCCCTTCGATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:11.5:1:31:1:1:0:48.5:4:1:0:3.5 0/1:6:2:1,1:3,1:0.3333:2,2:17.5:1:29:1:1:2.44949:49.5:4:0.3333:0:4.5 -GL000225.1 72788 . TG GA 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGCCTGTCCCGGGTGCCT;RSEQ=CCCTTCGATTCTGAAGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:14:0:31:0:1:0:60:2:1:0:0 0/1:6:2:1,1:3,1:0.3333:2,2:10.5:1:29:1:1:2.44949:49.5:4:0.3333:0:3.5 -GL000225.1 72828 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATCTGAATCCTGGACTCC;RSEQ=GGGGGACCCTCCAGCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:31.5:1:29:1:1:0:60:4:1:0:2.5 -GL000225.1 72862 . C T 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGCCAGCTCTTCCCTGG;RSEQ=GGCAATGCCTGGAAAGCGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:9:1:27:1:1:0:60:4:0.6667:0:4.5 -GL000225.1 72962 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCTGCCTTCTTGTGGGCC;RSEQ=CGTCTCCCGGGCCAGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:31:1:1:0:60:4:1:0:5 -GL000225.1 72975 . C G 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=GTGGGCCCCGTCTCCCGGGC;RSEQ=AGGGCCAAGATTCCCGCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:0:30.5:1:1:0:60:4:1:0:5 -GL000225.1 72995 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCAAGATTCCCGCTG;RSEQ=TGCTGCCTCAGCTGGAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:0:31:1:1:0:60:4:1:0:5 -GL000225.1 72997 . G T 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGGCCAAGATTCCCGCTGTT;RSEQ=CTGCCTCAGCTGGAGTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:22:0:28:1:1:0:60:4:1:0:5 -GL000225.1 73011 . A C 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGTTGCTGCCTCAGCTGG;RSEQ=GTGACCTCTCATTCTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:28.5:1:1:0:60:4:1:0:5 -GL000225.1 73142 . C G 51 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GCTCCCAGGGCCTCGCTTTG;RSEQ=CTCGGGGTCCAAACGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:2:0:30:0:1:0:27:2:1:0:6 1/1:3:3:1,2:0,0:1:0,2:34.3:1:32.3:1:1:0:55.7:6:1:0:5 -GL000225.1 73146 . G A 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=CCAGGGCCTCGCTTTGCCTC;RSEQ=GGGTCCAAACGAGTCTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:24:0:33:0:1:0:60:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:37.3:1:31:1:1:0:55.7:6:1:0:5 -GL000225.1 73150 . T A 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GGCCTCGCTTTGCCTCGGGG;RSEQ=CCAAACGAGTCTCCTTCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:20:0:32:0:1:0:60:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:35.7:1:30.3:1:1:0:55.7:6:1:0:5 -GL000225.1 73156 . C T 48 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GCTTTGCCTCGGGGTCCAAA;RSEQ=GAGTCTCCTTCGCCATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:8.3:1:31:1:1:0:60:6:1:0:3.3 1/1:3:3:1,2:0,0:1:0,2:29.7:1:30.7:1:1:0:55.7:6:1:0:5 -GL000225.1 73182 . C A 32 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCCTTCGCCATCCCCGTCCC;RSEQ=GGGCTTCCGTGGGGAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:0:32:0:1:0:60:4:1:0:1.5 0/0:1:0:0,0:0,1:0:0,0:18:0:32:0:1:0:49:2:1:0:6 -GL000225.1 73259 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGGTCAGAATTTCACGGA;RSEQ=GGACACGGGCAGAGAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:0:31:0:1:0:60:4:1:0:5.5 -GL000225.1 73281 . GC AG 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACGGGCAGAGAGAAGCC;RSEQ=CGTGCTCCGTGCACCTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37.5:1:30.3:1:1:0:60:4:1:0:4.5 -GL000225.1 73291 . G A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGAAGCCGCCGTGCTCC;RSEQ=TGCACCTCAGCCGGCCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28.5:1:29.5:1:1:0:60:4:1:0:4.5 -GL000225.1 73314 . T C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCTCAGCCGGCCTGTGCA;RSEQ=TGCGGCAGGAGCAGCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:29:1:1:0:60:4:1:0:4.5 -GL000225.1 73534 . G C 27 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=TGGAGAGCCTAAGAGGAAGG;RSEQ=GGCGAGGGGGAAGGGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:27.5:1:1:0:46:4:1:0:4 0/0:4:0:0,0:1,3:0:2,0:6.3:1:26.5:1:1:0:36.5:8:1:0:5.3 -GL000225.1 73539 . AG A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGCCTAAGAGGAAGGGGGCG;RSEQ=GGGGAAGGGGTGAGGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:17.5:1:30.5:1:1:0:46:4:1:0:4 1/0:4:2:1,1:0,2:0.5:0,2:16.5:1:27.5:1:1:0:49:4:0.5:0:4.5 -GL000225.1 73553 . A AG 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGGGCGAGGGGGAAGGGGTG;RSEQ=GGGGGCGCGTTTCTGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:31.5:1:29:0:1:1:46:4:0.5:0:4 0/0:4:0:0,0:1,3:0:2,0:24.8:1:29:1:1:0:36.5:8:1:0:5.3 -GL000225.1 73557 . GG TGT 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.57576;SOR=0.437;LSEQ=CGAGGGGGAAGGGGTGAGGG;RSEQ=CGCGTTTCTGGGGCTGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:14:0:32.3:1:1:1:31:4:1:0:4 0/1:7:2:1,1:0,2:0.2857:0,2:5.6:1:31.3:1:1:0:29:4:0.1428:0.3636:2 -GL000225.1 73566 . CT TG 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGGGGTGAGGGGGCGCGTTT;RSEQ=GGGGCTGGCTCTCCGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27.5:1:27.8:1:1:0:38.5:3:1:0:4 0/1:6:2:0,2:1,2:0.3333:2,0:35:0:31.8:1:1:0:24:4:0.5:0:5 -GL000225.1 73567 . T G 30 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5;SOR=0.23975;LSEQ=GGGGTGAGGGGGCGCGTTTC;RSEQ=GGGGCTGGCTCTCCGGACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:30:0:30.5:1:1:1:46:4:0.5:0:4 0/1:6:1:0,1:1,1:0.1667:2,0:30:0:31:0:1:0:49:2:0.3333:0:5 -GL000225.1 73571 . G A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TGAGGGGGCGCGTTTCTGGG;RSEQ=CTGGCTCTCCGGACCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27:1:32.8:1:1:0:38.5:8:1:0:4 0/1:6:2:1,1:1,3:0.3333:2,2:14:1:31.5:1:1:2.45:29:4:0.3333:0:2 -GL000225.1 73582 . G A 61 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07619;SOR=Inf;LSEQ=GTTTCTGGGGCTGGCTCTCC;RSEQ=GACCTCTCCAGGAATGCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21.5:1:30.8:1:1:0:38.5:8:1:0:4 1/0:6:4:1,3:1,1:0.6667:2,2:32.5:1:30.8:1:1:2.44949:36.5:8:0.6667:0:4.8 -GL000225.1 73586 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=CTGGGGCTGGCTCTCCGGAC;RSEQ=TCTCCAGGAATGCCGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.5:1:31.5:1:1:0:38.5:8:1:0:4 0/1:6:2:1,1:1,3:0.3333:2,2:11:0:31.5:1:1:2.45:49:4:0.3333:0:4.5 -GL000225.1 73598 . G C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGGACCTCTCCAGGAAT;RSEQ=CCGTGGGAACTGGAAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:28:0:33:0:1:0:31:2:1:0:7 1/1:3:3:0,3:0,0:1:0,0:24:1:32:1:1:0:25.7:6:1:0:4.3 -GL000225.1 73602 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGACCTCTCCAGGAATGCCG;RSEQ=GGGAACTGGAAGCCACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:31:0:32:0:1:0:24:4:1:0:5 -GL000225.1 73608 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCCAGGAATGCCGTGGGAA;RSEQ=TGGAAGCCACTCTCTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:18:0:34:0:1:0:31:2:1:0:6 1/1:2:2:0,2:0,0:1:0,0:25:0:32:0:1:0:24:4:1:0:5 -GL000225.1 73884 . A G 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGATGGACTACCGTGTGC;RSEQ=GCAACATGGGGAGTCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:31:0:1:0:32.5:4:1:0:7.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 73917 . A G 61 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCTGCAGTGTGGCCGGTTT;RSEQ=GAAACTGGGAAGGAGAGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,0:0.8:0,2:15:1:30.8:1:1:0:42.3:8:0.8:0:5.5 1/1:1:1:1,0:0,0:1:0,0:19:0:34:0:1:0:40:2:1:0:6 -GL000225.1 73926 . G C 33 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCCGGTTTAGAAACTGG;RSEQ=AAGGAGAGCGAATGCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,1:0.4:2,0:34.5:1:33:1:1:0:32.5:4:0.4:0:5 0/0:1:0:0,0:1,0:0:0,0:28:0:33:0:1:0:40:2:1:0:6 -GL000225.1 73939 . T G 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=Inf;LSEQ=AAACTGGGAAGGAGAGCGAA;RSEQ=GCACCATGCTGGTCTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:1,1:0.625:2,0:24.4:1:28.6:1:0.28571:0:30.8:4:0.5714:0:4.8 1/1:5:5:3,2:0,0:1:0,2:14:1:30.2:1:1:0:56:10:1:0:4.6 -GL000225.1 73945 . A G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.3172;LSEQ=GGAAGGAGAGCGAATGCACC;RSEQ=TGCTGGTCTTCCACCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:7,1:0.1111:2,0:2:0:29:0:1:0:60:2:0.1111:0:4 0/1:14:2:1,1:8,4:0.1429:2,2:24.5:1:30:1:1:1.89743:50:4:0.1429:0:5 -GL000225.1 73948 . C G 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=AGGAGAGCGAATGCACCATG;RSEQ=TGGTCTTCCACCCTTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:8,1:0:2,0:22.9:1:32.2:1:1:0:40.3:18:1:0:5.1 0/1:14:2:1,1:8,4:0.1429:2,2:18:0:29.5:1:1:1.89743:60:4:0.1429:0:5 -GL000225.1 73949 . T C 85 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22829;SOR=3.31368;LSEQ=GGAGAGCGAATGCACCATGC;RSEQ=GGTCTTCCACCCTTCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:4,1:0.2222:2,0:12:1:33:0:1:0:60:4:0.2222:0:4 1/0:14:7:5,2:3,3:0.5:2,2:13.6:1:30.3:1:0.59207:2.32:35.9:14:0.5:0:4 -GL000225.1 73958 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48506;SOR=Inf;LSEQ=ATGCACCATGCTGGTCTTCC;RSEQ=CCCTTCCCTGCATGTTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:11,3:0:2,0:21.4:1:30.3:1:1:0:42.1:28:1:0:4.3 0/1:16:2:1,1:10,4:0.125:2,2:17.5:1:30.5:1:1:2.34522:34:4:0.125:0:2.5 -GL000225.1 73965 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48485;SOR=Inf;LSEQ=ATGCTGGTCTTCCACCCTTC;RSEQ=CTGCATGTTTCCGGGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:12,4:0:2,0:22.6:1:31.4:1:1:0:43.1:32:1:0:3.9 0/1:17:2:1,1:11,4:0.1176:2,2:31.5:1:31:1:0.51471:2.56905:60:4:0.1176:0:3.5 -GL000225.1 73966 . C A 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22727;SOR=Inf;LSEQ=TGCTGGTCTTCCACCCTTCC;RSEQ=TGCATGTTTCCGGGTGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:12,3:0:2,0:23.6:1:31.7:1:1:0:44.5:30:0.9375:0:3.9 0/1:17:3:2,1:10,4:0.1765:2,2:31.3:1:30.3:1:1:1.23316:53.3:6:0.1875:0:4.7 -GL000225.1 73972 . G A 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.85068;LSEQ=TCTTCCACCCTTCCCTGCAT;RSEQ=TTTCCGGGTGCCCGCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:1,0:11,5:0.0588:2,0:34:0:27:0:1:0:27:2:0.0588:0:5 0/1:19:2:1,1:11,6:0.1053:2,2:35:0:30.5:1:1:1.77272:60:4:0.1111:0:3.5 -GL000225.1 73979 . G T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.65988;SOR=0.59672;LSEQ=CCCTTCCCTGCATGTTTCCG;RSEQ=GTGCCCGCAGAGCTCCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:2,1:9,6:0.1667:2,2:36.3:1:29.7:1:1:1.31:47.3:6:0.1667:0:2.7 0/1:19:2:1,1:9,6:0.1053:2,2:39:1:29.5:1:1:1.46382:60:4:0.1053:0:5 -GL000225.1 73983 . C A 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.60386;SOR=0.45405;LSEQ=TCCCTGCATGTTTCCGGGTG;RSEQ=CCGCAGAGCTCCGGGAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:0.1111:2,2:22:0:32:0:1:1.61828:50:4:0.1111:0:1.5 0/1:19:1:1,0:11,7:0.0526:2,0:39:0:31:0:1:0:40:2:0.0526:0:4 -GL000225.1 73984 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22973;SOR=0;LSEQ=CCCTGCATGTTTCCGGGTGC;RSEQ=CGCAGAGCTCCGGGAGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,6:0.1111:2,2:28.5:1:28.5:1:1:1.30929:53.5:4:0.1111:0:4.5 0/0:19:0:0,0:12,7:0:2,0:30.8:1:31.2:1:1:0:46.5:38:1:0:4.6 -GL000225.1 73985 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48649;SOR=Inf;LSEQ=CCTGCATGTTTCCGGGTGCC;RSEQ=GCAGAGCTCCGGGAGCAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:30.2:1:30.9:1:1:0:44.2:36:1:0:3.8 0/1:19:2:1,1:11,6:0.1053:2,2:43:0:31.5:1:1:1.77272:60:4:0.1053:0:5 -GL000225.1 73986 . G T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60386;SOR=3.09542;LSEQ=CTGCATGTTTCCGGGTGCCC;RSEQ=CAGAGCTCCGGGAGCAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:9,7:0.0556:2,0:37:0:32:0:1:0:24:2:0.0556:0:4 0/1:19:3:2,1:10,6:0.1579:2,2:25:1:29.3:1:1:1.19:47:6:0.1579:0:5.7 -GL000225.1 73987 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48649;SOR=Inf;LSEQ=TGCATGTTTCCGGGTGCCCG;RSEQ=AGAGCTCCGGGAGCAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:29.5:1:32.2:1:1:0:43.9:38:1:0:3.8 0/1:19:2:1,1:11,6:0.1053:2,2:47:1:29:1:1:1.77272:60:4:0.1053:0:5 -GL000225.1 73989 . G T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9458;LSEQ=CATGTTTCCGGGTGCCCGCA;RSEQ=AGCTCCGGGAGCAAACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:0.1053:2,2:30.5:1:28:1:1:1.40151:50:4:0.1053:0:3 0/1:20:2:1,1:11,7:0.1:2,2:28:1:29:1:1:1.53525:50:4:0.1:0:5 -GL000225.1 73990 . A G 50 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23269;SOR=Inf;LSEQ=ATGTTTCCGGGTGCCCGCAG;RSEQ=GCTCCGGGAGCAAACAGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,8:0:2,0:30.2:1:30.5:1:1:0:45.1:36:0.9474:0:3.8 0/1:21:3:2,1:10,8:0.1429:2,2:38:0:32:1:1:1.57:50.3:6:0.1429:0:5.7 -GL000225.1 73992 . C A 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.606;SOR=3.0847;LSEQ=GTTTCCGGGTGCCCGCAGAG;RSEQ=TCCGGGAGCAAACAGTCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:1,0:10,9:0.05:2,0:47:0:32:0:1:0:27:2:0.05:0:5 0/1:21:3:2,1:10,8:0.1429:2,2:36:1:27.7:1:1:1.57:41:6:0.1429:0:5.3 -GL000225.1 73994 . C G 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4878;SOR=Inf;LSEQ=TTCCGGGTGCCCGCAGAGCT;RSEQ=CGGGAGCAAACAGTCAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:0:2,0:30.5:1:31.3:1:1:0:43.8:40:1:0:3.8 0/1:21:2:1,1:11,8:0.0952:2,2:36:1:32.5:1:1:1.35399:50:4:0.0952:0:5 -GL000225.1 73995 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23171;SOR=0;LSEQ=TCCGGGTGCCCGCAGAGCTC;RSEQ=GGGAGCAAACAGTCAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:11,7:0.1:2,0:28:1:31.5:1:0.18947:0:36:4:0.1:0:5 0/0:21:0:0,0:11,8:0:2,0:27.4:1:30.4:1:1:0:45.4:38:0.9048:0:4.3 -GL000225.1 73998 . G C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0573;LSEQ=GGGTGCCCGCAGAGCTCCGG;RSEQ=AGCAAACAGTCAGCATGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:0.1:2,2:35:1:31.5:1:1:1.23603:50:4:0.1053:0:3 0/1:19:2:1,1:10,7:0.1053:2,2:23.5:1:31.5:1:1:1.40151:50:4:0.1053:0:5 -GL000225.1 74001 . C G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59459;SOR=2.32256;LSEQ=TGCCCGCAGAGCTCCGGGAG;RSEQ=AAACAGTCAGCATGACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:11,8:0.05:2,0:30:0:33:0:0.45:0:23:2:0.05:0:4 0/1:18:2:1,1:8,6:0.1111:2,2:36:1:31:1:1:1.30929:50:4:0.1111:0:5 -GL000225.1 74004 . A C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22973;SOR=Inf;LSEQ=CCGCAGAGCTCCGGGAGCAA;RSEQ=CAGTCAGCATGACACATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:30.9:1:30.2:1:1:0:43.9:38:1:0:3.7 0/1:18:2:1,1:9,7:0.1111:2,2:40.5:1:30.5:1:1:1.26772:50:4:0.1111:0:6.5 -GL000225.1 74005 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48649;SOR=0;LSEQ=CGCAGAGCTCCGGGAGCAAA;RSEQ=AGTCAGCATGACACATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:10,7:0.1053:2,0:12.5:1:30:1:0.21053:0:44.5:4:0.1053:0:5 0/0:18:0:0,0:10,8:0:2,0:29.4:1:31.5:1:1:0:47.5:36:1:0:4.7 -GL000225.1 74006 . A C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22973;SOR=Inf;LSEQ=GCAGAGCTCCGGGAGCAAAC;RSEQ=GTCAGCATGACACATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:30.1:1:30.1:1:1:0:43.9:18:1:0:3.7 0/1:18:2:1,1:9,7:0.1111:2,2:33.5:1:31.5:1:1:1.26772:60:4:0.1111:0:5 -GL000225.1 74008 . T A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2139;SOR=Inf;LSEQ=AGAGCTCCGGGAGCAAACAG;RSEQ=CAGCATGACACATCTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:30.8:1:29.5:1:1:0:44.2:17:1:0:3.8 0/1:16:2:1,1:8,6:0.125:2,2:31.5:1:31:0:1:1.30929:60:4:0.125:0:5 -GL000225.1 74014 . T A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48663;SOR=0;LSEQ=CCGGGAGCAAACAGTCAGCA;RSEQ=GACACATCTCTGAACTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:28.5:1:30.5:1:1:1:53.5:4:0.1111:0:4.5 0/0:16:0:0,0:9,7:0:2,0:29.1:1:30.1:1:1:0:45.9:32:1:0:4.8 -GL000225.1 74026 . G A 54 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03796;SOR=Inf;LSEQ=AGTCAGCATGACACATCTCT;RSEQ=AACTGATCAACAAAGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,8:0:2,0:21.7:1:31.6:1:1:0:43.4:32:0.9412:0:3.6 0/1:15:4:3,1:5,6:0.2667:2,2:27:1:27.3:1:0.56923:3.31:37.8:8:0.2667:0:5.3 -GL000225.1 74030 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48768;SOR=0;LSEQ=AGCATGACACATCTCTGAAC;RSEQ=GATCAACAAAGTGATGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:33.5:1:29.5:1:1:1:44:4:0.125:0:5 0/0:13:0:0,0:7,6:0:2,0:24.1:1:29.8:1:1:0:44.2:26:1:0:4.8 -GL000225.1 74031 . G C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20635;SOR=Inf;LSEQ=GCATGACACATCTCTGAACT;RSEQ=ATCAACAAAGTGATGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:0:2,0:21:1:31.7:1:1:0:46.7:30:1:0:3.6 0/1:13:2:1,1:6,5:0.1538:2,2:31:1:32:1:1:1.18321:50:4:0.1538:0:6.5 -GL000225.1 74035 . A T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=GACACATCTCTGAACTGATC;RSEQ=ACAAAGTGATGTAACTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:6:0:31.5:1:1:1:60:4:0.1429:0:2 0/0:13:0:0,0:6,6:0:2,0:20.8:1:29.3:1:1:0:45.3:24:0.9231:0:4.7 -GL000225.1 74042 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=0;LSEQ=CTCTGAACTGATCAACAAAG;RSEQ=GATGTAACTCTTTTCTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:0.2:2,2:13.5:1:29.5:1:1:1:46.5:4:0.2222:0:3.5 0/0:10:0:0,0:5,5:0:2,0:19.9:1:28.7:1:1:0:43.2:20:1:0:5 -GL000225.1 74046 . G A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GAACTGATCAACAAAGTGAT;RSEQ=TAACTCTTTTCTAGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:24:1:28:1:1:1.83:44:4:0.25:0:5 0/0:7:0:0,0:3,4:0:2,0:23.7:1:30:1:1:0:44.6:14:1:0:5.1 -GL000225.1 74051 . T A 57 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26573;SOR=5.69965;LSEQ=GATCAACAAAGTGATGTAAC;RSEQ=CTTTTCTAGGCTCTGCCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:2,2:0.1667:2,0:25:0:32:0:1:0:47:2:0.2:0:5 1/0:7:4:2,2:1,2:0.5714:2,2:22:1:28.5:1:1:1.81:38:8:0.5714:0:4.8 -GL000225.1 74055 . T G 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=AACAAAGTGATGTAACTCTT;RSEQ=TCTAGGCTCTGCCTAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:27:1:32:1:1:0:41:6:0.75:0:4 1/1:5:4:1,3:0,1:0.8:0,2:22.8:1:31:1:1:0:40.3:8:0.8:0:5 -GL000225.1 74071 . A C 49 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTCTAGGCTCTGCCTA;RSEQ=AGGGGCTTTGTGACATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:13.7:1:29:1:1:0:42.3:6:1:0:4.3 1/0:4:3:0,3:0,0:0.75:0,0:6.7:1:31:1:1:0:46.7:6:0.75:0:5.7 -GL000225.1 74105 . T C 28 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGCTGTGCACTGATCAC;RSEQ=CAGGTGATGGGACTTTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18.5:1:28:1:1:0:33.5:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 74792 . C A 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=AGCACTGATCCCGAGGTGAT;RSEQ=CAACTCTTGCCTGGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:16.7:1:33:0:1:0:38.7:6:1:0:1.3 1/0:5:3:2,1:1,1:0.6:2,2:14.7:1:29:1:1:1.73:43.7:6:0.6:0:2.3 -GL000225.1 74798 . C G 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=GATCCCGAGGTGATCCAACT;RSEQ=TTGCCTGGTCTCTGCCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:13:1:31.5:1:1:1:43.5:4:0.5:0:1.5 0/0:6:0:0,0:3,3:0:2,0:18.3:1:31.2:1:1:0:42.5:12:1:0:2.7 -GL000225.1 74814 . C A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=AACTCTTGCCTGGTCTCTGC;RSEQ=TACTGGGGACATTGTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:22.5:1:29.5:1:1:1.73:29:4:0.4:0:3.5 0/0:6:0:0,0:3,3:0:2,0:34.3:1:31.2:1:1:0:42.5:12:1:0:2.7 -GL000225.1 74819 . G A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=TTGCCTGGTCTCTGCCTACT;RSEQ=GGGACATTGTGACATATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:27.5:1:28:1:1:1:29:4:0.3333:0:3.5 0/0:6:0:0,0:3,3:0:2,0:39.3:1:30.5:1:1:0:42.5:12:1:0:2.7 -GL000225.1 74820 . G T 57 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02098;SOR=Inf;LSEQ=TGCCTGGTCTCTGCCTACTG;RSEQ=GGACATTGTGACATATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:24.1:1:30.9:1:1:0:41.1:14:1:0:2.6 1/0:6:4:2,2:1,1:0.6667:2,2:38.5:1:28.5:1:1:1:42.8:8:0.6667:0:2.3 -GL000225.1 74824 . C T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=TGGTCTCTGCCTACTGGGGA;RSEQ=ATTGTGACATATCTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:0:2,0:26.4:1:32.3:1:1:0:41.1:14:1:0:2.6 0/1:6:2:1,1:2,2:0.3333:2,2:48:0:29.5:1:1:1:42:4:0.3333:0:3.5 -GL000225.1 74854 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=TATCTCTGCACTGATCTCCC;RSEQ=GGTGCTGTAACTTTAGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:35.5:1:31.5:1:1:1.41:51.5:4:0.2857:0:3.5 0/0:6:0:0,0:3,3:0:2,0:23.3:1:29.3:1:1:0:42.5:12:1:0:2.7 -GL000225.1 74858 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=TCTGCACTGATCTCCCAGGT;RSEQ=CTGTAACTTTAGTCTAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:0.2857:2,2:39.5:1:30:1:1:1.41:51.5:4:0.2857:0:3.5 0/0:6:0:0,0:3,3:0:2,0:19.3:1:31.3:1:1:0:42.5:12:1:0:2.7 -GL000225.1 74859 . CT AA 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CTGCACTGATCTCCCAGGTG;RSEQ=GTAACTTTAGTCTAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:32.7:1:32:1:1:0:41.3:12:1:0:2.8 0/1:6:2:1,1:2,2:0.3333:2,2:13.5:1:28.3:1:1:1:42:4:0.3333:0:2.5 -GL000225.1 74882 . T G 33 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAACTTTAGTCTAGGCTCTG;RSEQ=CTACACGGCATTGTGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:21.5:1:33:0:1:0:34.5:4:0.5:0:3.5 1/1:1:1:0,1:0,0:1:0,0:13:0:34:0:1:0:40:2:1:0:2 -GL000225.1 74908 . C G 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCATTGTGACATATCACT;RSEQ=CACTGATCACCCAGTTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:5.3:1:31:1:1:0:44:6:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 75251 . T C 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTTGTGACATATCTCTGCAC;RSEQ=GATCACCCAGGTGATGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:16.5:1:32:0:1:0:27:4:1:0:5 1/0:4:2:1,1:1,1:0.5:2,2:34:1:28.5:1:1:1:31:4:0.5:0:5 -GL000225.1 75271 . CTG C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGATCACCCAGGTGATGTAA;RSEQ=TTGTCTAGGCTCCACCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:37.5:1:32:0:1:0:27:4:1:0:5 1/0:3:2:1,1:0,1:0.6667:0,2:38.5:1:31:1:1:0:31:4:0.6667:0:5 -GL000225.1 75291 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTGTTGTCTAGGCTCCACCT;RSEQ=CAGGGGGTATTGTGACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:33:1:29.5:1:1:0:27:4:1:0:5 1/0:3:2:1,1:0,1:0.6667:0,2:27:1:32.5:1:1:0:31:4:0.6667:0:5 -GL000225.1 75403 . A C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAATGATCACCCAGGTG;RSEQ=CATACCAGTTGTCAAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:33.5:1:1:0:60:4:1:0:2 -GL000225.1 75458 . A G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCGATGTATCTCTGCAAC;RSEQ=ACCACCTAGGTAATGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13.5:1:29.5:1:1:0:60:4:1:0:2 -GL000225.1 76885 . C T 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGATTTATGACATATCTCTG;RSEQ=GCTGATCACCCAGGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:43:0:34:0:1:0:35:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:14:0:30.5:1:1:0:60:4:1:0:2 -GL000225.1 76893 . A C 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GACATATCTCTGCGCTGATC;RSEQ=CCCAGGTGATGTAACTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:1:31.5:1:1:0:35:4:1:0:2 0/0:2:0:0,0:1,1:0:2,0:22:0:31:1:1:0:60:4:1:0:2 -GL000225.1 77596 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCAGGTGATGTAATAATT;RSEQ=TCTGGGCTTTGCCTACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9:0:30.5:1:1:0:21:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 77600 . G C 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTGATGTAATAATTGTCT;RSEQ=GGCTTTGCCTACAGGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:13:0:31.5:1:1:0:21:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 77623 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGCCTACAGGGGGCTTT;RSEQ=TGATATACATTTCCACTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:0:33:1:1:0:21:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 77644 . C G 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATATACATTTCCACTGAT;RSEQ=AAACAGGTGATGTAACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:32.5:1:32:1:1:0:21:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 77651 . G T 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCCACTGATCAAACAG;RSEQ=TGATGTAACCTTTGTCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25.5:1:29.5:1:1:0:21:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 78160 . A G 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCACAGAGAGAACTGAG;RSEQ=CCTCCCTTGCACGTCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18.5:1:30:1:1:0:60:4:1:0:4 -GL000225.1 78186 . CT TG 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCACGTCAGCCAGGGTG;RSEQ=CAATGAGCGCAGGTCTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:45.5:1:30.8:1:1:0:60:4:1:0:3 -GL000225.1 78195 . C A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCAGGGTGCTCAATGAG;RSEQ=GCAGGTCTAGCCAGGAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:46:1:30:0:1:0:60:4:1:0:3 -GL000225.1 78410 . G A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTCCACCCAGCCCAGGGG;RSEQ=GGATGCATTTTCCTGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:30.5:1:1:0:60:4:1:0:3.5 -GL000225.1 78414 . T C 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCCAGCCCAGGGGGGGA;RSEQ=GCATTTTCCTGGGCTGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:1:30.5:1:1:0:60:4:1:0:3.5 -GL000225.1 78466 . T A 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGGGTGATCAGGCGGGG;RSEQ=GGGGTGGTGGAAAGGCATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:40:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:22:1:27:1:1:0:60:4:1:0:3.5 -GL000225.1 78622 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAGAATGGCAGTTCTCC;RSEQ=CTGGGTGGAGCCTCTCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:38:1:32.5:1:1:1:44:4:0.3333:0:6 0/0:2:0:0,0:1,1:0:2,0:23:1:29.5:1:1:0:60:4:1:0:1.5 -GL000225.1 78625 . GG AT 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAATGGCAGTTCTCCGCT;RSEQ=GTGGAGCCTCTCACCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:42:1:31:1:1:1:44:4:0.3333:0:5 0/0:2:0:0,0:1,1:0:2,0:23:1:29.5:1:1:0:60:4:1:0:1.5 -GL000225.1 78628 . T C 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGCAGTTCTCCGCTGGG;RSEQ=GGAGCCTCTCACCAGGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:44:1:32:0:1:1:44:4:0.3333:0:5 0/0:2:0:0,0:1,1:0:2,0:23:1:26:0:1:0:60:4:1:0:1.5 -GL000225.1 78643 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGTGGAGCCTCTCACCA;RSEQ=GCCTAGACCTAGAAGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:39.5:1:30.5:1:1:1:44:4:0.3333:0:5 0/0:1:0:0,0:0,1:0:0,0:44:0:30:0:1:0:60:2:1:0:2 -GL000225.1 78652 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCTCACCAGGCCTAGAC;RSEQ=TAGAAGGCAGGAATCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:30.5:1:29.5:1:1:1:44:4:0.3333:0:5 0/0:2:0:0,0:1,1:0:2,0:19.5:1:31.5:1:1:0:42.5:4:1:0:4.5 -GL000225.1 78690 . T G 52 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AGGCCGGTCAGCCTGGTGGA;RSEQ=GGGGCGGGGGGAAGACACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:26.5:1:31.5:1:1:0:60:4:1:0:0 1/1:3:3:2,1:0,0:1:0,2:30.7:1:33.3:1:1:0:48.3:6:1:0:5.7 -GL000225.1 78695 . CG C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGTCAGCCTGGTGGATGGGG;RSEQ=GGGGGAAGACACGTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:20.5:1:33:0:1:0:60:4:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:31:0:33:1:1:0:60:4:0.6667:0:5 -GL000225.1 78706 . C A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGGATGGGGCGGGGGGAAGA;RSEQ=ACGTCCCTCCATAGCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:10.5:1:33.5:1:1:0:60:4:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:28:0:31:1:1:0:60:4:0.6667:0:5 -GL000225.1 78710 . T C 52 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TGGGGCGGGGGGAAGACACG;RSEQ=CCCTCCATAGCCAGCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:6.5:1:31:0:1:0:60:4:1:0:0 1/1:3:3:2,1:0,0:1:0,2:25.7:1:33:1:1:0:48.3:6:1:0:5.7 -GL000225.1 78720 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAGACACGTCCCTCCATA;RSEQ=CCAGCCAGGTGTTCCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:1:0:31:0:1:0:60:2:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:14:0:30:1:1:0:60:4:0.6667:0:5 -GL000225.1 78725 . C A 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGTCCCTCCATAGCCAG;RSEQ=CAGGTGTTCCCCGGGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:9:0:29:1:1:0:60:4:0.6667:0:5 -GL000225.1 78776 . T A 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGCCCCGACCCGACCCC;RSEQ=TCCCAACCCCGCGTCCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:32:0:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 78811 . A G 51 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTAAAGCTCCTCTAGCAGA;RSEQ=CCCAGTATTCTTCCTCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:33.7:1:32.7:1:1:0:53.3:6:1:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 78860 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCCAGCGAGGCGGCCTCCT;RSEQ=CAAGGCCTCCAGCTCCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:50:0:30:0:1:0:40:2:0.5:0:8 1/1:2:2:1,1:0,0:1:0,2:11.5:1:27.5:1:1:0:27:4:1:0:4 -GL000225.1 78878 . G C 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAAGGCCTCCAGCTCCC;RSEQ=CGGGTCCTCCGTTTCTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:32:0:28:0:1:0:40:2:1:0:8 1/1:2:2:1,1:0,0:1:0,2:29.5:1:29.5:1:1:0:27:4:1:0:4 -GL000225.1 78894 . T A 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=TCCCGCGGGTCCTCCGTTTC;RSEQ=AGGAAAGGTTGTGCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:8,2:0.1667:2,2:5:0:29:1:0.45455:3.4638:47:4:0.1667:0:4 0/0:7:0:0,0:6,1:0:2,0:17.3:1:30.9:1:1:0:35.1:14:1:0:5.4 -GL000225.1 78903 . T A 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25296;SOR=0;LSEQ=TCCTCCGTTTCTAGGAAAGG;RSEQ=TGTGCCTGCTGCAGAAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:8,3:0.2143:2,2:13.7:1:29.7:1:1:1.30524:50.7:6:0.2143:0:7 0/0:9:0:0,0:7,2:0:2,0:19.7:1:30.7:1:1:0:36.3:18:1:0:4.8 -GL000225.1 78906 . T C 92 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03443;SOR=8.34969;LSEQ=TCCGTTTCTAGGAAAGGTTG;RSEQ=GCCTGCTGCAGAAACTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:7,3:0.2:2,2:8.3:1:30:1:1:1.15267:48.3:6:0.2:0:8 1/0:10:7:6,1:1,1:0.7:2,2:23.7:1:33.1:1:0.41667:4.58:38:14:0.7:0:5.4 -GL000225.1 78909 . C T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=0;LSEQ=GTTTCTAGGAAAGGTTGTGC;RSEQ=TGCTGCAGAAACTCCGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:11,3:0.125:2,2:14:1:32:1:0.45:3.31654:42.5:4:0.125:0:8 0/0:10:0:0,0:8,2:0:2,0:21.3:1:31.9:1:1:0:38.7:20:1:0:5 -GL000225.1 78912 . C A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TCTAGGAAAGGTTGTGCCTG;RSEQ=TGCAGAAACTCCGGGCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:10,3:0.1333:2,2:26:1:32:1:0.47619:3.02781:56:4:0.1429:0:6.5 0/0:10:0:0,0:8,2:0:2,0:23.1:1:33.5:1:1:0:38.7:20:1:0:5 -GL000225.1 78915 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11905;SOR=Inf;LSEQ=AGGAAAGGTTGTGCCTGCTG;RSEQ=AGAAACTCCGGGCTCGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:19.7:1:32.8:1:1:0:46.3:36:1:0:5.1 0/1:10:2:1,1:7,1:0.2:2,2:17:0:31:1:0.37778:5.29155:40.5:4:0.2222:0:2.5 -GL000225.1 78920 . A T 62 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62208;SOR=0.36155;LSEQ=AGGTTGTGCCTGCTGCAGAA;RSEQ=CTCCGGGCTCGCCAGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:3,1:9,5:0.2222:2,2:21.8:1:31.3:1:1:1.62:53.5:8:0.2222:0:5.8 0/1:11:1:1,0:8,2:0.0909:2,0:16:0:32:0:1:0:60:2:0.0909:0:8 -GL000225.1 78923 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15172;SOR=Inf;LSEQ=TTGTGCCTGCTGCAGAAACT;RSEQ=CGGGCTCGCCAGGAGCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:25.9:1:32:1:1:0:46.3:36:1:0:5.1 0/1:12:2:1,1:8,2:0.1667:2,2:23.5:1:29:1:0.45455:3.4638:27:4:0.1667:0:6 -GL000225.1 78924 . C T 74 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12845;SOR=0;LSEQ=TGTGCCTGCTGCAGAAACTC;RSEQ=GGGCTCGCCAGGAGCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:3,2:10,4:0.2632:2,2:30:1:32:1:1:1.62034:48.4:10:0.2632:0:7 0/0:12:0:0,0:9,3:0:2,0:26.3:1:30.1:1:1:0:37.8:11:1:0:5.3 -GL000225.1 78926 . GG CT 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.79699;LSEQ=TGCCTGCTGCAGAAACTCCG;RSEQ=CTCGCCAGGAGCTCATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,6:0.0952:2,2:32:1:32.3:1:1:1.77272:42.5:4:0.1:0:7 0/1:13:1:1,0:9,3:0.0769:2,0:35:0:32.5:0:1:0:40:2:0.0769:0:6 -GL000225.1 78927 . G T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50588;SOR=0;LSEQ=GCCTGCTGCAGAAACTCCGG;RSEQ=CTCGCCAGGAGCTCATCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,6:0.0952:2,2:21.5:1:31.5:1:1:1.77272:47.5:4:0.1053:0:5.5 0/0:14:0:0,0:10,3:0:2,0:23.6:1:30.5:1:1:0:41:12:1:0:4.9 -GL000225.1 78930 . C T 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07207;SOR=Inf;LSEQ=TGCTGCAGAAACTCCGGGCT;RSEQ=GCCAGGAGCTCATCCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:27.4:1:31.3:1:1:0:45.3:42:1:0:5 0/1:16:3:2,1:9,4:0.1875:2,2:24.3:1:29.3:1:1:1.11662:31:6:0.1875:0:6 -GL000225.1 78931 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49528;SOR=0;LSEQ=GCTGCAGAAACTCCGGGCTC;RSEQ=CCAGGAGCTCATCCAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,8:0.0909:2,2:39:0:31.5:1:1:1.23603:47:4:0.0909:0:4 0/0:17:0:0,0:9,4:0:2,0:20.6:1:30.8:1:1:0:42.5:26:0.7647:0:4.2 -GL000225.1 78933 . C A 62 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36341;SOR=0.2895;LSEQ=TGCAGAAACTCCGGGCTCGC;RSEQ=AGGAGCTCATCCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:3,1:10,8:0.1818:2,2:31.8:1:31:1:0.61613:2.31:51.3:8:0.1818:0:7.3 0/1:17:1:1,0:10,5:0.0588:2,0:29:0:32:0:1:0:60:2:0.0625:0:8 -GL000225.1 78939 . C T 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09673;SOR=Inf;LSEQ=AACTCCGGGCTCGCCAGGAG;RSEQ=TCATCCAGCAGCAGGCCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:32.8:1:32:1:1:0:43.8:40:1:0:5.5 0/1:18:3:2,1:9,5:0.1667:2,2:22.3:1:29.7:1:1:1.10:31.3:6:0.1765:0:4.3 -GL000225.1 78944 . CC GA 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48846;SOR=0;LSEQ=CGGGCTCGCCAGGAGCTCAT;RSEQ=AGCAGCAGGCCGGAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:0.0952:2,2:25:0:32.8:1:1:1.35399:47:4:0.0952:0:3 0/0:19:0:0,0:12,7:0:2,0:23.6:1:30.5:1:1:0:45.4:18:1:0:4.9 -GL000225.1 78945 . C A 45 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23171;SOR=0;LSEQ=GGGCTCGCCAGGAGCTCATC;RSEQ=AGCAGCAGGCCGGAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:1,2:10,6:0.1429:2,2:27:1:28.7:1:0.54592:3.12168:50.7:6:0.1579:0:7 0/0:20:0:0,0:12,8:0:2,0:22.7:1:29.8:1:1:0:46.4:19:1:0:4.9 -GL000225.1 78951 . CAGG C 34 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.50786;LSEQ=GCCAGGAGCTCATCCAGCAG;RSEQ=CCGGAGGGGAGTGCAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:2,0:10,9:0.0909:2,0:44.5:1:34:0:0.48571:0:60:4:0.0909:0:7.5 0/1:21:1:1,0:11,8:0.0476:2,0:48:0:31:0:1:0:60:2:0.0476:0:8 -GL000225.1 78954 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.48837;SOR=0;LSEQ=AGGAGCTCATCCAGCAGCAG;RSEQ=CCGGAGGGGAGTGCAGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,8:0.0909:2,2:31:1:29:1:1:1.23603:39:4:0.1:0:6.5 0/0:21:0:0,0:12,8:0:2,0:23.3:1:30.8:1:1:0:46.6:40:1:0:4.9 -GL000225.1 78956 . C G 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4926;SOR=0;LSEQ=GAGCTCATCCAGCAGCAGGC;RSEQ=GGAGGGGAGTGCAGAAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:13,9:0.0833:2,2:43:0:31:1:1:1.42202:47.5:4:0.0833:0:5.5 0/0:20:0:0,0:9,6:0:2,0:29.7:1:28.9:1:1:0:48:14:0.7778:0:5.2 -GL000225.1 78957 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4716;SOR=2.10531;LSEQ=AGCTCATCCAGCAGCAGGCC;RSEQ=GAGGGGAGTGCAGAAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:1,3:13,7:0.1667:2,2:28.3:1:30.5:1:0.27207:5.17077:43.5:8:0.1739:0:6.3 0/1:20:6:3,3:9,5:0.3:2,2:28:1:30.2:1:0.64241:1.74629:55.2:12:0.3158:0:4.3 -GL000225.1 78960 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4926;SOR=0;LSEQ=TCATCCAGCAGCAGGCCGGA;RSEQ=GGGAGTGCAGAAGAGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:13,9:0.0833:2,2:31:1:30:1:1:1.42202:39:4:0.0833:0:6.5 0/0:20:0:0,0:12,8:0:2,0:27.9:1:30.8:1:1:0:47.5:40:1:0:5.2 -GL000225.1 78963 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21212;SOR=Inf;LSEQ=TCCAGCAGCAGGCCGGAGGG;RSEQ=AGTGCAGAAGAGCGCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:28.7:1:31:1:1:0:44:48:1:0:5.2 0/1:21:2:1,1:11,8:0.0952:2,2:32.5:1:28:1:1:1.35399:50:4:0.0952:0:7 -GL000225.1 78964 . A T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21212;SOR=Inf;LSEQ=CCAGCAGCAGGCCGGAGGGG;RSEQ=GTGCAGAAGAGCGCCCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:28.4:1:30.3:1:1:0:44:48:1:0:5.2 0/1:21:2:1,1:11,8:0.0952:2,2:25.5:1:28:1:1:1.35399:59.5:4:0.1:0:5.5 -GL000225.1 78966 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=AGCAGCAGGCCGGAGGGGAG;RSEQ=GCAGAAGAGCGCCCCGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:13,9:0.0833:2,2:40.5:1:30.5:1:1:1.42202:47.5:4:0.0833:0:5.5 0/0:21:0:0,0:12,9:0:2,0:28.1:1:28:1:1:0:47.2:20:1:0:5 -GL000225.1 78972 . A C 104 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20865;SOR=0.40898;LSEQ=AGGCCGGAGGGGAGTGCAGA;RSEQ=GAGCGCCCCGGCTCCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:6,4:2,2:0.4545:2,2:34.6:1:31.6:1:1:1.46:39.1:20:0.4545:0:5.4 0/1:20:5:3,2:4,2:0.25:2,2:40.4:1:31:1:1:1.29868:54:10:0.25:0:3.6 -GL000225.1 78975 . G A 44 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23171;SOR=0;LSEQ=CCGGAGGGGAGTGCAGAAGA;RSEQ=CGCCCCGGCTCCTGGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:10,6:0.1429:2,2:30.3:1:28.3:1:1:1.19:39.3:6:0.1579:0:6.3 0/0:20:0:0,0:10,6:0:2,0:31.9:1:30.8:1:1:0:47.1:32:0.8:0:4.8 -GL000225.1 78976 . C T 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0931;SOR=6.38883;LSEQ=CGGAGGGGAGTGCAGAAGAG;RSEQ=GCCCCGGCTCCTGGAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:10,7:0.0476:2,0:27:0:32:0:1:0:20:2:0.0526:0:7 0/1:20:5:3,2:7,4:0.25:2,2:42.8:1:29.8:1:1:1.15538:54:10:0.3333:0:3.6 -GL000225.1 78977 . G A 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.6628;SOR=1.65554;LSEQ=GGAGGGGAGTGCAGAAGAGC;RSEQ=CCCCGGCTCCTGGAGCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:11,8:0.0952:2,0:31:1:31:1:0.50476:0:60:4:0.0952:0:7.5 0/1:20:3:2,1:10,7:0.15:2,2:32.3:1:28.3:1:1:1.38:50.7:6:0.15:0:5.3 -GL000225.1 78979 . C T 31 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.59059;LSEQ=AGGGGAGTGCAGAAGAGCGC;RSEQ=CCGGCTCCTGGAGCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:11,8:0.087:2,0:29:1:31.5:1:0.50476:0:60:4:0.0952:0:7.5 0/1:19:1:1,0:10,8:0.0526:2,0:29:0:27:0:1:0:60:2:0.0526:0:8 -GL000225.1 78982 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24086;SOR=0.30295;LSEQ=GGAGTGCAGAAGAGCGCCCC;RSEQ=GCTCCTGGAGCACCTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:7,8:0.2857:2,2:29.2:1:30.5:1:0.63512:2.20:45:12:0.2857:0:5.8 0/1:19:2:2,0:8,7:0.1053:2,0:30.5:1:28:1:0.48529:0:45.5:4:0.1053:0:7.5 -GL000225.1 78983 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20854;SOR=Inf;LSEQ=GAGTGCAGAAGAGCGCCCCG;RSEQ=CTCCTGGAGCACCTGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:0:2,0:23.6:1:31.1:1:1:0:46.3:21:1:0:5 0/1:19:2:1,1:10,7:0.1053:2,2:22:1:26.5:1:1:1.40151:43.5:4:0.1053:0:3.5 -GL000225.1 78994 . A G 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92509;LSEQ=AGCGCCCCGGCTCCTGGAGC;RSEQ=CCTGGGAGGGCGCCGGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:2,3:7,7:0.25:2,2:30.6:1:31.2:1:1:1.46843:33:10:0.2632:0:6.6 0/1:17:4:2,2:6,6:0.2353:2,2:35.5:1:29.8:1:1:1:45.5:8:0.25:0:5.3 -GL000225.1 79002 . G T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48649;SOR=0;LSEQ=GGCTCCTGGAGCACCTGGGA;RSEQ=GGCGCCGGGATGCCTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:7,10:0.1053:2,2:12.5:1:31.5:1:1:1.40:51.5:4:0.1053:0:5 0/0:19:0:0,0:9,10:0:2,0:21.7:1:30.3:1:1:0:51.8:38:1:0:4.9 -GL000225.1 79003 . G T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22973;SOR=0;LSEQ=GCTCCTGGAGCACCTGGGAG;RSEQ=GCGCCGGGATGCCTTGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:8,8:0.1111:2,0:25.5:1:32:0:0.47712:0:33.5:4:0.1111:0:7 0/0:19:0:0,0:9,10:0:2,0:21.1:1:29.9:1:1:0:51.8:38:1:0:4.9 -GL000225.1 79006 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=CCTGGAGCACCTGGGAGGGC;RSEQ=CCGGGATGCCTTGCATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,9:0.1111:2,2:8.5:1:28:1:1:1.27:51.5:4:0.1176:0:5 0/0:18:0:0,0:8,10:0:2,0:20.1:1:30.6:1:1:0:52.2:36:1:0:4.9 -GL000225.1 79008 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60117;SOR=3.31312;LSEQ=TGGAGCACCTGGGAGGGCGC;RSEQ=GGGATGCCTTGCATCTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:1,0:6,10:0.0588:2,0:16:0:27:0:0.41176:0:33:2:0.0588:0:5 0/1:17:3:1,2:6,8:0.1765:2,2:17.3:1:30:1:1:1.46561:59.7:6:0.1765:0:5.7 -GL000225.1 79009 . G A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.83181;LSEQ=GGAGCACCTGGGAGGGCGCC;RSEQ=GGATGCCTTGCATCTGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:5,9:0.0667:2,0:25:0:29:0:1:0:60:2:0.0667:0:4 0/1:17:2:1,1:6,9:0.1176:2,2:9:1:28:1:1:1.46:49.5:4:0.1176:0:6 -GL000225.1 79011 . G C 51 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10122;SOR=0;LSEQ=AGCACCTGGGAGGGCGCCGG;RSEQ=ATGCCTTGCATCTGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:5,7:0.2:2,0:21.3:1:32.7:1:0.50549:0:46.3:6:0.2:0:6 0/0:16:0:0,0:6,10:0:2,0:19:1:30:1:1:0:52.6:15:1:0:4.6 -GL000225.1 79014 . G T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.6838;LSEQ=ACCTGGGAGGGCGCCGGGAT;RSEQ=CCTTGCATCTGCCCCTGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:5,6:0.0769:2,0:11:0:31:0:1:0:27:2:0.0769:0:6 0/1:16:2:1,1:5,9:0.125:2,2:7.5:1:27:1:1:1.73:46:4:0.125:0:4 -GL000225.1 79026 . C A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GCCGGGATGCCTTGCATCTG;RSEQ=CCCTGCCACATGGATGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:2,4:0.1429:2,0:4:0:31:0:0.42857:0:60:2:0.1429:0:6 0/1:14:2:1,1:4,8:0.1429:2,2:31:1:28.5:1:1:1.90:60:4:0.1429:0:6 -GL000225.1 79036 . A G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=CTTGCATCTGCCCCTGCCAC;RSEQ=TGGATGCCTCCGGGGTCGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:14:0:25:0:1:0:20:2:0.25:0:7 0/1:6:2:1,1:2,2:0.3333:2,2:16:0:32.5:1:1:1:26:4:0.3333:0:7.5 -GL000225.1 79037 . T C 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57143;SOR=2.68677;LSEQ=TTGCATCTGCCCCTGCCACA;RSEQ=GGATGCCTCCGGGGTCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:15:0:33:0:1:0:60:2:0.25:0:6 1/0:6:3:1,2:2,1:0.5:2,2:42.7:1:29:1:1:3.10575:60:6:0.5:0:6 -GL000225.1 79041 . T G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57143;SOR=2.68677;LSEQ=ATCTGCCCCTGCCACATGGA;RSEQ=GCCTCCGGGGTCGTGGGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:9:0:27:0:1:0:20:2:0.25:0:7 1/0:6:3:2,1:1,2:0.5:2,2:16.3:1:30.7:1:1:3.11:27.7:6:0.5:0:7.3 -GL000225.1 79047 . C T 63 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=CCCTGCCACATGGATGCCTC;RSEQ=GGGGTCGTGGGCTGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:0.6:2,2:11.3:1:28:1:1:1.73:46.7:6:0.6:0:5.7 1/0:6:4:2,2:1,1:0.6667:2,2:38:1:31.8:1:1:1:43:8:0.6667:0:6.8 -GL000225.1 79052 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCACATGGATGCCTCCGGGG;RSEQ=CGTGGGCTGGGGAGGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:29.3:1:29:1:1:0:60:8:1:0:2.5 0/1:5:2:1,1:1,2:0.4:2,2:32:0:33:1:1:1.73:26:4:0.4:0:7.5 -GL000225.1 79055 . T C 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=CATGGATGCCTCCGGGGTCG;RSEQ=GGGCTGGGGAGGTGGAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23.5:1:29.5:1:1:1:60:4:0.5:0:5 1/0:5:3:1,2:1,1:0.6:2,2:40.3:1:30.7:1:1:1.7321:60:6:0.6:0:6 -GL000225.1 79057 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TGGATGCCTCCGGGGTCGTG;RSEQ=GCTGGGGAGGTGGAGCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:29.3:1:29.8:1:1:0:60:8:1:0:2.5 0/1:5:2:1,1:1,2:0.4:2,2:28.5:1:32.5:1:1:1.73:26:4:0.4:0:7.5 -GL000225.1 79063 . GG CT 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCTCCGGGGTCGTGGGCTGG;RSEQ=AGGTGGAGCTGCCCCGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:29.3:1:30:1:1:0:60:8:1:0:2.5 0/1:5:2:1,1:1,2:0.4:2,2:21.5:1:31.8:1:1:1.73:26:4:0.4:0:6.5 -GL000225.1 79089 . C T 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGCTGCCCCGGCTTGGTG;RSEQ=TCCCACGGCTCCCCTGCGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:32.7:1:30.7:1:1:0:60:6:0.75:0:4.7 1/1:3:3:1,2:0,0:1:0,2:6.3:1:29:1:1:0:60:6:1:0:6 -GL000225.1 79097 . G C 52 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGGCTTGGTGCTCCCACG;RSEQ=CTCCCCTGCGACCTGGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:31.7:1:33:1:1:0:60:6:1:0:4.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 79145 . C A 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCCCACCATGGACTCC;RSEQ=CTGGGACGCGGGTGGTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:38:1:29.5:1:1:0:60:4:0.6667:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 79170 . T A 47 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGCGGGTGGTGCAAGCAC;RSEQ=CCTTGGCCCTGTGGCCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:13.3:1:29.7:1:1:0:53.3:6:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 79277 . GC TT 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCCCGGCTTTTGCCCGGGT;RSEQ=GGAGGCCACCGAGGAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:2:0:29:0:1:0:40:2:1:0:3 1/0:4:2:1,1:1,1:0.5:2,2:18:1:29.3:1:1:1:43:4:0.5:0:6.5 -GL000225.1 79282 . G T 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTTTTGCCCGGGTGCGGA;RSEQ=GCCACCGAGGAGCCTCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:7:0:31:0:1:0:40:2:1:0:3 1/0:4:2:1,1:1,1:0.5:2,2:24:1:32:0:1:1:21:4:0.5:0:1.5 -GL000225.1 79295 . C G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGCGGAGGCCACCGAGGAG;RSEQ=CTCAGGGTGGGAGAGCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:20:0:32:0:1:0:40:2:1:0:3 1/0:4:2:1,1:1,1:0.5:2,2:35:1:32.5:1:1:1:43:4:0.5:0:6.5 -GL000225.1 79298 . C G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGAGGCCACCGAGGAGCCT;RSEQ=AGGGTGGGAGAGCGCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:23:0:33:0:1:0:40:2:1:0:3 1/0:4:2:1,1:1,1:0.5:2,2:38:1:31.5:1:1:1:43:4:0.5:0:6.5 -GL000225.1 79324 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGAGCGCCCCTTCCGGA;RSEQ=GAGCCGGGGTGGCATAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:32.5:1:1:0:43:4:1:0:6.5 -GL000225.1 79332 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCTTCCGGAGGAGCCGG;RSEQ=GTGGCATAGCCAAAATCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:31.5:1:1:0:43:4:1:0:6.5 -GL000225.1 80088 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCCCCAGCCGGAATTTCAC;RSEQ=GACGGACACTGGCAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:43:0:32:0:1:0:60:2:0.5:0:5 1/1:2:2:1,1:0,0:1:0,2:6:0:30.5:1:1:0:49:4:1:0:3.5 -GL000225.1 80116 . G A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACTGGCAGAGAGAGGCCGGC;RSEQ=GGCACCCGTGCAACTCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:14:1:29.5:1:1:0:60:4:0.6667:0:3 0/0:2:0:0,0:1,1:0:2,0:34:0:31:0:1:0:49:4:1:0:3.5 -GL000225.1 80120 . A T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GCAGAGAGAGGCCGGCGGGC;RSEQ=CCCGTGCAACTCAGCTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:44:0:30:0:1:0:35:2:0.3333:0:7 1/1:2:2:1,1:0,0:1:0,2:38:0:29.5:1:1:0:49:4:1:0:3.5 -GL000225.1 80129 . A C 60 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GGCCGGCGGGCACCCGTGCA;RSEQ=CTCAGCTGGCCTGTGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:2,1:0.5714:2,2:11.3:1:30:1:1:1.41:40.8:8:0.5714:0:5.5 0/0:2:0:0,0:1,1:0:2,0:44.5:1:29.5:1:1:0:49:4:1:0:3.5 -GL000225.1 80150 . T C 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CTCAGCTGGCCTGTGCACTG;RSEQ=GGCAGGTGCAGCCAGGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,1:0.2857:2,2:25.5:1:31.5:1:1:1.7321:34:4:0.2857:0:6 1/1:2:2:1,1:0,0:1:0,2:23.5:1:28.5:1:1:0:49:4:1:0:3.5 -GL000225.1 80176 . C A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAGCCAGGAGGCCTGCA;RSEQ=GGACAGCCAGCCAGCGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:32:0:32:0:1:1:60:4:0.3333:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 80177 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGCCAGGAGGCCTGCAC;RSEQ=GACAGCCAGCCAGCGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:26:0:32.5:1:1:1:34:4:0.4:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 80180 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGGAGGCCTGCACGGA;RSEQ=AGCCAGCCAGCGGCTCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:23:0:32:0:1:1:34:4:0.3333:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 80184 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGGAGGCCTGCACGGACAGC;RSEQ=AGCCAGCGGCTCTTATAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:19:0:31:1:1:1:34:4:0.3333:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 80198 . T C 33 v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GACAGCCAGCCAGCGGCTCT;RSEQ=ATAAAGGCCCGAAGGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:5:0:33:0:1:1.41418:34:4:0.3333:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 80288 . CC TG 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCACGGAAGGATCCCAGGG;RSEQ=TCGAGTCCTGTGGCAGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:29:1:24:1:1:0:60:1:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:13:0:32.8:1:1:0:58:4:1:0:6.5 -GL000225.1 80292 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGGAAGGATCCCAGGGCCTC;RSEQ=AGTCCTGTGGCAGGGGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:29:1:24.5:1:1:0:60:1:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:16:0:32:0:1:0:58:4:1:0:6.5 -GL000225.1 80295 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAGGATCCCAGGGCCTCGAG;RSEQ=CCTGTGGCAGGGGTGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:29:1:29.5:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:1:0,2:19:0:33.5:1:1:0:58:4:1:0:6.5 -GL000225.1 80300 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TCCCAGGGCCTCGAGTCCTG;RSEQ=GGCAGGGGTGTGGTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:20.7:1:29.3:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:24:0:33:1:1:0:58:4:1:0:6.5 -GL000225.1 80343 . CC TG 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GTGGGAGGGCGTGGTGATGG;RSEQ=GTGGTGGGGCCGGAGACACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:25:1:30.7:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:1:0,2:9.5:1:29:1:1:0:58:4:1:0:5.5 -GL000225.1 80444 . A C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTGCTCCAGGAATCCCG;RSEQ=GGGAACTGGAAGCCACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 80500 . C A 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAGCAGGGAGAAACCGG;RSEQ=CTGCGAGGGTGGAGGGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:7:0:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 80593 . T G 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGAGGCAGTGCCTGTGGG;RSEQ=GTCGCCATTGCCAGCGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:14:0:28:0:1:0:33:2:1:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:10:0:32.5:1:1:0:43:4:0.6667:0:2.5 -GL000225.1 80595 . TCGCCATTGCCAGCGCAGTCTCACAAAG ACTCCGTGGCCTGGACAGACTCACACAC 49 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GGAGGCAGTGCCTGTGGGTG;RSEQ=GCAGGCGTTTGGCTCTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:12:0:28:0:1:0:33:2:1:0:0 1/1:3:3:1,2:0,0:1:0,2:17.7:1:31.2:1:1:0:46:6:1:1:3.3 -GL000225.1 80667 . C A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCACGTAGGAGACCAGAGC;RSEQ=AGACCCCAGAGAGAAGATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24:1:32:0:1:0:46:4:1:0:5.5 -GL000225.1 80684 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AGCCAGACCCCAGAGAGAAG;RSEQ=TGCCTCCACGGCGTGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:23.5:1:31:1:1:1:40:4:0.5:0:7 0/0:4:0:0,0:2,2:0:2,0:15.5:1:31.5:1:1:0:51:8:1:0:4.3 -GL000225.1 80692 . A C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=6.40831;LSEQ=CCCAGAGAGAAGATGCCTCC;RSEQ=CGGCGTGATGGCCTGACGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:25:0:33:0:1:0:33:2:0.25:0:4 1/0:4:3:2,1:0,0:0.75:0,2:23.7:1:32.3:1:1:0:50.7:6:0.75:0:4 -GL000225.1 80694 . G T 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CAGAGAGAAGATGCCTCCAC;RSEQ=GCGTGATGGCCTGACGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21.3:1:30.3:1:1:0:35.5:8:1:0:5.5 1/0:4:2:1,1:1,1:0.5:2,2:17:0:32:1:1:1:56:4:0.5:0:3 -GL000225.1 80720 . TG CA 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=ATGGCCTGACGATGGATTCC;RSEQ=TGTGCGGCAACATGGGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:0.5:0,2:23.5:1:30.3:1:1:0:40:4:0.5:0:6 0/0:4:0:0,0:2,2:0:2,0:18:1:30.3:1:1:0:48:8:1:0:4.8 -GL000225.1 80727 . G A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GACGATGGATTCCTGTGTGC;RSEQ=GCAACATGGGAAGTCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:36:1:30.7:1:1:0:34:6:1:0:4.3 1/0:4:2:1,1:1,1:0.5:2,2:18:1:28.5:1:1:1:40:4:0.5:0:6.5 -GL000225.1 80729 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CGATGGATTCCTGTGTGCGG;RSEQ=AACATGGGAAGTCTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:36.7:1:32.3:1:1:0:34:6:1:0:4.3 1/0:4:2:1,1:1,1:0.5:2,2:18:1:28:1:1:1:40:4:0.5:0:6.5 -GL000225.1 80738 . A G 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTGTGCGGCAACATGGG;RSEQ=AGTCTGCAGTGTGGCCGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:31:1:31.7:1:1:0:34:6:1:0:4.3 1/1:3:3:1,2:0,0:1:0,2:13:1:29.3:1:1:0:45:6:1:0:5.7 -GL000225.1 84065 . G A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCATTGTGACATATTTCT;RSEQ=TACTGATCAACCAGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:27:1:1:0:42:4:1:0:8 -GL000225.1 84079 . GG AT 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTGTACTGATCAACCA;RSEQ=TGATGTAACTCTTGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:28.8:1:1:0:42:4:1:0:7 -GL000225.1 84082 . G T 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTACTGATCAACCAGGT;RSEQ=ATGTAACTCTTGTCTAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21.5:1:27:1:1:0:42:4:1:0:7 -GL000225.1 85124 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAGGTGATGGGACTCTTGTC;RSEQ=AGGCTCTGCCTACAGGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12.5:1:31.5:1:1:0:39:4:1:0:5.5 0/0:1:0:0,0:1,0:0:0,0:20:0:33:0:1:0:42:2:1:0:4 -GL000225.1 85134 . C A 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GACTCTTGTCTAGGCTCTGC;RSEQ=TACAGGGGCATTGTGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22.5:1:32:1:1:0:39:4:1:0:5.5 0/0:1:0:0,0:1,0:0:0,0:30:0:32:0:1:0:42:2:1:0:4 -GL000225.1 85139 . G T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTGTCTAGGCTCTGCCTACA;RSEQ=GGGCATTGTGACATATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27.5:1:31.5:1:1:0:39:4:1:0:5.5 0/0:1:0:0,0:1,0:0:0,0:35:0:34:0:1:0:42:2:1:0:4 -GL000225.1 85142 . G T 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCTAGGCTCTGCCTACAGGG;RSEQ=CATTGTGACATATCTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:30.5:1:31:1:1:0:39:4:1:0:5.5 0/0:2:0:0,0:1,1:0:2,0:20:1:31:1:1:0:42:4:1:0:2.5 -GL000225.1 85171 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATATCTCTGCAGTGATCAC;RSEQ=CAGGTGATGTAACTCTTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:37:1:30.5:1:1:0:39:4:1:0:5.5 0/0:2:0:0,0:1,1:0:2,0:29:1:30:1:1:0:42:4:1:0:2.5 -GL000225.1 85609 . C A 79 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACTCTTCCCTAGGATCTG;RSEQ=CTACAGGGTGCTTTGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:20:0:32:0:1:0:25:2:1:0:4 1/1:6:6:5,1:0,0:1:0,2:10.2:1:30.7:1:1:0:41.3:12:1:0:5 -GL000225.1 85611 . T C 81 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTTCCCTAGGATCTGCC;RSEQ=ACAGGGTGCTTTGTGACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:22:0:33:0:1:0:25:2:1:0:4 1/1:6:6:5,1:0,0:1:0,2:12.2:1:31.7:1:1:0:41.3:12:1:0:5 -GL000225.1 85614 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTCCCTAGGATCTGCCTAC;RSEQ=GGGTGCTTTGTGACATATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:8.5:1:29.3:1:1:0:25.3:8:1:0:3.5 0/1:11:2:1,1:7,2:0.1818:2,2:16.5:1:32:0:0.49091:3.05504:31:4:0.1818:0:5.5 -GL000225.1 85620 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28051;SOR=0.22393;LSEQ=TAGGATCTGCCTACAGGGTG;RSEQ=TTTGTGACATATCCCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:5,0:0.375:0,2:7.3:1:30:1:0.375:0:38.7:6:0.4286:0:4.3 0/1:18:2:1,1:9,7:0.1111:2,2:11.5:1:31.5:1:1:1.26772:60:4:0.1111:0:5.5 -GL000225.1 85625 . T A 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCTGCCTACAGGGTGCTTTG;RSEQ=GACATATCCCTGCAATGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:13.6:1:30.3:1:1:0:40.7:18:1:0:3 0/1:19:2:1,1:10,7:0.1053:2,2:16.5:1:32:1:1:1.40151:60:4:0.1053:0:5.5 -GL000225.1 85627 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51954;SOR=Inf;LSEQ=TGCCTACAGGGTGCTTTGTG;RSEQ=CATATCCCTGCAATGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:0:2,0:13.1:1:29.5:1:1:0:44.2:22:1:0:2.6 0/1:19:2:1,1:10,7:0.1053:2,2:15:0:33.5:1:1:1.40151:44:4:0.1111:0:3.5 -GL000225.1 85629 . A T 59 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01204;SOR=0;LSEQ=CCTACAGGGTGCTTTGTGAC;RSEQ=TATCCCTGCAATGATCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:6,1:0.3636:2,2:14.5:1:29.5:1:0.49091:4.9538:44:8:0.3636:0:4.3 0/0:19:0:0,0:11,8:0:2,0:19.4:1:31.2:1:1:0:41.1:38:1:0:3.5 -GL000225.1 85631 . A T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52273;SOR=Inf;LSEQ=TACAGGGTGCTTTGTGACAT;RSEQ=TCCCTGCAATGATCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:15.8:1:29.2:1:1:0:42.6:24:1:0:2.5 0/1:21:2:1,1:11,8:0.0952:2,2:19:0:32:0:1:1.35399:44:4:0.0952:0:3.5 -GL000225.1 85660 . T C 154 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38776;SOR=Inf;LSEQ=ATGATCACCCAGGTGATATA;RSEQ=CACTTGCCAAGGCTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:18:11,7:1,0:0.9474:0,2:31.2:1:30.3:1:1:0:40.8:17:0.9444:0:2.6 1/1:30:30:15,15:0,0:1:0,2:30.8:1:31.5:1:1:0:43.6:60:1:0:3.2 -GL000225.1 85664 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50905;SOR=Inf;LSEQ=TCACCCAGGTGATATATCAC;RSEQ=TGCCAAGGCTCTGCCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:28.9:1:30:1:1:0:41.3:42:1:0:2.3 0/1:31:2:1,1:15,14:0.0645:2,2:29.5:1:29:1:1:1.06901:60:4:0.0645:0:2 -GL000225.1 85665 . T A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50905;SOR=Inf;LSEQ=CACCCAGGTGATATATCACT;RSEQ=GCCAAGGCTCTGCCTACAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:29.2:1:28.9:1:1:0:41.3:20:1:0:2.3 0/1:31:2:1,1:15,14:0.0645:2,2:44:1:29.5:1:1:1.06901:59:4:0.0645:0:4 -GL000225.1 85666 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50905;SOR=Inf;LSEQ=ACCCAGGTGATATATCACTT;RSEQ=CCAAGGCTCTGCCTACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:0:2,0:29.6:1:29.8:1:1:0:41.3:9.5:1:0:2.3 0/1:31:2:1,1:15,14:0.0645:2,2:23:0:31.5:1:1:1.06901:23:4:0.0667:0:4 -GL000225.1 85671 . G T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50508;SOR=Inf;LSEQ=GGTGATATATCACTTGCCAA;RSEQ=GCTCTGCCTACAGGGGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:29.4:1:29.6:1:1:0:40.4:10:1:0:2.5 0/1:31:2:1,1:15,14:0.0645:2,2:40:1:29.5:1:1:1.06901:53.5:4:0.0667:0:4.5 -GL000225.1 85673 . C T 29 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16763;SOR=0;LSEQ=TGATATATCACTTGCCAAGG;RSEQ=TCTGCCTACAGGGGCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:0.0909:2,2:28:0:29.5:1:1:1.21106:46:4:0.0952:0:3 0/0:31:0:0,0:16,15:0:2,0:29.4:1:31.6:1:1:0:43.2:30:1:0:3.1 -GL000225.1 85678 . CC GT 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50508;SOR=Inf;LSEQ=TATCACTTGCCAAGGCTCTG;RSEQ=TACAGGGGCATTGCAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:29.8:1:30.5:1:1:0:40.4:21:1:0:2.5 0/1:31:2:1,1:14,14:0.0645:2,2:10:0:32.5:0:1:1:23:4:0.0645:0:3 -GL000225.1 85679 . C T 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13243;SOR=Inf;LSEQ=ATCACTTGCCAAGGCTCTGC;RSEQ=TACAGGGGCATTGCAATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:29.6:1:29.3:1:1:0:40.4:6.333:1:0:2.5 0/1:31:4:2,2:13,12:0.129:2,2:20.3:1:30.8:1:1:1.08033:32:8:0.1379:0:3.8 -GL000225.1 85682 . C G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15837;SOR=0;LSEQ=ACTTGCCAAGGCTCTGCCTA;RSEQ=AGGGGCATTGCAATGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,7:0.0952:2,2:28:1:32.5:1:1:1.26772:22:4:0.0952:0:6 0/0:31:0:0,0:16,15:0:2,0:26.2:1:31.3:1:1:0:43.2:62:1:0:3 -GL000225.1 85690 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51531;SOR=Inf;LSEQ=AGGCTCTGCCTACAGGGGCA;RSEQ=TGCAATGTATCTCTGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:29.5:1:27.9:1:1:0:42.5:5.333:1:0:2.2 0/1:30:2:1,1:14,14:0.0667:2,2:19.5:1:30:1:1:1:60:4:0.069:0:5.5 -GL000225.1 85704 . T A 86 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13277;SOR=4.10314;LSEQ=GGGGCATTGCAATGTATCTC;RSEQ=GCACTGATCACCTAGGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:34.5:1:30.5:1:1:1.12:22:4:0.1111:0:6 0/1:21:7:3,4:6,8:0.3333:2,2:13.7:1:30.7:1:1:1:57.9:14:0.3333:0:3.7 -GL000225.1 85705 . G A 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21923;SOR=0;LSEQ=GGGCATTGCAATGTATCTCT;RSEQ=CACTGATCACCTAGGTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:0.1053:2,2:14:1:25:1:1:1.12:53.5:4:0.1053:0:2.5 0/0:21:0:0,0:9,12:0:2,0:16.7:1:32:1:1:0:46.2:42:1:0:2.5 -GL000225.1 85723 . AG TT 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=CTGCACTGATCACCTAGGTC;RSEQ=GTAACTCTTGTCTAGGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22:1:29:1:1:1:22:4:0.5:0:5 1/0:3:2:0,2:1,0:0.6667:0,0:20:1:32:0:0.33333:0:46.5:4:0.6667:0:5.5 -GL000225.1 85734 . G T 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCTAGGTCAGGTAACTCTT;RSEQ=TCTAGGCTCTGCCTACAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:12:1:29:1:1:1:22:4:0.5:0:5 1/1:1:1:0,1:0,0:1:0,0:21:0:32:0:1:0:46:2:1:0:7 -GL000225.1 86554 . A T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCAACTCTTGTCTAGG;RSEQ=TCTGCCTACAGGGGGTATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,1:0.4:2,2:5.5:1:30:1:1:1:27:4:0.4:0:2 -GL000225.1 86567 . G C 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTAGGATCTGCCTACAGG;RSEQ=GGTATTGTGAAATATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:31:0:30:1:1:0:43:4:0.5:0:8 -GL000225.1 86573 . T A 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATCTGCCTACAGGGGGTAT;RSEQ=GTGAAATATCTCTGCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:37:0:28.5:1:1:0:43:4:0.5:0:8 -GL000225.1 86576 . G T 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTACAGGGGGTATTGT;RSEQ=AAATATCTCTGCACTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:40:0:28:1:1:0:43:4:0.5:0:8 -GL000225.1 86590 . C A 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTGTGAAATATCTCTGCA;RSEQ=TGATCAACTAGGTGATGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:44:0:30.5:1:1:0:43:4:0.5:0:8 -GL000225.1 86603 . T G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCACTGATCAACTAGG;RSEQ=GATGTAACTCTTGTCTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:31:0:32:1:1:0:43:4:0.6667:0:8 -GL000225.1 86605 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCACTGATCAACTAGGTG;RSEQ=TGTAACTCTTGTCTAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:29:0:30.5:1:1:0:43:4:0.6667:0:8 -GL000225.1 86610 . A G 34 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGATCAACTAGGTGATGTA;RSEQ=CTCTTGTCTAGGCTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:24:0:34:0:1:0:43:4:0.6667:0:8 -GL000225.1 88948 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGGTGGAAAGGCATGAGAG;RSEQ=TCTGCCTGGGCTGTTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:24:0:30:1:1:0:60:4:0.6667:0:5 0/0:1:0:0,0:0,1:0:0,0:14:0:34:0:1:0:22:2:1:0:1 -GL000225.1 89002 . G T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCCGCCTACCCGCACGTGC;RSEQ=CAGTAGGCGGCCCACTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:1:0:30:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:28.5:1:31.5:1:1:0:60:4:1:0:1.5 -GL000225.1 89232 . C A 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCTGCCCCGACCCGACC;RSEQ=CGTCCCAACCCAGAGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:17:0:32:0:1:0:58:4:0.6667:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 89234 . G A 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CCCTGCCCCGACCCGACCCC;RSEQ=TCCCAACCCAGAGAGATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:18.3:1:31.7:1:1:0:58.7:6:1:0:3 0/0:1:0:0,0:0,1:0:0,0:1:0:29:0:1:0:60:2:1:0:8 -GL000225.1 89249 . GA CC 49 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCCCGTCCCAACCCAGAGA;RSEQ=TAAATCTCTTCCTGCAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:16.7:1:31.1:1:1:0:58.7:6:1:0.6667:2.7 1/1:1:1:0,1:0,0:1:0,0:17:0:33.5:0:1:0:60:2:1:0:7 -GL000225.1 89401 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCGGGCTCGCCAGGAGCTCA;RSEQ=CCATCAGCAGGACGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:44:0:33:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:17:0:31.5:1:1:0:60:4:1:0:4.5 -GL000225.1 89403 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGCTCGCCAGGAGCTCACC;RSEQ=ATCAGCAGGACGGAGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:46:0:35:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:19:0:32:0:1:0:60:4:1:0:4.5 -GL000225.1 89405 . T G 34 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTCGCCAGGAGCTCACCCA;RSEQ=CAGCAGGACGGAGGGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:48:0:30:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:21:0:34:0:1:0:60:4:1:0:4.5 -GL000225.1 89413 . A T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAGCTCACCCATCAGCAGG;RSEQ=CGGAGGGGAGTGCAGAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:45:0:31:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:1:0,2:21.5:1:31.5:1:1:0:60:4:1:0:4.5 -GL000225.1 89522 . T G 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAGGAGCACGGGCTGGC;RSEQ=AGGTGGATCTGCCCCGGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:28.5:1:1:0:60:4:1:0:4 -GL000225.1 89538 . G A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTAGGTGGATCTGCCCC;RSEQ=GCTTGTGGTTCCCACGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:19.5:1:28.5:1:1:0:60:4:1:0:4 -GL000225.1 89772 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTGAGGGTGGGAGAGTGC;RSEQ=GCTTCTGGAAGAGCCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:46:0:32:0:1:0:40:2:1:0:8 1/0:3:2:1,1:1,0:0.6667:0,2:25.5:1:29.5:1:1:0:60:4:0.6667:0:4.5 -GL000225.1 89787 . C T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=AGTGCCGCTTCTGGAAGAGC;RSEQ=GGGGCAGCGTAGGCAAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:11:1:31:1:1:0:49.8:8:1:0:6.3 0/1:8:2:1,1:3,3:0.25:2,2:8.5:1:29.5:1:1:1:50.5:4:0.25:0:5.5 -GL000225.1 89792 . CA TG 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=CGCTTCTGGAAGAGCCGGGG;RSEQ=GCGTAGGCAAAATCCCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:13.5:1:32.3:1:1:0:49.8:8:1:0:6.3 0/1:8:2:1,1:3,3:0.25:2,2:46.5:1:31:1:1:1:60:4:0.25:0:3.5 -GL000225.1 89801 . C A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=AAGAGCCGGGGCAGCGTAGG;RSEQ=AAAATCCCTGCGTGCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:0.3333:2,2:11.5:1:29:1:1:1:42.5:4:0.3333:0:6.5 0/0:8:0:0,0:4,4:0:2,0:19.4:1:33.3:1:1:0:41.1:16:1:0:2.5 -GL000225.1 89804 . A G 33 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGCCGGGGCAGCGTAGGCAA;RSEQ=ATCCCTGCGTGCCAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:22:0:33:1:1:1:57:4:0.3333:0:5 0/1:6:2:1,1:2,2:0.3333:2,2:6:0:33.5:1:1:1:33:4:0.3333:0:1 -GL000225.1 89810 . T C 61 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=GGCAGCGTAGGCAAAATCCC;RSEQ=GCGTGCCAGGGCAGGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:21.3:1:30.8:1:1:1:49.8:8:0.6667:0:5.8 1/0:4:2:1,1:0,0:0.5:0,2:34:0:31.5:1:1:0:60:4:0.5:0:3.5 -GL000225.1 89813 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AGCGTAGGCAAAATCCCTGC;RSEQ=TGCCAGGGCAGGTTGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:19:0:32:0:1:1:57:4:0.3333:0:5 0/0:4:0:0,0:2,2:0:2,0:31.3:1:30.8:1:1:0:55.3:8:1:0:4 -GL000225.1 89815 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CGTAGGCAAAATCCCTGCGT;RSEQ=CCAGGGCAGGTTGGGAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:0.3333:2,2:25.5:1:30:1:1:1:42.5:4:0.3333:0:6.5 0/0:4:0:0,0:2,2:0:2,0:30.3:1:33:1:1:0:55.3:8:1:0:4 -GL000225.1 89817 . CA TG 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TAGGCAAAATCCCTGCGTGC;RSEQ=GGGCAGGTTGGGAGATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:14:0:32.5:1:1:1:57:4:0.4:0:4 0/0:4:0:0,0:2,2:0:2,0:28.5:1:31.8:1:1:0:55.3:8:1:0:4 -GL000225.1 89818 . A T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AGGCAAAATCCCTGCGTGCC;RSEQ=GGGCAGGTTGGGAGATCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,1:0:2,0:28.5:1:29.5:1:1:0:42.5:4:0.6667:0:6.5 1/0:4:2:1,1:1,1:0.5:2,2:29:0:30:1:1:1:50.5:4:0.5:0:4.5 -GL000225.1 89837 . C A 28 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CAGGGCAGGTTGGGAGATCC;RSEQ=CTCTGCCGGTGCAGCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:29.3:1:31.3:1:1:0:41.7:6:1:0:6.3 1/0:4:2:1,1:1,1:0.5:2,2:10:0:28.5:1:1:1:50.5:4:0.5:0:4.5 -GL000225.1 89842 . G A 29 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CAGGTTGGGAGATCCCCTCT;RSEQ=CCGGTGCAGCCTGGCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:17:0:29.5:1:1:0:42.5:4:0.6667:0:6.5 0/0:4:0:0,0:2,2:0:2,0:3.5:1:31.8:1:1:0:55.3:8:1:0:4 -GL000225.1 89847 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAGATCCCCTCTGCCGG;RSEQ=GCAGCCTGGCTGGGCTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:12:0:32:1:1:0:42.5:4:0.6667:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 89850 . A T 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATCCCCTCTGCCGGTGC;RSEQ=GCCTGGCTGGGCTGGAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:17.7:1:31.3:1:1:0:41.7:6:1:0:6.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 89966 . T C 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AGGAAGCCCCATTCCCCAAG;RSEQ=GCCGGTGTTGGCGATGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:31:1:1:0:60:4:1:0:4.5 0/1:3:1:0,1:1,1:0.3333:2,0:29:0:32:0:1:0:45:2:0.3333:0:7 -GL000225.1 89979 . G T 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.33333;SOR=0;LSEQ=CCCCAAGTGCCGGTGTTGGC;RSEQ=ATGGCGACCCACGAGGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:44.5:1:30:1:1:0:60:4:1:0:4.5 0/0:2:0:0,0:0,1:0:0,0:11:0:32:0:1:0:60:2:0.5:0:0 -GL000225.1 90022 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGACACCCGCCAGGGACC;RSEQ=CGATACACCGGCCGCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:8:0:31.5:1:1:0:60:4:1:0:4.5 1/1:1:1:1,0:0,0:1:0,0:14:0:32:0:1:0:60:2:1:0:8 -GL000225.1 90025 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACCCGCCAGGGACCGCG;RSEQ=TACACCGGCCGCCTGCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5:0:31.5:1:1:0:60:4:1:0:4.5 1/1:1:1:1,0:0,0:1:0,0:17:0:32:0:1:0:60:2:1:0:8 -GL000225.1 90070 . G T 29 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACCCTGCCAGCCTTCCCC;RSEQ=GGTGCCTGGCTCTTTGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:43:0:34:0:1:0:60:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:27:1:29:1:1:0:60:4:1:0:5.5 -GL000225.1 90080 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCTTCCCCGGGTGCCTGG;RSEQ=TCTTTGATTCTGAAACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:48:0:31:0:1:0:60:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:27:1:28.5:1:1:0:60:4:1:0:5.5 -GL000225.1 90119 . G GGA 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCTGAATCCTGGACTCCG;RSEQ=GAGGCCCGTCTCTCTGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:9:0:33:0:1:0:60:2:1:0:6 1/0:3:2:1,1:0,1:0.6667:0,2:38.5:1:31:1:1:0:31:4:0.6667:0:1.5 -GL000225.1 90126 . C G 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCCTGGACTCCGGGAGGCC;RSEQ=GTCTCTCTGGCCAGCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:2:0:29:0:1:0:60:2:1:0:6 1/0:3:2:1,1:0,1:0.6667:0,2:35:0:30:1:1:0:31:4:0.6667:0:1.5 -GL000225.1 90276 . TTCC T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGGTCCAGGGCCGAGA;RSEQ=CACTGGTGCTCCCTCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:32:1:1:0:60:4:1:0:1.5 -GL000225.1 90495 . G A 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GCTTCCGCAGGGAGGGTGCC;RSEQ=TCCGAAGGTGTCGGGAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:0:31.5:1:1:0:54.5:4:1:0:2 0/0:3:0:0,0:1,2:0:2,0:12.3:1:28:1:1:0:59.7:6:1:0:4 -GL000225.1 90498 . C T 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TCCGCAGGGAGGGTGCCGTC;RSEQ=GAAGGTGTCGGGAGGGTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:0:31.5:1:1:0:54.5:4:1:0:2 0/0:3:0:0,0:1,2:0:2,0:13.3:1:28.7:1:1:0:59.7:6:1:0:4 -GL000225.1 90499 . G A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CCGCAGGGAGGGTGCCGTCC;RSEQ=AAGGTGTCGGGAGGGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13:0:32:1:1:0:54.5:4:1:0:2 1/0:3:2:1,1:0,1:0.6667:0,2:5.5:1:27.5:1:1:0:60:4:0.6667:0:2.5 -GL000225.1 90519 . C T 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAGGTGTCGGGAGGGTCAT;RSEQ=GCGGGGAGCCCCGTCCGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:25.5:1:29.5:1:1:0:60:4:0.6667:0:2.5 -GL000225.1 90879 . T C 65 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGTTTTGGGAGCTGGCTCT;RSEQ=CGGACCTCTCAAGGAATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:4,0:0,0:1:0,0:8.8:1:32.8:1:1:0:37:8:1:0:6.3 -GL000225.1 90885 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGAGCTGGCTCTTCGGAC;RSEQ=TCTCAAGGAATCCCGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:3,0:0.4:0,2:10.5:1:29.5:1:0.4:0:50:4:0.4:0:6.5 -GL000225.1 90890 . A C 70 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGCTCTTCGGACCTCTC;RSEQ=AGGAATCCCGTGGGAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:4,1:0,0:1:0,2:17.8:1:30.2:1:1:0:41.6:10:1:0:6.2 -GL000225.1 90896 . T A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTCGGACCTCTCAAGGAA;RSEQ=CCCGTGGGAACTGGAAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:5.5:1:28.5:1:1:0:45:4:1:0:6.5 0/1:6:2:1,1:3,1:0.3333:2,2:21.5:1:28.5:1:1:2.44949:50:4:0.3333:0:6.5 -GL000225.1 90900 . GT TC 53 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CGGACCTCTCAAGGAATCCC;RSEQ=GGGAACTGGAAGCCACTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:28.8:1:1:0:45:4:1:0:5.5 1/0:8:4:2,2:2,2:0.5:2,2:17.3:1:26.5:1:1:1:32.5:8:0.5:0.25:5.3 -GL000225.1 90907 . C A 57 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CTCAAGGAATCCCGTGGGAA;RSEQ=TGGAAGCCACTCTCTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:29.5:1:1:0:45:4:1:0:5.5 1/0:8:4:2,2:2,2:0.5:2,2:20.8:1:28.5:1:1:1:32.5:8:0.5:0:5.3 -GL000225.1 90916 . A G 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=2.04824;LSEQ=TCCCGTGGGAACTGGAAGCC;RSEQ=CTCTCTGGGCTCCCACGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:3,2:0.1667:2,0:2:0:29:0:1:0:21:2:0.1667:0:8 0/1:10:3:2,1:3,3:0.3:2,2:21:1:29.7:1:1:1.85:53:6:0.3333:0:5.3 -GL000225.1 90918 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.47712;SOR=Inf;LSEQ=CCGTGGGAACTGGAAGCCAC;RSEQ=CTCTGGGCTCCCACGCGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:0:2,0:9.6:1:30:1:1:0:42:16:1:0:5.8 0/1:10:2:1,1:4,4:0.2:2,2:29.5:1:30.5:1:1:1:51.5:4:0.2222:0:5 -GL000225.1 90933 . G T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21739;SOR=Inf;LSEQ=GCCACTCTCTGGGCTCCCAC;RSEQ=CGTCTTCAGCAGGGAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,6:0:2,0:19.5:1:29.5:1:1:0:40.5:22:1:0:5 0/1:11:2:1,1:4,5:0.1818:2,2:16:1:27.5:1:1:1.22:57.5:4:0.2:0:5.5 -GL000225.1 90934 . C T 42 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59006;SOR=0.31536;LSEQ=CCACTCTCTGGGCTCCCACG;RSEQ=GTCTTCAGCAGGGAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:4,3:0.25:2,2:11.7:1:27:1:1:2.41422:43.3:6:0.25:0:6.3 0/1:11:1:0,1:5,5:0.0909:2,0:25:0:30:0:1:0:24:2:0.0909:0:7 -GL000225.1 90935 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=CACTCTCTGGGCTCCCACGC;RSEQ=TCTTCAGCAGGGAGAAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:4,6:0.1667:2,0:22.5:1:31.5:1:0.45455:0:40.5:4:0.1818:0:3.5 0/0:11:0:0,0:5,6:0:2,0:28.1:1:28.5:1:1:0:42.9:10:1:0:5.6 -GL000225.1 90941 . A T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21739;SOR=Inf;LSEQ=CTGGGCTCCCACGCGTCTTC;RSEQ=GCAGGGAGAAGCCGGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:26.9:1:28.9:1:1:0:38.8:11:1:0:5.2 0/1:11:2:1,1:3,4:0.1818:2,2:27.5:1:31.5:1:1:1.29:50:4:0.1818:0:6.5 -GL000225.1 90942 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21739;SOR=Inf;LSEQ=TGGGCTCCCACGCGTCTTCA;RSEQ=CAGGGAGAAGCCGGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:27.6:1:31.3:1:1:0:38.8:24:1:0:5.2 0/1:11:2:1,1:4,5:0.1818:2,2:25:1:28.5:1:1:1.22:57.5:4:0.1818:0:5.5 -GL000225.1 90946 . G A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21739;SOR=Inf;LSEQ=CTCCCACGCGTCTTCAGCAG;RSEQ=GAGAAGCCGGCCTGGGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:0:2,0:30.3:1:29.5:1:1:0:38.8:11:1:0:5.2 0/1:11:2:1,1:4,5:0.1818:2,2:22.5:1:31.5:1:1:1.22:50:4:0.1818:0:6.5 -GL000225.1 90952 . G A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15495;SOR=0.17231;LSEQ=CGCGTCTTCAGCAGGGAGAA;RSEQ=CCGGCCTGGGAGGGTGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:5,6:1,0:0.9167:0,2:34.1:1:28.1:1:1:0:37.5:10:0.9091:0:5.3 1/0:11:7:3,4:0,0:0.6364:0,2:26.4:1:27.1:1:1:0:36.3:14:0.6364:0:5.9 -GL000225.1 90965 . G T 61 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20644;SOR=3.42921;LSEQ=GGGAGAAGCCGGCCTGGGAG;RSEQ=GTGGAGGGGAGTGTGGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:4,7:0.1875:2,2:31.7:1:30.7:1:0.53846:3.19:48:6:0.2:0:5 0/1:11:5:1,4:2,4:0.4545:2,2:20:1:26.6:1:1:1.87936:44.2:4:0.4:0:5.2 -GL000225.1 90966 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=GGAGAAGCCGGCCTGGGAGG;RSEQ=TGGAGGGGAGTGTGGAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,8:0.1176:2,2:31:1:31:1:1:1.31:21:4:0.125:0:6 0/0:11:0:0,0:3,8:0:2,0:24.7:1:30.3:1:1:0:44.4:22:1:0:4.8 -GL000225.1 90969 . G C 62 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13236;SOR=0;LSEQ=GAAGCCGGCCTGGGAGGGTG;RSEQ=AGGGGAGTGTGGAACTGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:1,3:6,7:0.2353:2,2:38.8:1:31.3:1:0.60294:2.43937:22:8:0.2353:0:4.5 0/0:11:0:0,0:3,8:0:2,0:23.9:1:29.9:1:1:0:44.4:10:1:0:4.8 -GL000225.1 90971 . GG AA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=AGCCGGCCTGGGAGGGTGGA;RSEQ=GGAGTGTGGAACTGAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:15.5:1:30.3:1:1:1.46:39:4:0.125:0:2.5 0/0:11:0:0,0:3,8:0:2,0:23.6:1:30.2:1:1:0:45.7:10:1:0:4.7 -GL000225.1 90972 . G T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1455;SOR=Inf;LSEQ=GCCGGCCTGGGAGGGTGGAG;RSEQ=GGAGTGTGGAACTGAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:6,9:0:2,0:34.3:1:29.1:1:1:0:36.5:6.5:1:0:4.8 0/1:11:2:1,1:2,6:0.1818:2,2:45.5:1:30.5:1:1:2.65:57.5:4:0.1818:0:4.5 -GL000225.1 90973 . G C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.63544;LSEQ=CCGGCCTGGGAGGGTGGAGG;RSEQ=GAGTGTGGAACTGAACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,8:0.1176:2,2:15:0:32.5:1:1:1.31:45:4:0.1333:0:5.5 0/1:11:2:0,2:2,5:0.1818:2,0:24:0:31:1:1:0:32.5:4:0.1818:0:5 -GL000225.1 90976 . GT CA 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50345;SOR=0;LSEQ=GCCTGGGAGGGTGGAGGGGA;RSEQ=GTGGAACTGAACCTCCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,9:0.1111:2,2:35:0:32.8:1:1:1.46:42:4:0.1111:0:4.5 0/0:12:0:0,0:4,7:0:2,0:19.5:1:32.3:1:1:0:45.4:22:1:0:4.5 -GL000225.1 90977 . T A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15172;SOR=Inf;LSEQ=CCTGGGAGGGTGGAGGGGAG;RSEQ=GTGGAACTGAACCTCCGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,10:0:2,0:28:1:30.3:1:1:0:36.3:32:1:0:4.6 0/1:12:2:1,1:3,7:0.1667:2,2:20.5:1:30.5:1:1:2.16:37.5:4:0.1667:0:6.5 -GL000225.1 90989 . C T 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49754;SOR=0;LSEQ=GAGGGGAGTGTGGAACTGAA;RSEQ=CTCCGTGGGAGTCTTGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:27:0:32.5:1:1:1.46:49:4:0.125:0:6 0/0:12:0:0,0:4,8:0:2,0:17.6:1:30.6:1:1:0:41.9:11:1:0:4.6 -GL000225.1 90994 . G C 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47868;LSEQ=GAGTGTGGAACTGAACCTCC;RSEQ=TGGGAGTCTTGAGTGTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:22:0:33.5:1:1:1.46:49:4:0.125:0:6 0/1:12:2:1,1:3,7:0.1667:2,2:24.5:1:33:1:1:2.16:40:4:0.1667:0:4 -GL000225.1 91000 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11077;SOR=Inf;LSEQ=GGAACTGAACCTCCGTGGGA;RSEQ=TCTTGAGTGTTCCAGGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:0:2,0:22.4:1:32.6:1:1:0:35.2:34:1:0:4.7 0/1:9:2:1,1:3,4:0.2222:2,2:14:0:32:0:1:1.29:34:4:0.2222:0:2.5 -GL000225.1 91002 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52923;SOR=0;LSEQ=AACTGAACCTCCGTGGGAGT;RSEQ=TTGAGTGTTCCAGGCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:22:1:30.5:1:1:1.46:47:4:0.125:0:6 0/0:9:0:0,0:4,5:0:2,0:19.6:1:32.6:1:1:0:42:18:1:0:4.4 -GL000225.1 91003 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52923;SOR=0;LSEQ=ACTGAACCTCCGTGGGAGTC;RSEQ=TGAGTGTTCCAGGCCCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:13:0:32.5:1:1:1.46:49:4:0.125:0:6 0/0:9:0:0,0:4,5:0:2,0:19.4:1:31.3:1:1:0:42:18:1:0:4.4 -GL000225.1 91004 . T G 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52923;SOR=0;LSEQ=CTGAACCTCCGTGGGAGTCT;RSEQ=GAGTGTTCCAGGCCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:7,7:0.1765:2,0:24.3:1:31.7:1:0.22794:0:34:6:0.1765:0:4.7 0/0:9:0:0,0:4,5:0:2,0:19.3:1:30.3:1:1:0:42:18:1:0:4.4 -GL000225.1 91005 . G C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52923;SOR=0;LSEQ=TGAACCTCCGTGGGAGTCTT;RSEQ=AGTGTTCCAGGCCCTCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:27:1:30.5:1:1:1.46:27:4:0.1176:0:2.5 0/0:9:0:0,0:4,5:0:2,0:19.2:1:32.4:1:1:0:42:18:1:0:4.4 -GL000225.1 91008 . T A 68 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12855;SOR=0;LSEQ=ACCTCCGTGGGAGTCTTGAG;RSEQ=GTTCCAGGCCCTCTCCGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:3,2:4,8:0.2941:2,2:24.2:1:29.6:1:0.59276:2.80:32:10:0.3125:0:6.4 0/0:9:0:0,0:4,5:0:2,0:18.9:1:30:1:1:0:42:18:1:0:4.4 -GL000225.1 91009 . G C 41 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52923;SOR=0;LSEQ=CCTCCGTGGGAGTCTTGAGT;RSEQ=TTCCAGGCCCTCTCCGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:6,8:0.1765:2,2:19.3:1:26.3:1:1:1.46561:43.7:2:0.125:0:5 0/0:9:0:0,0:4,5:0:2,0:18.8:1:31.4:1:1:0:42:18:1:0:4.4 -GL000225.1 91018 . C CCT 51 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.25824;SOR=0;LSEQ=GAGTCTTGAGTGTTCCAGGC;RSEQ=CTCTCCGTGAAGGAGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:2,2:0.3333:2,0:39.3:1:32.8:1:0.42857:0:33.3:6:0.4286:0.1111:4.3 0/0:5:0:0,0:1,2:0:2,0:28:1:30.3:1:1:0:50:6:0.6:0:5 -GL000225.1 91019 . C CGG 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10989;SOR=Inf;LSEQ=AGTCTTGAGTGTTCCAGGCC;RSEQ=TCTCCGTGAAGGAGGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,6:0:2,0:21.3:1:31.3:1:1:0:30.3:7:1:0:4.4 0/1:5:2:1,1:1,1:0.4:2,2:41:1:29.8:1:1:1:45.5:4:0.5:0:5.5 -GL000225.1 91028 . A G 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=TGTTCCAGGCCCTCTCCGTG;RSEQ=AGGAGGCAGTGCCTGTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:32.8:1:31.2:1:1:0:29:10:1:0:5.2 1/0:4:2:1,1:1,1:0.5:2,2:41:1:31:1:1:1:45.5:4:0.5:0:5.5 -GL000225.1 91034 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AGGCCCTCTCCGTGAAGGAG;RSEQ=CAGTGCCTGTGGGTGTCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:28.6:1:29:1:1:0:29:4:1:0:5.2 1/0:4:2:1,1:1,1:0.5:2,2:41:1:30:1:1:1:45.5:4:0.5:0:5.5 -GL000225.1 91054 . T C 31 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GCAGTGCCTGTGGGTGTCGC;RSEQ=GTTGCCGGGACAATCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:23.5:1:30:1:1:0:32:4:1:0:7.5 1/0:4:2:1,1:1,1:0.5:2,2:21:1:31.5:1:1:1:45.5:4:0.5:0:5.5 -GL000225.1 91067 . A G 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCGCTGTTGCCGGGACA;RSEQ=TCTCACACACGCAGCCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10.5:1:30.5:1:1:0:32:4:1:0:7.5 1/1:4:4:3,1:0,0:1:0,2:8.8:1:32.8:1:1:0:33.3:8:1:0:5.5 -GL000225.1 91165 . A G 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGGCGTGATGGCCTGAC;RSEQ=TTGGATTCCCGTGTGCGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:28.5:1:1:0:42.5:4:1:0:4.5 -GL000225.1 91187 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATTCCCGTGTGCGGCAA;RSEQ=ATGGGGAGTCTGCAGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:13:0:34:0:1:0:24:2:1:0:6 1/1:2:2:1,1:0,0:1:0,2:47.5:1:32:1:1:0:42.5:4:1:0:4.5 -GL000225.1 91210 . G A 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GGGGAGTCTGCAGTGTGGCC;RSEQ=GTTTGGAAACTGGCAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:20.5:1:31.5:1:1:0:42:4:1:0:3.5 1/1:3:3:1,2:0,0:1:0,2:22.7:1:29.3:1:1:0:41.7:6:1:0:5 -GL000225.1 91248 . A G 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAGAGCAAAGGCACCATGCC;RSEQ=GTCTTCCACCCTTCCCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:0.5:0,0:27:0:33:0:1:0:24:2:0.5:0:6 1/1:3:3:1,2:0,0:1:0,2:35:1:30.7:1:1:0:53.3:6:1:0:4.3 -GL000225.1 91250 . T C 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAGCAAAGGCACCATGCCAG;RSEQ=CTTCCACCCTTCCCTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35:1:32:0:1:0:42:4:1:0:3.5 1/0:3:2:1,1:0,1:0.6667:0,2:25.5:1:33:0:1:0:60:4:0.6667:0:3.5 -GL000225.1 91259 . C T 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CACCATGCCAGTCTTCCACC;RSEQ=TTCCCTGCATGTTTCCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:47:0:33:0:1:0:60:2:0.5:0:1 1/0:3:2:1,1:0,1:0.6667:0,2:16.5:1:31.5:1:1:0:60:4:0.6667:0:3.5 -GL000225.1 91441 . T G 50 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GTCTAGACTCTGCCTATGGG;RSEQ=GCATTGTGAGATATCTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:12.3:1:32:1:1:0:48.7:6:1:0:3 0/0:1:0:0,0:1,0:0:0,0:33:0:32:0:1:0:60:2:1:0:0 -GL000225.1 91485 . T A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GATCAACCAGGTGATGTAAC;RSEQ=CTTGTGTTGGATCAGCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:30:1:1:0:26:4:1:0:4.5 0/0:1:0:0,0:1,0:0:0,0:24:0:33:0:1:0:60:2:1:0:0 -GL000225.1 92344 . C G 34 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGTGACATATCTCTGCA;RSEQ=TGATCTCCCAGGTACTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:20:1:34:0:1:0:60:4:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92358 . A G 33 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCACTGATCTCCCAGGT;RSEQ=CTGTAACTTTAGTCTAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:1:33.5:1:1:0:60:4:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92360 . T C 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACTGATCTCCCAGGTAC;RSEQ=GTAACTTTAGTCTAGGTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:36:1:32:0:1:0:60:4:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92370 . G T 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAGGTACTGTAACTTTA;RSEQ=TCTAGGTTCTGGCTACACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:46:1:31.5:1:1:0:60:4:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92380 . T C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAACTTTAGTCTAGGTTC;RSEQ=GGCTACACGGCATTGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45:1:31:1:1:0:60:4:1:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92386 . C A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGTCTAGGTTCTGGCTA;RSEQ=ACGGCATTGTGACATATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:39:1:30:1:1:0:60:4:0.6667:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92389 . G A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTAGGTTCTGGCTACAC;RSEQ=GCATTGTGACATATCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:36:1:30:1:1:0:60:4:0.6667:0:8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92419 . C T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATCTCTGCACTGATCAC;RSEQ=CAGGTGATATATCTCTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:20.5:1:29.5:1:1:1:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92435 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCACCCAGGTGATATATCTC;RSEQ=CTTCTAGGATCTGCCTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92718 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGTACCACTTGTCAAGG;RSEQ=TCTGCCTACAGGGACATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:33.5:1:1:0:41:4:1:0:4.5 -GL000225.1 92744 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACAGGGACATTGCGATGT;RSEQ=TCTCTGCACTGATCACCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:0:32.5:1:1:0:41:4:1:0:4.5 -GL000225.1 92757 . T C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGATGTATCTCTGCACTGA;RSEQ=CACCTAGGTCATGTAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31:1:1:0:41:4:1:0:4.5 -GL000225.1 92766 . T A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCACTGATCACCTAGG;RSEQ=CATGTAACCCTTGTCTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20.5:1:28.5:1:1:0:41:4:1:0:4.5 -GL000225.1 92819 . T C 34 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCATTGTGACATGTCTCTG;RSEQ=ACTGATCATCCAAGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:34:0:1:0:20:4:1:0:4 1/1:1:1:1,0:0,0:1:0,0:4:0:33:0:1:0:52:2:1:0:4 -GL000225.1 92823 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTGACATGTCTCTGTACT;RSEQ=ATCATCCAAGTGATGTAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:30.5:1:1:0:20:4:1:0:4 1/1:1:1:1,0:0,0:1:0,0:8:0:29:0:1:0:52:2:1:0:4 -GL000225.1 92847 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCAAGTGATGTAACTCTT;RSEQ=TCTAGGATCTGCCTAAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17:0:33.5:1:1:0:20:4:1:0:4 1/1:1:1:1,0:0,0:1:0,0:18:0:33:0:1:0:52:2:1:0:4 -GL000225.1 92856 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTAACTCTTATCTAGGAT;RSEQ=TGCCTAAAGGGACTTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:8:0:33.5:1:1:1:20:4:0.5:0:4 1/1:1:1:1,0:0,0:1:0,0:9:0:32:0:1:0:52:2:1:0:4 -GL000225.1 92866 . GG TA 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTAGGATCTGCCTAAAG;RSEQ=ACTTTGTGACATAACTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15.5:1:30.8:1:1:0:44.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92883 . T C 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGACTTTGTGACATAAC;RSEQ=CTGCACTGATCATCCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:32.5:1:1:0:44.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92887 . C T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTTGTGACATAACTCTG;RSEQ=ACTGATCATCCAGGTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:30.5:1:1:0:44.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 92907 . A C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGATCATCCAGGTGATG;RSEQ=GGCTTTTGTCTAGGCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:45.5:1:31.5:1:1:0:44.5:4:1:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 130941 . CCCAAAG TCCAAC 32 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACTCTTGTCTACCCTCTG;RSEQ=GGGGCATTGTGAAATATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:32.1:1:1:0:22:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 130973 . T A 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTGAAATATCTCTGCAC;RSEQ=AATCACCCAGGTGATTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:41:1:30:1:1:0:22:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 130975 . A T 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAAATATCTCTGCACTA;RSEQ=TCACCCAGGTGATTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:40.5:1:30:1:1:0:22:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 130999 . T A 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGTGATTCAACTCTTG;RSEQ=CTAGGATTTGCCTACAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:28.5:1:1:0:22:4:1:0:7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 131006 . TT AC 30 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCAACTCTTGTCTAGGA;RSEQ=TGCCTACAGGGGTTATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11.5:1:30.8:1:1:0:22:4:1:0.5:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 131540 . T A 74 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGATCACCCAAGTGATGTA;RSEQ=CCATTGTCCAGGCTTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1:0,2:18.6:1:32:0:1:0:45.2:10:1:0:5.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 131549 . C T 71 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGTGATGTATCCATTGTC;RSEQ=AGGCTTTGCCTACAGGGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:1,1:0.7143:2,2:20.4:1:30.8:1:1:1.41:37.6:10:0.7143:0:6 1/1:1:1:1,0:0,0:1:0,0:2:0:32:0:1:0:41:2:1:0:8 -GL000225.1 131559 . C G 72 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCCATTGTCCAGGCTTTGC;RSEQ=TACAGGGGTCTTTGTGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:0,0:0.7143:0,2:37.6:1:31.2:1:1:0:45.2:10:0.7143:0:5.6 1/1:1:1:1,0:0,0:1:0,0:12:0:14:0:1:0:41:0:0:0:8 -GL000225.1 131567 . GT G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGCTTTGCCTACAGGG;RSEQ=CTTTGTGACATAGCTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:0,0:0.2857:0,2:48:1:32.5:1:1:0:45:4:0.2857:0:5.5 0/0:1:0:0,0:1,0:0:0,0:21:0:26:0:1:0:41:2:1:0:8 -GL000225.1 131568 . T G 76 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=CCAGGCTTTGCCTACAGGGG;RSEQ=CTTTGTGACATAGCTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:0,0:0.7143:0,2:37.2:1:32.8:1:1:0:38.8:10:0.7143:0:5.8 0/0:1:0:0,0:1,0:0:0,0:21:0:26:0:1:0:41:2:1:0:8 -GL000225.1 131571 . T C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTTTGCCTACAGGGGTCT;RSEQ=TGTGACATAGCTTTGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:29:0:33:0:1:1.41418:29:4:0.2857:0:6 0/0:1:0:0,0:1,0:0:0,0:24:0:28:0:1:0:41:2:1:0:8 -GL000225.1 131575 . G C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCCTACAGGGGTCTTTGT;RSEQ=ACATAGCTTTGCACTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:33:0:33:0:1:1.41418:29:4:0.3333:0:6 0/0:1:0:0,0:1,0:0:0,0:28:0:18:0:1:0:41:0:0:0:8 -GL000225.1 131581 . G C 72 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGGGGTCTTTGTGACATA;RSEQ=CTTTGCACTGATCACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:1,1:0.7143:2,2:39.2:1:31.4:1:1:1.41:45.2:10:0.7143:0:5.6 1/1:1:1:1,0:0,0:1:0,0:34:0:28:0:1:0:41:2:1:0:8 -GL000225.1 131600 . G A 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTTGCACTGATCACCCA;RSEQ=GTGATGTAACACATCTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:9:0:32.5:1:1:1.41418:29:4:0.2857:0:6 0/0:1:0:0,0:1,0:0:0,0:48:0:28:0:1:0:41:2:1:0:8 -GL000225.1 131675 . T A 86 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATCACTTAGGTGATGTA;RSEQ=CACTTTTATAAGCACTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:9:1:30.5:1:1:0:32.5:4:1:0:5 1/1:7:7:7,0:0,0:1:0,0:10.1:1:30.7:1:1:0:41.4:14:1:0:4.9 -GL000225.1 131687 . G T 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11924;LSEQ=GTGATGTATCACTTTTATAA;RSEQ=CACTGCCTACAGGGAATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:3,0:0.5:0,2:9:1:30.3:1:1:0:37.3:6:0.5:0:5.3 1/0:17:9:5,4:4,4:0.5294:2,2:13:1:28.9:1:1:1.23:42.6:18:0.5294:0:3.8 -GL000225.1 131709 . A T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11102;SOR=0;LSEQ=ACTGCCTACAGGGAATTTTG;RSEQ=CAAATCTCTGCACTGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:10,5:0.1176:2,2:35:1:31:1:1:1.91491:23:4:0.1176:0:3.5 0/0:33:0:0,0:17,16:0:2,0:23.2:1:28.5:1:1:0:44.2:66:1:0:3.7 -GL000225.1 131711 . A G 56 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67314;SOR=0.62834;LSEQ=TGCCTACAGGGAATTTTGAC;RSEQ=AATCTCTGCACTGATCACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:3,0:8,6:0.1765:2,0:18.7:1:31.3:1:0.51471:0:43.7:6:0.1765:0:4.7 0/1:34:4:1,3:16,14:0.1176:2,2:30:1:28:1:0.60117:3.31312:33.3:8:0.1176:0:4.5 -GL000225.1 131713 . A G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10692;SOR=0;LSEQ=CCTACAGGGAATTTTGACAA;RSEQ=TCTCTGCACTGATCACCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:11,5:0.1111:2,2:36.5:1:32.5:1:1:2.09766:23:4:0.1111:0:3.5 0/0:36:0:0,0:18,18:0:2,0:24.6:1:28.9:1:1:0:45.4:35:1:0:3.8 -GL000225.1 131716 . T G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11515;SOR=0;LSEQ=ACAGGGAATTTTGACAAATC;RSEQ=CTGCACTGATCACCTAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:12,5:0.1053:2,2:31.5:1:30:1:1:2.28037:51:4:0.1053:0:5 0/0:36:0:0,0:18,18:0:2,0:27.3:1:29.3:1:1:0:45.4:72:1:0:3.8 -GL000225.1 131717 . C G 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=2;SSF=0.15062;SOR=Inf;LSEQ=CAGGGAATTTTGACAAATCT;RSEQ=TGCACTGATCACCTAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:0:2,0:23.7:1:32.6:1:1:0:39.2:40:1:0:3.4 0/1:37:5:3,2:15,17:0.1351:2,2:32.4:1:30.6:1:0.65988:1.68:40:10:0.1351:0:4.8 -GL000225.1 131719 . G A 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15311;SOR=Inf;LSEQ=GGGAATTTTGACAAATCTCT;RSEQ=CACTGATCACCTAGGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:0:2,0:25.5:1:33:1:1:0:39.2:40:1:0:3.4 0/1:38:5:3,2:15,18:0.1316:2,2:33.4:1:28.2:1:0.65251:1.77:40:10:0.1351:0:4.8 -GL000225.1 131721 . A T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11105;SOR=0;LSEQ=GAATTTTGACAAATCTCTGC;RSEQ=CTGATCACCTAGGTGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:12,6:0.1:2,2:32:1:32:1:1:1.92731:35.5:4:0.1:0:4 0/0:39:0:0,0:18,21:0:2,0:28.3:1:29.3:1:1:0:45.8:78:1:0:3.9 -GL000225.1 131729 . C T 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51787;SOR=Inf;LSEQ=ACAAATCTCTGCACTGATCA;RSEQ=CTAGGTGATGTAACTCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:16,10:0:2,0:25.8:1:32.1:1:1:0:40.5:52:1:0:3.8 0/1:41:2:1,1:18,21:0.0488:2,2:17:0:28.5:1:1:1.16:58:4:0.05:0:5.5 -GL000225.1 131732 . A C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51662;SOR=Inf;LSEQ=AATCTCTGCACTGATCACCT;RSEQ=GGTGATGTAACTCTTGTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:16,11:0:2,0:26.6:1:30.1:1:1:0:40.4:54:1:0:3.9 0/1:42:2:1,1:18,22:0.0476:2,2:35.5:1:29.5:1:1:1.22:51:4:0.0488:0:4 -GL000225.1 131736 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51925;SOR=Inf;LSEQ=TCTGCACTGATCACCTAGGT;RSEQ=ATGTAACTCTTGTCTACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:16,11:0:2,0:28.6:1:32.4:1:1:0:40.4:54:1:0:3.9 0/1:43:2:1,1:18,23:0.0465:2,2:35.5:1:28.5:1:1:1.27:51:4:0.0476:0:4 -GL000225.1 131737 . A T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51549;SOR=Inf;LSEQ=CTGCACTGATCACCTAGGTG;RSEQ=TGTAACTCTTGTCTACCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:0:2,0:28.1:1:30.8:1:1:0:40.4:56:1:0:3.9 0/1:43:2:1,1:18,23:0.0465:2,2:30:1:29:1:1:1.27:50:4:0.0465:0:5 -GL000225.1 131744 . T A 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17694;SOR=0;LSEQ=GATCACCTAGGTGATGTAAC;RSEQ=CTTGTCTACCCTCTGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:14,13:0.0645:2,2:16:0:30:0:1:1.07415:53:4:0.0645:0:4.5 0/0:42:0:0,0:17,19:0:2,0:32.7:1:29.8:1:1:0:46.2:72:0.8571:0:4 -GL000225.1 131748 . G T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50457;SOR=Inf;LSEQ=ACCTAGGTGATGTAACTCTT;RSEQ=TCTACCCTCTGCCCAAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:28.7:1:32.4:1:1:0:40.1:62:1:0:4 0/1:42:2:1,1:18,21:0.0476:2,2:31:1:31.5:1:1:1.16:44.5:4:0.0488:0:5.5 -GL000225.1 131750 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50274;SOR=Inf;LSEQ=CTAGGTGATGTAACTCTTGT;RSEQ=TACCCTCTGCCCAAGGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,14:0:2,0:28.1:1:31.8:1:1:0:40.6:60:0.9677:0:4 0/1:41:2:1,1:17,22:0.0488:2,2:29:0:33.5:1:1:1.29:52:4:0.0488:0:5.5 -GL000225.1 131755 . C G 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18192;SOR=0;LSEQ=TGATGTAACTCTTGTCTACC;RSEQ=TCTGCCCAAGGGGGCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:14,13:0.0645:2,2:27:0:29.5:1:1:1.07415:53:4:0.0645:0:4.5 0/0:41:0:0,0:18,23:0:2,0:30.4:1:31.1:1:1:0:45.9:82:1:0:4.1 -GL000225.1 131756 . T C 61 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12644;SOR=Inf;LSEQ=GATGTAACTCTTGTCTACCC;RSEQ=CTGCCCAAGGGGGCATTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:28.9:1:30.8:1:1:0:40.1:62:1:0:4 0/1:40:4:2,2:15,20:0.1:2,2:40.8:1:30.8:1:1:1.32:41.5:8:0.1:0:5.3 -GL000225.1 131759 . GC CT 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50158;SOR=Inf;LSEQ=GTAACTCTTGTCTACCCTCT;RSEQ=CCAAGGGGGCATTGTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:0:2,0:30.6:1:32.4:1:1:0:40.2:58:1:0:4.3 0/1:38:2:1,1:15,21:0.0526:2,2:43.5:1:30.3:1:1:1.39:52:4:0.0526:0:4 -GL000225.1 131760 . C T 150 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.98105;LSEQ=TAACTCTTGTCTACCCTCTG;RSEQ=CCAAGGGGGCATTGTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:26:13,13:2,1:0.8966:2,2:31.9:1:30.3:1:1:1.95415:42.1:52:0.8966:0:4.5 1/1:38:34:14,20:0,0:0.8947:0,2:28.4:1:29.6:1:1:0:45.1:68:0.9444:0:4.1 -GL000225.1 131765 . G C 152 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.89048;LSEQ=CTTGTCTACCCTCTGCCCAA;RSEQ=GGGGCATTGTGAAATATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:24:12,12:2,2:0.8571:2,2:31.3:1:31.3:1:1:1:41.7:48:0.8571:0:4.4 1/1:38:32:13,19:0,0:0.8421:0,2:24.4:1:30.4:1:1:0:45.9:64:0.8421:0:4 -GL000225.1 131771 . A T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49821;SOR=Inf;LSEQ=TACCCTCTGCCCAAGGGGGC;RSEQ=TTGTGAAATATCTCTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:29.5:1:30.1:1:1:0:40.8:56:1:0:4.3 0/1:35:2:1,1:12,21:0.0571:2,2:34:1:30.5:1:1:1.72:51:4:0.0571:0:5 -GL000225.1 131781 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21771;SOR=0;LSEQ=CCAAGGGGGCATTGTGAAAT;RSEQ=TCTCTGCACTGATCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:10,13:0.08:2,2:30:1:32.5:1:1:1.29:40.5:4:0.08:0:5.5 0/0:28:0:0,0:9,17:0:2,0:18.8:1:29.6:1:1:0:49.6:52:0.9286:0:3.7 -GL000225.1 131786 . T A 61 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18819;SOR=0.21298;LSEQ=GGGGCATTGTGAAATATCTC;RSEQ=GCACTGATCACCCAGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:2,2:8,11:0.1739:2,2:29:1:30.8:1:1:1.36:47.5:8:0.1818:0:5.8 0/1:24:1:0,1:8,15:0.0417:2,0:20:0:33:0:1:0:60:2:0.0417:0:4 -GL000225.1 131788 . C G 65 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10777;SOR=0;LSEQ=GGCATTGTGAAATATCTCTG;RSEQ=ACTGATCACCCAGGTGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:2,2:8,10:0.1818:2,2:27:1:32.5:1:1:1.24:47.5:8:0.1818:0:5.8 0/0:21:0:0,0:8,13:0:2,0:17.6:1:32.3:1:1:0:51.5:42:1:0:3.9 -GL000225.1 131790 . C G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48897;SOR=0;LSEQ=CATTGTGAAATATCTCTGCA;RSEQ=TGATCACCCAGGTGATTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:0.0909:2,2:19.5:1:32:1:1:1.21:53.5:4:0.0909:0:5 0/0:20:0:0,0:8,11:0:2,0:15.8:1:31.8:1:1:0:51.2:38:0.95:0:3.8 -GL000225.1 131794 . T A 61 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80845;LSEQ=GTGAAATATCTCTGCACTGA;RSEQ=CACCCAGGTGATTGAACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:2,2:5,10:0.2105:2,2:21:1:30.8:1:0.60268:1.92:47.5:8:0.2105:0:5.8 0/1:17:3:1,2:5,9:0.1765:2,2:7.7:1:30.7:1:1:1.10434:58.7:6:0.1765:0:4.3 -GL000225.1 131808 . G C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGATCACCCAGGTGATT;RSEQ=AACTCTTGTCTAGGATCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:4,8:0,0:1:0,2:13.8:1:31.9:1:1:0:40.3:24:1:0:5.1 1/1:7:7:0,7:0,0:1:0,0:11.6:1:32.7:1:1:0:46.1:14:1:0:5 -GL000225.1 131817 . T A 70 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGTGATTGAACTCTTG;RSEQ=CTAGGATCTGCCCACAGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1:0,2:13.2:1:30.2:1:1:0:37.6:10:1:0:5.6 1/1:4:4:0,4:0,0:1:0,0:7.5:1:30.3:1:1:0:45.3:8:1:0:5.8 -GL000225.1 131824 . T A 31 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GATTGAACTCTTGTCTAGGA;RSEQ=CTGCCCACAGGGTGTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:0.5:0,0:11:0:31.5:1:1:0:40:4:0.5:0:5.5 1/0:2:1:0,1:0,1:0.5:0,0:6:0:31:0:1:0:40:2:0.5:0:5 -GL000225.1 131830 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTCTTGTCTAGGATCTGCC;RSEQ=ACAGGGTGTATTTTGAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5:0:29:0:1:0:40:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000225.1 132905 . T C 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=GATCACACAGCTGATGTAAC;RSEQ=CTTGTCTAGGCTCTGGCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:30:1:1:0:29:4:1:0:6.5 0/0:4:0:0,0:3,1:0:2,0:26.5:1:31:1:1:0:24.8:8:1:0:3.3 -GL000225.1 132913 . A T 28 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=AGCTGATGTAACTCTTGTCT;RSEQ=GGCTCTGGCTACAGGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:16.5:1:28.5:1:1:0:29:4:1:0:6.5 0/0:4:0:0,0:3,1:0:2,0:28.3:1:28.5:1:1:0:24.8:8:1:0:3.3 -GL000225.1 132942 . T A 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACAGGGGGCTTGTGACAC;RSEQ=TCTCTGCACTGATCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:47:0:33:0:1:0:29:2:1:0:6 1/1:4:4:2,2:0,0:1:0,2:32.3:1:31.3:1:1:0:23.5:8:1:0:4 -GL000225.1 132953 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTGACACTTCTCTGCACT;RSEQ=ATCACCCAGGTGATGTAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:36:0:33:0:1:0:29:2:1:0:6 1/0:4:2:1,1:1,1:0.5:2,2:36:1:29:1:1:1:22:4:0.5:0:4 -GL000225.1 132969 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTGATCACCCAGGTGATG;RSEQ=AACCCTTGTCTAGGCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:36:1:31:1:1:0:22:4:0.5:0:4 -GL000225.1 133012 . C A 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGGGGCATTGTGACATA;RSEQ=CTCTGCACTGATCACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:1:0,0:21.5:1:29:1:1:0:22.5:4:1:0:4.5 -GL000225.1 133684 . G A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACCGGGGTTATTGTGACGT;RSEQ=TCTCTGCACTGTTCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:12:0:28:0:1:0:41:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:18.3:1:31.3:1:1:0:36:6:1:0:5.3 -GL000225.1 133696 . T A 91 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGACGTGTCTCTGCACTG;RSEQ=TCACCCAGGTGATGTAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:24:0:29:0:1:0:41:2:1:0:7 1/1:9:8:4,4:0,0:0.8889:0,2:14.1:1:30.6:1:1:0:33.5:16:0.8889:0:4.8 -GL000225.1 133701 . C T 40 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51648;SOR=Inf;LSEQ=CGTGTCTCTGCACTGTTCAC;RSEQ=CAGGTGATGTAACTCTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,0:0:0,0:2:1:31.3:1:1:0:51.7:6:0.75:0:5.7 0/1:11:3:2,1:2,4:0.2727:2,2:9.3:1:25.7:1:0.52381:3.39:45.7:2:0.2:0:5 -GL000225.1 133705 . G T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53044;SOR=0.48387;LSEQ=TCTCTGCACTGTTCACCCAG;RSEQ=TGATGTAACTCTTGTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:5:0:31:0:1:0:44:2:0.25:0:8 0/1:15:2:1,1:7,6:0.1333:2,2:11:0:30.5:1:1:1.1547:24:4:0.1333:0:3.5 -GL000225.1 133707 . G T 26 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGCACTGTTCACCCAGGT;RSEQ=ATGTAACTCTTGTCTAGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,1:0:2,0:16.3:1:32:1:1:0:45.3:6:0.75:0:6.3 0/1:17:2:1,1:7,8:0.1176:2,2:5:0:26.5:1:1:1.13:53:4:0.1176:0:4 -GL000225.1 133710 . G C 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACTGTTCACCCAGGTGAT;RSEQ=TAACTCTTGTCTAGGCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:17.8:1:32.8:1:1:0:49:8:1:0:6 0/1:19:2:0,2:9,8:0.1053:2,0:26:1:32.5:1:0.47368:0:43.5:4:0.1053:0:4 -GL000225.1 133716 . C G 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCACCCAGGTGATGTAACT;RSEQ=TTGTCTAGGCTCCACCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:0:2,0:23.5:1:32.5:1:1:0:49:8:1:0:6 0/1:22:3:2,1:9,9:0.1364:2,2:36:1:31.3:1:1:1.94:31.3:6:0.1364:0:5.7 -GL000225.1 133721 . C A 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGGTGATGTAACTCTTGT;RSEQ=TAGGCTCCACCTACAGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:14.9:1:32:1:1:0:49.4:16:1:0:5.9 0/1:22:2:1,1:10,10:0.0909:2,2:19:0:27.5:1:1:1:53:4:0.0909:0:4 -GL000225.1 133724 . GG TT 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTGATGTAACTCTTGTCTA;RSEQ=CTCCACCTACAGGGGGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:17.1:1:33.1:1:1:0:49.4:16:1:0:5.9 0/1:22:2:1,1:8,9:0.0909:2,2:25:1:30.5:1:1:1.12:46:4:0.0909:0:6 -GL000225.1 133732 . C T 65 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0084;SOR=0;LSEQ=AACTCTTGTCTAGGCTCCAC;RSEQ=TACAGGGGGTATTGTGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:2,2:6,2:0.3333:2,2:13.8:1:32.5:1:0.54747:2.71347:47.5:8:0.3333:0:6.3 0/0:24:0:0,0:12,11:0:2,0:29.1:1:32.1:1:1:0:39.9:46:0.9583:0:3.9 -GL000225.1 133735 . CA C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51919;SOR=Inf;LSEQ=TCTTGTCTAGGCTCCACCTA;RSEQ=GGGGGTATTGTGACGTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,6:0:2,0:14.9:1:31:1:1:0:47:32:0.9412:0:5 0/1:28:2:1,1:15,10:0.0714:2,2:40:1:31:1:1:1.47706:27:4:0.0741:0:5 -GL000225.1 133737 . GG AA 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.52643;SOR=Inf;LSEQ=TTGTCTAGGCTCCACCTACA;RSEQ=GGGTATTGTGACGTATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:15.8:1:31.7:1:1:0:47:32:1:0:5 0/1:28:2:1,1:14,11:0.0714:2,2:23:0:32.3:1:1:1.2613:46:4:0.0714:0:3 -GL000225.1 133739 . G A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13737;SOR=0;LSEQ=GTCTAGGCTCCACCTACAGG;RSEQ=GGTATTGTGACGTATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:8,5:0.1176:2,0:22:1:32:0:0.52381:0:38:4:0.1176:0:6 0/0:28:0:0,0:16,12:0:2,0:28.4:1:31.4:1:1:0:40.6:56:1:0:3.7 -GL000225.1 133741 . G T 90 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28202;SOR=2.79836;LSEQ=CTAGGCTCCACCTACAGGGG;RSEQ=TATTGTGACGTATCTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:9,5:0.1176:2,2:24.5:1:28.5:1:1:1.73197:42:4:0.1176:0:7.5 0/1:29:8:5,3:11,10:0.2759:2,2:35.4:1:30:1:0.69682:1.49:39.1:16:0.2759:0:2.6 -GL000225.1 133744 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14154;SOR=0;LSEQ=GGCTCCACCTACAGGGGGTA;RSEQ=TGTGACGTATCTCTGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:0.1111:2,2:27.5:1:29:1:1:1.61828:42:4:0.1111:0:7.5 0/0:29:0:0,0:16,13:0:2,0:29.3:1:30.3:1:1:0:40.6:58:1:0:3.8 -GL000225.1 133745 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51711;SOR=Inf;LSEQ=GCTCCACCTACAGGGGGTAT;RSEQ=GTGACGTATCTCTGCACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:21.5:1:30.6:1:1:0:46.2:36:1:0:5.2 0/1:29:2:1,1:15,12:0.069:2,2:45:1:29.5:1:1:1.24034:46:4:0.069:0:6 -GL000225.1 133750 . C T 50 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14983;SOR=0.18546;LSEQ=ACCTACAGGGGGTATTGTGA;RSEQ=GTATCTCTGCACTGATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:3,0:7,6:0.1667:2,0:31.7:1:31.7:1:0.25:0:41.7:6:0.1667:0:7 0/1:29:1:0,1:16,11:0.0345:2,0:11:0:31:0:0.42857:0:21:2:0.0345:0:5 -GL000225.1 133754 . T C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52128;SOR=Inf;LSEQ=ACAGGGGGTATTGTGACGTA;RSEQ=CTCTGCACTGATCACCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,7:0:2,0:25.6:1:31.6:1:1:0:46.6:34:0.9444:0:5 0/1:30:2:1,1:15,13:0.0667:2,2:20.5:1:30.5:1:1:1.14834:48:4:0.0667:0:4 -GL000225.1 133755 . C G 33 v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54729;SOR=0.28376;LSEQ=CAGGGGGTATTGTGACGTAT;RSEQ=TCTGCACTGATCACCCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,5:0.1111:2,2:29:0:33.5:1:1:1.54914:45:4:0.1111:0:5.5 0/1:30:1:1,0:15,13:0.0333:2,0:22:0:34:0:1:0:25:2:0.0333:0:5 -GL000225.1 133758 . TGC CCT 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1301;SOR=0;LSEQ=GGGGTATTGTGACGTATCTC;RSEQ=ACTGATCACCCAGGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:0.1111:2,2:19:0:32.3:1:1:1.61828:50:4:0.1111:0:2 0/0:31:0:0,0:16,15:0:2,0:25.9:1:29.9:1:1:0:41.1:30:1:0:3.7 -GL000225.1 133760 . C T 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11565;SOR=0;LSEQ=GGTATTGTGACGTATCTCTG;RSEQ=ACTGATCACCCAGGTGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:9,4:0.1176:2,2:34:0:30.5:1:1:2.12136:45:4:0.1333:0:5.5 0/0:32:0:0,0:16,16:0:2,0:24.7:1:31.2:1:1:0:40.6:31:1:0:3.7 -GL000225.1 133766 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52128;SOR=Inf;LSEQ=GTGACGTATCTCTGCACTGA;RSEQ=CACCCAGGTGATGTAACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:30.7:1:31.3:1:1:0:45.6:36:1:0:4.8 0/1:30:2:1,1:15,13:0.0667:2,2:39.5:1:31:1:1:1.14834:46:4:0.0667:0:3 -GL000225.1 133768 . A T 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23446;SOR=0.37013;LSEQ=GACGTATCTCTGCACTGATC;RSEQ=CCCAGGTGATGTAACATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:10,4:0.2222:2,2:37.5:1:31.8:1:0.56863:2.36467:48:8:0.2222:0:5.3 0/1:32:3:1,2:16,13:0.0938:2,2:35.7:1:30:1:0.58871:2.39417:42.3:6:0.0938:0:2.7 -GL000225.1 133771 . C T 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51711;SOR=Inf;LSEQ=GTATCTCTGCACTGATCACC;RSEQ=AGGTGATGTAACATTTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:31.6:1:32.1:1:1:0:45.6:36:1:0:4.8 0/1:29:2:1,1:14,13:0.069:2,2:30:1:27.5:1:1:1.07415:46:4:0.069:0:6 -GL000225.1 133772 . A C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51711;SOR=Inf;LSEQ=TATCTCTGCACTGATCACCC;RSEQ=GGTGATGTAACATTTATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:31.5:1:31:1:1:0:45.6:36:1:0:4.8 0/1:29:2:1,1:14,13:0.069:2,2:13.5:1:32:0:1:1.07415:53:4:0.0714:0:3 -GL000225.1 133773 . G C 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14154;SOR=0;LSEQ=ATCTCTGCACTGATCACCCA;RSEQ=GTGATGTAACATTTATCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:11,5:0.1111:2,2:34:1:31:1:1:2.09766:42:4:0.1111:0:7.5 0/0:29:0:0,0:15,14:0:2,0:23.8:1:30.6:1:1:0:42.3:58:1:0:3.6 -GL000225.1 133774 . G T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1516;SOR=0;LSEQ=TCTCTGCACTGATCACCCAG;RSEQ=TGATGTAACATTTATCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:0.1053:2,2:37.5:1:30.5:1:1:1.77272:49.5:4:0.1053:0:6 0/0:29:0:0,0:15,14:0:2,0:23.6:1:30.7:1:1:0:42.3:58:1:0:3.6 -GL000225.1 133779 . G C 67 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1415;SOR=Inf;LSEQ=GCACTGATCACCCAGGTGAT;RSEQ=TAACATTTATCTAGGCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:32.1:1:32.5:1:1:0:45.2:34:1:0:5.1 0/1:29:5:3,2:12,12:0.1724:2,2:5:0:29.2:1:1:1.48:48.8:10:0.1724:0:2.2 -GL000225.1 133782 . A G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51919;SOR=Inf;LSEQ=CTGATCACCCAGGTGATGTA;RSEQ=CATTTATCTAGGCTCTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:31.9:1:30.5:1:1:0:45.2:34:1:0:5.1 0/1:28:2:1,1:13,13:0.0714:2,2:19:1:29:1:1:1:46:4:0.0714:0:6 -GL000225.1 133783 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51711;SOR=Inf;LSEQ=TGATCACCCAGGTGATGTAA;RSEQ=ATTTATCTAGGCTCTGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:0:2,0:30.1:1:32.2:1:1:0:45.2:36:1:0:4.9 0/1:29:2:1,1:13,14:0.069:2,2:22.5:1:28.5:1:1:1.07:46:4:0.0714:0:3 -GL000225.1 133784 . A G 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76704;LSEQ=GATCACCCAGGTGATGTAAC;RSEQ=TTTATCTAGGCTCTGCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:37.5:1:30.5:1:1:1.26772:49.5:4:0.1111:0:6 0/1:23:2:1,1:8,11:0.087:2,2:24.5:1:27:1:1:1.35:40:4:0.087:0:6.5 -GL000225.1 133790 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21764;SOR=0;LSEQ=CCAGGTGATGTAACATTTAT;RSEQ=TAGGCTCTGCCTACAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:18.5:1:29:1:1:1.26772:42.5:4:0.1111:0:7.5 0/0:20:0:0,0:9,11:0:2,0:27:1:30.8:1:1:0:41.5:40:1:0:4 -GL000225.1 133791 . T C 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23186;SOR=Inf;LSEQ=CAGGTGATGTAACATTTATC;RSEQ=AGGCTCTGCCTACAGGGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:26.9:1:30.2:1:1:0:44.9:36:1:0:5.1 0/1:20:3:1,2:8,8:0.15:2,2:31:1:29:1:1:1.9301:46.7:6:0.15:0:6 -GL000225.1 133792 . A G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68673;SOR=0.62559;LSEQ=AGGTGATGTAACATTTATCT;RSEQ=GGCTCTGCCTACAGGGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:8,6:0.2222:2,2:30.5:1:31.8:1:1:1.31198:48:8:0.2222:0:5.3 0/1:20:3:1,2:8,9:0.15:2,2:24:1:32.7:1:1:1.72884:42.3:6:0.15:0:2.7 -GL000225.1 133793 . G A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21764;SOR=0;LSEQ=GGTGATGTAACATTTATCTA;RSEQ=GCTCTGCCTACAGGGGCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:12.5:1:29.5:1:1:1.26772:54:4:0.1111:0:4 0/0:20:0:0,0:9,11:0:2,0:25.8:1:29.6:1:1:0:41.5:19:1:0:4 -GL000225.1 133794 . G A 43 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60618;SOR=2.92044;LSEQ=GTGATGTAACATTTATCTAG;RSEQ=CTCTGCCTACAGGGGCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:9,8:0.0556:2,0:32:0:31:0:1:0:29:2:0.0556:0:5 0/1:20:3:2,1:7,10:0.15:2,2:30.3:1:27.7:1:0.56579:2.71:35.3:6:0.15:0:4 -GL000225.1 133795 . C T 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.89165;LSEQ=TGATGTAACATTTATCTAGG;RSEQ=TCTGCCTACAGGGGCGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:0.1111:2,2:18.5:1:29:1:1:1.26772:42.5:4:0.1111:0:7.5 0/1:20:2:1,1:8,10:0.1:2,2:32:1:30:1:1:1.24:48:4:0.1:0:4 -GL000225.1 133797 . C G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48649;SOR=Inf;LSEQ=ATGTAACATTTATCTAGGCT;RSEQ=TGCCTACAGGGGCGTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:23.8:1:31.4:1:1:0:44.9:36:1:0:5.1 0/1:19:2:1,1:6,9:0.1053:2,2:38.5:1:31:1:1:1.46:47.5:4:0.1053:0:2.5 -GL000225.1 133802 . T A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2139;SOR=0;LSEQ=ACATTTATCTAGGCTCTGCC;RSEQ=ACAGGGGCGTTTTGACATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:28:1:28.5:1:1:1:49.5:4:0.125:0:6 0/0:18:0:0,0:8,10:0:2,0:25:1:28.5:1:1:0:41.8:36:1:0:3.9 -GL000225.1 133804 . C G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2139;SOR=0;LSEQ=ATTTATCTAGGCTCTGCCTA;RSEQ=AGGGGCGTTTTGACATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,7:0.125:2,2:12:0:33:1:1:1.15:50:4:0.125:0:1.5 0/0:18:0:0,0:8,10:0:2,0:24.2:1:30.5:1:1:0:41.8:36:1:0:3.9 -GL000225.1 133805 . A T 83 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00723;SOR=Inf;LSEQ=TTTATCTAGGCTCTGCCTAC;RSEQ=GGGGCGTTTTGACATAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:22.4:1:30.1:1:1:0:44:32:1:0:4.9 0/1:17:7:3,4:5,5:0.4118:2,2:33.1:1:29.7:1:1:1.31092:45.9:14:0.4118:0:4.4 -GL000225.1 133808 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48506;SOR=0;LSEQ=ATCTAGGCTCTGCCTACAGG;RSEQ=GCGTTTTGACATAGCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:27.5:1:30:1:1:1:51:4:0.125:0:5 0/0:14:0:0,0:7,7:0:2,0:29.4:1:30.2:1:1:0:41.9:28:1:0:3.9 -GL000225.1 133810 . C A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=CTAGGCTCTGCCTACAGGGG;RSEQ=GTTTTGACATAGCTCTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,5:0.1429:2,2:20:1:29:1:1:1:49.5:4:0.1538:0:6 0/0:14:0:0,0:6,7:0:2,0:29:1:30.7:1:1:0:43.6:26:1:0:3.9 -GL000225.1 133811 . G A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.64831;SOR=0.42986;LSEQ=TAGGCTCTGCCTACAGGGGC;RSEQ=TTTTGACATAGCTCTGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:5,5:0.2857:2,2:21.5:1:29.5:1:1:1:46.8:8:0.2857:0:6.3 0/1:14:2:1,1:5,5:0.1429:2,2:22:1:29:1:1:1:50:4:0.1429:0:6 -GL000225.1 133825 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47619;SOR=Inf;LSEQ=AGGGGCGTTTTGACATAGCT;RSEQ=TGCACAGATCACCTAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:21.7:1:31.7:1:1:0:40.4:22:1:0:4.5 0/1:11:2:1,1:4,5:0.1818:2,2:31:0:31.5:1:1:1.22:43:4:0.1818:0:4 -GL000226.1 74 . G A 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=GTGGACATTTGGATAGATTT;RSEQ=AAGATTTCGTTGGAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:0:0,0:29.3:1:32.8:1:1:0:21.3:12:1:0:0.5 0/1:7:2:2,0:5,0:0.2857:0,0:44:1:29:1:1:0:20:4:0.2857:0:1 -GL000226.1 97 . T A 27 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49858;SOR=Inf;LSEQ=GATTTCGTTGGAAACGGGAA;RSEQ=ATCTTCATATCAAATCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:0:2,0:15.5:1:29.6:1:1:0:28.5:22:1:0:0.3 0/1:16:2:1,1:10,4:0.125:2,2:9:0:27.5:1:1:2.34522:40:4:0.125:0:5 -GL000226.1 99 . T C 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26847;SOR=Inf;LSEQ=TTTCGTTGGAAACGGGAATA;RSEQ=CTTCATATCAAATCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:0:2,0:16:1:30.7:1:1:0:28.5:22:1:0:0.3 0/1:18:3:2,1:11,4:0.1667:2,2:7.7:1:28.7:1:1:1.34973:40.7:6:0.1667:0:4.7 -GL000226.1 108 . C A 105 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00375;SOR=Inf;LSEQ=AAACGGGAATATCTTCATAT;RSEQ=AAATCTAGACAGAAGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:16.6:1:31.6:1:1:0:29.5:28:1:0:0 0/1:31:13:7,6:12,6:0.4194:2,2:9.6:1:28.5:1:0.70977:1.68419:37.3:26:0.4333:0:4.3 -GL000226.1 120 . G A 70 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30956;SOR=Inf;LSEQ=CTTCATATCAAATCTAGACA;RSEQ=AAGCATTCTCAGAAACGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:19.3:1:31.4:1:1:0:35.3:36:1:0:0.4 0/1:45:5:3,2:23,17:0.1111:2,2:20.4:1:30.4:1:1:1.11:33.2:10:0.1111:0:4.8 -GL000226.1 128 . C G 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAATCTAGACAGAAGCATT;RSEQ=TCAGAAACGTCTTTGTGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:23.3:1:31.3:1:1:0:34.5:38:1:0:0.6 0/1:45:2:1,1:24,19:0.0444:2,2:15.5:1:33:1:1:1.25655:37:4:0.0444:0:2.5 -GL000226.1 134 . AA GT 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGACAGAAGCATTCTCAGA;RSEQ=CGTCTTTGTGATGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:29.2:1:29.7:1:1:0:35.3:36:1:0:0.7 0/1:49:2:1,1:25,22:0.0408:2,2:32.5:1:27.8:1:1:1.13339:42:4:0.0408:0:4.5 -GL000226.1 135 . A T 70 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31322;SOR=Inf;LSEQ=AGACAGAAGCATTCTCAGAA;RSEQ=CGTCTTTGTGATGTTTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:0:2,0:30:1:29.2:1:1:0:35.3:36:1:0:0.7 0/1:49:5:3,2:22,20:0.102:2,2:24:1:30.4:1:1:1.35:24.8:10:0.1111:0:3.6 -GL000226.1 137 . G T 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00761;SOR=Inf;LSEQ=ACAGAAGCATTCTCAGAAAC;RSEQ=TCTTTGTGATGTTTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:29.8:1:30.8:1:1:0:34.6:38:1:0:0.7 0/1:54:16:8,8:19,19:0.2963:2,2:32.2:1:30.5:1:1:1:34.8:32:0.2963:0:3.8 -GL000226.1 139 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAAGCATTCTCAGAAACGT;RSEQ=TTTGTGATGTTTGCATTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:0:2,0:27.1:1:31.5:1:1:0:33.4:44:1:0:0.8 0/1:53:2:1,1:25,26:0.0377:2,2:20:0:28.5:1:1:1.04:45.5:4:0.0392:0:2 -GL000226.1 144 . T C 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00602;SOR=0;LSEQ=CATTCTCAGAAACGTCTTTG;RSEQ=GATGTTTGCATTCAACTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:2,2:6,12:0.1818:2,2:22:1:27.3:1:0.60191:1.93:37:3:0.1429:0:3.3 0/0:53:0:0,0:25,28:0:2,0:30:1:29.5:1:1:0:41.2:106:1:0:2 -GL000226.1 145 . G A 80 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09599;SOR=Inf;LSEQ=ATTCTCAGAAACGTCTTTGT;RSEQ=ATGTTTGCATTCAACTCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:0:2,0:30.7:1:30.5:1:1:0:33.4:21:1:0:0.8 0/1:54:8:4,4:21,22:0.1481:2,2:41.4:1:26.9:1:1:1.05:39.9:7:0.1321:0:4 -GL000226.1 150 . T C 80 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17137;SOR=Inf;LSEQ=CAGAAACGTCTTTGTGATGT;RSEQ=TGCATTCAACTCATAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:0:2,0:32.5:1:29.6:1:1:0:33.4:44:1:0:0.8 0/1:53:6:3,3:22,25:0.1132:2,2:21.3:1:31.3:1:1:1.13:55.3:12:0.1132:0:2.3 -GL000226.1 152 . G A 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55104;SOR=Inf;LSEQ=GAAACGTCTTTGTGATGTTT;RSEQ=CATTCAACTCATAGAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:0:2,0:33.1:1:31.1:1:1:0:33.4:21:1:0:0.8 0/1:53:3:1,2:24,26:0.0566:2,2:24.3:1:29.3:1:1:1.8257:56.7:6:0.0566:0:1.3 -GL000226.1 162 . C G 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31553;SOR=Inf;LSEQ=TGTGATGTTTGCATTCAACT;RSEQ=ATAGAGTTGAACATTCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:0:2,0:31:1:31.7:1:1:0:34.5:48:1:0:1 0/1:55:5:2,3:23,26:0.0909:2,2:29.2:1:30.8:1:1:1.32007:33:10:0.0909:0:1.4 -GL000226.1 177 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07895;SOR=0;LSEQ=CAACTCATAGAGTTGAACAT;RSEQ=CCCTTTCAGAGAGCAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:6,14:0.0909:2,2:35.5:1:29:1:1:2.24:49:4:0.0952:0:2.5 0/0:55:0:0,0:25,30:0:2,0:21.9:1:29.1:1:1:0:43:54:1:0:2 -GL000226.1 201 . G A 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53947;SOR=Inf;LSEQ=TTTCAGAGAGCAGCTTTGAA;RSEQ=CACTCTTTTTGTAGTACGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:0:2,0:18.3:1:31.4:1:1:0:37.4:13:1:0:1.7 0/1:26:3:0,3:10,13:0.1154:2,0:21.3:1:31.7:1:0.26154:0:50.7:6:0.1154:0:2.7 -GL000226.1 216 . T C 57 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16176;SOR=0.20975;LSEQ=TTGAAGCACTCTTTTTGTAG;RSEQ=ACGTGCAAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:0,3:0.5714:0,2:14:1:28.8:1:0.42857:0:36:3:0.5:0:3.5 0/1:10:2:1,1:2,6:0.2:2,2:23:0:34:0:1:2.65:60:4:0.2:0:4 -GL000226.1 218 . C T 102 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCACTCTTTTTGTAGTA;RSEQ=GTGCAAGTGGATATTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:13.3:1:31.8:1:1:0:30:12:1:0:2.7 1/1:10:10:3,7:0,0:1:0,2:17.1:1:30.8:1:1:0:43.6:20:1:0:2.8 -GL000226.1 226 . T G 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25824;SOR=Inf;LSEQ=CTTTTTGTAGTACGTGCAAG;RSEQ=GGATATTTGGAGTCCTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:7:1:31.2:1:1:0:32:10:1:0:2.6 0/1:9:3:1,2:1,5:0.3333:2,2:6:1:30:1:1:2.24:43:6:0.3333:0:2.3 -GL000226.1 230 . T C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24242;SOR=0.16477;LSEQ=TTGTAGTACGTGCAAGTGGA;RSEQ=ATTTGGAGTCCTCTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:4:1:32.7:1:1:0:39.7:6:0.75:0:3.7 0/1:7:2:1,1:1,4:0.2857:2,2:9:0:33.5:1:1:3.16:60:4:0.2857:0:4 -GL000226.1 932 . G A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATTTGGAGCACCTTGAC;RSEQ=CCTACGGTGAAAAGGGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:0.75:0,2:33.7:1:31.3:1:1:0:35.7:6:0.75:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000226.1 946 . G C 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGACGCCTACGGTGAAAA;RSEQ=GGAAATATCTTCCCATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:25:1:32.5:1:1:1:43:4:0.5:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000226.1 5913 . A G 33 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AATATCTTCCTATAAAATCT;RSEQ=GACAGAAGCATTCTCAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:1:33:0:1:0:20:4:1:0:2 0/0:1:0:0,0:0,1:0:0,0:33:0:28:0:1:0:20:2:1:0:0 -GL000226.1 6029 . T G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGTATATGGAAGTGGAC;RSEQ=TTTCGGACGGTTTGAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:33.5:1:30.5:1:1:0:20:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000226.1 6944 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28409;SOR=Inf;LSEQ=ATATCAAATCTAGACAGAAG;RSEQ=ATTCTCAGAAACGTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:15,6:0:2,0:22.8:1:31.4:1:1:0:34.9:20:1:0:0.6 0/1:35:3:1,2:21,11:0.0857:2,2:11.3:1:26:1:0.54118:3.66543:47.7:6:0.0857:0:1 -GL000226.1 6951 . A G 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09842;LSEQ=ATCTAGACAGAAGCATTCTC;RSEQ=GAAACGTCTTTGTGATGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:14,8:0.0435:2,0:15:0:31:0:1:0:49:2:0.0455:0:1 0/1:42:2:1,1:24,16:0.0476:2,2:25:1:29.5:1:1:1.48518:43:4:0.0476:0:2.5 -GL000226.1 6958 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53017;SOR=Inf;LSEQ=CAGAAGCATTCTCAGAAACG;RSEQ=CTTTGTGATGTTTGCATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:0:2,0:26.2:1:30.2:1:1:0:38.3:54:1:0:0.7 0/1:47:2:1,1:26,19:0.0426:2,2:28.5:1:27.5:1:1:1.35916:43:4:0.0435:0:2.5 -GL000226.1 6971 . T G 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.27639;LSEQ=AGAAACGTCTTTGTGATGTT;RSEQ=GCATTCAACTCATAGAGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:1:1,0:20,12:0.0303:2,0:5:0:32:0:1:0:40:2:0.0303:0:1 0/1:52:2:1,1:28,22:0.0385:2,2:11.5:1:29.5:1:1:1.26678:42:4:0.0385:0:1.5 -GL000226.1 6983 . A C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16411;SOR=0;LSEQ=GTGATGTTTGCATTCAACTC;RSEQ=TAGAGTTGAACATTCCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:20,17:0.05:2,2:18.5:1:30.5:1:1:1.17156:47.5:4:0.05:0:2 0/0:58:0:0,0:29,29:0:2,0:28.6:1:29.6:1:1:0:39.7:57:1:0:0.6 -GL000226.1 6986 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15628;SOR=0;LSEQ=ATGTTTGCATTCAACTCATA;RSEQ=AGTTGAACATTCCGTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:21,20:0.0465:2,2:40.5:1:33:1:1:1.04883:49:4:0.0465:0:1 0/0:65:0:0,0:34,31:0:2,0:26:1:31.3:1:1:0:39.1:130:1:0:0.8 -GL000226.1 6988 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15341;SOR=0;LSEQ=GTTTGCATTCAACTCATAGA;RSEQ=TTGAACATTCCGTTTCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:21,20:0.0465:2,2:23.5:1:29:1:1:1.04883:47.5:4:0.0465:0:2 0/0:66:0:0,0:34,32:0:2,0:25.9:1:30.9:1:1:0:39.2:32:1:0:0.8 -GL000226.1 7000 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.26029;SOR=0.36506;LSEQ=CTCATAGAGTTGAACATTCC;RSEQ=TTTCAGAGAGCAGCTTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:3,2:18,21:0.1087:2,2:22.2:1:30.6:1:0.65754:1.73:40.8:10:0.1111:0:1 0/1:71:3:2,1:30,35:0.0423:2,2:27.7:1:28.3:1:0.59773:2.31:43:6:0.0423:0:2 -GL000226.1 7001 . T A 31 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.30148;LSEQ=TCATAGAGTTGAACATTCCG;RSEQ=TTCAGAGAGCAGCTTTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:0,1:23,21:0.0217:2,0:17:0:33:0:0.48889:0:20:2:0.0222:0:3 0/1:71:2:1,1:33,36:0.0282:2,2:21.5:1:31:0:1:1.09:47.5:4:0.0282:0:1 -GL000226.1 7006 . G A 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10445;SOR=2.4516;LSEQ=GAGTTGAACATTCCGTTTCA;RSEQ=AGAGCAGCTTTGAGGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:6:3,3:17,22:0.1333:2,2:28.5:1:29.7:1:1:1.29:35.8:12:0.1395:0:1.2 0/1:69:19:9,10:22,28:0.2754:2,2:30.1:1:30.3:1:1:1.14:40.1:38:0.2794:0:1.1 -GL000226.1 7019 . AG A 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18484;SOR=0;LSEQ=CGTTTCAGAGAGCAGCTTTG;RSEQ=GCACTCTTTTTGTAGTATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:15,27:0.0444:2,2:31:1:33.5:1:1:1.77:42.5:4:0.0455:0:0 0/0:59:0:0,0:20,36:0:2,0:28.7:1:30.8:1:1:0:40.4:112:0.9492:0:0.8 -GL000226.1 7036 . T C 64 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.38038;SOR=3.26592;LSEQ=TTGAGGCACTCTTTTTGTAG;RSEQ=ATGTGCAAGTGGATATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:1:1,0:13,24:0.0256:2,0:23:0:31:0:0.36842:0:20:2:0.0263:0:4 0/1:50:4:2,2:17,29:0.08:2,2:36.3:1:32:1:0.62916:1.69:32.3:8:0.0816:0:6 -GL000226.1 7048 . G C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19684;SOR=0;LSEQ=TTTTGTAGTATGTGCAAGTG;RSEQ=ATATTTGGAGCGCTCTGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:10,22:0.0588:2,2:42.5:1:32.5:1:1:2.14:45:4:0.0588:0:1.5 0/0:42:0:0,0:16,26:0:2,0:27.4:1:31:1:1:0:38:84:1:0:1.4 -GL000226.1 7050 . T C 64 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3692;SOR=3.5148;LSEQ=TTGTAGTATGTGCAAGTGGA;RSEQ=ATTTGGAGCGCTCTGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:1,0:10,23:0.0294:2,0:9:0:34:0:0.32353:0:20:2:0.0313:0:4 0/1:41:4:2,2:14,23:0.0976:2,2:32:1:32.3:1:0.63661:1.62:32.3:8:0.1026:0:6 -GL000226.1 7062 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49854;SOR=Inf;LSEQ=CAAGTGGATATTTGGAGCGC;RSEQ=CTGAGGCCTACGGTGAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:7,19:0:2,0:25.2:1:30.3:1:1:0:42:52:1:0:0.7 0/1:33:2:1,1:12,19:0.0606:2,2:30:1:29.5:1:1:1.56:21:4:0.0606:0:5 -GL000226.1 7069 . C T 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49686;SOR=Inf;LSEQ=ATATTTGGAGCGCTCTGAGG;RSEQ=CTACGGTGAAAAAGCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:6,18:0:2,0:20:1:30.8:1:1:0:42.8:23:1:0:0.7 0/1:30:2:1,1:10,18:0.0667:2,2:15:1:31.5:1:1:1.76:43.5:4:0.069:0:7 -GL000226.1 7071 . TA CT 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49927;SOR=Inf;LSEQ=ATTTGGAGCGCTCTGAGGCC;RSEQ=CGGTGAAAAAGCAAATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:5,18:0:2,0:18.7:1:29:1:1:0:43:46:1:0:0.7 0/1:30:2:1,1:10,18:0.0667:2,2:25.5:1:32:1:1:1.76:38:4:0.069:0:1.5 -GL000226.1 7076 . T G 71 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05287;SOR=Inf;LSEQ=GAGCGCTCTGAGGCCTACGG;RSEQ=GAAAAAGCAAATATCTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:4,13:0:2,0:19.1:1:29.2:1:1:0:42.9:16:1:0:0.7 0/1:21:5:2,3:5,11:0.2381:2,2:19.6:1:30.8:1:1:1.44:35.6:10:0.2381:0:5 -GL000226.1 7107 . C G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATCTTCCCATAACCACTA;RSEQ=ACAGAAACATTCTCAGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:3.3:1:31.7:1:1:0:31.3:6:1:0:1.3 1/0:3:2:0,2:0,1:0.6667:0,0:5.5:1:31.5:1:1:0:32:4:0.6667:0:2.5 -GL000226.1 7159 . A G 41 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATGCACTCACCTAACAGA;RSEQ=AAGAACCTTCCTTTTGACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:1:0,0:19:1:26:1:1:0:20:6:1:0:1.7 -GL000226.1 13317 . C G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAGTTGAACCTTTCTATTGA;RSEQ=AGAGCAGTTTTGAAACAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23.5:1:32.5:1:1:0:44:4:1:0:1.5 1/1:2:2:1,1:0,0:1:0,2:31:1:32.5:1:1:0:42:4:1:0:1 -GL000226.1 13322 . C G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAACCTTTCTATTGACAGAG;RSEQ=AGTTTTGAAACAGTCTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:31.5:1:1:0:44:4:1:0:1.5 0/0:2:0:0,0:1,1:0:2,0:26:1:33.5:1:1:0:42:4:1:0:1 -GL000226.1 14167 . A C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGTTGAACATTGCCTTTC;RSEQ=TAGAGCAGGTTTGAAACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:31:0:28:0:1:0:20:2:0.5:0:2 1/1:2:2:1,1:0,0:1:0,2:14.5:1:31.5:1:1:0:43.5:4:1:0:2.5 -GL000226.1 14212 . T C 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTGTAGTATATGGAAGTGGA;RSEQ=GTTTCGGACGGTTGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:10.5:1:32:1:1:0:20:4:0.6667:0:1 1/0:3:2:1,1:0,0:0.6667:0,2:7:0:32.5:1:1:0:43.5:4:0.6667:0:2.5 -GL000226.1 14311 . A C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.22429;SOR=0;LSEQ=TGTTTGTGATGTGTGTACTC;RSEQ=ACTAACAGAGTTGAACCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:14,7:0.087:2,2:19.5:1:31.5:1:1:1.93655:20:4:0.087:0:2 0/0:25:0:0,0:19,6:0:2,0:25.2:1:29.5:1:1:0:21.8:50:1:0:1 -GL000226.1 14343 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50868;SOR=Inf;LSEQ=TGAACCTTTCTTTTTACAGA;RSEQ=CAGTTTTGAAACACTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:21,15:0:2,0:25.3:1:32.1:1:1:0:22.9:72:0.973:0:1.5 0/1:52:2:1,1:34,15:0.0385:2,2:22.5:1:31:1:0.53333:2.22676:41.5:4:0.0392:0:2.5 -GL000226.1 14358 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51628;SOR=Inf;LSEQ=ACAGAGCAGTTTTGAAACAC;RSEQ=CTTTTTGTAGAATCTGCGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:0:2,0:32.9:1:30.6:1:1:0:23.1:68:1:0:1.6 0/1:52:2:1,1:33,17:0.0385:2,2:34:1:28.5:1:1:1.91492:20:4:0.0392:0:1.5 -GL000226.1 14359 . C G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=1.31588;LSEQ=CAGAGCAGTTTTGAAACACT;RSEQ=TTTTTGTAGAATCTGCGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:1,0:19,14:0.0294:2,0:46:0:32:0:1:0:20:2:0.0294:0:7 0/1:52:2:1,1:33,17:0.0385:2,2:30:1:30.5:1:1:1.91492:20:4:0.0385:0:2.5 -GL000226.1 14363 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5131;SOR=Inf;LSEQ=GCAGTTTTGAAACACTCTTT;RSEQ=TGTAGAATCTGCGAGGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:20,13:0:2,0:33.9:1:29.9:1:1:0:23.2:66:1:0:1.6 0/1:49:2:1,1:30,17:0.0408:2,2:28:1:32:1:1:1.74325:20:4:0.0408:0:2.5 -GL000226.1 14376 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52681;SOR=Inf;LSEQ=ACTCTTTTTGTAGAATCTGC;RSEQ=AGGGGAAATTTGGATAGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:0:2,0:34.7:1:30.2:1:1:0:23.7:58:1:0:2 0/1:49:2:1,1:27,20:0.0408:2,2:25.5:1:28:1:1:1.34163:20:4:0.0408:0:2.5 -GL000226.1 14382 . AA GT 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13766;SOR=0;LSEQ=TTTGTAGAATCTGCGAGGGG;RSEQ=ATTTGGATAGATTTCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:0.0667:2,2:17.5:1:27.4:1:1:1:20:4:0.0667:0.0333:6 0/0:50:0:0,0:26,24:0:2,0:31.3:1:28.9:1:1:0:23.6:49:1:0:2 -GL000226.1 14383 . A T 161 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04621;SOR=Inf;LSEQ=TTGTAGAATCTGCGAGGGGA;RSEQ=ATTTGGATAGATTTCAGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:26:13,13:1,1:0.8966:2,2:30.3:1:28.7:1:1:1:22.2:25:0.9259:0:2.1 1/1:50:50:26,24:0,0:1:0,2:30.8:1:28.6:1:1:0:23.6:49:1:0:2 -GL000226.1 14388 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13766;SOR=0;LSEQ=GAATCTGCGAGGGGAAATTT;RSEQ=GATAGATTTCAGGATTTCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:0.0667:2,2:15.5:1:29.5:1:1:1:20:4:0.0714:0:6 0/0:50:0:0,0:25,25:0:2,0:28.3:1:30.3:1:1:0:23.6:49:1:0:2 -GL000226.1 14389 . G C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13766;SOR=0;LSEQ=AATCTGCGAGGGGAAATTTG;RSEQ=ATAGATTTCAGGATTTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:0.0667:2,2:32.5:1:33.5:1:1:1:42:4:0.069:0:2 0/0:50:0:0,0:25,25:0:2,0:27.8:1:30.5:1:1:0:23.6:100:1:0:2 -GL000226.1 14390 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5216;SOR=Inf;LSEQ=ATCTGCGAGGGGAAATTTGG;RSEQ=TAGATTTCAGGATTTCGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:0:2,0:24.6:1:29.7:1:1:0:23.5:30:1:0:2.2 0/1:50:2:1,1:24,24:0.04:2,2:36:1:29:1:1:1:20:4:0.04:0:3.5 -GL000226.1 14398 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14002;SOR=0;LSEQ=GGGGAAATTTGGATAGATTT;RSEQ=AGGATTTCGTTGGAAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:13,16:0.0645:2,2:15.5:1:28:1:1:1.22:20:4:0.0645:0:6 0/0:51:0:0,0:25,26:0:2,0:22.3:1:30.5:1:1:0:23.5:50:1:0:2 -GL000226.1 14407 . G T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01162;SOR=0;LSEQ=TGGATAGATTTCAGGATTTC;RSEQ=TTGGAAACGGGAATATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:8,13:0.16:2,2:26.8:1:29.5:1:1:1.59:20:8:0.16:0:2.5 0/0:48:0:0,0:21,24:0:2,0:18.2:1:29.1:1:1:0:23:90:0.9375:0:2.1 -GL000226.1 14412 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53893;SOR=Inf;LSEQ=AGATTTCAGGATTTCGTTGG;RSEQ=AACGGGAATATCTTCATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:0:2,0:17.2:1:29.7:1:1:0:23.5:46:1:0:2.2 0/1:43:2:1,1:19,22:0.0465:2,2:14:1:30.5:1:1:1.15:20:4:0.0476:0:3.5 -GL000226.1 14415 . C G 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54413;SOR=Inf;LSEQ=TTTCAGGATTTCGTTGGAAA;RSEQ=GGGAATATCTTCATACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:5,13:0:2,0:18.8:1:29.9:1:1:0:24.1:36:0.9474:0:1.7 0/1:40:3:1,2:14,21:0.075:2,2:14:1:31:1:1:1.32357:21.3:6:0.0769:0:3 -GL000226.1 14418 . G T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29232;SOR=Inf;LSEQ=CAGGATTTCGTTGGAAACGG;RSEQ=AATATCTTCATACAAAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:4,13:0:2,0:20.6:1:30.8:1:1:0:23:34:1:0:2 0/1:30:3:1,2:7,20:0.1:2,2:9.3:1:28.7:1:1:1.41:27:6:0.1:0:3.3 -GL000226.1 14431 . C T 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=2.05485;LSEQ=GAAACGGGAATATCTTCATA;RSEQ=AAAATCTCGACAGAAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,1:0.9:0,0:31.7:1:28.2:1:1:0:20.4:18:0.9:0:2.7 1/1:20:19:0,19:0,0:0.95:0,1:27.1:1:28.4:1:1:0:20.1:38:1:0:2.8 -GL000226.1 14452 . C A 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52923;SOR=Inf;LSEQ=AAAATCTCGACAGAAGCATT;RSEQ=TCAGAAACTTCTTTGTGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:0:0,0:25.8:1:33.2:1:1:0:20.4:18:1:0:2.4 0/1:17:2:0,2:0,15:0.1176:1,0:19.5:1:31.5:1:1:0:20:4:0.1176:0:4 -GL000226.1 14474 . G C 52 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61715;LSEQ=CAGAAACTTCTTTGTGATAT;RSEQ=TGCATTCAAGTCACAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:0.3333:0,0:22.5:1:33.5:1:1:0:20:4:0.3333:0:3.5 0/1:13:3:0,3:0,10:0.2308:0,0:16.3:1:33.3:1:1:0:20.7:6:0.2308:0:4 -GL000226.1 14477 . C T 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACTTCTTTGTGATATGTG;RSEQ=ATTCAAGTCACAGAGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:0:0,0:24.7:1:33.2:1:1:0:20.7:12:1:0:1.8 0/1:13:2:0,2:0,11:0.1538:0,0:15.5:1:29.5:1:1:0:20:4:0.1538:0:3 -GL000228.1 116725 . C G 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CCCTGTAGCCATATCCTTGA;RSEQ=AAAAGTGACATCACCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:29.5:1:30:1:1:0:46.5:4:0.6667:0:4 0/0:2:0:0,0:1,0:0:0,0:8:0:32:0:1:0:31:2:0.5:0:3 -GL000228.1 116744 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAAAGTGACATCACCTGG;RSEQ=TGATCAGTGTGGAGATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:10:0:31.5:1:1:1.7321:47:4:0.4:0:6 0/0:2:0:0,0:2,0:0:0,0:31:1:33:0:1:0:35.5:4:1:0:2.5 -GL000228.1 116751 . G C 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13333;SOR=Inf;LSEQ=TGACATCACCTGGGTGATCA;RSEQ=TGTGGAGATATGTCACAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:24.8:1:33.2:1:1:0:40:12:1:0:5.8 1/0:4:2:1,1:2,0:0.5:0,2:6.5:1:30.5:1:1:0:23:4:0.5:0:4 -GL000228.1 116754 . T C 34 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69379;LSEQ=CATCACCTGGGTGATCAGTG;RSEQ=GGAGATATGTCACAATGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:2,2:0.3333:2,0:27:1:34:1:0.46667:0:26.5:4:0.3333:0:7.5 0/1:4:1:1,0:1,1:0.25:2,0:37:0:33:0:1:0:31:2:0.25:0:3 -GL000228.1 116763 . G C 33 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=GGTGATCAGTGTGGAGATAT;RSEQ=TCACAATGTCTCCAGTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:29:0:33:1:1:1.8258:47:4:0.25:0:6 0/0:5:0:0,0:3,2:0:2,0:20.6:1:31.4:1:1:0:29.6:10:1:0:3 -GL000228.1 116771 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=GTGTGGAGATATGTCACAAT;RSEQ=TCTCCAGTAGGCAGAGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:21:1:28.5:1:1:1.8258:31:4:0.25:0:7 0/0:6:0:0,0:4,2:0:2,0:20.5:1:32.5:1:1:0:31.2:12:1:0:2.8 -GL000228.1 116775 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=GGAGATATGTCACAATGTCT;RSEQ=CAGTAGGCAGAGCCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:21.5:1:28.5:1:1:1.8258:46.5:4:0.25:0:4 0/0:6:0:0,0:4,2:0:2,0:21.8:1:32:1:1:0:31.2:12:1:0:2.8 -GL000228.1 116776 . C T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=GAGATATGTCACAATGTCTC;RSEQ=AGTAGGCAGAGCCTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:21:1:28:1:1:1.8258:31:4:0.25:0:7 0/0:6:0:0,0:4,2:0:2,0:22.2:1:31.7:1:1:0:31.2:12:1:0:2.8 -GL000228.1 116788 . CC AT 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=AATGTCTCCAGTAGGCAGAG;RSEQ=TAGACAAGAGTTACATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:29:1:31.9:1:1:0:36.6:16:1:0:5.6 0/1:7:2:1,1:2,3:0.2857:2,2:25:0:31.5:1:1:1.41:23:4:0.2857:0:3 -GL000228.1 116792 . G T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TCTCCAGTAGGCAGAGCCTA;RSEQ=ACAAGAGTTACATCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:24:1:29:1:1:1:22:4:0.25:0:6.5 0/0:7:0:0,0:2,3:0:2,0:20.4:1:30.6:1:1:0:36.2:10:0.7143:0:3.4 -GL000228.1 116796 . A G 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=CAGTAGGCAGAGCCTAGACA;RSEQ=GAGTTACATCACCTGGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:28:1:32.5:1:1:1:22:4:0.25:0:6.5 0/0:7:0:0,0:3,3:0:2,0:23.2:1:31.2:1:1:0:31.2:12:0.8571:0:3.3 -GL000228.1 116799 . G A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07692;SOR=Inf;LSEQ=TAGGCAGAGCCTAGACAAGA;RSEQ=TTACATCACCTGGGTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:29:1:32.1:1:1:0:36.6:16:1:0:5.6 0/1:7:3:2,1:1,3:0.4286:2,2:30:1:29.7:1:0.48571:4.45:33.7:6:0.4286:0:2.3 -GL000228.1 116802 . A G 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=GCAGAGCCTAGACAAGAGTT;RSEQ=CATCACCTGGGTGATCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,3:0.2222:2,2:31:0:32:1:1:1.41:47:4:0.2222:0:6 0/0:7:0:0,0:3,4:0:2,0:22.3:1:29.1:1:1:0:32.4:14:1:0:3 -GL000228.1 116810 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=TAGACAAGAGTTACATCACC;RSEQ=GGGTGATCAGGGCAGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:27:1:29:1:1:2.24:40:4:0.2222:0:5 0/0:7:0:0,0:3,3:0:2,0:23:1:31.2:1:1:0:31.2:12:0.8571:0:3.2 -GL000228.1 116811 . G C 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=AGACAAGAGTTACATCACCT;RSEQ=GGTGATCAGGGCAGAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:22:0:29.5:1:1:2.24:47:4:0.2222:0:6 0/0:7:0:0,0:3,4:0:2,0:23.1:1:30.6:1:1:0:32.4:14:1:0:3 -GL000228.1 116815 . G C 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=AAGAGTTACATCACCTGGGT;RSEQ=ATCAGGGCAGAGATATGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:0.25:2,2:18:0:30.5:1:1:1.83:47:4:0.25:0:6 0/0:4:0:0,0:1,3:0:2,0:40:1:31.8:1:1:0:37.5:8:1:0:3 -GL000228.1 116821 . G C 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TACATCACCTGGGTGATCAG;RSEQ=GCAGAGATATGTCACAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:12:0:29:1:1:2.24:47:4:0.2222:0:6 0/0:5:0:0,0:1,4:0:2,0:32.8:1:29.8:1:1:0:37.8:10:1:0:2.4 -GL000228.1 116827 . G A 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=0;LSEQ=ACCTGGGTGATCAGGGCAGA;RSEQ=ATATGTCACAATGCCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:27:0:29.5:1:1:2.24:40:4:0.2222:0:5 0/0:5:0:0,0:1,4:0:2,0:33.4:1:31:1:1:0:37.8:10:1:0:2.4 -GL000228.1 116830 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=0;LSEQ=TGGGTGATCAGGGCAGAGAT;RSEQ=TGTCACAATGCCCCCTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:0.2222:2,2:31.5:1:31:1:1:2.24:22:4:0.2222:0:6.5 0/0:5:0:0,0:1,4:0:2,0:32.8:1:29.4:1:1:0:37.8:10:1:0:2.4 -GL000228.1 116835 . A T 46 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=GATCAGGGCAGAGATATGTC;RSEQ=CAATGCCCCCTGTAAGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:26.7:1:29.3:1:1:0:29.3:14:1:0:5.7 1/0:5:3:1,2:0,2:0.6:0,2:24.3:1:29.3:1:1:0:36.3:6:0.6:0:1.7 -GL000228.1 116840 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=GGGCAGAGATATGTCACAAT;RSEQ=CCCCCTGTAAGCAGATCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:2,3:0.2857:2,0:26.5:1:30:1:1:0:25.5:4:0.3333:0:5 0/0:5:0:0,0:1,4:0:2,0:29:1:32.4:1:1:0:37.8:10:1:0:2.4 -GL000228.1 116920 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTCACAATGCCCCTGTAGG;RSEQ=AGAGCCTAGACAAGAGTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5:0:31.5:1:1:0:44.5:4:1:0:3 -GL000228.1 116941 . A C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCCTAGACAAGAGTTAC;RSEQ=TAACCCAGGTGATCCGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:26:0:31.5:1:1:0:44.5:4:0.6667:0:3 -GL000228.1 116958 . T A 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATAACCCAGGTGATCCG;RSEQ=ACAGAGTGATGTCACAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:39:1:29:1:1:1:44.5:4:0.5:0:3 -GL000228.1 116991 . G C 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACAACGCCCTCTGTAGGCA;RSEQ=AGACTAGAAAAGAGTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:7:1:31:1:1:1.7321:44.5:4:0.4:0:3 -GL000228.1 117012 . T C 63 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTAGAAAAGAGTTACAT;RSEQ=ACCTGGGTGATCAGTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:32.8:1:31.8:1:1:0:41.3:8:1:0:5.5 -GL000228.1 117029 . C A 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTACCTGGGTGATCAGTG;RSEQ=AGAGATATGTCACAATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:30.5:1:27.5:1:1:1:25:4:0.3333:0:4.5 -GL000228.1 117042 . C A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAGTGCAGAGATATGTCA;RSEQ=AATGCCCCCTGTAGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:10:0:33:0:1:0:36:2:1:0:6 1/0:6:3:2,1:1,2:0.5:2,2:26.7:1:29.7:1:1:3.11:25.3:6:0.5:0:5.3 -GL000228.1 117050 . C T 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGATATGTCACAATGCCC;RSEQ=CTGTAGGCAGAGCATAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:18:0:33:0:1:0:36:2:1:0:5 0/1:7:2:1,1:1,3:0.2857:2,2:12:1:30.5:1:1:2.45:45.5:4:0.2857:0:4.5 -GL000228.1 117056 . G T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTCACAATGCCCCCTGTA;RSEQ=GCAGAGCATAGAGAAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:24:0:34:0:1:0:36:2:1:0:5 0/1:6:2:1,1:2,2:0.3333:2,2:18:1:32:0:1:1:45.5:4:0.3333:0:4.5 -GL000228.1 117097 . GT TA 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCATCACCTGGGTGATCAGT;RSEQ=AGAGATATGTCACAATGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:36:0:30:0:1:0:36:2:1:0:5 0/1:5:2:1,1:1,2:0.4:2,2:41:1:27.8:1:1:1.73:45.5:4:0.4:0:3.5 -GL000228.1 117113 . A G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTGTAGAGATATGTCACA;RSEQ=TGTCCCCTGTAGGCAGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:20:0:26:0:1:0:36:2:1:0:5 1/0:4:2:1,1:1,1:0.5:2,2:22:1:29.5:1:1:1:26:4:0.5:0:6.5 -GL000228.1 117120 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGATATGTCACAATGTCCC;RSEQ=TGTAGGCAGAGCACAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:13:0:26:0:1:0:36:2:1:0:5 1/0:4:2:1,1:1,1:0.5:2,2:22:1:28.5:1:1:1:26:4:0.5:0:6.5 -GL000228.1 117171 . G T 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.8918;LSEQ=ACCTGGGTGATCAGTGCAGA;RSEQ=ATATGTCACAATGTCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:12.5:1:33:0:1:0:34:4:0.5:0:3.5 1/0:9:6:6,0:2,1:0.6667:2,0:12:1:31.2:1:0.33333:0:31.5:12:0.6667:0:3.2 -GL000228.1 117178 . CA C 75 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.64297;LSEQ=TGATCAGTGCAGAGATATGT;RSEQ=CAATGTCCCCTGTAGGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:20.5:1:32.5:1:1:0:34:4:0.5:0:3.5 0/1:13:5:5,0:4,2:0.3846:2,0:15:1:32.6:1:0.45455:0:35:10:0.3846:0.1538:3.2 -GL000228.1 117180 . CAATGTC AATGTT 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49474;SOR=Inf;LSEQ=ATCAGTGCAGAGATATGTCA;RSEQ=CCCTGTAGGCAAAGCCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:11:1:31.5:1:1:0:31.8:16:1:0:3.9 0/1:12:2:1,1:7,2:0.1667:2,2:16:1:30.6:1:0.49091:3.05504:26.5:4:0.1818:0.0833:4 -GL000228.1 117186 . C T 45 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.04769;LSEQ=GCAGAGATATGTCACAATGT;RSEQ=CCCTGTAGGCAAAGCCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:7:0:28:1:1:2.23609:32:4:0.2222:0:5.5 0/1:13:3:2,1:8,2:0.2308:2,2:11.7:1:28.7:1:1:1.88511:46.7:6:0.2308:0:3.7 -GL000228.1 117195 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48506;SOR=Inf;LSEQ=TGTCACAATGTCCCCTGTAG;RSEQ=CAAAGCCTAGGCAAGAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,5:0:2,0:15.3:1:30:1:1:0:33.1:13:1:0:4.3 0/1:16:2:2,0:10,4:0.125:2,0:25.5:1:31:0:1:0:31.5:4:0.125:0:3 -GL000228.1 117202 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48589;SOR=Inf;LSEQ=ATGTCCCCTGTAGGCAAAGC;RSEQ=TAGGCAAGAGTTACATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:19.1:1:31.1:1:1:0:34.9:30:1:0:4.5 0/1:17:2:1,1:12,3:0.1176:2,2:27.5:1:30:1:0.42647:3.6058:41.5:4:0.1176:0:3 -GL000228.1 117204 . A G 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21169;SOR=0;LSEQ=GTCCCCTGTAGGCAAAGCCT;RSEQ=GGCAAGAGTTACATCACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:9,4:0.1333:2,2:25:0:31:1:1:2.12136:39:4:0.1429:0:4.5 0/0:17:0:0,0:13,4:0:2,0:31.5:1:29:1:1:0:34.9:34:1:0:3.5 -GL000228.1 117207 . C G 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4958;SOR=Inf;LSEQ=CCCTGTAGGCAAAGCCTAGG;RSEQ=AAGAGTTACATCACCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:22.3:1:30.7:1:1:0:34.9:14:1:0:4.5 0/1:20:2:1,1:14,4:0.1:2,2:35:1:29.5:1:0.44737:3.24034:28:4:0.1:0:4 -GL000228.1 117211 . A T 47 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05668;SOR=0;LSEQ=GTAGGCAAAGCCTAGGCAAG;RSEQ=GTTACATCACCTTTGTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:8,3:0.1875:2,2:29.3:1:30:1:1:1.30524:40:6:0.2143:0:5.3 0/0:24:0:0,0:14,5:0:2,0:24.3:1:29.7:1:1:0:33.8:38:0.7917:0:4.1 -GL000228.1 117213 . T C 34 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50244;SOR=Inf;LSEQ=AGGCAAAGCCTAGGCAAGAG;RSEQ=TACATCACCTTTGTCATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:0:2,0:23.4:1:29.2:1:1:0:37.5:16:1:0:5.4 0/1:24:2:1,1:16,6:0.0833:2,2:7:0:34:0:0.50725:2.54484:25:4:0.0833:0:4.5 -GL000228.1 117215 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1777;SOR=0;LSEQ=GCAAAGCCTAGGCAAGAGTT;RSEQ=CATCACCTTTGTCATCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:11,5:0.1111:2,2:31:1:31:1:1:2.09766:25:4:0.1176:0:6 0/0:24:0:0,0:17,7:0:2,0:29.3:1:28.5:1:1:0:34.2:48:1:0:4 -GL000228.1 117222 . C T 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0769;SOR=0;LSEQ=CTAGGCAAGAGTTACATCAC;RSEQ=TTTGTCATCAGTTCAGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:10,6:0.1429:2,2:40.3:1:31.7:1:1:1.19:40:6:0.15:0:5.3 0/0:27:0:0,0:17,9:0:2,0:29.1:1:30.5:1:1:0:34.3:52:0.963:0:4.2 -GL000228.1 117224 . T C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13625;SOR=0.28525;LSEQ=AGGCAAGAGTTACATCACCT;RSEQ=TGTCATCAGTTCAGGGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:5,1:8,7:0.2857:2,2:22.2:1:32.5:1:0.33591:4.10:42.8:12:0.2857:0:6.3 0/1:30:3:2,1:16,11:0.1:2,2:20.3:1:32:1:1:1.36:44.7:6:0.1:0:6.7 -GL000228.1 117233 . G C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.74469;SOR=1.35413;LSEQ=TTACATCACCTTTGTCATCA;RSEQ=TTCAGGGATATGTGAAAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:11,8:0.16:2,2:20:1:34:1:1:1.35584:43.3:8:0.1667:0:7.3 0/1:34:7:4,3:14,11:0.2059:2,2:27.1:1:30.7:1:1:1.05:36.6:14:0.2059:0:5.3 -GL000228.1 117243 . A G 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50273;SOR=Inf;LSEQ=TTTGTCATCAGTTCAGGGAT;RSEQ=TGTGAAAACGCCCCTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:29:1:28.9:1:1:0:39.8:12:1:0:5.7 0/1:35:2:1,1:18,15:0.0571:2,2:14.5:1:27.5:1:1:1.19373:27:4:0.0571:0:5.5 -GL000228.1 117247 . GA TG 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50502;SOR=Inf;LSEQ=TCATCAGTTCAGGGATATGT;RSEQ=AAACGCCCCTGTAGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:0:2,0:29.3:1:31.2:1:1:0:39.8:25:1:0:5.7 0/1:36:2:1,1:19,15:0.0556:2,2:16:1:26.4:1:1:1.2583:27:4:0.0556:0.0278:4.5 -GL000228.1 117248 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00386;SOR=0.18284;LSEQ=CATCAGTTCAGGGATATGTG;RSEQ=AAACGCCCCTGTAGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:20:10,10:4,2:0.7692:2,2:30.8:1:30.9:1:0.65217:1.94818:39:19:0.76:0:5.8 0/1:35:13:7,6:12,9:0.3714:2,2:25:1:30.6:1:1:1.13836:41.5:26:0.3824:0:4.8 -GL000228.1 117250 . A C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1776;SOR=0;LSEQ=TCAGTTCAGGGATATGTGAA;RSEQ=ACGCCCCTGTAGGCAGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:13,11:0.0769:2,2:34:1:33:1:1:1.17422:24.5:4:0.0769:0:6.5 0/0:35:0:0,0:19,16:0:2,0:25.3:1:29.1:1:1:0:35.4:34:1:0:4.8 -GL000228.1 117253 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50273;SOR=Inf;LSEQ=GTTCAGGGATATGTGAAAAC;RSEQ=CCCCTGTAGGCAGAGCTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,12:0:2,0:29.8:1:30.5:1:1:0:39.8:24:0.96:0:5.8 0/1:35:2:1,1:18,15:0.0571:2,2:18.5:1:29:1:1:1.19373:23:4:0.0571:0:4 -GL000228.1 117257 . C A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50565;SOR=Inf;LSEQ=AGGGATATGTGAAAACGCCC;RSEQ=TGTAGGCAGAGCTTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:0:2,0:30.8:1:32:1:1:0:40.4:50:1:0:5.8 0/1:35:2:1,1:18,15:0.0571:2,2:23.5:1:27.5:1:1:1.19373:40:4:0.0571:0:5.5 -GL000228.1 117263 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49854;SOR=Inf;LSEQ=ATGTGAAAACGCCCCTGTAG;RSEQ=CAGAGCTTAGACAAGAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:29.5:1:30.9:1:1:0:40.2:25:1:0:5.8 0/1:33:2:1,1:16,15:0.0606:2,2:7:0:31.5:1:1:1.06462:41.5:4:0.0606:0:3 -GL000228.1 117266 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49499;SOR=Inf;LSEQ=TGAAAACGCCCCTGTAGGCA;RSEQ=AGCTTAGACAAGAGTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:0:2,0:28.5:1:31.5:1:1:0:40.2:52:1:0:5.8 0/1:31:2:1,1:14,15:0.0645:2,2:41.5:1:29.5:1:1:1.07:42:4:0.0645:0:6.5 -GL000228.1 117268 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24242;SOR=Inf;LSEQ=AAAACGCCCCTGTAGGCAGA;RSEQ=CTTAGACAAGAGTTACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:0:2,0:28.7:1:31.5:1:1:0:40.1:24:1:0:5.9 0/1:30:3:2,1:12,15:0.1:2,2:14.3:1:27.7:1:0.58621:2.43:23.7:6:0.1:0:3.7 -GL000228.1 117270 . T C 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.89276;LSEQ=AACGCCCCTGTAGGCAGAGC;RSEQ=TAGACAAGAGTTACATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:1,0:10,13:0.0417:2,0:38:0:32:0:0.45833:0:40:2:0.0435:0:4 0/1:26:2:1,1:10,13:0.0769:2,2:32.5:1:31.5:1:1:1.29:31.5:4:0.0833:0:5.5 -GL000228.1 117272 . A G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70078;SOR=0.5768;LSEQ=CGCCCCTGTAGGCAGAGCTT;RSEQ=GACAAGAGTTACATCACCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:20:8,12:1,0:0.8696:0,2:27.2:1:31.4:1:0.42857:0:39.4:40:0.8696:0:6.2 1/0:24:19:8,11:1,2:0.7917:2,2:30.9:1:31.3:1:1:1.43:36.5:38:0.7917:0:5.6 -GL000228.1 117274 . A T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48986;SOR=Inf;LSEQ=CCCCTGTAGGCAGAGCTTAG;RSEQ=CAAGAGTTACATCACCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:29.4:1:30:1:1:0:39.9:44:1:0:6.2 0/1:24:2:1,1:9,13:0.0833:2,2:42.5:1:30:1:1:1.42:43:4:0.087:0:7.5 -GL000228.1 117275 . C T 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05142;LSEQ=CCCTGTAGGCAGAGCTTAGA;RSEQ=AAGAGTTACATCACCTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:7,9:0.2:2,2:39:1:29:1:1:1.27:43.3:8:0.2:0:7.3 0/1:24:5:2,3:8,11:0.2083:2,2:32.8:1:29.8:1:1:1.08701:40.6:10:0.2083:0:6.4 -GL000228.1 117279 . A G 125 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.27798;LSEQ=GTAGGCAGAGCTTAGACAAG;RSEQ=GTTACATCACCTAGTTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:7,7:1,1:0.7368:2,2:31:1:31.2:1:1:1:41.4:28:0.7778:0:6.8 1/0:23:18:9,9:1,2:0.7826:2,2:25.3:1:30:1:1:1.94:37.3:17:0.7727:0:5.6 -GL000228.1 117286 . T C 129 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43814;SOR=2.13482;LSEQ=GAGCTTAGACAAGAGTTACA;RSEQ=CACCTAGTTGATCAGTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:6,7:0,1:0.7222:0,2:24:1:30.9:1:1:0:42.8:26:0.7647:0:6.7 1/1:20:17:7,10:1,2:0.85:2,2:24.9:1:31.7:1:1:1.38:37.6:34:0.85:0:5.9 -GL000228.1 117296 . G T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62539;LSEQ=AAGAGTTACATCACCTAGTT;RSEQ=ATCAGTGCAGAGATATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:6,7:1,0:0.8667:0,2:21.2:1:28.4:1:1:0:44.3:26:0.8667:0:6.6 1/1:15:12:4,8:1,2:0.8:2,2:25.3:1:29.4:1:1:1:40.2:24:0.8:0:6.4 -GL000228.1 117312 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48188;SOR=0;LSEQ=AGTTGATCAGTGCAGAGATA;RSEQ=TTCACAATACCCCCTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:4,7:0.1538:2,2:7:1:30.5:1:1:1.67:43:4:0.1538:0:6.5 0/0:11:0:0,0:3,8:0:2,0:18.1:1:30.1:1:1:0:36.2:22:1:0:6.4 -GL000228.1 117322 . C A 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.57576;SOR=2.28835;LSEQ=TGCAGAGATATTTCACAATA;RSEQ=CCCCTGTAGGCAGATCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:11.5:1:29.5:1:1:0:41.5:4:0.5:0:6.5 1/0:7:5:2,3:1,1:0.7143:2,2:11.4:1:28.6:1:1:1.41418:36.2:10:0.7143:0:7.4 -GL000228.1 117325 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=AGAGATATTTCACAATACCC;RSEQ=CTGTAGGCAGATCCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:0.3333:2,0:17:0:32:0:1:0:40:2:0.3333:0:7 1/0:4:2:1,1:1,1:0.5:2,2:13:1:28.5:1:1:1:34.5:4:0.5:0:8 -GL000228.1 117454 . G A 47 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCAGTGCAGAGATTTGTC;RSEQ=AAATTCCCTGTAGGCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:0.75:0,0:39:1:30:1:1:0:30.7:6:0.75:0:2.7 1/1:1:1:0,1:0,0:1:0,0:1:0:29:0:1:0:40:2:1:0:1 -GL000228.1 117474 . C A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATTCCCTGTAGGCAGTG;RSEQ=TTATAAAAGTGTTACATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:45:1:31.5:1:1:0:26:4:0.6667:0:3 0/0:1:0:0,0:0,1:0:0,0:21:0:34:0:1:0:40:2:1:0:1 -GL000228.1 118092 . C A 32 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.57733;LSEQ=CCCTGTAGGCAGATCCTAGA;RSEQ=AAGAGTTACATGACCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:27.5:1:32.5:1:1:0:34.5:4:0.6667:0:5.5 1/0:2:1:1,0:1,0:0.5:0,0:26:0:26:0:1:0:35:2:0.5:0:3 -GL000228.1 118104 . G C 65 d7;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATCCTAGACAAGAGTTACAT;RSEQ=ACCTGGGTGATCAGTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:34.3:1:32.5:1:1:0:34:8:1:0:6 1/0:2:1:1,0:0,0:0.5:0,0:14:0:26:0:1:0:35:2:0.5:0:3 -GL000228.1 118106 . C A 26 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=CCTAGACAAGAGTTACATGA;RSEQ=CTGGGTGATCAGTGCAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:0.4:0,2:18.5:1:26:1:0.4:0:36:4:0.4:0:5.5 0/0:4:0:0,0:3,1:0:2,0:9.8:1:27.3:1:1:0:33.5:8:1:0:3.3 -GL000228.1 118111 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ACAAGAGTTACATGACCTGG;RSEQ=TGATCAGTGCAGAGATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:15:1:29.5:1:1:2.44949:40:4:0.3333:0:6 0/0:4:0:0,0:3,1:0:2,0:9.8:1:27.3:1:1:0:33.5:8:1:0:3.3 -GL000228.1 118120 . G T 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=ACATGACCTGGGTGATCAGT;RSEQ=CAGAGATATGTCACAATGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,2:0.2857:2,2:19:1:27.5:1:1:1:27:4:0.2857:0:6.5 0/0:4:0:0,0:2,2:0:2,0:11.5:1:29.5:1:1:0:33.5:8:1:0:2.8 -GL000228.1 118121 . C T 27 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=CATGACCTGGGTGATCAGTG;RSEQ=AGAGATATGTCACAATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:15:0:27.5:1:1:1:40:4:0.25:0:6 0/0:4:0:0,0:2,2:0:2,0:12:1:30:1:1:0:33.5:8:1:0:2.8 -GL000228.1 118122 . A C 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=0;LSEQ=ATGACCTGGGTGATCAGTGC;RSEQ=GAGATATGTCACAATGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:18.5:1:29:1:1:1:36:4:0.25:0:5.5 0/0:4:0:0,0:2,2:0:2,0:12.5:1:28.5:1:1:0:33.5:8:1:0:2.8 -GL000228.1 118126 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=0;LSEQ=CCTGGGTGATCAGTGCAGAG;RSEQ=TATGTCACAATGCCACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:19:1:29.5:1:1:1:27:4:0.2857:0:6.5 0/0:4:0:0,0:2,2:0:2,0:14.5:1:28.8:1:1:0:33.5:8:1:0:2.8 -GL000228.1 118131 . T C 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATCAGTGCAGAGATATG;RSEQ=CACAATGCCACTGTAGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:19:1:30.5:1:1:1:27:4:0.25:0:6.5 0/0:3:0:0,0:1,2:0:2,0:23.3:1:28.7:1:1:0:31:6:1:0:2.3 -GL000228.1 118143 . TG CA 30 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=GAGATATGTCACAATGCCAC;RSEQ=TAGGCAGAGCCTAGACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:30.2:1:29.3:1:1:0:32.7:12:1:0:4.7 1/0:4:2:1,1:0,2:0.5:0,2:40:0:30.5:1:1:0:29:4:0.5:0:2 -GL000228.1 118153 . G T 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=ACAATGCCACTGTAGGCAGA;RSEQ=CCTAGACAAGAGTTACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:33.5:1:31.7:1:1:0:32.7:12:1:0:4.7 0/1:5:2:0,2:1,2:0.4:2,0:14.5:1:31:0:1:0:39.5:4:0.4:0:6.5 -GL000228.1 118158 . G A 47 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GCCACTGTAGGCAGAGCCTA;RSEQ=ACAAGAGTTACATGACCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:0.6:0,2:38.7:1:29.7:1:1:0:34:6:0.6:0:3 0/0:5:0:0,0:1,4:0:2,0:32.4:1:32.2:1:1:0:34.4:10:1:0:3.6 -GL000228.1 118163 . G T 48 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=TGTAGGCAGAGCCTAGACAA;RSEQ=AGTTACATGACCTAGGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:40.2:1:31:1:1:0:33.8:10:1:0:4.2 1/0:5:3:1,2:0,2:0.6:0,2:30:1:30.3:1:1:0:32.3:6:0.6:0:3.3 -GL000228.1 118201 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77722;LSEQ=GATCAGTGCAGAGATACATC;RSEQ=CAATGCCCCTGTAGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:17:0:32:0:0.4:0:33.5:4:0.4:0:5.5 0/1:3:1:0,1:0,2:0.3333:0,0:34:0:32:0:1:0:40:2:0.3333:0:7 -GL000228.1 118237 . C T 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAGAGCCTTGACAAGTGGTA;RSEQ=ATCACCTGGGTGATCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:29:1:32.5:1:1:0:35:4:1:0:4.5 0/0:1:0:0,0:1,0:0:0,0:29:0:33:0:1:0:24:2:1:0:1 -GL000228.1 118265 . TGTCACAAAGCACCCTGTAAGCAGATCCTAGAGAAGAGTTATATCACCTGGGTGATCAGTGCAGAG T 48 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=GGGTGATCATTGCAGGGATA;RSEQ=ATATGTCACAAGCCCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:29:1:34:0:1:0:35:4:1:0:4.5 1/1:3:3:2,1:0,0:1:0,2:31.3:1:30.4:1:1:0:37.3:6:1:1:2.7 -GL000228.1 118323 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20308;SOR=0;LSEQ=TTATATCACCTGGGTGATCA;RSEQ=TGCAGAGATATGTCACAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:8,2:0.1667:2,2:25.5:1:31.5:1:0.45455:3.4638:38:4:0.1667:0:4.5 0/0:14:0:0,0:8,5:0:2,0:15.9:1:31.9:1:1:0:33.9:26:1:0:5.4 -GL000228.1 118324 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48308;SOR=Inf;LSEQ=TATATCACCTGGGTGATCAG;RSEQ=GCAGAGATATGTCACAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:8,2:0:2,0:23.1:1:31.6:1:1:0:27.8:20:0.8333:0:5.7 0/1:14:2:1,1:7,4:0.1429:2,2:6:0:32.5:1:1:1.67325:44:4:0.1538:0:6.5 -GL000228.1 118330 . GA TG 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49194;SOR=Inf;LSEQ=ACCTGGGTGATCAGTGCAGA;RSEQ=TATGTCACAAGCCCCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,3:0:2,0:21.1:1:32.8:1:1:0:30.1:26:0.9286:0:5.4 0/1:18:2:1,1:8,5:0.1111:2,2:13:0:32.8:1:1:1.54914:41:4:0.1333:0:5 -GL000228.1 118331 . A G 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.15349;SOR=0.32039;LSEQ=CCTGGGTGATCAGTGCAGAG;RSEQ=TATGTCACAAGCCCCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:5,2:5,2:0.5:2,2:26.9:1:32.4:1:1:1:27.4:14:0.5:0:5.4 0/1:17:4:3,1:6,5:0.2353:2,2:27.3:1:31:1:0.6044:2.36:29.5:8:0.2667:0:5.5 -GL000228.1 118334 . T G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.472;SOR=0.47285;LSEQ=GGGTGATCAGTGCAGAGATA;RSEQ=GTCACAAGCCCCCTGTAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:5,2:5,2:0.5:2,2:28.1:1:32.7:1:1:1:27.4:14:0.5:0:5.4 0/1:19:6:4,2:7,6:0.3158:2,2:25.5:1:32:1:1:1.67:33.3:12:0.3158:0:5.3 -GL000228.1 118335 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51111;SOR=Inf;LSEQ=GGTGATCAGTGCAGAGATAT;RSEQ=TCACAAGCCCCCTGTAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,4:0:2,0:25.4:1:32.4:1:1:0:30.1:28:1:0:5.3 0/1:22:2:1,1:11,9:0.0909:2,2:9:0:32:0:1:1.21106:44:4:0.0909:0:3.5 -GL000228.1 118342 . G T 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.5164;SOR=0.61416;LSEQ=AGTGCAGAGATATGTCACAA;RSEQ=CCCCCTGTAGGCAGAGCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:5,3:5,1:0.5333:2,2:27:1:30.9:1:0.58042:2.77987:26.8:16:0.5333:0:5.4 0/1:22:9:5,4:7,6:0.4091:2,2:24.9:1:29.3:1:1:1.07:34.2:18:0.4091:0:5.2 -GL000228.1 118343 . C A 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.46566;SOR=2.23644;LSEQ=GTGCAGAGATATGTCACAAG;RSEQ=CCCCTGTAGGCAGAGCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:7,4:0.2:2,0:40:1:31.3:1:0.50549:0:28.7:6:0.2143:0:6.3 0/1:22:8:5,3:7,7:0.3636:2,2:25.4:1:29.6:1:0.67492:1.63:37.8:16:0.3636:0:6.1 -GL000228.1 118346 . CC AT 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.29596;SOR=2.41906;LSEQ=CAGAGATATGTCACAAGCCC;RSEQ=TGTAGGCAGAGCCTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:7,5:0.1875:2,0:41.3:1:32:1:0.50549:0:28.7:6:0.2:0:5.3 0/1:22:8:5,3:7,7:0.3636:2,2:28.4:1:29.5:1:0.67492:1.63:37.8:16:0.3636:0:5.1 -GL000228.1 118347 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=AGAGATATGTCACAAGCCCC;RSEQ=TGTAGGCAGAGCCTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,5:0:2,0:23.6:1:31:1:1:0:30.6:24:1:0:5 0/1:22:2:1,1:6,6:0.0909:2,2:41.5:1:30:1:1:1:24:4:0.1429:0:3 -GL000228.1 118348 . T A 47 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06128;SOR=0;LSEQ=GAGATATGTCACAAGCCCCC;RSEQ=GTAGGCAGAGCCTAGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:8,4:0.1875:2,2:14:1:29.7:1:1:1:42:6:0.2:0:4 0/0:23:0:0,0:12,11:0:2,0:28:1:30.1:1:1:0:34.6:46:1:0:5 -GL000228.1 118352 . G C 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.4595;LSEQ=TATGTCACAAGCCCCCTGTA;RSEQ=GCAGAGCCTAGACAAGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,5:0.125:2,2:43.5:1:31.5:1:1:1.54914:25:4:0.1333:0:6 0/1:23:4:2,2:10,9:0.1739:2,2:26:1:26.3:1:1:1.10603:43.5:3:0.1429:0:5.3 -GL000228.1 118358 . G T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25366;SOR=Inf;LSEQ=ACAAGCCCCCTGTAGGCAGA;RSEQ=CCTAGACAAGAGTTATATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:0:2,0:30.1:1:32:1:1:0:27.8:34:1:0:4.9 0/1:24:3:2,1:11,10:0.125:2,2:26.3:1:31:1:1:1.77:25:6:0.125:0:3.7 -GL000228.1 118360 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56243;SOR=0.34207;LSEQ=AAGCCCCCTGTAGGCAGAGC;RSEQ=TAGACAAGAGTTATATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:0.1111:2,2:32.5:1:31.5:1:1:1.61828:44:4:0.1111:0:3.5 0/1:25:1:1,0:12,12:0.04:2,0:27:0:32:0:1:0:27:2:0.04:0:7 -GL000228.1 118362 . A T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50101;SOR=Inf;LSEQ=GCCCCCTGTAGGCAGAGCCT;RSEQ=GACAAGAGTTATATCACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,8:0:2,0:26.7:1:29.1:1:1:0:27.6:36:0.9474:0:4.8 0/1:26:2:1,1:13,11:0.0769:2,2:36:0:31.5:1:1:1.17422:41:4:0.0769:0:4.5 -GL000228.1 118363 . G T 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76051;SOR=0.70017;LSEQ=CCCCCTGTAGGCAGAGCCTA;RSEQ=ACAAGAGTTATATCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:5,4:6,4:0.4737:2,2:29.7:1:29.3:1:1:1.18851:23:18:0.4737:0:5.2 0/1:26:10:5,5:9,6:0.3846:2,2:34.2:1:28.3:1:0.69683:1.47557:33:20:0.4:0:5.1 -GL000228.1 118364 . A T 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50101;SOR=Inf;LSEQ=CCCCTGTAGGCAGAGCCTAG;RSEQ=CAAGAGTTATATCACCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:28:1:29.3:1:1:0:27.6:38:1:0:4.8 0/1:26:2:1,1:13,11:0.0769:2,2:46:0:30.5:1:1:1.17422:44:4:0.0769:0:5.5 -GL000228.1 118365 . C G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.48703;LSEQ=CCCTGTAGGCAGAGCCTAGA;RSEQ=AAGAGTTATATCACCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:10,8:0.0526:2,0:7:0:34:0:1:0:27:2:0.0526:0:4 0/1:26:2:2,0:12,12:0.0769:2,0:8.5:1:33.5:1:0.48308:0:25.5:4:0.0769:0:5 -GL000228.1 118372 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50101;SOR=Inf;LSEQ=GGCAGAGCCTAGACAAGAGT;RSEQ=ATATCACCTGGGTGATCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:0:2,0:27.4:1:29.3:1:1:0:27.6:38:1:0:4.8 0/1:26:2:1,1:13,11:0.0769:2,2:33.5:1:30:1:1:1.17422:44:4:0.08:0:3.5 -GL000228.1 118373 . A G 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.72028;SOR=0.67283;LSEQ=GCAGAGCCTAGACAAGAGTT;RSEQ=TATCACCTGGGTGATCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:4,1:7,7:0.2632:2,2:24.8:1:32.4:1:0.33781:3.73:26.4:10:0.2632:0:5 0/1:26:5:3,2:10,9:0.1923:2,2:31.4:1:29.4:1:1:1.33:31.4:10:0.1923:0:5.2 -GL000228.1 118378 . A G 95 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.22965;LSEQ=GCCTAGACAAGAGTTATATC;RSEQ=CCTGGGTGATCAGTGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:5,1:7,7:0.3:2,2:23.2:1:29.2:1:0.32456:4.63:26.5:12:0.3:0:4.8 0/1:26:9:6,3:8,9:0.3462:2,2:29.6:1:30.1:1:0.42911:2.18:32.2:18:0.3462:0:5 -GL000228.1 118383 . G C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17576;SOR=0;LSEQ=GACAAGAGTTATATCACCTG;RSEQ=GTGATCAGTGCAGTGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,7:0.1:2,2:24:0:33:1:1:1.53525:44:4:0.1:0:3.5 0/0:27:0:0,0:15,12:0:2,0:25.2:1:30.7:1:1:0:33.1:54:1:0:4.8 -GL000228.1 118384 . G T 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77101;SOR=1.29291;LSEQ=ACAAGAGTTATATCACCTGG;RSEQ=TGATCAGTGCAGTGATATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:4,4:9,4:0.381:2,2:23.8:1:29.4:1:0.64582:2.16102:22.8:16:0.381:0:5.4 0/1:27:12:6,6:9,6:0.4444:2,2:21.7:1:29.9:1:0.70682:1.4774:31.5:24:0.4444:0:4.8 -GL000228.1 118389 . C T 28 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49491;SOR=Inf;LSEQ=AGTTATATCACCTGGGTGAT;RSEQ=AGTGCAGTGATATGTCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:11,9:0:2,0:22.5:1:31.4:1:1:0:27.6:40:0.9524:0:4.6 0/1:26:2:1,1:13,11:0.0769:2,2:18:0:28:1:1:1.17422:43:4:0.0769:0:5 -GL000228.1 118402 . T A 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70102;SOR=0.67313;LSEQ=GGGTGATCAGTGCAGTGATA;RSEQ=GTCACAATGCTGTGTAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:3,1:6,8:0.2222:2,2:23.3:1:30.5:1:0.57647:3.71:24.5:8:0.2222:0:4.3 0/1:25:4:2,2:11,10:0.16:2,2:21.8:1:31:1:1:1.09581:33:8:0.16:0:5.5 -GL000228.1 118405 . C A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5703;SOR=0.36672;LSEQ=TGATCAGTGCAGTGATATGT;RSEQ=ACAATGCTGTGTAGCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:23.5:1:28:1:1:1.13:22:4:0.1176:0:5.5 0/1:22:1:1,0:11,10:0.0455:2,0:1:0:23:0:1:0:44:2:0.0455:0:4 -GL000228.1 118413 . T C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32174;SOR=0.26388;LSEQ=GCAGTGATATGTCACAATGC;RSEQ=GTGTAGCCAGAGCCTAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:4,8:0,0:0.9231:0,2:29.6:1:29.7:1:1:0:26.3:24:1:0:4.1 1/0:12:9:6,3:0,0:0.75:0,2:24.7:1:28.8:1:1:0:24.6:8:0.7273:0:4.9 -GL000228.1 118422 . A G 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17143;SOR=Inf;LSEQ=TGTCACAATGCTGTGTAGCC;RSEQ=GAGCCTAGACAAAAGTTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:0:2,0:30.8:1:30.7:1:1:0:26:24:1:0:4.2 0/1:9:2:2,0:3,4:0.2222:2,0:35.5:1:28:1:0.44444:0:24:4:0.2222:0:4.5 -GL000228.1 118433 . A T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.47033;LSEQ=TGTGTAGCCAGAGCCTAGAC;RSEQ=AAAGTTACAGCACCTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:2,6:2,2:0.6667:2,2:24.4:1:28.6:1:0.54747:2.71347:26.8:16:0.6667:0:4.5 1/0:8:6:5,1:1,1:0.75:2,2:33.2:1:29.8:1:0.46429:3.87:24.8:12:0.75:0:4.2 -GL000228.1 118437 . G T 60 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80935;LSEQ=TAGCCAGAGCCTAGACAAAA;RSEQ=TTACAGCACCTGGGAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:2,2:2,6:0.3333:2,2:34:1:30.3:1:0.54747:2.71:24.5:8:0.3333:0:3.5 0/1:7:2:1,1:4,1:0.2857:2,2:26.5:1:31.5:1:1:3.1622:26:4:0.2857:0:5 -GL000228.1 118482 . C A 76 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.0101;SOR=27.24464;LSEQ=AGAGATATGTCACAATGTCC;RSEQ=CAGTAGGCAGAGACCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:1,6:0.125:2,0:20:0:32:0:1:0:27:2:0.125:0:3 1/1:7:6:3,3:0,1:0.8571:0,2:24.7:1:29.7:1:1:0:25.5:12:0.8571:0:3.3 -GL000228.1 118510 . G T 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10256;SOR=9.83818;LSEQ=CAGAGACCAGGCAAGAGTTG;RSEQ=ATCACCTCGGGATCAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,5:0.1667:0,0:48:0:29:0:1:0:27:2:0.1667:0:3 1/0:7:5:1,4:0,2:0.7143:0,2:34.4:1:27.8:1:1:0:25.8:10:0.7143:0:2.6 -GL000228.1 118541 . T C 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.10989;SOR=0;LSEQ=GATCAGTGCAGAGATATGTC;RSEQ=CAATCCCCCTGTGGGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:12:1:32:0:0.4:0:23.5:4:0.4:0:6 0/0:9:0:0,0:2,6:0:2,0:23.8:1:29.3:1:1:0:25.8:16:0.8889:0:2.8 -GL000228.1 118577 . C A 45 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CACAGCCTAGACAAGAGTTA;RSEQ=ATCACCTCGGTTAACAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:35.5:1:31.5:1:1:0:26:4:1:0:3.5 1/0:4:3:1,2:0,1:0.75:0,2:32:1:29:1:1:0:25.3:6:0.75:0:3.3 -GL000228.1 118651 . T A 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=4.4496;LSEQ=TACACAAGTATTACATCACT;RSEQ=AGGTGATCAGTGCAGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:0.3333:2,0:4:0:30:0:1:0:25:2:0.3333:0:5 1/0:4:3:3,0:0,0:0.75:0,0:8.7:1:29.7:1:1:0:32.3:6:0.75:0:5.3 -GL000228.1 118666 . G T 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24476;SOR=5.98921;LSEQ=TCACTTAGGTGATCAGTGCA;RSEQ=AGATATGTCACAATACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:1,2:0.5:2,0:14.3:1:32.3:1:0.4:0:24.7:6:0.5:0:6.3 1/1:8:7:6,1:1,0:0.875:0,2:18.6:1:29.3:1:1:0:28.9:14:0.875:0:5.4 -GL000228.1 118669 . A T 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53846;SOR=0.31377;LSEQ=CTTAGGTGATCAGTGCAGAG;RSEQ=TATGTCACAATACCCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:13.5:1:32:0:1:2.44949:25:4:0.3333:0:4 0/1:8:1:1,0:6,1:0.125:2,0:18:0:32:0:1:0:24:2:0.125:0:6 -GL000228.1 118674 . T G 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=GTGATCAGTGCAGAGATATG;RSEQ=CACAATACCCCCTGTAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:27.5:1:31:1:1:2.44949:44:4:0.3333:0:3.5 0/0:8:0:0,0:7,1:0:2,0:26:1:29.9:1:1:0:28:16:1:0:5.3 -GL000228.1 118682 . CC TG 96 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.28006;SOR=4.0655;LSEQ=TGCAGAGATATGTCACAATA;RSEQ=CCCTGTAAGCAGAGCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:1,2:0.5:2,0:31.3:1:33:1:0.4:0:24.7:6:0.5:0:5.3 1/1:11:9:6,3:0,0:0.8182:0,2:28.8:1:30.5:1:1:0:30.1:18:0.8182:0.0909:4.3 -GL000228.1 118689 . T G 99 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61262;SOR=2.37986;LSEQ=ATATGTCACAATACCCCCTG;RSEQ=AAGCAGAGCCTAGACAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:1,2:0.5:2,0:37.3:1:32.3:1:0.4:0:24.7:6:0.5:0:5.3 1/0:14:10:6,4:1,2:0.7143:2,2:31.1:1:29.9:1:0.55944:2.75:29.5:20:0.7143:0:4.1 -GL000228.1 118702 . G T 30 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07143;SOR=0;LSEQ=CCCCCTGTAAGCAGAGCCTA;RSEQ=ACAAGAGTTACATCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:0.3333:2,2:44:0:30.5:1:1:2.44949:44:4:0.3333:0:3.5 0/0:15:0:0,0:7,8:0:2,0:30.6:1:29.5:1:1:0:27.9:30:1:0:4.1 -GL000228.1 118704 . C G 45 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52632;SOR=Inf;LSEQ=CCCTGTAAGCAGAGCCTAGA;RSEQ=AAGAGTTACATCACCTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:0:2,0:45.5:1:33:1:1:0:31.2:12:1:0:4.2 0/1:15:3:1,2:6,6:0.2:2,2:29.3:1:28.7:1:1:1.91151:25:6:0.2:0:4.7 -GL000228.1 118722 . G T 32 v4;pSTD;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20949;SOR=0.18301;LSEQ=GACAAGAGTTACATCACCTG;RSEQ=GTGATCAGTGCAGAGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:24:0:32:0:1:1.41418:44:4:0.2857:0:3.5 0/1:16:1:0,1:7,8:0.0625:2,0:34:0:27:0:1:0:31:2:0.0625:0:7 -GL000228.1 118729 . A C 30 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11077;SOR=0;LSEQ=GTTACATCACCTGGGTGATC;RSEQ=GTGCAGAGATATGTGACAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:25.5:1:30:1:1:1.29:24:4:0.2222:0:5.5 0/0:17:0:0,0:7,10:0:2,0:28.3:1:29.1:1:1:0:27.9:34:1:0:4 -GL000228.1 118733 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52923;SOR=Inf;LSEQ=CATCACCTGGGTGATCAGTG;RSEQ=AGAGATATGTGACAAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:0:2,0:17:1:31.8:1:1:0:29:18:1:0:4 0/1:17:2:1,1:6,9:0.1176:2,2:33.5:1:30.5:1:1:1.46:22:4:0.1176:0:3.5 -GL000228.1 118736 . A G 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.58154;SOR=0.45234;LSEQ=CACCTGGGTGATCAGTGCAG;RSEQ=GATATGTGACAAGGCCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:14:1:30:1:1:1.29:25:4:0.2222:0:3 0/1:18:2:1,1:6,10:0.1111:2,2:32:1:31:1:1:1.62:24:4:0.1176:0:3.5 -GL000228.1 118741 . T A 29 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12;SOR=0;LSEQ=GGGTGATCAGTGCAGAGATA;RSEQ=GTGACAAGGCCCCTTTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:0.2222:2,2:25.5:1:29:1:1:1.29:24:4:0.2222:0:5.5 0/0:16:0:0,0:5,11:0:2,0:26.1:1:28.9:1:1:0:27.8:15:1:0:3.7 -GL000228.1 118754 . C A 30 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05848;SOR=0;LSEQ=AGAGATATGTGACAAGGCCC;RSEQ=TTTAAGCAGAGCCTAGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:25.5:1:30.5:1:0.4:0:24:4:0.4:0:5.5 0/0:14:0:0,0:2,12:0:2,0:23.9:1:31.4:1:1:0:29.4:28:1:0:3.4 -GL000228.1 118757 . T G 82 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60294;SOR=2.43937;LSEQ=GATATGTGACAAGGCCCCTT;RSEQ=AAGCAGAGCCTAGACAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:0.25:0,0:31:0:28:0:1:0:25:2:0.25:0:6 0/1:13:6:0,6:1,6:0.4615:2,0:28.3:1:31.8:1:1:0:29.3:12:0.4615:0:3.7 -GL000228.1 118777 . G C 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.17741;LSEQ=TAAGCAGAGCCTAGACAATA;RSEQ=TTACATCACCTGAGTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:1,3:0.2:2,0:50:0:32:0:1:0:25:2:0.25:0:6 0/1:11:4:0,4:1,6:0.3636:2,0:26.5:1:33:1:1:0:30:8:0.3636:0:3.5 -GL000228.1 118781 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=CAGAGCCTAGACAATAGTTA;RSEQ=ATCACCTGAGTGATCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:31:1:31.4:1:1:0:32:10:1:0:4.2 0/1:9:2:1,1:0,7:0.2222:0,2:32.5:1:27:1:0.22222:0:42.5:4:0.25:0:3 -GL000228.1 118802 . A G 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.44444;SOR=Inf;LSEQ=ATCACCTGAGTGATCAGTGC;RSEQ=GAGATCTGTCACAATGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:26.8:1:29.6:1:1:0:32:4:1:0:4.2 0/1:5:2:1,1:0,3:0.4:0,2:47.5:1:29.5:1:0.4:0:42.5:4:0.4:0:3 -GL000228.1 118808 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGAGTGATCAGTGCAGAGAT;RSEQ=TGTCACAATGCCCCTTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,2:0:2,0:37:1:31.7:1:1:0:37:6:0.75:0:3.7 1/0:4:2:1,1:0,2:0.5:0,2:41.5:1:30:1:1:0:42.5:4:0.5:0:3 -GL000228.1 118837 . AG A 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TGCCCCTTTAGGCAGAGCTT;RSEQ=ACTAGAGTTACATCACCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:21:1:30.7:1:1:0:48.7:6:1:0:3.3 1/1:2:2:1,1:0,0:1:0,2:11.5:1:30.5:1:1:0:42.5:4:1:0:3 -GL000228.1 118844 . A T 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=TTAGGCAGAGCTTAGACTAG;RSEQ=GTTACATCACCTGGGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:19:0:27:1:1:0:43:4:0.6667:0:5 0/0:2:0:0,0:1,1:0:2,0:6.5:1:29.5:1:1:0:42.5:4:1:0:3 -GL000228.1 118858 . G T 28 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTAGAGTTACATCACCTG;RSEQ=GTGATCAGTGCAGAGATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:5:0:28:1:1:0:43:4:0.6667:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000228.1 119280 . G C 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCACCTGGGTGATCAGTGCA;RSEQ=AGATATGTCAGAAAGCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:25:0:34:0:1:0:25:2:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:16.5:1:29:1:1:0:44.5:4:0.6667:0:5.5 -GL000228.1 119282 . G T 25 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACCTGGGTGATCAGTGCAGA;RSEQ=ATATGTCAGAAAGCCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:27:0:34:0:1:0:25:2:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:16.5:1:25:1:1:0:44.5:4:0.6667:0:5.5 -GL000228.1 119291 . G C 38 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGTGCAGAGATATGTCA;RSEQ=AAAGCCCCCATACACAGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:36:0:33:0:1:0:25:2:1:0:5 1/1:3:3:2,1:0,0:1:0,2:24:1:24:1:1:0:38.7:2:1:0:5.3 -GL000229.1 5913 . A T 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCACTGTGTCTGTCTTC;RSEQ=GTCTTACTCTCTTTCTCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:28.5:1:32.5:1:1:0:33.5:4:1:0:4 1/1:1:1:1,0:0,0:1:0,0:22:0:33:0:1:0:60:2:1:0:4 -GL000229.1 5958 . A C 29 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTGTCTCTCTCTCCCC;RSEQ=TCTCTTTCTGTTTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:29.5:1:1:0:27:4:1:0:3.5 1/0:2:1:1,0:1,0:0.5:0,0:30:0:26:0:1:0:60:2:0.5:0:4 -GL000229.1 5964 . TTC T 30 d7;v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GTCTCTCTCTCCCCATCTCT;RSEQ=TGTTTCTCTCTCTCTCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:25:1:30:1:1:0:27:4:1:0:3.5 0/1:3:1:1,0:1,1:0.3333:2,0:23:0:25:0:1:0:60:2:0.3333:0:4 -GL000229.1 5977 . T TCC 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0.55247;LSEQ=CATCTCTTTCTGTTTCTCTC;RSEQ=CTCTCTATCTCTCACTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:25:1:26.8:1:1:0:27:4:0.6667:0:3.5 1/0:4:2:1,1:1,1:0.5:2,2:12:0:27.3:1:1:1:50:4:0.5:0:3 -GL000229.1 5980 . CTCTA C 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=8.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=CTCTTTCTGTTTCTCTCTCT;RSEQ=TCTCTCACTCTCTCCATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:14.8:1:27.5:1:1:0:42:3:1:0:3.8 1/0:4:2:1,1:1,1:0.5:2,2:21.5:1:30:1:1:1:33:4:0.5:0:3 -GL000229.1 6000 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=CTCTATCTCTCACTCTCTCC;RSEQ=TCTCTCTCTCTTTCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,2:0.3333:0,0:25:0:32:0:0.33333:0:60:2:0.5:0:3 1/0:4:2:1,1:0,2:0.5:0,2:36.5:1:30:1:1:0:33:4:0.5:0:3 -GL000229.1 6022 . GTC G 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=1;SOR=1.28664;LSEQ=CTCTCTCTCTTTCTGTTTCT;RSEQ=TCTCTCTGTCTGTCTCTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,1:0.3333:0,0:48:0:32:0:1:0:60:2:0.5:0:3 0/1:5:2:1,1:1,1:0.4:2,2:41.5:1:32.5:1:1:1:33:4:0.5:0:3 -GL000229.1 6068 . G C 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=CTGTCTGTTTCTCTCTCTTT;RSEQ=TCTCTCTCTCTTTCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:0.25:2,0:9:0:33:0:1:0:54:2:0.25:0:5 0/1:5:2:1,1:1,2:0.4:2,2:13:1:30:1:1:1.73:43.5:4:0.4:0:3 -GL000229.1 6178 . C T 31 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.5;SOR=0.23975;LSEQ=CTCTCTGTCTCTGTCTCTCT;RSEQ=TCTTTCTGTCTGTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:14:1:31:1:1:0:25:4:0.5:0:1.5 0/1:6:1:1,0:3,2:0.1667:2,0:12:0:31:0:1:0:21:2:0.1667:0:2 -GL000229.1 6261 . A C 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCTGTCAGTCTGTCAGAC;RSEQ=CCCCGTGCCGGGGAGGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:20.5:1:31.5:1:1:0:29:8:0.8:0:2.3 1/1:4:4:2,2:0,0:1:0,2:21.3:1:30.3:1:1:0:30:8:1:0:2.8 -GL000229.1 6272 . G C 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTGTCAGACACCCCGTGCCG;RSEQ=GGAGGGCCCTGCCCCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:0.6:0,2:13:1:30:1:1:0:30.3:6:0.6:0:2.3 1/0:5:3:1,2:1,1:0.6:2,2:22.7:1:29.3:1:1:1.7321:33:6:0.6:0:3 -GL000229.1 6293 . C A 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GGAGGGCCCTGCCCCTTCCA;RSEQ=GAAAGTGAGAAGCGCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:18.5:1:28.5:1:1:0:60:4:1:0:0 1/0:4:2:0,2:1,1:0.5:2,0:25.5:1:31.5:1:1:0:30:4:0.5:0:3.5 -GL000229.1 7097 . G A 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCATAGACTCTTCTACTTG;RSEQ=GTTTTAGGAGGGGTCAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:28:1:31:1:1:0:27:4:1:0:2 -GL000229.1 7099 . T A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGACTCTTCTACTTGGG;RSEQ=TTTAGGAGGGGTCAGTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:1:30:1:1:0:27:4:1:0:2 -GL000229.1 7269 . G C 34 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCCACCCCGGTGTGCCTCC;RSEQ=TCTTCTCTCCCCTTCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:0.4:2,0:27:1:34:0:1:0:53.5:4:0.4:0:1 1/1:1:1:1,0:0,0:1:0,0:23:0:32:0:1:0:47:2:1:0:1 -GL000229.1 7393 . C T 28 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGATGGGGGTGGCCCGGTCC;RSEQ=ACTTCCCCAGAGGCAGCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24:1:31:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:28:1:1:0:27:4:1:0:3.5 -GL000229.1 7536 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACCCTGGCTGGGTCTCA;RSEQ=TCACCTTTTATCATGATGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31:1:30:1:1:0:56:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 7651 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTTGCCCAAAATAGAAA;RSEQ=GCTTTCTGAAAACTAATACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:31:0:28:0:1:0:48:2:1:0:4 1/1:2:2:1,1:0,0:1:0,2:31:1:30.5:1:1:0:27:4:1:0:2.5 -GL000229.1 7808 . AT A 49 d7;v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CAGTTTTCAGGAAGACGTAT;RSEQ=TTTTCCCCAAGACATGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:44:1:31.3:1:1:0:42.7:6:1:0.3333:1.3 1/0:2:1:1,0:0,1:0.5:0,0:35:0:32:0:1:0:44:2:0.5:0:0 -GL000229.1 7841 . T A 28 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATGTTAGCTGCGGTTTTC;RSEQ=CCTGTTGTTAACTAACGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:14:1:28.5:1:1:0:50:4:0.3333:0:2 0/0:2:0:0,0:2,0:0:0,0:26.5:1:33:0:1:0:52:4:1:0:0 -GL000229.1 7922 . T C 64 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66515;SOR=0.4601;LSEQ=TACTAGACTTCAGAACATCT;RSEQ=ATGTTCTAGAAATCCGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:3,1:13,6:0.1739:2,2:32.8:1:32:1:1:1.37:47:8:0.1739:0:2.8 0/1:23:2:1,1:15,6:0.087:2,2:30.5:1:31:1:0.52569:2.39047:56:4:0.087:0:3.5 -GL000229.1 7935 . T C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7776;LSEQ=AACATCTTATGTTCTAGAAA;RSEQ=CCGTAAGCGATTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:16,8:0.0769:2,2:25.5:1:31:1:1:1.94371:54:4:0.0769:0:2 0/1:33:2:1,1:17,14:0.0606:2,2:28.5:1:29:1:1:1.20712:60:4:0.0606:0:1.5 -GL000229.1 7938 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3716;SOR=3.38513;LSEQ=ATCTTATGTTCTAGAAATCC;RSEQ=TAAGCGATTGCTGCTGCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:1,0:16,9:0.0385:2,0:30:0:27:0:1:0:49:2:0.0385:0:1 0/1:33:4:2,2:16,13:0.1212:2,2:28.5:1:28.8:1:1:1.223:53.8:8:0.1212:0:2.5 -GL000229.1 7944 . G A 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38576;SOR=0.3345;LSEQ=TGTTCTAGAAATCCGTAAGC;RSEQ=ATTGCTGCTGCTGCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:2,2:14,7:0.16:2,2:23.3:1:29.5:1:0.60158:1.94205:42:8:0.16:0:4 0/1:34:2:1,1:17,15:0.0588:2,2:30.5:1:28.5:1:1:1.12916:56:4:0.0588:0:3.5 -GL000229.1 7946 . T A 58 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21235;SOR=0.30944;LSEQ=TTCTAGAAATCCGTAAGCGA;RSEQ=TGCTGCTGCTGCTCTTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:2,2:13,7:0.1667:2,2:22.3:1:29:1:0.61462:1.80766:42:8:0.1667:0:4 0/1:35:2:1,1:17,16:0.0571:2,2:30.5:1:28.5:1:1:1.06069:56:4:0.0571:0:3.5 -GL000229.1 7978 . CTTG C 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.18355;SOR=2.22562;LSEQ=CTCTTGCTGCTGCTGCTGCT;RSEQ=TTGCTGTTGTTGTTGTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:1,6:11,9:0.2593:2,2:25.6:1:31.6:1:0.09138:6.84428:40.1:14:0.2593:0.037:3.6 0/1:34:15:6,9:11,8:0.4412:2,2:27.8:1:31.9:1:0.49053:2.01816:54:30:0.4412:0.2353:2.1 -GL000229.1 7982 . T C 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TGCTGCTGCTGCTGCTCTTG;RSEQ=TGCTGTTGTTGTTGTTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:11:6,5:6,10:0.4074:2,2:16.5:1:30.5:1:0.45165:1.95:52.2:10:0.3846:0:1.5 0/0:36:0:0,0:12,16:0:2,0:26.9:1:29.7:1:1:0:56.8:56:1:0:1.1 -GL000229.1 7985 . CTGT C 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=1;SOR=0.78445;LSEQ=TGCTGCTGCTGCTCTTGTTG;RSEQ=TGTTGTTGTTGTTTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:11,14:0.0741:2,2:39:1:33:1:1:1.26:39.5:4:0.0741:0:5 0/1:34:2:1,1:14,18:0.0588:2,2:3:1:28.6:1:1:1.28:56:4:0.0593:0.0656:2.5 -GL000229.1 7988 . T C 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.76307;SOR=0.77264;LSEQ=TGCTGCTGCTCTTGTTGCTG;RSEQ=TGTTGTTGTTGTTTTCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:1,6:10,8:0.2593:2,2:26:1:31.4:1:0.09:6.94718:40.1:14:0.28:0:3.6 0/1:33:7:1,6:14,12:0.2121:2,2:35.4:1:33.1:1:0.09523:6.63652:50.3:14:0.2121:0:3 -GL000229.1 7995 . T A 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.291;SOR=0.2091;LSEQ=GCTCTTGTTGCTGTTGTTGT;RSEQ=GTTGTTTTCAAAGCACAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:7,10:0.15:2,2:20.3:1:29.7:1:1:1.37728:51.7:6:0.15:0:3 0/1:29:1:0,1:12,16:0.0345:2,0:36:0:32:0:1:0:45:2:0.0345:0:4 -GL000229.1 8013 . A C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13942;SOR=0.27997;LSEQ=GTTGTTGTTTTCAAAGCACA;RSEQ=CTCGGCCACCGTTTATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:1,8:3,1:0.6923:2,2:36:1:32.1:1:0.05175:16.09965:36.9:18:0.6923:0:4 0/1:16:6:0,6:4,6:0.375:2,0:13:1:32.8:1:0.23352:0:48.7:12:0.375:0:3.3 -GL000229.1 8015 . T C 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23774;SOR=0.2928;LSEQ=TGTTGTTTTCAAAGCACAAC;RSEQ=CGGCCACCGTTTATGGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:1,8:3,1:0.6923:2,2:35.8:1:32.1:1:0.05175:16.09965:36.9:18:0.6923:0:4 0/1:13:5:0,5:3,5:0.3846:2,0:13.2:1:32.8:1:0.23077:0:47:10:0.3846:0:3.4 -GL000229.1 8042 . C G 76 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04396;SOR=0;LSEQ=CCGTTTATGGGATCAAAAGC;RSEQ=TTATAAAATATGTGTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:1,4:2,2:0.5556:2,2:18.4:1:32.8:1:0.52381:3.38757:33:10:0.5556:0:4 0/0:6:0:0,0:2,4:0:2,0:22.2:1:31:1:1:0:59:12:1:0:0.2 -GL000229.1 8104 . G C 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=8;SSF=1;SOR=0;LSEQ=CCTCCTCTCTCTGTCTCTCT;RSEQ=TCTCTCTTTCTCCGTCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:2,6:0.2:2,0:30:0:32:1:1:0:48.5:4:0.2:0:6 0/0:2:0:0,0:0,2:0:0,0:32.5:1:33:0:1:0:60:4:1:0:0 -GL000229.1 8114 . C A 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTCTCTGTCTCTCTTT;RSEQ=TCCGTCTTCTCTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:2,6:0.2:2,0:40:0:30.5:1:1:0:48.5:4:0.2:0:6 0/0:2:0:0,0:0,2:0:0,0:22.5:1:34:0:1:0:60:4:1:0:0 -GL000229.1 8117 . C T 48 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTCTGTCTCTCTTTCTC;RSEQ=GTCTTCTCTCTGTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:2,5:0.3:2,0:45:1:30.7:1:1:0:45.3:6:0.3:0:5.3 0/0:2:0:0,0:0,2:0:0,0:19.5:1:32:0:1:0:60:4:1:0:0 -GL000229.1 8125 . C A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCTCTTTCTCCGTCTTCT;RSEQ=TCTGTCTCTGTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:2,6:0.2:2,0:44:1:32:0:1:0:48.5:4:0.2:0:6 0/0:2:0:0,0:0,2:0:0,0:11.5:1:33.5:1:1:0:60:4:1:0:0 -GL000229.1 8129 . G T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=TCTTTCTCCGTCTTCTCTCT;RSEQ=TCTCTGTCTCTCTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:1,5:0.2222:2,0:40:1:31.5:1:1:0:48.5:4:0.25:0:6 0/0:1:0:0,0:0,1:0:0,0:17:0:33:0:1:0:60:2:1:0:0 -GL000229.1 8147 . C T 32 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGTCTCTGTCTCTCTCTCT;RSEQ=TGCCTATTTCTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,4:0.25:2,0:22:1:32:0:1:0:48.5:4:0.2857:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8276 . GTC G 33 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCTCTGCCTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,0:0.4:0,2:23:0:33.5:1:1:0:37.5:4:0.4:0:0 0/0:1:0:0,0:1,0:0:0,0:28:0:30:0:1:0:45:2:1:0:7 -GL000229.1 8294 . CTCCCTG GTC 30 d7;v4;NM4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=2;SSF=0.04762;SOR=Inf;LSEQ=CTGTCTCTCTCTCTCTCTCT;RSEQ=TCTGTCTCTTTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,2:0:2,0:30.3:1:32:1:1:0:31.3:8:1:0:0 1/1:2:2:2,0:0,0:1:0,0:28.5:1:30.5:1:1:0:52.5:4:1:0.5:6 -GL000229.1 8316 . C G 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.06061;SOR=Inf;LSEQ=CCCTGTCTGTCTCTTTCTCT;RSEQ=TGTCTCTCTCTTTCTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,2:0.25:2,2:15.5:1:32:1:1:1.41418:60:4:0.2857:0:2 1/1:3:3:2,1:0,0:1:0,2:22.3:1:31.3:1:1:0:55:6:1:0:5.3 -GL000229.1 8318 . G GTCTCTGTC 59 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=5.000;MSILEN=2;SSF=0.23636;SOR=0;LSEQ=CTGTCTGTCTCTTTCTCTCT;RSEQ=TCTCTCTCTTTCTGTTTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:1,0:0.5:0,2:25.3:1:29.7:1:1:0:31.3:8:0.5714:0.25:0 0/0:3:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8373 . T A 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.16667;SOR=Inf;LSEQ=TCTTTCTCTGTCTGTCTCTC;RSEQ=GTCTGTCTCTCTCTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27:1:30.5:1:1:0:60:8:1:0:0.8 1/0:5:3:1,2:1,1:0.6:2,2:29.7:1:29.7:1:1:1.7321:60:6:0.6:0:4.3 -GL000229.1 8378 . G GTCTC 62 d7;pSTD;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=8.000;MSILEN=2;SSF=0.16667;SOR=0;LSEQ=CTCTGTCTGTCTCTCTGTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:27:1:31.3:1:1:0:60:8:1:0:0.8 0/1:5:2:1,1:1,2:0.4:2,2:24:0:32.1:1:1:1.73:60:4:0.4:0:0.5 -GL000229.1 8384 . CTC TTCTT 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.16667;SOR=Inf;LSEQ=CTGTCTCTCTGTCTGTCTCT;RSEQ=TCTCTGTCTCTCTGTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:27:1:32.3:1:1:0:60:8:1:0:0.8 1/0:5:3:1,2:1,1:0.6:2,2:19.3:1:29.2:1:1:1.7321:60:6:0.6:0.2:4.3 -GL000229.1 8417 . T A 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGTCTCTGTGTCTCTCTC;RSEQ=CTCTGCCTGTCTCTCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:18:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8469 . T G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTTACTCTCTTTCTCC;RSEQ=CCGGCCTGTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:41.5:1:32:1:1:1:45:4:0.5:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8472 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTACTCTCTTTCTCCTCC;RSEQ=GCCTGTCTGTCTCTCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:38.5:1:30:1:1:1:45:4:0.5:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8479 . CTGTCTCTCTCTG C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTTTCTCCTCCGGCCTGT;RSEQ=TCTCTCTCTCTGTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:30.5:1:31.5:1:1:1:45:4:0.5:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8501 . C ATT 48 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=GTCTCTCTCTGTCTCTCTCT;RSEQ=TGTTTCTCTCTGTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:3,2:0.375:2,2:12.7:1:30.9:1:1:2.60168:55.7:6:0.375:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8565 . CTGTGTGTA C 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGTCTCTTTGTCTGTCTGT;RSEQ=TCTCTCTTTCTCTGTCTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:4,3:0.3:2,2:11:1:29.8:1:1:2.41422:55.7:6:0.3:0.3:1.3 0/0:1:0:0,0:1,0:0:0,0:26:0:33:0:1:0:60:2:1:0:0 -GL000229.1 8569 . G C 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTTTGTCTGTCTGTCTGT;RSEQ=TGTATCTCTCTTTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:1,2:0.2857:2,0:25:1:32.5:1:0.4:0:43.5:4:0.4:0:4 0/0:1:0:0,0:1,0:0:0,0:23:0:34:0:1:0:60:2:1:0:0 -GL000229.1 8597 . T C 31 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTCTTTCTCTGTCTCGCTGT;RSEQ=TCTGTCTCTCTTCCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:1,3:0.3333:2,0:25:1:31.5:1:0.4:0:43.5:4:0.3333:0:4 1/1:1:1:1,0:0,0:1:0,0:8:0:32:0:1:0:26:2:1:0:2 -GL000229.1 8601 . G GTCTC 31 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=5.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=TTCTCTGTCTCGCTGTTTCT;RSEQ=TCTCTCTTCCTGTCTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:25:1:31.4:1:1:2.45:43.5:4:0.3333:0.1667:4 1/1:1:1:1,0:0,0:1:0,0:13:0:32.8:0:1:0:26:2:1:0:2 -GL000229.1 8609 . T G 47 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGCTGTTTCTGTCTCTCT;RSEQ=CCTGTCTGTCTGTCTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:1,3:0.4286:2,2:17.3:1:29.7:1:1:1.41:38:6:0.4286:0:3.3 1/1:1:1:1,0:0,0:1:0,0:24:0:34:0:1:0:26:2:1:0:2 -GL000229.1 8624 . T G 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCTCTTCCTGTCTGTCTGTC;RSEQ=GTAGGTCTCTCTCTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:0.4:0,2:21:1:29.5:1:0.4:0:27:4:0.4:0:3 0/0:1:0:0,0:1,0:0:0,0:34:0:32:0:1:0:26:2:1:0:2 -GL000229.1 8668 . T TTTGC 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGTTTTTTTCTCTCTCTC;RSEQ=CTGTCTGTTTCTCTGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:27:1:31.5:1:1:0:43.5:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8758 . GTC G 28 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.02778;SOR=Inf;LSEQ=CTTTCTCTGCCTGTCTGTCT;RSEQ=TCTCTCTCTCTCCTTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:21.1:1:29.4:1:1:0:51.4:14:1:0:0.6 1/1:2:2:0,2:0,0:1:0,0:22:1:28.5:1:1:0:52.5:4:1:0:1.5 -GL000229.1 8794 . T C 49 v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03333;SOR=Inf;LSEQ=TTGTCTGTTTCTCTCTCTCT;RSEQ=TGTCTCTGTTTCTCTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:3,3:0.1429:2,0:37:0:32:0:1:0:31:2:0.1429:0:3 1/1:3:3:1,2:0,0:1:0,2:26.7:1:31:1:1:0:55:6:1:0:1.3 -GL000229.1 8858 . ATCTG CTGTCTA 30 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=CTCTCTCTGTCTCTTTCTCT;RSEQ=TCTCTCTCCTTCTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:22:1:30.2:1:1:1:52.5:4:0.5:0.2:2.5 0/0:1:0:0,0:1,0:0:0,0:6:0:32:0:1:0:60:2:1:0:1 -GL000229.1 8893 . T TC 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTCTCTGTCTGTCCA;RSEQ=TGTCTCTGTCTCTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:11:1:30.5:1:1:0:42.5:4:1:0.5:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8917 . G GTGTT 63 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTGTCTCTGTGTGTGTGT;RSEQ=TCTGCCTTCTGTCTTACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,1:0.8:0,2:25.8:1:31.5:1:0.4:0:47:8:0.8:0.2:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000229.1 8954 . G A 42 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=CTCTCTTTCTCTGACTGTCT;RSEQ=CCTGTCTGCCTGTCTGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,0:0.6:0,2:33:1:27:1:1:0:49.7:6:0.75:0:4 1/0:3:2:2,0:1,0:0.6667:0,0:24:1:29.5:1:1:0:60:4:0.6667:0:5.5 -GL000229.1 8959 . T C 58 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=8;SSF=1;SOR=0.54771;LSEQ=TTTCTCTGACTGTCTGCCTG;RSEQ=CTGCCTGTCTGTCTCTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,1:0.8:0,2:26.3:1:29.3:1:0.4:0:47:8:0.8:0:3.5 1/0:3:2:2,0:1,0:0.6667:0,0:29:1:33.5:1:1:0:60:4:0.6667:0:5.5 -GL000229.1 8963 . C T 54 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.09375;LSEQ=TCTGACTGTCTGCCTGTCTG;RSEQ=CTGTCTGTCTCTCTCTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:1,2:0.5714:2,2:22.3:1:27.3:1:0.48571:4.45:47:8:0.5714:0:3.5 1/0:4:3:2,1:1,0:0.75:0,2:22.7:1:29.3:1:1:0:60:6:0.75:0:4.7 -GL000229.1 8982 . C A 67 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=1.23147;LSEQ=GCCTGTCTGTCTCTCTCTGT;RSEQ=TGTCTCTCTCTCTTTCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:1,2:0.5:2,2:14:1:30:1:1:1:56.3:6:0.5:0:3.7 1/0:9:5:4,1:2,2:0.5556:2,2:22:1:29.2:1:0.52381:3.39:60:10:0.5556:0:3.6 -GL000229.1 8995 . T C 33 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=TCTCTGTCTGTCTCTCTCTC;RSEQ=TTCTGTCTCTGTCTCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:0:2,0:22:1:31.8:1:1:0:52.8:10:1:0.2:2.2 0/1:10:2:1,1:5,3:0.2:2,2:17:0:33:1:1:1.58108:60:4:0.2:0:1 -GL000229.1 9006 . GTC G 80 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=1.45647;LSEQ=CTCTCTCTCTTTCTGTCTCT;RSEQ=TCTCTTTCTGTTTCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:28:1:34:0:1:0:49.5:4:0.5:0:1 1/0:10:6:4,2:2,2:0.6:2,2:27.2:1:31:1:1:1.86:59.3:12:0.6:0:3.2 -GL000229.1 9024 . C T 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.55944;SOR=4.03195;LSEQ=CTGTCTCTCTTTCTGTTTCT;RSEQ=TCTGTCTCTGTCCATCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:0.25:2,0:42:0:32:0:1:0:60:2:0.25:0:2 1/0:10:6:4,2:2,2:0.6:2,2:28.7:1:30.2:1:1:1.86:59.3:12:0.6:0:3.2 -GL000229.1 9074 . GTCTC G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCTGTGTCTTTATCTGTCT;RSEQ=TCTCTCTCTTTCTGTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:23:0:34:0:1:0:39:2:1:0:0 0/1:5:2:0,2:2,1:0.4:2,0:34:1:31:1:0.4:0:48:4:0.4:0:1 -GL000229.1 9907 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22619;SOR=0.14055;LSEQ=GGTCTTCGTCGGCTAAAGTA;RSEQ=AAAGGGATGGCGACTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:13:0:33:0:1:0:51:4:0.6667:0:5.5 0/1:6:1:1,0:3,2:0.1667:2,0:29:0:27:0:1:0:40:2:0.1667:0:6 -GL000229.1 9912 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TCGTCGGCTAAAGTACAAAG;RSEQ=GATGGCGACTTCCACCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:21.8:1:31.5:1:1:0:55.5:8:1:0:3.3 0/1:5:2:1,1:2,1:0.4:2,2:7.5:1:30:0:1:1.7321:60:4:0.4:0:4.5 -GL000229.1 9916 . G T 25 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=CGGCTAAAGTACAAAGGGAT;RSEQ=GCGACTTCCACCCACAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:22:0:32:0:1:1:51:4:0.5:0:5.5 0/1:6:2:1,1:2,2:0.3333:2,2:10.5:1:25.5:1:1:1:41.5:4:0.3333:0:5.5 -GL000229.1 9938 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CGACTTCCACCCACAAGGTC;RSEQ=CCACTGAACTGTGAAGATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:24:1:31.2:1:1:0:56.4:10:1:0:3.2 0/1:6:2:1,1:1,3:0.3333:2,2:26:0:32:1:1:2.45:60:4:0.3333:0:4.5 -GL000229.1 9950 . T C 74 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24242;SOR=6.06919;LSEQ=ACAAGGTCCCCACTGAACTG;RSEQ=GAAGATGTGGAGCGTAGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:20.5:1:31.5:1:1:1.7321:51:4:0.4:0:5.5 1/1:6:5:2,3:0,1:0.8333:0,2:29.4:1:32:1:1:0:56.6:10:0.8333:0:4.2 -GL000229.1 9959 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CCACTGAACTGTGAAGATGT;RSEQ=GAGCGTAGGTCAGAGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:19.6:1:31.4:1:1:0:56.4:10:1:0:3.8 0/1:6:2:1,1:1,3:0.3333:2,2:5:0:30.5:1:1:2.45:60:4:0.3333:0:4.5 -GL000229.1 9962 . G A 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CTGAACTGTGAAGATGTGGA;RSEQ=CGTAGGTCAGAGAGGGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:19:1:31.2:1:1:0:56.4:10:1:0:3.8 0/1:6:2:1,1:1,3:0.3333:2,2:30:0:32:0:1:2.45:60:4:0.3333:0:3.5 -GL000229.1 9964 . G A 29 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53981;LSEQ=GAACTGTGAAGATGTGGAGC;RSEQ=TAGGTCAGAGAGGGGACCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:6.5:1:29.5:1:1:1.73:51:4:0.4:0:5.5 0/1:4:1:0,1:1,2:0.25:2,0:49:0:31:0:1:0:43:2:0.25:0:5 -GL000229.1 9983 . A T 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CGTAGGTCAGAGAGGGGACC;RSEQ=GGAGGGGAGACGTCCTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:33:1:32:1:1:0:60:6:1:0:2.7 1/0:4:2:1,1:0,2:0.5:0,2:9:0:32.5:1:1:0:60:4:0.5:0:3.5 -GL000229.1 9989 . GG TA 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TCAGAGAGGGGACCAGGAGG;RSEQ=AGACGTCCTGACAGGCGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:38.5:1:29.5:1:1:0:60:4:0.6667:0:3 0/0:4:0:0,0:1,2:0:2,0:15.7:1:31.7:1:1:0:60:6:0.75:0:2.7 -GL000229.1 9994 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=GAGGGGACCAGGAGGGGAGA;RSEQ=GTCCTGACAGGCGATGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:38.5:1:30.5:1:1:1:60:4:0.5:0:3 1/0:3:2:0,2:1,0:0.6667:0,0:29:1:30.5:1:0.33333:0:51.5:4:0.6667:0:3 -GL000231.1 23714 . T C 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGAAACAAAATGTGTATG;RSEQ=GACTAACTTGATTGTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:19.5:1:31:1:1:0:56:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000231.1 24049 . C T 30 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCACTGCAAGCTCCGCCTCC;RSEQ=GGGTTCATGCCATCCTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19:1:27:1:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:20.5:1:30:1:1:0:60:4:0.6667:0:1.5 -GL000231.1 24433 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACTTCCCTTTCTAGCAA;RSEQ=GGAGAACTTTGATTGGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:0.25:0,0:7:1:30:1:1:0:45:4:0.25:0:3 0/0:2:0:0,0:2,0:0:0,0:24.5:1:29.5:1:1:0:60:4:1:0:0.5 -GL000231.1 24460 . C T 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CTTTGATTGGATTTTTCCTG;RSEQ=CTACAGACAGGAATGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:4,1:0.375:2,0:28.7:1:29.3:1:1:0:59:6:0.375:0:2.7 1/1:2:2:2,0:0,0:1:0,0:15:1:32:0:1:0:43.5:4:1:0:1.5 -GL000231.1 24498 . T A 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.64427;SOR=0.55197;LSEQ=TCTGCTGTTTTCTTTTTTAA;RSEQ=CCCGAGGGGACTGAGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:11,2:1,2:0.8125:2,2:25.5:1:29.2:1:0.13571:8.86:51.1:12:0.8:0:3.8 1/0:10:7:5,2:2,1:0.7:2,2:17.4:1:26.9:1:1:1.22:46:6:0.6667:0:5.4 -GL000231.1 24503 . AG A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.53202;SOR=0;LSEQ=TGTTTTCTTTTTTAATCCCG;RSEQ=GGGACTGAGCCTGAGGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:13,4:0.1053:2,0:11.5:1:32.5:1:1:0:41:4:0.1053:0.0526:3 0/0:10:0:0,0:7,3:0:2,0:17.9:1:28.8:1:1:0:50.2:9:1:0:3.8 -GL000231.1 24526 . G C 74 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72786;LSEQ=GGACTGAGCCTGAGGGCCTC;RSEQ=AGCGCGGCCAGACTCCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:4,1:9,3:0.2941:2,2:24.8:1:32.2:1:1:1.31:35.8:10:0.2941:0:4.8 0/1:13:3:3,0:6,2:0.2308:2,0:33.3:1:31.7:1:1:0:46:6:0.25:0:5 -GL000231.1 24529 . C T 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.17931;SOR=Inf;LSEQ=CTGAGCCTGAGGGCCTCGAG;RSEQ=GCGGCCAGACTCCCCAAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:12,4:0:2,0:30.6:1:31.5:1:1:0:50.4:32:0.9412:0:3.3 0/1:13:2:1,1:9,2:0.1538:2,2:45.5:1:30:1:0.42308:3.87298:58:4:0.1538:0:8 -GL000231.1 24537 . GA CC 102 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47949;SOR=0.52981;LSEQ=GAGGGCCTCGAGCGCGGCCA;RSEQ=CTCCCCAAACCCCCAACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:7,2:3,2:0.5625:2,2:36.2:1:32.4:1:0.58042:2.19:42.7:18:0.5625:0:3.8 0/1:15:6:6,0:3,1:0.4:2,0:31.2:1:31.2:1:0.4:0:38.3:12:0.4286:0.0667:3.7 -GL000231.1 24545 . A C 106 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.09682;LSEQ=CGAGCGCGGCCAGACTCCCC;RSEQ=AACCCCCAACTGGTGATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:8,2:4,2:0.625:2,2:33.8:1:31.7:1:0.6044:1.91:44.4:20:0.625:0:3.9 1/0:17:11:8,3:5,1:0.6471:2,2:29.7:1:30.8:1:1:1.81053:41.2:22:0.6875:0:4.3 -GL000231.1 24551 . C A 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23269;SOR=0;LSEQ=CGGCCAGACTCCCCAAACCC;RSEQ=CAACTGGTGATTGTGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:2,1:12,6:0.1429:2,2:11.3:1:27.7:1:1:1:58:6:0.1429:0:3.7 0/0:19:0:0,0:12,5:0:2,0:27.4:1:29.9:1:1:0:46.1:34:0.8947:0:2 -GL000231.1 24563 . TGTGGTG T 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=6.000;MSILEN=3;SSF=1;SOR=0.83632;LSEQ=CCAAACCCCCAACTGGTGAT;RSEQ=GTGGTGGTGGTGGTTTTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:3,3:14,6:0.2308:2,2:18.3:1:30.1:1:0.62785:2.25281:51.8:12:0.2308:0.0769:3.7 0/1:25:5:3,2:11,7:0.2:2,2:21.8:1:28.1:1:1:1.04547:36.6:10:0.2:0.08:3.6 -GL000231.1 24603 . T TCTG 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.20413;SOR=Inf;LSEQ=TTTTGTGTTCCAGCTTCTGT;RSEQ=CTGTTGTTGTTGCTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:23,14:0:2,0:24.1:1:30:1:1:0:56.2:36:1:0:1.2 0/1:31:2:1,1:16,13:0.0645:2,2:27:0:32.7:1:1:1.22249:51:4:0.0667:0:4 -GL000231.1 24604 . C CTGCTGT 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.74591;SOR=1.25514;LSEQ=TTTGTGTTCCAGCTTCTGTT;RSEQ=TGTTGTTGTTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:3,2:20,12:0.1282:2,2:27.4:1:32.5:1:1:1.10792:38.6:10:0.1351:0.0256:3.8 0/1:32:5:2,3:16,11:0.1563:2,2:37.2:1:30.5:1:0.63126:2.12814:35.8:10:0.1563:0:1.8 -GL000231.1 24613 . T TTGTTTCTGA 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.49545;SOR=0;LSEQ=CAGCTTCTGTTCTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:29,21:0.0385:2,2:24:1:30.8:1:1:1.37225:55.5:4:0.0385:0.0192:2.5 0/0:49:0:0,0:25,24:0:2,0:20.6:1:29.5:1:1:0:53.6:98:1:0:1 -GL000231.1 24616 . C T 88 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.01327;SOR=0;LSEQ=CTTCTGTTCTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:4,3:23,17:0.1296:2,2:25.3:1:31.7:1:1:1.01439:41.6:14:0.1489:0:3.9 0/0:49:0:0,0:19,17:0:2,0:20.1:1:31.8:1:1:0:57.9:72:1:0:0.4 -GL000231.1 24628 . C G 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=0.96049;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGGTGCTGTCGTCATTGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:6:1,5:27,26:0.1017:2,2:33.3:1:32.2:1:0.19791:5.06761:49:12:0.1053:0:2.3 0/1:51:5:2,3:22,24:0.098:2,2:26.4:1:30.4:1:1:1.36654:44.4:10:0.1042:0:3 -GL000231.1 24638 . C T 77 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28862;SOR=0.38107;LSEQ=GCTGCTGCTGCTGGTGCTGT;RSEQ=GTCATTGTTTTGGTATTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:6:3,3:22,28:0.1053:2,2:28.8:1:29.8:1:1:1.27:39.3:12:0.1091:0:4.2 0/1:47:2:1,1:20,25:0.0426:2,2:34:0:29.5:1:1:1.24:51:4:0.0435:0:4 -GL000231.1 24641 . CA TG 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45008;SOR=0.45789;LSEQ=GCTGCTGCTGGTGCTGTCGT;RSEQ=TTGTTTTGGTATTTTACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:2,3:22,28:0.0909:2,2:33.2:1:31.2:1:1:1.17509:38.6:10:0.0926:0:3.4 0/1:46:2:1,1:19,25:0.0435:2,2:30:0:29.5:1:1:1.31:51:4:0.0455:0:3 -GL000231.1 24664 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51097;SOR=0;LSEQ=TGTTTTGGTATTTTACAGAC;RSEQ=CAGGGGGTGTATGTGCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:21,29:0.0385:2,2:24.5:1:29.5:1:1:1.37:60:4:0.0385:0:1 0/0:36:0:0,0:15,21:0:2,0:27.4:1:29.2:1:1:0:55.5:35:1:0:0.9 -GL000231.1 24665 . CAG C 112 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.35718;SOR=1.5998;LSEQ=GTTTTGGTATTTTACAGACT;RSEQ=GGGGTGTATGTGCTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:14:5,9:17,20:0.2745:2,2:31.4:1:31.3:1:0.54635:1.51742:52.1:28:0.28:0:0.8 0/1:37:14:6,8:9,14:0.3784:2,2:29.6:1:29.6:1:1:1.16:53.8:28:0.3889:0.027:1.2 -GL000231.1 24676 . T C 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.56483;SOR=2.96009;LSEQ=TTACAGACTCAGGGGGTGTA;RSEQ=GTGCTTGTTTGTTAGATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:0,1:19,29:0.0204:2,0:17:0:29:0:1:0:40:2:0.0208:0:2 0/1:34:2:0,2:14,18:0.0588:2,0:9:1:30.5:1:0.50089:0:40.5:4:0.0606:0:3.5 -GL000231.1 24695 . A G 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52715;SOR=0;LSEQ=ATGTGCTTGTTTGTTAGATC;RSEQ=GCTTACTACTGCTTCCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:0,2:9,21:0.0606:2,0:9:0:32:0:1:0:48:4:0.0645:0:4.5 0/0:19:0:0,0:6,12:0:2,0:18.7:1:29:1:1:0:58.6:8:1:0:0.9 -GL000231.1 24698 . T G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33117;SOR=2.00803;LSEQ=TGCTTGTTTGTTAGATCAGC;RSEQ=TACTACTGCTTCCGGATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:2,6:5,13:0.2759:2,2:20.8:1:32.6:1:1:1.14757:55.1:16:0.2759:0:1.3 0/1:16:7:2,5:2,6:0.4375:2,2:19.7:1:27.7:1:1:1.19:58:6:0.4:0:2.1 -GL000231.1 25212 . A G 51 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAAAGATGAAAAAAATA;RSEQ=AGAGAAAGACAAAAAGCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:3,1:0.4286:2,2:13:1:32.3:1:0.48571:4.4496:51:6:0.4286:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000231.1 25225 . A G 52 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATAAAGAGAAAGACAA;RSEQ=AAGCACGGGGTGAACGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:4,1:0.375:2,2:26:1:33:0:0.46429:5.78427:51:6:0.375:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000231.1 25231 . C G 51 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGAAAGACAAAAAGCA;RSEQ=GGGGTGAACGTTTCTCTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:4,1:0.375:2,2:32:1:32.7:1:0.46429:5.78427:51:6:0.375:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000231.1 25253 . G A 30 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGAACGTTTCTCTTGCC;RSEQ=CCTCCCAGGGTGTACCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:0.2222:2,2:10.5:1:30:1:1:1.29098:31:4:0.2222:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000231.1 25272 . G T 29 v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCTCCCAGGGTGTACCTT;RSEQ=GACCCAATAGGAGGGAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:29:1:29:1:1:1:54:4:0.25:0:4.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000231.1 25278 . A C 47 v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGTGTACCTTGGACCC;RSEQ=ATAGGAGGGAGGGAGCTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:1,3:0.4286:2,2:25.3:1:29.7:1:0.48571:4.45:47:6:0.4286:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000231.1 25298 . A G 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAGGAGGGAGGGAGCTTG;RSEQ=CTGGGTGGGTTTTCAGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:27.3:1:31.3:1:1:0:45.7:6:0.75:0:4 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -GL000231.1 25313 . A G 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGACTGGGTGGGTTTTC;RSEQ=GTGCTAAATCCTCCCGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,1:0.5:0,2:8:1:30:1:1:0:54.5:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -MT 73 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04665;SOR=3.09344;LSEQ=GGTATTTTCGTCTGGGGGGT;RSEQ=TGCACGCGATAGCATTGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:31:15,16:8,10:0.6327:2,2:26.3:1:31.5:1:1:1.17:59.2:30:0.625:0:1.3 1/1:32:27:11,16:2,3:0.8438:2,2:27:1:31.4:1:1:1.03:58.5:54:0.8438:0:1.2 -MT 75 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51392;SOR=0;LSEQ=TATTTTCGTCTGGGGGGTAT;RSEQ=CACGCGATAGCATTGCGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:21,25:0.0417:2,2:30:1:30:0:1:1.19:60:4:0.0417:0:1 0/0:32:0:0,0:13,19:0:2,0:26.1:1:32.1:1:1:0:58.8:64:1:0:1 -MT 150 . C T 95 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:37,22:0:2,0:21.5:1:31.1:1:1:0:60:118:1:0:1.6 0/1:19:9:5,4:4,6:0.4737:2,2:29.3:1:30.1:1:0.65628:1.81:60:18:0.4737:0:3.1 -MT 152 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.06779;LSEQ=CTTTGATTCCTGCCTCATCC;RSEQ=ATTATTTATCGCACCTACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:36:18,18:15,5:0.6429:2,2:21.8:1:31.2:1:0.09199:2.94184:60:72:0.6429:0:2.6 0/1:19:2:1,1:8,9:0.1053:2,2:38.5:1:30.5:1:1:1.12:60:4:0.1053:0:1.5 -MT 178 . A G 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TTATCGCACCTACGTTCAAT;RSEQ=TTACAGGCGAACATACTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:33:19,14:20,9:0.5323:2,2:23.7:1:32.1:1:0.43363:1.62437:60:66:0.5323:0:2.8 0/0:19:0:0,0:10,9:0:2,0:22.8:1:29.3:1:1:0:60:38:1:0:1.9 -MT 185 . G A 85 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57479;LSEQ=ACCTACGTTCAATATTACAG;RSEQ=CGAACATACTTACTAAAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:7:5,2:35,25:0.1045:2,2:27.4:1:30.3:1:0.69262:1.77:60:14:0.1061:0:1.7 0/1:16:1:0,1:9,6:0.0625:2,0:44:0:28:0:0.4375:0:60:2:0.0625:0:1 -MT 189 . A G 77 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=ACGTTCAATATTACAGGCGA;RSEQ=CATACTTACTAAAGTGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:41,27:0:2,0:24.8:1:29.9:1:1:0:60:136:1:0:1.8 0/1:16:5:3,2:5,6:0.3125:2,2:32:1:33.2:1:1:1.73:60:10:0.3125:0:5.2 -MT 194 . CT TC 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAATATTACAGGCGAACATA;RSEQ=TACTAAAGTGTGTTAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:40,29:0:2,0:25.2:1:31.5:1:1:0:60:138:1:0:1.7 0/1:18:7:5,2:5,6:0.3889:2,2:23:1:31.3:1:0.36652:2.82:60:14:0.3889:0.1111:3.9 -MT 195 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00528;SOR=0.13608;LSEQ=AATATTACAGGCGAACATAC;RSEQ=TACTAAAGTGTGTTAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:34:18,16:21,13:0.5:2,2:25.9:1:31.4:1:0.62425:1.42821:60:68:0.5:0:2.7 0/1:17:2:1,1:4,6:0.1176:2,2:12:1:31.5:1:1:1.45:60:4:0.1667:0:3 -MT 204 . T C 90 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=GGCGAACATACTTACTAAAG;RSEQ=GTGTTAATTAATTAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:33,30:0:2,0:29:1:29.7:1:1:0:60:126:1:0:1.6 0/1:18:7:4,3:5,6:0.3889:2,2:21.1:1:32.4:1:1:1.56:60:14:0.3889:0:4 -MT 207 . G A 77 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=GAACATACTTACTAAAGTGT;RSEQ=TTAATTAATTAATGCTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:33,30:0:2,0:29.4:1:31.7:1:1:0:60:126:1:0:1.6 0/1:17:6:4,2:5,6:0.3529:2,2:25.3:1:30:1:0.61991:2.28:60:12:0.3529:0:4 -MT 225 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5666;SOR=0;LSEQ=GTGTTAATTAATTAATGCTT;RSEQ=TAGGACATAATAATAACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:3:1,2:33,36:0.0417:2,2:15.7:1:28.3:1:1:1.81855:60:6:0.0423:0:2.7 0/0:25:0:0,0:14,11:0:2,0:16.7:1:31.4:1:1:0:60:50:1:0:2.3 -MT 228 . G A 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47856;SOR=1.65545;LSEQ=TTAATTAATTAATGCTTGTA;RSEQ=GACATAATAATAACAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:7:3,4:32,35:0.0946:2,2:22.7:1:30.6:1:1:1.21581:60:14:0.0946:0:2.7 0/1:27:4:2,2:13,10:0.1481:2,2:10.8:1:30.8:1:1:1.28731:60:8:0.1481:0:2.8 -MT 247 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00752;SOR=Inf;LSEQ=AGGACATAATAATAACAATT;RSEQ=AATGTCTGCACAGCCACTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:33,40:0:2,0:23.3:1:31.8:1:1:0:59.7:146:1:0:1.8 0/1:32:4:2,2:17,11:0.125:2,2:16.5:1:30.3:1:1:1.52399:60:8:0.125:0:3.3 -MT 263 . A G 183 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52284;SOR=Inf;LSEQ=AATTGAATGTCTGCACAGCC;RSEQ=CTTTCCACACAGACATCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:64:29,35:1,0:0.9697:0,2:24.4:1:30.5:1:0.46154:0:59.6:15:0.9836:0:2 1/1:41:41:23,18:0,0:1:0,2:25.2:1:30.8:1:1:0:59.6:82:1:0:2.6 -MT 295 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18976;SOR=2.06721;LSEQ=GACATCATAACAAAAAATTT;RSEQ=CACCAAACCCCCCCTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:8:5,3:22,28:0.1379:2,2:28.5:1:31:1:0.45263:2.09:60:16:0.1538:0:3.8 0/1:40:10:6,4:15,14:0.25:2,2:29.7:1:29.5:1:0.72575:1.39:58.5:20:0.2564:0:3 -MT 302 . A AC 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.7678;SOR=1.24613;LSEQ=TAACAAAAAATTTCCACCAA;RSEQ=CCCCCCCTCCCCCGCTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:7:4,3:23,27:0.1207:2,2:20.6:1:32:1:0.69681:1.55:57.1:14:0.1296:0.0345:3.7 0/1:41:6:6,0:14,20:0.1463:2,0:31.2:1:29.7:1:0.0202:0:60:12:0.15:0:4.7 -MT 310 . T C 121 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.04943;LSEQ=AATTTCCACCAAACCCCCCC;RSEQ=CCCCCGCTTCTGGCCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:20:18,2:1,2:0.3571:2,2:11.1:1:28.1:1:0.06663:14.31:56.7:9:0.4737:0:2.7 0/1:38:14:14,0:2,1:0.3684:2,1:18.6:1:20.4:1:0.17647:0:58.9:1.8:0.36:0:4.2 -MT 340 . C T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.05929;SOR=Inf;LSEQ=CTGGCCACAGCACTTAAACA;RSEQ=ATCTCTGCCAAACCCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:27,34:0:2,0:20.5:1:30.7:1:1:0:59.7:11.2:1:0:0.9 0/1:40:3:2,1:15,22:0.075:2,2:14.7:1:24.3:1:0.56468:2.85:60:2:0.0571:0:3 -MT 357 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14687;SOR=Inf;LSEQ=ACACATCTCTGCCAAACCCC;RSEQ=AAAACAAAGAACCCTAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:32,37:0:2,0:24.8:1:30:1:1:0:59.7:33.5:1:0:0.6 0/1:44:2:1,1:17,24:0.0455:2,2:12.5:1:32:0:1:1.40:60:4:0.0488:0:1.5 -MT 434 . C G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.50815;SOR=0;LSEQ=TATGCACTTTTAACAGTCAC;RSEQ=CCCCAACTAACACATTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:31,33:0.0303:2,2:13:1:27.5:1:1:1.06:60:4:0.0308:0:3 0/0:48:0:0,0:22,26:0:2,0:24:1:30:1:1:0:60:47:1:0:0.5 -MT 462 . C T 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.56581;SOR=1.48078;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:7:2,5:28,27:0.1129:2,2:30.6:1:29.6:1:0.42674:2.5548:60:14:0.1167:0:2.7 0/1:44:7:3,4:20,17:0.1591:2,2:34.7:1:30.1:1:0.69267:1.55258:60:14:0.1591:0:1.9 -MT 477 . T C 148 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCTCCCACTCCCATACTAC;RSEQ=AATCTCATCAATACAACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:26:13,13:16,16:0.4483:2,2:21.4:1:31.6:1:1:1:60:52:0.4643:0:1.3 0/0:49:0:0,0:24,25:0:2,0:23.3:1:28.7:1:1:0:60:23.5:1:0:0.6 -MT 488 . AT GC 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4989;SOR=0;LSEQ=CCATACTACTAATCTCATCA;RSEQ=ACAACCCCCGCCCATCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:28,27:0.0351:2,2:13:1:29.9:1:1:1.03639:60:4:0.0364:0.0175:1.5 0/0:48:0:0,0:24,24:0:2,0:23.1:1:29.3:1:1:0:60:47:1:0:0.7 -MT 489 . T C 96 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42318;SOR=1.60786;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:7:3,4:25,23:0.125:2,2:25.3:1:32.7:1:0.70487:1.43953:60:14:0.1321:0:2.9 0/1:48:9:5,4:19,20:0.1875:2,2:11.6:1:30.6:1:1:1.31:60:18:0.1915:0:1.8 -MT 491 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50222;SOR=0;LSEQ=TACTACTAATCTCATCAATA;RSEQ=AACCCCCGCCCATCCTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:27,27:0.0357:2,2:26.5:1:29.5:1:1:1:60:4:0.0364:0:3.5 0/0:44:0:0,0:22,22:0:2,0:24.9:1:30.8:1:1:0:60:43:1:0:0.7 -MT 497 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20495;SOR=Inf;LSEQ=TAATCTCATCAATACAACCC;RSEQ=CGCCCATCCTACCCAGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:27,28:0:2,0:24.5:1:30.5:1:1:0:60:54:1:0:0.9 0/1:46:2:1,1:22,22:0.0435:2,2:34:1:30:1:1:1:60:4:0.0455:0:1 -MT 508 . A G 96 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=ATACAACCCCCGCCCATCCT;RSEQ=CCCAGCACACACACACCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:25,29:0:2,0:25.8:1:28.3:1:1:0:60:26:1:0:0.7 0/1:48:9:5,4:16,23:0.1875:2,2:27.3:1:30.3:1:0.47716:1.77:60:8:0.1778:0:1.1 -MT 513 . G GCA 123 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0;SOR=30.93227;LSEQ=ACCCCCGCCCATCCTACCCA;RSEQ=CACACACACACCGCTGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:25,33:0.0169:2,0:41:0:32:0:1:0:60:2:0.0175:0:4 0/1:48:17:7,10:14,17:0.3542:2,2:26.5:1:30.3:1:1:1.1725:60:34:0.3542:0.0833:0.6 -MT 525 . C T 31 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57047;SOR=2.82863;LSEQ=CCTACCCAGCACACACACAC;RSEQ=GCTGCTAACCCCATACCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:25,35:0.0164:2,0:1:0:27:0:1:0:60:2:0.0167:0:1 0/1:44:2:1,1:18,23:0.0455:2,2:27:0:31.5:1:1:1.27:60:4:0.0465:0:1.5 -MT 533 . A G 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0047;SOR=0;LSEQ=GCACACACACACCGCTGCTA;RSEQ=CCCCATACCCCGAACCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:9:4,5:20,27:0.1607:2,2:26.2:1:32.8:1:1:1.08:60:18:0.1607:0:1.9 0/0:43:0:0,0:19,24:0:2,0:28.3:1:29.6:1:1:0:60:86:1:0:0.5 -MT 709 . G A 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75198;SOR=0.70614;LSEQ=TTACACATGCAAGCATCCCC;RSEQ=TTCCAGTGAGTTCACCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:4,8:5,7:0.5:2,2:22.7:1:31.2:1:1:1.40739:53.3:24:0.5:0:2.2 0/1:17:7:3,4:0,6:0.4118:0,2:21.7:1:28.1:1:0.19231:0:52.7:14:0.4118:0:1.7 -MT 750 . A G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCACCACGATCAAAAGG;RSEQ=ACAAGCATCAAGCACGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:12,11:0,0:1:0,2:25.8:1:31.4:1:1:0:58.9:46:1:0:1.7 1/1:16:16:6,10:0,0:1:0,2:28.8:1:30.8:1:1:0:58.2:32:1:0:1.8 -MT 769 . G A 47 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04228;SOR=Inf;LSEQ=GAACAAGCATCAAGCACGCA;RSEQ=CAATGCAGCTCAAAACGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:23.8:1:31.8:1:1:0:59.4:27:1:0:1.1 0/1:16:3:1,2:6,7:0.1875:2,2:38:1:30:1:1:1.659:60:6:0.1875:0:3 -MT 1243 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0991;SOR=Inf;LSEQ=CCCCGATCAACCTCACCACC;RSEQ=CTTGCTCAGCCTATATACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:0:2,0:32.1:1:30.1:1:1:0:51:50:1:0:0 0/1:12:2:1,1:4,6:0.1667:2,2:30:1:30.5:1:1:1.45:58.5:4:0.1667:0:1 -MT 1355 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGCCCATGAGGTGGCAA;RSEQ=AAATGGGCTACATTTTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:11,14:0.0741:2,2:29.5:1:31.5:1:1:1.26:60:4:0.0769:0:1 0/0:8:0:0,0:3,5:0:2,0:30.4:1:31:1:1:0:60:16:1:0:0.1 -MT 1438 . A G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGATTTAGCAGTAAACT;RSEQ=AGAGTAGAGTGCTTAGTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:13,11:0,0:1:0,2:24.3:1:30.7:1:1:0:53.3:48:1:0:1.1 1/1:13:13:7,6:0,0:1:0,2:28.9:1:29.3:1:1:0:48.5:12:1:0:1.4 -MT 1494 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09512;SOR=Inf;LSEQ=GCGTACACACCGCCCGTCAC;RSEQ=CTCCTCAAGTATACTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:11,17:0:2,0:26.6:1:31.1:1:1:0:50.6:27:1:0:0.5 0/1:13:2:1,1:3,8:0.1538:2,2:30.5:1:29.5:1:1:2.45:27:4:0.1667:0:1.5 -MT 1559 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTATATAGAGGAGACAA;RSEQ=TCGTAACATGGTAAGTGTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:17,18:0.0541:2,2:21.5:1:28.5:1:1:1.06:49:4:0.0541:0:2 0/0:8:0:0,0:3,5:0:2,0:26.8:1:32.5:1:1:0:54:16:1:0:0.1 -MT 1719 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06083;SOR=Inf;LSEQ=CTTACTACCAGACAACCTTA;RSEQ=CCAAACCATTTACCCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:0:2,0:21.9:1:31.7:1:1:0:60:40:1:0:0 0/1:14:3:2,1:6,5:0.2143:2,2:34:1:31.3:1:1:1.61:60:6:0.2143:0:1 -MT 1811 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11905;SOR=Inf;LSEQ=GGGAAAGATGAAAAATTATA;RSEQ=CCAAGCATAATATAGCAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,11:0:2,0:20.4:1:29.8:1:1:0:59.4:34:0.9444:0:0.1 0/1:10:2:1,1:4,4:0.2:2,2:36.5:1:32.5:1:1:1:60:4:0.2:0:1 -MT 1836 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13306;SOR=Inf;LSEQ=GCATAATATAGCAAGGACTA;RSEQ=CCCCTATACCTTCTGCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:18.9:1:30.2:1:1:0:57.9:40:1:0:0.3 0/1:12:2:1,1:4,6:0.1667:2,2:15.5:1:30.5:1:1:1.45:60:4:0.1667:0:1 -MT 1843 . T C 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16774;SOR=Inf;LSEQ=ATAGCAAGGACTAACCCCTA;RSEQ=ACCTTCTGCATAATGAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:0:2,0:24.5:1:28.6:1:1:0:54.2:17:1:0:0.4 0/1:13:2:1,1:6,5:0.1538:2,2:14:0:32.5:1:1:1.18321:52:4:0.1538:0:1.5 -MT 1888 . G A 115 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00043;SOR=0.04706;LSEQ=GAAATAACTTTGCAAGGAGA;RSEQ=CCAAAGCTAAGACCCCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:9,7:7,5:0.5714:2,2:31.1:1:28.9:1:1:1.08558:40.9:15:0.5769:0:1 0/1:18:1:1,0:7,10:0.0556:2,0:44:0:32:0:0.44444:0:40:2:0.0556:0:1 -MT 1990 . G A 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00265;SOR=0;LSEQ=GAAGATTTATAGGTAGAGGC;RSEQ=ACAAACCTACCGAGCCTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:7,5:5,6:0.5217:2,2:24.2:1:30.6:1:0.68427:1.64:51.5:24:0.5217:0:1.2 0/0:11:0:0,0:5,6:0:2,0:20.6:1:28.2:1:1:0:51.5:10:1:0:0 -MT 2294 . A G 34 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17235;SOR=Inf;LSEQ=ATCTATCACCCTATAGAAGA;RSEQ=CTAATGTTAGTATAAGTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:20.3:1:29.7:1:1:0:60:38:1:0:0.3 0/1:14:2:1,1:7,5:0.1429:2,2:19.5:1:34:0:1:1.36624:60:4:0.1429:0:1 -MT 2706 . A G 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15794;SOR=3.60062;LSEQ=GCCCGTGAAGAGGCGGGCAT;RSEQ=ACACAGCAAGACGAGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:17:8,9:4,5:0.6538:2,2:27.5:1:32.1:1:1:1.11:60:34:0.6538:0:1.1 1/1:16:14:6,8:1,1:0.875:2,2:20.3:1:30.9:1:1:1.30929:60:28:0.875:0:1.2 -MT 2836 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GGCGACCTCGGAGCAGAACC;RSEQ=AACCTCCGAGCAGTACATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:0:2,0:32:1:31.5:1:1:0:60:38:1:0:0.1 0/1:13:2:1,1:8,3:0.1538:2,2:33.5:1:31:1:1:2.4495:60:4:0.1667:0:1 -MT 3010 . G A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01395;SOR=0.14624;LSEQ=ATGTTGGATCAGGACATCCC;RSEQ=ATGGTGCAGCCGCTATTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:17:9,8:3,4:0.7083:2,2:17.8:1:30.5:1:1:1.47:55.2:34:0.7083:0:1.2 0/1:12:3:2,1:5,4:0.25:2,2:17:1:28:1:1:1.54:60:6:0.25:0:1 -MT 3106 . CN C 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGTCGGTTTCTATCTA;RSEQ=TTCAAATTCCTCCCTGTACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:11,10:0,0:1:0,2:19.8:1:30.9:1:1:0:59.9:42:1:0.1905:0.1 1/1:14:14:6,8:0,0:1:0,2:21.9:1:32.3:1:1:0:60:28:1:0.2143:0.4 -MT 3480 . A G 52 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11674;SOR=5.98438;LSEQ=GCCATAAAACTCTTCACCAA;RSEQ=GAGCCCCTAAAACCCGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:1:0,1:50,37:0.0114:2,0:31:0:14:0:0.43182:0:60:0:0:0:1 0/1:46:3:3,0:19,24:0.0652:2,0:12.7:1:33:1:0.10145:0:60:6:0.0652:0:1 -MT 3505 . A G 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTAAAACCCGCCACATCT;RSEQ=CCATCACCCTCTACATCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:53,47:0:2,0:26.5:1:28.8:1:1:0:60:99:1:0:0.2 0/1:56:12:6,6:19,23:0.2143:2,2:20.8:1:31.9:1:1:1.21:60:24:0.2143:0:1.2 -MT 3512 . C T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55135;SOR=0;LSEQ=ACCCGCCACATCTACCATCA;RSEQ=CCTCTACATCACCGCCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:3:1,2:54,47:0.0288:2,2:28:1:25:1:0.60042:2.28004:60:2:0.0198:0:1.7 0/0:53:0:0,0:25,28:0:2,0:22.5:1:31.4:1:1:0:60:106:1:0:0.6 -MT 3528 . C T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACCCTCTACATCACCGC;RSEQ=CCGACCTTAGCTCTCACCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:54,57:0.0177:2,2:20:1:31.5:1:1:1.06:60:4:0.018:0:1 0/0:54:0:0,0:26,28:0:2,0:22.7:1:30.6:1:1:0:60:53:1:0:0.6 -MT 3594 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09611;SOR=Inf;LSEQ=CCCATACCCAACCCCCTGGT;RSEQ=AACCTCAACCTAGGCCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:36,42:0:2,0:23.2:1:31.4:1:1:0:60:18.5:1:0:0.3 0/1:36:2:1,1:13,21:0.0556:2,2:17.5:1:29.5:1:1:1.59:60:4:0.0556:0:1.5 -MT 3643 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCCACCTCTAGCCTAGCC;RSEQ=TTTACTCAATCCTCTGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:34,26:0.0323:2,2:21:1:30:1:1:1.30197:60:4:0.0323:0:1 0/0:27:0:0,0:13,14:0:2,0:24.7:1:30.3:1:1:0:60:54:1:0:0.1 -MT 3812 . A G 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACCCTTATCACAACAC;RSEQ=AGAACACCTCTGATTACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:26,18:0.0435:2,2:33:0:32:0:1:1.43267:60:4:0.0444:0:1 0/0:20:0:0,0:12,8:0:2,0:22.6:1:28.4:1:1:0:60:19:1:0:0.2 -MT 3915 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTCGACCTTGCCGAAGG;RSEQ=GAGTCCGAACTAGTCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:19,30:0.0392:2,2:33.5:1:29.5:1:1:1.56:60:4:0.0392:0:1 0/0:11:0:0,0:5,6:0:2,0:19.5:1:30.7:1:1:0:53.9:22:1:0:0.1 -MT 4016 . T G 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTATTATAATAAACACCC;RSEQ=CACCACTACAATCTTCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:17,14:0.0606:2,2:26.5:1:26:1:1:1.20712:49:4:0.0606:0:2 0/0:16:0:0,0:10,6:0:2,0:28.3:1:29.5:1:1:0:41.3:32:1:0:0.3 -MT 4093 . A G 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02107;SOR=Inf;LSEQ=CAACATATTTTGTCACCAAG;RSEQ=CCCTACTTCTAACCTCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,23:0:2,0:23.7:1:29:1:1:0:51.2:20.5:1:0:0.3 0/1:28:4:2,2:11,13:0.1429:2,2:20.5:1:30.3:1:1:1.17:54.5:8:0.1538:0:1 -MT 4216 . T C 74 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCTAGCATTACTTATATGA;RSEQ=ATGTCTCCATACCCATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:3,1:0.6:2,2:23.3:1:29:1:0.19048:10.29391:31.3:5:0.5556:0:1.8 1/1:1:1:1,0:0,0:1:0,0:26:0:33:0:1:0:40:2:1:0:1 -MT 4769 . A G 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCATTAATAATCATAAT;RSEQ=GCTATAGCAATAAAACTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:12,2:0,0:1:0,2:25.9:1:31.4:1:1:0:31.5:28:1:0:1 1/1:9:9:9,0:0,0:1:0,0:26.9:1:31.9:1:1:0:31.3:18:1:0:1 -MT 4917 . A G 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCAAATCTCTCCCTCACTA;RSEQ=ACGTAAGCCTTCTCCTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:20:9,11:11,15:0.4348:2,2:26:1:31.8:1:1:1.11:59.5:40:0.4348:0:1.1 0/0:43:0:0,0:22,21:0:2,0:18.3:1:29.4:1:1:0:60:42:1:0:0.2 -MT 5007 . G A 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04236;SOR=0;LSEQ=CCCAGCTACGCAAAATCTTA;RSEQ=CATACTCCTCAATTACCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:4,4:16,17:0.1951:2,2:24:1:31.4:1:1:1.06:59.8:16:0.1951:0:1 0/0:22:0:0,0:9,13:0:2,0:22.7:1:31.6:1:1:0:57.5:44:1:0:0.2 -MT 5046 . G A 60 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00534;SOR=Inf;LSEQ=ACATAGGATGAATAATAGCA;RSEQ=TTCTACCGTACAACCCTAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:19,20:0:2,0:28.9:1:32.4:1:1:0:51.3:78:1:0:0.2 0/1:16:4:1,3:5,7:0.25:2,2:12:1:30.3:1:1:2.04824:51.8:8:0.25:0:1 -MT 5164 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGACCCTACTACTATCTC;RSEQ=CACCTGAAACAAGCTAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:27,19:0.0417:2,2:5:0:31.5:1:1:1.41046:52:4:0.0426:0:0.5 0/0:20:0:0,0:11,9:0:2,0:24.9:1:30.5:1:1:0:43.1:40:1:0:0.1 -MT 5237 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08235;SOR=Inf;LSEQ=TCCCTAGGAGGCCTGCCCCC;RSEQ=CTAACCGGCTTTTTGCCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:17,19:0:2,0:23.4:1:31.3:1:1:0:32.6:72:1:0:0.1 0/1:15:2:1,1:9,4:0.1333:2,2:9.5:1:28:1:1:2.12136:21:4:0.1333:0:1.5 -MT 5279 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26203;SOR=4.07983;LSEQ=TGGGCCATTATCGAAGAATT;RSEQ=ACAAAAAACAATAGCCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:1:0,1:24,28:0.0189:2,0:1:0:23:0:1:0:60:2:0.0192:0:1 0/1:27:2:1,1:15,10:0.0741:2,2:6:1:27.5:1:1:1.47706:60:4:0.0769:0:1 -MT 5325 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1129;SOR=Inf;LSEQ=CCACCATCATAGCCACCATC;RSEQ=CCCTCCTTAACCTCTACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:40,42:0:2,0:26.3:1:30.2:1:1:0:56.5:164:1:0:0.3 0/1:42:2:1,1:20,19:0.0476:2,2:32:1:30.5:1:1:1.05134:60:4:0.0488:0:1 -MT 5390 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.05132;SOR=Inf;LSEQ=TCAATCACACTACTCCCCAT;RSEQ=TCTAACAACGTAAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:35,36:0:2,0:24.3:1:29.6:1:1:0:59.3:142:1:0:0.1 0/1:43:3:1,2:19,21:0.0698:2,2:23.7:1:30.7:1:1:1.78563:51.3:6:0.0714:0:2.3 -MT 5393 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1402;SOR=Inf;LSEQ=ATCACACTACTCCCCATATC;RSEQ=AACAACGTAAAAATAAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:36,35:0:2,0:24:1:29.5:1:1:0:59.3:34.5:1:0:0.2 0/1:43:2:1,1:19,22:0.0465:2,2:29.5:1:30.5:1:1:1.15:44:4:0.0488:0:1 -MT 5426 . T C 50 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.05037;SOR=Inf;LSEQ=ATAAAATGACAGTTTGAACA;RSEQ=ACAAAACCCACCCCATTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:31,39:0:2,0:23.8:1:29.2:1:1:0:59.1:140:1:0:0.2 0/1:42:3:1,2:16,23:0.0714:2,2:34.7:1:31.7:1:1:1.38076:51.3:6:0.0732:0:2.3 -MT 5429 . A G 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13367;SOR=Inf;LSEQ=AAATGACAGTTTGAACATAC;RSEQ=AAACCCACCCCATTCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:33,39:0:2,0:23.4:1:29.8:1:1:0:59.1:71:1:0:0.2 0/1:42:2:1,1:17,23:0.0476:2,2:34:0:31.5:1:1:1.34:60:4:0.05:0:2 -MT 5460 . G A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00044;SOR=Inf;LSEQ=CATTCCTCCCCACACTCATC;RSEQ=CCCTTACCACGCTACTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:29,35:0:2,0:26.3:1:30.9:1:1:0:59.2:128:1:0:0.2 0/1:27:6:2,4:8,13:0.2222:2,2:31:1:28.7:1:1:1.22149:60:12:0.2222:0:1 -MT 5610 . G C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06022;SOR=Inf;LSEQ=GGACTGCAAAACCCCACTCT;RSEQ=CATCAACTGAACGCAAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:0:2,0:31.4:1:32.7:1:1:0:43.7:46:1:0:0.1 0/1:8:2:1,1:2,4:0.25:2,2:16:1:29:1:1:1.83:27:4:0.2857:0:1 -MT 6221 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14856;SOR=Inf;LSEQ=ATAAGCTTCTGACTCTTACC;RSEQ=CCCTCTCTCCTACTCCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:33,22:0:2,0:24.5:1:30.7:1:1:0:57.7:54:1:0:0.1 0/1:35:2:1,1:17,15:0.0571:2,2:22.5:1:28:0:1:1.12916:50:4:0.0588:0:1 -MT 6291 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49677;SOR=0;LSEQ=GAACAGGTTGAACAGTCTAC;RSEQ=CTCCCTTAGCAGGGAACTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:27,24:0.0377:2,2:47:0:31:1:1:1.1225:60:4:0.0377:0:1 0/0:47:0:0,0:25,22:0:2,0:28.7:1:30:1:1:0:59.6:46:1:0:0.1 -MT 6371 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16079;SOR=Inf;LSEQ=TTACACCTAGCAGGTGTCTC;RSEQ=TCTATCTTAGGGGCCATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:29,30:0:2,0:25:1:31.3:1:1:0:59.7:28.5:1:0:0.1 0/1:40:2:2,0:16,22:0.05:2,0:30.5:1:31:0:0.19615:0:60:4:0.0526:0:1 -MT 6518 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00388;SOR=Inf;LSEQ=CTCCCAGTCCTAGCTGCTGG;RSEQ=ATCACTATACTACTAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:31,26:0:2,0:25.6:1:32.5:1:1:0:59.6:114:1:0:0.1 0/1:40:6:2,4:18,16:0.15:2,2:17:1:28.2:1:0.66142:2.20556:47:12:0.1538:0:1.2 -MT 6541 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51418;SOR=0;LSEQ=CACTATACTACTAACAGACC;RSEQ=CAACCTCAACACCACCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:30,26:0.0345:2,2:20.5:1:31.5:1:1:1.15099:60:4:0.0345:0:1 0/0:39:0:0,0:18,21:0:2,0:22.7:1:30.3:1:1:0:57.7:78:1:0:0.3 -MT 6548 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05686;SOR=Inf;LSEQ=CTACTAACAGACCGCAACCT;RSEQ=AACACCACCTTCTTCGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:28,28:0:2,0:24.3:1:31.9:1:1:0:59.3:112:1:0:0.1 0/1:36:3:1,2:14,18:0.0833:2,2:13.3:1:29:1:1:1.53673:56.7:6:0.0857:0:1 -MT 6565 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.52629;SOR=0;LSEQ=CCTCAACACCACCTTCTTCG;RSEQ=CCCCGCCGGAGGAGGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:20,22:0.0455:2,2:20:1:30:1:1:1.10:60:4:0.0455:0:1 0/0:26:0:0,0:10,16:0:2,0:28.7:1:28.2:1:1:0:59.7:25:1:0:0.2 -MT 6909 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49714;SOR=Inf;LSEQ=GAAGCAATATGAAATGATCT;RSEQ=CTGCAGTGCTCTGAGCCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:30.5:1:32.2:1:1:0:56.2:44:1:0:0.1 0/1:28:2:1,1:14,12:0.0714:2,2:41:1:27.5:1:1:1.16024:60:4:0.0741:0:1 -MT 7028 . C T 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1451;SOR=6.57383;LSEQ=GACACGTACTACGTTGTAGC;RSEQ=CACTTCCACTATGTCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:3,1:3,3:0.4:2,2:24.3:1:32:1:0.57143:2.69:33.5:8:0.4444:0:1 1/1:6:5:3,2:0,1:0.8333:0,2:15.6:1:29:1:1:0:32.2:10:0.8333:0:1 -MT 7051 . T C 74 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=CTTCCACTATGTCCTATCAA;RSEQ=AGGAGCTGTATTTGCCATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:4,2:0.4545:2,2:31.4:1:32.2:1:1:1.88:32.2:10:0.4545:0:1 0/0:4:0:0,0:3,1:0:2,0:28.5:1:29.8:1:1:0:35.3:8:1:0:0.8 -MT 7235 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52893;SOR=0;LSEQ=CGACGTTACTCGGACTACCC;RSEQ=GATGCATACACCACATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:19,19:0.05:2,2:24.5:1:31:1:1:1:60:4:0.0513:0:1.5 0/0:23:0:0,0:11,12:0:2,0:24:1:29.9:1:1:0:57.3:46:1:0:0.1 -MT 7364 . A G 31 v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02463;SOR=Inf;LSEQ=AAAGTCCTAATAGTAGAAGA;RSEQ=CCCTCCATAAACCTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:0:2,0:26:1:29.6:1:1:0:38.4:48:1:0:0 0/1:5:2:1,1:0,3:0.4:0,2:29:0:31:1:0.4:0:27:4:0.4:0:2 -MT 7771 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGACGCTCAGGAAATAGA;RSEQ=ACCGTCTGAACTATCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:27,21:0.04:2,2:25:1:31:1:1:1.2792:49:4:0.04:0:1 0/0:23:0:0,0:11,12:0:2,0:19.2:1:29.4:1:1:0:49.8:22:1:0:0.1 -MT 7867 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.05198;SOR=Inf;LSEQ=GACGAGGTCAACGATCCCTC;RSEQ=CTTACCATCAAATCAATTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:22,25:0:2,0:24.3:1:31.2:1:1:0:59:46:1:0:0.1 0/1:29:3:1,2:14,12:0.1034:2,2:11.7:1:28.7:1:0.5977:2.2674:60:6:0.1034:0:1.3 -MT 8003 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGACTCCTTGACGTTGAC;RSEQ=ATCGAGTAGTACTCCCGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:18,17:0.0541:2,2:39.5:1:31.5:1:1:1.05721:50:4:0.0541:0:1 0/0:17:0:0,0:6,11:0:2,0:23.4:1:29.6:1:1:0:48.2:34:1:0:0.2 -MT 8038 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCGATTGAAGCCCCCATTCG;RSEQ=ATAATAATTACATCACAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:18,21:0.0488:2,2:16.5:1:31.5:1:1:1.16:55:4:0.0488:0:1 0/0:13:0:0,0:7,6:0:2,0:20:1:27.2:1:1:0:54.2:5.5:1:0:0.2 -MT 8170 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12685;SOR=Inf;LSEQ=CCGGGGGTATACTACGGTCA;RSEQ=TGCTCTGAAATCTGTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:0:2,0:20.6:1:30.5:1:1:0:60:56:1:0:0.1 0/1:16:2:1,1:5,9:0.125:2,2:26:0:33.5:1:1:1.73:60:4:0.125:0:1.5 -MT 8229 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCGTCCTAGAATTAATTC;RSEQ=CCTAAAAATCTTTGAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:17,10:0.069:2,2:44.5:1:30.5:1:1:1.66781:60:4:0.069:0:1 0/0:11:0:0,0:3,8:0:2,0:23.1:1:30.8:1:1:0:50.4:22:1:0:0.5 -MT 8251 . G A 63 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=CTAAAAATCTTTGAAATAGG;RSEQ=CCCGTATTTACCCTATAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:23.8:1:30.4:1:1:0:49:29:1:0:0.1 1/0:9:5:2,3:2,2:0.5556:2,2:23:1:27.4:1:1:1.43328:46.8:10:0.5556:0:1 -MT 8610 . T C 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00756;SOR=Inf;LSEQ=CTGATCATTCTATTTCCCCC;RSEQ=CTATTGATCCCCACCTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:0:2,0:24.6:1:29.9:1:1:0:50.6:18:1:0:0.2 0/1:25:5:1,4:8,12:0.2:2,2:23:1:29.8:1:0.62055:2.57368:48.4:10:0.2083:0:2.2 -MT 8614 . T C 70 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00821;SOR=Inf;LSEQ=TCATTCTATTTCCCCCTCTA;RSEQ=TGATCCCCACCTCCAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:0:2,0:25.2:1:30.7:1:1:0:51.2:74:1:0:0.3 0/1:25:5:1,4:8,12:0.2:2,2:20.6:1:30.4:1:0.62055:2.57368:48.4:10:0.2174:0:2.2 -MT 8697 . G A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00114;SOR=0.10232;LSEQ=AAACTAACCTCAAAACAAAT;RSEQ=ATAACCATACACAACACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:21:10,11:10,14:0.4667:2,2:23.2:1:28.7:1:0.76854:1.27:59.3:42:0.4667:0:1.2 0/1:25:2:2,0:13,10:0.08:2,0:19.5:1:30:0:0.5:0:42:4:0.0833:0:1 -MT 8860 . A G 81 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATCCCCTTATGAGCGGGC;RSEQ=CAGTGATTATAGGCTTTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1:0,2:21.3:1:31.7:1:1:0:33.5:12:1:0:1 1/1:4:4:1,3:0,0:1:0,2:31:1:32.5:1:1:0:33.5:8:1:0:1 -MT 9115 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14675;SOR=Inf;LSEQ=TTATCATCTTCACAATTCTA;RSEQ=TTCTACTGACTATCCTAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:0:2,0:24.8:1:28.2:1:1:0:50.8:7.25:1:0:0.5 0/1:21:2:1,1:13,6:0.0952:2,2:49.5:1:32:1:1:2.08171:49:4:0.1:0:2 -MT 9150 . A G 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01536;SOR=0;LSEQ=CTAGAAATCGCTGTCGCCTT;RSEQ=ATCCAAGCCTACGTTTTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:8:6,2:12,11:0.2581:2,2:20.5:1:32.4:1:0.41203:2.66:49.3:16:0.2667:0:1 0/0:23:0:0,0:13,10:0:2,0:27.8:1:27.7:1:1:0:50.7:22:1:0:0.3 -MT 9540 . T C 48 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02879;SOR=Inf;LSEQ=GCCTAGCCCCTACCCCCCAA;RSEQ=TAGGAGGGCACTGGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,27:0:2,0:26.1:1:30:1:1:0:60:25:1:0:0.1 0/1:24:3:2,1:11,9:0.125:2,2:16.7:1:30.7:1:1:1.60:60:6:0.1304:0:1 -MT 9698 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16923;SOR=Inf;LSEQ=CAAATAATTCAAGCACTGCT;RSEQ=ATTACAATTTTACTGGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:3,12:0:2,0:22.3:1:28.6:1:1:0:48.1:30:1:0:0.1 0/1:11:2:1,1:3,6:0.1818:2,2:27.5:1:30.5:1:1:1.87:54.5:4:0.1818:0:1 -MT 9891 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19048;SOR=Inf;LSEQ=AACTAATATTTCACTTTACA;RSEQ=CCAAACATCACTTTGGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:9,11:0:2,0:24:1:30.4:1:1:0:60:40:1:0:0.5 0/1:16:2:1,1:7,7:0.125:2,2:30.5:1:30.5:1:1:1:60:4:0.1333:0:2 -MT 9899 . T C 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00414;SOR=0;LSEQ=TTTCACTTTACATCCAAACA;RSEQ=CACTTTGGCTTCGAAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:7,7:0.3636:2,2:27.9:1:29.8:1:0.67492:1.62835:60:7:0.3333:0:1 0/0:19:0:0,0:9,10:0:2,0:24.7:1:29.1:1:1:0:60:38:1:0:0.3 -MT 10250 . A T 25 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.84324;LSEQ=GTAGCTATTACCTTCTTATT;RSEQ=TTTGATCTAGAAATTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:17,20:0.0513:2,0:9:1:25:0:0.49528:0:60:4:0.0541:0:1 0/1:23:1:0,1:11,11:0.0435:2,0:1:0:24:0:1:0:60:2:0.0435:0:1 -MT 10398 . A G 83 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00271;SOR=Inf;LSEQ=TACAAAAAGGATTAGACTGA;RSEQ=CCGAATTGGTATATAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:0:2,0:21.9:1:29.8:1:1:0:60:38:1:0:0.3 0/1:14:6:2,4:5,3:0.4286:2,2:6:1:32.3:1:0.59207:3.04364:51:12:0.4286:0:1.3 -MT 10457 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCATTAAATTATGATAA;RSEQ=CATATTTACCAAATGCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:0.08:2,2:25.5:1:33:1:1:1.0871:60:4:0.08:0:2 0/0:12:0:0,0:7,5:0:2,0:16.8:1:27.4:1:1:0:52.7:24:1:0:0.3 -MT 10463 . T C 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00035;SOR=0;LSEQ=TTAAATTATGATAATCATAT;RSEQ=TACCAAATGCCCCTCATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:6,8:7,3:0.5833:2,2:30.1:1:32.3:1:0.23967:2.96235:60:28:0.5833:0:1.2 0/0:13:0:0,0:7,6:0:2,0:17.5:1:28.2:1:1:0:53.2:26:1:0:0.3 -MT 10537 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51152;SOR=0;LSEQ=TCTAGGAATACTAGTATATC;RSEQ=CTCACACCTCATATCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:13,14:0.069:2,2:14.5:1:28:1:1:1.07:60:4:0.069:0:1 0/0:19:0:0,0:6,13:0:2,0:24.2:1:31.6:1:1:0:56.3:38:1:0:0.2 -MT 10550 . A G 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0769;SOR=Inf;LSEQ=GTATATCGCTCACACCTCAT;RSEQ=TCCTCCCTACTATGCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:25.6:1:28.8:1:1:0:59.1:26:1:0:0.3 0/1:21:3:1,2:7,11:0.1429:2,2:21:1:30.7:1:1:1.25853:60:6:0.15:0:1 -MT 10601 . T C 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0491;SOR=0;LSEQ=CTATCGCTGTTCATTATAGC;RSEQ=ACTCTCATAACCCTCAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:3,2:11,7:0.2174:2,2:30.2:1:30.6:1:1:1.04547:60:10:0.2174:0:1 0/0:23:0:0,0:13,10:0:2,0:22.8:1:29.7:1:1:0:60:46:1:0:0.3 -MT 10688 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12057;SOR=Inf;LSEQ=GCCGCCTGCGAAGCAGCGGT;RSEQ=GGCCTAGCCCTACTAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:27.8:1:32:1:1:0:60:62:1:0:0 0/1:17:2:1,1:7,8:0.1176:2,2:38.5:1:30:1:1:1.13:60:4:0.1176:0:1.5 -MT 10866 . T G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.11107;SOR=Inf;LSEQ=CCACAGCCTAATTATTAGCA;RSEQ=CATCCCTCTACTATTTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,23:0:2,0:22.9:1:30.8:1:1:0:60:98:1:0:0.2 0/1:25:2:1,1:12,11:0.08:2,2:28.5:1:30.5:1:1:1.0871:60:4:0.08:0:1 -MT 10873 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11712;SOR=Inf;LSEQ=CTAATTATTAGCATCATCCC;RSEQ=CTACTATTTTTTAACCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,23:0:2,0:22.5:1:30.4:1:1:0:60:48:1:0:0.2 0/1:26:2:1,1:12,12:0.0769:2,2:37.5:1:32:0:1:1:60:4:0.0769:0:1 -MT 10876 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12033;SOR=Inf;LSEQ=ATTATTAGCATCATCCCTCT;RSEQ=CTATTTTTTAACCAAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:26,22:0:2,0:22.5:1:28.6:1:1:0:60:96:1:0:0.2 0/1:26:2:1,1:12,12:0.0769:2,2:47:1:32:1:1:1:60:4:0.0769:0:1 -MT 11192 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGCCAGAACGCCTGAAC;RSEQ=CAGGCACATACTTCCTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:20,22:0.0455:2,2:23.5:1:29.5:1:1:1.10:60:4:0.0465:0:1 0/0:16:0:0,0:9,7:0:2,0:16.3:1:30.3:1:1:0:60:32:1:0:0.3 -MT 11195 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGAACGCCTGAACGCA;RSEQ=GCACATACTTCCTATTCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:17,23:0.0476:2,2:5.5:1:30:1:1:1.34:60:4:0.0476:0:2 0/0:15:0:0,0:9,6:0:2,0:16.6:1:30.7:1:1:0:60:30:1:0:0.3 -MT 11238 . TA T 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTAGTAGGCTCCCTTCCCC;RSEQ=CTCATCGCACTAATTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:17,22:0.0488:2,2:15:0:30:1:1:1.29:60:4:0.0488:0:3 0/0:12:0:0,0:7,5:0:2,0:22.7:1:28.2:1:1:0:59.5:24:1:0:0.6 -MT 11251 . A G 151 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10504;SOR=0.30913;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:31:13,18:6,9:0.6739:2,2:29:1:30.6:1:1:1.08:60:30:0.6818:0:1.4 0/1:13:5:3,2:5,3:0.3846:2,2:22.8:1:31.4:1:1:1.10211:60:10:0.3846:0:1.4 -MT 11294 . C A 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.56923;SOR=0;LSEQ=GCTCACTAAACATTCTACTA;RSEQ=TCACTCTCACTGCCCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:3:2,1:20,26:0.0612:2,2:29.3:1:25.7:1:0.58087:2.55:60:2:0.0417:0:3 0/0:16:0:0,0:8,7:0:2,0:24.2:1:30.8:1:1:0:60:30:0.9375:0:0.3 -MT 11447 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11106;SOR=Inf;LSEQ=CCCCCATCGCTGGGTCAATA;RSEQ=TACTTGCCGCAGTACTCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,19:0:2,0:25.8:1:32.1:1:1:0:59.2:84:0.9767:0:0.1 0/1:22:2:1,1:12,8:0.0909:2,2:32.5:1:28.5:1:1:1.47192:60:4:0.0909:0:1 -MT 11467 . A G 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=GTACTTGCCGCAGTACTCTT;RSEQ=AAACTAGGCGGCTATGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:29,25:0:2,0:23.7:1:29.2:1:1:0:59.4:108:1:0:0.1 0/1:27:8:5,3:9,10:0.2963:2,2:26.5:1:30.9:1:0.67762:1.81:60:16:0.2963:0:1 -MT 11541 . TC T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54774;SOR=0;LSEQ=AAAACACATAGCCTACCCCT;RSEQ=CTTGTACTATCCCTATGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:25,30:0.0351:2,2:34:1:30.5:1:1:1.20:60:4:0.0357:0:0 0/0:29:0:0,0:9,18:0:2,0:25.6:1:31:1:1:0:60:54:0.931:0:0.3 -MT 11674 . C T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.01229;SOR=Inf;LSEQ=ACAGCCATTCTCATCCAAAC;RSEQ=CCCTGAAGCTTCACCGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:0:2,0:26.1:1:31.1:1:1:0:52.9:86:1:0:0.4 0/1:23:4:1,3:12,7:0.1739:2,2:30.8:1:29.3:1:0.28063:4.78091:57.3:8:0.1818:0:1.3 -MT 11719 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01601;SOR=4.96938;LSEQ=ATTCTCATAATCGCCCACGG;RSEQ=CTTACATCCTCATTACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:29:13,16:11,9:0.58:2,2:21.2:1:29:1:0.56718:1.49167:53:28:0.5714:0:1.1 1/1:24:21:12,9:1,2:0.875:2,2:24.9:1:28.6:1:0.57609:2.56:55:20:0.8696:0:1 -MT 11812 . A G 50 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04634;SOR=Inf;LSEQ=TCTCAAGGACTTCAAACTCT;RSEQ=CTCCCACTAATAGCTTTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:20,21:0:2,0:24:1:28.2:1:1:0:59.6:82:1:0:0.3 0/1:24:3:1,2:9,12:0.125:2,2:28:1:32:1:1:1.47566:60:6:0.1304:0:1 -MT 11947 . A G 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0119;SOR=Inf;LSEQ=AATATCACTCTCCTACTTAC;RSEQ=GGACTCAACATACTAGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:22,15:0:2,0:23.9:1:29.7:1:1:0:59.2:17.5:1:0:0.1 0/1:28:5:2,3:13,10:0.1786:2,2:13.4:1:28.4:1:0.63889:1.90363:60:10:0.1852:0:1 -MT 12372 . G A 42 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0119;SOR=Inf;LSEQ=ACTATAACCACCCTAACCCT;RSEQ=ACTTCCCTAATTCCCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:25,29:0:2,0:25.7:1:31.2:1:1:0:60:26:1:0:0.2 0/1:17:3:2,1:7,7:0.1765:2,2:35:1:27:1:1:1.92:60:6:0.2:0:1.3 -MT 12414 . T C 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTACCACCCTCGTTAACCC;RSEQ=AACAAAAAAAACTCATACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:30,24:0:2,0:20.6:1:29.3:1:1:0:60:26:0.9811:0:0.1 1/0:20:10:5,5:6,4:0.5:2,2:22:1:30.5:1:1:1.46966:60:20:0.5:0:1.3 -MT 12479 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53112;SOR=0;LSEQ=ATCCACCTTTATTATCAGTC;RSEQ=CTTCCCCACAACAATATTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:21,21:0.0455:2,2:21.5:1:30.5:1:1:1:60:4:0.0455:0:1 0/0:25:0:0,0:15,10:0:2,0:23.1:1:29.2:1:1:0:60:24:1:0:0.4 -MT 12612 . A G 53 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.58292;LSEQ=TCCATAATATTCATCCCTGT;RSEQ=GCATTGTTCGTTACATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:4:2,2:15,15:0.1176:2,2:20.3:1:26.8:1:1:1:60:3:0.0909:0:1 0/1:14:1:0,1:5,8:0.0714:2,0:25:0:26:0:1:0:60:2:0.0714:0:1 -MT 12621 . C T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08067;SOR=Inf;LSEQ=TTCATCCCTGTAGCATTGTT;RSEQ=GTTACATGGTCCATCATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:16,17:0:2,0:23.7:1:31:1:1:0:60:66:0.9706:0:0.9 0/1:14:2:1,1:5,7:0.1429:2,2:36:1:26.5:1:1:1.37:60:4:0.1429:0:4.5 -MT 12633 . C A 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATTGTTCGTTACATGGTC;RSEQ=ATCATAGAATTCTCACTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:24:12,12:4,5:0.7273:2,2:20.9:1:30:1:1:1.24:60:48:0.7273:0:1.1 0/0:14:0:0,0:7,7:0:2,0:25.9:1:30.5:1:1:0:60:13:1:0:0.9 -MT 12687 . C A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCAAACATTAATCAGTT;RSEQ=TTCAAATATCTACTCATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:15,15:0.0625:2,2:43:0:30:1:1:1:60:4:0.0625:0:1.5 0/0:13:0:0,0:6,7:0:2,0:17.1:1:30.1:1:1:0:60:12:1:0:0.5 -MT 12705 . C T 45 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01552;SOR=Inf;LSEQ=TTCTTCAAATATCTACTCAT;RSEQ=TTCCTAATTACCATACTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:19,17:0:2,0:21.9:1:32:1:1:0:60:72:1:0:0.4 0/1:13:3:2,1:6,4:0.2308:2,2:12.7:1:28.7:1:1:1.30:60:6:0.2308:0:1.3 -MT 12766 . T C 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15;SOR=Inf;LSEQ=TATTCCAACTGTTCATCGGC;RSEQ=GAGAGGGCGTAGGAATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:0:2,0:23:1:30.4:1:1:0:60:68:1:0:0.1 0/1:22:2:1,1:13,7:0.0909:2,2:43:1:27:1:1:1.80284:60:4:0.0909:0:1.5 -MT 13020 . T C 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09985;SOR=Inf;LSEQ=GGCAAATCAGCCCAATTAGG;RSEQ=CTCCACCCCTGACTCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:37,42:0:2,0:23.6:1:29.9:1:1:0:59.8:78:1:0:0.1 0/1:37:2:1,1:21,14:0.0541:2,2:21:0:33.5:1:1:1.4832:55:4:0.0556:0:1 -MT 13105 . A G 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00679;SOR=Inf;LSEQ=GCACTATAGTTGTAGCAGGA;RSEQ=TCTTCTTACTCATCCGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:26,33:0:2,0:22.7:1:30.6:1:1:0:60:118:1:0:0.2 0/1:48:6:3,3:20,22:0.125:2,2:31.5:1:29.8:1:1:1.10:57.7:12:0.125:0:1.3 -MT 13209 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06128;SOR=Inf;LSEQ=ACTCTGTTCGCAGCAGTCTG;RSEQ=GCCCTTACACAAAATGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:0:2,0:27.6:1:31.3:1:1:0:60:82:1:0:0.1 0/1:14:2:1,1:5,7:0.1429:2,2:20.5:1:29.5:1:1:1.37:60:4:0.1429:0:1 -MT 13368 . G A 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATACTATTTATGTGCTCCGG;RSEQ=TCCATCATCCACAACCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:18:7,11:6,6:0.6:2,2:23.9:1:30.8:1:0.71062:1.54757:46.5:36:0.6207:0:1 0/0:22:0:0,0:11,11:0:2,0:24.8:1:30.9:1:1:0:60:44:1:0:0.1 -MT 13506 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0905;SOR=Inf;LSEQ=CCTTTCCTCACAGGTTTCTA;RSEQ=TCCAAAGACCACATCATCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:17,19:0:2,0:24.1:1:32.1:1:1:0:57.9:72:1:0:0.1 0/1:16:2:1,1:6,8:0.125:2,2:33:0:31.5:1:1:1.31:60:4:0.125:0:1.5 -MT 13650 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09653;SOR=Inf;LSEQ=ACAGGTCAACCTCGCTTCCC;RSEQ=ACCCTTACTAACATTAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:0:2,0:23.1:1:31:1:1:0:60:29.5:1:0:0.2 0/1:28:2:1,1:13,13:0.0714:2,2:35.5:1:28.5:1:1:1:60:4:0.0714:0:1.5 -MT 13708 . G A 90 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43374;SOR=0.33719;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:8:3,5:27,21:0.1429:2,2:19.1:1:30:1:0.45074:2.11375:60:16:0.1509:0:1.5 0/1:19:1:1,0:10,8:0.0526:2,0:23:0:24:0:1:0:60:2:0.0526:0:1 -MT 13734 . T C 64 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00542;SOR=Inf;LSEQ=GGAAGCCTATTCGCAGGATT;RSEQ=CTCATTACTAACAACATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:33,30:0:2,0:24.6:1:29.9:1:1:0:60:62:1:0:0.3 0/1:25:4:2,2:10,11:0.16:2,2:24.5:1:32:1:1:1.10:60:8:0.1667:0:1.3 -MT 13759 . G A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10298;SOR=Inf;LSEQ=TTACTAACAACATTTCCCCC;RSEQ=CATCCCCCTTCCAAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:37,36:0:2,0:24.8:1:30.5:1:1:0:60:35.5:1:0:0.2 0/1:35:2:1,1:15,18:0.0571:2,2:14:0:30:0:1:1.19:60:4:0.0588:0:1.5 -MT 13789 . T C 54 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00793;SOR=Inf;LSEQ=TCCAAACAACAATCCCCCTC;RSEQ=ACCTAAAACTCACAGCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:35,39:0:2,0:25.8:1:28.6:1:1:0:59.8:17.5:1:0:0.2 0/1:33:4:2,2:13,16:0.1212:2,2:25.8:1:27.3:1:1:1.22:60:3:0.0968:0:1 -MT 13934 . C T 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=6e-05;SOR=Inf;LSEQ=CGGATTCTACCCTAGCATCA;RSEQ=ACACCGCACAATCCCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:25,25:0:2,0:24.3:1:31.8:1:1:0:60:49:1:0:0.1 0/1:35:10:5,5:12,13:0.2857:2,2:26.1:1:29.5:1:1:1.08:60:20:0.2857:0:1 -MT 14139 . A G 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00324;SOR=Inf;LSEQ=CTCATCCTAACCCTACTCCT;RSEQ=ATCACATAACCTATTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:29,31:0:2,0:27.6:1:29.7:1:1:0:60:120:1:0:0.1 0/1:30:5:3,2:14,11:0.1667:2,2:26.4:1:31:1:1:1.17:60:10:0.1667:0:1 -MT 14258 . G A 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00826;SOR=Inf;LSEQ=ACAAAGCCCCCGCACCAATA;RSEQ=GATCCTCCCGAATCAACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:33,26:0:2,0:24.9:1:31.4:1:1:0:59.3:58:1:0:0.2 0/1:27:4:2,2:14,9:0.1481:2,2:30.5:1:31.3:1:1:1.52962:60:8:0.16:0:1 -MT 14306 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54362;SOR=0;LSEQ=CTCCTTCATAAATTATTCAG;RSEQ=TTCCTACACTATTAAAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:34,36:0.0278:2,2:7:0:31:1:1:1.06:60:4:0.0286:0:1.5 0/0:38:0:0,0:20,18:0:2,0:22.6:1:31.6:1:1:0:60:76:1:0:0.1 -MT 14362 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29849;SOR=3.56924;LSEQ=CCATCATACTCTTTCACCCA;RSEQ=AGCACCAATCCTACCTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:0,1:51,48:0.01:2,0:1:0:24:0:0.49:0:60:2:0.0101:0:1 0/1:57:2:1,1:27,28:0.0351:2,2:27.5:1:27:1:1:1.04:60:4:0.0351:0:1 -MT 14470 . T C 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00437;SOR=Inf;LSEQ=ATAGCCATCGCTGTAGTATA;RSEQ=CCAAAGACAACCATCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:25,37:0:2,0:30.2:1:30.8:1:1:0:60:124:1:0:0.1 0/1:23:4:2,2:7,12:0.1739:2,2:26.3:1:32.5:1:1:1.67:60:8:0.1739:0:1 -MT 14560 . G A 59 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0123;SOR=Inf;LSEQ=TTCAGAATAATAACACACCC;RSEQ=ACCACACCGCTAACAATCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:21,28:0:2,0:28.1:1:31.4:1:1:0:60:98:1:0:0.1 0/1:26:4:2,2:13,9:0.1538:2,2:37.5:1:29.8:1:1:1.42378:60:8:0.1538:0:1.8 -MT 14583 . C A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52918;SOR=0;LSEQ=CACACCGCTAACAATCAATA;RSEQ=TAAACCCCCATAAATAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:20,23:0.0444:2,2:9:1:32:1:1:1.15:50:4:0.0444:0:1.5 0/0:26:0:0,0:13,12:0:2,0:23:1:31.1:1:1:0:58.8:50:0.9615:0:0.3 -MT 14691 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14962;SOR=Inf;LSEQ=CATTATTCTCGCACGGACTA;RSEQ=AACCACGACCAATGATATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:22,20:0:2,0:25:1:32.2:1:1:0:59.5:84:1:0:0.3 0/1:27:2:1,1:11,14:0.0741:2,2:27.5:1:28.5:1:1:1.26:51:4:0.08:0:1.5 -MT 14766 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01204;SOR=4.42215;LSEQ=AATGACCCCAATACGCAAAA;RSEQ=TAACCCCCTAATAAAATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:30:18,12:13,7:0.6:2,2:24.1:1:30.5:1:0.77368:1.23283:59.7:29:0.5918:0:1.3 1/1:31:27:12,15:1,3:0.871:2,2:22.3:1:29.7:1:0.62072:2.34:60:26:0.8667:0:1.6 -MT 14769 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14246;SOR=Inf;LSEQ=GACCCCAATACGCAAAACTA;RSEQ=CCCCCTAATAAAATTAATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:29,18:0:2,0:23.9:1:28.2:1:1:0:59.8:10.75:1:0:0.9 0/1:29:2:1,1:12,15:0.069:2,2:17:0:32.5:1:1:1.24:60:4:0.069:0:2.5 -MT 14798 . T C 84 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.73766;LSEQ=TAAAATTAATTAACCACTCA;RSEQ=TCATCGACCTCCCCACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:6:2,4:27,23:0.1071:2,2:24.7:1:32.5:1:0.41406:2.31289:60:12:0.1111:0:1.8 0/1:37:3:2,1:15,19:0.0811:2,2:33.7:1:32:1:0.5843:2.47:60:6:0.0833:0:1.7 -MT 14803 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56127;SOR=3.09806;LSEQ=TTAATTAACCACTCATTCAT;RSEQ=GACCTCCCCACCCCATCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:30,28:0.0169:2,0:1:0:25:0:0.49153:0:60:2:0.0169:0:1 0/1:39:2:1,1:18,19:0.0513:2,2:29.5:1:30.5:1:1:1.05:60:4:0.0513:0:2.5 -MT 14887 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51928;SOR=0;LSEQ=CTGATCCTCCAAATCACCAC;RSEQ=GGACTATTCCTAGCCATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:21,22:0.0435:2,2:37.5:1:31:1:1:1.05:60:4:0.0444:0:2.5 0/0:29:0:0,0:13,16:0:2,0:22.3:1:30.4:1:1:0:59.5:58:1:0:0.2 -MT 14905 . G A 127 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.07795;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:21:11,10:9,14:0.4773:2,2:27.4:1:29.1:1:0.54519:1.69:60:42:0.4773:0:1.3 0/1:31:2:1,1:13,16:0.0645:2,2:2.5:1:24.5:1:1:1.22:60:4:0.0645:0:1 -MT 15324 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12367;SOR=Inf;LSEQ=CTTCATTATTGCAGCCCTAG;RSEQ=AACACTCCACCTCCTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:23,24:0:2,0:21.6:1:31.8:1:1:0:60:22.5:1:0:1.1 0/1:26:2:1,1:11,13:0.0769:2,2:29:1:26.5:1:1:1.17:60:4:0.0769:0:2 -MT 15326 . A G 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCATTATTGCAGCCCTAGCA;RSEQ=CACTCCACCTCCTATTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:22,25:0,0:1:0,2:21.4:1:31.3:1:1:0:60:14.667:1:0:1.1 1/1:27:27:11,16:0,0:1:0,2:30.2:1:31.6:1:1:0:60:26:1:0:1.1 -MT 15355 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18526;SOR=Inf;LSEQ=CTCCTATTCTTGCACGAAAC;RSEQ=GGATCAAACAACCCCCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:19,24:0:2,0:23.9:1:30.5:1:1:0:60:86:1:0:0.7 0/1:33:2:1,1:13,18:0.0606:2,2:10:0:32.5:1:1:1.37:60:4:0.0606:0:1.5 -MT 15452 . C A 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48948;SOR=0.5377;LSEQ=CCCTCGGCTTACTTCTCTTC;RSEQ=TTCTCTCCTTAATGACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:22:11,11:9,5:0.6111:2,2:19.4:1:30.9:1:0.50067:1.77077:60:44:0.6111:0:1.1 0/1:11:5:3,2:2,4:0.4545:2,2:34.6:1:28.4:1:0.5671:2.70:60:4:0.4:0:1.2 -MT 15607 . A G 121 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=0.0527;LSEQ=CTCCGATCCGTCCCTAACAA;RSEQ=CTAGGAGGCGTCCTTGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:15:6,9:6,9:0.5:2,2:22:1:31.1:1:1:1:60:30:0.5357:0:1.1 0/1:21:1:0,1:11,9:0.0476:2,0:26:0:34:0:0.47619:0:60:2:0.0476:0:1 -MT 15627 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52087;SOR=0;LSEQ=ACTAGGAGGCGTCCTTGCCC;RSEQ=ATTACTATCCATCCTCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:0.0556:2,2:35.5:1:31:1:1:1.26:60:4:0.0571:0:1 0/0:22:0:0,0:11,11:0:2,0:25:1:29.4:1:1:0:60:44:1:0:0.1 -MT 15698 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1918;SOR=Inf;LSEQ=AACAACAAAGCATAATATTT;RSEQ=GCCCACTAAGCCAATCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:0:2,0:24.8:1:29.8:1:1:0:60:33:1:0:0.1 0/1:27:2:1,1:10,15:0.0741:2,2:30.5:1:29:1:1:1.48:60:4:0.0741:0:1.5 -MT 15884 . G C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16173;SOR=Inf;LSEQ=AAAACAAAATACTCAAATGG;RSEQ=CCTGTCCTTGTAGTATAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:10,16:0:2,0:23.5:1:31.3:1:1:0:60:52:1:0:0.1 0/1:18:2:1,1:6,10:0.1111:2,2:25.5:1:32:1:1:1.62:60:4:0.1111:0:1.5 -MT 15928 . G A 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49357;SOR=0.55327;LSEQ=TACACCAGTCTTGTAAACCG;RSEQ=AGATGAAAACCTTTTTCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:8,10:0.3333:2,2:26.8:1:30.8:1:1:1:60:18:0.3333:0:1.1 0/1:14:3:1,2:6,5:0.2143:2,2:28:1:29.7:1:1:2.2554:60:6:0.2143:0:1 -MT 16019 . C T 71 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14485;SOR=0;LSEQ=AGATTCTAATTTAAACTATT;RSEQ=TCTGTTCTTTCATGGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:2,3:16,13:0.1471:2,2:28:1:31:1:0.64809:1.813:60:10:0.1563:0:1.8 0/0:22:0:0,0:13,9:0:2,0:21.4:1:30.6:1:1:0:60:21:1:0:0.3 -MT 16069 . C T 74 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22689;SOR=0.23018;LSEQ=GTACCACCCAAGTATTGACT;RSEQ=ACCCATCAACAACCGCTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:6:2,4:13,14:0.1818:2,2:23.3:1:28.8:1:0.66478:1.82342:60:12:0.1818:0:1.8 0/1:21:1:0,1:9,11:0.0476:2,0:21:0:29:0:1:0:60:2:0.0476:0:1 -MT 16086 . T C 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00311;SOR=Inf;LSEQ=ACTCACCCATCAACAACCGC;RSEQ=ATGTATTTCGTACATTACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:0:2,0:22.9:1:29.4:1:1:0:60:66:1:0:0.5 0/1:23:6:2,4:8,9:0.2609:2,2:26.7:1:31.2:1:0.66002:1.73456:60:12:0.2609:0:1.2 -MT 16110 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49675;SOR=0;LSEQ=TATTTCGTACATTACTGCCA;RSEQ=CCACCATGAATATTGTACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:0.0645:2,2:6:0:32.5:1:1:1.22249:60:4:0.0645:0:1.5 0/0:25:0:0,0:13,12:0:2,0:19.5:1:31.1:1:1:0:60:11.5:1:0:0.9 -MT 16126 . T C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0027;SOR=0.15883;LSEQ=GCCAGCCACCATGAATATTG;RSEQ=ACGGTACCATAAATACTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:8,8:10,6:0.5:2,2:18.8:1:32.7:1:0.72239:1.63996:60:32:0.5:0:2.9 0/1:30:4:2,2:13,13:0.1333:2,2:15.5:1:33:1:1:1:60:8:0.1333:0:1.5 -MT 16129 . G C 69 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01438;SOR=Inf;LSEQ=AGCCACCATGAATATTGTAC;RSEQ=GTACCATAAATACTTGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:21,15:0:2,0:19.8:1:30.6:1:1:0:60:72:1:0:1.6 0/1:29:5:3,2:12,12:0.1724:2,2:31.6:1:29.8:1:1:1.48:60:10:0.1724:0:1.6 -MT 16163 . A G 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGACCACCTGTAGTACATA;RSEQ=AAACCCAATCCACATCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:21:12,9:17,9:0.4468:2,2:29:1:32.1:1:0.76341:1.40609:60:42:0.4468:0:3.4 0/0:43:0:0,0:24,19:0:2,0:26.5:1:30.3:1:1:0:60:86:1:0:1.1 -MT 16179 . CA C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.09047;SOR=Inf;LSEQ=CATAAAAACCCAATCCACAT;RSEQ=AAACCCCCTCCCCATGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:33,21:0:2,0:24.4:1:30.5:1:1:0:60:108:1:0:1.7 0/1:45:3:1,2:20,22:0.0667:2,2:25:1:29.7:1:1:1.79505:60:6:0.0714:0:3.7 -MT 16186 . C T 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCAATCCACATCAAAACC;RSEQ=CCTCCCCATGCTTACAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:25:14,11:21,11:0.4386:2,2:24.4:1:29.9:1:0.5851:1.48921:60:24:0.4286:0:3.2 0/0:40:0:0,0:19,20:0:2,0:25.6:1:30.4:1:1:0:60:38:1:0:1.4 -MT 16189 . T C 143 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19993;SOR=0.54074;LSEQ=CAATCCACATCAAAACCCCC;RSEQ=CCCCATGCTTACAAGCAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:24:13,11:22,12:0.4138:2,2:25.2:1:31.2:1:0.58632:1.53936:60:48:0.4138:0:3.2 0/1:40:11:5,6:14,14:0.275:2,2:27.6:1:27.1:1:1:1.1944:60:4.5:0.25:0:2.8 -MT 16190 . C A 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51446;SOR=0;LSEQ=AATCCACATCAAAACCCCCT;RSEQ=CCCATGCTTACAAGCAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:36,23:0.0328:2,2:32:0:28:1:1:1.55335:60:4:0.0328:0:1.5 0/0:41:0:0,0:19,22:0:2,0:24.6:1:30.7:1:1:0:60:40:1:0:1.5 -MT 16192 . C T 104 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TCCACATCAAAACCCCCTCC;RSEQ=CATGCTTACAAGCAAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:37,24:0:2,0:22.8:1:31.6:1:1:0:60:122:1:0:1.5 0/1:41:11:6,5:13,17:0.2683:2,2:15.9:1:30.3:1:0.7254:1.55:60:22:0.275:0:1.7 -MT 16223 . C T 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAAGTACAGCAATCAACC;RSEQ=TCAACTATCACACATCAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:34,31:0:2,0:25.4:1:31.2:1:1:0:60:130:1:0:1.2 0/1:27:13:6,7:7,7:0.4815:2,2:24:1:27.8:1:1:1.16002:60:12:0.48:0:3.2 -MT 16224 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07661;SOR=Inf;LSEQ=GCAAGTACAGCAATCAACCC;RSEQ=CAACTATCACACATCAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:34,30:0:2,0:25.9:1:30:1:1:0:60:128:1:0:1.2 0/1:25:2:0,2:11,12:0.08:2,0:19:1:33:0:0.48667:0:60:4:0.0833:0:1 -MT 16234 . C T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.55139;SOR=0;LSEQ=CAATCAACCCTCAACTATCA;RSEQ=ACATCAACTGCAACTCCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:3:1,2:36,34:0.0411:2,2:35.7:1:27.7:1:0.61451:2.09666:60:6:0.0411:0:1 0/0:32:0:0,0:15,16:0:2,0:18.4:1:30.3:1:1:0:60:14.5:0.9667:0:1.5 -MT 16248 . C T 80 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=CTATCACACATCAACTGCAA;RSEQ=TCCAAAGCCACCCCTCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:34,39:0:2,0:24.7:1:31.8:1:1:0:60:72:1:0:1.2 0/1:30:6:2,4:11,13:0.2:2,2:22.3:1:31:1:0.67247:1.66358:60:12:0.2:0:3.2 -MT 16263 . T C 163 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCAACTCCAAAGCCACCCC;RSEQ=CACCCACTAGGATACCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:37:17,20:15,18:0.5286:2,2:27.7:1:31.3:1:1:1.02:60:74:0.5286:0:1.6 0/0:30:0:0,0:15,15:0:2,0:22.3:1:30.2:1:1:0:60:60:1:0:1.5 -MT 16264 . C T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08614;SOR=Inf;LSEQ=GCAACTCCAAAGCCACCCCT;RSEQ=ACCCACTAGGATACCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:32,39:0:2,0:26.3:1:32:1:1:0:60:142:1:0:1.2 0/1:30:2:1,1:14,14:0.0667:2,2:32.5:1:26.5:1:1:1:60:4:0.0667:0:4 -MT 16270 . C T 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07435;SOR=Inf;LSEQ=CCAAAGCCACCCCTCACCCA;RSEQ=TAGGATACCAACAAACCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:32,36:0:2,0:26.4:1:32.4:1:1:0:60:136:1:0:1.3 0/1:26:2:1,1:15,9:0.0769:2,2:38.5:1:29.5:1:1:1.63293:60:4:0.0769:0:4 -MT 16278 . C T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07491;SOR=Inf;LSEQ=ACCCCTCACCCACTAGGATA;RSEQ=CAACAAACCTACCCACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:29,36:0:2,0:25.3:1:31.8:1:1:0:60:130:1:0:1.2 0/1:25:2:1,1:14,9:0.08:2,2:46.5:1:28.5:1:1:1.52748:60:4:0.08:0:4 -MT 16292 . C T 101 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGATACCAACAAACCTACC;RSEQ=ACCCTTAACAGTACATAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:26,34:0:2,0:23.5:1:31.8:1:1:0:60:120:1:0:1.4 0/1:28:11:6,5:11,6:0.3929:2,2:24:1:29.3:1:0.70114:1.50442:60:22:0.3929:0:1.7 -MT 16294 . C T 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GATACCAACAAACCTACCCA;RSEQ=CCTTAACAGTACATAGTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:26:13,13:12,21:0.4407:2,2:21.8:1:30.1:1:0.4264:1.73:60:25:0.431:0:1 0/0:29:0:0,0:17,12:0:2,0:23.9:1:30.8:1:1:0:60:58:1:0:1.2 -MT 16311 . T C 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00157;SOR=Inf;LSEQ=CCACCCTTAACAGTACATAG;RSEQ=ACATAAAGCCATTTACCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:23,30:0:2,0:22.8:1:29.3:1:1:0:60:106:1:0:1.4 0/1:30:6:4,2:12,12:0.2:2,2:19.8:1:32.7:1:0.6567:1.96:60:12:0.2069:0:2 -MT 16316 . A G 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTAACAGTACATAGTACAT;RSEQ=AAGCCATTTACCGTACATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:29:12,17:10,13:0.5577:2,2:20.2:1:31.1:1:1:1.08794:60:28:0.549:0:1.9 0/0:31:0:0,0:16,15:0:2,0:21.5:1:27.4:1:1:0:60:14.5:1:0:1.1 -MT 16325 . T C 85 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=Inf;LSEQ=ACATAGTACATAAAGCCATT;RSEQ=ACCGTACATAGCACATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:24,25:0:2,0:22.8:1:29.2:1:1:0:60:48:1:0:1.3 0/1:30:7:3,4:13,10:0.2333:2,2:27.3:1:30.4:1:0.67458:1.70145:60:14:0.2333:0:1.9 -MT 16343 . A G 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06869;SOR=Inf;LSEQ=TTTACCGTACATAGCACATT;RSEQ=CAGTCAAATCCCTTCTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,23:0:2,0:24.3:1:28.9:1:1:0:60:48:1:0:1 0/1:35:3:1,2:18,14:0.0857:2,2:20.7:1:26.7:1:0.58197:2.50361:60:2:0.0588:0:1.7 -MT 16362 . T C 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00829;SOR=Inf;LSEQ=TACAGTCAAATCCCTTCTCG;RSEQ=CCCCATGGATGACCCCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:27,25:0:2,0:25.1:1:29.3:1:1:0:60:16.333:1:0:0.8 0/1:35:5:3,2:15,15:0.1429:2,2:11:1:32:1:1:1.48:60:10:0.1471:0:1.2 -MT 16365 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51097;SOR=0;LSEQ=AGTCAAATCCCTTCTCGTCC;RSEQ=CATGGATGACCCCCCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:27,23:0.0385:2,2:14.5:1:30.5:1:1:1.17028:60:4:0.0385:0:3 0/0:36:0:0,0:18,18:0:2,0:21.1:1:28.6:1:1:0:58.9:8:1:0:0.6 -MT 16390 . G A 133 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00012;SOR=0.05048;LSEQ=GATGACCCCCCTCAGATAGG;RSEQ=GTCCCTTGACCACCATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:10,12:20,18:0.3667:2,2:20.4:1:30:1:0.78917:1.32692:60:21:0.3621:0:1.5 0/1:36:1:0,1:19,16:0.0278:2,0:13:0:33:0:0.47222:0:60:2:0.0286:0:2 -MT 16456 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07279;SOR=Inf;LSEQ=GTGCTACTCTCCTCGCTCCG;RSEQ=GCCCATAACACTTGGGGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:33,36:0:2,0:21.9:1:30.8:1:1:0:59.9:22:1:0:0.6 0/1:26:2:2,0:10,14:0.0769:2,0:11.5:1:28.5:1:0.20308:0:60:4:0.0769:0:1.5 -MT 16519 . T C 175 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0051;SOR=0.05973;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:46:24,22:0,1:0.9787:0,2:25.2:1:31.8:1:0.48936:0:58.2:92:0.9787:0:1.2 1/0:18:13:7,6:3,2:0.7222:2,2:24.2:1:31.5:1:1:1.26799:56.7:26:0.7222:0:1.5 -MT 16524 . A G 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00514;SOR=Inf;LSEQ=GTTCCTACTTCAGGGTCATA;RSEQ=AGCCTAAATAGCCCACACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:23,22:0:2,0:25.4:1:30.2:1:1:0:58.2:90:1:0:1.1 0/1:18:4:2,2:8,6:0.2222:2,2:36.5:1:32.5:1:1:1.31198:53.3:8:0.2222:0:2 -X 450736 . C CTG 62 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCCAGCAGCAGGACGCTGA;RSEQ=TGCGTGAGTGATGCAGCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:28.5:1:31.4:1:1:0:60:8:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 450894 . TAA T 88 MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAATATGATTTAGGCAATGT;RSEQ=AAAAAAAAAACAAAACCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:1:0,2:28.3:1:29.6:1:1:0:59.4:16:1:0.25:0.4 1/0:4:3:3,0:0,0:0.75:0,0:10.7:1:30.2:1:1:0:60:6:0.75:0.25:0 -X 451056 . C T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55527;SOR=Inf;LSEQ=GTGGGTGTCTCCACGCCTTC;RSEQ=GTGCAAACTGTGTGTATTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:54,28:0:2,0:25.1:1:30.7:1:1:0:60:164:1:0:0.1 0/1:186:3:1,2:121,62:0.0161:2,2:8.3:1:26:1:0.27256:3.87256:60:6:0.0164:0:1 -X 451096 . C T 184 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GACAGATGAATGGTTTGTCT;RSEQ=TGGGATGATACTTTTCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:95,67:0:2,0:24.4:1:31.5:1:1:0:60:80:1:0:0.2 0/1:334:69:39,30:142,123:0.2066:2,2:25.3:1:30.2:1:0.68617:1.13:60:138:0.2104:0:1.3 -X 451139 . T C 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13413;SOR=0;LSEQ=TGCAGCCTGCAGATAACATC;RSEQ=AACGAGGGGAGAAGGATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:88,95:0.0108:2,2:39:0:31.5:1:1:1.08:60:4:0.011:0:1 0/0:321:0:0,0:141,179:0:2,0:29.3:1:28.6:1:1:0:59.9:28.091:0.9968:0:0.9 -X 451142 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.68303;LSEQ=AGCCTGCAGATAACATCTAA;RSEQ=GAGGGGAGAAGGATTATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:27:14,13:72,82:0.1492:2,2:27:1:30.2:1:0.67925:1.23:60:26:0.1512:0:1.3 0/1:313:123:50,73:88,99:0.393:2,2:30.3:1:29.2:1:0.294:1.29668:60:23.6:0.4014:0:1.3 -X 451164 . G C 92 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01424;SOR=Inf;LSEQ=AGGGGAGAAGGATTATGTGA;RSEQ=CAGTGGTGGCTGAGGTCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:65,87:0:2,0:26.3:1:31.3:1:1:0:59.6:18:1:0:0.7 0/1:241:9:4,5:92,139:0.0373:2,2:16.8:1:29.3:1:1:1.21:57.8:8:0.0352:0:2.8 -X 451175 . T A 47 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65319;SOR=2.47698;LSEQ=ATTATGTGAGCAGTGGTGGC;RSEQ=GAGGTCTCTCTCTCTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:1:0,1:49,75:0.0079:2,0:45:0:15:0:1:0:40:0:0:0:8 0/1:207:4:3,1:73,125:0.0193:2,2:6.3:1:23.5:1:0.15061:5.10:60:3:0.0168:0:2 -X 452780 . C T 32 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAAGGCAAGCACACAC;RSEQ=CACAGCCATGAGCCCTCACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:34:0:32:0:1:0:56:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 1314656 . T C 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6004;SOR=0.39896;LSEQ=CATATTGGCCAGGCTGGTCT;RSEQ=GAACTCGTGACCTCGTGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:0.4:0,0:31.5:1:30.5:1:1:0:58.5:8:0.4:0:1.5 0/1:5:1:1,0:4,0:0.2:0,0:3:0:30:0:1:0:60:2:0.25:0:1 -X 1314694 . G C 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCCTGCCTTGGTCTCC;RSEQ=CAAGTGCTGGGATGACAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:14,0:0.1176:1,0:16.5:1:25:1:1:0:57:4:0.1176:0:2 0/0:7:0:0,0:7,0:0:0,0:32.1:1:30.6:1:1:0:60:14:1:0:0.3 -X 1314764 . T G 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62822;SOR=1.3207;LSEQ=TTTCTTATAATCCACCATCA;RSEQ=AAGAGTGGGCATTGTATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:24:24,0:14,0:0.6316:1,1:18.7:1:32.8:1:1:0:60:48:0.6316:0:1.3 1/0:36:25:25,0:11,0:0.6944:0,1:19:1:31.5:1:1:0:60:24:0.6857:0:1 -X 1314857 . GG AT 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1438;LSEQ=TCACAGACATTGTGCAAGCA;RSEQ=TCCCTCCACCCACGGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:79:58,21:126,50:0.3062:2,2:24.1:1:30.5:1:0.88004:1.10:60:158:0.3123:0.0349:1 0/1:353:21:15,6:220,112:0.0595:2,2:26.3:1:29.9:1:0.81223:1.27:60:42:0.06:0.0085:1.1 -X 1314858 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0296;SOR=0;LSEQ=CACAGACATTGTGCAAGCAG;RSEQ=TCCCTCCACCCACGGGCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:4:2,2:126,51:0.0159:2,2:9.3:1:25:1:0.58169:2.45661:60:3:0.017:0:2 0/0:352:0:0,0:219,114:0:2,0:24.6:1:30.7:1:1:0:60:65.6:1:0:0.2 -X 1314931 . C T 138 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAGAAGGAGGAGAGACA;RSEQ=CATCAGAAGGATGGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:0:0,0:238,232:0:2,0:24.4:1:31.4:1:1:0:60:46:1:0:0.2 0/1:705:28:13,15:352,325:0.0397:2,2:26:1:28.9:1:0.57019:1.2493:60:27:0.0386:0:1.3 -X 1315104 . G C 152 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06184;SOR=0.51182;LSEQ=TTACATCTCATCCCTAACCA;RSEQ=TCTCCCTCATTTTTTGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:25:0,25:1,50:0.3289:1,1:24.4:1:32.8:1:1:0:60:50:0.3289:0:1.1 0/1:120:24:0,24:10,86:0.2:2,1:19.4:1:30.8:1:0.20875:0:60:11:0.188:0:1.1 -X 1315114 . T C 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.03709;SOR=Inf;LSEQ=TCCCTAACCAGTCTCCCTCA;RSEQ=TTTTTGGTGTTCGTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:0,73:0:1,0:21.8:1:30.5:1:1:0:60:146:1:0:0.3 0/1:96:6:0,6:2,88:0.0625:1,0:23.8:1:32.8:1:1:0:60:12:0.0645:0:1 -X 1315127 . G GT 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22197;SOR=4.28819;LSEQ=TCCCTCATTTTTTGGTGTTC;RSEQ=TTTTTTTTTCTTGGTTCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:0,58:0.0169:1,0:46:0:29:0:1:0:60:2:0.0172:0:0 0/1:72:5:0,5:2,64:0.0694:1,0:39.2:1:28.2:1:1:0:60:10:0.0704:0:0.6 -X 1317136 . GGAAGGCAGGACACCCTCCCTCCCACCTC G 31 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCCTCCCTCCCACCTCCCA;RSEQ=GAAGGCAGGACAGCCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:7:0:32:0:1:0:40:2:1:0:0 1/0:4:2:2,0:2,0:0.5:0,0:7.5:1:31.8:1:1:0:48.5:4:0.5:0.5:1 -X 1317177 . G C 51 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCACCTCGAAGGCAGGACA;RSEQ=CCTCCCTCCCACCTCCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:24.5:1:32.5:1:1:0:44.5:4:1:0:0.5 0/1:11:3:2,1:7,1:0.2727:2,2:10.7:1:32.7:1:0.49091:3.05504:48.7:6:0.3:0:1 -X 1317404 . T C 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17136;SOR=0.82497;LSEQ=AAGGCTATGGGACACTGCCG;RSEQ=GTAACAAGCATTACCCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:127:84,43:163,104:0.3207:2,2:25.3:1:31.2:1:0.37293:1.25:60:126:0.3223:0:1.1 0/1:735:206:119,87:311,218:0.2803:2,2:23.8:1:30.7:1:0.80315:1.04295:60:205:0.2824:0:1.2 -X 1317589 . AACATAC A 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00158;SOR=Inf;LSEQ=TTTCCTGTTTGGACTGGAGA;RSEQ=ACATACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:85,186:0:2,0:21.1:1:29.2:1:1:0:59.5:66.75:1:0:0.4 0/1:456:14:1,13:166,276:0.0307:2,1:26.7:1:27.6:1:0.02203:7.7971:57.9:28:0.0312:0.0044:1.1 -X 1317599 . T C 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGACTGGAGAAACATACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:31:16,15:38,105:0.1455:2,2:17.4:1:29.6:1:0.00962:2.93:59.6:9.333:0.1854:0:1.5 0/0:355:0:0,0:86,164:0:2,0:21.6:1:24.8:1:1:0:59.3:3.902:0.9343:0:0.4 -X 1317688 . G C 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29371;SOR=Inf;LSEQ=CTGTCCAGAGTTTTCCTTCC;RSEQ=GAGGGTTCACAGTCTCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:0,37:0:1,0:24.8:1:31.4:1:1:0:60:74:1:0:0.2 0/1:62:4:0,4:1,57:0.0645:1,0:25.8:1:30.3:1:1:0:60:8:0.0667:0:1 -X 1321079 . G C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04141;SOR=0.12512;LSEQ=ATTGGTTCTCTTTCTCTGGA;RSEQ=ACCCCTCAGAGACACAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:0.8462:0,0:23.7:1:32.6:1:1:0:60:22:0.8462:0:1 0/1:13:5:5,0:8,0:0.3846:0,0:29.6:1:32.2:1:1:0:60:10:0.4167:0:1 -X 1321215 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.55126;SOR=Inf;LSEQ=TGAAACAGCGAATCCCACAG;RSEQ=CCGCACCTGGGGGACGCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:75,12:0:2,0:25.1:1:31.7:1:1:0:60:86:1:0:0.1 0/1:171:2:2,0:140,29:0.0117:2,0:32.5:1:32:0:1:0:60:4:0.012:0:1 -X 1321222 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55341;SOR=Inf;LSEQ=GCGAATCCCACAGCCCGCAC;RSEQ=TGGGGGACGCTCAGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:86,16:0:2,0:24.1:1:30.4:1:1:0:60:50:1:0:0.1 0/1:207:3:2,1:165,39:0.0145:2,2:23.3:1:25.3:1:0.47674:2.1061:60:2:0.01:0:2.3 -X 1321243 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10108;SOR=0;LSEQ=TGGGGGACGCTCAGCCACCA;RSEQ=CGCCCTGAGTCGCGGCCGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:108,35:0.0138:2,2:24.5:1:30.5:1:0.43621:3.0565:60:4:0.0139:0:1 0/0:310:0:0,0:226,83:0:2,0:23.8:1:29.1:1:1:0:60:27.091:1:0:0.3 -X 1321433 . G A 62 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26418;SOR=3.65519;LSEQ=GAAGAAATAACGGAAGCGAC;RSEQ=TCCCTCCTCTCTGAGCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:1,0:65,162:0.0044:2,0:1:0:25:0:0.28947:0:60:2:0.0045:0:1 0/1:378:6:5,1:121,251:0.0159:2,2:8.5:1:24.3:1:0.01707:10.31:60:5:0.0135:0:1 -X 1321517 . G GT 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=CCTCCCCTTAATACCTTATG;RSEQ=GTCTCGGGGTTCACCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:1,63:0:1,0:21.2:1:30.6:1:1:0:60:20.333:1:0:0.1 0/1:63:12:0,12:3,48:0.1905:2,0:21.8:1:30.3:1:1:0:60:24:0.1967:0.0476:0.1 -X 1324241 . G T 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAGGTAAGGAGATGAAG;RSEQ=GGTACTGAAAAGTGTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:24.5:1:31.5:1:1:0:60:4:1:0:1.5 -X 1325301 . G T 110 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0.053;LSEQ=AAGGAAGTACTGAAAAGCAT;RSEQ=GTGAGCTGGCTTTACAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:12:10,2:167,91:0.0444:2,2:20:1:30.9:1:0.22848:2.72:60:24:0.0446:0:1.1 0/0:408:1:0,1:257,150:0.0025:2,0:1:0:25:0:0.3701:0:60:2:0.0025:0:1 -X 1325426 . C T 219 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCTCTGCGTCTAGGAGGCA;RSEQ=CCCGAAGTGTGACCTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:148:65,83:143,160:0.3282:2,2:25.8:1:30.4:1:0.54676:1.14091:60:296:0.3311:0:1.1 0/0:697:0:0,0:311,386:0:2,0:26.3:1:30.6:1:1:0:60:48.786:1:0:0.2 -X 1325519 . G T 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58284;SOR=0.38573;LSEQ=TTTAAAACGATGACCATTCA;RSEQ=CAACAAAACAAAAAAGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:15,125:0.0141:2,2:28.5:1:32:1:0.21337:8.10:60:4:0.0142:0:1 0/0:183:1:0,1:48,134:0.0055:2,0:31:0:31:0:1:0:60:2:0.0056:0:1 -X 1327620 . G A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1448;SOR=0;LSEQ=CTTTACACTTTTGTTCTCAA;RSEQ=CATTCCCAATCGCTGACGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:90,16:0.0185:2,2:41.5:1:31:1:0.29128:5.48736:60:4:0.0187:0:1 0/0:175:0:0,0:143,32:0:2,0:22:1:31.8:1:1:0:60:86.5:1:0:0.1 -X 1327635 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29504;SOR=Inf;LSEQ=CTCAAGCATTCCCAATCGCT;RSEQ=ACGGCTCAGAAGAGCGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:118,26:0:2,0:25.1:1:32:1:1:0:60:47:1:0:0 0/1:240:3:2,1:187,50:0.0125:2,2:12:1:23:1:0.51328:1.86425:60:2:0.0086:0:1 -X 1327655 . T A 110 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00086;SOR=Inf;LSEQ=GACGGCTCAGAAGAGCGATT;RSEQ=TGAGCCCCCTGGGCGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:161,51:0:2,0:23.3:1:30.2:1:1:0:60:105:1:0:0 0/1:346:16:10,6:232,98:0.0462:2,2:26.4:1:27.5:1:0.57792:1.41889:60:15:0.044:0:1.3 -X 1327837 . G A 88 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02384;SOR=Inf;LSEQ=CGCATGAAGTTCACGGTGAG;RSEQ=CAACTCTATTTTTTTATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:33,180:0:2,0:24.3:1:31.9:1:1:0:60:105.5:1:0:0.1 0/1:311:8:1,7:76,226:0.0257:2,2:21.5:1:29.6:1:0.68445:2.34893:60:16:0.026:0:1.3 -X 1327868 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51258;SOR=Inf;LSEQ=TTTTTATTTTTTTAAATTTA;RSEQ=TTTTCTTTTTGAGACAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:6,104:0:2,0:20.7:1:30.9:1:1:0:60:220:1:0:0 0/1:155:2:1,1:26,127:0.0129:2,2:26.5:1:30:1:0.31898:4.81:60:4:0.013:0:1 -X 1331145 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AATCAATCAATCAATAGATA;RSEQ=ACACACACACGCACACATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:0.6667:0,0:15.5:1:31.5:1:0.33333:0:60:4:0.6667:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 1331182 . C T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACAGTTCCTAGTTCTGGC;RSEQ=ACCGAAAGCTCATATAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:39:1:31.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 1331279 . A G 73 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54118;SOR=0.62768;LSEQ=TGTTTTGTCCCAGCTACTTG;RSEQ=GAAGCTGAGGCAGGAGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:7:7,0:24,0:0.2258:1,0:28.6:1:26.3:1:1:0:58.6:2.5:0.1786:0:2 0/1:39:6:6,0:32,1:0.1538:1,0:24.5:1:23:1:1:0:52.8:1:0.0909:0:2.3 -X 1331309 . C CAG 95 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02824;SOR=0.21774;LSEQ=GCAGGAGAATTGCTTGAACC;RSEQ=GGAAAAAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:9:9,0:36,0:0.1915:1,0:25.7:1:30.2:1:1:0:57.8:18:0.2045:0:0.6 0/1:62:3:3,0:58,1:0.0484:1,0:19:1:29.7:1:1:0:50.7:6:0.0517:0:0.3 -X 1331332 . G A 120 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.88166;SOR=0.93761;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAGAAGAAAGAAACCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:29:29,0:67,4:0.2685:2,1:12.1:1:26:1:0.32001:0:51.8:3.143:0.3284:0:2.2 0/1:125:32:32,0:76,4:0.256:2,1:10.7:1:24.1:1:0.57669:0:49.5:2.556:0.2911:0:2.1 -X 1331495 . G C 245 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=253.11094;LSEQ=CAGCCTCCCAGCAGAAAGAC;RSEQ=GCAGCTCCCCACAGCAGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:1:0,1:218,253:0.0021:2,0:36:0:28:0:1:0:60:2:0.0021:0:1 0/1:937:326:157,169:271,336:0.3479:2,2:25.7:1:29.4:1:0.33475:1.15:60:107.667:0.3496:0:1.2 -X 1331616 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49851;SOR=Inf;LSEQ=GCAGAGGTCACCATCGATTT;RSEQ=AAAAAGTCAGAAAGGAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:4,93:0:1,0:24.9:1:28.4:1:1:0:60:96:1:0:0.1 0/1:106:2:1,1:6,98:0.0189:2,2:25:1:27.5:1:0.1283:15.20:60:4:0.0189:0:1 -X 3085317 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1752;LSEQ=GACCTCCCGTGGACTTTTCA;RSEQ=GCAGCCCCCACGGTGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:5,1:22,1:0.2069:1,2:25.3:1:30.5:1:0.37685:4.10691:60:12:0.2069:0:1 0/1:17:4:4,0:13,0:0.2353:1,0:28:1:31.5:1:1:0:60:8:0.2353:0:1 -X 3085398 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49975;SOR=Inf;LSEQ=TCAGTGCAAGGGCTGGGGAA;RSEQ=GAGGGCTATTATTTGCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:87,35:0:2,0:23.7:1:31.9:1:1:0:60:121:1:0:0.2 0/1:137:2:1,1:87,48:0.0146:2,2:14:1:30:1:1:1.80409:60:4:0.0147:0:2 -X 3085419 . G T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.23616;SOR=0;LSEQ=GAGGGCTATTATTTGCACAT;RSEQ=GGGAGGCATGAGCATCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:103,60:0.0121:2,2:17:0:32:0:1:1.7107:60:4:0.0123:0:2 0/0:174:0:0,0:97,77:0:2,0:24.4:1:30.7:1:1:0:60:86:1:0:0.3 -X 3085464 . C T 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21276;SOR=0.74332;LSEQ=GTTTCGCTGCAGAGAATCTA;RSEQ=ATGTACCAGAGATGAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:61:28,33:71,76:0.2933:2,2:28.5:1:29:1:0.76298:1.10052:60:29.5:0.2878:0:1.2 0/1:191:45:21,24:70,76:0.2356:2,2:30.9:1:28.1:1:1:1.05237:60:44:0.2328:0:1.2 -X 3573359 . A C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50885;SOR=Inf;LSEQ=GAGCCCCGTGGTGCTGGAGA;RSEQ=GCGCCCCCGGTTGCGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:11,32:0:2,0:24.5:1:31.3:1:1:0:60:86:1:0:0.1 0/1:60:2:1,1:19,39:0.0333:2,2:37:1:29.5:1:1:2.03:60:4:0.0339:0:1 -X 5699290 . G C 197 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATACTCTCTCCTCTCCTGAA;RSEQ=AGAATGAATGGCCAGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:75:75:61,14:0,0:1:0,2:19.8:1:31.7:1:1:0:60:150:1:0:1.1 1/0:61:31:24,7:25,5:0.5082:2,2:24:1:30.8:1:0.74904:1.44935:60:62:0.5082:0:1.1 -X 5699307 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61414;SOR=0.47326;LSEQ=GAAGAGAATGAATGGCCAGG;RSEQ=ATCTTCAGGAAGGGGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:59,23:0.0238:2,2:24.5:1:28.5:1:0.49225:2.53241:60:4:0.0238:0:1.5 0/1:88:1:0,1:64,23:0.0114:2,0:1:0:23:0:0.27273:0:60:2:0.0115:0:1 -X 5699379 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07872;SOR=0;LSEQ=GCGTCTACAGCAAGCAGCAT;RSEQ=AAGGTGGATTCTCACGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:1,2:97,84:0.0163:2,2:28.3:1:28.7:1:0.5998:2.29932:60:6:0.0164:0:2 0/0:244:0:0,0:125,119:0:2,0:26.5:1:30.9:1:1:0:60:80.333:1:0:0.6 -X 5699394 . C T 233 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCATGAAGGTGGATTCTCA;RSEQ=GCATTTTAACCCAAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:199:102,97:0,0:1:0,2:25:1:30.6:1:1:0:60:198:1:0:1.2 1/0:253:147:79,68:52,54:0.581:2,2:24.3:1:30:1:0.52405:1.21:60:146:0.5794:0:1.1 -X 5699496 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23775;SOR=Inf;LSEQ=CAAGGCAACACAGCCCTTGG;RSEQ=CCGCCTGCTTGGCTCTAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:24,68:0:2,0:25.2:1:31.8:1:1:0:60:91:0.9891:0:0.1 0/1:89:2:1,1:24,63:0.0225:2,2:35.5:1:28:1:0.48519:2.59:60:4:0.0227:0:1 -X 5699512 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49673;SOR=0;LSEQ=TTGGGCCGCCTGCTTGGCTC;RSEQ=AATTACAACCTTGATGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:12,56:0.0286:2,2:13:1:30.5:1:0.33913:4.52:60:4:0.0286:0:1 0/0:66:0:0,0:13,53:0:2,0:23.8:1:28.6:1:1:0:60:132:1:0:0.2 -X 8703231 . T C 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.17462;SOR=0.42297;LSEQ=TTTTTTGTTTTGTTTTGTTT;RSEQ=CATTCTGCCCATGTATGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:26:26,0:10,0:0.7222:0,1:22.8:1:31.1:1:1:0:60:12:0.7059:0:1.1 1/0:25:13:13,0:12,0:0.52:0,1:23.8:1:31.8:1:1:0:60:26:0.52:0:1.2 -X 8703411 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25734;LSEQ=GATAAAGGGGTAGGACCCTC;RSEQ=GGTGCAGCTAGTAAGACGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:356:257:117,140:45,54:0.7219:2,2:24.3:1:30.5:1:1:1.00:59.8:127.5:0.7203:0:1.1 0/1:325:130:61,69:96,99:0.4:2,2:25.1:1:30.1:1:0.73429:1.09656:60:64:0.4013:0:1.1 -X 8703727 . C CT 32 v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTGGTTTTTCTTTTCTTT;RSEQ=TTTTTTTTTTTCCTGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,3:0.2857:0,0:32:1:32:0:1:0:60:4:0.3333:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 11316961 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=0;LSEQ=ATGCAGCCCCAGCCACCTGT;RSEQ=CACCCCATGCAGCCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:31,40:0.0274:2,2:28.5:1:28:1:1:1.29:60:4:0.0282:0:2 0/0:112:0:0,0:56,56:0:2,0:24.3:1:30.9:1:1:0:59.7:27:1:0:0.1 -X 11316968 . A C 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14726;SOR=0;LSEQ=CCCAGCCACCTGTGCACCCC;RSEQ=TGCAGCCCCTGCCGCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:28,39:0.029:2,2:28.5:1:26.5:1:1:1.39:60:4:0.0308:0:2 0/0:110:0:0,0:52,58:0:2,0:23.2:1:28.7:1:1:0:59.9:35.667:1:0:0.1 -X 11503157 . C CA 31 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAAACAAACAACAACAA;RSEQ=AAAAAAAAAACATATCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:0:31.5:1:1:0:60:4:1:0:0 -X 13078706 . TA T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.27069;SOR=Inf;LSEQ=CTTAAGAATCTTCTAGTACT;RSEQ=AAAAAAGTAGGCCATTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:87,40:0:2,0:22.7:1:28.3:1:1:0:60:126:1:0:0.2 0/1:181:3:2,1:117,61:0.0166:2,2:15.3:1:28.2:1:1:1.04:60:6:0.0168:0.011:0.7 -X 13078775 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.74663;LSEQ=TGGAGAAGTAGAGATGATGA;RSEQ=AAGTGAAAAAGGCTTTACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:70:35,35:84,97:0.2789:2,2:30.6:1:29.9:1:0.67298:1.15:60:69:0.2782:0:1.1 1/0:289:149:76,73:70,70:0.5156:2,2:26.9:1:29.5:1:0.90652:1.04:60:148:0.5193:0:1.1 -X 14852765 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.1556;LSEQ=TACAGAACTAGGTCCCTTTG;RSEQ=TGTTTTAGGAGTTTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:193:163:101,62:21,9:0.8446:2,2:28.7:1:32:1:0.53706:1.42977:47.3:53.333:0.8421:0:1.8 0/1:256:117:66,51:84,54:0.457:2,2:30.3:1:31.5:1:0.52372:1.20114:48.9:57.5:0.4545:0:1.7 -X 14852812 . T G 244 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01567;LSEQ=TGAAGGATTCTTGTCCTTTT;RSEQ=ATCTTGGTGTTGATGATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:227:226:111,115:0,0:0.9956:0,2:25.3:1:31.3:1:1:0:44.6:74.333:0.9955:0:1.6 1/0:285:222:100,122:27,36:0.7789:2,2:23.2:1:31.2:1:0.77599:1.09:44:444:0.7789:0:1.4 -X 14852826 . T A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25143;SOR=Inf;LSEQ=CCTTTTTATCTTGGTGTTGA;RSEQ=GATGGTTTTGAGTCTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:99,123:0:2,0:23.6:1:29.6:1:1:0:45.9:36:1:0:1.3 0/1:252:3:2,1:103,146:0.0119:2,2:13.7:1:26:1:0.57247:2.82:53.3:6:0.0122:0:1.7 -X 14852912 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.49765;SOR=0;LSEQ=AGATTTCTTCACTGGTGCTT;RSEQ=TTCTTCAGTTTCCTCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:23,70:0.0211:2,2:14.5:1:30.5:1:0.44345:3.00:60:4:0.0211:0:1 0/0:90:0:0,0:28,62:0:2,0:21.1:1:30.2:1:1:0:60:44:1:0:0.3 -X 14852936 . A G 136 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00837;SOR=3.1147;LSEQ=TTCAGTTTCCTCATCATCAA;RSEQ=ATCATCATCATCATCATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:11:3,8:31,42:0.1294:2,2:19.3:1:32.2:1:0.51255:1.95338:60:22:0.131:0:1.1 0/1:66:21:9,12:18,26:0.3182:2,2:18.4:1:31.1:1:1:1.08:60:42:0.3231:0:1.1 -X 14853076 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23172;SOR=0;LSEQ=CCTCTTCATCTTCTGACTCT;RSEQ=CATCTTCCTCCACAGCTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:97,63:0.0123:2,2:41:0:30.5:1:1:1.53542:46:4:0.0126:0:1.5 0/0:174:0:0,0:104,70:0:2,0:25.1:1:32.1:1:1:0:57.6:348:1:0:0.2 -X 14853120 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4987;SOR=0;LSEQ=TGCTGTCCACTAATATGCAC;RSEQ=GGCCCTGAATCACACTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:96,94:0.0104:2,2:37:1:30:1:1:1.02117:60:4:0.0105:0:1 0/0:190:0:0,0:102,88:0:2,0:26.7:1:30.3:1:1:0:58.4:189:1:0:0.1 -X 14853439 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16279;SOR=Inf;LSEQ=TGTCCATGTCCATCGAATCT;RSEQ=CCATCAGGTGGCTACATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:20,31:0:2,0:21.3:1:29.5:1:1:0:60:16:1:0:0.1 0/1:35:2:1,1:13,20:0.0571:2,2:7:1:30:1:1:1.52:60:4:0.0571:0:1 -X 15172106 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50301;SOR=Inf;LSEQ=TGTCTGGTATCCTCATCTGC;RSEQ=ATAAAACATGCAGAGCTAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:93,31:0:2,0:25.7:1:31.2:1:1:0:60:61:1:0:0.3 0/1:151:2:1,1:93,56:0.0132:2,2:34.5:1:28.5:1:1:1.65484:60:4:0.0133:0:1 -X 15172121 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20086;SOR=0;LSEQ=TCTGCCATAAAACATGCAGA;RSEQ=CTAGTGTTTAATTAAAGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:113,39:0.013:2,2:33:1:29:1:0.45327:2.87362:60:4:0.0131:0:1 0/0:189:0:0,0:116,73:0:2,0:27.6:1:31.8:1:1:0:60:188:1:0:0.3 -X 15172127 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18868;SOR=0;LSEQ=ATAAAACATGCAGAGCTAGT;RSEQ=TTTAATTAAAGCTTGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:113,46:0.0124:2,0:20.5:1:30.5:1:0.08758:0:60:4:0.0127:0:1 0/0:209:0:0,0:128,81:0:2,0:27.7:1:31.4:1:1:0:60:68.667:1:0:0.4 -X 15172189 . A G 222 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.92736;SOR=1.02558;LSEQ=GATCTACATGGTTCTGTTGA;RSEQ=GAGTAGACATTCCTGAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:234:132:64,68:52,49:0.5641:2,2:27.8:1:31.5:1:0.69257:1.12697:60:264:0.5641:0:1.1 1/0:256:146:74,72:55,54:0.5703:2,2:26.2:1:30.9:1:1:1.01:60:145:0.5754:0:1.1 -X 15808477 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18796;SOR=Inf;LSEQ=GCAGGGTTCTGGAAGACGAG;RSEQ=CGCCGAAGGGTACCTCCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:130,0:0:1,0:24.2:1:32.8:1:1:0:60:260:1:0:0 0/1:100:2:2,0:98,0:0.02:1,0:32:1:32:0:1:0:60:4:0.0202:0:1 -X 15808562 . G T 56 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27289;SOR=2.6852;LSEQ=CGCCTGCGCGTGCCCGTCTC;RSEQ=ACTCTTAGGCCCGCCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:2:0,2:321,151:0.0042:2,0:1.5:1:24.5:1:0.10373:0:60:4:0.0043:0:1 0/1:444:5:1,4:273,166:0.0113:2,2:7.8:1:24.2:1:0.07339:6.55172:60:10:0.0115:0:1 -X 15808586 . C T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01541;SOR=Inf;LSEQ=CTTAGGCCCGCCCTTTCCTG;RSEQ=CAGACCTGGAGGGGCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:644:0:0,0:366,278:0:2,0:25:1:31.5:1:1:0:60:106.333:1:0:0.1 0/1:658:7:1,6:356,295:0.0106:2,2:14.6:1:25.9:1:0.05168:7.22233:60:14:0.0109:0:1 -X 15808795 . T C 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTCCTTCCTGGTGCGCGC;RSEQ=CTGGTGCCCTCCCCGGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:193:148:12,136:5,40:0.7668:2,2:26.3:1:31:1:0.55193:1.41392:60:36:0.7701:0:1.1 1/1:154:154:3,151:0,0:1:0,1:22.7:1:31.2:1:1:0:60:76:1:0:1.1 -X 15808816 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=0;LSEQ=CTGGTGCCCTCCCCGGACTT;RSEQ=CACGGGCGGCTGTGGCTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:11,144:0.0127:2,2:29:1:30.5:1:0.14748:12.58:60:4:0.0131:0:1 0/0:99:0:0,0:2,97:0:1,0:24.8:1:32:1:1:0:60:48.5:1:0:1 -X 15808933 . A G 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51628;SOR=0;LSEQ=CTGTTCTGTAATTAAAATAC;RSEQ=GGAAGCAAGGTTTCTCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:2,0:110,28:0.0143:2,0:6:1:30:1:1:0:60:4:0.0147:0:1 0/0:95:0:0,0:85,10:0:2,0:22.6:1:30.4:1:1:0:60:94:1:0:0.2 -X 15817224 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCTGAGGCAGGAGAATC;RSEQ=CTTGAACCCAGGAGGCGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:15:0:31.5:1:1:1:60:4:0.5:0:1 -X 15817963 . A G 206 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGACCAAGGATTTGCAGC;RSEQ=CTCAGTTTAATAAAACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:182,30:0:2,0:24.2:1:29.9:1:1:0:60:69.667:1:0:0.1 1/0:163:123:110,13:34,2:0.7546:2,2:24.7:1:29.8:1:0.52345:2.00166:60:122:0.7578:0:1 -X 15818114 . AT A 240 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTTAAAGTGAATGAAGTT;RSEQ=TTTATTGGAATATTATCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:125,272:0:2,0:23.8:1:30.2:1:1:0:60:55.714:0.9949:0:0.1 1/0:431:262:85,177:59,110:0.6079:2,2:24.2:1:29.9:1:0.60258:1.11661:59.9:524:0.6107:0.0719:0.1 -X 15821745 . CGT C 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.05119;SOR=Inf;LSEQ=AAAATGTGTCATTTTGCTCT;RSEQ=GTGTGTGTGTATTTGTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:160,6:0:1,0:25.3:1:29.6:1:1:0:60:54.333:1:0:0.1 0/1:153:4:4,0:138,11:0.0261:2,0:22:1:29.6:1:1:0:60:8:0.0267:0.0065:0 -X 15821979 . T A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.34352;SOR=3.45164;LSEQ=CTTCACCATAATAACTCTCA;RSEQ=GAAGAGTTGCCTATCTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:1:1,0:63,231:0.0034:2,0:1:0:25:0:0.21695:0:60:2:0.0034:0:1 0/1:258:3:3,0:61,194:0.0116:2,0:11:1:25.3:1:0.01473:0:60:6:0.0117:0:1 -X 15822013 . C T 174 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTTGGGAGGTTGGAGTGAG;RSEQ=TGAGATCACGCCATTGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:16,122:0:2,0:26.4:1:31.9:1:1:0:59.9:33.5:1:0:0.2 1/0:104:65:4,61:1,38:0.625:1,2:21.1:1:29:1:0.64804:2.47:59.8:20.667:0.6263:0:2 -X 15822022 . C T 160 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=171.71584;LSEQ=GTTGGAGTGAGCTGAGATCA;RSEQ=GCCATTGCACTCCAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:1:1,0:12,113:0.0079:2,0:32:0:28:0:0.10317:0:60:2:0.0081:0:1 1/0:82:48:4,44:1,32:0.5854:1,2:24.2:1:28.8:1:0.64357:2.88:59.7:11:0.5789:0:2.3 -X 15822066 . C CA 42 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.29871;SOR=4.90613;LSEQ=GCAAGAGCGGAACTCCATCT;RSEQ=AAAAAGAAAAAAAAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:1:0,1:27,55:0.0115:2,0:34:0:28:0:1:0:60:2:0.0141:0:1 0/1:55:3:0,3:21,31:0.0545:2,0:26.3:1:26.7:1:0.27879:0:60:6:0.0652:0:4 -X 15822072 . GA G 98 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.97548;LSEQ=GCGGAACTCCATCTCAAAAA;RSEQ=AAAAAAAAAAAGAGTTGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:5,4:36,42:0.1023:2,2:22:1:31.2:1:0.72936:1.45:60:18:0.1034:0.0455:1.2 0/1:50:5:3,2:18,25:0.1:2,2:28:1:30.6:1:0.64127:2.05:60:10:0.1:0:2.4 -X 15822104 . TA T 115 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.0188;SOR=0.12165;LSEQ=AGAGTTGCCTATCTTGAACT;RSEQ=AAAAAAAAAAACAAAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:13:9,4:61,21:0.1354:2,2:29.7:1:31.2:1:0.73854:1.28741:60:26:0.1368:0.0208:1 0/1:54:1:0,1:41,8:0.0185:2,0:23:0:32:0:0.18:0:60:2:0.0204:0:0 -X 15822154 . G T 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.25328;SOR=0;LSEQ=TCAGTTTGCCAGTGTTTTAA;RSEQ=TTTTTCATCTATGTGCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:2,1:154,34:0.0156:2,2:10.7:1:26.3:1:0.45709:2.25263:60:2:0.0121:0:2 0/0:162:0:0,0:129,32:0:2,0:22.4:1:30.8:1:1:0:59.9:11.385:1:0:0.3 -X 15822390 . G GT 138 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.02778;SOR=0.4501;LSEQ=GTAGGCATGTCAGAGTTTGG;RSEQ=TTTTTTTTTTCTCTTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:26:9,17:50,170:0.1048:2,2:27.1:1:29.5:1:0.22297:1.80:60:25:0.102:0:0.7 0/1:240:12:0,12:53,174:0.05:2,0:32.9:1:28.1:1:0.07353:0:60:11:0.0468:0.0042:0.8 -X 15822401 . C T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01573;SOR=0;LSEQ=AGAGTTTGGGTTTTTTTTTT;RSEQ=TCTTTTTCTTGTCATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:7:2,5:36,162:0.0341:2,2:6.7:1:26.9:1:0.61592:1.79:57.1:6:0.0305:0:2.4 0/0:184:0:0,0:29,154:0:2,0:21.4:1:31.6:1:1:0:60:29.5:1:0:0.2 -X 15822422 . TG T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49794;SOR=0;LSEQ=TCTTTTTCTTGTCATTTCAT;RSEQ=TTTGTTTGGAAAGAATCATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:6,102:0.0182:2,2:24.5:1:29.5:1:0.12377:15.81:60:4:0.0187:0.0091:0.5 0/0:105:0:0,0:3,102:0:1,0:20.6:1:31.2:1:1:0:60:104:1:0:0.2 -X 15826162 . CA C 124 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACAGAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAGAGAAAAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:41,1:0:1,0:20.7:1:30.4:1:1:0:59.5:41:1:0:0.2 1/0:29:15:15,0:14,0:0.5172:1,1:29.1:1:31.9:1:1:0:60:30:0.5172:0:0 -X 15826556 . T C 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACAACAACAACAAACTTTA;RSEQ=TGATGAACAAATACAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:0,63:0:1,0:25:1:30.2:1:1:0:60:126:1:0:0 1/0:42:21:0,21:0,21:0.5:1,1:30.6:1:31.7:1:1:0:60:20:0.4878:0:1 -X 15827504 . C T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26715;SOR=0;LSEQ=AATGCTGACGTTTTTGAGTT;RSEQ=CCCTTTTGGGAGAGGCGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:24,229:0.0117:2,2:12:1:30:1:0.26623:4.72:60:6:0.0118:0:1 0/0:186:0:0,0:23,163:0:2,0:22.2:1:31.2:1:1:0:60:185:1:0:0.6 -X 15827524 . T G 192 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCTTTTGGGAGAGGCGCA;RSEQ=GTTTCCATTTCAAATGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:6,170:0:1,0:23.6:1:30.6:1:1:0:60:57.667:1:0:0.1 1/0:115:79:0,79:1,35:0.687:1,1:24.2:1:30.5:1:0.31304:0:60:78:0.6842:0:1.3 -X 15827563 . C T 152 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTCATCAGACATCTGCTGC;RSEQ=TTCTTGCTGCTGCTCTCGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:1,85:0:1,0:22.5:1:32.4:1:1:0:60:85:1:0:0.1 1/0:50:32:0,32:0,18:0.64:1,1:22.8:1:30.4:1:1:0:60:64:0.64:0:1.8 -X 15836644 . A G 118 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=5e-05;SOR=Inf;LSEQ=AATGTTAGCCTGGACAAACA;RSEQ=CATTTGATGAATGGCTGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:222,60:0:2,0:23.8:1:29.6:1:1:0:60:93:1:0:0.1 0/1:280:14:11,3:206,60:0.05:2,2:21.9:1:31.1:1:1:1.07:60:28:0.0507:0:2 -X 15836648 . T G 241 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAGCCTGGACAAACAACAT;RSEQ=TGATGAATGGCTGGTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:236,73:0:2,0:23.1:1:29.7:1:1:0:60:60.8:1:0:0.1 1/0:304:198:154,44:78,28:0.6513:2,2:23.2:1:31.7:1:0.47926:1.26:60:197:0.6502:0:1.2 -X 15838366 . C T 285 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=421.23541;LSEQ=GCAGCCCTTTCTCTGTTTAA;RSEQ=GGACGATGGTATGCAGGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1087:5:1,4:561,519:0.0046:2,2:22.2:1:28.4:1:0.20223:4.31817:60:10:0.0046:0:1.2 1/0:1147:759:385,374:198,189:0.6617:2,2:24.2:1:29.8:1:0.90069:1.01768:59.6:150.8:0.6626:0:1.2 -X 15840686 . G A 139 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTAGAGCACGTTTGAAATC;RSEQ=TGGGAACCAAATTATGACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:0:1,0:22.5:1:30.2:1:1:0:60:76:1:0:0.1 1/0:31:23:23,0:8,0:0.7419:0,1:20.3:1:30.8:1:1:0:60:46:0.7419:0:1.1 -X 15841422 . G A 46 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3718;SOR=0.32906;LSEQ=ATTATGGTTGCTACATACTC;RSEQ=GATAGAAGGCTATGAACGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:2,1:51,219:0.011:2,2:21:1:29.3:1:0.09738:8.49:60:6:0.0112:0:1 0/0:275:1:1,0:66,208:0.0036:2,0:1:0:23:0:0.24364:0:60:2:0.0037:0:1 -X 15841443 . G T 26 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24633;SOR=Inf;LSEQ=GATAGAAGGCTATGAACGCA;RSEQ=ATGGGTTCGCAAGTCTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:0,171:0:1,0:30.1:1:31.1:1:1:0:60:27.5:1:0:0.1 0/1:169:2:1,1:11,156:0.0118:2,2:6:0:26.5:1:0.13736:13.62:60:4:0.012:0:1.5 -X 17952872 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23658;SOR=Inf;LSEQ=TGTTTTCACTGTGCCAGAAG;RSEQ=TTAAAGAAGTCTGGTTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:36,49:0:2,0:26:1:29.9:1:1:0:60:27.333:1:0:0.2 0/1:81:2:1,1:33,46:0.0247:2,2:8.5:1:29:1:1:1.39:60:4:0.0247:0:1 -X 17952885 . G A 21 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.21961;SOR=Inf;LSEQ=CCAGAAGATTAAAGAAGTCT;RSEQ=GTTTTCATGCCTCCTTTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:29,43:0:2,0:25.2:1:30.7:1:1:0:60:71:1:0:0.2 0/1:64:2:1,1:27,35:0.0313:2,2:14:1:21.5:1:1:1.29:60:4:0.0313:0:1.5 -X 20146514 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22197;SOR=Inf;LSEQ=TATATAAGGGAGACTTTCAC;RSEQ=TCCTTAGGCTATGTGAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:31,111:0:2,0:21.4:1:31.9:1:1:0:60:141:1:0:0.1 0/1:127:2:1,1:21,103:0.0157:2,2:29.5:1:29:1:0.31987:4.82:60:4:0.016:0:1 -X 20148450 . G A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22581;SOR=0;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AATTCTCAAAATATAAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:12,0:0.1875:0,0:11.3:1:22:1:1:0:46.7:2:0.1538:0:2.3 0/0:15:0:0,0:13,1:0:1,0:27:0:13:0:1:0:40:0:0:0:5 -X 20148516 . C T 72 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05835;SOR=Inf;LSEQ=ATTATTTAATTCAGACAATT;RSEQ=TCAAAATACAACCTTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:73,1:0:1,0:27.3:1:31.4:1:1:0:60:73:1:0:0.2 0/1:75:5:5,0:68,2:0.0667:1,0:29:1:31.2:1:1:0:60:10:0.0694:0:1 -X 20148543 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=TACAACCTTATTTAAGTGTC;RSEQ=CATGTTCTTAAAATTAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:129,13:0:2,0:21.1:1:31:1:1:0:60:141:1:0:0.1 0/1:150:2:1,1:135,12:0.0133:2,2:20:1:30:1:0.16742:10.84885:60:4:0.0137:0:1 -X 20154346 . C G 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCTTTATAAACACGTGTG;RSEQ=GTGCACACACACACACACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:46:0:30.5:1:1:0:60:4:1:0:1 -X 20156750 . T TA 90 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10829;SOR=3.87358;LSEQ=ACCTCCTTTACCTGATGGTT;RSEQ=AAAAAAAAGAAAAGGAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:2:1,1:130,317:0.0044:2,2:7:1:28.5:1:0.49886:2.43:60:4:0.0045:0.0022:0.5 0/1:470:8:1,7:138,319:0.017:2,2:30.8:1:30.3:1:0.44545:3.02261:60:16:0.0171:0:0 -X 20159636 . C T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2778;SOR=0;LSEQ=CCAGCCGCGGGCAGGCAGGG;RSEQ=GGGAAGGAAAAAGGGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:3:1,2:200,25:0.0131:2,2:9.7:1:27:1:0.03769:15.61773:60:6:0.0136:0:1.3 0/0:153:0:0,0:139,14:0:2,0:25.5:1:31.2:1:1:0:60:50:1:0:0.1 -X 20159853 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56892;SOR=2.93641;LSEQ=GGGCGACACGAGGGAGCGCG;RSEQ=GGGACCAAGTAGGTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:0,1:43,172:0.0046:2,0:28:0:27:0:1:0:49:2:0.0049:0:1 0/1:148:2:1,1:24,122:0.0135:2,2:17:1:28:1:0.31026:5.00:27:4:0.0138:0:1 -X 20159910 . G A 84 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00044;SOR=Inf;LSEQ=CGGGAGAGGCTGGCGACCCA;RSEQ=CTCTTCAGAGATCCGCCTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:5,136:0:1,0:26.2:1:31.9:1:1:0:45.9:27.2:1:0:0.1 0/1:73:7:1,6:2,64:0.0959:1,2:16.3:1:30.1:1:0.26426:5.12:32:14:0.0986:0:1 -X 21705268 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53464;SOR=0;LSEQ=AAAGGGAAGGGCCCCCTGTC;RSEQ=CATGATCACGTGAGTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:20,18:0.05:2,2:31.5:1:30:1:1:1.10818:60:4:0.05:0:1 0/0:22:0:0,0:12,10:0:2,0:27.3:1:30.7:1:1:0:60:44:1:0:0.1 -X 22516092 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=TTGATCTGTGGCTCCAGGAA;RSEQ=GTTATTCTGAAATATCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:20:1:31.8:1:1:0:60:16:1:0:0 1/0:4:2:2,0:2,0:0.5:0,0:7:1:30.5:1:1:0:60:4:0.5:0:1 -X 22516183 . G A 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00088;SOR=0;LSEQ=ATCACATATTGCTGATCTTT;RSEQ=CTTCTACTGAGCACTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:12,0:35,0:0.2553:1,0:27.4:1:27.7:1:1:0:60:11:0.2444:0:1 0/0:35:0:0,0:35,0:0:1,0:22.1:1:31.7:1:1:0:60:70:1:0:0.1 -X 22516304 . A T 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04559;SOR=Inf;LSEQ=TGAGGTTGGAAAGAGTAATA;RSEQ=AGGGAGACAGTTTTTATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:185,158:0:2,0:25.9:1:30.2:1:1:0:60:342:1:0:0.1 0/1:297:4:1,3:146,147:0.0135:2,2:24.3:1:26.8:1:0.62253:2.96979:60:8:0.0136:0:1.3 -X 22516340 . G A 210 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=368.82897;LSEQ=ATAATACACATGCCTATCTT;RSEQ=CCAGAATTGCTGGTGGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:1:0,1:162,177:0.0029:2,0:18:0:31:0:1:0:60:2:0.003:0:1 1/0:281:147:67,80:55,78:0.5231:2,2:28.3:1:29.2:1:0.54638:1.19:60:294:0.5269:0:1.1 -X 22516401 . A G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50621;SOR=0;LSEQ=ATCACCCAACATACTCTGGT;RSEQ=CTTATGAGGTTCCAGTTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:46,98:0.0137:2,2:34:1:33:1:0.54171:2.12:60:4:0.0138:0:1 0/0:113:0:0,0:32,81:0:2,0:20.6:1:28.9:1:1:0:60:112:1:0:0.4 -X 23465760 . C T 70 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=3.65648;LSEQ=GAAAATAATTCCTGGAAATA;RSEQ=ATAAAGATGAAAATAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:3,0:0.5556:0,0:17.8:1:30.2:1:1:0:60:10:0.625:0:1 1/1:6:5:5,0:1,0:0.8333:0,0:31.8:1:30.2:1:1:0:60:10:0.8333:0:1 -X 24197670 . C T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51572;SOR=0;LSEQ=GATTCTATACATGTGTCTGA;RSEQ=GTTGGACATGTTGGACATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:0.0606:2,2:23.5:1:30:1:1:1.06462:60:4:0.0625:0:1 0/0:21:0:0,0:11,10:0:2,0:24.2:1:28.6:1:1:0:60:20:1:0:0.1 -X 25314412 . GT G 32 d7;v4;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTCTGGCTAATTTTGTAGG;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:14:1:32.1:1:1:0:60:4:0.6667:0.3333:3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 25314578 . A T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05877;SOR=0;LSEQ=CTTTCTTTTTTTTTTTTTTT;RSEQ=AATTTTGAATTTTGCTGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:32,1:0.0833:1,0:18:1:21.7:1:1:0:60:2:0.0571:0:1.3 0/0:55:0:0,0:49,6:0:2,0:24.2:1:26.4:1:1:0:60:26.5:1:0:0.9 -X 25314722 . T C 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-04;SOR=0.55192;LSEQ=TTAAGTGTATCTTAGCAGAC;RSEQ=TGGCTACTGTTCCACTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:122:54,68:65,72:0.471:2,2:27.1:1:31.8:1:0.61966:1.13627:60:121:0.4745:0:1.1 0/1:331:109:56,53:98,123:0.3293:2,2:24.9:1:30.5:1:0.24239:1.32:60:53.5:0.3272:0:1.1 -X 25314763 . A G 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03097;SOR=0;LSEQ=TTGAGTTATGAAGCATGTAC;RSEQ=GCTAGCAAGGTTTCTGTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:4:2,2:62,114:0.0222:2,2:17.5:1:30.3:1:0.61649:1.83:60:8:0.0227:0:1 0/0:247:0:0,0:92,155:0:2,0:26.2:1:30.2:1:1:0:60:60.75:1:0:0.4 -X 25314812 . C T 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.00286;SOR=Inf;LSEQ=GGGAGTAACAGTATCTACTA;RSEQ=TGACCACTCCCTCTTCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:9,68:0:2,0:22.8:1:32.2:1:1:0:60:154:0.9872:0:0.2 0/1:108:11:3,8:19,78:0.1019:2,2:17.5:1:29.5:1:0.69208:1.53:60:22:0.1019:0:1.5 -X 25648085 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.21121;SOR=Inf;LSEQ=CGATCTCTTGAGTTAAATTT;RSEQ=TATTTCTTGAAGAGAAGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:86,31:0:2,0:25.9:1:31.5:1:1:0:60:234:1:0:0.2 0/1:100:2:1,1:69,29:0.02:2,2:23:1:27:1:0.51212:2.35623:60:4:0.02:0:1 -X 25648094 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22416;SOR=Inf;LSEQ=GAGTTAAATTTCTATTTCTT;RSEQ=AAGAGAAGTGACTACAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:88,36:0:2,0:27:1:31.8:1:1:0:60:123:1:0:0.3 0/1:112:2:1,1:73,37:0.0179:2,2:8.5:1:30:1:1:1.96019:60:4:0.0179:0:2 -X 25648134 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22828;SOR=Inf;LSEQ=AACTCATTTGAGGATGACTG;RSEQ=AAAGAAAGATATCAAAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:109,85:0:2,0:22.2:1:30.9:1:1:0:60:63.667:1:0:0.6 0/1:178:2:1,1:93,82:0.0112:2,2:20:1:28.5:1:1:1.13334:60:4:0.0113:0:2.5 -X 25648137 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49918;SOR=0;LSEQ=TCATTTGAGGATGACTGGAA;RSEQ=GAAAGATATCAAAGCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:108,87:0.0102:2,2:19.5:1:27.5:1:1:1.24:60:4:0.0102:0:2 0/0:185:0:0,0:97,88:0:2,0:22.2:1:29.7:1:1:0:60:45.25:1:0:0.7 -X 25648140 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21984;SOR=Inf;LSEQ=TTTGAGGATGACTGGAAAGA;RSEQ=AGATATCAAAGCTCTATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:116,92:0:2,0:22.3:1:29.7:1:1:0:60:51:0.9951:0:0.7 0/1:185:2:1,1:96,87:0.0108:2,2:20.5:1:30:1:1:1.10286:60:4:0.011:0:1.5 -X 25648157 . T C 211 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01859;SOR=1.57264;LSEQ=AGAAAGATATCAAAGCTCTA;RSEQ=TTAGAATCTATTTGATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:108:52,56:70,64:0.4463:2,2:25:1:31.5:1:0.6051:1.17708:60:53:0.4492:0:1.6 1/0:211:118:60,58:46,47:0.5592:2,2:22.9:1:30.8:1:0.89009:1.06:60:58:0.555:0:1.5 -X 25648222 . T C 198 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45939;SOR=1.17338;LSEQ=TTGAGTTTCCGTATCCATAA;RSEQ=TGGTTTTAAGTAAACTCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:80:30,50:41,67:0.4255:2,2:22.3:1:32.3:1:1:1.0198:60:160:0.4278:0:1.8 0/1:172:80:33,47:38,54:0.4651:2,2:27.4:1:31.4:1:1:1.00223:60:79:0.4647:0:1.5 -X 26064958 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21327;SOR=0;LSEQ=CTGAAACAAGACAACGCCTT;RSEQ=CAAACTCTTATACCAACCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:35,27:0.0313:2,2:40.5:1:31:1:1:1.29098:60:4:0.0313:0:1 0/0:74:0:0,0:42,32:0:2,0:28.4:1:29.2:1:1:0:59.7:73:1:0:0.1 -X 26065016 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18242;SOR=0;LSEQ=GCTTCTCCCCTTTCTAGGTC;RSEQ=TGTGGCAGCCATCTTGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:17,24:0.0465:2,2:17.5:1:29:1:1:1.40:60:4:0.0476:0:1 0/0:57:0:0,0:22,34:0:2,0:22.4:1:30.6:1:1:0:59.4:27:0.9818:0:0.2 -X 26065100 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=0;LSEQ=TGTTACCTCCAGGATTGATG;RSEQ=CATGAAGCTACAGATGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:2,9:0.1538:2,2:27:1:29:1:0.42308:3.87:60:4:0.1538:0:1 0/0:11:0:0,0:2,9:0:2,0:10.5:1:28.7:1:1:0:60:10:1:0:0.4 -X 26520791 . T A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGGAAAGGGAAAAAGAA;RSEQ=AAATGTGTATACAGATAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9:0:31.5:1:1:0:60:4:1:0:1 -X 26522072 . A T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TTCTGAAATCAGACAATGCC;RSEQ=TTCAAACTCTTATACCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:25,20:0:2,0:21.8:1:30.4:1:1:0:54.6:90:1:0:0.1 0/1:60:2:1,1:31,27:0.0333:2,2:40:1:30:1:1:1.1455:29:4:0.0345:0:2.5 -X 26522091 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50051;SOR=Inf;LSEQ=CATTCAAACTCTTATACCAA;RSEQ=CTCTGGAGTTGGGCGACATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,23:0:2,0:26:1:32.3:1:1:0:54.4:98:1:0:0.1 0/1:60:2:1,1:30,28:0.0333:2,2:33.5:1:30:1:1:1.07017:29:4:0.0339:0:2.5 -X 26693427 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=CTACAATTCTTATGGATCAC;RSEQ=TATAAACATGAGGTCAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:76,39:0.0171:2,2:17:1:30.5:1:1:1.93689:60:4:0.0174:0:1 0/0:104:0:0,0:67,37:0:2,0:22.9:1:30.5:1:1:0:60:208:1:0:0.4 -X 26693438 . A G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49836;SOR=Inf;LSEQ=ATGGATCACCTATAAACATG;RSEQ=GGTCAAGTTGAGAAACTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:78,51:0:2,0:26.6:1:30:1:1:0:60:63.5:1:0:0.5 0/1:135:2:1,1:84,49:0.0148:2,2:17.5:1:26.5:1:1:1.70705:60:4:0.0148:0:1.5 -X 26693462 . T A 66 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0625;SOR=Inf;LSEQ=CAAGTTGAGAAACTCCTTTT;RSEQ=AAGATAACTCAGTATGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:96,75:0:2,0:25.5:1:28.9:1:1:0:60:33.2:1:0:0.7 0/1:190:5:4,1:109,76:0.0263:2,2:23.2:1:28.8:1:0.6499:2.78:60:10:0.0266:0:1.4 -X 26693505 . G A 228 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00621;LSEQ=AATAGTTTGATTACAAAAAG;RSEQ=ATGATGTCCAAATAATTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:200:199:103,96:0,0:0.995:0,2:25.3:1:29.9:1:1:0:60:65.333:0.9949:0:1.1 1/0:256:141:73,68:60,54:0.5508:2,2:26:1:29:1:0.90038:1.03488:60:46:0.5498:0:1.1 -X 28677096 . T TTATC 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64667;SOR=2.06488;LSEQ=TTTGACCCCATGGAAAAAAA;RSEQ=TAACGTTCAGAACTACCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:65:58,7:2,0:0.9559:0,2:22.5:1:30:1:1:0:56:64:0.9697:0.2941:0.3 1/1:46:45:39,6:1,0:0.9783:0,2:21.5:1:30.2:1:1:0:55.3:90:0.9783:0.2826:0.3 -X 28677132 . C CT 116 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.51217;SOR=0.72964;LSEQ=CCAGTAACAGGAAGAAGAGA;RSEQ=TTTTTTTTTTTATTGAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:13:13,0:95,24:0.0977:2,1:20:1:31.4:1:0.12436:0:57.1:26:0.1016:0.0301:0.4 0/1:123:9:7,2:89,22:0.0732:2,2:25.1:1:29.7:1:1:1.15436:55:18:0.0732:0:1 -X 28677134 . T C 33 v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.24362;SOR=Inf;LSEQ=AGTAACAGGAAGAAGAGACT;RSEQ=TTTTTTTTTATTGAGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:110,26:0:2,0:22.1:1:30.1:1:1:0:58.3:135:1:0:0.4 0/1:135:2:1,1:103,28:0.0148:2,2:29:0:33.5:1:0.38984:3.63249:60:4:0.015:0:1 -X 28677326 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=TCCTGCAAAGCACCGATAGC;RSEQ=GCACTCTGGAAGCGCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:44,116:0:2,0:25.1:1:30.2:1:1:0:60:79:1:0:0.2 0/1:173:2:1,1:66,105:0.0116:2,2:18:1:29:0:1:1.59:60:4:0.0116:0:2 -X 28677353 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18314;SOR=0;LSEQ=TGGAAGCGCAGATCTGTTTT;RSEQ=AAGTCCTGAGCAATTTCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:25,73:0.02:2,2:23:1:31:1:0.45434:2.88:60:4:0.02:0:1 0/0:133:0:0,0:52,81:0:2,0:26.1:1:29:1:1:0:59.6:132:1:0:0.1 -X 28677529 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49637;SOR=Inf;LSEQ=AGCGGCTTTTGTAGCCAGTT;RSEQ=CTTCCCGGGTGTTTTACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:36,27:0:2,0:20.8:1:32.3:1:1:0:59.6:126:1:0:0.1 0/1:66:2:0,2:30,34:0.0303:2,0:18:1:28:1:0.4965:0:60:4:0.0303:0:1 -X 28677536 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49706;SOR=Inf;LSEQ=TTTGTAGCCAGTTGCTTCCC;RSEQ=GGTGTTTTACCACCAGTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:38,30:0:2,0:22:1:30.5:1:1:0:59.8:136:1:0:0.1 0/1:73:2:1,1:33,38:0.0274:2,2:20.5:1:29.5:1:1:1.15:60:4:0.0278:0:1 -X 32172371 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53846;SOR=3.18702;LSEQ=AAAGGTAAAATTTAGAAGTG;RSEQ=AAAGGTATCTTTATCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:7,0:0.125:0,0:27:0:32:0:1:0:60:2:0.125:0:1 0/1:6:2:2,0:4,0:0.3333:0,0:23.5:1:31:1:1:0:60:4:0.3333:0:1 -X 32172584 . A C 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00019;SOR=0.46548;LSEQ=TCAAATAACTTGTTACAAAG;RSEQ=AATTTTCATCCTAAAACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:87:38,49:53,55:0.4462:2,2:25.9:1:31.9:1:0.47344:1.24119:60:86:0.4456:0:1.1 0/1:246:67:30,37:79,100:0.2724:2,2:21.9:1:31.5:1:1:1.03:60:66:0.2716:0:1.1 -X 32223980 . T C 114 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12559;LSEQ=GTCCTTTATCATCATCTGCC;RSEQ=TCTCTCCCACCTAAGTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:12:10,2:14,2:0.4286:2,2:25.8:1:31.8:1:1:1.38301:60:24:0.4286:0:1.1 0/1:24:11:9,2:9,4:0.4583:2,2:33.2:1:29.7:1:0.6494:1.94:60:22:0.4583:0:1 -X 32224078 . C T 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21777;SOR=Inf;LSEQ=TTTGGTTGTGAACTAAAGGC;RSEQ=GACAAAGATGATCACTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:45,31:0:2,0:26.3:1:30.6:1:1:0:60:75:1:0:0.1 0/1:67:2:2,0:36,29:0.0299:2,0:33:1:33:0:0.50158:0:60:4:0.0308:0:1 -X 32224251 . T C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50165;SOR=0;LSEQ=GGCAGCTTTGAAAATGTCTG;RSEQ=ACAGCCCATGGTTTCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:26,39:0.0299:2,2:9:0:32.5:1:1:1.49:60:4:0.0303:0:1 0/0:54:0:0,0:30,24:0:2,0:20.3:1:28.8:1:1:0:60:108:1:0:0.1 -X 32224292 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21777;SOR=Inf;LSEQ=AGGGCTTTGAAATAACACCA;RSEQ=CAGTGGTCTTACGGTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:29,39:0:2,0:20.9:1:30.1:1:1:0:60:21.667:1:0:0.3 0/1:60:2:1,1:31,27:0.0333:2,2:40.5:1:32:1:1:1.1455:60:4:0.0339:0:1.5 -X 32224322 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50359;SOR=Inf;LSEQ=TACGGTTGAAGTGTGGTTCA;RSEQ=GGCCAGTGCATGTGAGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:24,24:0:2,0:28.1:1:31.8:1:1:0:60:96:1:0:0 0/1:62:2:2,0:35,25:0.0323:2,0:41.5:1:31.5:1:0.51084:0:60:4:0.0328:0:1 -X 32224384 . C T 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01325;SOR=Inf;LSEQ=GAAGATACAGAGTCAGAAGA;RSEQ=GAACAGGAGGAGGATGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:47,20:0:2,0:20.3:1:31.1:1:1:0:60:66:1:0:0.6 0/1:66:6:3,3:34,26:0.0909:2,2:19.5:1:28.7:1:1:1.30232:60:12:0.0909:0:1.2 -X 32224435 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21516;LSEQ=ATATCTGGAAAGCGATCTGC;RSEQ=CCTGGAGGTGGTAGCAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:111:64,47:9,4:0.8952:2,2:26.4:1:30.7:1:0.55597:1.64595:58.6:110:0.8943:0:1.1 1/0:113:73:39,34:21,19:0.646:2,2:27.3:1:30.6:1:1:1.04:58.1:146:0.6577:0:1.1 -X 32224450 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49828;SOR=Inf;LSEQ=TCTGCTCCTGGAGGTGGTAG;RSEQ=AAGGTTCCACAGAAAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:73,57:0:2,0:27:1:32.2:1:1:0:58.8:129:1:0:1 0/1:135:2:1,1:68,65:0.0148:2,2:5.5:1:27.5:1:1:1.04582:60:4:0.0149:0:1.5 -X 32224452 . A G 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00731;SOR=Inf;LSEQ=TGCTCCTGGAGGTGGTAGCA;RSEQ=GGTTCCACAGAAAAAAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:73,59:0:2,0:26.6:1:30.4:1:1:0:58.8:65:1:0:0.9 0/1:142:8:5,3:68,66:0.0563:2,2:21:1:32.6:1:0.71948:1.61:60:16:0.0563:0:1 -X 32224478 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22237;SOR=0;LSEQ=CACAGAAAAAAGTAAAACTT;RSEQ=CTGCTGATGAAGATGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:70,55:0.0155:2,2:25:1:29:1:1:1.27028:60:4:0.0155:0:1.5 0/0:144:0:0,0:78,66:0:2,0:25.8:1:31.7:1:1:0:59.2:143:1:0:0.5 -X 32224525 . T A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24931;SOR=Inf;LSEQ=GATGATGATGATTTTGATGA;RSEQ=GAGGAAACTGAAGAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:64,57:0:2,0:21.5:1:30.1:1:1:0:60:120:1:0:0.2 0/1:135:3:2,1:66,65:0.0222:2,2:28.7:1:30:1:1:1.96:60:6:0.0226:0:1 -X 32224567 . A G 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24505;SOR=Inf;LSEQ=CCAGTGAAGAAATCTATATG;RSEQ=GATACTCCAGCCAAAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:57,70:0:2,0:27.1:1:30.6:1:1:0:59.8:126:1:0:0.1 0/1:125:2:1,1:56,67:0.016:2,2:14:0:29:1:1:1.19:60:4:0.0161:0:1 -X 32224583 . AA T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.24289;SOR=Inf;LSEQ=TATGAGATACTCCAGCCAAA;RSEQ=TGCACAAAAGTCAAATCGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:54,70:0:2,0:29:1:30.3:1:1:0:59.4:248:1:0:0.1 0/1:121:2:1,1:51,68:0.0165:2,2:49:0:30.8:1:1:1.33:60:4:0.0168:0:0 -X 34405705 . T C 93 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1107;SOR=4.96624;LSEQ=TAGAGTCTCTACCCAAGAGC;RSEQ=CCTTGAGCAACTGAGAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:5,0:10,0:0.3333:0,0:32.4:1:32:1:1:0:60:10:0.3571:0:1 1/0:11:8:8,0:3,0:0.7273:0,0:17.9:1:31.1:1:1:0:60:16:0.7273:0:1.1 -X 34405933 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13788;SOR=Inf;LSEQ=GTCGGCCAACACCCTGCGAG;RSEQ=TGTGTTCAAGAAGTATGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:104,174:0:2,0:25.9:1:31.5:1:1:0:60:26.8:1:0:0.1 0/1:366:4:2,2:142,218:0.0109:2,2:28.8:1:24.5:1:0.64963:1.53:60:3:0.0084:0:1 -X 39769863 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18477;SOR=0;LSEQ=GGCCCAGGCAGGGCTCGAAC;RSEQ=CTGACTCCAGCCCCTTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:21,25:0.0417:2,2:29.5:1:29:1:1:1.19:60:4:0.0426:0:1 0/0:63:0:0,0:35,28:0:2,0:27.5:1:30.5:1:1:0:60:126:1:0:0.4 -X 39769887 . A G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49939;SOR=Inf;LSEQ=ACTCCAGCCCCTTCCCACCT;RSEQ=GAGGGAGGCCCGGCTTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:16,25:0:2,0:27.4:1:29.7:1:1:0:60:82:1:0:0.2 0/1:50:2:1,1:24,24:0.04:2,2:16.5:1:31:1:1:1:60:4:0.0417:0:1 -X 39911657 . C A 197 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0.45279;LSEQ=GTAGCCAGTTTCGTGGCCTA;RSEQ=AAAACAGAAAGGAAAATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:93:34,59:82,149:0.287:2,2:25:1:30.2:1:0.89832:1.05:60:92:0.2857:0:1 0/1:396:61:22,39:127,208:0.154:2,2:25.4:1:30.9:1:0.88594:1.08219:60:122:0.1552:0:1.2 -X 39911827 . TTTTTTTTG T 87 v4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=19.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CATTTTTTTTTTTTTTTTTT;RSEQ=GAGACGGAATCTCGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:0,20:0:1,0:9.2:1:31.3:1:1:0:45.1:40:1:0:1.2 1/0:12:8:1,7:0,5:0.6667:0,2:20.1:1:29:1:1:0:42.5:16:0.6667:0.5833:1 -X 39911835 . G T 83 InGap;LongAT STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0031;SOR=0;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=GAGACGGAATCTCGCTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:0.7:0,0:19.3:1:29.7:1:1:0:43.6:14:0.7:0:1.1 0/0:9:0:0,0:0,1:0:0,0:1:0:30:0:1:0:40:2:1:0:0 -X 39913076 . T C 120 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATCTGCTCAAAGCGCATT;RSEQ=CTAACTCCTGTCACCTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:177,36:0:2,0:23.5:1:30:1:1:0:60:70:0.9953:0:0.1 0/1:184:16:11,5:137,31:0.087:2,2:21.8:1:30.1:1:0.31799:1.99991:60:32:0.087:0:1.1 -X 39913655 . C T 149 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAAATGATGGCAGAGCCA;RSEQ=GTGGCATTTTTTCCTATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:7,144:0:1,0:22.4:1:30.1:1:1:0:60:150:1:0:0.1 0/1:139:29:2,27:7,103:0.2086:2,2:19.3:1:30.7:1:1:1.09:60:58:0.2117:0:1.1 -X 39914540 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21086;SOR=Inf;LSEQ=TTTCAGCCTTTGTGATTTCT;RSEQ=CCTAGTCAAATTCCAATCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:149,20:0:2,0:25.1:1:32.3:1:1:0:60:168:1:0:0 0/1:144:2:1,1:124,18:0.0139:2,2:21:1:28.5:1:0.24728:6.73343:60:4:0.0141:0:1 -X 39916715 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07646;SOR=Inf;LSEQ=CGGGCTGTGGATGTCTTGGT;RSEQ=AGGGGGAAACACATGTGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:0,51:0:1,0:23:1:31.4:1:1:0:60:50:1:0:0.1 0/1:20:2:0,2:0,18:0.1:1,0:28:1:31.5:1:1:0:60:4:0.1:0:1 -X 39920974 . C T 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCCTACTCCCCCTACA;RSEQ=GGCCACCCTTCCACCCGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:27:0:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 39920989 . C G 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACACGGCCACCCTTCCAC;RSEQ=CGAAACAGTACAAGCAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:12:0:33:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 39921336 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11549;SOR=Inf;LSEQ=CCCTCCCCTCGCCCACCACA;RSEQ=TCCGCAGGCCCCGCCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:171,32:0:2,0:23.3:1:31.4:1:1:0:60:24.375:1:0:0.1 0/1:105:2:1,1:84,19:0.019:2,2:25.5:1:27.5:1:0.34615:4.33469:60:4:0.0194:0:1 -X 39921348 . C T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13965;SOR=5.29513;LSEQ=CCACCACAGTCCGCAGGCCC;RSEQ=GCCCCCCAGCCTGCAGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:0,1:196,61:0.0039:2,0:1:0:15:0:0.24031:0:60:0:0:0:1 0/1:148:3:2,1:111,34:0.0203:2,2:24.3:1:30.3:1:0.55773:1.62631:60:6:0.0204:0:1.3 -X 39921349 . GC G 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.55715;SOR=3.48576;LSEQ=CACCACAGTCCGCAGGCCCC;RSEQ=CCCCCAGCCTGCAGCCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:1,0:200,64:0.0038:2,0:35:0:34:0:1:0:60:2:0.0038:0:0 0/1:153:2:1,1:116,35:0.0131:2,2:20:1:30.5:1:0.41641:3.28196:60:4:0.0134:0:0 -X 39921707 . C A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57582;SOR=2.74898;LSEQ=CCTTCTAACAGCCGCTGCTT;RSEQ=CCCTCCTCCTCCCCACGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:1,0:41,172:0.0046:2,0:1:0:24:0:0.19626:0:60:2:0.0049:0:1 0/1:158:2:1,1:35,120:0.0127:2,2:26.5:1:27.5:1:0.40715:3.39:60:4:0.0127:0:1 -X 39921860 . C A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GCTGCCACCCAGAAGACATG;RSEQ=TCCTCTAGGACAGGGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:93,15:0:2,0:24.2:1:32:1:1:0:60:53:1:0:0.1 0/1:62:11:8,3:42,9:0.1774:2,2:19.7:1:27.1:1:0.43214:1.73243:60:4.5:0.15:0:1 -X 39921867 . A G 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53607;SOR=0;LSEQ=CCCAGAAGACATGCTCCTCT;RSEQ=GGACAGGGGAGTGACGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:105,14:0.0164:2,0:22:1:31:1:1:0:60:4:0.0167:0:1 0/0:69:0:0,0:60,9:0:2,0:21.1:1:28.9:1:1:0:60:68:1:0:0.2 -X 39922359 . A G 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25931;SOR=1.21914;LSEQ=GGTGACGGGGTGGCGGGCGG;RSEQ=TGGGAGACGGGAGAAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:100:39,61:83,140:0.3086:2,2:24.9:1:29.8:1:0.80433:1.08:60:15.667:0.2984:0:1.4 0/1:278:98:34,64:73,106:0.3525:2,2:24.1:1:29.5:1:0.36686:1.29513:60:15.333:0.3433:0:1.4 -X 39922384 . G T 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50191;SOR=0;LSEQ=AGACGGGAGAAGAAGCGGGC;RSEQ=TTACACAGTTGTAGCCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:54,145:0.01:2,2:24.5:1:32:1:0.47338:2.67:60:4:0.0101:0:2 0/0:171:0:0,0:50,121:0:2,0:21.8:1:29.9:1:1:0:60:84.5:1:0:0.5 -X 39923462 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0941;SOR=Inf;LSEQ=CCGCTCCACTGCTGCGCCCC;RSEQ=ACGGCTTCCCCTCACCGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:82,4:0:1,0:23.7:1:31.3:1:1:0:60:85:1:0:0.2 0/1:39:2:2,0:36,1:0.0513:1,0:42.5:1:30:1:1:0:60:4:0.0541:0:1 -X 39923499 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16349;SOR=Inf;LSEQ=GACTCTGTCTACGGGGGCAG;RSEQ=GCGCCGCACATCCACATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:142,9:0:2,0:23.7:1:32:1:1:0:60:49.333:1:0:0.1 0/1:103:2:1,1:93,8:0.0194:2,2:12.5:1:27:1:0.1679:11.01924:60:4:0.0206:0:1 -X 39923713 . G A 134 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCACCCGGAGGGTGGGGCT;RSEQ=TGAGGCATGTCCGAGGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:754:0:0,0:403,351:0:2,0:24.8:1:32.2:1:1:0:60:106.714:1:0:0.1 0/1:764:25:15,10:394,344:0.0327:2,2:21.5:1:29:1:0.54769:1.31:60:50:0.033:0:1.2 -X 39923898 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09401;SOR=Inf;LSEQ=TTAATGAAGCCCGAAGGTCG;RSEQ=CATGAGAAGGCAGGATCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:75,256:0:2,0:21.7:1:30.8:1:1:0:60:35.778:1:0:0.2 0/1:277:3:2,1:54,220:0.0108:2,2:6:1:24.3:1:0.10504:8.06:60:6:0.0111:0:1 -X 39930099 . C G 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00544;SOR=0;LSEQ=TCTTTCACAGACGCCTCGTT;RSEQ=CTGGTTGCCACCATTCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:9:9,0:140,3:0.0592:1,0:21.7:1:30.9:1:1:0:60:8:0.0541:0:1.1 0/0:119:0:0,0:119,0:0:1,0:22.6:1:30.8:1:1:0:60:22.8:1:0:0.1 -X 39931158 . C CT 45 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTAAGCAACCTTTTTT;RSEQ=TTTTTTTTTTCCTTTCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:0,3:3,25:0.0968:2,0:16.3:1:29:1:1:0:60:6:0.0968:0.0323:0.3 0/0:8:0:0,0:1,7:0:2,0:20.5:1:32.8:1:1:0:60:16:1:0:0.9 -X 39931492 . A G 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26646;SOR=0;LSEQ=TTCAAATTACCACAAGCTTC;RSEQ=TTCACCAAATCTGCCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:3:2,1:118,4:0.024:1,2:15:1:22.3:1:0.11616:13.79441:60:2:0.0163:0:2.3 0/0:90:0:0,0:88,2:0:1,0:21.6:1:30.4:1:1:0:60:180:1:0:0 -X 39932907 . T C 176 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=85.43527;LSEQ=GATGCGGAGGCTGGGCGGCC;RSEQ=GCACTCGACACTGACCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:1:0,1:301,308:0.0016:2,0:49:0:28:0:1:0:60:2:0.0017:0:1 0/1:519:64:34,30:225,229:0.1233:2,2:24.6:1:29.4:1:0.689:1.15:60:31:0.1213:0:1.1 -X 39933339 . A G 277 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=1.64351;LSEQ=AACAGAGGAGGTGAGCTGCC;RSEQ=TCTTTTCTGTCTTGAACCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:795:539:251,288:118,138:0.678:2,2:26.5:1:30.9:1:0.93937:1.02:60:88.833:0.6773:0:1.1 1/0:754:585:299,286:78,89:0.7759:2,2:23.2:1:30.2:1:0.33508:1.19:60:116:0.7744:0:1.2 -X 39933358 . G A 87 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11031;SOR=0.2662;LSEQ=CATCTTTTCTGTCTTGAACC;RSEQ=CTGTCTTCCGGGCATGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:8:3,5:341,408:0.0106:2,2:18.8:1:29.1:1:0.7342:1.39238:60:16:0.0107:0:1.8 0/0:706:2:1,1:340,364:0.0028:2,2:37.5:1:29.5:1:1:1.07:60:4:0.0029:0:2 -X 39934488 . C T 99 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACTCCTTCAAGGCAGCAGCA;RSEQ=CCAAAGACACTGCCAACTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:16,98:0:2,0:24.4:1:31.4:1:1:0:60:56:1:0:0.1 0/1:65:11:5,6:8,46:0.1692:2,2:16.4:1:28.8:1:0.03481:4.64:60:22:0.1719:0:1.2 -X 39935599 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17307;SOR=Inf;LSEQ=ACTCAGCCCTGCTCTGAACT;RSEQ=CCACCCCTCCCCCATTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:102,11:0:2,0:24.9:1:32.4:1:1:0:60:112:1:0:0.2 0/1:81:2:1,1:66,13:0.0247:2,2:17.5:1:27.5:1:0.31759:4.92929:60:4:0.025:0:1 -X 39936970 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.79754;LSEQ=TTAAAACTGTAAATCAAGAG;RSEQ=GGCCTACTAGGCGGGAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:86,0:0.0227:1,2:12.5:1:28.5:1:0.02273:0:60:4:0.0233:0:1.5 0/1:55:1:1,0:53,1:0.0182:1,0:5:0:28:0:1:0:60:2:0.0185:0:2 -X 39937038 . G T 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.26229;SOR=0;LSEQ=CGGTGGCTGTGAGAAGTTGA;RSEQ=GGGGGCTTCAGCATGGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:1,2:209,72:0.0105:2,2:25.7:1:24.7:1:0.16732:5.76185:60:2:0.0071:0:1.3 0/0:217:0:0,0:156,59:0:2,0:22.3:1:31:1:1:0:60:70.667:0.9953:0:0.1 -X 39937053 . G T 34 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08347;SOR=Inf;LSEQ=GTTGAGGGGGGCTTCAGCAT;RSEQ=GGCGTGGGCTCCACTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:260,120:0:2,0:22.7:1:31.4:1:1:0:60:62.333:1:0:0.1 0/1:296:3:1,2:190,102:0.0101:2,2:12.3:1:22:1:0.28454:3.70796:60:2:0.0069:0:2.3 -X 39945625 . A T 153 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCACAAATCTTAAAAACTC;RSEQ=GCCATAAACAGCTGAGGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:138,116:0:2,0:24.3:1:30.3:1:1:0:60:253:1:0:0.2 0/1:247:33:18,15:104,110:0.1336:2,2:26.8:1:30.4:1:0.57757:1.27:60:66:0.1347:0:1.2 -X 39945696 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21268;SOR=Inf;LSEQ=AACACGGTGACACTCACGGC;RSEQ=CCGTGGGCCTTCTCCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:56,114:0:2,0:24.2:1:30.8:1:1:0:60:84:1:0:0.1 0/1:146:2:2,0:55,89:0.0137:2,0:15.5:1:29.5:1:0.15078:0:60:4:0.0141:0:1.5 -X 40594768 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=GAGCGGGCAGAGTCGCCACC;RSEQ=CCTACCGCCGGGCCGCCTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:0:2,0:29.2:1:31.2:1:1:0:60:50:1:0:0.2 0/1:30:2:1,1:19,9:0.0667:2,2:15.5:1:29.5:1:1:2.05485:60:4:0.0667:0:1.5 -X 41031175 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49451;SOR=Inf;LSEQ=TAAATATGCCACCCCTTAGA;RSEQ=ATGGAGCAAGAGTACTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,23:0:2,0:29.7:1:31.6:1:1:0:60:86:1:0:0.1 0/1:45:2:1,1:19,24:0.0444:2,2:23:1:28:1:1:1.26:60:4:0.0444:0:1 -X 44732755 . AG A 92 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.05904;SOR=Inf;LSEQ=TCACTGCGGGCCCCGGTCCG;RSEQ=GGGGGGTGTCGGCGTTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:155,102:0:2,0:25.2:1:31.2:1:1:0:60:84.667:1:0:0.2 0/1:533:8:4,4:323,201:0.015:2,2:19.8:1:30.7:1:0.49214:1.60542:60:16:0.0152:0.0038:0.3 -X 44732959 . G A 26 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63212;SOR=0.59553;LSEQ=GCGCTCGGCGGACTGGACAG;RSEQ=TACGGGCCGCCGTCACTCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:64,121:0.0107:2,2:45.5:1:31:1:1:1.88:60:4:0.0109:0:2 0/0:313:2:2,0:115,196:0.0064:2,0:1:0:26.5:1:0.13898:0:60:4:0.0064:0:1 -X 44732963 . G A 55 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41401;SOR=3.13439;LSEQ=TCGGCGGACTGGACAGGTAC;RSEQ=GGCCGCCGTCACTCGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:0,1:56,118:0.0057:2,0:9:0:32:0:1:0:60:2:0.0058:0:1 0/1:282:5:3,2:98,179:0.0177:2,2:24.6:1:24:1:0.35312:2.73:60:1.5:0.0109:0:1 -X 44732995 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17577;SOR=0;LSEQ=CTCGCCCGGTCGGCTCCGGA;RSEQ=GGGCAGTAGCCGCTCTCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:36,91:0.0155:2,2:21:1:28.5:1:0.49297:2.51:60:4:0.0157:0:1 0/0:178:0:0,0:57,121:0:2,0:21.1:1:29.5:1:1:0:60:34.6:1:0:0.2 -X 44733054 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15619;SOR=Inf;LSEQ=TGTCTCTGGCGGCGGCGGGG;RSEQ=GGGCACCTCGGTTTGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:111,38:0:2,0:21.7:1:31.3:1:1:0:60:28.8:1:0:0.2 0/1:228:4:1,3:177,47:0.0175:2,2:9.5:1:26.5:1:0.03392:11.13495:60:8:0.0175:0:1.3 -X 44820500 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25585;SOR=Inf;LSEQ=TTTTAGGGCTTTATTTTTTG;RSEQ=TTACATATTTGTATTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:187,41:0:2,0:24.6:1:32.4:1:1:0:60:456:1:0:0.1 0/1:278:3:1,2:216,59:0.0108:2,2:6.3:1:26.7:1:0.12227:7.25206:60:6:0.0108:0:1 -X 44833826 . T C 154 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTACTGGGAGGTGGGTGTGG;RSEQ=GGGAATCTTGTTACCGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:105,23:0:2,0:25:1:29.9:1:1:0:60:127:1:0:0.1 0/1:172:28:25,3:122,22:0.1628:2,2:20.4:1:32.2:1:0.77015:1.50:60:27:0.1579:0:2.1 -X 44833829 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18674;SOR=0;LSEQ=CTGGGAGGTGGGTGTGGTGG;RSEQ=AATCTTGTTACCGTGTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:111,25:0.0144:2,2:15:1:27.5:1:0.34243:4.37335:60:4:0.0148:0:1 0/0:182:0:0,0:152,30:0:2,0:24.6:1:31.4:1:1:0:60:364:1:0:0.8 -X 44833841 . C A 213 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=238.08263;LSEQ=TGTGGTGGGAATCTTGTTAC;RSEQ=GTGTTTGTTAAGTGTATTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:127,38:0.006:2,0:32:0:16:0:0.23494:0:60:0:0:0:2 1/0:228:135:111,24:72,21:0.5921:2,2:24.9:1:30.1:1:0.40005:1.35:60:44:0.5893:0:1.3 -X 44833842 . G A 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.17404;SOR=0;LSEQ=GTGGTGGGAATCTTGTTACC;RSEQ=TGTTTGTTAAGTGTATTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:128,38:0.0119:2,2:7:0:32:1:0.41146:3.33787:60:4:0.012:0:1.5 0/0:234:0:0,0:188,46:0:2,0:24.7:1:31.2:1:1:0:60:77:1:0:0.8 -X 44834045 . C CT 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAAATTAATTGAGCTCTTG;RSEQ=TTTTTTTTGTTAATTACTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:31,139:0:2,0:22.1:1:31.2:1:1:0:60:20.25:0.9939:0:0.1 0/1:232:25:4,21:53,150:0.1078:2,2:25.3:1:28.6:1:0.33475:1.8506:60:50:0.1082:0.0043:0 -X 44870342 . TTG T 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.65566;SOR=0.49636;LSEQ=TTTTGTTTGTGCTTGATTTT;RSEQ=TGTGTGTGTGTAATAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:0,3:50,182:0.0128:2,0:23:1:31.2:1:1:0:60:6:0.0128:0.0043:2.3 0/0:314:2:1,1:85,227:0.0064:2,2:48:1:32:0:0.47339:2.66:60:4:0.0064:0:0 -X 44894091 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18713;SOR=0;LSEQ=ATGTATTTATTATTATTTTA;RSEQ=ACCTTACATACCTGAAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:142,41:0.0108:2,2:13:1:28:1:0.40347:3.43386:60:4:0.0109:0:1 0/0:242:0:0,0:178,64:0:2,0:21.5:1:31.1:1:1:0:60:47.4:1:0:0.1 -X 44896821 . G T 61 Cluster75bp STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02771;SOR=0;LSEQ=AGACTGTGATAATGTTTGAT;RSEQ=CTTTGTTATTCTTACTTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:353:4:2,2:258,91:0.0113:2,2:24.3:1:30.8:1:0.2841:2.82525:60:8:0.0114:0:1.3 0/0:510:0:0,0:358,150:0:2,0:24.5:1:31.6:1:1:0:60:83.667:0.998:0:0.1 -X 44896832 . C G 235 Cluster75bp STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0083;LSEQ=ATGTTTGATGCTTTGTTATT;RSEQ=TTACTTAATTTGCCCCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:160:105,55:176,88:0.3765:2,2:25.9:1:32.2:1:0.83288:1.04748:60:320:0.3791:0:1.7 0/0:606:3:2,1:396,206:0.005:2,2:26:1:27:1:1:1.04:60:2:0.0034:0:1.7 -X 44896888 . C T 228 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGATTTTTTTGTCTTTCCT;RSEQ=ATCCTTTGCAGTTCAATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:233:106,127:207,233:0.3447:2,2:26.8:1:29:1:0.74538:1.06429:60:115.5:0.3463:0:1.5 0/0:1036:0:0,0:511,524:0:2,0:25.6:1:31.2:1:1:0:60:128.375:0.999:0:0.2 -X 44897039 . TG T 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00076;SOR=Inf;LSEQ=CAGATAATTTAATGGAGTTC;RSEQ=GGCGTTACTTCTTAGGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:1,58:0:1,0:21.7:1:30.9:1:1:0:60:58:1:0:0.1 0/1:84:13:0,13:1,70:0.1548:1,1:26.6:1:31:1:1:0:60:26:0.1566:0:0.1 -X 44911107 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21336;SOR=0;LSEQ=TCTTTATGTTTTTTCCATGT;RSEQ=GAGTGTGGCAAATATGTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:24,117:0.014:2,2:22:1:27:1:0.3201:4.80:60:4:0.014:0:1 0/0:166:0:0,0:28,137:0:2,0:25.2:1:30:1:1:0:60:164:1:0:0 -X 44913052 . T A 172 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTAAGTCATTTATGTAAAT;RSEQ=TTTTTAAATCATTTACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:226,77:0:2,0:24.3:1:29.9:1:1:0:60:49.5:1:0:0.1 0/1:427:69:47,22:240,118:0.1616:2,2:22.8:1:28.2:1:0.88974:1.05:60:138:0.162:0:1.1 -X 44919532 . G A 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.18816;SOR=Inf;LSEQ=CTTTTGATTTAATTGCAAAG;RSEQ=GAATCTAGATCAAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:4,58:0:2,0:23.8:1:31.2:1:1:0:60:61:1:0:0 0/1:48:2:0,2:0,46:0.0417:1,0:18:1:33:0:1:0:60:4:0.0417:0:1 -X 44920068 . A G 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AGAAGTTTCAGCTGCCCTGA;RSEQ=ATTGTGCAGTTTGAACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:7,102:0:2,0:23.7:1:30.1:1:1:0:60:53.5:1:0:0.1 0/1:147:20:3,17:11,116:0.1361:2,2:18.3:1:30.9:1:0.40777:1.85:60:19:0.1319:0:1.1 -X 44920541 . A AT 121 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.66087;SOR=1.35387;LSEQ=ATTTAACCAAATATTCTTTA;RSEQ=TTTTTTTTTTAAATCGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:7:6,1:174,47:0.0303:2,2:20.3:1:29.8:1:1:1.62:60:14:0.0314:0.0087:0 0/1:394:16:14,2:273,104:0.0406:2,2:24.3:1:30.4:1:0.25426:2.66:60:32:0.041:0.0025:0.1 -X 44920542 . T A 39 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=0.04889;SOR=0;LSEQ=TTTAACCAAATATTCTTTAA;RSEQ=TTTTTTTTTAAATCGATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:3:2,1:172,52:0.013:2,2:11.3:1:24.7:1:0.55145:1.64973:60:2:0.0087:0:1.3 0/0:399:0:0,0:283,109:0:2,0:21.8:1:29.9:1:1:0:60:195:0.9848:0:0.1 -X 44922446 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=TTTTTTTTTGAAACCGACTT;RSEQ=TGCTTTTTCAAGGAAGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:0:2,0:24.9:1:28.8:1:1:0:60:9:1:0:0 1/0:4:2:2,0:2,0:0.5:0,0:6.5:1:31.5:1:1:0:60:4:0.5:0:1.5 -X 44922654 . GT G 49 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.30613;SOR=0.21646;LSEQ=CCAGCATTTACTTTTCCTTT;RSEQ=TTTTTTGACAGATGAGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:195,83:0.0107:2,2:37.7:1:31:1:1:1.17398:60:6:0.0107:0:0 0/0:430:1:0,1:278,151:0.0023:2,0:19:0:26:0:0.35349:0:60:2:0.0023:0:0 -X 44929077 . C A 182 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTTCAGGAAACATATTGA;RSEQ=GGTGCCTGAAACAAGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:0:0,0:257,326:0:2,0:25.5:1:31:1:1:0:60:582:1:0:0.1 0/1:850:67:30,37:374,409:0.0788:2,2:26.6:1:30.1:1:0.70275:1.12763:60:134:0.0793:0:1.1 -X 44929587 . T A 35 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.06015;SOR=0;LSEQ=ATACCCCAGCTCAGCAGAAG;RSEQ=TCTGAAGGCATGCAGGTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:3,0:94,171:0.0112:2,0:8:1:22.3:1:0.04648:0:60:2:0.0075:0:3.3 0/0:416:0:0,0:153,262:0:2,0:38:0:14:0:1:0:60:0:0:0:2 -X 44929611 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16764;SOR=0;LSEQ=GAAGGCATGCAGGTTAGTGT;RSEQ=GGAAAGTTCATCAAAGTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:54,131:0.0107:2,2:49.5:1:27.5:1:0.50285:2.41:60:4:0.0109:0:1.5 0/0:269:0:0,0:76,193:0:2,0:25.3:1:30.3:1:1:0:60:66.25:1:0:0.1 -X 44929647 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51776;SOR=Inf;LSEQ=GTGAAAATGTTTGACTTACT;RSEQ=GCATGATCAGAATGCTGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:13,73:0:2,0:23.4:1:31:1:1:0:60:42:1:0:0.2 0/1:129:2:1,1:20,107:0.0155:2,2:12.5:1:28:1:0.30015:5.25:60:4:0.0157:0:1 -X 44935874 . A AT 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19896;SOR=0;LSEQ=TAATTAGGACTTAATTCAGG;RSEQ=TTCTTTTTTTTTTTTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:0,2:137,0:0.0144:1,0:29:1:31:0:1e-04:0:60:4:0.0147:0:2 0/0:172:0:0,0:167,4:0:1,0:15:0:9:0:1:0:60:0:0:0:2 -X 44935920 . AT A 49 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08262;SOR=Inf;LSEQ=AAATAAATGTACAACTGATT;RSEQ=CCCTTTTTTTTTTTTTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:242,91:0:2,0:24.9:1:27.7:1:1:0:59.7:5.055:1:0:0.7 0/1:485:5:3,2:317,160:0.0103:2,2:26.4:1:21.2:1:1:1.31999:60:1.5:0.0073:0:1.4 -X 44935924 . CT C 240 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.08955;SOR=0.79266;LSEQ=AAATGTACAACTGATTATCC;RSEQ=TTTTTTTTTTTTCCAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:368:191:131,60:76,25:0.519:2,2:26.3:1:30.7:1:0.2789:1.39082:59.8:22.875:0.5244:0.0489:0.8 0/1:525:242:156,86:90,33:0.461:2,2:30.3:1:30.4:1:0.09944:1.50184:59.9:59.5:0.4732:0:0.7 -X 44937801 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15909;SOR=0;LSEQ=TGTCTCTTTGTTTTGCTATC;RSEQ=TTTAACTTTTCCAGCACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:28,145:0.0114:2,2:17:1:33.5:1:0.30476:5.11:60:4:0.0115:0:1 0/0:263:0:0,0:62,200:0:2,0:21.4:1:29.8:1:1:0:60:261:1:0:0.1 -X 44937821 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08564;SOR=0;LSEQ=TTTTAACTTTTCCAGCACTG;RSEQ=CAGATACTTTTCTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:1,2:9,123:0.0222:2,2:12:1:24:1:0.2076:6.64:60:2:0.0154:0:1 0/0:170:0:0,0:14,156:0:2,0:21.1:1:31.1:1:1:0:60:23.286:1:0:0.1 -X 44937849 . C CT 70 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.21007;SOR=5.15032;LSEQ=TTTTCTTTTTTTTCTTTTTT;RSEQ=TTTTTTTTTCTTTTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:0,1:5,75:0.0123:2,0:32:0:32:0:1:0:60:2:0.0125:0:0 0/1:82:5:0,5:0,77:0.061:1,0:33.2:1:30.3:1:1:0:60:10:0.0625:0.0122:0 -X 44938316 . TA T 123 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.21301;SOR=1.88227;LSEQ=AATGCTTTACCTTCTTCCTT;RSEQ=AAAAAAAAAAGCACTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:8:6,2:80,6:0.0825:2,2:28.5:1:30.4:1:0.13717:4.33231:57.5:16:0.0825:0:0.5 0/1:131:19:17,2:100,11:0.145:2,2:23.2:1:29.1:1:1:1.06897:60:18:0.1395:0.0534:0.3 -X 44938317 . A T 45 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=1.1128;LSEQ=ATGCTTTACCTTCTTCCTTT;RSEQ=AAAAAAAAAAGCACTTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:2,0:80,6:0.0206:2,0:13.5:1:31.5:1:1:0:60:4:0.0206:0:1 0/1:131:3:2,1:100,11:0.0229:2,2:3:1:28.7:1:0.28596:4.44573:60:4:0.0231:0:1.3 -X 44938331 . C T 36 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.65506;SOR=0.4984;LSEQ=TCCTTTAAAAAAAAAAAGCA;RSEQ=TTAAAATATTATCCCAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:1,2:121,20:0.0208:2,2:13:1:23:1:0.06099:11.75054:60:2:0.0155:0:1.7 0/1:191:2:1,1:153,36:0.0105:2,2:21:1:15:0:0.35073:4.20585:60:0:0:0:2 -X 44938563 . G A 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAATTGCTAAATATGCACA;RSEQ=TACCAGGCCTCCTCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:165,245:0:2,0:26.3:1:31.9:1:1:0:60:50.25:1:0:0.1 0/1:577:88:32,56:205,284:0.1525:2,2:25.1:1:29.5:1:0.34858:1.2627:60:176:0.1536:0:1.2 -X 44941741 . G T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27679;SOR=Inf;LSEQ=ATACTATTCAATCTAGATAT;RSEQ=AACTTTTTTTCAGTTGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:125,25:0:2,0:23.3:1:32.2:1:1:0:60:74:1:0:0.1 0/1:223:3:1,2:164,56:0.0135:2,2:11.3:1:25.7:1:0.1665:5.80061:60:6:0.0136:0:1 -X 44942135 . A AT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=CTTCTGTTTCATTTATTGTC;RSEQ=TTTTTTTTAAGTTGACATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:2,103:0:1,0:25.6:1:30.9:1:1:0:60:51.5:1:0:0.1 0/1:88:2:0,2:4,82:0.0227:1,0:21.5:1:31.5:1:1:0:60:4:0.0238:0:0 -X 44942631 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51224;SOR=Inf;LSEQ=TTTTCTGATTGGAACACAAG;RSEQ=GTTTTGAAGAAATGGTAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:99,10:0:2,0:22.5:1:31.3:1:1:0:60:218:1:0:0 0/1:153:2:1,1:124,27:0.0131:2,2:9:1:28.5:1:0.33351:4.528:60:4:0.0133:0:1 -X 44942636 . TG T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51184;SOR=Inf;LSEQ=TGATTGGAACACAAGGGTTT;RSEQ=AAGAAATGGTAAACTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:107,15:0:2,0:23.3:1:31.7:1:1:0:60:39.667:1:0:0 0/1:170:2:0,2:137,31:0.0118:2,0:8.5:1:24.5:1:0.03676:0:60:4:0.012:0.0059:0.5 -X 44942641 . A T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51188;SOR=Inf;LSEQ=GGAACACAAGGGTTTTGAAG;RSEQ=AATGGTAAACTTCCACAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:112,18:0:2,0:24.1:1:30.1:1:1:0:60:129:1:0:0 0/1:181:2:1,1:141,38:0.011:2,2:13.5:1:24.5:1:0.38545:3.67592:60:4:0.0115:0:1 -X 44945086 . A AT 48 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.31427;SOR=0.23882;LSEQ=ATTGCACCACTGGAGCTCCA;RSEQ=TTTTTTTTCTTTTCACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:3,0:210,70:0.0106:2,0:26:1:30.7:1:1:0:60:6:0.0109:0:0 0/0:394:1:1,0:279,114:0.0025:2,0:28:0:32:0:1:0:60:2:0.0026:0:0 -X 44945281 . C T 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26604;SOR=Inf;LSEQ=TAGAAAGCAGTAATTGTAAA;RSEQ=GACAACTTACCAAGCTGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:14,150:0:2,0:24.1:1:30:1:1:0:60:163:1:0:0.1 0/1:224:3:1,2:30,191:0.0134:2,2:22.7:1:25.3:1:0.36176:3.16:60:6:0.0135:0:1 -X 44949209 . T C 40 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27104;SOR=Inf;LSEQ=TATGCTTTAAAAAAGTTAAT;RSEQ=TATAAAGGATTATATCCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:26,137:0:2,0:22.5:1:30.4:1:1:0:60:80.5:1:0:0.1 0/1:232:3:1,2:55,174:0.0129:2,2:31:1:25.3:1:0.56522:1.58:60:2:0.0088:0:2.3 -X 44949284 . A T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02718;SOR=Inf;LSEQ=TAAAAGTTGTAAGAAGAATG;RSEQ=CTCCTTGCATAGAATTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:1,44:0:1,0:23:1:30.4:1:1:0:60:90:1:0:0 0/1:49:6:1,5:1,42:0.1224:1,2:22:1:29.8:1:0.23214:7.76:60:12:0.1224:0:1 -X 44949951 . G GT 164 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.90043;SOR=1.03998;LSEQ=CTTTGGGTTGCTTTATAACT;RSEQ=TTTTTTTTTTTCCTAGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:30:22,8:187,51:0.1119:2,2:23.8:1:29.3:1:0.49041:1.33181:60:60:0.1186:0.0187:0.3 0/1:371:43:30,13:220,98:0.1159:2,2:28.8:1:30.3:1:1:1.03:60:86:0.1246:0:0.4 -X 44966570 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50181;SOR=Inf;LSEQ=CATTAGAATCAAGTCTCTTG;RSEQ=CATTATTTCTAGTTGGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:89,12:0:2,0:24.1:1:31:1:1:0:60:49.5:1:0:0.1 0/1:121:2:1,1:99,20:0.0165:2,2:15:1:24:1:0.31818:4.85513:60:4:0.0171:0:1 -X 44966795 . T C 207 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTGAAGTAAGTAATTGTT;RSEQ=TTATCCACAGTTGTTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:181,287:0:2,0:26.8:1:29.9:1:1:0:60:92.6:1:0:0.1 0/1:578:109:46,63:173,296:0.1886:2,2:24.7:1:30.7:1:0.32463:1.25:60:26.25:0.1845:0:1.1 -X 44966805 . GT G 199 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTAATTGTTTTTATCCACA;RSEQ=TGTTTTATAAAGCCTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:140,263:0:2,0:25.5:1:29.8:1:1:0:60:66.167:0.9975:0:0.1 0/1:490:89:33,56:134,267:0.1816:2,2:25.2:1:30.8:1:0.53739:1.17:60:178:0.1835:0.0306:1 -X 44970742 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4046;SOR=2.91282;LSEQ=CTGGTTTTTGTAGCTATCTC;RSEQ=TAAGGCTGCTGGCTGAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:1,0:47,150:0.0051:2,0:1:0:25:0:0.24242:0:60:2:0.0051:0:1 0/1:274:4:3,1:73,197:0.0146:2,2:6:1:28.5:1:0.06617:8.02:60:8:0.0149:0:1.3 -X 44970751 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20302;SOR=0;LSEQ=GTAGCTATCTCGTAAGGCTG;RSEQ=TGGCTGAAAACTGTGTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:34,140:0.0114:2,2:28:0:31.5:1:0.35909:4.07:60:4:0.0115:0:1.5 0/0:214:0:0,0:50,164:0:2,0:23.9:1:31.8:1:1:0:60:70.333:1:0:0.1 -X 47004740 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51493;SOR=Inf;LSEQ=GGGAGGGCAGCGCGCTTGGC;RSEQ=CTTCTCCCCTCCCCCCGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:100,7:0:2,0:25.9:1:29.8:1:1:0:60:106:1:0:0.1 0/1:155:2:1,1:142,11:0.0129:2,2:21.5:1:28.5:1:0.14931:12.40307:60:4:0.0131:0:1 -X 47004760 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56332;SOR=0.31836;LSEQ=GCTTCTCCCCTCCCCCCGAT;RSEQ=TGCCTCCAGTCTCGGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:133,27:0.0123:2,2:10:1:28.5:1:0.31669:4.8554:60:4:0.0124:0:1.5 0/0:253:1:0,1:205,47:0.004:2,0:1:0:24:0:0.18972:0:60:2:0.004:0:1 -X 47004789 . G T 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.42293;SOR=2.91681;LSEQ=GTCTCGGACTTGGTTGTTGC;RSEQ=CGCTCCGGCTCCGGCTGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:0,1:177,100:0.0036:2,0:1:0:25:0:0.36331:0:60:2:0.0036:0:1 0/1:481:5:1,4:298,178:0.0104:2,2:5.4:1:28:1:0.07042:6.67128:60:10:0.0105:0:1 -X 47004966 . G T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61412;SOR=2.11814;LSEQ=GGCGCGAGGGCGGACTTCGG;RSEQ=TCGGGGGAGATGCGCGGAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:1:0,1:28,145:0.0057:2,0:40:0:12:0:1:0:60:0:0:0:1 0/1:165:2:1,1:23,140:0.0121:2,2:37:1:30.5:1:0.27051:5.98:60:4:0.0122:0:1 -X 47007061 . C CCTGTGCT 63 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=2.000;MSILEN=2;SSF=0.2652;SOR=0;LSEQ=GCACCTGTTGTGAGCCAGGA;RSEQ=CTGTGCTAGGCTCTGATAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:0,4:0,14:0.2222:1,0:13.8:1:31.6:1:1:0:60:8:0.2222:0.1667:0 0/0:10:0:0,0:0,10:0:0,0:22:1:31.8:1:1:0:60:20:1:0:0.2 -X 47028893 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12725;SOR=Inf;LSEQ=CTCATCTGAGGAGCAGAGTG;RSEQ=GGAGGTGAGGAGGGGGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:98,190:0:2,0:22.9:1:30.3:1:1:0:60:95:1:0:0.1 0/1:330:4:1,3:116,209:0.0121:2,2:12.8:1:29.8:1:1:1.66271:60:8:0.0124:0:1 -X 47030378 . C T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14544;SOR=Inf;LSEQ=GCGGCCAGCTCCTAGGCCTG;RSEQ=CCAGACTGACTGCCCGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:164,78:0:2,0:26.2:1:31.7:1:1:0:60:59.5:1:0:0.2 0/1:341:4:1,3:208,129:0.0117:2,2:7.3:1:25.8:1:0.30283:4.81517:60:8:0.0119:0:1.3 -X 47030466 . AGGC A 151 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.02117;SOR=2.43202;LSEQ=CGGGCTCCGAGACTCAGCGT;RSEQ=GGCGGCGGCGGCACAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:565:9:6,3:281,275:0.0159:2,2:20.1:1:31.7:1:0.5048:1.96:60:18:0.0161:0.0035:0.4 0/1:818:31:21,10:428,358:0.0379:2,2:20.4:1:30.5:1:0.19705:1.76:60:62:0.0385:0.0098:0.3 -X 47030585 . TGAG T 113 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.08692;SOR=0.46357;LSEQ=GAGGAGGAGGAGGAGGAGGA;RSEQ=GAGGAGGAGGAGAAGGCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:14:5,9:184,226:0.033:2,2:21.9:1:29.7:1:0.59117:1.4642:60:28:0.0339:0.0094:0.4 0/1:578:9:4,5:260,308:0.0156:2,2:20.7:1:31.1:1:1:1.05511:58.3:18:0.016:0.0069:1.2 -X 47030674 . G A 58 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.13528;SOR=5.00144;LSEQ=TGACGTACGTGCCCCCCATG;RSEQ=CCCCGGGCAGGAGGCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:1:1,0:130,193:0.0031:2,0:1:0:28:0:0.40432:0:60:2:0.0032:0:1 0/1:394:6:5,1:167,221:0.0152:2,2:8.8:1:22.5:1:0.09016:6.59:60:5:0.0131:0:1 -X 47032418 . G T 45 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.36315;SOR=3.14931;LSEQ=CGAAAGAGGCGGAGGAGACT;RSEQ=TGTGCACATCACCGATGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:1,0:123,14:0.0072:2,0:4:0:31:0:1:0:60:2:0.0075:0:1 0/1:133:3:2,1:108,22:0.0226:2,2:13:1:29:1:0.43695:2.43334:60:6:0.0227:0:1 -X 47032420 . G T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11451;SOR=Inf;LSEQ=AAAGAGGCGGAGGAGACTGT;RSEQ=TGCACATCACCGATGACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:126,17:0:2,0:21.4:1:31.9:1:1:0:60:70.5:1:0:0.2 0/1:136:3:2,1:110,23:0.0221:2,2:10.7:1:28.3:1:0.44415:2.37188:60:6:0.0221:0:1.3 -X 47032432 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23172;SOR=0;LSEQ=GAGACTGTGTGCACATCACC;RSEQ=ATGACCCCTCGGGATCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:143,30:0.0114:2,2:15.5:1:28:1:0.32374:4.70556:60:4:0.0119:0:1 0/0:188:0:0,0:146,42:0:2,0:21.7:1:29.5:1:1:0:60:93:1:0:0.2 -X 47032461 . G T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0346;SOR=0;LSEQ=TCGGGATCCAGAGGCCTCCA;RSEQ=CCAGCCTCAGGTACCCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:4:2,2:190,78:0.0147:2,2:10.8:1:28.8:1:0.58353:2.42689:60:8:0.0151:0:1.3 0/0:358:0:0,0:237,121:0:2,0:23.9:1:31.6:1:1:0:60:43.75:1:0:0.2 -X 47034511 . AC A 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.71481;SOR=1.19943;LSEQ=GGTTGCTTTGCCGCACTTGA;RSEQ=CCCCCCCCAAACAAATACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:11:5,6:202,261:0.0231:2,2:27.7:1:31.1:1:1:1.08:58.2:22:0.0246:0:0.5 0/1:761:21:12,9:332,407:0.0276:2,2:24.2:1:30.1:1:0.27665:1.63:60:9.5:0.0265:0.0053:0.5 -X 47034546 . C T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.67928;SOR=0.61429;LSEQ=AATACTACTTTGTAATCGAG;RSEQ=GCTCCCCATCGCCTGATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:1,2:98,176:0.0108:2,2:12.7:1:23.3:1:1:1.11322:60:2:0.0078:0:1.7 0/0:451:3:2,1:146,299:0.0067:2,2:25.3:1:29:1:0.25479:4.08:60:6:0.007:0:3 -X 47035783 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50047;SOR=Inf;LSEQ=TCCGCTCTCCGACCTCCCTC;RSEQ=GTTCCCTGTCCCTCATCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:120,13:0:2,0:22.7:1:30.9:1:1:0:60:65.5:1:0:0.1 0/1:152:2:1,1:128,21:0.0132:2,2:17.5:1:29:1:0.27099:5.97834:60:4:0.0133:0:1 -X 47038395 . T G 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21804;SOR=0;LSEQ=GCCACCATTGCCTAGGGGCT;RSEQ=TCCTTCCTGGGGCACTGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:102,6:0.0182:2,2:7:0:33.5:1:0.12377:15.80921:60:4:0.0185:0:1 0/0:125:0:0,0:104,21:0:2,0:21.3:1:29.4:1:1:0:60:61.5:1:0:0.1 -X 47038449 . G T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13644;SOR=Inf;LSEQ=TCTCTTCATCCAAGTTTGGA;RSEQ=GGTGCAGTGGGAAATCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:199,80:0:2,0:22.9:1:31.4:1:1:0:60:138.5:1:0:0.1 0/1:362:4:2,2:235,123:0.011:2,2:25.8:1:28.5:1:0.61088:1.90698:60:8:0.0113:0:1 -X 47038767 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1679;SOR=0;LSEQ=AGGCTGGATCAGCAGACACT;RSEQ=CCACTGGGTGGCCGGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:85,94:0.011:2,2:32:1:30.5:1:1:1.11:60:4:0.011:0:1 0/0:260:0:0,0:120,140:0:2,0:23.1:1:31.2:1:1:0:60:31.5:1:0:0.2 -X 47038780 . C T 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3007;SOR=Inf;LSEQ=AGACACTGCCACTGGGTGGC;RSEQ=GGGAGCTGAGCCAGGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:67,79:0:2,0:25.5:1:30.4:1:1:0:60:145:1:0:0.1 0/1:251:3:1,2:112,136:0.012:2,2:16.3:1:29:1:1:1.64392:60:6:0.0121:0:1 -X 47039178 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24686;SOR=Inf;LSEQ=AGCGGCAGTTGCAAAGGCAC;RSEQ=GAGTGAGTGGGGGCAGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:115,5:0:1,0:22.3:1:29.7:1:1:0:60:59:1:0:0.1 0/1:119:2:1,1:109,8:0.0168:2,2:8:1:29.5:1:0.14613:12.90462:60:4:0.0168:0:1 -X 47039188 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49928;SOR=Inf;LSEQ=GCAAAGGCACGGAGTGAGTG;RSEQ=GGGCAGAGGAAAGGGAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:130,10:0:2,0:24:1:31:1:1:0:60:34:1:0:0.1 0/1:153:2:1,1:129,22:0.0131:2,2:10.5:1:26:1:0.2789:5.75698:60:4:0.0133:0:1 -X 47039479 . C A 36 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62984;SOR=2.50352;LSEQ=GGGCCGGGCAGCCAGGGTCC;RSEQ=GGCCCCCGGGGTGGAGACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:1:1,0:64,140:0.0049:2,0:1:0:25:0:0.31707:0:60:2:0.005:0:1 0/1:247:3:3,0:63,181:0.0121:2,0:8.7:1:23.3:1:0.01844:0:60:6:0.0123:0:2 -X 47039481 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2522;SOR=Inf;LSEQ=GCCGGGCAGCCAGGGTCCCG;RSEQ=CCCCCGGGGTGGAGACGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:64,134:0:2,0:22.5:1:31.4:1:1:0:60:48.5:1:0:0.1 0/1:229:3:2,1:60,166:0.0131:2,2:5.3:1:26.7:1:0.17901:5.48:60:6:0.0133:0:1.3 -X 47039558 . CG C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21103;SOR=Inf;LSEQ=TGGAAATCGGGCAATGGAGC;RSEQ=GGGGCCTCCCCGGGCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:133,50:0:2,0:23.8:1:30:1:1:0:60:60:1:0:0.1 0/1:156:2:2,0:115,39:0.0128:2,0:12.5:1:31.1:1:1:0:60:4:0.013:0.0064:0 -X 47039570 . C T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21086;SOR=Inf;LSEQ=AATGGAGCCGGGGGCCTCCC;RSEQ=GGGCCTGACCCTTCTGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:156,66:0:2,0:22.7:1:30.6:1:1:0:60:110:1:0:0.1 0/1:189:2:2,0:136,51:0.0106:2,0:12:1:32.5:1:1:0:60:4:0.0107:0:1 -X 47039579 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11017;SOR=Inf;LSEQ=GGGGGCCTCCCCGGGCCTGA;RSEQ=CCTTCTGTCCCTGCCTCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:176,64:0:2,0:23.5:1:31.5:1:1:0:60:39:1:0:0.1 0/1:222:3:1,2:164,55:0.0135:2,2:7.3:1:26.7:1:0.16265:5.90483:60:6:0.0136:0:1.3 -X 47039832 . A G 191 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCAGGGACATGGCCTCCA;RSEQ=TGAAGGCAGTCGCATCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:236,318:0:2,0:24.7:1:30.4:1:1:0:60:68.25:1:0:0.1 0/1:741:74:35,39:307,360:0.0999:2,2:22.9:1:30.9:1:0.90233:1.05:60:148:0.1007:0:1.1 -X 47039959 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4973;SOR=Inf;LSEQ=AGACCTGGGCTTTCTCAACC;RSEQ=TCCTGCACCCTCTCTGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:8,82:0:2,0:22.4:1:32.1:1:1:0:60:180:1:0:0.1 0/1:92:2:1,1:10,80:0.0217:2,2:24.5:1:26:1:0.22599:7.68:60:4:0.0217:0:1 -X 47040531 . TG T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19633;SOR=Inf;LSEQ=AGAAATACTAGCCCCACGTG;RSEQ=GGACAGATGCTTCTAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:96,19:0:2,0:20.3:1:31.5:1:1:0:59.6:37.333:1:0:0.8 0/1:92:2:1,1:70,19:0.0217:2,2:11.5:1:28.5:1:0.39316:3.6161:60:4:0.0225:0.0109:0.5 -X 47040552 . G GT 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.62187;SOR=0.49307;LSEQ=GGGACAGATGCTTCTAGCAG;RSEQ=TTCCCCACCCCCCACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:2,0:88,30:0.0167:2,0:24.5:1:28.5:1:1:0:60:4:0.0192:0:2.5 0/0:121:1:1,0:77,43:0.0083:2,0:20:0:27:0:1:0:60:2:0.0089:0:0 -X 47040634 . T C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37078;LSEQ=GCCTCCCAAGGTGGGGAGGG;RSEQ=ACCTGGGCCACCTCCGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:165:84,81:111,104:0.4342:2,2:25.4:1:31.5:1:0.91775:1.02912:60:54:0.4309:0:1.1 0/1:488:108:63,45:207,173:0.2213:2,2:28.5:1:31.1:1:0.51143:1.17:60:26:0.2176:0:1.3 -X 47041002 . C T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07596;SOR=Inf;LSEQ=TCCTGGCATCTACCAACAAT;RSEQ=AGCCGAGGCGAGCAGTAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:167,181:0:2,0:23.8:1:31.3:1:1:0:60:48.714:1:0:0.1 0/1:471:5:1,4:223,243:0.0106:2,2:14.8:1:24.6:1:0.37533:3.66187:60:10:0.0108:0:1 -X 47041119 . C T 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06903;SOR=Inf;LSEQ=GGCATGGGCAGACACTGAGC;RSEQ=CTGTTCTCCTGTCTGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:196,146:0:2,0:25.8:1:30.9:1:1:0:60:41.75:1:0:0.2 0/1:425:5:1,4:249,171:0.0118:2,2:11.4:1:23.2:1:0.16434:5.80245:60:4:0.0097:0:1.8 -X 47041731 . C T 59 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14705;SOR=Inf;LSEQ=AAGACAGCTCAACAGGTGAA;RSEQ=ACCAGGGTCCAGCAGTCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:93,186:0:2,0:25.1:1:31.7:1:1:0:60:38.857:1:0:0.2 0/1:399:4:2,2:155,240:0.01:2,2:21.8:1:29.5:1:0.6479:1.55:60:8:0.0101:0:1.3 -X 47041743 . G A 53 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15432;SOR=Inf;LSEQ=CAGGTGAACACCAGGGTCCA;RSEQ=CAGTCACTGGCTGGCTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:74,156:0:2,0:26.2:1:32:1:1:0:60:75.667:1:0:0.2 0/1:346:4:3,1:129,213:0.0116:2,2:8.8:1:26.8:1:0.15721:4.93:60:8:0.0119:0:1 -X 47041753 . G A 32 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.5742;SOR=0.35792;LSEQ=CCAGGGTCCAGCAGTCACTG;RSEQ=CTGGCTGTGTGGTGTCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:54,139:0.0102:2,2:22.5:1:32:0:0.48559:2.56:60:4:0.0104:0:1 0/0:274:1:0,1:89,184:0.0036:2,0:17:0:32:0:1:0:60:2:0.0037:0:1 -X 47044372 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.22039;SOR=Inf;LSEQ=CTGGCCCGTGTTTGAGGATG;RSEQ=AGGGCAGTGGGTCAGCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:126,26:0:2,0:23.7:1:31.8:1:1:0:60:75:1:0:0 0/1:135:2:1,1:109,24:0.0148:2,2:8.5:1:28:1:0.3372:4.47028:60:4:0.0149:0:1 -X 47044386 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49884;SOR=Inf;LSEQ=AGGATGCAGGGCAGTGGGTC;RSEQ=GCAGATAGAGTTAGTAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:140,54:0:2,0:22.8:1:29.6:1:1:0:60:37.8:1:0:0.1 0/1:200:2:1,1:138,60:0.01:2,2:11:1:28.5:1:0.51804:2.28935:60:4:0.0101:0:1 -X 47045549 . G A 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08933;SOR=0;LSEQ=GCCCAAGAGGAGGAAGTACG;RSEQ=CGGCATATCCACAGCCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:2,1:124,144:0.0111:2,2:30.7:1:30:1:0.59901:2.32:60:6:0.0113:0:1 0/0:334:0:0,0:146,188:0:2,0:19:0:16:0:1:0:60:0:0:0:1 -X 47045611 . C T 24 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0.8081;LSEQ=AGGGGGTCTGGAGCCCGGGG;RSEQ=CGGGGCCGGCAGGCCGACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:94,95:0.0105:2,2:28.5:1:30.5:1:1:1.01:60:4:0.0106:0:1 0/0:236:2:0,2:114,120:0.0085:2,0:1:0:24:1:0.49845:0:60:4:0.0086:0:1 -X 47045615 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09586;SOR=0;LSEQ=GGTCTGGAGCCCGGGGCCGG;RSEQ=GCCGGCAGGCCGACCACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:1,2:110,88:0.0149:2,2:27:1:29:1:0.5879:2.48883:60:6:0.0152:0:1 0/0:237:0:0,0:117,120:0:2,0:23.1:1:29.9:1:1:0:60:46.4:1:0:0.2 -X 47045690 . C T 64 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47708;SOR=2.28513;LSEQ=CCTACTCGGGACGGGCTGGG;RSEQ=AGTGACAACATTGGCAGTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:2:0,2:185,150:0.0059:2,0:1:0:26.5:1:0.2027:0:60:4:0.006:0:1 0/1:448:6:2,4:248,194:0.0134:2,2:12.5:1:24.8:1:0.41265:2.55143:60:12:0.0136:0:1 -X 47045752 . G A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04463;SOR=Inf;LSEQ=GAAAGAGGGCAGCGGCCTGG;RSEQ=CCGCAAGAAGCAGGGCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:218,180:0:2,0:24:1:31.4:1:1:0:60:78.6:1:0:0.2 0/1:561:6:3,3:280,275:0.0107:2,2:23.7:1:29.5:1:1:1.01815:60:12:0.0108:0:1.3 -X 47046082 . C A 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00752;SOR=Inf;LSEQ=GTTGGATGGCTGGGACGGGG;RSEQ=CTTGCTCTTGTCGGCCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:0,58:0:1,0:23.8:1:31.6:1:1:0:60:57:1:0:0 0/1:37:5:0,5:1,31:0.1351:1,0:16.6:1:31.2:1:1:0:60:10:0.1389:0:1 -X 47424615 . C T 240 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=271.39922;LSEQ=GCCCTTACAGACAGCTGACC;RSEQ=GTGTCCCCTTGCTTTATACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:1:0,1:317,312:0.0016:2,0:1:0:31:0:0.49683:0:60:2:0.0016:0:1 0/1:825:248:136,112:308,268:0.3006:2,2:24.5:1:30.2:1:0.76067:1.06:60:61:0.2994:0:1.2 -X 47425058 . G A 94 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAATAATCAATTTTTTT;RSEQ=TTATTAATTATAAATATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:0,1:0.8889:0,0:28.3:1:31.5:1:1:0:60:16:0.8889:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 47426008 . G T 61 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24894;SOR=4.45112;LSEQ=TCTCGGTTCTCTGATTCCTG;RSEQ=CAGTGATTTCACAGCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:1:0,1:255,132:0.0026:2,0:7:0:14:0:0.34278:0:60:0:0:0:4 0/1:527:6:2,4:324,197:0.0114:2,2:7.5:1:23.7:1:0.20822:3.28169:60:5:0.0096:0:1.2 -X 47426848 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27714;SOR=Inf;LSEQ=TCAGGTGAGGTGGCATGTGT;RSEQ=CGTGGATGGGGGTGGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:53,149:0:2,0:25.2:1:31.9:1:1:0:60:100:1:0:0.2 0/1:300:3:1,2:96,201:0.01:2,2:32:1:29.3:1:1:1.05:60:6:0.0101:0:1 -X 47426857 . G T 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.65288;SOR=0.6624;LSEQ=GTGGCATGTGTGCGTGGATG;RSEQ=GGGTGGCAGGCCCGGCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:43,137:0.011:2,2:24.5:1:29:1:0.42608:3.16:60:4:0.0111:0:1 0/0:274:2:1,1:87,185:0.0073:2,2:41.5:1:29.5:1:0.53999:2.12:60:4:0.0075:0:1 -X 47428044 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18844;SOR=0;LSEQ=AGGAAGGTAAAGAACAGTGC;RSEQ=ACTCCTGATGCTCGGTAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:148,30:0.0111:2,2:23:1:29:1:0.31558:4.86957:60:4:0.0114:0:1 0/0:234:0:0,0:188,45:0:2,0:21.6:1:30:1:1:0:60:32.286:1:0:0.1 -X 47428570 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21994;SOR=Inf;LSEQ=GGTGGCAGAGCTGTGGCCAG;RSEQ=CAGGGGGCTTTAATGGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:3,104:0:1,0:24.9:1:31.6:1:1:0:60:106:1:0:0.1 0/1:95:2:1,1:5,88:0.0211:2,2:42:1:30.5:1:0.12296:16.16:60:4:0.0213:0:1 -X 47428842 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49878;SOR=Inf;LSEQ=GGGCTCCTGGTCAGGATCAG;RSEQ=GGGATGAGTGGTATAGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:138,8:0:2,0:25.9:1:29.8:1:1:0:60:28.2:1:0:0.1 0/1:155:2:1,1:137,16:0.0129:2,2:16.5:1:30:1:0.20796:8.33596:60:4:0.0132:0:1 -X 47428883 . C T 58 Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95948;LSEQ=ACCAATGGGAACCTCCCAGG;RSEQ=AGGGTGAGAGGCATGGCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:4:0,4:219,98:0.0125:2,0:1:0:24.3:1:0.00979:0:60:8:0.0127:0:1 0/1:418:5:0,5:267,146:0.012:2,0:9.6:1:25:1:0.00589:0:60:10:0.0121:0:1 -X 47430163 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49888;SOR=Inf;LSEQ=ATCCTCTGGGCCTTGATACT;RSEQ=ACAGTACCCCAGCTCGCTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:142,2:0:1,0:25.4:1:32.3:1:1:0:60:47:1:0:0.8 0/1:154:2:1,1:151,1:0.013:1,2:25.5:1:27.5:1:0.02589:107.40534:60:4:0.0131:0:1 -X 47430165 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27802;LSEQ=CCTCTGGGCCTTGATACTGA;RSEQ=AGTACCCCAGCTCGCTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:149:117:114,3:32,0:0.7852:1,1:25:1:30.6:1:1:0:60:22.4:0.7887:0:1.1 1/0:165:83:83,0:79,3:0.503:1,1:22.2:1:30.1:1:0.12047:0:60:82:0.5:0:1.1 -X 47430209 . A T 51 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20565;SOR=0.23547;LSEQ=AACCTTCCAAGTCCCTCAAT;RSEQ=CAAAATTCCTTGGGCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:4:1,3:277,117:0.0101:2,2:7.3:1:25.5:1:0.08379:7.06371:60:3:0.0077:0:2.5 0/0:420:1:0,1:291,128:0.0024:2,0:1:0:24:0:0.30714:0:60:2:0.0024:0:1 -X 47430457 . A T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24505;LSEQ=CTTGGGTGGGTGACTCTGGG;RSEQ=TAGAGGAAGACTGAGATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:176:31,145:11,32:0.8037:2,2:23.4:1:29.9:1:0.27941:1.60406:60:87:0.8056:0:1.1 1/0:270:135:28,107:34,101:0.5:2,2:28.4:1:29.4:1:0.46957:1.28521:60:66.5:0.5038:0:1.1 -X 47430479 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50267;SOR=Inf;LSEQ=AGAGGAAGACTGAGATGGAG;RSEQ=CAGATGTGAATATGAAAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:23,132:0:2,0:21.7:1:31.5:1:1:0:60:37.75:1:0:0.8 0/1:186:2:1,1:21,162:0.0108:2,2:12:1:27.5:1:0.22427:7.56:60:4:0.011:0:2 -X 47430509 . A AGTGT 140 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=18.000;MSILEN=2;SSF=0;SOR=0.06409;LSEQ=ATATGAAAGCTCAGAGGTAT;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:24:11,13:10,53:0.2474:2,2:27.8:1:30.6:1:0.00556:4.39:60:48:0.25:0.0309:0.5 0/1:98:2:1,1:13,81:0.0204:2,2:24.5:1:29.9:1:0.27171:6.04:60:4:0.0208:0.0102:0.5 -X 47430577 . GTA G 25 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.23029;SOR=Inf;LSEQ=GGACTGTTGGGGGTGTGTGT;RSEQ=TGTGTGTTTCGCCATGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:82,15:0:2,0:21.7:1:29.2:1:1:0:59.6:47.5:1:0:1.5 0/1:90:2:2,0:71,17:0.0222:2,0:31.5:1:25.5:1:1:0:45:4:0.0227:0.0111:3 -X 47430615 . TGTGTGTGT GGG 190 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=30;MSI=18.000;MSILEN=2;SSF=0.20131;SOR=0.7304;LSEQ=CATGAGGCTGGGACTGTTGG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:64:61,3:32,3:0.4156:2,1:26.8:1:31.8:1:0.66262:1.89:59.8:128:0.4267:0.0779:0.1 0/1:161:55:47,8:57,10:0.3416:2,2:20.4:1:30.3:1:1:1.03:60:110:0.3503:0.118:0.1 -X 47430623 . T G 135 MSI6;DIFF0.2 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=2;SSF=0.01811;SOR=0.42017;LSEQ=GACTGTTGGGTGTGTGTGTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:23:17,6:42,4:0.3286:2,2:7.7:1:29.9:1:0.07298:3.62708:58.9:22:0.3333:0:2 0/1:106:18:14,4:69,19:0.1698:2,2:11.2:1:28.3:1:1:1.03723:58.4:8:0.1569:0:2.4 -X 47430670 . TG T 229 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCCATGAGGCTGGGGCTGT;RSEQ=GGATGCCCACAGGGCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:248,118:0:2,0:23:1:31:1:1:0:59.9:35.6:1:0:0.5 0/1:427:186:115,71:144,96:0.4356:2,2:26.2:1:30.4:1:0.76416:1.08:59.8:45.5:0.4417:0.0515:0.7 -X 47443791 . T A 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22581;SOR=Inf;LSEQ=GGGGTTCTTGCTAAACTGAC;RSEQ=TAGCAAGGCTCTCGGCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:22.2:1:30.8:1:1:0:60:32:1:0:0 0/1:16:3:2,1:10,3:0.1875:2,2:19:1:30.3:1:1:1.60994:60:6:0.1875:0:1.3 -X 48649423 . A G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24739;SOR=0;LSEQ=TGGAGTGGGAGGAGGGGGAA;RSEQ=GGAGGAAGAGGAGCAGGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:133,8:0.014:2,2:24.5:1:30.5:1:0.12233:15.72782:60:4:0.0144:0:4 0/0:144:0:0,0:130,13:0:2,0:26.1:1:29.4:1:1:0:60:19.429:1:0:1.9 -X 48649425 . GA AG 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24384;SOR=0;LSEQ=GAGTGGGAGGAGGGGGAAAG;RSEQ=GGAAGAGGAGCAGGTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:130,8:0.0143:2,2:24.5:1:28.8:1:0.12487:15.37797:60:4:0.0146:0:3 0/0:143:0:0,0:129,14:0:2,0:26.8:1:31:1:1:0:60:34.75:1:0:1.9 -X 48649426 . A AG 235 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11323;SOR=Inf;LSEQ=AGTGGGAGGAGGGGGAAAGG;RSEQ=GGAAGAGGAGCAGGTGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:180:177:154,23:1,0:0.9833:0,2:23.5:1:31.5:1:1:0:60:176:1:0.2667:2 1/1:191:191:160,31:0,0:1:0,2:21.8:1:31.1:1:1:0:59.9:62.667:1:0.2565:2 -X 48649449 . T G 257 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.13628;LSEQ=AAGAGGAGCAGGTGAAAGGA;RSEQ=GTGGGGTGGAAGGATTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:272:271:206,65:0,1:0.9963:0,2:23.1:1:31.8:1:0.24265:0:60:134.5:0.9963:0:2.1 1/1:309:308:218,90:0,0:0.9968:0,2:22.4:1:31.1:1:1:0:60:307:1:0:2.1 -X 48649456 . T G 254 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77837;SOR=0.8129;LSEQ=GCAGGTGAAAGGATGTGGGG;RSEQ=GGAAGGATTTCTGTGTCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:305:216,89:0,1:0.9839:0,2:23:1:30.9:1:0.29412:0:60:75.25:0.9869:0:2 1/1:354:347:239,108:0,2:0.9802:0,2:23.2:1:30.2:1:0.09872:0:60:56.833:0.9855:0:2 -X 48652569 . T A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.29512;SOR=Inf;LSEQ=TGGTGGCTCCGCTCAGCTCA;RSEQ=GAGGGCACAGAGCATGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:16,94:0:2,0:26.2:1:30.2:1:1:0:60:109:1:0:0.1 0/1:184:3:2,1:49,132:0.0163:2,2:6.7:1:24:1:0.18641:5.33:60:2:0.0114:0:3.3 -X 48652595 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51576;SOR=Inf;LSEQ=CACAGAGCATGGCCTCCAGA;RSEQ=GAGGGGTGGTGTCCTTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:6,70:0:2,0:24.3:1:30.9:1:1:0:60:24.333:1:0:0.1 0/1:112:2:1,1:22,88:0.0179:2,2:17.5:1:28:1:0.37001:3.93:60:4:0.018:0:1 -X 48652792 . G A 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATGCCTGTGGCTCTCTGAT;RSEQ=ACAGTGCATGGCTGCAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:24:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 48687685 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.501;SOR=Inf;LSEQ=TGTGGTGGTGGGCGCCAGTG;RSEQ=CGTGGGCAAGAGTGCGCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:54,40:0:2,0:24.3:1:31.2:1:1:0:60:93:1:0:0.1 0/1:111:2:1,1:63,46:0.018:2,2:34.5:1:30:1:1:1.36561:60:4:0.0187:0:1.5 -X 48891721 . C T 67 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40863;SOR=3.61213;LSEQ=AGTGATGGCTGGTGTGGCCA;RSEQ=GCCTTGACTACTGTACACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:161,67:0.0044:2,0:5:0:27:0:1:0:60:2:0.0045:0:1 0/1:320:5:2,3:208,107:0.0156:2,2:19.6:1:29.2:1:0.34375:2.90535:60:10:0.016:0:1 -X 48892463 . G A 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24169;SOR=3.85464;LSEQ=ATTAGCACTGCTTTATGTCA;RSEQ=CCTAGTTTTTTTTTTTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:1:1,0:122,220:0.0029:2,0:1:0:26:0:0.3586:0:60:2:0.0032:0:1 0/1:448:5:4,1:154,285:0.0112:2,2:9.4:1:23:1:0.05632:7.37:60:4:0.01:0:2.4 -X 48892482 . C T 52 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0668;SOR=Inf;LSEQ=AGCCTAGTTTTTTTTTTTTT;RSEQ=CTCTCCTTCACACTTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:82,197:0:2,0:21.8:1:30.5:1:1:0:59.7:20.462:1:0:0.8 0/1:338:5:3,2:102,230:0.0148:2,2:9.2:1:22.4:1:0.17716:3.37:60:1.5:0.0093:0:2.2 -X 48892694 . A G 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAACAAAAAAAATTAGCC;RSEQ=AGCATGGTGGCCTGCACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:29.6:1:30.4:1:1:0:60:7:1:0:1 1/1:3:3:0,3:0,0:1:0,0:29:1:31.7:1:1:0:60:6:1:0:1 -X 48893174 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26364;SOR=Inf;LSEQ=ATCTCCTGACCTTGTGATCT;RSEQ=CCCGCCTCAGCCTCCCAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:134,7:0:1,0:25.4:1:31.9:1:1:0:59.1:46:1:0:0.1 0/1:189:3:2,1:174,10:0.0159:2,2:6.3:1:27.3:1:0.16714:8.4634:60:6:0.0164:0:1 -X 48894095 . C T 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCAGCACTTTGGGAGGC;RSEQ=GAGGCAGGCAGATCACAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:0.2857:0,0:30:1:33:0:1:0:57:4:0.3333:0:1 0/0:1:0:0,0:1,0:0:0,0:44:0:32:0:1:0:60:2:1:0:0 -X 48894299 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50335;SOR=Inf;LSEQ=ATAGCACCATTGCGCTCCAG;RSEQ=CTGGGTGACAGAGCAAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:105,8:0:2,0:23.2:1:31.5:1:1:0:59.8:36.667:1:0:0.1 0/1:139:2:2,0:128,9:0.0144:2,0:17.5:1:28:0:1:0:60:4:0.0149:0:1 -X 48894610 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24501;SOR=Inf;LSEQ=AGGCCAAGGCAGGTGGATCA;RSEQ=TTGAAGTCAGGAGTTCAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:7,119:0:2,0:28.2:1:32.6:1:1:0:59.6:125:1:0:0.1 0/1:124:2:1,1:13,109:0.0161:2,2:14:1:30.5:1:0.21387:8.12:60:4:0.0161:0:1.5 -X 48894615 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21861;SOR=Inf;LSEQ=AAGGCAGGTGGATCACTTGA;RSEQ=GTCAGGAGTTCAAGACCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:4,115:0:1,0:26.9:1:31.6:1:1:0:59.6:58.5:1:0:0.1 0/1:105:2:0,2:8,95:0.019:2,0:13:1:32:0:1:0:60:4:0.019:0:2.5 -X 48894787 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51237;SOR=Inf;LSEQ=AGCCAAGATCGCACCGCTGC;RSEQ=CTCCAGCCAGGGTGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:74,13:0:2,0:21.2:1:30.4:1:1:0:60:42.5:1:0:0.1 0/1:123:2:1,1:113,8:0.0163:2,2:25:1:29:1:0.14154:13.376:60:4:0.0164:0:1 -X 48894826 . G GA 67 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.72871;SOR=0.69993;LSEQ=AGTGAGACTCTGTCTTAAAA;RSEQ=AAAAAAAAGGTAAAAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:4:4,0:145,57:0.0194:2,0:48.8:1:26.9:1:0.57738:0:55:3:0.0148:0.0049:0 0/1:366:5:3,2:253,107:0.0137:2,2:22:1:29.1:1:0.63724:1.5742:60:10:0.014:0.0055:0 -X 48894950 . G A 62 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16262;SOR=Inf;LSEQ=AAGATGCTCATCTCGGCCGG;RSEQ=TGTGGTGGCTCACGCCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:105,189:0:2,0:23.4:1:31.7:1:1:0:60:293:1:0:0.1 0/1:471:5:4,1:175,291:0.0106:2,2:9.8:1:26.8:1:0.07152:6.63:60:10:0.0107:0:1 -X 48894958 . G A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06181;SOR=0;LSEQ=CATCTCGGCCGGGTGTGGTG;RSEQ=CTCACGCCTGTAATCCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:2,1:78,177:0.0116:2,2:17.7:1:29.3:1:0.22786:4.51:60:6:0.0119:0:1 0/0:393:0:0,0:135,258:0:2,0:22.3:1:31.2:1:1:0:60:48.125:1:0:0.1 -X 48894992 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19674;SOR=0;LSEQ=TCCCAGTACTTTGGGAGGCC;RSEQ=AGGCAGGCAGATCACGAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:18,120:0.0143:2,2:11.5:1:27.5:1:0.25385:6.52:60:4:0.0144:0:1 0/0:175:0:0,0:29,144:0:2,0:20.3:1:30.5:1:1:0:60:172:0.9885:0:0.1 -X 48895250 . A T 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30375;SOR=0.46744;LSEQ=AAAAAAAAAAAAAGATTATC;RSEQ=TCTCTTGGTACTTCTCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:5:2,3:257,114:0.0131:2,2:9.8:1:27.8:1:0.17677:3.36901:60:4:0.014:0:1.4 0/0:648:4:0,4:396,246:0.0062:2,0:1:0:24.8:1:0.0221:0:60:8:0.0076:0:1 -X 48896013 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.22194;SOR=0;LSEQ=GAGAGGGGACAAGGCAGAAC;RSEQ=GGACTCAAAGGGGTGAATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:34,99:0.0148:2,2:20:1:29.5:1:0.45274:2.88:60:4:0.0153:0:1 0/0:151:0:0,0:40,111:0:2,0:21.6:1:30.2:1:1:0:60:302:1:0:0.1 -X 49070676 . G A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1836;SOR=Inf;LSEQ=ATAGTGAAGAGGCCAGTGAA;RSEQ=ACCATGTTGAGGATGTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:0:1,0:26.1:1:33.1:1:1:0:60:60:1:0:0.1 0/1:23:2:2,0:19,2:0.087:2,0:27:1:31.5:1:1:0:60:4:0.0952:0:1 -X 49070718 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49849;SOR=Inf;LSEQ=GCATAGTTGAAGGGAGCAGT;RSEQ=TGCTCATAGTGCTGCAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:53,12:0:2,0:21.1:1:31.3:1:1:0:60:130:1:0:0.2 0/1:74:2:1,1:60,12:0.027:2,2:28:1:27:1:0.32247:4.84379:60:4:0.0274:0:1 -X 49070759 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50811;SOR=Inf;LSEQ=AAAATCAGGTTGAGATGGAG;RSEQ=CTGAGGCAGAGATGCCGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:76,49:0:2,0:24.9:1:31.5:1:1:0:60:124:0.992:0:0.1 0/1:167:2:1,1:106,59:0.012:2,2:17.5:1:26.5:1:1:1.78986:60:4:0.012:0:1 -X 49070776 . G A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06865;SOR=0;LSEQ=GAGCCTGAGGCAGAGATGCC;RSEQ=CCACACCCAACCAAATATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:2,1:84,61:0.0203:2,2:37:1:30.7:1:1:1.45:60:6:0.0207:0:1 0/0:212:0:0,0:130,82:0:2,0:25.2:1:30:1:1:0:60:52:1:0:0.6 -X 49070813 . G A 207 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCCCTGGCCTGGGCTGAG;RSEQ=CGAGTCTGGGGACTTGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:87,84:0:2,0:25.9:1:31.3:1:1:0:60:56:1:0:0.1 1/0:265:137:68,69:66,62:0.517:2,2:26:1:29.2:1:0.80613:1.07986:60:274:0.5229:0:1.2 -X 49070891 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.27273;LSEQ=CCCATTATGGATACTGGAAA;RSEQ=TTTAGTTCTTGATTACTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:1:1,0:18,61:0.0125:2,0:1:0:27:0:0.2375:0:60:2:0.0125:0:1 0/1:126:2:1,1:34,90:0.0159:2,2:7.5:1:27.5:1:0.48:2.62:60:4:0.0163:0:3 -X 50350674 . T C 90 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGGGGTGGCAGCTCCTC;RSEQ=TCCTCCTCCTCTGCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:1:0,2:26.5:1:30:1:1:0:60:16:1:0:1.4 1/1:7:7:7,0:0,0:1:0,0:20.7:1:28.9:1:1:0:57.9:6:1:0:1.4 -X 50350728 . T TTCC 149 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=8.000;MSILEN=3;SSF=0.45299;SOR=0.40462;LSEQ=TCTTCCTCTTCTTCTTCTTC;RSEQ=TCCTCCTCCTCCTCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:30:18,12:2,0:0.9375:0,2:21.3:1:30.1:1:0.51613:0:59.7:29:0.9355:0.375:0.3 1/1:42:36:19,17:5,1:0.8571:2,2:22.8:1:28.9:1:0.21424:4.33701:59.4:35:0.8537:0.3571:0.4 -X 50350742 . CCTCCTCCTGTTGCTTC GTTGCTTCTGCTGCTGCTGT 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.50548;SOR=Inf;LSEQ=TTCTTCTTCCTCCTCCTCCT;RSEQ=TGCTGCTGCTGTTGCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:22,15:0:2,0:26.6:1:30.9:1:1:0:59.7:74:1:0:0.3 0/1:50:2:1,1:26,22:0.04:2,2:38.5:1:32.7:1:1:1.17786:60:4:0.0408:0:6 -X 50350758 . C CTGCTGCTGCTGT 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=2.000;MSILEN=1;SSF=0.75069;SOR=0.66486;LSEQ=TCCTCCTCCTCCTGTTGCTT;RSEQ=TGCTGCTGCTGTTGCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:44:23,21:3,1:0.9167:2,2:27.4:1:31:1:0.61417:2.68696:59.8:88:0.9167:0.25:0.2 1/1:58:51:26,25:4,0:0.8793:0,2:30.1:1:30.8:1:0.11744:0:59.9:50:0.9434:0.2069:0.2 -X 50648296 . A AAAATAAAT 80 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=41;MSI=12.000;MSILEN=4;SSF=0.02098;SOR=0;LSEQ=AGCGAAACTTCGTCTCAAAT;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:17.2:1:31.1:1:1:0:60:12:0.75:0.375:0.2 0/0:5:0:0,0:3,0:0:0,0:20.3:1:28.3:1:1:0:60:6:0.6:0:0 -X 50648447 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50053;SOR=Inf;LSEQ=GTCTCTATACCATGGCTCGT;RSEQ=CAAGGTGGACTGCCCGCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:77,53:0:2,0:26.3:1:28.7:1:1:0:60:260:1:0:0.2 0/1:149:2:1,1:81,66:0.0134:2,2:30.5:1:32.5:1:1:1.22557:60:4:0.014:0:1.5 -X 50648608 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50185;SOR=Inf;LSEQ=GAAATTAGACATTATCAGAA;RSEQ=TCCACTGAACTTCTGATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:94,57:0:2,0:22.9:1:32.4:1:1:0:59.1:302:1:0:0.1 0/1:178:2:1,1:109,66:0.0112:2,2:36.5:1:31:1:1:1.64658:60:4:0.0115:0:1 -X 50648628 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5789;SOR=0.37322;LSEQ=GTCCACTGAACTTCTGATTC;RSEQ=CAAACTTCCCTTCCAGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:109,66:0.0113:2,2:14.5:1:28.5:1:1:1.64658:60:4:0.0116:0:1 0/0:236:1:1,0:141,94:0.0042:2,0:14:0:27:0:1:0:60:2:0.0043:0:2 -X 50648864 . T A 39 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62881;SOR=2.50955;LSEQ=TTTCAGAATACACCATGATG;RSEQ=GAAACATTTCATTCTCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:1:1,0:31,89:0.0083:2,0:1:0:26:0:0.26446:0:60:2:0.0092:0:1 0/1:146:3:2,1:44,95:0.0205:2,2:10.3:1:25:1:0.24517:4.27:60:6:0.0244:0:1 -X 50648874 . C A 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0634;SOR=Inf;LSEQ=CACCATGATGTGAAACATTT;RSEQ=ATTCTCAAAAAAAAAAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:22,78:0:2,0:17:1:29.8:1:1:0:60:9:1:0:0.2 0/1:118:5:0,5:31,80:0.0424:2,0:30.6:1:24.4:1:0.3223:0:60:1.5:0.0316:0:2.8 -X 50648931 . A AT 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.087;LSEQ=GGTAGTTCTGAACGTTAGAT;RSEQ=TTTTTTTTTCCATGGGGTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:5,32:0.0513:2,2:16:0:31.5:1:0.28745:5.93:60:4:0.0556:0:0 0/1:36:2:0,2:1,33:0.0556:1,0:13.5:1:31.5:1:1:0:60:4:0.0556:0.0278:0.5 -X 50920174 . T C 61 d7;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.2;SOR=0;LSEQ=GCAGGTGTTCTCCCCATGTG;RSEQ=GGAGACGAGAGATCATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:1:0,2:31.3:1:30.5:1:1:0:60:8:1:0:1 0/0:1:0:0,0:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 -X 51231291 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19615;SOR=0;LSEQ=AGTTTTTGGTAGTGGTAGGG;RSEQ=TTGGAGGATGGAGGGATTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:11,5:0.1111:2,2:8.5:1:29.5:1:1:2.09766:60:4:0.1111:0:1 0/0:22:0:0,0:11,11:0:2,0:26.4:1:30:1:1:0:60:21:1:0:0.2 -X 52862090 . G A 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23682;SOR=0.34894;LSEQ=GAAACTGAAGTCTCTGGCAT;RSEQ=CATTTTCTCAGTCAGCCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:4:2,2:150,135:0.0138:2,2:20.5:1:30.3:1:1:1.1107:60:8:0.0139:0:2.3 0/0:411:2:1,1:210,199:0.0049:2,2:11:0:30:0:1:1.05516:60:4:0.0049:0:1 -X 52862973 . C T 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAAAAACCACTCAGTGCC;RSEQ=GACTGAAAAGTCCTCTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:148,190:0:2,0:26.8:1:29.9:1:1:0:60:55.333:1:0:0.5 0/1:504:28:11,17:195,279:0.0556:2,2:31.5:1:30.5:1:1:1.08001:60:56:0.0562:0:1.3 -X 52863021 . T C 231 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4441;SOR=Inf;LSEQ=ACCCTCCACTTGTCTGTGTA;RSEQ=CTTATACTTCCTGGATGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:143:142:29,113:0,0:0.993:0,2:22.1:1:31.1:1:1:0:60:70:0.9929:0:1 1/1:179:179:43,136:0,0:1:0,2:20.6:1:30.9:1:1:0:60:58.667:1:0:1.1 -X 53222043 . A AC 252 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00084;SOR=0.6086;LSEQ=GGCGGGTAGCAGGGATGGCC;RSEQ=CCCCCCTACCCGCCCACCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:391:285:99,186:52,51:0.7289:2,2:27.5:1:30.9:1:0.00655:1.91232:59.7:46.5:0.7323:0.0384:0.7 1/0:477:296:91,205:77,100:0.6205:2,2:26.9:1:30.7:1:0.00552:1.73258:59.3:41.286:0.6188:0.0168:0.7 -X 53222050 . T C 95 P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06065;SOR=2.07648;LSEQ=AGCAGGGATGGCCACCCCCC;RSEQ=ACCCGCCCACCCCCCAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:11:3,8:98,201:0.0355:2,2:9:1:25.1:1:1:1.29915:57.3:2.667:0.0299:0:1.9 0/1:366:26:15,11:100,240:0.071:2,2:8.9:1:20.4:1:0.00418:3.26:55.2:1.167:0.0432:0:2.5 -X 53222448 . TCCG T 109 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.00476;SOR=10.88424;LSEQ=CTCCCCACCCCGATCCACCT;RSEQ=CCGCCGCCGCCTCTCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:1:0,1:183,291:0.0021:2,0:33:0:32:0:1:0:60:2:0.0021:0:0 0/1:582:13:8,5:249,320:0.0223:2,2:21.4:1:29.7:1:0.26106:2.05:60:26:0.0227:0.0069:0.3 -X 53222840 . C T 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGAGGTTGCAGGAACAAG;RSEQ=GGCATTAGAGGCTGCCCTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:237,188:0:2,0:24:1:30.9:1:1:0:60:59.714:1:0:0.1 0/1:467:33:19,14:209,225:0.0707:2,2:24.1:1:30:1:0.36703:1.46:60:66:0.0717:0:1 -X 53223092 . C A 60 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11139;SOR=0.1842;LSEQ=TGAAGAACCAGGCCCTATTC;RSEQ=TCCTCCGCCAACCCCAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:5:3,2:64,207:0.0181:2,2:8:1:26.2:1:0.09411:4.82:60:4:0.0148:0:1.8 0/0:296:1:1,0:68,227:0.0034:2,0:1:0:27:0:0.23311:0:60:2:0.0034:0:1 -X 53223093 . T C 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24984;SOR=Inf;LSEQ=GAAGAACCAGGCCCTATTCC;RSEQ=CCTCCGCCAACCCCAAACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:59,203:0:2,0:22.7:1:29.9:1:1:0:60:42.667:1:0:0.1 0/1:285:3:1,2:61,220:0.0105:2,2:30.7:1:29.7:1:0.52377:1.80:60:6:0.0109:0:1 -X 53223249 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49838;SOR=Inf;LSEQ=AAATTGGAGAACAAGGGGCA;RSEQ=GGCCGAGCCTAAACTGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:120,35:0:2,0:23.3:1:31.9:1:1:0:60:154:1:0:0.1 0/1:155:2:1,1:122,31:0.0129:2,2:26:1:30.5:1:0.37134:3.88935:60:4:0.0131:0:1 -X 53223485 . C T 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13296;SOR=Inf;LSEQ=AGAGGCCAGAGCCTGCCTGG;RSEQ=GCGGCCTTGCCAGCTGATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:105,173:0:2,0:24:1:30.1:1:1:0:60:68.5:1:0:0.1 0/1:347:4:2,2:133,210:0.0115:2,2:28.8:1:30.3:1:0.644:1.58:60:8:0.0117:0:1 -X 53223548 . G A 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10411;SOR=0;LSEQ=GGCCTCGCCCTCGGGCAGCC;RSEQ=CACAGGCAGTCTCTGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:1,2:99,82:0.0163:2,2:36:1:30.7:1:0.59291:2.40335:60:6:0.0165:0:1 0/0:206:0:0,0:116,90:0:2,0:23.6:1:30.5:1:1:0:60:67.667:1:0:0.2 -X 53224020 . G T 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12223;SOR=Inf;LSEQ=TCCCAAACCAGGAGAACTGA;RSEQ=GCTCAGGGGACAAGCGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:132,70:0:2,0:25.7:1:31.6:1:1:0:60:66.333:0.995:0:0.1 0/1:201:3:2,1:136,62:0.0149:2,2:31:1:26.3:1:1:1.09626:60:2:0.0102:0:2 -X 53224036 . G T 47 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1171;SOR=0;LSEQ=CTGAGGCTCAGGGGACAAGC;RSEQ=GTCTGCTCATGGCCACCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:1,2:170,78:0.012:2,2:16.3:1:29.7:1:0.23905:4.33071:60:6:0.012:0:1 0/0:261:0:0,0:175,86:0:2,0:22.8:1:29.1:1:1:0:60:51.2:1:0:0.1 -X 53224366 . C T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00839;SOR=0;LSEQ=ATGAGCCATCTCACAGAAGC;RSEQ=AGGGCAGGCGTTAAGAGACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:6:1,5:214,142:0.0166:2,2:14.8:1:26.8:1:0.04251:7.49592:60:12:0.0169:0:1.2 0/0:438:0:0,0:270,168:0:2,0:24.8:1:30.4:1:1:0:60:61.571:1:0:0.1 -X 53224479 . C T 69 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08738;SOR=0.29731;LSEQ=GCCTTCTCCCTCCAGGAGTG;RSEQ=GCTGTCAGTACCTGTAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:596:6:3,3:326,264:0.0101:2,2:14.7:1:27:1:1:1.2344:60:5:0.0086:0:1.3 0/0:996:3:0,3:521,470:0.003:2,0:10:1:24.3:1:0.10739:0:60:2:0.002:0:1 -X 53225026 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49899;SOR=Inf;LSEQ=AACCCATCCCAGCAACCCAG;RSEQ=ACATCCCAGTGTATATGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:115,24:0:2,0:24:1:31.6:1:1:0:60:22.167:1:0:0.1 0/1:150:2:1,1:123,25:0.0133:2,2:14.5:1:27:1:0.31758:4.84411:60:4:0.0135:0:1 -X 53225058 . C T 53 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37953;SOR=3.4802;LSEQ=TATATGCCATCTCTTCCCAG;RSEQ=TGGACTGAAGGCCTGGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:0,1:181,84:0.0038:2,0:1:0:29:0:0.31955:0:60:2:0.0038:0:1 0/1:308:4:1,3:214,90:0.013:2,2:15:1:26.8:1:0.08382:7.08283:60:8:0.0131:0:1 -X 53225501 . T C 89 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCTGCTAGCAATGCCTACA;RSEQ=ATACAACCTGTATTGTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1:0,0:17.7:1:32:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 53225751 . A G 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05419;SOR=0;LSEQ=CAACAAAAGAGGGGAGAGTC;RSEQ=ATACAGTAACACAGGAGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:50,2:0,0:1:0,1:24.8:1:30.3:1:1:0:60:104:1:0:1 1/1:50:46:46,0:3,0:0.92:0,1:24.3:1:30.5:1:1:0:60:92:0.9388:0:1 -X 53225847 . G T 48 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.65304;SOR=2.73886;LSEQ=TTTGGAATAGGGCAGGGAAG;RSEQ=GAAGCAGCAGCTGGACCTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:1:0,1:170,70:0.0041:2,0:46:0:14:0:0.29461:0:60:0:0:0:4 0/1:354:4:1,3:228,122:0.0113:2,2:23.8:1:24.3:1:0.12818:5.57856:60:3:0.0087:0:1 -X 53225904 . C T 78 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53248;SOR=1.70725;LSEQ=GGTGGGCTTTCTCCTCCCAG;RSEQ=GTTCAGCAATGGTCAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:3:0,3:273,205:0.0062:2,0:2.3:1:23:1:0.0802:0:60:2:0.0042:0:1.3 0/1:660:7:1,6:349,302:0.0106:2,2:7.6:1:28.1:1:0.05496:6.91677:60:14:0.0107:0:1 -X 53226091 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30441;SOR=2.50056;LSEQ=TTCCACCTGCCGCTGGAGCT;RSEQ=CTGGGCCTCAGGCACCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:2:0,2:226,272:0.004:2,0:20.5:1:32:0:0.50362:0:60:4:0.004:0:1 0/1:603:6:5,1:279,318:0.01:2,2:12:1:27:1:0.10484:5.68:60:12:0.0101:0:1.2 -X 53226311 . T C 209 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=ATGGAACCTTGTCCCACCTA;RSEQ=CTTCTTACCCTCCAAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:104:104:17,87:0,0:1:0,2:20.8:1:31.3:1:1:0:60:103:1:0:1 1/1:108:94:13,81:4,9:0.8704:2,2:21.4:1:30.9:1:0.21583:2.7358:60:188:0.8704:0:1.1 -X 53227343 . A G 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGGATCAGGTCTATAC;RSEQ=TCTTTGTCCTGTTCTTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:3,5:0,0:1:0,2:20.4:1:31.4:1:1:0:60:16:1:0:1 1/1:3:3:1,2:0,0:1:0,2:30.7:1:30.3:1:1:0:60:6:1:0:1 -X 53227592 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4986;SOR=0;LSEQ=TTCTGCCAAATGGTATTCAC;RSEQ=GTCTACCCCTTGCAGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:149,28:0.0112:2,2:25.5:1:29:1:0.29854:5.24651:60:4:0.0113:0:1 0/0:179:0:0,0:147,31:0:2,0:20:1:30.3:1:1:0:60:177:0.9944:0:0 -X 53228148 . C A 247 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.11589;LSEQ=CCCCACTTCCTCCAGAAAGG;RSEQ=CCATGCTCACCGCAGGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:321:318:165,153:0,0:0.9907:0,2:24.7:1:29.9:1:1:0:60:62.6:0.9968:0:1.1 1/1:411:380:214,166:15,16:0.9246:2,2:22.4:1:28.9:1:0.45356:1.37:60:62.333:0.9235:0:1.2 -X 53230934 . C A 42 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3214;SOR=0.25349;LSEQ=GCCCAGCAGGCAACTGTGGG;RSEQ=AGGTTCAAGGTTGAGTGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:3,0:123,135:0.0115:2,0:6.3:1:27:1:0.11112:0:60:6:0.0118:0:1 0/0:341:1:1,0:155,185:0.0029:2,0:1:0:26:0:0.45748:0:60:2:0.003:0:1 -X 53231196 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18341;SOR=0;LSEQ=TGGCTGTTGAGATAGAGATT;RSEQ=TCCTGTATACAGACCTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:47,150:0.0101:2,2:33:1:31.5:1:0.42516:3.17:60:4:0.0101:0:1 0/0:265:0:0,0:66,198:0:2,0:22.1:1:29.7:1:1:0:60:43:0.9961:0:0.1 -X 53239607 . G T 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04612;SOR=Inf;LSEQ=GGTACTCACTGGCACACCAT;RSEQ=GGACATGAGGGTGTTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:279,175:0:2,0:25.9:1:31.3:1:1:0:60:40.273:1:0:0.1 0/1:678:7:2,5:385,286:0.0103:2,2:13.9:1:25.4:1:0.14537:3.35954:60:6:0.009:0:1 -X 53241443 . T C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGACTTTAATATGCTATCC;RSEQ=GTGTTCTTCTGCCACCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:36.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 53243777 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.20059;SOR=0;LSEQ=CACAGAGACCCAAAACCTAA;RSEQ=ACTATGGCTGAGCTAAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:123,28:0.0131:2,2:22:1:27:1:0.34417:4.33397:60:4:0.0132:0:1 0/0:188:0:0,0:166,22:0:2,0:21.4:1:31.6:1:1:0:60:93:1:0:0.1 -X 53244906 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04948;SOR=0;LSEQ=GGTTAATGCGAACTGGTCCA;RSEQ=TGCCATGCAGGGGAATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:4:2,2:229,72:0.0131:2,2:10.5:1:24:1:0.24858:3.16571:60:3:0.0099:0:2.5 0/0:340:0:0,0:243,97:0:2,0:21.2:1:31.2:1:1:0:60:55.667:1:0:0.1 -X 53244924 . C T 74 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13069;SOR=5.22114;LSEQ=CAGTGCCATGCAGGGGAATG;RSEQ=TTATTGAAGGGACAAGAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:1:0,1:292,135:0.0023:2,0:1:0:26:0:0.31776:0:60:2:0.0023:0:1 0/1:496:6:2,4:321,169:0.0121:2,2:18.7:1:28.8:1:0.18977:3.78755:60:12:0.0122:0:1.3 -X 53246252 . C T 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50866;SOR=Inf;LSEQ=GGATAATGGAACAGGGAACA;RSEQ=AGCCTTAGCCAGAAGGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:126,22:0:2,0:22.5:1:31.8:1:1:0:60:296:1:0:0.1 0/1:197:2:1,1:158,37:0.0102:2,2:6:0:28:1:0.34937:4.22702:60:4:0.0103:0:1 -X 53246260 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18015;SOR=0;LSEQ=GAACAGGGAACACAGCCTTA;RSEQ=CCAGAAGGAAGGAGAGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:130,30:0.0123:2,2:25:1:30:1:0.34706:4.27924:60:4:0.0126:0:1.5 0/0:219:0:0,0:170,49:0:2,0:22.6:1:31.6:1:1:0:60:42.8:1:0:0.2 -X 53246268 . G T 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14052;SOR=Inf;LSEQ=AACACAGCCTTAGCCAGAAG;RSEQ=AAGGAGAGGACTCCCTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:144,47:0:2,0:23:1:30.8:1:1:0:60:94.5:1:0:0.1 0/1:259:4:1,3:192,63:0.0154:2,2:11.3:1:24:1:0.05215:9.04679:60:8:0.0157:0:1 -X 53246599 . C G 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=0;LSEQ=ACAGCCCCTGTTCCACTGGT;RSEQ=TTTAGCACTGACACCAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:13:0,13:3,31:0.2766:2,1:16.5:1:32.5:1:0.55023:0:60:26:0.2826:0:1 0/0:41:0:0,0:0,41:0:1,0:22.1:1:32.6:1:1:0:60:82:1:0:0 -X 53247209 . G A 30 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5978;SOR=0.42807;LSEQ=TATTTATATGTGAGGGAGTA;RSEQ=GCCTGTAGAAAGGGCAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:32,132:0.012:2,2:5:1:30:1:0.35904:4.08:60:4:0.0122:0:1 0/0:193:1:1,0:42,150:0.0052:2,0:1:0:24:0:0.2228:0:60:2:0.0052:0:1 -X 53247366 . TA T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23527;SOR=Inf;LSEQ=GTGCCCCTTCCATTGCAGCC;RSEQ=AAGATCTAATATCCAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:162,35:0:2,0:23.7:1:28.1:1:1:0:60:97.5:0.9949:0:0.1 0/1:187:2:1,1:151,34:0.0107:2,2:9.5:1:27:1:0.34012:4.39175:60:4:0.0108:0.0053:1 -X 53247651 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23834;SOR=Inf;LSEQ=TATCTTTGGGTCCAGTCTTA;RSEQ=GGGAGAACAGAGGAATACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:14,127:0:2,0:22.8:1:31.3:1:1:0:60:140:1:0:0.1 0/1:135:2:1,1:18,115:0.0148:2,2:10.5:1:28:1:0.26258:6.25:60:4:0.015:0:1.5 -X 53249916 . G T 43 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10231;SOR=0;LSEQ=TCACAGAAGAGAGAATAAAG;RSEQ=CCTAGCTAGGTAAAGTACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:1,2:174,34:0.0142:2,2:7.7:1:27.3:1:0.07606:10.06025:60:6:0.0147:0:1 0/0:239:0:0,0:196,43:0:2,0:22.6:1:30.8:1:1:0:60:38.833:1:0:0.1 -X 53254122 . G T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17987;SOR=0;LSEQ=GAGGCTTGGACCGCCCTTAA;RSEQ=GACTCATGGCGCCGCCGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:0,2:24,124:0.0133:2,0:12:1:26:1:1:0:60:4:0.0133:0:1 0/0:203:0:0,0:48,155:0:2,0:20.9:1:30.3:1:1:0:60:66.667:1:0:0.1 -X 54976727 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23404;SOR=Inf;LSEQ=GAGCCATAGGTTAAACTCCC;RSEQ=CAGCTCCCTTACATGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,16:0:2,0:23.3:1:30.7:1:1:0:60:48:1:0:0 0/1:23:2:1,1:7,14:0.087:2,2:17.5:1:29:1:1:1.94:60:4:0.1053:0:1 -X 57960211 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1489;SOR=0;LSEQ=TACTAAAGGGGAAGGGGAGG;RSEQ=CAAAAAATAAACTTGTGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:30,15:0.0426:2,2:9:1:30:1:1:1.96856:60:4:0.0426:0:1 0/0:74:0:0,0:49,25:0:2,0:26.9:1:28.6:1:1:0:60:73:1:0:0.1 -X 57960284 . G C 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51113;SOR=Inf;LSEQ=GTTAGTAGCCACTGAGGTAC;RSEQ=CAATTCATTTCTGCAATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:39,39:0:2,0:25:1:30.4:1:1:0:60:38:1:0:0.1 0/1:109:2:1,1:55,52:0.0183:2,2:14.5:1:26:1:1:1.05717:60:4:0.0185:0:1.5 -X 57960356 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51129;SOR=Inf;LSEQ=TAGACATCTTTTTCTCGGTT;RSEQ=ACGCCAGGTCTTGCAAGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:46,37:0:2,0:25.6:1:31.4:1:1:0:60:82:1:0:0.1 0/1:116:2:1,1:66,48:0.0172:2,2:33:1:28:1:1:1.37115:60:4:0.0174:0:2 -X 57960389 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52067;SOR=Inf;LSEQ=GCAAGTATCCCAAGGCCTTG;RSEQ=TTAGGATCACTACCGTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:57,48:0:2,0:25.5:1:31.9:1:1:0:60:104:0.9905:0:0.2 0/1:163:2:1,1:87,74:0.0123:2,2:24.5:1:30.5:1:1:1.1745:60:4:0.0124:0:2 -X 57960431 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13618;SOR=0;LSEQ=CCTTAGAGCAGCTGGCCAAG;RSEQ=TGGGTACCTGGTCCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:41,54:0.0206:2,2:26:1:29:1:1:1.31:60:4:0.0208:0:1 0/0:165:0:0,0:74,91:0:2,0:25.7:1:30.5:1:1:0:60:54:1:0:0.1 -X 57960449 . A G 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53114;SOR=Inf;LSEQ=AGGTGGGTACCTGGTCCCTC;RSEQ=GGGCCAAGAACTGAGAACGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:33,49:0:2,0:24.2:1:30.7:1:1:0:60:164:1:0:0.2 0/1:139:2:1,1:57,80:0.0144:2,2:26.5:1:26.5:1:1:1.40:60:4:0.0148:0:1.5 -X 57960605 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5068;SOR=Inf;LSEQ=CAATCCCCTCATCCTCCTCA;RSEQ=CTTCCGTTTCCCCTGGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:61,32:0:2,0:23.1:1:30.6:1:1:0:60:92:1:0:0.2 0/1:122:2:1,1:70,50:0.0164:2,2:36.5:1:27:1:1:1.39605:60:4:0.0165:0:2.5 -X 57960627 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18164;SOR=0;LSEQ=TTCCGTTTCCCCTGGAGCAT;RSEQ=TCCCTCCAGAACCTCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:0,2:60,40:0.0194:2,0:14:1:29.5:1:0.16715:0:60:4:0.02:0:1 0/0:138:0:0,0:74,63:0:2,0:28.2:1:31.3:1:1:0:60:67.5:1:0:0.2 -X 57960679 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.5118;SOR=Inf;LSEQ=TCTGGAGCCTCTTCTTGGGA;RSEQ=CAGCTTTCTGGAGAAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:43,60:0:2,0:25.5:1:32:1:1:0:60:50.5:1:0:0.1 0/1:144:2:1,1:68,74:0.0139:2,2:9.5:1:26.5:1:1:1.09:60:4:0.0142:0:1.5 -X 57960680 . C T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51282;SOR=Inf;LSEQ=CTGGAGCCTCTTCTTGGGAG;RSEQ=AGCTTTCTGGAGAAATATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:42,59:0:2,0:25.8:1:32.2:1:1:0:60:202:1:0:0.1 0/1:143:2:1,1:67,74:0.014:2,2:28:0:31:1:1:1.10:60:4:0.0143:0:1.5 -X 57960717 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20292;SOR=0;LSEQ=ATGGGCAGCGCAGTTGTGTT;RSEQ=TTGCTGGTGGATGGAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:19,50:0.0282:2,2:40.5:1:29.5:1:0.48692:2.59:60:4:0.0282:0:1 0/0:86:0:0,0:29,57:0:2,0:25.3:1:30.8:1:1:0:60:42:1:0:0.2 -X 57961120 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49901;SOR=Inf;LSEQ=CCAAGCTCTCGAGTGGCCCC;RSEQ=AGATTCCGTCTCATCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:16,30:0:2,0:27.4:1:30.4:1:1:0:60:22:1:0:0.3 0/1:55:2:1,1:20,33:0.0364:2,2:34.5:1:29:1:1:1.63:60:4:0.0385:0:1 -X 58559786 . T C 57 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGGTTTCTAAACTGCTC;RSEQ=ATCAAAAGAAAGGTTAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:10.3:1:28.8:1:1:0:39.5:8:1:0:6.5 -X 58559808 . GG CT 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAAAGAAAGGTTAAACTC;RSEQ=TGAGTTGAACGCACACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:33.3:1:30.3:1:1:0:39.5:8:1:0:5.5 -X 58559820 . G A 59 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACTCGGTGAGTTGAAC;RSEQ=CACACATCACAAAGTAGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:44.3:1:29.8:1:1:0:39.5:8:1:0:5.5 -X 58559844 . G T 63 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATCACAAAGTAGTTTCTG;RSEQ=GAATGATTCTGTCTAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:26.3:1:31.5:1:1:0:39.5:8:1:0:5.5 -X 58559863 . T G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAATGATTCTGTCTAGTT;RSEQ=TTATATGAACATATTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:7:0:33.5:1:1:1:41:4:0.5:0:6 -X 58561388 . G T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08386;SOR=0;LSEQ=TTCTGACCATGCTTCCGTTT;RSEQ=GTTTTTATATGAAGTTATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:0.125:2,2:13:0:31.5:1:1:1.30929:37:4:0.125:0:3 0/0:38:0:0,0:24,14:0:2,0:11.7:1:31.1:1:1:0:35.4:76:1:0:4.1 -X 58561396 . T G 176 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.44048;SOR=3.06575;LSEQ=ATGCTTCCGTTTGGTTTTTA;RSEQ=ATGAAGTTATTTCCTTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:8,7:1,0:0.9375:0,2:19.4:1:31.9:1:1:0:37.1:30:1:0:3.3 1/1:48:47:27,20:0,1:0.9792:0,2:16.9:1:31.7:1:0.4375:0:37.4:94:0.9792:0:4.5 -X 58561419 . C A 177 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTATTTCCTTTACTAC;RSEQ=GTAGGCCTCAAAGCAGTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:8,8:0,0:1:0,2:29.3:1:31.1:1:1:0:36.7:32:1:0:3.7 1/1:57:55:29,26:0,0:0.9649:0,2:31.2:1:30.7:1:1:0:38.1:110:0.9649:0:4.7 -X 58561423 . G C 32 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04566;SOR=0;LSEQ=TTATTTCCTTTACTACCGTA;RSEQ=GCCTCAAAGCAGTCCAAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,7:0.125:2,2:25:0:32.5:1:1:1.15:60:4:0.1333:0:3.5 0/0:57:0:0,0:30,27:0:2,0:30.9:1:31.3:1:1:0:38.6:114:1:0:4.7 -X 58561435 . G A 44 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTACCGTAGGCCTCAAAGCA;RSEQ=TCCAAATCTCCATTTGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:17:1:31.6:1:1:0:36.7:15:1:0:3.7 0/1:57:3:2,1:28,26:0.0526:2,2:13:0:28:1:1:1.84:31:6:0.0526:0:3 -X 58561448 . T A 163 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCAGTCCAAATCTCCA;RSEQ=TTGCAGATTCTACAATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:20:1:32.3:1:1:0:32.2:12:1:0:5.3 1/1:45:44:21,23:0,0:0.9778:0,2:20.9:1:30:1:1:0:39.9:88:0.9778:0:5.3 -X 58561450 . T C 158 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAGTCCAAATCTCCATT;RSEQ=GCAGATTCTACAATAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:18.7:1:31.3:1:1:0:32.2:12:1:0:5.3 1/1:41:39:19,20:0,0:0.9512:0,2:21.2:1:29.9:1:1:0:39.5:78:0.975:0:5.5 -X 58561464 . T A 127 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTTGCAGATTCTACAA;RSEQ=AAGAGTGTTTCCAATCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:29.5:1:32:0:1:0:37.5:4:1:0:8 1/1:22:22:9,13:0,0:1:0,2:16.5:1:28.5:1:1:0:35.4:21:1:0:6.9 -X 58561469 . G T 119 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGCAGATTCTACAATAAGA;RSEQ=TGTTTCCAATCTGCTCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24.5:1:31.5:1:1:0:37.5:4:1:0:8 1/1:17:17:5,12:0,0:1:0,2:15.9:1:29.2:1:1:0:36.4:34:1:0:7.4 -X 58561475 . C A 103 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTACAATAAGAGTGTTT;RSEQ=CAATCTGCTCTATCAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18.5:1:31.5:1:1:0:37.5:4:1:0:8 1/1:13:11:2,9:0,0:0.8462:0,2:12.9:1:29.9:1:1:0:34.5:22:0.8462:0:7.6 -X 58561479 . T C 108 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAATAAGAGTGTTTCCAA;RSEQ=CTGCTCTATCAATAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:14.5:1:32.5:1:1:0:37.5:4:1:0:8 1/1:11:11:2,9:0,0:1:0,2:11.9:1:31.5:1:1:0:37.1:22:1:0:7.9 -X 58561490 . A T 46 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTCCAATCTGCTCTATC;RSEQ=ATAGGAATGTTCACTTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:14:0:29:0:1:0:44:2:1:0:8 1/1:3:3:0,3:0,0:1:0,0:12:1:29.3:1:1:0:40.7:6:1:0:8 -X 58562295 . T A 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCAGTCCAAATCTCCA;RSEQ=TTGCAGATTCTACAAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29.5:1:31.5:1:1:0:40:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 58562297 . T C 31 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAGTCCAAATCTCCATT;RSEQ=GCAGATTCTACAAAAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:31.5:1:31.5:1:1:0:40:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 58562316 . G T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGCAGATTCTACAAAAAGA;RSEQ=TGTTTCCAATCTGCTCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:0:32.5:1:1:0:40:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 58562322 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTACAAAAAGAGTGTTT;RSEQ=CAATCTGCTCTATCAATAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18:0:32:0:1:0:40:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 58562326 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAAGAGTGTTTCCAA;RSEQ=CTGCTCTATCAATAGGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:14:0:33:1:1:0:40:4:1:0:6.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 61719754 . T G 119 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCCAAGCCCGCTAAATA;RSEQ=CCACTTGCACATTGTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:4:0:31:0:1:0:40:2:1:0:2 1/1:13:13:9,4:0,0:1:0,2:23.1:1:32.4:1:1:0:37:26:1:0:1.1 -X 61719765 . A G 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02372;SOR=0;LSEQ=CGCTAAATATCCACTTGCAC;RSEQ=TTGTAGAAAAAGTGTGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:13:1:29:1:1:1:40:4:0.5:0:1.5 0/0:19:0:0,0:11,8:0:2,0:21.5:1:29.6:1:1:0:36:38:1:0:0.8 -X 61720628 . A T 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCCAAATATCCACCTGC;RSEQ=GATTCTACCAAAAGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:32:0:1:0:45.5:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 61720868 . C A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTCCATGAGTTGAATGC;RSEQ=ATCCTCACAAAGTCGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:3.7:1:31.3:1:1:0:37.7:6:1:0:4.3 1/1:2:2:2,0:0,0:1:0,0:7:1:31:0:1:0:22.5:4:1:0:5.5 -X 61720872 . C A 72 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATGAGTTGAATGCCATC;RSEQ=TCACAAAGTCGTTTCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1:0,0:5.2:1:31.4:1:1:0:38.8:10:1:0:4 1/1:4:4:3,1:0,0:1:0,2:6.5:1:31.8:1:1:0:26.3:8:1:0:5 -X 61720882 . C A 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45833;SOR=0;LSEQ=GAATGCCATCCTCACAAAGT;RSEQ=GTTTCTGAGAATGCTTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:11,2:0,0:1:0,2:10.2:1:29.5:1:1:0:37.8:26:1:0:3.5 1/1:11:10:9,1:0,0:0.9091:0,2:8.2:1:30.1:1:1:0:33.5:20:1:0:3.6 -X 61720900 . T C 144 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTCGTTTCTGAGAATGCTTC;RSEQ=ATCTAGTTTTTATGTGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:18,4:0,0:1:0,2:20.1:1:31.8:1:1:0:38:44:1:0:3.6 1/1:25:24:21,3:0,0:0.96:0,2:16.9:1:31.6:1:1:0:36.3:48:0.96:0:3.6 -X 61720915 . T G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.89489;LSEQ=GCTTCTATCTAGTTTTTATG;RSEQ=GAAGATATTTCCTTTTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:20,8:0.0667:2,2:42:1:32:1:0.51724:2.41524:33:4:0.0667:0:4 0/1:50:3:2,1:34,13:0.06:2,2:31:1:30.7:1:1:1.30036:36.3:6:0.06:0:5 -X 61720921 . TA T 174 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.55881;LSEQ=ATCTAGTTTTTATGTGAAGA;RSEQ=TTTCCTTTTCCACCACAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:33:22,11:0,1:0.9706:0,2:28.6:1:30.7:1:0.35294:0:42.2:66:0.9706:0.1471:4.2 1/1:58:55:38,17:2,1:0.9483:2,2:24.4:1:30.2:1:1:1.12:39.8:110:0.9483:0.1379:4 -X 61720932 . C A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54393;SOR=Inf;LSEQ=ATGTGAAGATATTTCCTTTT;RSEQ=CACCACAGGCCTCAAAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:0:2,0:29.2:1:31.3:1:1:0:41.6:78:1:0:4.3 0/1:74:2:1,1:46,26:0.027:2,2:18.5:1:28:1:1:1.75484:24:4:0.027:0:6 -X 61720935 . C T 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28342;SOR=0.26594;LSEQ=TGAAGATATTTCCTTTTCCA;RSEQ=CACAGGCCTCAAAGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:24,15:0.0465:2,2:19.5:1:29.5:1:1:1.58108:44.5:4:0.0465:0:4.5 0/1:79:1:1,0:46,29:0.0127:2,0:13:0:32:0:1:0:40:2:0.0128:0:6 -X 61720936 . C A 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54152;SOR=Inf;LSEQ=GAAGATATTTCCTTTTCCAC;RSEQ=ACAGGCCTCAAAGCCCTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:26,17:0:2,0:27.8:1:30.9:1:1:0:41.4:42:1:0:4.5 0/1:80:2:1,1:48,30:0.025:2,2:29.5:1:30.5:1:1:1.59024:51.5:4:0.025:0:6 -X 61720961 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1111;SOR=0;LSEQ=GCCTCAAAGCCCTCCAAATG;RSEQ=CCACTTGCAGATTCTCGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:26,20:0.0417:2,2:23.5:1:29:1:1:1.29283:40:4:0.0417:0:6 0/0:95:0:0,0:54,41:0:2,0:30.8:1:29:1:1:0:41.9:94:1:0:4.7 -X 61720966 . T A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGCCCTCCAAATGTCCAC;RSEQ=TGCAGATTCTCGAAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:25,20:0:2,0:27.9:1:30:1:1:0:40.9:44:1:0:4.4 0/1:92:2:1,1:51,39:0.0217:2,2:18.5:1:28.5:1:1:1.30383:43.5:4:0.0217:0:6.5 -X 61720972 . A C 41 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5536;SOR=Inf;LSEQ=CTCCAAATGTCCACTTGCAG;RSEQ=TTCTCGAAAAAGAGTGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:19,20:0:2,0:30.4:1:30.1:1:1:0:41.7:38:1:0:4.6 0/1:91:3:2,1:48,38:0.033:2,2:12.7:1:26.3:1:1:1.58:27:2:0.023:0:4 -X 61720976 . TC CA 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAATGTCCACTTGCAGATTC;RSEQ=GAAAAAGAGTGTTTCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:19,20:0:2,0:28.6:1:29.6:1:1:0:41.7:78:1:0:4.6 0/1:89:2:1,1:48,39:0.0225:2,2:19:1:28:1:1:1.22788:46.5:4:0.0227:0.0112:4.5 -X 61720977 . C A 185 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24856;SOR=2.38158;LSEQ=AATGTCCACTTGCAGATTCT;RSEQ=GAAAAAGAGTGTTTCATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:35:17,18:1,1:0.8974:2,2:28.5:1:29.3:1:1:1.05721:42.1:34:0.8947:0:4.8 1/1:88:84:47,37:0,0:0.9545:0,2:30.1:1:29:1:1:0:43.3:168:0.9655:0:4.8 -X 61720981 . A T 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.64156;SOR=1.33537;LSEQ=TCCACTTGCAGATTCTCGAA;RSEQ=AAGAGTGTTTCATAGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:3,4:14,15:0.1944:2,2:26.3:1:30.1:1:1:1.23694:42.9:14:0.2059:0:5.6 0/1:86:21:11,10:35,29:0.2442:2,2:27.6:1:29:1:1:1.09598:40.4:42:0.25:0:5.8 -X 61720987 . T G 188 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0199;SOR=5.40344;LSEQ=TGCAGATTCTCGAAAAAGAG;RSEQ=GTTTCATAGCTGCTCTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:28:12,16:1,1:0.8235:2,2:23.2:1:30:1:1:1.32044:42.2:13:0.8387:0:5 1/1:80:77:40,37:0,0:0.9625:0,2:24.8:1:30:1:1:0:44.2:76:0.9744:0:5 -X 61720989 . T C 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGATTCTCGAAAAAGAGTG;RSEQ=TTCATAGCTGCTCTTTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,19:0:2,0:22.9:1:29.8:1:1:0:43:32:1:0:4.8 0/1:79:2:1,1:39,38:0.0253:2,2:33:0:31:1:1:1.02598:40:4:0.0253:0:8 -X 61720993 . AT GG 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTCGAAAAAGAGTGTTTC;RSEQ=AGCTGCTCTTTCAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:12,17:0:2,0:21.9:1:30.8:1:1:0:43.8:28:1:0:4.9 0/1:72:2:1,1:35,35:0.0278:2,2:24.5:1:28.8:1:1:1:40:4:0.0278:0:6 -X 61720994 . T G 190 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61962;SOR=1.73282;LSEQ=TCTCGAAAAAGAGTGTTTCA;RSEQ=AGCTGCTCTTTCAAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:26:10,16:1,1:0.9286:2,2:20.3:1:30.9:1:1:1.57244:43.8:12:0.9231:0:5.3 1/1:71:68:34,34:0,0:0.9577:0,2:20.5:1:31.3:1:1:0:44.5:136:0.9855:0:5.1 -X 61721004 . T G 178 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14924;SOR=3.8935;LSEQ=GAGTGTTTCATAGCTGCTCT;RSEQ=TCAAAAGGAAAGTTCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:20:6,14:1,1:0.8696:2,2:12.9:1:32.7:1:1:2.2361:45:40:0.8696:0:5.7 1/1:55:53:25,28:0,1:0.9636:0,2:14.6:1:31.1:1:1:0:44.3:106:0.9636:0:5.6 -X 61721009 . A G 172 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11429;SOR=Inf;LSEQ=TTTCATAGCTGCTCTTTCAA;RSEQ=AGGAAAGTTCAACTCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:6,16:1,1:0.9167:2,2:8.5:1:31.9:1:0.50725:2.54484:42:44:0.9167:0:5.9 1/1:46:46:21,25:0,0:1:0,2:11.4:1:31.3:1:1:0:45:92:1:0:5.7 -X 61721022 . C T 75 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=CTTTCAAAAGGAAAGTTCAA;RSEQ=TCTGGGAGTTGAATACAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:1,1:0.6667:2,2:13.3:1:30.3:1:1:2.44949:34.3:8:0.6667:0:6.8 1/0:9:6:3,3:0,0:0.6667:0,2:3:1:29.3:1:1:0:47:8:-0.0278:0:6.3 -X 61721025 . TG CT 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TCAAAAGGAAAGTTCAACTC;RSEQ=GGAGTTGAATACAAACATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:20:0:32.8:1:1:1.73:28:4:0.4:0:6 0/0:3:0:0,0:0,3:0:0,0:6.7:1:30:1:1:0:47.3:6:1:0:6 -X 61721028 . G A 48 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGAAAGTTCAACTCTGG;RSEQ=AGTTGAATACAAACATCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:21.7:1:30.3:1:1:1.7321:25.7:6:0.6:0:6.3 0/0:1:0:0,0:0,1:0:0,0:15:0:33:0:1:0:40:2:1:0:5 -X 61721032 . T G 50 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAGTTCAACTCTGGGAGT;RSEQ=GAATACAAACATCACAAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:20.3:1:31.7:1:1:1.7321:25.7:6:0.6:0:6.3 0/0:1:0:0,0:0,1:0:0,0:11:0:31:0:1:0:40:2:1:0:5 -X 61721036 . T C 50 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GTTCAACTCTGGGAGTTGAA;RSEQ=ACAAACATCACAAAGTAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:19:1:32:1:1:0:25.7:6:1:0:6.3 0/0:1:0:0,0:0,1:0:0,0:7:0:29:0:1:0:40:2:1:0:5 -X 61721163 . A G 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCAAAGAAAGATGGTTTC;RSEQ=AAACTGCTCCATCAAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:29.5:1:1:0:48:4:1:0:6 -X 61721170 . C G 33 pSTD;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GAAAGATGGTTTCAAAACTG;RSEQ=TCCATCAAAAGGATTGTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:33.5:1:1:0:41.5:4:1:0:5 0/0:6:0:0,0:3,3:0:2,0:6.7:1:33:1:1:0:49.5:12:1:0:4.5 -X 61721178 . AA GC 66 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCAAAACTGCTCCATCA;RSEQ=AGGATTGTTCAACTCTGTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:15:0:33.8:1:1:0:41.5:4:1:0:4 1/0:6:4:2,2:0,0:0.6667:0,2:18:1:33.3:1:1:0:49.3:8:0.6667:0:3.8 -X 61721191 . A C 108 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCAAAAGGATTGTTCA;RSEQ=CTCTGTGAGTTGAATGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:27:0:33.5:1:1:0:41.5:4:1:0:4 1/1:10:10:5,5:0,0:1:0,2:21.4:1:32.7:1:1:0:48.3:20:1:0:2.9 -X 61721199 . A G 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGATTGTTCAACTCTGTG;RSEQ=GTTGAATGCAGTCATCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:27:1:32:1:1:0:41.5:4:1:0:4 0/1:10:2:1,1:4,4:0.2:2,2:24.5:1:32:0:1:1:50:4:0.2222:0:4 -X 61721220 . C G 86 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGAATGCAGTCATCACAG;RSEQ=AAACTTTCTGAGAATGCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:1:31:1:1:0:41.5:4:1:0:4 1/1:7:7:3,4:0,0:1:0,2:5.6:1:30.9:1:1:0:48.6:14:1:0:3.6 -X 61722177 . TT CA 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAATGTCCACTTGTAGA;RSEQ=CTGCGAAAAGAATATTTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:35:0:33:0:1:0:55:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:29:0:32:1:1:0:53.3:6:1:0:7 -X 61722181 . G A 48 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTCCACTTGTAGATTCT;RSEQ=CGAAAAGAATATTTCAAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:38:0:30:0:1:0:55:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:32:0:30.7:1:1:0:53.3:6:1:0:7 -X 61722189 . A C 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTAGATTCTGCGAAAAG;RSEQ=ATATTTCAAAACTGCTCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:37:0:34:0:1:0:55:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:40:0:32.7:1:1:0:53.3:6:1:0:7 -X 61722192 . A G 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGATTCTGCGAAAAGAAT;RSEQ=TTTCAAAACTGCTCTATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:34:0:34:0:1:0:55:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:38.7:1:31.7:1:1:0:53.3:6:1:0:7 -X 61722198 . A G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCGAAAAGAATATTTCA;RSEQ=AACTGCTCTATGAAAAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:28:0:34:0:1:0:55:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:32.7:1:32.3:1:1:0:53.3:6:1:0:7 -X 61722203 . G A 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAGAATATTTCAAAACT;RSEQ=CTCTATGAAAAGCAATGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:23:0:30:0:1:0:55:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:27.7:1:28.7:1:1:0:53.3:6:1:0:7 -X 61722222 . T G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCTATGAAAAGCAATGT;RSEQ=AAACTCTGTGGCTCGAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:4:0:34:0:1:0:55:2:1:0:7 1/1:3:3:1,2:0,0:1:0,2:8.7:1:31:1:1:0:53.3:6:1:0:7 -X 63404910 . G T 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08361;SOR=Inf;LSEQ=CTCCACCCACCACCTCCTTG;RSEQ=TTTCTCAATTTCTCTCCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:143,14:0:2,0:23.9:1:31.2:1:1:0:60:38.25:1:0:0.1 0/1:123:3:1,2:104,16:0.0244:2,2:11.3:1:23.3:1:0.05578:12.53396:60:2:0.0167:0:1.3 -X 63404927 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09434;SOR=Inf;LSEQ=TTGGTTTCTCAATTTCTCTC;RSEQ=AAGGGCAATCCCAACAACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:171,42:0:2,0:23.5:1:30.9:1:1:0:60:41.6:1:0:0.1 0/1:179:3:2,1:136,40:0.0168:2,2:20.3:1:29:1:0.54408:1.69429:60:6:0.017:0:1 -X 63405225 . C G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15573;SOR=Inf;LSEQ=TGGGAGAGAAATAACTCTTA;RSEQ=ACCTGGGGTGATGATGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:2,77:0:1,0:24.9:1:32.1:1:1:0:60:78:1:0:0.1 0/1:52:2:0,2:1,49:0.0385:1,0:5:1:30.5:1:1:0:60:4:0.0385:0:1 -X 63409673 . A AC 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.40817;SOR=0.2798;LSEQ=GGTTTTCAAGTTAAACAACA;RSEQ=CCCCCACCCCCCCACCCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:5:5,0:216,59:0.0179:2,0:25.4:1:27.6:1:0.58758:0:60:4:0.0149:0:1.8 0/0:198:1:1,0:153,44:0.0051:2,0:14:0:28:0:1:0:60:2:0.0052:0:0 -X 63409681 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.07322;SOR=Inf;LSEQ=AGTTAAACAACAACCCCCAC;RSEQ=CCCCCACCCTTCTGCCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:230,87:0:2,0:11.1:1:28.4:1:1:0:57.9:17.647:1:0:1.2 0/1:229:3:2,1:164,61:0.0131:2,2:11.7:1:24:1:1:1.34241:60:2:0.0095:0:2 -X 63409685 . C T 38 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.31958;SOR=3.99902;LSEQ=AAACAACAACCCCCACCCCC;RSEQ=CACCCTTCTGCCCAACCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:1:0,1:235,95:0.003:2,0:1:0:25:0:0.29003:0:60:2:0.0031:0:1 0/1:250:3:1,2:174,73:0.012:2,2:20.3:1:24:1:0.21498:4.73334:60:2:0.0083:0:1 -X 63410110 . T C 188 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTGTGAGGGACGAGCTAG;RSEQ=TGAGGCCCAGATTCCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:0:0,0:378,403:0:2,0:24.7:1:29.8:1:1:0:60:194.25:0.9987:0:0.1 0/1:703:64:28,36:302,336:0.091:2,2:25.7:1:31.4:1:0.60196:1.15537:60:31:0.0895:0:1.2 -X 63412291 . C G 200 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTACCTCTCCTGCTACTAC;RSEQ=TTCTCCCCTGTTTCTGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1214:0:0,0:600,613:0:2,0:24.1:1:31.6:1:1:0:60:79.867:0.9992:0:0.1 0/1:955:98:49,49:427,430:0.1026:2,2:25:1:30.3:1:1:1.01:60:97:0.1024:0:1.2 -X 63412690 . A C 179 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGGCTTGGGCATAGAGGG;RSEQ=AACTTCTCAGCCACAGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:0:0,0:298,284:0:2,0:26.3:1:29.9:1:1:0:60:57.2:1:0:0.1 0/1:480:47:26,21:226,206:0.0979:2,2:26.7:1:32.3:1:0.75936:1.13:60:94:0.0985:0:1.3 -X 63415639 . A T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07302;SOR=Inf;LSEQ=ACAGGTCCCTGGTTCCAAAA;RSEQ=GGTTGGGAACCGCTGCCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:220,78:0:2,0:23.9:1:30:1:1:0:60:48.667:1:0:0.2 0/1:215:3:0,3:156,56:0.014:2,0:14.7:1:23.7:1:0.0199:0:60:2:0.0094:0:1.3 -X 63415940 . C T 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00136;SOR=0;LSEQ=TGCTTTCCAGAGCCTTGACG;RSEQ=CCCAGTTAGAAGACAGTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:16:0,16:1,63:0.2:1,1:27.7:1:30:1:1:0:60:15:0.1899:0:1.3 0/0:38:0:0,0:0,37:0:1,0:22.1:1:31.4:1:1:0:60:74:1:0:0.1 -X 63419338 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11108;SOR=Inf;LSEQ=GTGGCCTAACCTCTCTGACA;RSEQ=TCAAATGCCTTATCTGTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:0:1,0:22.9:1:32.4:1:1:0:60:118:1:0:0.1 0/1:30:2:1,1:27,1:0.0667:1,2:33:1:30:1:0.13103:19.44777:60:4:0.0667:0:1 -X 63425821 . G A 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGCGGAACCACTGGCTGG;RSEQ=GCTCCCCACTCCCGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:43:0,43:5,126:0.2457:1,1:25.6:1:30:1:0.33471:0:60:13.333:0.2395:0:1.2 0/0:149:0:0,0:5,142:0:1,0:23.7:1:30.4:1:1:0:60:146:0.9932:0:0.1 -X 65042284 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50723;SOR=Inf;LSEQ=TCCTGCGCCACACCCCAGCC;RSEQ=CCACGCTGCCTCCGCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:38,27:0:2,0:27.7:1:30.9:1:1:0:60:64:1:0:0.2 0/1:87:2:1,1:45,40:0.023:2,2:21:1:28:1:1:1.12347:60:4:0.0244:0:1 -X 65042289 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50953;SOR=Inf;LSEQ=CGCCACACCCCAGCCGCCAC;RSEQ=CTGCCTCCGCCTCCGGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:36,27:0:2,0:29.6:1:30.7:1:1:0:60:30.5:1:0:0.2 0/1:87:2:1,1:44,41:0.023:2,2:27:0:32:0:1:1.07227:60:4:0.0238:0:1.5 -X 65042321 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23946;SOR=Inf;LSEQ=TCCGGTGAGCTGACTTGTCT;RSEQ=CCAAGAGAACACTTATATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:28,32:0:2,0:23.4:1:30.7:1:1:0:60:14:1:0:0.2 0/1:58:2:1,1:22,34:0.0345:2,2:36:1:27:1:1:1.53:60:4:0.0357:0:1 -X 66764783 . C A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.10218;SOR=Inf;LSEQ=GCAGGGCAGATCTTGTCCAC;RSEQ=GTGTGTCTTCTTCTGCACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:49,1:0:1,0:26.3:1:31.1:1:1:0:60:49:1:0:0.1 0/1:24:2:1,1:21,1:0.0833:1,2:42:0:31:1:0.16304:15.19615:60:4:0.087:0:1.5 -X 66764892 . G T 50 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27343;SOR=0;LSEQ=CAGGTGGGCAGCTAGCTGCA;RSEQ=CGACTACCGCATCATCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:251,28:0.0106:2,2:23:1:32:1:0.27876:4.4421:60:6:0.0109:0:1 0/0:195:0:0,0:170,25:0:2,0:22.6:1:31.9:1:1:0:60:96.5:1:0:0.1 -X 66765242 . GGCA G 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.52719;SOR=1.26983;LSEQ=GCAGCAAGAGACTAGCCCCA;RSEQ=GCAGCAGCAGCAGCAGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:637:21:16,5:343,268:0.033:2,2:23.2:1:31:1:0.07594:2.50:58.6:20:0.0324:0.0094:0.6 0/1:506:21:13,8:264,219:0.0415:2,2:23.1:1:32.1:1:0.65534:1.35:59.8:42:0.0426:0.0079:0.4 -X 66765627 . G A 255 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0.66435;LSEQ=AGCAGCGGGAGAGCGAGGGA;RSEQ=GCCTCGGGGGCTCCCACTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:936:338:179,159:303,292:0.3611:2,2:24.1:1:30.4:1:0.5857:1.08:60:36.556:0.3568:0:1.1 0/1:839:229:111,118:319,291:0.2729:2,2:22.2:1:30.1:1:0.35234:1.16514:60:75.333:0.272:0:1.2 -X 66766125 . G A 36 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08322;SOR=Inf;LSEQ=GGACCGCCGCCCCCTCCGCC;RSEQ=CCTCCCCATCCCCACGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:140,171:0:2,0:25.5:1:30.6:1:1:0:60:43.429:1:0:0.2 0/1:242:3:1,2:107,132:0.0124:2,2:28.3:1:23.3:1:1:1.61811:60:2:0.0084:0:2.7 -X 66766220 . T C 42 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32365;SOR=3.88343;LSEQ=GCAGTGCCGCTATGGGGACC;RSEQ=GGCGAGCCTGCATGGCGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:1:1,0:193,187:0.0026:2,0:12:0:12:0:1:0:60:0:0:0:1 0/1:296:3:1,2:150,143:0.0101:2,2:26.7:1:26.7:1:0.61621:2.09282:60:6:0.0103:0:1 -X 66766359 . C T 142 MSI6 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=3;SSF=0;SOR=0.08815;LSEQ=GGTGGTGGTGGGGGTGGTGG;RSEQ=GGCGGCGGCGGCGGCGGCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:31:5,26:14,55:0.2981:2,2:10.4:1:28.8:1:0.78497:1.32005:60:6.75:0.2872:0:1.5 0/1:84:3:1,2:25,49:0.0357:2,2:20:1:19.3:1:1:1.02014:60:0.5:0.0141:0:2 -X 66766638 . G A 67 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0095;SOR=Inf;LSEQ=TCCAGAAATGTCGCCTTTCG;RSEQ=CCCAGGGCAGAGTCACTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:0:0,0:178,354:0:2,0:24.2:1:31.3:1:1:0:60:43.333:1:0:0.1 0/1:456:6:5,1:160,290:0.0132:2,2:5.5:1:26:1:0.02521:9.02:60:12:0.0133:0:1.5 -X 66766692 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5274;SOR=0;LSEQ=CTAGCGGCTCCTACCTGCGC;RSEQ=AACACTCAGATTGCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:7,166:0.0114:1,2:6.5:1:27.5:1:0.08959:22.25:60:4:0.0119:0:1 0/0:107:0:0,0:10,97:0:2,0:25.3:1:31.2:1:1:0:60:106:1:0:0.1 -X 66789057 . G T 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00727;SOR=0;LSEQ=GTGGGGGATTTTGTGTGTGG;RSEQ=GGGGGGTTGGGGGTTGAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:15:0,15:1,31:0.3191:1,1:23.9:1:25.9:1:1:0:60:2.75:0.2619:0:1.4 0/0:16:0:0,0:2,14:0:2,0:17.6:1:29.6:1:1:0:58.8:32:1:0:2.5 -X 66863453 . T G 136 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTGTTTGTACAGGCAAT;RSEQ=TAGGCAGTGAAGGTGGTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:2,18:0,0:1:0,2:29.4:1:31.6:1:1:0:60:40:1:0:1 1/1:2:2:0,2:0,0:1:0,0:17:1:32.5:1:1:0:60:4:1:0:1 -X 66906007 . T C 61 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.20704;SOR=0.23698;LSEQ=TCTTCCTCCTCCTTCCTCTC;RSEQ=CCCCCTTCTCCCTCATTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:4:1,3:68,208:0.0141:2,2:28.3:1:30.8:1:1:1.02:60:8:0.0145:0:1 0/0:296:1:1,0:93,201:0.0034:2,0:49:0:29:0:0.31864:0:60:2:0.0035:0:1 -X 66909171 . C G 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50476;SOR=Inf;LSEQ=AGTAGACTAGACAGATTATT;RSEQ=AGAGAGTGGAGGGCAGAAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:11,0:8,0:0.5789:0,0:24.9:1:32:1:1:0:60:22:0.6111:0:1 1/1:2:2:2,0:0,0:1:0,0:44.5:1:27.5:1:1:0:60:4:1:0:1.5 -X 66909568 . C T 62 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0133;SOR=Inf;LSEQ=ACATATTGTTAATTGCTTGA;RSEQ=GAATTTAAATCCCTTGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:3,101:0:1,0:24.6:1:30.1:1:1:0:60:103:1:0:0.1 0/1:55:4:0,4:3,48:0.0727:2,0:12.5:1:31.3:1:1:0:60:8:0.0727:0:1.5 -X 66914801 . T C 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27818;SOR=Inf;LSEQ=AGAAGTAATAGTGGTTACCA;RSEQ=TCATGTAGTTGTGAGTATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:0,14:0,7:0.6667:0,1:23:1:32.3:1:1:0:60:28:0.6667:0:1 1/1:5:5:1,4:0,0:1:0,2:10.6:1:32:1:1:0:60:10:1:0:1 -X 66931037 . A T 30 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01502;SOR=Inf;LSEQ=AGAGTTTTCCTCTGCAAGCT;RSEQ=TGAAAAATTTGGGTTTAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:32,0:0:1,0:25.9:1:28:1:1:0:60:64:1:0:0 0/1:5:2:2,0:3,0:0.4:0,0:40.5:1:30:1:1:0:60:4:0.4:0:1 -X 66931567 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15444;SOR=Inf;LSEQ=GTGGGAGCATGAGATAAGGG;RSEQ=GATCATATTTAGTGAACGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:40,194:0:2,0:21.7:1:30.7:1:1:0:60:45.8:1:0:0.1 0/1:152:2:1,1:27,123:0.0132:2,2:19.5:1:28.5:1:0.33548:4.49:60:4:0.0133:0:1 -X 66937278 . C T 58 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72849;SOR=1.49886;LSEQ=TCAGACTTAGCTCAACCCGT;RSEQ=AGTACCCAGACTGACCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:3:0,3:268,109:0.0079:2,0:1:0:24.3:1:0.02512:0:60:6:0.0081:0:1 0/1:424:5:1,4:269,150:0.0118:2,2:8.8:1:25.2:1:0.06061:7.14079:60:10:0.012:0:1 -X 66937538 . G A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50699;SOR=0;LSEQ=TGGTTGGTGGTGATGGTGAT;RSEQ=GGGTGACAGTGAAGCTTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:24,170:0.0102:2,2:15:1:27.5:1:0.2394:6.96:60:4:0.0104:0:1 0/0:151:0:0,0:21,130:0:2,0:23.1:1:30.1:1:1:0:60:36.75:1:0:0.1 -X 66937707 . A G 114 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGAACCAATCCTAGTCAT;RSEQ=TTTCTGGTCTGCTTTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:0,6:0.6471:0,0:31.7:1:33.1:1:1:0:60:22:0.6875:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 66941517 . C A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09057;SOR=Inf;LSEQ=AAAACAAACAAACAGACAAA;RSEQ=AAACAAAAAAACCTTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:106,2:0:1,0:23.5:1:31.6:1:1:0:60:53:1:0:0.5 0/1:47:2:1,1:42,2:0.0426:1,2:29:0:29:1:0.12754:17.3476:60:4:0.0426:0:1 -X 66941597 . T G 280 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12576;SOR=0;LSEQ=TTGGAAAACCTGGCGAGGGA;RSEQ=GGCAATCAGAGACATTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:485:485:356,129:0,0:1:0,2:23.4:1:31.4:1:1:0:60:79.833:1:0:1.1 1/1:267:265:210,55:1,0:0.9925:0,2:22.4:1:31.1:1:1:0:60:87.333:0.9924:0:1.1 -X 66942476 . A G 85 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31495;SOR=0;LSEQ=ACTCCTTTCAGATCGGATCC;RSEQ=GCTATCCTTTCCCCTGAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:8:8,0:28,0:0.2222:1,0:29.3:1:28.5:1:1:0:60:16:0.2286:0:1.1 0/0:7:0:0,0:7,0:0:0,0:26:1:30.7:1:1:0:60:14:1:0:0 -X 66943154 . C CTCTGTGTGTGTG 76 d7;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=25.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTCATGTGAGTTTGTCTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,0:0.8333:0,2:13:1:33:1:1:0:56:10:0.8333:0.6667:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 66943362 . A AACACACAC 132 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=14.000;MSILEN=2;SSF=0.05863;SOR=3.11043;LSEQ=CTCTCTCGCTGTCTCTCTCT;RSEQ=ACACACACACACACACACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:16,1:3,0:0.3696:0,1:28.9:1:32.3:1:1:0:60:34:0.3696:0:0.1 1/0:20:13:13,0:1,0:0.65:0,1:21.5:1:29.6:1:1:0:57.7:26:0.65:0.25:0.7 -X 66943769 . C A 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0041;SOR=0;LSEQ=AACTCTGCACTACTCCTCTG;RSEQ=AGTGCCTTGGGGAATTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:12:0,12:6,145:0.0736:1,0:24.2:1:29.3:1:1:0:60:11:0.0679:0:1.3 0/0:107:0:0,0:1,106:0:1,0:22.3:1:31.5:1:1:0:59.8:34.667:1:0:0.2 -X 69254637 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00223;SOR=0.19621;LSEQ=ACCTGTTTCCTCAATCATCA;RSEQ=ATGGGAGGCCCAAGGGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:56:49,7:5,1:0.9032:2,2:24.2:1:30.3:1:0.57987:1.39:60:55:0.9016:0:1.1 1/0:42:27:25,2:14,1:0.6429:1,2:23:1:28.6:1:1:1.11705:60:8:0.6154:0:1.2 -X 69254663 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22072;SOR=Inf;LSEQ=AGGCCCAAGGGGCACTGTGA;RSEQ=TCAGTGAGGGGAGTCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:80,21:0:2,0:23.6:1:30.2:1:1:0:60:100:1:0:0.7 0/1:90:2:1,1:72,16:0.0222:2,2:21.5:1:29.5:1:0.34382:4.39586:60:4:0.0222:0:1 -X 69254673 . G T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.22547;SOR=Inf;LSEQ=GGCACTGTGAATCAGTGAGG;RSEQ=GAGTCCAGGCCCAGGGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:92,28:0:2,0:23.7:1:30.6:1:1:0:60:23:1:0:0.6 0/1:109:2:1,1:84,23:0.0183:2,2:20:1:25:1:0.39348:3.59616:60:4:0.0187:0:1 -X 69254701 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49887;SOR=0;LSEQ=GGCCCAGGGGAGGGGTGGTG;RSEQ=AAGCTGAATAAGCTTCTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:125,71:0.0101:2,2:8:1:27.5:1:1:1.75518:60:4:0.0103:0:2 0/0:191:0:0,0:120,71:0:2,0:24.1:1:31.3:1:1:0:60:62.667:1:0:0.3 -X 69254760 . C G 213 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01604;SOR=0.64534;LSEQ=CAAGTTGTTACATGCCCTCT;RSEQ=TGGGGAATCAGTGACTTCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:102:50,52:115,122:0.3009:2,2:25.4:1:32:1:1:1.02:60:204:0.3054:0:1.1 0/1:313:68:34,34:121,124:0.2173:2,2:24:1:30.8:1:1:1.02:60:136:0.2201:0:1.1 -X 69254912 . A G 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07537;SOR=Inf;LSEQ=GCAGGGGTGGGCGGGGGAAC;RSEQ=GGGGCACGGTGAAGCTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:3,38:0:2,0:23.5:1:30.8:1:1:0:60:40:1:0:0.2 0/1:31:3:0,3:0,28:0.0968:1,0:14.3:1:23.7:1:1:0:60:2:0.069:0:1.7 -X 70338399 . A G 127 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05812;SOR=0.09823;LSEQ=CCAGGCCCCACCTCCTCTGC;RSEQ=GTCGGTATTGTCCGATGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:18,1:5,0:0.7917:0,1:20.3:1:30:1:1:0:60:38:0.9048:0:1.3 0/1:4:1:1,0:3,0:0.25:0,0:4:0:29:0:1:0:60:2:0.25:0:1 -X 70338517 . C T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07128;SOR=Inf;LSEQ=GCCGCCGTCCTCTCAACCAC;RSEQ=GCCCCCCTTTTCGGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:208,8:0:1,0:25.4:1:30.6:1:1:0:60:35:1:0:0.3 0/1:154:3:1,2:138,13:0.0195:2,2:15:1:29.3:1:0.02521:20.27672:60:6:0.02:0:1 -X 70338524 . C CT 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.18836;SOR=Inf;LSEQ=TCCTCTCAACCACCGCCCCC;RSEQ=TTTTCGGCTCCCTCTCCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:225,12:0:2,0:25.3:1:30.9:1:1:0:60:78:1:0:0.3 0/1:183:2:2,0:155,26:0.0109:2,0:13.5:1:31:1:1:0:60:4:0.0112:0.0055:0.5 -X 70339385 . G C 133 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAATCTAAGAAGGAGCAAA;RSEQ=GCCCTGGGTTGGGAAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:76,123:0:2,0:23.2:1:31.3:1:1:0:60:65.333:1:0:0.1 0/1:201:22:7,15:50,127:0.1095:2,2:24:1:30:1:0.80323:1.18:60:44:0.1111:0:1.1 -X 70339498 . C T 257 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.49013;LSEQ=GGCAGGACCACCTGTCTGCC;RSEQ=CTTCTTCCCACCCTGAGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:479:323:214,109:93,62:0.6743:2,2:23.4:1:30.9:1:0.18672:1.31:60:160.5:0.6786:0:1.1 1/0:431:217:141,76:137,74:0.5035:2,2:22.7:1:29.6:1:1:1.00:60:42.4:0.5048:0:1.1 -X 70340322 . C G 60 d7;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCTAGGAGCAGAAGGTT;RSEQ=TTTGAGTGGACAAAAGATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:29.5:1:30:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 70340738 . A G 202 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00224;SOR=0.39107;LSEQ=AAAGTGCTGGGATTACAGGC;RSEQ=TGAGCCACCGCACCCAGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:134:107:91,16:24,3:0.7985:2,2:23.1:1:30:1:0.76372:1.40322:57.6:106:0.797:0:1.1 1/0:89:54:48,6:32,3:0.6067:2,2:21.6:1:29.2:1:1:1.32915:57.6:53:0.6092:0:1.1 -X 70340742 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51643;SOR=0;LSEQ=TGCTGGGATTACAGGCATGA;RSEQ=CCACCGCACCCAGCCAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:123,21:0.0137:2,2:15:0:31.5:1:0.27955:5.74574:60:4:0.0137:0:3 0/0:99:0:0,0:84,15:0:2,0:21.6:1:31.3:1:1:0:58.6:32:1:0:0.6 -X 70341122 . T TACTTTATCTGCTTC 223 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00906;SOR=0.65706;LSEQ=GTTCTCTTCATCTTTTCATT;RSEQ=ACTTTATCTGCTTCATCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:296:162:112,50:74,57:0.5473:2,2:26.6:1:30.5:1:0.0284:1.72:59.9:324:0.5529:0.0912:0.8 0/1:348:154:97,57:104,90:0.4425:2,2:21:1:30.3:1:0.08175:1.47:59.8:308:0.4451:0.2213:0.9 -X 70341169 . A C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.42928;LSEQ=CCCCTCTTCCCTCCCCTGGT;RSEQ=CCCATAGGATGGAATGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:607:422:251,171:122,62:0.6952:2,2:26:1:31.1:1:0.12297:1.33993:59.9:210:0.6965:0:1.1 0/1:552:273:155,118:155,122:0.4946:2,2:26.9:1:30.7:1:0.86377:1.03:59.9:38:0.4908:0:1.2 -X 70341973 . C T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11021;SOR=0;LSEQ=AACTTTGGATCTGGAATCTA;RSEQ=GGGTTGGGTCTTAGAATGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:191,52:0.0122:2,2:22:1:28.7:1:0.51872:1.83124:60:6:0.0123:0:1.3 0/0:266:0:0,0:197,69:0:2,0:22.7:1:30.4:1:1:0:60:265:1:0:0.2 -X 70342029 . T C 179 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=55.54252;LSEQ=CCATGGTGAATGAGTTGGAC;RSEQ=TAGCTGTTTCTATCTGGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:1:0,1:358,212:0.0018:2,0:23:0:31:0:0.37303:0:60:2:0.0018:0:1 0/1:641:57:31,26:341,243:0.0889:2,2:27.7:1:30.7:1:0.5761:1.17665:60:114:0.09:0:1.2 -X 70342820 . A G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=8e-05;SOR=0.36905;LSEQ=AGGCATTGAAAGCAGAGCAT;RSEQ=TCTGCAGAAATGATCTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:156:106:39,67:16,34:0.6795:2,2:25.2:1:32.3:1:0.59456:1.24:60:105:0.6863:0:1.1 0/1:121:53:20,33:25,43:0.438:2,2:23.6:1:31.5:1:1:1.04:60:52:0.437:0:1.1 -X 70343621 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32569;LSEQ=CTGCCTAGACTCAGTTACCC;RSEQ=CCACTGTCATCAGAAAGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:245:177:25,152:8,60:0.7224:2,2:23.9:1:31.6:1:0.68254:1.23:60:176:0.7243:0:1.5 0/1:179:82:12,70:9,88:0.4581:2,2:21.9:1:31.7:1:0.35191:1.67:60:81:0.4602:0:1.6 -X 70343812 . T G 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCATTTTCACTGCATAAA;RSEQ=CGCAACAAAGATGTTACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:23,10:0.0571:2,2:45.5:1:32:1:0.53613:2.24016:60:4:0.0588:0:1 0/0:11:0:0,0:8,3:0:2,0:21.9:1:31:1:1:0:60:22:1:0:0 -X 70344215 . GGCA G 86 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.09373;SOR=3.90477;LSEQ=CAGAGCACAAGGAGGCTGAA;RSEQ=GCAGCAGCAGCAAGCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:2:1,1:66,247:0.0063:2,2:23:1:31:1:0.38069:3.72:60:4:0.0064:0:0 0/1:287:7:3,4:67,211:0.0244:2,2:25.6:1:30.9:1:0.36829:2.35:60:14:0.0249:0.007:0.3 -X 70344331 . G C 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.25542;SOR=0.58042;LSEQ=AGAGCCTCTTTTGCCTGGGG;RSEQ=AGGGGGGTAGTATTTTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:40:8,32:3,16:0.678:2,2:24.9:1:32.2:1:1:1.33:60:39:0.6964:0:1.1 1/0:31:17:0,17:2,12:0.5484:2,1:22.9:1:30.5:1:0.1957:0:60:16:0.5517:0:1.1 -X 70344762 . TG T 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0.95603;LSEQ=CATTATGCCTGCTTTTGGCA;RSEQ=TTTTTTTGCCCCCTCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:8:3,5:101,75:0.0165:2,2:24.1:1:31.4:1:0.29734:2.23455:60:16:0.0168:0:0.1 0/1:508:8:5,3:143,119:0.0157:2,2:29:1:30.9:1:0.73281:1.39:60:16:0.0297:0:0.3 -X 70344763 . G T 248 InGap STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTATGCCTGCTTTTGGCAT;RSEQ=TTTTTTTGCCCCCTCATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:486:294:161,133:101,75:0.6049:2,2:22.2:1:30.3:1:0.6316:1.11221:60:97:0.6113:0:1.1 0/0:508:0:0,0:143,119:0:2,0:23.3:1:31.8:1:1:0:60:261:0.9703:0:0.1 -X 70345593 . C T 122 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=23.8901;LSEQ=AGTAAGCCCCATACTGCCCT;RSEQ=CCTCCCTCTCCCTTCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:736:1:1,0:257,476:0.0014:2,0:10:0:32:0:0.3515:0:60:2:0.0014:0:2 0/1:698:22:7,15:271,402:0.0315:2,2:24.4:1:27.5:1:0.51103:1.44383:60:21:0.031:0:1.1 -X 70345683 . T G 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00433;SOR=0.46759;LSEQ=GTGGTCCTCTAAACCTTTGC;RSEQ=TCACTGTCCCCTTCCCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:88:10,78:4,40:0.6667:2,2:24.4:1:31.8:1:0.77339:1.28:60:87:0.6692:0:1.1 0/1:114:55:3,52:7,52:0.4825:2,2:25.1:1:31.5:1:0.32445:2.31681:60:110:0.4911:0:1.2 -X 70345850 . C T 45 v4;q23 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04704;SOR=Inf;LSEQ=CTAGTCAACTAGTTATCTTC;RSEQ=CTGTCTTGACTGGTCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:269,109:0:2,0:24.4:1:30.7:1:1:0:60:46.25:1:0:0.2 0/1:331:4:1,3:234,93:0.0121:2,2:10.8:1:22.5:1:0.07513:7.49606:60:3:0.0092:0:1 -X 70345867 . C T 58 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02701;SOR=Inf;LSEQ=TTCCCTGTCTTGACTGGTCC;RSEQ=TTTCAACTGTCCCCTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:0:0,0:318,165:0:2,0:25:1:31.2:1:1:0:60:79.5:1:0:0.2 0/1:458:5:1,4:293,160:0.0109:2,2:15.8:1:25:1:0.05764:7.29371:60:4:0.0088:0:1 -X 70346022 . G A 77 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0389;SOR=7.70823;LSEQ=CAGGTGTGGGCCTAAGCCCA;RSEQ=CCCCTTTCCCACATTCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:682:1:1,0:295,386:0.0015:2,0:1:0:27:0:0.43402:0:60:2:0.0015:0:1 0/1:714:8:6,2:307,399:0.0112:2,2:9.8:1:25.8:1:0.14745:3.89:60:7:0.01:0:1.9 -X 70346404 . G T 28 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59062;SOR=2.4475;LSEQ=GCGGCTACGGAGGGTCATAA;RSEQ=GACAGGCGTAGAGGCTCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:0,1:20,130:0.0066:2,0:15:0:13:0:1:0:60:0:0:0:1 0/1:125:2:1,1:18,105:0.016:2,2:17:0:28.5:1:0.28194:5.70:60:4:0.0163:0:1 -X 70347029 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=ACAAAGCTCTGGCGAATGCC;RSEQ=GTGGAAGTGGCCTGGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:88,149:0:2,0:24.2:1:30.3:1:1:0:60:58.25:1:0:0.1 0/1:198:2:1,1:68,128:0.0101:2,2:15:1:29:1:1:1.88:60:4:0.0102:0:1 -X 70347039 . G A 23 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19006;SOR=Inf;LSEQ=GGCGAATGCCGGTGGAAGTG;RSEQ=CCTGGGAAGAGCATGCACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:85,133:0:2,0:23.9:1:31.8:1:1:0:60:108:1:0:0.1 0/1:169:2:2,0:60,107:0.0118:2,0:10.5:1:23:1:0.13321:0:60:4:0.012:0:1 -X 70347614 . C T 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=0;LSEQ=CAGTCTGTTTTGTCCCATCT;RSEQ=CCTTTTCTTGTCTCAAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:15:15,0:69,1:0.1765:1,1:27.5:1:30.6:1:1:0:60:30:0.1765:0:1.1 0/0:64:0:0,0:63,1:0:1,0:28:1:31.4:1:1:0:60:128:1:0:0.1 -X 70347654 . CT C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.24989;SOR=Inf;LSEQ=CCTTCATCCCTCACTTTCTC;RSEQ=TTTTTTCTTTTCTCCCCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:161,20:0:2,0:23.2:1:31.3:1:1:0:60:362:1:0:0.2 0/1:201:3:2,1:171,27:0.0149:2,2:10:1:30.7:1:0.36395:3.14074:60:6:0.0152:0.005:0.3 -X 70348317 . G C 150 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGGGGTGGGGTTTTGCTA;RSEQ=TGGGGCAGTGACCAGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:224,304:0:2,0:23.1:1:31.7:1:1:0:60:51.8:1:0:0.5 0/1:559:27:10,17:229,303:0.0483:2,2:28.7:1:31.6:1:0.69076:1.28425:60:54:0.0491:0:1.2 -X 70348344 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38285;LSEQ=AGTGACCAGGGCAGGGGGCT;RSEQ=GTTGTGATCCTCTGACCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:379:270:109,161:49,60:0.7124:2,2:21.9:1:29.9:1:0.42264:1.20566:60:269:0.7173:0:1.1 0/1:368:179:81,98:85,104:0.4864:2,2:22.6:1:29.2:1:1:1.01:60:88.5:0.4863:0:1.1 -X 70348874 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16651;SOR=Inf;LSEQ=TTCTCTCCCATGCCCCTGCC;RSEQ=TACACTTGCATGCATGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:153,16:0:2,0:25.9:1:30.3:1:1:0:60:168:1:0:0.2 0/1:117:2:1,1:103,12:0.0171:2,2:12:1:28:1:0.21073:8.28552:60:4:0.0177:0:1 -X 70349947 . A C 268 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.45607;LSEQ=AGCAATGACCTGCAAGACCC;RSEQ=GTGTTGAGTAGTGCCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:702:474:226,248:104,122:0.6752:2,2:26.1:1:30.2:1:0.68649:1.07:60:66.714:0.6778:0:1.1 0/1:781:380:180,200:185,213:0.4866:2,2:26.2:1:29.8:1:0.82947:1.04:60:189:0.4884:0:1.1 -X 70350143 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16483;SOR=Inf;LSEQ=ATAGGAACCTTGAGAAAAGG;RSEQ=GAGGGGCAGTTAAGTAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:7,102:0:2,0:23.9:1:31.2:1:1:0:60:35.333:1:0:0.1 0/1:75:2:1,1:6,67:0.0267:2,2:16.5:1:30:1:0.1791:10.42:60:4:0.027:0:1 -X 70351838 . C T 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGCCAGTGTTGTCCTTCTC;RSEQ=GTCATCTCCGATCTCTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:166,28:0:2,0:23.9:1:30.7:1:1:0:60:63.667:1:0:0.1 0/1:139:14:11,3:104,21:0.1007:2,2:17.1:1:30.4:1:0.7095:1.3475:60:28:0.1007:0:1.4 -X 70351847 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18554;SOR=Inf;LSEQ=TTGTCCTTCTCCGTCATCTC;RSEQ=GATCTCTCCTACCATCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:190,34:0:2,0:24.5:1:30.7:1:1:0:60:73.667:1:0:0.1 0/1:170:2:1,1:138,30:0.0118:2,2:11.5:1:29:1:0.33234:4.54158:60:4:0.0118:0:1.5 -X 70352417 . T C 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.40293;LSEQ=GCTTAGGGAGTGGACCAAGA;RSEQ=TGAGGGGTAGAAAGGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:641:445:150,295:67,127:0.6942:2,2:24:1:31.9:1:0.85611:1.03744:60:62.571:0.7019:0:1.2 0/1:557:266:102,164:108,182:0.4776:2,2:24:1:31.5:1:0.7935:1.05:60:132:0.4862:0:1.1 -X 70352491 . G A 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGAAGCATCATAGGAAAGT;RSEQ=GAAAATCAGAGGATAAGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:53:12,41:15,108:0.3011:2,2:21.1:1:30.9:1:0.10886:2.10:60:106:0.3046:0:2.1 0/0:71:0:0,0:6,65:0:2,0:25.9:1:29.8:1:1:0:60:22.667:1:0:0.6 -X 70352516 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00673;SOR=0.39702;LSEQ=ATCAGAGGATAAGAGTGGGC;RSEQ=TGGCTGAGCAAGAGGCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:89:33,56:8,33:0.6846:2,2:20.2:1:31.3:1:0.06661:2.42:60:88:0.6822:0:1.5 0/1:52:24:3,21:7,21:0.4615:2,2:23.3:1:30.3:1:0.3087:2.29667:60:23:0.451:0:1 -X 70352617 . CCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT C 221 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=12.000;MSILEN=5;SSF=0.18862;SOR=0.75649;LSEQ=TTTCTCCTCTCCTCTTCTCT;RSEQ=CTCTTCTCTTCTCTTCTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:213:129:102,27:67,17:0.6056:2,2:23:1:31.6:1:1:1.04305:59.7:63.5:0.6077:0.1737:0.4 1/0:188:101:75,26:56,2:0.5372:1,2:22.3:1:31.4:1:0.00019:9.60559:59.6:202:0.5489:0.1436:0.3 -X 70353062 . GGT G 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02505;SOR=Inf;LSEQ=CTCAAACTGCGGCTCAACCT;RSEQ=GAGAAGGCCAGCTGGGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:0:0,0:207,287:0:2,0:25.1:1:31.2:1:1:0:60:37:1:0:0.1 0/1:455:5:4,1:178,272:0.011:2,2:14.4:1:26.4:1:0.08585:6.09:60:10:0.011:0.0066:0.6 -X 70353126 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16828;SOR=Inf;LSEQ=GAAATGCGGAGTGCAAAAGC;RSEQ=TCAGGTTGGGGAGAATGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:30,172:0:2,0:24.6:1:31.4:1:1:0:60:27.857:1:0:0.1 0/1:141:2:1,1:33,106:0.0142:2,2:5:1:27:1:0.42543:3.18:60:4:0.0144:0:1 -X 70354102 . C A 110 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.83362;SOR=1.19336;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=TCAAGCATGAACTCAGGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:12:12,0:81,3:0.1224:1,0:15.2:1:29.6:1:1:0:60:11:0.1429:0:1.5 0/1:98:14:12,2:77,5:0.1429:2,2:12.6:1:29.1:1:0.26975:2.53395:60:28:0.1972:0:1.6 -X 70354111 . G T 19 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.24911;LSEQ=AAAAAAAAAAACTCAAGCAT;RSEQ=AACTCAGGCGTCCCAACTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:2,0:159,12:0.0113:2,0:26.5:1:31:0:1:0:60:4:0.0144:0:2 0/1:142:2:1,1:122,15:0.0141:2,2:16:1:19:1:0.2177:7.90698:50:1:0.0096:0:3.5 -X 70354133 . A T 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3507;SOR=3.33174;LSEQ=ACTCAGGCGTCCCAACTCAG;RSEQ=TTGGAACTAAGCTTTCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:0,1:224,62:0.0035:2,0:1:0:14:0:0.21951:0:60:0:0:0:1 0/1:260:3:2,1:188,69:0.0115:2,2:24.3:1:20.7:1:1:1.36059:60:2:0.0085:0:3.7 -X 70354508 . T C 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11048;SOR=Inf;LSEQ=TTGTGTCCTCTGCTGAGGCC;RSEQ=TTTTCTATCTTCACCTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:174,95:0:2,0:22.1:1:30.8:1:1:0:60:88.667:0.9925:0:0.1 0/1:251:3:2,1:176,72:0.012:2,2:19.3:1:30.3:1:1:1.22117:60:6:0.012:0:1 -X 70354651 . A G 198 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=48.92425;LSEQ=CTAGCATCTCGCAAGGTAGC;RSEQ=TGGAGGAAAACAAGCGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:731:2:2,0:351,377:0.0027:2,0:43.5:1:17:1:0.23349:0:60:1:0.0014:0:1.5 0/1:759:90:40,50:308,361:0.1186:2,2:24.9:1:30.6:1:0.82216:1.06642:60:89:0.1191:0:1.2 -X 70355258 . CTT C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.16051;LSEQ=CTGGGGTTTTGAGCAAATCA;RSEQ=AACTTTCCTTACATTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:47:0,47:0,11:0.7966:0,1:24.4:1:32.5:1:1:0:59.8:94:0.8103:0.1186:0.1 0/1:42:16:0,16:0,26:0.381:1,1:22.3:1:32.4:1:1:0:60:32:0.3902:0.0476:0.1 -X 70355882 . A T 91 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29945;SOR=0.27545;LSEQ=CACACGCCCCCCGCCCCGTT;RSEQ=GTTCATCTCCTCTCCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:7,1:3,0:0.7273:0,2:29.9:1:30.4:1:1:0:60:16:0.7273:0:1.9 0/1:5:2:2,0:3,0:0.4:0,0:12:1:29.5:1:1:0:60:4:0.5:0:2 -X 70355942 . G C 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56918;SOR=0.71118;LSEQ=GCCTCCACACCTCTCCCTGT;RSEQ=CCCCACCCTTCACTCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:23:23,0:9,0:0.697:0,1:28.5:1:31.5:1:1:0:60:46:0.7188:0:1.3 1/0:21:13:12,1:7,0:0.619:0,1:26.2:1:31.3:1:1:0:60:26:0.619:0:1.2 -X 70356039 . C T 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60276;SOR=2.26496;LSEQ=ACCATCTCTCCTGAATCTGC;RSEQ=TATGACTTTCTTTCTACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:1,0:190,12:0.0049:2,0:5:0:20:0:1:0:60:2:0.005:0:1 0/1:180:2:1,1:164,14:0.0111:2,2:9.5:1:30:1:0.16015:11.3518:60:4:0.0112:0:1 -X 70356561 . G A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18423;SOR=Inf;LSEQ=TCTCACTTCATGACGCTCCG;RSEQ=TTTCTGGTTTGTGGGAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:85,167:0:2,0:26.4:1:31.4:1:1:0:60:49.4:1:0:0.3 0/1:190:2:2,0:55,133:0.0105:2,0:21.5:1:25.5:1:0.08889:0:60:4:0.0106:0:1 -X 70356642 . T C 244 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02251;SOR=0.64683;LSEQ=AAAATTAACCATATACGAAT;RSEQ=CAGCTCCTCTTTACCTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:298:210:174,36:70,17:0.7047:2,2:23.1:1:31.7:1:0.62068:1.17:60:209:0.7085:0:1.1 1/0:211:128:109,19:64,19:0.6066:2,2:22.4:1:31.1:1:0.14649:1.70:60:41.667:0.6039:0:1.3 -X 70356704 . C T 132 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCAGCTACAACCCACTCA;RSEQ=CCTCTTCCTCTGCCACTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:0:0,0:471,284:0:2,0:26.1:1:31.5:1:1:0:60:82.889:1:0:0.3 0/1:600:25:16,9:342,232:0.0417:2,2:29.4:1:28.5:1:0.83543:1.21:60:24:0.0405:0:1.4 -X 70356829 . A G 216 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTATAACACACCTTAACT;RSEQ=CAGGCAAGGCTCCATAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:976:130:57,73:390,454:0.1332:2,2:23.4:1:30.9:1:0.63737:1.10004:60:25:0.1297:0:1.1 0/0:922:0:0,0:447,474:0:2,0:24:1:28.5:1:1:0:60:130.571:1:0:0.2 -X 70360588 . GAGC G 132 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.40605;SOR=0.72845;LSEQ=GTTCAACAGCCATCCTACCT;RSEQ=AGCAGCAGCAGCAGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:21:10,11:297,416:0.0285:2,2:25.7:1:30.2:1:0.65585:1.27:60:42:0.0293:0.0068:0.4 0/1:764:16:8,8:335,408:0.0209:2,2:26.6:1:31.1:1:0.80139:1.22:60:32:0.0216:0.0039:0.3 -X 70360620 . G A 57 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.50361;SOR=1.69337;LSEQ=CAGCAGCAACAGCAGCAACA;RSEQ=CAACAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:3:3,0:169,321:0.0061:2,0:1:0:25.3:1:0.04198:0:60:6:0.0063:0:1.3 0/1:488:5:4,1:179,303:0.0102:2,2:22.8:1:24.6:1:0.0687:6.75:60:4:0.0085:0:1.2 -X 70360623 . ACAG A 83 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=0.87445;LSEQ=CAGCAACAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:7:4,3:154,303:0.0151:2,2:22.7:1:29.6:1:0.23585:2.62:60:14:0.0153:0.0043:0.3 0/1:455:6:1,5:156,291:0.0132:2,2:22.2:1:31.4:1:0.66941:2.67564:60:12:0.0135:0.0022:0 -X 70360647 . ACAG A 111 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.51001;SOR=1.39244;LSEQ=CAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:9:1,8:55,219:0.0313:2,2:28.7:1:31.4:1:1:2.00507:60:18:0.0318:0:0.4 0/1:279:12:3,9:62,205:0.043:2,2:29.3:1:31.2:1:1:1.10:59.2:24:0.0435:0.0072:0.4 -X 70360666 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.23993;SOR=0;LSEQ=AACAGCAGCAGCAGCAGCAG;RSEQ=AGTACCACATCCGGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:0,2:14,165:0.011:2,0:8.5:1:28:1:1:0:60:4:0.0116:0:1.5 0/0:188:0:0,0:29,159:0:2,0:24.5:1:31.7:1:1:0:59.9:46:1:0:0.1 -X 70360679 . GGCA G 109 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.32504;SOR=0.57437;LSEQ=GCAGCAGCAGTACCACATCC;RSEQ=GCAGCAGCAGCAGCAGATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:11:0,11:11,133:0.071:2,0:30.5:1:31.6:1:1:0:60:22:0.0743:0.0129:0 0/1:143:6:1,5:16,121:0.042:2,2:33.5:1:31.5:1:0.5388:1.51:60:12:0.0432:0:0 -X 70361077 . TAGC T 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.72464;SOR=1.67699;LSEQ=AAGTATCTTTTGTGTTCTTA;RSEQ=AGCAGCAGCAACAGCAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:233,48:0.0105:2,2:24.3:1:29.7:1:0.43469:2.41735:60:6:0.0109:0.0035:0.3 0/1:287:5:4,1:221,62:0.0174:2,2:5.3:1:26:1:1:1.12:44.8:6:0.0138:0.0146:1.8 -X 70361097 . ACAG A 124 MSI6;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.01878;SOR=0.32869;LSEQ=TAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:17:9,8:273,112:0.0422:2,2:24.1:1:30.5:1:0.17218:2.16206:60:16:0.0411:0.0074:0.5 0/1:421:6:3,3:275,140:0.0143:2,2:29.7:1:31.7:1:0.41284:1.96096:60:12:0.0145:0:0.3 -X 70361100 . G A 76 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.21191;SOR=0.40008;LSEQ=CAGCAGCAGCAACAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:7:6,1:271,115:0.0172:2,2:14.6:1:27.4:1:0.67893:2.54:60:6:0.0162:0:2 0/0:433:3:1,2:279,145:0.0069:2,2:20:1:23:1:0.27345:3.83504:60:2:0.0049:0:1 -X 70361127 . ACAG A 96 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.14054;SOR=2.22633;LSEQ=CAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:650:5:4,1:395,243:0.0077:2,2:32.8:1:31.2:1:0.65457:2.46:60:10:0.0078:0:0 0/1:648:11:4,7:357,277:0.017:2,2:20.3:1:28:1:0.22727:2.2526:56.5:22:0.0172:0.0093:0.5 -X 70361130 . G A 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.10726;SOR=3.54492;LSEQ=CAGCAGCAGCAACAGCAACA;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:2:2,0:395,260:0.003:2,0:25:1:31:1:0.52101:0:60:4:0.0032:0:1 0/1:659:7:4,3:361,284:0.0106:2,2:12.9:1:24.6:1:1:1.05:55.4:2.5:0.0079:0:1.1 -X 70361273 . C T 138 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.01847;LSEQ=ACAGCTGCCCAGGTTGGGCA;RSEQ=GCAGCCAGTGAACTGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:1:0,1:153,342:0.002:2,0:27:0:32:0:1:0:60:2:0.002:0:1 0/1:373:24:7,17:102,247:0.0643:2,2:18.5:1:30.3:1:1:1.00288:60:48:0.0652:0:1.3 -X 70361608 . T C 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98343;LSEQ=GTTGCAGTGAGCCAAGATCA;RSEQ=GCCACTGCACTCCAGCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:85:60:60,0:24,1:0.7059:1,1:28.5:1:32:1:0.29412:0:57.9:59:0.7108:0:1.2 1/0:84:59:59,0:25,0:0.7024:1,1:24.2:1:30.9:1:1:0:56.6:58:0.7073:0:1.4 -X 70361619 . T C 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00696;SOR=Inf;LSEQ=CCAAGATCATGCCACTGCAC;RSEQ=CCAGCCTGGGGGACAGAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:98,3:0:1,0:25.8:1:31:1:1:0:57.6:32.667:1:0:1.1 0/1:107:8:6,2:97,2:0.0748:1,2:21.1:1:24.5:1:0.02741:15.12369:59.4:3:0.0577:0:2.9 -X 70361651 . C CA 201 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.08695;SOR=0.7186;LSEQ=GACAGAGCGAGACTCCATCT;RSEQ=AAAAAAAAAAACGGATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:104:82,22:69,26:0.4581:2,2:25.6:1:30.1:1:0.32404:1.40:59.5:103:0.4619:0.0044:0.5 0/1:225:85:64,21:85,30:0.3778:2,2:25.8:1:29.3:1:0.87068:1.08:58.8:84:0.3818:0.0222:0.8 -X 70361967 . G A 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3806;LSEQ=ATACCTGAACAGCTTTCCTC;RSEQ=TGCATACCCACACCCCTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:798:566:335,231:131,96:0.7093:2,2:23.7:1:30.2:1:0.74964:1.06:60:69.75:0.7099:0:1.1 0/1:561:270:160,110:177,114:0.4813:2,2:26.1:1:29.7:1:0.73044:1.0673:60:134:0.4846:0:1.1 -X 70362490 . G A 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTGCAGTGGC;RSEQ=CGATCTCGGCTCACTGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:14:1:31:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 70510544 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53115;SOR=Inf;LSEQ=AACCATACTCCAAGAAAGCA;RSEQ=CATCAACATCACCACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:0:2,0:25.2:1:29.2:1:1:0:59.5:10:1:0:0.1 0/1:39:2:1,1:21,16:0.0513:2,2:39.5:1:30.5:1:1:1.30327:60:4:0.0513:0:2.5 -X 70715155 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=ATTTGTAAGACCATCTGTAG;RSEQ=TTGATGGCCTCGATCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:0:2,0:30.8:1:32.7:1:1:0:60:20:1:0:0 0/1:16:2:1,1:12,2:0.125:2,2:25.5:1:29:1:0.35:5.09912:60:4:0.125:0:1 -X 70715270 . G C 33 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1876;SOR=0;LSEQ=CTAGAAAGGGGAGAAGCCAT;RSEQ=TCGCCCAATTCCAGAGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:54,53:0.0183:2,2:35:0:33:1:1:1.0187:60:4:0.0185:0:2.5 0/0:142:0:0,0:69,73:0:2,0:24.5:1:31.4:1:1:0:58.7:284:1:0:0.2 -X 70715273 . G A 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50352;SOR=Inf;LSEQ=GAAAGGGGAGAAGCCATGTC;RSEQ=CCCAATTCCAGAGGTTGGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:57,58:0:2,0:26.3:1:30.6:1:1:0:59.8:37.333:0.9912:0:0.2 0/1:143:2:1,1:68,73:0.014:2,2:14:0:31:1:1:1.07:50.5:4:0.0143:0:1.5 -X 70715329 . CT C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49939;SOR=Inf;LSEQ=CATTGTCTGATTTCAAAAGC;RSEQ=TTTCCCGTAAACGCCAGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:27,41:0:2,0:21.5:1:30.2:1:1:0:59.9:67:1:0:0.1 0/1:79:2:1,1:29,47:0.0253:2,2:23.5:1:30.5:1:1:1.61:60:4:0.0253:0:0 -X 71788795 . C T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20087;SOR=0;LSEQ=GACCCAGCGTATGCCAGAAG;RSEQ=TAGAAACAGAAGCCAGCAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:114,51:0.012:2,2:21.5:1:29:1:0.52709:2.22342:60:4:0.012:0:1 0/0:205:0:0,0:121,84:0:2,0:25.7:1:31.4:1:1:0:60:50.25:1:0:0.2 -X 71788870 . T C 145 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGGCTGGAGTAATAAACA;RSEQ=ATTCTGTTCTTCCACTGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:118,133:0:2,0:27:1:29.1:1:1:0:60:40.833:0.9959:0:0.1 0/1:260:23:10,13:114,123:0.0885:2,2:22.3:1:32.2:1:0.8275:1.20402:60:46:0.0895:0:1.1 -X 72744762 . C CT 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01167;SOR=0;LSEQ=CCTTTTGCTTCCTCTCAGCC;RSEQ=TTTTTTTTAGTCTGATGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:6:3,3:107,35:0.0405:2,2:24.7:1:29.2:1:0.17621:3.02932:60:12:0.0414:0.0068:0.5 0/0:160:0:0,0:118,40:0:2,0:23.7:1:30.3:1:1:0:60:51.667:0.9936:0:0.2 -X 72744860 . C T 63 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12395;SOR=Inf;LSEQ=ATTTGACAAAACATAGCATG;RSEQ=GACTTCAATGGTACGTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:134,156:0:2,0:25.3:1:30.3:1:1:0:60:40.429:0.9965:0:0.1 0/1:301:4:2,2:129,167:0.0133:2,2:20.5:1:31.8:1:1:1.29:60:8:0.0135:0:1.3 -X 72744866 . C A 46 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2487;SOR=0;LSEQ=CAAAACATAGCATGCGACTT;RSEQ=AATGGTACGTTCTTCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:133,152:0.0104:2,2:22.3:1:29.3:1:1:1.74674:60:6:0.0106:0:1 0/0:287:0:0,0:124,163:0:2,0:25:1:30.8:1:1:0:60:70.75:1:0:0.2 -X 72745416 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21892;SOR=Inf;LSEQ=ACATCATCTAATACACTATA;RSEQ=ACATATTTGTAAAACTTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:116,87:0:2,0:26.9:1:31.5:1:1:0:59.9:32.833:1:0:0.1 0/1:179:2:1,1:90,87:0.0112:2,2:26.5:1:29.5:1:1:1.0343:60:4:0.0112:0:1 -X 72745947 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50104;SOR=Inf;LSEQ=CCCGGGGTGAGGCTGCCGCT;RSEQ=CTGCCCCCGGAGCCGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:57,91:0:2,0:22.2:1:31.6:1:1:0:60:147:1:0:0.7 0/1:171:2:1,1:63,106:0.0117:2,2:24.5:1:29:1:1:1.68:60:4:0.012:0:1.5 -X 72745977 . T G 218 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00027;SOR=0;LSEQ=GAGCCGCAGCCGCCGCTCAG;RSEQ=CTCGGAGCTGCCATTGTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:115:115:33,82:0,0:1:0,2:26.4:1:31.3:1:1:0:60:56.5:1:0:1.1 1/1:134:121:41,80:4,8:0.903:2,2:26.5:1:31.6:1:1:1.02:59.9:120:0.9091:0:1.1 -X 73434855 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50567;SOR=Inf;LSEQ=GAAAAGTGCCAGTGGAAGGA;RSEQ=AAAGTTATGGCTTTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:86,53:0:2,0:23.8:1:31.4:1:1:0:60:45.333:1:0:0.1 0/1:177:2:1,1:107,68:0.0113:2,2:39.5:1:28.5:1:1:1.56932:60:4:0.0114:0:1 -X 73434946 . GT TG 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20871;SOR=0;LSEQ=AATATGAGCACAAGGATTGG;RSEQ=TTACTTTCAAATCAGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:92,105:0.0101:2,2:40.5:1:32.5:1:1:1.14:60:4:0.0102:0:2 0/0:236:0:0,0:103,131:0:2,0:25.6:1:30.8:1:1:0:60:468:0.9957:0:0.5 -X 73434947 . T G 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19831;SOR=0.76822;LSEQ=ATATGAGCACAAGGATTGGG;RSEQ=TTACTTTCAAATCAGCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:82:40,42:54,63:0.408:2,2:25.9:1:31.4:1:0.77356:1.11:60:40:0.4082:0:1.1 0/1:237:82:34,48:70,84:0.346:2,2:24.4:1:31.1:1:0.58403:1.17566:60:81:0.3476:0:1.1 -X 73434975 . C A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11035;SOR=0;LSEQ=CAAATCAGCTGACTACTCTC;RSEQ=TTCTATGAAGCTGGGTCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:3:3,0:67,96:0.0181:2,0:8.3:1:21:1:0.07312:0:60:2:0.0125:0:1.7 0/0:179:0:0,0:73,106:0:2,0:23.2:1:31.1:1:1:0:60:178:1:0:0.4 -X 73516031 . C CTT 31 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATATAATGTTTTAACATTAA;RSEQ=TTTTTTTTTTTTTTGAGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:0:31.5:1:1:0:60:4:1:0:1.5 -X 73516050 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTTTTTTTTTTGAGA;RSEQ=AGTCTTGCTCTGTGGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:44:0:30:0:1:0:55:2:1:0:1 1/1:2:2:1,1:0,0:1:0,2:22.5:1:28.5:1:1:0:60:4:1:0:1.5 -X 73516287 . A G 115 P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05878;SOR=0;LSEQ=GCCCGCCTCGGCCTCCCAAA;RSEQ=TGCTGGGATTACAGGTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1:0,0:21.4:1:32.6:1:1:0:57.7:24:1:0:1 1/0:17:12:12,0:5,0:0.7059:0,0:27.5:1:32.3:1:1:0:56.6:24:0.7059:0:1.3 -X 73516407 . G T 38 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07908;SOR=0;LSEQ=TGAATATTCATCAGCAAACA;RSEQ=ATTTAGTTCTGTTTCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:3:1,2:41,48:0.0326:2,2:25.7:1:24:1:1:1.69881:60:2:0.0225:0:1.3 0/0:121:0:0,0:57,64:0:2,0:27.4:1:30.7:1:1:0:60:120:1:0:0.5 -X 73516451 . T A 169 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00077;SOR=0;LSEQ=AACTTCTACTTCTACCTTCA;RSEQ=CTCAGGCAAGGAGCTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:62:23,39:0,0:1:0,2:24.3:1:28.4:1:1:0:60:19.667:1:0:1.1 1/1:70:59:19,40:1,9:0.8429:2,2:24.9:1:28.9:1:0.26076:4.21:60:58:0.8406:0:1.1 -X 74604188 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50452;SOR=Inf;LSEQ=GTAATTCGCCAAAATGACGA;RSEQ=CACAAAGGGAAAGAGGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:43,56:0:2,0:25:1:30.1:1:1:0:55.6:198:1:0:0.1 0/1:125:2:1,1:50,73:0.016:2,2:32:0:33.5:1:1:1.46:60:4:0.016:0:1 -X 74604200 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2026;SOR=0;LSEQ=AATGACGAACACAAAGGGAA;RSEQ=GAGGAGAGGCACCCAATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:37,54:0.0215:2,2:15:1:27:1:1:1.45:53.5:4:0.022:0:1 0/0:113:0:0,0:47,66:0:2,0:22.3:1:30.2:1:1:0:54.7:112:1:0:0.1 -X 74604266 . C T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49993;SOR=Inf;LSEQ=TGGAGTTGTTCCTTTGGCCA;RSEQ=GTATATGCAAATCTATAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:32,24:0:2,0:25.3:1:31.1:1:1:0:42.9:112:1:0:0.1 0/1:67:2:1,1:39,26:0.0299:2,2:45.5:1:30:1:1:1.49067:22:4:0.0308:0:1.5 -X 74604293 . A G 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49804;SOR=Inf;LSEQ=GCAAATCTATAAGAAAGGTG;RSEQ=TATTGTAGACATCAAGGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:33,24:0:2,0:28:1:29.9:1:1:0:38.5:56:1:0:0 0/1:65:2:1,1:32,31:0.0308:2,2:12:1:27:1:1:1.03176:27:4:0.0313:0:1 -X 74604357 . C T 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49683;SOR=Inf;LSEQ=CCCCACAAGTGTTACCATGG;RSEQ=AAAACTGGAAGAGTCTACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:0:2,0:24.9:1:31.6:1:1:0:33.5:15.333:1:0:0 0/1:55:2:1,1:17,36:0.0364:2,2:14:1:25:0:1:2.09:40:4:0.0364:0:1 -X 74604425 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17857;SOR=Inf;LSEQ=TGTAAACAAACAAGTTAAGG;RSEQ=CAAGATTCTTGCCAAGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:7,21:0:2,0:19:1:31.4:1:1:0:41.3:56:1:0:0 0/1:21:2:0,2:8,11:0.0952:2,0:14.5:1:29.5:1:0.50476:0:40:4:0.1:0:1 -X 74802478 . A G 126 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0214;SOR=0.34049;LSEQ=GGCATTTATCCCAGATAAAT;RSEQ=AAAACATATGATAAGATGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:14:10,4:36,25:0.1867:2,2:23.6:1:33.2:1:0.54557:1.72:60:28:0.1892:0:1.1 0/1:111:8:5,3:74,29:0.0721:2,2:18.3:1:31.3:1:0.68774:1.52474:60:16:0.0727:0:1.6 -X 74802536 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52032;SOR=Inf;LSEQ=GTGGTGGCAGTGCGGAGCCC;RSEQ=GTGAGGCTCTATTCAACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:62,53:0:2,0:28.4:1:30.6:1:1:0:60:114:1:0:0.2 0/1:176:2:1,1:89,84:0.0114:2,2:38.5:1:30.5:1:1:1.0592:60:4:0.0114:0:2 -X 74802567 . C A 93 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01205;SOR=Inf;LSEQ=ATTCAACGGGGACGTGGAGC;RSEQ=TGAAGCCGGCGCTGGCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:51,52:0:2,0:22.6:1:31.3:1:1:0:60:102:1:0:0.1 0/1:151:9:3,6:65,76:0.0596:2,2:14.4:1:29.4:1:0.5123:1.70464:60:18:0.0604:0:1.6 -X 74802569 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51534;SOR=Inf;LSEQ=TCAACGGGGACGTGGAGCCT;RSEQ=AAGCCGGCGCTGGCGCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:50,53:0:2,0:22.1:1:31.6:1:1:0:60:206:1:0:0.1 0/1:150:2:1,1:66,82:0.0133:2,2:15:1:28.5:1:1:1.24:60:4:0.0135:0:2 -X 74802910 . C A 39 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07755;SOR=0;LSEQ=CACTCCAACAAAGAGAACAA;RSEQ=AGTTATTGGAATGTCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:125,131:0.0116:2,2:31.3:1:25:1:0.61637:2.09:60:2:0.0078:0:1 0/0:347:0:0,0:158,189:0:2,0:26.4:1:31:1:1:0:59.9:68.4:1:0:0.1 -X 74803004 . C A 38 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34096;SOR=0.28612;LSEQ=TTCTTCCTCTTTTAGCCTTT;RSEQ=AGTTTTTCTCTTTCAGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:2,1:77,95:0.0171:2,2:20.3:1:24.3:1:0.58969:2.46:60:2:0.0116:0:3.3 0/0:202:1:1,0:82,119:0.005:2,0:1:0:22:0:0.41089:0:60:2:0.005:0:1 -X 74803054 . C T 31 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59908;SOR=0.43172;LSEQ=CTTTATCTCTTTCAGTTTTC;RSEQ=GAAATCCCATAGATGTGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:94,55:0.0132:2,2:6:1:31:1:1:1.70267:60:4:0.0134:0:1 0/0:174:1:0,1:97,76:0.0057:2,0:1:0:24:0:0.44253:0:60:2:0.0058:0:1 -X 74803062 . C A 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2518;SOR=Inf;LSEQ=CTTTCAGTTTTCCGAAATCC;RSEQ=ATAGATGTGACATGGAGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:102,65:0:2,0:22.8:1:31.1:1:1:0:60:54.667:0.9939:0:0.1 0/1:194:3:2,1:110,81:0.0155:2,2:36.7:1:29.7:1:1:1.47:60:6:0.0155:0:1 -X 74803507 . T A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.22646;SOR=Inf;LSEQ=ATGACCATCTTGATTTGTTG;RSEQ=TTTTCTCCAAGTTCTTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:98,103:0:2,0:25:1:30.1:1:1:0:60:200:1:0:0.1 0/1:183:2:1,1:83,98:0.0109:2,2:20:1:26.5:1:1:1.18:60:4:0.011:0:2 -X 74803555 . T A 146 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAATACCCCAGGAAGAGGCC;RSEQ=CCTTAGCAGAGACTGCCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:120,122:0:2,0:25.3:1:30.4:1:1:0:60:120:1:0:0.1 0/1:227:28:14,14:106,93:0.1233:2,2:23.5:1:30.4:1:0.84054:1.13913:60:56:0.1239:0:1.3 -X 74803679 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62888;SOR=2.54798;LSEQ=TCCAATTCCACAGCCCTTCC;RSEQ=ACCAGCAGATGAAGATCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:1,0:115,130:0.0041:2,0:1:0:27:0:0.47154:0:60:2:0.0041:0:1 0/1:291:3:2,1:150,138:0.0103:2,2:8.3:1:28:1:1:1.84:60:6:0.0103:0:1 -X 74803832 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=0;LSEQ=AGGCTCAACCACAGGTTTGT;RSEQ=TGCCACACCCCCTGCCTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:90,77:0.0118:2,2:46:1:30:1:1:1.16775:60:4:0.0119:0:1 0/0:157:0:0,0:81,76:0:2,0:21.6:1:31:1:1:0:60:77.5:1:0:0.1 -X 74803836 . C G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22669;SOR=Inf;LSEQ=TCAACCACAGGTTTGTCTGC;RSEQ=ACACCCCCTGCCTGGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:93,77:0:2,0:25.5:1:31.7:1:1:0:60:84:1:0:0.2 0/1:155:2:1,1:82,71:0.0129:2,2:35:1:32:0:1:1.15385:60:4:0.0131:0:1 -X 74803877 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23893;SOR=0;LSEQ=TCACTAACGTGAAAGCCTTA;RSEQ=AGAAATCTCCAGGACTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:116,68:0.0108:2,2:32:1:31:1:1:1.70068:60:4:0.0108:0:1 0/0:194:0:0,0:116,78:0:2,0:23.3:1:31.2:1:1:0:60:193:1:0:0.1 -X 74803898 . T C 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAAATCTCCAGGACTTCAG;RSEQ=GAGAAAGGAAGTCATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:54:36,18:110,61:0.24:2,2:27.5:1:31:1:0.87032:1.11:60:53:0.2366:0:1.1 0/0:256:0:0,0:160,96:0:2,0:25.9:1:29.4:1:1:0:59.9:84.333:1:0:0.1 -X 74804297 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50089;SOR=0;LSEQ=GATCAAACTTATAGATATTG;RSEQ=ACAACAGACTGCACAGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:79,119:0.01:2,2:10.5:1:30.5:1:1:1.50:60:4:0.0101:0:1 0/0:175:0:0,0:65,110:0:2,0:25.2:1:32.1:1:1:0:60:350:1:0:0.1 -X 74804791 . C T 43 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36157;SOR=3.17186;LSEQ=AGCTGCTGACCCGCTCATTG;RSEQ=CAAAAATTCACCACAGTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:1,0:146,140:0.0035:2,0:33:0:12:0:1:0:60:0:0:0:2 0/1:273:3:1,2:141,127:0.011:2,2:29.7:1:27.3:1:0.60633:2.21415:60:6:0.011:0:1 -X 74804896 . G A 114 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTCCAAAAACACCCATCCAG;RSEQ=CAGGGGGATATGGTGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:149,217:0:2,0:26:1:31.6:1:1:0:59.8:44.75:1:0:0.1 0/1:360:16:5,11:152,192:0.0444:2,2:25.8:1:28.6:1:0.44042:1.73911:60:32:0.0451:0:1.3 -X 76297518 . C G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCCAGTCCCAGTGCTGGCTG;RSEQ=TGCCCCTCCCCCAAGGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:0.5:2,0:18.5:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 76297592 . C A 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTGGTCACAGGCTAGGGT;RSEQ=CCTCCCCACAGGAGTTTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:29.7:1:31:1:1:0:60:6:1:0:0.3 0/1:9:2:1,1:5,2:0.2222:2,2:25.5:1:27.5:1:1:2.23609:60:4:0.2222:0:1 -X 76297682 . C T 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63089;SOR=0.59928;LSEQ=ACACAGATTGGGACAATAGG;RSEQ=CACGGGACACTAAACCATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:13,9:1,1:0.9167:2,2:26.1:1:28.9:1:1:1.42:60:44:0.9167:0:1.1 1/1:15:13:7,6:1,1:0.8667:2,2:15.5:1:29.3:1:1:1.15:60:26:0.8667:0:1.3 -X 76775992 . C T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AACTCTGGCAAAAATTCCTA;RSEQ=GTAGATGTCCAGAATATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:0.3333:0,0:31.5:1:29:1:1:0:60:4:0.3333:0:1 0/0:4:0:0,0:4,0:0:0,0:16.8:1:30.3:1:1:0:60:8:1:0:0 -X 76776740 . G A 30 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.57178;SOR=2.81939;LSEQ=AATTGCTGGGTTACGGTTTG;RSEQ=CATTATCCATCCATTTTACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:1,0:85,3:0.0112:1,0:48:0:29:0:1:0:60:2:0.0114:0:1 0/1:64:2:2,0:62,0:0.0313:1,0:22:1:30:1:1:0:60:4:0.0313:0:1 -X 76777682 . C T 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24868;SOR=Inf;LSEQ=GCATAGGGAACCCTCAACAA;RSEQ=AAGGCACTTGAAATTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:225,53:0:2,0:23.4:1:32.2:1:1:0:60:277:1:0:0.1 0/1:281:3:2,1:209,69:0.0107:2,2:29.7:1:29.7:1:1:1.51204:60:6:0.0108:0:1.3 -X 76777926 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2347;SOR=Inf;LSEQ=TAAAACTTGAAATTCTACAT;RSEQ=ACCTACTGGTTTAGAAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:14,127:0:2,0:21.7:1:32.3:1:1:0:60:140:1:0:0 0/1:133:2:1,1:14,117:0.015:2,2:11:1:30:1:0.2136:8.11:60:4:0.0156:0:1 -X 76778062 . CT C 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=CTTTAACCCCTAAAGGTGTA;RSEQ=TTTTTTTTCTGATAATTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:0.2:0,0:26:1:32:1:1:0:60:4:0.2:0:0 0/0:7:0:0,0:1,6:0:2,0:16.3:1:29.9:1:1:0:60:14:1:0:0 -X 76812822 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49821;SOR=Inf;LSEQ=TTTTATTATCCTTGAAAAAT;RSEQ=CTGAAATATAGCCTTAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:121,9:0:2,0:22.8:1:30.1:1:1:0:60:64:1:0:0.1 0/1:134:2:1,1:125,7:0.0149:2,2:17:1:31:1:0.11626:16.76993:60:4:0.0149:0:1 -X 76812834 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50104;SOR=Inf;LSEQ=TGAAAAATTCTGAAATATAG;RSEQ=CTTAATCAGATGACTAAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:134,23:0:2,0:22.7:1:31.9:1:1:0:60:77.5:1:0:0.1 0/1:181:2:1,1:152,26:0.011:2,2:12:1:27:1:0.27821:5.75576:60:4:0.0112:0:1 -X 76813413 . C A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGGAGGAGGACAGCAGG;RSEQ=AGATACCAGAGTAAACAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:0,7:0.2222:0,2:26:0:30.5:1:0.22222:0:60:4:0.2857:0:2 0/0:1:0:0,0:0,1:0:0,0:35:0:33:0:1:0:60:2:1:0:0 -X 76814070 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22718;SOR=Inf;LSEQ=CCTCTCTGTAATACACATAT;RSEQ=TTCCATATCTCTAAAATATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:168,28:0:2,0:22.4:1:32.2:1:1:0:60:97:1:0:0.1 0/1:179:2:1,1:149,28:0.0112:2,2:5:1:28.5:1:0.29854:5.24651:60:4:0.0113:0:1 -X 76814401 . GT G 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03494;SOR=0;LSEQ=ATATGACTTTTTGATACTTA;RSEQ=TTTTTTTTAACTATCAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:6:0,6:4,67:0.0779:2,0:24.7:1:31.6:1:1:0:60:12:0.08:0.026:0.2 0/0:60:0:0,0:2,58:0:1,0:26.2:1:30.2:1:1:0:60:120:1:0:0 -X 76829870 . T A 55 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13485;SOR=Inf;LSEQ=AGGAATTTGATATATCGCTC;RSEQ=GCTTACTGGTAAGAACAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:45,215:0:2,0:23.8:1:30.1:1:1:0:60:51:1:0:0.1 0/1:332:4:3,1:78,250:0.012:2,2:10.5:1:27.8:1:0.04643:9.53:60:8:0.0123:0:1 -X 76845212 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22167;SOR=0;LSEQ=ATGATAGAGTTGTGAGACTG;RSEQ=GTAGTTTTGTTTCTTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:165,15:0.011:2,2:28.5:1:31:1:0.16854:10.6831:60:4:0.0111:0:1 0/0:204:0:0,0:184,20:0:2,0:22.6:1:30.8:1:1:0:60:101:1:0:0.1 -X 76845263 . A T 65 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14129;SOR=4.79036;LSEQ=TTGTATGGTATGTTTAAATC;RSEQ=GTATTTTTAAAATTACGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:1:0,1:289,181:0.0021:2,0:1:0:29:0:0.38641:0:60:2:0.0021:0:1 0/1:594:6:1,5:360,228:0.0101:2,2:7.8:1:25.3:1:0.03676:7.86806:60:12:0.0103:0:1 -X 76848940 . C T 64 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATAAGTTCAAGTTGCAA;RSEQ=AGGTAGAAGCAGAAATTTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:0.3333:0,0:28.5:1:32.3:1:1:0:60:8:0.3333:0:1 0/0:1:0:0,0:1,0:0:0,0:17:0:32:0:1:0:60:2:1:0:2 -X 76849126 . A T 34 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33842;SOR=3.54549;LSEQ=TAAGCAATAAAAACATAATC;RSEQ=AAAGGTTAATTTATATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:0,1:209,80:0.0034:2,0:2:0:26:0:0.27931:0:60:2:0.0035:0:1 0/1:247:3:1,2:170,74:0.0121:2,2:15.3:1:22:1:0.22476:4.5628:60:2:0.0082:0:1.3 -X 76855053 . AAAAC A 101 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=5.000;MSILEN=4;SSF=0.33261;SOR=1.73473;LSEQ=TCCCTTTTTTCTTCTTTCTA;RSEQ=AAACAAACAAACAAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:6:1,5:205,309:0.0115:2,2:30.7:1:31.7:1:0.41039:3.31093:60:12:0.0117:0:0 0/1:555:11:6,5:244,299:0.0198:2,2:27.3:1:29.2:1:0.55529:1.47:60:22:0.0202:0.0036:0.4 -X 76855295 . G GA 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.65646;SOR=0.86158;LSEQ=TTCATCAAAATAACCCTAGA;RSEQ=AAAAAAAAATGACCACTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:25:8,17:169,339:0.0466:2,2:27.6:1:29.7:1:1:1.05926:60:50:0.0473:0.0019:0 0/1:544:22:6,16:202,318:0.0404:2,2:28.3:1:28.6:1:0.37164:1.69239:60:21:0.0393:0.0018:0.6 -X 76874208 . GA G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.23734;SOR=Inf;LSEQ=ATTATTAAACTTTAAGCTCA;RSEQ=AAATATGTTGGGATTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:151,19:0:2,0:22.3:1:30.2:1:1:0:60:340:1:0:0.1 0/1:162:2:1,1:137,23:0.0123:2,2:19:1:29:1:0.27513:5.85239:60:4:0.0126:0.0062:0.5 -X 76875758 . T C 122 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCTATGTAGATCATGGTC;RSEQ=AGGACTATACTAGAATAAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:115,3:0:1,0:24.6:1:31.3:1:1:0:60:236:1:0:0.1 0/1:88:16:16,0:69,3:0.1818:1,1:19.6:1:30.5:1:1:0:60:32:0.1818:0:1.1 -X 76876036 . T A 40 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12023;SOR=0;LSEQ=GAAAAATAACACAATTAATA;RSEQ=ATAATAAAACTGAAAATGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:3:2,1:55,173:0.013:2,2:10:0:25.3:1:0.15138:6.23:60:2:0.0089:0:1.3 0/0:236:0:0,0:67,169:0:2,0:24.1:1:28.1:1:1:0:60:46.2:1:0:0.1 -X 76888654 . T A 164 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATATAAACACATTTTTTA;RSEQ=TCAACTTGCTTCTTTATGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:237,105:0:2,0:23:1:30.6:1:1:0:60:113:1:0:0.1 0/1:390:44:37,7:243,102:0.1128:2,2:21.8:1:30.1:1:0.07355:2.21:60:43:0.1105:0:1.2 -X 76891446 . A G 193 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.06702;LSEQ=AATTTGATAACCATATTTCT;RSEQ=TGAACCTGCACTAAAGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:2:2,0:420,349:0.0026:2,0:28.5:1:24:1:0.50384:0:60:1:0.0013:0:1 0/1:896:73:40,33:444,379:0.0815:2,2:27.8:1:31.2:1:0.90321:1.03:60:72:0.0816:0:1.2 -X 76907781 . TTCC T 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.74865;SOR=0.86596;LSEQ=TTTTCATCTTCCTCCTCCTC;RSEQ=TCCTCCTCCTCCTCTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:19:5,14:161,344:0.0361:2,2:24.1:1:30.3:1:0.80262:1.30986:60:38:0.0367:0.0095:0.2 0/1:700:22:9,13:246,428:0.0314:2,2:31.2:1:29.9:1:0.65979:1.20:59.8:21:0.0305:0.0014:0.1 -X 76918804 . A G 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01446;SOR=Inf;LSEQ=CCTCAGCTTCCCAAAGTGCT;RSEQ=GGATTACAGGCATAAGCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:324,88:0:2,0:23.4:1:28.3:1:1:0:60:44.778:0.9975:0:0.1 0/1:405:6:3,3:297,99:0.0148:2,2:7:1:30.7:1:0.1739:2.99011:60:12:0.0149:0:1.7 -X 76919127 . A T 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5001;SOR=0;LSEQ=TATTTTGCCTGTTGACAACT;RSEQ=CTGCAACTTATGAAAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:1,73:0.0263:1,2:18:1:26.5:1:0.05228:51.98:60:4:0.0263:0:1 0/0:64:0:0,0:1,63:0:1,0:24.3:1:30.4:1:1:0:60:128:1:0:0 -X 76919991 . T C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=5.23071;LSEQ=CTCAAGTGATCCACCTGCTT;RSEQ=GGCCTCCCAAAGTCCTGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:12:12,0:67,0:0.1519:1,0:23.9:1:29.8:1:1:0:60:11:0.141:0:1.6 0/1:41:20:20,0:21,0:0.4878:1,1:22.1:1:31.6:1:1:0:60:40:0.4878:0:1.1 -X 76931638 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11513;SOR=Inf;LSEQ=ACTCCTGGTTTTTACAACCT;RSEQ=CTTGCTGTTCCGTTGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:137,34:0:2,0:23.4:1:31.8:1:1:0:60:56:1:0:0.1 0/1:163:3:1,2:125,35:0.0184:2,2:16.3:1:27.7:1:0.1294:7.02983:60:6:0.0185:0:1 -X 76931656 . G T 44 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.12211;SOR=0;LSEQ=CTGCTTGCTGTTCCGTTGCT;RSEQ=CTGTTTGTGCCCATGCCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:1,2:191,63:0.0117:2,2:14.7:1:28:1:0.15845:6.01097:60:6:0.0117:0:1 0/0:260:0:0,0:170,87:0:2,0:21.4:1:31.3:1:1:0:60:63.25:0.9883:0:0.1 -X 76931666 . C T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3573;SOR=0.30938;LSEQ=TTCCGTTGCTGCTGTTTGTG;RSEQ=CCATGCCTAGGGTGTGTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:1,2:202,88:0.0102:2,2:5.3:1:28:1:0.22424:4.56413:60:6:0.0103:0:1 0/0:314:1:1,0:193,119:0.0032:2,0:24:0:32:0:1:0:60:2:0.0033:0:1 -X 76931741 . GTCA G 108 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.04225;SOR=3.56565;LSEQ=CTATTCTCAGGATCATTGTC;RSEQ=TCATCATCATCCACTGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:3:3,0:357,310:0.0045:2,0:20:1:30.7:1:0.25306:0:60:6:0.0046:0.0015:0.3 0/1:823:13:7,6:415,394:0.0158:2,2:27.8:1:29.4:1:1:1.11:60:26:0.016:0.0024:0.2 -X 76932438 . G A 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGCCTGGCCAACATGGC;RSEQ=AAATCCCGTCTCTACTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:0:30.5:1:1:0:60:4:1:0:1.5 -X 76937963 . G C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.75158;LSEQ=TTCCAAAGAAGTAAAACTCT;RSEQ=CTCTTTCCCAGAAAGCTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:42:18,24:175,159:0.1117:2,2:24.6:1:30.6:1:0.25622:1.466:60:41:0.1108:0:1.1 0/1:445:187:92,95:146,111:0.4202:2,2:24.4:1:30.8:1:0.12346:1.35724:60:92.5:0.4195:0:1.1 -X 76939830 . A G 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GATGTATGTTCATATACTTT;RSEQ=TTACTCTTTTCACTGTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:703:62:29,33:326,315:0.0882:2,2:25:1:32.2:1:0.59547:1.17739:60:61:0.0879:0:1.1 0/0:896:0:0,0:452,444:0:2,0:24.1:1:28.7:1:1:0:60:111:1:0:0.1 -X 76940534 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=5.76716;LSEQ=AGGAAGGGGAAATTTAATTC;RSEQ=AAATTGATAACATTCATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:49:15,34:108,259:0.1178:2,2:25:1:31:1:0.86852:1.06:60:98:0.1189:0:1.1 0/1:473:206:65,141:97,170:0.4355:2,2:25.4:1:30.6:1:0.28437:1.23718:60:412:0.4355:0:1.1 -X 76940627 . AT A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20954;SOR=Inf;LSEQ=GGACACTGGTGTGGGCAAAG;RSEQ=TTATTGAGCATATTACACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:0,61:0:1,0:28.1:1:30.1:1:1:0:60:29.5:1:0:0.2 0/1:52:2:0,2:0,50:0.0385:1,0:15.5:1:30.5:1:1:0:60:4:0.0385:0.0192:1 -X 76944240 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21497;SOR=0;LSEQ=CATCTTTCTTCAAGACTGTG;RSEQ=CCTCAAAGGCCTGGTATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:2,0:162,29:0.0103:2,0:30.5:1:31.5:1:1:0:60:4:0.0109:0:1 0/0:225:0:0,0:182,43:0:2,0:23.6:1:30.2:1:1:0:60:15.071:1:0:0.1 -X 76949226 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50745;SOR=Inf;LSEQ=TAAACAAAAGGCAGAAAAGT;RSEQ=GAGGTATTTTTAGTAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:137,9:0:2,0:26.5:1:32.4:1:1:0:60:72:1:0:0 0/1:191:2:1,1:160,29:0.0105:2,2:14.5:1:29:1:0.29016:5.44152:60:4:0.0106:0:1 -X 76952289 . C G 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30048;SOR=0.50763;LSEQ=GTTGAGATTGAGCAGTGGGT;RSEQ=TCAACAAGGAAGCACATCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:12:0,12:1,73:0.1395:1,0:26.8:1:32.8:1:1:0:60:24:0.1412:0:1.1 0/1:66:5:0,5:1,60:0.0758:1,0:29.2:1:30:1:1:0:60:10:0.0758:0:1 -X 76953957 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23734;SOR=Inf;LSEQ=TGAAGTATAATGACAACTGG;RSEQ=TATCAGTAGCCTTCGACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:163,27:0:2,0:22.3:1:31.2:1:1:0:60:94:1:0:0.1 0/1:181:2:1,1:153,26:0.011:2,2:21:1:28:1:0.2768:5.7935:60:4:0.0111:0:1 -X 76972553 . T TA 97 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.81103;SOR=0.8806;LSEQ=AATGGTTACCTCCATAAGTG;RSEQ=AAAAAAAAAATAGAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:8:5,3:139,42:0.0423:2,2:22.3:1:28.1:1:0.39807:1.97749:60:16:0.0432:0.0106:0.1 0/1:267:10:8,2:187,70:0.0375:2,2:32.8:1:29.2:1:1:1.50:60:20:0.0382:0:0.4 -X 77041281 . A C 27 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCCCCCCACCCCATCCCC;RSEQ=CCCCCACCCCCGTCGGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:0:0,0:10.8:1:29:1:1:0:60:8:1:0:2 0/1:10:2:2,0:8,0:0.2:0,0:12:0:27:0:1:0:40:4:0.2:0:2.5 -X 77041336 . G T 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50455;SOR=Inf;LSEQ=CGAAACCCTTCTCACCTAAA;RSEQ=AGAAAACGATGCCTCTTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:58,4:0:2,0:23.8:1:32.5:1:1:0:60:61:1:0:0.2 0/1:80:2:1,1:75,2:0.025:1,2:22.5:1:24.5:1:0.07498:30.84276:60:4:0.0263:0:1 -X 77041377 . A G 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21688;SOR=0;LSEQ=GCTAAGCAACACACAGGCCT;RSEQ=ACCCACCAAGCGAACGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:135,57:0.0103:2,2:7.5:1:29:1:0.50964:2.35662:60:4:0.0104:0:1.5 0/0:222:0:0,0:153,69:0:2,0:20.9:1:28:1:1:0:60:110:1:0:0.1 -X 85302305 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49667;SOR=Inf;LSEQ=TCAAATGGCGATAAGCACTG;RSEQ=GGGTCCCAGCCCCTCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:0:2,0:28:1:30.2:1:1:0:60:12:1:0:0.2 0/1:32:2:1,1:14,16:0.0625:2,2:24.5:1:28.5:1:1:1.14:60:4:0.0625:0:1 -X 85302315 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19831;SOR=0;LSEQ=ATAAGCACTGCGGGTCCCAG;RSEQ=CCCTCCCTGTAACTGCCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:14,11:0.0741:2,2:19.5:1:28.5:1:1:1.2613:60:4:0.0769:0:1 0/0:33:0:0,0:16,17:0:2,0:34.2:1:30.9:1:1:0:60:66:1:0:0.2 -X 86830845 . C T 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00352;SOR=1.80337;LSEQ=GCAAATCTTGGATTTCACTT;RSEQ=CATTTAACTAAAAATGAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:54:23,31:64,76:0.2784:2,2:27.1:1:29.5:1:0.74874:1.13427:60:53:0.2804:0:2 0/1:285:117:54,63:85,82:0.4105:2,2:26.5:1:29.3:1:0.47016:1.20853:60:116:0.4128:0:1.9 -X 86830854 . TA T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.16756;SOR=0;LSEQ=GGATTTCACTTCCATTTAAC;RSEQ=AAAATGAGGGGCTAAAAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:84,103:0.0106:2,2:36:1:31:1:1:1.22:60:4:0.0107:0:0 0/0:272:0:0,0:127,145:0:2,0:26.2:1:28.7:1:1:0:60:67:1:0:0.9 -X 86830863 . G A 205 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00111;SOR=1.94015;LSEQ=TTCCATTTAACTAAAAATGA;RSEQ=GGGCTAAAAAGCAAATAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:52:21,31:67,78:0.264:2,2:21.8:1:30.5:1:0.51765:1.26649:60:51:0.2656:0:2 0/1:263:108:49,59:69,86:0.4106:2,2:27.2:1:30.4:1:0.90039:1.04:60:107:0.41:0:2 -X 86831002 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1707;SOR=0;LSEQ=GTGTTGGTTTGAAAATTTGG;RSEQ=AAATACTGTGATAACATAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:0.125:1,0:42.5:1:30:0:1:0:60:4:0.125:0:1 0/0:22:0:0,0:0,22:0:1,0:25:1:31.2:1:1:0:60:44:1:0:0.2 -X 87956364 . AT A 29 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTTGGTTGATTCAGCTGTTG;RSEQ=TTTTTTTTTTTTTTTTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:1:0:28.5:1:1:0:50:4:1:0:0 1/0:4:2:1,1:1,1:0.5:2,2:34:1:29:1:1:1:60:4:0.5:0:2 -X 87956989 . C A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=TTCGATTTTCAGCACTTTCT;RSEQ=ATTGATTCCTTCTCATCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:0.1538:2,2:17:0:31:1:1:1.67325:60:4:0.1667:0:1.5 0/0:14:0:0,0:7,7:0:2,0:21.4:1:30.9:1:1:0:60:28:1:0:0.2 -X 87957056 . G T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23256;SOR=Inf;LSEQ=AGGCTGCTGACTCTTGGATG;RSEQ=GGTTTTTGTGGGGGCCTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:0:2,0:29.4:1:31.4:1:1:0:60:44:1:0:0.2 0/1:21:2:1,1:9,10:0.0952:2,2:20:0:29.5:1:1:1.11:60:4:0.0952:0:1 -X 87957083 . T A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12644;SOR=Inf;LSEQ=TGTGGGGGCCTTTTTTGTCG;RSEQ=TGTTGCTTTCTGCTTGTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:0:2,0:20.2:1:29.8:1:1:0:60:38:1:0:0.1 0/1:11:2:1,1:4,5:0.1818:2,2:5.5:1:25.5:1:1:1.22:60:4:0.1818:0:1.5 -X 90689704 . G A 92 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.71525;SOR=1.47899;LSEQ=CTCCGTTGGACTGTCCTGCG;RSEQ=AGAGAAACCCCAGCCCATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:4,2:5,2:0.4615:2,2:18.8:1:30.3:1:1:1.22862:60:12:0.4615:0:1.2 1/0:16:9:7,2:5,2:0.5625:2,2:19.7:1:29.2:1:1:1.37:60:18:0.5625:0:1 -X 91136946 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4985;SOR=Inf;LSEQ=CATTACTCGTCTGAATAGAA;RSEQ=CAGGAAAGTGGAAAATAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:67,100:0:2,0:24.5:1:29.5:1:1:0:58.1:82.5:1:0:0.1 0/1:167:2:1,1:65,100:0.012:2,2:32:1:27.5:1:1:1.53:60:4:0.0122:0:1 -X 91420433 . TTG T 153 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75898;SOR=0.89152;LSEQ=ATCTTGCCTATGGGATTTTA;RSEQ=TCTGTACAGGGTATTTGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:31:22,9:49,24:0.2981:2,2:32.8:1:31:1:0.81919:1.20:41.5:62:0.2981:0.0288:0.4 0/1:102:28:19,9:47,27:0.2745:2,2:26.3:1:30:1:0.81738:1.21:41.5:56:0.2745:0.0392:0.6 -X 91420465 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49862;SOR=Inf;LSEQ=GGTATTTGTAATCACAAAAC;RSEQ=TATCTTTTTTTCTTTGCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:86,50:0:2,0:24.7:1:31.4:1:1:0:50.1:135:1:0:0.3 0/1:144:2:0,2:83,59:0.0139:2,0:10:1:27:1:0.17774:0:60:4:0.0143:0:2.5 -X 91420476 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5006;SOR=Inf;LSEQ=TCACAAAACCTATCTTTTTT;RSEQ=CTTTGCTCTATTACATACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:83,55:0:2,0:24.1:1:29.9:1:1:0:50.7:137:1:0:0.3 0/1:158:2:1,1:88,67:0.0127:2,2:43.5:1:32:1:1:1.31111:60:4:0.0131:0:1 -X 91420506 . T C 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.90433;SOR=0.95425;LSEQ=ATTACATACATAAGTCCCCA;RSEQ=TTAAACAGAATTAGGCAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:46:22,24:56,50:0.3026:2,2:25:1:31.8:1:0.59993:1.2202:35.6:92:0.3026:0:1.1 0/1:181:53:27,26:69,59:0.2928:2,2:24.6:1:30:1:0.74551:1.12543:35.2:52:0.2938:0:1.1 -X 91420556 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22487;SOR=0;LSEQ=AAGATTCAATTCCAGAGGTC;RSEQ=TTGGCTTTGTTGTAAAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:57,84:0.014:2,2:25.5:1:29:1:1:1.47:53.5:4:0.0142:0:1.5 0/0:158:0:0,0:60,98:0:2,0:26.1:1:30.6:1:1:0:49.5:157:1:0:0.3 -X 91420566 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4995;SOR=Inf;LSEQ=TCCAGAGGTCGTTGGCTTTG;RSEQ=TGTAAAATCCCATGACTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:42,85:0:2,0:27.2:1:30.2:1:1:0:47.6:126:1:0:0.3 0/1:141:2:1,1:52,87:0.0142:2,2:21:1:28.5:1:1:1.67:54.5:4:0.0142:0:1 -X 92181851 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.5112;SOR=Inf;LSEQ=CTGTTCTCCTTAGCCAAGGA;RSEQ=TAGTTGTATGTCCCAGACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:71,35:0:2,0:25.6:1:32.6:1:1:0:52.3:212:1:0:0.6 0/1:147:2:1,1:88,57:0.0136:2,2:17.5:1:28:1:1:1.53912:60:4:0.0138:0:3 -X 92181892 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.51344;SOR=Inf;LSEQ=GTGAATTCATACCTGAAACA;RSEQ=AAAAAAAGGAGAAATCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:71,63:0:2,0:26.1:1:31.4:1:1:0:56.9:66:1:0:1 0/1:190:2:1,1:93,95:0.0105:2,2:29.5:1:28:1:1:1.02:60:4:0.0106:0:3 -X 92181907 . T C 221 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAACACAAAAAAAGGAGAAA;RSEQ=CATTTTAAGTTAATTTATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:139:70,69:0,0:1:0,2:25:1:31.1:1:1:0:58.2:138:1:0:1.1 1/0:183:95:45,50:42,46:0.5191:2,2:22.7:1:30.5:1:1:1.01442:59.1:46.5:0.5167:0:1.5 -X 92181917 . T C 142 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGGAGAAATCATTTTAAG;RSEQ=TAATTTATTCTATTGGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:62,73:0:2,0:25.4:1:29.2:1:1:0:58.1:32.75:1:0:1 0/1:160:22:11,11:62,76:0.1375:2,2:23:1:31.9:1:0.81825:1.22:58.9:44:0.1392:0:2.3 -X 93324980 . A G 248 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72393;SOR=0.92955;LSEQ=CTTTGTTTCAATTTATTTTA;RSEQ=CCCATGAACACCTTTTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:307:215:95,120:42,49:0.7003:2,2:25.1:1:32.1:1:0.80182:1.08242:60:214:0.711:0:1.1 1/0:295:202:95,107:36,56:0.6847:2,2:26.8:1:31.9:1:0.25474:1.38:60:404:0.6894:0:1.1 -X 93325029 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49859;SOR=Inf;LSEQ=TTTCTCTTTATGTCTGATTG;RSEQ=TATGGCAAAATCCAGGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:58,114:0:2,0:24:1:31.9:1:1:0:60:344:1:0:0.6 0/1:175:2:1,1:59,114:0.0114:2,2:29:1:28.5:1:1:1.92:60:4:0.0116:0:1.5 -X 93325074 . G A 79 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01314;SOR=Inf;LSEQ=ATAAGCTATGCATTCAAGAC;RSEQ=CCAGGTCCTTGAAACCATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:12,52:0:2,0:22:1:31.6:1:1:0:60:128:1:0:0.1 0/1:63:6:2,4:10,47:0.0952:2,2:25:1:30.8:1:0.32007:2.31:60:12:0.0984:0:1.2 -X 93325079 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4958;SOR=0;LSEQ=CTATGCATTCAAGACGCCAG;RSEQ=TCCTTGAAACCATACATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:10,48:0.0333:2,2:6.5:1:28.5:1:0.33559:4.62:60:4:0.0333:0:1.5 0/0:59:0:0,0:11,48:0:2,0:24:1:31.4:1:1:0:60:118:1:0:0.2 -X 93434358 . GT G 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49908;SOR=0;LSEQ=CCTGAAGTGGCTTAGGAAAT;RSEQ=TTTTTTAACCTGTCAATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:116,70:0.0106:2,2:24.5:1:28.5:1:1:1.65244:60:4:0.0107:0.0053:0 0/0:177:0:0,0:105,72:0:2,0:23.2:1:29.4:1:1:0:60:176:1:0:0.3 -X 93434435 . G A 220 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.46176;LSEQ=TCAATAAACTTATTTTCTTC;RSEQ=TTGGGGACCTGTTATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:153:79,74:45,52:0.612:2,2:24.7:1:30.4:1:0.43853:1.23:60:152:0.6154:0:1.1 0/1:285:120:59,61:84,79:0.4211:2,2:22.7:1:29.8:1:0.7193:1.09897:60:39:0.4179:0:1.3 -X 93434463 . C G 98 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00181;SOR=Inf;LSEQ=CCTGTTATGGAAAAGCAATT;RSEQ=CACTGCAGAAATTAATTAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:103,124:0:2,0:25.8:1:30.9:1:1:0:60:55.75:1:0:0.6 0/1:237:10:5,5:106,120:0.0422:2,2:17.3:1:29.8:1:1:1.13:60:20:0.0427:0:1.8 -X 93434491 . G T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50003;SOR=Inf;LSEQ=GAAATTAATTAGCTGACAGA;RSEQ=AAATCTTCCCATACAAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:63,104:0:2,0:27.8:1:31.6:1:1:0:60:82.5:1:0:0.5 0/1:186:2:1,1:70,114:0.0108:2,2:21.5:1:29:0:1:1.62:60:4:0.0108:0:2.5 -X 93434496 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49886;SOR=Inf;LSEQ=TAATTAGCTGACAGAGAAAT;RSEQ=TTCCCATACAAATGAATGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:61,100:0:2,0:26.8:1:31.5:1:1:0:60:52.667:1:0:0.5 0/1:170:2:1,1:62,106:0.0118:2,2:27:1:28.5:1:1:1.70:60:4:0.0121:0:1 -X 97019100 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=CCACTTATCAGCAAAACCCT;RSEQ=GGCAACTGAGCTGGGGCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:96,32:0:2,0:24.8:1:31.2:1:1:0:60:24.6:1:0:0.1 0/1:137:2:1,1:92,43:0.0146:2,2:27:1:27:1:0.54079:2.12659:60:4:0.0147:0:1.5 -X 97019115 . G A 39 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24843;SOR=Inf;LSEQ=ACCCTGGGCAACTGAGCTGG;RSEQ=GCAGAATCAGCAGCTGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:109,54:0:2,0:23.8:1:30.7:1:1:0:60:53.333:0.9938:0:0.2 0/1:174:3:1,2:113,58:0.0172:2,2:17:1:25:1:0.27349:3.86388:60:2:0.0117:0:1.3 -X 97019120 . A T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24517;SOR=0;LSEQ=GGGCAACTGAGCTGGGGCAG;RSEQ=ATCAGCAGCTGAAACTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:117,60:0.0112:2,2:21:1:30:1:1:1.94226:60:4:0.0112:0:1.5 0/0:182:0:0,0:115,67:0:2,0:24.8:1:28.9:1:1:0:60:181:1:0:0.3 -X 97019123 . C A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2453;SOR=0;LSEQ=CAACTGAGCTGGGGCAGAAT;RSEQ=AGCAGCTGAAACTTTCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:118,64:0.0109:2,2:14.5:1:29:0:1:1.83732:60:4:0.0109:0:1.5 0/0:187:0:0,0:119,68:0:2,0:25:1:30.6:1:1:0:60:61.333:1:0:0.3 -X 97019199 . G A 40 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67118;SOR=1.67962;LSEQ=TTAACTTTTTCCATCCTCAT;RSEQ=CGTCATTGCTAAGGGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:2:2,0:163,162:0.0061:2,0:22.5:1:27.5:1:0.49851:0:60:4:0.0062:0:1.5 0/1:293:3:2,1:148,142:0.0102:2,2:9.3:1:25.7:1:1:1.91:60:6:0.0105:0:1.7 -X 97019201 . G A 230 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.19151;LSEQ=AACTTTTTCCATCCTCATGC;RSEQ=TCATTGCTAAGGGATTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:324:179:91,88:70,74:0.5525:2,2:27.5:1:30.5:1:0.73738:1.09:60:178:0.5528:0:1.1 1/0:293:214:109,105:40,39:0.7304:2,2:26.2:1:29.8:1:1:1.01:60:70.333:0.7301:0:1.1 -X 97019268 . C A 29 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57643;SOR=2.73563;LSEQ=TCCACCCTGGTAATCAGTGC;RSEQ=TTACATACAATGGTAGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:1:1,0:79,150:0.0043:2,0:5:0:14:0:0.34783:0:60:0:0:0:1 0/1:169:2:1,1:58,109:0.0118:2,2:23:1:29:1:1:1.87:60:4:0.0119:0:1 -X 97019326 . G A 173 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50795;SOR=0.70448;LSEQ=CTTTTCAAGAAAGGTGACTG;RSEQ=TAAGAATTTCTCAGGGACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:47:5,42:1,13:0.7705:1,2:24.9:1:31.2:1:1:1.54:60:46:0.7667:0:1.1 1/0:47:33:5,28:2,12:0.7021:2,2:21.6:1:29.8:1:1:1.07:60:32:0.6957:0:1.1 -X 97157710 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49826;SOR=Inf;LSEQ=GGATATGGCAATCCTTGCTT;RSEQ=TTGACAAGGATCCTTTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:15,3:0:2,0:22.5:1:32.6:1:1:0:60:36:1:0:0.1 0/1:24:2:1,1:18,4:0.0833:2,2:18:1:30.5:1:0.38043:4.13522:60:4:0.0833:0:1 -X 97157753 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12957;SOR=0;LSEQ=CTGAACTTTAGTCAGGCTCC;RSEQ=GAAACTTCTTCTAGGCCTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:18,12:0.0625:2,2:36.5:1:30:1:1:1.48061:60:4:0.0625:0:1 0/0:56:0:0,0:30,26:0:2,0:25:1:29.7:1:1:0:60:55:1:0:0.1 -X 100056870 . G A 44 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2124;SOR=4.11607;LSEQ=ACAAACTTATTAGTAATAAT;RSEQ=ATGGTAGTATCTTTGATGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:1:1,0:178,225:0.0025:2,0:1:0:26:0:0.44307:0:60:2:0.0025:0:1 0/1:395:4:2,2:185,206:0.0101:2,2:11.5:1:22:1:1:1.11:60:3:0.0077:0:2 -X 100057572 . C T 225 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCTATGCCTCCACCACCAC;RSEQ=TCAGGGAGTTAAGTGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:665:178:96,82:263,224:0.2677:2,2:27:1:30.1:1:1:1.00288:60:88:0.2687:0:1.1 0/0:787:0:0,0:406,380:0:2,0:24.6:1:30.4:1:1:0:59.9:28.111:1:0:0.2 -X 100594828 . G T 26 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22321;SOR=0;LSEQ=CTATTTGATATGCCAGTGTT;RSEQ=TGTGGGAAGTATAATTCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:102,38:0.0141:2,2:29.5:1:26:1:0.47528:2.66253:60:4:0.0142:0:6 0/0:158:0:0,0:120,38:0:2,0:21:1:30.9:1:1:0:60:51.667:1:0:0.1 -X 100594834 . G T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50074;SOR=Inf;LSEQ=GATATGCCAGTGTTGTGTGG;RSEQ=AAGTATAATTCTTTTTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:112,51:0:2,0:20.3:1:30.3:1:1:0:60:31.6:1:0:0.2 0/1:186:2:1,1:132,52:0.0108:2,2:14:0:30:0:0.4898:2.52391:60:4:0.0109:0:1 -X 100594872 . G T 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13169;SOR=Inf;LSEQ=TAAAAAAGAGCTTCCTTTTG;RSEQ=CCGGAACTGCCATCTTTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:177,131:0:2,0:28:1:30.9:1:1:0:60:33.222:1:0:0.2 0/1:379:4:1,3:211,164:0.0106:2,2:12.5:1:25.8:1:0.32462:3.84681:60:8:0.0108:0:1 -X 100595660 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50634;SOR=Inf;LSEQ=TGTGTCTACACTGTTAACCA;RSEQ=CATGCTGTTGGCATTGTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:23,27:0:2,0:31.1:1:32.2:1:1:0:60:49:1:0:0 0/1:67:2:1,1:27,38:0.0299:2,2:14:1:29.5:1:1:1.40:60:4:0.0299:0:1 -X 100604681 . C T 49 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01681;SOR=Inf;LSEQ=AATTTCAGGCACAATAATTT;RSEQ=TTGGCCTTTGCTCAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:26,0:0:1,0:23.3:1:31.2:1:1:0:60:25:1:0:0.2 0/1:10:3:3,0:7,0:0.3:0,0:15.3:1:31.3:1:1:0:60:6:0.3:0:1 -X 100604757 . T G 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.12934;SOR=0.58919;LSEQ=AGATGTAGAGAGGGGCCTTT;RSEQ=TGTATTGAGTGGGAGCACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:46:46,0:32,2:0.575:2,1:26:1:32.5:1:0.17753:0:60:92:0.575:0:1 0/1:61:27:27,0:34,0:0.4426:1,1:20.1:1:32.8:1:1:0:60:54:0.4426:0:1 -X 100608120 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18309;SOR=Inf;LSEQ=CAGTCTTTGGTGGCTGAATG;RSEQ=CCAGCTAAATGGGCAAGTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:195,44:0:2,0:26.8:1:30.6:1:1:0:60:16.071:1:0:0.3 0/1:180:2:1,1:129,49:0.0111:2,2:15.5:1:28.5:1:0.47952:2.61628:60:4:0.0113:0:1.5 -X 100608191 . G A 219 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=249.91529;LSEQ=AAAGCACTTACCTCATGCCA;RSEQ=CAACTGTACATGATGGTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:1:1,0:281,208:0.002:2,0:1:0:29:0:1:0:60:2:0.0021:0:1 0/1:472:160:87,73:175,136:0.339:2,2:25.5:1:30:1:0.69666:1.07952:60:79:0.3376:0:1.2 -X 100609517 . G GA 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0291;SOR=0;LSEQ=GGCAGAAAACGCTAGAATGA;RSEQ=AAAAAAAAGAAAAGGAGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:5:4,1:158,13:0.0284:2,2:21.2:1:30.4:1:0.34258:3.00912:60:10:0.0286:0.017:0.4 0/0:179:0:0,0:161,18:0:2,0:20.8:1:31.8:1:1:0:60:88.5:1:0:0.8 -X 100609547 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.53694;LSEQ=AAAAGGAGAGGATTAAAACT;RSEQ=TAACACCTACCCATGTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:171:130,41:133,46:0.4886:2,2:22.6:1:28.8:1:0.71277:1.10:60:84.5:0.487:0:1.1 1/1:370:325:238,87:32,12:0.8784:2,2:22:1:28.5:1:1:1.03:60:161.5:0.8801:0:1.1 -X 100611131 . C T 78 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01679;SOR=Inf;LSEQ=GCAGCTGCTGAGTCTGGAAG;RSEQ=GGTGGCGCATCTCCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:596:0:0,0:259,337:0:2,0:23.7:1:30.6:1:1:0:60:48.667:1:0:0.1 0/1:680:7:2,5:310,359:0.0103:2,2:21:1:28:1:0.46043:2.15643:60:14:0.0104:0:1 -X 100611283 . T C 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49875;SOR=Inf;LSEQ=GAAAGGCAAGGAACTAGTCT;RSEQ=CTCCTTTTGGCTCTGCATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:52,148:0:2,0:23.2:1:29.8:1:1:0:60:49:1:0:0.2 0/1:200:2:1,1:53,145:0.01:2,2:15:1:33:0:0.46809:2.72:60:4:0.0104:0:1 -X 100611285 . T C 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCAAGGAACTAGTCTTC;RSEQ=CCTTTTGGCTCTGCATAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:50,142:0:2,0:23.2:1:29.9:1:1:0:60:31:1:0:0.2 0/1:192:59:14,45:38,93:0.3073:2,2:20.7:1:29.8:1:0.48684:1.31152:60:28.5:0.3032:0:1.2 -X 100611299 . C A 34 v4;q23;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62252;SOR=0.3392;LSEQ=GTCTTCTCCTTTTGGCTCTG;RSEQ=ATAATAGCAATAAAGGGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:3:2,1:35,107:0.0205:2,2:15.7:1:21.7:1:0.16015:6.02:60:2:0.0141:0:2 0/0:142:1:1,0:36,105:0.007:2,0:1:0:24:0:0.26056:0:60:2:0.0072:0:1 -X 100612389 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=TGTCTTGAGCGTCCTTGAGG;RSEQ=AGCTGCTGCAGAACAGTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:177,17:0:2,0:24.2:1:32.2:1:1:0:60:37.8:1:0:0.1 0/1:195:2:1,1:169,23:0.0103:2,2:5.5:1:26:1:0.23268:7.21356:60:4:0.0104:0:1 -X 100613489 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.49849;SOR=Inf;LSEQ=AACAGAACCCAGGAAGTGAA;RSEQ=TGAGATGAGTTTTGAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:80,79:0:2,0:22:1:31.9:1:1:0:60:38.75:1:0:0.1 0/1:163:2:1,1:79,82:0.0123:2,2:14.5:1:28.5:1:1:1.04:60:4:0.0124:0:1 -X 100613537 . G T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.252;SOR=Inf;LSEQ=GAGGAAGTGGGACGGGCACA;RSEQ=CATCAAGGAGCTATTAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:156,67:0:2,0:24.5:1:32:1:1:0:60:73.333:1:0:0.1 0/1:256:3:1,2:154,97:0.0117:2,2:23:1:26.7:1:0.56222:3.16052:60:6:0.0121:0:1 -X 100613750 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24301;SOR=Inf;LSEQ=ACACCTGCATCCCACCTGCC;RSEQ=AAACTTGAGAGAGAAAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:38,160:0:2,0:23:1:31.3:1:1:0:60:27.286:1:0:0.1 0/1:193:2:1,1:43,148:0.0104:2,2:40.5:1:29.5:1:0.4049:3.41:60:4:0.0104:0:1 -X 100613923 . C T 48 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACCTGAGGTCAGGAGTT;RSEQ=GAGACCAGCCTGGCCAACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:1,10:0.2143:2,2:11.7:1:30.7:1:0.3956:4.28:51.7:6:0.2143:0:1 0/0:2:0:0,0:0,2:0:0,0:29:1:30:1:1:0:54:4:1:0:0 -X 100614139 . CA C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50041;SOR=0;LSEQ=CCGTCTCAGAAAAACAAAAA;RSEQ=AAAAAAATGGTGTAATTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:2,0:89,2:0.0215:1,0:29.5:1:31:1:1:0:60:4:0.022:0:0 0/0:79:0:0,0:79,0:0:1,0:24.5:1:30.3:1:1:0:60:158:1:0:0.1 -X 100614867 . GTA G 51 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.55484;SOR=0;LSEQ=TGTTGAAAGTAGAAAAAAGT;RSEQ=TATATATATATACACACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:18,3:0.125:2,0:16.3:1:32.3:1:1:0:60:6:0.125:0.0833:0 0/0:8:0:0,0:8,0:0:0,0:21.6:1:30.5:1:1:0:60:16:1:0:0 -X 100614965 . TTA T 71 MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.22742;SOR=0.24059;LSEQ=CATATATACACTTGTGTGTG;RSEQ=TATATATATATAAATATATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:5:5,0:87,5:0.0515:2,0:30.6:1:30.6:1:1:0:60:10:0.0515:0.0103:0 0/1:78:1:1,0:73,3:0.0128:1,0:20:0:32:0:1:0:60:2:0.013:0:0 -X 100614997 . T TATAA 68 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=4.000;MSILEN=4;SSF=0.01981;SOR=Inf;LSEQ=ATAAATATATATAAAATATA;RSEQ=ATAAATAAATAAATATATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:150,31:0:2,0:20.5:1:30.1:1:1:0:59.7:362:1:0:0.4 0/1:154:5:3,2:114,35:0.0325:2,2:11.4:1:29.5:1:0.59422:2.15868:56:10:0.0325:0.0195:1.8 -X 100615009 . AAT A 121 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.6918;SOR=0.80076;LSEQ=AAAATATATATAAATAAATA;RSEQ=ATATATATATATAGAGAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:16:13,3:169,65:0.064:2,2:26.5:1:30.4:1:0.56821:1.66:59.7:32:0.064:0.004:0.1 0/1:212:11:7,4:141,61:0.0519:2,2:10.9:1:28.7:1:0.73922:1.31908:60:22:0.0521:0.033:0.4 -X 100615023 . TAG T 91 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.82034;SOR=1.12816;LSEQ=TAAATAAATATATATATATA;RSEQ=AGAGAGAGAGTTCCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:9:8,1:227,98:0.0268:2,2:30.4:1:32.4:1:0.29021:3.44:60:18:0.0269:0:0 0/1:332:10:4,6:213,108:0.0301:2,2:22.3:1:27.4:1:0.09884:2.94783:59.5:9:0.0273:0.009:0.9 -X 100615025 . G T 197 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.24317;SOR=1.2268;LSEQ=AATAAATATATATATATATA;RSEQ=AGAGAGAGAGTTCCTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:95:69,26:163,76:0.277:2,2:20.2:1:29.8:1:0.51046:1.24:59.3:94:0.2848:0:1.1 0/1:344:110:75,35:146,81:0.3198:2,2:18.2:1:29.1:1:0.54152:1.19:60:220:0.3323:0:1.2 -X 100615027 . G T 51 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.21428;SOR=0.24497;LSEQ=TAAATATATATATATATAGA;RSEQ=AGAGAGAGTTCCTCCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:4:3,1:248,110:0.011:2,2:11:1:25.5:1:1:1.33:50.3:3:0.0084:0:2 0/0:367:1:1,0:236,130:0.0027:2,0:7:0:24:0:1:0:60:2:0.0028:0:2 -X 100615217 . A G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1791;SOR=Inf;LSEQ=TTCATATGCCCACGTCCCTG;RSEQ=GCTCAGAACAAATCTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:53,208:0:2,0:22.5:1:30.8:1:1:0:60:129.5:1:0:0.1 0/1:192:2:1,1:36,154:0.0104:2,2:35:1:29:1:0.34909:4.23:60:4:0.0105:0:1 -X 100615478 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.22721;LSEQ=TCTGATGAGGATGCTGATCA;RSEQ=GGGAATTATGCCGCAGCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:198:113:98,15:81,4:0.5707:1,2:22.8:1:30.7:1:0.05174:3.08399:60:55.5:0.5692:0:1 0/1:173:40:36,4:110,23:0.2312:2,2:21.6:1:30.4:1:0.32776:1.88:60:39:0.2281:0:1.1 -X 100615505 . G T 171 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0189;LSEQ=TATGCCGCAGCACTTTTTGC;RSEQ=TGTAGGGAGTGGGCAGGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:44:37,7:209,55:0.1429:2,2:25.5:1:31.4:1:0.54558:1.39:60:88:0.1443:0:1 0/0:320:1:0,1:224,95:0.0031:2,0:1:0:28:0:0.3:0:60:2:0.0031:0:1 -X 100615777 . T A 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34265;SOR=3.46702;LSEQ=AGAAAAGGTAGGAGGGTTTG;RSEQ=CAAGATACCAAGCACTCTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:1,0:66,227:0.0034:2,0:1:0:25:0:0.22789:0:60:2:0.0034:0:1 0/1:256:3:3,0:78,175:0.0117:2,0:8.7:1:20.3:1:0.03087:0:60:2:0.0079:0:1 -X 100615793 . T A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21329;SOR=Inf;LSEQ=TTTGTCAAGATACCAAGCAC;RSEQ=CTTCTCTTCTCTCCCAACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:33,175:0:2,0:24.2:1:30:1:1:0:60:40.6:1:0:0.1 0/1:179:2:1,1:40,136:0.0112:2,2:16:1:30:1:0.40862:3.37:60:4:0.0114:0:1 -X 100616989 . C T 102 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=ACATGGTTGCTGAGAGCCTT;RSEQ=TATCTTTCCATCGAGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:64,0:0:1,0:22.7:1:31.3:1:1:0:60:63:1:0:0 0/1:45:11:10,1:34,0:0.2444:1,2:25.3:1:29.7:1:0.24444:0:60:22:0.25:0:1.2 -X 100617372 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=5.64174;LSEQ=GCATGCCAGGTCACATAGCT;RSEQ=GGAGAGCAGATTACCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:43:12,31:12,31:0.5:2,2:27.8:1:30.3:1:1:1:60:86:0.5:0:1 1/1:47:40:8,32:3,4:0.8511:2,2:23.6:1:29.9:1:0.32963:2.91644:60:80:0.8511:0:1.1 -X 100617706 . A T 151 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAGAAGAGAGAGATCAC;RSEQ=TCTGACATGGAGGAGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:99,254:0:2,0:23.4:1:30.5:1:1:0:60:49.429:1:0:0.2 0/1:376:35:8,27:105,236:0.0931:2,2:23.9:1:29.6:1:0.43901:1.50008:60:34:0.0914:0:1.1 -X 100624728 . TTTCTTTG T 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATACAAACTTTCCTTTG;RSEQ=TTATTTGTCTTTCTTTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:0.4444:0,0:40.3:1:31:1:1:0:60:8:0.5:0:0 0/0:1:0:0,0:1,0:0:0,0:14:0:31:0:1:0:60:2:1:0:0 -X 100624842 . A AT 48 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05427;SOR=Inf;LSEQ=TCTTTTCTCCCCTTCTATCC;RSEQ=TTTTTTTCTTCTTTTCTCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:39,2:0:1,0:15.9:1:29.4:1:1:0:60:19.5:1:0:0.2 0/1:26:3:3,0:23,0:0.1154:1,0:10:1:30.8:1:1:0:60:6:0.1154:0.0769:0 -X 100624920 . C T 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60357;SOR=0.44391;LSEQ=TCCTTCTTTCCTTTTCCTCC;RSEQ=GTCTATCTCCTCTTCCTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:141,14:0.0127:2,2:5.5:1:28:1:0.18251:9.76438:60:4:0.013:0:1 0/0:176:1:0,1:149,26:0.0057:2,0:1:0:24:0:0.15341:0:60:2:0.0058:0:1 -X 100624939 . C T 61 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13095;SOR=Inf;LSEQ=CCGTCTATCTCCTCTTCCTT;RSEQ=CTTTCCTTCTTTCTTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:170,45:0:2,0:22.8:1:30.9:1:1:0:60:106.5:0.9953:0:0.1 0/1:264:4:2,2:201,59:0.0152:2,2:8.5:1:30.8:1:0.22923:3.3868:60:8:0.0154:0:2 -X 100624945 . C T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25566;SOR=Inf;LSEQ=ATCTCCTCTTCCTTCCTTTC;RSEQ=TTCTTTCTTTGGAAACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:178,59:0:2,0:22.8:1:30.5:1:1:0:60:46.4:1:0:0.1 0/1:288:3:2,1:207,78:0.0104:2,2:14.3:1:24.3:1:1:1.32554:60:2:0.0071:0:1.7 -X 100626506 . C T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50218;SOR=0;LSEQ=CTTGGTTCAGCATCCTTGTC;RSEQ=ACCTCAACTTCTATTCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:143,16:0.0124:2,2:11.5:1:27:0:0.20062:8.70277:60:4:0.0127:0:1 0/0:135:0:0,0:124,11:0:2,0:23.9:1:29.3:1:1:0:60:32.75:1:0:0.1 -X 100626751 . A G 47 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25053;SOR=Inf;LSEQ=GCTCTTTTCTGAATTTCCTT;RSEQ=GGTACTAGAAGCCTTTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:27,139:0:2,0:23.1:1:30.8:1:1:0:60:54.333:1:0:0.1 0/1:187:3:1,2:46,138:0.016:2,2:15.7:1:29.7:1:1:1.50:60:6:0.016:0:1 -X 100626764 . C A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60556;SOR=0.44953;LSEQ=TTTCCTTAGGTACTAGAAGC;RSEQ=TTTTGCTGTGGCTTCAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:19,111:0.0152:2,2:9:1:29.5:1:0.28105:5.72:60:4:0.0153:0:1 0/0:146:1:1,0:28,117:0.0068:2,0:1:0:25:0:0.19863:0:60:2:0.0069:0:1 -X 100626864 . C T 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06531;SOR=0.28375;LSEQ=ACATATCCAATACGACCCAA;RSEQ=ACATACCCAGTCAAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:0,14:0,10:0.5833:0,1:33:1:27.6:1:1:0:60:13:0.5652:0:1.1 0/1:18:5:0,5:0,13:0.2778:1,0:22.8:1:27.6:1:1:0:60:10:0.2778:0:1.2 -X 100627125 . G T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGCTTTTTCTAATATAA;RSEQ=GATGAAACTTAGAACTATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:19.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 100629354 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12367;SOR=Inf;LSEQ=GAGATGTTCTGAATATGAAG;RSEQ=AAAGAAGCTAAGATTCTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:47,0:0:1,0:26.3:1:31.3:1:1:0:60:94:1:0:0 0/1:26:2:2,0:24,0:0.0769:1,0:32:1:28.5:1:1:0:60:4:0.08:0:1 -X 100629673 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19116;SOR=Inf;LSEQ=AAAGATTAAGAGGGATTAAG;RSEQ=AACCAGATGATTAGATTTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:15,171:0:2,0:23.1:1:32.4:1:1:0:60:185:1:0:0.1 0/1:145:2:1,1:15,128:0.0138:2,2:12.5:1:26.5:1:0.2092:8.29:60:4:0.0139:0:1 -X 100629748 . G GA 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.29004;SOR=0;LSEQ=GGACCTGTCATGTGGGGGAA;RSEQ=AAAAAAAAATCCTTCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:5,39:0.0833:2,0:27.5:1:31.3:1:1:0:60:8:0.0851:0:0 0/0:27:0:0,0:0,27:0:1,0:19.1:1:31.1:1:1:0:60:54:1:0:0.1 -X 100630054 . T A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51143;SOR=0;LSEQ=CCTCCTCCTACCAACGAAAA;RSEQ=TTACCTCTTCCCCAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:170,27:0.0101:2,2:32:1:32:1:0.26222:6.20101:60:4:0.0101:0:1 0/0:144:0:0,0:122,22:0:2,0:22.3:1:29.8:1:1:0:60:143:1:0:0.1 -X 100630321 . C A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25242;SOR=Inf;LSEQ=TGCTGTTGATAATGAAAGTT;RSEQ=CTGAGGACCCAGGACATTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:55,200:0:2,0:25.5:1:31.2:1:1:0:60:84:1:0:0.1 0/1:294:3:3,0:87,204:0.0102:2,0:5.3:1:20.7:1:0.02802:0:60:2:0.0069:0:1.7 -X 100630329 . C G 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAATGAAAGTTCCTGAGGA;RSEQ=CCAGGACATTAATCCTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:42,184:0:2,0:25.9:1:31.1:1:1:0:60:55.5:1:0:0.1 0/1:250:21:5,16:58,171:0.084:2,2:22.4:1:32:1:1:1.08503:60:42:0.0864:0:1.1 -X 100630500 . G A 81 MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATGCACACTGAATTGGGGGG;RSEQ=GATTGGTTCGATGTTGTGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:0.5:0,0:25.8:1:31.5:1:1:0:60:12:0.5:0:1 1/0:2:1:0,1:0,1:0.5:0,0:16:0:33:0:1:0:60:2:0.5:0:1 -X 100645467 . T C 239 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=83.77603;LSEQ=GCCTATTAGATTACTGTACC;RSEQ=CTCCCCCGGAACAGTGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:606:4:2,2:334,267:0.0066:2,2:20.5:1:30.8:1:1:1.25046:60:8:0.0067:0:1 0/1:661:237:129,108:221,202:0.3585:2,2:25.8:1:30.4:1:0.62595:1.09:60:117.5:0.3615:0:1.1 -X 101870343 . AAGTGGGTGGCTCTTAAAAGTGACTTTGAGTTGGGTAGAATTATTGCTGAGGAAGCTTTATGCTTTCTGTCTACGAATGTGGCATGTAAGCTCGATGTTCTTGAGCATGATAGTCACTCAG A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21187;SOR=Inf;LSEQ=CATAATTATGTTTTCAGATA;RSEQ=AGTGGATGGCGCACAGATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:51,0:0:1,0:22.1:1:30.3:1:1:0:60:50:1:0:0.1 0/1:44:2:1,1:41,1:0.0455:1,2:17:1:28.1:1:0.08985:29.33286:60:4:0.0455:0.0455:0 -X 101870511 . G A 54 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05018;SOR=Inf;LSEQ=CAAAGAGCCCCACCAGGTAG;RSEQ=CCTCTCACACTTCCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:0:0,0:214,213:0:2,0:24.2:1:31.3:1:1:0:60:52.375:0.9952:0:0.1 0/1:387:4:2,2:178,205:0.0103:2,2:20.8:1:27:1:1:1.15:60:8:0.0105:0:1 -X 101870739 . AT A 50 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.53295;LSEQ=CGGGCTACCTTGGTGGCCAG;RSEQ=TTTTTTTTTGTTTGTTTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:3:0,3:1,77:0.037:1,0:29:1:32:0:1:0:60:6:0.038:0:0 0/1:50:1:0,1:1,48:0.02:1,0:16:0:32:0:1:0:60:2:0.0208:0:0 -X 101870747 . TTTG T 30 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=0.5052;SOR=0;LSEQ=CTTGGTGGCCAGATTTTTTT;RSEQ=TTTGTTTTATAATTTTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:0,2:1,58:0.0328:1,0:19.5:1:30:1:1:0:60:4:0.0333:0.0164:0.5 0/0:46:0:0,0:1,45:0:1,0:22.7:1:29.3:1:1:0:60:45:1:0:0.4 -X 102721317 . G A 71 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03116;SOR=Inf;LSEQ=AGATGTGGAAGTGATCAGGT;RSEQ=CAACTCGAATTTTTCATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:37,30:0:2,0:25.8:1:31.6:1:1:0:60:66:1:0:0.1 0/1:79:6:5,1:48,25:0.0759:2,2:24.8:1:27.8:1:0.65762:2.58:60:12:0.0759:0:1 -X 102721326 . A T 87 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00728;SOR=Inf;LSEQ=AGTGATCAGGTGCAACTCGA;RSEQ=TTTTTCATACAAGCAAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:42,36:0:2,0:27.6:1:29.7:1:1:0:60:18.5:1:0:0.1 0/1:88:8:6,2:50,30:0.0909:2,2:27.4:1:29:1:0.70524:1.79:60:16:0.092:0:1 -X 102721361 . GGGT G 81 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03879;SOR=Inf;LSEQ=AAAGCCCGAGTCAGCGTGAG;RSEQ=GGTGGTGGTGGGGCAGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:45,54:0:2,0:27.6:1:31.2:1:1:0:60:98:1:0:0.1 0/1:132:6:3,3:60,65:0.0455:2,2:22.2:1:31.6:1:1:1.08:60:12:0.0455:0.0076:0.5 -X 102721388 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52257;SOR=Inf;LSEQ=GGTGGTGGGGCAGGGAGAGA;RSEQ=TGCCATTGCTTGGAGTTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:27,42:0:2,0:25.8:1:32.1:1:1:0:60:138:1:0:0.1 0/1:109:2:1,1:42,65:0.0183:2,2:47.5:1:29.5:1:1:1.54:60:4:0.0183:0:1.5 -X 102721403 . GT G 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13889;SOR=0;LSEQ=AGAGACTGCCATTGCTTGGA;RSEQ=TACTTAGGACACAGTCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:17,32:0.0392:2,2:29:1:33:1:1:1.86:60:4:0.0392:0:0 0/0:85:0:0,0:27,58:0:2,0:26.1:1:29.4:1:1:0:60:170:1:0:0.2 -X 104140863 . T G 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39439;SOR=0.40489;LSEQ=CTCCCCTTTCTCGGTCCCAT;RSEQ=GCAGCCATCTTGCTATTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:1,3:5,6:0.2667:2,2:10.8:1:31:1:0.6044:2.35829:53.8:8:0.2667:0:1 0/1:16:2:1,1:7,7:0.125:2,2:8:1:31:1:1:1:60:4:0.125:0:1 -X 105425922 . C T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11108;SOR=0;LSEQ=GCAAGATGGCTGTCACGGGA;RSEQ=CTAGAAAGGGGAGAAGCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:0,2:16,12:0.0667:2,0:5:1:28.5:1:0.2092:0:60:4:0.0667:0:1 0/0:59:0:0,0:34,25:0:2,0:21.8:1:31.3:1:1:0:57.3:118:1:0:0.3 -X 106444086 . T C 82 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00423;SOR=Inf;LSEQ=GTCAAATGCAAAAGACAGCC;RSEQ=CAAAGGTACGCCCATATTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:0:1,0:28.2:1:31.6:1:1:0:60:66:1:0:0.1 0/1:31:7:7,0:24,0:0.2258:1,0:23.6:1:29.3:1:1:0:60:14:0.2333:0:1 -X 106444141 . C CA 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49781;SOR=Inf;LSEQ=AAAACTCTGGAAAAGTAGAG;RSEQ=AAAAAAACCCTCAAAAAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:59,17:0:2,0:23.3:1:31.9:1:1:0:60:37:1:0:0.2 0/1:83:2:1,1:67,14:0.0241:2,2:9.5:1:26.9:1:0.33059:4.65785:60:4:0.0244:0.012:0 -X 106444209 . G A 175 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCATAAAAACCTTTTACA;RSEQ=ACATGCAAGTAAGAAAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:111,100:0:2,0:25.8:1:31.6:1:1:0:60:69.333:1:0:0.1 0/1:238:67:34,33:86,85:0.2815:2,2:29.3:1:28.9:1:1:1.02:60:32.5:0.2766:0:1.1 -X 106515857 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24878;SOR=Inf;LSEQ=ATTTCTACGACTATGACGGC;RSEQ=GGGAGGATTTCTACCGCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:128,149:0:2,0:24.9:1:30.6:1:1:0:60:276:1:0:0.2 0/1:284:3:2,1:131,149:0.0106:2,2:14:1:27.7:1:0.60234:2.27:60:6:0.0106:0:1 -X 106515879 . C A 32 v4;q23;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.47338;LSEQ=GGAGGATTTCTACCGCTCCA;RSEQ=GACGCCCAGCGAGGACATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:2:2,0:116,116:0.0085:2,0:1:0:29:0:0.49789:0:60:4:0.0087:0:1 0/1:239:3:3,0:101,134:0.0126:2,0:9:1:20.7:1:0.08208:0:60:2:0.0084:0:1 -X 106515914 . T G 115 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ACATCTGGAAGAAATTCGAG;RSEQ=TGGTGCCGCCGCCCTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:79,94:0:2,0:25.2:1:29.7:1:1:0:60:56.667:1:0:0.1 0/1:144:13:6,7:57,74:0.0903:2,2:22.6:1:31.1:1:1:1.11:60:26:0.0909:0:1.2 -X 106515938 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19084;SOR=Inf;LSEQ=TGCCGCCGCCCTGGGACTTG;RSEQ=GTCCCGCAGCCGGGAACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:57,79:0:2,0:22.9:1:30.8:1:1:0:60:67:1:0:0.1 0/1:106:2:1,1:41,63:0.0189:2,2:19.5:1:27.5:1:1:1.53:60:4:0.0192:0:1 -X 106515940 . T A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50739;SOR=0;LSEQ=CCGCCGCCCTGGGACTTGGG;RSEQ=CCCGCAGCCGGGAACCCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:56,74:0.0152:2,2:23:1:29:1:1:1.32:60:4:0.0155:0:1 0/0:100:0:0,0:38,61:0:2,0:23.8:1:28.9:1:1:0:60:98:1:0:0.2 -X 106516025 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50027;SOR=0;LSEQ=GGGACGAGACGGAATCCCAG;RSEQ=ACTACTGGAAAGCTTGGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:62,58:0.0164:2,2:21:1:30:0:1:1.06835:60:4:0.0167:0:1 0/0:106:0:0,0:62,44:0:2,0:22:1:30.5:1:1:0:60:105:1:0:0.2 -X 106516056 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49844;SOR=Inf;LSEQ=AGCTTGGGACGCGAACTACG;RSEQ=CTCCCTCATCCGCCGTGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:77,84:0:2,0:26.6:1:31.3:1:1:0:60:79.5:1:0:0.2 0/1:161:2:1,1:86,73:0.0124:2,2:31:1:28:1:1:1.17688:60:4:0.0127:0:1 -X 106516061 . C A 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=GGGACGCGAACTACGCCTCC;RSEQ=TCATCCGCCGTGACTGCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:75,85:0:2,0:27.5:1:31.6:1:1:0:60:79:1:0:0.2 0/1:168:2:1,1:86,80:0.0119:2,2:31:0:29:1:1:1.07451:60:4:0.012:0:1.5 -X 106516102 . G A 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62444;SOR=2.72762;LSEQ=TGGAGCGGCTTCTCCACCCA;RSEQ=GAGCCGCTGGAGAGAGCGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:1,0:51,84:0.0074:2,0:1:0:25:0:0.38235:0:60:2:0.0076:0:1 0/1:151:3:2,1:64,84:0.0199:2,2:10.3:1:28.3:1:0.5811:2.61:60:6:0.02:0:1.3 -X 106516106 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49846;SOR=Inf;LSEQ=GCGGCTTCTCCACCCAGGAG;RSEQ=CGCTGGAGAGAGCGGTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:46,83:0:2,0:26.9:1:31.6:1:1:0:60:128:1:0:0.2 0/1:136:2:1,1:57,77:0.0147:2,2:45:1:29.5:1:1:1.35:60:4:0.0147:0:1 -X 106516125 . G C 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00164;SOR=Inf;LSEQ=GCCGCTGGAGAGAGCGGTGA;RSEQ=TGACCTGCTTGCCGTTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:30,67:0:2,0:24.3:1:31.9:1:1:0:60:96:0.9897:0:0.1 0/1:105:10:2,8:38,57:0.0952:2,2:24.7:1:32.7:1:0.3115:2.6449:60:20:0.0962:0:1 -X 106516195 . C A 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57376;SOR=2.70412;LSEQ=GCCACCCCCGACTACACTCC;RSEQ=GAGCTCGAAGCCGGCAACCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:10,23:0.0294:2,0:47:0:18:0:1:0:60:0:0:0:1 0/1:26:2:1,1:10,14:0.0769:2,2:10:0:32.5:1:1:1.38:60:4:0.0769:0:1.5 -X 106516319 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17457;SOR=Inf;LSEQ=AAGAAATCGACGTGACAGTA;RSEQ=AGAAGAGGCAGTCTTTGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:45,17:0:2,0:22:1:30.4:1:1:0:60:61:1:0:0.1 0/1:45:2:1,1:32,11:0.0444:2,2:23:1:27.5:1:0.46667:2.82843:60:4:0.0444:0:1 -X 106516387 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20052;SOR=Inf;LSEQ=CGTGCAGACCTTCTGGATCC;RSEQ=CGCATGAATCTCTTCCACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:76,43:0:2,0:25.4:1:30.6:1:1:0:60:58.5:1:0:0.1 0/1:97:2:1,1:58,37:0.0206:2,2:23:1:29.5:1:1:1.56003:60:4:0.0206:0:1 -X 106516395 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20278;SOR=Inf;LSEQ=CCTTCTGGATCCCCGCATGA;RSEQ=TCTCTTCCACATCTCCATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:80,50:0:2,0:24.4:1:30.4:1:1:0:60:260:1:0:0.1 0/1:107:2:1,1:62,43:0.0187:2,2:31.5:1:28.5:1:1:1.4368:60:4:0.0187:0:1.5 -X 106516409 . T C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49968;SOR=0;LSEQ=GCATGAATCTCTTCCACATC;RSEQ=CCATCCACCAGCAACAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:78,64:0.0139:2,2:16.5:1:31.5:1:1:1.21706:60:4:0.0144:0:1 0/0:129:0:0,0:69,60:0:2,0:24.7:1:29.1:1:1:0:60:31.25:1:0:0.1 -X 106516443 . CT C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.20271;SOR=Inf;LSEQ=ACAGCACAACTATGCTGCCC;RSEQ=TTTCCTCCAGAAAGCTGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:84,90:0:2,0:26.8:1:30.4:1:1:0:60:86:1:0:0.2 0/1:143:2:1,1:60,81:0.014:2,2:34:1:31:1:1:1.35:60:4:0.0141:0:0 -X 106516447 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20793;SOR=Inf;LSEQ=CACAACTATGCTGCCCCTTT;RSEQ=CCTCCAGAAAGCTGCTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:80,90:0:2,0:27.6:1:29.7:1:1:0:60:84:1:0:0.2 0/1:143:2:1,1:60,81:0.014:2,2:39.5:1:32:1:1:1.35:60:4:0.0143:0:1 -X 106516475 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16031;SOR=Inf;LSEQ=AAAGCTGCTTCCAAGAAGGG;RSEQ=CTCCAAAGAGGATGCCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:70,85:0:2,0:25.6:1:31.8:1:1:0:60:154:1:0:0.1 0/1:104:2:1,1:39,63:0.0192:2,2:39:0:31:0:1:1.61:60:4:0.0192:0:1 -X 106516721 . G A 29 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.04369;LSEQ=CCCTGAGGGACGAGGTACCC;RSEQ=CCCTGGCCAGCTGCTCTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:29,42:0.0274:2,2:20.5:1:29.5:1:1:1.44:60:4:0.029:0:1 0/1:35:1:1,0:13,21:0.0286:2,0:1:0:26:0:0.4:0:60:2:0.0286:0:1 -X 106516786 . T A 97 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAGGCCACGGAATACTTACA;RSEQ=GAACTGGCGGAAGCCGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:7,23:0:2,0:23.3:1:30.1:1:1:0:60:29:1:0:0.1 1/0:19:10:4,6:4,5:0.5263:2,2:29.9:1:29.4:1:1:1.18851:60:20:0.5263:0:1.1 -X 106516931 . CT C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTTAAAAAGACACAAGTTTT;RSEQ=TTTTGATCTCCCTCTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:1,7:0:2,0:30.6:1:29.9:1:1:0:60:16:1:0:0.4 0/1:8:2:1,1:2,4:0.25:2,2:28:0:30.5:1:1:1.83:60:4:0.25:0:0 -X 106518947 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49806;SOR=Inf;LSEQ=ACTGATGTTTCACCTGAATA;RSEQ=CTTGTATTTTATAAGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:20,49:0:2,0:26.8:1:31:1:1:0:60:33.5:1:0:0.1 0/1:77:2:1,1:26,49:0.026:2,2:6:1:27:1:1:1.87:60:4:0.0263:0:1 -X 106519338 . G GA 59 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.68604;SOR=0.6008;LSEQ=TGTTAACTCTTTCTGTACAA;RSEQ=AAAAAAAAAACCTCTTGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:4:2,2:25,11:0.0976:2,2:30.5:1:29.7:1:0.58393:2.22215:60:8:0.1:0.0244:1 0/1:33:2:2,0:19,12:0.0606:2,0:25.5:1:30.5:1:0.52273:0:60:4:0.0645:0.0303:0 -X 106846417 . CCAG C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.22492;SOR=0;LSEQ=TCCACAGCCCGTAACCTTAA;RSEQ=CAGCAGCAGCAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:21,16:0.0476:2,2:36:1:31.5:1:1:1.30327:60:4:0.05:0:0 0/0:46:0:0,0:24,20:0:2,0:24.4:1:30.1:1:1:0:58.3:21:0.9545:0:0.4 -X 106846425 . A C 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.77375;SOR=0.80174;LSEQ=CCGTAACCTTAACCAGCAGC;RSEQ=GCAGCAACAACAACAGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:6:6,0:111,119:0.0254:2,0:7:0:28.8:1:0.0139:0:28:5:0.0216:0:3 0/1:293:6:6,0:142,144:0.0205:2,0:7:0:28:1:0.02974:0:29.5:5:0.0175:0:3.3 -X 106846426 . G T 124 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.69578;SOR=1.19777;LSEQ=CGTAACCTTAACCAGCAGCA;RSEQ=CAGCAACAACAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:11:9,2:107,117:0.0458:2,2:8:0:30.2:1:0.03247:4.89:34.4:10:0.0422:0:5.8 0/1:294:16:13,3:136,142:0.0544:2,2:7.9:1:31.2:1:0.01815:4.50:38:32:0.055:0:5.9 -X 106846430 . C CAACAACAACAGCAGCAGCAGCAACAACAACAGCAGCAGCAACAACAACAGCAGACAATAACAAAAGCAACGATAGCAACAGTATCAGCAACAGCAACAGCATCAGCAACAACAGCAACAATAGCAGCAGTAAA 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=53;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCTTAACCAGCAGCAGCAG;RSEQ=AACAACAACAGCAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:64:24,40:96,81:0.2656:2,2:21.8:1:29.6:1:0.02835:1.96973:41.1:128:0.2723:0.2656:3.2 0/0:293:0:0,0:148,145:0:2,0:13.5:1:31.6:1:1:0:39.7:47.833:1:0.0034:2.7 -X 106846435 . A G 108 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.47108;SOR=0.64543;LSEQ=AACCAGCAGCAGCAGCAACA;RSEQ=CAACAGCAGCAGCAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:10:9,1:113,124:0.0405:2,2:13.4:1:32.7:1:0.0095:9.81:29.1:20:0.0412:0:2.6 0/1:302:8:6,2:143,151:0.0265:2,2:15.5:1:32:1:0.169:3.16:31.3:16:0.0268:0:3.3 -X 106846436 . C T 196 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.72669;SOR=1.06652;LSEQ=ACCAGCAGCAGCAGCAACAA;RSEQ=AACAGCAGCAGCAGCAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:95:50,45:72,78:0.3846:2,2:16.2:1:28.9:1:0.51353:1.20:38.6:30.667:0.3849:0:3.4 0/1:305:122:68,54:83,100:0.4:2,2:16.1:1:28.3:1:0.08067:1.52:38.6:39.667:0.398:0:3.3 -X 106846438 . A G 149 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CAGCAGCAGCAGCAACAACA;RSEQ=CAGCAGCAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:112,116:0:2,0:20.8:1:29.8:1:1:0:41.2:44.6:1:0:2.4 0/1:306:25:13,12:138,142:0.0817:2,2:19.2:1:32.1:1:0.83703:1.11:36.9:50:0.0839:0:6 -X 106846439 . C G 214 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.93067;SOR=1.02354;LSEQ=AGCAGCAGCAGCAACAACAA;RSEQ=AGCAGCAGCAGCAACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:97:50,47:66,80:0.388:2,2:19.2:1:30.9:1:0.36022:1.29:38.9:23.25:0.3859:0:3.4 0/1:310:122:68,54:78,101:0.3935:2,2:19.1:1:31:1:0.04584:1.63:38.6:39.667:0.3927:0:3.3 -X 106846441 . G A 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.87849;SOR=1.08554;LSEQ=CAGCAGCAGCAACAACAACA;RSEQ=CAGCAGCAGCAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:20:10,10:112,117:0.08:2,2:21.7:1:29:1:1:1.04:34.5:19:0.0779:0:6.1 0/1:313:27:14,13:139,147:0.0863:2,2:22.1:1:29.6:1:0.84126:1.14:38.6:54:0.0891:0:5.6 -X 106846442 . C T 189 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.64712;SOR=1.09672;LSEQ=AGCAGCAGCAACAACAACAG;RSEQ=AGCAGCAGCAACAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:75:29,46:93,84:0.2976:2,2:22.5:1:28:1:0.05356:1.75219:35:24:0.2927:0:2 0/1:312:99:37,62:115,97:0.3173:2,2:22.4:1:28.6:1:0.00725:1.98223:33.2:98:0.3234:0:2 -X 106846444 . G A 58 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=1.08804;LSEQ=CAGCAGCAACAACAACAGCA;RSEQ=CAGCAGCAACAACAACAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:0,3:123,130:0.0117:2,0:10.9:1:29.5:1:0.24821:0:27.3:8:0.0119:0.0117:2 0/1:314:4:0,4:153,156:0.0127:2,0:13:1:29.3:1:0.12298:0:29.5:8:0.0131:0.0127:2 -X 106846447 . G GCAGCAACAACAACAGCAGACAATAACAAAAGCAACGATAGCAACAGTAT 188 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CAGCAACAACAACAGCAGCA;RSEQ=CAGCAACAACAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:77:28,49:96,84:0.2996:2,2:35.6:1:30:1:0.01432:1.99461:34.7:154:0.3056:0.2996:2 0/0:313:0:0,0:154,157:0:2,0:22.8:1:31.5:1:1:0:40.3:43.429:0.9935:0:2.6 -X 106846448 . C T 59 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.03885;SOR=0;LSEQ=AGCAACAACAACAGCAGCAG;RSEQ=AGCAACAACAACAGCAGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:4:4,0:120,133:0.0156:2,0:10:1:29.5:1:0.05284:0:31:8:0.0159:0:3 0/0:320:0:0,0:156,164:0:2,0:22.2:1:31.4:1:1:0:40.2:31:1:0:2.6 -X 106846456 . A G 98 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.43882;SOR=1.62569;LSEQ=CAACAGCAGCAGCAGCAACA;RSEQ=CAACAGCAGCAGCAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:5:1,4:121,132:0.0194:2,2:13.6:1:33:1:0.37384:3.65055:27.4:10:0.0195:0:2.8 0/1:321:10:2,8:154,157:0.0312:2,2:16.5:1:29.7:1:0.10527:3.90866:29.8:9:0.0284:0:2.8 -X 106846457 . C T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.76491;SOR=0.8999;LSEQ=AACAGCAGCAGCAGCAACAA;RSEQ=AACAGCAGCAGCAACAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:23:10,13:111,123:0.0895:2,2:34.3:1:25.4:1:0.82786:1.17244:35:4.75:0.0757:0:5.8 0/1:320:26:14,12:141,152:0.0813:2,2:35.1:1:27.8:1:0.68332:1.26:37.2:25:0.0791:0:5.9 -X 106846459 . A AGAG 105 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.25054;SOR=0.57632;LSEQ=CAGCAGCAGCAGCAACAACA;RSEQ=CAGCAGCAGCAACAACAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:11:10,1:107,135:0.0426:2,2:37.5:1:30.5:1:0.00327:12.52:33.5:22:0.0444:0.0155:5.9 0/1:320:8:5,3:140,162:0.025:2,2:34.5:1:30.9:1:0.48061:1.92:36:16:0.0257:0:4.8 -X 106846460 . C CAGT 203 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.86355;SOR=0.95784;LSEQ=AGCAGCAGCAGCAACAACAA;RSEQ=AGCAGCAGCAACAACAACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:101:55,46:62,79:0.3915:2,2:21.4:1:29.5:1:0.11871:1.52:38.2:49.5:0.4041:0.1008:3.4 0/1:320:122:68,54:76,103:0.3813:2,2:20.7:1:29.4:1:0.02593:1.70:38.3:121:0.398:0.1031:3.3 -X 106846465 . G T 75 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.35006;SOR=2.05521;LSEQ=CAGCAGCAACAACAACAGCA;RSEQ=CAGCAACAACAACAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:3:0,3:92,87:0.0164:2,0:12:0:31.7:1:0.11888:0:27.3:6:0.0169:0:2 0/1:211:7:0,7:108,94:0.0332:2,0:12:0:27:1:0.00551:0:30.7:6:0.0296:0:2.1 -X 106846468 . G A 78 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.52464;SOR=0.5766;LSEQ=CAGCAACAACAACAGCAGCA;RSEQ=CAACAACAACAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:6:0,6:86,85:0.0339:2,0:24.2:1:30.3:1:0.029:0:31:12:0.0347:0:6.7 0/1:202:4:0,4:103,94:0.0198:2,0:24:1:30.3:1:0.05473:0:32.3:8:0.0206:0:7 -X 106846474 . A G 142 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.55087;SOR=0.81809;LSEQ=CAACAACAGCAGCAGCAACA;RSEQ=CAACAGCAGCAGCAGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:27:13,14:60,71:0.1667:2,2:13.4:1:30:1:0.83542:1.10:32.1:12.5:0.1582:0:5.6 0/1:185:26:16,10:73,78:0.1405:2,2:12.9:1:31:1:0.28856:1.70:33.9:52:0.1429:0:6 -X 106846477 . ACAG A 31 v4;MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=1.84001;LSEQ=CAACAGCAGCAGCAACAACA;RSEQ=CAGCAGCAGCAGCAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:1,0:70,82:0.0065:2,0:48:0:34:0:0.46405:0:60:2:0.0067:0:0 0/1:168:2:0,2:80,85:0.0119:2,0:18.5:1:31.2:1:0.49787:0:51.5:4:0.012:0.006:0 -X 106846480 . G A 28 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.59528;SOR=0.42142;LSEQ=CAGCAGCAGCAACAACAACA;RSEQ=CAGCAGCAGCAGCAGCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:60,76:0.0144:2,2:25.5:1:28.5:1:1:1.26:60:4:0.0149:0:1 0/0:164:1:1,0:77,85:0.0061:2,0:45:0:23:0:0.47853:0:60:2:0.0064:0:6 -X 106846481 . C T 122 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.86879;SOR=0.9005;LSEQ=AGCAGCAGCAACAACAACAG;RSEQ=AGCAGCAGCAGCAGCAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:21:10,11:51,65:0.1533:2,2:14:0:26.5:1:0.81395:1.16:36:9.5:0.1439:0:5.9 0/1:157:22:14,8:59,75:0.1401:2,2:13:1:27.5:1:0.10824:2.21:35.4:44:0.1438:0:6 -X 108880224 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51566;SOR=Inf;LSEQ=GGGAACTAAATTTATTCCAG;RSEQ=CAGTTAAAGATTCAGAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:0:2,0:27.2:1:28.8:1:1:0:60:36:1:0:0.3 0/1:56:2:1,1:26,28:0.0357:2,2:34:1:30:1:1:1.08:60:4:0.0357:0:1 -X 108880251 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18365;SOR=0;LSEQ=AAGATTCAGAATGTGTTATT;RSEQ=CTCCCAGAACAATGACACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:13,23:0.0526:2,2:10.5:1:27:1:1:1.74:60:4:0.0541:0:1 0/0:50:0:0,0:21,29:0:2,0:24.5:1:30.5:1:1:0:60:100:1:0:0.3 -X 108880269 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18045;SOR=0;LSEQ=TTCCTCCCAGAACAATGACA;RSEQ=CGAGGACATAATTTTTCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:8,23:0.0606:2,2:21:1:31.5:1:0.47727:2.77:60:4:0.0645:0:1 0/0:44:0:0,0:15,29:0:2,0:26.6:1:30.8:1:1:0:60:88:1:0:0.3 -X 108880333 . CT C 67 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.18438;SOR=0.26276;LSEQ=CTGAACCATTTATGTGCCGT;RSEQ=TTTTTTTTTTTACAGAATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:0,4:1,7:0.3333:2,0:32.3:1:33.5:1:1:0:60:8:0.3333:0:0 0/1:18:2:0,2:3,13:0.1111:2,0:20:1:33.5:1:1:0:60:4:0.1176:0:0 -X 109590175 . G T 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=GGCCGATTCGTGGGTCGGTG;RSEQ=GTCGTGGGCCGTGGGTCGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:0,12:0.1429:0,2:7.5:1:28:1:0.14286:0:60:4:0.1429:0:1 0/0:13:0:0,0:4,9:0:2,0:19.2:1:29.9:1:1:0:60:26:1:0:0 -X 110437571 . G A 28 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50226;SOR=0;LSEQ=TGGGTAGTCATGGAATACTT;RSEQ=GCTGGTGGCTCTCTGACTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:0.0667:2,2:26.5:1:28:1:1:1.14834:60:4:0.069:0:1 0/0:22:0:0,0:12,10:0:2,0:26:1:29.6:1:1:0:60:21:1:0:0.1 -X 111353206 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GCAAGACCATCTGTAGCTTA;RSEQ=TGGCCTTGATCCTGGAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:0:2,0:28.1:1:32.4:1:1:0:60:16:1:0:0.3 0/1:9:2:1,1:4,3:0.2222:2,2:9:1:29.5:1:1:1.29098:60:4:0.2222:0:1 -X 112058737 . T C 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATAAGAAGCAGAGGATGGC;RSEQ=GAGCCCGAGGCATAGCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:0:2,0:18.3:1:31.7:1:1:0:60:12:1:0:0.2 0/1:13:2:1,1:8,3:0.1538:2,2:22:0:32:0:1:2.4495:60:4:0.1538:0:1.5 -X 112058796 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=0.93845;LSEQ=TGCTGTGGCTGCTGCTGCTG;RSEQ=TGTTGTTGGTGGTGATGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:0,2:21,9:0.0625:2,0:8.5:1:19.5:1:0.11089:0:60:1:0.0345:0:2 0/1:34:2:1,1:18,14:0.0588:2,2:22.5:1:29.5:1:1:1.27615:60:4:0.0588:0:1.5 -X 112058838 . TTGC T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.49474;SOR=0;LSEQ=TGATGGTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGACTCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:21,17:0.05:2,2:30:1:30:1:1:1.22874:60:4:0.0541:0:0 0/0:36:0:0,0:19,17:0:2,0:26.9:1:29.1:1:1:0:60:35:1:0:0.2 -X 114303670 . C A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49484;SOR=Inf;LSEQ=GCAGCAGCCACCATCTCAAC;RSEQ=GTCCCTCAAGGGCCAAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:19,18:0:2,0:22.6:1:30:1:1:0:60:74:1:0:0.1 0/1:41:2:1,1:18,21:0.0488:2,2:9.5:1:31:1:1:1.16:60:4:0.05:0:1 -X 114303720 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14423;SOR=Inf;LSEQ=CGCAACCCTCCCAGGGGCAG;RSEQ=GTCTGCCGTCCAGGCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:27,13:0:2,0:23.2:1:31.1:1:1:0:60:80:1:0:0.1 0/1:25:2:1,1:14,9:0.08:2,2:6.5:1:27:1:1:1.52748:60:4:0.0833:0:2 -X 114303816 . T C 33 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50284;SOR=0;LSEQ=CAGGCACCAGATCGTGCACG;RSEQ=CCAGGAGGACTTGGAGACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:2,0:79,25:0.0189:2,0:7:1:33:1:1:0:60:4:0.019:0:1 0/0:86:0:0,0:61,24:0:2,0:23.6:1:28.7:1:1:0:60:27.333:1:0:0.3 -X 114304092 . A G 40 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24917;SOR=0;LSEQ=TAGTCTGGCCCAGCTGCTAC;RSEQ=CCCACAGCTCAACATCTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:3:1,2:106,133:0.0123:2,2:47.3:1:25.7:1:1:1.59104:60:2:0.0086:0:1.3 0/0:228:0:0,0:112,116:0:2,0:27:1:29.5:1:1:0:60:56:1:0:0.1 -X 114304447 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5028;SOR=Inf;LSEQ=TAAAGGGTCATCTCCAAACC;RSEQ=TTTTAGATGTTTTTTATTAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:43,72:0:2,0:25:1:29.9:1:1:0:60:37.333:0.9912:0:0.1 0/1:141:2:1,1:49,90:0.0142:2,2:34:1:30.5:1:1:1.83:60:4:0.0143:0:1.5 -X 115503918 . T C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19679;LSEQ=CAGTCCCATTCCAGTGATAA;RSEQ=CTGAGCTTCCATTTGAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:125:60,65:61,72:0.4845:2,2:23.5:1:31.4:1:0.80303:1.09:60:250:0.4864:0:1.1 0/1:257:40:16,24:97,119:0.1556:2,2:22.9:1:31.6:1:0.60659:1.22174:60:80:0.1569:0:1.2 -X 115503945 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24371;SOR=0;LSEQ=TTCCATTTGAAGTTTTCAAA;RSEQ=GGCTTTAATATAAATCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:70,104:0.0114:2,2:27.5:1:30.5:1:1:1.48:60:4:0.0114:0:2.5 0/0:180:0:0,0:70,110:0:2,0:22.9:1:30.8:1:1:0:60:59:1:0:0.3 -X 115761425 . C CT 30 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTTCATTCCTTTTCATT;RSEQ=TTTTTTTTTTTTCTATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:30.5:1:1:0:53.5:4:1:0:0 -X 115761903 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=AGGCTGCAGACCCTTGGATG;RSEQ=GGTTTTTGTGGGGGCCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:0:2,0:33:1:31:1:1:0:60:48:1:0:0.3 0/1:20:2:1,1:10,8:0.1:2,2:19.5:1:29:1:1:1.23603:60:4:0.1:0:1 -X 115761919 . C CTTG 30 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.18937;SOR=Inf;LSEQ=GATGGGGTTTTTGTGGGGGC;RSEQ=TTGTTGTTGTTGTTGTTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:0:2,0:31.2:1:30.6:1:1:0:60:23:1:0:0.3 0/1:19:2:1,1:9,8:0.1053:2,2:47:1:30.5:1:1:1.11803:60:4:0.1053:0:0 -X 118708829 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52427;SOR=Inf;LSEQ=GCCGGGAGCGGGCGCCAGTG;RSEQ=CGGCCTAGGGGGACCCCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:22,7:0:2,0:21.8:1:30.3:1:1:0:60:13.5:1:0:0.2 0/1:48:2:1,1:35,11:0.0417:2,2:17.5:1:26.5:1:0.44149:3.08979:60:4:0.0455:0:1.5 -X 118708841 . G T 45 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05221;SOR=0;LSEQ=CGCCAGTGCCGGCCTAGGGG;RSEQ=ACCCCTGTCTGTCTTCCCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:3:1,2:30,8:0.0732:2,2:5:1:28.7:1:0.14212:7.02909:60:6:0.0769:0:1.3 0/0:67:0:0,0:47,20:0:2,0:23.2:1:30.4:1:1:0:60:21.333:1:0:0.4 -X 118708898 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51718;SOR=Inf;LSEQ=CTCCAGCCGGAGTCAGCGGG;RSEQ=CTCCGTCCGAGAACAACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:65,48:0:2,0:26.2:1:31.4:1:1:0:60:112:0.9912:0:0.2 0/1:169:2:1,1:94,73:0.0118:2,2:44.5:1:29.5:1:1:1.28572:60:4:0.012:0:1 -X 118708909 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17511;SOR=0;LSEQ=GTCAGCGGGGCTCCGTCCGA;RSEQ=AACAACATAATGGTGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:58,47:0.0187:2,2:37.5:1:29.5:1:1:1.2316:60:4:0.0187:0:1 0/0:148:0:0,0:79,69:0:2,0:28.2:1:30.9:1:1:0:60:296:1:0:0.2 -X 118708927 . G T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17861;SOR=0;LSEQ=GAGAACAACATAATGGTGTG;RSEQ=AACGCGGTCATTTTCGGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:48,42:0.0217:2,2:14.5:1:27.5:1:1:1.14119:60:4:0.0222:0:1 0/0:125:0:0,0:62,63:0:2,0:27.2:1:29.6:1:1:0:60:30.25:1:0:0.1 -X 121137409 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48538;SOR=Inf;LSEQ=TTTTTGTTGATGTTGTTATT;RSEQ=TTGCTTTTTGCTTGTTTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:23:1:31.9:1:1:0:60:16:1:0:0 0/1:11:2:1,1:6,3:0.1818:2,2:15.5:1:27.5:1:1:1.87089:60:4:0.1818:0:1.5 -X 121138010 . C A 31 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=GGTGTGTTGGGCTGTGGGGA;RSEQ=AAGTCTTGGGACGAAGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:32:0:31.5:1:1:1.73:60:4:0.4:0:2 0/0:6:0:0,0:2,4:0:2,0:31:1:31.3:1:1:0:60:12:1:0:0.7 -X 121138020 . G A 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.43179;LSEQ=GCTGTGGGGACAAGTCTTGG;RSEQ=ACGAAGCCTTCCATCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:1,0:0.8333:0,2:19.2:1:27.8:1:1:0:60:4:0.8:0:1.6 1/0:6:4:1,3:1,1:0.6667:2,2:27.8:1:29.8:1:1:2.44949:60:8:0.6667:0:1 -X 121138094 . T C 33 d7;v4;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=TATAGAAGTTGATGCTGCCC;RSEQ=TCCCCTGCCCAGGGAGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:31.2:1:28.2:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:33:1:1:0:60:4:1:0:1.5 -X 122035670 . C T 68 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.0202;SOR=0;LSEQ=AACTGTTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:3,2:7,7:0.2632:2,2:30.4:1:29.6:1:1:1.47:60:10:0.2632:0:1.2 0/0:20:0:0,0:9,11:0:2,0:31.4:1:32.4:1:1:0:58:19:1:0:0.3 -X 122035682 . C G 33 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.21764;SOR=0;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGCTGCTGTTGTTGTTTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:0.1111:2,2:20:0:33:0:1:1:37:4:0.1111:0:2.5 0/0:20:0:0,0:9,11:0:2,0:32.2:1:31.8:1:1:0:58:19:1:0:0.3 -X 122035688 . C T 71 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.01707;SOR=0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGTTGTTTTGTATCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:6,7:0.2778:2,2:20.8:1:30.6:1:1:1.26799:50.8:10:0.2778:0:1.8 0/0:20:0:0,0:9,11:0:2,0:31.6:1:30.9:1:1:0:58:9:1:0:0.3 -X 122648282 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15138;SOR=Inf;LSEQ=TCTCGCTCGCCGAGCTCCAG;RSEQ=CGAAGGAGAAGGGGGGTAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:59,25:0:2,0:20.2:1:31:1:1:0:58.9:20:1:0:0.1 0/1:54:2:1,1:34,18:0.037:2,2:26.5:1:28.5:1:1:1.86542:60:4:0.037:0:1.5 -X 122648298 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15203;SOR=Inf;LSEQ=CCAGCCGAAGGAGAAGGGGG;RSEQ=TAAGTAAGGAGGTCTCTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:75,40:0:2,0:22.2:1:30.6:1:1:0:59.2:27.75:1:0:0.1 0/1:74:2:1,1:45,27:0.027:2,2:11:1:28:1:1:1.65465:54.5:4:0.027:0:1 -X 122648346 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20503;SOR=Inf;LSEQ=TCCTACAAAGCGGACTGCCC;RSEQ=CAAACCGACCAGTGGTAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:91,80:0:2,0:27:1:30.7:1:1:0:60:33.2:1:0:0.1 0/1:142:2:1,1:78,62:0.0141:2,2:29:1:29.5:1:1:1.25601:60:4:0.0144:0:1.5 -X 122648427 . G T 25 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51624;SOR=0;LSEQ=GCGCCCTCTACTGGAGGGGT;RSEQ=AAGAAACCTCATCGTTACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:0,2:121,76:0.0101:2,0:17:1:25.5:1:0.15243:0:60:4:0.0104:0:1 0/0:136:0:0,0:72,63:0:2,0:22.4:1:30.5:1:1:0:52.3:44:0.9925:0:0.4 -X 122648443 . T C 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17525;SOR=Inf;LSEQ=GGGTGAAGAAACCTCATCGT;RSEQ=ACAGGCCTGGTACTGTGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:146,88:0:2,0:24.8:1:29.2:1:1:0:51.1:77:1:0:0.5 0/1:169:2:1,1:93,74:0.0118:2,2:29:0:30.5:1:1:1.25504:60:4:0.0122:0:1 -X 122648453 . GT TC 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19631;SOR=Inf;LSEQ=ACCTCATCGTTACAGGCCTG;RSEQ=ACTGTGGCGCTCCGTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:153,93:0:2,0:26.2:1:31:1:1:0:51:29.75:1:0:0.5 0/1:197:2:1,1:111,83:0.0102:2,2:26:0:31.8:1:1:1.33533:59.5:4:0.0104:0:1.5 -X 122648454 . T C 209 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62001;SOR=0.89706;LSEQ=CCTCATCGTTACAGGCCTGG;RSEQ=ACTGTGGCGCTCCGTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:93:60,33:95,62:0.372:2,2:25:1:32.1:1:0.59038:1.19:50:92:0.3725:0:1.2 0/1:196:68:40,28:71,55:0.3469:2,2:24.2:1:31.6:1:0.76311:1.11:51.6:33:0.3455:0:1.1 -X 122648598 . A G 28 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17491;SOR=Inf;LSEQ=CGCAGCTATCGGTGCTTTGC;RSEQ=GGAGGCAAGTGAGGCCTATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:188,77:0:2,0:22:1:30.2:1:1:0:34.7:52:1:0:0.1 0/1:191:2:1,1:128,61:0.0105:2,2:6:0:28:1:0.545:2.08954:25:4:0.0105:0:1 -X 122696472 . CA C 34 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5263;SOR=0;LSEQ=ATGTCCATGAAGGAGGTGGA;RSEQ=AGCAGATGCTGAGCCTGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:35,15:0.0385:2,2:17.5:1:34:1:0.52489:2.29131:60:4:0.0385:0:2.5 0/0:31:0:0,0:24,7:0:2,0:23.6:1:29:1:1:0:60:62:1:0:0.2 -X 122696563 . C T 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGGCCGTGTGCGACATCTCG;RSEQ=CCCACGGCCTGAAGATAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:107:55,52:0,0:1:0,2:29.6:1:30:1:1:0:60:106:1:0:1.1 0/1:117:32:18,14:43,42:0.2735:2,2:27.6:1:29.2:1:0.67937:1.25:60:64:0.2807:0:1 -X 122696575 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23439;SOR=Inf;LSEQ=ACATCTCGCCCCACGGCCTG;RSEQ=AGATAGCCGCAACTTTCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:61,61:0:2,0:26.1:1:30.2:1:1:0:60:121:1:0:0.9 0/1:115:2:1,1:57,56:0.0174:2,2:37.5:1:30.5:1:1:1.0177:60:4:0.0175:0:1.5 -X 123019821 . G A 140 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATCTTGAAAATAGTGCCAC;RSEQ=CAGTCTACAAATTCTGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:199,202:0:2,0:24.7:1:30.9:1:1:0:60:65.833:1:0:0.1 0/1:337:26:13,13:164,147:0.0772:2,2:19.3:1:29.8:1:0.83983:1.11528:60:52:0.0778:0:1 -X 123022371 . C A 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19028;SOR=Inf;LSEQ=GTTTTAAGCTGTGAGATTTT;RSEQ=ATGTTTTTTAGATGTGCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:212,20:0:2,0:23.8:1:31.5:1:1:0:60:115:1:0:0.1 0/1:180:2:1,1:166,11:0.0111:2,2:44:0:30:0:0.12994:14.48902:60:4:0.0112:0:1.5 -X 123022775 . C CT 57 MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATAACATTCAGATTATCC;RSEQ=TTTTTTTTTTTGAGACGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:0,4:0,15:0.2105:1,0:24:1:28.8:1:1:0:60:8:0.2222:0.0526:0.5 0/0:2:0:0,0:0,2:0:0,0:25.5:1:33:0:1:0:60:4:1:0:0 -X 123022854 . T C 30 v4;MAF0.05;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCTTGGCTCACTGCAACCTC;RSEQ=GCCTCCCAGGTTCAAGTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:0.25:0,0:6:1:30:1:1:0:60:4:0.25:0:1 1/1:1:1:0,1:0,0:1:0,0:31:0:30:0:1:0:59:2:1:0:1 -X 123024901 . G A 29 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04983;SOR=Inf;LSEQ=TTAGCATAGGTAGCATAACA;RSEQ=AGGGAACTTTTTTAACCTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:0:1,0:22.8:1:32.8:1:1:0:60:66:1:0:0 0/1:10:2:2,0:8,0:0.2:0,0:27:1:29:1:1:0:60:4:0.2:0:1 -X 123034227 . A G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02901;SOR=2.48988;LSEQ=TGCTTTGCTGGTTTGTTTTT;RSEQ=TTCTTTCGCTTGCTCCTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:24:24,0:41,0:0.3692:1,1:27.5:1:32.5:1:1:0:60:48:0.375:0:1 1/0:42:25:24,1:16,1:0.5952:1,1:23.4:1:32:1:1:1.49:60:50:0.5952:0:1 -X 123034247 . A AT 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16418;SOR=Inf;LSEQ=ATTCTTTCGCTTGCTCCTTA;RSEQ=TTTTTTCATTTTAACTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:80,0:0:1,0:25:1:30.1:1:1:0:60:79:1:0:0.3 0/1:55:2:1,1:49,4:0.0364:2,2:27:1:28.5:1:0.17508:11.06826:60:4:0.0377:0:0.5 -X 123034284 . G T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22607;SOR=Inf;LSEQ=ATATTTTGCTATTGAGTTGT;RSEQ=ATAATGAAAATAATTGTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:139,16:0:2,0:24.2:1:32:1:1:0:60:76.5:1:0:0.2 0/1:141:2:1,1:108,31:0.0142:2,2:17:1:26.5:1:0.40365:3.44472:60:4:0.0143:0:1 -X 123034497 . G T 57 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12408;SOR=0;LSEQ=GCAGATCTAGTGAATGCTCA;RSEQ=AAAGACAGTATGCAAGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:2,2:143,244:0.0102:2,2:28.5:1:28.5:1:0.62941:1.70:60:8:0.0104:0:1.3 0/0:385:0:0,0:156,228:0:2,0:26.8:1:31.3:1:1:0:59.9:127:1:0:0.5 -X 123034511 . A C 225 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4448;SOR=1.13391;LSEQ=TGCTCAGAAAGACAGTATGC;RSEQ=AGATGAGTCAAGTCAGACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:143:43,100:90,144:0.3793:2,2:24.6:1:31.5:1:0.11979:1.45205:59.6:142:0.3797:0:1.1 0/1:342:140:52,88:83,118:0.4094:2,2:25.2:1:31.3:1:0.49966:1.18974:60:280:0.4167:0:1.1 -X 123034551 . T C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18729;SOR=Inf;LSEQ=TCATTACAGAAAGGTATGCA;RSEQ=TGCTGTTTTTAAAAAGCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:77,174:0:2,0:23.4:1:30.4:1:1:0:60:61.75:1:0:0.4 0/1:192:2:1,1:65,125:0.0104:2,2:30:1:31:1:1:1.92:60:4:0.0104:0:1 -X 123034598 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18019;SOR=Inf;LSEQ=CCAGATGTGGTGGCTCATAC;RSEQ=TGTAATCCCAGCACTTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:20,81:0:2,0:24.3:1:32.2:1:1:0:60:202:1:0:0.1 0/1:75:2:1,1:12,61:0.0267:2,2:27.5:1:28:1:0.31856:4.92:60:4:0.0267:0:1.5 -X 123040729 . C T 33 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1402;SOR=Inf;LSEQ=TGAGTCATCCTCATATCTCC;RSEQ=GGCACTTGTTGGGTGCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:69,2:0:1,0:25.8:1:31.1:1:1:0:60:142:1:0:0 0/1:43:2:2,0:41,0:0.0465:1,0:18:1:33:0:1:0:60:4:0.0476:0:1 -X 123041043 . A G 141 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ATGTCTTAATCTAACTCTAT;RSEQ=GTAGGCATGTTATGTTGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:75,184:0:2,0:24:1:30.2:1:1:0:52.9:128.5:1:0:0.1 0/1:285:24:6,18:85,176:0.0842:2,2:19.9:1:30.8:1:0.50223:1.44709:58.2:48:0.0854:0:1.1 -X 123041111 . G C 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAACTGACTTTAAGTAATCA;RSEQ=GATTGAATTCCATTAGCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:37:4,33:2,43:0.4512:1,2:21.3:1:29.4:1:0.40174:2.58:43.5:36:0.4557:0:1 0/0:63:0:0,0:4,51:0:2,0:25.2:1:30.8:1:1:0:56.3:110:0.8871:0:0.1 -X 123156220 . CA C 80 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GACAGAGTGAGACTGTGTCT;RSEQ=AAAAAAAAAAAAAAAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:5,0:0.5:0,0:26.2:1:31:1:1:0:52.2:12:0.5:0.0833:1.2 1/0:2:1:1,0:1,0:0.5:0,0:41:0:33:0:1:0:54:2:0.5:0:2 -X 123159372 . G C 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTAGGAAATGGAACCAAC;RSEQ=ATTACATGGAACACCACAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:32:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 123159474 . T C 33 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.1888;LSEQ=AAAATGTTTAGGTATTTGTA;RSEQ=TTTAGATTATTATTTTTGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:11,1:0.1429:2,0:23.5:1:33.5:1:1:0:60:4:0.1538:0:2 0/1:6:1:1,0:5,0:0.1667:0,0:1:0:29:0:1:0:60:2:0.2:0:2 -X 123159533 . A G 98 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10123;SOR=0;LSEQ=TGTGTTTGGTAACGTGCTAT;RSEQ=GTATGATGTTTTGGGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:8,0:57,1:0.1212:1,0:28.6:1:32.9:1:1:0:60:16:0.1231:0:1.4 0/0:29:0:0,0:29,0:0:1,0:28.8:1:28.7:1:1:0:60:58:1:0:0.1 -X 123159810 . TCA T 77 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.21742;SOR=0.20397;LSEQ=TTATTTTGTTTCCTAAGATC;RSEQ=CACACACACAGATTTAAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:5:1,4:151,293:0.0111:2,2:34:1:33.2:1:0.66645:2.05856:60:10:0.0112:0:0.6 0/0:438:1:0,1:149,288:0.0023:2,0:33:0:29:0:1:0:60:2:0.0023:0:0 -X 123159901 . C A 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52081;SOR=0;LSEQ=GAGCTGATTGGTATGGTAAG;RSEQ=CTTCTGAGTAAATGTGGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:0,2:0,81:0.0241:1,0:28.5:1:27:1:1:0:60:4:0.0247:0:1 0/0:53:0:0,0:1,52:0:1,0:22.6:1:31.5:1:1:0:60:106:1:0:0 -X 123159978 . AAATAATAAT A 44 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=34;MSI=14.000;MSILEN=3;SSF=0.52105;SOR=0;LSEQ=TTACACTGCTGTAAAGTTGC;RSEQ=AATAATAATAATAATAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:0.2308:0,0:38:1:28:1:1:0:60:6:0.2308:0:0 0/0:7:0:0,0:0,7:0:0,0:14.7:1:30.3:1:1:0:60:14:1:0:0 -X 123165385 . G T 29 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ATGCCTGGCTAGTGTTTTTT;RSEQ=TTTGTTTGTTTGTTTGTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:22.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 123176358 . G T 56 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12675;SOR=Inf;LSEQ=TTAGTGTTAGAGACTTACTT;RSEQ=GAAGTTTTCTTTATTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:184,41:0:2,0:23.6:1:32:1:1:0:60:450:1:0:0.1 0/1:257:4:2,2:192,61:0.0156:2,2:11.5:1:28:1:0.25266:3.13039:60:8:0.0157:0:1.5 -X 123176582 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16239;SOR=Inf;LSEQ=TATTAAATTGTAAGCATTAG;RSEQ=CTGGGCATGGTGGCTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:31,149:0:2,0:21.9:1:31.6:1:1:0:59.9:89:1:0:0.1 0/1:122:2:1,1:15,105:0.0164:2,2:7.5:1:28:1:0.24604:6.81:60:4:0.0165:0:1 -X 123179265 . GA G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1765;SOR=Inf;LSEQ=TATTGTCTTAGATTTGAGAT;RSEQ=AAAAGATTCTCATTTAAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:51,193:0:2,0:24.6:1:30.2:1:1:0:60:80.333:1:0:0.1 0/1:178:2:1,1:45,131:0.0112:2,2:35:1:31.5:1:0.45115:2.89:60:4:0.0114:0:0.5 -X 123181404 . A G 26 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5235;SOR=0;LSEQ=ATTGTGTGACCAACTTGGTC;RSEQ=CCATTAATTAGGATATAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:18,148:0.0118:2,2:31:1:26.5:1:0.214:8.03:60:4:0.0121:0:1 0/0:107:0:0,0:13,94:0:2,0:24:1:29.3:1:1:0:60:214:1:0:0.1 -X 123181551 . G A 28 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02222;SOR=Inf;LSEQ=TTCTTATTTTCAACCTGCGT;RSEQ=GACTAGTATTAAGAGTGGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:0:0,0:29.1:1:27.5:1:1:0:60:7:1:0:0.8 1/1:2:2:0,2:0,0:1:0,0:10.5:1:28.5:1:1:0:60:4:1:0:1 -X 123182770 . C CT 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.24721;SOR=0;LSEQ=CAAAATACTGGGGAATTCTG;RSEQ=TTTTTTTGTGCTTGTAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:118,14:0.0149:2,2:22:1:30:1:0.2121:8.17647:60:4:0.0152:0.0075:0.5 0/0:135:0:0,0:112,23:0:2,0:24.9:1:32:1:1:0:60:66.5:1:0:0.1 -X 123182980 . C A 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24964;SOR=0;LSEQ=ATTATGTAATTTCTACTCAG;RSEQ=AAGTTTGCATATTTCGTGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:3,0:83,193:0.0108:2,0:14:1:21.7:1:0.02858:0:60:2:0.0072:0:1.7 0/0:259:0:0,0:67,192:0:2,0:24.2:1:31.6:1:1:0:60:63.75:1:0:0.1 -X 123184000 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0965;SOR=Inf;LSEQ=TAAGTTTTGTGGTATATTGG;RSEQ=ACTAATTATGCATCGTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:253,67:0:2,0:24.3:1:31.9:1:1:0:60:79:1:0:0.2 0/1:273:3:1,2:206,64:0.011:2,2:10.3:1:27.7:1:0.14603:6.38196:60:6:0.0112:0:1 -X 123184027 . C T 171 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.0195;LSEQ=TATGCATCGTTTTTCCTTCC;RSEQ=CCATTCAGTGATGCGATAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:51:33,18:337,165:0.0922:2,2:20.4:1:30.2:1:0.75562:1.11382:60:50:0.0921:0:1.1 0/0:507:1:0,1:308,196:0.002:2,0:1:0:23:0:0.3901:0:60:2:0.002:0:1 -X 123184219 . C A 41 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25006;SOR=0;LSEQ=GCGTGGCTGTCTGCACCTCT;RSEQ=ATTCATGAGTTATCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:2,1:47,216:0.0113:2,2:5:1:26:1:0.08822:9.08:60:6:0.0113:0:1 0/0:243:0:0,0:53,190:0:2,0:21.7:1:31.6:1:1:0:60:120.5:1:0:0.1 -X 123184284 . T A 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00697;SOR=0;LSEQ=TGGAAGCCTCCCCTTTATTC;RSEQ=TTTCTATCTTCTCTGTAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:11:1,10:2,72:0.1294:1,2:24.8:1:31.3:1:0.34369:3.52:60:22:0.131:0:1 0/0:50:0:0,0:1,49:0:1,0:23.4:1:29.7:1:1:0:60:49:1:0:0 -X 123184939 . A C 35 v4;q23;Bias;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.31718;SOR=4.07948;LSEQ=AATACATAGAGTTTTAATGC;RSEQ=TTGTCTCATCTTTTTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:1:0,1:359,11:0.0027:1,0:11:0:14:0:0.03235:0:60:0:0:0:3 0/1:276:3:0,3:255,14:0.0109:2,0:13.3:1:22.7:1:0.00021:0:60:2:0.0076:0:2.7 -X 123185446 . C CT 31 v4;MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.13256;LSEQ=ATGGAAATTCTTTTTTTTTT;RSEQ=TTTTTTTTTTCTGAGACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:0,2:0,25:0.0741:1,0:18.5:1:31.5:1:1:0:60:4:0.08:0:0 0/1:12:1:0,1:0,10:0.0833:0,0:28:0:32:0:1:0:60:2:0.0833:0:0 -X 123189846 . G GT 174 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.11506;SOR=2.31746;LSEQ=AATTAAATAAGCTTGATTTG;RSEQ=TTTTTTTTTTCCTTTAACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:81:54:54,0:15,0:0.6667:1,1:26.9:1:30.4:1:1:0:59.9:108:0.675:0.0123:0.3 1/1:34:28:28,0:1,0:0.8235:0,1:22.8:1:30.8:1:1:0:59.8:56:0.8235:0.0588:0.6 -X 123190746 . CT C 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCTTATGCTATAATTAGG;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:1:28:1:1:0:60:4:1:0.5:0.5 -X 123191922 . A G 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00131;SOR=0;LSEQ=AAAAATATTCCTTGTAGCAC;RSEQ=GTAAATTGTGAATAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:15:0,15:0,109:0.121:1,1:21.8:1:29.9:1:1:0:60:14:0.1176:0:1 0/0:69:0:0,0:1,68:0:1,0:24.8:1:31.5:1:1:0:59.9:138:1:0:0.1 -X 123191949 . ACCCACTCC A 73 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=1;SSF=0.00272;SOR=Inf;LSEQ=TGTGAATAGAATGGAGAGCC;RSEQ=CCCACTCCCCCAATTTTTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:0,79:0:1,0:28.6:1:30.6:1:1:0:60:12.167:1:0:0.5 0/1:37:5:0,5:1,31:0.1351:1,0:31:1:31.8:1:1:0:59:10:0.1471:0:0.2 -X 123191970 . AT A 50 v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.54715;SOR=0;LSEQ=CCCACTCCCCCACTCCCCCA;RSEQ=TTTTTTTTTTAAATATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:0,3:0,50:0.0556:1,0:18.7:1:32:1:1:0:60:6:0.06:0:0.3 0/0:26:0:0,0:1,25:0:1,0:16.9:1:30.3:1:1:0:58.3:52:1:0:0.7 -X 123191982 . A T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCCAATTTTTTTTTTT;RSEQ=AATATGCTTTCTACTTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:0,39:0.0488:1,0:17:1:29.5:1:1:0:60:4:0.0513:0:2.5 0/0:19:0:0,0:1,18:0:1,0:16.6:1:30.2:1:1:0:57.6:38:1:0:1 -X 123195035 . A C 178 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=2.49384;LSEQ=TTTGAGTTAAGGCTAGTATG;RSEQ=TAATTGTCTAAGACCACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:29:22,7:186,58:0.1062:2,2:25.1:1:31.3:1:1:1.0203:60:28:0.1045:0:1.1 0/1:214:49:37,12:120,44:0.229:2,2:19.8:1:31.8:1:0.854:1.13:60:98:0.23:0:1.1 -X 123195339 . C A 43 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04306;SOR=Inf;LSEQ=GTTTTCATATAAATATTATG;RSEQ=TATGTAAAAAGATGTAATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:8,42:0:2,0:24.7:1:32.2:1:1:0:60:49:1:0:0.2 0/1:28:3:1,2:0,25:0.1071:1,2:17:1:27.3:1:0.10714:0:60:6:0.1071:0:1 -X 123196540 . AT A 32 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTATAGGACTATCCAA;RSEQ=TTTTTTTTGTTATTTCAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:0.1176:1,0:11.5:1:32:0:1:0:60:4:0.125:0:0 0/0:8:0:0,0:8,0:0:0,0:26.8:1:31.4:1:1:0:60:16:1:0:0 -X 123196884 . G GT 69 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14151;SOR=3.41769;LSEQ=ATAGTGTTACTAAGAAATGA;RSEQ=TTTTTTTTCCCTAAATGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:2:0,2:184,301:0.0041:2,0:42.5:1:30.5:1:0.52889:0:60:4:0.0041:0:0 0/1:360:5:1,4:140,214:0.0139:2,2:30:1:29.8:1:0.65215:2.61083:60:10:0.014:0:0 -X 123197072 . T TA 89 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.81254;SOR=1.20508;LSEQ=AAAGGTAAGATTATTTTGTG;RSEQ=AAAAAAAACCTTTAAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:602:9:3,6:210,381:0.015:2,2:34.2:1:29.7:1:1:1.1022:60:18:0.0152:0.0017:0.2 0/1:501:9:3,6:183,309:0.018:2,2:32.3:1:28.1:1:1:1.18411:60:18:0.0181:0.002:0.2 -X 123197557 . T C 182 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08347;SOR=0.27899;LSEQ=GTGTATTTATTTATCATGAT;RSEQ=AGAAAAGCACCTTAAAATGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:55:54,1:6,0:0.9016:0,1:26.7:1:31.5:1:1:0:60:54:0.9:0:1 1/0:14:10:10,0:4,0:0.7143:0,0:30.7:1:32:1:1:0:60:20:0.7143:0:1.1 -X 123199712 . A T 55 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04379;SOR=Inf;LSEQ=TTGATGGTTCTTAATGTATA;RSEQ=TTAATATTTATAGGGTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:0:0,0:262,181:0:2,0:24.7:1:30:1:1:0:60:54.375:1:0:0.1 0/1:375:4:1,3:230,141:0.0107:2,2:14.3:1:27.5:1:0.16002:4.87313:60:8:0.0107:0:1 -X 123199726 . G T 65 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01923;SOR=Inf;LSEQ=TGTATAATTAATATTTATAG;RSEQ=GTGAAGAACCTGATGAAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:299,238:0:2,0:23.7:1:30.8:1:1:0:60:75.714:1:0:0.1 0/1:448:5:2,3:258,185:0.0112:2,2:28:1:28.4:1:0.65388:2.08842:60:10:0.0113:0:1 -X 123199914 . GTTTACTGCA G 65 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=1.222;MSILEN=1;SSF=0.29991;SOR=0;LSEQ=CGTTGTGGGGGCATTTTAAA;RSEQ=TTTACTGCATTCTGTTAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:4:4,0:79,66:0.0268:2,0:23.3:1:32.8:1:0.12973:0:60:8:0.027:0:0 0/0:82:0:0,0:36,46:0:2,0:23:1:29.9:1:1:0:60:81:1:0:0.1 -X 123200482 . ATTG A 74 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00128;SOR=Inf;LSEQ=GGTATGATTTTTAATTAAAA;RSEQ=TTGTTCACATTTGAAGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:0:1,0:22.2:1:30.4:1:1:0:60:35:1:0:0.1 0/1:15:5:0,5:0,10:0.3333:0,0:24:1:32:0:1:0:60:10:0.3333:0:0 -X 123200860 . G A 44 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACATTGTACTTGTAGT;RSEQ=CTGGATATTACCTTAAATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:22:1:28:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 123202318 . C CTATA 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.00108;SOR=0;LSEQ=CAGAAGTAGAGTTAATAAAG;RSEQ=TATGAGATAATGTTTTACAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:14:13,1:98,0:0.125:1,1:28.2:1:29.5:1:0.125:0:60:28:0.1308:0.0268:0 0/0:69:0:0,0:68,1:0:1,0:21.6:1:32.7:1:1:0:60:138:1:0:0.1 -X 123204992 . T A 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09357;SOR=Inf;LSEQ=TTTCCTCTTTTTTTTTTTTT;RSEQ=AAATAGGCCTTCACTATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:272,78:0:2,0:22.7:1:28.3:1:1:0:59.9:14.217:0.9849:0:0.6 0/1:297:3:2,1:207,86:0.0101:2,2:25:1:20.3:1:1:1.20268:60:2:0.0072:0:1 -X 123204993 . A T 64 P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.46912;SOR=0.49208;LSEQ=TTCCTCTTTTTTTTTTTTTT;RSEQ=AATAGGCCTTCACTATTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:5:2,3:278,77:0.0135:2,2:19.2:1:27.6:1:0.07502:5.38197:60:10:0.0145:0:1.4 0/0:299:2:1,1:210,86:0.0067:2,2:29:1:27.5:1:0.49936:2.43358:60:4:0.0071:0:1.5 -X 123210120 . T TA 47 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.77173;LSEQ=GCATGTTTCATAGTGAGAAT;RSEQ=AAAAAAAATACATGGTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:3,0:223,57:0.0106:2,0:14.3:1:29.7:1:1:0:60:6:0.0108:0.0071:0.3 0/0:244:2:1,1:191,51:0.0082:2,2:23:1:28:1:0.3815:3.71881:60:4:0.0083:0:0 -X 123210377 . G A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08062;SOR=Inf;LSEQ=AATGCAACGCTAGTTTTTAT;RSEQ=CATGGCTGCCATTGAATTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:40,173:0:2,0:24.2:1:32.1:1:1:0:60:105.5:1:0:0.1 0/1:163:3:2,1:36,124:0.0184:2,2:7.3:1:29:1:0.13592:6.78:60:6:0.0186:0:1 -X 123211740 . T C 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.152;SOR=Inf;LSEQ=ACGTGTTTACATGACTAACC;RSEQ=AAAATTTGTCTTATTGTCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:206,17:0:2,0:23.7:1:31.2:1:1:0:59.9:110.5:1:0:0 0/1:143:2:1,1:121,20:0.014:2,2:31.5:1:32:1:0.27302:5.92857:60:4:0.0141:0:1 -X 123214947 . T TC 52 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTTGCTGGGGTTTTTTT;RSEQ=CCCCTTTATATTTTTATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:36:1:33.3:1:1:0:60:6:1:0:0 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 123217056 . T TTG 89 MAF0.05;MSI6;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=0.60268;SOR=0.39967;LSEQ=TAAGTGGCGTGTGTGTGTGT;RSEQ=TGTGTGTGTGTGTGTGTATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:7,0:0.4667:0,0:33.7:1:31.8:1:1:0:60:14:0.4667:0.0667:0 0/1:4:1:1,0:3,0:0.25:0,0:22:0:33:0:1:0:60:2:0.25:0:0 -X 123217226 . G A 35 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0765;SOR=Inf;LSEQ=TTATTGACTTTTTTATTATA;RSEQ=TCCCTCAAATATTTATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:226,37:0:2,0:24.1:1:32.2:1:1:0:60:86.667:1:0:0.1 0/1:195:3:2,1:155,37:0.0154:2,2:16:1:22.3:1:0.48005:2.08501:60:2:0.0104:0:1 -X 123217527 . A G 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03469;SOR=0;LSEQ=ATTAATACACAAAAAAGTTT;RSEQ=TACTTCAGCAACTTTATAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:12:0,12:1,75:0.1364:1,0:22.6:1:32.3:1:1:0:60:24:0.1463:0:1.1 0/0:31:0:0,0:0,31:0:1,0:23.3:1:30.2:1:1:0:60:62:1:0:0 -X 123220306 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13573;SOR=Inf;LSEQ=TGTAAGGCTGAGTTTGAGTA;RSEQ=TGAAGTAATATGCCTATGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:145,5:0:1,0:24.2:1:32.3:1:1:0:60:74:1:0:0.1 0/1:88:2:1,1:80,6:0.0227:2,2:19:1:28.5:1:0.15361:12.42128:60:4:0.023:0:1 -X 123224615 . G A 76 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.00295;SOR=Inf;LSEQ=CAAACACCTCTTGATTATAA;RSEQ=TAAGTACATTTGATCATTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:895:0:0,0:393,502:0:2,0:24.7:1:32.1:1:1:0:60:178:1:0:0.1 0/1:692:7:5,2:308,377:0.0101:2,2:7.4:1:27.4:1:0.2538:3.06:60:14:0.0102:0:1 -X 123227822 . G T 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63297;SOR=0.41656;LSEQ=CTGCTGCCTAGATATTAATA;RSEQ=TCACGACATTAGTTCAGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:197,40:0.0125:2,2:23:1:28.7:1:0.07997:9.70673:60:6:0.0126:0:1 0/0:191:1:1,0:150,40:0.0052:2,0:5:0:30:0:1:0:60:2:0.0053:0:1 -X 123229169 . T A 137 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATATTTTCAGTTACTATC;RSEQ=GGTTTGTAGATATAGCTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:219,87:0:2,0:23.5:1:30.7:1:1:0:60:75.5:1:0:0.1 0/1:263:24:16,8:176,63:0.0913:2,2:23.9:1:29.9:1:0.47403:1.39494:60:48:0.092:0:1 -X 123234405 . C CCT 75 MSI6;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.52599;SOR=1.79033;LSEQ=CTTTTAACGAGATTTTCTCC;RSEQ=CTCTCTCTCTCTCATTAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:4:2,2:350,189:0.0073:2,2:21:1:28.9:1:0.61574:1.84969:60:8:0.0075:0.0018:0 0/1:459:6:4,2:290,163:0.0131:2,2:17.7:1:29.1:1:1:1.12:60:12:0.0134:0.0065:1.3 -X 123414449 . A T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4966;SOR=Inf;LSEQ=ATCTTTTTAATTGTGAACTA;RSEQ=AGGCCGACAAAGATGATCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:40,23:0:2,0:24.3:1:30.1:1:1:0:58.8:62:1:0:0.1 0/1:67:2:1,1:39,26:0.0299:2,2:36.5:1:29:1:1:1.49067:60:4:0.0299:0:1 -X 123414542 . G A 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50005;SOR=0;LSEQ=TTTAGAGGCTGGTGCAAAGG;RSEQ=TGACTTGCACATTGTTGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:39,36:0.026:2,2:12:1:29.5:1:1:1.08219:52:4:0.026:0:1 0/0:65:0:0,0:33,32:0:2,0:25.7:1:30.8:1:1:0:60:64:1:0:0.1 -X 123414650 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20568;SOR=Inf;LSEQ=GTAAATGGTTTCCACTGGGG;RSEQ=CTTTGAAATAACACCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:60,37:0:2,0:26.4:1:31.8:1:1:0:60:96:1:0:0.1 0/1:81:2:1,1:46,33:0.0247:2,2:26.5:1:30.5:1:1:1.38811:60:4:0.0247:0:1 -X 123414651 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.214;SOR=Inf;LSEQ=TAAATGGTTTCCACTGGGGG;RSEQ=TTTGAAATAACACCACCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:60,37:0:2,0:26.6:1:32.2:1:1:0:60:47.5:1:0:0.1 0/1:84:2:1,1:47,35:0.0238:2,2:6.5:1:28:1:1:1.33807:60:4:0.0238:0:1 -X 123414690 . T A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5025;SOR=0;LSEQ=CTGGTCTTATGGTTGAACTG;RSEQ=GGTTCAGGGCCAGTGCATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:81,78:0.0124:2,2:35.5:1:30.5:1:1:1.03823:60:4:0.0126:0:1.5 0/0:134:0:0,0:72,62:0:2,0:25.5:1:29.5:1:1:0:59.4:133:1:0:0.1 -X 123414692 . G T 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5034;SOR=0;LSEQ=GGTCTTATGGTTGAACTGTG;RSEQ=TTCAGGGCCAGTGCATATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:84,78:0.0122:2,2:21.5:1:29.5:1:1:1.07641:60:4:0.0123:0:1.5 0/0:134:0:0,0:70,64:0:2,0:26:1:30.9:1:1:0:59.2:268:1:0:0.1 -X 123480610 . G A 66 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10266;SOR=5.78331;LSEQ=ACAGCGAGAGCGTGCCAGGC;RSEQ=TGTACTGCCTATGTGTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:1:1,0:213,268:0.0021:2,0:1:0:27:0:0.44398:0:60:2:0.0021:0:1 0/1:421:5:3,2:175,240:0.0119:2,2:16.8:1:28.8:1:0.6544:2.05:60:10:0.0121:0:1.2 -X 123480687 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.16581;SOR=Inf;LSEQ=GTGGGCGGTGGGCAACAGCA;RSEQ=CTGGGGCCAGGGTGGAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:55,150:0:2,0:25.5:1:31.9:1:1:0:60:50.25:0.995:0:0.2 0/1:142:2:1,1:33,107:0.0141:2,2:29:1:28.5:1:0.42283:3.21:60:4:0.0146:0:1 -X 123480720 . G T 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53769;SOR=0;LSEQ=TGGAGGCCGAGGCAGGCAGG;RSEQ=GCGCCGGCGTTAGCAGCTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:9,109:0.0167:2,2:9:0:28:1:0.16036:11.54:60:4:0.0167:0:1 0/0:67:0:0,0:4,63:0:2,0:22:1:30.7:1:1:0:60:134:1:0:0.1 -X 123488238 . G C 159 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19273;SOR=1.9096;LSEQ=TCTCTCAGTGGACAGTTCTA;RSEQ=CTCCATGTCCAAGCAGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:32:0,32:0,40:0.4384:1,1:27.5:1:31.8:1:1:0:60:64:0.4571:0:1.1 1/0:30:18:0,18:0,12:0.6:0,1:18.6:1:29.6:1:1:0:60:17:0.6296:0:1.1 -X 123499949 . T TAGAA 97 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGTGACTATGTGAAATCT;RSEQ=AGCATATCAAAAGTAGGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:0,2:0.8182:0,0:30.6:1:30.9:1:1:0:60:18:0.8182:0:0.6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 123499991 . T G 94 P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATTAAATGAACAATTAT;RSEQ=TACCAAATGATACCAATATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1:0,0:19.4:1:31.4:1:1:0:60:16:1:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 123500066 . C A 50 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTATTTTCTAAGAGACTA;RSEQ=AATATACTTGGGAAGTTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:15.3:1:32:0:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 123500274 . A T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTTATGCACAAGGCTCA;RSEQ=TTTGAAAAGTAAATAAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:39:1:31.3:1:1:0:60:6:1:0:2.7 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 123503943 . C A 108 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTACACAAATGTTACTTCT;RSEQ=TTAGCATCCCTAGCACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:142,13:0:2,0:23.6:1:31.2:1:1:0:60:37.75:1:0:0.1 0/1:130:15:12,3:101,14:0.1154:2,2:26.9:1:27.7:1:0.4154:1.7939:60:30:0.1172:0:1 -X 123504227 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52268;SOR=0;LSEQ=GCTCAGAGTTATGAGTCAAC;RSEQ=TGTTCATAACCATATAATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:2,0:23,172:0.0102:2,0:5:1:30.5:1:0.01554:0:60:4:0.0103:0:1 0/0:126:0:0,0:19,107:0:2,0:21.2:1:31.5:1:1:0:60:252:1:0:0.1 -X 123505272 . C A 45 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93983;LSEQ=AACACCTTGTACTTTATTTT;RSEQ=TATAATTTAAATATATGCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:2,1:100,165:0.0112:2,2:15:1:29:1:0.55966:3.28:60:6:0.0113:0:1 0/1:190:2:2,0:67,121:0.0105:2,0:1:0:23.5:1:0.13066:0:60:4:0.0107:0:1 -X 123505439 . GA G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.10784;SOR=10.41485;LSEQ=AGCTTTGAAACGAGGATTGG;RSEQ=AAAAGTAATTCCGTAGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:0,13:0.0714:1,0:43:0:30:0:1:0:60:2:0.0714:0:0 1/0:4:2:0,2:0,2:0.5:0,0:12:1:32:1:1:0:60:4:0.5:0.25:0.5 -X 125161355 . C T 47 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CAGAGACTGTGGCCAGCCCT;RSEQ=CCCCTAGGGGCTCAGATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:0.5:2,2:20:1:30:1:1:3.11:60:6:0.6:0:1.3 0/0:4:0:0,0:0,4:0:0,0:14.8:1:31.8:1:1:0:60:8:1:0:0.3 -X 125161775 . A G 32 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAAGCAGATTCCAGCTGA;RSEQ=AGGCTGTAAGATTCTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:38:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 125318839 . A T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.30508;SOR=4.59413;LSEQ=ATAAATACAAAGGGGATTTT;RSEQ=AAATAAATCTTTAAGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:1:0,1:136,41:0.0056:2,0:1:0:23:0:0.23596:0:60:2:0.0058:0:1 0/1:118:3:1,2:87,28:0.0254:2,2:25.3:1:28.3:1:0.15863:6.09544:60:6:0.0259:0:1.3 -X 125318842 . A T 34 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.27886;SOR=0;LSEQ=AATACAAAGGGGATTTTAAA;RSEQ=TAAATCTTTAAGCCAGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:139,47:0.0159:2,2:16:1:22:1:0.16531:5.84701:60:2:0.0106:0:3 0/0:125:0:0,0:91,34:0:2,0:23.1:1:29.7:1:1:0:60:124:1:0:0.1 -X 125318941 . A G 201 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02466;SOR=0.63294;LSEQ=CAAGAAATAGGTAATAAGAA;RSEQ=GACTGAAAAAATTACCTTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:90:40,50:155,191:0.2059:2,2:25.1:1:31.1:1:1:1.01437:60:89:0.2046:0:1.1 0/1:298:42:19,23:126,129:0.1409:2,2:26.8:1:30.6:1:0.73937:1.18171:60:41:0.1385:0:1.1 -X 125499259 . T A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23426;SOR=Inf;LSEQ=CTTATTAGATGCCAAGATAT;RSEQ=GATTATTACTGGTTCTTTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:78,43:0:2,0:24.8:1:29.7:1:1:0:60:120:1:0:0.3 0/1:114:2:1,1:72,40:0.0175:2,2:41.5:1:29.5:1:1:1.79012:60:4:0.0177:0:1.5 -X 125499267 . A T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24317;SOR=Inf;LSEQ=ATGCCAAGATATTGATTATT;RSEQ=CTGGTTCTTTAAGGTAAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:77,51:0:2,0:25.7:1:28.1:1:1:0:60:41.667:1:0:0.2 0/1:126:2:1,1:73,51:0.0159:2,2:10:0:30:1:1:1.42719:60:4:0.016:0:2 -X 125499312 . A G 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24278;SOR=0;LSEQ=TGTAAATTAAATATGCTAAT;RSEQ=AAAGTGGCACCATTACATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:78,73:0.0131:2,2:5:1:27.5:1:1:1.068:60:4:0.0131:0:1 0/0:157:0:0,0:72,85:0:2,0:24.6:1:29.1:1:1:0:60:156:1:0:0.6 -X 125499336 . A C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.67905;LSEQ=GTGGCACCATTACATATATT;RSEQ=ATGATAACCAGTCATACATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:52:28,24:35,60:0.3537:2,2:25:1:30.9:1:0.05593:1.99:60:51:0.3566:0:1.1 1/0:124:83:38,45:18,23:0.6694:2,2:28.1:1:31.2:1:1:1.08:60:82:0.6721:0:1.1 -X 125499396 . T C 29 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54573;SOR=0;LSEQ=TTTGAATTCAAAGCATAAGC;RSEQ=GAAGAATAATTCATAGATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:21,65:0.0227:2,2:12.5:1:29:1:0.43966:3.05:60:4:0.023:0:1 0/0:46:0:0,0:14,32:0:2,0:21.4:1:28.8:1:1:0:60:22:1:0:0.4 -X 127677424 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTTGGGCTTGGGGGAC;RSEQ=AGTTTTGGAACCAAGCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:0:32:0:1:0:60:4:1:0:1.5 -X 131623188 . C T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14125;SOR=Inf;LSEQ=GGTATAAAATGTCAAGTCTA;RSEQ=AGACACGCGCACGCTGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:26,18:0:2,0:20.7:1:31.8:1:1:0:60:88:1:0:0.1 0/1:27:2:1,1:17,8:0.0741:2,2:26:1:27.5:1:1:2.0616:60:4:0.0741:0:1 -X 132127787 . C A 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08593;SOR=Inf;LSEQ=AATCAAGGCAAAAATAATTA;RSEQ=GTGGAAGCTCTAAATTGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:185,127:0:2,0:27:1:30.9:1:1:0:60:155:0.9936:0:0.2 0/1:249:3:2,1:144,101:0.012:2,2:24.7:1:28.3:1:1:1.40:60:6:0.0122:0:1 -X 132127845 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.87935;LSEQ=GAAACATTCTTCTCCCTGAG;RSEQ=TCTAATATCAAAAAACATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:100:48,52:123,128:0.2849:2,2:26.1:1:29.6:1:0.90609:1.04091:60:99:0.2837:0:1.2 1/0:288:154:70,84:61,73:0.5347:2,2:23.1:1:29:1:1:1.00273:60:50.333:0.5336:0:1.1 -X 132127908 . G A 33 v4;q23;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25864;SOR=0;LSEQ=TTTTGGGAAGTTCTGTGTTT;RSEQ=ACTATGAAGCCAGATTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:3:2,1:58,120:0.0166:2,2:5.3:1:21:1:0.25555:4.10:60:2:0.0113:0:2.3 0/0:142:0:0,0:46,96:0:2,0:21.7:1:31.1:1:1:0:60:141:1:0:0.5 -X 132127915 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17782;SOR=Inf;LSEQ=AAGTTCTGTGTTTGACTATG;RSEQ=AGCCAGATTCCTAGACCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:48,120:0:2,0:22.3:1:29.8:1:1:0:60:55:1:0:0.2 0/1:123:2:1,1:35,86:0.0163:2,2:5:0:32.5:1:0.5014:2.44:60:4:0.0163:0:1.5 -X 132127924 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17318;SOR=Inf;LSEQ=GTTTGACTATGAAGCCAGAT;RSEQ=CCTAGACCCATCTATTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:35,105:0:2,0:23.3:1:29.5:1:1:0:60:45.667:1:0:0.2 0/1:101:2:1,1:27,72:0.0198:2,2:32.5:1:28.5:1:0.4796:2.64:60:4:0.0198:0:1 -X 132467696 . A C 189 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGAGTAGCAGTGCTTTC;RSEQ=AACTAAATCGGAGACCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:148,109:0:2,0:26.2:1:30.2:1:1:0:60:127.5:1:0:0.1 0/1:189:74:45,29:62,53:0.3915:2,2:25.6:1:30.5:1:0.3706:1.32:60:36:0.385:0:2 -X 132467723 . T A 190 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCGGAGACCACTGGCATAA;RSEQ=CTGGAAGAAACACTGCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:126,124:0:2,0:29:1:30.4:1:1:0:60:124:1:0:0.1 0/1:219:89:48,41:67,63:0.4064:2,2:27.1:1:29.4:1:0.78347:1.10:60:88:0.4055:0:1.8 -X 132467759 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1964;SOR=Inf;LSEQ=CATTTGCAGGAAGGCCAGAA;RSEQ=GCCTCATGTCTTTCTCCGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:79,138:0:2,0:23.1:1:31.2:1:1:0:60:216:0.9954:0:0.1 0/1:174:2:1,1:71,101:0.0115:2,2:21:1:31.5:1:1:1.42:60:4:0.0115:0:1 -X 132467761 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19426;SOR=Inf;LSEQ=TTTGCAGGAAGGCCAGAAGG;RSEQ=CTCATGTCTTTCTCCGTACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:76,134:0:2,0:23.3:1:31:1:1:0:60:41:1:0:0.1 0/1:166:2:1,1:66,98:0.012:2,2:21.5:1:31.5:1:1:1.48:60:4:0.0123:0:1 -X 133300745 . T C 86 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07092;SOR=5.03608;LSEQ=TGAAGCCGATGGAGCGGAGT;RSEQ=GCAGCACCTGGTGGCCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:2,0:43,1:0.0435:1,0:34.5:1:31.5:1:1:0:60:4:0.0455:0:1 0/1:37:7:7,0:30,0:0.1892:1,0:24.9:1:30.9:1:1:0:60:14:0.1892:0:1.6 -X 133300776 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20833;SOR=Inf;LSEQ=GTGGCCGCCGAACAGCAGAA;RSEQ=GCGCAGTTTACTGCACAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:77,1:0:1,0:21.7:1:32.5:1:1:0:60:77:1:0:0.1 0/1:66:2:1,1:63,1:0.0303:1,2:5:1:28:1:0.06014:44.90018:60:4:0.0308:0:1 -X 133301028 . G A 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.50138;LSEQ=CAGACTTAAGGGCCAGTGGG;RSEQ=GAAGGCTGTCAACCCATTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:2:2,0:61,205:0.0075:2,0:1:0:26.5:1:0.05459:0:60:4:0.0076:0:1 0/1:179:2:1,1:41,136:0.0112:2,2:10.5:1:27.5:1:0.41523:3.29:60:4:0.0116:0:1 -X 133301064 . C A 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53386;SOR=0;LSEQ=ATTGTCAGATCAGCATCAGG;RSEQ=TGTTATCAAGTCTGTTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:0,2:5,146:0.013:1,0:12:1:31.5:1:1:0:60:4:0.0146:0:1 0/0:89:0:0,0:3,86:0:1,0:24.9:1:30.7:1:1:0:60:8.889:1:0:0.2 -X 133741142 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18735;SOR=Inf;LSEQ=ATAAAAAAGACAGATGATCA;RSEQ=TTTTGGCCAGAACCACCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:119,90:0:2,0:25.5:1:31.7:1:1:0:59.9:68.667:1:0:0.2 0/1:160:2:1,1:94,64:0.0125:2,2:24.5:1:28:1:1:1.46511:60:4:0.0127:0:1.5 -X 133741194 . A AG 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50888;SOR=0;LSEQ=TGCCAAAATAATGAACACAA;RSEQ=GGGAAAGAGAAGAGGCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:72,120:0.0103:2,2:18:1:30:1:1:1.66:60:4:0.0104:0:0 0/0:146:0:0,0:54,92:0:2,0:23.3:1:29.6:1:1:0:60:28.2:1:0:0.2 -X 136523405 . G T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57703;SOR=2.71987;LSEQ=GGGACAGGACCAAGAACTAG;RSEQ=GGCTCAGACATTTACAACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:1:1,0:143,67:0.0047:2,0:6:0:12:0:1:0:60:0:0:0:2 0/1:156:2:1,1:101,53:0.0128:2,2:13:1:28:1:1:1.89732:60:4:0.0132:0:1 -X 136523442 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09211;SOR=Inf;LSEQ=ACTGCAGGCATTTTCTCTTC;RSEQ=TCTTCTTCACGGGAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:176,130:0:2,0:27.9:1:31.4:1:1:0:60:50:1:0:0.1 0/1:253:3:1,2:138,110:0.0119:2,2:12.7:1:28.3:1:0.5875:2.50008:60:6:0.012:0:1 -X 136523528 . C T 44 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06417;SOR=Inf;LSEQ=CGCCTTGTGAGGGCCAAGCA;RSEQ=TCCAGGTATTTTACAGCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:181,149:0:2,0:24.3:1:31.9:1:1:0:60:54:1:0:0.1 0/1:222:3:1,2:110,109:0.0135:2,2:15.3:1:28.3:1:1:2.0122:60:6:0.0138:0:1 -X 136523931 . C G 158 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAATGCGTTGGTTGTGTAA;RSEQ=TGATCAGTAGGCAAGTTTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:208,281:0:2,0:25.5:1:32.1:1:1:0:59.7:162:1:0:0.1 0/1:396:33:14,19:153,210:0.0833:2,2:23.2:1:31.4:1:1:1.01:60:66:0.0846:0:1.1 -X 136524003 . G A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0794;SOR=0;LSEQ=TGATGGCCTGCATCTGGGCC;RSEQ=CTCGCTGGGCCGCAGCTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:5:3,2:85,221:0.0161:2,2:22:1:26.8:1:0.13954:3.88:60:10:0.0163:0:1 0/0:221:0:0,0:77,144:0:2,0:26.6:1:30.5:1:1:0:59.1:43.2:1:0:0.3 -X 138188496 . G A 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ACCCAAGGCCATCCAGCTGG;RSEQ=CAGCCACAGAGTTGGCGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:0.5:2,0:12.5:1:31:1:1:0:60:4:0.5:0:1 0/0:2:0:0,0:1,1:0:2,0:22:0:33.5:1:1:0:60:4:1:0:0.5 -X 138992339 . G T 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18363;SOR=0;LSEQ=ATGATTTGAACTCATGTTAA;RSEQ=AGAGGGTGTCAAATTGAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:0.069:2,2:11.5:1:31.5:1:1:1.07415:60:4:0.069:0:1 0/0:38:0:0,0:21,17:0:2,0:27.1:1:31.4:1:1:0:59.5:76:1:0:0.1 -X 139479299 . C T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.176;SOR=Inf;LSEQ=AAGCTGAGCAGTGACGAGAC;RSEQ=AGCAACCCTCACCTCTCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:82,28:0:2,0:27:1:31.6:1:1:0:60:220:1:0:0.1 0/1:80:2:1,1:60,18:0.025:2,2:33.5:1:31:1:0.42089:3.27133:60:4:0.026:0:1.5 -X 139479364 . G T 44 v4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64352;SOR=0.46277;LSEQ=TAGAAAGTGGTACAATCACT;RSEQ=AACACCCTGATATACCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:158,78:0.0125:2,2:10:1:28.3:1:0.26019:4.02563:60:6:0.0126:0:1 0/0:172:1:0,1:111,60:0.0058:2,0:1:0:22:0:0.35465:0:60:2:0.0058:0:1 -X 139479523 . C A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49887;SOR=0;LSEQ=TTGGAGTTCAATTTAATTAG;RSEQ=ACAGTAAAGAAGAAGATCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:78,107:0.0106:2,2:36:1:30.5:1:1:1.37:60:4:0.0108:0:1 0/0:180:0:0,0:76,104:0:2,0:25.1:1:32.2:1:1:0:60:360:1:0:0.1 -X 139479534 . A G 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.2479;SOR=Inf;LSEQ=TTTAATTAGCACAGTAAAGA;RSEQ=GAAGATCCATTACTGTTTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:80,99:0:2,0:26.6:1:31:1:1:0:60:358:1:0:0.1 0/1:178:2:1,1:81,95:0.0112:2,2:23.5:1:32:1:1:1.17:60:4:0.0114:0:2 -X 139479551 . T C 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49867;SOR=0;LSEQ=AGAAGAAGATCCATTACTGT;RSEQ=TGCAACTGTAGGAAGCAACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:81,99:0.011:2,2:23.5:1:30.5:1:1:1.22:60:4:0.011:0:1.5 0/0:178:0:0,0:89,89:0:2,0:25.2:1:30:1:1:0:60:356:1:0:0.1 -X 139479570 . C T 30 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61728;SOR=2.08171;LSEQ=TTTGCAACTGTAGGAAGCAA;RSEQ=AGAGTTACCTTGTATGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:92,103:0.0051:2,0:1:0:24:0:1:0:60:2:0.0052:0:1 0/1:189:2:1,1:91,96:0.0106:2,2:16:0:30.5:1:1:1.05:60:4:0.0107:0:2 -X 139479605 . A G 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22345;SOR=Inf;LSEQ=TGAATGTCATTGACAAGGAG;RSEQ=AATTCGGTTGTTGCAATCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:87,111:0:2,0:26:1:30.1:1:1:0:60:197:1:0:0.1 0/1:178:2:1,1:81,95:0.0112:2,2:49.5:1:28.5:1:1:1.17:60:4:0.0114:0:2 -X 139479663 . G C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20974;SOR=Inf;LSEQ=GACGAAACTTTTACACTTGT;RSEQ=CATGGACCTATGATAGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:67,91:0:2,0:26.1:1:32:1:1:0:60:51.667:1:0:0.1 0/1:134:2:1,1:52,80:0.0149:2,2:43.5:1:30.5:1:1:1.53:60:4:0.0152:0:1 -X 139479797 . C T 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTAGAGATCCAAATCTACT;RSEQ=CTATCAGTAAGTAAAGATCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:25:15,10:64,59:0.1689:2,2:24.6:1:29.8:1:0.51541:1.38:60:24:0.1678:0:1 0/0:98:0:0,0:56,42:0:2,0:24.7:1:30.8:1:1:0:60:97:1:0:0.2 -X 139479802 . C T 77 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00286;SOR=Inf;LSEQ=AGATCCAAATCTACTCCTAT;RSEQ=AGTAAGTAAAGATCATGCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:83,70:0:2,0:22.4:1:31.4:1:1:0:60:75.5:1:0:0.3 0/1:95:6:5,1:51,38:0.0632:2,2:21.8:1:30:1:0.39536:3.68:60:12:0.0638:0:1 -X 139479898 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21702;SOR=Inf;LSEQ=ACAGAGTTGAAGTTCTAAGC;RSEQ=CTGGTTGTGATCTTTTGCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:84,92:0:2,0:24.1:1:30.6:1:1:0:60:175:1:0:0.1 0/1:154:2:1,1:73,78:0.013:2,2:35.5:1:30:1:1:1.07:60:4:0.0132:0:1 -X 139479907 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5023;SOR=0;LSEQ=AAGTTCTAAGCGCTGGTTGT;RSEQ=ATCTTTTGCGTGAAAAAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:83,96:0.011:2,2:37.5:1:30:1:1:1.16:60:4:0.0112:0:1 0/0:152:0:0,0:73,79:0:2,0:24.6:1:31.1:1:1:0:60:151:1:0:0.1 -X 139479930 . G T 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5037;SOR=0;LSEQ=CTTTTGCGTGAAAAAATAAT;RSEQ=TCCTGTGGTATGGATCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:77,105:0.0109:2,2:12:1:30:1:1:1.36:60:4:0.0109:0:1 0/0:150:0:0,0:72,78:0:2,0:25.7:1:31.4:1:1:0:60:74:1:0:0.1 -X 139480142 . G A 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATACTTTCTAAGTCTTGT;RSEQ=AAAATGCAGTTGTGTTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:42,36:0.025:2,2:17:0:31:1:1:1.16441:60:4:0.0253:0:1 0/0:36:0:0,0:19,17:0:2,0:23.8:1:31.3:1:1:0:60:72:1:0:0.1 -X 139586707 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15982;SOR=Inf;LSEQ=AGCAGTTTCCAGTCGGCGCC;RSEQ=AAGCGCTTGCTGATCTCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:173,97:0:2,0:25.5:1:30.8:1:1:0:60:44:0.9962:0:0.1 0/1:181:2:1,1:107,72:0.011:2,2:31:1:28.5:1:1:1.48274:60:4:0.0113:0:1 -X 139586766 . G A 62 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.14078;SOR=0;LSEQ=CTCCAGGGCCATTTTGCGCC;RSEQ=CTGCCCGCGGGACCATACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:4:2,2:160,192:0.0112:2,2:19:1:31:1:1:1.20:60:8:0.0116:0:1 0/0:263:0:0,0:121,142:0:2,0:27.2:1:30.6:1:1:0:60:42.833:1:0:0.2 -X 139586803 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15898;SOR=Inf;LSEQ=ACCATGAAGGCGTTCATGGG;RSEQ=CGTTTCACACGGTCCTGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:73,163:0:2,0:24:1:31.2:1:1:0:60:58:1:0:0.1 0/1:157:2:1,1:56,99:0.0127:2,2:23.5:1:28:1:1:1.76:60:4:0.0131:0:1 -X 139586813 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15142;SOR=Inf;LSEQ=CGTTCATGGGCCGTTTCACA;RSEQ=GGTCCTGGTCTGTACCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:48,160:0:2,0:23.4:1:30.1:1:1:0:60:103:1:0:0.1 0/1:133:2:1,1:42,89:0.015:2,2:29:1:28:1:0.54375:2.11:60:4:0.0153:0:1 -X 140462166 . C T 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATAGAAATCCTCAGAAC;RSEQ=CTCTACCCCAAATCAACAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:15:0:33:0:1:0:56:4:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 140462644 . A T 27 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49804;SOR=0;LSEQ=TAAGACAAGAAATTTCTAAG;RSEQ=TCACAACAGAATTGAAGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:43,26:0.0282:2,2:38:1:27:1:1:1.64163:60:4:0.029:0:1.5 0/0:63:0:0,0:44,19:0:2,0:19.7:1:28.3:1:1:0:60:20:1:0:0.1 -X 140462686 . C CA 212 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01075;SOR=0.49016;LSEQ=TAGAGACACAAAAATCCCTC;RSEQ=AAAAAAATCAATCCAGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:165:134:73,61:18,13:0.8121:2,2:29.8:1:30.1:1:0.84168:1.15599:59.9:32.5:0.8176:0.0485:0.4 1/0:137:93:48,45:27,17:0.6788:2,2:31.2:1:30.1:1:0.3585:1.48464:59.5:186:0.6788:0.0365:0.2 -X 140462705 . G T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19484;SOR=Inf;LSEQ=CCAAAAAAATCAATCCAGGA;RSEQ=CCGTTTTTTTTTTAAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:86,87:0:2,0:27.2:1:31.3:1:1:0:59.8:18.222:1:0:0.3 0/1:138:2:1,1:67,69:0.0145:2,2:33.5:1:27.5:1:1:1.03:60:4:0.0147:0:1 -X 140462708 . G GT 112 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.26754;SOR=0.55606;LSEQ=AAAAAATCAATCCAGGAGCC;RSEQ=TTTTTTTTTTAAATGAACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:15:8,7:75,80:0.0872:2,2:35.5:1:28.7:1:0.79064:1.22:60:14:0.0843:0:0.5 0/1:139:7:4,3:64,68:0.0504:2,2:36.9:1:30.7:1:0.71459:1.41:60:14:0.0504:0:0.6 -X 140462745 . G A 30 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50223;SOR=0;LSEQ=ACAAAATTGATGGCTAGTTA;RSEQ=ACTAATAAAGAAGAAAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:39,58:0.0202:2,2:10:0:30:0:1:1.48:60:4:0.0204:0:1.5 0/0:81:0:0,0:31,50:0:2,0:18.8:1:30.3:1:1:0:60:19.25:1:0:0.3 -X 140519098 . C T 31 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTTATATAACAGCAGCC;RSEQ=CTGCACCGCCACTCCCAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:0.5:0,0:10.5:1:31:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:0:0,0:1:0:30:0:1:0:60:2:1:0:0 -X 140519337 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21245;SOR=Inf;LSEQ=AGCATGATGAGCTATCAGTA;RSEQ=CTGGCTTCTATGTACACATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:105,64:0:2,0:25.4:1:31.7:1:1:0:60:55.333:1:0:0.5 0/1:145:2:1,1:85,58:0.0138:2,2:25:1:31:0:1:1.46153:60:4:0.014:0:1 -X 140519367 . G A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25473;LSEQ=ATGTACACATAATCTACCTC;RSEQ=TTTCATGATACAATCTTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:197:125:61,64:38,34:0.6345:2,2:23.4:1:29.7:1:0.65777:1.17166:60:40.667:0.6289:0:1.1 0/1:157:48:23,25:61,48:0.3057:2,2:27.9:1:29.2:1:0.38808:1.37846:60:47:0.3013:0:1.1 -X 141805871 . C T 49 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGCAGTGACTCTCCAAAAC;RSEQ=GCCGAGGCCTAGACCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:30.3:1:31.3:1:1:0:53:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 141806035 . C G 75 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.73838;SOR=1.51998;LSEQ=CGCCTTTCAAACTCTTATAC;RSEQ=AACCTCTGGAGTTGGGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:4,2:12,11:0.2069:2,2:31.2:1:29.2:1:0.66284:1.80:60:12:0.2143:0:1 0/1:21:6:3,3:8,7:0.2857:2,2:24.5:1:29.3:1:1:1.1356:60:12:0.2857:0:1 -X 141806066 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23256;SOR=Inf;LSEQ=GTTGGGCAACATGGCTTCTC;RSEQ=CCTTTCTGTGTCCTGTGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:0:2,0:27.3:1:30.5:1:1:0:60:44:1:0:0.2 0/1:21:2:1,1:9,10:0.0952:2,2:27:1:28.5:1:1:1.11:60:4:0.1:0:1 -X 141806238 . T G 53 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCTCTGCCATGGCTCCA;RSEQ=CTGGTCCCTCCATTCGGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:1:0,0:25.3:1:33.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -X 142682796 . C G 107 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.09662;LSEQ=AATTTCAGGTGAACTTGCCT;RSEQ=TCAAAATAAATCAGACCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:10,0:10,1:0.4762:2,0:19.1:1:32.4:1:1:0:56.5:20:0.4762:0:1.6 1/0:10:5:5,0:4,1:0.5:2,0:33.6:1:32:1:1:0:60:10:0.5:0:1.2 -X 142682875 . C T 203 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AAGCAGTTAACACCACTTCC;RSEQ=GAAAGGCATACAAAAATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:87:87:84,3:0,0:1:0,1:23.7:1:31.6:1:1:0:60:174:1:0:1.7 1/1:68:55:51,4:13,0:0.8088:1,2:24.4:1:31.3:1:1:0:60:110:0.8088:0:1.8 -X 142682931 . T C 254 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GATTCCTCCCAGCATACTAC;RSEQ=CAACAGCAGCTTATAAAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:316:316:233,83:0,0:1:0,2:25.1:1:30.7:1:1:0:60:44.143:1:0:1.3 1/0:240:191:139,52:33,16:0.7958:2,2:24.8:1:29.9:1:0.47934:1.29:60:62.667:0.7932:0:1.3 -X 145042055 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17487;SOR=Inf;LSEQ=ACTATTATCCTTAGAGACAA;RSEQ=TCAAAATAATATAACTTAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:93,51:0:2,0:23.8:1:30.4:1:1:0:60:71:1:0:0.2 0/1:104:2:1,1:65,37:0.0192:2,2:12:1:27.5:1:1:1.74668:60:4:0.0198:0:2.5 -X 145042082 . G T 44 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30904;SOR=4.37774;LSEQ=TAATATAACTTAAAATAAAT;RSEQ=GAAGCCAACAATTTAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:113,79:0.0052:2,0:1:0:15:0:0.41451:0:60:0:0:0:1 0/1:134:3:1,2:77,54:0.0224:2,2:27.3:1:28:1:0.57109:2.82958:60:6:0.0231:0:1 -X 145042095 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16435;SOR=Inf;LSEQ=AATAAATGGAAGCCAACAAT;RSEQ=TAGAAATGCATGCAAAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:119,90:0:2,0:26.6:1:30:1:1:0:60:208:1:0:0.3 0/1:143:2:1,1:76,65:0.014:2,2:40.5:1:27.5:1:1:1.16795:60:4:0.0143:0:2 -X 145042104 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=9.49077;LSEQ=AAGCCAACAATTTAGAAATG;RSEQ=ATGCAAAAAAGACATAGGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:49:29,20:83,79:0.2311:2,2:27.2:1:29.5:1:0.41427:1.38:60:98:0.2356:0:1.1 1/0:155:115:59,56:19,21:0.7419:2,2:26.3:1:28.2:1:0.7163:1.16:60:114:0.755:0:1.2 -X 145042124 . TA T 70 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0686;SOR=0;LSEQ=CATGCAAAAAAGACATAGGT;RSEQ=AAAAAAATAGTTTCTATGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:5:2,3:87,101:0.0259:2,2:21.2:1:30.4:1:1:1.29039:60:10:0.0265:0:0.4 0/0:154:0:0,0:70,84:0:2,0:25.8:1:28.1:1:1:0:60:50.333:1:0:0.8 -X 145042128 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.19391;SOR=Inf;LSEQ=CAAAAAAGACATAGGTTAAA;RSEQ=AAAATAGTTTCTATGTAGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:86,104:0:2,0:26.7:1:30.2:1:1:0:60:189:1:0:0.3 0/1:150:2:1,1:64,84:0.0133:2,2:22.5:1:30:1:1:1.31:60:4:0.0134:0:2 -X 145701066 . G A 123 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27211;SOR=0.30435;LSEQ=AGCAGCAGTCCTGGGCAGCC;RSEQ=TGCGGCCCTCGCCTGCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:16:16,0:19,0:0.4571:1,1:23.9:1:30.9:1:1:0:38.8:32:0.4571:0:1 0/1:10:2:2,0:8,0:0.2:0,0:16.5:1:32:0:1:0:40:4:0.2:0:1 -X 145701530 . T G 237 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=240.90522;LSEQ=GGATACGATCAGCTTCTCCC;RSEQ=CTCGATGCTGTGCTGTAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1184:2:1,1:584,598:0.0017:2,2:17.5:1:31:1:1:1.02:53.5:4:0.0017:0:1 0/1:755:219:109,110:257,278:0.2901:2,2:25.1:1:30.5:1:0.68861:1.07:55.5:53.75:0.2905:0:1.7 -X 145701553 . A T 212 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGATGCTGTGCTGTAGACGC;RSEQ=GCTTTCCCCGGACGGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1184:0:0,0:612,572:0:2,0:24.9:1:30.5:1:1:0:58.6:61.316:1:0:0.1 0/1:711:130:65,65:288,293:0.1828:2,2:24.6:1:30.3:1:1:1.02:57.2:42.333:0.1804:0:1.2 -X 145701579 . C T 224 v4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=503.79954;LSEQ=CCCCGGACGGCCTCCTGCTG;RSEQ=CTGAACAGCTCCTTCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1165:1:0,1:629,534:9e-04:2,0:1:0:23:0:0.45962:0:60:2:9e-04:0:1 0/1:733:220:109,111:258,255:0.3001:2,2:24.2:1:28.9:1:0.87218:1.0303:56.7:54:0.3034:0:1.6 -X 145701908 . G A 53 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.02218;SOR=Inf;LSEQ=GGACGTGTTCAGCTGCTGCT;RSEQ=CAGCTGCTGGGTGGAGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:0:0,0:217,371:0:2,0:27.8:1:31.9:1:1:0:36:57.8:1:0:0.1 0/1:371:4:2,2:135,231:0.0108:2,2:22.8:1:26.8:1:0.6289:1.71:49.5:8:0.0108:0:1 -X 145701991 . G A 111 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCGGAGCCGCGGGCCTTG;RSEQ=CCCTGGTGACCGGGGCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:4,122:0:1,0:26.1:1:32:1:1:0:27.8:30.5:1:0:0.1 0/1:49:13:0,13:0,36:0.2653:1,1:23.2:1:30.1:1:1:0:27:26:0.2653:0:1.3 -X 145702036 . G T 72 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=GGGCGCACTCCTTCTCGGAG;RSEQ=GGGGCGGGCCCTGCTTGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:13,73:0:2,0:24.6:1:30.5:1:1:0:29.4:27.667:1:0:0.3 0/1:24:5:2,3:1,18:0.2083:1,2:25:1:31.2:1:0.09881:10.22:32.2:10:0.2083:0:2 -X 145702075 . G A 61 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00075;SOR=Inf;LSEQ=TCTGGTTCGCGAGCATCTGC;RSEQ=CCCGGTTCCTGGTCATGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:38,40:0:2,0:23.1:1:31.1:1:1:0:32.9:38:1:0:0.3 0/1:17:4:4,0:3,10:0.2353:2,0:28:1:30.8:1:0.01471:0:40:8:0.2353:0:1.5 -X 145702378 . T C 105 v4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCAGGACCAGATGGATTCC;RSEQ=AGCCGAATTCTACCAGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:0,75:0:1,0:24.2:1:28.4:1:1:0:48.2:74:1:0:0.1 0/1:30:9:0,9:0,21:0.3:1,0:21.9:1:33.2:1:1:0:38.8:18:0.3:0:1 -X 145961889 . G C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.02391;LSEQ=TTCTCAGCTTCAATGTCAGT;RSEQ=GCTCAGAGGATGTCTCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:99:48,51:100,140:0.292:2,2:27.4:1:30.6:1:0.27901:1.32:60:198:0.2991:0:1.1 1/0:225:125:61,64:49,51:0.5556:2,2:27.1:1:30:1:1:1.008:60:124:0.5586:0:1.2 -X 147332664 . G T 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15793;SOR=Inf;LSEQ=TTTCAAATATAAATGTGTAC;RSEQ=TATGCAGTTACAGACGTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:74,89:0:2,0:25.3:1:30.8:1:1:0:60:162:1:0:0.5 0/1:108:2:1,1:50,56:0.0185:2,2:11:0:32.5:1:1:1.12:60:4:0.0185:0:1.5 -X 147332680 . G A 189 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01279;SOR=0.50911;LSEQ=GTACGTATGCAGTTACAGAC;RSEQ=TGACTGTAAATATGAAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:71:29,42:31,38:0.5071:2,2:25:1:30.8:1:0.73288:1.18008:60:142:0.5145:0:1.1 0/1:102:35:13,22:32,35:0.3431:2,2:31.8:1:29.9:1:0.40129:1.54064:60:70:0.3431:0:1 -X 147582812 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12821;SOR=Inf;LSEQ=AGCCACCTCTGGCCCCGGCC;RSEQ=CGCTGACTCCTAGGTCGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:0:2,0:18.9:1:32.1:1:1:0:60:16:1:0:0.3 0/1:5:2:1,1:1,2:0.4:2,2:23:0:32:0:1:1.73:60:4:0.4:0:1.5 -X 149924637 . C T 27 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6269;SOR=1.72633;LSEQ=TCTTCTTATAAACTACTTTA;RSEQ=CTGCAGATATGGGGGTTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:0,2:123,50:0.0114:2,0:1:0:26:0:0.08709:0:60:4:0.0117:0:1 0/1:102:2:1,1:71,29:0.0196:2,2:21.5:1:27.5:1:0.50379:2.42403:60:4:0.0196:0:1 -X 149924638 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13655;SOR=Inf;LSEQ=CTTCTTATAAACTACTTTAC;RSEQ=TGCAGATATGGGGGTTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:127,53:0:2,0:23.5:1:30.8:1:1:0:60:29:1:0:0.2 0/1:106:2:1,1:74,30:0.0189:2,2:20:1:29:1:0.50135:2.44291:60:4:0.0192:0:1 -X 149924662 . C A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16251;SOR=Inf;LSEQ=AGATATGGGGGTTGGGGTGG;RSEQ=AGCCCTTTTCCCTGTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:163,85:0:2,0:27.2:1:31.5:1:1:0:60:23.8:1:0:0.2 0/1:168:2:1,1:104,61:0.0119:2,2:12:1:27.5:1:1:1.69915:60:4:0.012:0:1 -X 149924692 . G A 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0707;SOR=Inf;LSEQ=CCCTGTTTCCACGTAGAGGT;RSEQ=GTAGAAAGGCGTGTGGAAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:189,149:0:2,0:25:1:31.4:1:1:0:60:168:0.997:0:0.3 0/1:240:3:2,1:138,99:0.0125:2,2:19.3:1:27.7:1:1:1.43:60:6:0.0126:0:1 -X 149924738 . C T 186 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31066;SOR=0.80542;LSEQ=CAGGGCTACAGTGTATAGAC;RSEQ=CTGTTAGTCCAGCAGTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:74:36,38:124,131:0.2249:2,2:27:1:30.1:1:1:1.00:60:73:0.2288:0:1 0/1:264:50:22,28:104,108:0.1894:2,2:25.3:1:28.7:1:0.53378:1.22464:60:24:0.1846:0:1.2 -X 149924781 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18338;SOR=Inf;LSEQ=GCAGGTGCTTGAATCACAGA;RSEQ=CAGGTGCCCCTTTGAAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:87,149:0:2,0:23.7:1:29.4:1:1:0:60:117:1:0:0.3 0/1:178:2:1,1:63,113:0.0112:2,2:36:0:33.5:1:1:1.79:60:4:0.0114:0:1.5 -X 150724479 . C T 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23256;SOR=0;LSEQ=GGACCTAGAAAGGGGAGAAG;RSEQ=CATGTTGCCCAGCTCCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:0.0952:2,2:13:0:31.5:1:1:1.66897:51:4:0.0952:0:1.5 0/0:22:0:0,0:11,11:0:2,0:29:1:31.7:1:1:0:56.1:44:1:0:0.2 -X 155208866 . T C 97 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00699;SOR=0;LSEQ=CTGGGCCACTCAACATGGGT;RSEQ=TCCTTCTTCCTGATGTTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:1:0,2:40.9:1:32.4:1:1:0:60:16:1:0:1.3 0/1:7:2:1,1:3,2:0.2857:2,2:20:1:29.5:1:1:1.41418:60:4:0.2857:0:1 -X 155209025 . G T 26 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCTACTTTGATTCTCTAG;RSEQ=AACTTCAGTTGTTTCTTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:14:1:29.5:1:1:0:60:4:1:0:0 0/1:5:2:1,1:1,2:0.4:2,2:22:1:26:1:1:1.73:60:4:0.4:0:1 -Y 7194144 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGATTTGAAGCCGGAGAACA;RSEQ=CCTGCTGGATAGGGATGGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:0:2,0:28.1:1:29.7:1:1:0:59.5:21:1:0:0.3 0/1:104:2:1,1:46,56:0.0192:2,2:46:1:28.5:1:1:1.22:60:4:0.0194:0:1 -Y 9342245 . T C 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01975;SOR=0;LSEQ=TCCTGCCAAAACCCGGGCAG;RSEQ=CATGTTCAGCCAAACAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:28,31:0.0328:2,2:41:1:32.5:1:1:1.11:43:4:0.0333:0:1 0/0:370:0:0,0:160,210:0:2,0:27.4:1:28.3:1:1:0:33.6:51.857:1:0:0.2 -Y 9342265 . G A 30 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0183;SOR=0;LSEQ=TCATGTTCAGCCAAACAGCT;RSEQ=AATGAGCTCAGGTAGGAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:17,25:0.0455:2,2:20.5:1:30.5:1:1:1.46:43:4:0.0465:0:1 0/0:278:0:0,0:101,176:0:2,0:22.1:1:30.8:1:1:0:31.9:137.5:1:0:0.1 -Y 13457407 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCACTCGAATT;RSEQ=TTTCCATTCCTTTCGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:31:1:1:0:59.5:4:1:0:4 -Y 13457418 . TTTCGAT AG 32 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=13;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ACTCGAATTGTTTCCATTCC;RSEQ=TCCATTCCATTTCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32.5:1:32.5:1:1:0:59.5:4:1:0:3 -Y 13457446 . C A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTTCATTCCATT;RSEQ=CATTCCATTCCATTGCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:9.5:1:28.5:1:1:0:59.5:4:1:0:4 -Y 13457725 . C G 33 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.46429;SOR=0;LSEQ=CCACTAGTGTTGATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:10:1:33:0:1:1.7321:34:4:0.4:0:8 0/0:3:0:0,0:2,1:0:2,0:13:1:30.7:1:1:0:37.7:6:1:0:4.3 -Y 13457731 . C A 29 d7;v4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.44444;SOR=0;LSEQ=GTGTTGATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:0.4:2,2:10.5:1:29:1:1:1:48:4:0.4:0:2.5 0/0:4:0:0,0:3,1:0:2,0:14.5:1:30.8:1:1:0:37.3:8:1:0:4 -Y 13457745 . C A 28 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.48718;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:29:1:32.2:1:1:0:38.4:10:1:0:5.6 0/1:8:2:1,1:3,2:0.25:2,2:35:0:28.5:1:1:1.41418:43:4:0.25:0:4 -Y 13457748 . T C 30 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.48718;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:30.8:1:31.4:1:1:0:38.4:10:1:0:5.6 0/1:8:2:1,1:4,2:0.25:2,2:17:0:30.5:1:1:1.8258:22:4:0.25:0:3 -Y 13457750 . C G 34 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.2;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:35:1:34:1:1:1.41418:34:4:0.2857:0:8 0/0:8:0:0,0:5,3:0:2,0:26.1:1:31.5:1:1:0:31.1:16:1:0:4.4 -Y 13457752 . A G 30 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,3:0:2,0:24.2:1:31.3:1:1:0:44:12:0.8571:0:4.5 0/1:8:2:1,1:4,2:0.25:2,2:42:0:30.5:1:1:1.8258:43:4:0.25:0:4 -Y 13457755 . C T 31 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.2;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:7:0:31.5:1:1:1.41418:50:4:0.2857:0:3 0/0:8:0:0,0:5,3:0:2,0:31.1:1:31.8:1:1:0:31.1:16:1:0:4.4 -Y 13457758 . T C 32 v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:29.1:1:31.4:1:1:0:41.7:14:1:0:4.9 0/1:8:2:1,1:4,2:0.25:2,2:48:0:32:1:1:1.8258:43:4:0.25:0:4 -Y 13457760 . CC GA 32 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.2;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCCACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:13:0:32.3:1:1:1.41418:50:4:0.2857:0:2 0/0:8:0:0,0:4,2:0:2,0:34.7:1:32.2:1:1:0:31:12:0.75:0:4 -Y 13457767 . A T 31 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCACTCGGATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:30.6:1:31.4:1:1:0:41.7:14:1:0:4.6 0/1:8:2:1,1:4,2:0.25:2,2:35.5:1:31.5:1:1:1.8258:22:4:0.25:0:3 -Y 13457769 . T G 33 v4;pSTD;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.2;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCACTCGGATTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:31:0:33.5:1:1:1.41418:48:4:0.2857:0:2.5 0/0:8:0:0,0:5,3:0:2,0:36.5:1:30.3:1:1:0:31.1:16:1:0:4.1 -Y 13457772 . AT CC 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.2;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGATTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:42:1:31:1:1:1.41418:34:4:0.2857:0:7 0/0:8:0:0,0:4,2:0:2,0:36.7:1:29.8:1:1:0:27.2:12:0.75:0:4.2 -Y 13457775 . C G 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.56923;SOR=0.38278;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CACTCGGATTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:0.2857:2,2:40:1:32.5:1:1:1.41418:34:4:0.2857:0:7 0/1:8:1:1,0:3,2:0.125:2,0:43:0:34:0:1:0:20:2:0.1667:0:7 -Y 13457781 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=GATTGATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:34:1:30:1:1:1:34:4:0.3333:0:7 0/0:8:0:0,0:5,3:0:2,0:31.1:1:30.5:1:1:0:31.1:16:1:0:4.1 -Y 13457792 . A T 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.48571;SOR=Inf;LSEQ=ATTCCACTCGGATTGATTCC;RSEQ=TTCCATTCCATTCCTTTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:20.7:1:30.8:1:1:0:44:12:1:0:3.8 0/1:9:2:1,1:4,2:0.2222:2,2:12.5:1:32.5:1:1:1.8258:22:4:0.2222:0:3 -Y 13457802 . A T 29 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.13333;SOR=0;LSEQ=GATTGATTCCATTCCATTCC;RSEQ=TTCCTTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:13:1:29:1:1:1:34:4:0.5:0:7 0/0:6:0:0,0:3,3:0:2,0:16.2:1:29.5:1:1:0:28:12:1:0:3.8 -Y 13457807 . T A 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCACTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:8:1:29:1:1:1:34:4:0.5:0:7 1/0:4:2:1,1:1,1:0.5:2,2:17:1:32:0:1:1:28:4:0.5:0:6.5 -Y 13457938 . TTCAATTCAATTCCACTCCACTCCAC T 57 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCACTCCGTTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:1:0,2:9.8:1:28.7:1:1:0:44.3:8:1:1:3.5 -Y 13457943 . TTCAATTCCACTCCACTCCAC T 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCAA;RSEQ=TCCACTCCACTCCGTTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:10:1:30.2:1:1:0:23:4:1:1:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13457968 . C T 60 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCACTCCACTCCACTCCA;RSEQ=TCCACTCCGTTCCGTTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5:0:32:0:1:0:23:4:1:0:2 1/1:5:4:2,2:1,0:0.8:0,2:8:1:30.3:1:1:0:44.3:8:0.8:0:3.5 -Y 13457982 . G A 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ACTCCACTCCACTCCGTTCC;RSEQ=TTCCGTTCCGTTCCGTTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:19:0:34:0:1:0:23:4:1:0:2 0/1:7:2:1,1:3,2:0.2857:2,2:9:0:32:0:1:1.41418:41:4:0.2857:0:2.5 -Y 13457995 . C G 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCGTTCCGTTCCGTTCCGTT;RSEQ=CGTTCCGTTCCGTTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:32:0:34:0:1:0:23:4:1:0:2 0/1:7:2:1,1:3,2:0.2857:2,2:22:0:32.5:1:1:1.41418:41:4:0.2857:0:2.5 -Y 13457996 . C T 49 d7;v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.44444;SOR=0;LSEQ=CGTTCCGTTCCGTTCCGTTC;RSEQ=GTTCCGTTCCGTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:33:0:32:0:1:0:23:4:1:0:2 0/1:7:3:1,2:3,1:0.4286:2,2:33.7:1:31.3:1:0.48571:4.4496:48:6:0.4286:0:3.7 -Y 13458007 . G A 50 d7;v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.44444;SOR=0;LSEQ=GTTCCGTTCCGTTCCGTTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:24:0:33:0:1:0:23:4:1:0:2 0/1:7:3:1,2:3,1:0.4286:2,2:24:0:31.7:1:0.48571:4.4496:48:6:0.4286:0:3.7 -Y 13458010 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCGTTCCGTTCCGTTCCGTT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:21:0:33:0:1:0:23:4:1:0:2 0/1:7:2:1,1:3,2:0.2857:2,2:21:0:31:1:1:1.41418:60:4:0.2857:0:4 -Y 13458021 . C CATTCCATTCGGTTTA 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.5;SOR=0;LSEQ=CGTTCCGTTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:23:1:31.8:1:1:0:23:4:1:1:2 1/0:7:4:2,2:2,1:0.5714:2,2:9.2:1:29.7:1:1:1.81007:46.3:4:0.5:0.5:3.3 -Y 13458026 . C T 49 d7;v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.44444;SOR=0;LSEQ=CGTTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCACTGTGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:5:0:30:0:1:0:23:4:1:0:2 0/1:7:3:1,2:3,1:0.4286:2,2:5:0:31:1:0.48571:4.4496:48:6:0.4286:0:3.7 -Y 13458156 . C T 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TATTCCATTCCATTCCATTC;RSEQ=ATTCCGTTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14:0:30.5:1:1:0:28:4:1:0:3 -Y 13458164 . TC AT 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCGT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:23:0:30:1:1:0:28:4:1:0:2 -Y 13458403 . T C 98 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.02747;SOR=Inf;LSEQ=TTCCATTCCTTTCCATTCCA;RSEQ=TCCATTCCATTCCCTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:21.7:1:28.7:1:1:0:40:6:1:0:5.3 1/1:11:9:5,4:1,1:0.8182:2,2:20.3:1:31.1:1:1:1.22:44:18:0.8182:0:6.1 -Y 13458406 . C G 98 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.02747;SOR=Inf;LSEQ=CATTCCTTTCCATTCCATTC;RSEQ=ATTCCATTCCCTTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:20.7:1:27.3:1:1:0:40:2:1:0:5.3 1/1:11:9:5,4:1,1:0.8182:2,2:23.3:1:31:1:1:1.22:44:18:0.8182:0:6.1 -Y 13458408 . T A 85 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.19231;SOR=Inf;LSEQ=TTCCTTTCCATTCCATTCCA;RSEQ=TCCATTCCCTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:20:1:24.3:1:1:0:40:2:1:0:5.3 1/0:11:7:4,3:2,1:0.6364:2,2:26.6:1:30.4:1:1:1.44135:41.1:14:0.6364:0:6.1 -Y 13458410 . C A 92 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.02747;SOR=Inf;LSEQ=CCTTTCCATTCCATTCCATT;RSEQ=CATTCCCTTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:19.3:1:27.3:1:1:0:40:2:1:0:5.3 1/1:11:9:5,4:1,1:0.8182:2,2:27.3:1:29.3:1:1:1.22:44:18:0.8182:0:6.1 -Y 13458417 . C ATTCCACTCGTGTTGATTGCGTTTCCATTCCACTGGATTACA 47 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCACTCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:17.3:1:23.7:1:1:0:40:2:1:0:5.3 0/1:13:3:2,1:5,5:0.2308:2,2:26:1:30.1:1:1:1.90:47.3:6:0.25:0.2308:1.7 -Y 13458421 . CATTCC T 79 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=10;MSI=3.000;MSILEN=5;SSF=0.25;SOR=Inf;LSEQ=CATTCCATTCCATTCCCTTC;RSEQ=ATTCCACTCGGAATGATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:16.7:1:21:1:1:0:40:0.5:1:0:5.3 0/1:13:6:3,3:2,2:0.4615:2,2:36:1:30.9:1:1:1:41.3:12:0.5:0:4.8 -Y 13458422 . A C 62 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52857;SOR=Inf;LSEQ=ATTCCATTCCATTCCCTTCC;RSEQ=TTCCATTCCACTCGGAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:15.3:1:20.7:1:1:0:40:0.5:1:0:5.3 0/1:13:4:2,2:0,0:0.3077:0,2:9:1:31.3:1:1:0:41:8:1:0:2.8 -Y 13458435 . C A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCTTCCATTCCATTCCACT;RSEQ=GGAATGATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24.5:1:32:0:1:0:29:4:1:0:4.5 0/1:28:2:1,1:12,14:0.0714:2,2:23.5:1:29.5:1:1:1.16:41:4:0.0741:0:6.5 -Y 13458448 . T C 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCACTCGGAATGATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:33.5:1:30.5:1:1:0:29:4:1:0:4.5 0/1:28:2:1,1:12,14:0.0714:2,2:20:1:30:1:1:1.16:22:4:0.0741:0:1.5 -Y 13458451 . C A 31 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CACTCGGAATGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:30.5:1:32:1:1:0:29:4:1:0:4.5 0/1:28:2:1,1:11,14:0.0714:2,2:17.5:1:31:1:1:1.26:60:4:0.0741:0:2.5 -Y 13458455 . C A 30 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CGGAATGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:26.5:1:30.5:1:1:0:29:4:1:0:4.5 0/1:28:2:1,1:12,14:0.0714:2,2:15:0:30.5:1:1:1.16:60:4:0.0769:0:1 -Y 13458456 . C A 31 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGAATGATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:25.5:1:31:1:1:0:29:4:1:0:4.5 0/1:27:2:1,1:11,14:0.0741:2,2:24:0:31.5:1:1:1.26:46:4:0.0741:0:1 -Y 13458457 . A T 29 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GAATGATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:24.5:1:30:1:1:0:29:4:1:0:4.5 0/1:27:2:1,1:11,13:0.0741:2,2:23.5:1:29.5:1:1:1.17:57:4:0.0741:0:4 -Y 13458460 . C G 62 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:21.5:1:30.5:1:1:0:29:4:1:0:4.5 0/1:25:4:2,2:9,12:0.16:2,2:14.3:1:31.3:1:1:1.32:57:8:0.16:0:4.3 -Y 13458461 . CA AC 29 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GATTCCATTCCATTCCATTC;RSEQ=TTCCATTCCATTCCATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:20.5:1:31.5:1:1:0:29:4:1:0:4.5 0/1:25:2:1,1:10,13:0.08:2,2:18.5:1:29.8:1:1:1.29:57:4:0.08:0:3 -Y 13458462 . A C 52 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:19.5:1:29.5:1:1:0:29:4:1:0:4.5 0/1:25:3:1,2:9,11:0.12:2,2:9.3:1:33:1:1:1.60281:35.7:6:0.1364:0:2.7 -Y 13458465 . C A 25 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTACATTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:21:0:27:0:1:0:37:2:0.5:0:8 0/1:24:2:1,1:9,12:0.0833:2,2:15:0:25:1:1:1.32:54:4:0.087:0:6 -Y 13458472 . A C 28 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTACATTACATTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:14:0:26:0:1:0:37:2:1:0:8 0/1:12:2:1,1:5,5:0.1667:2,2:8.5:1:28.5:1:1:1:57:4:0.1667:0:3 -Y 13458473 . T A 28 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTACATTACATTTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:13:0:26:0:1:0:37:2:1:0:8 0/1:11:2:1,1:4,5:0.1818:2,2:7:0:28:1:1:1.22:54:4:0.1818:0:6 -Y 13458475 . C G 32 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTACATTACATTTCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:11:0:26:0:1:0:37:2:1:0:8 0/1:11:2:1,1:4,5:0.1818:2,2:6:1:32:1:1:1.22:52.5:4:0.1818:0:1.5 -Y 13458628 . T C 52 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TTCCGGTTTATTCCATTCCA;RSEQ=TCCATTCTGTTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:3:0:28:0:1:0:58:2:1:0:6 1/0:6:3:2,1:2,1:0.5:2,2:11.3:1:33.3:1:1:1:26.7:6:0.5:0:1.7 -Y 13458646 . C A 29 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=0.10989;SOR=0;LSEQ=CATTCCATTCTGTTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:7:1:29:1:1:1.7321:34:4:0.5:0:4.5 0/0:9:0:0,0:5,4:0:2,0:16.6:1:29.6:1:1:0:38.2:8:1:0:3.7 -Y 13458647 . A G 32 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.50549;SOR=Inf;LSEQ=ATTCCATTCTGTTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:11.2:1:24.2:1:1:0:41.2:4:1:0:4.6 0/1:9:2:1,1:4,3:0.2222:2,2:21.5:1:32:1:1:1.29098:48:4:0.2222:0:1.5 -Y 13458648 . TT AA 27 d7;v4;pSTD;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.48571;SOR=Inf;LSEQ=TTCCATTCTGTTCCATTCCA;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,2:0:2,0:12.2:1:25.6:1:1:0:41.2:1.5:0.75:0:4.6 0/1:9:2:1,1:3,3:0.2222:2,2:11:0:27.8:1:1:1:42.5:4:0.2222:0:5 -Y 13458650 . C T 28 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.14286;SOR=0;LSEQ=CCATTCTGTTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,1:0.3333:2,2:11:1:28.5:1:1:1.7321:34:4:0.4:0:4.5 0/0:9:0:0,0:4,4:0:2,0:15:1:31.8:1:1:0:37.6:16:0.8889:0:3.1 -Y 13458657 . A C 31 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.11053;SOR=0;LSEQ=GTTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:0.2857:2,0:6.5:1:31:1:1:0:51:4:0.2857:0:6.5 0/0:13:0:0,0:7,6:0:2,0:11.8:1:29:1:1:0:35.5:26:1:0:3.9 -Y 13458673 . T C 44 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.21739;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCACTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,5:0:2,0:19.7:1:29.5:1:1:0:43.5:22:1:0.0833:4.4 0/1:12:3:0,3:6,2:0.25:2,0:19.7:1:28.3:1:0.06061:0:40.7:6:0.25:0:4.7 -Y 13458676 . C T 45 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.22;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCACTCCACTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,6:0:2,0:20.4:1:29.1:1:1:0:41.9:10:0.9091:0.0833:4.3 0/1:13:3:1,2:4,5:0.2308:2,2:24.7:1:29:1:1:1.53983:40.7:6:0.2308:0:5.3 -Y 13458683 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.17235;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCACTCCACTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,5:0.1429:2,2:23.5:1:30:1:1:1:47:4:0.1538:0:7.5 0/0:19:0:0,0:7,10:0:2,0:16.9:1:30.8:1:1:0:39.4:34:0.8947:0:3.9 -Y 13458684 . T C 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.49621;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAC;RSEQ=CCACTCCACTCCACTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:0:2,0:23:1:26.5:1:1:0:43.8:3.333:0.9091:0.0714:4.1 0/1:19:2:1,1:7,10:0.1053:2,2:9.5:1:28.5:1:1:1.40:51:4:0.1053:0:1.5 -Y 13458686 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.61972;SOR=2.37744;LSEQ=CATTCCATTCCATTCCACTC;RSEQ=ACTCCACTCCACTCCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:6,7:0.0714:2,0:14:1:32:1:1:0:43:2:0.0833:0.0714:1 0/1:19:3:2,1:5,9:0.1579:2,2:30:1:30:1:0.53676:3.33:37.3:6:0.1579:0:4.3 -Y 13458688 . C T 59 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.3662;SOR=3.35166;LSEQ=TTCCATTCCATTCCACTCCA;RSEQ=TCCACTCCACTCCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:6,7:0.0714:2,0:16:1:32:1:1:0:43:2:0.0769:0.0714:1 0/1:19:4:2,2:6,9:0.2105:2,2:26:1:29.8:1:1:1.47:32.3:8:0.2105:0:4.3 -Y 13458689 . T A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.18018;SOR=0;LSEQ=TCCATTCCATTCCACTCCAC;RSEQ=CCACTCCACTCCACTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:0.125:2,2:32:1:28:1:1:1.30929:47.5:4:0.1667:0:4.5 0/0:21:0:0,0:9,12:0:2,0:19:1:28:1:1:0:38.8:20:1:0:4.2 -Y 13458692 . A T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.24324;SOR=Inf;LSEQ=ATTCCATTCCACTCCACTCC;RSEQ=CTCCACTCCACTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,7:0:2,0:21.9:1:27.1:1:1:0:42.4:14:0.9333:0:4.1 0/1:21:3:1,2:8,10:0.1429:2,2:17.3:1:27.3:1:1:1.56568:38:6:0.1429:0:3.7 -Y 13458693 . C T 57 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.11332;SOR=Inf;LSEQ=TTCCATTCCACTCCACTCCA;RSEQ=TCCACTCCACTCCATTCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,7:0:2,0:19.1:1:29.6:1:1:0:41.7:14:0.9333:0:3.6 0/1:21:4:1,3:8,9:0.1905:2,2:21.8:1:28.5:1:0.60301:2.55208:37.8:8:0.1905:0:3.5 -Y 13458694 . T A 24 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=1.58153;LSEQ=TCCATTCCACTCCACTCCAC;RSEQ=CCACTCCACTCCATTCCACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:1,0:8,8:0.0588:2,0:23:0:26:0:1:0:58:2:0.0667:0:6 0/1:22:2:1,1:8,12:0.0909:2,2:19:1:24.5:1:1:1.47:41.5:4:0.0909:0:6.5 -Y 13458695 . C G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.49929;SOR=Inf;LSEQ=CCATTCCACTCCACTCCACT;RSEQ=CACTCCACTCCATTCCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:21.4:1:28.8:1:1:0:42.4:7:1:0:4 0/1:22:2:1,1:8,11:0.0909:2,2:7:0:33.5:1:1:1.35:31:4:0.0909:0:4 -Y 13458697 . A T 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.49929;SOR=Inf;LSEQ=ATTCCACTCCACTCCACTCC;RSEQ=CTCCACTCCATTCCACTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:21.9:1:27.6:1:1:0:42.4:7:1:0:4 0/1:22:2:1,1:8,11:0.0909:2,2:20:0:29:1:1:1.35:27:4:0.0909:0:3.5 -Y 13458698 . C T 59 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.21703;SOR=0.31004;LSEQ=TTCCACTCCACTCCACTCCA;RSEQ=TCCACTCCATTCCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:1,3:7,5:0.25:2,2:28.3:1:29.8:1:0.56923:3.83897:41.3:8:0.2667:0:4 0/1:22:2:2,0:7,13:0.0909:2,0:20.5:1:32:0:0.15584:0:26:4:0.0909:0:4 -Y 13458699 . T TCTAATCCATC 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.18354;SOR=0;LSEQ=TCCACTCCACTCCACTCCAC;RSEQ=CCACTCCATTCCACTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:20:0:31.4:1:1:1.13:40:4:0.125:0:0 0/0:22:0:0,0:9,13:0:2,0:20.8:1:28.5:1:1:0:38.4:44:1:0:4.2 -Y 13458700 . C T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.18354;SOR=0;LSEQ=CCACTCCACTCCACTCCACT;RSEQ=CACTCCATTCCACTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:7,8:0.1176:2,2:28:1:29.5:1:1:1.13:47:4:0.1176:0:6 0/0:22:0:0,0:9,13:0:2,0:20.9:1:30.8:1:1:0:38.4:44:1:0:4.2 -Y 13458701 . C A 26 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=5;SSF=0.18354;SOR=0;LSEQ=CACTCCACTCCACTCCACTC;RSEQ=ACTCCATTCCACTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:6,9:0.1176:2,0:13:0:26:1:0.20588:0:40:4:0.1333:0:4 0/0:22:0:0,0:9,13:0:2,0:21:1:30.3:1:1:0:38.4:44:1:0:4.2 -Y 13458705 . C A 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.15766;SOR=0;LSEQ=CCACTCCACTCCACTCCACT;RSEQ=CATTCCACTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:5,8:0.1333:2,0:17:0:29:1:0.2:0:40:4:0.1538:0:4 0/0:22:0:0,0:9,13:0:2,0:20.6:1:30.8:1:1:0:38.4:44:1:0:4.2 -Y 13458708 . TT CC 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15766;SOR=0;LSEQ=CTCCACTCCACTCCACTCCA;RSEQ=CCACTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:25.5:1:31.8:1:1:1.15:47.5:4:0.1538:0:3.5 0/0:22:0:0,0:9,13:0:2,0:19.8:1:29.2:1:1:0:38.4:44:1:0:4.2 -Y 13458711 . C A 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18018;SOR=0;LSEQ=CACTCCACTCCACTCCATTC;RSEQ=ACTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:5,9:0.125:2,0:23:0:30.5:1:0.175:0:40:4:0.1333:0:4 0/0:21:0:0,0:8,13:0:2,0:20:1:30.6:1:1:0:38.1:42:1:0:4.1 -Y 13458715 . C A 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49206;SOR=Inf;LSEQ=CCACTCCACTCCATTCCACT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:0:2,0:23.6:1:28.8:1:1:0:42.8:7:1:0:3.9 0/1:20:2:1,1:6,12:0.1:2,2:28.5:1:29:1:1:1.93:44:4:0.1:0:4.5 -Y 13458733 . T C 68 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=0.18192;SOR=4.28301;LSEQ=CTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:0.1538:2,2:20:1:30.5:1:1:1.18:47:4:0.1818:0:6 0/1:11:5:3,2:1,3:0.4545:2,2:10.8:1:29.4:1:0.52381:3.76:36:10:0.4545:0.0909:4.2 -Y 13458742 . A C 29 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.18301;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,4:0:2,0:9.4:1:27.6:1:1:0:40.5:7:0.875:0:3.9 0/1:8:2:1,1:2,3:0.25:2,2:6.5:1:29:1:1:1.41:31:4:0.25:0:4 -Y 13458743 . T C 50 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=1;SOR=0.9371;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:4,2:0.3:2,0:12.3:1:32:1:0.16667:0:36.7:6:0.3333:0.1:4.3 0/1:7:2:0,2:2,2:0.2857:2,0:9:1:31:1:0.46667:0:51.5:4:0.2857:0:5.5 -Y 13459070 . A C 33 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTTCTTTCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:25:0:33:0:1:0:31:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13459096 . C T 29 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CATTTCTTTCCATTGCATTC;RSEQ=ATTCCGTTCCAGTCGGGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:8:0:29:1:1:0:31:4:0.6667:0:2 0/0:2:0:0,0:1,1:0:2,0:10:0:32:1:1:0:34:4:1:0:5.5 -Y 13459102 . GT CC 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TTTCCATTGCATTCCATTCC;RSEQ=TCCAGTCGGGTTGATTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:9:1:31:1:1:0:40.7:6:1:0:1.3 1/1:2:2:1,1:0,0:1:0,2:17:0:32.8:1:1:0:34:4:1:0:4.5 -Y 13459105 . C G 34 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCATTGCATTCCATTCCGTT;RSEQ=CAGTCGGGTTGATTCCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:20:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:1:0,2:19:0:34:0:1:0:34:4:1:0:4.5 -Y 13459139 . T G 31 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:25:1:31.5:1:1:1:34:4:0.5:0:4.5 -Y 13459141 . C CGGAAG 32 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:31.5:1:32:1:1:1:27:4:0.5:0:2.5 -Y 13459155 . C G 34 d7;v4;pSTD;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCAATCCATTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:21:0:34:0:1:1:27:4:0.5:0:2.5 -Y 13459268 . TT CA 27 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:5.5:1:27.7:1:1:0:59.5:4:0.6667:0.3333:5.5 -Y 13459288 . T C 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCACTGCACTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:22:1:29.5:1:1:0:59.5:4:0.5:0:5.5 -Y 13459327 . A T 29 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:0.6667:0,2:11:0:29:1:1:0:59.5:4:0.6667:0:5.5 -Y 13459511 . G T 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCTTCCCATTCCATTCC;RSEQ=TTCCGTTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:10.7:1:30:1:1:0:47.3:6:1:0:4.3 0/1:16:2:1,1:7,7:0.125:2,2:13:0:30:1:1:1:36:4:0.125:0:4 -Y 13459540 . C T 69 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.53044;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:37.7:1:31:1:1:0:47.3:6:1:0:4.3 0/1:16:5:2,3:6,5:0.3125:2,2:38.8:1:30:1:1:1.73457:26.4:10:0.3125:0:4 -Y 13459541 . A G 48 d7;v4;MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.01032;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:38:1:30.7:1:1:0:47.3:6:1:0:4.3 0/1:16:2:1,1:7,7:0.125:2,2:35:0:31.5:1:1:1:48.5:4:0.125:0:3 -Y 13459545 . C GGGTTA 71 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.53044;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:39:1:31.3:1:1:0:47.3:6:1:0:4.3 0/1:16:5:2,3:6,5:0.3125:2,2:37.8:1:30.8:1:1:1.73457:26.4:10:0.3125:0:4 -Y 13459546 . A G 61 d7;v4;MSI6 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.03612;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:39.7:1:23.3:1:1:0:47.3:2:1:0:4.3 0/1:16:4:2,2:6,6:0.25:2,2:29.3:1:30.5:1:1:1:48:8:0.25:0:2.8 -Y 13459548 . T A 28 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.01754;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:46.5:1:28.5:1:1:0:51:4:0.6667:0:5 0/0:16:0:0,0:8,8:0:2,0:28.3:1:30.1:1:1:0:35.5:32:1:0:2.8 -Y 13459551 . A G 62 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.53044;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:37.7:1:25.7:1:1:0:47.3:2:1:0:4.3 0/1:16:5:3,2:5,6:0.3125:2,2:25.6:1:27:1:1:1.73:43.4:4:0.2667:0:3 -Y 13459565 . C G 31 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCGATTCCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:0:2,0:23.7:1:23:1:1:0:47.3:2:1:0:4.3 0/1:16:2:1,1:6,6:0.125:2,2:21.5:1:31.5:1:1:1:20:4:0.125:0:4.5 -Y 13459570 . C T 50 d7;v4 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.02198;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCGATTCCATTCCATTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:18.7:1:32:1:1:0:47.3:6:1:0:4.3 0/1:12:2:1,1:5,5:0.1667:2,2:6:0:28.5:1:1:1:48.5:4:0.1667:0:3 -Y 13459575 . G GGGTTA 48 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00833;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTGCGTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:18.3:1:30.4:1:1:0:47.3:6:1:0.3333:4.3 0/0:7:0:0,0:2,2:0:2,0:6.3:1:30.5:1:1:0:34.3:8:0.5714:0:3.8 -Y 13459577 . T A 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TTCCATTCCATTCCATTCGA;RSEQ=TCCATTCCATTGCGTTCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13:0:29.5:1:1:0:51:4:1:0:5 1/0:3:2:1,1:1,0:0.6667:0,2:9.5:1:32:0:1:0:20:4:0.6667:0:4.5 -Y 13460483 . T A 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TAAGCAAGAGTTACATCACC;RSEQ=AGATGATCAGTGCAGAGATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:22:1:29.5:1:1:0:25:4:1:0:3 0/0:2:0:0,0:1,1:0:2,0:22.5:1:28.5:1:1:0:38:4:1:0:1 -Y 13487311 . GC G 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGTGCCTTCGCTCTCCTT;RSEQ=CAGTTTCCAAACCGGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:31:1:1:0:43:4:1:0:6 -Y 13487342 . C T 30 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCGGCCACACTGCAGACT;RSEQ=CCCAAGTTGCCGCATAAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:42:0:30.5:1:1:0:43:4:1:0:6 -Y 13487347 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACACTGCAGACTCCCCA;RSEQ=GTTGCCGCATAAGGGAATCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:37:0:31.5:1:1:0:43:4:1:0:6 -Y 13487357 . T C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTCCCCAAGTTGCCGCA;RSEQ=AAGGGAATCCATCGTCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:27:0:33.5:1:1:0:43:4:1:0:6 -Y 13487368 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCCGCATAAGGGAATCC;RSEQ=TCGTCAGGCCATCACGCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:0:32.5:1:1:0:43:4:1:0:6 -Y 13487371 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGCATAAGGGAATCCATC;RSEQ=TCAGGCCATCACGCCGGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:13:0:32:0:1:0:43:4:1:0:6 -Y 13487484 . G A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACAGTCCCGGCAACGGC;RSEQ=ACACCCACAGGCACTGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:12:0:31.5:1:1:0:60:4:1:0:1 -Y 13487707 . T C 32 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03571;SOR=0;LSEQ=TCGCCCCCTTCCTCTTCGTC;RSEQ=CTCCGGCCCCACCACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:26.5:1:32.5:1:1:0:37.5:4:1:0:5 0/0:6:0:0,0:4,2:0:2,0:22.7:1:31:1:1:0:45.3:12:1:0:2.2 -Y 13487725 . GCATCACCACGCCCTCCCTCCCCACCCCACA CAAGCACCATGCCCTTCCCCTCAACCCTCC 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.10714;SOR=0;LSEQ=TCTCTCCGGCCCCACCACCA;RSEQ=ACCCCCCGGCCACAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:33.5:1:29.5:1:1:0:50:4:1:0.6667:3 0/0:5:0:0,0:1,1:0:2,0:39.5:1:32.5:1:1:0:60:4:0.4:0:0 -Y 13487743 . T C 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=CAGCATCACCACGCCCTCCC;RSEQ=CCCCACCCCACAACCCCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:26:1:31:1:1:0:46:4:1:0:6.5 0/0:5:0:0,0:1,1:0:2,0:43.5:1:27:1:1:0:60:4:0.4:0:0 -Y 13487749 . C T 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CACCACGCCCTCCCTCCCCA;RSEQ=CCCACAACCCCCCGGCCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:7:1:28.5:1:1:0:31:4:0.6667:0:6 0/1:6:2:1,1:3,1:0.3333:2,2:34:1:27.5:1:1:2.44949:31:4:0.3333:0:6.5 -Y 13487755 . A C 58 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GCCCTCCCTCCCCACCCCAC;RSEQ=ACCCCCCGGCCACAGGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:19:1:30.7:1:1:0:39.7:6:1:0:6.7 1/0:6:4:3,1:1,1:0.6667:2,2:21.5:1:29:1:1:2.45:29.8:8:0.6667:0:6.5 -Y 13487761 . C A 27 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=CCTCCCCACCCCACAACCCC;RSEQ=CGGCCACAGGCCTCGACGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:19.3:1:31:1:1:0:48:6:1:0:5.7 0/1:5:2:1,1:2,1:0.4:2,2:29.5:1:27:1:1:1.7321:31:4:0.4:0:6.5 -Y 13487763 . G A 31 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TCCCCACCCCACAACCCCCC;RSEQ=GCCACAGGCCTCGACGCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:26:1:31.5:1:1:0:42:4:0.6667:0:7.5 0/0:5:0:0,0:3,2:0:2,0:24.4:1:29:1:1:0:43.6:10:1:0:4 -Y 13487767 . A G 47 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=CACCCCACAACCCCCCGGCC;RSEQ=CAGGCCTCGACGCCCTGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:21.3:1:30.3:1:1:0:48:6:1:0:5.7 1/0:6:3:2,1:1,2:0.5:2,2:23.7:1:30:1:1:3.11:32.7:6:0.5:0:6.7 -Y 13487778 . C T 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0.20187;LSEQ=CCCCCGGCCACAGGCCTCGA;RSEQ=GCCCTGGGACCCTTCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:27.5:1:29:0:1:0:43.5:4:0.6667:0:4.5 0/1:8:2:1,1:3,3:0.25:2,2:11:0:30:0:1:1:21:4:0.25:0:7.5 -Y 13487798 . G C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGCCCTGGGACCCTTCCGGG;RSEQ=TGGGGCTGGCTGTCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:41:1:33.5:1:1:0:43.5:4:1:0:4.5 0/1:6:2:1,1:1,3:0.3333:2,2:31:0:31.5:1:1:2.45:21:4:0.3333:0:7.5 -Y 13487804 . CT TG 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=GGGACCCTTCCGGGGTGGGG;RSEQ=GGCTGTCCCAGGGCTCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:35:1:34.5:1:1:0:43.5:4:1:0:4.5 0/1:5:2:1,1:1,2:0.4:2,2:37:1:30:1:1:1.73:21:4:0.4:0:6.5 -Y 13487805 . T A 33 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=GGACCCTTCCGGGGTGGGGC;RSEQ=GGCTGTCCCAGGGCTCACCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:34:1:33:0:1:0:43.5:4:1:0:4.5 0/0:5:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13487816 . G A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGTGGGGCTGGCTGTCCCA;RSEQ=GGCTCACCGCCATTCATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:23:1:32.5:1:1:0:43.5:4:1:0:4.5 0/1:5:2:1,1:1,2:0.4:2,2:33.5:1:29:1:1:1.73:21:4:0.4:0:6.5 -Y 13487824 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTGGCTGTCCCAGGGCTCAC;RSEQ=GCCATTCATGAAGGGGTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:15:1:31:0:1:0:43.5:4:1:0:4.5 1/0:4:2:1,1:0,2:0.5:0,2:25.5:1:28.5:1:1:0:21:4:0.5:0:6.5 -Y 13487826 . C G 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GGCTGTCCCAGGGCTCACCG;RSEQ=CATTCATGAAGGGGTGGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:0:0,0:13:1:33:0:1:0:43.5:4:1:0:4.5 1/0:4:2:1,1:0,2:0.5:0,2:23.5:1:29.5:1:1:0:21:4:0.5:0:6.5 -Y 13488013 . T C 30 d7;v4;MAF0.05;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGCTCCCCGCGATGGCC;RSEQ=TCCCGACAACTTCGGACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:18.5:1:30.5:1:1:0:44:4:1:0:7.5 1/1:1:1:0,1:0,0:1:0,0:8:0:34:0:1:0:36:2:1:0:1 -Y 13488131 . C T 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTGCTTTGAGCGGAACC;RSEQ=GTACCCGGGCATCGCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:30:1:31:1:1:0:40:4:1:0:6.5 -Y 13488144 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGAACCCGTACCCGGGCAT;RSEQ=GCCACCAGAGAACGGCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:39:0:31.5:1:1:0:40:4:1:0:6.5 -Y 13488152 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTACCCGGGCATCGCCACCA;RSEQ=AGAACGGCTGGCCCAGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:31:0:31.5:1:1:0:40:4:0.6667:0:6.5 -Y 13488157 . CG GA 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGCATCGCCACCAGAGAA;RSEQ=GCTGGCCCAGGCCATCGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:0.6667:0,2:25:0:32.5:0:1:0:40:4:0.6667:0:5.5 -Y 13488170 . C G 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGAACGGCTGGCCCAGG;RSEQ=CATCGACATTCCGGAGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:13:0:33.5:1:1:0:40:4:1:0:5.5 -Y 13488186 . GC TT 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCCATCGACATTCCGGA;RSEQ=CCAGAGTCCAGATTTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:27:1:28.3:1:1:1:49.5:4:0.5:0:4.5 -Y 13488203 . G T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCCCAGAGTCCAGATTT;RSEQ=GTTTCAGAATGCGAGGTCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:36.5:1:29.5:1:1:1:49.5:4:0.5:0:4.5 -Y 13488215 . C T 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGATTTGGTTTCAGAATG;RSEQ=GAGGTCACGCCAGCTGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:7:0:32:0:1:0:21:4:0.5:0:1.5 -Y 13488353 . A T 60 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCGAGCCTTTGAGAAGG;RSEQ=TCGCTTTCCAGGCATCGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:13.3:1:30.3:1:1:1:60:8:0.6667:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488367 . A T 31 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGATCGCTTTCCAGGC;RSEQ=TCGCCGCCAGGGAAGAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:14:1:31:0:1:1:40:4:0.3333:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488370 . G A 60 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATCGCTTTCCAGGCATC;RSEQ=CCGCCAGGGAAGAGGTGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:30.3:1:30.3:1:1:1:60:8:0.6667:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488373 . G A 30 d7;v4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGCTTTCCAGGCATCGCC;RSEQ=CCAGGGAAGAGGTGGCCAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:0.3333:2,2:8:1:30:1:1:1:40:4:0.3333:0:2.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488377 . G A 63 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCCAGGCATCGCCGCCA;RSEQ=GGAAGAGGTGGCCAGAGAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:0.6667:2,2:37.3:1:31.8:1:1:1:60:8:0.6667:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488410 . A T 60 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAGAGACGGGCCTCCCAG;RSEQ=GTCCAGGATTCAGATCTGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:1:0,2:15.3:1:30:1:1:0:60:8:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488484 . T G 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTGACAGGGCGCCCGCGCAG;RSEQ=CAGGCGGCCTGTGCAAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:9.5:1:28.5:1:1:0:60:4:1:0:7.5 1/1:2:2:1,1:0,0:1:0,2:6:0:30:1:1:0:39:4:1:0:7 -Y 13488489 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AGGGCGCCCGCGCAGTCAGG;RSEQ=GGCCTGTGCAAAGCGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:10:1:28.3:1:1:0:49:6:1:0:7 1/1:2:2:1,1:0,0:1:0,2:11:0:29.5:1:1:0:39:4:1:0:7 -Y 13488494 . T G 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=GCCCGCGCAGTCAGGCGGCC;RSEQ=GTGCAAAGCGGCCCCAGGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:15:1:28.7:1:1:0:49:6:1:0:7 1/1:2:2:1,1:0,0:1:0,2:16:0:29.5:1:1:0:39:4:1:0:7 -Y 13488500 . A C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GCAGTCAGGCGGCCTGTGCA;RSEQ=AGCGGCCCCAGGCGGGTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:21:1:29:1:1:0:49:6:1:0:7 1/1:2:2:1,1:0,0:1:0,2:22:0:31.5:1:1:0:39:4:1:0:7 -Y 13488505 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CAGGCGGCCTGTGCAAAGCG;RSEQ=CCCCAGGCGGGTGTCACCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:30.5:1:30:1:1:0:60:4:0.6667:0:7.5 0/0:2:0:0,0:1,1:0:2,0:27:0:32:1:1:0:39:4:1:0:7 -Y 13488510 . AGG TAT 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GGCCTGTGCAAAGCGGCCCC;RSEQ=CGGGTGTCACCCTGCTCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:37.5:1:30.5:1:1:0:60:4:0.6667:0:5.5 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488527 . C T 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCCAGGCGGGTGTCACCCTG;RSEQ=TCCCTCGTGGGTCGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:35:0:31.5:1:1:1:60:4:0.5:0:5.5 0/0:2:0:0,0:1,1:0:2,0:30:0:34:0:1:0:39:4:1:0:7 -Y 13488541 . G A 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCCTGCTCCCTCGTGGGTC;RSEQ=CCTTCGCCCACACCGGCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:0.75:0,2:23.7:1:31.3:1:1:0:49:6:0.75:0:5.3 1/1:2:2:1,1:0,0:1:0,2:16:0:32:0:1:0:39:4:1:0:7 -Y 13488550 . C A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=CCTCGTGGGTCGCCTTCGCC;RSEQ=ACACCGGCGCGTTGGGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:0:2,0:18.3:1:32.5:1:1:0:49.5:8:1:0:5.8 1/1:2:2:1,1:0,0:1:0,2:7:0:32:0:1:0:39:4:1:0:7 -Y 13488563 . T G 49 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCGCCCACACCGGCGCGT;RSEQ=GGGAACGGGGCTTCCCACAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:1:0,2:8.3:1:31:1:1:0:44.7:6:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488573 . G T 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCGGCGCGTTGGGAACGGG;RSEQ=CTTCCCACACCCCACGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:0.4:2,2:7:1:29.5:1:1:1.7321:58:4:0.5:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13488596 . G A 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCCCACACCCCACGTGCCCT;RSEQ=CACGACTGGGGCTCTCCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:19:0:30.5:1:1:1:58:4:0.5:0:5 0/0:3:0:0,0:1,2:0:2,0:6.3:1:30.7:1:1:0:53.3:6:1:0:1.7 -Y 13488597 . CA TG 30 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCCACACCCCACGTGCCCTG;RSEQ=CGACTGGGGCTCTCCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:20.5:1:30.3:1:1:1:56:4:0.5:0:4 0/0:3:0:0,0:1,2:0:2,0:7.3:1:30:1:1:0:53.3:6:1:0:1.7 -Y 13488598 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCACACCCCACGTGCCCTGC;RSEQ=CGACTGGGGCTCTCCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,0:0.5:0,2:17:0:32.5:1:1:0:58:4:1:0:5 0/0:3:0:0,0:1,2:0:2,0:8.3:1:27.7:1:1:0:53.3:6:1:0:1.7 -Y 13488601 . A C 63 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CACCCCACGTGCCCTGCACG;RSEQ=CTGGGGCTCTCCCACAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:15.8:1:31.8:1:1:0:57:8:0.8:0:4.5 0/0:3:0:0,0:1,2:0:2,0:11.3:1:28:1:1:0:53.3:6:1:0:1.7 -Y 13488650 . TCCC CCA 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGCCAGGGAGCGAGGGCCG;RSEQ=CGTGCTCCAGCCCAGCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:46:0:32:0:1:0:43:2:1:0:5 0/1:5:2:1,1:1,2:0.4:2,2:22:0:29.9:1:1:1.73:55.5:4:0.4:0:4 -Y 13488664 . C T 29 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGCCGTCCCCGTGCTCCAG;RSEQ=CCAGCCAGGCCGCGCCAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:32:0:33:0:1:0:43:2:1:0:5 0/1:5:2:1,1:1,2:0.4:2,2:35:0:29:1:1:1.73:55.5:4:0.4:0:5 -Y 13488675 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGCTCCAGCCCAGCCAGGC;RSEQ=GCGCCAGGAGAGGGGATCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:21:0:32:0:1:0:43:2:1:0:5 0/1:5:2:1,1:1,2:0.4:2,2:34:0:31:1:1:1.73:55.5:4:0.4:0:5 -Y 13488681 . A G 30 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGCCCAGCCAGGCCGCGCC;RSEQ=GGAGAGGGGATCTCCCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:15:0:32:0:1:0:43:2:1:0:5 1/0:4:2:1,1:1,1:0.5:2,2:28:0:30.5:1:1:1:55.5:4:0.5:0:5 -Y 13488685 . G A 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCAGCCAGGCCGCGCCAGGA;RSEQ=AGGGGATCTCCCAACCTGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:11:0:32:0:1:0:43:2:1:0:5 1/0:3:2:1,1:0,1:0.6667:0,2:24:0:31:1:1:0:55.5:4:0.6667:0:5 -Y 13488709 . TC GT 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATCTCCCAACCTGTCCCG;RSEQ=ACGCCAGGATTTTGCCTACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:9:0:32:1:1:0:33:4:1:0:3 -Y 13488715 . CA GG 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAACCTGTCCCGTCACGC;RSEQ=GGATTTTGCCTACACCGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0.6667:0,2:15:0:32.3:1:1:0:33:4:1:0:2 -Y 13488730 . A G 47 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGCCAGGATTTTGCCTAC;RSEQ=CCGCCCCGGCTCCTCCAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:14:0:32:0:1:0:27:2:1:0:6 1/0:6:3:2,1:2,1:0.5:2,2:9:1:30:1:1:1:28.7:6:0.5:0:6.7 -Y 13488738 . G T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTTTGCCTACACCGCCCC;RSEQ=GCTCCTCCAGAAGGGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:13.5:1:31:0:1:0:27:4:1:0:4.5 0/1:10:2:1,1:6,2:0.2:2,2:14.5:1:32:0:1:2.64575:21:4:0.2:0:6 -Y 13488747 . A G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0.32733;LSEQ=TACACCGCCCCGGCTCCTCC;RSEQ=GAAGGGGCGCTCTCCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:0.5:0,0:31:0:31:0:1:0:27:2:0.5:0:6 0/1:9:2:2,0:5,2:0.2222:2,0:22:1:30:1:1:0:35.5:4:0.2222:0:7.5 -Y 13488757 . C A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CGGCTCCTCCAGAAGGGGCG;RSEQ=TCTCCCACCCTCAGGCTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:22.3:1:32:1:1:0:31.3:6:1:0:4.7 0/1:8:2:1,1:4,1:0.25:2,2:33.5:1:30:1:1:3.1622:21:4:0.25:0:6 -Y 13488779 . C G 46 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=CTCCCACCCTCAGGCTCCTC;RSEQ=GTGGCCTCCGCACCCGGGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:26:1:27.7:1:1:0:31.3:6:1:0:4.7 1/0:5:3:2,1:0,0:0.6:0,2:35:1:29.3:1:1:0:23:6:0.75:0:6.3 -Y 13488782 . G T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=CCACCCTCAGGCTCCTCCGT;RSEQ=GCCTCCGCACCCGGGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:23:1:29.3:1:1:0:31.3:6:1:0:4.7 0/1:5:2:1,1:3,0:0.4:0,2:27:1:29:1:0.4:0:21:4:0.4:0:6 -Y 13488788 . C T 28 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0.17288;LSEQ=TCAGGCTCCTCCGTGGCCTC;RSEQ=GCACCCGGGCAAAAGCCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:0.6667:0,0:24.5:1:28.5:1:1:0:33.5:4:0.6667:0:4 0/1:5:1:1,0:3,1:0.2:2,0:40:0:29:0:1:0:27:2:0.2:0:7 -Y 13488789 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=CAGGCTCCTCCGTGGCCTCC;RSEQ=CACCCGGGCAAAAGCCGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:16:1:28:1:1:0:31.3:6:1:0:4.7 0/1:5:2:2,0:2,1:0.4:2,0:28.5:1:31.5:1:1:0:42:4:0.4:0:7 -Y 13488792 . C A 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTCCTCCGTGGCCTCCGCA;RSEQ=CCGGGCAAAAGCCGGGAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:20.5:1:28.5:1:1:0:33.5:4:1:0:4 0/1:5:2:1,1:3,0:0.4:0,2:17:1:28.5:1:0.4:0:21:4:0.4:0:6 -Y 13488853 . G A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52569;SOR=Inf;LSEQ=GCCTGCCGGTTGCTTGCGCG;RSEQ=TGGGACAGCCTGGGCCCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,5:0:2,0:6.3:1:32.6:1:1:0:50:14:0.875:0:3.6 0/1:15:2:1,1:4,9:0.1333:2,2:9:0:31.5:1:1:2.12:21:4:0.1429:0:5.5 -Y 13488859 . C A 45 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26847;SOR=Inf;LSEQ=CGGTTGCTTGCGCGGTGGGA;RSEQ=AGCCTGGGCCCGCTCAAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,6:0:2,0:10.7:1:32.9:1:1:0:46.7:20:0.9091:0:4.1 0/1:18:3:1,2:6,9:0.1667:2,2:10.3:1:28.7:1:1:1.3127:55:6:0.1667:0:6.3 -Y 13488861 . G C 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51232;SOR=Inf;LSEQ=GTTGCTTGCGCGGTGGGACA;RSEQ=CCTGGGCCCGCTCAAGCGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,5:0:2,0:10.4:1:32.1:1:1:0:42.7:20:0.9091:0:4 0/1:18:2:1,1:6,9:0.1111:2,2:17:0:32.5:1:1:1.46:21:4:0.1111:0:5.5 -Y 13488865 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50968;SOR=Inf;LSEQ=CTTGCGCGGTGGGACAGCCT;RSEQ=GGCCCGCTCAAGCGGGGCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:0:2,0:14.3:1:32.3:1:1:0:42.8:24:1:0:4.3 0/1:19:2:1,1:7,10:0.1053:2,2:11:1:30:1:1:1.40:44.5:4:0.1053:0:4.5 -Y 13488868 . C A 59 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05242;SOR=0.11485;LSEQ=GCGCGGTGGGACAGCCTGGG;RSEQ=CCGCTCAAGCGGGGCCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:4,5:0.3077:2,2:16.8:1:29.5:1:1:1.23:52.8:8:0.3077:0:4.5 0/1:22:1:0,1:9,12:0.0455:2,0:24:0:32:0:1:0:50:2:0.0455:0:4 -Y 13488870 . C A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13109;SOR=0;LSEQ=GCGGTGGGACAGCCTGGGCC;RSEQ=GCTCAAGCGGGGCCACAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:4,7:0.1538:2,0:11:1:32:1:0.19231:0:32.5:4:0.1538:0:5 0/0:22:0:0,0:8,11:0:2,0:17.4:1:30.4:1:1:0:49.6:38:0.8636:0:3.8 -Y 13488871 . G T 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63275;SOR=2.16737;LSEQ=CGGTGGGACAGCCTGGGCCC;RSEQ=CTCAAGCGGGGCCACAGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:6,6:0.0667:2,0:27:0:31:0:1:0:55:2:0.0714:0:1 0/1:22:3:2,1:6,10:0.1364:2,2:11.7:1:31:1:0.54592:3.12:57:6:0.1364:0:3 -Y 13488874 . C G 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63089;SOR=0.59928;LSEQ=TGGGACAGCCTGGGCCCGCT;RSEQ=AAGCGGGGCCACAGGGCCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:23:0:32.5:1:1:1.15:60:4:0.1333:0:3 0/1:24:2:0,2:10,12:0.0833:2,0:24.5:1:32.5:1:0.49275:0:45:4:0.0833:0:6 -Y 13488878 . C T 60 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.38858;LSEQ=ACAGCCTGGGCCCGCTCAAG;RSEQ=GGGGCCACAGGGCCAAGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:6,8:0.125:2,0:17:1:31:0:0.46667:0:29.5:4:0.1333:0:6 0/1:24:4:1,3:8,10:0.1667:2,2:19.3:1:30:1:0.61613:2.31239:39.3:8:0.1667:0:4.8 -Y 13488879 . G T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.64383;LSEQ=CAGCCTGGGCCCGCTCAAGC;RSEQ=GGGCCACAGGGCCAAGGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,6:0.125:2,2:15.5:1:31:1:1:1:30.5:4:0.1333:0:7 0/1:24:2:1,1:9,13:0.0833:2,2:35:0:31:0:1:1.42:60:4:0.0833:0:3.5 -Y 13488886 . C G 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.51417;SOR=Inf;LSEQ=GGCCCGCTCAAGCGGGGCCA;RSEQ=AGGGCCAAGGTGTGCTTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,7:0:2,0:26.8:1:31.4:1:1:0:45.5:13:0.9286:0:4.6 0/1:24:2:1,1:9,13:0.0833:2,2:35:0:31:1:1:1.42:57.5:4:0.0833:0:7.5 -Y 13488887 . A C 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51417;SOR=Inf;LSEQ=GCCCGCTCAAGCGGGGCCAC;RSEQ=GGGCCAAGGTGTGCTTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,6:0:2,0:26:1:29.7:1:1:0:44:13:0.9286:0:4.5 0/1:24:2:1,1:9,12:0.0833:2,2:16:0:30:1:1:1.32:40:4:0.0833:0:4 -Y 13488891 . C A 73 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09341;SOR=0.20821;LSEQ=GCTCAAGCGGGGCCACAGGG;RSEQ=CAAGGTGTGCTTGCGCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:2,3:7,5:0.2941:2,2:27.2:1:31.8:1:0.61991:2.00863:47.6:10:0.2941:0:4.8 0/1:26:2:1,1:10,14:0.0769:2,2:23.5:1:30:1:1:1.38:60:4:0.0769:0:3.5 -Y 13488894 . A T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.63211;LSEQ=CAAGCGGGGCCACAGGGCCA;RSEQ=GGTGTGCTTGCGCCACCCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:38:1:14.5:1:1:1.13389:45.5:0:0:0:6 0/1:26:2:1,1:10,14:0.0769:2,2:34.5:1:28:1:1:1.38:21:4:0.0769:0:5.5 -Y 13488895 . G A 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15061;SOR=0;LSEQ=AAGCGGGGCCACAGGGCCAA;RSEQ=GTGTGCTTGCGCCACCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:0.1176:2,2:32.5:1:32.5:1:1:1.13389:48:4:0.125:0:4.5 0/0:26:0:0,0:11,15:0:2,0:26.6:1:31.4:1:1:0:48:52:1:0:3.5 -Y 13488897 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51052;SOR=Inf;LSEQ=GCGGGGCCACAGGGCCAAGG;RSEQ=GTGCTTGCGCCACCCGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,8:0:2,0:26:1:29.9:1:1:0:46.5:15:1:0:4.6 0/1:26:2:1,1:10,14:0.0769:2,2:17.5:1:30:0:1:1.38:60:4:0.0769:0:3.5 -Y 13488900 . G A 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51684;SOR=Inf;LSEQ=GGGCCACAGGGCCAAGGTGT;RSEQ=CTTGCGCCACCCGCGTCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:27.9:1:32.8:1:1:0:45.3:32:1:0:4.8 0/1:26:2:1,1:10,14:0.0769:2,2:29:0:30:0:1:1.38:45:4:0.0769:0:4 -Y 13488902 . T C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=GCCACAGGGCCAAGGTGTGC;RSEQ=TGCGCCACCCGCGTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:14:1:33.5:1:1:1:54:4:0.125:0:4.5 0/0:24:0:0,0:10,14:0:2,0:24.9:1:30.5:1:1:0:48.1:48:1:0:3.8 -Y 13488904 . GC CT 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50769;SOR=Inf;LSEQ=CACAGGGCCAAGGTGTGCTT;RSEQ=GCCACCCGCGTCCCAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:0:2,0:27.2:1:32.6:1:1:0:45.3:32:1:0:4.8 0/1:24:2:1,1:9,13:0.0833:2,2:25:0:31.5:1:1:1.42:51:4:0.0833:0:3 -Y 13488905 . C T 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6786;SOR=0.67345;LSEQ=ACAGGGCCAAGGTGTGCTTG;RSEQ=GCCACCCGCGTCCCAGGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:7,7:0.1765:2,2:26.3:1:24.7:1:1:1.9219:39.3:2:0.125:0:5.3 0/1:24:3:1,2:8,11:0.125:2,2:20.3:1:30.7:1:1:1.43071:46.7:6:0.1364:0:4 -Y 13488911 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1707;SOR=0;LSEQ=CCAAGGTGTGCTTGCGCCAC;RSEQ=CGCGTCCCAGGGGAGTCCGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:0.125:2,2:20.5:1:30.5:1:1:1:48:4:0.125:0:4.5 0/0:22:0:0,0:10,12:0:2,0:18.3:1:30.1:1:1:0:49.4:21:1:0:3.8 -Y 13488913 . G T 80 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06419;SOR=Inf;LSEQ=AAGGTGTGCTTGCGCCACCC;RSEQ=CGTCCCAGGGGAGTCCGTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,7:0:2,0:24.7:1:29.8:1:1:0:45.1:14:0.9333:0:4.9 0/1:23:6:3,3:6,9:0.2609:2,2:22:1:31.2:1:1:1.47:51.2:12:0.2727:0:4.8 -Y 13488914 . C G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49929;SOR=Inf;LSEQ=AGGTGTGCTTGCGCCACCCG;RSEQ=GTCCCAGGGGAGTCCGTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,8:0:2,0:24.1:1:30:1:1:0:44.3:14:0.9333:0:4.8 0/1:22:2:1,1:8,11:0.0909:2,2:9:0:32.5:1:1:1.35:60:4:0.0909:0:2 -Y 13488915 . G A 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4955;SOR=Inf;LSEQ=GGTGTGCTTGCGCCACCCGC;RSEQ=TCCCAGGGGAGTCCGTGTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,7:0:2,0:23.8:1:30.9:1:1:0:45.1:30:0.9375:0:4.9 0/1:21:2:1,1:8,11:0.0952:2,2:13.5:1:26:1:1:1.35:21:4:0.0952:0:5.5 -Y 13488924 . G T 59 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04338;SOR=0;LSEQ=GCGCCACCCGCGTCCCAGGG;RSEQ=AGTCCGTGTTGGGGCTGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:2,2:5,5:0.2667:2,2:28:1:29.8:1:1:1:45.3:8:0.2667:0:5.3 0/0:16:0:0,0:6,8:0:2,0:8.4:1:31.6:1:1:0:44.7:28:0.875:0:4.4 -Y 13488927 . T C 32 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=CCACCCGCGTCCCAGGGGAG;RSEQ=CCGTGTTGGGGCTGGGGCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:0.1429:2,2:19:0:32.5:1:1:1:54:4:0.1538:0:4.5 0/0:13:0:0,0:6,7:0:2,0:9.2:1:28.7:1:1:0:43.8:26:1:0:5.1 -Y 13488928 . C A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.20308;SOR=Inf;LSEQ=CACCCGCGTCCCAGGGGAGT;RSEQ=CGTGTTGGGGCTGGGGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:0:2,0:15:1:29.9:1:1:0:42.1:13:1:0:5 0/1:12:2:1,1:5,5:0.1667:2,2:11:1:27.5:1:1:1:35.5:4:0.1667:0:7 -Y 13488930 . G A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCGCGTCCCAGGGGAGTCC;RSEQ=TGTTGGGGCTGGGGCAGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:0.1667:2,2:26:1:31:1:1:1.4491:30.5:4:0.1667:0:7 0/0:5:0:0,0:2,3:0:2,0:18.2:1:30:1:1:0:51.2:10:1:0:6.6 -Y 13488932 . GT TG 31 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCGTCCCAGGGGAGTCCGT;RSEQ=TGGGGCTGGGGCAGGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:0.1818:2,2:13:0:31.5:1:1:1.22474:54:4:0.1818:0:3.5 0/0:5:0:0,0:1,2:0:2,0:19:1:30:1:1:0:47:6:0.6:0:6 -Y 13488933 . T G 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58042;SOR=2.76;LSEQ=GCGTCCCAGGGGAGTCCGTG;RSEQ=TGGGGCTGGGGCAGGGGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:2,2:0.3333:2,2:17.7:1:30:1:1:1.81:28.7:6:0.4286:0:5 1/0:5:3:1,2:0,0:0.6:0,2:18.7:1:30.7:1:1:0:47:6:1:0:6 -Y 13488938 . G A 58 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.1049;SOR=0;LSEQ=CCAGGGGAGTCCGTGTTGGG;RSEQ=CTGGGGCAGGGGTTCCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:0.5:2,2:14:1:29.3:1:1:1:45.3:8:0.5:0:5.3 0/0:5:0:0,0:2,3:0:2,0:12.4:1:30.6:1:1:0:51.2:10:1:0:6.2 -Y 13488939 . C G 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51049;SOR=4.09114;LSEQ=CAGGGGAGTCCGTGTTGGGG;RSEQ=TGGGGCAGGGGTTCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:4,3:0.125:2,0:20:0:34:0:1:0:40:2:0.125:0:5 0/1:5:2:1,1:1,2:0.4:2,2:16.5:1:29:1:1:1.73:45.5:4:0.4:0:5 -Y 13488941 . G A 27 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=GGGGAGTCCGTGTTGGGGCT;RSEQ=GGGCAGGGGTTCCCAGGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:11.1:1:30.9:1:1:0:43.6:16:1:0:4.9 0/1:5:2:1,1:1,2:0.4:2,2:5:1:27.5:1:1:1.73:57.5:4:0.4:0:6.5 -Y 13488943 . G A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=GGAGTCCGTGTTGGGGCTGG;RSEQ=GCAGGGGTTCCCAGGGCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:4,3:0.125:2,0:16:0:33:0:1:0:40:2:0.125:0:5 1/0:4:2:1,1:0,2:0.5:0,2:12.5:1:27.5:1:1:0:45.5:4:0.5:0:5 -Y 13488946 . A C 46 d7;v4;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=GTCCGTGTTGGGGCTGGGGC;RSEQ=GGGGTTCCCAGGGCCCAGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:8:1:29.3:1:1:1.7321:40.3:6:0.6:0:6 1/0:4:2:0,2:1,1:0.5:2,0:3:0:26.5:1:1:0:52.5:4:0.5:0:7.5 -Y 13489043 . G A 74 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCCTCTGCGCGGCAGGGGC;RSEQ=GATGCAAGGCATCCCGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:13.2:1:32:1:1:0:33.8:10:0.8333:0:6.8 1/1:1:1:1,0:0,0:1:0,0:12:0:32:0:1:0:25:2:1:0:5 -Y 13489056 . C G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGGCGGATGCAAGGCAT;RSEQ=CCGGCGCCCTCCAAGGCGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:8,1:0.1818:2,2:14:1:31:1:0.34545:6:25:4:0.1818:0:7 0/0:4:0:0,0:3,0:0:0,0:17:1:32.3:1:1:0:41.7:6:0.75:0:3.3 -Y 13489059 . GGCGCCCTCCAAGGCGCTTCAGG AGGGCCTTCCCAGGCACTCAAGT 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=GGGCGGATGCAAGGCATCCC;RSEQ=AGCCGGGGCGCTCGTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:0.1818:2,2:18.5:1:29:1:0.49091:3.05504:55:4:0.1818:0.1818:4.5 0/0:6:0:0,0:6,0:0:0,0:12.8:1:31:1:1:0:37.2:12:1:0:4.8 -Y 13489061 . C T 47 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GCGGATGCAAGGCATCCCGG;RSEQ=GCCCTCCAAGGCGCTTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:6,1:0.3:2,2:15.3:1:29.7:1:1:2.64575:28.7:6:0.3:0:6.7 0/0:6:0:0,0:6,0:0:0,0:14.8:1:32.7:1:1:0:37.2:12:1:0:4.8 -Y 13489069 . A C 86 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.659;LSEQ=AAGGCATCCCGGCGCCCTCC;RSEQ=AGGCGCTTCAGGAGCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:6,1:1,1:0.7778:2,2:28.3:1:30.9:1:0.41667:4.58:32.6:14:0.7778:0:6.4 1/1:7:6:6,0:1,0:0.8571:0,0:19:1:30.5:1:1:0:34:12:0.8571:0:6 -Y 13489077 . T C 111 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28783;SOR=0.2187;LSEQ=CCGGCGCCCTCCAAGGCGCT;RSEQ=CAGGAGCCGGGGCGCTCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:8,5:0,1:0.9286:0,2:25.1:1:30:1:0.42857:0:34.5:26:0.9286:0:6.3 1/0:11:8:7,1:1,1:0.7273:2,2:16.9:1:31.6:1:0.37778:5.29:34.1:16:0.7273:0:5.8 -Y 13489084 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52205;SOR=0;LSEQ=CCTCCAAGGCGCTTCAGGAG;RSEQ=CGGGGCGCTCGTCTGCACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,9:0.0833:2,2:23:1:31:1:1:1.21106:44.5:4:0.0909:0:6.5 0/0:14:0:0,0:10,3:0:2,0:21.3:1:32.3:1:1:0:37.5:26:0.9286:0:5.1 -Y 13489085 . C T 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1791;SOR=0.33;LSEQ=CTCCAAGGCGCTTCAGGAGC;RSEQ=GGGGCGCTCGTCTGCACTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:10:6,4:8,7:0.4:2,2:20.4:1:29.4:1:1:1.30:34.7:9:0.375:0:5.6 0/1:17:3:2,1:10,4:0.1765:2,2:20:1:30.7:1:1:1.23316:29.7:6:0.1765:0:5 -Y 13489086 . G A 68 NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14005;SOR=0;LSEQ=TCCAAGGCGCTTCAGGAGCC;RSEQ=GGGCGCTCGTCTGCACTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:3,2:13,10:0.1786:2,2:18:1:29.4:1:1:1.15:43.2:10:0.1786:0:5 0/0:17:0:0,0:12,5:0:2,0:18.5:1:30.3:1:1:0:36.6:34:1:0:4.9 -Y 13489088 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.52367;SOR=0;LSEQ=CAAGGCGCTTCAGGAGCCGG;RSEQ=GCGCTCGTCTGCACTCCCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:15,12:0.069:2,2:41.5:1:30.5:1:1:1.24034:25:4:0.0714:0:7 0/0:17:0:0,0:12,5:0:2,0:20.1:1:30.8:1:1:0:36.6:34:1:0:4.9 -Y 13489090 . C T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51711;SOR=0;LSEQ=AGGCGCTTCAGGAGCCGGGG;RSEQ=GCTCGTCTGCACTCCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:15,12:0.069:2,2:11:0:31.5:1:1:1.24034:45:4:0.0714:0:7.5 0/0:18:0:0,0:12,6:0:2,0:20.4:1:31.3:1:1:0:37.7:36:1:0:4.8 -Y 13489091 . G A 45 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26729;SOR=0;LSEQ=GGCGCTTCAGGAGCCGGGGC;RSEQ=CTCGTCTGCACTCCCCTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:1,2:14,11:0.1034:2,2:31:1:29:1:0.58333:2.46268:33.3:6:0.1034:0:5.3 0/0:19:0:0,0:11,7:0:2,0:20.4:1:30.6:1:1:0:37.9:36:0.9474:0:4.7 -Y 13489092 . C T 46 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27878;SOR=0;LSEQ=GCGCTTCAGGAGCCGGGGCG;RSEQ=TCGTCTGCACTCCCCTCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:1,2:15,13:0.0968:2,2:14.7:1:29.3:1:0.59956:2.24752:34:6:0.0968:0:5.3 0/0:19:0:0,0:12,7:0:2,0:20.9:1:31.7:1:1:0:37.1:38:1:0:4.8 -Y 13489094 . C T 25 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.79298;LSEQ=GCTTCAGGAGCCGGGGCGCT;RSEQ=GTCTGCACTCCCCTCCGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:16,14:0.0625:2,2:13.5:1:25.5:1:1:1.13808:38:4:0.0625:0:7 0/1:20:1:1,0:11,8:0.05:2,0:16:0:32:0:1:0:59:2:0.05:0:8 -Y 13489095 . G A 72 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.38371;SOR=0.27571;LSEQ=CTTCAGGAGCCGGGGCGCTC;RSEQ=TCTGCACTCCCCTCCGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:3,2:14,13:0.1563:2,2:21.8:1:31.2:1:1:1.38:36.4:10:0.1563:0:5.6 0/1:21:1:1,0:12,8:0.0476:2,0:35:0:27:0:1:0:40:2:0.0476:0:5 -Y 13489099 . G A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50804;SOR=0;LSEQ=AGGAGCCGGGGCGCTCGTCT;RSEQ=CACTCCCCTCCGGCCTGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:16,14:0.0625:2,2:21.5:1:28.5:1:1:1.13808:21:4:0.0645:0:5.5 0/0:22:0:0,0:14,8:0:2,0:22.7:1:31.6:1:1:0:36.2:44:1:0:4.7 -Y 13489103 . T A 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49875;SOR=0;LSEQ=GCCGGGGCGCTCGTCTGCAC;RSEQ=CCCCTCCGGCCTGCTGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:2,0:15,15:0.0625:2,0:31:1:29:1:0.48589:0:38:4:0.0625:0:7.5 0/0:25:0:0,0:15,10:0:2,0:22.7:1:30:1:1:0:37.5:50:1:0:5 -Y 13489104 . C T 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19661;SOR=Inf;LSEQ=CCGGGGCGCTCGTCTGCACT;RSEQ=CCCTCCGGCCTGCTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:0:2,0:24.8:1:31:1:1:0:39.9:64:1:0:5.3 0/1:26:2:1,1:13,9:0.0769:2,2:20:0:29.5:1:1:1.42202:21:4:0.0769:0:4 -Y 13489107 . C G 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22938;SOR=Inf;LSEQ=GGGCGCTCGTCTGCACTCCC;RSEQ=TCCGGCCTGCTGCTGGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:0:2,0:27:1:31.5:1:1:0:39.9:62:1:0:5.2 0/1:29:2:1,1:14,13:0.069:2,2:8:0:29:1:1:1.07415:40:4:0.069:0:8 -Y 13489109 . C T 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=GCGCTCGTCTGCACTCCCCT;RSEQ=CGGCCTGCTGCTGGATGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:16,14:0.0625:2,2:29:1:30:1:1:1.13808:44.5:4:0.0625:0:6.5 0/0:31:0:0,0:15,14:0:2,0:23:1:31:1:1:0:39.3:58:0.9355:0:5.2 -Y 13489110 . C T 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.32669;SOR=2.16126;LSEQ=CGCTCGTCTGCACTCCCCTC;RSEQ=GGCCTGCTGCTGGATGAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:4:2,2:15,15:0.1176:2,2:22.5:1:31.8:1:1:1:43.3:8:0.1176:0:5 0/1:31:7:3,4:13,11:0.2258:2,2:27.9:1:31:1:0.68508:1.55268:37.9:14:0.2258:0:4.6 -Y 13489111 . G A 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.52114;LSEQ=GCTCGTCTGCACTCCCCTCC;RSEQ=GCCTGCTGCTGGATGAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:0,2:17,15:0.0588:2,0:16:1:28.5:1:0.48485:0:41.5:4:0.0588:0:4 0/1:32:1:0,1:16,13:0.0313:2,0:42:0:33:0:0.46667:0:40:2:0.0313:0:5 -Y 13489116 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23279;SOR=0;LSEQ=TCTGCACTCCCCTCCGGCCT;RSEQ=CTGCTGGATGAGCTCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:15,17:0.0571:2,2:31:0:31.5:1:1:1.13:46:4:0.0588:0:4.5 0/0:37:0:0,0:19,18:0:2,0:22.9:1:31.5:1:1:0:39.1:74:1:0:4.9 -Y 13489117 . CT TA 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49335;SOR=Inf;LSEQ=CTGCACTCCCCTCCGGCCTG;RSEQ=GCTGGATGAGCTCCTGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,17:0:2,0:28.6:1:32.2:1:1:0:39.5:66:0.9706:0:5.2 0/1:37:2:1,1:18,17:0.0541:2,2:26.5:1:30.5:1:1:1.05721:58:4:0.0556:0:6.5 -Y 13489118 . T A 46 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.24195;SOR=Inf;LSEQ=TGCACTCCCCTCCGGCCTGC;RSEQ=GCTGGATGAGCTCCTGGCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,18:0:2,0:28.4:1:30.6:1:1:0:39.6:68:1:0:5.2 0/1:39:3:2,1:17,17:0.0769:2,2:11:1:29.3:1:1:1.96:29:6:0.0811:0:4.7 -Y 13489120 . C A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22029;SOR=0;LSEQ=CACTCCCCTCCGGCCTGCTG;RSEQ=TGGATGAGCTCCTGGCGAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:2,0:13,17:0.0571:2,0:31:1:28:1:0.21169:0:38:4:0.0625:0:7.5 0/0:39:0:0,0:20,19:0:2,0:24.2:1:31.7:1:1:0:38.7:78:1:0:4.8 -Y 13489122 . G C 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22029;SOR=0;LSEQ=CTCCCCTCCGGCCTGCTGCT;RSEQ=GATGAGCTCCTGGCGAGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:14,16:0.0571:2,2:20:0:32:1:1:1.14:46:4:0.0588:0:3 0/0:39:0:0,0:20,19:0:2,0:25.1:1:31:1:1:0:38.7:78:1:0:4.8 -Y 13489123 . G A 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.71623;SOR=1.51107;LSEQ=TCCCCTCCGGCCTGCTGCTG;RSEQ=ATGAGCTCCTGGCGAGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:2,1:13,17:0.0882:2,2:25.3:1:29:1:0.57936:2.54:40.7:6:0.0909:0:7.7 0/1:39:5:2,3:16,14:0.1282:2,2:38.4:1:29.6:1:0.65815:1.68811:28.2:10:0.1282:0:4.4 -Y 13489124 . A G 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21347;SOR=0;LSEQ=CCCCTCCGGCCTGCTGCTGG;RSEQ=TGAGCTCCTGGCGAGCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:14,17:0.0588:2,2:19.5:1:33:0:1:1.21:27:4:0.0606:0:5.5 0/0:39:0:0,0:19,18:0:2,0:25.4:1:29.2:1:1:0:38.2:74:1:0:4.8 -Y 13489128 . G A 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23514;SOR=0.30767;LSEQ=TCCGGCCTGCTGCTGGATGA;RSEQ=CTCCTGGCGAGCCCGGAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:13,15:0.1515:2,2:41.2:1:30.6:1:1:1.28981:49.8:10:0.1515:0:4.8 0/1:39:2:1,1:19,18:0.0513:2,2:41:1:30:1:1:1.05412:50:4:0.0513:0:4 -Y 13489130 . T A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.65512;SOR=0.5452;LSEQ=CGGCCTGCTGCTGGATGAGC;RSEQ=CCTGGCGAGCCCGGAGTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:1,2:14,16:0.0909:2,2:40.3:1:31:1:1:1.7216:50:6:0.0909:0:4.7 0/1:39:2:1,1:19,18:0.0513:2,2:41:1:29:1:1:1.05412:50:4:0.0513:0:4 -Y 13489131 . C A 29 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.71713;LSEQ=GGCCTGCTGCTGGATGAGCT;RSEQ=CTGGCGAGCCCGGAGTTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:1:1,0:14,17:0.0303:2,0:23:0:30:0:0.46875:0:52:2:0.0303:0:4 0/1:39:2:1,1:17,17:0.0513:2,2:37:1:29.5:1:1:1:58:4:0.0513:0:6.5 -Y 13489132 . C T 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24108;SOR=Inf;LSEQ=GCCTGCTGCTGGATGAGCTC;RSEQ=TGGCGAGCCCGGAGTTTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:16,18:0:2,0:27.5:1:31.8:1:1:0:40.5:68:0.9714:0:5.2 0/1:39:3:1,2:16,15:0.0769:2,2:36.3:1:30.3:1:1:2.08761:26.3:6:0.0833:0:4.7 -Y 13489134 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20657;SOR=0;LSEQ=CTGCTGCTGGATGAGCTCCT;RSEQ=GCGAGCCCGGAGTTTCTGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:13,17:0.0606:2,2:40.5:1:30:1:1:1.30:45:4:0.0606:0:7.5 0/0:39:0:0,0:19,20:0:2,0:29.6:1:30.8:1:1:0:38.7:78:1:0:4.6 -Y 13489135 . GC G 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1996;SOR=0;LSEQ=TGCTGCTGGATGAGCTCCTG;RSEQ=GAGCCCGGAGTTTCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:12,16:0.0625:2,2:26.5:1:29.8:1:1:1.32:40:4:0.0625:0.0313:5 0/0:39:0:0,0:16,17:0:2,0:30.6:1:29.7:1:1:0:37.6:32:0.8421:0:4.3 -Y 13489136 . C T 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81323;LSEQ=GCTGCTGGATGAGCTCCTGG;RSEQ=GAGCCCGGAGTTTCTGCAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:0,2:12,16:0.0625:2,0:40.5:1:31.5:1:0.50345:0:28.5:4:0.0625:0:5 0/1:39:2:1,1:16,17:0.0513:2,2:27:1:31.5:1:1:1.06:58:4:0.0526:0:6 -Y 13489137 . G A 59 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03432;SOR=0;LSEQ=CTGCTGGATGAGCTCCTGGC;RSEQ=AGCCCGGAGTTTCTGCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:2,2:10,17:0.129:2,2:20.5:1:29.5:1:0.63045:1.67:36.5:8:0.129:0:5 0/0:39:0:0,0:18,19:0:2,0:30.4:1:30.1:1:1:0:38.1:74:0.9487:0:4.6 -Y 13489139 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.50128;SOR=Inf;LSEQ=GCTGGATGAGCTCCTGGCGA;RSEQ=CCCGGAGTTTCTGCAGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:11,18:0:2,0:30.2:1:32:1:1:0:41.6:28:0.9655:0:4.9 0/1:39:2:1,1:18,19:0.0513:2,2:28:1:28.5:1:1:1.05:53:4:0.0513:0:2 -Y 13489140 . C A 28 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=1.55778;LSEQ=CTGGATGAGCTCCTGGCGAG;RSEQ=CCGGAGTTTCTGCAGCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:0,1:11,17:0.0333:2,0:31:0:31:0:1:0:33:2:0.0345:0:6 0/1:39:2:1,1:17,18:0.0513:2,2:23:0:28:1:1:1.06:33:4:0.0513:0:3.5 -Y 13489142 . C T 85 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00616;LSEQ=GGATGAGCTCCTGGCGAGCC;RSEQ=GGAGTTTCTGCAGCAGGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:2,3:8,14:0.1786:2,2:36.8:1:30.8:1:1:1.16:38.4:10:0.1786:0:4.4 0/1:39:7:3,4:15,14:0.1795:2,2:32.7:1:30.3:1:1:1.41449:38.1:14:0.1842:0:4.6 -Y 13489143 . G A 88 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18409;LSEQ=GATGAGCTCCTGGCGAGCCC;RSEQ=GAGTTTCTGCAGCAGGCGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:1,4:9,14:0.1786:2,2:34:1:31.8:1:0.62637:2.4947:44.2:10:0.1852:0:5 0/1:39:8:4,4:15,16:0.2051:2,2:31.1:1:29.4:1:1:1.06:36.5:16:0.2051:0:6 -Y 13489144 . G A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17622;SOR=0;LSEQ=ATGAGCTCCTGGCGAGCCCG;RSEQ=AGTTTCTGCAGCAGGCGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:9,16:0.0714:2,2:27.5:1:30.5:1:1:1.74:46:4:0.0714:0:4.5 0/0:38:0:0,0:18,20:0:2,0:32.3:1:30.4:1:1:0:38.2:37:1:0:4.7 -Y 13489146 . G A 50 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25288;SOR=Inf;LSEQ=GAGCTCCTGGCGAGCCCGGA;RSEQ=TTTCTGCAGCAGGCGCAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:0:2,0:29.6:1:32.2:1:1:0:41.5:56:1:0:5 0/1:37:3:2,1:13,17:0.0811:2,2:36:1:31.7:1:0.57936:2.54:50:6:0.0811:0:7.3 -Y 13489148 . T G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50446;SOR=Inf;LSEQ=GCTCCTGGCGAGCCCGGAGT;RSEQ=TCTGCAGCAGGCGCAACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:0:2,0:29.6:1:30:1:1:0:42.1:26:1:0:5 0/1:37:2:1,1:16,18:0.0541:2,2:40:0:32.5:1:1:1.12:45:4:0.0541:0:7.5 -Y 13489150 . C T 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17411;SOR=0;LSEQ=TCCTGGCGAGCCCGGAGTTT;RSEQ=TGCAGCAGGCGCAACCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:30:1:31:1:1:1.74:49.5:4:0.0741:0:5 0/0:37:0:0,0:17,20:0:2,0:33.3:1:30.8:1:1:0:38.1:36:1:0:4.6 -Y 13489152 . G A 60 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02762;SOR=0;LSEQ=CTGGCGAGCCCGGAGTTTCT;RSEQ=CAGCAGGCGCAACCTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:1,3:9,14:0.1481:2,2:26.5:1:30.3:1:1:1.88548:46:8:0.1481:0:6.8 0/0:37:0:0,0:16,21:0:2,0:33:1:31.4:1:1:0:39.2:36:1:0:4.5 -Y 13489153 . C T 35 v4;q23;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.075;SOR=0;LSEQ=TGGCGAGCCCGGAGTTTCTG;RSEQ=AGCAGGCGCAACCTTTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:2,1:9,16:0.1071:2,2:20:1:22.7:1:0.54335:3.39:42.3:2:0.0769:0:4 0/0:37:0:0,0:16,21:0:2,0:32.8:1:31.8:1:1:0:39.2:74:1:0:4.5 -Y 13489155 . G T 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50192;SOR=Inf;LSEQ=GCGAGCCCGGAGTTTCTGCA;RSEQ=CAGGCGCAACCTTTCCTAGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:11,17:0:2,0:24.9:1:32.2:1:1:0:42.7:56:1:0:5.1 0/1:37:2:1,1:15,20:0.0541:2,2:23.5:1:28:1:1:1.32:49:4:0.0541:0:4.5 -Y 13489156 . CAGGCGCAACC AGGCACAACG 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49977;SOR=Inf;LSEQ=CGAGCCCGGAGTTTCTGCAG;RSEQ=TTTCCTAGAAACGGAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:11,18:0:2,0:23.6:1:31.6:1:1:0:42.2:28:1:0:5.2 0/1:37:2:1,1:14,19:0.0541:2,2:43:1:30.2:1:1:1.35:40:4:0.0541:0:6 -Y 13489157 . A G 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19519;SOR=0;LSEQ=GAGCCCGGAGTTTCTGCAGC;RSEQ=GGCGCAACCTTTCCTAGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:10,17:0.069:2,2:26:1:31:1:1:1.67:21:4:0.0714:0:4 0/0:36:0:0,0:15,21:0:2,0:29.5:1:30.3:1:1:0:39.4:35:1:0:4.4 -Y 13489160 . C T 80 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18923;LSEQ=CCCGGAGTTTCTGCAGCAGG;RSEQ=GCAACCTTTCCTAGAAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:1,4:10,12:0.1786:2,2:31.2:1:30.4:1:0.61848:3.20152:38.8:10:0.1786:0:5.8 0/1:34:7:2,5:11,16:0.2059:2,2:34.6:1:28.6:1:0.68182:1.69268:31.7:6:0.1818:0:4.4 -Y 13489161 . G T 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19989;SOR=0;LSEQ=CCGGAGTTTCTGCAGCAGGC;RSEQ=CAACCTTTCCTAGAAACGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:10,16:0.0714:2,2:13.5:1:28.5:1:1:1.57:45:4:0.0714:0:7.5 0/0:34:0:0,0:11,18:0:2,0:28.6:1:30.3:1:1:0:43.4:13.5:0.8438:0:4.3 -Y 13489163 . A C 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49656;SOR=Inf;LSEQ=GGAGTTTCTGCAGCAGGCGC;RSEQ=ACCTTTCCTAGAAACGGAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:11,17:0:2,0:20.1:1:29.4:1:1:0:41.9:27:1:0:5.3 0/1:34:2:1,1:11,19:0.0588:2,2:38.5:1:31:1:1:1.70:45:4:0.0588:0:7.5 -Y 13489166 . C G 47 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61995;SOR=2.56229;LSEQ=GTTTCTGCAGCAGGCGCAAC;RSEQ=TTTCCTAGAAACGGAGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:8,16:0.037:2,0:14:0:11:0:0.36:0:60:0:0:0:6 0/1:33:3:2,1:10,20:0.0909:2,2:20.3:1:29.7:1:0.53812:3.82:58.7:6:0.0909:0:6.7 -Y 13489167 . T A 28 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18562;SOR=0;LSEQ=TTTCTGCAGCAGGCGCAACC;RSEQ=TTCCTAGAAACGGAGGCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:0.0741:2,2:7.5:1:28.5:1:1:1.74:45:4:0.08:0:7.5 0/0:35:0:0,0:12,23:0:2,0:25.7:1:30.3:1:1:0:40.9:70:1:0:4.6 -Y 13489169 . T C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50273;SOR=Inf;LSEQ=TCTGCAGCAGGCGCAACCTT;RSEQ=CCTAGAAACGGAGGCCCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,17:0:2,0:17.3:1:28.5:1:1:0:43.3:12:1:0:5.5 0/1:35:2:1,1:11,22:0.0571:2,2:29.5:1:29.5:1:1:1.96:55:4:0.0571:0:7 -Y 13489171 . C A 31 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.42885;LSEQ=TGCAGCAGGCGCAACCTTTC;RSEQ=TAGAAACGGAGGCCCCGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:1,0:8,15:0.0417:2,0:1:0:25:0:0.375:0:46:2:0.0417:0:5 0/1:34:2:1,1:11,21:0.0588:2,2:20:1:31:0:1:1.87:21:4:0.0588:0:5.5 -Y 13489172 . T A 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51111;SOR=Inf;LSEQ=GCAGCAGGCGCAACCTTTCC;RSEQ=AGAAACGGAGGCCCCGGGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:0:2,0:18.1:1:29:1:1:0:43.1:44:1:0:5.6 0/1:33:2:1,1:11,20:0.0606:2,2:36:0:31.5:1:1:1.78:21:4:0.0625:0:5.5 -Y 13489174 . G A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.15805;LSEQ=AGCAGGCGCAACCTTTCCTA;RSEQ=AAACGGAGGCCCCGGGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:6,12:0.0526:2,0:1:0:26:0:0.36842:0:45:2:0.0556:0:8 0/1:33:2:1,1:11,20:0.0606:2,2:26:1:28.5:1:1:1.78:40:4:0.0606:0:8 -Y 13489178 . C T 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.89877;LSEQ=GGCGCAACCTTTCCTAGAAA;RSEQ=GGAGGCCCCGGGGGAGCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:3,10:0.0714:2,0:19:0:27:0:0.28571:0:40:2:0.0769:0:5 0/1:31:2:1,1:10,19:0.0645:2,2:23.5:1:29:1:1:1.86:45:4:0.0645:0:7.5 -Y 13489179 . G T 28 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23362;SOR=0.21548;LSEQ=GCGCAACCTTTCCTAGAAAC;RSEQ=GAGGCCCCGGGGGAGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:3,9:0.1429:2,2:13.5:1:28.5:1:0.50549:2.74:59.5:4:0.1429:0:5 0/1:30:1:0,1:9,17:0.0333:2,0:6:0:32:0:1:0:52:2:0.0333:0:4 -Y 13489187 . C T 88 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.44515;SOR=2.39303;LSEQ=TTTCCTAGAAACGGAGGCCC;RSEQ=GGGGGAGCTGGAGGCCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:0.1538:2,2:30.5:1:24:1:1:2.45:40.5:1:0.0833:0:5.5 0/1:26:8:3,5:5,11:0.3077:2,2:17.1:1:29.4:1:1:1.30:50.9:16:0.32:0:6.9 -Y 13489188 . G T 32 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.10526;SOR=0;LSEQ=TTCCTAGAAACGGAGGCCCC;RSEQ=GGGGAGCTGGAGGCCTTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:4,6:0.1538:2,0:9.5:1:32:1:0.51515:0:43:4:0.1538:0:6 0/0:26:0:0,0:8,15:0:2,0:16.4:1:30.7:1:1:0:44.6:46:0.8846:0:4.6 -Y 13489189 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.54386;SOR=Inf;LSEQ=TCCTAGAAACGGAGGCCCCG;RSEQ=GGGAGCTGGAGGCCTTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:0:2,0:19.9:1:30.8:1:1:0:42.8:26:1:0:5.8 0/1:26:2:1,1:8,16:0.0769:2,2:12.5:1:28:1:1:1.94:45:4:0.0769:0:7.5 -Y 13489192 . G C 33 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10476;SOR=0;LSEQ=TAGAAACGGAGGCCCCGGGG;RSEQ=AGCTGGAGGCCTTCGAAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:3,5:0.1667:2,0:27.5:1:33.5:1:1:0:30:4:0.1818:0:7 0/0:24:0:0,0:8,15:0:2,0:14.9:1:30.5:1:1:0:42.4:46:0.9583:0:4.8 -Y 13489194 . G C 30 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACGGAGGCCCCGGGGGA;RSEQ=CTGGAGGCCTTCGAAGAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:22.8:1:32.5:1:1:0:39.7:20:1:0:6 0/1:22:2:1,1:7,11:0.0909:2,2:29.5:1:30.5:1:1:1.54:55:4:0.0952:0:7 -Y 13489206 . C G 63 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8106;LSEQ=CCGGGGGAGCTGGAGGCCTT;RSEQ=GAAGAGGCCGCCTTGCTGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:1,3:0.5:2,2:16:1:31:1:1:1:33.3:8:0.5:0:5.8 0/1:9:4:1,3:2,3:0.4444:2,2:7:1:31.5:1:1:1.8525:25.8:8:0.4444:0:5.3 -Y 13489207 . G T 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=CGGGGGAGCTGGAGGCCTTC;RSEQ=AAGAGGCCGCCTTGCTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:2,4:0.25:2,0:25:0:30:0:1:0:39:4:0.25:0:5.5 0/0:6:0:0,0:1,3:0:2,0:30.3:1:32:1:1:0:52.5:8:0.6667:0:4.5 -Y 13489211 . A G 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GGAGCTGGAGGCCTTCGAAG;RSEQ=GGCCGCCTTGCTGGAAGCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:0.3333:2,0:21:0:33:0:1:0:39:4:0.3333:0:5.5 0/0:6:0:0,0:1,3:0:2,0:26.3:1:30.8:1:1:0:52.5:8:0.6667:0:4.5 -Y 13489220 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.41421;LSEQ=GGCCTTCGAAGAGGCCGCCT;RSEQ=GCTGGAAGCACCCTTCAGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,1:0.4:2,0:12:0:31:0:1:0:39:4:0.4:0:5.5 0/1:5:1:0,1:1,2:0.2:2,0:31:0:31:0:1:0:50:2:0.2:0:7 -Y 13489234 . T A 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=4.4496;LSEQ=CCGCCTTGCTGGAAGCACCC;RSEQ=TCAGCGAGGAAGAATACCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,0:0.3333:0,0:19:0:14:0:1:0:60:0:0:0:6 1/0:4:3:1,2:0,1:0.75:0,2:25:1:31.7:1:1:0:56.7:6:0.75:0:6.7 -Y 13489239 . C T 32 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TTGCTGGAAGCACCCTTCAG;RSEQ=GAGGAAGAATACCGGACTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,2:0:0,0:31.5:1:33:1:1:0:33.5:4:1:0:7 1/0:4:2:1,1:0,2:0.5:0,2:24:1:32:0:1:0:60:4:0.5:0:6.5 -Y 13489255 . A G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGCGAGGAAGAATACCGG;RSEQ=CTCTGCTGGAGGAGCTTTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:15.5:1:32.5:1:1:0:33.5:4:1:0:7 1/1:2:2:1,1:0,0:1:0,2:8:1:31:1:1:0:60:4:1:0:6.5 -Y 13489393 . T G 31 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=1;SOR=0.32198;LSEQ=CCCCCTCCACCGGGCTGACC;RSEQ=GCCTGGGATTCCTGCCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0.6667:0,0:13.5:1:31.5:1:1:0:42:4:0.6667:0:7 0/1:3:1:1,0:0,0:0.3333:0,0:19:0:32:0:1:0:40:2:0.5:0:6 -Y 13489409 . C A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GACCTGCCTGGGATTCCTGC;RSEQ=TTCTAGGTCTAGGCCTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:0.5:0,2:15.5:1:29:1:1:0:60:4:0.5:0:4.5 0/0:4:0:0,0:3,1:0:2,0:21:1:32.3:1:1:0:39.3:8:1:0:5.3 -Y 13489423 . C T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=TCCTGCCTTCTAGGTCTAGG;RSEQ=CTGGTGAGAGGCTCCACACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:0:2,0:28:1:31.8:1:1:0:48.8:10:1:0:6 0/1:7:2:1,1:4,1:0.2857:2,2:26.5:1:28.5:1:1:3.1622:50:4:0.2857:0:6.5 -Y 13489425 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.89792;LSEQ=CTGCCTTCTAGGTCTAGGCC;RSEQ=GGTGAGAGGCTCCACACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:3,1:0.1667:2,0:1:0:31:0:1:0:39:2:0.1667:0:6 0/1:7:2:2,0:3,2:0.2857:2,0:36.5:1:31:1:1:0:40:4:0.2857:0:4.5 -Y 13489442 . C G 30 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=1.18545;LSEQ=GCCTGGTGAGAGGCTCCACA;RSEQ=AGCGGAGAACTGCCATTCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:0.25:2,2:9.5:1:32:1:0.46429:3.87298:39:4:0.25:0:6.5 0/1:7:2:1,1:4,1:0.2857:2,2:26.5:1:30.5:1:1:3.1622:50:4:0.2857:0:6.5 -Y 13489447 . G T 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.55528;LSEQ=GTGAGAGGCTCCACACAGCG;RSEQ=AGAACTGCCATTCTTTCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:14.5:1:28:1:1:2.64575:39:4:0.2:0:6.5 0/1:7:2:1,1:4,1:0.2857:2,2:26.5:1:27.5:1:1:3.1622:50:4:0.2857:0:6.5 -Y 13489448 . A T 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=TGAGAGGCTCCACACAGCGG;RSEQ=GAACTGCCATTCTTTCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:31.5:1:29:1:1:2.64575:60:4:0.2:0:4.5 0/0:7:0:0,0:5,2:0:2,0:30.9:1:29:1:1:0:46.3:14:1:0:3.6 -Y 13489452 . C T 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=AGGCTCCACACAGCGGAGAA;RSEQ=TGCCATTCTTTCCTGGGCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:7:0:32:0:1:2.64575:50:4:0.2:0:3.5 0/0:7:0:0,0:5,2:0:2,0:29.1:1:30.6:1:1:0:46.3:14:1:0:3.6 -Y 13489464 . C G 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=GCGGAGAACTGCCATTCTTT;RSEQ=CTGGGCATCCTGGGGATCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:0.2:2,2:26:1:30.5:1:1:2.64575:60:4:0.2:0:4.5 0/0:8:0:0,0:6,2:0:2,0:21.8:1:29.4:1:1:0:43.5:16:1:0:3.8 -Y 13489474 . CT AC 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GCCATTCTTTCCTGGGCATC;RSEQ=GGGGATCCCAGAGCCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:4,3:0.2222:2,0:46:1:31:1:0.5:0:40:4:0.2222:0:6.5 0/0:5:0:0,0:4,1:0:2,0:25.2:1:28.4:1:1:0:41.2:10:1:0:4.8 -Y 13489475 . T C 26 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50549;SOR=4.64888;LSEQ=CCATTCTTTCCTGGGCATCC;RSEQ=GGGGATCCCAGAGCCGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:3,3:0.1111:2,0:11:0:32:0:1:0:40:2:0.1429:0:8 0/1:5:2:2,0:1,1:0.4:2,0:26.5:1:26.5:1:1:0:41:4:0.4:0:3 -Y 13489477 . G T 30 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.88331;LSEQ=ATTCTTTCCTGGGCATCCTG;RSEQ=GGATCCCAGAGCCGGCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:0.2222:2,2:42:1:30:1:1:2.23609:39:4:0.2222:0:6.5 0/1:5:1:0,1:4,0:0.2:0,0:42:0:32:0:0.2:0:60:2:0.2:0:7 -Y 13489486 . G C 32 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15267;LSEQ=TGGGCATCCTGGGGATCCCA;RSEQ=AGCCGGCCCAGGTACCAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,1:0.2222:2,2:42:1:32.5:1:1:3.1622:39:4:0.2222:0:6.5 0/1:4:1:0,1:3,0:0.25:0,0:33:0:34:0:0.25:0:60:2:0.25:0:7 -Y 13489492 . G A 30 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=TCCTGGGGATCCCAGAGCCG;RSEQ=CCCAGGTACCAGCAGGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:13.5:1:30.5:1:1:1.8258:50:4:0.25:0:3.5 0/0:5:0:0,0:4,1:0:2,0:17:1:30.4:1:1:0:41.2:10:1:0:4 -Y 13489515 . G A 32 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CAGGTACCAGCAGGTGGGCC;RSEQ=CCTACTGCGCACCCGCGGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:0.3333:2,0:35:1:32:0:1:0:40:4:0.3333:0:8 0/0:6:0:0,0:4,2:0:2,0:13.3:1:31.3:1:1:0:47.3:12:1:0:3.5 -Y 13489517 . C G 33 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.43179;LSEQ=GGTACCAGCAGGTGGGCCGC;RSEQ=TACTGCGCACCCGCGGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:0.3333:0,2:16.5:1:33:1:0.33333:0:39:4:0.3333:0:6.5 0/1:6:1:0,1:4,1:0.1667:2,0:2:0:30:0:0.33333:0:60:2:0.1667:0:7 -Y 13489528 . C G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=GTGGGCCGCCTACTGCGCAC;RSEQ=CGCGGGTTTGCGGGCAGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:0,0:0.6:0,2:17.7:1:31.3:1:1:0:39.7:6:0.6:0:7 1/0:4:2:2,0:1,1:0.5:2,0:34.5:1:30:1:1:0:40:4:0.5:0:5 -Y 13489538 . G C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TACTGCGCACCCGCGGGTTT;RSEQ=CGGGCAGCCGCCTGGGCTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:0:2,0:15.3:1:33.3:1:1:0:36.9:16:1:0:5.9 0/1:8:2:1,1:3,3:0.25:2,2:23:1:32.5:1:1:1:46:4:0.25:0:6 -Y 13489548 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63512;SOR=0.53515;LSEQ=CCGCGGGTTTGCGGGCAGCC;RSEQ=CCTGGGCTTTGGGAGCAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:5,2:0.3:2,0:28.3:1:30.7:1:1:0:40.3:6:0.3:0:6.7 0/1:11:2:0,2:5,4:0.1818:2,0:13:1:30.5:1:0.45455:0:25.5:4:0.1818:0:6.5 -Y 13489553 . G A 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08701;LSEQ=GGTTTGCGGGCAGCCGCCTG;RSEQ=GCTTTGGGAGCAGCCGGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,1:0.2:2,2:11.5:1:29:1:0.41667:4.58262:48.5:4:0.2:0:7 0/1:14:3:2,1:4,6:0.2143:2,2:6.3:1:29.3:1:0.55944:2.75:43.3:6:0.2143:0:4.3 -Y 13489557 . T G 97 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69683;SOR=1.47557;LSEQ=TGCGGGCAGCCGCCTGGGCT;RSEQ=TGGGAGCAGCCGGGGCAGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:5,1:4,1:0.5455:2,2:25.8:1:33.5:1:1:1.22:33.5:12:0.5455:0:4.8 1/0:14:9:4,5:3,2:0.6429:2,2:22.3:1:30.7:1:1:1.79176:37.8:8:0.6154:0:6 -Y 13489566 . G A 48 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2381;SOR=Inf;LSEQ=CCGCCTGGGCTTTGGGAGCA;RSEQ=CCGGGGCAGAGCTCTCATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:0:2,0:25.3:1:32.1:1:1:0:37.3:24:1:0:5.1 0/1:16:3:1,2:8,5:0.1875:2,2:31:1:30.3:1:0.55:2.96927:44.7:6:0.2:0:5.7 -Y 13489569 . G C 87 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13025;SOR=0.27421;LSEQ=CCTGGGCTTTGGGAGCAGCC;RSEQ=GGGCAGAGCTCTCATGCCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:7,0:0,0:0.5833:0,0:26.7:1:31.1:1:1:0:34.1:14:0.5833:0:5 0/1:15:4:2,2:1,1:0.2667:2,2:25:1:30.5:1:1:1:34.8:8:0.3077:0:5.3 -Y 13489571 . G T 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49194;SOR=Inf;LSEQ=TGGGCTTTGGGAGCAGCCGG;RSEQ=GCAGAGCTCTCATGCCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,4:0:2,0:24.7:1:30.9:1:1:0:37.9:28:1:0:4.5 0/1:18:2:1,1:9,7:0.1111:2,2:32.5:1:32:0:1:1.26772:30:4:0.1176:0:5.5 -Y 13489572 . G A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66446;SOR=0.62006;LSEQ=GGGCTTTGGGAGCAGCCGGG;RSEQ=CAGAGCTCTCATGCCTTTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:8,3:0.2143:2,2:18.7:1:29.7:1:1:1.30524:42.3:6:0.2143:0:4.7 0/1:21:3:2,1:10,8:0.1429:2,2:18:1:31:1:1:1.57:43.3:6:0.1429:0:4.7 -Y 13489577 . G C 31 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TTGGGAGCAGCCGGGGCAGA;RSEQ=CTCTCATGCCTTTCCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,4:0.1333:2,2:8.5:1:31:1:1:1.89743:30:4:0.1333:0:2.5 0/0:21:0:0,0:10,9:0:2,0:22.5:1:32.2:1:1:0:39.2:38:0.9048:0:4 -Y 13489579 . T G 33 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.38773;LSEQ=GGGAGCAGCCGGGGCAGAGC;RSEQ=CTCATGCCTTTCCACCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:9,4:0.0667:2,0:23:0:32:0:1:0:40:2:0.0667:0:4 0/1:22:2:1,1:12,8:0.0909:2,2:28:0:33:1:1:1.47192:45:4:0.0952:0:5 -Y 13489581 . T C 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.38773;LSEQ=GAGCAGCCGGGGCAGAGCTC;RSEQ=CATGCCTTTCCACCACCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:9,5:0.0667:2,0:21:0:32:0:1:0:40:2:0.0667:0:4 0/1:22:2:1,1:11,8:0.0909:2,2:26.5:1:32.5:1:1:1.35399:45:4:0.0952:0:5 -Y 13489583 . A T 28 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1417;SOR=0;LSEQ=GCAGCCGGGGCAGAGCTCTC;RSEQ=TGCCTTTCCACCACCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:8,5:0.1333:2,0:13:0:28.5:1:0.52381:0:40:4:0.1333:0:5 0/0:24:0:0,0:13,10:0:2,0:20.3:1:30.4:1:1:0:38.9:46:1:0:4.3 -Y 13489586 . C T 65 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.13717;SOR=Inf;LSEQ=GCCGGGGCAGAGCTCTCATG;RSEQ=CTTTCCACCACCCCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:23.4:1:31.3:1:1:0:37.4:30:1:0:4.3 0/1:25:5:2,3:11,8:0.2:2,2:24:1:28:1:0.62992:2.00028:40.4:10:0.2083:0:6 -Y 13489593 . A C 29 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.16241;LSEQ=CAGAGCTCTCATGCCTTTCC;RSEQ=CCACCCCACCCCCGCCTGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:8,5:0.0667:2,0:25:0:33:0:1:0:40:2:0.0667:0:6 0/1:26:2:2,0:13,11:0.0769:2,0:25:0:29:1:0.49231:0:44:4:0.0769:0:4 -Y 13489594 . C A 43 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1303;SOR=0.16781;LSEQ=AGAGCTCTCATGCCTTTCCA;RSEQ=CACCCCACCCCCGCCTGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:7,5:0.2:2,0:9.7:1:27.7:1:0.50549:0:40:6:0.2:0:5 0/1:26:1:1,0:14,11:0.0385:2,0:17:0:32:0:1:0:43:2:0.0385:0:8 -Y 13489595 . CA AG 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52439;SOR=Inf;LSEQ=GAGCTCTCATGCCTTTCCAC;RSEQ=CCCCACCCCCGCCTGACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:17.7:1:29.9:1:1:0:37.4:14:1:0:4.3 0/1:26:2:1,1:14,10:0.0769:2,2:14:0:32.8:1:1:1.38168:29:4:0.0833:0:6.5 -Y 13489602 . C G 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.10476;SOR=0;LSEQ=CATGCCTTTCCACCACCCCA;RSEQ=CCCCGCCTGACCACCCACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:0.1667:2,2:25.5:1:29:1:1:1.4491:40.5:4:0.1818:0:6 0/0:24:0:0,0:14,10:0:2,0:17.4:1:31:1:1:0:37.4:23:1:0:5 -Y 13489604 . C G 32 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09244;SOR=0;LSEQ=TGCCTTTCCACCACCCCACC;RSEQ=CCGCCTGACCACCCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,3:0.1818:2,2:15:0:32:0:1:1.29098:30:4:0.1818:0:2.5 0/0:24:0:0,0:11,8:0:2,0:14.7:1:30.1:1:1:0:40.1:18:0.8571:0:4.9 -Y 13489605 . C A 68 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.63994;SOR=2.56921;LSEQ=GCCTTTCCACCACCCCACCC;RSEQ=CGCCTGACCACCCACCCCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:6,4:0.0909:2,0:9:0:28:0:1:0:40:2:0.0909:0:5 0/1:24:5:4,1:10,9:0.2083:2,2:20.2:1:29.6:1:0.35771:3.43:36.2:10:0.2174:0:6.2 -Y 13489607 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTCCACCACCCCACCCCC;RSEQ=CCTGACCACCCACCCCCACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:0:2,0:12.3:1:25.3:1:1:0:36.2:2.667:1:0:4.5 0/1:23:2:0,2:12,8:0.087:2,0:12:0:31:0:0.19481:0:47:4:0.1053:0:5 -Y 13489608 . C A 30 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10417;SOR=0;LSEQ=TTTCCACCACCCCACCCCCG;RSEQ=CTGACCACCCACCCCCACCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:5,4:0.1818:2,0:6:1:30:1:0.49091:0:24.5:4:0.1818:0:4 0/0:22:0:0,0:13,8:0:2,0:17.1:1:31.2:1:1:0:35.6:20:1:0:4.8 -Y 13489612 . ACCA TACTCC 26 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09677;SOR=0;LSEQ=CACCACCCCACCCCCGCCTG;RSEQ=CCCACCCCCACCACCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:0.2:2,2:28:1:26:1:1:1.58108:40.5:4:0.25:0.1:6 0/0:21:0:0,0:12,9:0:2,0:17.6:1:28:1:1:0:36.5:6:1:0:4.8 -Y 13489613 . CCACCCA ACACC 30 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCACCCCACCCCCGCCTGA;RSEQ=CCCCCACCACCACCCACCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,3:0:2,0:4.7:1:28.7:1:1:0:38.6:6:1:0:4.1 0/1:21:2:1,1:10,8:0.0952:2,2:35:0:30.6:1:1:1.23603:29:4:0.1053:0:6.5 -Y 13489616 . CCCACCCCCACCACCACCCACCACCCCCGGA GGCCCAAGCCACCCCCACCCAACCCCTACCCCACACCCCCAGG 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=ACCCCACCCCCGCCTGACCA;RSEQ=AAATGCGTCCTCCCCTGGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:3.3:1:31.3:1:1:0:38.3:12:1:0:4 0/1:22:2:0,2:8,7:0.0909:2,0:30.5:1:28.7:1:0.47059:0:37.5:4:0.1333:0.0909:7 -Y 13489619 . ACCCC CGTCCTCACCCA 32 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=CCACCCCCGCCTGACCACCC;RSEQ=CACCACCACCCACCACCCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:0:2,0:8.5:1:32.3:1:1:0:35.5:12:1:0:3.8 0/1:20:2:1,1:8,5:0.1:2,2:40:0:32:1:1:1.54914:21:4:0.1333:0:2.5 -Y 13489628 . A C 73 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCTGACCACCCACCCCCACC;RSEQ=CCACCCACCACCCCCGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:5:3,2:2,1:0.5:2,2:32.8:1:31.6:1:1:1.28664:40.8:10:0.625:0:6.4 -Y 13489629 . CCACCCA C 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACCACCCACCCCCACCA;RSEQ=CCACCCCCGGAAAATGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:4,1:0.2:2,2:21:0:33:0:1:3.1622:21:4:0.2857:0:2.5 -Y 13489634 . CA AC 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CACCCACCCCCACCACCACC;RSEQ=CCACCCCCGGAAAATGCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:10:2:1,1:3,1:0.2:2,2:42.5:1:31.3:1:1:2.44949:41.5:4:0.3333:0:6.5 -Y 13489644 . G T 29 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=CACCACCACCCACCACCCCC;RSEQ=GAAAATGCGTCCTCCCCTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,7:0.125:2,2:7:0:29.5:1:1:1.15:50:4:0.1333:0:4 0/0:16:0:0,0:9,6:0:2,0:18.6:1:28.6:1:1:0:36.7:14:0.9333:0:5.8 -Y 13489653 . G A 49 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22973;SOR=0;LSEQ=CCACCACCCCCGGAAAATGC;RSEQ=TCCTCCCCTGGGCTGGGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:8,6:0.1579:2,2:11.7:1:31.3:1:0.57647:2.51691:38.7:6:0.1579:0:5 0/0:18:0:0,0:10,5:0:2,0:15.1:1:28.7:1:1:0:42.1:14:0.875:0:5.5 -Y 13489655 . C T 46 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22973;SOR=0;LSEQ=ACCACCCCCGGAAAATGCGT;RSEQ=CTCCCCTGGGCTGGGTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:9,7:0.1579:2,2:14.3:1:29.3:1:0.58204:2.44724:35:6:0.1667:0:5.7 0/0:19:0:0,0:11,8:0:2,0:14:1:30.5:1:1:0:39.6:38:1:0:5.6 -Y 13489658 . C T 50 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=ACCCCCGGAAAATGCGTCCT;RSEQ=CCCTGGGCTGGGTGGAGACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:10,7:0.15:2,2:17.3:1:31.7:1:0.56579:2.70974:35:6:0.15:0:5.7 0/0:19:0:0,0:10,9:0:2,0:14.2:1:29.9:1:1:0:43.3:38:1:0:5.9 -Y 13489665 . G C 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19346;SOR=Inf;LSEQ=GAAAATGCGTCCTCCCCTGG;RSEQ=CTGGGTGGAGACCCCCGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,10:0:2,0:21.1:1:32.3:1:1:0:42.2:40:0.9524:0:4.4 0/1:17:2:1,1:7,6:0.1176:2,2:19.5:1:28.5:1:1:1.1547:51.5:4:0.125:0:5.5 -Y 13489668 . G A 60 NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36341;SOR=0.2895;LSEQ=AATGCGTCCTCCCCTGGGCT;RSEQ=GGTGGAGACCCCCGTCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:2,2:10,8:0.1818:2,2:22.3:1:30:1:1:1.2373:43.5:8:0.1818:0:4.3 0/1:17:1:0,1:9,7:0.0588:2,0:22:0:31:0:0.47059:0:51:2:0.0625:0:8 -Y 13489669 . G T 42 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24291;SOR=0;LSEQ=ATGCGTCCTCCCCTGGGCTG;RSEQ=GTGGAGACCCCCGTCCCATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:2,1:9,8:0.1364:2,2:19.3:1:26.7:1:1:1.73:46:6:0.1364:0:2.7 0/0:17:0:0,0:8,8:0:2,0:16.7:1:29.7:1:1:0:44.1:32:0.9412:0:5.7 -Y 13489680 . C A 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5367;SOR=3.80587;LSEQ=CCTGGGCTGGGTGGAGACCC;RSEQ=CGTCCCATGAAACACCGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:9,9:0.0526:2,0:43:0:12:0:1:0:60:0:0:0:7 0/1:11:2:1,1:3,6:0.1818:2,2:26.5:1:32:0:1:1.87:60:4:0.1818:0:4 -Y 13489681 . C A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.17838;LSEQ=CTGGGCTGGGTGGAGACCCC;RSEQ=GTCCCATGAAACACCGTGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:8,8:0.1579:2,2:21.3:1:32:0:1:1.9301:36.7:6:0.1667:0:5 0/1:11:2:1,1:3,5:0.1818:2,2:39.5:1:31.5:1:1:1.58:21:4:0.2:0:8 -Y 13489682 . G T 32 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5367;SOR=3.80587;LSEQ=TGGGCTGGGTGGAGACCCCC;RSEQ=TCCCATGAAACACCGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:9,9:0.0526:2,0:45:0:28:0:1:0:60:2:0.0588:0:7 0/1:11:2:1,1:3,5:0.1818:2,2:28.5:1:32:0:1:1.58:60:4:0.1818:0:4 -Y 13489684 . CCCATGAAACACCGTGCCCGCA GCTGCGAAACACTAGGCCCCAG 54 P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.26787;SOR=0;LSEQ=GGCTGGGTGGAGACCCCCGT;RSEQ=CAGCGTCCAGGCCTGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:2,2:5,10:0.2105:2,2:32.3:1:27.1:1:0.60268:1.92:47.8:8:0.2105:0.2105:2 0/0:11:0:0,0:4,7:0:2,0:32:1:30:1:1:0:49.5:10:1:0:6.4 -Y 13489686 . CATG TGCT 49 v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25794;SOR=0;LSEQ=CTGGGTGGAGACCCCCGTCC;RSEQ=AAACACCGTGCCCGCACAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:6,8:0.1765:2,2:24.7:1:31.2:1:1:1.46561:44.7:6:0.1765:0.0588:3.7 0/0:11:0:0,0:4,7:0:2,0:32.2:1:30.6:1:1:0:49.5:22:1:0:6.4 -Y 13489687 . A G 94 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70072;SOR=1.50631;LSEQ=TGGGTGGAGACCCCCGTCCC;RSEQ=TGAAACACCGTGCCCGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:1,1:0.5333:2,2:25.5:1:31.6:1:1:1.58108:38:16:0.6154:0:5.6 1/0:11:7:3,4:1,3:0.6364:2,2:33.1:1:29.9:1:1:2.09:45.9:14:0.6364:0:6.7 -Y 13489688 . T C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29402;SOR=4.40795;LSEQ=GGGTGGAGACCCCCGTCCCA;RSEQ=GAAACACCGTGCCCGCACAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:3,5:0.0667:2,0:28:0:33:0:0.44444:0:45:2:0.1:0:7 0/1:12:3:1,2:3,6:0.25:2,2:33.7:1:32:0:1:1:57.7:6:0.2727:0:5 -Y 13489696 . C T 62 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93989;LSEQ=ACCCCCGTCCCATGAAACAC;RSEQ=GTGCCCGCACAGCGTCCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:4,4:0.2857:2,2:28.8:1:31.3:1:0.57576:2.74155:47:8:0.2857:0:5.3 0/1:11:3:1,2:3,5:0.2727:2,2:27.7:1:28.3:1:1:1.18052:53:6:0.2727:0:7.7 -Y 13489698 . T G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04718;SOR=6.57028;LSEQ=CCCCGTCCCATGAAACACCG;RSEQ=GCCCGCACAGCGTCCAGGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:3,2:1,1:0.3846:2,2:31.2:1:31.6:1:1:1.41:44.8:10:0.4545:0:6.2 1/1:11:9:3,6:1,1:0.8182:2,2:29.4:1:30.1:1:1:1.87089:47.9:18:0.8182:0:6.7 -Y 13489701 . C T 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CGTCCCATGAAACACCGTGC;RSEQ=CGCACAGCGTCCAGGCCTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:0.1818:2,2:23.5:1:29.5:1:1:1.22:51:4:0.1818:0:6 0/1:11:2:1,1:3,5:0.1818:2,2:24:1:28.5:1:1:1.58:55.5:4:0.2:0:6.5 -Y 13489705 . A G 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43338;LSEQ=CCATGAAACACCGTGCCCGC;RSEQ=CAGCGTCCAGGCCTGACACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:3,4:0.3636:2,2:29.3:1:30.5:1:1:1.30:43.3:8:0.3636:0:6.3 0/1:11:5:2,3:1,4:0.4545:2,2:23.2:1:30.8:1:1:2.41:40.8:10:0.4545:0:7.4 -Y 13489709 . C A 28 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58621;SOR=2.42568;LSEQ=GAAACACCGTGCCCGCACAG;RSEQ=GTCCAGGCCTGACACCCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:5,10:0.0625:2,0:47:0:29:0:0.375:0:31:2:0.0625:0:8 0/1:14:2:1,1:4,8:0.1429:2,2:26.5:1:28.5:1:1:1.90:21:4:0.1429:0:8 -Y 13489710 . G A 28 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22581;SOR=Inf;LSEQ=AAACACCGTGCCCGCACAGC;RSEQ=TCCAGGCCTGACACCCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:0:2,0:20:1:30.9:1:1:0:46.2:32:1:0:4.5 0/1:15:2:1,1:5,8:0.1333:2,2:23:1:28:1:1:1.55:55.5:4:0.1333:0:6.5 -Y 13489718 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=TGCCCGCACAGCGTCCAGGC;RSEQ=TGACACCCCTCTGGCCGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:0.1176:2,2:7.5:1:31:0:1:1.46:43:4:0.1176:0:5 0/0:16:0:0,0:7,9:0:2,0:14.5:1:31.1:1:1:0:46.9:32:1:0:6.1 -Y 13489724 . C T 48 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60117;SOR=0.32162;LSEQ=CACAGCGTCCAGGCCTGACA;RSEQ=CCCTCTGGCCGCTCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:5,9:0.1765:2,2:24.3:1:30.3:1:0.53676:3.33:55:6:0.1765:0:4.3 0/1:16:1:0,1:6,8:0.0625:2,0:33:0:31:0:1:0:53:2:0.0625:0:7 -Y 13489726 . C T 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48387;SOR=Inf;LSEQ=CAGCGTCCAGGCCTGACACC;RSEQ=CTCTGGCCGCTCGCCTCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:0:2,0:15.3:1:31.3:1:1:0:45.8:32:1:0:4.6 0/1:16:2:1,1:6,8:0.125:2,2:14:0:29.5:1:1:1.31:33:4:0.1333:0:8 -Y 13489727 . C T 47 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.60153;SOR=2.89897;LSEQ=AGCGTCCAGGCCTGACACCC;RSEQ=TCTGGCCGCTCGCCTCCTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:4,9:0.0714:2,0:29:0:28:0:0.35714:0:31:2:0.0714:0:8 0/1:16:3:1,2:6,7:0.1875:2,2:6.3:1:29.7:1:1:1.659:30:6:0.1875:0:8 -Y 13489730 . T C 62 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.31677;LSEQ=GTCCAGGCCTGACACCCCTC;RSEQ=GGCCGCTCGCCTCCTCTGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:4,4:0.2727:2,2:18:1:31.7:1:1:1.87936:45:6:0.2727:0:5.7 0/1:12:4:1,3:4,3:0.3333:2,2:23:1:31:1:0.54545:3.51553:57:8:0.3333:0:4.8 -Y 13489731 . G A 29 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.47826;SOR=Inf;LSEQ=TCCAGGCCTGACACCCCTCT;RSEQ=GCCGCTCGCCTCCTCTGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:0:2,0:21.5:1:31.4:1:1:0:44.6:22:1:0:5.1 0/1:12:2:1,1:4,6:0.1667:2,2:19:0:29.5:1:1:1.45:33:4:0.1667:0:8 -Y 13489734 . C G 101 NM4 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03964;SOR=0;LSEQ=AGGCCTGACACCCCTCTGGC;RSEQ=GCTCGCCTCCTCTGCGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:4,6:0,0:1:0,2:23.2:1:30.6:1:1:0:45.1:20:1:0:5 1/0:12:7:3,4:1,2:0.5833:2,2:15.4:1:30:1:1:1.44:38.1:14:0.5833:0:7.4 -Y 13489735 . G A 49 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21739;SOR=Inf;LSEQ=GGCCTGACACCCCTCTGGCC;RSEQ=CTCGCCTCCTCTGCGCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:20.6:1:31.1:1:1:0:45.4:22:1:0:5.3 0/1:12:3:1,2:3,4:0.25:2,2:25.3:1:31:1:1:1.44135:59:6:0.3:0:4 -Y 13489738 . C A 31 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=CTGACACCCCTCTGGCCGCT;RSEQ=GCCTCCTCTGCGCCTCCGCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:0.1818:2,2:27.5:1:31:1:1:1.87:43:4:0.1818:0:5 0/0:11:0:0,0:5,6:0:2,0:20.2:1:30:1:1:0:45.7:10:1:0:5.8 -Y 13489739 . G A 46 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.60687;LSEQ=TGACACCCCTCTGGCCGCTC;RSEQ=CCTCCTCTGCGCCTCCGCGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:2,6:0.2727:2,2:22.3:1:29.3:1:0.49091:4.95:55:6:0.2727:0:4.3 0/1:11:2:1,1:4,4:0.1818:2,2:18:0:30:0:1:1:46.5:4:0.1818:0:5.5 -Y 13489749 . C T 50 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09023;SOR=0;LSEQ=CTGGCCGCTCGCCTCCTCTG;RSEQ=GCCTCCGCGCCACCGTACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:4,3:0.3:2,0:8.3:1:31.7:1:0.2:0:40:6:0.3:0:4 0/0:11:0:0,0:5,6:0:2,0:18.5:1:30.3:1:1:0:45.2:22:1:0:5.8 -Y 13489751 . C A 47 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21429;SOR=Inf;LSEQ=GGCCGCTCGCCTCCTCTGCG;RSEQ=CTCCGCGCCACCGTACCCGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:10.4:1:30.6:1:1:0:45:20:1:0:5.1 0/1:11:3:1,2:4,4:0.2727:2,2:9.3:1:30:1:1:1.87936:59:6:0.2727:0:4 -Y 13489755 . C A 58 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09412;SOR=Inf;LSEQ=GCTCGCCTCCTCTGCGCCTC;RSEQ=GCGCCACCGTACCCGGCCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,4:0:2,0:6.5:1:30.6:1:1:0:45.3:16:0.8889:0:4.4 0/1:11:4:2,2:3,4:0.3636:2,2:25:1:29:1:1:1.30:38.5:8:0.3636:0:7.8 -Y 13489766 . AC CG 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=5.78427;LSEQ=CTGCGCCTCCGCGCCACCGT;RSEQ=CCGGCCCGCCTGTGCCCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,0:0.3333:0,0:33:0:29:0:1:0:48:2:0.3333:0:7 1/1:5:4:2,2:0,0:0.8:0,2:25:1:30.9:1:1:0:38.5:8:0.8:0:6.8 -Y 13489774 . C G 60 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCGCGCCACCGTACCCGGCC;RSEQ=GCCTGTGCCCCTGCAGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:0:0,0:7:0:33:0:1:0:42:2:0.5:0:6 1/0:7:4:2,2:2,1:0.5714:2,2:21:1:30:1:1:1.81007:38.5:8:0.5714:0:6.8 -Y 13489778 . T C 84 d7;v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02778;SOR=Inf;LSEQ=GCCACCGTACCCGGCCCGCC;RSEQ=GTGCCCCTGCAGCCTCCCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23:1:31:1:1:0:45:4:1:0:6.5 1/1:7:7:4,3:0,0:1:0,2:12.3:1:30:1:1:0:37.7:14:1:0:6.7 -Y 13489788 . C T 27 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=CCGGCCCGCCTGTGCCCCTG;RSEQ=AGCCTCCCAGCTGCCCCCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:12:1:32.2:1:1:0:39:10:1:0:7.2 0/1:7:2:1,1:2,3:0.2857:2,2:15:0:27:1:1:1.41:44:4:0.2857:0:6.5 -Y 13489793 . T C 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=CCGCCTGTGCCCCTGCAGCC;RSEQ=CCCAGCTGCCCCCATGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:15:1:30:1:1:0:39:10:1:0:7.2 0/1:7:2:1,1:2,2:0.2857:2,2:10:0:31:1:1:1:44:4:0.2857:0:6.5 -Y 13489795 . C T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.62671;LSEQ=GCCTGTGCCCCTGCAGCCTC;RSEQ=CAGCTGCCCCCATGGAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:10.5:1:30.5:1:1:1.73:32.5:4:0.4:0:8 0/1:7:2:1,1:2,3:0.2857:2,2:17.5:1:31.5:1:1:1.41:47:4:0.2857:0:8 -Y 13489803 . CC AA 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=CCCTGCAGCCTCCCAGCTGC;RSEQ=CCATGGAGTGCCTGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:1,3:0.2:2,0:18:0:30:0:0.4:0:36:2:0.2:0:7 0/1:5:2:1,1:1,2:0.4:2,2:26.5:1:31.8:1:1:1.73:47:4:0.5:0:7 -Y 13489804 . C A 60 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0.41421;LSEQ=CCTGCAGCCTCCCAGCTGCC;RSEQ=CCATGGAGTGCCTGGTGGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,0:0.8:0,2:22.5:1:30.3:1:1:0:39.8:8:1:0:7 1/0:5:3:1,2:0,0:0.6:0,2:26.3:1:30.3:1:1:0:40.7:6:1:0:7.7 -Y 13489813 . T G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=TCCCAGCTGCCCCCATGGAG;RSEQ=GCCTGGTGGTGGAACGCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:0,2:0.25:0,0:27:0:32:0:0.33333:0:36:2:0.25:0:7 0/1:5:2:1,1:1,2:0.4:2,2:35.5:1:31.5:1:1:1.73:47:4:0.4:0:7 -Y 13489820 . T C 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=TGCCCCCATGGAGTGCCTGG;RSEQ=GGTGGAACGCACACCTCTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:2,0:0.5:0,0:38:1:31.5:1:0.33333:0:34.5:4:0.5:0:7.5 1/0:5:3:1,2:1,1:0.6:2,2:42:1:31.3:1:1:1.7321:40.7:6:0.6:0:7.7 -Y 13489823 . T C 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=CCCCATGGAGTGCCTGGTGG;RSEQ=GGAACGCACACCTCTAGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,0:0.25:0,0:40:0:32:0:1:0:29:2:0.25:0:8 0/1:5:2:0,2:2,1:0.4:2,0:45.5:1:31:1:0.4:0:36.5:4:0.4:0:7.5 -Y 13489832 . C G 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.4697;SOR=Inf;LSEQ=GTGCCTGGTGGTGGAACGCA;RSEQ=ACCTCTAGCTCTCTTTGCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,0:0.7143:0,2:27.2:1:30.8:1:1:0:34.4:10:0.7143:0:7 1/1:5:5:2,3:0,0:1:0,2:45:1:30.8:1:1:0:43.2:10:1:0:7.4 -Y 13489842 . T C 32 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16484;SOR=Inf;LSEQ=GTGGAACGCACACCTCTAGC;RSEQ=CTCTTTGCCGGCCTCCTGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:20.1:1:30.6:1:1:0:40.3:16:1:0:5.9 0/1:6:2:1,1:1,3:0.3333:2,2:36:1:32:0:1:2.45:41:4:0.3333:0:7.5 -Y 13489867 . C A 49 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68493;LSEQ=TTGCCGGCCTCCTGGCTAGA;RSEQ=CTGCGCTCATTGCGCACCCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:2,3:0.375:2,2:25:1:31:1:1:2.60:48.7:6:0.375:0:6.3 0/1:7:2:1,1:2,3:0.2857:2,2:11.5:1:28:1:1:1.41:47:4:0.2857:0:7 -Y 13489870 . G A 27 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.55944;SOR=2.75172;LSEQ=CCGGCCTCCTGGCTAGACCT;RSEQ=CGCTCATTGCGCACCCAGGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:3,3:0.1429:2,0:17:0:29:0:1:0:36:2:0.1429:0:7 0/1:6:2:1,1:2,2:0.3333:2,2:8.5:1:27:1:1:1:47:4:0.4:0:7 -Y 13489881 . G A 30 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.5321;LSEQ=GCTAGACCTGCGCTCATTGC;RSEQ=CACCCAGGCTGACGTGCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:2,2:0.3333:2,0:21.5:1:30.5:1:0.46667:0:41.5:4:0.3333:0:7 0/1:5:1:0,1:3,1:0.2:2,0:2:0:27:0:0.4:0:50:2:0.2:0:7 -Y 13489887 . A C 68 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.44721;LSEQ=CCTGCGCTCATTGCGCACCC;RSEQ=GGCTGACGTGCAACGGAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,0:0.8333:0,2:24.2:1:29.6:1:1:0:51.4:10:0.8333:0:6.4 1/0:3:2:1,1:0,0:0.6667:0,2:13.5:1:31.5:1:1:0:43:4:0.6667:0:5 -Y 13489893 . ACGTGCAACGGAGACCGCTGTCC TCATGTAAGGGAGCCCGCTGGCT 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCATTGCGCACCCAGGCTG;RSEQ=TCTCTGTGCCCTTGTCCGTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:0.3333:2,2:28.5:1:29.6:1:1:2.45:50:4:0.3333:0.3333:7 0/0:2:0:0,0:2,0:0:0,0:26.5:1:31:0:1:0:34:4:1:0:7.5 -Y 13489895 . G A 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGCGCACCCAGGCTGAC;RSEQ=TGCAACGGAGACCGCTGTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:31:1:31:1:1:1.73:43.5:4:0.4:0:6.5 0/0:2:0:0,0:2,0:0:0,0:28.5:1:31.5:1:1:0:34:4:1:0:7.5 -Y 13489901 . C G 49 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACCCAGGCTGACGTGCAA;RSEQ=GGAGACCGCTGTCCTCTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:32.3:1:31:1:1:1.7321:45:6:0.6:0:6.7 1/1:2:2:2,0:0,0:1:0,0:34.5:1:31:1:1:0:34:4:1:0:7.5 -Y 13489906 . A C 50 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGCTGACGTGCAACGGAG;RSEQ=CCGCTGTCCTCTCTGTGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:0.6:2,2:28.7:1:32:1:1:1.7321:37.3:6:0.6:0:7 1/1:2:2:2,0:0,0:1:0,0:39.5:1:34:0:1:0:34:4:1:0:7.5 -Y 13489913 . T G 72 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTGCAACGGAGACCGCTG;RSEQ=CCTCTCTGTGCCCTTGTCCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:26.8:1:31.4:1:1:0:44.4:10:1:0:6.6 1/1:3:3:2,1:0,0:1:0,2:32.3:1:30.7:1:1:0:37.7:6:1:0:7.3 -Y 13489923 . G T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=GAGACCGCTGTCCTCTCTGT;RSEQ=CCCTTGTCCGTCCGTGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:18.7:1:32.2:1:1:0:43.7:12:1:0:6.7 1/0:3:2:1,1:1,0:0.6667:0,2:28:1:28:1:1:0:45.5:4:0.6667:0:7.5 -Y 13489954 . T G 32 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.32198;LSEQ=TCCGTGAAATTCCGGCTGAG;RSEQ=CTCTCCCAACACCTTCCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:0.6667:0,0:12:1:32:1:1:0:45.5:4:0.6667:0:6.5 0/1:3:1:1,0:1,1:0.3333:2,0:19:0:33:0:1:0:22:2:0.3333:0:7 -Y 13489989 . T G 30 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGAAGCTCTTTTGTCAAA;RSEQ=CCTGGAGAATACTTATATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:40:2:1:0:7 1/1:2:2:0,2:0,0:1:0,0:16:1:30.5:1:1:0:42.5:4:1:0:7.5 -Y 13490031 . T C 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGATGATCGGTTCAGAAA;RSEQ=ATGTCACAATGCCCCCTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:0,2:0.6:0,2:28.7:1:32:1:1:0:47.3:6:0.6:0:4.3 -Y 13490048 . T A 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATGTCACAATGCCCCC;RSEQ=CCCTGCGGAGCCTAGAGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:0,3:0.4:0,2:40:1:30:1:0.4:0:48.5:4:0.4:0:3.5 -Y 13490074 . C A 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGAGCCTAGAGAAGATTTG;RSEQ=ATCATTTGGGTGATCAGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:19:0:31.5:1:1:0:48.5:4:0.5:0:3.5 -Y 13568215 . G T 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCACTGTGATTTGCCCAATT;RSEQ=TTGCTTTAGCACTGGACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:0:2,0:26.2:1:31.9:1:1:0:46.5:32:1:0:0 0/1:98:2:1,1:59,37:0.0204:2,2:29:1:30.5:1:1:1.5867:42:4:0.0206:0:1 -Y 13568257 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAGAAGTTGTTGGTAGTG;RSEQ=ATCCAAAGGCACGTTTTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:0:2,0:24.6:1:32.1:1:1:0:45.9:36:1:0:0 0/1:127:2:1,1:63,61:0.0157:2,2:7.5:1:28:0:1:1.03253:48.5:4:0.0161:0:1.5 -Y 13568303 . T A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAAGCCTTAAGACACCGTG;RSEQ=CTTCAGGTGGGTGTGGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:0:2,0:27.4:1:30:1:1:0:54.2:40:1:0:0.1 0/1:183:2:1,1:91,90:0.0109:2,2:27.5:1:27.5:1:1:1.01105:30:4:0.011:0:1 -Y 13569835 . T TA 28 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGAGAACAACAAAAACT;RSEQ=AAAAAAAAAAAGACAGATAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:41.5:1:28.5:1:1:0:46.5:4:1:0:2 -Y 13572613 . T G 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATTTTTATGGCATCTGCTG;RSEQ=GTGAATTTTCCTAGGGTGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:36:1:29.5:1:1:1:46.5:4:0.6667:0:2.5 -Y 13572626 . A G 28 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCTGTGTGAATTTTCCT;RSEQ=GGGTGCTGGGCTGGTTGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:0.5:2,2:23:1:28.5:1:1:1:46.5:4:0.6667:0:2.5 -Y 13572922 . A C 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20598;SOR=0.26612;LSEQ=AAGGTAGAGGGGGGCAACAC;RSEQ=TAATGCCTTTGCTGTGGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:10,0:2,1:0.7692:2,0:24.2:1:30.3:1:0.23077:0:33.5:9:0.75:0:2.6 0/1:11:5:5,0:6,0:0.4545:0,0:16:1:30.8:1:1:0:37:10:0.4545:0:2.6 -Y 13572932 . T C 131 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12916;SOR=0.27566;LSEQ=GGGGCAACACATAATGCCTT;RSEQ=GCTGTGGGAGCTTCATCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:16,1:2,1:0.85:2,1:21.4:1:32.1:1:0.28421:6.73:36.6:34:0.85:0:2.4 1/0:15:9:9,0:6,0:0.6:0,0:16.2:1:31:1:1:0:41.9:18:0.6:0:2.4 -Y 13572999 . A G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.18076;LSEQ=TCCTCCCTCTTTCCACAGGG;RSEQ=CATGCTACCCCTGTCATTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:104:96:81,15:6,1:0.9231:2,2:29.7:1:31:1:1:1.11001:32.9:47:0.9307:0:2.1 1/0:123:84:73,11:33,4:0.6829:2,2:28.7:1:30.1:1:1:1.24094:34.7:20:0.678:0:2 -Y 13573033 . A C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18406;LSEQ=TCATTCCAGGAGTTTATTAT;RSEQ=CTTCAGACACAGCTACTTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:113:82,31:13,5:0.8626:2,2:28.5:1:30.6:1:1:1.02:32.8:112:0.8682:0:1.9 1/0:187:100:75,25:69,17:0.5348:2,2:28.4:1:30.1:1:0.48231:1.35075:32.5:99:0.5351:0:1.9 -Y 13573061 . A G 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00079;SOR=0;LSEQ=CACAGCTACTTATGTTTTTA;RSEQ=TTCCCTCACAGGATGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:7:6,1:73,56:0.0515:2,2:23.4:1:30.9:1:0.23827:4.56:30.1:14:0.053:0:2.6 0/0:236:0:0,0:149,87:0:2,0:24.1:1:29.6:1:1:0:40:58:1:0:0.8 -Y 13573108 . G C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13709;LSEQ=AGAAAGTTTCAAGATCTTCT;RSEQ=TCTGAGGAAAATGAATCCAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:123:92:31,61:19,12:0.748:2,2:26:1:31.2:1:0.0106:3.08494:27.3:29.667:0.7417:0:1.6 0/1:302:87:23,64:114,101:0.2881:2,2:28.7:1:31:1:2e-05:3.12894:27:174:0.289:0:1.7 -Y 13573152 . C A 188 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11963;LSEQ=TCTATCTCAGGTTCTAGCCC;RSEQ=GGTATTCGTATTCCTGATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:66:5,61:11,15:0.7097:2,2:35.2:1:31.2:1:0.00024:8.66733:24.8:65:0.7143:0:1.8 0/1:280:63:2,61:91,126:0.225:2,1:31.3:1:30.9:1:0:21.8773:26.4:62:0.2246:0:1.9 -Y 13573216 . G A 107 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=2e-05;SOR=0.08602;LSEQ=AGGAGCTGATAAGCAAAGAT;RSEQ=ATGAAATTCAAGATTTTCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:0,11:2,7:0.55:2,0:16.7:1:31:1:0.18947:0:24.2:22:0.55:0:2.1 0/1:87:8:0,8:18,61:0.092:2,0:4.5:1:29.3:1:0.19683:0:25.9:16:0.0941:0:2 -Y 13573240 . C T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00078;SOR=0.07082;LSEQ=AAATTCAAGATTTTCCTGAG;RSEQ=AGCAATTGCTTAACATTGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:2,4:1,7:0.4286:2,2:11.3:1:29.8:1:0.53846:3.19:27.8:12:0.4286:0:2.2 0/1:63:3:2,1:12,48:0.0476:2,2:8.7:1:28.7:1:0.12145:7.65:23:6:0.0484:0:2 -Y 13573271 . G T 72 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18063;SOR=0.28188;LSEQ=TAACATTGTTTCAGTTATAA;RSEQ=GTAGTAGAAACTCTGTTTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:1,5:0.4:2,2:28.8:1:30.3:1:0.5:4.17:34.8:8:0.4:0:1.8 0/1:39:6:2,4:5,28:0.1538:2,2:26.8:1:28:1:0.2902:2.71:27.3:12:0.1579:0:1.7 -Y 13574387 . C G 67 v4;DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04009;SOR=0.17321;LSEQ=GTCCGGCTGTGTGTGCTGCT;RSEQ=TGTTGTGAACTCCGTGGTTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:3,0:6,9:0.1667:2,0:6:1:32:1:0.20588:0:30.3:6:0.1667:0:3 0/1:152:5:4,1:70,77:0.0329:2,2:9.2:1:29:1:0.20069:4.36:31.4:4:0.0268:0:3.8 -Y 13574411 . C A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGAACTCCGTGGTTTGAA;RSEQ=ATGAAAGAAATGTACCTTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:0:2,0:26.3:1:31.9:1:1:0:51.4:16:1:0:0.8 0/1:127:2:1,1:52,73:0.0157:2,2:20.5:1:30:1:1:1.40:60:4:0.0164:0:1.5 -Y 13574414 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAACTCCGTGGTTTGAACAT;RSEQ=AAAGAAATGTACCTTCTTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:0:2,0:28.4:1:31.4:1:1:0:48.6:15:1:0:0.9 0/1:124:2:1,1:50,72:0.0161:2,2:16.5:1:26.5:1:1:1.44:60:4:0.0164:0:1.5 -Y 13574421 . A G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01899;SOR=0.21215;LSEQ=GTGGTTTGAACATGAAAGAA;RSEQ=TGTACCTTCTTTCACTCTGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:5,6:0.3125:2,2:26.4:1:32.4:1:1:1.73:32.2:10:0.3125:0:2.6 0/1:127:11:7,4:43,73:0.0866:2,2:28.1:1:30.8:1:0.10976:2.94:38.7:10:0.08:0:2.9 -Y 13574443 . A T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00511;SOR=0.19655;LSEQ=GTACCTTCTTTCACTCTGTC;RSEQ=TCTTTCTTTTCTTTGAGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:4,4:4,5:0.4706:2,2:29.9:1:30.9:1:1:1.23:34.5:16:0.4706:0:2.1 0/1:89:13:7,6:20,56:0.1461:2,2:33.8:1:30.2:1:0.05706:3.22:36.2:26:0.1477:0:2.6 -Y 13574523 . A G 33 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTTCACAGTCACTGATGT;RSEQ=TAATTAAAAACCTGATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:0:0,0:21:1:31:1:1:0:53.7:6:1:0:0 0/1:29:2:1,1:6,21:0.069:2,2:12.5:1:33.5:1:0.43103:3.32:42.5:4:0.069:0:1 -Y 13800083 . A G 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGTTCTGGAGTGGA;RSEQ=TGGACTCAAATAGAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:11:0:31:1:1:0:29:4:1:0:3 -Y 13800090 . C G 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTGGAGTGGAATGGACT;RSEQ=AAATAGAAAGGAATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:18:0:30.5:1:1:0:29:4:1:0:3 -Y 13800093 . A G 30 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGAGTGGAATGGACTCAA;RSEQ=TAGAAAGGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:30:1:1:0:29:4:1:0:3 -Y 13801072 . T A 28 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11921;SOR=0;LSEQ=TTGGATAGAACGGAATGGAA;RSEQ=TGAATGGAGTCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:18,19:0.0513:2,2:8:0:28.5:1:1:1.05:56.5:4:0.0541:0:5.5 0/0:73:0:0,0:40,33:0:2,0:7:1:29:1:1:0:46.8:35.5:1:0:3.8 -Y 13801073 . T TGAATGGAGTCGAATGGAATAGCCAAATGTAATGGACTCAAATG 29 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=2.000;MSILEN=1;SSF=0.13135;SOR=0;LSEQ=TGGATAGAACGGAATGGAAT;RSEQ=GAATGGAGTCGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:19,21:0.0476:2,0:18.5:1:29.2:1:0.4878:0:30:4:0.0476:0.0476:4 0/0:73:0:0,0:40,33:0:2,0:8:1:28.7:1:1:0:46.8:23.333:1:0:3.8 -Y 13801077 . T C 51 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1872;SOR=0.26669;LSEQ=TAGAACGGAATGGAATTGAA;RSEQ=GGAGTCGAATGGAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:4:2,2:19,20:0.093:2,2:13:0:25.8:1:1:1.05:52.8:3:0.0714:0:4.8 0/1:76:2:1,1:42,32:0.0263:2,2:10.5:1:28.5:1:1:1.30775:53.5:4:0.027:0:4.5 -Y 13801081 . GT TA 30 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12647;SOR=0;LSEQ=ACGGAATGGAATTGAATGGA;RSEQ=CGAATGGAATAGAATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:19,21:0.0465:2,2:18:0:30:1:1:1.10:52:4:0.0476:0:4 0/0:77:0:0,0:42,33:0:2,0:15.6:1:30.9:1:1:0:46.3:36.5:0.9733:0:3.9 -Y 13801082 . T A 171 DIFF0.2 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04245;SOR=0.25659;LSEQ=CGGAATGGAATTGAATGGAG;RSEQ=CGAATGGAATAGAATCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:40:19,21:1,0:0.9302:0,2:17:1:30.1:1:0.4878:0:49.6:80:0.9756:0:4 1/0:79:61:34,27:8,8:0.7722:2,2:16.7:1:29:1:0.78067:1.26:45.4:122:0.7722:0:3.9 -Y 13801084 . G T 180 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90316;LSEQ=GAATGGAATTGAATGGAGTC;RSEQ=AATGGAATAGAATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:41:20,21:1,0:0.9318:0,2:18.8:1:29.8:1:1:0:50:82:0.9318:0:3.9 1/1:80:74:41,33:1,3:0.925:2,2:18.3:1:29.1:1:0.33:3.67:45.9:36:0.9474:0:3.8 -Y 13801089 . G T 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54081;SOR=Inf;LSEQ=GAATTGAATGGAGTCGAATG;RSEQ=AATAGAATCAAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:22,24:0:2,0:22.4:1:31.5:1:1:0:49.1:92:1:0:3.8 0/1:85:2:1,1:45,38:0.0235:2,2:5:0:27.5:1:1:1.18184:45:4:0.0238:0:3 -Y 13801093 . A G 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5352;SOR=Inf;LSEQ=TGAATGGAGTCGAATGGAAT;RSEQ=GAATCAAATGGAATGGCATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:23,25:0:2,0:24.9:1:29.8:1:1:0:48.8:96:1:0:3.8 0/1:85:2:0,2:46,37:0.0235:2,0:12:0:32:0:0.20756:0:40:4:0.0235:0:7 -Y 13801098 . C G 47 v4;NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0478;SOR=0;LSEQ=GGAGTCGAATGGAATAGAAT;RSEQ=AAATGGAATGGCATCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:1,2:23,24:0.06:2,2:26.3:1:30:1:1:1.89276:40.3:6:0.0612:0:5 0/0:86:0:0,0:46,39:0:2,0:26.4:1:31:1:1:0:46.3:84:0.9882:0:3.9 -Y 13801099 . A G 33 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53306;SOR=Inf;LSEQ=GAGTCGAATGGAATAGAATC;RSEQ=AATGGAATGGCATCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:24,26:0:2,0:26.4:1:30.1:1:1:0:48.2:100:1:0:3.8 0/1:87:2:0,2:46,39:0.023:2,0:18:0:33:0:0.21919:0:40:4:0.0238:0:7 -Y 13801106 . A T 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53306;SOR=Inf;LSEQ=ATGGAATAGAATCAAATGGA;RSEQ=TGGCATCGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:24,26:0:2,0:26.8:1:30.7:1:1:0:48.2:100:1:0:3.8 0/1:87:2:0,2:45,40:0.023:2,0:25:0:31:1:0.23015:0:40:4:0.0238:0:7 -Y 13801109 . GC AT 31 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53013;SOR=Inf;LSEQ=GAATAGAATCAAATGGAATG;RSEQ=ATCGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:24,26:0:2,0:26.6:1:31.8:1:1:0:48.2:100:1:0:3.8 0/1:85:2:0,2:44,39:0.0235:2,0:29:0:31:0:0.22969:0:40:4:0.0238:0:6 -Y 13801113 . C A 24 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52149;SOR=Inf;LSEQ=AGAATCAAATGGAATGGCAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,26:0:2,0:24.6:1:30.7:1:1:0:48.1:102:0.9808:0:3.7 0/1:82:2:2,0:40,40:0.0244:2,0:13.5:1:24.5:1:0.49413:0:53.5:4:0.025:0:3.5 -Y 13801114 . G A 32 v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52149;SOR=Inf;LSEQ=GAATCAAATGGAATGGCATC;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,26:0:2,0:24.2:1:30.6:1:1:0:48.1:102:1:0:3.7 0/1:82:2:0,2:42,38:0.0244:2,0:33:0:32:0:0.23487:0:40:4:0.0247:0:6 -Y 13801126 . A C 184 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.79847;SOR=0.76426;LSEQ=ATGGCATCGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:32:13,19:4,1:0.8421:2,2:26:1:32.6:1:0.15896:5.58474:48.9:64:0.8421:0:4.5 1/1:76:61:30,31:6,7:0.8026:2,2:27.8:1:31.1:1:1:1.13:45.3:60:0.8:0:4.3 -Y 13801128 . G C 176 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.79954;SOR=0.8317;LSEQ=GGCATCGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:32:13,19:4,1:0.8421:2,2:24.3:1:30.8:1:0.15896:5.58474:48.9:64:0.8649:0:4.5 1/1:76:62:31,31:6,7:0.8158:2,2:26.6:1:29.7:1:1:1.16:45.1:19.667:0.8082:0:4.3 -Y 13801134 . G GAATGTGCTCGAATGGAATGGAATCGTATGGATTGATATCA 88 NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=6e-05;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:5,3:8,17:0.2286:2,2:11.6:1:29.4:1:0.21338:3.40:53.5:16:0.2286:0.2286:4.1 0/0:75:0:0,0:37,38:0:2,0:20.9:1:31.2:1:1:0:43.6:150:1:0:4.1 -Y 13801138 . G GTGCTC 152 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=12.000;MSILEN=5;SSF=1;SOR=0.95425;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:15:3,12:8,4:0.4545:2,2:21.1:1:32.2:1:0.02199:7.29602:46.9:30:0.4545:0:4.9 0/1:70:31:16,15:13,13:0.4429:2,2:23.5:1:30.8:1:1:1.07:42.7:62:0.4429:0:4.5 -Y 13801153 . G C 143 MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.52477;SOR=0.58669;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:15:3,12:3,0:0.8333:0,2:6.1:1:30.3:1:0.02451:0:46.1:30:0.8333:0:5.3 1/0:43:32:14,18:7,3:0.7442:2,2:6:1:28.7:1:0.27716:2.92226:43.2:31:0.7561:0:4.8 -Y 13801157 . T TGGATTGATATCAAATGGAAA 107 v4;NM4;MSI6 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.00959;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGAACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:5.9:1:31.2:1:1:0:44.2:26:1:0:4.5 0/1:32:12:3,9:9,7:0.375:2,2:9.9:1:30:1:0.13582:3.66753:44.7:24:0.375:0.375:4.3 -Y 13801161 . AT TTGATATCAAGTGGAAA 102 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=GGAATGGAATGAACTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:3,7:3,0:0.7692:0,2:9:1:30.8:1:0.06993:0:47.1:20:0.7692:0.7692:5 0/0:24:0:0,0:10,14:0:2,0:5.8:1:29:1:1:0:39.3:23:1:0.0417:4 -Y 13801163 . G GGAAACGAATAGAATGGAATGGAATCAGTTGGAGTA 28 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.05;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGAACTCGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,0:0.5:0,0:38:1:28.5:1:1:0:33:4:0.5:0.5:3 0/0:12:0:0,0:4,5:0:2,0:9.3:1:30.8:1:1:0:34:18:0.75:0.25:3.4 -Y 13801167 . T G 50 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.86755;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGAACTCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:2,0:0.3333:0,0:2:1:32:1:0.33333:0:56:2:0.3333:0.3333:3 0/1:10:3:0,3:6,1:0.3:2,0:6.3:1:31.7:1:0.03333:0:40:6:0.3:0.3:2.7 -Y 13801168 . G A 26 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0.6009;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGAACTCGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:2,0:0.3333:0,0:1:1:31:1:0.33333:0:56:2:0.3333:0.3333:3 0/1:9:2:2,0:3,4:0.2222:2,0:6.5:1:26:1:0.44444:0:26:4:0.2222:0:5 -Y 13801479 . T C 33 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAAGCGAATGGAATG;RSEQ=AATCAAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:25.5:1:33:1:1:0:45:4:1:0:4.5 -Y 13801484 . A C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCGAATGGAATGTAATC;RSEQ=AATGGAATGGAATGGAATAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:33:1:1:0:45:4:1:0:4.5 -Y 13801499 . G C 33 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TAATCAAATGGAATGGAATG;RSEQ=AATACAAAGGAATGGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:33.5:1:1:0:45:4:1:0:4.5 -Y 13802287 . A G 33 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGGACCAGAATGCA;RSEQ=TGGACTGGAATAAAGTGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:21:0:33:1:1:0:43:4:1:0:2.5 -Y 13802302 . G A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCAATGGACTGGAATAAA;RSEQ=TGGACACAAATGTAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:32:0:1:0:43:4:1:0:2.5 -Y 13802700 . ATC TGG 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTGCAATAGTATGGAATGGA;RSEQ=GAATGGAATGGACTAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16:1:29:1:1:0:60:4:1:0.5:3.5 -Y 13802743 . C G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGGACTCAAATGTAGTG;RSEQ=ATTGCAATGTAATTGATTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:5.5:1:30:1:1:0:60:4:1:0:3.5 -Y 13833050 . AC TG 32 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATGTAATGGACTTGAA;RSEQ=GAATGGACTGAAATAGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:43:0:32.5:0:1:0:20:2:1:0:6 1/1:2:2:2,0:0,0:1:0,0:18:1:32.3:1:1:0:32:4:1:0:4.5 -Y 13833059 . C A 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGACTTGAAACGAATGGA;RSEQ=TGAAATAGAATAGACTCAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:37:0:33:0:1:0:20:2:1:0:6 1/1:2:2:2,0:0,0:1:0,0:26:1:31:1:1:0:32:4:1:0:4.5 -Y 13833063 . A T 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAAACGAATGGACTGA;RSEQ=ATAGAATAGACTCAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:33:0:30:0:1:0:20:2:1:0:6 1/1:2:2:2,0:0,0:1:0,0:29:1:31:1:1:0:32:4:1:0:4.5 -Y 13833091 . T C 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTCAAAAGCAATGGTCT;RSEQ=GAATGGCATTTATTCGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:5:0:32:0:1:0:20:2:1:0:6 1/1:4:4:3,1:0,0:1:0,2:5:0:32.3:1:1:0:41:8:1:0:1 -Y 13833229 . CTG TTTC 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TTGCATTGTAATTGATTTGA;RSEQ=GAATGGAATCACATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:4,0:0,0:1:0,0:23.3:1:30.1:1:1:0:27.8:8:1:0.75:7 -Y 13833242 . A G 69 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGACTGGAATGGAATC;RSEQ=CATGGAATGTAATCAAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:11:0:32:0:1:0:40:2:1:0:8 1/1:5:5:5,0:0,0:1:0,0:12:1:30:1:1:0:28.8:10:1:0:7.2 -Y 13833257 . A G 44 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCACATGGAATGTAATC;RSEQ=AATGGAATGGAATTGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:26:0:32:0:1:0:40:2:1:0:8 1/0:5:3:3,0:2,0:0.6:0,0:20.7:1:28.3:1:1:0:23.7:6:0.6:0:6.7 -Y 13833271 . T G 65 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAATCAAATGGAATGGAAT;RSEQ=GAATGCAATAGAATGGAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:40:0:34:0:1:0:40:2:1:0:8 1/1:5:4:4,0:0,1:0.8:0,0:35.3:1:32.5:1:0.2:0:30:8:0.8:0:7.5 -Y 13833275 . T G 31 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAATGGAATGGAATTGAA;RSEQ=GCAATAGAATGGAGTAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:40:0:34:0:1:0:40:2:1:0:8 0/1:5:2:2,0:2,1:0.4:2,0:31:1:31:1:1:0:23.5:4:0.4:0:7 -Y 13833284 . A G 64 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATTGAATGCAATAGA;RSEQ=TGGAGTAGAATGGAATGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:31:0:34:0:1:0:40:2:1:0:8 1/0:7:4:3,1:2,1:0.5714:2,2:15:1:32:1:1:1.41:24.3:8:0.5714:0:7.5 -Y 13833286 . G T 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTGAATGCAATAGAAT;RSEQ=GAGTAGAATGGAATGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:29:0:32:0:1:0:40:2:1:0:8 1/1:7:6:5,1:0,1:0.8571:0,2:22.7:1:30.3:1:0.28571:0:28.3:12:0.8571:0:7.7 -Y 13833289 . G A 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGAATGCAATAGAATGGA;RSEQ=TAGAATGGAATGCAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:26:0:32:0:1:0:40:2:1:0:8 1/1:7:6:5,1:0,1:0.8571:0,2:22.7:1:30.3:1:0.28571:0:28.3:12:0.8571:0:7.7 -Y 13833304 . A G 50 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAGTAGAATGGAATGCA;RSEQ=TGGAATGGAATGGAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:0:0,0:12.7:1:32:0:1:0:38.3:6:1:0:7 0/1:24:3:2,1:12,9:0.125:2,2:21.3:1:32:1:1:1.48:35.3:6:0.125:0:7.3 -Y 13833307 . G A 131 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAGTAGAATGGAATGCAATG;RSEQ=AATGGAATGGAGTGGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:1:0,0:13.7:1:32:0:1:0:38.3:6:1:0:7 1/1:23:22:12,10:0,1:0.9565:0,2:15.2:1:29.6:1:0.47826:0:40.9:44:0.9565:0:6.6 -Y 13833315 . T C 140 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGCAATGGAATGGAA;RSEQ=GGAGTGGAATCGAGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:24.5:1:33.5:1:1:0:37.5:4:1:0:6.5 1/1:26:25:13,12:0,1:0.9615:0,2:19.8:1:30.2:1:1:0:42.3:50:0.9615:0:6.5 -Y 13833317 . G A 135 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=1;SOR=1.14495;LSEQ=GAATGCAATGGAATGGAATG;RSEQ=AGTGGAATCGAGTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:0.8:0,2:13.8:1:30:1:1:0:48:8:0.8:0:7.3 1/1:28:23:12,11:2,3:0.8214:2,2:19.6:1:30:1:1:1.61:43.1:22:0.8148:0:5.9 -Y 13833320 . T G 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCAATGGAATGGAATGGAG;RSEQ=GGAATCGAGTGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:0:2,0:12.5:1:29.5:1:1:0:46.8:12:1:0:5.5 0/1:42:2:1,1:20,20:0.0476:2,2:22.5:1:30.5:1:1:1:49.5:4:0.0488:0:6.5 -Y 13833329 . G GTGGACGGTAGGAATCGTACAGAACGGAAAGAAATGGAACGGAATGGAATGCACTCGAATGGAAAGGAGTCCAA 133 v4;NM4 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.02344;SOR=Inf;LSEQ=ATGGAATGGAGTGGAATCGA;RSEQ=TGGAATGGAATCGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:16.8:1:32:1:1:0:46.4:18:1:0:6 0/1:54:21:7,14:17,16:0.3889:2,2:19.6:1:30.5:1:0.26336:2.09531:45.8:42:0.3962:0.3889:6.6 -Y 13833333 . A T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAGTGGAATCGAGTGG;RSEQ=ATGGAATCGAATGGAATGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:20.2:1:30.1:1:1:0:46.4:18:1:0:6 0/1:54:2:1,1:23,29:0.037:2,2:21:1:26.5:1:1:1.26:33:4:0.037:0:7 -Y 13833349 . A G 179 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAATGGAATCGAATGGA;RSEQ=TGAACTGGAATGGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:2,7:0,0:1:0,2:27.4:1:32.3:1:1:0:46.4:18:1:0:6 1/1:53:49:22,27:0,2:0.9245:0,2:26:1:31.9:1:0.49961:0:44.9:98:0.9245:0:6.1 -Y 13833354 . C A 171 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCGAATGGAATGAA;RSEQ=TGGAATGGAATGGACACTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:2,7:0,0:1:0,2:28:1:30.9:1:1:0:46.4:18:1:0:6 1/1:51:51:23,28:0,0:1:0,2:25.2:1:30.3:1:1:0:45.1:50:1:0:6.1 -Y 13833370 . A G 138 d7;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.57091;SOR=0;LSEQ=TGAACTGGAATGGAATGGAC;RSEQ=CTAATGGAATGGACTGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:32.2:1:32:1:1:0:51.5:12:1:0:7.5 1/0:31:24:10,14:2,1:0.7742:2,2:28.1:1:30.3:1:0.56923:2.69485:45:23:0.7667:0:7 -Y 13833372 . T G 145 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53476;SOR=1.7662;LSEQ=AACTGGAATGGAATGGACAC;RSEQ=AATGGAATGGACTGGAAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,0:0.8333:0,2:29.6:1:30.8:1:1:0:49.8:10:0.8333:0:7.4 1/1:30:27:11,16:0,0:0.9:0,2:26.7:1:30.7:1:1:0:45.8:54:1:0:7 -Y 13833375 . T A 145 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGACACTAA;RSEQ=GGAATGGACTGGAAGAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1:0,2:27.2:1:31.2:1:1:0:51.5:12:1:0:7.5 1/1:27:26:11,15:0,0:0.963:0,2:24:1:30.9:1:1:0:46:52:0.963:0:7 -Y 13833390 . G C 145 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAATGGAATGGACTGGAA;RSEQ=AAAATGGAATCGAATTGATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:15:0:33.8:1:1:0:50.8:10:1:0:7.4 1/1:23:22:8,14:0,0:0.9565:0,2:14.5:1:32.7:1:1:0:45.7:44:0.9565:0:7 -Y 13833397 . G A 135 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGACTGGAAGAAAATG;RSEQ=AATCGAATTGATTAGAATCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1:0,0:8:0:32:0:1:0:50.8:10:1:0:7.4 1/1:21:21:8,13:0,0:1:0,2:8:1:30.9:1:1:0:45.5:42:1:0:6.9 -Y 13841112 . A T 28 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=AAGGAAGAGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:20:0:28.5:1:1:0:31:4:1:0:1 -Y 13842515 . A C 34 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGACTGCAGTGGATTGGA;RSEQ=TAGAATGGAATTCAATGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:6:0:34:0:1:0:38:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13842606 . TGGAACAAAATGGAAAGGAATGGACCGGAATGGAAAGGAAC T 62 d7;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATCGAATGGAATGGAC;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:1:0,0:6.5:1:31.3:1:1:0:29.3:8:1:1:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13842621 . A T 50 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTGGAACAAAATGGAA;RSEQ=GGAATGGACCGGAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:0.75:0,2:8.7:1:31.7:1:1:0:49:6:0.75:0:4.7 -Y 13842630 . C A 54 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAAATGGAAAGGAATGGA;RSEQ=CGGAATGGAAAGGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:3,1:0,0:0.8:0,2:17.5:1:27:1:1:0:42.8:3:0.75:0:5 -Y 13842638 . G T 44 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.38286;LSEQ=GAAAGGAATGGACCGGAATG;RSEQ=AAAGGAACGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:2,3:0.125:2,0:5:0:31:0:1:0:45:2:0.1667:0:4 0/1:18:3:2,1:9,6:0.1667:2,2:5:1:28:1:1:1.31:33.3:6:0.1667:0:4.7 -Y 13842641 . A T 100 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69415;SOR=0.62145;LSEQ=AGGAATGGACCGGAATGGAA;RSEQ=GGAACGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:4,2:0,1:0.6667:0,2:8.2:1:28.5:1:0.42857:0:41.2:12:1:0.1111:3.8 1/0:20:11:7,4:2,2:0.55:2,2:7.4:1:29:1:1:1.68:35.2:22:0.5789:0:4.4 -Y 13842646 . C T 87 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41471;SOR=3.4011;LSEQ=TGGACCGGAATGGAAAGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:6,3:0.0714:2,0:13:1:32:1:1:0:20:2:0.1111:0.0714:1 0/1:38:8:8,0:20,10:0.2105:2,0:6:1:29.3:1:0.08213:0:32.5:16:0.2162:0:5.3 -Y 13842648 . G C 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11246;SOR=0.21318;LSEQ=GACCGGAATGGAAAGGAACG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:10,2:0.1875:2,2:5.7:1:31.7:1:0.51648:2.32631:36:6:0.2:0.0625:3 0/1:44:2:2,0:30,11:0.0455:2,0:11.5:1:33.5:1:1:0:32:4:0.0455:0:5.5 -Y 13842696 . T A 47 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.61093;SOR=0.53663;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATCAACCCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:37,29:0.0294:2,2:14:0:29.5:1:1:1.27125:34:4:0.0303:0:3 0/1:188:3:2,1:100,85:0.016:2,2:43:1:30:1:1:1.70:32:6:0.016:0:5 -Y 13842697 . G T 61 v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.33019;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATCAACCCGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:38,30:0:2,0:31.2:1:31.9:1:1:0:36.7:136:1:0:3.2 0/1:191:5:2,3:99,85:0.0262:2,2:19.8:1:26.6:1:0.66518:1.74191:41.2:10:0.0263:0:2.8 -Y 13842701 . T C 34 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.06656;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATCAACCCGAGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:2,0:36,31:0.029:2,0:42:1:34:0:0.49787:0:40:4:0.029:0:6.5 0/0:197:0:0,0:104,93:0:2,0:29:1:29.1:1:1:0:38.3:48.25:1:0:3.4 -Y 13842703 . G A 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.16368;SOR=0.17058;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATCAACCCGAGTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:36,30:0.029:2,2:27:1:29.5:1:1:1.19677:32:4:0.029:0:6 0/0:199:1:0,1:101,89:0.005:2,0:14:0:32:0:0.4712:0:30:2:0.0051:0:7 -Y 13842707 . C T 29 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1659;SOR=0.17231;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=AACCCGAGTGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:2,0:35,30:0.029:2,0:35.5:1:29.5:1:0.49796:0:32:4:0.029:0:6.5 0/0:197:1:0,1:101,90:0.0051:2,0:42:0:29:0:0.47396:0:22:2:0.0052:0:7 -Y 13842709 . ACCCGAGTG TGCC 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGAATGGAATGGAATCA;RSEQ=GAATGGAATGGAGTGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:35,32:0:2,0:31.5:1:30.4:1:1:0:36.7:134:0.9571:0:3.1 0/1:199:2:1,1:102,93:0.0101:2,2:33.5:1:30.1:1:1:1.09626:40:4:0.0101:0:2.5 -Y 13842710 . C T 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57543;SOR=Inf;LSEQ=ATGGAATGGAATGGAATCAA;RSEQ=CCGAGTGGAATGGAATGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:36,32:0:2,0:31.3:1:31.9:1:1:0:36.7:136:1:0:3.2 0/1:200:4:2,2:100,92:0.02:2,2:34.8:1:24.5:1:1:1.08648:38:3:0.0155:0:2 -Y 13842711 . C G 88 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68453;SOR=2.49577;LSEQ=TGGAATGGAATGGAATCAAC;RSEQ=CGAGTGGAATGGAATGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:1:1,0:32,32:0.0143:2,0:7:0:32:0:1:0:24:2:0.0147:0:7 0/1:200:7:2,5:97,89:0.035:2,2:32.9:1:31.6:1:0.26925:2.71134:37.4:14:0.0359:0:5.9 -Y 13842715 . G C 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0665;SOR=0;LSEQ=ATGGAATGGAATCAACCCGA;RSEQ=TGGAATGGAATGGAGTGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:29,28:0.0286:2,2:18:0:31:1:1:1.03511:26.5:4:0.0323:0:4.5 0/0:200:0:0,0:93,86:0:2,0:29:1:30.7:1:1:0:38.6:28.833:0.9665:0:3.4 -Y 13842716 . T C 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5756;SOR=Inf;LSEQ=TGGAATGGAATCAACCCGAG;RSEQ=GGAATGGAATGGAGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:35,29:0:2,0:28.6:1:30.2:1:1:0:37.2:128:0.9846:0:3.2 0/1:198:4:2,2:90,86:0.0202:2,2:30:1:30:1:1:1.04626:44:8:0.0215:0:2.8 -Y 13842717 . GG AC 80 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.25821;LSEQ=GGAATGGAATCAACCCGAGT;RSEQ=AATGGAATGGAGTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:30,30:0.0286:2,2:13.5:1:32.3:1:1:1:55.5:4:0.0303:0:3.5 0/1:196:7:4,3:89,85:0.0357:2,2:28.1:1:28.6:1:1:1.27:43.7:14:0.0378:0:3.6 -Y 13842718 . G C 218 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55115;SOR=0.81077;LSEQ=GAATGGAATCAACCCGAGTG;RSEQ=AATGGAATGGAGTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:69:49:24,25:8,5:0.7101:2,2:29.3:1:32.3:1:0.5374:1.65304:37.4:98:0.7656:0:2.8 1/0:197:131:66,65:11,15:0.665:2,2:29.7:1:31:1:0.5225:1.38:38.8:42.667:0.7314:0:3 -Y 13842720 . A G 72 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.33275;SOR=Inf;LSEQ=ATGGAATCAACCCGAGTGGA;RSEQ=TGGAATGGAGTGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:35,32:0:2,0:27.3:1:30.6:1:1:0:37.1:134:1:0.0145:3.1 0/1:200:5:2,3:93,90:0.025:2,2:29.8:1:31.2:1:0.68077:1.54642:40.8:10:0.0269:0:4.8 -Y 13842722 . G C 90 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45438;SOR=2.85146;LSEQ=GGAATCAACCCGAGTGGAAT;RSEQ=GAATGGAGTGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:1:0,1:36,32:0.0143:2,0:16:0:29:0:0.47826:0:40:2:0.0145:0:6 0/1:201:8:2,6:95,87:0.0398:2,2:19:1:30.3:1:0.16288:3.25695:43.3:16:0.0419:0:4.1 -Y 13842723 . G C 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00468;SOR=0.06477;LSEQ=GAATCAACCCGAGTGGAATG;RSEQ=AATGGAGTGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:3,2:32,29:0.0725:2,2:19.2:1:33:1:1:1.35:31:10:0.0735:0.0145:2.2 0/0:201:1:1,0:94,96:0.005:2,0:44:0:27:0:0.49738:0:22:2:0.0052:0:3 -Y 13842724 . A C 30 v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69798;LSEQ=AATCAACCCGAGTGGAATGG;RSEQ=ATGGAGTGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:1:1,0:35,33:0.0143:2,0:42:0:34:0:1:0:34:2:0.0147:0:4 0/1:200:2:1,1:95,96:0.01:2,2:20.5:1:30:1:1:1.01:34:4:0.0108:0:4.5 -Y 13842725 . A T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATCAACCCGAGTGGAATGGA;RSEQ=TGGAGTGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:36,33:0:2,0:24.3:1:30.7:1:1:0:37.1:138:1:0.0143:3.2 0/1:199:2:1,1:93,95:0.0101:2,2:31:0:31:0:1:1.02:47:4:0.0106:0:2 -Y 13842726 . T G 60 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57529;SOR=Inf;LSEQ=TCAACCCGAGTGGAATGGAA;RSEQ=GGAGTGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:35,32:0:2,0:23.9:1:30.3:1:1:0:36.9:66:0.9851:0.0147:3.2 0/1:195:4:2,2:90,90:0.0205:2,2:34.8:1:30.3:1:1:1:60:8:0.0222:0:2.5 -Y 13842727 . GG AC 32 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06758;SOR=0;LSEQ=CAACCCGAGTGGAATGGAAT;RSEQ=AGTGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:36,31:0.029:2,2:15:0:32.3:1:1:1.15877:44:4:0.029:0:3 0/0:195:0:0,0:89,89:0:2,0:25.8:1:30.2:1:1:0:38.4:58.333:0.9459:0.0051:3.3 -Y 13842728 . G C 32 v4;pSTD;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0.71677;LSEQ=AACCCGAGTGGAATGGAATG;RSEQ=AGTGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:1:1,0:35,31:0.0145:2,0:16:0:34:0:1:0:40:2:0.0149:0:7 0/1:192:2:1,1:89,90:0.0104:2,2:28:0:32:1:1:1.01:38:4:0.0112:0:3 -Y 13842730 . G A 97 NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.03094;LSEQ=CCCGAGTGGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:10:6,4:28,26:0.1493:2,2:17.1:1:29.4:1:0.73822:1.39:34.7:20:0.1515:0.0149:4.8 0/0:188:1:1,0:77,79:0.0053:2,0:4:1:32:1:0.49682:0:37:2:0.0062:0.0053:0 -Y 13842731 . T A 133 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65373;SOR=1.39022;LSEQ=CCGAGTGGAATGGAATGGAG;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:4,2:31,30:0.0896:2,2:24.7:1:31:1:0.6747:1.92:46:12:0.0923:0:3.2 0/1:191:23:11,12:82,79:0.1204:2,2:21.7:1:29.6:1:0.82639:1.13157:39.7:46:0.1299:0:3.9 -Y 13842732 . G C 60 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00432;SOR=0;LSEQ=CGAGTGGAATGGAATGGAGT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:4:1,3:33,28:0.0597:2,2:21:1:30.3:1:0.34071:3.47184:33.3:8:0.0606:0:5.3 0/0:190:0:0,0:93,92:0:2,0:23.3:1:29.9:1:1:0:38.7:36:0.989:0.0053:3.2 -Y 13842733 . G A 48 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60415;SOR=0.50677;LSEQ=GAGTGGAATGGAATGGAGTG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:33,30:0.0303:2,2:36.5:1:29.5:1:1:1.09839:44:4:0.0303:0:4.5 0/1:193:3:1,2:92,92:0.0155:2,2:20.7:1:30.3:1:1:1.99286:22:6:0.0161:0:3 -Y 13842782 . G T 31 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATCAACCTGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:5,7:0:2,0:32.5:1:31.7:1:1:0:38.2:24:0.8571:0:4.8 0/1:53:2:1,1:22,25:0.0377:2,2:24.5:1:31.5:1:1:1.13:43.5:4:0.0392:0:4.5 -Y 13842787 . G A 27 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATCAACCTGAGTGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,8:0:2,0:33.6:1:30.8:1:1:0:39.7:26:1:0:4.7 0/1:51:2:1,1:22,25:0.0392:2,2:5:0:27.5:1:1:1.13:60:4:0.0408:0:2.5 -Y 13842792 . C T 26 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=AACCTGAGTGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:0:2,0:32.7:1:31.6:1:1:0:39.7:26:1:0:4.7 0/1:43:2:0,2:21,19:0.0465:2,0:38:1:26.5:1:0.4878:0:33:4:0.0488:0:6 -Y 13842801 . T C 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATGGAATCAACCTGAG;RSEQ=GGAATGGAATGGAATGCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,7:0:2,0:28.4:1:29.6:1:1:0:40.8:24:1:0:4.8 0/1:38:2:1,1:17,15:0.0526:2,2:21.5:1:33:1:1:1.12916:31:4:0.0556:0:6.5 -Y 13842802 . GG AC 25 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAATGGAATCAACCTGAGT;RSEQ=AATGGAATGGAATGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,7:0:2,0:27.3:1:31.2:1:1:0:39.7:24:0.9231:0:4.8 0/1:38:2:1,1:17,16:0.0526:2,2:18:1:25.3:1:1:1.06069:38:4:0.0571:0.0263:4.5 -Y 13842803 . G C 127 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.81542;LSEQ=GAATGGAATCAACCTGAGTG;RSEQ=AATGGAATGGAATGCAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:3,4:2,4:0.5385:2,2:27.7:1:30.1:1:1:1.45:44:6:0.5:0:5.7 0/1:37:18:11,7:5,11:0.4865:2,2:28.4:1:30.5:1:0.10047:3.33:40.1:17:0.5:0:5.1 -Y 13842804 . A C 52 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.55466;SOR=Inf;LSEQ=AATGGAATCAACCTGAGTGG;RSEQ=ATGGAATGGAATGCAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:22.9:1:29.8:1:1:0:38.6:28:1:0:4.5 0/1:38:3:0,3:17,18:0.0789:2,0:23.3:1:33.3:1:0.23826:0:39.7:6:0.0789:0:4.7 -Y 13842805 . AT GG 81 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.42338;SOR=2.88627;LSEQ=ATGGAATCAACCTGAGTGGA;RSEQ=GGAATGGAATGCAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:4,8:0.0714:2,0:32:0:28.5:0:0.38462:0:45:2:0.0769:0:5 0/1:38:7:5,2:12,19:0.1842:2,2:27:1:28.9:1:0.20741:3.81:48.3:14:0.1842:0:3.7 -Y 13842808 . G C 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAATCAACCTGAGTGGAATG;RSEQ=AATGGAATGCAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:0:2,0:21.6:1:31.2:1:1:0:38.5:26:1:0:4.2 0/1:37:2:1,1:15,19:0.0541:2,2:11.5:1:31:1:1:1.26:41.5:4:0.0571:0:3 -Y 13842815 . A C 52 v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.05551;SOR=0.10349;LSEQ=CCTGAGTGGAATGGAATGGA;RSEQ=TGCAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:3,5:0.25:2,2:17:1:33:1:1:1.18052:45.3:6:0.25:0:5 0/1:32:1:1,0:10,15:0.0313:2,0:26:0:30:0:0.42308:0:20:2:0.0313:0:3 -Y 13842816 . T A 33 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CTGAGTGGAATGGAATGGAA;RSEQ=GCAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:0:2,0:17.7:1:28.4:1:1:0:39.5:10:1:0:4.2 0/1:31:2:0,2:13,16:0.0645:2,0:22:1:33:0:0.49677:0:38.5:4:0.0645:0:4.5 -Y 13842818 . C A 50 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1096;SOR=0.20041;LSEQ=GAGTGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:2,3:0.2727:2,2:17:1:31.7:1:1:1.28664:45.7:6:0.2727:0:5.3 0/1:30:2:0,2:7,5:0.0667:2,0:10:0:31:1:0.46154:0:35.5:4:0.0741:0:4.5 -Y 13842821 . T C 31 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.72056;LSEQ=TGGAATGGAATGGAATGCAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:4,6:0.0909:2,0:15:0:31:0:1:0:24:2:0.0909:0:1 0/1:30:2:0,2:12,15:0.0667:2,0:17:1:31:0:0.49754:0:24:4:0.0667:0:1 -Y 13842828 . G C 71 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=1.10763;LSEQ=GAATGGAATGCAATGGAATG;RSEQ=AATGGAATGGAATGGGATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,6:0.2:2,2:13:1:21:1:1:2.65:42.5:1:0.1111:0:5.5 0/1:23:5:3,2:4,11:0.2174:2,2:9:1:30.6:1:0.2898:3.81:50.4:10:0.2174:0:3.8 -Y 13842831 . T TGGAATGCAAA 31 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGGAATGCAATGGAATGGAA;RSEQ=GGAATGGAATGGGATAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:0:2,0:9.3:1:30.9:1:1:0:40.3:14:1:0.1429:3.9 0/1:21:2:1,1:6,13:0.0952:2,2:15.5:1:31.3:1:1:2.08:59:4:0.1053:0.0952:4 -Y 13843684 . G C 30 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATGGAATGAAAAGGAAT;RSEQ=GAATAGAAAGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5:0:30.5:1:1:0:35:4:1:0:3.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13843709 . G T 29 d7;v4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.16667;SOR=0;LSEQ=AGAAAGGAATGGAATGGAAT;RSEQ=GAAAGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:21.5:1:29:1:1:1:35:4:0.6667:0:3.5 0/0:5:0:0,0:3,2:0:2,0:18.4:1:30.6:1:1:0:42:10:1:0:3.6 -Y 13843713 . AG CA 30 d7;v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AGGAATGGAATGGAATGGAA;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:30:0:30.8:1:1:1:31:4:0.5:0:3 0/0:5:0:0,0:2,2:0:2,0:21.8:1:29:1:1:0:38.5:8:1:0:3 -Y 13843718 . T C 29 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0.6977;LSEQ=TGGAATGGAATGGAAAGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:0.5:2,2:34:0:29:1:1:1:31:4:0.5:0:3 0/1:5:2:1,1:2,1:0.4:2,2:25.5:1:29.5:1:1:1.7321:37:4:0.4:0:2.5 -Y 13843723 . T C 29 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.46429;SOR=Inf;LSEQ=TGGAATGGAAAGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:0:2,0:39:0:24.5:1:1:0:31:1:0.5:0:3 0/1:5:2:1,1:2,1:0.4:2,2:20.5:1:29:1:1:1.7321:37:4:0.4:0:2.5 -Y 13843731 . AATG TACGGAATA 29 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.5;SOR=Inf;LSEQ=AAAGGAATGGAATGGAATGG;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:33:1:25:1:1:0:32.3:2:1:0:3.7 0/1:6:2:1,1:2,2:0.3333:2,2:30.5:1:29.1:1:1:1:40:4:0.3333:0:3.5 -Y 13843737 . A G 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.5;SOR=Inf;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:24:1:31:1:1:0:32.3:6:1:0:3.7 0/1:6:2:1,1:2,2:0.3333:2,2:26:1:30:1:1:1:48:4:0.3333:0:4 -Y 13843738 . T A 29 pSTD;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.08333;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:0.6667:0,2:26:0:29.5:1:1:0:31:4:0.6667:0:3 0/0:6:0:0,0:3,3:0:2,0:22.5:1:27.7:1:1:0:41.7:12:1:0:3.3 -Y 13843745 . G T 26 d7;v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:16:1:27:1:1:0:32.3:2:1:0:3.7 1/0:4:2:1,1:1,1:0.5:2,2:26:1:26:1:1:1:48:4:0.5:0:4 -Y 13843748 . T C 31 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:13:1:29.3:1:1:0:32.3:6:1:0:3.7 1/0:4:2:1,1:1,1:0.5:2,2:26:0:31:1:1:1:40:4:0.5:0:3.5 -Y 13843750 . G A 30 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAGTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:0:2,0:11:1:30.3:1:1:0:32.3:6:1:0:3.7 1/0:4:2:1,1:0,0:0.5:0,2:24:0:30:1:1:0:40:4:0.5:0:3.5 -Y 13843773 . A ATATTCCGAGT 31 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAGTGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0.5:0,2:19:1:31.1:1:1:0:40:4:0.5:0.5:3.5 -Y 13843959 . G GGAATGGAATGGAATGGAATGCCAATGGTTTGGAATGGATTCAACTTGAATATAATT 28 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=13.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:0.3333:2,2:35:1:28.4:1:1:1:21:4:0.3333:0.3333:6 -Y 13843985 . GA AT 54 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=ATGGAATAGACTGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:12:4:2,2:5,3:0.3333:2,2:37:1:27.4:1:1:1.59564:42:8:0.3333:0:4.3 -Y 13843988 . T C 63 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATAGACTGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:12:4:2,2:2,2:0.3333:2,2:39:1:31.5:1:1:1:42:8:0.3333:0:4.3 -Y 13843997 . C A 61 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGGAATGGAATAGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:13:4:2,2:5,4:0.3077:2,2:48:1:30.5:1:1:1.22862:42:8:0.3333:0:4.3 -Y 13844004 . G A 29 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATAGACTGGAAT;RSEQ=GAATGGAATGGAAAGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:5,5:0.1429:2,2:22:0:29:1:1:1:50:4:0.1429:0:3 -Y 13844005 . G GAACGA 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATAGACTGGAATG;RSEQ=AATGGAATGGAAAGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:6,5:0.1429:2,2:44:1:28.9:1:1:1.18321:41:4:0.1538:0:4 -Y 13844008 . T C 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATAGACTGGAATGGAA;RSEQ=GGAATGGAAAGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:6,6:0.1429:2,2:37.5:1:30.5:1:1:1:43:4:0.1429:0:5.5 -Y 13844010 . G A 28 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATAGACTGGAATGGAATG;RSEQ=AATGGAAAGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:6,6:0.1429:2,2:35.5:1:28.5:1:1:1:43:4:0.1429:0:5.5 -Y 13844012 . A C 31 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATAGACTGGAATGGAATGGA;RSEQ=TGGAAAGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:6,6:0.1429:2,2:14:0:31.5:1:1:1:50:4:0.1429:0:3 -Y 13844018 . A C 59 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:4:2,2:3,3:0.2857:2,2:41.8:1:29.8:1:1:1:38:8:0.2857:0:5.8 -Y 13844023 . T C 55 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAAAGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:4:2,2:5,5:0.2857:2,2:41.5:1:27.8:1:1:1:38:8:0.2857:0:5.8 -Y 13844054 . G A 30 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:15:1:30:1:1:1.73:45:4:0.4:0:5.5 -Y 13844063 . T C 29 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAAAGGTAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:0.4:2,2:16.5:1:29.5:1:1:1.73:31:4:0.4:0:6 -Y 13844064 . G T 30 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAAAGGTATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,1:0.4:2,2:5:1:30:1:1:1:45:4:0.4:0:5.5 -Y 13844068 . T C 30 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAAAGGTATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:0,1:0.6667:0,0:15:1:30:1:1:0:35.5:4:0.6667:0:6.5 -Y 13844567 . A G 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAAATGGAACAGAGTGGA;RSEQ=TCGAGTGGAACGGAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:6:0:32.5:1:1:0:36:4:1:0:2 -Y 13844578 . C A 32 d7;v4;pSTD;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTGGAATCGAGTGGAA;RSEQ=GGAATAGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:32.5:1:1:0:36:4:1:0:2 -Y 13850258 . A C 31 d7;v4;pSTD;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGACTCGAATGGAATGG;RSEQ=AACGAAAGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12:0:31:1:1:0:47:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13850290 . T A 31 d7;v4;pSTD;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:12:0:31.5:1:1:0:47:4:1:0:2 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13851242 . A G 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACGAATGGAATGGAATC;RSEQ=AATGGAATGCAATCCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:15.5:1:30:0:1:0:60:4:1:0:1.5 -Y 13851603 . T A 59 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAGAATAGACTGGAATGG;RSEQ=ATTGAATGGAATCGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:10:1:31:0:1:0:50:4:1:0:8 1/1:4:4:3,1:0,0:1:0,2:8.3:1:29.5:1:1:0:35:8:1:0:8 -Y 13851606 . T G 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATAGACTGGAATGGTAT;RSEQ=GAATGGAATCGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:13:1:33.5:1:1:0:50:4:1:0:8 1/1:4:4:3,1:0,0:1:0,2:11.3:1:33.3:1:1:0:35:8:1:0:8 -Y 13851610 . T G 66 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACTGGAATGGTATTGAA;RSEQ=GGAATCGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:17:1:33.5:1:1:0:50:4:1:0:8 1/1:5:4:3,1:0,1:0.8:0,2:15.3:1:33.3:1:0.4:0:35:8:0.8:0:8 -Y 13851616 . C G 82 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55944;SOR=2.75172;LSEQ=GGAATGGTATTGAATGGAAT;RSEQ=GAATGGAATGGAATTGACCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:0,1:0.6667:0,0:13:1:32.8:1:0.2:0:55:8:0.8:0:6.8 1/1:7:6:5,1:0,0:0.8571:0,2:15.5:1:32:1:1:0:43.3:12:0.8571:0:7.3 -Y 13851632 . G T 27 v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=GAATCGAATGGAATGGAATT;RSEQ=ACCCAAATGTAATAGACTTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:5,6:0.1429:2,0:12.5:1:27.5:1:0.48718:0:27:4:0.1538:0:6.5 0/0:14:0:0,0:8,6:0:2,0:20.5:1:30.7:1:1:0:46.6:28:1:0:5.7 -Y 13851634 . C A 117 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.22249;LSEQ=ATCGAATGGAATGGAATTGA;RSEQ=CCAAATGTAATAGACTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:5,8:0,0:0.9286:0,2:16.9:1:30.4:1:1:0:46.5:26:1:0:5.5 1/1:17:16:10,6:0,0:0.9412:0,2:19.6:1:29.4:1:1:0:50:32:0.9412:0:5.4 -Y 13851646 . A G 137 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTGACCCAAATGTAAT;RSEQ=GACTTGAAAGGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:6,9:0,0:1:0,2:23.7:1:31.6:1:1:0:47.7:30:1:0:5.5 1/1:23:23:12,11:0,0:1:0,2:22.7:1:30.4:1:1:0:50.9:46:1:0:4.8 -Y 13851655 . A T 141 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36364;SOR=Inf;LSEQ=CCAAATGTAATAGACTTGAA;RSEQ=GGAATGGAATCAAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:5,10:0,0:0.9375:0,2:29.4:1:30.5:1:1:0:47.7:30:1:0:5.3 1/1:28:28:15,13:0,0:1:0,2:22.9:1:29.4:1:1:0:50.4:56:1:0:4.4 -Y 13851668 . A T 146 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAAAGGAATGGAATCA;RSEQ=ATAGAATGGACTCAAAAGCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:7,12:0,0:1:0,2:23.1:1:29.7:1:1:0:48.1:38:1:0:4.5 1/1:34:34:17,17:0,0:1:0,2:20.4:1:28.7:1:1:0:51.1:68:1:0:3.9 -Y 13851695 . A T 64 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCAAAAGCAATGGTC;RSEQ=CAAATGGAATTTATTTGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:14.5:1:32:1:1:0:42.3:8:1:0:7.5 1/1:3:3:1,2:0,0:1:0,2:5.3:1:29:1:1:0:60:6:1:0:4 -Y 13851697 . A G 64 d7;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GACTCAAAAGCAATGGTCAC;RSEQ=AATGGAATTTATTTGAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:1:0,2:13.5:1:32.3:1:1:0:42.3:8:1:0:7.5 1/0:2:1:0,1:1,0:0.5:0,0:9:0:32:0:1:0:60:2:0.5:0:4 -Y 13851701 . G T 50 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAGCAATGGTCACAAAT;RSEQ=GAATTTATTTGAATAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:15.3:1:31.7:1:1:0:47.3:6:1:0:7.3 1/1:1:1:0,1:0,0:1:0,0:5:0:31:0:1:0:60:2:1:0:4 -Y 13851974 . A T 28 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATGGAATCGAATGGAATGGA;RSEQ=TCAAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:3,1:0.2857:2,2:8:0:28:1:1:2.44949:52:4:0.2857:0:5 -Y 13851976 . CA AG 27 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCGAATGGAATGGAAT;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:2:1,1:3,2:0.25:2,2:12:1:27:1:1:1.41418:50:4:0.3333:0:4 -Y 13851977 . A G 68 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCGAATGGAATGGAATC;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:8:5:3,2:0,0:0.625:0,2:12.2:1:29.6:1:1:0:44.6:10:1:0:5.8 -Y 13851986 . G T 26 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATCAAATGGAAT;RSEQ=GAATGGAATGGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:15:2:1,1:6,6:0.1333:2,2:21:1:26.5:1:1:1:50:4:0.1538:0:4 -Y 13851989 . A C 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATGGAATCAAATGGAATGGA;RSEQ=TGGAATGGAATGGAATCAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:16:2:1,1:7,6:0.125:2,2:23:0:31:1:1:1.1547:52:4:0.125:0:5 -Y 13852006 . C T 56 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=AATTCGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:17:4:2,2:6,5:0.2353:2,2:28.8:1:28.3:1:1:1.18545:40.5:8:0.2667:0:4.8 -Y 13852009 . T C 74 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGGAATGGAATCAA;RSEQ=TCGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:16:6:3,3:3,4:0.375:2,2:28.8:1:28.7:1:1:1.30:43.7:5:0.4167:0:5.2 -Y 13852011 . C T 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATCAATT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:16:2:1,1:6,7:0.125:2,2:38:1:29.5:1:1:1.15:41.5:4:0.1333:0:7 -Y 13852014 . A T 60 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGGAATCAATTCGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:15:4:2,2:4,5:0.2667:2,2:30.5:1:30:1:1:1.23:49.8:8:0.2857:0:3.3 -Y 13852017 . G T 54 d7;v4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATCAATTCGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:15:5:2,3:5,4:0.3333:2,2:33.6:1:23.4:1:1:1.79176:45.4:4:0.2857:0:3.8 -Y 13852025 . TG A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAATTCGAATGGAATGGAA;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:7:0:31:0:1:0:47:2:1:0:3 0/1:17:2:1,1:6,8:0.1176:2,2:49:1:30:1:1:1.31:41.5:4:0.1333:0:6 -Y 13852040 . T C 28 d7;v4;MSI6 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.02857;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:18.5:1:29:1:1:0:43.5:4:1:0:3 0/1:19:2:1,1:7,9:0.1053:2,2:32.5:1:28:1:1:1.27:31:4:0.1053:0:4.5 -Y 13852050 . T G 30 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.00585;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:28.5:1:30.5:1:1:0:43.5:4:1:0:3 0/0:17:0:0,0:7,10:0:2,0:22.4:1:28.6:1:1:0:37.9:34:1:0:4.8 -Y 13852071 . CAACTG TAACCTGAACA 31 pSTD;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=0.01099;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATAGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:29:0:31.4:1:1:0:43.5:4:1:0:3 0/0:12:0:0,0:5,7:0:2,0:14.3:1:29.8:1:1:0:34.5:24:1:0:4.8 -Y 13852076 . G C 60 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATCAACT;RSEQ=GAATGGAATAGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:5:3,2:0,1:0.8333:0,2:20:1:26.2:1:1:0:30.6:4:0.8:0:4.8 -Y 13852082 . G C 43 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAATGGAATCAACTGGAATG;RSEQ=AATAGAATGGAATGGAACGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:23:0:32.5:1:1:0:43.5:4:1:0:3 1/0:4:3:1,2:0,1:0.75:0,2:25.7:1:27.3:1:1:0:28.3:2:0.6667:0:5.3 -Y 13852100 . C T 46 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TGGAATAGAATGGAATGGAA;RSEQ=GGAAAGGACCCAAACGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:5:0:32:1:1:0:43.5:4:1:0:3 1/1:3:3:1,2:0,0:1:0,2:7.7:1:29.3:1:1:0:28.3:6:1:0:5.3 -Y 13853242 . G T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGAATGGCATGGAAT;RSEQ=GAATGGACCCAAATGTAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:8:0:31:0:1:0:22:4:1:0:7 -Y 13853251 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCATGGAATGGAATGGAC;RSEQ=CAAATGTAGTGGAAACAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:17:0:32:1:1:0:22:4:1:0:7 -Y 13853259 . AG TA 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGAATGGACCCAAATGT;RSEQ=TGGAAACAAAAGGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:26:0:31:0:1:0:22:4:1:0:6 -Y 13853266 . A T 31 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACCCAAATGTAGTGGAA;RSEQ=CAAAAGGAATGGACTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:32:0:31:0:1:0:22:4:1:0:6 -Y 13853271 . A G 32 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATGTAGTGGAAACAAA;RSEQ=GGAATGGACTCAAATAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:29.5:1:32.5:1:1:0:22:4:1:0:6 -Y 13866464 . G A 29 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATCGAACTGAATGGAAT;RSEQ=GAATGGAAAAGAATGGACGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:10:0:29:0:1:0:52:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13866490 . C G 31 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAGAATGGACGTCAATG;RSEQ=AATGGAGTCGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:36:0:31:1:1:0:52:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13866504 . G A 26 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATGCAATGGAGTCGAAT;RSEQ=GAATGGAACCGAATGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:38.5:1:26:1:1:0:52:4:1:0:6 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13866520 . CA GT 26 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAACCGAATG;RSEQ=ATGGAATTGAAGGGAATTGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:1:0,0:21.5:1:26:1:1:0:52:4:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13866539 . T C 25 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATGGAATTGAAGGGAAT;RSEQ=GAAAGGAATAGAATAGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:25.5:1:1:0:42:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13866548 . T A 28 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGAAGGGAATTGAAAGGAA;RSEQ=AGAATAGAATGGAGTGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:9.5:1:28.5:1:1:0:42:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13866929 . TGAATAGAAA CGAAT 29 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAGATTAATGGAAAGATAT;RSEQ=GGAATGGAATGAACTCAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:1:0,0:9.5:1:29.2:1:1:0:33.5:4:1:0.5:5 -Y 13866949 . GA TG 73 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATAGAAAGGAATGGAAT;RSEQ=ACTCAAATGGAATGGACTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:7:1:31:1:1:0:37:4:1:0.5:4.5 1/1:5:5:4,1:0,0:1:0,2:15.8:1:31.5:1:1:0:35.8:10:1:0:3.2 -Y 13866955 . A G 71 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAGGAATGGAATGAACTC;RSEQ=AATGGAATGGACTGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:11:1:32.5:1:1:0:37:4:1:0:4.5 1/1:6:5:4,1:1,0:0.8333:0,2:17.8:1:30.6:1:1:0:34.2:10:0.8333:0:4.4 -Y 13866978 . T C 140 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08895;SOR=7.67408;LSEQ=TGGAATGGACTGGAATGGAA;RSEQ=GGACTCGAATGGAATGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:4,4:2,1:0.7273:2,2:18.3:1:32.4:1:1:1.87936:40.3:16:0.7273:0:6.6 1/1:23:22:15,7:1,0:0.9565:0,2:21.3:1:31.4:1:1:0:41.2:44:0.9565:0:5.8 -Y 13867011 . TCTGGAAT ATTGAAC 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.50823;LSEQ=AATGGACTGGAATGGAATGG;RSEQ=GGAATGGACTGCAGAGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:6,5:0,0:0.9167:0,2:36.5:1:30.9:1:1:0:41.7:22:0.9167:0.0833:3.9 1/1:26:22:11,11:1,0:0.8462:0,2:32.6:1:28.9:1:1:0:41.6:44:0.8462:0.2308:4.3 -Y 13867030 . C G 135 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGGAATGGAATGGACTG;RSEQ=AGAGGAATGGTCTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:5,5:0,0:1:0,2:30.4:1:31.5:1:1:0:43.9:20:1:0:6.9 1/1:25:23:10,13:1,1:0.92:2,2:26.3:1:30:1:1:1.28628:40.7:46:0.92:0:6.6 -Y 13867041 . T A 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATGGACTGCAGAGGAATGG;RSEQ=CTCGAATGGAATGGAAACGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:5,5:0,0:1:0,2:19.4:1:30.2:1:1:0:43.9:20:1:0:6.9 1/1:24:23:9,14:1,0:0.9583:0,2:21.2:1:28.3:1:0.41667:0:41:46:0.9583:0:6.7 -Y 13867045 . G GAATGGAATGGAAACGAATGGAATGGAATTGAATGGAATGGACTTGAAATGGATAAGAAATGAAAAGAATGTAATGGAATCGGATGGAATGGAATTGAATGTATTGGAGTCGAGTAGAACAGAATTGAATGGAATGGCATCA 79 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=42;MSI=3.000;MSILEN=1;SSF=0.14783;SOR=Inf;LSEQ=GACTGCAGAGGAATGGTCTC;RSEQ=AATGGAATGGAAACGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:0:2,0:15.7:1:31.2:1:1:0:45.7:20:1:0:6.6 0/1:24:6:0,6:9,9:0.25:2,0:33.8:1:30.8:1:0.05185:0:36.7:12:0.25:0.25:4.7 -Y 13867053 . T A 128 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.34216;LSEQ=AGGAATGGTCTCGAATGGAA;RSEQ=GGAAACGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:3,4:0,1:0.875:0,2:12.4:1:31.3:1:1:0:43.3:14:0.875:0:7.1 1/1:21:19:7,12:1,1:0.9048:2,2:18.8:1:30.2:1:1:1.66897:38.5:38:0.9048:0:6.7 -Y 13867062 . A G 118 d7;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.69906;LSEQ=CTCGAATGGAATGGAAACGA;RSEQ=TGGAATGGAATTGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:0.8:0,2:9.5:1:31.5:1:1:0:39.8:8:0.8:0:7.8 1/1:16:14:3,11:1,1:0.875:2,2:15.9:1:31.2:1:0.45:3.31654:37:28:0.875:0:6.6 -Y 13867074 . T G 88 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=GGAAACGAATGGAATGGAAT;RSEQ=GAATGGAATGGACATTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:6:0:31:0:1:0:40:2:1:0:3 1/0:9:7:0,7:1,1:0.7778:2,0:11.9:1:31.4:1:0.22222:0:39:14:0.7778:0:5.7 -Y 13867077 . A G 51 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACGAATGGAATGGAATTGA;RSEQ=TGGAATGGACATTAAAGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:0:0,0:3:0:33:0:1:0:40:2:1:0:3 0/1:8:3:0,3:0,5:0.375:0,0:9:0:32.7:1:1:0:38.7:6:0.375:0:5.7 -Y 13867279 . T C 65 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGAGTGTAATTGAAAGA;RSEQ=ATCGAATGGAATGGAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:4,0:0,0:1:0,0:6.8:1:32.5:1:1:0:41.5:8:1:0:6 -Y 13867296 . T C 58 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AGATATCGAATGGAATGGAA;RSEQ=GGACTCGAATGGAATGGCCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:1:0,0:14:0:33:0:1:0:59:2:1:0:8 1/0:8:4:2,2:4,0:0.5:0,2:11.5:1:29.3:1:0.42857:0:51:8:0.5:0:7.8 -Y 13867297 . G T 49 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GATATCGAATGGAATGGAAT;RSEQ=GACTCGAATGGAATGGCCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:15:0:31:0:1:0:59:2:1:0:8 0/1:8:3:3,0:2,2:0.375:2,0:24.7:1:31.3:1:0.42857:0:45.3:6:0.375:0:6 -Y 13867314 . C A 85 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGACTCGAATGGAATGG;RSEQ=CTGGAATGGAATGAACTCGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:24:1:31.5:1:1:0:39.5:4:1:0:7 1/1:8:8:6,2:0,0:1:0,2:31.9:1:28.6:1:1:0:46.3:16:1:0:6.9 -Y 13867326 . T C 59 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.46667;SOR=Inf;LSEQ=TGGAATGGCCTGGAATGGAA;RSEQ=GAACTCGAATGGAATGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:36:1:31.5:1:1:0:39.5:4:1:0:7 1/0:8:4:4,0:2,2:0.5:2,0:22.3:1:29.8:1:0.42857:0:41.5:8:0.5:0:6 -Y 13867328 . AACTCGAAT GATTGAAC 78 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GAATGGCCTGGAATGGAATG;RSEQ=GGAATGGACTGGAGTGGGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:29:1:29.8:1:1:0:35.7:6:1:0.3333:5.3 1/0:11:7:2,5:0,0:0.6364:0,2:30.4:1:28:1:1:0:44.6:14:0.6364:0.2727:5.9 -Y 13867351 . T A 90 d7;v4;NM4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51648;SOR=0;LSEQ=TCGAATGGAATGGACTGGAG;RSEQ=GGGATGGACTCGAATGGAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:24.3:1:29:1:1:0:35.7:6:1:0:6.7 1/0:12:8:2,6:2,2:0.6667:2,2:22:1:30.1:1:0.54747:2.71347:44:16:0.6667:0:6.9 -Y 13867354 . G A 108 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGAATGGACTGGAGTGG;RSEQ=ATGGACTCGAATGGAAAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:23.3:1:28.3:1:1:0:35.7:6:1:0:6.7 1/1:14:13:5,8:0,0:0.9286:0,2:19:1:29.2:1:1:0:39.2:26:0.9286:0:4.9 -Y 13867380 . A G 100 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGAATGGAAAGGAAACGA;RSEQ=TTGAATAGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:24:0:32:0:1:0:28:2:1:0:6 1/1:9:9:3,6:0,0:1:0,2:17.3:1:31.6:1:1:0:39.6:18:1:0:5.2 -Y 13867382 . T G 78 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATGGAAAGGAAACGAAT;RSEQ=GAATAGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:22:0:31:0:1:0:28:2:1:0:6 1/0:8:6:1,5:1,1:0.75:2,2:15.7:1:30.2:1:0.46429:3.87298:31.7:12:0.75:0:5.2 -Y 13867387 . A G 81 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAGGAAACGAATTGAAT;RSEQ=GAATGGAATGGAATGGAAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:17:0:32:0:1:0:28:2:1:0:6 1/1:6:6:1,5:0,0:1:0,2:16.7:1:31.7:1:1:0:42.3:12:1:0:5.3 -Y 13867395 . A G 51 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AACGAATTGAATAGAATGGA;RSEQ=TGGAATGGAAACAATACAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:9:0:33:0:1:0:28:2:1:0:6 1/0:6:3:1,2:0,3:0.5:0,2:9:0:32.7:1:1:0:48.7:6:0.5:0:5.3 -Y 13868013 . A T 28 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:12.5:1:28.5:1:1:0:36:4:0.5:0:4.5 -Y 13868021 . G C 30 d7;v4;NM4;MSI6;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:20.5:1:30.5:1:1:0:36:4:0.5:0:4.5 -Y 13868040 . A G 62 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAA;RSEQ=GAATAGAATGGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:1,3:0,0:1:0,2:39.3:1:31.3:1:1:0:31:8:1:0:5.5 -Y 13868070 . A G 32 d7;v4;pSTD;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGAATCGGATGGAAC;RSEQ=GAATGGAATGGAGTTGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:0.5:0,2:11:0:32:0:1:0:36:4:0.5:0:4.5 -Y 13868369 . T TCGAATGGAATGGAATGGAATGGAACGGAACTACGGAATAGAATGGAATGGAATTAACC 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=3.000;MSILEN=1;SSF=0.02098;SOR=0;LSEQ=TAGAATCGAATTGTATGGCA;RSEQ=CGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:1,1:0.75:2,2:15.2:1:29:1:1:1:43.3:12:0.75:0.75:3.3 0/0:5:0:0,0:3,2:0:2,0:6.8:1:27.4:1:1:0:37:4:1:0:3.4 -Y 13868375 . G A 68 InIns STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.00145;SOR=0;LSEQ=CGAATTGTATGGCATCGAAT;RSEQ=GAATGGAATGGAATGGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:3,2:10,6:0.2381:2,2:5.6:1:29.6:1:1:1.10551:33.8:10:0.2381:0:3.2 0/0:51:0:0,0:11,15:0:2,0:2.4:1:29.6:1:1:0:40.3:25:0.5:0:2.4 -Y 13868378 . A G 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATTGTATGGCATCGAATGGA;RSEQ=TGGAATGGAATGGAACGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:0:2,0:7.6:1:30.5:1:1:0:35.9:23:1:0:2.1 0/1:54:2:1,1:29,23:0.037:2,2:8:0:32:1:1:1.25542:50:4:0.037:0:2 -Y 13868390 . G T 31 v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.08205;SOR=0;LSEQ=CGAATGGAATGGAATGGAAT;RSEQ=GAACGGAACGGAACGGAACG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:12,11:0.0741:2,2:21:0:31:1:1:1.0871:40:4:0.0769:0:4 0/0:66:0:0,0:35,31:0:2,0:17:1:30:1:1:0:40.7:65:1:0:2.5 -Y 13868394 . C T 130 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.81857;SOR=0.8843;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAACGGAACGGAACGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:11:5,6:8,8:0.3929:2,2:21.5:1:31.1:1:1:1.19191:37.3:22:0.44:0:2.5 0/1:66:24:12,12:22,18:0.3636:2,2:22.2:1:28.5:1:0.79775:1.21838:37.2:23:0.3538:0:2.8 -Y 13868396 . G C 34 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAATGGAACG;RSEQ=AACGGAACGGAACGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:24.2:1:32:1:1:0:37:56:1:0:2.1 0/1:66:2:1,1:34,30:0.0303:2,2:23:0:34:0:1:1.13118:50:4:0.0308:0:2 -Y 13868399 . C T 52 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0.84035;LSEQ=TGGAATGGAATGGAACGGAA;RSEQ=GGAACGGAACGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:13,13:0.0714:2,2:27:1:30.5:1:1:1:39:4:0.0741:0:3 0/1:66:4:2,2:32,27:0.0606:2,2:27:1:26.3:1:1:1.18198:36.5:3:0.0462:0:3.5 -Y 13868400 . G A 49 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.55274;SOR=Inf;LSEQ=GGAATGGAATGGAACGGAAC;RSEQ=GAACGGAACGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:27.8:1:31.3:1:1:0:37:56:1:0:2.1 0/1:67:3:1,2:32,30:0.0448:2,2:30.7:1:31.3:1:0.61319:2.10935:38.7:6:0.0455:0:2.3 -Y 13868408 . A T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=ATGGAACGGAACGGAACGGA;RSEQ=CGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:0:2,0:34:1:30.6:1:1:0:37:56:1:0:2.1 0/1:68:2:1,1:34,31:0.0294:2,2:31:1:26.5:1:1:1.09526:50:4:0.0299:0:2 -Y 13868449 . T C 46 v4;NM4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.54835;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATCGACCCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,12:0:2,0:7.1:1:30.3:1:1:0:37.5:44:1:0.1304:1.9 0/1:52:3:2,1:23,26:0.0577:2,2:9:1:29.3:1:0.60294:2.23:46.7:6:0.0577:0:4 -Y 13868452 . A C 74 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.16325;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=ATGGAATCGACCCAAAAGTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:5,9:0.125:2,2:5:0:31:1:1:1.73:56:4:0.1333:0:3 0/1:35:5:3,2:12,17:0.1429:2,2:5:0:32:1:0.63435:2.08:44.6:10:0.1429:0:3.4 -Y 13868454 . T A 28 v4;pSTD;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=0.11594;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATCGACCCAAAAGTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:5,9:0.125:2,2:5:0:28.5:1:1:1.73:48:4:0.1429:0:1 0/0:30:0:0,0:13,16:0:2,0:5.9:1:29.6:1:1:0:42.8:28:0.9655:0:2.8 -Y 13868491 . G C 49 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.4;SOR=0;LSEQ=TAATGGACTCAAATGGAATG;RSEQ=ACTCAAATAGAAAGGACTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:14.3:1:31.3:1:1:0:39.3:6:0.75:0:6.7 0/0:2:0:0,0:1,1:0:2,0:7:1:29:1:1:0:23:4:1:0:7.5 -Y 13868493 . C G 49 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATGGACTCAAATGGAATGGA;RSEQ=TCAAATAGAAAGGACTCGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:16.3:1:31.3:1:1:0:39.3:6:0.75:0:6.7 0/0:2:0:0,0:1,1:0:2,0:9:1:28.5:1:1:0:23:4:1:0:7.5 -Y 13868504 . A T 27 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGGAATGGACTCAAATAGAA;RSEQ=GGACTCGAAAGCAATGGTCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:30:0:33:0:1:0:40:2:0.25:0:6 1/1:2:2:1,1:0,0:1:0,2:20:1:27.5:1:1:0:23:4:1:0:7.5 -Y 13868509 . T A 48 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TGGACTCAAATAGAAAGGAC;RSEQ=CGAAAGCAATGGTCTCGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:25.3:1:30.3:1:1:0:39.3:6:0.75:0:6.7 0/0:2:0:0,0:1,1:0:2,0:25:1:28:1:1:0:23:4:1:0:7.5 -Y 13868511 . G A 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GACTCAAATAGAAAGGACTC;RSEQ=AAAGCAATGGTCTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:23:0:32:0:1:0:40:2:0.25:0:6 1/1:2:2:1,1:0,0:1:0,2:27:1:28:1:1:0:23:4:1:0:7.5 -Y 13868516 . C G 49 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AAATAGAAAGGACTCGAAAG;RSEQ=AATGGTCTCGAATGGAATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0.75:0,2:27.7:1:31.3:1:1:0:39.3:6:0.75:0:6.7 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13868525 . C T 28 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGACTCGAAAGCAATGGTCT;RSEQ=GAATGGAATTTATTCGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:0.25:2,0:9:0:32:0:1:0:40:2:0.25:0:6 1/1:2:2:1,1:0,0:1:0,2:41:1:28.5:1:1:0:23:4:1:0:7.5 -Y 13868527 . AA GT 47 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACTCGAAAGCAATGGTCTCG;RSEQ=TGGAATTTATTCGAATAGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:0.75:0,2:34.7:1:30.1:1:1:0:39.3:6:0.75:0.25:6 0/0:2:0:0,0:1,1:0:2,0:43:1:29:1:1:0:23:4:1:0:7.5 -Y 13868534 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGCAATGGTCTCGAATGGAA;RSEQ=TTATTCGAATAGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:45.5:1:29.5:1:1:0:44:4:1:0:7 1/1:2:2:1,1:0,0:1:0,2:49.5:1:31.5:1:1:0:23:4:1:0:7.5 -Y 13868544 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCGAATGGAATTTATTCGAA;RSEQ=AGAATGGAATCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:35.5:1:29.5:1:1:0:44:4:1:0:7 0/0:2:0:0,0:1,1:0:2,0:40.5:1:30:1:1:0:23:4:1:0:7.5 -Y 13868546 . G C 31 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAATGGAATTTATTCGAATA;RSEQ=AATGGAATCGAATGGAATGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:33.5:1:31.5:1:1:0:44:4:1:0:7 0/0:2:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13868551 . G T 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAATTTATTCGAATAGAATG;RSEQ=AATCGAATGGAATGCAATAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:28.5:1:30.5:1:1:0:44:4:1:0:7 1/1:2:2:1,1:0,0:1:0,2:33.5:1:29:0:1:0:23:4:1:0:7.5 -Y 13868655 . C T 32 d7;v4;pSTD;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATGGATAGCAATGTAAT;RSEQ=GATTCGAATTGAATGGAATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:10:0:32:0:1:0:25.5:4:1:0:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13868665 . T TC 47 d7;v4;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GCAATGTAATCGATTCGAAT;RSEQ=GAATGGAATCAAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:17.7:1:30:1:1:0:27:6:1:0:5.7 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13868676 . AA GC 33 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCGAATTGAATGGAATC;RSEQ=ATGGAATGTAATCAAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0.6667:0,2:33:0:33.8:1:1:0:25.5:4:1:0:4.5 0/0:1:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13868714 . T A 29 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TGGAATGGAATGGAATGCAA;RSEQ=GGAATGGAATAGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:22.3:1:28.5:1:1:0:27.3:8:1:0:4.3 1/0:3:2:1,1:0,1:0.6667:0,2:36:1:29.5:1:1:0:52.5:4:0.6667:0:4 -Y 13868715 . G A 48 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GGAATGGAATGGAATGCAAT;RSEQ=GAATGGAATAGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:24:1:30.7:1:1:0:27:6:0.75:0:5 0/0:3:0:0,0:1,2:0:2,0:26.7:1:28.7:1:1:0:42:6:1:0:2.7 -Y 13868720 . G T 49 NM4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GGAATGGAATGCAATGGAAT;RSEQ=GAATAGAATGGAATGCAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:0.75:0,2:19:1:31.3:1:1:0:27:6:0.75:0:5 0/0:3:0:0,0:1,2:0:2,0:25:1:28.7:1:1:0:42:6:1:0:2.7 -Y 13868722 . A T 28 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=AATGGAATGCAATGGAATGG;RSEQ=ATAGAATGGAATGCAATGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:18.3:1:31.5:1:1:0:27.3:8:1:0:4.3 1/0:3:2:1,1:0,0:0.6667:0,2:36:1:28:1:1:0:52.5:4:0.6667:0:4 -Y 13868724 . T C 31 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TGGAATGCAATGGAATGGAA;RSEQ=AGAATGGAATGCAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:0:2,0:17.3:1:30.5:1:1:0:27.3:8:1:0:4.3 1/0:3:2:1,1:0,1:0.6667:0,2:36:1:31:1:1:0:52.5:4:0.6667:0:4 -Y 13869055 . G A 30 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGACTC;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:14.5:1:30:1:1:0:60:4:1:0:4.5 -Y 13869057 . A C 31 d7;v4;NM4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGGAATGGACTCGA;RSEQ=TGGAATGGAATGGAATGGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:16.5:1:31.5:1:1:0:60:4:1:0:4.5 -Y 13869069 . G A 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=GGACTCGAATGGAATGGAAT;RSEQ=GAATGGACTCGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:0:0,0:5:0:33:0:1:0:33:2:1:0:5 1/1:2:2:1,1:0,0:1:0,2:28.5:1:30.5:1:1:0:60:4:1:0:4.5 -Y 13869083 . T C 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGGAATGGAATGGACTCGAA;RSEQ=GGAATGGAATGGAATGGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:11.5:1:32:0:1:0:34.5:4:1:0:5.5 0/1:5:2:1,1:3,0:0.4:0,2:32:0:32:1:0.4:0:60:4:0.4:0:4.5 -Y 13869087 . A ATGGAC 45 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.53981;LSEQ=ATGGAATGGACTCGAATGGA;RSEQ=TGGAATGGAATGGACTTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:0.6667:0,2:14:1:30.9:1:1:0:40.5:4:0.6667:0.3333:6.5 1/0:6:3:2,1:1,1:0.5:2,2:7.7:1:28.9:1:1:1.73:29.3:4:0.4815:0.5185:5.3 -Y 13869095 . G GAGTGA 30 d7;v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GACTCGAATGGAATGGAATG;RSEQ=AATGGACTTGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,0:0:0,0:19:1:32.3:1:1:0:39.7:6:0.75:0:6 0/1:11:2:2,0:6,3:0.1818:2,0:10:1:30.7:1:1:0:36.5:4:0.1818:0.0909:6 -Y 13869101 . AC A 48 d7;v4;NM4;P0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.07095;SOR=0.09902;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=TTGAATGGAATGGACTGGAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,0:0.5:0,2:20.3:1:30.8:1:1:0:35.3:6:0.5:0.3333:5 0/1:13:1:0,1:6,2:0.0769:2,0:15:0:25:0:0.33333:0:23:2:0.0769:0:6 -Y 13869103 . TT AC 61 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.13745;LSEQ=TGGAATGGAATGGAATGGAC;RSEQ=GAATGGAATGGACTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:3,2:0.1667:2,0:14:0:32:0:1:0:50:2:0.1667:0:6 0/1:13:4:4,0:4,2:0.3077:2,0:17.8:1:30.9:1:0.46667:0:28.3:8:0.3636:0:5.5 -Y 13869104 . T C 62 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.73871;LSEQ=GGAATGGAATGGAATGGACT;RSEQ=GAATGGAATGGACTGGAGTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,1:0.3333:2,2:23:1:32:0:1:1.7321:42:4:0.4:0:7 0/1:15:4:3,1:1,4:0.2667:2,2:14.3:1:31.3:1:0.20635:8.35:42:8:0.4444:0:5.8 -Y 13869123 . T A 48 v4;NM4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.048;SOR=0.09188;LSEQ=TTGAATGGAATGGACTGGAG;RSEQ=GGAATGGACTCGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:4,2:0.3333:2,2:26.7:1:30.3:1:1:1:35.3:6:0.3333:0:5 0/1:25:1:0,1:13,11:0.04:2,0:35:0:26:0:0.48:0:23:2:0.0435:0:6 -Y 13869133 . T A 119 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22393;SOR=3.09454;LSEQ=TGGACTGGAGTGGAATGGAC;RSEQ=CGAATGGAATGGAAAAGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:3,2:0.4444:2,2:31.8:1:30:1:1:1.85:47.5:8:0.4444:0:6.8 1/0:25:18:10,8:3,4:0.72:2,2:30.1:1:28.7:1:0.67277:1.63:35:36:0.72:0:5.3 -Y 13869135 . G C 29 v4;NM4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACTGGAGTGGAATGGACTC;RSEQ=AATGGAATGGAAAAGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:0:2,0:31.7:1:30.2:1:1:0:42.2:18:1:0:6.1 0/1:25:2:1,1:12,11:0.08:2,2:36:1:29.5:1:1:1.0871:33:4:0.087:0:7 -Y 13869143 . T A 69 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18407;SOR=0.29606;LSEQ=TGGAATGGACTCGAATGGAA;RSEQ=GGAAAAGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:4,1:0.4444:2,2:30.5:1:30.3:1:0.52381:3.38757:38.5:8:0.4444:0:5.8 0/1:27:5:2,3:12,10:0.1852:2,2:32.4:1:29.8:1:0.64831:1.76109:34.6:10:0.1852:0:5 -Y 13869148 . AA GC 108 v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.29897;LSEQ=TGGACTCGAATGGAATGGAA;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:2,2:0.375:2,2:43:1:32.2:1:1:1.81:44.7:6:0.375:0:5.7 0/1:25:11:5,6:4,5:0.44:2,2:41.5:1:31.3:1:1:1.04:31.5:22:0.44:0:4.9 -Y 13869149 . A C 68 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1695;SOR=0.26284;LSEQ=GGACTCGAATGGAATGGAAA;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:0,0:0.5:0,2:24.5:1:30.5:1:1:0:38.5:8:1:0:5.8 0/1:25:5:2,3:2,2:0.2:2,2:28.6:1:29.6:1:1:1.43328:34.6:10:0.4545:0:5 -Y 13869152 . A G 71 P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1695;SOR=0.26284;LSEQ=CTCGAATGGAATGGAAAAGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:3,1:0.5:2,2:21.5:1:31.3:1:1:2.60168:38.5:8:0.5714:0:5.8 0/1:25:5:2,3:10,10:0.2:2,2:25.6:1:30.8:1:1:1.47601:34.6:10:0.2083:0:5 -Y 13869153 . T C 31 v4;NM4;MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.05303;SOR=0;LSEQ=TCGAATGGAATGGAAAAGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:0.25:2,2:42:1:31.5:1:1:1.8258:55:4:0.25:0:5 0/0:25:0:0,0:12,13:0:2,0:34:1:28.2:1:1:0:35.3:7.333:1:0:4.6 -Y 13869162 . ATG A 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAAAAGAATGGAATGGA;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:28.7:1:28.4:1:1:0:44.4:6:1:0:5.9 0/1:26:2:1,1:11,13:0.0769:2,2:22:1:32:1:1:1.17:34:4:0.0769:0:1 -Y 13869170 . G A 98 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=0.71151;SOR=1.45099;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:2,4:0.3333:2,2:31.3:1:31:1:0.52381:3.39:55.3:6:0.3333:0:5.3 0/1:26:11:5,6:7,8:0.4231:2,2:24.4:1:28.5:1:1:1.04806:31.5:10:0.4:0:4.9 -Y 13869190 . G A 66 d7;v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=0.33308;SOR=3.9895;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:2,3:0.1667:2,0:15:0:25:0:1:0:24:2:0.1667:0:6 0/1:13:6:3,3:1,5:0.4615:2,2:9:1:25.7:1:0.54545:4.34:28.7:5:0.4545:0:5 -Y 13869200 . G A 30 d7;v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.15152;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAAATGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,1:0.4:2,0:33.5:1:30.5:1:0.4:0:35.5:4:0.4:0:4 0/0:7:0:0,0:2,5:0:2,0:9.7:1:29.3:1:1:0:34.9:14:1:0:5.1 -Y 13869214 . T G 31 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.33333;SOR=0;LSEQ=GGAATGGAATGGAATGGAAA;RSEQ=GAATGGAATGGAATGGAATA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:20:0:31.5:1:1:0:35.5:4:1:0:4 0/0:1:0:0,0:0,1:0:0,0:18:0:32:0:1:0:23:2:1:0:7 -Y 13869219 . G A 32 d7;v4;pSTD;NM4;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.33333;SOR=0;LSEQ=GGAATGGAATGGAAATGAAT;RSEQ=GAATGGAATGGAATAGGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:1:0,0:15:0:32.5:1:1:0:35.5:4:1:0:4 0/0:1:0:0,0:0,1:0:0,0:13:0:32:0:1:0:23:2:1:0:7 -Y 13869429 . G A 31 MSI6 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.04762;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:5:1:31.5:1:1:0:52:4:1:1:0.5 0/0:5:0:0,0:1,4:0:2,0:14.2:1:29.4:1:1:0:36.4:10:1:0.6:2 -Y 13869433 . TG CA 32 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GAATGGAATGGAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:9:1:32:1:1:0:52:4:1:1:0.5 0/1:5:2:1,1:0,3:0.4:0,2:24:0:32.5:1:0.4:0:55:4:0.4:0:3 -Y 13869434 . G C 42 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.42857;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:10:1:33:1:1:0:52:4:1:1:0.5 1/0:5:3:0,3:0,0:0.6:0,0:16:1:26.7:1:1:0:24:6:1:0.6:0.7 -Y 13869438 . TG AGCAATAGAATGGAATGGATCGTTATGGAAAGACATC 92 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.07692;SOR=Inf;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GAATGGAATGGAATTGACTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:13:1:32:1:1:0:52:4:1:1:0.5 1/1:11:9:3,6:1,1:0.8182:2,2:30.1:1:29.3:1:1:1.87089:40.3:18:0.8182:0.8182:1.2 -Y 13869445 . G A 28 d7;v4;pSTD;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATTGACTCGAATGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:0:2,0:3:0:32:1:1:0:52:4:1:0:0.5 0/1:13:2:1,1:4,7:0.1538:2,2:6:0:28.5:1:1:1.67:39:4:0.1538:0:2 -Y 13869483 . T C 107 d7;v4;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGACTGGAATGGAA;RSEQ=GGACTATAATGGAATGGCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:1:0,0:1:0:31:0:1:0:52:2:1:0:1 1/1:12:12:5,7:0,0:1:0,2:5.1:1:30:1:1:0:46.4:24:1:0:1.8 -Y 13869778 . TAGAATGGAATGCAATAAATGCAAA T 30 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCATGGAATGGAATGGAA;RSEQ=GGAGTGGAATCAAGTGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:1:0,2:10.5:1:30.1:1:1:0:48:4:1:1:1 -Y 13869837 . T G 32 v4;NM4;MSI6;P0.05 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:0.25:2,2:36.5:1:32.5:1:1:1:45:4:0.25:0:5.5 0/0:2:0:0,0:1,1:0:2,0:7:0:32:0:1:0:48:4:1:0:1 -Y 13869843 . G T 80 MSI6;P0.05 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:1,1:0.75:2,2:21:1:31.3:1:1:1:34.7:12:0.75:0:3.2 1/1:2:2:1,1:0,0:1:0,2:1:0:31.5:1:1:0:48:4:1:0:1 -Y 13869847 . T A 73 d7;MSI6;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1:0,2:21.4:1:31.8:1:1:0:39.2:10:1:0:3.8 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13869863 . G C 48 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAAGGGAATGGACCCAAATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:13.3:1:30.3:1:1:0:40:6:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13869867 . G T 47 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGACCCAAATGGAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:1:0,2:9.3:1:30:1:1:0:40:6:1:0:5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 13869877 . C TGGAATGGATGGATT 29 d7;v4;NM4;P0.05 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TGGAATGGAAGGGAATGGAC;RSEQ=CAAATGGAATGGATTCGAGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:1:0,2:17.5:1:29.5:1:1:0:45:4:1:1:5.5 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 -Y 15372143 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACAAAACAACTATCAGTA;RSEQ=AAACAGTTACTCACCTCACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:19,7:0:2,0:20.5:1:30.2:1:1:0:60:25:1:0:0.3 0/1:174:2:1,1:106,66:0.0115:2,2:34:1:28.5:1:1:1.60147:60:4:0.0115:0:1 -Y 15372253 . G A 44 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAGCTTCTCTCAATGTCT;RSEQ=ATATTGCTTCAGAATTTTCA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:3,10:0:2,0:21.5:1:32.3:1:1:0:60:26:1:0:0.1 0/1:121:4:2,2:36,81:0.0331:2,2:5:1:22:1:0.58902:2.23:60:3:0.0254:0:1 -Y 15409551 . C A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAATGGCTACCAATACCCC;RSEQ=AAAGAGAAACTGCAGCAGTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:20,7:0:2,0:20:1:29.3:1:1:0:60:12.5:1:0:0 0/1:162:2:1,1:112,47:0.0123:2,2:19.5:1:28:1:0.5087:2.36855:60:4:0.0126:0:1 -Y 15414854 . T G 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTTAACAGAGCAGAAGT;RSEQ=GTTATTTTCTTGGTGACCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:0:2,0:25.3:1:30.9:1:1:0:60:32:1:0:0.2 0/1:132:2:1,1:39,91:0.0152:2,2:26:1:31:1:0.51585:2.32:60:4:0.0152:0:2 -Y 15414856 . T A 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTTAACAGAGCAGAAGTTG;RSEQ=TATTTTCTTGGTGACCTGAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:0:2,0:24.1:1:29.3:1:1:0:60:15:1:0:0.2 0/1:123:2:1,1:34,87:0.0163:2,2:24:1:31:0:0.4898:2.54:60:4:0.0163:0:2 -Y 15435442 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAAAAACTTACTCTCAAT;RSEQ=ATTCCTGGAAGGAGGAAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:11,2:0:2,0:24.2:1:33.1:1:1:0:60:26:1:0:0 0/1:85:2:1,1:67,16:0.0235:2,2:16.5:1:27.5:1:0.3619:4.09268:60:4:0.0238:0:1.5 -Y 15435453 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCTCAATGATTCCTGGAA;RSEQ=GAGGAAGCCTGGTATTGTGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:13,3:0:2,0:25.6:1:32.6:1:1:0:60:32:1:0:0 0/1:112:2:1,1:86,24:0.0179:2,2:22:1:28.5:1:0.39817:3.53106:60:4:0.0179:0:1 -Y 15436447 . TA T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTATAAAAGTTTAAAGATAG;RSEQ=AAATATATATTCAATCTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:18.1:1:28.1:1:1:0:60:14:1:0:0 0/1:87:2:1,1:68,17:0.023:2,2:12:1:26:1:0.37289:3.91578:60:4:0.023:0.0115:0.5 -Y 15438098 . C T 32 v4;q23;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAGTTACTCAATGCGGACT;RSEQ=ACGTAAATACTAGGTGTGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:27,20:0:2,0:25.6:1:31.9:1:1:0:60:94:1:0:0.1 0/1:246:3:0,3:153,90:0.0122:2,0:6:1:20.7:1:0.05294:0:59:2:0.0084:0:1.3 -Y 15438169 . T C 32 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01656;SOR=0;LSEQ=GTATGGTGAAGTTGGTGGTC;RSEQ=TGGAGGTGGACATTTATCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:27,26:0.0364:2,2:30:1:32.5:1:1:1.03776:60:4:0.0364:0:1.5 0/0:369:0:0,0:170,199:0:2,0:24.9:1:29.9:1:1:0:60:45.125:1:0:0.1 -Y 15447831 . A T 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGATTGTCTGCAATTAATA;RSEQ=ATTTGGTGAATCTCCATGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:25.5:1:30.9:1:1:0:60:20:1:0:0.1 0/1:102:2:1,1:45,55:0.0196:2,2:29.5:1:27:1:1:1.22:60:4:0.0198:0:1 -Y 15447876 . T C 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGGAAACAGCATCTGCTA;RSEQ=CAACTGATGAACATGATTAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:23.3:1:31:1:1:0:60:14:1:0:0 0/1:75:2:1,1:38,35:0.0267:2,2:35.5:1:30:1:1:1.08451:60:4:0.027:0:1 -Y 15470363 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTTGTTGGACTAGATGTT;RSEQ=TTTTCTTCTTGGCAGGACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:0:2,0:23.6:1:32.2:1:1:0:60:66:1:0:0.1 0/1:180:2:1,1:109,69:0.0111:2,2:43:1:29:1:1:1.57551:60:4:0.0111:0:1 -Y 15470913 . G GA 98 v4;MSI6;P0.05 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.65969;SOR=0.74011;LSEQ=AAACTTGATTACTGAAGAGT;RSEQ=AAAAAAAAAAACCCTTAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:9,2:0.1538:2,0:15:1:31.9:1:1:0:60:4:0.1538:0.0769:0 0/1:93:11:8,3:65,16:0.1183:2,2:30.2:1:28.4:1:0.69116:1.51582:60:22:0.125:0.0215:0.2 -Y 15470934 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAAAAAAACCCTTAAAG;RSEQ=TGGGCACCTACAGAACATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:22.3:1:32.1:1:1:0:59.2:36:1:0:0.4 0/1:165:2:1,1:118,45:0.0121:2,2:23.5:1:28:1:0.48108:2.60453:60:4:0.0128:0:1 -Y 15470936 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAAAAACCCTTAAAGCT;RSEQ=GGCACCTACAGAACATAACC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:12,6:0:2,0:23.1:1:29.7:1:1:0:59.2:17:1:0:0.4 0/1:174:4:2,2:119,51:0.023:2,2:16:1:23:1:0.58626:2.32068:60:3:0.0181:0:2.3 -Y 15471059 . G T 32 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01634;SOR=0;LSEQ=CAATACTAGGAAGTAATTTA;RSEQ=TTTTATTCTGTAGACTACTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:32,26:0.0333:2,2:16:0:32.5:1:1:1.22648:60:4:0.0339:0:1.5 0/0:406:0:0,0:195,210:0:2,0:24.8:1:31.5:1:1:0:56.3:80:0.9975:0:0.1 -Y 15471159 . G A 28 v4 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02511;SOR=0.05028;LSEQ=GCCTACTTGAGTAAGAGCAA;RSEQ=TCCACTAAATCTTCCTCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:6,15:0.087:2,0:12.5:1:28.5:1:0.11067:0:52:4:0.087:0:1.5 0/0:216:1:0,1:70,145:0.0046:2,0:3:0:28:0:1:0:49:2:0.0047:0:1 -Y 15471192 . TA T 32 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCTCAGGGTTATAGGTATT;RSEQ=AAAAAAAATTCTAAATTTGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:0:2,0:24.6:1:30.9:1:1:0:60:22:1:0:0 0/1:83:2:0,2:9,72:0.0241:2,0:23.5:1:32:0:1:0:60:4:0.0241:0:0 -Y 15471841 . G A 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCCTGTAAAGCATCCATAG;RSEQ=CTGATTTTGCTGCTGATACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:0:2,0:24.1:1:30.6:1:1:0:60:29:1:0:0.1 0/1:224:3:2,1:99,122:0.0134:2,2:18.7:1:26.7:1:0.58998:2.45:60:6:0.0137:0:1 -Y 15471877 . A G 29 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATACAACACACTGGAAAGAA;RSEQ=AAGAATGCTGTCAAAAACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:0:2,0:28.8:1:30.9:1:1:0:60:32:1:0:0.1 0/1:146:2:1,1:51,93:0.0137:2,2:6:0:29.5:1:1:1.82:60:4:0.0137:0:1 -Y 15472337 . G T 28 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0078;SOR=0;LSEQ=AACACCATGTATCTGCACTT;RSEQ=CTTCTGATTTATCAATAGAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:16,20:0.0526:2,2:22.5:1:28.5:1:1:1.24:54.5:4:0.0526:0:1 0/0:387:0:0,0:201,186:0:2,0:9:0:14:0:1:0:60:0:0:0:6 -Y 15472400 . G T 27 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.01033;SOR=0;LSEQ=CCTGAACTTTCCCAATACTT;RSEQ=AATAACACCTAAAAGGAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:11,15:0.0714:2,2:29.5:1:27.5:1:1:1.35:60:4:0.0714:0:1 0/0:243:0:0,0:89,154:0:2,0:23.1:1:30.9:1:1:0:59.2:486:1:0:0.1 -Y 15478164 . C T 42 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACCTTCCAAGAAAATACCA;RSEQ=GATTGGCCAGAATTAGGATC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:0:2,0:26.1:1:31.3:1:1:0:60:30:1:0:0.1 0/1:159:3:1,2:93,61:0.0189:2,2:13.7:1:27:1:0.56477:3.02729:60:6:0.0194:0:1.3 -Y 15478170 . G A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAAGAAAATACCACGATTG;RSEQ=CCAGAATTAGGATCTGCCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:13,6:0:2,0:22.7:1:30.2:1:1:0:60:18:1:0:0.2 0/1:183:2:1,1:105,76:0.0109:2,2:35.5:1:29.5:1:1:1.37908:60:4:0.0116:0:1.5 -Y 15478226 . C A 28 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00502;SOR=0;LSEQ=ATACTGAATAGCATAGCTTT;RSEQ=CTTTGTGGCTTTGTCTCCTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:0.1333:2,2:28:1:28.5:1:1:1.1547:60:4:0.1538:0:1 0/0:190:0:0,0:75,113:0:2,0:26.9:1:30.5:1:1:0:60:30.333:1:0:0.3 -Y 15478270 . C T 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCCATATTATGATGCATC;RSEQ=AACCTATAATTAAGAAGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:0:2,0:13.6:1:29.4:1:1:0:60:8:1:0:0.1 0/1:78:3:2,1:17,58:0.0385:2,2:13:1:24:1:0.14535:6.61:60:2:0.0263:0:2 -Y 15522866 . C A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTGGGAAAAATCTCAAC;RSEQ=ACCTACCTTTAAACTAGACT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:0:2,0:21.7:1:31.8:1:1:0:60:20:1:0:0.1 0/1:117:2:1,1:84,31:0.0171:2,2:7.5:1:26.5:1:0.47392:2.68283:60:4:0.0171:0:1 -Y 15522952 . C A 32 v4;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00502;SOR=0;LSEQ=TTTCCTTGGCTCGACAAAAG;RSEQ=TGGGGTCAACATAAAGGACA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:0.1333:2,2:19:0:32:1:1:1.15:60:4:0.1429:0:1.5 0/0:190:0:0,0:83,107:0:2,0:26.9:1:31.5:1:1:0:59.9:37:1:0:0.1 -Y 15581983 . G A 130 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19161;SOR=Inf;LSEQ=TAAGTCAAGCAAGAAATTTA;RSEQ=AAAGAGAATAACAATACCTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:0:0,0:23:1:32.6:1:1:0:60:16:1:0:0 0/1:79:19:15,4:45,15:0.2405:2,2:28.6:1:30.7:1:1:1.25:60:38:0.2468:0:1.1 -Y 15582103 . G A 32 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTAAAGATTCGTAGCAGC;RSEQ=AACAGCCTAGAAATAAAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:0:2,0:25.3:1:29.9:1:1:0:60:38:1:0:0 0/1:156:2:1,1:54,100:0.0128:2,2:16:0:32:0:1:1.84:60:4:0.0129:0:1.5 -Y 15591133 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGCGTCTGGTTGCTTTTA;RSEQ=CTTGCCTAGTAGGGTCTTCG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:0:2,0:19.8:1:32.4:1:1:0:60:28:1:0:0.1 0/1:114:2:1,1:69,43:0.0175:2,2:42:1:29.5:1:1:1.59771:60:4:0.0179:0:1 -Y 15591445 . T G 71 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGACTGTCAGGCTAACAGAC;RSEQ=CCTCTTCACTCTCGCGGCTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:15.7:1:29.7:1:1:0:60:14:1:0:0.1 0/1:52:5:4,1:35,12:0.0962:2,2:18.2:1:31:1:1:1.36:60:10:0.098:0:1 -Y 15591537 . G C 73 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAGTGAGCGACACTGCGCA;RSEQ=GATTTCATGGAAACAACAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:0:2,0:26.3:1:31.1:1:1:0:60:14:1:0:0 0/1:91:5:1,4:37,49:0.0549:2,2:42.8:1:31.6:1:0.3959:2.98877:60:10:0.0549:0:1.2 -Y 15860530 . G A 27 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAAATTCCGATCATGGGG;RSEQ=TCAAGGAGACTTGGAGAAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:0:2,0:22.7:1:31.6:1:1:0:60:20:1:0:0 0/1:113:2:1,1:69,42:0.0177:2,2:22:1:27.5:1:1:1.6353:60:4:0.018:0:1 -Y 15860590 . C A 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTAGCTGCACCTGAGGGTC;RSEQ=TACCCCTTTATCCATCATTT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:0:2,0:28.7:1:31.9:1:1:0:58.1:38:1:0:0.2 0/1:153:2:1,1:71,80:0.0131:2,2:20:1:29:1:1:1.13:60:4:0.0135:0:1 -Y 15860645 . G A 41 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=TAGTGTTTTCCTCCCCTGTG;RSEQ=CTGGCTTTCATGAACTTAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:25.7:1:31.9:1:1:0:60:20:1:0:0.1 0/1:101:3:2,1:32,66:0.0297:2,2:13.7:1:26.3:1:0.26145:4.06:60:6:0.03:0:1 -Y 19370898 . T C 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTCTGTTCTTGGATCTCTT;RSEQ=GGTTTGTTTGTATTCAGGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:0:2,0:26.7:1:30.5:1:1:0:60:36:1:0:0.1 0/1:154:2:1,1:67,84:0.013:2,2:41:1:29:1:1:1.25:60:4:0.0132:0:2 -Y 19370916 . G A 116 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36486;SOR=Inf;LSEQ=TTTGGTTTGTTTGTATTCAG;RSEQ=GAAGAGATCCATTAGAGATG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:0:2,0:25.6:1:31.4:1:1:0:60:26:1:0:0.1 0/1:138:15:8,7:57,66:0.1087:2,2:27.6:1:29.7:1:0.78513:1.32:60:30:0.1103:0:1.5 -Y 21636121 . G T 31 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGTTACTTCCCTCTAGG;RSEQ=CCAGGTATCTAATGAATAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:4,12:0:2,0:19.5:1:32.1:1:1:0:60:32:1:0:0.1 0/1:89:2:1,1:30,57:0.0225:2,2:12:0:31.5:1:1:1.89:60:4:0.023:0:1 -Y 21868363 . C T 28 v4;P0.05 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29267;SOR=0.23793;LSEQ=ATTCTGTCCAGGTCTGGAGG;RSEQ=TGTCCAGCCTGCAGCAGCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:15,7:0.0435:2,0:1:0:29:0:0.34783:0:57:2:0.0435:0:1 0/1:189:2:1,1:111,76:0.0106:2,2:28.5:1:28.5:1:1:1.4575:60:4:0.0106:0:1.5 -Y 21868539 . T A 25 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCCAGGTCTGGGCGGAAGG;RSEQ=GGTGCGGTGAAAGGTGCAGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:0:2,0:27.6:1:29.7:1:1:0:60:18:1:0:0 0/1:82:2:1,1:22,58:0.0244:2,2:7:1:25:1:0.48479:2.60:60:4:0.025:0:1 -Y 21868553 . G T 46 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAGGTGGTGCGGTGAAAG;RSEQ=TGCAGGGACAGACTGGGTTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:0:2,0:31:1:32:1:1:0:60:16:1:0:0 0/1:61:3:1,2:15,43:0.0492:2,2:17.7:1:29.3:1:1:1.42:60:6:0.0492:0:1 -Y 21868666 . C T 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGCCAACAGCCTACCCAAAC;RSEQ=ACACCTGTCTTACCAGAGCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,5:0:2,0:19.5:1:30.8:1:1:0:60:28:1:0:0 0/1:106:2:1,1:67,36:0.0189:2,2:14.5:1:29:1:1:1.84951:60:4:0.0194:0:1 -Y 21868785 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGGTAACAATAATTGAG;RSEQ=TGATGAACCAGGTCCTATCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:0:2,0:16.8:1:31.1:1:1:0:60:28:1:0:0.1 0/1:62:2:1,1:16,43:0.0323:2,2:9.5:1:26:1:0.48306:2.64:60:4:0.0328:0:1.5 -Y 21869246 . A G 33 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGAGACACTGAAGGGCCTC;RSEQ=CCCTCAGGCAGCCGCACGGG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:0:2,0:29.4:1:29.9:1:1:0:60:14:1:0:0 0/1:39:2:1,1:22,15:0.0513:2,2:30:0:33:1:1:1.45198:60:4:0.0526:0:1.5 -Y 21869593 . C G 31 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01392;SOR=0;LSEQ=GCGACGCAGCTGCAGGATAC;RSEQ=CTCCTTCTCCTTCTGTTCCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:21,29:0.0385:2,2:45:1:31.5:1:1:1.37:60:4:0.0408:0:1 0/0:385:0:0,0:165,220:0:2,0:26.1:1:30.2:1:1:0:60:76:1:0:0.1 -Y 21869679 . G A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGGTCAGCAGTCCACCCTC;RSEQ=CCCTTGTCTGGCATCCTAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:0:2,0:21.1:1:31.5:1:1:0:60:28:1:0:0 0/1:66:2:1,1:14,50:0.0303:2,2:7.5:1:28:1:0.40559:3.48:60:4:0.0303:0:1 -Y 21869784 . A T 37 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTCAGAGAGAAACCCAG;RSEQ=ACCCATCTTTTCCCCATCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:17,1:0:1,0:32.8:1:31.2:1:1:0:60:36:1:0:0.1 0/1:149:3:1,2:97,49:0.0201:2,2:6.3:1:23.7:1:0.26982:3.91997:60:2:0.0138:0:1 -Y 21870257 . C T 29 v4 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01329;SOR=0;LSEQ=GCCCCACAGGCAGGTCCCGG;RSEQ=CCACAGCCACCAGGCCCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:32,34:0.0294:2,2:33.5:1:29.5:1:1:1.06:60:4:0.0294:0:1 0/0:518:0:0,0:252,266:0:2,0:27.2:1:31.1:1:1:0:60:56.556:1:0:0.2 -Y 21870329 . C A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGGAATAGGGGAAAGAAA;RSEQ=TTTATTTAAATTATGTCAAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:5,28:0:2,0:24:1:32.3:1:1:0:60:32:1:0:0.2 0/1:205:3:2,1:56,146:0.0146:2,2:5.7:1:24:1:0.19354:5.17:60:2:0.01:0:1.3 -Y 21870904 . AT A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGTGGATGCTTCTGCCTAA;RSEQ=TTTTTTTGAAAAAGAGAAAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:0:2,0:25.9:1:29.4:1:1:0:60:22:1:0:0.2 0/1:155:2:0,2:48,105:0.0129:2,0:34:1:28.5:1:1:0:60:4:0.013:0:0 -Y 21871569 . C T 27 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGCTGAAGCTGATGGGCTT;RSEQ=AGGCACCTCTACACCCAGCT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:0:2,0:21.2:1:32:1:1:0:60:10:1:0:0 0/1:64:2:1,1:41,21:0.0313:2,2:23:1:27.5:1:1:1.93068:60:4:0.0313:0:2 -Y 21877385 . C T 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGCCCTTAGCTCTTCAAAG;RSEQ=CTGGAGAGTGTAAGTTGCAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:0:2,0:27.4:1:31.6:1:1:0:60:20:1:0:0 0/1:81:2:1,1:37,42:0.0247:2,2:42.5:1:26:0:1:1.13:60:4:0.0263:0:1 -Y 21877588 . G A 51 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCCCGAATCTTCAGTTTAT;RSEQ=CAGCATGGTGGGGAGCTCAT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:16,27:0:2,0:27:1:31.6:1:1:0:60:42:1:0:0.1 0/1:314:4:3,1:130,180:0.0127:2,2:9:1:25.8:1:0.3148:4.14:60:8:0.0129:0:1 -Y 21877709 . C T 43 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACAGTGTTCCCATGCTCAC;RSEQ=GGAGGTACTGTCGGCTACTA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:0:2,0:26.8:1:30:1:1:0:60:24:1:0:0 0/1:120:3:1,2:67,50:0.025:2,2:16.7:1:27.3:1:0.57821:2.65823:60:6:0.025:0:1 -Y 21877822 . G A 38 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAAGAAGCACGTGGTCTT;RSEQ=CACTTGATGCACTGGCGTTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:17,14:0:2,0:27.6:1:31.9:1:1:0:60:30:1:0:0.2 0/1:239:3:1,2:110,126:0.0126:2,2:38.7:1:24:1:1:1.74213:60:2:0.0084:0:1 -Y 21877909 . C G 29 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCCTGGGGGTGTTCAACCCA;RSEQ=ATATACTGTAAAGACTAGGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:0:2,0:22.9:1:29:1:1:0:60:10:1:0:0.2 0/1:94:2:1,1:28,64:0.0213:2,2:11.5:1:29:1:0.52414:2.26:60:4:0.0213:0:1 -Y 21878194 . G A 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGGCCTTTCGTAGACGTC;RSEQ=CTCCTCCTGAACCATAATGA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:0:2,0:19:1:30.9:1:1:0:60:14:1:0:0 0/1:37:2:1,1:22,13:0.0541:2,2:41:1:30.5:1:1:1.66733:60:4:0.0556:0:1 -Y 21878285 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGCAGCCATCTTGCAGAT;RSEQ=AGCTCCTCGTGGGAGAAGAC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:0:2,0:24.9:1:31.6:1:1:0:60:16:1:0:0.3 0/1:75:2:1,1:40,33:0.0267:2,2:18:1:31:1:1:1.20899:60:4:0.0274:0:1 -Y 21878324 . G T 28 d7;v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACAATAGCGCCGGAGCCG;RSEQ=CGGTAGTGTTCAATGCACTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:0:2,0:27.4:1:32.6:1:1:0:60:10:1:0:0.4 0/1:78:2:1,1:32,44:0.0256:2,2:28.5:1:28:1:1:1.37:60:4:0.026:0:1 -Y 21878469 . C T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTACCTGCAGGCCCACTG;RSEQ=ATGCTCACTCACCCAGTCAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:0:2,0:25.1:1:30.4:1:1:0:60:8:1:0:0 0/1:82:2:1,1:53,27:0.0244:2,2:35:1:28:1:1:1.94576:60:4:0.0247:0:1 -Y 21878550 . C T 30 v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTAAAACCACTGTGGTAAG;RSEQ=ACGAGGAAAAGTGATGACAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:0:2,0:25.8:1:31:1:1:0:60:12:1:0:0.2 0/1:149:2:1,1:70,77:0.0134:2,2:8:0:30.5:1:1:1.10:60:4:0.0138:0:1.5 -Y 21882771 . G T 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTTACTGGCACACCATGG;RSEQ=ACATCAAAGTGTTGGGATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:10,1:0:2,0:29.5:1:31.5:1:1:0:60:22:1:0:0 0/1:128:2:1,1:89,37:0.0156:2,2:16.5:1:28.5:1:0.50726:2.38686:60:4:0.0157:0:1 -Y 21882786 . G A 26 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATGGGACATCAAAGTGTTG;RSEQ=GATTCATGAGAGTGACAAGC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:10,3:0:2,0:27.6:1:29.5:1:1:0:60:12:1:0:0 0/1:157:2:1,1:102,53:0.0127:2,2:32:1:26.5:1:1:1.91602:60:4:0.013:0:1 -Y 21882929 . G T 31 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGGCTCACCCCTGCTCAC;RSEQ=TAGACAGAAGACACGTCAAG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:0:2,0:23.5:1:31:1:1:0:60:20:1:0:0 0/1:89:2:1,1:36,51:0.0225:2,2:31.5:1:31:1:1:1.41:60:4:0.0227:0:1 -Y 21883019 . T A 28 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGGGGTCATGCTCACCAA;RSEQ=GCAGATAGTTAATAGAGTAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:0:2,0:23.9:1:29.8:1:1:0:60:42:1:0:0 0/1:155:2:1,1:87,66:0.0129:2,2:33:1:28.5:1:1:1.31579:60:4:0.0131:0:1 -Y 21883247 . G A 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02646;SOR=0;LSEQ=TAGGGAGTAGGATACGATGA;RSEQ=GAGAGGCAAACTGAGCAAAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:0.4:2,2:22.5:1:29:1:1:1.73:60:4:0.4:0:1.5 0/0:23:0:0,0:3,20:0:2,0:22.7:1:30.6:1:1:0:60:46:1:0:0 -Y 22744451 . C CT 29 d7;v4;pSTD;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTGGACCAAGATCTCAAC;RSEQ=TTTTTTTTTATCTCCTCTCC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:0:0,0:41:1:33:0:1:0:60:4:1:0:0 0/1:93:2:1,1:69,22:0.0215:2,2:23:0:29:1:0.43548:3.08929:60:4:0.0215:0:0 -Y 22744561 . A G 30 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAGGTTATGCCATATCAG;RSEQ=GGGAAATTGAGAAAAAAGGT GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:0:2,0:27:1:30.4:1:1:0:60:34:1:0:0.1 0/1:189:2:1,1:79,108:0.0106:2,2:16.5:1:30:1:1:1.36:60:4:0.0106:0:1.5 -Y 22746399 . CG C 29 d7;v4;P0.05 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTATATTGGTTGGTCTA;RSEQ=GGACTATCAGGTAAAAATAA GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:0.4:2,2:13:1:29:1:1:1.7321:60:4:0.4:0:0 -Y 22930752 . C A 45 v4;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGAATTCCACACCTGGTGA;RSEQ=TCATGATGCTCGAACCATTC GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:0:2,0:21.7:1:31.6:1:1:0:60:54:1:0:0.1 0/1:166:3:2,1:82,81:0.0181:2,2:5.7:1:29:1:1:1.97:60:6:0.0182:0:1 -Y 22930880 . G GT 30 d7;v4;MSI6;P0.05 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGTAAGGTTTTTTTTGTT;RSEQ=TTTTTTTTTTCCCTTGTCTG GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:0:0,0:14.6:1:33.4:1:1:0:60:10:1:0:0 0/1:30:2:0,2:2,26:0.0667:2,0:22:1:30.5:1:1:0:60:4:0.069:0:0.5 +1 935833 . C G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCCAGGGGGCCGGGAGC;RSEQ=GGGGCTGGACGGAGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:17.7:1:32.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 936111 . C T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10178;SOR=0.30593;LSEQ=CGACAGAGCCGGGGGAAGGT;RSEQ=GGCGGCCGGGTCGGCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:18:8,10:3,3:6,18:0.75:2,2:25.8:1:30.1:1:1:1.23836:60:36:0.75:0:1.3 0/1:17:8:6,2:4,4:8,8:0.4706:2,2:34.5:1:30.3:1:0.60839:2.79:60:16:0.5:0:1 +1 936194 . A G 130 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10145;SOR=0;LSEQ=CCCGCAGAGCAGGGCCGGTG;RSEQ=TGGCGCGGGCCGGGCCGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:5,11:0,0:0,16:1:0,2:20.3:1:32.7:1:1:0:60:32:1:0:1.9 1/0:8:6:1,5:1,1:2,6:0.75:2,2:28.2:1:31:1:0.46429:3.87298:60:12:0.75:0:2.8 +1 936210 . C A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGATGGCGCGGGCCGGGC;RSEQ=GGACCACGAGGAGCAGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:21.6:1:31.8:1:1:0:60:16:1:0:2 1/1:6:6:1,5:0,0:0,6:1:0,2:22:1:30:1:1:0:60:12:1:0:2.8 +1 938116 . T G 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACAACCTCTGCTTCCTG;RSEQ=ATTCAAGCGATTCTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:18:0:32:0:1:0:33:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:28:1:1:0:28:4:1:0:1 +1 1001177 . G C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAAGGTGAAGCAAGTCAC;RSEQ=TGATCACAGGACAGCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:10,12:0,0:0,22:1:0,2:26.4:1:30.8:1:1:0:52.4:21:1:0:1.1 1/1:30:30:15,15:0,0:0,30:1:0,2:25.4:1:30.2:1:1:0:47.6:60:1:0:1.2 +1 1001194 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50786;SOR=Inf;LSEQ=CACGTGATCACAGGACAGCG;RSEQ=GCCCTTCCCTCTTAGGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:19,0:0:2,0:29.9:1:31:1:1:0:54.1:38:1:0:1.1 0/1:28:2:1,1:13,13:26,2:0.0714:2,2:13:1:30:1:1:1:60:4:0.0714:0:1 +1 2487055 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGGTTCCTGGTGTGCA;RSEQ=CAGGCGGTGCCAGAGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:28:1:1:0:60:4:1:0:1 +1 2487766 . T C 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCCGGAGTGGACTGGAA;RSEQ=GGTGCAGGGGGAGAACTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,1:5,2:0.2857:2,0:12:1:32.5:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 2487987 . ATTCTCT A 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=4.000;MSILEN=6;SSF=0.21247;SOR=Inf;LSEQ=AGCTTGTCACACCGAGGCGG;RSEQ=TTCTCTTTCTCTTTCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:168,8:176,0:0:1,0:24.3:1:31.3:1:1:0:60:87:1:0:0.1 0/1:151:2:2,0:133,16:149,2:0.0132:2,0:7:1:31:1:1:0:60:4:0.0135:0.0066:0.5 +1 2488153 . A G 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21719;SOR=0.88652;LSEQ=TCCCTGGAGATCCACCCCCA;RSEQ=AACCGACGTCTTGAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:414:182,232:238,295:533,414:0.4367:2,2:25.8:1:32.6:1:0.84343:1.0284:60:137:0.4368:0:1.1 0/1:874:356:166,190:238,279:517,356:0.4073:2,2:25.1:1:31.1:1:0.89021:1.02:59.9:355:0.4104:0:1.1 +1 2488248 . C A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09402;SOR=Inf;LSEQ=GCCTCCCACAGATCTCTTCC;RSEQ=CATGCCCCTGTCCTGGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:47,240:287,0:0:2,0:22.5:1:31.6:1:1:0:59.9:286:0.9931:0:0.1 0/1:242:3:2,1:59,180:239,3:0.0124:2,2:17:1:29.3:1:0.15741:6.05:60:6:0.0126:0:1.3 +1 2488608 . T C 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTGGGTGGGGTGGGGA;RSEQ=ACTCTCCATGCTCATGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:21:1:33:1:0.33333:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 2488930 . G A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.03875;LSEQ=GTTCCAGTTCCCAGGGCTCC;RSEQ=CGCTGCCAGGCAGCGTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:10,0:12,1:13,10:0.4348:1,0:27.8:1:30:1:1:0:60:20:0.4545:0:1 0/1:9:4:3,1:5,0:5,4:0.4444:0,2:32.3:1:30.5:1:0.44444:0:60:8:0.4444:0:1 +1 2489756 . C T 65 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72814;SOR=1.5104;LSEQ=AGGGGCCTCCCGCAGACTTG;RSEQ=GAAGTTCCCACTCTCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:3:1,2:270,137:407,3:0.0073:2,2:23.7:1:29.3:1:0.26635:3.92739:60:6:0.0075:0:1 0/1:455:5:2,3:279,171:450,5:0.011:2,2:13.4:1:28:1:0.37527:2.44237:60:10:0.0111:0:1 +1 2489962 . G A 55 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04308;SOR=Inf;LSEQ=TGGGCAGCCTGGATGCCCCC;RSEQ=CACCCTGCACCCTCTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:39,197:236,0:0:2,0:23.6:1:31.8:1:1:0:59.9:58:1:0:0.1 0/1:199:4:3,1:43,152:195,4:0.0201:2,2:6:1:27.5:1:0.03921:10.44:60:8:0.0204:0:1.3 +1 2490048 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1087;SOR=Inf;LSEQ=CCAACCCCATCTCCATGGAT;RSEQ=CACCCTGCAGGGGACGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:19,43:62,0:0:2,0:23.5:1:32:1:1:0:60:30:1:0:0.1 0/1:31:2:1,1:2,27:29,2:0.0645:2,2:22.5:1:26.5:1:0.1871:11.22:60:4:0.0645:0:1 +1 2490499 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20876;SOR=Inf;LSEQ=CTCATGCCAGGCTCAGCATG;RSEQ=CCAGTGCTCCCTGCGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:40,190:230,0:0:2,0:23.3:1:32.3:1:1:0:60:75.667:1:0:0.1 0/1:194:2:2,0:28,163:191,2:0.0103:2,0:8.5:1:27.5:1:0.02348:0:60:4:0.0103:0:1 +1 2490898 . C A 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGATGGGAAACCCGTTTG;RSEQ=GGGGTGGGTGTCTGGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,1:1,3:0.75:0,0:17.7:1:31.3:1:0.25:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 2490942 . C A 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGCGAGGACCTGCCTG;RSEQ=GGGACCCTGCCCTGGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:2,3:5,3:0.375:2,0:36.3:1:30.3:1:0.19643:0:60:6:0.4286:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 2491164 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01234;SOR=Inf;LSEQ=GGGGTTCAGCCTGGCAGGGC;RSEQ=CCCTGGCAGCAGTCCTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:144,13:157,0:0:2,0:23.9:1:30.4:1:1:0:60:156:1:0:0.4 0/1:80:4:4,0:64,12:76,4:0.05:2,0:28.3:1:29.3:1:1:0:60:8:0.05:0:1 +1 2491205 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59545;SOR=1.10454;LSEQ=CTGTGGATGCTGTCCTGGCC;RSEQ=GTGGATGGTGTCCCGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:138:102,36:116,42:158,138:0.4662:2,2:23.6:1:31.2:1:1:1.03:60:68:0.4674:0:1.1 0/1:224:110:76,34:78,36:114,110:0.4911:2,2:22.8:1:29.9:1:1:1.03:60:35.667:0.4886:0:1.2 +1 2491228 . C T 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.049;SOR=Inf;LSEQ=GGATGGTGTCCCGGCCTCCA;RSEQ=GTACCCCTCTCAGCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:296,130:426,0:0:2,0:24.2:1:31.4:1:1:0:60:141:1:0:0.4 0/1:380:4:1,3:242,134:376,4:0.0105:2,2:12.5:1:23.3:1:0.13555:5.39344:60:3:0.008:0:1.3 +1 2493074 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15336;SOR=Inf;LSEQ=TGAGTGAACACTGGGCGCTG;RSEQ=ACCTGCCTCTCCCACGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:229,25:254,0:0:2,0:23.4:1:32.6:1:1:0:60:83.667:1:0:0.1 0/1:164:2:1,1:138,24:162,2:0.0122:2,2:18.5:1:26.5:1:0.28243:5.65426:60:4:0.0125:0:1.5 +1 2493328 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16082;SOR=Inf;LSEQ=AGCTCTGTCACCCCAAGCCT;RSEQ=GGAGGTGGCCCCAGAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:4,170:174,0:0:1,0:23.7:1:31.7:1:1:0:59.7:86:1:0:0.2 0/1:117:2:0,2:8,107:115,2:0.0171:2,0:17.5:1:30.5:1:1:0:56:4:0.0172:0:2 +1 2494197 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.1269;SOR=Inf;LSEQ=CTTGGGGACGGTCTCCCAGG;RSEQ=AGAAGCAGGAGTTGTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:165,13:178,0:0:2,0:21.7:1:31:1:1:0:59.6:18.778:1:0:0.2 0/1:99:2:1,1:86,11:97,2:0.0202:2,2:11.5:1:26:1:0.22882:7.52868:60:4:0.0206:0:1 +1 2494214 . C T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16928;SOR=Inf;LSEQ=AGGGAGAAGCAGGAGTTGTG;RSEQ=CTCCGCCACCGCTGTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:187,24:211,0:0:2,0:25.5:1:31.9:1:1:0:59.8:25.375:1:0:0.2 0/1:148:2:1,1:120,26:146,2:0.0135:2,2:18:1:24.5:1:0.3326:4.54796:60:4:0.0136:0:1 +1 2494330 . G A 185 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.55565;LSEQ=TAGTCAAGGTGATCGTCTCC;RSEQ=TCCAGGTATTGATCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:805:3:3,0:388,411:799,3:0.0037:2,0:8.7:1:24:1:0.11542:0:60:6:0.0038:0:2.7 0/1:779:80:39,41:344,352:696,80:0.1027:2,2:25.4:1:29.4:1:1:1.02736:60:160:0.1044:0:1.2 +1 2494752 . C T 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35008;SOR=3.34176;LSEQ=GACGCCAGAGATACCTGGAG;RSEQ=GACGGCTGCTGAAAGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:1:0,1:83,215:298,1:0.0033:2,0:25:0:32:0:1:0:60:2:0.0034:0:2 0/1:270:3:1,2:76,190:266,3:0.0111:2,2:40.3:1:30:1:1:1.25:60:6:0.0112:0:2 +1 2494772 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49946;SOR=0;LSEQ=CGACGGCTGCTGAAAGAGGC;RSEQ=GTCCACCTGGCGGAACCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:33,164:197,2:0.0101:2,2:15:1:27.5:1:0.31323:4.91:60:4:0.0102:0:1.5 0/0:184:0:0,0:37,147:184,0:0:2,0:21.3:1:29.2:1:1:0:60:60.333:1:0:0.4 +1 2494779 . C A 21 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22287;SOR=Inf;LSEQ=TGCTGAAAGAGGCTGTCCAC;RSEQ=TGGCGGAACCACCGGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:18,157:175,0:0:2,0:24.6:1:33:1:1:0:59.8:174:1:0:0.5 0/1:157:2:1,1:22,132:154,2:0.0127:2,2:8:1:21.5:1:0.27395:5.89:60:4:0.013:0:1.5 +1 2494784 . GG AA 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20042;SOR=Inf;LSEQ=AAAGAGGCTGTCCACCTGGC;RSEQ=AACCACCGGAGCCCGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:13,148:161,0:0:2,0:25.4:1:31.8:1:1:0:59.8:322:1:0:0.6 0/1:131:2:1,1:13,116:129,2:0.0153:2,2:5.5:1:27:1:0.20305:8.64:60:4:0.0155:0.0076:0.5 +1 2494785 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28291;SOR=0.76815;LSEQ=AAGAGGCTGTCCACCTGGCG;RSEQ=AACCACCGGAGCCCGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:74:4,70:8,75:83,74:0.4713:2,2:25.3:1:30.8:1:0.37867:1.8595:59.6:36:0.4706:0:1.1 0/1:128:52:6,46:6,69:75,52:0.4063:2,2:22.3:1:30.1:1:0.54767:1.50:60:51:0.4048:0:1.3 +1 2496582 . G C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14326;SOR=0;LSEQ=CTGCTCCCAGGTCTGGCCTC;RSEQ=GTCACCAGCCACCTGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:55:20,35:0,0:0,55:1:0,2:27:1:29.5:1:1:0:60:54:1:0:1.3 1/1:34:32:16,16:0,0:0,32:0.9412:0,2:30.5:1:29.2:1:1:0:60:64:0.9412:0:1.2 +1 2496649 . C G 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99014;LSEQ=GGAGTGGCAGGTGCAGCCCC;RSEQ=GGTACTCACTCAGCCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:1,10:2,12:14,11:0.44:2,2:17.9:1:31.7:1:1:1.63407:60:22:0.44:0:2.5 0/1:16:7:3,4:0,9:9,7:0.4375:0,2:29.6:1:26:1:0.0625:0:60:6:0.4:0:2.4 +1 2496653 . A G 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49131;SOR=1.68671;LSEQ=TGGCAGGTGCAGCCCCCGGT;RSEQ=CTCACTCAGCCCCAGGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:2,12:14,7:0.3333:2,0:25:1:33:1:0.53333:0:60:14:0.3333:0:2.6 0/1:13:6:3,3:0,7:7,6:0.4615:0,2:34:1:28.7:1:0.06993:0:60:5:0.4167:0:2.5 +1 2498027 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGGCCCACCAGAACCA;RSEQ=CAGGGAGAGAGAGGCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:33.5:1:1:0:58:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 3189588 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=GCAGTTACACTAGTGCTGTG;RSEQ=TCGAGAGGGCAGCCGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:88,68:156,0:0:2,0:25.8:1:31.6:1:1:0:59.9:155:1:0:0.1 0/1:169:2:1,1:96,71:167,2:0.0118:2,2:46:1:28.5:1:1:1.34965:60:4:0.0118:0:1 +1 3189627 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.91746;LSEQ=TCTGCGTGGGAGAGGATGTG;RSEQ=GTTCAGAACCAGAAGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:0,1:80,90:170,1:0.0058:2,0:24:0:31:0:1:0:60:2:0.0059:0:1 0/1:179:2:1,1:81,96:177,2:0.0112:2,2:22:1:27.5:1:1:1.18:60:4:0.0112:0:1 +1 3189714 . A G 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01886;SOR=0.14547;LSEQ=CAGGGGCAGTGGGGAGCAGG;RSEQ=GCAGGGATGAGGTGGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:0,11:0,13:13,11:0.4583:1,0:30:1:31.5:1:1:0:60:22:0.4583:0:2 0/1:19:2:0,2:0,17:17,2:0.1053:1,0:36:1:27:1:1:0:60:4:0.1053:0:3 +1 3189732 . T A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCAGGGATGAGGTGGGC;RSEQ=CCATGGCAGAGCAGGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:0,22:0,0:0,22:1:0,1:21.9:1:28.8:1:1:0:60:21:1:0:1.5 1/1:17:17:0,17:0,0:0,17:1:0,1:25.9:1:29:1:1:0:60:34:1:0:1.2 +1 3625768 . G A 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCCACGGGCTCCCCCA;RSEQ=CTGCTGGCTCCGGGCTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:31.3:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 3638567 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0632;SOR=Inf;LSEQ=GACCACTGGTCTCACCCGCT;RSEQ=CCTCTCCCCCACTCCAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:60,14:74,0:0:2,0:21.5:1:31.6:1:1:0:60:148:1:0:0.1 0/1:50:3:2,1:35,12:47,3:0.06:2,2:20:1:31.3:1:1:1.44652:60:6:0.06:0:1.3 +1 3638574 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.75141;LSEQ=GGTCTCACCCGCTCCCTCTC;RSEQ=CCCACTCCAGTACTCCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:68,19:87,2:0.0225:2,2:15.5:1:29.5:1:0.40092:3.51368:60:4:0.0225:0:1 0/1:59:1:0,1:41,17:58,1:0.0169:2,0:1:0:25:0:0.30508:0:60:2:0.0172:0:2 +1 3638620 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22513;SOR=Inf;LSEQ=AAGAAACTCTACTGCCAGAT;RSEQ=GCCAAGACATGCCCCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:76,63:139,0:0:2,0:29.4:1:30.7:1:1:0:60:68.5:1:0:0.4 0/1:126:2:1,1:69,55:124,2:0.0159:2,2:35.5:1:27.5:1:1:1.25226:60:4:0.016:0:1.5 +1 3638661 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19947;SOR=Inf;LSEQ=GATCAAGGTGTCCACCCCGC;RSEQ=ACCCCCAGGCACCGCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:44,83:127,0:0:2,0:23:1:31.5:1:1:0:60:41.333:1:0:0.6 0/1:103:2:1,1:43,58:101,2:0.0194:2,2:13.5:1:31.5:1:1:1.34:60:4:0.0196:0:2 +1 3638663 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.19457;SOR=Inf;LSEQ=TCAAGGTGTCCACCCCGCCA;RSEQ=CCCCAGGCACCGCCATCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:39,82:121,0:0:2,0:23.6:1:31:1:1:0:60:59.5:1:0:0.6 0/1:96:2:1,1:40,54:94,2:0.0208:2,2:25:1:27.5:1:1:1.35:60:4:0.0213:0:1 +1 3638674 . C T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09285;SOR=1.8173;LSEQ=ACCCCGCCACCCCCAGGCAC;RSEQ=GCCATCCGGGCCATGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:64:16,48:8,23:31,64:0.6667:2,2:26.5:1:30.4:1:1:1.04299:60:31:0.6667:0:1.2 1/0:79:62:23,39:6,10:16,62:0.7848:2,2:21.1:1:29:1:1:1.01717:60:61:0.7922:0:1.2 +1 3638834 . C T 44 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=AGCATCCCGGACAGCACAGC;RSEQ=GGGGGCTGCCTAACTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:4,0:0:0,0:24.5:1:32:0:1:0:60:8:1:0:0 1/1:3:3:0,3:0,0:0,3:1:0,0:31.3:1:28.3:1:1:0:60:6:1:0:1 +1 3640535 . C G 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCCCAGGAGAGGTGGCCTG;RSEQ=AGGAGGCTGAGGCTGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:31:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:16:0:26:0:1:0:60:2:1:0:0 +1 3643681 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11497;SOR=Inf;LSEQ=CTGCTCCCCCATGTGCAGGT;RSEQ=GGGACGGAATTCACCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:27,4:31,0:0:2,0:21.9:1:32.7:1:1:0:60:62:1:0:0.1 0/1:34:4:3,1:24,6:30,4:0.1176:2,2:29.8:1:28.3:1:1:1.32135:60:8:0.1176:0:1 +1 3643776 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49749;SOR=Inf;LSEQ=CATCCTCATCATCATCACCC;RSEQ=GGAGATGCGGGAGTGAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:20,35:55,0:0:2,0:22.3:1:30.7:1:1:0:60:110:1:0:0.2 0/1:62:2:1,1:24,36:60,2:0.0323:2,2:27.5:1:27.5:1:1:1.49:60:4:0.0323:0:1 +1 4832839 . C T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05712;SOR=0.19528;LSEQ=CCCCTGGACGTGGGCAGTGG;RSEQ=GGGAAATGCATAGTCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:12:12,0:22,2:24,12:0.3333:2,0:23.6:1:27.4:1:0.54286:0:59.8:11:0.3235:0:1.1 0/1:23:2:2,0:21,0:21,2:0.087:1,0:25:1:29.5:1:1:0:60:4:0.087:0:1 +1 4832912 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.6413;LSEQ=CAGAGCCCAAAGGCCAGCCC;RSEQ=GTGGTTATTGGCCTCCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:64,47:111,1:0.0089:2,0:1:0:15:0:0.42857:0:60:0:0:0:1 0/1:137:2:1,1:87,48:135,2:0.0146:2,2:8:1:28.5:1:1:1.80409:60:4:0.0146:0:1 +1 4832916 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21418;SOR=0;LSEQ=GCCCAAAGGCCAGCCCCGTG;RSEQ=TTATTGGCCTCCTAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:71,55:126,2:0.0156:2,2:22.5:1:29:1:1:1.2883:60:4:0.0163:0:1 0/0:148:0:0,0:94,54:148,0:0:2,0:23.6:1:30.6:1:1:0:60:73:1:0:0.1 +1 4833021 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19836;SOR=0;LSEQ=GGCAAATTTAGCAAAAATAT;RSEQ=AGATACCCACCAGACTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:47,84:131,2:0.015:2,2:21:1:27:1:1:1.78:60:4:0.0153:0:1 0/0:165:0:0,0:56,108:164,0:0:2,0:23.1:1:30.8:1:1:0:60:40:1:0:0.2 +1 4833164 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=CCCTTGAGTCAGCTTTCAAA;RSEQ=GTTTGTCCAGAATTAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:10,0:0:0,0:30.2:1:28.2:1:1:0:60:4:1:0:0.8 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:15.5:1:28:1:0.33333:0:60:4:0.3333:0:1 +1 4834606 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGCAGGGCAGACGCCGTG;RSEQ=GTCTGTTTCACGGTAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:14.5:1:29.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 4834641 . T A 30 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTACCTCTCTTTGGACAT;RSEQ=CCTGTTTTCGTTCCCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:7:0:30.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 4849109 . A G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGAGTTACTGTACATAGA;RSEQ=TCAAGAGAGCAGTTTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:22:1:33.3:1:1:0:60:6:0.3333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:43:0:32:0:1:0:60:2:1:0:0 +1 4849384 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.13615;LSEQ=GAGTTCTAAGCCAAGACATG;RSEQ=GCTTGGGACTGGATTAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:137:55,82:141,164:305,137:0.31:2,2:25.8:1:30.5:1:0.2555:1.28109:60:33.25:0.3043:0:1.1 0/1:445:218:98,120:103,124:227,218:0.4899:2,2:25.5:1:30:1:1:1.01708:60:108:0.4887:0:1.2 +1 4849405 . T C 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.95871;LSEQ=GCTTGGGACTGGATTAACTC;RSEQ=TGTCAATATCTTGGATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:1:0,1:164,242:406,1:0.0025:2,0:50:0:30:0:1:0:60:2:0.0025:0:4 0/1:379:22:9,13:136,221:357,22:0.058:2,2:23.7:1:30.1:1:0.82339:1.12:60:21:0.0569:0:2.2 +1 4955718 . C G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48326;SOR=0.6909;LSEQ=GTGTCTGCAAGCAGGCCCCC;RSEQ=GCCCAGAGCCTTGGCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:20:18,2:23,2:25,20:0.4444:2,2:23.9:1:30.1:1:1:1.27077:60:40:0.4444:0:1.1 0/1:31:11:11,0:20,0:20,11:0.3548:1,0:18.7:1:28.2:1:1:0:60:10:0.3333:0:1 +1 4955818 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26642;SOR=Inf;LSEQ=GGCCACCATGCTGAGCAAGC;RSEQ=GCAGATAAAAAAACAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:101,80:181,0:0:2,0:26.8:1:30.2:1:1:0:60:44.25:0.9944:0:0.3 0/1:249:3:1,2:138,107:245,3:0.012:2,2:13:1:26:1:0.58375:2.56974:60:6:0.0122:0:1 +1 4955824 . TA T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.17308;SOR=0;LSEQ=CATGCTGAGCAAGCGGCAGA;RSEQ=AAAAAACAGACAAACCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:103,85:188,2:0.0105:2,2:49:0:32:1:1:1.21053:60:4:0.0106:0:0 0/0:266:0:0,0:148,118:266,0:0:2,0:26.8:1:28.4:1:1:0:59.9:65.5:1:0:0.5 +1 4955833 . A T 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAGCGGCAGATAAAAAAAC;RSEQ=GACAAACCGGAGAGCACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:18:9,9:90,91:181,18:0.0905:2,2:26.8:1:30.4:1:1:1.01:60:36:0.0914:0:1.2 0/0:278:0:0,0:147,131:278,0:0:2,0:27:1:29.7:1:1:0:59.9:68.5:1:0:0.5 +1 4955834 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07026;SOR=0;LSEQ=AAGCGGCAGATAAAAAAACA;RSEQ=ACAAACCGGAGAGCACGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:1,2:95,99:194,3:0.0152:2,2:27:1:29.3:1:1:1.91309:60:6:0.0152:0:1.7 0/0:279:0:0,0:147,131:278,0:0:2,0:27.1:1:30.8:1:1:0:60:68.5:0.9964:0:0.5 +1 4955841 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17066;SOR=0;LSEQ=AGATAAAAAAACAGACAAAC;RSEQ=GGAGAGCACGGCACTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:93,104:197,2:0.0101:2,2:29.5:1:31.5:1:1:1.12:60:4:0.0102:0:1 0/0:282:0:0,0:140,142:282,0:0:2,0:27.1:1:29.5:1:1:0:60:55.4:1:0:0.5 +1 4955847 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16724;SOR=0;LSEQ=AAAAACAGACAAACCGGAGA;RSEQ=CACGGCACTCAGAACGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:89,106:195,2:0.0102:2,2:19.5:1:29:1:1:1.19:60:4:0.0104:0:1.5 0/0:284:0:0,0:139,145:284,0:0:2,0:26.6:1:31.1:1:1:0:60:70:1:0:0.5 +1 4955862 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.45443;LSEQ=GGAGAGCACGGCACTCAGAA;RSEQ=GGAACAGGGGACTTTGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:36:11,25:65,84:149,36:0.1946:2,2:23.3:1:31.1:1:0.1876:1.75347:60:72:0.1957:0:1.1 0/1:259:118:52,66:66,75:141,118:0.4556:2,2:24.9:1:29.5:1:0.70768:1.11644:59.9:58:0.4531:0:1.2 +1 4955878 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26661;SOR=Inf;LSEQ=AGAACGGAACAGGGGACTTT;RSEQ=CAGTCCCCAGGAGCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:56,100:156,0:0:2,0:25.1:1:31.8:1:1:0:59.8:77:0.9872:0:0.4 0/1:217:3:1,2:86,127:213,3:0.0138:2,2:15.3:1:30.3:1:1:1.3525:60:6:0.0141:0:1 +1 4955947 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=ACAGATTCATGTTTTCTGTT;RSEQ=CTGCTCTGCCCCACAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:7,42:49,0:0:2,0:22.6:1:30.8:1:1:0:60:98:1:0:0.1 0/1:50:2:1,1:5,43:48,2:0.04:2,2:32.5:1:28:1:0.22776:7.94:60:4:0.0417:0:1 +1 4955972 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49209;SOR=0;LSEQ=TCTGCCCCACAGAACACCAG;RSEQ=TGTTAGGGCTGAATCGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:3,26:29,2:0.0645:2,2:16.5:1:28.5:1:0.24516:7.65:60:4:0.0667:0:1 0/0:29:0:0,0:1,28:29,0:0:1,0:25.4:1:32.1:1:1:0:60:58:1:0:0.1 +1 4956070 . T C 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGCTGTGTTTGAAGACAG;RSEQ=GCCTTTAAAGAGGTGGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,1:1,4:0.6667:0,0:23.8:1:31.3:1:1:0:60:8:0.6667:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:43:1:27:1:1:0:60:4:1:0:1 +1 5130529 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14962;SOR=Inf;LSEQ=CCTGAACCTTCTCCTAGGCC;RSEQ=ATCTGTGCACTTCCTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:25,0:0:2,0:30:1:30.5:1:1:0:60:24:1:0:0.1 0/1:43:5:3,2:19,19:38,5:0.1163:2,2:23.8:1:29.6:1:1:1.49:60:10:0.1163:0:1.2 +1 6226463 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGGCTGCAGAAGCCCC;RSEQ=CAAGGCAGGGGCTGGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 6226476 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCCACAAGGCAGGGGC;RSEQ=GGGAGAGAAGGGCCGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:32:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 6227936 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23973;SOR=Inf;LSEQ=CACCGTGGCGACGGAATCCA;RSEQ=CCCTGTCCCTCGCACAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:12,25:37,0:0:2,0:23.1:1:32.3:1:1:0:60:74:1:0:0 0/1:36:2:1,1:13,21:34,2:0.0556:2,2:20.5:1:24.5:1:1:1.59:60:4:0.0571:0:1.5 +1 7434493 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11682;SOR=Inf;LSEQ=TAGGGCAAACGAGAAAAGAG;RSEQ=CCAGCCTGCTGCTTAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:162,90:252,0:0:2,0:25.9:1:31.6:1:1:0:60:62:1:0:0.2 0/1:242:3:1,2:136,103:239,3:0.0124:2,2:14.7:1:27.7:1:0.5807:2.63031:60:6:0.0128:0:1.3 +1 7434541 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05718;SOR=Inf;LSEQ=GGCATGGGGAGAGGAGGAGG;RSEQ=GCCGCCAACAATGACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:0:0,0:175,185:360,0:0:2,0:25.7:1:30.9:1:1:0:60:71:1:0:0.3 0/1:346:4:3,1:168,174:342,4:0.0116:2,2:13.3:1:25.3:1:0.36709:3.10:60:8:0.0118:0:1 +1 7434544 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.3346;LSEQ=ATGGGGAGAGGAGGAGGGGC;RSEQ=GCCAACAATGACAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:51:25,26:144,159:303,51:0.1437:2,2:26.4:1:31:1:0.88031:1.06:60:50:0.1433:0:1.2 1/0:341:236:115,121:53,52:105,236:0.6921:2,2:25.5:1:29.8:1:0.81482:1.07218:59.8:58:0.6925:0:1.2 +1 7520069 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2321;SOR=Inf;LSEQ=CACAGAGTCTGGACCAGTGG;RSEQ=GAAGGGCAGCGCCATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:73,62:135,0:0:2,0:24:1:31:1:1:0:60:66.5:1:0:0.4 0/1:126:2:1,1:68,56:124,2:0.0159:2,2:33.5:1:30.5:1:1:1.2124:60:4:0.016:0:1.5 +1 7520123 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49858;SOR=Inf;LSEQ=CTTCAAAGGCAAGGCCATCT;RSEQ=CCAGCCGCTCACTGTGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:86,85:171,0:0:2,0:24.6:1:32.4:1:1:0:60:170:1:0:0.7 0/1:174:2:1,1:84,88:172,2:0.0115:2,2:25.5:1:27:1:1:1.05:60:4:0.0118:0:2 +1 7520128 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24776;SOR=0;LSEQ=AAGGCAAGGCCATCTGCCAG;RSEQ=CGCTCACTGTGGGTCCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:81,84:165,2:0.012:2,2:26.5:1:28.5:1:1:1.04:60:4:0.012:0:1 0/0:168:0:0,0:84,84:168,0:0:2,0:25.7:1:30.7:1:1:0:60:41:1:0:0.4 +1 7520129 . C T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22887;LSEQ=AGGCAAGGCCATCTGCCAGC;RSEQ=GCTCACTGTGGGTCCCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:167:91:45,46:35,39:74,91:0.5449:2,2:24.8:1:31.7:1:0.87571:1.09:60:182:0.5515:0:1.1 0/1:168:36:18,18:66,66:132,36:0.2143:2,2:26.8:1:30.2:1:1:1:60:72:0.2169:0:1.2 +1 7520187 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4983;SOR=0;LSEQ=TGTGTGTGGAGTCATGCACT;RSEQ=GGCCCCTGCAGCTTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:55,63:118,2:0.0167:2,2:29.5:1:28:1:1:1.14:60:4:0.0171:0:1 0/0:113:0:0,0:42,71:113,0:0:2,0:24.7:1:29.3:1:1:0:60:112:1:0:0.5 +1 7520247 . C G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11508;SOR=2.15532;LSEQ=GAGAGCTGGGGAGGGGCCCG;RSEQ=CGTCCTCTCCCGTGGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:12:3,9:8,34:42,12:0.2143:2,2:20.8:1:28.6:1:0.69256:1.41:60:5:0.1887:0:2.4 0/1:43:16:1,15:4,23:27,16:0.3721:2,1:18:1:32.1:1:0.63536:2.55798:60:32:0.3721:0:1.8 +1 7520258 . C T 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00372;SOR=0.22692;LSEQ=AGGGGCCCGCCGTCCTCTCC;RSEQ=GTGGCGGCCCCTCTGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:36:5,31:1,8:9,36:0.8:2,2:26.8:1:30.7:1:1:1.28:60:72:0.8:0:1.5 0/1:34:16:0,16:2,16:18,16:0.4706:2,1:17.3:1:30.3:1:0.48663:0:60:32:0.4706:0:1.8 +1 7520283 . C A 84 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.66409;SOR=0.46699;LSEQ=CGGCCCCTCTGCTTTGCATC;RSEQ=CTTTTGTCCACCTGGCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:2,27:29,7:0.1944:2,0:27.7:1:30:1:1:0:60:14:0.1944:0:3 0/1:10:1:0,1:0,9:9,1:0.1:0,0:3:0:27:0:1:0:60:2:0.1:0:3 +1 7520379 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02778;SOR=Inf;LSEQ=CTGACCTTGAATGAAAAGGG;RSEQ=ACACTTCATCCTCCGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:24.3:1:33.7:1:1:0:60:14:1:0:0.1 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:30:1:1:0:60:4:1:0:1.5 +1 8074334 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.44937;LSEQ=AAAACCACATACAACTTGAT;RSEQ=CTCTTCATGTGGTCCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:217:102,115:555,591:1146,217:0.1592:2,2:23.6:1:30.5:1:0.71166:1.05876:60:53.25:0.1594:0:1.1 0/1:1926:151:73,78:897,875:1772,151:0.0784:2,2:22.8:1:28.8:1:0.61166:1.0953:60:74.5:0.0782:0:1.1 +1 8075620 . T C 184 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=46.86555;LSEQ=CCCATGGCTCGGCCATTATG;RSEQ=AGAAATCCAGTTTTTAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1005:1:0,1:477,525:1002,1:0.001:2,0:25:0:15:0:1:0:57:0:0:0:8 0/1:1322:59:23,36:595,666:1261,59:0.0446:2,2:21.7:1:31.3:1:0.23195:1.398:60:58:0.0441:0:1.2 +1 8075894 . C T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.73819;LSEQ=GTAGACTTTCACTTAATTCT;RSEQ=ACAGCTCGTGAGGGTACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:15:0,15:0,22:22,15:0.4054:1,1:23.9:1:27.6:1:1:0:57.6:14:0.3889:0:1.1 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:34.3:1:28:1:1:0:60:6:0.3333:0:1 +1 8079897 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19956;SOR=Inf;LSEQ=GCTTCAGTGGTTAACAGTGT;RSEQ=GCTTTCTAAACTGGTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:145,3:148,0:0:1,0:24.4:1:28.3:1:1:0:60:48.333:1:0:0 0/1:120:2:1,1:116,2:118,2:0.0167:1,2:26.5:1:32:1:0.04958:47.56167:60:4:0.0169:0:1 +1 8080236 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49645;SOR=Inf;LSEQ=TAAATCTCAGAAGCCATCCA;RSEQ=GGGAGGAGGAGGGGCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:1,70:71,0:0:1,0:25:1:30.6:1:1:0:60:142:1:0:0.1 0/1:71:2:0,2:2,67:69,2:0.0282:1,0:20:1:28:1:1:0:60:4:0.0282:0:1.5 +1 8084992 . T TA 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATAAGAAAAGAAATGCAGT;RSEQ=AAAAAAATAGGTACGGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:800:0:0,0:519,279:798,0:0:2,0:25.3:1:29.6:1:1:0:60:48.875:1:0:0.1 0/1:996:31:20,11:587,378:965,31:0.0311:2,2:31.3:1:29:1:0.71348:1.17:60:62:0.0314:0:0.1 +1 8085030 . C T 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACTTGGGATGTTCAGTCT;RSEQ=AACAAATGTGTGTACCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1245:0:0,0:677,568:1245,0:0:2,0:25.1:1:32.1:1:1:0:60:68.167:1:0:0.1 0/1:1616:56:31,25:821,738:1559,56:0.0347:2,2:24.9:1:29.1:1:0.7856:1.11:60:55:0.0344:0:1.1 +1 8085328 . T C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.76878;SOR=0.71574;LSEQ=AATAAAGACTTAGCAAGCAC;RSEQ=AATACAGCACCATTCACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:20:0,20:0,16:16,20:0.5556:1,1:31.2:1:32.6:1:1:0:59.9:40:0.5556:0:1 0/1:17:8:0,8:0,9:9,8:0.4706:0,0:27.1:1:30.9:1:1:0:58.4:16:0.4706:0:1.1 +1 8958110 . A C 29 v3;MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TAATTTTTAACCTCCTTGTC;RSEQ=AATTTGTTTCCTCTAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:0,6:6,2:0.25:0,2:5.5:1:29:1:0.25:0:42:4:0.25:0:1.5 0/1:4:1:0,1:1,2:3,1:0.25:2,0:10:0:33:0:1:0:43:2:0.25:0:1 +1 9770415 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50156;SOR=0;LSEQ=GGACCCCACTGTTTTCCAGG;RSEQ=AGTCCCTTCCAAAGGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:101,6:107,2:0.0183:2,0:23:1:28.5:1:1:0:60:4:0.0189:0:1 0/0:91:0:0,0:88,3:91,0:0:1,0:20.8:1:30.3:1:1:0:60:29.333:1:0:0 +1 9770714 . C G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-04;SOR=4.49214;LSEQ=GAGAGAGAGAGAGAGAGAGA;RSEQ=ACAGATAGACAGACAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:7:2,5:57,205:262,7:0.0259:2,2:9.9:1:30.1:1:0.65015:1.44:58.6:14:0.0265:0:1 0/1:299:32:11,21:67,200:267,32:0.107:2,2:14:1:28.8:1:0.28776:1.56:59:15:0.1034:0:1.3 +1 9775554 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1228;SOR=0;LSEQ=CCTCAGCCTCCCACCTCCCA;RSEQ=TGGCTGCCTTGGGTGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:1,2:125,42:167,3:0.0176:2,2:15.3:1:30:1:0.16464:5.87607:60:6:0.0181:0:1 0/0:171:0:0,0:131,40:171,0:0:2,0:23.6:1:31.1:1:1:0:60:84.5:1:0:0.1 +1 9775957 . G A 80 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00214;SOR=Inf;LSEQ=CAGAAGTGAACGACTTTCGC;RSEQ=CCAAGATGTGCCAATTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:544:0:0,0:272,272:544,0:0:2,0:24.6:1:30.7:1:1:0:59.9:44.333:1:0:0.2 0/1:607:10:6,4:312,284:596,10:0.0165:2,2:20.5:1:24.2:1:0.75492:1.36:60:2.333:0.012:0:1.5 +1 9776339 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03915;SOR=Inf;LSEQ=ATAACCAAGTGGCGTGGGGC;RSEQ=TTGGGCATCAGTTTGTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:51,19:70,0:0:2,0:24.3:1:30.8:1:1:0:59.4:34:1:0:0.1 0/1:37:3:2,1:28,6:34,3:0.0811:2,2:28.7:1:32:1:0.47748:2.2687:60:6:0.0811:0:1 +1 9776442 . C T 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.68708;SOR=0.52996;LSEQ=ATAGGCAACCCTGCCCTGTG;RSEQ=CCCAGAACCCCGGGGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:4:2,2:258,101:359,4:0.011:2,2:28.3:1:29.8:1:0.3194:2.54688:60:8:0.0112:0:1 0/0:341:2:1,1:229,110:339,2:0.0059:2,2:4:0:29:0:0.54571:2.07699:60:4:0.006:0:1.5 +1 9776709 . C G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21885;SOR=Inf;LSEQ=GAGGCCCTCTGCACTCTGGG;RSEQ=TCCCAACGCCCTGGATAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:47,139:186,0:0:2,0:24:1:32.6:1:1:0:59.8:25.571:1:0:0.1 0/1:164:2:1,1:41,121:162,2:0.0122:2,2:32:1:27:1:0.44778:2.93:60:4:0.0126:0:1 +1 9776738 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1505;SOR=Inf;LSEQ=CCCTGGATAGGGCCTGGGTG;RSEQ=GAGTCGGGGAGCTGACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:29,98:127,0:0:2,0:22.3:1:31.4:1:1:0:59.5:41.333:1:0:0.2 0/1:81:2:1,1:4,75:79,2:0.0247:2,2:20:1:27.5:1:0.12037:16.88:60:4:0.0256:0:1.5 +1 9776903 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16827;SOR=Inf;LSEQ=AAACCAGCAGGAAGCCCTCC;RSEQ=CTCTCCCAAGGCCTAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:142,14:156,0:0:2,0:25.8:1:32:1:1:0:60:155:1:0:0.1 0/1:109:2:1,1:97,10:107,2:0.0183:2,2:24.5:1:27.5:1:0.19249:9.29614:60:4:0.0183:0:1 +1 9776926 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20746;SOR=Inf;LSEQ=CTCCCAAGGCCTAGGACAGG;RSEQ=AGTGGGCAGCTTGGGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:191,20:211,0:0:2,0:25.6:1:32.5:1:1:0:60:69.333:1:0:0.1 0/1:177:2:1,1:158,17:175,2:0.0113:2,2:33.5:1:29:1:0.19357:9.0608:60:4:0.0114:0:1.5 +1 9777247 . G A 29 v3;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=TCCATGTGCTACTGGCCATG;RSEQ=GTCCAGGGGCCCTTGGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:2,0:9,149:158,2:0.0125:2,0:13.5:1:29:1:0.00432:0:60:4:0.0129:0:1.5 0/0:96:0:0,0:4,92:96,0:0:1,0:22.3:1:30.6:1:1:0:60:95:1:0:0.1 +1 9777451 . G GGA 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00886;SOR=3.64216;LSEQ=ATGGCAGGTTTTCTGGGAAA;RSEQ=GATAGCATTGTGGACAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:11:11,0:34,2:36,11:0.234:2,0:20.8:1:31:1:1:0:60:22:0.234:0.0851:0.2 1/0:32:17:17,0:15,0:15,17:0.5313:1,1:18.8:1:30:1:1:0:60:34:0.5484:0.125:0.1 +1 9777521 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49856;SOR=0;LSEQ=CACCCGCCCCCAAGTGGTCA;RSEQ=GGGCCTCACCATAGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:139,22:161,2:0.0123:2,2:11.5:1:29.5:1:0.26305:6.2015:60:4:0.0126:0:1 0/0:158:0:0,0:122,36:158,0:0:2,0:23.5:1:30.1:1:1:0:60:30.6:1:0:0.2 +1 9777586 . G C 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTAACAGCCCTGCTTCCCC;RSEQ=GCCCCCAGCCTTCCTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:249,156:405,0:0:2,0:23.3:1:30:1:1:0:60:44:1:0:0.1 0/1:493:30:16,14:269,194:463,30:0.0609:2,2:29.4:1:28.6:1:0.70359:1.21279:60:29:0.0605:0:1.2 +1 9778707 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22214;SOR=Inf;LSEQ=TTAAGGGGGAGGGGAGAGGG;RSEQ=CTGGGCCTCTGCCTCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:90,16:106,0:0:2,0:24:1:30.7:1:1:0:60:16.667:1:0:0.1 0/1:95:2:1,1:78,15:93,2:0.0211:2,2:26.5:1:30.5:1:0.30997:5.06719:60:4:0.0215:0:1 +1 9778724 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24555;SOR=0;LSEQ=GGGGCTGGGCCTCTGCCTCC;RSEQ=CACCCATCATCCCGGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:109,28:137,2:0.0144:2,2:19.5:1:33:0:0.37493:3.84266:60:4:0.015:0:1 0/0:141:0:0,0:109,32:141,0:0:2,0:25.6:1:29.6:1:1:0:60:19.143:1:0:0.2 +1 9778738 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=2.00751;LSEQ=GCCTCCTCACCCATCATCCC;RSEQ=GCACCTTCTACAGCTGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:0,1:131,46:177,1:0.0056:2,0:1:0:26:0:0.26404:0:60:2:0.0058:0:1 0/1:179:2:1,1:132,45:177,2:0.0112:2,2:25.5:1:28.5:1:0.449:2.91248:60:4:0.0113:0:1 +1 9778739 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12192;SOR=Inf;LSEQ=CCTCCTCACCCATCATCCCG;RSEQ=CACCTTCTACAGCTGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:135,47:182,0:0:2,0:24.2:1:31.2:1:1:0:60:35.4:1:0:0.2 0/1:181:3:2,1:131,47:178,3:0.0166:2,2:28.3:1:30.7:1:1:1.39088:60:6:0.0171:0:1.3 +1 9778808 . C T 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17906;SOR=0.20117;LSEQ=ATGCTGTGCAAGACGGTGTC;RSEQ=AGCTCGGAGGTGAGCGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:4:1,3:209,167:376,4:0.0105:2,2:23:1:28.3:1:0.3289:3.74225:60:8:0.0107:0:1 0/0:469:1:0,1:258,209:467,1:0.0021:2,0:1:0:25:0:0.44872:0:60:2:0.0022:0:1 +1 9779862 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52854;SOR=0;LSEQ=CAGGGTCTCCCAGGGGTCTG;RSEQ=TTGGGAGATGTTAGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:2,0:117,4:121,2:0.0163:1,0:25.5:1:32:0:1:0:60:4:0.0165:0:1.5 0/0:74:0:0,0:67,7:74,0:0:2,0:24.9:1:31:1:1:0:60:148:1:0:0.2 +1 9779871 . T C 139 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98739;LSEQ=CCAGGGGTCTGGTTGGGAGA;RSEQ=GTTAGCTGGGCTCTGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:21:20,1:120,5:125,21:0.1429:1,1:28.8:1:31.8:1:1:1.19839:60:20:0.1418:0:1.1 0/1:92:13:13,0:69,10:79,13:0.1413:2,1:24.5:1:32.5:1:0.34674:0:60:26:0.1413:0:1.1 +1 9780462 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10279;SOR=Inf;LSEQ=TTTGCCTGCAGGGATGCTGC;RSEQ=CAGTCTGATGACATTTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:158,61:219,0:0:2,0:24.5:1:30.5:1:1:0:59.8:35.5:1:0:0.1 0/1:194:3:1,2:132,59:191,3:0.0155:2,2:11:1:29.7:1:0.23318:4.43619:60:6:0.0159:0:1 +1 9780743 . TG T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.03061;SOR=0;LSEQ=AGTGGGGTGGGGGTGTGGGG;RSEQ=GGGGGCATGGAGCCGGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:5:3,2:226,255:481,5:0.0103:2,2:30.2:1:30.8:1:0.67019:1.69:60:10:0.0105:0:0.2 0/0:489:0:0,0:225,257:482,0:0:2,0:23:1:30.2:1:1:0:59.6:39.167:0.9874:0:0.8 +1 9780987 . T C 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGGTGGGGAGGCGCACC;RSEQ=GGGGGCGGAGCTGGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:112,230:342,0:0:2,0:23.2:1:30.6:1:1:0:60:56:1:0:0.2 0/1:304:32:6,26:86,186:272,32:0.1053:2,2:22.8:1:29:1:0.1575:1.99954:60:64:0.1081:0:1.2 +1 9781004 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2506;SOR=0;LSEQ=ACCTGGGGGCGGAGCTGGGG;RSEQ=CAGACCACAGCCTCTGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:70,168:238,3:0.0124:2,2:15:1:28.7:1:0.21337:4.76:60:6:0.0128:0:1 0/0:216:0:0,0:65,151:216,0:0:2,0:22.7:1:31.2:1:1:0:60:432:1:0:0.3 +1 9781106 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21834;SOR=Inf;LSEQ=GGCCACCCACCACCCTGACC;RSEQ=TGGCTGGCCATCACCCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:124,51:175,0:0:2,0:23.4:1:31.6:1:1:0:60:42.75:1:0:0.1 0/1:154:2:1,1:107,45:152,2:0.013:2,2:29.5:1:28.5:1:0.50955:2.36278:60:4:0.0131:0:1 +1 9781144 . T C 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25052;SOR=Inf;LSEQ=TACCCTGACCACCTCCACCC;RSEQ=GACCCCGGCCGCCCCCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:185,83:268,0:0:2,0:24.8:1:31.5:1:1:0:59.9:43.667:1:0:0.1 0/1:296:3:1,2:218,75:293,3:0.0101:2,2:16:1:21.7:1:0.16686:5.77128:60:2:0.0068:0:2.3 +1 9781340 . G A 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06229;SOR=Inf;LSEQ=GGGCGCTCCCCACTTCTCCA;RSEQ=AGGGCAGCTGTGTCCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:171,259:430,0:0:2,0:23.5:1:32.4:1:1:0:60:429:0.9977:0:0.2 0/1:456:5:3,2:171,279:450,5:0.011:2,2:10.6:1:24.2:1:0.37527:2.44:55.2:4:0.0089:0:2.2 +1 9781363 . C A 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37121;SOR=3.04628;LSEQ=GGCAGCTGTGTCCTGGCTGC;RSEQ=AGGACGTGGGCTCTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:1:1,0:97,200:297,1:0.0034:2,0:1:0:26:0:0.32886:0:60:2:0.0034:0:1 0/1:295:3:1,2:76,216:292,3:0.0102:2,2:8.3:1:21:1:1:1.42:52:2:0.0069:0:3.3 +1 9781412 . C G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=3.00701;LSEQ=CCTTCCCGTGGGCTTGCTCC;RSEQ=TCCTGCCTGGCCTCCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:38:22,16:71,96:167,38:0.1854:2,2:19.8:1:30.7:1:0.10465:1.85:60:76:0.1881:0:1.1 0/1:172:70:32,38:38,64:102,70:0.407:2,2:21.9:1:30.7:1:0.27421:1.42:60:140:0.4118:0:1.1 +1 9781421 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21488;SOR=Inf;LSEQ=GGGCTTGCTCCCTCCTGCCT;RSEQ=GCCTCCCTCTGGCTGCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:103,92:195,0:0:2,0:23.2:1:32.2:1:1:0:60:47.75:1:0:0.3 0/1:169:2:1,1:78,89:167,2:0.0118:2,2:26.5:1:30.5:1:1:1.14:60:4:0.0119:0:1.5 +1 9781880 . A G 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02779;SOR=0;LSEQ=TCATCCTGGAGGCCTACTGC;RSEQ=GGGGCAGCACCCACCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:5:2,3:228,253:481,5:0.0103:2,2:33.4:1:21:1:1:1.35095:60:1.5:0.0063:0:2 0/0:507:0:0,0:212,294:506,0:0:2,0:23.6:1:29.6:1:1:0:60:55.222:0.998:0:0.2 +1 9782386 . C T 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGCAGGCAGCGGCGGCAG;RSEQ=GTGGGCATCATCTTTAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:662:0:0,0:301,361:662,0:0:2,0:25.3:1:30.8:1:1:0:59.5:54.167:1:0:0.1 0/1:859:30:17,13:392,435:827,30:0.0349:2,2:18.1:1:29.7:1:0.35547:1.45:54.8:60:0.0358:0:1.2 +1 9782556 . C T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.09754;LSEQ=GAGAACCTACCAGAAACTCA;RSEQ=GCTTCTCCTCCCACCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:78:46,32:204,101:305,78:0.2037:2,2:23:1:31.2:1:0.23018:1.40374:60:77:0.2042:0:1.2 0/1:382:169:120,49:140,73:213,169:0.4424:2,2:25.9:1:30.2:1:0.32011:1.28:60:338:0.4447:0:1.1 +1 9782766 . C T 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGCATGACCATCTCAGC;RSEQ=GGGGAAAGGGCTTTCCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:15,215:230,0:0:2,0:25.2:1:30:1:1:0:59.8:75.667:1:0:0.1 0/1:193:17:2,15:15,161:176,17:0.0881:2,2:25.4:1:29.2:1:0.6496:1.43:60:16:0.0856:0:1 +1 9783074 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25146;SOR=0;LSEQ=GCTTTTTAGCAATGTGGGCA;RSEQ=CAGCATCTTCTGTGGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:2,1:122,7:129,3:0.0227:2,2:24.3:1:28.3:1:0.17225:8.38576:60:6:0.0231:0:1 0/0:113:0:0,0:108,5:113,0:0:1,0:25.3:1:31.9:1:1:0:60:112:1:0:0.2 +1 9783405 . G A 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCAAGAGGTGTGGAGTG;RSEQ=GAGGGCCTCGCCTGTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:65,209:274,0:0:2,0:22.5:1:31.2:1:1:0:60:90.333:1:0:0.1 0/1:291:35:10,25:63,193:256,35:0.1203:2,2:21.7:1:29.9:1:0.67784:1.22:60:70:0.1232:0:1.2 +1 9783923 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5061;SOR=0;LSEQ=CCATGTTCTGTTGGTCAAAG;RSEQ=AAGTCACAGGGCCAGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:133,7:140,2:0.0141:2,2:29.5:1:29.5:1:0.10988:17.83657:60:4:0.0144:0:1 0/0:110:0:0,0:102,8:110,0:0:2,0:22.6:1:31.2:1:1:0:60:54:1:0:0.2 +1 9784224 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20661;SOR=Inf;LSEQ=CTGCTGGCCCCTCTGCCTAG;RSEQ=ACACAGCTCTGTGGCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:93,126:219,0:0:2,0:24.7:1:32.2:1:1:0:59.9:53.75:1:0:0.1 0/1:183:2:1,1:74,107:181,2:0.0109:2,2:7.5:1:27.5:1:1:1.44:60:4:0.0111:0:1 +1 9784241 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20866;SOR=Inf;LSEQ=TAGCACACAGCTCTGTGGCA;RSEQ=GGGTCCCCCAGCCCTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:93,105:198,0:0:2,0:25.3:1:32.6:1:1:0:59.9:197:1:0:0.1 0/1:167:2:1,1:82,83:165,2:0.012:2,2:12:1:27.5:1:1:1.01:60:4:0.0121:0:1 +1 9784247 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.21137;SOR=Inf;LSEQ=ACAGCTCTGTGGCAGGGGTC;RSEQ=CCCAGCCCTGCTGGCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:104,94:198,0:0:2,0:24.8:1:31.3:1:1:0:59.9:48.5:1:0:0.1 0/1:169:2:1,1:96,71:167,2:0.0118:2,2:19.5:1:27:1:1:1.34965:60:4:0.012:0:1 +1 9784279 . A G 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10244;SOR=Inf;LSEQ=TGGCTTCCTGTCTCCCCTGG;RSEQ=TTCTCTCCTGTCTGACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:181,76:257,0:0:2,0:22:1:30.4:1:1:0:59.8:35.714:1:0:0.1 0/1:227:3:2,1:166,58:224,3:0.0132:2,2:14.3:1:26.3:1:1:1.4286:60:2:0.009:0:1.3 +1 9784423 . C T 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=42.88676;LSEQ=GTCCCATTCATCCTCACCTA;RSEQ=GACTTTGTCCATGTGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:772:1:0,1:347,423:770,1:0.0013:2,0:46:0:14:0:1:0:30:0:0:0:1 0/1:891:47:24,23:384,459:843,47:0.0527:2,2:26.8:1:30:1:0.54786:1.25:37.7:94:0.053:0:1 +1 9786882 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=CTACTAACCATTTCATTCAG;RSEQ=GACTCTGAAGTCCCCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:160,13:173,2:0.0114:2,2:25.5:1:31:1:0.15402:11.89718:60:4:0.0115:0:1 0/0:169:0:0,0:141,28:169,0:0:2,0:21.1:1:28.9:1:1:0:60:55.333:1:0:0.2 +1 9787140 . C A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24909;SOR=Inf;LSEQ=CTGGGCCCAAGAGGAGGCGG;RSEQ=TGCGGGTCGTGGGGACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:53,195:248,0:0:2,0:22.3:1:32.3:1:1:0:60:26.556:0.9958:0:0.1 0/1:263:3:1,2:64,195:259,3:0.0114:2,2:19.7:1:23:1:1:1.52:60:2:0.0078:0:2.3 +1 9787143 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10859;SOR=0;LSEQ=GGCCCAAGAGGAGGCGGCTG;RSEQ=GGGTCGTGGGGACCAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:0,3:40,187:227,3:0.013:2,0:24:1:32.7:1:1:0:60:6:0.0134:0:1 0/0:251:0:0,0:58,193:251,0:0:2,0:23.1:1:29.4:1:1:0:60:49.2:1:0:0.2 +1 10114712 . AT A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50511;SOR=Inf;LSEQ=CAAGACTGTTGCCATTGTTC;RSEQ=TTACTACAATGCCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:28,10:38,0:0:2,0:18.5:1:29.9:1:1:0:58.7:18:1:0:0.1 0/1:51:2:1,1:34,15:49,2:0.0392:2,2:36.5:1:29.5:1:0.53333:2.22676:59:4:0.0408:0:1.5 +1 10114751 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52016;SOR=Inf;LSEQ=GCATGCTGGGTAACATTGTA;RSEQ=ACTCTTCCAGTCTAGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:27,25:52,0:0:2,0:30.6:1:32.1:1:1:0:59.1:51:1:0:0.1 0/1:81:2:1,1:42,37:79,2:0.0247:2,2:27.5:1:25.5:1:1:1.13335:59:4:0.0247:0:1.5 +1 10114788 . AT A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.17208;SOR=0;LSEQ=CATGGTAACACTTGCGGGGC;RSEQ=TTTTTTTGGAACAGTACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:18,28:46,2:0.0417:2,2:6:1:28:1:1:1.54:52:4:0.0426:0.0208:2 0/0:67:0:0,0:27,40:67,0:0:2,0:24.3:1:29.6:1:1:0:57.8:134:1:0:0.2 +1 10702618 . C A 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGACCGGCGCTGGGCCCAGG;RSEQ=CGGGTGGGAGGCAGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:6,2:0.25:2,2:21:1:27:1:1:1:60:4:0.25:0:2.5 1/1:1:1:1,0:0,0:0,1:1:0,0:7:0:29:0:1:0:60:2:1:0:1 +1 11168371 . A G 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10344;SOR=0;LSEQ=AGGAGGAACAAAAACATTTC;RSEQ=CTCTCTTCCTGGCAATCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:64,172:236,3:0.0126:2,2:9.3:1:24.3:1:1:1.34:60:2:0.0087:0:1 0/0:269:0:0,0:78,190:268,0:0:2,0:22.8:1:28.6:1:1:0:60:52.6:1:0:0.1 +1 11169271 . G T 49 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.41438;SOR=0.3963;LSEQ=TCACTAACACCACTGGACAT;RSEQ=GGGCTGACCACCACTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:4:2,2:233,67:300,4:0.0132:2,2:19.8:1:24.5:1:0.22266:3.45938:60:3:0.0103:0:1 0/0:381:2:1,1:271,108:379,2:0.0052:2,2:17.5:1:28:1:0.49087:2.50234:60:4:0.0053:0:1.5 +1 11169639 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11091;SOR=Inf;LSEQ=TCTTGTTGACCCCTCTCAGG;RSEQ=TATAACACAGCTGCTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:167,98:265,0:0:2,0:24.7:1:31.4:1:1:0:59.7:65.25:1:0:0.1 0/1:247:3:1,2:163,81:244,3:0.0121:2,2:21.3:1:26.3:1:0.26197:4.0002:60:6:0.0123:0:1.3 +1 11174067 . A T 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.44444;SOR=Inf;LSEQ=TGCCCCCAAGTGAAGAAGGA;RSEQ=GTGTTTGCTTCCCCTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:37.7:1:31.3:1:1:0:54:6:0.375:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:49:0:32:0:1:0:60:2:1:0:3 +1 11175116 . TA T 81 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.38909;SOR=0.29618;LSEQ=CAGGGATTTGAAAGACAACT;RSEQ=AAAAAAAAAAGAAACGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:0,6:4,15:19,6:0.24:2,0:32.3:1:31.5:1:0.5404:0:60:12:0.25:0:0.2 0/1:12:1:0,1:2,8:10,1:0.0833:2,0:30:0:32:0:1:0:60:2:0.0833:0:0 +1 11175344 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49876;SOR=Inf;LSEQ=ACAGCCTTGGTAGGGCCAGC;RSEQ=GGGGTTAAGAGTAAGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:163,28:191,0:0:2,0:22.4:1:30.5:1:1:0:60:46.75:1:0:0.1 0/1:195:2:1,1:171,22:193,2:0.0103:2,2:29:1:30:1:0.22252:7.62399:60:4:0.0105:0:1 +1 11175367 . G T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04363;SOR=0;LSEQ=GGTTAAGAGTAAGGCAGTTT;RSEQ=GGCTTAAGTCTGCCTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:4:1,3:228,70:298,4:0.0132:2,2:12.3:1:27:1:0.04513:9.67759:60:8:0.0135:0:1 0/0:357:0:0,0:261,96:357,0:0:2,0:22.5:1:30.7:1:1:0:60:177.5:1:0:0.1 +1 11175384 . C T 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17858;SOR=0.2004;LSEQ=TTTGGGCTTAAGTCTGCCTA;RSEQ=AGTGTCAGAGGAGGGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:4:2,2:279,117:396,4:0.01:2,2:12.3:1:25.5:1:0.58565:2.3788:60:3:0.0076:0:2 0/0:497:1:0,1:332,164:496,1:0.002:2,0:1:0:24:0:0.33199:0:60:2:0.002:0:1 +1 11175590 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24756;SOR=Inf;LSEQ=ACGGATGAAAAAATCAATAA;RSEQ=TACGTGATACTGTAAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:12,136:148,0:0:2,0:23.2:1:32.3:1:1:0:60:36:1:0:0.1 0/1:151:3:2,1:23,125:148,3:0.0199:2,2:8.7:1:26.7:1:0.07129:10.60:60:6:0.02:0:1.3 +1 11176987 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09689;SOR=0;LSEQ=AAAAGCCATATATTTAATTG;RSEQ=AAAACCAAATGAAACCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:243,54:297,3:0.01:2,2:17:1:25.7:1:0.09057:8.90563:60:6:0.0101:0:1 0/0:352:0:0,0:274,78:352,0:0:2,0:23.9:1:30.3:1:1:0:60:87:1:0:0.1 +1 11177200 . TTATACTCTAA T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04066;SOR=0;LSEQ=AAACTTTAATTTCAACATAA;RSEQ=TAAGCTGTCTTTGGTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:4:1,3:41,232:273,4:0.0144:2,2:33.5:1:31:1:0.48399:1.88:60:8:0.0147:0:0 0/0:338:0:0,0:78,258:336,0:0:2,0:21.4:1:27.7:1:1:0:60:66.2:0.997:0:0.1 +1 11181327 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.24141;LSEQ=GAGCTGGGGCTTTTCAGCCA;RSEQ=AGCAGCTTGGCCAGGTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:286:160,126:192,166:358,286:0.4441:2,2:25.2:1:29.8:1:0.57768:1.10:60:142:0.4472:0:1.1 0/1:681:110:60,50:315,256:571,110:0.1615:2,2:24:1:28.6:1:0.91697:1.02536:60:54:0.161:0:1.1 +1 11181963 . G T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5045;SOR=0;LSEQ=AGTGACAGACATACAGAGAG;RSEQ=AATGAGAAAAGCAGCGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:131,32:163,2:0.0121:2,2:10:1:25.5:1:0.36098:4.0466:60:4:0.0122:0:1 0/0:132:0:0,0:108,24:132,0:0:2,0:19.5:1:30.2:1:1:0:60:131:1:0:0.1 +1 11181978 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22181;SOR=Inf;LSEQ=GAGAGGAATGAGAAAAGCAG;RSEQ=GCTACGGAGATTCCCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:154,50:204,0:0:2,0:24:1:31.3:1:1:0:60:33:0.995:0:0.3 0/1:183:2:1,1:141,38:179,2:0.0109:2,2:21:1:27.5:1:0.38545:3.67592:60:4:0.0109:0:1 +1 11181985 . G A 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATGAGAAAAGCAGCGCTACG;RSEQ=AGATTCCCTGCCACGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:40:30,10:156,47:203,40:0.1646:2,2:22.5:1:30.4:1:0.83885:1.10591:60:39:0.1632:0:1.1 0/0:210:0:0,0:161,49:210,0:0:2,0:23:1:30.4:1:1:0:60:51.5:1:0:0.2 +1 11181995 . G T 46 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7253;LSEQ=CAGCGCTACGGAGATTCCCT;RSEQ=CCACGGAAGGGGCACTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:3:1,2:203,71:274,3:0.0108:2,2:12.3:1:29.3:1:0.17075:5.6748:60:6:0.011:0:1 0/0:254:2:0,2:176,76:252,2:0.0079:2,0:1:0:22.5:1:0.09346:0:60:4:0.008:0:1 +1 11182261 . G GT 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.97664;LSEQ=GCTCAGAACACAGGCAGACT;RSEQ=TTTTTTTTTTCTTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:8:0,8:8,116:124,8:0.0602:2,0:30.5:1:30.8:1:1:0:56:16:0.063:0:0 0/1:136:8:0,8:15,113:128,8:0.0588:2,0:21.8:1:29.8:1:0.59755:0:55.3:16:0.0615:0:0.1 +1 11182303 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1875;SOR=Inf;LSEQ=CAGAGTCTTGCTCTGTTGCC;RSEQ=AGGCTGGAGTGCAGTGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:36,0:0:1,0:21.3:1:32.9:1:1:0:48.5:35:1:0:0.2 0/1:28:2:1,1:0,26:26,2:0.0714:1,2:9.5:1:28:1:0.07143:0:40:4:0.0714:0:4 +1 11182322 . A C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18354;SOR=Inf;LSEQ=CCAGGCTGGAGTGCAGTGGC;RSEQ=CAATCTTGGCTCACTGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:0,22:22,0:0:1,0:14.3:1:30:1:1:0:35.5:21:1:0:0.3 0/1:17:2:1,1:0,15:15,2:0.1176:1,2:28.5:1:31:1:0.11765:0:40:4:0.1176:0:4 +1 11182339 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.083;SOR=Inf;LSEQ=GGCACAATCTTGGCTCACTG;RSEQ=AACCTCTGCCTCCTGGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:0,16:16,0:0:1,0:10.6:1:32.6:1:1:0:30.3:32:1:0:0 0/1:7:2:1,1:0,5:5,2:0.2857:0,2:28:0:31.5:1:0.28571:0:40:4:0.2857:0:4 +1 11182345 . C G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07353;SOR=Inf;LSEQ=ATCTTGGCTCACTGCAACCT;RSEQ=TGCCTCCTGGGTTCAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:12,0:0:0,0:14.3:1:32.4:1:1:0:31.3:24:1:0:0 0/1:5:2:1,1:0,3:3,2:0.4:0,2:22:0:33.5:1:0.4:0:40:4:0.4:0:4 +1 11185626 . A G 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGAAATCCCATCTCTACT;RSEQ=AAAATATAAAAATTAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:47:0:31.5:1:1:0:36.5:4:0.6667:0:2.5 +1 11185670 . T C 27 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGGCATGCGCCTGTAATC;RSEQ=CAGCTATTAGGGAGGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:6.5:1:27.5:1:1:0:36.5:4:0.6667:0:2.5 +1 11186291 . T TA 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCACAGAGACTATGATGG;RSEQ=AAAAAAAAAAAGAAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:14:1:28.5:1:1:1.73:60:6:0.6:0.2:0.3 0/0:1:0:0,0:1,0:1,0:0:0,0:50:0:28:0:1:0:60:2:1:0:0 +1 11187618 . A AT 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.63499;SOR=1.20763;LSEQ=ATAAAAACTTTTCTCATTTC;RSEQ=TTTTTTTTTAGTGGCAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:417:17:12,5:305,92:397,17:0.0408:2,2:19.6:1:31.6:1:0.56172:1.38018:60:34:0.0414:0.0096:0.2 0/1:512:25:17,8:345,140:485,25:0.0488:2,2:24.2:1:28.7:1:0.82146:1.1593:59.8:24:0.0479:0.0117:0.3 +1 11187838 . G A 56 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21844;SOR=4.71615;LSEQ=ACATCTCATGCCAGAGGATG;RSEQ=CCACTCGGATCAGCTCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:1:1,0:86,274:360,1:0.0028:2,0:1:0:26:0:0.241:0:60:2:0.0028:0:1 0/1:386:5:3,2:94,285:379,5:0.013:2,2:15.4:1:24.4:1:0.10489:4.53:60:4:0.0106:0:1 +1 11187882 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=ACCTGAAGCCAAGAGAAGAA;RSEQ=GAGAGAAGCATCAAGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:37,143:180,2:0.011:2,2:16:1:32.5:1:0.3749:3.83:60:4:0.011:0:2 0/0:169:0:0,0:32,137:169,0:0:2,0:24:1:30.8:1:1:0:60:41.25:1:0:1 +1 11187893 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46708;SOR=0;LSEQ=AGAGAAGAAGGAGAGAAGCA;RSEQ=CAAGAATCAGCTAACCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:170:170:36,134:0,0:0,170:1:0,2:23.9:1:31.8:1:1:0:59.7:55.667:1:0:1.1 1/1:149:148:33,115:0,0:0,148:0.9933:0,2:22.6:1:31.4:1:1:0:60:147:0.9932:0:1.1 +1 11188004 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23421;SOR=0;LSEQ=GGAAGAAAAACAATCCCACT;RSEQ=GCGCCCACCAGCTAAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:123,63:186,2:0.0106:2,2:32:1:31.5:1:1:1.94499:60:4:0.0109:0:1 0/0:201:0:0,0:136,64:200,0:0:2,0:21.8:1:29.5:1:1:0:60:99:1:0:0.2 +1 11188012 . C T 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37324;SOR=3.80951;LSEQ=AACAATCCCACTTGCGCCCA;RSEQ=CAGCTAAGGGACCAGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:0,1:137,75:212,1:0.0047:2,0:1:0:28:0:0.35681:0:60:2:0.0048:0:1 0/1:226:4:2,2:151,71:222,4:0.0177:2,2:17.8:1:25.5:1:0.59631:2.11905:60:3:0.0136:0:1 +1 11188013 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24928;SOR=Inf;LSEQ=ACAATCCCACTTGCGCCCAC;RSEQ=AGCTAAGGGACCAGGGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:139,77:216,0:0:2,0:23.2:1:31.1:1:1:0:60:35:1:0:0.2 0/1:232:3:1,2:154,75:229,3:0.0129:2,2:15.3:1:25.3:1:0.25637:4.07951:60:6:0.0131:0:1 +1 11188049 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65791;SOR=0.51471;LSEQ=GTCTATGAAGCCCCACAGTG;RSEQ=CTCCGACCCACCATCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:2,1:165,125:290,3:0.0102:2,2:24.3:1:29.7:1:1:1.51:60:6:0.0104:0:1 0/0:378:2:1,1:226,150:376,2:0.0053:2,2:16.5:1:28:1:1:1.50495:60:4:0.0054:0:1 +1 11189770 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10102;SOR=0;LSEQ=CATTAACATGGCCTACCAGA;RSEQ=TTGCATCCTTCCCTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:189,108:297,3:0.01:2,2:14.7:1:29:1:0.55668:3.48476:60:6:0.0102:0:1 0/0:343:0:0,0:232,111:343,0:0:2,0:24.6:1:31.4:1:1:0:60:170.5:1:0:0.1 +1 11190646 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26781;LSEQ=TTCTCGGTGCTCTCGGCCTC;RSEQ=CTCTCACTGTTGCTGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:727:295:156,139:238,192:430,295:0.4058:2,2:23.7:1:30.2:1:0.54396:1.10435:60:146.5:0.4115:0:1.1 0/1:945:146:81,65:422,375:797,146:0.1545:2,2:24:1:29.2:1:0.58934:1.11:60:47.667:0.1541:0:1.2 +1 11193560 . A AGTT 47 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAATTTTTTGTGGGTGAC;RSEQ=GTTGAGAGTTACTTCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:17.3:1:30:1:1:0:60:6:1:0.3333:0 1/1:1:1:0,1:0,0:0,1:1:0,0:13:0:31.7:0:1:0:60:2:1:0:0 +1 11194368 . G T 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72395;SOR=0.74003;LSEQ=AGAAGCTGCTGGGATGACAG;RSEQ=GCTGGAATATGACTTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:4:1,3:249,111:360,4:0.011:2,2:10.3:1:26:1:0.09283:6.69138:60:8:0.0112:0:1 0/0:368:3:0,3:243,122:365,3:0.0082:2,0:2.3:1:21:1:0.03857:0:60:2:0.0056:0:1 +1 11194604 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23134;SOR=Inf;LSEQ=AGCTACCGTTCATCTGATAG;RSEQ=CATGAGTCAACCCCTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:8,108:116,0:0:2,0:24.5:1:32:1:1:0:60:28:1:0:0.1 0/1:108:2:1,1:11,95:106,2:0.0185:2,2:7:1:26.5:1:0.2108:8.31:60:4:0.0189:0:1 +1 11205058 . C T 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.31724;LSEQ=CTGTAACTCTCTCCTGCCAT;RSEQ=GCAGTTAATTCAGCATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:852:451:232,219:197,204:401,451:0.5293:2,2:24.1:1:30.2:1:0.5368:1.10:59.9:40:0.5257:0:1.2 1/1:920:763:369,394:77,78:155,763:0.8293:2,2:24.6:1:29.5:1:0.79181:1.05403:60:189.75:0.8286:0:1.1 +1 11205273 . T A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11688;SOR=Inf;LSEQ=CTGAATGGCTTGAGAGGAGG;RSEQ=ATTATCCAATTTCTCATCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:1,50:51,0:0:1,0:23:1:28.9:1:1:0:59.6:102:1:0:0.1 0/1:27:2:0,2:1,24:25,2:0.0741:1,0:26.5:1:32:0:1:0:60:4:0.0741:0:1 +1 11206586 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19616;SOR=Inf;LSEQ=TGCTGGCAGTCTTCTGAGTA;RSEQ=AATGAATCAAAACCATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:60,1:61,0:0:1,0:24.9:1:32.7:1:1:0:60:122:1:0:0.1 0/1:49:2:1,1:47,0:47,2:0.0408:1,2:22.5:1:27:1:0.04082:0:60:4:0.0408:0:1 +1 11206670 . G A 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.43982;SOR=2.11865;LSEQ=AGCTTCTTTACCAAAGCACC;RSEQ=TGGGCTTAGAAGCACTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:2:1,1:257,76:333,2:0.006:2,2:11.5:1:29:1:0.4074:3.36602:60:4:0.006:0:1 0/1:318:4:2,2:241,73:314,4:0.0126:2,2:33.3:1:25.3:1:0.23731:3.28589:60:3:0.0096:0:1 +1 11206679 . G T 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05242;SOR=Inf;LSEQ=ACCAAAGCACCGTGGGCTTA;RSEQ=AAGCACTACAATCTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:296,109:405,0:0:2,0:22.6:1:32.7:1:1:0:60:100.25:1:0:0.1 0/1:374:4:2,2:267,103:370,4:0.0107:2,2:9:1:23:1:0.31416:2.58462:60:3:0.0081:0:1 +1 11207269 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAAATTACATTTTCCTC;RSEQ=AAACAATTGAAAATAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:19:1:27:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 11217114 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24053;SOR=Inf;LSEQ=AACAAAATGAGTCTGAAGTG;RSEQ=GAACTCCGTGTGGGGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:118,2:120,0:0:1,0:25.4:1:29.9:1:1:0:59.8:29:1:0:0.1 0/1:116:2:1,1:111,3:114,2:0.0172:1,2:19:1:32.5:1:0.06807:32.17955:60:4:0.0172:0:1 +1 11217138 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21181;SOR=0;LSEQ=CTCCGTGTGGGGGAAGCCTT;RSEQ=CTTTCAAATCCAAAGATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:152,23:175,2:0.0113:2,2:18.5:1:29.5:1:0.25347:6.4908:60:4:0.0115:0:1 0/0:207:0:0,0:177,30:207,0:0:2,0:21.9:1:30:1:1:0:60:40.4:1:0:0.1 +1 11227302 . TA T 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.66513;SOR=0.37921;LSEQ=CCTAGAACTTAAAGTATAAT;RSEQ=AAAAAAAAAAAGAAAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:6,0:42,0:42,6:0.1176:1,0:23:1:30.4:1:1:0:53.8:12:0.12:0.0392:0.3 0/1:21:1:1,0:20,0:20,1:0.0476:1,0:42:0:29:0:1:0:43:2:0.0476:0:0 +1 11227864 . C T 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTGGGTGTGGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:21:1:31.3:1:1:0:53.8:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 11259250 . C T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12413;SOR=Inf;LSEQ=TGACTCCAGTGAAGTGGCAC;RSEQ=AGGCAGTGGGAGAAGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:235,36:271,0:0:2,0:22:1:31.2:1:1:0:60:89.333:1:0:0.1 0/1:285:4:1,3:224,57:281,4:0.014:2,2:10.8:1:26.5:1:0.03042:11.64694:60:8:0.0143:0:1 +1 11264299 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CCTGTGGTATTTGTAACAAA;RSEQ=AGCAATAATTAGAATACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:22:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 11269272 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22455;SOR=Inf;LSEQ=TTTCTGGAAAAAACACCTGG;RSEQ=CTGGTTTTCGGTTGCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:143,3:146,0:0:1,0:24.1:1:31.5:1:1:0:60:47.667:1:0:0.1 0/1:132:2:1,1:127,3:130,2:0.0152:1,2:5.5:1:27:1:0.05991:36.7993:60:4:0.0153:0:1.5 +1 11269281 . C T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=AAAACACCTGGGCTGGTTTT;RSEQ=GGTTGCCCAGTTTAAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:171,9:180,0:0:2,0:22.9:1:32.3:1:1:0:60:89:1:0:0.1 0/1:153:11:11,0:132,10:142,11:0.0719:2,0:33:1:29.5:1:1:0:60:22:0.0719:0:1.1 +1 11269796 . T C 32 q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTCGGCAATGGGAAAAG;RSEQ=GATAAAGTGTTTGGAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:33:1:20.7:1:1:0:59.3:2:0.25:0:4.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 11270776 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24654;SOR=Inf;LSEQ=TGCCAATCCCTAATTTACAG;RSEQ=CAAAAAGCTACACAAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:99,10:109,0:0:2,0:25.4:1:32.1:1:1:0:60:53.5:1:0:0.1 0/1:108:2:1,1:88,18:106,2:0.0185:2,2:6.5:1:26.5:1:0.32226:4.78552:60:4:0.0192:0:1 +1 11272754 . CA C 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.73582;SOR=0.66093;LSEQ=AATAATGTGAGTTGAAATAA;RSEQ=AAAAAAATAGAAAGATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:5:4,1:103,10:113,5:0.0424:2,2:19:1:32:1:0.3924:2.54612:60:10:0.0435:0.0169:0.2 0/1:141:4:4,0:130,6:136,4:0.0284:1,0:23.5:1:30.6:1:1:0:60:8:0.0286:0.0071:0 +1 11273390 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49981;SOR=0;LSEQ=AGAATGAGGTCTCAGCTTTT;RSEQ=GCTGATCACCCAGGGACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:109,21:130,2:0.0152:2,2:19.5:1:30.5:1:0.30662:5.09448:60:4:0.0153:0:1 0/0:117:0:0,0:88,29:117,0:0:2,0:22.6:1:27.4:1:1:0:60:28.25:1:0:0.1 +1 11273413 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23007;SOR=Inf;LSEQ=TGATCACCCAGGGACTCAGA;RSEQ=GAAATCAGAAAATCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:155,56:211,0:0:2,0:22.5:1:32.5:1:1:0:60:422:1:0:0.1 0/1:195:2:1,1:138,55:193,2:0.0103:2,2:10.5:1:28.5:1:0.49294:2.49559:60:4:0.0105:0:1 +1 11273442 . C T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12387;SOR=0;LSEQ=AAAATCTCTCTGGAGGATGA;RSEQ=GTAGGCTACTCACCTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:4:1,3:212,116:328,4:0.012:2,2:12.5:1:28.5:1:0.1333:5.45413:60:8:0.0121:0:1 0/0:332:0:0,0:217,115:332,0:0:2,0:24.5:1:30.6:1:1:0:60:65.4:1:0:0.2 +1 11273651 . T G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=GAGAGAAAAGTCAGAGGAGC;RSEQ=GAGTCAGGTCCCTTTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:28,143:171,0:0:2,0:23.2:1:30.6:1:1:0:59.8:33.2:1:0:0.1 0/1:187:2:1,1:41,144:185,2:0.0107:2,2:12:0:32:0:0.39969:3.48:60:4:0.011:0:2 +1 11287785 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTGCCAGCTAATAAAAT;RSEQ=GAGAAGGAATAGCAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 11288618 . G A 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.95365;LSEQ=TTAAGGGGGAGGAAGGCATT;RSEQ=GGCTCAGGGGCACAGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:58:58,0:74,2:76,58:0.4328:1,1:27.2:1:28.3:1:0.50533:0:60:57:0.4351:0:1.9 1/1:108:91:91,0:17,0:17,91:0.8426:1,1:24.6:1:27.6:1:1:0:60:44.5:0.8396:0:2.1 +1 11288633 . G C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=6.45355;LSEQ=GCATTGGGCTCAGGGGCACA;RSEQ=AGAATGCACAATTAAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:70:65,5:93,6:99,70:0.4142:2,2:25.8:1:32.8:1:0.76347:1.19105:60:140:0.4167:0:1.8 1/1:151:124:117,7:26,1:27,124:0.8212:1,2:23.9:1:31.7:1:1:1.55156:60:123:0.82:0:1.8 +1 11288758 . G A 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.70983;LSEQ=CCATCACAGACTCGAATGAC;RSEQ=TTAAGGAACGTGGGCATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:788:319:168,151:233,234:467,319:0.4048:2,2:24.1:1:30.6:1:0.46784:1.12:60:52.167:0.4028:0:1.1 1/1:919:754:384,370:81,83:164,754:0.8205:2,2:25.3:1:29.5:1:0.73111:1.06:60:52.857:0.8204:0:1.2 +1 11289161 . G A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01084;SOR=Inf;LSEQ=AATAGCCTCTCACCATCAAG;RSEQ=AGTAAACGGTTTTTGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:0,4:0,10:10,4:0.2857:0,0:33.8:1:26:1:1:0:60:3:0.2308:0:1.3 1/1:5:5:0,5:0,0:0,5:1:0,0:13.4:1:31:1:1:0:60:10:1:0:1.2 +1 11290880 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08647;SOR=Inf;LSEQ=TTGCTACACGAGCCAATATC;RSEQ=TATAATTTCTCAGTAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:109,2:111,0:0:1,0:24.7:1:31.4:1:1:0:59.7:36:1:0:0 0/1:89:3:3,0:84,2:86,3:0.0337:1,0:24:1:30.3:1:1:0:60:6:0.0345:0:1 +1 11291380 . G A 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01272;SOR=0.09544;LSEQ=TCTGCGTGTACCCTGGTTCT;RSEQ=CTCAGTCTTCAGAAAATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:689:8:6,2:387,294:681,8:0.0116:2,2:15.6:1:26.1:1:0.47686:2.28:60:16:0.0118:0:1 0/0:894:1:1,0:457,436:893,1:0.0011:2,0:1:0:22:0:1:0:60:2:0.0011:0:1 +1 11291598 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51437;SOR=0;LSEQ=AGTGTTAGAGGCTGTAAGAA;RSEQ=AAAAGAGGTTTCCAGTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:0,2:5,85:90,2:0.0217:2,0:38:1:28.5:1:1:0:60:4:0.0222:0:1 0/0:63:0:0,0:1,62:63,0:0:1,0:23.3:1:30.3:1:1:0:60:20:1:0:0.2 +1 11292666 . T A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.8093;LSEQ=TGGAGGCCGGGCACGGTGGC;RSEQ=CATGCCTGTAATCCCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:53:2,51:3,73:76,53:0.4046:1,1:23.7:1:30.5:1:1:1.04757:54.8:106:0.4109:0:1.2 1/1:119:98:12,86:3,16:19,98:0.8235:2,2:22:1:29:1:0.70898:1.3401:56.4:48:0.8348:0:1.2 +1 11292753 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01549;SOR=5.70745;LSEQ=ACCAGCCTAGCCAACATGGT;RSEQ=AAACCCCATCTCTACTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:0,15:0,14:14,15:0.5172:1,1:15.7:1:32.3:1:1:0:41.7:30:0.5172:0:1.5 1/1:22:19:0,19:0,3:3,19:0.8636:0,1:24.7:1:31.3:1:1:0:42.3:38:0.8636:0:1.3 +1 11292881 . A G 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGAGGTTGCAGTGAGCC;RSEQ=AGATCACACCACTGCACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:3,3:0.5:2,0:26.3:1:31:1:1:0:45:6:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 11293367 . TA T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.17786;SOR=1.75272;LSEQ=AATATGTGAGACCTTTCATT;RSEQ=AAAAAAAAAATAGTATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:11:9,2:160,17:177,11:0.0585:2,2:24.9:1:31.5:1:0.30722:2.08097:60:22:0.0598:0.016:0 0/1:183:18:15,3:135,25:160,18:0.0984:2,2:25.3:1:30.3:1:1:1.07954:58.9:36:0.1006:0.0109:0.2 +1 11293959 . C T 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTCCTTTCCAAACATCTG;RSEQ=GATGATGTGCCTGAAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:5,1:2,0:2,6:0.75:0,2:17.8:1:32:0:1:0:55.3:12:0.75:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:16:1:27:1:1:0:60:6:1:0:1 +1 11294382 . T A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.51762;LSEQ=GACATTCTAGAGAGAGACTG;RSEQ=GTCCAACAGAAAAAGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:26,130:156,2:0.0127:2,2:26:1:29.5:1:0.31347:4.93:60:4:0.0127:0:1 0/0:152:1:1,0:26,116:142,1:0.0066:2,0:1:0:23:0:0.18881:0:60:2:0.0066:0:1 +1 11294474 . T A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0207;SOR=6.58532;LSEQ=ATACTCAATGAGCAACAGAC;RSEQ=TTTCTGCAACAGGCAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:0,7:0,21:21,7:0.25:1,0:23.1:1:29.3:1:1:0:60:6:0.2222:0:1.1 1/0:10:7:0,7:0,3:3,7:0.7:0,0:24.7:1:31.6:1:1:0:60:14:0.7:0:1 +1 11297762 . T C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00021;SOR=7.72507;LSEQ=GCCAGGGAAACATTTGGACC;RSEQ=TTGCAGACAAATGCGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:16:15,1:22,0:22,16:0.4211:1,1:27.8:1:32.1:1:0.42105:0:60:32:0.4211:0:1.2 1/1:34:29:27,2:5,0:5,29:0.8529:0,2:22.1:1:31:1:1:0:60:58:0.8529:0:1.1 +1 11297771 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49463;SOR=Inf;LSEQ=ACATTTGGACCTTTGCAGAC;RSEQ=AATGCGGCTTTTACCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:43,1:44,0:0:1,0:23.7:1:30.4:1:1:0:60:43:1:0:0.5 0/1:46:2:1,1:42,2:44,2:0.0435:1,2:41.5:1:29.5:1:0.12754:17.3476:60:4:0.0435:0:2 +1 11297779 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22013;SOR=0;LSEQ=ACCTTTGCAGACAAATGCGG;RSEQ=TTTTACCAGGTACCTCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:48,0:48,2:0.04:1,2:32.5:1:31:1:0.04:0:60:4:0.0408:0:2 0/0:56:0:0,0:53,3:56,0:0:2,0:21.9:1:32:1:1:0:60:112:1:0:0.6 +1 11298182 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51448;SOR=0;LSEQ=TCCCAGCTTCTACCTCCACT;RSEQ=CCATCAGCGTAGTGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:8,91:99,2:0.0196:2,2:26.5:1:27.5:1:0.17109:10.78:60:4:0.0208:0:1 0/0:70:0:0,0:6,64:70,0:0:2,0:21.4:1:32:1:1:0:60:140:1:0:0.1 +1 11298641 . G T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02655;SOR=0;LSEQ=CACTGTTCAGGAAATGATCC;RSEQ=CACAGTGGCGAACAAATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:4:2,2:148,232:380,4:0.0104:2,2:26:1:30.5:1:0.64544:1.57:60:8:0.0106:0:1.3 0/0:568:0:0,0:240,325:565,0:0:2,0:24.8:1:30.3:1:1:0:60:93.167:0.9947:0:0.1 +1 11298790 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=28.16803;LSEQ=TAATTCTACTTTCAACTAGA;RSEQ=ATTGATCAATACGATACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:13:0,13:0,25:25,13:0.3421:1,1:26.8:1:31.5:1:1:0:58.6:12:0.3243:0:1.3 1/1:33:31:0,31:0,2:2,31:0.9394:0,1:21.6:1:32.2:1:1:0:59.1:30:0.9375:0:1.3 +1 11300318 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50397;SOR=Inf;LSEQ=TTCCTTTCCCAAAGTTTCCA;RSEQ=CATCTCTCACTATCTTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:89,31:120,0:0:2,0:23.4:1:33.2:1:1:0:60:119:1:0:0.1 0/1:149:2:1,1:99,48:147,2:0.0134:2,2:27:1:31:1:0.55106:2.05168:60:4:0.0135:0:1 +1 11300344 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59447;SOR=0.41863;LSEQ=CTCACTATCTTGGCAAGAGC;RSEQ=GTTGTAATTTCTTACCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:134,54:188,2:0.0105:2,2:31:1:30:1:0.49624:2.46799:60:4:0.0106:0:1 0/0:226:1:0,1:146,79:225,1:0.0044:2,0:1:0:25:0:0.35398:0:60:2:0.0045:0:1 +1 11301714 . A G 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=6.67215;LSEQ=ATGCAAGTGAAGACTGTGGC;RSEQ=TCCACCTGCATTGCCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:236:102,134:166,202:368,236:0.3907:2,2:26.2:1:31:1:0.67517:1.07945:60:58:0.3893:0:1.1 1/1:777:630:291,339:69,76:145,630:0.8108:2,2:25.6:1:30.2:1:0.78224:1.05754:60:104:0.8114:0:1.2 +1 11302065 . G A 52 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTGAACAATGTGTTCATCAG;RSEQ=GACAAGAAGGCAGTACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:15:1:33.3:1:1:0:60:6:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:21:0:32:0:1:0:60:2:1:0:0 +1 11303116 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23076;SOR=Inf;LSEQ=CGTGGATCTGAAATAGAGCG;RSEQ=CCTTCCTCTCCAACCAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:172,20:192,0:0:2,0:23.4:1:30.3:1:1:0:59.8:191:1:0:0.1 0/1:178:2:1,1:145,31:176,2:0.0112:2,2:24:0:32.5:1:0.32806:4.61963:60:4:0.0113:0:1 +1 11303131 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06251;SOR=0;LSEQ=GAGCGTCCTTCCTCTCCAAC;RSEQ=AAATGGAGTGGAAGGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:5:1,4:204,64:268,5:0.0183:2,2:11.4:1:26.2:1:0.01456:12.60622:60:10:0.0187:0:1 0/0:250:0:0,0:185,65:250,0:0:2,0:23.4:1:30.1:1:1:0:60:40.667:1:0:0.1 +1 11303407 . T A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0932;SOR=0;LSEQ=TCCAGGTCAGGGTTAGGGTC;RSEQ=ACATATCAACAGTCAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:3:2,1:26,152:178,3:0.0166:2,2:15:1:23.3:1:0.06287:11.43:60:2:0.0114:0:1 0/0:217:0:0,0:47,170:217,0:0:2,0:23.7:1:27.7:1:1:0:60:35.167:1:0:0.1 +1 11308168 . G GA 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.24921;SOR=Inf;LSEQ=GACGCTATATATATGAGGAG;RSEQ=AAAAAAATCATCTTTACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:42,239:281,0:0:2,0:23.4:1:32:1:1:0:59.9:69.25:1:0:0.1 0/1:296:3:1,2:57,236:293,3:0.0101:2,2:32.3:1:30:1:0.48147:2.06:60:6:0.0103:0:0.3 +1 11313799 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24159;SOR=Inf;LSEQ=TATTTATTATGTTTCCTGCC;RSEQ=CAAAATGTCAGCTCCATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:131,4:135,0:0:1,0:20.5:1:31.2:1:1:0:60:66.5:1:0:0.1 0/1:131:2:1,1:125,4:129,2:0.0153:1,2:26:1:28.5:1:0.07516:28.06607:60:4:0.0153:0:1 +1 11314202 . AT A 33 v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.10475;LSEQ=TTTTATTTAATTCAGCTTCA;RSEQ=TTTTTTTTTTTGAGATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:0,31:31,2:0.0606:1,2:50:0:33:1:0.06061:0:60:4:0.0645:0:0 0/1:15:1:0,1:0,14:14,1:0.0667:1,0:39:0:32:0:1:0:47:2:0.0667:0:0 +1 11315975 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10369;SOR=Inf;LSEQ=GCTCCATGGCAAGGGCTTGT;RSEQ=GCTGCCCTTTAGGCCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:129,29:158,0:0:2,0:27.4:1:31.6:1:1:0:59.8:38.5:1:0:0.3 0/1:141:3:2,1:98,40:138,3:0.0213:2,2:22.7:1:30.3:1:1:1.22313:60:6:0.0213:0:1 +1 11315990 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49918;SOR=Inf;LSEQ=CTTGTGGCTGCCCTTTAGGC;RSEQ=AGGTGATTCTCTACGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:145,40:185,0:0:2,0:27.4:1:30.4:1:1:0:60:15.818:1:0:0.1 0/1:197:2:1,1:124,71:195,2:0.0102:2,2:20:1:28:1:1:1.7412:60:4:0.0104:0:1 +1 11316899 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.49934;SOR=Inf;LSEQ=AGCTCTTCTAACCAGCTTTT;RSEQ=TAAGGAATGAGCCTCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:66,4:70,0:0:2,0:26.7:1:31.4:1:1:0:60:140:1:0:0.1 0/1:81:2:1,1:74,5:79,2:0.0247:2,2:19:1:32.5:1:0.14352:13.60148:60:4:0.0253:0:1 +1 11317298 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49922;SOR=0;LSEQ=TACGCAGACTTCAACTAAAA;RSEQ=CTGGTGAGTGCCGGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:8,104:112,2:0.0175:2,2:7.5:1:29:1:0.15231:12.32:60:4:0.018:0:1 0/0:102:0:0,0:11,91:102,0:0:2,0:23.3:1:31.9:1:1:0:59.4:204:1:0:0.5 +1 11317320 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-04;SOR=4.36754;LSEQ=TGGTGAGTGCCGGCCAGGCA;RSEQ=GGTGGCTCAAGTCTGTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:31:2,29:0,28:28,31:0.5254:1,2:23.7:1:30.9:1:0.49269:0:55:62:0.5254:0:1.1 1/1:59:49:4,45:0,10:10,49:0.8305:0,2:22.8:1:29.8:1:1:0:58.1:98:0.8305:0:1 +1 11318548 . C T 69 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0171;SOR=Inf;LSEQ=GACTCTGTCCTTACCTATGG;RSEQ=CAAGATGCCACCTTTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:0:0,0:327,259:586,0:0:2,0:24.5:1:31.7:1:1:0:60:64.111:0.9983:0:0.1 0/1:679:7:3,4:366,306:672,7:0.0103:2,2:11.7:1:24.9:1:0.70802:1.59365:60:6:0.009:0:1.3 +1 11318714 . G T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50379;SOR=Inf;LSEQ=AACTGTGGTGGTGGGAGTGG;RSEQ=CTGGCATCTAAAGATTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:5,97:102,0:0:1,0:23.6:1:32:1:1:0:60:101:1:0:0.2 0/1:127:2:1,1:15,110:125,2:0.0157:2,2:5:0:31:0:0.23697:7.13:60:4:0.016:0:1.5 +1 11318763 . C G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=6e-04;SOR=5.05422;LSEQ=GCAGGAGGTATAGTTCAAAC;RSEQ=AAAGAAGACAAGTTACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:27:0,27:0,27:27,27:0.5:1,1:29:1:31.9:1:1:0:60:26:0.4906:0:1.1 1/1:43:36:2,34:0,7:7,36:0.8372:0,2:21.8:1:30.7:1:1:0:60:72:0.8372:0:1.1 +1 11319228 . C CA 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.48529;SOR=1.46527;LSEQ=CAAATCCTCACTTAGCTGTA;RSEQ=AAAAAAAAATGTAAACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:7:7,0:136,23:159,7:0.0419:2,0:33.6:1:31.2:1:0.59486:0:60:14:0.0432:0.006:0.1 0/1:199:12:8,4:148,38:186,12:0.0603:2,2:22.6:1:30:1:0.28568:1.93983:59.2:24:0.0609:0.0151:0.3 +1 11319587 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00017;SOR=5.5457;LSEQ=CCCCCTAGCCCTTGTCAGGC;RSEQ=GGGGATTCTAAAAAGGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:24:0,24:0,31:31,24:0.4364:1,1:25.5:1:29.6:1:1:0:60:11:0.4231:0:1.2 1/1:43:35:0,35:1,7:8,35:0.814:2,1:22.7:1:30.8:1:0.18605:0:60:34:0.8095:0:1.1 +1 11938050 . G A 73 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.6749;SOR=1.80915;LSEQ=CCCCCCAAGCTGGCAGCACC;RSEQ=GGGCCAGCTGCCCCCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,1:8,2:0.2:2,0:12.5:1:32.5:1:1:0:60:4:0.2:0:1 0/1:19:6:4,2:8,4:12,6:0.3158:2,2:13:1:28.5:1:1:1:60:12:0.3158:0:1.2 +1 11938146 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=0;LSEQ=GGCCTCAGCTCTGAAGCCCT;RSEQ=AGACGGCATGACCATCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:12,16:28,2:0.0667:2,2:29:1:30:0:1:1.32:60:4:0.0667:0:1 0/0:26:0:0,0:11,15:26,0:0:2,0:28.6:1:31:1:1:0:59.4:25:1:0:0.3 +1 11938203 . A G 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47478;LSEQ=TTGCTGCCGCAACTAGCAGT;RSEQ=CCTCGGGCTGGGCACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:1,8:9,3:0.25:2,0:10.7:1:31.3:1:1:0:60:6:0.25:0:1.7 0/1:12:4:0,4:2,6:8,4:0.3333:2,0:30:1:30.8:1:0.51515:0:60:8:0.3333:0:2.8 +1 11938210 . GC AA 59 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=3.65648;LSEQ=CGCAACTAGCAGTACCTCGG;RSEQ=TGGGCACCCTGAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:31:0:28:0:1:0:60:2:0.1667:0:2 0/1:9:4:0,4:1,4:5,4:0.4444:2,0:34.3:1:29.5:1:1:0:60:8:0.4444:0.1111:2 +1 11938265 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=AAGCTCTTCCGCATTTCTCT;RSEQ=GACAACCGCATGTTGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:6,0:0:0,0:17.3:1:33:0:1:0:57.3:12:1:0:0.8 1/0:4:2:1,1:0,2:2,2:0.5:0,2:18.5:1:27:1:1:0:60:4:0.5:0:1 +1 11938340 . T C 31 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCCCAGGGTGTCCAGGACAA;RSEQ=GCCCTGCAGTGGGTGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:7.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:30:0:1:0:60:2:1:0:1 +1 11972634 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.48617;SOR=0;LSEQ=TAGTGGCCCCGAATGGCTGG;RSEQ=CGCGCTGATATTTATTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:32:0:32:0:1:1.67325:30:4:0.1538:0:1.5 0/0:10:0:0,0:7,3:10,0:0:2,0:27.1:1:30.1:1:1:0:48.9:20:1:0:0.3 +1 11972651 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1567;SOR=Inf;LSEQ=TGGGCGCGCTGATATTTATT;RSEQ=TATACAAGACAAGGGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:16,0:0:2,0:23.1:1:31.4:1:1:0:53.4:32:1:0:0.3 0/1:11:2:2,0:6,3:9,2:0.1818:2,0:25:1:29:0:1:0:46.5:4:0.1818:0:1 +1 11972688 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50786;SOR=Inf;LSEQ=GGCAGGCAGGGTAAGGAAGG;RSEQ=GGTCGTCCAAGTGATTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:19,0:0:2,0:30.4:1:30.8:1:1:0:52.6:18:1:0:0.3 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:15:1:29:1:1:1.34838:37:4:0.0741:0:1 +1 12071513 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.47895;SOR=Inf;LSEQ=GTAGTCCTAATACTGCCTAT;RSEQ=ATCAGCTATCATGGTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:9,0:0:0,0:16.8:1:33.1:1:1:0:60:18:1:0:0 0/1:11:2:1,1:8,1:9,2:0.1818:2,2:21.5:1:30:1:0.34545:6:60:4:0.1818:0:1.5 +1 12071680 . A G 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.60961;LSEQ=TGCTGCCAGCCCTAAGTGCC;RSEQ=TGTGGGCTCCCCCAGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:15:5,10:9,16:25,15:0.375:2,2:21.3:1:30.5:1:1:1.12171:60:14:0.359:0:1.4 1/1:53:47:18,29:3,3:6,47:0.8868:2,2:21.6:1:30.6:1:0.67106:1.59616:60:94:0.8868:0:1.1 +1 14192526 . A G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07736;LSEQ=AGCCAAAATCCTTCACTTTA;RSEQ=TGAGCCTCAGTTCCCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:75:71:69,2:4,0:4,71:0.9467:0,1:26.7:1:33.8:1:1:0:59.8:142:0.9467:0:1 1/0:61:35:32,3:24,1:25,35:0.5738:1,2:23.2:1:31.9:1:0.63395:2.22243:60:34:0.5763:0:1.2 +1 14192575 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24144;SOR=0;LSEQ=TGTCACCCTGTTAAGTGATC;RSEQ=GGACTCAAGATATTTTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:109,46:155,2:0.0127:2,2:17:1:29.5:1:0.51045:2.35497:60:4:0.0128:0:1 0/0:162:0:0,0:114,47:161,0:0:2,0:23.3:1:29.3:1:1:0:60:52.667:0.9937:0:0.4 +1 14192672 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08493;LSEQ=CAAAAATCAGGAAAAATTAA;RSEQ=GTTGGACCCTCCTGGGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:315:289:135,154:13,13:26,289:0.9175:2,2:23.7:1:30.5:1:0.83839:1.14026:59.9:95.333:0.9167:0:1.1 0/1:392:190:86,104:102,100:202,190:0.4847:2,2:26.3:1:29.5:1:0.3132:1.23282:60:94:0.4833:0:1.1 +1 14192676 . G A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=AATCAGGAAAAATTAACGTT;RSEQ=GACCCTCCTGGGATCCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:145,166:311,0:0:2,0:23.3:1:31.3:1:1:0:59.9:61.2:1:0:1 0/1:392:15:8,7:181,196:377,15:0.0383:2,2:28.5:1:29.2:1:0.79452:1.24:60:30:0.0392:0:1 +1 14192818 . G T 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00554;SOR=0;LSEQ=CTGTTCATGGCTAATTCTTG;RSEQ=GTGGCTTCCATCACAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:0,8:1,32:33,8:0.1951:1,0:11.1:1:31.3:1:1:0:60:16:0.1951:0:1 0/0:38:0:0,0:2,35:37,0:0:2,0:25.9:1:30.3:1:1:0:60:17.5:1:0:0.1 +1 14192919 . A G 64 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACCTGCTCCATGCCAC;RSEQ=TGCCCCTCCTAGCCCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:26.8:1:32.3:1:1:0:58.5:8:0.8:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 14321714 . CAA C 31 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTAGACAGTGCAATAAGG;RSEQ=AAAAAAAAAAAAAATCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45:1:31:1:1:0:60:4:1:0:0 +1 14322547 . CT C 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=0;LSEQ=CATCACAACGGACTAGGAGG;RSEQ=GGCCTGATCCACGGAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:30.5:1:1:0:60:4:1:0:0.5 0/0:1:0:0,0:1,0:1,0:0:0,0:45:0:33:0:1:0:60:2:1:0:0 +1 14323295 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TCTGAGGAATCTGGGCAGCC;RSEQ=GGATGAGTGGGTTTCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:37.5:1:30.5:1:1:0:57.5:4:0.6667:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:30.5:1:31:1:1:0:60:4:1:0:0 +1 14323668 . TCAA T 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.5671;SOR=2.69977;LSEQ=CAGCAAAAACAACACCATCA;RSEQ=CAACAACAACAACAACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:32:0:34:0:1:2.44949:60:4:0.3333:0:0.5 1/0:5:3:3,0:2,1:3,3:0.6:2,0:5.3:1:29:1:1:0:47.3:6:0.6:0.4:1.7 +1 14323765 . A G 55 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65134;SOR=2.12461;LSEQ=ACTCACGAAGATGAGAAAGA;RSEQ=TCAATGAAAAAATGCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:23:1:31.5:1:1:1.37:26:4:0.1429:0:2 0/1:15:4:2,2:5,6:11,4:0.2667:2,2:15:1:27.8:1:1:1.19:25.3:8:0.2857:0:2.3 +1 14323796 . A C 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47601;LSEQ=AATGCTGAAAACCCAAAAGG;RSEQ=CAGAGTGCCTCCTTTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:43.5:1:32:1:1:1.45:26:4:0.1667:0:2 0/1:13:3:1,2:4,6:10,3:0.2308:2,2:41:1:29.7:1:1:1.30472:26.3:6:0.25:0:2 +1 15295906 . G C 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0589;SOR=2.12682;LSEQ=ATACGCTTGAAGCTACTGCT;RSEQ=TTTCTTTAGCCTGGTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:12:12,0:62,6:68,12:0.15:2,0:27.4:1:32.9:1:0.58373:0:60:24:0.15:0:1.1 0/1:84:23:22,1:58,3:61,23:0.2738:1,1:23.5:1:31.2:1:1:1.14:60:46:0.2738:0:1 +1 15295949 . A T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50114;SOR=Inf;LSEQ=GGGGCTGCTGCAGGGGGCCC;RSEQ=CCCTGAGCCAGCCCCTCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:119,43:162,0:0:2,0:23.4:1:30.2:1:1:0:60:53:1:0:0.3 0/1:187:2:1,1:135,50:185,2:0.0107:2,2:6.5:1:28:1:0.47214:2.68328:60:4:0.0107:0:1.5 +1 15295987 . G T 42 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13259;SOR=Inf;LSEQ=GGTCCCACAGCCCTGACGTA;RSEQ=AAGACTCTTTGCTGGTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:156,120:276,0:0:2,0:24.7:1:32.6:1:1:0:60:68:1:0:0.3 0/1:343:4:1,3:196,143:339,4:0.0117:2,2:23.8:1:21.3:1:0.31608:4.09576:60:3:0.0088:0:1.3 +1 15296019 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00331;SOR=1.67072;LSEQ=CTGGTAAATCTCGGAACTCA;RSEQ=TGGAAGCTTCCACAAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:67:32,35:135,141:276,67:0.1953:2,2:25.2:1:31.1:1:0.89231:1.04709:60:134:0.1976:0:1.1 0/1:433:125:58,67:156,152:308,125:0.2887:2,2:26.1:1:29.8:1:0.45842:1.1851:60:250:0.2907:0:1.1 +1 15296282 . T G 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41631;LSEQ=CCTAAAAAGAACCCATGCCC;RSEQ=AATGCACAAGTACTTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:13,3:0.1875:1,0:27:1:32.3:1:1:0:60:6:0.1875:0:1.7 0/1:4:1:0,1:0,3:3,1:0.25:0,0:42:0:30:0:1:0:60:2:0.25:0:2 +1 15847913 . T G 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=CCTCCCTGTGGTGCTGTGCT;RSEQ=CCATGGTCACGCTCCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:12:1:30.5:1:1:0:60:4:0.6667:0:1 0/1:4:1:1,0:2,1:3,1:0.25:2,0:19:0:33:0:1:0:58:2:0.25:0:1 +1 16174490 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49943;SOR=Inf;LSEQ=CGCCGCCCCGGCACCCGCCT;RSEQ=CCGGCGCTGACGGTCTCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:99,8:107,0:0:2,0:13.8:1:32.8:1:1:0:60:52.5:1:0:0.2 0/1:120:2:1,1:104,14:118,2:0.0167:2,2:15:0:31:1:0.23529:7.21024:60:4:0.0167:0:1.5 +1 16174524 . G T 74 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.13721;SOR=4.92914;LSEQ=TCTCGTACGAAGCCGGCGAG;RSEQ=GGGAGCCAGCAGCGGCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:1:1,0:274,102:376,1:0.0027:2,0:35:0:32:0:1:0:60:2:0.0027:0:1 0/1:463:6:2,4:334,123:457,6:0.013:2,2:15.2:1:29:1:0.05076:5.40732:60:12:0.0131:0:1.3 +1 16174686 . C A 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.65362;SOR=2.8279;LSEQ=GGCCGCGCTCGCTCCTCGGG;RSEQ=GCCGCTTCCCGCCCCGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:1,0:64,193:257,1:0.0039:2,0:1:0:26:0:0.25194:0:60:2:0.004:0:1 0/1:367:4:3,1:109,254:363,4:0.0109:2,2:16:1:27.3:1:0.08651:6.95:60:8:0.011:0:1 +1 16174695 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27924;SOR=Inf;LSEQ=CGCTCCTCGGGCGCCGCTTC;RSEQ=CGCCCCGGCCCGTTGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:37,149:186,0:0:2,0:20.1:1:31.6:1:1:0:60:92:0.9946:0:0.1 0/1:282:3:1,2:69,209:278,3:0.0106:2,2:20.3:1:26:1:1:1.51:60:2:0.0072:0:1 +1 16174707 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27661;SOR=Inf;LSEQ=GCCGCTTCCCGCCCCGGCCC;RSEQ=TTGCCGGCCCCTCCCGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:12,102:114,0:0:2,0:18.5:1:32.7:1:1:0:60:228:1:0:0.1 0/1:170:3:2,1:29,138:167,3:0.0176:2,2:8.7:1:26.3:1:0.08594:9.33:60:6:0.018:0:1.3 +1 16199094 . C CA 64 MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=AACAGAGCGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:1,1:2,4:0.6667:2,0:15:1:32.3:1:0.33333:0:40.3:8:0.6667:0:4 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:11:0:28:0:1:0:22:2:0.5:0:7 +1 16199587 . G A 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGCTTATGGTCCCCCACC;RSEQ=TCACTTCATGCACGAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:168,236:404,0:0:2,0:25.3:1:31.3:1:1:0:60:133.667:1:0:0.1 0/1:656:32:14,18:263,361:624,32:0.0488:2,2:27.6:1:29.8:1:0.85658:1.07:60:31:0.0476:0:1.1 +1 16200163 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACAAACAATACTTTAAC;RSEQ=TGGAAATGTGTACTTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:18:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 16200564 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50325;SOR=Inf;LSEQ=TGGAATTGTAGAGGATATTT;RSEQ=CTCTTCTGCCAGCTACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:113,7:120,0:0:2,0:24.5:1:31.9:1:1:0:60:39:1:0:0.1 0/1:147:2:1,1:126,19:145,2:0.0136:2,2:8.5:1:31:1:0.2544:6.48926:60:4:0.0138:0:1 +1 16200729 . A AT 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.18553;SOR=1.45061;LSEQ=TATTTTGTCTGGTCACTAAG;RSEQ=TTTTTTTTTTCTTGTGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:558:24:7,17:244,283:527,24:0.043:2,2:33.3:1:31.3:1:0.14115:2.09119:60:48:0.044:0:0 0/1:588:36:16,20:264,288:552,36:0.0612:2,2:27.6:1:30:1:0.73316:1.14557:60:72:0.0626:0:0.1 +1 16200909 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.97468;LSEQ=AGGTTGGTATGTCCTGACCT;RSEQ=TGTATATTAGCCCCTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:49,143:192,2:0.0103:2,2:24:1:18.5:1:0.45003:2.90:60:1:0.0052:0:1 0/1:199:2:1,1:53,144:197,2:0.0101:2,2:8.5:1:27.5:1:0.47008:2.70:60:4:0.0103:0:1 +1 16200933 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49828;SOR=0;LSEQ=ATATTAGCCCCTCTCCTAAC;RSEQ=CAAGTCAAACTCTCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:14,102:116,2:0.0169:2,2:9:0:31.5:1:0.23903:7.07:60:4:0.0172:0:1 0/0:111:0:0,0:19,92:111,0:0:2,0:23.9:1:30.5:1:1:0:59.7:54.5:1:0:0.1 +1 16202622 . T A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47687;LSEQ=AGACAAAGACAATGCTGAAG;RSEQ=GAATGTTTGCATGACTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:1,0:114,8:122,1:0.0081:2,0:35:0:14:0:1:0:60:0:0:0:3 0/1:167:2:1,1:143,22:165,2:0.012:2,2:17:1:28.5:1:0.2572:6.37932:60:4:0.0122:0:1 +1 16235724 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50469;SOR=Inf;LSEQ=AGAAATTCCAGTCTGAAAAT;RSEQ=TAGACCTATTAGTTATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:94,7:101,0:0:2,0:22:1:31:1:1:0:60:202:1:0:0 0/1:129:2:1,1:117,10:127,2:0.0155:2,2:22:1:27:1:0.16388:11.20338:60:4:0.0159:0:1 +1 16237577 . G GT 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.74445;SOR=0.74202;LSEQ=TTAGAAGAATTAATAACTTG;RSEQ=TTTTTTTTGGGAATTTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:5:3,2:189,65:254,5:0.0193:2,2:22.8:1:28.7:1:0.60648:1.93294:60:10:0.0195:0.0077:0 0/1:278:4:3,1:183,81:264,4:0.0144:2,2:27.8:1:28.3:1:1:1.33:60:8:0.0148:0.0036:0 +1 16237813 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19741;SOR=0;LSEQ=CCAGGTAAGACACAAGCAAG;RSEQ=TGAGTTTGAGTTACTCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:45,143:188,2:0.0105:2,2:23.5:1:30.5:1:0.42657:3.15:60:4:0.0105:0:1 0/0:237:0:0,0:74,162:236,0:0:2,0:22.7:1:31.4:1:1:0:59.9:77.667:1:0:0.1 +1 16237846 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22281;SOR=Inf;LSEQ=ACTCATCACACACACTGTTT;RSEQ=TGTTGCAGTGTATGAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:18,100:118,0:0:2,0:23.8:1:32.6:1:1:0:60:236:1:0:0.1 0/1:106:2:0,2:16,88:104,2:0.0189:2,0:10.5:1:31.5:1:1:0:60:4:0.0189:0:1 +1 16242620 . C A 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCGGCCCCCATTCCACTTA;RSEQ=AGAAACAGAAAGTGAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:0:0,0:338,114:452,0:0:2,0:24.7:1:32.3:1:1:0:60:112:0.9978:0:0.1 0/1:543:44:29,15:328,170:498,44:0.081:2,2:22.7:1:30.1:1:1:1.00:60:88:0.0819:0:1.2 +1 16242866 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23714;SOR=0;LSEQ=TTGGAAAGGTGATATTTAAT;RSEQ=GTGTAATGAATGAACATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:0,2:0,120:120,2:0.0164:1,0:21.5:1:31:1:1:0:60:4:0.0165:0:1 0/0:128:0:0,0:7,121:128,0:0:2,0:20.7:1:30.7:1:1:0:60:127:1:0:0 +1 16243005 . CTT C 32 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0.09804;SOR=Inf;LSEQ=ACATATATATTTTCTTACCT;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,9:9,0:0:0,0:18.9:1:19.9:1:1:0:54.2:0.8:0.6667:0:1.7 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:26.5:1:32:1:1:0:60:4:0.4:0:0 +1 16245362 . G A 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATACCCTATATGGACTTG;RSEQ=TTCATTCTAATTTATTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:134,39:173,0:0:2,0:23.7:1:31.6:1:1:0:60:85.5:1:0:0.1 0/1:256:30:22,8:166,59:225,30:0.1172:2,2:23.4:1:28.7:1:1:1.02302:60:60:0.119:0:1 +1 16245610 . GT G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.06659;LSEQ=TGTTTTTTAAGACTTGAAGG;RSEQ=TTTTTTTTTGCATATGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:60:5,55:15,95:110,60:0.3529:2,2:30.1:1:32.4:1:0.45534:1.7316:60:120:0.3571:0:0 0/1:201:7:0,7:37,157:194,7:0.0348:2,0:26.6:1:31.9:1:0.35315:0:60:14:0.0354:0:0 +1 16245803 . TA T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20918;SOR=Inf;LSEQ=CACTTGAGATGTTGATTTGA;RSEQ=AGATTACTATAGAAAACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:95,10:105,0:0:2,0:21.7:1:28.9:1:1:0:59.9:104:1:0:0.2 0/1:89:2:1,1:83,4:87,2:0.0225:1,2:26.5:1:29:1:0.10981:18.66298:60:4:0.0227:0:0 +1 16245997 . T C 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACACGACATTTCTGCCGATA;RSEQ=GGGCCTGTGGTAAAGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:672:0:0,0:317,355:672,0:0:2,0:25.9:1:30.7:1:1:0:59.9:95:1:0:0.1 0/1:943:34:14,20:415,493:908,34:0.0361:2,2:28.6:1:30.3:1:0.72636:1.20232:60:68:0.0366:0:1.2 +1 16247227 . CT C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.07604;SOR=Inf;LSEQ=TCACTACAGTGTGCATCACA;RSEQ=TTTTTTTTTAATAGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:19,0:0:1,0:32.2:1:33.3:1:1:0:59.3:38:1:0:0.1 0/1:15:3:3,0:11,1:12,3:0.2:2,0:35.3:1:32:1:1:0:60:6:0.2:0:0 +1 16247573 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50805;SOR=Inf;LSEQ=GCTCACGCCTGTAATCCCAG;RSEQ=ACTTTGGGAGGCCAAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:1,54:55,0:0:1,0:22:1:33.1:1:1:0:46.6:110:1:0:0.1 0/1:75:2:1,1:2,71:73,2:0.0267:1,2:9:1:30:1:0.07892:29.17:60:4:0.0267:0:2 +1 16247575 . C T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51137;SOR=Inf;LSEQ=TCACGCCTGTAATCCCAGCA;RSEQ=TTTGGGAGGCCAAGGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:1,51:52,0:0:1,0:21.7:1:33.9:1:1:0:45.8:104:1:0:0.1 0/1:74:2:1,1:1,71:72,2:0.027:1,2:7:1:30.5:1:0.05368:50.56:60:4:0.0274:0:2 +1 16247681 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07353;SOR=Inf;LSEQ=AAATACAAGAAAAATTAGCC;RSEQ=GGCTTGGTGGCGCGTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:12,0:0:0,0:28.2:1:31.9:1:1:0:55.8:24:1:0:0 0/1:5:2:0,2:0,3:3,2:0.4:0,0:8.5:1:32:0:1:0:46:4:0.4:0:1 +1 16248717 . A T 34 p8;q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10124;SOR=0;LSEQ=CATTAAAATTTGAAACTTGC;RSEQ=TCAAACACCTCTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:3:0,3:206,51:257,3:0.0115:2,0:6:1:21.7:1:0.00857:0:60:2:0.0083:0:1 0/0:299:0:0,0:241,57:298,0:0:2,0:5:0:14:0:1:0:45:0:0:0:3 +1 16248728 . C CT 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00458;SOR=0.49106;LSEQ=GAAACTTGCATCAAACACCT;RSEQ=TTTTTTTTTTTAAAGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:46:34,12:188,66:254,46:0.1489:2,2:30.3:1:31.1:1:1:1.00533:60:22:0.1522:0:0.4 0/1:367:29:21,8:250,81:331,29:0.079:2,2:26.8:1:29.3:1:0.66026:1.1752:58.2:13.5:0.0765:0:0.7 +1 16248740 . A T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.06498;LSEQ=AAACACCTCTTTTTTTTTTT;RSEQ=AAGGTGGATTTTGCAAATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:9:6,3:265,127:392,9:0.0224:2,2:21.1:1:25:1:1:1.04319:56:3.5:0.0179:0:2.4 0/1:504:12:9,3:325,166:491,12:0.0238:2,2:25.8:1:26.3:1:0.75872:1.53:60:11:0.0225:0:1.2 +1 16248910 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18744;SOR=0;LSEQ=TAATACAGAAACTTAAGATG;RSEQ=CATTAAATTTTATTTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:15,151:166,2:0.0118:2,2:19.5:1:32:0:0.18192:9.78:60:4:0.0118:0:1 0/0:222:0:0,0:37,185:222,0:0:2,0:21.9:1:31.2:1:1:0:60:221:1:0:0.1 +1 16249125 . C CT 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTGATAACTTTATGTA;RSEQ=TTTTTTTTTTGAGACAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,3:3,2:0.3333:0,0:33.5:1:28:1:1:0:44:4:0.3333:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 16254571 . G A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAAAGAACTAATATCTTT;RSEQ=TTATTTTTTGGCAGAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:593:0:0,0:383,210:593,0:0:2,0:25.1:1:32.4:1:1:0:60:196.667:1:0:0.1 0/1:702:37:23,14:403,259:662,37:0.0527:2,2:21.2:1:28.2:1:1:1.06:60:74:0.0532:0:1.2 +1 16255141 . GGA G 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1.01012;LSEQ=ACTTTTGATCCGGAGAGAGT;RSEQ=GAGAGAGAGACGCTTAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:534:8:3,5:308,218:526,8:0.015:2,2:31.4:1:33:1:0.28791:2.35093:60:16:0.0154:0:0.4 0/1:727:11:5,6:388,327:715,11:0.0151:2,2:31.7:1:31.3:1:0.76219:1.42314:60:22:0.0153:0:0.2 +1 16255644 . C T 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCAAGCCTGAGCAGCCTG;RSEQ=AGATGGGGTAAGTGCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:223,268:491,0:0:2,0:26.2:1:32:1:1:0:60:43.636:1:0:0.2 0/1:524:42:19,23:215,267:482,42:0.0802:2,2:25.2:1:27.4:1:1:1.03:60:41:0.0793:0:1.2 +1 16255972 . G T 53 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06279;SOR=Inf;LSEQ=TCTGTTGGGTCTGGCTCAAG;RSEQ=CCCAGCTCAGACCTACAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:217,182:399,0:0:2,0:23.5:1:31.5:1:1:0:60:78.8:1:0:0.8 0/1:433:5:2,3:245,183:428,5:0.0115:2,2:9.4:1:23.2:1:0.65556:2.00496:60:4:0.0094:0:1.6 +1 16256007 . T C 279 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01883;LSEQ=ACAAGCAAGACTGGGAGAAC;RSEQ=AGCAGGTGAATCTGTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:444:440:238,202:0,2:2,440:0.991:0,2:26.2:1:31.8:1:0.21245:0:60:72.333:0.9909:0:1.1 1/0:586:395:223,172:102,88:190,395:0.6741:2,2:25.7:1:30.8:1:0.53526:1.12:60:78:0.6713:0:1.2 +1 16257858 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12816;SOR=Inf;LSEQ=CCTGCCCCCAGGAGCAGACC;RSEQ=CGATAAAGAAGCTGCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:141,142:283,0:0:2,0:23.4:1:31.3:1:1:0:59.9:55.6:0.9964:0:0.1 0/1:331:4:2,2:161,166:327,4:0.0121:2,2:24.8:1:27.8:1:1:1.03:60:8:0.0122:0:0.8 +1 16258302 . A G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04698;LSEQ=GGAAAAACTCAAGCGGTCCA;RSEQ=TTCTCCTCGGGGAGAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:273:126,147:159,188:347,273:0.4389:2,2:23.1:1:32.7:1:0.93552:1.01:60:135.5:0.4407:0:1.1 0/1:763:27:15,12:351,385:736,27:0.0354:2,2:22.5:1:31.1:1:0.43996:1.37:60:54:0.0358:0:1 +1 16259335 . A G 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12528;SOR=Inf;LSEQ=GCACCAGAGGGCCTTGCCCC;RSEQ=GAGGACAGGGACAAGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:185,135:320,0:0:2,0:25.2:1:30.9:1:1:0:59.9:79:0.9968:0:0.1 0/1:351:4:2,2:197,148:345,4:0.0114:2,2:35.3:1:29:1:1:1.32996:60:8:0.0115:0:1 +1 16259465 . C A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05325;SOR=0;LSEQ=CACCTTATCCTGGAGAATCC;RSEQ=AGACAGATCTGCAACCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:4:3,1:195,188:383,4:0.0103:2,2:16.8:1:27.8:1:0.62346:2.89:60:8:0.0105:0:1 0/0:417:0:0,0:188,229:417,0:0:2,0:25.8:1:30.7:1:1:0:60:58.571:1:0:0.1 +1 16259813 . A G 284 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00716;LSEQ=AGAGCCATGTCCCTGAATCC;RSEQ=ACCAAGCTCAAGGTGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:588:586:299,287:0,0:0,586:0.9966:0,2:25.7:1:30.9:1:1:0:60:116.2:0.9983:0:1.1 1/0:646:437:202,235:96,112:208,437:0.6765:2,2:24.2:1:29.5:1:1:1.00:60:42.7:0.6724:0:1.2 +1 16260233 . G A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02294;SOR=Inf;LSEQ=GCCCCCCTACTAAGGTGACA;RSEQ=AGTGGATCACAAGGCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:112,118:230,0:0:2,0:23:1:32.4:1:1:0:60:56.5:1:0:0.1 0/1:206:5:3,2:105,96:201,5:0.0243:2,2:11.6:1:30:1:1:1.37:60:10:0.0245:0:1 +1 16260916 . C T 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCCAGGCACAGTCAATGC;RSEQ=GCTGCGAGTGCAGTGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:127,164:291,0:0:2,0:23.5:1:30.5:1:1:0:59.9:290:1:0:0.1 0/1:286:21:9,12:132,133:265,21:0.0734:2,2:24.5:1:29.3:1:0.65196:1.32201:60:20:0.0702:0:1.1 +1 16261327 . G A 76 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07239;SOR=6.34766;LSEQ=CCTGATTCTGTCACAGCATC;RSEQ=CAGCCTCCATCCAAAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:1:1,0:259,225:484,1:0.0021:2,0:1:0:25:0:1:0:60:2:0.0021:0:1 0/1:540:7:3,4:285,247:532,7:0.013:2,2:8.4:1:27.1:1:0.71011:1.53722:60:14:0.0132:0:1.1 +1 16261851 . C A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05753;SOR=Inf;LSEQ=GCCATCCTCATTCCCAAGGG;RSEQ=AAGCCACCCCAGCAGTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:138,198:336,0:0:2,0:24:1:32.2:1:1:0:60:66.2:1:0:0.1 0/1:324:4:3,1:132,186:318,4:0.0123:2,2:16.3:1:26.5:1:0.31288:4.21:60:8:0.0127:0:1 +1 16262047 . G A 39 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34286;SOR=3.46261;LSEQ=GTGAGAATGAACACTCCCAC;RSEQ=CTGCCCAGTATCACCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:1,0:114,144:258,1:0.0039:2,0:1:0:24:0:0.44402:0:60:2:0.004:0:1 0/1:226:3:2,1:97,126:223,3:0.0133:2,2:9.7:1:24.7:1:0.58275:2.59:60:6:0.0137:0:1 +1 16262067 . G A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09495;SOR=Inf;LSEQ=GCTGCCCAGTATCACCTACA;RSEQ=CATCCGGCCAGAAGCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:96,139:235,0:0:2,0:24:1:32.3:1:1:0:60:32.571:1:0:0.1 0/1:199:3:2,1:84,112:196,3:0.0151:2,2:26.3:1:23.7:1:0.57934:2.65:60:2:0.0103:0:1.3 +1 16262075 . C A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25132;SOR=0;LSEQ=GTATCACCTACAGCATCCGG;RSEQ=CAGAAGCGCTTCACTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:1,2:87,120:207,3:0.0142:2,2:21.7:1:24:1:1:1.44753:60:2:0.0099:0:2.3 0/0:186:0:0,0:82,104:186,0:0:2,0:24.8:1:30.6:1:1:0:60:22.25:1:0:0.2 +1 16262076 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21668;SOR=Inf;LSEQ=TATCACCTACAGCATCCGGC;RSEQ=AGAAGCGCTTCACTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:88,125:213,0:0:2,0:25.1:1:31.4:1:1:0:60:29.429:1:0:0.2 0/1:186:2:1,1:81,103:184,2:0.0108:2,2:31:1:30:1:1:1.27:60:4:0.011:0:1 +1 16262086 . T A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21726;SOR=Inf;LSEQ=AGCATCCGGCCAGAAGCGCT;RSEQ=CACTCTCCTCGGGCTCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:77,116:193,0:0:2,0:25.9:1:30.2:1:1:0:60:47.25:1:0:0.2 0/1:169:2:1,1:77,90:167,2:0.0118:2,2:16:1:24.5:1:1:1.17:60:4:0.0121:0:1 +1 16262194 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09553;SOR=Inf;LSEQ=GTGCCTGCACTGGCCTCCCA;RSEQ=CACCCTCCCGAGGAGGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:55,78:133,0:0:2,0:25.6:1:32.8:1:1:0:60:132:1:0:0.1 0/1:113:3:1,2:50,60:110,3:0.0265:2,2:25.7:1:23:1:1:1.65945:60:2:0.0182:0:1.3 +1 16262237 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19026;SOR=Inf;LSEQ=ATTATCACCTTCCTGTCGCT;RSEQ=GAGCCACAGCCCCTGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:74,73:147,0:0:2,0:23.3:1:30.7:1:1:0:60:48:0.9931:0:0.1 0/1:115:2:1,1:59,54:113,2:0.0174:2,2:27:1:29.5:1:1:1.09174:60:4:0.0174:0:1 +1 16262381 . G T 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.6252;SOR=2.75138;LSEQ=AGCCCAGGGCCGCGGATGGG;RSEQ=TGGTGAAGGTGCCACCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:0,1:152,107:259,1:0.0038:2,0:41:0:32:0:0.41538:0:60:2:0.004:0:4 0/1:286:3:1,2:148,135:283,3:0.0105:2,2:26:1:29.3:1:0.60847:2.18678:60:6:0.0107:0:1 +1 16262404 . C T 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGAAGGTGCCACCAGCCAG;RSEQ=AAGGCCCCTCAGCAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:164,112:276,0:0:2,0:25.7:1:31.7:1:1:0:59.9:26.6:1:0:0.4 0/1:295:23:10,13:146,125:271,23:0.078:2,2:31.1:1:27.7:1:0.38792:1.51622:60:46:0.0785:0:1.3 +1 16262459 . G GC 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.12814;SOR=5.34383;LSEQ=AGACACCAGATGCCAAAGCT;RSEQ=CCCCCACCCCCACCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:1,0:128,122:250,1:0.004:2,0:12:0:28:0:1:0:60:2:0.0043:0:0 0/1:286:6:6,0:138,139:277,6:0.021:2,0:34.7:1:28.1:1:0.02975:0:51.7:5:0.0183:0.0105:1.5 +1 16262477 . G C 40 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5539;SOR=1.54662;LSEQ=CTGCCCCCACCCCCACCCCT;RSEQ=CCCCCGTCCCTGTCCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:4:4,0:62,138:200,4:0.019:2,0:11.3:1:25:1:0.01029:0:52.5:3:0.0173:0:3 0/1:241:7:7,0:77,154:231,7:0.029:2,0:17:1:14.6:1:0.00058:0:51.9:0:0:0:4 +1 16262491 . C T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25063;SOR=Inf;LSEQ=ACCCCTGCCCCCGTCCCTGT;RSEQ=CCTGTCCCCCTTCCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:111,159:270,0:0:2,0:19.7:1:30.7:1:1:0:59.7:19.769:1:0:0.4 0/1:299:3:1,2:114,182:296,3:0.01:2,2:11.7:1:20.3:1:1:1.25181:56.7:2:0.0075:0:3 +1 16262650 . G A 63 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02732;SOR=0;LSEQ=AGCGGGGAGCTGTTTCAAGA;RSEQ=TACCGGTACGGCGACATCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:5:4,1:185,271:456,5:0.0108:2,2:6.8:1:27.2:1:0.16415:5.84:60:10:0.011:0:1 0/0:484:0:0,0:222,262:484,0:0:2,0:24.4:1:31:1:1:0:60:59.5:1:0:0.2 +1 16262717 . G A 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.69973;SOR=1.57447;LSEQ=CACACACTCAGTTTCCCGCC;RSEQ=CTTCCTCTGTTGGCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:2:1,1:120,188:308,2:0.0065:2,2:21.5:1:31.5:1:1:1.56:60:4:0.0067:0:1 0/1:395:4:3,1:170,221:391,4:0.0101:2,2:16.3:1:30:1:0.32313:3.89:60:8:0.0103:0:1.3 +1 16262784 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=GAGCCAGCCAGGTATCTCCC;RSEQ=ACTGTCTGTTGGGCATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:39,113:152,0:0:2,0:24.1:1:31.4:1:1:0:60:29.4:1:0:0.2 0/1:161:2:1,1:44,115:159,2:0.0124:2,2:11.5:1:28:1:0.48214:2.60:60:4:0.0127:0:1 +1 16262806 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19727;SOR=Inf;LSEQ=CTGTCTGTTGGGCATGTGCT;RSEQ=GTGGGGCTCAGCAGGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:19,87:106,0:0:2,0:26.9:1:30.3:1:1:0:60:34.333:1:0:0.1 0/1:86:2:1,1:14,69:83,2:0.0233:2,2:20:1:29:1:0.32353:4.80:60:4:0.0233:0:1 +1 16263452 . A G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGCTCTTGCTGGGTAGC;RSEQ=TCAGCAGGAGGCAGGTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:26.3:1:30.3:1:1:0:56.5:22:1:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:13.7:1:31.3:1:1:0:60:6:1:0:1 +1 16264264 . G A 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTCCAGCATGGCTCAGC;RSEQ=AGGGGCCATGAGCTCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:243,163:406,0:0:2,0:24.8:1:31.1:1:1:0:60:405:1:0:0.1 0/1:403:42:29,13:213,147:360,42:0.1042:2,2:25.8:1:29.5:1:0.24609:1.54:60:84:0.1058:0:1.1 +1 16264391 . G A 141 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.61488;LSEQ=ACTTCGTCTCTGGCAACAAC;RSEQ=TCCTGGCCCATCGGTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:938:2:1,1:447,488:935,2:0.0021:2,2:40.5:1:31.5:1:1:1.09:60:4:0.0022:0:1.5 0/1:957:29:13,16:448,480:928,29:0.0303:2,2:20:1:29.2:1:0.85075:1.14855:60:58:0.0307:0:1.1 +1 16264567 . G T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26038;SOR=0;LSEQ=GGAAGACGTAGGTAGTCCCT;RSEQ=CCAGCCCATCTCCCTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:1,2:34,173:207,3:0.0142:2,2:22:1:26.3:1:0.42296:2.53:60:2:0.0099:0:1.3 0/0:163:0:0,0:39,124:163,0:0:2,0:23.3:1:31.1:1:1:0:60:53.333:1:0:0.1 +1 16264590 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15165;SOR=Inf;LSEQ=AGCCCATCTCCCTGGCCTGT;RSEQ=ATGGAAGCATTAACTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:12,144:156,0:0:2,0:20.9:1:32.3:1:1:0:60:77:1:0:0.1 0/1:100:2:1,1:7,91:98,2:0.02:2,2:20:1:27.5:1:0.15434:12.23:60:4:0.0204:0:1 +1 16265152 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24423;SOR=0;LSEQ=TGGACCTGATACTGTGGGTT;RSEQ=GATGTGGGCTGCTGTTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:169,21:190,2:0.0104:2,2:29:1:32:0:0.21657:7.88555:60:4:0.0105:0:1 0/0:196:0:0,0:164,32:196,0:0:2,0:8:0:15:0:1:0:60:0:0:0:2 +1 16265153 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=Inf;LSEQ=GGACCTGATACTGTGGGTTG;RSEQ=ATGTGGGCTGCTGTTTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:173,24:197,0:0:2,0:25.6:1:31.3:1:1:0:60:38.4:1:0:0.2 0/1:197:2:1,1:163,32:195,2:0.0102:2,2:23.5:1:27.5:1:0.30768:5.03149:60:4:0.0105:0:1 +1 16265186 . C T 47 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68671;SOR=1.9145;LSEQ=GTTTGACTAGGAGGCCCCTG;RSEQ=TCACTGGCAGCTGGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:2:2,0:249,94:343,2:0.0058:2,0:16.5:1:17.5:1:1:0:60:1:0.003:0:2 0/1:362:4:1,3:254,104:358,4:0.011:2,2:17.5:1:23.8:1:0.07926:7.28166:60:3:0.0083:0:1.5 +1 16265422 . A G 279 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01761;LSEQ=TACACCCACAGGTGGGGCTG;RSEQ=TCAGGGTAGGTGGGCCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:459:453:147,306:1,1:2,453:0.9869:2,2:23.5:1:31.7:1:0.54523:2.07803:60:74.5:0.9889:0:1.1 1/0:423:241:81,160:59,123:182,241:0.5697:2,2:22.3:1:31:1:0.83503:1.06:60:240:0.5701:0:1.1 +1 16265427 . G A 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0493;SOR=Inf;LSEQ=CCACAGGTGGGGCTGATCAG;RSEQ=GTAGGTGGGCCTACTCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:131,296:427,0:0:2,0:22.9:1:30.9:1:1:0:60:37.818:1:0:1.1 0/1:382:4:3,1:119,259:378,4:0.0105:2,2:14.5:1:23.5:1:0.09795:6.49:60:3:0.008:0:1.8 +1 16265466 . C T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51213;SOR=0;LSEQ=CTGGTGCCCACTAGATCTGG;RSEQ=CCCAGAGGTGGGCAAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:16,180:196,2:0.0101:2,2:5:1:28:1:0.16474:10.94:60:4:0.0102:0:1.5 0/0:142:0:0,0:8,134:142,0:0:2,0:5:0:18:0:1:0:60:0:0:0:2 +1 16265662 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1503;SOR=Inf;LSEQ=TTCCAGTAGACATAGTCCTG;RSEQ=CACATTTGCTGGTTGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:171,13:184,0:0:2,0:26:1:32:1:1:0:60:183:1:0:0.1 0/1:117:2:2,0:112,3:115,2:0.0171:1,0:36:1:25:1:1:0:60:4:0.0172:0:1 +1 16265904 . T A 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCTCTCCCCACCTCATGAT;RSEQ=GTCATTGCCTCCGTGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1036:0:0,0:409,627:1036,0:0:2,0:25.1:1:30.5:1:1:0:59.9:78.692:1:0:0.2 0/1:1117:89:41,48:428,600:1028,89:0.0797:2,2:24.9:1:28.4:1:0.43454:1.20:60:43.5:0.0788:0:1.2 +1 16265967 . C A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12533;SOR=Inf;LSEQ=TGAATCTTCCCAGGGCTCTG;RSEQ=AGTAAAAACAAAGGACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:77,291:368,0:0:2,0:23.7:1:32.3:1:1:0:60:45:1:0:0.2 0/1:400:4:3,1:112,284:396,4:0.01:2,2:9:1:26.8:1:0.07355:7.56:60:8:0.0101:0:1 +1 16458607 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49635;SOR=0;LSEQ=TCCTCCAGCACGCGGGACAG;RSEQ=CCAAAGTCAGACACCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:49,18:67,2:0.029:2,2:36:1:31.5:1:0.47783:2.67652:60:4:0.0294:0:1 0/0:68:0:0,0:41,27:68,0:0:2,0:22.9:1:30.1:1:1:0:49.3:33:1:0:0.2 +1 16458654 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49678;SOR=0;LSEQ=GTTGCTGTTGACGAGGATGT;RSEQ=GCGGGCAGCCAGGTCACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:39,36:75,2:0.026:2,2:36.5:1:31:1:1:1.08219:36:4:0.0263:0:1 0/0:75:0:0,0:36,39:75,0:0:2,0:27.7:1:29.4:1:1:0:45.7:74:1:0:0.3 +1 16458660 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49807;SOR=Inf;LSEQ=GTTGACGAGGATGTTGCGGG;RSEQ=AGCCAGGTCACGGTGCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:37,33:70,0:0:2,0:25.7:1:31.9:1:1:0:45.8:69:1:0:0.1 0/1:78:2:1,1:38,38:76,2:0.0256:2,2:40.5:1:28.5:1:1:1:40:4:0.0256:0:2 +1 16458693 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50272;SOR=Inf;LSEQ=GTGCACATAGTTCATGTTGG;RSEQ=CAGGTACTTCATGCCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:25,39:64,0:0:2,0:27.7:1:31.7:1:1:0:49.9:128:1:0:0.1 0/1:80:2:1,1:34,44:78,2:0.025:2,2:29.5:1:27.5:1:1:1.29:29.5:4:0.025:0:1 +1 16458732 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=TGCGATGCCCCGCAGCATGC;RSEQ=CACCAGCTGCAGCACGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:17,33:50,0:0:2,0:24.4:1:31:1:1:0:60:49:1:0:0.1 0/1:50:2:1,1:21,27:48,2:0.04:2,2:25:1:32:1:1:1.28:60:4:0.0408:0:1 +1 16971069 . G C 63 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTGCAGGTGCCCTCGCA;RSEQ=TGGACTAAACTGGACCGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:19.8:1:31.8:1:1:0:29.8:8:1:0:1 1/1:3:3:1,2:0,0:0,3:1:0,2:33.3:1:32.3:1:1:0:26.7:6:1:0:1 +1 16971283 . T G 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCCCGCGCCCAGCCTCCGC;RSEQ=AGGGGACCCCCTCCGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:30:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:29.5:1:27.5:1:1:0:60:4:1:0:0.5 +1 16971804 . A T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=CTGGCAGCTGTCACTTTCAC;RSEQ=ATGCCCTTGGGCTGACTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:5,1:6,6:0.5:2,0:28.2:1:32.2:1:1:0:28.2:12:0.5:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:31:1:31:0:1:0:21:4:1:0:0 +1 16971862 . A G 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12255;SOR=2.03177;LSEQ=CCCAACCCCAGGGCACCTCA;RSEQ=GTGGCCCCACCAAACCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:21:21,0:43,0:43,21:0.3281:1,1:25.2:1:34.5:1:1:0:49.2:42:0.3387:0:2.2 1/0:32:16:13,3:15,1:16,16:0.5:1,2:18.4:1:32.6:1:0.59956:3.33655:53:32:0.5:0:2.6 +1 16971866 . G T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.98811;LSEQ=ACCCCAGGGCACCTCAAGTG;RSEQ=CCCCACCAAACCTTCCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:69:50:50,0:19,0:19,50:0.7246:1,1:25.2:1:31.2:1:1:0:50.3:100:0.7246:0:1.6 1/0:36:26:23,3:9,1:10,26:0.7222:2,2:23:1:30.4:1:1:1.16883:52.3:52:0.7222:0:2 +1 16971948 . C G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63443;SOR=1.14324;LSEQ=TGCTAGGCCCTTGCAACTGA;RSEQ=CTGTGGGACCTGAGGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:86:82,4:119,1:120,86:0.4175:1,1:34.2:1:32.8:1:0.16313:5.75907:49.4:42:0.4179:0:1.2 0/1:111:50:48,2:58,3:61,50:0.4505:1,1:32.7:1:31.2:1:1:1.24:49.1:49:0.4455:0:1.5 +1 16972189 . C A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.45041;LSEQ=CCCTGGTGAGTGCCCCCAAC;RSEQ=TTGATCCCCATCTGCCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1154:227:60,167:346,581:927,227:0.1967:2,2:34.3:1:31.1:1:0.00192:1.65685:26:112.5:0.1974:0:1.1 0/1:1158:115:43,72:410,632:1042,115:0.0993:2,2:35.3:1:29.9:1:0.76279:1.0862:26.5:37.333:0.0982:0:1.2 +1 16972221 . G A 175 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=16.21658;LSEQ=CTGCCTTCAGGAGGGGCTTG;RSEQ=CCCCATTCTCCTATTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1247:5:4,1:395,847:1242,5:0.004:2,2:7.6:1:25.4:1:0.03869:8.56:39.2:4:0.0032:0:1.2 0/1:1207:74:28,46:410,723:1133,74:0.0613:2,2:23.4:1:28.3:1:0.80341:1.07:33.9:73:0.0614:0:1.2 +1 16972294 . T C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57641;SOR=0.75584;LSEQ=TGGGCATGGGGCAGTGACCT;RSEQ=GGCCTCTTGAGCACAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:23:2,21:12,111:123,23:0.1575:2,2:47.3:1:28.2:1:1:1.13418:21.8:10.5:0.1469:0:1.8 0/1:97:12:1,11:3,82:85,12:0.1237:1,2:47:1:27.9:1:0.41562:2.45:22.3:11:0.1158:0:1.5 +1 16972300 . C T 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15059;SOR=0.43421;LSEQ=TGGGGCAGTGACCTTGGCCT;RSEQ=TTGAGCACAGCTGGGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:15:2,13:9,87:96,15:0.1351:2,2:45.5:1:29.6:1:0.64247:1.48:22:14:0.1308:0:2.1 0/1:79:5:0,5:2,72:74,5:0.0633:1,0:45.8:1:31.2:1:1:0:22.6:10:0.0633:0:2 +1 16972350 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22857;SOR=0;LSEQ=CATAGACATGGCCCACTTAG;RSEQ=CCTCTATTAGCACGTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:9,3:0.25:0,0:9.3:1:28:1:1:0:22.7:6:0.2727:0:2.3 0/0:9:0:0,0:1,8:9,0:0:2,0:13.7:1:29.3:1:1:0:30.3:8:1:0:0.3 +1 16972790 . GAAT AA 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=0;LSEQ=CCTTGTAGCTTTGATCCCCT;RSEQ=GAACAAACTGTGGACATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:11:10,1:104,22:126,11:0.0791:2,2:12:1:30.9:1:0.69024:2.11:34.7:22:0.0815:0.0288:0.6 0/0:142:0:0,0:99,42:141,0:0:2,0:11.1:1:31:1:1:0:28.2:69.5:0.9929:0:0.1 +1 16972920 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=0.72525;LSEQ=GGGGCACAGAGCTACAGCGC;RSEQ=GCTACAAGCGGTGGTGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1388:310:165,145:595,483:1078,310:0.2233:2,2:28.9:1:31.3:1:0.56034:1.0825:39.4:309:0.2251:0:1.1 0/1:1756:303:175,128:783,670:1453,303:0.1726:2,2:28.8:1:30:1:0.22856:1.17:38.5:302:0.1743:0:1.2 +1 16972940 . G A 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.33532;LSEQ=CGCTACAAGCGGTGGTGCCC;RSEQ=GGCCTTGGCAGGAGGATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1064:656:358,298:217,191:408,656:0.6165:2,2:30.5:1:31.2:1:0.70431:1.06:35.3:92.714:0.6181:0:1.1 0/1:1385:485:255,230:479,421:900,485:0.3502:2,2:29.3:1:30:1:0.82167:1.02621:37.2:68.286:0.3494:0:1.1 +1 16973057 . G A 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGGGGGCAGGGGAGCCTG;RSEQ=GCCGTGGCGTTACCTTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:612:0:0,0:276,336:612,0:0:2,0:31.5:1:31.3:1:1:0:37.2:46.077:1:0:0.1 0/1:758:31:16,15:325,401:726,31:0.0409:2,2:29.2:1:29.1:1:0.46694:1.32:27.4:30:0.0404:0:1.3 +1 16973184 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03245;SOR=0.56265;LSEQ=GCTGCGGCATTCTGGGCGCT;RSEQ=TGACCTCTTCCAGGAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:32:22,10:245,292:537,32:0.0562:2,2:30.6:1:28.7:1:0.01654:2.62:21.9:15:0.0533:0:1.8 0/1:956:31:21,10:448,476:924,31:0.0324:2,2:29:1:29.3:1:0.04364:2.23:22.5:62:0.0328:0:1.7 +1 16973358 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGACCGTGGGTGGCCTGTC;RSEQ=TGCCAGGCTTGGAGCCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:12,0:0:2,0:7:1:30.8:1:1:0:43.4:11:1:0:0.4 0/1:32:2:1,1:15,15:30,2:0.0625:2,2:19.5:1:28.5:1:1:1:60:4:0.0625:0:1.5 +1 16973620 . C T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CCTGCCGGGTGGGTAAGCGG;RSEQ=GCCGGGTCAAGCTGGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:1.5:1:30.5:1:1:0:20:4:1:0:0.5 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:47:1:30:1:1:1:20.5:4:0.3333:0:2 +1 16974386 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50476;SOR=Inf;LSEQ=CCACCGCGGGCGTACCTTGC;RSEQ=AGCGTTGGGACGCGCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:10.8:1:32.3:1:1:0:20.5:16:1:0:0.5 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:9.5:1:28:1:1:1.18321:22:4:0.1818:0:1.5 +1 16974415 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50537;SOR=Inf;LSEQ=GACGCGCAAATCCCGCATCA;RSEQ=CACCGATTTACGCCAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:28,34:62,0:0:2,0:7.5:1:32:1:1:0:20.7:61:1:0:0.5 0/1:81:2:1,1:43,36:79,2:0.0247:2,2:8.5:1:28:1:1:1.19181:20:4:0.025:0:1.5 +1 16974426 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52006;SOR=Inf;LSEQ=CCCGCATCAGCACCGATTTA;RSEQ=GCCAGAAAAATACGCGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:42,47:89,0:0:2,0:14.8:1:31.3:1:1:0:21.3:88:0.9888:0:0.6 0/1:138:2:1,1:71,65:136,2:0.0145:2,2:22:1:28:1:1:1.0916:21:4:0.0146:0:1 +1 16974449 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06238;SOR=0;LSEQ=CAGAAAAATACGCGTGCAAG;RSEQ=GAGGTGGGGGGGCGGGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:2,1:53,60:113,3:0.0254:2,2:30:1:26.3:1:0.6029:2.25:24.3:2:0.0179:0:1.7 0/0:178:0:0,0:92,86:178,0:0:2,0:28.2:1:29.7:1:1:0:22:58.333:1:0:0.5 +1 16974465 . G T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.27554;SOR=Inf;LSEQ=CAAGTGAGGTGGGGGGGCGG;RSEQ=CGTTGGGACGTGCTGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:57,62:119,0:0:2,0:21.8:1:31.2:1:1:0:21.8:10.9:1:0:0.7 0/1:176:3:2,1:89,84:173,3:0.017:2,2:20:1:23.7:1:1:1.88:21:2:0.0116:0:1.3 +1 16974471 . G A 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=2.00722;LSEQ=AGGTGGGGGGGCGGGCGTTG;RSEQ=GACGTGCTGCTGCGGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:0,1:56,60:116,1:0.0085:2,0:12:0:16:0:1:0:25:0:0:0:3 0/1:176:3:1,2:90,83:173,3:0.017:2,2:35.7:1:30:1:0.61031:2.15947:24.3:6:0.0174:0:1.3 +1 16974511 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1673;SOR=0.80581;LSEQ=GACGGGAGGAGGGTAGTCAC;RSEQ=GGCTTAGGGCTGGAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:127:73,54:167,160:327,127:0.2797:2,2:13.4:1:31.6:1:0.24947:1.29:23.7:126:0.2851:0:1.1 0/1:428:102:61,41:178,148:326,102:0.2383:2,2:13.1:1:29.7:1:0.3637:1.24:24.3:101:0.2365:0:1.1 +1 16974616 . G T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.26216;LSEQ=CGGCTCAGAGGCGCCCTGGT;RSEQ=CTTCACACTGCGGCCCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:1:0,1:21,22:43,1:0.0227:2,0:1:0:28:0:1:0:22:2:0.0233:0:2 0/1:70:2:1,1:36,32:68,2:0.0286:2,2:10:0:31:1:1:1.1231:20:4:0.029:0:2.5 +1 16974628 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28869;SOR=Inf;LSEQ=GCCCTGGTGCTTCACACTGC;RSEQ=GCCCGGCATGCGCGTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:24,26:50,0:0:2,0:20.9:1:30.5:1:1:0:21.7:15.667:1:0:0.9 0/1:82:3:2,1:39,38:77,3:0.0366:2,2:35.3:1:26:1:1:1.93:24.3:2:0.0256:0:2 +1 16974666 . C T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00261;SOR=0.16659;LSEQ=GCTTTTGCTACCAGATCCGG;RSEQ=GTTGTACAGACGACGTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:17:8,9:4,6:10,17:0.6296:2,2:7.4:1:28.9:1:1:1.32:21.9:16:0.6154:0:1.8 0/1:28:6:2,4:11,11:22,6:0.2143:2,2:10.5:1:29.3:1:0.65459:1.95193:20.5:12:0.2143:0:1.7 +1 16974780 . C T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTCGGCCTGATGGCTGCC;RSEQ=GCACCGGCCGCAGACTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:9:0:30.5:1:1:0:50:4:1:0:2 +1 16974786 . G C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGATGGCTGCCCGCACC;RSEQ=GCCGCAGACTGCTACCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:15:0:31:0:1:0:50:4:1:0:2 +1 16974817 . C G 109 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=0.04067;LSEQ=GCTACCACGGCGCGGGGGAG;RSEQ=AGTACCGCGGCACGGTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:6,5:17,9:26,11:0.2973:2,2:12.1:1:31.6:1:0.71298:1.55431:21.4:22:0.3056:0:2 0/1:61:1:0,1:21,38:59,1:0.0164:2,0:13:0:32:0:1:0:21:2:0.0164:0:2 +1 16974831 . G T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.4269;LSEQ=GGGGAGCAGTACCGCGGCAC;RSEQ=GTCAGCAAGACCCGCAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:0,1:55,35:90,1:0.011:2,0:1:0:27:0:0.3956:0:60:2:0.0114:0:1 0/1:192:3:0,3:94,95:189,3:0.0156:2,0:10:1:27:1:0.2464:0:46.7:6:0.0157:0:1 +1 16974869 . G C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.35192;LSEQ=GGGTGTCCAGTGCCAGCGCG;RSEQ=GTCCGCTGAGACGCCGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:78:49,29:92,94:186,78:0.2955:2,2:24.8:1:32.1:1:0.05822:1.72:21.5:156:0.3:0:1.3 0/1:545:70:36,34:239,236:475,70:0.1284:2,2:27.6:1:30.8:1:0.89856:1.05:22.3:140:0.1292:0:1.1 +1 16974928 . G A 49 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.87869;LSEQ=GTGCTCCCGGCCCCGCCAGG;RSEQ=CCCTAACCCTGGGGCGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:1,0:75,75:150,1:0.0066:2,0:1:0:26:0:1:0:60:2:0.0068:0:1 0/1:323:4:3,1:163,156:319,4:0.0124:2,2:5.3:1:24.8:1:0.62325:2.86:60:8:0.0125:0:1 +1 16975002 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97178;LSEQ=TTGAGACTACCCTGCCACGA;RSEQ=TTCGCTCCCGCTCCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:9:6,3:320,231:551,9:0.0161:2,2:5.7:1:30.1:1:0.74111:1.44:26:18:0.0163:0:1.7 0/1:1024:16:8,8:575,433:1008,16:0.0156:2,2:7.9:1:29.3:1:0.61694:1.32756:21.7:32:0.0157:0:1.4 +1 16975075 . G A 48 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30224;SOR=Inf;LSEQ=CTGGAGGAGAACTTCTGCCA;RSEQ=ACCCAGATGGGGATAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:114,96:210,0:0:2,0:11.5:1:31.7:1:1:0:22:25.25:1:0:0.2 0/1:373:4:2,2:210,159:369,4:0.0107:2,2:5.5:1:24:1:1:1.31974:27.3:3:0.0082:0:1.5 +1 16975084 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05366;SOR=0;LSEQ=AACTTCTGCCAGACCCAGAT;RSEQ=GGGATAGCCATGGGCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:3:2,1:74,53:127,3:0.0231:2,2:16.7:1:29:1:1:1.43:27.3:6:0.0242:0:2 0/0:213:0:0,0:120,93:213,0:0:2,0:6:1:29.1:1:1:0:21.3:41.6:1:0:0.1 +1 16975200 . C A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10577;SOR=0;LSEQ=CCCCATGACCCTGCCTCAGC;RSEQ=CTCACCACCAAAGGCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:3:2,1:110,115:225,3:0.0132:2,2:22.7:1:28.7:1:0.6168:2.08:21.7:6:0.0136:0:1 0/0:253:0:0,0:135,118:253,0:0:2,0:31.4:1:30.8:1:1:0:30.2:83.333:1:0:0.2 +1 16975202 . T C 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78098;SOR=0.78224;LSEQ=CCATGACCCTGCCTCAGCCC;RSEQ=CACCACCAAAGGCTGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:7:4,3:105,111:216,7:0.0311:2,2:21.6:1:32.7:1:0.71687:1.41:23:14:0.0315:0:1.3 0/1:245:6:3,3:128,111:239,6:0.0245:2,2:23.5:1:28.8:1:1:1.15248:21.7:5:0.0207:0:1.5 +1 16975228 . C T 188 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCAAAGGCTGGCTCCCTTAA;RSEQ=CGCAGTGAACTTTGTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:76:34,42:62,61:123,76:0.38:2,2:30.3:1:30.1:1:0.46771:1.2541:21.8:37:0.3776:0:1.1 0/0:198:0:0,0:108,90:198,0:0:2,0:28.9:1:30.8:1:1:0:30.2:197:1:0:0.1 +1 16976215 . G A 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56005;SOR=0.62266;LSEQ=GGGTGAGACCAAAGGTAAGA;RSEQ=CATAGTGCACAGGACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:1,0:19,31:50,1:0.0196:2,0:1:0:28:0:0.39216:0:60:2:0.0196:0:2 0/1:163:2:1,1:65,96:161,2:0.0123:2,2:5:1:27:1:1:1.47:60:4:0.0124:0:1 +1 16976216 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTGAGACCAAAGGTAAGAG;RSEQ=ATAGTGCACAGGACTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:18,29:47,0:0:2,0:14.6:1:33.5:1:1:0:57.9:94:1:0:0.2 0/1:152:2:1,1:59,90:149,2:0.0132:2,2:9:1:26:1:1:1.52:60:4:0.0134:0:1 +1 16976222 . G A 40 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96452;LSEQ=ACCAAAGGTAAGAGCATAGT;RSEQ=CACAGGACTGCTGGTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:1:1,0:13,23:36,1:0.027:2,0:1:0:23:0:0.37838:0:60:2:0.027:0:1 0/1:115:3:2,1:38,74:112,3:0.0261:2,2:6.3:1:25.7:1:0.27695:3.85:60:6:0.0261:0:1 +1 16976679 . G A 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CGCTGGCCAGCCGTCTTCAC;RSEQ=CGTGTCTCTGTGTTTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:2,2:0.5:2,0:41:1:32:0:1:0:22:4:0.5:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:24:1:30:1:1:0:46.7:6:1:0:1.7 +1 17012241 . G T 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06167;LSEQ=TGGAAGCTCGCCGTATGCCT;RSEQ=CAGACTTCTAGCTTCGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:989:987:455,532:0,0:0,987:0.998:0,2:21:1:30.6:1:1:0:43.4:122.375:0.999:0:1.1 1/1:1068:1034:502,532:18,16:34,1034:0.9682:2,2:22.6:1:29.2:1:0.72789:1.19203:43.3:128.25:0.9679:0:1.1 +1 17012702 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10835;SOR=0.51091;LSEQ=CGGGAGAGGCTGGCGACCCA;RSEQ=CTCTTCGGAGATCCGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:34:0,34:0,23:23,34:0.5965:1,1:22.7:1:26.9:1:1:0:49.8:16:0.5926:0:1.2 0/1:42:18:0,18:3,21:24,18:0.4286:2,1:27.4:1:28.4:1:0.24739:0:42:36:0.4286:0:1.7 +1 17012709 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06828;SOR=2.20874;LSEQ=GGCTGGCGACCCAGCTCTTC;RSEQ=GAGATCCGCCTGCGTCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:17:0,17:0,43:43,17:0.2833:1,1:24.1:1:29.8:1:1:0:44.9:16:0.2759:0:1.6 0/1:47:22:1,21:2,23:25,22:0.4681:2,1:25.5:1:28.6:1:1:1.80368:42.7:21:0.4565:0:2.1 +1 17012761 . C G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27679;SOR=1.62662;LSEQ=CAAAATGCTCTTCTGGTTTT;RSEQ=AATGTGGTGGGTGGCCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:12:0,12:2,53:55,12:0.1765:1,0:28.3:1:32.5:1:1:0:39.6:24:0.1791:0:1.7 0/1:54:14:1,13:3,36:39,14:0.2593:2,1:32.1:1:31.1:1:1:1.08172:46.8:28:0.2642:0:1.8 +1 17012933 . A ATTT 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=12.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTATTATTATTATTATTATT;RSEQ=TTATTATTATTAGCAGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:3,2:0.4:2,0:12:1:32:1:1:0:35:4:0.4:0.2:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 17083568 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.8489;LSEQ=TAATTCTCTTCTTCATTACT;RSEQ=TTTACTTGCAGGGGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:30,3:33,3:0.0833:2,0:27.7:1:29.7:1:1:0:20:6:0.0882:0:1 0/1:14:1:1,0:11,2:13,1:0.0714:2,0:35:0:24:0:1:0:22:2:0.0714:0:1 +1 17083671 . C G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.83031;SOR=0.85;LSEQ=CCTTGAGTACAAGTCTTGTC;RSEQ=TTGACTGTACTTACAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:24:15,9:50,0:50,24:0.3243:1,2:33:1:30.9:1:1e-05:0:38.4:48:0.3243:0:2 0/1:38:11:5,6:25,2:27,11:0.2895:2,2:26.5:1:29.9:1:0.0035:13.53977:28:10:0.2703:0:2.1 +1 17083685 . C A 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65315;SOR=0.79813;LSEQ=CTTGTCCTTGACTGTACTTA;RSEQ=AAGTTTTGTCCTCCCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:24:15,9:33,0:33,24:0.4211:1,2:19.3:1:30:1:0.00015:0:38.4:48:0.4286:0:2 0/1:30:11:5,6:17,2:19,11:0.3667:2,2:12.5:1:29.9:1:0.02751:9.25689:28:22:0.3667:0:2.1 +1 17085006 . C T 33 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.05455;SOR=0;LSEQ=GTGAGTTGCCCGGATGGCCC;RSEQ=CAGCCACGCGCAGCTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:19:0:33:1:1:0:48:4:0.6667:0:1.5 0/0:8:0:0,0:4,4:8,0:0:2,0:14:1:31.1:1:1:0:60:16:1:0:0.5 +1 17085253 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.12424;SOR=Inf;LSEQ=AGGGAGCCAGCCTTTGGTGG;RSEQ=GAGGGCTGAGGTAAGGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:148,163:311,0:0:2,0:35:1:30:1:1:0:27.1:102.667:1:0:0.2 0/1:327:4:2,2:148,175:323,4:0.0122:2,2:22.3:1:31.8:1:1:1.18:21:8:0.0125:0:2.3 +1 17085255 . A G 159 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=9.6942;LSEQ=GGAGCCAGCCTTTGGTGGTG;RSEQ=GGGCTGAGGTAAGGTCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:4:2,2:148,161:309,4:0.0127:2,2:4.5:1:32.3:1:1:1.09:22.5:8:0.0129:0:1.5 0/1:332:37:16,21:136,159:295,37:0.1114:2,2:34.8:1:30.6:1:0.86137:1.12225:22.6:74:0.1128:0:1.3 +1 17085412 . C T 101 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0105;SOR=4.63149;LSEQ=TTCTCCTCCAGTTGTGCATG;RSEQ=GGTTCGGAGGTAAATGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:831:3:0,3:378,450:828,3:0.0036:2,0:45.7:1:30.7:1:0.25521:0:22:6:0.0037:0:2.7 0/1:787:13:4,9:343,430:773,13:0.0165:2,2:15.5:1:27.3:1:0.40602:1.79349:33.8:26:0.0168:0:1.2 +1 17085482 . C A 53 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16662;SOR=5.65755;LSEQ=CAGGGTAGTCTCAACCATTT;RSEQ=CAGGCTCTGGTCCCAGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:1:1,0:240,263:503,1:0.002:2,0:1:0:23:0:0.47817:0:60:2:0.002:0:1 0/1:359:4:3,1:146,208:354,4:0.0111:2,2:6.8:1:26.5:1:0.31185:4.26:25:8:0.0116:0:1.3 +1 17085494 . C A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55627;SOR=0;LSEQ=AACCATTTCCAGGCTCTGGT;RSEQ=CCAGACATCAAAGCATGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:2,1:117,138:255,3:0.0116:2,2:10:1:25.3:1:0.59657:2.35:21.7:6:0.012:0:1.7 0/0:146:0:0,0:54,92:146,0:0:2,0:8.1:1:29.7:1:1:0:21.3:35.5:1:0:0.3 +1 17085569 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CCAGGGACTCACTGCAGCTT;RSEQ=TGCGGCGTCTCAGCGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:41.9:1:33:1:1:0:49:14:1:0:0.4 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:23:0:28.5:1:1:2.44949:47.5:4:0.3333:0:3.5 +1 17085784 . G T 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19852;LSEQ=CCTGGGGCCGCACGTCGTCT;RSEQ=TACAACGCCGGATCTGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:53,54:107,2:0.0182:2,2:16:0:32.5:1:1:1.02:60:4:0.0183:0:1 0/1:46:1:1,0:18,27:45,1:0.0217:2,0:3:0:26:0:0.41304:0:60:2:0.0222:0:1 +1 17085834 . G T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=3.52197;LSEQ=ACGCGCGTGCCGGGCCGCAG;RSEQ=GTGAAGCACCAGGGCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:24:22,2:239,257:496,24:0.0462:2,2:22.2:1:31.5:1:2e-05:11.79:20.2:48:0.0471:0:1.2 0/1:240:35:28,7:85,120:205,35:0.1458:2,2:20.9:1:30.3:1:3e-05:5.61:21.8:70:0.1489:0:1.3 +1 17085930 . C T 38 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0979;SOR=Inf;LSEQ=ACTCAGCCCTAGCCCGCCAG;RSEQ=CTCCAGCCCTAAGCCCGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:166,151:317,0:0:2,0:20.2:1:31.4:1:1:0:22.4:44.286:1:0:0.3 0/1:272:3:1,2:134,134:268,3:0.011:2,2:6.3:1:24.3:1:1:1.99507:20:6:0.0115:0:1 +1 17085966 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.212;SOR=Inf;LSEQ=CGTGACTACCCTCCTCCCGT;RSEQ=TCACCCGCAGCAGCACGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:89,118:207,0:0:2,0:22.7:1:32.1:1:1:0:21:40.4:1:0:1.3 0/1:178:2:1,1:69,105:174,2:0.0112:2,2:31.5:1:27.5:1:1:1.52:21:4:0.0118:0:2 +1 17085970 . C T 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09975;SOR=Inf;LSEQ=ACTACCCTCCTCCCGTCTCA;RSEQ=CCGCAGCAGCACGTCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:90,131:221,0:0:2,0:25.1:1:30.9:1:1:0:21.1:19.091:0.9953:0:1.3 0/1:193:3:1,2:74,116:190,3:0.0155:2,2:7.3:1:27.3:1:1:1.27429:23.3:6:0.0163:0:1.7 +1 17085992 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24896;SOR=0;LSEQ=CGCAGCAGCACGTCCCAACG;RSEQ=CCGCCCCCCCGCCCACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:1,2:94,136:230,3:0.0129:2,2:27.7:1:29:1:1:1.3805:22.7:6:0.0146:0:1 0/0:220:0:0,0:83,136:219,0:0:2,0:34.8:1:28.3:1:1:0:21.4:5.441:1:0:1.1 +1 17085995 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.1115;SOR=Inf;LSEQ=AGCAGCACGTCCCAACGCCC;RSEQ=CCCCCCCGCCCACCTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:92,138:230,0:0:2,0:36:1:26.7:1:1:0:21.2:3.6:0.9945:0:1.2 0/1:220:3:1,2:76,134:210,3:0.0136:2,2:25.7:1:27.3:1:1:1.13369:22.3:6:0.0172:0:1.3 +1 17086017 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10872;SOR=Inf;LSEQ=CCCCCCGCCCACCTCACTTG;RSEQ=ACGCGTATTTTTCTGGCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:90,135:225,0:0:2,0:20.8:1:28.8:1:1:0:21.1:4:1:0:1.2 0/1:211:3:1,2:77,126:203,3:0.0142:2,2:27.7:1:29.7:1:1:1.22103:20.3:6:0.0171:0:2 +1 17087108 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57307;SOR=0.37957;LSEQ=CTCCAAGCCTGGCAGGACAG;RSEQ=CCACCCACGGTCGTGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:13.5:1:28.5:1:1:1.18321:44:4:0.1538:0:1 0/1:16:1:1,0:8,7:15,1:0.0625:2,0:1:0:25:0:1:0:23:2:0.0625:0:1 +1 17087244 . AC A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00274;SOR=0.61326;LSEQ=CTCCCACCCTGCCCCTCTCC;RSEQ=CCCCACTCGCCTTTCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:984:122:66,56:460,401:861,122:0.124:2,2:20.2:1:31.7:1:0.92292:1.03:30.8:244:0.1258:0.0234:0.1 0/1:764:61:28,33:386,317:703,61:0.0798:2,2:18:1:30:1:0.18291:1.43441:30.4:60:0.0798:0.0209:0.2 +1 17087262 . C T 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=0.69277;LSEQ=CCACCCCCACTCGCCTTTCT;RSEQ=CTGGAAGAGGTCACAGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1512:434:243,191:557,521:1078,434:0.287:2,2:27:1:30.5:1:0.13871:1.19:28.4:53.25:0.2876:0:1.2 0/1:1174:256:132,124:479,437:916,256:0.2181:2,2:26:1:29.1:1:0.88748:1.02966:28.4:127:0.2207:0:1.2 +1 17087322 . A G 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGGGCGAGTGTTGAGTCC;RSEQ=TGGCAGCAGTTGGCAACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2093:0:0,0:1085,1007:2092,0:0:2,0:29.9:1:30.7:1:1:0:30.5:62.394:1:0:0.6 0/1:1695:31:18,13:825,839:1664,31:0.0183:2,2:32.7:1:30.5:1:0.3704:1.41:30.5:62:0.0186:0:1.5 +1 17087365 . C G 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06368;SOR=0.81823;LSEQ=CTGCTCACATTGTAGTGGAA;RSEQ=GCCCTGGAGAGAAGAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:873:570:302,268:158,144:302,570:0.6529:2,2:11.8:1:31.5:1:0.88669:1.03:27:94:0.6551:0:1.1 1/0:683:414:203,211:138,127:265,414:0.6061:2,2:10.9:1:30:1:0.47899:1.12923:26.9:40.4:0.6057:0:1.1 +1 17087395 . G A 106 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01208;SOR=0.11666;LSEQ=AGAAGAAGGCACAGGGTAAC;RSEQ=CCACGGCCCAGGCTCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:13:6,7:521,459:980,13:0.0131:2,2:18.3:1:28.8:1:0.78122:1.32387:21.8:26:0.0133:0:1.9 0/0:649:1:0,1:356,290:646,1:0.0015:2,0:26:0:25:0:0.44977:0:23:2:0.0016:0:2 +1 17087459 . A G 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55601;SOR=1.13056;LSEQ=TGGCCACTCACCAGCAGTCC;RSEQ=TTAAGGGCCCACAGCGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:957:66:29,37:462,429:891,66:0.069:2,2:15.8:1:31.8:1:0.25087:1.37354:22.2:132:0.07:0:1.3 0/1:647:50:27,23:317,279:596,50:0.0773:2,2:15.2:1:29.8:1:1:1.03:23.6:100:0.0781:0:1.2 +1 17087465 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00179;SOR=1.43467;LSEQ=CTCACCAGCAGTCCATTAAG;RSEQ=GCCCACAGCGACCAGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:238:112,126:342,320:662,238:0.2642:2,2:10.4:1:30.3:1:0.22753:1.20209:22.8:33:0.2637:0:1.1 0/1:600:204:109,95:203,191:394,204:0.34:2,2:10.4:1:28.1:1:0.66693:1.08:24.7:67:0.3401:0:1.1 +1 17087541 . GGTGCT G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08279;SOR=2.35328;LSEQ=GGGCACCACCGCATGTAGCA;RSEQ=GTAGCTCTGTGCCCCGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:7:4,3:277,341:618,7:0.0111:2,2:8:1:32.7:1:0.70647:1.64:34.6:14:0.0113:0.0064:1.6 0/1:581:15:7,8:269,296:565,15:0.0258:2,2:10.1:1:30.7:1:1:1.03855:32.9:30:0.0261:0.0138:1.3 +1 17087582 . G A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0015;SOR=3.01839;LSEQ=GGAGCACCTGGAAGTCATTC;RSEQ=ATGGCGAGCGCTGCCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1059:11:6,5:459,589:1048,11:0.0104:2,2:41.3:1:29.5:1:0.54887:1.54:34.3:10:0.0096:0:1.7 0/1:1009:31:15,16:433,545:978,31:0.0307:2,2:36.6:1:30.5:1:0.71491:1.18:33.6:62:0.0311:0:1.4 +1 17088194 . GC G 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.04666;SOR=Inf;LSEQ=GGCCAAGGTCACTGCCCCAT;RSEQ=CCACTGAGCCTCTGGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:118,15:133,0:0:2,0:20.7:1:32.1:1:1:0:36.3:32.25:1:0:0.1 0/1:117:4:3,1:100,13:113,4:0.0342:2,2:11:1:29.4:1:0.40363:2.53607:42.8:8:0.0351:0.0256:0 +1 17088343 . C A 125 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=28.81093;LSEQ=GAAGCAGCAGGAGTGGGAGC;RSEQ=ACTCCTCCAGGATGACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2091:1:1,0:804,1286:2090,1:5e-04:2,0:1:0:27:0:0.38498:0:60:2:5e-04:0:1 0/1:1617:22:10,12:651,944:1595,22:0.0136:2,2:25.3:1:28.2:1:0.66808:1.21:59.4:21:0.0131:0:1.2 +1 17345073 . G GC 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAACAAGCTGCAGGCCCT;RSEQ=CTGATGTCAGTTCCACGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:17:1:30.9:1:1:0:60:10:0.5:0.3:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 17345216 . C CT 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.33698;LSEQ=GGCAAGTAAAGGAACAGGTT;RSEQ=TTTTTTTTTTGTTAATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:3,0:63,0:63,3:0.0455:1,0:32.7:1:32.3:1:1:0:60:6:0.0455:0:0 0/1:50:3:3,0:47,0:47,3:0.06:1,0:25.7:1:32.3:1:1:0:60:6:0.0612:0:0.3 +1 17345905 . A G 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAGAAACTACCCTCTCT;RSEQ=TTAACCCTTTGTAAAACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:21.8:1:32.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 17350238 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCAAGGCATGGTTTGC;RSEQ=CCCCTTTGGGGTGACCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:0,17:1:0,1:24.2:1:30.7:1:1:0:58.4:34:1:0:1.1 1/1:8:8:7,1:0,0:0,8:1:0,2:30.8:1:31.5:1:1:0:60:16:1:0:1.1 +1 17350573 . T A 41 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6876;SOR=1.85593;LSEQ=CACTCGTAGAGCCCGTCCTG;RSEQ=ATGGGGAGAAAAGAGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:2:2,0:98,228:326,2:0.0061:2,0:1:0:26:1:0.0923:0:60:4:0.0062:0:1.5 0/1:355:4:4,0:118,233:351,4:0.0113:2,0:9.8:1:20.8:1:0.0135:0:60:3:0.0086:0:1 +1 17350931 . G A 27 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGATTCAAAAGCCTAGGG;RSEQ=CTGAAGCAGCAAGAGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:7:1:27:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 17350943 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCTAGGGGCTGAAGCAGCA;RSEQ=GAGTCTGTAGCTGCTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:35:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 17353988 . T G 94 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51049;SOR=0.24443;LSEQ=CTGGTTTCTTTTGAAAAAGA;RSEQ=GGAGTAGCCACACAGCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:3,7:0.7:0,0:21.9:1:33.6:1:1:0:60:14:0.7:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:31:0:33:0:1:0:60:2:0.3333:0:1 +1 17355387 . T C 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TGTTGGCTTTTCTCCCTTCC;RSEQ=TCCTTCTTCCTGCCTCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:0,18:0,0:0,18:1:0,1:20.7:1:33.9:1:1:0:60:36:1:0:1 1/1:11:11:0,11:0,0:0,11:1:0,0:20.4:1:31.7:1:1:0:60:22:1:0:1 +1 17359386 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.81156;SOR=1.14061;LSEQ=AGAAACCAGAACTTGCACCA;RSEQ=GGTTAGAATTTTGGATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:19:18,1:15,1:16,19:0.5429:1,1:22.4:1:31.7:1:1:1.19:59:18:0.5294:0:1.4 1/0:33:19:19,0:14,0:14,19:0.5758:1,1:28.2:1:32:1:1:0:59.7:38:0.5758:0:1.1 +1 17359676 . C A 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=ATCCAGTGGTATTTATGTAA;RSEQ=GTTCAACCTCCCTACACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:289:289:67,222:0,0:0,289:1:0,2:23.7:1:31.4:1:1:0:60:35.125:1:0:1.1 1/1:302:288:86,202:2,12:14,288:0.9536:2,2:23.8:1:29.6:1:0.36517:2.55:60:56.6:0.9529:0:1.1 +1 17370797 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTATTTTGGTATTATT;RSEQ=TTCTGAATCAGGTAACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:33:1:33:0:1:0:59:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 17370970 . C T 49 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GCTGGGATTACAGGCATGAG;RSEQ=CACTATACCCAGCTAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:37.7:1:31:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:2:0:31:0:1:0:60:2:1:0:0 +1 17371152 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38303;SOR=0.75273;LSEQ=TTGTTTTAAAAACAGAGCCA;RSEQ=CGGATGATCTCAGATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:70:67,3:36,1:37,70:0.6481:1,1:24.2:1:32.8:1:1:1.60532:59.9:140:0.6604:0:1.1 1/0:93:54:50,4:35,4:39,54:0.5806:2,2:19.3:1:31.9:1:0.7162:1.42:60:108:0.5806:0:1.1 +1 17371221 . C T 124 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=16.20435;LSEQ=CCTAAATCAAATCAAGAACT;RSEQ=TCCTTCAATAGCTGGCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:1:1,0:249,109:358,1:0.0028:2,0:23:0:13:0:1:0:60:0:0:0:7 0/1:461:20:11,9:275,166:441,20:0.0434:2,2:24.1:1:28.7:1:0.49208:1.35447:60:40:0.0436:0:1.3 +1 17371223 . C T 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATCAAATCAAGAACTCT;RSEQ=CTTCAATAGCTGGCTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:256,115:371,0:0:2,0:25.8:1:31.2:1:1:0:59.9:45.375:1:0:0.2 0/1:479:48:31,17:263,168:431,48:0.1002:2,2:22.5:1:29.4:1:0.75493:1.16:60:96:0.1004:0:1.1 +1 17371411 . G GA 82 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16391;SOR=0.30777;LSEQ=TTTTTAAAGTTCACAAAAAG;RSEQ=AAAAAAAAATTAGAAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:6:1,5:39,159:198,6:0.0294:2,2:26.5:1:31.8:1:1:1.22526:60:12:0.0299:0:0 0/0:217:2:0,2:56,159:215,2:0.0092:2,0:34:1:22:1:1:0:60:1:0.0047:0:0 +1 17371494 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2505;SOR=0.57572;LSEQ=ATAAACTCACACATTACTGA;RSEQ=ACATAATCTTCTTAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:28:0,28:0,16:16,28:0.6364:1,1:25.3:1:28.4:1:1:0:59.8:56:0.6512:0:1.1 1/0:32:16:0,16:1,15:16,16:0.5:1,1:24.2:1:27.8:1:1:0:60:15:0.5:0:1.1 +1 17372397 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCTTGAACCACTTGCTC;RSEQ=ATCCCACTCCTACTCTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 17378188 . C G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCCTCATAAGATAACC;RSEQ=GGGGGAGGGGGGGTCAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:29.5:1:1:0:60:4:1:0:3.5 +1 17380195 . TC T 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.1032;SOR=0;LSEQ=TCAAGTCCCCTTTCTGAACG;RSEQ=CCCCCCCCCCGCACCCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:8,0:7,0:7,8:0.5333:0,0:34.3:1:31.9:1:1:0:60:16:0.5333:0:0.6 0/0:4:0:0,0:4,0:4,0:0:0,0:15.5:1:29:1:1:0:60:8:1:0:3.5 +1 17380269 . G C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.02131;SOR=Inf;LSEQ=GCTGCTGCGAGGCGCAGAAA;RSEQ=ATAACTTGACAGGGATGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:44,0:0:1,0:20.9:1:33.9:1:1:0:60:88:1:0:0 0/1:40:5:5,0:35,0:35,5:0.125:1,0:36.4:1:32.6:1:1:0:60:10:0.1429:0:1 +1 17380326 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49835;SOR=0;LSEQ=ACTGCACCAGGGGGAGGAGG;RSEQ=CCTCCATCTCCCTGAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:144,5:149,2:0.0132:1,2:19.5:1:33.5:1:0.07815:26.38197:60:4:0.0135:0:1 0/0:149:0:0,0:136,13:149,0:0:2,0:22.4:1:29:1:1:0:60:48.667:1:0:0 +1 17380497 . G T 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.13116;LSEQ=AACCGGCGCCTCAAGGAGAG;RSEQ=GCGACCACCGCCGCCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:839:835:387,448:0,0:0,835:0.9952:0,2:25.9:1:29.9:1:1:0:59.9:58.643:0.9976:0:1.2 1/1:879:848:392,456:15,14:29,848:0.9647:2,2:24.4:1:29:1:0.57572:1.24604:60:83.8:0.9654:0:1.2 +1 17380653 . C A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11654;LSEQ=ACCAAGTGGGAGGCGGCTTC;RSEQ=GGTTTCCCGGGTGGGCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:45:0,45:0,57:57,45:0.4412:1,1:23.6:1:33.2:1:1:0:60:90:0.4455:0:1 0/1:60:5:1,4:2,53:55,5:0.0833:1,2:28.4:1:31.2:1:0.23334:6.24:60:10:0.0862:0:1 +1 19173167 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=TGAAGTCATCCTGGAGGAGG;RSEQ=TGGGTCCTTAATCTCATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:19:0:33.5:1:1:0:51:4:1:0:0.5 0/1:5:2:1,1:1,2:3,2:0.4:2,2:8:1:27.5:1:1:1.73:60:4:0.4:0:1 +1 19173614 . G T 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTGCAGAACAGTATGCCCAT;RSEQ=CAACCTCTTTTCTCTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:43.5:1:31:1:1:0:60:4:0.3333:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:32:0:1:0:60:2:1:0:1 +1 19173895 . G T 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGTCTGTGATACTTTGT;RSEQ=AGGCAGGCCTAGGAAACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:45.5:1:30:0:1:0:60:4:0.3333:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 19173896 . A AT 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCTGTGATACTTTGTG;RSEQ=GGCAGGCCTAGGAAACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:45.5:1:32.5:1:1:0:60:4:0.3333:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 20541290 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2436;SOR=Inf;LSEQ=TACCTAACGTGACCTACTTA;RSEQ=TTCTCAGACACAGTAATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:115,62:177,0:0:2,0:22.9:1:32.6:1:1:0:60:87.5:1:0:0.3 0/1:173:2:1,1:115,56:171,2:0.0116:2,2:42.5:1:30.5:1:0.55169:2.04436:60:4:0.0118:0:1 +1 20541370 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.86273;LSEQ=TGATTCGGCCACCCTCAGCT;RSEQ=GATCCTCCAATATCATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:324:232:120,112:49,43:92,232:0.716:2,2:25.6:1:31.8:1:0.8067:1.06333:59.9:115:0.7165:0:1.1 1/1:321:282:135,147:18,21:39,282:0.8785:2,2:26.7:1:30.6:1:0.86584:1.07:60:93:0.8774:0:1.2 +1 20541449 . T A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58302;SOR=2.58637;LSEQ=ACGTATTGACACTTGGGCAA;RSEQ=GGAAACAGAGATTGGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:1,0:35,122:157,1:0.0063:2,0:1:0:27:0:0.22785:0:60:2:0.0064:0:1 0/1:123:2:1,1:33,88:121,2:0.0163:2,2:30:1:28.5:1:0.47808:2.64:60:4:0.0165:0:1 +1 21958587 . G A 26 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGAAAGCTGGAGCCAACCTG;RSEQ=AGTCTGGGCCAGGCACATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:19.5:1:30:1:1:0:60:4:0.4:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:17.5:1:26.5:1:1:0:60:4:1:0:1.5 +1 21959132 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGCTCAGTGGTTCATG;RSEQ=CTGTAATCCCAGCACTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:1:28.5:1:1:0:51.5:4:1:0:1 +1 22234424 . G C 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.07622;LSEQ=CTGTGCCTCCGTTTCCTCAT;RSEQ=TGTAAAATGGGCACGATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:9,5:0.3571:0,0:24.8:1:31.6:1:1:0:60:10:0.3571:0:1 0/1:8:3:3,0:5,0:5,3:0.375:0,0:16.3:1:29.3:1:1:0:60:6:0.375:0:1 +1 22234542 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50122;SOR=Inf;LSEQ=CATGGTGAATGTTCTATAAG;RSEQ=GTTTGCTGCCTTTCGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:66,40:106,0:0:2,0:24.9:1:29.7:1:1:0:50.7:105:1:0:0.1 0/1:125:2:1,1:66,57:123,2:0.016:2,2:33:1:31.5:1:1:1.15653:47.5:4:0.0163:0:1 +1 22234557 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50479;SOR=Inf;LSEQ=ATAAGTGTTTGCTGCCTTTC;RSEQ=GCCGGAACCGCCATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:64,46:110,0:0:2,0:28.7:1:30.2:1:1:0:46.2:109:1:0:0.1 0/1:139:2:1,1:71,65:136,2:0.0144:2,2:25.5:1:28:0:1:1.0916:24:4:0.0146:0:1.5 +1 22234585 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50612;SOR=Inf;LSEQ=CCGCCATCTTCCAGTAATTC;RSEQ=CCAAAATGACGAACACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:48,46:94,0:0:2,0:29.5:1:30.9:1:1:0:43.8:46:1:0:0.1 0/1:122:2:1,1:55,65:120,2:0.0164:2,2:23:1:27.5:1:1:1.18:58.5:4:0.0164:0:1 +1 22234598 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17143;SOR=0;LSEQ=GTAATTCGCCAAAATGACGA;RSEQ=CACAAAGGGAAAGAGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:36,48:84,2:0.0233:2,2:13.5:1:33:1:1:1.33:50.5:4:0.0235:0:2 0/0:121:0:0,0:53,68:121,0:0:2,0:24:1:29.8:1:1:0:39.3:242:1:0:0.1 +1 22234654 . C T 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCCAGGCCTTTTAGAAAA;RSEQ=ATGGAGTTGTTCCTTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:13,20:33,0:0:2,0:43.2:1:33:1:1:0:21.2:66:1:0:0.1 1/0:20:11:6,5:5,4:9,11:0.55:2,2:42.2:1:29.9:1:1:1.03956:26.2:22:0.55:0:1 +1 22234689 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51234;SOR=0;LSEQ=TTGGCCACGTATATGCGAAT;RSEQ=TATAAGAAAGGTGATATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:11,19:30,2:0.0625:2,2:15.5:1:28:1:1:1.70:22.5:4:0.0625:0:1 0/0:21:0:0,0:10,11:21,0:0:2,0:16:1:30.8:1:1:0:22.7:42:1:0:0.5 +1 22587728 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07172;SOR=Inf;LSEQ=AGGAACTTCACTCTTCATAC;RSEQ=GGTAACAATGGGGGGCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:45,0:0:1,0:23.8:1:32.2:1:1:0:60:44:1:0:0.1 0/1:33:3:2,1:27,3:30,3:0.0909:2,2:16.3:1:31.7:1:0.33028:4.19592:60:6:0.0938:0:1 +1 22587762 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16746;SOR=Inf;LSEQ=GGCTGTAAGACAGAGCTGTA;RSEQ=GCAGGGGAGGGCATGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:72,24:96,0:0:2,0:23:1:30.8:1:1:0:60:95:1:0:0.1 0/1:67:2:1,1:49,15:64,2:0.0299:2,2:19.5:1:28:1:0.4289:3.19504:60:4:0.0313:0:2.5 +1 22587773 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18728;SOR=Inf;LSEQ=AGAGCTGTAAGCAGGGGAGG;RSEQ=CATGGTAGGCTTGGAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:81,34:115,0:0:2,0:24.2:1:31.6:1:1:0:60:114:0.9913:0:0.1 0/1:89:2:1,1:60,27:87,2:0.0225:2,2:9.5:1:26.5:1:0.53269:2.20033:60:4:0.0227:0:2 +1 22587781 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20425;SOR=Inf;LSEQ=AAGCAGGGGAGGGCATGGTA;RSEQ=GCTTGGAATTTAGAAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:91,43:134,0:0:2,0:24.4:1:32.4:1:1:0:60:133:1:0:0.2 0/1:111:2:1,1:72,37:109,2:0.018:2,2:38.5:1:29:1:1:1.93352:60:4:0.0183:0:2.5 +1 22587839 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11028;SOR=Inf;LSEQ=AGAATGGGTTATTTAGATGT;RSEQ=GGCCTCGGCGAGGGCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:131,98:229,0:0:2,0:24.2:1:31.5:1:1:0:60:44.8:1:0:0.6 0/1:212:3:1,2:108,101:209,3:0.0142:2,2:22:1:30.7:1:0.61277:2.1312:60:6:0.0142:0:1.7 +1 22587878 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13342;SOR=0.75015;LSEQ=CCCGGGGAAGGGGCCTTTCC;RSEQ=CTGGGCCAGAAGGGGGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:144:74,70:55,48:103,144:0.583:2,2:26.2:1:29.8:1:0.79679:1.08354:59.9:35:0.5785:0:1.2 1/0:213:109:49,60:57,47:104,109:0.5117:2,2:23:1:29.2:1:0.17136:1.48221:60:218:0.5142:0:1.2 +1 22587882 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10134;SOR=Inf;LSEQ=GGGAAGGGGCCTTTCCGCTG;RSEQ=GCCAGAAGGGGGGCATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:123,121:244,0:0:2,0:25.9:1:31.2:1:1:0:60:121:0.9959:0:0.8 0/1:215:3:1,2:103,109:212,3:0.014:2,2:14.7:1:29:1:1:1.88453:60:6:0.0142:0:2 +1 22587925 . T C 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09024;SOR=Inf;LSEQ=CGTGGACTTCCTGCAACCAT;RSEQ=GCCCCCCACACCTGTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:86,123:209,0:0:2,0:26.6:1:30.2:1:1:0:60:33.833:1:0:0.7 0/1:171:3:1,2:77,91:168,3:0.0175:2,2:21.7:1:22.3:1:1:1.68732:60:2:0.0118:0:2 +1 22587948 . C A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59198;SOR=2.4258;LSEQ=CCCCCACACCTGTGGCTGCC;RSEQ=TTTCCTCCCACTTGGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:1:1,0:58,105:163,1:0.0061:2,0:1:0:27:0:0.35976:0:60:2:0.0063:0:2 0/1:136:2:1,1:53,81:134,2:0.0147:2,2:38.5:1:30:1:1:1.52:60:4:0.0152:0:1.5 +1 22587949 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06082;SOR=1.77884;LSEQ=CCCCACACCTGTGGCTGCCC;RSEQ=TTCCTCCCACTTGGGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:27:9,18:45,87:132,27:0.1698:2,2:27.6:1:32.2:1:1:1.03427:60:26:0.1667:0:1.4 0/1:131:35:14,21:38,58:96,35:0.2672:2,2:29.2:1:31.1:1:1:1.02:60:70:0.2672:0:1.1 +1 22924270 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17273;SOR=Inf;LSEQ=CCGGCTACACGGAGAGACAG;RSEQ=GGCGGGACTTCCTGAGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:26,0:0:2,0:26.5:1:29.6:1:1:0:60:25:1:0:0 0/1:19:2:1,1:11,6:17,2:0.1053:2,2:34.5:1:29.5:1:1:1.77272:60:4:0.1053:0:1 +1 22926772 . G T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGAAGGGAAGGAAGGAA;RSEQ=GGATGAGGAAAGGAAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:27.5:1:1:0:60:4:1:0:1 +1 22927217 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14856;SOR=0;LSEQ=CCTTCCGCACCTTCTCCTCG;RSEQ=CCAGCGACGTGTGGAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:17,16:33,2:0.0571:2,2:31:0:31:0:1:1.06069:60:4:0.0588:0:1 0/0:55:0:0,0:25,30:55,0:0:2,0:30:1:31:1:1:0:59.9:54:1:0:0.2 +1 22927314 . A G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0021;SOR=Inf;LSEQ=CAACCGGGATGTGAGTGCCA;RSEQ=GCCCTGGCAGGTCCGCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:1,11:12,0:0:2,0:26.1:1:32.7:1:1:0:60:24:1:0:0 1/1:5:4:1,3:0,1:1,4:0.8:0,2:17.5:1:31:1:1:0:60:8:0.8:0:1.5 +1 22927326 . T G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05714;SOR=Inf;LSEQ=GAGTGCCAAGCCCTGGCAGG;RSEQ=CCGCGGGCGGTGGAGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:11,0:0:2,0:21.9:1:31.4:1:1:0:60:22:1:0:0 1/0:4:2:0,2:1,1:2,2:0.5:2,0:19:1:33:0:1:0:60:4:0.5:0:2 +1 23109291 . T C 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAAATTAATGCAA;RSEQ=GTAGGGAGCTTCAGAGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:30:1:1:0:60:4:1:0:1.5 1/0:2:1:1,0:1,0:1,1:0.5:0,0:43:0:29:0:1:0:60:2:0.5:0:1 +1 23110939 . G A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.18937;SOR=Inf;LSEQ=ACACGATCCGCACGTACCAG;RSEQ=TGTGCAACGTGTTTGAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:24,0:0:2,0:32.6:1:32.1:1:1:0:60:48:1:0:0.1 0/1:19:2:1,1:5,12:17,2:0.1053:2,2:36:0:29.5:1:1:2.28:60:4:0.1053:0:1 +1 23111036 . C T 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00216;SOR=0;LSEQ=CCACGTGGAGATGAAGTTTT;RSEQ=GGTGCGTGACTGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1:0,2:24.7:1:30.3:1:1:0:60:12:1:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:17.8:1:31.6:1:1:0:52.2:10:1:0:0.2 +1 23210476 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTGCCGTCCCCCCACCCACC;RSEQ=ACCTCACTGCCCACCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:1:29.5:1:1:0:60:4:1:0:1 +1 23232400 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAGTGGATTTCCCTCCA;RSEQ=GGAGGGACTGGCTCCCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:16:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 23232869 . G C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCTGGGTCTGGAGCCCA;RSEQ=TTCTCTGGACTCTTGGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36:0:34.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 23233284 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22051;SOR=Inf;LSEQ=GGCCATCAAGACGCTCAAGT;RSEQ=GGGCTACACGGAGAAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:35,13:48,0:0:2,0:26.4:1:31.7:1:1:0:60:96:1:0:0.1 0/1:43:2:1,1:27,14:41,2:0.0465:2,2:10:0:31.5:1:1:1.89743:60:4:0.0465:0:1.5 +1 23233370 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19698;SOR=0;LSEQ=ATCCCAACGTCATCCACCTG;RSEQ=AGGGTGTCGTGACCAAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:9,31:40,2:0.0476:2,2:16.5:1:28:1:0.42393:3.32:60:4:0.0488:0:1 0/0:52:0:0,0:21,31:52,0:0:2,0:26.2:1:29.6:1:1:0:60:25:1:0:0.1 +1 23234457 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2261;SOR=Inf;LSEQ=CTCCCAAAGCAAAACGATGG;RSEQ=CAGTTCACAGTCATCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:61,30:91,0:0:2,0:23.4:1:31:1:1:0:59.4:29.333:1:0:0.1 0/1:83:2:1,1:56,25:81,2:0.0241:2,2:47.5:1:29.5:1:0.531:2.21606:60:4:0.0244:0:1 +1 23234511 . G A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4988;SOR=Inf;LSEQ=CGGGGCATCGCAGCTGGCAT;RSEQ=AAGTACCTGGCAGACATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:57,63:120,0:0:2,0:25.9:1:32.5:1:1:0:52.7:119:1:0:0.1 0/1:130:2:1,1:66,62:128,2:0.0154:2,2:7.5:1:26.5:1:1:1.06404:60:4:0.0156:0:1.5 +1 23234521 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4983;SOR=Inf;LSEQ=CAGCTGGCATGAAGTACCTG;RSEQ=CAGACATGAACTATGTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:48,65:113,0:0:2,0:26:1:31.9:1:1:0:50.9:55.5:1:0:0.1 0/1:120:2:1,1:52,66:118,2:0.0167:2,2:21.5:1:28:1:1:1.27:46.5:4:0.0167:0:1 +1 23234621 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49468;SOR=Inf;LSEQ=CTTTGGGCTCTCACGCTTTC;RSEQ=AGAGGACGATACCTCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:10,31:41,0:0:2,0:24:1:28.8:1:1:0:57.3:82:1:0:0.2 0/1:44:2:1,1:12,30:42,2:0.0455:2,2:36:1:29:1:0.50846:2.44:56:4:0.0455:0:1 +1 23235533 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49889;SOR=Inf;LSEQ=AGGGCGGAAAGATCCCCATC;RSEQ=GCTGGACAGCCCCGGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:103,66:169,0:0:2,0:24.9:1:30.1:1:1:0:60:32.8:1:0:0.3 0/1:178:2:1,1:110,66:176,2:0.0112:2,2:32:1:28:1:1:1.66161:60:4:0.0114:0:1 +1 23235598 . C A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24859;SOR=Inf;LSEQ=GCCAGTGATGTGTGGAGCTA;RSEQ=GGCATTGTCATGTGGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:60,108:168,0:0:2,0:25.6:1:30.7:1:1:0:60:167:1:0:0.2 0/1:179:3:1,2:73,103:176,3:0.0168:2,2:26:1:30.3:1:1:1.41482:60:6:0.0169:0:1 +1 23235619 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24667;SOR=Inf;LSEQ=GGCATTGTCATGTGGGAGGT;RSEQ=ATGTCCTATGGGGAGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:29,84:113,0:0:2,0:23.9:1:31.9:1:1:0:60:55.5:1:0:0.1 0/1:112:2:1,1:28,82:110,2:0.0179:2,2:18:1:26.5:1:0.45254:2.90:60:4:0.0185:0:1 +1 23236826 . C T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22619;SOR=0.3156;LSEQ=TGGGCCTGGCAGAGGGTAGA;RSEQ=GCCCTCAGCCCATCCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:10,0:3,0:3,10:0.7692:0,0:27.2:1:32.5:1:1:0:60:20:0.7692:0:1 1/0:12:6:6,0:6,0:6,6:0.5:0,0:26.5:1:29.8:1:1:0:60:12:0.5:0:1 +1 23236849 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5122;SOR=Inf;LSEQ=CCTCAGCCCATCCACCCAAC;RSEQ=CCACTGCACTCCTGCATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:16,0:0:1,0:30.7:1:30.6:1:1:0:58.7:15:1:0:1 0/1:25:2:1,1:20,3:23,2:0.08:2,2:26:1:31:1:0.3:5.9161:60:4:0.0833:0:1 +1 23236881 . A T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24178;SOR=Inf;LSEQ=CTGCATTGTCCCAGGTAATC;RSEQ=ATGCCATTGAGCAGGACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:27,7:34,0:0:2,0:19:1:29.6:1:1:0:59.4:33:1:0:0.5 0/1:38:3:1,2:26,9:35,3:0.0789:2,2:19:1:26:1:0.19559:5.46678:60:6:0.0811:0:1.3 +1 23236925 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49656;SOR=Inf;LSEQ=CTGCCACCGCCCATGGACTG;RSEQ=CCGAGCGCCCTGCACCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:33,29:62,0:0:2,0:26.1:1:29.7:1:1:0:60:9.333:1:0:0.2 0/1:66:2:1,1:41,23:64,2:0.0303:2,2:44.5:1:29:1:1:1.76614:60:4:0.0308:0:2 +1 23236938 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.23497;SOR=Inf;LSEQ=TGGACTGCCCGAGCGCCCTG;RSEQ=ACCAACTCATGCTGGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:40,36:76,0:0:2,0:26:1:30.7:1:1:0:60:11.667:1:0:0.3 0/1:72:2:1,1:41,29:70,2:0.0278:2,2:19.5:1:30:1:1:1.40686:60:4:0.029:0:1 +1 23236979 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49731;SOR=Inf;LSEQ=TGGCAGAAGGACCGCAACCA;RSEQ=CGGCCCAAGTTCGGCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:33,43:76,0:0:2,0:26.3:1:30.9:1:1:0:60:24.333:1:0:0.3 0/1:81:2:1,1:35,44:79,2:0.0247:2,2:27.5:1:28.5:1:1:1.25:60:4:0.025:0:1 +1 23237021 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50252;SOR=Inf;LSEQ=GTCAACACGCTAGACAAGAT;RSEQ=ATCCGCAATCCCAACAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:11,26:37,0:0:2,0:22.6:1:32.2:1:1:0:60:74:1:0:0.2 0/1:48:2:1,1:12,34:46,2:0.0417:2,2:36.5:1:28:1:0.47252:2.76:60:4:0.0435:0:1 +1 23238023 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCAGCCTGAGGGGTGTTC;RSEQ=CTTGGGGACCTGGTGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 23880912 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01501;LSEQ=TGCCACTGACTGACCCCTAA;RSEQ=AGGAGAACTAATCAGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:253:181:164,17:61,10:71,181:0.7154:2,2:23.4:1:30.2:1:0.36446:1.58:60:35.2:0.7126:0:1.2 0/1:334:12:8,4:279,43:322,12:0.0359:2,2:18.5:1:29.3:1:0.07251:3.22799:60:24:0.0366:0:1.3 +1 23881005 . G A 301 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00735;LSEQ=GTGGGGAAGGACTTCGAGAG;RSEQ=GCAGAGGCTTCCCGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1198:904:507,397:165,128:293,904:0.7546:2,2:25.4:1:30.7:1:1:1.00938:59.9:44.2:0.7543:0:1.2 0/1:1541:34:16,18:788,717:1505,34:0.0221:2,2:25.4:1:29.2:1:0.60418:1.23623:60:68:0.0225:0:1.2 +1 23881310 . G A 32 d5;v3;MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGAGGCCGCGCTGCTGGC;RSEQ=GAGCGGCGGGGGCGCCGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:5:1:32:1:1:0:60:4:1:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:10:0:32:0:1:0:60:2:0.5:0:1 +1 23881587 . G A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCCGCCGGTGGGGAGCG;RSEQ=CTGTCTCCGGGGAGGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:30.5:1:1:0:60:4:1:0:1.5 +1 23884172 . T C 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=ACCAACTTGCTGGGCAAGCT;RSEQ=GCACCAGTCTCTGGTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:52,229:281,0:0:2,0:21.7:1:30.6:1:1:0:60:69.25:1:0:0.1 0/1:359:14:3,11:76,268:344,14:0.039:2,2:18:1:29.3:1:1:1.03971:60:28:0.0395:0:1.2 +1 23884206 . A AG 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37895;SOR=0.63355;LSEQ=GTTTCATCTCTGAAATAATG;RSEQ=GCAGAGCCCAGAACTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:140:6,134:2,6:8,140:0.9459:2,1:21.2:1:31.3:1:0.06097:7.23207:60:139:0.9456:0.2635:0.1 1/1:169:155:9,146:2,12:14,155:0.9172:2,2:24:1:30.7:1:0.22758:2.68124:59.7:76.5:0.9107:0.1953:0.1 +1 23885230 . C G 126 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00505;SOR=0.06954;LSEQ=GCCACTGCGGGAGGGCAGGG;RSEQ=CCAGGCGCATTTAAGGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:18:18,0:13,0:13,18:0.5806:1,1:26.2:1:30.4:1:1:0:58.3:17:0.6071:0:1.1 0/1:12:1:1,0:11,0:11,1:0.0833:0,0:47:0:30:0:1:0:60:2:0.0833:0:1 +1 23885431 . G A 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGGAGATACTCACCTGGA;RSEQ=GTGTCAGGACACGGCCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:983:0:0,0:615,367:982,0:0:2,0:25.8:1:32.2:1:1:0:60:60.375:0.999:0:0.5 0/1:1319:55:32,23:745,516:1261,55:0.0417:2,2:27.7:1:28.9:1:0.88959:1.03772:60:26.5:0.0408:0:1.5 +1 23885480 . A C 213 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGCTCCTTTTGTCGTTGG;RSEQ=GATGACAAGTTCCGGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1293:0:0,0:644,647:1291,0:0:2,0:26:1:31:1:1:0:60:63.55:0.9992:0:0.8 0/1:1809:137:72,65:837,833:1670,137:0.0757:2,2:25.4:1:30.1:1:0.59503:1.10:59.8:44.667:0.0754:0:2.2 +1 23885498 . T C 320 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.6595;LSEQ=GGAGATGACAAGTTCCGGAG;RSEQ=GAGCTCGGCTGTCTGATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1303:1024:508,516:135,144:279,1024:0.7859:2,2:25.4:1:30.9:1:0.73588:1.05:59.9:59.235:0.7843:0:1.1 1/1:1773:1523:752,771:116,134:250,1523:0.859:2,2:25.5:1:30.3:1:0.41285:1.13:60:88.588:0.8581:0:1.3 +1 23885599 . T C 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05614;LSEQ=TGCCTGGGTGTTCAGCCCTG;RSEQ=CCCGACTTCGAGGCTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1222:942:495,447:150,129:279,942:0.7709:2,2:24.9:1:31.4:1:0.73326:1.05001:59.9:33.889:0.7683:0:1.1 0/1:1437:228:120,108:617,590:1207,228:0.1587:2,2:22.6:1:30.1:1:0.71805:1.06:59.9:27.5:0.156:0:1.2 +1 23886073 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03954;SOR=2.61885;LSEQ=AAAATGGCCCGCCTCGGCCC;RSEQ=GCCCCCGCCGGCCCTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:12:0,12:1,54:55,12:0.1791:1,0:19.2:1:29:1:1:0:60:11:0.1667:0:1 0/1:41:15:0,15:0,26:26,15:0.3659:1,1:20.9:1:29.7:1:1:0:60:30:0.3659:0:1 +1 23886299 . GC G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=CCAGATCTTTGAGCTTCCCT;RSEQ=CCCCTGCCAGTCCGCCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:6,0:0:2,0:27:1:32:1:1:0:60:12:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:33.5:1:1:0:60:4:1:0:0.5 +1 23886338 . G GC 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGCCCAACACTGGTTCGA;RSEQ=CCACAGCTCCTCCGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,1:1,5:0.8333:0,2:33.4:1:31.4:1:1:0:60:10:0.8333:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 23887354 . A AG 52 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCACTGATTAACAGGACA;RSEQ=GGGGGCTCAGAGCCAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:15:1:33:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:31:1:1:0:60:4:1:0:0 +1 23889095 . G C 220 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTGCATCGCCCCAACCGC;RSEQ=AGCGGCTTGTGAATTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1448:0:0,0:737,711:1448,0:0:2,0:25.4:1:31:1:1:0:60:95.533:1:0:0.2 0/1:2006:138:66,72:943,919:1862,138:0.0688:2,2:27.8:1:31:1:0.53787:1.11933:60:276:0.0692:0:1.2 +1 23889161 . C CT 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.43539;SOR=1.25942;LSEQ=CAATTGGGGCCCTTTAAAGT;RSEQ=TTTTTTTTTCTTTCTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:953:23:8,15:324,603:927,23:0.0241:2,2:29.7:1:31:1:1:1.00745:60:46:0.0246:0:0.3 0/1:1291:39:16,23:491,757:1248,39:0.0302:2,2:31.6:1:28.6:1:0.86856:1.07:59.9:12:0.0284:8e-04:0.4 +1 23889378 . AT A 88 MAF0.05;MSI12;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.63336;SOR=0.34494;LSEQ=ATTCAATGTTGTGCTCTCTG;RSEQ=TTTTTTTTTTTTGAGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:0,14:14,7:0.3333:1,0:28.1:1:31.4:1:1:0:56.1:14:0.3684:0:1.4 0/1:7:1:0,1:1,5:6,1:0.1429:2,0:30:0:32:0:1:0:60:2:0.1429:0:1 +1 25228844 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49298;SOR=Inf;LSEQ=ACCATGGAGAACTGGTAGGA;RSEQ=CCAGAGGATGTCCCGTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,19:33,0:0:2,0:25.1:1:33:1:1:0:60:66:1:0:0.2 0/1:35:2:1,1:17,16:33,2:0.0571:2,2:23.5:1:27.5:1:1:1.06069:60:4:0.0606:0:1 +1 25254127 . G T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52159;SOR=Inf;LSEQ=CCACCTGGTTCTTCATGACG;RSEQ=CCGAGGCATTGCGCAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:16,0:0:2,0:26.7:1:30.6:1:1:0:60:15:1:0:0.3 0/1:27:2:1,1:15,10:25,2:0.0741:2,2:5.5:1:30:1:1:1.47706:60:4:0.0741:0:1 +1 25255982 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54755;SOR=0.59302;LSEQ=TCGCCGCGGCGTCTCGGGCA;RSEQ=CTCCCATCCCCACTGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:11:11,0:33,1:34,11:0.2444:1,0:19.4:1:32.4:1:1:0:60:22:0.2558:0:1 0/1:25:4:4,0:20,1:21,4:0.16:1,0:30.8:1:30.8:1:1:0:60:8:0.16:0:1 +1 25256029 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49847;SOR=Inf;LSEQ=CTGGCTCCCGCAGCTCAGAC;RSEQ=CCCGGAGCCCCAGGGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:76,10:86,0:0:2,0:26.1:1:30.5:1:1:0:60:172:1:0:0.2 0/1:95:2:1,1:84,9:93,2:0.0211:2,2:19.5:1:27:1:0.20045:8.90741:60:4:0.0213:0:1 +1 25256056 . C T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.76151;LSEQ=GCCCCAGGGCCGGCGCCCTC;RSEQ=CGCCCCGGGTCCCGCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:0,1:124,48:172,1:0.0058:2,0:1:0:24:0:0.28324:0:60:2:0.006:0:1 0/1:197:2:1,1:139,56:195,2:0.0102:2,2:9:0:31:1:0.49601:2.46912:60:4:0.0104:0:1.5 +1 25256089 . C T 82 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14739;SOR=5.49403;LSEQ=CGCACTCACCTTGAAGGCGA;RSEQ=GGGCAGCGTCTTGTTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:1:0,1:178,142:320,1:0.0031:2,0:1:0:27:0:0.44548:0:32:2:0.0031:0:1 0/1:414:7:3,4:228,178:406,7:0.0169:2,2:26.6:1:29.3:1:0.70437:1.7056:55.3:14:0.0172:0:1.1 +1 25256168 . G A 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06565;SOR=Inf;LSEQ=CTGTCGGTGCGCACGAGCTC;RSEQ=CCTGCGTGGTCCGCCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:112,195:307,0:0:2,0:26.4:1:31.1:1:1:0:58.9:50.167:1:0:0.1 0/1:361:5:3,2:125,231:356,5:0.0139:2,2:18.4:1:27.2:1:0.35133:2.76:49.4:10:0.014:0:1.2 +1 25256181 . G A 43 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67011;SOR=0.59096;LSEQ=CGAGCTCGCCTGCGTGGTCC;RSEQ=CCAGCACGTCCACCATCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:76,155:231,3:0.0128:2,2:6:1:27.3:1:0.2583:4.05:60:6:0.0132:0:1 0/0:264:2:2,0:87,175:262,2:0.0076:2,0:1:0:25.5:1:0.1128:0:37:4:0.0077:0:1 +1 25256191 . C A 40 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06025;SOR=Inf;LSEQ=TGCGTGGTCCGCCAGCACGT;RSEQ=CACCATCGAGCGCACCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:50,144:194,0:0:2,0:22.5:1:31.4:1:1:0:59.7:31.333:1:0:0.1 0/1:192:4:3,1:51,137:188,4:0.0208:2,2:11.3:1:20:1:0.06815:7.96:55.3:3:0.016:0:1.5 +1 25256202 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23182;SOR=Inf;LSEQ=CCAGCACGTCCACCATCGAG;RSEQ=GCACCTCGGGCCGGGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:25,108:133,0:0:2,0:20.8:1:30.7:1:1:0:60:43.333:1:0:0.1 0/1:124:2:1,1:25,97:122,2:0.0161:2,2:22.5:1:31:1:0.37674:3.82:60:4:0.0164:0:1 +1 25257366 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGCGCGGCTTTGGTCC;RSEQ=AGCCTCGGTGGCCCCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:28.5:1:1:0:60:4:1:0:2 +1 27022832 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19707;SOR=0;LSEQ=GGACTGGGCCCCGGGGCGGG;RSEQ=TGGGAGGGGGGGAGAAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:32,16:48,2:0.04:2,2:25:1:30:1:1:1.97043:60:4:0.0408:0:1 0/0:62:0:0,0:44,18:62,0:0:2,0:24.1:1:29.7:1:1:0:60:30:1:0:0.6 +1 27022840 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=7.000;MSILEN=1;SSF=0.15533;SOR=0;LSEQ=CCCCGGGGCGGGGTGGGAGG;RSEQ=GGGGAGAAGACGAAGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:37,22:59,2:0.0328:2,2:25.5:1:30:1:1:1.66686:60:4:0.0339:0:1.5 0/0:93:0:0,0:54,37:91,0:0:2,0:21:1:29.7:1:1:0:60:29.333:0.9778:0:0.5 +1 27022903 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52513;SOR=Inf;LSEQ=ACAGCGGGGATCATGGCCGC;RSEQ=CAGGTCGCCCCCGCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:48,65:113,0:0:2,0:24.9:1:30.7:1:1:0:59.7:27.25:1:0:0.4 0/1:181:2:1,1:83,95:178,2:0.011:2,2:28:0:31:0:1:1.14:60:4:0.0113:0:1 +1 27022905 . A C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52862;SOR=Inf;LSEQ=AGCGGGGATCATGGCCGCGC;RSEQ=GGTCGCCCCCGCCGCCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:47,65:112,0:0:2,0:24.6:1:31.3:1:1:0:59.7:55:1:0:0.4 0/1:185:2:1,1:85,98:183,2:0.0108:2,2:25.5:1:28:1:1:1.15:60:4:0.0111:0:1 +1 27022910 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52344;SOR=Inf;LSEQ=GGATCATGGCCGCGCAGGTC;RSEQ=CCCCCGCCGCCGCCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:46,63:109,0:0:2,0:23.6:1:31.4:1:1:0:59.7:108:1:0:0.3 0/1:172:2:1,1:76,94:170,2:0.0116:2,2:25:0:31.5:1:1:1.24:60:4:0.0117:0:1.5 +1 27022916 . G A 25 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.53292;SOR=Inf;LSEQ=TGGCCGCGCAGGTCGCCCCC;RSEQ=CCGCCGCCAGCAGCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:40,55:95,0:0:2,0:24.1:1:31:1:1:0:59.6:30.667:1:0:0.3 0/1:163:2:1,1:70,91:161,2:0.0123:2,2:5:0:25.5:1:1:1.30:60:4:0.0124:0:1 +1 27022935 . G A 27 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54233;SOR=Inf;LSEQ=CGCCGCCGCCAGCAGCCTGG;RSEQ=CAACCCGCCGCCGCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:27,41:68,0:0:2,0:22.5:1:32.2:1:1:0:60:33:1:0:0.2 0/1:126:2:1,1:53,71:124,2:0.0159:2,2:7:0:27.5:1:1:1.34:60:4:0.0161:0:1.5 +1 27022939 . CCCG C 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.0881;SOR=Inf;LSEQ=GCCGCCAGCAGCCTGGGCAA;RSEQ=CCGCCGCCGCCGCCCTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:24,38:62,0:0:2,0:21:1:31.9:1:1:0:60:124:0.9841:0:0.2 0/1:111:6:2,4:46,59:105,6:0.0541:2,2:31.8:1:32.7:1:0.69666:1.55332:60:12:0.0561:0:0.2 +1 27022978 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TCGGAGCTGAAGAAAGCCGA;RSEQ=CAGCAGCAGCGGGAGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:24,23:47,0:0:2,0:15.6:1:32.9:1:1:0:60:94:1:0:0.1 0/1:97:2:1,1:47,48:95,2:0.0206:2,2:12:0:30.5:1:1:1.02:60:4:0.0208:0:1.5 +1 27022998 . CG C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.15234;SOR=0;LSEQ=GCAGCAGCAGCGGGAGGAGG;RSEQ=GGGGGCGAGGCGGCGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:35,32:67,2:0.029:2,2:43:1:32:1:1:1.09232:60:4:0.0294:0:0 0/0:107:0:0,0:52,55:107,0:0:2,0:22.6:1:29.8:1:1:0:60:106:1:0:0.4 +1 27023007 . AGGC A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.14578;SOR=0;LSEQ=GCGGGAGGAGGCGGGGGGCG;RSEQ=GGCGGCGGCGGCAGCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:39,33:72,2:0.027:2,2:40:1:33.5:1:1:1.17914:60:4:0.0286:0:0 0/0:119:0:0,0:61,58:119,0:0:2,0:25.3:1:30.7:1:1:0:60:58.5:1:0:0.4 +1 27023009 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.52284;SOR=Inf;LSEQ=GGGAGGAGGCGGGGGGCGAG;RSEQ=CGGCGGCGGCGGCAGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:39,33:72,0:0:2,0:26.8:1:31.7:1:1:0:59.9:71:1:0:0.3 0/1:117:2:1,1:61,54:115,2:0.0171:2,2:17:0:31:0:1:1.12845:60:4:0.0177:0:1.5 +1 27023016 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51932;SOR=Inf;LSEQ=GGCGGGGGGCGAGGCGGCGG;RSEQ=GGCGGCAGCGGCCGAGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:50,40:90,0:0:2,0:26.2:1:31.4:1:1:0:59.9:180:1:0:0.3 0/1:137:2:1,1:73,62:135,2:0.0146:2,2:20.5:1:27:1:1:1.17601:60:4:0.0149:0:1.5 +1 27023019 . C T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.30289;SOR=0.2116;LSEQ=GGGGGGCGAGGCGGCGGCGG;RSEQ=GGCAGCGGCCGAGCGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:3:1,2:53,41:94,3:0.0309:2,2:13:1:28.7:1:0.58266:2.56048:60:6:0.0319:0:1 0/0:150:1:0,1:82,67:149,1:0.0067:2,0:1:0:26:0:0.45333:0:60:2:0.0068:0:1 +1 27023020 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51972;SOR=Inf;LSEQ=GGGGGCGAGGCGGCGGCGGC;RSEQ=GCAGCGGCCGAGCGCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:60,43:103,0:0:2,0:24.8:1:30.7:1:1:0:59.9:206:1:0:0.3 0/1:157:2:1,1:87,67:154,2:0.0127:2,2:23:0:32:1:1:1.2963:60:4:0.0129:0:1.5 +1 27023063 . G T 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65461;SOR=2.45295;LSEQ=TGAAGGCAGCCGCCGGGCAG;RSEQ=AAAGCGAGGGCCCCGCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:1:0,1:123,114:237,1:0.0042:2,0:1:0:24:0:0.48319:0:60:2:0.0043:0:1 0/1:390:4:1,3:195,191:386,4:0.0103:2,2:14.3:1:24.5:1:0.37051:3.05493:60:8:0.0104:0:1.5 +1 27023131 . C T 50 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41409;SOR=3.15458;LSEQ=CTGCAGGACGGGGCCGAGAG;RSEQ=AATGGGGGTGGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:1:0,1:107,135:242,1:0.0041:2,0:1:0:24:0:1:0:60:2:0.0042:0:1 0/1:388:5:1,4:182,197:379,5:0.0129:2,2:5.8:1:21.8:1:0.3745:3.68439:60:4:0.0108:0:1 +1 27023140 . TGGC T 83 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.00651;SOR=0.08781;LSEQ=GGGGCCGAGAGCAATGGGGG;RSEQ=GGCGGCGGCGGAGCCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:7:3,4:93,125:218,7:0.0311:2,2:20.7:1:29.6:1:1:1.01:60:6:0.0271:0.0089:0.1 0/0:357:1:1,0:169,182:351,1:0.0028:2,0:11:0:34:0:0.48295:0:60:2:0.0028:0:0 +1 27023143 . C T 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.3028;SOR=Inf;LSEQ=GCCGAGAGCAATGGGGGTGG;RSEQ=GGCGGCGGCGGAGCCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:89,120:209,0:0:2,0:17.2:1:30.6:1:1:0:59.8:40.8:0.9903:0:0.3 0/1:354:4:1,3:170,179:349,4:0.0113:2,2:9.3:1:27:1:0.6236:2.84174:60:8:0.0117:0:1.3 +1 27023144 . GGCGGCGGCGGAGCCGGCA G 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.02387;SOR=0;LSEQ=CCGAGAGCAATGGGGGTGGC;RSEQ=GCGGCGGCGGGCCCGGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:4:2,2:98,120:218,4:0.0179:2,2:20:1:31.2:1:1:1.22:60:8:0.0183:0.0179:0 0/0:342:0:0,0:169,169:338,0:0:2,0:18.9:1:31:1:1:0:59.8:66.6:0.9881:0:0.4 +1 27023148 . G A 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.68966;SOR=0.67498;LSEQ=GAGCAATGGGGGTGGCGGCG;RSEQ=CGGCGGAGCCGGCAGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:2,1:104,121:225,3:0.0129:2,2:14.3:1:27.7:1:0.59867:2.32:60:6:0.0133:0:1 0/0:344:3:1,2:171,169:340,3:0.0087:2,2:35.3:1:30.3:1:0.6228:2.01966:60:6:0.009:0:1.3 +1 27023160 . G A 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40996;SOR=3.38695;LSEQ=TGGCGGCGGCGGCGGAGCCG;RSEQ=CAGCGGCGGCGGGCCCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:1:1,0:151,117:268,1:0.0037:2,0:1:0:15:0:1:0:60:0:0:0:1 0/1:403:5:4,1:212,182:394,5:0.0124:2,2:14:1:26:1:0.38045:3.42:60:10:0.013:0:1.4 +1 27023167 . C T 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.65358;SOR=2.80848;LSEQ=GGCGGCGGAGCCGGCAGCGG;RSEQ=GGCGGGCCCGGCGCGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:1:0,1:163,114:277,1:0.0036:2,0:1:0:15:0:0.41367:0:60:0:0:0:2 0/1:398:4:2,2:224,170:394,4:0.0101:2,2:14.8:1:25.8:1:1:1.31671:60:8:0.0104:0:1 +1 27023170 . C T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08253;SOR=Inf;LSEQ=GGCGGAGCCGGCAGCGGCGG;RSEQ=GGGCCCGGCGCGGAGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:169,110:279,0:0:2,0:18.5:1:31.3:1:1:0:60:38.857:1:0:0.3 0/1:403:5:2,3:230,167:397,5:0.0124:2,2:22.2:1:26.8:1:0.65416:2.06212:60:4:0.0101:0:1.2 +1 27023175 . C T 73 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15121;SOR=4.86672;LSEQ=AGCCGGCAGCGGCGGCGGGC;RSEQ=CGGCGCGGAGCCGGACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:1:0,1:185,118:303,1:0.0033:2,0:1:0:30:0:0.39145:0:60:2:0.0034:0:1 0/1:445:7:1,6:257,180:437,7:0.0157:2,2:9:1:26.3:1:0.02337:8.53029:60:14:0.0161:0:1.1 +1 27023178 . G T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.08337;SOR=Inf;LSEQ=CGGCAGCGGCGGCGGGCCCG;RSEQ=CGCGGAGCCGGACCTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:198,123:321,0:0:2,0:21.2:1:31.8:1:1:0:60:39.125:0.9968:0:0.3 0/1:468:5:1,4:272,190:462,5:0.0107:2,2:12:1:28.2:1:0.16544:5.70691:57.4:10:0.011:0:1.2 +1 27023179 . C A 53 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.08481;SOR=Inf;LSEQ=GGCAGCGGCGGCGGGCCCGG;RSEQ=GCGGAGCCGGACCTGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:203,124:327,0:0:2,0:21.5:1:31.4:1:1:0:60:45.714:0.9938:0:0.3 0/1:484:5:3,2:282,195:477,5:0.0103:2,2:15.6:1:23:1:1:1.04:60:4:0.0085:0:2.2 +1 27023187 . C T 52 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.496;SOR=0.52683;LSEQ=CGGCGGGCCCGGCGCGGAGC;RSEQ=GGACCTGAAGAACTCGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:5:1,4:236,147:383,5:0.0129:2,2:9.6:1:22.6:1:0.07764:6.39262:60:1.5:0.0079:0:1 0/0:586:4:0,4:340,241:581,4:0.0068:2,0:1:0:22.5:1:0.03033:0:60:3:0.0052:0:1.5 +1 27023252 . C T 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAACAATAACCTCACGGAG;RSEQ=CGCCCGGCGGCGGCGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:0:0,0:310,300:610,0:0:2,0:25.7:1:31.5:1:1:0:59.9:54.455:0.9983:0:0.3 0/1:908:96:50,46:416,393:809,96:0.1057:2,2:22.4:1:28.7:1:0.91445:1.03:59.1:47:0.1056:0:1.4 +1 27023312 . G A 78 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02403;SOR=Inf;LSEQ=GGGCGCCTCCTCACTCAGCC;RSEQ=CGGCCGCCTTGCCGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:226,261:487,0:0:2,0:22.8:1:31:1:1:0:60:43.273:1:0:0.3 0/1:682:8:6,2:332,342:674,8:0.0117:2,2:5.4:1:26.1:1:0.17369:3.09:60:16:0.012:0:1.5 +1 27023450 . AGCG A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.6351;SOR=0.83135;LSEQ=CTGGCCTGGCAGCGCTGCAG;RSEQ=GCGGCGGCGGGGGCCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1126:20:12,8:637,468:1105,20:0.0178:2,2:22.7:1:32.4:1:1:1.10:60:40:0.0181:0.0036:0.2 0/1:1418:21:11,10:780,612:1392,21:0.0148:2,2:24.2:1:29.6:1:0.82595:1.15852:60:20:0.0144:0.0035:0.2 +1 27023928 . C T 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.63889;SOR=2.25723;LSEQ=GGCTGCGGCGGCGGCAGCTG;RSEQ=GGCGGCGGCCGCCTCGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:1:0,1:102,112:214,1:0.0047:2,0:1:0:26:0:1:0:60:2:0.0048:0:1 0/1:287:3:1,2:139,145:284,3:0.0105:2,2:8:1:29.3:1:1:1.91306:60:6:0.0108:0:1 +1 27023936 . G A 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.03548;SOR=0;LSEQ=CGGCGGCAGCTGCGGCGGCG;RSEQ=CCGCCTCGGGAGGGGCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:4:3,1:112,90:202,4:0.0193:2,2:8:1:28.3:1:0.63162:2.40:60:8:0.0201:0:1.3 0/0:268:0:0,0:146,122:268,0:0:2,0:23.4:1:30.5:1:1:0:59.9:32.5:1:0:0.4 +1 27023944 . G T 44 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.15144;LSEQ=GCTGCGGCGGCGGCCGCCTC;RSEQ=GGAGGGGCCCAACAAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:2:1,1:125,90:215,2:0.0092:2,2:35.5:1:33:1:1:1.38673:60:4:0.0094:0:2 0/1:283:3:1,2:158,121:279,3:0.0106:2,2:7.7:1:28.3:1:0.5822:2.60281:60:6:0.0108:0:1.7 +1 27023995 . C T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.69855;SOR=1.58811;LSEQ=CCCATGAGCCCCGGGAGCAG;RSEQ=GGCGGCGGGGGGCAGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:2:1,1:134,106:240,2:0.0083:2,2:29:1:30.5:1:1:1.26291:60:4:0.0084:0:1 0/1:306:4:2,2:168,133:301,4:0.0131:2,2:39.5:1:30.5:1:1:1.26217:60:8:0.0133:0:1 +1 27024022 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17951;SOR=0;LSEQ=GGGGGGCAGCCGCTCGCCCG;RSEQ=ACCCCTCAGGTACACAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:112,83:195,2:0.0101:2,2:27.5:1:31:1:1:1.3473:60:4:0.0102:0:1.5 0/0:270:0:0,0:145,124:269,0:0:2,0:26.1:1:29.9:1:1:0:59.9:25.9:0.9962:0:0.3 +1 27024030 . AG A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06729;SOR=0;LSEQ=GCCGCTCGCCCGGACCCCTC;RSEQ=GTACACAGCTGAGTGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:3:2,1:100,79:179,3:0.0165:2,2:19.3:1:29:1:1:1.58:60:6:0.0168:0.0055:0.3 0/0:264:0:0,0:137,127:264,0:0:2,0:21.9:1:30.5:1:1:0:59.8:131:1:0:0.3 +1 27024056 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51101;SOR=Inf;LSEQ=ACAGCTGAGTGGGGAGGGGG;RSEQ=TGGGGCGAGCGTGGTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:43,64:107,0:0:2,0:20.6:1:32:1:1:0:60:52.5:1:0:0.1 0/1:148:2:0,2:61,85:146,2:0.0135:2,0:43:1:30:1:0.51213:0:60:4:0.0141:0:1 +1 27056071 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20491;SOR=Inf;LSEQ=ACAGACTAAAAAAACCTGTG;RSEQ=ACTTGGGTTATATATTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:148,11:159,0:0:2,0:24.3:1:30.3:1:1:0:60:78.5:1:0:0.1 0/1:132:2:1,1:109,21:130,2:0.0152:2,2:22.5:1:27.5:1:0.30662:5.09448:60:4:0.0153:0:1 +1 27056093 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10971;SOR=Inf;LSEQ=CTTGGGTTATATATTCAGTG;RSEQ=CCAGAGGCCATCAAAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:201,44:245,0:0:2,0:23.7:1:31.2:1:1:0:60:34:1:0:0.1 0/1:226:3:1,2:168,55:223,3:0.0133:2,2:17.7:1:29.7:1:0.15749:6.04856:60:6:0.0135:0:1.3 +1 27056354 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25349;SOR=Inf;LSEQ=GGCCTCTCTTATACACAGCA;RSEQ=GTAGATGGTGATTGTGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:62,175:237,0:0:2,0:23.3:1:31.8:1:1:0:60:117.5:0.9958:0:0.2 0/1:280:3:1,2:83,194:277,3:0.0107:2,2:30.7:1:24:1:1:1.17:60:2:0.0073:0:1.3 +1 27057621 . A C 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGAGAGTCAGTGCTAAA;RSEQ=GTATATTTTCCTTTCCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:764:0:0,0:537,227:764,0:0:2,0:23.4:1:30.6:1:1:0:60:49.933:1:0:0.1 0/1:843:77:48,29:491,274:765,77:0.0913:2,2:23.8:1:30.5:1:0.80346:1.08254:59.9:154:0.0929:0:1.1 +1 27058079 . G A 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33013;SOR=0.26908;LSEQ=AACTGCCTATTCCCAGCAGC;RSEQ=CTTCCCTCCACCGCAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:2,1:40,154:194,3:0.0152:2,2:17.7:1:28:1:0.1155:7.59:60:6:0.0155:0:1 0/0:242:1:1,0:70,171:241,1:0.0041:2,0:1:0:25:0:0.29339:0:60:2:0.0042:0:1 +1 27059748 . C CT 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTGATTTTGTGTGAATA;RSEQ=TTTTTTTTTTTATTTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:13.5:1:28:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 27087177 . CA C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.12945;SOR=Inf;LSEQ=CAACGAGTGAAACACTGTCT;RSEQ=AAAAAAAAAATTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:24,0:0:1,0:26.1:1:30.4:1:1:0:59.1:48:1:0:0.1 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:8:1:30.5:1:1:0:60:4:0.1429:0.0714:0.5 +1 27087188 . A AAT 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0.50652;LSEQ=ACACTGTCTCAAAAAAAAAA;RSEQ=TTTTTTTTTTTAATAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:25,0:25,3:0.1:1,0:9.7:1:32.5:1:1:0:60:6:0.1:0.0667:0.7 0/1:19:1:1,0:16,1:17,1:0.0526:1,0:13:0:29.5:0:1:0:60:2:0.0588:0:4 +1 27088546 . A T 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCCATGCAAGTGGCTGCT;RSEQ=AAGAAAATGTAGATGGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:177,7:184,0:0:1,0:21.2:1:28.6:1:1:0:60:60.333:1:0:0.1 0/1:140:26:21,5:105,9:114,26:0.1857:2,2:21.4:1:29.7:1:0.13786:2.7522:60:52:0.1857:0:1.1 +1 27089389 . G T 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34183;SOR=3.47813;LSEQ=AATATTGAATGACATTGTTT;RSEQ=GTGTTCTAGAGTTGAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:1,0:151,27:178,1:0.0056:2,0:4:0:31:0:1:0:60:2:0.0057:0:1 0/1:156:3:2,1:131,22:153,3:0.0192:2,2:30.3:1:31.3:1:0.38238:2.94843:60:6:0.0195:0:1.3 +1 27089391 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20969;SOR=Inf;LSEQ=TATTGAATGACATTGTTTGG;RSEQ=GTTCTAGAGTTGAGAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:158,31:189,0:0:2,0:24.2:1:29.9:1:1:0:60:93.5:1:0:0.1 0/1:161:2:1,1:135,24:159,2:0.0124:2,2:27:1:27.5:1:0.28727:5.5318:60:4:0.013:0:1 +1 27089446 . G C 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGTGACTAACCAAGTCTT;RSEQ=TCTTCCTCCCCTCCCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:285,137:422,0:0:2,0:26.3:1:32.3:1:1:0:60:210:1:0:0.1 0/1:469:28:20,8:274,167:441,28:0.0597:2,2:30.6:1:31:1:0.4212:1.52:59.4:27:0.0588:0:1.4 +1 27092639 . A G 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00572;SOR=Inf;LSEQ=CTAGATGATCACACAGCACT;RSEQ=TTTGGCTCCAGTTCAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:186,29:215,0:0:2,0:22.9:1:28.6:1:1:0:60:106.5:1:0:0.1 0/1:201:7:5,2:150,43:193,7:0.0348:2,2:29.3:1:29.1:1:0.65592:1.39283:60:14:0.0352:0:1 +1 27092698 . A G 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTGTCTCTCTCACTTTCC;RSEQ=TCTTCTTCCTTAGGCCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:319,185:504,0:0:2,0:25:1:30.6:1:1:0:60:83:0.998:0:0.1 0/1:517:42:27,15:280,195:475,42:0.0812:2,2:23.9:1:30:1:0.62335:1.25:60:84:0.083:0:1.1 +1 27093096 . C A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20258;SOR=4.31129;LSEQ=ACTCCTTTCAACTTTGTGTC;RSEQ=TATCTTTTTCAGTGATAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:1:1,0:88,277:365,1:0.0027:2,0:1:0:26:0:0.24317:0:60:2:0.0028:0:1 0/1:342:4:2,2:91,247:338,4:0.0117:2,2:19.8:1:24.5:1:0.29874:2.71:60:3:0.0088:0:1 +1 27094156 . A G 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAACCTTATGAAGGTAGG;RSEQ=CAGGTGTTAGTAACCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:45,0:0:1,0:22.4:1:30.8:1:1:0:60:44:1:0:0 0/1:39:16:15,1:23,0:23,16:0.4103:1,1:26.5:1:31.6:1:0.41026:0:60:32:0.4103:0:1.1 +1 27094234 . G T 44 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62918;SOR=2.52397;LSEQ=TTCTGAGACCCTTAGCACAG;RSEQ=CTTTGAATCTGACCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:1,0:140,47:187,1:0.0053:2,0:22:0:32:0:1:0:60:2:0.0055:0:1 0/1:226:3:1,2:159,63:222,3:0.0133:2,2:5:1:28:1:0.20098:5.00567:60:6:0.0135:0:1 +1 27097515 . A G 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAAGAACTGTGGTTCTACA;RSEQ=AGATGAATACCTTACAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:149,14:163,0:0:2,0:23.7:1:30.8:1:1:0:60:326:1:0:0 0/1:139:23:21,2:103,13:116,23:0.1655:2,2:19.4:1:31.2:1:1:1.32:60:46:0.1667:0:1.1 +1 27097839 . C A 47 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.37589;SOR=3.67639;LSEQ=TAAGGATGGGGTCAGCGGCC;RSEQ=CACCAAGGCTGAGAGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:1:1,0:102,257:359,1:0.0028:2,0:1:0:25:0:0.28611:0:60:2:0.0029:0:1 0/1:394:4:2,2:126,264:390,4:0.0102:2,2:11:1:23.8:1:0.59853:2.09:60:3:0.0078:0:1 +1 27097856 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24907;SOR=Inf;LSEQ=GCCCCACCAAGGCTGAGAGG;RSEQ=CCTGTTGCCCTGGCCTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:56,220:276,0:0:2,0:23.4:1:31.9:1:1:0:60:54.2:1:0:0.1 0/1:290:3:2,1:63,224:287,3:0.0103:2,2:12:1:27:1:0.12719:7.05:60:6:0.0105:0:1 +1 27098890 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.51824;SOR=0;LSEQ=TCAGGCTTTAAAGGCCTTAG;RSEQ=AAGAACTTTCCCAAAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:2,0:79,0:79,2:0.0247:1,0:17:1:28:1:1:0:60:4:0.025:0:1 0/0:53:0:0,0:51,2:53,0:0:1,0:21.6:1:30.4:1:1:0:60:52:1:0:0.1 +1 27098928 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5061;SOR=0;LSEQ=GATTCTGGGTCGTTCGTGTG;RSEQ=TTGTGTGAGAGTTAAACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:172,23:195,2:0.0102:2,2:31:1:32.5:1:0.22936:7.34332:60:4:0.0102:0:1 0/0:154:0:0,0:136,18:154,0:0:2,0:20.5:1:29.2:1:1:0:60:76:1:0:0.1 +1 27098960 . C T 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1871;SOR=4.69788;LSEQ=TTAAACACTGTCATGCCAAG;RSEQ=AAACTACTCAACTTGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:1:0,1:268,91:359,1:0.0028:2,0:1:0:24:0:0.25556:0:60:2:0.0028:0:1 0/1:309:4:2,2:224,81:305,4:0.0129:2,2:18.3:1:23:1:0.29293:2.75474:60:3:0.0099:0:1.5 +1 27099238 . G T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09991;SOR=Inf;LSEQ=TCCCAGCCAGTGACTCCTGC;RSEQ=TGTCCTTTGTTATATTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:155,128:283,0:0:2,0:23.1:1:30.9:1:1:0:60:55.6:1:0:0.1 0/1:246:3:0,3:150,93:243,3:0.0122:2,0:5.7:1:27:1:0.0583:0:60:6:0.0123:0:1 +1 27099688 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12666;SOR=Inf;LSEQ=TAATAAGTACATGCTTTTCG;RSEQ=TGGTTGGGGCCTCTTTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:44,13:57,0:0:2,0:23.8:1:32.6:1:1:0:59.4:56:1:0:0.1 0/1:32:2:2,0:25,5:30,2:0.0625:2,0:22:1:29.5:1:1:0:60:4:0.0625:0:1 +1 27099776 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24081;SOR=Inf;LSEQ=TGAAGAGGGCCTGGGTCAAA;RSEQ=GGTAGATTACCAGGCTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:162,44:206,0:0:2,0:23.1:1:32.9:1:1:0:60:102:1:0:0.1 0/1:199:2:1,1:154,43:197,2:0.0101:2,2:26.5:1:28:1:0.39419:3.55169:60:4:0.0104:0:1 +1 27100243 . C T 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTCGGTGCTGCTATGGAT;RSEQ=AGGCTTCGCCACTGCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:651:0:0,0:352,299:651,0:0:2,0:24.7:1:32.2:1:1:0:60:58.182:1:0:0.2 0/1:676:36:18,18:349,291:640,36:0.0533:2,2:29:1:28.1:1:0.61026:1.19898:60:72:0.0537:0:1.1 +1 27100475 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19618;SOR=Inf;LSEQ=TCTAACGTGTTGAAGTCTAA;RSEQ=AAGCTCACTTTAGATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:13,170:183,0:0:2,0:20.1:1:32.1:1:1:0:59.7:35.6:1:0:0.1 0/1:146:2:0,2:10,134:144,2:0.0137:2,0:10:1:29:0:1:0:60:4:0.0139:0:1.5 +1 27102188 . A G 174 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=40.10535;LSEQ=CAACAGCATCATGACCTTCA;RSEQ=CCTCAGTCAGGTGAGTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:697:1:1,0:285,411:696,1:0.0014:2,0:30:0:14:0:0.41033:0:60:0:0:0:2 0/1:825:45:21,24:340,438:778,45:0.0545:2,2:23.8:1:31.8:1:0.75806:1.13:60:90:0.0554:0:1.1 +1 27105437 . G T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=2.00696;LSEQ=ACTGATACAGAAGACTTGGG;RSEQ=AGGTCTCTCAAGTCAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:1,0:165,26:191,1:0.0052:2,0:20:0:11:0:1:0:60:0:0:0:7 0/1:193:2:2,0:159,32:191,2:0.0104:2,0:26.5:1:30.5:1:1:0:60:4:0.0104:0:1 +1 27105469 . G A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37576;SOR=3.6842;LSEQ=GTCAATAATTCTGTTCTTAG;RSEQ=CCACTTTTCTCCCTTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:1:1,0:250,107:357,1:0.0028:2,0:15:0:26:0:1:0:60:2:0.0029:0:2 0/1:391:4:3,1:274,112:386,4:0.0102:2,2:24.8:1:24.5:1:1:1.23:60:3:0.0078:0:1.5 +1 27106967 . G A 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10033;SOR=0.1695;LSEQ=AGTGCAGAAGGGCAGTATCG;RSEQ=CAACCTCCTGGGCTTCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:5:2,3:229,233:462,5:0.0107:2,2:19.8:1:29.6:1:1:1.47303:60:10:0.0109:0:1.2 0/0:547:1:1,0:268,278:546,1:0.0018:2,0:1:0:23:0:0.49177:0:60:2:0.0018:0:1 +1 27106978 . G A 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13057;SOR=5.23055;LSEQ=GCAGTATCGGCAACCTCCTG;RSEQ=GCTTCCTAGAGGACAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:1:1,0:236,231:467,1:0.0021:2,0:1:0:28:0:1:0:60:2:0.0022:0:1 0/1:541:6:5,1:268,267:535,6:0.0111:2,2:13.3:1:25.5:1:0.21626:4.97:59.7:5:0.0095:0:1.2 +1 27107263 . TC T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.76894;SOR=1.11761;LSEQ=CATGACAGCCGTGGGACACC;RSEQ=CCCCCCCCGTGTGTGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:20:7,13:180,254:434,20:0.0441:2,2:28.8:1:31.7:1:0.64709:1.31531:59.4:40:0.0455:0.0044:0.2 0/1:592:29:13,16:247,312:559,29:0.049:2,2:29.7:1:29.6:1:1:1.03:60:28:0.0489:0.0017:0.5 +1 27107272 . CGT C 86 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.08585;SOR=5.51653;LSEQ=CGTGGGACACCTCCCCCCCC;RSEQ=GTGTGTGTGCGTGTGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:0,1:160,242:402,1:0.0024:2,0:20:0:28:0:1:0:60:2:0.0026:0:0 0/1:524:7:4,3:216,298:514,7:0.0134:2,2:28:1:30.9:1:0.4628:1.84:60:14:0.0139:0:0.1 +1 27107313 . T A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11431;SOR=0;LSEQ=AGAACTTAGAAACTGACTGT;RSEQ=GCCCTTTATTTATGCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:3:2,1:66,180:246,3:0.012:2,2:11:1:27.3:1:0.18191:5.41:60:6:0.0124:0:1 0/0:263:0:0,0:71,191:262,0:0:2,0:20.2:1:28.9:1:1:0:60:31.75:1:0:0.3 +1 27107332 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49835;SOR=Inf;LSEQ=TTGCCCTTTATTTATGCAAA;RSEQ=CCACCTCAGAATCCAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:15,135:150,0:0:2,0:24.1:1:29.5:1:1:0:60:49:1:0:0.2 0/1:152:2:1,1:28,122:150,2:0.0132:2,2:20:1:28.5:1:0.3462:4.30:60:4:0.0135:0:1 +1 27533330 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24384;SOR=Inf;LSEQ=TTAATAGTTAATGTCTCCTG;RSEQ=TATGATTCCATCCTGAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:110,33:143,0:0:2,0:21.7:1:31.2:1:1:0:59.7:46.667:1:0:0.2 0/1:140:2:1,1:103,35:138,2:0.0143:2,2:37:1:30.5:1:0.44954:2.9155:60:4:0.0147:0:1 +1 27533356 . C T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.26459;SOR=Inf;LSEQ=TTCCATCCTGAGCGGCTGTT;RSEQ=TCTTGAGCAGCGTTCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:141,75:216,0:0:2,0:25.5:1:32.1:1:1:0:59.8:71:1:0:0.2 0/1:290:3:0,3:176,111:287,3:0.0103:2,0:12.7:1:20.7:1:0.05977:0:60:2:0.007:0:1.3 +1 27533368 . G T 149 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02011;LSEQ=CGGCTGTTCTCTTGAGCAGC;RSEQ=TTCATTTATCTCCGTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:31:17,14:135,83:218,31:0.1245:2,2:26.1:1:30.1:1:0.55535:1.33784:59.7:30:0.1215:0:1.1 0/0:352:1:0,1:203,148:351,1:0.0028:2,0:1:0:26:0:0.4233:0:60:2:0.0029:0:1 +1 27533400 . C A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06282;SOR=0;LSEQ=CCGTCTGCCTTCTGTCCCAC;RSEQ=TAAGTGTGTGCCGCCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:126,130:256,3:0.0116:2,2:30.3:1:29.3:1:0.6192:2.06:52.7:6:0.0117:0:1 0/0:391:0:0,0:201,190:391,0:0:2,0:28.7:1:30.8:1:1:0:56.4:390:1:0:0.2 +1 27533640 . G T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01023;SOR=Inf;LSEQ=ACAAAGGCAGTCCAATTAAA;RSEQ=TAACACTGGCAACTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:62,61:123,0:0:2,0:21.4:1:31.8:1:1:0:32.2:19.5:1:0:0.1 0/1:157:8:4,4:72,77:149,8:0.051:2,2:32.3:1:29.3:1:1:1.07:30.3:16:0.051:0:1 +1 27533906 . AGATGAT A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=12.000;MSILEN=3;SSF=0.22117;SOR=0.67377;LSEQ=GTAAAACTTGCTGTTGATGA;RSEQ=GATGATGATGATGATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:30:10,20:27,30:57,30:0.3409:2,2:35.6:1:32.6:1:0.25707:1.78791:44:60:0.3488:0.0114:0.2 0/1:124:32:11,21:31,44:75,32:0.2581:2,2:30.9:1:30.2:1:0.52571:1.34136:40.6:31:0.252:0.0161:0.3 +1 27533961 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52543;SOR=Inf;LSEQ=ATTTTGATGATGAGGAAGCT;RSEQ=AAGAAAAAGTGCCAGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:38,45:83,0:0:2,0:22.4:1:32.2:1:1:0:35.3:166:1:0:0.1 0/1:134:2:1,1:58,74:132,2:0.0149:2,2:20:1:27.5:1:1:1.27:50.5:4:0.0153:0:1 +1 27533979 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.53848;SOR=Inf;LSEQ=CTGAAGAAAAAGTGCCAGTG;RSEQ=AGAAATCTATATGAGATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:41,42:83,0:0:2,0:20.1:1:30.6:1:1:0:32.1:166:1:0:0.1 0/1:149:2:1,1:73,74:147,2:0.0134:2,2:33:1:27.5:1:1:1.01:27.5:4:0.0135:0:1 +1 27534005 . CA C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52907;SOR=Inf;LSEQ=TCTATATGAGATACTCCAGC;RSEQ=AAAATGCACACAAGTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:51,41:92,0:0:2,0:24.8:1:30.9:1:1:0:26.6:91:1:0:0.1 0/1:153:2:1,1:84,67:151,2:0.0131:2,2:47:1:31:1:1:1.25186:29.5:4:0.0132:0:1.5 +1 27534028 . A G 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00417;SOR=Inf;LSEQ=AAATGCACACAAGTCAAATC;RSEQ=GAATGGAAAAGACTCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:62,57:119,0:0:2,0:25.6:1:30.9:1:1:0:33.7:118:1:0:0.1 0/1:182:12:7,5:92,78:170,12:0.0659:2,2:28.4:1:30:1:1:1.19:26.3:24:0.0659:0:1.1 +1 27534166 . T C 34 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53457;SOR=Inf;LSEQ=AGCAAAAATGCAAGCAAGTA;RSEQ=AGAAAAAGGGGGTTCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:29,0:0:2,0:20.1:1:30.2:1:1:0:39.9:58:1:0:0.3 0/1:52:2:1,1:19,31:50,2:0.0385:2,2:17:0:34:0:1:1.62:29:4:0.0385:0:2 +1 27534176 . G T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.97057;LSEQ=CAAGCAAGTATAGAAAAAGG;RSEQ=GGTTCTCTTCCCAAAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:16:10,6:13,14:27,16:0.3721:2,2:12.1:1:29.7:1:0.5282:1.77:25.7:15:0.3659:0:1 0/1:63:23:10,13:14,26:40,23:0.3651:2,2:17.5:1:28.6:1:0.59345:1.42:23.7:46:0.3651:0:1.2 +1 27939425 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24389;SOR=0;LSEQ=AGGGTTGATGCCCGGACAGG;RSEQ=TATGTCTGATCCCCGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:68,31:99,2:0.0198:2,2:26.5:1:29.5:1:0.53545:2.17486:60:4:0.02:0:1 0/0:103:0:0,0:71,32:103,0:0:2,0:21.7:1:30.5:1:1:0:60:50.5:1:0:0.2 +1 27939515 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51299;SOR=Inf;LSEQ=TACTCGAAGGTAGGCCTCTC;RSEQ=TCCGGGTCCAGACGCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:53,81:134,0:0:2,0:24.4:1:32.1:1:1:0:60:268:1:0:0.1 0/1:189:2:1,1:74,113:187,2:0.0106:2,2:26:1:28.5:1:1:1.52:60:4:0.0108:0:1 +1 27939747 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21465;SOR=0;LSEQ=AACCTGGGTAGGGGATTCGG;RSEQ=CCTTGGTGATGAGCTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:69,40:109,2:0.018:2,2:27.5:1:32:0:1:1.71605:60:4:0.0187:0:1 0/0:128:0:0,0:80,48:128,0:0:2,0:21.8:1:31.1:1:1:0:60:127:1:0:0.2 +1 27939759 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50384;SOR=Inf;LSEQ=GGATTCGGCCCTTGGTGATG;RSEQ=GCTCAGTGAGCAGGATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:76,56:132,0:0:2,0:25.5:1:30.6:1:1:0:59.8:65:1:0:0.1 0/1:163:2:1,1:99,62:161,2:0.0123:2,2:18:1:28.5:1:1:1.59197:60:4:0.0123:0:1 +1 27941982 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50328;SOR=Inf;LSEQ=GTCACGATGTAGATGGGCTC;RSEQ=TCCGACACCACGGCGTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:63,51:114,0:0:2,0:27.3:1:31.7:1:1:0:60:56:1:0:0.2 0/1:140:2:1,1:77,61:138,2:0.0143:2,2:13:0:32:0:1:1.26017:60:4:0.0149:0:1.5 +1 27941983 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50298;SOR=Inf;LSEQ=TCACGATGTAGATGGGCTCC;RSEQ=CCGACACCACGGCGTACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:62,51:113,0:0:2,0:27.6:1:31:1:1:0:60:112:1:0:0.2 0/1:138:2:1,1:75,61:136,2:0.0145:2,2:28.5:1:27:1:1:1.22765:60:4:0.0147:0:1 +1 27941986 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50328;SOR=Inf;LSEQ=CGATGTAGATGGGCTCCTCC;RSEQ=ACACCACGGCGTACAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:61,53:114,0:0:2,0:27.3:1:30.7:1:1:0:60:113:1:0:0.2 0/1:140:2:1,1:75,63:138,2:0.0143:2,2:39:0:30:1:1:1.18898:60:4:0.0146:0:1 +1 27942016 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50379;SOR=Inf;LSEQ=CGTACAGCTGCACCAGCTTG;RSEQ=CGTGCCGCAGCAGCTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:40,62:102,0:0:2,0:24.6:1:30.2:1:1:0:60:204:1:0:0.2 0/1:127:2:1,1:49,76:125,2:0.0157:2,2:37.5:1:32:1:1:1.55:60:4:0.0163:0:1.5 +1 27942017 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19731;SOR=0;LSEQ=GTACAGCTGCACCAGCTTGT;RSEQ=GTGCCGCAGCAGCTTCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:39,61:100,2:0.0196:2,2:32:0:32.5:1:1:1.56:60:4:0.0198:0:1.5 0/0:127:0:0,0:50,77:127,0:0:2,0:24.3:1:28.9:1:1:0:60:62.5:1:0:0.2 +1 27942263 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2066;SOR=Inf;LSEQ=CAGCGTGATGGAGCTGCGGC;RSEQ=GATCTCCCAGGCGTCCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:43,32:75,0:0:2,0:26.5:1:31.1:1:1:0:60:150:1:0:0.3 0/1:63:2:1,1:38,23:61,2:0.0317:2,2:47:0:31:1:1:1.63846:60:4:0.0317:0:1 +1 27942345 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=ATGAGCAGGTTGCACAGCCC;RSEQ=TCATTCACCTCTAGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:13,25:38,2:0.05:2,2:16.5:1:29:1:1:1.89:60:4:0.0513:0:1 0/0:28:0:0,0:6,22:28,0:0:2,0:21.5:1:31.3:1:1:0:60:56:1:0:0 +1 27943453 . C A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.417;LSEQ=CCCATGTCCAGTTTGCGGAT;RSEQ=TTGTAATGCTTCACATGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:0,1:49,73:122,1:0.0081:2,0:27:0:14:0:1:0:60:0:0:0:2 0/1:174:2:1,1:79,93:172,2:0.0115:2,2:27.5:1:30:1:1:1.18:60:4:0.0116:0:1 +1 27943462 . C A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51497;SOR=Inf;LSEQ=AGTTTGCGGATCTTGTAATG;RSEQ=TTCACATGATCGCCTCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:41,73:114,0:0:2,0:23.5:1:33.4:1:1:0:60:228:1:0:0.1 0/1:165:2:1,1:69,94:163,2:0.0121:2,2:21:0:29:1:1:1.36:60:4:0.0124:0:1.5 +1 28637962 . AT A 93 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=13.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAAAAAAATTAAAAAAAAAA;RSEQ=AATAATAATAATAATATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:0,0:0,8:0.7273:0,0:13.4:1:31:1:1:0:60:16:0.7273:0.2727:0.1 0/0:1:0:0,0:1,0:1,0:0:0,0:22:0:32:0:1:0:60:2:1:0:0 +1 28637963 . T A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AAAAAAATTAAAAAAAAAAA;RSEQ=AATAATAATAATAATATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:0,0:0,3:0.2727:0,0:17:1:31.3:1:1:0:54:6:0.2727:0:2.3 0/0:1:0:0,0:1,0:1,0:0:0,0:22:0:32:0:1:0:60:2:1:0:0 +1 28638126 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20986;SOR=0;LSEQ=AAACATGAATGAGTTTAAAT;RSEQ=ATATTCATTCCTAAGCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:17,28:45,2:0.0426:2,2:26:0:31.5:1:1:1.63:52:4:0.0426:0:1 0/0:55:0:0,0:27,28:55,0:0:2,0:27:1:30.9:1:1:0:56.5:110:1:0:0.2 +1 28638198 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19886;SOR=Inf;LSEQ=ATGCCAATACCTTTAACTCC;RSEQ=GATATCGTGTTCTCAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:2,16:18,0:0:2,0:22.5:1:32.7:1:1:0:58.8:36:1:0:0.1 0/1:15:2:1,1:0,13:13,2:0.1333:1,2:13.5:1:28.5:1:0.13333:0:60:4:0.1333:0:1 +1 28638259 . G A 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.7321;LSEQ=CCATCTTATGTATCAAGTCA;RSEQ=CATGAAATTGAAATACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:19:0:32:0:1:0:39:2:0.5:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:15:0:31:0:1:0:49:4:0.6667:0:1 +1 29644328 . C T 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00048;SOR=0;LSEQ=GCCCTGTTGCCCCGGAACCG;RSEQ=GACAAGAACCGCAGCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:6,4:7,3:10,10:0.5:2,2:26:1:30.5:1:1:1.52135:60:20:0.5:0:1.2 0/0:18:0:0,0:11,7:18,0:0:2,0:25.2:1:30:1:1:0:60:36:1:0:0.1 +1 29845899 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19548;SOR=Inf;LSEQ=AGGGTGTGAGAGGGGAGTGG;RSEQ=TTGTGCCCTCCCCACGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:28,13:41,0:0:2,0:26:1:32.2:1:1:0:60:82:1:0:0 0/1:33:2:2,0:18,13:31,2:0.0606:2,0:19:0:31:0:0.50758:0:60:4:0.0606:0:1 +1 29845932 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.17749;SOR=Inf;LSEQ=CACGGCCAAGTCTACTGGGC;RSEQ=CTGGGCTCTGGTTTCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:32,25:57,0:0:2,0:27.5:1:30.2:1:1:0:60:27.5:1:0:0.1 0/1:42:2:1,1:20,20:40,2:0.0476:2,2:30:1:28.5:1:1:1:60:4:0.0488:0:1 +1 30274816 . C A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18221;SOR=Inf;LSEQ=GTGGCAGGTGACCCTAGGAC;RSEQ=CCAACCTTCCTGCTCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:41,55:96,0:0:2,0:23.5:1:30.4:1:1:0:60:47:1:0:0.1 0/1:72:2:1,1:33,37:70,2:0.0278:2,2:21.5:1:24:1:1:1.12:60:4:0.029:0:1.5 +1 30274851 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18733;SOR=Inf;LSEQ=CTGGAGCTGCTGAAGTTAGG;RSEQ=TGGGCAGAGAGGGGGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:12,45:57,0:0:2,0:21.7:1:30.9:1:1:0:59.9:18:1:0:0.1 0/1:44:2:1,1:11,31:42,2:0.0455:2,2:32:1:28.5:1:0.47569:2.74:60:4:0.0455:0:1 +1 30534961 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50673;SOR=0;LSEQ=TCCAAGAATGAGGTGTGTGC;RSEQ=GTGTGTGTGCTGCCCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:36,0:36,2:0.0526:1,2:28:1:30:1:0.05263:0:60:4:0.0556:0:2 0/0:27:0:0,0:25,2:27,0:0:2,0:22.9:1:31.4:1:1:0:60:54:1:0:0.8 +1 30534979 . G A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98794;LSEQ=GCCGTGTGTGTGCTGCCCCA;RSEQ=TGCATTTTGTAAATGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:41:39,2:12,0:12,41:0.7736:0,1:25.1:1:30.6:1:1:0:60:82:0.7736:0:1.1 1/0:35:27:26,1:8,0:8,27:0.7714:0,1:27.4:1:29.9:1:1:0:60:54:0.7714:0:1.1 +1 30535114 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.55244;LSEQ=CTAGTGGAACCCAAGTCTCT;RSEQ=TACAAGTAGGGATCTTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:88:44,44:62,57:119,88:0.4251:2,2:28.1:1:29.2:1:0.7802:1.08728:60:28.333:0.425:0:1.2 1/0:214:140:72,68:34,40:74,140:0.6542:2,2:24.7:1:28.1:1:0.47468:1.24:60:45.667:0.6493:0:1.1 +1 30535142 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4987;SOR=Inf;LSEQ=AGGGATCTTGTATGGGGCCA;RSEQ=CAGCAAGCCCCAGTAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:78,99:177,0:0:2,0:23.3:1:32.3:1:1:0:60:58:1:0:0.5 0/1:182:2:1,1:78,102:180,2:0.011:2,2:12:0:31.5:1:1:1.31:60:4:0.011:0:2.5 +1 30535145 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24832;SOR=Inf;LSEQ=GATCTTGTATGGGGCCAGCA;RSEQ=CAAGCCCCAGTAGGAGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:74,93:167,0:0:2,0:24:1:31.9:1:1:0:60:22.857:1:0:0.5 0/1:176:3:2,1:72,101:173,3:0.017:2,2:29.7:1:27.7:1:0.57325:2.79:60:6:0.0176:0:1.7 +1 30535269 . G A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=GCATTTGAGAAATAGCTCTT;RSEQ=GCTTTCTACTGAGCCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:30,0:0:1,0:28.4:1:31.7:1:1:0:60:60:1:0:0.2 1/0:15:8:0,8:0,7:7,8:0.5333:0,0:26.9:1:30:1:1:0:60:7:0.5:0:1.1 +1 30535317 . G T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.10551;LSEQ=AGTGGCTTCCTTTTTTCTAA;RSEQ=AAAAAGGAAATGAGTTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:10,6:0.375:0,0:16.8:1:29.8:1:1:0:60:12:0.375:0:1.2 0/1:5:2:0,2:0,3:3,2:0.4:0,0:19.5:1:29:1:1:0:60:4:0.4:0:1.5 +1 30648945 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49789;SOR=Inf;LSEQ=ATTCATATCAAAAACACACC;RSEQ=ATAAATGTAACTGAAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:19,0:0:2,0:28.1:1:31.5:1:1:0:60:38:1:0:0.1 0/1:25:2:1,1:15,8:23,2:0.08:2,2:27.5:1:29:1:1:1.82581:60:4:0.0833:0:1 +1 30792845 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGCCATGGCTCCGAGC;RSEQ=TCCTCACCCCCCCATCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:31.5:1:1:0:35:4:1:0:1.5 +1 30794414 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCCTCCCAGCACCTTCA;RSEQ=GTCTGAGTGGGTTAAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:41.5:1:33:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 30794719 . G C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3125;SOR=0;LSEQ=CGTATTTCCCCATTTAATTG;RSEQ=TTGTATTCTCAGTGGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:22.5:1:32.8:1:1:0:57.5:22:1:0:2.2 1/1:5:4:4,0:1,0:1,4:0.8:0,0:38.3:1:32.8:1:1:0:58.5:8:0.8:0:1.3 +1 30794788 . A G 178 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=TCGGGTTTCTCTGGAAAATA;RSEQ=TGATTCCCTGGCAGGGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:35,2:0,0:0,37:1:0,2:22.4:1:34.2:1:1:0:60:74:1:0:1.2 0/1:25:10:10,0:14,1:15,10:0.4:1,0:22.2:1:33.1:1:1:0:60:20:0.4:0:1.1 +1 30794877 . C T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0969;SOR=Inf;LSEQ=CTGCACTGGGTCTTCCAGGA;RSEQ=ATCCCAGGGTGGCCCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:151,55:206,0:0:2,0:25.2:1:31.7:1:1:0:60:67.667:1:0:0.4 0/1:176:3:1,2:119,53:172,3:0.017:2,2:7.7:1:26:1:0.23285:4.44774:60:6:0.0176:0:1.7 +1 30794960 . A C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13381;LSEQ=AGTCCCAGGGTCACCTGCTG;RSEQ=AGAAAGGAAACCAGAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:457:424:201,223:13,19:32,424:0.9278:2,2:26.3:1:31.8:1:0.58225:1.32:60:34.333:0.93:0:1.2 1/0:410:259:130,129:77,74:151,259:0.6317:2,2:27.1:1:31.3:1:0.91856:1.03247:60:63.75:0.6328:0:1.2 +1 30795039 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24904;SOR=0;LSEQ=CCATCTTCGCTCCTCAGGGG;RSEQ=CTCTCCTGAGACAGCCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:1,2:53,134:187,3:0.0157:2,2:8.7:1:29.7:1:1:1.26:60:6:0.0161:0:2 0/0:177:0:0,0:53,124:177,0:0:2,0:22.5:1:30:1:1:0:60:34.4:1:0:0.5 +1 30795106 . T G 163 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.04538;LSEQ=GCTGGTGGGGAGGCTCTGAC;RSEQ=GTCACCCCAGGAAAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:40:0,40:0,1:1,40:0.9756:0,1:24.6:1:30.7:1:1:0:60:19:0.9744:0:1.3 1/0:47:30:0,30:0,17:17,30:0.6383:1,1:24.6:1:30.6:1:1:0:60:60:0.6383:0:1 +1 30795214 . G C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTCAGGGACCCAGAAGG;RSEQ=CTGTGCGCTGGTGACCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:0,8:1:0,2:20.8:1:29.6:1:1:0:60:7:1:0:1.6 1/1:3:3:0,3:0,0:0,3:1:0,0:22:1:28.3:1:1:0:60:6:1:0:1 +1 31581502 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14282;SOR=0;LSEQ=TACTGGAAGACGGCAGTTCT;RSEQ=GCCAAAAGACTCTATTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:49,71:120,2:0.0164:2,2:28.5:1:29:1:1:1.44:51.5:4:0.0172:0:1 0/0:200:0:0,0:91,108:199,0:0:2,0:29.3:1:30.5:1:1:0:53.8:98.5:1:0:0.2 +1 31581541 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52489;SOR=Inf;LSEQ=CATTTCTCACCAATCTCTAT;RSEQ=TTCATCTGTATATTTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:16,49:65,0:0:2,0:18.6:1:30.5:1:1:0:60:130:1:0:0 0/1:105:2:1,1:29,74:103,2:0.019:2,2:25.5:1:28:1:0.49176:2.53:60:4:0.0196:0:1 +1 33132188 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGTCTCGAACTCCTGA;RSEQ=CTCAGGTGATCTGCCCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:29.5:1:1:0:32.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 33132857 . G C 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGATTCCTCTTTGAAGTT;RSEQ=CTAGAGGATAGCAGTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:0,7:1:0,2:26.7:1:33.9:1:1:0:41.1:14:1:0:1 1/1:6:6:6,0:0,0:0,6:1:0,0:15.7:1:31.8:1:1:0:56.8:12:1:0:1.3 +1 33133016 . CT C 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55309;SOR=Inf;LSEQ=GATCATGTGACTTGCTTGAC;RSEQ=TATCAATCACTTGGACGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:43,44:87,0:0:2,0:28.5:1:31.6:1:1:0:46.7:86:1:0:0.1 0/1:169:3:2,1:79,87:166,3:0.0178:2,2:26:1:27:1:0.60763:2.19:60:6:0.018:0.0059:0.3 +1 33133063 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15806;SOR=0;LSEQ=TCCTTACCTCGCCCCCTTGT;RSEQ=TTGTATGCAATAAATATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:19,29:48,2:0.04:2,2:35.5:1:31.5:1:1:1.51:46.5:4:0.04:0:1 0/0:75:0:0,0:31,44:75,0:0:2,0:20.3:1:30.2:1:1:0:47.7:24:1:0:0.1 +1 34805896 . G A 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04805;SOR=0;LSEQ=CCTGGGAACCAGTGAATCCT;RSEQ=CCTCCACCCCATGTCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:24.2:1:28:1:1:0:60:12:0.4286:0:1.7 0/0:9:0:0,0:9,0:9,0:0:0,0:21.3:1:31.8:1:1:0:60:18:1:0:0 +1 34805927 . C T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09774;SOR=0.25186;LSEQ=ATGTCTGACTTGCACATCTC;RSEQ=GGAGGCCTCCTAATTAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:8,1:21,0:21,9:0.3:1,2:26.9:1:31.7:1:0.3:0:60:18:0.3:0:1.4 0/1:21:2:2,0:19,0:19,2:0.0952:1,0:16.5:1:32.5:1:1:0:60:4:0.1:0:1 +1 34806052 . TTGC T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.30321;SOR=0.56191;LSEQ=TGCTGCTGTTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:9:6,3:114,115:229,9:0.0378:2,2:26.4:1:30.7:1:0.49949:2.01:60:18:0.038:0:0.3 0/1:278:6:4,2:134,137:271,6:0.0216:2,2:28.3:1:30.5:1:0.44714:2.04:56.7:12:0.0219:0:0.3 +1 34806066 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.25383;SOR=Inf;LSEQ=CTGCTGTTGCTGCTGCTGCT;RSEQ=CTGCAACTGCTGTGGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:96,113:209,0:0:2,0:25.7:1:32.2:1:1:0:59.6:208:1:0:0.1 0/1:248:3:2,1:114,131:245,3:0.0121:2,2:28:1:28.3:1:0.60066:2.29:53.7:6:0.0123:0:1.3 +1 34806090 . C A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50156;SOR=Inf;LSEQ=CAACTGCTGTGGCTGTTGGC;RSEQ=TATGACTAGTACCTCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:52,108:160,0:0:2,0:23.4:1:32:1:1:0:59.8:159:1:0:0.1 0/1:188:2:1,1:67,119:186,2:0.0106:2,2:5.5:1:26.5:1:1:1.77:60:4:0.0109:0:1 +1 35013586 . A G 206 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATTACATATAACACCAGT;RSEQ=TAACAGCCAGTATTTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:220,227:447,0:0:2,0:26.7:1:29.6:1:1:0:60:148:0.9955:0:0.1 0/1:511:95:47,48:198,217:415,95:0.1859:2,2:26:1:31.4:1:0.82009:1.07:60:94:0.1858:0:1.1 +1 35013690 . C T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08719;SOR=Inf;LSEQ=CATGAGTTTCTAGATTGAAA;RSEQ=GGCCACCAAGTGCCAGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:13,110:123,0:0:2,0:25.1:1:30.6:1:1:0:60:122:1:0:0 0/1:99:3:1,2:14,82:96,3:0.0303:2,2:27:1:21.3:1:0.39251:2.89:60:2:0.0204:0:1 +1 35468329 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50241;SOR=Inf;LSEQ=GTGGTTTGGTCATCTTCATA;RSEQ=ATTTTTTATCACATCTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:97,52:149,0:0:2,0:22.5:1:32.3:1:1:0:60:148:1:0:0.1 0/1:178:2:0,2:127,49:176,2:0.0112:2,0:11.5:1:25.5:1:0.08094:0:60:4:0.0114:0:1 +1 35468380 . AT A 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.04213;SOR=Inf;LSEQ=AGTTATTAAATTTGGGGCAC;RSEQ=TTTTTTAGCACTAGCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:143,133:276,0:0:2,0:28.6:1:30.8:1:1:0:60:275:1:0:0.1 0/1:378:6:3,3:193,179:372,6:0.0159:2,2:28.5:1:31:1:1:1.07797:60:12:0.0161:0:0 +1 35468429 . A G 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TATAACACTTAAATGGCATT;RSEQ=TTCTACGATATAAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:93,130:223,0:0:2,0:23.4:1:30:1:1:0:60:446:1:0:0.1 0/1:304:18:10,8:115,169:284,18:0.0592:2,2:24.7:1:32.1:1:0.22558:1.83:60:36:0.0598:0:1.2 +1 35468440 . TA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.17556;SOR=0;LSEQ=AATGGCATTATTCTACGATA;RSEQ=AAAAAAGAGTTTTAATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:0,2:75,111:186,2:0.0106:2,0:45:1:31.5:1:0.51786:0:60:4:0.0106:0:0 0/0:260:0:0,0:102,157:259,0:0:2,0:22.7:1:28.8:1:1:0:60:128.5:1:0:0.2 +1 35468456 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18116;SOR=0;LSEQ=GATATAAAAAAAGAGTTTTA;RSEQ=TTATATCAAGAGCAAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:49,94:143,2:0.0138:2,2:41.5:1:31:1:1:1.91:60:4:0.0141:0:2 0/0:195:0:0,0:73,120:193,0:0:2,0:23:1:29.5:1:1:0:60:192:0.9948:0:0.2 +1 35468504 . C T 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02103;SOR=Inf;LSEQ=CAGCACAAGCTGGGCACCAT;RSEQ=GGCTCATGCCTGTAATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:18,49:67,0:0:2,0:23.9:1:31:1:1:0:60:134:1:0:0.1 0/1:91:7:3,4:18,65:83,7:0.0769:2,2:32.4:1:30.6:1:0.34717:2.67:60:14:0.0787:0:1.3 +1 35468538 . T C 48 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30478;LSEQ=AATCACAACAGCTTGGGAGG;RSEQ=TGAGGCGGGAGGATCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:7,34:41,2:0.0465:2,2:15:1:31.5:1:0.34109:4.61:54.5:4:0.0465:0:1.5 0/1:50:3:0,3:8,39:47,3:0.06:2,0:35.7:1:30.3:1:1:0:60:6:0.0612:0:1.3 +1 36411515 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21739;SOR=Inf;LSEQ=GCTATTTTTTTCCTTAGTAA;RSEQ=TATCCATGTTTATTTTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:31.2:1:32.1:1:1:0:60:24:1:0:0 0/1:11:2:1,1:8,1:9,2:0.1818:2,2:24:1:29.5:1:0.34545:6:60:4:0.2:0:1 +1 36411737 . A G 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=19.36825;LSEQ=CTGAAATCAGGCTGCACATC;RSEQ=TGAGCACATCATTTTCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:1:0,1:203,175:378,1:0.0026:2,0:13:0:14:0:0.46438:0:60:0:0:0:1 0/1:471:23:11,12:233,215:448,23:0.0488:2,2:22.2:1:29.7:1:0.83122:1.18182:60:46:0.0498:0:1.3 +1 36411799 . T C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08906;SOR=0;LSEQ=CTTGCTTTTTTCTCCTCACC;RSEQ=CTCTTATGTACCACTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:104,172:276,3:0.0107:2,2:32.7:1:32.3:1:0.55957:3.29:60:6:0.011:0:1 0/0:347:0:0,0:138,208:346,0:0:2,0:47:0:15:0:1:0:60:0:0:0:1 +1 36807481 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11874;LSEQ=CTTGGGTACCCAGCTCCGGG;RSEQ=GTCATGGATGGAGCTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:521:339:140,199:84,97:181,339:0.6507:2,2:25.5:1:29.7:1:0.26635:1.23042:60:66.8:0.6511:0:1.1 0/1:509:92:34,58:185,232:417,92:0.1807:2,2:22:1:28.8:1:0.20284:1.35948:60:91:0.1827:0:1.1 +1 36807563 . C T 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGTACTGGGAGCACTCCTC;RSEQ=GTCACCTTCGCCTTTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:132,252:384,0:0:2,0:26.9:1:30.5:1:1:0:60:191:0.9974:0:0.3 0/1:363:18:8,10:138,207:345,18:0.0496:2,2:22.7:1:30.4:1:0.80648:1.20:60:36:0.05:0:1.2 +1 36807628 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17827;SOR=Inf;LSEQ=ATAAACCCAGATGAAGGCAG;RSEQ=GCAGCAGACAGGAGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:19,98:117,0:0:2,0:22.7:1:30.1:1:1:0:60:38:1:0:0.1 0/1:86:2:1,1:18,66:84,2:0.0233:2,2:18:1:28.5:1:0.39508:3.60:60:4:0.0235:0:1 +1 36809375 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20904;SOR=Inf;LSEQ=TCTAACTGGCAGAGAAGCAG;RSEQ=CTGACTACTGGCTGCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:96,15:111,0:0:2,0:22.2:1:30.7:1:1:0:60:14.857:1:0:0.2 0/1:94:2:2,0:78,14:92,2:0.0213:2,0:36.5:1:29.5:1:1:0:60:4:0.0213:0:1 +1 36809436 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05527;SOR=Inf;LSEQ=CCTGAGGACGCAGCCTTGTG;RSEQ=CCGGTCAAGTGCCTGTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:215,116:331,0:0:2,0:26.7:1:31.8:1:1:0:59.9:40.375:1:0:0.2 0/1:314:4:2,2:186,124:310,4:0.0127:2,2:25.8:1:27.8:1:1:1.49797:60:8:0.0131:0:1 +1 36809726 . A G 148 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.81519;LSEQ=GGAGGCAGGACTCACTCAGG;RSEQ=ATGGTATACTCGGCAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:17:17,0:219,268:487,17:0.0337:2,1:25.1:1:14.1:1:0:0:58.5:0:0:0:5.1 0/1:545:64:41,23:218,255:473,64:0.1174:2,2:24.9:1:24.7:1:0.00763:2.08:57:1.909:0.0909:0:3 +1 36810011 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00149;SOR=0.18714;LSEQ=AGCTCCTGCCCGTGCTCCCC;RSEQ=CTCCCCTGTTCCTCAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:24:1,23:0,11:11,24:0.6667:0,1:26.4:1:28.7:1:1:0:60:23:0.6765:0:1.3 0/1:30:8:0,8:2,20:22,8:0.2667:2,0:23.3:1:28.8:1:1:0:60:16:0.2667:0:1.4 +1 36814216 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18504;SOR=Inf;LSEQ=GCCCCAGCACCTTGCCCAGG;RSEQ=CCTGCCCACAAATTTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:221,34:255,0:0:2,0:24.3:1:30.7:1:1:0:60:24.5:1:0:0.1 0/1:193:2:1,1:168,22:190,2:0.0104:2,2:21.5:1:26.5:1:0.22579:7.49067:60:4:0.011:0:1 +1 36814473 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90913;SOR=0.96227;LSEQ=CTATAGCAACAGGCACAAGA;RSEQ=ACGCAGGCAGGACACACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:48:7,41:53,268:321,48:0.1301:2,2:24.6:1:28.5:1:0.83645:1.15787:60:23:0.1271:0:1.1 0/1:318:40:7,33:45,232:277,40:0.1258:2,2:22.2:1:27.7:1:0.82077:1.09:60:80:0.1274:0:1 +1 36819825 . C CCT 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08528;SOR=Inf;LSEQ=TTCCCATGTTCATCCCATCC;RSEQ=GAGCCCTGGGATTCCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:131,0:131,0:0:1,0:22.2:1:31.6:1:1:0:59.8:262:1:0:0.1 0/1:104:3:3,0:100,1:101,3:0.0288:1,0:9.7:1:30.5:1:1:0:60:6:0.03:0.0096:0 +1 36819930 . G T 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=44.56253;LSEQ=TGTAGCCTGCCCCAGCCCCG;RSEQ=GGTAACTGTATGGATGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:877:1:0,1:518,358:876,1:0.0011:2,0:1:0:26:0:0.40935:0:60:2:0.0012:0:1 0/1:908:44:26,18:485,377:862,44:0.0485:2,2:20.8:1:29.6:1:0.75722:1.12:60:88:0.0492:0:1.2 +1 36820196 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09946;SOR=Inf;LSEQ=AGTTCGCGTGACCTGCGCGT;RSEQ=TGGATGGGGAATGAATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:2,49:51,0:0:1,0:27.9:1:32.7:1:1:0:59.6:24.5:1:0:0.2 0/1:24:2:1,1:1,21:22,2:0.0833:1,2:31:1:28.5:1:0.16304:15.20:60:4:0.0833:0:1 +1 36820750 . C T 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.25551;SOR=0;LSEQ=AGCTGCCTTCTGCTCAGCAG;RSEQ=AGCAAGAAAGGTGGCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:3:1,2:123,21:144,3:0.0204:2,2:20.3:1:21.3:1:0.0639:11.39223:60:2:0.0142:0:1.3 0/0:119:0:0,0:92,27:119,0:0:2,0:21.4:1:30.7:1:1:0:60:28.75:1:0:0.2 +1 36820752 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.09273;SOR=Inf;LSEQ=CTGCCTTCTGCTCAGCAGCA;RSEQ=CAAGAAAGGTGGCTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:131,25:156,0:0:2,0:23.1:1:32.4:1:1:0:59.8:38:1:0:0.2 0/1:130:3:3,0:98,29:127,3:0.0231:2,0:21:1:31:0:1:0:60:6:0.024:0:2 +1 36820783 . C T 113 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=19.11297;LSEQ=GGCTTTCTGTGGCCAGAAGG;RSEQ=GCAGCAGCAGGGTGTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:0,1:193,66:259,1:0.0038:2,0:1:0:26:0:0.25769:0:60:2:0.0039:0:1 0/1:232:16:12,4:148,68:216,16:0.069:2,2:18.4:1:28.3:1:0.78123:1.38:60:32:0.0693:0:1.3 +1 36820927 . G A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43392;SOR=0.8947;LSEQ=ATGAGGTCAGCGGTCTTATC;RSEQ=CTGAAGTCATGAGCACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:775:111:61,50:349,313:662,111:0.1432:2,2:23.7:1:29.5:1:0.68218:1.09:59.4:54.5:0.1427:0:1.2 0/1:907:118:64,54:435,353:788,118:0.1301:2,2:26.5:1:29:1:0.84345:1.03972:59.9:236:0.1314:0:1.2 +1 36821068 . G A 49 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06166;SOR=0;LSEQ=GGGTAGCGCAGGGCTTGGCT;RSEQ=TGAACTTGGCAGGGCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:4:2,2:106,259:365,4:0.0108:2,2:26.8:1:24.8:1:0.58373:2.44:60:3:0.0083:0:1.3 0/0:370:0:0,0:116,253:369,0:0:2,0:24.4:1:31.2:1:1:0:60:183.5:0.9973:0:0.1 +1 36821402 . A G 32 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCATGGCACCCAGATTCC;RSEQ=GTAATCACCAACAGAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:5.5:1:32.5:1:1:0:25:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 36824053 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11715;SOR=Inf;LSEQ=ACAGCAGAACAACCAGAACG;RSEQ=GGGAAGCAGGGGGCTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:22,193:215,0:0:2,0:24.4:1:31.3:1:1:0:60:42:1:0:0.2 0/1:207:3:1,2:18,185:203,3:0.0145:2,2:16.7:1:23:1:0.25308:5.07:60:2:0.01:0:1 +1 36824055 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24881;SOR=0;LSEQ=AGCAGAACAACCAGAACGGG;RSEQ=GAAGCAGGGGGCTTTTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:1,2:21,186:207,3:0.0143:2,2:22.3:1:24.3:1:0.28372:4.38:60:2:0.0096:0:2 0/0:198:0:0,0:15,183:198,0:0:2,0:22.2:1:30.2:1:1:0:60:38.6:1:0:0.1 +1 36824305 . C T 200 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGGCATGACAGGCCCTGTT;RSEQ=CTGAGGCACCCTCACCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:104:57,47:342,246:588,104:0.1503:2,2:25.5:1:29.9:1:0.52078:1.14611:60:208:0.1529:0:2.1 0/0:690:0:0,0:408,281:689,0:0:2,0:25.9:1:30.3:1:1:0:60:67.9:1:0:0.4 +1 36824321 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00035;SOR=1.49312;LSEQ=TGTTCCTGAGGCACCCTCAC;RSEQ=CCCATGTCTCACTTACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:843:182:106,76:357,304:661,182:0.2159:2,2:25.2:1:31.1:1:0.31433:1.19:60:90:0.2171:0:1.7 0/1:906:264:151,113:362,280:642,264:0.2914:2,2:25.3:1:29.2:1:0.88274:1.03:60:65:0.2921:0:1.2 +1 36826717 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09332;SOR=Inf;LSEQ=GCAGGACCACACACTGCTGT;RSEQ=GGTGGGCCACCTCACTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:199,7:206,0:0:1,0:24.5:1:32.2:1:1:0:60:40.2:1:0:0.1 0/1:172:3:2,1:163,6:169,3:0.0174:1,2:8.3:1:30.3:1:0.11785:12.96317:60:6:0.0175:0:1 +1 36853369 . GACAC G 92 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=13.000;MSILEN=2;SSF=0.75202;SOR=1.39564;LSEQ=TACCATGAGGAGAACGCTGG;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:5,2:5,5:10,7:0.3043:2,2:31.9:1:31.8:1:0.62207:2.37:60:14:0.3043:0.0435:0 0/1:21:8:4,4:4,2:6,8:0.381:2,2:38.5:1:30.9:1:0.62704:1.90258:60:16:0.381:0:0.3 +1 36931882 . C T 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=47.48833;LSEQ=GGGTAGTTTTTAGTCATGGG;RSEQ=TTATGGACCCTCCCCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:1:0,1:385,330:715,1:0.0014:2,0:1:0:26:0:0.46229:0:60:2:0.0014:0:1 0/1:689:43:21,22:357,289:646,43:0.0624:2,2:20:1:28.8:1:0.43233:1.29362:59.8:42:0.0618:0:1.2 +1 36933096 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32965;LSEQ=AAGGGACTTAGATGGGCCCA;RSEQ=CTGGACCTGAGGTTCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:178:133,45:274,124:398,178:0.3074:2,2:23.6:1:31.8:1:0.16625:1.34:59.8:88:0.3115:0:1.1 0/1:541:69:45,24:347,125:472,69:0.1275:2,2:23:1:30.8:1:0.1517:1.47939:60:33.5:0.1257:0:1.1 +1 36933198 . G A 206 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=134.95669;LSEQ=AGGCAGTTCCACAGAGGCAG;RSEQ=TGAGCAACAGCAGGAGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1567:1:1,0:792,773:1565,1:6e-04:2,0:1:0:15:0:1:0:60:0:0:0:1 0/1:1713:136:67,69:777,796:1573,136:0.0794:2,2:24.2:1:29.1:1:1:1.00527:60:135:0.0798:0:1.3 +1 36933317 . C T 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCTGGGTCTCCTCCCTC;RSEQ=GACCAGGGGATTCAAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:746:0:0,0:346,399:745,0:0:2,0:23:1:30.4:1:1:0:59.9:81.778:0.9986:0:0.1 0/1:682:51:20,31:284,346:630,51:0.0748:2,2:25.6:1:29.3:1:0.46576:1.27181:60:50:0.0743:0:1.1 +1 36933539 . C T 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=21.52715;LSEQ=GGCCATGGAGGACAAAGCCA;RSEQ=GGGAGGAGGCATTCAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1553:5:3,2:749,796:1545,5:0.0032:2,2:19.8:1:28.8:1:0.67835:1.59:60:10:0.0033:0:1 0/1:1722:112:51,61:790,820:1610,112:0.065:2,2:22:1:30:1:0.49476:1.15222:59.9:111:0.0654:0:1.3 +1 36933651 . G A 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCAGGCCTTCTGGGGCT;RSEQ=TGGGGGAACTGAGGATAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1249:0:0,0:603,645:1248,0:0:2,0:25.3:1:32.2:1:1:0:60:77:0.9992:0:0.1 0/1:1268:44:21,23:591,630:1221,44:0.0347:2,2:26.2:1:28.4:1:1:1.02742:60:88:0.035:0:1.2 +1 36934667 . T C 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTATGGTAGGAAGGCAA;RSEQ=GTTCCCTATACTTCTGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:291,22:313,0:0:2,0:21.9:1:31.4:1:1:0:60:103.333:1:0:0.1 0/1:238:32:29,3:184,22:206,32:0.1345:2,2:19:1:31.6:1:1:1.16:60:64:0.135:0:1 +1 36934976 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00048;SOR=0.26053;LSEQ=TCATGATTCAGGGTTAACCT;RSEQ=CACAATATCTTCTTTAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:40:2,38:17,101:118,40:0.2532:2,2:23.7:1:30:1:0.16051:3.17981:60:19:0.2452:0:1 0/1:99:8:0,8:9,82:91,8:0.0808:2,0:29.6:1:27.6:1:1:0:60:7:0.0729:0:1 +1 36935072 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGGCTATAGAAAAAGGA;RSEQ=CAGGTTAGACTGTAGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:86,27:113,2:0.0174:2,2:25:1:28:1:0.42929:3.14592:60:4:0.0182:0:1.5 0/0:54:0:0,0:46,8:54,0:0:2,0:22.6:1:30.5:1:1:0:60:108:1:0:0.1 +1 36935128 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.35529;LSEQ=GGATATGAAATGAGAACAAC;RSEQ=AAGGATCAAGAAAGGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:220:110:103,7:107,3:110,110:0.5:1,2:22.6:1:31.3:1:0.3323:2.41468:60:220:0.5023:0:1 0/1:172:45:43,2:124,3:127,45:0.2616:1,1:24.5:1:30:1:0.60689:1.91433:60:90:0.2632:0:1.2 +1 36936601 . A G 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=AGAGGCCGGGGATGGGAGGT;RSEQ=ACTTACTCAGGTCACACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:23:1:30.3:1:1:0:57.7:6:0.5:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:24:1:28:1:1:0:60:4:1:0:0 +1 36937059 . A G 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.23783;LSEQ=CTTTCTGAGAAGACCACCGG;RSEQ=GTGGGACGAGAGGTCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1298:656:368,288:355,285:640,656:0.5054:2,2:23.9:1:30.9:1:0.8232:1.03:59.9:33.526:0.5052:0:2 1/0:1476:1027:554,473:239,208:447,1027:0.6958:2,2:24.1:1:30.3:1:0.90952:1.02:60:84.583:0.6962:0:1.5 +1 36937065 . A G 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.47076;LSEQ=GAGAAGACCACCGGAGTGGG;RSEQ=CGAGAGGTCCCGGCTGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1313:604:332,272:394,314:708,604:0.46:2,2:24.2:1:31.5:1:0.82376:1.028:59.8:45.462:0.4567:0:2.1 0/1:1506:431:234,197:568,506:1074,431:0.2862:2,2:24.8:1:30.7:1:0.64767:1.06:60:142.667:0.2884:0:2.1 +1 36937392 . T C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.01113;LSEQ=CCCCCCTCCCCTTTTCCCTC;RSEQ=GTTCCCTTGTGCTAGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:6:1,5:17,141:158,6:0.0366:2,2:26.3:1:31.8:1:0.50792:1.65:60:12:0.0375:0:1 0/1:87:29:2,27:3,54:57,29:0.3333:2,2:18:1:29.7:1:1:1.33:60:58:0.3372:0:1.1 +1 36937414 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01588;SOR=Inf;LSEQ=TTCCCTTGTGCTAGGTTCTA;RSEQ=GAAGGAGGGCAGGAAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:31,106:137,0:0:2,0:22.7:1:32.2:1:1:0:59.3:67.5:1:0:0.1 0/1:47:3:0,3:12,31:43,3:0.0638:2,0:39:1:30:1:0.55652:0:52:6:0.0652:0:1 +1 36937496 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08055;SOR=Inf;LSEQ=ACACTGTGACGTGCGTTACA;RSEQ=TCTGTCCAAAAGCTAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:106,29:135,0:0:2,0:24.5:1:33:1:1:0:59.5:32.75:1:0:0.2 0/1:54:2:2,0:46,6:52,2:0.037:2,0:14:1:31:0:1:0:60:4:0.037:0:1 +1 36937614 . G A 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCCGGTTTGTAGGGATCT;RSEQ=TTTGGACTGCGGGAGGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:937:0:0,0:578,358:936,0:0:2,0:25.2:1:32:1:1:0:60:84.091:0.9989:0:0.2 0/1:934:38:24,14:556,338:894,38:0.0407:2,2:20.6:1:27:1:1:1.04:60:11.667:0.0381:0:1.4 +1 36937701 . T C 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACTGTCCTGGGGTCCAGC;RSEQ=GCCTCTGCCGCCACCATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1371:0:0,0:689,682:1371,0:0:2,0:24.9:1:31.2:1:1:0:60:123.636:1:0:0.2 0/1:1422:56:29,27:641,723:1364,56:0.0394:2,2:27.4:1:29.5:1:0.4976:1.21:60:55:0.039:0:1.3 +1 36937878 . C T 169 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.0981;LSEQ=CTCCAGGCTGGGGCTCCAGT;RSEQ=GCTCCAGTGGCCAGGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1443:2:0,2:706,735:1441,2:0.0014:2,0:1:0:26:0:0.49988:0:60:4:0.0014:0:1 0/1:1416:55:29,26:681,680:1361,55:0.0388:2,2:27.5:1:29.4:1:0.78359:1.11:60:110:0.0395:0:1.2 +1 36938060 . A T 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAGGGCCAGCTCGAGCCCG;RSEQ=CTTACCCTGCCCCCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:860:0:0,0:407,453:860,0:0:2,0:22:1:29.9:1:1:0:59.9:70.667:1:0:0.1 0/1:727:49:24,25:326,352:678,49:0.0674:2,2:24.4:1:28.2:1:1:1.04:60:48:0.0668:0:1.1 +1 36938269 . A G 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGTCCATGGTCCGCAGC;RSEQ=TGGGGGGCTCCAGTTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1395:0:0,0:718,674:1392,0:0:2,0:24.4:1:30.7:1:1:0:60:48.714:0.9978:0:0.2 0/1:1596:68:35,33:766,757:1523,68:0.0426:2,2:24.7:1:30:1:0.90164:1.05:59.9:21.667:0.0414:0:1.2 +1 36938873 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.54978;SOR=0;LSEQ=CTGGGTCTGTGTCCCCATTT;RSEQ=TCTGTCTCCAGCTGCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:99,1:100,2:0.0196:1,2:30.5:1:29.5:1:0.03902:70.20734:60:4:0.0206:0:1 0/0:52:0:0,0:51,1:52,0:0:1,0:20.3:1:31.2:1:1:0:60:104:1:0:0 +1 36940801 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTAGTAGAGGCGGGG;RSEQ=TTCGCCTTGCTGGCCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:2,0:55,0:55,2:0.0345:1,0:8:1:34:1:1:0:41:4:0.0364:0:1 0/0:16:0:0,0:16,0:16,0:0:1,0:23.3:1:29.7:1:1:0:48.8:32:1:0:0.1 +1 36940811 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04186;SOR=Inf;LSEQ=AGAGGCGGGGTTTCGCCTTG;RSEQ=TGGCCAGGCTGATCATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:68,0:68,0:0:1,0:22.6:1:32.8:1:1:0:48.2:33:1:0:0.4 0/1:18:2:2,0:16,0:16,2:0.1111:1,0:38.5:1:29:1:1:0:36.5:4:0.1176:0:1 +1 36941374 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16494;SOR=Inf;LSEQ=GACTCAGAGGCCTCACCTTC;RSEQ=TGTCTCACCCTTCAAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:5,237:242,0:0:1,0:25.2:1:33.5:1:1:0:59.8:59.5:1:0:0.2 0/1:166:2:1,1:4,160:164,2:0.012:1,2:16.5:1:29:1:0.05951:35.88:60:4:0.0124:0:1.5 +1 36941539 . G GT 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03612;SOR=0;LSEQ=AGTGTGTGCCTTTCCGCGGT;RSEQ=TAAGTGCTCTCACTGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:0,12:1,3:4,12:0.75:2,0:19:1:29.4:1:0.25:0:60:24:0.75:0.3125:0.3 0/0:3:0:0,0:1,2:3,0:0:2,0:42:1:32:1:1:0:60:6:1:0:0 +1 36944054 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGAGAATCGCTTGAACC;RSEQ=GGCAGGCGGAGGTTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:29.5:1:1:0:26.5:4:1:0:1 +1 36945307 . AG A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.37655;SOR=0.49261;LSEQ=ACACAAAATGATGCAAGTCA;RSEQ=GGCTTTTCACAGTGCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:0,17:0,29:29,17:0.3696:1,1:30.6:1:32.7:1:1:0:60:34:0.3696:0.0435:0.2 0/1:18:4:0,4:1,13:14,4:0.2222:1,0:21.5:1:32.3:1:1:0:55:8:0.2222:0.0556:0 +1 36945559 . G A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGAAGGAGAGAAAGCCA;RSEQ=CACAAAGTTACATCATCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:25.5:1:29.5:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:34:0:1:0:60:2:1:0:0 +1 40361220 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19675;SOR=Inf;LSEQ=CTTTCAAAATAAATCAGACC;RSEQ=TTGCAACAGGAAATTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:102,4:106,0:0:1,0:24.8:1:32:1:1:0:59.4:105:1:0:0 0/1:85:2:2,0:81,2:83,2:0.0235:1,0:33:1:31:0:1:0:60:4:0.0244:0:1 +1 40361307 . TA T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.63312;SOR=0.88191;LSEQ=AGGCATACAAAAATACAATA;RSEQ=AAAAAAAAAGACTCCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:35:23,12:304,118:422,35:0.0763:2,2:22.9:1:30.9:1:0.43839:1.34324:60:70:0.0769:0.0153:0.2 0/1:619:42:29,13:376,200:576,42:0.0679:2,2:21.9:1:30.1:1:0.73723:1.19:60:84:0.068:0.0097:0.3 +1 40362978 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25206;SOR=Inf;LSEQ=AAATGTGCAAATTACTAAAG;RSEQ=GGAGAGGGAGGTTAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:160,26:186,0:0:2,0:23.4:1:31.1:1:1:0:54.2:92:1:0:0.4 0/1:215:3:1,2:165,46:211,3:0.014:2,2:11:1:24.3:1:0.127:7.08677:46:6:0.0142:0:2 +1 40363054 . G C 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07111;LSEQ=TTTTGGTCAGTTAGTAGCCA;RSEQ=TGAGGTATGCAATTCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:555:551:318,233:1,0:1,551:0.9928:0,2:26.9:1:32.4:1:1:0:54.7:109.2:0.9945:0:1.1 1/1:701:636:365,271:32,29:61,636:0.9073:2,2:24.8:1:31.1:1:0.49946:1.22:53.7:69.667:0.9074:0:1.1 +1 40363648 . C A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62363;SOR=2.98346;LSEQ=CAATTTCTTCATTCTCTGTC;RSEQ=GAGAAAAGAGATCAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:1,0:61,206:267,1:0.0037:2,0:1:0:26:0:0.23134:0:60:2:0.0038:0:1 0/1:271:3:1,2:78,190:268,3:0.0111:2,2:15.3:1:28:1:1:1.22:60:6:0.0112:0:1.3 +1 40364803 . C A 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07278;SOR=7.71731;LSEQ=CTGATTACGCTGTGTTTGGA;RSEQ=TTCTGTCTTACCCAGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:18,0:18,1:0.0526:1,0:45:0:30:0:1:0:60:2:0.0526:0:1 0/1:16:5:5,0:11,0:11,5:0.3125:0,0:30.2:1:31:1:1:0:60:10:0.3125:0:1 +1 40364939 . C T 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11525;SOR=5.29755;LSEQ=GTGAGTGAACTAGAAGCTCA;RSEQ=AAACAGGTTCAGGTTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:1:0,1:229,97:326,1:0.0031:2,0:1:0:23:0:0.29969:0:60:2:0.0031:0:1 0/1:312:5:1,4:216,91:307,5:0.016:2,2:8.2:1:24.6:1:0.03139:9.42105:60:10:0.0161:0:1.2 +1 40364988 . C T 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAATGATTCAGCAGGCTT;RSEQ=CCTACATCCCAAACCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:576:0:0,0:305,271:576,0:0:2,0:25.9:1:31.7:1:1:0:60:63:1:0:0.1 0/1:724:28:15,13:378,318:696,28:0.0387:2,2:30.7:1:30:1:1:1.03016:60:56:0.0395:0:1.3 +1 40365174 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24239;SOR=Inf;LSEQ=GTGTGCAAATGGGGAAACTG;RSEQ=GGCCCAGATCAGCGAAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:39,143:182,0:0:2,0:23.3:1:31.7:1:1:0:60:59.667:1:0:0.1 0/1:177:2:1,1:38,137:175,2:0.0113:2,2:31:1:31.5:1:0.3931:3.57:60:4:0.0116:0:1 +1 40366454 . G T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.07884;SOR=0;LSEQ=ACCAACACACCCACGTGCCA;RSEQ=ACAGACACGGTTGGGGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:191,81:272,3:0.0109:2,2:18.3:1:27.3:1:0.21738:4.68597:60:6:0.011:0:1 0/0:365:0:0,0:227,136:363,0:0:2,0:25.1:1:30.8:1:1:0:60:50.857:0.9944:0:0.1 +1 40367111 . G A 87 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14906;SOR=2.7648;LSEQ=ACGAGTCGTAGTCCATGTCC;RSEQ=CTCCCTGCGGGAGGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:691:3:1,2:263,424:687,3:0.0043:2,2:48:1:30.3:1:1:1.24016:60:6:0.0044:0:1 0/1:755:9:5,4:302,444:746,9:0.0119:2,2:11.9:1:27.7:1:0.49751:1.84:60:18:0.0121:0:1 +1 40367433 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAGGCAGCCTGCAGCCAGC;RSEQ=CGCACCGCGGGACCCGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:21,0:0:2,0:14.7:1:32.1:1:1:0:60:42:1:0:0.6 0/1:46:2:1,1:23,21:44,2:0.0435:2,2:16.5:1:27.5:1:1:1.09307:60:4:0.0435:0:1.5 +1 40367518 . C T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18596;SOR=0;LSEQ=CACCTGGAGCGGACCGGCTC;RSEQ=CCGCCGGCTCGGGGCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:45,45:90,2:0.0215:2,2:45:0:30.5:1:1:1:60:4:0.0215:0:1 0/0:122:0:0,0:61,61:122,0:0:2,0:23.7:1:29.9:1:1:0:59.8:60:1:0:0.5 +1 40367535 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24099;SOR=Inf;LSEQ=CTCCCCGCCGGCTCGGGGCA;RSEQ=CCCGGCAGCCAGCACACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:49,49:98,0:0:2,0:25.5:1:32.6:1:1:0:59.8:23.5:1:0:0.5 0/1:95:2:1,1:45,48:93,2:0.0211:2,2:20.5:1:28:1:1:1.07:60:4:0.022:0:1.5 +1 40367541 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24599;SOR=Inf;LSEQ=GCCGGCTCGGGGCAGCCCGG;RSEQ=AGCCAGCACACACGCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:47,47:94,0:0:2,0:24.5:1:32.5:1:1:0:59.8:93:1:0:0.5 0/1:93:2:1,1:44,47:91,2:0.0215:2,2:29:1:29.5:1:1:1.07:60:4:0.0215:0:1 +1 40367555 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49697;SOR=Inf;LSEQ=GCCCGGCAGCCAGCACACAC;RSEQ=CACATGCGCGCCGCCGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:38,42:80,0:0:2,0:21.7:1:31.2:1:1:0:60:79:1:0:0.6 0/1:82:2:1,1:37,41:78,2:0.0244:2,2:36.5:1:29:1:1:1.11:60:4:0.025:0:1.5 +1 40367592 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGCGCGGCCCGCACTCAC;RSEQ=AGCGCGCCCCCCCCGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:22:11,11:1,0:1,22:0.9565:0,2:9.4:1:29.2:1:1:0:60:10:0.9524:0:1.5 1/1:20:20:9,11:0,0:0,20:1:0,2:14.5:1:29.5:1:1:0:60:40:1:0:1.5 +1 40367615 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGCGCCCCCCCCGCGCGCGC;RSEQ=CCCTCCCTCGCTCGCGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:8.5:1:27:1:1:1:60:4:0.3333:0:2.5 +1 40799236 . C T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19306;SOR=0.2797;LSEQ=CTTTGTGTTTGTCATTTTGG;RSEQ=GAATTACTGGAAGGTGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:0,4:6,7:13,4:0.2353:2,0:35:1:30:1:0.23739:0:45.8:8:0.2353:0:1 0/1:26:2:0,2:9,15:24,2:0.0769:2,0:23.5:1:29:1:0.52923:0:59:4:0.0769:0:1 +1 40799267 . A C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12556;SOR=Inf;LSEQ=AAGGTGGCGTTTCTGGCCGT;RSEQ=AGGCTGATATTCTTCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:6,14:20,0:0:2,0:22.4:1:30.6:1:1:0:51.8:40:1:0:0.3 0/1:27:4:2,2:6,17:23,4:0.1481:2,2:34:1:31.8:1:0.55829:2.71:58.8:8:0.1481:0:1.3 +1 41661496 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08565;SOR=3.9451;LSEQ=ATGTAGGAAATTCTACAGAT;RSEQ=CCACAAAAAAGCTATTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:3,2:5,4:9,5:0.3571:2,2:13:1:31:1:1:1.18:51.2:10:0.3571:0:1 1/0:23:16:9,7:4,3:7,16:0.6957:2,2:24.4:1:29.4:1:1:1.03541:59.7:32:0.6957:0:1.1 +1 41827670 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24419;SOR=Inf;LSEQ=CGCGCCGCAGAGCCGGCCGC;RSEQ=CTCGTGTACCTGGCCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:29,36:65,0:0:2,0:28.8:1:31.4:1:1:0:60:31.5:1:0:0.1 0/1:64:2:1,1:28,34:62,2:0.0313:2,2:47.5:1:30:0:1:1.21:60:4:0.0317:0:1.5 +1 41828044 . TG T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.10594;SOR=Inf;LSEQ=CGTCCGGCTGGGGAGGGGGC;RSEQ=GGGACGCCGACTGGGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:93,229:322,0:0:2,0:23.4:1:31.1:1:1:0:60:52.667:0.9968:0:0.2 0/1:292:3:2,1:95,193:288,3:0.0103:2,2:14:1:26.7:1:0.25849:4.04:60:6:0.0104:0.0034:1 +1 41829272 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTGGAGGAGTAGACCTG;RSEQ=GTCTCTTTCCGCATCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29:1:1:0:60:4:1:0:1.5 +1 43605219 . T G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2639;SOR=Inf;LSEQ=CCTGCCTTACCCTGCCTCCT;RSEQ=GTCTTGTATGCAATAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:17,22:39,0:0:2,0:24.4:1:30.5:1:1:0:55.8:78:1:0:0.2 0/1:55:3:1,2:21,31:52,3:0.0545:2,2:29.3:1:30:1:1:1.34762:51.3:6:0.0556:0:1 +1 43784874 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20363;SOR=0;LSEQ=GTCCTGGGCTCCCTCATCCC;RSEQ=AGTCTCTCCTGACTTCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:18,6:24,2:0.0769:2,2:22.5:1:29:1:0.47385:2.85369:60:4:0.0769:0:1.5 0/0:31:0:0,0:21,10:31,0:0:2,0:24.6:1:30.1:1:1:0:60:62:1:0:0.1 +1 43784956 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.83709;SOR=0.89172;LSEQ=GTGCTGGTCGGAGAGAACCT;RSEQ=GCCTCCAAGATTGCAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:24:12,12:8,11:19,24:0.5581:2,2:25.4:1:30.7:1:0.75995:1.36:60:23:0.5476:0:1.1 1/0:51:27:11,16:9,15:24,27:0.5294:2,2:26.6:1:30.6:1:1:1.14:60:54:0.5294:0:1.1 +1 43803120 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATAACAAGACTATTGTG;RSEQ=GGATTGTCTAAGTGAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:34:1:29:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 43803222 . G A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90381;LSEQ=TATTATACCATTCTATAATC;RSEQ=TTAGCACAGATACAGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:10,0:9,0:9,10:0.5263:0,0:20.3:1:29.9:1:1:0:60:20:0.5882:0:1.4 1/0:6:3:2,1:2,1:3,3:0.5:2,2:27:1:27.7:1:1:1:60:6:0.5:0:1.3 +1 43803416 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15696;SOR=Inf;LSEQ=CAGGGACAGGGACAGGACGT;RSEQ=GGGCTGTATCTGACAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:272,29:301,0:0:2,0:22:1:32.2:1:1:0:59.9:49.167:1:0:0.1 0/1:198:2:2,0:169,27:196,2:0.0101:2,0:13.5:1:32:0:1:0:60:4:0.0102:0:1 +1 43804069 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGCCCCAGCTCCAGCC;RSEQ=TACATAACCCCTAATCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:84,29:113,2:0.0174:2,0:18:1:28.5:1:1:0:60:4:0.0175:0:1 0/0:46:0:0,0:39,7:46,0:0:2,0:21.1:1:31:1:1:0:60:45:1:0:0.1 +1 43804117 . G T 25 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50557;SOR=0;LSEQ=AGGCAGTGAGAAGAAAAATG;RSEQ=CAGTACTAGAGACAGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:0,2:141,30:171,2:0.0116:2,0:7:1:25:0:0.03334:0:60:4:0.0118:0:1 0/0:136:0:0,0:123,13:136,0:0:2,0:25.6:1:30.5:1:1:0:60:44.333:1:0:0.1 +1 43804340 . G A 132 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=23.74263;LSEQ=TGCACCTCTGGGTGAAGAAT;RSEQ=TGTTCCTAAACCAGACTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:754:1:1,0:332,421:753,1:0.0013:2,0:1:0:24:0:0.44164:0:60:2:0.0013:0:1 0/1:817:25:12,13:365,426:791,25:0.0306:2,2:26.2:1:28.5:1:1:1.08:60:24:0.0299:0:1.2 +1 43804433 . G T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.1238;SOR=Inf;LSEQ=CCCTGCCCCCTCCACTTGCT;RSEQ=CCCCCAGTCCAGCTCCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:77,221:298,0:0:2,0:25.1:1:32.2:1:1:0:60:36.25:1:0:0.1 0/1:303:4:2,2:95,204:299,4:0.0132:2,2:26.5:1:24.8:1:0.59547:2.14:60:3:0.0101:0:1.5 +1 43804438 . C T 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12369;SOR=Inf;LSEQ=CCCCCTCCACTTGCTGCCCC;RSEQ=AGTCCAGCTCCCGGAATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:71,215:286,0:0:2,0:23.7:1:32.1:1:1:0:60:94.333:1:0:0.1 0/1:286:4:2,2:80,200:280,4:0.014:2,2:21:1:22:1:0.58179:2.49:60:3:0.0107:0:1 +1 43805557 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22213;SOR=Inf;LSEQ=AGCTCCTCTCCACAGAGATG;RSEQ=TGTGCAAATATAAGGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:129,23:152,0:0:2,0:21.9:1:32.2:1:1:0:59.7:29.4:1:0:0.1 0/1:136:2:1,1:102,32:134,2:0.0147:2,2:23:1:27:1:0.42778:3.15418:60:4:0.015:0:1 +1 43805564 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24775;SOR=0;LSEQ=CTCCACAGAGATGCTGTGCA;RSEQ=ATATAAGGGTTGGAGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:135,29:164,2:0.012:2,2:12.5:1:32:1:0.32968:4.59387:60:4:0.0125:0:1 0/0:167:0:0,0:122,45:167,0:0:2,0:21.7:1:29.3:1:1:0:60:40.75:1:0:0.1 +1 43812075 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0302;SOR=1.3347;LSEQ=AGCCTTGGGATTAGTCTCTG;RSEQ=GGCAGGCCTGATTCAATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:180:126,54:175,78:253,180:0.4147:2,2:24.3:1:30.4:1:0.91573:1.04:60:59:0.4165:0:1.1 0/1:506:246:170,76:165,92:257,246:0.4862:2,2:24.1:1:28.5:1:0.25743:1.25:60:48.2:0.4898:0:1.1 +1 43812643 . G A 51 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32586;LSEQ=ATGCCCACAGACCTCACTAC;RSEQ=CAGGGGATCCCTGGGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:3:3,0:95,284:379,3:0.0078:2,0:1:0:25.7:1:0.0165:0:60:6:0.008:0:1 0/1:386:4:2,2:122,260:382,4:0.0104:2,2:9.5:1:25.5:1:0.59652:2.13:60:8:0.0105:0:1 +1 43812663 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10963;SOR=Inf;LSEQ=GCAGGGGATCCCTGGGGTTG;RSEQ=CCATGCCTGTTAGCAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:46,222:268,0:0:2,0:25.2:1:31.8:1:1:0:60:52.6:1:0:0.1 0/1:247:3:1,2:53,189:242,3:0.0121:2,2:24.3:1:23.3:1:0.52784:1.78:60:2:0.0083:0:3.3 +1 43814730 . G A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61282;SOR=0.46869;LSEQ=GCCTGCGCCAGGGACTGGGC;RSEQ=CCGGGTGCGAGTGGGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:11,148:159,2:0.0124:2,0:31:1:31.5:1:1:0:60:4:0.0127:0:1 0/0:171:1:0,1:14,156:170,1:0.0058:2,0:22:0:31:0:1:0:60:2:0.0059:0:1 +1 43814733 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2487;SOR=Inf;LSEQ=TGCGCCAGGGACTGGGCGCC;RSEQ=GGTGCGAGTGGGGCGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:8,136:144,0:0:2,0:24.6:1:32:1:1:0:60:71:1:0:0.2 0/1:156:3:1,2:8,145:153,3:0.0192:2,2:17.7:1:26.7:1:0.16428:8.76:60:2:0.0131:0:1 +1 43814738 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49932;SOR=Inf;LSEQ=CAGGGACTGGGCGCCGGGTG;RSEQ=GAGTGGGGCGGGGCTCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:7,118:125,0:0:2,0:23.7:1:30.4:1:1:0:60:24:1:0:0.2 0/1:138:2:0,2:6,130:136,2:0.0145:1,0:10.5:1:31:0:1:0:60:4:0.0148:0:1 +1 43814864 . T C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34368;SOR=1.23903;LSEQ=GGCGAGGGGCGGGGCCAGAG;RSEQ=AGGGGCTGGCTGGATGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:78:69,9:88,12:100,78:0.4358:2,2:25.7:1:32.2:1:1:1.05:60:25:0.431:0:1.1 0/1:184:90:75,15:78,16:94,90:0.4891:2,2:21.6:1:31.5:1:1:1.03:60:89:0.4944:0:1.2 +1 43996593 . T A 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20854;SOR=0;LSEQ=GCAGAGGCGGCGGCTCCAGC;RSEQ=TCGGCTCCGGCTCGGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:26:0:30:1:1:1.11803:60:4:0.1053:0:1 0/0:22:0:0,0:12,10:22,0:0:2,0:23.1:1:30.2:1:1:0:60:44:1:0:0.7 +1 43996613 . GGGCTCC G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=24;MSI=5.000;MSILEN=6;SSF=0.23643;SOR=Inf;LSEQ=TTCGGCTCCGGCTCGGGCTC;RSEQ=GGCTCCGGCTCCGGCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:25,0:0:2,0:27.8:1:31.6:1:1:0:60:50:1:0:0.3 0/1:27:3:2,1:13,11:24,3:0.1111:2,2:37.7:1:30:1:1:1.66:60:6:0.1154:0:0 +1 44035232 . C G 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55045;SOR=0;LSEQ=GGGGGCAGGCAGAGCCAGCC;RSEQ=TAATACACACATTGCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:4,0:18,0:18,4:0.1818:1,0:21.8:1:29:1:1:0:60:8:0.1905:0:1.3 0/0:8:0:0,0:7,1:8,0:0:2,0:26:1:31.3:1:1:0:60:16:1:0:0 +1 44035352 . C T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00157;SOR=0.31254;LSEQ=ACAGCCACCATGCTATGTGC;RSEQ=GCAGGCGGAAATCCAGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:32:15,17:19,24:43,32:0.4267:2,2:20.9:1:31.5:1:1:1.11:60:64:0.4267:0:1 0/1:80:15:7,8:36,29:65,15:0.1875:2,2:27.9:1:29.3:1:0.57746:1.41246:60:14:0.1772:0:1.1 +1 44035353 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4969;SOR=Inf;LSEQ=CAGCCACCATGCTATGTGCC;RSEQ=CAGGCGGAAATCCAGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:34,41:75,0:0:2,0:23.3:1:31.5:1:1:0:60:150:1:0:0.5 0/1:78:2:1,1:41,35:76,2:0.0256:2,2:10.5:1:31:0:1:1.16904:60:4:0.026:0:1.5 +1 44035472 . G A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.91073;LSEQ=GAGCAGAGGGCAGGGGTCAA;RSEQ=GGGCCATGCAGACCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:3,13:1,9:10,16:0.6154:2,2:21.8:1:31.6:1:1:2.02:60:32:0.6154:0:1 1/0:27:16:4,12:2,9:11,16:0.5926:2,2:17.3:1:30.6:1:1:1.48:60:32:0.5926:0:1 +1 44044468 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTGCCTGACCTCTCGCTT;RSEQ=GTGTACCCACAGGTGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:9,3:12,2:0.1429:2,0:11.5:1:31:1:1:0:60:4:0.1429:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:18.7:1:31.3:1:1:0:60:6:1:0:0 +1 44054486 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52809;SOR=Inf;LSEQ=CGTGAACCTGACATGCGTGG;RSEQ=AGTGGGTGCACCCATGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:25,0:0:2,0:23.8:1:31.8:1:1:0:60:24:1:0:0.2 0/1:43:2:1,1:23,18:41,2:0.0465:2,2:10.5:1:29:1:1:1.27044:60:4:0.0513:0:1.5 +1 44054524 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.5311;SOR=Inf;LSEQ=CCTACGTGAAGTGGATGATG;RSEQ=GGGCCGAGGAGCTCACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:28,0:0:2,0:32.2:1:31.1:1:1:0:60:56:1:0:0.3 0/1:49:2:1,1:22,25:47,2:0.0408:2,2:15:1:27.5:1:1:1.13:60:4:0.0426:0:1 +1 44054536 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15211;SOR=0;LSEQ=GGATGATGGGGGCCGAGGAG;RSEQ=TCACCAAGGAGGATGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:12,14:26,2:0.0714:2,2:34:1:30:1:1:1.16:60:4:0.0769:0:1 0/0:43:0:0,0:19,24:43,0:0:2,0:25.7:1:31.1:1:1:0:60:42:1:0:0.4 +1 44056462 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGACAGGCCTGGCCAC;RSEQ=GTCCCTCACTTGTGCCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:28.5:1:1:0:60:4:1:0:1 +1 44057128 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48;SOR=0;LSEQ=TCACGACCGTGGGCAGCCTG;RSEQ=TGCCTGGCATCACCTACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:14:1:28:1:1:2.4495:60:4:0.1538:0:1 0/0:13:0:0,0:8,5:13,0:0:2,0:24.5:1:31.5:1:1:0:60:26:1:0:0.2 +1 44057257 . A G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.56182;SOR=0.62832;LSEQ=ATGCCGGCTGGGCAGCCAAC;RSEQ=GCAGAGAAGGGGAGGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:5,7:8,6:14,12:0.4615:2,2:25.7:1:29.2:1:0.6951:1.82171:60:11:0.44:0:1.1 0/1:23:8:3,5:7,8:15,8:0.3478:2,2:25.9:1:30.4:1:1:1.43469:60:16:0.3478:0:1.1 +1 44063224 . A G 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGAGAGAGGGAAGGAGAGAG;RSEQ=GGGAGGCAGGTCAGAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:37:0:34:0:1:0:60:2:1:0:1 0/1:5:2:1,1:2,1:3,2:0.4:2,2:28:1:28.5:1:1:1.7321:60:4:0.4:0:2 +1 44063250 . T C 86 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGTCAGAGGGAGTCAGG;RSEQ=GTCCTTGGCGAGAGTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:38:0:32:0:1:0:60:2:1:0:1 1/1:7:7:4,3:0,0:0,7:1:0,2:26.9:1:30.9:1:1:0:60:14:1:0:1.6 +1 44064319 . A G 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80718;LSEQ=GGTGCTGAGGCAGGACCCTC;RSEQ=AGTTTGCTGTGCCCACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:4,1:8,0:8,5:0.3846:0,2:32.6:1:29.2:1:0.38462:0:60:10:0.3846:0:1.2 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:25.3:1:30.5:1:1:0:60:8:0.3636:0:1 +1 44064455 . C G 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=TCCACTGCTGTGCATGTCTA;RSEQ=TGGAAGCTGCCTGTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:74,41:115,0:0:2,0:23.9:1:31.9:1:1:0:60:56.5:1:0:0.1 0/1:124:2:1,1:71,50:121,2:0.0161:2,2:7.5:1:28.5:1:1:1.41585:60:4:0.0164:0:2 +1 44064473 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23111;SOR=0;LSEQ=TACTGGAAGCTGCCTGTCCC;RSEQ=AGCAAGCAGCATGGCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:98,69:167,2:0.0118:2,2:38.5:1:32:1:1:1.41726:60:4:0.012:0:1 0/0:182:0:0,0:99,81:180,0:0:2,0:25.4:1:31:1:1:0:60:179:0.989:0:0.2 +1 44064479 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49992;SOR=Inf;LSEQ=AAGCTGCCTGTCCCCAGCAA;RSEQ=CAGCATGGCCAGATCCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:99,82:181,0:0:2,0:23.8:1:32.6:1:1:0:60:89.5:0.9944:0:0.1 0/1:201:2:1,1:109,88:197,2:0.01:2,2:36.5:1:31.5:1:1:1.23729:60:4:0.0102:0:1 +1 44079139 . C T 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CCACCCTCCGCCATCCCTGT;RSEQ=GCCGCATGTGCTGCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:11.8:1:32.5:1:1:0:60:8:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:35:0:32:1:1:0:60:4:0.6667:0:1.5 +1 44079338 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09296;SOR=Inf;LSEQ=ACCGACCTGGCGGACAACAT;RSEQ=GAGCGCCTCAAAGCCAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,21:49,0:0:2,0:28.3:1:30.3:1:1:0:60:23.5:1:0:0.4 0/1:22:2:1,1:11,9:20,2:0.0909:2,2:27:1:26.5:1:1:1.21106:60:4:0.0909:0:1.5 +1 44079411 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49793;SOR=0.55118;LSEQ=GATGTTCCCGCCCCCTACCA;RSEQ=GTGCCTGGCCCAGGCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:26:6,20:1,4:5,26:0.8387:2,2:22.3:1:30.3:1:1:1.19:60:52:0.8387:0:1.2 1/0:23:17:5,12:2,3:5,17:0.7391:2,2:21.1:1:30.4:1:1:1.56456:60:34:0.7391:0:1.1 +1 44081762 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCACCAGAGCAGCCTGAGG;RSEQ=GTGGGGTGTGCTGCGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:29:1:1:0:60:4:1:0:1 +1 44083015 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37479;SOR=3.35527;LSEQ=GCTGTGGCCTGTGGAGTGAA;RSEQ=GCAGGATGTGAGCATCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:12,0:6,0:6,12:0.6667:0,0:25.1:1:31.3:1:1:0:60:24:0.6667:0:1.3 1/1:8:7:7,0:1,0:1,7:0.875:0,0:16.6:1:30.7:1:1:0:60:14:0.875:0:1.3 +1 44083110 . C T 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15368;SOR=2.15728;LSEQ=CCACCCGCTTTCTCCATTCT;RSEQ=TGCAGTCCATCGACCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:72:53,19:12,1:13,72:0.8471:1,2:24:1:31:1:0.28395:4.24839:59.9:144:0.8471:0:1.1 1/1:91:84:61,23:6,1:7,84:0.9231:2,2:22:1:29.4:1:0.67068:2.24553:59.2:83:0.9222:0:1.1 +1 44083168 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50504;SOR=Inf;LSEQ=GAATTCAAACCTGGAGGTGA;RSEQ=CAAGCCCAAGAACCGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:63,71:134,0:0:2,0:29.2:1:30.3:1:1:0:59.9:268:1:0:0.4 0/1:169:2:1,1:85,82:167,2:0.0118:2,2:28:1:30.5:1:1:1.03638:60:4:0.0119:0:3 +1 44083190 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50193;SOR=Inf;LSEQ=AAGCCCAAGAACCGCTATGC;RSEQ=AATGTCATCGCCTACGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:50,77:127,0:0:2,0:28.2:1:31.4:1:1:0:59.9:126:1:0:0.3 0/1:151:2:1,1:63,86:149,2:0.0132:2,2:40:0:31.5:1:1:1.36:60:4:0.0134:0:1 +1 44083205 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=TATGCGAATGTCATCGCCTA;RSEQ=GACCACTCTCGAGTCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:38,77:115,0:0:2,0:25.2:1:30.8:1:1:0:59.9:56.5:0.9912:0:0.1 0/1:127:2:0,2:45,80:125,2:0.0157:2,0:38:1:27:1:0.53881:0:60:4:0.016:0:2.5 +1 44083507 . T C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42616;SOR=1.41292;LSEQ=CCCCTGCCCGAGACCATGGG;RSEQ=GATTTCTGGAGGATGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:96:80:51,29:11,5:16,80:0.8333:2,2:24.9:1:31.1:1:0.78165:1.24813:60:79:0.8316:0:2 1/1:105:92:62,30:8,5:13,92:0.8762:2,2:21.5:1:29.9:1:0.75611:1.29:60:29.667:0.8725:0:2.1 +1 44083519 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.36501;SOR=1.40129;LSEQ=ACCATGGGTGATTTCTGGAG;RSEQ=ATGGTGTGGGAACAGCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:88:53,35:12,7:19,88:0.8224:2,2:26.7:1:29.9:1:1:1.13076:60:87:0.8208:0:2 1/1:120:104:61,43:8,7:15,104:0.8667:2,2:24.8:1:27.6:1:0.78243:1.24:60:25:0.8621:0:1.9 +1 44083591 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10024;SOR=0;LSEQ=GAGAAGTCCCGGGTGAGGCT;RSEQ=CAGGGCCCTGCCAGGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:2,1:49,80:129,3:0.0227:2,2:10.3:1:28.3:1:0.55896:3.24:60:6:0.0231:0:2.3 0/0:151:0:0,0:57,94:151,0:0:2,0:22.7:1:31.2:1:1:0:60:49.333:1:0:0.7 +1 44083874 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGTGTTCCCGGGGTATTC;RSEQ=TGTGTTCCCCAGATGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:41:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 44084739 . C T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.54771;LSEQ=AGTGGCTCCAGTGAGAAGCG;RSEQ=GAGCTGCGTCAGTTTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:1,1:0.5:0,0:35:0:33:0:1:0:60:2:0.5:0:1 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:37.5:1:29:1:1:2.45:60:4:0.3333:0:1 +1 44084990 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18365;SOR=Inf;LSEQ=GCCGCACCGGCTGCTTCATC;RSEQ=TGATTGATGCCATGTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:54,0:54,0:0:1,0:23.6:1:30.2:1:1:0:60:108:1:0:0.1 0/1:41:2:2,0:39,0:39,2:0.0488:1,0:26.5:1:31.5:1:1:0:60:4:0.05:0:1 +1 44085022 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50335;SOR=Inf;LSEQ=ATGTTGGAGCGGATGAAGCA;RSEQ=GAGAAGACGGTGGACATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:65,21:86,0:0:2,0:25.9:1:30.6:1:1:0:60:27.667:1:0:0.1 0/1:107:2:1,1:73,32:105,2:0.0187:2,2:10.5:1:28:1:0.52372:2.26178:60:4:0.0187:0:1.5 +1 44085057 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50245;SOR=Inf;LSEQ=CATCTATGGCCACGTGACCT;RSEQ=CATGCGATCACAGAGGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:84,64:148,0:0:2,0:25.8:1:31.5:1:1:0:59.9:28.6:1:0:0.1 0/1:177:2:1,1:103,72:175,2:0.0113:2,2:28.5:1:27:1:1:1.42758:60:4:0.0114:0:1 +1 44085357 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4988;SOR=Inf;LSEQ=CTGCCTCTCAATAGTTGCTG;RSEQ=CCAGCTCCAAGGCCCACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:123,70:193,0:0:2,0:23.8:1:31.2:1:1:0:60:47.25:1:0:0.2 0/1:198:2:1,1:129,66:195,2:0.0101:2,2:33.5:1:29.5:1:1:1.94747:60:4:0.0105:0:1 +1 44085473 . C A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11313;SOR=0;LSEQ=ACCCGTGTGTGTCTGCAGCC;RSEQ=ATCCGTGGTGTGGAGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:2,1:76,129:205,3:0.0144:2,2:26:1:25:1:0.55757:3.37:60:2:0.01:0:1.3 0/0:221:0:0,0:77,144:221,0:0:2,0:24.9:1:30.8:1:1:0:60:54.25:1:0:0.1 +1 44085483 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62214;SOR=0.49324;LSEQ=GTCTGCAGCCCATCCGTGGT;RSEQ=TGGAGGGCTCTGACTACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:68,126:194,2:0.0102:2,2:15.5:1:28.5:1:1:1.85:60:4:0.0106:0:1 0/0:198:1:1,0:69,128:197,1:0.0051:2,0:1:0:22:0:0.35354:0:60:2:0.0051:0:1 +1 44085498 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49873;SOR=0;LSEQ=GTGGTGTGGAGGGCTCTGAC;RSEQ=ACATCAATGCCAGCTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:46,114:160,2:0.0123:2,2:34.5:1:30:1:0.49735:2.46:60:4:0.0126:0:1.5 0/0:154:0:0,0:43,111:154,0:0:2,0:25.4:1:28.3:1:1:0:60:76:1:0:0.1 +1 44086080 . T C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43829;SOR=0.6082;LSEQ=GAAGCCTGGCACCCCTCCCC;RSEQ=ATTCCTTCTCACCTGATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:43:37,6:9,0:9,43:0.8113:0,2:24.7:1:32.1:1:0.57446:0:60:86:0.8113:0:1.1 1/0:36:26:25,1:8,2:10,26:0.7222:2,1:23.1:1:28:1:0.18067:5.87:60:7.667:0.697:0:1.2 +1 44086136 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21263;SOR=Inf;LSEQ=TGTCCACAGGAGAAATGCCA;RSEQ=CAGTACTGGCCAGCAGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:113,36:149,0:0:2,0:23.8:1:32.1:1:1:0:60:298:1:0:0.3 0/1:128:2:1,1:87,39:126,2:0.0156:2,2:26.5:1:27.5:1:0.52904:2.21537:60:4:0.0157:0:1.5 +1 44086212 . C A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02094;SOR=Inf;LSEQ=TGGCTGAGTACAACATGCCC;RSEQ=AGTATATCCTGCGTGAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:201,184:385,0:0:2,0:28.1:1:31.6:1:1:0:60:76:1:0:0.1 0/1:332:5:2,3:168,158:326,5:0.0151:2,2:23.4:1:25.6:1:0.67742:1.5927:60:4:0.0123:0:1 +1 44086287 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52799;SOR=0;LSEQ=AGTGTGTCCATAACGCTGCC;RSEQ=GTCCACACGCTGGGTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:41,141:182,2:0.0109:2,2:20.5:1:32.5:1:0.40538:3.41:60:4:0.0111:0:1 0/0:112:0:0,0:32,80:112,0:0:2,0:20.9:1:29.6:1:1:0:60:224:1:0:0.1 +1 44086554 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19606;SOR=0;LSEQ=AGTTCCAGTTCACAGACTGG;RSEQ=CAGAGCAGGGCGTGCCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:65,67:132,2:0.0149:2,2:36.5:1:30.5:1:1:1.03:60:4:0.0152:0:1 0/0:168:0:0,0:90,78:168,0:0:2,0:29.3:1:30.7:1:1:0:59.7:55:1:0:0.1 +1 44086826 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49818;SOR=0;LSEQ=GCATCGTCCTGGAGCGCATG;RSEQ=GCTACGAGGGCGTGGTCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:35,17:52,2:0.037:2,2:13:1:28.5:1:1:2.02925:60:4:0.037:0:2 0/0:46:0:0,0:29,17:46,0:0:2,0:23.9:1:31:1:1:0:60:92:1:0:0.9 +1 44086831 . C T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.10533;LSEQ=GTCCTGGAGCGCATGCGCTA;RSEQ=GAGGGCGTGGTCGACATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:47:30,17:10,2:12,47:0.7966:2,2:24.3:1:31.2:1:0.3034:2.7896:59.2:94:0.7966:0:1.2 1/1:48:39:25,14:5,4:9,39:0.8125:2,2:25.1:1:29.2:1:0.7111:1.42:60:78:0.8125:0:1.1 +1 44087496 . C T 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.86091;LSEQ=GTAGCTGCCAGGGTCCAGCA;RSEQ=CTGCTCTTGGCCAGCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:21:21,0:4,0:4,21:0.84:0,1:18.4:1:32:1:1:0:60:42:0.84:0:1 1/1:11:9:9,0:2,0:2,9:0.8182:0,0:21.2:1:31:1:1:0:60:18:0.8182:0:1 +1 44087693 . C A 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11464;SOR=0;LSEQ=AACTACCGCTCCCCTCTCCT;RSEQ=CGCCACCCCCGCCGTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:2,1:64,122:186,3:0.0159:2,2:17:1:26.7:1:0.27957:3.78:60:6:0.016:0:1 0/0:199:0:0,0:79,120:199,0:0:2,0:22.4:1:30:1:1:0:60:98.5:1:0:0.2 +1 44087694 . C A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61627;SOR=0.4777;LSEQ=ACTACCGCTCCCCTCTCCTC;RSEQ=GCCACCCCCGCCGTGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:64,121:185,2:0.0107:2,2:12:1:29:1:1:1.88:60:4:0.0109:0:1 0/0:195:1:1,0:76,118:194,1:0.0051:2,0:1:0:24:0:0.39487:0:60:2:0.0051:0:1 +1 44087729 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49745;SOR=0;LSEQ=GGGGCTCCGGAGGGGACCCA;RSEQ=CTCCTCTGAGCCATACCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:11,65:76,2:0.0256:2,2:17:1:31.5:1:0.28571:5.70:60:4:0.026:0:1 0/0:72:0:0,0:9,63:72,0:0:2,0:23.1:1:31.7:1:1:0:60:71:1:0:0.1 +1 45795150 . A G 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11162;SOR=Inf;LSEQ=GGAGGCCTTGTAGTTGGGGG;RSEQ=GGGGGAGCAGAGAATCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:77,228:305,0:0:2,0:24.4:1:30.9:1:1:0:60:24.417:1:0:0.1 0/1:287:3:1,2:78,206:284,3:0.0105:2,2:14.7:1:22.3:1:1:1.32:60:2:0.0071:0:1.3 +1 45796269 . G C 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07349;LSEQ=GGTGAGGGCTGGCACTTTTT;RSEQ=CAAAAGAGATAAACCGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:661:659:222,437:0,0:0,659:0.997:0,2:25.6:1:31.5:1:1:0:59.9:53.917:0.9969:0:1.1 1/1:655:629:228,401:7,18:25,629:0.9603:2,2:26.7:1:30.1:1:0.52482:1.46:60:43.929:0.9594:0:1.2 +1 45796354 . G T 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTTGGCCAGGCATGGTG;RSEQ=CTCACGCCTATAATCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:1,107:108,0:0:1,0:22.8:1:32.8:1:1:0:57.6:107:1:0:0.4 0/1:66:21:1,20:0,44:44,21:0.3182:1,1:20.7:1:28.8:1:0.32308:0:58.1:20:0.3077:0:1.5 +1 45797505 . C G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=5.77543;LSEQ=GGAGGCAGGCACAGGTGGCA;RSEQ=TGTCCAGTGTTGGGAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:39:17,22:341,389:730,39:0.0506:2,2:29.5:1:33.2:1:0.74408:1.13425:60:78:0.0514:0:1.2 0/1:806:190:81,109:286,329:615,190:0.2357:2,2:26.2:1:31.3:1:0.36042:1.16957:60:94:0.238:0:1.2 +1 45798555 . T C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09055;LSEQ=TCACCCGTCAGTCCCTCTAT;RSEQ=GTTCCTATTTCCCCTACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:852:849:371,478:1,1:2,849:0.9965:2,2:24.2:1:30.9:1:1:1.28801:59.9:83.9:0.9964:0:1.1 1/1:958:922:388,534:18,17:35,922:0.9624:2,2:24.1:1:29.8:1:0.29837:1.45664:59.9:114.25:0.9621:0:1.2 +1 45798717 . G T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11204;SOR=Inf;LSEQ=ACACCCACCCCAAAGTAGAG;RSEQ=CTCTCATCTGGGGTCTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:187,130:317,0:0:2,0:24.1:1:31.5:1:1:0:60:78.25:1:0:0.1 0/1:297:3:2,1:164,129:293,3:0.0101:2,2:29.7:1:24.7:1:1:1.57:60:2:0.0069:0:1.3 +1 45798742 . A T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19915;SOR=4.387;LSEQ=CATCTGGGGTCTGACCCATG;RSEQ=CCCTTCCCTTCCTCCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:1:0,1:246,165:411,1:0.0024:2,0:1:0:26:0:0.40291:0:60:2:0.0025:0:1 0/1:379:4:1,3:223,151:374,4:0.0106:2,2:13.5:1:26.3:1:0.30858:4.4136:60:8:0.0107:0:1.5 +1 45798981 . C A 145 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02822;LSEQ=ATATGCCCGCCTGTCCAGGT;RSEQ=CATCTCATCTTCTGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:879:32:21,11:438,408:846,32:0.0364:2,2:21.5:1:29:1:0.14967:1.78:60:64:0.037:0:1.3 0/0:939:1:1,0:486,452:938,1:0.0011:2,0:1:0:21:0:1:0:60:2:0.0011:0:1 +1 45799280 . G A 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09076;SOR=0;LSEQ=ATCATCCCTGCACAGGCTGT;RSEQ=CATCAGGGTCTTGGGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:3:2,1:43,177:220,3:0.0135:2,2:8.7:1:27:1:0.10442:8.12:60:6:0.0135:0:1 0/0:272:0:0,0:74,198:272,0:0:2,0:23:1:31.2:1:1:0:60:67:1:0:0.2 +1 45799302 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.99576;LSEQ=ATCAGGGTCTTGGGACACAG;RSEQ=AGCCTGTGGCAGTATGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:0,1:23,132:155,1:0.0064:2,0:28:0:11:0:1:0:60:0:0:0:5 0/1:158:2:1,1:22,134:156,2:0.0127:2,2:14:1:27.5:1:0.27074:5.98:60:4:0.0129:0:1 +1 45799337 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50437;SOR=0;LSEQ=TGCTCCCACTTAGGGCTTCC;RSEQ=CCAACTAACCCCCTTAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:5,74:79,2:0.0247:2,2:25.5:1:29.5:1:0.14352:13.60:60:4:0.025:0:1 0/0:63:0:0,0:4,59:63,0:0:2,0:22.1:1:30.4:1:1:0:60:62:1:0:0.1 +1 45800156 . C T 204 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCTGTGACCACTTCCCA;RSEQ=GGCTGCTCGTGGCTTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:912:0:0,0:382,530:912,0:0:2,0:26.1:1:30.8:1:1:0:60:227:1:0:0.1 0/1:958:130:56,74:366,457:823,130:0.1357:2,2:27:1:29.1:1:0.77662:1.05825:60:42.333:0.1338:0:1.1 +1 45805566 . G C 91 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=1;SOR=0;LSEQ=ACCCAGCCACCCCACTACCC;RSEQ=CTACCCGCGGCCCACGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:18.4:1:32.6:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 45805796 . C T 39 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24892;SOR=Inf;LSEQ=CCGGACCCGGGACGTCTGAA;RSEQ=GGAAGTTCGACCCATCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:222,43:265,0:0:2,0:23.3:1:31.8:1:1:0:59.9:43.167:1:0:0.1 0/1:276:3:1,2:216,57:273,3:0.0109:2,2:6.3:1:25:1:0.1165:7.50362:60:6:0.011:0:1 +1 45805826 . C T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06377;SOR=Inf;LSEQ=ACCCATCGGCGACCCGACGG;RSEQ=GAGACCCCGCCCCATCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:304,137:441,0:0:2,0:24.8:1:31.1:1:1:0:60:62:1:0:0.1 0/1:493:5:1,4:322,166:488,5:0.0101:2,2:9.8:1:26.8:1:0.05031:7.72678:58.6:10:0.0102:0:1 +1 46509146 . G A 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01087;SOR=0;LSEQ=GCTTAGTATGTCAGTGCAGC;RSEQ=GCATGGCTGAGTCCTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:31.2:1:31.2:1:1:0:55:10:0.4545:0:1 0/0:13:0:0,0:12,1:13,0:0:1,0:23.5:1:30.2:1:1:0:60:26:1:0:0.2 +1 46511487 . G C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08557;SOR=1.79315;LSEQ=GGTCCGAGCCATGGGTCCTC;RSEQ=TTACTGTACATTAACTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:43:43,0:49,1:50,43:0.4574:1,1:23.6:1:31.3:1:1:0:60:20.5:0.4505:0:1.2 1/0:73:44:42,2:28,1:29,44:0.6027:1,1:19.1:1:31:1:1:1.32826:60:88:0.6027:0:1.1 +1 46511981 . T G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90275;LSEQ=TGAATAAAAGTGCTTTTACA;RSEQ=CCAGATTTTGGGTAGCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:20:15,5:7,2:9,20:0.6897:2,2:24.2:1:34.5:1:1:1.16055:58.9:40:0.6897:0:1.1 1/0:6:4:3,1:0,2:2,4:0.6667:0,2:22:1:33:1:0.4:0:60:8:0.6667:0:1 +1 46512162 . AAGGCGCATGTCTTATATTGATAACAAAGCCCTCTGACAGAAAGGTAT A 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATATTTACCACGTATAAAC;RSEQ=AGAGAGAACTTACTCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:325,124:449,0:0:2,0:23.1:1:30.4:1:1:0:60:43.9:1:0:0.1 0/1:559:41:24,17:344,174:518,41:0.0733:2,2:24.2:1:29.5:1:0.30932:1.39956:58.7:82:0.0741:0.0215:0.3 +1 46521517 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00169;SOR=1.31902;LSEQ=TGGATCAGGTCAGGTTTGAT;RSEQ=CTATTCATTTTTTTATCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1011:499:254,245:256,256:512,499:0.4936:2,2:22.9:1:29.1:1:0.80142:1.04:60:70.286:0.492:0:1.7 1/0:1104:621:330,291:259,222:481,621:0.5625:2,2:26:1:28:1:0.85509:1.02877:60:102.5:0.5616:0:1.8 +1 46521559 . A T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.63532;LSEQ=TCTCGGTTGTCCAAAGCTTG;RSEQ=TTCTTCAAATCCTGCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:905:446:211,235:203,256:459,446:0.4928:2,2:26.7:1:30.2:1:0.38568:1.13:60:222:0.495:0:1.8 1/0:1072:658:312,346:190,221:411,658:0.6138:2,2:24.9:1:29.1:1:0.75283:1.05:60:130.6:0.616:0:1.7 +1 46521724 . CT C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.70688;SOR=0.81396;LSEQ=GTGAGCACGGTCCTAATATC;RSEQ=TTTTTTTTTTCCCTTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:25:1,24:1,45:46,25:0.3378:1,1:31.6:1:33.1:1:1:1.86:57.1:50:0.3521:0:0.2 0/1:58:17:0,17:2,37:39,17:0.2931:2,1:21.6:1:31.7:1:1:0:56.4:34:0.2982:0.0345:0.2 +1 46521792 . G A 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6951;SOR=1.56986;LSEQ=GAGTGTAGTGGCATGATCTC;RSEQ=GCTCACTGCAACCTCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:0,6:0,8:8,6:0.4286:0,0:15:1:32.7:1:1:0:37.5:12:0.4286:0:1 1/0:11:6:0,6:0,5:5,6:0.5455:0,0:17.2:1:31.7:1:1:0:40.3:12:0.5455:0:1.3 +1 46521882 . C T 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=ACAGGCGCATGCCACCACAC;RSEQ=CGGCTAATTTTTGTATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:4,0:0:0,0:20.5:1:30.5:1:1:0:29:8:1:0:0.3 1/0:4:2:1,1:0,2:2,2:0.5:0,2:12:0:31:1:1:0:52.5:4:0.5:0:1.5 +1 46527300 . G A 59 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0.17288;LSEQ=ACACTAGGGATCAGGACCAG;RSEQ=CACTGTAGGGACCCAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:27.3:1:29.5:1:1:0:60:8:0.8:0:1 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:16:0:30:0:1:0:60:2:0.3333:0:1 +1 46527505 . C T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24929;SOR=0;LSEQ=GTTCCAATAGTAGGGCTGTG;RSEQ=AGTTTGAGGGGGTAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:3:3,0:124,10:134,3:0.0219:2,0:27.3:1:25.3:1:1:0:60:2:0.015:0:1 0/0:123:0:0,0:115,8:123,0:0:2,0:24.6:1:31.5:1:1:0:60:60.5:1:0:0.1 +1 46531652 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TAAAACAGCTAAAGATCATC;RSEQ=AGTGAATGATCGAAAATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:154,16:170,0:0:2,0:25.2:1:30.8:1:1:0:60:84:0.9941:0:0.1 0/1:190:2:1,1:167,21:188,2:0.0105:2,2:23.5:1:29:1:0.21871:7.79259:60:4:0.0106:0:1.5 +1 46532354 . C T 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=2.31595;LSEQ=GCACCTGTGATCCCAGCTAC;RSEQ=GGGGAGGCTGAGGCAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:15:0:34:0:1:0:60:2:0.1667:0:2 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:15:1:27.5:1:0.33333:0:59:4:0.4:0:1 +1 46532407 . G A 36 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47633;LSEQ=CAGAAGGTCAAGACTGCAGT;RSEQ=AGCCATATTCATGCCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:12,0:12,3:0.2:0,0:29.7:1:30:0:1:0:60:6:0.2:0:1.3 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:31.7:1:23:1:1:0:60:2:0.2:0:1.3 +1 46543047 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16531;SOR=Inf;LSEQ=TGTATAGAAAAAAGAATTAG;RSEQ=CAGACTGGAAATTATGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:80,1:81,0:0:1,0:25.1:1:32.3:1:1:0:60:39.5:1:0:0.1 0/1:56:2:2,0:54,0:54,2:0.0357:1,0:18:1:31:0:1:0:60:4:0.037:0:1 +1 46546208 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00116;SOR=3.25697;LSEQ=CTCCTGAGTTGCTGGGATTA;RSEQ=AGGCATGAGCCACCATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:12:12,0:85,1:86,12:0.1224:1,0:26.6:1:32.5:1:1:0:60:24:0.1224:0:1 0/1:102:32:32,0:69,1:70,32:0.3137:1,1:21.2:1:32.2:1:1:0:60:64:0.3137:0:1.1 +1 46546852 . T G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTAACTATGAAATGATGG;RSEQ=TATGTTATTAATAATTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:16.7:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 46597496 . CT C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.81139;SOR=0.94045;LSEQ=ATCAGACCCATCACGAGATT;RSEQ=TTTTTTTTTTCTCCCAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:35:28,7:189,63:252,35:0.1211:2,2:24.2:1:32.6:1:0.67497:1.33:59.8:70:0.1241:0.0208:0.3 0/1:401:46:35,11:268,86:354,46:0.1147:2,2:20.9:1:31.1:1:1:1.02:59.9:45:0.1134:0.0299:0.2 +1 46598253 . G A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00959;SOR=Inf;LSEQ=CTTGTCTGGGCGCTCCCGCC;RSEQ=GGGTGTAAGAACCAACCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:147,22:169,0:0:2,0:22.4:1:29.7:1:1:0:60:83.5:1:0:0.7 0/1:147:6:4,2:119,21:140,6:0.0408:2,2:14.3:1:28.3:1:0.23951:2.8064:60:12:0.0408:0:1 +1 46598269 . C A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=2.63808;LSEQ=CGCCGGGGTGTAAGAACCAA;RSEQ=CCGACCGCACCAACTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:33:30,3:136,36:172,33:0.161:2,2:24.7:1:29.4:1:0.14721:2.64:60:32:0.16:0:2.1 0/1:205:69:58,11:105,31:136,69:0.3366:2,2:24.1:1:29.8:1:0.27731:1.55:60:138:0.3382:0:2 +1 46598273 . A C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00108;SOR=1.90499;LSEQ=GGGGTGTAAGAACCAACCCG;RSEQ=CCGCACCAACTGCCCTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:110:87,23:88,25:113,110:0.4933:2,2:23.9:1:32.1:1:0.87142:1.07:60:220:0.4955:0:1.4 1/0:220:143:110,33:58,19:77,143:0.65:2,2:24.3:1:31.5:1:0.8681:1.09:60:142:0.6514:0:1.6 +1 46598520 . TC T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12764;SOR=Inf;LSEQ=TCCATCTCGACTTTCACGTC;RSEQ=CCCACCGCTCTCTAGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:45,271:316,0:0:2,0:22.9:1:31.3:1:1:0:60:78:1:0:0.1 0/1:364:4:3,1:73,285:358,4:0.011:2,2:13.3:1:26.3:1:0.03039:11.60:60:8:0.0112:0.0055:0.5 +1 46641741 . A G 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATTTTTAGTAGAGATGGG;RSEQ=TTTCACCGTGTTAGCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:17,0:17,4:0.1905:1,0:16:1:30:1:1:0:25.3:8:0.2:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:19:0:23:0:1:0:38:2:1:0:0 +1 46641827 . A G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2982;SOR=0.62437;LSEQ=AAAGTGCCGGGATTACAGGC;RSEQ=TGAGCCACCGCACCCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:16:16,0:107,6:113,16:0.124:2,1:28.6:1:30.9:1:1:0:48.9:15:0.119:0:2 0/1:111:9:8,1:96,6:102,9:0.0811:2,2:22.6:1:30.8:1:0.45627:1.98404:55.8:18:0.0826:0:1 +1 46641837 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.86436;SOR=1.10312;LSEQ=GATTACAGGCATGAGCCACC;RSEQ=CACCCAGCCTAGTGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:20:20,0:136,15:151,20:0.117:2,1:29:1:31:1:0.22153:0:51.2:19:0.1138:0:1.8 0/1:149:19:15,4:114,16:130,19:0.1275:2,2:20.1:1:28.9:1:0.28912:1.8904:56.6:18:0.1241:0:1.2 +1 46641839 . A G 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50008;SOR=0;LSEQ=TTACAGGCATGAGCCACCGC;RSEQ=CCCAGCCTAGTGGCTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:162,17:179,2:0.011:2,2:6.5:1:31.5:1:0.1895:9.28947:60:4:0.0114:0:1.5 0/0:162:0:0,0:139,23:162,0:0:2,0:21.5:1:29.3:1:1:0:56.5:80:1:0:0.3 +1 46641869 . C T 59 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21704;SOR=4.95219;LSEQ=GTGGCTCTGTTTTTTAAAAC;RSEQ=CCACCCTGGCTCACAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:1:0,1:285,96:381,1:0.0026:2,0:1:0:26:0:0.25393:0:60:2:0.0027:0:1 0/1:389:5:1,4:267,117:384,5:0.0129:2,2:5.8:1:25.8:1:0.03422:9.07337:60:10:0.0133:0:1.2 +1 46714305 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25076;SOR=Inf;LSEQ=GGACAGGGAAGGTGGGTAGA;RSEQ=CTGTTTGGACAGAAAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:84,186:270,0:0:2,0:23.3:1:32.4:1:1:0:60:66.5:1:0:0.1 0/1:300:3:1,2:102,195:297,3:0.01:2,2:18.3:1:28.3:1:1:1.046:60:6:0.0101:0:1 +1 46715874 . C CA 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90899;LSEQ=CCTGTCCCTGTACACTCCCT;RSEQ=AGTGCTTTCTAGAGTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:9:1,8:6,119:125,9:0.0672:1,2:16.7:1:28.7:1:0.39247:2.46:60:8:0.063:0.0299:0.2 0/1:114:7:0,7:5,102:107,7:0.0614:1,0:23.7:1:29.3:1:1:0:60:6:0.055:0:0 +1 46725447 . CA C 86 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.69387;SOR=1.64341;LSEQ=AACAAAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAGCTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:6,0:20,0:20,6:0.2308:1,0:17.5:1:33.3:1:1:0:58.2:12:0.2308:0.0385:0 0/1:12:4:4,0:6,0:6,4:0.3333:0,0:19.3:1:31.5:1:1:0:51.5:8:0.3333:0.0833:1 +1 46725941 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8242;LSEQ=AGAGCCTGTGGTCATGTCCA;RSEQ=TGAGTGGGCATTCCTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:13:2,11:5,11:16,13:0.4483:2,2:36:1:31.5:1:0.40996:2.42412:56.3:26:0.4483:0:1.2 0/1:15:6:1,5:0,9:9,6:0.4:0,2:12.5:1:31:1:0.4:0:60:12:0.4:0:1 +1 46726057 . A C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00109;SOR=0.12427;LSEQ=GAGCTAACTTTCTAACTCCT;RSEQ=AAGTAGGAACTTGCTATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:17:14,3:16,1:17,17:0.5:1,2:28.5:1:32.3:1:0.60117:3.31312:58.8:34:0.5152:0:1 0/1:28:3:3,0:25,0:25,3:0.1071:1,0:27:1:32.7:1:1:0:60:6:0.1071:0:1 +1 46726134 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22383;SOR=Inf;LSEQ=CAGCTGCCTCTGTTGCCTCC;RSEQ=GATCAGCAGGACACAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:162,28:190,0:0:2,0:25.5:1:29.9:1:1:0:60:46.5:1:0:0.1 0/1:172:2:1,1:140,30:170,2:0.0116:2,2:43:0:31:1:0.32885:4.60717:60:4:0.0119:0:1.5 +1 46726747 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23573;SOR=0;LSEQ=AGCCTGCTGCTTTCTTACGT;RSEQ=TATGCTCATTTATGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:27,114:141,2:0.014:2,2:8:1:28:1:0.35438:4.16:60:4:0.0144:0:1 0/0:151:0:0,0:37,114:151,0:0:2,0:21.9:1:31.5:1:1:0:60:150:1:0:0.1 +1 46726784 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.6027;SOR=2.26122;LSEQ=CAGGGTGGAGGGCAATGCAG;RSEQ=GGTAGAAGAAAAGAGAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:1,0:46,72:118,1:0.0084:2,0:14:0:32:0:0.39496:0:60:2:0.0085:0:1 0/1:106:2:0,2:47,57:104,2:0.0189:2,0:17.5:1:28.5:1:0.50171:0:60:4:0.019:0:2.5 +1 46727122 . G A 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20617;SOR=Inf;LSEQ=AAATCTCTTCACTGAGTATT;RSEQ=CCTTCCAAGGGCTGTGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:19,185:204,0:0:2,0:21.1:1:32.3:1:1:0:60:50:0.995:0:0 0/1:171:2:2,0:18,151:169,2:0.0117:2,0:18:1:23:1:0.01307:0:60:4:0.0118:0:1 +1 46732948 . C G 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03845;SOR=11.51618;LSEQ=GTTTCACCACACTGGCCAGG;RSEQ=TGGTCTGGAACTCCTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:1,0:37,0:37,1:0.0263:1,0:3:0:29:0:1:0:42:2:0.027:0:1 0/1:12:3:3,0:9,0:9,3:0.25:0,0:39.7:1:29.3:1:1:0:60:6:0.25:0:1 +1 46736508 . C A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24872;SOR=0;LSEQ=GCCTCCCAAACCATCCATGG;RSEQ=CAATCCTTTGGGGGCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:2,1:30,141:171,3:0.0172:2,2:23:1:29.7:1:0.08737:9.22:60:6:0.0175:0:1.3 0/0:162:0:0,0:44,118:162,0:0:2,0:22.3:1:30.4:1:1:0:60:53:1:0:0.1 +1 46738046 . G T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49846;SOR=0;LSEQ=ATTTAATACTGTAAAAGAGG;RSEQ=CTAGTCTTGGTCCTTTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:149,12:161,2:0.0123:2,2:20.5:1:25.5:1:0.1536:11.96969:60:4:0.0124:0:1 0/0:162:0:0,0:145,17:162,0:0:2,0:21.4:1:30.3:1:1:0:60:31.4:1:0:0.1 +1 46739188 . AT A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.81267;SOR=0.81194;LSEQ=CTCTAGGAGGAGGGTGGGAG;RSEQ=TTTTTTTTGTGCTAGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:10:3,7:146,269:415,10:0.0235:2,2:30.3:1:32:1:1:1.26577:60:20:0.0239:0.0024:0.3 0/1:417:8:6,2:159,250:409,8:0.0192:2,2:17.3:1:30:1:0.0626:4.70:59.4:16:0.0194:0:0.3 +1 46739286 . C T 69 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01703;SOR=Inf;LSEQ=TAGGGGACTGCTGGTTGCTG;RSEQ=TCTTCCCAGGTAAGATGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:0:0,0:290,255:545,0:0:2,0:24.9:1:32.2:1:1:0:60:48.545:1:0:0.1 0/1:629:7:2,5:350,272:622,7:0.0111:2,2:12.4:1:24.7:1:0.24992:3.21115:60:6:0.0097:0:1 +1 46739464 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.165;SOR=Inf;LSEQ=CCAAAGGGGGATATACCCCT;RSEQ=CCCTACTGTCTGTCTAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:26,156:182,0:0:2,0:23.2:1:31.3:1:1:0:60:59.667:1:0:0.1 0/1:125:2:1,1:13,110:123,2:0.016:2,2:10.5:1:26:1:0.21226:8.19:60:4:0.0163:0:1 +1 46739751 . A AT 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.12411;SOR=Inf;LSEQ=TAAAAAAATTTTTATTTTTA;RSEQ=TTTTTTTTCCCCCTAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:230,67:297,0:0:2,0:22.3:1:30:1:1:0:59.8:32:1:0:0.2 0/1:310:4:3,1:234,72:306,4:0.0129:2,2:13.3:1:29.8:1:1:1.08306:60:8:0.0132:0.0032:1 +1 46740131 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24184;SOR=Inf;LSEQ=TGAGTAGTATAGAGGCATGA;RSEQ=GGAGGAGCTGGTTGGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:122,48:170,0:0:2,0:23:1:32.6:1:1:0:59.8:55.667:1:0:0.1 0/1:165:2:1,1:122,40:162,2:0.0121:2,2:13:0:32:1:0.43865:3.02487:60:4:0.0121:0:1.5 +1 46740458 . C A 55 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02701;SOR=Inf;LSEQ=TCTTCAGGACCATCTTGTTC;RSEQ=TTAGTGCCTCTCTTTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:25,154:179,0:0:2,0:22.5:1:32.8:1:1:0:60:88.5:1:0:0.2 0/1:171:5:3,2:29,137:166,5:0.0292:2,2:10:1:23.8:1:0.04594:6.97:60:4:0.0241:0:1.4 +1 46740500 . A G 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00714;SOR=0;LSEQ=TCTGCCTCTAGCAGTAGCCA;RSEQ=GCTATGGGCCCAGAAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:8:0,8:0,78:78,8:0.093:1,0:32.8:1:32.8:1:1:0:60:16:0.0941:0:1 0/0:77:0:0,0:0,77:77,0:0:1,0:23.5:1:31.6:1:1:0:59.9:154:1:0:0 +1 46743451 . G A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06118;SOR=Inf;LSEQ=TTTTATGAGGATGGCTAAGC;RSEQ=CTGTATCTTTTGACATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:183,53:236,0:0:2,0:24.5:1:30.2:1:1:0:60:58:1:0:0.1 0/1:237:5:3,2:159,72:231,5:0.0211:2,2:29.4:1:30.2:1:0.65004:1.46968:60:10:0.0216:0:1 +1 46743900 . C T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38363;LSEQ=TGGGATGCTGCCTCCACTGC;RSEQ=ATCACCTTCGTCTTCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:299:124,175:150,200:350,299:0.4607:2,2:26.1:1:29.9:1:0.75007:1.05835:60:148.5:0.4633:0:1.1 0/1:835:206:96,110:276,353:629,206:0.2467:2,2:24.1:1:28.5:1:0.51864:1.12:59.8:50.5:0.2469:0:1.3 +1 46743923 . G A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCTTCGTCTTCCACCAGC;RSEQ=TTCTCATGAGGAGCAGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:0:0,0:201,321:522,0:0:2,0:25.2:1:31:1:1:0:60:86:1:0:0.5 0/1:646:29:13,16:237,380:617,29:0.0449:2,2:22:1:30.1:1:0.55945:1.30:58.5:58:0.0453:0:2.2 +1 46743991 . A T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50055;SOR=Inf;LSEQ=GTGTAGCTCTTAGAGGAAGG;RSEQ=GATAGGGAAAAGGGGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:19,145:164,0:0:2,0:22:1:31.4:1:1:0:60:40:1:0:0.2 0/1:186:2:1,1:32,152:184,2:0.0108:2,2:5.5:1:26.5:1:0.32415:4.69:60:4:0.011:0:2.5 +1 47882266 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49123;SOR=0;LSEQ=GCCCCGGGCCGCCGCCTCAC;RSEQ=CTGGCCGCCATCTACCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:25,2:27,2:0.069:2,2:26.5:1:30.5:1:0.19951:10.40842:60:4:0.0714:0:1 0/0:28:0:0,0:21,7:28,0:0:2,0:26.2:1:28.9:1:1:0:60:13:1:0:0 +1 47882385 . C A 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56877;SOR=2.92725;LSEQ=CGACTGCTTCGTCAAGGTGC;RSEQ=CCGCGAGCCGGGCAACCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:1:1,0:71,76:147,1:0.0068:2,0:1:0:26:0:0.48649:0:60:2:0.0068:0:1 0/1:102:2:1,1:47,53:100,2:0.0196:2,2:28:1:25.5:1:1:1.13:49.5:4:0.0204:0:1 +1 47882410 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52141;SOR=0;LSEQ=GAGCCGGGCAACCCGGGCAA;RSEQ=GGCAACTACTGGACGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:60,90:150,2:0.0132:2,2:31:0:32.5:1:1:1.50:31:4:0.0134:0:1.5 0/0:98:0:0,0:40,57:97,0:0:2,0:26.8:1:30.6:1:1:0:51.4:96:0.9897:0:0.2 +1 47882412 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52429;SOR=0;LSEQ=GCCGGGCAACCCGGGCAAGG;RSEQ=CAACTACTGGACGCTGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:59,92:151,2:0.0131:2,2:12:1:30:1:1:1.55:60:4:0.0135:0:1.5 0/0:96:0:0,0:39,56:95,0:0:2,0:26.9:1:30.7:1:1:0:51.2:46.5:0.9894:0:0.1 +1 47882441 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87017;LSEQ=GGACGCTGGACCCCGCGGCC;RSEQ=CAGACATGTTCGACAACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:34,86:120,2:0.0164:2,2:9.5:1:29.5:1:0.49316:2.51:36.5:4:0.0168:0:1 0/1:70:1:1,0:20,49:69,1:0.0143:2,0:1:0:23:0:0.3:0:37:2:0.0147:0:1 +1 47882497 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84536;LSEQ=CGCAAGCGCTTCAAGCGCGC;RSEQ=GAGCTGCCCGCGCACGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:19:0,19:1,7:8,19:0.7037:2,1:17.7:1:30.9:1:0.2963:0:60:18:0.6923:0:1.1 1/0:18:12:1,11:0,6:6,12:0.6667:0,2:19.2:1:29.8:1:1:0:60:24:0.6667:0:1 +1 47883019 . T C 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGCCGCCCTCGAGCGCCCCA;RSEQ=CTCTACCCCCCACCCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 47883024 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCGAGCGCCCCATCTCT;RSEQ=CCCCCCACCCTGGCTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:32.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 47903961 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCGCCCCCCGGGACGTG;RSEQ=TCCCCCACGGCCACGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:28.5:1:1:0:60:4:1:0:1 +1 47904190 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49606;SOR=0;LSEQ=GCGGAGCCCGCTGGTGAAGC;RSEQ=GCCCTACTCGTACATCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:45,17:62,2:0.0313:2,2:23.5:1:29.5:1:0.48661:2.60091:60:4:0.0317:0:1 0/0:63:0:0,0:43,20:63,0:0:2,0:23.3:1:30.2:1:1:0:50.8:30.5:1:0:0.3 +1 47904651 . C A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16304;SOR=Inf;LSEQ=CGGCCTACGGCGCACCCCCG;RSEQ=CGGGGCCGGCCCCGCATCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,7:13,0:0:2,0:24.2:1:31.6:1:1:0:58.8:26:0.9286:0:0.2 0/1:10:2:1,1:4,4:8,2:0.2:2,2:5.5:1:25:1:1:1:60:4:0.2222:0:1 +1 47904668 . T TCCGCAC 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=4.000;MSILEN=6;SSF=1;SOR=1.39711;LSEQ=CCGCCGGGGCCGGCCCCGCA;RSEQ=CCGCACCCGCACCCGCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:17:7,10:2,0:2,17:0.8947:0,2:23.8:1:31.6:1:0.21053:0:57.8:34:0.8947:0.2632:0.8 1/1:13:12:5,7:1,0:1,12:0.9231:0,2:20.7:1:27.9:1:0.46154:0:60:24:0.9231:0.2308:0.5 +1 47904682 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.49621;SOR=0;LSEQ=CCCGCATCCGCACCCGCACC;RSEQ=GCACGCCTTCGCTTTCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:19.5:1:31:1:1:1.40:60:4:0.1053:0:2.5 0/0:14:0:0,0:6,8:14,0:0:2,0:25.8:1:28.1:1:1:0:60:13:1:0:0.5 +1 47906425 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGATGGGGCTCTCCCAGAA;RSEQ=AGCTTAGCTCCCCAACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 47963691 . G GT 70 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CCCAGGTACCTTTCTCTTTG;RSEQ=TTCCTTCTTTTCCTGATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:14.6:1:30.3:1:1:0:56.4:10:1:0.6:0 1/0:6:4:3,1:1,1:2,4:0.6667:2,2:26.5:1:28.8:1:1:2.45:52.8:8:0.6667:0:0 +1 47963973 . G A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16256;SOR=0;LSEQ=TGTTTCCTAAAAGGCCTAGA;RSEQ=AATATGTATCAGGTGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:5,12:0,0:0,17:1:0,2:25.8:1:30.8:1:1:0:55.8:34:1:0:1.1 1/1:12:10:4,6:1,1:2,10:0.8333:2,2:21.1:1:29.6:1:1:1.4491:60:20:0.8333:0:1.2 +1 48909353 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49753;SOR=Inf;LSEQ=GATAGTATGAGATGCCACCC;RSEQ=GCGTTTACAGGAAAAGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:26,11:37,0:0:2,0:21.7:1:29.9:1:1:0:53.4:36:1:0:0.1 0/1:44:2:1,1:30,12:42,2:0.0455:2,2:27.5:1:29:1:0.50846:2.44164:24:4:0.0455:0:1 +1 48909415 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=CAAACTCTTATAACAACCTC;RSEQ=GGAGTTGGGCGACATGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:55,59:114,2:0.0172:2,2:24:1:28:1:1:1.07:51:4:0.0174:0:1 0/0:106:0:0,0:52,54:106,0:0:2,0:27.8:1:29.4:1:1:0:56.5:34.333:1:0:0.2 +1 48909461 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49804;SOR=0;LSEQ=CTTTCTAGGTCCCGTGACAG;RSEQ=CATCTTGCTATTACTCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:29,40:69,2:0.0282:2,2:25.5:1:28.5:1:1:1.37:29:4:0.0299:0:1.5 0/0:63:0:0,0:22,41:63,0:0:2,0:22.6:1:30.4:1:1:0:52.9:62:1:0:0.1 +1 48963214 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1985;SOR=0;LSEQ=ACAGCATGCCTGGTGACACT;RSEQ=TAGACTCTTCCAGTTTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:32,34:66,2:0.0294:2,2:40.5:1:30.5:1:1:1.06:60:4:0.0294:0:1.5 0/0:84:0:0,0:47,37:84,0:0:2,0:33.3:1:31.8:1:1:0:55.7:168:1:0:0.9 +1 48963247 . A G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTAGCCATGGTGACATTT;RSEQ=TGGGGCATTCCTTTTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:60:26,34:0,0:0,60:1:0,2:23.1:1:32.3:1:1:0:56.7:59:1:0:1 1/1:78:78:38,40:0,0:0,78:1:0,2:20.4:1:30.5:1:1:0:55.4:38:1:0:1.1 +1 48963298 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21168;SOR=Inf;LSEQ=CCCTTGATGTCTAGAATAGC;RSEQ=CCTTTCTTGTAGATTCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:17,27:44,0:0:2,0:22.9:1:30.2:1:1:0:59.3:13.667:1:0:0.5 0/1:38:2:1,1:12,24:36,2:0.0526:2,2:43:1:29:1:1:1.96:60:4:0.0541:0:1.5 +1 48963394 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2389;SOR=Inf;LSEQ=CAGGTGCCTCTCCTCTTTCC;RSEQ=TTTGTCTGCGTCATTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:33,24:57,0:0:2,0:20.6:1:31.4:1:1:0:60:27.5:1:0:0.2 0/1:55:2:1,1:30,23:53,2:0.0364:2,2:21.5:1:28:1:1:1.29798:60:4:0.0364:0:1 +1 48963398 . G A 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.10321;LSEQ=TGCCTCTCCTCTTTCCCTTT;RSEQ=TCTGCGTCATTTTGGCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:5,2:31,21:52,7:0.1167:2,2:23.9:1:29.9:1:0.69421:1.68:60:14:0.1186:0:1 0/1:55:7:3,4:28,20:48,7:0.1273:2,2:26.3:1:27.6:1:0.68617:1.84516:52.3:14:0.1273:0:1.3 +1 48963432 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.56505;LSEQ=GGCAAATTACTGGAAGATGG;RSEQ=AGTTCCAGCCAAAAGGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:31,32:63,2:0.0308:2,2:41.5:1:29:1:1:1.03:60:4:0.0317:0:1 0/1:57:1:0,1:29,27:56,1:0.0175:2,0:8:0:29:0:0.49123:0:60:2:0.0175:0:1 +1 48963511 . T C 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2881;SOR=0;LSEQ=GTTCAGAACTCTACCAGGAG;RSEQ=TGTACAAGAGCTTAGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:20,3:0.1304:1,0:21.3:1:35.3:1:1:0:60:6:0.1364:0:1 0/0:13:0:0,0:0,13:13,0:0:1,0:21.3:1:30.4:1:1:0:60:26:1:0:0 +1 48965535 . TAAAC T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCAGATGCATTTCGCTAA;RSEQ=AAGCATTGCAGCCAGCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 50870454 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAGCCGGGACCACAGGCAC;RSEQ=CGACACCACACCCGGCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:33:1:1:0:60:4:1:0:1 +1 50871167 . C T 61 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTATGGTTAGAAATGTA;RSEQ=ATGATAGGAACTCCAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:28.3:1:30.5:1:1:0:54.8:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 50871536 . T C 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03714;SOR=8.14923;LSEQ=TATTATATTGGAAAAATAAG;RSEQ=GGGAAGGGTGTTGGGGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:20:1,19:0,13:13,20:0.6061:1,1:28.1:1:28.8:1:1:0:40.4:19:0.5938:0:1.7 1/1:14:13:0,13:0,1:1,13:0.9286:0,1:27.8:1:27.5:1:1:0:39:12:0.9231:0:1.9 +1 50871575 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05806;SOR=8.22261;LSEQ=CTTCCCTTTCCTTTAATGTG;RSEQ=TGGGATCCTTCTTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:14:0,14:0,11:11,14:0.56:0,1:23.4:1:33.9:1:1:0:43:28:0.56:0:2.1 1/1:12:11:0,11:0,1:1,11:0.9167:0,0:23.7:1:30.9:1:1:0:39.5:22:0.9167:0:2.3 +1 50871649 . G C 60 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGATCTCTGAGACTAAG;RSEQ=ATTTGCTTCATGGTTGCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:13.8:1:34:0:1:0:35.8:8:1:0:1.3 1/1:4:4:0,4:0,0:0,4:1:0,0:28:1:30:1:1:0:48.3:8:1:0:1.5 +1 51434327 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49576;SOR=Inf;LSEQ=AGCAGGGCGGAGGGCGGGGC;RSEQ=TGGGCGGCGCCCGGCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:46,2:48,0:0:1,0:16.9:1:30:1:1:0:60:23:1:0:0.2 0/1:52:2:1,1:43,7:50,2:0.0385:2,2:12:1:27:0:0.28658:5.81258:60:4:0.04:0:1 +1 51434373 . C A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18889;SOR=0;LSEQ=CCGCGGCGCTGCAACTCTGC;RSEQ=GAGCCTCCTTAAAACTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:130,43:173,2:0.0114:2,2:34:0:33:1:0.44072:3.00017:60:4:0.0115:0:1 0/0:227:0:0,0:163,64:227,0:0:2,0:24.1:1:29.7:1:1:0:59.9:27.375:1:0:0.2 +1 51434393 . C T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.38227;SOR=3.38626;LSEQ=CGAGCCTCCTTAAAACTCTG;RSEQ=CGTTAAAATGGGGGCGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:1:0,1:185,83:268,1:0.0037:2,0:1:0:25:0:0.31227:0:60:2:0.0038:0:1 0/1:320:4:1,3:222,94:316,4:0.0125:2,2:12.5:1:26:1:0.08476:7.0371:60:8:0.0129:0:1 +1 51434469 . GA G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.78738;SOR=0.77585;LSEQ=AAAAAAAGCTGATGAGGTCG;RSEQ=AAAAAGGGAGAAGAAACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:7:4,3:214,187:401,7:0.0172:2,2:26.4:1:30.9:1:1:1.16:60:14:0.0174:0.0049:0 0/1:524:7:4,3:267,249:516,7:0.0134:2,2:31.3:1:30.6:1:1:1.24:60:14:0.0136:0:0 +1 51434554 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13509;SOR=Inf;LSEQ=AAAAAGCAGCAAGGGAGGGA;RSEQ=TGAAGGAAAAAAGCAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:38,135:173,0:0:2,0:22.5:1:32.1:1:1:0:60:33.6:1:0:0.1 0/1:223:4:3,1:52,167:219,4:0.0179:2,2:16.3:1:26.8:1:0.04735:9.51:60:8:0.0181:0:1 +1 51434560 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.5033;SOR=Inf;LSEQ=CAGCAAGGGAGGGAGTGAAG;RSEQ=AAAAAAGCAAAAAAGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:31,127:158,0:0:2,0:22.1:1:31.6:1:1:0:60:30.6:1:0:0.1 0/1:192:2:1,1:44,146:190,2:0.0104:2,2:29:1:26:1:0.41476:3.29:60:4:0.0108:0:1 +1 51434568 . C CA 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50557;SOR=Inf;LSEQ=GAGGGAGTGAAGGAAAAAAG;RSEQ=AAAAAAGGGGGCGACACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:19,117:136,0:0:2,0:22.8:1:31.7:1:1:0:60:18.429:1:0:0.1 0/1:173:2:1,1:35,136:171,2:0.0116:2,2:30.5:1:27.5:1:0.37384:3.85:60:4:0.0116:0:0 +1 51436157 . G T 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=GCACAAAATGGATTTGGAAG;RSEQ=ACTGCGCTGCAGGTTGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:14:5,9:170,265:435,14:0.0312:2,2:22.3:1:29.4:1:1:1.15439:60:28:0.0314:0:1 0/0:530:0:0,0:210,320:530,0:0:2,0:26.6:1:30.4:1:1:0:60:105:1:0:0.2 +1 51437709 . GA G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.2069;SOR=Inf;LSEQ=ATATTGCTATTATTTTCTGT;RSEQ=AAAAAGGTGAATTTTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:150,4:154,0:0:1,0:24:1:30.7:1:1:0:60:153:1:0:0.1 0/1:129:2:2,0:117,10:127,2:0.0155:2,0:45.5:1:31.5:1:1:0:60:4:0.0159:0:0 +1 51437902 . G A 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2224;SOR=0;LSEQ=AAATATGACTAAATCTTTAG;RSEQ=GACAGTTGTGGTCGTATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:572:572:193,379:0,0:0,572:1:0,2:26:1:31.4:1:1:0:60:113.4:1:0:1.1 1/1:511:509:188,321:0,0:0,509:0.9961:0,2:25.3:1:29.4:1:1:0:60:100.8:1:0:1.1 +1 51437916 . G A 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00462;SOR=Inf;LSEQ=CTTTAGGGACAGTTGTGGTC;RSEQ=TATCAATTTTTAATAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:496:0:0,0:153,343:496,0:0:2,0:25.6:1:31.5:1:1:0:60:81.667:1:0:1 0/1:432:7:3,4:145,280:425,7:0.0162:2,2:29.7:1:29:1:0.69532:1.45:60:14:0.0164:0:2.3 +1 51439494 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19648;SOR=Inf;LSEQ=AGTTACATAAATGGAAGGAC;RSEQ=GGCAGATATTTTAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:165,18:183,0:0:2,0:22.1:1:31:1:1:0:59.7:182:0.9945:0:0.1 0/1:147:2:1,1:131,14:145,2:0.0136:2,2:8.5:1:27.5:1:0.1943:9.0743:60:4:0.0138:0:1 +1 51439777 . C T 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11593;LSEQ=CACTTGGCTGCCAAAGAAGG;RSEQ=CACCTCCGGGTGGTGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:80:32,48:167,202:369,80:0.1782:2,2:22:1:30:1:0.45661:1.23951:60:79:0.1779:0:1.1 0/1:572:14:9,5:237,320:557,14:0.0245:2,2:33.3:1:27.2:1:0.16968:2.43:60:13:0.0232:0:1.2 +1 51440064 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=TAAGCAGCTAAATTTTCTGA;RSEQ=ACTGCATAAGTGAAAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:0,27:27,0:0:1,0:29.6:1:30.1:1:1:0:58.9:12.5:1:0:0.1 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:36:1:29:1:1:0:60:4:0.0909:0:1 +1 51440093 . C T 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.52015;LSEQ=AGTGAAAATCTTACAACAGG;RSEQ=TTATGAATATATTTAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:19.5:1:29:1:1:0:60:4:0.0952:0:1 0/1:15:2:0,2:0,13:13,2:0.1333:1,0:48:0:32:0:1:0:60:4:0.1333:0:1 +1 51441244 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24834;SOR=Inf;LSEQ=TCATCTACCACATGATCAAA;RSEQ=ATGTTTTATGTGAACGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:157,54:211,0:0:2,0:24.8:1:32.8:1:1:0:59.9:104.5:1:0:0.1 0/1:216:3:2,1:156,57:213,3:0.0139:2,2:24.7:1:23.3:1:1:1.3663:60:2:0.0093:0:1 +1 51441409 . A G 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03054;SOR=0;LSEQ=TTTTCAATAATTTATTTTCC;RSEQ=TGATAGTATAAAAGAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:5:2,3:100,222:322,5:0.0153:2,2:34.6:1:32.4:1:0.64904:1.48:60:10:0.0154:0:1 0/0:328:0:0,0:129,199:328,0:0:2,0:24.5:1:29.6:1:1:0:60:108.333:1:0:0.1 +1 53409305 . G T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11235;SOR=0;LSEQ=GTGTCTTCAAAAAGGCCAAC;RSEQ=AGATAGGCCTCACTTACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:3,1:14,8:22,4:0.1538:2,2:26.8:1:31.8:1:1:1.68:56:8:0.1538:0:1.3 0/0:23:0:0,0:15,8:23,0:0:2,0:23.7:1:30:1:1:0:60:46:1:0:0.1 +1 53409417 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15892;SOR=Inf;LSEQ=GACGCTGGAAGGGAGGTTTG;RSEQ=GAATCAGTTTAGTGGACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:29,17:46,0:0:2,0:24.4:1:32.1:1:1:0:60:92:1:0:0.1 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:22:1:26:1:1:1.07:48.5:4:0.0645:0:1 +1 53569399 . A G 141 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00111;SOR=0;LSEQ=GCAGAGCAGGGATTGCTATC;RSEQ=ATATTTTACCCAAAGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:17,7:0,0:0,24:1:0,2:18.5:1:30.9:1:1:0:60:48:1:0:1.3 0/1:7:3:2,1:3,1:4,3:0.4286:2,2:33.3:1:31:1:1:1.41418:60:6:0.4286:0:1 +1 53569492 . T C 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00082;SOR=Inf;LSEQ=CATTCCTCTTCTTACTTCTA;RSEQ=ACCTCATCACCCCATCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:12,20:32,0:0:2,0:23.1:1:29.5:1:1:0:60:64:1:0:0.2 0/1:26:8:3,5:8,10:18,8:0.3077:2,2:36.4:1:31.8:1:1:1.31876:60:16:0.3077:0:1 +1 53571288 . C G 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAGCATCCCACCTCCAG;RSEQ=AGACAGCGTGACTGGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:29.8:1:30:1:1:0:60:10:1:0:1.2 1/1:2:2:2,0:0,0:0,2:1:0,0:22:1:32.5:1:1:0:60:4:1:0:1 +1 53809833 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAGGTGAGTTGCTACAC;RSEQ=GAGAGGGCCTGCTGGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:16.5:1:31.5:1:1:1:60:4:0.5:0:2 +1 53809858 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCTGCTGGATGGGTCAG;RSEQ=GAGGAGGGAGGGTGCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:41.5:1:30:1:1:1:60:4:0.5:0:2 +1 53811817 . A G 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14267;SOR=Inf;LSEQ=CAGGACTTTCCCACTTTGGG;RSEQ=GAAGCCTATGCACCTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:185,28:213,0:0:2,0:25.2:1:30.3:1:1:0:60:52.25:1:0:0.1 0/1:131:2:1,1:110,19:129,2:0.0153:2,2:7.5:1:26:1:0.28303:5.66853:60:4:0.0154:0:1 +1 53811822 . C T 40 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.52628;LSEQ=CTTTCCCACTTTGGGAGAAG;RSEQ=CTATGCACCTGGGAGTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:2,1:194,33:227,3:0.013:2,2:26:1:25.3:1:0.38256:2.9203:56.7:2:0.0089:0:3.7 0/0:145:1:0,1:117,27:144,1:0.0069:2,0:1:0:22:0:0.1931:0:60:2:0.0069:0:1 +1 53811942 . G T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.15868;LSEQ=TTACTATGCAGGGTATGAGG;RSEQ=TCCTGAGGAGAGATTCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:210:98,112:231,259:490,210:0.3:2,2:27.6:1:30.3:1:0.93425:1.01928:59.9:209:0.3025:0:1.2 0/1:622:299:141,158:147,176:323,299:0.4807:2,2:27.5:1:29.2:1:0.6882:1.07:60:298:0.4846:0:1.1 +1 53812211 . C T 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAACAAGGCCAAGTGAA;RSEQ=GCCTGGTGACCAGATGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:20:1:32:0:1:0:48.5:4:0.2222:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 55878119 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=CAATTCAGAATACAATATGG;RSEQ=AGAGAAGGATTTACAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:5,0:5,2:0.2857:0,2:20.5:1:29:0:0.28571:0:60:4:0.2857:0:1.5 0/0:6:0:0,0:4,2:6,0:0:2,0:18.8:1:27.2:1:1:0:60:12:1:0:0 +1 57004147 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05521;SOR=3.46444;LSEQ=ACAAACACAAAGGGAAAGAG;RSEQ=AGAGGCACCCGATAGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:19:12,7:14,2:16,19:0.5429:2,2:21.1:1:30.2:1:0.1354:3.92625:41.1:18:0.5294:0:1.9 1/1:26:21:15,6:4,1:5,21:0.8077:2,2:25:1:29.1:1:1:1.57335:36.7:20:0.8:0:1.8 +1 57004178 . G T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00072;SOR=4.8929;LSEQ=GATAGATGTTCTCTAGGCCT;RSEQ=TTAGAAAACATGGAGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:30:25,5:24,5:29,30:0.5085:2,2:23.7:1:31.3:1:1:1.04:45:29:0.5:0:1.6 1/1:43:36:26,10:7,0:7,36:0.8372:0,2:21.8:1:29.8:1:0.17248:0:44.3:72:0.8372:0:1.5 +1 57004270 . TA T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21189;SOR=Inf;LSEQ=TAAGGGAATGGGTACTGCTC;RSEQ=AAAAGAATGCCCCACAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:128,92:220,0:0:2,0:23.6:1:29.2:1:1:0:59.6:219:0.9955:0:0.2 0/1:189:2:1,1:106,81:187,2:0.0106:2,2:24:1:27.5:1:1:1.30675:60:4:0.0108:0.0053:0.5 +1 57004417 . A T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02382;SOR=Inf;LSEQ=GCATATTGAGCACATTAAGC;RSEQ=CTCCAAGAGCTGAGATAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:4,40:44,0:0:2,0:25.6:1:30.4:1:1:0:52.9:88:1:0:0 0/1:30:4:1,3:4,22:26,4:0.1333:2,2:29.3:1:28.5:1:0.53841:1.79:58:8:0.1379:0:1 +1 58158593 . G C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05105;SOR=Inf;LSEQ=ACAATGCCTTTCAAACTCTT;RSEQ=TACCAACCTCTGGAGTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:27,0:0:2,0:30.7:1:33.1:1:1:0:48.9:54:1:0:0.3 0/1:26:4:2,2:13,9:22,4:0.1538:2,2:39.3:1:31.5:1:1:1.42378:29.5:8:0.16:0:1.3 +1 58158647 . C G 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02391;SOR=0;LSEQ=CCCCTTTCTAGGTCCCATAA;RSEQ=AGCCATCTTGCTATTACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:1,5:8,13:21,6:0.2222:2,2:32.3:1:32.7:1:0.62785:2.96583:50:12:0.2222:0:1 0/0:24:0:0,0:10,13:23,0:0:2,0:19.6:1:30.3:1:1:0:55.4:46:0.9583:0:0.3 +1 58160304 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCATTATTAGGCTTTTT;RSEQ=AAACTAAGGATATTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:28:1:31:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 59245595 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16211;SOR=Inf;LSEQ=TGGTCAAAATCATCTCACCT;RSEQ=CCGGGTTGCTGACATCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:13,237:250,0:0:2,0:24.4:1:30:1:1:0:59.9:61.5:1:0:0.1 0/1:169:2:1,1:15,152:167,2:0.0118:2,2:8:1:26.5:1:0.1809:9.84:60:4:0.012:0:1 +1 59245987 . T C 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTAAGTTATATCTGTAGG;RSEQ=AGAATTCAAGTTTCCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:21:1:32.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 59246115 . T G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTACTATCTTTTGAGACT;RSEQ=ATTCTATATTTAAACAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:23:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 59246773 . G A 45 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38344;SOR=0.29835;LSEQ=GAAACATCGCACTATCCTTT;RSEQ=GTAAGCAATTCCATATAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:4:2,2:65,264:329,4:0.012:2,2:5.3:1:22.8:1:0.18172:4.04:60:3:0.0093:0:1 0/0:278:1:1,0:66,211:277,1:0.0036:2,0:1:0:22:0:0.24101:0:60:2:0.0037:0:1 +1 59247596 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52778;SOR=0;LSEQ=TCGTGCACACTGGGGGCGCC;RSEQ=TCAGGACGCAACCCAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:2,0:82,1:83,2:0.0235:1,0:22:1:29.5:1:1:0:60:4:0.0238:0:1 0/0:51:0:0,0:51,0:51,0:0:1,0:21.5:1:29.9:1:1:0:60:102:1:0:0.1 +1 59247705 . AT A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00045;SOR=Inf;LSEQ=CAAGTCTGTCTCTCTGTGTT;RSEQ=TTTTTTTCTTCGTTGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:784:0:0,0:535,248:783,0:0:2,0:26.1:1:30.9:1:1:0:59.9:155.6:0.9987:0:0.2 0/1:964:13:8,5:628,323:951,13:0.0135:2,2:27.7:1:29.2:1:0.77168:1.2149:60:26:0.0136:0.001:0.2 +1 59247993 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=0.62016;LSEQ=CTCTCCGCCTTGATCCGCTC;RSEQ=TGGGACTCCATGTCGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:846:184:69,115:252,408:660,184:0.2175:2,2:21.7:1:30.9:1:0.9316:1.02938:60:91:0.2177:0:1.1 0/1:864:127:52,75:286,451:737,127:0.147:2,2:20.7:1:29.6:1:0.69394:1.09:60:254:0.1485:0:1.2 +1 59248077 . C A 52 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03326;SOR=Inf;LSEQ=GGCTCCTCCTTCAGGGCCTG;RSEQ=AGCCGCGGGTGCTGCACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:89,263:352,0:0:2,0:25.4:1:31.9:1:1:0:60:43:1:0:0.2 0/1:409:6:4,2:127,272:399,6:0.0147:2,2:18.2:1:20.5:1:0.08907:4.27:60:2:0.0101:0:1.3 +1 59248123 . GGCT G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.16758;SOR=0.31438;LSEQ=GCTGGGGCAGGTGGTGCGGC;RSEQ=GCTGCTGCTGCTGGGGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:6:1,5:20,134:154,6:0.0368:2,2:29.2:1:33.7:1:0.5763:1.34:60:12:0.037:0:0.3 0/1:169:2:1,1:42,124:166,2:0.0118:2,2:8:1:27:1:0.44753:2.93:60:4:0.0119:0.0059:0.5 +1 59248124 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24029;SOR=0;LSEQ=CTGGGGCAGGTGGTGCGGCG;RSEQ=CTGCTGCTGCTGCTGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:0,2:20,134:154,2:0.0123:2,0:23:1:32:0:1:0:60:4:0.0123:0:1 0/0:169:0:0,0:42,124:166,0:0:2,0:22.7:1:31.2:1:1:0:60:165:0.9821:0:0.2 +1 59248128 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=1.94434;LSEQ=GGCAGGTGGTGCGGCGGCTG;RSEQ=TGCTGCTGCTGGGGTTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:0,1:19,132:151,1:0.0066:2,0:8:0:32:0:1:0:60:2:0.0067:0:1 0/1:157:2:1,1:38,117:155,2:0.0127:2,2:36.5:1:29:1:0.43631:3.05:60:4:0.0131:0:1 +1 59248149 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26087;SOR=Inf;LSEQ=TGCTGCTGCTGGGGTTGCGC;RSEQ=GGAAAGGCCAGGCCGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:21,80:101,0:0:2,0:22.5:1:31.7:1:1:0:59.8:49.5:1:0:0.1 0/1:133:3:0,3:43,87:130,3:0.0226:2,0:16.3:1:26:1:0.55071:0:60:6:0.0231:0:1 +1 59248182 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51961;SOR=Inf;LSEQ=CCGGCCGCGCCGTAGGAGGG;RSEQ=GCCCCGCCGCCGCTGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:25,44:69,0:0:2,0:20.2:1:30.9:1:1:0:59.7:68:1:0:0.1 0/1:106:2:0,2:43,61:104,2:0.0189:2,0:18.5:1:30:0:0.51321:0:56.5:4:0.0194:0:1.5 +1 59248202 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.15833;SOR=0;LSEQ=CGCCCCGCCGCCGCTGCTCA;RSEQ=CGCGCCTGGGTTGAAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:30,26:56,2:0.0345:2,2:46.5:1:29:1:1:1.15099:60:4:0.0351:0:1 0/0:87:0:0,0:45,42:87,0:0:2,0:28.6:1:31.1:1:1:0:59.8:86:1:0:0.2 +1 59248221 . G A 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08274;SOR=Inf;LSEQ=AGCGCGCCTGGGTTGAAGTT;RSEQ=CTGAGGTTTGCGTAGACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:33,26:59,0:0:2,0:26.1:1:32.5:1:1:0:59.6:58:1:0:0.2 0/1:88:5:3,2:42,40:82,5:0.0568:2,2:23.6:1:28:1:1:1.42:60:10:0.0581:0:1.2 +1 59248242 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18171;SOR=0;LSEQ=CTGAGGTTTGCGTAGACCGG;RSEQ=GGCTCGCTGTGCAGGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:30,22:52,2:0.037:2,2:47:0:32:1:1:1.35569:60:4:0.037:0:1.5 0/0:72:0:0,0:32,40:72,0:0:2,0:24.6:1:30.6:1:1:0:60:71:1:0:0.2 +1 59248263 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22804;SOR=Inf;LSEQ=GGCTCGCTGTGCAGGCTGGC;RSEQ=CTGAAGCCGCCGCTGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:45,19:64,0:0:2,0:22.8:1:30.9:1:1:0:60:63:1:0:0.1 0/1:59:2:1,1:31,26:57,2:0.0339:2,2:38.5:1:29.5:1:1:1.18874:60:4:0.0345:0:1 +1 59248318 . A T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50055;SOR=Inf;LSEQ=AGGCTACCGCGGGAGCCACC;RSEQ=TGCCTGCCCCGTTGACCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:105,24:129,0:0:2,0:25.4:1:30.7:1:1:0:59.9:128:1:0:0.1 0/1:148:2:1,1:118,28:146,2:0.0135:2,2:21:0:32:0:0.35457:4.1585:60:4:0.0135:0:1.5 +1 59248324 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50157;SOR=Inf;LSEQ=CCGCGGGAGCCACCATGCCT;RSEQ=CCCCGTTGACCGGCTGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:113,24:137,0:0:2,0:26.1:1:32.5:1:1:0:59.9:136:1:0:0.1 0/1:161:2:1,1:129,30:159,2:0.0124:2,2:10:1:27:1:0.34899:4.24644:60:4:0.0125:0:2 +1 59248813 . G C 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGGGGCCGCAACAGGGCT;RSEQ=TGGCAAGCGGGGGACACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:266:266:36,230:0,0:0,266:1:0,2:25.7:1:33.1:1:1:0:59.9:87.667:1:0:1.1 1/1:257:257:44,213:0,0:0,257:1:0,2:23.1:1:31:1:1:0:60:41.833:1:0:1.1 +1 59248835 . G GC 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50392;SOR=0;LSEQ=GGCAAGCGGGGGACACCCGC;RSEQ=CCCCCCGGAGCCTTTGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:0,2:8,175:183,2:0.0108:1,0:20.5:1:32:1:1:0:60:4:0.0112:0.0054:1.5 0/0:151:0:0,0:5,146:151,0:0:1,0:23.5:1:31.5:1:1:0:60:36.75:1:0:1.1 +1 59249031 . T G 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCACTGAGCGCTCTTCG;RSEQ=GCGCAGCGGTTCCTCGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:2,6:0,0:0,8:1:0,2:32.3:1:27.3:1:1:0:59:3:1:0:1.9 1/1:2:2:0,2:0,0:0,2:1:0,0:31:1:31.5:1:1:0:60:4:1:0:1 +1 59249347 . G C 104 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAAGGCTTGCAAAAGTT;RSEQ=GCTCCGGGACTCTGCCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:0,9:1:0,2:18.7:1:32.9:1:1:0:52.4:18:1:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:13:0:31:0:1:0:60:2:1:0:1 +1 59249359 . C CTG 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAAAAGTTGGCTCCGGGACT;RSEQ=TGCCACTTGTCTCCGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:19.3:1:29.6:1:1:0:60:6:0.3333:0.1111:2.3 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:1 +1 59250418 . C G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43275;SOR=0.51266;LSEQ=AGGGGCGGTCTCCCGAGAGT;RSEQ=GGCCCCCCACGTTGAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:14,0:7,0:7,14:0.6667:0,1:20.2:1:31.6:1:1:0:57.1:13:0.65:0:2.2 1/0:8:4:3,1:3,1:4,4:0.5:2,2:20.5:1:29:1:1:1:60:3:0.4286:0:2.5 +1 59250439 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04858;SOR=Inf;LSEQ=GGCCCCCCACGTTGAGAACA;RSEQ=TCCGAAGTTTGCATCTCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:30,0:0:1,0:26.4:1:33.1:1:1:0:57.8:60:1:0:1.2 0/1:9:2:1,1:7,0:7,2:0.2222:0,2:23.5:1:32.5:1:0.22222:0:60:4:0.2222:0:2.5 +1 59250452 . A G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.73226;SOR=0.73534;LSEQ=GAGAACACTCCGAAGTTTGC;RSEQ=TCTCGGTCAAGTTCAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:23:23,0:14,0:14,23:0.6216:1,1:26.3:1:30.2:1:1:0:58.3:22:0.6111:0:1.7 1/0:11:6:6,0:5,0:5,6:0.5455:0,0:26:1:29.3:1:1:0:60:12:0.5455:0:1.8 +1 59250675 . C G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10766;LSEQ=TAACAGGGTCCAGATGGGAA;RSEQ=AAGCGTGTAGGCGATCCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1544:274:158,116:676,592:1268,274:0.1775:2,2:28.3:1:32.8:1:0.20419:1.19:60:273:0.1796:0:1.1 0/1:1631:37:22,15:844,747:1591,37:0.0227:2,2:25.7:1:30.9:1:0.5066:1.30:60:36:0.0224:0:1.2 +1 59250710 . G A 209 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=71.06509;LSEQ=TCCGAAACTCGGGGAACCCC;RSEQ=GTGTTAGTCTACTCCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1817:2:2,0:884,923:1807,2:0.0011:2,0:3.5:1:29.5:1:0.23974:0:60:4:0.0011:0:1 0/1:1885:137:65,72:881,865:1746,137:0.0727:2,2:23.9:1:29.5:1:0.53487:1.12811:60:67.5:0.0728:0:1.2 +1 59250778 . ACG A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.33631;SOR=0.75412;LSEQ=AACACAACACGCACAACATA;RSEQ=CGCGCGCGCGCGCACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1096:30:11,19:421,641:1062,30:0.0274:2,2:35.9:1:30.8:1:0.85074:1.13435:59.3:60:0.0279:9e-04:0.4 0/1:1155:24:9,15:477,644:1121,24:0.0208:2,2:34.8:1:29.5:1:0.68098:1.23425:59.8:48:0.021:0:0.1 +1 59250792 . G A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AACATAACGCGCGCGCGCGC;RSEQ=CACACACACACTCCATCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:910:0:0,0:310,578:888,0:0:2,0:25.8:1:30.5:1:1:0:60:25.118:1:0:0.2 0/1:936:29:16,13:348,558:906,29:0.031:2,2:19.1:1:27.8:1:0.08168:1.97:60:58:0.032:0:1.1 +1 59564093 . G GT 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=TTTTGTTTTGTTTTTTTGTT;RSEQ=TTTTTTTTTTTGAGTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,0:2,2:0.4:0,0:29.5:1:30:1:1:0:60:4:0.4:0:0 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19:1:30:1:1:0:60:4:0.5:0.25:0 +1 59564208 . GA G 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.4898;SOR=0;LSEQ=AGTAAGCTCATTTTAAAGGT;RSEQ=AAAAAAAAATAAAGCTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:23,0:23,2:0.08:1,0:30:1:32:1:1:0:60:4:0.08:0:0 0/0:24:0:0,0:22,2:24,0:0:2,0:12:0:16:0:1:0:60:0:0:0:1 +1 59564276 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2106;SOR=Inf;LSEQ=CACAGAGAGTAAATTATTGC;RSEQ=TCTGATTCCAAAGAACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:106,28:134,0:0:2,0:24.9:1:30.4:1:1:0:60:268:0.9926:0:0.1 0/1:115:2:1,1:82,31:113,2:0.0174:2,2:21.5:1:29:1:0.48085:2.61933:60:4:0.0174:0:1.5 +1 59564373 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38692;SOR=1.14823;LSEQ=AGTGTAGTTTTGCTAAATTA;RSEQ=CCTCTTTGGGGATTGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:157:87,70:84,94:178,157:0.4687:2,2:22.4:1:30.3:1:0.15464:1.39:60:38.25:0.4665:0:1.1 1/0:310:156:75,81:76,77:153,156:0.5032:2,2:26:1:28.5:1:0.82031:1.06575:59.8:25:0.4967:0:1.2 +1 59564403 . G A 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36252;SOR=3.15896;LSEQ=GGATTGAGTTGCAGCCTCAT;RSEQ=ACATAATGACTGGTGATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:1,0:136,171:307,1:0.0032:2,0:1:0:24:0:0.44481:0:60:2:0.0033:0:2 0/1:295:3:2,1:136,156:292,3:0.0102:2,2:14:1:25.3:1:0.60099:2.29:60:6:0.0102:0:1.7 +1 59564443 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59524;SOR=2.37553;LSEQ=CAGGTCCTTCTTAGAAACGT;RSEQ=CTGTTCATTTCTGGCTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:1,0:73,127:200,1:0.005:2,0:1:0:27:0:0.36816:0:60:2:0.005:0:1 0/1:170:2:1,1:61,107:168,2:0.0118:2,2:26.5:1:27:1:1:1.75:60:4:0.0118:0:1.5 +1 59564452 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50125;SOR=0;LSEQ=CTTAGAAACGTGCTGTTCAT;RSEQ=TCTGGCTAATGTTCCCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:54,115:169,2:0.0116:2,2:19.5:1:31.5:1:0.54111:2.12:60:4:0.0116:0:1 0/0:148:0:0,0:49,99:148,0:0:2,0:24.2:1:29.6:1:1:0:60:296:1:0:0.3 +1 59564892 . A T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGGAAAGGTTCATTAACC;RSEQ=GGAGCTTTATAACAGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:34:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 63789015 . G T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGCCGGACCGGGGGGCGAC;RSEQ=TGGGCGCGCCGGAGGCGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:1:0:33:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:48.5:1:30:1:1:0:60:4:1:0:1 +1 63789244 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21538;SOR=Inf;LSEQ=CGGCATCTGCGAGTTCATCA;RSEQ=CAACCGCTTCCCCTACTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:31,25:56,0:0:2,0:20.1:1:32.3:1:1:0:58.4:55:1:0:0.1 0/1:49:2:1,1:28,18:46,2:0.0408:2,2:10.5:1:25:1:1:1.54082:45.5:4:0.0426:0:1 +1 63789400 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49938;SOR=0;LSEQ=GGACCCGCAGTCCGAGGACA;RSEQ=GTTCGACAACGGCAGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:9,28:37,2:0.0513:2,2:42.5:1:30:1:0.45209:3.00:60:4:0.0513:0:1 0/0:31:0:0,0:6,25:31,0:0:2,0:23:1:30.1:1:1:0:45.1:62:1:0:0.1 +1 65300374 . GT G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24803;SOR=Inf;LSEQ=GAAGTAACAACAGTAAAAAT;RSEQ=TAGATCTGGGAACTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:39,152:191,0:0:2,0:23:1:30.5:1:1:0:60:94.5:1:0:0.1 0/1:190:2:1,1:47,141:188,2:0.0105:2,2:21:1:31:1:0.44244:2.98:60:4:0.0106:0:0.5 +1 65300398 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22227;SOR=Inf;LSEQ=GATCTGGGAACTTTAAAAAA;RSEQ=AACAGAAATATCAAGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:10,115:125,0:0:2,0:21.2:1:28.7:1:1:0:60:61.5:1:0:0.1 0/1:112:2:1,1:15,95:110,2:0.0179:2,2:12.5:1:28:1:0.26641:6.16:60:4:0.0179:0:1 +1 65300993 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22397;SOR=Inf;LSEQ=CACTGCATCATTTCCTCGCT;RSEQ=TCCCCTCTACCCATTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:179,13:192,0:0:2,0:21.9:1:32.5:1:1:0:60:95:1:0:0.1 0/1:173:2:1,1:157,14:171,2:0.0116:2,2:19:1:27:1:0.16635:10.86873:60:4:0.0118:0:1 +1 65301238 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.28435;SOR=1.51667;LSEQ=TTAACTTTGCAAGTATTTAC;RSEQ=TAAATGCCAAACAGATTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:13:3,10:22,150:172,13:0.0703:2,2:20.2:1:31.8:1:0.38969:2.04:60:26:0.071:0:1.1 0/1:204:21:3,18:25,158:183,21:0.1029:2,2:22.9:1:30.4:1:1:1.05:60:20:0.099:0:1.2 +1 65301490 . G A 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69008;LSEQ=ACAAGGCTGGTCCCTACCCA;RSEQ=TGCTACCCCACTTAACTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:2,2:4,6:0.6:2,2:25.5:1:25.3:1:1:1:60:2:0.5714:0:1.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:46:0:28:0:1:0:60:2:0.5:0:1 +1 65301611 . T G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89139;LSEQ=TCGTTGTGAAAGCAAGACTT;RSEQ=AGAGATTCACAAATAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:7,2:23,1:24,9:0.2727:1,2:26.7:1:33.7:1:0.17375:6.11937:60:18:0.2727:0:1.8 0/1:8:2:2,0:5,1:6,2:0.25:2,0:22:1:32.5:1:1:0:60:4:0.25:0:2 +1 65301669 . C A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03813;LSEQ=TAATGGGAAAGTGACATTTT;RSEQ=CATTATAATACATTCATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:13:13,0:51,3:54,13:0.194:2,1:17.2:1:26.8:1:1:0:60:12:0.1846:0:1.5 0/1:40:8:7,1:32,0:32,8:0.2:1,2:20.6:1:28.1:1:0.2:0:60:16:0.2:0:1.3 +1 65303659 . C T 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTGACGGTGTAATACTC;RSEQ=TTATCGGTTTCAATTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:950:0:0,0:520,430:950,0:0:2,0:25.4:1:32:1:1:0:60:85.364:1:0:0.1 0/1:980:49:26,23:517,413:930,49:0.05:2,2:26.5:1:29:1:0.7691:1.10726:60:15.333:0.0474:0:1.2 +1 65304470 . A C 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAATGGTGTACCTACCTCAC;RSEQ=GGCATAAGCACTCACTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:1,17:18,3:0.1429:1,0:18.7:1:30.3:1:1:0:60:6:0.1579:0:1 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:7:0:31:0:1:0:60:2:0.1429:0:1 +1 65305102 . TCA T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.80138;SOR=1.26664;LSEQ=GAGGGGCCTGGGTGGCCTCC;RSEQ=GGAGCCCTGCAGCTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:45:45,0:16,0:16,45:0.7377:1,1:27.5:1:32.7:1:1:0:59.3:90:0.7377:0.082:0.1 1/0:32:25:25,0:7,0:7,25:0.7813:0,1:20.3:1:31.1:1:1:0:59.8:50:0.7813:0.25:0.1 +1 65306996 . G GT 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.07245;SOR=0.45164;LSEQ=GGGGTCCACTTCAGTTGCTG;RSEQ=TTTTTTTTCTGAAACAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:17:9,8:326,413:739,17:0.0224:2,2:24:1:30:1:0.47242:1.42:60:34:0.0227:0.0013:0.1 0/1:878:9:4,5:389,479:868,9:0.0103:2,2:31.7:1:28.8:1:1:1.01512:60:18:0.0104:0:0.1 +1 65307409 . G A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10568;SOR=3.69441;LSEQ=TCCACTTACAGGTAGATTTC;RSEQ=TAAGTGTTTGTTACTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:6:0,6:0,41:41,6:0.1277:1,0:22.3:1:32.3:1:1:0:60:12:0.1304:0:1.3 0/1:14:5:0,5:0,9:9,5:0.3571:0,0:17.6:1:31.6:1:1:0:60:10:0.3571:0:1 +1 65309387 . T C 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGATGCCTGATACACAA;RSEQ=AGGAACTCCATACGTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:8,2:0.2:0,0:26.5:1:34.5:1:1:0:60:4:0.2:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 65309400 . C T 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACACAATAGGAACTCCATA;RSEQ=GTATTTGTGTGGTAATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:26:1:30.7:1:1:0:60:6:0.375:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 65309415 . ATTT A 66 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATACGTATTTGTGTGGTA;RSEQ=TGCTGAATAACAGGCACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:26.3:1:33:1:1:0:58.3:8:0.4444:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 65309958 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21043;SOR=Inf;LSEQ=ATCTCCTAGGGATTCAATTA;RSEQ=TGTCACTGCAGCCAGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:21,179:200,0:0:2,0:22.5:1:33.2:1:1:0:59.9:99:1:0:0.1 0/1:170:2:1,1:37,131:168,2:0.0118:2,2:9.5:1:29:1:0.39812:3.51:60:4:0.0119:0:1.5 +1 65310268 . GAAGGCAGGAGATC G 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00124;SOR=Inf;LSEQ=GCTCGTTCAAGGACTTAAGA;RSEQ=AAGACCATCCTGGCCAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:39,3:42,0:0:2,0:22.5:1:30.4:1:1:0:51.4:41:1:0:0 0/1:17:5:5,0:11,0:11,5:0.2941:0,0:10.8:1:31.5:1:1:0:49.4:10:0.3125:0.1765:0.2 +1 65310328 . CA C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.80311;SOR=0.8117;LSEQ=ACCCCGTCTCTACTAAAATA;RSEQ=AAAAAAAAATGACTCTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:12:12,0:130,3:133,12:0.0828:1,0:23.1:1:31.8:1:1:0:53.5:24:0.0839:0.0207:0.2 0/1:88:6:6,0:76,5:81,6:0.0682:2,0:23.2:1:31.8:1:1:0:56.2:12:0.069:0.0227:0.8 +1 65310361 . CCCCAG C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17645;SOR=Inf;LSEQ=ACTCTCTAAAAGGAGACCAA;RSEQ=CCCAGCCCTTCTCTCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:238,25:263,0:0:2,0:24.3:1:31.4:1:1:0:59.1:64.75:1:0:0.2 0/1:191:2:1,1:169,20:189,2:0.0105:2,2:10:1:28.5:1:0.20832:8.26978:60:4:0.0105:0.0052:0.5 +1 65310402 . G T 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11016;SOR=5.47083;LSEQ=TGCTGACTTGCCCCTGACTC;RSEQ=GGGTGGGGCCAGAGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:1:0,1:330,115:445,1:0.0022:2,0:1:0:26:0:0.26009:0:60:2:0.0023:0:1 0/1:411:5:2,3:284,122:406,5:0.0122:2,2:31.8:1:28.6:1:0.1673:3.48006:60:10:0.0125:0:1 +1 65310489 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11686;SOR=1.18826;LSEQ=GGGTCACTGAGCTTGATGAA;RSEQ=GGGCCACACTCACTGTCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1016:201:105,96:393,422:815,201:0.1978:2,2:26.5:1:31.1:1:0.34456:1.17:60:39.2:0.1958:0:1.2 0/1:1028:233:119,114:405,390:795,233:0.2267:2,2:25.6:1:30.3:1:1:1.01:60:232:0.2263:0:1.2 +1 65310747 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13664;SOR=Inf;LSEQ=ACAGGTGCCCCTTGGCTCCA;RSEQ=CTCCCTCATCACTGAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:23,0:0:1,0:21:1:33.2:1:1:0:60:46:1:0:0 0/1:14:2:1,1:0,12:12,2:0.1429:0,2:17:1:28:1:0.14286:0:60:4:0.1429:0:1 +1 65311075 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1384;SOR=Inf;LSEQ=TTTGTTCAACCACAGAGCCC;RSEQ=GGCCCCATGGAACCCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:115,4:119,0:0:1,0:24.7:1:31.8:1:1:0:59.9:118:1:0:0.4 0/1:71:2:2,0:66,3:69,2:0.0282:1,0:28.5:1:32.5:1:1:0:60:4:0.0286:0:1.5 +1 65311116 . GC CT 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18041;SOR=0.70007;LSEQ=CAGGCCCCTCTAGCTGCTTG;RSEQ=TAGCACCTCCTTCCTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:53:42,11:152,21:173,53:0.2345:2,2:22.7:1:31.8:1:0.12052:1.88975:59.8:106:0.2409:0.0398:0.9 0/1:187:33:28,5:137,17:154,33:0.1765:2,2:18.8:1:30.6:1:0.55154:1.43602:60:66:0.1784:0.0321:1 +1 65311214 . G C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00219;SOR=1.79657;LSEQ=ACCAAGTAGCTCAGGGCACT;RSEQ=GCCAGCTGTTTGGCAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1027:47:25,22:557,421:978,47:0.0458:2,2:28.9:1:31.7:1:0.6525:1.1641:60:94:0.0464:0:1.1 0/1:983:78:41,37:486,419:905,78:0.0793:2,2:29:1:30.3:1:0.90596:1.04672:60:77:0.0791:0:1.3 +1 65311262 . G A 188 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=103.35676;LSEQ=CATGGTGTGGTAAGGACATC;RSEQ=CTTTTCCGGTGCATGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1128:1:1,0:560,566:1126,1:9e-04:2,0:1:0:26:0:0.49778:0:60:2:9e-04:0:1 0/1:1094:92:47,45:492,509:1001,92:0.0841:2,2:25.3:1:28.9:1:0.74471:1.08:60:29.667:0.0826:0:1.2 +1 65312100 . TG T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54404;SOR=0;LSEQ=CTAGCACAGTGTAGGGTTCT;RSEQ=GCCAGCGTTGACAAGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:5,0:14,1:15,5:0.25:1,0:26:1:28.8:1:1:0:60:4:0.2:0.1:0.2 0/0:4:0:0,0:4,0:4,0:0:0,0:32.3:1:32.3:1:1:0:60:8:1:0:0 +1 65312354 . G A 94 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46665;SOR=1.5684;LSEQ=TCCACGTCGCGGACACAGAC;RSEQ=CCATAGAGGTACACGATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:777:6:5,1:389,382:771,6:0.0077:2,2:9.3:1:27.3:1:0.21722:4.90:60:12:0.0079:0:1 0/1:912:11:8,3:454,446:900,11:0.0121:2,2:14.5:1:27.3:1:0.22425:2.62:60:10:0.0111:0:1.1 +1 65312583 . C T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTGGCTGTCCAGAGGCACTG;RSEQ=CAAGCCTTGTTCTCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:8:1,7:1,27:28,8:0.2222:1,2:22.5:1:30.5:1:0.4:3.67:60:16:0.2222:0:1.4 0/1:18:4:1,3:1,13:14,4:0.2222:1,2:22.5:1:29.3:1:0.40523:3.89:60:8:0.2222:0:1 +1 65313414 . G A 97 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00374;SOR=11.85835;LSEQ=GTGCCCTGAAGTGATGGACC;RSEQ=TCTGGGAATGGGTCCTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:1,0:43,258:301,1:0.0033:2,0:1:0:26:0:0.1457:0:60:2:0.0034:0:1 0/1:263:10:3,7:42,211:253,10:0.038:2,2:22.1:1:29.2:1:0.38233:2.15:60:20:0.0386:0:1 +1 65316398 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50725;SOR=0;LSEQ=TTCTACTAAGATTTCCCCAA;RSEQ=CACAGCCTTCCTTCCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:155,13:168,2:0.0118:2,2:29:1:30.5:1:0.15837:11.52661:60:4:0.012:0:1 0/0:130:0:0,0:110,20:130,0:0:2,0:22.2:1:29.4:1:1:0:60:129:1:0:0.1 +1 65316675 . G A 160 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66181;SOR=0.87098;LSEQ=ACGTCTGCTGAGCCGGGGCC;RSEQ=TGGGACCGGTGTGCGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:35:1,34:5,112:117,35:0.2303:1,1:25.2:1:31.3:1:1:1.51409:60:70:0.2318:0:1.1 0/1:121:25:0,25:6,90:96,25:0.2066:2,1:23.5:1:30.9:1:0.3431:0:60:24:0.2:0:1.4 +1 65319411 . C A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01126;SOR=7.09166;LSEQ=TGAGGTAGGTACATAAACTG;RSEQ=CTGGGCCACAGTAGGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:4,0:14,5:19,4:0.1739:2,0:22.5:1:31.3:1:0.53924:0:60:8:0.1739:0:1 1/0:13:8:6,2:4,1:5,8:0.6154:2,2:20.8:1:28.4:1:1:1.30472:60:16:0.6154:0:1.1 +1 65319455 . T TG 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12451;SOR=2.4723;LSEQ=ATCCAGCAGCTCCTGCTACC;RSEQ=GTTCACTTGACAGGCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:6,3:15,14:29,9:0.2368:2,2:29.3:1:31.4:1:0.47571:1.84:60:18:0.2368:0:0.4 0/1:32:14:7,7:12,6:18,14:0.4375:2,2:32.3:1:31.2:1:0.4727:1.95606:60:28:0.4375:0:0.5 +1 65321028 . T C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27477;SOR=0;LSEQ=AAATGCTCACACTCAAGGGA;RSEQ=TGGATGTGAGTTGGGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:3,0:19,0:19,3:0.1304:1,0:28:1:33.7:1:1:0:60:6:0.1364:0:1 0/0:14:0:0,0:13,1:14,0:0:1,0:25:1:30.6:1:1:0:60:28:1:0:0.1 +1 65321250 . G A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00152;SOR=2.2921;LSEQ=CTGATGTTATCCGTGCGCAG;RSEQ=ATCTGCTTCTTGAGGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:22:13,9:337,222:559,22:0.0378:2,2:23:1:30.6:1:1:1.05082:60:44:0.0389:0:1.1 0/1:617:51:33,18:323,243:566,51:0.0827:2,2:23.8:1:29.2:1:0.30484:1.38:60:102:0.0836:0:1.1 +1 65321388 . G A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13772;SOR=1.2416;LSEQ=GCACCCTGCACCTGCTATTC;RSEQ=GGAAATGACCAGAAATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:127:47,80:121,226:347,127:0.2674:2,2:25.7:1:31.2:1:0.66614:1.10:60:126:0.2675:0:1.2 0/1:497:155:56,99:130,211:341,155:0.3119:2,2:24.5:1:29.6:1:0.69012:1.08899:60:154:0.3136:0:1.3 +1 65321419 . G A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00085;SOR=2.97677;LSEQ=AGAAATTACATGTTTAAAAT;RSEQ=GGGTCAGGCATGGGTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:13:3,10:56,210:266,13:0.0466:2,2:22.3:1:30.8:1:0.74112:1.12:60:26:0.0473:0:1.8 0/1:283:36:8,28:71,176:247,36:0.1272:2,2:24.3:1:29.1:1:0.5511:1.41031:60:35:0.1254:0:1.9 +1 65323142 . C T 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11506;LSEQ=GGCCCTACAGGGGGAGGATG;RSEQ=AGGGGTCTGGCTACTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:14,5:0.2632:1,0:15:1:29.8:1:1:0:60:10:0.2778:0:1.6 0/1:7:2:1,1:5,0:5,2:0.2857:0,2:41.5:1:28:1:0.28571:0:60:4:0.2857:0:1 +1 65324068 . C A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGTGCTGGTGAGAGAGGGC;RSEQ=GCCATGGTTCGTGTGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:21:0:32:0:1:0:60:2:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:15.5:1:28:1:1:0:60:4:0.6667:0:1 +1 65325970 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03159;SOR=1.5175;LSEQ=TGAGAGAGAAGAAATTCCCA;RSEQ=GGTTACATCATGTCTCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:58:13,45:61,151:212,58:0.214:2,2:24.8:1:30.4:1:0.4072:1.39671:60:57:0.2143:0:1.1 0/1:335:98:27,71:74,163:237,98:0.2925:2,2:20.8:1:29.5:1:0.60082:1.1932:60:97:0.2913:0:1.1 +1 65326011 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17221;SOR=Inf;LSEQ=AGCTTAAGTGGCTGACTCTG;RSEQ=AGGGAGGTGCACAGTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:16,144:160,0:0:2,0:21.4:1:28.3:1:1:0:60:79:1:0:0.3 0/1:114:2:1,1:15,97:112,2:0.0175:2,2:18.5:1:27:1:0.26207:6.29:60:4:0.018:0:1 +1 65326095 . TTGCA T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.28626;SOR=0;LSEQ=ATCAATACTAAATATACCCC;RSEQ=TGCATTTATTTATTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:0,4:0,28:28,4:0.125:1,0:21.8:1:32:1:1:0:60:8:0.129:0.0313:0 0/0:16:0:0,0:1,15:16,0:0:1,0:22.1:1:29.9:1:1:0:56.6:32:1:0:0.3 +1 65330682 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.08237;LSEQ=AGATACATAAAAGGGACAGG;RSEQ=TTAAGTTGCTTTCTTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:16:5,11:49,221:270,16:0.0559:2,2:28.1:1:31.1:1:0.19523:2.04:60:32:0.0563:0:1.1 0/1:328:64:13,51:63,200:263,64:0.1951:2,2:18.8:1:29.7:1:0.62205:1.23504:60:128:0.1988:0:1 +1 65332766 . T C 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATGCGTGGACACGCTGCTG;RSEQ=CACAAATGGTCTTGTTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:25:10,15:271,336:607,25:0.0394:2,2:21.6:1:31:1:0.68672:1.20946:60:24:0.0385:0:1 0/0:658:0:0,0:317,341:658,0:0:2,0:24.1:1:28.7:1:1:0:60:218.333:1:0:0.1 +1 65332927 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50098;SOR=Inf;LSEQ=AAAGTACATCTCCTTTTCAT;RSEQ=TACAGGTTAGGAGAAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:32,127:159,0:0:2,0:22.8:1:32.2:1:1:0:59.6:78.5:0.9937:0:0.1 0/1:184:2:1,1:42,140:182,2:0.0109:2,2:7.5:1:26.5:1:0.41376:3.31:60:4:0.0109:0:1 +1 65335062 . A G 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGTGTGAGATGGCCAGGAC;RSEQ=GCCATCCCTAGACACTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:931:0:0,0:459,472:931,0:0:2,0:25:1:31.2:1:1:0:60:185.2:1:0:0.1 0/1:1013:38:15,23:499,474:973,38:0.0375:2,2:26.8:1:29.8:1:0.18592:1.61344:60:76:0.0379:0:1.2 +1 65335095 . T C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=2.86393;LSEQ=CACTCGTTCTCAATATCATG;RSEQ=CCATCCTGCTCGGTCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:980:40:18,22:419,521:940,40:0.0408:2,2:24.3:1:32.1:1:1:1.02:59.4:80:0.0412:0:1.2 0/1:1095:119:52,67:454,521:975,119:0.1087:2,2:24.6:1:31:1:0.56094:1.12265:59.9:238:0.1106:0:1.2 +1 65335323 . G A 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1875;SOR=3.40927;LSEQ=AAACAGAGTTGGGTGTGAAG;RSEQ=GGCTCAGGAGATGTTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:0,3:0,29:29,3:0.0938:1,0:33.3:1:33.3:1:1:0:60:6:0.0968:0:1 0/1:15:4:0,4:0,11:11,4:0.2667:0,0:21.8:1:32:1:1:0:60:8:0.2667:0:1 +1 65339110 . C CT 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.70049;SOR=0.85345;LSEQ=AGAGGGGTTGCATCTGGAAT;RSEQ=TTTTTTTTCTCGTAGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:849:13:7,6:397,439:836,13:0.0153:2,2:25.2:1:32.2:1:0.78181:1.29:60:26:0.0155:0.0024:0.1 0/1:1069:14:7,7:510,542:1052,14:0.0131:2,2:32.9:1:29.9:1:1:1.06:60:28:0.0132:0:0 +1 65339243 . G A 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12329;SOR=Inf;LSEQ=TGAATGCCAATTGTGGCAAA;RSEQ=GGGACCCAGATGTGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:43,154:197,0:0:2,0:23.7:1:31.8:1:1:0:60:64.667:1:0:0.1 0/1:203:4:3,1:52,147:199,4:0.0197:2,2:14.3:1:23.3:1:0.0615:8.38:60:3:0.015:0:1 +1 65339294 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21275;SOR=Inf;LSEQ=TCACCAACAGTGGTCAGTGC;RSEQ=GGAGGCTGAAGTGCCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:5,68:73,0:0:2,0:22.9:1:30:1:1:0:60:72:1:0:0 0/1:63:2:1,1:4,57:61,2:0.0317:2,2:17.5:1:30:1:0.15361:12.86:60:4:0.0328:0:1.5 +1 65342806 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24586;SOR=0;LSEQ=GAGAGATACCTGAGGATAAC;RSEQ=ATGATTACCCAACAACTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:28,60:88,2:0.0222:2,2:31.5:1:31:1:0.54307:2.12:59.5:4:0.0222:0:1 0/0:91:0:0,0:35,56:91,0:0:2,0:25.7:1:28:1:1:0:59.6:90:1:0:0.1 +1 65344809 . G A 69 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01887;SOR=Inf;LSEQ=TCGTCATACAGGGCAAAGAG;RSEQ=TTGTGACAAAGAGGAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:198,348:546,0:0:2,0:24.7:1:31.8:1:1:0:59.4:77:0.9963:0:0.1 0/1:675:7:6,1:278,389:667,7:0.0104:2,2:10.4:1:24.6:1:0.04566:8.37:56.9:6:0.009:0:1.1 +1 65348485 . T C 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTCACTTCAACTCAGCACCA;RSEQ=GCATGGGAGGGCAGTCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:27.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 65348961 . G T 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04286;SOR=Inf;LSEQ=GGCAGCTGCCAGTACTCACG;RSEQ=CATGCCTGTGCAGCCCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:297,142:439,0:0:2,0:25.4:1:31.4:1:1:0:59.9:61.714:1:0:0.1 0/1:368:4:2,2:235,128:363,4:0.0109:2,2:9.5:1:23:1:0.61701:1.83279:60:3:0.0083:0:1.3 +1 65349304 . G A 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00228;SOR=0;LSEQ=CCCTGCCCCTTCCCTTCCTG;RSEQ=AAACCAAACATGTCAGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:11:1,10:1,35:36,11:0.234:1,2:29.2:1:31.9:1:0.41721:3.38:60:22:0.2444:0:1.3 0/0:32:0:0,0:0,32:32,0:0:1,0:25.6:1:30.9:1:1:0:60:15:1:0:0.1 +1 65349309 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CCCCTTCCCTTCCTGGAAAC;RSEQ=AAACATGTCAGATCTCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:1,42:43,2:0.0444:1,2:13.5:1:29:1:0.08788:30.05:60:4:0.0455:0:2.5 0/0:33:0:0,0:0,33:33,0:0:1,0:23.3:1:30.8:1:1:0:60:10:1:0:0.1 +1 65349608 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTATGGCAAGAATCAGC;RSEQ=TTTTAATTTCATGTCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:29.5:1:34:0:0.33333:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 65349817 . C G 34 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGACTTTGACGCAGCA;RSEQ=CAGGAGGGCAGGAGGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:26:0:34.5:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:8:0:31:0:1:0:60:2:1:0:0 +1 65351748 . C T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01358;SOR=0;LSEQ=CAAGGGAAGTTTAACTTTTA;RSEQ=TCTGTACCTCCTATACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:7,0:47,0:47,7:0.1296:1,0:21:1:31.6:1:1:0:60:14:0.1321:0:1 0/0:48:0:0,0:47,1:48,0:0:1,0:24.5:1:31.9:1:1:0:60:47:1:0:0 +1 65351797 . C T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.92679;LSEQ=GGTTTTTTTTAACCAGCATA;RSEQ=TCAACATTGGGAATGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:125,15:140,1:0.0071:2,0:1:0:25:0:0.11348:0:60:2:0.0072:0:1 0/1:147:2:1,1:131,14:145,2:0.0136:2,2:8.5:1:31.5:1:0.1943:9.0743:60:4:0.0138:0:1.5 +1 66041969 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24603;SOR=Inf;LSEQ=CATGTCTGCCTGACCCATGG;RSEQ=ACTCCACGAGTTGTGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:114,44:158,0:0:2,0:26.1:1:32.2:1:1:0:60:157:1:0:0.2 0/1:156:2:1,1:106,48:154,2:0.0128:2,2:11:1:26.5:1:0.53093:2.19601:60:4:0.0131:0:1 +1 66041983 . T C 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24809;SOR=0;LSEQ=CCATGGCACTCCACGAGTTG;RSEQ=GGTGGGTCTGATGAGCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:3:1,2:131,62:193,3:0.0153:2,2:38.3:1:28.7:1:0.24905:4.19181:60:6:0.0156:0:1 0/0:194:0:0,0:129,65:194,0:0:2,0:26.5:1:28.7:1:1:0:60:96:1:0:0.2 +1 66041989 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24828;SOR=Inf;LSEQ=CACTCCACGAGTTGTGGTGG;RSEQ=TCTGATGAGCTAGTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:142,70:212,0:0:2,0:26:1:31.2:1:1:0:59.9:41.4:1:0:0.2 0/1:215:3:2,1:136,76:212,3:0.014:2,2:16:1:23:1:1:1.12:58.3:2:0.0095:0:3.3 +1 66042078 . G T 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAATCCAGATCTGATTTG;RSEQ=GTCCCCATGCTCACAAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:202,192:394,0:0:2,0:26.2:1:31.2:1:1:0:60:77.8:1:0:0.1 0/1:337:88:41,47:126,123:249,88:0.2611:2,2:26.4:1:29.2:1:0.53727:1.17374:60:87:0.2613:0:1.1 +1 66042135 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25332;SOR=0;LSEQ=TCCTTTCCAACTTGGGCAGC;RSEQ=CTGAGCCACCAGACATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:84,159:243,3:0.0122:2,2:27:1:30.7:1:0.28035:3.76:60:6:0.0124:0:1 0/0:209:0:0,0:84,125:209,0:0:2,0:24.7:1:30:1:1:0:59.9:68.667:1:0:0.3 +1 66042192 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08857;SOR=Inf;LSEQ=GAGCCTTCCAAGTTGAAGGA;RSEQ=TTTGGGGCATTTTGGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:7,85:92,0:0:2,0:22.8:1:33:1:1:0:60:91:1:0:0 0/1:75:3:2,1:7,65:72,3:0.04:2,2:23.3:1:28:1:0.03643:17.13:60:6:0.0405:0:1.7 +1 66042199 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17191;SOR=Inf;LSEQ=CCAAGTTGAAGGACTTTGGG;RSEQ=CATTTTGGCCCTCTACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:7,77:84,0:0:2,0:23.1:1:32.1:1:1:0:60:83:1:0:0 0/1:60:2:1,1:4,54:58,2:0.0333:2,2:27.5:1:29.5:1:0.16102:12.19:60:4:0.0333:0:2 +1 66372769 . A G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01069;SOR=0.24734;LSEQ=AAAATGACCTTTCTTATTAC;RSEQ=TATACTTTTTTCCCCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:16,0:7,1:8,16:0.6667:2,1:23.3:1:29.9:1:0.33333:0:60:32:0.6667:0:1 0/1:46:15:13,2:30,1:31,15:0.3261:1,2:21.6:1:27.9:1:0.2444:4.44671:60:14:0.3111:0:1.1 +1 66372835 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52821;SOR=Inf;LSEQ=CATACAACTTCAAAAATTTT;RSEQ=GGGAGGAAGCACATTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:68,29:97,0:0:2,0:27.8:1:32:1:1:0:60:96:1:0:0.5 0/1:160:2:1,1:100,58:158,2:0.0125:2,2:36:1:29:1:1:1.71791:60:4:0.0127:0:1 +1 66372906 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.31943;LSEQ=AGCAGCAATAACTGAGTGCA;RSEQ=TAGTCCTGAATTTCTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:185:142:74,68:25,18:43,142:0.7676:2,2:27.2:1:30.7:1:0.60098:1.2746:60:70:0.765:0:1.1 1/0:275:141:68,73:68,66:134,141:0.5127:2,2:23.7:1:29:1:0.71803:1.10565:60:140:0.5128:0:1.1 +1 67356569 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.13306;SOR=Inf;LSEQ=GGAAGAAGAAGAAGAAGAAG;RSEQ=AGAAGCAGCAGCAGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:20,0:0:2,0:26.6:1:32.2:1:1:0:59.6:19:1:0:0.2 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:35:1:28:1:1:1:60:4:0.1667:0:1 +1 68598726 . A AGGCAGC 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.59333;SOR=1.38067;LSEQ=AAAGAACAACTGTCATGAAA;RSEQ=GGCAGCAGCAGCAACAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:26:13,13:4,3:7,26:0.7879:2,2:27.5:1:31:1:1:1.32179:56.7:52:0.7879:0.0909:0.1 1/1:86:72:42,30:8,5:13,72:0.8372:2,2:27.5:1:29.8:1:1:1.14107:57.5:144:0.8372:0.2558:0.4 +1 68598728 . G GCAGCGT 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07154;SOR=0;LSEQ=AGAACAACTGTCATGAAAAG;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:31,2:0.0606:2,2:49:1:32:1:1:1.06462:60:4:0.0645:0:0 0/0:89:0:0,0:52,37:89,0:0:2,0:25.5:1:29.9:1:1:0:57.3:28.667:1:0:0.4 +1 68598743 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=6;SSF=1;SOR=Inf;LSEQ=AAAAGGCAGCAGCAGCAACA;RSEQ=CAACAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:17,17:34,0:0:2,0:27.3:1:32.3:1:1:0:57.4:33:1:0:0.3 0/1:93:2:1,1:46,40:86,2:0.0215:2,2:22.5:1:28:1:1:1.14817:60:4:0.0227:0:4.5 +1 68598746 . A G 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.07556;SOR=0;LSEQ=AGGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:16,16:32,2:0.0571:2,2:5.5:1:31:1:1:1:60:4:0.0625:0:3 0/0:91:0:0,0:43,43:86,0:0:2,0:25.7:1:28.7:1:1:0:57.2:172:1:0:0.3 +1 68598752 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.5735;SOR=Inf;LSEQ=CAGCAGCAACAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,19:35,0:0:2,0:26.1:1:32.2:1:1:0:57.5:34:1:0:0.2 0/1:95:4:2,2:43,48:91,4:0.0421:2,2:20:1:29.3:1:1:1.11:46.5:8:0.0426:0:3 +1 68840797 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAGCCTTTGGGAACTG;RSEQ=TGGTGCTACATAGGGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:18.5:1:33.5:1:1:0:60:4:0.2857:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:34:0:31:0:1:0:60:2:1:0:0 +1 68841023 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25353;SOR=Inf;LSEQ=ATTTAACAATCTAGGAAGTT;RSEQ=ACAGCCACCAGCAGTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:152,58:210,0:0:2,0:25.5:1:32.1:1:1:0:59.9:51.5:1:0:0.1 0/1:248:3:1,2:143,102:245,3:0.0121:2,2:24.3:1:27.3:1:0.57365:2.7923:58.3:6:0.0122:0:1 +1 68841270 . T C 100 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01172;SOR=9.49755;LSEQ=TTACAATAAATTCATGGCCA;RSEQ=CAGATGGTATCAATTTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:1:0,1:226,149:375,1:0.0027:2,0:13:0:13:0:0.39894:0:37:0:0:0:2 0/1:404:10:6,4:221,171:392,10:0.0248:2,2:25.7:1:30.4:1:1:1.16:42.6:20:0.0253:0:1.1 +1 69777209 . C T 44 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.38437;LSEQ=CCGTCTCATCCTCTGTCCAG;RSEQ=TCTGTGCTCCGATGGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:16.3:1:28.3:1:1:0:60:6:0.6:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:48:0:32:0:1:0:60:2:0.3333:0:1 +1 69777307 . A G 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01767;SOR=0;LSEQ=ATTGATTCTTTCTCGTCATG;RSEQ=GTTTGTCTACTTTCAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:8,6:14,5:0.2632:2,2:28.2:1:30.6:1:0.62848:1.92739:60:10:0.2632:0:1.4 0/0:21:0:0,0:12,9:21,0:0:2,0:20.8:1:29.1:1:1:0:57.3:42:1:0:0 +1 69777322 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12338;SOR=0;LSEQ=TCATGAGTTTGTCTACTTTC;RSEQ=GTCTTTGAGGCTGCTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,7:18,2:0.1:2,2:39.5:1:30:1:1:1.53525:60:4:0.1:0:2 0/0:36:0:0,0:20,16:36,0:0:2,0:19.9:1:28.2:1:1:0:57.5:8:1:0:0.2 +1 69778029 . G T 68 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAACCCTCCAGTCTCCCC;RSEQ=GCTCCAGCAGGGGAAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:5:2,3:2,2:4,5:0.5556:2,2:21.6:1:29.6:1:1:1.43328:60:10:0.5556:0:1 +1 70742002 . A T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24858;SOR=Inf;LSEQ=GTAGTCTAGCATAGGTTGAA;RSEQ=CTAAAGGATAATGACAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:143,91:234,0:0:2,0:25.7:1:30.2:1:1:0:60:468:1:0:0.3 0/1:241:3:0,3:145,91:236,3:0.0124:2,0:14.3:1:21:1:0.05966:0:60:2:0.0085:0:1.3 +1 70742063 . G C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.08853;LSEQ=AGAAGATAAATAATGAATGG;RSEQ=CTTGCACACTATGCTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:81:42,39:102,105:207,81:0.2813:2,2:27:1:31.8:1:0.79334:1.11:60:80:0.2837:0:1.1 0/1:360:162:78,84:105,92:197,162:0.45:2,2:26.2:1:31.1:1:0.34164:1.22838:60:80:0.4533:0:1.2 +1 70742140 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50425;SOR=Inf;LSEQ=AATGGGAAATCTCAAATAAG;RSEQ=AACTGTCCTGCGCAATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:27,99:126,0:0:2,0:25.4:1:32.2:1:1:0:60:62:1:0:0.5 0/1:157:2:1,1:49,106:155,2:0.0127:2,2:40:1:27:1:0.53691:2.15:60:4:0.0129:0:1.5 +1 70742188 . T C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTCCTTAGAACAGTGTC;RSEQ=TTTAGTTTTTTAGGTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:3,50:0,0:0,53:1:0,2:21.9:1:33.2:1:1:0:60:52:1:0:1 1/1:51:51:4,47:0,0:0,51:1:0,2:22.9:1:31.6:1:1:0:60:102:1:0:1.1 +1 71762203 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41689;LSEQ=CTTGTTTTGGATTTTGCTAT;RSEQ=GTTCTCATTTGGATTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:668:155:73,82:234,279:513,155:0.232:2,2:27.7:1:31.4:1:0.78287:1.06:59.8:50.667:0.2324:0:1.1 0/1:796:89:39,50:336,370:706,89:0.1118:2,2:26.6:1:30.7:1:0.57343:1.16402:60:178:0.1128:0:1.2 +1 71762268 . A G 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04685;SOR=0;LSEQ=CTAAAGAGGGTGAGTATTTC;RSEQ=GGTGTTCATCGTTTGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:4:2,2:93,229:322,4:0.0123:2,2:19:1:25:1:0.58302:2.45:60:3:0.0093:0:1 0/0:373:0:0,0:117,256:373,0:0:2,0:24.2:1:30:1:1:0:60:185.5:1:0:0.2 +1 71762279 . G A 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.45119;SOR=2.39695;LSEQ=GAGTATTTCAGGTGTTCATC;RSEQ=TTTGGGAAAGGCAAGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:2:2,0:60,204:264,2:0.0075:2,0:1:0:26:0:0.05365:0:60:4:0.0076:0:1.5 0/1:281:5:1,4:73,202:275,5:0.0178:2,2:16:1:30.4:1:1:1.44376:60:10:0.018:0:1.6 +1 72058192 . C T 80 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAAACAACAAAATCTCA;RSEQ=CAAATCTACTGACTTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:19.2:1:31:1:1:0:60:12:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:17:0:32:0:1:0:60:2:1:0:1 +1 72058367 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCCATGTGTAAGGATTG;RSEQ=GTGATGTATAAGGAATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:119:119:117,2:0,0:0,119:1:0,1:24.6:1:30.2:1:1:0:60:118:1:0:1.8 1/1:71:71:69,2:0,0:0,71:1:0,1:22.7:1:29.7:1:1:0:60:142:1:0:2 +1 72058405 . T C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTCACATCAGGTTGAGTTT;RSEQ=AAAATGAACGTACTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:233:232:224,8:0,0:0,232:0.9957:0,1:23:1:32.6:1:1:0:60:231:1:0:1.4 1/1:185:185:178,7:0,0:0,185:1:0,1:24.6:1:31.1:1:1:0:60:91.5:1:0:1.4 +1 72058552 . G A 318 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20167;SOR=2.77853;LSEQ=AGCTTGTTGGCAGCCACACA;RSEQ=GTATAATTGCCGAAGTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1456:1449:744,705:1,1:2,1449:0.9952:2,2:26.4:1:31.1:1:1:1.06:60:79.5:0.9965:0:1.1 1/1:1729:1726:855,871:0,0:0,1726:0.9983:0,2:25.6:1:29.6:1:1:0:60:68.04:0.9982:0:1.1 +1 72058774 . CG TA 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=ACGCTGACGTTAGCATATAA;RSEQ=TGATAATGGTGCAATTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:1,132:133,0:0:1,0:24.9:1:32.4:1:1:0:60:32.25:1:0:1.1 0/1:94:8:1,7:1,85:86,8:0.0851:1,2:17.6:1:29.9:1:0.16381:11.43:60:16:0.086:0.0106:1 +1 72058775 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00177;SOR=0;LSEQ=CGCTGACGTTAGCATATAAC;RSEQ=TGATAATGGTGCAATTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:128:128:1,127:0,0:0,128:1:0,1:25.3:1:31.6:1:1:0:60:63:1:0:1.1 1/1:90:83:1,82:0,0:0,83:0.9222:0,1:24.2:1:30.6:1:1:0:60:166:1:0:1 +1 72058827 . G A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03643;SOR=0;LSEQ=TTAGTAGATTTGGGGGAGGT;RSEQ=AGGTTGCATGTCAGCTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:6:0,6:1,42:43,6:0.1224:1,0:20:1:31.7:1:1:0:60:12:0.125:0:2 0/0:36:0:0,0:2,34:36,0:0:2,0:23.9:1:31:1:1:0:60:35:1:0:0.6 +1 72076617 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17789;SOR=Inf;LSEQ=GCTGCTGAGAATCATTCAAG;RSEQ=CAGTTAAAGAAATTGCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:228,3:231,0:0:1,0:24.1:1:32.4:1:1:0:59.9:56.75:1:0:0 0/1:169:2:1,1:161,6:167,2:0.0118:1,2:37.5:1:32:0:0.08136:24.92023:60:4:0.012:0:1 +1 72076795 . G T 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACTGCGTCCGGGGGTCAC;RSEQ=GTGCCAGATTTAATTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1047:0:0,0:422,621:1043,0:0:2,0:24.7:1:30.6:1:1:0:60:79.231:0.9971:0:0.1 0/1:1092:51:22,29:454,586:1040,51:0.0467:2,2:24.6:1:29.5:1:1:1.02124:60:102:0.0472:0:1.1 +1 72076894 . A T 94 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00608;SOR=12.03464;LSEQ=TAATCCTCAACAGAAATATG;RSEQ=CACACATATATTTTTATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:1:0,1:8,191:199,1:0.005:1,0:30:0:14:0:1:0:60:0:0:0:1 0/1:157:9:0,9:10,138:148,9:0.0573:2,0:18.2:1:29.7:1:1:0:60:18:0.0581:0:1 +1 72241677 . AAAAT A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=44;MSI=12.000;MSILEN=4;SSF=0.65571;SOR=0.7884;LSEQ=CAGAGTAAGACTCTGTCTCA;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:31:31,0:28,0:28,31:0.5082:1,1:14.1:1:31.4:1:1:0:50.3:62:0.5082:0.2295:0.1 0/1:29:13:13,0:16,0:16,13:0.4483:1,1:18.2:1:30.9:1:1:0:45.9:26:0.4483:0.1724:0 +1 72241731 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49939;SOR=0;LSEQ=AATAAATAAATAAATGCATT;RSEQ=TGCCTACCGCATGAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:165,1:166,2:0.0119:1,2:11:1:29:1:0.02374:116.89256:40.5:4:0.012:0:1.5 0/0:154:0:0,0:153,1:154,0:0:1,0:22.6:1:31.3:1:1:0:58.2:308:1:0:0.1 +1 72242039 . G A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=2.55446;LSEQ=ATAAAGTTTTGTTGAAGTAC;RSEQ=TATGATTAATTCCATAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:271:212:27,185:7,52:59,212:0.7823:2,2:23.6:1:31.4:1:1:1.08:59.9:211:0.7815:0:1.1 1/1:316:285:33,252:8,23:31,285:0.9019:2,2:22.8:1:30.5:1:0.04291:2.64538:60:284:0.9016:0:1.1 +1 72400491 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGACTACAATACTTGCATA;RSEQ=CTTTTTTTAAATGTGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:10,0:10,2:0.1667:0,2:11:1:29:1:0.16667:0:60:4:0.1667:0:1.5 0/0:3:0:0,0:3,0:3,0:0:0,0:12.3:1:31:1:1:0:47.3:6:1:0:0 +1 72400656 . A G 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00417;SOR=Inf;LSEQ=CAACAAATATTTCAATGACA;RSEQ=CAAATATTTCAACATTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:132,1:133,0:0:1,0:24.1:1:30.8:1:1:0:59.7:43.333:1:0:0.1 0/1:115:7:7,0:107,1:108,7:0.0609:1,0:19.7:1:31.6:1:1:0:60:14:0.0619:0:1 +1 72401095 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23388;SOR=Inf;LSEQ=TTTTGCTGAATAATAGCACA;RSEQ=CATCAAATGCAAACATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:2,195:197,0:0:1,0:23.7:1:32.6:1:1:0:60:48.25:1:0:0.1 0/1:185:2:0,2:4,178:182,2:0.0108:1,0:11:1:29.5:1:1:0:60:4:0.0109:0:1 +1 72401185 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.38192;SOR=0.5557;LSEQ=CAAATGTGAAACAATACTTG;RSEQ=GTACAGTTTTTTTAAGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:14:0,14:0,20:20,14:0.4118:1,1:18.9:1:30.2:1:1:0:58.9:28:0.4242:0:1.1 0/1:18:5:0,5:0,13:13,5:0.2778:1,0:23.2:1:30.4:1:1:0:60:10:0.2778:0:1 +1 72646511 . C T 41 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33811;SOR=0.28151;LSEQ=CCTAGGGTTTAAAACTGTCT;RSEQ=AGGGAGGCTCTGCTTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:188,91:279,3:0.0106:2,2:13:1:26.3:1:0.25374:4.10923:54.7:6:0.0109:0:1.3 0/0:332:1:1,0:216,115:331,1:0.003:2,0:23:0:20:0:1:0:60:2:0.003:0:1 +1 72646585 . A AT 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.0469;SOR=1.92446;LSEQ=CTTGCAGCAGTTAGTTTGGG;RSEQ=TTTTTTTTTCTATAGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:15:8,7:245,247:492,15:0.0296:2,2:26.3:1:29.1:1:0.80045:1.15:52:14:0.0283:0.0039:0 0/1:541:30:13,17:240,270:510,30:0.0555:2,2:26.8:1:28.6:1:0.71147:1.16207:53.1:29:0.0551:0.0037:0.2 +1 72646658 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10837;SOR=Inf;LSEQ=ACTGTGGTGCTGATGGTGCA;RSEQ=CATGTCTGATGGGAATACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:65,193:258,0:0:2,0:24.8:1:31.3:1:1:0:59.4:35.857:0.996:0:0.1 0/1:237:3:1,2:59,175:234,3:0.0127:2,2:35.3:1:29.7:1:1:1.48:46:6:0.0132:0:1 +1 72747844 . C T 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00211;SOR=0.38772;LSEQ=CCAGCATAAACGGGCCGGGG;RSEQ=TCCGGGAAGAATCTGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:101:99,2:29,2:31,101:0.7652:2,1:26.3:1:29.9:1:0.23452:3.37:59:100:0.7634:0:1.1 1/0:79:44:44,0:32,2:34,44:0.557:2,1:22.5:1:29.5:1:0.18681:0:60:88:0.5789:0:1 +1 72748329 . TTTTC T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54451;SOR=0;LSEQ=TTGGTGGGTGGGTGGGTTTC;RSEQ=TTTCTTTCTTCCCCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:0,2:0,76:76,2:0.0256:1,0:39.5:1:28:1:1:0:60:4:0.027:0:0 0/0:41:0:0,0:0,41:41,0:0:1,0:20:1:28.3:1:1:0:45:7.2:1:0:0.5 +1 72748567 . G GTCCT 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.806;LSEQ=CGCCGGCGAGTGAGGGAGGA;RSEQ=GCGCGGCGGCGGGGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:5,5:4,2:6,10:0.625:2,2:28.9:1:30.3:1:0.63287:1.91506:60:20:0.625:0.1875:0 1/0:14:8:3,5:3,3:6,8:0.5714:2,2:23.1:1:28.5:1:1:1.60599:60:16:0.5714:0.1429:0 +1 72748596 . AGCG A 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.14584;SOR=0.15633;LSEQ=GCGGGGGAGGAGGCAGGGCG;RSEQ=GCGGCGGCGGCGGCTGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:2,2:7,8:15,4:0.2105:2,2:23:1:32.8:1:1:1.13:60:8:0.2222:0:0.3 0/1:26:1:0,1:11,14:25,1:0.0385:2,0:50:0:30:0:1:0:60:2:0.0385:0:0 +1 72748669 . A C 101 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00167;SOR=0;LSEQ=CAGCAGCAGAAGCAGCGCGG;RSEQ=GCGCTGCGCCGGCCGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:4,5:0,0:0,9:1:0,2:20.9:1:32:1:1:0:52.2:18:1:0:1.2 0/1:13:4:2,2:4,5:9,4:0.3077:2,2:26:1:29.8:1:1:1.23:60:8:0.3077:0:1 +1 75413421 . C T 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58204;SOR=2.44724;LSEQ=TTTCACTCCTATGTGAGTCT;RSEQ=ACGAGGGGAAGGGGTAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:8,0:8,1:0.1:0,0:2:0:30:0:1:0:60:2:0.1:0:1 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:33:1:32:0:1:0:60:4:0.2222:0:1 +1 75413501 . CTT C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01038;SOR=6.3069;LSEQ=AAAGTCCTTTCGAAAAAGAA;RSEQ=ATCAATCTGTAAAGAAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:2,1:29,8:37,3:0.075:2,2:27:1:34.7:1:0.54504:1.78205:60:6:0.0789:0:0.3 0/1:29:10:7,3:12,7:19,10:0.3448:2,2:28.1:1:31.4:1:1:1.35:60:20:0.3448:0:0.1 +1 75413522 . T A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49833;SOR=0;LSEQ=TTATCAATCTGTAAAGAAAC;RSEQ=GATTTACAGTTAACTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:37,11:48,2:0.04:2,2:40:0:31:1:0.42612:3.26364:60:4:0.0408:0:1 0/0:42:0:0,0:28,14:42,0:0:2,0:25.8:1:29.7:1:1:0:60:41:1:0:0.1 +1 75413622 . C T 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12412;SOR=2.1389;LSEQ=TAGAGAGCGTGCAGAAAGTC;RSEQ=CCTGCCCTCCCAGGGACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:8:3,5:62,57:119,8:0.063:2,2:29.3:1:30.3:1:0.48515:1.80449:60:16:0.0645:0:2.1 0/1:119:15:7,8:55,49:104,15:0.1261:2,2:31.5:1:29.2:1:0.78404:1.2801:60:30:0.1282:0:1.8 +1 75413644 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22667;SOR=Inf;LSEQ=CTGCCCTCCCAGGGACTCAG;RSEQ=GATGGCCCCAGACATGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:61,76:137,0:0:2,0:25.6:1:31:1:1:0:60:44.667:1:0:0.2 0/1:125:2:1,1:60,63:123,2:0.016:2,2:43:1:29.5:1:1:1.05:60:4:0.016:0:1 +1 75413656 . A G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00944;SOR=3.44807;LSEQ=GGACTCAGGGATGGCCCCAG;RSEQ=CATGATTTTAACAGTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:6:3,3:57,70:127,6:0.0451:2,2:28.8:1:33.2:1:1:1.23:60:12:0.0455:0:2.5 0/1:128:18:6,12:53,56:109,18:0.1406:2,2:23.8:1:30.9:1:0.30917:1.8836:60:36:0.1452:0:1.7 +1 77900050 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCATACAATTTACTAA;RSEQ=TAAACCTAATCATTTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:16,36:0,0:0,52:1:0,2:21.5:1:31.1:1:1:0:60:104:1:0:1.1 1/1:65:65:23,42:0,0:0,65:1:0,2:24.7:1:30.4:1:1:0:60:130:1:0:1.1 +1 78414346 . C A 21 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76179;LSEQ=AAAGGAAACACTATTTTAAA;RSEQ=CAAAAACAAAATTAAGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:3:2,1:117,34:151,3:0.0192:2,2:9:1:23:1:0.54127:1.71371:60:2:0.0147:0:2.3 0/1:204:3:3,0:147,53:200,3:0.0147:2,0:14:1:13.3:1:0.56885:0:58.3:0:0:0:4 +1 78414402 . GT G 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00598;SOR=0;LSEQ=CATCCATATATTTAACAAAG;RSEQ=TTTTTTCCCCCACACAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:6:3,3:252,206:458,6:0.0129:2,2:29.7:1:31.5:1:1:1.22276:60:12:0.0132:0:0.2 0/0:623:0:0,0:348,275:623,0:0:2,0:27:1:28.3:1:1:0:59.9:33.611:1:0:0.2 +1 78414768 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50159;SOR=Inf;LSEQ=ATTTAAAAGGCAAACACTCC;RSEQ=AAACAGACAAACAGTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:139,21:160,0:0:2,0:22.3:1:31.5:1:1:0:59.9:79:1:0:0.1 0/1:187:2:1,1:160,24:184,2:0.0107:2,2:25:1:28:1:0.25138:6.55235:60:4:0.0108:0:1 +1 78415029 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22355;SOR=0;LSEQ=GCTGTAACCACAATTATAAG;RSEQ=CCAACATCTCATTTCTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:18,124:142,2:0.0139:2,2:38:1:29.5:1:0.24728:6.73:60:4:0.0139:0:1 0/0:160:0:0,0:33,126:159,0:0:2,0:23.3:1:30.4:1:1:0:60:78.5:0.9937:0:0.1 +1 78415038 . T C 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.90526;LSEQ=ACAATTATAAGCCCAACATC;RSEQ=CATTTCTAATAAAAACAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:1,0:14,113:127,1:0.0078:2,0:28:0:33:0:0.11719:0:60:2:0.0078:0:1 0/1:135:2:1,1:21,112:133,2:0.0148:2,2:12.5:1:26:0:0.30039:5.23:60:4:0.0152:0:1.5 +1 78415120 . CA C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.01123;SOR=Inf;LSEQ=TTGTGTTTGCCCTTGTTGAC;RSEQ=AAAAAAAAAACCCCTAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:0,32:32,0:0:1,0:28.5:1:29.7:1:1:0:59.4:9.667:1:0:0.8 0/1:17:4:0,4:0,13:13,4:0.2353:1,0:30:1:30.8:1:1:0:60:8:0.2353:0:0.3 +1 78420772 . G GA 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54785;SOR=0;LSEQ=CTGGTTGACAAATGCAATTA;RSEQ=AAAAAAAAATTTCCTTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:3,0:47,0:47,3:0.06:1,0:19.3:1:30.3:1:1:0:60:6:0.06:0:0 0/0:27:0:0,0:27,0:27,0:0:1,0:22.5:1:31.3:1:1:0:60:54:1:0:0.1 +1 78422436 . TCA T 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.73906;SOR=0.7204;LSEQ=GTGAAGTCTGTAATTCTCTC;RSEQ=CACACACACACACCACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:5:0,5:15,74:89,5:0.0532:2,0:29.6:1:32:1:1:0:60:10:0.0543:0:0 0/1:103:4:0,4:22,76:98,4:0.0388:2,0:32.5:1:30.5:1:0.57466:0:60:8:0.0392:0:0.5 +1 78425794 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51291;SOR=Inf;LSEQ=ATGCATACAAATGTAGAATC;RSEQ=ACACTAGAAAATTTAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:84,14:98,0:0:2,0:23.3:1:29.7:1:1:0:59.4:18.6:1:0:0.1 0/1:139:2:1,1:108,28:136,2:0.0144:2,2:17:0:31.5:1:0.37734:3.80756:60:4:0.0145:0:1.5 +1 78425801 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51096;SOR=Inf;LSEQ=CAAATGTAGAATCAACACTA;RSEQ=AAAATTTAATAATGTAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:95,18:113,0:0:2,0:23.2:1:32.6:1:1:0:59.5:55.5:1:0:0.1 0/1:156:2:1,1:117,36:153,2:0.0128:2,2:20.5:1:29.5:1:0.42162:3.21944:60:4:0.013:0:1 +1 78426184 . CA C 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.45024;SOR=0.40206;LSEQ=AAAGGATTTACTGGGCCCTA;RSEQ=AAAAAAAGGATGACATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:5:2,3:50,225:275,5:0.0179:2,2:27.6:1:32.8:1:0.23281:2.98:60:10:0.0182:0:1.2 0/0:276:2:0,2:81,193:274,2:0.0072:2,0:24.5:1:33:0:1:0:60:4:0.0073:0:0 +1 78426212 . GA G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49859;SOR=Inf;LSEQ=AGGATGACATAGAAAAATCA;RSEQ=AAAACACAGTAATGGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:28,149:177,0:0:2,0:22.7:1:30.9:1:1:0:59.8:43.25:1:0:0.2 0/1:178:2:1,1:46,130:176,2:0.0112:2,2:26:1:29:1:0.45947:2.81:60:4:0.0114:0:1.5 +1 78426231 . A G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01495;SOR=Inf;LSEQ=AGAAAAACACAGTAATGGTT;RSEQ=AACAACTCTACGGCCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:19,105:124,0:0:2,0:22.5:1:30.6:1:1:0:60:123:1:0:0.1 0/1:135:7:2,5:28,100:128,7:0.0519:2,2:27.4:1:30.6:1:0.65124:1.42:60:14:0.0519:0:1.3 +1 78426284 . T C 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TACCCTCTTATAGTCACAAA;RSEQ=AACAAATTTTAGGTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:1,51:52,0:0:1,0:25.5:1:28.7:1:1:0:59.1:51:1:0:0 0/1:36:11:0,11:1,24:25,11:0.3056:1,0:25.5:1:31.1:1:1:0:60:10:0.2941:0:1.3 +1 78428596 . G A 104 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00755;SOR=6.16005;LSEQ=GCACCAGACTGCTGGCTTAT;RSEQ=CTTTTTATGGTTTCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:577:2:1,1:203,372:575,2:0.0035:2,2:20:0:30.5:1:1:1.83:55.5:4:0.0035:0:4.5 0/1:619:13:5,8:224,381:605,13:0.021:2,2:27.2:1:28.2:1:1:1.06:60:26:0.0212:0:1.7 +1 78428639 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25025;SOR=Inf;LSEQ=AAATCAAAAGACAGTAATTT;RSEQ=TCTAAAGGTTTCAAGGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:50,222:272,0:0:2,0:24.6:1:33.2:1:1:0:60:89.667:1:0:0.1 0/1:298:3:2,1:82,212:294,3:0.0101:2,2:18.7:1:26.7:1:0.19383:5.14:60:6:0.0101:0:1 +1 78428851 . A C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CTTAGTATGTTTAAACATAA;RSEQ=CTTAATGTGATTATAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:7,0:0:2,0:10.4:1:30.1:1:1:0:57:14:1:0:0 1/0:4:2:0,2:0,2:2,2:0.5:0,0:19:1:30.5:1:1:0:60:4:0.5:0:1 +1 78429084 . C A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00285;SOR=Inf;LSEQ=ATTAAAATCCTGCTCTTTCT;RSEQ=TAAATATACATGAGATCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:21,1:22,0:0:1,0:26.5:1:33.1:1:1:0:58.3:44:1:0:0.1 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:15.4:1:28.8:1:1:0:60:10:0.4167:0:1 +1 78429215 . A G 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=GCAACAGAAAGTGTCCAGAA;RSEQ=AATGAATAATGTGTTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:221,68:289,0:0:2,0:22.5:1:30.3:1:1:0:60:95.333:0.9965:0:0.1 0/1:291:14:11,3:215,62:277,14:0.0481:2,2:19.9:1:31:1:1:1.06:60:28:0.0488:0:1.1 +1 78429219 . G T 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37452;SOR=3.76064;LSEQ=CAGAAAGTGTCCAGAAAAAT;RSEQ=AATAATGTGTTAAAACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:0,1:235,73:308,1:0.0032:2,0:1:0:24:0:0.23948:0:60:2:0.0033:0:1 0/1:331:4:2,2:243,84:327,4:0.0121:2,2:12.5:1:26.8:1:0.27782:2.88181:60:8:0.0121:0:1 +1 78429408 . G C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGGATTACCAGCCTATAGA;RSEQ=AGGGAAAGACAAGAACGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:139,350:489,0:0:2,0:25.8:1:32.3:1:1:0:60:60.125:1:0:0.1 0/1:578:44:16,28:190,344:534,44:0.0761:2,2:25.1:1:31:1:1:1.03:60:88:0.0767:0:1.1 +1 78430093 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24739;SOR=Inf;LSEQ=CTAGCTTCTCAGGGTTTAAA;RSEQ=TAAAAAAAAGTATTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:30,114:144,0:0:2,0:21:1:31.7:1:1:0:59.8:27.8:1:0:0.2 0/1:143:2:1,1:28,112:140,2:0.014:2,2:22:1:28:1:0.3679:3.95:60:4:0.0145:0:1 +1 78430094 . TA T 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.62228;SOR=2.9892;LSEQ=TAGCTTCTCAGGGTTTAAAG;RSEQ=AAAAAAAGTATTTTAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:0,1:29,106:135,1:0.0074:2,0:42:0:33:0:1:0:60:2:0.0075:0:0 0/1:138:3:1,2:27,108:135,3:0.0217:2,2:19.3:1:30:1:0.49638:1.99:60:6:0.0224:0:0 +1 78430234 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19114;SOR=Inf;LSEQ=AAGTATAAAGGTGAAATAAA;RSEQ=GGATAACAATGTTAGAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:162,15:177,0:0:2,0:23.2:1:30.4:1:1:0:59.9:28.5:1:0:0.1 0/1:138:2:2,0:123,13:136,2:0.0145:2,0:16.5:1:30.5:1:1:0:60:4:0.0147:0:1 +1 78430689 . A AG 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19838;SOR=0.57839;LSEQ=AAATAATATATATTAACAAA;RSEQ=GAAGTGGACAAAAATGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:412:402:233,169:4,5:9,402:0.9757:2,2:25.6:1:32.2:1:0.50307:1.72:59.8:43.667:0.9776:0.0971:0.1 1/1:509:488:265,223:7,9:16,488:0.9587:2,2:25.7:1:30.5:1:0.45198:1.53:59.9:43.364:0.9675:0.1139:0.1 +1 78432313 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24762;SOR=Inf;LSEQ=TAAAGCAGTAACAAAGAGAA;RSEQ=AGACAAAATTCAAAGAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:141,17:158,0:0:2,0:22.7:1:33.2:1:1:0:60:78:1:0:0.1 0/1:157:2:1,1:122,33:155,2:0.0127:2,2:16:1:27:1:0.38731:3.65744:60:4:0.013:0:1 +1 78432503 . G C 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCATTATTGTTACTAGAAG;RSEQ=CTTAAAAAAAAAAAAAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:142,137:279,0:0:2,0:22.3:1:30.7:1:1:0:59.7:12.95:0.9962:0:0.5 0/1:349:80:41,39:128,134:262,80:0.2292:2,2:22.1:1:29:1:0.79847:1.10:59.7:7.889:0.2145:0:1.5 +1 78432647 . G GA 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.85124;SOR=0.88247;LSEQ=CCTCTGCCAATTACTAGTTA;RSEQ=AAAAAAAAAAATTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:14:6,8:128,169:297,14:0.0449:2,2:33.4:1:31.1:1:1:1.00983:58.2:28:0.047:0:0.6 0/1:402:16:9,7:177,206:383,16:0.0398:2,2:34.9:1:29.4:1:0.4548:1.49:59.7:15:0.0405:0:0.7 +1 78432658 . AT A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=4.91881;LSEQ=TACTAGTTAGAAAAAAAAAA;RSEQ=TTTTTTTTTGGTTGAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:12:6,6:128,143:271,12:0.0399:2,2:23.3:1:31.9:1:1:1.12:60:24:0.0407:0.0066:0.3 0/1:359:61:30,31:136,159:295,61:0.1699:2,2:21.5:1:29.6:1:0.67477:1.13:60:122:0.1743:0.0724:0.5 +1 78432659 . T A 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTAGTTAGAAAAAAAAAAA;RSEQ=TTTTTTTTTGGTTGAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:18:6,12:128,143:271,18:0.0598:2,2:13.7:1:30.3:1:0.33096:1.78673:60:36:0.061:0:1.1 0/0:359:0:0,0:136,159:295,0:0:2,0:22.6:1:29.3:1:1:0:59.7:48.167:0.8257:0:0.3 +1 78432670 . G T 42 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66564;SOR=0.56593;LSEQ=AAAAAAAAATTTTTTTTTTG;RSEQ=TTGAAAGATTCTAAAGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:148,148:296,3:0.01:2,2:11.3:1:26.7:1:1:1.99553:60:6:0.0103:0:1.3 0/0:351:2:1,1:168,181:349,2:0.0057:2,2:16:1:18.5:1:1:1.08:60:1:0.0029:0:2.5 +1 78433801 . T C 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATGAACAAAATCTTAACA;RSEQ=TGAAATTGTTACTTTAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:292,183:475,0:0:2,0:23.3:1:30.5:1:1:0:59.9:46.5:1:0:0.1 0/1:511:64:41,23:264,183:447,64:0.1252:2,2:21:1:30.9:1:0.49705:1.24:60:128:0.1262:0:1.1 +1 78434683 . A G 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12503;SOR=Inf;LSEQ=CACGTTTACATACTGAACAC;RSEQ=GGTAATAAATAAAAATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:227,138:365,0:0:2,0:24.7:1:30.9:1:1:0:59.9:72:1:0:0.1 0/1:393:4:2,2:216,173:389,4:0.0102:2,2:31.3:1:28.5:1:1:1.24784:60:8:0.0103:0:1 +1 78434821 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24587;SOR=Inf;LSEQ=CAACATCTGAAGCATCATTA;RSEQ=CTCATTTTTTTTCTACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:30,121:151,0:0:2,0:25.8:1:32.1:1:1:0:60:24.167:0.9932:0:0.1 0/1:150:2:1,1:37,111:148,2:0.0133:2,2:20:1:31:1:0.44376:2.97:60:4:0.0137:0:1 +1 78435700 . C A 57 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75434;SOR=0.72038;LSEQ=CCTCCAATTTTTGCTGCAAT;RSEQ=TAAAAAAAAAAAAGAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:6:5,1:94,295:389,6:0.0151:2,2:5.8:1:22.2:1:0.00439:15.56:60:5:0.0144:0:1.3 0/1:366:4:4,0:118,242:360,4:0.0109:2,0:1:0:22.3:1:0.01221:0:60:8:0.0121:0:1.3 +1 78435701 . TA T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.44553;SOR=0.83856;LSEQ=CTCCAATTTTTGCTGCAATC;RSEQ=AAAAAAAAAAAGAAAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:53:9,44:71,222:293,53:0.1468:2,2:29.7:1:31.5:1:0.2913:1.56171:59.9:106:0.1519:0.0055:0.3 0/1:349:44:8,36:100,192:292,44:0.1261:2,2:27.3:1:30.6:1:0.03753:2.33854:59.9:88:0.129:0:0.3 +1 78442593 . C G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCTTCTAGCGACTTCA;RSEQ=TTCTGGGTCCTTGCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:30:1:1:0:60:4:1:0:1 +1 78444734 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00354;SOR=Inf;LSEQ=CCTGTTCAGAGACTTCCTCT;RSEQ=AGCTAACAGCTAAGAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:24,157:181,0:0:2,0:24.1:1:32.6:1:1:0:59.9:89.5:0.9944:0:0.1 0/1:184:9:0,9:35,139:174,9:0.0489:2,0:15.3:1:28.6:1:0.21056:0:60:18:0.0495:0:1.1 +1 78444764 . C CGGCCG 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.45203;SOR=1.40394;LSEQ=CTAAGAAAGAAAGAAAATGG;RSEQ=GGCCGTCGAAGCTCTATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:17:1,16:9,80:89,17:0.1604:2,1:22.6:1:31.6:1:1:1.79156:59.4:34:0.1667:0.0472:0.1 0/1:85:18:2,16:6,61:67,18:0.2118:2,2:21.4:1:30.3:1:0.67473:1.27:59.7:36:0.2118:0.0706:0.1 +1 82939448 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.21048;SOR=Inf;LSEQ=TAGTCTCAAGGATCCATTTC;RSEQ=TGTTTAATAATGTTTACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:135,39:174,0:0:2,0:23.5:1:30.6:1:1:0:60:86:1:0:0.1 0/1:148:2:1,1:116,29:145,2:0.0135:2,2:25.5:1:29.5:1:0.36763:3.94968:60:4:0.0136:0:1 +1 82939464 . A T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11967;SOR=Inf;LSEQ=TTTCATGTTTAATAATGTTT;RSEQ=CATACCTGAAAAGAAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:153,58:211,0:0:2,0:26:1:28.7:1:1:0:60:210:1:0:0.2 0/1:206:3:1,2:147,56:203,3:0.0146:2,2:21:1:21.7:1:0.19188:5.20056:60:2:0.0099:0:1 +1 82939537 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.09837;LSEQ=AAGATCTGGTACTTTTGTAA;RSEQ=GGCTTCAAAGGAACTGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:95:45,50:138,154:292,95:0.2455:2,2:26.8:1:30.3:1:1:1.00:60:94:0.2442:0:1.2 0/1:473:192:97,95:134,147:281,192:0.4059:2,2:27.1:1:29.8:1:0.57468:1.12:60:191:0.4064:0:1.3 +1 82939621 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.34012;LSEQ=TTAGAGGAACCAGTTCAATT;RSEQ=ACTACATTTTGTAGATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:31:6,25:29,110:139,31:0.1824:2,2:22.2:1:32.5:1:1:1.09789:60:30:0.1775:0:1.3 0/1:180:77:23,54:27,76:103,77:0.4278:2,2:21.6:1:30.3:1:0.61671:1.20:59.8:76:0.4246:0:1.4 +1 82939664 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50174;SOR=0;LSEQ=TCAAATTCATCTAAGAAACC;RSEQ=ATGTAACACCTACTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:0,2:3,69:72,2:0.027:1,0:16:1:32:1:1:0:60:4:0.027:0:1 0/0:60:0:0,0:4,56:60,0:0:2,0:22.4:1:27.5:1:1:0:60:59:1:0:0.4 +1 83024609 . G T 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08641;SOR=0;LSEQ=AGAACATTGCTCTTTAATTT;RSEQ=TTAAAATAAGTATGGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:3:1,2:101,23:124,3:0.0236:2,2:7.3:1:27.7:1:0.09869:8.56924:60:6:0.0236:0:1 0/0:159:0:0,0:110,49:159,0:0:2,0:24.1:1:31.6:1:1:0:60:158:1:0:0.2 +1 83024629 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18945;SOR=0;LSEQ=GTTAAAATAAGTATGGTAAA;RSEQ=ACATTGCATATTATGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:129,46:175,2:0.0113:2,2:22:1:32:1:0.46167:2.78509:60:4:0.0114:0:1 0/0:229:0:0,0:142,86:228,0:0:2,0:24.4:1:29.3:1:1:0:60:56:0.9956:0:0.4 +1 83024692 . A G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=5.37792;LSEQ=GGCAACATGAAAACTTTAGT;RSEQ=AAGAGAACTCCAGTGTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:76:42,34:138,128:266,76:0.2222:2,2:25.5:1:31.9:1:0.69616:1.15:59.8:75:0.2226:0:1.1 1/0:343:208:95,113:67,68:135,208:0.6064:2,2:26.5:1:31:1:0.50735:1.17143:60:207:0.607:0:1.2 +1 83024780 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58349;SOR=2.57251;LSEQ=ACATTTTTGAAGACAGTTTT;RSEQ=TTGACTTCAATTTGGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:1,0:26,98:124,1:0.008:2,0:1:0:23:0:0.216:0:60:2:0.0082:0:2 0/1:98:2:1,1:20,76:96,2:0.0204:2,2:22:1:30.5:1:0.38439:3.73:60:4:0.0206:0:1 +1 84971721 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52925;SOR=Inf;LSEQ=CGGTTGAGTCCGGCCTCCAG;RSEQ=CGGAGCTGTTGAACCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:27,13:40,0:0:2,0:25.6:1:31.6:1:1:0:58.2:39:1:0:0.1 0/1:68:2:1,1:41,25:66,2:0.0294:2,2:45.5:1:28:1:1:1.62758:60:4:0.0303:0:1 +1 84971732 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5106;SOR=Inf;LSEQ=GGCCTCCAGCCGGAGCTGTT;RSEQ=AACCACTTTCTTCATAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:34,17:51,0:0:2,0:23.9:1:31.9:1:1:0:57.5:50:1:0:0.2 0/1:72:2:1,1:41,29:70,2:0.0278:2,2:9.5:1:26.5:1:1:1.40686:60:4:0.0286:0:1 +1 84971788 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52586;SOR=Inf;LSEQ=CAGACATGGTGCACGCGACG;RSEQ=CCGGGCCGATTCGTGGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:12,21:33,0:0:2,0:28:1:30.5:1:1:0:57.1:15.5:1:0:0.4 0/1:55:2:1,1:22,30:52,2:0.0364:2,2:15:1:30:0:1:1.36:60:4:0.0377:0:1.5 +1 84971819 . G A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.0087;SOR=0;LSEQ=TCGTGGGTCGGTGGGTCGTG;RSEQ=GCCGTGGGTCGGCGGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:1,5:6,13:19,6:0.24:2,2:24:1:29.5:1:0.63715:2.23947:56.7:5:0.2083:0:2 0/0:27:0:0,0:5,22:27,0:0:2,0:19.1:1:29.4:1:1:0:54.8:26:1:0:0.2 +1 84971833 . G C 67 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.18213;SOR=0.18282;LSEQ=GTCGTGGGCCGTGGGTCGGC;RSEQ=GGGCCAGACAACTCAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:1,4:1,13:14,5:0.2632:1,2:18.2:1:29.2:1:0.46784:3.02:56:10:0.2632:0:2.2 0/1:17:1:0,1:1,15:16,1:0.0588:1,0:19:0:32:0:1:0:46:2:0.0625:0:1 +1 85732941 . A C 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGACTGGCAAAGACTATT;RSEQ=GACTCTTGAAAATTTCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:0,1:1,4:0.8:0,0:27.5:1:31:1:0.2:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 85733374 . C T 216 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=62.25147;LSEQ=CACTAGAGTTTGCACAAGTT;RSEQ=CTTCTTCTTCTAACTGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1731:3:1,2:897,831:1728,3:0.0017:2,2:28:1:30:1:0.61123:2.15793:60:6:0.0018:0:1 0/1:1772:173:86,87:822,773:1595,173:0.0976:2,2:23.5:1:29.1:1:0.68905:1.07569:59.8:85.5:0.0982:0:1.1 +1 85733670 . A G 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCTACATTTTAGTCCTAC;RSEQ=ATAAAATTATTCAGATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:799:0:0,0:281,518:799,0:0:2,0:25.1:1:30.6:1:1:0:59.9:71.636:1:0:0.1 0/1:899:27:9,18:322,550:872,27:0.03:2,2:23.1:1:30.4:1:0.84024:1.17074:60:54:0.0303:0:1.2 +1 85733704 . TA T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06218;SOR=0;LSEQ=GATGTAAATGAAAAAGTAAC;RSEQ=AAAAAATGGAGTCACTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:5:2,3:100,338:438,5:0.0113:2,2:35.6:1:31.4:1:0.32539:2.25:60:10:0.0115:0:0 0/0:421:0:0,0:97,324:421,0:0:2,0:22:1:29:1:1:0:60:59.143:1:0:0.1 +1 85733737 . TGTTAA T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00078;SOR=Inf;LSEQ=TCACTGTCCATCTTGTGACT;RSEQ=AGATTACAAGCTAGTTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:11,205:216,0:0:2,0:24.8:1:32.5:1:1:0:59.9:107:1:0:0.1 0/1:182:9:1,8:10,163:173,9:0.0495:2,2:28.3:1:30.9:1:0.43687:2.03:60:18:0.0495:0:0 +1 85733929 . C T 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCTCATTTAAGGTACAG;RSEQ=GTACATATAAACTTAACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:23.9:1:28.3:1:1:0:60:8:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:21.5:1:31:0:1:0:60:4:1:0:1 +1 85736510 . AT A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04871;SOR=0.62087;LSEQ=CAGTGTCTTCTCTACTGAGT;RSEQ=TTTTTTTGCACGTAGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1426:45:26,19:648,731:1379,45:0.0316:2,2:24.3:1:31.4:1:0.17318:1.54:60:90:0.0318:0.0035:0.2 0/1:1614:32:15,17:742,840:1582,32:0.0198:2,2:26.8:1:29.8:1:1:1.00111:59.7:64:0.0199:0.0012:0.3 +1 85739749 . T C 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5352;SOR=0;LSEQ=GAATGCTCTTCCCTCAGTTC;RSEQ=GTCAAATCTTTCAGGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:3,1:13,0:13,4:0.2353:1,2:33:1:32.5:1:0.23529:0:60:8:0.2353:0:2 0/0:5:0:0,0:5,0:5,0:0:0,0:24.8:1:30.2:1:1:0:60:10:1:0:0 +1 85739751 . T C 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2719;SOR=0;LSEQ=ATGCTCTTCCCTCAGTTCTG;RSEQ=CAAATCTTTCAGGAATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:7,0:10,1:11,7:0.3889:2,0:22.4:1:32.1:1:1:0:60:14:0.3889:0:1.3 0/0:5:0:0,0:5,0:5,0:0:0,0:26:1:29.4:1:1:0:60:10:1:0:0 +1 85739778 . A G 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01124;SOR=0;LSEQ=TTTCAGGAATCAGTTTAAAT;RSEQ=TAACCTCTCCTGACCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:10,1:23,0:23,11:0.3235:1,2:22.6:1:33.2:1:0.32353:0:60:22:0.3235:0:1.7 0/0:15:0:0,0:15,0:15,0:0:1,0:18.9:1:28.1:1:1:0:60:30:1:0:0.1 +1 85739861 . A G 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=4e-05;SOR=0.13736;LSEQ=ATTCCTTCATAGTAATTGCA;RSEQ=TAATGAAAACAAAATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:31:31,0:77,0:77,31:0.287:1,1:23.2:1:33.3:1:1:0:60:62:0.2897:0:1.2 0/1:77:4:4,0:73,0:73,4:0.0519:1,0:19:1:29.5:1:1:0:60:8:0.0526:0:1 +1 85740024 . T C 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.63138;LSEQ=TCACTGCACTTATTTTGTGA;RSEQ=TTAAAACAATCCCCCTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1158:211:100,111:461,486:947,211:0.1822:2,2:27.2:1:32.7:1:0.76091:1.05288:60:51.75:0.1805:0:1.2 0/1:1519:405:215,190:556,557:1113,405:0.2666:2,2:27.4:1:31.5:1:0.2963:1.13:59.9:134:0.2659:0:1.1 +1 85741684 . T C 86 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84124;LSEQ=AAGCATCTCCAAGAACCCAG;RSEQ=TGGGGGGAAAGCATGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:10,0:10,6:0.375:0,0:16.7:1:33.3:1:1:0:60:12:0.375:0:1.8 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:21:0:33:0:1:0:60:2:0.3333:0:1 +1 85741734 . A T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGGGCAAGAATCAAAAC;RSEQ=CCACTTGGCAACAAAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:2,0:38,0:38,2:0.05:1,0:32:1:34:0:1:0:60:4:0.0513:0:1 0/0:16:0:0,0:16,0:16,0:0:1,0:21.3:1:31:1:1:0:59.9:32:1:0:0.2 +1 85741921 . G C 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09614;LSEQ=GACTCCAGGCTTCCGCTTTC;RSEQ=TCTCCCGCTGGGCTGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:911:903:559,344:1,0:1,903:0.9912:0,2:24.2:1:31.6:1:1:0:60:59.2:0.9966:0:1.3 1/1:1113:1019:620,399:58,32:90,1019:0.9155:2,2:24.8:1:30.5:1:0.57302:1.16625:60:126.375:0.9158:0:1.2 +1 85741968 . G C 195 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGCCCGCCCTGGGCACAGCT;RSEQ=CGTTACTCACGTCCTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1483:70:39,31:713,695:1408,70:0.0472:2,2:26.2:1:31.9:1:0.46286:1.23:60:140:0.0483:0:1.6 0/0:1926:0:0,0:969,953:1922,0:0:2,0:24.9:1:31.2:1:1:0:60:67.643:0.9984:0:0.8 +1 85742012 . G C 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.54438;LSEQ=TCAGTGAGGTCCTCCTCGGT;RSEQ=AGGGACGGTGCGGTGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1555:658:338,320:434,459:893,658:0.4232:2,2:24.3:1:32.1:1:0.30416:1.12:60:53.833:0.4211:0:1.3 0/1:1903:543:269,274:670,684:1354,543:0.2853:2,2:24.8:1:31:1:1:1.00:59.9:107.6:0.2853:0:1.3 +1 85742023 . C A 222 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=36.06713;LSEQ=CTCCTCGGTGAGGGACGGTG;RSEQ=GGTGGGCTCCATGGTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1519:5:3,2:741,772:1513,5:0.0033:2,2:34.6:1:24.4:1:0.68114:1.56:60:1.5:0.002:0:1.2 0/1:1850:197:99,98:815,837:1652,197:0.1065:2,2:23.8:1:29.2:1:0.82143:1.04:60:48.25:0.1058:0:1.2 +1 85742157 . G C 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00183;SOR=0;LSEQ=GAGGAGGCGGAGCGGGTCGG;RSEQ=AGAAAGACGGCCGCCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:10:0,10:14,221:235,10:0.0403:2,0:27.9:1:31:1:1:0:60:9:0.0378:0:1.1 0/0:236:0:0,0:13,223:236,0:0:2,0:24.1:1:31.1:1:1:0:60:77.667:1:0:0.2 +1 85742167 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24966;SOR=0;LSEQ=AGCGGGTCGGGAGAAAGACG;RSEQ=CCGCCCCTTCGGGAACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:3:1,2:8,194:202,3:0.0146:1,2:16.3:1:29:1:0.1266:11.70:60:6:0.0155:0:1 0/0:188:0:0,0:11,177:188,0:0:2,0:23:1:31.3:1:1:0:60:19.889:1:0:0.2 +1 85742264 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.06346;SOR=Inf;LSEQ=GCGAATCTACGCGACGCGAC;RSEQ=CGGAGCTCGGAGCAGCGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:1,44:45,0:0:1,0:24.8:1:33.1:1:1:0:60:90:0.9783:0:0.3 0/1:16:2:0,2:0,14:14,2:0.125:1,0:36.5:1:31.5:1:1:0:60:4:0.125:0:1 +1 85742338 . G C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCACGGCGAGGCGCGTC;RSEQ=CTTAGCAGAGCCCGCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:1,20:0,0:0,21:1:0,1:24.2:1:30.8:1:1:0:58.8:42:1:0:1 1/1:6:6:2,4:0,0:0,6:1:0,2:26.3:1:32:1:1:0:60:12:1:0:1.3 +1 85742389 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02206;SOR=Inf;LSEQ=GCCTATCGACGCCAGCCCGC;RSEQ=GGCCGATCCTGTTCCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:1,13:14,0:0:1,0:24:1:32:1:1:0:57.3:28:1:0:0.7 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:38:1:29:1:1:0:60:4:0.6667:0:1.5 +1 85746410 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18396;SOR=Inf;LSEQ=GGATTGGGCGGGACTGAATG;RSEQ=GGATTCCGGGAGTTTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:232,15:247,0:0:2,0:24.4:1:30.3:1:1:0:60:60.75:1:0:0.1 0/1:186:2:1,1:168,15:183,2:0.0108:2,2:22:1:28:1:0.16592:10.87684:60:4:0.0108:0:2 +1 85746472 . A G 192 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=77.54631;LSEQ=GCTTTTCAGACCATGTGTCA;RSEQ=TGTTCCCAAGATGAATTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:861:1:1,0:597,261:858,1:0.0012:2,0:40:0:34:0:1:0:60:2:0.0012:0:1 0/1:833:69:48,21:509,255:764,69:0.0828:2,2:22.7:1:31.5:1:0.68962:1.14:60:138:0.0832:0:1.1 +1 85746754 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01043;SOR=0.07988;LSEQ=ACACAGCCTCCATACCCCCT;RSEQ=AACTTCCAGGTGCTCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:88:87:1,86:0,0:0,87:0.9886:0,1:24:1:32.3:1:1:0:60:42.5:0.9884:0:1.1 1/1:39:34:1,33:0,5:5,34:0.8718:0,1:24.6:1:32.9:1:1:0:60:68:0.8718:0:1.1 +1 85746929 . T C 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=CAGACAGTGTATTAGTTTCC;RSEQ=AGGGCCATCATACCAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:32.3:1:34:0:1:0:60:6:0.4286:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:31:0:27:0:1:0:60:2:0.5:0:1 +1 87267422 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTTTCATTCTGGTGGGTT;RSEQ=GTGGTCTCACTGACTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:29.5:1:1:0:60:4:1:0:1 +1 87268589 . T G 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TAGAGTAAGGATAGATTTCA;RSEQ=TATTTCTTGCAAACTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:28:0:1:0:39:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:29.5:1:1:0:54.5:4:1:0:1 +1 88553551 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49392;SOR=Inf;LSEQ=TCTAGTTTCAGTCTTTGAGG;RSEQ=TGCTGACCCTTGGATGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:29,0:0:2,0:30.7:1:33:1:1:0:51.9:58:1:0:0.1 0/1:33:2:1,1:17,14:31,2:0.0606:2,2:27:1:27.5:1:1:1.20712:55:4:0.0606:0:1 +1 88553825 . C A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=0;LSEQ=CAACCTGATGCCAGTAGGAT;RSEQ=GGTCCTGTATAGGGTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:34:1:26:1:1:1.4491:55.5:4:0.1667:0:2.5 0/0:10:0:0,0:5,5:10,0:0:2,0:20.7:1:30.7:1:1:0:59.7:20:1:0:0.1 +1 88553882 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21212;SOR=Inf;LSEQ=GATCTCATCCAGTTGGGTGG;RSEQ=ACAAGGAGCAGGACCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:24,0:0:2,0:27.5:1:31.3:1:1:0:59:11:1:0:0.1 0/1:21:2:1,1:11,8:19,2:0.0952:2,2:30.5:1:27.5:1:1:1.35399:60:4:0.0952:0:1.5 +1 89294616 . G A 63 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30341;SOR=0.20446;LSEQ=TAACAGAAAGACTAATAAAA;RSEQ=GAATGTACTCTGTACCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:18.8:1:31.8:1:1:0:59.3:8:0.4:0:1 0/1:9:1:1,0:8,0:8,1:0.1111:0,0:7:0:30:0:1:0:60:2:0.125:0:1 +1 89294935 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50013;SOR=Inf;LSEQ=GCCATGTTGAGTGGCCCAGG;RSEQ=CAATTTGCTGAGAATGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:41,58:99,0:0:2,0:26.9:1:30.2:1:1:0:59.7:98:1:0:0.1 0/1:114:2:1,1:37,75:112,2:0.0175:2,2:11:1:26.5:1:1:2.01:60:4:0.0179:0:1 +1 89294985 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50268;SOR=Inf;LSEQ=CAATTTGAGAGAGATACCTT;RSEQ=ACATGTGCTATCAAAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:69,49:118,0:0:2,0:23.7:1:32.4:1:1:0:58.4:117:1:0:0.2 0/1:143:2:1,1:92,49:141,2:0.014:2,2:17.5:1:26.5:1:1:1.86882:60:4:0.0142:0:1 +1 89295007 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1869;SOR=0;LSEQ=CATGTGCTATCAAAAGTATT;RSEQ=GCTACACCAACAGCTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:86,76:162,2:0.0121:2,2:15:0:32.5:1:1:1.13072:51:4:0.0121:0:1.5 0/0:216:0:0,0:132,84:216,0:0:2,0:20.3:1:29.8:1:1:0:59.4:107:1:0:0.3 +1 89295015 . C T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00202;SOR=0.37711;LSEQ=ATCAAAAGTATTCGCTACAC;RSEQ=AACAGCTCCACCGAGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:32:14,18:80,68:148,32:0.1778:2,2:25.2:1:28.7:1:0.33213:1.50909:55.9:31:0.1751:0:1.1 0/1:226:17:9,8:125,83:208,17:0.0752:2,2:24.7:1:28.8:1:0.61243:1.3369:57.5:34:0.0766:0:1.1 +1 90228194 . G GCA 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGCGTGCACACATGCACAT;RSEQ=CACACACACACACCTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:21.5:1:29.8:1:1:1.40151:60:4:0.1053:0:0 0/0:6:0:0,0:3,3:6,0:0:2,0:26.5:1:31.3:1:1:0:60:12:1:0:0 +1 90228235 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCTATTCGGCTGTGCGA;RSEQ=GTCTCTGCGGCCCCGCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:27.5:1:30:1:1:1.11:57.5:4:0.0952:0:1.5 0/0:10:0:0,0:5,5:10,0:0:2,0:26.4:1:31.1:1:1:0:60:20:1:0:0.3 +1 90228243 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGCTGTGCGAGGTCTCTG;RSEQ=GGCCCCGCTGTCTCCGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:8,11:19,2:0.0952:2,2:15.5:1:29.5:1:1:1.35:60:4:0.0952:0:1 0/0:9:0:0,0:4,5:9,0:0:2,0:28.8:1:31.3:1:1:0:60:18:1:0:0.3 +1 90228266 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12121;SOR=Inf;LSEQ=CCCCGCTGTCTCCGGGCATC;RSEQ=AGGGTAACATCTCTTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:14,0:0:2,0:24.6:1:29.9:1:1:0:59.6:28:1:0:0.7 0/1:8:2:1,1:2,4:6,2:0.25:2,2:17.5:1:28:1:1:1.83:60:4:0.25:0:1.5 +1 90228304 . TCT GAAAAACGTAA 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.06061;SOR=0;LSEQ=CATTTCAGACCTGGGACTGG;RSEQ=GAAACTGTATAATGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:1,5:0,2:2,6:0.75:0,2:18.7:1:30.3:1:1:0:59.2:12:0.75:0.375:1.3 0/0:3:0:0,0:1,2:3,0:0:2,0:13:1:29.7:1:1:0:60:6:1:0:0.3 +1 90739719 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50174;SOR=Inf;LSEQ=GCTGCAAAGATATAACAACA;RSEQ=CAGCAGCAACAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:30,30:60,0:0:2,0:28.8:1:33.3:1:1:0:58.7:120:1:0:0.1 0/1:74:2:1,1:35,37:72,2:0.027:2,2:42:1:29:1:1:1.06:60:4:0.027:0:1 +1 90788757 . G C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52937;SOR=Inf;LSEQ=TGCTTTAATTCATGGTGGAA;RSEQ=TTGAAGGGGAGTCAGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:29,0:0:2,0:25.4:1:32.6:1:1:0:59.2:28:1:0:0.2 0/1:50:2:1,1:27,21:48,2:0.04:2,2:42:0:31.5:1:1:1.2792:60:4:0.0408:0:1 +1 90788816 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GAGAAAGACAGAGAGGAGGA;RSEQ=GTGCCAGGCTCTTCTCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:22.6:1:31.4:1:1:0:60:22:1:0:0 0/1:32:2:1,1:14,16:30,2:0.0625:2,2:42.5:1:29:1:1:1.14:60:4:0.0667:0:2 +1 90788954 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGGCCCCACCTCCAACA;RSEQ=TGGGGATCACAGTATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:20:1:31:0:1:0:60:4:1:0:1 +1 91182381 . GGGC G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=GCCGAGCCCAGCTGCTGGGG;RSEQ=GGCGGCGGCGGCTGCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:21:1:32.7:1:1:0:60:20:1:0:0.1 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:10.5:1:29.5:1:1:1:60:4:0.3333:0:0.5 +1 91183109 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=6;SSF=0.18068;SOR=0;LSEQ=GGCGAAGGCGAAGGCGAAGG;RSEQ=GCAGGCGAAGGCGAAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:28,40:68,2:0.0286:2,2:26.5:1:28:1:1:1.42:60:4:0.029:0:2 0/0:94:0:0,0:36,58:94,0:0:2,0:23.5:1:30.2:1:1:0:59.4:188:1:0:0.2 +1 92590826 . A G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.37616;SOR=2.54377;LSEQ=AAGAGCAGAAGAAAGAATAG;RSEQ=GGGGACCTGAGACACTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:4,0:4,5:0.5556:0,2:21.2:1:32.2:1:1:0:58:10:0.5556:0:1.2 1/0:13:10:10,0:3,0:3,10:0.7692:0,0:27.6:1:29.4:1:1:0:60:9:0.75:0:1.1 +1 92590965 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24242;SOR=Inf;LSEQ=CACTGCTCAAAGATTCTATT;RSEQ=TGCAGTTATGTACTGCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:29,21:50,0:0:2,0:25.7:1:31.3:1:1:0:60:15.667:1:0:0.1 0/1:49:2:1,1:21,26:47,2:0.0408:2,2:10.5:1:25:1:1:1.23:60:4:0.0408:0:1.5 +1 92591472 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50077;SOR=Inf;LSEQ=GCAACCAGTGTTGAAGAAGG;RSEQ=GGGAGCTTTGGAGAATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:91,81:172,0:0:2,0:25.5:1:30.6:1:1:0:60:56.333:1:0:0.1 0/1:196:2:1,1:98,96:194,2:0.0102:2,2:24:1:28.5:1:1:1.02073:60:4:0.0104:0:1 +1 92591758 . C A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58062;SOR=0.37845;LSEQ=GAGAACCAGGGGATGAGTTC;RSEQ=TTATTATTCTAGAGGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:93,88:181,2:0.0109:2,2:25.5:1:30:0:1:1.05652:60:4:0.0112:0:1 0/0:242:1:1,0:124,117:241,1:0.0041:2,0:1:0:26:0:1:0:60:2:0.0042:0:1 +1 92591780 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25795;SOR=Inf;LSEQ=TATTATTCTAGAGGGGCCAG;RSEQ=TGCTATGCTGCAACGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:110,90:200,0:0:2,0:21.8:1:32.6:1:1:0:59.5:99:1:0:0.2 0/1:251:3:1,2:130,118:248,3:0.012:2,2:14:1:28.7:1:0.60762:2.19669:52.7:6:0.0121:0:1 +1 92591916 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45993;SOR=1.22295;LSEQ=GTGGTTGTACATGGCCCCTT;RSEQ=AAGTACATTAAGCTGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:81:35,46:32,15:47,81:0.6328:2,2:23.8:1:30:1:0.00985:2.78073:60:39.5:0.632:0:1.1 1/0:171:116:61,55:24,29:53,116:0.6784:2,2:22.4:1:28.6:1:0.41025:1.34:60:57:0.6746:0:1.2 +1 92591929 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50891;SOR=Inf;LSEQ=GCCCCTTGAAGTACATTAAG;RSEQ=TGGACCAGCCTAGATTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:76,72:148,0:0:2,0:23.2:1:32.4:1:1:0:60:36:0.9931:0:0.5 0/1:199:2:1,1:104,91:195,2:0.0101:2,2:30:1:27.5:1:1:1.14208:60:4:0.0102:0:2 +1 92592037 . G A 31 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.72163;LSEQ=GTCTGAAATCTGCCTCTTGG;RSEQ=CCTCCCTTTTCTCCTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:70,97:167,2:0.0118:2,2:6.5:1:29.5:1:1:1.38:29:4:0.012:0:1.5 0/0:235:2:1,1:92,140:232,2:0.0085:2,2:27:0:31:0:1:1.52:50:4:0.0086:0:3 +1 92592064 . T GTA 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.29535;SOR=1.3401;LSEQ=TTTTCTCCTCTCCTCAATCC;RSEQ=CTTCACTCATGCAGACCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:111:69:20,49:10,30:40,69:0.6216:2,2:22.3:1:29.9:1:0.82426:1.22:56.7:138:0.6449:0.1261:1.1 1/0:157:108:31,77:18,30:48,108:0.6879:2,2:21:1:28.3:1:0.35013:1.48645:57.8:107:0.6859:0.1975:1.1 +1 92592082 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50288;SOR=Inf;LSEQ=CCTCTTCACTCATGCAGACC;RSEQ=CTTTATTTTCGCTATTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:12,62:74,0:0:2,0:22:1:30.9:1:1:0:59.9:17.5:1:0:0.9 0/1:92:2:1,1:18,72:90,2:0.0217:2,2:12:1:29.5:1:0.37219:3.92:60:4:0.0217:0:2 +1 92592222 . T C 94 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51049;SOR=0.24443;LSEQ=GTACACAATTAAATAGAGTT;RSEQ=TATGGAGTCTTTGCTGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:1,6:0,3:3,7:0.7:0,2:20.3:1:33.7:1:1:0:60:14:0.7:0:1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:39:0:15:0:1:0:60:0:0:0:3 +1 93307302 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.48538;SOR=Inf;LSEQ=TCAGTTATAGTTTAAAAAAT;RSEQ=TATATTCCTATCTTTTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:8,0:0:2,0:25:1:28.4:1:1:0:60:16:1:0:0 0/1:11:2:2,0:6,3:9,2:0.1818:2,0:24.5:1:31.5:1:1:0:60:4:0.1818:0:1 +1 93307331 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5013;SOR=Inf;LSEQ=TATCTTTTGTAGGTGGAACC;RSEQ=TCCCAAAATGTCCCTTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:24,0:0:2,0:16.1:1:29:1:1:0:36.5:23:1:0:0 0/1:32:2:1,1:23,7:30,2:0.0625:2,2:12.5:1:31.5:1:0.44355:3.1396:23.5:4:0.0625:0:1 +1 93307334 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50635;SOR=Inf;LSEQ=CTTTTGTAGGTGGAACCGTC;RSEQ=CAAAATGTCCCTTGCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:24,0:0:2,0:17.8:1:29.8:1:1:0:36.5:23:1:0:0 0/1:34:2:1,1:25,7:32,2:0.0588:2,2:15.5:1:31:1:0.42068:3.40681:26.5:4:0.0588:0:1 +1 94837386 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTGAAGCCGCAGACCTTC;RSEQ=TGGTGAGTGTTACAGCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:31.5:1:1:0:59:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 94838188 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24711;SOR=Inf;LSEQ=TAATAGCAAGATGTCTGTCA;RSEQ=GGGACCTAGAAAGGGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:40,31:71,0:0:2,0:21.3:1:30.9:1:1:0:48.6:34.5:1:0:0.2 0/1:79:3:2,1:46,30:76,3:0.038:2,2:22.3:1:29.3:1:1:1.30:33.3:6:0.0385:0:1 +1 94838220 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18652;SOR=0;LSEQ=AGGGGAGAAGCCATGTCGCC;RSEQ=AACTTCAGAAGTTGGTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:38,35:73,2:0.0267:2,2:37.5:1:31.5:1:1:1.08451:30:4:0.027:0:1 0/0:98:0:0,0:53,45:98,0:0:2,0:30.6:1:31.4:1:1:0:54.5:196:1:0:0.2 +1 94838271 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84067;LSEQ=GGCATTATCTGATTTCAGAA;RSEQ=CCGTTTCCTGTAAATGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:15,32:47,2:0.0408:2,2:4.5:1:31:1:1:2.10:60:4:0.0417:0:1.5 0/1:58:2:1,1:20,36:56,2:0.0345:2,2:24:1:27.5:1:1:1.78:60:4:0.0351:0:1 +1 96258741 . CT C 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.78549;LSEQ=AAGTTTGAAAAATGCTTAGT;RSEQ=TTTTTTTTTATTAGATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:4,0:36,0:36,4:0.1:1,0:24.3:1:33.3:1:1:0:60:8:0.1:0.025:0 0/1:25:2:2,0:23,0:23,2:0.08:1,0:32.5:1:32:0:1:0:60:4:0.08:0:0 +1 96258846 . G T 48 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.37664;SOR=3.60245;LSEQ=CTTTTCCATCTGTCATTCAG;RSEQ=GGAGATAGGTACCTACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:0,1:154,96:250,1:0.004:2,0:1:0:27:0:0.38645:0:60:2:0.004:0:1 0/1:281:4:1,3:170,107:277,4:0.0142:2,2:5.8:1:24.3:1:0.30309:4.74034:60:3:0.0109:0:1.3 +1 96258925 . T G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.86541;LSEQ=GAAGGACTAAGGGCTAATGA;RSEQ=TACAACATTTTTATTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:33:13,20:73,127:200,33:0.141:2,2:23.2:1:32.2:1:0.84597:1.13:60:66:0.1429:0:1 0/1:281:125:52,73:56,100:156,125:0.4448:2,2:22.8:1:31:1:0.3878:1.27:60:124:0.446:0:1.1 +1 96258941 . T TA 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25107;SOR=Inf;LSEQ=ATGATTACAACATTTTTATT;RSEQ=AAAAAAATGCCTTATGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:57,130:187,0:0:2,0:26.1:1:29:1:1:0:60:61.333:1:0:0.2 0/1:212:3:2,1:69,140:209,3:0.0142:2,2:24.3:1:22.7:1:0.26031:4.03:60:2:0.0096:0.0047:1 +1 99248468 . CT C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTTTTTTTTGAGTCACC;RSEQ=TTTTTTTTTTTCTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:31:1:1:0:49:4:1:0:0 +1 99250254 . T TCAA 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=3;SSF=0.00722;SOR=Inf;LSEQ=CATCATCATCATCATCATCA;RSEQ=CAACAACAACAAATCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,5:12,0:0:2,0:18.2:1:31:1:1:0:57.1:24:0.9231:0:0.1 1/0:7:4:2,2:1,2:3,4:0.5714:2,2:29.5:1:26.8:1:1:1.81:55:8:0.5714:0:0.3 +1 99250311 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07655;SOR=Inf;LSEQ=GGGTCAGCAGCCTCAAAGAC;RSEQ=GAAACTAGACAAACTCACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:23,0:0:2,0:24.8:1:30.3:1:1:0:52.6:10.5:1:0:0.2 0/1:18:3:2,1:9,6:15,3:0.1667:2,2:8.7:1:31.7:1:1:1.31:49.3:6:0.1667:0:1 +1 99250420 . G T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10359;SOR=0.38062;LSEQ=CACAATGTCTTTCCATCAAG;RSEQ=GTACAGAACTGGACGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:28:14,14:4,2:6,28:0.8235:2,2:31.7:1:30.3:1:0.66023:1.96046:60:56:0.8235:0:1.2 1/0:33:21:10,11:5,7:12,21:0.6364:2,2:36.4:1:29:1:1:1.26:58.6:42:0.6364:0:1.3 +1 99250459 . A G 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.8257;LSEQ=GATCAGATGGATGAACTGAC;RSEQ=GCAGTAGGCTTCAGAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:11,13:24,1:0.04:2,0:44:0:14:0:1:0:60:0:0:0:1 0/1:28:2:1,1:11,15:26,2:0.0714:2,2:22.5:1:31:1:1:1.35:60:4:0.0714:0:2 +1 99473971 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22186;SOR=0;LSEQ=TGTCCCTTGCTCAGAAGAAG;RSEQ=ATTGGGTAGCTCAAAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:16,11:27,2:0.069:2,2:28.5:1:30:0:1:1.43545:47.5:4:0.069:0:1 0/0:32:0:0,0:14,18:32,0:0:2,0:29.1:1:29.7:1:1:0:56.7:64:1:0:0.1 +1 99474093 . TAA T 28 v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAACTGATGAACAGCAAC;RSEQ=AAAAAAAAAAAAAAACTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:30:1:28:1:1:0:60:4:0.3333:0:1.5 0/0:2:0:0,0:0,2:2,0:0:0,0:4.5:1:30.5:1:1:0:60:4:1:0:0 +1 99589292 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49754;SOR=Inf;LSEQ=TAATTCCTGCTAGCATTTTA;RSEQ=TATATATTCCTCCAGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:79,6:85,0:0:2,0:28:1:33.6:1:1:0:59.6:170:1:0:0.1 0/1:90:2:1,1:73,14:87,2:0.0222:2,2:30.5:1:27.5:1:0.31027:5.072:60:4:0.0225:0:1.5 +1 99589379 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65351;SOR=0.9323;LSEQ=ATCTTAAGCACATGCTATCA;RSEQ=GCTATTTGGTAACTATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:343:188:116,72:92,63:155,188:0.5481:2,2:25.9:1:30.7:1:0.65895:1.10:60:46:0.5428:0:1.8 1/0:375:199:113,86:98,78:176,199:0.5307:2,2:23.1:1:29.5:1:0.83557:1.05:60:65.333:0.5297:0:1.7 +1 99589424 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50165;LSEQ=TTCAAGTTTTAAGGGAAAAT;RSEQ=GCTACAGGGGTTACTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:249:140,109:98,89:187,249:0.5685:2,2:26.2:1:30.7:1:0.43846:1.17:60:498:0.5685:0:1.6 0/1:440:175:82,93:138,126:264,175:0.3977:2,2:25.9:1:29.7:1:0.28441:1.24154:60:350:0.4014:0:1.7 +1 99589425 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01163;SOR=0.50654;LSEQ=TCAAGTTTTAAGGGAAAATC;RSEQ=CTACAGGGGTTACTTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:45:20,25:215,174:389,45:0.1032:2,2:26.9:1:30.3:1:0.20613:1.54296:60:90:0.1042:0:1.1 0/1:436:24:14,10:205,206:411,24:0.055:2,2:28.8:1:29.6:1:0.5298:1.41:60:48:0.0554:0:1 +1 99589496 . T A 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACATGTTCCATCAGAGTCTC;RSEQ=TCCCTAACTATCCCATGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:85,204:289,0:0:2,0:24.5:1:30.5:1:1:0:60:56.8:1:0:0.4 0/1:224:32:11,21:63,129:192,32:0.1429:2,2:25.7:1:30.3:1:0.84196:1.07:60:64:0.1468:0:1.1 +1 99589869 . T C 67 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACTGAAAAACATCTCCTTA;RSEQ=AGCTGAGGATTAGCTAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:20.5:1:33.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 99777865 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50321;SOR=Inf;LSEQ=AATTTATTTTAAAAACTGAG;RSEQ=ATACACTTAACCACACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:15,10:25,0:0:2,0:19.9:1:31.9:1:1:0:60:50:1:0:0.1 0/1:34:2:1,1:21,11:32,2:0.0588:2,2:20.5:1:28:1:1:1.8709:60:4:0.0606:0:1.5 +1 99780131 . T TG 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.63781;SOR=0.72041;LSEQ=TTGATACTCTTATCCAGGCT;RSEQ=GGGGCTCCCCTTATAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:23:23,0:25,2:27,23:0.46:2,1:22.8:1:32.2:1:0.49306:0:60:22:0.4583:0.12:0 0/1:29:11:11,0:18,0:18,11:0.3793:1,0:21.3:1:32.5:1:1:0:60:22:0.3793:0.069:0 +1 99780177 . T TA 73 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1426;SOR=0.21101;LSEQ=GGCAGTCAAGGTGAACTTCT;RSEQ=AAAAAAAAATCAGATCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:6:5,1:109,22:131,6:0.0438:2,2:31.8:1:28.5:1:1:1.01:57.5:12:0.0444:0:0.5 0/0:105:1:1,0:80,24:104,1:0.0095:2,0:29:0:29:0:1:0:60:2:0.0096:0:0 +1 99780188 . C A 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33699;SOR=3.56659;LSEQ=TGAACTTCTTAAAAAAAAAT;RSEQ=AGATCAGATCTCCTCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:1,0:123,31:154,1:0.0065:2,0:36:0:12:0:1:0:60:0:0:0:3 0/1:132:3:2,1:96,33:129,3:0.0227:2,2:11.7:1:24:1:1:1.45008:60:2:0.0155:0:2 +1 99780190 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.22607;SOR=Inf;LSEQ=AACTTCTTAAAAAAAAATCA;RSEQ=ATCAGATCTCCTCCAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:124,31:155,0:0:2,0:25.5:1:33.1:1:1:0:59.9:50.667:1:0:0.1 0/1:141:2:1,1:102,37:139,2:0.0142:2,2:21.5:1:27.5:1:0.46778:2.73354:60:4:0.0143:0:1 +1 99780284 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00955;SOR=0.67198;LSEQ=TGGCTATCCAGTTTCCTTCA;RSEQ=TGGCAGATAGGTTTCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:159:70,89:76,93:169,159:0.4818:2,2:27:1:33:1:0.91163:1.03892:60:318:0.4818:0:1.1 0/1:372:143:70,73:105,124:229,143:0.3844:2,2:23.4:1:31.5:1:0.59411:1.13:60:142:0.3838:0:1.1 +1 99780335 . T A 46 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62551;SOR=0.36919;LSEQ=CAATATTCAGTGATGTTATC;RSEQ=ATGAGATGCAGAAAGTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:2,1:76,154:230,3:0.0128:2,2:17.3:1:29.3:1:0.26021:4.03:60:6:0.0131:0:1.3 0/0:210:1:1,0:74,135:209,1:0.0048:2,0:1:0:29:0:0.35714:0:57:2:0.0048:0:1 +1 99780510 . T A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19231;SOR=Inf;LSEQ=CAAAACAATTATTTTAATTA;RSEQ=ACAATTGGTAAATAATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:7,0:0:2,0:26.9:1:27.3:1:1:0:57:14:1:0:0 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:26.5:1:32.5:1:1:0:60:4:0.3333:0:1 +1 101971074 . T C 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CTTATACTGACCACTGGAGT;RSEQ=GGGCGACATGGCTTCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:13:3,10:26,23:49,13:0.2097:2,2:27.9:1:30.8:1:0.06704:3.69123:45.1:26:0.2167:0:1 0/0:84:0:0,0:38,46:84,0:0:2,0:30.1:1:29.8:1:1:0:41.8:168:1:0:0.3 +1 101971096 . T C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03674;SOR=Inf;LSEQ=GGCGACATGGCTTCTCCCCT;RSEQ=TCTAGGTCCCGTGACAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:23,36:59,0:0:2,0:23.6:1:29.4:1:1:0:45.3:28.5:1:0:0.4 0/1:78:6:2,4:31,41:72,6:0.0769:2,2:23.5:1:29.2:1:1:1.50447:48:12:0.0779:0:1.3 +1 101971106 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17208;SOR=0;LSEQ=CTTCTCCCCTTTCTAGGTCC;RSEQ=GTGACAGCCATCTTGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:15,31:46,2:0.0417:2,2:34:1:30:1:1:2.03:48:4:0.0426:0:1 0/0:67:0:0,0:29,38:67,0:0:2,0:22.4:1:29.1:1:1:0:44:32.5:1:0:0.3 +1 101971113 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49561;SOR=Inf;LSEQ=CCTTTCTAGGTCCCGTGACA;RSEQ=CCATCTTGCCATTACTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:15,31:46,0:0:2,0:24.8:1:32.1:1:1:0:48.9:92:1:0:0.3 0/1:50:2:1,1:21,27:48,2:0.04:2,2:12:1:28:1:1:1.28:39:4:0.04:0:1 +1 102237818 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.17057;LSEQ=GGGAGCACAGGTTACTTATC;RSEQ=CTGTAAATATAATCTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:212:98,114:97,135:232,212:0.4775:2,2:25.5:1:31.3:1:0.38908:1.20:59.9:424:0.4796:0:1.1 0/1:520:70:33,37:207,243:450,70:0.1346:2,2:26.5:1:29.2:1:0.89782:1.05:60:69:0.1353:0:1.2 +1 103210619 . A T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05668;SOR=0.09767;LSEQ=ATCCTTTACTGGTTAGCGTA;RSEQ=AAGCAACACTCTTCCCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:0,7:1,1:2,7:0.7778:2,0:25.9:1:29.9:1:0.22222:0:59.6:14:0.7778:0:1 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:15.5:1:30.5:1:1:2.24:22.5:4:0.25:0:1 +1 103210685 . T TTGG 75 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGAGGATATCTAGGCC;RSEQ=TGGTTTTGGAGAGTCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:34:1:33.2:1:1:0:55:4:1:0:0 1/1:6:6:3,3:0,0:0,6:1:0,2:21.3:1:29.1:1:1:0:37.3:12:1:0.1667:0.3 +1 105976620 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50227;SOR=Inf;LSEQ=ATCTACCCTGAACTGAGAAT;RSEQ=GCCATCTCTCAATATGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:44,24:68,0:0:2,0:24.2:1:32:1:1:0:59.9:136:1:0:0.1 0/1:84:2:1,1:48,34:82,2:0.0238:2,2:10.5:1:27.5:1:1:1.40585:60:4:0.0244:0:1 +1 105976654 . G T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25203;SOR=Inf;LSEQ=ATGAGCCAGTGGCTGAAATT;RSEQ=GTGTGAGTGCCCATGGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:42,45:87,0:0:2,0:26.7:1:31.9:1:1:0:59.9:174:1:0:0.1 0/1:104:3:1,2:51,50:101,3:0.0288:2,2:26.7:1:31.3:1:1:2.02654:60:6:0.0297:0:1.3 +1 105976686 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49915;SOR=Inf;LSEQ=CATGGGTCGGTGTACAAGGA;RSEQ=TGTGATCCCCACAGTGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:31,48:79,0:0:2,0:26.3:1:33.1:1:1:0:60:158:1:0:0.1 0/1:90:2:1,1:44,44:88,2:0.0222:2,2:25.5:1:27.5:1:1:1:60:4:0.0227:0:1 +1 105977123 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16629;SOR=Inf;LSEQ=TGTACTGTGCTCACGAGGTT;RSEQ=TTCTGCAATCTACACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:5,48:53,0:0:2,0:26.6:1:33.1:1:1:0:60:52:1:0:0 0/1:37:2:1,1:7,28:35,2:0.0541:2,2:35:1:27.5:1:0.39039:3.81:60:4:0.0571:0:1 +1 106053681 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18638;SOR=Inf;LSEQ=ATTAAGAAAAACAACTTTGG;RSEQ=GTAACTAGAAAAAACATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:68,9:77,0:0:2,0:20.7:1:31.3:1:1:0:60:76:1:0:0 0/1:59:2:1,1:50,7:57,2:0.0339:2,2:16:1:25:1:0.25482:6.74709:60:4:0.0339:0:1.5 +1 106053803 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42503;LSEQ=AAAAGAGAAATTCAAATTGA;RSEQ=CTGATGGTTATAAGAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:120:50,70:87,99:186,120:0.3909:2,2:27.6:1:30.4:1:0.41095:1.22946:60:59:0.3946:0:1.8 0/1:327:70:35,35:123,134:257,70:0.2141:2,2:25.8:1:28.9:1:0.7882:1.09:60:69:0.213:0:1.5 +1 106053847 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.42564;LSEQ=TTTTGCTAGGGAGATGCCTA;RSEQ=ATTTTTATCTTTAAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:96:30,66:50,104:154,96:0.384:2,2:24.4:1:29.8:1:0.88965:1.05748:60:192:0.3855:0:1.9 0/1:234:49:16,33:67,118:185,49:0.2094:2,2:25.7:1:28.2:1:0.7378:1.1703:60:98:0.2112:0:1.7 +1 106053879 . T A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24768;SOR=Inf;LSEQ=TAAAAAATAACTATTTGTCT;RSEQ=AAATTTACCTTATGGTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:29,100:129,0:0:2,0:23.5:1:29.2:1:1:0:60:128:1:0:0.5 0/1:136:3:2,1:35,98:133,3:0.0221:2,2:5.3:1:25.3:1:0.17975:5.52:60:6:0.0226:0:1 +1 108079754 . TA T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15986;SOR=0.41772;LSEQ=AGAAAAGATCAGAAAACTCT;RSEQ=AGTCAGTGAGGCCTGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:18:18,0:12,0:12,18:0.6:0,1:28.6:1:32.2:1:1:0:60:36:0.6:0.0667:0 0/1:21:8:8,0:13,0:13,8:0.381:1,0:22.1:1:31:1:1:0:60:16:0.381:0.1429:0 +1 108079857 . G T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=0.49043;LSEQ=AATTAGAGAAATAATAAAAA;RSEQ=TATTTGTCATCACAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:212:113:87,26:77,22:99,113:0.533:2,2:21.9:1:31.4:1:1:1.04577:60:226:0.5381:0:1.4 0/1:212:76:56,20:105,31:136,76:0.3585:2,2:21.5:1:29.8:1:0.61639:1.20856:60:152:0.3602:0:1.4 +1 108079880 . G C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03255;SOR=0.69808;LSEQ=TTTGTCATCACAAATAAAAT;RSEQ=TTTAGCGATTGAATGAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:131:88,43:136,52:188,131:0.4094:2,2:25.2:1:31.8:1:0.32304:1.27696:60:42.667:0.4038:0:1.1 0/1:316:103:68,35:141,71:212,103:0.3259:2,2:24.3:1:31:1:1:1.0221:60:206:0.3259:0:1.1 +1 108079945 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.43446;LSEQ=GGTTACGAATACAAACATCA;RSEQ=AAGTCTTTTTCAGGGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:525:302:155,147:109,114:223,302:0.5752:2,2:24.3:1:30.1:1:0.59707:1.10:60:32.556:0.5723:0:1.3 0/1:551:204:100,104:171,174:345,204:0.3702:2,2:24.6:1:29.5:1:0.92973:1.02203:59.9:203:0.3732:0:1.3 +1 108080040 . G T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34401;LSEQ=GTTTTGTCCTGGTGTTGCAT;RSEQ=TATTAGTTCATCACATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:189:110:24,86:20,59:79,110:0.582:2,2:25.1:1:30.3:1:0.60369:1.21342:60:35.667:0.5753:0:2.2 0/1:164:53:8,45:21,90:111,53:0.3232:2,2:22.4:1:29.9:1:0.6637:1.31039:60:52:0.319:0:2.2 +1 108080046 . G T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32733;LSEQ=TCCTGGTGTTGCATGTATTA;RSEQ=TTCATCACATCCCCTTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:170:102:19,83:13,54:67,102:0.6:2,2:24:1:30.5:1:1:1.05132:60:50:0.5952:0:2.1 0/1:137:45:7,38:13,79:92,45:0.3285:2,2:20.5:1:29.8:1:0.80228:1.12:60:44:0.3235:0:2.2 +1 108080184 . C T 45 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8918;LSEQ=CCAGCAACTTATTGGAAATA;RSEQ=AACTGCTTGGACCTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:18.3:1:28.7:1:1:0:60:6:0.3333:0:1 1/0:4:2:1,1:0,2:2,2:0.5:0,2:4.5:1:26.5:1:1:0:60:4:0.5:0:1 +1 108080285 . GC G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGATTCTGATGTGTTTCA;RSEQ=CCACAACTGGGATGTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:27:1:34:0:1:0:60:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 109490457 . T C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08253;LSEQ=AGCTAGTTGTTTTGATCAAG;RSEQ=TTGCATTTATCAGCTATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:331:307:126,181:7,16:23,307:0.9275:2,2:25.3:1:32.6:1:0.38222:1.59:60:75.75:0.9266:0:1.1 1/0:577:296:138,158:122,156:278,296:0.513:2,2:25.3:1:30.9:1:0.55712:1.12:60:48.333:0.5124:0:1.2 +1 109491028 . T C 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAAGTCGCTGAGGGTAG;RSEQ=GGGTATTTTTCAAACATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:35.5:1:26.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 109853073 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53319;SOR=Inf;LSEQ=GACAGAACAGAAAGTCTGGC;RSEQ=CCTGCTGACTCCGGCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:22,25:47,0:0:2,0:26.4:1:30.6:1:1:0:60:94:1:0:0.2 0/1:82:2:1,1:43,37:80,2:0.0244:2,2:39.5:1:30:1:1:1.16002:60:4:0.025:0:2 +1 109853086 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53219;SOR=Inf;LSEQ=GTCTGGCACCTGCTGACTCC;RSEQ=GCCCTCCCTGTCACTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:20,25:45,0:0:2,0:30.9:1:31.4:1:1:0:60:90:1:0:0.2 0/1:78:2:1,1:36,40:76,2:0.0256:2,2:31.5:1:30:1:1:1.11:60:4:0.0263:0:1.5 +1 109853098 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5107;SOR=Inf;LSEQ=CTGACTCCGGCCCTCCCTGT;RSEQ=ACTTCATCACACAGCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,26:45,0:0:2,0:28.9:1:33:1:1:0:60:90:1:0:0.2 0/1:64:2:1,1:27,35:62,2:0.0313:2,2:14.5:1:26.5:1:1:1.29:60:4:0.0317:0:2 +1 109853105 . T C 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51446;SOR=Inf;LSEQ=CGGCCCTCCCTGTCACTTCA;RSEQ=CACACAGCAAATCTTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:18,23:41,0:0:2,0:29:1:31.4:1:1:0:60:82:1:0:0.2 0/1:61:2:1,1:25,34:59,2:0.0328:2,2:6.5:1:27:0:1:1.35:60:4:0.0328:0:1 +1 109956909 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATTAAACTCAGCTCAAAAT;RSEQ=ACTTTCATGGAATCCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:13,3:16,0:0:2,0:21.9:1:32.3:1:1:0:60:32:1:0:0.1 0/1:42:2:1,1:25,15:40,2:0.0476:2,2:18.5:1:28:1:1:1.64563:60:4:0.05:0:1 +1 110116309 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51482;SOR=0;LSEQ=CATTCATGTTGATATTATAC;RSEQ=TTTATGTTGATTACCGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:35,10:45,2:0.0426:2,2:8.5:1:31:1:0.41721:3.38437:60:4:0.0426:0:1 0/0:31:0:0,0:27,4:31,0:0:2,0:21.1:1:30:1:1:0:60:30:1:0:0 +1 110116413 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50629;SOR=Inf;LSEQ=ACAGATGAAGTAAGTTGGAA;RSEQ=GTAGCGTTTTGTTAGACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:18,36:54,0:0:2,0:23.1:1:30.1:1:1:0:59.5:26:1:0:0.1 0/1:72:2:1,1:27,43:70,2:0.0278:2,2:25:1:28:1:1:1.58:60:4:0.0278:0:1 +1 113234356 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18552;SOR=Inf;LSEQ=CCACCTCCCCGCCTCAGGCA;RSEQ=CTGCTCCCCATGCTTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:188,77:265,0:0:2,0:23:1:32.9:1:1:0:60:87.333:1:0:0.1 0/1:201:2:1,1:146,51:197,2:0.01:2,2:17:0:28:1:0.45531:2.84478:60:4:0.0101:0:1 +1 113234456 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.84898;SOR=1.03255;LSEQ=TCTGCACCCCGCACTCTCCC;RSEQ=TCTTTTACCTACTGGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:470:274:124,150:90,106:196,274:0.583:2,2:26.2:1:30.2:1:0.92526:1.02704:60:44.667:0.5852:0:1.1 1/0:562:332:150,182:106,122:228,332:0.5907:2,2:25.5:1:29.5:1:0.79582:1.05408:59.9:82:0.5942:0:1.2 +1 113234502 . T A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2492;SOR=Inf;LSEQ=TTGCCCTGGCACCTCCGTCC;RSEQ=CAGCCTCCCAGGCTGTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:78,199:277,0:0:2,0:24.5:1:30.1:1:1:0:59.9:54.4:1:0:0.6 0/1:293:3:2,1:89,201:290,3:0.0102:2,2:18:1:27.7:1:0.22863:4.49:60:6:0.0105:0:1.7 +1 113244237 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGAGTGGCCATCTCAAACAC;RSEQ=TCCCGCACTCCCTCCTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:30:1:32.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:27.5:1:1:0:60:4:1:0:1.5 +1 113245320 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50016;SOR=Inf;LSEQ=TTCTCAGGAATGTTTTCTGT;RSEQ=TAGACATGCACCAACAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:41,98:139,0:0:2,0:23:1:32.4:1:1:0:60:278:1:0:0.1 0/1:157:2:1,1:47,108:155,2:0.0127:2,2:19.5:1:28.5:1:0.51935:2.28:60:4:0.0128:0:1 +1 113245682 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19622;SOR=0;LSEQ=ACATCAGTGTCCGGGTAGGA;RSEQ=AGAGGCCGCAGTCGATCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:47,35:82,2:0.0238:2,2:32.5:1:28.5:1:1:1.33807:60:4:0.0241:0:1.5 0/0:105:0:0,0:60,45:105,0:0:2,0:23.9:1:30.4:1:1:0:60:34:1:0:0.2 +1 113245701 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21659;SOR=0;LSEQ=AGAGAGGCCGCAGTCGATCA;RSEQ=AGTCTTCCTGCCCTGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:52,44:96,2:0.0204:2,2:42:1:30.5:1:1:1.17979:60:4:0.0206:0:1 0/0:112:0:0,0:62,50:112,0:0:2,0:30.4:1:28.8:1:1:0:60:111:1:0:0.2 +1 113247563 . G A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCCTCAGTCCAGCTCACCC;RSEQ=CATGCCCTGCCCACCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:27:0:1:0:60:2:1:0:0 0/1:5:2:2,0:2,1:3,2:0.4:2,0:32.5:1:30:0:1:0:60:4:0.4:0:1 +1 115251293 . G GA 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.6944;SOR=1.66169;LSEQ=ACCCTATAAAAGGAAAAAAT;RSEQ=AAAAAAAATGAGAGAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:2:1,1:58,238:296,2:0.0067:2,2:16.5:1:28:1:0.35731:4.08:60:4:0.0068:0.0034:0.5 0/1:360:4:1,3:94,261:355,4:0.0111:2,2:8:1:23:1:1:1.08023:60:3:0.0084:0.0056:1 +1 115252054 . T TA 48 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.25787;SOR=0;LSEQ=AGATAGAGTGAGACTCTGCC;RSEQ=AAAAAAAAATAAAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:3,0:61,2:63,3:0.0455:1,0:7:1:30.3:1:1:0:60:6:0.0469:0.0303:0.7 0/0:50:0:0,0:48,2:50,0:0:1,0:27.2:1:29.7:1:1:0:58.8:11.5:1:0:0.2 +1 115252095 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50321;SOR=0;LSEQ=AAAATAAAAATGAAAAAAAT;RSEQ=CATAACAACAAAGAATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:186,6:192,2:0.0103:1,2:23.5:1:29.5:1:0.07104:28.80031:60:4:0.0105:0:1 0/0:160:0:0,0:154,5:159,0:0:1,0:20.8:1:32:1:1:0:59.7:78.5:1:0:0.1 +1 115256349 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23405;SOR=0;LSEQ=AGCTCTATCTTCCCTAGTGT;RSEQ=GTAACCTCATTTCCCCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:158,27:185,2:0.0107:2,2:5:1:29:1:0.27773:5.76461:60:4:0.0108:0:1 0/0:199:0:0,0:163,36:199,0:0:2,0:22.2:1:31:1:1:0:60:38.8:1:0:0.1 +1 115256669 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.10595;SOR=0.60974;LSEQ=TATTAAAAACCACAGGGAAT;RSEQ=CAATGCTATTGCCAAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:78:4,74:0,26:26,78:0.75:1,2:25.4:1:30.3:1:0.56983:0:60:156:0.7573:0:1.3 1/0:113:73:4,69:5,35:40,73:0.646:2,2:22.3:1:30.1:1:0.27547:2.44318:60:146:0.6518:0:1.2 +1 115258819 . G A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0725;SOR=0;LSEQ=CTGTTGGAAACCAGTAATCA;RSEQ=GGTTAATTGGCGAGCCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:3:1,2:48,176:224,3:0.0132:2,2:31:1:25.7:1:0.51962:1.83:60:2:0.0088:0:2 0/0:316:0:0,0:77,239:316,0:0:2,0:22.6:1:30.4:1:1:0:60:157:1:0:0.1 +1 116099481 . A T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24913;SOR=0;LSEQ=AAAAACCTATGGTGACTGTG;RSEQ=AGGCCCTGATGCCATGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:163,124:287,3:0.0103:2,2:9.3:1:23.7:1:1:1.52:49.7:2:0.0071:0:1 0/0:276:0:0,0:140,136:276,0:0:2,0:26.7:1:29.1:1:1:0:58.2:54.2:1:0:0.1 +1 116099527 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10672;SOR=Inf;LSEQ=TTGATATCATCTAGTGGTCA;RSEQ=AAAGTTATTGTAAAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:84,131:215,0:0:2,0:23.8:1:32:1:1:0:58.9:106.5:1:0:0.1 0/1:195:3:2,1:78,114:192,3:0.0154:2,2:8:1:28:1:0.56906:2.91:58.7:6:0.0156:0:1 +1 116099689 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=ATGTAAGCTGCATGCTGTGG;RSEQ=TCAAGCCTATAATCACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:3,14:17,2:0.1053:2,2:31.5:1:32:0:0.38596:4.18:60:4:0.1053:0:1 0/0:11:0:0,0:3,8:11,0:0:2,0:21.3:1:31:1:1:0:60:22:1:0:0.2 +1 116099916 . C T 49 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGAGCTATGATCACAC;RSEQ=ACTGCACTCTAGAGTGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:34.5:1:24.5:1:1:0:50.8:3:1:0:3.5 1/1:2:2:2,0:0,0:0,2:1:0,0:8:0:32:0:1:0:60:4:1:0:1.5 +1 116099991 . T G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27931;SOR=0;LSEQ=TGCATATATGTTACATACAA;RSEQ=GGTCACTACACTAACAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:19.5:1:32.4:1:1:0:60:10:1:0:1.5 1/1:19:16:11,5:2,1:3,16:0.8421:2,2:22.6:1:30.3:1:1:1.09:60:32:0.8421:0:1.1 +1 116100046 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50786;SOR=Inf;LSEQ=AATTCCCAGCTGCACCTCAA;RSEQ=TTGCACCAGAATTGCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:19,0:0:2,0:33.8:1:28.5:1:1:0:60:8.5:1:0:0.8 0/1:28:2:1,1:12,14:26,2:0.0714:2,2:16:1:29.5:1:1:1.16:60:4:0.0714:0:1.5 +1 116107025 . G GCCA 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=1;LSEQ=GGCGCCTGATCGCCGCCGCC;RSEQ=CCGCTGCCGCCGCCGCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:39.5:1:32:1:1:1.40151:60:4:0.1176:0:0 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:18:0:30.7:1:1:1.40151:54:4:0.1053:0:0.5 +1 116107027 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.48649;SOR=0;LSEQ=CGCCTGATCGCCGCCGCCGC;RSEQ=GCTGCCGCCGCCGCTACCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:18.5:1:29:1:1:1.40151:60:4:0.1053:0:1.5 0/0:19:0:0,0:11,8:19,0:0:2,0:26.9:1:30.1:1:1:0:59.4:38:1:0:0.4 +1 116333547 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00613;SOR=Inf;LSEQ=AATCTTTCGCCTGTCTTAGA;RSEQ=GGCACTCTAGCAGACGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:30,1:31,0:0:1,0:23.8:1:32.5:1:1:0:60:30:1:0:0.9 0/1:8:3:3,0:5,0:5,3:0.375:0,0:29.7:1:31:0:1:0:60:6:0.375:0:1.7 +1 116333581 . T G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACGAGGTGAGCCCTGCCTTG;RSEQ=AACAGGAAGGACCTTTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:39,3:0,0:0,42:1:0,2:22.7:1:31.9:1:1:0:60:84:1:0:1.3 1/1:21:20:20,0:1,0:1,20:0.9524:0,1:18.3:1:29.9:1:1:0:60:9:0.9474:0:1.9 +1 116333628 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.67613;LSEQ=AGGCCAATAATTTGTTGTGG;RSEQ=TTGCCAACTAAATTCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:20:15,5:73,29:102,20:0.1639:2,2:26:1:30.6:1:1:1.19:60:19:0.1583:0:1.5 0/1:77:37:27,10:27,13:40,37:0.4805:2,2:28.3:1:31.4:1:0.62762:1.30:60:36:0.4737:0:1.4 +1 116333734 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24902;LSEQ=CCCTGCTCTACTAATAGCAA;RSEQ=GCAGCTGTGGATGGCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:237:195:90,105:19,22:41,195:0.8228:2,2:24.9:1:30.4:1:1:1.00754:59.9:31.5:0.8182:0:1.1 1/0:198:106:51,55:42,50:92,106:0.5354:2,2:25.6:1:30.5:1:0.77609:1.10:59.7:212:0.5436:0:1.2 +1 116333773 . C A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.82895;LSEQ=GCAACCAGAAGGATGCTGGC;RSEQ=TAGTACAGATAGCACATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:30:8,22:47,105:152,30:0.1648:2,2:23.3:1:30.5:1:0.82808:1.22955:60:60:0.1685:0:2.2 0/1:146:63:24,39:35,48:83,63:0.4315:2,2:22.5:1:29.6:1:0.73368:1.18352:60:126:0.4315:0:2.1 +1 116333785 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07233;SOR=Inf;LSEQ=ATGCTGGCCTAGTACAGATA;RSEQ=CACATTGAATGTATTTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:37,117:154,0:0:2,0:27.9:1:32.3:1:1:0:60:76:1:0:1 0/1:111:3:2,1:39,69:108,3:0.027:2,2:26.7:1:29.3:1:0.55361:3.50:60:6:0.027:0:2 +1 116333793 . A C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=4.03741;LSEQ=CTAGTACAGATAGCACATTG;RSEQ=ATGTATTTATGCTGTAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:20:2,18:26,87:113,20:0.1504:2,2:32.5:1:33:1:0.24422:2.67369:60:40:0.1538:0:2.7 0/1:98:41:13,28:20,37:57,41:0.4184:2,2:27.5:1:31.6:1:0.82946:1.16244:60:40:0.4124:0:2.7 +1 116333796 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1676;SOR=Inf;LSEQ=GTACAGATAGCACATTGAAT;RSEQ=TATTTATGCTGTAGTCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:27,105:132,0:0:2,0:27.7:1:32.4:1:1:0:60:65:1:0:1 0/1:92:2:1,1:29,61:90,2:0.0217:2,2:8.5:1:26:1:0.54826:2.09:60:4:0.022:0:2.5 +1 116333816 . C G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=5.27514;LSEQ=GTATTTATGCTGTAGTCCGA;RSEQ=ACATCACGCACGCTGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:17:2,15:12,70:82,17:0.1717:2,2:27.4:1:33.2:1:1:1.28263:60:34:0.1735:0:2.7 1/0:59:31:7,24:7,21:28,31:0.5254:2,2:23.6:1:30.9:1:1:1.14027:60:62:0.5254:0:2.8 +1 116334594 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACCTGCAGACCATAAGC;RSEQ=TGAGTGTAAAGGCTGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:29:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 117273321 . CAAA C 91 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=17.000;MSILEN=1;SSF=1;SOR=1.66859;LSEQ=AACAGAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAAAAAAGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:2,0:2,7:0.4667:0,0:15.7:1:32.5:1:1:0:55.3:14:0.4667:0.2:1.3 1/0:5:3:3,0:0,0:0,3:0.6:0,0:10.7:1:31.4:1:1:0:60:6:0.6:0.2:1.3 +1 117273456 . TA T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23353;SOR=Inf;LSEQ=CTTTGCCCCTCAGCGGCAGG;RSEQ=ACTCTTTCCCTTGCTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:115,47:162,0:0:2,0:21.7:1:29.3:1:1:0:60:161:1:0:0.5 0/1:152:2:1,1:104,46:150,2:0.0132:2,2:17:1:28:1:0.52422:2.24745:58:4:0.0132:0:1 +1 117273500 . C T 32 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36397;SOR=3.13942;LSEQ=TGCTTGAACAGAAGACTGTG;RSEQ=CTGGGGCAAGAAGGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:1:0,1:179,125:304,1:0.0033:2,0:46:0:32:0:0.41311:0:60:2:0.0034:0:2 0/1:293:3:0,3:168,122:290,3:0.0102:2,0:15:1:20.7:1:0.07658:0:59.3:2:0.007:0:1.7 +1 117273534 . T A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06378;SOR=0.72267;LSEQ=GAAGAAGGGAAACCATGCAG;RSEQ=GAGATGGGCTCCCTGTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:346:266:136,130:40,37:77,266:0.7688:2,2:26.6:1:31:1:1:1.0333:60:65.5:0.7661:0:1.7 1/0:381:269:138,131:59,52:111,269:0.706:2,2:23.7:1:29:1:0.82146:1.07684:60:37.429:0.7005:0:1.7 +1 117273577 . G T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00116;SOR=0.51245;LSEQ=CTCTGGTACACAGACTGGAG;RSEQ=TGAAGCAAACAACAGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:254:205:83,122:17,32:49,205:0.8071:2,2:25.9:1:29.7:1:0.51688:1.28:60:40:0.8065:0:1.8 1/0:289:197:86,111:35,56:91,197:0.6817:2,2:26.6:1:29.4:1:0.44244:1.24:60:394:0.684:0:1.9 +1 117690272 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03968;LSEQ=TTGCATGCTTTTTTGTGGCC;RSEQ=AGGCACATTATTTTAGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:473:471:299,172:0,0:0,471:0.9958:0,2:23.7:1:30.3:1:1:0:55.2:41.818:0.9957:0:1.1 1/1:475:429:279,150:28,18:46,429:0.9032:2,2:25.8:1:29.6:1:0.62715:1.20:53.6:60.286:0.9017:0:1.1 +1 117690445 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07948;SOR=Inf;LSEQ=TTTAGGGTCATACAGGAGAA;RSEQ=CTGGATGTCTTCTTCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:51,242:293,0:0:2,0:22.2:1:32.4:1:1:0:59.8:57.6:1:0:0.1 0/1:222:3:2,1:41,176:217,3:0.0135:2,2:15:1:27:1:0.09835:8.47:60:6:0.0136:0:1 +1 117695988 . A G 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25217;SOR=0;LSEQ=CATTCACTTCCGGCATGCTG;RSEQ=AGGCTGCAGGGTCAAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:83,201:284,3:0.0105:2,2:45:1:26.7:1:0.21029:4.81:60:2:0.0072:0:1.3 0/0:250:0:0,0:95,154:249,0:0:2,0:22:1:29.3:1:1:0:59.9:48.8:1:0:0.2 +1 117695994 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66477;SOR=1.77742;LSEQ=CTTCCGGCATGCTGAAGGCT;RSEQ=CAGGGTCAAAAGTCAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:2:1,1:72,188:260,2:0.0076:2,2:38:0:29:1:0.48039:2.60:60:4:0.0077:0:1 0/1:223:3:2,1:80,140:220,3:0.0135:2,2:14.3:1:26.7:1:0.55615:3.48:60:6:0.0137:0:1 +1 117696032 . G A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26441;SOR=0;LSEQ=AAGGGCAGATGCCAAAGTCA;RSEQ=ACACGTAAGACAATATAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:1,2:23,122:145,3:0.0203:2,2:14.7:1:25.7:1:0.41419:2.63:60:6:0.0222:0:3.7 0/0:109:0:0,0:23,86:109,0:0:2,0:27.2:1:29.5:1:1:0:59.7:9.9:1:0:0.4 +1 117696034 . C A 45 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7005;SOR=1.36717;LSEQ=GGGCAGATGCCAAAGTCAGA;RSEQ=ACGTAAGACAATATAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:0,3:21,119:140,3:0.0208:2,0:22:1:14.3:1:1:0:60:0:0:0:4.7 0/1:106:3:1,2:21,82:103,3:0.0283:2,2:8.7:1:29:1:0.5061:1.94:58:6:0.0309:0:2.7 +1 117696037 . G A 111 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=20.65181;LSEQ=CAGATGCCAAAGTCAGACAC;RSEQ=TAAGACAATATAGCCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:0,1:21,117:138,1:0.0072:2,0:47:0:30:0:1:0:60:2:0.0074:0:1 0/1:99:13:3,10:17,69:86,13:0.1313:2,2:23.5:1:30.1:1:0.72244:1.22:60:26:0.1398:0:1 +1 117696063 . T A 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57357;SOR=2.7751;LSEQ=CAATATAGCCTTTGAAGCGC;RSEQ=AGGCCTTAAAAATGCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:0,1:2,85:87,1:0.0112:1,0:16:0:13:0:1:0:60:0:0:0:4 0/1:65:2:0,2:9,54:63,2:0.0308:2,0:10.5:1:25.5:1:1:0:60:4:0.0345:0:2.5 +1 117712517 . AAAAT A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.56717;SOR=0;LSEQ=ACAGAGCCAGACCCTGTCTC;RSEQ=AAATAAATAAATAATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:4:3,1:50,0:50,4:0.0741:1,2:12.3:1:31.4:1:0.07407:0:60:8:0.0741:0.037:0 0/0:16:0:0,0:16,0:16,0:0:1,0:22.8:1:29.8:1:1:0:58.1:32:1:0:0.1 +1 117712628 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05995;SOR=Inf;LSEQ=ATGCTATACTCTGAGGTTTT;RSEQ=TGGGTCAAAGCTCTGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:324,57:381,0:0:2,0:21.1:1:32.1:1:1:0:60:126:1:0:0.1 0/1:246:3:1,2:200,43:243,3:0.0122:2,2:18.7:1:27.3:1:0.08698:9.1758:60:6:0.0123:0:1 +1 117712844 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14779;SOR=Inf;LSEQ=AGTTCTCCATTCCTCTTGAT;RSEQ=TGCTGCTTTGCAACTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:35,238:273,0:0:2,0:24.7:1:32.3:1:1:0:59.8:90:1:0:0.1 0/1:171:2:1,1:29,140:169,2:0.0117:2,2:10:1:31.5:1:0.32095:4.76:60:4:0.0118:0:1 +1 117712862 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12328;SOR=Inf;LSEQ=ATGTGCTGCTTTGCAACTGG;RSEQ=GTACAAATCTGTTGTGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:11,208:219,0:0:2,0:23.6:1:31.3:1:1:0:59.9:35.5:1:0:0.1 0/1:119:2:0,2:11,106:117,2:0.0168:2,0:13.5:1:31:1:1:0:60:4:0.0169:0:1 +1 117753285 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5441;SOR=0;LSEQ=GTGGGATGTTAAGTCAAATC;RSEQ=AGTTAGGCTCTTGTCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:109,0:109,2:0.018:1,2:28:1:29.5:1:0.01802:0:60:4:0.0183:0:1 0/0:59:0:0,0:59,0:59,0:0:1,0:23:1:30.8:1:1:0:60:118:1:0:0.1 +1 117753455 . A G 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTATATACTACCTCCAGAAG;RSEQ=GGATCTGCCCCAGGGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1036:0:0,0:498,536:1034,0:0:2,0:25.3:1:31:1:1:0:60:48.238:1:0:0.1 0/1:823:51:26,25:388,384:772,51:0.062:2,2:29.3:1:30.6:1:1:1.03:60:102:0.0627:0:1.2 +1 117753543 . G A 174 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGCCGCTGCCTTCCTTGGT;RSEQ=ACTCACAACCAGCTCCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:48:9,39:98,255:353,48:0.1197:2,2:25.4:1:31.2:1:0.22468:1.66344:60:96:0.1228:0:1 0/0:337:0:0,0:108,229:337,0:0:2,0:22.4:1:30.2:1:1:0:60:47.143:1:0:0.1 +1 118145527 . G A 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.61915;LSEQ=TAAAGACTGTTTTGTCCCTC;RSEQ=GTTTCCCTAGGTATAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:2:2,0:170,321:491,2:0.0041:2,0:11.5:1:15:1:0.12126:0:60:0:0:0:3 0/1:427:39:16,23:141,247:388,39:0.0913:2,2:19:1:29.8:1:0.60285:1.22:60:78:0.0926:0:1 +1 118155620 . G A 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACCCTGTGGATTACGTGTAA;RSEQ=CTGAGTCATTCTTACAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:29:1:32:0:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:43:1:28:1:1:0:60:4:1:0:0 +1 118155826 . T TTG 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.26142;SOR=2.22465;LSEQ=AGGATTATTTCCATTTCAAG;RSEQ=TGTGTGTGTAGCACTTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:5:5,0:59,0:59,5:0.0781:1,0:22.4:1:31.1:1:1:0:60:10:0.0806:0.0156:0 0/1:25:4:4,0:20,1:21,4:0.16:1,0:23.5:1:31:1:1:0:60:8:0.16:0.08:0 +1 118156053 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20677;LSEQ=ACAGCATTAGTTCTTCCAGC;RSEQ=TTATCTCTCCACCCACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1229:221:115,106:527,480:1007,221:0.1798:2,2:24.3:1:30.5:1:0.94087:1.01198:60:109.5:0.1795:0:1.1 0/1:1292:56:29,27:607,627:1234,56:0.0433:2,2:24.9:1:29.6:1:0.78499:1.11:60:55:0.043:0:1.3 +1 118156191 . T A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16973;LSEQ=CTGTGTGTTGGCTTCTCACT;RSEQ=CTTAGTGGGAAGTGAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:53:12,41:52,257:309,53:0.1464:2,2:22.5:1:29.7:1:0.33012:1.44:60:106:0.1489:0:1.1 0/1:248:7:0,7:50,191:241,7:0.0282:2,0:15.4:1:29.7:1:0.35031:0:60:14:0.0287:0:1.3 +1 118160944 . GA G 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.62493;LSEQ=AATAGCAATTCTGTGAAACT;RSEQ=AAAAAAAAATTTCTTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:2,0:46,0:46,2:0.0417:1,0:10:1:32.6:1:1:0:60:4:0.0417:0.0208:0 0/1:38:1:1,0:37,0:37,1:0.0263:1,0:36:0:34:0:1:0:60:2:0.0263:0:0 +1 118160949 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.20224;SOR=Inf;LSEQ=CAATTCTGTGAAACTGAAAA;RSEQ=AAAAATTTCTTTTGGTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:52,0:52,0:0:1,0:24.3:1:31.3:1:1:0:60:104:1:0:0.2 0/1:43:2:2,0:41,0:41,2:0.0465:1,0:25.5:1:30.5:1:1:0:60:4:0.0465:0:1.5 +1 118160998 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49958;SOR=0;LSEQ=AGATGAGAGGAGATGGATTT;RSEQ=CATGAATTAGAGAGTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:124,5:129,2:0.0153:1,2:12.5:1:26:1:0.08984:22.73079:60:4:0.0154:0:1 0/0:117:0:0,0:113,4:117,0:0:1,0:25.6:1:32:1:1:0:60:234:1:0:0.1 +1 118161017 . A AG 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12483;SOR=0;LSEQ=TGCATGAATTAGAGAGTCTG;RSEQ=GGTTTTTTTTTAATGAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:4:3,1:174,29:203,4:0.0193:2,2:17.5:1:32.8:1:0.46807:1.9917:60:8:0.0195:0.0048:0.5 0/0:188:0:0,0:154,34:188,0:0:2,0:22.7:1:28.5:1:1:0:60:187:1:0:0.1 +1 118161019 . G GT 112 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.30475;SOR=1.60189;LSEQ=CATGAATTAGAGAGTCTGAG;RSEQ=TTTTTTTTTAATGAGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:10:9,1:171,30:201,10:0.0474:2,2:32.2:1:29:1:1:1.58:60:20:0.0481:0:0.1 0/1:203:15:14,1:149,39:188,15:0.0739:2,1:28.6:1:28.7:1:0.31202:3.65:60:30:0.0739:0.0049:0.2 +1 118161020 . T G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00237;SOR=0.41214;LSEQ=ATGAATTAGAGAGTCTGAGG;RSEQ=TTTTTTTTAATGAGCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:43:37,6:144,29:173,43:0.1972:2,2:20.2:1:32.2:1:0.81815:1.24:59.7:86:0.1991:0:1.2 0/1:207:19:13,6:151,36:187,19:0.0918:2,2:18.1:1:30.8:1:0.23178:1.92878:59.7:38:0.0931:0:1.3 +1 118161094 . GTC G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0;SOR=0.11196;LSEQ=AGGCATTCTAAAGGAAAAGA;RSEQ=TCTCTTCCTCTGTTCATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:137:78,59:311,237:548,137:0.2:2,2:27.7:1:32.7:1:1:1.01:59.8:274:0.2024:0.019:0.3 0/1:662:18:9,9:349,294:643,18:0.0272:2,2:21.1:1:31:1:0.81221:1.18676:59.7:36:0.0275:0.0045:0.4 +1 118161273 . T G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20243;SOR=Inf;LSEQ=TAAATAAGGCAGCAGGTGAA;RSEQ=AGAAGGCTCCTAAGGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:32,152:184,0:0:2,0:23.1:1:28.6:1:1:0:60:91:1:0:0.1 0/1:151:2:1,1:24,125:149,2:0.0132:2,2:8:0:32.5:1:0.30464:5.12:60:4:0.0133:0:2 +1 118163457 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACAGGTTCATGCTGCAAC;RSEQ=ATCATTCCCCTCTTCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 118165328 . T C 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80884;LSEQ=TTTAACTCATTGAGTCCTCA;RSEQ=GGCAACACTGAGCAGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:8,0:15,0:15,8:0.3478:1,0:32.3:1:30.5:1:1:0:60:7:0.3333:0:1 0/1:10:3:3,0:7,0:7,3:0.3:0,0:27:1:33.3:1:1:0:60:6:0.3:0:1 +1 118165462 . A T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07674;SOR=Inf;LSEQ=GCTTCTCACCCCTCACTTTC;RSEQ=GTTTCCCCAGCCAGAACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:244,51:295,0:0:2,0:23.8:1:30.4:1:1:0:59.9:58:1:0:0.1 0/1:219:3:1,2:172,44:216,3:0.0137:2,2:17.7:1:22:1:0.11249:7.71766:60:2:0.0093:0:2 +1 118165577 . C G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.56251;LSEQ=AGCCGGCTGCATGAGGTCCT;RSEQ=ACTGAAGTTGTACCTATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:148:73,75:444,415:859,148:0.1468:2,2:25.2:1:32.3:1:0.65631:1.09909:59.7:296:0.1492:0:1.2 0/1:850:75:38,37:405,369:774,75:0.0882:2,2:27:1:30.7:1:0.80953:1.06857:60:24:0.086:0:1.1 +1 118165609 . A G 177 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=66.4978;LSEQ=ACCTATCCACGGACGAGGCA;RSEQ=CTTTCCAACCTTGGAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:949:1:1,0:461,486:947,1:0.0011:2,0:24:0:13:0:0.48734:0:60:0:0:0:1 0/1:853:56:28,28:408,389:797,56:0.0657:2,2:26.2:1:30.6:1:0.89072:1.0488:60:27:0.064:0:1.2 +1 118165691 . C G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.36736;LSEQ=GAGGCAGGCATCAAAGTGCA;RSEQ=GACGTCCGGCTGAATGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:105:48,57:255,328:583,105:0.1526:2,2:22:1:32.2:1:0.74907:1.08:60:210:0.1551:0:1.1 0/1:645:40:13,27:180,230:410,40:0.062:2,2:26.5:1:30.4:1:0.18331:1.62373:60:80:0.0629:0:1.1 +1 118165973 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.20799;LSEQ=ATCTCCCTCTCCAACAAGAA;RSEQ=GGGAAGAACGTGGAGCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:231:133,98:245,172:417,231:0.3559:2,2:24.3:1:30.5:1:0.80311:1.04947:60:56.75:0.353:0:1.1 0/1:505:52:26,26:258,195:453,52:0.103:2,2:16.7:1:29.3:1:0.37704:1.32232:60:51:0.102:0:1 +1 118166096 . C T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14709;LSEQ=GACTGTTCCAATAATCCCAT;RSEQ=TCTGAGCACTTCCACCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1143:189:86,103:455,499:954,189:0.1654:2,2:25:1:30.3:1:0.63246:1.09197:59.9:36.8:0.1636:0:1.1 0/1:1025:29:17,12:497,497:994,29:0.0283:2,2:24.4:1:29.8:1:0.45188:1.42:60:58:0.0286:0:1.1 +1 118166195 . C T 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=47.73748;LSEQ=AGACTGATCGCCACCAAGAA;RSEQ=CCAGAAGAAATCAGAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:851:1:0,1:434,416:850,1:0.0012:2,0:1:0:27:0:0.49001:0:60:2:0.0012:0:1 0/1:713:38:16,22:330,344:674,38:0.0533:2,2:19.6:1:29.3:1:0.50519:1.31853:60:37:0.0528:0:1.1 +1 118166750 . A G 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00016;SOR=0;LSEQ=GCCTCCTTCTAGATGTAGGC;RSEQ=TTTGGCTTTTAAAGGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:20:1,19:0,32:32,20:0.3846:1,1:25.7:1:30.6:1:0.38462:0:58:9:0.3913:0:1.4 0/0:24:0:0,0:1,23:24,0:0:1,0:29.3:1:30.4:1:1:0:60:48:1:0:0.2 +1 118170155 . G A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0778;SOR=Inf;LSEQ=GAGCAAAGTAGTTATCCAAT;RSEQ=GTGAGACGAGACCCTGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:69,323:392,0:0:2,0:21.8:1:31.3:1:1:0:60:48:1:0:0 0/1:293:3:2,1:66,223:289,3:0.0102:2,2:5.7:1:26:1:0.13645:6.70:60:6:0.0104:0:1 +1 118170173 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17145;SOR=Inf;LSEQ=ATGGTGAGACGAGACCCTGA;RSEQ=GCTCATAGAGGCCATTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:22,232:254,0:0:2,0:23.8:1:30.4:1:1:0:60:126:1:0:0 0/1:180:2:1,1:17,161:178,2:0.0111:2,2:24:1:30:1:0.1905:9.23:60:4:0.0112:0:1 +1 118223693 . A G 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTTAACTTAGCATAGTA;RSEQ=TGAGAACAATGAATATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:11,0:11,3:0.2143:0,0:13.7:1:33.7:1:1:0:60:6:0.2143:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:49:0:31:0:1:0:60:2:1:0:0 +1 118223755 . C T 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00224;SOR=Inf;LSEQ=GATCCCTTAGAATATGTTTA;RSEQ=GGGTGGCTGTTTTGTCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:25,1:26,0:0:1,0:24.3:1:32.2:1:1:0:60:52:1:0:0.4 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:26:1:31.4:1:1:0:60:10:0.3846:0:1 +1 118223824 . AT A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51502;SOR=0;LSEQ=TTGTGAGATGGCAGGTGGGG;RSEQ=TTTGCTCCACACTGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:2,0:72,3:75,2:0.026:1,0:33:1:33:0:1:0:60:4:0.0274:0:0 0/0:52:0:0,0:50,2:52,0:0:1,0:20.9:1:29.5:1:1:0:60:25:1:0:0.2 +1 118223888 . C T 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66954;SOR=1.69842;LSEQ=ACACAGTTGCTAGTATCTAC;RSEQ=TACCCAGCATAGTTCTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:2:1,1:177,52:229,2:0.0087:2,2:19.5:1:21.5:1:0.407:3.38102:60:1:0.0044:0:2.5 0/1:205:3:1,2:143,59:202,3:0.0146:2,2:14:1:21.7:1:0.21168:4.80494:60:2:0.0101:0:2.7 +1 118223910 . C T 44 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04702;SOR=Inf;LSEQ=ACCCAGCATAGTTCTAGAGG;RSEQ=GTGTCAGTCAGTGCCTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:241,113:354,0:0:2,0:22.5:1:31.2:1:1:0:60:34.4:1:0:0.6 0/1:310:4:1,3:208,96:304,4:0.0129:2,2:5.5:1:22:1:0.09939:6.45758:60:3:0.0099:0:1.5 +1 118223911 . G A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05641;SOR=0.59913;LSEQ=CCCAGCATAGTTCTAGAGGC;RSEQ=TGTCAGTCAGTGCCTAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:44:27,17:216,98:314,44:0.1229:2,2:23.6:1:30.3:1:0.38865:1.38647:60:43:0.1222:0:1.1 0/1:323:25:16,9:204,93:297,25:0.0774:2,2:20.6:1:29.4:1:0.65707:1.23301:60:50:0.0789:0:1.2 +1 118223984 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.5362;LSEQ=TTGACATGGCTGGGCTGAGC;RSEQ=TCTTGGGCAACAGGATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:665:405:207,198:126,134:260,405:0.609:2,2:26.1:1:30.6:1:0.52546:1.11:60:56.857:0.6076:0:1.1 0/1:611:278:147,131:162,171:333,278:0.455:2,2:27.6:1:29.6:1:0.32964:1.18:59.8:54.6:0.4535:0:1.2 +1 118224030 . G A 52 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10616;SOR=5.62713;LSEQ=GGTGAGGTAACTTAGGTCTT;RSEQ=GTTAAGTCTGAGTTCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:1:1,0:201,322:523,1:0.0019:2,0:1:0:24:0:0.3855:0:60:2:0.0019:0:1 0/1:469:5:4,1:189,275:464,5:0.0107:2,2:19.2:1:22.4:1:0.16452:5.80:60:4:0.0086:0:1.6 +1 118224210 . G A 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47083;LSEQ=GATTGGGACTCCCAAGGCAG;RSEQ=AGCAGCAAATGGAGTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:0,6:0,9:9,6:0.4:0,0:18:1:30.7:1:1:0:60:12:0.4:0:1.2 1/0:6:3:0,3:1,2:3,3:0.5:2,0:8:1:28.3:1:1:0:60:6:0.5:0:1.3 +1 118224274 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCCTCCGAAGCTGGAGA;RSEQ=GGGATGCCTGCCCCAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:19.3:1:30.7:1:1:0:60:6:0.2727:0:1.3 0/0:3:0:0,0:0,3:3,0:0:0,0:18.7:1:29:1:1:0:60:6:1:0:1 +1 118225308 . C G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCCTGCAGCTAGGCTA;RSEQ=AGAGAGTTCTGGAAGAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:33:0:32.5:1:1:0:60:4:0.6667:0:2 +1 118225351 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGGGGGGGTGGGGAGAA;RSEQ=TGAGCTCCAGAGAAGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:28.5:1:1:0:60:4:1:0:2 +1 118346123 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09133;SOR=Inf;LSEQ=ATTTGACCCAGAAAGGCTTA;RSEQ=TCAGAGAGGCATCCACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:234,98:332,0:0:2,0:24.1:1:32.3:1:1:0:60:82:1:0:0.2 0/1:273:3:1,2:181,89:270,3:0.011:2,2:11:1:28.3:1:0.25844:4.04476:60:6:0.011:0:1 +1 118346219 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3513;SOR=1.13906;LSEQ=GAATGATCTAAGAGAGGTTT;RSEQ=CTGAAGCCAGCACTATATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:485:308:129,179:71,105:176,308:0.6351:2,2:25.5:1:30.2:1:0.77387:1.07:60:76:0.6333:0:1.1 1/0:507:337:159,178:70,100:170,337:0.6647:2,2:26.5:1:29:1:0.21953:1.28:59.9:111.333:0.6653:0:1.1 +1 119721104 . A G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.31874;SOR=2.28454;LSEQ=TGCCGCCCAGCGTTTACAGG;RSEQ=AAAGACTTCTGAAATCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:12,8:20,3:0.1304:2,2:15.7:1:31:1:1:1.32:47.7:6:0.1304:0:1 0/1:31:8:5,3:14,9:23,8:0.2581:2,2:26:1:30.4:1:1:1.07:45.6:16:0.2667:0:1.3 +1 119721191 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50351;SOR=0;LSEQ=GCTTCTCCCCTTTCTAGGTC;RSEQ=CGTGACAGCCATCTTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:16,21:37,2:0.0513:2,2:26.5:1:30:1:1:1.30:20.5:4:0.0526:0:1.5 0/0:29:0:0,0:11,18:29,0:0:2,0:30.3:1:29.3:1:1:0:37.2:13.5:1:0:0.2 +1 119721860 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGCTGTGCTCTACTTCT;RSEQ=GCCGGGCCTTAGCTGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:30.5:1:1:0:43:4:1:0:1 +1 120199071 . G T 38 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40604;SOR=2.16433;LSEQ=CATTGCCTGAGACTGGAGAA;RSEQ=TAGGAACGGACCCAGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:100,13:113,2:0.0174:2,2:17:1:26.5:1:0.2296:7.44943:60:4:0.0175:0:1 0/1:81:3:0,3:62,16:78,3:0.037:2,0:1:0:24:0:0.01136:0:60:6:0.037:0:1 +1 120199189 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.19144;LSEQ=GATAGACTAAAAGTAAATGA;RSEQ=TCCATCCCTGTAGGCTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:96:46,50:117,131:248,96:0.2791:2,2:24.3:1:30.9:1:0.90486:1.03:60:192:0.284:0:1.1 0/1:368:169:81,88:98,101:199,169:0.4592:2,2:25.7:1:29.6:1:0.83458:1.05397:60:83.5:0.4588:0:1.2 +1 120199277 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10676;SOR=Inf;LSEQ=GTCTCAGTTTCATTTCCATT;RSEQ=GCATGCTAATTTTCTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:39,114:153,0:0:2,0:24.4:1:31.6:1:1:0:60:50:0.9934:0:0.2 0/1:140:3:2,1:38,99:137,3:0.0214:2,2:14:1:24.3:1:0.19634:5.14:60:2:0.0148:0:1 +1 120428796 . A G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00416;SOR=0.04882;LSEQ=AAGGTAGGATCAGGCAAAGC;RSEQ=GAAGTTGACTATAAATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:15,1:1,0:1,16:0.9412:0,1:17.7:1:31.6:1:1:0:60:32:1:0:1 0/1:10:4:4,0:5,1:6,4:0.4:2,0:15.3:1:29.5:1:1:0:58.5:8:0.4:0:1 +1 120428831 . G A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02145;SOR=Inf;LSEQ=ATCTCCATGTTGGATTTTGA;RSEQ=GAGCTGATCATGAGGTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:33,0:0:1,0:26:1:32.6:1:1:0:59.3:15.5:1:0:0.6 0/1:22:4:4,0:17,1:18,4:0.1818:1,0:25.5:1:31.3:1:1:0:49.5:8:0.1818:0:1 +1 120428963 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04957;SOR=Inf;LSEQ=TCTGGATGATGCACGCATCA;RSEQ=CAATCCTTGCCACAAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:171,134:305,0:0:2,0:28.1:1:32.4:1:1:0:57.4:60:1:0:0.1 0/1:274:4:2,2:152,118:270,4:0.0146:2,2:23:1:27.8:1:1:1.28692:54.8:8:0.0148:0:1 +1 120429037 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22776;SOR=Inf;LSEQ=ATATTTGCACCTGCCCAGAA;RSEQ=ATGTGGACGACTGTGTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:48,130:178,0:0:2,0:26.2:1:32.7:1:1:0:59.7:177:1:0:0.1 0/1:163:2:1,1:52,109:161,2:0.0123:2,2:12.5:1:27:1:0.54594:2.09:38:4:0.0124:0:1.5 +1 120429074 . CT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49707;SOR=0;LSEQ=CATGGGGGAGTACCCAGAAC;RSEQ=TTCCTATTCCTTGGAGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:4,73:77,2:0.0253:2,2:27.5:1:31:1:0.12334:16.43:60:4:0.026:0:0 0/0:75:0:0,0:10,65:75,0:0:2,0:19.3:1:29.7:1:1:0:60:36.5:1:0:0 +1 120429124 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49734;SOR=0;LSEQ=TCAGCAAGTGTTTAAACAGA;RSEQ=GCACATTTTACTGTTAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:0,2:2,23:25,2:0.0741:2,0:13:1:32:0:1:0:60:4:0.0741:0:1 0/0:21:0:0,0:3,18:21,0:0:2,0:32.5:1:30.8:1:1:0:60:42:1:0:0 +1 120429340 . TAC T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.15548;SOR=5.79829;LSEQ=ACGCACATCTCTCTCTCTCA;RSEQ=ACACACACACACCCCTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:1,0:27,0:27,1:0.0357:1,0:13:0:33:0:1:0:60:2:0.0357:0:0 0/1:22:4:4,0:18,0:18,4:0.1818:1,0:28:1:30.7:1:1:0:60:8:0.1818:0.0455:0 +1 120429402 . A G 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07847;SOR=0;LSEQ=CTCTCTTCTAGTTAGAGGGT;RSEQ=GAATTGGAAATTAAGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:5:5,0:70,3:73,5:0.0641:1,0:27:1:33.6:1:1:0:60:10:0.0641:0:1 0/0:54:0:0,0:51,3:54,0:0:2,0:26.4:1:27.8:1:1:0:60:108:1:0:0 +1 120429478 . C T 36 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=0;LSEQ=GATTGATACTGATGATTGTT;RSEQ=CAGTACTCGTGTCCGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:0,3:180,116:296,3:0.01:2,0:5.3:1:23.3:1:0.06208:0:60:2:0.0068:0:2.3 0/0:291:0:0,0:164,125:289,0:0:2,0:28.4:1:30.3:1:1:0:59.7:143.5:0.9931:0:0.2 +1 120429512 . G A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGAATGGGGCAAAGCATACC;RSEQ=ATCACCCGAATAGCTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:0:0,0:206,187:393,0:0:2,0:26.3:1:30.4:1:1:0:59.9:34.727:1:0:0.1 0/1:358:15:7,8:171,172:343,15:0.0419:2,2:24.3:1:30.3:1:1:1.13581:55.6:30:0.0421:0:1.1 +1 120429554 . T A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.52598;LSEQ=GCCAGTGTGCCACAGGTAAG;RSEQ=TTCTCCTCACTCTTCATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:14:5,9:113,186:299,14:0.0447:2,2:28.9:1:30.4:1:1:1.09325:58.2:13:0.0421:0:1.2 0/1:260:61:23,38:75,124:199,61:0.2346:2,2:26.7:1:29.4:1:1:1.00:57.4:122:0.2355:0:1.1 +1 120458004 . A T 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCGCTGACCTCCTCCAGC;RSEQ=CCCCCAGGGGTAGGGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:0:0,0:418,295:713,0:0:2,0:22.8:1:29.9:1:1:0:59.9:100.857:1:0:0.2 0/1:609:92:50,42:285,230:515,92:0.1511:2,2:23.6:1:28.7:1:0.90954:1.04082:60:45:0.1513:0:1.2 +1 120460984 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02908;SOR=Inf;LSEQ=TCTATTCCCCTCGTCAGAGG;RSEQ=ATGCTTTGCAGGTAAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:548:0:0,0:395,153:548,0:0:2,0:25.4:1:32.4:1:1:0:59.9:108.6:1:0:0.1 0/1:387:4:1,3:256,127:383,4:0.0103:2,2:12.3:1:26:1:0.11226:6.01772:60:8:0.0104:0:1 +1 120461253 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=ACTCAGTGAAGAAACAAGGG;RSEQ=ATCAGAGCTGAGGCTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:2,122:124,0:0:1,0:24.3:1:32.7:1:1:0:59.8:248:1:0:0.1 0/1:117:12:1,11:7,98:105,12:0.1026:2,2:28:1:25.3:1:0.59113:1.27:60:5:0.0885:0:1.3 +1 120462279 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52318;SOR=0;LSEQ=AAAGTACTCAAGAAGGAGAA;RSEQ=GTAGTTAACCCTATGGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:14,137:151,2:0.0131:2,2:12.5:1:29.5:1:0.18705:9.49:60:4:0.0135:0:1.5 0/0:97:0:0,0:10,86:96,0:0:2,0:23.8:1:30.6:1:1:0:60:95:0.9896:0:0 +1 120462777 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.19067;SOR=Inf;LSEQ=GGGGTTTATGACTGGACAGG;RSEQ=CAAACACAGGGACAACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:155,33:188,0:0:2,0:23.9:1:31:1:1:0:59.8:36.6:0.9946:0:0.1 0/1:147:2:2,0:118,26:144,2:0.0136:2,0:15.5:1:28:1:1:0:60:4:0.014:0:1 +1 120463044 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02828;SOR=0.69704;LSEQ=AAAGGTGAAAACAATGCTCC;RSEQ=TATCAATCTGGCCACCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:129:40,89:159,324:483,129:0.2108:2,2:23.5:1:30.2:1:0.75117:1.09176:60:63.5:0.2106:0:1.1 0/1:478:75:25,50:134,267:401,75:0.1569:2,2:22.8:1:29:1:1:1.00374:60:17.75:0.1511:0:1.1 +1 120463056 . C T 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03598;SOR=Inf;LSEQ=AATGCTCCCTATCAATCTGG;RSEQ=CACCACCAGAAACTGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:135,340:475,0:0:2,0:25.2:1:31.2:1:1:0:60:66.857:1:0:0.3 0/1:368:4:2,2:112,252:364,4:0.0109:2,2:32.5:1:27.3:1:0.59071:2.24:60:8:0.011:0:1.5 +1 120463093 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56406;SOR=3.11204;LSEQ=TAATCAGAAGGTGTCCAGAG;RSEQ=CTCCACCACCGCTGCTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:0,1:26,232:258,1:0.0038:2,0:8:0:32:0:1:0:60:2:0.004:0:1 0/1:168:2:1,1:21,145:166,2:0.0119:2,2:41.5:1:28.5:1:0.24544:6.77:60:4:0.0123:0:1 +1 120464141 . A C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.54822;SOR=0;LSEQ=GAGTTATTCTTGAAGAGCAT;RSEQ=TATAGGTAACCCAAGGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:3:3,0:36,0:36,3:0.0732:1,0:21:1:32:1:1:0:60:6:0.075:0:1 0/0:17:0:0,0:17,0:17,0:0:1,0:23:1:27.9:1:1:0:58:34:1:0:0.4 +1 120464165 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06915;SOR=Inf;LSEQ=AGGTAACCCAAGGTCATTTA;RSEQ=GTCCTAAGGATTCCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:55,1:56,0:0:1,0:24.3:1:32.2:1:1:0:60:55:1:0:0.3 0/1:40:3:3,0:37,0:37,3:0.075:1,0:14.3:1:31.7:1:1:0:60:6:0.075:0:1 +1 120464481 . T C 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATGGCAGTCATAAACTAA;RSEQ=ACAGTGGTTTTCAACACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:21,196:217,0:0:2,0:22.4:1:28.7:1:1:0:60:107.5:1:0:0.1 0/1:166:16:2,14:18,132:150,16:0.0964:2,2:22.6:1:31.7:1:1:1.05:60:32:0.0976:0:1 +1 120464492 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16077;SOR=Inf;LSEQ=ATAAACTAATACAGTGGTTT;RSEQ=CAACACTTTCCACCATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:18,168:186,0:0:2,0:20.3:1:30.4:1:1:0:60:185:1:0:0.1 0/1:125:2:1,1:12,111:123,2:0.016:2,2:25.5:1:27:1:0.19794:8.93:60:4:0.0161:0:1 +1 120464827 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0728;SOR=Inf;LSEQ=TAGTCATCCCTACTTATACT;RSEQ=TGAATAGTGGCTTATTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:242,83:325,0:0:2,0:25.6:1:32.6:1:1:0:60:80.25:1:0:0.1 0/1:234:3:2,1:155,76:231,3:0.0128:2,2:21:1:26.7:1:1:1.01966:60:6:0.013:0:1 +1 120465222 . C T 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.3226;SOR=3.91176;LSEQ=TCCCCCAATTGACACTCTTC;RSEQ=CCCGCCACCTTTCCCCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:1:1,0:255,102:357,1:0.0028:2,0:29:0:34:0:1:0:60:2:0.0029:0:1 0/1:277:3:1,2:197,77:274,3:0.0108:2,2:10:1:24:1:0.19666:5.08185:60:6:0.011:0:1.3 +1 120465443 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2199;SOR=Inf;LSEQ=GCGGAGGAGGAGAGATGGGG;RSEQ=TAAAACAGAAGAGTGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:34,184:218,0:0:2,0:24.7:1:31.7:1:1:0:60:42.6:1:0:0.1 0/1:193:2:1,1:43,148:191,2:0.0104:2,2:10.5:1:27.5:1:0.4049:3.41:60:4:0.0104:0:1.5 +1 120468134 . C T 228 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCTCATCACAGACGCCATC;RSEQ=CGAGCTTTGTCGGCACAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:967:176:80,96:352,438:790,176:0.182:2,2:22.2:1:30.6:1:0.86696:1.04:60:34.2:0.1806:0:1.1 0/0:804:0:0,0:358,446:804,0:0:2,0:24.8:1:30:1:1:0:60:72.091:1:0:0.2 +1 120468333 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.03329;SOR=Inf;LSEQ=ACTCGCAGTCCCGGGGACTG;RSEQ=GGCAGAAGCAGCGGGGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:517:0:0,0:252,265:517,0:0:2,0:25.7:1:31.3:1:1:0:60:85.167:1:0:0.1 0/1:387:4:2,2:199,184:383,4:0.0103:2,2:27.8:1:25.3:1:1:1.08128:60:3:0.0079:0:1.3 +1 120468434 . C A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03071;SOR=Inf;LSEQ=CACCTTGCCCCGGAAAATCC;RSEQ=TGTGGAAATCAGTGAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:142,293:435,0:0:2,0:26:1:32.6:1:1:0:60:71.5:1:0:0.2 0/1:434:5:4,1:178,249:427,5:0.0115:2,2:12:1:25.8:1:0.16691:5.58:60:10:0.0117:0:1.2 +1 120468481 . T A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22493;SOR=0;LSEQ=TGGCATTGGTAGGAAAACAG;RSEQ=CATATTGGAAGTTTGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:28,141:169,2:0.0117:2,2:5.5:1:28.5:1:0.31125:4.97:60:4:0.0118:0:1 0/0:189:0:0,0:43,145:188,0:0:2,0:21.6:1:28.3:1:1:0:60:93:1:0:0.1 +1 120468487 . T C 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGTAGGAAAACAGTCATAT;RSEQ=GGAAGTTTGAGGTTTCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:32:3,29:14,95:109,32:0.227:2,2:26.6:1:29.3:1:0.7627:1.42131:60:31:0.223:0:1.2 0/0:154:0:0,0:34,119:153,0:0:2,0:22:1:29.5:1:1:0:60:152:0.9935:0:0.1 +1 120469077 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03609;SOR=1.42694;LSEQ=AGTTCTGTTCACAGATTGTA;RSEQ=GGAAGAGACAATGCCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:72:57,15:309,98:407,72:0.1503:2,2:25.6:1:31.9:1:0.65196:1.20:60:71:0.1492:0:1.1 0/1:496:100:71,29:269,127:396,100:0.2016:2,2:26.3:1:30.3:1:0.63008:1.16:60:99:0.2004:0:1.1 +1 120469388 . ACACT A 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15209;SOR=0;LSEQ=AATCTGAGCATAGAAAGAAA;RSEQ=CACTGCATCTCAACATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:0,20:20,5:0.2:1,0:20.6:1:32.4:1:1:0:60:10:0.2:0:0.2 0/0:12:0:0,0:0,12:12,0:0:0,0:28:1:32.9:1:1:0:60:24:1:0:0.2 +1 120471424 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAAAGGTAGACACTGAT;RSEQ=ATAACATCCATAAAGTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:40,0:0,0:0,40:1:0,1:22.5:1:30.4:1:1:0:59.5:19:1:0:1.2 1/1:22:22:21,1:0,0:0,22:1:0,1:23.2:1:30.8:1:1:0:60:44:1:0:1.1 +1 120471610 . C A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01066;SOR=Inf;LSEQ=GCTTCTCACCAGTAAAGGCA;RSEQ=TACGGCAAACACACAGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:667:0:0,0:396,270:666,0:0:2,0:26.2:1:32.5:1:1:0:60:50.231:1:0:0.2 0/1:592:6:3,3:334,252:586,6:0.0101:2,2:26:1:28.3:1:1:1.32474:60:12:0.0102:0:1 +1 120471857 . C T 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGAGGAAAGAGAAGAGGTA;RSEQ=AGAATTATGAAAATCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:0:0,0:150,437:587,0:0:2,0:23.7:1:32.3:1:1:0:60:57.7:1:0:0.1 0/1:480:50:10,40:131,297:428,50:0.1042:2,2:24.2:1:28.7:1:0.14098:1.76242:60:100:0.1057:0:1 +1 120471975 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08764;SOR=Inf;LSEQ=TGGGACCTTGTAGTTGGGCA;RSEQ=GGCAAAGCACACTCTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:0,63:63,0:0:1,0:23.3:1:31.8:1:1:0:59.9:62:1:0:0.1 0/1:27:2:1,1:0,25:25,2:0.0741:1,2:13:0:31.5:1:0.07407:0:49:4:0.0741:0:1.5 +1 120477998 . C A 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGGAATGAAGCTAGTCTT;RSEQ=CTATCTTTAATTTTATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:327,129:456,0:0:2,0:22.9:1:31.8:1:1:0:60:90.2:1:0:0.1 0/1:430:53:34,19:254,123:377,53:0.1233:2,2:20.6:1:28.2:1:0.6424:1.15359:60:106:0.1238:0:1.1 +1 120478285 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCATTACTGGAAACAGACCA;RSEQ=GAGAGCTAGTGAGATCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:210:210:19,191:0,0:0,210:1:0,2:22.7:1:30.6:1:1:0:60:420:1:0:1.1 1/1:134:113:15,98:5,16:21,113:0.8433:2,2:25.9:1:29.4:1:0.31277:2.02892:60:55.5:0.8409:0:1.2 +1 120478807 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTGAGGTGGCTTTATTTGGA;RSEQ=ACTTTGACAGGTTTGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:25.5:1:34:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:27:1:1:0:60:4:1:0:1 +1 120479872 . G T 63 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05032;SOR=7.39191;LSEQ=AGTTGTACAATCTCCTGGGA;RSEQ=GTCCATGACCTCTGCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:682:1:0,1:464,216:680,1:0.0015:2,0:1:0:26:0:0.31865:0:60:2:0.0015:0:1 0/1:558:6:2,4:357,195:552,6:0.0108:2,2:15.7:1:24.7:1:0.19339:3.65255:60:5:0.0091:0:1.8 +1 120480394 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.56567;SOR=0.32915;LSEQ=TATCTGCCCTTCCCTCTTAT;RSEQ=CCACAAAAAAATGATACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:187:186:167,19:0,0:0,186:0.9947:0,2:21.4:1:32:1:1:0:60:61:0.9946:0:1.1 1/1:124:122:103,19:1,1:2,122:0.9839:2,2:22.4:1:30.2:1:0.29767:5.31:60:39.667:0.9835:0:1 +1 120480583 . G A 164 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.99627;LSEQ=GACTCTGCTTTTTTCTGAAC;RSEQ=CAAGTACCTTTGTTTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1005:6:5,1:445,553:998,6:0.006:2,2:9.3:1:28.7:1:0.09529:6.20:60:12:0.006:0:1 0/1:882:50:24,26:377,454:831,50:0.0567:2,2:25.4:1:29.1:1:0.77073:1.11:60:24:0.0556:0:1.2 +1 120480703 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17414;SOR=Inf;LSEQ=TGAAGAAAAGAAGTTATATT;RSEQ=TGTTACAAGAAATCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:14,178:192,0:0:2,0:23.5:1:32.1:1:1:0:60:37.4:1:0:0.1 0/1:138:2:1,1:21,115:136,2:0.0145:2,2:17:1:31.5:1:0.2944:5.37:60:4:0.0147:0:1 +1 120482907 . A C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAAAAAAACAAAAAACA;RSEQ=AAAACAAAAATCTGTGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:31.8:1:33.5:1:1:0:54:12:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:29:1:1:0:60:4:1:0:1 +1 120483137 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14711;SOR=Inf;LSEQ=GAACAGGTATAATATTCAGC;RSEQ=GCTCTAGGGGAGCTGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:221,45:266,0:0:2,0:24.7:1:32.3:1:1:0:60:265:1:0:0.1 0/1:166:2:1,1:124,40:164,2:0.012:2,2:14:1:31.5:1:0.4341:3.07411:60:4:0.012:0:1 +1 120484421 . G A 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCTGAAGAGTAGCATCA;RSEQ=TTTAATCTTAGATTCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:81,275:356,0:0:2,0:23.5:1:32.2:1:1:0:60:38.556:0.9971:0:0.1 0/1:286:42:9,33:65,179:244,42:0.1469:2,2:21.4:1:30:1:0.56944:1.33022:60:84:0.1474:0:1 +1 120490948 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14519;SOR=Inf;LSEQ=GGTATGCCCAATGTCAGGCG;RSEQ=GAAAGGCGGCAGCCTCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:154,6:160,0:0:1,0:24.5:1:30.7:1:1:0:59.8:159:1:0:0.1 0/1:99:2:1,1:94,3:97,2:0.0202:1,2:12.5:1:32:1:0.07957:27.27949:60:4:0.0206:0:1 +1 120490993 . T C 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.31754;SOR=4.06578;LSEQ=TCTCCTCTGCTCCCTGTGTG;RSEQ=TTTCCTCTCCTCTGGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:1:1,0:270,74:344,1:0.0029:2,0:32:0:13:0:1:0:60:0:0:0:2 0/1:257:3:1,2:185,69:254,3:0.0117:2,2:9.7:1:30:1:0.18574:5.32096:60:6:0.0117:0:1 +1 120491301 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1382;SOR=Inf;LSEQ=AGCTATTCCACAGACAAACT;RSEQ=GTTGGCCCCCTGCTTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:3,106:109,0:0:1,0:23.8:1:31.5:1:1:0:59.7:53.5:1:0:0 0/1:65:2:0,2:4,59:63,2:0.0308:2,0:10.5:1:31:0:1:0:60:4:0.0313:0:1 +1 120491312 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13289;SOR=Inf;LSEQ=AGACAAACTGGTTGGCCCCC;RSEQ=GCTTTAGGAAGTTCCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:4,91:95,0:0:1,0:24.3:1:30.6:1:1:0:59.7:46.5:1:0:0 0/1:55:2:0,2:4,49:53,2:0.0364:2,0:12.5:1:31.5:1:1:0:60:4:0.0364:0:1 +1 120493101 . TA T 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.81422;LSEQ=TGGTTCCAGCCACATACAAT;RSEQ=AAAAAAAATTTCTTTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:6:5,1:257,46:303,6:0.0194:2,2:25.5:1:31.2:1:1:1.11701:60:12:0.0195:0.0065:0.2 0/1:253:4:2,2:196,53:249,4:0.0158:2,2:20.5:1:27.3:1:0.20695:3.67363:60:8:0.0159:0.004:0.3 +1 120495767 . T G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAACATGGAGAAACCCCGTC;RSEQ=CTACTAAAAATACAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:26:1:30.5:1:1:0:36:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 120496119 . A T 183 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=99.7442;LSEQ=GAGTCAAGCAGTATGCAACA;RSEQ=CAAGAAGACAAAGAGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:887:1:1,0:585,300:885,1:0.0011:2,0:17:0:27:0:1:0:60:2:0.0011:0:2 0/1:740:75:46,29:425,239:664,75:0.1014:2,2:26.8:1:29.5:1:0.70413:1.12089:60:36.5:0.1001:0:2.1 +1 120496127 . A C 200 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=58.06987;LSEQ=CAGTATGCAACAACAAGAAG;RSEQ=CAAAGAGCAGACGCAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:981:2:2,0:618,360:978,2:0.002:2,0:26.5:1:20:1:0.53472:0:60:1:0.001:0:5 0/1:847:90:54,36:470,286:756,90:0.1063:2,2:27.3:1:30.9:1:0.7308:1.09545:60:44:0.1056:0:2 +1 120497589 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17326;SOR=Inf;LSEQ=GCCCCATTTGACAACTTCAG;RSEQ=CTGTCACCAGTACTACAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:151,25:176,0:0:2,0:24.7:1:31.2:1:1:0:59.8:87:1:0:0.1 0/1:126:2:1,1:108,16:124,2:0.0159:2,2:11.5:1:27:1:0.25257:6.57871:60:4:0.016:0:1.5 +1 120497601 . A T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19867;SOR=Inf;LSEQ=AACTTCAGGCTGTCACCAGT;RSEQ=CTACAAGCCAACTGGCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:177,40:217,0:0:2,0:23.8:1:28.3:1:1:0:59.9:434:1:0:0.1 0/1:175:2:1,1:136,37:173,2:0.0114:2,2:20.5:1:25:1:0.38811:3.64068:60:4:0.0116:0:1 +1 120498086 . G C 98 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTAACAAAAGGCTGGAAAA;RSEQ=TGTTATAGCAATTTGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:20.1:1:35:1:1:0:60:14:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:19:0:33:0:1:0:60:2:1:0:1 +1 120501953 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07903;SOR=Inf;LSEQ=TTGAAAAGCAATATTCCTTT;RSEQ=GATGCTATATTCCCAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:228,58:286,0:0:2,0:23.8:1:32.1:1:1:0:60:94.333:1:0:0.1 0/1:216:3:2,1:156,56:212,3:0.0139:2,2:10.3:1:31.7:1:1:1.39056:60:6:0.0142:0:1 +1 120501957 . G T 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63279;SOR=0.41447;LSEQ=AAAGCAATATTCCTTTGGAT;RSEQ=CTATATTCCCAAAGTGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:233,60:293,3:0.0101:2,2:10:1:30.7:1:0.50091:1.9364:60:6:0.0102:0:1 0/0:237:1:0,1:173,61:234,1:0.0042:2,0:1:0:26:0:0.26383:0:60:2:0.0043:0:1 +1 120505996 . G C 124 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACACAAAATCATCAGATT;RSEQ=GCAGAGCTATTGTCTCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:0,14:1:0,1:27.3:1:32.6:1:1:0:60:28:1:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:36:0:33:0:1:0:60:2:1:0:1 +1 120506108 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0438;SOR=Inf;LSEQ=GGACTGTTTTTTAGGTATCT;RSEQ=AGCATATGCCAACAGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:42,6:48,0:0:2,0:18.8:1:32.1:1:1:0:60:96:1:0:0.1 0/1:42:4:4,0:34,3:37,4:0.0952:2,0:17.5:1:28:1:1:0:60:8:0.0952:0:1 +1 120506145 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2236;SOR=Inf;LSEQ=CTGAAACATCTGTGTAAACA;RSEQ=ATTTGAGAAACAGTGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:84,18:102,0:0:2,0:25.5:1:33.1:1:1:0:60:101:1:0:0.1 0/1:92:2:1,1:72,18:90,2:0.0217:2,2:37.5:1:33:1:0.37219:3.92026:60:4:0.0217:0:2 +1 120510372 . A AT 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1258;SOR=5.75029;LSEQ=AATATCATTCCCAATTTTCT;RSEQ=TTTTTTTTTCCTTAATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:1:0,1:5,69:74,1:0.0133:2,0:39:0:29:0:1:0:60:2:0.0137:0:0 0/1:41:3:0,3:1,37:38,3:0.0732:1,0:35.7:1:31:0:1:0:60:6:0.0769:0:0 +1 120510572 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52889;SOR=0;LSEQ=AGGTCACTTGTAAACACTGG;RSEQ=CATGTAGCAAGAGTAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:119,4:123,2:0.016:1,2:18:1:28.5:1:0.07871:26.7209:60:4:0.0161:0:1 0/0:75:0:0,0:74,1:75,0:0:1,0:22.5:1:32.1:1:1:0:60:150:1:0:0.1 +1 120512052 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49998;SOR=0;LSEQ=ATGGTAACTCAAAGAATATG;RSEQ=TGTTTGGGATGAAAGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:2,0:145,8:153,2:0.0129:2,0:26:1:27:1:1:0:60:4:0.0136:0:3 0/0:138:0:0,0:119,19:138,0:0:2,0:22.8:1:31.8:1:1:0:60:45:1:0:0.8 +1 120512104 . T C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05245;SOR=0;LSEQ=AATGCCCCCTGCCCCTTCCC;RSEQ=GTTTCTAGATCCGTCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:383:383:304,79:0,0:0,383:1:0,2:24.1:1:30.8:1:1:0:60:62.833:1:0:1.1 1/1:353:349:254,95:1,1:2,349:0.9887:2,2:25.5:1:29.7:1:0.47277:2.66:59.9:57.167:0.9885:0:1.1 +1 120512403 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49812;SOR=0;LSEQ=TACTTTTGATTAGGGCTCTT;RSEQ=AGTCTCAAAGGACTAGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:6,122:128,2:0.0154:1,2:23.5:1:31.5:1:0.10519:18.89:60:4:0.0155:0:1 0/0:127:0:0,0:22,105:127,0:0:2,0:19.8:1:30.9:1:1:0:60:62.5:1:0:0.1 +1 120512409 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23779;SOR=Inf;LSEQ=TGATTAGGGCTCTTGAGTCT;RSEQ=AAAGGACTAGTACCATACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:6,108:114,0:0:2,0:23.4:1:32.4:1:1:0:60:113:1:0:0.2 0/1:109:2:1,1:18,89:107,2:0.0183:2,2:10:0:30.5:1:0.31957:4.84:60:4:0.0185:0:1.5 +1 120529750 . A C 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGATGAAATCTCATACAGA;RSEQ=GAAACGACCTGCTCTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:55,272:327,0:0:2,0:22.3:1:31.9:1:1:0:60:162.5:1:0:0.1 0/1:285:28:5,23:50,207:257,28:0.0982:2,2:24.4:1:29.4:1:1:1.11071:60:56:0.0986:0:1 +1 120529778 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50567;SOR=0;LSEQ=CCTGCTCTGTTCCCACAGAA;RSEQ=ATGGTTATTAGAATAGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:9,166:175,2:0.0113:2,2:25.5:1:29.5:1:0.11011:17.55:60:4:0.0113:0:1 0/0:139:0:0,0:9,130:139,0:0:2,0:22.2:1:31.7:1:1:0:60:45.333:1:0:0.2 +1 120539727 . C T 27 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGCTGTCACAGTACTGG;RSEQ=CTGTGAAGCCCTGAGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:18:0:27:1:1:1:60:4:0.5:0:1 +1 120572806 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTTCCAACAATAACCAC;RSEQ=TTTGTGGTCTTGAATGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:44:1:31.5:1:1:0:20:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 120611715 . A G 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=CTCCTGCCGAGGAGGCGTGT;RSEQ=AGGGGTCCCGGGCCGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:7,0:7,6:0.4615:0,0:10.7:1:31:1:1:0:39.2:5:0.4167:0:2.3 0/0:2:0:0,0:2,0:2,0:0:0,0:9.5:1:29:0:1:0:51:4:1:0:0 +1 120611758 . G A 94 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36443;SOR=0.28796;LSEQ=CAGAGGCGGCGGGGAACCCC;RSEQ=GCGGTTGGCGGGGCACCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:11,0:11,8:0.4211:0,0:43.5:1:31.6:1:1:0:39.8:16:0.4211:0:2.1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:25:0:30:0:1:0:24:2:0.1667:0:2 +1 120611964 . G C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.33308;SOR=0.72597;LSEQ=TCACCATGCGCGGGGGCCGC;RSEQ=CAGCACAGCCAGAGCGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:41:15,26:14,19:33,41:0.5541:2,2:16:1:30:1:0.63912:1.27294:21.4:12.667:0.5352:0:2.6 0/1:76:36:11,25:23,17:40,36:0.4737:2,2:15.3:1:29.1:1:0.02237:3.02741:21.3:72:0.48:0:3 +1 120612006 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.25668;SOR=1.41005;LSEQ=AGCGCCCACAGCAGAGCGGG;RSEQ=CGCAGGGCGGGCATCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:49:21,28:21,30:51,49:0.49:2,2:42.9:1:30:1:1:1.07:21.6:23.5:0.4845:0:2.3 1/0:99:57:22,35:24,18:42,57:0.5758:2,2:38.7:1:28.9:1:0.10239:2.10475:22.7:114:0.5758:0:2.5 +1 120612043 . G T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.0085;SOR=2.46407;LSEQ=TCTCGGTCGCCTCCTCCTCC;RSEQ=CCGCCGCCGCCGCCGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:19:8,11:32,45:77,19:0.1979:2,2:6.1:1:29.2:1:1:1.02:21.5:8.5:0.1809:0:3.1 0/1:87:33:12,21:30,24:54,33:0.3793:2,2:9.1:1:28.1:1:0.1213:2.16758:21.6:66:0.3882:0:3.2 +1 120612046 . G T 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.00242;SOR=Inf;LSEQ=CGGTCGCCTCCTCCTCCGCC;RSEQ=CCGCCGCCGCCGCCTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:32,46:78,0:0:2,0:13.1:1:30.8:1:1:0:34:77:1:0:0.9 0/1:73:8:2,6:37,28:65,8:0.1096:2,2:8:1:28.5:1:0.13458:3.89261:21:16:0.1111:0:3.9 +1 120904666 . T C 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTAGACCCTCTCGTATCAA;RSEQ=GAGACAGCATGGCCCGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:9:0:33:1:1:1:55:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 120904788 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5078;SOR=0;LSEQ=GCCACGGGCGGGGTGAAGAA;RSEQ=CCACACCGCTACCGGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:31,34:65,2:0.0299:2,2:19:0:32.5:1:1:1.10:21:4:0.0299:0:1.5 0/0:49:0:0,0:24,25:49,0:0:2,0:25.4:1:31.6:1:1:0:37.7:48:1:0:0.6 +1 120904807 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50579;SOR=0;LSEQ=AGCCACACCGCTACCGGCCG;RSEQ=CACCGTGGCTCTGCGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:32,35:67,2:0.029:2,2:23:0:32:0:1:1.09:25:4:0.029:0:1.5 0/0:52:0:0,0:25,25:50,0:0:2,0:28.1:1:32:1:1:0:38.7:100:0.9615:0:0.7 +1 120904830 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15446;SOR=Inf;LSEQ=CCGTGGCTCTGCGGGAGATC;RSEQ=GGCGCTACCAGAAGTCTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:29,32:61,0:0:2,0:15.4:1:31.1:1:1:0:38.9:29.5:1:0:0.5 0/1:40:2:1,1:19,19:38,2:0.05:2,2:17.5:1:31.5:1:1:1:51:4:0.0513:0:1.5 +1 120904832 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16079;SOR=Inf;LSEQ=GTGGCTCTGCGGGAGATCCG;RSEQ=CGCTACCAGAAGTCTACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:28,31:59,0:0:2,0:13.8:1:32.8:1:1:0:38.2:118:1:0:0.5 0/1:40:2:1,1:19,19:38,2:0.05:2,2:26:0:31:1:1:1:22:4:0.0513:0:2.5 +1 120904844 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19674;SOR=Inf;LSEQ=GAGATCCGGCGCTACCAGAA;RSEQ=TCTACGGAGCTGCTGATCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,18:35,0:0:2,0:7:1:33.1:1:1:0:35.9:70:0.9459:0:0.3 0/1:30:2:1,1:14,14:28,2:0.0667:2,2:14:0:31.5:1:1:1:22:4:0.0667:0:2.5 +1 120905012 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.027;SOR=Inf;LSEQ=TTCGAAGACACGAACCTGTG;RSEQ=GCCATCCATGCCAAGCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:0:0,0:243,186:429,0:0:2,0:12.2:1:30.7:1:1:0:25.2:84.8:1:0:0.1 0/1:407:5:3,2:240,160:400,5:0.0123:2,2:21.8:1:29.6:1:1:1:22.6:10:0.0125:0:1.4 +1 121483753 . A G 33 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTCCATCGAAATGTTCAAAG;RSEQ=GGTCCACATATCCGCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18:0:33.5:1:1:0:24:4:1:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:32:0:1:0:21:2:1:0:0 +1 121483755 . G T 32 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCATCGAAATGTTCAAAGAG;RSEQ=TCCACATATCCGCTTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:32:0:1:0:24:4:1:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:25:0:33:0:1:0:21:2:1:0:0 +1 121483803 . C T 29 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAAAGAGTGTTTCCAAACTG;RSEQ=TGTATCAAAAGGAATCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:29.5:1:1:0:24:4:1:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:33:0:1:0:21:2:1:0:0 +1 121484099 . G T 83 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.40587;SOR=2.69862;LSEQ=GTAACTTCCTTGTGTTGTGT;RSEQ=TATTCAACTCACAGAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:1,7:8,2:0.2:2,0:42:0:30.5:1:1:0:22:4:0.2:0:2.5 0/1:17:7:2,5:1,9:10,7:0.4118:2,2:42.9:1:29.7:1:0.53676:3.33:22.7:14:0.4118:0:2.9 +1 121484106 . A G 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04103;SOR=0;LSEQ=CCTTGTGTTGTGTGTATTCA;RSEQ=CTCACAGAGTTGAACGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:0,7:7,3:0.3:0,2:46.3:1:32.7:1:0.3:0:24:6:0.3:0:3.3 0/0:17:0:0,0:3,14:17,0:0:2,0:46.9:1:29.2:1:1:0:24.5:34:1:0:2.7 +1 121484115 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=GTGTGTATTCAACTCACAGA;RSEQ=TTGAACGATCCTTTACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:10,0:0:2,0:38.4:1:33.8:1:1:0:24.7:20:1:0:2.6 0/1:18:2:1,1:2,14:16,2:0.1111:2,2:37.5:1:29.5:1:0.31373:5.92:25:4:0.1111:0:1 +1 121484121 . C T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19223;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=GATCCTTTACACAGAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:1,3:0,5:5,4:0.4:0,2:33.8:1:31.3:1:0.44444:0:21.8:8:0.4:0:2.8 0/1:18:8:2,6:1,8:9,8:0.4444:2,2:32.1:1:30.5:1:0.57647:2.52:22.6:16:0.4444:0:3 +1 121484125 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=AACTCACAGAGTTGAACGAT;RSEQ=CTTTACACAGAGCAGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:10,0:0:2,0:28.4:1:32.4:1:1:0:24.7:20:1:0:2.6 0/1:18:2:0,2:3,13:16,2:0.1111:2,0:26.5:1:32.5:1:1:0:37.5:4:0.1111:0:6.5 +1 121484137 . G A 28 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28388;SOR=0.24897;LSEQ=TGAACGATCCTTTACACAGA;RSEQ=CAGACTTGAAACACTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:0,8:8,2:0.2:0,2:16.5:1:28.5:1:0.2:0:21.5:4:0.2:0:3 0/1:18:1:0,1:3,14:17,1:0.0556:2,0:19:0:31:0:1:0:22:2:0.0588:0:4 +1 121484358 . C T 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAGTGGATATTCAGACC;RSEQ=CCTTGAGGCCTTCGTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:29.3:1:32.7:1:1:0:39.3:6:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 121484381 . C G 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGGCCTTCGTTGGAAAC;RSEQ=GTATTTTTTCATATTATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:48.3:1:31.7:1:1:0:39.3:6:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 121484383 . T G 81 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCCTTCGTTGGAAACCG;RSEQ=ATTTTTTCATATTATGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1:0,2:28.6:1:32:1:1:0:33.6:10:1:0:5 1/1:7:7:3,4:0,0:0,7:1:0,2:1.6:1:28.9:1:1:0:28.7:14:1:0:3.4 +1 121484388 . T C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCGTTGGAAACCGTATTT;RSEQ=TTCATATTATGCTAGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:0,6:1:0,2:23.8:1:33.7:1:1:0:33.8:12:1:0:4.5 1/1:12:12:6,6:0,0:0,12:1:0,2:5.7:1:29:1:1:0:29.3:24:1:0:2.9 +1 121484397 . A C 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01413;SOR=0.13384;LSEQ=AAACCGTATTTTTTCATATT;RSEQ=TGCTAGACAGAAGAATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:3,3:3,3:6,6:0.5:2,2:21:1:31.8:1:1:1:35.3:12:0.5:0:4.3 0/1:27:3:1,2:12,12:24,3:0.1111:2,2:11.3:1:28:1:1:1.95076:29:6:0.1111:0:3.3 +1 121484410 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATATTATGCTAGACAGAA;RSEQ=AATTCTCAGTAATTTCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:19,0:0:2,0:15.2:1:31.2:1:1:0:35.2:38:1:0:3.1 0/1:60:3:2,1:25,32:57,3:0.05:2,2:17.7:1:28:1:0.5834:2.52:38.3:6:0.0508:0:3.7 +1 121484423 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25455;SOR=Inf;LSEQ=GACAGAAGAATTCTCAGTAA;RSEQ=TTCCTTGTGTTGTGTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:27:16,11:0,1:1,27:0.9643:0,2:19:1:32.9:1:0.42857:0:34.4:54:0.9643:0:2.8 1/1:82:82:40,42:0,0:0,82:1:0,2:21.1:1:31.2:1:1:0:34.5:164:1:0:2.4 +1 121484430 . G C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GAATTCTCAGTAATTTCCTT;RSEQ=TGTTGTGTGTATTCAACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:22.8:1:32.6:1:1:0:35.4:60:1:0:2.3 0/1:99:3:2,1:48,48:96,3:0.0303:2,2:20:1:32.7:1:1:1.99:36.3:6:0.0303:0:3.3 +1 121484434 . T G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.05586;SOR=0;LSEQ=TCTCAGTAATTTCCTTGTGT;RSEQ=GTGTGTATTCAACTGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:19,12:31,2:0.0606:2,2:27:0:33.5:1:1:1.56069:36:4:0.0606:0:3.5 0/0:105:0:0,0:51,54:105,0:0:2,0:26:1:29.6:1:1:0:35.3:51.5:1:0:2.3 +1 121484436 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.05525;SOR=0;LSEQ=TCAGTAATTTCCTTGTGTTG;RSEQ=GTGTATTCAACTGACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:19,13:32,2:0.0588:2,2:29:0:33:1:1:1.44493:36:4:0.0588:0:3.5 0/0:109:0:0,0:52,57:109,0:0:2,0:26.6:1:29.3:1:1:0:35.7:218:1:0:2.3 +1 121484440 . T C 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59316;SOR=0.45642;LSEQ=TAATTTCCTTGTGTTGTGTG;RSEQ=ATTCAACTGACAGAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:21,15:36,2:0.0526:2,2:24.5:1:31:1:1:1.38742:35.5:4:0.0526:0:4 0/1:122:3:2,1:57,62:119,3:0.0246:2,2:24.3:1:31.7:1:0.60972:2.16:27.3:6:0.0248:0:5 +1 121484452 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTTGTGTGTATTCAACTGAC;RSEQ=GAGTTGAACTTTCATTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:29,22:51,0:0:2,0:25.2:1:31.6:1:1:0:41.1:102:1:0:1.9 0/1:158:2:1,1:76,80:156,2:0.0127:2,2:19.5:1:29:1:1:1.05:43.5:4:0.0128:0:3 +1 121484453 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTGTGTATTCAACTGACA;RSEQ=AGTTGAACTTTCATTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:30,23:53,0:0:2,0:24.8:1:33.2:1:1:0:41.1:106:1:0:1.8 0/1:158:2:1,1:76,80:156,2:0.0127:2,2:43:1:29:1:1:1.05:40:4:0.0128:0:2.5 +1 121484457 . T C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57426;SOR=Inf;LSEQ=GTGTATTCAACTGACAGAGT;RSEQ=GAACTTTCATTTAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:31,24:55,0:0:2,0:26:1:31.2:1:1:0:41.5:110:1:0:1.9 0/1:166:4:2,2:79,83:162,4:0.0241:2,2:13:1:30.8:1:1:1.05:27.8:8:0.0242:0:3.3 +1 121484459 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTATTCAACTGACAGAGTTG;RSEQ=ACTTTCATTTAGAGAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:31,26:57,0:0:2,0:26.1:1:31:1:1:0:41.7:114:1:0:1.9 0/1:172:2:1,1:82,88:170,2:0.0116:2,2:26:0:32.5:1:1:1.07:27.5:4:0.0118:0:2 +1 121484460 . A G 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67186;LSEQ=TATTCAACTGACAGAGTTGA;RSEQ=CTTTCATTTAGAGAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:1:1,0:30,27:57,1:0.0172:2,0:42:0:32:0:1:0:36:2:0.0172:0:3 0/1:172:2:0,2:83,87:170,2:0.0116:2,0:28.5:1:32.5:1:0.49769:0:44.5:4:0.0117:0:3 +1 121484461 . C A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.57446;SOR=Inf;LSEQ=ATTCAACTGACAGAGTTGAA;RSEQ=TTTCATTTAGAGAGAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:31,27:58,0:0:2,0:26.4:1:32.9:1:1:0:41.8:116:1:0:1.9 0/1:175:4:2,2:83,86:169,4:0.0229:2,2:21:1:29.5:1:1:1.04:34.8:8:0.0231:0:4 +1 121484463 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAACTGACAGAGTTGAACT;RSEQ=TCATTTAGAGAGAGCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:32,27:59,0:0:2,0:26.7:1:30.9:1:1:0:41.9:118:1:0:1.9 0/1:181:2:1,1:88,91:179,2:0.011:2,2:24.5:1:30:1:1:1.03:43:4:0.0112:0:2.5 +1 121484470 . A G 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.01734;SOR=0.20643;LSEQ=ACAGAGTTGAACTTTCATTT;RSEQ=GAGAGAGCAGATTTGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:6:2,4:34,25:59,6:0.0923:2,2:24.5:1:30.5:1:0.3946:2.67843:38.2:12:0.0938:0:3 0/1:196:4:2,2:91,98:189,4:0.0204:2,2:38.8:1:30.5:1:1:1.08:34.5:8:0.0204:0:2.8 +1 121484471 . G C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.57493;SOR=Inf;LSEQ=CAGAGTTGAACTTTCATTTA;RSEQ=AGAGAGCAGATTTGAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:36,29:65,0:0:2,0:25.5:1:32.9:1:1:0:41.8:130:1:0:1.9 0/1:199:4:2,2:92,99:191,4:0.0201:2,2:16:1:33:0:1:1.08:26.3:8:0.0204:0:2.5 +1 121484473 . G C 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.3411;SOR=Inf;LSEQ=GAGTTGAACTTTCATTTAGA;RSEQ=AGAGCAGATTTGAAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:36,30:66,0:0:2,0:25.3:1:33:1:1:0:41.8:132:1:0:1.9 0/1:205:6:3,3:95,104:199,6:0.0293:2,2:17.8:1:33.2:1:1:1.09:26.2:12:0.0296:0:3.3 +1 121484477 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57513;SOR=Inf;LSEQ=TGAACTTTCATTTAGAGAGA;RSEQ=CAGATTTGAAACACTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:38,33:71,0:0:2,0:23.6:1:32.6:1:1:0:41.3:142:1:0:1.8 0/1:213:4:2,2:100,109:209,4:0.0188:2,2:31.8:1:29:1:1:1.09:47:8:0.019:0:3.3 +1 121484480 . G C 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04858;SOR=0.10697;LSEQ=ACTTTCATTTAGAGAGAGCA;RSEQ=ATTTGAAACACTGTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:3:2,1:35,33:68,3:0.0423:2,2:14.3:1:33.7:1:1:1.87:45.7:6:0.0423:0:1.7 0/0:215:1:1,0:101,111:212,1:0.0047:2,0:11:0:33:0:0.47887:0:37:2:0.0047:0:2 +1 121484482 . T G 86 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.16029;LSEQ=TTTCATTTAGAGAGAGCAGA;RSEQ=TTGAAACACTGTTTTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:35,32:67,2:0.029:2,2:28:1:31.5:1:1:1.09232:35.5:4:0.029:0:4 0/1:209:7:4,3:95,104:199,7:0.0335:2,2:24.3:1:30.7:1:0.71273:1.46:36.1:14:0.0343:0:4.1 +1 121484486 . A T 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30762;SOR=3.9274;LSEQ=ATTTAGAGAGAGCAGATTTG;RSEQ=AACACTGTTTTTGTGGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:1:1,0:37,35:72,1:0.0137:2,0:16:0:26:0:1:0:36:2:0.0137:0:3 0/1:212:11:4,7:96,102:198,11:0.0519:2,2:27.8:1:28.5:1:0.5421:1.64322:31.9:22:0.0526:0:3 +1 121484487 . A T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.04698;LSEQ=TTTAGAGAGAGCAGATTTGA;RSEQ=ACACTGTTTTTGTGGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:1:0,1:39,35:74,1:0.0133:2,0:1:0:24:0:0.48:0:34:2:0.0133:0:3 0/1:215:3:1,2:101,111:212,3:0.014:2,2:27.3:1:26:1:1:1.81496:34:6:0.014:0:2.3 +1 121484489 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57525;SOR=Inf;LSEQ=TAGAGAGAGCAGATTTGAAA;RSEQ=ACTGTTTTTGTGGTATTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:39,34:73,0:0:2,0:23.5:1:31.8:1:1:0:40.1:72:1:0:1.9 0/1:222:4:1,3:103,115:218,4:0.018:2,2:30.3:1:28.5:1:0.62461:2.67598:40.3:8:0.0181:0:2.5 +1 121484490 . A C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57528;SOR=Inf;LSEQ=AGAGAGAGCAGATTTGAAAC;RSEQ=CTGTTTTTGTGGTATTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:39,33:72,0:0:2,0:23.5:1:29.9:1:1:0:40:144:0.9863:0:1.9 0/1:223:4:2,2:104,114:218,4:0.0179:2,2:36.3:1:30.3:1:1:1.10:35:8:0.018:0:2.8 +1 121484492 . T G 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAGAGCAGATTTGAAACAC;RSEQ=GTTTTTGTGGTATTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:39,34:73,0:0:2,0:23.8:1:31.1:1:1:0:39.6:146:1:0:1.9 0/1:222:3:2,1:103,116:219,3:0.0135:2,2:30:1:22.3:1:0.60392:2.24:35.7:2:0.0093:0:3.7 +1 121484493 . G C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGAGCAGATTTGAAACACT;RSEQ=TTTTTGTGGTATTTGCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:39,33:72,0:0:2,0:24.2:1:32:1:1:0:39.6:144:1:0:1.9 0/1:224:3:2,1:102,117:219,3:0.0134:2,2:32:1:32.3:1:0.60092:2.29:35:6:0.0136:0:5 +1 121484499 . G A 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.27431;LSEQ=AGATTTGAAACACTGTTTTT;RSEQ=TGGTATTTGCAAGTGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:1:1,0:36,30:66,1:0.0149:2,0:1:0:23:0:1:0:36:2:0.0149:0:4 0/1:211:4:2,2:99,107:206,4:0.019:2,2:29.8:1:27.8:1:1:1.08:38.5:8:0.0191:0:2.3 +1 121484503 . T A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33958;SOR=0;LSEQ=TTGAAACACTGTTTTTGTGG;RSEQ=ATTTGCAAGTGGAGATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:64:34,30:0,0:0,64:1:0,2:28.1:1:30.6:1:1:0:39:128:1:0:1.9 1/1:199:194:95,99:1,1:2,194:0.9749:2,2:25.7:1:29.1:1:1:1.0419:36.7:96:0.9897:0:2 +1 121484509 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTGTTTTTGTGGTATTTG;RSEQ=AAGTGGAGATTTCAAGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:33,29:62,0:0:2,0:28.7:1:31.6:1:1:0:39.3:30:1:0:1.9 0/1:184:2:1,1:89,93:182,2:0.0109:2,2:32:1:28.5:1:1:1.04:40.5:4:0.0113:0:2 +1 121484511 . A G 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.66788;LSEQ=CTGTTTTTGTGGTATTTGCA;RSEQ=GTGGAGATTTCAAGCGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:33,27:60,1:0.0164:2,0:32:0:33:0:0.45902:0:53:2:0.0164:0:2 0/1:182:2:1,1:87,93:180,2:0.011:2,2:9.5:1:32.5:1:1:1.07:34:4:0.0112:0:1.5 +1 121484512 . G T 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04702;SOR=0.10495;LSEQ=TGTTTTTGTGGTATTTGCAA;RSEQ=TGGAGATTTCAAGCGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:3:2,1:30,26:56,3:0.0508:2,2:36:1:32:1:1:1.72:48:6:0.0508:0:2.3 0/0:181:1:0,1:87,91:178,1:0.0055:2,0:49:0:28:0:1:0:44:2:0.0056:0:3 +1 121484513 . T G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTTTGTGGTATTTGCAAG;RSEQ=GGAGATTTCAAGCGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:31,26:57,0:0:2,0:30.6:1:30.2:1:1:0:39.4:114:0.9828:0:1.8 0/1:179:3:1,2:85,91:176,3:0.0168:2,2:30.7:1:31.3:1:1:1.86187:28.3:6:0.0169:0:3 +1 121484515 . G C 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTTGTGGTATTTGCAAGTG;RSEQ=AGATTTCAAGCGCTTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:29,26:55,0:0:2,0:31:1:31.5:1:1:0:39.1:54:1:0:1.8 0/1:176:2:1,1:84,90:174,2:0.0114:2,2:7:1:31:1:1:1.07:35:4:0.0116:0:5.5 +1 121484516 . A T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14758;SOR=0.15752;LSEQ=TTTGTGGTATTTGCAAGTGG;RSEQ=GATTTCAAGCGCTTTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:27,25:52,2:0.0364:2,2:29.5:1:31:1:1:1.07844:34:4:0.037:0:2.5 0/0:171:1:0,1:82,88:170,1:0.0058:2,0:46:0:29:0:1:0:36:2:0.0059:0:5 +1 121484519 . T C 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60153;SOR=0.49569;LSEQ=GTGGTATTTGCAAGTGGAGA;RSEQ=TTCAAGCGCTTTGGGGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:28,26:54,2:0.0357:2,2:43.5:1:32.5:1:1:1.07547:35:4:0.0364:0:2 0/1:167:3:1,2:80,84:164,3:0.018:2,2:37.3:1:30:1:1:1.8977:39.7:6:0.0183:0:4.3 +1 121484520 . T G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGTATTTGCAAGTGGAGAT;RSEQ=TCAAGCGCTTTGGGGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:28,27:55,0:0:2,0:29.8:1:30.9:1:1:0:39.5:110:0.9821:0:1.7 0/1:167:2:1,1:79,84:163,2:0.012:2,2:28.5:1:30:1:1:1.06:26:4:0.012:0:5 +1 121484521 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTATTTGCAAGTGGAGATT;RSEQ=CAAGCGCTTTGGGGCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:28,27:55,0:0:2,0:30.3:1:30.7:1:1:0:39.4:54:1:0:1.7 0/1:165:2:1,1:79,84:163,2:0.0121:2,2:33:0:32.5:1:1:1.06:32.5:4:0.0123:0:3.5 +1 121484522 . C G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06395;SOR=0;LSEQ=GTATTTGCAAGTGGAGATTT;RSEQ=AAGCGCTTTGGGGCCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:27,26:53,2:0.0364:2,2:41.5:1:33:1:1:1.03776:33.5:4:0.037:0:2 0/0:161:0:0,0:77,84:161,0:0:2,0:26.6:1:31.3:1:1:0:37.3:322:1:0:1.9 +1 121484527 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.71268;LSEQ=TGCAAGTGGAGATTTCAAGC;RSEQ=CTTTGGGGCCAAAGGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:1:0,1:27,26:53,1:0.0185:2,0:12:0:32:0:1:0:38:2:0.0185:0:4 0/1:151:2:1,1:72,77:149,2:0.0132:2,2:16.5:1:27:1:1:1.07:39.5:4:0.0135:0:2.5 +1 121484529 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGTGGAGATTTCAAGCGC;RSEQ=TTGGGGCCAAAGGCAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:26,27:53,0:0:2,0:28.1:1:31.5:1:1:0:39.6:106:1:0:1.7 0/1:140:2:1,1:63,74:137,2:0.0143:2,2:30.5:1:32.5:1:1:1.17:26.5:4:0.0146:0:3 +1 121484531 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.56285;SOR=Inf;LSEQ=AGTGGAGATTTCAAGCGCTT;RSEQ=GGGGCCAAAGGCAGAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:25,26:51,0:0:2,0:28:1:30.6:1:1:0:39.7:50:1:0:1.7 0/1:135:3:2,1:59,73:132,3:0.0222:2,2:14.7:1:30:1:0.58912:2.46:41.3:6:0.0231:0:2 +1 121484534 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGATTTCAAGCGCTTTGG;RSEQ=GCCAAAGGCAGAAAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:51,0:0:2,0:26.3:1:31.3:1:1:0:38.9:50:1:0:1.8 0/1:132:2:1,1:61,68:129,2:0.0152:2,2:19:0:31.5:1:1:1.11:22.5:4:0.0156:0:2 +1 121484537 . C A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58501;SOR=0.42408;LSEQ=GATTTCAAGCGCTTTGGGGC;RSEQ=AAAGGCAGAAAAGGAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:27,26:53,2:0.0357:2,2:19.5:1:30.5:1:1:1.03776:32.5:4:0.0364:0:2 0/1:130:2:1,1:62,65:127,2:0.0154:2,2:38:0:31:1:1:1.05:21:4:0.0157:0:2.5 +1 121484540 . A G 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.86011;LSEQ=TTCAAGCGCTTTGGGGCCAA;RSEQ=GGCAGAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:1,0:27,28:55,1:0.0179:2,0:11:0:28:0:1:0:49:2:0.0182:0:2 0/1:130:2:1,1:63,65:128,2:0.0154:2,2:18.5:1:32.5:1:1:1.03:39:4:0.0155:0:2.5 +1 121484550 . G C 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55511;SOR=Inf;LSEQ=TTGGGGCCAAAGGCAGAAAA;RSEQ=GAAATATCTTCGTATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:28,25:53,0:0:2,0:15.7:1:32.7:1:1:0:33.1:106:0.9815:0:2 0/1:126:3:2,1:59,62:121,3:0.0238:2,2:18.7:1:28.3:1:0.61585:2.09:34.3:6:0.024:0:4.3 +1 121484552 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGGCCAAAGGCAGAAAAGG;RSEQ=AATATCTTCGTATAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:26,24:50,0:0:2,0:15.7:1:30.8:1:1:0:31:49:1:0:2 0/1:127:2:1,1:60,65:125,2:0.0157:2,2:21:1:29.5:1:1:1.08:45:4:0.0157:0:2 +1 121484561 . C T 30 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18031;SOR=0.18253;LSEQ=GGCAGAAAAGGAAATATCTT;RSEQ=GTATAAAAACTAGACAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:25,19:44,2:0.0435:2,2:5:1:30:1:1:1.30786:44.5:4:0.0435:0:2 0/0:123:1:0,1:56,66:122,1:0.0081:2,0:26:0:25:0:1:0:21:2:0.0081:0:3 +1 121484564 . A T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15657;SOR=2.36232;LSEQ=AGAAAAGGAAATATCTTCGT;RSEQ=TAAAAACTAGACAGAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:4,0:23,21:44,4:0.0833:2,0:20.5:1:32.8:1:0.12095:0:22.8:8:0.0833:0:4.3 0/1:124:22:11,11:47,55:102,22:0.1774:2,2:17.2:1:28.8:1:0.81569:1.17:22.9:44:0.1803:0:4.1 +1 121484565 . T G 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.29592;SOR=0.36321;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGACAGAATCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:2,0:23,21:44,2:0.0435:2,0:10:1:34:1:0.49275:0:27.5:4:0.0435:0:3 0/1:124:2:1,1:57,65:122,2:0.0161:2,2:13.5:1:29.5:1:1:1.14:32.5:4:0.0163:0:3.5 +1 121484566 . A C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22883;SOR=2.09211;LSEQ=AAAAGGAAATATCTTCGTAT;RSEQ=AAAACTAGACAGAATCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:4:4,0:21,20:41,4:0.087:2,0:22.5:1:33.8:1:0.11742:0:22.8:8:0.087:0:4.3 0/1:126:21:10,11:49,55:104,21:0.1667:2,2:18.5:1:30.3:1:1:1.02:22:42:0.1667:0:4 +1 121484571 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATCATTCTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:27,22:49,0:0:2,0:16.3:1:32.8:1:1:0:23.8:48:1:0:2.5 0/1:128:2:1,1:59,65:124,2:0.0156:2,2:13:1:30:1:1:1.10:32.5:4:0.016:0:3.5 +1 121484572 . TA CC 49 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56107;SOR=Inf;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=GACAGAATCATTCTCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,20:48,0:0:2,0:16.9:1:30.5:1:1:0:23.3:23:0.9787:0:2.4 0/1:127:3:2,1:59,64:123,3:0.0236:2,2:7.3:1:31:1:0.6102:2.16:29:6:0.0238:0.0079:3 +1 121484574 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATCTTCGTATAAAAACTA;RSEQ=ACAGAATCATTCTCAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:28,20:48,0:0:2,0:17.9:1:32.9:1:1:0:23.4:47:1:0:2.5 0/1:124:2:1,1:61,61:122,2:0.0161:2,2:21:1:32:0:1:1:22.5:4:0.0161:0:3 +1 121484578 . G A 41 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60681;SOR=0.52185;LSEQ=CTTCGTATAAAAACTAGACA;RSEQ=AATCATTCTCAGTAACTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:26,18:44,2:0.0435:2,2:11:1:32.5:1:1:1.43267:25.5:4:0.0455:0:2.5 0/1:130:3:3,0:61,66:127,3:0.0231:2,0:12.3:1:26.3:1:0.11646:0:25.7:6:0.0236:0:4 +1 121484581 . T G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTATAAAAACTAGACAGAA;RSEQ=CATTCTCAGTAACTGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:27,18:45,0:0:2,0:23.9:1:30.6:1:1:0:22.4:21.5:1:0:2.7 0/1:126:2:1,1:60,64:124,2:0.0159:2,2:23.5:1:30.5:1:1:1.07:26.5:4:0.0161:0:5.5 +1 121484582 . C G 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05566;LSEQ=GTATAAAAACTAGACAGAAT;RSEQ=ATTCTCAGTAACTGCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:1:1,0:26,18:44,1:0.0222:2,0:17:0:34:0:1:0:22:2:0.0222:0:4 0/1:128:3:0,3:62,62:124,3:0.0234:2,0:9.7:1:30.7:1:0.24447:0:22.7:6:0.0234:0:3.7 +1 121484584 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAAAAACTAGACAGAATCA;RSEQ=TCTCAGTAACTGCTCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:28,20:48,0:0:2,0:24.6:1:31.2:1:1:0:22.4:96:1:0:2.8 0/1:133:2:2,0:63,68:131,2:0.015:2,0:11:1:33:0:0.23696:0:22.5:4:0.015:0:3 +1 121484588 . C G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACTAGACAGAATCATTCT;RSEQ=AGTAACTGCTCTGTGATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:27,20:47,0:0:2,0:27.6:1:32:1:1:0:22.1:22.5:1:0:2.8 0/1:135:2:2,0:66,67:133,2:0.0148:2,0:34.5:1:33.5:1:0.4963:0:24:4:0.0149:0:4 +1 121484589 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTAGACAGAATCATTCTC;RSEQ=GTAACTGCTCTGTGATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:27,20:47,0:0:2,0:28.1:1:31.2:1:1:0:22.1:46:1:0:2.8 0/1:138:2:1,1:68,68:136,2:0.0145:2,2:36.5:1:29:1:1:1:22:4:0.0146:0:2 +1 121484591 . T A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGACAGAATCATTCTCAG;RSEQ=AACTGCTCTGTGATGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:27,20:0,0:0,47:1:0,2:29:1:31:1:1:0:22.3:94:1:0:2.8 1/1:144:141:70,71:0,0:0,141:0.9792:0,2:27.2:1:28.9:1:1:0:23.3:69.5:0.9858:0:2.9 +1 121484596 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAATCATTCTCAGTAACT;RSEQ=CTCTGTGATGTGTGCGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:31,24:55,0:0:2,0:27.4:1:32:1:1:0:22.9:54:0.9818:0:2.9 0/1:154:2:1,1:73,78:151,2:0.013:2,2:12.5:1:27:0:1:1.07:22:4:0.0132:0:5 +1 121484597 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06821;SOR=0;LSEQ=AGAATCATTCTCAGTAACTG;RSEQ=TCTGTGATGTGTGCGTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:31,23:54,2:0.0357:2,2:11:0:32:0:1:1.34054:25.5:4:0.037:0:3.5 0/0:157:0:0,0:77,80:157,0:0:2,0:27.7:1:31.2:1:1:0:23.8:156:1:0:3 +1 121484599 . CT GC 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.43437;SOR=0.66986;LSEQ=AATCATTCTCAGTAACTGCT;RSEQ=GTGATGTGTGCGTTCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:7:2,5:32,20:52,7:0.1148:2,2:9.4:1:27.6:1:0.1222:3.90546:27.3:6:0.1034:0.0164:3.6 0/1:163:13:6,7:73,75:148,13:0.0798:2,2:14.1:1:30.5:1:1:1.13466:25.3:26:0.0813:0.0123:4 +1 121484602 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16373;SOR=1.5597;LSEQ=CATTCTCAGTAACTGCTCTG;RSEQ=GATGTGTGCGTTCAACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:48:29,19:8,16:24,48:0.6575:2,2:30:1:31.7:1:0.04507:3.00:23.5:96:0.6575:0:2.8 1/0:184:138:68,70:23,23:46,138:0.75:2,2:28.9:1:29.7:1:1:1.02926:23.8:45:0.7584:0:2.9 +1 121484611 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08387;SOR=0;LSEQ=TAACTGCTCTGTGATGTGTG;RSEQ=GTTCAACTCTCAGAGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:44,44:88,2:0.022:2,2:24.5:1:29.5:1:1:1:21:4:0.023:0:2.5 0/0:222:0:0,0:107,108:215,0:0:2,0:24.6:1:30.1:1:1:0:26.3:214:0.9683:0:2.6 +1 121484617 . A G 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.20724;SOR=0.20563;LSEQ=CTCTGTGATGTGTGCGTTCA;RSEQ=CTCTCAGAGTTTAACTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:49,50:99,2:0.0198:2,2:11.5:1:31:1:1:1.02:29:4:0.0198:0:3 0/0:243:1:0,1:116,126:242,1:0.0041:2,0:19:0:34:0:1:0:21:2:0.0042:0:3 +1 121484619 . T C 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20618;SOR=0.20479;LSEQ=CTGTGATGTGTGCGTTCAAC;RSEQ=CTCAGAGTTTAACTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:49,49:98,2:0.0198:2,2:13.5:1:32:1:1:1:23:4:0.02:0:1.5 0/0:244:1:0,1:117,125:242,1:0.0041:2,0:17:0:25:0:1:0:45:2:0.0042:0:5 +1 121484624 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08757;SOR=0;LSEQ=ATGTGTGCGTTCAACTCTCA;RSEQ=AGTTTAACTTTTCTTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:51,51:102,2:0.0189:2,2:33:1:32:1:1:1:29:4:0.0196:0:4 0/0:251:0:0,0:119,131:250,0:0:2,0:25.4:1:30.8:1:1:0:27.3:249:0.996:0:2.7 +1 121484625 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08942;SOR=0;LSEQ=TGTGTGCGTTCAACTCTCAG;RSEQ=GTTTAACTTTTCTTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:53,53:106,2:0.0185:2,2:14:1:30:1:1:1:20.5:4:0.0189:0:2.5 0/0:252:0:0,0:120,132:252,0:0:2,0:25.4:1:29:1:1:0:27.3:35:1:0:2.7 +1 121484636 . T G 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.01052;SOR=0.08308;LSEQ=AACTCTCAGAGTTTAACTTT;RSEQ=CTTTTCATTCAGCAGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:5:3,2:48,53:101,5:0.0472:2,2:31.2:1:32.8:1:0.66993:1.65:31.2:10:0.0476:0:2.4 0/0:246:1:1,0:115,129:244,1:0.0041:2,0:40:0:29:0:0.47347:0:23:2:0.0041:0:3 +1 121484650 . A G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.78615;SOR=1.11572;LSEQ=AACTTTTCTTTTCATTCAGC;RSEQ=GTTTGGAAACACTCTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:26:10,16:36,37:73,26:0.26:2,2:34.2:1:31.1:1:0.36922:1.54983:32.3:52:0.2653:0:2.7 0/1:213:60:28,32:69,82:151,60:0.2817:2,2:32.6:1:29.7:1:1:1.04:31.9:120:0.2844:0:3 +1 121484651 . G A 26 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23718;SOR=0.22979;LSEQ=ACTTTTCTTTTCATTCAGCA;RSEQ=TTTGGAAACACTCTGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:2,0:44,52:96,2:0.0204:2,0:8:1:26:0:0.21776:0:23:4:0.0204:0:3.5 0/0:211:1:1,0:95,113:208,1:0.0047:2,0:1:0:28:0:0.45933:0:27:2:0.0049:0:2 +1 121484654 . T A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.55359;SOR=Inf;LSEQ=TTTCTTTTCATTCAGCAGTT;RSEQ=GGAAACACTCTGTTTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:45,52:97,0:0:2,0:31.2:1:30.3:1:1:0:29.6:47.5:1:0:2.5 0/1:203:3:3,0:90,110:200,3:0.0148:2,0:9.7:1:25:1:0.09446:0:24.3:6:0.0153:0:3 +1 121484655 . G A 30 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23467;SOR=0.22764;LSEQ=TTCTTTTCATTCAGCAGTTT;RSEQ=GAAACACTCTGTTTGTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:42,49:91,2:0.0215:2,2:6.5:1:30.5:1:1:1.16:21:4:0.0222:0:4 0/0:202:1:1,0:91,110:201,1:0.005:2,0:12:0:22:0:0.45545:0:22:2:0.0051:0:5 +1 121484657 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTCATTCAGCAGTTTGG;RSEQ=AACACTCTGTTTGTAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:41,49:90,0:0:2,0:33:1:30.6:1:1:0:30.3:89:1:0:2.5 0/1:193:2:1,1:87,104:191,2:0.0104:2,2:41.5:1:28:1:1:1.19:49.5:4:0.0106:0:6 +1 121484660 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCATTCAGCAGTTTGGAAA;RSEQ=ACTCTGTTTGTAAAGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:40,49:89,0:0:2,0:32.5:1:31.8:1:1:0:30.4:28.667:1:0:2.4 0/1:189:2:1,1:87,100:187,2:0.0106:2,2:41.5:1:28.5:1:1:1.15:49.5:4:0.0107:0:6 +1 121484664 . CTGTT C 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.09299;SOR=0.14908;LSEQ=TTCAGCAGTTTGGAAACACT;RSEQ=TGTAAAGTCTGCACGTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:3:2,1:36,47:83,3:0.0349:2,2:9.7:1:30.7:1:0.58116:2.58:24.7:6:0.0361:0.0116:1.7 0/0:188:1:1,0:87,100:187,1:0.0053:2,0:35:0:27:0:0.46809:0:35:2:0.0054:0:4 +1 121484667 . T G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGTTTGGAAACACTCTG;RSEQ=TTGTAAAGTCTGCACGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:34,45:79,0:0:2,0:32.4:1:30:1:1:0:31.5:78:1:0:2.4 0/1:181:2:1,1:81,95:176,2:0.011:2,2:16.5:1:29:1:1:1.17:28:4:0.0114:0:3.5 +1 121484670 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTTGGAAACACTCTGTTT;RSEQ=TAAAGTCTGCACGTAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:33,43:76,0:0:2,0:32.2:1:32.6:1:1:0:31.7:152:1:0:2.4 0/1:177:2:1,1:83,90:173,2:0.0113:2,2:27.5:1:28.5:1:1:1.08:32.5:4:0.0114:0:3.5 +1 121484671 . T G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55567;SOR=Inf;LSEQ=GTTTGGAAACACTCTGTTTG;RSEQ=AAAGTCTGCACGTAGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:33,43:76,0:0:2,0:31.4:1:29.1:1:1:0:31.7:152:1:0:2.4 0/1:175:3:1,2:82,90:172,3:0.0171:2,2:12.3:1:31.7:1:1:1.81623:25:6:0.0171:0:3.7 +1 121484674 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09305;SOR=0;LSEQ=TGGAAACACTCTGTTTGTAA;RSEQ=GTCTGCACGTAGATATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:31,43:74,2:0.0263:2,2:33.5:1:30:1:1:1.38:37:4:0.0267:0:3.5 0/0:172:0:0,0:80,92:172,0:0:2,0:23.4:1:29.8:1:1:0:30.3:85:1:0:3 +1 121484675 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09305;SOR=0;LSEQ=GGAAACACTCTGTTTGTAAA;RSEQ=TCTGCACGTAGATATTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:31,43:74,2:0.0263:2,2:8.5:1:31.5:1:1:1.38:25.5:4:0.0263:0:3.5 0/0:172:0:0,0:80,91:171,0:0:2,0:22.9:1:31.4:1:1:0:30.5:84.5:0.9941:0:3 +1 121484676 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACACTCTGTTTGTAAAG;RSEQ=CTGCACGTAGATATTTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:32,43:75,0:0:2,0:27.3:1:30.3:1:1:0:31.9:150:0.9868:0:2.5 0/1:167:2:1,1:78,87:165,2:0.012:2,2:8.5:1:27:1:1:1.11:22:4:0.012:0:3.5 +1 121484677 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09937;SOR=0;LSEQ=AAACACTCTGTTTGTAAAGT;RSEQ=TGCACGTAGATATTTTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:31,43:74,2:0.0263:2,2:13.5:1:31:1:1:1.38:29:4:0.0263:0:4 0/0:164:0:0,0:78,85:163,0:0:2,0:22.7:1:30.8:1:1:0:30.9:39.75:0.9938:0:3 +1 121484679 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACTCTGTTTGTAAAGTCT;RSEQ=CACGTAGATATTTTGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:32,44:76,0:0:2,0:24.3:1:32.6:1:1:0:31.8:152:1:0:2.5 0/1:162:2:1,1:77,82:159,2:0.0123:2,2:41:1:29:1:1:1.06:24.5:4:0.0127:0:5 +1 121484681 . A C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55325;SOR=Inf;LSEQ=ACTCTGTTTGTAAAGTCTGC;RSEQ=CGTAGATATTTTGACCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:31,44:75,0:0:2,0:22.7:1:30:1:1:0:31.9:74:1:0:2.5 0/1:160:3:2,1:76,81:157,3:0.0188:2,2:17.7:1:32:1:0.61333:2.12:21:6:0.0188:0:5 +1 121484683 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGTTTGTAAAGTCTGCAC;RSEQ=TAGATATTTTGACCACTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:28,41:69,0:0:2,0:22.6:1:31.3:1:1:0:32.5:138:1:0:2.6 0/1:156:2:1,1:74,79:153,2:0.0128:2,2:11:1:28:1:1:1.07:27.5:4:0.0129:0:5 +1 121484685 . A G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64444;SOR=1.51211;LSEQ=TGTTTGTAAAGTCTGCACGT;RSEQ=GATATTTTGACCACTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:66:28,38:0,0:0,66:0.9706:0,2:20.8:1:31.3:1:1:0:32.6:65:0.9701:0:2.6 1/1:153:150:70,80:0,1:1,150:0.9804:0,2:18.8:1:31:1:1:0:31.3:300:0.9868:0:3.2 +1 121484688 . T A 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04095;SOR=6.85409;LSEQ=TTGTAAAGTCTGCACGTAGA;RSEQ=ATTTTGACCACTTAGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:1:0,1:28,36:64,1:0.0152:2,0:12:0:28:0:1:0:38:2:0.0154:0:5 0/1:146:14:6,8:60,69:129,14:0.0959:2,2:17.3:1:29.1:1:1:1.15823:32.1:28:0.0959:0:3.9 +1 121484690 . T A 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.96383;LSEQ=GTAAAGTCTGCACGTAGATA;RSEQ=TTTGACCACTTAGAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:11:7,4:21,31:52,11:0.1719:2,2:19.2:1:29.4:1:0.19353:2.54:33.2:22:0.1746:0:2.8 0/1:144:24:9,15:55,61:116,24:0.1667:2,2:14:1:30:1:0.50027:1.49842:30:48:0.1667:0:3.1 +1 121484697 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGCACGTAGATATTTTGAC;RSEQ=ACTTAGAGGCCTTCTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:24,31:55,0:0:2,0:13.2:1:31.3:1:1:0:33.9:54:1:0:2.6 0/1:116:2:1,1:54,60:114,2:0.0172:2,2:27:0:32.5:1:1:1.11:34:4:0.0175:0:5 +1 121484698 . A C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCACGTAGATATTTTGACC;RSEQ=CTTAGAGGCCTTCTTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:20,30:50,0:0:2,0:13.5:1:30:1:1:0:34.2:100:1:0:2.6 0/1:115:2:1,1:54,58:112,2:0.0174:2,2:5:1:29:1:1:1.07:32:4:0.0175:0:3.5 +1 121484712 . T G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67551;SOR=0.45454;LSEQ=TTGACCACTTAGAGGCCTTC;RSEQ=TTGGAAACGGTTTTTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:9,10:0,0:0,19:0.95:0,2:9.6:1:30.7:1:1:0:31.9:38:0.95:0:3.4 1/1:67:60:27,33:3,3:6,60:0.8955:2,2:18.4:1:30.1:1:1:1.21849:30.7:59:0.8939:0:4.3 +1 121484717 . A G 28 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTTAGAGGCCTTCTTTGG;RSEQ=AACGGTTTTTTCTCATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:10.5:1:30.2:1:1:0:29.7:26:1:0:3.5 0/1:58:2:1,1:29,26:55,2:0.0345:2,2:23:1:28.5:1:1:1.11325:41:4:0.0351:0:8 +1 121484723 . T G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.55505;SOR=1.52055;LSEQ=GAGGCCTTCTTTGGAAACGG;RSEQ=TTTTTCTCATGTAAGGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:1,5:0.8333:0,2:23.2:1:33.2:1:1:0:35.8:10:0.8333:0:5.2 1/1:52:46:28,18:1,1:2,46:0.8846:2,2:23.4:1:30.5:1:1:1.54:35.3:45:0.8824:0:4.8 +1 121484727 . T C 87 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0.82614;LSEQ=CCTTCTTTGGAAACGGTTTT;RSEQ=TCTCATGTAAGGCTAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:3,3:6,1:0.1429:2,0:19:0:34:0:1:0:59:2:0.1429:0:6 0/1:58:7:5,2:33,18:51,7:0.1207:2,2:23.6:1:31.3:1:1:1.36:36.7:14:0.1207:0:5.7 +1 121484729 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.08203;LSEQ=TTCTTTGGAAACGGTTTTTT;RSEQ=TCATGTAAGGCTAGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:0,0:0,6:0.8571:0,2:16.5:1:29.3:1:1:0:31.8:5:1:0:4 1/1:60:52:35,17:0,0:0,52:0.8667:0,2:20.2:1:29.4:1:1:0:37.5:51:0.8947:0:4.2 +1 121484732 . A C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76236;SOR=1.394;LSEQ=TTTGGAAACGGTTTTTTCTC;RSEQ=TGTAAGGCTAGACAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:5,1:2,5:7,6:0.4615:2,2:14.7:1:32.5:1:0.10256:9.84:45.7:12:0.5:0:4 1/0:66:36:25,11:18,12:30,36:0.5455:2,2:22.3:1:30.4:1:0.44877:1.51:43.9:72:0.5538:0:4.9 +1 121484734 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAACGGTTTTTTCTCAT;RSEQ=TAAGGCTAGACAGAAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:22,0:0:2,0:9:1:31.4:1:1:0:40.7:21:1:0:2.3 0/1:82:2:1,1:50,30:80,2:0.0244:2,2:6.5:1:28.5:1:1:1.65581:28.5:4:0.0253:0:3.5 +1 121484743 . G C 30 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTTTCTCATGTAAGGCTA;RSEQ=ACAGAAGAATTCCCAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:20,18:38,0:0:2,0:11.2:1:32.7:1:1:0:42.1:37:1:0:2 0/1:121:2:1,1:70,49:119,2:0.0165:2,2:34.5:1:30.5:1:1:1.42425:41:4:0.0169:0:8 +1 121484745 . C G 104 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46318;SOR=3.31611;LSEQ=TTTTCTCATGTAAGGCTAGA;RSEQ=AGAAGAATTCCCAGTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:1:0,1:20,18:38,1:0.025:2,0:13:0:28:0:0.48718:0:39:2:0.0263:0:2 0/1:127:10:7,3:67,50:117,10:0.0787:2,2:13.2:1:31.6:1:0.51955:1.73:46.1:20:0.08:0:2.9 +1 121484760 . T G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57463;SOR=Inf;LSEQ=CTAGACAGAAGAATTCCCAG;RSEQ=AACTTCCTTGTGTTGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:29,32:61,0:0:2,0:19.9:1:29.5:1:1:0:42:122:1:0:1.9 0/1:183:4:2,2:100,79:179,4:0.0219:2,2:36.8:1:30:1:1:1.26417:53:8:0.0223:0:4.5 +1 121484762 . A G 51 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59971;SOR=0.48548;LSEQ=AGACAGAAGAATTCCCAGTA;RSEQ=CTTCCTTGTGTTGTGTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:28,32:60,2:0.0323:2,2:11.5:1:32.5:1:1:1.14:25.5:4:0.0328:0:7 0/1:189:3:1,2:102,83:185,3:0.0159:2,2:31:1:32.3:1:0.5903:2.44634:42.3:6:0.016:0:6.3 +1 121484768 . T A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAATTCCCAGTAACTTCC;RSEQ=TGTGTTGTGTGCATTCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:32,37:69,0:0:2,0:24.3:1:31.1:1:1:0:42.4:138:1:0:2 0/1:198:2:1,1:105,91:196,2:0.0101:2,2:27.5:1:32:0:1:1.15301:56:4:0.0102:0:3 +1 121484770 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GAATTCCCAGTAACTTCCTT;RSEQ=TGTTGTGTGCATTCAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:33,38:71,0:0:2,0:25.3:1:32.2:1:1:0:42.1:70:1:0:2 0/1:199:2:1,1:104,92:196,2:0.0101:2,2:7.5:1:26.5:1:1:1.12973:24:4:0.0101:0:5 +1 121484775 . G T 30 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07489;SOR=0;LSEQ=CCCAGTAACTTCCTTGTGTT;RSEQ=TGTGCATTCAACTCACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:35,43:78,2:0.025:2,2:6:0:30.5:1:1:1.23:31:4:0.0253:0:2 0/0:211:0:0,0:111,100:211,0:0:2,0:27.7:1:31.3:1:1:0:45.5:104.5:1:0:1.9 +1 121484777 . G T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.32985;SOR=Inf;LSEQ=CAGTAACTTCCTTGTGTTGT;RSEQ=TGCATTCAACTCACAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:36,44:80,0:0:2,0:27.9:1:32.4:1:1:0:42:79:1:0:2.1 0/1:221:5:3,2:111,105:216,5:0.0226:2,2:16:1:27:1:1:1.42:53:10:0.0228:0:2.2 +1 121484779 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02685;SOR=0.54924;LSEQ=GTAACTTCCTTGTGTTGTGT;RSEQ=CATTCAACTCACAGAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:45:22,23:15,22:37,45:0.5488:2,2:29.5:1:29:1:0.50783:1.40:39.2:44:0.557:0:3.1 0/1:225:90:48,42:68,67:135,90:0.4:2,2:30.3:1:28.2:1:0.68485:1.13:39.5:180:0.4:0:3.4 +1 121484784 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07665;SOR=0;LSEQ=TTCCTTGTGTTGTGTGCATT;RSEQ=AACTCACAGAGTTGAACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:41,49:90,2:0.0217:2,2:17:1:31.5:1:1:1.19:46.5:4:0.022:0:2 0/0:239:0:0,0:122,114:236,0:0:2,0:29.2:1:30.5:1:1:0:45.8:46.2:0.9872:0:1.9 +1 121484791 . C G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5624;SOR=Inf;LSEQ=TGTTGTGTGCATTCAACTCA;RSEQ=AGAGTTGAACGTTCCCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:46,55:101,0:0:2,0:28.8:1:32.3:1:1:0:44.7:202:1:0:2.1 0/1:259:3:2,1:134,122:256,3:0.0116:2,2:44.3:1:31:1:1:1.82:46.3:6:0.0117:0:3.3 +1 121484794 . A T 66 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.96384;LSEQ=TGTGTGCATTCAACTCACAG;RSEQ=GTTGAACGTTCCCTTAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:0,2:47,54:101,2:0.0194:2,0:36.5:1:32:0:0.49895:0:32.5:4:0.02:0:2.5 0/1:267:5:1,4:139,121:260,5:0.0187:2,2:29:1:28.8:1:0.19154:4.57229:54.8:10:0.019:0:1.8 +1 121484796 . T A 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.31452;LSEQ=TGTGCATTCAACTCACAGAG;RSEQ=TGAACGTTCCCTTAGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:3:1,2:47,56:103,3:0.0283:2,2:23:1:30:1:1:1.67072:56.3:6:0.0288:0:1.3 0/1:271:10:6,4:138,123:261,10:0.0369:2,2:23.9:1:27.8:1:0.75429:1.34:42.7:9:0.0335:0:2.1 +1 121484800 . A G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05067;LSEQ=CATTCAACTCACAGAGTTGA;RSEQ=CGTTCCCTTAGACAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:1,2:47,59:106,3:0.0275:2,2:21.7:1:32.3:1:1:1.5867:35.7:6:0.028:0:1.7 0/1:277:8:4,4:142,127:269,8:0.0289:2,2:33.9:1:29.1:1:1:1.11766:50.5:7:0.0254:0:1.9 +1 121484801 . C G 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32095;SOR=0.39458;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=GTTCCCTTAGACAGAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:0,2:48,58:106,2:0.018:2,0:8:1:30.5:1:0.50156:0:39:4:0.018:0:4.5 0/0:279:2:1,1:145,130:275,2:0.0072:2,2:32:1:29.5:1:1:1.11494:34:4:0.0073:0:5.5 +1 121484802 . G T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32809;SOR=Inf;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTCCCTTAGACAGAGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:52,63:115,0:0:2,0:27.4:1:31.5:1:1:0:45.6:114:1:0:2.2 0/1:282:4:3,1:143,134:277,4:0.0142:2,2:15:1:31:1:0.62347:2.80:44:8:0.0143:0:3 +1 121484804 . TC T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19427;SOR=0.19553;LSEQ=CAACTCACAGAGTTGAACGT;RSEQ=CCTTAGACAGAGCAGATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:51,64:115,2:0.0169:2,2:26:1:31.5:1:1:1.25:47.5:4:0.0172:0.0085:1.5 0/0:299:1:1,0:151,145:296,1:0.0033:2,0:28:0:33:0:1:0:60:2:0.0034:0:1 +1 121484813 . C G 33 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18145;SOR=0.18539;LSEQ=GAGTTGAACGTTCCCTTAGA;RSEQ=AGAGCAGATTTGAAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:51,64:115,2:0.0168:2,2:42:0:33:1:1:1.25:21:4:0.0169:0:4 0/0:318:1:1,0:158,155:313,1:0.0031:2,0:26:0:33:0:1:0:25:2:0.0032:0:6 +1 121484815 . G C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13068;LSEQ=GTTGAACGTTCCCTTAGACA;RSEQ=AGCAGATTTGAAACACTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:3:2,1:50,68:118,3:0.0248:2,2:41:1:33:1:0.57639:2.70:40.3:6:0.0252:0:2.7 0/1:322:9:4,5:161,152:313,9:0.028:2,2:26.8:1:32.6:1:0.74509:1.32286:42:18:0.0283:0:1.8 +1 121484818 . C G 77 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67876;SOR=2.37687;LSEQ=GAACGTTCCCTTAGACAGAG;RSEQ=AGATTTGAAACACTCTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:1:0,1:53,70:123,1:0.0081:2,0:33:0:34:0:1:0:34:2:0.0082:0:2 0/1:316:6:3,3:156,154:310,6:0.019:2,2:23.7:1:30:1:1:1.01295:44.3:12:0.019:0:2.5 +1 121484823 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.079;SOR=0;LSEQ=TTCCCTTAGACAGAGCAGAT;RSEQ=TGAAACACTCTATTTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:54,70:124,2:0.0159:2,2:45.5:1:30.5:1:1:1.29:42:4:0.0161:0:5 0/0:321:0:0,0:161,160:321,0:0:2,0:24:1:29.5:1:1:0:48:320:1:0:1.8 +1 121484831 . CT GC 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.32173;SOR=0.39572;LSEQ=GACAGAGCAGATTTGAAACA;RSEQ=CTATTTGTGCAATTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:53,67:120,2:0.0164:2,2:36:1:31.5:1:1:1.26:60:4:0.0168:0:2 0/0:306:2:1,1:146,155:301,2:0.0065:2,2:13.5:1:29.8:1:1:1.06:46:4:0.0067:0:4.5 +1 121484832 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07777;SOR=0;LSEQ=ACAGAGCAGATTTGAAACAC;RSEQ=CTATTTGTGCAATTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:51,65:116,2:0.0167:2,2:45.5:1:31:1:1:1.27:35:4:0.0174:0:4.5 0/0:309:0:0,0:148,159:307,0:0:2,0:23.7:1:28.9:1:1:0:47.9:33.111:1:0:1.7 +1 121484835 . A T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00709;SOR=0.52721;LSEQ=GAGCAGATTTGAAACACTCT;RSEQ=TTTGTGCAATTTGCAAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:43:14,29:34,36:70,43:0.3772:2,2:27.2:1:30.2:1:0.11799:1.94477:38.3:20.5:0.3761:0:3.7 0/1:302:73:31,42:111,116:227,73:0.2417:2,2:29.3:1:30:1:0.34925:1.29532:37.1:146:0.2475:0:3.5 +1 121484839 . G C 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02221;SOR=0.09329;LSEQ=AGATTTGAAACACTCTATTT;RSEQ=TGCAATTTGCAAGTGTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:4:2,2:45,61:106,4:0.0364:2,2:31.3:1:34:1:1:1.35:49.3:8:0.0364:0:4.8 0/0:287:1:0,1:139,146:285,1:0.0035:2,0:32:0:33:0:1:0:54:2:0.0035:0:3 +1 121484841 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07412;SOR=0;LSEQ=ATTTGAAACACTCTATTTGT;RSEQ=CAATTTGCAAGTGTAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:44,60:104,2:0.0189:2,2:15:0:31:1:1:1.36:44.5:4:0.0192:0:5.5 0/0:282:0:0,0:137,144:281,0:0:2,0:24.6:1:31.4:1:1:0:47.5:69.25:0.9964:0:1.8 +1 121484842 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57666;SOR=Inf;LSEQ=TTTGAAACACTCTATTTGTG;RSEQ=AATTTGCAAGTGTAGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:43,57:100,0:0:2,0:27.3:1:32.8:1:1:0:48:99:1:0:2.2 0/1:281:4:2,2:134,141:275,4:0.0142:2,2:23.5:1:28.8:1:1:1.05:55:8:0.0144:0:2.3 +1 121484846 . T A 43 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61865;SOR=0.56627;LSEQ=AAACACTCTATTTGTGCAAT;RSEQ=TGCAAGTGTAGATTTCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:44,57:101,2:0.0194:2,2:16:1:28.5:1:1:1.29:37.5:4:0.0196:0:2.5 0/1:271:3:2,1:132,136:268,3:0.0111:2,2:14.3:1:27.7:1:0.61946:2.06:58.3:6:0.0113:0:2.3 +1 121484847 . T G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1355;SOR=0.6567;LSEQ=AACACTCTATTTGTGCAATT;RSEQ=GCAAGTGTAGATTTCAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:31:11,20:32,35:67,31:0.3131:2,2:27.2:1:32.3:1:0.28146:1.65377:39.4:62:0.3163:0:4.4 0/1:265:61:29,32:100,104:204,61:0.2302:2,2:29:1:30.9:1:0.88451:1.0608:36.8:60:0.2317:0:3.7 +1 121484849 . CA T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07298;SOR=0;LSEQ=CACTCTATTTGTGCAATTTG;RSEQ=AGTGTAGATTTCAAGCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:41,52:93,2:0.0208:2,2:45:1:30.5:1:1:1.27:57.5:4:0.0211:0:0.5 0/0:258:0:0,0:127,128:255,0:0:2,0:25.9:1:31.5:1:1:0:46.9:50:0.9921:0:1.8 +1 121484852 . G A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.82925;SOR=1.23256;LSEQ=TCTATTTGTGCAATTTGCAA;RSEQ=TGTAGATTTCAAGCGCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:7:2,5:43,49:92,7:0.07:2,2:28.6:1:31.3:1:0.45031:2.17757:41:14:0.07:0:4.9 0/1:259:22:10,12:118,119:237,22:0.0849:2,2:28.4:1:30.1:1:0.82448:1.18912:37.9:44:0.0853:0:4 +1 121484855 . T G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07635;SOR=0.6257;LSEQ=ATTTGTGCAATTTGCAAGTG;RSEQ=AGATTTCAAGCGCTTTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:31:11,20:31,33:64,31:0.3229:2,2:20:1:31.9:1:0.27493:1.6984:38.8:62:0.3229:0:4.1 0/1:257:59:29,30:102,96:198,59:0.2296:2,2:24.8:1:30.4:1:0.76863:1.09873:35.9:118:0.2332:0:3.7 +1 121484858 . A T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37339;SOR=1.72751;LSEQ=TGTGCAATTTGCAAGTGTAG;RSEQ=TTTCAAGCGCTTTAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:5:2,3:40,48:88,5:0.0538:2,2:25.8:1:30.4:1:1:1.24704:48.4:10:0.0538:0:3.4 0/1:257:23:9,14:120,114:234,23:0.0895:2,2:22.6:1:29.7:1:0.28374:1.6343:49:46:0.0898:0:3.1 +1 121484867 . G T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.3406;SOR=1.93157;LSEQ=TGCAAGTGTAGATTTCAAGC;RSEQ=CTTTAAGGTCAATGGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:4:2,2:38,49:87,4:0.043:2,2:27:1:31.3:1:1:1.29:47:8:0.0435:0:3.8 0/1:250:20:9,11:118,110:228,20:0.08:2,2:21.8:1:29.4:1:0.64401:1.30967:46.6:40:0.08:0:3.5 +1 121484872 . A T 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.17547;LSEQ=GTGTAGATTTCAAGCGCTTT;RSEQ=AGGTCAATGGCAGAAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:1:1,0:45,53:98,1:0.0101:2,0:30:0:28:0:0.46465:0:56:2:0.0101:0:3 0/1:253:3:2,1:126,122:248,3:0.0119:2,2:29.7:1:30.7:1:1:1.93:38.7:6:0.012:0:2.7 +1 121484875 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57733;SOR=Inf;LSEQ=TAGATTTCAAGCGCTTTAAG;RSEQ=TCAATGGCAGAAAAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:46,48:94,0:0:2,0:21.5:1:31.2:1:1:0:42.9:30.333:1:0:1.9 0/1:256:4:2,2:128,123:251,4:0.0156:2,2:11.8:1:27.5:1:1:1.0405:34.5:8:0.016:0:1.8 +1 121484880 . T C 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43627;SOR=1.24484;LSEQ=TTCAAGCGCTTTAAGGTCAA;RSEQ=GGCAGAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:26:17,9:27,41:68,26:0.268:2,2:22:1:31.3:1:0.03707:2.84:37.9:52:0.2737:0:2.4 0/1:249:78:41,37:81,83:164,78:0.3133:2,2:24.2:1:30.6:1:0.6812:1.13:42:156:0.3158:0:2.1 +1 121484881 . G A 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.19937;LSEQ=TCAAGCGCTTTAAGGTCAAT;RSEQ=GCAGAAAAGGAAATATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:1,0:47,49:96,1:0.0103:2,0:1:0:24:0:0.49485:0:48:2:0.0104:0:5 0/1:243:3:2,1:121,119:240,3:0.0123:2,2:24.7:1:30:1:1:1.96:39.7:6:0.0125:0:1.3 +1 121484883 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07675;SOR=0;LSEQ=AAGCGCTTTAAGGTCAATGG;RSEQ=AGAAAAGGAAATATCTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:45,46:91,2:0.0213:2,2:22:1:30.5:1:1:1.02:60:4:0.0215:0:3 0/0:244:0:0,0:124,118:242,0:0:2,0:23.1:1:31:1:1:0:40.2:47.4:0.9916:0:1.8 +1 121484891 . G A 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.13505;LSEQ=TAAGGTCAATGGCAGAAAAG;RSEQ=AAATATCTTCGTTTCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:1,0:48,47:95,1:0.0104:2,0:15:0:32:0:1:0:27:2:0.0105:0:4 0/1:254:3:1,2:128,122:250,3:0.0118:2,2:8.7:1:31.3:1:0.61616:2.09242:56:6:0.012:0:2.3 +1 121484892 . A T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56523;SOR=Inf;LSEQ=AAGGTCAATGGCAGAAAAGG;RSEQ=AATATCTTCGTTTCAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:49,46:95,0:0:2,0:21.8:1:30:1:1:0:36.9:30.667:0.9892:0:1.8 0/1:256:3:1,2:130,122:252,3:0.0117:2,2:19.3:1:27:1:0.6134:2.12503:40:6:0.0118:0:3 +1 121484893 . A T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32976;SOR=Inf;LSEQ=AGGTCAATGGCAGAAAAGGA;RSEQ=ATATCTTCGTTTCAAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:49,46:95,0:0:2,0:22.3:1:30.6:1:1:0:36.8:190:1:0:1.8 0/1:259:5:2,3:128,124:252,5:0.0193:2,2:21.6:1:28.4:1:0.6814:1.54578:46.8:10:0.0195:0:1.6 +1 121484896 . A T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01816;SOR=0;LSEQ=TCAATGGCAGAAAAGGAAAT;RSEQ=TCTTCGTTTCAAAACTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:1,2:46,42:88,3:0.0323:2,2:10:1:31.3:1:0.60848:2.17225:60:6:0.0323:0:1.7 0/0:258:0:0,0:132,126:258,0:0:2,0:22.4:1:28.3:1:1:0:36.6:257:1:0:1.7 +1 121484901 . C G 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11633;SOR=Inf;LSEQ=GGCAGAAAAGGAAATATCTT;RSEQ=GTTTCAAAACTAGACAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:50,43:93,0:0:2,0:24.3:1:30.5:1:1:0:35.3:45.5:0.9891:0:1.6 0/1:262:8:3,5:129,122:251,8:0.0305:2,2:18.5:1:30.8:1:0.49365:1.75849:42.3:16:0.0308:0:3.4 +1 121484904 . T G 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06276;SOR=0.12173;LSEQ=AGAAAAGGAAATATCTTCGT;RSEQ=TCAAAACTAGACAGAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:2,1:51,40:91,3:0.0319:2,2:24.7:1:32.3:1:1:1.56:31.3:6:0.033:0:2 0/0:252:1:1,0:132,115:247,1:0.004:2,0:6:0:33:0:1:0:20:2:0.004:0:7 +1 121484906 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56414;SOR=Inf;LSEQ=AAAAGGAAATATCTTCGTTT;RSEQ=AAAACTAGACAGAATCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:53,43:96,0:0:2,0:24.4:1:32.1:1:1:0:34.6:192:0.9897:0:1.7 0/1:255:3:1,2:129,119:248,3:0.0118:2,2:40.3:1:28:1:0.61039:2.16162:41:6:0.0119:0:2 +1 121484911 . CT TA 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0194;SOR=0;LSEQ=GAAATATCTTCGTTTCAAAA;RSEQ=AGACAGAATCATTCCCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:3:2,1:52,41:93,3:0.0306:2,2:15:1:30:1:1:1.57:39.3:6:0.0309:0.0102:1.3 0/0:264:0:0,0:140,123:263,0:0:2,0:24:1:31:1:1:0:33.6:86.667:0.9962:0:1.8 +1 121484913 . A C 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17943;SOR=0.18354;LSEQ=AATATCTTCGTTTCAAAACT;RSEQ=GACAGAATCATTCCCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:52,44:96,2:0.0204:2,2:23:1:32:1:1:1.17979:31:4:0.0206:0:4 0/0:264:1:0,1:138,122:260,1:0.0038:2,0:49:0:28:0:0.47126:0:40:2:0.0038:0:2 +1 121484941 . G C 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20731;SOR=0.20576;LSEQ=TCATTCCCACAAACTGCGTT;RSEQ=TGATGTGTTTGTTCAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:58,46:104,2:0.0189:2,2:19.5:1:33:1:1:1.25808:34:4:0.0192:0:2.5 0/0:255:1:0,1:129,125:254,1:0.0039:2,0:19:0:33:0:0.49412:0:33:2:0.0039:0:3 +1 121484942 . T C 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32267;SOR=Inf;LSEQ=CATTCCCACAAACTGCGTTG;RSEQ=GATGTGTTTGTTCAACTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:60,47:107,0:0:2,0:27.3:1:30.3:1:1:0:31.3:106:1:0:2.2 0/1:253:4:2,2:126,122:248,4:0.0158:2,2:31.5:1:29.5:1:1:1.03266:32.3:8:0.0158:0:3.5 +1 121484945 . T C 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56593;SOR=1.60705;LSEQ=TCCCACAAACTGCGTTGTGA;RSEQ=GTGTTTGTTCAACTCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:2,1:58,46:104,3:0.028:2,2:29.3:1:32:0:1:1.58:26.7:6:0.0283:0:2.3 0/1:248:11:4,7:117,119:236,11:0.0444:2,2:28.7:1:28.4:1:0.5404:1.71689:26.7:10:0.0412:0:3 +1 121484946 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08907;SOR=0;LSEQ=CCCACAAACTGCGTTGTGAT;RSEQ=TGTTTGTTCAACTCACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:59,45:104,2:0.0189:2,2:35.5:1:31:1:1:1.30771:42:4:0.0192:0:2.5 0/0:248:0:0,0:122,126:248,0:0:2,0:34:0:11:0:1:0:32:0:0:0:3 +1 121484949 . T C 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55627;SOR=Inf;LSEQ=ACAAACTGCGTTGTGATGTG;RSEQ=TTGTTCAACTCACAGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:59,47:106,0:0:2,0:26.6:1:30:1:1:0:31.3:52:1:0:2.3 0/1:243:3:2,1:118,121:239,3:0.0123:2,2:30.3:1:26.3:1:0.62033:2.04:33:6:0.0124:0:3.3 +1 121484951 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96263;LSEQ=AAACTGCGTTGTGATGTGTT;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:96:53,43:0,1:1,96:0.96:0,2:27.7:1:31.3:1:0.45361:0:31.4:95:0.9694:0:2.3 1/1:241:231:113,118:2,3:5,231:0.9585:2,2:29.1:1:29.8:1:1:1.43:31.6:56.75:0.9578:0:2.1 +1 121484954 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08743;SOR=0;LSEQ=CTGCGTTGTGATGTGTTTGT;RSEQ=CAACTCACAGAGTTTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:0,2:57,41:98,2:0.02:2,0:49:1:30.5:1:0.18242:0:46:4:0.0202:0:3 0/0:237:0:0,0:114,123:237,0:0:2,0:28.5:1:29.4:1:1:0:32.3:236:1:0:2.1 +1 121484957 . A T 75 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67879;SOR=2.57304;LSEQ=CGTTGTGATGTGTTTGTTCA;RSEQ=CTCACAGAGTTTAACCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:0,1:57,44:101,1:0.0098:2,0:6:0:33:0:0.44118:0:30:2:0.0098:0:2 0/1:241:6:5,1:109,126:235,6:0.0249:2,2:18.8:1:29.3:1:0.10361:5.74:24:12:0.025:0:3.7 +1 121484965 . A C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0836;SOR=0;LSEQ=TGTGTTTGTTCAACTCACAG;RSEQ=GTTTAACCTTTCTGTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:55,44:99,2:0.0194:2,2:38.5:1:31.5:1:1:1.24721:22:4:0.0194:0:3.5 0/0:252:0:0,0:122,128:250,0:0:2,0:22.5:1:29.1:1:1:0:33.5:49:0.9919:0:2.2 +1 121484966 . G C 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08106;SOR=0;LSEQ=GTGTTTGTTCAACTCACAGA;RSEQ=TTTAACCTTTCTGTTCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:55,45:100,2:0.0196:2,2:16:0:34.5:1:1:1.2198:47.5:4:0.0196:0:3.5 0/0:255:0:0,0:125,130:255,0:0:2,0:21.9:1:30.9:1:1:0:33.6:41.5:1:0:2.2 +1 121484972 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07685;SOR=0;LSEQ=GTTCAACTCACAGAGTTTAA;RSEQ=CTTTCTGTTCATAGAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:49,43:92,2:0.0208:2,2:20.5:1:29.5:1:1:1.13795:30:4:0.0213:0:3 0/0:249:0:0,0:120,124:244,0:0:2,0:20.1:1:30.6:1:1:0:34.1:80.333:0.9797:0:2.3 +1 121484973 . C T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00044;SOR=0;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCTGTTCATAGAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:6:3,3:47,41:88,6:0.0625:2,2:19.2:1:32.2:1:1:1.14467:28.2:12:0.0625:0:4.5 0/0:246:0:0,0:119,125:244,0:0:2,0:36:0:18:0:1:0:34:0:0:0:4 +1 121484979 . G T 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14212;SOR=1.52563;LSEQ=TCACAGAGTTTAACCTTTCT;RSEQ=TTCATAGAGCAGTTAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:23:12,11:33,30:63,23:0.2614:2,2:16.7:1:29.3:1:1:1.00824:23.7:22:0.2529:0:3.7 0/1:228:80:38,42:73,74:147,80:0.3509:2,2:15.1:1:29.7:1:0.78237:1.08991:24.2:160:0.3587:0:3.7 +1 121484989 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09108;SOR=0;LSEQ=TAACCTTTCTGTTCATAGAG;RSEQ=AGTTAGGAAACGCTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:45,45:90,2:0.0215:2,2:12.5:1:28:1:1:1:22.5:4:0.0217:0:4 0/0:214:0:0,0:98,116:214,0:0:2,0:19.6:1:30.9:1:1:0:34.4:70.333:1:0:2.8 +1 121484999 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTCATAGAGCAGTTAGGAA;RSEQ=CGCTCTGTTTGTAAAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:47,48:95,0:0:2,0:21.5:1:30.4:1:1:0:32.2:190:1:0:3 0/1:193:2:1,1:87,104:191,2:0.0104:2,2:29:1:31:1:1:1.19:26.5:4:0.0104:0:5.5 +1 121485001 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01682;SOR=0.50341;LSEQ=TCATAGAGCAGTTAGGAAAC;RSEQ=CTCTGTTTGTAAAGTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:73:38,35:0,0:0,73:0.7684:0,2:21.3:1:30.5:1:1:0:33.1:72:0.7742:0:2.6 1/0:200:125:61,64:2,3:5,125:0.625:2,2:24.1:1:28.8:1:1:1.43:37.4:61.5:0.6244:0:2.4 +1 121485002 . C G 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.18264;SOR=Inf;LSEQ=CATAGAGCAGTTAGGAAACG;RSEQ=TCTGTTTGTAAAGTCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:37,36:73,0:0:2,0:21.5:1:32.9:1:1:0:32.5:146:1:0:2.6 0/1:191:6:3,3:63,67:130,6:0.0314:2,2:17.2:1:30.5:1:1:1.06:33:12:0.0451:0:4.3 +1 121485006 . GT G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.09523;SOR=0;LSEQ=GAGCAGTTAGGAAACGCTCT;RSEQ=TTGTAAAGTCTGTAAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:40,48:88,2:0.0217:2,2:38:0:34:1:1:1.20:45:4:0.0225:0:1 0/0:205:0:0,0:94,111:205,0:0:2,0:23.7:1:28.6:1:1:0:33.8:50.25:1:0:3 +1 121485011 . T A 89 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00612;SOR=0.12888;LSEQ=GTTAGGAAACGCTCTGTTTG;RSEQ=AAAGTCTGTAAGTGGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:7:3,4:44,46:90,7:0.0722:2,2:15.1:1:32:1:1:1.27219:40.7:14:0.0722:0:3.9 0/0:203:2:2,0:90,111:201,2:0.0099:2,0:25:1:25:1:0.20417:0:30:4:0.0099:0:4 +1 121485012 . A C 136 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01037;SOR=5.39943;LSEQ=TTAGGAAACGCTCTGTTTGT;RSEQ=AAGTCTGTAAGTGGATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:48,47:95,2:0.0206:2,2:39:1:32:1:1:1.02106:24.5:4:0.0208:0:4.5 0/1:205:21:10,11:83,101:184,21:0.1024:2,2:24.6:1:31:1:0.82207:1.11:27.1:42:0.1034:0:4.7 +1 121485015 . G T 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00732;SOR=2.09093;LSEQ=GGAAACGCTCTGTTTGTAAA;RSEQ=TCTGTAAGTGGATATTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:24:11,13:37,36:73,24:0.2449:2,2:27.1:1:30.8:1:0.81467:1.21221:31.5:23:0.2396:0:3.9 0/1:215:87:40,47:61,67:128,87:0.4047:2,2:26.9:1:29.4:1:0.88942:1.06943:28.6:174:0.4065:0:4.2 +1 121485023 . G C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09375;SOR=0;LSEQ=TCTGTTTGTAAAGTCTGTAA;RSEQ=TGGATATTCTGACATCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:48,51:99,2:0.0196:2,2:40:0:33:1:1:1.06:37:4:0.02:0:2.5 0/0:230:0:0,0:110,116:226,0:0:2,0:25.7:1:31.2:1:1:0:35.5:36.667:0.9821:0:3 +1 121485026 . G C 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23463;SOR=0.22781;LSEQ=GTTTGTAAAGTCTGTAAGTG;RSEQ=ATATTCTGACATCTTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:49,53:102,2:0.0192:2,2:25.5:1:30.5:1:1:1.08:33:4:0.0192:0:3.5 0/0:226:1:1,0:108,116:224,1:0.0044:2,0:31:0:33:0:0.48444:0:21:2:0.0045:0:4 +1 121485029 . A T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55484;SOR=Inf;LSEQ=TGTAAAGTCTGTAAGTGGAT;RSEQ=TTCTGACATCTTGTGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:51,53:104,0:0:2,0:25.7:1:30.4:1:1:0:33.4:208:1:0:2.9 0/1:229:3:1,2:110,116:226,3:0.0131:2,2:32.3:1:30.3:1:1:1.89146:39.7:6:0.0133:0:4.7 +1 121485035 . A T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09866;SOR=0;LSEQ=GTCTGTAAGTGGATATTCTG;RSEQ=CATCTTGTGGCCTTCGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:48,54:102,2:0.0192:2,2:28.5:1:32:0:1:1.12:27:4:0.0198:0:4.5 0/0:226:0:0,0:109,117:226,0:0:2,0:28.5:1:28.8:1:1:0:35.7:225:1:0:3.1 +1 121485039 . C T 44 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.64904;SOR=0.67653;LSEQ=GTAAGTGGATATTCTGACAT;RSEQ=TTGTGGCCTTCGTTGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:47,53:100,2:0.0196:2,2:41.5:1:31:1:1:1.13:25.5:4:0.0196:0:5 0/1:225:3:2,1:103,114:217,3:0.0133:2,2:33.3:1:28:1:0.60682:2.21:23:6:0.0134:0:4.7 +1 121485047 . C A 90 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72882;SOR=1.74959;LSEQ=ATATTCTGACATCTTGTGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:42,50:92,2:0.0213:2,2:39:1:32:0:1:1.19:22.5:4:0.0215:0:4 0/1:218:8:4,4:101,109:210,8:0.0367:2,2:35.3:1:30.1:1:1:1.08:32.3:7:0.0335:0:3.9 +1 121485048 . T A 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30265;LSEQ=TATTCTGACATCTTGTGGCC;RSEQ=TCGTTGGAAACGGGATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:0,1:43,50:93,1:0.0106:2,0:21:0:33:0:1:0:24:2:0.0109:0:6 0/1:217:3:1,2:103,111:214,3:0.0138:2,2:34.7:1:30.3:1:1:1.85078:25:6:0.0141:0:4.7 +1 121485059 . C A 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.86058;LSEQ=CTTGTGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCCTATTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:3:2,1:37,44:81,3:0.0349:2,2:8.3:1:28:1:0.59479:2.35:41:6:0.0353:0:2.3 0/1:199:6:3,3:96,95:191,6:0.0302:2,2:29.2:1:28.5:1:1:1.01047:34.3:5:0.0254:0:3.8 +1 121485060 . G A 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.18677;LSEQ=TTGTGGCCTTCGTTGGAAAC;RSEQ=GGATTTCTTCCTATTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:1,0:37,39:76,1:0.013:2,0:1:0:30:0:0.49351:0:60:2:0.013:0:1 0/1:195:3:2,1:96,96:192,3:0.0154:2,2:16.3:1:29:1:1:1.99:48:6:0.0155:0:2.3 +1 121485061 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGGCCTTCGTTGGAAACG;RSEQ=GATTTCTTCCTATTCTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:37,39:76,0:0:2,0:30:1:31.5:1:1:0:31.8:152:1:0:3.2 0/1:193:2:1,1:96,95:191,2:0.0104:2,2:29.5:1:28.5:1:1:1.01047:25:4:0.0105:0:6 +1 121485063 . A T 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.18915;LSEQ=TGGCCTTCGTTGGAAACGGG;RSEQ=TTTCTTCCTATTCTGCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:0,1:34,37:71,1:0.0139:2,0:37:0:32:0:1:0:32:2:0.0141:0:5 0/1:182:3:1,2:88,90:178,3:0.0165:2,2:11.7:1:29.3:1:1:1.94859:48:6:0.0169:0:3 +1 121485066 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CCTTCGTTGGAAACGGGATT;RSEQ=CTTCCTATTCTGCTAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:34,38:72,0:0:2,0:29.2:1:30.8:1:1:0:30.9:144:1:0:3.3 0/1:168:2:1,1:80,86:166,2:0.0119:2,2:36:1:29.5:1:1:1.07:27.5:4:0.012:0:5.5 +1 121485068 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TCCTATTCTGCTAGACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:34,37:71,0:0:2,0:28.4:1:31.5:1:1:0:30.5:142:1:0:3.3 0/1:164:2:1,1:78,84:162,2:0.0122:2,2:40.5:1:30:1:1:1.08:34.5:4:0.0123:0:5 +1 121485071 . C A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10959;SOR=0.18803;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TATTCTGCTAGACAGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:69:33,36:0,0:0,69:0.9857:0,2:27:1:31.2:1:1:0:30.5:138:1:0:3.2 1/1:153:142:70,72:4,4:8,142:0.9281:2,2:24.8:1:29.6:1:1:1.02839:31.7:141:0.9276:0:3.7 +1 121485076 . C A 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29809;SOR=0.46056;LSEQ=AAACGGGATTTCTTCCTATT;RSEQ=TGCTAGACAGATGAATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:5:2,3:29,32:61,5:0.0758:2,2:35.2:1:29.8:1:1:1.35314:32.8:10:0.0758:0:3.6 0/1:138:5:3,2:65,68:133,5:0.0362:2,2:24.4:1:28.8:1:0.67829:1.56:29.2:10:0.0368:0:2.8 +1 121485078 . G C 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55216;SOR=Inf;LSEQ=ACGGGATTTCTTCCTATTCT;RSEQ=CTAGACAGATGAATTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:31,33:64,0:0:2,0:23.7:1:32:1:1:0:30.5:63:1:0:3.4 0/1:131:3:1,2:64,63:127,3:0.0229:2,2:19.3:1:23:1:1:2.02108:30.3:2:0.0156:0:5.3 +1 121485080 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGATTTCTTCCTATTCTGC;RSEQ=AGACAGATGAATTCTCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:30,33:63,0:0:2,0:22.3:1:30.1:1:1:0:30.6:126:1:0:3.4 0/1:128:2:1,1:63,63:126,2:0.0156:2,2:40.5:1:31.5:1:1:1:34.5:4:0.0157:0:5 +1 121485081 . A G 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23863;SOR=0.22971;LSEQ=GGATTTCTTCCTATTCTGCT;RSEQ=GACAGATGAATTCTCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:28,28:56,2:0.0345:2,2:31.5:1:31:1:1:1:49.5:4:0.0351:0:3 0/0:124:1:1,0:61,62:123,1:0.0081:2,0:40:0:29:0:1:0:34:2:0.0081:0:3 +1 121485082 . G C 34 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24062;SOR=0.23128;LSEQ=GATTTCTTCCTATTCTGCTA;RSEQ=ACAGATGAATTCTCAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:27,27:54,2:0.0351:2,2:35.5:1:34:1:1:1:33:4:0.0351:0:4 0/0:121:1:1,0:58,61:119,1:0.0083:2,0:26:0:27:0:0.49167:0:39:2:0.0083:0:4 +1 121485088 . T A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54895;SOR=0.56018;LSEQ=TTCCTATTCTGCTAGACAGA;RSEQ=GAATTCTCAGTAACTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:43:21,22:1,1:2,43:0.9348:2,2:21.3:1:31.3:1:1:1.04655:31:86:0.9556:0:3.4 1/1:99:88:46,42:4,1:5,88:0.8889:2,2:19.1:1:29.2:1:0.36856:3.6078:32.2:176:0.898:0:3.8 +1 121485091 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTATTCTGCTAGACAGATGA;RSEQ=TTCTCAGTAACTTCCTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:41,0:0:2,0:21.3:1:30.6:1:1:0:32.2:82:1:0:3.5 0/1:90:2:1,1:45,43:88,2:0.0222:2,2:11:1:33:0:1:1.046:32:4:0.0222:0:5 +1 121485099 . T A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66411;SOR=1.32055;LSEQ=CTAGACAGATGAATTCTCAG;RSEQ=AACTTCCTTGTGTTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:8,4:9,12:21,12:0.3636:2,2:17.6:1:29.5:1:0.28175:2.59:33.1:24:0.3636:0:4.7 0/1:65:28:15,13:21,16:37,28:0.4308:2,2:15.4:1:28:1:0.80704:1.13524:34.1:56:0.4308:0:4.9 +1 121485100 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGACAGATGAATTCTCAGT;RSEQ=ACTTCCTTGTGTTGTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:30,0:0:2,0:18.4:1:29.9:1:1:0:33.4:60:1:0:3.6 0/1:64:2:1,1:34,28:62,2:0.0313:2,2:19:1:29:1:1:1.21058:51:4:0.0317:0:3 +1 121485101 . A T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25015;SOR=1.8127;LSEQ=AGACAGATGAATTCTCAGTA;RSEQ=CTTCCTTGTGTTGTGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:6,2:8,12:20,8:0.2857:2,2:18:1:30.5:1:0.2087:4.26:35.3:16:0.2857:0:4.6 0/1:64:27:15,12:20,17:37,27:0.4219:2,2:14.1:1:28.3:1:1:1.06:34.5:54:0.4219:0:4.9 +1 121485106 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATGAATTCTCAGTAACTTC;RSEQ=TTGTGTTGTGTGTATTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:26,0:0:2,0:15:1:32:1:1:0:33.2:52:1:0:3.5 0/1:55:2:1,1:29,23:52,2:0.0364:2,2:15:1:30:0:1:1.25542:34.5:4:0.0377:0:5 +1 121485114 . G A 48 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03168;SOR=0;LSEQ=CTCAGTAACTTCCTTGTGTT;RSEQ=TGTGTATTCAACTCACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:9,8:17,3:0.15:2,2:6.7:1:30.3:1:1:2.16219:32.7:6:0.15:0:4.7 0/0:41:0:0,0:22,19:41,0:0:2,0:14.5:1:30.6:1:1:0:34.1:82:1:0:3.1 +1 121485120 . A T 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04084;SOR=0.10971;LSEQ=AACTTCCTTGTGTTGTGTGT;RSEQ=TTCAACTCACAGAGTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:9,7:16,4:0.2:2,2:12.8:1:31:1:1:1.26953:32.8:8:0.2:0:5.8 0/1:39:1:1,0:20,18:38,1:0.0256:2,0:8:0:32:0:1:0:28:2:0.0256:0:7 +1 121485125 . A C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.31837;SOR=Inf;LSEQ=CCTTGTGTTGTGTGTATTCA;RSEQ=CTCACAGAGTTGAACGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:12,20:32,0:0:2,0:5.5:1:28.9:1:1:0:25.1:31:1:0:2.3 0/1:77:4:2,2:38,35:73,4:0.0519:2,2:17:1:30.5:1:1:1.08454:39.8:8:0.0519:0:3 +1 121485126 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTGTGTTGTGTGTATTCAA;RSEQ=TCACAGAGTTGAACGATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:15,22:37,0:0:2,0:5:1:31.4:1:1:0:24.2:74:0.9737:0:2.1 0/1:93:2:1,1:49,40:89,2:0.0215:2,2:10:1:30.5:1:1:1.22225:29:4:0.0215:0:6.5 +1 121485132 . G C 71 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32594;SOR=Inf;LSEQ=TTGTGTGTATTCAACTCACA;RSEQ=AGTTGAACGATCCTTTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:30,39:69,0:0:2,0:7.1:1:31.6:1:1:0:26.5:138:1:0:2.1 0/1:180:5:3,2:89,84:173,5:0.0278:2,2:6.8:1:31:1:1:1.41:24.6:10:0.0282:0:4.8 +1 121485133 . A T 50 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.62775;LSEQ=TGTGTGTATTCAACTCACAG;RSEQ=GTTGAACGATCCTTTACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:32,43:75,1:0.0132:2,0:25:0:30:0:0.43421:0:44:2:0.0135:0:5 0/1:188:4:2,2:94,88:182,4:0.0213:2,2:7:1:25:1:1:1.06777:22.3:3:0.0161:0:2.3 +1 121485137 . G C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78123;SOR=0.87965;LSEQ=TGTATTCAACTCACAGAGTT;RSEQ=AACGATCCTTTACACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:5:1,4:43,59:102,5:0.0467:2,2:16.2:1:31.6:1:0.64663:2.89018:27:10:0.0472:0:4.4 0/1:242:10:6,4:117,111:228,10:0.0413:2,2:12.2:1:30.9:1:0.75005:1.42:31.6:20:0.0418:0:4.4 +1 121485139 . A G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55478;SOR=Inf;LSEQ=TATTCAACTCACAGAGTTGA;RSEQ=CGATCCTTTACACAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:56,70:126,0:0:2,0:9.4:1:29.3:1:1:0:27.4:41:1:0:2.1 0/1:273:3:2,1:134,132:266,3:0.011:2,2:8:1:32.7:1:1:1.97:28.7:6:0.011:0:4.3 +1 121485140 . C G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59165;SOR=0.75915;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=GATCCTTTACACAGAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:6:3,3:54,66:120,6:0.0451:2,2:12.3:1:32:1:1:1.22:24.8:12:0.0455:0:4.2 0/1:289:10:4,6:129,130:259,10:0.0346:2,2:11.4:1:28.5:1:0.74937:1.48628:22.5:20:0.0352:0:5 +1 121485141 . G C 76 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44265;SOR=2.75664;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=ATCCTTTACACAGAGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:1:1,0:62,76:138,1:0.0071:2,0:33:0:33:0:0.45324:0:44:2:0.0072:0:5 0/1:308:6:3,3:154,141:295,6:0.0195:2,2:11.3:1:29.5:1:1:1.09187:31.3:12:0.0199:0:2.5 +1 121485144 . C G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.83699;SOR=1.16272;LSEQ=AACTCACAGAGTTGAACGAT;RSEQ=CTTTACACAGAGCAGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:8:2,6:67,74:141,8:0.0526:2,2:13.1:1:30.8:1:0.28666:2.69939:22.4:16:0.0541:0:3.5 0/1:346:21:11,10:159,156:315,21:0.0607:2,2:11.7:1:31:1:1:1.08:31.4:42:0.0609:0:4.4 +1 121485145 . C G 63 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03319;SOR=0.10931;LSEQ=ACTCACAGAGTTGAACGATC;RSEQ=TTTACACAGAGCAGACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:4:2,2:72,92:164,4:0.0237:2,2:5:1:31.5:1:1:1.28:37.8:8:0.0242:0:3.3 0/0:380:1:0,1:185,188:373,1:0.0026:2,0:23:0:33:0:1:0:44:2:0.0027:0:1 +1 121485148 . T G 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09685;SOR=0;LSEQ=CACAGAGTTGAACGATCCTT;RSEQ=ACACAGAGCAGACTTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:81,105:186,2:0.0106:2,2:10.5:1:24:1:1:1.29:33.5:4:0.0106:0:2.5 0/0:415:0:0,0:201,210:411,0:0:2,0:13.9:1:27.9:1:1:0:28:101.75:0.9903:0:2.4 +1 121485151 . A G 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02789;SOR=0;LSEQ=AGAGTTGAACGATCCTTTAC;RSEQ=CAGAGCAGACTTGAAACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:3:2,1:89,111:200,3:0.0146:2,2:19.7:1:28:1:0.58822:2.48:30.7:6:0.0149:0:4.7 0/0:471:0:0,0:225,238:463,0:0:2,0:15:1:28.5:1:1:0:28.6:114.75:0.9871:0:2.4 +1 121485152 . C G 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45928;SOR=0.82816;LSEQ=GAGTTGAACGATCCTTTACA;RSEQ=AGAGCAGACTTGAAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:30:11,19:81,96:177,30:0.1442:2,2:15.7:1:31.5:1:0.42859:1.45478:30.1:29:0.1408:0:3.1 0/1:490:60:37,23:197,227:424,60:0.1224:2,2:19.5:1:31.2:1:0.03776:1.85:30:120:0.1242:0:3.4 +1 121485155 . A C 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08089;SOR=0.13958;LSEQ=TTGAACGATCCTTTACACAG;RSEQ=GCAGACTTGAAACACTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:3:2,1:95,118:213,3:0.0138:2,2:13.3:1:31.3:1:0.58884:2.47:23:6:0.014:0:4.3 0/0:516:1:1,0:246,266:512,1:0.0019:2,0:28:0:33:0:0.48148:0:24:2:0.002:0:6 +1 121485157 . C T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72171;SOR=0.85849;LSEQ=GAACGATCCTTTACACAGAG;RSEQ=AGACTTGAAACACTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:13:5,8:96,115:211,13:0.0578:2,2:28.5:1:27:1:0.77639:1.33395:28.1:12:0.0543:0:3.8 0/1:540:27:15,12:243,266:509,27:0.05:2,2:21.6:1:27.9:1:0.43802:1.37:29:54:0.0509:0:4.2 +1 121485158 . A G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00298;LSEQ=AACGATCCTTTACACAGAGC;RSEQ=GACTTGAAACACTCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:5:2,3:102,122:224,5:0.0218:2,2:13.6:1:29.6:1:1:1.25287:28:10:0.0221:0:3.4 0/1:548:12:6,6:257,277:534,12:0.0219:2,2:31:1:31.3:1:1:1.08:41.3:24:0.0222:0:2.8 +1 121485159 . G T 84 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02542;SOR=0.25142;LSEQ=ACGATCCTTTACACAGAGCA;RSEQ=ACTTGAAACACTCTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:8:3,5:100,120:220,8:0.0348:2,2:19.5:1:28.1:1:0.73214:1.38693:23.1:16:0.0351:0:3.6 0/0:558:5:2,3:267,281:548,5:0.009:2,2:25.4:1:29.2:1:1:1.42436:24.2:10:0.0091:0:3.6 +1 121485160 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67873;SOR=1.31434;LSEQ=CGATCCTTTACACAGAGCAG;RSEQ=CTTGAAACACTCTTTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:7:3,4:99,124:223,7:0.0298:2,2:24.9:1:32.3:1:1:1.06424:22.3:14:0.0299:0:4.6 0/1:567:22:10,12:260,277:537,22:0.0388:2,2:26.2:1:30.3:1:0.83065:1.12611:22.2:44:0.0394:0:4.5 +1 121485161 . C T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41847;SOR=1.83482;LSEQ=GATCCTTTACACAGAGCAGA;RSEQ=TTGAAACACTCTTTTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:104,130:234,3:0.0126:2,2:27.3:1:32:0:1:1.59696:28.7:6:0.0127:0:2 0/1:570:13:5,8:270,287:557,13:0.0228:2,2:19:1:30:1:0.57975:1.50416:24.7:26:0.023:0:3.1 +1 121485164 . G T 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.70153;SOR=0.70712;LSEQ=CCTTTACACAGAGCAGACTT;RSEQ=AAACACTCTTTTTGTGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:0,3:110,132:242,3:0.0122:2,0:24.7:1:28:1:0.25477:0:27.7:6:0.0123:0:1.7 0/0:578:5:3,2:274,296:570,5:0.0087:2,2:18.2:1:30.4:1:0.67574:1.62:26.6:10:0.0088:0:3 +1 121485165 . A T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.96911;LSEQ=CTTTACACAGAGCAGACTTG;RSEQ=AACACTCTTTTTGTGGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:15:8,7:104,129:233,15:0.0605:2,2:26.1:1:29.3:1:0.59668:1.42:25.3:30:0.0617:0:3.5 0/1:579:34:16,18:263,281:544,34:0.0587:2,2:27.6:1:28.1:1:1:1.05286:23.8:68:0.0593:0:3.6 +1 121485169 . ACT A 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.43325;SOR=0.56728;LSEQ=ACACAGAGCAGACTTGAAAC;RSEQ=CTTTTTGTGGAATTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:111,129:240,3:0.012:2,2:35.3:1:33.3:1:1:1.71725:26.3:6:0.0121:0:2.7 0/0:585:4:2,2:272,289:561,4:0.0068:2,2:36:1:28.8:1:1:1.06:26.8:8:0.0069:0.0017:4.8 +1 121485170 . C T 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51956;SOR=1.43897;LSEQ=CACAGAGCAGACTTGAAACA;RSEQ=TCTTTTTGTGGAATTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:6:2,4:111,129:240,6:0.024:2,2:28.5:1:29:1:0.68996:1.71729:24.2:12:0.0243:0:3.3 0/1:585:20:9,11:272,289:561,20:0.0342:2,2:28.7:1:30.3:1:0.82266:1.15005:27.8:40:0.0345:0:3.1 +1 121485171 . T A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78818;SOR=1.28755;LSEQ=ACAGAGCAGACTTGAAACAC;RSEQ=CTTTTTGTGGAATTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:4:1,3:112,129:241,4:0.016:2,2:38.3:1:27.5:1:0.62648:2.59535:22.8:8:0.0164:0:2 0/1:585:12:6,6:273,294:567,12:0.0205:2,2:30.1:1:28.5:1:1:1.08:22.8:24:0.0211:0:3 +1 121485172 . C A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02623;SOR=0;LSEQ=CAGAGCAGACTTGAAACACT;RSEQ=TTTTTGTGGAATTTGCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:2,1:112,135:247,3:0.012:2,2:32:1:28.7:1:0.59327:2.40:25.7:6:0.0122:0:4.7 0/0:589:0:0,0:282,304:586,0:0:2,0:31.4:1:30.8:1:1:0:28.3:40.857:0.9965:0:2.5 +1 121485173 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.27805;SOR=1.61681;LSEQ=AGAGCAGACTTGAAACACTC;RSEQ=TTTTGTGGAATTTGCAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:8:2,6:111,130:241,8:0.032:2,2:31.8:1:30.8:1:0.29813:2.55266:23.5:16:0.0324:0:4 0/1:591:30:13,17:270,288:558,30:0.0508:2,2:31.4:1:30.5:1:0.70834:1.22554:25.2:29:0.0497:0:3 +1 121485175 . T G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5811;SOR=0.70026;LSEQ=AGCAGACTTGAAACACTCTT;RSEQ=TTGTGGAATTTGCAAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:6:3,3:111,129:240,6:0.024:2,2:35.2:1:32.7:1:1:1.16:23.8:12:0.0246:0:3.2 0/1:591:10:6,4:279,301:580,10:0.0169:2,2:38.3:1:26.5:1:0.5337:1.62:22.9:2.333:0.012:0:4.2 +1 121485176 . T C 80 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.68048;SOR=2.52998;LSEQ=GCAGACTTGAAACACTCTTT;RSEQ=TGTGGAATTTGCAAGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:0,1:114,135:249,1:0.004:2,0:47:0:32:0:1:0:24:2:0.0041:0:7 0/1:596:6:3,3:283,306:589,6:0.0101:2,2:24:1:31:1:1:1.08:23.7:12:0.0103:0:4 +1 121485180 . G C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67251;SOR=0.84264;LSEQ=ACTTGAAACACTCTTTTTGT;RSEQ=GAATTTGCAAGTGGAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:9:4,5:116,136:252,9:0.0342:2,2:38.3:1:32.3:1:1:1.06594:21.8:18:0.035:0:4.7 0/1:621:18:7,11:288,307:595,18:0.029:2,2:34:1:29.7:1:0.47984:1.47325:21.6:36:0.0298:0:4.6 +1 121485181 . G T 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00796;SOR=Inf;LSEQ=CTTGAAACACTCTTTTTGTG;RSEQ=AATTTGCAAGTGGAGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:121,144:265,0:0:2,0:36.4:1:31.8:1:1:0:27.6:52:1:0:2.4 0/1:632:15:6,9:296,319:615,15:0.0237:2,2:32.7:1:27.2:1:0.60761:1.39113:27.9:30:0.0241:0:3.8 +1 121485186 . T G 83 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72932;SOR=0.8418;LSEQ=AACACTCTTTTTGTGGAATT;RSEQ=GCAAGTGGAGATTTCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:1,2:124,147:271,3:0.0109:2,2:35.3:1:31:1:1:1.68399:30.7:6:0.0111:0:5 0/0:650:6:4,2:308,334:642,6:0.0092:2,2:38.2:1:32.3:1:0.43545:2.17:24.5:12:0.0094:0:4 +1 121485187 . G A 82 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47316;LSEQ=ACACTCTTTTTGTGGAATTT;RSEQ=CAAGTGGAGATTTCAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:2:1,1:124,148:272,2:0.0073:2,2:39.5:1:30.5:1:1:1.19:23:4:0.0075:0:1 0/1:653:7:3,4:311,335:646,7:0.0107:2,2:43.1:1:29.3:1:1:1.23741:23.4:14:0.0108:0:2.4 +1 121485190 . A GG 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0.97643;LSEQ=CTCTTTTTGTGGAATTTGCA;RSEQ=GTGGAGATTTCAGCCGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:122,148:270,3:0.0109:2,2:31.3:1:31.7:1:1:1.64575:30.7:6:0.0109:0:5 0/1:657:7:4,3:309,338:647,7:0.0107:2,2:36.7:1:30.8:1:0.71501:1.46:24.9:14:0.0108:0:4.7 +1 121485191 . G T 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26691;SOR=0.53265;LSEQ=TCTTTTTGTGGAATTTGCAA;RSEQ=TGGAGATTTCAGCCGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:7:3,4:125,145:270,7:0.0251:2,2:42.1:1:31.3:1:1:1.14885:29.3:14:0.0254:0:4.3 0/1:666:9:3,6:311,334:645,9:0.0135:2,2:37:1:28.2:1:0.50793:1.86057:25.8:18:0.0137:0:3.3 +1 121485196 . G C 53 pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07796;SOR=0.13709;LSEQ=TTGTGGAATTTGCAAGTGGA;RSEQ=ATTTCAGCCGCTTTGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:127,149:276,3:0.0106:2,2:30:0:34:0:1:1.70157:21:6:0.0108:0:2 0/0:681:1:0,1:325,353:678,1:0.0015:2,0:34:0:32:0:1:0:33:2:0.0015:0:5 +1 121485199 . T A 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11254;SOR=Inf;LSEQ=TGGAATTTGCAAGTGGAGAT;RSEQ=TCAGCCGCTTTGAGGTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:133,154:287,0:0:2,0:34:1:31.2:1:1:0:27.9:286:1:0:2.5 0/1:689:7:4,3:325,355:680,7:0.0102:2,2:33.6:1:27.4:1:0.7152:1.46:24.6:14:0.0103:0:3.1 +1 121485202 . A T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.39501;SOR=0.62004;LSEQ=AATTTGCAAGTGGAGATTTC;RSEQ=GCCGCTTTGAGGTCAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:6:4,2:130,153:283,6:0.0208:2,2:34.3:1:32.7:1:0.42089:2.35:32:12:0.021:0:4.8 0/1:694:9:4,5:326,355:681,9:0.013:2,2:32.3:1:30.2:1:1:1.14766:24.3:18:0.0131:0:4.1 +1 121485204 . C A 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00996;SOR=0.137;LSEQ=TTTGCAAGTGGAGATTTCAG;RSEQ=CGCTTTGAGGTCAATGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:6:2,4:132,150:282,6:0.0206:2,2:38.3:1:29.7:1:0.68881:1.75668:30.7:12:0.0208:0:4 0/0:697:2:1,1:333,360:693,2:0.0029:2,2:26.5:1:30.5:1:1:1.08:22.5:4:0.0029:0:4.5 +1 121485205 . C T 126 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07922;SOR=3.83686;LSEQ=TTGCAAGTGGAGATTTCAGC;RSEQ=GCTTTGAGGTCAATGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:2:1,1:135,156:291,2:0.0068:2,2:37:0:32.5:1:1:1.15:32.5:4:0.007:0:5 0/1:700:18:8,10:327,354:681,18:0.0257:2,2:28.8:1:30.3:1:0.81505:1.15442:29.2:36:0.0262:0:3.9 +1 121485206 . G A 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0047;SOR=Inf;LSEQ=TGCAAGTGGAGATTTCAGCC;RSEQ=CTTTGAGGTCAATGGTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:139,159:298,0:0:2,0:29.4:1:31.6:1:1:0:28.7:73.5:1:0:2.5 0/1:706:16:8,8:328,355:683,16:0.0227:2,2:27.8:1:28.1:1:1:1.08:30.4:15:0.0214:0:4.8 +1 121485207 . C A 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.6994;SOR=0.69276;LSEQ=GCAAGTGGAGATTTCAGCCG;RSEQ=TTTGAGGTCAATGGTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:1,2:137,157:294,3:0.0101:2,2:30.7:1:31.3:1:1:1.74208:35:6:0.0102:0:3 0/0:715:5:3,2:337,365:702,5:0.007:2,2:25.4:1:30.2:1:0.67553:1.62:33.8:10:0.0071:0:2.6 +1 121485208 . T G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49669;SOR=1.59904;LSEQ=CAAGTGGAGATTTCAGCCGC;RSEQ=TTGAGGTCAATGGTAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:5:3,2:135,156:291,5:0.0168:2,2:37.4:1:27.4:1:0.6669:1.73:31.4:4:0.0136:0:3.6 0/1:715:19:10,9:328,363:691,19:0.0266:2,2:20.6:1:30:1:0.81668:1.23:38.6:38:0.0272:0:2.7 +1 121485213 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7755;SOR=1.13134;LSEQ=GGAGATTTCAGCCGCTTTGA;RSEQ=GTCAATGGTAGAAAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:17:8,9:128,152:280,17:0.057:2,2:24.7:1:32.6:1:1:1.06:24.5:34:0.0576:0:3.6 0/1:718:46:20,26:321,345:666,46:0.0641:2,2:25.2:1:30.2:1:0.54643:1.20924:23.6:92:0.0652:0:4.2 +1 121485214 . G T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0702;SOR=2.02751;LSEQ=GAGATTTCAGCCGCTTTGAG;RSEQ=TCAATGGTAGAAAAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:8:5,3:131,159:290,8:0.0268:2,2:25.3:1:29:1:0.47601:2.02:24.5:7:0.0236:0:3 0/1:717:38:18,20:323,351:674,38:0.053:2,2:30.4:1:28.8:1:1:1.02245:24.7:37:0.052:0:3.6 +1 121485217 . A C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24283;SOR=0.59789;LSEQ=ATTTCAGCCGCTTTGAGGTC;RSEQ=ATGGTAGAAAAGGAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:9:2,7:135,155:290,9:0.0301:2,2:20.4:1:33:1:0.18695:3.03814:21.4:18:0.0305:0:1.1 0/1:714:13:7,6:332,368:700,13:0.0182:2,2:21.6:1:31:1:0.78143:1.29:26.2:26:0.0185:0:1.3 +1 121485218 . A G 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15697;SOR=0.27835;LSEQ=TTTCAGCCGCTTTGAGGTCA;RSEQ=TGGTAGAAAAGGAAATATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:137,159:296,3:0.01:2,2:18.7:1:34.3:1:1:1.72026:22.3:6:0.0101:0:2.7 0/0:712:2:1,1:340,370:710,2:0.0028:2,2:12.5:1:33:0:1:1.09:21.5:4:0.0028:0:1 +1 121485219 . T A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.87328;SOR=0.95091;LSEQ=TTCAGCCGCTTTGAGGTCAA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:15:7,8:130,152:282,15:0.0502:2,2:19.9:1:31.5:1:1:1.02:23.8:14:0.0483:0:3.4 0/1:711:34:16,18:322,350:672,34:0.0478:2,2:19.1:1:29.6:1:1:1.03496:23.2:33:0.0472:0:3.8 +1 121485220 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.87848;SOR=1.09689;LSEQ=TCAGCCGCTTTGAGGTCAAT;RSEQ=GTAGAAAAGGAAATATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:15:7,8:124,151:275,15:0.0507:2,2:17.1:1:29.6:1:1:1.07:23.7:14:0.0484:0:2.1 0/1:705:39:16,23:315,340:655,39:0.0553:2,2:16.9:1:29.8:1:0.41403:1.33125:24.8:78:0.0557:0:2.1 +1 121485221 . G T 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70047;SOR=0.69974;LSEQ=CAGCCGCTTTGAGGTCAATG;RSEQ=TAGAAAAGGAAATATCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:1,2:135,153:288,3:0.0102:2,2:11:1:29.3:1:1:1.7614:21.7:6:0.0103:0:1.7 0/0:696:5:2,3:323,354:677,5:0.0072:2,2:13.8:1:24.6:1:1:1.36802:33.6:4:0.0059:0:2.2 +1 121485227 . A T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02391;SOR=1.39295;LSEQ=CTTTGAGGTCAATGGTAGAA;RSEQ=AGGAAATATCTTCGTATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:130:62,68:64,73:137,130:0.4779:2,2:19.8:1:30:1:0.90278:1.04:29:260:0.4797:0:3.5 1/0:619:347:171,176:122,144:266,347:0.5606:2,2:21.1:1:28.6:1:0.41548:1.15:29.2:114.667:0.5612:0:3.6 +1 121485230 . G T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33626;SOR=1.83067;LSEQ=TGAGGTCAATGGTAGAAAAG;RSEQ=AAATATCTTCGTATAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:4:0,4:125,131:256,4:0.0154:2,0:17.8:1:30:0:0.12322:0:24.5:8:0.0155:0:2.5 0/1:575:16:7,9:268,290:558,16:0.0278:2,2:14:1:28.4:1:0.80366:1.18782:33.3:32:0.0279:0:2.3 +1 121485232 . A T 82 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.44638;SOR=3.13406;LSEQ=AGGTCAATGGTAGAAAAGGA;RSEQ=ATATCTTCGTATAGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:1:0,1:119,130:249,1:0.004:2,0:2:0:29:0:1:0:26:2:0.004:0:2 0/1:567:7:2,5:267,290:557,7:0.0123:2,2:12:1:29.4:1:0.45372:2.29844:28.4:14:0.0125:0:3.1 +1 121485233 . A AC 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04841;SOR=0.42568;LSEQ=GGTCAATGGTAGAAAAGGAA;RSEQ=TATCTTCGTATAGAAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:13:9,4:108,125:233,13:0.0528:2,2:18:1:31.1:1:0.15344:2.59:31.2:26:0.0531:0.0122:2.1 0/1:561:13:7,6:258,289:547,13:0.0232:2,2:12.1:1:30.4:1:0.78054:1.31:27.1:26:0.0234:0.0053:1.7 +1 121485240 . C A 21 v3;p8;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5858;SOR=0.41884;LSEQ=GGTAGAAAAGGAAATATCTT;RSEQ=GTATAGAAACAAGACAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:88,96:184,2:0.0108:2,2:7:0:32:1:1:1.09:29:4:0.0108:0:1 0/0:442:2:2,0:205,233:438,2:0.0045:2,0:1:0:21.5:1:0.22076:0:24.5:4:0.0046:0:3.5 +1 121485241 . G C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03398;SOR=1.5018;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=TATAGAAACAAGACAGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:174:107:52,55:25,28:53,107:0.6149:2,2:19.7:1:32.3:1:1:1.06:29.4:214:0.6185:0:3.8 1/0:425:300:139,161:43,55:98,300:0.7059:2,2:20.2:1:30.7:1:0.72651:1.10:29.6:74:0.7115:0:3.6 +1 121485244 . T C 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.18806;SOR=Inf;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AGAAACAAGACAGAATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:84,80:164,0:0:2,0:18.1:1:29.9:1:1:0:31:328:1:0:3.3 0/1:399:6:2,4:188,198:386,6:0.015:2,2:28.8:1:31.3:1:0.68598:1.896:27.7:12:0.0153:0:4.7 +1 121485245 . A T 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32434;SOR=0.39922;LSEQ=AAAAGGAAATATCTTCGTAT;RSEQ=GAAACAAGACAGAATGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:79,75:154,2:0.0127:2,2:16:1:29.5:1:1:1.053:24.5:4:0.0128:0:5 0/0:391:2:1,1:187,199:386,2:0.0051:2,2:5:1:25:1:1:1.06:34.5:4:0.0052:0:4 +1 121485246 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00289;SOR=0.46716;LSEQ=AAAGGAAATATCTTCGTATA;RSEQ=AAACAAGACAGAATGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:34:19,15:54,54:108,34:0.2345:2,2:16.8:1:30.1:1:0.56257:1.26:34.2:68:0.2345:0:3 0/1:360:45:26,19:146,166:312,45:0.125:2,2:13.9:1:28.7:1:0.20208:1.55:28.6:90:0.1264:0:3.5 +1 121485248 . A G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01011;SOR=0.35982;LSEQ=AGGAAATATCTTCGTATAGA;RSEQ=ACAAGACAGAATGATTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:15:7,8:64,61:125,15:0.1064:2,2:25.1:1:30.6:1:0.79008:1.19751:38.1:14:0.1007:0:3.6 0/1:366:15:8,7:170,179:349,15:0.041:2,2:22.7:1:30.8:1:0.79587:1.20:28.1:30:0.0413:0:4.1 +1 121485250 . CA GT 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16523;SOR=0.54042;LSEQ=GAAATATCTTCGTATAGAAA;RSEQ=AGACAGAATGATTCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:10:7,3:63,60:123,10:0.073:2,2:27.9:1:31.8:1:0.3318:2.21:29.8:20:0.0741:0:3.4 0/1:368:15:5,10:178,170:348,15:0.0408:2,2:22.2:1:29:1:0.1975:2.08998:26.3:30:0.0409:0:2.7 +1 121485251 . A T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18223;SOR=1.49732;LSEQ=AAATATCTTCGTATAGAAAC;RSEQ=AGACAGAATGATTCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:116:60,56:3,3:6,116:0.8345:2,2:19.3:1:30.4:1:1:1.07:29.5:232:0.928:0:3.3 1/1:368:325:170,155:6,8:14,325:0.8832:2,2:18.3:1:28.7:1:0.58899:1.46:28.7:324:0.9337:0:3.3 +1 121485253 . G C 50 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62396;SOR=0.58591;LSEQ=ATATCTTCGTATAGAAACAA;RSEQ=ACAGAATGATTCTCAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:78,71:149,2:0.0131:2,2:34.5:1:32.5:1:1:1.09791:28:4:0.0132:0:7 0/0:390:3:2,1:201,185:386,3:0.0077:2,2:22.7:1:31.7:1:1:1.84:26:6:0.0077:0:4.3 +1 121485257 . G A 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.93243;LSEQ=CTTCGTATAGAAACAAGACA;RSEQ=AATGATTCTCAGAAACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:1:0,1:89,70:159,1:0.0063:2,0:15:0:33:0:0.44375:0:21:2:0.0063:0:5 0/1:416:5:2,3:223,183:406,5:0.012:2,2:23.4:1:30.6:1:0.66208:1.82516:30.8:10:0.0121:0:4.6 +1 121485260 . T C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45306;SOR=1.401;LSEQ=CGTATAGAAACAAGACAGAA;RSEQ=GATTCTCAGAAACTCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:8:2,6:96,69:165,8:0.0457:2,2:18.9:1:30.9:1:0.07852:4.14084:26.9:16:0.0457:0:3.1 0/1:445:28:14,14:231,185:416,28:0.0629:2,2:22.8:1:30.9:1:0.69528:1.24801:29.3:56:0.0629:0:3.5 +1 121485265 . C G 125 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17217;SOR=2.89823;LSEQ=AGAAACAAGACAGAATGATT;RSEQ=TCAGAAACTCCTTTGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:99,80:179,2:0.0109:2,2:26:1:34:0:1:1.23603:29:4:0.011:0:4.5 0/1:453:14:8,6:242,197:439,14:0.0309:2,2:22.8:1:32.9:1:1:1.09:27.5:28:0.0312:0:3.6 +1 121485267 . C G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78646;SOR=0.895;LSEQ=AAACAAGACAGAATGATTCT;RSEQ=AGAAACTCCTTTGTGATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:5:4,1:99,82:181,5:0.0269:2,2:26.2:1:33.6:1:0.38287:3.29:22.2:10:0.0272:0:3.6 0/1:456:11:5,6:245,200:445,11:0.0241:2,2:26:1:30.8:1:0.55489:1.46873:26.5:22:0.0242:0:3.1 +1 121485269 . G T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.80712;SOR=1.29234;LSEQ=ACAAGACAGAATGATTCTCA;RSEQ=AAACTCCTTTGTGATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:5:2,3:101,79:180,5:0.0269:2,2:23.4:1:29:1:0.65655:1.91092:24.6:10:0.027:0:2.6 0/1:464:16:7,9:243,202:445,16:0.0345:2,2:22.5:1:28.4:1:0.44953:1.54519:24.2:32:0.0347:0:3.6 +1 121485271 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08132;SOR=0;LSEQ=AAGACAGAATGATTCTCAGA;RSEQ=ACTCCTTTGTGATGTGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:102,83:185,2:0.0106:2,2:34:1:31.5:1:1:1.22755:60:4:0.0108:0:1 0/0:470:0:0,0:253,217:470,0:0:2,0:23:1:29.7:1:1:0:28.5:93:1:0:2.5 +1 121485272 . AC A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.35969;SOR=0.39431;LSEQ=AGACAGAATGATTCTCAGAA;RSEQ=TCCTTTGTGATGTGTGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:3:2,1:100,83:183,3:0.0158:2,2:35:1:32.7:1:1:1.66:21.3:6:0.0159:0:4.3 0/0:478:3:1,2:252,216:468,3:0.0063:2,2:26.3:1:30:1:0.59839:2.32926:26.7:6:0.0063:0:3.7 +1 121485273 . C A 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28252;SOR=0.49211;LSEQ=GACAGAATGATTCTCAGAAA;RSEQ=TCCTTTGTGATGTGTGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:4:2,2:100,83:183,4:0.0211:2,2:25:1:32.5:1:1:1.20361:39.8:8:0.0212:0:4 0/1:478:5:2,3:252,216:468,5:0.0105:2,2:12.4:1:30:1:0.66645:1.74792:22.6:10:0.0105:0:3.8 +1 121485275 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30366;SOR=2.17712;LSEQ=CAGAATGATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:3,0:101,88:189,3:0.0155:2,0:24.7:1:32.7:1:0.25131:0:23:6:0.0159:0:2 0/1:481:16:12,4:241,220:461,16:0.0333:2,2:22.3:1:30.4:1:0.08053:2.73:22:32:0.0338:0:2.4 +1 121485276 . C T 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15979;SOR=0.39606;LSEQ=AGAATGATTCTCAGAAACTC;RSEQ=TTTGTGATGTGTGCGTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:5:2,3:102,86:188,5:0.0255:2,2:21.8:1:31.8:1:0.66331:1.77376:29.6:10:0.0255:0:4 0/1:488:5:3,2:257,224:481,5:0.0102:2,2:17.6:1:30:1:1:1.31:23.2:10:0.0104:0:3.6 +1 121485283 . A C 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28048;SOR=0.48903;LSEQ=TTCTCAGAAACTCCTTTGTG;RSEQ=TGTGTGCGTTCAACTCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:4:2,2:107,96:203,4:0.0192:2,2:36:1:32:1:1:1.114:27.8:8:0.0194:0:3.5 0/0:527:5:2,3:280,239:519,5:0.0095:2,2:33.6:1:26.8:1:0.66611:1.75542:29:4:0.0077:0:3.6 +1 121485286 . T C 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.35779;SOR=0.3883;LSEQ=TCAGAAACTCCTTTGTGATG;RSEQ=GTGCGTTCAACTCACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:3:2,1:106,96:202,3:0.0146:2,2:35:1:32:1:1:1.81:28.7:6:0.0148:0:2.7 0/0:524:3:1,2:283,238:521,3:0.0057:2,2:24:1:30:1:0.59549:2.37433:29.3:6:0.0058:0:2.3 +1 121485288 . T G 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10495;SOR=0.29375;LSEQ=AGAAACTCCTTTGTGATGTG;RSEQ=GCGTTCAACTCACAGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:4:3,1:108,96:204,4:0.019:2,2:41.5:1:32.3:1:0.62481:2.66:32:8:0.019:0:3.3 0/0:530:3:3,0:284,241:525,3:0.0057:2,0:26.3:1:31.3:1:0.25428:0:28:6:0.0057:0:2.7 +1 121485290 . C T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62467;SOR=1.26772;LSEQ=AAACTCCTTTGTGATGTGTG;RSEQ=GTTCAACTCACAGAGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:12:7,5:108,96:204,12:0.0556:2,2:31:1:31.3:1:0.77396:1.24:24.2:24:0.0561:0:2.9 0/1:533:37:23,14:264,229:493,37:0.0694:2,2:25.5:1:29.3:1:0.39279:1.42:23.8:74:0.0703:0:3.3 +1 121485291 . G A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21505;SOR=0.46941;LSEQ=AACTCCTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:6:3,3:109,100:209,6:0.0276:2,2:35.2:1:30.7:1:1:1.08955:29.7:12:0.0276:0:3.3 0/1:532:7:5,2:277,239:516,7:0.0132:2,2:36.6:1:29.6:1:0.46012:2.15:27.3:14:0.0132:0:3 +1 121485294 . C G 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48982;SOR=0.61757;LSEQ=TCCTTTGTGATGTGTGCGTT;RSEQ=AACTCACAGAGTTTAACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:4:1,3:111,104:215,4:0.0182:2,2:35.5:1:32:1:0.36038:3.18635:28:8:0.0184:0:4 0/1:531:6:3,3:281,237:518,6:0.0113:2,2:35.7:1:31.2:1:1:1.18526:33.2:12:0.0114:0:3.5 +1 121485297 . C G 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15853;SOR=0.27959;LSEQ=TTTGTGATGTGTGCGTTCAA;RSEQ=TCACAGAGTTTAACCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:3:2,1:113,105:218,3:0.0134:2,2:10.7:1:33:1:1:1.85:25.3:6:0.0135:0:3.7 0/0:530:2:1,1:287,241:528,2:0.0038:2,2:23:1:33.5:1:1:1.19047:30:4:0.0038:0:2 +1 121485298 . T A 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.986;LSEQ=TTGTGATGTGTGCGTTCAAC;RSEQ=CACAGAGTTTAACCTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:3:3,0:113,108:221,3:0.0134:2,0:18.7:1:30.3:1:0.2476:0:24.7:6:0.0135:0:3.3 0/1:530:7:4,3:282,240:522,7:0.0132:2,2:30.1:1:30:1:1:1.13:25.6:14:0.0134:0:3.3 +1 121485303 . G C 112 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25284;SOR=2.53727;LSEQ=ATGTGTGCGTTCAACTCACA;RSEQ=AGTTTAACCTTTCTTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:2:2,0:111,106:217,2:0.0091:2,0:24:1:31:1:0.49822:0:22.5:4:0.0092:0:3 0/1:527:12:7,5:279,234:513,12:0.0228:2,2:33.3:1:31.3:1:1:1.17:30.3:24:0.0229:0:1.9 +1 121485312 . C T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28995;SOR=0.69437;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCTTTTCATAGAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:15:5,10:109,96:205,15:0.0682:2,2:39.4:1:29.5:1:0.18233:2.26258:23.9:14:0.066:0:2.6 0/1:538:26:12,14:274,237:511,26:0.0483:2,2:37.8:1:29.5:1:0.54687:1.34804:23.3:52:0.0489:0:2.5 +1 121485317 . T C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02457;SOR=0;LSEQ=CTCACAGAGTTTAACCTTTC;RSEQ=TTTCATAGAGCAGTTAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:1,2:117,106:223,3:0.0133:2,2:17:1:31:1:0.60729:2.20007:22.3:6:0.0134:0:1.7 0/0:549:0:0,0:291,255:546,0:0:2,0:28.6:1:29.6:1:1:0:25.9:90:0.9945:0:1.9 +1 121485318 . T G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.61247;SOR=1.18955;LSEQ=TCACAGAGTTTAACCTTTCT;RSEQ=TTCATAGAGCAGTTAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:22:11,11:106,95:201,22:0.0973:2,2:25.1:1:32:1:0.82592:1.11524:28.8:21:0.0938:0:1.9 0/1:554:63:26,37:263,225:488,63:0.1137:2,2:26:1:31:1:0.06187:1.66186:27.2:62:0.1131:0:2.2 +1 121485319 . T C 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.75174;SOR=0.80969;LSEQ=CACAGAGTTTAACCTTTCTT;RSEQ=TCATAGAGCAGTTAGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:4:3,1:114,108:222,4:0.0176:2,2:22.5:1:31:1:0.6226:2.83:25.5:8:0.0178:0:2.8 0/1:559:8:3,5:290,260:550,8:0.0143:2,2:37.3:1:31:1:0.4868:1.85692:21.5:16:0.0144:0:3.5 +1 121485323 . T C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52151;SOR=1.4479;LSEQ=GAGTTTAACCTTTCTTTTCA;RSEQ=AGAGCAGTTAGGAAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:6:3,3:111,104:215,6:0.0264:2,2:37.5:1:32:1:1:1.06696:31.2:12:0.0267:0:2.5 0/1:555:21:13,8:268,245:513,21:0.0378:2,2:33:1:31:1:0.50477:1.48:29.3:42:0.038:0:2.8 +1 121485328 . C T 39 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07089;SOR=0.13039;LSEQ=TAACCTTTCTTTTCATAGAG;RSEQ=AGTTAGGAAACACTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:107,108:215,3:0.0136:2,2:32:1:25:1:1:2.01:24:2:0.0092:0:3 0/0:560:1:1,0:284,267:551,1:0.0018:2,0:45:0:27:0:1:0:23:2:0.0018:0:1 +1 121485329 . A T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14291;SOR=0.51383;LSEQ=AACCTTTCTTTTCATAGAGC;RSEQ=GTTAGGAAACACTCTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:9:5,4:107,109:216,9:0.04:2,2:32.2:1:30.9:1:0.74829:1.27:39.2:18:0.0405:0:2.2 0/1:573:12:6,6:286,271:557,12:0.0209:2,2:29.7:1:28.3:1:1:1.05528:33.2:11:0.0194:0:2.2 +1 121485333 . A G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58141;SOR=0.83048;LSEQ=TTTCTTTTCATAGAGCAGTT;RSEQ=GGAAACACTCTGTTTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:12:5,7:110,106:216,12:0.0526:2,2:16.8:1:30:1:0.56797:1.45046:29.8:11:0.0491:0:3.2 0/1:567:25:12,13:280,257:537,25:0.0441:2,2:14.2:1:30.6:1:0.68891:1.17993:27.7:50:0.0444:0:3.1 +1 121485335 . G T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.70973;SOR=1.23291;LSEQ=TCTTTTCATAGAGCAGTTAG;RSEQ=AAACACTCTGTTTGTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:9:6,3:109,109:218,9:0.0393:2,2:22.8:1:28.1:1:0.49928:1.99:23.1:18:0.04:0:3.6 0/1:583:28:15,13:288,263:551,28:0.048:2,2:27.9:1:28.3:1:1:1.05:25:27:0.0469:0:3.4 +1 121485338 . A T 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68015;SOR=2.32795;LSEQ=TTTCATAGAGCAGTTAGGAA;RSEQ=CACTCTGTTTGTAAAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:0,1:114,112:226,1:0.0044:2,0:24:0:32:0:0.4978:0:27:2:0.0044:0:3 0/1:588:6:4,2:306,276:582,6:0.0102:2,2:25.7:1:27.5:1:0.6887:1.80:24.5:12:0.0103:0:2.8 +1 121485343 . CTGTT C 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.36796;SOR=0.41658;LSEQ=TAGAGCAGTTAGGAAACACT;RSEQ=TGTAAAGTCTGCAAGTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:2,1:109,111:220,3:0.0133:2,2:37.3:1:32.3:1:0.62161:2.03:29:6:0.0133:0.0044:2 0/0:539:3:0,3:275,256:531,3:0.0056:2,0:15.3:1:32.7:1:0.11342:0:25.3:6:0.0056:0.0019:3.3 +1 121485349 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17182;SOR=1.91405;LSEQ=AGTTAGGAAACACTCTGTTT;RSEQ=TAAAGTCTGCAAGTGGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:6:4,2:98,101:199,6:0.0283:2,2:14:1:27.8:1:0.445:2.05:22.8:12:0.0286:0:3.3 0/1:492:26:14,12:236,226:462,26:0.0528:2,2:19.9:1:27.9:1:0.84203:1.12:23.8:52:0.0534:0:3.4 +1 121485350 . T A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06356;SOR=Inf;LSEQ=GTTAGGAAACACTCTGTTTG;RSEQ=AAAGTCTGCAAGTGGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:106,106:212,0:0:2,0:21.6:1:29:1:1:0:27.8:105:1:0:1.8 0/1:480:9:3,6:241,230:471,9:0.0188:2,2:19.1:1:29.2:1:0.33183:2.09252:31.4:18:0.0188:0:2.3 +1 121485351 . A G 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.76387;SOR=1.33717;LSEQ=TTAGGAAACACTCTGTTTGT;RSEQ=AAGTCTGCAAGTGGATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:3:2,1:99,106:205,3:0.0144:2,2:11.7:1:29.7:1:0.61254:2.13:38.7:6:0.0145:0:3.7 0/1:471:9:6,3:232,226:458,9:0.0191:2,2:11.8:1:29.2:1:0.50429:1.95:25:18:0.0191:0:3.4 +1 121485354 . G C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58421;SOR=0.72235;LSEQ=GGAAACACTCTGTTTGTAAA;RSEQ=TCTGCAAGTGGATATTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:6:3,3:92,94:186,6:0.0309:2,2:24:1:31.8:1:1:1.02:22.2:12:0.0314:0:3.2 0/1:444:10:5,5:214,220:434,10:0.0225:2,2:17.9:1:31.1:1:1:1.03:22.1:20:0.0226:0:2.4 +1 121485355 . T C 62 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44449;SOR=0.58796;LSEQ=GAAACACTCTGTTTGTAAAG;RSEQ=CTGCAAGTGGATATTCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:2,1:91,97:188,3:0.0156:2,2:7.7:1:30.7:1:0.61332:2.12:38.7:6:0.0159:0:3.7 0/0:433:4:1,3:209,218:427,4:0.0092:2,2:13.3:1:31.3:1:0.62374:2.86999:21.8:8:0.0094:0:4.3 +1 121485356 . C A 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37778;SOR=0.44008;LSEQ=AAACACTCTGTTTGTAAAGT;RSEQ=TGCAAGTGGATATTCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:3:2,1:88,95:183,3:0.016:2,2:23:1:30:1:0.61108:2.15:25.3:6:0.016:0:1.3 0/0:424:3:2,1:200,214:414,3:0.0071:2,2:30.7:1:28.3:1:0.6127:2.14:25:6:0.0071:0:2.3 +1 121485358 . GC G 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22462;SOR=0.22031;LSEQ=ACACTCTGTTTGTAAAGTCT;RSEQ=AAGTGGATATTCAGACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:2,0:78,90:168,2:0.0116:2,0:16:1:31.2:1:0.21998:0:26.5:4:0.0118:0.0058:1 0/0:388:1:1,0:178,198:376,1:0.0026:2,0:21:0:33:0:0.4748:0:26:2:0.0026:0:2 +1 121485359 . C A 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.59015;SOR=0.44113;LSEQ=CACTCTGTTTGTAAAGTCTG;RSEQ=AAGTGGATATTCAGACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:78,90:168,2:0.0116:2,2:10:1:31.5:1:1:1.15:21.5:4:0.0118:0:1.5 0/0:388:2:1,1:178,198:376,2:0.0052:2,2:32:1:25.5:1:1:1.11:22.5:4:0.0052:0:2 +1 121485360 . A C 73 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10116;LSEQ=ACTCTGTTTGTAAAGTCTGC;RSEQ=AGTGGATATTCAGACCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:0,2:76,87:163,2:0.0121:2,0:22.5:1:34:0:0.50007:0:38.5:4:0.0123:0:5 0/1:375:5:1,4:175,194:369,5:0.0133:2,2:11.8:1:31.6:1:0.376:3.59742:24.2:10:0.0135:0:4.4 +1 121485364 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0882;SOR=0;LSEQ=TGTTTGTAAAGTCTGCAAGT;RSEQ=GATATTCAGACCTCCTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:0,2:71,80:151,2:0.0131:2,0:17.5:1:28.5:1:0.49931:0:27.5:4:0.0132:0:2 0/0:361:0:0,0:168,188:356,0:0:2,0:27.6:1:31:1:1:0:26:355:0.9889:0:1.9 +1 121485376 . C A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.80664;SOR=1.07158;LSEQ=CTGCAAGTGGATATTCAGAC;RSEQ=TCCTTGAGGCCTTCGTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:29:14,15:48,55:103,29:0.2071:2,2:30.7:1:30.8:1:1:1.07:32.1:28:0.2059:0:3 0/1:320:70:37,33:108,125:233,70:0.2188:2,2:29.3:1:30.2:1:0.34393:1.30:25.9:69:0.219:0:3.1 +1 121485378 . C G 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64646;SOR=0.66735;LSEQ=GCAAGTGGATATTCAGACCT;RSEQ=CTTGAGGCCTTCGTTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:2,0:60,68:128,2:0.0154:2,0:21:1:31:1:0.22552:0:22:4:0.0156:0:1.5 0/1:291:3:1,2:134,147:281,3:0.0103:2,2:16:1:30:1:1:1.81943:24.3:6:0.0106:0:2.7 +1 121485379 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78425;SOR=0.91249;LSEQ=CAAGTGGATATTCAGACCTC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:25:12,13:48,51:99,25:0.2:2,2:32.4:1:31.3:1:1:1.01945:30.7:24:0.1935:0:3.6 0/1:280:52:21,31:110,113:223,52:0.1857:2,2:29.9:1:29.9:1:0.28173:1.43511:26.4:51:0.1855:0:3.3 +1 121485380 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0985;SOR=0;LSEQ=AAGTGGATATTCAGACCTCC;RSEQ=TGAGGCCTTCGTTGGAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:0,2:58,64:122,2:0.0161:2,0:17:1:32.5:1:0.49803:0:25:4:0.0161:0:2 0/0:270:0:0,0:127,143:270,0:0:2,0:30.4:1:29.8:1:1:0:27.1:134:1:0:2 +1 121485381 . T A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31167;SOR=Inf;LSEQ=AGTGGATATTCAGACCTCCT;RSEQ=GAGGCCTTCGTTGGAAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:59,63:122,0:0:2,0:28.5:1:30.9:1:1:0:30:121:0.9918:0:2 0/1:264:4:2,2:123,136:259,4:0.0152:2,2:11.3:1:28.3:1:1:1.11:26.5:8:0.0153:0:2.5 +1 121485385 . G A 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33656;SOR=0.32334;LSEQ=GATATTCAGACCTCCTTGAG;RSEQ=CCTTCGTTGGAAACGGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:3:3,0:55,60:115,3:0.0252:2,0:28.3:1:28.7:1:0.1156:0:28.3:6:0.0259:0:3.7 0/0:242:2:1,1:109,127:236,2:0.0083:2,2:40.5:1:29.5:1:1:1.16:34:4:0.0085:0:3 +1 121485387 . C T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.89095;SOR=0.94581;LSEQ=TATTCAGACCTCCTTGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:26:14,12:41,45:86,26:0.2301:2,2:33.5:1:31.7:1:0.65714:1.28:32.7:52:0.2342:0:3.4 0/1:236:52:29,23:80,103:183,52:0.2203:2,2:31.7:1:30.7:1:0.15602:1.62:27.3:104:0.2222:0:3.3 +1 121485388 . T G 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2379;SOR=0.23054;LSEQ=ATTCAGACCTCCTTGAGGCC;RSEQ=TCGTTGGAAACGGGATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:50,55:105,2:0.0185:2,2:34.5:1:32.5:1:1:1.10:40:4:0.0189:0:1.5 0/0:232:1:0,1:107,124:231,1:0.0043:2,0:45:0:34:0:1:0:45:2:0.0044:0:2 +1 121485390 . C T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08906;SOR=0.14595;LSEQ=TCAGACCTCCTTGAGGCCTT;RSEQ=GTTGGAAACGGGATTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:3:2,1:44,51:95,3:0.03:2,2:38:1:29.7:1:0.59896:2.30:34.7:6:0.0306:0:2.7 0/0:224:1:0,1:104,117:221,1:0.0045:2,0:25:0:31:0:1:0:24:2:0.0045:0:3 +1 121485391 . G T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05628;LSEQ=CAGACCTCCTTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:5:1,4:45,46:91,5:0.0515:2,2:32.6:1:31.2:1:0.36389:3.86418:24.8:10:0.0521:0:2.8 0/1:221:12:5,7:98,110:208,12:0.0543:2,2:25.4:1:28.8:1:0.77386:1.24603:26.3:11:0.0507:0:2.6 +1 121485392 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09296;SOR=0;LSEQ=AGACCTCCTTGAGGCCTTCG;RSEQ=TGGAAACGGGATTTCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:46,48:94,2:0.0206:2,2:43.5:1:30:1:1:1.04:33:4:0.0206:0:3.5 0/0:220:0:0,0:102,113:215,0:0:2,0:26.6:1:29.2:1:1:0:27.6:106.5:0.9771:0:2 +1 121485398 . A G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1627;SOR=0.53942;LSEQ=CCTTGAGGCCTTCGTTGGAA;RSEQ=CGGGATTTCTTCATATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:10:5,5:37,39:76,10:0.1149:2,2:33.4:1:29.8:1:1:1.05:29.9:4:0.0941:0:3.8 0/1:199:13:5,8:90,96:186,13:0.0653:2,2:31.5:1:29.9:1:0.57341:1.49699:23.7:12:0.0612:0:4.2 +1 121485399 . C A 63 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.85179;LSEQ=CTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCATATTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:0,2:40,42:82,2:0.0235:2,0:24.5:1:34:0:0.49512:0:36:4:0.0241:0:3 0/1:199:4:1,3:93,100:193,4:0.0201:2,2:32.5:1:31.8:1:0.62274:2.77661:32.3:8:0.0204:0:3.3 +1 121485400 . G A 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42717;SOR=0.55514;LSEQ=TTGAGGCCTTCGTTGGAAAC;RSEQ=GGATTTCTTCATATTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:3:2,1:36,42:78,3:0.0357:2,2:30.3:1:31.7:1:0.59782:2.31:31.7:6:0.0357:0:3 0/1:199:4:2,2:93,102:195,4:0.0201:2,2:20.5:1:30:1:1:1.10:27.8:8:0.0203:0:2.5 +1 121485402 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGGCCTTCGTTGGAAACGG;RSEQ=ATTTCTTCATATTCTGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:40,44:84,0:0:2,0:23.2:1:31.8:1:1:0:32.2:27:1:0:2.3 0/1:196:2:1,1:92,102:194,2:0.0102:2,2:33:0:29.5:1:1:1.11:59.5:4:0.0104:0:1.5 +1 121485403 . A G 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55628;SOR=Inf;LSEQ=AGGCCTTCGTTGGAAACGGG;RSEQ=TTTCTTCATATTCTGCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:40,44:84,0:0:2,0:22.2:1:30.8:1:1:0:32.2:41:1:0:2.3 0/1:195:3:3,0:88,103:191,3:0.0154:2,0:23.3:1:28:1:0.10139:0:24.3:6:0.0155:0:4.7 +1 121485408 . T C 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TCATATTCTGCTAGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:36,40:76,0:0:2,0:19:1:31.5:1:1:0:33:75:0.9868:0:2.3 0/1:175:2:1,1:85,87:172,2:0.0114:2,2:7:0:29:1:1:1.02:24:4:0.0116:0:2 +1 121485411 . A C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.92623;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TATTCTGCTAGACAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:0,1:37,38:75,1:0.0132:2,0:4:0:32:0:1:0:24:2:0.0135:0:2 0/1:164:2:1,1:79,81:160,2:0.0122:2,2:17:1:29:1:1:1.03:23.5:4:0.0123:0:2.5 +1 121485413 . A G 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68391;SOR=0.62725;LSEQ=TGGAAACGGGATTTCTTCAT;RSEQ=TTCTGCTAGACAGAAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:3:2,1:33,36:69,3:0.0417:2,2:14.7:1:32.3:1:0.60915:2.16:25.7:6:0.0417:0:4.7 0/1:151:4:1,3:74,73:147,4:0.0265:2,2:21.5:1:31.3:1:0.61998:3.02075:23:8:0.0268:0:4.5 +1 121485416 . C A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38595;SOR=1.59847;LSEQ=AAACGGGATTTCTTCATATT;RSEQ=TGCTAGACAGAAGAATTCNN GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:7:1,6:31,29:60,7:0.1045:2,2:13:1:31.9:1:0.1078:6.26469:22.1:14:0.1061:0:2.4 0/1:127:20:7,13:58,46:104,20:0.1575:2,2:11:1:29:1:0.14116:2.32559:22.7:40:0.16:0:1.8 +1 121485422 . G T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5352;SOR=0.68366;LSEQ=GATTTCTTCATATTCTGCTA;RSEQ=ACAGAAGAATTCNNNNNNNN GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:2,3:25,25:50,5:0.0909:2,2:10.6:1:29.8:1:1:1.48909:26.8:10:0.0909:0:4 0/1:94:6:3,3:40,45:85,6:0.0638:2,2:11:1:30.3:1:1:1.12:32.2:12:0.0652:0:4.8 +1 121485424 . C A 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94043;LSEQ=TTTCTTCATATTCTGCTAGA;RSEQ=AGAAGAATTCNNNNNNNNNN GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:6:3,3:22,24:46,6:0.1132:2,2:4.7:1:29.8:1:1:1.09:41.5:12:0.1132:0:3.8 0/1:84:9:6,3:36,39:75,9:0.1071:2,2:8.3:1:28.3:1:0.48272:2.15:26.8:18:0.1071:0:3.2 +1 121485429 . G T 67 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69465;SOR=1.83561;LSEQ=TCATATTCTGCTAGACAGAA;RSEQ=AATTCNNNNNNNNNNNNNNN GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:18,14:32,2:0.0556:2,0:2:1:29.5:1:0.2139:0:21:4:0.0588:0:3 0/1:51:5:3,2:25,21:46,5:0.098:2,2:5.6:1:29.2:1:1:1.25:30.8:10:0.1:0:2 +1 145209330 . G C 94 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.48689;SOR=0.50469;LSEQ=TGTGGATCTGCCCAGGCGGC;RSEQ=GCGGCGGCGGCGGCGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:4,4:18,20:38,8:0.1739:2,2:15.4:1:31.4:1:1:1.11:50.4:16:0.1739:0:1.5 0/1:21:2:2,0:10,9:19,2:0.0952:2,0:2:1:29:1:0.48571:0:20.5:4:0.0952:0:1 +1 145209612 . GCCCCGCCAACCGCCGGGGTT G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=47;MSI=2.350;MSILEN=1;SSF=1;SOR=1.09789;LSEQ=CCGGGGGCCCCTCCCGTGGT;RSEQ=CCCCGCCAACCGCCGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:0,12:2,20:22,12:0.3529:2,0:45.2:1:32.3:1:0.52941:0:31.6:24:0.3529:0:0.1 0/1:16:6:4,2:2,8:10,6:0.375:2,2:13.5:1:29.7:1:0.11813:6.82:26.2:12:0.375:0.3125:0 +1 145273345 . T C 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.15528;SOR=3.46379;LSEQ=AGGACTGCCAGTACTCGACA;RSEQ=CTCATCCATGCTTTGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:2:1,1:179,183:362,2:0.0055:2,2:21.5:1:33.5:1:1:1.02:49:4:0.0056:0:2.5 0/1:319:6:3,3:157,156:313,6:0.0188:2,2:20.5:1:32.8:1:1:1.00639:34.3:12:0.0189:0:1.3 +1 145273703 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCAGGTGCGGTGGCG;RSEQ=ACGCTTGCAATCCCAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:1,10:11,2:0.1538:2,0:18:1:30:0:1:0:21.5:4:0.1538:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:33:0:1:0:21:2:1:0:0 +1 145281363 . CTTTAG TTTAT 48 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGAGTTTTGTTATCCTTC;RSEQ=GTAAGGAGTGCCAATGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:12:3:1,2:5,3:8,3:0.25:2,2:9:1:30.4:1:0.54545:2.97405:59:6:0.2727:0.0833:1.3 +1 145281408 . C T 60 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGATGCCTGCCTGTCTCATC;RSEQ=CTGTGCAAATGGAAGTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:13:4:2,2:5,4:9,4:0.3077:2,2:12.8:1:30:1:1:1.22862:59.3:8:0.3077:0:1.8 +1 145281824 . T G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02222;SOR=Inf;LSEQ=AGGGAAGTGAGAATTTTGTG;RSEQ=GGGGTGGGTTGCTAGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:8,0:0:2,0:9.5:1:30.6:1:1:0:56.9:16:1:0:0.4 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:32:0:1:0:60:4:1:0:1 +1 146788870 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATCTGCAGGCATAGGAG;RSEQ=GAACCAGAGGAATATGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:29:1:29.5:1:1:1.73:60:4:0.4:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:24:1:27.5:1:1:0:53:4:1:0:0.5 +1 147282258 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5312;SOR=0;LSEQ=TCCACTTGACAAGGTAAGTC;RSEQ=CATGGCCCAGCCCAAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:31,1:32,2:0.0588:1,0:19.5:1:33:1:1:0:60:4:0.0588:0:1 0/0:19:0:0,0:19,0:19,0:0:1,0:23.7:1:30.9:1:1:0:60:38:1:0:0.1 +1 147282416 . T C 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=AGTAAATATGTTCATAGATA;RSEQ=CTAGAGATGCAAGCGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:327,188:515,0:0:2,0:25.3:1:30.5:1:1:0:60:102:1:0:0.7 0/1:287:7:4,3:162,118:280,7:0.0244:2,2:20.7:1:30.6:1:1:1.02957:60:14:0.0249:0:2.3 +1 147282446 . C T 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04615;SOR=1.40176;LSEQ=CAAGCGGCCTAGGAGAAGGA;RSEQ=GGGACAGTTATGTCCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:634:479:262,217:78,75:153,479:0.7555:2,2:25.4:1:30.8:1:0.45654:1.16:59.9:94.8:0.7548:0:1.2 1/1:352:286:160,126:35,31:66,286:0.8125:2,2:25.3:1:29.6:1:0.68235:1.12:60:39.857:0.8087:0:1.2 +1 147282508 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.34837;LSEQ=GTGTCAAAACCTATTCCCGC;RSEQ=ACCACAAACCTCTTCTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:123:41,82:157,271:428,123:0.2232:2,2:28.1:1:29.5:1:0.52374:1.15836:60:29.75:0.2204:0:1.6 0/1:308:28:12,16:126,152:278,28:0.0909:2,2:28.4:1:27.9:1:0.84451:1.10488:60:56:0.0918:0:1.4 +1 147282541 . A G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04934;SOR=Inf;LSEQ=TTCTATTGCTCCAAATTCCC;RSEQ=GCTTTGGGAAAAAATGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:90,255:345,0:0:2,0:23.7:1:31.2:1:1:0:60:33.5:1:0:0.3 0/1:202:3:1,2:62,136:198,3:0.0149:2,2:19.3:1:29:1:1:1.10:60:6:0.0155:0:1 +1 148878150 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCATGAGCCACCATGCCCA;RSEQ=GCTGGAGTGCAGTGGCGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:30.5:1:1:0:48:4:1:0:2.5 +1 148888410 . AGTTTTGTTTT A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=40;MSI=10.000;MSILEN=5;SSF=1;SOR=1.06457;LSEQ=AACTCTCAACTCCAGACTAA;RSEQ=GTTTTGTTTTGTTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:0,9:0,14:14,9:0.36:1,0:36.8:1:31.9:1:1:0:34.7:18:0.36:0:0 0/1:8:3:0,3:1,4:5,3:0.375:2,0:26.7:1:31:1:1:0:30:6:0.375:0.125:0.3 +1 148889551 . TAA T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.45185;SOR=0;LSEQ=TCAGTATATTCCATTTTTTT;RSEQ=AAAAATGTACAAATATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:74:69,5:0,0:0,74:1:0,2:30.3:1:30.3:1:1:0:21.1:148:1:0:0.1 1/1:61:60:54,6:0,0:0,60:0.9836:0,2:30.2:1:29.4:1:1:0:21.1:120:0.9836:0:0.2 +1 148890360 . G T 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=AATCTGCTTCAATCATATGG;RSEQ=TGTTCTATCCAAATTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:31.3:1:32.5:1:1:0:40.5:8:1:0:0 1/0:4:2:1,1:0,2:2,2:0.5:0,2:10:0:31.5:1:1:0:22:4:0.5:0:1 +1 148891116 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCTGCCTCAGCCTCACG;RSEQ=ACAGCTGGGATTACAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:34:0:1:0:33:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 149785233 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20076;SOR=Inf;LSEQ=GGCAGTCTGCTTAGTACGGG;RSEQ=CATGCTGTCTCATTGATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:91,86:177,0:0:2,0:16.5:1:31.6:1:1:0:57.6:58:0.9943:0:0.2 0/1:145:2:1,1:74,68:142,2:0.0138:2,2:8:1:28:1:1:1.08758:60:4:0.014:0:1 +1 149857769 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25875;SOR=0;LSEQ=GAGCCTTTGGAGTCAAGCAG;RSEQ=CGGCGACTCGAGCGAGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:2,1:37,14:51,3:0.0556:2,2:16.7:1:30.3:1:1:1.31427:60:6:0.0556:0:1.3 0/0:40:0:0,0:27,13:40,0:0:2,0:18:1:30.1:1:1:0:60:80:1:0:0.1 +1 149857790 . C T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.50634;SOR=0;LSEQ=CGGCGACTCGAGCGAGCGAG;RSEQ=GCCAGGTCCCGGCAGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:40,25:65,2:0.0299:2,2:15:1:25.5:1:1:1.58836:51:4:0.0299:0:1.5 0/0:50:0:0,0:31,19:50,0:0:2,0:25.6:1:30.2:1:1:0:57.6:100:1:0:0.1 +1 149857797 . T C 139 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCGAGCGAGCGAGCGCCAGG;RSEQ=CCCGGCAGGGACTCACTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:23:14,9:35,23:58,23:0.284:2,2:22.4:1:30.9:1:1:1.02:50:22:0.275:0:1.1 0/0:56:0:0,0:35,21:56,0:0:2,0:27.2:1:28.7:1:1:0:53.9:112:1:0:0.1 +1 149858030 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19935;SOR=Inf;LSEQ=CCATGGCCTTGGACGAGATG;RSEQ=CGGTGTCGGGGTGGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:34,41:75,0:0:2,0:21.1:1:30.7:1:1:0:26.5:24:1:0:0.1 0/1:61:2:1,1:27,32:59,2:0.0328:2,2:8.5:1:27:1:1:1.18:21:4:0.0333:0:1.5 +1 149858103 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49929;SOR=0;LSEQ=CTCTTTGCGGCTGCGCTTGC;RSEQ=CTTCTTGCCGTCTTTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:25,56:81,2:0.0241:2,2:16.5:1:29:1:0.531:2.22:26:4:0.0247:0:1.5 0/0:72:0:0,0:26,46:72,0:0:2,0:17.8:1:30.3:1:1:0:37.6:144:1:0:0.2 +1 150546790 . A ATTT 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=7.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=TGATTTTAAAGAGGTTTTTG;RSEQ=TTTTACTTGGAGGTTTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:21.3:1:31.5:1:1:0:60:8:0.4:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:27.3:1:1:0:60:4:1:0.5:1 +1 150546865 . A T 92 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.73141;LSEQ=AAAACCCAACACCTCTAATT;RSEQ=GAATTGAAGAAAGGAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:13,0:13,9:0.4091:1,0:17.3:1:29.1:1:1:0:60:8:0.381:0:1.1 0/1:3:1:0,1:2,0:2,1:0.3333:0,0:25:0:31:0:0.33333:0:60:2:0.3333:0:2 +1 150547050 . A AT 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.99209;LSEQ=TGTATTTGAATAAAAGATTT;RSEQ=TTTTTTTTTCTCAGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:566:18:13,5:380,167:547,18:0.0318:2,2:18.6:1:30.1:1:1:1.14:60:36:0.0324:0.0071:0 0/1:507:16:9,7:344,147:491,16:0.0316:2,2:22.5:1:28.4:1:0.27118:1.81766:59.7:15:0.0302:0.0039:0.2 +1 150547292 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16564;SOR=Inf;LSEQ=TCACTGGGAGCGCCATCCTT;RSEQ=TAAGCAAATCCTCCCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:6,155:161,0:0:1,0:23.8:1:32.9:1:1:0:60:25.833:1:0:0.1 0/1:111:2:1,1:7,102:109,2:0.018:2,2:10.5:1:28:1:0.13956:13.70:60:4:0.0182:0:1 +1 150549754 . C T 39 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.31402;SOR=4.1797;LSEQ=CTGGCTAGGTTGCTAGGGTG;RSEQ=AACTCTAGGAAGTTACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:1:0,1:209,37:246,1:0.004:2,0:1:0:23:0:0.15385:0:60:2:0.0041:0:1 0/1:179:3:1,2:146,30:176,3:0.0168:2,2:7.7:1:25:1:0.08285:9.54653:60:6:0.017:0:1 +1 150549800 . TTGG T 93 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.18144;SOR=2.19121;LSEQ=TCCAACTGCATAAACTGGTT;RSEQ=TGGTGGTGGTGGTTGGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:580:5:4,1:352,222:574,5:0.0086:2,2:22.4:1:32.2:1:0.65369:2.52:60:10:0.0087:0.0017:0.4 0/1:481:9:4,5:290,182:472,9:0.0187:2,2:20.7:1:29.6:1:0.31978:1.98883:60:18:0.0191:0.0062:0.2 +1 150550019 . T TA 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46971;SOR=1.59788;LSEQ=AGTATGGGTTTCTGCTCTCT;RSEQ=ACAACACTACTATCCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:147:134:10,124:6,6:12,134:0.9116:2,2:23.3:1:30.3:1:0.00042:11.97619:60:32.5:0.9155:0.1497:0.1 1/1:105:99:8,91:2,4:6,99:0.9429:2,2:25.3:1:29.6:1:0.09994:5.52341:60:32:0.9412:0.1333:0.1 +1 150551256 . G A 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCAACCCACCCTTGGCG;RSEQ=GTGAGTCCGGGGAGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1104:0:0,0:700,402:1102,0:0:2,0:24.2:1:30.9:1:1:0:60:99.182:0.9982:0:0.1 0/1:827:35:25,10:500,289:789,35:0.0423:2,2:23.9:1:28.3:1:0.37374:1.44:60:34:0.0418:0:1.1 +1 150551295 . T C 212 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAAAAGGGAGTGAGGCC;RSEQ=TGGCGATTAATGAACCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1722:0:0,0:933,789:1722,0:0:2,0:25.6:1:31.2:1:1:0:60:73.87:1:0:0.2 0/1:1512:119:73,46:768,625:1393,119:0.0787:2,2:25.6:1:30.8:1:0.2117:1.29:60:238:0.0795:0:1.2 +1 150551491 . GTCC G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=1.03079;LSEQ=AGCGACTGCCGGTACAACTC;RSEQ=TCCTCCTCCTCTGCTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1721:22:8,14:807,887:1694,22:0.0128:2,2:31.4:1:31.8:1:0.39089:1.59174:60:44:0.013:0:0.1 0/1:1898:25:14,11:919,949:1868,25:0.0132:2,2:28.3:1:30.4:1:0.54987:1.31:59.8:50:0.0134:0.0016:0.3 +1 150551729 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.25145;SOR=0;LSEQ=CGAAGAAAAGCAGCCTCGCG;RSEQ=GGGTCGCGGTGACGTCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:100,181:281,3:0.0106:2,2:39.3:1:31.7:1:1:1.1046:60:6:0.0107:0:1 0/0:251:0:0,0:92,159:251,0:0:2,0:24.3:1:30.7:1:1:0:60:250:1:0:0.2 +1 150551732 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09679;SOR=Inf;LSEQ=AGAAAAGCAGCCTCGCGGGG;RSEQ=TCGCGGTGACGTCGGGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:99,179:278,0:0:2,0:24.4:1:31.7:1:1:0:60:45.333:1:0:0.2 0/1:237:3:2,1:87,147:234,3:0.0127:2,2:9.3:1:28.3:1:0.55806:3.36:60:6:0.0129:0:1.3 +1 150551777 . G A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.69252;LSEQ=CGCCAATGGGCGGCGGCCGC;RSEQ=CGACCCTCCGGGAGTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:95,71:166,2:0.0119:2,2:44:1:31:1:1:1.33566:60:4:0.0121:0:1 0/0:121:1:1,0:64,56:120,1:0.0083:2,0:1:0:25:0:1:0:60:2:0.0085:0:1 +1 150552042 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.08189;LSEQ=CCGCCTGGCTGAGAAAACTG;RSEQ=GGAAGACCCCGACTCCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:571:337:106,231:75,157:232,337:0.5902:2,2:22.1:1:31.2:1:0.85487:1.041:60:32.7:0.586:0:1.2 0/1:532:56:15,41:157,317:474,56:0.1053:2,2:20.4:1:29.7:1:0.36905:1.35298:60:55:0.1048:0:1.2 +1 150552150 . CT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGGTGGCGCCAGCGAACT;RSEQ=TTTTTTTTAAAAAAAGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:0,2:0,92:92,2:0.0213:1,0:32:1:33.5:1:1:0:60:4:0.0217:0:0 0/0:45:0:0,0:1,44:45,0:0:1,0:20.4:1:30.4:1:1:0:60:90:1:0:0.1 +1 150552202 . C T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04615;SOR=Inf;LSEQ=GGGAAAGGGGCGGCAGCTTC;RSEQ=GGAGGGTTGCGCACGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:1,19:20,0:0:1,0:21.5:1:29.4:1:1:0:60:40:1:0:0.3 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:5.5:1:30.5:1:1:0:60:4:0.3333:0:1 +1 150552330 . G T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87898;LSEQ=TTCGGAGGCTCTGAGTGCCG;RSEQ=TTACGTAACGGCGGCTCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:13,0:19,0:19,13:0.4063:1,1:20.6:1:29.3:1:1:0:60:12:0.4:0:1.9 0/1:24:9:9,0:15,0:15,9:0.375:1,0:25.7:1:27.2:1:1:0:58.6:8:0.3636:0:2 +1 150552392 . C G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88906;SOR=0.94832;LSEQ=CTCCTGGGCTCGAGCTCTTT;RSEQ=CATGAGCACCTCGGGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:53:50,3:66,1:67,53:0.4417:1,2:23.3:1:31.8:1:0.32002:3.91708:60:16.667:0.4386:0:1.3 0/1:91:39:37,2:49,3:52,39:0.4286:2,2:21.2:1:32.3:1:1:1.13:59.7:78:0.4333:0:1.3 +1 150552407 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19601;SOR=Inf;LSEQ=TCTTTCCATGAGCACCTCGG;RSEQ=CCTTCTCGTGGCTACCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:148,15:163,0:0:2,0:22:1:31.2:1:1:0:60:31.6:1:0:0.5 0/1:130:2:1,1:111,17:128,2:0.0154:2,2:24:1:26:0:0.25868:6.37397:60:4:0.0156:0:1.5 +1 150552622 . T G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=1.60385;LSEQ=TTGGGGACTTGTGGTTATTT;RSEQ=GCACAGCTCTCTACTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:273:88,185:169,286:455,273:0.374:2,2:23.4:1:31.3:1:0.20007:1.24188:60:67.25:0.3721:0:1.1 0/1:660:323:121,202:128,208:336,323:0.4894:2,2:26.2:1:30.5:1:0.87268:1.0273:60:106.667:0.4885:0:1.1 +1 150552718 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52143;SOR=0;LSEQ=AAGTGGACTAAGCTAAAACT;RSEQ=CCACAGCTAAACTATTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:1,114:115,2:0.0171:1,0:22:1:32:0:1:0:60:4:0.0172:0:1 0/0:75:0:0,0:2,73:75,0:0:1,0:24.7:1:32.2:1:1:0:59.8:150:1:0:0.2 +1 151272735 . T C 28 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12918;SOR=Inf;LSEQ=TAACACTAGGAAAAGGTGGG;RSEQ=CACTAAACTTTGCCTCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:51,39:90,0:0:2,0:23.5:1:29.6:1:1:0:59.9:180:1:0:0.2 0/1:51:2:1,1:28,21:49,2:0.0392:2,2:6:0:28.5:1:1:1.32572:60:4:0.0392:0:1 +1 151272748 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13572;SOR=Inf;LSEQ=AGGTGGGTCACTAAACTTTG;RSEQ=CTCCGCAAAATTTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:50,40:90,0:0:2,0:29.5:1:31.5:1:1:0:59.9:44:1:0:0.2 0/1:53:2:1,1:26,25:51,2:0.0377:2,2:6.5:1:27.5:1:1:1.03924:60:4:0.0385:0:1.5 +1 151678674 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCATAACGAGGGCATTC;RSEQ=TGTCTCCCAAGGCCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:15,6:21,2:0.087:2,2:31:1:29.5:1:0.52569:2.39047:60:4:0.0909:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:24.5:1:30:1:1:0:60:20:1:0:0.1 +1 151678707 . TTGC T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03312;SOR=Inf;LSEQ=CCCCAGCCAGCACCTTCTCT;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:22,16:38,0:0:2,0:27.3:1:30.9:1:1:0:59.9:76:1:0:0.3 0/1:19:3:1,2:8,8:16,3:0.1579:2,2:15.7:1:30:1:1:1.9301:55.3:6:0.1579:0.0526:0.7 +1 152330803 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53927;SOR=0;LSEQ=CACCGCGCCTAGCTGAGTCC;RSEQ=TTTTAAGTAGATGGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:119,20:139,2:0.0142:2,2:19:1:34:1:0.2766:5.83099:60:4:0.0143:0:1 0/0:78:0:0,0:65,13:78,0:0:2,0:20.9:1:30.5:1:1:0:60:77:1:0:0.1 +1 152330817 . G T 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54024;SOR=0;LSEQ=GAGTCCTTTTTAAGTAGATG;RSEQ=AATAAAATGCTGGCATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:157,35:192,2:0.0103:2,2:12:1:24.5:1:0.33748:4.43705:60:4:0.0104:0:1 0/0:107:0:0,0:87,20:107,0:0:2,0:20.9:1:30.5:1:1:0:60:106:1:0:0.1 +1 152330829 . G T 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTAGATGGAATAAAATGCT;RSEQ=GCATTTTATTTTTGATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:79:56,23:134,43:177,79:0.3086:2,2:21.9:1:30.7:1:0.44125:1.2786:59.9:158:0.3123:0:1.1 0/0:145:0:0,0:105,40:145,0:0:2,0:21.2:1:31:1:1:0:60:144:1:0:0.1 +1 152330869 . A G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TAATCATGGCTATTTTGTCA;RSEQ=CTCCCTATGTAGATGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:482:0:0,0:280,202:482,0:0:2,0:26.4:1:29.6:1:1:0:60:47.2:1:0:0.2 0/1:262:9:6,3:149,104:253,9:0.0344:2,2:30.3:1:31.1:1:0.74162:1.39:60:18:0.0346:0:1.6 +1 152330900 . CT C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00664;SOR=Inf;LSEQ=AGATGATTTCCCTTTCTATA;RSEQ=TTTTTTTCCATTTGATAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:284,270:554,0:0:2,0:26.6:1:31:1:1:0:60:68.25:1:0:0.2 0/1:323:5:2,3:166,152:318,5:0.0155:2,2:36.4:1:31.6:1:0.6738:1.63566:60:10:0.0156:0:0 +1 152330945 . T C 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTATTAATTCGTGTCCTAG;RSEQ=ATAATTTTATTTTCTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:186,266:452,0:0:2,0:24.3:1:29:1:1:0:60:89.4:1:0:0.2 0/1:281:44:18,26:98,139:237,44:0.1566:2,2:25.6:1:31.6:1:1:1.01832:60:88:0.1583:0:1.2 +1 152330982 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13809;SOR=Inf;LSEQ=CTTTTTCTAAGGAAAAGCCT;RSEQ=GGTGTATGAGAAAGTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:106,206:312,0:0:2,0:25.3:1:31.5:1:1:0:60:61.4:1:0:0.2 0/1:185:2:1,1:59,123:182,2:0.0108:2,2:28.5:1:30:1:0.54704:2.08:60:4:0.0109:0:1 +1 152331013 . G A 143 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.06305;LSEQ=AAAGTCTGAGAGTCTATGAG;RSEQ=TAGGAGTGCATAGGTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:26:7,19:46,140:186,26:0.1226:2,2:22.5:1:30.6:1:0.81109:1.12:60:52:0.125:0:1.1 0/0:115:1:1,0:28,86:114,1:0.0087:2,0:1:0:25:0:0.25217:0:60:2:0.0087:0:1 +1 153579668 . C T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=CTGACCTTTGGAGGTCAGGA;RSEQ=GGACCCAGAATCAGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:2,7:9,2:0.1818:2,2:10:0:29:1:0.49091:3.06:60:4:0.2222:0:1 0/0:6:0:0,0:1,5:6,0:0:2,0:27.7:1:28.5:1:1:0:60:12:1:0:0 +1 153907309 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.11281;SOR=Inf;LSEQ=TGCTGCTGCTGCTGCTGTTG;RSEQ=TGCTGCTGCTGCTGTTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:31,0:0:2,0:26.7:1:33.3:1:1:0:58.5:62:1:0:0.2 0/1:30:3:1,2:14,13:27,3:0.1:2,2:23:1:23.3:1:1:2.10086:60:2:0.069:0:1.3 +1 153918029 . GAC G 96 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=11.000;MSILEN=2;SSF=0.31902;SOR=0.44846;LSEQ=TCTTCATCACCTGGCCTCTG;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:8,0:18,0:18,8:0.2857:1,0:35.9:1:32:1:1:0:60:16:0.2857:0:0.5 0/1:20:3:3,0:14,1:15,3:0.15:1,0:21.7:1:32:0:1:0:60:6:0.1579:0:0 +1 153918113 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14486;SOR=Inf;LSEQ=AAATTTAGACTCCACTTCTG;RSEQ=GAGGTAAAGCCAGGAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:75,56:131,0:0:2,0:28.4:1:30.8:1:1:0:60:31.75:1:0:0.3 0/1:81:2:1,1:42,37:79,2:0.0247:2,2:41.5:1:30:1:1:1.13335:60:4:0.0247:0:1 +1 153918158 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53212;SOR=0;LSEQ=AGCCTCTTGATTTAATTCTG;RSEQ=GGCACAGACCTGTCCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:55,68:123,2:0.016:2,2:8.5:1:30.5:1:1:1.23:60:4:0.0163:0:1 0/0:73:0:0,0:34,39:73,0:0:2,0:26.8:1:30.3:1:1:0:60:146:1:0:0.1 +1 153918414 . T G 30 v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGTGACGGGAAGTTCGGG;RSEQ=TGGGGCAGAGGGCGCGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:5,2:0.2857:2,2:5:0:30.5:1:1:3.16:60:4:0.2857:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 154842199 . G GGCTGCTGCT 94 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=43;MSI=17.000;MSILEN=3;SSF=0.01771;SOR=0;LSEQ=GCTGAGACAGGGGATGCGGT;RSEQ=GCTGCTGCTGCTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:7,1:2,3:5,8:0.5714:2,2:31.6:1:31.6:1:0.21678:8.37:50.6:16:0.5714:0.1429:1 0/0:8:0:0,0:3,1:4,0:0:2,0:43:1:27.5:1:1:0:60:8:0.5:0:0 +1 155870416 . G A 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=62.63952;LSEQ=TCTTCCTTGGTGACCTTTAA;RSEQ=GGCAAAATGTGAGAAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:702:502:153,349:54,146:200,502:0.7151:2,2:23.6:1:31.5:1:0.40933:1.19:59.8:124.5:0.7155:0:1.1 1/1:476:473:171,302:0,0:0,473:0.9937:0,2:26.1:1:29.7:1:1:0:59.9:66.571:1:0:1.1 +1 155870489 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52415;SOR=0;LSEQ=CTGAATGCACCACCACCTTA;RSEQ=CACAAAGAAAGCTTCTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:1,167:168,2:0.0118:1,2:19:1:31.5:1:0.02346:118.34:60:4:0.0119:0:1 0/0:107:0:0,0:4,103:107,0:0:1,0:3:0:16:0:1:0:60:0:0:0:2 +1 155873960 . A G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=CCACCTTGGCCCCGCAAAGT;RSEQ=CTGGTGTGAGCCACCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:69:46:46,0:22,1:23,46:0.6667:1,1:24:1:31.6:1:0.33333:0:59.5:45:0.6716:0:1 1/1:32:32:32,0:0,0:0,32:1:0,1:23.5:1:31.8:1:1:0:58.5:31:1:0:1.1 +1 155874661 . C A 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02707;SOR=Inf;LSEQ=AGAAATGCCTATTTAAAACT;RSEQ=ATCTTACAGAGTAGTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:80,331:411,0:0:2,0:23.1:1:32.3:1:1:0:60:67.5:1:0:0.1 0/1:282:4:2,2:73,205:278,4:0.0142:2,2:17.5:1:24.5:1:0.28829:2.80:60:3:0.0107:0:1.5 +1 155874765 . G GT 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.36872;SOR=2.50565;LSEQ=AAACTGAGTCTTCAACTGAA;RSEQ=TTTTTTTTTCCACATAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:0,2:1,43:44,2:0.0435:1,0:46.5:1:30.5:1:1:0:60:4:0.0435:0:1 0/1:29:3:0,3:1,25:26,3:0.1034:1,0:13.3:1:28.4:1:1:0:60:6:0.1034:0.069:0.3 +1 155876706 . G T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGTTTGAGACCAGCCT;RSEQ=GGCAATAGAGCGAGACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 155880070 . G GA 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.57134;SOR=0;LSEQ=TGGCTTATGACATAAAGTCT;RSEQ=AAAAAAAAAGAAATATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:4,0:47,0:47,4:0.0784:1,0:26.8:1:29.8:1:1:0:60:8:0.0784:0:0 0/0:20:0:0,0:20,0:20,0:0:1,0:21.7:1:31.8:1:1:0:60:40:1:0:0.1 +1 155880159 . T C 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTCCAAAAAAGCCTCAAAA;RSEQ=ATAAATAGTTAGAAACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:159,29:188,0:0:2,0:22.2:1:30.6:1:1:0:60:93:1:0:0.1 0/1:151:33:27,6:90,28:118,33:0.2185:2,2:25.2:1:31.5:1:0.63917:1.40:60:66:0.22:0:1 +1 155880391 . T C 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGATAGCAAGTATCCCATC;RSEQ=GGTCATTTAAGTACTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:253,135:388,0:0:2,0:23.6:1:32:1:1:0:59.7:193:1:0:0 0/1:232:63:42,21:95,73:168,63:0.2716:2,2:25.1:1:29.5:1:0.1785:1.53:60:62:0.2696:0:1.1 +1 155880573 . C G 316 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=233.59457;LSEQ=TGTCCTCTTGGGGCCTTCCT;RSEQ=GGTTGCCCCGAGGAAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1706:1255:655,600:230,215:445,1255:0.7356:2,2:25.2:1:31.7:1:0.86853:1.02:60:65.053:0.7344:0:1.1 1/1:1298:1296:622,674:0,0:0,1296:0.9985:0,2:24.1:1:30.6:1:1:0:60:40.806:0.9984:0:1.1 +1 155880760 . C CA 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00012;SOR=1.44324;LSEQ=GGTGGCCCTAAGAAACCCCC;RSEQ=CATCTTCACCCTCCCTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1331:945:277,668:116,267:383,945:0.71:2,2:25.3:1:29.4:1:0.74025:1.04768:59.8:54.588:0.7117:0.1375:0.1 1/0:1070:834:255,579:127,109:236,834:0.7794:2,2:27:1:28.4:1:0:2.64294:59.9:54.6:0.7793:0.043:0.1 +1 155880952 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95746;LSEQ=CACGTCTGCGGTACCCAGAG;RSEQ=TTCCGCCCCCTCCCCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:0,23:1,10:11,23:0.6765:2,1:19.9:1:31.3:1:0.32353:0:58.8:46:0.6765:0:1.1 1/0:12:8:0,8:0,4:4,8:0.6667:0,0:15.1:1:31.4:1:1:0:60:16:0.6667:0:1.1 +1 156267399 . AT A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TAAGTAGTGTATCTATAGTG;RSEQ=TTTTTTTTTCCTTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:27.5:1:1:0:60:4:1:0.5:0.5 +1 156268330 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02646;SOR=Inf;LSEQ=CCAGGCTGGTCTCGAACTCC;RSEQ=GACCTCAAGTGATCTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:23,0:23,0:0:1,0:23.6:1:31.7:1:1:0:58.9:46:1:0:0 0/1:5:2:2,0:3,0:3,2:0.4:0,0:26.5:1:30.5:1:1:0:54.5:4:0.4:0:1 +1 156268452 . A T 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34459;SOR=3.42782;LSEQ=CAGCCGCTCCAGGTCTTTCA;RSEQ=TCACATTTGGATGATCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:98,42:140,1:0.0071:2,0:1:0:25:0:0.30496:0:60:2:0.0071:0:1 0/1:125:3:1,2:74,48:122,3:0.024:2,2:10.7:1:22.7:1:0.56334:3.05522:60:2:0.0165:0:1.3 +1 156268453 . T C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.215;SOR=Inf;LSEQ=AGCCGCTCCAGGTCTTTCAA;RSEQ=CACATTTGGATGATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:100,44:144,0:0:2,0:24.9:1:31.1:1:1:0:60:288:1:0:0.1 0/1:125:2:1,1:74,49:123,2:0.016:2,2:6.5:1:29.5:1:1:1.50505:60:4:0.0167:0:1.5 +1 156268463 . A T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2169;SOR=Inf;LSEQ=GGTCTTTCAATCACATTTGG;RSEQ=TGATCTTCCAGATCGTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:100,52:152,0:0:2,0:26:1:30.1:1:1:0:60:29.4:1:0:0.1 0/1:133:2:1,1:75,56:131,2:0.015:2,2:38:0:31:1:1:1.33629:60:4:0.0155:0:1 +1 156268473 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=TCACATTTGGATGATCTTCC;RSEQ=GATCGTCATAGAGTGATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:108,57:165,2:0.012:2,2:42.5:1:30.5:1:1:1.88708:60:4:0.0121:0:1 0/0:145:0:0,0:84,61:145,0:0:2,0:26:1:29.6:1:1:0:60:71.5:1:0:0.2 +1 156268495 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=ATCGTCATAGAGTGATCTGA;RSEQ=GATGTCCAGTCTCCTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:135,66:201,0:0:2,0:25.3:1:31.6:1:1:0:60:200:1:0:0.1 0/1:163:11:7,4:85,67:152,11:0.0675:2,2:21.1:1:29.4:1:0.75755:1.38:60:22:0.0679:0:1.2 +1 156268694 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52055;SOR=0;LSEQ=CTCTGAAGAGCCAAGGGTGG;RSEQ=TTCGGAAGTTGTGGATGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:48,143:191,2:0.0104:2,2:24.5:1:29:1:0.4443:2.96:60:4:0.0106:0:1 0/0:126:0:0,0:38,88:126,0:0:2,0:20.9:1:30.8:1:1:0:59.8:125:1:0:0.1 +1 156268892 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21923;SOR=Inf;LSEQ=CCATCTCCTCCTCGGCGCCC;RSEQ=ACTCTTCCTGGCAGTACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:6,15:21,0:0:2,0:27.4:1:30.6:1:1:0:60:42:1:0:0 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:25:1:29.5:1:1:1.11803:60:4:0.1053:0:1 +1 156450873 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTTCCCCGACCTCCTTC;RSEQ=TCAGGGTTCCCAGCATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:29.5:1:1:0:60:4:1:0:1 +1 156452096 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47253;SOR=0;LSEQ=GGTTTGCATGTGTGTGCGCA;RSEQ=AGGTGAGGGGCTACAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:6,0:6,2:0.25:0,2:14.5:1:31.5:1:0.25:0:60:4:0.25:0:1.5 0/0:6:0:0,0:5,1:6,0:0:2,0:23:1:31:1:1:0:60:12:1:0:0.2 +1 156452238 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17248;SOR=Inf;LSEQ=TATGGGCCCACCTCGATGAT;RSEQ=TCGGCGTTGGTGCGGCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:96,30:126,0:0:2,0:22.8:1:32:1:1:0:60:62:1:0:0.1 0/1:90:2:1,1:56,32:88,2:0.0222:2,2:16:1:27.5:1:1:1.73851:60:4:0.0227:0:1 +1 156452293 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17839;SOR=Inf;LSEQ=ACTCCGTGTACTTGAGCAGC;RSEQ=CCTTGTCCATGTCGGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:107,65:172,0:0:2,0:25.7:1:29.6:1:1:0:60:42:1:0:0.1 0/1:127:2:1,1:75,49:124,2:0.0157:2,2:23.5:1:28.5:1:1:1.52525:60:4:0.0161:0:1.5 +1 156452315 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51639;SOR=0;LSEQ=CTTGTCCATGTCGGTGCTGG;RSEQ=GTACTGGAACAGCTTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:120,72:192,2:0.0103:2,2:34.5:1:29.5:1:1:1.66202:60:4:0.0104:0:1 0/0:133:0:0,0:76,57:133,0:0:2,0:24.1:1:29.9:1:1:0:60:43.333:1:0:0.1 +1 156452435 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18434;SOR=Inf;LSEQ=CCGCTTGGTGAAAGTCACCT;RSEQ=CAGAGAAGGATGGGTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:74,133:207,0:0:2,0:23:1:32:1:1:0:60:68:1:0:0.1 0/1:157:2:1,1:56,99:155,2:0.0127:2,2:5:1:27:1:1:1.76:60:4:0.0129:0:1 +1 156452453 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.55479;SOR=0;LSEQ=CTGCAGAGAAGGATGGGTGG;RSEQ=CGGCCAGATCTGGCTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:2,1:39,102:141,3:0.0208:2,2:12.3:1:28:1:0.19518:5.16:60:6:0.021:0:1 0/0:81:0:0,0:20,61:81,0:0:2,0:24.9:1:31.1:1:1:0:60:162:1:0:0.1 +1 156452783 . A T 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTATGACCTAAGGCTTGCA;RSEQ=ATGGCTCTGGGATGGGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17.5:1:26.5:1:1:0:44:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 156468022 . GC G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGAGCCAGGATGCCCAG;RSEQ=CCTCCAGCCCAGGGGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 156785356 . T C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGAGGATGAAGAAACATGA;RSEQ=GCAGGAAGTCACCCTAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:24,0:0,0:0,24:1:0,1:24.6:1:33.2:1:1:0:60:48:1:0:1.1 1/1:6:6:6,0:0,0:0,6:1:0,0:18.7:1:33.3:1:1:0:60:12:1:0:1 +1 156785617 . G A 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.77539;LSEQ=AGGGAGTGAGTGGGCAACTC;RSEQ=GCGCATGAAGGAGGTACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1265:806:406,400:211,248:459,806:0.6372:2,2:25.1:1:31:1:0.14366:1.19:60:72.273:0.636:0:1.2 1/0:939:711:359,352:113,113:226,711:0.7572:2,2:24.5:1:29.7:1:0.93916:1.02:60:78:0.7589:0:1.2 +1 156785647 . TTC T 108 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.13752;SOR=2.01552;LSEQ=GGAGGTACTCCTCATTTTCG;RSEQ=TCTCTCTCTGTGCCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1296:9:4,5:580,707:1287,9:0.0069:2,2:23.7:1:29.6:1:1:1.02544:60:18:0.007:0.0015:0.8 0/1:1007:14:6,8:471,521:992,14:0.0139:2,2:29.5:1:28.6:1:0.79302:1.20515:60:28:0.0142:0:0.4 +1 156785653 . C G 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ACTCCTCATTTTCGTTCTCT;RSEQ=TCTCTGTGCCCCAGCCCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1266:43:17,26:547,672:1219,43:0.034:2,2:28.6:1:32.6:1:0.53505:1.24471:59.5:86:0.0343:0:1.9 0/0:988:0:0,0:463,524:987,0:0:2,0:25.7:1:31:1:1:0:60:108.667:0.999:0:0.7 +1 156785762 . AG A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52215;SOR=1.2034;LSEQ=GAGGGTGGGAGAGATGAGGG;RSEQ=CTGCACCACGCTGCCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:119:4,115:0,84:84,119:0.5862:1,1:22.5:1:33:1:0.1437:0:59.9:118:0.5842:0.1773:1.5 1/0:92:58:3,55:2,32:34,58:0.6304:2,2:23:1:30.7:1:1:1.14411:59.9:57:0.6264:0.1413:1.5 +1 156785771 . A G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.26236;SOR=1.38598;LSEQ=AGAGATGAGGGAGCTGCACC;RSEQ=CGCTGCCGCCCCAGGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:156:87:2,85:0,69:69,87:0.5577:1,1:26.2:1:32.5:1:0.50347:0:59.9:42.5:0.5629:0:2 1/0:77:49:3,46:1,27:28,49:0.6364:1,2:25.1:1:30.1:1:1:1.75:60:15.333:0.6216:0:2 +1 156785779 . G A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62103;SOR=1.22976;LSEQ=GGGAGCTGCACCACGCTGCC;RSEQ=CCCCAGGTTTCCACTCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:127:88:2,86:0,39:39,88:0.6929:1,1:27.7:1:30.2:1:1:0:60:87:0.696:0:1.9 1/0:68:50:2,48:1,16:17,50:0.7353:1,1:26.2:1:28.2:1:1:1.49015:60:11.5:0.7302:0:1.9 +1 156811493 . A C 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52365;SOR=0;LSEQ=TGGTGAAGATCCCATCTTTG;RSEQ=GGGACTCGGGGGCCATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:85,62:147,2:0.0134:2,2:6:1:31:1:1:1.368:60:4:0.0136:0:1 0/0:94:0:0,0:52,41:93,0:0:2,0:27.8:1:29.5:1:1:0:60:186:0.9894:0:0.2 +1 156811747 . C A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07665;SOR=Inf;LSEQ=GAACTCATCCCATCCAAACC;RSEQ=CTCTGCCCTTGGACAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:227,12:239,0:0:2,0:23.8:1:31.5:1:1:0:60:58.75:1:0:0.1 0/1:92:2:1,1:82,7:89,2:0.0217:2,2:18:0:29:1:0.16899:11.02463:60:4:0.022:0:1 +1 156830711 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09244;SOR=Inf;LSEQ=CGGCTGCCCCGCCTGAGCGA;RSEQ=GCGGGCGCCGCCGCGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:24,0:0:2,0:21.8:1:31.9:1:1:0:60:48:1:0:0.6 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:20:0:32:1:1:1.22474:60:4:0.1818:0:1.5 +1 156830741 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.09315;SOR=Inf;LSEQ=GCCGCGATGCTGCGAGGCGG;RSEQ=CGGCGCGGGCAGCTTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:113,27:140,0:0:2,0:14.7:1:30:1:1:0:60:34:1:0:0.3 0/1:62:2:1,1:43,17:60,2:0.0323:2,2:33.5:1:31:1:0.49974:2.48658:60:4:0.0328:0:2 +1 156830742 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09184;LSEQ=CCGCGATGCTGCGAGGCGGA;RSEQ=GGCGCGGGCAGCTTGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:114,28:142,2:0.0139:2,2:11.5:1:30.5:1:0.36334:4.01812:60:4:0.0139:0:1 0/1:66:1:0,1:46,19:65,1:0.0152:2,0:1:0:23:0:0.30303:0:60:2:0.0154:0:1 +1 156830745 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09217;SOR=Inf;LSEQ=CGATGCTGCGAGGCGGACGG;RSEQ=GCGGGCAGCTTGGCTGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:131,33:164,0:0:2,0:15.8:1:32.2:1:1:0:60:81:1:0:0.2 0/1:72:2:1,1:50,19:69,2:0.0278:2,2:15.5:1:30:0:0.48692:2.59047:60:4:0.0294:0:1.5 +1 156830747 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.131;LSEQ=ATGCTGCGAGGCGGACGGCG;RSEQ=GGGCAGCTTGGCTGGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:137,35:172,2:0.0115:2,2:10.5:1:29.5:1:0.37194:3.8736:60:4:0.0118:0:1 0/1:77:1:0,1:53,23:76,1:0.013:2,0:1:0:23:0:0.31169:0:60:2:0.0133:0:1 +1 156830758 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.09062;SOR=Inf;LSEQ=CGGACGGCGCGGGCAGCTTG;RSEQ=CTGGCACAGCTGGGCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:186,52:238,0:0:2,0:20.8:1:32.1:1:1:0:60:78.333:1:0:0.2 0/1:103:2:1,1:71,29:100,2:0.0194:2,2:33:0:31:1:0.50379:2.42403:60:4:0.0196:0:2.5 +1 156830781 . C T 56 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.17394;LSEQ=GGCACAGCTGGGCTGCGGGG;RSEQ=CGGGCAGCCTGCTGGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:4:2,2:279,78:357,4:0.0111:2,2:27.5:1:28:1:0.21407:3.56044:60:8:0.0113:0:1 0/1:154:2:1,1:109,42:151,2:0.013:2,2:28.5:1:28:1:0.48443:2.57663:60:4:0.0135:0:2.5 +1 156830838 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0082;SOR=Inf;LSEQ=CGGGCGCCGCACCCTGCCCC;RSEQ=ATGCCTGCTGCCCCCACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:477,231:708,0:0:2,0:24.8:1:30.2:1:1:0:60:63.364:0.9971:0:0.1 0/1:442:5:2,3:275,162:437,5:0.0113:2,2:17.4:1:25.8:1:0.36683:2.54066:60:10:0.0115:0:1 +1 156830989 . G A 42 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3028;SOR=0;LSEQ=GGGGACAGGCAGGCATTGCA;RSEQ=TGCCCCGAGGGCGCGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:4:3,1:76,292:368,4:0.0108:2,2:6.5:1:21.3:1:0.03143:11.42:60:3:0.0082:0:1.5 0/0:203:0:0,0:48,155:203,0:0:2,0:21.9:1:31.1:1:1:0:60:39.6:1:0:0.1 +1 156830995 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11769;SOR=Inf;LSEQ=AGGCAGGCATTGCAGTGCCC;RSEQ=GAGGGCGCGGACTCGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:52,263:315,0:0:2,0:21.7:1:29.5:1:1:0:60:25.25:1:0:0.2 0/1:165:2:1,1:31,132:163,2:0.0121:2,2:19:1:28:1:0.35122:4.21:60:4:0.0123:0:1 +1 156831060 . ACGCAGCCTTCGGCGCTGCCCGGGCGTTCCTC A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.01238;SOR=Inf;LSEQ=CACGGCGGAAGGCTGGCACC;RSEQ=CGCAGCCGCCGCTGCCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:0,83:83,0:0:1,0:23.3:1:30.5:1:1:0:60:166:1:0:0.1 0/1:26:3:0,3:0,23:23,3:0.1154:1,0:31.3:1:30.4:1:1:0:60:6:0.1154:0.0385:0 +1 156834269 . G T 106 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=22.04299;LSEQ=AGCTCAGCATGGGCCTGGGG;RSEQ=AGACCAGAAGGTCAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:735:1:1,0:258,473:731,1:0.0014:2,0:3:0:13:0:0.35383:0:60:0:0:0:3 0/1:445:13:3,10:158,272:430,13:0.0292:2,2:26.9:1:28.7:1:0.39127:1.93369:60:26:0.0297:0:1.1 +1 156834364 . G A 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=GGAGAAGTCAGGAAGCTCAG;RSEQ=GCTTTGAGGGGTCTAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:140,144:284,0:0:2,0:25.5:1:31.5:1:1:0:59.8:55.8:0.9964:0:0.2 0/1:95:7:3,4:42,46:88,7:0.0737:2,2:21.1:1:30.9:1:1:1.21489:60:14:0.0778:0:1 +1 156834656 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04598;SOR=Inf;LSEQ=CAGACTTGGGCTGCTAATGG;RSEQ=CTTGGCTGTCCCCGGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:79,375:454,0:0:2,0:24.3:1:32.1:1:1:0:59.9:49.444:0.9978:0:0.1 0/1:255:3:2,1:57,194:251,3:0.0118:2,2:20:1:28:1:0.13566:6.74:60:6:0.012:0:1.7 +1 156834668 . C A 23 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.27242;SOR=3.84327;LSEQ=GCTAATGGGCTTGGCTGTCC;RSEQ=CGGGGAATGATTGCGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:1,0:49,319:368,1:0.0027:2,0:1:0:25:0:0.1355:0:60:2:0.0028:0:1 0/1:193:2:1,1:31,160:191,2:0.0104:2,2:5.5:1:23:0:0.30484:5.10:60:4:0.0108:0:1 +1 156834682 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11965;SOR=Inf;LSEQ=CTGTCCCCGGGGAATGATTG;RSEQ=GAGGAGGGCCCAAGCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:25,235:260,0:0:2,0:22.7:1:30.4:1:1:0:59.9:129:1:0:0.1 0/1:138:2:1,1:17,119:136,2:0.0145:2,2:6:1:27.5:1:0.24468:6.83:60:4:0.0147:0:1 +1 156836592 . CG C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1018;SOR=Inf;LSEQ=TCTGGTTGCCTAGGCCGGGG;RSEQ=GGGGAGCCAGATGTCAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:328,36:364,0:0:2,0:21.9:1:29.3:1:1:0:60:25:0.9943:0:0.2 0/1:172:2:1,1:146,22:168,2:0.0116:2,2:29:1:29:1:0.25298:6.51268:60:4:0.0123:0:0 +1 156836805 . A AGT 96 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.55409;SOR=0.5948;LSEQ=TTCCAGGGGCAAGAGCACCA;RSEQ=GTGTGTGTGTGCCTGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:867:9:3,6:271,587:858,9:0.0104:2,2:25.1:1:30.4:1:1:1.08:60:18:0.0107:0.0023:0.1 0/0:484:3:2,1:154,326:480,3:0.0062:2,2:32.7:1:32.3:1:0.24508:4.22:60:6:0.0063:0:0.3 +1 156836817 . C T 57 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46335;SOR=1.84003;LSEQ=GAGCACCAAGTGTGTGTGTG;RSEQ=CTGTGTGCACTTGGGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:722:4:2,2:185,533:718,4:0.0055:2,2:9.5:1:29.5:1:0.27673:2.88:60:8:0.0058:0:1 0/1:394:4:2,2:108,281:389,4:0.0102:2,2:16.5:1:28.8:1:0.31269:2.59:60:8:0.0104:0:1.5 +1 156836838 . T C 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00058;SOR=Inf;LSEQ=CTGTGTGCACTTGGGTCTGT;RSEQ=GGATGACATTGGGTCACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:82,418:500,0:0:2,0:24.6:1:30.2:1:1:0:60:40.667:1:0:0.1 0/1:266:7:2,5:55,203:258,7:0.0263:2,2:32.7:1:28.4:1:0.6454:1.47:60:14:0.0266:0:1 +1 156837463 . CT C 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTTTTCTTTTCTTTT;RSEQ=TTTTTTTTTTTTATGAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:37.5:1:31.5:1:0.33333:0:57.5:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 156837802 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0873;SOR=Inf;LSEQ=TGTCCTCCCTTTCACCTGTA;RSEQ=ACGGTCCTCCCTGCTGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:373,55:428,0:0:2,0:24.6:1:33:1:1:0:59.9:60.143:1:0:0.1 0/1:180:2:1,1:155,23:178,2:0.0111:2,2:28.5:1:29:0:0.24953:6.61849:60:4:0.0112:0:1 +1 156838141 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01587;SOR=1.89611;LSEQ=CACTGAAAAGGCCTGGGGAA;RSEQ=GGGCACTGGCAAAGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:110:38,72:47,98:145,110:0.4314:2,2:25.2:1:30.9:1:0.78878:1.10:60:109:0.4343:0:1.1 1/0:83:49:13,36:7,27:34,49:0.5904:2,2:22.4:1:29.4:1:0.60838:1.39:60:48:0.5854:0:1.1 +1 156838571 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGAGGTTGAGGGACGGACA;RSEQ=AGATGGTTTAGACCCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:0,2:5,130:135,2:0.0146:1,0:18:1:29.5:1:1:0:60:4:0.015:0:1 0/0:35:0:0,0:0,35:35,0:0:1,0:23.3:1:31.2:1:1:0:60:70:1:0:0 +1 156838809 . TC T 68 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTACATCACTTTTCTCTC;RSEQ=CCTTCCTTCCTTCCTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:29:1:29.6:1:1:0:49.8:10:1:0.2:0.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 156841199 . T TA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAATAAAACATAAAA;RSEQ=AAAAAAAAAATGTGATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:17,2:0.1053:1,0:22.5:1:30:0:1:0:60:4:0.1053:0:1 0/0:9:0:0,0:9,0:9,0:0:0,0:21.7:1:30.3:1:1:0:60:18:1:0:1.2 +1 156841259 . A C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTAAAGGAGGAAGGCCATT;RSEQ=TCTGCTACATTCTCTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:78:77:77,0:0,0:0,77:0.9872:0,1:27.7:1:31.8:1:1:0:59.7:24.667:1:0:1.1 1/1:29:29:28,1:0,0:0,29:1:0,1:23:1:30.2:1:1:0:60:58:1:0:1.2 +1 156841639 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.11199;SOR=Inf;LSEQ=GGGGGGCTGGAAGAAAGGGT;RSEQ=GGATGTGTGTCTCCACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:7,161:168,0:0:1,0:23.7:1:31.5:1:1:0:59.9:41:1:0:0.2 0/1:85:2:1,1:2,81:83,2:0.0235:1,2:13:1:28.5:1:0.06975:33.24:60:4:0.0244:0:1 +1 156841674 . G A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=ACAGCTGCTCCCTCCCAGCT;RSEQ=TTTCCAGATTCCCATGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:3,90:93,0:0:1,0:23.9:1:32.4:1:1:0:59.7:92:1:0:0.1 0/1:31:6:0,6:0,25:25,6:0.1935:1,0:14.5:1:26.8:1:1:0:60:5:0.1667:0:1.3 +1 156843302 . T G 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAGGGCCTGCTGACCTG;RSEQ=TTCTCCCAGGCCTGCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:91,2:93,2:0.0211:1,2:6.5:1:29.5:1:0.06249:37.34509:60:4:0.0213:0:1.5 0/0:27:0:0,0:27,0:27,0:0:1,0:23.5:1:30.2:1:1:0:60:54:1:0:0.1 +1 156845492 . A AGTGT 251 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=20.000;MSILEN=2;SSF=0.01766;SOR=0.75226;LSEQ=CTGGGTCAAGGGCAGGGACG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1346:282:164,118:466,392:858,282:0.2095:2,2:30.3:1:30.9:1:0.26999:1.17:58:281:0.2207:0:0.5 0/1:740:123:73,50:288,204:492,123:0.1662:2,2:30.3:1:29.7:1:0.9186:1.03:57:122:0.1735:0:0.7 +1 156846073 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09539;SOR=Inf;LSEQ=GCTCCATCACATCAGGACAG;RSEQ=GTGGGGGGAGATGCAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:0:0,0:144,289:433,0:0:2,0:25:1:31:1:1:0:60:23.056:1:0:0.1 0/1:194:2:1,1:57,134:191,2:0.0103:2,2:29:1:28:1:0.51182:2.34:60:4:0.0108:0:1 +1 156846119 . G T 31 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.02403;SOR=Inf;LSEQ=ATGGCTGGATACCGGGGTGG;RSEQ=CGGGCTGCCCTGGGTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:461:0:0,0:260,200:460,0:0:2,0:22.3:1:31.2:1:1:0:59.9:24.556:1:0:0.1 0/1:188:3:1,2:108,77:185,3:0.016:2,2:7.3:1:20:1:0.57334:2.78986:60:2:0.0109:0:2 +1 156846233 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44614;SOR=1.09613;LSEQ=AGTGCTCGGCAGGACTTCCA;RSEQ=CGTGAGGCTGAGCTGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1141:263:158,105:507,370:877,263:0.2305:2,2:24.7:1:30.2:1:0.52199:1.10:60:130.5:0.2332:0:1.1 0/1:623:154:90,64:274,194:468,154:0.2472:2,2:23.2:1:29.1:1:1:1.00435:60:308:0.2492:0:1.1 +1 156848778 . C T 131 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.004;SOR=0;LSEQ=ACCCCTCTGGACAGCTGCCT;RSEQ=TACTGTTCTCTCAATCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:20:20,0:92,1:93,20:0.177:1,1:25.5:1:30.4:1:1:0:58.9:19:0.1712:0:3.1 0/0:38:0:0,0:37,1:38,0:0:1,0:26.5:1:30.6:1:1:0:60:37:1:0:1.6 +1 156848794 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05203;SOR=0.51035;LSEQ=GCCTCTACTGTTCTCTCAAT;RSEQ=CTCCACTTCCAGGTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:102:101,1:33,0:33,102:0.7556:1,1:26:1:31.2:1:1:0:59.7:101:0.7537:0:2.3 1/0:54:33:33,0:20,1:21,33:0.6111:1,1:22.7:1:29.7:1:0.38889:0:60:66:0.6226:0:2 +1 156848808 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00501;SOR=0.17843;LSEQ=CTCAATCCTCCACTTCCAGG;RSEQ=CCCCAGTCTCCTCTCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:182:178:169,9:0,0:0,178:0.978:0,2:23.4:1:32.2:1:1:0:59.9:43.5:0.9886:0:1.7 1/1:71:63:61,2:8,0:8,63:0.8873:0,1:23.5:1:30.7:1:1:0:60:30.5:0.8841:0:1.6 +1 156848909 . CA C 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCCCTCTCCTTTTCTTGTT;RSEQ=CAGATCCCATGGACCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1006:0:0,0:624,381:1005,0:0:2,0:25.4:1:30.1:1:1:0:59.9:82.75:0.999:0:0.3 0/1:571:99:59,40:268,202:470,99:0.1734:2,2:25.7:1:30.6:1:0.65632:1.11:59.5:98:0.1738:0.021:0.2 +1 156848995 . C T 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.46868;LSEQ=GGTCTGGGGCAGCTGCTGGC;RSEQ=GTGGCTAGCCAGGTCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1195:888:459,429:164,142:306,888:0.7431:2,2:25.9:1:31.1:1:0.59569:1.07936:59.9:97.667:0.7462:0:1.2 1/0:650:374:184,190:141,134:275,374:0.5754:2,2:24.9:1:29.5:1:0.63386:1.08641:60:61.333:0.5759:0:1.1 +1 156849047 . G T 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=ACCTGGCGGGTCTGCATTTT;RSEQ=TGCACCGGGACCTGGCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1254:27:14,13:655,570:1225,27:0.0215:2,2:21.8:1:30.3:1:1:1.06696:59.3:26:0.021:0:1.4 0/0:678:0:0,0:369,308:677,0:0:2,0:23.4:1:31.3:1:1:0:60:60.545:0.9985:0:0.4 +1 156849505 . G A 70 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGACTCCCTGGTTCAAGC;RSEQ=ATTCTCCTGCTTCAGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:4,1:6,3:9,5:0.3571:2,2:12.4:1:30.4:1:1:1.91:35.6:10:0.3571:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 156849658 . C T 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1144;SOR=0;LSEQ=TGATTGCCCACCTCGGCCTC;RSEQ=CAAAGTGCTGGGATTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:10:9,1:74,0:74,10:0.119:1,2:31.7:1:31.6:1:0.11905:0:51.2:20:0.1266:0:1.1 0/0:23:0:0,0:22,1:23,0:0:1,0:29.4:1:31:1:1:0:52:46:1:0:0.2 +1 156849675 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCAAAGTGCTGGGATTA;RSEQ=AGGCGTGAACCACCGAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:124,2:126,2:0.0156:1,0:23:1:33:1:1:0:60:4:0.016:0:1.5 0/0:39:0:0,0:37,2:39,0:0:2,0:24.6:1:31.5:1:1:0:55.3:38:1:0:0.1 +1 156849744 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03996;SOR=Inf;LSEQ=GGTAGGCTGTGCCTTGACGG;RSEQ=CTGTCCCAGGCGCCCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:0:0,0:412,151:563,0:0:2,0:25.1:1:30.8:1:1:0:59.9:27.15:1:0:0.1 0/1:294:3:2,1:214,76:290,3:0.0102:2,2:36:1:22.3:1:1:1.40613:60:2:0.0069:0:2.3 +1 156849775 . T C 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCCCCTGGAATTGATGCAG;RSEQ=GTCCGCCCGTGGCAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:839:0:0,0:532,306:838,0:0:2,0:25.7:1:29.6:1:1:0:59.9:48.294:1:0:0.1 0/1:507:97:61,36:268,142:410,97:0.1913:2,2:26.9:1:30.7:1:0.63833:1.11359:60:47.5:0.1896:0:1.2 +1 156850104 . G C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACTGTGTCCCCTCCACT;RSEQ=TGGCCCTTTTCTTCTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:101:101:1,100:0,0:0,101:1:0,1:24.4:1:33.8:1:1:0:60:202:1:0:2 1/1:27:27:0,27:0,0:0,27:1:0,1:20.7:1:32.6:1:1:0:60:54:1:0:1.8 +1 156850112 . T G 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCCTCCACTGTGGCCCT;RSEQ=TTCTTCTCTTCCTCCCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:90:90:0,90:0,0:0,90:1:0,1:22.7:1:32.8:1:1:0:60:180:1:0:2.1 1/1:21:21:0,21:0,0:0,21:1:0,1:18.9:1:32.5:1:1:0:58.2:42:1:0:2 +1 156850989 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCTGGCAAGTCTTCTTA;RSEQ=GATCTGATCCCAGTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:12,0:12,2:0.1429:0,2:21:1:30.5:1:0.14286:0:60:4:0.1429:0:2 0/0:3:0:0,0:3,0:3,0:0:0,0:12:1:32.3:1:1:0:60:6:1:0:1 +1 156851041 . T G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCAGCCCAAGCTTCCCA;RSEQ=AGTCGAGCCTTAATCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:38,3:0,0:0,41:1:0,2:23.9:1:34:1:1:0:59.5:82:1:0:1.1 1/1:8:8:8,0:0,0:0,8:1:0,0:27.3:1:31.8:1:1:0:60:16:1:0:1 +1 156851141 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGCAGCTAAGAAGCCCAGA;RSEQ=GAGTAGTGTGAGCTGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:227,0:227,0:0:1,0:25.2:1:32.4:1:1:0:60:55.75:1:0:0 0/1:88:19:19,0:67,2:69,19:0.2159:1,1:18.4:1:29.2:1:1:0:60:18:0.2118:0:1.1 +1 156852626 . T A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGCCTCTTGTCCAGGC;RSEQ=GGTTAGTGCTAATGGAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 157474475 . G C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGAAGCAGTTAAAATG;RSEQ=GTCTTCGTCCTTATCCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:33:1:1:0:49:4:1:0:1.5 +1 157474737 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGTTTGCTCCTTTTCTTC;RSEQ=TCTTTACCCAAAAAAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 157512453 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCATCAGGCAGGGGTAT;RSEQ=AGGGCACCTAGACTGCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:29:1:1:0:60:4:1:0:1 +1 157514097 . A G 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGTCAGATATGACGCTGT;RSEQ=AGGCATTGTTGCTGCCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:20.3:1:32.8:1:1:0:60:8:0.5714:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:9:0:33:0:1:0:60:2:1:0:1 +1 157514287 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74523;LSEQ=GTCAGGGTCACTGGGTTCCC;RSEQ=CTGATGGGCTGGAAGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:26,26:52,2:0.037:2,2:31:1:28.5:1:1:1:60:4:0.0377:0:1 0/1:36:1:1,0:17,18:35,1:0.0278:2,0:1:0:25:0:1:0:60:2:0.0278:0:1 +1 157516231 . C A 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGTGACAGAGCGAGACT;RSEQ=CATCTCAAAAAACCAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:27.5:1:1:0:46.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 157550066 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.0067;LSEQ=CCCCACAGTTTTGCATATTG;RSEQ=GTACTCGGGAAACTAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:767:255:109,146:219,290:509,255:0.3325:2,2:25.7:1:30.9:1:1:1.0115:59.9:62.75:0.3347:0:1.1 0/1:542:181:88,93:164,196:360,181:0.3339:2,2:24.4:1:29.9:1:0.52329:1.13:60:59.333:0.3315:0:1.2 +1 157550156 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05619;SOR=Inf;LSEQ=CTCCTGCAAAATAAAGCAAA;RSEQ=ACGCATTTTTGTCAGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:54,214:268,0:0:2,0:22.9:1:32.3:1:1:0:60:133:0.9963:0:0.1 0/1:168:3:1,2:40,125:165,3:0.0179:2,2:10.7:1:26.7:1:0.57051:1.56:60:6:0.0179:0:2.3 +1 157599744 . T C 121 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.47413;LSEQ=CAGGCTCCGTTTTCTGACCG;RSEQ=GTGAGCCACAGTATCTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:13,0:12,0:12,13:0.52:0,1:14.7:1:32.9:1:1:0:60:26:0.52:0:1.2 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:31:0:33:0:1:0:60:2:0.3333:0:1 +1 157599795 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50674;SOR=0;LSEQ=GGACCATGAATCTTCACTCC;RSEQ=CATGGCACTGATCTGGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:55,4:59,2:0.0328:2,2:11.5:1:30.5:1:0.15847:12.40977:60:4:0.0328:0:1 0/0:45:0:0,0:38,7:45,0:0:2,0:21.9:1:29.7:1:1:0:60:44:1:0:0.5 +1 157599839 . C A 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGCTGCTCCAGCCTGAT;RSEQ=CCAGGGTCTGGCCATCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:99,41:140,0:0:2,0:23.6:1:31.9:1:1:0:58:139:1:0:1 0/1:116:16:9,7:68,31:99,16:0.1379:2,2:24.7:1:26.8:1:0.39287:1.69762:60:15:0.1316:0:1.3 +1 157599858 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=0.45935;LSEQ=TCCCAGGGTCTGGCCATCTC;RSEQ=GAAGAAGCAGAACTGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:102:63,39:52,30:82,102:0.5543:2,2:26.6:1:31.5:1:0.87872:1.07259:55.4:101:0.558:0:2 0/1:168:61:39,22:65,42:107,61:0.3631:2,2:24.6:1:29.6:1:0.74246:1.14:55.6:60:0.3659:0:1.9 +1 157599866 . C T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04971;SOR=Inf;LSEQ=TCTGGCCATCTCCGAAGAAG;RSEQ=AGAACTGGAGCTGGACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:123,81:204,0:0:2,0:25.3:1:32:1:1:0:57.6:39.8:1:0:1.2 0/1:184:4:2,2:107,73:180,4:0.0217:2,2:9.5:1:26.5:1:1:1.46261:60:8:0.0219:0:1.3 +1 157599878 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20949;SOR=Inf;LSEQ=CGAAGAAGCAGAACTGGAGC;RSEQ=GGACTTCTGATCTCTCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:134,100:234,0:0:2,0:25.3:1:30.9:1:1:0:57:57.5:1:0:1.3 0/1:198:2:1,1:111,85:196,2:0.0101:2,2:22:0:32:0:1:1.30409:60:4:0.0102:0:1.5 +1 157599882 . C A 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGCAGAACTGGAGCTGGA;RSEQ=TTCTGATCTCTCTAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:32:18,14:115,87:202,32:0.1368:2,2:26.6:1:31.2:1:1:1.02799:53.5:64:0.1379:0:3 0/0:204:0:0,0:114,87:201,0:0:2,0:26.6:1:31.4:1:1:0:58.3:99.5:0.9851:0:0.9 +1 157599917 . A G 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37798;LSEQ=GAGAGAGCCGGGTCTCACAG;RSEQ=TCAGGGTCACTGGGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:251:133:72,61:59,59:118,133:0.5299:2,2:27.2:1:31.2:1:0.52912:1.18:49.7:32.25:0.5375:0:2.7 0/1:238:71:36,35:83,84:167,71:0.2983:2,2:25.5:1:30.4:1:1:1.04:50:70:0.2991:0:2.5 +1 157599937 . T A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.39859;LSEQ=ATCAGGGTCACTGGGCTCCC;RSEQ=TTGGTGGGCTGGGAGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:121:57,64:47,63:110,121:0.5238:2,2:26.3:1:30.4:1:0.51146:1.19:47.9:59.5:0.5242:0:2.9 0/1:207:63:28,35:67,76:143,63:0.3043:2,2:26.3:1:29.5:1:0.76402:1.10145:47.8:62:0.3039:0:2.7 +1 157599988 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.30072;LSEQ=ACTGGACGTGAAAACAGCTC;RSEQ=AGAGAGAAGAATCACAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:76:20,56:21,42:63,76:0.5429:2,2:25.3:1:31.7:1:0.45529:1.39656:44.6:75:0.5435:0:2.8 0/1:103:27:4,23:26,49:75,27:0.2621:2,2:22:1:31.6:1:0.08301:3.02131:45.6:26:0.26:0:2.8 +1 157600009 . G T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.20611;LSEQ=AGAGAGAAGAATCACAACAG;RSEQ=CCCAGAGCAATGAGGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:55:9,46:9,34:43,55:0.5612:2,2:25.8:1:29.5:1:0.60643:1.34871:43.6:26.5:0.5579:0:2.7 0/1:58:12:0,12:11,34:45,12:0.2069:2,0:25.3:1:29.3:1:0.09677:0:41.8:24:0.2069:0:2.6 +1 158506819 . G T 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACCTGAACAGGGAAAGA;RSEQ=AATTTGAATTGAAATTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:5,0:5,3:0.375:0,2:31:1:31.3:1:0.375:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 158507096 . AT A 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.31467;SOR=0.39022;LSEQ=GGGAATTTGAACCAAGCAGT;RSEQ=TTTTTTTTCAGACATAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:7:5,2:174,70:244,7:0.0279:2,2:29.6:1:32.4:1:1:1.01:60:14:0.028:0:1 0/1:181:2:1,1:122,57:179,2:0.011:2,2:30:1:32:0:0.53941:2.13054:50:4:0.011:0:1 +1 158507157 . A T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23008;LSEQ=TCTGAAGGTAAAGATTCAAG;RSEQ=TGTTTTTCAAGAGCGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:443:270:153,117:93,80:173,270:0.6095:2,2:26.5:1:29.8:1:0.55799:1.12:59.9:89:0.611:0:2.9 0/1:326:86:48,38:130,110:240,86:0.2638:2,2:27.5:1:29:1:0.80223:1.07:59.9:85:0.2681:0:2.6 +1 158507160 . T G 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.24759;LSEQ=GAAGGTAAAGATTCAAGATG;RSEQ=TTTTCAAGAGCGCACAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:447:269:153,116:97,80:177,269:0.6018:2,2:26.7:1:31.8:1:0.697:1.09:59.9:268:0.6063:0:2.8 0/1:331:90:49,41:131,110:241,90:0.2719:2,2:27.3:1:30.8:1:1:1.00:59.9:89:0.2722:0:2.6 +1 158507184 . A G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16335;LSEQ=TCAAGAGCGCACAGGTATAG;RSEQ=TTATATGTCAGCATTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:499:295:154,141:98,106:204,295:0.5912:2,2:26:1:31.8:1:0.36431:1.18:59.9:590:0.5948:0:2.5 0/1:367:70:37,33:147,150:297,70:0.1907:2,2:25.4:1:30.7:1:0.69049:1.14:59.7:34:0.1894:0:2.4 +1 158507222 . GA G 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.43527;LSEQ=GAAATGGTTTCCAGGGTTAT;RSEQ=AAAAAAATCTCTGCCTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:461:256:107,149:88,115:203,256:0.5553:2,2:26.7:1:32.1:1:0.77576:1.06543:59.9:255:0.5568:0.0542:1.3 0/1:341:120:55,65:99,122:221,120:0.3519:2,2:27.3:1:31.4:1:0.9094:1.04:59.7:240:0.355:0.0323:0.9 +1 158507360 . G C 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00632;SOR=Inf;LSEQ=CAATCTAAGATAAAATGACA;RSEQ=GTCTAGAGAAGTGTGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:47,0:0:1,0:23.3:1:31.4:1:1:0:59.7:46:1:0:0.4 0/1:20:4:0,4:1,15:16,4:0.2:1,0:28.3:1:29:1:1:0:60:8:0.2:0:1.5 +1 158507398 . G T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15723;SOR=0.22635;LSEQ=GTGGTTAGTTGTCAGGCTCT;RSEQ=AATGTAGGCATTATCTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:21:0,21:0,6:6,21:0.7778:0,1:27.6:1:29:1:1:0:59.1:42:0.7778:0:1.5 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:20:1:29:0:1:0:60:6:0.4286:0:1.7 +1 161284075 . CAG C 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00108;SOR=Inf;LSEQ=AGAGCTGAGCGGAGAAGCTC;RSEQ=AGCCTTTTAAAGAGACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:204,5:209,0:0:1,0:25.6:1:30.4:1:1:0:59.9:51.25:1:0:0.2 0/1:101:6:6,0:92,3:95,6:0.0594:1,0:35.2:1:30.3:1:1:0:60:12:0.0612:0:0.2 +1 161284164 . T C 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCGGGTGGCGGGGCCGCC;RSEQ=GGCGTCACTTCCGTCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:928:0:0,0:589,339:928,0:0:2,0:24.9:1:31.2:1:1:0:60:91.8:1:0:0.1 0/1:736:46:25,21:402,288:690,46:0.0625:2,2:23.8:1:29.5:1:0.64483:1.17224:59.4:22:0.061:0:1.3 +1 161284224 . A AGT 200 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCTGTTGCTGAGGTGACTTC;RSEQ=GTGGGACTGGGAGTTGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1372:0:0,0:632,737:1369,0:0:2,0:25.9:1:31.1:1:1:0:59.9:61.227:0.9985:0:0.2 0/1:1122:107:49,58:501,513:1014,107:0.0954:2,2:22.3:1:29.7:1:0.54204:1.15583:59.9:214:0.0968:0.0223:0.4 +1 161284297 . T C 223 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=153.91929;LSEQ=CACGTTTTGCTGATAACTGT;RSEQ=TATCCTGTGCCTGGGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:634:2:1,1:177,455:632,2:0.0032:2,2:19.5:1:20:1:0.48301:2.57:60:1:0.0016:0:2 0/1:478:157:47,110:101,220:321,157:0.3285:2,2:22.5:1:30.6:1:0.75318:1.07433:60:314:0.3298:0:1.1 +1 161284376 . TC T 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.55368;SOR=0;LSEQ=CCTAGAGACCCCTTTTCCCG;RSEQ=CCCCCCAGCCGCTCCGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:3:0,3:1,121:122,3:0.024:1,0:30:1:26.7:1:1:0:60:2:0.0165:0:1.7 0/0:69:0:0,0:0,69:69,0:0:1,0:20.5:1:30.3:1:1:0:60:22:1:0:0.3 +1 161293487 . TATTTA ATTTTTTT 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=Inf;LSEQ=TTCTAAGTCTGGAGATTATT;RSEQ=TTTTTTTTTTTGAGACGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:0:0,0:192,440:632,0:0:2,0:20.7:1:30.3:1:1:0:54.7:47.615:0.9984:0:0.1 0/1:540:18:10,8:158,356:514,18:0.0333:2,2:14.4:1:27.4:1:0.03695:2.81:59.2:36:0.034:0.0185:1.4 +1 161293492 . A AT 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.63011;SOR=0.87102;LSEQ=AGTCTGGAGATTATTTATTT;RSEQ=TTTTTTTTTTTGAGACGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:43:9,34:131,352:483,43:0.081:2,2:28.2:1:30.4:1:0.47243:1.40512:53.3:20.5:0.0812:0:0.1 0/1:449:32:8,24:110,281:391,32:0.0713:2,2:25.3:1:29:1:0.83857:1.17393:53.5:64:0.0753:0.0022:0.2 +1 161293508 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.04856;SOR=Inf;LSEQ=ATTTATTTTTTTTTTTGAGA;RSEQ=GGAGTCTCGCTCTGTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:52,256:308,0:0:2,0:21.9:1:30:1:1:0:50.4:43:1:0:0.2 0/1:274:4:1,3:57,211:268,4:0.0146:2,2:19:1:29.3:1:1:1.23:48.3:8:0.015:0:2.5 +1 161298109 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15772;SOR=Inf;LSEQ=GCTTGGTATTGCAAAATATT;RSEQ=ACTTAATAAAACGTTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:235,37:272,0:0:2,0:23.7:1:32.1:1:1:0:60:67:0.9963:0:0.1 0/1:181:2:1,1:145,34:179,2:0.011:2,2:18.5:1:27:1:0.35021:4.21781:60:4:0.0113:0:1 +1 161310519 . C T 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTCATTGGCCCTAGTCTC;RSEQ=GCCTCCTTTGAAACTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:53,254:307,0:0:2,0:22.1:1:30.1:1:1:0:60:152.5:1:0:0.1 0/1:223:17:5,12:41,165:206,17:0.0762:2,2:16.8:1:29.8:1:0.35511:1.67:60:34:0.0773:0:1.2 +1 161326293 . T C 117 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=19.09341;LSEQ=GAGCCAAGATTGCACCACTA;RSEQ=ACTCCAGCCTGGGTGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:2,0:65,1:66,2:0.0294:1,0:29:0:31.5:1:1:0:28:4:0.0294:0:1 0/1:32:12:12,0:20,0:20,12:0.375:1,0:25.3:1:32.7:1:1:0:43:24:0.3871:0:1.3 +1 161326331 . G T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.01103;SOR=5.09097;LSEQ=AGAATGAGACTCTGTCTCAA;RSEQ=AAAAAAAGAAAACAAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:4:4,0:143,3:146,4:0.0267:1,0:16.5:1:32.5:1:1:0:60:8:0.0268:0:1 0/1:73:9:9,0:64,0:64,9:0.1233:1,0:20.9:1:29.7:1:1:0:50.6:18:0.125:0:1.3 +1 161326716 . G A 25 v3;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14136;SOR=Inf;LSEQ=CCTTCATTACTGGGTTTAGT;RSEQ=CTGTTCTTTTTTTTTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:18,260:278,0:0:2,0:22.7:1:30.5:1:1:0:59.4:9.296:1:0:0.4 0/1:168:2:2,0:11,155:166,2:0.0119:2,0:9:1:25:1:0.00556:0:52:4:0.0126:0:1 +1 161326722 . CT C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.86034;SOR=0.91886;LSEQ=TTACTGGGTTTAGTGCTGTT;RSEQ=TTTTTTTTTTTCCCAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:25:0,25:9,201:210,25:0.1055:1,1:24.6:1:32.4:1:0.60275:0:58.6:50:0.1101:0.0084:0.2 0/1:133:13:2,11:5,115:120,13:0.0977:1,2:29.5:1:30.9:1:0.14007:4.11:57.6:26:0.1008:0:0.5 +1 161332361 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTTTCAGATCTCCTTGGAG;RSEQ=AGTAGAGTACCTGGTAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:21.5:1:31.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:28:1:1:0:45:4:1:0:1 +1 161369021 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08258;SOR=Inf;LSEQ=GAGGAAACCGACCCATCGCA;RSEQ=TCTCGGCCGAAGAGGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:26,0:0:2,0:31.5:1:31.3:1:1:0:60:25:1:0:0.3 0/1:11:2:1,1:7,2:9,2:0.1818:2,2:22.5:1:28:0:0.49091:3.05504:60:4:0.1818:0:1 +1 161448241 . C G 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=AGTCAGGGATAGTATGAGAT;RSEQ=CTGCCTAGAATTTACAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:17,0:0:2,0:25.1:1:33:1:1:0:53.9:34:1:0:0.2 1/0:12:8:5,3:3,1:4,8:0.6667:2,2:16.5:1:32.4:1:1:1.71671:60:16:0.6667:0:1 +1 161448285 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22356;SOR=0;LSEQ=TCTTCTGTATCAGACAACGT;RSEQ=TTTCAAACTCTTATACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:29,2:0.0645:2,2:40.5:1:30.5:1:1:1.22249:60:4:0.0645:0:1 0/0:34:0:0,0:18,16:34,0:0:2,0:27.9:1:28.2:1:1:0:50.9:33:1:0:0.4 +1 161449051 . C CCCG 26 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATGCCCGAGCCCCCCCC;RSEQ=CCCCGGACGGTGGGCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:11:1:26:1:1:0:60:4:1:0.5:1 +1 161449129 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATGGCACCCAGTCCTAT;RSEQ=GACCGCCCAAAGGCTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:30:1:31.5:1:1:0:60:4:1:0:2 +1 162039394 . G T 31 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGGACTTTCACCTGCTC;RSEQ=GCTGGCAGCGCGGGCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:31.5:1:1:0:60:4:1:0:1.5 +1 162688638 . A T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAGAGTTTGAAAATTATT;RSEQ=TATTAGGTGATTATTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:3,0:31,0:31,3:0.0882:1,0:37.7:1:31:1:1:0:54:6:0.0909:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:20.4:1:28:1:1:0:60:10:1:0:0 +1 162722812 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.1036;SOR=Inf;LSEQ=CTTGTTCAATATTCAGTGAT;RSEQ=TTCTTCCTAGGGGGCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:266,30:296,0:0:2,0:23.5:1:28.8:1:1:0:59.9:97.667:1:0:1 0/1:141:2:1,1:117,22:139,2:0.0142:2,2:19.5:1:27.5:1:0.30061:5.22358:60:4:0.0143:0:2 +1 162722846 . C G 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.31499;LSEQ=GCTTGGAAATAAAAATAAAA;RSEQ=CATGTCCTCTCTTTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:598:593:471,122:0,0:0,593:0.9916:0,2:24.2:1:32.8:1:1:0:60:52.909:0.9915:0:1.1 1/1:314:312:222,90:0,0:0,312:0.9936:0,2:22.6:1:31.2:1:1:0:59.9:77:0.9935:0:1.1 +1 162723162 . T C 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00171;SOR=Inf;LSEQ=ATGTTTTCAGGGAGAGAATT;RSEQ=AGGACTTAGCCACATGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:1,87:88,0:0:1,0:21.9:1:28.4:1:1:0:59.9:87:1:0:0.2 0/1:24:4:0,4:0,20:20,4:0.1667:1,0:33.5:1:32.8:1:1:0:60:8:0.1667:0:1.3 +1 162725380 . C T 34 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0398;SOR=Inf;LSEQ=ACGCTGTGCAAGCTTATACC;RSEQ=TTGAAACTCACATAGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:394,94:488,0:0:2,0:24:1:31.8:1:1:0:59.9:243:1:0:0.1 0/1:254:3:1,2:188,62:250,3:0.0118:2,2:7:1:22:1:0.15848:6.01116:60:2:0.0079:0:2 +1 162725655 . A C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATAATCAATCAACCAATC;RSEQ=GTATTTATTTAGTTCTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:141:141:2,139:0,0:0,141:1:0,1:25.9:1:30.4:1:1:0:59.7:140:1:0:1 1/1:61:61:0,61:0,0:0,61:1:0,1:22.3:1:29.8:1:1:0:60:60:1:0:1.1 +1 162729523 . C T 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11315;SOR=Inf;LSEQ=ATGCCGGGTAAAAGCTCTTC;RSEQ=ACGAATGTGTGGTTAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:188,30:218,0:0:2,0:25.7:1:31.4:1:1:0:60:53.5:1:0:0.1 0/1:111:2:1,1:86,23:109,2:0.018:2,2:14:1:22:1:0.38722:3.6819:60:4:0.0185:0:1 +1 162729529 . T A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.11992;SOR=Inf;LSEQ=GGTAAAAGCTCTTCCACGAA;RSEQ=GTGTGGTTAACTCAGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:223,46:269,0:0:2,0:23:1:31:1:1:0:60:268:1:0:0.1 0/1:143:2:1,1:111,30:141,2:0.014:2,2:10:0:28:1:0.38777:3.65654:60:4:0.0142:0:1 +1 162730148 . T TTG 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=23;MSI=12.000;MSILEN=2;SSF=0.46429;SOR=Inf;LSEQ=TTATCTTTTTACCAGCACAG;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:3,3:0.5:0,2:27.3:1:31:1:1:0:60:6:0.6:0.1667:0.7 1/1:2:2:1,1:0,0:0,2:1:0,2:2:1:32.5:1:1:0:60:6:0.8858:0.6875:1.5 +1 162730759 . T TA 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.01186;SOR=Inf;LSEQ=TCATTTAGAAATGAGATTTC;RSEQ=AAAAAAAAAAATGAAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:20,0:20,1:0.0476:1,0:18:0:12:0:1:0:41:0:0:0:7 1/1:2:2:2,0:0,0:0,2:1:0,0:24:1:28.6:1:1:0:60:4:1:0.5:0 +1 162731291 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05453;SOR=Inf;LSEQ=AGTGGGAGCAAGGTGATGAA;RSEQ=GAGGAATGCACATGCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:73,315:388,0:0:2,0:22.6:1:31.6:1:1:0:59.9:387:1:0:0.1 0/1:238:3:1,2:53,182:235,3:0.0126:2,2:31.7:1:26.3:1:0.53963:1.71:60:2:0.0085:0:1 +1 162731404 . C T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGTGTGACTAGTTTTAA;RSEQ=TGTGGAGGGGATGGGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:46:0,46:0,0:0,46:1:0,1:25.3:1:29.5:1:1:0:58.1:10.5:1:0:1.3 1/1:12:12:1,11:0,0:0,12:1:0,2:16.3:1:29.9:1:1:0:60:24:1:0:1 +1 162735473 . A G 103 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATTCTGTCTATATTTTC;RSEQ=CTGAATTTGGGTCCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:0,14:1:0,1:17.8:1:27.2:1:1:0:60:6:1:0:1.6 1/1:1:1:1,0:0,0:0,1:1:0,0:8:0:29:0:1:0:60:2:1:0:1 +1 162736463 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATAGAAAAACTCACCATTA;RSEQ=TCTGTCTGACACATGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:11:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162736690 . C T 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTAGCCGGGCGTAGTGG;RSEQ=GCATGCCTGTAATCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:21.2:1:29:1:1:0:29.5:12:0.8571:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162736734 . G C 101 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGGCTGAGGCAGAATT;RSEQ=CTTGAACCTGGGAGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:24.9:1:29.4:1:1:0:39.3:4.5:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:2:0:30:0:1:0:60:2:1:0:1 +1 162736821 . G GA 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.67882;SOR=0.65107;LSEQ=AGAACAAGACTCTATCTCAG;RSEQ=AAAAAAAAAAAGTAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:31:31,0:10,0:10,31:0.7209:0,1:28.7:1:31.1:1:1:0:56:62:0.7381:0:1.3 1/0:8:5:5,0:1,0:1,5:0.625:0,0:24.8:1:29.6:1:1:0:54.6:10:0.625:0:1.2 +1 162736856 . C AAAAA 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.05572;SOR=0.27616;LSEQ=AGTAATAAAACAGTAGCAAG;RSEQ=AAAACAGTAGCAAGAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:33:31,2:16,0:16,33:0.44:1,2:25.2:1:31.2:1:1:0:57.1:66:0.4853:0:2.5 0/1:17:3:2,1:3,0:3,3:0.1765:0,2:12.7:1:31.6:1:1:0:49.3:6:0.1765:0:1.3 +1 162736899 . G A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCAGAAGTATTAAGGTG;RSEQ=CATCTTCCATAATTATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:2,0:191,4:195,2:0.0102:1,0:7:1:30.5:1:1:0:60:4:0.0111:0:1 0/0:75:0:0,0:73,2:75,0:0:1,0:20.2:1:30.2:1:1:0:59.1:17.75:1:0:0.5 +1 162737116 . C G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.2083;LSEQ=GCCATCATTGTCATCATCCT;RSEQ=TGGAGGCAGTTCTGGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1191:315:119,196:355,518:873,315:0.2645:2,2:26.2:1:32.3:1:0.38351:1.12866:59.8:104:0.2649:0:1.1 0/1:761:53:19,34:292,414:706,53:0.0696:2,2:26.2:1:31.1:1:0.47153:1.26176:60:52:0.0693:0:1.1 +1 162737241 . A G 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00219;SOR=0;LSEQ=GTAAAAGGCAAATTGCAAAC;RSEQ=TTTATTAATGGTTGGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:18:0,18:7,146:153,18:0.1053:1,1:25.9:1:29.2:1:1:0:60:8:0.0988:0:1.2 0/0:71:0:0,0:3,68:71,0:0:1,0:20.3:1:30.4:1:1:0:60:142:1:0:0 +1 162737338 . G C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTCTCATTTTTAGAGTGGA;RSEQ=ATGTTGGAACCTTCCTAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:0,23:0,0:0,23:1:0,1:25:1:32:1:1:0:60:22:1:0:1.1 1/1:5:5:0,5:0,0:0,5:1:0,0:24:1:32:1:1:0:60:10:1:0:1.4 +1 162739830 . CT C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAGCAACAGGGAGATAAT;RSEQ=TTTTTTTTTAAGTGTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:10,1:11,3:0.2143:2,0:29.3:1:32.7:1:1:0:60:6:0.2143:0.0714:0 0/0:1:0:0,0:1,0:1,0:0:0,0:7:0:31:0:1:0:58:2:1:0:0 +1 162740009 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53674;SOR=0;LSEQ=TAAAGAGTTATTTCATTTGA;RSEQ=TGGGAGAGCTGAGTTTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:155,4:159,2:0.0124:1,2:7:1:28:1:0.06134:34.76925:60:4:0.0125:0:1 0/0:91:0:0,0:88,3:91,0:0:1,0:23.9:1:31.7:1:1:0:60:90:1:0:0 +1 162740121 . G A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14707;LSEQ=AGGATGCTGGATGATGAAAT;RSEQ=ACAGTCAGCCTTTCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1055:262:179,83:476,316:792,262:0.2483:2,2:24.5:1:29.2:1:0.01869:1.43:60:130:0.249:0:1.1 0/1:756:35:21,14:420,301:721,35:0.0463:2,2:27.5:1:28:1:0.86293:1.07:60:34:0.0452:0:1.2 +1 162740327 . T C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10041;LSEQ=GGATGATGTGGTGGGCAGGG;RSEQ=GTCAAGGGAGAAACCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:684:680:209,471:0,1:1,680:0.9942:0,2:23.4:1:30.1:1:1:0:60:39:0.9955:0:1.1 1/1:469:443:146,297:9,17:26,443:0.9446:2,2:25:1:29.5:1:0.83335:1.07678:59.9:43.3:0.9454:0:1.2 +1 162740740 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAAGCTAAAGACATTCC;RSEQ=AAATTCCCAGTGGTGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:33.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162741494 . A G 35 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGGAAATAAGTTATTAA;RSEQ=CCTTCAACCTTTAATATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:8,2:0.2:0,0:13:1:35.5:1:1:0:60:4:0.2:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162741769 . A G 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TCCTTCCTGAAGAGATCTCC;RSEQ=AAGACACTCCACGGAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:298,74:372,0:0:2,0:23.2:1:30.5:1:1:0:60:185:1:0:0.1 0/1:215:10:7,3:157,48:205,10:0.0465:2,2:18.8:1:28.8:1:0.70414:1.39941:60:20:0.0469:0:1 +1 162741794 . C T 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00122;SOR=14.5272;LSEQ=CACTCCACGGAATGAGGGCT;RSEQ=GTTGCCCTTGTCTTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:0,1:374,160:534,1:0.0019:2,0:1:0:27:0:0.30093:0:60:2:0.0019:0:1 0/1:339:9:4,5:220,109:329,9:0.0265:2,2:25.1:1:28:1:0.17123:2.51543:60:18:0.0269:0:1 +1 162741795 . G A 106 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=17.67208;LSEQ=ACTCCACGGAATGAGGGCTC;RSEQ=TTGCCCTTGTCTTCCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:1:0,1:383,163:546,1:0.0018:2,0:41:0:34:0:0.29982:0:60:2:0.0019:0:1 0/1:350:11:6,5:224,113:337,11:0.0314:2,2:31.4:1:30.9:1:0.51901:1.64944:60:22:0.032:0:1.1 +1 162742117 . C T 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGAACAAAGAGTCCCTTC;RSEQ=AGAGGTGGATTCACAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:28,273:301,0:0:2,0:22.3:1:32.4:1:1:0:60:74.25:0.9966:0:0.2 0/1:174:23:5,18:15,136:151,23:0.1322:2,2:19.6:1:27.7:1:0.15025:2.50:60:46:0.1329:0:1.2 +1 162742180 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCATTGTCCTCTGGATT;RSEQ=CAGTATTGGGTCAACCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:79:1,78:0,0:0,79:1:0,1:23.7:1:32:1:1:0:60:158:1:0:1 1/1:43:43:2,41:0,0:0,43:1:0,1:20.9:1:31.3:1:1:0:60:86:1:0:1.1 +1 162742510 . A G 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAATGAATCACCAACTA;RSEQ=GATAAGGAGGAGTACTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:32:1:30.7:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162742843 . G C 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTTATACTGTTACTAATA;RSEQ=ACAGGAGTTTCTTATAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:12:1:29.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162743418 . G T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.5722;LSEQ=ACATTTTGAATTTTCCTTTA;RSEQ=GTATTTCATCTTTAGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:482:481:123,358:0,0:0,481:0.9979:0,2:23.9:1:30.6:1:1:0:59.9:159.333:0.9979:0:1.1 1/1:276:275:80,195:1,0:1,275:0.9964:0,2:24.1:1:29.7:1:0.29348:0:60:274:0.9964:0:1.1 +1 162743851 . TTG CTCC 62 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TTATGCTCCTTTTCTTCTAT;RSEQ=AGCAACCCTCAAAATGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:26.5:1:31.3:1:1:0:60:8:1:0.25:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162745047 . T TAA 55 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGAGTGACTCCATGGCTT;RSEQ=AAAAAAAAAAAGGTAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:0,0:0,4:0.5:0,0:25.3:1:27.6:1:1:0:60:8:0.5714:0.125:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162748025 . A C 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAGATTCCTCTATCTCTA;RSEQ=CATAAAAACCATTGACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:27.8:1:31.5:1:1:0:58.3:8:0.8:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162748147 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCAAATAGCTTATGGCTGC;RSEQ=TTTTTTTCAGCTCTTGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:23,0:0,0:0,23:1:0,1:25.5:1:30.2:1:1:0:58.1:22:1:0:1 1/1:6:6:6,0:0,0:0,6:1:0,0:12.5:1:27.2:1:1:0:60:5:1:0:1.2 +1 162748285 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11471;SOR=Inf;LSEQ=TTGCCTGTGGTGGGGGAAGG;RSEQ=GTATAGCTGCAGATTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:231,16:247,0:0:2,0:23.5:1:31.2:1:1:0:60:48.4:1:0:0.1 0/1:127:2:1,1:113,12:125,2:0.0157:2,2:21:0:31.5:1:0.19498:9.08719:60:4:0.0161:0:1.5 +1 162748518 . A T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01877;SOR=Inf;LSEQ=CTTCCGAGACCAAGGGAGGC;RSEQ=GGTAAGAACTGTTGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:0:0,0:125,417:542,0:0:2,0:24.5:1:31.7:1:1:0:59.9:76.429:1:0:0.2 0/1:320:4:1,3:90,226:316,4:0.0125:2,2:22.5:1:25:1:1:1.19404:60:3:0.0095:0:3 +1 162748543 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12039;SOR=Inf;LSEQ=AGAACTGTTGGGGATGAATG;RSEQ=ATGTGGACCTGTGTACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:51,300:351,0:0:2,0:24:1:32.3:1:1:0:59.9:116:1:0:0.4 0/1:187:2:1,1:41,144:185,2:0.0107:2,2:12:1:29:0:0.39969:3.48:60:4:0.0109:0:1 +1 162748566 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.09937;SOR=Inf;LSEQ=GTGGACCTGTGTACCTTGAA;RSEQ=GATGGAGAATGGCAAGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:24,203:227,0:0:2,0:23.5:1:31.9:1:1:0:59.8:112.5:1:0:0.7 0/1:105:2:1,1:10,93:103,2:0.019:2,2:32.5:1:31:0:0.19945:8.92:60:4:0.0194:0:2 +1 162748588 . C A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00284;SOR=0;LSEQ=ATGGAGAATGGCAAGTCCTG;RSEQ=CTTAGCAGGAGTGGGCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:145:145:4,141:0,0:0,145:1:0,1:23.3:1:30.4:1:1:0:59.9:47.333:1:0:1.1 1/1:67:62:4,58:0,5:5,62:0.9254:0,2:26.1:1:28.9:1:1:0:60:124:0.9254:0:1.1 +1 162749761 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGTAGGAAAAATGGACAC;RSEQ=ACACCCATTTCAGTTATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:79,3:0,0:0,82:1:0,1:22.8:1:31.7:1:1:0:60:81:1:0:1 1/1:30:30:30,0:0,0:0,30:1:0,1:25.9:1:31.3:1:1:0:58.8:29:1:0:1.1 +1 162750158 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12259;SOR=Inf;LSEQ=GAGAGACAGAGGCTTGTTTG;RSEQ=TTTGCCCTCTTTTCCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:0,116:116,0:0:1,0:28.8:1:32.7:1:1:0:60:22.2:1:0:0.5 0/1:63:2:1,1:3,58:61,2:0.0317:1,2:12:1:27:1:0.12391:16.89:60:4:0.0317:0:1 +1 162750208 . C T 104 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00101;SOR=0;LSEQ=CCCTACCCCTGACTCATATA;RSEQ=ACTTTTTTTTTTTTTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:20:0,20:0,0:0,20:0.4545:0,1:13.3:1:24.1:1:1:0:60:2.333:0.4:0:1.9 0/0:15:0:0,0:0,1:1,0:0:0,0:11:0:34:0:1:0:60:2:0.0667:0:0 +1 162830985 . CCCTCCCTA C 86 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTGAAAGCTCTCTTCGT;RSEQ=CCTCCCCTGGTCAGGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:25.5:1:33.3:1:1:0:60:12:0.6667:0.1111:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 162831191 . ATC A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.51389;SOR=0;LSEQ=AGTGTGTAACTGTGTTCTCA;RSEQ=TCTCTCTCTCCTACCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:2,0:152,9:161,2:0.0123:2,0:25.5:1:31:1:1:0:51:4:0.0126:0:3 0/0:114:0:0,0:106,8:114,0:0:2,0:21.6:1:30.2:1:1:0:59.6:27.5:1:0:0.4 +1 162831227 . ATT A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0;SOR=0.38827;LSEQ=CCCTTTCCTCGTTTCTCTCC;RSEQ=TTTTTTTTTTCTCTCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:127:92,35:140,40:180,127:0.3567:2,2:24.7:1:31.3:1:0.28493:1.33024:59.9:126:0.361:0.0506:0.3 0/1:243:43:30,13:129,45:174,43:0.177:2,2:26.4:1:29.7:1:0.56769:1.2409:59.1:86:0.1799:0.0288:0.3 +1 162831317 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.99295;LSEQ=CAGCCTCAAAAGAAAGCACC;RSEQ=TTTTTTCTGTCATGACTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:651:446:195,251:93,110:203,446:0.6851:2,2:27.9:1:30.6:1:0.67016:1.08811:59.7:43.6:0.6845:0:1.2 1/0:493:337:150,187:71,83:154,337:0.6836:2,2:26.5:1:29.5:1:0.76976:1.06628:59.9:55.167:0.6881:0:1.2 +1 162831391 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22087;SOR=0.74669;LSEQ=ATTATGTGTTATTGCACACC;RSEQ=TACTGACCTTCCCCAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:72:17,55:49,148:197,72:0.2677:2,2:24.6:1:31.1:1:0.87425:1.07088:60:144:0.2677:0:1.3 0/1:182:39:8,31:43,99:142,39:0.2143:2,2:22.1:1:30.1:1:0.31499:1.67856:60:78:0.2167:0:1.6 +1 162831535 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00611;SOR=Inf;LSEQ=AACAGCTACCGTAGAAGGTT;RSEQ=AGCAGAGCTATTGTTTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:0,22:22,0:0:1,0:23.4:1:32.3:1:1:0:60:44:1:0:0 1/0:6:3:0,3:0,3:3,3:0.5:0,0:15.3:1:30:1:1:0:60:6:0.6:0:1 +1 162831722 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCCTACTAACCACAATCA;RSEQ=TGCCCAGCAAATAAATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:12.5:1:28.5:1:1:0:49.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 163276396 . A G 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TATGTTGAAATCCCAATCCC;RSEQ=AATACTTCAGAATGTGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:10:1:30.5:1:1:0:60:4:1:0:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:33:0:31:0:1:0:60:2:1:0:0 +1 163276534 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=AAAAGGAAATTTGGACACAA;RSEQ=AATACACACAAGAATGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:22.7:1:31.9:1:1:0:60:14:1:0:0.1 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:8.5:1:30:1:1:2.23609:60:4:0.2222:0:1 +1 165043980 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06291;SOR=Inf;LSEQ=TAGTTGGCCTCACACTGCTA;RSEQ=GATTCTGATAATTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:207,161:368,0:0:2,0:25.5:1:32.1:1:1:0:60:91:1:0:0.1 0/1:244:3:1,2:138,103:241,3:0.0123:2,2:19:1:26.3:1:0.57889:2.6689:60:6:0.0126:0:1 +1 165044038 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=8.30878;LSEQ=AACTCTCTAATTCTTAGTTG;RSEQ=AAATGTTTCATGCCTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:10:5,5:179,216:395,10:0.0247:2,2:17.9:1:28.2:1:1:1.21:60:20:0.0253:0:1.4 0/1:264:46:25,21:107,111:218,46:0.1742:2,2:25.8:1:28.3:1:0.62677:1.23:60:92:0.1749:0:1.1 +1 165044089 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02774;SOR=2.81649;LSEQ=TACTCAACAGAGATTATTAA;RSEQ=AACAGCACGATGATCCGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:8:2,6:89,191:280,8:0.0278:2,2:33.4:1:32.9:1:1:1.3964:60:16:0.0284:0:1.5 0/1:201:15:6,9:73,113:186,15:0.0746:2,2:28.6:1:32.3:1:1:1.03:60:30:0.0746:0:1.5 +1 165044147 . G A 187 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTGTTTGTTTATTTTTTGG;RSEQ=AATAGCGCAAATGTTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:62:11,51:8,38:46,62:0.5741:2,2:22.3:1:31.5:1:1:1.02:60:124:0.5741:0:1.1 0/0:74:0:0,0:17,57:74,0:0:2,0:25.2:1:30.4:1:1:0:60:73:1:0:0.2 +1 165267008 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12795;SOR=Inf;LSEQ=GAACCAGGGAGAAGAAGGCT;RSEQ=ACTCTACTGAGCCACTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:19,16:35,0:0:2,0:24:1:31.8:1:1:0:60:34:1:0:0.2 0/1:20:2:1,1:10,8:18,2:0.1:2,2:22.5:1:26.5:1:1:1.23603:60:4:0.1:0:1.5 +1 165267095 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08021;SOR=Inf;LSEQ=TTATAGCTGTGGGAACTCAG;RSEQ=CAAGTCATTCAGCCTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:24,0:0:2,0:19:1:32.2:1:1:0:60:48:1:0:0.2 0/1:10:2:1,1:2,6:8,2:0.2:2,2:15.5:1:26.5:1:1:2.65:60:4:0.2:0:1 +1 165470814 . T C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CCAGTCTACACCAGTCATTG;RSEQ=ACCACGAGGATCTGGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:6,6:7,7:14,12:0.4615:2,2:28.6:1:32.3:1:1:1:60:24:0.4615:0:2.2 0/1:13:6:4,2:4,3:7,6:0.4615:2,2:25:1:29.8:1:1:1.45:60:12:0.4615:0:2 +1 165470830 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTACCACGAGGATCTGG;RSEQ=AGACAGCAGGAGTCAGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:17,19:0,0:0,36:1:0,2:28.3:1:29:1:1:0:60:72:1:0:1.4 1/1:14:14:8,6:0,0:0,14:1:0,2:29.8:1:28.3:1:1:0:60:28:1:0:1.6 +1 165645675 . C T 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50835;SOR=1.59861;LSEQ=GCAATACTGTAGACATCAAG;RSEQ=GAACGGGTACTATTCAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:3,4:8,9:17,7:0.2917:2,2:16.4:1:30.1:1:1:1.17684:60:14:0.2917:0:1 0/1:15:6:3,3:5,4:9,6:0.4:2,2:17.7:1:28.3:1:1:1.23147:60:12:0.4:0:1 +1 165645833 . G T 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.41203;SOR=2.12538;LSEQ=GCACATTGAGCACATTAAGC;RSEQ=CTCTAAGACCCAAGATAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:1,3:7,4:11,4:0.2667:2,2:15:1:32.5:1:0.28205:4.676:56.8:8:0.2667:0:1 0/1:9:4:3,1:2,3:5,4:0.4444:2,2:35.3:1:31.3:1:0.52381:3.76:60:8:0.4444:0:1 +1 165871268 . C G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATCAGGAAGTCAGGAGAT;RSEQ=GAGACCATCCTGGCTAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:33.5:1:1:0:28.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 165872043 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49333;SOR=0;LSEQ=GGAGGCAGCGTGCAGCCCAG;RSEQ=CCTCTCGGGGCCCAGATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:15,21:36,2:0.0526:2,2:25:1:29.5:1:1:1.39:60:4:0.0588:0:1 0/0:37:0:0,0:19,18:37,0:0:2,0:27.1:1:31.1:1:1:0:60:36:1:0:0.2 +1 166245037 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCATGCCCAGCCACCAC;RSEQ=GAAGCCACTTCTGTCTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:30.5:1:30.5:1:1:0:50:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 166245453 . T C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02546;SOR=0.38368;LSEQ=GTGGCATCCCTCTGCCCTCA;RSEQ=GGGGTGGCATACCACCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:109:93:58,35:12,4:16,93:0.8532:2,2:25.6:1:31.6:1:0.40653:1.80116:51.9:92:0.8519:0:1.1 1/0:45:31:19,12:8,6:14,31:0.6889:2,2:26.2:1:30.8:1:1:1.18:52.7:62:0.6889:0:1.2 +1 166245498 . C T 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TGTTCACTGGAGGCCTCTTC;RSEQ=GAGCAAGAGAGACTTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:102,55:157,0:0:2,0:25.7:1:30.2:1:1:0:55.3:30.4:1:0:0.5 0/1:85:9:6,3:50,26:76,9:0.1059:2,2:12.3:1:29.7:1:1:1.04:59.2:18:0.1059:0:1.4 +1 166245515 . A T 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13602;SOR=Inf;LSEQ=TTCCGAGCAAGAGAGACTTT;RSEQ=AGTTTGCTCCCTTGAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:114,58:172,0:0:2,0:25.1:1:29.3:1:1:0:56.2:171:1:0:0.4 0/1:101:2:1,1:64,35:99,2:0.0198:2,2:8:0:26:1:1:1.81693:60:4:0.0202:0:1 +1 166245568 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18606;SOR=Inf;LSEQ=CCATTCCACGGCAGCTTTGG;RSEQ=AGTAGGTGAGTCTTCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:134,100:234,0:0:2,0:26.6:1:32:1:1:0:59.6:57.5:1:0:0.2 0/1:178:2:1,1:97,78:175,2:0.0112:2,2:25.5:1:26.5:1:1:1.24204:60:4:0.0114:0:1 +1 166245656 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14915;SOR=Inf;LSEQ=GTGTGGATCATGGGTTGCTC;RSEQ=GTTCTCTTGTTCATCTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:147,151:298,0:0:2,0:24.3:1:30.8:1:1:0:59.6:58.6:1:0:0.1 0/1:188:2:1,1:96,90:186,2:0.0106:2,2:36.5:1:29.5:1:1:1.06633:60:4:0.0109:0:1 +1 166245662 . C A 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56293;SOR=3.16525;LSEQ=ATCATGGGTTGCTCAGTTCT;RSEQ=TTGTTCATCTTAACAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:1:1,0:151,152:303,1:0.0033:2,0:39:0:11:0:1:0:60:0:0:0:4 0/1:193:2:1,1:102,89:191,2:0.0104:2,2:15:0:30.5:1:1:1.14525:44:4:0.0106:0:1.5 +1 166245975 . C A 28 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7;LSEQ=TGCTCCGGTTCTCTCCTAGT;RSEQ=CGGAAAATCCTCCAGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:85,108:193,2:0.0103:2,2:5.5:1:28:1:1:1.27:24:4:0.0104:0:1.5 0/0:139:1:0,1:62,76:138,1:0.0072:2,0:2:0:20:0:1:0:50:2:0.0073:0:4 +1 166246002 . TA T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51713;SOR=0;LSEQ=ATCCTCCAGACTCCTGCCCA;RSEQ=AACACCCATGCTACTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:74,122:196,2:0.0101:2,2:16.5:1:30:1:1:1.64:60:4:0.0102:0:0.5 0/0:134:0:0,0:45,88:133,0:0:2,0:23.7:1:28.9:1:1:0:51.4:132:1:0:0.2 +1 166246010 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52134;SOR=0;LSEQ=GACTCCTGCCCATAAACACC;RSEQ=ATGCTACTGGGGTGGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:66,127:193,2:0.0102:2,2:28:1:28.5:1:1:1.92:55.5:4:0.0104:0:1 0/0:127:0:0,0:45,82:127,0:0:2,0:25.4:1:31:1:1:0:50.9:126:1:0:0.2 +1 166246021 . G A 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATAAACACCCATGCTACTGG;RSEQ=GTGGTCCTGTCAGAATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:68,123:191,0:0:2,0:28.9:1:31.5:1:1:0:49.3:94.5:1:0:0.1 0/1:115:12:4,8:30,71:101,12:0.1043:2,2:28.6:1:28.8:1:0.75078:1.18:54.3:11:0.0973:0:1.3 +1 166246061 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.15771;SOR=Inf;LSEQ=CTCTGCTGCCCGTAGCTGCT;RSEQ=CTCTGTTAGCTATACTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:62,127:189,0:0:2,0:26.7:1:32.8:1:1:0:57.2:378:1:0:0.1 0/1:125:2:0,2:39,84:123,2:0.016:2,0:25:1:31.5:1:1:0:59:4:0.0164:0:1 +1 168652905 . G C 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00445;SOR=0;LSEQ=TGTATAGGGTGTCTGACAAC;RSEQ=CCTGTTGGAGGGTCTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:5,3:5,5:10,8:0.4444:2,2:24.1:1:29:1:0.66406:1.62:46.1:7:0.4118:0:1.5 0/0:14:0:0,0:9,5:14,0:0:2,0:12.5:1:28.9:1:1:0:59.3:28:1:0:0.4 +1 168653061 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=GAACTAACAGGAGGAAAGGC;RSEQ=ATGTCTGCTGGTCTGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:4,6:10,2:0.1667:2,0:35:1:30.5:1:0.51515:0:60:4:0.1667:0:1 0/0:7:0:0,0:1,6:7,0:0:2,0:28:1:28.9:1:1:0:60:14:1:0:0 +1 169022617 . C T 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTTATATCACTGAGGAAG;RSEQ=TGGGTGGGAAACTGAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:11,0:11,3:0.2143:0,0:37.7:1:29.7:1:1:0:60:6:0.2143:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 169022734 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09219;SOR=Inf;LSEQ=AATTTATTATATTAATAGTG;RSEQ=TAATCCTGATATTGTAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:46,1:47,0:0:1,0:27:1:33.5:1:1:0:60:94:1:0:0.1 0/1:21:2:2,0:19,0:19,2:0.0952:1,0:37:1:31.5:1:1:0:60:4:0.1:0:1 +1 169022820 . G T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.29083;SOR=0;LSEQ=AAAGCCTGGTGACATCATAG;RSEQ=AAATCAAATATTCCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:170,87:257,3:0.0115:2,2:17.7:1:21.7:1:0.27048:3.886:60:2:0.0078:0:2.3 0/0:160:0:0,0:99,59:158,0:0:2,0:24.7:1:29.8:1:1:0:60:51.667:1:0:0.1 +1 169022903 . A T 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATTACATAGTTTTTAGTA;RSEQ=ATGGAAGCAGGGTAGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:224,207:431,0:0:2,0:25:1:30.8:1:1:0:59.9:214.5:1:0:0.1 0/1:338:49:31,18:157,132:289,49:0.145:2,2:25.4:1:28.8:1:0.27812:1.45:60:48:0.1463:0:1.1 +1 169022969 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1197;SOR=Inf;LSEQ=CCGCATTTGGAATAAAATCC;RSEQ=AAGTCCAAATCCTTTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:134,228:362,0:0:2,0:26.2:1:30.4:1:1:0:59.9:119.667:1:0:0.1 0/1:192:2:1,1:67,123:190,2:0.0104:2,2:15.5:1:29.5:1:1:1.83:60:4:0.0108:0:1.5 +1 169023065 . A AT 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.04995;SOR=8.08958;LSEQ=TTCTTTTTATTTATTTACTT;RSEQ=TTTTTTTTGTTACAGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:0,58:58,1:0.0169:1,0:35:0:31:0:1:0:60:2:0.0172:0:0 0/1:32:4:0,4:1,27:28,4:0.125:1,0:25.8:1:29.5:1:1:0:60:8:0.129:0:0.3 +1 169024855 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTTTCTTTCTCTTTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:31.5:1:1:0:34:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 169431170 . C T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0.80411;LSEQ=AAACCTAACATTTTGAACCC;RSEQ=CTTCTGTAGTATTACTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:30:29,1:2,0:2,30:0.9375:0,1:21:1:32.1:1:1:0:60:60:0.9375:0:1.5 1/1:13:12:12,0:1,0:1,12:0.9231:0,0:20.3:1:31.2:1:1:0:56.7:24:0.9231:0:1.4 +1 169431218 . A C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00114;SOR=0.22475;LSEQ=GTAGAGGAACTAGTATTTCT;RSEQ=CAAGGTCCTTTTCAAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:58:56,2:28,2:30,58:0.6591:2,1:24.4:1:32.7:1:0.60303:1.98:60:116:0.6591:0:1.3 0/1:30:9:9,0:20,1:21,9:0.3:1,0:28.7:1:30.2:1:1:0:60:18:0.3:0:1.7 +1 169431363 . C T 265 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.0964;LSEQ=TTTCTATCATTTAAGCACAA;RSEQ=AGTACCTTGAATAAGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:530:513:245,268:7,9:16,513:0.9679:2,2:26.2:1:29.5:1:0.80421:1.18:59.9:84.5:0.9694:0:1.1 1/0:398:296:154,142:48,54:102,296:0.7437:2,2:25:1:28.2:1:0.42224:1.22:60:48.333:0.7398:0:1.1 +1 169431437 . CT C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.45197;SOR=1.46019;LSEQ=TAATATTTTACACTGATGTG;RSEQ=TTTTTTTTTCTGAGACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:8:3,5:62,183:245,8:0.0314:2,2:31.4:1:32:1:0.42712:1.77:57.5:16:0.0325:0:0.8 0/1:177:8:1,7:48,120:168,8:0.0452:2,2:22:1:33:1:0.44607:2.78723:60:16:0.046:0:0.3 +1 169431460 . C G 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTTTTTTCTGAGACAGTCT;RSEQ=TCTATCCCACGCAGGAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:29,142:171,0:0:2,0:23.5:1:32.3:1:1:0:59.7:20.375:1:0:0.3 0/1:113:17:3,14:23,73:96,17:0.1504:2,2:29.8:1:31.7:1:0.75816:1.46568:57.8:34:0.1532:0:1.2 +1 169431599 . A G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGTTTTGCCTTGTTGGCC;RSEQ=GGCTGATCTCGATCTCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:13,3:0.1875:1,0:31:1:33:0:1:0:60:6:0.1875:0:1.3 0/0:4:0:0,0:0,4:4,0:0:0,0:20:1:31.3:1:1:0:60:8:1:0:0 +1 169637303 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.083;SOR=Inf;LSEQ=AGCAGTGGAGGGAGAGGTGC;RSEQ=GGCAGGAACCGGGGCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:3,13:16,0:0:2,0:23.2:1:30.8:1:1:0:60:32:1:0:0.7 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:12:1:28.5:1:1:1.41:60:4:0.2857:0:1 +1 169637325 . C T 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30472;LSEQ=GCAGGAACCGGGGCTGCATG;RSEQ=GGTGCTTGTGGGCCAGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:4,6:0.6:0,0:18.8:1:32:0:1:0:60:12:0.6:0:1.8 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:20:1:27.5:1:1:0:60:4:0.6667:0:1.5 +1 169637363 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAGTTCCAGGTGGCATGG;RSEQ=CTTGGTGGACCCCACACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:28:1:32:0:1:0:60:4:0.4:0:3.5 0/0:2:0:0,0:0,2:2,0:0:0,0:32.5:1:32.5:1:1:0:60:4:1:0:1 +1 170599573 . T C 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25075;SOR=Inf;LSEQ=TGGGCATTTAGTACTATAAA;RSEQ=TTCTCTCTTTTGGGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:4,0:4,6:0.6:0,2:18:1:32.2:1:0.2:0:44.7:12:0.6:0:1.3 1/1:4:4:2,2:0,0:0,4:1:0,2:27.5:1:32.3:1:1:0:58.3:8:1:0:1 +1 170600293 . TGTGTTGGGCTGTGGGGACAA T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06061;SOR=Inf;LSEQ=TCTGACCGCAGGCCAGCTGG;RSEQ=GTGTTGGGACTGAGCCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:29.6:1:32.6:1:1:0:56.2:10:1:0:0.2 1/0:6:4:2,2:2,0:2,4:0.6667:0,2:25.8:1:30.9:1:0.46667:0:43.5:8:0.6667:0.3333:0.8 +1 170600344 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=TGAGCCGTCCAGCCTCCCTG;RSEQ=CTCCAGCAGGGGAAAAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:20.8:1:32:1:1:0:52.2:10:1:0:0 0/1:10:2:1,1:4,4:8,2:0.2:2,2:31:0:29.5:1:1:1:31:4:0.2222:0:1 +1 170835642 . T A 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00154;SOR=Inf;LSEQ=TCCAAATCGTTTGCCTTAGA;RSEQ=TACTTGCAGCAGGTTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:156,25:181,0:0:2,0:22.5:1:30.8:1:1:0:60:44.25:1:0:0.1 0/1:122:7:7,0:93,22:115,7:0.0574:2,0:19.1:1:27.6:1:0.34885:0:60:6:0.05:0:1.3 +1 170835762 . G A 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.17661;LSEQ=GCTTAAGAAAAGGACCACTG;RSEQ=GATTTTCACCTACTGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:570:425:184,241:63,81:144,425:0.7456:2,2:27.6:1:31:1:0.92287:1.01869:59.9:84:0.7447:0:1.1 0/1:455:155:72,83:147,153:300,155:0.3407:2,2:26.5:1:28.9:1:0.62181:1.10732:60:18.375:0.3303:0:1.1 +1 170835872 . A C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05364;SOR=0.2835;LSEQ=TAAAACTTTCATTAACTTGC;RSEQ=GAATTCTCATTCTCCAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:11:0,11:2,64:66,11:0.1429:1,0:21.8:1:28.9:1:1:0:60:22:0.1447:0:1.1 0/1:67:3:0,3:4,60:64,3:0.0448:2,0:19.7:1:31.7:1:1:0:60:6:0.0462:0:1 +1 170987149 . T TC 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CAGACCAGACAAGTGGGCTT;RSEQ=CCCCCCAGCAAAGCACACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:27.5:1:30.5:1:1:1.29098:58:4:0.2222:0:0 0/0:5:0:0,0:3,2:5,0:0:2,0:35.2:1:29.6:1:1:0:58.4:10:1:0:0.2 +1 170987152 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.52381;SOR=0;LSEQ=ACCAGACAAGTGGGCTTTCC;RSEQ=CCCAGCAAAGCACACCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:8,2:0.2:2,2:49.5:1:32:0:1:1.58108:60:4:0.2:0:1 0/0:5:0:0,0:3,2:5,0:0:2,0:37:1:29.8:1:1:0:58.4:10:1:0:0.2 +1 170987278 . T C 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TCAGAAACCCTATACAGGAG;RSEQ=GAGCCCACAGGCATCAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:16.5:1:30.5:1:1:0:60:8:1:0:0 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:16.5:1:33.5:1:1:0:60:4:0.3333:0:1 +1 170987501 . C CA 33 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAGCAACAACAGCACCAA;RSEQ=AAAAAAAAAAAAGTCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:23:1:33:0:1:2.45:57:4:0.4:0:0.5 0/0:1:0:0,0:0,1:1,0:0:0,0:20:0:15:0:1:0:41:0:0:0:0 +1 171001567 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.54774;LSEQ=CGTGAGTTTGTCTAGAGTCG;RSEQ=TCTTTGAGGCTCTGACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:11,15:26,2:0.0714:2,2:23.5:1:29.5:1:1:1.35:60:4:0.0769:0:1.5 0/1:25:1:1,0:10,14:24,1:0.04:2,0:1:0:25:0:0.44:0:20:2:0.0417:0:1 +1 171001707 . G T 56 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=CAGTTTGCTGGGGGTTCACT;RSEQ=CAGGCCCTACTCATCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:15.8:1:31.3:1:1:0:50.5:8:1:0:0 1/1:5:4:1,3:0,1:1,4:0.8:0,2:20.3:1:28:1:1:0:35.8:8:0.8:0:1 +1 171002234 . A G 49 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=TGTTGGGCTGCGGAGGGACA;RSEQ=GTCTTGGGACCAAGCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:1,3:0.75:0,2:21.3:1:31.3:1:1:0:45:6:0.75:0:1 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:3:0:28:0:1:0:60:2:0.3333:0:1 +1 171207295 . A G 99 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01282;SOR=0;LSEQ=AGCAGGCACCCATCTTTGCT;RSEQ=TTTTCCAGCCTCCTTGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:23:1:33.1:1:1:0:46.8:16:1:0:1.4 0/1:10:4:2,2:3,3:6,4:0.4:2,2:10.5:1:27:1:1:1:56:3:0.3333:0:1 +1 171207326 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18947;SOR=Inf;LSEQ=TCCTTGAGTGATATCTCCAG;RSEQ=CACAGGAGCGAATCAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:11,0:0:2,0:22:1:32.1:1:1:0:44.2:22:1:0:1 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:29:1:27.5:1:1:1.29:52.5:4:0.2222:0:1 +1 171207335 . C T 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00749;SOR=0;LSEQ=GATATCTCCAGGCACAGGAG;RSEQ=GAATCAGATGAATAAGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:4,3:4,2:6,7:0.5385:2,2:24.4:1:27.7:1:1:1.45385:38.1:14:0.5385:0:1.9 0/0:10:0:0,0:4,6:10,0:0:2,0:32:1:30.7:1:1:0:54.2:20:1:0:0.7 +1 171207408 . T C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6948;LSEQ=ACAGAAGAGGAACCTGACCA;RSEQ=TGAAAGAAAAACAAACAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:8,3:2,1:3,11:0.7857:2,2:22.8:1:31.9:1:1:1.31:50.2:10:0.7692:0:1.2 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:27.6:1:30.4:1:1:1.41418:45.6:10:0.7143:0:1 +1 171207507 . G A 74 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01678;SOR=6.99305;LSEQ=CAAGGGTCAGCGGCCTCAAA;RSEQ=ACCAAAACTAGACAAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:22,26:48,2:0.04:2,2:41:1:31:1:1:1.18:57.5:4:0.0417:0:1 0/1:26:6:2,4:11,9:20,6:0.2308:2,2:33.8:1:29:1:0.64472:2.36181:53.8:12:0.2308:0:1.8 +1 171207510 . CA C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12995;SOR=Inf;LSEQ=GGGTCAGCGGCCTCAAAGAC;RSEQ=AAACTAGACAAACTCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:21,26:47,0:0:2,0:25.1:1:29.8:1:1:0:54.4:22.5:1:0:0.5 0/1:27:2:1,1:11,14:25,2:0.0741:2,2:20.5:1:29:1:1:1.26:60:4:0.0769:0:0 +1 171207680 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAATTAGGCTTCAGAAGA;RSEQ=GGGTAATAAAAAACTACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:41:1:30:1:1:0:50.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 171208014 . C T 90 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21569;SOR=0;LSEQ=TTATAAAAAGAGCAAAGCTA;RSEQ=AATTGATTGGAGTACCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:22.4:1:30.1:1:1:0:50.9:16:1:0:1.4 1/0:10:7:3,4:2,1:3,7:0.7:2,2:30.4:1:28.4:1:1:2.41422:56.1:14:0.7:0:1.3 +1 171208094 . C T 49 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGATATTATCCAGGAAAA;RSEQ=TTACCAAATCTAGCAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:13:0:32:0:1:0:51:2:1:0:2 1/0:5:3:0,3:1,1:2,3:0.6:2,0:19:1:31:0:0.4:0:54:6:0.75:0:1.7 +1 171281278 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=Inf;LSEQ=TTCGGGCCCTGTATTTTTAA;RSEQ=CTCTTTGTCAATTTGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:21:1:32.7:1:1:0:60:20:1:0:0 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:17.5:1:32.5:1:1:1.41:43.5:4:0.3333:0:1 +1 171308832 . A G 216 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=197.85223;LSEQ=GCTGATGCCAAGGTCATGAA;RSEQ=GATGCAAAGATGAAGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:873:1:1,0:452,420:872,1:0.0011:2,0:32:0:14:0:1:0:60:0:0:0:1 0/1:664:123:69,54:269,271:540,123:0.1852:2,2:31:1:31.2:1:0.23079:1.29:42.3:246:0.1866:0:1.2 +1 171309078 . C G 197 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=143.82059;LSEQ=TTTGCCTGGGCCATTGAAAT;RSEQ=GCTGATGAAGACTACGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:1:0,1:215,349:564,1:0.0018:2,0:6:0:14:0:1:0:60:0:0:0:2 0/1:448:91:31,60:138,219:357,91:0.2031:2,2:25.2:1:30.4:1:0.46812:1.21909:32.1:90:0.2045:0:1.1 +1 171393502 . T C 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=TTAAAACCCTTTAATGCATT;RSEQ=CCATTTCACCCAAACATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:37.8:1:33.6:1:1:0:60:10:0.4167:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:50:0:29:0:1:0:60:2:1:0:1 +1 171393700 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08985;SOR=Inf;LSEQ=TCACATTTTCTCCTCCTTGC;RSEQ=TATTCCCCATTCCCAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:162,87:249,0:0:2,0:25:1:31.1:1:1:0:59.9:30.125:1:0:0.3 0/1:203:3:1,2:128,72:200,3:0.0148:2,2:18.7:1:23.3:1:0.30083:3.53233:60:2:0.0101:0:1.3 +1 171393787 . T C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.23012;LSEQ=GTTCCAGCCTCTCCTCTTTA;RSEQ=GACCTCAAGAAGCGAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:153:60,93:74,95:169,153:0.4752:2,2:24:1:30.5:1:0.4295:1.20666:60:75.5:0.4794:0:2 1/0:278:186:76,110:38,53:91,186:0.6691:2,2:24.9:1:29.8:1:0.89725:1.03762:60:92:0.6691:0:1.9 +1 171393800 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.86177;LSEQ=CTCTTTATGACCTCAAGAAG;RSEQ=GAGTGAAAACCTGTCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:86:33,53:80,113:193,86:0.3082:2,2:28.3:1:29.5:1:0.69253:1.13651:60:20.5:0.3015:0:2.8 1/0:246:138:55,83:41,67:108,138:0.561:2,2:26:1:28.8:1:0.79329:1.08:60:45:0.5556:0:2.2 +1 171393826 . G C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22467;LSEQ=AAAACCTGTCTCCCAAGTCA;RSEQ=AGTGCCTTACACACCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:67:20,47:58,97:155,67:0.3018:2,2:23.4:1:32.1:1:0.28919:1.40304:60:66:0.307:0:2.9 0/1:170:15:4,11:53,102:155,15:0.0882:2,2:34:1:32:1:0.77566:1.42608:60:30:0.0898:0:3.1 +1 171393833 . T A 32 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58743;SOR=2.50643;LSEQ=GTCTCCCAAGTCAGAGTGCC;RSEQ=TACACACCTGAAGGCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:1,0:61,135:196,1:0.0051:2,0:1:0:26:0:0.31472:0:60:2:0.0052:0:1 0/1:158:2:1,1:50,106:156,2:0.0127:2,2:5:0:32:0:0.54277:2.11:60:4:0.0127:0:2.5 +1 171393861 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17652;SOR=Inf;LSEQ=CTGAAGGCTCGCCTAGGGCA;RSEQ=GATATGCACAGATAGGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:24,94:118,0:0:2,0:23.2:1:31.5:1:1:0:60:58:1:0:0.6 0/1:86:2:1,1:19,65:84,2:0.0233:2,2:24.5:1:29.5:1:0.41313:3.36:60:4:0.0233:0:2.5 +1 171393911 . T C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29852;SOR=2.07536;LSEQ=CAAGCACAGACTAAGCAACA;RSEQ=AGCCCAGCAGTCAGGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:0,7:2,45:47,7:0.1296:1,0:20.4:1:30.4:1:1:0:60:6:0.1154:0:1 0/1:21:5:1,4:1,15:16,5:0.2381:1,2:23:1:33.6:1:0.42857:3.46:60:10:0.2381:0:1.6 +1 171394212 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACAAATGTTCTATTGTT;RSEQ=TACTAGCCATGATAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 171395913 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCAGCTGTTCACCTCTTG;RSEQ=GGTGTAGCCCGGTTCCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 172415351 . GA G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31203;LSEQ=TTTTGAATATAACGAAAGCA;RSEQ=TTATCAGAGGTTCAATAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:282:169:119,50:84,29:113,169:0.5993:2,2:23.7:1:32.5:1:0.50113:1.2162:59.8:55.333:0.595:0.1135:0.2 0/1:148:47:33,14:70,31:101,47:0.3176:2,2:26.7:1:31.3:1:1:1.04:60:94:0.3176:0.0068:0 +1 172415451 . C T 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43374;LSEQ=TAACACTGCATGGATCAGCA;RSEQ=GAGTAAGGACAGTCTAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:450:273:123,150:84,93:177,273:0.6067:2,2:26.3:1:30.7:1:0.62949:1.10126:59.9:44.5:0.6082:0:1.2 0/1:347:139:62,77:91,116:207,139:0.4006:2,2:24.9:1:29.3:1:0.91256:1.03:60:138:0.4047:0:1.2 +1 172415546 . C T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00122;SOR=3.09203;LSEQ=GCATAATGAGTAAAGCTGGC;RSEQ=AAACAGGACTGCAATGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:22:4,18:28,123:151,22:0.1272:2,2:25.3:1:29.5:1:1:1.02426:60:44:0.1287:0:1.1 0/1:77:24:7,17:13,40:53,24:0.3117:2,2:23.6:1:28.9:1:0.78026:1.26:60:48:0.3243:0:1.1 +1 172772482 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19644;SOR=Inf;LSEQ=CAACATGGCTTCTTCCCTTC;RSEQ=TAGGTCCCGTGACAGCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:30,46:76,0:0:2,0:26.6:1:32.6:1:1:0:39.1:75:1:0:0.1 0/1:61:2:1,1:28,31:59,2:0.0328:2,2:43.5:1:30:1:1:1.11:48:4:0.0328:0:1 +1 173344256 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10145;SOR=Inf;LSEQ=TTTCTAGGTCCTGTGACAGC;RSEQ=ATCTTGCTATTACTCGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:3,13:16,0:0:2,0:18.1:1:30.3:1:1:0:36.8:7:1:0:0.2 0/1:8:2:1,1:4,2:6,2:0.25:2,2:13.5:1:26.5:1:1:1.8258:60:4:0.25:0:1 +1 173485336 . C T 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTTGTCCCTTGGTCTTTGG;RSEQ=TCATTTCTATTTGAATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:19:7,12:7,4:11,19:0.6333:2,2:23.4:1:29.9:1:0.25677:2.88672:60:38:0.6333:0:1.1 0/0:27:0:0,0:14,13:27,0:0:2,0:27.9:1:31:1:1:0:60:54:1:0:0.1 +1 173485363 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16194;SOR=Inf;LSEQ=CTATTTGAATTCCCCACACC;RSEQ=AGTGAAATGTCAGGACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:23,0:0:2,0:18.7:1:28.8:1:1:0:60:46:1:0:0.6 0/1:16:2:1,1:3,11:14,2:0.125:2,2:20.5:1:29:1:0.45:3.32:60:4:0.125:0:1 +1 174099191 . T C 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=GGAAGTTCTCCTGAATAGCC;RSEQ=GAAGTGTGTTTTCCAGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:18.9:1:30.6:1:1:0:28.4:14:1:0:0.1 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:13:0:28.5:1:1:1.41418:27.5:4:0.2857:0:1 +1 175869554 . A C 297 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02604;SOR=0.77331;LSEQ=CAGTGGGCTTGAGCTCATCT;RSEQ=ACCAGATCTTGGTGTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:888:601:318,283:157,129:286,601:0.6768:2,2:26.2:1:32.2:1:0.61432:1.083:60:149.25:0.6769:0:1.1 1/0:550:340:172,168:111,94:205,340:0.6182:2,2:28.1:1:31:1:0.4273:1.15308:59.9:112.333:0.6172:0:1.1 +1 175869673 . AG A 42 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.55441;SOR=0;LSEQ=GTGGTAAAGAGTTTGGATTC;RSEQ=GGATCAAACTCACTTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:31,262:293,3:0.0101:2,2:7.7:1:26.9:1:0.03373:16.57:60:6:0.0102:0.0068:0.3 0/0:155:0:0,0:28,127:155,0:0:2,0:20.8:1:30.2:1:1:0:59.8:76.5:1:0:0.1 +1 175869807 . C G 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06479;SOR=0;LSEQ=ACATTGTGCAACTCAGTGAG;RSEQ=CCTCACACATTGAACACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:10,7:0.4118:0,0:22.1:1:29.6:1:1:0:60:6:0.375:0:1.3 0/0:7:0:0,0:0,7:7,0:0:0,0:19.9:1:31:1:1:0:60:14:1:0:0.1 +1 175914184 . T C 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AACAAATCCAAAACCCATGA;RSEQ=GACTTTGGGGAGAGACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:305,23:328,0:0:2,0:28.3:1:32:1:1:0:32.1:81:1:0:0 0/1:161:13:10,3:127,21:148,13:0.0807:2,2:28.2:1:30.6:1:0.41382:1.80631:37.2:26:0.0813:0:1.1 +1 175914531 . A G 141 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=TATCTCCACAGTTAACTTGG;RSEQ=AGCCTTCAAGGTAAACTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:1,21:0,0:0,22:1:0,1:27.9:1:31.7:1:1:0:58.9:44:1:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:44:0:33:0:1:0:60:2:0.5:0:1 +1 175916267 . T C 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=9e-05;SOR=0.05347;LSEQ=TCAGTACAATGGTGTATTTC;RSEQ=ATAATCCTGTTTCAGTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:595:594:421,173:0,1:1,594:0.9983:0,2:24.7:1:31.5:1:0.29244:0:60:65:0.9983:0:1.1 1/1:425:412:279,133:7,5:12,412:0.9694:2,2:23.3:1:30.5:1:0.53745:1.50:60:102:0.9691:0:1.1 +1 175955557 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAACCCAGTAGCATAACTG;RSEQ=CTCATCAATATACTAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 175955996 . T C 226 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18093;LSEQ=ACATACCACATACCAATTTA;RSEQ=ATTTTAAAATTTAATCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:227:120:108,12:101,6:107,120:0.5286:2,2:25.3:1:32.8:1:0.32528:1.86538:60:240:0.531:0:1.1 0/1:125:21:21,0:96,8:104,21:0.168:2,1:22:1:31.9:1:0.34979:0:60:42:0.1694:0:1 +1 175956248 . AAAT A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.00375;SOR=Inf;LSEQ=TATTTTCACTTCCTGAAAAC;RSEQ=AATAATAATAGTATTTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:0:0,0:155,367:522,0:0:2,0:22:1:30.6:1:1:0:58.9:73.571:1:0:0.1 0/1:342:6:2,4:101,234:335,6:0.0175:2,2:22.2:1:29.4:1:1:1.16:60:12:0.0178:0.0058:0.3 +1 175957231 . TA T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTCAGGGTTTCTACACAA;RSEQ=AAAAAGGGAAGGACTAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:2,0:62,1:63,2:0.0308:1,0:24.5:1:29.5:1:1:0:60:4:0.0317:0:0 0/0:24:0:0,0:23,1:24,0:0:1,0:18.5:1:27.5:1:1:0:58.5:23:1:0:0.4 +1 175957897 . G A 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAATCACTTGAACCTGGG;RSEQ=GGCAGATGCTGCAGTGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:30:1:30.8:1:1:0:27.3:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 175958358 . T TA 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.75272;LSEQ=CTACTTTAATTGGACAAGAT;RSEQ=AAAAAAAAAATCTACTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:7:6,1:121,0:121,7:0.0547:1,2:28.4:1:29.3:1:0.05469:0:60:14:0.0547:0.0078:0 0/1:48:2:2,0:46,0:46,2:0.0417:1,0:15:1:28.5:1:1:0:60:4:0.0417:0.0208:0 +1 175958420 . C T 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13103;SOR=5.48487;LSEQ=AATATTATAGTTTACATACA;RSEQ=CCTCAGTGACATTACAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:1:0,1:370,37:407,1:0.0025:2,0:1:0:25:0:0.09314:0:60:2:0.0025:0:2 0/1:225:3:2,1:201,21:222,3:0.0133:2,2:15:1:31:1:0.26666:4.72798:60:6:0.0136:0:1.7 +1 175958637 . T A 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00047;SOR=0;LSEQ=TAAAACAAAACAAAATTAGA;RSEQ=AAATGTAGTAAATGCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:17:4,13:85,371:456,17:0.0359:2,2:19.3:1:29.1:1:0.53931:1.34:60:7.5:0.0326:0:1.3 0/0:293:0:0,0:59,233:292,0:0:2,0:23.1:1:27.7:1:1:0:59.9:72:1:0:0.1 +1 175958683 . GT G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14146;SOR=Inf;LSEQ=AGCAAAGTTAATTTTAACTG;RSEQ=TTTTGGTTTTTTCATTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:4,171:175,0:0:1,0:21.4:1:30.6:1:1:0:60:57.333:1:0:0 0/1:106:2:0,2:1,103:104,2:0.0189:1,0:27:1:32:1:1:0:60:4:0.0189:0:0 +1 175997035 . TA T 85 MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=1.46382;LSEQ=CCTGAAACTGGGTAATTTAT;RSEQ=AAAAAAAAAAAAAGAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:0,6:0,6:6,6:0.4:0,0:24.2:1:33:0:1:0:56.5:12:0.4615:0:0.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:49:0:29:0:1:0:60:2:0.5:0:0 +1 176012392 . C T 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGTCAACACTCCAACACCT;RSEQ=TTCTCATGCTCCTGGAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1045:0:0,0:425,620:1045,0:0:2,0:25.1:1:32.3:1:1:0:60:44.435:1:0:0.1 0/1:692:29:12,17:280,379:659,29:0.0419:2,2:24.3:1:29.1:1:1:1.04655:60:28:0.0415:0:1.3 +1 176012466 . G GA 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.88711;SOR=0.94391;LSEQ=TCTCAAAATGAATAAAGCAA;RSEQ=AAAAAAAAAAACCTGATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:38:6,32:46,243:289,38:0.1111:2,2:26.3:1:30.4:1:1:1.00957:59.7:37:0.1246:0.0058:0.3 0/1:199:21:2,19:31,133:164,21:0.1055:2,2:25.4:1:28.2:1:0.37751:2.2067:57.9:9.5:0.1056:0.0151:0.4 +1 176012482 . A G 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=4e-04;SOR=Inf;LSEQ=GCAAGAAAAAAAAAAACCTG;RSEQ=TATCAATTTATTGTTACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:24,260:284,0:0:2,0:21.7:1:31.1:1:1:0:59.8:39.571:1:0:0.3 0/1:141:7:0,7:5,128:133,7:0.0496:1,0:28:1:29.3:1:1:0:60:6:0.0441:0:1 +1 176012495 . G A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00411;SOR=Inf;LSEQ=AAACCTGATATCAATTTATT;RSEQ=TTACGGGGAGAGGGAAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:11,185:196,0:0:2,0:24.5:1:31.9:1:1:0:59.8:20.778:1:0:0.3 0/1:100:5:0,5:2,92:94,5:0.05:1,0:20.4:1:31.6:1:1:0:60:10:0.0521:0:1 +1 176012709 . T C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00056;SOR=0.21167;LSEQ=GGAAAAAAAAGCATTTGGTA;RSEQ=TGCATAGGTGTTACACAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:53:47,6:57,6:63,53:0.4569:2,2:26.9:1:32.4:1:0.76916:1.21074:59.5:106:0.4569:0:1.2 0/1:40:6:5,1:34,0:34,6:0.15:1,2:32.5:1:31.3:1:0.15:0:60:12:0.1538:0:1 +1 176012807 . G A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62586;LSEQ=AAAGTTTTAACAAACCAAAT;RSEQ=TATGATTCATATAACATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:674:673:496,177:0,0:0,673:0.9985:0,2:24.1:1:28.9:1:1:0:60:95.143:0.9985:0:1.1 1/1:422:421:298,123:0,0:0,421:0.9976:0,2:22.3:1:28:1:1:0:60:139.333:0.9976:0:1.1 +1 176014960 . G A 43 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATGTTGAGATATGTGCA;RSEQ=GCTAGGGGAAAAATTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:15.7:1:27.7:1:1:0:59.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 176015104 . GA G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.32842;SOR=2.89059;LSEQ=GAACTTTAATTTGGCAACCA;RSEQ=AAAAAAAAAAAGGCTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:7,0:20,0:20,7:0.25:1,0:20.7:1:33.4:1:1:0:60:14:0.2692:0.1071:0.1 1/0:6:3:3,0:2,1:3,3:0.5:2,0:19.3:1:33:1:1:0:60:6:0.5:0.1667:0.3 +1 176015573 . T G 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0033;SOR=Inf;LSEQ=TAAATACCTTCAAATTGTAC;RSEQ=AGACCTCATATCCAGATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:2,156:158,0:0:1,0:25.2:1:28.7:1:1:0:60:316:1:0:0 0/1:76:5:0,5:0,71:71,5:0.0658:1,0:33.8:1:31:1:1:0:60:10:0.0667:0:1.2 +1 176050138 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAATTTGGCATATAGAA;RSEQ=CTCAGGAACTTGCCTAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:51,1:0,0:0,52:1:0,1:22.4:1:30.8:1:1:0:60:51:1:0:1.1 1/1:29:29:28,1:0,0:0,29:1:0,1:22.1:1:29.1:1:1:0:60:28:1:0:1.1 +1 176050428 . A T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05306;SOR=Inf;LSEQ=GCAGTTCGACTGTCATCTAT;RSEQ=TGAAAAAAAAAAAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:101,305:406,0:0:2,0:18.4:1:27.5:1:1:0:59.1:6.66:0.9972:0:0.5 0/1:246:3:0,3:77,166:243,3:0.0122:2,0:19:1:20.3:1:0.55402:0:51.3:2:0.0093:0:3.3 +1 176050429 . T A 30 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.71015;SOR=1.30682;LSEQ=CAGTTCGACTGTCATCTATA;RSEQ=GAAAAAAAAAAAAAAAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:0,4:95,289:384,4:0.0102:2,0:28:1:15:1:0.57603:0:56.3:0:0:0:3 0/1:225:3:1,2:68,154:222,3:0.0133:2,2:19.3:1:24.3:1:1:1.13:60:2:0.0112:0:1.7 +1 176050446 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12901;SOR=Inf;LSEQ=ATATGAAAAAAAAAAAAAAA;RSEQ=GACAAAACAGATGAATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:49,232:281,0:0:2,0:18.9:1:30.6:1:1:0:58.4:17.733:1:0:0.7 0/1:158:2:1,1:33,123:156,2:0.0127:2,2:37:1:30:1:0.38515:3.69:60:4:0.0133:0:3 +1 176050447 . G A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37893;SOR=0.60425;LSEQ=TATGAAAAAAAAAAAAAAAA;RSEQ=ACAAAACAGATGAATTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:18:16,2:10,229:239,18:0.07:1,2:7.5:1:19.4:1:0:170.65:55:1.571:0.046:0:1.8 0/1:138:6:6,0:9,122:131,6:0.0435:2,0:8.7:1:22.7:1:0:0:53.3:2:0.0315:0:2.5 +1 176050449 . C A 54 p8;q25;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.77673;SOR=1.14622;LSEQ=TGAAAAAAAAAAAAAAAAGA;RSEQ=AAAACAGATGAATTGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:8:8,0:8,223:231,8:0.0332:1,0:7.6:1:18.3:1:0:0:52.5:1:0.0174:0:2.3 0/1:132:5:5,0:7,118:125,5:0.0379:2,0:6:1:24.2:1:0:0:51:4:0.0325:0:2.6 +1 176050676 . A T 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATAATTCCTTGGAAAAA;RSEQ=AATAATAACAATAATAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:17.3:1:29.2:1:1:0:60:12:0.8571:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 176069548 . C T 32 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65322;SOR=2.13568;LSEQ=AAAAAAAAAAAAAAAAAAGA;RSEQ=TGGAGAGAGATAAATTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:2:2,0:130,128:258,2:0.0076:2,0:10:1:15:1:0.49819:0:35:0:0:0:5 0/1:186:3:1,2:86,97:183,3:0.0161:2,2:7.7:1:20.7:1:1:1.76796:57.7:2:0.0133:0:2 +1 176069628 . T A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33676;SOR=3.57444;LSEQ=CCTTTGTTATTTTTAAGTGT;RSEQ=TGCCTACATTTTAGACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:1,0:72,130:202,1:0.0049:2,0:1:0:23:0:0.35961:0:60:2:0.005:0:1 0/1:172:3:2,1:69,100:169,3:0.0174:2,2:23:1:26.7:1:0.56974:2.88:60:6:0.0175:0:1 +1 176069648 . C T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21548;SOR=Inf;LSEQ=TTGCCTACATTTTAGACTAA;RSEQ=CCTGCTTGTTCCTGTGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:29,87:116,0:0:2,0:20.8:1:31.1:1:1:0:59.9:115:1:0:0.1 0/1:101:2:1,1:33,66:99,2:0.0198:2,2:10:0:29.5:1:1:1.99:37.5:4:0.0202:0:1 +1 176085412 . C G 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAGGGCCAGCTACTTGA;RSEQ=AGGCTGAGGTAGGAGAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:13.2:1:32.8:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 176103954 . C T 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57425;SOR=0;LSEQ=TAACATTATAGTATTCTACT;RSEQ=GCTAACTCTTCCTGGCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:8:8,0:38,1:39,8:0.1702:1,0:25.5:1:31:1:1:0:60:16:0.1778:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:22.3:1:32.2:1:1:0:60:12:1:0:0 +1 176104082 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55936;SOR=3.34668;LSEQ=GCATGGAAAAGGCTCCTAAA;RSEQ=GACTAGACCATATGCATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:1:1,0:244,63:307,1:0.0032:2,0:2:0:30:0:1:0:60:2:0.0033:0:1 0/1:185:2:1,1:144,39:183,2:0.0108:2,2:12.5:1:28:1:0.3866:3.65885:60:4:0.011:0:1.5 +1 176104087 . A T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05659;SOR=Inf;LSEQ=GAAAAGGCTCCTAAAGGACT;RSEQ=GACCATATGCATACTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:272,73:345,0:0:2,0:23.4:1:29.2:1:1:0:60:85.25:1:0:0.1 0/1:216:3:1,2:165,48:213,3:0.0139:2,2:19:1:29.7:1:0.1346:6.79546:60:6:0.014:0:1 +1 176104265 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16216;SOR=Inf;LSEQ=TATAGTAGATATTTCAAATA;RSEQ=AAGATATATAAATCAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:30,214:244,0:0:2,0:24.3:1:32.6:1:1:0:60:243:1:0:0.1 0/1:165:2:1,1:33,129:162,2:0.0121:2,2:36.5:1:29:1:0.37266:3.87:60:4:0.0122:0:1 +1 176105710 . CA C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.33117;SOR=0.81359;LSEQ=ATTAAATAGAGAGAGAAAGA;RSEQ=AAAAAAAAAAAGCCTAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:83:15,68:90,282:372,83:0.1751:2,2:31.1:1:31.6:1:0.25237:1.44571:59.9:166:0.1808:0.0042:0.3 0/1:326:48:9,39:77,185:262,48:0.1472:2,2:28.3:1:30.6:1:0.16105:1.80049:59.9:96:0.1524:0.0031:0.3 +1 176105755 . T A 24 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63702;SOR=1.63464;LSEQ=CCAAAATGGCATCACCATGA;RSEQ=CATAAAATAAATTTACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:2:2,0:8,213:221,2:0.009:1,0:12:1:14:0:0.00182:0:60:0:0:0:7 0/1:137:2:2,0:4,130:134,2:0.0146:1,0:7:1:24:1:0.00163:0:60:4:0.015:0:4.5 +1 176117805 . T G 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAAAACTATATCCTACC;RSEQ=AAGGCTTTATTATCTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:26:1:27.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 176118219 . G A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07607;SOR=1.36881;LSEQ=TGCATGTGATTCCTACAATA;RSEQ=AAAATTATAATTTTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:98:32,66:114,237:351,98:0.2183:2,2:20.8:1:30.4:1:1:1.01:60:97:0.219:0:1.1 0/1:282:78:27,51:74,130:204,78:0.2766:2,2:19.9:1:29.6:1:0.88972:1.07496:59.7:156:0.2786:0:1.1 +1 176118238 . T C 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12888;SOR=Inf;LSEQ=AGAAAATTATAATTTTTCTT;RSEQ=TAAAAAATATAACTGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:72,236:308,0:0:2,0:22:1:30.5:1:1:0:60:307:1:0:0.2 0/1:173:2:1,1:54,117:171,2:0.0116:2,2:7:0:30.5:1:0.53603:2.16:60:4:0.0118:0:1 +1 176131963 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0707;SOR=Inf;LSEQ=GTCTTTTTTATTGCAATAAA;RSEQ=TTCATCATTTAAAATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:317,82:399,0:0:2,0:22.9:1:32.7:1:1:0:60:65.5:0.9975:0:0.1 0/1:283:3:1,2:214,66:280,3:0.0106:2,2:8.3:1:27:1:0.14445:6.43049:60:6:0.0108:0:1 +1 176132292 . C T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGCTCCCTACTGTCTTA;RSEQ=AGTTATAACTTAAACACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:1,42:0,0:0,43:1:0,1:24.3:1:28.5:1:1:0:59.3:20.5:1:0:1.5 1/1:9:9:0,9:0,0:0,9:1:0,0:12.3:1:28.8:1:1:0:60:18:1:0:1 +1 176132602 . C T 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGGCTTGAGTGATCCTC;RSEQ=CACCTTGGCCTCCCAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:4,1:5,4:0.4444:2,2:28.8:1:31:1:1:1.29098:60:8:0.4444:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 176134531 . T G 29 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=21.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GTGTGTGTGTGTAGGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 176145008 . G T 43 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.41274;SOR=2.58858;LSEQ=AGCACACAATTTTGGGGATC;RSEQ=AAATATTTTTAAAATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:2:0,2:363,119:482,2:0.0041:2,0:1:0:24.5:1:0.06211:0:60:4:0.0042:0:1 0/1:376:4:1,3:271,99:370,4:0.0106:2,2:10.8:1:21.8:1:0.06351:8.15766:60:3:0.0081:0:1.8 +1 176145159 . GA G 90 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.30985;SOR=1.67272;LSEQ=TGTAGCTATTAGTAGGGGGG;RSEQ=AAAAAAAGGCTTAATTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:828:8:4,4:231,588:819,8:0.0097:2,2:24.9:1:30:1:0.23334:2.54:60:16:0.0099:0:0 0/1:498:8:1,7:161,329:490,8:0.0161:2,2:33.1:1:30.3:1:0.44729:3.41914:60:16:0.0163:0:0.1 +1 176145277 . T C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00145;SOR=3.7918;LSEQ=AATAAATTTATTTTTGCTTA;RSEQ=ATTTTTACATTATCAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:55:0,55:1,50:51,55:0.5189:1,1:19.2:1:32.4:1:0.48113:0:59.3:26.5:0.5096:0:1.1 1/1:41:33:0,33:0,8:8,33:0.8049:0,1:22.1:1:32.4:1:1:0:60:66:0.8049:0:1 +1 176153442 . A G 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCCAACCTATCCCCACA;RSEQ=GTGAGTAATTAGTGCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:33.7:1:33.3:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 176153658 . T C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=3.08249;LSEQ=ACATGTCAAGAAAAAAAATA;RSEQ=GACTGTAACATAATCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:82:78,4:84,7:91,82:0.4713:2,1:25.4:1:32.3:1:0.54179:1.62:60:81:0.4709:0:1 1/0:109:80:75,5:26,3:29,80:0.7339:2,2:21.3:1:31.6:1:0.43637:1.72:60:160:0.7339:0:1.1 +1 176153673 . C T 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56768;SOR=2.9798;LSEQ=AAATATGACTGTAACATAAT;RSEQ=AAAGTTGGTTTAAAACACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:0,1:220,25:245,1:0.0041:2,0:1:0:24:0:0.10569:0:60:2:0.0041:0:1 0/1:166:2:1,1:141,23:164,2:0.012:2,2:25:1:24.5:1:0.269:6.02262:60:4:0.0121:0:1 +1 176153853 . A AT 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.76272;LSEQ=AAAGAAAAGAAAAATAATTG;RSEQ=TTTTTTTTTAAAAGTAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:6:2,4:75,294:369,6:0.016:2,2:28:1:30.8:1:0.60704:1.96:60:12:0.0162:0:0 0/1:245:3:0,3:61,181:242,3:0.0122:2,0:34:1:30:1:0.57581:0:60:6:0.0124:0:0 +1 176175885 . C A 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00227;SOR=0;LSEQ=TGGACACCGCCCCGCCGCCG;RSEQ=TACCCGATACGGCGGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:13:5,8:49,176:225,13:0.0546:2,2:24.8:1:31.4:1:0.17753:2.24:59.6:26:0.0563:0:1.3 0/0:153:0:0,0:51,102:153,0:0:2,0:20.3:1:32.1:1:1:0:60:152:1:0:0.3 +1 176175938 . G A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.30262;SOR=4.62817;LSEQ=CGCACCGGGCCCCCGAGGCC;RSEQ=CCCGAGCCGGCGGCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:1,0:70,25:95,1:0.0104:2,0:1:0:27:0:1:0:60:2:0.011:0:1 0/1:64:3:2,1:46,15:61,3:0.0469:2,2:12.3:1:28.3:1:1:1.52217:57.3:6:0.0492:0:2 +1 176175999 . G T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41914;SOR=2.41212;LSEQ=CTGCCGCCGAAACCGCCACG;RSEQ=AAGGCGGCGACGGGGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:2:0,2:296,129:425,2:0.0047:2,0:1:0:27:0:0.09362:0:60:4:0.0048:0:1 0/1:356:4:2,2:233,119:352,4:0.0112:2,2:28.3:1:26:1:0.60733:1.95408:60:8:0.0113:0:1 +1 176176119 . A C 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=GGCGGCTACCAGACATCGTG;RSEQ=CTCCCTCCCCTCCAGCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:219,296:515,0:0:2,0:25.3:1:29.8:1:1:0:59.9:84.833:1:0:0.1 0/1:433:13:5,8:173,247:420,13:0.03:2,2:25.5:1:31.3:1:1:1.12039:60:26:0.0302:0:1.4 +1 177199560 . A G 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03219;SOR=5.57707;LSEQ=TTGTGCTGCTTATAAGTTGA;RSEQ=GACAAATCAGGCAGCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:2,1:15,9:24,3:0.1111:2,2:20.3:1:28:1:1:1.19:60:2:0.0833:0:1.3 0/1:19:8:3,5:5,6:11,8:0.4211:2,2:35.5:1:30.3:1:1:1.36508:60:16:0.4211:0:1 +1 177294186 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13876;SOR=Inf;LSEQ=TGCTGCCTGGCATTTACAGG;RSEQ=AAGGACTTCTGAAATCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:30,18:48,0:0:2,0:26.4:1:29.6:1:1:0:47.4:23:1:0:0.1 0/1:29:2:1,1:18,9:27,2:0.069:2,2:31:1:30:1:1:1.94942:22:4:0.069:0:1 +1 177294353 . G A 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13364;SOR=0;LSEQ=AATTTGTTTCCTCTAGGATC;RSEQ=AGGCCATCGAGCTACAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:1,4:3,11:14,5:0.2632:2,2:24.8:1:30:1:1:1.086:26:10:0.2632:0:1.2 0/0:10:0:0,0:5,5:10,0:0:2,0:25.3:1:29.3:1:1:0:52:20:1:0:0.2 +1 177294420 . G A 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24242;SOR=0.1257;LSEQ=CTCAACTCACAACTTCTACC;RSEQ=AGGACTCCTGAACTGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:1,0:1,4:0.8:0,0:36.5:1:31.8:1:0.2:0:55.3:8:0.8:0:1 0/1:7:2:0,2:1,4:5,2:0.2857:2,0:47.5:1:31:1:1:0:60:4:0.2857:0:1 +1 177392910 . C T 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCCAGGATTTTACCTTA;RSEQ=CTGCATGCTAGCAAGTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:28.5:1:32.5:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:33:0:28:0:1:0:60:2:1:0:0 +1 177394601 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCATGCGCGCGCGCGCGCG;RSEQ=GTGTGTGTGTGTGTGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:30.5:1:28.5:1:1:0:52:4:0.6667:0:1.5 +1 178163144 . G T 50 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCAATCGTTAAACACTTG;RSEQ=ATCAAATCATAACTAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:19.7:1:31.7:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:19:0:31:0:1:0:60:2:1:0:1 +1 178163570 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1347;SOR=Inf;LSEQ=GAGTAGTGTCTTCCAACACA;RSEQ=CCACCAACTATGCCTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:12,201:213,0:0:2,0:26.4:1:30.5:1:1:0:60:105.5:1:0:0.1 0/1:124:2:1,1:11,111:122,2:0.0161:2,2:13.5:1:29:1:0.18489:9.70:60:4:0.0165:0:1 +1 179084149 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2042;SOR=Inf;LSEQ=CCATAGGTAGCAATTTCCCA;RSEQ=AACAATACCCCAAAAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:20,0:0:2,0:30.5:1:32.7:1:1:0:60:40:1:0:0 0/1:17:2:1,1:7,8:15,2:0.1176:2,2:42:0:31:1:1:1.13:60:4:0.1176:0:1.5 +1 179086078 . C A 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGCTCAAGCAACTCCC;RSEQ=TGCCTCAGCCTTCAGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:32:1:1:0:60:4:1:0:1.5 +1 179095667 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50769;SOR=0;LSEQ=CTCAGCTGCACTGCGTGACA;RSEQ=AGGTCCATGGTACCAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:62,66:128,2:0.0154:2,2:28.5:1:29.5:1:1:1.06:60:4:0.0156:0:1 0/0:98:0:0,0:52,46:98,0:0:2,0:24.7:1:31.1:1:1:0:60:31.667:1:0:0.2 +1 180810083 . TA T 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.15958;LSEQ=TAACATGCCGTGCTAAGCAC;RSEQ=AAAAAAATAGCAACAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:4:4,0:203,12:215,4:0.0183:2,0:38:1:33.5:1:1:0:60:8:0.0186:0:0 0/1:142:3:3,0:132,7:139,3:0.0211:2,0:42.3:1:29:1:1:0:60:6:0.0213:0:0 +1 180810185 . G C 126 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=28.90293;LSEQ=GCATTAATTGGTTCTTAATA;RSEQ=TATTGTTAAGTGTACTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:871:1:0,1:417,453:870,1:0.0011:2,0:46:0:35:0:1:0:60:2:0.0012:0:2 0/1:590:19:9,10:267,303:570,19:0.0322:2,2:25.9:1:29.7:1:1:1.02:60:8.5:0.0292:0:1.5 +1 180810233 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.38919;SOR=1.12833;LSEQ=GGCTTAAAATGGTAAATTTT;RSEQ=TTTGTTTTTACCACAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:236:88,148:153,214:367,236:0.3914:2,2:23.1:1:30.1:1:0.30701:1.20205:60:77.667:0.3936:0:1.1 0/1:390:164:64,100:94,131:225,164:0.4205:2,2:24.1:1:28.9:1:0.60256:1.12085:60:328:0.4282:0:1.2 +1 180810249 . G GT 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.8659;LSEQ=TTTTGTTTGTTTTTACCACA;RSEQ=TTTTTTTTTAAAGGCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:11:3,8:168,304:472,11:0.0227:2,2:33.5:1:30.5:1:0.75385:1.47257:60:22:0.023:0:0.3 0/1:304:6:1,5:108,188:296,6:0.0197:2,2:27:1:30.3:1:0.42389:2.86415:60:12:0.0203:0:0.7 +1 180810259 . A T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26301;SOR=1.88639;LSEQ=TTTTACCACAGTTTTTTTTT;RSEQ=AAGGCATAAAAATAGAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:6:2,4:134,268:402,6:0.0147:2,2:18:1:28.2:1:1:1:60:12:0.0147:0:1.2 0/1:256:7:3,4:80,169:249,7:0.0273:2,2:26.3:1:28.1:1:0.68503:1.58:60:14:0.0275:0:1.1 +1 181474675 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCCACCATGCCTGGCTAA;RSEQ=ATTTTGTATTTTTTTTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:30:0:1:0:21:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 181475237 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.13846;SOR=Inf;LSEQ=TGTCACTGAATTCTAGAACA;RSEQ=AGAGTCAGAGTCCTGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:16,0:0:2,0:15.4:1:31.9:1:1:0:60:32:1:0:0.1 0/1:10:2:1,1:4,4:8,2:0.2:2,2:5.5:1:28:1:1:1:60:4:0.2:0:1 +1 181475244 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51567;SOR=0;LSEQ=GAATTCTAGAACAGAGAGTC;RSEQ=GAGTCCTGGACAGACTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:15,2:0.1176:2,2:29:1:29.5:1:1:1.46:60:4:0.1176:0:1 0/0:10:0:0,0:5,5:10,0:0:2,0:16.3:1:28.2:1:1:0:60:20:1:0:0.1 +1 181801200 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CAAATGAGTTCAACTAACAA;RSEQ=TTCTACCAAGGACCCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:11:1:31:1:1:0:48.4:10:1:0:0.6 1/0:4:2:1,1:0,2:2,2:0.5:0,2:17.5:1:31.5:1:1:0:26:4:0.6667:0:1 +1 181801585 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAACCAGGGCGGTGCGCAG;RSEQ=GCTTGTGGGACAGGGCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:32.5:1:1:0:52:4:1:0:1.5 +1 181801766 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCACGCTTGAATTCTTGC;RSEQ=GGGCTTCAGCCGCCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:31:1:1:0:54.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 181818020 . G A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAGGCGCCCATTGAAAA;RSEQ=AAACCATAATAAGCGTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:25,16:0,0:0,41:1:0,2:28.9:1:30.8:1:1:0:53.9:82:1:0:1 1/1:14:14:7,7:0,0:0,14:1:0,2:25.8:1:28.1:1:1:0:55.6:13:1:0:1.1 +1 181818150 . G A 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGGTGCAGCGGCCCATGTGA;RSEQ=AGCCACATGGGAAAGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:3,10:0,2:2,13:0.8667:0,2:22.7:1:29.7:1:1:0:60:12:0.8571:0:1.2 1/1:3:3:0,3:0,0:0,3:1:0,0:29.3:1:30:1:1:0:60:6:1:0:1 +1 181818482 . C A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTAACGTGCTAAGCTCC;RSEQ=TGGGTGGGTGAAGGGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:5,3:8,3:0.2727:2,2:29:1:32.3:1:0.54545:2.97405:60:6:0.3:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:43.5:1:32:1:1:0:60:4:1:0:0.5 +1 181818912 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23494;SOR=Inf;LSEQ=CTCCTGGTGCCACCAAACTG;RSEQ=GTGAGACCCTCCAACACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:28,31:59,0:0:2,0:26.5:1:31:1:1:0:60:28.5:1:0:0.1 0/1:56:2:1,1:23,31:54,2:0.0357:2,2:21.5:1:28.5:1:1:1.34:60:4:0.0364:0:1.5 +1 181818999 . C T 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.13645;LSEQ=GCTCCTTGAGGTCAGAGGTC;RSEQ=CAGAAGCAGGAGGCATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:2,10:12,3:0.2:2,0:31.3:1:29:1:1:0:60:6:0.2:0:1.7 0/1:9:2:0,2:2,5:7,2:0.2222:2,0:9.5:1:26:1:1:0:60:4:0.2222:0:2 +1 181819067 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28871;SOR=Inf;LSEQ=GACATTTCCAGGCATGGAAG;RSEQ=GAATCAGATGAATAGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:6,8:3,3:6,14:0.7:2,2:23.9:1:30.6:1:1:1.31413:59.4:28:0.7:0:1.7 1/1:5:5:3,2:0,0:0,5:1:0,2:17.2:1:31:1:1:0:60:10:1:0:1.6 +1 181819068 . G A 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28871;SOR=0;LSEQ=ACATTTCCAGGCATGGAAGC;RSEQ=AATCAGATGAATAGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:3,3:6,8:14,6:0.3:2,2:33.7:1:31.2:1:1:1.31:60:12:0.3:0:1 0/0:5:0:0,0:3,2:5,0:0:2,0:17:1:33.2:1:1:0:60:10:1:0:1.6 +1 181819083 . G A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.21278;LSEQ=GAAGCGAATCAGATGAATAG;RSEQ=GCTGGAAGTGAATCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:3,6:7,4:11,9:0.45:2,2:24:1:31.6:1:0.36985:3.27423:59:18:0.45:0:2 1/0:6:3:3,0:2,1:3,3:0.5:2,0:26.3:1:30:1:1:0:60:6:0.5:0:1.7 +1 181819187 . T C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00182;SOR=0;LSEQ=AATGACACCATCAACAAAAA;RSEQ=AACAACAAAACGGGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:79:44,35:0,0:0,79:1:0,2:26.8:1:32.3:1:1:0:55.4:158:1:0:2.1 1/1:45:39:23,16:3,3:6,39:0.8667:2,2:25.2:1:30.8:1:0.68613:1.43:54.9:78:0.8667:0:1.9 +1 181819202 . C T 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=AAAAATAACAACAAAACGGG;RSEQ=CCCCACAAAAACCCCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:22:11,11:39,35:74,22:0.2292:2,2:27.7:1:29.3:1:1:1.11303:54.9:44:0.2316:0:2.6 0/0:51:0:0,0:25,26:51,0:0:2,0:29.2:1:29.5:1:1:0:53.2:50:1:0:1.6 +1 181819206 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11881;SOR=Inf;LSEQ=ATAACAACAAAACGGGCCCC;RSEQ=ACAAAAACCCCATCTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:50,46:96,0:0:2,0:30.3:1:31.8:1:1:0:53.9:95:1:0:2 0/1:51:2:1,1:24,25:49,2:0.0392:2,2:32.5:1:29.5:1:1:1.04:60:4:0.04:0:3 +1 181819208 . CA C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54375;SOR=0;LSEQ=AACAACAAAACGGGCCCCCA;RSEQ=AAAACCCCATCTGAGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:50,44:94,2:0.0208:2,2:32.5:1:32:1:1:1.13485:60:4:0.0208:0:2 0/0:51:0:0,0:25,26:51,0:0:2,0:31.1:1:28.6:1:1:0:52.8:50:1:0:1.6 +1 181819234 . G C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=CCCCATCTGAGGGTCAGCAG;RSEQ=CTCAAAGACCAAAACTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:104:104:50,54:0,0:0,104:1:0,2:27.7:1:31.5:1:1:0:54.1:25:1:0:1.9 1/1:58:50:21,29:3,5:8,50:0.8621:2,2:27.2:1:30.4:1:1:1.20:52.2:24:0.8571:0:1.7 +1 181819362 . G T 60 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57964;LSEQ=ACAACATCTCTCCATCAAGG;RSEQ=TGCAGAACTGGATGGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:1,3:0,9:9,4:0.3077:0,2:23.5:1:30:1:0.30769:0:58.8:8:0.3077:0:1 0/1:5:1:0,1:1,3:4,1:0.2:2,0:48:0:29:0:1:0:60:2:0.2:0:1 +1 182695805 . C CAA 32 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAAAGCGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAGATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:14.5:1:32.3:1:1:0:60:4:0.5:0.25:2 0/0:1:0:0,0:1,0:1,0:0:0,0:26:0:32:0:1:0:60:2:1:0:0 +1 182696005 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10947;SOR=Inf;LSEQ=CAGCAGGTCCCTTGTCTCAA;RSEQ=GGGCCCTGTAGCCATTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:149,32:181,0:0:2,0:23.4:1:30.4:1:1:0:59.9:35.2:1:0:0.2 0/1:90:2:1,1:69,19:88,2:0.0222:2,2:27:1:29:1:0.397:3.5649:60:4:0.0225:0:2 +1 182696024 . A T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55391;SOR=0;LSEQ=AAGGGCCCTGTAGCCATTAC;RSEQ=GGCATGAGGTGTTTGATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:1,2:188,68:256,3:0.0116:2,2:24.3:1:31.7:1:0.17859:5.48584:60:6:0.012:0:1.3 0/0:132:0:0,0:95,37:132,0:0:2,0:23.1:1:29.3:1:1:0:60:25.4:1:0:0.3 +1 182696047 . C CT 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=0.25195;LSEQ=CATGAGGTGTTTGATATAGA;RSEQ=TTTTTTTTATCATGGACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:179:114,65:143,80:223,179:0.4431:2,2:24.3:1:31.1:1:1:1.01915:59.8:58.667:0.4456:0.0792:0.7 0/1:210:35:19,16:115,59:174,35:0.1667:2,2:23.7:1:30.2:1:0.2461:1.6374:60:70:0.1683:0.019:0.9 +1 182696117 . C G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.30093;LSEQ=GGGGCCATGTACACCCGCCA;RSEQ=AGGTTGGAACAGTGAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:301:152,149:172,173:345,301:0.4652:2,2:26:1:32.1:1:0.87501:1.03:60:42:0.4623:0:1.1 0/1:357:74:33,41:144,138:282,74:0.2073:2,2:24.7:1:30.6:1:0.36134:1.29549:60:73:0.2098:0:1.3 +1 182696160 . T A 49 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01545;SOR=Inf;LSEQ=ATAACTTTTCAGCTCCTCCC;RSEQ=CTCTCATTCCAACATTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:517:0:0,0:194,323:517,0:0:2,0:24.2:1:30.3:1:1:0:60:46:1:0:0.4 0/1:283:4:3,1:115,164:279,4:0.0141:2,2:7.5:1:24.5:1:0.31146:4.26:56:3:0.0108:0:1.8 +1 184327212 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14296;SOR=Inf;LSEQ=TATTTATCTTTCTCACATTT;RSEQ=AGAAATAGAGCCATTAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:148,65:213,0:0:2,0:23.8:1:32.4:1:1:0:60:70:1:0:0.4 0/1:130:2:1,1:94,34:128,2:0.0154:2,2:27:1:30.5:1:0.4675:2.73938:60:4:0.0156:0:1 +1 184327245 . A T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06051;SOR=Inf;LSEQ=ATTAAAATATTAAGAAAAAA;RSEQ=TTAAAGTTTTCGGCACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:202,125:327,0:0:2,0:24:1:30.6:1:1:0:60:162.5:0.9969:0:0.5 0/1:213:3:1,2:119,91:210,3:0.0141:2,2:10.3:1:29:1:0.58185:2.60374:60:6:0.0142:0:1 +1 184327256 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01577;SOR=0.6416;LSEQ=AAGAAAAAAATTAAAGTTTT;RSEQ=GGCACATAAAAGTTAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:139:78,61:136,83:219,139:0.3872:2,2:27.8:1:30.5:1:0.27063:1.28052:60:68.5:0.387:0:1.1 0/1:222:64:34,30:84,73:157,64:0.2883:2,2:28.5:1:29.3:1:1:1.01524:60:63:0.2903:0:1.2 +1 184327286 . T TA 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.66536;LSEQ=AAGTTAAATTCCTCTTCATG;RSEQ=AAAAAAAACTAAAGGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:5:2,3:194,195:389,5:0.0127:2,2:29.6:1:30.2:1:1:1.4908:60:10:0.0128:0:0.6 0/0:236:2:1,1:104,130:234,2:0.0085:2,2:25.5:1:19:1:1:1.25:60:1:0.0043:0.0042:1 +1 184327323 . T G 196 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAGAAAAAGTAAGAATATA;RSEQ=TCTTCTTAATAACCTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:76:28,48:71,145:216,76:0.2603:2,2:25.8:1:31.5:1:0.57385:1.19:60:24.333:0.2544:0:1.1 0/0:150:0:0,0:48,101:149,0:0:2,0:22.5:1:29.2:1:1:0:60:48.667:0.9932:0:0.3 +1 184327784 . AT A 29 v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAAAATGTGTAGTGGAAG;RSEQ=TTTTTTTTTTTTTTTTCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:3,2:0.4:0,2:24:1:29:1:0.4:0:60:4:0.4:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 184951494 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGATGATGCTCCCCGTGGG;RSEQ=CCACAGCTACTGGGCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:13,13:26,2:0.0714:2,2:11:1:28.5:1:1:1:60:4:0.0714:0:1 0/0:13:0:0,0:8,5:13,0:0:2,0:19.5:1:29.7:1:1:0:60:26:1:0:0.2 +1 184951525 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1301;SOR=Inf;LSEQ=TGGGCAGGGTGGGAAAGAAC;RSEQ=CTGACTCCGGTCCAAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:14,17:31,0:0:2,0:29.3:1:29.9:1:1:0:60:30:1:0:0.1 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:25:1:29.5:1:1:1.26772:60:4:0.1111:0:1 +1 185195864 . CT C 75 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.67277;SOR=0.54696;LSEQ=TCTCATTTAAGCTTCTGAGA;RSEQ=TTTTTTTTTTTTTTTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:5,0:5,5:0.3846:0,0:33:1:32.4:1:1:0:56.2:10:0.3846:0:1.6 0/1:12:3:3,0:4,0:4,3:0.25:0,0:41.7:1:30.7:1:1:0:60:6:0.2727:0:1.3 +1 185195953 . C T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00443;SOR=0.23717;LSEQ=TGGTTTAGCTCTCAGCAGCC;RSEQ=GCTCCTGAGCTCTGAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:31:22,9:11,5:16,31:0.6596:2,2:29:1:32.9:1:1:1.11:27.2:62:0.6739:0:1.1 0/1:29:9:5,4:11,9:20,9:0.3103:2,2:24.1:1:29.1:1:1:1.02:27.9:18:0.3103:0:1.2 +1 185520465 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00104;SOR=0.43782;LSEQ=ACTTCTTCATTAGAAAGAAC;RSEQ=AAATAAATGCTTCTTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:86:75,11:231,42:273,86:0.2396:2,2:20.7:1:30.2:1:0.60582:1.24:59.9:85:0.2408:0:1.1 0/1:190:23:20,3:142,25:167,23:0.1211:2,2:26.3:1:29.6:1:1:1.17:60:46:0.1223:0:1 +1 185520600 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.18979;LSEQ=TGACCTCAACTTACCTGTTC;RSEQ=GTTGGATTTCTTGATACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:981:221:87,134:335,423:758,221:0.2253:2,2:26.8:1:31.6:1:0.21715:1.21956:60:220:0.2263:0:1.1 0/1:609:237:95,142:161,210:371,237:0.3892:2,2:24.8:1:29.8:1:0.44887:1.14571:59.9:78:0.3887:0:1.2 +1 185520654 . C G 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00031;SOR=0;LSEQ=TGTGAAGTTTCTGCAACAGT;RSEQ=CTATGGTCTTTCACCTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:23:6,17:172,417:589,23:0.0375:2,2:22.9:1:30.3:1:1:1.16837:60:10.5:0.0347:0:1 0/0:281:0:0,0:89,192:281,0:0:2,0:23.2:1:30.4:1:1:0:60:139.5:1:0:0.4 +1 185520693 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07991;SOR=Inf;LSEQ=GTGCCTTTGCTTATGCTAAC;RSEQ=CAGGGCATGCCCTCCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:47,241:288,0:0:2,0:24.7:1:31.6:1:1:0:59.9:71:1:0:0.2 0/1:114:2:1,1:18,94:112,2:0.0175:2,2:25:1:27.5:1:0.30678:5.11:60:4:0.0179:0:1 +1 185520694 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18353;SOR=5.35018;LSEQ=TGCCTTTGCTTATGCTAACC;RSEQ=AGGGCATGCCCTCCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:1,0:46,239:285,1:0.0035:2,0:1:0:26:0:0.16434:0:60:2:0.0035:0:1 0/1:108:2:1,1:17,89:106,2:0.0185:2,2:8.5:1:28:1:0.30685:5.12:60:4:0.0187:0:1 +1 185520728 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGAGCCTGCTGTGATCT;RSEQ=GATGTTTGCATATCCCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:8,133:141,2:0.014:2,2:23:1:29:1:0.12233:15.73:60:4:0.0143:0:1 0/0:48:0:0,0:4,44:48,0:0:2,0:24.2:1:30.8:1:1:0:60:96:1:0:0.1 +1 187529093 . G C 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCCTCTTCTGTAGGGCT;RSEQ=CTGTGGATTGCTGGGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:3,3:0.5:2,2:24.3:1:32:1:1:1:51.7:6:0.5:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 187529404 . T C 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGTAAATCTGCTTGTC;RSEQ=GCAGAGACTGCGGCCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:31:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:41:0:32:0:1:0:60:2:1:0:1 +1 188226895 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAGTGCTGATTGGTGC;RSEQ=TTTACAATCCTTTAGTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:36:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 188227425 . GC AA 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAGGTTAAAAATACAGG;RSEQ=CCAAAGGTGAGTAATAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:39.5:1:29.5:1:1:0:36:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 188744693 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGGCTGGGGTGGTCTCA;RSEQ=ATGGAGATGAGTAACTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:32:1:1:0:49:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 188746793 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00234;SOR=0.20778;LSEQ=GACAAAAAGTTATCTCCTTG;RSEQ=GATTTTAAGTTAATTTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:71:53:53,0:18,0:18,53:0.7465:1,1:20.9:1:31.4:1:1:0:59.8:25.5:0.7391:0:2.2 0/1:24:9:9,0:15,0:15,9:0.375:1,0:24.3:1:31:1:1:0:60:18:0.375:0:2.1 +1 188746835 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25717;LSEQ=TGCAGTCTGTTTTTTAATTC;RSEQ=TTAGTTAATTTATTTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:162:116:104,12:42,3:45,116:0.716:2,2:25.5:1:30:1:0.56119:1.61101:60:57:0.717:0:1.4 0/1:74:29:25,4:41,4:45,29:0.3919:2,2:21:1:28.7:1:0.70379:1.62863:60:28:0.3836:0:1.4 +1 188746974 . A C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21977;LSEQ=AAACACATTTTTATTAAATT;RSEQ=ATCACTGGCTCTTAATTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:475:322:125,197:58,95:153,322:0.6779:2,2:24.1:1:32.3:1:0.91968:1.04:60:160:0.678:0:1.1 0/1:285:90:42,48:80,115:195,90:0.3158:2,2:24.7:1:30.3:1:0.43983:1.26:60:89:0.3134:0:1.1 +1 188746979 . C A 45 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05407;SOR=Inf;LSEQ=CATTTTTATTAAATTAATCA;RSEQ=TGGCTCTTAATTCATATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:162,282:444,0:0:2,0:25.2:1:32.9:1:1:0:59.9:221:1:0:0.8 0/1:271:3:2,1:113,154:267,3:0.0111:2,2:6.3:1:28.7:1:0.57692:2.72:60:6:0.0112:0:1 +1 188952643 . A G 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52723;SOR=0;LSEQ=TTAAATTTTTTCAAAAAAAC;RSEQ=GCTCCTGGATTCATTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:0,2:88,58:146,2:0.0134:2,0:19:1:24.5:1:0.16271:0:54.5:4:0.0143:0:5 0/0:91:0:0,0:57,32:89,0:0:2,0:22.2:1:30.1:1:1:0:56.9:88:0.9778:0:0.1 +1 188952660 . AT A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=8.38249;LSEQ=AACAGCTCCTGGATTCATTG;RSEQ=TTTTTTTTTTGAGGGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:64:34,30:75,58:133,64:0.3168:2,2:26.5:1:31.2:1:0.7598:1.14021:58.9:128:0.3184:0.0396:0.3 1/0:118:94:55,39:12,7:19,94:0.7966:2,2:28.2:1:30.3:1:0.80121:1.21351:56.6:93:0.7949:0:0.1 +1 188952697 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16128;SOR=Inf;LSEQ=CTTTTTGTGTCTTTATCTCC;RSEQ=TCAATTCCTCTCTGATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:82,102:184,0:0:2,0:26.8:1:30.7:1:1:0:58.6:45:0.9836:0:0.4 0/1:126:2:1,1:60,64:124,2:0.0159:2,2:29:1:32:1:1:1.07:60:4:0.016:0:1 +1 188952784 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=27.88658;LSEQ=CCTCTCTAGCTCTTTTAATT;RSEQ=TGATGTTAGAGTGTCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:0,4:0,16:16,4:0.2:1,0:6.8:1:30.8:1:1:0:44.3:8:0.2:0:1 1/1:18:16:0,16:0,2:2,16:0.8889:0,1:21.1:1:31.1:1:1:0:51.4:32:0.8889:0:1.1 +1 188955252 . T C 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55944;SOR=2.75172;LSEQ=TTCCTGAGATTGTCTAGTTT;RSEQ=CATCTTTGAGGCTGCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:6,1:0.1429:2,0:9:0:32:0:1:0:60:2:0.1429:0:1 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:11:1:33:0:1:1:60:4:0.3333:0:1 +1 188955404 . G T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14087;SOR=6.4591;LSEQ=GGCTGCTGCAGTATTCTGGA;RSEQ=GTTCACTTCAGGCCCTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:4,5:9,5:0.3571:2,2:24:1:30.4:1:1:1.18452:50.8:10:0.3846:0:1 1/1:5:4:3,1:1,0:1,4:0.8:0,2:34.5:1:30.5:1:1:0:52:8:0.8:0:1 +1 188955897 . C T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGAAGAGGCACTCTGGC;RSEQ=GCAGACTGCCACAGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:2,2:5,6:11,4:0.2667:2,2:36.3:1:32.3:1:1:1.19:32.3:8:0.2667:0:1.3 0/0:2:0:0,0:1,1:2,0:0:2,0:46.5:1:30:1:1:0:52:4:1:0:0 +1 188955985 . T A 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCCAGCAGGGGAAAAG;RSEQ=ATGGCCTGGAGCTATAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:3,2:0.4:0,2:28.5:1:32.5:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 188956278 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18357;SOR=Inf;LSEQ=ATCCGTGAGTTGCACAGTTC;RSEQ=ATGAAAAAAGCAGTTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:11,15:26,0:0:2,0:25.4:1:32.1:1:1:0:60:52:1:0:0.2 0/1:20:2:1,1:7,11:18,2:0.1:2,2:6.5:1:28:1:1:1.54:60:4:0.1053:0:1 +1 189241655 . T A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGAAATCATATTAAAAA;RSEQ=ATTCTAAGACAGAATGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:28.5:1:1:0:60:4:1:0:1 +1 189243366 . T A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28792;SOR=1.83934;LSEQ=GAGAAGCGAGATAGAGATAG;RSEQ=TAATTTTCAGTAACCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:17:16,1:47,2:49,17:0.2576:1,1:23.9:1:31.2:1:1:1.45952:60:34:0.2576:0:1 0/1:23:9:9,0:12,2:14,9:0.3913:2,0:15.7:1:29.9:1:0.50198:0:60:18:0.3913:0:1 +1 189243405 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTCTACTTAAGTAATAA;RSEQ=CTTTGTAATCTCTAGGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:122,25:147,2:0.0134:2,2:20:1:29:1:0.31952:4.80487:60:4:0.0135:0:1.5 0/0:68:0:0,0:55,13:68,0:0:2,0:23.2:1:32.1:1:1:0:60:136:1:0:0.3 +1 189243491 . A G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.2334;LSEQ=ATGAATTACATCTAGCAGCT;RSEQ=TACAGTAAATAGTAAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:156:81,75:150,149:299,156:0.3429:2,2:26.9:1:32:1:0.76721:1.07:60:155:0.3468:0:1.1 1/0:234:126:65,61:53,55:108,126:0.5385:2,2:26.4:1:31:1:0.79319:1.11:60:252:0.5385:0:1.1 +1 189243520 . A C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATAGTAAGTGGTGAGACTGG;RSEQ=TATTATTTTCGCAGGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:196,258:454,0:0:2,0:25.9:1:30.8:1:1:0:60:74.667:1:0:0.4 0/1:234:13:6,7:99,122:221,13:0.0556:2,2:25.4:1:31.5:1:1:1.06:60:26:0.0556:0:1.1 +1 189243571 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10402;SOR=Inf;LSEQ=AATATATTTCCTTCTATGGG;RSEQ=TAACTTACTATCCCAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:58,151:209,0:0:2,0:24.4:1:30.8:1:1:0:60:51.25:1:0:0.2 0/1:100:2:1,1:24,74:98,2:0.02:2,2:31:0:32.5:1:0.43939:3.04:60:4:0.0202:0:1.5 +1 189243810 . A G 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGTGAGTATATATGAAT;RSEQ=TTAATGTATATTAAATACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:17.7:1:33.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 190733725 . T C 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAAATTCTGCTCTGAGC;RSEQ=TCTAGCAGATACATTATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:18.8:1:30.5:1:1:0:57.8:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 190734020 . C T 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCCTTTTGGAAAATGGTA;RSEQ=ATGAAGAAGAACATCTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:724:0:0,0:428,296:724,0:0:2,0:24.8:1:32.4:1:1:0:60:240.333:1:0:0.6 0/1:376:21:16,5:204,151:355,21:0.0559:2,2:26.7:1:29.5:1:0.11188:2.36:60:42:0.0565:0:1.7 +1 190734051 . G A 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21534;LSEQ=ACATCTAAGTAAAGAGTCCA;RSEQ=AATATTTCAAAGGTAACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:767:578:312,266:98,91:189,578:0.7536:2,2:25.8:1:30.5:1:0.61539:1.09:60:288:0.7539:0:1.1 0/1:426:169:80,89:124,133:257,169:0.3967:2,2:26:1:29.5:1:0.92107:1.03715:60:55.333:0.399:0:1.1 +1 190734074 . A C 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTTCAAAGGTAACCTTAT;RSEQ=GGTTTCCCATAAACATCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:783:0:0,0:378,403:781,0:0:2,0:25:1:30.1:1:1:0:60:110.571:0.9974:0:0.7 0/1:400:32:18,14:168,200:368,32:0.08:2,2:22.6:1:30.3:1:0.27168:1.53:60:64:0.0806:0:1.6 +1 190734156 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08628;SOR=Inf;LSEQ=TCTCAATTTTTTGAATGACT;RSEQ=ACAGCAATGCCTATTATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:68,252:320,0:0:2,0:23.2:1:32:1:1:0:60:39:0.9968:0:0.1 0/1:134:2:1,1:34,96:130,2:0.0149:2,2:26.5:1:28:1:0.46149:2.80:60:4:0.0152:0:1 +1 191168873 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=AGCCTCAAAGATTGAGTTTA;RSEQ=ACAAACTTATGAAGATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:15.5:1:34:0:1:1:38:4:0.3333:0:1 0/0:3:0:0,0:1,2:3,0:0:2,0:19.7:1:29.3:1:1:0:60:6:1:0:0 +1 191549641 . T C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCCATTAGTTATTCTTCC;RSEQ=GATCCTCTCCCTCCTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:4,7:0,0:0,11:1:0,2:15.5:1:29.3:1:1:0:60:22:1:0:1.1 1/1:6:6:2,4:0,0:0,6:1:0,2:15.3:1:30.2:1:1:0:51:12:1:0:1 +1 192220536 . C T 104 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01471;SOR=0;LSEQ=CATTGGTCAAGTCCCTCTTC;RSEQ=GTAGGGCTGCTACAGTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:6,4:0,0:0,10:1:0,2:19.9:1:31.4:1:1:0:52.3:20:1:0:1.1 0/1:7:3:1,2:2,2:4,3:0.4286:2,2:19.7:1:31.3:1:1:1.81007:45.7:6:0.4286:0:1 +1 192221363 . T G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10051;SOR=0.21865;LSEQ=TAAGAGGCTGTTGAGAATCT;RSEQ=TGCAGCTCTGGGGTTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:21:15,6:7,4:11,21:0.6563:2,2:24.6:1:32.3:1:0.7026:1.41:60:42:0.6563:0:1 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:21.5:1:31.5:1:1:0:60:4:0.2857:0:1 +1 193090865 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTGCTCAGGTACGCGCG;RSEQ=ACCTGACGCCGCTTGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:22:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 193091233 . AAGG A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.2806;SOR=3.77288;LSEQ=GTTGGTTCGTCGCGGCGGCG;RSEQ=AGGAGGAGGAAGAGGGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:1,0:111,5:116,1:0.0085:1,0:45:0:29:0:1:0:60:2:0.0088:0:0 0/1:63:2:1,1:55,6:61,2:0.0317:2,2:36:1:29:1:0.21147:8.56132:60:4:0.0323:0:0 +1 193091281 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14501;SOR=Inf;LSEQ=CAAGAGAAGAAGGAGGCAGG;RSEQ=GCGGCGGCAGCGGCGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:260,27:287,0:0:2,0:23.9:1:32:1:1:0:59.9:40:1:0:0.1 0/1:177:2:1,1:146,29:175,2:0.0113:2,2:35:1:28.5:1:0.31106:4.96692:60:4:0.0116:0:1 +1 193091490 . G T 131 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=GGCATGGCTGTGGCCCAGGG;RSEQ=TGGCAGGGCAGAGTTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:767:21:6,15:224,521:745,21:0.0274:2,2:22:1:30:1:1:1.07476:60:42:0.0276:0:1.2 0/0:421:0:0,0:131,290:421,0:0:2,0:22.8:1:30.7:1:1:0:60:139.333:1:0:0.1 +1 193091493 . G A 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05262;SOR=7.54205;LSEQ=ATGGCTGTGGCCCAGGGGTG;RSEQ=CAGGGCAGAGTTGGGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:1:1,0:210,521:731,1:0.0014:2,0:1:0:26:0:0.28825:0:60:2:0.0014:0:1 0/1:391:4:2,2:113,274:387,4:0.0102:2,2:24.8:1:27.3:1:0.58435:2.42:60:8:0.0105:0:1 +1 193094120 . CT C 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49092;SOR=1.59696;LSEQ=ATTCATTATTAGATTTTATA;RSEQ=TTTTTTTTGTTAGCTATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:5:4,1:165,1:166,5:0.0292:1,2:23:1:32.8:1:0.05779:36.99945:60:10:0.0296:0:0 0/1:87:4:4,0:82,1:83,4:0.046:1,0:28.8:1:32.1:1:1:0:60:8:0.046:0.0115:0 +1 193094213 . T TA 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.30296;SOR=0.58076;LSEQ=AGTTGAATTAGAATTGTCAG;RSEQ=AAAAAAAATCTTGCCTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:18:14,4:524,310:834,18:0.0211:2,2:21.1:1:27.3:1:0.22578:2.07:60:17:0.0202:0.0059:0 0/1:567:7:4,3:348,212:560,7:0.0123:2,2:28.3:1:27.4:1:1:1.23066:60:14:0.0125:0:0.1 +1 193094368 . TTATC T 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=GTAAGTAGAATTCATTTTAC;RSEQ=TATCTATTTATCAGTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:0:0,0:130,453:583,0:0:2,0:25:1:29.1:1:1:0:60:582:1:0:0.9 0/1:381:52:14,38:97,232:329,52:0.1365:2,2:25.6:1:29.7:1:0.74596:1.1345:59.5:104:0.1394:0.0052:0.2 +1 193094375 . T C 284 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.04513;LSEQ=GAATTCATTTTACTTATCTA;RSEQ=CTATTTATCAGTTTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:532:516:105,411:3,13:16,516:0.9699:2,2:24.3:1:31.6:1:1:1.11:60:72.714:0.9714:0:1.1 1/0:348:206:62,144:36,106:142,206:0.592:2,2:25.5:1:30.9:1:0.3961:1.27:60:205:0.5959:0:1.1 +1 193098964 . A G 64 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AGAAAATTATTAAAAGTAAC;RSEQ=TGTTTAATACATTTTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:20.5:1:32:0:1:0:47.8:8:1:0:1 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:18:1:32.5:1:1:0:52:4:0.6667:0:1 +1 193104168 . ATATGTGTGTG A 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAAAAAATCTTGTCCATAT;RSEQ=TATGTGTGTGTGTATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:13:1:31:1:1:0:52.7:6:0.5:0.3333:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 193104439 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.11696;SOR=Inf;LSEQ=CCATATAGAAGTATATAAAA;RSEQ=ACCTAAAGCATTTCACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:205,23:228,0:0:2,0:22.1:1:30.3:1:1:0:59.8:75:1:0:0.1 0/1:119:2:2,0:108,9:117,2:0.0168:2,0:14.5:1:32:1:1:0:60:4:0.0168:0:1 +1 193104712 . G A 217 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCAGAAGCAAAGAAACCAC;RSEQ=AATTGAGGTAAAGAAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:815:134:45,89:268,413:681,134:0.1644:2,2:28.6:1:30.8:1:0.24362:1.28301:60:66:0.1632:0:1.1 0/0:525:0:0,0:219,306:525,0:0:2,0:26.5:1:29.7:1:1:0:60:74:1:0:0.1 +1 193104827 . G A 212 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.02745;LSEQ=CCTGAGGAGCTTTTTTTCTG;RSEQ=AAAAATTTTTGTGGTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:104:3,101:0,2:2,104:0.9811:0,1:26.3:1:31.7:1:1:0:59.6:208:0.9811:0:1.1 1/0:55:32:0,32:0,23:23,32:0.5818:1,1:26:1:31:1:1:0:60:64:0.5818:0:1.1 +1 193105216 . A G 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCCGTGTTGGCCAGGCT;RSEQ=CAGAATTCTTTCTTTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:32.8:1:32.2:1:1:0:55.2:10:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 193119588 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29639;SOR=0;LSEQ=CAGTGTGGCCTGATGTTTAA;RSEQ=GGTAAGGGTTGGCAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:40,257:297,3:0.01:2,2:25:1:24:1:0.35754:3.19:60:2:0.0068:0:2 0/0:179:0:0,0:26,153:179,0:0:2,0:21.1:1:30.4:1:1:0:60:178:1:0:0.1 +1 193119940 . G C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATTAAAATGTTATTATA;RSEQ=TGCCTGTCTCTTACCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:30.5:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:30:1:1:0:60:4:1:0:2.5 +1 193119992 . A G 22 d5;v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGGTTAATAAATATTGA;RSEQ=TTCCCAGAATAGTATCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:12:1:33.5:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:22.5:1:1:0:60:1:1:0:2.5 +1 193120667 . T C 39 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTGACAGATTTTAAGGCT;RSEQ=GCAATGTGTTAAAATATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:23.3:1:25:1:1:0:60:2:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 193121496 . C CT 111 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05924;SOR=0.23749;LSEQ=AAAATCTTAACAATAAGCCT;RSEQ=TTTTTTTTCGTAGAAACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1025:13:7,6:624,388:1012,13:0.0127:2,2:16.4:1:30.1:1:0.57681:1.37802:60:26:0.0129:0.0049:0.3 0/0:658:2:1,1:391,265:656,2:0.003:2,2:24:1:29.5:1:1:1.47454:60:4:0.0031:0.0015:0.5 +1 193172859 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09584;SOR=Inf;LSEQ=GAGATATGAGATTTCTTTGG;RSEQ=ATAATTAAAGTGTTTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:334,73:407,0:0:2,0:21.3:1:30.5:1:1:0:60:100.75:1:0:0.1 0/1:183:2:1,1:144,37:181,2:0.0109:2,2:29.5:1:26.5:1:0.37309:3.85365:60:4:0.0112:0:1 +1 193173335 . GTGTATATATA G 68 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACACACACATATATATAC;RSEQ=TGTATATATATGTATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:30.6:1:29.5:1:1:0:47.2:10:0.7143:0.1429:2.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 193173356 . TG CA 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATATATATGTATATATA;RSEQ=TATATATACACGTATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:35.4:1:32.7:1:1:0:47.2:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 193181175 . A AT 105 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24003;SOR=0.33606;LSEQ=TTTTATGACACAGAGTTGTG;RSEQ=TTTTTTTTCTTTTTCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:820:11:7,4:530,279:809,11:0.0134:2,2:20.2:1:30.4:1:1:1.0854:60:22:0.0136:0.0024:0.5 0/0:440:2:2,0:281,157:438,2:0.0045:2,0:8.5:1:31.5:1:0.53996:0:60:4:0.0046:0.0023:1 +1 193181412 . T G 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00028;SOR=Inf;LSEQ=TCCACTGGCTTAAAATATTT;RSEQ=TTAGATCAAAAGTTAAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:182,113:295,0:0:2,0:23.2:1:31.3:1:1:0:60:146.5:1:0:0.1 0/1:104:6:4,2:70,28:98,6:0.0577:2,2:28.5:1:32.5:1:1:1.24726:60:12:0.0583:0:1 +1 193202001 . C G 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01766;LSEQ=CAAGATTGCACCACTGCACT;RSEQ=TAGCCTGGGCAATAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:75:75,0:1,0:1,75:0.9868:0,1:25.2:1:32.9:1:1:0:54.2:36.5:0.9865:0:1.2 1/0:34:19:19,0:14,1:15,19:0.5588:1,1:24.6:1:30.4:1:0.44118:0:54.6:18:0.5455:0:1.4 +1 193202032 . CA C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30491;SOR=1.40951;LSEQ=AATAAGAAAAAACTCTGTCT;RSEQ=AAAAAAAAAAATATTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:26:26,0:153,4:157,26:0.1405:1,1:24.3:1:33.4:1:1:0:59.7:52:0.1421:0.0162:0.3 0/1:96:18:16,2:67,5:72,18:0.1875:2,2:20.1:1:31.8:1:0.62359:1.66417:59.3:36:0.1875:0.0521:0.3 +1 193202297 . CTA C 102 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.78095;SOR=1.14498;LSEQ=CAAGACTGGTAAGATAGTCT;RSEQ=TATATATATCTTTTCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:986:9:3,6:297,680:977,9:0.0091:2,2:27.9:1:32.2:1:1:1.14:58.7:18:0.0092:0.001:0 0/1:479:5:1,4:161,313:474,5:0.0104:2,2:26.6:1:30.8:1:0.66672:2.05483:58.2:10:0.0105:0.0042:0 +1 193202953 . G A 86 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACACTTTTATTGAATTTAA;RSEQ=TGTCCTTTAACAAAATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:0,7:1:0,2:14.6:1:30.9:1:1:0:60:14:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 193203035 . C T 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=AATTACCTTATTTCTTTAAC;RSEQ=GGGAGTAAAAGTTGAGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:9,1:12,0:12,10:0.4545:0,2:28.5:1:32.9:1:0.45455:0:60:20:0.4545:0:1.2 0/0:3:0:0,0:3,0:3,0:0:0,0:23.3:1:29.7:1:1:0:60:6:1:0:0.3 +1 193203268 . C T 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0;LSEQ=CTTAAACTTATGCCTCAAGA;RSEQ=TGGTAGGATAATTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:22:7,15:221,282:503,22:0.0418:2,2:18.1:1:30.7:1:0.28227:1.67775:56.4:44:0.0437:0:1 0/0:304:0:0,0:128,176:304,0:0:2,0:24.1:1:30.5:1:1:0:54.1:20.714:1:0:0.4 +1 193203305 . TCACACACACACACA T 176 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=23.000;MSILEN=2;SSF=0;SOR=0.13907;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CACACACACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:53:9,44:55,55:110,53:0.2524:2,2:29.8:1:30.9:1:4e-05:4.84294:46:52:0.2723:0.0905:0.5 0/1:112:5:0,5:36,54:90,5:0.0446:2,0:25.6:1:31:1:0.15289:0:40.8:10:0.0467:0.0089:0.6 +1 193203368 . T G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATATATATATTTAAAAT;RSEQ=TATATATTTATTTATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:0,2:1,66:67,2:0.029:1,0:24:1:34.5:1:1:0:41:4:0.0299:0:1.5 0/0:29:0:0,0:0,29:29,0:0:1,0:30.4:1:30.1:1:1:0:46.5:58:1:0:0.7 +1 193203397 . T TTATAATATATATAATTTATTATATATATATTATA 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=4.000;MSILEN=2;SSF=0.00025;SOR=0;LSEQ=TATTTATATATATAATTTAA;RSEQ=TATAATATATATAATATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:1,14:0,16:16,15:0.4839:1,1:20.9:1:29.5:1:0.48387:0:57.3:30:0.5357:0.3226:0.4 0/0:18:0:0,0:0,18:18,0:0:1,0:16.9:1:30.1:1:1:0:57.6:36:1:0:0.4 +1 193203413 . ATACA T 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01238;SOR=Inf;LSEQ=TTAATTATAATATATATAAT;RSEQ=TATTATATATATAATATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,9:9,0:0:0,0:16.8:1:32.3:1:1:0:57.2:18:1:0:0.2 1/0:10:5:0,5:0,5:5,5:0.5:0,0:10.4:1:30.1:1:1:0:60:10:0.5:0.3:0.4 +1 193203471 . AAT A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATTTAAAACACACACATA;RSEQ=ATATATATATATATTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:46.5:1:32:1:1:0:60:4:0.25:0:0 0/0:1:0:0,0:0,1:1,0:0:0,0:15:0:32:0:1:0:60:2:1:0:0 +1 193203491 . A AAATTAT 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATATATATATATATTTA;RSEQ=AATTATAATTCTTCTCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:34.5:1:31.5:1:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 193205272 . T A 218 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02037;LSEQ=GGAAGGATTGATAAGACTCT;RSEQ=TCACATGAATGTTTATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:200:197:196,1:3,0:3,197:0.985:0,1:25.1:1:28.7:1:1:0:60:196:0.9849:0:1.2 1/0:102:58:58,0:43,1:44,58:0.5686:1,1:23.2:1:27.9:1:0.43137:0:60:57:0.5758:0:1.1 +1 193218808 . C CT 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.73105;SOR=0.60147;LSEQ=TGGAATAAAGAAATTTTTTT;RSEQ=TTTTTTTTTATTTTGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:8:8,0:324,51:375,8:0.0209:2,0:30.9:1:33.3:1:0.60432:0:60:16:0.0211:0.0026:0.3 0/1:158:2:1,1:135,20:155,2:0.0127:2,2:6:1:29:1:0.25037:6.61168:60:4:0.0128:0.0063:0.5 +1 193218843 . C G 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAGTAAAAATGATAACTTCT;RSEQ=TCCACCCTCTCTATAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:736:0:0,0:557,177:734,0:0:2,0:24.1:1:32.2:1:1:0:60:55.462:0.9986:0:0.1 0/1:379:30:25,5:244,104:348,30:0.0792:2,2:21.2:1:31.1:1:0.1451:2.13:60:29:0.0777:0:1 +1 193219691 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGTTTTCTAGAAAACAG;RSEQ=ATTTTATTCTGTTGATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:120,5:125,2:0.0157:1,2:14:1:28.5:1:0.09261:22.00022:60:4:0.0159:0:1 0/0:49:0:0,0:45,4:49,0:0:2,0:24.3:1:31.2:1:1:0:60:48:1:0:0 +1 195110131 . G C 29 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTATCTTTACTCCACAATCC;RSEQ=AAATAGACTCTTTGGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:22:1:29.5:1:1:0:51.5:4:0.6667:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:28:0:32:0:1:0:36:2:1:0:1 +1 195112308 . G A 31 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAAGAAAGAAAGAAAGA;RSEQ=AAAGAAAGGAAGGAAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:6:0:31.5:1:1:1:48:4:0.6667:0:1 +1 197974705 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=CCACCAGAATCTAGGGAAGA;RSEQ=GCATGGAACAGATTCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:27,0:0:2,0:35.1:1:32.9:1:1:0:60:54:1:0:0.2 0/1:22:2:1,1:12,8:20,2:0.0909:2,2:35.5:1:30:1:1:1.47192:60:4:0.0909:0:1 +1 198167238 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGATAGGTGGTGGGTGGG;RSEQ=AGGATTGGAACCTCCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:23,29:52,2:0.037:2,2:22:1:28.5:1:1:1.26:60:4:0.037:0:1 0/0:19:0:0,0:9,10:19,0:0:2,0:30.7:1:31.1:1:1:0:57.7:38:1:0:0 +1 198167287 . T C 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01067;SOR=0;LSEQ=GTGGGGGGATATGGATTTGG;RSEQ=CCTGGCTGGCCGGCATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:2,10:9,16:25,12:0.3243:2,2:21.9:1:30.4:1:0.27934:2.74057:42.4:11:0.3235:0:1 0/0:17:0:0,0:7,10:17,0:0:2,0:23.8:1:29.1:1:1:0:57.8:34:1:0:0.1 +1 199066099 . G T 26 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=Inf;LSEQ=CCTCTTCACTGCTGAGAAAG;RSEQ=AGGACTCTGCCCCTTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:17:1:30:1:1:0:60:8:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:26.5:1:26.5:1:1:1:48:4:0.5:0:1 +1 199416906 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=CCACAGAGACTGCAACCACC;RSEQ=CTCCCACTAGGGGCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:24.5:1:29:1:1:1.4491:49:4:0.1667:0:1 0/0:6:0:0,0:2,4:6,0:0:2,0:22.8:1:30.8:1:1:0:60:12:1:0:0.2 +1 199417365 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGGTTGGGACACTGGG;RSEQ=CCTGGTGGCATGGGTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:41,40:81,2:0.0241:2,2:20:1:29:1:1:1.0247:60:4:0.0247:0:1.5 0/0:39:0:0,0:21,18:39,0:0:2,0:23:0:14:0:1:0:60:0:0:0:4 +1 199417387 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTGGCATGGGTTTACAA;RSEQ=TGGGATCTTCCAATCCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:43,45:88,2:0.0222:2,2:15:0:32.5:1:1:1.05:51:4:0.0227:0:1.5 0/0:41:0:0,0:21,20:41,0:0:2,0:26.3:1:31.6:1:1:0:59.9:82:1:0:0.3 +1 199417587 . A G 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCTTCTAGTCAATTTTGATG;RSEQ=GAGAACCTGGACACCTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:17:1:29.3:1:1:0:60:8:0.6667:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:1:0:30:0:1:0:60:2:1:0:1 +1 202065925 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11931;SOR=Inf;LSEQ=ATTGTCACCATCGTCATCGT;RSEQ=ATCAGCAGCAGCAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:29,25:54,0:0:2,0:26.5:1:32.3:1:1:0:59.7:108:1:0:0.9 0/1:29:2:2,0:14,13:27,2:0.069:2,0:13.5:1:32:0:0.48768:0:60:4:0.069:0:1 +1 202065930 . G T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.00071;SOR=0.18503;LSEQ=CACCATCGTCATCGTCATCA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:40:20,20:8,5:13,40:0.7547:2,2:27.7:1:31.1:1:0.53554:1.58593:59.6:80:0.7547:0:1.2 0/1:28:10:4,6:11,7:18,10:0.3571:2,2:30.2:1:29.6:1:0.4328:2.28381:60:20:0.3571:0:1.3 +1 202065942 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0.81247;LSEQ=CGTCATCAGCAGCAGCAGCA;RSEQ=CAGCAACAGCAGCCCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:22,25:47,2:0.0408:2,2:26:1:28.5:1:1:1.13:60:4:0.0408:0:2 0/1:30:1:0,1:14,15:29,1:0.0333:2,0:44:0:29:0:1:0:60:2:0.0333:0:2 +1 202066564 . G A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CCTGAAGAGTGCATGGCGGC;RSEQ=GTGGTGGGGGTGGCGGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:2,4:0.6667:2,2:28.8:1:32.8:1:1:1:60:8:0.6667:0:1.3 0/0:2:0:0,0:1,1:2,0:0:2,0:16.5:1:28:1:1:0:60:4:1:0:0 +1 202188543 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09007;SOR=Inf;LSEQ=GAGAAAGCTGCTGGTCCACT;RSEQ=CAGGAGCCAAAGGATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:199,81:280,0:0:2,0:23.5:1:32.1:1:1:0:60:55:0.9964:0:0.9 0/1:121:2:2,0:83,36:119,2:0.0165:2,0:14.5:1:32:0:1:0:60:4:0.0167:0:2.5 +1 202188549 . G T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00676;LSEQ=GCTGCTGGTCCACTGCAGGA;RSEQ=CCAAAGGATTATTTGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:118:86,32:120,56:176,118:0.4014:2,2:24.5:1:30.7:1:0.43652:1.25:60:58:0.3986:0:1.8 0/1:134:54:40,14:52,28:80,54:0.403:2,2:25:1:29.7:1:0.34294:1.53:60:53:0.4015:0:1.9 +1 202188616 . G T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00742;SOR=1.62562;LSEQ=ATGCCTAATTAAGAGAACAG;RSEQ=GAGCGCTGTGAGCAACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:538:404:219,185:71,63:134,404:0.7509:2,2:25:1:29.6:1:0.84174:1.05:59.9:49.5:0.75:0:1.7 1/1:307:255:145,110:33,19:52,255:0.8306:2,2:24.6:1:29:1:0.44189:1.31644:60:254:0.8301:0:1.6 +1 202188641 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.9454;SOR=0.9821;LSEQ=GCTGTGAGCAACAGCCTTCA;RSEQ=TGATTGGGTGCCGGCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:600:229:113,116:184,187:371,229:0.3817:2,2:25.2:1:32.2:1:1:1.01006:59.8:75.333:0.3837:0:1.9 0/1:363:137:68,69:118,107:225,137:0.3774:2,2:24.7:1:31.3:1:0.66471:1.11867:60:136:0.3788:0:1.9 +1 202188719 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28105;SOR=3.73937;LSEQ=ATTGTAGCAGCTGGGGGAGA;RSEQ=ATTGACACTAGGCAGTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:1:1,0:95,219:314,1:0.0032:2,0:1:0:25:0:0.30476:0:60:2:0.0032:0:2 0/1:170:2:1,1:52,116:168,2:0.0118:2,2:20:1:27.5:1:0.5276:2.22:60:4:0.012:0:1 +1 202188932 . A G 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATTCTATACTAATAATT;RSEQ=TAATTCAGTTAGATGAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:1,3:4,5:0.5556:2,0:28.8:1:31.8:1:0.44444:0:60:10:0.5556:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:44:0:28:0:1:0:60:2:1:0:0 +1 202189472 . A G 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCCTGCCTCAGCCTCTC;RSEQ=AGTAACTGGGATTACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:27:1:1:0:57:4:1:0:1 +1 203027354 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAGGAGGAGGGAGAGCACG;RSEQ=GAGGAGGAGGTTGGGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 203054310 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.1;SOR=0;LSEQ=TTTTAGGCTCTGACTCAGGC;RSEQ=CTGGGATTAATCCTCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:13:1:31.7:1:1:0:60:6:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:23:1:30.5:1:1:0:60:4:1:0:0 +1 203054523 . A T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CGACCCTGTCTGGCACCTGC;RSEQ=CCAACCCTCTGAGCCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:0,12:1:0,2:20.9:1:30.3:1:1:0:60:11:1:0:1.3 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:16.4:1:31.8:1:1:0:60:10:0.8333:0:1.2 +1 203054782 . G A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04416;SOR=Inf;LSEQ=GCAGGGTGCTTCTCTTCAGG;RSEQ=CCTCGAAGGCCTCATTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:44,95:139,0:0:2,0:24.9:1:31.8:1:1:0:60:138:1:0:0 0/1:77:3:2,1:31,43:74,3:0.039:2,2:26.7:1:23.3:1:0.57323:2.74:60:2:0.0267:0:1.3 +1 203054785 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13555;SOR=Inf;LSEQ=GGGTGCTTCTCTTCAGGGCC;RSEQ=CGAAGGCCTCATTCACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:41,92:133,0:0:2,0:24.9:1:30.6:1:1:0:60:266:1:0:0 0/1:78:2:1,1:31,45:76,2:0.0256:2,2:22.5:1:26.5:1:1:1.44:60:4:0.0256:0:1 +1 203224948 . T G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49657;SOR=0;LSEQ=GATTATCACTTTAAGGTGGA;RSEQ=AATGATGAAAATGAGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:38,30:68,2:0.0286:2,2:47.5:1:33:1:1:1.26235:48:4:0.029:0:1 0/0:67:0:0,0:33,34:67,0:0:2,0:22.6:1:28.5:1:1:0:54.1:32.5:1:0:0.2 +1 203224985 . G T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0614;SOR=0;LSEQ=ACCAGTTATCTTTAATAACG;RSEQ=CCAGTTTAGGGGCTGCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:3,2:36,28:64,5:0.0725:2,2:21.8:1:26.2:1:1:1.16:40.4:4:0.0597:0:1 0/0:59:0:0,0:26,33:59,0:0:2,0:27.3:1:30.5:1:1:0:54.8:118:1:0:0.1 +1 203225148 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16625;SOR=Inf;LSEQ=CACACTACCAGTGGTCTTAC;RSEQ=GCTGAAGTGTGGTTCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:161,107:268,0:0:2,0:26.5:1:30:1:1:0:57.3:52.6:1:0:0.1 0/1:185:2:1,1:113,70:183,2:0.0108:2,2:19.5:1:27.5:1:1:1.60989:49:4:0.011:0:1 +1 203225183 . G T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26131;SOR=0;LSEQ=CAGGGCCAGTGCATATTAGT;RSEQ=GACAGCACTTAGGACGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:132,160:292,3:0.0102:2,2:24:1:23.7:1:0.59249:2.42:60:2:0.0069:0:1.3 0/0:227:0:0,0:122,105:227,0:0:2,0:28.9:1:30.7:1:1:0:57:112.5:1:0:0.2 +1 203225204 . T C 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2548;SOR=0;LSEQ=GACAGCACTTAGGACGAAGA;RSEQ=GCAGAGCCAGAAGATGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:101,157:258,3:0.0115:2,2:29:1:23.7:1:1:1.28541:44.7:2:0.0078:0:1.3 0/0:217:0:0,0:100,117:217,0:0:2,0:25.5:1:29.4:1:1:0:53.1:107.5:1:0:0.2 +1 203225245 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50626;SOR=0;LSEQ=GGAGGAAGATGTGAAACTCT;RSEQ=AAGTATATCTGGAAAGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:76,117:193,2:0.0103:2,2:22:1:30.5:1:1:1.54:49:4:0.0104:0:1 0/0:152:0:0,0:65,86:151,0:0:2,0:23.2:1:28:1:1:0:44.1:36.75:1:0:0.1 +1 203225284 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50369;SOR=0;LSEQ=GTCTGCCCCTGGAGGTGGTA;RSEQ=CAAGTTTCCAGAGGAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:62,89:151,2:0.0131:2,2:24:1:30:1:1:1.43:51:4:0.0133:0:1 0/0:124:0:0,0:49,75:124,0:0:2,0:26.1:1:31.5:1:1:0:40.5:40.333:1:0:0.2 +1 203225306 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18927;SOR=Inf;LSEQ=AAGTTTCCAGAGGAAAAAGT;RSEQ=AAACTTGCTGCTGATGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:60,77:137,0:0:2,0:24.5:1:30:1:1:0:50.4:274:1:0:0.2 0/1:106:2:1,1:49,54:103,2:0.0189:2,2:28.5:1:31:0:1:1.10:45.5:4:0.0189:0:1 +1 203225322 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50522;SOR=0;LSEQ=AAGTAAAACTTGCTGCTGAT;RSEQ=CAAATGATGATGAAGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:54,68:122,2:0.0161:2,2:20.5:1:30:1:1:1.26:60:4:0.0165:0:1 0/0:97:0:0,0:44,53:97,0:0:2,0:22.2:1:31.2:1:1:0:54.1:96:1:0:0.1 +1 203225459 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52597;SOR=0;LSEQ=CAGAAGTCAAATCAGAATGG;RSEQ=AAGGACTCAAAACCGTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:65,74:139,2:0.0142:2,2:22.5:1:29:1:1:1.14:26.5:4:0.0143:0:1 0/0:87:0:0,0:43,44:87,0:0:2,0:29.5:1:29.5:1:1:0:45.5:86:1:0:0.4 +1 203225539 . A C 125 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=31.000;MSILEN=1;SSF=1;SOR=1.10877;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AACCAGAAAAAAACTCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:0,12:4,0:4,12:0.5455:0,0:28.4:1:31.8:1:0.00055:0:38.9:11:0.5789:0:1.6 1/0:28:16:1,15:12,0:12,16:0.5714:0,1:26:1:31.3:1:0:0:39.1:32:0.5926:0:1.1 +1 203225545 . G A 44 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.60788;SOR=2.92807;LSEQ=AAAAAAAAAAAAAAAAACCA;RSEQ=AAAAAAACTCCTAAAACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:1,0:2,17:19,1:0.05:2,0:26:0:26:0:0.15:0:38:2:0.0526:0:3 0/1:22:3:3,0:4,15:19,3:0.1364:2,0:7.3:1:28.3:1:0.02273:0:55:6:0.15:0:3.3 +1 204150630 . A T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07437;SOR=Inf;LSEQ=TGGCATGGTGCAGGCTGAGG;RSEQ=ACCTGGTCAGATATCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:49,43:92,0:0:2,0:29.4:1:30.1:1:1:0:60:29.667:1:0:0 0/1:35:2:1,1:17,16:33,2:0.0571:2,2:28:1:25:1:1:1.06069:60:4:0.0571:0:1 +1 204150667 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02365;SOR=Inf;LSEQ=AGGGTGATCAGATATTGAGG;RSEQ=TGGGGATTATTTGCTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:30,42:72,0:0:2,0:24.8:1:32.2:1:1:0:59.9:144:1:0:0 0/1:30:3:1,2:10,17:27,3:0.1:2,2:25:1:26.7:1:1:1.17019:58:6:0.1:0:1 +1 204314471 . C G 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTTCCTAACAAGGAGGC;RSEQ=AGGACAGCTTGACCACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204315882 . C CT 25 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGATATTTCTCCCATTTG;RSEQ=TTTTTTTTTTTTTAACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:14:1:25.3:1:1:0:23.5:4:1:0.3333:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204316065 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CTGATCATTTTCCTTCACAC;RSEQ=TTTCAGGAAGCTATCTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:1,3:0.75:0,2:27.7:1:32:1:1:0:26:6:0.75:0:1 0/0:3:0:0,0:2,1:3,0:0:2,0:21.3:1:29.7:1:1:0:28.3:6:1:0:0.7 +1 204316082 . C T 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CACGTTTCAGGAAGCTATCT;RSEQ=GGCTCTTAGAGTGCTTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:9:0:33:0:1:0:24:2:0.3333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:30.5:1:1:0:29.5:4:1:0:1 +1 204316204 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAACATTGTAGACTCTTCC;RSEQ=GTTTTGCCGTGGTAACGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:72,107:179,2:0.011:2,2:27.5:1:30.5:1:1:1.48:22.5:4:0.0111:0:1 0/0:89:0:0,0:34,55:89,0:0:2,0:32.6:1:30.3:1:1:0:27:178:1:0:0.1 +1 204316222 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10717;SOR=Inf;LSEQ=CCAGTTTTGCCGTGGTAACG;RSEQ=GTGTGGGGCATTCCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:79,109:188,0:0:2,0:25.9:1:31.1:1:1:0:24.7:187:1:0:0.1 0/1:92:2:1,1:34,56:90,2:0.0217:2,2:30.5:1:30.5:1:1:1.64:25.5:4:0.0217:0:1 +1 204316350 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.14936;SOR=Inf;LSEQ=AAAAGGCCTAGAGAACATAC;RSEQ=TCGGGTGCCTCTCCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:6,17:23,0:0:2,0:28.2:1:30.9:1:1:0:42.8:46:1:0:0.1 0/1:15:2:1,1:7,6:13,2:0.1333:2,2:8:0:32.5:1:1:1.1547:42:4:0.1333:0:1.5 +1 204316427 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19212;SOR=Inf;LSEQ=TGGCAGTTATGGCCGAAAGG;RSEQ=TCCCATTTGCTTTTGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:3,13:16,0:0:2,0:19.4:1:33:1:1:0:52.9:32:1:0:0.1 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:25:1:28:1:1:1.18:54:4:0.1538:0:1 +1 204316458 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=TTTTGAAAGAAGAGAAATAT;RSEQ=GCTCTGTTCTGCCTGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,6:8,2:0.2:2,2:25:1:30.5:1:1:2.65:57:4:0.2:0:1 0/0:11:0:0,0:2,9:11,0:0:2,0:16.3:1:30.4:1:1:0:53:22:1:0:0.1 +1 204317602 . T G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGAATGGTACCAGCTAG;RSEQ=GAACCCCACACAAACCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:31:1:1:0:60:4:1:0:1 +1 204494283 . C T 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATCTAGAGAGTGCTCTAC;RSEQ=TGATAACCATTGGGGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:12.5:1:34:0:1:0:50.5:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204494436 . C T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67313;SOR=0.56281;LSEQ=TACTCTTAATTAAATCAGAA;RSEQ=TAGAAAGTAGTCAGAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:18:18,0:20,0:20,18:0.4737:1,1:26.5:1:32.5:1:1:0:59.9:36:0.4865:0:1 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:7.5:1:31.5:1:1:0:60:4:0.3333:0:1 +1 204494576 . T C 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATAGGGAATTTTCTGCA;RSEQ=TAGAATAGATGTTATAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:261,54:315,0:0:2,0:24.8:1:30.8:1:1:0:60:38.375:1:0:0.1 0/1:193:14:11,3:145,34:179,14:0.0725:2,2:15.6:1:31.5:1:0.73422:1.16219:60:28:0.0737:0:1 +1 204494594 . A AT 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.88206;LSEQ=CATTAGAATAGATGTTATAA;RSEQ=TTTTTTTTTCTATTTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:9:7,2:353,109:462,9:0.0191:2,2:22.6:1:31.3:1:1:1.08:60:18:0.0194:0.0042:0.2 0/1:356:6:5,1:255,95:350,6:0.0169:2,2:29.2:1:30.3:1:1:1.86:60:12:0.0171:0:0 +1 204494738 . G A 126 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=27.54397;LSEQ=CAATCAGGTAAATCATTTTC;RSEQ=GTATTTCTAGTTTTTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:779:1:1,0:252,521:773,1:0.0013:2,0:1:0:28:0:0.32687:0:60:2:0.0014:0:1 0/1:584:20:7,13:208,354:562,20:0.0342:2,2:23.2:1:29.2:1:1:1.09105:60:19:0.0351:0:1.4 +1 204495253 . G A 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=0.406;LSEQ=AATTACCTGGATATGGTGGC;RSEQ=TGCACCTGTAGTCCCAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:13,0:1,0:1,13:0.9286:0,1:19.2:1:31.7:1:1:0:59.8:26:0.9286:0:1 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:6.8:1:31:1:1:0:59:10:0.8333:0:1.2 +1 204495379 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCGACAGAGCAAGACCTT;RSEQ=CCTCAAAAAACAAAAGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:2,0:87,3:90,2:0.0217:1,0:37.5:1:31.5:1:1:0:59.5:4:0.0217:0:1 0/0:45:0:0,0:43,2:45,0:0:1,0:23.4:1:31.4:1:1:0:60:44:1:0:0.1 +1 204495586 . AT A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01154;SOR=Inf;LSEQ=AGCCATCAAATAAAATTCTC;RSEQ=TTTTTTTGTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:112,256:368,0:0:2,0:22:1:30.2:1:1:0:57.4:35.8:1:0:0.6 0/1:336:6:3,3:106,223:329,6:0.0179:2,2:19.2:1:29.3:1:0.39512:2.10:60:12:0.0184:0.003:0.2 +1 204495595 . G GT 189 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.30534;SOR=0.82169;LSEQ=ATAAAATTCTCATTTTTTTT;RSEQ=TTTTTTTTTTTTTTGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:87:18,69:58,120:178,87:0.2771:2,2:28.7:1:29.4:1:0.05955:1.84864:54.1:16.4:0.2808:0:1 0/1:284:68:17,51:66,96:162,68:0.2394:2,2:25.4:1:28.6:1:0.0247:2.05626:54.5:33:0.2651:0.007:1.1 +1 204495610 . G T 86 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00084;SOR=0;LSEQ=TTTTTGTTTTTTTTTTTTTT;RSEQ=AGATGGAGTCTCCCTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:11:6,5:35,146:181,11:0.057:2,2:6.5:1:25.1:1:0.0134:4.95:58.2:2.667:0.0485:0:1.6 0/0:192:0:0,0:43,143:186,0:0:2,0:18.2:1:29:1:1:0:55.3:7.857:0.9821:0:1 +1 204500257 . G A 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGAGTGGGTGGGATTTAGA;RSEQ=TGTTAGAGGTCAAGAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:24.5:1:33:0:1:0:57:4:0.6667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:29:0:33:0:1:0:21:2:1:0:0 +1 204500961 . C CA 43 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATAGCAAAACTCCGTCTC;RSEQ=AAAAAAAAAAGACTCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:8,1:9,3:0.25:2,2:8:1:27.4:1:0.45455:3.4638:60:6:0.25:0.1667:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204501383 . C T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.1426;LSEQ=CTGCTACTACAGGTATGTCA;RSEQ=ATCATATTTCTTCAGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:702:347:132,215:136,217:353,347:0.4943:2,2:25.6:1:29.2:1:0.93804:1.02078:59.9:56.833:0.4921:0:1.1 0/1:483:59:21,38:160,262:422,59:0.1222:2,2:22.4:1:27.8:1:0.77573:1.10485:60:118:0.1237:0:1.1 +1 204506107 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGGGGAAAAATCCAGATTT;RSEQ=AAGATCCCATAACCCTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:12.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204506174 . CT C 45 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTAAAAAGCCATACACT;RSEQ=TTTCCTTTTGTTTGTGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:25.7:1:28.7:1:1:0:59:2:0.2857:0:0.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204506887 . CTG C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTTTGGGTTTGTGTGTAC;RSEQ=TGTGTGTGTGTTTGAGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:1,10:11,2:0.1538:2,0:22.5:1:32.5:1:1:0:60:4:0.1538:0.0769:0 0/0:3:0:0,0:2,1:3,0:0:2,0:20.3:1:32:1:1:0:60:6:1:0:0.3 +1 204507207 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0179;SOR=Inf;LSEQ=CTTTATTTGATGACTGTTGT;RSEQ=AACTTGAGTTCTCTTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:127,0:127,0:0:1,0:25.6:1:33.1:1:1:0:60:254:1:0:0.1 0/1:46:3:3,0:42,1:43,3:0.0652:1,0:14.7:1:29.3:1:1:0:60:6:0.0652:0:1 +1 204508159 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCGCACGCCACCACACCC;RSEQ=GCTAATTTTGTATTTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:29.5:1:1:0:26.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204511602 . C A 82 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCATTTAGAAATTCTTTTAG;RSEQ=ACAAGGTCATTGTTCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:9:1:31.8:1:1:0:60:12:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204512100 . T C 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=0.17641;LSEQ=TCACATTTGAAGGGAAGTGG;RSEQ=TTTTTTTCTTTTGAAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:329:318:64,254:2,9:11,318:0.9666:2,2:24.6:1:32.8:1:1:1.13:60:44.429:0.9658:0:1.1 1/1:219:183:46,137:7,29:36,183:0.8356:2,2:21.6:1:31.3:1:0.53009:1.39:60:44.75:0.8326:0:1.1 +1 204512139 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09688;SOR=Inf;LSEQ=GTAACATTCTTGGTTACTCT;RSEQ=GACCACACATTATATTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:11,145:156,0:0:2,0:23.5:1:30.8:1:1:0:60:77:1:0:1.1 0/1:71:2:1,1:1,68:69,2:0.0282:1,2:22:1:28.5:1:0.05594:48.43:60:4:0.0286:0:2 +1 204512195 . A T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05354;SOR=0.10696;LSEQ=CTCCTATGGCGTTAAATACC;RSEQ=TCTGTATGCATGTGATACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:55:1,54:0,1:1,55:0.9821:0,1:23:1:30.3:1:1:0:60:54:0.9818:0:1.4 1/1:20:17:0,17:0,3:3,17:0.85:0,1:22.3:1:29.5:1:1:0:60:34:0.85:0:1.3 +1 204513256 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCATATTTCTTTAATAA;RSEQ=CATCCTTGACCATTTTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204513402 . G A 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=CTTACCTTTTAAACTCTTCA;RSEQ=TACTGTTTCTTAGGTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:18.3:1:32:0:1:0:60:6:0.3:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:30.5:1:31.5:1:1:0:60:4:1:0:1 +1 204513647 . G GT 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.79129;SOR=1.13125;LSEQ=GAATACAGAAACTCATGTTT;RSEQ=TTTTTTTTCTGTTAGGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:8:6,2:282,156:438,8:0.0179:2,2:28.5:1:31:1:0.71789:1.66:60:16:0.0181:0:0 0/1:297:6:4,2:170,120:290,6:0.0202:2,2:37.7:1:30:1:1:1.41:60:12:0.0203:0:0.2 +1 204515299 . G C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCACGTTTAACAATTTG;RSEQ=AGCTTTTCTACTCTGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:34:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204515863 . C T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16188;LSEQ=GCAGTTGTCTTTTTTGCTTT;RSEQ=AGTTAATTAGCCTCATCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:541:520:376,144:14,5:19,520:0.9612:2,2:23.3:1:30.2:1:1:1.0722:60:103:0.9626:0:1.1 1/1:360:288:204,84:51,21:72,288:0.8:2,2:24.3:1:29.1:1:1:1:60:143:0.7989:0:1.1 +1 204516025 . A G 297 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10523;LSEQ=GGTATGAATCTTTAGCAAGA;RSEQ=CTATTTTGCACCAGCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:567:553:168,385:1,13:14,553:0.9753:1,2:24.4:1:32.7:1:0.07563:5.66:59.9:137.25:0.9751:0:1.1 1/1:448:361:113,248:21,66:87,361:0.8058:2,2:25.7:1:31.3:1:0.24017:1.43:60:89.25:0.8041:0:1.1 +1 204518457 . A C 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGCTCCTGTCGTTAGACCT;RSEQ=AAGATGCGTATATAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1205:0:0,0:520,685:1205,0:0:2,0:24.5:1:29.9:1:1:0:59.9:69.882:1:0:0.1 0/1:792:40:19,21:332,420:752,40:0.0505:2,2:25.9:1:30.7:1:0.74475:1.14:59.5:39:0.0499:0:1.1 +1 204518820 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13417;SOR=Inf;LSEQ=TTATAGCATAATGGTAGTAC;RSEQ=AACATAAAAATGCATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:52,262:314,0:0:2,0:25.1:1:31.8:1:1:0:59.7:77.5:1:0:0.7 0/1:182:2:1,1:41,138:179,2:0.011:2,2:25.5:1:27:1:0.41123:3.34:60:4:0.011:0:1.5 +1 204518824 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12658;SOR=Inf;LSEQ=AGCATAATGGTAGTACGAAC;RSEQ=TAAAAATGCATTTATTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:46,241:287,0:0:2,0:25.6:1:31.5:1:1:0:59.7:574:1:0:0.8 0/1:159:2:1,1:32,125:157,2:0.0126:2,2:30:1:30:0:0.37306:3.86:60:4:0.0127:0:1.5 +1 204518842 . C A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.12317;LSEQ=ACATAAAAATGCATTTATTC;RSEQ=GTTCACTTACCACATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:231:226:30,196:0,5:5,226:0.9784:0,2:22.4:1:32:1:1:0:59.7:74.333:0.9781:0:1 1/1:111:94:18,76:3,14:17,94:0.8468:2,2:20.7:1:29.9:1:1:1.10:60:188:0.8468:0:1.1 +1 204519187 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAGCAATAGAATGTTT;RSEQ=TGTCACCCCAAAACACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:19.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 204700134 . A G 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGAGGAAGAGAGCCCC;RSEQ=GGATGAAGCCAAATGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:0:31.5:1:1:0:60:4:1:0:1.5 +1 204851121 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5068;SOR=0;LSEQ=GCCAGAATCCCCCTTACTCC;RSEQ=GATGTTTCCTCTTAGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:13,14:27,2:0.069:2,2:28:0:32.5:1:1:1.07:49:4:0.069:0:1.5 0/0:20:0:0,0:10,10:20,0:0:2,0:30.3:1:28.9:1:1:0:60:9:1:0:0.2 +1 206646274 . G T 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGAGGGGCTTCAAGGGAAC;RSEQ=TGGGGAGCCAGGACAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:4,3:0.4286:2,0:16.7:1:34:0:1:0:51:6:0.4286:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:33:0:1:0:60:2:1:0:2 +1 206646311 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=GCAGCAGGTGGAACAGGTGC;RSEQ=GGCTGTGGGCTGAGGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:7,2:0.2222:2,0:8.5:1:34:0:1:0:40.5:4:0.2222:0:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:29:1:30.5:1:1:0:60:4:0.6667:0:1.5 +1 206646427 . C A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=4.31797;LSEQ=CTCCCTTGCTTGTGGAATGG;RSEQ=CACATGGAGCCCTTCTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:24:24,0:69,1:70,24:0.2553:1,1:27.6:1:29.4:1:1:0:59.9:23:0.25:0:1.1 1/0:35:21:19,2:14,0:14,21:0.6:1,2:24.1:1:27.8:1:0.50588:0:60:20:0.5882:0:1 +1 206646493 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10408;SOR=Inf;LSEQ=CAGGCCACCAGCGGCCACCC;RSEQ=GTGCCAGGAATGGAATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:232,21:253,0:0:2,0:21.5:1:32.3:1:1:0:59.9:62.25:1:0:0.1 0/1:121:2:1,1:98,21:119,2:0.0165:2,2:18:1:31.5:1:0.33182:4.5826:60:4:0.0168:0:1.5 +1 206646832 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02852;SOR=Inf;LSEQ=GGCATAGGGAGCTGAAAACG;RSEQ=CTCCTTGAGAGGATGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:2,88:90,0:0:1,0:24.2:1:32.2:1:1:0:59.5:44:1:0:0.1 0/1:19:2:1,1:1,16:17,2:0.1053:1,2:31.5:1:28.5:1:0.20468:11.66:60:4:0.1053:0:1 +1 206647450 . A G 124 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24901;SOR=0.21587;LSEQ=CAACAAGCCATCCCCTGCAG;RSEQ=AGATCAGAGTGTCAGGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:15:15,0:6,0:6,15:0.7143:0,1:21.5:1:31.8:1:1:0:60:30:0.7143:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:21:0:33:0:1:0:60:2:0.3333:0:2 +1 206647613 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.14126;SOR=Inf;LSEQ=GGAGAGGGTGGCTGCTCCCC;RSEQ=GTGGGAGTGGGACATGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:245,78:323,0:0:2,0:23.3:1:31.6:1:1:0:59.9:106.667:1:0:0.1 0/1:195:2:1,1:146,47:193,2:0.0103:2,2:30.5:1:29.5:1:0.43267:3.08415:60:4:0.0103:0:1 +1 206647742 . A G 323 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04327;LSEQ=CTGCGGCCCCGCGAGGTGCA;RSEQ=GTGAGGGAGTTTGAGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1093:1091:592,499:1,0:1,1091:0.9982:0,2:23.7:1:32.1:1:1:0:60:82.923:0.9981:0:1.5 1/1:688:660:342,318:15,13:28,660:0.9593:2,2:24.6:1:30.8:1:1:1.0728:60:219:0.9591:0:1.7 +1 206647787 . T C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.06655;LSEQ=AAGCTGAACCACCAGAACAT;RSEQ=GTCAAGCTCTTTGCGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1045:577:241,336:203,262:465,577:0.5522:2,2:27.4:1:30.8:1:0.57072:1.08015:60:63.111:0.5536:0:1.8 1/1:680:567:243,324:53,59:112,567:0.8338:2,2:26.2:1:29.6:1:0.40516:1.19741:59.9:50.545:0.8348:0:1.7 +1 206648037 . C G 67 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03294;SOR=6.78039;LSEQ=CAGAGGGCTTCCTGGAATAA;RSEQ=TGACTTTGGATTCCAGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:2,0:62,11:73,2:0.0267:2,0:18:1:35:0:1:0:60:4:0.0267:0:1 0/1:25:4:4,0:18,2:20,4:0.16:2,0:27.5:1:33.5:1:1:0:60:8:0.16:0:1 +1 206648147 . T G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11928;LSEQ=GCTCCAGGCTGAGCCACTTC;RSEQ=TCCTGGTGGGTGGGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:119:89,30:213,73:286,119:0.2931:2,2:24.8:1:30.5:1:1:1.02:60:118:0.2943:0:1.1 0/1:234:11:8,3:157,66:223,11:0.047:2,2:27.8:1:29.7:1:1:1.12:60:10:0.0439:0:1.2 +1 206648378 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.89407;SOR=0.97777;LSEQ=GCCTCCACCCTCAGACCAGC;RSEQ=GCAGGCCTGGGACAGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:652:354:100,254:77,219:296,354:0.5429:2,2:23.8:1:31.3:1:0.53691:1.12:60:117:0.5476:0:1.1 1/0:348:187:69,118:50,111:161,187:0.5374:2,2:24.6:1:29.7:1:0.25957:1.30:60:61.333:0.5364:0:1.1 +1 206648769 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATGAGGAGTTGTTTAAT;RSEQ=AGTATGGTTTCAAGTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:35.5:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 206649372 . T C 97 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=4e-05;SOR=24.9836;LSEQ=TGCCCCCTAAGCCCCATGCA;RSEQ=GTCTCTGTCCTTCTGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:2,0:53,1:54,2:0.0357:1,0:20.5:1:34.5:1:1:0:54.5:4:0.037:0:1 1/0:16:8:8,0:8,0:8,8:0.5:0,0:20.6:1:32.6:1:1:0:60:16:0.5333:0:1.1 +1 206649411 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00756;SOR=Inf;LSEQ=GTCCCATGGCTCTGTCAGCC;RSEQ=ATGGGAACTCCTGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:89,3:92,0:0:1,0:23.7:1:31.3:1:1:0:59.9:45:1:0:0.1 0/1:40:4:4,0:36,0:36,4:0.1:1,0:20.3:1:32.3:1:1:0:60:8:0.1026:0:1.3 +1 206649528 . C T 143 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.61642;LSEQ=CCCCGTCTGTCCCCAGTGGC;RSEQ=GGCATGAACCACCTGCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:4:1,3:373,254:627,4:0.0063:2,2:17.3:1:26.5:1:0.30958:4.39551:60:3:0.0048:0:1.5 0/1:449:26:15,11:254,169:423,26:0.0579:2,2:22.3:1:30.5:1:0.83858:1.10193:60:52:0.059:0:1 +1 206649720 . C A 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83984;LSEQ=TACCTGGTGGGTGAGCTGCT;RSEQ=GAGACCCGCTGCCCTATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:5:4,1:160,327:487,5:0.0102:2,2:14:1:26.8:1:0.04443:8.14:60:10:0.0104:0:1.4 0/0:351:3:3,0:135,212:347,3:0.0085:2,0:1:0:23:1:0.06049:0:60:6:0.0086:0:1 +1 206649952 . G A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.2875;SOR=1.70031;LSEQ=CACCTGCAGGCGGTGAAAGG;RSEQ=GGTCTGACAGGTCTCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:10:10,0:196,23:219,10:0.0437:2,0:22.6:1:30.8:1:0.60394:0:60:20:0.045:0:1.2 0/1:97:7:7,0:81,9:90,7:0.0722:2,0:30.3:1:26:1:1:0:60:6:0.0667:0:1 +1 206649975 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10286;SOR=Inf;LSEQ=TCTGACAGGTCTCAGGCCCT;RSEQ=GCCAGCCCTCCGGCTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:265,58:323,0:0:2,0:25.2:1:30.9:1:1:0:59.9:52.833:1:0:0.2 0/1:153:2:1,1:129,22:151,2:0.0131:2,2:26.5:1:28.5:1:0.2789:5.75698:60:4:0.0132:0:1.5 +1 206650065 . A G 265 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGCTTCGAAAGCCCCAGCA;RSEQ=AAAGCGTTCGGGGTGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1088:277:161,116:447,364:811,277:0.2546:2,2:25.7:1:32.7:1:0.40086:1.13:60:91.333:0.2537:0:1.1 0/0:817:0:0,0:422,395:817,0:0:2,0:25.1:1:29.6:1:1:0:60:101.125:1:0:0.2 +1 206650245 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07888;SOR=Inf;LSEQ=CCCTGGCCCTTCCCCCACCG;RSEQ=TCCTTGCTGTGTCTTCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:13,188:201,0:0:2,0:24:1:32.1:1:1:0:59.9:32.5:1:0:0.1 0/1:79:2:1,1:7,69:76,2:0.0253:2,2:17.5:1:27.5:1:0.1958:9.29:60:4:0.026:0:1 +1 206650852 . C CA 149 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGGCTGAGGGAAGTGTAG;RSEQ=GGGGGGAGAGGCAGTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:28:25,3:12,0:12,28:0.7:0,2:26.8:1:31:1:0.54089:0:58.8:56:0.7:0.2:0.4 1/1:1:1:1,0:0,0:0,1:1:0,0:48:0:29:0:1:0:60:2:1:0:0 +1 206651107 . G A 246 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=239.29067;LSEQ=CGCAGGTACCGGATCACCAC;RSEQ=GAGAAGCCGGCTGGGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1481:3:2,1:790,686:1476,3:0.002:2,2:26:1:32.3:1:1:1.74:60:6:0.0021:0:1 0/1:956:313:155,158:348,294:642,313:0.3274:2,2:26.2:1:29.7:1:0.18966:1.20634:59.9:51.167:0.3269:0:1.1 +1 206651350 . C T 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCCCATCTGGTTGCTGGAA;RSEQ=GAGTTCTTCCAGCTCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:37,86:123,0:0:2,0:25.4:1:30.5:1:1:0:59.6:29.75:1:0:0.2 0/1:37:10:5,5:6,21:27,10:0.2703:2,2:22.7:1:30.4:1:0.12494:3.37:60:20:0.2703:0:1 +1 206651351 . G A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0124;SOR=4.46246;LSEQ=TCCCATCTGGTTGCTGGAAC;RSEQ=AGTTCTTCCAGCTCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:6:4,2:37,83:120,6:0.0476:2,2:24.2:1:29:1:0.08725:4.43:60:12:0.0484:0:1 0/1:38:7:0,7:12,19:31,7:0.1842:2,0:31.6:1:30.4:1:0.07448:0:60:14:0.1892:0:1 +1 206651439 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12155;SOR=Inf;LSEQ=TCTCTTAGAACGCTCCTATT;RSEQ=CCTGCTTAAGGAGGATAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:183,44:227,0:0:2,0:22.8:1:32.4:1:1:0:60:55.75:1:0:0.1 0/1:122:2:1,1:103,17:120,2:0.0164:2,2:22:1:28:1:0.27435:5.91666:60:4:0.0167:0:1 +1 206651467 . C T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.40998;SOR=1.4626;LSEQ=AAGGAGGATAGGTCTGGGCC;RSEQ=CCACCCCTGACAGTCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:15:12,3:277,45:322,15:0.0445:2,2:27.4:1:32.1:1:0.45717:1.53663:60:30:0.0456:0:1.1 0/1:188:12:10,2:149,27:176,12:0.0638:2,2:29.9:1:30.8:1:1:1.10313:60:24:0.0656:0:1.1 +1 206652159 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.0093;SOR=Inf;LSEQ=ATGACAGAGAAAACCACCCC;RSEQ=GTCCCTCCCTCTGCAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:190,9:199,0:0:1,0:24.8:1:30.9:1:1:0:59.8:23.875:1:0:0.2 0/1:54:3:2,1:47,4:51,3:0.0556:2,2:25:1:30:1:0.25722:5.53743:60:6:0.0556:0:1.3 +1 206652189 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0869;SOR=Inf;LSEQ=TCTGCAAAACAGAGCCCTGT;RSEQ=TATGGGCAACGCTTAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:281,24:305,0:0:2,0:24.1:1:32:1:1:0:59.9:42.571:1:0:0.2 0/1:128:2:1,1:114,11:125,2:0.0156:2,2:34:1:30.5:1:0.18073:9.96588:60:4:0.0156:0:1 +1 206652524 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=5.45571;LSEQ=TTCTCCTCCCCACATTTTCC;RSEQ=CTGAGACAGGAGTTTGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:8:0,8:24,200:224,8:0.0343:2,0:20.9:1:32.5:1:1:0:60:16:0.0357:0:1.1 0/1:141:23:5,18:16,101:117,23:0.1631:2,2:29.6:1:30:1:0.3417:1.75:60:22:0.1618:0:1.2 +1 206653097 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0389;SOR=Inf;LSEQ=TGGGAGGCTCAGGGTGAGTT;RSEQ=TGAAGCCTGAGGTGGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:152,8:160,0:0:2,0:26.5:1:32.4:1:1:0:59.9:159:1:0:0.2 0/1:83:3:2,1:74,6:80,3:0.0361:2,2:33.3:1:30.7:1:0.23488:5.91375:60:6:0.0366:0:1.3 +1 206653132 . G T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13452;SOR=Inf;LSEQ=GGAGATTGGCAGTGAGGGGT;RSEQ=AGTGTGAGCTGGAAATAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:253,50:303,0:0:2,0:22.5:1:32.2:1:1:0:60:59.6:1:0:0.1 0/1:176:2:1,1:139,35:174,2:0.0114:2,2:6:0:31:1:0.36818:3.92994:60:4:0.0116:0:1.5 +1 206653671 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGGCAGGCCGGAGGGGG;RSEQ=GGCAGGCCAGAGGGGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:2,0:185,10:195,2:0.0101:2,0:30:1:32.5:1:1:0:60:4:0.0109:0:1.5 0/0:99:0:0,0:92,7:99,0:0:2,0:23.4:1:27.6:1:1:0:59.9:10:1:0:0.3 +1 206653699 . A G 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14647;SOR=5.13564;LSEQ=CAGAGGGGGAGGCCGGCAGG;RSEQ=GGTGGAGGCCAGTATCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:1:1,0:292,36:328,1:0.003:2,0:19:0:12:0:1:0:60:0:0:0:1 0/1:194:3:2,1:155,35:190,3:0.0155:2,2:26:1:23.3:1:0.46363:2.20302:60:2:0.0109:0:1.3 +1 206653717 . TGG T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04552;SOR=Inf;LSEQ=GGAGGTGGAGGCCAGTATCC;RSEQ=GATGCTGTCTGCATGCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:379,98:477,0:0:2,0:23.6:1:32.1:1:1:0:59.9:78.5:0.9958:0:0.1 0/1:267:3:1,2:206,57:263,3:0.0112:2,2:10.3:1:28.9:1:0.12467:7.15677:60:6:0.0117:0.0075:0.3 +1 206653753 . G T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00321;SOR=Inf;LSEQ=TGCACGGTGCTGAGTCCCCC;RSEQ=ATCAAGGCAGCTCTGACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:852:0:0,0:595,257:852,0:0:2,0:24.5:1:30.4:1:1:0:59.9:64.538:1:0:0.1 0/1:534:6:2,4:358,170:528,6:0.0112:2,2:12.7:1:27.3:1:0.09169:4.19931:60:12:0.0115:0:1.2 +1 206658266 . G T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66392;SOR=1.79396;LSEQ=GCCCAGCATGTGCCAACAGA;RSEQ=CTCTCTGCCTCCCACCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:2:0,2:203,70:273,2:0.0073:2,0:1:0:25.5:1:0.06784:0:60:4:0.0075:0:1 0/1:231:3:1,2:155,73:228,3:0.013:2,2:27.3:1:27:1:0.24678:4.21742:60:6:0.0135:0:1 +1 206658275 . C T 35 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09501;SOR=Inf;LSEQ=GTGCCAACAGAGCTCTCTGC;RSEQ=TCCCACCTTGGCTGCTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:234,102:336,0:0:2,0:23.2:1:31.6:1:1:0:59.9:83:1:0:0.2 0/1:283:3:1,2:179,101:280,3:0.0106:2,2:5.3:1:22.7:1:0.3003:3.52798:60:2:0.0072:0:1.3 +1 206664396 . A T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62962;SOR=2.76434;LSEQ=CTTCTCAGATGCAATCTTGA;RSEQ=GTAACTGGATTTACTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:14:1,13:0,8:8,14:0.6364:0,1:20.2:1:31:1:1:0:60:28:0.6364:0:1.6 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:25.6:1:29.6:1:1:0:60:10:0.8333:0:1.8 +1 206664407 . T G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60268;SOR=3.30211;LSEQ=CAATCTTGAAGTAACTGGAT;RSEQ=TACTTCTGGTATGGACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:1,6:7,8:0.5333:2,0:21.4:1:31.9:1:0.46667:0:60:16:0.5333:0:2 1/1:5:4:0,4:0,1:1,4:0.8:0,0:30.5:1:32:1:1:0:60:8:0.8:0:2 +1 206664519 . T TC 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTGAACCTTCCCTGCC;RSEQ=CCCCCCGCTCCTCTGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:41.5:1:32.5:1:1:1.73:60:4:0.4:0:0.5 0/0:2:0:0,0:1,1:2,0:0:2,0:43.5:1:28:1:1:0:60:4:1:0:0 +1 206665052 . C T 204 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=96.14094;LSEQ=GTGCGTGCAGAAGTATCAAG;RSEQ=GTCCTTAGTCACACACGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1019:2:0,2:462,552:1014,2:0.002:2,0:1:0:26:1:0.50361:0:60:4:0.002:0:1 0/1:791:126:58,68:303,362:665,126:0.1593:2,2:24.3:1:29.3:1:0.92267:1.02:60:125:0.1607:0:1.2 +1 206665247 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00554;SOR=Inf;LSEQ=GTGGACCAGGCAGTTGGCTG;RSEQ=GAGATTTCTGTAGCTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,65:65,0:0:1,0:26.9:1:32:1:1:0:58.8:64:1:0:0.1 0/1:15:3:0,3:0,12:12,3:0.2:0,0:26.7:1:28.3:1:1:0:60:6:0.2:0:1 +1 206665896 . C G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGTGTGGCGAGGGCTGA;RSEQ=CTCCAACCCCTGATTTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:20.5:1:29:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 206666734 . T G 208 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=198.50578;LSEQ=AAGTGCTGGGGAGAAAGCGG;RSEQ=TGTGTATCTGTGTGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:738:1:0,1:259,477:736,1:0.0014:2,0:19:0:35:0:1:0:60:2:0.0014:0:1 0/1:522:111:43,68:159,252:411,111:0.2126:2,2:25.9:1:30.7:1:1:1.00:59.7:54.5:0.2137:0:1.2 +1 206666785 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00478;SOR=Inf;LSEQ=AGCAGAGTATGCTGAGGTTA;RSEQ=AGCCTGAGGGGTTTGGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:55,268:323,0:0:2,0:23.3:1:32.1:1:1:0:60:79.75:1:0:0.1 0/1:171:5:0,5:28,138:166,5:0.0292:2,0:12.2:1:25.6:1:0.59286:0:60:1.5:0.0182:0:1.4 +1 206667175 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10589;SOR=Inf;LSEQ=TTTGGTGGGGCTGCAGAGGA;RSEQ=GGTGGGCCTCCCAGGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:211,16:227,0:0:2,0:27.9:1:33.6:1:1:0:60:226:1:0:0.1 0/1:110:2:2,0:100,8:108,2:0.0182:2,0:30.5:1:29.5:1:1:0:60:4:0.0183:0:1 +1 206667209 . C T 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13697;SOR=5.34529;LSEQ=GGAAAAGGGTCTGGGCAGGG;RSEQ=AACTTCCAGCCTCAGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:1,0:310,51:361,1:0.0028:2,0:49:0:32:0:1:0:60:2:0.0028:0:1 0/1:205:3:2,1:171,30:201,3:0.0146:2,2:24.3:1:23.3:1:0.39173:2.83001:60:2:0.0101:0:2.3 +1 206667268 . C T 74 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25919;SOR=2.16155;LSEQ=GGCAGCATGCAAGAGCTCTG;RSEQ=GAGGGGATGAAGCTGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:866:5:0,5:497,364:861,5:0.0058:2,0:10.6:1:27.8:1:0.01383:0:60:10:0.0059:0:1.4 0/1:645:8:2,6:377,260:637,8:0.0124:2,2:10.8:1:24.9:1:0.07058:4.34044:60:7:0.011:0:1.4 +1 206667441 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02161;SOR=1.68939;LSEQ=GATGACACGTGTCCATTTTC;RSEQ=AAGAAGCCCTGTTGAAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:122:6,116:2,107:109,122:0.5281:1,1:26.3:1:30.8:1:0.28679:2.76:60:29.5:0.5221:0:1.1 1/0:136:89:3,86:1,46:47,89:0.6544:1,1:24.6:1:30.4:1:1:1.60:60:28.667:0.6515:0:1.1 +1 206669136 . C A 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCATTTAAACTCCTTTC;RSEQ=CCTCCTAAACCTTGGCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:24.4:1:30.6:1:1:0:60:10:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 206669442 . T C 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAGCCTGTACCTTTTCTTG;RSEQ=AGGCTAAATAGAGTCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1244:0:0,0:603,641:1244,0:0:2,0:25.1:1:28.9:1:1:0:60:72.176:1:0:0.2 0/1:805:52:30,22:351,402:753,52:0.0646:2,2:22.1:1:31.1:1:0.15061:1.56:58.8:16.333:0.0613:0:1.2 +1 206669465 . C T 167 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=44.00396;LSEQ=GCTAAATAGAGTCCCAGCAC;RSEQ=TCCTGATGTCTGAGCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1190:2:1,1:541,646:1187,2:0.0017:2,2:19.5:1:30:1:1:1.19:60:4:0.0017:0:1 0/1:753:52:25,27:313,387:700,52:0.0691:2,2:27.8:1:29.3:1:0.66649:1.14:60:104:0.0701:0:1.1 +1 206669607 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10696;SOR=Inf;LSEQ=ACCTCCCTCCTGGCTGCTGG;RSEQ=CAGGATGTCGCCAGCATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:5,137:142,0:0:1,0:25:1:31.1:1:1:0:59.9:34.5:1:0:0.1 0/1:70:2:1,1:4,64:68,2:0.0286:2,2:16:1:28:1:0.13872:14.42:60:4:0.029:0:1 +1 206670258 . G GGGAA 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCTGTGTCTGCAAGGCA;RSEQ=GGCTCTCAGCTGGGTGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:30.6:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 206941864 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2041;SOR=1.63893;LSEQ=AGAGGTAATAAATATTCTAT;RSEQ=AGAGAGGTACAATAAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:33:32,1:59,0:59,33:0.3587:1,1:25.5:1:33.1:1:0.3587:0:60:66:0.3587:0:1.1 0/1:48:23:23,0:25,0:25,23:0.4792:1,1:22.1:1:32.4:1:1:0:60:46:0.4792:0:1 +1 206943297 . A G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0219;SOR=2.57342;LSEQ=TCCAGCTCCATGTCCATCAC;RSEQ=CTTAGGGGACAAGCTGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:10:2,8:58,223:281,10:0.0344:2,2:30.9:1:30.4:1:1:1.04024:58.4:9:0.0314:0:1.8 0/1:238:20:6,14:59,159:218,20:0.084:2,2:30.9:1:31.1:1:0.79533:1.15:60:40:0.0847:0:1.3 +1 206943351 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGATTTATCCAAATGCCT;RSEQ=GCCTCACAGCTCCCAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:98:3,95:0,0:0,98:1:0,1:27.2:1:29.9:1:1:0:59.7:48:1:0:1.3 1/1:60:60:2,58:0,0:0,60:1:0,1:21.5:1:29.9:1:1:0:60:120:1:0:1.1 +1 206944077 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02453;SOR=Inf;LSEQ=TGCCTAGCAGCCACCCCCAA;RSEQ=GCCTGCTCAAAGAGAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:61,0:0:1,0:24.2:1:32.6:1:1:0:60:29.5:1:0:0.4 0/1:26:3:3,0:23,0:23,3:0.1154:1,0:14.3:1:31.7:1:1:0:60:6:0.1154:0:1 +1 206944112 . T A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23063;SOR=0.5716;LSEQ=AAATGAGCAAGAGATCTGAC;RSEQ=CCAGGAGTCTTTCCTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:34:33,1:71,0:71,34:0.3238:1,1:26.6:1:30.6:1:0.32381:0:60:33:0.3267:0:1 0/1:42:9:9,0:31,2:33,9:0.2143:2,0:30.3:1:31:1:1:0:60:18:0.2143:0:1 +1 206944233 . A G 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=2.00069;LSEQ=GGGGGCAGCTGCAAGGGAAA;RSEQ=AACTGATCTGCTACTTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:734:500:348,152:151,83:234,500:0.6812:2,2:23.1:1:32.9:1:0.17525:1.26:59.9:82.333:0.6823:0:1.1 1/1:533:432:291,141:61,40:101,432:0.8105:2,2:23.7:1:31.3:1:0.19977:1.35:60:85.4:0.8102:0:1.2 +1 206944645 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.40506;LSEQ=CCTGCAATCAGGAAGCAGAG;RSEQ=CTCCCTTCCCTTAATCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:476:345:241,104:88,43:131,345:0.7248:2,2:25.5:1:31.8:1:0.58009:1.13:59.9:42.125:0.7216:0:1.1 1/1:345:298:205,93:29,18:47,298:0.8638:2,2:24.2:1:30.9:1:0.40086:1.37:60:41.571:0.8635:0:1.1 +1 206944830 . C A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30668;SOR=4.5687;LSEQ=GAAATGCGGTCTTTTTGATG;RSEQ=CCTTTCATTTAGAGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:1:1,0:81,292:373,1:0.0027:2,0:1:0:26:0:0.21925:0:60:2:0.0028:0:1 0/1:248:3:2,1:58,186:244,3:0.0121:2,2:26.3:1:26.3:1:0.1472:6.35:60:6:0.0127:0:1 +1 206944845 . AT A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.36747;SOR=0.59159;LSEQ=TGATGCCCTTTCATTTAGAG;RSEQ=TTTTTTTTTTAAATAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:16:1,15:27,192:219,16:0.0681:2,1:24.9:1:31.7:1:0.70091:2.10416:59.7:32:0.0702:0:0.9 0/1:145:6:0,6:22,116:138,6:0.0414:2,0:28.5:1:32:0:0.59076:0:60:12:0.0429:0:0.8 +1 206944857 . A T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5241;SOR=0;LSEQ=ATTTAGAGATTTTTTTTTTT;RSEQ=AATAAAATTGGCTCTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:0,2:9,173:182,2:0.0109:1,0:7:1:30:0:1:0:55:4:0.0113:0:2 0/0:116:0:0,0:11,105:116,0:0:2,0:20.8:1:29.3:1:1:0:60:37.667:1:0:0.9 +1 206944861 . A C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.63344;SOR=1.19846;LSEQ=AGAGATTTTTTTTTTTAAAT;RSEQ=AAATTGGCTCTGGCCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:160:126:3,123:4,30:34,126:0.7875:2,1:23:1:32.2:1:0.03745:5.38787:59.8:30.5:0.7871:0:1.2 1/1:98:80:4,76:3,15:18,80:0.8163:2,2:23.9:1:31.1:1:0.11353:3.73018:60:79:0.8144:0:1.3 +1 206944936 . T C 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGTGATGGGACCATCAC;RSEQ=TAAATCAGGTCCTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:0,3:1,46:47,3:0.06:1,0:23.7:1:35.3:1:1:0:60:6:0.0612:0:1.7 0/0:16:0:0,0:1,15:16,0:0:1,0:22.7:1:29.1:1:1:0:60:15:1:0:0.6 +1 206944952 . T G 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.18019;SOR=0;LSEQ=TCACTTAAATCAGGTCCTCC;RSEQ=CCTCAGAGTCAAGTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:8:0,8:1,30:31,8:0.2051:1,0:27.9:1:33.8:1:1:0:60:16:0.2105:0:1.3 0/0:10:0:0,0:1,9:10,0:0:2,0:22.2:1:29.6:1:1:0:60:20:1:0:0.3 +1 206945046 . C A 38 q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTGCGGAGCTACATT;RSEQ=GGCTTTAAGGGACACCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:3,3:0.5:0,2:16:1:24.3:1:1:0:54:2:0.4:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 206945311 . A C 71 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTCACCTCGAATCAGAC;RSEQ=TTTCTTTACTTCTCCTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:26.3:1:33.5:1:1:0:60:8:1:0:1.3 1/1:5:5:5,0:0,0:0,5:1:0,0:21:1:30.8:1:1:0:50:10:1:0:1.4 +1 206945381 . G A 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.40032;SOR=2.3994;LSEQ=ATAAGTTTCTCAGCACGAGA;RSEQ=AGAACGCATTTACTTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:9,6:0.4:0,0:12.8:1:30.7:1:1:0:60:12:0.4:0:1.2 1/0:8:5:3,2:3,0:3,5:0.625:0,2:22.8:1:28.2:1:0.46429:0:54.6:10:0.625:0:1.4 +1 206945573 . C T 65 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00299;SOR=Inf;LSEQ=AGGAGAATGTCTAGTTCAGG;RSEQ=AGTCCCAGGAAGAGAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:0:0,0:427,194:621,0:0:2,0:22.9:1:32:1:1:0:59.9:68:1:0:0.1 0/1:483:7:2,5:306,170:476,7:0.0145:2,2:15.9:1:23.3:1:0.10466:4.48545:60:6:0.0127:0:1.1 +1 206945848 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19575;SOR=Inf;LSEQ=CCCCTGATGTGTAGACCTTC;RSEQ=CCTCTCTGTCCCCCTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:33,168:201,0:0:2,0:23.6:1:30.1:1:1:0:59.9:200:1:0:0.1 0/1:160:2:1,1:25,133:158,2:0.0125:2,2:22.5:1:32:1:0.29945:5.24:60:4:0.0126:0:1.5 +1 209632204 . C T 59 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCGCCAAGCATGAAGCA;RSEQ=GTTGGCACTAGCTCCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:31.5:1:29.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 209632430 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25784;SOR=0.67659;LSEQ=CACTGTAGGATCATGTTCGT;RSEQ=GTACTACAGAAAGCAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:54:49,5:73,5:78,54:0.406:2,2:21.6:1:31.8:1:0.7397:1.48516:60:108:0.4122:0:1 0/1:57:18:17,1:32,7:39,18:0.3158:2,1:28.2:1:30.4:1:0.41358:3.65:60:36:0.3214:0:1.1 +1 209632472 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0.55448;SOR=0;LSEQ=CTTGATTTACAGTGAGAGGA;RSEQ=CAGCAATTAGAGGGAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:2,1:224,53:277,3:0.0107:2,2:37:1:30.3:1:0.47552:2.10636:60:6:0.0109:0:1 0/0:148:0:0,0:111,37:148,0:0:2,0:21.9:1:31:1:1:0:60:48.333:1:0:0.3 +1 209632563 . T C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31548;SOR=1.11251;LSEQ=ATTATTTTGACTGGTGGGTC;RSEQ=CTGGCGGGTGAACATCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:968:335:184,151:354,279:633,335:0.3461:2,2:25.8:1:31.1:1:0.78585:1.04124:60:110.667:0.3466:0:1.1 0/1:653:242:132,110:212,199:411,242:0.3706:2,2:25.8:1:30.2:1:0.46666:1.13:60:79.667:0.3711:0:1.1 +1 209632658 . C A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06484;SOR=6.90763;LSEQ=TTTCATTGAGCATGTGCTAC;RSEQ=TATTCTTTAAGACCTAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:1:1,0:75,332:407,1:0.0025:2,0:1:0:25:0:0.18627:0:60:2:0.0025:0:1 0/1:239:4:2,2:60,175:235,4:0.0167:2,2:16.3:1:24.5:1:0.2769:2.90:60:3:0.0127:0:1 +1 209634354 . T G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTAGCTGGCATTACAGAC;RSEQ=TCCACCACCATGCCTAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:28.5:1:1:0:55:4:1:0:1 +1 209744020 . TA T 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGTCACAAACTGGGTGGC;RSEQ=AAATGACAGAAATTTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:7:1:32.8:1:1:0:60:4:0.6667:0.3333:0 1/1:2:2:2,0:0,0:0,2:1:0,0:3:1:27.8:1:1:0:60:4:0.9333:0.8667:0 +1 209744147 . G T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23522;SOR=0.44711;LSEQ=ATGTTTCTCTCCTAGATTTG;RSEQ=GTGATTTGCTTGCAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:14:7,7:7,9:16,14:0.4667:2,2:21.4:1:29.2:1:1:1.27:59.6:28:0.4828:0:1.1 0/1:18:5:2,3:6,7:13,5:0.2778:2,2:33.6:1:27.6:1:1:1.26799:60:10:0.2941:0:1.2 +1 209745395 . T G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTACTTACAATTCCACA;RSEQ=TCCATGCTCCACAATCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:34:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 209745400 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTACAATTCCACATTCCA;RSEQ=GCTCCACAATCCCCAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:33:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 209865797 . T A 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTGGTGGATGGAAAATT;RSEQ=CTAAGAGGAAACATCAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:18:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:30:1:1:0:60:4:1:0:1.5 +1 209865952 . C CGGGGGT 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.65566;SOR=0.54922;LSEQ=GGAATCGGGTATTAAAATGG;RSEQ=GGGGGGGGGGGTGGGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:20.8:1:30:1:1:0:60:10:0.3846:0.0769:0 0/1:8:2:2,0:6,0:6,2:0.25:0,0:30.5:1:28.1:1:1:0:60:4:0.25:0:0 +1 209866075 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.28371;SOR=0;LSEQ=GGAGCCTGACTAAAGTTTGG;RSEQ=CAGAAAAATCTTTGTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:3:2,1:22,30:52,3:0.0545:2,2:28.3:1:30.3:1:0.57461:2.68:60:6:0.0556:0:1 0/0:34:0:0,0:14,20:34,0:0:2,0:25.7:1:30.5:1:1:0:60:33:1:0:0 +1 211401831 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49761;SOR=0;LSEQ=CGCCTTTCAAACTCTTATAC;RSEQ=AACCTCTGGAGTTGTGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:22,18:40,2:0.0476:2,2:14.5:1:29:1:1:1.21636:50.5:4:0.0488:0:1 0/0:35:0:0,0:17,18:35,0:0:2,0:29.7:1:30.2:1:1:0:38.9:34:1:0:0.2 +1 211401892 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19192;SOR=Inf;LSEQ=GTCCCATGACAGCCATCCTG;RSEQ=TATTACTCACCTTCGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:25,0:0:2,0:21.2:1:33.3:1:1:0:48.9:50:1:0:0.1 0/1:20:2:1,1:5,12:17,2:0.1:2,2:12.5:1:32.5:1:1:2.28:39.5:4:0.1:0:1 +1 212225343 . T C 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04525;SOR=3.09476;LSEQ=CTCCTCTTTCCCTTTGTGTT;RSEQ=GTCATTTTGGCGAATTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:89:76:41,35:0,0:0,76:0.8539:0,2:17.4:1:30.1:1:1:0:44.8:24.333:0.8488:0:1.2 1/1:96:91:49,42:0,0:0,91:0.9479:0,2:20.3:1:29.6:1:1:0:40.1:182:0.9479:0:1.1 +1 212225354 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49797;SOR=Inf;LSEQ=CTTTGTGTTTGTCATTTTGG;RSEQ=GAATTACTGGAAGATGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:47,52:99,0:0:2,0:26.9:1:30.1:1:1:0:45.8:32:1:0:1.1 0/1:105:2:1,1:51,52:103,2:0.019:2,2:25.5:1:30:1:1:1.02:43.5:4:0.019:0:1.5 +1 212225370 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2402;SOR=0;LSEQ=TTGGCGAATTACTGGAAGAT;RSEQ=GCGGTTCCGGCCGAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:46,64:110,2:0.0179:2,2:39.5:1:28.5:1:1:1.39:48:4:0.0179:0:2 0/0:116:0:0,0:52,64:116,0:0:2,0:36.1:1:30.8:1:1:0:44:232:1:0:0.9 +1 212225419 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.21547;SOR=Inf;LSEQ=TGAAATTCTGGGTCAACAGC;RSEQ=TTTTTTTCCTTTCATTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:28,73:101,0:0:2,0:21.6:1:31:1:1:0:56.2:100:1:0:0.6 0/1:88:2:1,1:20,66:86,2:0.0227:2,2:11.5:1:28.5:1:0.42241:3.24:50:4:0.023:0:1.5 +1 212225962 . G T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTCCACACTCCAGCCTG;RSEQ=GCAACAGAGCGAGACTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:30:1:1:0:34:4:1:0:1.5 +1 214977161 . T TA 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.2042;SOR=Inf;LSEQ=GCGATCCTCATTTCATAAAT;RSEQ=AAAAAAAAAATTTCAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:20,0:0:1,0:17.1:1:31.2:1:1:0:60:40:1:0:0.2 0/1:17:2:2,0:14,1:15,2:0.1176:1,0:34:1:27:0:1:0:60:4:0.1176:0:0.5 +1 214977284 . T C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00552;SOR=1.8901;LSEQ=CCAATAATTTTTCATGTAAT;RSEQ=GTACACAAAGAAAGTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:60:39,21:82,39:121,60:0.3315:2,2:18.8:1:31.1:1:0.73908:1.13136:60:120:0.3333:0:1.5 0/1:159:77:52,25:44,38:82,77:0.4843:2,2:22.4:1:29.9:1:0.07765:1.79:60:154:0.4904:0:1.4 +1 214977365 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=2.74674;LSEQ=TAATCTATATTGGGTTTGGT;RSEQ=AAAAACAAATTATTATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:112:48,64:93,115:208,112:0.3489:2,2:24.1:1:32.2:1:0.81358:1.07799:60:224:0.3567:0:1.3 1/0:245:146:67,79:43,53:96,146:0.5959:2,2:25.8:1:30.9:1:0.89557:1.05:60:145:0.5967:0:1.3 +1 218806217 . C T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25889;SOR=0;LSEQ=GAAGAGGCACTCTGGTCACT;RSEQ=GGGTTTTCAGCATTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:2,2:5,6:11,4:0.2667:2,2:15:1:30.5:1:1:1.19:60:8:0.2667:0:1 0/0:9:0:0,0:4,5:9,0:0:2,0:24.2:1:29.3:1:1:0:60:18:1:0:0.1 +1 218807505 . G GT 63 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=1.04727;LSEQ=AGGATTCACACGCTTATTAT;RSEQ=TTTTTTTTTTTTTTATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:3,2:2,4:6,5:0.4167:2,2:40.6:1:27.2:1:0.5671:2.70:54.8:4:0.4444:0.0833:1.2 0/1:7:3:1,2:1,3:4,3:0.4286:2,2:24:1:28.3:1:1:1.41:54:6:0.4286:0.1429:0.7 +1 219421879 . A G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03788;LSEQ=AAGTTATCAAATTATAAAGC;RSEQ=TGCCAGGAATTAAAGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:417:416:283,133:0,0:0,416:0.9976:0,2:25:1:30.4:1:1:0:60:58.429:1:0:1.2 1/1:284:267:167,100:10,7:17,267:0.9401:2,2:24.4:1:30:1:0.79926:1.17:60:132.5:0.9397:0:1.6 +1 219421928 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.91272;LSEQ=AATTATGAAAGTTGTCAAGA;RSEQ=TGTGTCATTATGGCACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:565:111:55,56:231,222:453,111:0.1965:2,2:25.8:1:30.3:1:0.83247:1.05932:60:110:0.1971:0:1.6 1/0:390:213:107,106:88,89:177,213:0.5462:2,2:26.8:1:29.2:1:1:1.02:60:29.429:0.5379:0:1.6 +1 219422204 . A G 73 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=AGATAAACGCAAAGAAAATA;RSEQ=ATCCTATAATCTAGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:0,7:7,5:0.4167:0,0:17.2:1:31.8:1:1:0:60:10:0.4167:0:1.6 1/1:1:1:0,1:0,0:0,1:1:0,0:29:0:32:0:1:0:60:2:1:0:2 +1 219991301 . AT A 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49522;SOR=0.44638;LSEQ=TTTTTCAGTCTCTTTGCCTC;RSEQ=TTTTTTCCATTTTGTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:7:3,4:391,270:661,7:0.0105:2,2:17.6:1:32.7:1:0.4533:1.92887:60:14:0.0106:0:0.4 0/0:426:2:1,1:247,177:424,2:0.0047:2,2:15.5:1:27.9:1:1:1.39435:60:4:0.0047:0.0023:0 +1 219991332 . A ATGG 106 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00131;SOR=0;LSEQ=TTTTGTGCCTTAATCAGAAG;RSEQ=AGGAGGAGGAGGAGAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:13:7,6:374,340:714,13:0.0178:2,2:5.2:1:28.7:1:1:1.06:58:12:0.0168:0.0165:0.8 0/0:492:0:0,0:243,241:484,0:0:2,0:23.5:1:28.7:1:1:0:59.7:47.4:0.9854:0:0.1 +1 219991341 . G GAGA 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.0485;SOR=0.54505;LSEQ=TTAATCAGAAGAAGGAGGAG;RSEQ=AGGAGAAAGTGCTTTTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:706:685:347,338:12,4:16,685:0.9703:2,2:25.7:1:31.1:1:0.07486:2.91828:59.7:170.25:0.9756:0.1813:0.1 1/1:488:462:227,235:14,10:24,462:0.9467:2,2:25.6:1:29.4:1:0.40929:1.44823:59.6:91.4:0.9462:0.1516:0.1 +1 219991450 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62878;SOR=1.71004;LSEQ=AGAATTATGCCTCAGTAAAC;RSEQ=TACTACATGACATCATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:2:1,1:46,216:262,2:0.0076:2,2:13:1:26.5:1:0.32492:4.66:60:4:0.0076:0:1 0/1:155:2:1,1:32,121:153,2:0.0129:2,2:13:1:28:1:0.38157:3.74:60:4:0.0129:0:1 +1 220440200 . G A 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGGTCCCTGGCTCCCTCT;RSEQ=TTACAAAGTCAGGGAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:950:0:0,0:471,479:950,0:0:2,0:25.8:1:32.2:1:1:0:46.7:78.167:1:0:0.1 0/1:658:34:17,17:303,320:623,34:0.0517:2,2:22.5:1:28.2:1:1:1.06:51.9:68:0.0522:0:1.1 +1 220440885 . C CT 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=4.87334;LSEQ=TCTTCCAAAGCCCATTGCCT;RSEQ=TTTTTGATTCTTCATTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:814:96:42,54:350,366:716,96:0.1179:2,2:31.2:1:30.6:1:0.38467:1.22919:56:47:0.1181:0.0049:0.1 0/1:580:229:109,120:177,172:349,229:0.3948:2,2:27.7:1:29.7:1:0.49653:1.13267:54.9:75.333:0.3965:0.0431:0.1 +1 220440986 . T C 99 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00125;SOR=13.76841;LSEQ=CTGTTTTGGGTGTTATTCAG;RSEQ=GGCCTGGAGGCAGGATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:0,1:268,265:533,1:0.0019:2,0:3:0:27:0:0.49813:0:60:2:0.0019:0:1 0/1:397:10:2,8:194,192:386,10:0.0252:2,2:26.3:1:29.9:1:0.10511:4.02885:50.9:20:0.0254:0:1.2 +1 220441229 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1245;SOR=Inf;LSEQ=GTTTTAGCCTCAACAGGCCC;RSEQ=GAAATGCAGTTTTCTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:33,166:199,0:0:2,0:21.3:1:30.8:1:1:0:59.9:98.5:1:0:0.1 0/1:109:2:1,1:27,80:107,2:0.0183:2,2:8:1:28:1:0.44954:2.93:57.5:4:0.0185:0:1 +1 220473809 . A G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCTGTTCTGTACAAAGC;RSEQ=GCCTCTGCTTGAGGTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:110:110:74,36:0,0:0,110:1:0,2:21.7:1:29.2:1:1:0:59.3:26.5:1:0:1.1 1/1:56:56:36,20:0,0:0,56:1:0,2:24.5:1:29.7:1:1:0:60:112:1:0:1.1 +1 220473844 . C A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.54389;SOR=0;LSEQ=TTATGGCTTACTGCTCATAG;RSEQ=AGCAGCAACAACAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:96,81:177,2:0.0112:2,2:5.5:1:30:1:1:1.18405:60:4:0.0113:0:1.5 0/0:96:0:0,0:49,47:96,0:0:2,0:25.9:1:31.2:1:1:0:60:95:1:0:0.7 +1 221053536 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49425;SOR=0;LSEQ=CTGGCTTCCCGCAGCGGCTG;RSEQ=CTCCGCTCTCAGCCGCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:28,14:42,2:0.0455:2,2:35:1:32.5:1:1:1.96644:60:4:0.0455:0:2 0/0:44:0:0,0:33,11:44,0:0:2,0:21.6:1:27.3:1:1:0:60:13.667:1:0:0.4 +1 221053545 . T C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13854;SOR=2.21025;LSEQ=CGCAGCGGCTGTCTCCGCTC;RSEQ=CAGCCGCCTACCACCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:7:4,3:29,13:42,7:0.1429:2,2:33.7:1:31:1:0.66845:1.65457:60:14:0.1458:0:1.3 0/1:48:13:10,3:24,11:35,13:0.2708:2,2:28.7:1:30.6:1:0.72786:1.51:60:26:0.2708:0:1 +1 221053572 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20918;SOR=Inf;LSEQ=CCTACCACCACCATCACCCG;RSEQ=AACAACAACAGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:60,45:105,0:0:2,0:21.9:1:32.2:1:1:0:59.9:51.5:1:0:0.4 0/1:89:2:1,1:55,32:87,2:0.0225:2,2:12.5:1:29:1:1:1.70775:60:4:0.0235:0:1.5 +1 221053574 . A C 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.03088;SOR=0;LSEQ=TACCACCACCATCACCCGCA;RSEQ=CAACAACAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:5,1:54,46:100,6:0.0566:2,2:25.2:1:33.3:1:0.22369:4.21:60:12:0.0577:0:1 0/0:93:0:0,0:57,36:93,0:0:2,0:24.2:1:28.9:1:1:0:59.9:186:1:0:0.3 +1 221053589 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22709;SOR=Inf;LSEQ=CCGCAACAACAACAGCAGCA;RSEQ=CAACAGCCGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:54,52:106,0:0:2,0:28.6:1:32.6:1:1:0:59.9:34.333:1:0:0.4 0/1:97:2:1,1:54,41:95,2:0.0206:2,2:36.5:1:29:1:1:1.31328:60:4:0.0211:0:1 +1 221053641 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23412;SOR=Inf;LSEQ=CGCCCCGGGCTGGCGCCCTG;RSEQ=AGCCCCCGGCCTCGGGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:31,41:72,0:0:2,0:21.7:1:31.7:1:1:0:60:35:1:0:0.3 0/1:68:2:1,1:26,40:66,2:0.0294:2,2:12:1:26:1:1:1.53:60:4:0.0308:0:1 +1 221345640 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09667;SOR=Inf;LSEQ=TCACATCACTTCTTATTCCT;RSEQ=GAGCTTCTTCTCTGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:159,46:205,0:0:2,0:22:1:31.7:1:1:0:60:40:1:0:0 0/1:93:2:1,1:71,20:91,2:0.0215:2,2:13.5:1:28:1:0.40252:3.48859:60:4:0.0217:0:1 +1 221345742 . A G 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5845;SOR=0.91264;LSEQ=ATATCTTGTTTATGCTGTCT;RSEQ=TGACATAGTTATCTCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:494:371:179,192:59,64:123,371:0.751:2,2:28.1:1:32.4:1:1:1.01:60:370:0.7505:0:1.1 1/0:379:278:147,131:54,47:101,278:0.7335:2,2:25.1:1:31.2:1:1:1.02382:60:277:0.7347:0:1.2 +1 221345779 . G C 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGTCAGTGGAAATAATT;RSEQ=TTCATGACCCCTTCTCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:171,270:441,0:0:2,0:24:1:32.1:1:1:0:60:87.2:0.9977:0:0.6 0/1:349:26:13,13:140,179:319,26:0.0745:2,2:29.8:1:31.3:1:0.54668:1.28:60:52:0.0751:0:1.9 +1 222474589 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1836;SOR=0;LSEQ=AAGGAAGAGTAAATGGGAAG;RSEQ=TGTTTAATGAGTACAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:12,9:21,2:0.087:2,2:27.5:1:32:1:1:1.31655:60:4:0.0952:0:1.5 0/0:30:0:0,0:16,14:30,0:0:2,0:28:1:29.3:1:1:0:59.6:60:1:0:0.2 +1 222474717 . T C 28 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTTAAAAATGGTTAAGA;RSEQ=GGTAAATTTCATGTTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:38.5:1:28:0:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:3:0:26:0:1:0:60:2:1:0:1 +1 222642095 . C G 52 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCAGGGTCACCCCAACCA;RSEQ=TATAACCGGACCATCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:25:1:34.3:1:1:0:21.3:6:1:0:1 1/1:3:3:0,3:0,0:0,3:1:0,0:24.7:1:33.3:1:1:0:23.7:6:1:0:1.3 +1 224137928 . T C 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATGTGTGCATAGCGGG;RSEQ=CCACTGCTGCTGCCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:0,2:2,5:0.7143:0,2:36:1:32.2:1:1:0:20.2:10:0.8333:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 224486006 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.52821;SOR=0;LSEQ=CCCACAAGTGTTACCACCAC;RSEQ=AAACTGGAAGAGTCTATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:17,11:28,2:0.0667:2,2:31:0:33:1:1:1.52251:60:4:0.0667:0:1 0/0:17:0:0,0:11,6:17,0:0:2,0:30.9:1:29.3:1:1:0:56.9:34:1:0:0.1 +1 224639577 . C T 60 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTAAAAATTGACAGATTA;RSEQ=ACATAGGAATCTGGACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:20.5:1:30.3:1:1:0:60:8:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:12:1:32:0:1:0:60:4:1:0:1 +1 224639728 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50311;SOR=0;LSEQ=ACGCTTTCCTATTGCCTCCC;RSEQ=GATACTGAGGTTGACTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:14,24:38,2:0.05:2,2:28:1:31.5:1:1:1.69:60:4:0.05:0:1 0/0:30:0:0,0:14,16:30,0:0:2,0:28.2:1:28.9:1:1:0:60:14:1:0:0.1 +1 224803669 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAAGAACCGGGAGGGG;RSEQ=GGCTGCGGCGTTTAGGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:28.5:1:1:0:60:4:1:0:1.5 +1 224804029 . AGGC A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.58768;SOR=2.14825;LSEQ=TACAGTTCTCGCAGTGGCAA;RSEQ=GGCGGCGGCGGCGGCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:22.5:1:32:1:1:1.19087:60:4:0.0833:0:0.5 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:41.5:1:28:1:1:1:60:4:0.1667:0:0 +1 226064490 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGAGTAGCCGGGATTACA;RSEQ=GCGCCGACCACCACACCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:27:1:32:0:1:0:38:4:0.2:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:18:0:33:0:1:0:30:2:1:0:0 +1 226064639 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1415;SOR=Inf;LSEQ=GATTACAGGCATGAGCCACC;RSEQ=TACCTGGCCCAGCTTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:176,56:232,0:0:2,0:22.9:1:30.2:1:1:0:59.6:45.4:1:0:0.1 0/1:141:2:1,1:94,45:139,2:0.0142:2,2:17:1:28:1:0.54762:2.07707:59:4:0.0142:0:1 +1 226064642 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15416;SOR=Inf;LSEQ=TACAGGCATGAGCCACCGTA;RSEQ=CTGGCCCAGCTTCTGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:180,59:239,0:0:2,0:24:1:31.9:1:1:0:59.7:46.8:1:0:0.1 0/1:155:2:1,1:104,49:153,2:0.0129:2,2:33.5:1:29:1:0.54252:2.11124:60:4:0.0131:0:1 +1 226064745 . G T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.18635;LSEQ=ATTCTAGTCCGTACTCTCCA;RSEQ=TCACATGTCTCAACCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:584:244:108,136:153,184:337,244:0.4178:2,2:25:1:30.4:1:0.80036:1.04704:60:80.333:0.417:0:1.6 1/0:347:212:102,110:60,75:135,212:0.611:2,2:23.4:1:29:1:0.51034:1.16:60:41.4:0.6053:0:1.3 +1 226064750 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39889;LSEQ=AGTCCGTACTCTCCAGTCAC;RSEQ=TGTCTCAACCCCTTGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:124:51,73:194,241:435,124:0.2214:2,2:26:1:31.1:1:0.53861:1.15193:60:61:0.221:0:2.2 0/1:334:34:16,18:136,163:299,34:0.1018:2,2:21.7:1:30.4:1:0.85828:1.07:60:68:0.104:0:2.1 +1 226064797 . G T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29531;SOR=3.57316;LSEQ=CCCAAGGGCCTTAAAGATAC;RSEQ=ACAGGCTGAGAGCTCTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:1,0:83,218:301,1:0.0033:2,0:35:0:16:0:0.27815:0:60:0:0:0:3 0/1:170:2:1,1:57,111:168,2:0.0118:2,2:31.5:1:25:1:1:1.94:60:4:0.0121:0:1.5 +1 226064799 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1323;SOR=Inf;LSEQ=CAAGGGCCTTAAAGATACGA;RSEQ=AGGCTGAGAGCTCTGCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:78,215:293,0:0:2,0:23.3:1:32.1:1:1:0:60:96.667:1:0:0.7 0/1:168:2:1,1:57,109:166,2:0.0119:2,2:10:1:30.5:1:1:1.90:60:4:0.012:0:2 +1 226064846 . A G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00593;SOR=2.44936;LSEQ=GTAATCACAGGCATAGCTAT;RSEQ=TGAGTATTCTGGCCTTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:52:4,48:7,57:64,52:0.4483:2,2:27.1:1:32.1:1:0.75211:1.46887:60:51:0.4435:0:1.2 1/0:69:46:11,35:4,19:23,46:0.6667:2,2:17.5:1:31.1:1:0.75803:1.48:60:92:0.6667:0:1 +1 226252084 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08947;SOR=Inf;LSEQ=AAAGCAGACTGCCCGCAAAT;RSEQ=GACCGGTGGTAAAGCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:149,134:283,0:0:2,0:15.3:1:30.8:1:1:0:39.3:93.333:1:0:0.1 0/1:230:3:2,1:123,103:226,3:0.013:2,2:13.7:1:25.3:1:1:1.67:35:6:0.013:0:1.3 +1 226252089 . G A 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59837;SOR=2.32889;LSEQ=AGACTGCCCGCAAATCGACC;RSEQ=GTGGTAAAGCACCCAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:1,0:118,113:231,1:0.0043:2,0:1:0:26:0:1:0:35:2:0.0044:0:1 0/1:200:2:2,0:104,94:198,2:0.01:2,0:10:1:24.5:1:0.4993:0:26.5:4:0.0101:0:1 +1 226252232 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCTCTCTTGTATGTATCCA;RSEQ=ATAATTTAACAAAAAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:102:102:2,100:0,0:0,102:1:0,1:25:1:28.8:1:1:0:60:101:1:0:1.1 1/1:54:54:2,52:0,0:0,54:1:0,1:22.3:1:27.5:1:1:0:60:26:1:0:1.1 +1 226252252 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07481;SOR=Inf;LSEQ=CATAATTTAACAAAAAGATG;RSEQ=ATAACAGGAAAACTTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:2,79:81,0:0:1,0:23.7:1:31.8:1:1:0:60:26:1:0:1.1 0/1:31:2:0,2:0,29:29,2:0.0645:1,0:34:1:26:1:1:0:60:4:0.0645:0:2 +1 226252283 . CT C 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.57437;SOR=0;LSEQ=AACTTTTTGCTTTAGAGAAA;RSEQ=TTTTTTTTTCATTTGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:1,43:44,4:0.0833:1,0:31.8:1:34.5:1:1:0:60:8:0.0889:0:1.5 0/0:12:0:0,0:0,12:12,0:0:0,0:22.2:1:29.8:1:1:0:60:24:1:0:0.9 +1 226253127 . T G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAATAAATAGGGCTTTGA;RSEQ=GAATTTCTTGCTAAGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:31,1:0,0:0,32:1:0,1:26.1:1:33:1:1:0:59.3:64:1:0:1 1/1:5:5:5,0:0,0:0,5:1:0,0:14.2:1:32:1:1:0:60:10:1:0:1 +1 226253316 . G T 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.94487;LSEQ=CCACTTACCTTTTTGTGCTA;RSEQ=TTATGTTTTTGGTAACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:563:562:380,182:0,0:0,562:0.9982:0,2:24.4:1:30.8:1:1:0:59.3:111.4:1:0:1.1 1/1:532:531:345,186:0,0:0,531:0.9981:0,2:24.4:1:29.4:1:1:0:59.5:87.5:1:0:1.1 +1 226253419 . G A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12268;SOR=Inf;LSEQ=GTCCACTGAACTTCTGATTC;RSEQ=CAAACTTCCCTTCCAGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:89,73:162,0:0:2,0:11.5:1:30.3:1:1:0:33.3:53:1:0:0.1 0/1:161:3:2,1:96,62:158,3:0.0186:2,2:5.3:1:27.7:1:1:1.29:37.3:6:0.0186:0:1 +1 226253688 . T C 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00134;SOR=Inf;LSEQ=AAGGTCATACACGTAGAAAA;RSEQ=GGCAAAACCATAATTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:11,360:371,0:0:1,0:24.7:1:30.8:1:1:0:59.8:184.5:1:0:0 0/1:239:7:2,5:9,223:232,7:0.0293:1,2:21:1:29.7:1:0.03573:9.67:60:14:0.0295:0:1 +1 226253926 . T C 77 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTCAGGTCCTGAAGAAACA;RSEQ=ATAGGTAGAGAGAGCTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:18.6:1:33.4:1:1:0:60:10:0.5556:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226254036 . T C 60 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGATTGGATTGGCAAGAT;RSEQ=GGGGGAACGGTGCTTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:23.8:1:26:1:1:0:60:4:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226259065 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19247;SOR=Inf;LSEQ=TTTGCAGGAGGCAAGTGAGG;RSEQ=CTATCTGGTTGGCCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:219,26:245,0:0:2,0:33.2:1:31.6:1:1:0:48.8:48:1:0:0.1 0/1:192:2:1,1:167,23:190,2:0.0104:2,2:36.5:1:28:1:0.23495:7.12893:22.5:4:0.0105:0:1 +1 226549058 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16465;SOR=Inf;LSEQ=TTCTGAGGTGGTTTAGTACA;RSEQ=GTACTACCCATCAGCAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:171,4:175,0:0:1,0:26.3:1:33.8:1:1:0:59:174:1:0:0.1 0/1:120:2:1,1:109,9:118,2:0.0167:2,2:11:1:29:1:0.16036:11.54243:60:4:0.0168:0:1 +1 226549326 . G A 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3011;SOR=3.5154;LSEQ=CTCCCCCAGGCTGGCAGGAC;RSEQ=CTCAGTGCCAGCCTGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:1:0,1:24,186:210,1:0.0047:2,0:38:0:32:0:1:0:60:2:0.0048:0:1 0/1:121:2:1,1:16,103:119,2:0.0165:2,2:12:0:31.5:1:0.26226:6.28:60:4:0.0167:0:1.5 +1 226549404 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCGGGGCTGGCAGGAT;RSEQ=CTCAATGCCAGCCTGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:10,54:64,2:0.0303:2,2:26:0:31:1:0.30769:5.20:60:4:0.0313:0:1.5 0/0:21:0:0,0:1,20:21,0:0:1,0:23.6:1:32.3:1:1:0:60:42:1:0:0 +1 226549498 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04648;SOR=Inf;LSEQ=TGGGGGAAGGCTCATACCCT;RSEQ=TAAGCCAGGCTATGCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:50,10:60,0:0:2,0:27.6:1:33.2:1:1:0:59.5:120:1:0:0 0/1:17:2:2,0:13,2:15,2:0.1176:2,0:21.5:1:28.5:1:1:0:60:4:0.1176:0:2 +1 226550437 . G A 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGGTTAAAGCCGAAACCC;RSEQ=TGCATCTGGTTACTGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:24.8:1:32:1:1:0:54.3:8:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226550442 . T C 68 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAGCCGAAACCCGTGCA;RSEQ=CTGGTTACTGGTGCCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:29.8:1:34:1:1:0:54.3:8:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226550553 . ATT A 125 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.63581;SOR=0.50047;LSEQ=TCCTGCTATAGAGCTTGCCT;RSEQ=TTTTTTTTTTTTTTACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:15:15,0:6,0:6,15:0.5769:0,1:28.1:1:32.2:1:1:0:56.5:30:0.5769:0.0385:0.4 0/1:5:2:2,0:3,0:3,2:0.4:0,0:45.5:1:30.5:1:1:0:60:4:0.4:0:0 +1 226550639 . AAAC A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AACCACCACCACCACCCCCC;RSEQ=AACAACAACAACGCACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:108,5:113,2:0.0174:1,0:37.5:1:31.5:1:1:0:60:4:0.0174:0:0 0/0:46:0:0,0:43,3:46,0:0:2,0:27.9:1:29.2:1:1:0:60:45:1:0:0.2 +1 226550741 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09519;SOR=1.32248;LSEQ=TTCTCAGGACAGCAAGCCCC;RSEQ=GGCTTCTGTGCTGTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:101:61,40:318,138:456,101:0.1804:2,2:23.3:1:30.3:1:0.07706:1.50991:60:49.5:0.1793:0:1.1 0/1:377:85:59,26:199,93:292,85:0.2255:2,2:20.8:1:29.4:1:0.89484:1.06:60:170:0.2273:0:1.2 +1 226550924 . G C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42797;SOR=1.12395;LSEQ=GCTCTCGAAACCAACAGTTT;RSEQ=ATTAGGAGAATAAGATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:237:60,177:85,192:277,237:0.4611:2,2:23.4:1:32.3:1:0.20134:1.30531:59.9:78:0.4615:0:1.1 0/1:308:151:48,103:44,113:157,151:0.4903:2,2:25.1:1:31.4:1:0.5338:1.20:60:302:0.4903:0:1.1 +1 226551178 . A G 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGACCCCTGGCCTTTTAC;RSEQ=TGACCTTGTGCTTTTGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:1,3:2,10:12,4:0.25:2,2:25.8:1:33.3:1:1:1.61:60:8:0.2857:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:43:0:28:0:1:0:60:2:1:0:0 +1 226551460 . T C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.5992;SOR=1.4494;LSEQ=TTGCATTTCCTGAAGTATCC;RSEQ=TGTATCTCCCTTGTTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:55:53,2:23,2:25,55:0.6875:2,1:23.5:1:31.5:1:0.5853:2.28:60:54:0.7013:0:2 1/0:21:16:14,2:5,0:5,16:0.7619:0,2:23.8:1:30.1:1:1:0:58.8:15:0.75:0:2.1 +1 226551506 . T C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26013;SOR=1.47139;LSEQ=GAATTGGATTCTGCTACTTA;RSEQ=AAGAAAAGAATCCTAATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:38:37,1:138,2:140,38:0.2135:1,1:26.5:1:32.2:1:0.5157:1.85721:60:37:0.2114:0:2.4 0/1:77:22:22,0:52,3:55,22:0.2857:2,1:22.4:1:31.2:1:0.55338:0:60:21:0.2838:0:2.1 +1 226551529 . C G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49193;SOR=1.18371;LSEQ=GAAAAGAATCCTAATTGGTG;RSEQ=GTCCAGTAACTGCAGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:280:180:177,3:96,2:98,180:0.6429:1,1:24.4:1:31.3:1:1:1.23:60:44:0.6447:0:1.5 1/0:119:81:79,2:37,1:38,81:0.6807:1,1:24.2:1:29.9:1:1:1.07:60:15.2:0.6786:0:1.5 +1 226553467 . C CA 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAGAGTGAGACTCCATGT;RSEQ=AAAAAAAAAAACAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:4,0:23,1:24,4:0.1379:1,0:13.5:1:32:1:1:0:57.8:8:0.1429:0.069:0.8 0/0:6:0:0,0:6,0:6,0:0:0,0:18.8:1:31.3:1:1:0:58.7:12:1:0:1.8 +1 226553485 . AC CA 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.43518;SOR=1.61071;LSEQ=GTCAAAAAAAAAAACAAAAA;RSEQ=AAACAAACAAAAAAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:28:28,0:29,1:30,28:0.459:1,1:17.9:1:31.9:1:1:0:55.3:56:0.4828:0:2.3 1/0:19:11:11,0:6,0:6,11:0.5789:0,0:11.7:1:31.4:1:1:0:59.6:22:0.5789:0:2.2 +1 226553486 . C A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.56754;SOR=0;LSEQ=TCAAAAAAAAAAACAAAAAA;RSEQ=AAACAAACAAAAAAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:4:4,0:27,1:28,4:0.0645:1,0:8.8:1:26.3:1:1:0:51.3:3:0.1034:0:2.5 0/0:20:0:0,0:7,0:7,0:0:0,0:22.3:1:27.7:1:1:0:58.9:2.5:1:0:0.7 +1 226553490 . C A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32284;SOR=1.71872;LSEQ=AAAAAAAAACAAAAAACAAA;RSEQ=AAACAAAAAAAAAACTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:31:31,0:30,1:31,31:0.4844:1,1:18.9:1:31.1:1:1:0:55.4:62:0.5082:0:2.3 1/0:21:13:13,0:7,0:7,13:0.619:0,1:13.8:1:30.8:1:1:0:59.7:26:0.6842:0:2.1 +1 226553494 . C CA 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.02748;LSEQ=AAAAACAAAAAACAAACAAA;RSEQ=AAAAAAAAAACTACTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:33:33,0:30,1:31,33:0.4714:1,1:21.5:1:31.9:1:0.48437:0:56.5:66:0.5077:0.0571:2.7 0/1:23:11:11,0:10,0:10,11:0.4783:0,0:21.1:1:30.9:1:1:0:59.6:22:0.5238:0:2.9 +1 226553779 . G A 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48394;SOR=0.48478;LSEQ=TAAACAGAATCTTGGGATTA;RSEQ=CACAAAAGAGACCCAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:6:5,1:142,371:513,6:0.0116:2,2:8.2:1:27.8:1:0.00801:12.99:60:12:0.0117:0:1 0/0:355:2:2,0:105,248:353,2:0.0056:2,0:1:0:20.5:1:0.09025:0:60:1:0.0029:0:1 +1 226553934 . A C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33171;SOR=2.14972;LSEQ=CTGGGCCAGTGGCTCCACTT;RSEQ=CCTAAGCCTCCACCTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:22:0,22:0,16:16,22:0.5789:1,1:24.8:1:32.4:1:1:0:60:44:0.5789:0:1.1 1/0:12:9:0,9:0,3:3,9:0.75:0,0:22.2:1:32:1:1:0:58:18:0.8182:0:1 +1 226554736 . G C 87 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACCAGAGAAAAATGAAC;RSEQ=CAAGCATTGTGTTTTTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:24:1:31.1:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226554951 . T C 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAAGCTGAGGTGCTGGCT;RSEQ=GGAAGGCTGCCTTGCAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:6:6,0:29,0:29,6:0.1714:1,0:23.7:1:31.3:1:1:0:60:12:0.1765:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:25:1:29.3:1:1:0:60:8:1:0:0 +1 226555302 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00288;SOR=0.71368;LSEQ=GCAGGTTGTCAAGCATTTCC;RSEQ=CCTTGGCCTGGAGGAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1005:330:118,212:240,434:674,330:0.3284:2,2:23.3:1:31.2:1:1:1.01:60:164:0.3313:0:1.1 0/1:638:165:62,103:179,291:470,165:0.2586:2,2:25.3:1:29.8:1:0.92598:1.02186:60:40.25:0.2593:0:1.1 +1 226555401 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07146;SOR=Inf;LSEQ=AAAACCTACATGCAGAGAAG;RSEQ=TCCAACACAGTGAATGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:7,178:185,0:0:1,0:25.6:1:32.5:1:1:0:60:91.5:1:0:0.1 0/1:68:2:1,1:1,65:66,2:0.0294:1,2:13.5:1:28.5:1:0.05838:46.32:60:4:0.0303:0:1.5 +1 226555712 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10692;SOR=Inf;LSEQ=TTTCCCCAGTGGATTTGGTA;RSEQ=AACAGGGGCAGGAAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:31,5:36,0:0:2,0:23.3:1:32.3:1:1:0:59.4:35:1:0:0.1 0/1:18:2:2,0:15,1:16,2:0.1111:1,0:39.5:1:31.5:1:1:0:44:4:0.1176:0:1 +1 226556094 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGGCCAGGCTTTCTCTT;RSEQ=TAGCAGGTGGGTGCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:174:174:26,148:0,0:0,174:1:0,2:20.6:1:33.1:1:1:0:60:173:1:0:1.1 1/1:87:87:12,75:0,0:0,87:1:0,2:21.7:1:31.4:1:1:0:60:86:1:0:1.1 +1 226557669 . G GA 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCTCAAAAAAGAAAAA;RSEQ=AAAGAAAAATCCCACCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:19.3:1:29.7:1:1:0:53:6:1:0.3333:3.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226557878 . T C 115 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30609;SOR=0.24398;LSEQ=AACAGAGAGGGTAACCAACG;RSEQ=CTTCAAGTTTATGGTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:13:13,0:9,0:9,13:0.5909:0,1:24.8:1:31.2:1:1:0:60:12:0.5714:0:1.3 0/1:4:1:1,0:2,1:3,1:0.25:2,0:13:0:33:0:1:0:60:2:0.3333:0:1 +1 226558285 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13813;SOR=Inf;LSEQ=GTGATCGCAGGAGAGCTGGA;RSEQ=CGGGCAGCCCACCCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:51,266:317,0:0:2,0:22.7:1:31:1:1:0:60:34.222:1:0:0.1 0/1:188:2:1,1:38,148:186,2:0.0106:2,2:32:1:28.5:1:0.37274:3.86:60:4:0.0108:0:1 +1 226558301 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1143;SOR=Inf;LSEQ=TGGACCGGGCAGCCCACCCT;RSEQ=AGGCCCCCAACAGGAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:25,207:232,0:0:2,0:24.2:1:32.2:1:1:0:60:45.4:1:0:0.1 0/1:119:2:1,1:13,104:117,2:0.0168:2,2:7:1:26.5:1:0.22233:7.75:60:4:0.0171:0:1 +1 226558318 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09686;SOR=Inf;LSEQ=CCTCAGGCCCCCAACAGGAG;RSEQ=AGTCAGGAGCCTGCTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:11,176:187,0:0:2,0:23.4:1:32.4:1:1:0:60:61.333:1:0:0.1 0/1:85:2:0,2:4,79:83,2:0.0235:1,0:21.5:1:29:0:1:0:60:4:0.0241:0:1 +1 226561548 . A G 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGGGTGGGCCGGGCACG;RSEQ=TGGCTCACACCTATATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,1:3,3:0.5:2,0:23:1:31:1:1:0:56:6:0.5:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226561761 . G C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12324;SOR=2.75043;LSEQ=GCAAAAGTGCAACCACTCCA;RSEQ=GCCCCAACACTCACACAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:47:45,2:29,0:29,47:0.6184:1,1:22.9:1:31.9:1:0.52175:0:60:94:0.6184:0:1.1 1/1:22:18:18,0:4,0:4,18:0.8182:0,1:22.9:1:31.9:1:1:0:60:36:0.8182:0:1 +1 226561850 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28469;SOR=3.69339;LSEQ=TGAAACAGAAACAAGAACAG;RSEQ=CAGACAGCTCTTCACTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:0,1:314,47:361,1:0.0028:2,0:2:0:28:0:0.1326:0:60:2:0.0028:0:1 0/1:197:2:1,1:163,32:195,2:0.0102:2,2:9:1:27:1:0.30768:5.03149:60:4:0.0103:0:1.5 +1 226564691 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.037;SOR=1.95203;LSEQ=TGAAGGACTATTATTCTCCT;RSEQ=TCAACATTTGGTAGTATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:67:66,1:79,1:80,67:0.4497:1,1:22:1:31.6:1:1:1.1955:59.5:21.333:0.4414:0:1.1 1/0:65:40:39,1:25,0:25,40:0.6154:1,1:25.8:1:30.8:1:1:0:60:39:0.619:0:1.1 +1 226564735 . G T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03198;SOR=Inf;LSEQ=TATGATGCCACCTGATCCAC;RSEQ=ATGTGGATTTTCTAGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:317,55:372,0:0:2,0:23.4:1:30.6:1:1:0:59.9:371:1:0:0.2 0/1:174:3:1,2:142,29:171,3:0.0172:2,2:11:1:25:1:0.08227:9.59886:60:6:0.0174:0:1.3 +1 226564740 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10602;SOR=Inf;LSEQ=TGCCACCTGATCCACGATGT;RSEQ=GATTTTCTAGAATAAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:341,65:406,0:0:2,0:23.7:1:32.1:1:1:0:59.9:49.75:0.9975:0:0.2 0/1:197:2:1,1:157,38:195,2:0.0102:2,2:19.5:1:27:1:0.35756:4.09123:60:4:0.0103:0:1.5 +1 226565036 . T C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.02588;SOR=Inf;LSEQ=AGGAGGGTGTCAGATACACA;RSEQ=GTGTGGGTCAGCTGTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:0:0,0:121,374:495,0:0:2,0:23.5:1:30.4:1:1:0:60:40.25:1:0:0.1 0/1:333:4:2,2:94,234:328,4:0.012:2,2:18.3:1:30.3:1:0.58231:2.48:60:8:0.0125:0:1 +1 226566726 . A C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18931;SOR=1.47658;LSEQ=TGTTTTTGATCTCTGTGATT;RSEQ=GATTTCATTCCCCAGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:217:146:145,1:71,0:71,146:0.6728:1,1:22.4:1:32.3:1:1:0:60:292:0.6791:0:1.1 1/0:101:76:76,0:24,1:25,76:0.7525:1,1:26.3:1:30.3:1:0.24752:0:60:18:0.7423:0:1.1 +1 226567008 . C G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00024;SOR=1.68053;LSEQ=AAAAGCACCTACAGTTTTCT;RSEQ=TCCCCTTGAGGTGCTAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:834:145:39,106:188,501:689,145:0.1739:2,2:22.8:1:32.3:1:1:1.01989:59.9:71.5:0.1742:0:1.1 0/1:463:121:41,80:104,238:342,121:0.2613:2,2:24.7:1:31:1:0.49504:1.17:60:120:0.2609:0:1.1 +1 226567172 . A C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14745;LSEQ=GTGAGGACAAAGGCACGACC;RSEQ=CACTGCCCCAGGTATGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:58:47,11:138,47:185,58:0.2377:2,2:22.3:1:30.7:1:0.37922:1.45:60:18.333:0.2311:0:1 0/1:137:6:6,0:111,19:130,6:0.0438:2,0:28.5:1:31.5:1:0.59491:0:60:12:0.0451:0:1 +1 226567178 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13984;SOR=Inf;LSEQ=ACAAAGGCACGACCACACTG;RSEQ=CCCAGGTATGCTGCGGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:209,53:262,0:0:2,0:23.8:1:32.1:1:1:0:60:51.4:1:0:0.3 0/1:157:2:1,1:128,27:155,2:0.0127:2,2:9.5:1:28:1:0.32582:4.6735:60:4:0.0129:0:1 +1 226567209 . G T 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08673;SOR=6.04033;LSEQ=CTGCGGGCATTTGGATGTGT;RSEQ=CTCCTAGTCAGCTGGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:1:0,1:308,142:450,1:0.0022:2,0:1:0:26:0:0.31707:0:60:2:0.0023:0:1 0/1:302:4:3,1:205,93:298,4:0.0132:2,2:34:1:26.5:1:1:1.36:60:3:0.0101:0:1.5 +1 226567563 . C G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57473;SOR=1.13649;LSEQ=GGGAGAGGTTCCGTGGACAA;RSEQ=AACCTGGCCACCAATGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:78:67,11:249,79:328,78:0.1916:2,2:20.1:1:33.1:1:0.06819:1.93:60:38:0.1891:0:1.1 0/1:179:38:29,9:117,24:141,38:0.2123:2,2:18.8:1:30.5:1:0.35214:1.50917:60:18:0.2057:0:1.1 +1 226567882 . G GA 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.83729;LSEQ=TCCTCTGTTCAAATTGAAAG;RSEQ=AAAAAAAACCAAAATACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:6:1,5:92,349:441,6:0.0134:2,2:18.7:1:30.1:1:1:1.31729:60:12:0.0138:0.0045:0.3 0/1:267:3:1,2:61,203:264,3:0.0112:2,2:26.3:1:29:1:0.54893:1.66:60:6:0.0113:0.0037:0.3 +1 226568608 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11485;SOR=Inf;LSEQ=TACAGTACAAAGCAGCAACA;RSEQ=TGAGAGCAAATACTGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:78,1:79,0:0:1,0:26.1:1:32.5:1:1:0:60:78:1:0:0.1 0/1:41:2:1,1:39,0:39,2:0.0488:1,2:47:1:30.5:1:0.04878:0:60:4:0.05:0:1 +1 226568665 . T C 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01611;SOR=0.46684;LSEQ=CAGCGATGATGATGTTAAGA;RSEQ=CCAGTTTTTCAGCGCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:52:51,1:156,6:162,52:0.243:1,1:25.6:1:32.4:1:1:1.96:60:51:0.2417:0:1.1 0/1:123:16:15,1:104,3:107,16:0.1301:1,1:22.3:1:31.3:1:0.43157:2.29062:60:32:0.1322:0:1.1 +1 226568972 . A G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04262;SOR=Inf;LSEQ=TGCTGCTCCCCAGTAAGGGG;RSEQ=GGTGGAGGAGCAGGTGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:40,286:326,0:0:2,0:24:1:31.6:1:1:0:60:53.333:1:0:0.1 0/1:176:3:1,2:29,144:173,3:0.017:2,2:23.3:1:29.7:1:0.43117:2.47:60:6:0.0174:0:1 +1 226569028 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06905;SOR=Inf;LSEQ=GGGAAAAGCCTATGAAAATA;RSEQ=ACTCGCGAGAAAACAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:1,107:108,0:0:1,0:21.6:1:32.8:1:1:0:60:216:1:0:0.1 0/1:39:2:1,1:0,37:37,2:0.0513:1,2:40:1:29.5:1:0.05128:0:60:4:0.0513:0:1 +1 226570786 . C T 75 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24924;SOR=2.01403;LSEQ=GGAGCCGAGGCTGTGGAGGG;RSEQ=GGAGGCGTGGCCGCCACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:788:5:0,5:410,373:783,5:0.0063:2,0:1:0:26.6:1:0.02505:0:51.8:10:0.0065:0:1.6 0/1:551:7:3,4:290,254:544,7:0.0127:2,2:22:1:26.9:1:0.71096:1.52114:56:14:0.0129:0:1.4 +1 226570840 . T C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=1.6977;LSEQ=GGGGGGAATATACGGTCCTG;RSEQ=TTTTTAACCTTCAATTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:723:441:177,264:127,153:280,441:0.61:2,2:27.5:1:32.6:1:0.18838:1.23768:56:48:0.6119:0:1.1 1/0:574:417:185,232:74,83:157,417:0.7265:2,2:25:1:31.3:1:0.57319:1.11785:55.4:68.5:0.7261:0:1.2 +1 226572794 . C T 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTGCGATACTAGGAGATA;RSEQ=GTGAACCCTGGATCCAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:31.5:1:28.5:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226573274 . G A 145 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=6.40495;LSEQ=CACTTGGTCCAGGCAGTGAC;RSEQ=TCCCCAGTGCAGTAATAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1401:7:6,1:644,748:1392,7:0.005:2,2:6.1:1:24.9:1:0.05443:6.96:60:6:0.0043:0:1.9 0/1:930:29:13,16:437,464:901,29:0.0312:2,2:24.6:1:29.9:1:0.71099:1.15897:59.1:58:0.0316:0:1.3 +1 226573364 . A G 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80978;SOR=1.03038;LSEQ=GCACCGAACACCATGCCATC;RSEQ=GCTACTCGGTCCAAGATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:683:329:112,217:108,243:351,329:0.4817:2,2:25.8:1:30.7:1:0.36822:1.16:60:64.8:0.4836:0:1.3 0/1:462:226:85,141:86,150:236,226:0.4892:2,2:24.5:1:29.1:1:0.84724:1.05:59.9:74.333:0.4901:0:1.4 +1 226573402 . T C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0625;SOR=1.45929;LSEQ=CTGCAGCCAGTGGAGAAACA;RSEQ=GTCAGAGGGCAAATGCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:433:72:16,56:76,284:360,72:0.1663:2,2:25.7:1:29.7:1:0.87484:1.07:59.6:23:0.1627:0:1.9 0/1:235:53:10,43:46,136:182,53:0.2255:2,2:24.2:1:30.1:1:0.3666:1.45222:60:106:0.2265:0:1.9 +1 226573424 . T A 34 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55575;SOR=0;LSEQ=TCAGAGGGCAAATGCGGGAC;RSEQ=ACAAAAAAGGACACTTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:43,248:291,3:0.0102:2,2:5:1:21.7:1:0.06219:11.38:49.3:2:0.007:0:3.7 0/0:163:0:0,0:32,131:163,0:0:2,0:23.3:1:27.7:1:1:0:60:53.333:1:0:0.6 +1 226573924 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12255;SOR=Inf;LSEQ=TCCTTGCAATTAATACCAGC;RSEQ=GGTGTTCACACGGAGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:217,3:220,0:0:1,0:23.5:1:30.7:1:1:0:59.8:72.333:1:0:0.1 0/1:119:2:1,1:114,3:117,2:0.0168:1,2:21.5:1:28:1:0.06637:33.03137:60:4:0.0172:0:1 +1 226574309 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGACTCCCAGTCATGCT;RSEQ=CTGTGGACACCAAATTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:0,77:77,2:0.0253:1,2:14.5:1:28.5:1:0.02532:0:60:4:0.0256:0:1.5 0/0:24:0:0,0:2,22:24,0:0:2,0:30.4:1:30.3:1:1:0:60:48:1:0:0.1 +1 226576127 . T C 106 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66214;SOR=0.38123;LSEQ=ACTCAGCCCTTGCTCAAGCC;RSEQ=GGCTGCAGGTCAGACACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:10,0:30,0:30,10:0.25:1,0:32.3:1:32.1:1:1:0:60:20:0.25:0:1 0/1:9:1:1,0:7,1:8,1:0.1111:2,0:49:0:29:0:1:0:60:2:0.1111:0:1 +1 226576270 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.4743;SOR=0.88321;LSEQ=TAAAGGTCTTAATAAGTGGG;RSEQ=CACAACTCCTTGAATTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:176:155,21:331,46:377,176:0.3177:2,2:24.6:1:31.6:1:1:1.03:60:57.667:0.3163:0:1.1 0/1:278:81:66,15:174,23:197,81:0.2914:2,2:22.4:1:30.2:1:0.17739:1.71568:60:39.5:0.2894:0:1 +1 226576296 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47544;SOR=0.89832;LSEQ=CTCCTTGAATTGTCTTCCCA;RSEQ=AATGAGAAAGAGAATCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:894:164:114,50:497,230:727,164:0.1834:2,2:23.6:1:30.2:1:0.85232:1.06:60:163:0.1844:0:1.1 0/1:536:90:61,29:290,155:445,90:0.1679:2,2:21.7:1:29:1:0.71542:1.12:60:29:0.1648:0:1.2 +1 226576496 . T A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04588;SOR=Inf;LSEQ=TGAGAGACAGCCAGAGCCAT;RSEQ=AAAAGTCTGACACCCAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:100,386:486,0:0:2,0:23.5:1:28.8:1:1:0:59.9:161:1:0:0.1 0/1:272:3:2,1:67,202:269,3:0.011:2,2:11:1:20.7:1:0.15937:5.98:58.7:2:0.0074:0:3.3 +1 226576774 . TA T 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCAGACCCCGTCTGAGGT;RSEQ=AAAAAAAAAAAGAAACCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:24:1:33:0:1:0:60:4:0.4:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226578047 . G T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3264;SOR=0.80902;LSEQ=AGTGGTATGGAACCTGTAGG;RSEQ=CCTTTGGGCCTCCCTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:109:95,14:168,53:221,109:0.3293:2,2:23.3:1:30.5:1:0.01977:2.14:59.7:218:0.3344:0:1.8 0/1:190:54:37,17:102,34:136,54:0.2842:2,2:22.4:1:28.2:1:0.36965:1.37602:60:108:0.2872:0:1.9 +1 226578099 . T C 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03955;LSEQ=CCCCCAGGGCAACCCCGCAG;RSEQ=GCTCCACCCACCCTTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:695:691:448,243:0,3:3,691:0.9942:0,2:26:1:31:1:0.04419:0:59.3:45.067:0.9956:0:1.2 1/1:469:409:253,156:32,28:60,409:0.8721:2,2:26.5:1:30.5:1:0.25718:1.42:59.3:408:0.8737:0:1.2 +1 226579788 . TACGTTGAGCTAGCAC T 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=TCACTTTATTTTTAATCACT;RSEQ=CCTAAAGCCCCCATTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:382,10:392,0:0:1,0:24:1:28.8:1:1:0:60:129.667:1:0:0 0/1:181:8:7,1:162,10:172,8:0.0442:2,2:28.5:1:31.6:1:0.40243:2.29927:60:16:0.0447:0:0 +1 226579812 . C T 51 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02026;SOR=Inf;LSEQ=TTGAGCTAGCACCCTAAAGC;RSEQ=CCCATTTCTTCTTTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:562:0:0,0:483,79:562,0:0:2,0:24.5:1:31:1:1:0:60:50.091:1:0:0.1 0/1:342:4:1,3:275,63:338,4:0.0117:2,2:7.8:1:25.5:1:0.02384:12.95846:60:8:0.0118:0:1 +1 226580021 . G T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48737;SOR=0.89456;LSEQ=CATCCTGGCCTTTGCCTGGA;RSEQ=AATCAAACAGACAGCAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:725:135:33,102:152,438:590,135:0.1862:2,2:24.2:1:29:1:0.82697:1.07255:59.6:66.5:0.1847:0:1.2 0/1:465:79:19,60:123,262:385,79:0.1699:2,2:25.2:1:27.6:1:0.18192:1.48133:59.9:78:0.1714:0:1.2 +1 226580093 . C T 162 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97315;LSEQ=GGAGCCCCGTCCTCTTCTAC;RSEQ=TCCCCAGGATCCTTCCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:40:0,40:8,176:184,40:0.1786:1,1:25.3:1:30.5:1:0.35608:0:60:80:0.1802:0:1.4 0/1:126:22:1,21:9,95:104,22:0.1746:2,1:22.2:1:30.2:1:1:1.98053:60:44:0.176:0:1.5 +1 226580187 . T C 104 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67255;SOR=0.46046;LSEQ=TAACAACCGTGGTCAGCTAA;RSEQ=AGAGCTTCTTTTCTGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:9:0,9:0,41:41,9:0.18:1,0:14.9:1:32.9:1:1:0:60:18:0.18:0:1.4 0/1:11:1:0,1:1,9:10,1:0.0909:2,0:26:0:33:0:1:0:60:2:0.0909:0:1 +1 226589709 . C T 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13689;LSEQ=TAAAGGCTACATTCCAAGCA;RSEQ=CTGGAAAAACAAAATACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:14:14,0:8,0:8,14:0.6364:0,1:20.1:1:30:1:1:0:53.4:13:0.619:0:1.1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:17:1:31.5:1:1:0:60:4:0.6667:0:1 +1 226589809 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08629;SOR=Inf;LSEQ=TACGCTTGATCTGCACATGT;RSEQ=GGAGAGGGCAAGCTGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:116,3:119,0:0:1,0:25:1:32.7:1:1:0:60:38.667:1:0:0.3 0/1:50:2:1,1:47,1:48,2:0.04:1,2:46:0:30:1:0.07918:33.61413:60:4:0.04:0:2.5 +1 226589833 . T C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02614;SOR=1.93167;LSEQ=GAGGGCAAGCTGGGGGAGGT;RSEQ=TGCTTTGCTCTCTGAGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:37:34,3:149,11:160,37:0.1878:2,2:21.1:1:31.7:1:0.72947:1.19406:60:17.5:0.1832:0:1.1 0/1:97:30:27,3:63,4:67,30:0.3093:2,2:21.4:1:30.6:1:0.67297:1.73904:60:29:0.3053:0:1.2 +1 226589851 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27815;SOR=3.77772;LSEQ=GTTTGCTTTGCTCTCTGAGA;RSEQ=GAGGCCCTCCTGGGAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:1:0,1:236,35:271,1:0.0037:2,0:1:0:25:0:0.13235:0:60:2:0.0038:0:1 0/1:145:2:1,1:128,15:143,2:0.0138:2,2:30.5:1:28.5:1:0.2092:8.29356:60:4:0.0139:0:2 +1 226589958 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.56195;LSEQ=GTCTTCTTGACTTTCTGCTG;RSEQ=TCATCCCACCGAAGCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1046:366:203,163:385,294:679,366:0.3499:2,2:25.6:1:30.5:1:0.74384:1.05141:52.1:90.5:0.3525:0:1.1 0/1:771:179:99,80:334,255:589,179:0.2322:2,2:27.2:1:29.3:1:0.79634:1.05833:52:178:0.2336:0:1.2 +1 226590413 . G A 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACACACTGCTACATTTA;RSEQ=TGGTGAGCTGCCTCATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:1,3:4,3:0.4286:2,0:37.7:1:32.3:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 226595403 . A AGGGCCC 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=3.000;MSILEN=1;SSF=0.14987;SOR=0;LSEQ=AGGCCCCAAGTGCCGCTCCG;RSEQ=GGGCCCGGGCCCGCTCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:8,1:17,0:17,9:0.3462:1,2:15:1:32.4:1:0.34615:0:60:18:0.3462:0.0769:0.2 0/0:6:0:0,0:6,0:6,0:0:0,0:8.3:1:30.2:1:1:0:60:12:1:0:0 +1 226595647 . C G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.51078;LSEQ=CCATCCTCCCCTAGCTGCCG;RSEQ=CAAAGCTCCGGAAGCCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1032:363:136,227:252,416:668,363:0.3517:2,2:25.9:1:31.6:1:0.94644:1.01109:59.9:44.375:0.3522:0:1.2 0/1:779:169:66,103:268,340:608,169:0.2169:2,2:24.1:1:30.2:1:0.25454:1.2298:60:27.167:0.2128:0:1.2 +1 226596686 . T A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGAAATTGTGGTAATGAC;RSEQ=GCACCTGTTGCTATCAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:19:0:32.5:1:1:0:43:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 227595966 . G A 69 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0.2582;LSEQ=TTCAGTTGTCACTTGTCTGA;RSEQ=TGCTTTCCACCATCCGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:29.8:1:29.8:1:1:0:60:10:0.8333:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:29:0:25:0:1:0:23:2:0.5:0:1 +1 227596235 . A T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07687;SOR=0.68201;LSEQ=ATAGAAAACCATAAACAGTT;RSEQ=ACTTAGACAGATACATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:72:46,26:216,120:336,72:0.1765:2,2:26.4:1:30.2:1:1:1.01736:59.9:71:0.1762:0:1.8 0/1:306:39:19,20:158,109:267,39:0.1275:2,2:25.5:1:28.4:1:0.22864:1.52364:59.1:78:0.1291:0:1.6 +1 227596280 . A G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0078;SOR=0.69012;LSEQ=GAAGCTATAAATGATACACA;RSEQ=TGTGCCTCTGGTTTTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:550:324:184,140:124,101:225,324:0.5891:2,2:24.1:1:32.5:1:0.72685:1.07:59.9:63.8:0.5875:0:1.3 0/1:360:179:93,86:90,91:181,179:0.4972:2,2:24.4:1:31.4:1:0.67495:1.09:59.8:178:0.5014:0:1.3 +1 227596405 . G T 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTCTGTCACACACATT;RSEQ=CCTATATCCCACACCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:8,143:151,2:0.0131:2,2:6.5:1:31:1:0.11455:16.91:60:4:0.0134:0:1 0/0:67:0:0,0:2,65:67,0:0:1,0:23.9:1:32.6:1:1:0:60:134:1:0:0 +1 227596565 . C A 60 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22474;LSEQ=AACGTTTTTGTTCCCCAGTG;RSEQ=ATATAAAAGTTATGTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,4:4,4:0.4444:0,0:22.3:1:30.3:1:1:0:53.5:8:0.4444:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:15:0:32:0:1:0:60:2:0.5:0:1 +1 228161888 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCTCGGCCGCTTCAGCA;RSEQ=GTCCAGCTCCTGCCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 228163949 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20216;SOR=Inf;LSEQ=CATCTGGGCGTGGTGGGGTC;RSEQ=TCCAGTGTGGGATCCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:21,19:40,0:0:2,0:27.6:1:31.6:1:1:0:29:39:1:0:0.1 0/1:34:2:1,1:15,17:32,2:0.0588:2,2:45.5:1:28.5:1:1:1.13:36:4:0.0588:0:1.5 +1 228163964 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1875;SOR=Inf;LSEQ=GGGTCCTCCAGTGTGGGATC;RSEQ=ATGTCCGTGGGGTTCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:17,19:36,0:0:2,0:20.7:1:31.4:1:1:0:29.9:35:1:0:0.1 0/1:28:2:1,1:11,15:26,2:0.0714:2,2:17:1:30.5:1:1:1.35:44:4:0.0741:0:1 +1 228164114 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08523;SOR=Inf;LSEQ=GAGGAGCCTGGTAGTTCCAG;RSEQ=TCGCCCACACTTTCAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:23,0:0:2,0:19.3:1:31:1:1:0:21.1:22:1:0:0.1 0/1:10:2:2,0:6,2:8,2:0.2:2,0:25:1:33.5:1:1:0:20.5:4:0.2:0:1 +1 228512409 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1411;SOR=Inf;LSEQ=TGTACATCCAGTTGGCATCA;RSEQ=ATGTGTTGTGAGTGAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:47,12:59,0:0:2,0:21.3:1:32.8:1:1:0:60:118:1:0:0 0/1:36:2:1,1:24,10:34,2:0.0556:2,2:8:0:30.5:1:0.52381:2.33552:60:4:0.0556:0:1.5 +1 228512422 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13704;SOR=Inf;LSEQ=GGCATCAGATGTGTTGTGAG;RSEQ=GAAAACAGCTCAGGGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:51,23:74,0:0:2,0:21.1:1:29.7:1:1:0:60:148:1:0:0 0/1:44:2:1,1:27,15:42,2:0.0455:2,2:35.5:1:30.5:1:1:1.77473:60:4:0.0455:0:1 +1 228512513 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.146;SOR=Inf;LSEQ=ATGTGATCTGGTAGAAGTGA;RSEQ=TTTATCACTCAATGCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:41,73:114,0:0:2,0:21.9:1:32.4:1:1:0:59.7:56:1:0:0.1 0/1:71:2:1,1:29,40:69,2:0.0282:2,2:27.5:1:25:0:1:1.37:60:4:0.0282:0:1 +1 228607395 . T C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGAATTCTTAAATTGAATTC;RSEQ=ACTTTAATAATTTAATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:335:335:333,2:0,0:0,335:1:0,1:25.3:1:31.4:1:1:0:60:54.833:1:0:1.1 1/1:132:121:119,2:11,0:11,121:0.9167:0,1:23.9:1:30.8:1:1:0:60:39.333:0.9147:0:1.1 +1 228607443 . G T 48 v3;q25;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0457;SOR=5.00469;LSEQ=ATACCACTGCTGTGGATTGT;RSEQ=GTTTTTTTTTTCAAATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:896:2:0,2:703,190:893,2:0.0022:2,0:13.5:1:26.5:1:0.04583:0:60:4:0.0023:0:1.5 0/1:451:5:0,5:317,129:446,5:0.0111:2,0:11.6:1:21:1:0.0022:0:60:1.5:0.0069:0:2.6 +1 228607444 . G GT 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.1391;SOR=1.39956;LSEQ=TACCACTGCTGTGGATTGTG;RSEQ=TTTTTTTTTTCAAATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:908:55:47,8:656,189:845,55:0.0606:2,2:28.5:1:30.9:1:0.23748:1.69:59.9:110:0.0615:0:0.4 0/1:459:38:30,8:292,128:420,38:0.0828:2,2:28.2:1:30.1:1:0.26842:1.64:60:76:0.0844:0:0.5 +1 228608991 . G T 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCAGAAGGTACGCTGAG;RSEQ=GCCTCATTCCCTGGCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 228612444 . A G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00104;SOR=0.04129;LSEQ=ACAGGGTGAACACAGGATTC;RSEQ=CCAGCCTCCCACCCTAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:121:120:117,3:1,0:1,120:0.9917:0,1:24.2:1:30:1:1:0:59.8:119:0.9917:0:1.1 1/1:29:24:23,1:5,0:5,24:0.8276:0,1:23.3:1:30.6:1:1:0:60:48:0.8276:0:1.2 +1 228612838 . G T 333 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00146;LSEQ=CGCTGGAAGGGCAACTTGCG;RSEQ=ATTAGCAGCTCAGTGGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2826:2824:1398,1426:1,0:1,2824:0.9993:0,2:25:1:29.1:1:0.49522:0:59.7:99.857:0.9993:0:1.2 1/0:1823:1222:571,651:299,299:598,1222:0.6703:2,2:24.1:1:28.2:1:0.19427:1.14002:59.8:202.667:0.6722:0:1.2 +1 228612892 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27681;LSEQ=ATCTCGCGAAGCGCCACCGT;RSEQ=CCGGGCCGGTAGCGGTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2573:252:120,132:1127,1191:2318,252:0.0979:2,2:24.8:1:28.9:1:0.79083:1.04089:59.7:41:0.0974:0:1.6 0/1:1577:46:23,23:723,805:1528,46:0.0292:2,2:20.7:1:28:1:0.76555:1.11:59.9:92:0.0296:0:1.8 +1 228613052 . T C 320 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02028;LSEQ=CGAAACTGTTGGCCCCGCGG;RSEQ=GTCCTCTGCCCAGACCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1361:1357:506,851:1,1:2,1357:0.9971:2,2:27.3:1:30.8:1:1:1.68107:60:78.824:0.997:0:1.1 1/1:866:756:304,452:42,66:108,756:0.873:2,2:26.1:1:29.9:1:0.83417:1.06:60:74.6:0.8746:0:1.2 +1 228613129 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10806;SOR=Inf;LSEQ=ATTGGCTGGCCTCAGGTGGC;RSEQ=TGATGGCCCACTGCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:10,330:340,0:0:1,0:27:1:32.5:1:1:0:59.9:339:1:0:0.4 0/1:167:2:1,1:10,155:165,2:0.012:2,2:13:1:29.5:1:0.12777:14.83:60:4:0.0122:0:2 +1 228613442 . G A 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTCACTCTTGTTGCCCA;RSEQ=GCTGGAGTGCAATAGCGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:14.7:1:28.7:1:1:0:58.3:2:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 228613471 . T C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATAGCGTGATCTCTGCT;RSEQ=ACTGCAACCTCCACCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:10.7:1:31.7:1:1:0:38.3:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 228617063 . G A 62 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CCTCACTTTTCCAGTCATAA;RSEQ=GGCTTTTGCTTTTAGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:32:1:31:1:1:0:60:8:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:41:0:31:0:1:0:60:2:1:0:0 +1 228617397 . G A 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAGATTTCCTCTGCAAACT;RSEQ=AAGAGAATGTGAGATACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:46:45,1:301,8:309,46:0.1296:1,1:20.8:1:28.8:1:1:1.20:59.7:92:0.1311:0:1.2 0/0:120:0:0,0:119,1:120,0:0:1,0:23.6:1:31.6:1:1:0:60:39:1:0:0.3 +1 228617425 . CA TT 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGTGAGATACAAACATTCCC;RSEQ=CAAGGAACTGGTCTGTCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:501,48:549,0:0:2,0:24.6:1:31.5:1:1:0:59.9:77.429:1:0:0.6 0/1:246:35:30,5:200,11:211,35:0.1423:2,2:20:1:30.7:1:0.05906:3.01166:60:70:0.1458:0.0163:1.8 +1 228617431 . G T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0931;SOR=6.63993;LSEQ=ATACAAACATTCCCCACAAG;RSEQ=AACTGGTCTGTCGAGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:1:1,0:558,70:628,1:0.0016:2,0:2:0:29:0:1:0:60:2:0.0016:0:2 0/1:287:3:2,1:258,26:284,3:0.0105:2,2:15.7:1:28.3:1:0.25732:4.91234:60:6:0.0107:0:1.7 +1 228617493 . T G 347 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01619;LSEQ=TTTTTCTCTGTCTCCTCGTT;RSEQ=TCTCTCCTTATGGTCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1837:1833:1135,698:0,4:4,1833:0.9978:0,2:25.4:1:32.1:1:0.02121:0:60:75.375:0.9978:0:1.1 1/1:1129:995:601,394:77,57:134,995:0.8813:2,2:24.9:1:31.2:1:0.5125:1.13:60:98.5:0.8826:0:1.2 +1 228617641 . A T 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATCAGCAAACAATATGCT;RSEQ=TCGCTTCTCCAATTTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1333:0:0,0:399,934:1333,0:0:2,0:23.4:1:30.2:1:1:0:60:165.625:1:0:0.1 0/1:742:41:10,31:228,473:701,41:0.0553:2,2:22.3:1:29.3:1:0.30703:1.49354:60:19.5:0.0532:0:1.1 +1 228618328 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTAAAAAAGAATCCTGCCA;RSEQ=GTGTTCAGTGTTTTTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 228623243 . C G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAATACCAGCTCCTAGTGT;RSEQ=ACTGTCATTTTGTACATTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:174:174:0,174:0,0:0,174:1:0,1:24.8:1:32.6:1:1:0:59.8:42.5:1:0:1.1 1/1:71:58:1,57:0,13:13,58:0.8169:1,1:21.4:1:31.1:1:1:0:60:116:0.8169:0:1.1 +1 228645900 . A G 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58678;SOR=2.50021;LSEQ=AGGCTGTCACCAAGGCACAG;RSEQ=AGAAGGACGGCAAGAAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:1:1,0:52,26:78,1:0.0127:2,0:13:0:13:0:1:0:60:0:0:0:2 0/1:64:2:1,1:41,21:62,2:0.0313:2,2:40:1:30.5:1:1:1.93068:57:4:0.0317:0:1 +1 228646169 . C A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16907;SOR=Inf;LSEQ=CTGGCCAAGCACGCCGTGTC;RSEQ=GAGGGCACCAAGGCTGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:63,57:120,0:0:2,0:25.2:1:29.8:1:1:0:44.5:39:0.9915:0:0.2 0/1:85:2:1,1:48,35:83,2:0.0235:2,2:11:0:28:1:1:1.36624:60:4:0.0244:0:1 +1 228646227 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52641;SOR=0;LSEQ=AGTGAGGCGTTCCTCGGCGT;RSEQ=CTGAACCCAAAGGCTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:37,69:106,2:0.0185:2,2:14.5:1:31:1:1:1.85:45.5:4:0.0187:0:1 0/0:66:0:0,0:27,39:66,0:0:2,0:26.3:1:29.8:1:1:0:55.7:32:1:0:0.2 +1 228646356 . CGT C 30 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=14.000;MSILEN=2;SSF=0.47253;SOR=0;LSEQ=GGGTGCGGCCGAATCTGAGC;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:37.5:1:30:1:1:0:60:4:0.25:0:0 0/0:6:0:0,0:0,5:5,0:0:0,0:21:1:32.2:1:1:0:60:10:0.8333:0:0 +1 228652228 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13384;SOR=Inf;LSEQ=GCTTCTTGCCGTCCTTCTTC;RSEQ=GCGCCTTGGTAATGGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:30,61:91,0:0:2,0:33.3:1:30.9:1:1:0:48.4:44.5:1:0:0.1 0/1:53:2:1,1:19,32:51,2:0.0377:2,2:33:1:28.5:1:1:1.67:39:4:0.0377:0:1 +1 229106423 . C CTG 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00297;SOR=0.1238;LSEQ=CAGCTGGTGAAGTAAGTACT;RSEQ=TGGATGGTGGCGACTCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:20:9,11:14,15:29,20:0.4082:2,2:27.1:1:32.6:1:1:1.13768:59.8:40:0.4082:0.0408:0.2 0/1:26:2:1,1:15,8:23,2:0.0769:2,2:26:0:32.5:1:1:1.82581:60:4:0.0769:0:0.5 +1 229223719 . G C 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=GGGGTTTCAAGAAAGGCTCA;RSEQ=AGTCAGCCTCACTTCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,1:3,7:0.7:2,0:39.7:1:33.1:1:0.3:0:60:14:0.7:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:24:0:33:0:1:0:60:2:1:0:0 +1 229223863 . AC A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.55426;SOR=0;LSEQ=CGGAGTCAGTGTGGGCTGTA;RSEQ=CCCCGGGGTCAGGAGTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:219,56:275,3:0.0108:2,2:32:1:31.9:1:0.49901:1.94987:48.7:6:0.0109:0.0036:0.3 0/0:145:0:0,0:111,34:145,0:0:2,0:24.4:1:31.2:1:1:0:47.4:144:1:0:0.1 +1 229223956 . G A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=22;MSI=1.000;MSILEN=1;SSF=0.16152;SOR=0;LSEQ=GTCAGGAGTCAGCGTGGGCT;RSEQ=TACCCCCTGGGGTCAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:4:3,1:152,233:385,4:0.0103:2,2:17.5:1:26:1:0.30583:4.58:37.8:8:0.0104:0:1 0/0:247:0:0,0:101,146:247,0:0:2,0:24.4:1:30.8:1:1:0:41.4:34.286:1:0:0.2 +1 229223985 . G A 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01314;LSEQ=GGGGTCAGGAGTCAGTGTGG;RSEQ=CTGTATCCCGGTGGCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:4:2,2:85,223:308,4:0.0128:2,2:21.8:1:29:1:0.31075:2.61:52.5:8:0.013:0:1 0/1:154:2:1,1:45,107:152,2:0.013:2,2:33:1:23:0:0.50955:2.36:50:4:0.0132:0:1 +1 229226129 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCCAGTGATCCTCCCAC;RSEQ=TCAGCCTCCCAAAGTACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:45:1:33:0:1:0:45.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 230355248 . C G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22022;SOR=0.41982;LSEQ=GGTCCAGTCCCTTGTCCTCC;RSEQ=TTCTGAGTCACTGGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:14,1:17,0:17,15:0.4688:1,1:22.3:1:30.7:1:0.46875:0:60:30:0.4839:0:1 0/1:15:4:4,0:11,0:11,4:0.2667:0,0:42:1:29.3:1:1:0:60:8:0.2667:0:1.3 +1 230355372 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14682;SOR=Inf;LSEQ=TGGATCCCCCTCCTGGGCCC;RSEQ=GCATAGATGGCCTGCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:192,105:297,0:0:2,0:25.5:1:31.1:1:1:0:60:73.25:1:0:0.3 0/1:185:2:1,1:117,66:183,2:0.0108:2,2:47.5:1:30.5:1:1:1.76686:60:4:0.011:0:1 +1 230355438 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.002;SOR=0.55309;LSEQ=ACCTTTCTTGAGACTTCTGA;RSEQ=GTGGATGCATTCCAGATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:111:57,54:159,164:323,111:0.2558:2,2:26.9:1:30.7:1:0.7418:1.09:60:110:0.2552:0:2.1 0/1:307:49:27,22:120,137:257,49:0.1596:2,2:22.2:1:29.7:1:0.34938:1.40:60:98:0.1612:0:1.4 +1 230355441 . G A 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCTTGAGACTTCTGACGT;RSEQ=GATGCATTCCAGATGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:114:56,58:154,162:316,114:0.2651:2,2:26.5:1:29.9:1:1:1.02:60:56:0.2623:0:2.1 0/0:304:0:0,0:143,161:304,0:0:2,0:25.8:1:30.4:1:1:0:60:75:1:0:0.4 +1 230355443 . A G 119 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=22.30154;LSEQ=TCTTGAGACTTCTGACGTGG;RSEQ=TGCATTCCAGATGTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:1,0:208,223:431,1:0.0023:2,0:32:0:15:0:0.4838:0:60:0:0:0:1 0/1:304:15:6,9:134,154:288,15:0.0493:2,2:10.9:1:30.7:1:0.79188:1.30406:60:30:0.0508:0:2.3 +1 230355453 . G C 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-04;SOR=Inf;LSEQ=TCTGACGTGGATGCATTCCA;RSEQ=ATGTGGGGGCATTCTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:193,231:424,0:0:2,0:25.9:1:32.5:1:1:0:60:211:1:0:0.6 0/1:298:8:4,4:128,162:290,8:0.0268:2,2:17.4:1:31.1:1:0.73604:1.26:60:16:0.0271:0:2.3 +1 230355471 . G A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07843;SOR=0;LSEQ=CAGATGTGGGGGCATTCTTT;RSEQ=CAAAGTGCTTGTGGCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:5:3,2:162,221:383,5:0.0129:2,2:24.2:1:27.4:1:0.65449:2.04:60:10:0.0129:0:1.8 0/0:279:0:0,0:120,159:279,0:0:2,0:26.2:1:31:1:1:0:60:68.75:1:0:0.3 +1 230355496 . T A 36 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64578;SOR=0.47085;LSEQ=GTGCTTGTGGCTGTCTTCAT;RSEQ=CATGGTATTCTCCACTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:96,196:292,3:0.0102:2,2:5.3:1:23:1:0.25699:4.06:60:2:0.0069:0:2.3 0/0:208:1:1,0:74,133:207,1:0.0048:2,0:1:0:21:0:0.36058:0:60:2:0.0049:0:1 +1 230355501 . G A 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50159;LSEQ=TGTGGCTGTCTTCATTCATG;RSEQ=TATTCTCCACTGCCCTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:83,192:275,3:0.0108:2,2:24.3:1:29:1:0.22239:4.60:60:6:0.0109:0:1.3 0/0:184:1:0,1:64,119:183,1:0.0054:2,0:26:0:32:0:1:0:60:2:0.0056:0:1 +1 230355561 . C T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13474;SOR=Inf;LSEQ=GTCCCTTAAAACACAATTTG;RSEQ=CTAGATTCTTCCAAAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:3,72:75,0:0:1,0:21.7:1:31.2:1:1:0:60:24:1:0:0.1 0/1:44:2:1,1:2,40:42,2:0.0455:1,2:7:0:31:1:0.13319:16.53:60:4:0.0455:0:1 +1 230459862 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCACACAGGTCACCCCTC;RSEQ=GGGAAGCCCACCCAGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:9.5:1:27:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 230459926 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CACTAGCCTCAGGCCTCACT;RSEQ=ACTGCACTGTCTTCTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27.5:1:30:0:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 230723061 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACTGCTCATCCATGATT;RSEQ=CAAGTGATTGCTGTTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 230724462 . T C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.00298;SOR=0.18688;LSEQ=CAGGTAAGTAGGTAGTTGTG;RSEQ=AGGTAAGTAAGTAGGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:17:11,6:22,10:32,17:0.3469:2,2:26.9:1:31.2:1:1:1.19548:49.2:16:0.3404:0:1.2 0/1:45:4:2,2:27,14:41,4:0.0889:2,2:20.8:1:26.3:1:0.60761:1.89894:41:3:0.0698:0:1.3 +1 230724514 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16671;SOR=Inf;LSEQ=TAGGTGGGCAGGTAAGTAGG;RSEQ=AGATGTGCAGGTAAGTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:68,53:121,0:0:2,0:22.2:1:28.5:1:1:0:55.9:39.333:1:0:0.4 0/1:84:2:1,1:42,40:82,2:0.0238:2,2:24:0:31:1:1:1.04941:47:4:0.0241:0:1 +1 230724540 . G T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0156;SOR=Inf;LSEQ=TGCAGGTAAGTAGGTAGGTG;RSEQ=GCAGGTAAGTAGGTAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:68,67:135,0:0:2,0:25.3:1:31:1:1:0:56.9:44:1:0:0.3 0/1:106:5:0,5:51,50:101,5:0.0472:2,0:14:1:24.8:1:0.05751:0:25.4:4:0.04:0:3.4 +1 230724570 . T C 91 v3;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00049;SOR=Inf;LSEQ=TAGGTAGGTGTGTAGGTAAG;RSEQ=AGGTAGGTGTGTGGATAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:56,63:119,0:0:2,0:27.1:1:27.9:1:1:0:57.8:38.667:1:0:0.2 0/1:94:9:0,9:40,45:85,9:0.0957:2,0:23.7:1:29:1:0.00916:0:28.9:18:0.1:0:2.7 +1 230724588 . G GGTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=37;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=AGTAGGTAGGTGTGTGGATA;RSEQ=GTAGGTGTGCAGGTAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:47:13,34:33,30:63,47:0.4234:2,2:22.7:1:30.2:1:0.01137:2.84876:59.7:94:0.4312:0.3333:0.1 0/0:64:0:0,0:25,30:55,0:0:2,0:21.4:1:30.4:1:1:0:54.1:17.333:1:0:0.7 +1 230724609 . G C 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.0128;SOR=Inf;LSEQ=GTAGGTGTGCAGGTAAGTAG;RSEQ=TAGGTGTGTAGGTAAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:26,44:70,0:0:2,0:14:1:31.6:1:1:0:58.4:34:1:0:0.2 0/1:37:4:2,2:10,23:33,4:0.1081:2,2:14.3:1:28.5:1:0.5821:2.24:56.5:3:0.0857:0:1.3 +1 230724624 . A AGCAGGTAGGTGTGTGGATAAGTAGTAGGTGTGCAG 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTAGGTAGGTGTGTAGGTA;RSEQ=GTAAGTAGGTGGGCAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:14,36:50,0:0:2,0:10.6:1:31.6:1:1:0:58.1:100:1:0:0.1 1/0:20:10:5,5:2,8:10,10:0.5:2,2:20.7:1:28.9:1:0.34985:3.72:41.6:20:0.5:0.5:1.1 +1 231473151 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCCCTCCAGAGGCGGCGGCG;RSEQ=CTCCGGCGGCAGCAGCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:41,30:71,2:0.0274:2,2:30:0:32:0:1:1.36072:60:4:0.0274:0:1.5 0/0:33:0:0,0:13,20:33,0:0:2,0:27.7:1:31.5:1:1:0:60:66:1:0:0.2 +1 232455307 . A T 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTAAAAGAACTCAGATTGC;RSEQ=TATGAAATGCATCTCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:137,40:177,0:0:2,0:23.4:1:30.5:1:1:0:60:176:1:0:0.2 0/1:97:12:9,3:63,22:85,12:0.1237:2,2:25.3:1:30.5:1:1:1.05:60:24:0.1237:0:1 +1 232455324 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14564;SOR=Inf;LSEQ=TGCATATGAAATGCATCTCT;RSEQ=TCTTCTTGCTTTTGATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:180,59:239,0:0:2,0:24.8:1:30.7:1:1:0:60:38.833:1:0:0.2 0/1:148:2:1,1:97,49:146,2:0.0135:2,2:13.5:1:26.5:1:1:1.96983:60:4:0.0136:0:1.5 +1 232455397 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05098;SOR=Inf;LSEQ=GAAGCTTTTCCTATGCTCTG;RSEQ=TGACACGAACAAACCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:487:0:0,0:259,227:486,0:0:2,0:26.1:1:32.5:1:1:0:60:80:0.9979:0:0.5 0/1:288:3:1,2:145,140:285,3:0.0104:2,2:19.3:1:26.7:1:0.6185:2.06637:60:6:0.0105:0:1.7 +1 232455403 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05034;SOR=1.35123;LSEQ=TTTCCTATGCTCTGCTGACA;RSEQ=GAACAAACCATCAATCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:182:95,87:158,150:308,182:0.3714:2,2:26.7:1:30.4:1:0.8522:1.04:60:59.667:0.3691:0:1.1 0/1:295:131:64,67:82,82:164,131:0.4441:2,2:24.4:1:29.2:1:0.90681:1.04674:60:25.2:0.436:0:1.1 +1 232455440 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0429;SOR=Inf;LSEQ=ATTGCCTGGATTTCCTGAAC;RSEQ=TCTCAGTACAGAGGCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:178,249:427,0:0:2,0:25.7:1:32.2:1:1:0:60:46.444:1:0:0.5 0/1:231:3:2,1:97,131:228,3:0.013:2,2:22.3:1:29.7:1:0.57789:2.69:60:6:0.0132:0:1.7 +1 232455454 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11273;SOR=Inf;LSEQ=CTGAACCTCTCAGTACAGAG;RSEQ=CTTCCAGGCCAAGAAGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:143,224:367,0:0:2,0:24.6:1:31.6:1:1:0:60:35.7:1:0:0.4 0/1:186:2:0,2:73,111:184,2:0.0108:2,0:19:1:31:0:0.52055:0:60:4:0.0108:0:1 +1 232455466 . A G 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03537;SOR=Inf;LSEQ=GTACAGAGGCTTCCAGGCCA;RSEQ=GAAGGGTTGAGAAAGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:115,193:308,0:0:2,0:24.2:1:30.9:1:1:0:60:50.333:1:0:0.4 0/1:152:3:2,1:55,94:149,3:0.0197:2,2:31.7:1:26.3:1:0.55646:3.39:60:2:0.0132:0:1.3 +1 232455500 . A G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=0.17099;LSEQ=AGGCCTCCTTCCAGCTGAGG;RSEQ=CAGTGAAGTGTGGTAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:39:8,31:27,104:131,39:0.2294:2,2:23.7:1:31.6:1:1:1.00597:60:38:0.2289:0:1.1 0/1:83:4:0,4:20,59:79,4:0.0482:2,0:27:1:31.5:1:0.5678:0:60:8:0.0482:0:1 +1 232455839 . AAC A 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=CATGCACACACACACACACA;RSEQ=ACACACACATGCACACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:22.5:1:33:0:1:0:60:4:0.5:0:0 0/0:2:0:0,0:1,1:2,0:0:2,0:31:1:26:1:1:0:60:4:1:0:0.5 +1 232522227 . G T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGTCACACCTGTCCCTG;RSEQ=AGCCAAGTGCAGCTTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:27:1:1:0:60:4:1:0:1 +1 233163436 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53131;SOR=0;LSEQ=CAGAGAGTAAATATTTTAAG;RSEQ=ATTGTGGGCCACATGTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:27,2:0.069:2,2:31.5:1:28.5:1:1:1.07415:60:4:0.069:0:1 0/0:16:0:0,0:9,7:16,0:0:2,0:35:1:31.5:1:1:0:60:32:1:0:0.2 +1 234162957 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00063;SOR=0.49324;LSEQ=CTCTGTCTCCCACCACCACA;RSEQ=GCTTGATGGCCTGCATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:107:54,53:121,122:243,107:0.3057:2,2:29.1:1:31.1:1:1:1.03:59.7:214:0.3092:0:1.1 0/1:230:41:18,23:100,89:189,41:0.1783:2,2:23.8:1:29.5:1:0.30712:1.43343:58:40:0.1778:0:1.2 +1 234162987 . T C 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15677;SOR=Inf;LSEQ=CCTGCATCTGGGCTGCTCAC;RSEQ=GGGCCACAGAGGGCAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:116,166:282,0:0:2,0:25.8:1:30.7:1:1:0:59.9:46:0.9964:0:0.4 0/1:186:2:1,1:79,105:184,2:0.0108:2,2:5:0:29.5:1:1:1.33:42:4:0.011:0:2.5 +1 234162998 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16786;SOR=Inf;LSEQ=GCTGCTCACTGGGCCACAGA;RSEQ=GGCAGTGGCAGCTGGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:93,144:237,0:0:2,0:24.2:1:31.8:1:1:0:59.9:474:1:0:0.4 0/1:165:2:1,1:65,98:163,2:0.0121:2,2:36.5:1:28:1:1:1.50:60:4:0.0123:0:1 +1 234163017 . C T 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51528;SOR=0;LSEQ=AGGGCAGTGGCAGCTGGGTG;RSEQ=TGAGATGGGAAGCTGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:45,120:165,2:0.012:2,2:7.5:1:26.5:1:0.47623:2.65:60:4:0.0122:0:1 0/0:115:0:0,0:38,77:115,0:0:2,0:20.5:1:30.6:1:1:0:60:37.333:1:0:0.3 +1 234164879 . G A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCCAGTGAGCTTGGGGCTGG;RSEQ=TGATAACATCGATTAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:29.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:17:0:33:0:1:0:60:2:1:0:0 +1 234271868 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTAGGAAGCCTTCCCT;RSEQ=AAACCCAAGTACAGCTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 234272690 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05411;SOR=Inf;LSEQ=TGTATCTCTAAGGGTTCCTT;RSEQ=TGTGAACCTTCTTCAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:61,0:0:1,0:22.8:1:31.7:1:1:0:60:122:1:0:0.1 0/1:19:2:2,0:17,0:17,2:0.1053:1,0:19:1:32:0:1:0:60:4:0.1053:0:1 +1 234272887 . C G 215 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTAACAGATGCATGCACA;RSEQ=GTACCTGTCACAAAATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:0:0,0:388,402:790,0:0:2,0:25.1:1:30.8:1:1:0:60:51.667:0.9949:0:0.1 0/1:447:125:64,61:159,162:321,125:0.2796:2,2:25.4:1:31:1:0.83306:1.07:60:250:0.2834:0:1.2 +1 234273318 . G T 47 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AACCTTGGCTTTGAATGAAA;RSEQ=GAAAGAGAGAGAGACACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:25.3:1:30:1:1:0:60:6:0.75:0:1.3 0/0:2:0:0,0:1,1:2,0:0:2,0:8:0:33:1:1:0:60:4:1:0:0.5 +1 234800899 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATAGGTACACACAGCCT;RSEQ=TCTCTCTCTCTCTCCCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 234802093 . T A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31722;SOR=1.80358;LSEQ=TCCAGATCATACCAATCACC;RSEQ=CTGAGAAGCCCAATCACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:38:37,1:23,0:23,38:0.623:1,1:22.7:1:30.7:1:1:0:60:76:0.623:0:1 1/0:24:18:18,0:6,0:6,18:0.75:0,1:18.1:1:29.7:1:1:0:60:36:0.75:0:1.2 +1 234802147 . C T 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AACATAAATCAACGTGAGGA;RSEQ=CTGAGAGCTCGCTTGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:108,18:126,0:0:2,0:20.7:1:32.1:1:1:0:60:62:1:0:0.2 0/1:63:10:8,2:47,6:53,10:0.1587:2,2:23.9:1:28.5:1:0.602:1.93392:60:20:0.1613:0:1.4 +1 234802267 . A G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54399;SOR=1.11005;LSEQ=TTCCTTTTTCAAAGACTGGG;RSEQ=ACACTTAAAAATATCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:497:326:150,176:83,88:171,326:0.6559:2,2:27.6:1:31.8:1:0.63641:1.10644:60:325:0.6579:0:1.1 1/0:321:218:108,110:52,48:100,218:0.6791:2,2:28.2:1:29.9:1:0.71799:1.10305:60:23.222:0.6742:0:1.2 +1 234802365 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28983;SOR=3.64602;LSEQ=GACTCTGGCTCCTGGATGGC;RSEQ=TCAAACCTGCCCTTGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:1:0,1:41,144:185,1:0.0054:2,0:39:0:13:0:1:0:60:0:0:0:5 0/1:103:2:1,1:29,72:101,2:0.0194:2,2:26:1:29:1:0.49971:2.46:60:4:0.0196:0:1.5 +1 234802408 . C T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70895;SOR=1.23426;LSEQ=CCGAGGCTGGTCTGGGAGTA;RSEQ=CATTTGCAAATGGCTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:100:61:2,59:3,36:39,61:0.61:2,1:21.8:1:30.7:1:0.37545:2.43541:59.4:122:0.61:0:1.1 1/0:44:29:0,29:1,14:15,29:0.6591:1,1:21.7:1:29.1:1:0.34091:0:60:58:0.6591:0:1 +1 236306018 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05769;SOR=Inf;LSEQ=AACGACTCGCTGCCGCCCAC;RSEQ=CTGACCCCGGCCGTGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:18,12:30,0:0:2,0:22:1:29.9:1:1:0:60:29:1:0:0.4 0/1:10:2:1,1:4,4:8,2:0.2:2,2:36.5:1:31:1:1:1:60:4:0.2:0:1.5 +1 236306034 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGCTGACCCCGGCCGTG;RSEQ=CCCCCTACGTGAAGCTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:17,11:28,2:0.0667:2,2:38:1:29.5:1:1:1.52251:60:4:0.069:0:1 0/0:10:0:0,0:5,5:10,0:0:2,0:23.6:1:31:1:1:0:60:20:1:0:0.7 +1 236306036 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.04991;SOR=Inf;LSEQ=ACGCTGACCCCGGCCGTGCC;RSEQ=CCCTACGTGAAGCTTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:16,10:26,0:0:2,0:28.8:1:29:1:1:0:60:7.667:1:0:0.4 0/1:8:2:1,1:3,3:6,2:0.25:2,2:28:0:31:1:1:1:60:4:0.25:0:1.5 +1 236306564 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAGAAGGCAGGGGAGGG;RSEQ=TGGAGGCCGCCGCTCACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 236306825 . A G 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGTTGGCAGGGTGAGACC;RSEQ=TGTTGGTTTTGATGAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:28:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:9:1:28:1:1:0:60:4:1:0:1 +1 240656797 . G A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAACGAGAAAAGAGAG;RSEQ=GGCTGGCTGTGAAGGGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:33.7:1:32.7:1:1:0:53:6:0.375:0:1.3 0/0:2:0:0,0:0,2:2,0:0:0,0:8.5:1:31.5:1:1:0:60:4:1:0:0 +1 240656824 . C A 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGAAGGGCCGTAGAGTA;RSEQ=GGGATCAATCTTACTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:9.3:1:32.8:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 240683271 . T G 96 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62542;SOR=1.71116;LSEQ=ATGCCTGTAATCCCAGCTAC;RSEQ=CAGGAGGCTGAGGCATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:8,0:13,0:13,8:0.3636:1,0:26.4:1:32:0:1:0:42.3:16:0.381:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:4.5:1:29.5:1:1:0:51.5:4:0.5:0:1.5 +1 240683374 . C G 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00205;SOR=Inf;LSEQ=TGGGCAACAAGAGCAAAACT;RSEQ=CATCCCAAAAAATAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:96,6:102,0:0:2,0:23.5:1:32.6:1:1:0:55.2:204:1:0:0.1 0/1:59:6:6,0:50,3:53,6:0.1017:2,0:11.3:1:31.8:1:1:0:38.2:12:0.1017:0.0339:0.7 +1 240683382 . A AAAAATAAAATAAAAT 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=10.000;MSILEN=5;SSF=0;SOR=Inf;LSEQ=AAGAGCAAAACTCCATCCCA;RSEQ=AAAATAAAATAAAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:81,8:89,0:0:2,0:22.3:1:30.3:1:1:0:57.9:88:0.7788:0:0 0/1:99:42:33,9:34,4:38,42:0.4242:2,2:9.8:1:28.5:1:0.23358:2.29461:50.3:41:0.4184:0.4242:0.6 +1 240683489 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.66694;SOR=0.95033;LSEQ=CAAACTTACTTCTTCAGTAT;RSEQ=CAATTTTTGTGTGTATGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:807:378:185,193:221,206:427,378:0.4684:2,2:26.6:1:28.9:1:0.43784:1.11905:60:188:0.4724:0:1.1 0/1:610:278:137,141:162,170:332,278:0.4557:2,2:27.3:1:27.9:1:0.93526:1.02:60:91.667:0.4591:0:1.1 +1 240683509 . T TA 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAATTTTTGTGTGTATGAG;RSEQ=ATGCCAAGCACATGGTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:0:0,0:347,423:770,0:0:2,0:25.3:1:28.9:1:1:0:60:109:0.9987:0:0.5 0/1:571:38:18,20:239,292:531,38:0.0665:2,2:24.3:1:29:1:0.86638:1.10:60:76:0.0671:0.0158:1.2 +1 240683595 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13024;SOR=Inf;LSEQ=TAGAGTTGGGATGAGCTCTG;RSEQ=TGGTCAACTAGTCCATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:27,174:201,0:0:2,0:23.3:1:32:1:1:0:59.9:49.25:1:0:0.2 0/1:114:2:1,1:17,95:112,2:0.0175:2,2:23:1:25.5:1:0.29204:5.46:60:4:0.018:0:1 +1 240683666 . C T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1256;SOR=0.40298;LSEQ=GCAGGGGGACAAATAACCAC;RSEQ=TCAACCTTTACTGTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:23:0,23:1,32:33,23:0.4107:1,1:21.8:1:30.6:1:1:0:60:22:0.4:0:1.3 0/1:23:5:0,5:0,18:18,5:0.2174:1,0:23:1:30.2:1:1:0:60:10:0.2273:0:1 +1 241661227 . A ATTT 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTCCTTTAAGGTTGATCC;RSEQ=TTTTTGTGTGCTGTCTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1375:0:0,0:602,772:1374,0:0:2,0:26.3:1:30.8:1:1:0:45.6:123.909:0.9993:0:0.1 0/1:857:21:8,13:358,478:836,21:0.0245:2,2:24.5:1:29.5:1:0.82407:1.21678:48.2:42:0.0247:0.0058:0.1 +1 241661327 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10296;SOR=Inf;LSEQ=AGTGATATTTGGTTTCCTAA;RSEQ=GCAAAAGGTGACATAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:31,296:327,0:0:2,0:24.9:1:32:1:1:0:60:80.75:1:0:0.1 0/1:155:2:1,1:16,137:153,2:0.0129:2,2:17:1:29:1:0.20796:8.34:60:4:0.0132:0:1 +1 241663809 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61432;SOR=1.86657;LSEQ=GTTGATCCTTTCTGTATTGG;RSEQ=CTGGATTCCCACCACGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:2:1,1:185,157:342,2:0.0058:2,2:10.5:1:18.5:1:1:1.17778:41:1:0.003:0:3.5 0/1:185:2:1,1:89,94:183,2:0.0108:2,2:14.5:1:26.5:1:1:1.06:23:4:0.0109:0:1 +1 241663821 . C T 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11603;SOR=Inf;LSEQ=TGTATTGGCCTGGATTCCCA;RSEQ=CACGCAGTTTTCTGTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:145,155:300,0:0:2,0:8:1:30.8:1:1:0:36.9:149:0.9967:0:0.1 0/1:156:2:0,2:70,84:154,2:0.0128:2,0:10.5:1:22.5:1:0.50207:0:41:4:0.0132:0:1 +1 241663863 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.05264;SOR=Inf;LSEQ=AACTGAAGCATCCCCCAGCA;RSEQ=CCTGGCTGAGTGTAACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:126,230:356,0:0:2,0:32.7:1:30.7:1:1:0:51.9:8.128:1:0:0.4 0/1:215:3:2,1:73,139:212,3:0.014:2,2:38.7:1:22.7:1:0.2792:3.78:27.3:2:0.0104:0:1.3 +1 241663893 . T TTGAG 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=4.000;MSILEN=4;SSF=0.09201;SOR=0;LSEQ=GTGTAACACATTTTTAATCT;RSEQ=TGAGTGAGTGAGAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:6:0,6:128,287:415,6:0.0141:2,0:33.7:1:29.5:1:0.18414:0:57.5:12:0.0157:0:0 0/0:242:0:0,0:76,166:242,0:0:2,0:26:1:28.1:1:1:0:50.2:10:1:0:0.4 +1 241665510 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05385;SOR=0.23541;LSEQ=AGACAGGCTTGTAGGGAGGC;RSEQ=TTTTATTTTTCTTAAACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:21:21,0:16,0:16,21:0.5676:1,1:20.1:1:30.3:1:1:0:60:42:0.5676:0:1 0/1:13:3:3,0:9,1:10,3:0.2308:2,0:25.7:1:30.7:1:1:0:60:6:0.25:0:1 +1 241666973 . G A 58 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTATCAAATGACTTGCT;RSEQ=AAATCCAGACATACACTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:7,1:8,4:0.3333:2,0:35.5:1:29:1:1:0:60:8:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 241667233 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00056;SOR=0.47399;LSEQ=TGCTGGAACAGTGCGCCTTG;RSEQ=GCATCCAGCTGCGGGATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:139:138,1:138,2:140,139:0.4947:1,1:25.4:1:30.6:1:1:2.00:60:138:0.4946:0:2 0/1:139:44:43,1:93,1:94,44:0.3165:1,1:24.4:1:30.4:1:0.53761:2.14958:60:88:0.3212:0:2 +1 241667244 . G T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.91794;SOR=1.04434;LSEQ=TGCGCCTTGCGCATCCAGCT;RSEQ=CGGGATAACTTTAAACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:343:238:234,4:104,1:105,238:0.6939:1,1:22:1:30.9:1:1:1.77515:60:28.75:0.6907:0:1.7 1/0:165:116:113,3:46,3:49,116:0.703:2,1:24.1:1:30.3:1:0.36321:2.44:60:57:0.7037:0:1.4 +1 241667523 . C T 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAGAGCTTCAAATTTATT;RSEQ=GGAGCAGTGACAAAAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1101:0:0,0:432,668:1100,0:0:2,0:25.5:1:30.5:1:1:0:45.5:90.667:0.9991:0:0.1 0/1:693:18:7,11:294,379:673,18:0.026:2,2:25:1:29.2:1:0.81148:1.21865:48.4:36:0.0262:0:1.1 +1 241669668 . C T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTATAGAACCATAAGGTA;RSEQ=GACAATGCCACTGATAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:1,20:21,5:0.1923:1,0:18.4:1:30.6:1:1:0:60:10:0.1923:0:2.2 0/0:3:0:0,0:0,3:3,0:0:0,0:18.7:1:29.3:1:1:0:60:6:1:0:0.3 +1 241669842 . C T 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTTATTTTTTGGGATG;RSEQ=CTCAGACAACTTTGGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:20.7:1:29.7:1:1:0:48.3:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 241671638 . C T 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60191;SOR=1.93443;LSEQ=GGCACAGAAAGGCTAAATGA;RSEQ=TTTCCTATGGTCCCATAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:12,6:0.3333:0,0:27.5:1:30.7:1:1:0:50.7:12:0.3529:0:1.7 1/0:4:2:2,0:1,1:2,2:0.5:2,0:22:1:28.5:1:1:0:60:4:0.5:0:1 +1 241675074 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACATACACTAAATTCA;RSEQ=GTGTCCTAAAAATAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:49,0:49,2:0.0392:1,2:19.5:1:31.5:1:0.03922:0:60:4:0.0392:0:1.5 0/0:13:0:0,0:13,0:13,0:0:1,0:20.9:1:32.2:1:1:0:60:26:1:0:0.2 +1 241675119 . G C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00107;SOR=0.26485;LSEQ=GGATTGAAACATAAAACCAA;RSEQ=ATTCCTTCAAGAAATAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:49:49,0:31,0:31,49:0.6125:1,1:25.4:1:32.1:1:1:0:60:48:0.6076:0:1.1 0/1:41:12:12,0:29,0:29,12:0.2927:1,0:17.7:1:32.7:1:1:0:60:24:0.2927:0:1.1 +1 241676239 . A G 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTGTGTGTGTGTGTGTGT;RSEQ=TATGAGAAACACACACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:11:1:31.7:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 241676255 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTATATGAGAAACACACA;RSEQ=TTTCTGTTCATTTTTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 241676758 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.083;SOR=0.56112;LSEQ=TAAGCACCATATTAATATCA;RSEQ=CACTAAAAATAATGCTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:138:78:78,0:59,1:60,78:0.5652:1,1:24.2:1:32:1:0.43478:0:60:77:0.5662:0:1.1 0/1:57:24:24,0:33,0:33,24:0.4211:1,1:26.3:1:30:1:1:0:60:23:0.4107:0:1.1 +1 241677035 . T A 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAAATTAATCAGAAAAATA;RSEQ=TTCAAATTTACAATTTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:607:0:0,0:157,450:607,0:0:2,0:23.4:1:30.3:1:1:0:60:45.692:1:0:0.1 0/1:306:22:7,15:88,196:284,22:0.0719:2,2:21.4:1:29.8:1:1:1.04:60:44:0.0719:0:1.1 +1 241680247 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCATAAGCCACCGTGCCC;RSEQ=GCCTTAAATTTTAAAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:3,0:16,0:16,3:0.1579:1,0:13.3:1:31.7:1:1:0:60:6:0.1667:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:23.8:1:24.3:1:1:0:52.5:3:1:0:0.3 +1 241680555 . T C 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGGGCGCCATAATACTTA;RSEQ=CATTTGGCACCTTTAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1176:0:0,0:565,610:1175,0:0:2,0:25.3:1:30.5:1:1:0:60:47.958:1:0:0.1 0/1:827:28:15,13:390,409:799,28:0.0339:2,2:25.3:1:31.2:1:0.70209:1.21:60:56:0.0342:0:1.1 +1 241682757 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19935;SOR=5.16523;LSEQ=AGGCCCGCCACGCCGGCACG;RSEQ=GCGCTAAGCCCAGAGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:1:1,0:53,0:53,1:0.0185:1,0:26:0:32:0:1:0:60:2:0.0185:0:1 0/1:22:2:1,1:19,1:20,2:0.0909:1,2:25:1:27.5:1:0.17749:13.78761:60:4:0.0909:0:1 +1 241682821 . C T 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24939;SOR=4.15414;LSEQ=CTCTCCCGCCAAGTCGCGGG;RSEQ=GCCCAGGCCGGCAGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:1:0,1:329,48:377,1:0.0026:2,0:1:0:27:0:0.12963:0:60:2:0.0027:0:1 0/1:183:2:1,1:155,26:181,2:0.0109:2,2:7.5:1:28:1:0.274:5.86897:60:4:0.011:0:1 +1 241683101 . C A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27965;SOR=0;LSEQ=TTGTCAGAAACCGTTCCGCC;RSEQ=ACCGGCCTCCGCTCTTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:1,2:20,170:190,3:0.0155:2,2:15.7:1:28.7:1:0.29355:4.20:60:6:0.0159:0:1 0/0:127:0:0,0:24,103:127,0:0:2,0:21:1:30.8:1:1:0:60:62.5:1:0:0.1 +1 242373248 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGATTACAGGCACCCAA;RSEQ=ACTACATCCAGCTAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:1:29:1:1:0:55:4:1:0:1 +1 242375779 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAGACCTGGAGCCAACA;RSEQ=ATGCTCCCAGGAACTCGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:29:1:1:0:60:4:1:0:1 +1 242376422 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGGGCTCCCTTCCCCCGTGG;RSEQ=GATTCCTCACAATTGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:47:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 242505879 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTGAACTTTCCTTACCT;RSEQ=TCAGTGATGTCCCAGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:76:6,70:0,0:0,76:1:0,2:26.1:1:29.4:1:1:0:24.6:18:1:0:1.3 1/1:45:45:2,43:0,0:0,45:1:0,1:23.8:1:28.2:1:1:0:24.9:44:1:0:1.2 +1 242505965 . G A 136 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05766;SOR=0;LSEQ=CCTCAGGTAACCAAAGTGAC;RSEQ=TGGAGATTTAAAGTTATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:0,19:1:0,1:7.3:1:32.2:1:1:0:21.6:38:1:0:1.9 1/0:13:10:0,10:0,3:3,10:0.7692:0,0:10.4:1:31.1:1:1:0:21:20:0.7692:0:2 +1 242506053 . CA C 73 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=AGAAATCCAATACAAAGAGA;RSEQ=AAAAAAAAAAGGTCATTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:36.4:1:31.6:1:1:0:29.2:10:1:0:0.2 1/0:2:1:0,1:0,1:1,1:0.5:0,0:49:0:30:0:1:0:23:2:1:0:0 +1 242508851 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19388;SOR=Inf;LSEQ=TGTTAGCCAGGCACAAAAGG;RSEQ=TCACTCCCCAGGAAATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:50,18:68,0:0:2,0:22.9:1:32.2:1:1:0:32.4:33:1:0:0.4 0/1:54:2:1,1:33,19:52,2:0.037:2,2:15:0:31:1:1:1.71824:30:4:0.0392:0:1.5 +1 242508913 . G A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11488;SOR=Inf;LSEQ=ATCCACCTGGAGTACCCTCT;RSEQ=TTGGCAGAATATGACTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:24,0:0:2,0:9:1:31.5:1:1:0:40.7:48:1:0:0.3 0/1:28:4:3,1:12,12:24,4:0.1429:2,2:12.8:1:26:1:0.6:2.89:39:8:0.1429:0:1.3 +1 243213669 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTGGCCCATGAGTGGCG;RSEQ=TCATGATCTTCAGCAAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:37,38:75,2:0.026:2,0:9.5:1:28.5:1:0.49419:0:21.5:4:0.0263:0:1 0/0:28:0:0,0:10,18:28,0:0:2,0:15.3:1:30.7:1:1:0:23:56:1:0:0.3 +1 243213717 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGCAGGGCGCACCAGG;RSEQ=TCACCCTAACCAGGATAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:55,53:108,2:0.0182:2,2:39:1:31:1:1:1.0374:22:4:0.0183:0:1 0/0:35:0:0,0:14,21:35,0:0:2,0:30.9:1:31.1:1:1:0:24.6:70:1:0:0.7 +1 243213751 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08067;SOR=Inf;LSEQ=GATAACCAGACCATCAGCCA;RSEQ=ATGCTGAGCGAGCGGTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:47,45:92,0:0:2,0:28.8:1:32.6:1:1:0:26.8:45:1:0:0.2 0/1:37:2:1,1:15,20:35,2:0.0541:2,2:29.5:1:28.5:1:1:1.32:22:4:0.0556:0:1 +1 243213760 . C G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ACCATCAGCCAGATGCTGAG;RSEQ=GAGCGGTGGTACACCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:41,37:78,2:0.025:2,2:40.5:1:33:1:1:1.10668:26:4:0.0253:0:1 0/0:33:0:0,0:14,18:32,0:0:2,0:27.6:1:31.4:1:1:0:23.9:64:0.9697:0:0.9 +1 243213761 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=48.17195;LSEQ=CCATCAGCCAGATGCTGAGC;RSEQ=AGCGGTGGTACACCCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:3,1:38,34:72,4:0.0526:2,2:21.3:1:27:1:0.61971:2.65:23.3:3:0.04:0:1.3 1/0:31:23:10,13:3,5:8,23:0.7419:2,2:29.8:1:30.1:1:1:1.27:24.4:46:0.7419:0:1.2 +1 243430907 . GA G 48 v3;MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.27218;SOR=5.05351;LSEQ=AGAGCCAAACTCCCTCTCAA;RSEQ=AAAAAAAAAAAAAAGTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:10,0:10,1:0.0833:0,0:13:0:35:0:1:0:60:2:0.0833:0:0 0/1:9:3:2,1:5,1:6,3:0.3333:2,2:17.3:1:30.3:1:1:2.23609:60:6:0.3333:0:0.7 +1 243431125 . G T 49 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30171;SOR=0;LSEQ=ACACAATCAGTTATACAAGG;RSEQ=ATACACTTGACATGCAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:4:1,3:92,120:212,4:0.0185:2,2:24.8:1:24.8:1:0.63608:2.29197:30:3:0.0143:0:1.5 0/0:132:0:0,0:61,71:132,0:0:2,0:30.2:1:30.1:1:1:0:35.1:131:1:0:0.1 +1 243431146 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15924;SOR=Inf;LSEQ=ATACACTTGACATGCAGACA;RSEQ=CCCATCATTGACTGCACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:74,115:189,0:0:2,0:27.7:1:32.4:1:1:0:36.5:36.8:1:0:0.1 0/1:126:2:1,1:57,67:124,2:0.0159:2,2:30.5:1:30.5:1:1:1.17:29.5:4:0.0159:0:2 +1 243431159 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.16098;SOR=Inf;LSEQ=GCAGACAGCCCATCATTGAC;RSEQ=GCACTAAGTCCAGTTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:52,95:147,0:0:2,0:28.4:1:31.2:1:1:0:38.9:48:1:0:0.1 0/1:99:2:1,1:40,57:97,2:0.0202:2,2:17.5:1:31.5:1:1:1.42:29.5:4:0.0206:0:2 +1 243431167 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51562;SOR=0;LSEQ=CCCATCATTGACTGCACTAA;RSEQ=TCCAGTTTGGCTTTTATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:38,89:127,2:0.0155:2,2:33:1:31.5:1:0.5149:2.32:29.5:4:0.0161:0:1 0/0:88:0:0,0:36,52:88,0:0:2,0:25.6:1:31.3:1:1:0:38.9:87:1:0:0.1 +1 243431184 . T A 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52524;SOR=0;LSEQ=TAAGTCCAGTTTGGCTTTTA;RSEQ=GGAAAAGTTGATAAAGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:23,74:97,2:0.0202:2,2:5.5:1:26:0:0.42795:3.17:41.5:4:0.0204:0:1 0/0:61:0:0,0:20,41:61,0:0:2,0:19.2:1:29.3:1:1:0:43.5:29.5:1:0:0.1 +1 243662668 . T G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGCCTACACCCTGTTTT;RSEQ=GTTCTAGAATTACCTGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:20.5:1:31.5:1:1:0:40.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 243662773 . T C 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51933;SOR=0;LSEQ=AAGAGATGGCTCTCTGGCCA;RSEQ=GTCCTAACACCAGACTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:9,4:0.3077:0,0:28:1:32.5:1:1:0:60:8:0.3077:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:18.5:1:31.3:1:1:0:60:8:1:0:0 +1 243662917 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51863;SOR=0;LSEQ=ATGAGGCACAAACTTTTCAT;RSEQ=TAATTTCCACATTTTTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:164,10:174,2:0.0114:2,2:23.5:1:29:1:0.12143:15.67998:60:4:0.0114:0:1 0/0:117:0:0,0:104,13:117,0:0:2,0:23.6:1:27.9:1:1:0:60:57.5:1:0:0.1 +1 243662942 . G GT 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTCCACATTTTTAGCAACAG;RSEQ=TTTTTTTCTCCAACAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:229,69:298,0:0:2,0:22.5:1:31.5:1:1:0:60:98.333:1:0:0.1 0/1:223:14:9,5:149,60:209,14:0.0628:2,2:23.6:1:27.9:1:0.55577:1.37754:59.6:13:0.0594:0.0135:0.1 +1 243663126 . G A 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0285;SOR=Inf;LSEQ=AAATAAATGATTTACAAAGA;RSEQ=ATATTTACATTCATCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:0:0,0:178,326:504,0:0:2,0:26.3:1:32.6:1:1:0:59.9:99.8:1:0:0.1 0/1:353:4:2,2:139,210:349,4:0.0113:2,2:15:1:22.8:1:1:1.51:60:3:0.0086:0:1.5 +1 243668671 . A G 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CATCTATTTTAATTTTACAC;RSEQ=TTCATTTTTTGCAACATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:101,323:424,0:0:2,0:23.5:1:30.9:1:1:0:60:41.4:1:0:0.1 0/1:292:13:4,9:72,207:279,13:0.0445:2,2:27.6:1:31.8:1:0.74771:1.28:60:26:0.0451:0:1.1 +1 243668676 . T A 45 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.14835;SOR=0;LSEQ=ATTTTAATTTTACACATTCA;RSEQ=TTTTTGCAACATTATCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:4:3,1:87,292:379,4:0.0104:2,2:12:1:22.5:1:0.0419:9.99:60:3:0.008:0:2.3 0/0:266:0:0,0:64,202:266,0:0:2,0:24.6:1:29.3:1:1:0:60:132:1:0:0.1 +1 243669012 . TCTGT CCTG 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATCCACAGCATCCAAAG;RSEQ=ATAGAATTCATCATCGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:30.4:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 243675543 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15599;SOR=Inf;LSEQ=TGATCTTGAAAATATCAGAT;RSEQ=AGTTTTTAAAAGACTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:171,9:180,0:0:2,0:26:1:32.5:1:1:0:59.8:59:1:0:0.1 0/1:118:2:1,1:108,8:116,2:0.0169:2,2:24:1:30:1:0.14733:12.78678:60:4:0.0171:0:1 +1 243708979 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAAAAAATATTTTGTGAAA;RSEQ=TGTAATTTTCTGTGTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:0,2:5,159:164,2:0.012:1,0:18.5:1:29:1:1:0:60:4:0.0123:0:1 0/0:82:0:0,0:1,81:82,0:0:1,0:23.7:1:31.9:1:1:0:59.6:81:1:0:0.1 +1 243709071 . G A 157 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21622;SOR=0;LSEQ=CTATTTTTCCTAATATGCTT;RSEQ=TAAGAACTAGCTTCAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:0,29:0,0:0,29:1:0,1:24.9:1:32.5:1:1:0:59:58:1:0:1 1/1:8:7:0,7:0,1:1,7:0.875:0,0:4.3:1:30.1:1:1:0:55.7:14:0.875:0:1 +1 243715975 . A C 122 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=27.74403;LSEQ=ATATTTGAATTAATTTCCAT;RSEQ=TCTCAATTTTTAACCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:1:1,0:362,80:442,1:0.0023:2,0:13:0:15:0:1:0:60:0:0:0:5 0/1:270:16:12,4:202,52:254,16:0.0593:2,2:23.3:1:30.7:1:0.74994:1.29355:60:32:0.0593:0:1.2 +1 243716481 . CA C 53 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAGGGGCAGGTCGTA;RSEQ=AAAAAAAAAAAATCCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,4:4,3:0.375:0,0:32:1:33.7:1:1:0:60:6:0.375:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 243716654 . A C 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGATTATAGAGCACATAA;RSEQ=GTGCACTGTACATTCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:29.7:1:32:0:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 243726955 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13216;SOR=Inf;LSEQ=ACTACAGTTAACTTTTAATG;RSEQ=TTAAATGGTTTACTTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:247,47:294,0:0:2,0:23.8:1:32.6:1:1:0:60:293:0.9966:0:0 0/1:169:2:1,1:130,37:167,2:0.0118:2,2:15:1:27.5:1:0.40018:3.48013:60:4:0.012:0:1 +1 243776811 . C A 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.58366;SOR=0;LSEQ=TAAAAACAATCATTACATCT;RSEQ=ATCAGAAATAATTTCGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:4:4,0:137,4:141,4:0.0276:1,0:34.8:1:28.3:1:1:0:60:8:0.028:0:1 0/0:37:0:0,0:37,0:37,0:0:1,0:23.1:1:30.2:1:1:0:60:17.5:1:0:0 +1 243777066 . G A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33695;LSEQ=AAATAAAAAAAAGAAAAAAT;RSEQ=TTACATTATAATCCTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:262:40,222:51,308:359,262:0.4212:2,2:21.3:1:30.9:1:0.73129:1.09:60:130:0.4235:0:1 0/1:371:73:21,52:66,232:298,73:0.1968:2,2:17.6:1:28.5:1:0.28014:1.42:60:72:0.1973:0:1.1 +1 243777087 . CTTATAA C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.00385;SOR=Inf;LSEQ=TTACATTATAATCCTGTATT;RSEQ=TTATAATAGTACTAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:0:0,0:11,350:361,0:0:1,0:25.8:1:30.9:1:1:0:60:89.25:1:0:0.5 0/1:179:5:0,5:15,159:174,5:0.0279:2,0:27.6:1:32.4:1:1:0:60:10:0.0281:0:0.8 +1 243777495 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCACAACAGAACCCAACC;RSEQ=AACAGAGTTGGTTTATATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 243801190 . T C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78696;SOR=1.2142;LSEQ=GAAAAAGAATCAGACTGGCA;RSEQ=TGGCTGTCTCATTAGCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:23:1,22:0,34:34,23:0.3966:1,1:23.9:1:34.1:1:0.40351:0:58.5:46:0.4107:0:1 0/1:18:8:0,8:0,10:10,8:0.4444:0,0:21.9:1:33.1:1:1:0:60:16:0.4444:0:1.1 +1 243801283 . G C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACCTAGAATTCCTCAGC;RSEQ=AAATTATCAGTTGTGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:1,13:0,0:0,14:1:0,1:24.1:1:30.1:1:1:0:60:6:1:0:1.3 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:33:0:1:0:60:4:1:0:1 +1 243809387 . T A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11341;SOR=Inf;LSEQ=AATAGAAGATGGTAAATGAT;RSEQ=TAAATATTTTCCTTTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:46,341:387,0:0:2,0:24.5:1:30.8:1:1:0:59.7:386:1:0:0 0/1:197:2:1,1:23,172:195,2:0.0102:2,2:37:0:28:1:0.22936:7.34:60:4:0.0103:0:1 +1 243809488 . C T 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06046;SOR=0;LSEQ=CATACACTCTCACCATCACC;RSEQ=CAAAGTGAAAATAATCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:12:1,11:0,53:53,12:0.1846:1,2:25.9:1:30.8:1:0.18462:0:60:24:0.1905:0:1.3 0/0:18:0:0,0:0,18:18,0:0:1,0:24.8:1:30.1:1:1:0:60:17:1:0:0.1 +1 243827672 . G T 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCACGCCTGGCTGATTTTTT;RSEQ=TGTGTGTGTTTTTTTAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:25.3:1:30:1:1:0:50.7:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 243828306 . T A 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAACTCACAGCTTTCTATGG;RSEQ=TCTCCACTCAAGATTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:87:87:2,85:0,0:0,87:1:0,1:22.4:1:31.7:1:1:0:60:86:1:0:1 1/0:28:19:0,19:0,9:9,19:0.6786:0,1:24.2:1:29.9:1:1:0:60:38:0.6786:0:1.1 +1 245977251 . T A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTAAAATATTCATTGTAG;RSEQ=TGCTTTTAGGTGATTGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:29:1:1:0:60:4:1:0:1.5 +1 245977880 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15821;SOR=Inf;LSEQ=TGAAATGGATGCTGCTGCAA;RSEQ=ATTTTATTTAAACAACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:65,16:81,0:0:2,0:22.9:1:33:1:1:0:60:80:1:0:0.4 0/1:54:2:1,1:43,9:52,2:0.037:2,2:29.5:1:30:1:0.33892:4.58502:60:4:0.037:0:1 +1 245977881 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01166;SOR=0.29242;LSEQ=GAAATGGATGCTGCTGCAAG;RSEQ=TTTTATTTAAACAACATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:25:18,7:48,10:58,25:0.3012:2,2:21.5:1:31.1:1:0.37372:1.85169:60:50:0.3086:0:1.1 0/1:54:6:5,1:39,9:48,6:0.1111:2,2:28.3:1:30.2:1:1:1.15:60:12:0.1132:0:1 +1 245977996 . C T 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50046;SOR=1.13301;LSEQ=GCCGGCTCTGCTAAGAGCTC;RSEQ=GATGAGGAATAAACTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:396:257:147,110:81,58:139,257:0.649:2,2:24:1:31.1:1:0.9152:1.04494:60:127.5:0.6489:0:1.1 1/0:260:176:89,87:45,39:84,176:0.6769:2,2:24.2:1:29.3:1:0.69164:1.12739:59.9:43:0.6719:0:1.2 +1 245978063 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12089;SOR=Inf;LSEQ=TTCCCAGCAGACCTGTTTCC;RSEQ=TTGGCTTCCAGATCCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:122,211:333,0:0:2,0:25.5:1:32.1:1:1:0:59.9:46.571:1:0:0.5 0/1:178:2:1,1:73,103:176,2:0.0112:2,2:5:0:31:1:1:1.41:60:4:0.0114:0:1.5 +1 245978110 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5581;SOR=0;LSEQ=CTTATCCCTTATCCCACCAT;RSEQ=CACACACACACACGCACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:0,3:24,125:149,3:0.0195:2,0:26:1:30:1:1:0:60:6:0.0199:0:1 0/0:63:0:0,0:14,49:63,0:0:2,0:23:0:14:0:1:0:60:0:0:0:3 +1 245978150 . G A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.51254;SOR=0.72832;LSEQ=ACACACGCACACACATGCAC;RSEQ=CACACACACGCAAGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:43:0,43:0,23:23,43:0.6515:1,1:20.4:1:29.7:1:1:0:59.3:20.5:0.6406:0:1.1 1/0:33:19:1,18:1,12:13,19:0.5758:1,1:21.6:1:28:1:1:1.48061:58.2:8.5:0.5667:0:1.5 +1 245978192 . G GCA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.52767;SOR=0;LSEQ=ACACGCACGCACACACGCAT;RSEQ=CACACACACACACTCTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:0,2:0,23:23,2:0.08:1,0:26:1:30.3:1:1:0:57.5:4:0.0909:0:0.5 0/0:14:0:0,0:1,13:14,0:0:1,0:28.8:1:31.1:1:1:0:57.5:13:1:0:1.1 +1 246979806 . G A 31 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAGAGGCGGGATTTTGTC;RSEQ=TCTTGCTCAGGCGGGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:31.5:1:1:0:60:4:1:0:1.5 +1 246981262 . C G 64 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60839;SOR=2.34872;LSEQ=TAGGGAGTATATGGGGGGAA;RSEQ=GTATTGTGGTTGGGGAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,1:3,2:0.2857:2,2:12:0:34.5:1:1:1.7321:34.5:4:0.2857:0:3.5 1/0:8:4:3,1:2,0:2,4:0.5:0,2:11:1:32:1:1:0:35.5:8:0.5:0:4 +1 246981266 . T C 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GAGTATATGGGGGGAACGTA;RSEQ=TGTGGTTGGGGAGTATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:1,0:1,6:0.8571:0,2:14.3:1:34.3:1:1:0:28.5:12:0.8571:0:2.7 1/1:8:8:7,1:0,0:0,8:1:0,2:14.1:1:30.8:1:1:0:36.1:7:1:0:3 +1 246981282 . TG T 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.30245;SOR=0.23847;LSEQ=CGTATTGTGGTTGGGGAGTA;RSEQ=GGGGGGAACGTACTGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:2,1:3,4:0.5714:2,2:24.3:1:33.5:1:1:1.81007:31.3:8:0.5714:0:3.3 0/1:9:2:1,1:6,1:7,2:0.2222:2,2:19:1:30.5:1:0.41667:4.58262:32.5:4:0.25:0:2 +1 246981292 . C G 22 v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=0.45719;LSEQ=TTGGGGAGTATGGGGGGGAA;RSEQ=GTACTGTGGTTGGGGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,0:1,2:0.4:0,2:16.5:1:33:0:1:0:34.5:4:0.6667:0:3.5 0/1:9:2:2,0:5,2:7,2:0.2222:2,0:17:1:22:1:1:0:30.5:1:0.125:0:4 +1 247249055 . TCCACACAGGAGGG T 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=0.14787;SOR=6.52396;LSEQ=AAATTTAACCTCTGGCCCCC;RSEQ=CCACACAGGGGCCACACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:13,2:15,2:0.1176:2,0:27.5:1:34:0:1:0:29:4:0.1176:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:23:1:29.1:1:1:0:31.5:4:0.5:0.25:0.5 +1 247249155 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACACATAACCTGGGTGAG;RSEQ=CGCTGCCAGCGGCTGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:36,27:63,2:0.0308:2,2:25:1:29.5:1:1:1.32735:41.5:4:0.0313:0:1.5 0/0:31:0:0,0:17,14:31,0:0:2,0:25.6:1:30.6:1:1:0:46.2:62:1:0:0.2 +1 247249186 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10109;SOR=Inf;LSEQ=GGCTGTTGGCCTCAGCGTTC;RSEQ=CTTGCAAGGCATTCAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:42,32:74,0:0:2,0:24.8:1:31.1:1:1:0:58.4:73:1:0:0.2 0/1:35:2:1,1:20,13:33,2:0.0571:2,2:8:1:28.5:1:1:1.51907:40.5:4:0.0571:0:1 +1 247249268 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=AGCCCTGCCCCAACCTTGAC;RSEQ=CAGACAGTGGGTGGCATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:21,34:55,0:0:2,0:24.9:1:30.5:1:1:0:59.2:26.5:1:0:0.1 0/1:22:2:1,1:5,15:20,2:0.0909:2,2:27.5:1:30.5:1:0.48052:2.83:60:4:0.0909:0:1 +1 247250360 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGAAGGAGATGCAGGGT;RSEQ=AAGCAGCAGTGTGGATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:48.5:1:29:0:1:0:60:4:1:0:1.5 +1 247294628 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52159;SOR=0;LSEQ=CCCACGGATTGGAAGATCCC;RSEQ=CTCGCAAACCCACGCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:27.5:1:30:1:1:1.0801:60:4:0.0741:0:1 0/0:16:0:0,0:7,9:16,0:0:2,0:29.9:1:28.9:1:1:0:60:32:1:0:0.3 +1 247294658 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12945;SOR=Inf;LSEQ=CCACGCCACCGAGGCCTGCC;RSEQ=TCCCAACCCTGGAACGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:24,0:0:2,0:29.3:1:31.1:1:1:0:60:48:1:0:0.3 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:21.5:1:28.5:1:1:1.37:60:4:0.1429:0:1 +1 247298458 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14634;SOR=Inf;LSEQ=CAGAAAGCTAGAAGCAAGAG;RSEQ=AAACTATTCCAAAAGCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:20,5:25,0:0:2,0:18.2:1:32.6:1:1:0:60:50:1:0:0 0/1:16:2:1,1:11,3:14,2:0.125:2,2:22:1:28:1:0.45:3.31654:60:4:0.1333:0:1 +1 247298525 . C CA 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTGAAGAAGACAGAGACA;RSEQ=AAAAAACCCTCCAAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:50,43:93,0:0:2,0:30.1:1:32.3:1:1:0:59.4:92:1:0:0.2 0/1:78:20:10,10:27,31:58,20:0.2564:2,2:28:1:30.6:1:0.80151:1.15:57.8:40:0.2632:0.0128:0.3 +1 247485932 . A G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTCTGACTCCTCAGAGC;RSEQ=CCCGAGTAAGCAAGTCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:0,15:1:0,2:21.9:1:30.1:1:1:0:60:6.5:1:0:1.1 1/1:9:9:4,5:0,0:0,9:1:0,2:31.4:1:30.7:1:1:0:60:18:1:0:1.1 +1 247554732 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAACCATAATCAATCAC;RSEQ=ACTGCATTCCAGCCTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 247554949 . T G 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26316;SOR=Inf;LSEQ=GACAGAGATTACTAAGAGGA;RSEQ=ATAGTAAAGGTGAAAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:9,0:3,0:3,9:0.75:0,0:28.2:1:34.1:1:1:0:60:18:0.75:0:1.1 1/1:7:7:7,0:0,0:0,7:1:0,0:35.9:1:32.6:1:1:0:60:14:1:0:1.1 +1 247555049 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52968;SOR=0;LSEQ=GAACCTTCTCCTAGACCCAT;RSEQ=TGTGCATTTCCTTATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:30,28:58,2:0.0333:2,2:18:1:29:1:1:1.07017:60:4:0.0333:0:1 0/0:35:0:0,0:16,19:35,0:0:2,0:29.6:1:30.7:1:1:0:60:70:1:0:0.1 +1 247555079 . A G 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00059;SOR=0;LSEQ=CCTTATAAAATCCAGCTTTA;RSEQ=CAAGAATCCTGCTAAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:15:6,9:9,24:33,15:0.3125:2,2:23.9:1:32.9:1:0.50411:1.76:55.1:30:0.3125:0:1.1 0/0:28:0:0,0:9,19:28,0:0:2,0:21.4:1:28.9:1:1:0:60:56:1:0:0.1 +1 248567495 . ACGTGTG A 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.05455;SOR=Inf;LSEQ=GTCCCTGTGCTATTACATAT;RSEQ=TGTGTGTGTGTATAAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:5,2:7,1:0.1111:2,0:12:0:33:0:1:0:26:2:0.1111:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:30:1:1:0:25:4:1:0:2.5 +1 248567496 . CGTGTGT C 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCCTGTGCTATTACATATA;RSEQ=GTGTGTGTGTATAAAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:1,2:3,3:0.2308:2,0:15.3:1:34:0:0.4:0:37.3:6:0.3:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +1 248567502 . T TGTGTGTGGCAGAGGCCGCTATTACATGTAC 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=8.000;MSILEN=2;SSF=0.54067;SOR=0;LSEQ=TGCTATTACATATACGTGTG;RSEQ=GTGTGTGTGTATAAAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:2,4:4,3:7,6:0.3333:2,2:24.8:1:27.2:1:0.59207:2.46629:40.3:5:0.4167:0.3333:1.3 0/0:4:0:0,0:2,2:4,0:0:2,0:8.3:1:30.3:1:1:0:34.5:8:1:0:1.8 +1 248567529 . G C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.96475;LSEQ=GTGTATAAAATGGGAGTAAG;RSEQ=GTGAACAGACAGCAGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:9,11:2,2:4,20:0.8333:2,2:17.8:1:31.1:1:1:1.21199:35.1:40:0.8333:0:1.6 1/1:11:10:4,6:1,0:1,10:0.9091:0,2:18:0:31.6:1:0.45455:0:38.8:20:0.9091:0:1.4 +1 248567539 . C G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71029;LSEQ=TGGGAGTAAGGGTGAACAGA;RSEQ=AGCAGAGACCACTGTTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:4,4:7,8:15,8:0.3478:2,2:8:0:30.5:1:1:1.14:30.6:7:0.3333:0:2 0/1:11:3:1,2:4,4:8,3:0.2727:2,2:8:0:32.7:1:1:1.87936:28.7:6:0.2727:0:2.3 +10 1509949 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1901;SOR=Inf;LSEQ=AAATAAAAATAAATGTTGAT;RSEQ=CTGGTGGATTGTAAAATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:103,27:130,0:0:2,0:20.2:1:32.7:1:1:0:60:129:1:0:1 0/1:101:2:1,1:79,20:99,2:0.0198:2,2:25.5:1:27.5:1:0.37426:3.87913:60:4:0.0198:0:2 +10 1509976 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=GATTGTAAAATCCCCTACCA;RSEQ=TTCCGTTATTCCATCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:142,57:199,2:0.01:2,2:24.5:1:32.5:1:0.49488:2.47835:60:4:0.0101:0:3 0/0:199:0:0,0:148,50:198,0:0:2,0:25:1:31.3:1:1:0:60:65:1:0:1.3 +10 1509981 . G C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATCCCCTACCACTTCC;RSEQ=TTATTCCATCCTGTGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:219:157,62:0,0:0,219:1:0,2:28.5:1:32:1:1:0:60:108.5:1:0:1.3 1/1:211:211:157,54:0,0:0,211:1:0,2:26.4:1:30.5:1:1:0:60:51.75:1:0:1.4 +10 1510047 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00845;SOR=0.65789;LSEQ=GGGAGACTGGCTCTGACATA;RSEQ=CGCTGTGTCCCTCTTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:145:71,74:78,84:162,145:0.4693:2,2:26.1:1:30.1:1:0.9093:1.03:60:290:0.4754:0:1.3 0/1:389:143:73,70:131,114:245,143:0.3676:2,2:26.2:1:28.9:1:0.67411:1.10162:60:70.5:0.3672:0:1.4 +10 1510148 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23018;SOR=Inf;LSEQ=ATTCTAAATGCTCCCCCACC;RSEQ=CAGGGATTGAAACGTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:32,103:135,0:0:2,0:20.9:1:31.3:1:1:0:60:26:1:0:0.1 0/1:125:2:1,1:26,97:123,2:0.016:2,2:6:1:28.5:1:0.38671:3.68:60:4:0.0165:0:1 +10 1510172 . T G 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=GGATTGAAACGTTCTTCCTA;RSEQ=AATTATAGTGGAATCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:5,62:67,0:0:2,0:23.3:1:28.8:1:1:0:60:134:1:0:0.1 0/1:56:11:2,9:6,38:44,11:0.1964:2,2:14.1:1:29.4:1:0.6538:1.40:60:10:0.1852:0:1 +10 1510208 . C T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.378;SOR=0.50355;LSEQ=AAAAGTCTAGCCGGCTAATG;RSEQ=GTGGAGCTTCTGTGCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:0,11:0,23:23,11:0.3235:1,0:16.4:1:29.9:1:1:0:60:22:0.3235:0:1 0/1:26:5:0,5:1,20:21,5:0.1923:1,0:31:1:29.8:1:1:0:60:10:0.1923:0:1 +10 2158398 . T C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02485;SOR=3.53747;LSEQ=AAAAAGAGGAGAGGGGACTT;RSEQ=GCGTGGTTCCTGCCTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:16:16,0:21,1:22,16:0.4211:1,1:23.7:1:31.8:1:1:0:60:32:0.4211:0:1.1 1/0:29:21:20,1:8,0:8,21:0.7241:0,1:21.6:1:31:1:1:0:60:42:0.7241:0:1 +10 2158524 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTAAGAGTATTTATGCTAA;RSEQ=GATGCAAATAAAAGGTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:286:286:172,114:0,0:0,286:1:0,2:26.6:1:30.9:1:1:0:59.9:70.5:1:0:1.4 1/1:321:296:171,125:15,10:25,296:0.9221:2,2:26.7:1:29.5:1:1:1.09621:60:58.2:0.9209:0:1.5 +10 2158567 . C A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=14.39329;LSEQ=AAGGTGTTCTGAACTTTTAA;RSEQ=CATGTCTTGCAGACATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:19:10,9:169,183:352,19:0.0512:2,2:27.4:1:29.3:1:0.81487:1.20:60:38:0.0521:0:1.5 0/1:388:170:86,84:105,112:217,170:0.4381:2,2:24.5:1:29.1:1:0.68307:1.09:60:169:0.4424:0:1.6 +10 2158572 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14359;LSEQ=GTTCTGAACTTTTAACCATG;RSEQ=CTTGCAGACATAAATTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:173:80,93:91,102:193,173:0.4727:2,2:23.7:1:31.2:1:0.91651:1.03705:60:27.833:0.4652:0:1.5 0/1:378:43:23,20:161,174:335,43:0.1138:2,2:24.5:1:30:1:0.52113:1.24:60:20.5:0.1114:0:1.6 +10 2158638 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23612;SOR=0;LSEQ=AAATGGGAAAAATGACATTT;RSEQ=ATTTGGAATTTAAACACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:53,144:197,2:0.0101:2,2:25:1:28.5:1:0.47008:2.70:60:4:0.0103:0:1.5 0/0:210:0:0,0:66,144:210,0:0:2,0:23.9:1:31:1:1:0:60:69:1:0:0.4 +10 3096943 . C T 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATTTTCAGGATACAAAGAGT;RSEQ=CCCCCACCACTGCAGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:28.5:1:33:0:1:0:60:4:0.6667:0:1 0/0:3:0:0,0:2,1:3,0:0:2,0:25.7:1:31:1:1:0:60:6:1:0:0.3 +10 3096948 . C A 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=0;LSEQ=CAGGATACAAAGAGTCCCCC;RSEQ=ACCACTGCAGAGTCTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:17.5:1:32:0:1:0:60:4:0.5:0:1.5 0/0:3:0:0,0:2,1:3,0:0:2,0:27.3:1:31:1:1:0:60:6:1:0:0.3 +10 3097046 . TA T 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51111;SOR=0;LSEQ=ATTTACAATTCAATTATGTA;RSEQ=ATGCTAAGACCTTGTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:31,0:31,2:0.0606:1,2:14:1:24.5:1:0.06061:0:60:4:0.0606:0.0303:0.5 0/0:22:0:0,0:22,0:22,0:0:1,0:22.5:1:28.1:1:1:0:60:44:1:0:0 +10 3097129 . A T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50409;SOR=Inf;LSEQ=GAAACCTAAGACCCACATGG;RSEQ=GGGGGAGGAAGTTTCTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:106,41:147,0:0:2,0:24.4:1:30.1:1:1:0:60:17.375:0.9929:0:0.4 0/1:183:2:1,1:126,55:181,2:0.0109:2,2:13:1:25.5:1:0.51955:2.27938:58:4:0.0111:0:4 +10 3097134 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50288;SOR=Inf;LSEQ=CTAAGACCCACATGGAGGGG;RSEQ=AGGAAGTTTCTAGCTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:117,45:162,0:0:2,0:24.9:1:31.5:1:1:0:60:31.4:1:0:0.5 0/1:195:2:1,1:133,59:192,2:0.0103:2,2:19:1:26.5:1:0.52401:2.24379:60:4:0.0105:0:1.5 +10 3097135 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20231;SOR=0;LSEQ=TAAGACCCACATGGAGGGGG;RSEQ=GGAAGTTTCTAGCTTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:117,45:162,2:0.0122:2,2:32:0:33:0:0.48354:2.58256:60:4:0.0127:0:1.5 0/0:200:0:0,0:137,63:200,0:0:2,0:23.8:1:28.7:1:1:0:60:65.667:1:0:0.4 +10 3097180 . G A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=Inf;LSEQ=CAATGCTGGAAGGAATTCAG;RSEQ=TGAAATATTCCATGGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:146,111:257,0:0:2,0:25.3:1:31.3:1:1:0:60:50.4:1:0:0.8 0/1:314:13:7,6:167,134:301,13:0.0414:2,2:30:1:28.4:1:1:1.06799:60:26:0.0419:0:1.7 +10 3097212 . T C 246 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00452;LSEQ=ATGGCCTTCTGACTGCTCTC;RSEQ=GGTGCCTGTTGTGAAGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:281:280:144,136:0,0:0,280:0.9964:0,2:25.2:1:30.3:1:1:0:60:69:0.9964:0:1.1 1/0:325:181:88,93:72,72:144,181:0.5569:2,2:27.3:1:29.7:1:0.82396:1.05661:60:89.5:0.5576:0:1.2 +10 3097396 . G C 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73303;SOR=1.44322;LSEQ=TGGCACTTGAGGTTTCCTCC;RSEQ=TGATTTTCTTCCAGACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:0,7:0,17:17,7:0.2917:1,0:27:1:33.9:1:1:0:60:14:0.3043:0:1.1 0/1:16:6:1,5:0,10:10,6:0.375:0,2:18.5:1:29.3:1:0.375:0:60:5:0.3333:0:1 +10 3280406 . T C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0743;SOR=0.14828;LSEQ=ATGAGACTGATTTCAAGACA;RSEQ=GGGCCAGCCGGGCATTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:2,10:0.8333:0,0:20:1:30.4:1:1:0:60:9:0.8182:0:1.8 0/1:10:4:4,0:5,1:6,4:0.4:2,0:34.5:1:32.5:1:1:0:60:8:0.4:0:2.3 +10 3280416 . G A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0805;SOR=0.16427;LSEQ=TTTCAAGACATGGGCCAGCC;RSEQ=GGCATTCCTCCCGGTACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:9,0:2,0:2,9:0.8182:0,0:26.7:1:30.3:1:1:0:60:18:0.8182:0:2 0/1:10:4:4,0:5,1:6,4:0.4:2,0:34.5:1:30.3:1:1:0:60:8:0.4:0:2.3 +10 3280590 . A G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.02581;LSEQ=CAGAGAAGGAGATGTGGGGG;RSEQ=AAAAGCCTGTGCTAGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:375:347:212,135:15,13:28,347:0.9253:2,2:25.3:1:31.4:1:0.43019:1.36:60:68.4:0.9243:0:1.5 0/1:369:89:48,41:161,118:279,89:0.2412:2,2:27.5:1:30.4:1:0.54128:1.16494:60:178:0.2459:0:1.4 +10 3280619 . T C 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0125;SOR=0;LSEQ=GTGCTAGTCTGGAAGTGGAG;RSEQ=CTGGAGCTTAGATTAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:4,2:237,213:450,6:0.0131:2,2:18.3:1:32.2:1:0.68851:1.80:60:12:0.0135:0:1.2 0/0:489:0:0,0:252,237:489,0:0:2,0:23:0:14:0:1:0:60:0:0:0:5 +10 3280664 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03768;LSEQ=TTGACAGAAGGAATTCCCCA;RSEQ=CGCAGTCCCGTTCCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:411:374:167,207:15,21:36,374:0.91:2,2:25.1:1:30.2:1:0.86089:1.13:60:40.556:0.9125:0:1.4 0/1:462:127:65,62:155,179:334,127:0.2749:2,2:25.8:1:29:1:0.40395:1.21:60:126:0.2775:0:1.3 +10 3280942 . G A 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGAGCTGGAGCTGGGC;RSEQ=GCCCTGCCCTGTGGCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:25.6:1:33.8:1:1:0:60:10:1:0:1.6 1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:32:0:1:0:60:2:1:0:2 +10 3280961 . G A 52 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCCCTGCCCTGTGGCAGC;RSEQ=GGAATAAGAGGAGACAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:16.7:1:33:1:1:0:60:6:1:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:3:0:28:0:1:0:60:2:1:0:2 +10 3281573 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAGAGAGTCTGCAGGCC;RSEQ=TCAGTCAATCACACCGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 5094232 . C T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATGAAGCCGTGGACCCT;RSEQ=GCAGTGTTACAGTTCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:30:1:1:0:32.5:4:1:0:1.5 +10 5505007 . C T 37 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCCAAACTCCCAGGCCATG;RSEQ=TCTAAATGCTGGGCTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:33:0:30:0:1:0:60:2:1:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:25:1:23.7:1:1:0:60:2:1:0:1 +10 5505165 . G C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01822;SOR=3.41754;LSEQ=CAGCTCACACAACTGCACTC;RSEQ=TGCCCAGACGTCCCTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:24:14,10:11,7:18,24:0.5714:2,2:24.9:1:30.8:1:1:1.11937:60:23:0.575:0:2.3 1/1:45:37:22,15:4,4:8,37:0.8222:2,2:31.5:1:30.5:1:0.70429:1.45:60:74:0.8222:0:1.9 +10 5505210 . T C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCACGCTGACTCCCCAGCTT;RSEQ=CTCTAGGCCACCCCCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:24,24:0,0:0,48:1:0,2:23.5:1:30.8:1:1:0:58.6:23:1:0:2.1 1/1:47:47:18,29:0,0:0,47:1:0,2:21.3:1:29.2:1:1:0:59.3:22.5:1:0:2 +10 5505293 . G A 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63325;SOR=2.38223;LSEQ=GCAGCCGGCAGCTTCCAGGA;RSEQ=TAATTCATCAGATTCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:0,6:0,5:5,6:0.5455:0,0:25.5:1:33:1:1:0:60:12:0.5455:0:1.3 1/0:8:6:2,4:0,2:2,6:0.75:0,2:24.5:1:29.8:1:1:0:60:12:0.75:0:1.3 +10 5909907 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=GACTTTGCACCTTCTTAGGG;RSEQ=AAGAGTGTTGCTTTTACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:6,1:7,2:0.2222:2,2:34.5:1:28.5:1:0.41667:4.58262:27:4:0.2222:0:1 0/0:8:0:0,0:6,2:8,0:0:2,0:19.8:1:28.4:1:1:0:42:7:1:0:0 +10 6175914 . C T 34 v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=CCTGGTGTTGGGGCTCTGCC;RSEQ=CTGGTCTGGCTGAGCAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:47:0:34:0:1:0:60:4:0.4:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:26:0:33:0:1:0:60:2:0.5:0:1 +10 6176061 . TA T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.66948;LSEQ=ATGAAGGTTCTTTGCAACAT;RSEQ=AAAAAAATAATAAAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:1:1,0:53,14:67,1:0.0147:2,0:33:0:33:0:1:0:60:2:0.0149:0:0 0/1:82:2:1,1:63,17:80,2:0.0244:2,2:16:1:27.1:1:0.39295:3.63032:60:4:0.0247:0.0122:0.5 +10 6176070 . TAATAA T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=CTTTGCAACATTAAAAAAAA;RSEQ=AATAAAATAAACCTGTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:69,22:91,0:0:2,0:20.2:1:29.3:1:1:0:60:182:1:0:0.7 0/1:99:2:1,1:72,25:97,2:0.0202:2,2:15.5:1:29:1:0.45826:2.84362:60:4:0.0206:0.0101:1 +10 6176112 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.27635;LSEQ=TGCATATTTGCCAGGGGCTG;RSEQ=GCTTTCTGAGAGTGGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:152:99,53:52,36:88,152:0.6333:2,2:25.9:1:30.8:1:0.40572:1.29:60:151:0.6371:0:1.1 0/1:214:69:41,28:85,59:144,69:0.3224:2,2:26.6:1:29.1:1:1:1.02:60:138:0.3255:0:1.2 +10 6176145 . G A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02111;SOR=Inf;LSEQ=TGGACAGGGAACAGCTGAGC;RSEQ=TGCTTGACGGCTCTGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:157,121:278,0:0:2,0:28.7:1:30.7:1:1:0:60:91.667:1:0:0.9 0/1:241:5:2,3:130,106:236,5:0.0207:2,2:21.6:1:30.2:1:0.66062:1.83495:60:10:0.0207:0:1.8 +10 6176166 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.0356;SOR=0.6471;LSEQ=TGCTTGACGGCTCTGGGGTC;RSEQ=TCAGGGCCTCCGTCTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:88:41,47:89,88:177,88:0.3321:2,2:24.9:1:30:1:0.60328:1.15872:60:28.333:0.3244:0:1.1 0/1:222:54:21,33:77,89:166,54:0.2432:2,2:27.6:1:28.8:1:0.34955:1.35766:60:17:0.2339:0:1.1 +10 6176208 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49842;SOR=0;LSEQ=TGACACTGTCCTGGGCTCAG;RSEQ=GGGCTGTGGAGGCCCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:42,104:146,2:0.0135:2,2:26.5:1:29.5:1:0.49807:2.46:60:4:0.0137:0:1 0/0:143:0:0,0:49,94:143,0:0:2,0:26.7:1:29.5:1:1:0:60:46.667:1:0:0.4 +10 6176223 . C A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1153;SOR=Inf;LSEQ=CTCAGCGGGCTGTGGAGGCC;RSEQ=CAAGTGACGCTGTGAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:28,88:116,0:0:2,0:24.8:1:31:1:1:0:60:57:1:0:0.4 0/1:111:3:1,2:30,78:108,3:0.027:2,2:30.3:1:26:1:1:1.30:60:2:0.0185:0:1.7 +10 6743894 . T A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=CTTTTTGCAGGCAGGGGTAA;RSEQ=GCTATGTTCTGTGTGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:8,0:0:0,0:26.1:1:31.8:1:1:0:60:16:1:0:0.6 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:5.5:1:30.5:1:1:0:60:4:0.3333:0:1 +10 6744002 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51158;SOR=Inf;LSEQ=AGTGATGATGATGACAATGA;RSEQ=CATGATGATGACGATGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:29,28:57,0:0:2,0:27.9:1:31.9:1:1:0:59.4:27.5:1:0:0.4 0/1:81:2:1,1:43,36:79,2:0.0247:2,2:43.5:1:30.5:1:1:1.19181:60:4:0.0247:0:1.5 +10 6744019 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51284;SOR=Inf;LSEQ=TGAGCATGATGATGACGATG;RSEQ=CCTTGATGGTGTTGCTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:22,32:54,0:0:2,0:26:1:29.4:1:1:0:59.4:53:1:0:0.3 0/1:78:2:1,1:34,42:76,2:0.0256:2,2:11.5:1:29.5:1:1:1.23:60:4:0.0256:0:1.5 +10 6744024 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14838;SOR=0;LSEQ=ATGATGATGACGATGACCTT;RSEQ=ATGGTGTTGCTGCTAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:17,31:48,2:0.04:2,2:19.5:1:31.5:1:1:1.80:60:4:0.04:0:1 0/0:79:0:0,0:34,45:79,0:0:2,0:24.7:1:30.4:1:1:0:60:78:1:0:0.2 +10 6744105 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48667;SOR=Inf;LSEQ=TACATGGCATGACAACATGC;RSEQ=TGAAATGTTTCATGGTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:11,0:0:0,0:22.7:1:32.5:1:1:0:60:22:1:0:0 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:26:1:29:0:1:0:60:4:0.1429:0:1 +10 8087393 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1918;SOR=0;LSEQ=CGGCGGCCACAGTGGCGAAC;RSEQ=CTGCCTGTCATTTCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:25,2:0.0741:2,2:30.5:1:33:0:1:1.74:60:4:0.0741:0:1 0/0:34:0:0,0:17,17:34,0:0:2,0:29.1:1:28.3:1:1:0:60:33:1:0:0.4 +10 8087409 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49156;SOR=Inf;LSEQ=GAACTCTGCCTGTCATTTCT;RSEQ=CCTTCAGATCTCCGGGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:9,18:27,0:0:2,0:27.1:1:32.3:1:1:0:60:26:1:0:0.2 0/1:29:2:1,1:10,16:26,2:0.069:2,2:26.5:1:28:1:1:1.57:60:4:0.069:0:1 +10 8087428 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23256;SOR=0;LSEQ=TGCCTTCAGATCTCCGGGCG;RSEQ=GTCAGGAAAAAAAATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:5,14:19,2:0.0952:2,2:23.5:1:33:0:0.5:2.65:60:4:0.0952:0:1 0/0:22:0:0,0:7,15:22,0:0:2,0:26:1:30:1:1:0:60:44:1:0:0.1 +10 8097556 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13255;SOR=Inf;LSEQ=CCCCCGACCTCCCAGGCGGA;RSEQ=CGCCCTCCCTCCCCGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:52,10:62,0:0:2,0:17.5:1:31.4:1:1:0:60:30:1:0:0.1 0/1:36:2:1,1:28,6:34,2:0.0556:2,2:28:0:31:1:0.35556:4.39698:60:4:0.0571:0:1.5 +10 8097570 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.06002;SOR=Inf;LSEQ=GGCGGACCGCCCTCCCTCCC;RSEQ=GCGCGCGGGTTCCGGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:83,18:101,0:0:2,0:19.3:1:31:1:1:0:60:49.5:1:0:0.2 0/1:66:3:3,0:51,12:63,3:0.0455:2,0:20.3:1:32:0:1:0:60:6:0.0455:0:1 +10 8097603 . G T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.65859;SOR=1.90908;LSEQ=CGGGCCCGGCGAGAGGGCGC;RSEQ=AGCACAGCCGAGGCCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:2:1,1:203,43:246,2:0.0081:2,2:19.5:1:27.5:1:0.32395:4.67849:60:4:0.0083:0:1.5 0/1:196:3:1,2:149,44:193,3:0.0153:2,2:11.3:1:25.3:1:0.13791:6.68766:60:6:0.0155:0:1.3 +10 8098185 . A G 59 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGTCTCGGGATGTCCCCA;RSEQ=GCGCGGGGTGCCCTGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:24:1:29.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 8100125 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44795;SOR=0.52033;LSEQ=CAGGTACTCCGGGGACCGCC;RSEQ=GGATGAGAGAGTGGGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:60:59,1:4,0:4,60:0.9375:0,1:24.7:1:30.8:1:1:0:60:120:0.9375:0:4.1 1/1:35:31:31,0:4,0:4,31:0.8857:0,1:27.2:1:30.2:1:1:0:60:62:0.8857:0:3.9 +10 8100129 . TGA ATT 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12383;LSEQ=TACTCCGGGGACCGCCAGGA;RSEQ=GAGAGTGGGCCTGAGCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:60:60,0:5,0:5,60:0.9091:0,1:26.8:1:31.8:1:1:0:60:120:0.9231:0.0303:2.1 1/1:49:45:45,0:4,0:4,45:0.9184:0,1:22.4:1:30.2:1:1:0:60:90:0.9184:0.3265:1.4 +10 8100647 . C T 162 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02231;LSEQ=TCCCGTGGCAGCATGACCGC;RSEQ=CTGGGTGGAGCCTCCTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:949:39:19,20:445,465:910,39:0.0411:2,2:27.3:1:30.8:1:1:1.00735:60:38:0.0409:0:1.1 0/0:1049:1:0,1:529,518:1047,1:0.001:2,0:1:0:25:0:0.49523:0:60:2:0.001:0:1 +10 8100727 . TC T 93 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.03292;SOR=4.83941;LSEQ=CGAGTACAGCTCCGGACTCT;RSEQ=CCCCCCAGCAGCCTGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:2:0,2:292,411:703,2:0.0028:2,0:12.5:1:29:1:0.51404:0:60:4:0.0029:0.0014:1 0/1:662:9:5,4:278,375:653,9:0.0136:2,2:25:1:29.4:1:0.50736:1.68:60:18:0.014:0.003:0.2 +10 8100866 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18487;SOR=Inf;LSEQ=TCCCCTTTTCCTCAATCCAG;RSEQ=GCCGCACCCAGAGGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:14,102:116,0:0:2,0:22.8:1:30.5:1:1:0:60:57:1:0:0.2 0/1:88:2:1,1:18,68:86,2:0.0227:2,2:9:1:28:1:0.38715:3.70:60:4:0.0238:0:1 +10 8102887 . G A 47 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTCACAGTCGTGAAAACC;RSEQ=AGAACAGCACACCTGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:19.7:1:30:1:1:0:60:6:1:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:10:0:24:0:1:0:60:2:1:0:1 +10 8105745 . G A 48 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.01621;SOR=22.11438;LSEQ=CCCCTTCTGCGGGCGCCTCC;RSEQ=TGTGTGTCGGGGGAACGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:19,0:19,2:0.0952:1,0:15:1:32:0:1:0:60:4:0.1:0:1 1/0:4:3:3,0:1,0:1,3:0.75:0,0:7.7:1:30.7:1:1:0:60:6:0.75:0:1 +10 8106135 . A G 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGGATGGATTCCATGCTG;RSEQ=CCATTCTGGGTTTCTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:53,181:234,0:0:2,0:21.8:1:29.5:1:1:0:59.8:57.5:1:0:0.1 0/1:231:25:5,20:59,147:206,25:0.1082:2,2:23.1:1:30.9:1:0.47994:1.60244:60:50:0.1096:0:1.2 +10 8106248 . TTTTC T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTTTTTTTTTTTTTCCT;RSEQ=TTTCTTTCTTTTCTTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:0,2:2,27:29,2:0.0645:2,0:13:1:31.3:1:1:0:60:4:0.0645:0.0323:0.5 0/0:15:0:0,0:3,12:15,0:0:2,0:13.7:1:27.8:1:1:0:53.5:14:1:0:0.7 +10 8106272 . TTC T 27 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=18.000;MSILEN=1;SSF=0.56459;SOR=2.4775;LSEQ=CTTTCTTTCTTTTCTTCTTC;RSEQ=TTTTTTTTTTTTTTTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:0,2:0,12:12,2:0.1333:0,0:15.5:1:28:1:1:0:38:4:0.1538:0.0667:5 0/1:7:2:1,1:0,2:2,2:0.2857:0,2:12.5:1:27.5:1:1:0:60:4:0.6667:0.1429:1 +10 8106274 . C T 101 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=17.000;MSILEN=1;SSF=0.00151;SOR=0;LSEQ=TTCTTTCTTTTCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:0,10:0,0:0,10:0.8333:0,0:13.8:1:30.5:1:1:0:49.5:20:1:0:3.5 0/0:6:0:0,0:0,1:1,0:0:0,0:12:0:28:0:1:0:60:2:1:0:4 +10 8106353 . G A 47 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATCCATGTTTCTTAAGTC;RSEQ=CTTGTGAACATTTTAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:16.7:1:22.7:1:1:0:53:2:1:0:3 1/0:4:3:1,2:0,1:1,3:0.75:0,2:10.3:1:30:1:1:0:60:6:0.75:0:1 +10 8106856 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAAACTTTTTAAGCATG;RSEQ=GGGATCCTTGAGAAAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:30:1:1:0:60:4:1:0:1 +10 8107572 . A G 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACATGACTTTAATCTTTG;RSEQ=CAATCCTGGATATCGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:32.5:1:1:0:60:4:1:0:1.5 +10 8110938 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTGGTGCTTGGCTTTGC;RSEQ=CCTCCTTTGCTGTGAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:37.5:1:30.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 8111168 . C T 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGACTGCCAGGGAGGAGG;RSEQ=CCCGGCTTCCTGCTCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:10.3:1:29.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 8111409 . C T 255 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06855;LSEQ=TTTAACATTTGTTTTGATTT;RSEQ=ACCCTCTCCTCTCTCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:348:336:255,81:8,4:12,336:0.9655:2,2:24.5:1:30.4:1:0.49661:1.57:59.8:111:0.9652:0:1.2 1/0:405:266:188,78:99,40:139,266:0.6568:2,2:21.5:1:28.4:1:1:1.0268:60:65.5:0.665:0:1.1 +10 8111621 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03114;LSEQ=TGATGGTGACCAGCAAACAG;RSEQ=GTCACCACCACCCTCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:258:240:30,210:3,15:18,240:0.9302:2,2:23.1:1:30.6:1:0.71122:1.39797:60:119:0.937:0:1.1 0/1:189:55:5,50:16,118:134,55:0.291:2,2:27:1:29.7:1:0.79924:1.35386:60:110:0.2926:0:1.1 +10 8111850 . GA G 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.03333;SOR=0;LSEQ=GGGCCTGTGTGGTTTATAAG;RSEQ=AAAAAAAAAAATCTTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,0:0,6:0.8571:0,0:31.3:1:30.7:1:1:0:60:12:0.8571:0:0.7 0/0:3:0:0,0:1,2:3,0:0:2,0:24:1:29.7:1:1:0:60:6:1:0:1.7 +10 8115687 . T A 84 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00178;LSEQ=GTAAAAAAAAAAAAAAAAAA;RSEQ=TGATCTTTGTTTAGATTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:577:14:12,2:421,138:559,14:0.0243:2,2:20.4:1:19.5:1:0.53458:1.96:57.5:0.75:0.0117:0:2.9 0/1:576:14:10,4:380,176:556,14:0.0243:2,2:16.7:1:22.2:1:1:1.16:60:1.8:0.017:0:1.9 +10 8116079 . C T 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GCAGTATCATGAAGCCTAAA;RSEQ=GCGATGGATATATGTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:40:0,40:0,19:19,40:0.678:1,1:17.7:1:30.5:1:1:0:60:19:0.6667:0:1.1 0/0:29:0:0,0:3,26:29,0:0:2,0:23:1:29:1:1:0:60:28:1:0:0.2 +10 8116241 . G GA 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGGGTCTCTAGTGCTGT;RSEQ=AAAAAAAAAATGCTGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:16:1:32:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 8596688 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11853;SOR=Inf;LSEQ=TGGGAGCTCAAGGCAGTGTT;RSEQ=ACCCATCAAGGCCTGACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:193,97:290,0:0:2,0:25.8:1:32:1:1:0:60:95.667:1:0:0.1 0/1:281:3:1,2:162,116:278,3:0.0107:2,2:18:1:27.7:1:0.57417:2.78293:60:6:0.0108:0:1.3 +10 8596711 . G T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02848;SOR=Inf;LSEQ=CCATCAAGGCCTGACAGTAA;RSEQ=AGGAGGATGGATGAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:218,169:387,0:0:2,0:25.6:1:32.5:1:1:0:60:95.75:1:0:0.1 0/1:375:5:2,3:197,173:370,5:0.0133:2,2:25.6:1:26.2:1:0.66886:1.70565:60:10:0.0135:0:1.6 +10 8596776 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.58626;LSEQ=CCTGTTCCCTGGCCTGACCT;RSEQ=CCTCTGCACTCATTTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:16:7,9:140,213:353,16:0.0431:2,2:28:1:30.7:1:0.79695:1.18:60:32:0.044:0:1.3 0/1:317:109:49,60:96,111:207,109:0.3438:2,2:26.2:1:28.6:1:0.81362:1.05886:60:26.25:0.342:0:1.1 +10 9959556 . C T 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.02718;SOR=0;LSEQ=ATGTTTTAAATATATCCTGT;RSEQ=TAAAATAGAAATCAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:6,1:13,1:14,7:0.3333:1,2:15.1:1:32.3:1:1:2.08171:60:14:0.35:0:1 0/0:14:0:0,0:13,0:13,0:0:1,0:19.5:1:31.8:1:1:0:60:26:1:0:0 +10 9959688 . A C 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00156;SOR=Inf;LSEQ=CTAGTTGATTAGTAGTAAGG;RSEQ=GCAGTGCTTCAGGGCATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:120,50:170,0:0:2,0:23.3:1:30.3:1:1:0:60:55.667:1:0:1.2 0/1:215:12:9,3:133,70:203,12:0.0558:2,2:30.5:1:30.8:1:0.75496:1.58:60:24:0.0563:0:3.1 +10 9959704 . A G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=5e-05;SOR=0.056;LSEQ=AAGGAGCAGTGCTTCAGGGC;RSEQ=TGCATCTCATTGTGGTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:233:232:152,80:0,0:0,232:0.9957:0,2:23.6:1:30.7:1:1:0:60:115:0.9957:0:1.3 1/1:265:246:149,97:10,9:19,246:0.9283:2,2:25.5:1:30.1:1:0.62787:1.38:60:492:0.9283:0:1.3 +10 9959736 . T C 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=Inf;LSEQ=GTGGTATTATCAAAACTGTC;RSEQ=CAACCACACATTCACATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:193,147:340,0:0:2,0:25.8:1:31.1:1:1:0:60:41.5:1:0:0.9 0/1:366:15:9,6:190,161:351,15:0.041:2,2:24.3:1:28.1:1:0.79336:1.27:60:14:0.0385:0:2.9 +10 9959785 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.30823;LSEQ=TCAGGTTTCCAAGTCGGAAA;RSEQ=GGAGTCCTGAATTTTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:137:63,74:101,114:215,137:0.3892:2,2:25.7:1:30.4:1:0.91284:1.04056:60:67.5:0.3879:0:1.3 1/0:361:215:95,120:65,81:146,215:0.5956:2,2:26.1:1:29.7:1:1:1.01361:60:214:0.5961:0:1.2 +10 9959931 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.79208;SOR=1.22335;LSEQ=TTTTCCTTTATTGGAATTTC;RSEQ=GTGACACGTAGGAATCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:0,15:0,17:17,15:0.4688:1,1:20.6:1:31.3:1:1:0:59.1:30:0.4688:0:2.5 1/0:25:13:0,13:0,11:11,13:0.52:0,1:26.5:1:30.5:1:1:0:60:26:0.52:0:2.4 +10 9959939 . G T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39045;SOR=1.86462;LSEQ=TATTGGAATTTCCGTGACAC;RSEQ=TAGGAATCATCATATTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:0,12:0,17:17,12:0.4138:1,0:22.6:1:30.3:1:1:0:58.9:24:0.4138:0:2.9 1/0:21:12:0,12:0,9:9,12:0.5714:0,0:24.8:1:30.7:1:1:0:60:24:0.5714:0:2.6 +10 9959979 . C T 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00934;SOR=15.97969;LSEQ=GGGAATTTGAGGATGTCTGT;RSEQ=TCTTTGTTTTAATTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:0,5:0,13:13,5:0.2778:1,0:26.6:1:30.8:1:1:0:60:10:0.2778:0:4.2 1/1:8:7:1,6:0,1:1,7:0.875:0,2:17.6:1:26.3:1:1:0:60:6:0.8571:0:3.4 +10 9959999 . T G 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04076;SOR=13.80899;LSEQ=CTCTTTGTTTTAATTTCTCT;RSEQ=TAAATTTTTTTTATTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:18:1:34:0:1:0:60:6:0.2308:0:5 1/1:6:5:1,4:0,1:1,5:0.8333:0,2:24.2:1:30.8:1:1:0:60:10:0.8333:0:3.6 +10 9960005 . T C 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.10577;SOR=8.9635;LSEQ=GTTTTAATTTCTCTTTAAAT;RSEQ=TTTTTTATTTCCAGAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:12:1:35.3:1:1:0:60:6:0.2727:0:5 1/1:5:4:1,3:0,1:1,4:0.8:0,2:29.5:1:31:1:1:0:60:8:0.8:0:3.5 +10 9960282 . A G 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGATTTCTGCAATTTTG;RSEQ=TGCACCCATCACCTGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:26.3:1:33.3:1:1:0:59.3:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 10136339 . C G 225 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAATAATACAGAAAGGCTC;RSEQ=ATAAATGTGAGTTTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:260,240:500,0:0:2,0:24.7:1:31.4:1:1:0:60:82.333:0.998:0:0.1 0/1:465:198:92,106:136,131:267,198:0.4258:2,2:24.8:1:29.6:1:0.34971:1.19568:60:197:0.4283:0:1.1 +10 10136473 . G A 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATCTGTTGATAATTCTAGC;RSEQ=TGAGAGAAAAATGTTAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:1,80:81,0:0:1,0:22.1:1:32.7:1:1:0:60:80:1:0:0 0/1:48:18:0,18:1,29:30,18:0.375:1,1:23.8:1:31.1:1:1:0:60:36:0.375:0:1.6 +10 10136486 . G T 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTAGCGTGAGAGAAAAAT;RSEQ=TTAAACTTCATTTATTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:1,61:62,0:0:1,0:21.8:1:32.4:1:1:0:60:61:1:0:0 0/1:34:13:0,13:0,21:21,13:0.3824:1,1:22.4:1:30.6:1:1:0:60:26:0.3939:0:1.8 +10 10216156 . T C 92 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00691;SOR=10.94865;LSEQ=CTGATGAGAAACCACTGAAG;RSEQ=TCCTGGGGAAGCAAAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:0,1:129,35:164,1:0.0061:2,0:1:0:32:0:0.21818:0:60:2:0.0061:0:1 0/1:143:9:5,4:98,34:132,9:0.0629:2,2:24.1:1:29.2:1:0.25121:2.29026:60:18:0.0647:0:1.1 +10 10216373 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03482;SOR=0.54466;LSEQ=TGAATGAAACCAATGAGGTC;RSEQ=ATTTTAGAGAGATACCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:59:31,28:27,18:45,59:0.5619:2,2:23.2:1:30.5:1:0.5506:1.35087:59.3:28.5:0.5588:0:1.1 0/1:95:39:25,14:34,22:56,39:0.4105:2,2:22:1:29.4:1:0.8309:1.15:60:38:0.4086:0:1.1 +10 10216430 . A G 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGCACGTATTTTATGTAT;RSEQ=AGGTTCGCTACCCTAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:73,65:138,0:0:2,0:25.7:1:29.4:1:1:0:59.9:137:1:0:0.4 0/1:142:24:13,11:62,54:116,24:0.169:2,2:25.8:1:30.1:1:1:1.03:59.7:48:0.1702:0:1 +10 10216431 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49828;SOR=Inf;LSEQ=ATGCACGTATTTTATGTATA;RSEQ=GGTTCGCTACCCTAACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:74,66:140,0:0:2,0:25.3:1:30.8:1:1:0:59.9:69:1:0:0.4 0/1:143:2:1,1:75,66:141,2:0.014:2,2:31:1:30:1:1:1.13534:60:4:0.0141:0:1.5 +10 10216438 . C A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1122;SOR=0;LSEQ=TATTTTATGTATAAGGTTCG;RSEQ=TACCCTAACAGCTCCACCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:2,1:72,76:148,3:0.0199:2,2:48:1:31.3:1:0.61505:2.10:60:6:0.0207:0:1 0/0:161:0:0,0:82,79:161,0:0:2,0:23.2:1:30.8:1:1:0:60:160:1:0:0.4 +10 10216761 . TA T 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATAAAGATGCCAATTTG;RSEQ=AAAAAAAAAATAATAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:28.3:1:32.3:1:1:0:46.7:6:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 10439699 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52164;SOR=Inf;LSEQ=AGAGCCTCTGGAGGGAGTGT;RSEQ=CCCCTGCTGACTCCGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:27,21:48,0:0:2,0:22.8:1:31.8:1:1:0:60:23:1:0:0.3 0/1:76:2:1,1:39,35:74,2:0.0263:2,2:13.5:1:26:1:1:1.1127:60:4:0.0263:0:2 +10 10439732 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27547;SOR=Inf;LSEQ=CCGGCAGTTTGGACTTCTGG;RSEQ=CTCCAGAACTCTGAGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:22,20:42,0:0:2,0:32.1:1:31.5:1:1:0:60:41:1:0:0.2 0/1:64:3:2,1:31,30:61,3:0.0469:2,2:12:1:27:1:1:1.92:60:6:0.0476:0:1 +10 10439734 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15769;SOR=0;LSEQ=GGCAGTTTGGACTTCTGGCC;RSEQ=CCAGAACTCTGAGACAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:21,19:40,2:0.0476:2,2:31:0:33:0:1:1.10263:60:4:0.05:0:1.5 0/0:63:0:0,0:32,31:63,0:0:2,0:28.1:1:29.2:1:1:0:58:30.5:1:0:0.2 +10 10923338 . TA T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.27044;SOR=Inf;LSEQ=ACTACCTATTTCCTTCAGAA;RSEQ=AAAATAAATTTTTAACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:72,12:84,0:0:2,0:23.9:1:29.1:1:1:0:60:168:0.9882:0:0.2 0/1:122:3:1,2:103,16:119,3:0.0246:2,2:15.7:1:25.7:1:0.05666:12.41384:60:6:0.0248:0.0164:0.7 +10 10923359 . A AT 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50799;SOR=Inf;LSEQ=AAAAATAAATTTTTAACTTC;RSEQ=TTTTTTTCCTGAAGTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:101,26:127,0:0:2,0:24.8:1:30.9:1:1:0:60:254:1:0:0.5 0/1:168:2:1,1:127,39:166,2:0.0119:2,2:17:1:27:1:0.42059:3.22807:60:4:0.0119:0:0.5 +10 10923431 . T A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0088;LSEQ=GCTGTTAGTAAAATATGAGA;RSEQ=ACTTCAAACTTAATGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:347:326:180,146:10,11:21,326:0.9395:2,2:25:1:30:1:0.50759:1.35:60:39.75:0.9381:0:1.2 0/1:445:53:27,26:192,200:392,53:0.1191:2,2:29.5:1:29.2:1:0.8838:1.08:60:52:0.119:0:1.3 +10 10923503 . C T 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AACCCACCCTCCAGATTTAG;RSEQ=ATCCTGAAACATTTTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:79,158:237,0:0:2,0:24.3:1:32.2:1:1:0:60:78:1:0:0.5 0/1:264:18:7,11:86,160:246,18:0.0682:2,2:23.2:1:28.4:1:0.79996:1.18:60:36:0.0692:0:1.5 +10 10925636 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCATCTGCTGTACTGAGA;RSEQ=GGTGCGGAGTCCTGTGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:29:1:1:0:60:4:1:0:1 +10 14379777 . G A 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCAGAAACAAGGCAAGG;RSEQ=TGACCATTCTCAGCACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:17.5:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 14379945 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGATGGAATCTATTAAAT;RSEQ=CTAATAAGCAAGTTTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:18,8:0,0:0,26:1:0,2:22.5:1:28.9:1:1:0:60:52:1:0:1.1 1/1:32:32:20,12:0,0:0,32:1:0,2:26.5:1:28.1:1:1:0:60:64:1:0:1 +10 15008967 . A G 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCTTGAACTCCTGACCTC;RSEQ=AGTGATCCACGCGCCTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:20:1:27:1:1:0:41.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 15009109 . T C 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01099;SOR=0;LSEQ=TGGGAGAAGAGGTGGTCGTT;RSEQ=AGCTGGGCACATTCAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:10,0:1,0:1,10:0.9091:0,0:28.9:1:32.5:1:1:0:57.8:20:0.9091:0:2.3 0/0:3:0:0,0:2,1:3,0:0:2,0:39.3:1:29.7:1:1:0:60:6:1:0:0 +10 15009164 . G T 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08757;SOR=0.17113;LSEQ=GCAACTGTGCTCTGCTAAAT;RSEQ=AATCTTTTGCGGTAGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:25:25,0:2,0:2,25:0.9259:0,1:19:1:30.1:1:1:0:60:11.5:0.92:0:1.6 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:17:1:31.3:1:1:0:56.7:12:0.6667:0:1.8 +10 15009184 . C CA 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.3884;SOR=0.58069;LSEQ=GAATCTTTTGCGGTAGACCA;RSEQ=AAAAAAAAAGCTTTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:23:23,0:6,0:6,23:0.7667:0,1:28.8:1:30.1:1:1:0:60:10.5:0.7778:0:0.9 1/0:26:17:17,0:7,0:7,17:0.6538:0,1:18.6:1:30.9:1:1:0:58.8:34:0.6538:0.1923:0.6 +10 15009285 . G T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12762;SOR=Inf;LSEQ=TTACTTTTTATTTTAACCAT;RSEQ=AATTAGAAAGAGGTTAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:177,85:262,0:0:2,0:24:1:32.1:1:1:0:60:86.333:1:0:0.3 0/1:303:4:1,3:195,104:299,4:0.0132:2,2:10.8:1:25.8:1:0.12798:5.5921:60:8:0.0133:0:1.3 +10 15009339 . CA C 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCAATTATACCTTACAAA;RSEQ=AAAGTGTTAGAACAACTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:0:0,0:211,181:392,0:0:2,0:26.6:1:30.5:1:1:0:60:97:0.9974:0:0.7 0/1:501:25:12,13:241,234:475,25:0.0499:2,2:27.4:1:31.3:1:0.83945:1.1155:59.3:50:0.0501:0.006:0.1 +10 15009368 . A G 268 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06697;LSEQ=TAGAACAACTCGTGACTTTG;RSEQ=TAGTATATCCCAGGCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:360:172,188:4,6:10,360:0.973:2,2:24.8:1:31.6:1:0.75352:1.37:59.9:119:0.9728:0:1.1 1/0:446:315:147,168:57,74:131,315:0.7063:2,2:25.7:1:30.8:1:0.60204:1.14:60:104:0.7059:0:1.2 +10 15009466 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50446;SOR=0;LSEQ=CTCCCGTTTATACAGTGTGG;RSEQ=TCTTCTTAACTTATTTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:16,102:118,2:0.0167:2,2:23:1:31.5:1:0.26429:6.22:60:4:0.0169:0:1 0/0:95:0:0,0:14,81:95,0:0:2,0:23.1:1:29:1:1:0:58.4:30.667:1:0:0.8 +10 15009504 . T C 137 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=1;SSF=0.36158;SOR=0.62886;LSEQ=TTCTCTTGGCTACTAAGATA;RSEQ=TTTTTTTTTTTTTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:19:1,18:0,0:0,19:0.413:0,1:7.6:1:32.4:1:1:0:58.5:18:0.439:0:1.1 0/1:36:11:1,10:0,9:9,11:0.3056:0,2:8.4:1:32.7:1:1:0:59.1:22:0.3438:0:1.5 +10 15009535 . A G 102 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0419;SOR=0;LSEQ=TTTTTTTGAGACAGAGTCTC;RSEQ=CTCTGTCACCCAGGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:17.9:1:34:1:1:0:44.4:16:1:0:2.9 1/0:12:6:0,6:0,6:6,6:0.5:0,0:12.8:1:32.8:1:1:0:54.3:12:0.5:0:1.8 +10 15009590 . A G 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CTCGGCTCAGTGCAACCTCC;RSEQ=CCTCCCGGGTTCAAGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:12:1:31:1:1:0:60:4:1:0:1.5 0/1:4:1:0,1:0,3:3,1:0.25:0,0:50:0:34:0:1:0:29:2:0.25:0:2 +10 15009719 . A T 44 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATAACTTTTGACTCCCCA;RSEQ=AACAACTACTAGTAACCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:26.7:1:28:1:1:0:60:6:1:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 15549548 . A C 144 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04435;SOR=0;LSEQ=CCATCGTTTACATCTGACCA;RSEQ=ATTCCTCCCCCGTCACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:20,0:0,0:0,20:1:0,1:34.4:1:33.5:1:1:0:60:40:1:0:1.1 1/0:12:9:9,0:3,0:3,9:0.75:0,0:21.2:1:32:1:1:0:60:18:0.75:0:1 +10 15549612 . A C 113 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00391;SOR=7.23301;LSEQ=TTGACTGCCTCAGCCTTAGC;RSEQ=GGAATCACCCCTGACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:2,0:31,23:54,2:0.0357:2,0:40:1:33:0:0.50714:0:60:4:0.0364:0:1 0/1:75:16:10,6:31,28:59,16:0.2133:2,2:25.9:1:28.4:1:0.57667:1.50:60:15:0.2027:0:1.2 +10 15549894 . A G 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAAGATGCACATAAACT;RSEQ=CTTAGTGGAGGGCTTCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:26.7:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 15950149 . G A 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=211.49016;LSEQ=CTACGTAAAAGGGGTAGCAC;RSEQ=GGAGCCGAGAGAAATTCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:598:3:3,0:294,300:594,3:0.005:2,0:1:0:26.3:1:0.1225:0:60:6:0.0051:0:1 1/0:766:396:194,202:176,194:370,396:0.517:2,2:25:1:29.8:1:0.7178:1.06:60:197:0.5205:0:1.2 +10 16154458 . A C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00233;SOR=1.64864;LSEQ=ATAGGAGAGAAGTGATCCAG;RSEQ=TACAAATACCCAAGGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:155:88,67:93,67:160,155:0.4921:2,2:27.6:1:32.4:1:0.8206:1.05661:60:37.75:0.4887:0:1.6 1/0:317:195:116,79:70,50:120,195:0.6151:2,2:27.3:1:31.6:1:0.90616:1.05:60:390:0.619:0:1.5 +10 16154522 . C G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00041;SOR=1.697;LSEQ=TTTCCAAGGCATCTTCTCAT;RSEQ=ATGTTCACTTTCAGTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:161:68,93:95,105:200,161:0.4448:2,2:23.9:1:31.6:1:0.33939:1.23666:60:52.667:0.4401:0:1.9 1/0:380:219:93,126:75,85:160,219:0.5763:2,2:26:1:30.9:1:0.40418:1.19487:59.9:438:0.5794:0:1.8 +10 16154527 . TCACTTTCAGTCCAGGCAAGCAATTGA T 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00773;SOR=Inf;LSEQ=AAGGCATCTTCTCATCATGT;RSEQ=CACTATGGAATCCAAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:149,191:340,0:0:2,0:25.9:1:31.8:1:1:0:60:47.571:0.997:0:0.9 0/1:364:8:2,6:151,204:355,8:0.022:2,2:34.5:1:32.3:1:0.47577:2.21616:59.4:16:0.0221:0:2.3 +10 16154569 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24848;SOR=Inf;LSEQ=ATTGACACTATGGAATCCAA;RSEQ=CTGATAATGAGTTCGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:63,142:205,0:0:2,0:23.3:1:32.1:1:1:0:60:33.167:1:0:0.8 0/1:213:3:1,2:63,147:210,3:0.0141:2,2:27.7:1:28.7:1:1:1.17:60:6:0.0142:0:1.7 +10 16154583 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.91124;SOR=1.04483;LSEQ=ATCCAAGCTGATAATGAGTT;RSEQ=GGAGGTATAAACAGGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:161:89:20,69:20,51:71,89:0.5528:2,2:21:1:30.3:1:0.46417:1.35034:60:178:0.5597:0:1.7 1/0:165:93:28,65:17,55:72,93:0.5636:2,2:24.9:1:30:1:0.38271:1.39:59.9:186:0.5636:0:1.7 +10 16154624 . T A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11992;SOR=Inf;LSEQ=GAAGTACAATGTAGAATGTC;RSEQ=ACCCATCAAGAAAGGGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:5,58:63,0:0:2,0:26.5:1:29:1:1:0:60:62:1:0:0.5 0/1:67:4:1,3:11,52:63,4:0.0597:2,2:15.5:1:30.3:1:0.55504:1.56:60:8:0.0597:0:2.3 +10 16154704 . T C 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0078;SOR=10.96685;LSEQ=AGAAAATTGGGAAAGACAGA;RSEQ=CAAGGCTAAGTCCAATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:0,6:0,15:15,6:0.2727:1,0:26.2:1:32.3:1:1:0:60:12:0.2857:0:1 1/1:11:9:0,9:0,2:2,9:0.8182:0,0:16:1:30.3:1:1:0:60:18:0.8182:0:1.1 +10 16762523 . T C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.2632;LSEQ=AGGGAAGAACTCTAATTTTA;RSEQ=AGTTAAACTCAGGGTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:290:187:111,76:54,48:102,187:0.6448:2,2:26.4:1:32.4:1:0.32078:1.30:59.7:61.333:0.6434:0:1.2 0/1:350:113:65,48:128,108:236,113:0.3229:2,2:24.1:1:31.4:1:0.64549:1.14:60:226:0.3238:0:1.1 +10 16762607 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23413;SOR=Inf;LSEQ=GAGTTTCTCATATAAATAAG;RSEQ=ATCCTACACAGAATACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:54,146:200,0:0:2,0:23.8:1:28.6:1:1:0:60:199:1:0:0.2 0/1:188:2:1,1:59,127:186,2:0.0106:2,2:31.5:1:28.5:1:0.5376:2.14:60:4:0.0106:0:1 +10 17054256 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18076;SOR=Inf;LSEQ=GGCTGCCATGGGACCTAGAA;RSEQ=GGGGAGAAGCCATATTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:25,0:0:2,0:12.4:1:29.3:1:1:0:31.1:11.5:1:0:0 0/1:19:2:1,1:11,6:17,2:0.1053:2,2:24.5:1:28.5:1:1:1.77272:30.5:4:0.1111:0:1.5 +10 17054570 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGCTTTGAGAGTGTGTG;RSEQ=TAGTAGGATAATGCATGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:29.5:1:1:0:33:4:1:0:1 +10 18471750 . CA C 30 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=GACAGAATGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAACAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:35.7:1:31:1:1:0:48.4:14:1:0:1.1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19:1:30.5:1:1:0:60:4:0.5:0.25:1.5 +10 18471794 . C T 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00075;SOR=25.95982;LSEQ=ATAATTTCCTTCACCTGAAG;RSEQ=GTTAACATTATTAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:1,0:25,0:25,1:0.0385:1,0:39:0:32:0:1:0:60:2:0.0435:0:1 1/0:13:7:7,0:6,0:6,7:0.5385:0,0:21.1:1:29.9:1:1:0:60:14:0.5833:0:1.1 +10 18471920 . G T 33 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6823;LSEQ=AATAGTATACAAATTGAATT;RSEQ=TAACATCTTTTTTTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:0,3:186,84:270,3:0.011:2,0:13:1:21:1:0.0316:0:60:2:0.0078:0:2.7 0/0:266:2:0,2:185,79:264,2:0.0075:2,0:23:1:13:0:0.09193:0:50:0:0:0:6.5 +10 18471923 . A G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.94541;LSEQ=AGTATACAAATTGAATTGTA;RSEQ=CATCTTTTTTTTTTTAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:10:5,5:190,88:278,10:0.0344:2,2:27.9:1:31.1:1:0.30105:2.15282:60:9:0.0317:0:2 0/1:275:135:98,37:78,35:113,135:0.4909:2,2:22.1:1:30.4:1:0.57569:1.19:59.6:18.286:0.4848:0:2 +10 18471927 . CT C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.66521;SOR=0.85105;LSEQ=TACAAATTGAATTGTAACAT;RSEQ=TTTTTTTTTTAATTAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:30:19,11:179,92:271,30:0.099:2,2:26:1:32:1:0.8398:1.12597:58.9:60:0.1014:0.0132:0.1 0/1:269:23:14,9:167,74:241,23:0.0855:2,2:26.3:1:30.7:1:0.48123:1.44864:59.1:46:0.0868:0:0.6 +10 18471961 . T G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=41.86894;LSEQ=TTAGGAGAAGCAGAGGGGCA;RSEQ=TGTGGTTGAGAGATTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:18:10,8:251,195:446,18:0.0388:2,2:20.8:1:32.4:1:1:1.02969:59.4:36:0.0398:0:1.8 1/0:480:302:172,130:103,73:176,302:0.6292:2,2:25.1:1:31:1:0.77387:1.06625:59.6:36.75:0.6269:0:1.6 +10 18472087 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21201;SOR=Inf;LSEQ=TCATCTGTAAAACGCAGATC;RSEQ=CAGTATCAACCCACACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:17,116:133,0:0:2,0:22.9:1:31.4:1:1:0:60:65.5:1:0:0.1 0/1:114:2:1,1:11,101:112,2:0.0175:2,2:30.5:1:27.5:1:0.20028:8.84:60:4:0.018:0:1 +10 19229312 . CA TG 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=ATGTCTTTTGCATCTGGCTT;RSEQ=TTTACTTAGTATAATGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:37,0:37,0:0:1,0:25.7:1:33.1:1:1:0:60:74:1:0:0 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:21.2:1:32:1:1:0:60:10:0.4167:0.0833:1 +10 19229394 . A G 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTTTTTATTGCCAAATAGT;RSEQ=TTCCATTGTGTGTGTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:111,9:120,0:0:2,0:23.3:1:28.3:1:1:0:60:39:1:0:0.1 0/1:102:26:24,2:71,5:76,26:0.2549:2,2:24:1:32.1:1:1:1.18128:60:52:0.2574:0:1 +10 19229559 . G A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62539;SOR=2.7218;LSEQ=TCTGACCCTGAACTCCACTG;RSEQ=AAGCAATTGCACTGTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:1:1,0:84,136:220,1:0.0045:2,0:1:0:27:0:0.38462:0:60:2:0.0046:0:1 0/1:245:3:2,1:101,141:242,3:0.0122:2,2:14.3:1:28:1:0.5741:2.78:60:6:0.0125:0:1 +10 19229606 . C T 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGAGTATACATCAACTCT;RSEQ=GACTGGCACCACTGGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:79,92:171,0:0:2,0:24.2:1:30.8:1:1:0:60:56:1:0:0.1 0/1:198:59:28,31:66,73:139,59:0.298:2,2:26.7:1:30.3:1:1:1.00097:50.9:118:0.298:0:2.6 +10 19229638 . G A 174 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=68.42517;LSEQ=CTGGAAGTTTGTGCACATTC;RSEQ=TTTTTTCATGAATTACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:1,0:88,78:166,1:0.006:2,0:2:0:27:0:1:0:60:2:0.0061:0:1 0/1:201:59:32,27:71,71:142,59:0.2935:2,2:22.5:1:29.6:1:0.64317:1.18:42.5:58:0.2915:0:3.3 +10 19229645 . C G 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGTGCACATTCGTTTTTT;RSEQ=ATGAATTACAGGATCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:90,75:165,0:0:2,0:24.6:1:32.2:1:1:0:60:164:0.9939:0:0.1 0/1:226:68:36,32:79,79:158,68:0.3009:2,2:20.5:1:30.8:1:0.77197:1.12:44.9:67:0.2991:0:3.1 +10 19229675 . C G 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGATCCAAATGTCAAACTA;RSEQ=CAAATGGGTGAGACACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:113,89:202,0:0:2,0:25.6:1:31.5:1:1:0:60:66.333:1:0:0.1 0/1:276:79:42,37:108,89:197,79:0.2862:2,2:26.3:1:31:1:0.89373:1.06875:50.5:78:0.2836:0:2.4 +10 19229823 . C G 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCACAGCAGCCACCGATG;RSEQ=TAGTGCTGGAGACCGTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:125,125:250,0:0:2,0:23.9:1:32.6:1:1:0:60:61.5:1:0:0.1 0/1:322:75:41,34:112,134:246,75:0.2329:2,2:22.2:1:29.8:1:0.18736:1.44:60:17.75:0.2247:0:1.2 +10 19229864 . GC AT 70 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01213;SOR=0;LSEQ=AGACCAATAATGCTGTTTCT;RSEQ=ATCATCTTCCAACTTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:5:2,3:101,136:237,5:0.0207:2,2:6.4:1:30.4:1:1:1.11351:60:10:0.0209:0.0124:0.8 0/0:340:0:0,0:152,188:340,0:0:2,0:24.4:1:31.2:1:1:0:59.9:67:1:0:0.3 +10 19229929 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18483;SOR=0;LSEQ=CACAGGAAAAGCCACCAGTT;RSEQ=CTTGAGTCACTCAGCAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:48,133:181,2:0.0109:2,2:11.5:1:31:1:0.4649:2.75:60:4:0.011:0:1.5 0/0:242:0:0,0:87,155:242,0:0:2,0:41:0:16:0:1:0:42:0:0:0:1 +10 19229941 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCAGTTACTTGAGTCACT;RSEQ=AGCAACACTGGTCACTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:29,115:144,0:0:2,0:24.3:1:32.8:1:1:0:59.7:288:1:0:0.2 0/1:194:28:8,20:51,114:165,28:0.1443:2,2:21.8:1:27.6:1:1:1.1178:57.5:56:0.1451:0:1.1 +10 19229961 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=CAGCAACACTGGTCACTTTT;RSEQ=GAAAGAATATTAAAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:7,73:80,0:0:2,0:23.8:1:32.2:1:1:0:59.5:79:0.9875:0:0.1 0/1:90:2:1,1:16,72:88,2:0.0222:2,2:32.5:1:28.5:1:0.34382:4.40:50.5:4:0.0225:0:1 +10 19229962 . G GA 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAACACTGGTCACTTTTG;RSEQ=AAAGAATATTAAAAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:7,71:78,0:0:2,0:23.7:1:32.6:1:1:0:59.5:77:1:0:0.1 0/1:87:31:5,26:10,46:56,31:0.3563:2,2:29.1:1:29.7:1:1:1.12882:54.8:62:0.3605:0.0575:0.7 +10 19229980 . G GA 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03113;SOR=Inf;LSEQ=TGGAAAGAATATTAAAAAGA;RSEQ=AAAAAAAATCTGTTAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:3,52:55,0:0:2,0:17.8:1:32.5:1:1:0:59.3:110:1:0:0.1 0/1:67:6:0,6:10,51:61,6:0.0896:2,0:25:1:31.8:1:0.58043:0:57.2:12:0.0952:0:0.2 +10 19230013 . GTATA G 72 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=28;MSI=16.000;MSILEN=2;SSF=0.18361;SOR=0.16646;LSEQ=TTAAAAATATATGTGTGTAT;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:0,5:0,14:14,5:0.2381:1,0:35:1:31.4:1:1:0:55.4:10:0.2381:0:0.2 0/1:21:1:0,1:0,20:20,1:0.0476:1,0:41:0:24:0:1:0:40:2:0.0476:0:3 +10 19230027 . ATATATATATATATATATACATATA G 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.0022;SOR=Inf;LSEQ=GTGTATGTATATATATATAT;RSEQ=CATACACACAATGGAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:14,0:0:1,0:28:1:31.7:1:1:0:58.1:28:1:0:0.4 1/0:15:8:0,8:0,7:7,8:0.5333:0,0:24.5:1:31.2:1:1:0:52.9:16:0.5333:0.1333:0.3 +10 19230044 . TAC T 57 v3;MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=17.000;MSILEN=2;SSF=0.14783;SOR=6.04934;LSEQ=TATATATATATATATATATA;RSEQ=ATATACATACACACAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:0,13:13,1:0.0714:1,0:12:0:33:0:1:0:56:2:0.0714:0:1 0/1:12:4:0,4:0,2:2,4:0.3333:0,0:20.8:1:28.6:1:1:0:56.8:8:0.6667:0.0833:0.5 +10 20006337 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGCAGATGGTGATGAAGAA;RSEQ=ACAGTGTATAATTTGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 20007127 . A C 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=3.000;MSILEN=3;SSF=0.01806;SOR=0;LSEQ=AAGGAAAAAGAAGACGAAGA;RSEQ=GAAGAGGAAGAAGAAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:5,3:3,2:5,8:0.6154:2,2:11.5:1:30.8:1:1:1.10:57.9:16:0.6154:0:1 0/0:6:0:0,0:3,3:6,0:0:2,0:25.8:1:28.5:1:1:0:60:12:1:0:0 +10 21399813 . C G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49242;SOR=1.96262;LSEQ=GTCCAATTAAAGTAACACTG;RSEQ=CAACTTTGAAAATGTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:4,3:4,3:7,7:0.5:2,2:32.1:1:29.9:1:1:1:43.6:6:0.4615:0:1.4 1/0:24:16:8,8:4,4:8,16:0.6667:2,2:32.5:1:30.6:1:1:1:41.1:32:0.6667:0:1.3 +10 21399869 . G A 56 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46625;LSEQ=AAAATCACAAGCATTCCTAT;RSEQ=CAGCAATAACAGACAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:2,4:6,4:0.4:2,2:16.5:1:24.8:1:1:1.86:43.5:3:0.3333:0:1.8 1/0:8:4:1,3:0,4:4,4:0.5:0,2:15.8:1:28.3:1:1:0:42.8:8:0.5:0:2 +10 21401670 . TA T 97 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=1.12028;LSEQ=CCCTAGAACTTAAAGTATAA;RSEQ=AAAAAAAAAAAAGAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:3,1:4,4:0.4444:2,0:16.5:1:33:0:1:0:52:8:0.4444:0:0 0/1:19:9:5,4:6,2:8,9:0.4737:2,2:27.9:1:30.7:1:0.61991:2.27808:54.9:18:0.5:0:0.2 +10 21401731 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49787;SOR=Inf;LSEQ=TACAGCCAGTGATTTCCCTT;RSEQ=GGGGCTTTGAAATTACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:20,11:31,0:0:2,0:27.2:1:31.1:1:1:0:60:14.5:1:0:0.6 0/1:38:2:1,1:19,17:36,2:0.0526:2,2:34:1:29.5:1:1:1.11437:60:4:0.0556:0:4 +10 21401765 . T C 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00056;SOR=0.15241;LSEQ=TACACCACCCAGTCTTACAG;RSEQ=TGAAGTGTGGTTCAGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:22:13,9:8,5:13,22:0.6286:2,2:26.5:1:32.8:1:1:1.10447:60:21:0.6176:0:1.1 0/1:35:7:3,4:15,13:28,7:0.2:2,2:31.6:1:30.3:1:0.69057:1.51957:60:14:0.2:0:1 +10 21401876 . A T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03285;SOR=Inf;LSEQ=ATGTGAAACTCTTAAGTGTA;RSEQ=CTGGAAAGTGATCTGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:14,19:33,0:0:2,0:26.2:1:30.4:1:1:0:45.8:66:1:0:0 0/1:26:4:2,2:7,15:22,4:0.1538:2,2:35.5:1:30.3:1:0.59064:2.08:40:8:0.1538:0:1 +10 21402110 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49126;SOR=Inf;LSEQ=AGGAAACTGAAGAAAAAGTG;RSEQ=CAGTGAAGAAATCTATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:26,0:0:2,0:21.8:1:32.2:1:1:0:59.1:52:1:0:0 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:34.5:1:28.5:1:1:1.34838:60:4:0.0769:0:1.5 +10 22434438 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49462;SOR=Inf;LSEQ=CACCTGGCATTTACAGAAAA;RSEQ=GGCCTCTGAAATCAGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:28,19:47,0:0:2,0:19.1:1:30.7:1:1:0:51.7:94:1:0:0.1 0/1:47:2:1,1:27,18:45,2:0.0426:2,2:33:1:30:1:1:1.48675:44.5:4:0.0435:0:2.5 +10 22434503 . C G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51326;SOR=0;LSEQ=TCTGGAGTTAGGCGTCATGG;RSEQ=TTCTCCCCTTTCTAGGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:33,35:68,2:0.0286:2,2:44.5:1:32.5:1:1:1.06:49:4:0.0286:0:1 0/0:48:0:0,0:20,27:47,0:0:2,0:24.9:1:30.9:1:1:0:55.7:94:0.9792:0:0.1 +10 26579975 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23259;SOR=0;LSEQ=TGCAGTGCAAACTCTTCTTC;RSEQ=TGGGAAATCAGAGAGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:109,46:155,2:0.0127:2,2:9:0:33:1:0.51045:2.35497:60:4:0.0128:0:2.5 0/0:168:0:0,0:108,60:168,0:0:2,0:26.7:1:29.1:1:1:0:60:32.6:1:0:0.2 +10 26580036 . T G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03685;SOR=1.93093;LSEQ=GAGTTGGCCAAAGCCATTCA;RSEQ=CTGGACAGGGTCAGAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:19:10,9:102,115:217,19:0.0805:2,2:24.7:1:32.6:1:0.6422:1.25:60:38:0.0819:0:1.2 0/1:221:32:15,17:90,99:189,32:0.1448:2,2:27.7:1:32.1:1:1:1.03017:60:64:0.1475:0:1.2 +10 26580105 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22923;SOR=Inf;LSEQ=ATGCAAAAGTTTAAACCCAA;RSEQ=TCCAGACTGGTCCAAAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:40,89:129,0:0:2,0:23.6:1:32.6:1:1:0:60:63.5:1:0:0.1 0/1:119:2:1,1:37,80:117,2:0.0168:2,2:14:1:27.5:1:0.53853:2.15:60:4:0.0168:0:1.5 +10 28301440 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49745;SOR=0;LSEQ=AACAATTCTTCTCTGGGTCT;RSEQ=GTCACTGGATTGAAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:44,32:76,2:0.0256:2,2:26.5:1:32.5:1:1:1.36929:60:4:0.0256:0:1 0/0:72:0:0,0:42,30:72,0:0:2,0:25.8:1:29.1:1:1:0:60:71:1:0:0.2 +10 29107838 . C T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTGCCAGCCCAAGGAG;RSEQ=GTTTCTCTTACAGTTTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:0,14:1:0,1:24.7:1:29.9:1:1:0:60:28:1:0:1.7 1/1:6:6:6,0:0,0:0,6:1:0,0:25.8:1:26.3:1:1:0:60:12:1:0:2.3 +10 29107866 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAGTTTACACAAGAAGT;RSEQ=GTTAAAAAACAAAGAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:20,0:0,0:0,20:1:0,1:23.2:1:32.9:1:1:0:60:40:1:0:2 1/1:10:10:10,0:0,0:0,10:1:0,0:23:1:28.3:1:1:0:60:4:1:0:2.2 +10 29107904 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13326;SOR=Inf;LSEQ=GAGCTGATCTGATATCCAAT;RSEQ=AAGTCACATTTGATTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:60,0:0:1,0:22.2:1:29.3:1:1:0:59.5:120:1:0:1.3 0/1:35:2:2,0:32,1:33,2:0.0571:1,0:34:0:33:0:1:0:60:4:0.0571:0:2 +10 29107937 . C G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTACTTCCTTGTGAAAAT;RSEQ=CTTACTCAATAGGCTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:100:97,3:0,0:0,100:1:0,1:26.7:1:33.1:1:1:0:59.7:200:1:0:1.1 1/1:77:77:72,5:0,0:0,77:1:0,2:23.2:1:31.7:1:1:0:60:76:1:0:1.1 +10 29108055 . A T 278 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00624;LSEQ=AACATGTTAAAATACCTGTT;RSEQ=TGGTTTTAGGGGATTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:564:562:267,295:2,0:2,562:0.9965:0,2:27:1:30.5:1:0.22704:0:59.9:92.667:0.9964:0:1.1 1/0:475:302:149,153:90,83:173,302:0.6358:2,2:26.7:1:29.6:1:0.63361:1.11319:60:74.5:0.6368:0:1.1 +10 29108209 . C G 185 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=AAAATTGGTATAAGTAGAGA;RSEQ=ATAATTTGGGCCAAGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:51:0,51:0,0:0,51:1:0,1:24.6:1:32.7:1:1:0:60:102:1:0:1 1/0:35:24:0,24:0,11:11,24:0.6857:0,1:23.8:1:30.9:1:1:0:60:48:0.6857:0:1.1 +10 29109847 . C CAG 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAACTTCTATTTTAGAGT;RSEQ=GGGGTGTACGTGCAGGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:31.3:1:1:0:60:4:1:0:0 +10 29188056 . T C 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.68427;SOR=0.60896;LSEQ=AACCCAGGTACCTTTCTCTT;RSEQ=GGCTTCTTTCTTTTTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:4,2:5,0:5,6:0.5455:0,2:18.5:1:32.5:1:0.45455:0:25.2:12:0.5455:0:1.2 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:17.2:1:31.6:1:1:0:27.6:10:0.4167:0:1.2 +10 29188110 . G A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GCGTTTCAGGAAGCTGTCTC;RSEQ=GCTCTTAGAGTGCTTAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:41,5:46,0:0:2,0:25.3:1:31.1:1:1:0:31:92:1:0:0.2 0/1:31:11:9,2:17,3:20,11:0.3548:2,2:25.5:1:29.6:1:1:1.2497:22.7:22:0.3548:0:1 +10 29188387 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAACATATATCGGGTGCC;RSEQ=CTCCTCTTTCTCTTTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:0,11:1:0,2:19:1:30.3:1:1:0:37.5:10:1:0:1.1 1/1:20:20:8,12:0,0:0,20:1:0,2:18.3:1:28.2:1:1:0:41.4:19:1:0:1.1 +10 29965811 . A T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.10738;LSEQ=GACCCTTGGGTCTTGGAAAC;RSEQ=CCTGTGGAGATTTAGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:149:78,71:99,102:201,149:0.4257:2,2:23.9:1:30.8:1:0.58996:1.13:60:73.5:0.4224:0:1.1 1/0:341:208:105,103:65,68:133,208:0.61:2,2:26.4:1:29.2:1:0.82449:1.07:60:103:0.6077:0:1.2 +10 29965818 . G T 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGTCTTGGAAACACCTGTG;RSEQ=AGATTTAGCCTTGGTAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:166,179:345,0:0:2,0:25.8:1:31.3:1:1:0:60:42.125:1:0:0.5 0/1:349:26:11,15:160,163:323,26:0.0745:2,2:23.7:1:27.8:1:0.54388:1.33742:60:52:0.0756:0:1.2 +10 29965868 . T A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32798;SOR=3.76821;LSEQ=TCCCAGGTCATCAGAACCCA;RSEQ=CTGCCTCCTAGACTAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:1:1,0:95,177:272,1:0.0037:2,0:1:0:26:0:0.35165:0:60:2:0.0037:0:1 0/1:219:3:2,1:84,132:216,3:0.0137:2,2:10.3:1:26:1:0.5628:3.13:59:6:0.014:0:4 +10 30692028 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00606;SOR=Inf;LSEQ=AAGTGCAGGATTACAGGCGT;RSEQ=AGCCAGCATGCCAGGCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:8,0:0:0,0:18.9:1:29.6:1:1:0:59:7:1:0:0.9 1/1:3:3:3,0:0,0:0,3:1:0,0:15:1:27.7:1:1:0:60:6:1:0:2 +10 30692068 . C A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTGTATTGATATAT;RSEQ=TCACATATGGTTATCTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:25,0:0,0:0,25:1:0,1:23.4:1:29.4:1:1:0:58.5:50:1:0:1 1/1:16:16:16,0:0,0:0,16:1:0,1:19.3:1:28.6:1:1:0:60:32:1:0:1.3 +10 30692132 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22517;SOR=Inf;LSEQ=GTTTTCACAACTGGATGGTG;RSEQ=GTACATGGCAAAGGTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:74,24:98,0:0:2,0:21.6:1:30.5:1:1:0:59.5:31.667:1:0:0.3 0/1:89:2:1,1:70,17:87,2:0.0225:2,2:20.5:1:27:1:0.36542:4.03012:60:4:0.0227:0:1 +10 30692136 . C T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49756;SOR=Inf;LSEQ=TCACAACTGGATGGTGGGTA;RSEQ=ATGGCAAAGGTGTAATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:78,25:103,0:0:2,0:22.3:1:31.7:1:1:0:59.5:50.5:1:0:0.3 0/1:103:2:1,1:78,23:101,2:0.0194:2,2:10:1:23:1:0.41348:3.34106:60:4:0.0196:0:1.5 +10 30692361 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20797;SOR=Inf;LSEQ=TTTCTCAATGGTCATGGGCC;RSEQ=AGTCTTACGCAGCTTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:113,119:232,0:0:2,0:26.2:1:31.4:1:1:0:59.8:32.143:1:0:0.2 0/1:195:2:1,1:89,104:193,2:0.0103:2,2:19.5:1:29.5:1:1:1.17:56.5:4:0.0105:0:1 +10 30692382 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09128;SOR=Inf;LSEQ=AGTCTTACGCAGCTTGGAGG;RSEQ=CAGCCGCATGGAGACCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:108,102:210,0:0:2,0:25:1:31:1:1:0:59.8:20:1:0:0.2 0/1:173:3:1,2:86,84:170,3:0.0173:2,2:25:1:29:1:0.62063:2.03944:60:6:0.0175:0:1 +10 30692387 . C G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=TACGCAGCTTGGAGGCCAGC;RSEQ=GCATGGAGACCGCAACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:110,93:203,0:0:2,0:25:1:30.2:1:1:0:59.8:32.833:1:0:0.2 0/1:171:12:7,5:82,77:159,12:0.0702:2,2:25.5:1:27.4:1:0.76857:1.31:60:11:0.0647:0:1.3 +10 30692531 . A T 44 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20255;SOR=4.31249;LSEQ=CACAGCACTGCTCCTCACAC;RSEQ=CCTCCAGCATCCAGTAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:1:0,1:126,153:279,1:0.0035:2,0:1:0:26:0:1:0:60:2:0.0037:0:1 0/1:264:4:0,4:136,123:259,4:0.0152:2,0:6.8:1:22:1:0.05304:0:60:3:0.0117:0:1 +10 30692597 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=TCTCCCTTTGCACGCACTGG;RSEQ=AGTAGGCGCAGTGCACGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:66,120:186,0:0:2,0:24:1:30.5:1:1:0:59.6:45.5:1:0:0.1 0/1:187:2:1,1:77,108:185,2:0.0107:2,2:45:1:28.5:1:1:1.40:60:4:0.0112:0:1 +10 30692599 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=TCCCTTTGCACGCACTGGAA;RSEQ=TAGGCGCAGTGCACGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:63,117:180,0:0:2,0:23.8:1:32.2:1:1:0:59.6:59:1:0:0.1 0/1:181:2:1,1:73,106:179,2:0.011:2,2:11.5:1:29.5:1:1:1.45:60:4:0.0112:0:1.5 +10 30692610 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0499;SOR=Inf;LSEQ=GCACTGGAAGTAGGCGCAGT;RSEQ=CACGCAGCGCTACTCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:50,108:158,0:0:2,0:21.6:1:32:1:1:0:60:51.667:1:0:0.1 0/1:144:4:3,1:50,90:140,4:0.0278:2,2:12.3:1:25.3:1:0.14114:5.34:60:8:0.028:0:1.3 +10 30692614 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22256;SOR=Inf;LSEQ=TGGAAGTAGGCGCAGTGCAC;RSEQ=CAGCGCTACTCCAAGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:44,101:145,0:0:2,0:22:1:31.3:1:1:0:60:47.333:1:0:0.1 0/1:130:2:1,1:46,82:128,2:0.0154:2,2:14:1:28.5:1:1:1.77:60:4:0.0156:0:1 +10 30692623 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22227;SOR=Inf;LSEQ=GCGCAGTGCACGCAGCGCTA;RSEQ=TCCAAGGGGAGCAAGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:37,88:125,0:0:2,0:22.4:1:32.8:1:1:0:60:124:1:0:0.1 0/1:112:2:1,1:36,74:110,2:0.0179:2,2:10.5:1:27.5:1:1:2.04:60:4:0.018:0:2 +10 30692649 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18366;SOR=Inf;LSEQ=GGGGAGCAAGCTCTGCAGGA;RSEQ=GCGCTGATCCCCTGGCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:21,61:82,0:0:2,0:26:1:30.3:1:1:0:60:81:1:0:0.1 0/1:62:2:0,2:20,40:60,2:0.0323:2,0:18.5:1:29:1:1:0:60:4:0.0323:0:2 +10 30692681 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2099;SOR=Inf;LSEQ=CTGGCGTCTGCGGGTCCTCG;RSEQ=GCCTTCGCAGCATAGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:23,45:68,0:0:2,0:23.4:1:31.1:1:1:0:60:67:1:0:0.2 0/1:58:2:1,1:21,35:56,2:0.0345:2,2:32.5:1:29.5:1:1:1.65:60:4:0.0345:0:2 +10 30692717 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21957;SOR=0;LSEQ=CAGCTCCACACTCGGGCAGC;RSEQ=CACAGGCAGGGCGGGAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:17,30:47,2:0.0408:2,2:43:1:31:1:1:1.74:60:4:0.0426:0:1 0/0:55:0:0,0:23,32:55,0:0:2,0:26.9:1:30.2:1:1:0:60:54:1:0:0.2 +10 31902215 . C A 31 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50171;SOR=0;LSEQ=AGGCCTGGGAAGTACACTGT;RSEQ=ATTAACTGTTACATTGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:38,19:57,2:0.0339:2,2:7:0:31.5:1:1:1.9749:60:4:0.0345:0:1.5 0/0:47:0:0,0:29,18:47,0:0:2,0:27.2:1:31.1:1:1:0:60:94:1:0:0.2 +10 31902242 . T C 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.11572;LSEQ=TGTTACATTGCCATGGCCCC;RSEQ=GCTGTTGCTGTTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:40,27:67,2:0.029:2,2:11:1:31:1:1:1.47282:60:4:0.0299:0:1 0/1:62:2:1,1:36,24:60,2:0.0323:2,2:20.5:1:28:1:1:1.48993:60:4:0.0323:0:1 +10 31902253 . TTGC T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.11993;SOR=0;LSEQ=CATGGCCCCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGTAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:4:2,2:37,30:67,4:0.0563:2,2:33.5:1:30.8:1:1:1.22967:60:8:0.058:0:0.3 0/0:68:0:0,0:35,33:68,0:0:2,0:26.5:1:30.1:1:1:0:58.9:136:1:0:0.2 +10 31902801 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGTTTTGGCTGGTTCCA;RSEQ=TAGGGAGAGATTTTGTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 34717415 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10769;SOR=Inf;LSEQ=ATAGTGAGATCCCATCTCTA;RSEQ=AAGAAAAAAGAGGCCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:43,1:44,0:0:1,0:23:1:30.8:1:1:0:59.5:43:1:0:0.2 0/1:22:2:2,0:20,0:20,2:0.0909:1,0:25:1:33:0:1:0:60:4:0.0909:0:1 +10 34717559 . C A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.67014;LSEQ=TTCACTGTTCAGAAAGAAGA;RSEQ=GACAACAGCTGTGTTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:187:119,68:123,78:201,187:0.4807:2,2:25.3:1:31:1:0.67509:1.11:60:186:0.4806:0:1.8 1/0:351:250:157,93:59,42:101,250:0.7123:2,2:25.1:1:29.7:1:0.46851:1.20:59.9:61.5:0.711:0:1.8 +10 34717596 . G C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.85309;LSEQ=TCTCTGGAGTAAAGAGGTTA;RSEQ=AGCCCTGCCAATGGGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:236:126,110:134,124:258,236:0.4777:2,2:26.4:1:32.3:1:0.78689:1.06:60:117:0.4776:0:1.7 1/0:426:268:141,127:81,75:156,268:0.6291:2,2:27.1:1:31.1:1:0.91988:1.03:60:133:0.6318:0:1.8 +10 34717713 . T C 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50442;SOR=0;LSEQ=TTTTTTCCTACATTATAAAC;RSEQ=AAAGGAAATCATGCAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:13,111:124,2:0.0159:2,2:17.5:1:26.5:1:0.21067:8.26:60:4:0.016:0:1 0/0:100:0:0,0:22,78:100,0:0:2,0:21.4:1:27.7:1:1:0:60:99:1:0:0.4 +10 34717740 . G A 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04871;SOR=2.10021;LSEQ=AATCATGCAGAAACACTAAC;RSEQ=CTAAATTTTATGTAAGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:36:0,36:0,36:36,36:0.4932:1,1:26.9:1:30.4:1:1:0:60:72:0.5:0:1 1/0:55:37:3,34:0,18:18,37:0.6727:1,2:26.9:1:28.7:1:0.54305:0:60:74:0.6727:0:1.1 +10 36853842 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATGGAAGTTGTAGCTGAAAC;RSEQ=TGTCCTCTGAGAGAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1:0,1:24.3:1:30.7:1:1:0:60:26:1:0:2.5 0/1:16:2:2,0:14,0:14,2:0.125:1,0:7.5:1:31:0:1:0:60:4:0.125:0:2 +10 36853858 . G C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAACGTGTCCTCTGAGAGAG;RSEQ=CTGGCGCTCTCTCCGCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:24,0:0,0:0,24:1:0,1:21:1:32.7:1:1:0:60:48:1:0:2.4 0/1:22:3:3,0:19,0:19,3:0.1364:1,0:10.7:1:33.3:1:1:0:60:6:0.15:0:2.3 +10 36853878 . T C 167 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGGCGCTCTCTCCGCCCG;RSEQ=CCTGGTACACCCTTCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:36,0:0,0:0,36:1:0,1:24.4:1:32.4:1:1:0:60:35:1:0:1.9 0/1:37:10:8,2:27,0:27,10:0.2703:1,2:15.1:1:32.4:1:0.06757:0:60:20:0.2857:0:1.6 +10 36853977 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51038;SOR=Inf;LSEQ=TGCACAGGGATCCTGGCTGC;RSEQ=CCCTCCATAATTTATGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:83,63:146,0:0:2,0:24:1:30.6:1:1:0:60:35.5:1:0:0.5 0/1:199:2:1,1:125,72:197,2:0.0101:2,2:21:1:30.5:1:1:1.73098:60:4:0.0102:0:2 +10 36854039 . T G 230 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00295;LSEQ=TGCTTCCGTTACCTTGTAAC;RSEQ=GCTTAGAATCTACTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:206:205:100,105:0,0:0,205:0.9951:0,2:25.8:1:30:1:1:0:59.6:19.5:1:0:1.3 0/1:400:150:72,78:122,128:250,150:0.375:2,2:27:1:29.4:1:0.91784:1.03248:59.7:74:0.3785:0:1.2 +10 36854068 . T C 34 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1119;SOR=0;LSEQ=TCTACTTATTTAACACACAG;RSEQ=CATCTTGATGCCGATGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:86,101:187,2:0.0106:2,0:5:0:34:0:0.21547:0:46.5:4:0.0111:0:2 0/0:375:0:0,0:175,200:375,0:0:2,0:28.1:1:28.1:1:1:0:59.2:25.786:1:0:0.7 +10 36854110 . C CTT 141 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0;SOR=0.1597;LSEQ=CTCCACTAGTTACTTACCTT;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:28:14,14:22,21:43,28:0.3333:2,2:21.4:1:29.5:1:1:1.04696:56:13:0.3333:0.0833:2 0/1:150:11:4,7:48,69:117,11:0.0733:2,2:18.8:1:28.9:1:1:1.21555:53.1:22:0.0853:0.02:2.5 +10 36854169 . T C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCCCGGCTGGAGTGCAGTGG;RSEQ=GCAATCTCGACTCACTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:0,18:0,0:0,18:1:0,1:33.5:1:28.4:1:1:0:35.4:17:1:0:2.3 1/1:18:18:0,18:0,0:0,18:1:0,1:38.5:1:27.1:1:1:0:43.5:8:1:0:1.6 +10 36854193 . A C 136 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTCGACTCACTGCAACCA;RSEQ=CCCCTCCCAGGTTTAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:0,19:1:0,1:32.1:1:32.1:1:1:0:38.3:38:1:0:2.2 0/1:19:4:0,4:0,15:15,4:0.2105:1,0:25:1:31.3:1:1:0:41.8:8:0.2857:0:1.8 +10 36854328 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATTGGCCAGGCTGGTCA;RSEQ=GAACTCCTGACCTAGTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:9:1:31:0:1:0:32.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 37564987 . T C 62 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACAGGGTCCTCATTAGAAGT;RSEQ=GTTAATTGAACTCATTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:18:1:31:1:1:0:60:8:1:0:1 1/0:2:1:1,0:0,1:1,1:0.5:0,0:28:0:33:0:1:0:60:2:0.5:0:1 +10 37565327 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGAGGAGGTCTAGGCCTC;RSEQ=GAGGTTTTGGAGAGTCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:25:1:30.5:1:1:0:24.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 38372664 . A G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.78657;LSEQ=TTCCTCACAGTGTCAGTGCT;RSEQ=TATGATTGTTTAATTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:19:8,11:53,70:123,19:0.1338:2,2:22.5:1:32.2:1:1:1.04079:46.8:38:0.1367:0:1 0/1:133:63:28,35:33,37:70,63:0.4737:2,2:23.8:1:30.6:1:0.86185:1.11395:42:126:0.4773:0:1.1 +10 38378777 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAAGATTCCAAGTTGTGG;RSEQ=CCGTCCTGCCCACATTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:38,4:0,0:0,42:1:0,2:24.1:1:31:1:1:0:56.3:20:1:0:1.1 1/1:43:43:38,5:0,0:0,43:1:0,2:24.3:1:30.6:1:1:0:54.3:42:1:0:1.4 +10 38378785 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49524;SOR=Inf;LSEQ=TCCAAGTTGTGGACCGTCCT;RSEQ=CCCACATTCTGCATCATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:46,4:50,0:0:2,0:22.9:1:33.2:1:1:0:56:100:1:0:0.9 0/1:52:2:1,1:43,7:50,2:0.0385:2,2:11:1:27.5:1:0.28658:5.81258:36.5:4:0.0385:0:2.5 +10 38378814 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.25896;LSEQ=CTGCATCATGATGTCAAAAT;RSEQ=GCATCTGATGTTCTTTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:7:6,1:65,15:80,7:0.0805:2,2:29:1:32.1:1:1:1.38:50.9:14:0.0824:0:1.4 0/1:109:46:38,8:44,19:63,46:0.422:2,2:20.8:1:31.9:1:0.1777:2.04:56.6:92:0.422:0:1.4 +10 38378828 . T G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50907;SOR=Inf;LSEQ=CAAAATAGCATCTGATGTTC;RSEQ=TTGCATTTTCATTGAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:82,24:106,0:0:2,0:25:1:32:1:1:0:57.7:212:1:0:0.4 0/1:143:2:1,1:98,43:141,2:0.014:2,2:9:0:32.5:1:0.52221:2.26452:60:4:0.014:0:1.5 +10 38378831 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50944;SOR=Inf;LSEQ=AATAGCATCTGATGTTCTTT;RSEQ=CATTTTCATTGAAGTAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:83,27:110,0:0:2,0:25.5:1:32.8:1:1:0:57.8:109:1:0:0.4 0/1:149:2:2,0:100,47:147,2:0.0134:2,0:27:1:29:0:1:0:52:4:0.0135:0:1.5 +10 38378917 . A AT 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.54813;SOR=0.74599;LSEQ=AGTGATTAAAGGATTGTGTG;RSEQ=TTTTTTTTTTGGCATTCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:13:6,7:103,104:207,13:0.0591:2,2:31.9:1:29.9:1:1:1.15469:55.2:12:0.0553:0:0.4 0/1:313:14:7,7:147,149:296,14:0.0447:2,2:27.4:1:28.6:1:1:1.01:57.9:28:0.0465:0:0.1 +10 38379011 . C T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.03871;LSEQ=TTGATAAAGTTGTTAGTTTA;RSEQ=GTAAAGTCTTGAAATAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:6:0,6:6,63:69,6:0.08:2,0:38.8:1:31.8:1:1:0:52.5:12:0.0811:0:1.2 1/0:83:46:3,43:6,31:37,46:0.5542:2,2:22.8:1:29.5:1:0.17829:2.74012:49.1:92:0.5542:0:1 +10 38379117 . G GT 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.52727;SOR=4.02871;LSEQ=TTACTTGTTTTTTATTCATA;RSEQ=TTTTTTTTTTTCACTAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:1,11:12,1:0.0714:2,0:25:0:32:0:1:0:44:2:0.0714:0:0 0/1:8:2:0,2:0,5:5,2:0.25:0,0:44.5:1:30.5:1:1:0:38:4:0.2857:0:0 +10 38539531 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5045;SOR=Inf;LSEQ=GAGTTCCTCAATCATTTCCC;RSEQ=GGGAGTGAGCCTTTTGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:0,15:15,0:0:1,0:14:1:31.3:1:1:0:21.1:30:1:0:0.1 0/1:22:2:0,2:1,19:20,2:0.0909:1,0:17:1:29:1:1:0:21.5:4:0.0952:0:1.5 +10 38542415 . C T 96 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00425;SOR=9.83443;LSEQ=AACTTTAAATCTCCATGTCA;RSEQ=TTTGGTTACCTGAGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:32,0:32,2:0.0588:1,0:26.5:1:24:1:1:0:29.5:1:0.0303:0:2 0/1:23:9:9,0:14,0:14,9:0.3913:1,0:18.6:1:30.3:1:1:0:33.9:18:0.3913:0:1.2 +10 38542536 . G C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49761;SOR=0;LSEQ=ACTGCTAGTTTAGGTTGCAT;RSEQ=CATCCTGTGACTTGGCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:52,39:91,2:0.0215:2,2:11:1:33.5:1:1:1.32915:60:4:0.0215:0:1 0/0:88:0:0,0:42,43:85,0:0:2,0:11.8:1:30.4:1:1:0:22.1:84:0.9655:0:0.5 +10 38542588 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.01041;LSEQ=TAGTGCCCCTAATCATCCTC;RSEQ=TACCTCATTCTTATGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:19:10,9:100,107:207,19:0.0841:2,2:33.4:1:30.6:1:0.81234:1.19:21.9:38:0.0848:0:1.1 0/1:275:132:61,71:65,77:142,132:0.48:2,2:31.7:1:29.9:1:1:1.02:25.2:43:0.476:0:1.2 +10 38542638 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20599;SOR=0;LSEQ=ACGGTGAAGTTTCCCACACA;RSEQ=CATGTCCTCAGGGACCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:49,70:119,2:0.0165:2,2:19.5:1:32.5:1:1:1.42:21.5:4:0.0169:0:1 0/0:145:0:0,0:59,85:144,0:0:2,0:18.3:1:29:1:1:0:26.9:35:0.9929:0:0.5 +10 38743433 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49123;SOR=0;LSEQ=AGTGGTGCTAAAGCCATCAT;RSEQ=AGCAATGACATCATCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:15,12:27,2:0.069:2,2:25.5:1:28:1:1:1.24034:22:4:0.069:0:1 0/0:28:0:0,0:17,11:28,0:0:2,0:18.1:1:30.4:1:1:0:26:13:1:0:0.2 +10 38743615 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10853;SOR=0;LSEQ=AGCTCCATACTGAGTAGAAG;RSEQ=CTTTGGGCCAGAGTATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:3,1:8,11:19,4:0.1739:2,2:17:1:30.3:1:0.31677:3.88:31.3:8:0.1739:0:1 0/0:22:0:0,0:11,11:22,0:0:2,0:15.1:1:29.8:1:1:0:36:44:1:0:0.1 +10 38743659 . A G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09201;SOR=Inf;LSEQ=TGCCAGACACCACCTGTGTC;RSEQ=GTTCCTGTAGTGCCTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,19:34,0:0:2,0:36.9:1:31.3:1:1:0:28.8:33:1:0:0.2 0/1:29:3:2,1:13,13:26,3:0.1034:2,2:34.3:1:30.7:1:1:1.95:21.3:6:0.1034:0:1 +10 38744080 . G T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.148;SOR=0.28237;LSEQ=CTGACAGTCCGGTTATCCTG;RSEQ=TTGGGGTGACCCTGGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:6:2,4:19,22:41,6:0.1277:2,2:23.8:1:30.3:1:0.67795:1.70791:35.7:12:0.1333:0:1.2 0/1:51:2:0,2:27,22:49,2:0.0392:2,0:10:1:30.5:1:0.21647:0:44:4:0.0392:0:1 +10 38744437 . CC AA 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATGTGTGGGGTTGCGGGC;RSEQ=TGGGCTTTCAGGGCAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:32.5:1:33.5:1:1:0:41.5:4:1:0:0.5 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:26.5:1:31:0:1:2.45:24:4:0.3333:0:1.5 +10 39011138 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCATTCTAGGAGTTTGCT;RSEQ=TCCTTCAGACACAGCTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:20,2:0,0:0,22:1:0,2:11.5:1:25.9:1:1:0:26.5:21:1:0:1.1 1/1:11:11:11,0:0,0:0,11:1:0,0:9.2:1:24.8:1:1:0:28:22:1:0:1.2 +10 39011653 . TTTG T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TTAATTCCAGTCCTGCTTTT;RSEQ=TTGTTGTTGTTGTTGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:33:1:31:1:1:0:51.3:8:1:0:0.3 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26.5:1:28.5:1:1:0:31:4:0.6667:0:1.5 +10 39011707 . C A 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TTTTCCCCACTGTTTCCTCC;RSEQ=CCCCGATTTTTTTTTCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:17.3:1:30.7:1:1:0:52:6:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:21:0:30.5:1:1:0:31:4:0.6667:0:1.5 +10 39012293 . G T 31 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13843;SOR=0;LSEQ=TTATTTTCAGCCTTCTACTA;RSEQ=TCGAAAGCGGCCTCATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:80,53:133,2:0.0148:2,2:7:0:31.5:1:1:1.50467:21:4:0.0149:0:1.5 0/0:227:0:0,0:126,101:227,0:0:2,0:23.5:1:30.8:1:1:0:41:74.667:1:0:0.1 +10 39012324 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05252;SOR=0;LSEQ=CCTCATGAAGGGGAAGCCGA;RSEQ=GGTGCCGAGACCACAAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:3:1,2:86,94:180,3:0.0164:2,2:20:1:28.3:1:1:1.82399:29.3:6:0.0171:0:1 0/0:304:0:0,0:144,160:304,0:0:2,0:25.7:1:30.6:1:1:0:35.7:303:1:0:0.2 +10 39012451 . AT A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20588;SOR=0;LSEQ=TTTTTATAGTTTGTATTTTA;RSEQ=TATGGGAATAATTGCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:1,5:6,3:0.3333:2,0:21.3:1:33:1:1:0:36.7:6:0.3333:0:0 0/0:9:0:0,0:3,6:9,0:0:2,0:3.1:1:28.7:1:1:0:44.2:18:1:0:0.1 +10 39128837 . T A 58 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCAATGGAATCGAATGGA;RSEQ=TGTAATCAAATGGAATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:29:1:1:0:25.5:4:1:0:8 1/1:4:4:3,1:0,0:0,4:1:0,2:21.5:1:29:1:1:0:25.3:8:1:0:7.8 +10 39128840 . T C 61 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATGGAATCGAATGGATTG;RSEQ=AATCAAATGGAATGGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:30.5:1:1:0:25.5:4:1:0:8 1/1:4:4:3,1:0,0:0,4:1:0,2:23:1:30.8:1:1:0:25.3:8:1:0:7.8 +10 39128845 . A C 66 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=GAATCGAATGGATTGTAATC;RSEQ=AATGGAATGGAATGCAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:18.5:1:31:1:1:0:25.5:4:0.6667:0:8 1/1:5:5:4,1:0,0:0,5:1:0,2:21.4:1:28.8:1:1:0:24.4:10:1:0:7.8 +10 39128879 . A C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATGCAATGGAATGGAAT;RSEQ=GAATGGAATGCAATAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:38.4:1:32.8:1:1:0:23.2:10:1:0:5.2 1/1:6:6:4,2:0,0:0,6:1:0,2:39.7:1:29.8:1:1:0:22.3:12:1:0:7.8 +10 39128883 . T C 61 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5671;SOR=2.69977;LSEQ=TGCAATGGAATGGAATAGAA;RSEQ=GGAATGCAATAGAAGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:42:0:32:1:1:1.7321:25.5:4:0.4:0:8 1/0:6:4:3,1:1,1:2,4:0.6667:2,2:39.8:1:30.8:1:1:2.45:22.8:8:0.6667:0:8 +10 39128892 . A G 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=ATGGAATAGAATGGAATGCA;RSEQ=TAGAAGGGAATGGAGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:34.3:1:34.3:1:1:1.73:25:6:0.6:0:6.7 1/1:6:6:4,2:0,0:0,6:1:0,2:38.2:1:30.7:1:1:0:22.3:12:1:0:7.8 +10 39128894 . A G 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATAGAATGGAATGCAAT;RSEQ=GAAGGGAATGGAGGGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:32.4:1:33.4:1:1:0:23.2:10:1:0:5.2 1/1:6:6:4,2:0,0:0,6:1:0,2:36.2:1:29.5:1:1:0:22.3:12:1:0:7.8 +10 39128908 . G T 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5671;SOR=0.3704;LSEQ=TGCAATAGAAGGGAATGGAG;RSEQ=GGAATCAAGTGGAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:0,0:0,3:0.6:0,2:19.3:1:28:1:1:0:21.7:6:0.6:0:3.3 0/1:6:2:1,1:0,0:0,2:0.3333:0,2:14.5:1:26.5:1:1:0:21.5:4:0.3333:0:7.5 +10 39128925 . G T 40 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GAGGGGAATCAAGTGGAATG;RSEQ=AATAGAATTGAATGGAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:2.3:1:30.3:1:1:0:21.7:6:1:0:3.3 1/1:3:3:2,1:0,0:0,3:1:0,2:12:1:25.3:1:1:0:21:6:1:0:8 +10 39128929 . A G 43 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCAAGTGGAATGGAAT;RSEQ=GAATTGAATGGAATTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:8:1:27.3:1:1:0:21:6:1:0:8 +10 42358793 . A T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCGTTCC;RSEQ=TTTGATTCCTTTCCAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:2,2:0.5:2,0:42.5:1:29.5:1:1:0:28.5:4:0.5:0:2.5 +10 42358799 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCGTTCCATTTGA;RSEQ=TCCTTTCCAGTTGATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:29.5:1:31:1:1:0:36.5:4:0.5:0:4 +10 42358831 . GT TC 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=ATTCCATTCCATTCCAATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:32:0:31.8:1:1:0:36.5:4:0.6667:0:3 +10 42358835 . T G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTGTAT;RSEQ=CCATTCCATTCCAATCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:29:0:33:0:1:0:36.5:4:0.6667:0:3 +10 42360866 . C A 41 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:30:0:30:0:1:0:29:2:1:0:2 0/1:7:3:1,2:1,3:4,3:0.4286:2,2:23.3:1:26.3:1:1:1.41:28.7:6:0.4286:0:3 +10 42360883 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGGGTTGATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:30:0:1:0:29:2:1:0:2 0/1:7:2:0,2:1,2:3,2:0.2857:2,0:46:0:31:1:1:0:24:4:0.2857:0:3 +10 42360886 . CC GT 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATTCCATTCCATTCCGTT;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:50:0:32:0:1:0:29:2:1:0:2 0/1:7:2:0,2:1,2:3,2:0.2857:2,0:42:0:30.5:1:1:0:24:4:0.4:0:2 +10 42360887 . C CATTGT 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCGTTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:49:0:30:0:1:0:29:2:1:0:2 0/1:7:3:1,2:0,0:0,3:0.4286:0,2:43.7:1:30.1:1:1:0:28.7:6:1:0:3 +10 42364672 . TCCATTCCAGTCCATTCGGGTTGATTCCATTCCATTCCATTCCTTTCCATTCCTTTCCATTCATTT C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=5.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=TCCATTCCATTCCGTTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:32:0:1:0:21:2:1:0:3 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:31.5:1:1:0:20:4:1:1:4.5 +10 42364766 . T G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.72384;SOR=0.76062;LSEQ=TTCCATTCCATTCTATTCGG;RSEQ=TTGATTCCATTCCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:2,3:3,1:4,5:0.4167:2,2:26.8:1:33.6:1:0.52381:3.76419:25.8:10:0.4167:0:3.4 0/1:20:7:4,3:7,3:10,7:0.35:2,2:31.1:1:30.6:1:0.64367:1.692:22.6:14:0.35:0:4 +10 42364769 . G A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCTATTCGGTTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:8,4:0,0:0,12:1:0,2:29.8:1:30.8:1:1:0:24.4:24:1:0:3 1/1:20:20:13,7:0,0:0,20:1:0,2:32.8:1:28.5:1:1:0:23.4:40:1:0:3.1 +10 42364799 . C T 64 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.06636;SOR=0.16516;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:1,1:2,4:0.5714:2,0:14:0:32.3:1:0.33333:0:22:8:0.6667:0:3.3 0/1:18:3:3,0:9,6:15,3:0.1667:2,0:10:1:25:1:0.51471:0:21:2:0.125:0:4.3 +10 42365017 . T G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=GTATTCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:30.5:1:1:0:41.5:4:1:0:3 +10 42365048 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGATGATTGCATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:28.5:1:1:0:41.5:4:1:0:3 +10 42365073 . G C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTGCATTCCATTCCATT;RSEQ=CAGTCGGGTTGATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:31.5:1:1:0:41.5:4:1:0:3 +10 42378531 . AA GC 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCATTCCAGTCGGGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:29.5:1:1:0:32:4:1:0:2.5 +10 42378542 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTCCAATCCATTCCA;RSEQ=TCGGGATGATTCCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:29:1:1:0:32:4:1:0:2.5 +10 42380256 . T C 34 v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.53981;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTGCACTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,0:1,2:0.4:0,2:26:0:34:1:1:0:20:4:0.4:0:3 0/1:4:1:0,1:1,2:3,1:0.25:2,0:16:0:33:0:1:0:20:2:0.25:0:3 +10 42380272 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=TCCATTCCATTCCATTGCAC;RSEQ=CGGGTTGATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:23.2:1:28.8:1:1:0:20.4:4:1:0:2.6 1/0:4:2:1,1:0,2:2,2:0.5:0,2:32.5:1:29:1:1:0:21:4:0.5:0:2.5 +10 42380279 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=CATTCCATTGCACTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:16.2:1:28.4:1:1:0:20.4:4:1:0:2.6 1/0:4:2:1,1:0,2:2,2:0.5:0,2:25.5:1:31:1:1:0:21:4:0.5:0:2.5 +10 42383493 . C T 46 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAACAATCATCGAATGGAC;RSEQ=CAAATGGAATTATCCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:10.3:1:29.3:1:1:0:25.7:6:1:0:4.7 +10 42383504 . T C 48 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATGGACCCAAATGGAAT;RSEQ=ATCCTCAAATGGAATAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:21.3:1:30.3:1:1:0:25.7:6:1:0:4.7 +10 42383520 . A G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTATCCTCAAATGGAAT;RSEQ=GAATGGAATTATCGAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:34.5:1:32.5:1:1:0:25:4:0.6667:0:4.5 +10 42383569 . G A 42 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCATCGAATGGACTCGA;RSEQ=TGGAATCATCGAATGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:14.7:1:26.7:1:1:0:25.7:6:1:0:4.3 +10 42385145 . G A 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGAATGGAATCAGATGG;RSEQ=ATCATCGAATGGACTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:0,6:1:0,2:1.8:1:30.3:1:1:0:22:12:1:0:4.5 1/1:7:7:6,1:0,0:0,7:1:0,2:7.7:1:29:1:1:0:23.7:14:1:0:5.3 +10 42385151 . C T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGAATCAGATGGGATCAT;RSEQ=GAATGGACTTGAATGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:9,0:0:2,0:6.6:1:28.9:1:1:0:21.8:8:1:0:4 0/1:27:2:1,1:14,10:24,2:0.0741:2,2:6:1:29:1:1:1.38168:25.5:4:0.0741:0:4.5 +10 42385159 . C A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54167;SOR=Inf;LSEQ=AGATGGGATCATCGAATGGA;RSEQ=TTGAATGGAATCATTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:22,0:0:2,0:8.4:1:31.7:1:1:0:28.1:21:1:0:3.8 0/1:42:2:1,1:20,20:40,2:0.0476:2,2:7:1:29.5:1:1:1:28:4:0.0488:0:4.5 +10 42385161 . T G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29169;SOR=0;LSEQ=ATGGGATCATCGAATGGACT;RSEQ=GAATGGAATCATTGAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:10,13:0,0:0,23:1:0,2:10:1:30.3:1:1:0:28.9:22:1:0:3.7 1/1:45:41:23,18:0,2:2,41:0.9111:0,2:11.8:1:30.8:1:0.21041:0:27.7:40:0.9091:0:4 +10 42385164 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53982;SOR=Inf;LSEQ=GGATCATCGAATGGACTTGA;RSEQ=TGGAATCATTGAATGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:29,0:0:2,0:10.7:1:30.5:1:1:0:29.2:58:1:0:3.7 0/1:54:2:1,1:28,24:52,2:0.037:2,2:15:0:33:0:1:1.16333:22:4:0.0385:0:4 +10 42385189 . G T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.94051;LSEQ=ATCATTGAATGGACTCGAAA;RSEQ=GAATCATTATTGAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:0,1:28,26:54,1:0.0179:2,0:31:0:27:0:0.49091:0:30:2:0.0182:0:6 0/1:119:2:1,1:62,54:116,2:0.0168:2,2:39:1:30.5:1:1:1.1468:31:4:0.0168:0:5 +10 42385190 . GA AG 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41975;LSEQ=TCATTGAATGGACTCGAAAG;RSEQ=ATCATTATTGAATGGAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:1,0:28,27:55,1:0.0179:2,0:30:0:34:0:1:0:25:2:0.0179:0:4 0/1:119:3:2,1:61,55:116,3:0.0252:2,2:19.3:1:30.2:1:1:1.79:22.7:6:0.0254:0:4 +10 42385191 . A G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17245;SOR=0.22563;LSEQ=CATTGAATGGACTCGAAAGG;RSEQ=ATCATTATTGAATGGAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:55:28,27:0,0:0,55:0.9821:0,2:27.1:1:32.4:1:1:0:27.7:110:1:0:3.2 1/1:120:111:59,52:3,3:6,111:0.925:2,2:26.9:1:30.9:1:1:1.13:28:110:0.9483:0:3.3 +10 42385195 . A T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55322;SOR=Inf;LSEQ=GAATGGACTCGAAAGGAATC;RSEQ=TTATTGAATGGAATTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:29,27:56,0:0:2,0:30.4:1:31.6:1:1:0:27.6:112:1:0:3.3 0/1:124:3:1,2:65,56:121,3:0.0242:2,2:21:1:31.3:1:0.59884:2.30612:20.7:6:0.0244:0:4 +10 42385197 . T G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8595;SOR=0.94475;LSEQ=ATGGACTCGAAAGGAATCAT;RSEQ=ATTGAATGGAATTGAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:16:7,9:22,17:39,16:0.2857:2,2:34.1:1:33.3:1:0.55315:1.64832:25.9:32:0.2857:0:4.3 0/1:124:34:17,17:48,41:89,34:0.2742:2,2:31.7:1:31.1:1:0.84019:1.16923:28.9:33:0.2705:0:3.8 +10 42385198 . A G 77 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66731;SOR=2.30197;LSEQ=TGGACTCGAAAGGAATCATT;RSEQ=TTGAATGGAATTGAATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:1,0:28,27:55,1:0.0179:2,0:22:0:34:0:1:0:23:2:0.0179:0:3 0/1:124:5:4,1:62,57:119,5:0.0403:2,2:31.2:1:33.4:1:0.37008:3.64:33:10:0.041:0:3.2 +10 42385200 . T G 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACTCGAAAGGAATCATTAT;RSEQ=GAATGGAATTGAATGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:29,27:56,0:0:2,0:33.8:1:31.5:1:1:0:27.6:112:1:0:3.3 0/1:124:2:1,1:65,57:122,2:0.0161:2,2:14:0:29:1:1:1.13914:27.5:4:0.0161:0:3 +10 42385201 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCGAAAGGAATCATTATT;RSEQ=AATGGAATTGAATGGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:29,27:56,0:0:2,0:34.4:1:33.1:1:1:0:27.6:112:1:0:3.3 0/1:124:2:1,1:63,57:120,2:0.0161:2,2:31.5:1:30:1:1:1.10435:23:4:0.0163:0:4 +10 42385215 . G A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18094;SOR=Inf;LSEQ=ATTATTGAATGGAATTGAAT;RSEQ=GAATCATCGAATGGTCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:29,27:56,0:0:2,0:37.6:1:32.5:1:1:0:27.6:112:1:0:3.3 0/1:131:6:3,3:67,58:125,6:0.0458:2,2:15.8:1:29.3:1:1:1.1539:26.2:12:0.0458:0:3 +10 42385224 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAATTGAATGGAATCATC;RSEQ=AATGGTCTCGAATGGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:28,26:54,0:0:2,0:36.1:1:31.7:1:1:0:27.9:108:1:0:3.3 0/1:130:2:1,1:68,59:127,2:0.0154:2,2:13:1:29.5:1:1:1.15127:21:4:0.0155:0:2.5 +10 42385229 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGAATGGAATCATCGAATG;RSEQ=TCTCGAATGGAATCATTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:28,26:54,0:0:2,0:32.8:1:32.1:1:1:0:27.9:108:1:0:3.3 0/1:130:2:1,1:68,60:128,2:0.0154:2,2:38.5:1:31:1:1:1.13224:25:4:0.0154:0:4 +10 42385236 . A T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0066;SOR=0;LSEQ=GAATCATCGAATGGTCTCGA;RSEQ=TGGAATCATTATCAAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:50:26,24:0,0:0,50:1:0,2:28.6:1:31.2:1:1:0:28.4:100:1:0:3.3 1/1:127:111:59,52:8,8:16,111:0.874:2,2:26:1:29.5:1:1:1.13:27.9:222:0.874:0:3.2 +10 42385239 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55714;SOR=Inf;LSEQ=TCATCGAATGGTCTCGAATG;RSEQ=AATCATTATCAAATGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:26,24:50,0:0:2,0:25.6:1:32:1:1:0:28.4:100:1:0:3.3 0/1:122:3:2,1:62,56:118,3:0.0246:2,2:21.3:1:26.3:1:1:1.80:24.3:6:0.025:0:4.3 +10 42385243 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGAATGGTCTCGAATGGAAT;RSEQ=ATTATCAAATGGAATCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,22:48,0:0:2,0:22.2:1:32.2:1:1:0:28.7:96:0.9796:0:3.3 0/1:117:2:1,1:60,53:113,2:0.0171:2,2:44:1:29:1:1:1.13085:20:4:0.0172:0:5 +10 42385246 . TA CT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGGTCTCGAATGGAATCAT;RSEQ=TCAAATGGAATCGAATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:24,22:46,0:0:2,0:20.4:1:29.7:1:1:0:29:92:1:0:3.2 0/1:112:2:1,1:56,52:108,2:0.0179:2,2:11:1:31.3:1:1:1.07617:23.5:4:0.0182:0.0089:3 +10 42385248 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08859;SOR=0;LSEQ=GGTCTCGAATGGAATCATTA;RSEQ=CAAATGGAATCGAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:22,21:43,2:0.0444:2,2:21:1:31:1:1:1.04655:24.5:4:0.0444:0:4 0/0:105:0:0,0:54,51:105,0:0:2,0:20.3:1:29:1:1:0:29:104:1:0:3.1 +10 42385249 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCTCGAATGGAATCATTAT;RSEQ=AAATGGAATCGAATGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:23,22:45,0:0:2,0:17.8:1:31.9:1:1:0:29.1:90:1:0:3.2 0/1:100:2:1,1:50,47:97,2:0.02:2,2:38:1:30.5:1:1:1.0632:20:4:0.0202:0:5 +10 42385255 . G A 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02987;SOR=Inf;LSEQ=AATGGAATCATTATCAAATG;RSEQ=AATCGAATGGAATCACCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:20,20:40,0:0:2,0:13.6:1:31.5:1:1:0:28.5:80:1:0:3.2 0/1:86:10:5,5:40,36:76,10:0.1163:2,2:25:1:28.9:1:1:1.10975:31.4:20:0.1176:0:3.2 +10 42385257 . A G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05642;SOR=Inf;LSEQ=TGGAATCATTATCAAATGGA;RSEQ=TCGAATGGAATCACCGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:19,19:38,0:0:2,0:12.2:1:30.2:1:1:0:28:76:1:0:3.2 0/1:84:8:4,4:40,36:76,8:0.0952:2,2:21.3:1:31.5:1:1:1.10972:34.3:16:0.0952:0:2.8 +10 42385258 . T A 57 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02976;SOR=0.10093;LSEQ=GGAATCATTATCAAATGGAA;RSEQ=CGAATGGAATCACCGAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:4:2,2:17,15:32,4:0.1111:2,2:7:1:28.8:1:1:1.12939:34:8:0.1111:0:4 0/1:82:1:1,0:43,38:81,1:0.0122:2,0:1:0:24:0:1:0:22:2:0.0123:0:3 +10 42385271 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56794;SOR=Inf;LSEQ=AATGGAATCGAATGGAATCA;RSEQ=CGAATAGAATCGAATGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:14,0:0:2,0:6.9:1:31.6:1:1:0:24.6:28:1:0:3 0/1:43:3:1,2:21,18:39,3:0.0698:2,2:12.7:1:30:1:0.59756:2.28772:29:6:0.0698:0:3.3 +10 42385611 . C T 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAAATGGAATTCAAAGGAAT;RSEQ=ATCATCAAATGGAACCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:26.5:1:32:0:1:0:20.5:4:1:0:2.5 +10 42387277 . G A 50 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCGAATGGAATAATCATC;RSEQ=AATGGAATCTAATGGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:25:1:31.7:1:1:0:24.7:6:1:0:3.7 +10 42387288 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATCATCGAATGGAATCT;RSEQ=ATGGAATCATTGAACAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:35:0:33:0:1:0:26:4:0.6667:0:2.5 +10 42387732 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCATCATCAAATGGAATC;RSEQ=AATGGAATCATCATCGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:17:1:30.5:1:1:0:23:4:1:0:3 +10 42387782 . A C 40 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATCATTGAACGGAATTG;RSEQ=ATGGAATCATCATCGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:27:1:25.7:1:1:0:22.7:2:1:0:3.7 +10 42390326 . A G 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AACGAATGGAATCATCATCG;RSEQ=ATGGAATCGAATGGAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:30:1:1:0:21.5:4:1:0:4 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:18:0:32:0:1:0:20:2:0.3333:0:3 +10 42390333 . T A 28 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GGAATCATCATCGAATGGAA;RSEQ=CGAATGGAATCATCAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:28.5:1:1:0:21.5:4:1:0:4 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:25:0:31:0:1:0:20:2:0.3333:0:3 +10 42390341 . A G 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CATCGAATGGAATCGAATGG;RSEQ=ATCATCAAATGGAATCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29:1:29.5:1:1:0:21.5:4:1:0:4 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:45.5:1:30.5:1:1:0:24.5:4:0.6667:0:1 +10 42390400 . T C 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AATCGAATAGAATTATGGAA;RSEQ=GAAATCCAATGTGATCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13:1:33:1:1:0:21.5:4:1:0:4 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:24:0:1:0:20:2:1:0:3 +10 42391617 . G C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCGAATGGACTCGAATG;RSEQ=AATAATCATTGAACGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:33.5:1:1:0:20:4:1:0:4.5 +10 42391631 . CG TA 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATGGAATAATCATTGAA;RSEQ=GAATCAAATGGAATCATCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:46:0:29.8:1:1:0:20:4:1:0:3.5 +10 42391638 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAATCATTGAACGGAATC;RSEQ=AATGGAATCATCGTCGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:30.5:1:1:0:20:4:1:0:3.5 +10 42394926 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATAATCCA;RSEQ=GGACTCGAATGCAATCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:30.5:1:1:0:59:4:1:0:2.5 +10 42394931 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATAATCCATGGAC;RSEQ=CGAATGCAATCATCTTCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41.5:1:31:1:1:0:59:4:1:0:2.5 +10 42396143 . A G 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGAATCATCGAGTGGAATC;RSEQ=AATGGAATCATGATCAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:36:0:29:0:1:0:20:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:32:1:1:0:28:4:1:0:2 +10 42396152 . C T 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGTGGAATCAAATGGAAT;RSEQ=ATGATCAAATGGAATCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:45:0:27:0:1:0:20:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:30.5:1:1:0:28:4:1:0:2 +10 42396883 . A C 41 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATGGAATCATCATCCAA;RSEQ=GGAAGCTAATGGAATCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:18.3:1:26.3:1:1:0:32.3:2:1:0:2.3 +10 42396909 . TG T 46 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATGGAATCAACATCGAA;RSEQ=GAATCGAATGGAAACACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:12.7:1:29.6:1:1:0:32.3:6:1:0.3333:2.3 +10 42397909 . T C 33 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTCTCAGTAACTTCTTTG;RSEQ=GTTGTGTTTAATTCAAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:33:1:1:0:24:4:1:0:1.5 +10 42398642 . T G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03347;SOR=0.09529;LSEQ=TCCTTTAGACAGAGCAGATT;RSEQ=GAAACACTCTTTTTGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:4,6:0,1:1,10:0.9091:0,2:20.5:1:31.3:1:1:0:22.9:20:0.9091:0:4.1 0/1:13:6:1,5:3,4:7,6:0.4615:2,2:25.7:1:27:1:0.55944:3.3873:21.3:5:0.4167:0:4.2 +10 42398648 . A T 83 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03347;SOR=10.4945;LSEQ=AGACAGAGCAGATTTGAAAC;RSEQ=CTCTTTTTGTGGAATTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:4,6:10,1:0.0909:2,0:37:0:32:0:1:0:30:2:0.0909:0:2 1/0:13:7:3,4:1,5:6,7:0.5385:2,2:33.3:1:29.6:1:0.55944:3.39:24.1:14:0.5385:0:1.6 +10 42398677 . T A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28205;SOR=0.18851;LSEQ=GTGGAATTTGCAAGTGGAGA;RSEQ=TTCAAGAGATTTGAGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:2,4:0,1:1,6:0.8571:0,2:34.8:1:31.3:1:1:0:22.7:12:0.8571:0:6 1/0:8:4:0,4:2,2:4,4:0.5:2,0:33.8:1:31.3:1:0.42857:0:21.8:8:0.5:0:6.3 +10 42398681 . A T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54545;SOR=0.23036;LSEQ=AATTTGCAAGTGGAGATTTC;RSEQ=AGAGATTTGAGACCAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:0,1:1,5:0.8333:0,2:40.6:1:30.8:1:1:0:22.8:10:0.8333:0:6.8 1/0:6:3:0,3:0,3:3,3:0.5:0,0:43.7:1:22:1:1:0:20.7:2:0.4:0:7 +10 42398684 . A C 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45455;SOR=0;LSEQ=TTGCAAGTGGAGATTTCAAG;RSEQ=GATTTGAGACCAATGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1:0,2:33.5:1:32:1:1:0:24:12:1:0:6 1/1:5:4:0,4:0,0:0,4:0.8:0,0:32.3:1:30.5:1:1:0:23:8:0.8:0:5.8 +10 42398686 . A C 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGTGGAGATTTCAAGAG;RSEQ=TTTGAGACCAATGGTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:39.4:1:34.2:1:1:0:22.8:10:1:0:6.8 1/1:3:3:0,3:0,0:0,3:1:0,0:40.7:1:31.7:1:1:0:20.7:6:1:0:7 +10 42398692 . GA CG 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.4831;LSEQ=GGAGATTTCAAGAGATTTGA;RSEQ=CCAATGGTAGAAAGGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,0:0,3:0.6:0,2:36.7:1:32.2:1:1:0:22:6:0.6:0:6 0/1:5:2:0,2:1,1:2,2:0.4:2,0:40:0:33:0:1:0:21:4:0.4:0:6 +10 42398698 . T A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TTCAAGAGATTTGAGACCAA;RSEQ=GGTAGAAAGGAAATATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:27.4:1:31.8:1:1:0:22.8:10:1:0:6.2 0/1:5:2:1,1:0,3:3,2:0.4:0,2:11:1:32:1:0.4:0:20.5:4:0.4:0:5 +10 42398712 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GACCAATGGTAGAAAGGAAA;RSEQ=ATCTTCGTATAAAAACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:13.4:1:30.2:1:1:0:22.8:10:1:0:6.2 0/1:5:2:1,1:0,3:3,2:0.4:0,2:26:1:33:0:0.4:0:20.5:4:0.4:0:5 +10 42398725 . A C 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACTAGACAGAATCATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:4.7:1:28.7:1:1:0:22:6:1:0:6 1/0:4:2:1,1:0,2:2,2:0.5:0,2:39:1:33:1:1:0:20.5:4:0.6667:0:5 +10 42398744 . T A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAACTAGACAGAATCATTC;RSEQ=CAGAAACTACTTTGTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:29.5:1:1:0:20.5:4:1:0:5 +10 42398779 . CA AG 26 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATGTGTGTGTTCAACTCA;RSEQ=GAGTTTAACATTTCTGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:1:26.6:1:1:0:20.5:4:1:0.5:4.5 +10 42399297 . CC AG 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=TTCCTTTAGACAGACCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:32.5:1:1:0:26.5:4:1:0:4 +10 42399313 . CC GT 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACCTTCCTTTAGACAGA;RSEQ=AGATTTGAAACACTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:31.5:0:1:0:26.5:4:1:0:3 +10 42399320 . T G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTTAGACAGACCAGATT;RSEQ=GAAACACTCTTTTTGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:31.5:1:1:0:26.5:4:1:0:3 +10 42399371 . G A 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATTTCAATCGCTTTGAG;RSEQ=CCAATTGTAGGAAAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:21:1:1:0:25:1:1:0:5 1/0:4:3:1,2:0,1:1,3:0.75:0,2:23:0:30:1:1:0:23.3:6:1:0:5.3 +10 42399376 . T A 49 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAATCGCTTTGAGGCCAA;RSEQ=TGTAGGAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:32.5:1:1:0:25:4:1:0:5 1/1:3:3:1,2:0,0:0,3:1:0,2:28:0:31.3:1:1:0:23.3:6:1:0:5.3 +10 42399382 . G A 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTTGAGGCCAATTGTAG;RSEQ=AAAGGAAATATCTTCTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:28.5:1:1:0:25:4:1:0:5 1/1:3:3:1,2:0,0:0,3:1:0,2:25.3:1:30.3:1:1:0:23.3:6:1:0:5.3 +10 42399391 . T C 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAATTGTAGGAAAGGAAA;RSEQ=ATCTTCTTATAAAAACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:23.5:1:1:0:25:1:1:0:5 1/1:3:3:1,2:0,0:0,3:1:0,2:16.3:1:30.7:1:1:0:23.3:6:1:0:5.3 +10 42399398 . T G 48 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGGAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:7.3:1:18.3:1:1:0:24:0.5:1:0:5.3 1/1:3:3:1,2:0,0:0,3:1:0,2:9.3:1:30.7:1:1:0:23.3:6:1:0:5.3 +10 42399430 . CT AC 51 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4;SOR=Inf;LSEQ=GACAAAATCATTCTCAGAAA;RSEQ=ACTTTGTGATGTGTGTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:0,0:0,3:0.75:0,2:23.3:1:32.2:1:1:0:28:6:0.75:0:2.7 +10 42399434 . T A 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATCATTCTCAGAAACTAC;RSEQ=TTGTGATGTGTGTGTTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:38:0:28:0:1:0:22:2:1:0:4 1/0:4:2:1,1:2,0:2,2:0.5:0,2:26:0:32.5:1:1:0:32:4:0.5:0:2.5 +10 42399677 . G A 74 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAGACACTCTTTTTGTA;RSEQ=AACTTCCAAGTGCATACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:32:0:30:0:1:0:32:2:1:0:6 1/1:6:6:3,3:0,0:0,6:1:0,2:12.2:1:28.8:1:1:0:29.8:12:1:0:6.2 +10 42399680 . C G 79 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACACTCTTTTTGTAGAA;RSEQ=TTCCAAGTGCATACTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:35:0:33:0:1:0:32:2:1:0:6 1/1:6:6:3,3:0,0:0,6:1:0,2:15.2:1:30.7:1:1:0:29.8:12:1:0:6.2 +10 42399690 . C A 74 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTAGAACTTCCAAGTG;RSEQ=ATACTTAGAGTGCTTTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:36:0:28:0:1:0:32:2:1:0:6 1/1:6:6:3,3:0,0:0,6:1:0,2:25.2:1:29:1:1:0:29.8:12:1:0:6.2 +10 42399697 . A T 78 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAACTTCCAAGTGCATACTT;RSEQ=GAGTGCTTTGAAGCCTACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:29:0:28:0:1:0:32:2:1:0:6 1/1:6:6:3,3:0,0:0,6:1:0,2:31:1:30.2:1:1:0:29.8:12:1:0:6.2 +10 42399719 . A T 65 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AGTGCTTTGAAGCCTACGGT;RSEQ=GACAACTTAATATCTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:7:0:23:0:1:0:32:2:1:0:6 1/0:6:4:3,1:0,2:2,4:0.6667:0,2:18.5:1:32.5:1:0.4:0:24.5:8:0.6667:0:6.3 +10 42399726 . TT GA 79 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGCCTACGGTAGACAAC;RSEQ=AATATCTTCATGTAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:0,6:1:0,2:13.8:1:30.7:1:1:0:29.8:12:1:0.3333:5.5 +10 42400207 . GC A 88 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGCAAGTGGAGATTTCA;RSEQ=GCTTTGAGGCCAATGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:13:1:30:1:1:0:24.5:8:1:0.25:3.3 1/1:10:9:3,6:0,0:0,9:0.9:0,2:13.6:1:28:1:1:0:29.3:18:1:0.4:3.1 +10 42400248 . AA GC 111 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGAAATATCTTCGTAT;RSEQ=AAACTAGACAGAATCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:36.5:1:33.3:1:1:0:24.5:8:1:0:3 1/1:12:11:4,7:0,0:0,11:0.9167:0,2:32.5:1:32.2:1:1:0:27.8:22:0.9167:0:2.6 +10 42400278 . A C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAATCATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:6,0:0:2,0:9.3:1:30.8:1:1:0:23.5:12:1:0:3.3 0/1:15:2:1,1:9,4:13,2:0.1333:2,2:5.5:1:28:1:1:2.12136:21:4:0.1333:0:2.5 +10 42400284 . TG GT 61 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08891;SOR=0.08002;LSEQ=CATTCTCAGAAACTACTTTG;RSEQ=ATGTGTGCATTCAACTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:1,1:2,4:0.6667:2,0:10.3:1:30.7:1:0.33333:0:24.5:8:0.6667:0.5:3.5 0/1:9:1:0,1:8,0:8,1:0.1111:0,0:21:0:31:0:0.11111:0:30:2:0.1111:0:5 +10 42400290 . G T 81 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.86497;LSEQ=CAGAAACTACTTTGTGATGT;RSEQ=TGCATTCAACTCACAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:17:1:32.5:1:1:1:21.5:4:0.5:0:4 0/1:13:6:6,0:4,3:7,6:0.4615:2,0:19.5:1:31.7:1:0.19231:0:23.3:12:0.4615:0:4.3 +10 42400293 . CA TG 31 v3;MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1548;SOR=0.13451;LSEQ=AAACTACTTTGTGATGTGTG;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,1:3,2:0.4:2,0:7:1:31.3:1:0.4:0:25.5:4:0.4:0.2:3.5 0/1:14:1:0,1:10,2:12,1:0.0714:2,0:12:0:32:0:0.23077:0:30:2:0.0714:0:4 +10 42400294 . A G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.74434;LSEQ=AACTACTTTGTGATGTGTGC;RSEQ=TTCAACTCACAGAGTTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:0,0:0,5:0.8333:0,2:10.8:1:32.2:1:1:0:22:10:1:0:5 1/0:14:11:9,2:2,0:2,11:0.7857:0,2:16.5:1:30.7:1:1:0:23.6:22:0.8462:0:5.6 +10 42400307 . A T 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.65951;SOR=0.59896;LSEQ=TGTGTGCATTCAACTCACAG;RSEQ=GTTTAACCTTACTTTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:4,2:6,3:0.3333:2,0:16:1:32:0:0.5:0:21.7:6:0.3333:0:8 0/1:22:5:3,2:10,7:17,5:0.2273:2,2:21.2:1:30:1:1:1.05:24:10:0.2273:0:7.2 +10 42400315 . C G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6664;SOR=1.60411;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTACTTTTCATAGAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:5,2:3,0:3,7:0.7:0,2:24.3:1:32.1:1:1:0:22:14:0.7:0:4 1/0:24:19:11,8:3,2:5,19:0.7917:2,2:24.3:1:29.8:1:1:1.08701:24.1:18:0.7826:0:3.5 +10 42400318 . A T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCACAGAGTTTAACCTT;RSEQ=CTTTTCATAGAGCAGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:8,2:0,0:0,10:1:0,2:27.2:1:32.8:1:1:0:21.9:20:1:0:5.2 1/1:26:26:16,10:0,0:0,26:1:0,2:26.3:1:29.4:1:1:0:24:52:1:0:4.1 +10 42400328 . G C 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66709;SOR=0.61463;LSEQ=GTTTAACCTTACTTTTCATA;RSEQ=AGCAGTTTGGAAACACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:5,3:8,3:0.2727:2,0:37:1:33.7:1:0.49091:0:21.7:6:0.2727:0:8 0/1:27:5:3,2:14,8:22,5:0.1852:2,2:42.2:1:32:1:1:1.15993:24:10:0.1852:0:7.2 +10 42400331 . CA TT 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66709;SOR=0.61463;LSEQ=TAACCTTACTTTTCATAGAG;RSEQ=GTTTGGAAACACTCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:5,3:8,3:0.2727:2,0:41:1:31.5:1:0.49091:0:21.7:6:0.2727:0:7 0/1:27:5:3,2:14,8:22,5:0.1852:2,2:46.2:1:30.3:1:1:1.15993:24:10:0.1923:0:6.2 +10 42400337 . G C 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66028;SOR=0.56443;LSEQ=TACTTTTCATAGAGCAGTTT;RSEQ=GAAACACTCTTTTTGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:5,3:8,3:0.2727:2,0:44.3:1:32.7:1:0.49091:0:21.7:6:0.2727:0:7 0/1:29:5:3,2:14,10:24,5:0.1724:2,2:46.8:1:30.6:1:1:1.07:24:10:0.1724:0:6.2 +10 42400386 . A T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1753;SOR=4.06332;LSEQ=TGGATATTTGGACCTCTTTG;RSEQ=GGCCTTCGTTGGAAACGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:3,1:4,6:0.6:2,2:14.3:1:28.8:1:1:1.44135:22.3:12:0.6:0:3.5 1/1:15:13:5,8:2,0:2,13:0.8667:0,2:22.2:1:28:1:0.2:0:22.9:26:0.8667:0:2.8 +10 42400387 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16304;SOR=0;LSEQ=GGATATTTGGACCTCTTTGA;RSEQ=GCCTTCGTTGGAAACGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:5,3:8,2:0.2:2,0:8.5:1:28.5:1:1:0:20:4:0.2:0:7 0/0:14:0:0,0:6,8:14,0:0:2,0:20.9:1:30.3:1:1:0:22.9:28:1:0:3 +10 42400389 . C T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16304;SOR=0;LSEQ=ATATTTGGACCTCTTTGAGG;RSEQ=CTTCGTTGGAAACGGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:5,3:8,2:0.2:2,0:6.5:1:28.5:1:1:0:20:4:0.2:0:7 0/0:14:0:0,0:6,8:14,0:0:2,0:19.2:1:29:1:1:0:22.9:13:1:0:3 +10 42400390 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15;SOR=0;LSEQ=TATTTGGACCTCTTTGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:8,2:0.2:2,2:19.5:1:33:1:1:2.64575:25:4:0.2:0:2.5 0/0:15:0:0,0:6,9:15,0:0:2,0:17.2:1:30.2:1:1:0:22.9:30:1:0:3.2 +10 42400410 . CTTCAC TTCAT 69 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=CTTCGTTGGAAACGGGATTT;RSEQ=ATAATGTTAGACAGAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:2,0:0:2,0:13:0:34.5:1:1:0:25:4:0.6667:0:2.5 0/1:14:6:3,3:3,4:7,6:0.4286:2,2:8.2:1:26.9:1:1:1.30:24.3:12:0.5:0.2857:2.7 +10 42400411 . T C 42 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=TTCGTTGGAAACGGGATTTC;RSEQ=TCACATAATGTTAGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:8.3:1:31.3:1:1:0:24.3:6:1:0:3 0/1:8:3:0,3:4,1:5,3:0.375:2,0:17.3:1:27:1:0.14286:0:23:6:0.375:0:6 +10 42400415 . CA AG 46 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTGGAAACGGGATTTCTTCA;RSEQ=TAATGTTAGACAGAAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:8:0:34:0:1:0:25:4:1:0:2.5 0/1:8:3:2,1:1,0:1,3:0.375:0,2:11:1:29.5:1:1:0:21:6:0.4286:0:3 +10 42400424 . A C 60 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGATTTCTTCACATAATGTT;RSEQ=GACAGAAGAATTCTCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:8:0:27:0:1:0:28:2:1:0:0 0/1:10:4:3,1:1,5:6,4:0.4:2,2:19:1:30:1:0.19048:10.29:22:8:0.4444:0:3 +10 42400425 . G C 55 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTTCTTCACATAATGTTA;RSEQ=ACAGAAGAATTCTCAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:27:0:1:0:28:2:1:0:0 0/1:10:4:0,4:4,2:6,4:0.4:2,0:26:1:27.5:1:0.07619:0:25:8:0.4444:0:6.3 +10 42400448 . C A 74 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=AGAAGAATTCTCAGTAACTT;RSEQ=TTTGTGTTGTGTGTATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:30:0:1:0:28:2:1:0:0 1/0:10:6:2,4:3,1:4,6:0.6:2,2:35.7:1:28.8:1:0.52381:4.91839:24.2:12:0.6667:0:5.3 +10 42400455 . T G 97 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=TTCTCAGTAACTTCTTTGTG;RSEQ=TGTGTGTATTCAACTCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:39:0:28:0:1:0:28:2:1:0:0 1/1:10:9:4,5:1,0:1,9:0.9:0,2:40:1:30.8:1:1:0:23.1:18:0.9:0:4.6 +10 42400478 . T A 55 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGTATTCAACTCACAGAG;RSEQ=TGAACCTTCCTTTAGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:39:0:31:0:1:0:28:2:1:0:0 0/1:9:4:0,4:4,1:5,4:0.4444:2,0:18.5:1:27.8:1:0.04762:0:25:3:0.375:0:6.3 +10 42400491 . T C 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACAGAGTTGAACCTTCCTT;RSEQ=AGACAGAGCAGATTTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:26:0:30:0:1:0:28:2:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:20:1:32.5:1:1:2.44949:25.5:4:0.3333:0:5.5 +10 42400495 . C A 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTTGAACCTTCCTTTAGA;RSEQ=AGAGCAGATTTGAGACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:22:0:34:0:1:0:28:2:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:16:1:31.5:1:1:2.44949:25.5:4:0.3333:0:5.5 +10 42400575 . T C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61771;SOR=1.77896;LSEQ=GCCAAAGGAAGAAAAGGAAA;RSEQ=ATCTTCGTATAAAAACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:2,4:1,1:2,6:0.75:2,2:8.7:1:33.2:1:1:1.8258:24.5:12:0.75:0:3.7 1/1:13:11:4,7:0,2:2,11:0.8462:0,2:7.8:1:29.2:1:1:0:22.7:22:0.8462:0:3.9 +10 42400592 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=AGACAGAATCATTCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,6:8,0:0:2,0:23.5:1:29.5:1:1:0:23.6:16:0.8889:0:3.5 0/1:23:2:1,1:9,12:21,2:0.087:2,2:18:1:28:1:1:1.32:21.5:4:0.087:0:4 +10 42400609 . A C 72 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.87376;LSEQ=AACTAGACAGAATCATTCTC;RSEQ=GAAACTACTTTGTGATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:3,5:8,1:0.1111:2,0:46:0:32:0:1:0:33:2:0.1111:0:4 0/1:26:5:3,2:8,13:21,5:0.1923:2,2:31:1:31.4:1:0.61957:2.35:35.4:10:0.1923:0:3.8 +10 42400616 . A T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05714;SOR=0;LSEQ=CAGAATCATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,4:6,2:0.2222:2,2:47:0:31.5:1:1:1.83:24.5:4:0.2222:0:4 0/0:27:0:0,0:12,15:27,0:0:2,0:37.7:1:29.1:1:1:0:26:54:1:0:3.6 +10 42400637 . A C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTGTGATGTGTGCGTTCA;RSEQ=CTCACAGAGTTTAAGCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:9,0:0:2,0:31.7:1:30.1:1:1:0:23.6:18:1:0:3.6 0/1:27:2:1,1:11,14:25,2:0.0741:2,2:15.5:1:33:0:1:1.26:30.5:4:0.0741:0:3.5 +10 42400642 . CA AG 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATGTGTGCGTTCAACTCA;RSEQ=GAGTTTAAGCTTTCTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:3,6:0,0:0,9:1:0,2:25.7:1:31.8:1:1:0:23.6:18:1:0:2.6 1/1:27:27:12,15:0,0:0,27:1:0,2:27.9:1:31.1:1:1:0:26:54:1:0:2.6 +10 42400669 . C T 82 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=0;LSEQ=TAAGCTTTCTTTTCATAGAG;RSEQ=AGTTTGGAAACACTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:4.3:1:29.5:1:1:0:21.5:8:1:0:2.5 1/0:12:8:4,4:2,1:3,8:0.6667:2,2:9.9:1:27.5:1:1:1.87936:21.5:16:0.6667:0:2.6 +10 42401962 . T G 28 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAACTAGACAGGATCATTC;RSEQ=CAGAAACCACGTTGTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:28:1:1:0:25:4:1:0:8 +10 42401983 . G C 29 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAACCACGTTGTGATCT;RSEQ=TGCGTTCAACTCACAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:29.5:1:1:0:25:4:1:0:8 +10 42402015 . T C 46 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGAGTTTAACCTTTCTT;RSEQ=CCATAGAGCAGTTATGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:30.3:1:29.3:1:1:0:28.7:6:1:0:7.3 +10 42402017 . C T 45 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTTTAACCTTTCTTTC;RSEQ=ATAGAGCAGTTATGAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:29.7:1:29:1:1:0:28.7:6:1:0:7.3 +10 42402037 . C G 47 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATAGAGCAGTTATGAAACA;RSEQ=TCTCTTTGTAGTATTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:20:1:29.7:1:1:0:28.7:6:1:0:7.3 +10 42402049 . T A 28 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=ATGAAACACTCTCTTTGTAG;RSEQ=ATTTGCAATGGTGTATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:5:0:30.5:1:1:0:36:4:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:13.5:1:28:1:1:0:29.5:4:1:0:7.5 +10 42527255 . TCAAA CAAC 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCCACAAAAAGAGAGTT;RSEQ=TCTGCTCTATCTAAAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:19.5:1:28.9:1:1:2.45:22:4:0.3333:0:3.5 +10 42527266 . C G 72 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGAGAGTTTCAAATCTGCT;RSEQ=TATCTAAAGGAAGGTTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:0,6:1:0,2:30:1:28:1:1:0:20.8:5:1:0:4 +10 42527268 . A T 72 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTTTCAAATCTGCTCT;RSEQ=TCTAAAGGAAGGTTCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:0,6:1:0,2:32:1:28:1:1:0:20.8:12:1:0:4 +10 42527279 . G A 78 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCTCTATCTAAAGGAA;RSEQ=GTTCAACTCTGAGAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:0,6:1:0,2:28.7:1:30.5:1:1:0:20.8:12:1:0:4 +10 42527982 . G A 32 d5;v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTGTGAGTTGAATACAC;RSEQ=CAACACAAAGAAGTTACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:6:1:32:0:1:0:20.5:4:1:0:3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:12:0:24:0:1:0:21:2:0.5:0:4 +10 42528020 . A G 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68272;LSEQ=TGAGAATTCTTCTGTCTAGC;RSEQ=TTATATGAAGAAATCCCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:36:1:32.3:1:1:1.73:23:6:0.6:0:1.7 1/0:12:6:2,4:2,4:6,6:0.5:2,2:31:1:30.8:1:1:1:22.2:12:0.5:0:2.8 +10 42528023 . A G 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.81093;LSEQ=GAATTCTTCTGTCTAGCATT;RSEQ=TATGAAGAAATCCCGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:2,2:4,1:0.2:2,0:34:0:34:0:1:0:21:2:0.2:0:2 0/1:12:2:0,2:4,5:9,2:0.1667:2,0:33.5:1:30:1:0.49091:0:22:4:0.1667:0:2.5 +10 42528029 . AG A 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.06713;LSEQ=TTCTGTCTAGCATTATATGA;RSEQ=AAATCCCGTTTCCAACGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:42:0:31.5:1:1:1.7321:22.5:4:0.4:0:2.5 0/1:12:5:2,3:2,5:7,5:0.4167:2,2:38.8:1:30.8:1:1:1.60:22.2:10:0.4167:0:2 +10 42528054 . T A 68 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23276;LSEQ=TCCCGTTTCCAACGAAGGCC;RSEQ=CAAAGAGGTCCAAATATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:23.5:1:32:0:1:1.7321:22.5:4:0.4:0:2.5 0/1:11:5:2,3:2,4:6,5:0.4545:2,2:15.8:1:29.6:1:1:1.30:22.2:10:0.4545:0:2 +10 42529281 . ACAACGAG GAAAGAA 45 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACTTGCAAATTCCACA;RSEQ=TTTTTCAAAACTGCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:19.7:1:28.6:1:1:0:25:6:1:0.6667:4 +10 42529307 . TC AA 97 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28006;SOR=4.0655;LSEQ=AGTTTTTCAAAACTGCTCTG;RSEQ=TAAAGGAAGGTTCAACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:21.5:1:32.8:1:0.4:0:20.5:4:0.4:0:5 1/0:12:9:6,3:1,2:3,9:0.75:2,2:21.3:1:30.7:1:0.52273:3.53:22.2:18:0.75:0:5.4 +10 42529322 . A C 106 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12874;SOR=5.91384;LSEQ=CTCTGTCTAAAGGAAGGTTC;RSEQ=ACTCTGTGAGTTGAATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:35.5:1:33.5:1:1:2.44949:20.5:4:0.3333:0:5 1/0:13:10:6,4:1,2:3,10:0.7692:2,2:32.7:1:32:1:0.55944:2.75:22:20:0.7692:0:5.3 +10 42529331 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52941;SOR=Inf;LSEQ=AAGGAAGGTTCAACTCTGTG;RSEQ=GTTGAATACACACAACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:6,0:0:2,0:41.2:1:32.2:1:1:0:23.2:12:1:0:5 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:44:0:31:1:1:1.4491:23:4:0.1818:0:5.5 +10 42529332 . G C 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10704;SOR=0.11825;LSEQ=AGGAAGGTTCAACTCTGTGA;RSEQ=TTGAATACACACAACACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:1,1:2,4:0.6667:2,2:40.5:1:33.8:1:1:2.45:24.5:8:0.6667:0:5 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:44:0:32:1:1:1.4491:27:4:0.1667:0:3.5 +10 42529347 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52941;SOR=Inf;LSEQ=TGTGAGTTGAATACACACAA;RSEQ=ACAAAGTAGTTACTGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:6,0:0:2,0:37.3:1:33.8:1:1:0:23.2:12:1:0:5 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:36:1:29:1:1:1.4491:25:4:0.1667:0:6 +10 42529354 . T A 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10704;SOR=0.11825;LSEQ=TGAATACACACAACACAAAG;RSEQ=AGTTACTGAGAATTCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:0,0:0,4:0.6667:0,2:34.8:1:31.8:1:1:0:24.5:8:0.6667:0:5 0/1:12:2:1,1:0,0:0,2:0.1667:0,2:29.5:1:31.5:1:1:0:27:4:0.1667:0:3.5 +10 42529356 . G T 97 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10704;SOR=8.45724;LSEQ=AATACACACAACACAAAGTA;RSEQ=TTACTGAGAATTCTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:26.5:1:32.5:1:1:2.44949:20.5:4:0.3333:0:5 1/1:12:10:6,4:1,1:2,10:0.8333:2,2:28.8:1:29.2:1:1:1.45:22:20:0.8333:0:5.3 +10 42529358 . T G 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10704;SOR=0.11825;LSEQ=TACACACAACACAAAGTAGT;RSEQ=ACTGAGAATTCTTCTGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:1,1:2,4:0.6667:2,2:32.8:1:33.8:1:1:2.45:24.5:8:0.6667:0:5 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:25.5:1:33:1:1:1.4491:27:4:0.1667:0:3.5 +10 42529381 . A G 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00894;SOR=0;LSEQ=TGAGAATTCTTCTGTCTAGC;RSEQ=TTATATGAAGAAATCCCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:6,4:10,4:0.2857:2,2:17:1:33.3:1:1:1.45647:27.8:8:0.2857:0:3.5 0/0:28:0:0,0:14,13:27,0:0:2,0:4.5:1:28.3:1:1:0:24.8:26:0.963:0:5.1 +10 42529384 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08907;SOR=0;LSEQ=GAATTCTTCTGTCTAGCATT;RSEQ=TATGAAGAAATCCCGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:21:0:34:0:1:1.4491:31:4:0.1667:0:2 0/0:27:0:0,0:13,14:27,0:0:2,0:6.3:1:28.1:1:1:0:25.6:54:1:0:5 +10 42529394 . A C 31 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29311;SOR=0.26933;LSEQ=GTCTAGCATTATATGAAGAA;RSEQ=TCCCGTTTCCAACGAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:10,10:20,2:0.0909:2,2:10:0:31:1:1:1:24:4:0.0909:0:3 0/1:39:1:0,1:16,22:38,1:0.0256:2,0:7:0:25:0:1:0:24:2:0.0256:0:5 +10 42529407 . C T 30 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22521;SOR=0.21599;LSEQ=TGAAGAAATCCCGTTTCCAA;RSEQ=GAAGGCCTCAAAGAAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:23:0:30:1:1:1.14834:24:4:0.0667:0:3 0/1:67:1:0,1:27,39:66,1:0.0149:2,0:20:0:24:0:1:0:24:2:0.0149:0:5 +10 42529410 . A T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55266;SOR=Inf;LSEQ=AGAAATCCCGTTTCCAACGA;RSEQ=GGCCTCAAAGAAGTCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:21.2:1:30.3:1:1:0:26.7:29:1:0:4.8 0/1:71:3:1,2:28,40:68,3:0.0423:2,2:18:1:28.3:1:1:1.39361:23.7:6:0.0423:0:5 +10 42529419 . A T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.07753;SOR=3.30404;LSEQ=GTTTCCAACGAAGGCCTCAA;RSEQ=GAAGTCCAAATATGCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:24:13,11:3,3:6,24:0.8:2,2:29.7:1:30.2:1:1:1.18:24.7:23:0.7931:0:5 1/1:72:67:29,38:1,4:5,67:0.9306:2,2:28.3:1:29.5:1:0.39324:3.01:25.9:134:0.9306:0:4.9 +10 42529425 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACGAAGGCCTCAAAGAAGT;RSEQ=CAAATATGCACTTGCAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:35.7:1:31.9:1:1:0:26.7:60:1:0:4.8 0/1:72:2:0,2:30,39:69,2:0.0278:2,0:36:1:31:0:0.50503:0:25:4:0.0282:0:5.5 +10 42529430 . T A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34377;SOR=1.9544;LSEQ=AGGCCTCAAAGAAGTCCAAA;RSEQ=ATGCACTTGCAGACTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:24:13,11:3,3:6,24:0.8:2,2:38.7:1:31:1:1:1.18:24.7:48:0.8:0:5 1/1:71:63:28,35:1,4:5,63:0.8873:2,2:36.2:1:29.9:1:0.38431:3.15:25.9:126:0.9:0:4.9 +10 42529432 . T A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77566;LSEQ=GCCTCAAAGAAGTCCAAATA;RSEQ=GCACTTGCAGACTTTACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:28:15,13:1,1:2,28:0.9333:2,2:40.4:1:31.5:1:1:1.15:24.4:56:0.9333:0:4.8 1/1:71:65:28,37:2,3:5,65:0.9155:2,2:37:1:29.4:1:1:1.13:25.8:20.667:0.9254:0:4.9 +10 42529443 . A G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07753;SOR=3.30404;LSEQ=GTCCAAATATGCACTTGCAG;RSEQ=CTTTACAAACAGAGTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:24:13,11:3,3:6,24:0.8:2,2:41.5:1:32.1:1:1:1.18:24.7:48:0.8:0:5 1/1:72:67:29,38:1,4:5,67:0.9306:2,2:37.5:1:31.1:1:0.39324:3.01:25.9:66:0.9296:0:4.9 +10 42529447 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.946;LSEQ=AAATATGCACTTGCAGACTT;RSEQ=ACAAACAGAGTGTTTCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:5,1:11,13:24,6:0.2:2,2:38.5:1:30:1:0.17548:5.60:22.5:5:0.1724:0:5.7 0/1:68:13:7,6:21,34:55,13:0.1912:2,2:36.2:1:31.5:1:0.35666:1.87:23.8:26:0.194:0:6 +10 42529451 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08788;SOR=0;LSEQ=ATGCACTTGCAGACTTTACA;RSEQ=ACAGAGTGTTTCCAAACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:36.5:1:33.5:1:1:1.14834:21.5:4:0.069:0:4.5 0/0:70:0:0,0:29,41:70,0:0:2,0:36.4:1:29.9:1:1:0:25.7:69:1:0:4.8 +10 42529452 . A C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCACTTGCAGACTTTACAA;RSEQ=CAGAGTGTTTCCAAACTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,13:29,0:0:2,0:37.4:1:30.7:1:1:0:27:58:0.9667:0:4.7 0/1:70:2:0,2:29,39:68,2:0.0286:2,0:43:1:30.5:1:0.50766:0:34.5:4:0.0286:0:4 +10 42529454 . A T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CACTTGCAGACTTTACAAAC;RSEQ=GAGTGTTTCCAAACTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:35.6:1:31.6:1:1:0:26.7:60:1:0:4.8 0/1:70:2:1,1:28,40:68,2:0.0286:2,2:6:0:31.5:1:1:1.42:31:4:0.0286:0:3 +10 42529458 . T G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCAGACTTTACAAACAGAG;RSEQ=GTTTCCAAACTGCTCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:31.6:1:30.7:1:1:0:26.7:60:1:0:4.8 0/1:70:2:1,1:28,40:68,2:0.0286:2,2:28.5:1:28.5:1:1:1.42:24.5:4:0.029:0:6 +10 42529459 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08788;SOR=0;LSEQ=GCAGACTTTACAAACAGAGT;RSEQ=TTTCCAAACTGCTCTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:28.5:1:34:0:1:1.14834:21.5:4:0.0667:0:4.5 0/0:70:0:0,0:28,41:69,0:0:2,0:30:1:31.6:1:1:0:25.8:68:0.9855:0:4.8 +10 42529463 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTTACAAACAGAGTGTTT;RSEQ=CAAACTGCTCTATGAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:26.6:1:32.3:1:1:0:26.7:60:1:0:4.8 0/1:69:2:1,1:28,39:67,2:0.029:2,2:11:1:28:1:1:1.39:30:4:0.0294:0:5 +10 42529465 . A C 34 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.22118;SOR=0.21279;LSEQ=TTTACAAACAGAGTGTTTCC;RSEQ=AACTGCTCTATGAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:25:1:34:1:1:1.14834:59:4:0.0667:0:4 0/1:68:1:1,0:27,40:67,1:0.0147:2,0:34:0:27:0:0.41176:0:31:2:0.0147:0:4 +10 42529467 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACAAACAGAGTGTTTCCAA;RSEQ=CTGCTCTATGAAAAGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:22.6:1:30.1:1:1:0:26.7:29:1:0:4.8 0/1:68:2:1,1:27,39:66,2:0.0294:2,2:19.5:1:29:1:1:1.44:24.5:4:0.0299:0:6 +10 42529468 . C G 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58379;SOR=0.42841;LSEQ=ACAAACAGAGTGTTTCCAAA;RSEQ=TGCTCTATGAAAAGAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:19.5:1:34.5:1:1:1.14834:21.5:4:0.0667:0:4.5 0/1:68:2:1,1:27,39:66,2:0.0294:2,2:13.5:1:33.5:1:1:1.44:31:4:0.0294:0:3 +10 42529470 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09152;SOR=0;LSEQ=AAACAGAGTGTTTCCAAACT;RSEQ=CTCTATGAAAAGAAAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,13:27,2:0.0667:2,2:20:1:29.5:1:1:1.07415:59:4:0.0667:0:4 0/0:68:0:0,0:28,40:68,0:0:2,0:20.3:1:31.1:1:1:0:25.4:21.667:1:0:4.8 +10 42529474 . T G 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5791;SOR=0.40781;LSEQ=AGAGTGTTTCCAAACTGCTC;RSEQ=ATGAAAAGAAAGGTTAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:14,11:25,2:0.0741:2,2:16:1:33:1:1:1.2613:59:4:0.0741:0:4 0/1:64:2:1,1:24,37:61,2:0.0313:2,2:27:1:29:1:1:1.53:30:4:0.0317:0:3.5 +10 42529476 . T C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18673;SOR=2.33564;LSEQ=AGTGTTTCCAAACTGCTCTA;RSEQ=GAAAAGAAAGGTTAAACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:4,0:9,12:21,4:0.1538:2,0:17.8:1:32.5:1:0.09565:0:22.8:8:0.1538:0:6 0/1:60:18:9,9:15,27:42,18:0.3:2,2:16:1:30.5:1:0.39098:1.78:24.3:36:0.3051:0:5.4 +10 42529477 . G T 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.58601;SOR=0.44122;LSEQ=GTGTTTCCAAACTGCTCTAT;RSEQ=AAAAGAAAGGTTAAACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:13,11:24,2:0.0769:2,2:13:1:30.5:1:1:1.17422:59:4:0.0769:0:4 0/1:57:2:1,1:22,33:55,2:0.0351:2,2:24:1:27:1:1:1.49:30:4:0.0351:0:3.5 +10 42529486 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTGCTCTATGAAAAGAAA;RSEQ=GTTAAACTCTGTGAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:17,0:0:2,0:10.8:1:32.4:1:1:0:28.9:34:1:0:5 0/1:38:2:1,1:13,23:36,2:0.0526:2,2:12.5:1:29.5:1:1:1.74:21:4:0.0526:0:6 +10 42529492 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTATGAAAAGAAAGGTTAA;RSEQ=CTCTGTGAGTTGAATGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:12,0:0:2,0:7.8:1:30.1:1:1:0:25.5:24:1:0:4.9 0/1:32:2:0,2:13,17:30,2:0.0625:2,0:9.5:1:32:1:0.50202:0:34.5:4:0.0625:0:4 +10 42529493 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTATGAAAAGAAAGGTTAAA;RSEQ=TCTGTGAGTTGAATGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:11,0:0:2,0:7.4:1:32.5:1:1:0:25.8:22:1:0:5 0/1:31:2:1,1:12,17:29,2:0.0645:2,2:8:1:28:1:1:1.40:30:4:0.0645:0:3.5 +10 42529528 . C G 51 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACATCACAAAGTAGTT;RSEQ=TTTAGAATGATTCTGTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:20:0:34:0:1:0:20:2:1:0:7 1/1:3:3:3,0:0,0:0,3:1:0,0:19.3:1:32.7:1:1:0:20.7:6:1:0:7.3 +10 42529531 . T G 64 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCACAAAGTAGTTCTT;RSEQ=AGAATGATTCTGTCTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:23:0:34:0:1:0:20:2:1:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:17.3:1:32:1:1:0:21.5:8:1:0:7.5 +10 42529545 . C G 62 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTTTAGAATGATTCTGT;RSEQ=TAGTTTTTATACGAAGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:37:0:34:0:1:0:20:2:1:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:31.3:1:31.3:1:1:0:21.5:8:1:0:7.5 +10 42529565 . C T 45 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTTTTTATACGAAGATA;RSEQ=TTCCTTTTCTACAATTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:44:0:33:0:1:0:20:2:1:0:7 1/0:4:3:2,1:0,0:0,3:0.75:0,2:42.7:1:29:1:1:0:21.3:6:0.75:0:7.3 +10 42529576 . A G 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAAGATACTTCCTTTTCT;RSEQ=CAATTGGCCTAGAAGCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:33:0:34:0:1:0:20:2:1:0:7 1/0:4:2:2,0:1,1:2,2:0.5:2,0:35:0:31:1:1:0:20:4:0.5:0:7 +10 42529578 . A C 57 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATACTTCCTTTTCTAC;RSEQ=ATTGGCCTAGAAGCGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:31:0:33:0:1:0:20:2:1:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:36:1:28.5:1:1:0:21.5:8:1:0:7.5 +10 42529581 . T A 51 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATACTTCCTTTTCTACAAT;RSEQ=GGCCTAGAAGCGCTTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:28:0:30:0:1:0:20:2:1:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:33.8:1:25.8:1:1:0:21.5:8:1:0:7.5 +10 42529620 . C A 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCACTTGCAAATTCCA;RSEQ=AAAAAGAGTGTTTCAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:30.5:1:1:0:22:4:1:0:8 +10 42529624 . A C 32 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTTGCAAATTCCACAAA;RSEQ=AGAGTGTTTCAAATCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:32:1:1:0:22:4:1:0:8 +10 42529908 . A C 118 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTTATATGAAGATATTT;RSEQ=CATTTCTAACATTGGCGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:14:14:6,8:0,0:0,14:1:0,2:14.9:1:31.1:1:1:0:28.6:28:1:0:3.2 +10 42529912 . T G 122 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATATGAAGATATTTACAT;RSEQ=TCTAACATTGGCGTCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:14:14:6,8:0,0:0,14:1:0,2:18.9:1:32.1:1:1:0:28.6:28:1:0:3.2 +10 42529916 . A T 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAAGATATTTACATTTCT;RSEQ=ACATTGGCGTCAAATCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:23:0:29.5:1:1:1.37:23.5:4:0.1429:0:4 +10 42529918 . C G 120 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATATTTACATTTCTAA;RSEQ=ATTGGCGTCAAATCGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:14:14:6,8:0,0:0,14:1:0,2:24.9:1:31.6:1:1:0:28.6:28:1:0:3.2 +10 42530586 . T A 66 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTTTAATACGAAGATAT;RSEQ=TCCTTTTCTACCATTGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:26:0:33:0:1:0:30:2:1:0:8 1/1:5:5:2,3:0,0:0,5:1:0,2:24.2:1:28.6:1:1:0:25.4:10:1:0:7.2 +10 42530597 . C T 65 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAAGATATTTCCTTTTCTA;RSEQ=CATTGTCCTCGAAGCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:18.3:1:31:1:1:0:30:6:1:0:6.7 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:35.2:1:28.4:1:1:1.41418:25.4:10:0.7143:0:7.2 +10 42530599 . A G 29 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGATATTTCCTTTTCTACC;RSEQ=TTGTCCTCGAAGCGCTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:20.3:1:30.7:1:1:0:30:6:1:0:6.7 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:10.5:1:29:1:1:1.41:20:4:0.2857:0:7.5 +10 42530600 . T C 60 d5;NM7.25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=AGATATTTCCTTTTCTACCA;RSEQ=TGTCCTCGAAGCGCTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:21.3:1:34:1:1:0:30:6:1:0:6.7 1/0:7:4:1,3:2,1:3,4:0.5714:2,2:41.3:1:30:1:0.48571:4.4496:26.3:8:0.5714:0:7.5 +10 42530605 . C T 68 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCTTTTCTACCATTGTC;RSEQ=TCGAAGCGCTTCAAATCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:26.3:1:32:1:1:0:30:6:1:0:6.7 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:43:1:29.4:1:1:1.41418:25.4:10:0.7143:0:7.2 +10 42530614 . C T 81 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACCATTGTCCTCGAAGCG;RSEQ=TTCAAATCTGCACTAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:31.3:1:31.7:1:1:0:30:6:1:0:6.7 1/1:7:7:3,4:0,0:0,7:1:0,2:38.4:1:29.1:1:1:0:23.9:14:1:0:7.3 +10 42530617 . C G 86 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTGTCCTCGAAGCGCTT;RSEQ=AAATCTGCACTAGCAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:32.3:1:34.3:1:1:0:30:6:1:0:6.7 1/1:7:7:3,4:0,0:0,7:1:0,2:38:1:30.7:1:1:0:23.9:14:1:0:7.3 +10 42530627 . C T 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=CGAAGCGCTTCAAATCTGCA;RSEQ=TAGCAAATTCCACAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:26:0:32.5:1:1:0:30:4:0.5:0:6 0/0:9:0:0,0:3,6:9,0:0:2,0:29.1:1:30.2:1:1:0:23.7:18:1:0:6.4 +10 42530635 . T C 32 d5;v3;pSTD;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCAAATCTGCACTAGCAAA;RSEQ=TCCACAAAAAGAGTGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:17.8:1:32.3:1:1:0:29.3:8:1:0:6 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:41:0:32:1:1:2.24:20:4:0.2222:0:7.5 +10 42530640 . C G 32 d5;v3;pSTD;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCTGCACTAGCAAATTCCA;RSEQ=AAAAAGAGTGTTTCAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:15.3:1:34.5:1:1:0:29.3:8:1:0:6 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:36:0:32:1:1:2.24:20:4:0.2222:0:7.5 +10 42530642 . A C 33 d5;v3;pSTD;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGCACTAGCAAATTCCACA;RSEQ=AAAGAGTGTTTCAAATCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:14.3:1:32.8:1:1:0:29.3:8:1:0:6 0/1:9:2:1,1:2,4:6,2:0.2222:2,2:34:0:33:1:1:1.83:20:4:0.2222:0:7.5 +10 42530647 . A G 31 d5;v3;pSTD;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTAGCAAATTCCACAAAAAG;RSEQ=GTGTTTCAAATCTGCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:11.8:1:33:1:1:0:29.3:8:1:0:6 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:29:0:31.5:1:1:2.24:20:4:0.2222:0:7.5 +10 42530657 . A C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=CCACAAAAAGAGTGTTTCAA;RSEQ=TCTGCTCTCTCTAAAGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:36:0:35:0:1:0:27:2:1:0:4 0/1:7:2:0,2:2,3:5,2:0.2857:2,0:22.5:1:31:1:1:0:24.5:4:0.2857:0:5.5 +10 42530676 . C AG 48 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=AATCTGCTCTCTCTAAAGAA;RSEQ=GTTCAACTCTGTGAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:0,2:2,3:0.6:0,2:20.3:1:30.9:1:1:0:21:6:0.6:0.4:6.3 +10 42530677 . G GT 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCTCTCTCTAAAGAAC;RSEQ=TTCAACTCTGTGAGTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:30.5:1:30:1:1:0:21.5:4:0.6667:0:4 +10 42531902 . G T 70 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACATCACAAAGTAGTT;RSEQ=CAGAGAATGATTCTGTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:0,5:1:0,2:18.8:1:30.4:1:1:0:24.8:10:1:0:4.8 +10 42531904 . A T 72 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACATCACAAAGTAGTTGC;RSEQ=GAGAATGATTCTGTCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:0,5:1:0,2:20.8:1:31.4:1:1:0:24.8:10:1:0:4.8 +10 42531907 . G C 64 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCACAAAGTAGTTGCAGA;RSEQ=AATGATTCTGTCTAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:8:4:2,2:3,1:4,4:0.5:2,2:23.3:1:32.3:1:1:2.60168:26:8:0.5:0:5.3 +10 42531912 . A C 52 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGTAGTTGCAGAGAATG;RSEQ=TTCTGTCTAATTTTTACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:3:2,1:3,2:5,3:0.375:2,2:8:0:33.3:1:1:1.29:25:6:0.375:0:4.3 +10 42531919 . C G 74 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAGAGAATGATTCTGT;RSEQ=TAATTTTTACACGAAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:5:3,2:3,2:5,5:0.5:2,2:11.4:1:32:1:1:1:27:10:0.5:0:3.8 +10 42531922 . AT A 74 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGAATGATTCTGTCTA;RSEQ=TTTTACACGAAGATATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:10:5:3,2:3,2:5,5:0.5:2,2:34.4:1:32:1:1:1:24.8:10:0.5:0:4.8 +10 42531951 . T A 99 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAAGATATTTCCATTTCAA;RSEQ=GATTGGCCTCAAATCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:33:1:1:0:40:4:1:0:2.5 1/1:10:10:6,4:0,0:0,10:1:0,2:19.7:1:30:1:1:0:25.9:20:1:0:4.3 +10 42531956 . G A 64 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=ATATTTCCATTTCAATGATT;RSEQ=GCCTCAAATCGCTTCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:30:1:1:0:40:4:1:0:2.5 1/0:10:5:3,2:3,2:5,5:0.5:2,2:19.6:1:27.8:1:1:1:27:10:0.5:0:3.8 +10 42531957 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTCCATTTCAATGATTG;RSEQ=CCTCAAATCGCTTCAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:33.5:1:1:0:40:4:1:0:2.5 0/1:10:2:1,1:5,3:8,2:0.2:2,2:12:1:28.5:1:1:1.58108:30:4:0.2:0:5.5 +10 42532523 . A G 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAGAGTGTTTCCAAACT;RSEQ=CTCTATGAAAAGAAAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:14:1:30:1:1:0:26.5:4:0.6667:0:8 +10 42532533 . A G 72 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCAAACTACTCTATGAA;RSEQ=AGAAAGGTTAAACTCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:8:5:3,2:1,2:3,5:0.625:2,2:14.4:1:31.2:1:1:2.60:27.6:10:0.625:0:7.8 +10 42532542 . T G 94 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTCTATGAAAAGAAAGGT;RSEQ=AAACTCTGTGAGCTGAACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:9:8:4,4:0,1:1,8:0.8889:0,2:18.8:1:31.5:1:1:0:26:16:0.8889:0:7 +10 42532552 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAAGGTTAAACTCTGT;RSEQ=AGCTGAACGCACACATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:22.5:1:27.5:1:1:1.29:25:4:0.2222:0:5.5 +10 42532554 . G A 78 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAAGGTTAAACTCTGTGA;RSEQ=CTGAACGCACACATCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:6:3,3:1,2:3,6:0.6667:2,2:32.8:1:30.3:1:1:1.85:26.3:12:0.6667:0:7.5 +10 42532564 . C G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACTCTGTGAGCTGAACGCA;RSEQ=ACATCACAAAGTAGTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:34.5:1:30.5:1:1:1.29:25:4:0.2222:0:5.5 +10 42532566 . C G 81 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTGTGAGCTGAACGCACA;RSEQ=ATCACAAAGTAGTTTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:6:3,3:1,2:3,6:0.6667:2,2:37.7:1:31.7:1:1:1.85:26.3:12:0.6667:0:7.5 +10 42532569 . C G 81 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGAGCTGAACGCACACAT;RSEQ=ACAAAGTAGTTTCTGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:6:3,3:1,2:3,6:0.6667:2,2:36.7:1:31.5:1:1:1.85:26.3:12:0.6667:0:7.5 +10 42532576 . T C 95 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACGCACACATCACAAAG;RSEQ=AGTTTCTGAGAATGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:9:8:4,4:0,0:0,8:0.8889:0,2:33.3:1:31.9:1:1:0:26:16:0.8889:0:7 +10 42532608 . T C 70 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGATTCTGTGTAGTTTTTA;RSEQ=ACGAACATATTTACATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:4,1:0,0:0,5:1:0,2:8.4:1:30.4:1:1:0:29:10:1:0:7 +10 42534646 . TC AT 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCTGTGTAGTTTTAAT;RSEQ=GAAGATATTTCCATTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16.5:1:31.2:1:1:0:21.5:4:1:0.5:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 42534662 . T G 32 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTCGAAGATATTTCCAT;RSEQ=TCTAAGATTGGCCTCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28:1:32:1:1:0:21.5:4:1:0:5.5 1/0:2:1:1,0:0,0:0,1:0.5:0,0:5:0:33:0:1:0:27:2:0.5:0:7 +10 42534675 . C G 29 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCATTTCTAAGATTGGC;RSEQ=TCAAATCCCTTGAAATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:35:1:30.5:1:1:0:21.5:4:1:0:5.5 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:23:1:29.5:1:1:0:24.5:4:0.6667:0:6 +10 42534683 . C G 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAAGATTGGCCTCAAATC;RSEQ=CTTGAAATCTCCACTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:35:1:29:1:1:0:21.5:4:1:0:5.5 1/1:3:3:3,0:0,0:0,3:1:0,0:25:1:30.3:1:1:0:24:6:1:0:6 +10 42534717 . A T 43 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTGCAAATTCCACAAAAAG;RSEQ=GTGTTTCAAAACTGCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:14:0:32:0:1:0:20:2:1:0:5 1/1:3:3:3,0:0,0:0,3:1:0,0:35.3:1:27.3:1:1:0:24:6:1:0:6 +10 42534720 . G T 44 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAATTCCACAAAAAGAGT;RSEQ=TTTCAAAACTGCTCTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:11:0:33:0:1:0:20:2:1:0:5 1/0:5:3:3,0:1,1:2,3:0.6:2,0:34:1:28.3:1:0.4:0:24:6:0.6:0:6 +10 42534752 . A C 60 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGAATAAAGGAAGGTTC;RSEQ=ACTCTGTGAGTTGAATGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:3,1:0,0:0,4:1:0,2:13:1:30.3:1:1:0:24.8:8:1:0:3.8 +10 42597079 . T C 45 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATAATCCA;RSEQ=GGACTCGAATGCAATCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:0,3:1:0,0:38.3:1:28.7:1:1:0:21.3:6:1:0:3 +10 42597103 . A T 57 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=CTCGAATGCAATCATCATCG;RSEQ=ATAGAATCGAATGGAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:1,1:0.5:0,0:1:0:31:0:1:0:28:2:0.5:0:3 1/0:6:4:1,3:1,1:2,4:0.6667:2,2:11.3:1:28.8:1:1:2.44949:23:8:0.6667:0:2.5 +10 42597106 . A G 44 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=GAATGCAATCATCATCGAAT;RSEQ=GAATCGAATGGAATCATCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:1,1:0.5:0,0:15:0:31:0:1:0:22:2:0.5:0:2 0/1:7:3:1,2:1,3:4,3:0.4286:2,2:9:1:28:1:1:1.41:22:6:0.4286:0:3.7 +10 42597110 . T A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAATCATCATCGAATAGAA;RSEQ=CGAATGGAATCATCGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:31.5:1:1:0:25:4:1:0:2.5 0/1:7:2:1,1:1,4:5,2:0.2857:2,2:16:1:27.5:1:1:3.16:22.5:4:0.2857:0:3.5 +10 42597186 . C T 48 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAATCATCATCAGATGGAAA;RSEQ=GAATGGAATCATCATTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:11.5:1:33:1:1:0:25:4:1:0:2.5 1/0:4:3:1,2:1,0:1,3:0.75:0,2:10.3:1:30.7:1:1:0:22:6:0.75:0:3.7 +10 42599566 . C G 82 d5;v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.66417;LSEQ=TCATTCAATGGACTCGAATG;RSEQ=AATAATCATTGAACGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:12.5:1:33.5:1:1:0:23.5:4:0.6667:0:1.5 1/0:9:7:4,3:0,0:0,7:0.7778:0,2:2.6:1:29.3:1:1:0:21.4:14:0.7778:0:3.6 +10 42599603 . A G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00082;SOR=Inf;LSEQ=AATCGAATGGAATCATCATC;RSEQ=GATGGAAACGAATGGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:7,2:4,2:6,9:0.6:2,2:38:1:32.1:1:1:1.68:22.2:18:0.6:0:2.8 1/1:28:28:16,12:0,0:0,28:1:0,2:34.5:1:29.6:1:1:0:22.5:27:1:0:3.3 +10 42599611 . A T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=GGAATCATCATCAGATGGAA;RSEQ=CGAATGGAATCATCATCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:11,4:15,0:0:2,0:38.8:1:31.2:1:1:0:22.7:30:1:0:2.3 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:45:0:29:1:1:1.34838:25:4:0.0714:0:3 +10 42599612 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54056;SOR=Inf;LSEQ=GAATCATCATCAGATGGAAA;RSEQ=GAATGGAATCATCATCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:11,4:15,0:0:2,0:39.4:1:32.7:1:1:0:22.7:30:1:0:2.3 0/1:28:3:3,0:13,11:24,3:0.1071:2,0:44:1:33:0:0.24786:0:20:6:0.1071:0:5.3 +10 42599622 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11628;SOR=0;LSEQ=CAGATGGAAACGAATGGAAT;RSEQ=ATCATCGAATGGAAATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:10,3:13,2:0.1333:2,2:46:1:30:1:0.47619:3.02781:23.5:4:0.1333:0:4 0/0:28:0:0,0:16,12:28,0:0:2,0:41.1:1:31.8:1:1:0:22.5:56:1:0:3.3 +10 42599624 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0.53488;SOR=Inf;LSEQ=GATGGAAACGAATGGAATCA;RSEQ=CATCGAATGGAAATGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:11,4:15,0:0:2,0:39.7:1:31.7:1:1:0:22.7:30:1:0:2.3 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:46:0:32:1:1:1.34838:21:4:0.0714:0:4 +10 42599627 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.54056;SOR=Inf;LSEQ=GGAAACGAATGGAATCATCA;RSEQ=CGAATGGAAATGAAAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:11,4:15,0:0:2,0:37.9:1:31.6:1:1:0:22.7:30:1:0:2.3 0/1:28:3:2,1:14,11:25,3:0.1071:2,2:38:1:31:1:1:1.55:24:6:0.1111:0:3 +10 42599644 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54017;SOR=Inf;LSEQ=TCATCGAATGGAAATGAAAG;RSEQ=AGTCATCATCTAATGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:11,4:15,0:0:2,0:24.4:1:31.6:1:1:0:22.7:30:1:0:2.3 0/1:29:2:1,1:16,11:27,2:0.069:2,2:36.5:1:27.5:1:1:1.43545:22.5:4:0.069:0:3.5 +10 42599660 . G T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGGAGTCATCATCTAATG;RSEQ=AATCGCATGGAATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:8,4:12,0:0:2,0:12.5:1:31.7:1:1:0:22.8:24:1:0:2.3 0/1:25:2:1,1:14,9:23,2:0.08:2,2:10:0:28.5:1:1:1.52748:21:4:0.08:0:4 +10 42599664 . C T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52688;SOR=0;LSEQ=GAGTCATCATCTAATGGAAT;RSEQ=GCATGGAATCATCATCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:7,4:0,0:0,11:1:0,2:9.3:1:29.9:1:1:0:22.6:22:1:0:2.3 1/1:20:18:11,7:1,1:2,18:0.9:2,2:8.6:1:29.6:1:1:1.54:21.9:36:0.9:0:3.6 +10 42599680 . C A 42 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=GAATCGCATGGAATCATCAT;RSEQ=AAATGGAATCGAATGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:10:1:29:1:1:0:21.5:4:0.6667:0:2 1/0:4:3:3,0:1,0:1,3:0.75:0,0:16.3:1:26.7:1:1:0:21:6:0.75:0:3.7 +10 42600026 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATGGAATCATCGAATGGA;RSEQ=TCGAATGGAATAATCATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:7:0:34:0:1:0:24:2:1:0:3 1/0:4:2:1,1:1,1:2,2:0.5:2,2:26.5:1:28:1:1:1:47:4:0.5:0:3.5 +10 42600054 . T A 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATAATCATTGAACGGAAT;RSEQ=GAATGGAATCATCATCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:35:0:30:0:1:0:24:2:1:0:3 1/0:4:2:1,1:1,1:2,2:0.5:2,2:26.5:1:28:1:1:1:47:4:0.5:0:3.5 +10 43052740 . G GA 30 d5;v3;MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.46429;SOR=0.17288;LSEQ=TAAAATATTTGTTTCCTAGT;RSEQ=AAAAAAAAAAAAAAAACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:15:1:30.5:1:1:0:51.5:4:1:0:0.5 0/1:5:1:1,0:1,0:1,1:0.2:0,0:11:0:30:0:1:0:60:2:0.25:0:5 +10 43052870 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20419;SOR=Inf;LSEQ=GACTTTACATAAACAACTTT;RSEQ=TCAACTGTGTTAGTTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:133,35:168,0:0:2,0:21.4:1:32.4:1:1:0:58.6:83:1:0:0.1 0/1:139:2:1,1:105,32:137,2:0.0144:2,2:18.5:1:28:1:0.41977:3.24648:60:4:0.0144:0:1.5 +10 43052937 . CA C 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.28647;SOR=3.00419;LSEQ=AAATGAAGAATATTGAATGC;RSEQ=AAAAAAATCAAACAATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:2:1,1:206,168:374,2:0.0053:2,2:18.5:1:31:1:1:1.22552:42.5:4:0.0053:0:5 0/1:379:6:3,3:205,167:372,6:0.0158:2,2:24:1:32.8:1:1:1.22687:46.2:12:0.016:0:0.3 +10 43052980 . G A 249 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AATCACTCAATTCTAATCGT;RSEQ=TAAATGCTGAAGTAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:329:329:136,193:0,0:0,329:1:0,2:27.6:1:29.8:1:1:0:46.9:64.8:1:0:1.1 1/0:372:249:105,144:54,69:123,249:0.6694:2,2:24.6:1:28.7:1:0.82378:1.07309:48.2:248:0.6685:0:1.1 +10 43053033 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22559;SOR=0;LSEQ=AGTTACTTCAATGAAAATGC;RSEQ=AAGAACATCAGATGCTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:48,143:191,2:0.0103:2,2:25.5:1:29:1:0.4443:2.96:49:4:0.0104:0:1.5 0/0:215:0:0,0:70,145:215,0:0:2,0:26.3:1:30:1:1:0:52.6:214:1:0:0.6 +10 43053085 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49669;SOR=Inf;LSEQ=TGCAGAATGTGGGTCGGACG;RSEQ=CCCACAAGTTGGAATCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:7,66:73,0:0:2,0:23.6:1:32:1:1:0:60:35.5:1:0:0.1 0/1:75:2:1,1:17,55:72,2:0.0267:2,2:15:1:30.5:1:0.42984:3.17:60:4:0.027:0:1 +10 43059514 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49849;SOR=Inf;LSEQ=GTGAGGAAGCTTTTTAAGGG;RSEQ=TTTGCTTATATTTATTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:71,72:143,0:0:2,0:31.3:1:32.3:1:1:0:45.7:27.6:1:0:0.1 0/1:149:2:1,1:67,80:147,2:0.0134:2,2:8.5:1:26:1:1:1.19:60:4:0.0136:0:1 +10 43059566 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50051;SOR=0;LSEQ=CACTGCGGACACTCAGGTGG;RSEQ=AGCAGGAAGGAAAGTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:30,70:100,2:0.0196:2,2:13.5:1:29.5:1:0.51757:2.31:60:4:0.0204:0:1 0/0:87:0:0,0:27,60:87,0:0:2,0:20.5:1:31.2:1:1:0:57.6:174:1:0:0.1 +10 43572511 . C A 29 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GGCGCAGCCGGCGCTTACCT;RSEQ=GCTTCAGTCCCGCGACCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:29:1:1:0:60:4:1:0:2 0/0:3:0:0,0:3,0:3,0:0:0,0:21:1:25.7:1:1:0:60:2:1:0:2.3 +10 43572644 . G A 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75056;LSEQ=CCAGACTGAGCGCCGCACCC;RSEQ=CCATCCAGACCCGCCGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:2,1:122,76:198,3:0.0149:2,2:15.3:1:28.7:1:1:1.24:60:6:0.0155:0:1.3 0/1:178:2:1,1:103,72:175,2:0.0112:2,2:29:0:30.5:1:1:1.42758:60:4:0.0115:0:1 +10 43572659 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10862;SOR=Inf;LSEQ=CACCCGCCATCCAGACCCGC;RSEQ=GGCCCTAGCCGCAGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:162,101:263,0:0:2,0:26.1:1:31:1:1:0:59.9:262:1:0:0.3 0/1:241:3:1,2:141,97:238,3:0.0124:2,2:15:1:27.7:1:0.56983:2.8943:60:6:0.0128:0:1 +10 43572664 . C T 34 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3594;SOR=3.2021;LSEQ=GCCATCCAGACCCGCCGGCC;RSEQ=TAGCCGCAGTCCCTCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:0,1:184,109:293,1:0.0034:2,0:23:0:12:0:0.37415:0:60:0:0:0:2 0/1:277:3:0,3:160,114:274,3:0.0108:2,0:6:1:21.7:1:0.07424:0:60:2:0.0074:0:2 +10 43572796 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30799;SOR=4.48338;LSEQ=AAAGGTGAGTTCTGCCGGCC;RSEQ=CCGGCTCCCGCAGGGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:1:1,0:149,221:370,1:0.0027:2,0:1:0:28:0:0.40431:0:60:2:0.0028:0:1 0/1:250:3:2,1:96,151:247,3:0.012:2,2:15.7:1:26.7:1:0.5629:3.13:60:6:0.0123:0:1.3 +10 43572832 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04875;LSEQ=GCCAGGGCGAAGTTGGCGCC;RSEQ=AGCAGCGGAGCGGGCGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:227:210:56,154:2,15:17,210:0.9251:2,2:23.2:1:30.6:1:0.25045:2.72:60:41:0.9234:0:1.1 0/1:134:50:12,38:21,63:84,50:0.3731:2,2:24.3:1:29.7:1:1:1.05514:60:49:0.374:0:1.1 +10 43595781 . G T 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAATAATTGAGTGTTCAT;RSEQ=TTCTCAGGAACAGAGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:111,2:113,0:0:1,0:24.5:1:32.4:1:1:0:59.8:112:1:0:0.3 0/1:59:14:14,0:45,0:45,14:0.2373:1,1:28.1:1:30.1:1:1:0:60:13:0.2241:0:1.3 +10 43595836 . A AT 217 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.00034;SOR=0.46461;LSEQ=ATCGGAATTTTAAATTAATG;RSEQ=TTTTTTTTTTTTTTGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:110:104,6:120,15:135,110:0.3957:2,2:26.7:1:32:1:0.16774:2.16:59.1:54:0.406:0:1 0/1:176:41:38,3:106,15:121,41:0.233:2,2:29.2:1:30.9:1:0.56596:1.79:59.9:82:0.2398:0:1 +10 43595968 . A G 298 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15383;LSEQ=AAGCTGTATGTGGACCAGGC;RSEQ=GCCGGCACGCCCTTGCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:981:907:399,508:28,46:74,907:0.9246:2,2:25:1:30.4:1:0.33091:1.29:59.9:52.353:0.9261:0:1.1 1/0:891:582:267,315:138,164:302,582:0.6532:2,2:25.7:1:29.9:1:1:1.01:59.9:63.667:0.6526:0:1.2 +10 43596179 . G A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02168;LSEQ=TCAGTGTCCGCAGTAAGGGA;RSEQ=CCGCCCCAACACCCACCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:544:491:176,315:18,34:52,491:0.9026:2,2:26.9:1:29.4:1:1:1.06:60:34.071:0.9034:0:1.3 0/1:481:80:34,46:159,242:401,80:0.1663:2,2:24:1:28.3:1:0.70804:1.12:60:79:0.1667:0:1.3 +10 43596241 . C T 190 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAGCCGCCCTTATCACAGC;RSEQ=GCTGACACTGAAGCTTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:87:7,80:9,79:88,87:0.4943:2,2:25.8:1:29.5:1:0.79406:1.30003:59.8:16.4:0.4881:0:1.9 0/0:136:0:0,0:16,120:136,0:0:2,0:22.2:1:29.2:1:1:0:60:44.333:1:0:0.5 +10 43596307 . G T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08002;LSEQ=GAAGGCGTCAGGGGTTAAGT;RSEQ=AGGCTGGCCTGCCTCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:52:0,52:1,5:6,52:0.8966:2,1:21.9:1:28.7:1:0.10345:0:59.7:25:0.8929:0:1.4 0/1:30:12:1,11:1,17:18,12:0.4:1,2:27.8:1:28:1:1:1.52:60:24:0.4138:0:1 +10 43597256 . C A 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGGGACAGGCTAGCAAAAAG;RSEQ=AAAGAGAATGCCAGAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:3,0:3,1:0.25:0,0:23:0:13:0:1:0:60:0:0:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:28:1:1:0:60:4:1:0:1 +10 43597626 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGGCAGCAGGGCTGTGCAG;RSEQ=AGAGGTAAGGAGGTGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:113,3:116,2:0.0169:1,2:18:1:31.5:1:0.06693:32.74837:60:4:0.0172:0:1 0/0:38:0:0,0:36,2:38,0:0:2,0:22.1:1:32:1:1:0:60:76:1:0:0.1 +10 43597885 . G A 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=17.92699;LSEQ=AGTGGCCAGGCTGTGCCCGC;RSEQ=TATACTTCTCCTTCTTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1725:1:1,0:852,868:1720,1:6e-04:2,0:1:0:25:0:0.49564:0:60:2:6e-04:0:1 0/1:1360:14:9,5:663,680:1343,14:0.0103:2,2:25.4:1:28.9:1:0.29498:1.85:60:13:0.0096:0:1.1 +10 43598125 . G A 39 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52748;LSEQ=CACAGTGCCTGCTACTGCTG;RSEQ=TCTTGCTCTGCGAGCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:1,2:45,211:256,3:0.0116:2,2:20.7:1:25:1:0.44519:2.33:51.7:2:0.0079:0:1.3 0/0:163:1:1,0:28,134:162,1:0.0061:2,0:1:0:23:0:0.17791:0:60:2:0.0063:0:1 +10 43598126 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14665;SOR=Inf;LSEQ=ACAGTGCCTGCTACTGCTGG;RSEQ=CTTGCTCTGCGAGCCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:45,211:256,0:0:2,0:25.2:1:30.1:1:1:0:59.9:127:1:0:0.3 0/1:160:2:1,1:27,130:157,2:0.0125:2,2:34:1:28:1:0.32211:4.75:60:4:0.0127:0:1 +10 43598195 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04081;LSEQ=TCATGCCATCAGTTCATTCA;RSEQ=TATTCCAGAAGTACCTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:62:0,62:0,7:7,62:0.8986:0,1:21.5:1:33:1:1:0:60:124:0.8986:0:1.1 0/1:39:10:0,10:0,29:29,10:0.2564:1,0:25.6:1:32.6:1:1:0:60:20:0.2632:0:1 +10 43600210 . AGCACAGTCAT A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=CTGCAAACTGCAAACTCGTA;RSEQ=CGCTGCAAACTGCAAACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:22:21,1:19,1:20,22:0.5238:1,1:21.7:1:31.7:1:1:1.10:58.6:44:0.5238:0.0952:0.3 0/0:16:0:0,0:14,2:16,0:0:2,0:20.9:1:32.4:1:1:0:58.1:32:1:0:0.2 +10 43600304 . C T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93469;LSEQ=CCTGGGGCCGCGGCGGTGTG;RSEQ=GCCCCGCTCTGACCGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:2,1:147,24:171,3:0.0172:2,2:15.3:1:30:1:0.3739:3.03484:51.7:6:0.0176:0:2.3 0/1:62:1:1,0:56,5:61,1:0.0161:2,0:10:0:31:0:1:0:60:2:0.0161:0:1 +10 43600324 . GCC G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0;SOR=0.08907;LSEQ=CGCCCCGCTCTGACCGCAGA;RSEQ=CCCTTCCCGAGGAAAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:232:204:162,42:25,3:28,204:0.8793:2,2:24.2:1:32.9:1:0.3087:2.15459:59.9:203:0.8788:0.1509:0.1 0/1:115:45:34,11:60,10:70,45:0.3913:2,2:22.5:1:31.6:1:0.21735:1.92957:59.7:90:0.3913:0.1043:0.2 +10 43600343 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13866;SOR=Inf;LSEQ=AGCCCCCTTCCCGAGGAAAG;RSEQ=GGCTGGCCCGGTCCCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:214,70:284,0:0:2,0:26.4:1:31.5:1:1:0:59.9:34.5:1:0:0.1 0/1:169:2:2,0:125,42:167,2:0.0118:2,0:30.5:1:27.5:1:1:0:60:4:0.0118:0:1.5 +10 43600689 . A G 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07587;LSEQ=CCCAGTGTCTGTCTCCGGCC;RSEQ=CAGTTCGTTTCTCGGTCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:628:576:167,409:14,38:52,576:0.9172:2,2:25.2:1:31.2:1:0.87329:1.11:60:40.143:0.9198:0:1.2 0/1:397:181:67,114:68,148:216,181:0.4559:2,2:25.5:1:30.6:1:0.28752:1.28:60:362:0.4606:0:1.1 +10 43601325 . T TC 55 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTGGTGGGCAGAGCCA;RSEQ=CCAGGTGCCCAGCGGCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:12.8:1:27.6:1:1:0:60:8:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43601415 . G C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGATGTACACCTGGCCTC;RSEQ=GAGCTCGGCTCTGCCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:1,3:0.75:0,2:18:1:31:1:1:0:48:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43601749 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17886;LSEQ=CTGTGTGGGACGTGCAGCAT;RSEQ=CTAAGGTCTCTGGTTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:160:149:127,22:11,0:11,149:0.9313:0,2:22.6:1:32.4:1:0.3638:0:60:148:0.9308:0:1.1 1/0:109:77:63,14:27,5:32,77:0.7064:2,2:23.2:1:29.9:1:1:1.198:60:18.25:0.6952:0:1.1 +10 43601794 . G T 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32382;SOR=3.87767;LSEQ=CTGAGGGGCCCATCTCGCCT;RSEQ=CACTGACCAACGCCCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:1:0,1:267,83:350,1:0.0028:2,0:1:0:28:0:0.23932:0:60:2:0.0029:0:1 0/1:274:3:1,2:185,86:271,3:0.0109:2,2:23.7:1:30:1:0.24233:4.27708:60:6:0.0111:0:1.3 +10 43603007 . TCACACACA T 31 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=21.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GACCTTTAACCCCCCATGCC;RSEQ=CACACACACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:20.5:1:31:1:1:1:30.5:4:0.5:0:0.5 +10 43604148 . A C 86 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGCACAGACACCACACA;RSEQ=ATGCATACTACACACTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:2,0:2,6:0.6667:0,0:24:1:33.5:1:1:0:60:12:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43604390 . A T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.2494;LSEQ=TGCGTGTTTGCACCAGTGTG;RSEQ=GTGCAGGGCTGTGTCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:194:175:161,14:17,1:18,175:0.9021:1,2:21.9:1:30.2:1:1:1.47565:60:57.333:0.9053:0:1.1 1/0:115:80:71,9:31,4:35,80:0.6957:2,2:26.3:1:29.1:1:1:1.02:60:160:0.7018:0:1.1 +10 43604718 . G A 41 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55708;SOR=0;LSEQ=CTGTCTGGGGAAGATTGAAA;RSEQ=GCCAAGGGACATGGGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:65,228:293,3:0.0101:2,2:6.3:1:26:1:0.12953:6.96:60:2:0.0068:0:1 0/0:170:0:0,0:39,131:170,0:0:2,0:23.9:1:30.6:1:1:0:60:169:1:0:0.1 +10 43604745 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54142;SOR=0;LSEQ=GGACATGGGGGCACAGGGAG;RSEQ=CAGGTGACACTGCCTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:14,158:172,2:0.0115:2,2:9:1:29.5:1:0.16544:10.94:60:4:0.0118:0:1.5 0/0:95:0:0,0:10,85:95,0:0:2,0:19.8:1:30.9:1:1:0:60:46.5:1:0:0.1 +10 43604950 . A G 90 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAAAATGCAAGAGCAAT;RSEQ=CTGGGTAAATCTGCATATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:19.1:1:32.1:1:1:0:60:14:0.875:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43605246 . TAAA T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAGTAATAAATATTCAT;RSEQ=GAAGATGAGGCATGAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28.5:1:31.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43605860 . T G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTTTTTGCTGTGGTCAC;RSEQ=TGTGGGCCTGGGAGAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:28.7:1:32.7:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43605902 . A G 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGCTCTGGCCCGCCCCC;RSEQ=TCTCGCCATCTGTGGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:28:1:29.3:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43606650 . C T 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=46.76776;LSEQ=AAGGTGTTCCCCTGTGCCCC;RSEQ=CTAGATCGGGAAAGTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1068:2:0,2:596,470:1066,2:0.0019:2,0:5.5:1:19.5:1:0.19509:0:57:1:0.001:0:5 0/1:903:73:42,31:469,360:829,73:0.0808:2,2:26.3:1:29.3:1:0.90255:1.04:60:146:0.0822:0:1.9 +10 43606687 . A G 316 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02407;LSEQ=TGTGTGGAAAACTGCCAGGC;RSEQ=TTCAGTGGCATCAACGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1219:1212:646,566:2,0:2,1212:0.9943:0,2:25.2:1:30.9:1:0.50187:0:60:70.294:0.9975:0:1.1 1/1:1105:891:457,434:113,99:212,891:0.8063:2,2:25.4:1:30.1:1:0.6465:1.08387:60:98:0.807:0:1.2 +10 43607471 . T G 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00041;SOR=0;LSEQ=GGGCAGCTCAGCTGGTGCTG;RSEQ=TCCCTGTCCTTGGGCACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:14:11,3:111,4:115,14:0.1085:1,2:27.8:1:31.3:1:0.02778:7.35353:60:28:0.1085:0:1.1 0/0:94:0:0,0:85,9:94,0:0:2,0:21.1:1:29.2:1:1:0:60:188:1:0:0.2 +10 43607503 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17387;SOR=Inf;LSEQ=GGGCACTAGCTGGACGCTGG;RSEQ=CCCAGGCCAGCCCCCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:199,35:234,0:0:2,0:23.5:1:31:1:1:0:60:25:1:0:0.1 0/1:170:2:1,1:139,28:167,2:0.0118:2,2:32.5:1:30:0:0.3146:4.89556:60:4:0.012:0:1 +10 43607518 . C T 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32223;SOR=3.91974;LSEQ=GCTGGGCCCAGGCCAGCCCC;RSEQ=TGTGACCCTGCTTGTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:1:1,0:261,52:313,1:0.0032:2,0:40:0:16:0:1:0:55:0:0:0:8 0/1:242:3:1,2:184,55:239,3:0.0124:2,2:17.3:1:24:1:0.13911:6.62346:60:6:0.0125:0:1 +10 43607540 . C T 122 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=29.06467;LSEQ=GTGACCCTGCTTGTCTGCCA;RSEQ=CTGCAGATGTGGCCGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:1:0,1:332,126:458,1:0.0022:2,0:1:0:29:0:0.27669:0:60:2:0.0022:0:1 0/1:351:21:12,9:222,108:330,21:0.0598:2,2:20.9:1:28:1:0.34746:1.5397:60:20:0.0583:0:1 +10 43607714 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05857;SOR=Inf;LSEQ=GGGAGGCCTGCAGGGGCGAT;RSEQ=GCACCGGTGGAAACGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:121,320:441,0:0:2,0:23.5:1:31.1:1:1:0:59.9:54.125:1:0:0.4 0/1:281:3:2,1:79,199:278,3:0.0107:2,2:21.7:1:26:1:0.20044:5.00:60:6:0.0109:0:1.3 +10 43607756 . GTGGC ATGG 237 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGGGCCCTGCCAGCCTGGG;RSEQ=TCTCCCTGCTCCAGGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:184:184:10,174:0,0:0,184:1:0,2:21.8:1:31.6:1:1:0:59.8:183:1:0.2717:1.1 1/0:109:81:7,74:4,24:28,81:0.7431:2,2:20.4:1:30:1:0.46838:1.75175:59.4:162:0.75:0.2661:1.2 +10 43608522 . G C 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTCAGTTCTATGCATCAA;RSEQ=CTGAGCCTCCTGTGCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1986:0:0,0:979,1006:1985,0:0:2,0:24.6:1:32.6:1:1:0:60:59.152:0.9995:0:0.1 0/1:1538:36:21,15:744,751:1495,36:0.0234:2,2:20.2:1:30.8:1:0.31807:1.41:60:35:0.0232:0:1.1 +10 43608653 . G A 204 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=83.78393;LSEQ=CCCAGAAGTCGGCACACACA;RSEQ=ATTTCAGAAGCAGAGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2135:2:2,0:1061,1067:2128,2:9e-04:2,0:1:0:25.5:1:0.24894:0:60:4:9e-04:0:1 0/1:1687:123:61,62:765,795:1560,123:0.0729:2,2:23.8:1:29.5:1:0.92558:1.02:59.9:60.5:0.0725:0:1.2 +10 43608807 . G T 195 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=150.51838;LSEQ=AAATGTTAGGAGGGGGCCTG;RSEQ=CTTCACCCATGGCTTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1880:1:0,1:909,968:1877,1:5e-04:2,0:1:0:25:0:1:0:60:2:5e-04:0:1 0/1:1482:110:56,54:688,683:1371,110:0.0742:2,2:25.2:1:28.8:1:0.92122:1.03:59.9:54:0.0739:0:1.1 +10 43610119 . G A 317 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02021;LSEQ=CGGTCAGCTACTCCTCTTCC;RSEQ=GTGCCCGCCGGCCCTCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1333:1222:611,611:56,53:109,1222:0.9167:2,2:24.2:1:31:1:0.84168:1.05658:60:33.914:0.9173:0:1.1 0/1:1008:183:97,86:449,373:822,183:0.1815:2,2:23.9:1:29.6:1:0.74285:1.06716:60:60:0.1816:0:1.2 +10 43610366 . G A 331 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00901;LSEQ=ACAGTCTGTGGGGTGGGACT;RSEQ=TGATGAGGTGCCGTTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2281:2273:1133,1140:2,2:4,2273:0.9965:2,2:24.7:1:29.7:1:1:1.00618:59.8:80.179:0.9973:0:1.3 1/0:1973:1418:713,705:288,262:550,1418:0.7187:2,2:23.3:1:28.6:1:0.42165:1.08686:59.8:58.083:0.7182:0:1.3 +10 43610455 . T C 333 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00616;LSEQ=CAGTGTGGATGGAGGGGCAC;RSEQ=GAAGTCAGAAGGGGGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2005:1998:944,1054:2,1:3,1998:0.9965:2,2:24.4:1:30.4:1:0.60553:2.23219:60:59.545:0.9975:0:1.2 1/0:1783:1136:543,593:302,339:641,1136:0.6371:2,2:23.1:1:29.7:1:0.80473:1.03:59.9:102.273:0.6381:0:1.3 +10 43610558 . C T 340 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00506;LSEQ=ATCCTGGAGCCTCCTTGTCC;RSEQ=GGCCAGGCAGGCCTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1926:1921:946,975:1,1:2,1921:0.9974:2,2:24.6:1:31.2:1:1:1.03065:59.9:75.84:0.9974:0:1.2 1/0:1689:1115:555,560:281,290:571,1115:0.6602:2,2:24.3:1:29.9:1:0.83704:1.02:59.7:100.364:0.6615:0:1.2 +10 43610671 . G T 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGAAGTAACAGAGGCTCA;RSEQ=AGCCAAGGGTGTGAGTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1593:0:0,0:768,823:1591,0:0:2,0:25.6:1:32.6:1:1:0:59.9:78.55:0.9987:0:0.1 0/1:1261:76:36,40:588,597:1185,76:0.0603:2,2:24.5:1:28.2:1:0.72397:1.09427:59.9:75:0.0601:0:1.1 +10 43611708 . A G 340 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02018;LSEQ=TGGACACTTCCACTGTAGTC;RSEQ=GAGGTCCTGGGCTGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2260:2245:1138,1107:7,1:8,2245:0.9934:2,2:24.2:1:30.6:1:0.07012:6.80477:59.9:82.148:0.9942:0:1.1 1/0:1788:1343:674,669:224,218:442,1343:0.7511:2,2:24.5:1:29.7:1:0.86944:1.01989:59.9:88.533:0.7503:0:1.2 +10 43611865 . T C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.9653;LSEQ=GGGGCCTGGCTGTGGGGTCC;RSEQ=GCCCAGGGCAGAGACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1856:156:73,83:875,822:1697,156:0.0841:2,2:24.5:1:30.2:1:0.27682:1.21017:60:38:0.0835:0:1.2 0/1:1477:667:335,332:399,403:802,667:0.4516:2,2:23.9:1:29.6:1:0.87514:1.02:60:73.111:0.4513:0:1.1 +10 43612226 . C T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGGGGGAGTCTCCGGGG;RSEQ=GGGGGGCGGGTGAGGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:33,186:219,0:0:2,0:22.5:1:24.7:1:1:0:59.7:3.469:1:0:0.6 0/1:145:14:2,12:18,108:126,14:0.0966:2,2:22.8:1:27.6:1:1:1:58.1:6:0.1062:0:2.5 +10 43612609 . C T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCACAAGTTTGGCTCT;RSEQ=GATGGGCACATGCACCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:28.3:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43613741 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1722;SOR=Inf;LSEQ=GAACTTGGGCAAGGCGATGC;RSEQ=GGTCCATCCTGACCTGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:169,46:215,0:0:2,0:21.9:1:30.5:1:1:0:60:106.5:1:0:0.1 0/1:153:2:1,1:119,32:151,2:0.0131:2,2:14.5:1:28.5:1:0.38596:3.67763:60:4:0.0131:0:1.5 +10 43613843 . G T 285 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00557;LSEQ=AACGCCTCCCCGAGTGAGCT;RSEQ=CGAGACCTGCTGTCAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:669:667:362,305:0,0:0,667:0.997:0,2:25.1:1:30.4:1:1:0:60:46.643:0.9969:0:1.1 1/0:702:456:233,223:139,107:246,456:0.6496:2,2:24:1:29.2:1:0.17856:1.24292:59.8:90.2:0.6508:0:1.2 +10 43614230 . G A 47 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGTTCGGGGCTGGGCCC;RSEQ=TGGGGCAGGGAGCTCTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:31:1:29.7:1:1:0:60:6:1:0:1.7 1/1:1:1:0,1:0,0:0,1:1:0,0:15:0:25:0:1:0:60:2:1:0:1 +10 43614460 . G A 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGCGTGTGTGGGTGTGTGC;RSEQ=AGAGGGATAGGGAACCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:16.7:1:29.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43614885 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CCCCTTACTCATTGGGTGGC;RSEQ=GGGCCTGGGGACCCTGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:186,8:194,0:0:1,0:24.6:1:31.6:1:1:0:60:193:1:0:0.1 0/1:132:10:8,2:105,16:121,10:0.0758:2,2:23.1:1:29.6:1:0.62741:1.63345:60:20:0.0781:0:1.2 +10 43614902 . C T 74 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02364;SOR=9.47462;LSEQ=GGCCGGGCCTGGGGACCCTG;RSEQ=GGCCTCCCACCCCTGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:1,0:224,40:264,1:0.0038:2,0:34:0:27:0:1:0:60:2:0.0038:0:1 0/1:202:7:3,4:147,47:194,7:0.0347:2,2:8.9:1:26.4:1:0.07051:4.1333:60:6:0.0309:0:1.6 +10 43614971 . G A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00565;SOR=Inf;LSEQ=GCCCAGGGCCCCCTCTCTCC;RSEQ=CCCCCAGGCCCGCTCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:791:0:0,0:459,328:787,0:0:2,0:26.5:1:30.4:1:1:0:59.9:36.476:0.9961:0:0.2 0/1:580:6:4,2:311,263:574,6:0.0103:2,2:26.3:1:26.7:1:0.69287:1.69:60:12:0.0105:0:1 +10 43615094 . C T 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGCAGCCGCAACTCCAG;RSEQ=TCCCTGGACCACCCGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1195:0:0,0:582,613:1195,0:0:2,0:25.6:1:32.3:1:1:0:60:41.679:1:0:0.2 0/1:924:83:40,43:424,416:840,83:0.0898:2,2:22.5:1:28.6:1:0.73066:1.09556:60:40.5:0.089:0:1.2 +10 43615212 . G T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0737;SOR=Inf;LSEQ=AGGTGCGTGCATATGGCTCT;RSEQ=CACCCAGCCAGCCCCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:109,299:408,0:0:2,0:23.4:1:31.8:1:1:0:60:44.333:0.995:0:0.2 0/1:297:3:1,2:89,204:293,3:0.0101:2,2:19:1:21.3:1:1:1.15:58:2:0.0068:0:3.3 +10 43615223 . G A 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.31385;SOR=4.19745;LSEQ=TATGGCTCTGCACCCAGCCA;RSEQ=CCCCGGCCAGGCCACACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:1:0,1:68,256:324,1:0.0031:2,0:48:0:13:0:1:0:60:0:0:0:6 0/1:234:3:1,2:58,173:231,3:0.0128:2,2:10.3:1:21.3:1:1:1.49:58:2:0.0087:0:3.3 +10 43615284 . T C 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05141;SOR=Inf;LSEQ=CCCACACCCTGGCCTGCCAC;RSEQ=CCCCCACCATGCCACACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:18,106:124,0:0:2,0:25:1:29.3:1:1:0:59.9:16.714:1:0:0.3 0/1:75:3:2,1:11,61:72,3:0.04:2,2:16:1:26.3:1:0.07585:10.54:60:2:0.0282:0:1.3 +10 43615364 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09218;SOR=Inf;LSEQ=TCACCACGCCCCTGCCATGT;RSEQ=ACACCCTGACTCCACCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:51,35:86,0:0:2,0:23.4:1:31.5:1:1:0:59.7:13.333:1:0:1 0/1:38:2:1,1:20,16:36,2:0.0526:2,2:15.5:1:29:0:1:1.24262:60:4:0.0541:0:1.5 +10 43615382 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0035;LSEQ=GTCACACCCTGACTCCACCA;RSEQ=GCCCCTGCCATGCCACACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:80:76:56,20:3,1:4,76:0.95:2,2:28.6:1:30.6:1:1:1.07052:59.8:14.2:0.9467:0:1.3 0/1:37:2:1,1:24,11:35,2:0.0541:2,2:34.5:1:31:0:1:2.13205:60:4:0.0556:0:1.5 +10 43615386 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=4.000;MSILEN=1;SSF=0.00239;SOR=Inf;LSEQ=CACCCTGACTCCACCACGCC;RSEQ=CTGCCATGCCACACCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:64,18:82,0:0:2,0:28.2:1:31.4:1:1:0:59.8:40:1:0:1.1 0/1:37:5:4,1:23,9:32,5:0.1351:2,2:29.6:1:28.2:1:1:1.55:60:4:0.1143:0:1.2 +10 43615505 . G A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.6008;LSEQ=CTGCCTGGCCATGGCCTGAC;RSEQ=ACTCGTGCTATTTTTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:34:23,11:262,151:413,34:0.0759:2,2:24.1:1:30.1:1:0.71247:1.20:60:33:0.0755:0:1.1 0/1:386:68:48,20:194,123:317,68:0.1762:2,2:22.2:1:28.7:1:0.16746:1.52:60:21.667:0.1711:0:1.2 +10 43615633 . C G 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03112;LSEQ=GATGTTTATGAAGAGGATTC;RSEQ=TACGTGAAGAGGAGCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:562:511:207,304:21,29:50,511:0.9093:2,2:24.1:1:31:1:0.88056:1.06335:60:55.778:0.9078:0:1.2 0/1:591:140:58,82:186,264:450,140:0.2369:2,2:27.2:1:30.4:1:1:1.00:60:280:0.2385:0:1.1 +10 43615654 . G A 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28671;SOR=3.01821;LSEQ=TACGTGAAGAGGAGCCAGGT;RSEQ=CCCAGTCCCGGGGATGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:2:2,0:143,275:418,2:0.0048:2,0:4:1:19:1:0.11865:0:60:1:0.0024:0:3 0/1:421:6:4,2:152,263:415,6:0.0143:2,2:15.2:1:26:1:0.20025:3.45:60:12:0.0144:0:1.5 +10 43617517 . C A 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.30756;SOR=4.51757;LSEQ=GTTACAGAAACACCCTTATA;RSEQ=ATGTAGTGGGGCCACGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:1:1,0:105,313:418,1:0.0024:2,0:1:0:27:0:0.25298:0:60:2:0.0024:0:1 0/1:280:3:2,1:62,215:277,3:0.0107:2,2:9.7:1:23.7:1:0.13182:6.87:60:2:0.0072:0:1.3 +10 43618751 . G A 67 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGGCCTGCATTCTCACC;RSEQ=CTTTAAGTGTGAGAATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:13.2:1:29:1:1:0:56.4:10:0.8333:0:2.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43620134 . C T 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09804;SOR=0;LSEQ=GACCTGAGCACAGTGGCCCA;RSEQ=GGGCTGGGATCCTGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:11,1:4,0:4,12:0.75:0,2:36.1:1:32.7:1:1:0:60:24:0.75:0:1.1 0/0:2:0:0,0:2,0:2,0:0:0,0:32.5:1:29:1:1:0:60:4:1:0:0 +10 43620316 . T C 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12731;SOR=0;LSEQ=TTGGATCATATTGGCCTGTC;RSEQ=GCTCTTCCCACCAGGTACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:4:1,3:246,105:351,4:0.0113:2,2:16.3:1:24:1:0.08574:6.98591:60:3:0.0086:0:2 0/0:310:0:0,0:212,97:309,0:0:2,0:23:1:29.7:1:1:0:60:76.25:1:0:0.2 +10 43620497 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12677;SOR=Inf;LSEQ=GACTCCAGCCTCACCCCAGG;RSEQ=CAGTAGTTTTAGCCCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:17,172:189,0:0:2,0:22.7:1:32.3:1:1:0:60:46.25:1:0:0.1 0/1:105:2:1,1:15,88:103,2:0.019:2,2:26.5:1:29.5:1:0.28278:5.71:60:4:0.0192:0:1 +10 43620551 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=12.37447;LSEQ=GGCCACAGTGGGATTGTGCA;RSEQ=AGAGAGAGAGTCATGCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:7:0,7:0,60:60,7:0.1029:1,0:18.9:1:31.1:1:1:0:60:14:0.1045:0:1 1/0:37:22:1,21:0,15:15,22:0.5946:1,1:17.5:1:29.9:1:1:0:60:44:0.5946:0:1.2 +10 43621712 . A G 67 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAGATGAGGCGTCCCCCA;RSEQ=GGCTGCCCTCCAGGCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:27.3:1:33.5:1:1:0:59.3:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 43621996 . G T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12449;SOR=0;LSEQ=TAGTTGTGGCACATGGCTTG;RSEQ=AGTGACCGGCCATCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:4:2,2:224,94:318,4:0.0124:2,2:25.3:1:27.3:1:0.58546:2.37576:60:8:0.0126:0:1 0/0:303:0:0,0:197,106:303,0:0:2,0:25.4:1:30.6:1:1:0:60:59.6:1:0:0.2 +10 43622217 . T C 299 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTAGCACCGCTGTCCCCT;RSEQ=TGCACTATCCTTCCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:584:584:201,383:0,0:0,584:1:0,2:24.1:1:32.6:1:1:0:60:96.333:1:0:1.1 1/0:631:489:184,305:56,84:140,489:0.775:2,2:24.2:1:31:1:0.62275:1.10489:60:488:0.7783:0:1.1 +10 43622368 . T A 178 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00031;SOR=0;LSEQ=ACTATGTTTTTCTAAAAGGA;RSEQ=GTGAAAATAAGTGTAATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:2,46:0,0:0,48:1:0,1:24:1:31.9:1:1:0:59.1:96:1:0:1 1/0:14:9:0,9:1,4:5,9:0.6429:2,0:21.9:1:30:1:0.35714:0:60:18:0.6429:0:1 +10 43623474 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51807;SOR=0;LSEQ=CACGAGTTTGGTTTGAACAT;RSEQ=AAAGGGAGTTTTGCCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:95,3:98,2:0.02:1,2:15:1:28:1:0.07879:27.56815:60:4:0.0204:0:1 0/0:66:0:0,0:64,2:66,0:0:1,0:22.8:1:30.8:1:1:0:60:65:1:0:0.1 +10 43623479 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5641;SOR=3.06441;LSEQ=GTTTGGTTTGAACATCAAAG;RSEQ=GAGTTTTGCCAAGGCCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:1,0:106,5:111,1:0.0089:1,0:30:0:32:0:1:0:60:2:0.0091:0:1 0/1:74:2:1,1:70,2:72,2:0.027:1,2:19.5:1:27:1:0.07997:28.75679:60:4:0.027:0:1 +10 43623783 . G A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.5233;LSEQ=CTGAGAATGGAAAGTCTACC;RSEQ=GCCCTTTCTTTGTGAACGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:26,138:164,2:0.012:2,2:18:1:31.5:1:0.29967:5.23:60:4:0.0121:0:1 0/0:158:1:0,1:18,139:157,1:0.0063:2,0:15:0:32:0:1:0:60:2:0.0064:0:1 +10 43623812 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45063;SOR=0.6434;LSEQ=TTTGTGAACGTCACATTGGC;RSEQ=GAGCCGTGTTCAGTTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:11:0,11:3,77:80,11:0.1209:1,0:23.3:1:30.3:1:1:0:60:22:0.1222:0:1 0/1:74:6:0,6:2,65:67,6:0.0811:1,0:23.2:1:29:1:1:0:60:12:0.0811:0:1 +10 43624105 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGGATTTTTCTAGTTGCC;RSEQ=CCAAACAAGGCAAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:27.3:1:32:0:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 44126388 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51825;SOR=Inf;LSEQ=ACCACCGTCTTCCAGTAATT;RSEQ=GACAAAATGACAAACACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:52,58:110,0:0:2,0:27.9:1:30.7:1:1:0:60:109:1:0:0.1 0/1:165:2:1,1:80,83:163,2:0.0121:2,2:18.5:1:28:1:1:1.04:60:4:0.0124:0:1 +10 44126421 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18309;SOR=0;LSEQ=AACACAAAGGGAAAGAGGAG;RSEQ=GGCTCCTGGTAGATGTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:34,55:89,2:0.022:2,2:22.5:1:29:1:1:1.61:60:4:0.022:0:1 0/0:121:0:0,0:55,66:121,0:0:2,0:21.5:1:29.2:1:1:0:59.9:39.333:1:0:0.1 +10 44126599 . G C 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAGAGTCTACAGTGTTAC;RSEQ=CAGCAGGCCGTCGGCATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:21,32:53,0:0:2,0:27.1:1:30.9:1:1:0:60:52:1:0:0.1 1/0:41:21:7,14:7,13:20,21:0.5122:2,2:24.6:1:30.1:1:1:1.07497:53.8:42:0.525:0:1.2 +10 44237687 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50006;SOR=0;LSEQ=TAATGCATGTTGTCTTTTTA;RSEQ=AACAAATTCATGACCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:88,26:114,2:0.0171:2,2:16:1:27.5:1:0.41289:3.34011:60:4:0.0175:0:2 0/0:102:0:0,0:68,34:102,0:0:2,0:19.2:1:31:1:1:0:60:204:1:0:0 +10 44237699 . G T 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24015;SOR=Inf;LSEQ=TCTTTTTACAACAAATTCAT;RSEQ=ACCATCAGAAGATATCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:100,41:141,0:0:2,0:21.8:1:31.8:1:1:0:60:69.5:1:0:0.1 0/1:136:2:1,1:81,53:134,2:0.0147:2,2:7:0:30.5:1:1:1.52336:60:4:0.0148:0:1 +10 44728442 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04784;SOR=Inf;LSEQ=GGATGGGGTTTTTGTGGGGG;RSEQ=CTTTGTTGTTGTTATTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,10:20,0:0:2,0:29.9:1:32.4:1:1:0:55.6:40:1:0:0.2 0/1:21:5:3,2:8,8:16,5:0.2381:2,2:21.8:1:28:1:1:1.47:45.8:10:0.2381:0:1.4 +10 44728592 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09023;SOR=Inf;LSEQ=GATTCGCTCCTGTGCCTGGA;RSEQ=ATGTCATTCAAGGAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:10,0:0:2,0:27.2:1:31.5:1:1:0:43.4:20:1:0:0 0/1:11:4:2,2:1,6:7,4:0.3636:2,2:34.3:1:29.8:1:0.49091:4.95:39.3:8:0.3636:0:1.8 +10 44728597 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16374;SOR=Inf;LSEQ=GCTCCTGTGCCTGGAGATGT;RSEQ=ATTCAAGGAGGCTGGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:23.9:1:30.3:1:1:0:44.9:22:1:0:0 0/1:8:2:1,1:1,5:6,2:0.25:2,2:40.5:1:27.5:1:0.46429:3.87:49.5:4:0.25:0:2 +10 44728797 . T C 47 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=ATTTTGTCCCTTGGTGGTGA;RSEQ=GGTGGTGTGCTTCACTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:10:1:31.7:1:1:0:60:6:1:0:0 1/0:5:3:1,2:1,1:2,3:0.6:2,2:26.3:1:30:1:1:1.7321:57.7:6:0.6:0:1 +10 44728977 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=TCTGGCTGGAGTTATTGGAG;RSEQ=TCCTGCAGGGAAGCCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:22:1:30.8:1:1:0:60:10:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:35:0:30:1:1:0:36:4:1:0:1 +10 44729300 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TGGTCGCCCCTCCCCCTGGG;RSEQ=GTTCAGTAGGCTTAAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:8,0:0:2,0:33.8:1:31.3:1:1:0:58.3:16:1:0:0.1 0/1:8:2:1,1:3,3:6,2:0.25:2,2:30:0:32:0:1:1:20:4:0.3333:0:2.5 +10 44729307 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=Inf;LSEQ=CCCTCCCCCTGGGAGTTCAG;RSEQ=AGGCTTAAGCAGATTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:8,0:0:2,0:35.3:1:29.4:1:1:0:58.3:16:1:0:0.1 0/1:10:2:1,1:4,4:8,2:0.2:2,2:37:0:33:0:1:1:20:4:0.2:0:2.5 +10 44729599 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12606;SOR=Inf;LSEQ=AACCTGGATACGCTGGTTGC;RSEQ=GGTGAAGGACTCACCCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:14,0:0:2,0:30.9:1:30.7:1:1:0:60:28:1:0:0.2 0/1:20:4:2,2:6,10:16,4:0.2:2,2:21.8:1:26.3:1:1:1.62:60:3:0.1579:0:1.5 +10 44729641 . A ATTT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.49275;SOR=Inf;LSEQ=TTATGGTTTTTTTTTTCATT;RSEQ=TTTATTATTATTATTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:24.5:1:30.5:1:1:0:54.3:20:1:0:0.1 0/1:14:2:0,2:5,7:12,2:0.1429:2,0:48.5:1:31.8:1:0.50549:0:60:4:0.1429:0:0 +10 44729642 . T TTTA 47 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=38;MSI=13.000;MSILEN=3;SSF=0.04743;SOR=0;LSEQ=TATGGTTTTTTTTTTCATTA;RSEQ=TTATTATTATTATTATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:2,3:5,3:0.3333:2,2:14.7:1:30.1:1:1:1.28664:48.7:6:0.3333:0.1111:0.3 0/0:14:0:0,0:5,9:14,0:0:2,0:29.2:1:30.7:1:1:0:60:28:1:0:0.4 +10 45071312 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAAGGGACGGCAGCTTC;RSEQ=CCCCAGGGCAGGCCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 45072488 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48649;SOR=Inf;LSEQ=GAGTGAAACAGTGCTGAGGG;RSEQ=CCCAGGCCCAGGGACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:19,0:0:2,0:23.3:1:31.2:1:1:0:60:38:1:0:0.4 0/1:19:2:1,1:11,6:17,2:0.1053:2,2:10.5:1:28:1:1:1.77272:60:4:0.1053:0:1 +10 45072521 . G A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01727;SOR=0.21012;LSEQ=GACAGGCAGCTCTGTGGCTC;RSEQ=CACCCTCATCCGCTGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:4,7:7,7:14,11:0.44:2,2:28.5:1:30.5:1:0.68875:1.71101:60:22:0.44:0:1.1 0/1:29:4:1,3:15,10:25,4:0.1379:2,2:27:1:29:1:0.2994:4.27461:60:8:0.1379:0:1 +10 45072584 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50202;SOR=Inf;LSEQ=TCCCACCCTTTTTCTGATCC;RSEQ=CATGAATTTGTGAGCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:18.2:1:31.4:1:1:0:60:26:1:0:0.5 0/1:19:2:1,1:6,11:17,2:0.1053:2,2:25.5:1:28:1:1:1.77:60:4:0.1053:0:1 +10 45385828 . A C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19156;LSEQ=CCCTGGGGCCCCAGCAGCCG;RSEQ=TAGGGTGGTAGCCAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:15:15,0:6,0:6,15:0.7143:0,1:21.5:1:33.3:1:1:0:60:30:0.7143:0:1.1 1/0:4:3:3,0:1,0:1,3:0.75:0,0:22.7:1:32:1:1:0:60:6:0.75:0:1 +10 45385937 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=3.13934;LSEQ=AGGTTTTAAGCCTGAGATAC;RSEQ=GGCAGATGCCAATGGTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:51:42,9:43,10:53,51:0.4904:2,2:22.3:1:30:1:1:1.08:60:102:0.4904:0:1.1 1/0:105:79:61,18:21,4:25,79:0.7524:2,2:22.9:1:29.6:1:0.58155:1.54311:60:158:0.7524:0:1 +10 45386046 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68952;SOR=1.07812;LSEQ=TGTTCTGAAGCAGAAGAAAC;RSEQ=GATGGTGCCCATGAACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:147:73,74:75,76:151,147:0.4933:2,2:26:1:30.3:1:1:1.00036:60:72.5:0.4899:0:1.1 1/0:330:169:79,90:81,80:161,169:0.5121:2,2:24.7:1:29.2:1:0.58181:1.15298:60:168:0.5122:0:1.1 +10 45386322 . G T 62 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=GGTGTAACTGGGTCCACCAG;RSEQ=GCAGCAATTGCAGGTTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:33:0:34:0:1:0:60:2:1:0:0 1/1:4:4:1,3:0,0:0,4:1:0,2:22.5:1:31:1:1:0:60:8:1:0:1.8 +10 45386352 . C A 27 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GCAGGTTCAGCAAGGAGCCT;RSEQ=TGGATCTGTGGCCAGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:27.5:1:1:0:60:4:1:0:2.5 +10 49842541 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16371;SOR=Inf;LSEQ=GAAACCATTGTAGGAAACTG;RSEQ=GTCTCTAAGAAGAGCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:115,27:142,0:0:2,0:21:1:31.2:1:1:0:60:70:1:0:0.1 0/1:97:2:1,1:82,13:95,2:0.0206:2,2:21.5:1:28:1:0.26912:6.11521:60:4:0.0211:0:1.5 +10 49842556 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50032;SOR=0;LSEQ=AACTGGGTCTCTAAGAAGAG;RSEQ=CGCTGACTCAGCCCTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:126,47:173,2:0.0114:2,2:34.5:1:30.5:1:0.47448:2.66329:60:4:0.0116:0:1.5 0/0:155:0:0,0:113,42:155,0:0:2,0:21.2:1:31:1:1:0:60:50.667:1:0:0.1 +10 49842601 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12311;SOR=Inf;LSEQ=CTGTGGCTGGGGGTGGGTGA;RSEQ=CCTGGGCTTCCGCTTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:164,133:297,0:0:2,0:26.2:1:32:1:1:0:60:28.7:1:0:0.5 0/1:295:3:1,2:157,135:292,3:0.0102:2,2:14:1:27.7:1:0.5988:2.31946:60:6:0.0103:0:1.7 +10 49842643 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12057;SOR=0;LSEQ=CTAGAGGGTAGTGTGGCTGG;RSEQ=AGGGCATCTGTCTAGACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:1,2:119,168:287,3:0.0103:2,2:13.7:1:26:1:1:1.41503:60:6:0.0106:0:2 0/0:296:0:0,0:131,165:296,0:0:2,0:25:1:31.4:1:1:0:59.9:295:1:0:0.5 +10 49842655 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34347;LSEQ=GTGGCTGGCAGGGCATCTGT;RSEQ=TAGACACTCTCTGAGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:271:186:75,111:31,52:83,186:0.6863:2,2:25.1:1:30.1:1:0.68665:1.13:60:36.2:0.683:0:1.1 0/1:252:108:44,64:60,84:144,108:0.4286:2,2:22.9:1:29.6:1:0.89784:1.03882:59.6:53:0.4274:0:1.2 +10 49843065 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGAATGGGAAAAAATAC;RSEQ=TGTATGTTGTGAAAGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:31:1:1:0:55:4:1:0:1.5 +10 49977719 . C G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3961;SOR=1.16836;LSEQ=CATATCTTGGAATGCTGAAC;RSEQ=CAACACCCATGCCTCTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:113:59,54:89,93:182,113:0.3831:2,2:28.2:1:31.1:1:0.63234:1.14:60:55.5:0.3801:0:1.1 0/1:283:119:65,54:90,74:164,119:0.4205:2,2:25.9:1:29.9:1:1:1.01036:60:58.5:0.4164:0:1.2 +10 49977746 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00769;SOR=0.63703;LSEQ=CCATGCCTCTTTAGGGGACC;RSEQ=ATTGCTCCAGGACCCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:291:172:79,93:56,63:119,172:0.5911:2,2:24.4:1:31.7:1:0.90498:1.04628:60:85:0.5903:0:1.1 0/1:288:138:71,67:70,79:149,138:0.4792:2,2:26.7:1:30.7:1:0.4795:1.20:60:68:0.4789:0:1.1 +10 49977805 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50064;SOR=Inf;LSEQ=CATATTAATCTGGACCAAGA;RSEQ=AGAAAGTGGGGAACAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:47,100:147,0:0:2,0:23.8:1:32.4:1:1:0:60:294:1:0:0.5 0/1:168:2:1,1:54,112:166,2:0.0119:2,2:26:1:29.5:1:0.5489:2.06:60:4:0.0119:0:1.5 +10 49977882 . G A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02325;LSEQ=AGCGTGGACTTAAAGGCTAG;RSEQ=TCGTTAAGTGAAGAATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:27:0,27:0,16:16,27:0.6279:1,1:28:1:31.7:1:1:0:60:54:0.6279:0:1 1/0:30:19:1,18:0,11:11,19:0.6333:0,1:21.1:1:29.2:1:1:0:60:18:0.6207:0:1.1 +10 49977973 . C A 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=GGGCCCAGCCCGCTGGCCAA;RSEQ=CTGGTGACCCTGTGCTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:32.3:1:29.7:1:1:0:60:6:0.6:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:35.5:1:26:1:1:0:60:4:0.6667:0:1 +10 52388952 . G A 80 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAAGGTACAGTATTTGC;RSEQ=TATAACCTCCCCATATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:23.3:1:31:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 52389217 . T A 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50027;SOR=0;LSEQ=ACAAAGTGAAAATGAGGAAT;RSEQ=CTCATTCTGTAAATGAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:156,21:177,2:0.0112:2,2:23:0:28:1:0.23131:7.27962:60:4:0.0113:0:1.5 0/0:159:0:0,0:131,28:159,0:0:2,0:19.6:1:29.5:1:1:0:59.5:38.75:1:0:0.1 +10 52389659 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09488;LSEQ=TCTGAATCACCTGCCTCAGA;RSEQ=CTGCAGCAAAGTTTCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:173:83,90:66,76:142,173:0.5492:2,2:22.9:1:29.9:1:0.82113:1.06:57.3:56.667:0.5502:0:1.1 0/1:281:29:15,14:124,127:251,29:0.1032:2,2:19.4:1:29.1:1:0.84665:1.10:56.1:58:0.1074:0:1.2 +10 52389662 . G A 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67098;SOR=1.68197;LSEQ=GAATCACCTGCCTCAGAGCT;RSEQ=CAGCAAAGTTTCTGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:2:2,0:146,165:311,2:0.0064:2,0:12:1:18.5:1:0.22278:0:60:1:0.0032:0:3.5 0/1:281:3:3,0:138,140:278,3:0.0107:2,0:8:1:23.7:1:0.24733:0:60:6:0.0109:0:1.3 +10 52390008 . C T 45 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13511;SOR=0;LSEQ=TCATCGCCAGTTTGAAATGG;RSEQ=GATAGAGCAGGTAACACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:4:1,3:149,160:309,4:0.0127:2,2:9:1:22.5:1:0.62389:2.78523:60:3:0.0097:0:1 0/0:245:0:0,0:121,124:245,0:0:2,0:25:1:30.6:1:1:0:59.7:244:1:0:0.1 +10 52390506 . A T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0959;LSEQ=AAATCTGGATCCTTAATAAC;RSEQ=TCACTCAATTCATCCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:347:202:110,92:76,69:145,202:0.5821:2,2:25:1:31.3:1:0.74387:1.09:60:100:0.5831:0:1.1 0/1:383:45:26,19:202,135:337,45:0.1175:2,2:25:1:29.8:1:0.87168:1.09319:60:90:0.1194:0:1 +10 52390836 . A G 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01591;LSEQ=CCTTGCTCGCTTCCGTATCC;RSEQ=TATTCTACAATTCTTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:356:354:134,220:0,1:1,354:0.9944:0,2:25.2:1:31.5:1:1:0:59.8:353:0.9972:0:1.1 1/0:384:283:111,172:50,51:101,283:0.737:2,2:25.6:1:30.5:1:0.07879:1.51743:59.7:46.167:0.7387:0:1.1 +10 52390900 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25128;SOR=Inf;LSEQ=GCTTGGCATAGTAGTCTAGG;RSEQ=CGACCCCTCGAAGTAGACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:108,132:240,0:0:2,0:24.4:1:31.8:1:1:0:60:79:1:0:0.5 0/1:272:3:1,2:130,139:269,3:0.011:2,2:19.7:1:25.7:1:1:1.86637:60:6:0.0114:0:1 +10 52390994 . C A 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60706;SOR=0.45326;LSEQ=GGCTCCTGGCTGAGGCTGAA;RSEQ=GCCGGGGTCAGCATCGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:50,111:161,2:0.0123:2,2:10:1:33:1:0.5292:2.21:60:4:0.0126:0:1 0/0:179:1:1,0:65,113:178,1:0.0056:2,0:1:0:23:0:0.36872:0:60:2:0.0058:0:1 +10 52391028 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24634;SOR=0;LSEQ=TCGCGGCACCAGACGCAGGG;RSEQ=CCAGCGCGGCTCGCCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:13,87:100,2:0.0196:2,2:22.5:1:29:1:0.25684:6.49:60:4:0.0202:0:1 0/0:103:0:0,0:24,79:103,0:0:2,0:24.6:1:31:1:1:0:60:206:1:0:0.1 +10 52391216 . A G 73 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATCAGCCCCGCCGACATG;RSEQ=CGAAACTCCGTCTCTACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:19.8:1:31.6:1:1:0:59.2:10:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:3:0:28:0:1:0:60:2:1:0:1 +10 52833765 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACGTCGCTAGGATCGTAGC;RSEQ=CAACATTCTCCAGGCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:16:1:31:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 52834254 . A C 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06797;SOR=Inf;LSEQ=AGGAAGCTTTGGCACTCGGG;RSEQ=GGCAGCGGCGACTTTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:59,27:86,0:0:2,0:23.9:1:30:1:1:0:60:42:1:0:0.1 0/1:109:5:2,3:60,43:103,5:0.0459:2,2:25.8:1:30.6:1:0.64884:2.07855:60:10:0.0472:0:1 +10 52834260 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.56421;LSEQ=CTTTGGCACTCGGGAGGCAG;RSEQ=GGCGACTTTGGGGAAAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:1:1,0:58,29:87,1:0.0114:2,0:27:0:12:0:1:0:60:0:0:0:3 0/1:113:2:1,1:62,49:111,2:0.0177:2,2:19:1:27:1:1:1.26264:60:4:0.018:0:1 +10 52834329 . GC G 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.5862;LSEQ=CGGAGCAGCGGCAGGAAGGA;RSEQ=CCCCGGCAGCCCGGAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:64,60:124,2:0.0159:2,2:35.5:1:32.5:1:1:1.06615:60:4:0.0164:0:0.5 0/0:107:1:0,1:54,51:105,1:0.0093:2,0:20:0:33:0:0.49057:0:60:2:0.0095:0:0 +10 52834362 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51092;SOR=0;LSEQ=CGGAGGAGCATGGGCACCTT;RSEQ=CGGGATTTACAGTACGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:65,66:131,2:0.015:2,2:14:0:32.5:1:1:1.02:60:4:0.015:0:1 0/0:96:0:0,0:50,46:96,0:0:2,0:25.4:1:31.1:1:1:0:60:47:1:0:0.1 +10 52834391 . A T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62634;LSEQ=ACAGTACGCGCTCCAGGAGA;RSEQ=GATCGAGGAGCTGAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:57,58:115,2:0.0171:2,2:32.5:1:30:1:1:1.02:60:4:0.0171:0:1 0/1:93:1:0,1:45,47:92,1:0.0108:2,0:1:0:25:0:1:0:60:2:0.011:0:1 +10 52834437 . G T 29 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12184;LSEQ=GCTCTCATCGACGAGCTGGA;RSEQ=CTGGAGTTGGATCAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:2,0:52,57:109,2:0.0179:2,0:35.5:1:23.5:1:0.2344:0:44.5:1:0.0091:0:3.5 0/1:100:2:1,1:47,51:98,2:0.02:2,2:47:0:29:0:1:1.08:60:4:0.0202:0:1 +10 52834447 . G T 41 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25151;SOR=0;LSEQ=ACGAGCTGGAGCTGGAGTTG;RSEQ=ATCAGAAGGACGAACTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:3:1,2:53,55:108,3:0.027:2,2:6:1:26.3:1:1:1.91633:60:6:0.0278:0:1 0/0:94:0:0,0:44,50:94,0:0:2,0:26.4:1:30.3:1:1:0:60:93:1:0:0.1 +10 52834529 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12498;SOR=Inf;LSEQ=CCGACCAGCCACCCAGCAGG;RSEQ=GCAGAAGCAGAGCGCGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:53,43:96,0:0:2,0:24.7:1:31.2:1:1:0:60:95:1:0:0.2 0/1:53:2:1,1:21,30:51,2:0.0377:2,2:18.5:1:27.5:1:1:1.42:60:4:0.0377:0:1 +10 52834585 . A T 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52492;SOR=0;LSEQ=CGCGCACCAAGCGGCAGGCG;RSEQ=TCTCCGCCGAGCCCACCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:50,42:92,2:0.0213:2,2:14:0:28.5:1:1:1.18826:60:4:0.0215:0:1 0/0:58:0:0,0:26,32:58,0:0:2,0:22.1:1:29.6:1:1:0:60:116:1:0:0.1 +10 52834616 . A T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20835;SOR=Inf;LSEQ=GCCCACCGCCTTCGACATCC;RSEQ=GGATCTCAGCCATGTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:63,40:103,0:0:2,0:24.8:1:31:1:1:0:60:102:1:0:0.2 0/1:87:2:1,1:51,34:85,2:0.023:2,2:5:1:28.5:1:1:1.4928:60:4:0.023:0:1 +10 52834639 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49793;SOR=Inf;LSEQ=ATCTCAGCCATGTGACCCTG;RSEQ=CCTTCTACCCCAAGAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:71,47:118,0:0:2,0:23.8:1:31.5:1:1:0:60:58:1:0:0.2 0/1:120:2:1,1:77,41:118,2:0.0167:2,2:9:1:26.5:1:1:1.86764:60:4:0.0168:0:1 +10 52834679 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24746;SOR=0;LSEQ=ACAGTAAGCAGGGGTGACGC;RSEQ=CCGGGTCCATGTGGCGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:3:1,2:71,72:143,3:0.0204:2,2:25:1:27.3:1:1:1.9634:60:6:0.0208:0:2.7 0/0:145:0:0,0:89,55:144,0:0:2,0:25.3:1:29.8:1:1:0:60:288:0.9931:0:0.2 +10 52834694 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4986;SOR=0;LSEQ=GACGCGCCGGGTCCATGTGG;RSEQ=GCCCTGGCGATGGGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:81,85:166,2:0.0119:2,2:19.5:1:29:1:1:1.05:60:4:0.0123:0:1 0/0:163:0:0,0:94,69:163,0:0:2,0:23.1:1:29.7:1:1:0:59.8:162:1:0:0.1 +10 52834707 . G A 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.61989;SOR=0.48734;LSEQ=CATGTGGCGCCCTGGCGATG;RSEQ=GGAGCTGCGGGTCTCTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:83,95:178,2:0.011:2,2:21:1:33:1:1:1.14:60:4:0.0114:0:1 0/0:185:1:1,0:104,79:183,1:0.0054:2,0:2:0:24:0:1:0:60:2:0.0055:0:1 +10 52834721 . T C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.87329;LSEQ=GCGATGGGGAGCTGCGGGTC;RSEQ=CTGTATTGTCTGTCGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:1:1,0:83,98:181,1:0.0055:2,0:27:0:8:0:0.46154:0:60:0:0:0:3 0/1:196:2:1,1:103,91:194,2:0.0102:2,2:34.5:1:29:1:1:1.13115:60:4:0.0106:0:1 +10 52834808 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24894;SOR=Inf;LSEQ=ATTTTAACGGGCACTTCTTG;RSEQ=GGGGCTGTGCACGTTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:101,110:211,0:0:2,0:25.3:1:30.5:1:1:0:60:34.167:1:0:0.2 0/1:224:3:1,2:108,112:220,3:0.0134:2,2:30:1:29:1:1:1.92311:60:6:0.0136:0:1 +10 52834856 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4998;SOR=Inf;LSEQ=ACTCACTGCACATACGTTGC;RSEQ=TTCGTGTCTTTGTCAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:59,99:158,0:0:2,0:26.3:1:32.6:1:1:0:59.8:157:1:0:0.2 0/1:175:2:1,1:67,106:173,2:0.0114:2,2:34:1:29.5:1:1:1.58:60:4:0.0114:0:1 +10 52834870 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=CGTTGCCTTCGTGTCTTTGT;RSEQ=AGATGTCAAGGTATTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:47,88:135,0:0:2,0:23.5:1:32.3:1:1:0:59.7:134:1:0:0.2 0/1:148:2:1,1:49,97:146,2:0.0135:2,2:22.5:1:28:1:1:1.97:60:4:0.0139:0:1 +10 52834872 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2187;SOR=0;LSEQ=TTGCCTTCGTGTCTTTGTCA;RSEQ=ATGTCAAGGTATTATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:40,85:125,2:0.0157:2,2:24:1:29:1:0.54318:2.11:60:4:0.016:0:1 0/0:144:0:0,0:48,96:144,0:0:2,0:25.8:1:31.1:1:1:0:60:288:1:0:0.1 +10 53238115 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10966;LSEQ=TCTTTAATTGCCTTAAGGAA;RSEQ=AATCTGAATCTATAATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:383:344:153,191:13,26:39,344:0.8982:2,2:24.9:1:30.6:1:0.23278:1.60:60:171:0.9:0:1.1 0/1:383:188:86,102:80,115:195,188:0.4909:2,2:23:1:29.2:1:0.35571:1.21:60:93:0.4908:0:1.1 +10 53238190 . A C 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAATTTTTATAAGAATGCA;RSEQ=AAACTGGCCCCCTTGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:36,129:165,0:0:2,0:25.4:1:30.8:1:1:0:60:81.5:1:0:0.4 0/1:151:23:7,16:39,89:128,23:0.1523:2,2:25.9:1:31.4:1:1:1.00159:60:46:0.1523:0:1.5 +10 53238191 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23034;SOR=Inf;LSEQ=TAATTTTTATAAGAATGCAA;RSEQ=AACTGGCCCCCTTGATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:35,127:162,0:0:2,0:25.5:1:30.7:1:1:0:60:53:1:0:0.4 0/1:150:2:1,1:45,103:148,2:0.0133:2,2:35:1:30:1:0.52072:2.27:60:4:0.0134:0:1.5 +10 53238223 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52917;SOR=0;LSEQ=TTGATGATTCAAACTACTTC;RSEQ=GGCCAAATCCTTGACCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:13,89:102,2:0.0192:2,2:11.5:1:29.5:1:0.25224:6.63:60:4:0.0194:0:1 0/0:62:0:0,0:7,55:62,0:0:2,0:21.1:1:29.6:1:1:0:59.6:30:1:0:0.4 +10 53793287 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50587;SOR=0;LSEQ=ATCACCTTTTTAGCTATTTA;RSEQ=CTATTCCCAGCCTTGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:2,0:114,18:132,2:0.0149:2,0:34.5:1:32:0:1:0:60:4:0.0155:0:2.5 0/0:104:0:0,0:88,16:104,0:0:2,0:24.9:1:31.7:1:1:0:60:208:1:0:0.1 +10 53793313 . G T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04423;SOR=Inf;LSEQ=CCCAGCCTTGGAGACAGTCT;RSEQ=TCCTCCAGTTTTATGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:145,61:206,0:0:2,0:25.3:1:32.2:1:1:0:60:102:1:0:0.1 0/1:176:4:2,2:125,47:172,4:0.0227:2,2:26.5:1:28.8:1:0.30962:2.64248:60:8:0.0229:0:1 +10 53793329 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2563;SOR=0;LSEQ=GTCTGTCCTCCAGTTTTATG;RSEQ=AGGTTGAGCTACTGTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:168,93:261,3:0.0114:2,2:12.7:1:28.7:1:0.29454:3.59444:60:6:0.0115:0:1 0/0:215:0:0,0:141,74:215,0:0:2,0:25.6:1:31.3:1:1:0:60:106.5:1:0:0.3 +10 53793416 . G A 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGAATTCAGAAACTCTAAA;RSEQ=TATATGTAAAGCAGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:436:436:217,219:0,0:0,436:1:0,2:24.5:1:30.6:1:1:0:60:86.2:1:0:1.1 1/1:499:416:217,199:40,43:83,416:0.8337:2,2:24.6:1:29.3:1:0.54847:1.17:60:40.6:0.8303:0:1.1 +10 53793523 . A G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.05199;LSEQ=ACAAGTGGTAAATTTCATGC;RSEQ=CGTCCGTGTGAACAGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:159:158:42,116:1,0:1,158:0.9937:0,2:23.5:1:31.2:1:0.27044:0:55.9:51.667:0.9936:0:1.1 1/1:165:147:43,104:3,13:16,147:0.8909:2,2:23.6:1:30.1:1:0.56008:1.79:57.2:28.4:0.8931:0:1.2 +10 53793528 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2438;SOR=Inf;LSEQ=TGGTAAATTTCATGCACGTC;RSEQ=GTGTGAACAGACCACCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:32,110:142,0:0:2,0:22.7:1:29.8:1:1:0:55.5:46.333:1:0:1.1 0/1:139:2:1,1:31,106:137,2:0.0144:2,2:13:1:28.5:1:0.40872:3.38:60:4:0.0147:0:2 +10 54610432 . G A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6009;LSEQ=CCCTGATGGAGAGACGTTGC;RSEQ=ATCATTGGAGAAGAGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:20:0:29:0:1:0:60:2:0.3333:0:1 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:8:1:27:1:1:2.23609:60:4:0.2222:0:1 +10 54610457 . T C 93 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16486;SOR=6.30681;LSEQ=TTGGAGAAGAGGCACTCTGG;RSEQ=CTTTTGTGTTTTCAGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:6,1:0.1429:2,0:30:0:34:0:1:0:47:2:0.1429:0:1 1/0:15:8:5,3:4,3:7,8:0.5333:2,2:19.9:1:31.1:1:1:1.23:37.9:16:0.5333:0:1 +10 54610668 . C G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10922;SOR=0;LSEQ=TGCAGTTTGCTGGGGGTTCA;RSEQ=TTCAGGGCCTATTCATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:10,10:20,3:0.1304:2,2:25:1:33:1:1:1.94:41:6:0.1304:0:1.3 0/0:24:0:0,0:14,10:24,0:0:2,0:31.7:1:30.8:1:1:0:59.1:23:1:0:0.1 +10 54611200 . T G 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03492;SOR=Inf;LSEQ=TGGGCTGTGGGGACAAGTCT;RSEQ=GGGACCAAGCCGTCCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:15,0:0:2,0:28.1:1:30.6:1:1:0:43.6:30:1:0:0.1 0/1:13:4:2,2:3,6:9,4:0.3077:2,2:36.5:1:29.5:1:1:1.89:53.3:8:0.3077:0:1 +10 54611217 . G GC 77 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19039;SOR=0.19631;LSEQ=TCTTGGGACCAAGCCGTCCA;RSEQ=CCCCCCCAGCTCTAGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:2,4:4,4:8,6:0.375:2,2:27.7:1:29.9:1:0.62704:1.90258:49.7:12:0.375:0.0625:0.2 0/1:10:1:0,1:3,6:9,1:0.1:2,0:12:0:32:0:1:0:30:2:0.1:0:0 +10 54611276 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0119;SOR=Inf;LSEQ=CTATGGAGATGGGTGCCACC;RSEQ=TTTCCCAACCCAGTGAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:6,0:0:2,0:25.8:1:33:1:1:0:60:12:1:0:0.7 1/1:3:3:1,2:0,0:0,3:1:0,2:21:1:32:1:1:0:60:6:1:0:1 +10 54611291 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCACCATTTCCCAACCCAGT;RSEQ=AGCTTAGTGCATTAGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:1,4:0.8:0,2:21.3:1:30.3:1:1:0:60:8:0.8:0:1.3 0/0:1:0:0,0:0,1:1,0:0:0,0:22:0:32:0:1:0:60:2:1:0:1 +10 54611336 . C T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.4;SOR=0;LSEQ=AGTCCCAGTGTTGGCTGCTG;RSEQ=TCCTCTCACAAGGAGCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:20:1:29:1:1:0:60:4:0.6667:0:2 0/0:2:0:0,0:1,0:1,0:0:0,0:29:0:33:0:1:0:60:2:1:0:0 +10 54611395 . A G 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=AGCCACAGCCAGTGCTGGTC;RSEQ=CCCCTCACCTCAGGAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1:0,2:24.8:1:28.6:1:1:0:60:4:1:0:1.2 0/0:2:0:0,0:2,0:2,0:0:0,0:27:1:27:1:1:0:60:4:1:0:0 +10 54611637 . G C 45 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTGCCTTATGTGGCTCTCAG;RSEQ=TGGGCCACTGCACCACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:26:1:28.7:1:1:0:60:2:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:36:0:28:0:1:0:60:2:1:0:0 +10 56060068 . G A 116 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=36.178;LSEQ=TCCACTTTCTAGGTCCGGTA;RSEQ=CAGCCATTTTGCAATTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:1:1,0:14,24:38,1:0.0256:2,0:28:0:27:0:0.38462:0:32:2:0.0256:0:1 1/0:34:17:7,10:6,11:17,17:0.5:2,2:22.2:1:28.6:1:1:1.27:36.2:34:0.5:0:1.1 +10 56851227 . GAATTAATCC TAAA 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTATAGTAGAGGTCTAAAGT;RSEQ=TTGTGGGTAACAATTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,0:58,0:0:1,0:23.8:1:32.6:1:1:0:60:116:1:0:0.1 1/0:48:24:23,1:23,1:24,24:0.5:1,1:21.6:1:29.5:1:1:1:59.8:48:0.5:0.1042:1.1 +10 56851276 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2121;SOR=Inf;LSEQ=TAGATTAAGCACTCAGTGAT;RSEQ=CATAACTTTCAAGAGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:113,34:147,0:0:2,0:24.5:1:32:1:1:0:60:146:1:0:0.1 0/1:126:2:1,1:92,32:124,2:0.0159:2,2:34.5:1:30:1:0.45676:2.84645:57.5:4:0.0161:0:1.5 +10 56851396 . C A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=20.50607;LSEQ=CTTCTGTGAAAGGTAACTAT;RSEQ=ATTTAAATATGAGGAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:11:5,6:152,179:331,11:0.0322:2,2:22.9:1:29.7:1:1:1.01894:60:22:0.0326:0:1.4 0/1:283:115:48,67:78,90:168,115:0.4064:2,2:26.5:1:28.5:1:0.46636:1.2089:60:114:0.4057:0:1.1 +10 59601231 . C T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AACACTACAACTGCAAGGCC;RSEQ=CTTCTTTGCCCTATCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:13.3:1:33:0:1:0:41:6:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:24:1:31:1:1:1:35:4:0.5:0:1 +10 60094679 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTACACTTCCCAGTGTGCC;RSEQ=GGCGGGGCGGGGCGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:28.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 60095105 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=GGAAGGGTGGGCCGGGGTGC;RSEQ=GGCAGGGAGCTGAAGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,16:24,0:0:2,0:23.3:1:30.9:1:1:0:60:48:1:0:0.4 0/1:20:2:0,2:5,13:18,2:0.1:2,0:28:1:31:0:1:0:60:4:0.1111:0:1 +10 60095143 . T C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGGCCGGGCCAGCGGGCA;RSEQ=CGGACAGGTGAGGTGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1:0,2:21.7:1:31.2:1:1:0:60:20:1:0:1.1 1/1:9:9:0,9:0,0:0,9:1:0,0:17.8:1:31.2:1:1:0:60:18:1:0:1.1 +10 60277451 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17756;SOR=Inf;LSEQ=TAGATTTGAATCTTGATGCT;RSEQ=CATTTTAATAGGGAGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:171,59:230,0:0:2,0:24.2:1:28.7:1:1:0:60:229:1:0:0.1 0/1:168:2:1,1:113,53:166,2:0.0119:2,2:29:1:30.5:1:0.54085:2.12161:60:4:0.012:0:2 +10 60277489 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=44.96975;LSEQ=TGGGAGAATCCATCACTTGG;RSEQ=GACCTCATTTCTCAAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:21:14,7:205,128:333,21:0.0593:2,2:24.9:1:29:1:0.81754:1.25:60:20:0.0575:0:1.6 1/0:286:212:121,91:42,32:74,212:0.7413:2,2:25.5:1:29:1:1:1.01:60:424:0.7439:0:1.6 +10 60277549 . A C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=26.00523;LSEQ=ACCTCCTGAGGTAGTTTTGA;RSEQ=AATGAAGAGGAAAAAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:37:19,18:197,226:423,37:0.0803:2,2:27.5:1:32.5:1:0.60945:1.21:60:74:0.0811:0:1.4 1/0:397:276:136,140:53,66:119,276:0.6952:2,2:25.4:1:31.5:1:0.44239:1.21:60:137:0.6954:0:1.5 +10 60277750 . ATAT A 81 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.00025;SOR=49.72797;LSEQ=GAACATGCACAGCTATCTAA;RSEQ=TATTATTGGCCTCCCTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:0,22:22,1:0.0435:1,0:42:0:32:0:1:0:60:2:0.0476:0:0 1/0:8:6:1,5:0,2:2,6:0.75:0,2:29.7:1:31.5:1:1:0:60:12:0.75:0:0 +10 60278140 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATAATAGTCCTACTTTA;RSEQ=GGTGATATTGTGAATGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:28:1:1:0:60:4:1:0:1 +10 63661533 . C CA 54 v3;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04071;SOR=Inf;LSEQ=CCGATCCCGGCACCCCCCGG;RSEQ=ACCCCCCAACCCCCCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:117,269:386,0:0:2,0:23.6:1:30.6:1:1:0:59.8:10.697:0.9972:0:0.4 0/1:518:6:6,0:161,345:506,6:0.0116:2,0:8.5:1:21.2:1:0.00113:0:60:2:0.0084:0.0058:1.3 +10 63661534 . AC A 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0.94262;LSEQ=CGATCCCGGCACCCCCCGGC;RSEQ=CCCCCAACCCCCCAGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:4:2,2:108,264:372,4:0.0106:2,2:29.8:1:29.3:1:0.58372:2.44:60:8:0.0114:0.0026:0 0/1:501:5:3,2:156,339:495,5:0.01:2,2:25:1:29.2:1:0.33282:3.25:60:10:0.011:0.002:0.2 +10 63661732 . G GT 45 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=0.15275;SOR=3.69948;LSEQ=GTGGCGGTGGGGGGCCCTGA;RSEQ=TTTTTTTTTTTTTTTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:2,1:16,11:27,3:0.1:2,2:35:1:24:1:1:1.36:56:2:0.069:0:1 0/1:10:3:2,1:5,2:7,3:0.3:2,2:18:1:29:1:1:1.22183:54.3:6:0.3:0:3 +10 63661854 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49984;SOR=Inf;LSEQ=GTCTGTGTGTAAATGTGTCT;RSEQ=GGAATAGATGTTTGTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:124,28:152,0:0:2,0:22.4:1:32:1:1:0:60:75:1:0:0.2 0/1:169:2:1,1:129,38:167,2:0.0118:2,2:23:0:31.5:1:0.40934:3.36384:60:4:0.0118:0:1 +10 63661905 . T TC 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.03673;SOR=Inf;LSEQ=TTATTTATTTGGTGTTTTTT;RSEQ=CCCCCCCTGCAGTGGGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:229,102:331,0:0:2,0:24.5:1:30.5:1:1:0:60:32.1:1:0:0.2 0/1:416:6:4,2:270,140:410,6:0.0144:2,2:26.5:1:30:1:1:1.04:60:12:0.0149:0.0024:0 +10 63662172 . G T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09919;SOR=0;LSEQ=AGAAATAGCGACCATGGCGA;RSEQ=GTGGTAAACCTGTCTGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:74,211:285,3:0.0104:2,2:25.3:1:25:1:0.1712:5.66:60:2:0.007:0:1.7 0/0:333:0:0,0:97,236:333,0:0:2,0:25.9:1:30.5:1:1:0:59.9:82.25:1:0:0.2 +10 63698147 . T G 31 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGCCAAATTCTCTCTT;RSEQ=ACTAATGTTGAGACTGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:1:31.5:1:1:0:60:4:1:0:1 +10 63699895 . A C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.04128;LSEQ=GAGAGTGGATCATTTCCCTC;RSEQ=AACCTATAAATAACGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:168:158:119,39:5,4:9,158:0.9405:2,2:23.3:1:30.9:1:0.23777:2.43:60:38.5:0.9448:0:1.1 0/1:181:71:51,20:81,29:110,71:0.3923:2,2:23.9:1:30.5:1:0.86434:1.09478:60:142:0.3944:0:1.2 +10 63700223 . G A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=Inf;LSEQ=GGCGTATATAGTAACTTTTC;RSEQ=GTTGAAGATTTTTCTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:37,128:165,0:0:2,0:22.8:1:31.2:1:1:0:59.8:330:1:0:1 0/1:181:2:1,1:44,135:179,2:0.011:2,2:5:1:29:1:0.43646:3.05:60:4:0.0111:0:1 +10 63700228 . A T 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.029;SOR=0.59573;LSEQ=ATATAGTAACTTTTCGGTTG;RSEQ=AGATTTTTCTGGAAACACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:149:98:18,80:13,37:50,98:0.6577:2,2:21.4:1:28.4:1:0.2927:1.55672:60:48:0.6575:0:1.7 1/0:165:88:20,68:19,58:77,88:0.5333:2,2:22.4:1:27.5:1:0.8548:1.11306:60:43:0.5276:0:1.7 +10 63700245 . A G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05088;SOR=0.56565;LSEQ=TTGAAGATTTTTCTGGAAAC;RSEQ=CTATCATTTATATATAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:101:65:7,58:4,32:36,65:0.6436:2,2:21.6:1:32.5:1:1:1.03538:60:130:0.6436:0:2 1/0:109:55:4,51:8,46:54,55:0.5046:2,2:23:1:31.3:1:0.23678:2.20158:60:26.5:0.4953:0:2 +10 63759692 . G A 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05956;SOR=4.13881;LSEQ=TTCTGTGGGGCTGGATGGGT;RSEQ=AAGTGGGGCTGGGAGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:3,0:47,2:49,3:0.0577:1,0:14:1:29.7:1:1:0:60:6:0.0577:0:1 0/1:44:9:9,0:34,1:35,9:0.2045:1,0:30.7:1:29:1:1:0:60:18:0.2045:0:1.1 +10 63759735 . A G 101 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0066;SOR=11.18128;LSEQ=GCATCCCCCAGACTGTAACA;RSEQ=GGATGAGAGTCTTTTTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:1,0:123,1:124,1:0.008:1,0:4:0:32:0:1:0:60:2:0.008:0:1 0/1:108:9:9,0:97,2:99,9:0.0833:1,0:19.7:1:32.1:1:1:0:60:18:0.0833:0:1 +10 63760085 . G A 34 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24905;SOR=0;LSEQ=ATATGCGATGAGTTTGGTGA;RSEQ=TCTTTTTTTTTTTTTCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:73,204:277,3:0.0107:2,2:7:1:22:1:0.17582:5.55:60:2:0.0079:0:1.3 0/0:268:0:0,0:88,180:268,0:0:2,0:23.9:1:30.3:1:1:0:59.6:23.364:1:0:0.6 +10 63760101 . C T 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20699;SOR=4.22232;LSEQ=GTGAGTCTTTTTTTTTTTTT;RSEQ=CTACCTGATTCTTGTGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:1:1,0:42,174:216,1:0.0046:2,0:13:0:9:0:0.19816:0:35:0:0:0:5 0/1:208:4:2,2:50,154:204,4:0.0192:2,2:29:1:23:1:0.26069:3.06:60:3:0.0147:0:3.5 +10 63760113 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1064;SOR=Inf;LSEQ=TTTTTTTTCCTACCTGATTC;RSEQ=TGTGCGTGTGTGCCTAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:28,133:161,0:0:2,0:24.5:1:30.2:1:1:0:58.6:52.667:1:0:0.9 0/1:146:3:0,3:33,110:143,3:0.0205:2,0:24.3:1:32:1:1:0:60:6:0.0207:0:1.3 +10 63809527 . G A 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51049;SOR=4.09114;LSEQ=GTGTTTGTAAAATGAGTACA;RSEQ=TGTAAAAATGTCCTAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:7,3:0.3:0,0:34.7:1:32.3:1:1:0:60:6:0.3:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:26.5:1:31.5:1:1:0:60:4:0.6667:0:1 +10 63810452 . C T 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0337;SOR=0.18832;LSEQ=AATAGATTAGCTTTGGGAAA;RSEQ=GTGTACAGAAATGTATACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:15:15,0:6,0:6,15:0.7143:0,1:29.2:1:30.9:1:1:0:60:14:0.7:0:1.5 0/1:13:4:4,0:9,0:9,4:0.3077:0,0:30:1:30.5:1:1:0:60:8:0.3077:0:1 +10 63810458 . C A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03797;LSEQ=TTAGCTTTGGGAAACGTGTA;RSEQ=AGAAATGTATACTCTACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:7,0:16,0:16,7:0.3043:1,0:24.3:1:31.1:1:1:0:60:14:0.3043:0:1 0/1:16:5:5,0:11,0:11,5:0.3125:0,0:22:1:28:1:1:0:60:10:0.3125:0:1 +10 63810562 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49749;SOR=0;LSEQ=TTCTCTGAACAATTAGAAGG;RSEQ=ATCACTGTAGTGAGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:94,4:98,2:0.02:1,2:13.5:1:28:1:0.09798:21.13062:60:4:0.0202:0:1 0/0:99:0:0,0:89,10:99,0:0:2,0:23.5:1:30.6:1:1:0:60:198:1:0:0.1 +10 63816832 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17668;SOR=Inf;LSEQ=CTATGTCTTGGTAAGCATCC;RSEQ=GGGGCTGTGCCTCGTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:147,44:191,0:0:2,0:23.7:1:31.5:1:1:0:60:62.667:1:0:0.1 0/1:139:2:1,1:105,32:137,2:0.0144:2,2:23.5:1:28:1:0.41977:3.24648:60:4:0.0146:0:1 +10 63816834 . G T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.65281;LSEQ=ATGTCTTGGTAAGCATCCTG;RSEQ=GGCTGTGCCTCGTCTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:147,46:193,2:0.0103:2,2:27:1:31.5:1:0.4249:3.1722:60:4:0.0105:0:1 0/0:149:1:0,1:111,37:148,1:0.0067:2,0:1:0:27:0:0.25503:0:60:2:0.0068:0:1 +10 63816842 . C T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13156;SOR=0;LSEQ=GTAAGCATCCTGGGGCTGTG;RSEQ=CTCGTCTGATGTGGTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:4:2,2:160,55:215,4:0.0183:2,2:25:1:28.3:1:0.2783:2.89236:60:8:0.0186:0:1.3 0/0:177:0:0,0:130,47:177,0:0:2,0:24.1:1:30.9:1:1:0:59.8:176:1:0:0.2 +10 63817096 . G A 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGTGAGTATACTTGTTTTC;RSEQ=TTTCTGAATTATCAGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:108,225:333,0:0:2,0:24.6:1:31.4:1:1:0:60:165.5:1:0:0.1 0/1:362:30:11,19:114,218:332,30:0.0829:2,2:20.7:1:29.7:1:0.842:1.11:58.9:60:0.0836:0:1.2 +10 63817135 . G GA 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=TGCTCAGATTCTTTGAATTG;RSEQ=AAAAAATAATTTTGACTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:18,128:146,0:0:2,0:24.1:1:31.9:1:1:0:60:47.667:1:0:0.1 0/1:154:2:1,1:28,124:152,2:0.013:2,2:17:1:25:1:0.34216:4.37:60:4:0.0132:0.0065:0.5 +10 63818914 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5071;SOR=0;LSEQ=GTATTTCTTTTTTTCTCTTT;RSEQ=TCGTTGAAAAAAAAAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:114,18:132,2:0.0149:2,2:31.5:1:31.5:1:0.26439:6.1914:60:4:0.0152:0:1 0/0:102:0:0,0:85,17:102,0:0:2,0:22.1:1:30.7:1:1:0:60:101:1:0:0.2 +10 63818920 . GA G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.3001;LSEQ=CTTTTTTTCTCTTTCTCGTT;RSEQ=AAAAAAAAATGTTTTAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:162:109:85,24:50,3:53,109:0.6728:2,2:22:1:32.4:1:0.00742:4.67027:60:218:0.6728:0.1235:0.1 0/1:113:43:38,5:50,14:64,43:0.3805:2,2:28.4:1:31.9:1:0.20535:2.11:60:86:0.3805:0:0 +10 63829539 . C T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.13769;LSEQ=ACCAGCGCTGCCACTTGTAC;RSEQ=CGCAGACATTATGAAAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:428:251:96,155:72,105:177,251:0.5864:2,2:26.9:1:30.9:1:0.61688:1.10688:60:40.833:0.5861:0:1.1 0/1:503:82:38,44:167,254:421,82:0.163:2,2:26:1:28.9:1:0.27096:1.31:60:40:0.1623:0:1.2 +10 63829930 . A T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAAAGTAAGCACTTCTC;RSEQ=TAATATTAGCATTGAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:41:1:29.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 63844810 . G C 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACATGAATGAAAATAAAAT;RSEQ=TTTTCAGATGGGCAGCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:31.5:1:32.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:28.5:1:1:0:60:4:1:0:1 +10 63845705 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18589;SOR=Inf;LSEQ=ACCTCTGGAAGACATGTGCT;RSEQ=CCTCGAGGTCCTTCTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:26,100:126,0:0:2,0:25.7:1:31.7:1:1:0:60:30.5:1:0:0 0/1:96:2:1,1:18,76:94,2:0.0208:2,2:10.5:1:27.5:1:0.35833:4.14:60:4:0.0215:0:2 +10 63847565 . G A 60 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTTTTTTGTTTTTATTA;RSEQ=GTTTCATAATTATTTTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:10.8:1:30.3:1:1:0:60:8:1:0:1.5 +10 63851593 . C T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04501;SOR=Inf;LSEQ=ACCGCTGCAGCTTCTCCAAG;RSEQ=ATCACCTTAACCCCCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:279,183:462,0:0:2,0:25.3:1:32.3:1:1:0:59.9:114.5:1:0:0.1 0/1:396:4:2,2:225,166:391,4:0.0101:2,2:17:1:26.8:1:1:1.35435:60:8:0.0102:0:1 +10 63852297 . GA G 86 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.56723;SOR=1.52163;LSEQ=TTGGACCTTGTGATTGCAGG;RSEQ=AAAAGGCCCGGGCAGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:5:4,1:320,303:623,5:0.008:2,2:32.4:1:32:1:0.37428:3.78:60:10:0.0081:0.0016:0.2 0/1:580:7:3,4:294,277:571,7:0.0121:2,2:33.1:1:30.7:1:0.7181:1.41431:60:14:0.0123:0:0 +10 63852823 . G C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18794;SOR=Inf;LSEQ=CAGCAGTCCAAAGCGGCATG;RSEQ=CCAACAGAGCTTCACTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:21,126:147,0:0:2,0:24:1:31.7:1:1:0:59.7:23.5:1:0:0.2 0/1:113:2:1,1:12,99:111,2:0.0177:2,2:6.5:1:29:1:0.21776:7.97:60:4:0.018:0:1 +10 63852965 . C G 93 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTGATTTTTGTGGGACAACT;RSEQ=TAGCCCACAAACTGACTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:3,8:0.7273:0,0:22.1:1:31.1:1:1:0:60:16:0.7273:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:38:0:32:0:1:0:60:2:1:0:1 +10 65825669 . A AG 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.18542;SOR=0;LSEQ=TATTTAATGCATACAAGACA;RSEQ=GGGGGGGGCAGGGTAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:2,0:19,9:28,2:0.0667:2,0:26:1:33.5:1:1:0:36:4:0.0741:0:0.5 0/0:39:0:0,0:21,18:39,0:0:2,0:20.5:1:29:1:1:0:41.4:38:1:0:0.2 +10 65825674 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.50128;SOR=Inf;LSEQ=AATGCATACAAGACAAGGGG;RSEQ=GGGCAGGGTAAGGAGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:21,8:29,0:0:2,0:28.9:1:30.9:1:1:0:46.9:58:1:0:0.2 0/1:39:2:1,1:20,17:37,2:0.0513:2,2:11.5:1:27.5:1:1:1.17156:23:4:0.0526:0:1 +10 65825677 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18542;SOR=0;LSEQ=GCATACAAGACAAGGGGGGG;RSEQ=CAGGGTAAGGAGGGTGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:20,8:28,2:0.0667:2,2:34:1:29.5:1:0.51724:2.41524:52.5:4:0.0667:0:1 0/0:39:0:0,0:21,18:39,0:0:2,0:23.9:1:30.7:1:1:0:41.4:78:1:0:0.2 +10 65825866 . A G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=TCACTATTTCTTCTACTGCT;RSEQ=TCTACTACGAACTTCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:0,2:2,4:0.6667:0,2:19.8:1:32.5:1:1:0:26:8:0.6667:0:1 1/0:4:2:1,1:0,2:2,2:0.5:0,2:35:0:33.5:1:1:0:22:4:0.5:0:1 +10 66345180 . G GAA 92 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.76646;SOR=0.73234;LSEQ=AATCCAGGAGCTGTTTTTCT;RSEQ=AAAAAAAAAAAAAATTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:2,5:6,7:13,7:0.2917:2,2:25.7:1:30.6:1:0.64241:2.06372:60:14:0.3182:0:0.3 0/1:39:9:4,5:12,11:23,9:0.2308:2,2:22.2:1:29.3:1:1:1.35045:56.1:18:0.2308:0:1 +10 68050400 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4962;SOR=0;LSEQ=CTATTTATTTTTTACAATAT;RSEQ=AGATTATCGTCTGCAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:54,7:61,2:0.0317:2,2:29:1:29:1:0.23963:7.28402:60:4:0.0317:0:1 0/0:60:0:0,0:50,10:60,0:0:2,0:22:1:30.6:1:1:0:60:120:1:0:0.3 +10 68050444 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49796;SOR=Inf;LSEQ=AAGTACTAGAGTTTTGATTT;RSEQ=CACCTACCTGATATGACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:82,34:116,0:0:2,0:27.2:1:31.8:1:1:0:59.8:22.2:0.9911:0:0.8 0/1:120:2:1,1:79,39:118,2:0.0167:2,2:8:0:31:1:1:2.01284:60:4:0.0169:0:1.5 +10 68050445 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24476;SOR=0;LSEQ=AGTACTAGAGTTTTGATTTG;RSEQ=ACCTACCTGATATGACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:82,34:116,2:0.0169:2,2:21:1:31:1:0.50703:2.39153:60:4:0.0174:0:2.5 0/0:120:0:0,0:79,41:120,0:0:2,0:26.9:1:31.2:1:1:0:60:59:1:0:0.4 +10 68050459 . G A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15398;LSEQ=GATTTGCACCTACCTGATAT;RSEQ=ACATACAGAAATAGGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:157:87:56,31:44,26:70,87:0.5541:2,2:24.1:1:29.3:1:0.86866:1.07:59.6:174:0.5577:0:1.7 0/1:144:23:14,9:74,46:120,23:0.1597:2,2:26.5:1:27.8:1:1:1.03394:60:46:0.1608:0:1.5 +10 68050521 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1794;LSEQ=TCAATGCATAAATGAATAAA;RSEQ=GATCTCAACATGGCTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:211:107:63,44:44,60:104,107:0.5071:2,2:25.5:1:31.1:1:0.01932:1.95:60:52.5:0.5024:0:1.6 0/1:219:34:16,18:97,87:184,34:0.1553:2,2:26.8:1:30.3:1:0.5792:1.253:60:68:0.156:0:1.6 +10 68050533 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.85247;SOR=0.92678;LSEQ=TGAATAAATGATCTCAACAT;RSEQ=GCTTTTGACAGAAGTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:15:9,6:100,101:201,15:0.0691:2,2:22.6:1:29.6:1:0.59415:1.51:60:30:0.0698:0:1.8 0/1:233:15:7,8:112,106:218,15:0.0644:2,2:23.9:1:29.5:1:0.79353:1.20657:60:30:0.0649:0:1.8 +10 68050569 . T A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25252;SOR=Inf;LSEQ=GAGTCACAAATTATTCGAAA;RSEQ=TGATGTCAACAGTGAGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:74,106:180,0:0:2,0:27.1:1:30.6:1:1:0:60:179:1:0:0.5 0/1:210:3:2,1:94,113:207,3:0.0143:2,2:15.3:1:21.3:1:0.59361:2.39:60:2:0.0096:0:2.3 +10 68050758 . A G 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07619;SOR=0;LSEQ=CCTCAGATCAGGATTACAAA;RSEQ=TATGATAACCTATATGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:26.5:1:31.3:1:1:0:58.5:8:0.6667:0:2.8 0/0:4:0:0,0:0,4:4,0:0:0,0:29.5:1:29.3:1:1:0:60:8:1:0:0.5 +10 68821161 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGTAATTTTTAGATGTG;RSEQ=TATCAGAGTTCCTTTATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:36.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 68821307 . G T 96 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTCCCTTGTCCCTTAACA;RSEQ=GCATATCAAAAAATGAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:0,9:1:0,0:25:1:30.6:1:1:0:60:18:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:12:0:31:0:1:0:60:2:1:0:1 +10 68821469 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21284;SOR=Inf;LSEQ=AAAGAGAAACGATATTTCAG;RSEQ=AGTTGTGTGCATATTCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:80,28:108,0:0:2,0:25.9:1:32.3:1:1:0:60:107:1:0:0.1 0/1:93:2:1,1:72,19:91,2:0.0215:2,2:36:1:27.5:1:0.38569:3.71925:60:4:0.022:0:1 +10 68821487 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4998;SOR=0;LSEQ=AGCAGTTGTGTGCATATTCT;RSEQ=ATATGTATCTTTGTTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:106,45:151,2:0.0131:2,2:8.5:1:29:1:0.5123:2.3408:60:4:0.0134:0:1.5 0/0:137:0:0,0:99,37:136,0:0:2,0:22.9:1:28.2:1:1:0:60:272:1:0:0.2 +10 68821572 . T C 253 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03156;LSEQ=TTCATTACAAAACAAATTCC;RSEQ=CATTGGCAGATAAGCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:281:272:130,142:4,5:9,272:0.968:2,2:26.1:1:31.4:1:1:1.14:59.9:67:0.9675:0:1.1 0/1:302:147:76,71:73,79:152,147:0.4868:2,2:26.1:1:30.1:1:0.56374:1.16:60:72.5:0.4849:0:1.1 +10 68821716 . AT A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00259;SOR=0.15692;LSEQ=GCTTATTTACTGTAAAAAAA;RSEQ=CAATCTTAGGAAATAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:36:2,34:1,2:3,36:0.878:2,2:21.6:1:32.2:1:0.21873:7.61228:60:72:0.878:0.2195:0 1/0:23:12:0,12:0,11:11,12:0.5217:0,0:22.3:1:31.8:1:1:0:60:24:0.5217:0.2174:0 +10 68821717 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.53224;SOR=0;LSEQ=CTTATTTACTGTAAAAAAAA;RSEQ=CAATCTTAGGAAATAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:1,2:3,2:0.0488:2,0:17:1:31.5:1:1:0:60:4:0.0488:0:1 0/0:23:0:0,0:0,11:11,0:0:0,0:25.3:1:29.9:1:1:0:60:22:0.4783:0:0 +10 68821956 . CAG C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAAGAACGTTAAAACCCA;RSEQ=AGAGTAAATTGTTTAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:19:1:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 69553534 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTAATTCGCCAAAATAA;RSEQ=AAACACAAAGGGAAAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:14,4:18,2:0.1:2,2:23:1:29:1:0.44737:3.24034:60:4:0.1053:0:1 0/0:5:0:0,0:4,1:5,0:0:2,0:19.6:1:32:1:1:0:60:10:1:0:0 +10 69553736 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14101;SOR=0;LSEQ=AGTCTACAGTGTTACTGCAT;RSEQ=CTGTTGGCATTGTTATAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:14,29:43,2:0.0444:2,2:23:1:29.5:1:1:2.04:60:4:0.0444:0:1 0/0:74:0:0,0:33,41:74,0:0:2,0:25.2:1:30.6:1:1:0:59.2:17.5:1:0:0.3 +10 69553768 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.518;SOR=Inf;LSEQ=GTTATAAACACACGAGTTAA;RSEQ=GGCAAGATTCTTGCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:4,24:28,0:0:2,0:27:1:31.4:1:1:0:60:56:1:0:0.1 0/1:44:2:1,1:14,28:42,2:0.0455:2,2:29.5:1:28:1:1:1.97:55.5:4:0.0465:0:1 +10 69553779 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49854;SOR=Inf;LSEQ=ACGAGTTAAGGGCAAGATTC;RSEQ=TGCCAGGAGAATTAATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:2,24:26,0:0:2,0:26.1:1:30.8:1:1:0:59.3:52:1:0:0 0/1:33:2:1,1:10,21:31,2:0.0606:2,2:15:1:29.5:1:1:2.05:60:4:0.0625:0:1 +10 69554894 . G C 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCACATTTCTGGAGACC;RSEQ=GGAAGTCCAAGATCAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 69555026 . T TA 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTCTCAATCCTCTTTCA;RSEQ=AAGAGCACTAATCCCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:30.5:1:1:0:60:4:1:0:0.5 +10 69760514 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.1957;SOR=0;LSEQ=TGGATGCAGACACGTACAGA;RSEQ=AGAAGGCCAAGGTCTACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:10:0:31.5:1:1:1.37:60:4:0.1538:0:1 0/0:17:0:0,0:11,6:17,0:0:2,0:16:1:31.4:1:1:0:60:34:1:0:0.1 +10 70332066 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01694;SOR=0.6776;LSEQ=ACCAATGACTCTGTTTCCTG;RSEQ=GCCCTTTCATTTTTTCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:293:152:101,51:94,47:141,152:0.5188:2,2:24.7:1:30:1:1:1.00987:59.7:304:0.5223:0:1.1 0/1:346:146:96,50:119,81:200,146:0.422:2,2:24.8:1:29.5:1:0.26243:1.31:60:292:0.4269:0:1.1 +10 70332152 . C CA 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.01467;LSEQ=GTCAGGAAGGAAGATGTAAA;RSEQ=AAAAAAAAGAAAAACAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:10:6,4:406,225:631,10:0.0156:2,2:26:1:31:1:0.7505:1.20259:60:20:0.0158:0.0016:0.3 0/1:886:14:10,4:531,339:870,14:0.0158:2,2:12.6:1:28.9:1:0.58327:1.60:60:28:0.016:0.009:0.6 +10 70332580 . A G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.62884;SOR=0.92812;LSEQ=TGATTCGGTTCCAATGCAAG;RSEQ=CACCCAAGTCCTTCCTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:183:104,79:135,131:266,183:0.4076:2,2:22.7:1:31.8:1:0.21227:1.28:59.9:90.5:0.4086:0:1 0/1:426:166:85,81:118,142:260,166:0.3897:2,2:23.8:1:31:1:0.27401:1.26:60:332:0.3915:0:1.1 +10 70332672 . T A 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2359;SOR=1.35644;LSEQ=AAGAGACAACTCAGTTTTGG;RSEQ=CCCAAAGAGTTGAGGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:30:13,17:234,238:472,30:0.0598:2,2:24.5:1:28.8:1:0.57442:1.28507:60:14:0.0571:0:1.3 0/1:592:47:24,23:275,270:545,47:0.0794:2,2:28.5:1:28.6:1:1:1.02:60:46:0.0786:0:1.2 +10 70332862 . C T 147 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=12.19339;LSEQ=TGCTCCTTTTCCCCAAAGAG;RSEQ=AACCCCCAAAGTTACCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:893:3:1,2:494,396:890,3:0.0034:2,2:7.3:1:26.7:1:0.58862:2.49245:60:6:0.0034:0:1.3 0/1:962:38:21,17:509,413:922,38:0.0395:2,2:27.3:1:28.1:1:1:1.00:60:76:0.0399:0:1.1 +10 70333502 . G A 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGTGCTATACAGATTTT;RSEQ=CCTTTGGGCTCAGGACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:557:0:0,0:265,291:556,0:0:2,0:25.3:1:32.2:1:1:0:59.5:54.6:0.9982:0:0.1 0/1:623:24:12,12:289,309:598,24:0.0385:2,2:21.5:1:27.4:1:1:1.07:60:48:0.0391:0:1.1 +10 70333741 . G C 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGAGGGAGCTCCCAGGTCA;RSEQ=TGTAACCAGCACAGTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:959:0:0,0:496,461:957,0:0:2,0:24.3:1:32.5:1:1:0:58.3:62.8:0.9979:0:0.1 0/1:1111:69:37,32:523,518:1041,69:0.0621:2,2:25.5:1:31.6:1:0.62035:1.15:55.6:138:0.0624:0:1.1 +10 70334006 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10534;SOR=Inf;LSEQ=CCATCTGTTGTTGTGCCTCT;RSEQ=GAGGTAAGCAAACAGTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:92,164:256,0:0:2,0:25.9:1:31.3:1:1:0:60:63:0.996:0:0.1 0/1:231:3:1,2:78,149:227,3:0.013:2,2:25:1:30.3:1:1:1.04677:60:6:0.0131:0:1.7 +10 70334034 . G T 24 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57864;SOR=2.68197;LSEQ=GCAAACAGTCAAGGGGCTGG;RSEQ=AGACAGCTGACACTTGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:61,134:195,1:0.0051:2,0:45:0:10:0:1:0:60:0:0:0:5 0/1:147:2:1,1:43,102:145,2:0.0136:2,2:7.5:1:24:0:0.51048:2.36:60:4:0.0136:0:1 +10 70334316 . T G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAAATTGTATGAAATGTG;RSEQ=TTTTGCAGAGATTTCCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:33.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 70360784 . T A 44 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13196;SOR=Inf;LSEQ=GAGGGAAAAGAAGCCCAAAG;RSEQ=TTTAAAGGTAATCAGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:127,185:312,0:0:2,0:27.1:1:29.8:1:1:0:60:155:1:0:0.1 0/1:384:4:4,0:149,230:379,4:0.0104:2,0:6:1:22:1:0.02487:0:60:3:0.008:0:1.3 +10 70404379 . T C 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18208;LSEQ=AGGGGCTTTACATTTAGTTG;RSEQ=TATTAAATTTTAATCTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:63:59,4:74,4:78,63:0.4468:2,2:22.2:1:32.4:1:1:1.2522:60:126:0.4468:0:1 0/1:149:19:16,3:118,12:130,19:0.1275:2,2:22.6:1:32.1:1:0.40973:1.83485:60:38:0.1275:0:1.2 +10 70404402 . G T 40 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84646;LSEQ=TTAAATTTTAATCTTCTATG;RSEQ=CTGTTATTCAGATATTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:0,3:170,39:209,3:0.0142:2,0:1:0:26.3:1:0.00733:0:60:6:0.0144:0:1 0/1:250:3:2,1:193,54:247,3:0.012:2,2:28:1:25.3:1:0.52706:1.78226:50.3:2:0.0082:0:4 +10 70404938 . G T 64 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06191;SOR=0;LSEQ=TGAGTTGTGATCATCTCAAG;RSEQ=GGAGAAGTAACGTTTTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:5:0,5:245,199:444,5:0.0111:2,0:7.2:1:27.6:1:0.01884:0:60:10:0.0113:0:1 0/0:437:0:0,0:215,221:436,0:0:2,0:24.5:1:30.2:1:1:0:60:47.444:0.9977:0:0.1 +10 70405237 . G A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09301;LSEQ=TCAAAGTCAGAGAAGGATGA;RSEQ=GAATCAGAGCAGAGAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:330:181:94,87:79,70:149,181:0.5485:2,2:23.7:1:31.1:1:0.91187:1.04442:54.8:362:0.5502:0:1 0/1:435:44:19,25:203,188:391,44:0.1011:2,2:23.3:1:30:1:0.34007:1.41962:53.6:88:0.1021:0:1.2 +10 70405539 . A G 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCATCCAAGATTGACACCA;RSEQ=TAAAAGTATTGCTCAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:190,198:388,0:0:2,0:25.1:1:31:1:1:0:59.8:193:1:0:0.1 0/1:432:28:15,13:194,210:404,28:0.0648:2,2:25:1:31.6:1:0.69646:1.25:60:56:0.0657:0:1 +10 70405855 . A G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.61042;LSEQ=AATCAGGAGAAGGGCACAAT;RSEQ=CAACAGAAACCACCTTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:616:281:159,122:192,143:335,281:0.4562:2,2:23.9:1:31.9:1:0.87048:1.03018:59.3:45.833:0.453:0:1.1 1/1:843:729:400,329:65,48:113,729:0.8648:2,2:25.1:1:31.2:1:0.61281:1.11365:59.3:80:0.8633:0:1.1 +10 70405901 . T C 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAATAATCATGGTTCATCA;RSEQ=TAACAAAACAAAAGAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:682:0:0,0:329,353:682,0:0:2,0:26:1:30.7:1:1:0:59.8:84.25:1:0:0.3 0/1:976:36:21,15:487,452:939,36:0.0369:2,2:23.3:1:31.5:1:0.49892:1.30:60:72:0.0373:0:1.1 +10 70406345 . C T 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00873;SOR=0;LSEQ=AAGCTTATAATTCTCAGGTA;RSEQ=AGTTAACGGTGAATGCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:545:6:2,4:277,262:539,6:0.011:2,2:21.8:1:28.7:1:0.44034:2.11168:59.5:12:0.0111:0:1.2 0/0:653:0:0,0:324,329:653,0:0:2,0:1:0:13:0:1:0:60:0:0:0:1 +10 70406390 . C T 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01262;SOR=Inf;LSEQ=AAGCCCATCCTTTGACCCAG;RSEQ=CCTCCTCTCCACCTAACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:0:0,0:289,252:541,0:0:2,0:25.9:1:31.7:1:1:0:59.9:66.625:1:0:0.1 0/1:751:9:3,6:384,358:742,9:0.012:2,2:18.4:1:25:1:0.32778:2.14313:60:8:0.0108:0:1.2 +10 70406518 . A T 255 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00444;LSEQ=CCTGGTATCTCTCATGAAAC;RSEQ=CCCTTACCGGAGTCAGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:662:305:172,133:190,167:357,305:0.4607:2,2:24.5:1:30.9:1:0.43401:1.14:60:37.125:0.4562:0:1.1 0/0:797:3:0,3:411,381:792,3:0.0038:2,0:1:0:23.7:1:0.11224:0:60:6:0.0038:0:1 +10 70406783 . G A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25183;SOR=Inf;LSEQ=GTGAGTACTTGTGTGCATGT;RSEQ=TTCTTATTTCACCTGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:59,181:240,0:0:2,0:25.9:1:31.9:1:1:0:59.9:47:1:0:0.2 0/1:274:3:1,2:80,191:271,3:0.0109:2,2:12.3:1:25:1:1:1.19:60:2:0.0074:0:2.7 +10 70406855 . AT A 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ATTCATCTTTTTTGTGTGAT;RSEQ=TTTTTCCCCATTCTTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,65:65,0:0:1,0:21:1:30.4:1:1:0:60:20.667:1:0:0.6 0/1:57:13:0,13:0,44:44,13:0.2281:1,1:22.5:1:30.4:1:1:0:59.6:12:0.2143:0.0351:0.1 +10 70406864 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.05677;LSEQ=TTTTGTGTGATATTTTTTCC;RSEQ=CATTCTTATTCTAACTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:28:0,28:0,21:21,28:0.5714:1,1:21.9:1:30.6:1:1:0:60:56:0.5714:0:1.1 0/1:44:3:0,3:0,41:41,3:0.0682:1,0:28.7:1:27.7:1:1:0:60:6:0.0682:0:1.3 +10 70411536 . G A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13059;LSEQ=GGGGAACAAAAAGTATAAAA;RSEQ=TAGCTTCTCCTGTCCCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:80:69,11:81,13:94,80:0.4598:2,2:22.9:1:30.6:1:1:1.01:60:39:0.4561:0:1.1 0/1:191:19:12,7:139,33:172,19:0.0995:2,2:13.2:1:29.4:1:0.08135:2.44315:60:38:0.1011:0:1.2 +10 70412132 . AAG A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05586;LSEQ=TTTAACAAGAGTAAATTACG;RSEQ=AGTGTCTAATTTTTGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:48:48,0:32,0:32,48:0.6:1,1:21.9:1:30.9:1:1:0:60:96:0.6076:0.1875:0 0/1:66:5:5,0:61,0:61,5:0.0758:1,0:25:1:28.6:1:1:0:60:10:0.0769:0:0.2 +10 70412165 . A G 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01377;SOR=Inf;LSEQ=TTTTGAACTTCTGTACATCT;RSEQ=TATCTTATATACATTAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:125,10:135,0:0:2,0:23.5:1:28.6:1:1:0:59.9:44:1:0:0 0/1:132:6:6,0:118,8:126,6:0.0455:2,0:17:1:32.7:1:1:0:60:12:0.0458:0:1 +10 70412425 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20189;SOR=0;LSEQ=ATTTATACATTTACAATAGC;RSEQ=AGAGTGATCTTTATTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:6,141:147,2:0.0134:1,2:15.5:1:31.5:1:0.09206:21.83:60:4:0.0136:0:1 0/0:182:0:0,0:14,166:180,0:0:2,0:24.4:1:32:1:1:0:60:360:0.9945:0:0.1 +10 70426168 . A G 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCAAAGGAAAAGCCATA;RSEQ=CATTCCTCAGATGGCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:38.3:1:34.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 70427335 . A G 69 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTGGCTAATATGTCTCC;RSEQ=CTATAAATACAAAAAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:30.8:1:34.5:1:1:0:55.3:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 70432603 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24909;SOR=0;LSEQ=ACCTGAAATGTTCTCTCTGA;RSEQ=GTATTGTAATGCTTCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:204,52:256,3:0.0116:2,2:13.3:1:24.3:1:0.49835:1.95559:60:2:0.0079:0:1 0/0:245:0:0,0:183,61:244,0:0:2,0:22.9:1:30.8:1:1:0:60:60:0.9959:0:0.1 +10 70440769 . C T 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTCTCCGTTATAGGAAC;RSEQ=TGTTACATTGTAACCAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:24.5:1:32.3:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 70440826 . G T 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCAGCAAGAACGTTGTTT;RSEQ=CATTTATTCCAAGTGTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:16.3:1:30.3:1:1:0:60:6:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:48:0:30:0:1:0:33:2:1:0:1 +10 70442868 . GA G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.309;SOR=0.50379;LSEQ=AAATAAGTGGAAAATAAAGT;RSEQ=AAAAAAAGAAATAAGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:31:0,31:0,7:7,31:0.8158:0,1:29.5:1:33:1:1:0:60:62:0.8158:0.0263:0 1/0:16:11:0,11:0,5:5,11:0.6875:0,0:26.6:1:31.4:1:1:0:60:22:0.6875:0.0625:0 +10 70443936 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGAGGATTGCTTGAGCCC;RSEQ=GGGAGTTCTAGACCAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:29.5:1:1:0:52:4:1:0:2 +10 70446673 . C G 67 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTTTTGAGAGGGAGT;RSEQ=TTGCTCTGTCACCCAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:16.3:1:33.5:1:1:0:59.8:8:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 70450264 . T C 51 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCCAGCTACTCGGGAGG;RSEQ=TGAGGCAAGAGAATGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:25.7:1:32.7:1:1:0:37:6:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:27:0:33:0:1:0:28:2:1:0:2 +10 70450272 . A G 54 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTACTCGGGAGGTTGAGGCA;RSEQ=GAGAATGGCATGAGCCGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:32.7:1:34.3:1:1:0:37:6:1:0:2 1/1:2:2:2,0:0,0:0,2:1:0,0:20:1:32.5:1:1:0:38.5:4:1:0:1.5 +10 70450869 . G T 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17969;SOR=0.20217;LSEQ=GATGGCCCTGGCATTTCACA;RSEQ=CTTGGCGAAGTGGCTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:4:2,2:167,185:352,4:0.0112:2,2:11.8:1:29.5:1:1:1.11:60:8:0.0116:0:1.3 0/0:437:1:0,1:214,222:436,1:0.0023:2,0:1:0:26:0:1:0:60:2:0.0023:0:1 +10 70451383 . A T 200 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGAGGCTAAAGAAGCTAAG;RSEQ=ATAAGAAAATGAAGGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:131:61,70:435,407:842,131:0.1345:2,2:24.6:1:28.5:1:0.30183:1.22623:59.4:31.75:0.1333:0:1.1 0/0:1342:0:0,0:648,694:1342,0:0:2,0:25.2:1:29.1:1:1:0:60:77.941:1:0:0.1 +10 70451687 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50124;SOR=0;LSEQ=TCACCCATTTCAAGTCTGAG;RSEQ=TAAAAAAATAATAATGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:0,2:1,85:86,2:0.0227:1,0:26:1:32:0:1:0:60:4:0.0233:0:1 0/0:73:0:0,0:2,71:73,0:0:1,0:23.3:1:32:1:1:0:60:146:1:0:0.1 +10 71539221 . T C 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGATGGAGGCTTGTCTA;RSEQ=CCCTCACAGTACCAAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:13.7:1:33.7:1:1:0:51.7:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 71539455 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10449;SOR=Inf;LSEQ=TGCTGCTATATAAGAGAATC;RSEQ=AGCCTGGGAGAAGAAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:118,28:146,0:0:2,0:23.5:1:31.2:1:1:0:59.9:145:1:0:0.1 0/1:131:3:1,2:99,29:128,3:0.0229:2,2:18.3:1:28:1:0.13928:6.69909:53.7:6:0.0229:0:1 +10 71539581 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17971;SOR=0.79115;LSEQ=CTTTTTCAGAGCTCAAGAGC;RSEQ=GGCTGCTGAGAGCTAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:118:56,62:95,114:209,118:0.3609:2,2:25.4:1:31.2:1:0.73066:1.08:59.9:58:0.358:0:1.1 0/1:311:96:38,58:92,123:215,96:0.3087:2,2:25.6:1:29.8:1:0.62052:1.14115:60:192:0.3117:0:1.1 +10 71539648 . GCAA G 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.69398;SOR=0.60678;LSEQ=AGACTGTAAACTTATTGACA;RSEQ=CAACAACAACAACAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:4:2,2:38,128:166,4:0.0235:2,2:28.5:1:32:1:0.2357:3.34:60:8:0.0235:0:0.3 0/1:139:2:1,1:40,97:137,2:0.0144:2,2:33:1:34:0:0.50443:2.41:60:4:0.0144:0:0.5 +10 71539671 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51098;SOR=0;LSEQ=ACAACAACAACAACAAAAAC;RSEQ=CAAAAATCAATAACACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:19,104:123,2:0.016:2,2:22:1:32.5:1:0.29548:5.36:60:4:0.0161:0:1 0/0:90:0:0,0:22,68:90,0:0:2,0:21.9:1:29:1:1:0:60:44:1:0:0.2 +10 71539687 . C T 25 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56357;SOR=3.06389;LSEQ=AAACACAAAAATCAATAACA;RSEQ=CTGGCAGGCTACTCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:0,1:8,79:87,1:0.0112:2,0:38:0:16:0:1:0:60:0:0:0:1 0/1:59:2:1,1:11,46:57,2:0.0339:2,2:6:1:25:1:0.36821:4.05:60:4:0.0345:0:1 +10 72471033 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27273;SOR=0;LSEQ=GACTCCTATCCCCATCCATG;RSEQ=CTGGAGACAAAAGGAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:2,1:15,22:37,3:0.075:2,2:17.3:1:29:1:0.56468:2.85:60:6:0.0769:0:1 0/0:26:0:0,0:14,12:26,0:0:2,0:32.2:1:30.5:1:1:0:60:52:1:0:0.1 +10 72488413 . G A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCCTGTGAGAAAAAGG;RSEQ=ATTATCTAGAGCAGTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:0,12:1:0,0:19.5:1:30.1:1:1:0:60:24:1:0:2 1/1:5:5:5,0:0,0:0,5:1:0,0:10.4:1:28.8:1:1:0:60:10:1:0:1.8 +10 72488445 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45161;SOR=0;LSEQ=CAGTGCTCTTCAAACTTGCC;RSEQ=ATGCCTGCCAGTCAGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:15,2:0,0:0,17:1:0,2:27.6:1:31.7:1:1:0:60:34:1:0:1.8 1/1:14:13:9,4:1,0:1,13:0.9286:0,2:19.2:1:29.5:1:1:0:60:26:0.9286:0:1.4 +10 72488598 . C T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.547;SOR=3.42051;LSEQ=TCCTGGAGGAGTGCCCACTG;RSEQ=TGCCTCCCCAGGGCCGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:0,1:3,20:23,1:0.0417:2,0:11:0:32:0:1:0:60:2:0.0435:0:1 0/1:15:2:0,2:2,11:13,2:0.1333:2,0:12.5:1:31:0:1:0:60:4:0.1333:0:1 +10 72764857 . C T 84 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15158;SOR=0.15935;LSEQ=AAATGGAACTGGCCTGGAAG;RSEQ=CCACAGACCTGGGTGTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:4,3:2,3:5,7:0.5833:2,2:28.1:1:30.1:1:1:1.89:60:14:0.5833:0:1 0/1:6:1:0,1:4,1:5,1:0.1667:2,0:1:0:22:0:0.33333:0:60:2:0.1667:0:1 +10 72765013 . G A 31 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATCCTGTTTGCATGATCTCT;RSEQ=CCAGCCGTCAAGTGCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:5:1:31.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:33:1:27.5:1:1:0:60:4:1:0:0 +10 72845178 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0.11373;SOR=Inf;LSEQ=GAGGCACAGAGCAGGGCTCT;RSEQ=TCAGGTGAGAGCTGGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:24,32:56,0:0:2,0:29:1:32.4:1:1:0:60:55:1:0:0.1 0/1:29:2:1,1:11,16:27,2:0.069:2,2:9:0:31:1:1:1.44:60:4:0.069:0:1.5 +10 74677495 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50082;SOR=Inf;LSEQ=GAACTTGGCTGCCACTTTGG;RSEQ=AAGAGAATCACCTTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:64,53:117,0:0:2,0:26:1:31.4:1:1:0:35:38:0.9913:0:0.1 0/1:137:2:1,1:78,57:135,2:0.0146:2,2:17.5:1:28:1:1:1.36522:27:4:0.0148:0:1.5 +10 74677675 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23464;SOR=Inf;LSEQ=ATTTGACTTCTGTACATTTT;RSEQ=GGCTGGAGTATCTTGTATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:40,117:157,0:0:2,0:29.7:1:30.3:1:1:0:36.4:156:1:0:0.1 0/1:148:2:1,1:41,105:146,2:0.0135:2,2:33.5:1:30.5:1:0.48842:2.54:25:4:0.0138:0:1 +10 74677694 . A G 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49938;SOR=0;LSEQ=TTGGCTGGAGTATCTTGTAT;RSEQ=GATTTCTTCACTGGTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:48,124:172,2:0.0115:2,2:37.5:1:27.5:1:0.48508:2.57:33.5:4:0.0116:0:2 0/0:160:0:0,0:49,111:160,0:0:2,0:23.7:1:29.5:1:1:0:40.3:79:1:0:0.2 +10 74677784 . GTCA G 93 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.01821;SOR=0.11548;LSEQ=TCATCTTCATCTTCTTCATC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:8:5,3:53,45:98,8:0.0748:2,2:21.1:1:31.2:1:0.72626:1.41:44.1:16:0.0762:0.0187:0 0/0:109:1:1,0:61,47:108,1:0.0092:2,0:29:0:32:0:1:0:32:2:0.0093:0:0 +10 74677845 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23098;SOR=0;LSEQ=TTACTTTTTTCTGTGGAACC;RSEQ=TGCTACCACCTCCAGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:81,60:141,2:0.014:2,2:21:1:34:1:1:1.34711:24:4:0.0141:0:1 0/0:154:0:0,0:79,75:154,0:0:2,0:27:1:29.8:1:1:0:35.3:76:1:0:0.1 +10 74678221 . C T 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55077;LSEQ=AAAGTGATCATCTTTGTCAG;RSEQ=CTTAATTCACAACCAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:53,15:68,2:0.0286:2,2:31:0:32:0:0.40745:3.45312:45:4:0.0286:0:1.5 0/1:63:1:0,1:46,16:62,1:0.0159:2,0:1:0:25:0:0.26984:0:22:2:0.0161:0:1 +10 74678247 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50695;SOR=Inf;LSEQ=TTCACAACCAAAAAGATAGT;RSEQ=CTGGGGCCTCAGGAGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:69,23:92,0:0:2,0:22.8:1:30.3:1:1:0:55.3:29.667:1:0:0.1 0/1:121:2:1,1:81,38:119,2:0.0165:2,2:16:1:32:0:0.54256:2.11707:46.5:4:0.0171:0:1 +10 74678257 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51357;SOR=Inf;LSEQ=AAAAGATAGTTCTGGGGCCT;RSEQ=AGGAGGCTCATGTCCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:80,33:113,0:0:2,0:22.1:1:32.1:1:1:0:55.8:226:1:0:0.1 0/1:161:2:1,1:98,61:159,2:0.0124:2,2:46:1:25.5:1:1:1.6016:43:4:0.0124:0:1 +10 74678258 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51225;SOR=Inf;LSEQ=AAAGATAGTTCTGGGGCCTC;RSEQ=GGAGGCTCATGTCCATGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:83,33:116,0:0:2,0:21.9:1:30.5:1:1:0:55.9:57:0.9913:0:0.1 0/1:164:2:1,1:100,62:162,2:0.0122:2,2:35:1:29:1:1:1.60797:34.5:4:0.0122:0:1 +10 74678300 . C A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27976;SOR=Inf;LSEQ=TCGAATCTTCCATCGGGTGG;RSEQ=GGCACACACTTAGGTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:103,86:189,0:0:2,0:27.3:1:30.7:1:1:0:56.9:30.5:1:0:0.2 0/1:286:3:2,1:147,136:283,3:0.0105:2,2:12:1:26:1:1:1.85:51.3:6:0.0107:0:1.3 +10 74678348 . T A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25472;SOR=Inf;LSEQ=GGATGGAGATAAACCACCAC;RSEQ=GCTCAAGAGAACAGCCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:54,95:149,0:0:2,0:23.6:1:30.3:1:1:0:59.4:36.25:1:0:0.1 0/1:182:3:3,0:64,114:178,3:0.0165:2,0:13:1:21.3:1:0.04929:0:60:2:0.0113:0:1.3 +10 74959528 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52966;SOR=Inf;LSEQ=CAATGATTTAAAAGATTCCT;RSEQ=TGTTAAAAATAACATAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:92,19:111,0:0:2,0:25:1:30.4:1:1:0:60:36:1:0:0.1 0/1:185:2:1,1:140,43:183,2:0.0108:2,2:17:1:26.5:1:0.42009:3.23006:60:4:0.0109:0:1 +10 74959550 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15534;SOR=0;LSEQ=GTTAAAAATAACATAGGCAG;RSEQ=TTTTCAGTCGGGTGCTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:135,45:180,2:0.011:2,2:32:1:28:1:0.44266:2.97817:60:4:0.0113:0:1 0/0:279:0:0,0:188,91:279,0:0:2,0:24:1:30.9:1:1:0:60:68.75:1:0:0.1 +10 74959663 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14275;SOR=Inf;LSEQ=CCCTGATGGTGTCATCGAGA;RSEQ=CAACTGGAAGGAGGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:94,152:246,0:0:2,0:26:1:32.3:1:1:0:59.9:40:1:0:0.1 0/1:339:4:2,2:153,182:335,4:0.0118:2,2:31:1:25:1:1:1.19:60:3:0.009:0:1.3 +10 74959723 . G T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56021;SOR=0.30376;LSEQ=CTTTAAAAAGTCTCTTCTTT;RSEQ=GGGTATCTATGCTTATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:0,2:67,99:166,2:0.0119:2,0:12.5:1:30:1:0.51761:0:60:4:0.0121:0:1 0/0:275:1:0,1:126,148:274,1:0.0036:2,0:1:0:26:0:1:0:60:2:0.0037:0:1 +10 74959725 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29508;SOR=Inf;LSEQ=TTAAAAAGTCTCTTCTTTGG;RSEQ=GTATCTATGCTTATGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:68,99:167,0:0:2,0:23.5:1:31.2:1:1:0:60:54.667:1:0:0.1 0/1:278:3:1,2:124,151:275,3:0.0108:2,2:14.3:1:26:1:1:1.63957:60:6:0.0111:0:1 +10 74959806 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51143;SOR=Inf;LSEQ=TATTAAAGATCCAAAAGGTG;RSEQ=CCAGGCGCAGTGGCTCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:50,80:130,0:0:2,0:24.6:1:31.6:1:1:0:56.9:64:1:0:0.1 0/1:180:2:1,1:67,111:178,2:0.0111:2,2:28.5:1:28:1:1:1.65:46.5:4:0.0112:0:1 +10 74959829 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50719;SOR=Inf;LSEQ=AGGCGCAGTGGCTCATGCCT;RSEQ=TAATCCCAGCACTTTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:25,51:76,0:0:2,0:20.6:1:32.4:1:1:0:54.8:152:1:0:0 0/1:101:2:1,1:35,64:99,2:0.0198:2,2:21:1:29.5:1:1:1.82:60:4:0.0198:0:1.5 +10 74959834 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51337;SOR=Inf;LSEQ=CAGTGGCTCATGCCTGTAAT;RSEQ=CCAGCACTTTGGGAGGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:19,44:63,0:0:2,0:21.2:1:31.5:1:1:0:53.7:126:1:0:0 0/1:91:2:1,1:28,61:89,2:0.022:2,2:18:0:31:1:0.53822:2.16:60:4:0.0227:0:4.5 +10 74959839 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51055;SOR=Inf;LSEQ=GCTCATGCCTGTAATCCCAG;RSEQ=ACTTTGGGAGGCCGAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:14,40:54,0:0:2,0:20.5:1:32.4:1:1:0:52.6:108:1:0:0 0/1:76:2:1,1:18,56:74,2:0.0263:2,2:13:0:32.5:1:0.44:3.05:60:4:0.0274:0:4.5 +10 74959846 . GG AA 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51145;SOR=Inf;LSEQ=CCTGTAATCCCAGCACTTTG;RSEQ=AGGCCGAGGCGGGTAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:6,32:38,0:0:2,0:21.8:1:31.6:1:1:0:49.5:76:1:0:0 0/1:55:2:1,1:10,43:53,2:0.0364:2,2:5:0:31:1:0.36296:4.15:60:4:0.0364:0:3.5 +10 74960524 . G A 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AATCGAACAGTTTTATATCA;RSEQ=TGTTGAGCAGGAGGAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:216,239:455,0:0:2,0:25.5:1:32.6:1:1:0:60:64:0.9978:0:0.1 0/1:441:17:7,10:218,206:424,17:0.0385:2,2:23.1:1:29.2:1:0.46449:1.51037:60:34:0.0391:0:1 +10 74960672 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24874;SOR=Inf;LSEQ=ACGTCACAGTTTTTGCTCTG;RSEQ=ATGGCGACATGGACCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:133,159:292,0:0:2,0:22.5:1:32:1:1:0:59.5:72:1:0:0.1 0/1:296:3:1,2:135,158:293,3:0.0101:2,2:9:1:28.7:1:1:1.7059:60:6:0.0102:0:1 +10 74960675 . G T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24875;SOR=Inf;LSEQ=TCACAGTTTTTGCTCTGCAT;RSEQ=GCGACATGGACCAGAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:133,160:293,0:0:2,0:22.5:1:31.4:1:1:0:59.6:72.25:0.9966:0:0.1 0/1:297:3:2,1:132,162:294,3:0.0101:2,2:31:1:31.3:1:0.59068:2.45:60:6:0.0101:0:1 +10 74960683 . G A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11984;SOR=Inf;LSEQ=TTTGCTCTGCATGGCGACAT;RSEQ=GACCAGAAGGAGAGAGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:133,158:291,0:0:2,0:23.7:1:31.5:1:1:0:59.5:47.5:1:0:0.1 0/1:284:3:3,0:126,154:280,3:0.0106:2,0:13.3:1:25:1:0.09351:0:57.3:6:0.0106:0:1 +10 79127430 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4902;SOR=Inf;LSEQ=TCAAGATACAGAACAACTCT;RSEQ=CCCCAAAAACTATCTTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:26,0:0:2,0:26:1:32.5:1:1:0:59.2:52:1:0:0.1 0/1:26:2:1,1:11,13:24,2:0.0769:2,2:21:1:28:1:1:1.17:60:4:0.08:0:1 +10 79127539 . A C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTACCTATCCAAGGAAGT;RSEQ=ACATAAATGAAATTGATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:1,10:0.9091:0,0:26.5:1:33.3:1:1:0:60:20:0.9091:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:34.5:1:30.5:1:1:0:60:4:1:0:1 +10 80848835 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49692;SOR=Inf;LSEQ=TGTACAAACGAGTATCCTGT;RSEQ=GACATGGTTGTCTGCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:37,27:64,0:0:2,0:30.3:1:31:1:1:0:60:31:1:0:0.2 0/1:69:2:1,1:37,30:67,2:0.029:2,2:26.5:1:31.5:1:1:1.22956:60:4:0.029:0:1 +10 80848893 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23913;SOR=Inf;LSEQ=CGCTGAGCAGGTACCTGGGC;RSEQ=GGTGCCACACTTGGGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:12,23:35,0:0:2,0:21.2:1:30.4:1:1:0:60:16.5:1:0:0.3 0/1:34:2:1,1:14,18:32,2:0.0588:2,2:35:1:29.5:1:1:1.28:60:4:0.0606:0:1 +10 81002050 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCCCGGGGCGGGGCAGG;RSEQ=CCGCGCGCAGCCGCCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:12.5:1:28.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 81003146 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75993;LSEQ=CATTAGCGGAGCCTCCGCCT;RSEQ=TGATTGGCTTCGCCCGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:14.5:1:32.3:1:1:0:60:8:0.8:0:1 1/0:16:12:9,3:2,1:3,12:0.75:2,2:17.6:1:29.4:1:1:1.46:60:11:0.7857:0:1.1 +10 81003154 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54023;SOR=Inf;LSEQ=GAGCCTCCGCCTATGATTGG;RSEQ=TTCGCCCGGGAAGCTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:10.4:1:31.9:1:1:0:60:20:1:0:0.4 0/1:20:2:1,1:10,7:17,2:0.1:2,2:13.5:1:27:1:1:1.40151:60:4:0.1053:0:1 +10 83458193 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAACCTACAATTAATTGGA;RSEQ=TACCAGAAGGAGATGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:34.4:1:33.6:1:1:0:50.9:16:1:0:0.1 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:42.5:1:29.5:1:1:1.13389:48.5:4:0.1176:0:1 +10 84195177 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=CTGGACTCATTGATTTTTTG;RSEQ=AGGGCTTTTTGTGTCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:60,59:119,0:0:2,0:29.6:1:32:1:1:0:56.2:58.5:1:0:0.2 0/1:130:2:1,1:59,69:128,2:0.0154:2,2:20.5:1:30.5:1:1:1.17:60:4:0.0157:0:1.5 +10 84195201 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49816;SOR=Inf;LSEQ=GCTTTTTGTGTCTTTATCTC;RSEQ=TTCAGTTCTTCTCTGATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:50,62:112,0:0:2,0:20.5:1:32.6:1:1:0:55.9:55:1:0:0.2 0/1:118:2:1,1:46,70:116,2:0.0169:2,2:18.5:1:29.5:1:1:1.52:36:4:0.0171:0:1.5 +10 84198314 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47895;SOR=0;LSEQ=ACAGGCAGCTGCAGTTGGTG;RSEQ=TGGTCACCCCTCACCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:9,2:0.1818:2,2:9:0:32.5:1:0.49091:3.05504:60:4:0.1818:0:1 0/0:9:0:0,0:7,2:9,0:0:2,0:23.4:1:32:1:1:0:60:18:1:0:0 +10 84198390 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49492;SOR=0;LSEQ=CTGTAACAATCTGCGCTTTC;RSEQ=GGGGTTGGGATGCTAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:27,2:0.069:2,2:15:1:28.5:1:1:1.07415:60:4:0.0714:0:1 0/0:24:0:0,0:15,9:24,0:0:2,0:27.5:1:28.4:1:1:0:60:23:1:0:0.1 +10 84198427 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49153;SOR=0;LSEQ=GCCCTTGGTGGCATGGGTTC;RSEQ=TGAGTGGGATCTTCCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:28,2:0.0667:2,2:41.5:1:31:1:1:1:60:4:0.0667:0:1 0/0:29:0:0,0:13,16:29,0:0:2,0:28.4:1:29:1:1:0:59.7:28:1:0:0.2 +10 85224770 . C A 65 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22619;SOR=7.11489;LSEQ=TCTACAATCCCAAATAGACT;RSEQ=TTTAGCAGCAGTGACTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:47:0:30:0:1:0:60:2:0.3333:0:1 1/1:6:5:3,2:0,1:1,5:0.8333:0,2:30.4:1:28.4:1:1:0:56.2:10:0.8333:0:1.2 +10 85224968 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92145;LSEQ=AAACTCTTATACCAAACTCT;RSEQ=GACTTGGGCAACATGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:16:8,8:16,11:27,16:0.3721:2,2:30.9:1:29.1:1:0.75156:1.44176:46.4:15:0.3571:0:1.1 0/1:34:12:8,4:12,10:22,12:0.3529:2,2:30.3:1:26.7:1:0.71698:1.64:44.3:11:0.3438:0:1.4 +10 85225048 . T TACAC 44 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=15.000;MSILEN=2;SSF=0.08152;SOR=Inf;LSEQ=TATAGTTCATAAAAAATGTA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:3,10:13,0:0:2,0:34.5:1:28.8:1:1:0:60:26:1:0:0.4 0/1:11:3:0,3:1,7:8,3:0.2727:2,0:16.7:1:28.3:1:1:0:56:6:0.2727:0.1818:4 +10 85225073 . AC CCAT 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=1;LSEQ=CACACACACACACACACACA;RSEQ=ATTATTATATATGTATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:1,7:8,3:0.25:2,0:25.7:1:31.1:1:1:0:60:6:0.25:0:1.3 0/1:8:2:0,2:0,3:3,2:0.25:0,0:18:1:31.6:0:1:0:60:4:0.25:0:1 +10 85225074 . C T 39 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=13.000;MSILEN=2;SSF=0.26213;SOR=5.42517;LSEQ=CACACACACACACACACACA;RSEQ=ATTATTATATATGTATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:0,7:7,1:0.0909:0,0:23:0:24:0:1:0:52:2:0.125:0:4 0/1:8:3:0,3:0,3:3,3:0.375:0,0:27:1:25:1:1:0:54:6:0.5:0:5.3 +10 85225096 . C T 42 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.22222;SOR=7.2181;LSEQ=TTATTATATATGTATATACA;RSEQ=ACATTATATTGTATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:23:1:29.5:1:1:0:56:4:0.25:0:3 1/0:4:3:0,3:0,1:1,3:0.75:0,0:48.7:1:27:1:1:0:54:6:0.75:0:5.3 +10 85225107 . GTA G 64 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.04762;SOR=Inf;LSEQ=GTATATACACACATTATATT;RSEQ=TATATATATGTATATACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:4,1:0.2:0,0:37:0:32:0:1:0:52:2:0.2:0:4 1/1:4:4:0,4:0,0:0,4:1:0,0:39.5:1:32:1:1:0:55.5:8:1:0:4 +10 85225139 . G A 50 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=1;SOR=2.44949;LSEQ=GTATATACACACATTATATT;RSEQ=TATATATATAAGTCAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:8:0:33:0:1:0:52:2:0.5:0:4 1/0:4:3:0,3:0,1:1,3:0.75:0,0:9.3:1:32:0:1:0:54:6:0.75:0:5.3 +10 86028463 . A C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08789;SOR=0.58043;LSEQ=CTATGTGTCCATTTATTCTT;RSEQ=CGCTAACTTTATTAATAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:40:35,5:43,5:48,40:0.4545:2,2:23.4:1:32.7:1:1:1.22568:60:80:0.4545:0:1 0/1:83:27:22,5:45,11:56,27:0.3253:2,2:20.6:1:30.4:1:1:1.07:60:54:0.3253:0:1.1 +10 86028479 . TA T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24338;SOR=Inf;LSEQ=TCTTACGCTAACTTTATTAA;RSEQ=ACTCCAAGATGGCTCCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:98,35:133,0:0:2,0:22.2:1:28.8:1:1:0:60:65.5:1:0:0.3 0/1:130:2:1,1:91,37:128,2:0.0154:2,2:29:1:27.9:1:0.50078:2.44019:60:4:0.0155:0.0077:0.5 +10 86028579 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=0.38599;LSEQ=CATTCCCAATAACCATAAAA;RSEQ=AAAAATCTTGAGTTGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:156:76,80:83,98:181,156:0.4629:2,2:26.4:1:32:1:0.66176:1.12:60:51:0.4622:0:1.8 0/1:401:100:45,55:152,149:301,100:0.2494:2,2:25.2:1:31.3:1:0.35758:1.24614:60:99:0.2506:0:1.8 +10 86028605 . C G 256 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02309;LSEQ=TCTTGAGTTGGGGCTTGATT;RSEQ=GACCACTTCTAAACAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:295:282:110,172:8,5:13,282:0.9559:2,2:26.8:1:31.5:1:0.14665:2.49381:60:93:0.9555:0:1.5 0/1:331:110:48,62:102,117:219,110:0.3323:2,2:28:1:30.8:1:0.64017:1.12566:60:54:0.3303:0:1.8 +10 86028662 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49882;SOR=0;LSEQ=TAAAATGATAGTTGGCTTAA;RSEQ=ACTCCCATTAATCCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:28,108:136,2:0.0145:2,2:26.5:1:30.5:1:0.37734:3.81:60:4:0.0146:0:1.5 0/0:128:0:0,0:33,95:128,0:0:2,0:22.8:1:27.7:1:1:0:60:63:1:0:0.4 +10 86331958 . G T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16261;SOR=0.31949;LSEQ=TGGGGTCCTTTTCCACACTG;RSEQ=GAAAAGTTTGTTCTTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:3,4:4,6:10,7:0.4118:2,2:27.6:1:31.6:1:1:1.12:49.7:14:0.4118:0:2.1 0/1:28:5:1,4:11,12:23,5:0.1786:2,2:20.6:1:27.8:1:0.35531:3.51527:60:10:0.1852:0:2 +10 86331960 . A G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00776;SOR=0.10947;LSEQ=GGGTCCTTTTCCACACTGGG;RSEQ=AAAGTTTGTTCTTTTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:4,5:9,7:0.4375:2,2:26.1:1:33.6:1:1:1.06235:49.7:14:0.4375:0:2.1 0/1:27:2:0,2:12,13:25,2:0.0741:2,0:26.5:1:25.5:1:0.48718:0:60:4:0.0769:0:3 +10 86332020 . A G 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTACAATTTTTGGGTCCAC;RSEQ=TTGCCTTTATGAGCTGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:11.5:1:30.5:1:1:0:60:4:1:0:0 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:14.5:1:33:0:1:0:60:4:0.25:0:3 +10 88127039 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGCCAGAGGGGGCCGGCCGC;RSEQ=GCAAGCATCTCAGAGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 88635779 . C A 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACATTACAATTGAACAATG;RSEQ=CTCAGCTATACATTTACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:0:0,0:341,305:646,0:0:2,0:20.4:1:31.5:1:1:0:48.2:128.2:0.9984:0:0.1 0/1:607:72:34,38:275,256:531,72:0.1186:2,2:9.1:1:27.2:1:0.53027:1.20023:32.5:23:0.1156:0:1.1 +10 88635888 . C T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GTATGTGTGTATATAAAAAG;RSEQ=ACTATTTCTTGCTTCTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:92,331:423,0:0:2,0:23:1:32.2:1:1:0:60:83.6:0.9976:0:0.1 0/1:432:14:4,10:106,309:415,14:0.0324:2,2:18.7:1:28.5:1:0.7612:1.17:60:28:0.0329:0:1.1 +10 88649763 . C T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=15.5776;LSEQ=TTTCTCATTGAAAATTGTCA;RSEQ=GAAACAATGAGCTTTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:8:8,0:107,19:126,8:0.0597:2,0:15.9:1:30.9:1:0.60048:0:60:16:0.0611:0:1 1/0:130:65:55,10:60,5:65,65:0.5:2,2:23.3:1:29.9:1:0.27195:2.16904:60:64:0.4961:0:1.1 +10 88650068 . G GT 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.47422;SOR=1.96097;LSEQ=AATTATTAAACTTGTCTGCG;RSEQ=TTTTTTTTTCATTCATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:3:0,3:5,73:78,3:0.037:2,0:35:1:31:1:1:0:60:6:0.037:0:0 0/1:71:5:0,5:5,61:66,5:0.0704:2,0:31.4:1:30:1:1:0:60:10:0.0735:0:0 +10 88652022 . G A 43 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13812;SOR=Inf;LSEQ=GGACCCATGAGACAAAGAAG;RSEQ=GAGGGGCCATATGAAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:73,212:285,0:0:2,0:23.1:1:31:1:1:0:58.8:46.5:1:0:0.1 0/1:376:4:3,1:111,261:372,4:0.0106:2,2:7:1:21.5:1:0.08501:7.01:56.3:3:0.0083:0:2 +10 88659494 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25359;SOR=Inf;LSEQ=TATTTTATGAATACTAAAAA;RSEQ=ACATATCAGTTTAAAATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:189,26:215,0:0:2,0:24.7:1:33:1:1:0:60:52.75:1:0:0.1 0/1:254:3:2,1:201,50:251,3:0.0118:2,2:27:1:23:1:0.49103:2.00347:60:2:0.0079:0:1 +10 88659758 . T A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATTTTTTCATTTCAATTG;RSEQ=TTACATTGTTTACTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:566:0:0,0:338,228:566,0:0:2,0:24.5:1:30.2:1:1:0:56.4:187.667:1:0:0.1 0/1:804:35:18,17:446,320:766,35:0.0435:2,2:21.7:1:28.6:1:0.48491:1.31585:53.7:34:0.0429:0:1.2 +10 88659788 . G A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTACTTTTATTGTCAGGTCC;RSEQ=TTTTTTGATGGCAGCATTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:314,222:536,0:0:2,0:31:1:31.1:1:1:0:51.4:267:0.9981:0:0.1 0/1:800:24:12,12:445,331:776,24:0.03:2,2:27.3:1:29.5:1:0.53254:1.34389:54.2:48:0.0302:0:1.1 +10 88660269 . CA C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTTCAGAAGACAGTTGC;RSEQ=AAAAAGAAGAGTAATAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:20.5:1:31.5:1:1:1:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 88661887 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGCCCTCCCAAATTGCTGG;RSEQ=ATTACAGGCGTGAGCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:29.5:1:1:0:39.5:4:1:0:1 +10 88671873 . A G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03129;SOR=Inf;LSEQ=ACAGGATATATTATCCAATG;RSEQ=TAAGACTAATTTGGATAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:63,0:63,0:0:1,0:22.4:1:30.3:1:1:0:60:126:1:0:0.1 0/1:30:3:3,0:27,0:27,3:0.1:1,0:22.7:1:30:1:1:0:60:6:0.1:0:1 +10 88671946 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49889;SOR=Inf;LSEQ=ACCTCAAGGTTTTTCTTAGG;RSEQ=TTTTATAGTTTTTCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:176,18:194,0:0:2,0:22.9:1:31.5:1:1:0:60:63.667:1:0:0.1 0/1:201:2:1,1:178,21:199,2:0.01:2,2:15:1:27:1:0.20741:8.30351:60:4:0.0101:0:1 +10 88672153 . G A 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTTTATTGGTAAGTTAAAC;RSEQ=TTCCTATAGACATGAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:668:0:0,0:249,418:667,0:0:2,0:27.2:1:31.6:1:1:0:50.2:165.75:1:0:0.1 0/1:662:30:11,19:234,398:632,30:0.0453:2,2:32.9:1:28.8:1:1:1.01551:52.9:14:0.0429:0:1.3 +10 88672247 . AT A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.13236;SOR=Inf;LSEQ=CAGGGAACAATAATGGACAC;RSEQ=TTTTTTCTCCTTATTTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:0,160:160,0:0:1,0:22.9:1:30.8:1:1:0:60:79:1:0:0.1 0/1:92:2:0,2:2,88:90,2:0.0217:1,0:36:1:31.5:1:1:0:60:4:0.022:0:1 +10 88676749 . CA C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.88397;LSEQ=GACAGAGCGAGACTCCATCT;RSEQ=AAAAAAAAAAAGTACATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:9:8,1:46,2:48,9:0.1552:1,2:25.7:1:33.1:1:0.40889:2.8045:58.9:18:0.1552:0:0.2 0/1:43:6:6,0:36,1:37,6:0.1395:1,0:25:1:29.8:1:1:0:58.5:12:0.1429:0.0233:0.3 +10 88677218 . C G 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01096;SOR=Inf;LSEQ=AGGAAACCTAGTAGAATACA;RSEQ=GGTTTGAATAAAACATAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:1,84:85,0:0:1,0:20.8:1:29.7:1:1:0:59.3:27.333:1:0:0.1 0/1:60:5:0,5:0,55:55,5:0.0833:1,0:23.6:1:30:1:1:0:60:10:0.0847:0:1 +10 88678748 . A T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATTTATTGTAGAAGTACAG;RSEQ=TATATGTGTAAATGTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:39,0:0,0:0,39:1:0,1:23.9:1:31.7:1:1:0:60:78:1:0:1.1 1/1:28:28:27,1:0,0:0,28:1:0,1:22.8:1:30:1:1:0:60:56:1:0:1 +10 88678807 . C T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12312;SOR=Inf;LSEQ=ATTCACGACTTGGTGTCAGG;RSEQ=GAATTAAAGTTTCACTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:92,0:92,0:0:1,0:23.4:1:32.3:1:1:0:59.8:29.667:1:0:0.4 0/1:102:4:4,0:96,2:98,4:0.0392:1,0:26.3:1:31.3:1:1:0:60:8:0.0392:0:1 +10 88678882 . G T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02355;SOR=0;LSEQ=ATGAGCATTACTTCTCCCTA;RSEQ=CCTATCTCTGATGATAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:4:1,3:247,115:362,4:0.0109:2,2:9:1:28.8:1:0.10044:6.40833:60:8:0.0111:0:1 0/0:566:0:0,0:346,220:566,0:0:2,0:24.1:1:31:1:1:0:60:69.75:1:0:0.1 +10 88679155 . CA C 47 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.24759;SOR=0;LSEQ=GCTCATCGAGACCTAAAGAG;RSEQ=AAAACATCCTCATCAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:3:2,1:53,73:126,3:0.0233:2,2:6.3:1:29.7:1:0.57495:2.73:40.7:6:0.0234:0.0155:0 0/0:122:0:0,0:50,72:122,0:0:2,0:7.3:1:28.6:1:1:0:31:121:1:0:0.2 +10 88679356 . TG T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00195;SOR=Inf;LSEQ=TAGTTACATAAATGTATAGT;RSEQ=GGGGGGATTTTGTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:2,41:43,0:0:1,0:24.8:1:31:1:1:0:58.7:42:1:0:0 0/1:33:7:0,7:1,25:26,7:0.2121:1,0:19.9:1:31.1:1:1:0:60:14:0.2121:0:0 +10 88681318 . G A 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88463;LSEQ=GCCCTTGAATACCAGGGTGG;RSEQ=CACCAAACGCTACATGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:4:3,1:171,144:315,4:0.0125:2,2:20.5:1:26.8:1:0.62888:2.52:54.8:3:0.0097:0:1.3 0/1:453:5:4,1:221,227:448,5:0.011:2,2:12.4:1:26.6:1:0.2136:4.10:39.6:10:0.0112:0:1 +10 88681402 . A T 50 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06817;SOR=Inf;LSEQ=CTACATCATGGCTGACATCT;RSEQ=CAGCTTCGGCCTAATCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:113,164:277,0:0:2,0:15.8:1:28.8:1:1:0:43.1:68.25:1:0:0.1 0/1:342:5:0,5:162,175:337,5:0.0146:2,0:5.4:1:21.6:1:0.0624:0:43.6:4:0.0118:0:1.2 +10 88681458 . A G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTGTATCACAGGAGGTGGG;RSEQ=GTTTGAGTAGTTTCTGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:566:0:0,0:208,358:566,0:0:2,0:29.2:1:31.2:1:1:0:50.6:42.538:1:0:0.1 0/1:755:28:12,16:301,426:727,28:0.0371:2,2:27.4:1:30.6:1:1:1.06:45.1:27:0.037:0:1.3 +10 88682999 . T ATGTATATA 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.03471;SOR=Inf;LSEQ=CATACATCTACTATTAAGAG;RSEQ=GAATCATAGTGTCTATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:63,1:64,0:0:1,0:22.6:1:34.1:1:1:0:60:128:1:0:0.1 0/1:32:3:3,0:29,0:29,3:0.0938:1,0:22.7:1:28.7:1:1:0:60:6:0.0938:0.0313:0.7 +10 88683122 . T C 222 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGTGCCCATGTTTTCTCA;RSEQ=TCCCTTATAGGGATCGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:266,132:398,0:0:2,0:25.4:1:31.1:1:1:0:53.5:198:1:0:0.1 0/1:495:134:85,49:223,138:361,134:0.2707:2,2:26.9:1:31.5:1:0.75534:1.07:52.4:133:0.2698:0:1.1 +10 88866050 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28252;SOR=Inf;LSEQ=GGGATTATAGGCATGAGCCA;RSEQ=TGTTCCCGGCCAGAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:44,21:65,0:0:2,0:21.8:1:32.4:1:1:0:55.9:64:1:0:0.1 0/1:102:3:1,2:63,36:99,3:0.0294:2,2:16:1:25.3:1:0.55383:3.45539:60:6:0.0294:0:1 +10 88866085 . TCA T 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGGAATAATTGTTAGACAAC;RSEQ=CAGTGTCTGCCATATTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:18:11,7:69,46:115,18:0.1353:2,2:29.6:1:33.2:1:1:1.05:59.4:36:0.1374:0:0.3 0/0:233:0:0,0:127,105:232,0:0:2,0:25.6:1:30.7:1:1:0:59.9:76.333:0.9957:0:0.3 +10 88866129 . C G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=13.83862;LSEQ=CAGAAAATAACTGACTTGCT;RSEQ=TCTGCTGTCTTACTGTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:3:1,2:83,78:161,3:0.0183:2,2:14.7:1:32.3:1:0.61361:2.11873:60:6:0.0186:0:1 0/1:248:51:22,29:90,107:197,51:0.2056:2,2:27.3:1:31.3:1:0.75535:1.10829:60:50:0.2049:0:1.1 +10 88866168 . AT A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06326;SOR=Inf;LSEQ=TAATATATTTTTTTAACGCA;RSEQ=TTACAAAAGGGGGGGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:46,68:114,0:0:2,0:24.9:1:30.2:1:1:0:59.9:37:1:0:0.1 0/1:133:5:1,4:38,90:128,5:0.0376:2,2:16.6:1:30.1:1:1:1.68296:60:10:0.0382:0.0226:0.2 +10 88866177 . A AG 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.21645;LSEQ=TTTTTAACGCAATTTACAAA;RSEQ=GGGGGGGAACATTCTTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:97:54:16,38:18,23:41,54:0.5567:2,2:28.4:1:31.7:1:0.19564:1.84634:59.7:108:0.5567:0.0722:0.2 0/1:113:24:6,18:26,63:89,24:0.2124:2,2:30.2:1:30.2:1:0.80153:1.2358:59.8:23:0.213:0.0088:0.1 +10 89153971 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11905;SOR=Inf;LSEQ=TCCTCCCTTACCCTTGATGT;RSEQ=CCCTCGTAGTCATTTCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:18,0:0:2,0:36.2:1:30.5:1:1:0:48.6:17:1:0:0.2 0/1:10:2:1,1:4,4:8,2:0.2:2,2:34.5:1:31:1:1:1:27.5:4:0.2:0:1 +10 89623860 . CT C 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAACACGGCGGCGGCGGCGG;RSEQ=GGCACATCCAGGGACCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:0,6:1:0,2:32.3:1:32.5:1:1:0:33.7:12:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29.5:1:1:0:24.5:4:1:0:0 +10 89653686 . A G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10071;SOR=0.56966;LSEQ=CTCCAGCTATAGTGGGGAAA;RSEQ=CTTTCTTTTCATAACTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:31:28,3:52,5:57,31:0.3523:2,2:24.2:1:32.9:1:1:1.1129:60:30:0.3448:0:1.1 0/1:89:21:18,3:61,7:68,21:0.236:2,2:19.8:1:31.8:1:0.69473:1.44584:60:42:0.2386:0:1.1 +10 89653834 . C T 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=26.5594;LSEQ=CCTGCAGAAAGACTTGAAGG;RSEQ=GTATACAGGAACAATATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:1:0,1:234,261:495,1:0.002:2,0:1:0:27:0:1:0:60:2:0.0021:0:1 0/1:550:28:11,17:235,287:522,28:0.0509:2,2:26.6:1:28.6:1:0.69711:1.26491:38.8:27:0.0503:0:1.1 +10 89653911 . T A 31 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24872;SOR=0;LSEQ=TCAAATATTGATGTTTATAT;RSEQ=CATGTTGTGTTTTCATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:2,1:50,161:211,3:0.014:2,2:14.7:1:20:1:0.1471:6.37:60:2:0.0096:0:1.3 0/0:203:0:0,0:52,151:203,0:0:2,0:23.5:1:28.8:1:1:0:60:202:1:0:0.1 +10 89685391 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50522;SOR=Inf;LSEQ=TGAAAGTTATCTGCTTGTTA;RSEQ=AGTGAGGTAGAGTTAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:23,87:110,0:0:2,0:22.4:1:32.4:1:1:0:60:220:1:0:0.1 0/1:140:2:1,1:37,101:138,2:0.0143:2,2:27:0:31:1:0.47061:2.71:60:4:0.0144:0:1 +10 89690770 . TA T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15663;SOR=0;LSEQ=TTCTTCCTAAGTGCAAAAGA;RSEQ=ACTTTATATCACTTTTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:120,73:193,2:0.0102:2,2:29:0:30.5:1:1:1.63941:60:4:0.0103:0:0.5 0/0:300:0:0,0:194,106:300,0:0:2,0:24:1:28.3:1:1:0:60:600:1:0:0.1 +10 89690952 . T TTTATC 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94981;LSEQ=ATTATCGAGTGAGATACATA;RSEQ=TTAAGAATTATCTTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:14:0,14:2,50:52,14:0.2059:1,1:26.3:1:29.4:1:1:0:60:28:0.209:0.0588:0 0/1:81:16:0,16:2,63:65,16:0.1975:1,1:26.4:1:30.5:1:1:0:60:32:0.2078:0.037:0.1 +10 89692731 . G GT 103 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.02444;SOR=0.27644;LSEQ=TGTTAATTAAAAATTCAAGA;RSEQ=TTTTTTTTTCTTATTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:13:12,1:191,67:258,13:0.0476:2,1:24.4:1:27.9:1:0.19545:4.19:60:5.5:0.0406:0:0.2 0/1:294:4:3,1:208,80:288,4:0.0136:2,2:33.8:1:30.5:1:1:1.15:60:8:0.0137:0:0.3 +10 89692844 . C T 190 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTTTTGTGAAGATCTTGAC;RSEQ=AATGGCTAAGTGAAGATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:85:49,36:55,53:108,85:0.4404:2,2:7.6:1:29.7:1:0.38482:1.31:26.5:84:0.4421:0:1.1 0/0:194:0:0,0:101,92:193,0:0:2,0:6.8:1:29.4:1:1:0:26:63.333:0.9948:0:0 +10 89693036 . T C 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12019;SOR=0;LSEQ=ATTTTTTGATGTTTTTCCTT;RSEQ=CCTCTTCCTGGATCTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:3:1,2:41,184:225,3:0.0131:2,2:33.7:1:25.3:1:0.45871:2.23:49.3:2:0.0088:0:2.3 0/0:234:0:0,0:74,160:234,0:0:2,0:22.8:1:28.9:1:1:0:56.1:77:1:0:0.1 +10 89711813 . T A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11695;SOR=0;LSEQ=CAGTTACCATAGCAATTTAG;RSEQ=GAAATAACTATAATGGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:130,24:154,3:0.0191:2,2:19.7:1:24.3:1:0.40785:2.68535:60:2:0.0132:0:1.3 0/0:163:0:0,0:129,33:162,0:0:2,0:23.4:1:29.1:1:1:0:60:161:0.9938:0:0.1 +10 89711833 . AT A 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.6922;SOR=1.70121;LSEQ=TGAAATAACTATAATGGAAC;RSEQ=TTTTTTTCAATTTGGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:2:1,1:176,59:235,2:0.0084:2,2:10.5:1:30.3:1:0.44304:2.96644:60:4:0.0085:0.0042:0 0/1:280:4:3,1:201,75:276,4:0.0143:2,2:34.3:1:31.3:1:1:1.12:60:8:0.0144:0:0 +10 89711855 . C CT 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.2516;LSEQ=TTTTTTTCAATTTGGCTTCT;RSEQ=TTTTTTTTCTGTCCACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:4:3,1:230,83:313,4:0.0126:2,2:30:1:31.5:1:1:1.08:60:8:0.0129:0:0 0/1:381:6:5,1:248,125:373,6:0.0157:2,2:29:1:30.7:1:0.66815:2.52:60:12:0.016:0.0026:0 +10 89717709 . AGCCGT A 238 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATGTACTTTGAGTTCCCTC;RSEQ=TACCTGTGTGTGGTGATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:209:90,119:114,144:258,209:0.4475:2,2:25.8:1:31:1:0.85131:1.04668:35.3:418:0.4553:0.0771:0 0/0:579:0:0,0:271,307:578,0:0:2,0:25:1:31.4:1:1:0:38.7:191.667:0.9983:0:0.2 +10 89717776 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10377;SOR=0;LSEQ=CAGAACAAGATGCTAAAAAA;RSEQ=GTTTGTACTTTACTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:1,2:60,188:248,3:0.012:2,2:8.7:1:29.3:1:0.56792:1.56:37.7:6:0.0121:0:1 0/0:282:0:0,0:84,198:282,0:0:2,0:28.1:1:30.6:1:1:0:45.5:69.5:1:0:0.1 +10 89720251 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGTAGCTCATTTGAAATG;RSEQ=AGAAAAAATTAAATCCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:18.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 89720617 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22772;SOR=Inf;LSEQ=ATTAATTAAATATGTCATTT;RSEQ=ATTTCTTTTTCTTTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:82,4:86,0:0:1,0:23.1:1:31.2:1:1:0:56.5:20.5:1:0:0.6 0/1:79:2:2,0:58,15:73,2:0.0253:2,0:21:1:29:0:1:0:52:4:0.0328:0:1 +10 89720907 . T G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.35757;LSEQ=TAAACATTTTGTGGGGGTTG;RSEQ=TGACTTGTATGTATGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:53:27,26:41,87:128,53:0.2912:2,2:11.3:1:31.1:1:0.01907:2.19:32.5:106:0.2961:0:1.1 0/1:266:34:13,21:88,144:232,34:0.1278:2,2:12.1:1:31.2:1:1:1.01:30.4:68:0.1288:0:1.1 +10 89721094 . C T 81 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCCTTTTCCTAATTCTT;RSEQ=GTTGTTTGCTGAAATCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:18.7:1:31.5:1:1:0:58.5:12:1:0:1.2 1/1:1:1:0,1:0,0:0,1:1:0,0:26:0:31:0:1:0:60:2:1:0:1 +10 89725230 . A AT 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.69215;LSEQ=CACAAATTACAAAAGTCTGA;RSEQ=TTTTTTTTTATCAAGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:3:1,2:10,49:59,3:0.0484:2,2:13:1:28.2:1:0.44937:2.41:29.3:6:0.0484:0.0161:0 0/1:59:2:1,1:6,51:57,2:0.0339:2,2:16:1:31.5:1:0.22501:7.95:31:4:0.0339:0:0 +10 89725293 . CT C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.08219;LSEQ=TGAATAAACTGAAAATGGAC;RSEQ=TTTTTTTTTTAATGGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:11:0,11:13,116:129,11:0.0786:2,0:38.6:1:32.8:1:0.599:0:25.4:22:0.0827:0:0.1 0/1:142:12:0,12:7,122:129,12:0.0845:2,0:29.6:1:30.8:1:1:0:22.9:24:0.0896:0:0.1 +10 90918714 . G T 191 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=95.57489;LSEQ=GCACTCCCCCCCTGCCGTGG;RSEQ=TATACATGTCATAATATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:1:1,0:188,206:394,1:0.0025:2,0:4:0:25:0:0.47848:0:60:2:0.0026:0:1 0/1:466:91:46,45:174,201:375,91:0.1953:2,2:29.1:1:29.5:1:0.48505:1.18:60:182:0.197:0:1.1 +10 90918802 . AAG A 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.79689;SOR=0.8553;LSEQ=AGTTGATATTTGAAGAAAGA;RSEQ=AGAGAGAGAGAGAAAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:8:0,8:23,104:127,8:0.0593:2,0:28.3:1:31.5:1:0.35053:0:60:16:0.0602:0:0.4 0/1:137:7:2,5:34,95:129,7:0.0511:2,2:34.4:1:30.1:1:1:1.12:60:14:0.0519:0:0 +10 90918806 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.49807;SOR=Inf;LSEQ=GATATTTGAAGAAAGAAAGA;RSEQ=AGAGAGAGAGAAAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:21,108:129,0:0:2,0:24.5:1:32:1:1:0:60:42:1:0:0.2 0/1:130:2:1,1:31,96:127,2:0.0154:2,2:20:1:27:1:0.43605:3.06:60:4:0.0155:0:1 +10 91613683 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53846;SOR=Inf;LSEQ=GGCTCTGCACCCTTCCGGCC;RSEQ=CTAAGACAAGGCCTCAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:9,0:0:2,0:19.7:1:29.8:1:1:0:60:8:1:0:0.2 0/1:18:2:1,1:5,11:16,2:0.1111:2,2:13.5:1:27:1:1:2.10:60:4:0.125:0:1 +10 93654341 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=TTTGATCTTTCTTATAAGTG;RSEQ=ATAGAAGAAAATGCTGACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:14,3:17,0:0:2,0:23.6:1:31.9:1:1:0:45.4:16:1:0:0.1 0/1:13:2:1,1:11,0:11,2:0.1538:0,2:32:1:27:1:0.15385:0:51:4:0.1538:0:1 +10 93654381 . C T 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45634;SOR=2.12022;LSEQ=TATGCTGCCTTCTCTCTCTC;RSEQ=TTCAGCTACATAAAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:2,1:24,12:36,3:0.0769:2,2:11.7:1:28.7:1:1:1:34:6:0.0811:0:1 0/1:33:5:3,2:14,14:28,5:0.1515:2,2:15.4:1:28.4:1:1:1.48:53.2:10:0.1563:0:1 +10 93654415 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49515;SOR=0;LSEQ=AAGGGAAAGCACCCCTGTCC;RSEQ=ATGATCATGTGACTTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:27,23:50,2:0.0385:2,2:45:0:33:1:1:1.17028:60:4:0.0385:0:1.5 0/0:52:0:0,0:24,28:52,0:0:2,0:27:1:28.5:1:1:0:58.1:51:1:0:0.3 +10 93878432 . A G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00423;SOR=0.59028;LSEQ=ATGGCTGCACTCTTGCTGAG;RSEQ=CATGTTGGTCGACATTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:80:57,23:145,78:223,80:0.264:2,2:29:1:31:1:0.33596:1.33:28.5:19:0.255:0:6.1 0/1:418:73:52,21:211,134:345,73:0.1746:2,2:29.5:1:31.2:1:0.11148:1.57:29.7:146:0.1794:0:6.1 +10 93878434 . A T 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00576;SOR=0.60016;LSEQ=GGCTGCACTCTTGCTGAGAC;RSEQ=TGTTGGTCGACATTGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:80:57,23:150,82:232,80:0.2564:2,2:31:1:31.6:1:0.33715:1.35:28.5:160:0.2572:0:6.1 0/1:426:73:52,21:213,139:352,73:0.1714:2,2:31.5:1:30.5:1:0.11071:1.61:29.7:72:0.1735:0:6.1 +10 93878441 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0081;SOR=0.61808;LSEQ=CTCTTGCTGAGACATGTTGG;RSEQ=CGACATTGCCTCCGAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:79:56,23:155,97:252,79:0.2387:2,2:36.5:1:31.7:1:0.14182:1.52:28.5:38.5:0.2355:0:6.1 0/1:450:73:52,21:220,157:377,73:0.1622:2,2:37.6:1:31.6:1:0.04933:1.76:29.7:146:0.1663:0:6.1 +10 93878444 . A T 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00354;SOR=0.58914;LSEQ=TTGCTGAGACATGTTGGTCG;RSEQ=CATTGCCTCCGAGCCCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:80:57,23:160,101:261,80:0.2346:2,2:37.7:1:29.9:1:0.11274:1.56:28.5:160:0.236:0:6.1 0/1:471:72:51,21:233,165:398,72:0.1529:2,2:39.1:1:29.3:1:0.05076:1.72:29.6:144:0.1552:0:6.1 +10 93878447 . T C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00479;SOR=0.59464;LSEQ=CTGAGACATGTTGGTCGACA;RSEQ=TGCCTCCGAGCCCACTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:80:57,23:160,107:267,80:0.2305:2,2:38.4:1:32.3:1:0.0865:1.65:28.5:79:0.2303:0:6.1 0/1:483:73:52,21:240,170:410,73:0.1511:2,2:40.4:1:31.8:1:0.05084:1.75:29.7:146:0.1534:0:6.1 +10 93878455 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00597;SOR=0.61449;LSEQ=TGTTGGTCGACATTGCCTCC;RSEQ=AGCCCACTTTAGCCCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:83:58,25:178,118:296,83:0.2184:2,2:33.9:1:29.9:1:0.12427:1.54:29.1:82:0.2187:0:6 0/1:512:75:52,23:245,191:436,75:0.1465:2,2:35.6:1:29.5:1:0.04213:1.76:29.4:150:0.1491:0:6.2 +10 93878496 . C CTGATGGTTG 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2751;SOR=0.75201;LSEQ=TCTGTATCAGAAATGCTGTT;RSEQ=CTTTGGGAACCACAGGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:37:22,15:159,154:313,37:0.1051:2,2:10.6:1:29.5:1:0.38529:1.42:32.3:74:0.1072:0.0938:6.2 0/1:493:40:23,17:218,234:452,40:0.0811:2,2:9.7:1:28.5:1:0.32244:1.45:31.9:80:0.0823:0.071:6.3 +10 93878609 . A G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34723;SOR=1.17164;LSEQ=AGTTGGTCTCTTCCCATGGC;RSEQ=ATGGCCATCTGCCACCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:145:96,49:100,57:157,145:0.4801:2,2:24.9:1:30.5:1:0.71756:1.12:53:47.333:0.4781:0:1.1 1/0:354:184:119,65:108,61:169,184:0.5198:2,2:24.1:1:29.4:1:0.91171:1.03:52:60.333:0.5201:0:1.1 +10 93878628 . GAC G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=3.45141;LSEQ=CAATGGCCATCTGCCACCAT;RSEQ=ACTGGTACTGCTTTGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:13:9,4:242,111:353,13:0.0355:2,2:29.6:1:33.3:1:1:1.03:59.2:26:0.0359:0.0027:0 0/1:434:49:35,14:247,138:385,49:0.1129:2,2:25.6:1:31.3:1:0.34429:1.40:58.7:98:0.1148:0.023:0 +10 93878957 . T G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.90003;SOR=0.95746;LSEQ=AGCATCATATTCCTACACAT;RSEQ=ATTACATTCACCCATCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:859:30:18,12:371,458:829,30:0.0349:2,2:12.6:1:32.9:1:0.13419:1.85:44.4:60:0.0353:0:7.7 0/1:1075:36:23,13:472,567:1039,36:0.0335:2,2:9.3:1:32.1:1:0.03994:2.12:44:72:0.0339:0:7.7 +10 93878970 . CA TG 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.81986;SOR=1.05737;LSEQ=TACACATTATTACATTCACC;RSEQ=TCTTTCTGTTTGTCACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:35:21,14:392,474:866,35:0.0388:2,2:21.8:1:32.8:1:0.11828:1.81:43.7:70:0.0391:0:6.6 0/1:1098:45:28,17:487,563:1050,45:0.041:2,2:20.2:1:32:1:0.0466:1.90:44.1:90:0.0414:0:6.5 +10 93878975 . TT CC 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64869;SOR=1.14158;LSEQ=ATTATTACATTCACCCATCT;RSEQ=CTGTTTGTCACTCTTATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:902:34:21,13:386,480:866,34:0.0377:2,2:26.1:1:32.5:1:0.05405:2.01:43.4:68:0.0384:0:5.7 0/1:1098:47:29,18:485,563:1048,47:0.0428:2,2:23.8:1:31.6:1:0.05112:1.87:44.2:94:0.0433:0.0018:5.6 +10 93879006 . A C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.0037;LSEQ=ACTCTTATCTCCAGCCTGGG;RSEQ=AAAGTTCTCCTTATTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:839:81:39,42:316,442:758,81:0.0965:2,2:26.2:1:32.7:1:0.28764:1.30:46.2:80:0.097:0:5.3 0/1:1053:102:56,46:404,546:950,102:0.0969:2,2:27.6:1:32:1:0.02053:1.64:44.8:101:0.0967:0:5.2 +10 93879018 . T C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.93428;SOR=1.02134;LSEQ=AGCCTGGGAAAAGTTCTCCT;RSEQ=ATTTGTTTAGATCCTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:737:72:33,39:242,422:664,72:0.0977:2,2:25.5:1:32.5:1:0.12501:1.47:46.5:71:0.0982:0:5.6 0/1:934:93:51,42:331,510:841,93:0.0996:2,2:24.4:1:31.2:1:0.00525:1.87:45.2:186:0.1009:0:5.3 +10 93879022 . T A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.86741;SOR=1.03977;LSEQ=TGGGAAAAGTTCTCCTTATT;RSEQ=GTTTAGATCCTTTTGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:70:34,36:223,402:625,70:0.1007:2,2:22.4:1:29.9:1:0.03722:1.70:46.7:34:0.0997:0:5.6 0/1:882:92:52,40:300,490:790,92:0.1043:2,2:20.8:1:28.5:1:0.00071:2.12:45.6:184:0.105:0:5.3 +10 93879038 . CA TG 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50073;SOR=0.82405;LSEQ=TATTTGTTTAGATCCTTTTG;RSEQ=CTTTCAGATCCCCTTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:29:10,19:168,341:509,29:0.0538:2,2:18.5:1:31.7:1:0.84197:1.07:46.4:28:0.0525:0:5.9 0/1:648:29:15,14:219,400:619,29:0.0448:2,2:19.6:1:31:1:0.07827:1.95:43.1:58:0.0453:0:6 +10 93879045 . A T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89154;SOR=0.96062;LSEQ=TTAGATCCTTTTGCACTTTC;RSEQ=GATCCCCTTGGAGCAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:26:8,18:167,345:512,26:0.0483:2,2:13.9:1:31.7:1:1:1.08897:46:52:0.049:0:6.1 0/1:645:30:15,15:218,397:615,30:0.0465:2,2:14.8:1:29.1:1:0.12045:1.82:42.4:14:0.0438:0:5.9 +10 93879049 . C A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.78385;SOR=0.90793;LSEQ=ATCCTTTTGCACTTTCAGAT;RSEQ=CCCTTGGAGCAGTAGAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:27:9,18:160,337:497,27:0.0515:2,2:9.6:1:29.3:1:1:1.05:45.2:26:0.0506:0:5.9 0/1:617:29:16,13:206,382:588,29:0.047:2,2:9.7:1:28.2:1:0.04543:2.28:42.4:58:0.0474:0:5.9 +10 93879078 . A C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.6775;LSEQ=GCAGTAGAGTACCTTGTAGA;RSEQ=CATAAGAGTGGAAAAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:132:22,110:22,115:137,132:0.4907:2,2:19.9:1:30.7:1:1:1.05:28.1:21:0.4809:0:1 1/1:265:217:37,180:10,37:47,217:0.8189:2,2:20.3:1:30.8:1:0.52882:1.31339:26.8:216:0.8182:0:1.1 +10 95374453 . T G 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TTCTGCTGTTATACTTTGAT;RSEQ=AGCCCAGTTCTCTGTGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:0:0,0:188,176:364,0:0:2,0:25.7:1:29.6:1:1:0:60:59.667:1:0:0.1 0/1:488:19:11,8:232,237:469,19:0.0389:2,2:29.2:1:30.9:1:0.49349:1.40:60:38:0.0396:0:1 +10 95374469 . G A 149 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=30.16274;LSEQ=TGATTAGCCCAGTTCTCTGT;RSEQ=GTGAGAAGGAAATAAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:1:1,0:179,171:350,1:0.0028:2,0:1:0:25:0:1:0:60:2:0.0029:0:1 0/1:454:36:19,17:193,225:418,36:0.0793:2,2:24.5:1:29:1:0.48885:1.30:60:72:0.0798:0:1.1 +10 95374519 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08913;SOR=0;LSEQ=TTGGAGGTGGTTTTGGTCTG;RSEQ=GGCTGTCCATGGTGAGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:89,152:241,3:0.0123:2,2:8.7:1:28:1:1:1.17034:60:6:0.0124:0:1 0/0:301:0:0,0:116,185:301,0:0:2,0:24.3:1:30.1:1:1:0:60:99.333:1:0:0.2 +10 96163397 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.4955;SOR=Inf;LSEQ=CGGGGCCGGGGCCGGAGCCG;RSEQ=GGTCTTGGTGGGAGTCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:16,0:0:2,0:28.9:1:29.2:1:1:0:60:7:1:0:0.9 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:34:1:29.5:1:1:1.10554:60:4:0.0952:0:1 +10 96163412 . T TCGGAGC 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=5.000;MSILEN=6;SSF=0.75012;SOR=1.28783;LSEQ=AGCCGGGGTCTTGGTGGGAG;RSEQ=CGGAGCCGGAGCCGGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:6,3:5,2:7,9:0.5625:2,2:24.3:1:30.7:1:1:1.23276:60:18:0.6429:0.1875:0.9 1/0:24:15:7,8:4,4:8,15:0.625:2,2:26.3:1:30.6:1:1:1.13623:58:30:0.6522:0:0.3 +10 96202765 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49984;SOR=Inf;LSEQ=TCCTCAGGAAAAACAAAGTT;RSEQ=GGGACACACACTATGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:76,22:98,0:0:2,0:23.3:1:29.6:1:1:0:60:196:1:0:0.1 0/1:112:2:1,1:81,28:109,2:0.0179:2,2:10:0:32.5:1:0.45602:2.86004:60:4:0.0182:0:1.5 +10 96202869 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25764;SOR=Inf;LSEQ=TGTTTAACCAGAACCAAGAT;RSEQ=TTCACCCCCATAGAATGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:85,119:204,0:0:2,0:24.9:1:32.1:1:1:0:60:101:1:0:0.1 0/1:255:3:2,1:106,146:252,3:0.0118:2,2:29:1:22.3:1:0.57565:2.74:60:2:0.0079:0:1 +10 96202896 . G A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22715;SOR=0;LSEQ=CCCATAGAATGTACATGCAC;RSEQ=GCACTAGAGGACTGCATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:40,96:136,2:0.0145:2,2:5:1:30:1:0.50746:2.38:60:4:0.0146:0:1 0/0:151:0:0,0:46,105:151,0:0:2,0:23.2:1:29.9:1:1:0:60:302:1:0:0.1 +10 97753910 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAGACCGGTGGTGGCCTC;RSEQ=AATGGCTGGGCGCACTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:9,2:11,0:0:2,0:22.7:1:31.5:1:1:0:59.8:22:1:0:0 0/1:24:2:1,1:20,2:22,2:0.0833:2,2:32:1:28.5:1:0.23913:8.36492:60:4:0.0833:0:1 +10 97754105 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGCACTTGTAAGAAAGATC;RSEQ=AAGACTTTAAGACTTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:22.4:1:32.8:1:1:0:40:16:1:0:0.1 0/1:20:2:0,2:2,16:18,2:0.1:2,0:27:1:32.5:1:1:0:29:4:0.1:0:1 +10 97759626 . A G 47 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TCTGGGTGAAGCAGGCTGGC;RSEQ=CTTCAGTTGAACCCAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:27.3:1:30.3:1:1:0:46.3:6:1:0:1 1/0:6:3:2,1:3,0:3,3:0.5:0,2:22:1:30:1:1:0:60:6:0.5:0:1 +10 97759760 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49524;SOR=Inf;LSEQ=TTAATTCTCTTGGCAAGAAT;RSEQ=TTGCCCTTCTTTGTTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:36,14:50,0:0:2,0:18.7:1:32.4:1:1:0:58.9:100:1:0:0.1 0/1:52:2:1,1:34,16:50,2:0.0385:2,2:14:1:30.5:1:1:2.0917:47.5:4:0.0392:0:1 +10 97949207 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21132;SOR=0;LSEQ=ATAATTGATGAACTTGGCTT;RSEQ=CACTTTGGGAAGAGAACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:31,16:47,2:0.0408:2,2:20:1:31:1:1:1.90979:35.5:4:0.0426:0:1 0/0:57:0:0,0:38,19:57,0:0:2,0:28:0:14:0:1:0:28:0:0:0:7 +10 97949368 . C A 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09112;SOR=0;LSEQ=ATGATGGGTTTGAGTGTTTT;RSEQ=TATTCTGATTTGACTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:2,1:48,84:132,3:0.0221:2,2:22.7:1:26.7:1:0.55486:3.47:49:6:0.0222:0:1 0/0:165:0:0,0:70,95:165,0:0:2,0:23.2:1:30.6:1:1:0:59:81.5:1:0:0.1 +10 97949454 . A AATC 161 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=13.000;MSILEN=3;SSF=0;SOR=0.13794;LSEQ=TTCAGTTTCCTCATCATCAA;RSEQ=ATCATCATCATCATCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:35:17,18:10,11:21,35:0.625:2,2:35.4:1:31.4:1:1:1.04:40:34:0.6415:0.0536:0.1 0/1:49:9:4,5:15,25:40,9:0.1837:2,2:34.2:1:30.6:1:0.71994:1.33:36.7:18:0.1837:0:0.2 +10 97949572 . A C 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCACTTTCCAGATATCCTTA;RSEQ=GAGTTTCACATCCTCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:48,16:64,0:0:2,0:28.4:1:30.2:1:1:0:43.5:128:1:0:0.1 0/1:102:26:18,8:54,22:76,26:0.2549:2,2:32:1:29.9:1:1:1.08997:41.8:25:0.2475:0:1.1 +10 97949707 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20294;SOR=Inf;LSEQ=TGGTGGTGTTATTTCAAAGA;RSEQ=CCCAAGGGAAACTGTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:104,93:197,0:0:2,0:26.5:1:32.1:1:1:0:47.8:97.5:1:0:0.1 0/1:162:2:1,1:85,75:160,2:0.0123:2,2:8.5:1:29:1:1:1.13245:42.5:4:0.0125:0:1 +10 97949788 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25391;SOR=Inf;LSEQ=CTGCCTTCATAATTCATTGC;RSEQ=TCTGCTTCAACAATGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:119,106:225,0:0:2,0:19.4:1:31.7:1:1:0:39.1:55.25:0.9955:0:0.1 0/1:268:3:2,1:139,126:265,3:0.0112:2,2:15.7:1:27.7:1:1:1.81:37.7:6:0.0113:0:1 +10 97949868 . C A 31 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33374;SOR=0.27472;LSEQ=GGATAACTGGTGCTCATTTT;RSEQ=ATCATTATCCACCTTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:3,0:108,142:250,3:0.0119:2,0:11.3:1:20:1:0.08317:0:32.3:2:0.008:0:1 0/0:305:1:1,0:131,173:304,1:0.0033:2,0:1:0:23:0:0.43279:0:35:2:0.0033:0:1 +10 97949883 . T A 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32947;SOR=0.26815;LSEQ=ATTTTCATCATTATCCACCT;RSEQ=AAAGTGATCATCTTTGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:2,1:69,101:170,3:0.0173:2,2:25.7:1:27.7:1:0.56875:2.91:43.3:6:0.0175:0:1 0/0:213:1:1,0:89,123:212,1:0.0047:2,0:1:0:23:0:0.42254:0:21:2:0.0048:0:1 +10 97949903 . G A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18317;SOR=0;LSEQ=TAAAGTGATCATCTTTGTCG;RSEQ=CCTTTAGTTCACAACTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:37,67:104,2:0.0189:2,2:22:1:25:0:1:1.80:25.5:4:0.019:0:1 0/0:141:0:0,0:63,78:141,0:0:2,0:21:1:30.7:1:1:0:28.6:46:1:0:0 +10 98319855 . A G 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05434;SOR=Inf;LSEQ=TCTGTACATCTGCCTGGTGT;RSEQ=ATTCTGTCCTGCGTGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:31,7:38,0:0:2,0:22.1:1:28.7:1:1:0:60:76:1:0:0.2 0/1:37:4:3,1:27,6:33,4:0.1081:2,2:26.5:1:32.3:1:1:1.48199:60:8:0.1081:0:1 +10 98319912 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12974;SOR=0;LSEQ=CATTTATCTCCGTCTGCCTT;RSEQ=TTTCCCACCTAAATGCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:47,23:70,2:0.0278:2,2:19:0:32.5:1:1:2.02168:44.5:4:0.0286:0:1 0/0:127:0:0,0:78,49:127,0:0:2,0:27:1:30.6:1:1:0:56:62.5:1:0:0.1 +10 98319949 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15803;SOR=0;LSEQ=GTGCTGCCACCCCATGGAAG;RSEQ=TTCGATGGACATGGACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:52,27:79,2:0.0247:2,2:31.5:1:29:1:1:1.90939:32.5:4:0.0263:0:1 0/0:122:0:0,0:72,50:122,0:0:2,0:28.9:1:29:1:1:0:49.9:60:1:0:0.1 +10 98320021 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50073;SOR=Inf;LSEQ=TTGTGAACTAAAGGCCAACA;RSEQ=AGATGATCACTTTAAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:108,44:152,0:0:2,0:22.7:1:30.9:1:1:0:31.5:304:0.9935:0:0.1 0/1:175:2:1,1:115,58:173,2:0.0114:2,2:12.5:1:26.5:1:1:1.97448:41:4:0.0115:0:1 +10 98320153 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24665;SOR=0;LSEQ=AATGAATTATGAAGGCAGTC;RSEQ=AATTAAATAACACTGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:74,109:183,2:0.0108:2,2:28:1:28:1:1:1.47:60:4:0.0111:0:2 0/0:187:0:0,0:90,97:187,0:0:2,0:20.8:1:30.3:1:1:0:34.7:61.333:1:0:0.1 +10 98320268 . T C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00068;SOR=0;LSEQ=AGTGTGGTTCAGGGCCAGTG;RSEQ=ATATTAGTGGACAGCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:81:43,38:0,0:0,81:1:0,2:12.5:1:31.7:1:1:0:26.6:39.5:1:0:1.1 1/1:82:71:38,33:5,6:11,71:0.8659:2,2:12.3:1:30.8:1:0.74933:1.38:26.7:142:0.8659:0:1.1 +10 98320336 . G A 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02954;SOR=Inf;LSEQ=GAAGATGAACAGGAGGAGGC;RSEQ=AAATTCTTAAGGATATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:52,68:120,0:0:2,0:26:1:30.9:1:1:0:43.3:119:1:0:0.4 0/1:125:6:3,3:55,64:119,6:0.048:2,2:18.7:1:29.8:1:1:1.16:37.8:12:0.048:0:1.3 +10 98320393 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19524;SOR=0;LSEQ=GGAGGTGGTAGCAAGGTTCC;RSEQ=CAGAAAAAAGTAAAACTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:0,2:41,62:103,2:0.019:2,0:19.5:1:33.5:1:0.51941:0:58.5:4:0.0192:0:1 0/0:132:0:0,0:63,69:132,0:0:2,0:24.4:1:29.1:1:1:0:41.9:131:1:0:0.2 +10 98320419 . A C 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26015;SOR=Inf;LSEQ=AAAAGTAAAACTTGCTGCTG;RSEQ=TGAAGATGATGATGATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:45,52:97,0:0:2,0:25.8:1:30.9:1:1:0:43.7:194:1:0:0.1 0/1:127:3:1,2:58,66:124,3:0.0236:2,2:21:1:29:1:1:1.7501:48:6:0.0238:0:2 +10 98320423 . AGAT A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.03563;SOR=0;LSEQ=GTAAAACTTGCTGCTGATGA;RSEQ=GATGATGATGATGATGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:4:2,2:39,53:92,4:0.0417:2,2:32:1:33.3:1:1:1.35:58.8:8:0.0417:0:0.5 0/0:123:0:0,0:58,65:123,0:0:2,0:26.4:1:30.5:1:1:0:43.4:60.5:1:0:0.3 +10 98320426 . T A 57 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.69833;SOR=1.56578;LSEQ=AAACTTGCTGCTGATGAAGA;RSEQ=GATGATGATGATGATGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:34,53:87,2:0.0215:2,2:13.5:1:31.5:1:1:1.55:36:4:0.023:0:1 0/1:120:4:2,2:55,61:116,4:0.0333:2,2:26.8:1:28.8:1:1:1.11:47.3:8:0.0336:0:1 +10 98320441 . T C 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=8e-05;SOR=Inf;LSEQ=GAAGATGATGATGATGATGA;RSEQ=GACGATTTTGATGAGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:33,53:86,0:0:2,0:27.4:1:30.1:1:1:0:48.9:20.5:1:0:0.1 0/1:111:16:8,8:40,55:95,16:0.1441:2,2:29.8:1:31.6:1:0.59408:1.37:47.5:32:0.1495:0:1.1 +10 98320574 . CA C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50274;SOR=Inf;LSEQ=CAACACTAAGATCAAAAGGA;RSEQ=AAAATCCTTCAAAAACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:12,19:31,0:0:2,0:22.8:1:30.8:1:1:0:47.6:30:1:0:0.1 0/1:41:2:1,1:19,20:39,2:0.0488:2,2:14:0:33.5:1:1:1.05:60:4:0.05:0:0 +10 98320668 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.49315;SOR=Inf;LSEQ=CAAAAATGCAAGCAAGTATA;RSEQ=AAAAAGTGCATTGAACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:17,19:36,0:0:2,0:29.1:1:31.5:1:1:0:60:35:1:0:0.1 0/1:37:2:1,1:20,15:35,2:0.0541:2,2:28:1:27:1:1:1.32286:60:4:0.0556:0:1 +10 98320693 . G C 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05561;SOR=Inf;LSEQ=AGTGCATTGAACAGTTCAGG;RSEQ=CACTACTGGTAAATTAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:20,22:42,0:0:2,0:30.8:1:31.3:1:1:0:60:41:1:0:0.1 0/1:44:5:3,2:19,20:39,5:0.1136:2,2:24.8:1:30:1:1:1.56:47.4:10:0.119:0:1 +10 98403534 . GA G 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51163;SOR=Inf;LSEQ=TTCCATGAGTTCATGGATGG;RSEQ=AAGTCAGGCCCGCCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:56,34:90,0:0:2,0:26.5:1:30.1:1:1:0:60:89:1:0:1 0/1:126:2:1,1:76,48:124,2:0.0159:2,2:36:0:30:1:1:1.57732:60:4:0.016:0:1 +10 98403546 . C T 207 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGGATGGGAAAGTCAGGCC;RSEQ=GCCTCCCTGTGGGCCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:103:103:60,43:0,0:0,103:1:0,2:25.2:1:31.1:1:1:0:60:102:1:0:1.1 1/0:143:86:50,36:31,26:57,86:0.6014:2,2:26.4:1:29.8:1:0.73114:1.16:60:85:0.5986:0:1.1 +10 98403616 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50321;SOR=Inf;LSEQ=TTGTAACACTCAATATAGCC;RSEQ=ATTCCAGAAATTCCCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:36,57:93,0:0:2,0:26.6:1:31.9:1:1:0:60:186:1:0:0.5 0/1:115:2:1,1:44,69:113,2:0.0174:2,2:31.5:1:28.5:1:1:1.56:60:4:0.0174:0:1 +10 98403745 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCCGCATGCTTAGCATTTG;RSEQ=TAGCGAATGATGGTAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,0:0,13:0.9286:0,1:23.6:1:31.3:1:1:0:60:26:1:0:1 1/1:4:4:0,4:0,0:0,4:1:0,0:23.5:1:31.3:1:1:0:60:8:1:0:1 +10 99803871 . A T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CTTCTGGCTCCCAGTTAGGC;RSEQ=GCTCGGGGGTGAAAGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:16.4:1:31.9:1:1:0:60:14:1:0:0.1 1/0:4:2:1,1:2,0:2,2:0.5:0,2:10:0:31.5:1:1:0:50:4:0.5:0:2 +10 99804006 . G A 191 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCCATGCATGTGCTGTAC;RSEQ=CTAACAACAACAATAGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:75:75:68,7:0,0:0,75:1:0,2:23.2:1:30.7:1:1:0:60:36.5:1:0:1.1 1/0:62:39:35,4:21,2:23,39:0.629:2,2:23.6:1:29.8:1:1:1.19652:60:38:0.623:0:1.1 +10 99804118 . CAGCAACAACAGTAGTGT AACAG 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03822;SOR=0;LSEQ=CAGCAGCAAAACAGCAGCAA;RSEQ=CAACAGCAGCAGCGACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:4:1,3:152,156:308,4:0.0128:2,2:16.8:1:27.5:1:0.62286:2.91415:46.8:3:0.0099:0.0064:1.3 0/0:393:0:0,0:201,192:393,0:0:2,0:24.5:1:31.1:1:1:0:57.8:48.125:1:0:1.7 +10 99804130 . T C 100 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04877;SOR=7.09741;LSEQ=AGCAGCAACAGCAACAACAG;RSEQ=AGTGTCAACAGCAGCAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:0,1:127,131:258,1:0.0038:2,0:34:0:14:0:1:0:40:0:0:0:8 0/1:343:9:5,4:165,165:330,9:0.0262:2,2:8.3:1:31.6:1:1:1.25:49.7:18:0.0271:0:5 +10 99804133 . T C 97 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12487;SOR=3.52322;LSEQ=AGCAACAGCAACAACAGTAG;RSEQ=GTCAACAGCAGCAGCGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:2:1,1:118,129:247,2:0.0079:2,2:35:1:10:1:1:1.09:45:0:0:0:5 0/1:329:9:5,4:159,161:320,9:0.0274:2,2:11.3:1:30.9:1:0.7501:1.26:49.7:18:0.028:0:5 +10 99804135 . T A 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01219;SOR=Inf;LSEQ=CAACAGCAACAACAGTAGTG;RSEQ=CAACAGCAGCAGCGACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:117,123:240,0:0:2,0:23.3:1:29.5:1:1:0:57.6:23:1:0:1.6 0/1:325:9:5,4:156,157:313,9:0.0277:2,2:13.3:1:29.6:1:1:1.26:49.7:18:0.029:0:5 +10 99804142 . C CAGCAAT 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.01215;SOR=Inf;LSEQ=AACAACAGTAGTGTCAACAG;RSEQ=AGCAGCGACAGCAGCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:104,126:230,0:0:2,0:22:1:32.1:1:1:0:55.9:56.5:1:0:1.9 0/1:311:9:5,4:146,155:301,9:0.0289:2,2:21.3:1:31.1:1:0.74476:1.33:49.7:18:0.0294:0:5 +10 99804144 . G GCAGCAAAA 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01271;LSEQ=CAACAGTAGTGTCAACAGCA;RSEQ=CAGCGACAGCAGCAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:226:171:87,84:15,37:52,171:0.7566:2,2:26.1:1:31:1:0.00663:2.54:56.8:342:0.7703:0.1947:2.1 0/1:320:12:1,11:156,152:308,12:0.0375:2,2:30.8:1:28.8:1:0.00557:11.22732:49.1:24:0.0382:0.0031:3.5 +10 99804147 . GCGACAGCAGCAA AAACAG 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06873;SOR=0;LSEQ=CAGTAGTGTCAACAGCAGCA;RSEQ=CAACAGCAGCAGCGACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:2,1:98,111:209,3:0.014:2,2:13.3:1:25.2:1:0.60297:2.26:48:2:0.0098:0.0093:2 0/0:307:0:0,0:145,161:306,0:0:2,0:23.2:1:30.9:1:1:0:54.8:42.714:1:0:2.4 +10 99804149 . G A 171 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=19.08319;LSEQ=GTAGTGTCAACAGCAGCAGC;RSEQ=ACAGCAGCAACAACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:74,84:158,2:0.0123:2,2:9.5:1:32.5:1:1:1.13:43:4:0.0128:0:5 0/1:307:59:31,28:54,80:134,59:0.1922:2,2:8.4:1:29.2:1:0.11932:1.64:49.2:118:0.1954:0:3 +10 99804153 . G A 147 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=20.76009;LSEQ=TGTCAACAGCAGCAGCGACA;RSEQ=CAGCAACAACAGCAGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:1:0,1:76,84:160,1:0.0061:2,0:11:0:31:0:1:0:42:2:0.0064:0:3 0/1:272:31:17,14:53,77:130,31:0.114:2,2:17.7:1:29.8:1:0.16472:1.76:39.1:62:0.1938:0:3.3 +10 99804156 . G A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.09684;SOR=Inf;LSEQ=CAACAGCAGCAGCGACAGCA;RSEQ=CAACAACAGCAGCAGCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:66,79:145,0:0:2,0:21.7:1:32.4:1:1:0:52:47.333:1:0:3.2 0/1:275:6:2,4:70,92:162,6:0.0218:2,2:22.5:1:25:1:0.70133:1.51808:49.7:5:0.0301:0:4.5 +10 99804159 . A G 212 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CAGCAGCAGCGACAGCAGCA;RSEQ=CAACAGCAGCAGCGACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:96:45,51:9,23:32,96:0.7273:2,2:22.6:1:32.2:1:0.06741:2.24:54.8:18.2:0.7165:0:3.5 0/0:279:0:0,0:69,83:152,0:0:2,0:21.5:1:29:1:1:0:54.4:151:0.9869:0:0.8 +10 99804161 . A G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04429;LSEQ=GCAGCAGCGACAGCAGCAAC;RSEQ=ACAGCAGCAGCGACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:153:94:45,49:34,24:58,94:0.6144:2,2:21.5:1:30.1:1:0.24258:1.53815:53.9:22.5:0.625:0:3.6 0/1:291:19:4,15:93,95:188,19:0.0653:2,2:31.5:1:26.8:1:0.02777:3.6504:48.6:3.75:0.0769:0:4.5 +10 99804170 . AG GA 81 Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00125;SOR=0;LSEQ=ACAGCAGCAACAACAGCAGC;RSEQ=CGACAGCAGCAACAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:6:0,6:65,40:105,6:0.0448:2,0:35.8:1:31.6:1:0.00414:0:47.2:12:0.055:0:7 0/0:269:0:0,0:133,132:265,0:0:2,0:22.5:1:29.6:1:1:0:53:87.333:1:0:2.4 +10 99804171 . G A 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0;SOR=0.03749;LSEQ=CAGCAGCAACAACAGCAGCA;RSEQ=CGACAGCAGCAACAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:74:38,36:26,3:29,74:0.5606:2,2:18.1:1:30.2:1:0.00025:8.06537:50.4:148:0.74:0:4.1 0/1:266:12:1,11:130,120:250,12:0.0451:2,2:30:1:30.1:1:0.00529:11.83475:47.8:24:0.0474:0:4.2 +10 99804173 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04197;LSEQ=GCAGCAACAACAGCAGCAGC;RSEQ=ACAGCAGCAACAACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:139:85:43,42:27,3:30,85:0.6115:2,2:17.1:1:30.6:1:0.00015:8.6458:47.6:170:0.7522:0:4.6 0/1:261:16:2,14:127,112:239,16:0.0613:2,2:22.9:1:28.9:1:0.00156:7.88477:45.6:7:0.0576:0:5.5 +10 99804177 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.55528;SOR=Inf;LSEQ=CAACAACAGCAGCAGCGACA;RSEQ=CAGCAACAACAGCAGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:81,66:147,0:0:2,0:17.3:1:31:1:1:0:41.1:8.188:1:0:4.2 0/1:268:3:1,2:132,132:264,3:0.0112:2,2:24.3:1:30.3:1:1:1.995:27.7:6:0.0115:0:4 +10 99804182 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20103;LSEQ=ACAGCAGCAGCGACAGCAGC;RSEQ=ACAACAGCAGCAATAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:67:35,32:60,47:107,67:0.3807:2,2:14.3:1:30:1:0.64171:1.16613:33:15.75:0.3728:0:5.5 0/1:292:32:14,18:130,128:258,32:0.1096:2,2:9.7:1:27.9:1:0.57485:1.3046:42.9:7:0.0993:0:6.3 +10 99804184 . C T 74 q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00033;SOR=0;LSEQ=AGCAGCAGCGACAGCAGCAA;RSEQ=AACAGCAGCAATAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:8:0,8:97,73:170,8:0.0449:2,0:27:1:24.9:1:0.00151:0:41.6:3:0.0349:0:7 0/0:301:0:0,0:151,150:301,0:0:2,0:18.3:1:30.9:1:1:0:48.5:74.25:1:0:2.8 +10 99804186 . A G 87 Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07975;SOR=0.28151;LSEQ=CAGCAGCGACAGCAGCAACA;RSEQ=CAGCAGCAATAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:6:0,6:97,71:168,6:0.0343:2,0:33.7:1:34:0:0.00671:0:47.2:12:0.0345:0:7 0/0:304:3:2,1:149,149:298,3:0.0099:2,2:9:0:30.7:1:1:2.00:23.3:6:0.0101:0:3 +10 99804187 . C T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.1082;LSEQ=AGCAGCGACAGCAGCAACAA;RSEQ=AGCAGCAATAGCAGCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:9:2,7:95,74:169,9:0.0506:2,2:4.3:1:27:1:0.08126:4.45806:40.6:18:0.0526:0:5.3 0/1:305:17:8,9:144,144:288,17:0.0557:2,2:6.6:1:27.1:1:1:1.12457:27.1:7.5:0.0503:0:4.3 +10 99804192 . G A 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.00369;SOR=0;LSEQ=CGACAGCAGCAACAACAGCA;RSEQ=CAATAGCAGCAACAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:6:0,6:85,77:162,6:0.0311:2,0:27.7:1:32:0:0.01323:0:47.2:12:0.0339:0:7 0/0:294:0:0,0:127,145:272,0:0:2,0:18.2:1:30.6:1:1:0:47.9:23.727:0.9812:0:3 +10 99804194 . AAT GACAAC 118 Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=4e-05;SOR=0.08164;LSEQ=GACAGCAGCAACAACAGCAG;RSEQ=AGCAGCAACAACAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:15:15,0:85,77:162,15:0.0777:2,1:34.4:1:30.4:1:0.00016:0:33.2:30:0.0847:0:5.3 0/0:294:2:2,0:127,145:272,2:0.0068:2,0:34:0:29.4:1:0.22074:0:36.5:4:0.0075:0:5 +10 99804196 . T C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16947;SOR=0.34006;LSEQ=AGCAGCAACAACAGCAGCAA;RSEQ=AGCAGCAACAACAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:6:0,6:84,82:166,6:0.0306:2,0:23.7:1:34.3:1:0.0288:0:47.2:12:0.037:0:7 0/1:283:3:2,1:105,130:235,3:0.0106:2,2:19:0:31.3:1:0.58934:2.47:23.3:6:0.0134:0:3 +10 99804203 . A G 93 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56962;SOR=0.76269;LSEQ=ACAACAGCAGCAATAGCAGC;RSEQ=ACAACAGCAGCAATAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:15:9,6:111,91:202,15:0.0691:2,2:23.4:1:27.1:1:0.79214:1.23:44:6.5:0.0616:0:4.1 0/1:280:15:15,0:109,127:236,15:0.0536:2,1:27.8:1:23.9:1:2e-05:0:42.7:6.5:0.0533:0:2.8 +10 99804204 . A G 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.41151;SOR=0.38479;LSEQ=CAACAGCAGCAATAGCAGCA;RSEQ=CAACAGCAGCAATAGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:4:2,2:117,95:212,4:0.0185:2,2:14.8:1:28.8:1:1:1.23038:30.3:3:0.0141:0:2.3 0/0:278:2:1,1:122,126:248,2:0.0072:2,2:6.5:1:29.5:1:1:1.03:29:4:0.0081:0:4.5 +10 99804205 . C T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00094;SOR=0.1443;LSEQ=AACAGCAGCAATAGCAGCAA;RSEQ=AACAGCAGCAATAGCAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:15:15,0:105,96:201,15:0.0691:2,1:28.1:1:27.7:1:0.00016:0:33.2:6.5:0.0613:0:5.3 0/1:284:3:2,1:124,128:252,3:0.0106:2,2:17.7:1:27.7:1:0.61911:2.06:37.3:6:0.012:0:5.7 +10 99804207 . A ACAACAAGAGGAGCAACAAAAGTAGCTGCAACAATAACAAAAGCAACAGCAGCAACAACAG 87 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.78422;SOR=1.22714;LSEQ=CAGCAGCAATAGCAGCAACA;RSEQ=CAGCAGCAATAGCAGCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:5:0,5:105,90:195,5:0.0231:2,0:61.4:1:32.8:1:0.02285:0:30.4:10:0.0235:0.0231:0.2 0/1:283:8:2,6:121,120:241,8:0.0283:2,2:46.3:1:29.3:1:0.28134:3.01276:33.4:16:0.0324:0.0283:1 +10 99804208 . CAGCAGCAAT C 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00029;SOR=4.86286;LSEQ=AGCAGCAATAGCAGCAACAA;RSEQ=AGCAGCGACAACAGCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:5:1,4:120,91:211,5:0.0231:2,2:36:1:31.6:1:0.17165:5.23832:21.6:10:0.0239:0:4.2 0/1:280:29:13,16:111,112:223,29:0.1036:2,2:24.1:1:30.1:1:0.69479:1.21882:49.8:13.5:0.1102:0.0214:2.5 +10 99804211 . CAGCAAT C 124 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0;LSEQ=AGCAATAGCAGCAACAACAG;RSEQ=AGCAGCGACAACAGCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:18:9,9:120,85:205,18:0.0789:2,2:5.3:1:29.8:1:0.61967:1.40952:41.9:36:0.0829:0.0789:5.3 0/0:273:0:0,0:112,109:221,0:0:2,0:21.8:1:29:1:1:0:48.3:21.1:1:0.0037:3.1 +10 99804213 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.22851;LSEQ=CAATAGCAGCAACAACAGCA;RSEQ=CAATAGCAGCGACAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:146:91,55:29,26:55,146:0.6518:2,2:24.6:1:29.9:1:0.25926:1.48:38.6:47.667:0.7371:0:6.4 0/1:271:81:46,35:66,72:138,81:0.2989:2,2:25.2:1:28.9:1:0.21075:1.43:43:39.5:0.3744:0:6.5 +10 99804214 . C T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07221;SOR=2.5911;LSEQ=AATAGCAGCAACAACAGCAG;RSEQ=AATAGCAGCGACAACAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:5:2,3:118,78:196,5:0.0223:2,2:17:0:30.2:1:0.39419:2.25976:25:10:0.0253:0:4 0/1:286:16:7,9:104,99:203,16:0.0559:2,2:17.1:1:28.3:1:0.61179:1.34879:25.7:32:0.0714:0:4.1 +10 99804215 . A G 62 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00556;SOR=0;LSEQ=ATAGCAGCAACAACAGCAGC;RSEQ=ATAGCAGCGACAACAGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:6:2,4:105,67:172,6:0.0291:2,2:15.2:1:24:1:0.21823:3.11385:22.5:2:0.023:0:5.7 0/0:280:0:0,0:110,102:212,0:0:2,0:23.1:1:28.8:1:1:0:48.8:20.2:1:0.0036:3.1 +10 99804216 . A ACAG 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02039;SOR=0.17616;LSEQ=TAGCAGCAACAACAGCAGCA;RSEQ=TAGCAGCGACAACAGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:8:3,5:31,17:48,8:0.0379:2,2:8.5:1:25.5:1:0.24081:2.97594:42.5:3:0.0335:0.0237:5.9 0/0:291:2:0,2:68,70:138,2:0.0069:2,0:22.5:1:20.5:1:0.49681:0:44.5:4:0.0091:0:7.5 +10 99804217 . T CAGC 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.25153;LSEQ=AGCAGCAACAACAGCAGCAA;RSEQ=AGCAGCGACAACAGCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:211:127:75,52:31,17:48,127:0.6019:2,2:29.2:1:32.6:1:0.60359:1.26264:39.1:254:0.7095:0:6.6 0/1:291:80:46,34:68,70:138,80:0.2749:2,2:27.4:1:31.2:1:0.26254:1.39:42:160:0.3636:0.0378:6.2 +10 99804224 . G A 108 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAACAGCAGCAATAGCAGC;RSEQ=ACAACAGCAATAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:15:11,4:115,83:198,15:0.067:2,2:6.7:1:27.7:1:0.28796:1.98:37.1:14:0.0707:0:2.9 0/0:314:0:0,0:106,102:208,0:0:2,0:26.3:1:28.7:1:1:0:52:9.947:0.913:0:3 +10 99804228 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09481;LSEQ=CAGCAGCAATAGCAGCGACA;RSEQ=CAGCAATAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:240:201:108,93:26,7:33,201:0.8375:2,2:26.8:1:32:1:0.00758:3.18401:40.9:17.273:0.8482:0:5.8 0/1:324:106:57,49:103,92:195,106:0.3272:2,2:29.5:1:31.3:1:0.90415:1.04:41.9:34.333:0.354:0:6 +10 99804234 . ATAGCAGCAGCAACAA GCAAAACAG 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13831;SOR=0.36824;LSEQ=GCAGCAATAGCAGCGACAAC;RSEQ=CAACAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:8:3,5:136,99:235,8:0.0328:2,2:25.9:1:29:1:0.29286:2.28171:30.8:7:0.0292:0.0164:3.6 0/1:325:4:1,3:159,143:302,4:0.0123:2,2:47.5:1:31.4:1:0.35106:3.32357:22.3:8:0.0134:0:2.3 +10 99804235 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04794;LSEQ=AATAGCAGCGACAACAGCAA;RSEQ=AGCAGCAGCAACAACAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:244:228:123,105:8,2:10,228:0.9344:2,2:26.3:1:32.1:1:0.19187:3.39921:40.5:37:0.961:0:5.5 0/1:314:127:63,64:73,79:152,127:0.4045:2,2:28.6:1:31.4:1:0.81087:1.07:43.9:62.5:0.4647:0:5.7 +10 99804237 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0;SOR=0.0441;LSEQ=TAGCAGCGACAACAGCAATA;RSEQ=CAGCAGCAACAACAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:243:229:123,106:8,1:9,229:0.9424:2,2:26.7:1:30.1:1:0.04402:6.85253:40.4:75.333:0.9617:0:5.5 0/1:309:129:65,64:74,76:150,129:0.4175:2,2:28.5:1:29:1:0.90465:1.04:44.1:258:0.464:0:5.7 +10 99804243 . GCAACAA G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=3;SSF=0;SOR=0.16115;LSEQ=CGACAACAGCAATAGCAGCA;RSEQ=CAACAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:49:22,27:15,5:20,49:0.1863:2,2:16.6:1:31.1:1:0.03307:3.61251:42.2:48:0.1846:0.0913:3.4 0/1:310:11:4,7:85,84:169,11:0.0355:2,2:29.9:1:29.1:1:0.53609:1.76532:42.4:10:0.0348:0:5.4 +10 99804247 . CAACAAC T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=3.000;MSILEN=3;SSF=0;SOR=0.19901;LSEQ=GACAACAGCAATAGCAGCAG;RSEQ=AGCAGCAGCAACAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:263:194:110,84:15,5:20,194:0.7376:2,2:27.5:1:31.6:1:0.15324:2.2827:40.1:388:0.7462:0.0342:4.6 0/1:310:111:57,54:85,84:169,111:0.3581:2,2:28.9:1:30.2:1:0.90304:1.04:44.4:222:0.3868:0:4.7 +10 99804249 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.622;SOR=1.40842;LSEQ=CAGCAATAGCAGCAGCAACA;RSEQ=CAACAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:6:6,0:4,2:6,6:0.0259:2,0:18.2:1:27.3:1:0.45455:0:26.8:5:0.5:0:6.5 0/1:305:11:6,5:74,76:150,11:0.0361:2,2:17.5:1:30.5:1:0.76559:1.23:51.6:10:0.0641:0:4 +10 99804250 . C T 45 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.67557;SOR=0.7807;LSEQ=AGCAATAGCAGCAGCAACAA;RSEQ=AACAGCAGCAGCAACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:33,36:69,2:0.025:2,2:4.5:1:28.5:1:1:1.09:25:4:0.0303:0.025:4 0/1:204:4:0,4:89,103:192,4:0.0196:2,0:15:1:22.5:1:0.1275:0:47.5:3:0.016:0.0049:3.5 +10 99804253 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0.04976;LSEQ=AATAGCAGCAGCAACAACAA;RSEQ=AGCAGCAGCAACAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:85:66:31,35:10,9:19,66:0.7765:2,2:12.6:1:24.8:1:0.79567:1.25112:44.7:2.474:0.7705:0:2.7 0/1:213:31:8,23:88,91:179,31:0.1455:2,2:13.3:1:21.9:1:0.01888:2.76745:48:2.1:0.1066:0:3 +10 99804255 . G A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=3e-04;SOR=Inf;LSEQ=TAGCAGCAGCAACAACAACA;RSEQ=CAGCAGCAACAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:152,131:283,0:0:2,0:23.9:1:31.7:1:1:0:41.7:15.647:0.9963:0.0035:4.6 0/1:332:13:6,7:150,167:317,13:0.0392:2,2:14:1:29.4:1:1:1.04777:54.2:26:0.0417:0:3.4 +10 99804258 . GCAGCAACAGCAGCAACAACAGCAGCAACAACAA G 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=3.000;MSILEN=3;SSF=1e-05;SOR=Inf;LSEQ=CAGCAGCAACAACAACAGCA;RSEQ=CAGCAACAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:159,142:301,0:0:2,0:22.9:1:32.1:1:1:0:42.5:36.625:1:0:4.4 0/1:345:19:9,10:155,171:326,19:0.0551:2,2:25.5:1:31.7:1:1:1.00713:55.1:38:0.0569:0.0116:0.7 +10 99804263 . A G 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.76208;SOR=0.70587;LSEQ=GCAACAACAACAGCAGCAGC;RSEQ=ACAGCAGCAACAACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:6:2,4:157,141:298,6:0.0197:2,2:25.2:1:27.7:1:0.42983:2.22127:22:5:0.017:0:4.3 0/1:357:5:2,3:161,176:337,5:0.014:2,2:27.4:1:29.6:1:1:1.37091:24.4:10:0.0148:0:4 +10 99804284 . A G 71 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.7406;SOR=0.69871;LSEQ=ACAGCAGCAACAACAGCAGC;RSEQ=ACAACAACAGCAACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:5:1,4:158,157:315,5:0.0156:2,2:4.8:1:30.6:1:0.37111:4.00993:21.6:10:0.0159:0:4.2 0/1:366:4:1,3:163,184:347,4:0.0109:2,2:6.5:1:26.3:1:0.6261:2.65079:22.3:3:0.0088:0:4.3 +10 99804304 . C A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12725;SOR=Inf;LSEQ=AACAACAACAGCAACAGCAG;RSEQ=AACAGCAGCAGCAACAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:125,163:288,0:0:2,0:27:1:31.9:1:1:0:51.4:25.182:1:0:1.8 0/1:330:4:3,1:146,179:325,4:0.0121:2,2:14:1:25.3:1:0.33228:3.66:50.5:8:0.0123:0:4 +10 99804306 . ACAG A 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.01607;SOR=Inf;LSEQ=CAACAACAGCAACAGCAGCA;RSEQ=CAGCAGCAACAACAATAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:125,169:294,0:0:2,0:26.2:1:32:1:1:0:51.9:48:1:0:1.6 0/1:328:7:5,2:143,178:321,7:0.0213:2,2:17.7:1:28.3:1:0.2507:3.10:51:14:0.0215:0.0122:1.3 +10 99804318 . ACAACAATAGCAACAACAGTAGTGG A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.56935;SOR=0.67604;LSEQ=CAGCAGCAACAGCAGCAGCA;RSEQ=CAATAACAGCAGCAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:7:1,6:126,170:296,7:0.023:2,2:15.9:1:29.6:1:0.24533:4.4299:25.7:14:0.0241:0.023:1.9 0/1:319:5:0,5:141,173:314,5:0.0157:2,0:17.2:1:24.1:1:0.06896:0:28:10:0.016:0.0157:1.8 +10 99804341 . G A 38 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62447;SOR=0.35625;LSEQ=ACAATAGCAACAACAGTAGT;RSEQ=GCAATAACAGCAGCAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:104,146:250,3:0.0116:2,2:19.7:1:24:1:0.57352:2.80:55:2:0.0082:0:3.3 0/0:241:1:1,0:100,136:236,1:0.0041:2,0:1:0:24:0:0.42616:0:58:2:0.0044:0:1 +10 99804349 . C G 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75149;SOR=0.67561;LSEQ=AACAACAGTAGTGGCAATAA;RSEQ=AGCAGCAAAACAGCAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:6:0,6:94,146:240,6:0.0243:2,0:7:0:32.8:1:0.08518:0:20:12:0.0253:0:2 0/1:242:4:0,4:105,133:238,4:0.0165:2,0:7:0:26.3:1:0.13505:0:20:8:0.0167:0:2 +10 99804357 . A AC 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.75253;SOR=0.70714;LSEQ=TAGTGGCAATAACAGCAGCA;RSEQ=AACAGCAACAGCAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:6:0,6:88,142:230,6:0.0254:2,0:16:0:33.2:1:0.08669:0:20:12:0.0259:0:2 0/1:221:4:0,4:97,120:217,4:0.0181:2,0:16:0:28:1:0.13282:0:20:8:0.0185:0:2 +10 99804365 . ACAG A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.1559;SOR=2.65549;LSEQ=ATAACAGCAGCAAAACAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:4:2,2:84,149:233,4:0.0169:2,2:19.8:1:26:1:0.62254:1.77:56.3:3:0.0129:0.0042:1 0/1:206:9:4,5:80,109:189,9:0.0437:2,2:23.1:1:30.2:1:1:1.09:60:18:0.0464:0.0194:0.4 +10 99804369 . C T 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.75864;SOR=0.7759;LSEQ=CAGCAGCAAAACAGCAACAG;RSEQ=AGCAGCAGCAGCAACAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:6:0,6:80,140:220,6:0.0264:2,0:25:0:29.5:1:0.09205:0:20:12:0.0274:0:2 0/1:194:4:0,4:75,106:181,4:0.0206:2,0:25:0:22.5:1:0.14794:0:20:3:0.0165:0:2 +10 99804377 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.59947;SOR=2.31219;LSEQ=AAACAGCAACAGCAGCAGCA;RSEQ=CAGCAACAGCAACAATCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:1,0:76,136:212,1:0.0047:2,0:1:0:25:0:0.3615:0:60:2:0.0048:0:1 0/1:185:2:1,1:71,112:183,2:0.0108:2,2:22.5:1:27.5:1:1:1.57:60:4:0.011:0:1 +10 103248941 . G T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62546;SOR=2.66031;LSEQ=GAAAACATTCATTTAGACTT;RSEQ=TATGTACCAATATTTTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:1,0:90,39:129,1:0.0077:2,0:45:0:12:0:1:0:60:0:0:0:1 0/1:148:3:1,2:90,55:145,3:0.0203:2,2:24.3:1:26.7:1:0.55909:3.24585:60:6:0.0207:0:1 +10 103249002 . G A 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62689;SOR=2.62922;LSEQ=AGTATCTAGGACTCCCCCCA;RSEQ=ACAACTCTTTTTTTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:1,0:107,102:209,1:0.0048:2,0:1:0:26:0:1:0:60:2:0.0048:0:1 0/1:241:3:2,1:130,107:237,3:0.0124:2,2:10:1:21.7:1:1:1.64:60:2:0.0085:0:2.3 +10 103249009 . C CT 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.18223;SOR=0.4615;LSEQ=AGGACTCCCCCCAGACAACT;RSEQ=TTTTTTTTTCTTTCCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:9:5,4:107,101:208,9:0.0413:2,2:31.3:1:32:1:1:1.18:60:18:0.0425:0:0.3 0/1:257:5:3,2:139,112:251,5:0.0195:2,2:30.8:1:29.2:1:1:1.21:60:10:0.0197:0:0 +10 103249036 . A G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32658;LSEQ=TTTCTTTCCCAGAATCAAGA;RSEQ=TAAAAGCAACCCAGACAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:90:38,52:54,54:108,90:0.4545:2,2:27.3:1:33.1:1:0.31722:1.36623:60:180:0.4569:0:1.1 0/1:267:57:31,26:113,97:210,57:0.2135:2,2:24.4:1:31.1:1:1:1.02:60:56:0.2129:0:1.2 +10 104263913 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05921;SOR=0;LSEQ=CTGCCCTACGCACCCCGATG;RSEQ=CGGAGCTGCGGCCTAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:144,151:295,3:0.0101:2,2:42.7:1:25.3:1:0.61627:2.09:60:2:0.0069:0:2 0/0:465:0:0,0:210,255:465,0:0:2,0:24.8:1:30.9:1:1:0:59.9:65.429:1:0:0.4 +10 104263934 . GC G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.07976;SOR=Inf;LSEQ=CGGAGCTGCGGCCTAGCGGC;RSEQ=CCCCGGCCCCACCGCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:178,138:316,0:0:2,0:20.2:1:31.1:1:1:0:59.5:18.75:0.9967:0:0.8 0/1:446:5:3,2:228,211:439,5:0.0112:2,2:23.8:1:32.8:1:1:1.39:60:10:0.0115:0:0.4 +10 104264107 . C T 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.09268;LSEQ=TACTGGTATGCTCTGGGCCG;RSEQ=GGGGAGACGGACAGGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:640:604:254,350:17,17:34,604:0.9438:2,2:25.5:1:29.4:1:0.37746:1.37723:60:32.556:0.9467:0:1.2 1/0:924:562:230,332:164,197:361,562:0.6082:2,2:25.6:1:28.5:1:0.19516:1.20143:59.9:61.444:0.6117:0:1.2 +10 104264280 . C T 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0398;SOR=6.85697;LSEQ=GGACAAAGGGGTTAACGGAG;RSEQ=CCGTGGGTACTGAGGGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:0,2:0,31:31,2:0.0606:1,0:35.5:1:31:1:1:0:60:4:0.0625:0:1 0/1:19:6:1,5:2,11:13,6:0.3158:2,2:28.8:1:27.8:1:1:1.09:60:5:0.2778:0:1 +10 104268626 . T C 108 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06319;SOR=0.0847;LSEQ=ACAATCCCTGCCAATCTCAT;RSEQ=TGGGATCGGTAATTTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:2,10:0.8333:0,0:24.9:1:32.6:1:1:0:57.3:20:0.8333:0:1.1 0/1:4:1:1,0:2,1:3,1:0.25:2,0:18:0:32:0:1:0:60:2:0.25:0:1 +10 104268800 . G C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.61165;SOR=0.46643;LSEQ=TCTGGAGAGATGTGGCCTCT;RSEQ=TTTAGTTACCTTTCACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:99:99,0:0,0:0,99:0.99:0,1:21.4:1:32.7:1:1:0:60:98:1:0:1.1 1/1:94:92:90,2:1,1:2,92:0.9787:2,1:23.3:1:31:1:0.06314:36.94:59.9:45:0.9783:0:1.3 +10 104268859 . GC A 160 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.22854;LSEQ=CTTTAGGTTTACAAAGTAGA;RSEQ=GCCTTAGCTTGACATTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:1,0:273,88:361,1:0.0027:2,0:13:0:32:0:1:0:60:2:0.0028:0:0 0/1:400:40:31,9:264,95:359,40:0.1:2,2:21.9:1:30.2:1:0.7055:1.24:60:80:0.1013:0.0225:0.5 +10 104268877 . G C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.43648;LSEQ=GAGCGCCTTAGCTTGACATT;RSEQ=TCTGATTTCCAGGCTTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:39:29,10:317,158:475,39:0.0759:2,2:25.2:1:32.1:1:0.37835:1.44:60:38:0.0748:0:1.2 0/1:563:124:81,43:289,148:437,124:0.2202:2,2:23.4:1:31:1:0.91457:1.03652:60:248:0.2226:0:1.2 +10 104269217 . G A 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04682;SOR=0.20699;LSEQ=CTCATGCCAAGGTGGTCCTC;RSEQ=TTAACACCTGATTCCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:36:0,36:0,3:3,36:0.9231:0,1:20.6:1:30.6:1:1:0:60:35:0.9211:0:1.2 1/0:17:12:0,12:0,5:5,12:0.7059:0,0:21.8:1:31.5:1:1:0:60:24:0.7059:0:1 +10 104309647 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.1821;SOR=0;LSEQ=TACTGAGGCCACCATAAAAA;RSEQ=GGGGAGAACTTTAGACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:2,0:174,24:198,2:0.01:2,0:18:1:32:0:1:0:60:4:0.0101:0:1 0/0:268:0:0,0:232,36:268,0:0:2,0:20.1:1:31.3:1:1:0:60:133:1:0:0.1 +10 104352124 . C CCATTT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTAATAGCCTGTCCTTTT;RSEQ=AAGTCTGACAGAACTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:14,1:15,2:0.1176:1,0:18:1:29.7:1:1:0:60:4:0.1333:0.0588:0 0/0:1:0:0,0:1,0:1,0:0:0,0:15:0:32:0:1:0:60:2:1:0:0 +10 104353308 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22529;SOR=0;LSEQ=CTGTGGTCTCCCAACTGGAG;RSEQ=TGACTCAGAGAGCCTGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:2,0:119,34:153,2:0.0129:2,0:8.5:1:29:1:1:0:60:4:0.0133:0:1 0/0:171:0:0,0:134,37:171,0:0:2,0:24.8:1:30.1:1:1:0:60:33.2:1:0:0.1 +10 104353345 . TG T 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1.31192;LSEQ=GGTAGCTGACCTTCTTGGGG;RSEQ=GGGGGTGGCCATTAACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:185,104:289,3:0.0103:2,2:39.7:1:32.7:1:1:1.12:60:6:0.0106:0:0 0/1:372:5:2,3:240,127:367,5:0.0134:2,2:16.4:1:26.8:1:0.34789:2.82612:60:10:0.0139:0.0081:1.2 +10 104353519 . TG T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1089;SOR=0;LSEQ=GGAGCGCGGCTCCCTGGGCC;RSEQ=GGGGTGGGAGTCCCTCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:2,1:59,141:200,3:0.0148:2,2:37:1:33:1:0.21537:4.74:60:6:0.0152:0:0 0/0:221:0:0,0:65,156:221,0:0:2,0:24:1:30.7:1:1:0:60:72.667:1:0:0.1 +10 104353527 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24549;SOR=0;LSEQ=GCTCCCTGGGCCTGGGGGTG;RSEQ=GAGTCCCTCCACTACCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:57,132:189,2:0.0104:2,2:15.5:1:26:1:0.51623:2.30:60:4:0.0106:0:2 0/0:195:0:0,0:59,135:194,0:0:2,0:23.2:1:30.5:1:1:0:60:193:0.9948:0:0.2 +10 104353681 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07583;SOR=Inf;LSEQ=GCCTGGGGCAGCAAACAGGG;RSEQ=AGGCTGTAGGCCCAGCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:248,99:347,0:0:2,0:23.9:1:32.1:1:1:0:60:48.571:1:0:0.2 0/1:469:5:2,3:307,157:464,5:0.0107:2,2:10.4:1:25:1:0.34333:2.92583:60:10:0.0108:0:1.2 +10 104356822 . A G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0517;SOR=0;LSEQ=TCAGTAAATACTGTAAGAGC;RSEQ=GTGGCTGAAAGGGTGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:130:130:121,9:0,0:0,130:1:0,2:23.8:1:30.5:1:1:0:60:129:1:0:1.1 1/1:120:116:106,10:4,0:4,116:0.9667:0,2:23.3:1:29.7:1:1:0:60:115:0.9664:0:1.1 +10 104359350 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49867;SOR=Inf;LSEQ=ACAAGAGGACGACTTTTTTC;RSEQ=GAAGGGCCTGTCCCTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:28,157:185,0:0:2,0:24.4:1:30.6:1:1:0:60:36:1:0:0.1 0/1:187:2:0,2:28,155:183,2:0.0107:2,0:26.5:1:31.5:1:1:0:60:4:0.0108:0:1.5 +10 104359359 . T G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24287;SOR=Inf;LSEQ=CGACTTTTTTCTGAAGGGCC;RSEQ=GTCCCTGTGGATTGCATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:17,142:159,0:0:2,0:22.9:1:30.9:1:1:0:60:78.5:1:0:0.1 0/1:155:2:1,1:22,131:153,2:0.0129:2,2:23:1:28:1:0.27558:5.85:60:4:0.013:0:1 +10 104359884 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACCCTAGAGGTCAGATC;RSEQ=GCTTCCTGCCAACCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:15.5:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 104374618 . A G 35 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCAGCCTGGGTAATAGA;RSEQ=CGAGACACCATCTCAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:17:1:35:1:1:0:56.5:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 104374636 . TA T 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGAGACACCATCTCAAT;RSEQ=AAAAAAAAAAAAAAATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:18.5:1:31.5:1:1:0:58:4:0.6667:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 104374815 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGTGGCAGCCACCTCTTG;RSEQ=GGGCATTGTGAGGAGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:16,0:16,2:0.1111:1,0:37.5:1:30.5:1:1:0:60:4:0.1176:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:16.3:1:32.3:1:1:0:60:6:1:0:0 +10 104374963 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12293;SOR=Inf;LSEQ=GGAGCCCAGCTGGAGACTCC;RSEQ=ATCTTGCTCCTCCCTGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:153,28:181,0:0:2,0:24.3:1:31.2:1:1:0:59.8:59.333:1:0:0.1 0/1:180:3:1,2:138,39:177,3:0.0167:2,2:18.3:1:24.3:1:0.1304:6.97623:60:2:0.0114:0:1 +10 104375258 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.59131;LSEQ=AGCCCCCTCCCCCAGCAGGC;RSEQ=TCCTCCAGGGCCTCCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:0,3:0,104:104,3:0.028:1,0:13.3:1:32.7:1:1:0:60:6:0.0288:0:1 0/1:87:26:0,26:1,60:61,26:0.2989:1,1:20.2:1:30.5:1:1:0:60:52:0.3023:0:1.1 +10 104377762 . T C 24 d5;v3;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCCTTCCTTTGCTCTTC;RSEQ=GGCTGGAGCGAGCTTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:24.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 104378563 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05848;SOR=Inf;LSEQ=GCCATGTCCCGGGCTGCTGC;RSEQ=TCTGCCCCTGTGGAGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:14,0:0:1,0:25.6:1:29.1:1:1:0:60:28:1:0:0.1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:35.5:1:31.5:1:1:0:60:4:0.4:0:1 +10 104378688 . CGT C 167 MSI12;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=46;MSI=24.000;MSILEN=2;SSF=0;SOR=0.14335;LSEQ=TCCCAAGTGTCCTCAGGTAG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:34:30,4:76,1:77,34:0.2378:1,2:24.3:1:32.9:1:0.03003:9.90233:55.4:33:0.2391:0.035:0.7 0/1:141:6:6,0:93,3:96,6:0.0426:1,0:27.7:1:33:1:1:0:56.7:12:0.0441:0:0.3 +10 104378750 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=12.25341;LSEQ=TGTGTGTAATGTTCAAGCAC;RSEQ=TTTTCCTGGGACAGTCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:12:8,4:258,150:408,12:0.0284:2,2:21.4:1:28.7:1:1:1.16:57.8:5:0.0264:0:1.1 0/1:450:119:67,52:184,145:329,119:0.2644:2,2:22.1:1:28.7:1:1:1.02:59.5:16:0.2712:0:1.2 +10 104378927 . GC G 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.25459;SOR=0;LSEQ=TCAGCAGCTCAAGAACCTTG;RSEQ=CCCCACAGGACTTCGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:2,1:50,233:283,3:0.0105:2,2:18:1:30:1:0.08615:9.21:60:6:0.0107:0.0035:0.3 0/0:239:0:0,0:53,186:239,0:0:2,0:23.4:1:30.6:1:1:0:60:78.667:1:0:0.1 +10 104385132 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTAGAACAGAGAGTTTGGT;RSEQ=AGGAGACGTGGACCAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:27:1:1:0:60:4:1:0:1 +10 104386854 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5859;SOR=0.395;LSEQ=TCTCCTCCATGGTCAGAAGA;RSEQ=AGGTATAACGCTTGGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:116,10:126,2:0.0156:2,2:18:1:29:1:0.16511:11.10804:60:4:0.0156:0:1 0/0:161:1:1,0:142,18:160,1:0.0062:2,0:4:0:29:0:1:0:60:2:0.0063:0:1 +10 104386876 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26268;SOR=Inf;LSEQ=GGTATAACGCTTGGTGGTTG;RSEQ=CAAAAAGATCATACATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:145,43:188,0:0:2,0:23.3:1:31.4:1:1:0:60:187:0.9947:0:0.1 0/1:251:3:2,1:187,60:247,3:0.012:2,2:29.3:1:28:1:0.5696:1.55528:60:6:0.0121:0:1 +10 104386934 . T C 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCTTGTGCCTTCACAGAT;RSEQ=CTGTTGACCGAAGAGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:0:0,0:332,203:535,0:0:2,0:26.2:1:30.6:1:1:0:60:40.154:1:0:0.3 0/1:688:49:24,25:366,273:639,49:0.0712:2,2:27.2:1:30.7:1:0.29573:1.39581:60:48:0.0712:0:1.3 +10 104387019 . T C 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09553;LSEQ=AAGTAAGCTTGTTTGACTTT;RSEQ=CCTGACAACAGGTCCCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:431:406:131,275:10,13:23,406:0.942:2,2:25.1:1:31.5:1:0.26345:1.61291:60:134.333:0.9416:0:1.1 1/0:553:336:126,210:88,129:217,336:0.6076:2,2:25.3:1:30.3:1:0.47597:1.13668:60:66.2:0.6085:0:1.1 +10 104387103 . G T 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17196;SOR=0.29;LSEQ=TGTGTGCGTGTGTACCTGTG;RSEQ=TGCGTGTGTGCTTGCATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:7:0,7:3,100:103,7:0.0636:1,0:16.7:1:30:1:1:0:60:14:0.0636:0:1 0/1:104:2:0,2:1,101:102,2:0.0192:1,0:45.5:1:31.5:1:1:0:60:4:0.0192:0:1 +10 104389928 . G A 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.20745;SOR=0.2375;LSEQ=ACTAGCCTGGGCTGGGCCCT;RSEQ=CAGTGGCCAGCAGGGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:4:3,1:117,269:386,4:0.0103:2,2:20.8:1:26.5:1:0.08854:6.86:60:8:0.0104:0:1.5 0/0:408:1:1,0:127,280:407,1:0.0025:2,0:1:0:25:0:0.31373:0:60:2:0.0025:0:2 +10 104389932 . T G 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07118;LSEQ=GCCTGGGCTGGGCCCTGCAG;RSEQ=GGCCAGCAGGGAGCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:365:363:101,262:0,0:0,363:0.9945:0,2:24.3:1:31:1:1:0:60:120:0.9972:0:1.1 1/1:389:361:103,258:10,15:25,361:0.928:2,2:24.5:1:30.1:1:0.25637:1.6675:60:89.25:0.9273:0:1.1 +10 105362209 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTCTCCAGGCTGTCTGA;RSEQ=TTGCCTTCGTTCTGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 105363289 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GGCTCTGAGTCAAAGCCGAA;RSEQ=GCAGGGATGTCATACTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:20:1:34:0:1:0:60:4:0.3333:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:34.4:1:30.4:1:1:0:60:10:1:0:0 +10 105517075 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5091;SOR=Inf;LSEQ=TGTGCCATGGTGATTAGCAT;RSEQ=GGGTGCACTAGAATCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:80,29:109,0:0:2,0:23.8:1:31.5:1:1:0:60:108:1:0:0.2 0/1:147:2:1,1:103,42:145,2:0.0136:2,2:12:0:30.5:1:0.50089:2.43545:60:4:0.0137:0:1.5 +10 105517091 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17136;SOR=0;LSEQ=GCATGGGGTGCACTAGAATC;RSEQ=AGGACTCTGGAGACCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:88,44:132,2:0.0149:2,2:37.5:1:29.5:1:1:1.98892:60:4:0.0149:0:1 0/0:189:0:0,0:125,64:189,0:0:2,0:25.2:1:30.8:1:1:0:60:188:1:0:0.4 +10 105517105 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1602;SOR=0;LSEQ=AGAATCCAGGACTCTGGAGA;RSEQ=CCAGGCCCGGGTGCATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:98,56:154,2:0.0128:2,2:37.5:1:30.5:1:1:1.74332:60:4:0.0129:0:1 0/0:233:0:0,0:144,89:233,0:0:2,0:25.1:1:30.9:1:1:0:59.8:76.667:1:0:0.5 +10 105517112 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28148;SOR=Inf;LSEQ=AGGACTCTGGAGACCCAGGC;RSEQ=CGGGTGCATTTTCTGCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:102,67:169,0:0:2,0:25.9:1:30.8:1:1:0:60:41.25:1:0:0.4 0/1:259:3:2,1:150,104:254,3:0.0116:2,2:46.7:1:28.7:1:1:1.38:60:6:0.0118:0:2 +10 105517162 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00053;SOR=1.81525;LSEQ=CAGACTGACTGAGACCATGA;RSEQ=AAGAGACAGGCTTTTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:121:62,59:66,62:128,121:0.4859:2,2:24:1:30.9:1:1:1.01296:60:242:0.4939:0:1.1 1/0:337:213:101,112:64,59:123,213:0.632:2,2:25.7:1:29.5:1:0.42981:1.20222:60:70:0.6306:0:1.2 +10 105517238 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.61885;SOR=0.48478;LSEQ=ACAATCCATCCAGGACGGAG;RSEQ=GTTGGGGGTAGGTGTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:47,100:147,2:0.0133:2,2:28.5:1:28:1:0.54199:2.12:60:4:0.0135:0:1 0/0:154:1:1,0:46,106:152,1:0.0065:2,0:1:0:22:0:0.30719:0:60:2:0.0066:0:1 +10 105517249 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22685;SOR=Inf;LSEQ=AGGACGGAGGGTTGGGGGTA;RSEQ=GTGTTCAGGAGCTGATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:35,92:127,0:0:2,0:22.5:1:31.1:1:1:0:60:41.333:1:0:0.3 0/1:116:2:1,1:29,84:113,2:0.0172:2,2:13.5:1:31.5:1:0.45538:2.86:60:4:0.0175:0:1.5 +10 108316062 . G C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.97308;LSEQ=ACTTCTGCCTCCTACTAATG;RSEQ=TCTTTGGCTTAAAAATGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:19:7,12:209,244:453,19:0.0402:2,2:23.1:1:32.2:1:0.48716:1.46721:60:38:0.0412:0:1.2 0/1:523:143:69,74:188,192:380,143:0.2734:2,2:25.7:1:30.9:1:0.84463:1.05005:60:46.667:0.2708:0:1.1 +10 108316278 . A G 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04096;SOR=18.0326;LSEQ=TTGAGATTAGTTAAGTGGTT;RSEQ=TTTGGCTGAAAGGGATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,9:9,1:0.1:0,0:14:0:34:0:1:0:60:2:0.1111:0:1 1/0:4:3:0,3:0,1:1,3:0.75:0,0:23.7:1:31:1:1:0:60:6:0.75:0:1 +10 109599389 . A T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68275;SOR=0.94151;LSEQ=AGAACTCTGTATGGAACCCT;RSEQ=GACTTTACATAGTAATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:199:91,108:102,107:209,199:0.4866:2,2:24.7:1:30.7:1:0.55285:1.13101:60:398:0.4901:0:1.6 0/1:456:215:103,112:114,125:239,215:0.4715:2,2:25.1:1:29.7:1:1:1.01:60:214:0.4735:0:1.5 +10 109599439 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20411;LSEQ=GACTCTGTAATCTAGCTTCT;RSEQ=GAAATGTCCTTGACAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:94:27,67:62,104:166,94:0.3615:2,2:25.4:1:31.4:1:0.17537:1.47714:60:93:0.3619:0:2.6 0/1:300:31:12,19:98,170:268,31:0.1033:2,2:22.8:1:30.8:1:0.84538:1.10:60:62:0.1044:0:2.5 +10 109599452 . A T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64016;SOR=1.10519;LSEQ=AGCTTCTAGAAATGTCCTTG;RSEQ=CAACCAAGGTGCTCAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:94:23,71:42,76:118,94:0.4434:2,2:25.6:1:29.9:1:0.09923:1.70166:60:30.333:0.4439:0:2.5 0/1:252:118:39,79:47,87:134,118:0.4683:2,2:23.9:1:28.7:1:0.79055:1.09392:60:236:0.4701:0:1.8 +10 109599593 . A AAG 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68079;SOR=0.4864;LSEQ=GATGGGGAGAGAGAGACAGA;RSEQ=AGAAAATGAGCAATCAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:0,7:1,14:15,7:0.3182:1,0:14:1:33.4:1:1:0:60:14:0.3182:0.0455:0 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:9.5:1:27.3:1:1:0:60:4:0.1818:0.0909:0.5 +10 110550348 . A C 99 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0079;SOR=0.07215;LSEQ=TAGTCCCAGGAAAAGTCAGC;RSEQ=AGGTCATCTGTGAGTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:8,1:9,9:0.5:2,2:16.8:1:31.3:1:0.57647:3.70691:60:18:0.5294:0:1 0/1:16:1:1,0:13,2:15,1:0.0625:2,0:7:0:30:0:1:0:60:2:0.0625:0:1 +10 110550481 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=TGAGAAGTGTGGTGTTAGCA;RSEQ=AAACAGAGGAATGGATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:5,11:16,2:0.1111:2,2:16:1:30.5:1:1:2.10:60:4:0.1111:0:1.5 0/0:11:0:0,0:2,9:11,0:0:2,0:20.4:1:26.4:1:1:0:60:10:1:0:0 +10 110550558 . A G 32 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GTTTAGAAGACTGCAAAGAC;RSEQ=TTCTTACGGTGCTATAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:5:1:32:1:1:0:60:4:0.6667:0:1.5 0/0:3:0:0,0:0,3:3,0:0:0,0:17:1:31:1:1:0:60:6:1:0:0 +10 110806492 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAAAGAGAGAAAGAGAC;RSEQ=GGAAGTCAGAGAAAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:28.5:1:1:0:53:4:1:0:1 +10 110807162 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04965;SOR=Inf;LSEQ=CTAACCAGTCAGGGATAGTG;RSEQ=GAGATGGCGCCTGGAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:18,6:24,0:0:2,0:31.8:1:32.8:1:1:0:52.8:48:1:0:0 0/1:23:4:2,2:14,5:19,4:0.1739:2,2:17.5:1:28.8:1:0.55731:2.66173:39.3:8:0.1739:0:1.8 +10 110807229 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49614;SOR=Inf;LSEQ=ATGCCTTTCAAACTCTTATA;RSEQ=CAACCTCTGGAGTTGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:23,31:54,0:0:2,0:26:1:30.9:1:1:0:35.8:26:1:0:0.2 0/1:58:2:1,1:29,25:54,2:0.0345:2,2:35.5:1:29.5:1:1:1.15692:29.5:4:0.0345:0:1 +10 110807255 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49515;SOR=Inf;LSEQ=TCTGGAGTTGGGCAACATGG;RSEQ=TTCTCCCCTTTCTAGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:18,34:52,0:0:2,0:35.4:1:33.2:1:1:0:37.4:104:1:0:0.3 0/1:52:2:1,1:20,30:50,2:0.0385:2,2:38.5:1:28.5:1:1:1.49:33:4:0.0385:0:1 +10 110982543 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49883;SOR=0;LSEQ=GTGAAAAATAGAAGGAATAT;RSEQ=AGAATCTAGCTCTTATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:40,1:41,2:0.0465:1,0:10:1:30.5:1:1:0:60:4:0.0476:0:1.5 0/0:35:0:0,0:35,0:35,0:0:1,0:21.6:1:27.6:1:1:0:60:34:1:0:0.1 +10 110982703 . C T 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.0911;LSEQ=AAGCCCATTTATGCCCTTCG;RSEQ=TGCCTCAAAAAAGAGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:39:19,20:186,164:350,39:0.1003:2,2:27:1:30.2:1:0.61616:1.19329:60:78:0.1016:0:1.2 1/0:500:346:165,181:73,81:154,346:0.692:2,2:27.1:1:29.3:1:1:1.01:59.9:172:0.6949:0:1.2 +10 110982789 . C T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24779;SOR=0;LSEQ=GAAGCCTGCACTCAGAGACT;RSEQ=ACTGCTATTGGTCAGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:3:1,2:33,132:165,3:0.0178:2,2:25.3:1:23:1:0.49488:1.99:60:2:0.012:0:2 0/0:167:0:0,0:39,127:166,0:0:2,0:23.9:1:30.9:1:1:0:60:82:0.9939:0:0.2 +10 111440147 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16811;SOR=Inf;LSEQ=AAAATGATGGGACCCTCTTT;RSEQ=TAGCCTTGGGGAAAATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:247,29:276,0:0:2,0:23.2:1:32.6:1:1:0:60:275:0.9964:0:0 0/1:193:2:1,1:166,25:191,2:0.0104:2,2:33:0:31:1:0.25189:6.53064:60:4:0.0106:0:1.5 +10 111440222 . G A 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AAAGTGCTTTCACTGTGGAG;RSEQ=AGGGCTAACTGATTGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:757:0:0,0:446,310:756,0:0:2,0:25.5:1:31.3:1:1:0:43:83:0.9987:0:0.1 0/1:656:20:10,10:362,274:636,20:0.0305:2,2:27:1:28.3:1:0.64806:1.32059:41.9:19:0.0295:0:1.1 +10 111440605 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.56154;LSEQ=CAAGTCAGACTTCATTACAG;RSEQ=AAGAGATTAGTACTGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:519:265:134,131:130,123:253,265:0.5106:2,2:23:1:31.7:1:0.86087:1.0332:50.9:87.333:0.5127:0:1.1 0/1:482:178:81,97:159,144:303,178:0.3693:2,2:25.1:1:30.2:1:0.15677:1.32149:51.5:177:0.3718:0:1.1 +10 111440719 . T A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89986;SOR=0.94575;LSEQ=CTTGTGGACATCTAGTCACT;RSEQ=GTAAACAATGTGCTGAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:61:33,28:34,40:74,61:0.4519:2,2:10.1:1:30.1:1:0.38941:1.38:38.3:122:0.4552:0:1.1 0/1:121:53:28,25:29,39:68,53:0.438:2,2:8.4:1:27.4:1:0.27768:1.50:37.9:106:0.438:0:1.2 +10 111440966 . G T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCAATATAATCTTTGAAT;RSEQ=TCTGGATTTTTCAGGGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:1,11:0,0:0,12:1:0,2:35.8:1:30.3:1:1:0:32.1:24:1:0:1.3 1/1:4:4:1,3:0,0:0,4:1:0,2:35:1:29.5:1:1:0:41.8:8:1:0:1.3 +10 111441034 . C T 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53451;LSEQ=AATTAATTGAAACCATAGAC;RSEQ=AAGAAGCATCATATTATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:3,6:0.6667:0,0:19:1:28.8:1:1:0:43.3:12:0.6667:0:1.8 1/0:2:1:0,1:0,1:1,1:0.5:0,0:2:0:28:0:1:0:27:2:0.5:0:2 +10 111500499 . A T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTATGTCCATTGGAGAA;RSEQ=AAAATAAACAGATGTGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:20:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 111500571 . T G 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=GGAGCATGGTGGGGATTGAG;RSEQ=TTCTGGTAACATTTCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:25.5:1:33:0:1:0:60:4:0.2222:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:37:0:33:0:1:0:60:2:1:0:1 +10 111500811 . A T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25178;SOR=Inf;LSEQ=TGTTTAAACCTCCTATGAAT;RSEQ=TTCATCTCATTTGAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:183,78:261,0:0:2,0:24.2:1:28.8:1:1:0:60:64.25:1:0:0.2 0/1:297:3:1,2:198,95:293,3:0.0101:2,2:22.3:1:23.7:1:0.25101:4.14647:60:2:0.007:0:2.3 +10 111500900 . T A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00068;SOR=1.53823;LSEQ=TGGGGTACTTTGGGCAGCAA;RSEQ=CCTTATCTACATGTTATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:209:97,112:103,131:234,209:0.4718:2,2:24.1:1:29.8:1:0.63339:1.10:60:68.667:0.4747:0:1.1 1/0:596:345:160,185:111,135:246,345:0.5789:2,2:24.1:1:29.2:1:0.8018:1.05:60:85.25:0.5789:0:1.1 +10 111501026 . G A 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.85164;SOR=1.09354;LSEQ=TTAATAACTTGCAATTAGGA;RSEQ=GCATTAAGCCTACTGCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:28:0,28:0,39:39,28:0.4179:1,1:26.6:1:33:1:1:0:60:56:0.4179:0:1.9 0/1:50:22:1,21:1,27:28,22:0.44:1,1:22.6:1:30.7:1:1:1.28:60:21:0.4375:0:1.8 +10 111501039 . C T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68379;SOR=0.81999;LSEQ=ATTAGGAGGCATTAAGCCTA;RSEQ=TGCTACCAAAATCACAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:28:0,28:0,31:31,28:0.4746:1,1:21.3:1:29.9:1:1:0:60:56:0.4746:0:1.9 0/1:40:17:1,16:1,22:23,17:0.425:1,1:19.9:1:29.9:1:1:1.36:60:34:0.425:0:2 +10 111501067 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.97997;LSEQ=AAAATCACAGAATCTTAGCA;RSEQ=TAATATTGTCACTTCATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:21:0,21:0,12:12,21:0.6364:0,1:16.4:1:32.8:1:1:0:60:42:0.6364:0:1.1 1/0:19:12:1,11:0,7:7,12:0.6316:0,2:20.8:1:31.6:1:1:0:60:24:0.6316:0:1.1 +10 111567417 . C A 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.50089;SOR=Inf;LSEQ=TAATTTACCAAAATGACAAA;RSEQ=ACAAAGGGAAACAGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:13,1:14,0:0:1,0:20.3:1:31.1:1:1:0:60:13:1:0:0.1 0/1:20:2:1,1:11,7:18,2:0.1:2,2:6.5:1:31.5:1:1:1.53525:60:4:0.1053:0:1.5 +10 111567538 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24349;SOR=Inf;LSEQ=GTAATATTGTAGACATCAAG;RSEQ=GAATGAGCACTGTTCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:125,49:174,0:0:2,0:20.5:1:30.8:1:1:0:60:86:1:0:0.1 0/1:170:2:1,1:113,55:168,2:0.0118:2,2:22:1:27:1:0.55162:2.04516:60:4:0.012:0:1.5 +10 111567639 . A C 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGTTGGCATGGTTGTAAA;RSEQ=AAACAAGTTAAGGGCAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:67,122:189,0:0:2,0:24.1:1:30.6:1:1:0:59.7:188:1:0:0.1 0/1:231:42:12,30:77,112:189,42:0.1818:2,2:20.6:1:31.8:1:0.16326:1.71489:43.2:84:0.1834:0:1.1 +10 112948994 . G A 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.31595;LSEQ=TTTGATCATAAAGGGAATAC;RSEQ=TAATAAACTTGTAACTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:3,2:5,4:0.4444:2,2:35.3:1:30.5:1:1:1.85:60:8:0.4444:0:1.3 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:21.5:1:31:0:1:0:60:4:0.6667:0:1 +10 112949020 . T A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=AACTTGTAACTACAATCTAT;RSEQ=GAATGCTCAGGGTGCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,3:10,2:0.1667:2,2:45:0:31:1:1:2.16028:60:4:0.1667:0:1.5 0/0:9:0:0,0:7,2:9,0:0:2,0:23.3:1:29.8:1:1:0:60:18:1:0:0.4 +10 114710162 . TC T 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCTCCTGTATCTTCGGCT;RSEQ=CCCCCCCCTTTGCTCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:23.5:1:32.4:1:1:0:43.5:4:0.6667:0.3333:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:8:0:32:0:1:0:60:2:1:0:1 +10 114710208 . G GT 49 d5;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GACTTCTTGTTGTTGTTGGT;RSEQ=TTTTTTTTTTTTTTACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:42.3:1:31.3:1:1:0:60:6:1:0:3 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:17:0:1:0:60:0:0:0:1 +10 114710243 . A T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCCTTTTTTATTTATT;RSEQ=TTTTTTTGCACATTGATCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:13.5:1:26:1:1:0:60:4:0.5:0:3.5 0/0:1:0:0,0:1,0:1,0:0:0,0:24:0:29:0:1:0:60:2:1:0:0 +10 114710450 . AT A 62 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.71889;SOR=1.40758;LSEQ=GGCAAAACTTTTTGGGGGTG;RSEQ=TTTTTTTGGCTTTTCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:3:3,0:317,59:376,3:0.0079:2,0:8.3:1:31.9:1:1:0:60:6:0.008:0.0053:0.7 0/1:360:4:4,0:290,66:356,4:0.0111:2,0:19.3:1:31.1:1:1:0:60:8:0.0112:0.0056:0.3 +10 114710507 . G GA 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.35533;SOR=1.36899;LSEQ=CAAAATTGCTGCTGGTGGGT;RSEQ=AAAAAAAAATGCCGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:958:16:10,6:565,369:934,16:0.0167:2,2:27.4:1:29.8:1:1:1.09:60:32:0.0171:0.001:0 0/1:1188:27:12,15:689,469:1158,27:0.0227:2,2:29.8:1:29.8:1:0.16433:1.83533:60:54:0.0232:0:0.3 +10 114710869 . AC A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06909;SOR=1.3138;LSEQ=TTGTAACCCTGTTTTTTTCT;RSEQ=CCCCCCCTCGACCTCGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:160:127,33:151,47:198,160:0.442:2,2:23.6:1:31.6:1:0.52464:1.20:59.9:79:0.454:0.0856:0.4 1/0:398:203:165,38:164,31:195,203:0.5101:2,2:23.4:1:30.6:1:0.50865:1.21777:59.8:32.833:0.509:0.0955:0.3 +10 114711041 . G A 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.99914;LSEQ=GTTTGGAAGAAGGTGAGTAC;RSEQ=CCCCGCGCGCCCCGCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:4:2,2:96,292:388,4:0.0102:2,2:15:1:24:1:0.26118:3.03:60:3:0.0077:0:1.3 0/1:590:6:5,1:203,381:584,6:0.0102:2,2:9.3:1:28.8:1:0.02251:9.35:59.2:12:0.0103:0:1.2 +10 114711066 . G A 111 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01241;SOR=5.47316;LSEQ=GCGCGCCCCGCAGCCGCCCG;RSEQ=AGCCGCCCCCCGGGCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:2,0:32,132:164,2:0.012:2,0:1:0:26:1:0.04096:0:60:4:0.0123:0:1 0/1:255:16:3,13:78,161:239,16:0.0627:2,2:9.3:1:27.8:1:0.40514:2.09408:60:7:0.056:0:1.2 +10 114711399 . G A 50 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69085;SOR=1.71485;LSEQ=GCGCCCGGCCCCCGCCCGCT;RSEQ=CCCGCCCGCCCGCGCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:2,0:36,116:152,2:0.013:2,0:1:0:22.5:1:0.05967:0:60:4:0.0133:0:1 0/1:181:4:3,1:52,125:177,4:0.0221:2,2:6.5:1:25.3:1:0.08431:7.12:60:8:0.0223:0:1 +10 114711755 . C T 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATGACTCTGTGGCTCTT;RSEQ=CTTTGCTCTCTCTCCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:16:0:27:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:30:1:1:0:59.5:4:1:0:1.5 +10 114712594 . G C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCCTCCCCCACCGGCCT;RSEQ=TGCCCCCTGCCCTCACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:32:1:1:0:60:4:1:0:1 +10 114724100 . A AAAAAAC 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=TGCTTATTGAATAGGTGCTT;RSEQ=AAAAACAAAAACAAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:17,0:17,0:0:1,0:23.9:1:29:1:1:0:57.7:34:1:0:0 0/1:13:2:2,0:11,0:11,2:0.1538:0,0:8.5:1:28.2:1:1:0:60:4:0.1538:0.0769:1 +10 114724470 . GATA G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13339;SOR=Inf;LSEQ=CCGCCCCTTCCCCCAACTGA;RSEQ=ATGATGATGATGATGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:32,191:223,0:0:2,0:23.4:1:30.7:1:1:0:58.5:30.857:1:0:0.3 0/1:282:4:0,4:47,231:278,4:0.0142:2,0:29.3:1:30.4:1:1:0:56:8:0.0148:0.0035:0 +10 114724473 . A G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=11.46608;LSEQ=CCCCTTCCCCCAACTGAGAT;RSEQ=ATGATGATGATGATGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:15:2,13:31,173:204,15:0.0685:2,2:21.5:1:32.2:1:1:1.16397:56.9:30:0.0701:0:1.2 0/1:266:122:22,100:23,116:139,122:0.4586:2,2:25.2:1:30.2:1:0.86973:1.11:58.9:60:0.4706:0:1.3 +10 114724525 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.20382;SOR=Inf;LSEQ=TGGTGGTGGTGGTGATGGTG;RSEQ=TGGTGGTGGTGATGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,65:65,0:0:1,0:20.2:1:31.7:1:1:0:53.8:20.667:1:0:0.6 0/1:54:2:0,2:1,51:52,2:0.037:1,0:10.5:1:30.5:1:1:0:60:4:0.037:0:4 +10 114724569 . GGT G 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=0.5045;SOR=0;LSEQ=GTGATGGTGGTGGTGGTGGT;RSEQ=GGGGGGGGGTTGAATCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:20.5:1:27.5:1:1:0:53.5:4:0.1053:0.0455:0.5 0/0:15:0:0,0:1,13:14,0:0:1,0:21.3:1:30.1:1:1:0:48.9:13:0.9286:0:0.5 +10 114849059 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50574;SOR=0;LSEQ=TGGAGCTTCTATAGAAATGT;RSEQ=GGTTAGGGCAGAAAGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:2,0:165,4:169,2:0.0117:1,0:8:1:32:1:1:0:60:4:0.0119:0:1 0/0:134:0:0,0:129,4:133,0:0:1,0:23:1:32:1:1:0:59.9:132:0.9925:0:0.1 +10 114849353 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.02143;LSEQ=AGCTAGCTCTAAAATGAAGC;RSEQ=GCCCACCCAAAGTTTACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:22:2,20:125,349:474,22:0.0444:2,2:27:1:30.3:1:0.08122:3.57535:60:44:0.0445:0:1 0/1:578:91:23,68:143,344:487,91:0.1574:2,2:24.3:1:29.4:1:0.45221:1.22855:60:44.5:0.1561:0:1.1 +10 114849399 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00197;SOR=Inf;LSEQ=AGGGCAGGGCCCATCCACTG;RSEQ=GATCCCTGAATTCTTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:5,185:190,0:0:1,0:23.4:1:30.3:1:1:0:59.9:94:1:0:0.1 0/1:211:10:0,10:4,197:201,10:0.0474:1,0:29.5:1:30.7:1:1:0:60:20:0.0476:0:1 +10 114849463 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1816;SOR=Inf;LSEQ=GATGTCTGGGTGTGCTGACC;RSEQ=CTGATAGGGATATCATAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:3,64:67,0:0:1,0:19.5:1:32.5:1:1:0:60:66:0.9851:0:0.1 0/1:51:2:1,1:2,47:49,2:0.0392:1,2:25.5:1:26:1:0.11529:19.40:60:4:0.0392:0:1 +10 114886564 . C T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37135;SOR=3.90498;LSEQ=GCCCGCGGCCGGCGCGGGCC;RSEQ=TGGGCAGCATCTGGGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:0,1:82,66:148,1:0.0067:2,0:1:0:25:0:0.44966:0:60:2:0.0069:0:1 0/1:155:4:1,3:86,65:151,4:0.0258:2,2:12.5:1:27:1:0.31995:3.93585:60:8:0.0265:0:1.3 +10 114886565 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=CCCGCGGCCGGCGCGGGCCC;RSEQ=GGGCAGCATCTGGGCGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:84,71:155,0:0:2,0:18.3:1:30.8:1:1:0:60:50.667:1:0:0.2 0/1:159:2:1,1:90,67:157,2:0.0126:2,2:27:0:32:0:1:1.34074:60:4:0.0127:0:1.5 +10 114886655 . CGGCG C 46 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=1;SSF=1;SOR=0.8688;LSEQ=TAGATGGTAAGCGCGGCCGG;RSEQ=GGCGGGCGGGCAGGGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:51,68:119,2:0.0163:2,2:32.5:1:32.5:1:1:1.33:60:4:0.0167:0:0.5 0/1:212:3:1,2:93,114:207,3:0.0142:2,2:8.7:1:29.4:1:1:1.62793:60:6:0.0142:0.0094:0.7 +10 114886662 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAGCGCGGCCGGCGGCGGG;RSEQ=GGGCGGGCAGGGGTGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:36,56:92,0:0:2,0:15.6:1:30.9:1:1:0:60:91:1:0:0.3 0/1:187:2:1,1:80,103:183,2:0.0107:2,2:14:0:28:0:1:1.29:60:4:0.0108:0:1.5 +10 114886663 . G A 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55308;SOR=Inf;LSEQ=AAGCGCGGCCGGCGGCGGGC;RSEQ=GGCGGGCAGGGGTGCGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:36,51:87,0:0:2,0:15.6:1:30.6:1:1:0:59.9:42.5:1:0:0.4 0/1:178:3:1,2:77,97:174,3:0.0169:2,2:10:1:24.7:1:1:1.58366:60:6:0.0171:0:1.3 +10 114886843 . AT A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GGGGTGGATGCAGTAGATTT;RSEQ=TTTTTTTAGCCTCTCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:5,0:0:2,0:13.8:1:29.6:1:1:0:60:10:1:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:34.5:1:32:1:1:1.73:60:4:0.4:0:0 +10 114889261 . T A 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGTTTTTAAAATTTTTTT;RSEQ=AAAAAATTAAATCTGCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:22:1:30:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 114889436 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12342;SOR=Inf;LSEQ=ACTCGGCCAGGAATCTGGAG;RSEQ=CATTTCGATCTTTTTAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:60,0:0:1,0:22.8:1:31.5:1:1:0:59.9:14:1:0:0.4 0/1:33:2:1,1:29,2:31,2:0.0606:2,2:22.5:1:26:1:0.17614:12.04172:60:4:0.0645:0:1 +10 114889834 . T A 42 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05135;SOR=Inf;LSEQ=TTGACCATTAAACCTATGCT;RSEQ=TTTCCCCCCCCTTAATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:31,379:410,0:0:2,0:23.2:1:30.8:1:1:0:59.9:67.333:1:0:0.2 0/1:374:4:3,1:48,322:370,4:0.0107:2,2:12.8:1:21:1:0.0087:19.83:60:3:0.0081:0:1.3 +10 114889837 . TC T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00029;SOR=0.54472;LSEQ=ACCATTAAACCTATGCTTTT;RSEQ=CCCCCCCTTAATTTAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:385:293:6,287:16,76:92,293:0.761:2,1:25.5:1:31.9:1:0:9.98964:59.9:145.5:0.7618:0.0727:0.3 1/0:328:208:7,201:21,96:117,208:0.6341:2,1:26.6:1:31:1:1e-05:6.2429:60:207:0.635:0.0396:0.2 +10 114889900 . GC TA 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07667;SOR=0.53883;LSEQ=AGAATAAATGGTCAACTCAA;RSEQ=TATGCCCTTTCTTTGAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:58:0,58:0,48:48,58:0.5472:1,1:23.7:1:30.4:1:1:0:60:116:0.5524:0.066:0.9 0/1:61:24:0,24:1,36:37,24:0.3934:1,1:18:1:30:1:1:0:60:48:0.3934:0.0656:1.1 +10 114890223 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGATAAGGCTTTAACAGTAG;RSEQ=AGGGCTGTGTAAACTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:27.5:1:1:0:60:4:1:0:1.5 +10 114900499 . A G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGATTTGGGCCCTGCC;RSEQ=GTTTCTTGTAAGTGGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:37.7:1:31:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 114900559 . A C 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAGCCTGCGTGCCTCCTGG;RSEQ=GGTGGGGCCTTGGGGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:31:1:31.7:1:1:0:47:6:0.6:0:2.3 1/1:2:2:2,0:0,0:0,2:1:0,0:11.5:1:32.5:1:1:0:53.5:4:1:0:3 +10 114900595 . T C 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TAGGAGGTCCCCACAACATG;RSEQ=GGAAACGCAGTAGGCATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:3,0:3,4:0.5714:0,2:12.8:1:31.3:1:1:0:50.3:8:0.5714:0:2.3 1/1:2:2:2,0:0,0:0,2:1:0,0:47.5:1:32.5:1:1:0:53.5:4:1:0:3 +10 114900627 . T C 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.09375;LSEQ=AGGCATGGGAGATTGAAGTC;RSEQ=CCACTTCTGACTCACCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:3,0:3,4:0.5714:0,2:15:1:32.5:1:1:0:60:8:0.5714:0:1.8 1/0:4:3:2,1:1,0:1,3:0.75:0,2:18.7:1:29.3:1:1:0:55.7:6:0.75:0:2.3 +10 114901194 . TG T 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.8125;LSEQ=GGACTTTGGGGGAACGGTGG;RSEQ=GGGGGGCCCCTGTTGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:8:0,8:2,118:120,8:0.0404:1,0:17.3:1:26.4:1:1:0:56.3:7:0.0363:0.0202:2.4 0/1:121:4:0,4:2,74:76,4:0.0331:1,0:13.3:1:27.2:1:1:0:60:8:0.0333:0.0165:1.3 +10 114901200 . GG T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.80968;SOR=0.93731;LSEQ=GACTTTGGGGGAACGGTGGT;RSEQ=CCCCTGTTGCTTTTCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:70:0,70:2,118:120,70:0.3535:1,1:27.3:1:32.2:1:0.53216:0:59.8:140:0.3627:0.0101:0.1 0/1:121:41:0,41:2,74:76,41:0.3388:1,1:24.9:1:31:1:0.54082:0:60:82:0.3417:0.0413:0.1 +10 114901201 . G T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.79042;SOR=0.81266;LSEQ=GGGGGAACGGTGGTGGGGGG;RSEQ=CCCCTGTTGCTTTTCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:11:0,11:1,99:100,11:0.0991:1,0:11.9:1:27.7:1:1:0:57.3:10:0.0926:0:2 0/1:61:5:0,5:2,54:56,5:0.082:1,0:13.4:1:27.2:1:1:0:60:10:0.0833:0:1.2 +10 114903850 . T TGAA 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.10566;SOR=Inf;LSEQ=CATGTTTATTATTTATTCTG;RSEQ=GTGTGTGTCTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:31,265:296,0:0:2,0:22.1:1:30.6:1:1:0:58.9:73:0.9966:0:0.2 0/1:270:3:2,1:32,235:267,3:0.0111:2,2:15.7:1:29.3:1:0.04266:14.41:60:6:0.0112:0.0037:0.7 +10 114903859 . C G 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00211;SOR=Inf;LSEQ=TATTTATTCTGTGTGTGTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:21,209:230,0:0:2,0:22.1:1:31.3:1:1:0:58.8:8.2:0.9809:0:0.2 0/1:206:8:1,7:18,178:196,8:0.0388:2,2:23.3:1:25.3:1:0.54913:1.41:44.5:1.667:0.0267:0:2.5 +10 114904036 . G A 74 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69008;LSEQ=ACTGGCACTTAGCATTCCGC;RSEQ=ACCATGGTCCCCAGAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:4,6:0.6:0,0:17:1:28.8:1:1:0:60:5:0.625:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:32:0:27:0:1:0:22:2:0.5:0:1 +10 114904534 . A T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCCCAGATTATTTGACTA;RSEQ=CTTTTGCAACTTAAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 114910412 . G C 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGGAAATTGTCTTCTTA;RSEQ=ATGCCACTAATAATGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:13.5:1:31.5:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 +10 114910586 . A G 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05799;SOR=Inf;LSEQ=GCTTTAATGACATTATGAGA;RSEQ=TCATTATGTTTAATTTATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:114,0:114,0:0:1,0:25.1:1:30.5:1:1:0:59.7:113:1:0:0.1 0/1:73:3:3,0:69,1:70,3:0.0411:1,0:10.7:1:27.3:1:1:0:60:2:0.0278:0:1.3 +10 114910667 . G GT 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.34082;LSEQ=TCATGTGAGTGTTACGTGCT;RSEQ=TTTTTTTTTTTCTTTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:128:119,9:192,20:212,128:0.3351:2,2:28.8:1:30.6:1:0.54918:1.38:59.6:256:0.3432:0:0.3 0/1:403:59:49,10:271,55:326,59:0.1464:2,2:25.8:1:29.6:1:1:1.00555:59.7:118:0.1497:0:0.3 +10 114911022 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08236;SOR=Inf;LSEQ=ACCCAGCCTGTGTGGGCTCT;RSEQ=CACTCCCTTACAAAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:2,159:161,0:0:1,0:24.5:1:30.7:1:1:0:59.8:79.5:1:0:0.4 0/1:125:3:0,3:2,120:122,3:0.024:1,0:16:1:32:1:1:0:60:6:0.0242:0:1 +10 114911035 . AAG A 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.07979;SOR=0;LSEQ=GGGCTCTTCACTCCCTTACA;RSEQ=AGAGAGAGAGTGCACAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:0,5:2,125:127,5:0.0379:1,0:30:1:34:0:1:0:57.2:10:0.0394:0:0.4 0/0:92:0:0,0:1,91:92,0:0:1,0:24.4:1:30.8:1:1:0:59.9:91:1:0:0.4 +10 114911079 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.71418;SOR=1.88733;LSEQ=AGAATCTCACTGTACCACCG;RSEQ=GGGTTAGAACAGAACTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:59:1,58:0,6:6,59:0.8939:0,1:22.2:1:30.1:1:1:0:60:28.5:0.9194:0:1.1 1/1:34:32:0,32:0,2:2,32:0.9412:0,1:19.5:1:29.7:1:1:0:60:31:0.9394:0:1.1 +10 114912534 . C T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=ACCCAAAGGACCTTATGTTC;RSEQ=GGATTAGGTTCCGCAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:22.6:1:31.4:1:1:0:54.4:10:0.625:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:3.5:1:26.5:1:1:0:60:4:1:0:0 +10 114917603 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GTGTCCCTCCAGCTGGGGTA;RSEQ=AATGCAAGGGCATTTGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:19,0:0:1,0:21.9:1:33:1:1:0:58.4:38:1:0:0.6 0/1:13:2:1,1:11,0:11,2:0.1538:0,2:25.5:1:26:1:0.15385:0:60:4:0.1538:0:1.5 +10 114917721 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19941;SOR=Inf;LSEQ=TCTCCTTCCAGGTGCGCCCA;RSEQ=ACACTCTTCTCACATCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:182,6:188,0:0:1,0:25.3:1:33.3:1:1:0:60:61.667:1:0:0.1 0/1:153:2:2,0:148,3:151,2:0.0131:1,0:39.5:1:30.5:1:1:0:60:4:0.0134:0:1 +10 114917782 . AAAG A 97 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.3071;SOR=1.83178;LSEQ=TTTCATCTCTTCATCTAGGG;RSEQ=AAGAAGAAGAGGAAAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:629:5:4,1:396,227:623,5:0.0079:2,2:36.8:1:32.2:1:0.65801:2.29:60:10:0.0081:0:0.2 0/1:691:10:4,6:401,280:681,10:0.0145:2,2:30.6:1:29.4:1:0.3328:2.14582:60:20:0.0146:0:0.3 +10 114917909 . G T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06171;SOR=Inf;LSEQ=TAGGTTTCCATCTGGGGGAG;RSEQ=CAGGAGAAATTCAAGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:99,289:388,0:0:2,0:24.9:1:31.7:1:1:0:60:54.429:0.9948:0:0.1 0/1:393:5:2,3:115,272:387,5:0.0127:2,2:12.8:1:27.2:1:0.6372:1.57:60:10:0.0131:0:1 +10 114917998 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54688;SOR=0;LSEQ=TAATTAATTGCTTCATGACT;RSEQ=CCCTTTTAAAGCTAGTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:2,96:98,2:0.02:1,2:24:1:26.5:1:0.05939:39.37:54:4:0.0206:0:1 0/0:52:0:0,0:0,52:52,0:0:1,0:26.6:1:32.1:1:1:0:60:51:1:0:0 +10 114918624 . A AT 55 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.70794;SOR=1.31046;LSEQ=GGTTTCGTATGTTTCAGTAG;RSEQ=TTTTTTTTTTCAGTTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:4:0,4:4,108:112,4:0.0345:1,0:23.5:1:27.7:1:1:0:60:3:0.0283:0.0172:0.5 0/1:67:3:0,3:1,63:64,3:0.0448:1,0:31:1:27.7:1:1:0:60:6:0.0484:0:1.3 +10 114918646 . GT G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.25545;SOR=0.43216;LSEQ=TTTTTTTTTCAGTTGCTTCT;RSEQ=TTTTTTTTTTTAATTTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:12:0,12:1,66:67,12:0.1519:1,0:31:1:33:1:1:0:60:24:0.1538:0:0.8 0/1:42:3:0,3:2,37:39,3:0.0714:2,0:18:1:28.1:1:1:0:60:6:0.075:0.0238:0 +10 114918783 . TA T 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTTTAAAAGAGACTGGT;RSEQ=AAAAAAAAAATGGAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:38:1:28:1:1:0:60:4:0.25:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 114919469 . CT C 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.06879;SOR=6.68646;LSEQ=GAATAAGAATGTGACTTTTA;RSEQ=TTTTTTTTTTTAATTAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:3,0:21,0:21,3:0.12:1,0:8.3:1:26.7:1:1:0:60:2:0.0833:0.08:1 1/0:6:3:3,0:3,0:3,3:0.5:0,0:23:1:33:0:1:0:56.7:6:0.5:0:0.7 +10 114919482 . A G 108 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12189;SOR=0.16076;LSEQ=ACTTTTACTTTTTTTTTTTT;RSEQ=ATTAAAGAAAGTTAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:11:11,0:16,0:16,11:0.3929:1,0:22.6:1:31.3:1:1:0:60:10:0.3704:0:1 0/1:11:1:1,0:10,0:10,1:0.0909:0,0:10:0:34:0:1:0:60:2:0.1111:0:1 +10 114919602 . CCCTCTTTC TCTCTCTT 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.73911;SOR=1.43681;LSEQ=TTTCTCTTCCCCCCCCCCCC;RSEQ=TCTCTCTCTCTCTCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:4:4,0:153,31:184,4:0.0205:2,0:10.8:1:29.7:1:1:0:52.3:8:0.0301:0.0154:1.5 0/1:171:5:4,1:130,27:157,5:0.0292:2,2:16.8:1:30.4:1:1:1.20221:57.4:10:0.0394:0.0234:1 +10 114919603 . C T 153 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=0.01184;SOR=1.8644;LSEQ=TTCTCTTCCCCCCCCCCCCC;RSEQ=CTCTTTCTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:41:34,7:91,25:116,41:0.2316:2,2:16.7:1:24.9:1:0.65469:1.33:55.3:1.278:0.217:0:3.3 0/1:161:58:43,15:68,0:68,58:0.3602:1,2:8.9:1:26.2:1:0:0:55.6:2.867:0.4343:0:2.2 +10 114919608 . T C 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00041;SOR=0;LSEQ=TTCCCCCCCCCCCCCCCTCT;RSEQ=TCTCTCTCTCTCTCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:12:6,6:130,39:169,12:0.0642:2,2:17.2:1:29.2:1:0.07558:3.30618:53.3:5:0.0654:0:3.7 0/0:187:0:0,0:118,59:177,0:0:2,0:11:1:27.6:1:1:0:57.6:8.316:1:0:1.3 +10 114920089 . A G 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08669;SOR=0;LSEQ=CCTAGGTAGAAGCAAATGAC;RSEQ=TCACCTTCTCCCCTCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:8,2:3,3:6,10:0.625:2,2:27.4:1:30.7:1:0.29945:3.63:60:20:0.625:0:1.2 0/0:3:0:0,0:1,2:3,0:0:2,0:34.7:1:30.7:1:1:0:51.7:6:1:0:0.7 +10 114920107 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01846;SOR=Inf;LSEQ=ACATCACCTTCTCCCCTCCT;RSEQ=TTCTCTCTCTCTTTTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,7:22,0:0:2,0:22.5:1:31:1:1:0:60:10:1:0:0.5 1/0:4:2:1,1:0,2:2,2:0.5:0,2:37.5:1:29.5:1:1:0:60:4:0.5:0:1 +10 114921129 . A G 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=3e-04;SOR=Inf;LSEQ=TATGTGTGTATATATGTAGC;RSEQ=TTGGTTCCAAAAGGAATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:100,1:101,0:0:1,0:18.9:1:31.2:1:1:0:60:202:1:0:0.1 0/1:61:8:8,0:51,2:53,8:0.1311:1,0:18.5:1:30.4:1:1:0:60:16:0.1379:0:1 +10 114925316 . G GA 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.91404;SOR=1.04141;LSEQ=TCTCTCCCCTGTTTCTAGGA;RSEQ=AAAAAAAAAGTGCGTTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1271:40:22,18:675,555:1230,40:0.0315:2,2:25.6:1:29:1:1:1.00:60:9:0.0289:0:0.7 0/1:1497:49:25,24:814,630:1444,49:0.0327:2,2:29.2:1:28.7:1:0.46779:1.24019:59.7:48:0.0324:0:0.2 +10 114925675 . T C 233 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=187.85637;LSEQ=CTTCCTTACATTCCCACAGC;RSEQ=CCCTGGCCGGGACCCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1914:1:0,1:912,997:1909,1:5e-04:2,0:26:0:13:0:1:0:60:0:0:0:5 0/1:2326:207:102,105:1084,1032:2116,207:0.089:2,2:22.7:1:30.4:1:0.61058:1.08123:59.9:206:0.0912:0:1.3 +10 114925758 . T C 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTCGTGAACCCCGCTGCTT;RSEQ=GTTTATGGTTTTGTTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1123:0:0,0:404,719:1123,0:0:2,0:25.9:1:30.3:1:1:0:59.9:43.92:1:0:0.2 0/1:1455:103:42,61:532,813:1345,103:0.0708:2,2:23.2:1:29.3:1:0.83474:1.05:60:50.5:0.071:0:1.4 +10 114925845 . T C 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02478;SOR=Inf;LSEQ=ACTCTCTTAATTTTGTGCCA;RSEQ=GTGGCTACATTAGTTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:2,217:219,0:0:1,0:25.4:1:30.6:1:1:0:60:72:1:0:0.1 0/1:202:5:0,5:1,196:197,5:0.0248:1,0:27.4:1:30.4:1:1:0:60:10:0.025:0:1 +10 116005765 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51296;SOR=Inf;LSEQ=CAGTCTGAGAATATTGGGTG;RSEQ=TCAGTACATGCTCCATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:56,47:103,0:0:2,0:27:1:31.1:1:1:0:56.2:24.75:1:0:0.2 0/1:146:2:1,1:84,60:144,2:0.0137:2,2:41.5:1:29:1:1:1.3967:59:4:0.0139:0:1 +10 116005775 . G A 21 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51287;SOR=Inf;LSEQ=ATATTGGGTGGTCAGTACAT;RSEQ=CTCCATCCTCCAGGAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:58,48:106,0:0:2,0:26.5:1:31:1:1:0:55.3:12.25:1:0:0.3 0/1:150:2:2,0:82,66:148,2:0.0133:2,0:8.5:1:21.5:1:0.50389:0:60:4:0.0135:0:1 +10 116005831 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.51501;SOR=Inf;LSEQ=CTGGACTACCTGCCCCCGCC;RSEQ=CCCGCCCAAGATGATTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:33,57:90,0:0:2,0:15.6:1:29.5:1:1:0:56.4:14:1:0:0.5 0/1:131:2:2,0:56,73:129,2:0.0153:2,0:19:1:28:1:0.19413:0:42:4:0.0167:0:1 +10 116006000 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13753;SOR=0;LSEQ=CTGGGCATGGTGGCTCACGC;RSEQ=TGTAATCCCAGCACTTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:36,91:127,2:0.0155:2,2:32.5:1:29.5:1:0.49297:2.51:60:4:0.0157:0:1 0/0:218:0:0,0:60,158:218,0:0:2,0:23.4:1:31:1:1:0:56:71.667:1:0:0.2 +10 116006007 . C A 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05096;SOR=0;LSEQ=TGGTGGCTCACGCCTGTAAT;RSEQ=CCAGCACTTCGGGAGGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:3:2,1:23,84:107,3:0.0273:2,2:14:1:27:1:0.12881:7.13:53.7:6:0.0278:0:1 0/0:185:0:0,0:42,142:184,0:0:2,0:22.5:1:30.4:1:1:0:55.3:91:0.9945:0:0.2 +10 116006031 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27711;SOR=Inf;LSEQ=GCACTTCGGGAGGCCGAGGC;RSEQ=GTCGTATCACCTGAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:5,61:66,0:0:2,0:24.6:1:30.7:1:1:0:44.4:65:1:0:0.1 0/1:100:3:0,3:7,89:96,3:0.03:2,0:10:1:30.7:1:1:0:58.3:6:0.0309:0:1 +10 116006285 . C A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37908;SOR=1.80684;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=GAGTATCATGGGTTGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:5:5,0:103,36:139,5:0.0342:2,0:15.2:1:24:1:0.33152:0:47.2:1.5:0.0254:0:2.2 0/1:116:7:5,2:74,35:109,7:0.0603:2,2:16.4:1:29.6:1:1:1.18:55.6:14:0.0737:0:1.6 +10 116006436 . T C 115 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0289;SOR=3.78188;LSEQ=AGCAAATTCATCAAAACCAT;RSEQ=AAATTCCCAAAACAAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:3:2,1:144,187:331,3:0.009:2,2:8:1:27:1:0.58299:2.59:30.7:2:0.0061:0:1.7 0/1:452:15:4,11:190,247:437,15:0.0332:2,2:10.6:1:29.6:1:0.2891:2.11213:32.6:30:0.0338:0:1.3 +10 116006522 . C G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42108;SOR=1.49725;LSEQ=GAACCAGGGCTGCTGTATAA;RSEQ=CTTTCAGGAACATGCTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:10:1,9:66,170:236,10:0.0407:2,2:25.8:1:32.8:1:0.29401:3.48156:47:20:0.0415:0:1.2 0/1:268:16:6,10:69,183:252,16:0.0597:2,2:26.3:1:31.3:1:0.39571:1.59:42:32:0.0597:0:1.3 +10 116006533 . C A 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.39276;LSEQ=GCTGTATAACCTTTCAGGAA;RSEQ=ATGCTACTAAAATTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:45,152:197,2:0.0101:2,2:12.5:1:29:1:0.40978:3.35:57.5:4:0.0102:0:1 0/1:215:3:2,1:53,159:212,3:0.014:2,2:21.7:1:29:1:0.16153:5.94:37:6:0.0142:0:1.7 +10 116006545 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23864;SOR=0;LSEQ=TTCAGGAACATGCTACTAAA;RSEQ=TTTATTTTACCATTGACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:27,131:158,2:0.0125:2,2:11.5:1:28:1:0.32028:4.78:60:4:0.0125:0:1 0/0:167:0:0,0:33,134:167,0:0:2,0:21.8:1:30:1:1:0:57.1:334:1:0:0.2 +10 116007159 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCATCCCAGGTTCAAG;RSEQ=GATTCTCCTGCCTCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 117807835 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01001;SOR=2.97123;LSEQ=TCAAGGTCTGAACAGAGGGA;RSEQ=GAGAGAAAAGTAAATAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:7:5,2:115,70:185,7:0.0363:2,2:34:1:30.4:1:0.71326:1.52:58.6:6:0.0313:0:1.9 0/1:258:26:15,11:131,100:231,26:0.1008:2,2:22.9:1:30.9:1:1:1.04:60:52:0.1008:0:1.7 +10 117807881 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=19.27878;LSEQ=GAGGGCAGGAATCATATTTC;RSEQ=CTGTTTCCCAAAGATAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:10:7,3:137,126:263,10:0.0366:2,2:18.4:1:32.2:1:0.34222:2.14:59:20:0.037:0:1.5 0/1:368:156:76,80:99,112:211,156:0.4239:2,2:25.8:1:29.4:1:0.752:1.07:59.8:77:0.4242:0:1.6 +10 117807917 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29039;LSEQ=AGCGTCCATCACATGATAGG;RSEQ=CTCCAGTGAACTTTCTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:243:131:57,74:46,66:112,131:0.5391:2,2:23.9:1:29.7:1:0.79462:1.10:60:42.667:0.5378:0:1.1 0/1:324:82:33,49:101,140:241,82:0.2531:2,2:26.6:1:28.4:1:0.89683:1.07101:60:81:0.2531:0:1.8 +10 117807951 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24889;SOR=Inf;LSEQ=TCTAATAGAGGAAGGAATGA;RSEQ=CCTGAGGGAAACCCAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:45,108:153,0:0:2,0:22.7:1:32.3:1:1:0:60:50:1:0:0.6 0/1:166:3:2,1:53,110:163,3:0.0181:2,2:17.7:1:22.7:1:0.25522:4.11:60:2:0.0123:0:1 +10 117807957 . G T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24869;SOR=Inf;LSEQ=AGAGGAAGGAATGAGCCTGA;RSEQ=GGAAACCCAGTTCATCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:33,102:135,0:0:2,0:22.6:1:31.6:1:1:0:59.9:66.5:0.9925:0:0.6 0/1:148:3:2,1:45,99:144,3:0.0203:2,2:15:1:23.7:1:0.23968:4.35:60:2:0.0139:0:2 +10 117808099 . C T 82 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33714;SOR=0.23734;LSEQ=GACCAGCCTGGCCAACATGG;RSEQ=GAAACCCTGTCTCTACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:0,6:0,8:8,6:0.4286:0,0:29.7:1:32:0:1:0:36.3:12:0.4286:0:1 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:30:0:31:0:1:0:27:2:0.1429:0:1 +10 117888157 . A T 28 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGCAGGAGAATGGCGTG;RSEQ=ACCTGGGAGGCAGAGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:6.5:1:28.5:1:0.33333:0:38.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 117888193 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=CTTGCAGTGAGCCAAGACTG;RSEQ=GCCACTGCACTCCAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:31.8:1:32.8:1:1:0:33.4:10:1:0:0.4 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:32:0:1:0:52.5:4:1:0:1.5 +10 117888236 . CAAAAAA C 30 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=26.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=GACTGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,1:6,0:0:2,0:14:1:31.7:1:1:0:36.8:12:0.8571:0:1.3 0/1:5:2:2,0:1,0:1,2:0.4:0,0:20.5:1:30.4:1:1:0:55:4:0.4:0.2:1.5 +10 117888327 . C T 61 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01291;SOR=Inf;LSEQ=AGTTGTTAAAACTACATATG;RSEQ=TGTTAAGGTTTTCCTCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:86,5:91,0:0:2,0:23.3:1:31.7:1:1:0:59.6:17.2:1:0:0.3 0/1:88:6:5,1:71,11:82,6:0.0682:2,2:25.7:1:23.8:1:1:1.28686:58.3:2:0.05:0:3.2 +10 117888366 . AT A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.75669;SOR=1.07485;LSEQ=AATGTTATTAGAAAAGCAAT;RSEQ=TTTTTTTAAAAAGGCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:90:73,17:70,37:107,90:0.4569:2,2:23.7:1:31.5:1:0.01627:2.26:60:180:0.4615:0.0761:0.1 0/1:179:85:64,21:61,33:94,85:0.4749:2,2:25.2:1:30.4:1:0.14464:1.64:59.9:170:0.4749:0.095:0.7 +10 117888425 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.23524;LSEQ=TGAATCATTTTATGTCTAAA;RSEQ=CAATTGCTCAAAGTTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:18:9,9:194,182:376,18:0.0457:2,2:26.7:1:30.1:1:1:1.06573:60:17:0.0435:0:1.8 0/1:389:158:83,75:122,109:231,158:0.4062:2,2:25.9:1:28.9:1:1:1.01136:60:51.667:0.4026:0:1.7 +10 117888438 . G C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00041;SOR=1.65605;LSEQ=GTCTAAACCAATTGCTCAAA;RSEQ=TTTACTTCATATAGCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:160:73,87:122,116:238,160:0.402:2,2:27.9:1:32.8:1:0.30664:1.2527:59.8:159:0.4046:0:1.1 1/0:408:215:105,110:93,99:192,215:0.527:2,2:27:1:31.3:1:1:1.02:60:70.667:0.5274:0:1.1 +10 117888465 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.8841;LSEQ=TCATATAGCAGTAGGTGTGA;RSEQ=TTAGCCTCACTTTCTACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:15:7,8:141,190:331,15:0.0434:2,2:29.3:1:30.2:1:0.79403:1.18:60:14:0.0409:0:1.9 0/1:333:123:49,74:93,114:207,123:0.3694:2,2:27.8:1:29.5:1:0.42109:1.23123:60:60.5:0.3712:0:1.8 +10 117888566 . C G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30236;SOR=0.69385;LSEQ=CCTGTGACAAATTCTAGAAT;RSEQ=CGCAACCTGGAATATTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:37:1,36:2,26:28,37:0.5692:2,1:24:1:32.8:1:0.57308:2.72623:60:74:0.5692:0:1.1 0/1:67:32:4,28:3,32:35,32:0.4776:2,2:21.3:1:31.8:1:0.70137:1.51:60:31:0.4769:0:1 +10 117888887 . T C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATGCAAGGTTAGTTTAATAT;RSEQ=TAAAAATATATGTAATTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:32:0:1:0:25:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:30:1:1:0:60:4:1:0:2.5 +10 117888908 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAATATATGTAATTCAC;RSEQ=GCACTAACAGAATACAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:28:1:1:0:60:4:1:0:2.5 +10 118257049 . T C 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAAATTTGACAAGGAGG;RSEQ=TAAAAATACAGGGCCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:30.8:1:33.6:1:1:0:56.2:10:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:19:0:34:0:1:0:53:2:1:0:1 +10 118257169 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTGAAGAGCATTGTCTG;RSEQ=TTTCAGAAGACTTTTCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:5,9:0,0:0,14:1:0,2:19.2:1:32.2:1:1:0:55.3:28:1:0:1.1 1/1:14:13:6,7:0,1:1,13:0.9286:0,2:17.4:1:31.1:1:1:0:49:26:0.9286:0:1.2 +10 118510678 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49661;SOR=0;LSEQ=ACTAGTAGTGGGTGACAATG;RSEQ=CAAAACTGTCCCAAAATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:31,2:0.0606:2,2:33:1:29:1:1:1.06462:60:4:0.0606:0:1 0/0:27:0:0,0:16,11:27,0:0:2,0:26.7:1:30.4:1:1:0:59.5:54:1:0:0.1 +10 119379087 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05076;LSEQ=GGTAAGCGGTCTGAAGACTC;RSEQ=ATTATGGAAAAACTGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:332:304:135,169:14,14:28,304:0.9157:2,2:27.1:1:30.6:1:0.69196:1.25099:60:75:0.9146:0:1.1 0/1:446:158:78,80:135,152:287,158:0.3543:2,2:27.7:1:29.6:1:0.6918:1.10:60:157:0.3552:0:1.2 +10 119379171 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49977;SOR=Inf;LSEQ=TGGGGAATATTGAGATAGGT;RSEQ=GGTTAAGCCTTCTCTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:25,95:120,0:0:2,0:21.9:1:30.6:1:1:0:60:119:1:0:0.4 0/1:135:2:1,1:28,105:133,2:0.0148:2,2:10:0:32:0:0.38474:3.70:60:4:0.015:0:1.5 +10 119379381 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCAGCCAACAGCAAACTA;RSEQ=AGCAGCTCAGCTGGGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:13:1:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 121649371 . C G 43 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.02341;LSEQ=GAGTGTTGCTTTTACACTAA;RSEQ=CAGTCAGGGATAGGATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:8,1:9,1:0.1:2,0:6:0:35:0:1:0:49:2:0.1111:0:1 0/1:16:3:2,1:10,3:13,3:0.1875:2,2:29:1:27.7:1:1:1.60994:37.3:6:0.1875:0:1.3 +10 121649420 . T G 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15374;SOR=Inf;LSEQ=GGTGTTTACAGGAAAAGGCT;RSEQ=CTGAAATCAGACAACGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:23,10:33,0:0:2,0:16.8:1:30.6:1:1:0:47.1:32:1:0:0.6 0/1:57:5:3,2:32,20:52,5:0.0877:2,2:24.4:1:33.2:1:1:1.06545:55.8:10:0.0877:0:2 +10 121649458 . C A 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08233;SOR=Inf;LSEQ=CTTTCAAACTCTTATATCAA;RSEQ=CTCTGGAGTTGGGCGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:36,31:67,0:0:2,0:29:1:32.2:1:1:0:55:134:1:0:0.9 0/1:103:6:3,3:50,47:97,6:0.0583:2,2:36.3:1:28.2:1:1:1.06322:56.5:12:0.0583:0:2.3 +10 121649505 . T C 179 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCTTTCTAGGTCCTGTGA;RSEQ=GGCCATCTTGCTATTATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:23,33:0,0:0,56:1:0,2:21.7:1:30.9:1:1:0:54.2:112:1:0:1.1 1/0:70:49:21,28:7,14:21,49:0.7:2,2:19.3:1:30.1:1:0.59607:1.49:51.9:98:0.7206:0:1.3 +10 121649535 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49059;SOR=Inf;LSEQ=GCTATTATTCACCTTCGGGC;RSEQ=CTGTATTTTTAACCTCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:5,15:20,0:0:2,0:18.8:1:32:1:1:0:49.4:40:1:0:1 0/1:23:2:1,1:4,17:21,2:0.087:2,2:19.5:1:27.5:1:0.39526:3.91:43.5:4:0.087:0:2 +10 121932750 . T G 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=3.4267;LSEQ=GCTTCAAAAGGGCAGCATCA;RSEQ=TATGGAGAATGTTTTGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:75:58,17:40,15:55,75:0.5769:2,2:26.9:1:32.7:1:0.68066:1.28:60:150:0.5814:0:1.8 1/1:131:108:73,35:14,8:22,108:0.8244:2,2:24.6:1:31.5:1:0.80471:1.19:60:107:0.8231:0:2 +10 121932799 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.31825;LSEQ=GGTGAAACATAACAACTCAC;RSEQ=GTAAACATCTGTCGTACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:109:60,49:51,39:90,109:0.5477:2,2:26.3:1:30.1:1:0.88623:1.06758:60:35.333:0.5408:0:2.2 1/1:200:168:93,75:17,15:32,168:0.84:2,2:26.8:1:29.3:1:0.84807:1.09:60:55:0.8376:0:1.9 +10 121932833 . C A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01818;SOR=0.63381;LSEQ=GTACCTTGTATAGAGCTGAA;RSEQ=TCCAGCACACATTGATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:225:131:62,69:43,51:94,131:0.5822:2,2:25.4:1:30.8:1:0.89236:1.07:60:130:0.5856:0:1.8 0/1:224:105:52,53:57,62:119,105:0.4688:2,2:24.9:1:29.6:1:0.89352:1.07:60:51.5:0.4703:0:1.9 +10 121932919 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1936;SOR=Inf;LSEQ=ACTTTTTCTCAGTTGTCCTT;RSEQ=GGGTCCTCACTCACTATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:25,93:118,0:0:2,0:25.2:1:31.5:1:1:0:60:117:0.9915:0:0.3 0/1:94:2:1,1:24,68:92,2:0.0213:2,2:24.5:1:28:1:0.46328:2.80:60:4:0.0215:0:1 +10 121932975 . T C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01373;SOR=0.1611;LSEQ=ACTTTATTTTTATTTAGTCA;RSEQ=ATATAAGATAACGCCTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:18:0,18:0,13:13,18:0.5806:1,1:27.7:1:33:1:1:0:60:36:0.6:0:1 0/1:17:3:0,3:0,14:14,3:0.1765:1,0:17.3:1:32.7:1:1:0:60:6:0.1765:0:1 +10 122114724 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24053;SOR=Inf;LSEQ=ATTACTGGAAGATGGCGGTT;RSEQ=CGGCCGAAAGGGAAAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:56,63:119,0:0:2,0:35.3:1:31.3:1:1:0:46.8:38.667:0.9915:0:0.8 0/1:116:2:1,1:51,63:114,2:0.0172:2,2:41:1:28:1:1:1.23:49.5:4:0.0174:0:1 +10 122114727 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49793;SOR=0;LSEQ=ACTGGAAGATGGCGGTTCCG;RSEQ=CCGAAAGGGAAAGTTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:56,62:118,2:0.0167:2,2:29:1:32:0:1:1.11:28.5:4:0.0169:0:2 0/0:118:0:0,0:52,66:118,0:0:2,0:33.6:1:30.4:1:1:0:48.5:58:1:0:0.5 +10 122114728 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24476;SOR=Inf;LSEQ=CTGGAAGATGGCGGTTCCGG;RSEQ=CGAAAGGGAAAGTTCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:57,63:120,0:0:2,0:35.1:1:31:1:1:0:46.9:23:1:0:0.9 0/1:118:2:1,1:51,65:116,2:0.0169:2,2:31:0:31:1:1:1.27:33:4:0.0171:0:1 +10 122114730 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25751;LSEQ=GGAAGATGGCGGTTCCGGCC;RSEQ=AAAGGGAAAGTTCATTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:122:84:39,45:18,20:38,84:0.6885:2,2:34.9:1:30.5:1:1:1.03816:48.3:83:0.686:0:1.2 0/1:119:43:21,22:31,45:76,43:0.3613:2,2:32.9:1:28.8:1:0.44439:1.38:50.2:86:0.3613:0:1.1 +10 122302038 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68284;SOR=1.94945;LSEQ=CTCCTCCAAAATGTTTATGA;RSEQ=AGATGGGATTTGGAATTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:9,0:9,0:9,9:0.5:0,0:16.3:1:33.9:1:1:0:60:18:0.5:0:1.1 1/0:9:6:5,1:3,0:3,6:0.6667:0,2:21.7:1:32.5:1:1:0:60:12:0.6667:0:1 +10 122302203 . G A 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.89293;LSEQ=CAGTTCTTTTCTTGCACTCA;RSEQ=CCTACATTCTCAATTCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:1:1,0:177,122:299,1:0.0033:2,0:1:0:25:0:1:0:60:2:0.0034:0:1 0/1:300:29:16,13:161,109:270,29:0.0967:2,2:23.3:1:28.8:1:0.69301:1.19937:60:28:0.0946:0:1.8 +10 122302242 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11327;SOR=1.29653;LSEQ=CAGGCGCTGCTGAGTAATTA;RSEQ=GTGGTAAAAGCTTTTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:293:149:77,72:80,64:144,149:0.5085:2,2:25.6:1:30.5:1:0.55837:1.1682:60:36.25:0.507:0:1.1 1/0:356:204:105,99:81,71:152,204:0.573:2,2:25:1:29.5:1:0.74866:1.07543:60:203:0.5767:0:1.2 +10 122302313 . T A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24834;SOR=Inf;LSEQ=GACTGTCGATGATGCTTCAT;RSEQ=GTGGGCATTTGGATCAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:71,133:204,0:0:2,0:24.7:1:29.9:1:1:0:60:24.5:1:0:0.4 0/1:210:3:2,1:79,128:207,3:0.0143:2,2:19.3:1:27:1:0.56048:3.22:60:6:0.0143:0:1.3 +10 122302318 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=TCGATGATGCTTCATTGTGG;RSEQ=CATTTGGATCAGTTAGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:61,127:188,0:0:2,0:25.1:1:31.6:1:1:0:60:61.667:0.9946:0:0.4 0/1:191:2:1,1:68,120:188,2:0.0105:2,2:21:1:26.5:1:1:1.76:60:4:0.0106:0:1 +10 122302325 . G T 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=TGCTTCATTGTGGGCATTTG;RSEQ=ATCAGTTAGACCCCTGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:55,121:176,2:0.0112:2,2:29:0:28.5:1:0.53145:2.19:60:4:0.0113:0:1 0/0:168:0:0,0:54,114:168,0:0:2,0:23.3:1:30.1:1:1:0:60:55:1:0:0.4 +10 122302341 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22263;SOR=Inf;LSEQ=TTTGGATCAGTTAGACCCCT;RSEQ=ATTGTGGGGCAAAAGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:30,106:136,0:0:2,0:24.6:1:31.7:1:1:0:60:44.333:1:0:0.4 0/1:122:2:1,1:29,91:120,2:0.0164:2,2:5.5:1:26.5:1:0.43287:3.10:60:4:0.0167:0:1.5 +10 122302362 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26397;SOR=0.67405;LSEQ=ATTGTGGGGCAAAAGATGGC;RSEQ=TCATCTTCCAAAATTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:38:4,34:12,48:60,38:0.3878:2,2:21.3:1:31.7:1:0.27006:2.10979:60:76:0.3878:0:1 0/1:77:23:2,21:8,46:54,23:0.2987:2,2:25.1:1:29.3:1:0.71409:1.81322:60:22:0.2895:0:1.2 +10 122302563 . G C 42 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCATCCCCAGGACGGTG;RSEQ=GTGAGTGTGGGTGTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:24.7:1:27:1:1:0:47.7:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 123239112 . G A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.22888;LSEQ=GTCCTACTGGTCCACAGCCA;RSEQ=TACGCACGGCAGGTGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:40:20,20:399,326:725,40:0.0521:2,2:26:1:29.9:1:0.62504:1.2236:59.5:39:0.0512:0:1.1 1/0:865:466:235,231:211,187:398,466:0.5387:2,2:25.5:1:29.7:1:0.45342:1.109:60:154.333:0.539:0:1.2 +10 123239349 . G T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10147;SOR=Inf;LSEQ=TTCCCAGTGCTGTCCTGTTT;RSEQ=GGGACAGGCAGACACAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:217,85:302,0:0:2,0:22.3:1:32.1:1:1:0:60:99.667:1:0:0.1 0/1:265:3:1,2:171,91:262,3:0.0113:2,2:5.3:1:27:1:0.28226:3.73856:60:6:0.0114:0:1 +10 123239751 . G A 170 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=51.02142;LSEQ=CCAGCCCACCTGACTTCCAC;RSEQ=AAGACCTCCCTGAGACCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1477:1:1,0:686,789:1475,1:7e-04:2,0:1:0:25:0:0.46545:0:60:2:7e-04:0:1 0/1:1705:57:29,28:769,878:1647,57:0.0334:2,2:22.6:1:29.2:1:0.58994:1.18:59.8:18:0.0322:0:1.1 +10 123240276 . GA G 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTGAAGGTTCGAGATTCA;RSEQ=AAGTGTCCTTTGCTCCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:819:0:0,0:394,424:818,0:0:2,0:23:1:30.5:1:1:0:59.9:61.923:1:0:1 0/1:969:49:22,27:442,478:920,49:0.0506:2,2:23:1:30.9:1:0.7695:1.13469:59.7:98:0.0513:0.0103:0.9 +10 123240287 . T C 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51265;SOR=0.55692;LSEQ=CGAGATTCAGAAAGTGTCCT;RSEQ=TGCTCCCCAAGGCATCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:805:802:392,410:0,0:0,802:0.9963:0,2:23.7:1:32.7:1:1:0:59.9:79.2:0.9962:0:1.1 1/1:899:893:425,468:1,1:2,893:0.9933:2,2:23.9:1:30.9:1:1:1.10106:60:110.625:0.9933:0:1.1 +10 123240429 . G GA 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.24573;SOR=1.33173;LSEQ=TTTAACATTGGTAAGCGGTT;RSEQ=AAAAAAAAAATCAAAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:33:13,20:273,302:575,33:0.0537:2,2:29:1:31.4:1:0.37768:1.38998:58.9:66:0.0549:0:0.1 0/1:654:46:21,25:294,310:604,46:0.0703:2,2:30.1:1:29.7:1:0.76043:1.12882:60:92:0.0734:0.0015:0.2 +10 123240625 . A G 297 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.0383;LSEQ=ACAGAGACCACAGGGCCGGC;RSEQ=AAGCTGAAAATATTTACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:810:767:344,423:19,23:42,767:0.9469:2,2:24.7:1:31:1:1:1.01578:59.8:190.75:0.9478:0:1.5 0/1:1006:408:188,220:277,314:591,408:0.4056:2,2:24.2:1:30:1:0.84655:1.0323:59.7:407:0.4078:0:1.3 +10 123240645 . C T 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08496;LSEQ=AAAGCTGAAAATATTTACTC;RSEQ=CTGGCCCTTTACAGAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:795:365:168,197:189,240:429,365:0.4591:2,2:24.9:1:30.9:1:0.61643:1.08:59.8:72:0.4615:0:1.9 0/1:938:63:31,32:402,472:874,63:0.0672:2,2:24.3:1:29.1:1:0.69505:1.14:59.5:14.75:0.0638:0:1.9 +10 123240667 . T C 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TGGCCCTTTACAGAAAGCAG;RSEQ=TGCCGACCCCTGTTCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:770:0:0,0:361,408:769,0:0:2,0:25.2:1:30.4:1:1:0:59.8:152.8:0.9987:0:1 0/1:892:16:9,7:406,469:875,16:0.0179:2,2:27.9:1:31.1:1:0.45933:1.48:60:32:0.018:0:1.6 +10 123240903 . GACACACACAC G 279 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=16.000;MSILEN=2;SSF=0;SOR=0.2042;LSEQ=GGCAACTAGACATTTTTAAA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:624:355:226,129:108,40:148,355:0.5689:2,2:30.3:1:33:1:0.04912:1.53985:59.6:710:0.5754:0.0721:0.1 0/1:599:127:71,56:112,62:174,127:0.212:2,2:31.8:1:31.2:1:0.15224:1.42308:58.9:254:0.2145:0:0.2 +10 123241122 . C G 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATTTTGTCCTAAATGGAA;RSEQ=CGTTTTTCTTGAGCATATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1562:0:0,0:729,831:1560,0:0:2,0:24.8:1:31.8:1:1:0:60:64:0.9987:0:0.1 0/1:1814:86:40,46:831,893:1724,86:0.0474:2,2:23.5:1:31.1:1:0.82521:1.07015:60:85:0.0474:0:1.1 +10 123241211 . T C 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0;SOR=Inf;LSEQ=AATATGGCATTCTGCTTTTT;RSEQ=ATTTTAGGGTACTAGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1083:0:0,0:544,538:1082,0:0:2,0:24.6:1:29.7:1:1:0:60:97.364:0.9991:0:0.1 0/1:1393:57:30,27:698,636:1334,57:0.0409:2,2:25.1:1:31.3:1:1:1.01:60:114:0.0412:0:1.1 +10 123241323 . G A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04387;LSEQ=CATTAAAATAGAACTTTAGT;RSEQ=CTTTTCCCGGTTTCTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:924:484:185,299:236,203:439,484:0.5238:2,2:26.9:1:29.5:1:0:1.87766:55.1:160.333:0.5286:0:3.4 0/1:1632:75:38,37:781,774:1555,75:0.046:2,2:26.9:1:27.7:1:1:1.02:53.2:36.5:0.0473:0:3.6 +10 123241332 . G A 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19777;SOR=0.42166;LSEQ=AGAACTTTAGTGCTTTTCCC;RSEQ=GTTTCTTTCTTTTTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:793:790:352,438:0,0:0,790:0.9962:0,2:22.6:1:30.9:1:1:0:55.3:40.579:1:0:2.9 1/1:1456:1443:700,743:1,1:2,1443:0.9911:2,2:25.7:1:29.1:1:1:1.06141:57.1:25.236:0.9978:0:1.9 +10 123241348 . A T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.00037;SOR=0.63003;LSEQ=TCCCGGTTTCTTTCTTTTTT;RSEQ=TTTTTATTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:137:109,28:121,232:353,137:0.2773:2,2:14.1:1:29.2:1:0:7.43:53.4:67.5:0.2813:0:2.9 0/1:1048:204:172,32:342,494:836,204:0.1947:2,2:17:1:26.9:1:0:7.75:51.8:28.143:0.2054:0:3.2 +10 123241354 . AT TA 240 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0;SOR=0.03789;LSEQ=TTTCTTTCTTTTTTATTTTT;RSEQ=TTTTTTTTTTTTTGAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:266:80,186:10,15:25,266:0.6584:2,2:22.7:1:29.8:1:0.36541:1.54753:48.5:265:0.9075:0:3.8 0/1:929:63:19,44:237,343:580,63:0.0678:2,2:21.7:1:28.6:1:0.10559:1.599:48.9:126:0.0903:0:3.4 +10 123241361 . T A 241 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0;SOR=0.02779;LSEQ=CTTTTTTATTTTTATTTTTT;RSEQ=TTTTTTTGAGACGGAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:369:253:73,180:89,27:116,253:0.6856:2,2:20.3:1:30.3:1:0:8.0761:47.1:125.5:0.6858:0:3.8 0/1:826:47:16,31:372,407:779,47:0.0569:2,2:19.7:1:28.7:1:0.07222:1.76969:45.7:94:0.057:0:3.7 +10 123241369 . G T 91 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00739;SOR=8.77148;LSEQ=TTTTTATTTTTTTTTTTTTT;RSEQ=AGACGGAGTCTCGCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:1:1,0:71,164:235,1:0.0042:2,0:14:0:10:0:0.30508:0:60:0:0:0:3 0/1:555:20:15,5:168,364:532,20:0.036:2,2:7.5:1:21.1:1:0.00012:6.48:52.7:1.5:0.0253:0:3.7 +10 123241373 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=61.01897;LSEQ=TATTTTTTTTTTTTTTGAGA;RSEQ=GGAGTCTCGCTCTGTCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:19:5,14:48,134:182,19:0.0936:2,2:17.7:1:28.8:1:1:1.00297:51.2:8.5:0.0885:0:2.5 1/1:443:383:116,267:12,43:55,383:0.8646:2,2:18.6:1:28.1:1:0.26653:1.56:52.3:17.238:0.8808:0:2.3 +10 123241383 . C T 124 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03569;SOR=0.45956;LSEQ=TTTTTTGAGACGGAGTCTCG;RSEQ=TCTGTCGCCAAGGCTGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:17:3,14:29,106:135,17:0.1118:2,2:16.1:1:30.4:1:1:1.27477:31.9:34:0.1181:0:2.6 0/1:293:16:0,16:61,215:276,16:0.0546:2,1:19.1:1:29.9:1:0.02846:0:31.3:32:0.0593:0:2.6 +10 123241496 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGTAGCTGGGATTACAGG;RSEQ=GCACACCAACACGCCCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:89:89:55,34:0,0:0,89:1:0,2:24.9:1:30.7:1:1:0:42.2:21.25:1:0:1.2 1/1:63:63:32,31:0,0:0,63:1:0,2:23.3:1:28.5:1:1:0:41.6:8:1:0:1.3 +10 123241505 . A C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20152;SOR=Inf;LSEQ=GGGATTACAGGTGCACACCA;RSEQ=CACGCCCGGCTAATTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:61,28:89,0:0:2,0:25.2:1:29.4:1:1:0:41:13.833:1:0:1.1 0/1:73:2:1,1:45,25:70,2:0.0274:2,2:8:0:33:0:1:1.78446:52.5:4:0.0303:0:2.5 +10 123241593 . C T 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62342;SOR=3.01927;LSEQ=GAACTCCTGACCTCATGATC;RSEQ=GCCTGCCTCGGCCTCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:1:0,1:210,27:237,1:0.0042:2,0:1:0:25:0:0.11765:0:43:2:0.0043:0:1 0/1:238:3:1,2:211,24:235,3:0.0126:2,2:5:1:26:1:0.03223:17.1438:33.7:6:0.0127:0:3.3 +10 123241616 . G A 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCCTCGGCCTCCCAAAGT;RSEQ=CTGGGATTACAGGCATGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:293,111:404,0:0:2,0:21.8:1:32.3:1:1:0:48:133.667:0.9975:0:0.1 0/1:470:21:14,7:315,132:447,21:0.0447:2,2:22.8:1:27.8:1:0.80726:1.19269:52:42:0.0455:0:1.2 +10 123241794 . C T 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=8.60587;LSEQ=AAGAAGAAAGTTGGTTTCTT;RSEQ=CCCCCCTTGAACCGTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1635:102:50,52:754,774:1528,102:0.0624:2,2:26:1:30.4:1:1:1.01312:59.8:50:0.0625:0:1.2 0/1:1963:715:346,369:601,638:1239,715:0.3642:2,2:23.2:1:29.2:1:0.96256:1.00462:60:101.143:0.3646:0:1.2 +10 123242026 . T C 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=5.58873;LSEQ=TTCTAAAATACTTGGGGGAC;RSEQ=TTAACTTTTTTCTTGTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1272:628:350,278:361,280:641,628:0.4937:2,2:25.5:1:32:1:0.86529:1.02405:60:77.5:0.4917:0:1.1 1/1:1394:1178:656,522:114,98:212,1178:0.8451:2,2:24.7:1:30.5:1:0.6526:1.08:60:68.294:0.8444:0:1.1 +10 123242508 . G A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0369;SOR=Inf;LSEQ=TTTAGTAGAGACAGGGTTTC;RSEQ=CCATGTTGGCCAGGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:96,10:106,0:0:2,0:25.6:1:30.9:1:1:0:44.5:105:0.9906:0:0.1 0/1:85:4:3,1:81,0:81,4:0.0471:1,2:28.8:1:31.3:1:0.04706:0:26.3:8:0.0476:0:1.3 +10 123242549 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21668;SOR=Inf;LSEQ=TCGAACTCCTGGCCTCAGGT;RSEQ=ATCTGCCCTCCTCGGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:155,27:182,0:0:2,0:24.3:1:32.2:1:1:0:51.5:90:1:0:0.4 0/1:159:2:1,1:137,20:157,2:0.0126:2,2:14.5:1:26.5:1:0.24743:6.71025:60:4:0.0128:0:1 +10 123242589 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06636;LSEQ=CCAAAATGCTGGGATTACAG;RSEQ=CGAGAGCATAAATATTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:154:105,49:137,59:196,154:0.44:2,2:23.8:1:30.1:1:0.72842:1.08337:58.5:153:0.4435:0:1.1 0/1:405:20:11,9:258,127:385,20:0.0494:2,2:22.9:1:27.7:1:0.33139:1.65996:57.9:40:0.05:0:1.1 +10 123242724 . T C 315 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=7.84908;LSEQ=GAAAGAGGCTGCAAGGCATA;RSEQ=AGCATTACCAACAGGATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1143:585:308,277:294,263:557,585:0.5118:2,2:24.9:1:32.3:1:1:1.00535:59.9:145.25:0.5128:0:1.4 1/1:1210:1079:534,545:65,64:129,1079:0.8917:2,2:24.9:1:31.3:1:0.8528:1.03653:60:106.9:0.8916:0:1.5 +10 123242780 . G C 314 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=8.66394;LSEQ=GGTAACAGAAGCTGGTGTTA;RSEQ=AAAACTTCATTGTATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1084:557:303,254:263,260:523,557:0.5138:2,2:23.4:1:32.4:1:0.1804:1.18:59.9:184.667:0.5149:0:1.5 1/1:1149:1036:538,498:58,52:110,1036:0.9017:2,2:23.9:1:31.4:1:0.92019:1.03244:60:128.5:0.9025:0:1.5 +10 123242897 . A G 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTTTTTCCCATGCACACC;RSEQ=AAATGCAAGTGAATACTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1470:0:0,0:737,733:1470,0:0:2,0:23.8:1:30.7:1:1:0:60:104:1:0:0.2 0/1:1695:56:32,24:792,842:1634,56:0.033:2,2:24.4:1:29.8:1:0.22235:1.42:60:112:0.0334:0:1.1 +10 123243197 . G A 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59581;SOR=1.03868;LSEQ=CCAAGGACAAGGGGCTTCTA;RSEQ=AAGGAAGTTCTTACCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1476:724:376,348:401,349:750,724:0.4905:2,2:24.6:1:30.6:1:0.56627:1.06338:59.9:102.429:0.4914:0:1.1 1/0:1742:871:448,423:445,419:864,871:0.5:2,2:23.9:1:29.6:1:1:1.00278:59.9:61.214:0.4991:0:1.2 +10 123244834 . C T 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACCAGGGGCCTTCAAAAA;RSEQ=GAGATACATCAGGAGAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:192,23:215,0:0:2,0:22.4:1:31.9:1:1:0:60:52.75:1:0:0.1 0/1:224:19:15,4:169,36:205,19:0.0848:2,2:14.3:1:28.7:1:0.75389:1.25052:60:38:0.0872:0:1.2 +10 123245077 . T C 129 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=18.09767;LSEQ=AGGAGAAAGCACGGCATTAC;RSEQ=AACCCATCCACGTTGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:1:0,1:96,281:377,1:0.0026:2,0:40:0:15:0:1:0:60:0:0:0:2 0/1:415:19:7,12:123,273:396,19:0.0458:2,2:25.3:1:30.5:1:0.61669:1.29:60:38:0.0468:0:1.1 +10 123245108 . G A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2486;SOR=0;LSEQ=CGTTGCCAAAACCTAAACAC;RSEQ=CCCAGCTGAGACATAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:3:2,1:24,195:219,3:0.0135:2,2:16.3:1:21.3:1:0.03686:15.85:60:2:0.0092:0:2.7 0/0:214:0:0,0:43,171:214,0:0:2,0:21.8:1:30.6:1:1:0:59.9:29.571:1:0:0.2 +10 123245179 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52459;SOR=0;LSEQ=GGCCCTCCTGCAGTTCCTCC;RSEQ=ATGTGCTCTTTCCTGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:0,54:54,2:0.0357:1,2:16.5:1:30:1:0.03571:0:60:4:0.037:0:1 0/0:34:0:0,0:1,33:34,0:0:1,0:20.7:1:27.8:1:1:0:60:33:1:0:0.1 +10 123246612 . G A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62785;SOR=2.60278;LSEQ=AGTTGCACATCCATGAATAT;RSEQ=TTCAAGGGAAGGACTTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:13:13,0:7,0:7,13:0.65:0,1:23.7:1:29.1:1:1:0:60:26:0.65:0:1 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:27.8:1:28:1:1:0:60:10:0.8333:0:1.6 +10 123246648 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=TCCGCTCTGGCAGGGGGAGG;RSEQ=CAGCAGTTCCACCTTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:39,0:39,0:0:1,0:24.5:1:30.9:1:1:0:60:78:1:0:0.3 0/1:16:2:2,0:14,0:14,2:0.125:1,0:16.5:1:29.5:1:1:0:60:4:0.1333:0:1 +10 123246732 . TTTCTAAGGCCAGCTCCTGCACC T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01305;SOR=1.88535;LSEQ=GCCTACCATAAAATCTGTCC;RSEQ=TTCTACGAATGTGTGAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:147:80:70,10:67,0:67,80:0.5442:1,2:25.1:1:32.2:1:0.002:0:59.4:160:0.5479:0.0816:0.1 1/0:127:88:81,7:38,1:39,88:0.6929:1,2:22.4:1:31.3:1:0.43328:3.26022:59.3:176:0.6929:0.126:0.1 +10 123246744 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09031;SOR=Inf;LSEQ=ATCTGTCCTTTCTAAGGCCA;RSEQ=CTCCTGCACCTTCTACGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:73,3:76,0:0:1,0:23.8:1:33.4:1:1:0:60:75:1:0:0.1 0/1:119:3:2,1:41,3:44,3:0.0252:2,2:13:1:26.7:1:0.23891:6.3241:60:6:0.0652:0:1 +10 123247037 . C T 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28544;SOR=1.48165;LSEQ=TGTTTAAGAGCTGATATTCT;RSEQ=GGTTTTTACTAGTCAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:39:3,36:1,50:51,39:0.4333:1,2:23.3:1:30:1:0.3124:4.10:59.6:18.5:0.4253:0:2 1/0:47:25:0,25:2,20:22,25:0.5319:2,1:21.5:1:30.2:1:0.21369:0:58.6:50:0.5319:0:1.8 +10 123247044 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0.15986;LSEQ=GAGCTGATATTCTCGGTTTT;RSEQ=ACTAGTCAGTCAATAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:69:3,66:0,8:8,69:0.8961:0,1:26.3:1:32.4:1:1:0:59.8:33.5:0.8933:0:1.6 1/0:40:23:0,23:0,17:17,23:0.575:1,1:19.3:1:31.1:1:1:0:58.4:22:0.5641:0:1.9 +10 123247176 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTCCCTAGCACACAGATG;RSEQ=TCCTTGACCAGTTATTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:1,4:5,3:0.375:2,2:35:1:30.3:1:1:1.83:60:6:0.375:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:6.5:1:31:1:1:0:60:4:1:0:0 +10 123247550 . G A 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATTGTTGATATCTCTGGC;RSEQ=AGTCCAAAGTCTGCTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:707:0:0,0:357,349:706,0:0:2,0:25.1:1:31:1:1:0:59.9:87.25:0.9986:0:0.1 0/1:839:34:17,17:430,374:804,34:0.0405:2,2:26.4:1:29.7:1:0.72793:1.14954:60:68:0.0409:0:1.1 +10 123247669 . AC A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.15107;LSEQ=GAGAAATAACTAATTTCAAA;RSEQ=ACCGCCAGAACAAAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:99:19,80:21,104:125,99:0.442:2,2:22.5:1:30.6:1:0.72604:1.18:60:48.5:0.4389:0.0893:0 0/1:263:28:9,19:47,188:235,28:0.1065:2,2:16.9:1:29.2:1:0.1467:1.89:59.8:56:0.1073:0.0418:0.1 +10 123247751 . T TA 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00312;SOR=6.6064;LSEQ=ATGTTAAAAACCAGTTGCGG;RSEQ=ATACTATAAGAAATACAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:0,4:0,43:43,4:0.0851:1,0:35.3:1:32.5:1:1:0:60:8:0.087:0:0 0/1:31:12:0,12:0,19:19,12:0.3871:1,0:24.8:1:30.3:1:1:0:60:24:0.4:0.0968:0 +10 123256312 . A C 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31962;SOR=3.96795;LSEQ=CAATTCAGCAAAACATTTTT;RSEQ=GTTATTACAACCCATGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:1:0,1:7,121:128,1:0.0075:2,0:20:0:10:0:1:0:60:0:0:0:1 0/1:103:3:0,3:9,86:95,3:0.0291:2,0:22:1:29:1:1:0:60:6:0.0375:0:1.3 +10 123256346 . A T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.11322;LSEQ=ATGCTTTTTTTTTTTTTTTT;RSEQ=AAGTTTAACATACAGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:0,2:0,78:78,2:0.025:1,0:17.5:1:29.5:1:1:0:60:4:0.0253:0:1.5 0/1:36:1:0,1:2,33:35,1:0.0278:2,0:17:0:29:0:1:0:60:2:0.0286:0:3 +10 123258192 . A G 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17694;SOR=Inf;LSEQ=CAGCTACTGTTAGTTGCCAA;RSEQ=GACTTAGTTGAAACAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:14,174:188,0:0:2,0:24.6:1:32.3:1:1:0:59.9:187:1:0:0.1 0/1:137:2:1,1:10,125:135,2:0.0146:2,2:5.5:1:29.5:1:0.15468:11.97:60:4:0.0146:0:1 +10 123263118 . AT A 61 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.34363;SOR=0.24357;LSEQ=AGCTCTGCTTTCAAGGAGTT;RSEQ=TTTTTTTTTTAAATCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:16,0:16,4:0.2:1,0:12.8:1:30.6:1:1:0:60:8:0.2:0.05:0 0/1:18:1:1,0:16,1:17,1:0.0556:1,0:21:0:29:0:1:0:60:2:0.0556:0:4 +10 123263850 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGGATCCCCTCTCAGAC;RSEQ=ACCCGGATCATGGATCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 123274653 . A G 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTACCTGTCTCCGCAGGGGG;RSEQ=TACGTTTGGTCAGCTTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:37:23,14:341,160:501,37:0.0688:2,2:25.9:1:32:1:0.46971:1.29658:60:74:0.0703:0:1.1 0/0:673:0:0,0:410,262:672,0:0:2,0:24:1:28.5:1:1:0:59.9:28.217:0.9985:0:0.2 +10 123276652 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50011;SOR=Inf;LSEQ=TGATCATAAATGTGAGTGTG;RSEQ=GATCTCACTGTGTGTGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:69,6:75,0:0:2,0:24.1:1:32:1:1:0:59.9:150:1:0:0.1 0/1:88:2:1,1:79,7:86,2:0.0227:2,2:8:1:26.5:1:0.1745:10.62357:60:4:0.023:0:1 +10 123276689 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5055;SOR=Inf;LSEQ=AATTTCCAAGGCAGTTTTCT;RSEQ=ATCCCTGAGGGATCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:126,32:158,0:0:2,0:22.4:1:30.5:1:1:0:59.9:157:1:0:0.1 0/1:200:2:1,1:143,55:198,2:0.01:2,2:23:1:32.5:1:0.48261:2.58568:60:4:0.01:0:1 +10 123276696 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25592;SOR=Inf;LSEQ=AAGGCAGTTTTCTTATCCCT;RSEQ=AGGGATCATTTTTAACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:142,39:181,0:0:2,0:22.8:1:32.4:1:1:0:59.8:180:1:0:0.1 0/1:222:3:1,2:152,67:219,3:0.0135:2,2:14:1:28.3:1:0.22865:4.50281:60:6:0.0138:0:1 +10 123277742 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAACTCATAAGGATCAAC;RSEQ=ATGCAACCAAAGAAATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:47.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 123278438 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24731;SOR=Inf;LSEQ=CACACCGCAAGAAAACAAAC;RSEQ=CCATTACGTCTAAACAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:1,139:140,0:0:1,0:23.9:1:30.5:1:1:0:60:69:1:0:0.1 0/1:139:2:1,1:9,128:137,2:0.0144:2,2:8:1:27.5:1:0.13919:13.54:60:4:0.015:0:1 +10 123279179 . C T 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGGGGGACAGAGTATCA;RSEQ=GATCTCTACTTTTATAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:0,7:1:0,2:18.3:1:28.4:1:1:0:60:6:1:0:1.4 1/1:2:2:1,1:0,0:0,2:1:0,2:8:1:28.5:1:1:0:60:4:1:0:1 +10 123279686 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.49888;SOR=Inf;LSEQ=GCCGGTGAGGCGATCGCTCT;RSEQ=GTGGAGAGAGGGAAGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:24,168:192,0:0:2,0:25.6:1:31.4:1:1:0:59.9:47:1:0:0.4 0/1:200:2:1,1:34,164:198,2:0.01:2,2:45:0:30:1:0.3201:4.77:60:4:0.0102:0:1 +10 123279745 . C T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00281;SOR=0;LSEQ=ATGAGAGACCAATAAATAAG;RSEQ=TGTGTTGTCCAGAGGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:63:5,58:0,0:0,63:1:0,2:19.6:1:30.5:1:1:0:59.7:126:1:0:1.4 1/1:51:44:3,41:0,7:7,44:0.8627:0,2:21.6:1:29.3:1:1:0:60:88:0.8627:0:1.1 +10 123279795 . C T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01553;LSEQ=CATGCCAGAAAAGCCTCAAG;RSEQ=CTGCTGGCTGACACCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:23:0,23:0,2:2,23:0.92:0,1:21.5:1:29.7:1:1:0:60:10.5:0.913:0:1.9 0/1:16:2:0,2:0,14:14,2:0.125:1,0:11:1:26:1:1:0:60:4:0.1333:0:2 +10 123279866 . C T 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=ACGACTTCAAAGGAGACTGC;RSEQ=GGAGCGCGACCCTTGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:16.7:1:31:1:1:0:58.3:12:1:0:1.8 1/1:5:4:0,4:0,1:1,4:0.8:0,0:22.3:1:31.5:1:1:0:60:8:0.8:0:1.3 +10 123298158 . T C 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=55.08122;LSEQ=GACCCGTATTCATTCTCCAC;RSEQ=ACACAGGTATAATTTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:45:21,24:302,344:646,45:0.065:2,2:24.5:1:31.8:1:1:1.00332:60:90:0.066:0:1 1/0:863:685:313,372:79,95:174,685:0.7937:2,2:24.8:1:31:1:1:1.01:60:170.25:0.7965:0:1.2 +10 123310501 . G T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAACACTTTGGGAGGCC;RSEQ=AGGCAGGCGGATCACGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:6:0:32:1:0.33333:0:52.5:4:0.3333:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:5.5:1:30:1:1:0:52.5:4:1:0:1.5 +10 123310505 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=AACACTTTGGGAGGCCGAGG;RSEQ=AGGCGGATCACGAGGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:6,0:0:2,0:14.7:1:33.3:1:1:0:46.5:12:1:0:0.8 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:31:1:1:0:52.5:4:1:0:1.5 +10 123310664 . AT GC 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02154;SOR=Inf;LSEQ=GAATCGCTTGAACCTGGGAG;RSEQ=GGAGGTTGCAGTGAACCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:60,0:0:1,0:25.4:1:30.6:1:1:0:36.8:29:1:0:0 0/1:54:5:5,0:49,0:49,5:0.0926:1,0:12.8:1:30.2:1:1:0:35.6:10:0.0943:0.037:0.6 +10 123310732 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26707;SOR=Inf;LSEQ=CGACAGAGCGAGACTCCATC;RSEQ=CAAAAAAAAAATGTAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:171,38:209,0:0:2,0:21.1:1:29.8:1:1:0:56.5:68.667:1:0:0.1 0/1:287:3:2,1:223,60:283,3:0.0105:2,2:31.7:1:29.3:1:0.51448:1.85359:58:6:0.0106:0:1.3 +10 123310733 . CA C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.67916;SOR=0.84612;LSEQ=GACAGAGCGAGACTCCATCG;RSEQ=AAAAAAAAATGTAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:11:11,0:170,44:214,11:0.0489:2,0:27.6:1:33.4:1:0.12785:0:54.8:22:0.0493:0.0089:0 0/1:312:13:11,2:229,69:298,13:0.0417:2,2:16.6:1:31.9:1:0.73957:1.65:58.2:26:0.0418:0.0096:0.5 +10 123310871 . A G 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGCCACCGCATGGTTGGC;RSEQ=TTGGGTTCCCCCCGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:706:0:0,0:339,367:706,0:0:2,0:24.6:1:30.7:1:1:0:59.9:63.182:1:0:0.2 0/1:956:61:27,34:440,453:893,61:0.0638:2,2:26.6:1:30.3:1:0.5087:1.22286:60:60:0.0638:0:1.1 +10 123311192 . GA G 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATGTCTACCAACAGGAA;RSEQ=AAAAAAAAAAAGTGTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:37:1:31.7:1:1:0:60:6:0.375:0:0.3 0/0:2:0:0,0:0,1:1,0:0:0,0:23:0:32:0:1:0:60:2:0.5:0:0 +10 123323962 . A G 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAGACAGGTGACAGGCAG;RSEQ=ACTTCCCTCCATGCTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:0:0,0:342,190:532,0:0:2,0:25.4:1:30.3:1:1:0:60:87.667:1:0:0.1 0/1:658:80:49,31:354,223:577,80:0.1216:2,2:23.7:1:29.9:1:1:1.0043:59.9:39:0.1204:0:1.2 +10 123324186 . C A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51432;SOR=0;LSEQ=GACCTTCTCCATAGCAAAGT;RSEQ=AACAACCCAGGAACCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:4,93:97,2:0.0202:1,0:33:0:33:0:1:0:60:4:0.0206:0:1 0/0:68:0:0,0:3,65:68,0:0:1,0:21.8:1:31.8:1:1:0:60:136:1:0:0.1 +10 123324410 . C T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTACCAATTGTGTAGCAC;RSEQ=CAAAGACTCTTTTTCCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:1,3:0.75:0,2:45.7:1:30.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 123325169 . C A 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCTAGCGACTCCCCTGG;RSEQ=GCAGCCACGTACACTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:0:0,0:206,340:546,0:0:2,0:23.6:1:30.8:1:1:0:59.9:135.5:0.9982:0:0.1 0/1:663:36:17,19:258,368:626,36:0.0543:2,2:19.1:1:29.6:1:0.49104:1.28:60:35:0.0532:0:1.2 +10 123325267 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21468;SOR=Inf;LSEQ=AGACAGATGGGAAGGAGGGA;RSEQ=AGGAGAGAACGTCCAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:23,148:171,0:0:2,0:21.3:1:32.7:1:1:0:59.9:170:0.9942:0:0 0/1:149:2:1,1:23,124:147,2:0.0134:2,2:30:1:27:1:0.29712:5.30:60:4:0.0135:0:1 +10 123325397 . G C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00399;SOR=Inf;LSEQ=AAGTCAGGAAGTATCTGGAA;RSEQ=AGCAACCAGAGGATACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:0,19:19,0:0:1,0:24.9:1:32.3:1:1:0:60:38:1:0:0 1/0:8:4:0,4:0,3:3,4:0.5:0,0:17:1:30:1:1:0:60:8:0.5:0:1.3 +10 123353869 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGCAAGTTAAAAATGCT;RSEQ=GGGTTGGCATAACCAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:25:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 123488385 . C T 119 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGTGGTTGTGGGGGGATGG;RSEQ=GGGGGACTCCAGCACGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:10,8:0,0:0,18:1:0,2:24.2:1:28.7:1:1:0:60:17:1:0:1.9 0/1:19:4:2,2:9,6:15,4:0.2105:2,2:33.5:1:28.5:1:1:1.4677:60:8:0.2222:0:1.8 +10 123488416 . A G 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=AGCACGCTGCCTCCTTCTTA;RSEQ=CCAAGCTGGCCACTGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:4,6:4,5:9,10:0.5263:2,2:30.3:1:30.8:1:1:1.18851:60:9:0.5:0:2.4 0/0:22:0:0,0:12,10:22,0:0:2,0:26:1:27.4:1:1:0:58.2:21:1:0:1 +10 123488457 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTGATGCCGAGTCCAT;RSEQ=TGCCTTTCACCTGGTGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:6,9:0,0:0,15:1:0,2:20.9:1:33.1:1:1:0:60:30:1:0:2.1 1/1:14:14:4,10:0,0:0,14:1:0,2:19:1:31.4:1:1:0:60:28:1:0:1.4 +10 124402897 . G T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGACCCCCCCACGCCGA;RSEQ=AAGAGGAGCCTCGGTAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 124403514 . TGCTGTGCTGCTGTGTTGCTGTGCG T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=2.000;MSILEN=1;SSF=0.0089;SOR=Inf;LSEQ=AGAACAGGGAGTGCATCTGC;RSEQ=GCTGTGCTGCTGTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:21,0:0:2,0:32.4:1:32.4:1:1:0:60:42:1:0:0.3 0/1:22:7:4,3:9,6:15,7:0.3182:2,2:42.3:1:32.1:1:1:1.11896:55.7:14:0.3182:0:0.9 +10 124403561 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.52205;SOR=Inf;LSEQ=TGTGCTGCTGTGTTGCTGTG;RSEQ=GGCTGTGATGCTGCGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:14,0:0:2,0:22.4:1:27.7:1:1:0:55.8:3.667:1:0:0.6 0/1:24:2:1,1:8,14:22,2:0.0833:2,2:20:1:27.5:1:1:1.71:55:4:0.087:0:1 +10 124403644 . C CTGTGCGGCTGTGCGGT 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=2.000;MSILEN=1;SSF=0.50893;SOR=Inf;LSEQ=GCTGCTGTCATGCTGTGATG;RSEQ=TGTGCGGCTGTGCGGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:21.2:1:31.4:1:1:0:60:10:1:0:0 0/1:11:3:0,3:5,3:8,3:0.2727:2,0:22.3:1:22.5:1:0.18182:0:28:6:0.3:0.2727:2 +10 124403657 . CG TT 23 v3;pSTD;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=4.000;MSILEN=8;SSF=0.5;SOR=Inf;LSEQ=TGTGATGCTGTGCGGCTGTG;RSEQ=GCTGTGCGGCTGTGCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:16.2:1:27.3:1:1:0:60:5:1:0:0 0/1:10:2:0,2:5,2:7,2:0.2:2,0:14:0:23.3:1:0.16667:0:31:4:0.2222:0:1 +10 124403674 . G T 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=4.000;MSILEN=8;SSF=0.00049;SOR=0;LSEQ=GTGCGGCTGTGCGGCTGTGC;RSEQ=GCTGTGCTGCTGTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:3,4:2,1:3,7:0.7:2,2:11:1:30.9:1:1:2.41422:60:14:0.7:0:4.1 0/0:13:0:0,0:6,7:13,0:0:2,0:32.4:1:28.6:1:1:0:51.2:12:1:0:0.5 +10 124403681 . C T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=3;SSF=0.00022;SOR=0;LSEQ=TGTGCGGCTGTGCGGCTGTG;RSEQ=TGCTGTGTTGCTGTGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:3,5:2,1:3,8:0.7273:2,2:16.1:1:29.6:1:0.54545:2.97405:60:16:0.8:0:4.1 0/0:13:0:0,0:6,7:13,0:0:2,0:33.5:1:31.6:1:1:0:51.2:26:1:0:0.5 +10 124403689 . T C 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=15;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=TGTGCGGCTGTGCTGCTGTG;RSEQ=TGCTGTGCGGCTGTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:4,5:2,1:3,9:0.75:2,2:22.3:1:33.2:1:1:2.31595:60:18:0.8182:0:4 0/0:13:0:0,0:6,7:13,0:0:2,0:23:0:14:0:1:0:60:0:0:0:1 +10 124403716 . T G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00483;SOR=0.06982;LSEQ=GCGGCTGTGCTGCTGTGTTG;RSEQ=GGGCATGGACGAGGGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:4,6:1,2:3,10:0.7692:2,2:40.3:1:31.1:1:1:1.30:60:20:0.7692:0:3.8 0/1:12:2:0,2:5,5:10,2:0.1667:2,0:22:1:32:0:0.4697:0:60:4:0.1667:0:2 +10 124403778 . G A 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=GGATTTCTGGCCCAGTCTGG;RSEQ=GCTAGGTCAACAGATGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:2,3:0.6:0,2:8.7:1:30.7:1:1:0:60:6:0.6:0:3 1/0:4:2:0,2:0,2:2,2:0.5:0,0:17:1:32:0:1:0:60:4:0.5:0:2 +10 124896966 . C T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19548;SOR=0;LSEQ=CCGGCCTGGCCGCGTCCCTG;RSEQ=ACCTCACCGAGACGCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:43,30:73,2:0.0267:2,2:38:0:30.5:1:1:1.4263:46:4:0.0267:0:1.5 0/0:94:0:0,0:54,40:94,0:0:2,0:23.6:1:31.1:1:1:0:55.4:188:1:0:0.2 +10 124896975 . G T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.65628;LSEQ=CCGCGTCCCTGCACCTCACC;RSEQ=AGACGCAGGTCAAGATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:0,1:49,39:88,1:0.0112:2,0:1:0:23:0:0.44944:0:44:2:0.0112:0:1 0/1:108:2:1,1:61,45:106,2:0.0185:2,2:18.5:1:25.5:1:1:1.35167:50:4:0.0187:0:2 +10 124897022 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50827;SOR=Inf;LSEQ=AACCGCCGCAACAAGTGGAA;RSEQ=CGGCAGCTGGCGGCGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:32,47:79,0:0:2,0:28.1:1:32.5:1:1:0:56.4:158:0.9753:0:0.1 0/1:109:2:1,1:44,63:107,2:0.0183:2,2:20:1:27.5:1:1:1.43:60:4:0.0185:0:1.5 +10 124897048 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49652;SOR=Inf;LSEQ=GCTGGCGGCGGAGCTGGAGG;RSEQ=GGCCAACCTGAGCCATGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:18,48:66,0:0:2,0:21.8:1:30.3:1:1:0:58.3:65:1:0:0.1 0/1:69:2:1,1:21,46:67,2:0.029:2,2:34.5:1:31.5:1:0.53922:2.16:54:4:0.029:0:1.5 +10 126423706 . G A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01014;SOR=0.16719;LSEQ=CTCCCCCAACGTGAGAGGAA;RSEQ=AACAAAAAACAAAGATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:3,8:2,5:7,11:0.6111:2,2:17.8:1:30.7:1:1:1.06284:60:22:0.6111:0:1.4 0/1:25:5:2,3:9,11:20,5:0.2:2,2:16.4:1:28.8:1:1:1.21734:60:10:0.2:0:1 +10 126553456 . G C 92 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02424;SOR=0;LSEQ=CTGCTTGTCTGAGCCTCGGT;RSEQ=TCTCTTGCAGTCCAAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:0,7:1:0,2:20.9:1:33.1:1:1:0:60:14:1:0:1.1 0/1:4:1:0,1:0,3:3,1:0.25:0,0:31:0:33:0:1:0:60:2:0.25:0:1 +10 126556006 . G A 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62254;SOR=1.10743;LSEQ=CTGGTGTGATTCCATCCTGC;RSEQ=GGGCTGTTCTCTTGAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:171:90:62,28:65,16:81,90:0.5263:2,2:23.5:1:30.7:1:0.11489:1.82823:58.9:29:0.537:0:2.2 1/0:261:144:101,43:77,39:116,144:0.5517:2,2:20.9:1:28.9:1:0.59148:1.19:58.9:19.571:0.5502:0:2.1 +10 126556015 . C G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.85438;SOR=1.04964;LSEQ=TTCCATCCTGCGGGGCTGTT;RSEQ=TCTTGAGCAGTGGTCGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:191:101:62,39:65,21:86,101:0.5288:2,2:27.7:1:31.1:1:0.0422:1.9401:58.7:11.625:0.5225:0:2 1/0:318:172:110,62:87,58:145,172:0.5409:2,2:22.5:1:30.8:1:0.48738:1.18:59.1:27.667:0.5533:0:1.9 +10 126556100 . G A 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56804;SOR=0.33647;LSEQ=ATGGAAGATTCGATGGACAT;RSEQ=CACATGAGTCCTCTGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:59,130:189,2:0.0104:2,2:8:1:25:1:0.53072:2.19:60:4:0.0106:0:1 0/0:284:1:1,0:94,189:283,1:0.0035:2,0:1:0:23:0:0.33451:0:60:2:0.0036:0:1 +10 126556118 . G A 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.24624;LSEQ=ATGCACATGAGTCCTCTGAG;RSEQ=CCCCAGAACTATCTTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:40,103:143,2:0.0138:2,2:11.5:1:25.5:1:0.48697:2.56:56:4:0.014:0:1 0/1:175:3:3,0:48,124:172,3:0.0171:2,0:1:0:20.7:1:0.02372:0:60:2:0.0117:0:1 +10 126556124 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2146;SOR=0;LSEQ=ATGAGTCCTCTGAGGCCCCA;RSEQ=AACTATCTTTTCAGTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:36,98:134,2:0.0147:2,2:9.5:1:32.5:1:0.47157:2.70:60:4:0.0147:0:1 0/0:157:0:0,0:42,115:157,0:0:2,0:24.9:1:30.8:1:1:0:56.5:77.5:1:0:0.1 +10 126556186 . A G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11573;SOR=Inf;LSEQ=TCACTTTAAGGTGGATAATG;RSEQ=TGAAAATGAGCACCAGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:34,46:80,0:0:2,0:22.6:1:31:1:1:0:45.8:79:0.9875:0:0.1 0/1:78:3:1,2:32,43:75,3:0.0385:2,2:21.3:1:32.7:1:1:1.48109:60:6:0.039:0:1 +10 126556239 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24191;SOR=Inf;LSEQ=TCAGTTCATGGGCTGGTGCA;RSEQ=AGGATGATTGCACATTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:43,35:78,0:0:2,0:23.7:1:32.9:1:1:0:55:156:1:0:0.2 0/1:76:2:1,1:39,35:74,2:0.0263:2,2:9.5:1:26.5:1:1:1.1127:49.5:4:0.0267:0:1 +10 126556276 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24476;SOR=Inf;LSEQ=GTTGAAGCAGAGGCAGTGAA;RSEQ=TAGAAGGCGGTCCAATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:44,28:72,0:0:2,0:24.3:1:30.4:1:1:0:59.5:35:1:0:0.1 0/1:71:2:1,1:47,22:69,2:0.0282:2,2:17:1:29:1:0.54608:2.11156:60:4:0.0294:0:1 +10 126556320 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21654;SOR=0;LSEQ=ACACTGGCAACTTTGAAAAT;RSEQ=TCTGTTTAGTCAACGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:76,40:116,2:0.0169:2,2:26:1:30.5:1:1:1.88906:52:4:0.0174:0:1 0/0:135:0:0,0:83,52:135,0:0:2,0:23.7:1:31.2:1:1:0:57.1:44:1:0:0.2 +10 126556374 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21071;SOR=0;LSEQ=GAAATCACACCACCAGTGGT;RSEQ=TTACAGTTGTAGTGTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:100,75:175,2:0.0113:2,2:16:1:29.5:1:1:1.33112:40.5:4:0.0113:0:1 0/0:208:0:0,0:117,90:207,0:0:2,0:25.7:1:30.8:1:1:0:44.3:68:0.9951:0:0.1 +10 126556376 . TA T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.25426;SOR=Inf;LSEQ=AATCACACCACCAGTGGTCT;RSEQ=CAGTTGTAGTGTGGCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:100,81:181,0:0:2,0:26.4:1:28.8:1:1:0:45.1:59.333:1:0:0.1 0/1:217:3:1,2:116,98:214,3:0.0138:2,2:23.7:1:28.3:1:0.59597:2.3582:35:6:0.014:0.0046:0.3 +10 126556402 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50026;SOR=Inf;LSEQ=TGTAGTGTGGCTCAGGGCCA;RSEQ=TGCATATTAGTGGACAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:82,78:160,0:0:2,0:27.1:1:32.7:1:1:0:40.5:320:1:0:0.1 0/1:180:2:1,1:92,86:178,2:0.0111:2,2:9:1:31.5:1:1:1.06933:50:4:0.0112:0:1 +10 126556562 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22583;SOR=0;LSEQ=AGTAAAACTTGCTGCTGATG;RSEQ=AGATGATGATGATCATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:37,43:80,2:0.0244:2,2:31:1:30.5:1:1:1.16:52.5:4:0.0247:0:1 0/0:90:0:0,0:32,58:90,0:0:2,0:25.2:1:30:1:1:0:52.7:180:1:0:0.1 +10 126556573 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50083;SOR=Inf;LSEQ=CTGCTGATGAAGATGATGAT;RSEQ=ATCATGATGAAGATGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:34,37:71,0:0:2,0:26.6:1:32:1:1:0:53.9:142:1:0:0.1 0/1:85:2:1,1:29,54:83,2:0.0235:2,2:24:1:27.5:1:1:1.85:55.5:4:0.0235:0:1 +10 126556614 . TGAA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=GATGATGAAGATGAAGATGA;RSEQ=GAAGATGATGATGAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:13,25:38,2:0.05:2,2:33:1:31:1:1:1.89:60:4:0.05:0:0.5 0/0:65:0:0,0:36,29:65,0:0:2,0:23.3:1:31.2:1:1:0:60:64:1:0:0.1 +10 126556646 . G GTGA 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.67278;SOR=1.20879;LSEQ=TGATGAAGATGAAGATGGTG;RSEQ=TGATGATGAAGAAGATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:23:14,9:5,10:15,23:0.6053:2,2:22.8:1:32.1:1:0.18367:3.02:59.1:46:0.6216:0.1316:0 1/0:60:39:27,12:11,10:21,39:0.65:2,2:27.3:1:29.6:1:0.26335:2.02:59.9:78:0.65:0.1333:0.1 +10 126556677 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31142;SOR=Inf;LSEQ=GAAGATGATGATGAAGATGA;RSEQ=GAGGAAACTGAAGAAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:22,17:39,0:0:2,0:25.7:1:30.5:1:1:0:58.5:12:1:0:0.1 0/1:88:4:3,1:56,28:84,4:0.0455:2,2:16.3:1:30.3:1:1:1.49:42:8:0.0455:0:1.3 +10 126556741 . C T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5221;SOR=Inf;LSEQ=ATACTTCAGCCAAAAATGCA;RSEQ=AAAAGTCAAATCAGAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:46,37:83,0:0:2,0:28.1:1:32:1:1:0:31.8:40.5:1:0:0.9 0/1:130:2:1,1:71,57:128,2:0.0154:2,2:8:1:24.5:1:1:1.24349:48:4:0.0156:0:1.5 +10 126556775 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12422;SOR=0;LSEQ=GAATGGAAAAGACTCAAAAC;RSEQ=GTCAACACCAAGATCAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:55,48:103,2:0.019:2,2:30.5:1:30.5:1:1:1.14434:31:4:0.0192:0:2 0/0:192:0:0,0:108,84:192,0:0:2,0:22.2:1:29.5:1:1:0:37.8:63:1:0:1 +10 126556782 . A G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00288;SOR=0;LSEQ=AAAGACTCAAAACCGTCAAC;RSEQ=CCAAGATCAAAAAGACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:108:108:58,50:0,0:0,108:1:0,2:24:1:31:1:1:0:34.9:216:1:0:1.1 1/1:200:186:105,81:6,7:13,186:0.93:2,2:24.2:1:29.9:1:0.56768:1.51:40:61:0.9289:0:1.1 +10 126556846 . C A 31 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12146;SOR=0;LSEQ=ACTCCTAAAATACCAAAGAC;RSEQ=TAGTTCTGTAGAAGATATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:44,54:98,2:0.02:2,2:5:0:31:1:1:1.22:24:4:0.0202:0:2.5 0/0:186:0:0,0:84,102:186,0:0:2,0:24.7:1:30.3:1:1:0:56.1:45.5:1:0:0.6 +10 126558870 . A T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGGAGGAAATGCCTGTG;RSEQ=AGGATAAGGAGAGGAAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 127191022 . C T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08071;SOR=6.25561;LSEQ=CCCAGGCTGGAGTGCAGTGG;RSEQ=GCAGGCACACATATTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:1:0,1:264,103:367,1:0.0027:2,0:1:0:26:0:0.28261:0:60:2:0.0028:0:1 0/1:238:4:3,1:170,64:234,4:0.0168:2,2:23:1:29.5:1:1:1.13:60:8:0.0169:0:1.5 +10 127191122 . T C 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17646;SOR=0.84983;LSEQ=CTGTGCCCCTGCCATGCTGC;RSEQ=TAGTAATGGGGATGCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:710:454:202,252:121,135:256,454:0.6394:2,2:24.3:1:31.9:1:0.48113:1.11797:60:74.667:0.6391:0:1.1 1/0:544:327:149,178:98,119:217,327:0.6011:2,2:24.4:1:30.8:1:0.93019:1.02:59.9:162.5:0.6052:0:1.2 +10 127191232 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14632;SOR=Inf;LSEQ=GATAATTGATGTTCTCCAGA;RSEQ=TCTTCTCTTTCTTGCCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:19,140:159,0:0:2,0:23.5:1:30.2:1:1:0:60:38.75:1:0:0.1 0/1:99:2:1,1:15,82:97,2:0.0202:2,2:24:0:31.5:1:0.2985:5.33:60:4:0.0204:0:1.5 +10 127191254 . GTT G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=9.000;MSILEN=1;SSF=0.72646;SOR=0.83736;LSEQ=CTTCTCTTTCTTGCCATACA;RSEQ=TTTTTTTAACTTCAATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:37:1,36:8,60:68,37:0.3426:2,1:26.9:1:33:1:0.1549:4.74634:59.7:74:0.3491:0.0093:0.1 0/1:56:17:0,17:3,36:39,17:0.3036:2,1:24.5:1:31.7:1:0.54556:0:60:34:0.3091:0.0179:0.1 +10 127191355 . T C 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=ATTTAATTAATTAATTTATT;RSEQ=GTTTTTGAGACGGAGTTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:0,7:7,5:0.4167:0,2:5:1:30:1:0.41667:0:60:10:0.4167:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:24:1:28:1:1:0:60:4:1:0:1 +10 128270435 . G T 48 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGACTGATTCGGACAG;RSEQ=TGCTGTGGAAGGAGACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:15.3:1:30.3:1:1:0:56.3:6:1:0:1.7 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:28:1:1:0:60:4:1:0:2.5 +10 128270440 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACTGATTCGGACAGGTGCT;RSEQ=TGGAAGGAGACCTGGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:27:1:33:1:1:0:60:4:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:27.5:1:1:0:60:4:1:0:2.5 +10 128270475 . A G 28 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCGCCTTACTGCTGCAC;RSEQ=GTGGCAGCATCTCAGTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:35.5:1:28:1:1:0:60:4:1:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:4:0:29:0:1:0:60:2:1:0:3 +10 128270643 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49973;SOR=0;LSEQ=ATTCCCGGCATCCACAGCAG;RSEQ=TCCTCTCCCAGGTCACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:136,50:186,2:0.0106:2,2:8:1:28:1:0.47002:2.70309:60:4:0.0108:0:1.5 0/0:171:0:0,0:129,42:171,0:0:2,0:21.1:1:31.4:1:1:0:60:56:1:0:0.5 +10 128270664 . C T 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20168;SOR=4.33151;LSEQ=TCCTCTCCCAGGTCACCCTG;RSEQ=AGCTGCTGTGGGACTTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:161,92:253,1:0.0039:2,0:10:0:32:0:1:0:60:2:0.004:0:1 0/1:237:4:1,3:152,81:233,4:0.0169:2,2:12.8:1:24.3:1:0.12881:5.58754:60:8:0.0172:0:1.5 +10 128270699 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=1.87443;LSEQ=TTGTTCCTGGGGTTAGCCTA;RSEQ=AGTCTGCTGCCATGGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:148:77,71:125,89:214,148:0.4088:2,2:26.8:1:32.2:1:0.23817:1.29411:59.9:147:0.4118:0:1.2 1/0:363:205:111,94:90,68:158,205:0.5647:2,2:26.5:1:30.9:1:0.59655:1.12047:59.9:101.5:0.5718:0:1.2 +10 128270786 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24923;SOR=0;LSEQ=TGTGGTATGTAACAAAGAGC;RSEQ=ATGGGTAGTACAGCACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:3:2,1:53,127:180,3:0.0164:2,2:10.3:1:30.7:1:0.2153:4.75:60:6:0.0169:0:1 0/0:168:0:0,0:50,118:168,0:0:2,0:24.2:1:30.7:1:1:0:60:167:1:0:0.3 +10 128271072 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGACACCAGCGTTCACTG;RSEQ=GAAAATGTCGGCTGTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:30.5:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 129140160 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAGTCAGGGGCCCATCT;RSEQ=GCATACGACCCATGTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,1:5,2:0.2857:2,0:18.5:1:34.5:1:1:0:60:4:0.2857:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:32:0:29:0:1:0:60:2:1:0:0 +10 129140353 . TTGTTGTTGCTGCTGCTGCTGCTGC T 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=6.000;MSILEN=3;SSF=0.01904;SOR=Inf;LSEQ=TGCTGCTGTTGCTGTTGCTG;RSEQ=TGTTGTTGTTAAAGGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:63,63:126,0:0:2,0:27.6:1:30.1:1:1:0:59.6:30.5:1:0:0.1 0/1:161:7:3,4:73,80:153,7:0.0435:2,2:28.4:1:29.9:1:1:1.21519:55.3:14:0.0446:0.0062:0.3 +10 129140368 . C T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.2204;SOR=0;LSEQ=TGCTGTTGTTGTTGCTGCTG;RSEQ=TGCTGCTGCTGTTGTTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:52,58:110,2:0.0179:2,2:29:0:29:1:1:1.11:60:4:0.0187:0:2.5 0/0:126:0:0,0:53,67:120,0:0:2,0:25.8:1:31:1:1:0:58.6:29:1:0:0.3 +10 129140429 . C A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24051;SOR=0;LSEQ=AGATCTATTGTGAGTCCTCG;RSEQ=AGGCATGGGTCCTATTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:2,1:7,30:37,3:0.075:2,2:14:1:28.3:1:0.12146:7.95:60:6:0.0769:0:1 0/0:39:0:0,0:6,33:39,0:0:2,0:19.9:1:30.8:1:1:0:59.9:38:1:0:0.1 +10 129140507 . G A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13484;LSEQ=TGCAGCCAGTGATTCCTGCC;RSEQ=GTGCTGTGGCAAGGCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:8,7:0.4667:0,0:26.6:1:33.9:1:1:0:60:14:0.4667:0:1 1/0:4:2:0,2:0,2:2,2:0.5:0,0:15.5:1:32:0:1:0:60:4:0.5:0:1 +10 129534864 . A C 44 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCCTTCCGGGTTGAGGG;RSEQ=GCGAGGACTCCAGACGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:19:0:34:0:1:0:60:2:1:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:18.3:1:28:1:1:0:60:6:1:0:1 +10 129536033 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.52465;SOR=0;LSEQ=GCTTCAAGAAGGTGCCCCGC;RSEQ=ACGAGGACGACCCAGGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:11,32:43,2:0.0444:2,2:24.5:1:32:0:0.46667:2.83:24:4:0.0455:0:1 0/0:27:0:0,0:8,19:27,0:0:2,0:29:1:29.9:1:1:0:38.8:54:1:0:0.1 +10 129536050 . T A 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53247;SOR=0;LSEQ=CGCGACGAGGACGACCCAGG;RSEQ=AACAGCGGCGCGCCGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:9,25:34,2:0.0556:2,2:38:0:29:1:0.48413:2.69:54:4:0.0556:0:1 0/0:20:0:0,0:4,16:20,0:0:2,0:32.3:1:27.8:1:1:0:46.1:40:1:0:0.1 +10 129878570 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11077;SOR=Inf;LSEQ=TACAATTTTAAAGCCTGTTA;RSEQ=AATGCATCCTTTTTACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:17,0:0:2,0:23.6:1:31.5:1:1:0:60:34:1:0:0 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:20.5:1:31:0:1:2.23609:60:4:0.25:0:1 +10 130262786 . C T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCCTCCTCCTCCACCATC;RSEQ=TCCCCTCTAGACTTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:26:1:30.5:1:1:0:22:4:1:0:0.5 0/1:14:2:0,2:5,7:12,2:0.1429:2,0:38:1:30:1:0.50549:0:22.5:4:0.1538:0:2.5 +10 130262813 . CA C 76 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=1.11808;LSEQ=CTAGACTTCTCCTCCTCCTC;RSEQ=CCATCCTCCCCTCTAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:27.5:1:31:1:1:1.73:23:4:0.4:0:1 0/1:14:6:2,4:3,5:8,6:0.4286:2,2:31.3:1:29.7:1:1:1.18452:27.8:12:0.4615:0:0.2 +10 130262890 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTCCTCCCCATCCTCC;RSEQ=GCCTTCCCCTCCTCATTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:29:1:1:0:46.5:4:1:0:1 +10 132314567 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTCTCTGGGCTGAGGAA;RSEQ=ATGAAGGTGAAATCCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:13.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +10 132314713 . G A 84 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTAAGTTGACATAGCTT;RSEQ=TGCATCAGTTTGGGCCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:23:1:29.3:1:1:0:60:8:1:0:1 1/1:8:8:8,0:0,0:0,8:1:0,0:23:1:28:1:1:0:60:16:1:0:1 +10 132314843 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19444;SOR=Inf;LSEQ=TCAGCGTTCCCTCCAGGAAG;RSEQ=CACCAGGGCTCTCCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:21,24:45,0:0:2,0:26.5:1:31.3:1:1:0:60:44:1:0:0.2 0/1:36:2:1,1:14,20:34,2:0.0556:2,2:32.5:1:29.5:1:1:1.41:60:4:0.0556:0:1 +10 132314861 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGCCACCAGGGCTCTCCTTC;RSEQ=TCCCCTCCATGAAAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:12,16:28,2:0.0667:2,2:18.5:1:30:1:1:1.32:60:4:0.0667:0:2 0/0:14:0:0,0:6,8:14,0:0:2,0:24.7:1:30.1:1:1:0:60:28:1:0:0.3 +10 133191478 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATGGCTGTGTTCCTTCCTGC;RSEQ=GCAAATGACTGTGGAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:6:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:28:1:1:0:60:4:1:0:1 +10 133191575 . C T 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57576;SOR=2.74155;LSEQ=TCATGGAGATCCTTTGGGCA;RSEQ=CCCTAATGCAATTCTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:32.3:1:31.3:1:1:0:60:8:0.5:0:1 1/0:4:3:3,0:1,0:1,3:0.75:0,0:18:1:32:1:1:0:60:6:0.75:0:2 +10 133191600 . C T 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=AATGCAATTCTCCCCATTTC;RSEQ=GAAGCCAAAGTGATCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:26.2:1:31.3:1:1:0:60:24:1:0:0.3 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:18:1:31.6:1:1:0:60:14:0.7778:0:1.4 +10 133191708 . T C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=16.78459;LSEQ=CCCAAGGCCCTGCAGGTCCA;RSEQ=CCCCGCAGGTCTCTGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:9:7,2:91,9:100,9:0.0826:2,2:21.9:1:31.8:1:0.22487:2.84982:60:18:0.0826:0:1 1/0:114:69:47,22:34,11:45,69:0.6053:2,2:19.2:1:31:1:0.52662:1.44219:60:138:0.6053:0:1.1 +10 133191723 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24154;SOR=Inf;LSEQ=GTCCATCCCCGCAGGTCTCT;RSEQ=CCACCTCAGACCTGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:128,36:164,0:0:2,0:22.1:1:32.3:1:1:0:59.8:81:1:0:0.1 0/1:159:2:1,1:104,53:157,2:0.0126:2,2:23.5:1:26.5:1:1:1.9534:60:4:0.0127:0:1.5 +10 133191727 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24635;SOR=Inf;LSEQ=ATCCCCGCAGGTCTCTGCCA;RSEQ=CTCAGACCTGGGCCCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:134,38:172,0:0:2,0:23.2:1:32.1:1:1:0:59.9:85:1:0:0.1 0/1:170:2:1,1:107,61:168,2:0.0118:2,2:32.5:1:28:1:1:1.74792:60:4:0.0119:0:2 +10 133191828 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=27.82008;LSEQ=TGACCTCCAGCCTTAACATT;RSEQ=GCTGCTCTCTGGCTGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:16:10,6:179,201:380,16:0.0404:2,2:23.9:1:29.3:1:0.30784:1.87:60:32:0.0408:0:1.9 1/0:383:207:105,102:86,89:175,207:0.5405:2,2:26.4:1:29.4:1:0.83731:1.07:60:102.5:0.5423:0:1.9 +10 133191851 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=33.18254;LSEQ=TGCTCTCTGGCTGAGACTCT;RSEQ=TCATCTCACCTCATCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:14:7,7:147,214:361,14:0.0373:2,2:24.4:1:28.8:1:0.58285:1.45:60:13:0.0357:0:2.2 1/0:360:203:93,110:70,87:157,203:0.5639:2,2:24.7:1:29.6:1:0.83163:1.05:60:66.667:0.565:0:2 +10 133191905 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2201;SOR=Inf;LSEQ=AACCCGTTACTTCCTTCTGA;RSEQ=CATCTTCCCTGACCCCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:47,138:185,0:0:2,0:25.7:1:32.4:1:1:0:60:25.429:1:0:0.2 0/1:164:2:1,1:55,107:162,2:0.0122:2,2:14.5:1:25:1:1:1.94:60:4:0.0123:0:3 +10 133191920 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20412;SOR=Inf;LSEQ=TCTGAGCATCTTCCCTGACC;RSEQ=CACATCCACTCCAGCATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:31,114:145,0:0:2,0:21.5:1:31.5:1:1:0:60:47.333:1:0:0.2 0/1:120:2:1,1:32,86:118,2:0.0167:2,2:6.5:1:27:1:0.47605:2.66:60:4:0.0171:0:1.5 +10 133191928 . A T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.03758;LSEQ=TCTTCCCTGACCCCACATCC;RSEQ=CTCCAGCATGGGGAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:7:1,6:25,92:117,7:0.0565:2,2:22.3:1:28.6:1:1:1.62477:60:6:0.0508:0:1.4 1/0:101:61:17,44:6,34:40,61:0.604:2,2:20.7:1:27.6:1:0.15239:2.17:60:19.333:0.5979:0:1.6 +10 133191934 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50063;SOR=0;LSEQ=CTGACCCCACATCCACTCCA;RSEQ=CATGGGGAAGGAATTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:16,81:97,2:0.0202:2,2:11.5:1:29:1:0.3154:4.94:60:4:0.0206:0:1 0/0:84:0:0,0:16,68:84,0:0:2,0:20.4:1:31.1:1:1:0:60:83:1:0:0.9 +10 133192043 . C CT 48 v3;MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.58204;SOR=3.61082;LSEQ=CACTGTCCCTGTTTCCATTT;RSEQ=TTTTTTTTTTTTTTTCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,8:8,1:0.1:0,0:34:0:31:0:1:0:60:2:0.1111:0:3 0/1:10:3:0,3:0,7:7,3:0.3:0,0:15.3:1:30.8:1:1:0:60:6:0.3333:0.1:0 +10 134198942 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17715;SOR=Inf;LSEQ=AATAGCGGCCTCTCCTCCAC;RSEQ=TGCTCCCTCTGTCATTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:84,11:95,0:0:2,0:23.8:1:30.8:1:1:0:60:18:1:0:0.1 0/1:71:2:1,1:60,9:69,2:0.0282:2,2:12.5:1:28:1:0.26358:6.37705:60:4:0.0282:0:1 +10 134199067 . T C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2106;LSEQ=ACTTTTTTCTACTTCCTCTT;RSEQ=CACACTTTTCCTTTGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:314:283:128,155:15,13:28,283:0.9013:2,2:25:1:31.4:1:0.43142:1.39571:60:140.5:0.9035:0:1.3 1/0:394:259:119,140:64,71:135,259:0.6574:2,2:25.7:1:29.8:1:0.83164:1.0603:60:50.8:0.6546:0:1.3 +10 134199109 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.41085;LSEQ=AACATTCGCATCCTCTCTGT;RSEQ=GGTTCATTTGCTGATGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:96:31,65:58,92:150,96:0.3902:2,2:27.9:1:30.8:1:0.3426:1.32038:60:95:0.3942:0:1.8 0/1:303:63:20,43:93,146:239,63:0.2079:2,2:25.7:1:30:1:0.31025:1.36813:60:126:0.21:0:1.7 +10 134199206 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50204;SOR=0;LSEQ=GGGGTCCCCTTGGGCCCTGG;RSEQ=TGGTGCTGCTGGTGCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:1,47:48,2:0.04:1,2:24:1:28:1:0.07918:33.61:60:4:0.0408:0:1 0/0:39:0:0,0:3,36:39,0:0:2,0:24.5:1:31.3:1:1:0:60:38:1:0:0.1 +10 134913210 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08245;SOR=Inf;LSEQ=GCCTCTGTAGCCACAGCTCC;RSEQ=GGGCGGCTCCTCCCCGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:31,0:0:2,0:26.6:1:30.9:1:1:0:60:62:1:0:0.3 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:8:1:28:1:1:1.67325:60:4:0.1538:0:2 +10 134913223 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07536;SOR=Inf;LSEQ=CAGCTCCGGGGCGGCTCCTC;RSEQ=CCGCACACCCAGCCCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:33,0:0:2,0:29.4:1:31.9:1:1:0:60:66:1:0:0.3 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:36.5:1:29:1:1:1.67325:60:4:0.1538:0:1 +10 134913229 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00438;SOR=Inf;LSEQ=CGGGGCGGCTCCTCCCCGCA;RSEQ=ACCCAGCCCAGTCCCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:33,0:0:2,0:29.4:1:33.2:1:1:0:60:66:1:0:0.3 0/1:13:4:3,1:5,4:9,4:0.3077:2,2:29.3:1:29:1:1:2.25:60:8:0.3077:0:1.5 +10 134913291 . C T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04556;SOR=0;LSEQ=ACAGCCCAGTACAGTCACCT;RSEQ=CAGGGCCCAGACACAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:3,4:7,8:0.5333:2,2:19:1:27.3:1:1:1.23147:60:7:0.5:0:1 0/0:6:0:0,0:3,3:6,0:0:2,0:17.8:1:31.5:1:1:0:60:12:1:0:1.2 +10 134913358 . A G 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=TTGCCAGGGGTCCACCCTGC;RSEQ=GTTTCTGGAACCCTCCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:36:0:33:0:1:0:60:2:0.3333:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:26:1:28.5:1:1:0:60:4:0.6667:0:1 +11 324163 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGTATGGCTAGCCTCC;RSEQ=GTTGGAAAATTTTTACCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:48.5:1:32:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 324170 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCTAGCCTCCCGTTGGA;RSEQ=AATTTTTACCATCTTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:33:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 325034 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAAGGGGGCAGGGTACGGA;RSEQ=GGTGAGTCGTCCAAGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:12,18:30,0:0:2,0:25.7:1:30.5:1:1:0:59.1:60:1:0:0 0/1:64:2:1,1:33,29:62,2:0.0313:2,2:29:0:32:0:1:1.13563:59.5:4:0.0323:0:1 +11 325114 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26504;SOR=Inf;LSEQ=CCTTTCCCTCTTAGGTAGCC;RSEQ=AGCAGAGAGAGAAGGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:23,0:0:2,0:22.4:1:31.3:1:1:0:54.7:46:1:0:0 0/1:34:3:2,1:14,17:31,3:0.0882:2,2:9:1:27.7:1:0.59091:2.37:38.7:6:0.0882:0:1.3 +11 353042 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTAAATCTCTTCATTCCT;RSEQ=CCTTCCTTTGTGGGTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:28.5:1:1:0:60:4:1:0:1.5 +11 353861 . G T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCATGACTTCTATCATG;RSEQ=AGGGTCCAGCCCTACGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:28.5:1:1:0:55.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 354119 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1718;LSEQ=CAAGCAAGTCATGTGACCAT;RSEQ=GGACAGGGGCCCTTCCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:17:9,8:1,1:2,17:0.8947:2,2:30:1:31.1:1:1:1.12:50.9:16:0.8889:0:1.3 1/1:22:20:8,12:1,1:2,20:0.9091:2,2:27:1:31.3:1:1:1.47192:58.9:40:0.9091:0:1.1 +11 354508 . G GA 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCTGTCTCAAAAAAAAA;RSEQ=AAAAAAAAAAAGAAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,0:1,2:0.5:0,2:22:1:29:1:1:0:58:4:0.6667:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:18:0:33:0:1:0:60:2:1:0:1 +11 355039 . CTAA C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGATTAATAATGTTTATA;RSEQ=TGATTGATATGTCCATGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:33.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 528208 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACGCGTGGCCTTGTGGGATC;RSEQ=CTGTGGCGGACTCTCAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:22:1:30:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:31.5:1:1:0:60:4:1:0:2.5 +11 528237 . C T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACTCTCAGCTATCAGAGGG;RSEQ=TCCATCACTCCATCGTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:44:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:30:1:1:0:60:4:1:0:2.5 +11 528575 . A G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCCACCGAGGAAGGGGGCCA;RSEQ=CCCCCTCCCCGCGTCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21:1:33.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:21:0:28:0:1:0:60:2:1:0:0 +11 531572 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGAGCAACCAGCCATGA;RSEQ=GCAGGCGTGGGGCAAGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 532546 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51195;SOR=0;LSEQ=GGCGGGGCACAAGGGAGGCT;RSEQ=CTGACCGCAGGCCAGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:173,13:186,2:0.0106:2,2:21.5:1:28.5:1:0.14376:12.86069:60:4:0.0108:0:1 0/0:135:0:0,0:129,6:135,0:0:1,0:22.9:1:31.5:1:1:0:60:26:1:0:0.3 +11 532567 . C T 39 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.85228;LSEQ=CTGACCGCAGGCCAGGAGAC;RSEQ=GGCAGGGGCGGGGAGCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:228,57:285,3:0.0104:2,2:25:1:25:1:0.49201:1.99433:60:2:0.0071:0:1 0/0:225:2:1,1:181,42:223,2:0.0089:2,2:6.5:1:21.5:1:0.34639:4.27087:60:1:0.0046:0:4 +11 532923 . A C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13382;SOR=0.42601;LSEQ=CTGGACTCTGGCCATCTCGA;RSEQ=GTGCCCAGGGCCACCCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:31:2,29:1,27:28,31:0.5254:1,2:27.6:1:30.8:1:1:1.84:60:62:0.5254:0:1.1 0/1:22:7:1,6:0,15:15,7:0.3182:1,2:26.4:1:29.9:1:0.31818:0:60:14:0.3182:0:1 +11 533223 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5035;SOR=0;LSEQ=CCCAGGACTGCAGGGCGTGA;RSEQ=CCCAGACCCCGGCCCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:2,0:141,31:172,2:0.0114:2,0:19:1:31:1:1:0:60:4:0.0116:0:1.5 0/0:143:0:0,0:111,32:143,0:0:2,0:22.3:1:31.4:1:1:0:60:46.667:1:0:0.1 +11 533308 . CG C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.79317;SOR=0.85004;LSEQ=CCGCTGGGTCACATGGGTCC;RSEQ=GGGGGTCCCAGAGGGTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:7:4,3:341,230:571,7:0.0121:2,2:23:1:30.4:1:1:1.11175:60:14:0.0124:0:0.1 0/1:680:7:3,4:374,299:673,7:0.0103:2,2:30.6:1:30.4:1:0.70596:1.66649:60:14:0.0105:0:0.3 +11 533994 . A G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11112;SOR=Inf;LSEQ=TCAGGACCTTCCGTGGGGGG;RSEQ=GTTCACACAGCCAGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:39,150:189,0:0:2,0:23.9:1:31.8:1:1:0:60:188:1:0:0.2 0/1:176:3:2,1:35,138:173,3:0.017:2,2:21.7:1:29:1:0.11234:7.76:60:6:0.0171:0:1 +11 534242 . A G 321 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05739;LSEQ=GGGTCGTATTCGTCCACAAA;RSEQ=TGGTTCTGGATCAGCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1056:933:454,479:51,67:118,933:0.8835:2,2:27.1:1:32.6:1:0.28296:1.24:59.8:65.643:0.8854:0:1.1 0/1:1063:322:154,168:360,378:738,322:0.3029:2,2:24.5:1:31.6:1:0.78953:1.03894:59.5:321:0.306:0:1.2 +11 534287 . G A 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42214;SOR=0.56576;LSEQ=AGCGCACTCTTGCCCACACC;RSEQ=CCGGCGCCCACCACCACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:745:9:7,2:293,443:736,9:0.0121:2,2:12.9:1:27.8:1:0.0347:5.28:59.7:18:0.0122:0:1.9 0/0:728:5:4,1:305,416:721,5:0.0069:2,2:19:1:27.2:1:0.1693:5.44:60:10:0.007:0:1 +11 534403 . GCCCAGGCCCAGC G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=1;SSF=0.00202;SOR=0.16303;LSEQ=GGAGGGCCCTGCTCAGCCAG;RSEQ=CCCAGGCCCCACAGGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:21:0,21:0,45:45,21:0.3182:1,1:30.2:1:33.4:1:1:0:59.3:42:0.3231:0:0.4 0/1:43:3:0,3:0,40:40,3:0.0698:1,0:43:1:32.3:1:1:0:60:6:0.0732:0:0 +11 534409 . GCCCAGC G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=4.000;MSILEN=1;SSF=0.001;SOR=0.19039;LSEQ=CCCTGCTCAGCCAGGCCCAG;RSEQ=CCCAGGCCCCACAGGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:31:0,31:0,8:8,31:0.5167:0,1:27.5:1:32:1:1:0:60:14.5:0.8056:0.0167:0.2 0/1:36:6:0,6:0,26:26,6:0.1667:1,0:18.7:1:33.2:1:1:0:60:12:0.1875:0.0278:0 +11 535026 . C T 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGCACTGGGGCTGAGG;RSEQ=CCCCGGCCTGGTCCGCGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 1782844 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12119;SOR=Inf;LSEQ=CTGCCTGTCACCTGGAAACT;RSEQ=CTGGCCCAGCTCCCCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:15,25:40,0:0:2,0:29.4:1:31.7:1:1:0:60:39:1:0:0.1 0/1:47:4:3,1:18,25:43,4:0.0851:2,2:12.8:1:25.3:1:0.31124:4.05:60:8:0.0851:0:1 +11 1782850 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49333;SOR=Inf;LSEQ=GTCACCTGGAAACTGCTGGC;RSEQ=CAGCTCCCCCAAGTCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:14,24:38,0:0:2,0:27.1:1:29.9:1:1:0:60:18:1:0:0 0/1:38:2:1,1:14,22:36,2:0.0526:2,2:34.5:1:29:1:1:1.55:60:4:0.0541:0:1 +11 1782886 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.49245;SOR=Inf;LSEQ=AGTGAATGGCAACCCATTGC;RSEQ=CCCCGCCAGGTTGCACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:3,16:19,0:0:2,0:17.9:1:31.1:1:1:0:60:18:1:0:0.1 0/1:23:2:1,1:4,17:21,2:0.087:2,2:12.5:1:27.5:1:0.39526:3.91:60:4:0.087:0:1 +11 2154188 . G A 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGCTGCAGGATGGTGGC;RSEQ=CCGGGCTGCAGACTTGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:353,78:431,0:0:2,0:25.5:1:30.3:1:1:0:60:46.889:1:0:0.1 0/1:364:51:32,19:232,81:313,51:0.1401:2,2:25.7:1:29.4:1:0.12668:1.69787:59.9:102:0.1425:0:1.1 +11 2154234 . C T 74 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05108;SOR=4.73097;LSEQ=TGCTCACTTCCGATTGCTGG;RSEQ=CATCTCTGGGGGGGCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:871:2:0,2:543,326:869,2:0.0023:2,0:1:0:27:1:0.14154:0:60:4:0.0024:0:1 0/1:742:8:3,5:427,307:734,8:0.0108:2,2:22.1:1:24.9:1:0.29116:2.3155:60:7:0.0096:0:1.3 +11 2154683 . G T 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6899;LSEQ=TCCCAGAGGCCACAGGAAAC;RSEQ=CTGGGCGCCCGAAGCCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:4:2,2:283,99:382,4:0.0104:2,2:24.5:1:29.8:1:0.28105:2.84934:60:8:0.0105:0:1 0/0:279:2:1,1:216,61:277,2:0.0072:2,2:42:1:29:1:0.39568:3.52023:60:4:0.0074:0:1 +11 2154964 . G A 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGCCCCCGGAGGCTGAAG;RSEQ=GGGAGCAAACCACCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:24,230:254,0:0:2,0:24.4:1:31.7:1:1:0:59.9:253:1:0:0.1 0/1:174:42:6,36:15,116:131,42:0.2414:2,2:26.3:1:30.2:1:0.59621:1.29:60:41:0.2412:0:1.2 +11 2156213 . G A 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAACGCACGTCCCTTGTCA;RSEQ=AATGTCCAAAAGGTGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:21.7:1:31.3:1:1:0:48.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 2156536 . G A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66574;SOR=1.08117;LSEQ=CCCCTGGCTTGAGGTTGGGC;RSEQ=TCCTCACCGGTCACTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:202:168,34:122,21:143,202:0.5855:2,2:24.8:1:30.5:1:0.6555:1.17519:60:100:0.5848:0:1.1 1/0:230:139:109,30:63,27:90,139:0.6043:2,2:22.7:1:29.4:1:0.16168:1.55:60:68.5:0.6009:0:1.1 +11 2156741 . T G 228 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACCAGCATCGACTTCCCCA;RSEQ=TGGGATTCCCATTGGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1040:130:55,75:420,490:910,130:0.125:2,2:24.2:1:32.6:1:0.45178:1.16866:60:129:0.1261:0:1.1 0/0:1037:0:0,0:485,552:1037,0:0:2,0:24.9:1:29.3:1:1:0:59.9:44.087:1:0:0.2 +11 2156821 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13234;SOR=0;LSEQ=CAAGCCCCAGGCCAGAGGTG;RSEQ=CCCTCCCAAACCAAATTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:4:2,2:66,300:366,4:0.0108:2,2:24.8:1:29.3:1:0.15552:4.52:60:8:0.011:0:1 0/0:299:0:0,0:72,226:298,0:0:2,0:22.4:1:30.2:1:1:0:59.9:32.111:1:0:0.1 +11 2156930 . G A 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00333;SOR=0.159;LSEQ=AACACACAGGTCATAATGCC;RSEQ=AGGTGAGGGCGCAGGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:21:0,21:1,16:17,21:0.5526:1,1:21.9:1:31.8:1:0.44737:0:60:42:0.5676:0:1 0/1:25:4:0,4:2,19:21,4:0.16:2,0:30.5:1:31:1:1:0:60:8:0.16:0:1 +11 2157044 . C G 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65944;SOR=1.88324;LSEQ=TACACGAGGGGTGACCATCT;RSEQ=CACGGTCATTATTGCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:3,3:2,5:7,6:0.4615:2,2:17.2:1:31.2:1:0.59207:2.32:60:12:0.4615:0:1.3 1/0:8:5:2,3:1,2:3,5:0.625:2,2:26.6:1:32:1:1:1.29:60:10:0.625:0:1 +11 2161488 . G C 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGACGCGAGTTCGGTCTC;RSEQ=GGGGCCACCACGATAATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1107:0:0,0:502,600:1102,0:0:2,0:24.5:1:30.2:1:1:0:60:49.091:0.9963:0:0.2 0/1:1017:92:40,52:410,510:920,92:0.0905:2,2:25.2:1:30:1:0.91249:1.04506:60:184:0.0917:0:1.2 +11 2161858 . A G 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCTCCAGCCGCTTTCCCCAC;RSEQ=AATGAGATCTTTGCAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:11:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:47:0:31:1:1:0:60:4:1:0:1 +11 2164799 . G C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37143;SOR=0;LSEQ=TCGTCTTTAAAATTAGGGAA;RSEQ=CCGGGTTAGTGGCCTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:22,0:0,0:0,22:1:0,1:26.1:1:32.6:1:1:0:60:44:1:0:1 1/1:13:12:12,0:1,0:1,12:0.9231:0,0:16.8:1:32.3:1:1:0:60:24:0.9231:0:1.3 +11 2164915 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50006;SOR=0;LSEQ=AGTGTAAGTCTGGAAAAGCC;RSEQ=GCCGGGACTGATGTGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:136,10:146,2:0.0135:2,2:24:1:28:1:0.14359:13.01473:60:4:0.0138:0:1.5 0/0:131:0:0,0:116,15:131,0:0:2,0:23.7:1:30.5:1:1:0:60:262:1:0:0.4 +11 2164921 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22987;SOR=Inf;LSEQ=AGTCTGGAAAAGCCCGCCGG;RSEQ=ACTGATGTGTTTTGACGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:155,16:171,0:0:2,0:22.2:1:31.6:1:1:0:60:170:1:0:0.6 0/1:158:2:1,1:133,23:156,2:0.0127:2,2:9:1:27.5:1:0.28154:5.68215:60:4:0.0127:0:2 +11 2164990 . G A 279 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGACCCGTCGAAATGGTGA;RSEQ=TATATTTAGAAGACTTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:566:566:343,223:0,0:0,566:1:0,2:24.6:1:30.6:1:1:0:60:69.75:1:0:1.1 1/0:579:436:257,179:81,61:142,436:0.753:2,2:24.5:1:29.2:1:0.696:1.08:60:108:0.7539:0:1.1 +11 2165138 . G A 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3738;SOR=0.25904;LSEQ=TGTTGAGCTCAAGCTTCCCG;RSEQ=GCAGCGGAAGGAAGGCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:4:3,1:95,266:361,4:0.011:2,2:20:1:27.3:1:0.06079:8.34:60:8:0.0111:0:1.3 0/0:350:1:1,0:106,243:349,1:0.0029:2,0:1:0:23:0:0.30571:0:60:2:0.0029:0:1 +11 2165143 . C T 60 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21512;SOR=0.24583;LSEQ=AGCTCAAGCTTCCCGGGCAG;RSEQ=GGAAGGAAGGCGCTGCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:4:2,2:74,242:316,4:0.0125:2,2:14.3:1:30.3:1:0.24006:3.26:60:8:0.0128:0:1.5 0/0:323:1:0,1:93,229:322,1:0.0031:2,0:36:0:26:0:1:0:60:2:0.0031:0:1 +11 2165173 . T G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.3316;LSEQ=GCGCTGCCGGGGATTCACCT;RSEQ=GGCTGGGGCGCGCGCGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:76:4,72:10,72:82,76:0.481:2,2:24.1:1:32.3:1:0.16433:2.48627:60:152:0.481:0:1 0/1:128:30:4,26:10,87:97,30:0.2344:2,2:19.6:1:31.1:1:0.73926:1.34:60:60:0.2362:0:1.1 +11 2166847 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCGCTCATGCTTGAAAA;RSEQ=GCATGCCTGGACTTTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 2582118 . T C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATGGGGGAGGGCTTCAC;RSEQ=GCAGGGAGAGTGAGGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:20:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:29.5:1:1:0:60:4:1:0:1.5 +11 2583116 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49717;SOR=Inf;LSEQ=GTGGCCAGGGCCTCAGGAGG;RSEQ=ACACAGAGGGCCCCACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:40,38:78,0:0:2,0:26.1:1:31.3:1:1:0:60:38:1:0:0.2 0/1:82:2:1,1:43,37:80,2:0.0244:2,2:17.5:1:28:1:1:1.16002:60:4:0.0247:0:2.5 +11 2583141 . A G 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGGGCCCCACTCAAGGTC;RSEQ=CGGGCTGCACGTTCCATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:37,45:82,0:0:2,0:25.8:1:30.2:1:1:0:60:164:1:0:0.1 0/1:89:24:11,13:33,32:65,24:0.2697:2,2:23.5:1:31.3:1:0.81197:1.21604:60:48:0.2727:0:1.2 +11 2583173 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23238;SOR=0;LSEQ=TTCCATGGGGCCTGGGGAAG;RSEQ=AGCCGAGCAGAAGGATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:23,36:59,2:0.0328:2,2:12:0:31:1:1:1.55:60:4:0.0333:0:1.5 0/0:65:0:0,0:29,36:65,0:0:2,0:26.6:1:30.8:1:1:0:60:64:1:0:0.3 +11 6502636 . G C 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02876;SOR=Inf;LSEQ=AGGGCGGAGCTGACGTCGCA;RSEQ=CCAGGGCAGGGCGATACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:14,0:0:1,0:22.1:1:32.1:1:1:0:60:13:1:0:0.1 0/1:22:7:6,1:14,1:15,7:0.3182:1,2:12.6:1:31.6:1:1:2.2361:60:14:0.3333:0:1.7 +11 6502694 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15556;SOR=0;LSEQ=AGCGAGAGGTTACTTCCGGG;RSEQ=CGGCACCGAGAAGCTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:34,14:48,2:0.04:2,2:24:1:29:1:0.51429:2.38049:60:4:0.0417:0:1 0/0:76:0:0,0:54,22:76,0:0:2,0:20.4:1:30.2:1:1:0:60:75:1:0:0.6 +11 6502727 . C G 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGAAACGGAAGTGGCGTA;RSEQ=GGCATGCGCCGGTGGCGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:49,38:87,0:0:2,0:25.7:1:30.7:1:1:0:60:86:0.9885:0:0.3 0/1:146:36:20,16:65,45:110,36:0.2466:2,2:23.5:1:30.4:1:0.84587:1.1544:60:72:0.25:0:2.1 +11 6502734 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14959;SOR=0;LSEQ=CGGAAGTGGCGTACGGCATG;RSEQ=GCCGGTGGCGTGATGGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:52,43:95,2:0.0206:2,2:30:1:31:1:1:1.20692:60:4:0.0211:0:1 0/0:153:0:0,0:86,67:153,0:0:2,0:27.6:1:30:1:1:0:59.8:50:1:0:0.7 +11 6502738 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52549;SOR=Inf;LSEQ=AGTGGCGTACGGCATGCGCC;RSEQ=GTGGCGTGATGGAGCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:54,45:99,0:0:2,0:26.2:1:29.8:1:1:0:60:23.75:1:0:0.2 0/1:161:2:1,1:89,70:159,2:0.0124:2,2:20:1:30.5:1:1:1.26951:60:4:0.0127:0:2.5 +11 6502744 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53604;SOR=Inf;LSEQ=GTACGGCATGCGCCGGTGGC;RSEQ=TGATGGAGCGGCAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:53,46:99,0:0:2,0:27.8:1:31.1:1:1:0:60:98:1:0:0.3 0/1:174:2:1,1:94,77:171,2:0.0115:2,2:16:0:32:0:1:1.21936:60:4:0.0117:0:2.5 +11 6502754 . GGCA G 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.61499;SOR=0.53926;LSEQ=CGCCGGTGGCGTGATGGAGC;RSEQ=GCAGCAGCAGCAACAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:49,50:99,2:0.0198:2,2:30.5:1:31:1:1:1.02:60:4:0.0204:0:0 0/1:186:2:1,1:91,91:182,2:0.0108:2,2:36:1:31:1:1:1:60:4:0.0111:0:0 +11 6502780 . C A 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAGCAGCAACAGCAACTG;RSEQ=GAAACGTAAGTGAGAACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:40,49:89,0:0:2,0:26.8:1:31.2:1:1:0:60:178:1:0:0.3 0/1:169:46:22,24:52,71:123,46:0.2722:2,2:24.4:1:29.6:1:0.60188:1.25:60:92:0.2771:0:1.8 +11 6707260 . A G 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08081;SOR=0;LSEQ=TTGGCTCTCTTCTTTTTCTG;RSEQ=TCATTTTCTTTCATGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:3,0:3,4:0.5714:0,2:32.8:1:29:1:0.14286:0:60:3:0.5:0:1.5 0/0:5:0:0,0:4,1:5,0:0:2,0:21.6:1:27.6:1:1:0:60:10:1:0:0 +11 6707395 . C T 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49885;SOR=Inf;LSEQ=TTTCCCTACAGCAATGCTAA;RSEQ=AGCATGCTGAGTAACATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:44,28:72,0:0:2,0:18.8:1:29.5:1:1:0:59.8:6.2:1:0:0.3 0/1:82:2:1,1:44,35:79,2:0.0244:2,2:15:0:26.5:1:1:1.25356:60:4:0.027:0:1 +11 7206403 . C T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0147;SOR=0.18985;LSEQ=CCAATAGCTAATTTAGAAGT;RSEQ=ACATACAATGCTGATTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:13:13,0:9,0:9,13:0.5909:0,1:25.8:1:31.9:1:1:0:60:26:0.5909:0:1 0/1:24:5:5,0:19,0:19,5:0.2083:1,0:22.6:1:30.4:1:1:0:60:10:0.2174:0:1 +11 7206465 . G C 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00067;SOR=Inf;LSEQ=AGAAAGCAGCAAAATGCTTC;RSEQ=CAATTTCATATGAATAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:69,18:87,0:0:2,0:23.1:1:30.4:1:1:0:60:86:0.9885:0:0.1 0/1:113:13:9,4:69,30:99,13:0.115:2,2:20.6:1:29.5:1:1:1.02204:60:26:0.1182:0:1.2 +11 7206563 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=6e-05;SOR=0.49199;LSEQ=TGTTATAACATGGGCAGTGC;RSEQ=AAAATGCTGGGCTACTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:234:125:65,60:53,55:108,125:0.5342:2,2:27:1:31.7:1:0.69449:1.12:59.9:61.5:0.5325:0:1.2 0/1:308:111:57,54:100,97:197,111:0.3604:2,2:26.5:1:31:1:1:1.02:60:222:0.3627:0:1.1 +11 8246137 . C T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.02427;SOR=0;LSEQ=CAGGCGGGCAGATGGACAGA;RSEQ=GGGCCTGGAGGCCAGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:5:1,4:295,194:489,5:0.0101:2,2:9:1:28.6:1:0.16276:6.06174:60:10:0.0102:0:1.2 0/0:543:0:0,0:315,227:542,0:0:2,0:23.7:1:30.2:1:1:0:60:179.667:0.9981:0:0.3 +11 8246181 . A G 200 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTTACTGAACTTGGGATTC;RSEQ=AAGGTGCCATTGAGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:751:0:0,0:392,358:750,0:0:2,0:26.1:1:31:1:1:0:60:186.5:0.9987:0:0.2 0/1:842:109:56,53:393,339:732,109:0.1295:2,2:24.8:1:29.6:1:0.68128:1.09707:59.9:108:0.13:0:1.2 +11 8246326 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=6e-05;SOR=0.39428;LSEQ=GTCCCAGTGGGTAAGGGGGG;RSEQ=GCTGCAGACAGAAGCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:86:12,74:10,101:111,86:0.4365:2,2:24.4:1:30.7:1:0.36215:1.63:60:13.333:0.4211:0:1.1 0/1:167:39:5,34:24,104:128,39:0.2335:2,2:24.5:1:30.1:1:0.47565:1.56534:60:38:0.2303:0:1.1 +11 8246343 . G A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15738;SOR=0.44913;LSEQ=GGGGGCTGCAGACAGAAGCC;RSEQ=GCCTGGCCTATGAGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:15:0,15:5,128:133,15:0.1014:1,1:26.1:1:32.9:1:1:0:60:30:0.1027:0:1 0/1:104:5:0,5:2,97:99,5:0.0481:1,0:25:1:29.8:1:1:0:60:10:0.049:0:1.6 +11 8246382 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.13383;SOR=Inf;LSEQ=GCTATGTGGGAGGTGGTGGG;RSEQ=GGAGTTTGTTCCTTGAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,65:65,0:0:1,0:22.1:1:30.9:1:1:0:59.8:20.667:1:0:0.5 0/1:38:2:0,2:0,36:36,2:0.0526:1,0:25.5:1:31:0:1:0:60:4:0.0541:0:1.5 +11 8248426 . A T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50315;SOR=0;LSEQ=CATACACACACGCAACCCGC;RSEQ=TTTGCGTGCACGCCTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:136,4:140,2:0.0141:1,2:23:1:33:1:0.06942:30.52118:60:4:0.0143:0:1 0/0:116:0:0,0:113,3:116,0:0:1,0:23.8:1:29.3:1:1:0:60:22.2:1:0:0.6 +11 8248440 . C G 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=69.51844;LSEQ=ACCCGCATTTGCGTGCACGC;RSEQ=TCCGCCGTGCTCCTGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:0,1:162,9:171,1:0.0058:2,0:2:0:13:0:0.05814:0:60:0:0:0:4 0/1:148:43:39,4:97,7:104,43:0.2905:2,2:29:1:29:1:0.7312:1.41765:60:20.5:0.2847:0:1.8 +11 8248457 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5959;SOR=2.36647;LSEQ=CGCCTCCGCCGTGCTCCTGG;RSEQ=CCATCCCAGCAGGCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:0,1:210,20:230,1:0.0043:2,0:19:0:14:0:0.09091:0:60:0:0:0:4 0/1:196:2:1,1:165,29:194,2:0.0102:2,2:24.5:1:28:1:0.28336:5.61102:60:4:0.0104:0:1 +11 8248482 . C T 171 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.78264;LSEQ=CCCAGCAGGCCTCAGGCTGG;RSEQ=GTCTGGGGAGTGTGTTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:4:0,4:271,80:351,4:0.0113:2,0:1:0:26.5:1:0.00297:0:60:8:0.0115:0:1.5 0/1:331:66:47,19:190,75:265,66:0.1994:2,2:22.6:1:28.4:1:1:1.02406:60:65:0.2006:0:1.5 +11 8248574 . G T 194 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGGTGATACACGTTGTCCC;RSEQ=GGCCCGCATCACCATCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:74:38,36:408,400:808,74:0.0839:2,2:26.6:1:31.4:1:0.90392:1.03:59.9:148:0.0846:0:1.2 0/0:1008:0:0,0:508,496:1004,0:0:2,0:24.8:1:29.5:1:1:0:60:76.231:0.997:0:0.2 +11 8248650 . G A 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10277;SOR=5.77793;LSEQ=CCTGTGGTGCCAAAGAGCCT;RSEQ=CCGAGGGAAGGGCGCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:1:1,0:169,352:521,1:0.0019:2,0:1:0:21:0:0.32567:0:60:2:0.0019:0:1 0/1:456:5:3,2:163,288:451,5:0.011:2,2:21:1:27.4:1:0.35911:2.64:60:10:0.0111:0:1.2 +11 8248698 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19447;SOR=Inf;LSEQ=AGCATTCTGGGAAGCTGGGT;RSEQ=GGCAGGGGGAAAGGAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:32,193:225,0:0:2,0:24.2:1:31.5:1:1:0:60:111.5:1:0:0.1 0/1:178:2:0,2:25,151:176,2:0.0112:2,0:29.5:1:32:0:1:0:60:4:0.0114:0:1 +11 8251654 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54017;SOR=0;LSEQ=AGTCCAAGGGCATAACGACC;RSEQ=GGGCCTTCCCCTCAGGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:27,0:27,2:0.069:1,2:23:1:30:1:0.06897:0:60:4:0.069:0:1 0/0:15:0:0,0:15,0:15,0:0:1,0:20:1:31.5:1:1:0:58:30:1:0:0 +11 8251803 . A G 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGAGCTTTCTGAGCAGG;RSEQ=CAAGGGCTTGGGAGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:261,120:381,0:0:2,0:25.8:1:30:1:1:0:60:62.5:1:0:0.1 0/1:346:19:14,5:204,123:327,19:0.0549:2,2:27.5:1:30.4:1:0.46416:1.69:60:18:0.0533:0:1 +11 8251810 . C A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02651;SOR=Inf;LSEQ=CTTTCTGAGCAGGACAAGGG;RSEQ=TTGGGAGGCCAGGGTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:290,141:431,0:0:2,0:25.4:1:32.6:1:1:0:60:70.833:1:0:0.1 0/1:406:5:3,2:249,150:399,5:0.0123:2,2:18.2:1:26.4:1:1:1.10638:60:10:0.0126:0:1.4 +11 8251921 . G C 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0873;LSEQ=CCCAGGCGGCAGTCACAGCA;RSEQ=GCACACTTGAGGCAGTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:864:769:388,381:56,37:93,769:0.89:2,2:25.1:1:30.9:1:0.07958:1.48552:59.9:68.909:0.8886:0:1.1 0/1:974:403:213,190:292,279:571,403:0.4138:2,2:24.1:1:30.3:1:0.60313:1.07:59.9:806:0.4172:0:1.2 +11 8284838 . A G 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.09586;LSEQ=GTGTGCCTGCGCGCCGCGGC;RSEQ=GGGGGCGAGGGGGTGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:560:556:391,165:0,0:0,556:0.9929:0,2:26.7:1:30.2:1:1:0:60:45.333:0.9927:0:1.7 1/1:460:457:301,156:0,0:0,457:0.9935:0,2:25.9:1:29.3:1:1:0:60:49.778:0.9978:0:1.5 +11 8284860 . G T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29389;LSEQ=GGGGCGAGGGGGTGAGGGGC;RSEQ=TCGAGACCCCGGCCCGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:850:483:305,178:236,131:367,483:0.5682:2,2:25.1:1:31.3:1:0.77346:1.05135:59.9:79.5:0.5706:0:1.8 0/1:800:223:131,92:354,222:576,223:0.2788:2,2:23.1:1:29.4:1:0.51843:1.11971:60:43.6:0.2788:0:1.8 +11 8284981 . A C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61321;SOR=2.13202;LSEQ=CGACTCGGGGCGCGCTTTGG;RSEQ=GGGGCGGCCGGTCTTCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:375:373:98,275:1,0:1,373:0.9947:0,2:22.9:1:30:1:0.26471:0:60:45.625:0.9973:0:1.8 1/1:399:398:116,282:1,0:1,398:0.9975:0,2:22.4:1:29.2:1:0.29323:0:60:55.857:0.9974:0:1.8 +11 8284995 . T C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTTGGAGGGGCGGCCGGTC;RSEQ=TCGGGCAGCTAGCGGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:284:284:52,232:0,0:0,284:1:0,2:22.6:1:32.5:1:1:0:60:55.8:1:0:2 1/1:286:261:46,215:4,21:25,261:0.9126:2,2:24.2:1:30.9:1:1:1.12:60:86:0.9149:0:2.1 +11 8285009 . G A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGTCTTCGGGCAGCTAGC;RSEQ=GGCTCTAATTACCCGCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:22,197:219,0:0:2,0:23.2:1:31.3:1:1:0:60:218:1:0:1.8 0/1:201:20:2,18:14,167:181,20:0.0995:2,2:27:1:31.3:1:0.66391:1.32:60:40:0.1005:0:2.8 +11 8285124 . A C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69184;SOR=0.56723;LSEQ=CTCACCTACTTTTGTGCCTC;RSEQ=GAATTGGAAGGAACTACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:0,25:0,4:4,25:0.8621:0,1:24.4:1:30.6:1:1:0:60:50:0.8621:0:1.1 1/0:18:14:0,14:0,4:4,14:0.7778:0,1:23.8:1:28.7:1:1:0:60:13:0.7647:0:1.1 +11 8289880 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04833;SOR=Inf;LSEQ=GGTGCTGAGGGCTCTGCCGC;RSEQ=GCTAGCGGGGTGGACTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:70,19:89,0:0:2,0:16.4:1:31.1:1:1:0:60:178:1:0:0.1 0/1:52:3:2,1:41,8:49,3:0.0577:2,2:12.7:1:29.3:1:0.44158:2.5037:60:6:0.0577:0:1 +11 8289881 . G T 30 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.55937;SOR=3.23732;LSEQ=GTGCTGAGGGCTCTGCCGCC;RSEQ=CTAGCGGGGTGGACTCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:1,0:73,20:93,1:0.0106:2,0:18:0:17:0:1:0:60:0:0:0:2 0/1:59:2:1,1:46,11:57,2:0.0339:2,2:7.5:1:30:1:0.36821:4.04707:57.5:4:0.0345:0:1 +11 8289932 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02711;SOR=Inf;LSEQ=CGCAGTCTCCGCCCCACGTC;RSEQ=CGCGTGCCCCCGGGCACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:235,132:367,0:0:2,0:25.7:1:31.1:1:1:0:60:90.75:1:0:0.2 0/1:349:5:2,3:222,122:344,5:0.0143:2,2:11.8:1:28.2:1:0.35386:2.72115:60:10:0.0143:0:1.2 +11 8289940 . C T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02867;SOR=Inf;LSEQ=CCGCCCCACGTCCCGCGTGC;RSEQ=CCCGGGCACCGGCACCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:274,173:447,0:0:2,0:24.7:1:31.1:1:1:0:60:48.667:1:0:0.2 0/1:434:5:1,4:257,172:429,5:0.0115:2,2:18.2:1:24.6:1:0.16317:5.95394:60:10:0.0116:0:1 +11 8290069 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.7823;LSEQ=TCCGACTCCCGCCGCCGGCC;RSEQ=CCTGCGCTGCTCCCGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:1:1,0:34,83:117,1:0.0085:2,0:1:0:26:0:0.29661:0:60:2:0.0087:0:1 0/1:133:2:1,1:43,88:131,2:0.015:2,2:14.5:1:27:1:1:2.03:60:4:0.0152:0:1 +11 8290075 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.09758;SOR=0;LSEQ=TCCCGCCGCCGGCCGCCTGC;RSEQ=CTGCTCCCGCCGGCCCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:2,1:22,69:91,3:0.0319:2,2:9.3:1:29.3:1:0.15923:6.12:60:6:0.033:0:1 0/0:109:0:0,0:33,76:109,0:0:2,0:11.7:1:30.8:1:1:0:60:218:1:0:0.3 +11 8291041 . C T 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCCAGGCTGGGCCACAGTG;RSEQ=TCTCCATCCGGTCACCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 8589648 . A G 219 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGGTACTTCCTTAGTACA;RSEQ=AATAATTGCCATCCAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:102,127:229,0:0:2,0:27.6:1:30.7:1:1:0:59.9:458:1:0:0.1 1/0:265:137:64,73:61,67:128,137:0.517:2,2:26.6:1:30.9:1:0.90245:1.03835:60:67.5:0.5172:0:1.1 +11 8852106 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24821;SOR=Inf;LSEQ=AATTCAGCGAGGGCTGCATT;RSEQ=CCTTACTGCCTGATGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:115,9:124,0:0:2,0:24.6:1:32.2:1:1:0:60:40.333:1:0:0.1 0/1:134:3:2,1:116,15:131,3:0.0224:2,2:30.7:1:30.3:1:0.31924:3.80636:60:6:0.0224:0:1 +11 8852112 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=GCGAGGGCTGCATTGCCTTA;RSEQ=TGCCTGATGGTGGAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:121,18:139,0:0:2,0:24.8:1:32.5:1:1:0:60:138:1:0:0.1 0/1:154:2:1,1:127,25:152,2:0.013:2,2:5.5:1:28:1:0.31008:5.00107:60:4:0.0134:0:1 +11 8852239 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16652;SOR=0.83542;LSEQ=CCCAACTCCTAAAGTATCTT;RSEQ=CCGCCTGTTCCTCCCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:457:251:108,143:100,106:206,251:0.5492:2,2:25.1:1:30.1:1:0.25786:1.2485:60:49.2:0.5479:0:1.2 1/0:569:287:123,164:127,153:280,287:0.5044:2,2:24.9:1:29.3:1:0.55498:1.10655:59.8:94.667:0.509:0:1.1 +11 8852338 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=GAGGCTGAGCCTGAGCCCAT;RSEQ=AGAACAGCATGCAGACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:3,76:79,0:0:1,0:23.2:1:32.8:1:1:0:60:78:1:0:0.1 0/1:88:2:1,1:10,76:86,2:0.0227:2,2:19.5:1:30.5:1:0.23563:7.30:60:4:0.023:0:1 +11 9681965 . T A 32 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37384;SOR=0.40749;LSEQ=CCTTTCGGCCGGAACCGCCA;RSEQ=CTTCCAGTAATTCGCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:3,0:31,31:62,3:0.0462:2,0:15.7:1:20.7:1:0.2399:0:47.3:2:0.0385:0:3 0/1:104:2:2,0:51,49:100,2:0.0192:2,0:17.5:1:16.5:1:0.49583:0:45:1:0.0119:0:5 +11 9846278 . C G 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAATGGCAAAATACAAGAT;RSEQ=AGGTTGTGGGGTGGGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 9848396 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGAGTGATCTCGGCTC;RSEQ=TTTTGCTCTTGTTGCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:29:1:1:0:59:4:1:0:1 +11 11863712 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55002;SOR=Inf;LSEQ=CCCTCCCCCGGCAGGGCGGA;RSEQ=AGGAGCGGCCGGAGTCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:43,38:81,0:0:2,0:26:1:32.7:1:1:0:60:162:1:0:0.2 0/1:158:2:1,1:82,74:156,2:0.0127:2,2:29.5:1:28.5:1:1:1.10739:60:4:0.0129:0:1.5 +11 11863756 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53386;SOR=Inf;LSEQ=GTGCCCGGCGAGGAGAACCA;RSEQ=CTGGTCCCGAAAGAGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:39,50:89,0:0:2,0:29.4:1:29.8:1:1:0:60:43.5:1:0:0.2 0/1:154:2:1,1:68,84:152,2:0.013:2,2:42:0:31.5:1:1:1.23:60:4:0.0132:0:1 +11 12262281 . T C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCTAGCCACCCTGGCC;RSEQ=GGCATGGGCTCTGGCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:22:1:1:0:60:1:1:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:6:1:29.5:1:1:0:60:4:1:0:1 +11 12264025 . T C 29 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59916;SOR=0.43406;LSEQ=TCTGTCCGTGTCTGGGTGAC;RSEQ=TCCTTTCTTCCCCTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:54,9:63,2:0.0308:2,2:7.5:1:29.5:1:0.28606:5.74461:60:4:0.0328:0:1 0/1:74:1:0,1:56,17:73,1:0.0135:2,0:1:0:29:0:0.24324:0:60:2:0.0135:0:1 +11 12264074 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23094;SOR=0;LSEQ=GGGTGGGTTCCTCCTCCCTC;RSEQ=GCCCACCCCCTGTCTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:112,41:153,2:0.0129:2,2:28.5:1:29.5:1:0.46979:2.71101:60:4:0.0129:0:1 0/0:167:0:0,0:102,65:167,0:0:2,0:27.4:1:29.8:1:1:0:60:54.667:1:0:0.4 +11 12264140 . A C 244 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.0047;LSEQ=GGCCCCCGGCTGCCTCCCTC;RSEQ=CCCACTTCTTGGAAGCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:248:247:124,123:1,0:1,247:0.996:0,2:26.1:1:30.8:1:1:0:60:48.4:0.9959:0:1.1 1/0:269:144:71,73:66,57:123,144:0.5353:2,2:26.6:1:30.1:1:0.53939:1.18973:60:143:0.5458:0:1.2 +11 12264214 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.88237;LSEQ=TCTCCTTTCTCACCTTCACT;RSEQ=CAGAAGAGGGCTCAGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:1:1,0:40,93:133,1:0.0075:2,0:1:0:23:0:0.30597:0:60:2:0.0076:0:3 0/1:143:2:1,1:53,88:141,2:0.014:2,2:34.5:1:28.5:1:1:1.65:60:4:0.0141:0:1.5 +11 13127828 . G T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23699;SOR=Inf;LSEQ=CCTGAGAAATGAAGAGACTC;RSEQ=ATTTGAGAAATACACAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:108,38:146,0:0:2,0:23.7:1:30.6:1:1:0:60:72:1:0:0.1 0/1:139:2:1,1:88,49:137,2:0.0144:2,2:11.5:1:23.5:1:1:1.78785:60:4:0.0147:0:1.5 +11 13127893 . C A 203 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTCTGGAGGCCCTCACAAC;RSEQ=GAAAAGTGTGCATAAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:161,145:306,0:0:2,0:27.7:1:30.4:1:1:0:59.9:75.5:1:0:0.1 0/1:292:108:57,51:95,89:184,108:0.3699:2,2:26:1:30.1:1:0.90361:1.05:59.9:107:0.3715:0:1.6 +11 13127942 . A T 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGGAACCTGTCAAGGATT;RSEQ=AAAAAGTGCTACCAGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:83,133:216,0:0:2,0:24.3:1:29.6:1:1:0:59.8:107:1:0:0.1 1/0:202:113:47,66:41,48:89,113:0.5594:2,2:25.4:1:28.3:1:0.5688:1.19838:60:226:0.565:0:1.5 +11 13127951 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2293;SOR=Inf;LSEQ=TGTCAAGGATTAAAAAAGTG;RSEQ=TACCAGAGCACAGGAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:68,123:191,0:0:2,0:23.3:1:32.5:1:1:0:59.8:46.75:1:0:0.1 0/1:176:2:1,1:70,104:174,2:0.0114:2,2:34:1:28:1:1:1.48:60:4:0.0116:0:1.5 +11 13127964 . G A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11631;SOR=Inf;LSEQ=AAAAGTGCTACCAGAGCACA;RSEQ=GAGAGATGGCAGATGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:38,113:151,0:0:2,0:23:1:31.6:1:1:0:59.8:150:1:0:0.1 0/1:145:3:3,0:49,93:142,3:0.0207:2,0:13:1:20.7:1:0.04441:0:60:2:0.0139:0:1.7 +11 15511463 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20154;SOR=Inf;LSEQ=TGGAACTGTCTGATCTTTGG;RSEQ=GAAATCCACACTTGGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:116,26:142,0:0:2,0:25.2:1:31.8:1:1:0:60:141:0.993:0:0.5 0/1:117:2:1,1:85,30:115,2:0.0171:2,2:23.5:1:28:1:0.46139:2.80361:60:4:0.0174:0:1 +11 15511476 . T C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00191;SOR=1.97714;LSEQ=TCTTTGGCGAAATCCACACT;RSEQ=GGGAGACATTCTGGAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:94:63,31:68,22:90,94:0.5109:2,2:23.1:1:30.9:1:0.25441:1.51743:60:93:0.5082:0:1.1 1/0:178:120:82,38:32,26:58,120:0.6742:2,2:19.7:1:29.1:1:0.09736:1.75:60:29:0.6705:0:1.2 +11 15511590 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.56919;SOR=0.91747;LSEQ=GTTCCGTTCACACTACAGCT;RSEQ=CCAGGTTAGGACCTCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:398:203:93,110:85,110:195,203:0.5101:2,2:24.6:1:30.3:1:0.68726:1.09:60:100.5:0.5128:0:1.1 0/1:391:191:88,103:105,95:200,191:0.4885:2,2:23.5:1:28.7:1:0.22511:1.29279:59.9:20.222:0.4789:0:1.1 +11 15511846 . T C 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=3.38757;LSEQ=CCTACATTACTCCAAAAAAC;RSEQ=CTAACAGGGCTGTATGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:36.5:1:33.5:1:1:0:60:4:0.4:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:17.5:1:31.5:1:1:0:60:4:0.6667:0:1 +11 17457039 . C G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01428;SOR=Inf;LSEQ=CTTTAGAAACAAGGAGAAAA;RSEQ=TAGACCCTTTTCCACTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:149,5:154,0:0:1,0:24.4:1:32.3:1:1:0:58.6:37.5:1:0:0.1 0/1:117:5:5,0:106,6:112,5:0.0427:2,0:30.2:1:33:0:1:0:54.2:10:0.0427:0:1 +11 17457183 . A C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=1.90267;LSEQ=GAAAGATGGGTGAATGTAAT;RSEQ=ATGTGTAGGAAGATGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1107:53:27,26:591,463:1054,53:0.0479:2,2:11.6:1:32.5:1:0.48118:1.22894:36:52:0.0475:0:4.8 0/1:1122:98:53,45:534,489:1023,98:0.0873:2,2:10.4:1:30.8:1:0.75156:1.08:34.7:97:0.0873:0:5 +11 17457210 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=2.02893;LSEQ=AGGAAGATGATGCTGGGAAC;RSEQ=TCTGTTCTTCACATGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1084:51:26,25:556,476:1032,51:0.047:2,2:32.3:1:30.7:1:0.77391:1.12302:35:24.5:0.0459:0:5.1 0/1:1087:99:52,47:519,466:985,99:0.0911:2,2:32.1:1:29.9:1:1:1.00664:33.8:48.5:0.0897:0:5.1 +11 17457213 . TGT CAC 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.11539;LSEQ=AAGATGATGCTGGGAACCTC;RSEQ=TCTTCACATGGCTGCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1088:49:25,24:558,479:1037,49:0.045:2,2:28.5:1:31.8:1:0.76995:1.11821:35.1:98:0.0457:0:3.1 0/1:1080:98:50,48:516,464:980,98:0.0907:2,2:28.2:1:30.9:1:0.8321:1.0675:33.8:196:0.0913:0:3.1 +11 17457422 . C G 127 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=15.38846;LSEQ=CCCCGGACACAGGGACTTCA;RSEQ=GCATTCCAAATAAGACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:875:1:1,0:414,459:873,1:0.0011:2,0:1:0:32:0:0.47483:0:60:2:0.0012:0:1 0/1:924:16:8,8:443,462:905,16:0.0173:2,2:14.8:1:31.8:1:1:1.04:26.9:32:0.0174:0:6.7 +11 17457424 . CA AG 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGACACAGGGACTTCACG;RSEQ=TTCCAAATAAGACTCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:841:0:0,0:403,436:839,0:0:2,0:24.3:1:32.1:1:1:0:54.4:43.158:0.9976:0:0.1 0/1:914:29:21,8:433,452:885,29:0.0317:2,2:13.2:1:31.1:1:0.01398:2.74:36.6:58:0.0321:0.0142:6.7 +11 17457434 . A T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00374;SOR=2.20245;LSEQ=GGACTTCACGCATTCCAAAT;RSEQ=AGACTCAAAGTTCCCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:20:15,5:351,385:736,20:0.0264:2,2:7.9:1:30.2:1:0.02156:3.29:38.6:19:0.0256:0:7.5 0/1:833:47:30,17:393,392:785,47:0.0564:2,2:13.5:1:30.3:1:0.0725:1.76:33.9:94:0.0571:0:6.6 +11 17457456 . T C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00105;SOR=2.36094;LSEQ=GACTCAAAGTTCCCAGGGAG;RSEQ=AACAGGGCCAACATGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:21:16,5:252,290:542,21:0.0373:2,2:29.5:1:33.4:1:0.01245:3.67:38.1:42:0.0379:0:7.5 0/1:632:53:33,20:276,303:579,53:0.0839:2,2:22.5:1:32.9:1:0.04514:1.81:33.3:106:0.084:0:6.7 +11 17457466 . A T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00389;SOR=2.14377;LSEQ=TCCCAGGGAGTAACAGGGCC;RSEQ=ACATGCCAAAAAGAGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:529:21:16,5:230,278:508,21:0.0397:2,2:36.9:1:30.4:1:0.00658:3.86:38.1:9.5:0.0365:0:7.5 0/1:577:47:30,17:229,300:529,47:0.0815:2,2:27.6:1:30.6:1:0.00879:2.31:34.6:94:0.0823:0:6.9 +11 17457479 . G A 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.08215;SOR=1.58827;LSEQ=CAGGGCCAACATGCCAAAAA;RSEQ=AGAGACCCCTGCACTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:510:28:18,10:199,282:481,28:0.0549:2,2:25.4:1:30.3:1:0.01908:2.55:33.6:56:0.0558:0:7.6 0/1:497:42:27,15:196,259:455,42:0.0845:2,2:25.9:1:30.2:1:0.00938:2.37:35:84:0.085:0:7.3 +11 17457487 . CC TT 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59977;SOR=1.15276;LSEQ=ACATGCCAAAAAGAGAGACC;RSEQ=TGCACTCAAAGCAATACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:29:18,11:181,284:465,29:0.0586:2,2:21.3:1:30:1:0.0183:2.56:33.8:58:0.0599:0.002:6.7 0/1:478:32:22,10:185,259:444,32:0.0669:2,2:25.7:1:30.1:1:0.00486:3.07:36.8:64:0.0672:0:6.7 +11 17457495 . C T 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4231;SOR=1.26538;LSEQ=AAAAGAGAGACCCCTGCACT;RSEQ=AAAGCAATACCAGTGCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:28:18,10:171,270:441,28:0.0594:2,2:19.4:1:29.2:1:0.00951:2.84:33.9:56:0.0606:0:6.6 0/1:432:32:21,11:157,243:400,32:0.0741:2,2:19.5:1:28.9:1:0.00469:2.95:36.7:64:0.0742:0:6.8 +11 17457506 . C T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79645;SOR=1.10512;LSEQ=CCCTGCACTCAAAGCAATAC;RSEQ=AGTGCCACGGTGGCAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:31:20,11:146,244:390,31:0.0735:2,2:15.8:1:30.1:1:0.00391:3.03:32.9:62:0.074:0:6.5 0/1:422:34:20,14:141,244:385,34:0.0806:2,2:11.4:1:28.1:1:0.01578:2.47:38.6:68:0.0813:0:6.2 +11 17457532 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39776;SOR=0.78233;LSEQ=CACGGTGGCAGATGGACATC;RSEQ=CCATGGGAAGAGACCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:29:13,16:126,235:361,29:0.0744:2,2:30.6:1:29.5:1:0.31578:1.51:25.7:13.5:0.0712:0:7.4 0/1:406:24:9,15:132,250:382,24:0.0591:2,2:26.3:1:29:1:0.8261:1.14:28.1:48:0.0605:0:7.4 +11 17457546 . C T 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.80364;SOR=0.92162;LSEQ=GACATCGCCATGGGAAGAGA;RSEQ=CAACTGTAGATAGTGATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:36:15,21:142,260:402,36:0.0822:2,2:29.7:1:31.1:1:0.47097:1.31:25.4:72:0.0826:0:7.5 0/1:446:34:12,22:141,271:412,34:0.0762:2,2:27.4:1:28.6:1:1:1.05:27.1:68:0.0767:0:7.6 +11 17457559 . G A 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90118;SOR=0.94898;LSEQ=GAAGAGACCAACTGTAGATA;RSEQ=TGATGTGGGGAGATATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:36:15,21:145,277:422,36:0.0786:2,2:32.8:1:31.4:1:0.36974:1.36:25.4:72:0.0791:0:7.5 0/1:454:34:12,22:148,272:420,34:0.0749:2,2:32.2:1:30.1:1:1:1.00:27.1:68:0.0757:0:7.6 +11 17457575 . TGGGACAG AAAACAC 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.88671;SOR=1.05417;LSEQ=GATAGTGATGTGGGGAGATA;RSEQ=TTTGAACTTGTGTTCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:25:11,14:130,237:367,25:0.0636:2,2:32.8:1:32.1:1:0.39583:1.43:26.8:50:0.0643:0.0025:3.9 0/1:404:27:10,17:145,231:376,27:0.0668:2,2:32.4:1:30.6:1:1:1.06694:27.6:54:0.0677:0:3.9 +11 17457590 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88027;SOR=0.92192;LSEQ=AGATATGGGACAGTTTGAAC;RSEQ=TGTGTTCTTATTCCAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:24:11,13:128,199:327,24:0.0682:2,2:24.8:1:32.5:1:0.52411:1.31:26.5:23:0.0673:0:8 0/1:364:23:8,15:144,197:341,23:0.0632:2,2:29:1:31.3:1:0.52126:1.3694:27:46:0.0642:0:8 +11 17457614 . C T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46336;SOR=1.55213;LSEQ=GTTCTTATTCCAGAACTGCT;RSEQ=CATCTCTTCTTTGGCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:7:2,5:135,187:322,7:0.0211:2,2:16:0:32.3:1:0.70369:1.80179:24.1:14:0.0219:0:8 0/1:308:10:3,7:139,158:297,10:0.0325:2,2:16:0:30.5:1:0.34972:2.04821:24.5:20:0.033:0:8 +11 17457697 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=AGTGGGCTCGGAGGCAATGA;RSEQ=AACCAACATGTCTCAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:120,168:288,0:0:2,0:25:1:32.3:1:1:0:58.4:143:0.9965:0:0.1 0/1:286:11:5,6:122,153:275,11:0.0385:2,2:27:1:29.4:1:1:1.04:57.5:22:0.0387:0:1.4 +11 17457739 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22107;SOR=0;LSEQ=GCACAGCCATCTTGGGTTCT;RSEQ=GTCTGGATGGAAGTGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:52,116:168,2:0.0118:2,2:13.5:1:29:1:0.5276:2.22:60:4:0.0121:0:1.5 0/0:191:0:0,0:68,123:191,0:0:2,0:26.4:1:30.3:1:1:0:59.9:94.5:1:0:0.2 +11 17733984 . C A 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27356;LSEQ=TTGTGTTGTTTAGTAAACAG;RSEQ=GCATGTGTATTTCAAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:775:326:186,140:243,203:446,326:0.4206:2,2:24.3:1:30.5:1:0.50946:1.11:60:39.75:0.419:0:1.1 0/1:767:127:72,55:352,286:638,127:0.1656:2,2:24.9:1:28.7:1:0.77021:1.06:60:41.333:0.1645:0:1.1 +11 17734179 . G C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=0.31497;LSEQ=GCCTCAGCTTCCCCTACCTG;RSEQ=TGGGCAGTCTCAGCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:63:5,58:15,64:79,63:0.4437:2,2:25.2:1:33.5:1:0.08792:2.7009:59.6:62:0.4429:0:1.1 0/1:105:21:2,19:14,70:84,21:0.2:2,2:31.1:1:32.3:1:0.51817:1.88997:60:42:0.2:0:1 +11 17740991 . A AC 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTGCGGCCACCCCGGGG;RSEQ=CCCCCCCAAGCCCCGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25:1:34.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 17741244 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51831;SOR=0;LSEQ=GCACTTTGCTATCTACAGCC;RSEQ=GGGCTCCCGAGCGGCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:129,12:141,2:0.014:2,2:28:1:29.5:1:0.17414:10.3683:60:4:0.0141:0:1.5 0/0:95:0:0,0:86,9:95,0:0:2,0:23.5:1:28.8:1:1:0:60:46.5:1:0:0.1 +11 17741265 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52183;SOR=0;LSEQ=GGGCTCCCGAGCGGCAGAAA;RSEQ=TTCCGGCCACTCTCTGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:169,29:198,2:0.01:2,2:19.5:1:27:1:0.27814:5.74661:60:4:0.0102:0:1 0/0:129:0:0,0:107,22:129,0:0:2,0:24.6:1:31.7:1:1:0:60:258:1:0:0.1 +11 17741542 . G A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01271;SOR=Inf;LSEQ=TTCCCCGCGGCGGTGCACCC;RSEQ=GCCCCGGGCGCACGTGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:114,307:421,0:0:2,0:24.5:1:30.5:1:1:0:59.9:37.273:1:0:0.1 0/1:396:6:4,2:121,268:389,6:0.0152:2,2:22.5:1:27.7:1:0.0827:4.41:60:12:0.0154:0:1 +11 17741786 . G A 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05751;SOR=0.23295;LSEQ=AGGTGGAGATCCTGCGCAAC;RSEQ=CCATCCGCTATATCGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:8:5,3:253,434:687,8:0.0115:2,2:17.1:1:29.5:1:0.15487:2.85:60:16:0.0117:0:1.1 0/0:740:2:2,0:295,443:738,2:0.0027:2,0:1:0:24.5:1:0.16076:0:60:4:0.0028:0:1 +11 17741838 . CGC AG 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10933;SOR=Inf;LSEQ=GCTGCGCGACCAGGACGCCG;RSEQ=CCCCTGGCGCCGCAGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:48,203:251,0:0:2,0:23.7:1:31.1:1:1:0:59.9:502:1:0:0.1 0/1:231:3:2,1:61,167:228,3:0.013:2,2:16.7:1:29.7:1:0.18139:5.43:60:6:0.013:0.0043:1.3 +11 17741892 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49811;SOR=Inf;LSEQ=GGGCCCGCTGCCCCCGGGCC;RSEQ=CGGCGGCGAGCACTACAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:49,0:0:2,0:18.5:1:31.3:1:1:0:60:48:1:0:0.3 0/1:57:2:1,1:35,19:54,2:0.0351:2,2:39:1:29:1:1:1.821:60:4:0.0364:0:1 +11 17741955 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2181;SOR=Inf;LSEQ=GCGCTCCAACTGCTCCGACG;RSEQ=CATGGTAAGGCCGGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:58,43:101,0:0:2,0:27.3:1:30.9:1:1:0:60:15.833:1:0:0.3 0/1:89:2:1,1:47,40:87,2:0.0225:2,2:14.5:1:30.5:1:1:1.17286:60:4:0.023:0:1 +11 17742320 . C G 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00512;SOR=Inf;LSEQ=CCCACCCGTAATTACCCCCC;RSEQ=AACCAGGACAGGTCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:143,3:146,0:0:1,0:23.1:1:31.1:1:1:0:60:35.5:1:0:0.2 0/1:80:5:5,0:72,3:75,5:0.0625:1,0:29.4:1:29:1:1:0:60:10:0.0633:0:1 +11 17742398 . G C 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTACAGGAATTGGTGTTC;RSEQ=GGCCTCGAGCCGTCCCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:0:0,0:375,192:567,0:0:2,0:24.2:1:29.8:1:1:0:60:39.5:0.9946:0:0.1 0/1:536:22:15,7:327,185:512,22:0.041:2,2:26.9:1:29.5:1:0.82182:1.21:59.6:21:0.0397:0:1.3 +11 17742600 . TC T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTGGCCTCTATCTAGGACGC;RSEQ=CCACCCCCACTCACACACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:116,305:421,0:0:2,0:24.3:1:31.1:1:1:0:60:41.1:1:0:0.2 0/1:334:14:4,10:99,221:320,14:0.0419:2,2:20:1:30.3:1:1:1.11953:60:28:0.0428:0.012:0.1 +11 17742681 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAAGTAGCTCCCTGTCTTTT;RSEQ=GATTGTCCCGGACTCTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:172:90,82:11,12:23,172:0.8776:2,2:22.2:1:31.7:1:0.82478:1.20:60:171:0.886:0:1.1 1/1:116:116:76,40:0,0:0,116:1:0,2:24.5:1:30.8:1:1:0:60:232:1:0:1.1 +11 17742690 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51923;SOR=0;LSEQ=CCCTGTCTTTTGGATTGTCC;RSEQ=GGACTCTAACTAAAGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:2,0:113,71:184,2:0.0108:2,0:13.5:1:32.5:1:0.52543:0:60:4:0.0109:0:1.5 0/0:123:0:0,0:92,31:123,0:0:2,0:24.3:1:30.5:1:1:0:60:60.5:1:0:1 +11 17746770 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCACTCCAGCTCTGGGCA;RSEQ=TAGAGCAAGACTCCATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:32,0:0,0:0,32:1:0,1:21.7:1:30.8:1:1:0:56.4:64:1:0:1 1/1:11:11:11,0:0,0:0,11:1:0,0:21.1:1:29.2:1:1:0:54.6:10:1:0:1.1 +11 17746976 . G T 173 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01879;LSEQ=CAAGAGGGAAGGGAACAGCT;RSEQ=GAGACTGGATCACACCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1193:50:27,23:634,509:1143,50:0.0419:2,2:23.4:1:30.7:1:0.88491:1.06097:60:100:0.0427:0:1.2 0/0:1219:1:0,1:651,567:1218,1:8e-04:2,0:1:0:24:0:0.46596:0:60:2:8e-04:0:1 +11 18586080 . TA T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.85725;SOR=1.10919;LSEQ=ATGTAAGAAAAGGCCATCTT;RSEQ=AAAAAAAAAAAGCCAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:13:8,5:54,25:79,13:0.1383:2,2:23.6:1:31.2:1:0.751:1.3455:60:26:0.1429:0.0426:0.6 0/1:172:26:15,11:90,49:139,26:0.1512:2,2:23.2:1:30.3:1:0.51139:1.3444:60:52:0.152:0.0233:0.4 +11 18586122 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18861;LSEQ=AGAAAGAGCTAAAATTACTA;RSEQ=ATTAAATGAGTTTAATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:60:36,24:43,32:75,60:0.4348:2,2:26.7:1:28.8:1:0.8607:1.12:60:11:0.4508:0:1.3 0/1:222:28:16,12:96,96:192,28:0.1261:2,2:27.1:1:27.1:1:0.5467:1.33:60:8.333:0.1225:0:1.3 +11 18586184 . C A 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13539;SOR=Inf;LSEQ=AAAAGAATTTGTGATTAAGT;RSEQ=ATATGAATGTCAAATTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:64,84:148,0:0:2,0:25.1:1:31.8:1:1:0:60:296:1:0:0.3 0/1:192:4:3,1:72,116:188,4:0.0208:2,2:18.3:1:23.3:1:0.30125:4.79:60:3:0.0159:0:1.5 +11 18586344 . C CAT 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33308;SOR=0.25066;LSEQ=GCCAAAATAAGGTTTTCCCA;RSEQ=GACAAAATGAAGGCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:0,6:0,7:7,6:0.4615:0,0:21.7:1:30.3:1:1:0:60:12:0.4615:0.1538:0.3 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:14:0:31.5:0:1:0:60:2:0.1667:0:0 +11 19498582 . T A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCTCCATCATATTGCAT;RSEQ=CCCAAGGGGTCCTTTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:0,16:1:0,1:15.1:1:29.2:1:1:0:60:32:1:0:1.8 1/1:4:4:4,0:0,0:0,4:1:0,0:18:1:28.8:1:1:0:60:8:1:0:1.8 +11 19498649 . G T 167 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00279;SOR=0;LSEQ=TGGCCAGTCTTGGGTCAAGC;RSEQ=AAATGATTTTTTTGGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:39,0:0,0:0,39:1:0,1:19.6:1:31.6:1:1:0:60:38:1:0:2 1/0:26:20:20,0:6,0:6,20:0.7692:0,1:21:1:31:1:1:0:60:40:0.7692:0:2.1 +11 19498655 . A AT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50982;SOR=0;LSEQ=GTCTTGGGTCAAGCGAAATG;RSEQ=TTTTTTTGGATAAGACTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:2,0:44,0:44,2:0.0435:1,0:12:1:29.5:1:1:0:60:4:0.0455:0.0217:2 0/0:32:0:0,0:32,0:32,0:0:1,0:19.8:1:28.1:1:1:0:60:15:1:0:1.4 +11 19498686 . C T 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAGACTATCCAAACCCTTC;RSEQ=CAAGGTAAAGTCAGGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:71:71,0:0,0:0,71:1:0,1:26.3:1:33:1:1:0:60:70:1:0:1.5 1/0:54:29:29,0:25,0:25,29:0.537:1,1:30:1:30.5:1:1:0:60:58:0.537:0:1.6 +11 19498860 . C G 262 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.00759;LSEQ=TTTTGCCACTTACATTACAC;RSEQ=AAAACCTCCTAGAAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:358:355:137,218:0,1:1,355:0.9916:0,2:25.8:1:31:1:1:0:59.9:87.75:0.9943:0:1.5 0/1:414:195:92,103:93,124:217,195:0.471:2,2:24.9:1:29.8:1:0.42754:1.19:60:96.5:0.4684:0:1.7 +11 19498866 . C T 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.00016;SOR=Inf;LSEQ=CACTTACATTACACCAAAAC;RSEQ=TCCTAGAAGGCAGGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:122,217:339,0:0:2,0:24.5:1:32.2:1:1:0:59.9:66.8:0.9911:0:1.6 0/1:392:14:6,8:167,210:377,14:0.0357:2,2:32:1:29.8:1:1:1.06017:60:28:0.0361:0:3 +11 19498907 . T C 244 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACTGATTTTGTTTGCATTA;RSEQ=TTATTATATTTTGTGCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:167:167:36,131:0,0:0,167:1:0,2:24.2:1:33.1:1:1:0:60:82.5:1:0:2.3 1/0:219:114:37,77:26,78:104,114:0.5205:2,2:25.9:1:31.2:1:0.23556:1.44:60:113:0.5231:0:2.4 +11 19498915 . AT A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50677;SOR=Inf;LSEQ=TTGTTTGCATTATTTATTAT;RSEQ=TTTGTGCATTGAAACAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:26,120:146,0:0:2,0:24.4:1:30.3:1:1:0:60:28.2:1:0:2.3 0/1:189:2:1,1:50,137:187,2:0.0106:2,2:12:1:31:1:0.46792:2.72:60:4:0.0107:0.0053:4 +11 19498936 . T A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTTGTGCATTGAAACAGTT;RSEQ=ATCAGCAAGGATTTATTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:13,93:0,0:0,106:1:0,2:24.2:1:31.1:1:1:0:60:105:1:0:2.3 1/1:124:102:21,81:4,18:22,102:0.8226:2,2:24.2:1:29.1:1:1:1.17:60:204:0.8226:0:2 +11 19499060 . G A 106 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13725;SOR=0;LSEQ=TGTGAATTTTGCATTCAGAC;RSEQ=GAACTGGGTCTATGTGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:26.6:1:30.9:1:1:0:60:10:1:0:1 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:29:1:31.2:1:1:0:60:10:0.7143:0:1 +11 19499168 . T C 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAAATTTACAACCTTCA;RSEQ=GAGGGTCCCCAGCATAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:16.3:1:31.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 20245648 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGGTAAAGCATAGTGCA;RSEQ=TTGTGTTATTTTTAAGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 20245673 . TG T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTATTTTTAAGATTGCAAA;RSEQ=AGAGGAATTCAATCTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 20246591 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51603;SOR=Inf;LSEQ=CCATGGTAATGATGCTTAGT;RSEQ=CAGTCGCAAGTCATTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:36,20:56,0:0:2,0:26:1:31.6:1:1:0:60:55:0.9821:0:0.2 0/1:85:2:1,1:48,35:83,2:0.0235:2,2:20.5:1:25.5:1:1:1.36624:60:4:0.0238:0:1 +11 20246592 . C T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17529;SOR=0;LSEQ=CATGGTAATGATGCTTAGTG;RSEQ=AGTCGCAAGTCATTGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:38,21:59,2:0.0328:2,2:20.5:1:25:1:1:1.79094:60:4:0.0339:0:1.5 0/0:84:0:0,0:48,36:84,0:0:2,0:27:1:31.2:1:1:0:60:168:1:0:0.1 +11 20246597 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50714;SOR=Inf;LSEQ=TAATGATGCTTAGTGCAGTC;RSEQ=CAAGTCATTGAAAGATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:44,25:69,0:0:2,0:24.1:1:30.2:1:1:0:60:68:1:0:0.2 0/1:92:2:1,1:50,40:90,2:0.0217:2,2:19:1:27.5:1:1:1.24694:60:4:0.0217:0:1 +11 20246599 . A G 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18734;SOR=0;LSEQ=ATGATGCTTAGTGCAGTCGC;RSEQ=AGTCATTGAAAGATTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:46,25:71,2:0.0274:2,2:17.5:1:27.5:1:1:1.82385:60:4:0.0278:0:1 0/0:95:0:0,0:51,43:94,0:0:2,0:27.4:1:29.4:1:1:0:60:188:0.9895:0:0.1 +11 20246743 . C A 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06372;SOR=0;LSEQ=AGATTGATACTAGTGGGAAC;RSEQ=CCTTGGAGATTACTTAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:0,10:0,13:13,10:0.4348:1,0:22.7:1:32:0:1:0:60:20:0.4348:0:1 0/0:7:0:0,0:1,6:7,0:0:2,0:20.4:1:31:1:1:0:60:14:1:0:0 +11 20575654 . G C 157 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01919;LSEQ=GTGCTAGGTGTGGGGTTAGA;RSEQ=TGGGGAGCAAGATGGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:33:32,1:48,3:51,33:0.3929:2,1:30.2:1:31.2:1:1:1.99:60:10:0.3704:0:1.1 0/1:83:1:1,0:72,10:82,1:0.012:2,0:16:0:33:0:1:0:60:2:0.012:0:1 +11 20575682 . A T 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGATGGAGATGATGCTGC;RSEQ=TTATCAGAGTTTATTATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:124,38:162,0:0:2,0:21.2:1:30.1:1:1:0:60:80:1:0:0.3 0/1:155:45:30,15:79,31:110,45:0.2903:2,2:19.7:1:28.6:1:0.56373:1.27213:60:90:0.2941:0:1.1 +11 20575717 . A T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62659;SOR=2.66007;LSEQ=TATCTAGAAATTAGGTAAGC;RSEQ=TTTAAAGGGTGATAAGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:1:0,1:159,103:262,1:0.0038:2,0:1:0:23:0:0.39544:0:60:2:0.0039:0:2 0/1:298:3:1,2:176,119:295,3:0.0101:2,2:16.7:1:27:1:0.56835:2.94715:60:6:0.0101:0:1.3 +11 20575787 . G C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65717;SOR=0.92633;LSEQ=AGTGTACTGGCCAGCATCCT;RSEQ=CCCACACATCCCCTCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:329:168:68,100:74,87:161,168:0.5106:2,2:24.1:1:31.3:1:0.31919:1.24998:59.8:55:0.5156:0:1.2 0/1:411:202:97,105:95,111:206,202:0.4915:2,2:26.1:1:29.9:1:0.76609:1.08:60:32.667:0.4864:0:1.2 +11 20575883 . C G 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGAATATTTAAAATGAAAAC;RSEQ=TTGCAAGATGATAGTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:7,68:75,0:0:2,0:24.5:1:32.7:1:1:0:60:24:1:0:0.1 0/1:103:20:4,16:16,66:82,20:0.1942:2,2:19.5:1:30:1:1:1.03:60:19:0.19:0:1.4 +11 20575937 . G A 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05015;SOR=Inf;LSEQ=TCAAAGTCATATGGTTTTCA;RSEQ=TGTGAAGATGTCAGGATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:1,23:24,0:0:1,0:22.1:1:32.7:1:1:0:60:23:1:0:0 0/1:25:5:0,5:1,19:20,5:0.2:1,0:20:1:31.2:1:1:0:60:10:0.2174:0:2.2 +11 20575982 . CCCTT C 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=4;SSF=0.23077;SOR=0;LSEQ=CCCTCCCTCCCTCCCTCCCT;RSEQ=CCTTCCTTCCTTTGCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,6:6,3:0.375:0,0:24.3:1:29:1:1:0:60:6:0.375:0.25:0.7 0/0:5:0:0,0:0,5:5,0:0:0,0:24.6:1:31.8:1:1:0:60:10:1:0:1 +11 20576595 . T C 33 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGTGGGGATTATTACAA;RSEQ=TCAAGGTGAGATTTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:33:0:1:0:53:4:1:0:1 +11 21635224 . A T 33 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37212;SOR=0.32948;LSEQ=ATACCACCTGAGGCTTAATC;RSEQ=AATATTTTCTGATTAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:2,1:135,79:214,3:0.0138:2,2:11.3:1:21:1:1:1.17:60:2:0.0093:0:1 0/0:218:1:0,1:136,80:216,1:0.0046:2,0:1:0:21:0:0.37327:0:60:2:0.0047:0:1 +11 21635226 . A G 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01232;SOR=1.64241;LSEQ=ACCACCTGAGGCTTAATCAA;RSEQ=TATTTTCTGATTAGCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:83:58,25:81,56:137,83:0.3739:2,2:26.9:1:32.3:1:0.11536:1.60:60:40.5:0.3682:0:1.9 0/1:218:108:70,38:66,44:110,108:0.4954:2,2:24.7:1:31.5:1:0.48702:1.23:60:107:0.4977:0:1.7 +11 21635282 . C G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.10544;LSEQ=TCTAATAAACTGACAATCAG;RSEQ=GGTAATGGGAGCTGCTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:101:53,48:95,101:196,101:0.3378:2,2:25.7:1:31.4:1:0.54167:1.17:60:202:0.3459:0:2.3 1/0:303:157:78,79:72,73:145,157:0.5182:2,2:24.9:1:30:1:1:1.00:60:156:0.5235:0:1.6 +11 21635295 . T G 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAATCAGCGGTAATGGGAGC;RSEQ=GCTAGACAGGAGGGAAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:94:47,47:88,102:190,94:0.3298:2,2:27.1:1:30.7:1:0.61402:1.16:59.6:188:0.3333:0:2.3 0/0:304:0:0,0:141,163:304,0:0:2,0:25:1:29.5:1:1:0:59.9:59.8:1:0:0.8 +11 21635306 . A G 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24927;SOR=Inf;LSEQ=AATGGGAGCTGCTAGACAGG;RSEQ=GGGAAGACCCTTCTTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:126,145:271,0:0:2,0:25.4:1:30.6:1:1:0:59.8:37.714:1:0:0.8 0/1:287:3:1,2:131,152:283,3:0.0105:2,2:33.7:1:25.7:1:1:1.72054:60:2:0.0071:0:2 +11 21635308 . G A 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00023;SOR=Inf;LSEQ=TGGGAGCTGCTAGACAGGAG;RSEQ=GAAGACCCTTCTTTGGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:124,142:266,0:0:2,0:25.3:1:30.7:1:1:0:59.8:37:1:0:0.8 0/1:285:13:7,6:125,147:272,13:0.0456:2,2:19.7:1:29.7:1:0.58509:1.37:60:26:0.0464:0:1.9 +11 21635345 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24802;SOR=Inf;LSEQ=TGTTAGGGCCACTCTGTGAC;RSEQ=AGTCATTGCTCAGGCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:65,125:190,0:0:2,0:25.3:1:31.7:1:1:0:60:380:1:0:0.5 0/1:189:2:1,1:68,119:187,2:0.0106:2,2:11.5:1:27:1:1:1.74:60:4:0.0108:0:2.5 +11 21635346 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=GTTAGGGCCACTCTGTGACC;RSEQ=GTCATTGCTCAGGCTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:62,124:186,0:0:2,0:25.6:1:31.2:1:1:0:60:185:1:0:0.5 0/1:187:2:1,1:67,118:185,2:0.0107:2,2:9.5:1:29:1:1:1.76:60:4:0.0108:0:1.5 +11 23122594 . CT C 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.04444;SOR=0;LSEQ=TTGAAATAGTTTCAATAGAC;RSEQ=TTTTTGTATGTAAGCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:4:2,2:156,229:385,4:0.0102:2,2:31.5:1:32.5:1:1:1.47:60:8:0.0103:0:0.8 0/0:460:0:0,0:200,260:460,0:0:2,0:26.7:1:29.4:1:1:0:60:56.5:1:0:0.5 +11 23122604 . T C 218 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAATAGACCTTTTTTGTA;RSEQ=GTAAGCAAACTCAACAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:151,223:374,0:0:2,0:25.5:1:30.4:1:1:0:59.9:73.8:0.9973:0:0.1 0/1:450:164:68,96:119,167:286,164:0.3644:2,2:25.5:1:29.7:1:1:1.00598:60:163:0.3679:0:1.1 +11 23122634 . C CA 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=0.17648;LSEQ=CTCAACAAATTATTTTTAGT;RSEQ=AAAAAATTTATTTCTTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:108:37,71:49,102:151,108:0.4154:2,2:27.4:1:31.1:1:0.78993:1.08:60:216:0.4303:0.0538:0.1 0/1:333:37:11,26:111,185:296,37:0.1111:2,2:25.1:1:29.1:1:0.46942:1.41675:60:11.333:0.1043:0.003:0.2 +11 23122704 . T C 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGTAACTAGCACACAGTTA;RSEQ=CACTTAATAGATGCTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:3,61:64,0:0:1,0:24.4:1:30:1:1:0:60:63:1:0:0.4 0/1:70:27:4,23:6,37:43,27:0.3857:2,2:21.5:1:31.2:1:1:1.07:60:54:0.3857:0:1 +11 23122721 . A C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00121;SOR=0.18267;LSEQ=TTATCACTTAATAGATGCTT;RSEQ=AGTGAATGAATGACTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:22:0,22:2,28:30,22:0.4231:2,1:25.2:1:33.2:1:0.50226:0:60:44:0.4231:0:1.2 0/1:43:5:0,5:2,36:38,5:0.1163:2,0:28.2:1:32.2:1:1:0:60:10:0.1163:0:1 +11 23122852 . A C 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTCTCAGCAATAAATA;RSEQ=TTTTCCCAAATGTTTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:27.6:1:34:1:1:0:60:10:0.5556:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:29:0:18:0:1:0:60:0:0:0:1 +11 24881825 . C T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AACCCCAGGCAGAGGCTCAG;RSEQ=GACAGAATCTGATCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,2:2,2:0.5:0,0:18:1:29.5:1:0.33333:0:60:4:0.5:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:32.6:1:29.8:1:1:0:60:10:1:0:0.4 +11 24882079 . T C 50 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCACCCTATACAGGAG;RSEQ=GATCCTACTGGCAACAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:44:1:31.5:1:1:0:59:4:1:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:17.3:1:32:1:1:0:60:6:1:0:1 +11 24882340 . C A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1396;SOR=0;LSEQ=AAGGCCCCCCCAAAAACCCT;RSEQ=CCCAAGGGTCAGCAGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:19,19:0,0:0,38:1:0,2:32.5:1:28.9:1:1:0:58.8:76:1:0:1.1 1/1:54:50:22,28:0,0:0,50:0.9259:0,2:27.5:1:27.9:1:1:0:59.2:15.667:0.9216:0:1.3 +11 24882358 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50476;SOR=Inf;LSEQ=CTCCCCAAGGGTCAGCAGCC;RSEQ=CAAAGACCCAAGCTGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:18,21:39,0:0:2,0:30:1:30.5:1:1:0:58.8:38:1:0:1 0/1:52:2:1,1:21,29:50,2:0.0385:2,2:35.5:1:32:1:1:1.37:51:4:0.0392:0:2.5 +11 24882489 . T C 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCCATCAAGGGTGCAGAAC;RSEQ=GGATGGAGGATCAGATGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:6.5:1:29:1:1:0:60:4:1:0:0 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:30.5:1:28:1:1:1.22474:60:4:0.1818:0:1 +11 24882587 . G A 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATGTTCTAACCCAATGC;RSEQ=AAGAAGCTAAGAACTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:23.4:1:32.4:1:1:0:57.8:10:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:28:0:32:0:1:0:36:2:1:0:1 +11 25022127 . T C 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65618;SOR=0.47503;LSEQ=ATACAGGGCCCAAAGGTGAG;RSEQ=AACAGCAAAATAGCTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:3,1:8,5:13,4:0.2353:2,2:15.8:1:32.5:1:1:1.81:49.5:8:0.25:0:2 0/1:16:2:1,1:10,4:14,2:0.125:2,2:27.5:1:33:0:1:2.34522:45.5:4:0.125:0:1.5 +11 25022172 . T C 80 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09848;SOR=0.15357;LSEQ=CTTAGAAAGGGGAGAAGCCA;RSEQ=GTTGCCCAACTCCAGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:8,7:15,6:0.2857:2,2:35:1:31.3:1:0.65944:1.70:41.3:12:0.2857:0:1.7 0/1:18:1:1,0:10,7:17,1:0.0556:2,0:31:0:34:0:1:0:31:2:0.0556:0:2 +11 25023468 . C T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTGCTTGTACTGCTGTTCTC;RSEQ=CTTCTCCTTTCCCTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:8:0:33.5:1:1:0:23:4:1:0:0.5 1/0:4:2:1,1:1,1:2,2:0.5:2,2:31.5:1:30.5:1:1:1:60:4:0.5:0:1 +11 27795538 . T C 216 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=152.34398;LSEQ=TTCTAAAGAGGTGCATTCTA;RSEQ=TGATTGTAGGATTTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:1:1,0:170,265:435,1:0.0023:2,0:31:0:13:0:0.3922:0:60:0:0:0:1 0/1:450:117:48,69:146,186:332,117:0.26:2,2:25.4:1:31.5:1:0.58951:1.12806:60:234:0.2629:0:1.1 +11 27795598 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49893;SOR=0;LSEQ=GCACATCTGCCGGTAGCACA;RSEQ=CATTGTTTTGCATAAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:37,147:184,2:0.0108:2,2:39.5:1:31.5:1:0.36774:3.93:60:4:0.011:0:1 0/0:177:0:0,0:37,140:177,0:0:2,0:45:0:14:0:1:0:60:0:0:0:5 +11 27795708 . T G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01544;SOR=Inf;LSEQ=GGTGGTGGTTGGGTGAGGGA;RSEQ=CACAGTGAGAAGGGAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:2,25:27,0:0:2,0:27.4:1:28.7:1:1:0:60:12.5:1:0:0.3 0/1:10:3:0,3:1,6:7,3:0.3:2,0:43:1:31.7:1:1:0:60:6:0.3:0:1 +11 30098621 . TT A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.33779;SOR=1.19837;LSEQ=AGAAGTTAATATAACCATAG;RSEQ=TTTTCCTTCAGAAGTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:78:44,34:105,80:185,78:0.2943:2,2:26.4:1:31.7:1:1:1.01415:60:156:0.2977:0.0226:1 0/1:357:119:66,53:132,104:236,119:0.3333:2,2:24.6:1:29.8:1:1:1.01918:59.5:238:0.3352:0.0448:1.1 +11 30098622 . T A 59 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.19564;SOR=0.39491;LSEQ=GAAGTTAATATAACCATAGT;RSEQ=TTTTCCTTCAGAAGTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:6:4,2:105,81:186,6:0.0313:2,2:13:1:23.2:1:0.70002:1.54:59.2:1:0.0161:0:2.3 0/1:239:3:2,1:131,104:235,3:0.0126:2,2:12:1:25.3:1:1:1.58:58.3:2:0.0085:0:2.3 +11 30098650 . G C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.8723;SOR=0.97437;LSEQ=TCAGAAGTTGAGTTATTTGA;RSEQ=TTTTCTAAGGCACTTTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:106:51,55:90,105:195,106:0.3522:2,2:23.5:1:31.9:1:0.8091:1.08:60:34.333:0.3456:0:2.2 0/1:387:134:64,70:125,128:253,134:0.3463:2,2:27.4:1:31.3:1:0.83081:1.06791:59.6:268:0.3463:0:2.2 +11 30098715 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAATATAAGTTAGAAAATG;RSEQ=AAGTCTAGTTTTTGATACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:162:162:48,114:0,0:0,162:1:0,2:23.4:1:30.6:1:1:0:59.9:80:1:0:1.4 1/1:210:178:61,117:11,20:31,178:0.8476:2,2:24.2:1:29.4:1:1:1.05465:60:177:0.8469:0:1.3 +11 30098849 . G T 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0033;SOR=0;LSEQ=AGACTAAAAATTGTGTAAAT;RSEQ=TAGACAGCATATACCTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:8,8:0.5:0,0:22.6:1:31.3:1:1:0:60:16:0.5:0:1 0/0:13:0:0,0:0,13:13,0:0:1,0:22.2:1:32.8:1:1:0:60:26:1:0:0.4 +11 30254268 . T G 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GAAATAGTTTCCATGGTGCT;RSEQ=TCTTTTTTCTCTGCAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:27.6:1:32.6:1:1:0:60:10:0.5556:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:8:1:32:0:1:0:60:4:1:0:0 +11 30254550 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04563;SOR=0.70061;LSEQ=CTGGATTAAAAATTCTTATA;RSEQ=GCAAACTGCATATCCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:126:61,65:62,63:125,126:0.498:2,2:27.1:1:31.1:1:0.89976:1.04843:60:125:0.498:0:1.2 0/1:283:116:51,65:77,87:164,116:0.4099:2,2:26:1:30:1:0.62863:1.12753:60:232:0.4143:0:1.1 +11 30254607 . A G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12064;SOR=Inf;LSEQ=AAGTATACAGCTTTCAAGGG;RSEQ=GAAAAATGTCCACAAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:84,131:215,0:0:2,0:25:1:31.1:1:1:0:60:106.5:1:0:0.5 0/1:211:3:1,2:77,131:208,3:0.0142:2,2:25.3:1:29.7:1:1:1.17473:60:6:0.0144:0:2 +11 30254683 . A C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.99107;LSEQ=CATGTTAACTTAAGCATTAA;RSEQ=ATTTAAAATTATATATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:18:0,18:1,29:30,18:0.375:1,1:25.4:1:33:1:1:0:60:36:0.375:0:1.2 0/1:59:22:3,19:3,34:37,22:0.3729:2,2:24.5:1:32:1:0.6614:1.77:60:44:0.3729:0:1 +11 32106583 . C T 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00083;SOR=Inf;LSEQ=GGTGCAATATATCAGTAGAC;RSEQ=TAACAGAATGAATATCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:31,0:0:1,0:26.7:1:31.5:1:1:0:60:62:1:0:0 0/1:31:10:10,0:21,0:21,10:0.3226:1,0:26.8:1:32.3:1:1:0:60:20:0.3226:0:1.2 +11 32106694 . C T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0735;SOR=0;LSEQ=ACTTTGTGACTTCCACGAGA;RSEQ=ACTGACCATCACACAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:1,2:96,74:170,3:0.0172:2,2:32.3:1:24.7:1:0.58274:2.58051:60:2:0.0116:0:1.3 0/0:240:0:0,0:126,114:240,0:0:2,0:28.6:1:31:1:1:0:60:59:1:0:0.1 +11 32106837 . G A 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03855;SOR=Inf;LSEQ=AAAAAGATGTTAGCATGAGG;RSEQ=ATTTCTGATCAGGGTCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:97,74:171,0:0:2,0:26.9:1:31.1:1:1:0:60:33.2:1:0:0.1 0/1:224:6:4,2:119,98:217,6:0.0268:2,2:27.7:1:29.5:1:0.6934:1.64:60:12:0.0273:0:1.2 +11 32106872 . TA T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18178;SOR=0;LSEQ=TCAAGCTGTGTTCTGATCAC;RSEQ=ATGACTTGTCGGCTTGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:82,109:191,2:0.0104:2,2:12:1:27.5:1:1:1.33:60:4:0.0105:0.0052:0.5 0/0:259:0:0,0:131,128:259,0:0:2,0:27.1:1:28.7:1:1:0:60:85.333:1:0:0.2 +11 32106903 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18462;SOR=0;LSEQ=CGGCTTGTGGGATGGAGGAG;RSEQ=AATGAGTGTCTTTGGTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:65,100:165,2:0.012:2,0:14:1:27:1:0.15951:0:60:4:0.0121:0:1 0/0:221:0:0,0:101,116:217,0:0:2,0:22.9:1:31.1:1:1:0:60:107.5:0.9817:0:0.1 +11 32106983 . G T 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24651;SOR=Inf;LSEQ=AGGAGTCGACAGCAGCAGTT;RSEQ=ATGGCAAGATGGTACTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:65,43:108,0:0:2,0:24.6:1:32.4:1:1:0:59.9:53:1:0:0.1 0/1:107:2:1,1:52,53:105,2:0.0187:2,2:8:0:26:1:1:1.02:60:4:0.019:0:1 +11 32107011 . T C 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGGTACTCAGAAATGGCA;RSEQ=TGATGTAATTTAGGACGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:74,36:110,0:0:2,0:24.5:1:30.8:1:1:0:59.9:35.667:1:0:0.1 0/1:113:25:17,8:58,30:88,25:0.2212:2,2:32.4:1:31.7:1:1:1.10:60:50:0.2252:0:1.5 +11 32107062 . C T 165 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=72.89342;LSEQ=GAGACAGCACACAATTAGAA;RSEQ=AAAGAATTGGCAGAGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:0,1:131,100:231,1:0.0043:2,0:1:0:26:0:0.43534:0:60:2:0.0044:0:1 0/1:249:60:29,31:105,84:189,60:0.241:2,2:26.2:1:28:1:0.37346:1.33463:60:120:0.2459:0:1.4 +11 32107091 . G T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2487;SOR=Inf;LSEQ=GGCAGAGGGGGTCGACTTGG;RSEQ=AAGAAAGGTGTGGATATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:149,138:287,0:0:2,0:29.1:1:31.8:1:1:0:60:56.4:1:0:0.2 0/1:289:3:1,2:142,144:286,3:0.0104:2,2:27.7:1:25:1:1:1.96776:60:6:0.0107:0:1 +11 32107172 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23364;SOR=Inf;LSEQ=GACTTTCTACGATACCATAG;RSEQ=GGAAGAGATGCCCATGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:34,98:132,0:0:2,0:25.4:1:30.3:1:1:0:60:65:1:0:0 0/1:124:2:1,1:46,76:122,2:0.0161:2,2:32.5:1:26:1:1:1.65:60:4:0.0163:0:1 +11 32409549 . AACAC A 29 d5;v3;pSTD;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=17.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAAAAAACAAAACACAACAC;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:39:0:29:1:1:0:60:4:0.6667:0:0 +11 32410774 . A G 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGCAACAAAGAGACAGGC;RSEQ=CAAGTTCAACTATCAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:35,187:222,0:0:2,0:21.8:1:30.2:1:1:0:59.8:73:1:0:0.1 0/1:239:46:7,39:33,160:193,46:0.1925:2,2:18.6:1:31.5:1:1:1.14845:60:92:0.1925:0:1.2 +11 32413417 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49743;SOR=0;LSEQ=TCAACTGAGTCTAAACCTTA;RSEQ=AACTTTTACACTAGTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:2,0:73,2:75,2:0.026:1,0:15.5:1:32.5:1:1:0:60:4:0.026:0:1 0/0:71:0:0,0:69,2:71,0:0:1,0:27.2:1:31.5:1:1:0:60:22.667:1:0:0.1 +11 32413470 . T A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28287;SOR=Inf;LSEQ=ATCACAATTTCATTCCACAA;RSEQ=AGTTTAAAAAAATAATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:126,48:174,0:0:2,0:23.1:1:30:1:1:0:60:57:1:0:0.1 0/1:269:3:2,1:182,83:265,3:0.0112:2,2:19.7:1:28:1:1:1.096:60:6:0.0113:0:1.3 +11 32413662 . A G 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0908;SOR=0;LSEQ=CTAACAATGTGGGCACAGTG;RSEQ=GGCCCACAAGGCTGACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:1,2:37,130:167,3:0.0176:2,2:26.3:1:30.3:1:0.53426:1.75:60:6:0.0179:0:1 0/0:207:0:0,0:48,159:207,0:0:2,0:23.6:1:29.7:1:1:0:60:102.5:1:0:0.1 +11 32414094 . T C 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61902;SOR=2.06171;LSEQ=AGATTATGGGGGGAAAATAC;RSEQ=GGAAAAACTAAACACATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:1,0:181,8:189,1:0.0053:1,0:9:0:33:0:1:0:60:2:0.0054:0:1 0/1:185:2:1,1:174,9:183,2:0.0108:1,2:11.5:1:28.5:1:0.10546:18.38814:60:4:0.011:0:1 +11 32414333 . G T 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=24.36905;LSEQ=CACATATTCTATTTGAAAAT;RSEQ=ATACTGGAAAAGGGGATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:2:1,1:71,182:253,2:0.0078:2,2:16.5:1:28.5:1:0.48578:2.55:60:4:0.0078:0:1 0/1:292:47:14,33:62,183:245,47:0.161:2,2:16.4:1:28.1:1:0.58636:1.25:60:94:0.1621:0:1.1 +11 32414518 . TA T 30 v3;MAF0.05;MSI12;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=1.22183;LSEQ=CTCACATCTAGCTCTGCCAT;RSEQ=AAAAAAAAAAAAAAGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:32:1:30.5:1:1:0:60:4:0.2857:0:0.5 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:39:0:28:0:1:0:60:2:0.3333:0:0 +11 32417796 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12621;SOR=Inf;LSEQ=CCAAGACTGGACAGCGGGCA;RSEQ=ACTTACCAGTGTGCTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:247,100:347,0:0:2,0:23.9:1:32.3:1:1:0:60:114.667:1:0:0.1 0/1:387:4:1,3:261,122:383,4:0.0103:2,2:20.5:1:26:1:0.101:6.38503:60:8:0.0105:0:1 +11 32417945 . T C 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCTACTCCAGGCACACG;RSEQ=CGCACATCCTGCAGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:476:0:0,0:174,300:474,0:0:2,0:23.8:1:29.8:1:1:0:59.9:51.667:0.9979:0:0.1 0/1:575:69:28,41:175,328:503,69:0.12:2,2:25.9:1:31.1:1:0.3505:1.28:60:138:0.1223:0:1.1 +11 32418019 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49831;SOR=Inf;LSEQ=AACATTCACGTAGGTCTTGA;RSEQ=GGAGAGTGAGCACTGGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:6,108:114,0:0:2,0:24.9:1:31.1:1:1:0:59.8:37:1:0:0.2 0/1:121:2:1,1:18,101:119,2:0.0165:2,2:23:1:24:1:0.2905:5.49:60:4:0.0168:0:1 +11 32421470 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26817;SOR=Inf;LSEQ=GGCAGTGCGGCCCCCTTCCC;RSEQ=CTGGGGCCTGTCTGTGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:140,59:199,0:0:2,0:25.6:1:30.4:1:1:0:60:98.5:1:0:0.1 0/1:276:3:2,1:191,81:272,3:0.0109:2,2:27:1:31.3:1:1:1.17826:60:6:0.0112:0:1 +11 32421493 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06415;SOR=0;LSEQ=GGGGCCTGTCTGTGTGCTCA;RSEQ=CTGAATGCCTCTGAAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:161,96:257,3:0.0115:2,2:10.3:1:28:1:0.55864:3.33805:60:6:0.0118:0:1 0/0:388:0:0,0:234,154:388,0:0:2,0:25.3:1:30.7:1:1:0:60:42.111:1:0:0.2 +11 32421627 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14242;SOR=Inf;LSEQ=GGGAAAAAGGCTCAGTGTGG;RSEQ=TCACAGTCGCCATTTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:62,156:218,0:0:2,0:23:1:32.9:1:1:0:60:217:1:0:0.1 0/1:300:4:2,2:94,201:295,4:0.0133:2,2:39.5:1:29.3:1:0.59595:2.13:60:8:0.0134:0:1 +11 32437699 . T C 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAGTTAAGACTGAAAGC;RSEQ=TTGACTGATCTAACAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:12:1:31:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 32437841 . A C 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0;LSEQ=TCCAGGGGCATGTTGATGAG;RSEQ=AATGCTACTCCCTCCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:14,0:19,0:19,14:0.4242:1,1:17.6:1:31.9:1:1:0:60:13:0.4063:0:1.1 0/0:25:0:0,0:25,0:25,0:0:1,0:26.9:1:28.8:1:1:0:60:24:1:0:0.2 +11 32437902 . G A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=GAATAAGAAGAGGTGGGGGC;RSEQ=GGGGAGAGAGATTCTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:82,3:85,0:0:1,0:25.4:1:29.7:1:1:0:59.6:84:0.9882:0:0.3 0/1:84:9:9,0:71,4:75,9:0.1071:2,0:30.4:1:29.1:1:1:0:60:18:0.1084:0:2.1 +11 32437914 . T G 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=43.02806;LSEQ=GTGGGGGCGGGGGAGAGAGA;RSEQ=TCTTCCCATCCACCAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:1,0:116,13:129,1:0.0077:2,0:32:0:35:0:1:0:60:2:0.0079:0:2 0/1:135:34:32,2:92,9:101,34:0.2519:2,2:24.2:1:31.7:1:0.72977:1.56:59.7:68:0.2537:0:1.4 +11 32437946 . C T 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25612;SOR=Inf;LSEQ=ACCAAATGCTACCCTGATTA;RSEQ=CCACGTCAGTCCTAACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:174,69:243,0:0:2,0:23.1:1:31.8:1:1:0:60:80:1:0:0.1 0/1:297:3:1,2:227,67:294,3:0.0101:2,2:6:1:25.7:1:0.13587:6.7197:60:6:0.0101:0:1 +11 32438788 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCACTTCTTGATAAGA;RSEQ=AGTGGAATGGTTAACAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:20.5:1:31:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 32439001 . T C 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGAGGAAAGCGTTCTAATG;RSEQ=CACAGAGAGCTTTGCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:41:40,1:67,0:67,41:0.3796:1,1:27.2:1:32.1:1:0.37963:0:60:19.5:0.3679:0:1 0/0:85:0:0,0:85,0:85,0:0:1,0:24.4:1:29.8:1:1:0:60:170:1:0:0.1 +11 32439016 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5023;SOR=0;LSEQ=TAATGTCACAGAGAGCTTTG;RSEQ=CCTTTCTTCTAAAACTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:133,8:141,2:0.014:2,2:10:1:29.5:1:0.12233:15.72782:60:4:0.014:0:1.5 0/0:119:0:0,0:109,10:119,0:0:2,0:23:1:31.5:1:1:0:60:118:1:0:0.1 +11 32439038 . T C 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTCTTCTAAAACTGTACT;RSEQ=TCTTCATAAGTTCTAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:188,50:238,0:0:2,0:21.3:1:30.9:1:1:0:60:237:1:0:0.2 0/1:230:26:21,5:149,55:204,26:0.113:2,2:20:1:30.6:1:0.48328:1.55:60:52:0.115:0:1 +11 32449274 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08772;SOR=Inf;LSEQ=CGCCGCTCCTTCTTCAGCTC;RSEQ=AAAGAGTAATTGTCCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:20.6:1:30.2:1:1:0:60:26:1:0:0.1 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:17.5:1:29:1:1:0:60:4:0.3333:0:1 +11 32449417 . C G 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07273;SOR=Inf;LSEQ=TGCCCGCAGTCAGGGCTGCC;RSEQ=GGCTGGGGCGTTCCCAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:118,8:126,0:0:2,0:26.9:1:31.3:1:1:0:60:125:1:0:0.1 0/1:92:3:3,0:81,7:88,3:0.0326:2,0:35.3:1:24.7:1:1:0:60:2:0.0227:0:2 +11 32449420 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17795;SOR=Inf;LSEQ=CCGCAGTCAGGGCTGCCCGG;RSEQ=TGGGGCGTTCCCAAGTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:126,9:135,0:0:2,0:26.2:1:31.9:1:1:0:60:32.75:1:0:0.1 0/1:99:2:2,0:88,9:97,2:0.0202:2,0:39.5:1:30.5:1:1:0:60:4:0.0204:0:2 +11 32449459 . CG C 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.111;SOR=Inf;LSEQ=GCCGGCTCATGCGTCCCCTC;RSEQ=GGGTCCCAAGGACCCAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:216,65:281,0:0:2,0:21.4:1:29.7:1:1:0:60:69.25:1:0:0.2 0/1:261:3:1,2:188,69:257,3:0.0115:2,2:9.7:1:29.3:1:0.18194:5.40709:60:6:0.0118:0.0038:1.3 +11 32449486 . C T 208 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=213.25914;LSEQ=CCAAGGACCCAGACGCAGAG;RSEQ=CCAGCGCCTTCCTACCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:1:0,1:274,158:432,1:0.0023:2,0:17:0:14:0:0.36721:0:60:0:0:0:1 0/1:477:158:92,66:189,128:317,158:0.3312:2,2:23.4:1:28.5:1:0.84299:1.05913:59.9:38.5:0.3305:0:1.2 +11 32449661 . G A 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00753;SOR=Inf;LSEQ=CCCAAGGGCTCGGGGTGCGA;RSEQ=GCTGCGGGCAGGGGTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:49,140:189,0:0:2,0:21:1:31.3:1:1:0:60:36.8:1:0:0.2 0/1:203:8:1,7:49,146:195,8:0.0394:2,2:24.5:1:31.4:1:0.68227:2.3415:60:16:0.0404:0:1 +11 32449704 . G A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51262;SOR=0;LSEQ=GACACGAGATCCTGAGCCTG;RSEQ=GGCACTGGGGCCTGGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:5,86:91,2:0.0215:2,2:22.5:1:33:1:0.12553:15.79:60:4:0.0222:0:1 0/0:65:0:0,0:1,64:65,0:0:1,0:24.8:1:30.4:1:1:0:60:64:1:0:0.2 +11 32449799 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01694;SOR=Inf;LSEQ=ATTCCCCTAGCAGTCGCTGC;RSEQ=CTGTGCACCAAAAAGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:23,0:0:2,0:24.3:1:31.6:1:1:0:60:22:1:0:0.3 0/1:9:3:3,0:3,3:6,3:0.3333:2,0:21.3:1:32:0:0.46429:0:60:6:0.3333:0:1 +11 32449992 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24906;SOR=0;LSEQ=GGAATTCCTGGGGGAGAGGA;RSEQ=GATAGCACGGAAGAAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:2,1:178,52:230,3:0.0129:2,2:35.3:1:25.7:1:0.54071:1.70705:60:2:0.0087:0:1.3 0/0:219:0:0,0:159,60:219,0:0:2,0:23.5:1:31.4:1:1:0:60:438:1:0:0.1 +11 32450193 . T A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1197;SOR=0;LSEQ=AGCGGCGGAGAGAAGCACAG;RSEQ=GTCAGCGGTGCTCTCGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:3,0:74,199:273,3:0.0109:2,0:8.3:1:22.3:1:0.0211:0:60:2:0.0073:0:1.3 0/0:283:0:0,0:87,196:283,0:0:2,0:24.9:1:29.4:1:1:0:60:140.5:1:0:0.2 +11 32450199 . C T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37268;SOR=3.94235;LSEQ=GGAGAGAAGCACAGTGTCAG;RSEQ=GGTGCTCTCGCAAGACGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:0,1:67,179:246,1:0.004:2,0:33:0:32:0:1:0:60:2:0.0041:0:1 0/1:254:4:1,3:72,177:249,4:0.0157:2,2:9:1:26:1:1:1.21941:60:8:0.0161:0:1.3 +11 32450209 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24672;SOR=0;LSEQ=ACAGTGTCAGCGGTGCTCTC;RSEQ=CAAGACGGGGCAGTGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:43,144:187,2:0.0106:2,2:43.5:1:30.5:1:0.41236:3.32:60:4:0.0108:0:1 0/0:191:0:0,0:46,145:191,0:0:2,0:23.8:1:31.2:1:1:0:59.9:94.5:1:0:0.2 +11 32450244 . CG C 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGTCTGAACCAGCCACGGG;RSEQ=GGGGGGGTGTGCGCTGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:40:3,37:8,47:55,40:0.4211:2,2:26.5:1:32.2:1:0.34719:2.08397:60:80:0.4255:0.0105:0.1 0/0:67:0:0,0:8,59:67,0:0:2,0:17.3:1:29.7:1:1:0:59.9:32.5:1:0:0.3 +11 32451920 . TG GC 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACCCACTATTGCCCGGAG;RSEQ=AAGGCCGAATTTCTGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:74,1:75,0:0:1,0:23.9:1:29.8:1:1:0:60:24:1:0:0.2 0/1:44:17:17,0:26,0:26,17:0.3864:1,1:24.5:1:31.3:1:1:0:59.7:34:0.4048:0.0682:1.1 +11 32451950 . A AAG 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.51786;SOR=0;LSEQ=ATTTCTGAAAGGACACTAAA;RSEQ=AGAGAGAGAGAGAAAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:2,0:110,1:111,2:0.0177:1,0:30.5:1:33.5:0:1:0:60:4:0.018:0:0 0/0:75:0:0,0:72,0:72,0:0:1,0:23.8:1:29.6:1:1:0:58.6:35:0.9589:0:0.5 +11 32451997 . G A 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGAGAGAGAGAGAGAGAG;RSEQ=GAGGGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:194,58:252,0:0:2,0:23.8:1:28.8:1:1:0:55.6:6.412:0.9864:0:0.6 0/1:267:32:15,17:184,47:231,32:0.1199:2,2:12.5:1:27.3:1:0.00023:4.40496:46.1:7:0.1197:0:2.8 +11 32451999 . A G 35 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72452;SOR=0.74481;LSEQ=AGAGAGAGAGAGAGAGAGGG;RSEQ=GGGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:4:4,0:196,64:260,4:0.0148:2,0:31.8:1:17.8:1:0.5751:0:41.8:0.333:0.0043:0:4.8 0/1:271:3:3,0:194,66:260,3:0.0111:2,0:37.7:1:23.7:1:0.5749:0:32.7:2:0.0084:0:2.7 +11 32452001 . GGAGA G 201 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=18.000;MSILEN=2;SSF=0.23406;SOR=0.79311;LSEQ=AGAGAGAGAGAGAGAGGGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:86:54,32:73,11:84,86:0.281:2,2:26.7:1:31.4:1:0.00037:3.90082:54.7:42:0.2867:0.0294:0.8 0/1:317:75:53,22:111,46:157,75:0.2366:2,2:26.7:1:30.4:1:1:1.00163:56.2:36.5:0.2355:0.0252:0.6 +11 32452158 . G A 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01996;SOR=Inf;LSEQ=CCTGCTCCGCAACTGTCCGT;RSEQ=CCCGGCGAGGGCCGTGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:74,268:342,0:0:2,0:23.3:1:32.1:1:1:0:60:67.4:1:0:0.1 0/1:290:5:4,1:74,211:285,5:0.0172:2,2:9:1:24.2:1:0.01959:11.30:60:10:0.0177:0:1 +11 32452240 . GC G 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0122;SOR=Inf;LSEQ=CAGAACTCGGGCCCAAGGAT;RSEQ=CCGTGGCCCGCGAGCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,64:64,0:0:1,0:23.9:1:30.4:1:1:0:60:15:0.9836:0:0.1 0/1:48:5:0,5:0,43:43,5:0.1042:1,0:19.6:1:32:1:1:0:60:10:0.1087:0.0208:0.2 +11 32456298 . G A 230 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=301.24598;LSEQ=CAGCTGGGCAGGTAGGGCGC;RSEQ=TTAGGAAACATCCTGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:820:1:1,0:410,407:817,1:0.0012:2,0:1:0:28:0:1:0:60:2:0.0012:0:1 0/1:813:218:107,111:291,304:595,218:0.2681:2,2:25.2:1:29.7:1:1:1.01:59.7:108:0.2697:0:1.2 +11 32456446 . G A 44 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.3802;SOR=0.28862;LSEQ=ACTGCTCCTCGTGCGGCTCC;RSEQ=CGCCGCCCCAGCTCGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:4:3,1:96,274:370,4:0.0107:2,2:5.3:1:22.3:1:0.05846:8.50:60:3:0.0081:0:1.8 0/0:322:1:1,0:114,207:321,1:0.0031:2,0:1:0:29:0:0.35714:0:60:2:0.0032:0:1 +11 32456484 . AGGC A 81 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03632;SOR=5.15308;LSEQ=TCCTGTTTGATGAAGGAGTG;RSEQ=GGCGGCGGCGGGGGTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:0,2:31,151:182,2:0.0109:2,0:23.5:1:34:0:1:0:60:4:0.011:0:0 0/1:130:7:3,4:35,86:121,7:0.0538:2,2:24.4:1:29:1:0.42285:1.83:60:14:0.056:0.0077:0.4 +11 32456487 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.2725;SOR=0;LSEQ=TGTTTGATGAAGGAGTGAGG;RSEQ=GGCGGCGGCGGGGGTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:1,2:28,142:170,3:0.0171:2,2:23.3:1:30.3:1:0.42533:2.52:60:6:0.0176:0:1 0/0:121:0:0,0:31,83:114,0:0:2,0:21.1:1:28.9:1:1:0:60:15.286:1:0:0.3 +11 32456496 . C G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51095;SOR=0;LSEQ=AAGGAGTGAGGCGGCGGCGG;RSEQ=GGGGGTGGCGGCGGAGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:17,110:127,2:0.0155:2,2:28:0:33:0:0.26054:6.32:60:4:0.0157:0:1.5 0/0:93:0:0,0:21,71:92,0:0:2,0:20.5:1:29.5:1:1:0:60:22:0.9888:0:0.3 +11 32456618 . AGCC A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.18611;SOR=0;LSEQ=GCCGCTCACAGGCAGGGCAC;RSEQ=GCCGCCGCCACCCAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:74,28:102,2:0.0183:2,0:11:1:33.4:1:1:0:60:4:0.019:0.0092:0.5 0/0:143:0:0,0:86,57:143,0:0:2,0:22.8:1:31.1:1:1:0:60:27.6:1:0:0.3 +11 32456619 . G A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07966;SOR=0;LSEQ=CCGCTCACAGGCAGGGCACA;RSEQ=CCGCCGCCGCCACCCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:2,1:74,28:102,3:0.0275:2,2:10.7:1:25.7:1:1:1.31774:60:2:0.019:0:1.7 0/0:143:0:0,0:86,57:143,0:0:2,0:22.8:1:31.1:1:1:0:60:27.6:1:0:0.3 +11 32456627 . C T 41 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1;SOR=1.32983;LSEQ=AGGCAGGGCACAGCCGCCGC;RSEQ=GCCACCCAGGGAGGGGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:98,36:134,2:0.0147:2,2:37.5:1:28:1:0.47157:2.69885:60:4:0.0147:0:2 0/1:154:3:1,2:92,59:151,3:0.0195:2,2:4:1:26.3:1:0.56281:3.09526:60:6:0.0195:0:1.7 +11 32456648 . C T 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81859;LSEQ=GCCACCCAGGGAGGGGACGG;RSEQ=GGGCAGCAGCGCGTTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:125,55:180,2:0.011:2,2:25.5:1:30:1:0.52189:2.26137:60:4:0.0112:0:1 0/0:222:2:1,1:127,93:220,2:0.009:2,2:6:1:27.5:1:1:1.36363:60:4:0.0093:0:1 +11 32456694 . C A 196 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGTCGGAGCCCATTTGCTG;RSEQ=GGCTCAGACCCGGACGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:196,123:319,0:0:2,0:26.3:1:31:1:1:0:59.9:52.167:0.9905:0:0.2 0/1:320:106:54,52:122,92:214,106:0.3313:2,2:24.3:1:29.2:1:0.3401:1.27598:60:34.333:0.3291:0:1.2 +11 32456809 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.97591;LSEQ=CCCGGACTCCCTGCTGCTCT;RSEQ=GCTGCTGTAGGCACCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:1:1,0:78,113:191,1:0.0052:2,0:1:0:14:0:0.41146:0:60:0:0:0:5 0/1:195:2:1,1:86,107:193,2:0.0103:2,2:10.5:1:28:1:1:1.24:60:4:0.0103:0:1.5 +11 32456815 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4987;SOR=0;LSEQ=CTCCCTGCTGCTCTGGCTGC;RSEQ=GTAGGCACCCAGGCCCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:73,112:185,2:0.0107:2,2:22.5:1:28:1:1:1.53:60:4:0.011:0:1 0/0:183:0:0,0:81,102:183,0:0:2,0:22.3:1:29.3:1:1:0:60:60:1:0:0.2 +11 32456820 . G A 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61171;SOR=2.14758;LSEQ=TGCTGCTCTGGCTGCTGTAG;RSEQ=CACCCAGGCCCGGAGCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:1:1,0:71,112:183,1:0.0054:2,0:1:0:16:0:0.3913:0:60:0:0:0:1 0/1:173:2:2,0:75,96:171,2:0.0116:2,0:18.5:1:24:1:0.19667:0:60:4:0.012:0:1 +11 32456830 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21599;SOR=Inf;LSEQ=GCTGCTGTAGGCACCCAGGC;RSEQ=CGGAGCGGAGCGTGTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:64,122:186,0:0:2,0:22.9:1:30.5:1:1:0:60:36.2:1:0:0.3 0/1:162:2:0,2:66,94:160,2:0.0123:2,0:17.5:1:25.5:1:0.51415:0:60:4:0.013:0:1 +11 32456836 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=0;LSEQ=GTAGGCACCCAGGCCCGGAG;RSEQ=GGAGCGTGTGCTGAGACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:0,2:62,115:177,2:0.011:2,0:9:1:29:1:0.54466:0:60:4:0.0115:0:1 0/0:165:0:0,0:69,96:165,0:0:2,0:23.4:1:29.3:1:1:0:59.9:32:1:0:0.2 +11 32456844 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49873;SOR=0;LSEQ=CCAGGCCCGGAGCGGAGCGT;RSEQ=TGCTGAGACGCCGGCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:63,107:170,2:0.0116:2,2:25.5:1:29.5:1:1:1.69:60:4:0.0119:0:1 0/0:165:0:0,0:72,93:165,0:0:2,0:23.7:1:30.6:1:1:0:59.9:19.625:1:0:0.2 +11 32456892 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49808;SOR=Inf;LSEQ=GTGGAAGCCGGGTCCTGCAG;RSEQ=AAGAGGAAGTCCAGGATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:50,80:130,0:0:2,0:27.2:1:32.6:1:1:0:60:260:1:0:0.2 0/1:131:2:1,1:54,75:129,2:0.0153:2,2:30.5:1:31:1:1:1.39:60:4:0.0156:0:1 +11 32548278 . T C 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCTAAAATAATGCACTTAAT;RSEQ=AAATGTCAATTATGCTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:20:1:31:0:1:0:60:4:1:0:0.5 1/1:2:2:2,0:0,0:0,2:1:0,0:30:1:32.5:1:1:0:60:4:1:0:1.5 +11 32548407 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07568;SOR=0;LSEQ=ATGTGTTGTAAAGGTGTTCT;RSEQ=AAGAGACTGAGTGTCAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:19,2:0.0952:2,2:29.5:1:28:1:1:1.66897:60:4:0.1:0:1 0/0:54:0:0,0:30,24:54,0:0:2,0:28.4:1:31.3:1:1:0:59.5:53:1:0:0.2 +11 32548470 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22711;SOR=0;LSEQ=CATCCTTCTGGGAAAGATCA;RSEQ=ATGGGTCTGTTTGGAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:24,2:0.0769:2,2:41:0:32:0:1:1:60:4:0.0769:0:1 0/0:28:0:0,0:10,18:28,0:0:2,0:23.9:1:30.3:1:1:0:60:56:1:0:0.1 +11 35053622 . C A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00554;SOR=Inf;LSEQ=TCATGATAGGCATGTGATGA;RSEQ=GAGTGAACCAGGAAAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:34,1:35,0:0:1,0:26.2:1:32.7:1:1:0:60:70:1:0:0.5 0/1:28:6:6,0:22,0:22,6:0.2143:1,0:29.8:1:29.3:1:1:0:60:12:0.2222:0:2 +11 35053634 . G A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=30.26483;LSEQ=TGTGATGACGAGTGAACCAG;RSEQ=AAAAGGGCAAGAGGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:16:16,0:28,1:29,16:0.3556:1,1:24.8:1:30.9:1:1:0:60:32:0.3556:0:1.1 1/1:37:35:35,0:2,0:2,35:0.9459:0,1:26.4:1:28.9:1:1:0:60:34:0.9444:0:1.2 +11 35053783 . G A 206 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=56.62771;LSEQ=GAGGCAGAACAGAAAGCAAA;RSEQ=AAGGAGGGTCTAGGGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:2:1,1:216,176:392,2:0.0051:2,2:15.5:1:22.5:1:1:1.22663:60:1:0.0026:0:3 0/1:581:130:75,55:241,209:450,130:0.2238:2,2:25.5:1:29.4:1:0.42501:1.18:60:260:0.2257:0:1.8 +11 35053817 . A T 214 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAACTGCAAAGAGATTTCC;RSEQ=TTCTAGTGCTCACACTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:214,199:413,0:0:2,0:25.5:1:30.4:1:1:0:59.9:67.833:1:0:0.1 0/1:612:151:77,74:229,232:461,151:0.2467:2,2:25.6:1:29.6:1:0.85129:1.05:60:150:0.2467:0:1.7 +11 35053931 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=GTCTGCTCTGGATGAGGAAA;RSEQ=GAGAGTAAATGTATGAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:21,122:143,0:0:2,0:23.2:1:31.7:1:1:0:60:142:1:0:0.1 0/1:152:2:1,1:27,122:149,2:0.0132:2,2:33.5:1:28.5:1:0.33748:4.46:60:4:0.0132:0:1 +11 35242375 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTGCAGTGGC;RSEQ=CGACCTCGGCCCACTGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:37:1:32.5:1:1:0:45:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 35242423 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGAGTTCAAGCGATTCT;RSEQ=CTGCCTCAGCCTCCTGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16:1:33:0:1:0:45:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 35242653 . C T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04608;SOR=0;LSEQ=TATACCAAAATGTGATTACA;RSEQ=CTTACACGGTGTTTAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:7,0:7,6:0.4615:0,0:26.5:1:31.7:1:1:0:60:12:0.4615:0:2.2 0/0:9:0:0,0:9,0:9,0:0:0,0:17.4:1:31.7:1:1:0:60:18:1:0:0.9 +11 35242660 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66564;SOR=0.49436;LSEQ=AAATGTGATTACACCTTACA;RSEQ=GGTGTTTAGCAAACATTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:14:14,0:2,0:2,14:0.8235:0,1:20.2:1:31.8:1:1:0:58.3:28:0.8235:0:1.6 1/0:13:9:9,0:4,0:4,9:0.6923:0,0:20.1:1:30.8:1:1:0:60:18:0.6923:0:1.2 +11 35242907 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.53683;LSEQ=TTAATAATATTATACCAAAG;RSEQ=CATCTACAAGATTCAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:162:85,77:87,88:175,162:0.4807:2,2:25.1:1:29.9:1:0.663:1.12:60:161:0.4879:0:1.1 0/1:434:144:63,81:139,150:289,144:0.3318:2,2:24.9:1:28.8:1:0.41455:1.19094:59.9:143:0.3357:0:1.1 +11 36128516 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAAGAATATACCCTGGG;RSEQ=GCTGCTGGTCCAAGGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:28.5:1:1:0:60:4:1:0:2.5 +11 39206459 . G A 47 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATGTTCTTATTTGGAAACAG;RSEQ=GTTGTGGCAGATGTAATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:20:1:30:1:1:0:60:6:1:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:25:0:30:0:1:0:60:2:0.5:0:1 +11 39588291 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCGACAATAAGGGAAT;RSEQ=AAAGCTGGCCACCCAAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:29:1:1:0:46.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 39878822 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=33.03521;LSEQ=TACTAATGTAATAGAAAGAA;RSEQ=ATTGATTATTTAAACTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:23:11,12:135,118:253,23:0.0833:2,2:29.2:1:29.8:1:0.66627:1.24706:60:46:0.0842:0:1 1/0:318:239:124,115:39,40:79,239:0.7516:2,2:23.2:1:28.4:1:0.79526:1.11:60:118.5:0.7548:0:1.1 +11 39878886 . C A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12705;SOR=Inf;LSEQ=CTTTTGTCTCTCTAGATTTC;RSEQ=TAACCCCTTGTTAAGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:84,154:238,0:0:2,0:26.4:1:32.4:1:1:0:60:118:1:0:0.1 0/1:273:4:2,2:98,171:269,4:0.0147:2,2:28.5:1:28.8:1:0.6254:1.74:60:8:0.0148:0:1.3 +11 39878908 . A T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06268;SOR=Inf;LSEQ=AACCCCTTGTTAAGAGAATG;RSEQ=TTATGTTCATGTTTACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:48,123:171,0:0:2,0:24.4:1:30.9:1:1:0:60:170:1:0:0.1 0/1:191:5:2,3:61,125:186,5:0.0262:2,2:22.8:1:29:1:0.66553:1.36:60:10:0.0265:0:1.2 +11 39878930 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49858;SOR=Inf;LSEQ=TATGTTCATGTTTACAGTTT;RSEQ=AAAGACTCAAAATTGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:22,88:110,0:0:2,0:22.7:1:32.4:1:1:0:60:220:1:0:0.1 0/1:119:2:1,1:26,90:116,2:0.0168:2,2:31:1:28.5:1:0.40678:3.42:60:4:0.0171:0:1 +11 39878942 . ATTG TTT 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=19.57387;LSEQ=GTTTACAGTTTGAAAGACTC;RSEQ=TAAAAATTTCAGTCCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:10:2,8:10,67:77,10:0.1149:2,2:20.8:1:32:1:0.62328:1.66:60:20:0.1176:0.0115:0.1 1/0:90:65:10,55:2,21:23,65:0.7222:2,2:21.6:1:30.2:1:0.72434:1.90:59.8:130:0.7386:0.1333:0.2 +11 39880947 . C T 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTGAAGGTTGCAGTGAG;RSEQ=AGAGATTGCGCCACTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35:0:29.5:1:1:0:60:4:1:0:1.5 +11 39894251 . GACCT TAC 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24377;SOR=Inf;LSEQ=CTTCCTCCAAAAATTGATCT;RSEQ=CTGTTATTTCACTAACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:86,15:101,0:0:2,0:22.6:1:32.1:1:1:0:60:49.5:1:0:0.4 0/1:99:2:1,1:80,17:97,2:0.0202:2,2:35.5:1:30.7:1:0.3321:4.60182:60:4:0.0202:0:1 +11 39894253 . CCT C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=60.36254;LSEQ=TCCTCCAAAAATTGATCTGA;RSEQ=CTGTTATTTCACTAACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:10:9,1:82,15:97,10:0.0935:2,2:20.4:1:33.4:1:1:1.64:60:20:0.0943:0.028:0 1/1:119:103:79,24:11,3:14,103:0.8655:2,2:24:1:31.1:1:1:1.11292:60:206:0.8879:0.1849:0.1 +11 39894274 . C T 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCTGTTATTTCACTAACCC;RSEQ=CTCTACTCACAAAAATTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:49:37,12:67,25:92,49:0.3475:2,2:24.2:1:31.6:1:0.84148:1.15:60:98:0.3475:0:1.1 0/0:166:0:0,0:118,47:165,0:0:2,0:25.2:1:30.4:1:1:0:60:330:1:0:0.1 +11 39894277 . CTACTCACAAAAAT C 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03594;SOR=Inf;LSEQ=TGTTATTTCACTAACCCCCT;RSEQ=TTGCCTCATGCCAAGCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:103,40:143,0:0:2,0:26.6:1:31:1:1:0:60:286:1:0:0.4 0/1:180:6:4,2:122,51:173,6:0.0333:2,2:17.3:1:30.7:1:1:1.19482:59.2:12:0.0337:0.0111:0.2 +11 39894373 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=38.17139;LSEQ=ACCTACTATGGGTATGTTGC;RSEQ=AGAGCTTTAGAAGGATAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:28:10,18:92,126:218,28:0.1138:2,2:26.2:1:31.1:1:0.54823:1.31285:60:56:0.1148:0:1.1 1/1:304:253:107,146:25,26:51,253:0.8322:2,2:26.3:1:29.7:1:0.43927:1.31081:60:125.5:0.8367:0:1.1 +11 39894484 . T C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=0.09994;LSEQ=TGATTTGATGACAAATGATA;RSEQ=AAATCATTTATCAATCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:1,22:0,11:11,23:0.6765:0,1:26.3:1:32.7:1:1:0:60:46:0.6765:0:1.1 0/1:30:5:0,5:1,24:25,5:0.1667:1,0:28.6:1:31.2:1:1:0:60:10:0.1667:0:1 +11 41939837 . T C 85 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGCTAGATAGCATGCT;RSEQ=ACTCACTGCCTGCCTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:11.3:1:34:0:1:0:60:8:1:0:1 1/0:9:7:1,6:0,2:2,7:0.7778:0,2:30.6:1:30.6:1:1:0:60:14:0.7778:0:1.1 +11 42138390 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1479;SOR=Inf;LSEQ=ACAGATTAAAGGAGAGGTGA;RSEQ=ATTGAATGAGAAGTAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:48,4:52,0:0:2,0:26.8:1:32.4:1:1:0:59.5:104:1:0:0.4 0/1:33:2:1,1:26,5:31,2:0.0606:2,2:18:1:26:1:0.33523:4.83744:60:4:0.069:0:1 +11 42138434 . C T 171 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01073;LSEQ=AACATATGTACAATCCTGTG;RSEQ=CTTTAGTACCCTTTTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:55:34,21:34,20:54,55:0.5046:2,2:23.7:1:29.6:1:1:1.04956:60:110:0.514:0:1 0/1:94:1:0,1:59,34:93,1:0.0106:2,0:1:0:22:0:0.37234:0:60:2:0.0108:0:2 +11 42138471 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49928;SOR=Inf;LSEQ=ATTTAGATCTATCACTTTCA;RSEQ=CTGATCTCACATGATTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:74,62:136,0:0:2,0:30.8:1:30.9:1:1:0:60:135:1:0:0.8 0/1:149:2:1,1:85,62:147,2:0.0134:2,2:40:1:28.5:1:1:1.368:60:4:0.0137:0:1 +11 42138495 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24633;SOR=Inf;LSEQ=ATCTCACATGATTATGAAAG;RSEQ=TTGCTAGGCACGCCCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:81,90:171,0:0:2,0:23.5:1:31.9:1:1:0:59.8:170:1:0:0.8 0/1:169:2:1,1:89,78:167,2:0.0118:2,2:27.5:1:27.5:1:1:1.14013:60:4:0.012:0:1 +11 42138498 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49853;SOR=0;LSEQ=TCACATGATTATGAAAGGTT;RSEQ=CTAGGCACGCCCATCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:80,88:168,2:0.0118:2,2:35.5:1:29.5:1:1:1.10:60:4:0.0119:0:2 0/0:168:0:0,0:90,78:168,0:0:2,0:24.6:1:31.3:1:1:0:60:55:1:0:0.7 +11 42138514 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0481;SOR=1.56218;LSEQ=GGTTGCTAGGCACGCCCATC;RSEQ=TCATACAACAATGGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:86:40,46:37,43:80,86:0.5119:2,2:21.8:1:31:1:1:1.01:59.6:85:0.5152:0:1.1 1/0:169:105:55,50:27,37:64,105:0.6213:2,2:23.9:1:29.6:1:0.20878:1.50:59.9:34:0.6145:0:1.1 +11 42138579 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=GGGATGCAGAGTCATTGGTG;RSEQ=TTTAAAATTATGCATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:45,83:128,0:0:2,0:25.1:1:32.5:1:1:0:59.7:41.667:1:0:0.3 0/1:137:2:1,1:54,81:135,2:0.0146:2,2:32:0:31.5:1:1:1.50:60:4:0.0148:0:1 +11 42138604 . CTT C 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03068;SOR=Inf;LSEQ=AAATTATGCATTTATTCTCT;RSEQ=AGCCATAGGTAGGATAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:29,57:86,0:0:2,0:23.5:1:30.8:1:1:0:60:172:1:0:0.1 0/1:98:6:2,4:34,58:92,6:0.0612:2,2:12.5:1:29.5:1:1:1.17059:59.2:12:0.0619:0.0306:0.2 +11 42138732 . G C 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.58042;SOR=3.65648;LSEQ=TAAGATATTATATGATGGAG;RSEQ=ATGTTATATGATGGATGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:19.8:1:30:1:1:0:50.4:4:0.4444:0:2.4 1/1:5:4:0,4:0,1:1,4:0.8:0,0:20.3:1:30.8:1:1:0:60:8:0.8:0:1.3 +11 43266834 . C A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.04777;LSEQ=CTCCAAAGGACACAACTTTA;RSEQ=AATAAAAGCAAGTACTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:191:86,105:98,118:216,191:0.467:2,2:24.3:1:30.3:1:1:1.01396:60:37.2:0.465:0:1.1 1/0:506:325:160,165:83,96:179,325:0.6423:2,2:25.5:1:29.3:1:0.57661:1.12:60:45.429:0.6424:0:1.2 +11 44368381 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.16408;LSEQ=GGATTCCTGGAGCTGTCCTC;RSEQ=TAGCTGCAAGTACCTGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:174:93,81:114,100:214,174:0.4485:2,2:28.1:1:31:1:1:1.01:60:173:0.447:0:1.8 1/0:428:273:131,142:76,79:155,273:0.6379:2,2:26.1:1:30.3:1:0.84122:1.04273:60:135.5:0.6392:0:1.7 +11 44368416 . G T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-04;SOR=1.7066;LSEQ=TGGCACCTTTACACATCAGT;RSEQ=CCTCCCTCCCTCTGCCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:155:66,89:91,102:193,155:0.4454:2,2:24.3:1:30.3:1:0.44819:1.20242:60:76.5:0.4513:0:1.9 1/0:351:203:80,123:64,82:146,203:0.5783:2,2:26:1:28.5:1:0.44106:1.19936:59.9:19.3:0.571:0:1.9 +11 44368605 . T C 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10294;SOR=0;LSEQ=TTTGTTGGCTGGCTTTGCCT;RSEQ=CGGGAGGTGTGAGCCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:6,7:0.5385:0,0:32.1:1:31.6:1:1:0:60:14:0.5385:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:20.5:1:29.8:1:1:0:60:8:1:0:0 +11 44458019 . A G 55 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGGCATGGCACATAGTA;RSEQ=CCTCCTATGAATGTTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:37:1:27.5:1:1:0:60:3:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 47286171 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21151;SOR=0;LSEQ=ATATCCTCCTTGTGGAACCC;RSEQ=GCCCAGTTCTAAGATCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:39,14:53,2:0.0364:2,2:31.5:1:31.5:1:0.47475:2.72554:60:4:0.037:0:1 0/0:64:0:0,0:50,14:64,0:0:2,0:26.6:1:30.2:1:1:0:60:128:1:0:0.1 +11 47286271 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19558;SOR=0;LSEQ=TTATACAAGCAGTTTTGAAG;RSEQ=AATCATGCTTGCATTTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:104,84:188,2:0.0105:2,2:12.5:1:29.5:1:1:1.23669:60:4:0.0105:0:1.5 0/0:239:0:0,0:121,118:239,0:0:2,0:24.7:1:27.9:1:1:0:60:118.5:1:0:0.3 +11 47286290 . T C 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAATCATGCTTGCATTTCT;RSEQ=ATTTCATGAGTGAGGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:95,95:190,0:0:2,0:27.1:1:29.8:1:1:0:60:94:1:0:0.1 0/1:250:26:13,13:112,112:224,26:0.104:2,2:27.7:1:30.9:1:1:1:60:52:0.1057:0:1.1 +11 47286347 . TC T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5061;SOR=Inf;LSEQ=GCTCTGCTTGTCAAGTCTCC;RSEQ=CCCTCCCTATCCGCTACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:52,86:138,0:0:2,0:24.8:1:31.6:1:1:0:59.9:68:1:0:0.2 0/1:177:2:1,1:68,107:175,2:0.0113:2,2:18.5:1:29:1:1:1.57:60:4:0.0114:0:0 +11 47286414 . G A 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03738;SOR=Inf;LSEQ=GACATGGACTGAGCACATTT;RSEQ=AGGTGTTCATTCCGTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:3,27:30,0:0:2,0:24.7:1:31.7:1:1:0:60:14:1:0:0.1 0/1:42:6:1,5:4,32:36,6:0.1429:2,2:36.2:1:31:1:0.55683:1.58:60:12:0.1463:0:1 +11 51579537 . C T 28 v3;p8;NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54872;SOR=0.31415;LSEQ=TAATACCGTAGGCCACAAAG;RSEQ=AGTCCAAATCTCCAATTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:5:1:28:1:1:1.22474:26.5:4:0.1818:0:7.5 0/1:16:1:0,1:8,7:15,1:0.0625:2,0:1:0:21:0:1:0:30:2:0.0625:0:7 +11 51579554 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.62122;LSEQ=AAGCAGTCCAAATCTCCAAT;RSEQ=GCAGATTGTACAAAAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:9,5:0,0:0,14:0.9333:0,2:19.5:1:32.6:1:1:0:25.1:28:1:0:6.6 1/1:24:23:11,12:0,0:0,23:0.9583:0,2:20.3:1:29.9:1:1:0:28.3:46:0.9583:0:6.5 +11 51579562 . G C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.55509;LSEQ=CAAATCTCCAATTGCAGATT;RSEQ=TACAAAAAGAGTGTTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:8,6:0,0:0,14:0.9333:0,2:27.3:1:32.7:1:1:0:25:28:0.9333:0:6.6 1/1:26:23:12,11:0,1:1,23:0.8846:0,2:28.2:1:31.1:1:1:0:27.4:46:0.8846:0:6.6 +11 51579573 . G T 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGCAGATTGTACAAAAAGA;RSEQ=TGTTTACAAACTGCACTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:9,6:0,0:0,15:1:0,2:38.7:1:31.6:1:1:0:25.1:30:1:0:6.7 1/1:26:25:13,12:0,0:0,25:0.9615:0,2:37.4:1:29.6:1:1:0:27.7:24:0.96:0:6.5 +11 51579583 . A C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAAGAGTGTTTACAA;RSEQ=CTGCACTATCCATAGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:10,6:0,0:0,16:1:0,2:41.7:1:32.3:1:1:0:24.9:32:1:0:6.4 1/1:31:30:14,16:0,0:0,30:0.9677:0,2:36.2:1:30.9:1:1:0:25.8:60:0.9677:0:6.1 +11 51579588 . A T 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAAGAGTGTTTACAAACTGC;RSEQ=CTATCCATAGGAATGTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:9,7:1,0:1,16:0.9412:0,2:39:1:31:1:1:0:24.8:32:0.9412:0:6.5 1/1:34:34:16,18:0,0:0,34:1:0,2:32.1:1:29.1:1:1:0:25.8:68:1:0:5.9 +11 51579594 . C T 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15137;SOR=0;LSEQ=TGTTTACAAACTGCACTATC;RSEQ=ATAGGAATGTTCAACTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:10,14:0,0:0,24:1:0,2:24.3:1:29.5:1:1:0:23.5:48:1:0:5 1/1:38:34:13,21:3,1:4,34:0.8947:2,2:25.9:1:27.5:1:0.29066:4.64893:25.1:33:0.8919:0:5.5 +11 51579599 . G C 34 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=ACAAACTGCACTATCCATAG;RSEQ=AATGTTCAACTCTGTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:24,0:0:2,0:23:1:31.3:1:1:0:23.5:48:1:0:5 0/1:40:2:2,0:14,24:38,2:0.05:2,0:9:0:34:0:0.15385:0:20:4:0.0513:0:6 +11 51579610 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12788;SOR=0;LSEQ=TATCCATAGGAATGTTCAAC;RSEQ=CTGTGAGTCGAATGCAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:9,14:23,2:0.08:2,2:25:1:30.5:1:1:1.53:21.5:4:0.08:0:5.5 0/0:44:0:0,0:15,29:44,0:0:2,0:19.7:1:27.8:1:1:0:25:21:1:0:5 +11 51579641 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54023;SOR=Inf;LSEQ=AATGCAATCATCACAAAGTA;RSEQ=TTTCTGAGAATGCTTCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:10,0:0:2,0:44.2:1:32.9:1:1:0:20.9:20:1:0:2.1 0/1:20:2:1,1:2,16:18,2:0.1:2,2:41:0:31.5:1:0.28421:6.73:22:4:0.1053:0:2.5 +11 51579658 . T C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTAGTTTCTGAGAATGCTTC;RSEQ=ATCTAGTTTTTATGTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1:0,2:29.8:1:33.8:1:1:0:20.9:20:1:0:2.1 1/1:20:20:3,17:0,0:0,20:1:0,2:29.9:1:32.6:1:1:0:21.4:40:1:0:3.2 +11 51579679 . TG T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTAGTTTTTATGTGAAGA;RSEQ=TTTCCTTTTCCACCACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:1,8:0,0:0,9:1:0,2:10.4:1:31.4:1:1:0:20.8:18:1:0.3333:2.1 1/1:14:13:2,11:0,0:0,13:0.9286:0,2:12.7:1:30.3:1:1:0:21.9:26:1:0.3571:2.5 +11 51580519 . C A 25 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGCTTCTATCTAGTATT;RSEQ=ATGTGAAGATATTTCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:25.5:1:1:0:25:4:1:0:4.5 +11 56503728 . C T 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1023;SOR=4.62268;LSEQ=GACCTAGCAATTCCAGCATG;RSEQ=GAATTGTGAGAGGACATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:10,0:10,3:0.2308:0,0:16.3:1:29.7:1:1:0:58:6:0.2308:0:1.3 1/0:10:6:6,0:4,0:4,6:0.6:0,0:22.5:1:28.7:1:1:0:57.3:12:0.6:0:1 +11 56503835 . T C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.26132;SOR=0;LSEQ=CCTGCAGGTCCTCTTCAGTG;RSEQ=CCTCTCCATTAAACCCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:66,40:0,0:0,106:1:0,2:27.6:1:31.6:1:1:0:58.3:52:1:0:1.5 1/1:140:137:89,48:1,2:3,137:0.9786:2,2:28.2:1:30.9:1:0.29012:3.67:59.2:136:0.9855:0:1.2 +11 56503851 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16923;SOR=0;LSEQ=AGTGTCCTCTCCATTAAACC;RSEQ=ATTAACATGTAGGATCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:74,51:125,2:0.0157:2,2:36:1:30:1:1:1.44661:60:4:0.0161:0:3 0/0:181:0:0,0:110,71:181,0:0:2,0:26.3:1:30.3:1:1:0:59.3:89.5:1:0:1 +11 56503873 . C T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29822;LSEQ=TTAACATGTAGGATCCTCAT;RSEQ=TGCTTCACATTGGTGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:52:27,25:48,36:84,52:0.3824:2,2:26:1:30.5:1:0.59707:1.23264:57.3:104:0.3852:0:1.9 0/1:206:32:15,17:93,81:174,32:0.1553:2,2:30:1:29.4:1:0.56521:1.29956:56.6:31:0.1535:0:1.8 +11 56503910 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50706;SOR=Inf;LSEQ=CTTTACCAGATTCTCCAGCA;RSEQ=CCAGGAGTAGCAGGCGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:39,66:105,0:0:2,0:25.2:1:31.6:1:1:0:58.5:104:1:0:0.6 0/1:139:2:1,1:53,84:137,2:0.0144:2,2:12:1:29:1:1:1.58:48:4:0.0144:0:3 +11 56503938 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50045;SOR=Inf;LSEQ=TAGCAGGCGGTCCATGGCAC;RSEQ=GTCGATGCTTGGCTGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:20,48:68,0:0:2,0:23.6:1:30:1:1:0:60:21.667:1:0:0.2 0/1:81:2:1,1:19,60:79,2:0.0247:2,2:16:1:27.5:1:0.43519:3.10:60:4:0.0247:0:1 +11 58009466 . T C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24391;SOR=Inf;LSEQ=ATGCATGTTGTGGTTGCCTA;RSEQ=TTGGCAACAGTGAGCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:59,0:0:1,0:24.1:1:31.7:1:1:0:60:58:1:0:0.1 0/1:61:3:3,0:55,3:58,3:0.0492:2,0:31:1:32.3:1:1:0:60:6:0.0492:0:1 +11 58009485 . G A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61878;SOR=2.06022;LSEQ=ATTTGGCAACAGTGAGCACT;RSEQ=CATCCTGAACTATCTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:1,0:85,6:91,1:0.0109:2,0:6:0:23:0:1:0:60:2:0.011:0:1 0/1:90:2:1,1:74,14:88,2:0.0222:2,2:24:1:26.5:1:0.30712:5.141:60:4:0.0225:0:1 +11 58009594 . T C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.55776;LSEQ=TGTCATGAAGAATTATTTTG;RSEQ=CCTCTTCAGTAACAAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:53:34,19:103,90:193,53:0.2154:2,2:27.4:1:31.7:1:0.21152:1.56:60:52:0.214:0:1.1 0/1:287:142:75,67:80,65:145,142:0.4948:2,2:25.3:1:30.7:1:0.72313:1.09912:60:70:0.493:0:1.1 +11 58009595 . C A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12806;SOR=Inf;LSEQ=GTCATGAAGAATTATTTTGT;RSEQ=CTCTTCAGTAACAAAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:136,109:245,0:0:2,0:27.5:1:31.5:1:1:0:59.9:60.25:1:0:0.3 0/1:286:4:3,1:151,131:282,4:0.014:2,2:11:1:25:1:0.62684:2.59:60:3:0.0108:0:1.8 +11 58010309 . A G 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.38392;LSEQ=TGAACATTTGTTCCACCAAT;RSEQ=CAGGCACGACAAGTTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:113:53,60:141,146:287,113:0.2811:2,2:24.6:1:32:1:0.73923:1.09306:49.3:226:0.2839:0:1.3 1/0:551:314:149,165:114,123:237,314:0.5699:2,2:25.8:1:31:1:0.93138:1.02632:47.9:77.5:0.5699:0:1.4 +11 58010357 . G A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTCCAAGTGCCAGAATTAC;RSEQ=TTTTGGATCTTTAATACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:124,201:325,0:0:2,0:25:1:31.3:1:1:0:57:64:1:0:0.5 0/1:422:21:9,12:154,247:401,21:0.0498:2,2:27.4:1:29.7:1:0.81871:1.20:41.4:42:0.0504:0:2.9 +11 58010380 . A T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.42333;LSEQ=TTGGATCTTTAATACAAGGA;RSEQ=CAATAGCTCTGGGCTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:58:22,36:61,124:185,58:0.2387:2,2:24.2:1:30.4:1:0.52699:1.24:56.4:57:0.2355:0:2.1 1/0:301:156:54,102:49,96:145,156:0.5183:2,2:23.2:1:29:1:0.9037:1.04:55.3:77:0.5151:0:2.2 +11 58010397 . A C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21976;SOR=0;LSEQ=GGAACAATAGCTCTGGGCTG;RSEQ=ATAGCTGGAGGCTTCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:53,137:190,2:0.0104:2,2:25.5:1:31.5:1:0.48446:2.57:60:4:0.0106:0:3.5 0/0:217:0:0,0:65,152:217,0:0:2,0:23.9:1:29.6:1:1:0:60:107.5:1:0:1.2 +11 58010432 . A T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.16023;LSEQ=CTCAAAACCACAAACATGGA;RSEQ=TACCCCTAAAAGAGACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:28:8,20:19,78:97,28:0.224:2,2:23.5:1:30.8:1:0.30866:1.64:59.7:27:0.2177:0:2.9 1/0:123:92:14,78:6,25:31,92:0.748:2,2:22.3:1:29.4:1:0.58241:1.33384:60:184:0.7541:0:2.3 +11 58010439 . T C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.81004;LSEQ=CCACAAACATGGAATACCCC;RSEQ=AAAAGAGACTCCTTTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:26:8,18:21,73:94,26:0.2167:2,2:24.6:1:32.9:1:0.43884:1.54:59.7:52:0.2185:0:3 1/0:110:63:12,51:8,38:46,63:0.5727:2,2:22.6:1:31.4:1:1:1.12:60:126:0.5727:0:2.7 +11 58010513 . A G 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00033;SOR=5.20008;LSEQ=GCTCTTGATGACAACATTGG;RSEQ=TCCATTCCCTTTGGGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:13:4,9:13,33:46,13:0.2203:2,2:23.3:1:31.4:1:1:1.13:60:12:0.2143:0:1.8 1/0:35:21:4,17:3,11:14,21:0.6:2,2:23.5:1:31.8:1:1:1.15416:60:42:0.6:0:1.8 +11 58010633 . ACTT A 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATTATAGAGATCTTTC;RSEQ=CTTTGGTTAAGTTTATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:3,2:0.4:2,0:26.5:1:31:1:1:0:60:4:0.4:0.2:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 58010711 . C T 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCTTTCTTGATTTCTTTT;RSEQ=CAGAGCGTTTGCTATTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:30.5:1:31.3:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 60617646 . T C 55 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGGACCGAGGCTGCAGC;RSEQ=GCACTAATGTCCTCCCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:23:1:27.5:1:1:0:60:3:1:0:1.8 1/1:2:2:2,0:0,0:0,2:1:0,0:15:1:32:0:1:0:60:4:1:0:1.5 +11 60617834 . C A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77086;SOR=1.21665;LSEQ=AGGCCTTCCATGGCCAACAA;RSEQ=CATGTCAGACACAGCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:5,7:3,9:12,12:0.5:2,2:25.3:1:30:1:0.66685:2.07:56.4:24:0.5455:0:1.1 1/0:20:11:5,6:3,6:9,11:0.55:2,2:26.9:1:28.6:1:0.66992:1.62:51.3:22:0.55:0:1.3 +11 60617845 . A G 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23077;SOR=Inf;LSEQ=GGCCAACAACCATGTCAGAC;RSEQ=CAGCACCTCAGGCCGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:7,13:20,0:0:2,0:25.1:1:30.2:1:1:0:57.9:40:1:0:0.7 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:29:0:29:1:1:1.40:45:4:0.1053:0:2 +11 61197460 . GC G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01617;SOR=0.14385;LSEQ=CGCTCTCCGCCCCAGGTCCC;RSEQ=CCCCCCCGCCGCCGGCGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:59:57:57,0:1,0:1,57:0.9661:0,1:24:1:32.8:1:1:0:60:114:0.9661:0.1864:0.2 1/1:30:24:24,0:6,0:6,24:0.8:0,1:25.3:1:32.3:1:1:0:60:48:0.8:0.0667:0.1 +11 61197664 . G A 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTTCGTCGCTGGTGAGGAGA;RSEQ=AGAACGTTCTAGCGTCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:961:0:0,0:458,502:960,0:0:2,0:25.8:1:32.6:1:1:0:60:79:1:0:0.1 0/1:1273:91:47,44:555,627:1182,91:0.0715:2,2:24.5:1:29.6:1:0.44583:1.21:60:44.5:0.0707:0:1.3 +11 61200952 . T A 146 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=23.90328;LSEQ=TTGGCTAAAATAATAAGACA;RSEQ=CCCAATTATTAGAACAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:541:1:0,1:265,275:540,1:0.0018:2,0:17:0:13:0:1:0:60:0:0:0:3 0/1:754:32:15,17:357,364:721,32:0.0424:2,2:30:1:29.3:1:0.85732:1.11138:60:64:0.0435:0:1.1 +11 61205337 . CT C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.07498;SOR=2.05163;LSEQ=TTAGGTATGGGACTAGGAGT;RSEQ=TTTTTTTTAAATCGGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:10:4,6:196,286:482,10:0.0203:2,2:26.3:1:33.2:1:1:1.02792:60:20:0.0205:0:0 0/1:563:23:9,14:219,321:540,23:0.0409:2,2:27.1:1:30.7:1:1:1.06117:60:46:0.0411:0.0036:0.1 +11 61205434 . G A 235 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTCTCTTTTATTAGACACA;RSEQ=CCTTCTCAACCTCTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:226:226:115,111:0,0:0,226:1:0,2:23.6:1:30.1:1:1:0:59.9:44.2:1:0:1.1 1/0:212:166:100,66:25,21:46,166:0.783:2,2:22.7:1:29.3:1:0.50109:1.27:59.9:82:0.781:0:1.1 +11 61205676 . C CT 165 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.06849;SOR=0.5949;LSEQ=CCTAGATAATTTTTTTCTTT;RSEQ=TTTTTTTTTTTTGAGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:43:0,43:4,40:44,43:0.4479:2,1:26:1:30.5:1:0.11643:0:55.3:42:0.4667:0.0208:0.5 0/1:120:39:0,39:8,59:67,39:0.325:2,1:26.5:1:29.3:1:0.02525:0:53.9:38:0.3423:0.0167:0.1 +11 61213355 . C T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11786;SOR=0;LSEQ=GTTTCGAGTTTTAAGATTCT;RSEQ=ATACCTGAGCATTGACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:203,73:276,3:0.0108:2,2:9:1:21.7:1:0.17695:5.52072:59.3:2:0.0073:0:1.7 0/0:289:0:0,0:212,77:289,0:0:2,0:23.7:1:30.5:1:1:0:59.9:578:1:0:0.1 +11 61213555 . C T 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACGTTGAGCTGTGCTCCA;RSEQ=GGCCTGGCATGGGGGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:81,183:264,0:0:2,0:25.9:1:30.4:1:1:0:59.9:65:1:0:0.2 0/1:337:35:10,25:107,195:302,35:0.1039:2,2:25.2:1:29.2:1:0.4596:1.37056:60:70:0.1051:0:1.1 +11 61213559 . C A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08826;SOR=0;LSEQ=GTTGAGCTGTGCTCCACGGC;RSEQ=TGGCATGGGGGTTCAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:2,1:74,176:250,3:0.0119:2,2:28:1:30:1:0.21549:4.72:60:6:0.0119:0:1 0/0:314:0:0,0:108,206:314,0:0:2,0:25.8:1:30.9:1:1:0:60:156:1:0:0.2 +11 61213583 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20422;SOR=0;LSEQ=CATGGGGGTTCAGTCTGTGG;RSEQ=TGGTAACTACTTATGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:41,129:170,2:0.0116:2,2:26.5:1:30:1:0.42982:3.12:60:4:0.012:0:1.5 0/0:208:0:0,0:54,153:207,0:0:2,0:21.9:1:29.6:1:1:0:60:102.5:1:0:0.2 +11 61213622 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61045;SOR=2.1561;LSEQ=GACGTTAGCCTTGCTTCCGG;RSEQ=TTCTTAGATGCCCAGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:1:0,1:6,72:78,1:0.0127:2,0:1:0:32:0:1:0:60:2:0.013:0:1 0/1:74:2:1,1:7,65:72,2:0.027:2,2:27.5:1:27.5:1:0.20585:8.75:60:4:0.0274:0:1 +11 61213623 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.49722;SOR=0;LSEQ=ACGTTAGCCTTGCTTCCGGC;RSEQ=TCTTAGATGCCCAGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:5,71:76,2:0.0256:2,2:25.5:1:29.5:1:0.14885:13.05:60:4:0.026:0:1 0/0:73:0:0,0:8,65:73,0:0:2,0:22.6:1:29.7:1:1:0:60:72:1:0:0.1 +11 61213920 . T C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGCTGTGCGTGCTGTA;RSEQ=GGAAAGCCTCCCGCCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31.5:1:31.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:31:0:1:0:60:4:1:0:1 +11 62098295 . T A 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00223;SOR=0.05206;LSEQ=GGAATTGTGGGTGTATACAT;RSEQ=TATCTGTAAAAGATGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:9,0:10,0:10,9:0.4737:0,0:15.1:1:29:1:1:0:60:18:0.4737:0:1.3 0/1:24:1:1,0:23,0:23,1:0.0417:1,0:41:0:30:0:1:0:60:2:0.0417:0:1 +11 62098371 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27885;SOR=Inf;LSEQ=TGTTCTCTTGAGCAGTGGTC;RSEQ=TTTATCTCCATCCACATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:50,30:80,0:0:2,0:24.9:1:30.7:1:1:0:42.6:79:1:0:1.7 0/1:122:3:2,1:71,48:119,3:0.0246:2,2:43.3:1:29.7:1:1:1.35:45:6:0.0252:0:3 +11 62098387 . A C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=GGTCGTTTATCTCCATCCAC;RSEQ=TTCTCTCCCACCTAAGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:97:97:59,38:0,0:0,97:1:0,2:27.7:1:31.8:1:1:0:39.5:96:1:0:1.7 1/1:143:122:68,54:11,10:21,122:0.8531:2,2:27.2:1:30.2:1:0.81539:1.14:42.4:60:0.8571:0:1.3 +11 62098407 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11944;LSEQ=ATTCTCTCCCACCTAAGTGC;RSEQ=TGCCACCACCCGATGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:58:34,24:25,23:48,58:0.5472:2,2:29.9:1:30.4:1:0.55833:1.30:37.6:28:0.549:0:2 0/1:144:18:12,6:60,66:126,18:0.125:2,2:24.1:1:29:1:0.20689:2.19:39.5:36:0.1268:0:2.1 +11 62098508 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52357;SOR=Inf;LSEQ=TAAAGGCCAACAAAGATGAT;RSEQ=ACTTTAAGGTGGATAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:52,43:95,0:0:2,0:25.3:1:31.7:1:1:0:58.8:46.5:0.9894:0:0.1 0/1:152:2:1,1:87,63:150,2:0.0132:2,2:7.5:1:26.5:1:1:1.37795:60:4:0.0132:0:1.5 +11 62098521 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51433;SOR=Inf;LSEQ=AGATGATCACTTTAAGGTGG;RSEQ=TAATGATGAAGATGAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:61,51:112,0:0:2,0:24.2:1:30.4:1:1:0:58.5:55:1:0:0.1 0/1:161:2:1,1:90,69:159,2:0.0124:2,2:17.5:1:29.5:1:1:1.30216:52.5:4:0.0126:0:1 +11 62098726 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11437;LSEQ=CACCAGTGTCTTACGGTTGA;RSEQ=GTGTGGCTTAGGGCTAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:226:158:73,85:34,34:68,158:0.6991:2,2:26.2:1:30.3:1:0.66367:1.16359:47:30.6:0.6955:0:2 0/1:244:51:23,28:87,106:193,51:0.209:2,2:28.2:1:29.9:1:1:1.00:46.4:102:0.2099:0:2 +11 62098734 . TT AC 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10798;SOR=0;LSEQ=TCTTACGGTTGACGTGTGGC;RSEQ=AGGGCTAGGGCATATTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:2,1:92,106:198,3:0.0149:2,2:23.7:1:31.2:1:0.60018:2.30:33:6:0.0152:0.005:2 0/0:220:0:0,0:97,123:220,0:0:2,0:25.2:1:28.7:1:1:0:52.1:35.667:1:0:1.3 +11 62098735 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06253;LSEQ=CTTACGGTTGACGTGTGGCT;RSEQ=AGGGCTAGGGCATATTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:197:92,105:0,0:0,197:0.9899:0,2:24.1:1:31.5:1:1:0:50.1:38.4:1:0:1.9 1/1:214:184:80,104:12,18:30,184:0.8598:2,2:24.9:1:30.8:1:0.84297:1.15:51.1:368:0.8638:0:1.5 +11 62098737 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23375;SOR=0;LSEQ=TACGGTTGACGTGTGGCTTA;RSEQ=GGCTAGGGCATATTAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:91,105:196,2:0.0101:2,2:34:1:31:1:1:1.15:60:4:0.0102:0:2 0/0:211:0:0,0:93,118:211,0:0:2,0:24.8:1:30.3:1:1:0:52.4:51.75:1:0:1.3 +11 62098753 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50032;SOR=Inf;LSEQ=CTTAGGGCTAGGGCATATTA;RSEQ=TGGACAGCACTTAGTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:66,89:155,0:0:2,0:24.1:1:32.4:1:1:0:50.1:76.5:1:0:1.7 0/1:175:2:1,1:74,99:173,2:0.0114:2,2:20.5:1:28.5:1:1:1.34:42:4:0.0116:0:2.5 +11 62098766 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49861;SOR=Inf;LSEQ=CATATTAGTGGACAGCACTT;RSEQ=GTAGCTGTGGAGGAAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:53,82:135,0:0:2,0:23:1:30.5:1:1:0:51.1:270:1:0:1.6 0/1:143:2:1,1:56,85:141,2:0.014:2,2:17.5:1:28:1:1:1.51:48:4:0.014:0:1 +11 62098773 . G A 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGACAGCACTTAGTAGCT;RSEQ=TGGAGGAAGATGCAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:41,74:115,0:0:2,0:24.6:1:32:1:1:0:54.1:27.75:1:0:1.4 0/1:119:23:6,17:35,61:96,23:0.1933:2,2:25.2:1:29.2:1:0.4653:1.61937:52.1:46:0.1933:0:1.7 +11 62098774 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49784;SOR=0;LSEQ=TGGACAGCACTTAGTAGCTG;RSEQ=GGAGGAAGATGCAAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:39,74:113,2:0.0174:2,2:11:1:28.5:1:1:1.89:41:4:0.0177:0:2.5 0/0:113:0:0,0:38,75:113,0:0:2,0:23.1:1:29.4:1:1:0:55.1:226:1:0:1 +11 62098899 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.56588;LSEQ=AAGTAAAACTTGCTGCCGAT;RSEQ=AAGATGATGATTATGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:1:1,0:39,34:73,1:0.0135:2,0:1:0:25:0:1:0:25:2:0.0135:0:1 0/1:95:2:1,1:46,47:93,2:0.0211:2,2:39:1:28:1:1:1.02:58.5:4:0.0213:0:1.5 +11 62098934 . A AGAT 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=8.000;MSILEN=3;SSF=3e-05;SOR=0.21887;LSEQ=GAAGATGATGATGATGATGA;RSEQ=GATGATGATGATGATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:50:33,17:6,9:15,50:0.7692:2,2:26.7:1:30.9:1:0.13121:2.86:59.4:49:0.7656:0.2:0.1 0/1:74:31:15,16:22,20:42,31:0.4189:2,2:29.5:1:30:1:0.81471:1.17076:60:62:0.4366:0.0541:0.1 +11 62098943 . T TGAC 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.00299;SOR=Inf;LSEQ=GATGATGATGAAGATGATGA;RSEQ=GATGATGATGATTTTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:45,27:72,0:0:2,0:20.7:1:30.5:1:1:0:59.6:71:1:0:0.1 0/1:71:8:4,4:29,32:61,8:0.1127:2,2:21.8:1:29:1:1:1.10:60:16:0.1159:0.0282:0 +11 62099052 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50984;SOR=Inf;LSEQ=AGTCAAATCAGAATGGAAAA;RSEQ=ACTCAAAGCCATCGTCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:82,50:132,0:0:2,0:22.2:1:32.3:1:1:0:37.7:131:1:0:0.4 0/1:179:2:1,1:103,74:177,2:0.0112:2,2:31.5:1:28.5:1:1:1.38926:22:4:0.0113:0:1 +11 62099066 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18098;LSEQ=GGAAAAGACTCAAAGCCATC;RSEQ=TCAACACCAAGATCAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:49:31,18:48,36:84,49:0.3684:2,2:10.8:1:30:1:0.58362:1.29:32.5:48:0.3692:0:1 0/1:200:19:13,6:100,80:180,19:0.095:2,2:12.6:1:29.4:1:0.33631:1.73:40.6:38:0.0969:0:1 +11 62099069 . A T 32 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06372;SOR=0;LSEQ=AAAGACTCAAAGCCATCGTC;RSEQ=ACACCAAGATCAAAAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:3:1,2:77,58:135,3:0.0217:2,2:6:1:20.7:1:0.57955:2.63662:48.3:2:0.0148:0:2 0/0:206:0:0,0:116,90:206,0:0:2,0:24.4:1:29.3:1:1:0:49.4:102:1:0:0.2 +11 62099172 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50697;SOR=Inf;LSEQ=ACGTTAAAGCAAACATGCAA;RSEQ=CAAGGATAGAAAAAGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:22,81:103,0:0:2,0:22.4:1:32.5:1:1:0:48.4:206:1:0:0 0/1:135:2:1,1:44,89:133,2:0.0148:2,2:8:1:30:0:1:2.01:60:4:0.015:0:1 +11 62100880 . A C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGTGTGCCTGCCCCCTA;RSEQ=GATCTTGAGGTGTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:32.5:1:1:0:27:4:1:0:1.5 +11 62789131 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03195;LSEQ=TGGGATCTCCTATCTGAGCT;RSEQ=TGAGGTCTCCTCCCTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:353:318:157,161:18,17:35,318:0.9008:2,2:25.8:1:29.4:1:0.85997:1.08553:60:317:0.9006:0:1.2 0/1:362:81:42,39:124,156:280,81:0.2238:2,2:21.6:1:28.9:1:0.25538:1.35:60:162:0.2244:0:1.1 +11 62789169 . T C 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGCCATCCATGCTTTGGG;RSEQ=GGAGAGCCTCGTTCCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:95,154:249,0:0:2,0:24:1:30.4:1:1:0:59.9:248:1:0:0.8 0/1:267:19:8,11:104,144:248,19:0.0712:2,2:24.7:1:28.4:1:1:1.01:60:18:0.0679:0:1.1 +11 63010648 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49746;SOR=0;LSEQ=CCGTGTCCTGAAGAACCTGC;RSEQ=TGCTATCAAGAAGCGCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:32,13:45,2:0.0426:2,2:30:1:33.5:1:0.51156:2.40879:60:4:0.0426:0:1 0/0:40:0:0,0:26,14:40,0:0:2,0:23.5:1:29.5:1:1:0:60:39:1:0:0.2 +11 63010898 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49893;SOR=Inf;LSEQ=AAAGGTTTTCCCTCTGGCCA;RSEQ=GATTTACCTGGACTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:102,55:157,0:0:2,0:23.2:1:31.1:1:1:0:60:77.5:1:0:0.1 0/1:167:2:2,0:102,63:165,2:0.012:2,0:34:1:32.5:1:0.52731:0:60:4:0.0121:0:1 +11 63011204 . A C 222 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATCTGCAAGCAAGTCCAGA;RSEQ=CTTCAATGCTCTGTATGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:130:130:41,89:0,0:0,130:1:0,2:23:1:31.7:1:1:0:60:129:1:0:1.1 0/1:141:42:10,32:30,69:99,42:0.2979:2,2:20.5:1:30.3:1:0.5412:1.38814:60:84:0.3:0:1.1 +11 63011241 . G C 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00201;SOR=Inf;LSEQ=GCAATGTACCCGCCATCAAT;RSEQ=GTTGCAACTGGAAGTGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:51,61:112,0:0:2,0:24.7:1:32.5:1:1:0:60:224:1:0:0.6 0/1:99:8:4,4:46,45:91,8:0.0808:2,2:18.9:1:30.5:1:1:1.022:60:16:0.0825:0:1.6 +11 63011334 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08172;SOR=0;LSEQ=AATGCCCTGACTGAGCTGCT;RSEQ=GCAAAGATCACCAACACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:2,1:69,67:136,3:0.0216:2,2:25:1:24:1:1:1.93:49.7:2:0.0152:0:2 0/0:180:0:0,0:94,84:178,0:0:2,0:24:1:30.7:1:1:0:60:177:0.9888:0:0.1 +11 63011410 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.48491;LSEQ=GAGGTGGTCTTCCTCAACAG;RSEQ=CTGCAGCAGTGCCATCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:1:0,1:87,52:139,1:0.0071:2,0:1:0:26:0:0.37857:0:60:2:0.0072:0:1 0/1:189:2:1,1:107,80:187,2:0.0106:2,2:16.5:1:27:1:1:1.3354:60:4:0.0108:0:1 +11 63011423 . C T 42 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13152;SOR=Inf;LSEQ=TCAACAGCCTGCAGCAGTGC;RSEQ=ATCAGGACCAGCAGGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:94,69:163,0:0:2,0:26:1:31.4:1:1:0:60:53.333:1:0:0.1 0/1:202:4:0,4:112,86:198,4:0.0198:2,0:6.8:1:21.3:1:0.03795:0:60:3:0.015:0:1 +11 63011426 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1974;SOR=0;LSEQ=ACAGCCTGCAGCAGTGCCAT;RSEQ=AGGACCAGCAGGACAGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:94,74:168,2:0.0118:2,2:32.5:1:28.5:1:1:1.26846:60:4:0.012:0:1 0/0:212:0:0,0:117,95:212,0:0:2,0:26.7:1:30.8:1:1:0:60:211:1:0:0.1 +11 63011476 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20032;SOR=0;LSEQ=GATGAACTGGGCCAAGCCAG;RSEQ=ACCCCTATAGACCTGTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:83,112:195,2:0.0101:2,2:21.5:1:32.5:1:1:1.35:60:4:0.0102:0:1 0/0:245:0:0,0:115,130:245,0:0:2,0:25.4:1:31.1:1:1:0:60:80.667:1:0:0.1 +11 63011599 . T TA 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.7057;SOR=0.55947;LSEQ=TTGTATCTTAGGGCGAAACT;RSEQ=AAAAAAAAAAACCTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:0,5:1,23:24,5:0.1724:1,0:28.4:1:31.4:1:1:0:60:10:0.1724:0:0.4 0/1:29:3:1,2:0,24:24,3:0.1034:1,2:43:1:30.3:1:0.11111:0:60:6:0.1034:0:0.7 +11 63011631 . G C 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02894;SOR=Inf;LSEQ=CCTCTGCCCCCACATAGTTC;RSEQ=TGTTTAAAGATCTTTTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:0,22:22,0:0:1,0:26.3:1:32.6:1:1:0:59.7:21:1:0:0.6 0/1:17:4:2,2:0,13:13,4:0.2353:1,2:23.3:1:32:1:0.04412:0:60:8:0.2353:0:1.3 +11 63011713 . A G 54 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CTTTGGTGCTTATTTGAAGT;RSEQ=CAGCATAAGGGAATCCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:24.5:1:27.3:1:1:0:47:3:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:31:0:1:0:60:2:1:0:0 +11 64002177 . T C 34 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGGGGCCGCGGAGGAG;RSEQ=CGCCCCCCGCGCCCGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:34:1:1:0:27:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 64002405 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCCGCCCGCCCGCCGTG;RSEQ=CCTCTCTCAAGGTTGGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 64126666 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20513;SOR=Inf;LSEQ=GCCGCCATGTAACCGGCGCC;RSEQ=CCCGGAGCCCGAGCCGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:148,34:182,0:0:2,0:15.5:1:30.6:1:1:0:60:35.4:0.9944:0:0.3 0/1:152:2:1,1:114,36:150,2:0.0132:2,2:27:0:31:0:0.42881:3.13729:60:4:0.0136:0:1.5 +11 64126679 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09959;SOR=Inf;LSEQ=CGGCGCCGCCCGGAGCCCGA;RSEQ=CCGCGCGGGCCCCAGCGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:192,56:248,0:0:2,0:22.3:1:32.9:1:1:0:60:30:0.9917:0:0.2 0/1:217:3:2,1:156,58:214,3:0.0138:2,2:28.3:1:24:1:1:1.34288:60:2:0.0094:0:1.7 +11 64126691 . C T 32 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.34318;SOR=3.45846;LSEQ=GAGCCCGAGCCGCGCGGGCC;RSEQ=CAGCGACCCGCCCGCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:1:0,1:246,97:343,1:0.0029:2,0:1:0:26:0:0.28488:0:60:2:0.003:0:1 0/1:300:3:0,3:206,91:297,3:0.01:2,0:10.7:1:20.7:1:0.03009:0:60:2:0.0068:0:1 +11 64126698 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AGCCGCGCGGGCCCCAGCGA;RSEQ=CCGCCCGCCATGGGGGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:283,109:392,0:0:2,0:26.5:1:32.2:1:1:0:60:77.4:1:0:0.2 0/1:359:12:7,5:230,115:345,12:0.0334:2,2:25.8:1:28.4:1:0.54659:1.42712:60:11:0.0312:0:1.4 +11 64126725 . C T 67 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18121;SOR=3.25706;LSEQ=GCCATGGGGGACGAGGACGA;RSEQ=GATGAGAGCTGCGCCGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:640:2:0,2:436,202:638,2:0.0031:2,0:1:0:28:1:0.10126:0:60:4:0.0032:0:1 0/1:692:7:2,5:420,265:685,7:0.0101:2,2:6.9:1:23.9:1:0.11672:3.95434:60:14:0.0102:0:1.1 +11 64126993 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20918;SOR=Inf;LSEQ=TCCTGCCTGCTCACTCTTGG;RSEQ=CCTGGGCCAGGCCACTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:26,149:175,0:0:2,0:24.5:1:31.9:1:1:0:60:34:1:0:0.1 0/1:148:2:1,1:30,116:146,2:0.0135:2,2:6.5:1:27:1:0.37617:3.82:60:4:0.0138:0:1 +11 64127230 . G T 26 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTCCCTTTCTTCCAATATGG;RSEQ=ATCCCCCTCCCACATTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:0,2:2,1:0.3333:0,0:4:0:29:0:0.33333:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:26.5:1:1:0:60:4:1:0:1 +11 64127560 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.18797;SOR=Inf;LSEQ=TGCACACCCTCCTGGGTTGG;RSEQ=ATCGCCCCCACCCCCCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:167,44:211,0:0:2,0:23:1:32:1:1:0:59.8:104.5:1:0:0.1 0/1:162:2:1,1:122,38:160,2:0.0123:2,2:12:1:30:1:0.42466:3.18205:60:4:0.0123:0:1 +11 64127565 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2681;SOR=0;LSEQ=ACCCTCCTGGGTTGGCATCG;RSEQ=CCCCACCCCCCAAGCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:3:1,2:178,60:238,3:0.0123:2,2:15.3:1:27.3:1:0.16333:5.87966:60:6:0.0126:0:1 0/0:175:0:0,0:131,44:175,0:0:2,0:23.7:1:31.1:1:1:0:60:57.333:1:0:0.1 +11 64127744 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=7.76476;LSEQ=GTGCAGCGCGCCAAGACGCA;RSEQ=GAGCACACGCGCACCGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:28:11,17:174,198:372,28:0.07:2,2:24.8:1:31.8:1:0.55638:1.3571:60:56:0.0702:0:1.1 0/1:322:119:44,75:84,119:203,119:0.3696:2,2:22.3:1:30.7:1:0.47976:1.20252:60:38.667:0.3671:0:1.2 +11 64127763 . C T 49 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09985;SOR=Inf;LSEQ=AAGAGCACACGCGCACCGAG;RSEQ=GCTCGGTGCTGGAGCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:151,176:327,0:0:2,0:25.3:1:31.1:1:1:0:59.9:80.75:1:0:0.2 0/1:284:3:1,2:111,170:281,3:0.0106:2,2:12:0:31:0:1:1.30469:60:6:0.0109:0:2.3 +11 64127881 . T G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6298;SOR=2.52904;LSEQ=CACACCACATCCCAACGGGG;RSEQ=TGGGGTGGCTGGGGGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:496:493:312,181:0,1:1,493:0.994:0,2:24.4:1:31.3:1:0.36842:0:59.9:43.818:0.9938:0:1.2 1/1:417:416:261,155:0,0:0,416:0.9976:0,2:23.8:1:30.7:1:1:0:60:82.2:0.9976:0:1.2 +11 64127902 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05988;SOR=0.68139;LSEQ=TGGGGTGGCTGGGGGCAGGC;RSEQ=AGGCCACCTGACGGGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:70:42,28:328,220:548,70:0.1129:2,2:24.4:1:30.3:1:1:1.01:60:69:0.1133:0:1.9 0/1:539:43:26,17:301,195:496,43:0.0798:2,2:25.3:1:29.3:1:1:1.00925:60:42:0.0791:0:1.9 +11 64128423 . G T 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41127;SOR=2.34849;LSEQ=CTTGGGGCCTGATCCACGGG;RSEQ=CCCTCCTTCTTTGTTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:5,0:25,2:27,5:0.1563:2,0:25.6:1:27.6:1:1:0:60:4:0.1333:0:1.2 0/1:13:4:3,1:9,0:9,4:0.3077:0,2:33.3:1:31:1:0.30769:0:60:8:0.3077:0:1.3 +11 64128494 . C T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28736;SOR=1.92122;LSEQ=TGCCCTGGAGACCCCCTCTA;RSEQ=AGGCAGATGACTTTCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:7:7,0:94,2:96,7:0.068:1,0:29.3:1:31.7:1:1:0:60:14:0.0693:0:1.1 0/1:73:9:9,0:61,3:64,9:0.1233:1,0:26.6:1:31:1:1:0:60:18:0.125:0:1 +11 64128537 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20704;SOR=Inf;LSEQ=GGTCTCCTTATCCTGAGCAG;RSEQ=GCCAGGAGCTGGAGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:185,24:209,0:0:2,0:21.5:1:30.8:1:1:0:59.8:28.857:1:0:0.1 0/1:175:2:1,1:148,25:173,2:0.0114:2,2:9:1:27:1:0.2758:5.82466:60:4:0.0118:0:1 +11 64129050 . GA T 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGGAAGTGGGGCTGGGG;RSEQ=GGTGGAAAGGTGGGGTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:216,275:491,0:0:2,0:24.2:1:31.6:1:1:0:59.9:121.75:1:0:0.1 0/1:543:23:8,15:220,291:511,23:0.0424:2,2:22.7:1:30.3:1:0.52098:1.41663:59.8:46:0.0431:0.0074:0.3 +11 64129051 . A T 51 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06207;SOR=Inf;LSEQ=CAGGGAAGTGGGGCTGGGGG;RSEQ=GGTGGAAAGGTGGGGTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:206,271:477,0:0:2,0:23.6:1:30.3:1:1:0:59.9:30.8:1:0:0.1 0/1:497:5:2,3:209,280:489,5:0.0101:2,2:24:1:22.2:1:1:1.11943:60:1.5:0.0064:0:1.2 +11 64129075 . AG A 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.05392;SOR=0;LSEQ=GGAAAGGTGGGGTGTGAGGC;RSEQ=GGGAGATGCAGGCCCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:4:3,1:165,225:390,4:0.0102:2,2:8.5:1:29:1:0.3168:4.08:60:8:0.0102:0.0051:0.5 0/0:422:0:0,0:185,237:422,0:0:2,0:22.8:1:30.5:1:1:0:59.9:37.364:1:0:0.2 +11 64129767 . C A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGCAGGTGACCTGCCCC;RSEQ=GACGGCACAGTAAATGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:43.5:1:33:1:1:0:56:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 64132498 . C T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCTCCCAAAATCCTGGGAT;RSEQ=ACAGGCATGAGCCACCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:27.3:1:29.1:1:1:0:54.3:10:1:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:22.7:1:30.7:1:1:0:49.7:6:1:0:1 +11 64132664 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18681;SOR=Inf;LSEQ=ACAGCTGCCCACCCCAAATG;RSEQ=CAGATGGGCCCTTGCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:169,9:178,0:0:2,0:23.7:1:32.4:1:1:0:59.8:43.5:1:0:0.1 0/1:136:2:1,1:127,7:134,2:0.0147:2,2:16.5:1:28:1:0.1146:17.03684:60:4:0.0152:0:1 +11 64132701 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0445;SOR=Inf;LSEQ=TCATGGAGGAACTGCCCAGT;RSEQ=AGGGTGGGCTGAGTGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:281,101:382,0:0:2,0:23.1:1:32:1:1:0:59.9:53.571:1:0:0.1 0/1:326:4:1,3:222,100:322,4:0.0123:2,2:15.8:1:25:1:0.09493:6.61804:60:8:0.0125:0:1 +11 64133166 . TC T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAAACCTTCTGTTAATT;RSEQ=CCTTCTATTCCATCATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:0,3:0,16:16,3:0.1579:1,0:30:1:33:0:1:0:60:6:0.1667:0:0 0/0:4:0:0,0:0,4:4,0:0:0,0:22.5:1:29.3:1:1:0:60:8:1:0:0 +11 64135435 . G A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11005;SOR=1.96615;LSEQ=CCAAGTGATTATAAAACCAG;RSEQ=TGGAATAAAAAGTGTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:16:16,0:71,1:72,16:0.1818:1,1:23.6:1:30.3:1:1:0:60:32:0.1839:0:1.1 0/1:59:18:17,1:40,1:41,18:0.3051:1,1:18.9:1:28.7:1:0.52075:2.31508:60:36:0.3103:0:1.1 +11 64135477 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17154;SOR=Inf;LSEQ=ATCCTGTGTGTACCAGAATG;RSEQ=AACTGGAACACCCCCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:184,2:186,0:0:1,0:26.8:1:32.2:1:1:0:60:30:1:0:0.2 0/1:132:2:2,0:128,2:130,2:0.0152:1,0:34:1:31:0:1:0:60:4:0.0153:0:1.5 +11 64135541 . GTC G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=2.82789;LSEQ=TTGCCTGGTTCCCCACCAGA;RSEQ=TCCTCACCCGCACCCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:70:46,24:317,112:429,70:0.14:2,2:23.9:1:31.7:1:0.19191:1.47548:59.6:69:0.142:0.034:0.2 0/1:485:153:101,52:221,108:329,153:0.3155:2,2:21.5:1:30.9:1:0.83562:1.05342:59.7:152:0.3207:0.0701:0.2 +11 64135748 . C T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.16842;SOR=5.49638;LSEQ=TGCAGGTGGGCTGGGCTGGG;RSEQ=TGGGTTGGGGGGAAATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:1:0,1:101,264:365,1:0.0027:2,0:1:0:31:0:1:0:60:2:0.0028:0:1 0/1:269:4:2,2:72,193:265,4:0.0149:2,2:17.5:1:29.8:1:0.30412:2.67:60:8:0.0154:0:1.3 +11 64135780 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15129;SOR=Inf;LSEQ=GAAATTGGTTTTAGGAGAGG;RSEQ=CTAGGCCCGGGGACTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:74,164:238,0:0:2,0:22.4:1:31.8:1:1:0:59.7:58.5:1:0:0.1 0/1:152:2:1,1:47,103:150,2:0.0132:2,2:15:1:26.5:1:0.53329:2.18:60:4:0.0141:0:1 +11 64135837 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15974;SOR=Inf;LSEQ=GCCCGCAGCGTGAGCTCAGC;RSEQ=AGGTCCTAAGCCTCTCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:117,66:183,0:0:2,0:26.8:1:30.7:1:1:0:60:182:1:0:0.1 0/1:123:2:1,1:83,38:121,2:0.0163:2,2:18.5:1:27:1:0.53539:2.16902:60:4:0.0164:0:1 +11 64135894 . A T 54 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06171;SOR=Inf;LSEQ=CCGCGGGGCTACCAGGTGGG;RSEQ=CCTCTGACGCGCCGCCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:237,153:390,0:0:2,0:24.3:1:29.8:1:1:0:60:77:1:0:0.2 0/1:393:5:1,4:243,145:388,5:0.0127:2,2:6.4:1:23.6:1:0.07069:6.67236:52.4:4:0.0104:0:1.6 +11 64135907 . C T 119 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00083;SOR=7.92287;LSEQ=AGGTGGGACCTCTGACGCGC;RSEQ=GCCTTCGCCTTCGCCTTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:2:0,2:268,180:448,2:0.0044:2,0:1:0:26:0:0.16304:0:60:4:0.0045:0:1.5 0/1:499:17:11,6:284,191:475,17:0.0341:2,2:26.2:1:29.2:1:0.80385:1.23:58.4:16:0.0328:0:1.5 +11 64136184 . C T 65 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3434;SOR=2.21908;LSEQ=TCCGTCCCCCAGGCTGGAGG;RSEQ=GAACACGCAGCGCGAAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:3:1,2:323,190:513,3:0.0058:2,2:10.3:1:25:1:0.55868:3.39164:60:2:0.004:0:1 0/1:546:7:1,6:305,233:538,7:0.0128:2,2:11.6:1:23.3:1:0.0473:7.82859:60:6:0.0113:0:1 +11 64136592 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGAACATGGCGAAACCCC;RSEQ=TCTCTACGAAAAATACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:25:1:32:0:1:0:57.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 64136667 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTACTTGGGAGGCTGAG;RSEQ=CACGAGAATCGCTTGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,1:8,2:0.2:2,0:29.5:1:30.5:1:1:0:49:4:0.2:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:37:0:32:0:1:0:37:2:1:0:0 +11 64136721 . C A 84 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.79106;LSEQ=TGCAGTGAGCCGAGGTGGTG;RSEQ=CACTGCATTCCAGCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:7,0:20,1:21,7:0.2414:1,0:36.4:1:30.1:1:1:0:59.7:14:0.2414:0:1.1 0/1:5:1:1,0:4,0:4,1:0.2:0,0:50:0:26:0:1:0:60:2:0.2:0:1 +11 64136772 . C CAAAG 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=5.000;MSILEN=4;SSF=0.19451;SOR=3.03565;LSEQ=GACTGTCTCCAAAAAAGTAA;RSEQ=AAAGAAAGAAAGAAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:41:41,0:9,0:9,41:0.82:0,1:23:1:31.4:1:1:0:59.5:82:0.82:0.22:0.2 1/1:30:28:28,0:2,0:2,28:0.9333:0,1:14.5:1:30.1:1:1:0:59.1:56:0.9333:0.4667:0.2 +11 64136839 . CG C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.5004;SOR=0;LSEQ=CATTGGCAGGGCCCGAAGGC;RSEQ=GGGGCGGGGCCTGGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:142,39:181,2:0.0109:2,2:23.5:1:31:1:0.39032:3.60751:60:4:0.0112:0:0.5 0/0:162:0:0,0:115,47:162,0:0:2,0:22.2:1:28.5:1:1:0:59.8:31.4:1:0:0.4 +11 64136845 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20813;SOR=Inf;LSEQ=CAGGGCCCGAAGGCCGGGGG;RSEQ=GGGGCCTGGGTGGTGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:150,56:206,0:0:2,0:24.4:1:29.2:1:1:0:59.9:9.842:1:0:0.3 0/1:175:2:1,1:117,53:170,2:0.0114:2,2:34:1:27.5:1:0.5306:2.19638:60:4:0.0124:0:1 +11 64136877 . C G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00723;SOR=1.97003;LSEQ=GGTGGGAGGGGGCTTGCCGC;RSEQ=GTGGGTGGGTGTTGACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:32:23,9:154,107:261,32:0.1085:2,2:25.7:1:28.8:1:0.18348:1.77:59.9:15:0.106:0:1.3 0/1:248:48:27,21:117,83:200,48:0.1935:2,2:29.5:1:29.1:1:0.87081:1.09598:60:47:0.1926:0:1.2 +11 64137167 . G A 177 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.29904;LSEQ=ACCACTACCCCGCCGCCCTC;RSEQ=CAGAACATCCTGTACGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:756:2:1,1:419,332:751,2:0.0026:2,2:41.5:1:30:1:1:1.26165:60:4:0.0027:0:1 0/1:800:65:36,29:408,322:730,65:0.0813:2,2:22.3:1:29.5:1:1:1.02068:60:64:0.0808:0:1.3 +11 64137875 . T C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.45145;LSEQ=AGGTGCGGAGCTGGAGGTCA;RSEQ=AGACCATGGTTGGGGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:786:66:27,39:304,416:720,66:0.084:2,2:25.8:1:31.8:1:0.89673:1.05549:59.7:32:0.0832:0:1 0/1:736:177:74,103:239,316:555,177:0.2405:2,2:25.2:1:31.1:1:0.79397:1.05267:60:58:0.24:0:1.2 +11 64138433 . G A 94 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0.2887;LSEQ=TAAAAAGAGAAAAATTAGCC;RSEQ=GGTGTGGTGGCGCGCGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:3,5:0,2:2,8:0.8:0,2:25.4:1:31.4:1:1:0:41.5:16:0.8889:0:1.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:1:0:20:0:1:0:32:2:0.5:0:2 +11 64138573 . CAAAAAAAAAAA C 49 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=25.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=GCGACAGAGGGAGACTCCGT;RSEQ=AAAAAAAAAAAAAAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,0:5,0:0:0,0:14:1:26.8:1:1:0:24:4:0.6667:0:1.6 0/1:7:3:3,0:1,0:1,3:0.4286:0,0:9.7:1:31.1:1:1:0:57:6:0.4286:0.2857:3 +11 64138602 . A G 34 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31965;SOR=2.15733;LSEQ=AAAAAAAAAAAAAAAAAGGG;RSEQ=GGTGAACCGAATCCGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:5:5,0:48,1:49,5:0.0926:1,0:25.4:1:23.8:1:1:0:45.6:1.5:0.0652:0:4.6 0/1:33:6:6,0:25,2:27,6:0.1818:2,0:23.3:1:13.2:1:1:0:45.8:0:0:0:4.3 +11 64138663 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19647;SOR=Inf;LSEQ=TGTCGGCCTTGACCTAGGCG;RSEQ=CTGGAGGCAAGGTCTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:206,27:233,0:0:2,0:26.7:1:30.9:1:1:0:59.9:37.833:1:0:0.3 0/1:186:2:1,1:163,21:184,2:0.0108:2,2:13.5:1:26.5:1:0.22313:7.6066:60:4:0.0109:0:1 +11 64138805 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.95203;LSEQ=TTCCTGAAGAGCGTGGAGAA;RSEQ=GCACCCCTGGCCAAGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:955:64:27,37:428,463:891,64:0.067:2,2:27.3:1:30.5:1:0.43719:1.26646:60:128:0.0677:0:1.3 0/1:999:221:92,129:368,407:775,221:0.2212:2,2:24.8:1:29.7:1:0.12684:1.26751:60:54.25:0.2203:0:1.1 +11 64138905 . T G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.30892;LSEQ=CGGGCCGAGCCCCCGTCGCC;RSEQ=CCAAAGGGGCCCCCCGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:57:33,24:315,319:634,57:0.0824:2,2:23:1:29.1:1:0.26929:1.39:59.7:8.5:0.0797:0:2.4 0/1:588:101:53,48:242,239:481,101:0.1718:2,2:24:1:29.5:1:0.74298:1.09:59.5:13.429:0.1688:0:2 +11 64138922 . C T 78 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20012;SOR=2.82914;LSEQ=GCCTCCAAAGGGGCCCCCCG;RSEQ=CGAGCCAACGGCCCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:708:3:0,3:351,354:705,3:0.0042:2,0:1:0:22.3:1:0.24899:0:60:2:0.003:0:1.3 0/1:588:7:3,4:294,287:581,7:0.0119:2,2:19.6:1:27.9:1:0.72241:1.36513:59.7:14:0.0127:0:1.6 +11 64139013 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08483;SOR=Inf;LSEQ=CCTGGGAGCCCGGCTCACTC;RSEQ=CGGAGGCCTCTGCCTGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:57,202:259,0:0:2,0:22:1:30.9:1:1:0:60:42.167:1:0:0.1 0/1:204:3:0,3:51,149:200,3:0.0147:2,0:24.7:1:25:1:0.57394:0:60:2:0.0101:0:2 +11 64410111 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49909;SOR=Inf;LSEQ=TGGTGGGTGGTGCTGAGGCT;RSEQ=GAGGAGACCCGGGCCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:43,41:84,0:0:2,0:21.9:1:30.5:1:1:0:60:41:1:0:0.1 0/1:95:2:1,1:48,45:93,2:0.0211:2,2:10:0:31.5:1:1:1.06598:60:4:0.0213:0:1.5 +11 64410135 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19103;SOR=0;LSEQ=GAGACCCGGGCCCCCTCGGC;RSEQ=GCCCCCAGCAGCAACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:34,60:94,2:0.0208:2,2:27.5:1:32:0:1:1.75:60:4:0.022:0:1.5 0/0:123:0:0,0:47,76:123,0:0:2,0:28:1:29.1:1:1:0:59.5:40:1:0:0.2 +11 64410183 . TGGC T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.50086;SOR=Inf;LSEQ=GGCAACAGCGGCAGCAGAGG;RSEQ=GGCGGCGGCGGTGGAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:15,47:62,0:0:2,0:18.7:1:31.1:1:1:0:60:30:1:0:0.3 0/1:75:2:0,2:23,49:72,2:0.0267:2,0:12:1:31:1:1:0:60:4:0.0267:0.0133:0.5 +11 64410192 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=1.32974;LSEQ=GGCAGCAGAGGTGGCGGCGG;RSEQ=GGCGGTGGAGGCGGCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:1,0:8,32:40,1:0.0244:2,0:1:0:26:0:0.21951:0:60:2:0.0263:0:1 0/1:62:2:1,1:18,42:60,2:0.0323:2,2:12.5:1:27.5:1:0.52247:2.30:60:4:0.0323:0:1 +11 64571710 . C T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01649;SOR=0;LSEQ=GGTTTGGGTAGAGGTGAGGC;RSEQ=TGTCCCCTTTGGGCTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:7:6,1:365,43:408,7:0.0169:2,2:19.7:1:29.6:1:0.54643:1.41338:60:6:0.0147:0:1 0/0:366:0:0,0:328,38:366,0:0:2,0:23.3:1:30.6:1:1:0:59.9:90.5:1:0:0.1 +11 64572018 . T C 318 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05019;LSEQ=CTCCGGCGGTGGTGATGCTG;RSEQ=GGGTGCTGGCACCTGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1419:1412:691,721:0,1:1,1412:0.9951:0,2:24.6:1:31:1:1:0:59.9:66.238:0.9986:0:1.1 1/1:1690:1538:723,815:74,73:147,1538:0.9101:2,2:24.2:1:30.1:1:0.48926:1.1426:59.9:58.154:0.9092:0:1.2 +11 64572403 . C G 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09933;LSEQ=GTCTCAGTCCCATCGGCACC;RSEQ=AAGGGGATGGGCAGATGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:669:590:208,382:31,46:77,590:0.8819:2,2:22.9:1:31.2:1:0.44846:1.23724:59.9:72.75:0.8818:0:1.1 0/1:630:268:91,177:126,234:360,268:0.4254:2,2:22.2:1:30:1:0.79965:1.04728:59.9:88.333:0.426:0:1.1 +11 64572460 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.03651;SOR=Inf;LSEQ=GTCTGACAAGCCCGTGGCTG;RSEQ=TGTCACCACCTGTAGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:171,252:423,0:0:2,0:25.9:1:33.1:1:1:0:60:83.6:1:0:0.5 0/1:330:4:1,3:137,189:326,4:0.0121:2,2:10:1:29.3:1:0.64276:2.16997:60:8:0.0122:0:1 +11 64572557 . A G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94251;LSEQ=AGAAAGGTGGCCCAGCCCAC;RSEQ=TGCAGCACAGGCGTGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:542:539:286,253:2,0:2,539:0.9945:0,2:24.8:1:30.8:1:0.50117:0:59.9:43.917:0.9943:0:1.2 1/1:511:508:287,221:1,0:1,508:0.9941:0,2:24.4:1:30.1:1:1:0:60:126:0.9941:0:1.4 +11 64572602 . G A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=5.21743;LSEQ=TCCTCCCATTTGCAGATGCC;RSEQ=TCGTAGAATCGCAGCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:58:24,34:310,332:642,58:0.0829:2,2:26.3:1:31.3:1:0.33881:1.32226:60:116:0.0841:0:1.5 0/1:733:235:123,112:260,238:498,235:0.3206:2,2:24.7:1:29.7:1:1:1.01:60:234:0.3245:0:1.6 +11 64573311 . G T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10916;SOR=Inf;LSEQ=GGGGGTAGCCCCAGGGACCT;RSEQ=GCGGGGGATGGAGCCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:24,177:201,0:0:2,0:22.6:1:31.5:1:1:0:60:200:1:0:0.1 0/1:185:3:1,2:25,156:181,3:0.0162:2,2:9.7:1:23.7:1:0.36855:3.09:60:2:0.0112:0:1.3 +11 64573313 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23355;SOR=Inf;LSEQ=GGGTAGCCCCAGGGACCTGG;RSEQ=GGGGGATGGAGCCCCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:22,170:192,0:0:2,0:22.8:1:30:1:1:0:60:31:0.9947:0:0.1 0/1:181:2:0,2:25,154:179,2:0.011:2,0:28.5:1:29.5:1:1:0:60:4:0.0114:0:1 +11 64573589 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17091;SOR=Inf;LSEQ=TGGCCTTGCTGCCTAGGGAC;RSEQ=GGATGGAAAGGGGATGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:77,5:82,0:0:2,0:24:1:31.6:1:1:0:59.6:26.333:1:0:0.1 0/1:59:2:2,0:54,2:56,2:0.0339:1,0:33.5:1:29:1:1:0:60:4:0.0364:0:1 +11 64573636 . G T 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.59748;SOR=2.34047;LSEQ=GCCAGGCCTCAGTCCTGGAC;RSEQ=AGGGTGGTTGGAAACTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:0,1:133,50:183,1:0.0054:2,0:1:0:25:0:0.27717:0:60:2:0.0055:0:2 0/1:158:2:1,1:115,41:156,2:0.0127:2,2:10:0:30.5:1:0.46223:2.78331:60:4:0.0127:0:2.5 +11 64573875 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21854;SOR=0;LSEQ=GGCAGAGGATCCTCAGGGAG;RSEQ=CAGCCCCAGCTGCCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:50,138:188,2:0.0105:2,2:15:1:28.5:1:0.46583:2.74:60:4:0.0108:0:2 0/0:217:0:0,0:62,155:217,0:0:2,0:23.8:1:30.8:1:1:0:60:107.5:1:0:0.1 +11 64573878 . G A 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62653;SOR=2.6356;LSEQ=AGAGGATCCTCAGGGAGGCA;RSEQ=CCCCAGCTGCCCTGCTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:1:1,0:44,133:177,1:0.0056:2,0:1:0:28:0:0.25281:0:60:2:0.0057:0:1 0/1:204:3:1,2:57,144:201,3:0.0147:2,2:31:1:22.3:1:1:1.26:60:2:0.01:0:1 +11 64574185 . TTCA T 109 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CACCAAGTGAACACCCCCTC;RSEQ=TCAGTGCTCCTGCCACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:0,10:1:0,0:30.4:1:33.1:1:1:0:55.1:20:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:24:0:31:0:1:0:60:2:1:0:1 +11 64574200 . G A 103 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCTTCATCAGTGCTCCT;RSEQ=CCACATTTGACCTCTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:0,12:1:0,0:28.1:1:29:1:1:0:55.9:24:1:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:13:0:31:0:1:0:60:2:1:0:1 +11 64574381 . AC A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.22591;SOR=Inf;LSEQ=AGTGAGACTGGATGGGCGAT;RSEQ=CCCCCAACACACAAAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:144,9:153,0:0:2,0:22.3:1:32.2:1:1:0:59.9:306:1:0:0.1 0/1:140:2:2,0:125,13:138,2:0.0143:2,0:24.5:1:30.5:1:1:0:60:4:0.0144:0:0 +11 64574397 . A T 34 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10448;SOR=0;LSEQ=CGATACCCCCCAACACACAA;RSEQ=GTTCTCTTCTCATCTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:3:1,2:175,26:201,3:0.0147:2,2:6.3:1:22:1:0.05007:13.1558:60:2:0.01:0:2 0/0:228:0:0,0:175,52:227,0:0:2,0:19.7:1:28.8:1:1:0:60:24.222:1:0:0.2 +11 64574773 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25984;SOR=Inf;LSEQ=ATCGGGCAGAGGTGGGGGTC;RSEQ=GAACCAACAGGGACCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:60,173:233,0:0:2,0:22.7:1:31.3:1:1:0:59.9:76.667:1:0:0.1 0/1:298:3:1,2:88,207:295,3:0.0101:2,2:30.7:1:31:0:1:1.18:60:6:0.0102:0:1 +11 64575295 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19765;SOR=Inf;LSEQ=AGGGGTGTGGCCCAAGAAAA;RSEQ=GGAGTCCCTTGGGTGGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:178,60:238,0:0:2,0:24.9:1:31:1:1:0:60:78.333:1:0:0.1 0/1:191:2:1,1:140,49:189,2:0.0105:2,2:14:1:32:1:0.45605:2.83851:60:4:0.0105:0:1 +11 64575346 . G T 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.21926;SOR=4.66979;LSEQ=GTATGAAGGGGACAAGGCTG;RSEQ=GGGGAGGGAACAATACCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:1:0,1:302,160:462,1:0.0022:2,0:1:0:15:0:0.34773:0:60:0:0:0:1 0/1:499:5:1,4:319,175:494,5:0.01:2,2:10.6:1:26:1:0.0581:7.26295:60:10:0.0101:0:1 +11 64575505 . C T 201 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04041;LSEQ=ACAGGGCGAGGTGGACATCC;RSEQ=GGAGACCCAGGGCCTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:862:94:44,50:311,456:767,94:0.109:2,2:23.5:1:30.8:1:0.26743:1.29:60:30.333:0.1067:0:1.1 0/0:1017:5:1,4:474,535:1009,5:0.0049:2,2:8.6:1:29.8:1:0.37875:3.53998:57:10:0.005:0:1 +11 64575740 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTCCCACGTGTTCAAA;RSEQ=ACTCTCTCCCTGTTTACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:1,30:31,2:0.0606:1,2:29:1:26:1:0.11932:21.57:60:4:0.0606:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:11.2:1:31.2:1:1:0:60:12:1:0:0.2 +11 64577021 . GA G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.15694;SOR=Inf;LSEQ=AGTTTCCCAACTGCAAAGAG;RSEQ=AAATAACACCTGCCGAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:158,15:173,0:0:2,0:22.2:1:30.3:1:1:0:59.9:56.667:1:0:0.1 0/1:114:2:1,1:103,8:111,2:0.0175:2,2:25.5:1:27.5:1:0.1536:12.19759:60:4:0.0182:0:0 +11 64577541 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10717;SOR=Inf;LSEQ=GCACCACGTCGTCGATGGAG;RSEQ=GCAGCGGGAACAGCGTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:70,224:294,0:0:2,0:22.3:1:30.4:1:1:0:60:97:1:0:0.2 0/1:267:3:1,2:67,196:263,3:0.0112:2,2:26:1:23:1:1:1.46:60:2:0.0078:0:1.3 +11 64577567 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19132;SOR=Inf;LSEQ=GGGAACAGCGTCTTCTGGGC;RSEQ=GCCTTCAGCCCCATGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:29,162:191,0:0:2,0:25.8:1:31.2:1:1:0:59.9:62.667:1:0:0.3 0/1:149:2:1,1:29,116:145,2:0.0134:2,2:35.5:1:30.5:1:0.36763:3.95:60:4:0.0134:0:1 +11 64577620 . G C 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.0064;SOR=Inf;LSEQ=GCGGCCTGCAAGGCAAGCCG;RSEQ=GGGAGGGAGGGTCGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:12,77:89,0:0:2,0:25.1:1:31.6:1:1:0:60:88:1:0:0.5 0/1:53:5:1,4:5,43:48,5:0.0943:2,2:31.8:1:30:1:0.46547:2.11:60:10:0.0962:0:1 +11 65375490 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20683;SOR=Inf;LSEQ=GCCACAGCAAGGCAGTCAAT;RSEQ=CCACGGTATGGCACCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:126,82:208,0:0:2,0:24.6:1:32.1:1:1:0:59.9:51:1:0:0.2 0/1:174:2:1,1:99,73:172,2:0.0115:2,2:42.5:1:30:1:1:1.35374:60:4:0.0117:0:1.5 +11 66625801 . TCC T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10145;SOR=Inf;LSEQ=TCGCCCAGCTCGGTCAGCTC;RSEQ=CGCCTGGACCTCACCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:16,0:0:2,0:22.8:1:31.6:1:1:0:60:32:1:0:0.2 0/1:8:2:1,1:3,3:6,2:0.25:2,2:36.5:1:29.5:1:1:1:60:4:0.25:0:2 +11 66626394 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGACATCGCCGCCTCCGC;RSEQ=CGCACTGCTGCCGAGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:28.5:1:1:0:60:4:1:0:1 +11 66676732 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGCTGCTGGTGTGGGGCC;RSEQ=GAGCTGGAGGAAGTATCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 66677336 . T C 264 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTGGCCAGGACACGGGCCA;RSEQ=TGTATGGTCACAAACCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:282:282:155,127:0,0:0,282:1:0,2:26.1:1:32.5:1:1:0:59.9:69.5:1:0:1.9 1/0:342:202:104,98:73,67:140,202:0.5906:2,2:24.6:1:31.2:1:0.91285:1.02662:59.9:201:0.6:0:1.8 +11 66677366 . T C 247 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAAACCATGCAGTTTGGTA;RSEQ=GGCTGGAACACCGGGTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:277:277:130,147:0,0:0,277:1:0,2:26:1:30.5:1:1:0:59.9:33.625:1:0:1.9 1/0:314:162:72,90:74,76:150,162:0.5159:2,2:26:1:30.5:1:0.42721:1.21633:60:324:0.5192:0:2 +11 66677428 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5048;SOR=0;LSEQ=TGACCACTCACTGCGGCAGA;RSEQ=CAACACAGCATGATCCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:41,107:148,2:0.0133:2,2:14:1:29:1:0.48295:2.59:60:4:0.0137:0:2 0/0:119:0:0,0:33,86:119,0:0:2,0:24.6:1:31:1:1:0:60:58.5:1:0:0.4 +11 66677453 . T C 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51128;SOR=0;LSEQ=ACAGCATGATCCATGCTGTC;RSEQ=TCAATTTACACAGAAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:13,82:95,2:0.0206:2,2:6:0:33.5:1:0.26912:6.12:60:4:0.0208:0:2 0/0:69:0:0,0:10,59:69,0:0:2,0:26.5:1:29.9:1:1:0:60:68:1:0:0.1 +11 67194847 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTGCTGGGATTACAGGTG;RSEQ=GAGCCACCGTGACCAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:32:0:1:0:55.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 67196182 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.519;SOR=0;LSEQ=GCGGCTCCGCACGCCCAGAG;RSEQ=GGGCTCCGACTCTTTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:32,159:191,2:0.0104:2,2:10.5:1:26.5:1:0.31347:4.91:60:4:0.0107:0:1 0/0:128:0:0,0:19,109:128,0:0:2,0:24.3:1:30:1:1:0:60:127:1:0:0.2 +11 67196237 . T C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=6.79897;LSEQ=AGATCCCGGTCTCTATTAAG;RSEQ=TCTGATCCCACCCTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:4,2:40,60:100,6:0.0566:2,2:30.7:1:33.7:1:0.23012:2.97:60:12:0.0583:0:1 0/1:65:19:10,9:25,21:46,19:0.2923:2,2:19.9:1:31.3:1:1:1.07028:60:18:0.2813:0:1.1 +11 67196456 . G A 87 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04841;SOR=3.68428;LSEQ=CCCTCGGTTTCTCACAGGAC;RSEQ=CATGTCCCCTTGCCGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:974:3:2,1:481,489:970,3:0.0031:2,2:17.3:1:27.7:1:0.62193:2.03:60:6:0.0032:0:1 0/1:888:10:7,3:426,451:877,10:0.0113:2,2:16.4:1:26.4:1:0.2142:2.47:59.1:4:0.0092:0:1.4 +11 67196544 . C G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=3.41005;LSEQ=AATGGAGTGGGGAAGGGGAA;RSEQ=TGGGGAGCACTGGAGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:807:81:41,40:346,375:721,81:0.1004:2,2:22.8:1:32.2:1:0.72524:1.11:60:19.25:0.0986:0:1.4 0/1:718:198:101,97:256,261:517,198:0.2758:2,2:23.8:1:31.2:1:0.73866:1.06:59.8:65:0.2798:0:1.3 +11 67196740 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13896;SOR=Inf;LSEQ=GGGCGCACCCTCCTCCTGGC;RSEQ=TCACAGCCTCCATCTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:70,195:265,0:0:2,0:24.8:1:32:1:1:0:60:28.444:1:0:0.1 0/1:158:2:1,1:42,114:156,2:0.0127:2,2:25.5:1:28.5:1:0.4715:2.69:60:4:0.0127:0:1 +11 67196744 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13822;SOR=Inf;LSEQ=GCACCCTCCTCCTGGCCTCA;RSEQ=AGCCTCCATCTGGAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:66,190:256,0:0:2,0:24.2:1:32.2:1:1:0:60:84.333:1:0:0.1 0/1:152:2:1,1:40,110:150,2:0.0132:2,2:31:1:30:1:0.46802:2.73:60:4:0.0132:0:1 +11 67196900 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17077;SOR=Inf;LSEQ=ACTGCCCCACCCTTGGCAGG;RSEQ=CCTAGGCCTCCTGATCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:237,41:278,0:0:2,0:23.4:1:31.2:1:1:0:60:45.333:0.9963:0:0.1 0/1:197:2:1,1:159,36:195,2:0.0102:2,2:8.5:1:26:1:0.34114:4.37026:60:4:0.0106:0:1 +11 67199034 . G A 35 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29255;SOR=0;LSEQ=CTGGGGGTCGCGGGGGGGCA;RSEQ=CGAGCCAGCAAAGGAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:3:2,1:37,208:245,3:0.0121:2,2:6:1:22.7:1:0.0653:11.06:60:2:0.0085:0:1 0/0:151:0:0,0:23,128:151,0:0:2,0:24:1:30.6:1:1:0:60:24.167:1:0:0.2 +11 67199035 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2922;SOR=0;LSEQ=TGGGGGTCGCGGGGGGGCAG;RSEQ=GAGCCAGCAAAGGAAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:1,2:32,206:238,3:0.0124:2,2:35.7:1:31.3:1:0.35838:3.20:60:6:0.0133:0:1 0/0:147:0:0,0:21,125:146,0:0:2,0:24.3:1:29.2:1:1:0:60:47.667:0.9931:0:0.2 +11 67199959 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16197;SOR=Inf;LSEQ=TCCCCACGGCAGCTCTGTGA;RSEQ=GCAGGTAGGGCGGGAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:249,18:267,0:0:2,0:25.8:1:33.3:1:1:0:60:52.4:1:0:0.1 0/1:181:2:2,0:168,11:179,2:0.011:2,0:27:1:31:1:1:0:60:4:0.011:0:1 +11 67200819 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.19826;LSEQ=CTCCTCCTCCAGCCGCCCTT;RSEQ=ACCGCAGAGAACCGGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:998:62:35,27:498,437:935,62:0.0621:2,2:26.5:1:28.7:1:0.6939:1.14:60:14.5:0.0592:0:1.1 0/1:879:284:163,121:335,260:595,284:0.3231:2,2:23.3:1:29:1:0.77144:1.05:59.9:141:0.3249:0:1.2 +11 67201008 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=3.28897;LSEQ=CTGTGGGGAAGCCAGGGCCA;RSEQ=CCCGGCCTGTGCAGTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:21:0,21:6,170:176,21:0.1066:1,1:24.4:1:30.3:1:1:0:60:20:0.1047:0:1 0/1:138:39:2,37:3,96:99,39:0.2826:1,2:20.7:1:28.5:1:0.62124:1.72:60:38:0.2794:0:1.1 +11 67201615 . C T 190 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0;SOR=22.91769;LSEQ=CCCAGGGCAGAGGGAGTGAC;RSEQ=GGGGGGCAAGCAGGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1264:5:0,5:653,604:1257,5:0.004:2,0:2.6:1:23.8:1:0.02595:0:60:4:0.0032:0:1.4 0/1:1030:86:45,41:501,441:942,86:0.0835:2,2:20.9:1:29.6:1:0.91041:1.03505:60:42:0.0834:0:1.2 +11 67202044 . G A 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.41877;LSEQ=TGTCGCATGGCCCTGCCTCC;RSEQ=CCCCCCAGGGCTTCACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:51:26,25:304,219:523,51:0.0885:2,2:26.1:1:30.4:1:0.37381:1.33404:60:50:0.0896:0:1.1 0/1:469:141:87,54:191,133:324,141:0.3006:2,2:23.6:1:29:1:0.6079:1.12:60:69.5:0.3082:0:1.1 +11 67202156 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=6.34231;LSEQ=CCTCAACAGTAGCCCCCGGG;RSEQ=CCCCGTCAGGTACTGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:701:48:19,29:286,366:652,48:0.0685:2,2:21:1:28.9:1:0.65162:1.1924:60:23:0.0671:0:1.2 0/1:685:218:92,126:211,255:466,218:0.3182:2,2:26.5:1:28.5:1:0.45853:1.13304:60:108:0.3181:0:1.2 +11 67202826 . G A 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20427;SOR=4.40228;LSEQ=CACGGAGGGCCGCCCGCCAC;RSEQ=CCCCGCGCTCAACTGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:0,19:19,2:0.0952:1,0:21.5:1:25.5:1:1:0:60:4:0.1:0:1 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:27.5:1:29.5:1:1:0:60:4:0.3333:0:1 +11 67203369 . G T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCGCCCTCCGTGTCACT;RSEQ=TCTCTGGCTTCCTCAGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:31.5:1:1:0:60:4:1:0:1 +11 67817154 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGTCCAGGCCACGCTGGTG;RSEQ=TCCTGGCCTTGGCCATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,3:10,2:0.1667:2,2:32.5:1:30:1:1:2.16028:60:4:0.1818:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:23.5:1:29.8:1:1:0:60:8:1:0:0 +11 67875171 . T C 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CTTAGAAAGTGTTTCTAAAA;RSEQ=ACAAATTTCAAGCCGCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21:1:32.5:1:1:0:60:4:1:0:1 0/1:5:1:1,0:3,1:4,1:0.2:2,0:12:0:33:0:1:0:60:2:0.2:0:1 +11 68132394 . A AC 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0.04415;LSEQ=CCGTATTTTGGGGCTGCTAC;RSEQ=CCCAGCTTTCCCCTGGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:82:69,13:2,1:3,82:0.9647:2,2:22.8:1:32.1:1:0.42133:2.61:33:164:0.9647:0.2235:0.1 1/0:50:27:21,6:19,4:23,27:0.54:2,2:23.1:1:30.1:1:0.73555:1.34894:34.3:54:0.54:0.14:0.1 +11 68132507 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50144;SOR=0;LSEQ=AAGCTTGGCCATCCCAGCAA;RSEQ=AGGGACAGTGTTCCTATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:56,80:136,2:0.0145:2,2:38.5:1:29:1:1:1.42:56:4:0.0148:0:1 0/0:117:0:0,0:51,66:117,0:0:2,0:25.4:1:30.7:1:1:0:49.9:57.5:1:0:0.2 +11 68132551 . C A 30 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.67133;LSEQ=TGCTGGGTCCACACATAGCA;RSEQ=AAAGACAAGACAAGCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:21,58:79,2:0.0247:2,2:7:1:30.5:1:0.47191:2.72:60:4:0.0263:0:1 0/1:60:1:1,0:18,41:59,1:0.0167:2,0:1:0:25:0:0.31667:0:60:2:0.0167:0:1 +11 68132731 . A G 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=CATAGGAGCTTGGTGGGAGG;RSEQ=AGCAGATGGGGAGATGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:28.4:1:32.2:1:1:0:46.2:10:0.8333:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:31:1:32.5:1:1:0:60:4:1:0:0 +11 68132743 . A AG 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGAGGAAGCAGATGGGG;RSEQ=GATGTCACTCCATGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:27:1:32:1:1:0:46.2:10:1:0.2:0.8 1/1:2:2:0,2:0,0:0,2:1:0,0:18:1:32:0:1:0:60:4:1:0:0 +11 68758369 . C A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTATACACAGCACATATAC;RSEQ=TATACACAGTAAACACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:53,1:0,0:0,54:1:0,1:26.7:1:29.9:1:1:0:60:17:1:0:1.3 1/1:58:58:53,5:0,0:0,58:1:0,2:20.5:1:29.4:1:1:0:60:57:1:0:1.1 +11 68758426 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19317;SOR=0;LSEQ=ACACGGACACACCGAGCACA;RSEQ=ATATAACGATGACCACGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:98,43:141,2:0.0139:2,2:24.5:1:32:1:0.52221:2.26452:60:4:0.0143:0:2 0/0:183:0:0,0:119,64:183,0:0:2,0:22.7:1:28.9:1:1:0:60:182:1:0:0.9 +11 68758434 . G T 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18495;SOR=0.2101;LSEQ=ACACCGAGCACATATATAAC;RSEQ=ATGACCACGAACTCACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:4:1,3:112,58:170,4:0.023:2,2:12.8:1:27:1:0.12439:5.73272:60:8:0.0231:0:2.5 0/0:204:1:0,1:126,77:203,1:0.0049:2,0:1:0:22:0:0.38235:0:60:2:0.005:0:2 +11 68758439 . C T 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03473;SOR=Inf;LSEQ=GAGCACATATATAACGATGA;RSEQ=CACGAACTCACAGTTGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:120,66:186,0:0:2,0:25.1:1:31.4:1:1:0:60:36.2:1:0:1.4 0/1:227:6:5,1:129,92:221,6:0.0264:2,2:33.7:1:29:1:0.40483:3.55:60:12:0.0267:0:2.2 +11 68758487 . T C 251 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACACAGTTAAAGGCAGTCC;RSEQ=ACCCTACAGCTCAGGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:261:261:129,132:0,0:0,261:1:0,2:26.5:1:31.3:1:1:0:59.9:31.625:1:0:1.9 1/0:316:203:93,110:53,59:112,203:0.6424:2,2:25.9:1:31:1:0.81428:1.06229:60:202:0.6495:0:1.6 +11 68758509 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05566;LSEQ=CCCTACAGCTCAGGGTGTGT;RSEQ=TAACAAGGTGAGGGACTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:212:92,120:11,11:22,212:0.906:2,2:26.5:1:29.8:1:0.65327:1.30284:59.9:25.5:0.9027:0:2.2 0/1:282:98:41,57:74,109:183,98:0.3475:2,2:23.2:1:29.5:1:0.89878:1.06:60:97:0.3502:0:2.1 +11 68758558 . TG T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49831;SOR=Inf;LSEQ=ACTCAGGTGGGAAGGGGAGC;RSEQ=GGGGGAGCCAGGTGAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:39,109:148,0:0:2,0:27.1:1:31.3:1:1:0:60:48.333:1:0:1.7 0/1:148:2:1,1:45,101:146,2:0.0135:2,2:16.5:1:26.5:1:0.52648:2.23:60:4:0.0136:0.0068:1 +11 68758581 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0.09222;LSEQ=GGGGAGCCAGGTGAGGGAGC;RSEQ=GGGTGCTGGCTGCAGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:102:21,81:2,8:10,102:0.9107:2,2:24:1:31.6:1:1:1.04:60:24.5:0.9074:0:1.6 0/1:79:38:12,26:7,34:41,38:0.481:2,2:27:1:30.1:1:0.18815:2.22:60:76:0.481:0:1.6 +11 68758590 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16246;SOR=Inf;LSEQ=GGTGAGGGAGCGGGGTGCTG;RSEQ=CTGCAGGAGAAGTGTGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:16,81:97,0:0:2,0:23.5:1:32.3:1:1:0:60:96:1:0:1.3 0/1:66:2:1,1:14,50:64,2:0.0303:2,2:24.5:1:28:1:0.40559:3.48:60:4:0.0303:0:2 +11 68758840 . A C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGAGACCAGGGGCCCCG;RSEQ=AGCTCTGAGAGAGGAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:9.5:1:31.5:1:1:0:60:4:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 68759641 . T G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCAGAGGACCCCTCCCGG;RSEQ=GGGGAGATGCTCAGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69069479 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02435;SOR=Inf;LSEQ=GGGCTGGGTTCCCTGCAGAT;RSEQ=GGAGGGCTAGGTGCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:151,80:231,0:0:2,0:25.3:1:31.8:1:1:0:59.9:56.75:0.9956:0:0.1 0/1:153:4:2,2:93,56:149,4:0.0261:2,2:19.3:1:27:1:0.63422:1.65492:60:8:0.0261:0:1.5 +11 69069489 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06841;SOR=Inf;LSEQ=CCCTGCAGATGGGAGGGCTA;RSEQ=GTGCCTGTCTCCTTGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:160,103:263,0:0:2,0:24.7:1:32.3:1:1:0:59.9:64.75:1:0:0.1 0/1:183:3:3,0:102,78:180,3:0.0164:2,0:28.7:1:26.3:1:0.2623:0:60:2:0.0111:0:2.3 +11 69069589 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17192;SOR=Inf;LSEQ=AGGAGAGGAAAGTGACTCAC;RSEQ=TGCCCCCCTTGCCTGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:97,154:251,0:0:2,0:23.4:1:32.3:1:1:0:60:61.75:0.996:0:0.1 0/1:179:2:1,1:78,98:176,2:0.0112:2,2:26.5:1:29.5:1:1:1.25:60:4:0.0112:0:1 +11 69069591 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.17319;SOR=Inf;LSEQ=GAGAGGAAAGTGACTCACCT;RSEQ=CCCCCCTTGCCTGTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:93,148:241,0:0:2,0:23.6:1:32:1:1:0:60:39.167:0.9958:0:0.1 0/1:173:2:1,1:75,95:170,2:0.0116:2,2:8.5:1:31:1:1:1.26:60:4:0.0116:0:1.5 +11 69069627 . G T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18216;SOR=Inf;LSEQ=TCCTCAGCAGCCACACCCAG;RSEQ=CTAGGCTCTCCCGCAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:33,106:139,0:0:2,0:24.7:1:31.4:1:1:0:60:45.333:1:0:0 0/1:104:2:0,2:37,65:102,2:0.0192:2,0:24:1:23.5:1:0.53715:0:60:4:0.0196:0:1.5 +11 69069783 . T C 73 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGTGTCCTCGTCTGTAG;RSEQ=CGGGCTGTCGGCAGGCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:23.8:1:31.6:1:1:0:60:10:0.5556:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69456000 . G C 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=GCAGAAGAGCGCGAGGGAGC;RSEQ=CGGGGCAGCAGAAGCGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:215,10:225,0:0:1,0:23.3:1:29.9:1:1:0:59.9:36.5:1:0:0.1 0/1:130:10:10,0:109,11:120,10:0.0769:2,0:29.8:1:31.8:1:1:0:60:20:0.0781:0:1.2 +11 69456326 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16022;SOR=Inf;LSEQ=AGACTTCCCTGCAACTTGTT;RSEQ=CCCAGACCCACGTTTCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:29,186:215,0:0:2,0:24.4:1:31.9:1:1:0:60:29.714:1:0:0.2 0/1:144:2:1,1:40,102:142,2:0.0139:2,2:16:1:31:1:0.4898:2.53:60:4:0.0142:0:1 +11 69456327 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1625;SOR=Inf;LSEQ=GACTTCCCTGCAACTTGTTG;RSEQ=CCAGACCCACGTTTCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:27,184:211,0:0:2,0:24.3:1:31:1:1:0:60:22.444:1:0:0.2 0/1:143:2:1,1:40,101:141,2:0.014:2,2:8:1:28:1:0.49266:2.51:60:4:0.0146:0:1 +11 69457746 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.10483;SOR=Inf;LSEQ=ATGGGGGGTGCGGGGGCGTG;RSEQ=GGGGGGGCGGCGCGACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:143,22:165,0:0:2,0:15.7:1:31.8:1:1:0:60:17.333:0.9936:0:0.2 0/1:150:3:1,2:119,26:145,3:0.02:2,2:11.3:1:25.7:1:0.09187:8.95221:60:6:0.0216:0:1.3 +11 69457756 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08322;SOR=Inf;LSEQ=CGGGGGCGTGCGGGGGGGCG;RSEQ=CGCGACCTGGCGGCGGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:218,53:271,0:0:2,0:17.6:1:31.9:1:1:0:60:66.75:1:0:0.2 0/1:211:3:1,2:160,48:208,3:0.0142:2,2:18.7:1:27.3:1:0.14048:6.58996:60:6:0.0149:0:1 +11 69458055 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06131;SOR=Inf;LSEQ=CCCCCCGCCCCCCGCGAGCC;RSEQ=CACGCAGGACCACGGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:105,322:427,0:0:2,0:24.4:1:31.6:1:1:0:60:41.7:1:0:0.2 0/1:279:3:2,1:77,199:276,3:0.0108:2,2:14.3:1:24.3:1:0.19417:5.13:57.7:2:0.0074:0:1 +11 69458074 . CG C 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12827;SOR=Inf;LSEQ=CGCACGCAGGACCACGGGGC;RSEQ=GGGAAGGTGCAGGCGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:37,211:248,0:0:2,0:21.4:1:31.3:1:1:0:60:48.6:0.9918:0:0.2 0/1:140:2:1,1:27,109:136,2:0.0143:2,2:7.5:1:26.7:1:0.36581:3.98:60:4:0.0145:0.0071:0 +11 69458081 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13213;SOR=Inf;LSEQ=AGGACCACGGGGCCGGGGAA;RSEQ=GTGCAGGCGGTGGCGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:28,183:211,0:0:2,0:20.1:1:31.8:1:1:0:60:34.167:1:0:0.2 0/1:121:2:1,1:20,99:119,2:0.0165:2,2:6:1:28:1:0.31818:4.86:60:4:0.0165:0:1 +11 69458455 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06417;SOR=Inf;LSEQ=CAGCATTCGCCAGCCCTCCC;RSEQ=TCCAACATCCAGGACCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:25,0:0:1,0:22:1:32.1:1:1:0:60:50:1:0:0.2 0/1:9:2:1,1:6,1:7,2:0.2222:2,2:30.5:1:29:1:0.41667:4.58262:60:4:0.25:0:1.5 +11 69462642 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95947;LSEQ=GATGTGGAGCCTCAGATACC;RSEQ=AGTGCTTCCCTTCAGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:54:52,2:72,2:74,54:0.4219:1,1:27.2:1:30.7:1:1:1.38102:59.7:53:0.4173:0:1.2 0/1:51:21:21,0:29,1:30,21:0.4118:1,1:18.1:1:30.1:1:1:0:60:42:0.4118:0:1 +11 69462664 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTTCCCTTCAGGCCGGG;RSEQ=CGCTTGCTCAGAGCCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:2,0:173,11:184,2:0.0107:2,0:21.5:1:29:1:1:0:60:4:0.0111:0:1.5 0/0:84:0:0,0:79,5:84,0:0:2,0:22.4:1:31.6:1:1:0:60:168:1:0:0.3 +11 69462666 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCCCTTCAGGCCGGGCC;RSEQ=CTTGCTCAGAGCCAGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:2,0:182,13:195,2:0.0102:2,0:20:1:29:1:1:0:60:4:0.0104:0:1.5 0/0:89:0:0,0:82,7:89,0:0:2,0:22.2:1:29.3:1:1:0:60:88:1:0:0.3 +11 69462856 . C T 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAGGAGCCCCAACAACTT;RSEQ=CTGTCCTACTACCGCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1550:0:0,0:751,799:1550,0:0:2,0:25.1:1:31.6:1:1:0:60:69.455:1:0:0.3 0/1:1291:57:27,30:592,641:1233,57:0.0442:2,2:28.5:1:29.1:1:1:1.02616:59.6:27.5:0.0432:0:1.2 +11 69462910 . G A 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26314;SOR=1.11933;LSEQ=AGAGTGATCAAGTGTGACCC;RSEQ=GTAAGTGAGGGTGATGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1016:393:153,240:228,394:622,393:0.3868:2,2:25.6:1:31.2:1:0.46522:1.10:60:55.143:0.3883:0:1.1 0/1:778:322:114,208:172,284:456,322:0.4139:2,2:25.6:1:30:1:0.54606:1.10487:59.9:52.667:0.4115:0:1.2 +11 69463478 . AG A 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTAAAATGACAATCAAA;RSEQ=GGTTTGTGGCATTTACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:22.5:1:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69465507 . C A 55 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCTGAAAAGGCAGGGTT;RSEQ=AAAGGGCCTCCTGTCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:23:1:27.5:1:1:0:60:8:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69465681 . A G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48236;SOR=1.70316;LSEQ=ACCAGGTGGGAGGTGGAGGC;RSEQ=TTTGGTCCTGAGTGTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:11:11,0:17,2:19,11:0.3667:2,0:19.8:1:28.9:1:0.51954:0:60:10:0.3448:0:1.3 1/0:10:5:5,0:5,0:5,5:0.5:0,0:10.6:1:30.2:1:1:0:60:10:0.5:0:1.2 +11 69465799 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12115;SOR=Inf;LSEQ=TTGCTCTTATAAAGGCTTCC;RSEQ=GGTCATGGCACCTGGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:262,33:295,0:0:2,0:22.7:1:29.9:1:1:0:59.9:41.143:1:0:0.1 0/1:158:2:1,1:134,22:156,2:0.0127:2,2:12.5:1:28.5:1:0.27074:5.97924:60:4:0.0127:0:1 +11 69465872 . CCT C 96 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.6057;SOR=1.39978;LSEQ=CTCTTCCCACCTCTCCCCAC;RSEQ=CTCTCTCTCAGGACTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:916:7:2,5:537,372:909,7:0.0076:2,2:36.6:1:31.9:1:0.13105:3.60389:60:14:0.0077:0:0 0/1:750:8:6,2:438,300:738,8:0.0107:2,2:32.3:1:32:1:0.48422:2.05:60:16:0.0108:0.0013:1 +11 69465987 . AGAG A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.43905;SOR=0.7594;LSEQ=AAGGCCGCCGAGGAGGAGGA;RSEQ=GAGGAGGAGGAGGTGGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1152:27:11,16:545,577:1122,27:0.0234:2,2:20.5:1:32.1:1:0.44317:1.3735:59.6:54:0.0238:0.0069:0.4 0/1:894:16:8,8:407,469:876,16:0.0179:2,2:24.3:1:31:1:0.80533:1.15:59.5:32:0.0182:0.0034:0.3 +11 69466115 . C A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.01721;LSEQ=GAGCCGGCCCCAGGTGCTCC;RSEQ=CTGACAGTCCCTCCTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:105:13,92:15,141:156,105:0.4023:2,2:19.1:1:29.8:1:0.54245:1.33:60:104:0.4094:0:1.2 0/1:187:76:13,63:12,99:111,76:0.4064:2,2:19.9:1:28.7:1:0.27437:1.70:60:37:0.4066:0:1.1 +11 69511849 . A C 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29984;SOR=0;LSEQ=GCATCTTGATTGGCAGATGG;RSEQ=GACAGGGAACGCCCCAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:4:4,0:149,4:153,4:0.0255:1,0:27.8:1:33.8:1:1:0:60:8:0.0261:0:1 0/0:88:0:0,0:86,2:88,0:0:1,0:24.6:1:28.7:1:1:0:60:176:1:0:0.1 +11 69512089 . T C 338 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.39411;LSEQ=TAATCCCTGGCAAATGCTCA;RSEQ=TTGGAATCATGTTTCATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1448:1334:560,774:50,63:113,1334:0.9213:2,2:24.7:1:32.6:1:0.69168:1.09687:59.9:77.471:0.921:0:1.1 1/1:1306:1261:537,724:20,22:42,1261:0.9655:2,2:24.4:1:31.3:1:0.52962:1.22546:59.9:113.636:0.9653:0:1.2 +11 69512114 . T C 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCATGTTTCATGCACACG;RSEQ=TGGTGTCCGGTTGCACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1077:0:0,0:372,702:1074,0:0:2,0:24.3:1:30.2:1:1:0:60:118.333:0.9972:0:0.9 0/1:935:41:12,29:350,542:892,41:0.0439:2,2:21.6:1:29.8:1:0.2514:1.55987:60:12.667:0.0413:0:2 +11 69512199 . G A 41 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26944;SOR=0;LSEQ=CGCTAATTCTTGCCTTCCCA;RSEQ=CCTGCCGTGCAGCTGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:3:2,1:18,233:251,3:0.0118:2,2:5.3:1:26.3:1:0.0169:25.02:60:6:0.012:0:1.3 0/0:181:0:0,0:20,161:181,0:0:2,0:25.4:1:31.2:1:1:0:60:44.25:1:0:0.1 +11 69513939 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21441;SOR=Inf;LSEQ=CCTAAAGCTAAACAGAACGT;RSEQ=GACTCAGGACTGTTCTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:167,11:178,0:0:2,0:22.8:1:32.3:1:1:0:60:58.333:1:0:0.1 0/1:154:2:1,1:135,17:152,2:0.013:2,2:14.5:1:29:1:0.22078:7.74581:60:4:0.0132:0:1 +11 69514371 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06623;SOR=Inf;LSEQ=AGAAAACAGGCAGCTCTGAG;RSEQ=AATCCACAGTGGACAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:81,255:336,0:0:2,0:23.4:1:32:1:1:0:59.9:83:0.997:0:0.1 0/1:230:3:1,2:50,177:227,3:0.013:2,2:12:1:27.3:1:0.53038:1.76:60:6:0.0133:0:1 +11 69514657 . C A 57 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAATCCAGGAGTTTGAGA;RSEQ=CAGCCTGGGCAACATGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:13.8:1:28.8:1:1:0:53.8:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69515423 . G A 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCCTTTATCATTCTAAG;RSEQ=CCTTCTGGTCTGCAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:32.4:1:27.4:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69515695 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.12159;SOR=Inf;LSEQ=CCTTGGCGACCCAGGACAGG;RSEQ=GCAGGCGGGAGCCGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:109,3:112,0:0:1,0:26.4:1:32.3:1:1:0:59.8:55:1:0:0.1 0/1:61:2:2,0:55,2:57,2:0.0328:1,0:10:1:30.5:1:1:0:60:4:0.0328:0:1 +11 69515696 . G A 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00811;SOR=11.94738;LSEQ=CTTGGCGACCCAGGACAGGC;RSEQ=CAGGCGGGAGCCGGAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:1:1,0:113,4:117,1:0.0085:1,0:46:0:29:0:1:0:60:2:0.0085:0:1 0/1:64:6:6,0:54,4:58,6:0.0938:2,0:26.5:1:26.8:1:1:0:60:12:0.0952:0:1.5 +11 69515734 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18953;SOR=Inf;LSEQ=GGCTGGGCAGTAAACACACT;RSEQ=CAGGACGGCCTCAGTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:188,50:238,0:0:2,0:21.9:1:31.9:1:1:0:60:58.5:1:0:0.1 0/1:184:2:1,1:135,47:182,2:0.0109:2,2:23:1:30:1:0.45474:2.85277:60:4:0.0112:0:1 +11 69515786 . G T 64 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29347;SOR=0.37093;LSEQ=TCTGCAAAGGTCACTGAACT;RSEQ=CAGGTGGGTGACGAGGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:6:2,4:343,214:557,6:0.0107:2,2:20:1:24.8:1:0.21281:3.19882:60:2:0.0073:0:1.2 0/0:503:2:0,2:321,180:501,2:0.004:2,0:1:0:22.5:1:0.13046:0:54.5:1:0.002:0:1 +11 69516025 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02225;SOR=Inf;LSEQ=AGAAATTAGTATCACTTTCT;RSEQ=CATACAGAAAACGAAATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:1,146:147,0:0:1,0:24.9:1:31.6:1:1:0:59.8:72.5:1:0:0.2 0/1:94:4:0,4:1,89:90,4:0.0426:1,0:17.8:1:28.8:1:1:0:60:8:0.0426:0:1 +11 69517971 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02002;SOR=Inf;LSEQ=TTTCTCTCCTTCAGGCCTCC;RSEQ=CCCGGGGACAGGCGCCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:323,109:432,0:0:2,0:23.1:1:30.3:1:1:0:60:53:1:0:0.1 0/1:262:4:2,2:174,84:258,4:0.0153:2,2:20.5:1:27.8:1:0.59965:2.06522:60:8:0.0159:0:1.8 +11 69518455 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17126;SOR=Inf;LSEQ=GCAGTCCACGACGCCGTCGG;RSEQ=ACGGATGCGCAGGAAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:181,69:250,0:0:2,0:25.9:1:32.5:1:1:0:60:82.333:1:0:0.2 0/1:177:2:1,1:117,58:175,2:0.0113:2,2:18.5:1:27.5:1:1:2.00866:60:4:0.0116:0:1 +11 69518486 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03773;SOR=Inf;LSEQ=AGGAAGCAGCTGGAGAGCCC;RSEQ=TGGGGGCCGGAGGTGTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:0:0,0:225,135:360,0:0:2,0:26.2:1:30.1:1:1:0:60:35:0.9972:0:0.2 0/1:286:4:3,1:167,115:282,4:0.014:2,2:11:1:27.3:1:0.64898:2.06:60:8:0.0141:0:1.5 +11 69518534 . G T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04354;SOR=Inf;LSEQ=AGGCGGATGGGGTCGCCCCA;RSEQ=CCGTAGTGCACGTGGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:178,171:349,0:0:2,0:25.3:1:32.6:1:1:0:60:86.25:1:0:0.2 0/1:295:4:1,3:150,140:290,4:0.0136:2,2:18.5:1:25.5:1:0.35926:3.20262:60:3:0.0106:0:1.5 +11 69518589 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25013;SOR=0;LSEQ=CGAGGGGGCGCCCGGCCACG;RSEQ=CCAGCCAGAGGCCGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:2,1:107,145:252,3:0.0118:2,2:34.7:1:32:0:0.57755:2.70:60:6:0.0118:0:2 0/0:232:0:0,0:101,131:232,0:0:2,0:23.4:1:30.2:1:1:0:60:24.778:1:0:0.2 +11 69518636 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25552;SOR=0;LSEQ=ACGTGGACCACCACACACCC;RSEQ=CTCCGCATGGCACCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:2,1:75,125:200,3:0.0148:2,2:28:1:29.3:1:0.55858:3.31:60:6:0.0154:0:1 0/0:166:0:0,0:67,98:165,0:0:2,0:26.8:1:30.2:1:1:0:60:54:1:0:0.2 +11 69518660 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18012;SOR=Inf;LSEQ=CGCATGGCACCTCCCTGGGG;RSEQ=TCTCGGCGCAGCTCCGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:51,107:158,0:0:2,0:24.8:1:32:1:1:0:60:18.75:1:0:0.2 0/1:117:2:1,1:45,70:115,2:0.0171:2,2:18.5:1:25:1:1:1.55:60:4:0.0172:0:2 +11 69529910 . AGAGG A 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=4.000;MSILEN=4;SSF=0.4;SOR=Inf;LSEQ=GGAAAGAAAGAAAGAAAGAG;RSEQ=GAGGGAGGGAGGAAGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:38:1:33.5:1:1:0:60:4:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:25:1:32.5:1:1:0:60:4:0.6667:0:0 +11 69530825 . G A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19886;SOR=Inf;LSEQ=ATCCACGCCCAGGCCACAGA;RSEQ=AATAGCCCCTTTAGGACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:4,14:18,0:0:2,0:21.7:1:31.9:1:1:0:60:36:1:0:0.3 0/1:15:2:1,1:3,10:13,2:0.1333:2,2:6:1:30.5:1:0.47619:3.03:60:4:0.1429:0:1 +11 69586371 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14323;SOR=Inf;LSEQ=AACAGCAGTTTAAGATGTGT;RSEQ=GTCCTGTCTTAGCGGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:97,4:101,0:0:1,0:25.1:1:33:1:1:0:60:49.5:1:0:0.1 0/1:62:2:2,0:58,2:60,2:0.0323:1,0:19:1:29:0:1:0:60:4:0.0328:0:1.5 +11 69588020 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.42158;LSEQ=AGAAAGTGCACCAAGGTGAC;RSEQ=CTCGGCACTGCCCTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:168:137,31:177,23:200,168:0.4553:2,2:26.1:1:31.7:1:0.07554:1.73866:60:83:0.4573:0:1.1 0/1:219:57:51,6:140,22:162,57:0.2603:2,2:24:1:30.4:1:0.64969:1.33:60:114:0.2627:0:1.1 +11 69588729 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGGGGCTGGAGAAGCCAC;RSEQ=AGCCTGCTAGCCATGTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:421:421:298,123:0,0:0,421:1:0,2:23.8:1:30.4:1:1:0:60:104.25:1:0:1.1 1/1:283:267:185,82:9,6:15,267:0.9435:2,2:22.6:1:29.3:1:0.56724:1.50:59.9:65.75:0.9427:0:1.1 +11 69589142 . G A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0.2887;LSEQ=CGGCGGCCGCACCCAGTCCC;RSEQ=GACCTTCAGACGCGAGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:1,0:1,8:0.8889:0,0:16.4:1:32.4:1:0.11111:0:60:16:0.8889:0:1.4 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25:1:30.5:1:1:0:60:4:0.6667:0:1.5 +11 69589182 . C G 52 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=GACCCCAGCGGTTCCCCAGC;RSEQ=TGGGCCAGGCCGGGGCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:1,1:2,3:0.6:2,0:36:1:33.3:1:0.4:0:60:6:0.6:0:2 1/0:2:1:0,1:0,1:1,1:0.5:0,0:28:0:30:0:1:0:60:2:0.5:0:2 +11 69589308 . A G 60 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCGGGAGGCGGCGCCCG;RSEQ=CCTCAGGGGTTGCGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:31:1:1:0:60:4:1:0:1 1/1:4:4:2,2:0,0:0,4:1:0,2:32:1:30.3:1:1:0:60:8:1:0:1 +11 69589450 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.58197;SOR=2.50361;LSEQ=GGTCTCAGAGTGTGACTGAG;RSEQ=GGGTTGGCCCGGCGGCCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:9,9:18,1:0.0526:2,0:1:0:27:0:1:0:60:2:0.0556:0:1 0/1:16:2:1,1:7,7:14,2:0.125:2,2:18:0:30:1:1:1:58:4:0.125:0:3.5 +11 69589509 . T C 39 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63709;SOR=0.43558;LSEQ=TTCGCGCCTGGCCGCGCCAC;RSEQ=CACTGTCGCGGGTGTCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:2,1:181,76:257,3:0.0115:2,2:22.3:1:25:1:1:1.18994:60:2:0.0079:0:1 0/0:198:1:1,0:130,67:197,1:0.0051:2,0:2:0:31:0:1:0:60:2:0.0053:0:1 +11 69589556 . G A 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=50.03179;LSEQ=CCGCCGATGCGGCCGTCGGG;RSEQ=AGCGCCTGGAGGTGGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:667:1:1,0:386,280:666,1:0.0015:2,0:1:0:26:0:1:0:60:2:0.0015:0:1 0/1:571:40:23,17:304,225:529,40:0.0701:2,2:29.2:1:28.8:1:1:1.00:60:80:0.071:0:1.1 +11 69589711 . C T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43352;SOR=2.18984;LSEQ=CGAGAGCGCCACCAGGCTCT;RSEQ=CCAGCGGCGCTCCAGCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:2:0,2:157,208:365,2:0.0054:2,0:1:0:19.5:1:0.50909:0:60:1:0.0028:0:1 0/1:337:4:1,3:149,184:333,4:0.0119:2,2:21.3:1:27.3:1:0.63185:2.42353:60:8:0.012:0:1 +11 69589804 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26286;SOR=0;LSEQ=CCAGGGCGCCAGCAAGGCCA;RSEQ=CAGGACCGCCGGGAGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:140,153:293,3:0.0101:2,2:24:1:32.3:1:0.60901:2.18:60:6:0.0104:0:1 0/0:225:0:0,0:101,123:224,0:0:2,0:19:1:31.4:1:1:0:59.8:36.333:0.9954:0:0.4 +11 69589820 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17159;SOR=Inf;LSEQ=GCCAGCAGGACCGCCGGGAG;RSEQ=AGCGCTACCGCGGCCGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:120,131:251,0:0:2,0:21.7:1:32.2:1:1:0:60:61.75:1:0:0.3 0/1:178:2:1,1:82,94:176,2:0.0112:2,2:18.5:1:27.5:1:1:1.15:60:4:0.0116:0:1.5 +11 69589836 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56527;SOR=3.05354;LSEQ=GGAGCAGCGCTACCGCGGCC;RSEQ=TCCCGGGCCCCGACATCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:1:1,0:95,95:190,1:0.0052:2,0:1:0:27:0:1:0:60:2:0.0053:0:1 0/1:126:2:1,1:60,64:124,2:0.0159:2,2:40.5:1:30.5:1:1:1.07:60:4:0.0159:0:1 +11 69589842 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14531;SOR=Inf;LSEQ=GCGCTACCGCGGCCGTCCCG;RSEQ=GCCCCGACATCCCGGCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:88,91:179,0:0:2,0:24.6:1:30.5:1:1:0:60:21.375:0.9884:0:0.3 0/1:112:2:1,1:56,54:110,2:0.0179:2,2:41:1:29:1:1:1.03671:60:4:0.0183:0:1 +11 69589865 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.51032;SOR=0;LSEQ=CCCGACATCCCGGCCCGAGG;RSEQ=CCGTGCGTCGGTCAGGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:62,64:126,2:0.0156:2,2:20.5:1:28.5:1:1:1.03:60:4:0.0159:0:1 0/0:93:0:0,0:46,46:92,0:0:2,0:23.6:1:31:1:1:0:60:184:0.9892:0:0.5 +11 69589868 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16886;SOR=Inf;LSEQ=GACATCCCGGCCCGAGGGCC;RSEQ=TGCGTCGGTCAGGCGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:61,63:124,0:0:2,0:24.5:1:30.6:1:1:0:60:123:1:0:0.3 0/1:87:2:1,1:42,43:85,2:0.023:2,2:9.5:1:28.5:1:1:1.02:60:4:0.0233:0:1.5 +11 69589929 . T G 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00223;SOR=Inf;LSEQ=GCAGAGCTGCGCCTGTGGCG;RSEQ=CCCGCGGGAGCGCACGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:6,14:20,0:0:2,0:20.6:1:30.6:1:1:0:60:40:1:0:0.3 0/1:14:6:3,3:2,6:8,6:0.4286:2,2:12.8:1:30.3:1:0.58042:2.76:60:12:0.4286:0:1.2 +11 69589956 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCGCACGGCCGACCTCG;RSEQ=GCAGGAGTGCGCAACCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,6:8,2:0.2:2,2:22:1:28.5:1:1:2.65:60:4:0.2:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:7.5:1:31:1:1:0:60:4:1:0:1.5 +11 69589959 . A G 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GCGCACGGCCGACCTCGGGC;RSEQ=GGAGTGCGCAACCGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:2,2:4,3:0.4286:2,0:27:1:32:1:0.42857:0:60:6:0.4286:0:1.3 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:32:0:1:0:60:4:1:0:1.5 +11 69591515 . TC T 74 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.62174;LSEQ=GCTGCCTCTGGGTCCTGGGG;RSEQ=CCCCAGATGAGCCTGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:6,0:6,5:0.4545:0,2:18.8:1:31.9:1:0.45455:0:60:10:0.5:0.0909:0 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:12:0:32:0:1:0:60:2:0.5:0:0 +11 69591699 . A C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTCCCTCAGCCTGGGGCCA;RSEQ=CCGAACACACCCTCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:261:261:254,7:0,0:0,261:1:0,1:25:1:32.3:1:1:0:59.9:64.25:1:0:1.1 1/1:168:152:139,13:15,1:16,152:0.9048:1,2:22.8:1:31.3:1:1:1.40036:60:37:0.9024:0:1.1 +11 69591784 . T TC 228 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=304.07178;LSEQ=GCAGAGGGACTCTGATGTCT;RSEQ=CCCCCGGCTTTTGATAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1105:1:1,0:644,457:1101,1:9e-04:2,0:20:0:32:0:1:0:60:2:9e-04:0:0 0/1:953:205:107,98:425,323:748,205:0.2151:2,2:23.7:1:29.8:1:0.26644:1.20487:59.8:33.167:0.2126:0.0346:0.2 +11 69591809 . C T 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38292;LSEQ=CGGCTTTTGATAGGATGAGG;RSEQ=TCCTTTCTTCCCAGGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1447:779:426,353:347,319:666,779:0.5384:2,2:25.6:1:30:1:0.34109:1.11:59.9:76.9:0.54:0:1.1 0/1:1241:383:198,185:438,419:857,383:0.3086:2,2:25.2:1:28.8:1:0.85389:1.02:59.8:53.714:0.3082:0:1.2 +11 69592058 . T G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29464;SOR=0;LSEQ=GGCTTCCACTTTGCTCCGGG;RSEQ=GCTCCCTGAGCACACTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:79:0,79:0,0:0,79:1:0,1:25.4:1:31.5:1:1:0:59.8:38.5:1:0:1.2 1/1:33:32:3,29:0,1:1,32:0.9697:0,2:22.2:1:30.1:1:1:0:60:31:0.9688:0:1.2 +11 69592140 . A T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35484;SOR=0;LSEQ=AACAAAAGCACAGGTAAGGA;RSEQ=GAATTGCGGATGAAGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:0,20:1:0,1:21.2:1:30.8:1:1:0:60:40:1:0:1.7 1/1:11:10:2,8:0,1:1,10:0.9091:0,2:20.3:1:29.9:1:1:0:60:20:0.9091:0:1.4 +11 69623641 . G T 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGCTGAAGGAGGCACCGA;RSEQ=ATTTTCACTTGTGTTGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:28.7:1:31:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69623866 . G A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03573;LSEQ=TCTGACCCTGGGCTCTCTGA;RSEQ=TCTGGGCTCTCTGACCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:27:27,0:86,3:89,27:0.2328:1,1:24.3:1:31.1:1:1:0:60:54:0.2348:0:1 0/1:46:11:11,0:35,0:35,11:0.2391:1,0:29.2:1:29.2:1:1:0:60:10:0.2222:0:1.5 +11 69623871 . G T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00148;SOR=Inf;LSEQ=CCCTGGGCTCTCTGAGTCTG;RSEQ=GCTCTCTGACCCCTGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:123,3:126,0:0:1,0:25.5:1:31:1:1:0:60:14.75:1:0:0.3 0/1:49:5:5,0:43,0:43,5:0.102:1,0:20.8:1:29.6:1:1:0:60:10:0.1042:0:1.2 +11 69623935 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.04787;SOR=Inf;LSEQ=CCTCACAGTCCCAGGCTCAG;RSEQ=AGAGCCTCCTCACCTGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:347,88:435,0:0:2,0:22:1:31.1:1:1:0:60:38.545:1:0:0.1 0/1:249:3:1,2:181,65:246,3:0.012:2,2:14.7:1:25.7:1:0.17714:5.52328:60:6:0.0122:0:1 +11 69624283 . A C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00328;SOR=0.21172;LSEQ=AGAGTTTTCAAAGAAAGTAA;RSEQ=CTCTCTCTCTCTCTCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:45:0,45:0,11:11,45:0.8036:0,1:14.6:1:31.3:1:1:0:55:21.5:0.7963:0:1.3 0/1:24:11:0,11:1,12:13,11:0.4583:1,0:17.5:1:29.9:1:1:0:59.1:10:0.4545:0:1.6 +11 69625025 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTCAGAGTCAAGAGGCTG;RSEQ=CACGCCAAGATGTCGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:2,0:165,7:172,2:0.0115:1,0:12.5:1:31:1:1:0:60:4:0.0116:0:1 0/0:85:0:0,0:78,7:85,0:0:2,0:22.4:1:31.4:1:1:0:59.8:27.333:1:0:0.1 +11 69625385 . C T 130 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.83169;LSEQ=GCCCCAGGCGTACTAGACAC;RSEQ=GTCCGGTACAGCCGGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:986:1:0,1:404,580:984,1:0.001:2,0:1:0:26:0:1:0:60:2:0.001:0:1 0/1:791:21:10,11:350,419:769,21:0.0265:2,2:17.5:1:29.8:1:1:1.09:58.5:42:0.027:0:1.3 +11 69625473 . G A 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=79.87438;LSEQ=CGGCGCTGTAGTGCTCCTGC;RSEQ=GGGATGAGATATCATGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:1:1,0:231,409:640,1:0.0016:2,0:1:0:29:0:0.36193:0:60:2:0.0016:0:1 0/1:468:52:21,31:170,246:416,52:0.1111:2,2:19.5:1:29.2:1:1:1.02009:60:25:0.1082:0:1.1 +11 69625496 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16188;SOR=4.8193;LSEQ=GATGAGATATCATGGTCAGT;RSEQ=CCCCGGGGAGACTGTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:1:1,0:142,320:462,1:0.0022:2,0:1:0:25:0:0.30886:0:60:2:0.0022:0:1 0/1:290:3:2,1:108,179:287,3:0.0103:2,2:16.3:1:26.7:1:0.55949:3.30:60:6:0.0106:0:1.7 +11 69625511 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10877;LSEQ=TCAGTGCCCCGGGGAGACTG;RSEQ=GGCAGCGTCAGGGCCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:355:301:62,239:14,40:54,301:0.8479:2,2:23.9:1:30.3:1:0.37225:1.34799:60:74.25:0.8462:0:1.1 0/1:202:76:25,51:35,91:126,76:0.3762:2,2:22.9:1:29.9:1:0.52518:1.27:60:75:0.375:0:1.1 +11 69625730 . G A 101 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=CCAGACAACTCCCAGCTCCT;RSEQ=CTCTCTGGGTTCCACCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:26.3:1:29.3:1:1:0:59.5:22:1:0:1.1 1/0:2:1:1,0:0,1:1,1:0.5:0,0:18:0:22:0:1:0:60:2:0.5:0:1 +11 69626472 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGCCTGGCATGAGGCAC;RSEQ=TGATCAATCAGTGCCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:22.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69627317 . C G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.702;SOR=1.35502;LSEQ=ACTGAGGCCCAGGGGTGGTG;RSEQ=CAGGCCCTACATTACAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:12:12,0:48,1:49,12:0.1967:1,0:26.9:1:29.8:1:1:0:59:11:0.1897:0:1.2 0/1:12:3:3,0:9,0:9,3:0.25:0,0:29.3:1:31.7:1:1:0:60:6:0.25:0:1 +11 69627441 . A T 32 v3;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0451;SOR=Inf;LSEQ=CCGACTTCCCCACCCCACAC;RSEQ=CTGGGTACACCATGTTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:358,69:427,0:0:2,0:24.6:1:30.5:1:1:0:60:141.333:1:0:0.6 0/1:237:3:0,3:187,47:234,3:0.0127:2,0:14:1:20.7:1:0.00895:0:60:2:0.0085:0:1 +11 69627451 . C A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10327;LSEQ=CACCCCACACACTGGGTACA;RSEQ=CATGTTAGTGTCTGGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:513:292:225,67:172,49:221,292:0.5692:2,2:24.2:1:30.5:1:0.91518:1.04518:60:584:0.5692:0:1.1 0/1:334:40:31,9:210,84:294,40:0.1198:2,2:23.1:1:28.9:1:0.57277:1.38:60:80:0.1205:0:1.1 +11 69627540 . G A 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTCGATCCTGCAGCAGGT;RSEQ=AGTCCTCTCAGGGCCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1360:0:0,0:643,716:1359,0:0:2,0:25.4:1:32.2:1:1:0:60:74.5:0.9993:0:0.2 0/1:1070:24:10,14:523,523:1046,24:0.0224:2,2:25.8:1:29.3:1:0.53667:1.39956:60:48:0.0226:0:1.2 +11 69627662 . A G 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14242;LSEQ=CAGGGGGCTCAGGCTCTCCC;RSEQ=AGGTGGGAGATTGGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:354:304:60,244:12,38:50,304:0.8588:2,2:24.8:1:31.8:1:0.4555:1.28325:59.9:100.333:0.8575:0:1.1 0/1:244:113:32,81:38,93:131,113:0.4631:2,2:25.5:1:30.2:1:1:1.03414:60:112:0.4609:0:1.2 +11 69627674 . T A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.2841;SOR=0;LSEQ=GCTCTCCCAAGGTGGGAGAT;RSEQ=GGGGGCAGTGTAGATCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:54,228:282,3:0.0105:2,2:13:1:21.3:1:0.09964:8.35:60:2:0.0071:0:2.3 0/0:183:0:0,0:52,131:183,0:0:2,0:23.9:1:29.3:1:1:0:60:90.5:1:0:0.7 +11 69627762 . A G 189 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGGTGTTGGCTCAGGGGCC;RSEQ=GGGCCATAGACTCCAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:1,64:0,0:0,65:1:0,1:22.2:1:31.4:1:1:0:59.7:31.5:1:0:1.1 0/1:17:8:0,8:0,9:9,8:0.4706:0,0:21.6:1:30.3:1:1:0:60:16:0.4706:0:1 +11 69628073 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGGGGGCTTCCGGAAGC;RSEQ=GGAGGAGGCTCAACCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:40.5:1:29:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69628099 . A G 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTCAACCTCTGGATGAC;RSEQ=GCCCCCCTGGGAGCAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:31.3:1:30.7:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69629390 . G A 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTCCTAGGCAAGCTGGCC;RSEQ=CACGCAGGACTGTGGTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:20:1:31.5:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:25:0:25:0:1:0:60:2:1:0:1 +11 69630842 . C A 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGATGGGGGAAACCTTTG;RSEQ=TAACCTGGCATTCTCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:15,1:16,4:0.2:1,0:12:1:29.5:1:1:0:60:8:0.2:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:35:0:28:0:1:0:60:2:1:0:0 +11 69630973 . G A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23096;LSEQ=AGGGTCTGGTCCTAGCTTGG;RSEQ=TCCCGTGTACCCTTGGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:84:84,0:79,2:81,84:0.5091:1,1:25.5:1:30.3:1:0.23947:0:60:83:0.5188:0:2.2 0/1:78:15:15,0:62,1:63,15:0.1923:1,1:16.1:1:30.1:1:1:0:60:30:0.1923:0:2.2 +11 69630978 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=0.30486;LSEQ=CTGGTCCTAGCTTGGGTCCC;RSEQ=TGTACCCTTGGCAAAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:183:154:153,1:28,1:29,154:0.8415:1,1:24.3:1:30.5:1:0.29256:5.39:60:153:0.8407:0:1.7 1/0:94:58:57,1:36,0:36,58:0.617:1,1:20.8:1:29.7:1:1:0:60:57:0.6129:0:1.3 +11 69633358 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=ACACCCCGGGCGCACCATGC;RSEQ=TTCTCCCGGGCCAGACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:10,0:0:2,0:14.6:1:32.5:1:1:0:60:20:1:0:0.1 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:31.5:1:1:0:60:4:1:0:1.5 +11 69633436 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.62244;SOR=1.77317;LSEQ=CCTTCTCCCGGGCCCGACCC;RSEQ=TCCCGGCGCCGCTTCCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:2:0,2:195,43:238,2:0.0083:2,0:1:0:23.5:1:0.03452:0:60:4:0.0084:0:2 0/1:136:2:1,1:102,32:134,2:0.0147:2,2:16.5:1:28.5:1:0.42778:3.15418:60:4:0.0148:0:1.5 +11 69633617 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20793;SOR=Inf;LSEQ=GACGCCGCCACGGCCGCCCG;RSEQ=ATCGCGCCGCAACCGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:51,119:170,0:0:2,0:13.4:1:32.8:1:1:0:60:340:1:0:0.3 0/1:143:2:1,1:58,83:141,2:0.014:2,2:38.5:1:29:0:1:1.43:60:4:0.0142:0:1 +11 69633631 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50274;SOR=0;LSEQ=CGCCCGCATCGCGCCGCAAC;RSEQ=GCGCCCCAGGGCCCGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:38,74:112,2:0.0175:2,2:40.5:1:32:0:1:1.94:60:4:0.018:0:1 0/0:93:0:0,0:35,57:92,0:0:2,0:16.4:1:29.9:1:1:0:59.6:184:0.9892:0:0.4 +11 69633633 . C A 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04488;SOR=5.23992;LSEQ=CCCGCATCGCGCCGCAACCG;RSEQ=GCCCCAGGGCCCGCTGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:2,0:36,67:103,2:0.019:2,0:1:0:27.5:1:0.12875:0:60:4:0.0192:0:1 0/1:86:8:3,5:31,47:78,8:0.093:2,2:18.1:1:29.4:1:1:1.09812:60:7:0.0843:0:1.1 +11 69633645 . C T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23106;SOR=Inf;LSEQ=CGCAACCGCGCCCCAGGGCC;RSEQ=GCTGCGGGCCAGCCGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:38,36:74,0:0:2,0:22.6:1:30.7:1:1:0:60:73:1:0:0.5 0/1:69:2:1,1:34,33:67,2:0.029:2,2:38:0:29:1:1:1.02986:60:4:0.0299:0:1 +11 69633650 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CCGCGCCCCAGGGCCCGCTG;RSEQ=GGGCCAGCCGGGCTCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:1,2:39,36:75,3:0.0385:2,2:26.3:1:28:1:0.61039:2.14595:60:6:0.0395:0:1 0/0:66:0:0,0:34,32:66,0:0:2,0:25.7:1:30.5:1:1:0:60:132:1:0:0.4 +11 69633669 . C T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63145;LSEQ=GCGGGCCAGCCGGGCTCCAG;RSEQ=AGGCTGAGCAGTAGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:51,46:97,2:0.0202:2,2:15.5:1:28:1:1:1.10754:60:4:0.0204:0:1.5 0/1:78:1:0,1:39,38:77,1:0.0128:2,0:1:0:23:0:1:0:60:2:0.0128:0:1 +11 69633682 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51037;SOR=0;LSEQ=GCTCCAGCAGGCTGAGCAGT;RSEQ=GCAGCCAGATTAGGCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:55,51:106,2:0.0185:2,2:31:1:31:1:1:1.07765:60:4:0.0187:0:1 0/0:78:0:0,0:38,40:78,0:0:2,0:28.4:1:28.8:1:1:0:60:77:1:0:0.4 +11 69633721 . CGCG C 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0.74588;LSEQ=TCGTGGCATCGCGCCCGCCC;RSEQ=GCGGCGGCGGCTGCAGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:4:2,2:28,32:60,4:0.0615:2,2:27.3:1:32:1:1:1.14:60:8:0.0615:0:0.3 0/1:43:2:1,1:18,22:40,2:0.0465:2,2:3.9:1:32:1:1:1.22:60:8:0.0438:0.0556:0.5 +11 69633828 . G A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13306;SOR=Inf;LSEQ=GCCTGGAGATGCTGACTCCG;RSEQ=CTTCGCGGGAAAGGTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:20,0:0:2,0:25.4:1:31.8:1:1:0:60:40:1:0:0.3 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:11:0:29:0:1:1.4491:60:4:0.1818:0:1.5 +11 69634091 . C A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCGGGGTTCGGGCCGGG;RSEQ=GCCGTCTGCATACACTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:31.5:1:1:0:60:4:1:0:1.5 +11 69656028 . A C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26564;SOR=0.35262;LSEQ=ACAACCACCAGCACCACCAC;RSEQ=ACACAACAGCATCATCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:5,6:2,1:3,11:0.7857:2,2:32:1:32.5:1:1:2.2554:60:22:0.7857:0:1.4 1/0:18:10:7,3:5,3:8,10:0.5556:2,2:30.2:1:29.1:1:1:1.37:60:9:0.5625:0:1.1 +11 69656104 . T C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15796;SOR=0;LSEQ=AACAACCACAAAAGCAGCAA;RSEQ=AACTACCACAACGACAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:11,4:15,2:0.1176:2,2:13:0:31.5:1:0.51471:2.56905:60:4:0.1176:0:1 0/0:25:0:0,0:13,12:25,0:0:2,0:28.8:1:29.1:1:1:0:60:50:1:0:0 +11 69656286 . A ACAACAG 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=3.000;MSILEN=6;SSF=0.34481;SOR=2.12004;LSEQ=CAGCATCAGCAGCAACCACA;RSEQ=CAACAGCAACAGCAACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:28:14,14:5,3:8,28:0.7778:2,2:35.5:1:32.3:1:0.69515:1.64336:59.6:56:0.7778:0:0.2 1/1:34:30:14,16:3,1:4,30:0.8824:2,2:35.5:1:30.7:1:0.60117:3.31312:60:60:0.8824:0:0.2 +11 69656312 . C A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=1;SOR=1.84836;LSEQ=GCAACAGCAACAACCACCAC;RSEQ=ACTACCACAACAAGAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:1,0:14,14:28,1:0.0345:2,0:1:0:26:0:1:0:55:2:0.0345:0:1 0/1:32:2:1,1:13,17:30,2:0.0625:2,2:37.5:1:29.5:1:1:1.30:60:4:0.0625:0:1 +11 69656411 . A AGAAACG 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.606;SOR=0.30817;LSEQ=ACAGCAACAACCACCACAAC;RSEQ=GCAACAACCACCACAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:11,7:18,3:0.1429:2,0:18.7:1:32.9:1:0.09023:0:44.3:6:0.15:0:0.3 0/1:21:1:0,1:14,6:20,1:0.0476:2,0:20:0:31.7:0:0.33333:0:60:2:0.0476:0:0 +11 69656500 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49425;SOR=0;LSEQ=CCACAAAACAACAGCAACAA;RSEQ=CACAACAGCAACAGCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:23,19:42,2:0.0455:2,2:24:0:32.5:1:1:1.20525:60:4:0.0476:0:1.5 0/0:44:0:0,0:22,22:44,0:0:2,0:21.7:1:29.3:1:1:0:60:13.667:1:0:0.4 +11 69656515 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.23101;SOR=Inf;LSEQ=AACAACCACAACAGCAACAG;RSEQ=ATCATCAACAGCAACAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:47,0:0:2,0:22.9:1:32.1:1:1:0:60:94:1:0:0.3 0/1:44:2:1,1:20,21:41,2:0.0455:2,2:21.5:1:25:0:1:1.05:60:4:0.0476:0:2 +11 69656529 . A T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.24118;SOR=Inf;LSEQ=CAACAGCATCATCAACAGCA;RSEQ=CAGCAACAACAACAACGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:43,0:0:2,0:26.9:1:29.9:1:1:0:60:86:1:0:0.2 0/1:42:2:1,1:21,19:40,2:0.0476:2,2:7.5:1:27:0:1:1.10263:60:4:0.0476:0:2 +11 69656545 . C T 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05609;SOR=Inf;LSEQ=AGCAACAGCAACAACAACAA;RSEQ=GGCAGCAACAATAATAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:21,21:42,0:0:2,0:28.5:1:30.9:1:1:0:60:84:1:0:0.1 0/1:45:5:2,3:21,19:40,5:0.1111:2,2:38:1:31.6:1:0.66515:1.63945:60:10:0.119:0:1.4 +11 69656564 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49413;SOR=0;LSEQ=ACGGCAGCAACAATAATAGC;RSEQ=ACAGCATATTCAACAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:18,22:40,2:0.0476:2,2:31.5:1:29:1:1:1.22:60:4:0.05:0:1 0/0:40:0:0,0:18,22:40,0:0:2,0:24.2:1:29.2:1:1:0:60:19:1:0:0.3 +11 69871665 . AATG A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATAGTGGTGATGGTGATGAC;RSEQ=ATGATGATGATGATGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:31:1:1:0:43:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69872433 . G A 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TAATGATGGCATTGATGATG;RSEQ=TGGTGGTGGTGGTGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:2,3:0.6:2,0:20:1:31.7:1:0.4:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69872459 . G A 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTGGTGGTGGTGGTGAC;RSEQ=GTGATGGTGGTGGTGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:34.5:1:32:1:0.4:0:48.5:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 69872725 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30705;SOR=0.23787;LSEQ=AGTGGCGACTGATATCACCC;RSEQ=TGCTGCCATCATTCAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:33:17,16:1,0:1,33:0.9706:0,2:23:1:32.4:1:1:0:60:66:0.9706:0:1.1 1/1:26:23:13,10:1,2:3,23:0.8846:2,2:26.7:1:29.9:1:0.58:2.51:58.5:46:0.8846:0:1.2 +11 71952339 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5175;SOR=0;LSEQ=AGAACTTGTAGGGCACTGCG;RSEQ=GTGTGTGCAGGGGGGCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:16,39:55,2:0.0351:2,2:7:1:29.5:1:0.51128:2.39:60:4:0.0351:0:1 0/0:37:0:0,0:11,26:37,0:0:2,0:18.6:1:29.7:1:1:0:60:74:1:0:0.9 +11 71952356 . CG C 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16171;SOR=5.50453;LSEQ=GCGGGTGTGTGCAGGGGGGC;RSEQ=GGGGGGGGGCAAAAAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:5,20:25,1:0.0357:2,0:45:0:31:0:1:0:60:2:0.04:0:0 0/1:23:4:0,4:2,17:19,4:0.1739:2,0:31.5:1:31.8:1:1:0:60:8:0.2:0:0.5 +11 71991307 . A C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGTGCTCTCGGTTGCACA;RSEQ=TAAACGGACGTTTAGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:173,271:444,0:0:2,0:24.5:1:30.9:1:1:0:59.8:73:1:0:0.1 0/1:431:19:10,9:175,237:412,19:0.0441:2,2:23.9:1:31.7:1:0.47838:1.50:58:38:0.0445:0:1.3 +11 71991390 . C T 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45101;SOR=0.39732;LSEQ=CCCTGTCTGCTGATGGTTTG;RSEQ=GCTGTGCCATGAGCGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:5:1,4:157,227:384,5:0.0129:2,2:16.4:1:29.6:1:0.65231:2.76031:60:10:0.013:0:1.2 0/0:389:2:1,1:169,218:387,2:0.0051:2,2:7:1:27:1:1:1.29:60:4:0.0052:0:1 +11 71991682 . G C 48 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11281;SOR=Inf;LSEQ=CAGGATGGTCTCGATCTCCT;RSEQ=ACCTCGTGATCCGCCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:30,1:31,0:0:1,0:11:1:33.8:1:1:0:36.2:62:1:0:0.1 0/1:30:3:3,0:27,0:27,3:0.1:1,0:6:1:30.3:1:1:0:36.7:6:0.1:0:2 +11 71991729 . G T 61 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44836;SOR=2.46198;LSEQ=CCCAAAGTGCTAGGATTACA;RSEQ=GCATGAGCCACCGTGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:125,31:156,2:0.0127:2,2:19:1:32:1:0.36507:3.9846:60:4:0.0127:0:1 0/1:163:5:1,4:126,32:158,5:0.0307:2,2:15.8:1:26.4:1:0.00872:15.397:60:10:0.0313:0:1 +11 71992099 . C T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CCATCCGAAGAAGCATAGAT;RSEQ=AAGATCCCAGTCCCGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:193,156:349,0:0:2,0:23.4:1:31.9:1:1:0:60:33.9:1:0:0.1 0/1:281:13:9,4:165,102:267,13:0.0463:2,2:21.2:1:29.4:1:0.77207:1.39:60:26:0.0469:0:1.1 +11 71992298 . A AT 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1253;SOR=0;LSEQ=CAAACCAGATCATAAGGGGA;RSEQ=TTTTTTTTTAAAACAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:4:1,3:17,118:135,4:0.0288:2,2:12.3:1:27:1:0.42952:2.30:60:8:0.0296:0:0 0/0:122:0:0,0:26,96:122,0:0:2,0:21.2:1:30.1:1:1:0:59.9:121:1:0:0.1 +11 71994119 . CT C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTGCTTAATCTGCCATA;RSEQ=TTTTTCTCTTTTTTCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:33.5:1:1:0:60:4:1:0:0.5 +11 72301370 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49648;SOR=Inf;LSEQ=CAGGCGCCGCTCAGCTCCGC;RSEQ=CCGGGCCCGCCGCCGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:16,16:32,0:0:2,0:23.3:1:31.5:1:1:0:60:64:1:0:0.2 0/1:38:2:1,1:18,18:36,2:0.0526:2,2:15:0:31:0:1:1:38:4:0.0526:0:1.5 +11 72326111 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51918;SOR=0;LSEQ=GACTCCGGCTTCAGTTGTTA;RSEQ=TCCAACAGGGCCGCGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:12,17:29,2:0.0645:2,2:37:1:30:1:1:1.40:60:4:0.069:0:1.5 0/0:19:0:0,0:7,12:19,0:0:2,0:24.7:1:31.7:1:1:0:60:38:1:0:0.2 +11 74401763 . C T 274 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.00226;LSEQ=GGAGTAGTACAGGCATAAAA;RSEQ=GGGGAAAGGCATTCCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:490:489:224,265:0,1:1,489:0.998:0,2:26.1:1:30.7:1:1:0:60:121.25:0.9979:0:1.1 1/0:502:263:134,129:120,119:239,263:0.5239:2,2:26.1:1:29.3:1:0.9288:1.03:59.9:64.75:0.5243:0:1.1 +11 74401849 . G A 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58372;SOR=2.57839;LSEQ=AGAAAGTTGTAGCAGTGGCG;RSEQ=CCTGGGAACGGGGATCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:1,0:67,163:230,1:0.0043:2,0:1:0:26:0:0.29437:0:60:2:0.0044:0:2 0/1:180:2:1,1:49,129:178,2:0.0111:2,2:5.5:1:28:1:0.47952:2.62:60:4:0.0112:0:1 +11 74401859 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19308;SOR=Inf;LSEQ=AGCAGTGGCGGCCTGGGAAC;RSEQ=GGGATCCCTTTGGTGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:44,148:192,0:0:2,0:23.8:1:31:1:1:0:59.9:95:1:0:0.2 0/1:151:2:1,1:35,114:149,2:0.0132:2,2:26:0:32.5:1:0.42119:3.23:60:4:0.0132:0:1.5 +11 74402547 . A C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTTGGCCCAGTTGTCAC;RSEQ=GGGCAGGAGAGGCCCGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 74790414 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4963;SOR=0;LSEQ=CCACTTTGGGAAGAGAACCA;RSEQ=CTTTTCCTATACTTGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:38,28:66,2:0.0294:2,2:43:1:30:1:1:1.35095:27:4:0.0299:0:1 0/0:68:0:0,0:42,26:68,0:0:2,0:26.5:1:31:1:1:0:37:67:1:0:0.1 +11 74790631 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50088;SOR=0;LSEQ=TCTTCACTGGTGCTTTTTCT;RSEQ=CAGTTTCCTCATCATCGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:53,59:112,2:0.0175:2,2:39:1:31:1:1:1.11:38.5:4:0.0175:0:1 0/0:97:0:0,0:43,54:97,0:0:2,0:29.7:1:29.3:1:1:0:47.8:96:1:0:0.2 +11 74790660 . C T 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.00017;SOR=18.60198;LSEQ=TCATCATCGAAATCATCCTC;RSEQ=TCCTCCTCTTCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:1:0,1:65,77:142,1:0.007:2,0:1:0:26:0:1:0:60:2:0.0073:0:1 0/1:120:14:5,9:45,61:106,14:0.1167:2,2:16.4:1:29:1:0.7759:1.3248:50.6:28:0.1186:0:1 +11 74790719 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51417;SOR=0;LSEQ=ATCATCTTCATCTGCAGCAA;RSEQ=TTTTTCTTTTTTCTGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:52,80:132,2:0.0149:2,2:33:1:30:1:1:1.53:60:4:0.0153:0:1 0/0:93:0:0,0:37,56:93,0:0:2,0:25.5:1:31.3:1:1:0:59.9:92:1:0:0.2 +11 74790730 . T C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.18651;SOR=Inf;LSEQ=CTGCAGCAAGTTTTTCTTTT;RSEQ=TCTGTGGAACCTTGCTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:50,73:123,0:0:2,0:25.1:1:30.4:1:1:0:59.9:60.5:1:0:0.1 0/1:94:2:1,1:36,55:91,2:0.0213:2,2:5:0:33:0:1:1.52:60:4:0.0213:0:0 +11 74790785 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18566;SOR=Inf;LSEQ=CTGCTTTCTAGATATACTCA;RSEQ=GAGTTTCACATCCTCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:55,50:105,0:0:2,0:23:1:31.3:1:1:0:59.5:51.5:1:0:0.1 0/1:80:2:1,1:46,32:78,2:0.025:2,2:8.5:1:28:1:1:1.43083:30.5:4:0.025:0:1 +11 74790792 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17627;SOR=Inf;LSEQ=CTAGATATACTCAAGAGTTT;RSEQ=ACATCCTCCTCTTCATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:59,55:114,0:0:2,0:22.7:1:31.6:1:1:0:59.3:27.5:1:0:0.1 0/1:83:2:1,1:48,33:81,2:0.0241:2,2:22.5:1:30.5:1:1:1.44782:60:4:0.0247:0:1 +11 74790806 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20998;SOR=Inf;LSEQ=GAGTTTCACATCCTCCTCTT;RSEQ=ATCTTCTGACTCTACATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:66,54:120,0:0:2,0:24.5:1:32.2:1:1:0:59.3:119:1:0:0.1 0/1:102:2:1,1:59,41:100,2:0.0196:2,2:36:1:29:0:1:1.43376:60:4:0.02:0:1 +11 74790951 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5236;SOR=0;LSEQ=GTACAGACATTTTCAAAGTT;RSEQ=CCAGTGTTACCTTAATTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:28,38:66,2:0.0294:2,2:31:1:28.5:1:1:1.35:60:4:0.0294:0:1 0/0:42:0:0,0:14,28:42,0:0:2,0:28.2:1:30.5:1:1:0:59.6:13:1:0:0.1 +11 74791304 . A C 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.91231;LSEQ=TGATAGTTGGGATGAGAAAC;RSEQ=CATGGGATTTCTGTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:32:1:33:0:1:0:60:6:0.2727:0:1 0/1:14:3:0,3:0,11:11,3:0.2143:0,0:17.3:1:31.7:1:1:0:60:6:0.2308:0:1 +11 76059229 . T C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.52244;LSEQ=ACATAGAATTATTAATAAAG;RSEQ=GTTTGTTCCCACTTACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:286:177:80,97:49,60:109,177:0.6189:2,2:27.1:1:31.1:1:1:1.01:60:58:0.6148:0:1.1 0/1:327:150:73,77:77,99:176,150:0.4587:2,2:23.8:1:30.3:1:0.43524:1.22:60:300:0.4587:0:1.1 +11 76059287 . CT C 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.12958;LSEQ=ATCAGGCTTCAACTGTGTAA;RSEQ=TTTTTTTTCCAAAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:2:0,2:84,116:200,2:0.0099:2,0:22.5:1:32:1:0.51175:0:60:4:0.0101:0:0.5 0/1:179:2:1,1:65,111:176,2:0.0112:2,2:28.5:1:31:1:1:1.70:60:4:0.0112:0:0 +11 76059298 . CA C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50528;SOR=0;LSEQ=ACTGTGTAACTTTTTTTTTC;RSEQ=AAAAAAAGAGATATGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:71,108:179,2:0.011:2,2:37:0:31.5:1:1:1.52:60:4:0.0112:0:0 0/0:144:0:0,0:52,91:143,0:0:2,0:23.4:1:29.6:1:1:0:60:142:1:0:0.3 +11 76302988 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCCCTGAACATGATCGT;RSEQ=TTCTTGTCCATCAAGTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:18.5:1:32.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 77034453 . TC T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50246;SOR=0;LSEQ=ACATGACTATTTAACATTCT;RSEQ=CCCAGTAACCATTACAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:25,172:197,2:0.0101:2,2:35:1:30.5:1:0.24481:6.76:60:4:0.0101:0:1.5 0/0:167:0:0,0:29,138:167,0:0:2,0:22.4:1:30.5:1:1:0:60:166:1:0:0 +11 77043421 . A AG 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AGGGAAGGGAAAGGAAGGGA;RSEQ=GGGAAGGGAAGGGAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:13.7:1:29.2:1:1:0:52.7:6:1:0.6667:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 77047515 . T G 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28352;SOR=3.17702;LSEQ=GCCTATTTCCTATTGAACCC;RSEQ=GAAGAGAAATAGAAGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:40.5:1:23.5:1:1:0:60:1:0.0476:0:4 0/1:8:2:0,2:0,6:6,2:0.25:0,0:35.5:1:32.5:1:1:0:60:4:0.25:0:1 +11 77051507 . T TA 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.41126;SOR=0.28143;LSEQ=GGGTAGAATAAAGTTATCGT;RSEQ=AAAAAAAAAATCATGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:6,0:44,0:44,6:0.1176:1,0:40.2:1:27.7:1:1:0:58.2:12:0.1224:0:0 0/1:28:1:1,0:24,2:26,1:0.0357:2,0:45:0:27:0:1:0:60:2:0.037:0:0 +11 77051605 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23218;SOR=0;LSEQ=ACCAATTCCACAGAGCCCAG;RSEQ=CTGAGATCTCACTGTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:2,0:174,16:190,2:0.0104:2,0:26.5:1:30:1:1:0:60:4:0.0105:0:1 0/0:207:0:0,0:187,20:207,0:0:2,0:24.8:1:30.6:1:1:0:60:68:1:0:0.2 +11 77051683 . G C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=0.6624;LSEQ=CCCAAGACTGCTTGGCCCTT;RSEQ=GCCTTACCTCACGGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:731:277:172,105:278,175:453,277:0.3789:2,2:24.2:1:31.1:1:0.8755:1.03:60:137.5:0.3798:0:1.1 0/1:973:280:157,123:420,271:691,280:0.2878:2,2:25.4:1:29.7:1:0.19413:1.21393:60:69:0.2875:0:1.1 +11 77051820 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.51007;LSEQ=ACGAGGTAACTGCAGGAATA;RSEQ=AGATAAAGGGTGAGAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:52:17,35:175,357:532,52:0.0889:2,2:24.5:1:29:1:1:1.00921:59.8:104:0.0903:0:1.1 0/1:690:211:68,143:162,315:477,211:0.3058:2,2:24.1:1:27.6:1:0.726:1.08142:60:41.2:0.3052:0:1.1 +11 77051859 . C A 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36543;SOR=0.32051;LSEQ=AACAATCAGAGTACACTGAG;RSEQ=CATAGCACTGGGTTTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:39,248:287,3:0.0103:2,2:14.7:1:22:1:0.0534:12.52:60:2:0.0071:0:1 0/0:300:1:1,0:54,245:299,1:0.0033:2,0:1:0:26:0:0.18333:0:60:2:0.0034:0:2 +11 77052071 . T C 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CTAAGATCTCTAGCTTGAAG;RSEQ=GATACAATAAAATTATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:21.3:1:30:1:1:0:60:6:0.4286:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:30.5:1:31:0:1:0:60:4:1:0:0 +11 77054749 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08511;SOR=Inf;LSEQ=ACAGAGAGCTCAGCATCACA;RSEQ=AAGACTCATAAATGGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:176,1:177,0:0:1,0:25.6:1:33.3:1:1:0:60:87.5:1:0:0.1 0/1:140:3:3,0:135,2:137,3:0.0214:1,0:29.3:1:29.3:1:1:0:60:6:0.0219:0:1.3 +11 77055059 . C A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49998;SOR=0;LSEQ=AGTACCAGACCTTAAGTACT;RSEQ=AGGAAACAAAGATGAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:7,128:135,2:0.0146:2,2:6:1:30.5:1:0.11378:17.17:60:4:0.015:0:1.5 0/0:121:0:0,0:3,118:121,0:0:1,0:22.5:1:31.8:1:1:0:60:59.5:1:0:0 +11 77060092 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02199;SOR=Inf;LSEQ=AGGCTGGAGAACTGCTTGAA;RSEQ=CTAGTAGGCGGAGGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:22,0:22,0:0:1,0:22.3:1:32.4:1:1:0:57:44:1:0:0.2 0/1:10:3:3,0:7,0:7,3:0.3:0,0:33.7:1:30.3:1:1:0:53.7:6:0.3333:0:1.3 +11 77060203 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2331;SOR=Inf;LSEQ=AAAACCTAGAACTGTTCCTG;RSEQ=TGACCTAACAAGGGCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:140,33:173,0:0:2,0:18.7:1:29.3:1:1:0:58.5:20.625:1:0:0.9 0/1:162:2:1,1:111,48:159,2:0.0123:2,2:17:0:33:0:0.51739:2.2991:60:4:0.0129:0:1 +11 77060417 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24423;SOR=Inf;LSEQ=AAATGCAGTTCTACACACAA;RSEQ=CTGTGAGTGTCAAAAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:41,154:195,0:0:2,0:23.8:1:30.4:1:1:0:60:64:0.9948:0:0.1 0/1:192:2:1,1:47,143:190,2:0.0104:2,2:32:1:28:0:0.43848:3.02:60:4:0.0107:0:1 +11 77060418 . C A 31 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=AATGCAGTTCTACACACAAT;RSEQ=TGTGAGTGTCAAAAACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:36,153:189,2:0.0105:2,2:5:0:31:1:0.35073:4.21:60:4:0.0106:0:1.5 0/0:189:0:0,0:45,144:189,0:0:2,0:23.7:1:30.9:1:1:0:60:36.8:1:0:0.2 +11 77064358 . A G 49 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.37769;LSEQ=CGTTCTCTCACTGTCACTGC;RSEQ=GGGGTATTTTTAGCAACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:3,0:25,0:25,3:0.1071:1,0:37:1:31.3:1:1:0:60:6:0.1071:0:1 0/1:14:2:2,0:11,1:12,2:0.1429:2,0:3.5:1:30.5:1:1:0:60:4:0.1429:0:1 +11 77064501 . CA C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.81433;SOR=0.8702;LSEQ=AGAACAAGGTTTATGAGAGG;RSEQ=AAAAAAAAGCAAAATCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:9:6,3:268,59:327,9:0.0267:2,2:18.7:1:30.2:1:0.37536:2.2643:60:3.5:0.0211:0.0119:0 0/1:386:9:7,2:279,96:375,9:0.0233:2,2:27.9:1:31.8:1:1:1.20:60:18:0.0235:0.0026:0 +11 77064672 . AT A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.06454;SOR=Inf;LSEQ=AGAAACAGAGACCATGAATC;RSEQ=TTTTTCCCAAATCAAGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:116,324:440,0:0:2,0:25.9:1:30.5:1:1:0:60:145.667:1:0:0.1 0/1:502:5:3,2:150,345:495,5:0.01:2,2:28.8:1:29.6:1:0.17005:3.44:60:10:0.0101:0.002:0.4 +11 77069746 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76897;SOR=1.31208;LSEQ=TTGGGACTATCTGCAAACCA;RSEQ=TGATAAATAAACACATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:14:14,0:29,0:29,14:0.3256:1,1:31.7:1:32.3:1:1:0:60:13:0.3333:0:1.9 0/1:18:7:7,0:9,1:10,7:0.3889:2,0:27.3:1:32.7:1:1:0:60:14:0.3889:0:1.9 +11 77069790 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63074;SOR=0.8177;LSEQ=TGTCTTTAATCATACAGAAA;RSEQ=TACCTTTAGTCAAGGTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:43:43,0:58,1:59,43:0.4216:1,1:18.8:1:31.2:1:1:0:59.1:86:0.43:0:1.3 0/1:67:25:25,0:39,2:41,25:0.3731:1,1:16.1:1:30:1:0.52214:0:60:50:0.3731:0:1.4 +11 77069989 . GCAT G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.70899;SOR=1.20093;LSEQ=CAATCACTGGTGGTGGGGTA;RSEQ=CATCATCATCATCATCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:803:12:5,7:359,431:790,12:0.0149:2,2:33.3:1:33.9:1:1:1.1659:60:24:0.0152:0:0.2 0/1:950:17:5,12:422,506:928,17:0.0179:2,2:25.9:1:30.3:1:0.22439:2.00017:59.4:34:0.0182:0.0021:0.2 +11 77070163 . CT C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21329;SOR=Inf;LSEQ=GAAACCCCATCCTGATATCC;RSEQ=TCTGAAATACACATTAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:2,65:67,0:0:1,0:21.5:1:30:1:1:0:60:15.75:1:0:0.2 0/1:58:2:1,1:0,56:56,2:0.0345:1,2:22:1:28:1:0.03448:0:60:4:0.0345:0.0172:0 +11 77085318 . C A 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05444;SOR=0;LSEQ=CTCTGCCTCTACCACACTGT;RSEQ=TTGATCCTTACCTCCACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:4:2,2:243,132:375,4:0.0106:2,2:31.8:1:28.3:1:0.61659:1.83783:60:8:0.0107:0:1 0/0:404:0:0,0:256,147:403,0:0:2,0:22.9:1:30.5:1:1:0:60:79.6:0.9975:0:0.1 +11 77087565 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCAAGGTGGGTGGATCA;RSEQ=GAGGTCAATAGGTCAAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:29:1:1:0:37:4:1:0:1 +11 77090037 . T C 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=AGAATCTAGACCTTCTAGCA;RSEQ=AAAACCTGTGTTCTCTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:43.7:1:33:1:1:0:60:6:0.375:0:1 1/1:4:4:3,1:0,0:0,4:1:0,2:17:1:31.3:1:1:0:60:8:1:0:1 +11 77090211 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00289;SOR=1.92144;LSEQ=TTTCTTCTCTCATCCCAGAC;RSEQ=AATAGGCATGTGAGCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:207:105:91,14:91,11:102,105:0.5072:2,2:22.9:1:31.1:1:0.67132:1.27125:60:34:0.5:0:1.1 1/0:161:107:93,14:46,8:54,107:0.6646:2,2:22.2:1:31:1:0.80985:1.15:60:214:0.6688:0:1.1 +11 77090466 . G A 58 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11475;SOR=5.31272;LSEQ=CATGCAAGACTAACAGGAAG;RSEQ=CACAGTCACAGGGGAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:1:1,0:82,280:362,1:0.0028:2,0:1:0:28:0:0.22865:0:60:2:0.0028:0:1 0/1:345:5:4,1:62,277:339,5:0.0145:2,2:6.8:1:25.2:1:0.00537:17.66:60:10:0.0148:0:1 +11 77090518 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98084;LSEQ=GAGCTAACTTTGACACTTGC;RSEQ=AGCAGCAAAAGATGCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:63:2,61:3,104:107,63:0.3706:1,1:23.2:1:33.3:1:1:1.14:59.9:126:0.375:0:1 0/1:112:41:0,41:4,67:71,41:0.3661:2,1:22:1:31.6:1:0.29461:0:60:40:0.367:0:1.1 +11 77579869 . G A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGGCGCTTAATTTGAACCC;RSEQ=GGTACCTTTCTCTCTGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:20:1:32:0:1:0:60:4:1:0:0.5 0/1:8:2:1,1:5,1:6,2:0.25:2,2:29:1:29:1:0.46429:3.87298:60:4:0.25:0:1 +11 77580044 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGCACGTTGGGTAATACC;RSEQ=TAGACTCTTCCAGTTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:18,0:0:2,0:34.9:1:31:1:1:0:57.9:36:1:0:0 0/1:51:2:1,1:27,22:49,2:0.0392:2,2:29:1:29:1:1:1.22232:60:4:0.0392:0:1 +11 77580208 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23151;SOR=Inf;LSEQ=AGGCCTAGAGGACATATATT;RSEQ=GGTGCATCTCCTCTTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:37,25:62,0:0:2,0:20.7:1:31.7:1:1:0:60:30:1:0:0.1 0/1:58:2:1,1:31,24:55,2:0.0345:2,2:15.5:1:29:1:1:1.28581:60:4:0.0351:0:1 +11 77580275 . CA C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49789;SOR=Inf;LSEQ=TGGAAGATGGTTGTTCCAGC;RSEQ=AAAGGTCCTGAGCCTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:38,43:81,0:0:2,0:27:1:30.3:1:1:0:60:162:1:0:0.1 0/1:88:2:1,1:36,50:86,2:0.0227:2,2:44.5:1:28:1:1:1.38:60:4:0.0227:0:1 +11 77580291 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49635;SOR=0;LSEQ=CAGCCAAAAGGTCCTGAGCC;RSEQ=TTTAAAATGCTTTTTCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:29,38:67,2:0.029:2,2:25:1:31:1:1:1.31:60:4:0.0308:0:1 0/0:68:0:0,0:26,42:68,0:0:2,0:27.4:1:29.1:1:1:0:59.9:67:1:0:0.3 +11 77580354 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=GATTTCGTTTATTTATCTCT;RSEQ=TTTCTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,13:13,0:0:1,0:8.5:1:30.5:1:1:0:57.2:12:1:0:0.3 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:20:1:31.5:1:1:0:57.5:4:0.3333:0:3 +11 77580548 . ACGGT A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTTTTATTTTTTGTAGAGAC;RSEQ=CGGTCTCCCTATGTTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:31.5:1:1:0:25.5:4:1:0:0.5 +11 78881609 . T C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2566;SOR=2.64395;LSEQ=CTCCTAAGCAGTGGAAATAG;RSEQ=GACACAGACATGCACACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:3,3:4,2:6,6:0.5:2,2:30.2:1:30.5:1:1:1.88578:60:12:0.5:0:1 1/0:15:11:7,4:3,1:4,11:0.7333:2,2:25.4:1:30.3:1:1:1.65645:60:22:0.7857:0:1.1 +11 81184872 . T A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATCTAGAGGCAAAGAGAA;RSEQ=CTGTATGATTCAAGGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 81185086 . T G 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63325;SOR=0.41977;LSEQ=AATTTAGAACATATCTCTAA;RSEQ=CTGTCTGATGTATAATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:6,0:6,6:0.5:0,0:35.3:1:34.8:1:1:0:60:12:0.5:0:1.2 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:27.5:1:33:0:1:0:60:4:0.2857:0:1 +11 81185227 . C CT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50263;SOR=Inf;LSEQ=TTTTGTTCTACCCAACTTTC;RSEQ=TTTTCTCCTTCCATGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:88,30:118,0:0:2,0:22.7:1:31.9:1:1:0:60:117:0.9915:0:0.1 0/1:144:2:1,1:105,37:142,2:0.0139:2,2:20.5:1:31.5:1:0.4595:2.81355:60:4:0.0139:0:0 +11 81185242 . G T 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=0;LSEQ=CTTTCCTTTTCTCCTTCCAT;RSEQ=TTTCCTTTACTAAAAATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:11:6,5:92,47:139,11:0.0733:2,2:27.9:1:30.7:1:0.51475:1.62566:60:22:0.0743:0:1.1 0/0:208:0:0,0:134,74:208,0:0:2,0:22.9:1:31.2:1:1:0:60:416:1:0:0.2 +11 81185331 . G T 237 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGACACTTTAAAAATAATT;RSEQ=TATAACAACCACGTAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:219:90,129:0,0:0,219:1:0,2:24.9:1:30.6:1:1:0:60:108.5:1:0:1.1 1/0:265:143:64,79:47,75:122,143:0.5396:2,2:24.3:1:29.6:1:0.32013:1.29:60:286:0.5396:0:1.1 +11 81185416 . T G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26101;SOR=Inf;LSEQ=TTGGCATTTGCTTTTTAGTA;RSEQ=TTTTAGAGATGGTTACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:15,46:61,0:0:2,0:24:1:29.8:1:1:0:59.5:29.5:1:0:0.3 0/1:82:3:1,2:17,62:79,3:0.0366:2,2:32.3:1:32.3:1:0.52954:1.81:60:6:0.037:0:1 +11 81185452 . TC T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.05466;SOR=0;LSEQ=CTCAAACATCCCAAAAGTCA;RSEQ=TTTGAAAGAGATCTCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:0,5:1,30:31,5:0.1389:1,0:34.6:1:31:1:1:0:60:10:0.1389:0:0 0/0:33:0:0,0:1,32:33,0:0:1,0:28.3:1:31.8:1:1:0:60:66:1:0:0 +11 81187272 . G T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATACAAGGTTTGTATTTG;RSEQ=ACATAATTGAGTTTGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 83267886 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATCCAGTGGAAGGCAAG;RSEQ=TGGGATGATGCGGGGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:29:1:1:0:60:4:1:0:1 +11 83269046 . C G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00401;SOR=0.2205;LSEQ=ACCAACTCCAAGCAGGAGGA;RSEQ=AATATGGAATCTATAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:56:56,0:5,0:5,56:0.918:0,1:24.8:1:34.2:1:1:0:60:112:0.918:0:1.1 1/0:55:39:38,1:16,0:16,39:0.7091:1,1:21.9:1:32:1:1:0:60:78:0.7091:0:1.1 +11 83269191 . C T 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1997;LSEQ=ACTGGCTCTAGTTGTAGTCC;RSEQ=TTACTTAGTCCAAAACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:568:500:258,242:36,32:68,500:0.8803:2,2:25.4:1:30.9:1:0.89734:1.05515:60:70.429:0.8788:0:1.1 1/0:624:371:188,183:134,119:253,371:0.5946:2,2:25.5:1:29.6:1:0.62457:1.09594:59.9:73.2:0.5922:0:1.1 +11 85956145 . TG T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.21886;SOR=0;LSEQ=CTGGGCGCGATTTGCGACAG;RSEQ=GGGGGGGCGGTGGAGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:24,0:24,2:0.0769:1,0:9:1:32:1:1:0:60:4:0.08:0.0385:0 0/0:29:0:0,0:26,3:29,0:0:2,0:16.9:1:31.1:1:1:0:59.5:58:1:0:0.5 +11 85956190 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50043;SOR=Inf;LSEQ=GGCAGCGGCAACTTTGCGGC;RSEQ=AGCTCGGGCCGGGCTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:83,6:89,0:0:2,0:23.4:1:30.9:1:1:0:59.9:88:1:0:0.1 0/1:104:2:1,1:91,11:102,2:0.0192:2,2:33:0:31:1:0.21845:7.96356:52.5:4:0.0194:0:2.5 +11 85956212 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50154;SOR=Inf;LSEQ=GCTCGGGCCGGGCTTGCTTG;RSEQ=CGGCGGTGTGGCGGAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:118,19:137,0:0:2,0:23.7:1:29.9:1:1:0:60:44.667:1:0:0.1 0/1:162:2:1,1:124,36:160,2:0.0123:2,2:18:1:29:1:0.40572:3.41116:60:4:0.0126:0:1 +11 85956421 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19178;SOR=0;LSEQ=GGCAGTTACGAGACTGCGGA;RSEQ=TGAAAGTTTTAAATTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:32,127:159,2:0.0124:2,2:21.5:1:33:1:0.36894:3.92:60:4:0.0127:0:1 0/0:206:0:0,0:61,145:206,0:0:2,0:21.8:1:31.1:1:1:0:60:67.667:1:0:0.2 +11 85956426 . A G 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19499;SOR=0;LSEQ=TTACGAGACTGCGGAGTGAA;RSEQ=GTTTTAAATTCTTTTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:29,115:144,2:0.0137:2,2:5:0:33:0:0.36986:3.92:60:4:0.0141:0:1 0/0:184:0:0,0:52,132:184,0:0:2,0:21:1:29.9:1:1:0:60:60.333:1:0:0.2 +11 85956427 . G T 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.25509;SOR=Inf;LSEQ=TACGAGACTGCGGAGTGAAA;RSEQ=TTTTAAATTCTTTTAAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:27,118:145,0:0:2,0:19.6:1:32.1:1:1:0:60:35.25:1:0:0.3 0/1:177:3:1,2:45,129:174,3:0.0169:2,2:7.7:1:25.7:1:1:1.43:60:2:0.0115:0:2 +11 85956438 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5061;SOR=Inf;LSEQ=GGAGTGAAAGTTTTAAATTC;RSEQ=TTTAAAACGGGGGGCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:16,94:110,0:0:2,0:19.3:1:30.4:1:1:0:60:54:1:0:0.3 0/1:142:2:1,1:29,111:140,2:0.0141:2,2:14.5:1:29.5:1:0.37908:3.78:60:4:0.0142:0:1.5 +11 85961166 . C T 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2605;SOR=0;LSEQ=AATATAAAATATCTACAAAC;RSEQ=TTCTAACCTGTAGCTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:7,1:8,5:0.3846:2,0:20.8:1:33.4:1:1:0:60:10:0.3846:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:38.3:1:31.5:1:1:0:60:8:1:0:0 +11 85961287 . TA T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.501;SOR=0;LSEQ=CCAGTAGAGTTATTTACTGC;RSEQ=AAAACAGTATTGCTGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:148,12:160,2:0.0123:2,0:24:1:34:0:1:0:60:4:0.0125:0:0 0/0:140:0:0,0:126,14:140,0:0:2,0:25:1:28.1:1:1:0:60:139:1:0:0.1 +11 85961525 . T A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11862;SOR=Inf;LSEQ=AGATCCTTTGGGCTGAATGC;RSEQ=AGGCTTCAGAAATTATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:64,230:294,0:0:2,0:24.6:1:29.1:1:1:0:60:97:1:0:0.1 0/1:285:3:3,0:67,215:282,3:0.0105:2,0:13:1:22:1:0.01434:0:60:2:0.007:0:2.3 +11 85961620 . G GT 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30167;SOR=0.38427;LSEQ=GTTACAATGTTTTCTGAAGG;RSEQ=TTTTTTTTTTTGTAGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:7:0,7:1,48:49,7:0.1186:1,0:17:1:29.2:1:1:0:60:14:0.125:0.0339:0 0/1:41:2:0,2:2,37:39,2:0.0488:2,0:36.5:1:26:1:1:0:60:4:0.0541:0:0.5 +11 85961646 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=22.16623;LSEQ=TTTTTTGTAGTTCAGACTGC;RSEQ=TATCTATTTTAGTCCATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:0,3:0,32:32,3:0.0857:1,0:15:1:32.3:1:1:0:60:6:0.0882:0:1 1/0:29:20:2,18:0,9:9,20:0.6897:0,2:21.4:1:29.5:1:1:0:59.5:19:0.6786:0:1.3 +11 85963130 . C T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20603;SOR=Inf;LSEQ=GAAGGGGATAGGTTAGTTTA;RSEQ=TGTCATTTTCTGGTTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:187,47:234,0:0:2,0:23.9:1:32.1:1:1:0:60:57.5:1:0:0.1 0/1:195:2:1,1:149,44:193,2:0.0103:2,2:6.5:1:29:1:0.4092:3.35969:60:4:0.0104:0:1.5 +11 85963147 . G A 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00182;SOR=Inf;LSEQ=TTACTGTCATTTTCTGGTTT;RSEQ=TAAGATACATTAATCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:229,79:308,0:0:2,0:25.1:1:32.2:1:1:0:60:76:1:0:0.1 0/1:260:8:7,1:181,70:251,8:0.0308:2,2:25.1:1:29.5:1:0.45231:2.70:60:16:0.031:0:1.1 +11 85963553 . G GT 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACTTGGTTGAAAGAATTGGC;RSEQ=TCCTTTTTTTTTTTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:16.3:1:29.9:1:1:0:60:8:1:0.2:0.8 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:34:0:1:0:60:2:1:0:0 +11 85963619 . C T 77 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTATTTATCATTCAAATAG;RSEQ=GTAAGAACTGGCTGTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:4,6:0.6:0,2:30.3:1:29.8:1:1:0:60:12:0.6:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 85963632 . T C 59 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAAATAGCGTAAGAACTGGC;RSEQ=GTGATTTTTTTAAAATTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:3,5:0.625:0,2:31.8:1:25.6:1:1:0:60:10:0.625:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 85965909 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGACCTCATGATCCGCA;RSEQ=GCCTTGGCCTCCCAAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:20.5:1:30.5:1:1:0:38:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 85965938 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCAAAATGCTGGGATTA;RSEQ=AGGCGTGAGCCACCGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:32.5:1:33.5:1:1:0:52:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 85966177 . G T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.63607;LSEQ=TCTGTAGTATATTTAAGATA;RSEQ=GATTGCGATTAAAATATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:210:167,43:99,28:127,210:0.6213:2,2:22.9:1:31:1:0.78323:1.10:60:69:0.6179:0:1.1 1/1:276:244:194,50:22,10:32,244:0.8841:2,2:23.7:1:29.8:1:0.17481:1.76:59.9:60:0.8824:0:1.1 +11 85966542 . A C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00823;SOR=0.10508;LSEQ=AGCTAGGCAAAAAGAAAAAG;RSEQ=AAAGAATCCATTGTGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:18:0,18:0,7:7,18:0.72:0,1:26.6:1:32.4:1:1:0:58.9:36:0.72:0:2 0/1:10:2:0,2:1,7:8,2:0.2:2,0:29.5:1:33.5:1:1:0:60:4:0.25:0:2 +11 85966560 . A G 43 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.03123;SOR=15.03322;LSEQ=AGAAAAGAATCCATTGTGGG;RSEQ=TGGATGTGCTGGTTGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:0,18:18,1:0.0526:1,0:7:0:34:0:1:0:60:2:0.0526:0:1 1/0:6:3:0,3:1,2:3,3:0.5:2,0:21.3:1:27.7:1:1:0:60:2:0.4:0:1 +11 85966575 . G A 112 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2451;SOR=0.203;LSEQ=GTGGGATGGATGTGCTGGTT;RSEQ=GGTGCAGATGTCTATAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:4,11:0.7333:0,0:24.7:1:32.6:1:1:0:60:22:0.7333:0:2.7 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:14:0:32:0:1:0:60:2:0.3333:0:3 +11 85966586 . T C 101 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.4714;LSEQ=GTGCTGGTTGGGTGCAGATG;RSEQ=CTATAGAGATAGGAGCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:0,9:0,4:4,9:0.6923:0,0:20:1:32:1:1:0:60:18:0.6923:0:2.9 1/0:2:1:0,1:0,1:1,1:0.5:0,0:3:0:28:0:1:0:60:2:0.5:0:3 +11 85967064 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTTATAGAGGTATGGGG;RSEQ=TAGAGCAGAGGTTAAACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:16.5:1:33:0:0.33333:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 85967298 . A G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.58396;LSEQ=CTCAAATCACCATTGTATAT;RSEQ=TTTGGTTGTATAAGGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:6:5,1:49,2:51,6:0.1053:1,2:30.5:1:31.8:1:0.28828:4.67695:60:12:0.1071:0:1.2 1/0:29:17:17,0:12,0:12,17:0.5862:0,1:14.5:1:30.9:1:1:0:60:34:0.5862:0:1.2 +11 85967605 . G A 48 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03453;SOR=Inf;LSEQ=CTTCTTTTGAATCCACAACT;RSEQ=TAAAAACTTGTAATGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:41,217:258,0:0:2,0:22.8:1:32.3:1:1:0:59.9:63.5:1:0:0.1 0/1:197:4:3,1:43,150:193,4:0.0203:2,2:5.5:1:24.3:1:0.04034:10.30:60:8:0.0203:0:1 +11 85967609 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0791;SOR=Inf;LSEQ=TTTTGAATCCACAACTGTAA;RSEQ=AACTTGTAATGTTAAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:36,198:234,0:0:2,0:23.3:1:31:1:1:0:59.9:77:1:0:0.1 0/1:177:3:1,2:34,140:174,3:0.0169:2,2:25:1:31:1:0.48582:2.05:60:6:0.0171:0:1 +11 85967709 . G A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22022;SOR=0.41982;LSEQ=TTGGATGAGTCTTTTGAGAC;RSEQ=TTTGTCACATTTGGGTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:0,15:0,17:17,15:0.4688:1,1:22.1:1:32.1:1:1:0:60:30:0.4688:0:1 0/1:15:4:0,4:1,10:11,4:0.2667:2,0:27.8:1:30:1:1:0:60:8:0.2667:0:1 +11 85968400 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14474;SOR=Inf;LSEQ=GTCTTTTTTTTTTTTTTTTT;RSEQ=CCTTTTCACCTCAAGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:34,1:35,0:0:1,0:21.3:1:28.7:1:1:0:59.7:10.667:1:0:1 0/1:22:2:2,0:20,0:20,2:0.0909:1,0:15:1:29:1:1:0:60:4:0.0909:0:1.5 +11 85968623 . C T 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26835;LSEQ=CAAGAGATCCAAATCTTCTC;RSEQ=TGTCAGTAAGTAAAGGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:830:454:221,233:181,193:374,454:0.547:2,2:25.9:1:30.7:1:0.94441:1.01:59.8:55.75:0.5452:0:1.1 0/1:781:191:87,104:276,314:590,191:0.2446:2,2:25.4:1:29.7:1:0.80251:1.05069:60:190:0.2442:0:1.1 +11 85969117 . T A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTATCTGTTAGTTATTT;RSEQ=TCCTGATCTTCTTACTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:37.5:1:29:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 85975154 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20358;SOR=Inf;LSEQ=TAGTAGTTTTTCTTTCACAA;RSEQ=ATGTTGAAAGTTCACAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:143,6:149,0:0:1,0:24.9:1:33.3:1:1:0:60:73.5:1:0:0 0/1:123:2:1,1:115,6:121,2:0.0163:1,2:20:1:31:0:0.11102:17.81892:60:4:0.0165:0:1 +11 85975481 . A ATATT 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=5.000;MSILEN=4;SSF=0.48034;SOR=0.45795;LSEQ=GAATAAAACAAGTAAAGACT;RSEQ=TATTTATTTATTTATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:15:0,15:0,17:17,15:0.4545:1,1:25.9:1:29.8:1:1:0:59.7:30:0.4688:0.0606:0.1 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:46:1:30.5:1:1:0:60:6:0.2727:0:0 +11 85977117 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.46096;LSEQ=ATATAAAACTTTTTGGTTTT;RSEQ=CATACAGGATTATGATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:527:331:199,132:126,70:196,331:0.6281:2,2:26.4:1:29:1:0.35528:1.19357:59.8:330:0.6286:0:1.1 1/1:507:433:257,176:41,27:68,433:0.854:2,2:26.4:1:27.9:1:1:1.03984:59.7:215.5:0.8569:0:1.1 +11 85977296 . T A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20549;SOR=Inf;LSEQ=TGAAACAATTTGCTATGTTG;RSEQ=GCTATTGAATATAAGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:42,160:202,0:0:2,0:21:1:30.2:1:1:0:60:66.333:1:0:0 0/1:168:2:1,1:43,123:166,2:0.0119:2,2:7:1:28.5:1:0.45637:2.84:60:4:0.0121:0:1 +11 85979270 . T G 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATGTTTATAAACAAAGTATC;RSEQ=ATCATAGGACAAAGATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:20.3:1:30:1:1:0:60:8:0.5:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:21.5:1:29:1:1:0:60:4:0.5:0:1 +11 85979624 . C A 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29443;SOR=2.66946;LSEQ=GTATGGTAACTGCAGTTAAG;RSEQ=TGTACTTCCATCGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:2:0,2:165,267:432,2:0.0046:2,0:8:1:14.5:1:0.52762:0:59:0:0:0:3 0/1:491:6:4,2:205,280:485,6:0.0122:2,2:10.3:1:25.3:1:0.40907:2.73:59.7:5:0.011:0:1.3 +11 85980945 . G T 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06833;SOR=0;LSEQ=TTATGTAACTATCTATGGTA;RSEQ=GAGGTTTTGGTCATTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:5:5,0:62,1:63,5:0.0735:1,0:18.2:1:32.2:1:1:0:60:10:0.0746:0:2 0/0:52:0:0,0:52,0:52,0:0:1,0:23.8:1:32.3:1:1:0:60:104:1:0:1 +11 85980958 . A G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=6.06202;LSEQ=TATGGTAGGAGGTTTTGGTC;RSEQ=TTTCCAGTTCTGGGCTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:53:52,1:25,0:25,53:0.6795:1,1:26.5:1:30:1:1:0:59.5:52:0.6933:0:1.1 1/1:70:65:62,3:5,0:5,65:0.9286:0,1:24.5:1:30:1:1:0:60:130:0.9286:0:1 +11 85981150 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2314;SOR=0;LSEQ=CCGTGCCATTTTACATTCCC;RSEQ=CCAGCAATGTATGAGAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:10,71:81,2:0.0241:2,2:17.5:1:31.5:1:0.2489:6.82:60:4:0.0247:0:2 0/0:89:0:0,0:15,74:89,0:0:2,0:21:1:29:1:1:0:60:43.5:1:0:0 +11 85988444 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GAAATTAGGTGTTTATGTTC;RSEQ=ATAACATAAACATTATCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:2,5:7,2:0.2222:2,0:19.5:1:30:0:1:0:60:4:0.2222:0:1 0/0:5:0:0,0:0,5:5,0:0:0,0:8.8:1:32:1:1:0:60:10:1:0:0.2 +11 85989348 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50116;SOR=0;LSEQ=AAGTGCTTTTCGTATGACTT;RSEQ=GAACATCTGCTTATTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:165,29:194,2:0.0102:2,2:25:1:30.5:1:0.28336:5.61102:60:4:0.0103:0:1 0/0:170:0:0,0:146,24:170,0:0:2,0:22.5:1:31.5:1:1:0:60:169:1:0:0.1 +11 86333286 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14555;SOR=Inf;LSEQ=GCCAATAGTCACATGGATAG;RSEQ=TTGTGCCAGAGCTAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:74,3:77,0:0:1,0:20.2:1:31.4:1:1:0:60:76:1:0:0.1 0/1:48:2:1,1:42,4:46,2:0.0417:2,2:17.5:1:31:0:0.19947:9.50264:60:4:0.0444:0:1 +11 86333332 . TA T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=CTGCATGTGGGTTCTCATTT;RSEQ=CGCCTCCCTATCAATGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:110,50:160,0:0:2,0:23:1:28.8:1:1:0:60:159:0.9876:0:0.1 0/1:164:2:1,1:108,54:162,2:0.0122:2,2:28.5:1:28:1:1:1.99095:60:4:0.0123:0:0 +11 86333335 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49851;SOR=Inf;LSEQ=CATGTGGGTTCTCATTTTAC;RSEQ=CCTCCCTATCAATGGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:112,55:167,0:0:2,0:23:1:30.5:1:1:0:60:166:1:0:0.1 0/1:168:2:1,1:110,56:166,2:0.0119:2,2:8.5:1:27.5:1:1:1.95587:60:4:0.012:0:1 +11 86333379 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11422;SOR=0;LSEQ=TAAAAATGCATTACATACTA;RSEQ=AGACACTGCCATATCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:1,2:160,133:293,3:0.0101:2,2:13.3:1:26.3:1:0.59361:2.39906:60:6:0.0104:0:1.7 0/0:313:0:0,0:182,130:312,0:0:2,0:24.7:1:31.3:1:1:0:60:38:1:0:0.5 +11 86333429 . TA T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.11922;LSEQ=CAGGGATTGTGGGAGGGCAT;RSEQ=AAAAAAAAAAAGTTGTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:83:33,50:104,99:203,83:0.2767:2,2:28.5:1:30.8:1:0.09035:1.58906:59.6:82:0.2742:0:0.3 0/1:322:14:7,7:149,156:305,14:0.0435:2,2:28.7:1:29.9:1:1:1.05:60:28:0.0439:0:0.4 +11 86333434 . A T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=12.000;MSILEN=1;SSF=0.01152;SOR=1.51477;LSEQ=ATTGTGGGAGGGCATTAAAA;RSEQ=AAAAAAAGTTGTTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:125:59,66:72,84:156,125:0.4433:2,2:22.6:1:29.2:1:0.90446:1.04:59.7:30.25:0.4353:0:1.2 1/0:320:175:81,94:72,73:145,175:0.5469:2,2:24.5:1:28.1:1:0.5752:1.14411:60:42.75:0.5463:0:1.1 +11 86333534 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=CTGGTAGATCTGATAGATTA;RSEQ=TGATTCAGTCAAAGGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:26,91:117,2:0.0168:2,2:21:1:29:1:0.40379:3.45:60:4:0.0174:0:1 0/0:108:0:0,0:30,77:107,0:0:2,0:21.9:1:31:1:1:0:60:34.667:0.9905:0:0.1 +11 86335117 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGAGACCAGGATTTTAT;RSEQ=CCTCTTTGAGGTCGGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:31:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 86805562 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTCTTTCAATTCCCTCC;RSEQ=CCTAGTCTTTCCTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:29.7:1:30.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 86805605 . A G 91 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03186;SOR=0.05395;LSEQ=TAGAAATTACAGTATAGGCT;RSEQ=GGTGTGGTGGTATGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:1,0:1,7:0.875:0,0:21.7:1:32.6:1:1:0:60:14:0.875:0:1.4 0/1:5:1:1,0:4,0:4,1:0.2:0,0:31:0:32:0:1:0:60:2:0.2:0:2 +11 86805759 . G T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=GATTCATCTTGTGTCTTTCT;RSEQ=AGCACTCAATGAATCTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:42,22:64,0:0:2,0:27.7:1:31.9:1:1:0:60:31:1:0:0.1 0/1:76:2:1,1:44,30:74,2:0.0263:2,2:13.5:1:23.5:1:1:1.45909:60:4:0.0267:0:1 +11 86805789 . C A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00761;SOR=Inf;LSEQ=TGAATCTGCAACCAGAACCT;RSEQ=AGGTGACTTATAGTTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:44,33:77,0:0:2,0:29:1:32.4:1:1:0:60:154:1:0:0.1 0/1:89:8:3,5:45,36:81,8:0.0899:2,2:25.5:1:30.1:1:0.46254:2.06624:60:16:0.092:0:1.1 +11 86805885 . A C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.06792;LSEQ=CATTTGTGTAGCTTCTTGTA;RSEQ=CATAGGATTTTGAAAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:46:12,34:2,1:3,46:0.9388:2,2:24.9:1:30.7:1:0.19263:5.43188:60:14.333:0.9348:0:1.1 1/0:32:16:5,11:4,12:16,16:0.5:2,2:27.9:1:31.5:1:1:1.35:60:32:0.5:0:1.1 +11 86806069 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52314;SOR=0;LSEQ=GCATGTTGTTCCCGGGGGTG;RSEQ=TCAATGGGTTTCCATCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:19,11:30,2:0.0625:2,2:27.5:1:32:1:1:1.69662:60:4:0.0645:0:2 0/0:19:0:0,0:13,6:19,0:0:2,0:24.3:1:28.8:1:1:0:60:18:1:0:0.3 +11 86806071 . C G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=0.07357;LSEQ=ATGTTGTTCCCGGGGGTGTT;RSEQ=AATGGGTTTCCATCAGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:27:19,8:1,3:4,27:0.871:2,2:25.3:1:30.4:1:0.11537:6.64:60:26:0.8667:0:1.3 0/1:19:6:4,2:9,4:13,6:0.3158:2,2:21.8:1:32.5:1:1:1.11798:60:12:0.3333:0:1 +11 86806128 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49474;SOR=0;LSEQ=AAGCATTTTACTTTATCACC;RSEQ=TTACCTAAAGCATAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:34,11:45,2:0.0426:2,2:17.5:1:30:1:0.44958:3.0025:60:4:0.0426:0:2.5 0/0:45:0:0,0:35,10:45,0:0:2,0:24:1:30.4:1:1:0:60:90:1:0:0.1 +11 86806164 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22936;SOR=0;LSEQ=AATTCAGCTCCTGCATGCTG;RSEQ=TGCTTGTTAACTGAGTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:49,12:61,2:0.0317:2,2:22:1:29.5:1:0.37276:3.96297:60:4:0.0328:0:1 0/0:68:0:0,0:49,19:68,0:0:2,0:27.9:1:31.8:1:1:0:59.8:136:1:0:0 +11 86806220 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49933;SOR=0;LSEQ=AATGATCTGTGCTTCATAAT;RSEQ=CTCCATGGATGGATTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:92,42:134,2:0.0147:2,2:24.5:1:31:1:0.53399:2.17663:60:4:0.015:0:1 0/0:123:0:0,0:71,52:123,0:0:2,0:23.2:1:31:1:1:0:59.8:246:1:0:0 +11 86806279 . CA C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10411;LSEQ=GGGAAATTCCTATCAGAACT;RSEQ=ACAATGTCAGATTCACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:197:177:111,66:11,9:20,177:0.8985:2,2:26.6:1:32.2:1:0.62788:1.37:59.7:354:0.8985:0.1168:0.1 0/1:157:75:38,37:40,42:82,75:0.4777:2,2:26.7:1:31:1:0.87356:1.08:59.4:150:0.4808:0.0764:0.1 +11 86806299 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50472;SOR=0;LSEQ=CAACAATGTCAGATTCACTT;RSEQ=AAATATTAACATTCTGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:117,71:188,2:0.0105:2,2:29:1:30:1:1:1.64332:60:4:0.0106:0:1 0/0:152:0:0,0:84,68:152,0:0:2,0:24.4:1:30.6:1:1:0:59.9:37:1:0:0.1 +11 86806422 . G A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00194;SOR=Inf;LSEQ=TCTACCACAATAAAAGCACT;RSEQ=CACTTGGTCATCAATACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:175,210:385,0:0:2,0:27.6:1:32.2:1:1:0:60:54:1:0:0.1 0/1:412:10:5,5:193,209:402,10:0.0243:2,2:26.3:1:27.9:1:1:1.08:60:20:0.0244:0:1.1 +11 86806471 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.23015;SOR=0;LSEQ=AGTTCAGCACTAACTCTCTC;RSEQ=CTTGGGGTTAAGTGGGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:46,136:182,2:0.0109:2,2:11:1:29:1:0.44666:2.94:60:4:0.011:0:1 0/0:199:0:0,0:63,136:199,0:0:2,0:22:1:28.7:1:1:0:60:198:1:0:0.1 +11 86806968 . A G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTGGAGCTGGCAGTGAGCCG;RSEQ=GATCGCGCCACTGCACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:12:1:33:0:1:0:22.5:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:31:0:1:0:21:2:1:0:1 +11 86807017 . CA C 135 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.06143;SOR=0.3902;LSEQ=AACAGAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAAAGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:18:16,2:9,2:11,18:0.5294:2,2:16.4:1:32.5:1:0.62208:1.74:51.8:36:0.5455:0.2059:1.9 0/1:43:13:12,1:22,5:27,13:0.3023:2,1:10.4:1:30.6:1:0.64337:2.67:54.7:26:0.3023:0.1628:1.9 +11 86807104 . C A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.1772;LSEQ=GAGTCTCCATATTGCCTTCT;RSEQ=TCTACTCCTGCATGACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:158:144:95,49:9,5:14,144:0.9114:2,2:29.2:1:28.7:1:1:1.08:59.7:23:0.9079:0:1.2 1/0:197:127:82,45:49,21:70,127:0.6447:2,2:26.3:1:27.6:1:0.52853:1.2789:59.8:17.143:0.6349:0:1.1 +11 86807151 . C CATATATATAAAGAAAT 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.05116;LSEQ=CCACATGGTGTCTCCTTCAC;RSEQ=AATATAAAGAAAACCTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:300:276:174,102:15,9:24,276:0.92:2,2:20.6:1:30.1:1:1:1.02:58.5:275:0.9197:0.5733:1.5 0/1:390:144:87,57:143,103:246,144:0.3692:2,2:20.6:1:28.5:1:0.67112:1.10:58.9:288:0.374:0.2026:1.1 +11 86807189 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.12527;LSEQ=CTTGTGCCAGTGTTGATGCT;RSEQ=AAACAGGACTACTACTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:189:111,78:141,101:242,189:0.4385:2,2:24.2:1:29.4:1:1:1.02:53.9:378:0.4426:0:2.1 0/1:551:49:30,19:272,230:502,49:0.0889:2,2:25.6:1:27.9:1:0.37029:1.33:55.6:48:0.0882:0:2 +11 86807217 . C CA 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.14324;LSEQ=ACTACTACTTGGAAAACTAG;RSEQ=AAAAGTTTTTTATCCGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:456:333:168,165:75,48:123,333:0.7303:2,2:28.6:1:30.4:1:0.05675:1.53314:52.2:110:0.7301:0.068:1.4 0/1:552:154:80,74:208,190:398,154:0.279:2,2:24.5:1:29.1:1:1:1.01261:53.2:76:0.2774:0.0598:1.2 +11 86807218 . A AA 82 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.08742;SOR=0.2344;LSEQ=CTACTACTTGGAAAACTAGC;RSEQ=AAAGTTTTTTATCCGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:7:4,3:239,209:448,7:0.0154:2,2:18:0:29.4:1:1:1.17:60:14:0.0156:0:1.3 0/0:550:2:1,1:285,262:547,2:0.0036:2,2:18:0:31.5:1:1:1.08761:60:4:0.0037:0:1.5 +11 86807219 . A AA 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.09687;SOR=0.16397;LSEQ=TACTACTTGGAAAACTAGCA;RSEQ=AAGTTTTTTATCCGTTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:5:3,2:236,214:450,5:0.011:2,2:18:0:31.2:1:1:1.36:60:10:0.0111:0:1.4 0/0:552:1:1,0:284,265:549,1:0.0018:2,0:18:0:24:0:1:0:55:2:0.0018:0:1 +11 86807222 . GT AG 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=0.29898;LSEQ=TACTTGGAAAACTAGCAAAA;RSEQ=TTTTTATCCGTTAAACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:47:28,19:198,196:394,47:0.1051:2,2:20.4:1:31.9:1:0.27999:1.46:59.3:94:0.1061:0:2.6 0/1:531:18:11,7:258,250:508,18:0.0339:2,2:22.5:1:30.4:1:0.47507:1.52:59.7:36:0.0338:0:2.4 +11 86807223 . TTTTTT GTTTTTA 67 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.73938;SOR=0.67125;LSEQ=ACTTGGAAAACTAGCAAAAG;RSEQ=ATCCGTTAAACTCTTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:5:4,1:198,196:394,5:0.0112:2,2:13.4:1:29.2:1:0.37205:3.95:59:10:0.0113:0.0022:2.6 0/0:531:4:2,2:258,250:508,4:0.0075:2,2:18:0:29.5:1:1:1.03194:60:8:0.0075:0:2.3 +11 86807228 . T A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11378;LSEQ=GAAAACTAGCAAAAGTTTTT;RSEQ=ATCCGTTAAACTCTTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:461:370:179,191:36,29:65,370:0.8026:2,2:26.6:1:29.4:1:0.34678:1.32374:53:122.333:0.8417:0:1.4 0/1:529:167:85,82:170,178:348,167:0.3157:2,2:24.1:1:28.3:1:0.70674:1.09:53.8:82.5:0.321:0:1.3 +11 86807229 . A AA 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15395;SOR=0.28424;LSEQ=AAAACTAGCAAAAGTTTTTT;RSEQ=TCCGTTAAACTCTTCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:6:3,3:223,225:448,6:0.0132:2,2:18:0:30.2:1:1:1.01:60:12:0.0132:0:2.5 0/0:528:2:1,1:263,263:526,2:0.0038:2,2:18:0:26.5:1:1:1:57.5:4:0.0038:0:2.5 +11 86807230 . TC AT 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16357;SOR=0.48946;LSEQ=AAACTAGCAAAAGTTTTTTA;RSEQ=CGTTAAACTCTTCTACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:12:7,5:214,221:435,12:0.0268:2,2:16:1:30:1:0.57202:1.44:58.3:24:0.027:0:2.7 0/1:527:7:3,4:258,261:519,7:0.0133:2,2:14.3:1:28.7:1:1:1.31732:60:14:0.0134:0.0038:2.1 +11 86807231 . C CC 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25901;SOR=0.34179;LSEQ=AACTAGCAAAAGTTTTTTAT;RSEQ=CGTTAAACTCTTCTACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:5:3,2:212,224:436,5:0.0112:2,2:17.4:1:31.4:1:0.67857:1.58:59:10:0.0114:0:4.4 0/0:521:2:1,1:254,260:514,2:0.0038:2,2:18:0:32:0:1:1.02:60:4:0.0039:0:5 +11 86807232 . C CC 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48167;SOR=0.51036;LSEQ=ACTAGCAAAAGTTTTTTATC;RSEQ=GTTAAACTCTTCTACAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:5:3,2:215,226:441,5:0.0112:2,2:17.2:1:31:1:0.67931:1.58:60:10:0.0113:0:4.6 0/0:523:3:2,1:255,264:519,3:0.0057:2,2:18:0:29.3:1:0.61859:2.07:60:6:0.0058:0:4.3 +11 87300037 . G T 59 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCCTTTTGAGCTCCTTG;RSEQ=GAGAGGGGCAGCAACCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:12:0:32:0:1:0:60:2:1:0:1 1/1:4:4:4,0:0,0:0,4:1:0,0:37.5:1:29.5:1:1:0:60:8:1:0:1 +11 87300291 . G C 84 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TGGGTGAGGCTTTCCTGCAG;RSEQ=ATCTCCAATAATTCCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1:0,2:33.5:1:32.8:1:1:0:54.8:12:1:0:1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:24.5:1:29.5:1:1:1:60:4:0.5:0:1 +11 87300400 . T C 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=TGCGGACCAGCAGTCTTAAG;RSEQ=TTTTCCTCCGAGTAGTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:20.8:1:33:1:1:0:60:8:1:0:1 0/0:4:0:0,0:3,1:4,0:0:2,0:19:1:24.3:1:1:0:60:3:1:0:0.3 +11 87300575 . A C 96 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=TCAGACACCCTATATAGGAG;RSEQ=AATCCTACTGGCATCAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:18:1:32:1:1:0:46:16:1:0:1.8 1/0:6:4:2,2:0,2:2,4:0.6667:0,2:15.5:1:30.8:1:0.46667:0:43.8:8:0.6667:0:1.3 +11 87300593 . G T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08081;SOR=0;LSEQ=AGAAATCCTACTGGCATCAG;RSEQ=TTGGTGCCCCTTGAGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,1:2,4:0.5714:2,2:23:1:28.8:1:1:2.44949:40.8:8:0.6667:0:1.8 0/0:5:0:0,0:2,3:5,0:0:2,0:27.4:1:33:1:1:0:52.2:10:1:0:0.8 +11 87300620 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=CCCCTTGAGATCAGAGGTTC;RSEQ=GGAAGAAAGAGCAGGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:32.1:1:31.9:1:1:0:51.6:14:1:0:1 0/1:10:2:2,0:6,2:8,2:0.2:2,0:45.5:1:31.5:1:1:0:46.5:4:0.2222:0:1.5 +11 87300621 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=CCCTTGAGATCAGAGGTTCC;RSEQ=GAAGAAAGAGCAGGCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:32.3:1:32.1:1:1:0:51.6:14:1:0:1 0/1:10:2:2,0:6,2:8,2:0.2:2,0:11.5:1:30.5:1:1:0:60:4:0.2:0:1 +11 87300858 . A G 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.61372;LSEQ=AACCCCATCCAAGGGTCAGC;RSEQ=GTCTCAAAGACCGAAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:2,3:5,3:0.375:2,0:27:1:31.3:1:0.46429:0:60:6:0.375:0:1 1/0:8:4:2,2:1,3:4,4:0.5:2,2:18:1:29.8:1:1:2.60:60:8:0.5:0:1 +11 88359126 . C A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTCCAGGTAGAATTCAG;RSEQ=GGCAACAGGCAGTGAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:18.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 88359287 . AT GG 85 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGAGAGCAGCCTTTACA;RSEQ=TTACACCAAATATAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:23.8:1:32.9:1:1:0:60:12:1:0.3333:0.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 88359488 . A G 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TTTCACAGATGTAAAACGTG;RSEQ=CAATTAAAGCAGAATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:86:86:79,7:0,0:0,86:1:0,2:22.5:1:31.5:1:1:0:60:85:1:0:1 1/0:57:45:43,2:11,1:12,45:0.7895:2,1:25.7:1:30.9:1:0.51504:1.93:60:44:0.7857:0:1.2 +11 88359567 . CA C 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=GCACTTAGTTTATAAATGCA;RSEQ=AACCTCTCCACTGTGACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:170,125:295,0:0:2,0:26.6:1:30.8:1:1:0:60:590:1:0:1.9 0/1:274:12:7,5:156,106:262,12:0.0438:2,2:25.5:1:32.1:1:1:1.051:60:24:0.0441:0.0073:0.9 +11 88359606 . TG CA 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08812;LSEQ=TCATAGAGATTTCTGACTTG;RSEQ=TTTATTTGAGTTTCATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:323:318:158,160:0,0:0,318:0.9845:0,2:24.6:1:31.6:1:1:0:59.9:636:0.9938:0.0991:1.7 1/1:336:285:152,133:0,1:1,285:0.8482:0,2:26:1:30.5:1:0.46853:0:59.9:570:0.8559:0.0655:1.8 +11 88359607 . G A 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38912;SOR=1.84337;LSEQ=CATAGAGATTTCTGACTTGT;RSEQ=TTTATTTGAGTTTCATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:4:1,3:0,0:0,4:0.0138:0,2:25.8:1:30:1:1:0:59.8:8:1:0:3.3 0/1:318:8:3,5:23,22:45,8:0.0252:2,2:6.8:1:27.3:1:0.70398:1.72443:60:7:0.1346:0:2.5 +11 88359631 . T A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03879;LSEQ=ATTTGAGTTTCATTTCTCCA;RSEQ=ACAATGTAATTTTTGGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:290:288:133,155:0,1:1,288:0.9931:0,2:24.5:1:30.6:1:1:0:59.9:287:0.9965:0:1.9 1/1:335:284:138,146:22,27:49,284:0.8478:2,2:25.9:1:29.3:1:0.64614:1.16:60:93.667:0.8515:0:1.9 +11 88359686 . G A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=TTACATTCTTTTATGTGTTC;RSEQ=GAAGTGTTGTGATTCTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:66,128:194,0:0:2,0:27.8:1:30.6:1:1:0:60:63.667:1:0:1.3 0/1:232:14:6,8:79,139:218,14:0.0603:2,2:29.5:1:28.5:1:0.77569:1.32:60:28:0.0606:0:2.1 +11 88359723 . G A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCTGTGAAATTGCTAG;RSEQ=AAAAAAGTGCAGAAGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:111:111:20,91:0,0:0,111:1:0,2:23.1:1:30.8:1:1:0:59.9:36:1:0:1.3 1/1:124:124:31,93:0,0:0,124:1:0,2:23.7:1:29.5:1:1:0:60:61:1:0:1.2 +11 88359907 . G A 48 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGTAATTAGGTTTAGAT;RSEQ=AGCTAATGAGGGTAGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:22.7:1:30.3:1:1:0:60:6:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:27:1:1:0:60:4:1:0:2 +11 88359919 . G A 25 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GTTTAGATGAGCTAATGAGG;RSEQ=TAGCCTGTTCATGATAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:25:1:30:1:1:0:60:6:1:0:0.7 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:25:0:1:0:60:4:1:0:2 +11 88360079 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTAGGCTGGAAAATGAG;RSEQ=CTTCACCAGAACCCAACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:8.5:1:32.5:1:1:0:46.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 90507372 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGAGACGTTGAGATCAT;RSEQ=TGGAGGAGAAGAGGCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:39:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 90507460 . C T 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53924;SOR=0.51761;LSEQ=ATGAGTTCGTCTAGTGTTGG;RSEQ=CTTTGAGGCTGCTGACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:4,1:0.2:2,0:47:0:30:0:1:0:46:2:0.2:0:1 0/1:18:2:1,1:10,6:16,2:0.1111:2,2:40.5:1:28.5:1:1:1.61828:47.5:4:0.1111:0:1 +11 90507501 . C A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGATGGGGTTTTTGTGGAGG;RSEQ=CTTTTTGATGTTGTTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:9.8:1:30.3:1:1:0:56.5:8:1:0:0.3 0/1:18:2:1,1:7,9:16,2:0.1111:2,2:39.5:1:28.5:1:1:1.27:57:4:0.1111:0:1 +11 90507561 . G A 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGCTTGTTTGTTTCTCCTGC;RSEQ=ATAGTCAGGTCCCTCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:29.7:1:31.3:1:1:1.73:50:6:0.6:0:1 1/0:5:3:1,2:0,2:2,3:0.6:0,2:25.7:1:31:1:1:0:56.3:6:0.75:0:1 +11 90507897 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08356;SOR=4.43716;LSEQ=AGCCACTTGTCTGGGATGCC;RSEQ=GGATTCCTCAGAACTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:8,5:5,7:12,13:0.52:2,2:27.8:1:30.5:1:0.43375:2.17:60:26:0.52:0:1.1 1/1:12:10:5,5:1,1:2,10:0.8333:2,2:27.9:1:29.2:1:1:1:59.4:20:0.8333:0:1.1 +11 90508050 . A C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19015;SOR=5.27797;LSEQ=AGACTGCAAGGAAGCCCCAC;RSEQ=CACTGAGGAAAGATGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:4,6:5,3:8,10:0.5556:2,2:30.4:1:30.8:1:0.63719:2.37182:55.7:20:0.5882:0:1.9 1/1:8:7:4,3:1,0:1,7:0.875:0,2:20.1:1:30.3:1:1:0:55.7:14:0.875:0:1.1 +11 90508316 . T G 100 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00191;SOR=30.28838;LSEQ=TCAAACAGCTTAGACAGAGG;RSEQ=CAGCTGCAGCCTGTGTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:8,2:0.2:2,2:17:1:30.5:1:1:1.58:60:4:0.2:0:1 1/1:11:10:6,4:1,0:1,10:0.9091:0,2:22.7:1:30.4:1:1:0:58.2:20:0.9091:0:1.4 +11 90508350 . G A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00333;SOR=0.0542;LSEQ=TGTTGGTCGCCCCTCCTGCC;RSEQ=GGAGTTCAGTAGGCTTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:5,4:1,1:2,9:0.8182:2,2:12.7:1:30.7:1:1:1.22:60:18:0.8182:0:1 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:25.5:1:27.5:1:1:1.4491:60:4:0.1667:0:1 +11 90508356 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TCGCCCCTCCTGCCGGGAGT;RSEQ=CAGTAGGCTTAAGCAGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:23.5:1:31.6:1:1:0:60:16:1:0:0.9 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:38.5:1:31:1:1:1.36624:60:4:0.1429:0:2 +11 93267819 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGCTCAACTCTGCAGTC;RSEQ=CTTCATCTCCCAAGGGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 93858111 . A G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27005;SOR=Inf;LSEQ=CCAACCTCTGGAGTTGGGCA;RSEQ=CATGGCTTCTCCCCTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:13,0:0:2,0:11:1:28.9:1:1:0:29.8:26:1:0:0 0/1:21:3:1,2:6,12:18,3:0.1429:2,2:25.7:1:29.7:1:1:1:24:6:0.1429:0:1 +11 94153641 . C G 70 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTAAGCCAGAAAAATAATT;RSEQ=AAGTCATTTTATATTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:24.6:1:30.4:1:1:0:60:4:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 94155446 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AACTCTTCCTCTTCCTCCTC;RSEQ=TCCTCATTCATGGTGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41.5:1:31:1:1:0:60:4:1:0:1 +11 94163159 . CAAAACA C 97 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=1;SSF=0.1092;SOR=0.26031;LSEQ=ATGTGCTGGACCACCTGAGG;RSEQ=AAAACAAAAACAAACACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:781:8:2,6:273,500:773,8:0.0102:2,2:32.4:1:32.6:1:0.71946:1.63705:60:16:0.0104:0.0013:0 0/0:745:2:1,1:290,453:743,2:0.0027:2,2:35:1:33:1:1:1.56:60:4:0.0027:0:0 +11 94169159 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21234;SOR=Inf;LSEQ=ATTACACGATTAAATCTTAA;RSEQ=TTATATATGAGCCACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:11,130:141,0:0:2,0:22.8:1:31.9:1:1:0:60:27.2:1:0:0.1 0/1:121:2:1,1:4,115:119,2:0.0165:1,2:19.5:1:27.5:1:0.08127:25.83:60:4:0.0167:0:1 +11 94170172 . G GA 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.71024;SOR=1.50859;LSEQ=TAAAAAAAGAGAGCAACCAA;RSEQ=AAAAAAAAAATCAAATCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:4,0:47,0:47,4:0.0784:1,0:31.5:1:30.7:1:1:0:60:8:0.0816:0.0196:0.5 0/1:35:4:4,0:31,0:31,4:0.1143:1,0:24.8:1:30.5:1:1:0:60:8:0.1143:0:0 +11 94170460 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23685;SOR=Inf;LSEQ=TAAAATAACTTAGAAAAACT;RSEQ=GCATACTTCTTTAGCTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:19,164:183,0:0:2,0:22.9:1:30.3:1:1:0:59.8:366:1:0:0.1 0/1:174:2:1,1:30,142:172,2:0.0115:2,2:16:1:28:1:0.32543:4.67:60:4:0.0116:0:1 +11 94170484 . TTC T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00179;SOR=Inf;LSEQ=TACTTCTTTAGCTAAAGATT;RSEQ=TGAGTCCTATCTGCAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:5,116:121,0:0:1,0:26.7:1:30.5:1:1:0:59.7:242:1:0:0 0/1:104:8:0,8:6,90:96,8:0.0769:2,0:28.3:1:29.3:1:1:0:60:16:0.0784:0.0192:0 +11 94179125 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=9.17272;LSEQ=AGGTTTATTTCATACAACAC;RSEQ=AAAAAATGAAAGCTAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:19:3,16:38,162:200,19:0.0856:2,2:20.6:1:32.1:1:1:1.24982:60:38:0.0864:0:1 0/1:231:107:25,82:28,94:122,107:0.4632:2,2:23.9:1:30.9:1:1:1.02:60:34.667:0.4602:0:1.1 +11 94180266 . T G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.81597;LSEQ=TTATATATTATAAAAATAGA;RSEQ=TTTTAAAGAACCGTGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:7:7,0:76,0:76,7:0.0833:1,0:20.7:1:33.6:1:1:0:60:14:0.0833:0:1.1 0/1:58:4:4,0:54,0:54,4:0.069:1,0:28:1:33:0:1:0:60:8:0.0741:0:1.3 +11 94189681 . T TA 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.07604;SOR=0;LSEQ=AAAATTGCACAATGTACTCT;RSEQ=AAAAAAAAAAACTCATATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:0,11:11,3:0.2:0,0:38:1:33:0:1:0:60:6:0.2:0:0 0/0:19:0:0,0:1,18:19,0:0:1,0:28.6:1:28.3:1:1:0:58.6:38:1:0:0.2 +11 94193020 . A G 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGAAATTAACCAGTGTC;RSEQ=TAGGCAAAATAAGAGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:41:1:34:0:1:0:60:4:0.2857:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 94193864 . TAAC T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0.09091;SOR=Inf;LSEQ=AGAGATACAAAGAAAGAGAA;RSEQ=AACATCAACAATAACAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:15,0:0:1,0:25.1:1:29.1:1:1:0:60:30:1:0:0 0/1:7:2:2,0:4,1:5,2:0.2857:2,0:28:1:32.5:1:1:0:60:4:0.2857:0:0 +11 94194303 . G T 127 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=50.25849;LSEQ=GAAGGTAAGGCCAAACTTTA;RSEQ=CAACTGCCAGCTTGCTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:0,1:3,138:141,1:0.007:1,0:30:0:14:0:1:0:60:0:0:0:4 0/1:79:21:0,21:2,56:58,21:0.2658:1,1:24.8:1:29.1:1:1:0:60:42:0.2692:0:1.3 +11 94197260 . A G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.71247;LSEQ=TAAGAACATTTTTTTACCTC;RSEQ=TAAAAATAACTAGCTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:51:34,17:326,190:516,51:0.0899:2,2:25.2:1:30.7:1:0.65123:1.17:52.6:50:0.0901:0:1 0/1:449:95:57,38:220,133:353,95:0.2116:2,2:29.2:1:30.2:1:0.72159:1.10251:55.4:190:0.2144:0:1 +11 94197568 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00067;SOR=Inf;LSEQ=GAGCTATATCATTTATCCTA;RSEQ=TGAGAAACTAATGTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:39,0:0:1,0:22.4:1:33:1:1:0:59.9:78:1:0:0.1 0/1:19:6:1,5:0,13:13,6:0.3158:1,2:36.3:1:29.7:1:0.31579:0:60:12:0.3158:0:1 +11 94203461 . T TA 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.15455;SOR=Inf;LSEQ=ATTCCTCTCTCTCAATGACT;RSEQ=AAAAAAAAAAATCTTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:26,0:26,0:0:1,0:25.3:1:32:1:1:0:59:52:0.963:0:0 0/1:18:2:2,0:14,2:16,2:0.1111:2,0:26:1:30.6:1:1:0:60:4:0.1176:0.0556:0 +11 94203801 . C A 160 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04473;LSEQ=CCCTTTAATACGCAGCAAAC;RSEQ=AACATGTCTGAAGTGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:37:15,22:145,252:397,37:0.0851:2,2:27.9:1:30.8:1:0.72199:1.18:60:36:0.0845:0:1.1 0/0:484:2:2,0:197,285:482,2:0.0041:2,0:1:0:24:0:0.16855:0:60:4:0.0041:0:1 +11 94203868 . A T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=2.80321;LSEQ=TTTCCTCAGGGTGATGTGCA;RSEQ=ACGAAAGCTTTCATATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:80:14,66:16,90:106,80:0.4301:2,2:24:1:28.5:1:0.6907:1.19:59.6:79:0.4293:0:1.1 1/0:153:104:21,83:5,44:49,104:0.6797:2,2:22.2:1:28.1:1:0.16702:2.22:60:103:0.6821:0:1 +11 94209348 . T C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00332;SOR=0.41887;LSEQ=ATGTTTTGTCTGATCTTGCA;RSEQ=TGACAACCTTGAAAGATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:58:58,0:92,0:92,58:0.3867:1,1:25.7:1:32.6:1:1:0:60:116:0.3867:0:1 0/1:96:20:20,0:76,0:76,20:0.2083:1,1:28.1:1:31.7:1:1:0:60:40:0.2105:0:1 +11 94209741 . C CT 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.54138;SOR=0;LSEQ=GTTGCAGGTTCTTTTTTTAT;RSEQ=TTTTTTTTTTAACTGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:0,22:22,3:0.1111:1,2:31:1:31:1:0.12:0:57.3:6:0.125:0:0 0/0:15:0:0,0:1,14:15,0:0:1,0:18.9:1:30.4:1:1:0:57.9:14:1:0:0.1 +11 94211833 . A T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58271;SOR=2.59969;LSEQ=TTCCAAACAGATACAAACTT;RSEQ=TCTCCAAATTTCTCAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:1,0:208,46:254,1:0.0039:2,0:26:0:13:0:1:0:47:0:0:0:7 0/1:197:2:0,2:154,41:195,2:0.0102:2,0:6.5:1:27.5:1:0.04677:0:60:4:0.0103:0:1 +11 94211916 . C T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTACCTAAACCATATAGCG;RSEQ=AATCTTTGTGCTTCCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:779:0:0,0:457,322:779,0:0:2,0:25.6:1:32.2:1:1:0:59.9:63.917:1:0:0.1 0/1:706:34:20,14:395,277:672,34:0.0482:2,2:27.5:1:28.8:1:1:1.00:58.4:68:0.0486:0:1.2 +11 94212048 . C T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.78628;LSEQ=ACAAAGTGCATCTGCCTATG;RSEQ=AAAATAATTTCAAAGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:45:14,31:110,298:408,45:0.0991:2,2:25.8:1:28.6:1:0.59767:1.22:60:90:0.1:0:1 0/1:396:93:28,65:101,201:302,93:0.2348:2,2:28.5:1:27.9:1:0.61365:1.16603:59.6:186:0.2366:0:1.2 +11 94212154 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57712;SOR=1.42072;LSEQ=TTCTACTTACAAAAACATAG;RSEQ=TGAGGATAGTGTCTTCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:9:0,9:0,55:55,9:0.1406:1,0:32.3:1:33.2:1:1:0:60:18:0.1429:0:1.1 0/1:37:7:0,7:0,30:30,7:0.1892:1,0:29:1:30.3:1:1:0:60:14:0.1944:0:2 +11 94212930 . TA T 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05804;SOR=0.60341;LSEQ=TAGTTCACCCATGGAAACCT;RSEQ=AAAAAAAAAAGTTACTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:504:45:16,29:162,297:459,45:0.0893:2,2:28.7:1:31.7:1:1:1.01:59.2:90:0.0904:0:0.3 0/1:412:23:8,15:142,243:385,23:0.0558:2,2:25.3:1:31.5:1:1:1.09545:56.7:46:0.0562:0:0.3 +11 94212977 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51772;SOR=0;LSEQ=CATACGGGACAAAAGCTGTT;RSEQ=TCCCTAAGATTCTCCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:0,2:18,169:187,2:0.0106:2,0:24.5:1:31:1:1:0:57.5:4:0.0106:0:1 0/0:127:0:0,0:18,109:127,0:0:2,0:21.5:1:29.9:1:1:0:59.8:254:1:0:0.2 +11 94219002 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55205;SOR=0;LSEQ=CTAAGAAAATAGCTTATATG;RSEQ=AAGGCAAAACAGTTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:119,6:125,2:0.0157:1,0:23:1:29:0:1:0:60:4:0.0157:0:1 0/0:64:0:0,0:57,7:64,0:0:2,0:23.8:1:30.6:1:1:0:60:128:1:0:0 +11 94219040 . CA C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17911;SOR=Inf;LSEQ=TGTTTACGTGTCTTATACAG;RSEQ=AATACCATACACAAGTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:187,44:231,0:0:2,0:23.6:1:30.7:1:1:0:60:230:1:0:0.1 0/1:170:2:1,1:130,38:168,2:0.0118:2,2:14:1:28.5:1:0.40724:3.3898:60:4:0.012:0.0059:0.5 +11 94219325 . T TA 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.64944;SOR=0.36608;LSEQ=TAAACTACAGATGAAAGAGA;RSEQ=AAAAAAAAACTCACAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:4:0,4:4,98:102,4:0.0377:1,0:32.8:1:32.3:1:1:0:60:8:0.0385:0:0 0/1:71:1:0,1:3,67:70,1:0.0141:1,0:41:0:33:0:1:0:60:2:0.0147:0:0 +11 94223855 . A G 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACACAAAGCATACAAAATC;RSEQ=GCTTTGAGCTTTCAGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:54:54,0:1,0:1,54:0.9818:0,1:24.3:1:29.4:1:1:0:60:26:1:0:1 1/1:41:41:41,0:0,0:0,41:1:0,1:21.9:1:30:1:1:0:60:82:1:0:1 +11 94225807 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=4.43891;LSEQ=TATTTAAAACATTCCAAATA;RSEQ=CCTTTTTGATGACTAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:14:14,0:84,1:85,14:0.1414:1,1:19.1:1:31.6:1:1:0:60:28:0.1414:0:1 0/1:99:42:39,3:53,4:57,42:0.4242:2,2:24.4:1:30:1:1:1.01904:60:41:0.4271:0:1 +11 94225920 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.62223;LSEQ=GCTTTAGAAACCCCAAATAA;RSEQ=AAGGGATTCCAGAAGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:58:33,25:278,234:512,58:0.1018:2,2:27.5:1:29.6:1:0.78132:1.11:60:28:0.0995:0:1.1 0/1:627:269:137,132:203,153:356,269:0.429:2,2:26.5:1:28.1:1:0.14441:1.27786:60:37.429:0.4246:0:1.2 +11 94532923 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51652;SOR=0;LSEQ=CAGAACAACGAGGAACTGCC;RSEQ=ACTTACGAGGAGGCCAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:14,7:21,2:0.087:2,2:22.5:1:31:1:1:1.93655:60:4:0.0909:0:1 0/0:14:0:0,0:10,4:14,0:0:2,0:24.9:1:27.7:1:1:0:60:6:1:0:0.2 +11 94532994 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49153;SOR=0;LSEQ=GCAGCAACAGCAGCAGGGGG;RSEQ=GGTGGGCCATGGTTACTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:12,16:28,2:0.0667:2,2:26:1:29.5:1:1:1.32:60:4:0.0667:0:1 0/0:30:0:0,0:13,17:30,0:0:2,0:25.4:1:30.3:1:1:0:60:60:1:0:0.2 +11 94770943 . G T 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00067;SOR=0;LSEQ=TCGCCTTCGTCCGCTTTCAC;RSEQ=ACCGGAGCGACGCGCAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:12:1,11:150,314:464,12:0.0252:2,2:15.9:1:25.8:1:0.1145:5.243:28.3:11:0.0237:0:1.3 0/0:404:0:0,0:168,236:404,0:0:2,0:26.3:1:29.8:1:1:0:48.1:79.8:1:0:0.2 +11 94771054 . A G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=0.23356;LSEQ=GCCGGGACCTGCCTCGCAGC;RSEQ=GCCAGGAAGAGCCACGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:48:5,43:15,63:78,48:0.381:2,2:22.3:1:32:1:0.21865:2.03678:42.2:96:0.384:0:1 0/1:112:14:4,10:27,71:98,14:0.125:2,2:22.6:1:29.9:1:1:1.05:44.2:28:0.1284:0:1 +11 94771066 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08739;SOR=Inf;LSEQ=CTCGCAGCAGCCAGGAAGAG;RSEQ=CACGCGGCAGGTCCTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:12,82:94,0:0:2,0:18.6:1:31.6:1:1:0:34.5:30.333:1:0:0.4 0/1:76:3:1,2:15,58:73,3:0.0395:2,2:19.7:1:27.7:1:0.51323:1.91:28:6:0.0411:0:1 +11 94771495 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05031;SOR=Inf;LSEQ=CCATCTCCAGATCTTGCTCA;RSEQ=GGTCCAGGTCTAGATCTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:277,76:353,0:0:2,0:24.7:1:31.1:1:1:0:43.7:352:1:0:0.1 0/1:320:4:4,0:223,93:316,4:0.0125:2,0:34.5:1:31.8:1:0.32678:0:22.5:8:0.0126:0:1.3 +11 94771564 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.4995;SOR=Inf;LSEQ=GGGAATCCAAGTCCAGGTCG;RSEQ=GATCCAAGAGTCCTCCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:99,65:164,0:0:2,0:14.9:1:30.8:1:1:0:35.2:328:1:0:0.1 0/1:179:2:1,1:98,78:176,2:0.0112:2,2:17:1:32:0:1:1.25478:28.5:4:0.0116:0:1 +11 94771664 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50786;SOR=0;LSEQ=TGATGGAGGACTTGGGGAAA;RSEQ=GGACTCCATACTCAGTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:0,2:1,117:118,2:0.0167:1,0:20.5:1:33:0:1:0:28.5:4:0.0168:0:1.5 0/0:90:0:0,0:1,89:90,0:0:1,0:29.5:1:30.7:1:1:0:27.2:89:1:0:0 +11 94800529 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17895;SOR=Inf;LSEQ=TGGGCGACGTGTACATCCCG;RSEQ=GGGAGCCCCACACCAAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:70,153:223,0:0:2,0:22.6:1:29.6:1:1:0:33.7:21.3:1:0:0.1 0/1:164:2:1,1:53,108:161,2:0.0122:2,2:16.5:1:31:0:1:2.03:48:4:0.0123:0:1 +11 94800534 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17872;SOR=Inf;LSEQ=GACGTGTACATCCCGCGGGA;RSEQ=CCCCACACCAAGGCGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:75,166:241,0:0:2,0:25.8:1:31.9:1:1:0:34.1:39.167:1:0:0.2 0/1:177:2:1,1:55,120:175,2:0.0113:2,2:18.5:1:27.5:1:0.5339:2.17:48:4:0.0114:0:1 +11 94800652 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6092;SOR=2.17969;LSEQ=ACGGACGCGAGCTGCGGGTG;RSEQ=AGGTGGCGCGCTATGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:1:1,0:44,170:214,1:0.0047:2,0:1:0:24:0:0.2093:0:60:2:0.0048:0:1 0/1:198:2:1,1:63,133:196,2:0.0101:2,2:10.5:1:27:1:0.5431:2.10:55.5:4:0.0102:0:1 +11 94800663 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23311;SOR=Inf;LSEQ=CTGCGGGTGCAGGTGGCGCG;RSEQ=TATGGCCGCCGGGACCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:28,130:158,0:0:2,0:19.5:1:33:1:1:0:54.2:30.6:1:0:0.2 0/1:148:2:1,1:45,101:146,2:0.0135:2,2:20:0:30.5:1:0.52648:2.23:30:4:0.0136:0:1.5 +11 94800704 . C G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49512;SOR=0;LSEQ=CCGCAGCCGCCAGGGAGAGC;RSEQ=ACGCGGCAGGTCCAGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,12:21,2:0.087:2,2:19:1:33:1:1:1.32:60:4:0.0909:0:1 0/0:18:0:0,0:8,10:18,0:0:2,0:17.7:1:31.1:1:1:0:60:36:1:0:0.1 +11 94800781 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06925;SOR=Inf;LSEQ=GGAGCCGCAGCCCCAGGCGG;RSEQ=GACACCGCAGCCGATCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:47,19:66,0:0:2,0:27.6:1:30.7:1:1:0:59.7:21:1:0:0.3 0/1:47:3:2,1:28,16:44,3:0.0638:2,2:17.3:1:29.3:1:1:1.14:60:6:0.0638:0:1.3 +11 94800810 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.19159;SOR=Inf;LSEQ=AGCCGATCCCGGGGTCCCAG;RSEQ=TGCTCCAGGTCCCGCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:52,27:79,0:0:2,0:30.2:1:31.3:1:1:0:60:12.167:1:0:0.3 0/1:62:2:1,1:34,26:60,2:0.0323:2,2:37.5:1:28.5:1:1:1.30197:60:4:0.0323:0:2 +11 94800857 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1719;SOR=Inf;LSEQ=CTATAGGGGTTCTCGCTATA;RSEQ=CCGGTCTCCCTACAGCCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:35,25:60,0:0:2,0:19.6:1:32.8:1:1:0:60:120:1:0:0.2 0/1:43:2:1,1:20,21:41,2:0.0465:2,2:28.5:1:28.5:1:1:1.05:60:4:0.0526:0:1.5 +11 94800902 . G GC 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTACAGCCGGTCGCGCTACA;RSEQ=CGCTCTCCCTACAGCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:54:38,16:1,0:1,54:0.9818:0,2:27.2:1:31.7:1:1:0:60:53:0.9815:0.2364:0.1 1/1:33:33:18,15:0,0:0,33:1:0,2:24.8:1:30.9:1:1:0:59.4:66:0.9706:0.2424:0.3 +11 94801011 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.20377;SOR=Inf;LSEQ=GCCGATATCACAGCAGCCGG;RSEQ=CTCACTCGAAGTCTGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:216,7:223,0:0:1,0:25.2:1:30.2:1:1:0:59.9:43.6:1:0:0.1 0/1:184:2:1,1:173,9:182,2:0.0109:1,2:36.5:1:30:1:0.10602:18.28336:60:4:0.0109:0:1 +11 94801633 . A AT 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTAACGCTGTCAAGAC;RSEQ=TGCTTCAACATTGCCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:29.5:1:1:0:40:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 95490325 . T C 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7092;SOR=0.6645;LSEQ=GGACTGGAAGGCTGCCCGTC;RSEQ=GCCTGCCCCTCTCTGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:4,4:6,8:14,8:0.3636:2,2:21.1:1:30.4:1:1:1.32:60:16:0.3636:0:1 0/1:11:3:1,2:3,5:8,3:0.2727:2,2:27:1:28.3:1:1:1.18052:60:6:0.2727:0:1 +11 95825203 . TTGC T 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.82668;SOR=1.18504;LSEQ=GCAGGCTGAGAAGATGGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:9:3,6:99,75:174,9:0.0492:2,2:27.3:1:30.2:1:0.18719:2.62613:60:18:0.0492:0:0 0/1:225:13:9,4:118,95:213,13:0.0578:2,2:23.4:1:31:1:0.39788:1.81:51.2:26:0.058:0.0044:0.7 +11 95825221 . C T 110 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.00595;SOR=6.10065;LSEQ=TGTTGCTGCTGCTGCTGCTG;RSEQ=TGTTGTTGCTGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:102,93:195,2:0.0102:2,2:36:0:32:0:1:1.09626:60:4:0.0107:0:1.5 0/1:254:15:8,7:128,111:239,15:0.0591:2,2:23.2:1:28.2:1:1:1.00897:55.2:14:0.0562:0:1.4 +11 95825233 . T TTGTTGTTGCTGCTGCTGCTGC 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=47;MSI=5.000;MSILEN=3;SSF=0.07007;SOR=Inf;LSEQ=TGCTGCTGCTGTTGTTGCTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:106,100:206,0:0:2,0:23.4:1:29.3:1:1:0:59.2:40.2:1:0:0.3 0/1:263:5:3,2:133,124:257,5:0.019:2,2:13:1:31:1:1:1.40:60:10:0.0197:0.0152:2 +11 95825254 . C T 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.01593;SOR=Inf;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:100,75:175,0:0:2,0:22.3:1:32.1:1:1:0:59.6:34:1:0:0.4 0/1:204:7:5,2:103,94:197,7:0.0343:2,2:23.4:1:27.9:1:0.45078:2.27:48:6:0.0306:0:1.7 +11 95825260 . TTGC T 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.52224;SOR=0.5525;LSEQ=TGCTGCTGCTGCTGCTGTTG;RSEQ=TGCTGCTGCTGCTGTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:6:3,3:93,66:159,6:0.0355:2,2:30.8:1:30.8:1:0.69516:1.40609:60:12:0.0366:0:0 0/1:201:4:2,2:107,90:197,4:0.0199:2,2:36.3:1:25.5:1:1:1.18786:55:3:0.0153:0:1 +11 95825282 . G A 41 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.36471;SOR=0.31958;LSEQ=GCTGCTGCTGCTGCTGTTGG;RSEQ=CTGAAATTGAGCTCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:2,1:103,92:195,3:0.015:2,2:6.3:1:26.3:1:1:1.78:59.3:6:0.0161:0:1 0/0:207:1:1,0:109,96:205,1:0.0048:2,0:1:0:23:0:1:0:60:2:0.0052:0:1 +11 95825332 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25103;SOR=0;LSEQ=TGTTGAGCTGAAATTGAACT;RSEQ=TGCTGTTGCTGTTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:2,1:116,120:236,3:0.0126:2,2:24.7:1:30.7:1:0.61872:2.06:46:6:0.0133:0:1 0/0:212:0:0,0:109,103:212,0:0:2,0:28.4:1:31.2:1:1:0:57.3:52:1:0:0.3 +11 95825356 . TTGC T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=0.9481;LSEQ=TGTTGCTGTTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:5:1,4:108,129:237,5:0.0207:2,2:24.6:1:30.6:1:0.38222:3.33438:46.2:10:0.021:0.0041:0.6 0/1:204:4:3,1:97,103:200,4:0.0196:2,2:28:1:31.3:1:0.36164:3.17:57:8:0.0199:0:0.3 +11 95825374 . TTGCTGCTGC T 148 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=13.000;MSILEN=3;SSF=0.00015;SOR=3.2626;LSEQ=TGTTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:17:6,11:75,90:165,17:0.0895:2,2:29.5:1:30.1:1:0.45574:1.52431:54.3:34:0.0924:0.0105:0 0/1:152:37:17,20:57,44:101,37:0.2434:2,2:32.1:1:28.6:1:0.33622:1.51934:51.8:36:0.2384:0.0263:0.3 +11 95825418 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07938;SOR=Inf;LSEQ=CTGCTGCTGCTGCTGCTGTT;RSEQ=CTGCTGTTGCTGTTGGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:56,78:134,0:0:2,0:24.9:1:32.4:1:1:0:55:66:1:0:0.2 0/1:102:3:2,1:38,61:99,3:0.0294:2,2:19.7:1:25.3:1:0.55946:3.17:52:6:0.0303:0:1.7 +11 95825797 . A G 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66406;SOR=0.6174;LSEQ=CCTGGTGATGGTCCAGCAGA;RSEQ=GAGGGCAAGGCTGACCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:1,4:3,2:5,5:0.5:2,2:26:1:31:1:0.52381:4.91839:60:10:0.5:0:1 0/1:8:3:2,1:3,2:5,3:0.375:2,2:24:1:25.3:1:1:1.29:60:2:0.2857:0:1 +11 99322049 . T C 85 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATGACCCCATGTTACATTA;RSEQ=ACAAAAGTTATGAGATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:16:1:33:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 99322082 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=AGATGAAATTCACATTAGCC;RSEQ=ATTCTAAGAACTAGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:9,0:0:0,0:33.6:1:30.3:1:1:0:55.6:18:1:0:1 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:20.5:1:28:1:1:0:60:4:0.6667:0:2 +11 99322134 . A T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1482;SOR=4.16771;LSEQ=TACAAATAGTACATCAAAAT;RSEQ=TTACAAATGGAATGTTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:14:14,0:11,0:11,14:0.56:0,1:21.6:1:30.8:1:1:0:57.1:13:0.5417:0:1 1/1:13:11:10,1:2,0:2,11:0.8462:0,2:23.7:1:28.8:1:1:0:60:4.5:0.8182:0:1.2 +11 99322304 . T A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=1.89569;LSEQ=CAGAGTTTTCTTACTGATAG;RSEQ=GGAAATTATTTTTATATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:88:44,44:87,83:170,88:0.3411:2,2:25.7:1:30.9:1:0.89591:1.04803:59.8:176:0.3451:0:1.9 0/1:228:113:64,49:63,52:115,113:0.4956:2,2:20.8:1:29.2:1:0.79124:1.08:59.9:112:0.4978:0:1.9 +11 99322321 . T C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00081;SOR=1.85337;LSEQ=TAGTGGAAATTATTTTTATA;RSEQ=GTTAGAAAGCATCATAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:90:42,48:85,92:177,90:0.3371:2,2:24.8:1:31:1:0.89705:1.05572:59.7:89:0.3358:0:1.9 0/1:241:117:64,53:60,64:124,117:0.4855:2,2:22.1:1:30.6:1:0.36742:1.29:60:116:0.4874:0:1.8 +11 99322382 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=GTCTGAAGGATTAGGCGGTA;RSEQ=ACATAAGAAATAAAATTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:65,124:189,2:0.0104:2,2:37.5:1:31:1:1:1.90:60:4:0.0105:0:1 0/0:187:0:0,0:77,110:187,0:0:2,0:26.1:1:30.6:1:1:0:60:92.5:1:0:0.6 +11 99322415 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49761;SOR=Inf;LSEQ=AAATTATCCTTACAGTTGAT;RSEQ=TAAGATATTTATGAATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:23,81:104,0:0:2,0:24.2:1:31.9:1:1:0:60:103:1:0:0.1 0/1:105:2:1,1:32,71:103,2:0.019:2,2:13.5:1:31.5:1:0.53187:2.20:60:4:0.0192:0:3 +11 99322486 . A C 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06899;SOR=3.63067;LSEQ=ATAAAAGCCTAACATGCTGT;RSEQ=TACACACTTTCTTTTTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:0,7:0,15:15,7:0.3182:1,0:24.3:1:33.4:1:1:0:54.3:14:0.3182:0:1 1/0:22:14:0,14:0,8:8,14:0.6364:0,1:25:1:31.4:1:1:0:60:28:0.6364:0:1 +11 99322609 . C A 49 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTCTTTTAAGTCACAAGACT;RSEQ=TTCACAATTACCTTGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:41.3:1:31.3:1:1:0:60:6:0.75:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:34:0:33:0:1:0:60:2:1:0:0 +11 100240074 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGGTGCAAGACCAGCC;RSEQ=GAGCAACATAGGGAGACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:28.5:1:1:0:60:4:1:0:1.5 +11 100353271 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=0;LSEQ=TGGTTTTCTAGCAATATTGG;RSEQ=CATTCCTTTGATTAATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:14,2:0.125:2,2:29:1:29:1:1:1.30929:60:4:0.125:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:19.2:1:30.3:1:1:0:60:20:1:0:0 +11 100850073 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.77031;LSEQ=TCTTTGATGACAGTCATTTT;RSEQ=GGACCACTTTTCAAAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:9:9,0:77,6:83,9:0.0978:2,0:26.3:1:29.1:1:1:0:60:18:0.0989:0:1.6 0/1:52:24:23,1:26,2:28,24:0.4615:2,1:21.8:1:27.7:1:1:1.75:60:48:0.4615:0:1.4 +11 100850129 . G T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0148;SOR=Inf;LSEQ=AAGTTATATAACTTTTTCTG;RSEQ=AGGAATCATCATGAATATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:213,66:279,0:0:2,0:22.9:1:31.3:1:1:0:59.9:54.8:1:0:0.2 0/1:213:5:2,3:153,55:208,5:0.0235:2,2:30:1:27.2:1:0.12586:4.1392:60:10:0.0238:0:1 +11 100850140 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=5.55883;LSEQ=CTTTTTCTGGAGGAATCATC;RSEQ=TGAATATCCATGGAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:21:13,8:209,78:287,21:0.0682:2,2:22.6:1:30.6:1:0.31516:1.646:60:42:0.0682:0:1.9 0/1:245:71:49,22:122,52:174,71:0.2898:2,2:22.6:1:29.8:1:0.87894:1.05315:60:142:0.291:0:1.8 +11 100850202 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=9.54606;LSEQ=GAGATGTTGTAGAGTTAATT;RSEQ=CCCAAAGCGACTCTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:35:17,18:275,246:521,35:0.0629:2,2:26:1:29.6:1:0.72723:1.18328:60:70:0.0635:0:1.4 0/1:437:171:93,78:133,133:266,171:0.3913:2,2:26.6:1:28.1:1:0.37919:1.19:60:170:0.3935:0:1.4 +11 100850334 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00103;SOR=3.5085;LSEQ=TGCTTGCTTCTAAAGTTCCT;RSEQ=CTTTACTCTTCTTGCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:61:1,60:1,43:44,61:0.581:1,1:26.9:1:32.8:1:1:1.39083:60:122:0.581:0:1 1/1:59:49:1,48:0,10:10,49:0.8305:0,1:24.3:1:32.6:1:1:0:60:98:0.8305:0:1 +11 100850432 . A AT 108 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=1.60791;LSEQ=AAAGTCAGAGGCTTTTCATT;RSEQ=TTTTTTTTTTTTACTATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:0,11:1,11:12,11:0.4783:2,0:22.3:1:31.4:1:1:0:57.8:22:0.4783:0.087:1 1/0:5:3:0,3:0,2:2,3:0.6:0,0:24.3:1:29.7:1:1:0:60:6:0.6:0:0.3 +11 100909580 . G GAT 60 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTATGAAATAATATGGATAA;RSEQ=ATAGTTTACTTTAACAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:10.5:1:30:1:1:0:60:8:0.5:0.375:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 100909809 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.39521;LSEQ=TGACCAAAACAAAAAGACAT;RSEQ=CCACAAAATTTAATTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:251:133:128,5:116,2:118,133:0.5299:1,1:23.8:1:33:1:0.45249:2.25863:60:266:0.5341:0:1 0/1:169:52:50,2:109,8:117,52:0.3077:2,1:25.2:1:32.2:1:0.72547:1.83:60:104:0.3095:0:1 +11 100909991 . T C 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.40221;LSEQ=TTCAAGCAGTACAGATGAAG;RSEQ=TGTTTGACAAGCTGTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1360:706:287,419:261,391:652,706:0.5191:2,2:27.9:1:32.9:1:0.82494:1.03:60:87.25:0.5201:0:1.1 0/1:1163:352:149,203:351,459:810,352:0.3027:2,2:26.4:1:31.3:1:0.79653:1.04182:60:57.667:0.2996:0:1.1 +11 100910132 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01048;SOR=0.38982;LSEQ=AAGGTGTTTTTTTCTTACCA;RSEQ=AGTGAAAATAACTCCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:126:68:0,68:0,58:58,68:0.5397:1,1:28.1:1:33.3:1:1:0:60:136:0.544:0:1 0/1:48:15:0,15:0,33:33,15:0.3125:1,1:24.8:1:32.1:1:1:0:60:30:0.3125:0:1 +11 100912230 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGATAAATCCTAAAAAA;RSEQ=AGAAACTTGAAAAGCATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:34:1:34:0:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 100912235 . A G 35 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAATCCTAAAAAATAGAA;RSEQ=CTTGAAAAGCATGCAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:15:1:35.5:1:1:0:55:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 100912252 . A T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACTTGAAAAGCATGCAA;RSEQ=TTTTAACTTTTGCTATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:39.5:1:32.5:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 100912510 . G GA 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.0211;SOR=0.29195;LSEQ=GAGTGGTCTATATTGAAAAT;RSEQ=AAAAAAAAACACAATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:26:26,0:34,0:34,26:0.4:1,1:30.5:1:31.5:1:1:0:59.4:52:0.4:0:2 0/1:31:5:5,0:20,2:22,5:0.1613:2,0:20.8:1:30.2:1:1:0:60:10:0.1613:0.0323:1.6 +11 100912527 . A C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03004;SOR=0.42843;LSEQ=AATGAAAAAAAAACACAATA;RSEQ=AAAGTCTGAGCAGCATGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:50:50,0:44,0:44,50:0.5319:1,1:24.9:1:30.2:1:1:0:59.5:6.143:0.5:0:2.1 0/1:46:15:15,0:29,2:31,15:0.3261:2,1:19.8:1:31.2:1:1:0:60:14:0.3182:0:1.9 +11 100912561 . C A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=0.38139;LSEQ=CATGATCCAAACACTTTTAA;RSEQ=ATACAAGTATTAATCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:84:84,0:70,0:70,84:0.5455:1,1:23.9:1:31:1:1:0:59.4:168:0.549:0:1.7 0/1:99:31:31,0:66,2:68,31:0.3131:1,1:24.4:1:30:1:1:0:60:30:0.3061:0:1.5 +11 100912565 . C A 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30279;SOR=4.76155;LSEQ=ATCCAAACACTTTTAACATA;RSEQ=AAGTATTAATCTGAGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:1,0:166,0:166,1:0.006:1,0:13:0:10:0:1:0:51:0:0:0:8 0/1:107:3:3,0:102,2:104,3:0.028:1,0:23.3:1:30.3:1:1:0:60:6:0.0291:0:1 +11 100912910 . C CTA 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=TTATAACATATATTTCTGAG;RSEQ=TATATAATGATTTCTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:16,281:297,0:0:2,0:23.9:1:33.4:1:1:0:59.9:58.4:1:0:0.1 0/1:185:12:0,12:9,164:173,12:0.0649:2,0:31:1:29.9:1:1:0:60:24:0.0659:0.0108:0.1 +11 100913165 . G A 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATGCTTCTTAAATACTT;RSEQ=GTTTGACTTAGTTTACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:17.6:1:33.8:1:1:0:60:10:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 100920568 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0531;SOR=Inf;LSEQ=TTATAATCCAAGACGTCTAC;RSEQ=TCATACATAACTATATAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:260,9:269,0:0:1,0:22.7:1:31.5:1:1:0:60:133.5:1:0:0.6 0/1:163:3:2,1:154,6:160,3:0.0184:1,2:19.3:1:25.3:1:0.12411:12.25267:60:2:0.0126:0:1.7 +11 100920575 . A T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3459;LSEQ=CCAAGACGTCTACCTCATAC;RSEQ=TAACTATATAATCATATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:301:174:164,10:121,6:127,174:0.5781:1,2:22.9:1:32.4:1:0.7983:1.22884:60:348:0.58:0:1.1 0/1:190:61:57,4:118,11:129,61:0.3211:2,2:22:1:30.9:1:0.77778:1.33:60:122:0.3245:0:1.1 +11 100920829 . GA G 76 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.7648;SOR=1.336;LSEQ=CACAAAAGAAAAAGCAACAG;RSEQ=AAAAAAATAGTGTCTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:5:2,3:170,476:646,5:0.0077:2,2:26.4:1:33.6:1:0.6117:1.86:60:10:0.0078:0:0 0/1:587:6:3,3:200,381:581,6:0.0102:2,2:22.8:1:29.5:1:0.42135:1.90:55.8:12:0.0104:0.0017:0.8 +11 100920897 . A C 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02448;SOR=Inf;LSEQ=GGTTTTGGTAATTACCTTAC;RSEQ=TATTATTGAAAATGACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:4,174:178,0:0:1,0:25.2:1:31.5:1:1:0:59.8:43.5:1:0:0 0/1:118:4:0,4:2,112:114,4:0.0339:1,0:13.8:1:31:1:1:0:60:8:0.0342:0:1.3 +11 100922062 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5283;SOR=0;LSEQ=TAATGTCATCATATCAAGAA;RSEQ=ACTAAATATGTGATCATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:183,6:189,2:0.0105:1,2:36:1:28.5:1:0.07214:28.32449:60:4:0.0105:0:2 0/0:116:0:0,0:116,0:116,0:0:1,0:45:0:13:0:1:0:60:0:0:0:2 +11 100922112 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13638;LSEQ=AACTTTCAAAATTATCCTAC;RSEQ=TGTACACTTAAAATAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:244:184,60:207,59:266,244:0.4775:2,2:22.4:1:30.8:1:0.53123:1.14376:59.8:488:0.4813:0:1 0/1:434:48:33,15:274,111:385,48:0.1106:2,2:23.2:1:29.6:1:0.73759:1.12172:60:47:0.109:0:1.1 +11 100922202 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.50975;LSEQ=TACAGCATCTGCCCACTGAC;RSEQ=TGTTTGTAGGATCTCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1416:128:69,59:705,579:1284,128:0.0904:2,2:21.7:1:30.3:1:0.85255:1.04114:59.9:41.667:0.0892:0:1.2 0/1:1252:250:138,112:520,479:999,250:0.1997:2,2:23.5:1:29.2:1:0.39567:1.13:60:61.5:0.1997:0:1.1 +11 100922387 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15508;SOR=Inf;LSEQ=ACATATAAATCTGAAAATAG;RSEQ=TATGCGTAGGGTAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:8,256:264,0:0:1,0:23:1:32.3:1:1:0:60:65:1:0:0.9 0/1:172:2:0,2:6,164:170,2:0.0116:1,0:27:1:28:1:1:0:60:4:0.0117:0:1.5 +11 100922404 . A T 213 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGGTATGCGTAGGGTAATA;RSEQ=AATGTTTTCAATCCCAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:181:181:1,180:0,0:0,181:1:0,1:25.9:1:28.5:1:1:0:60:35.2:1:0:1.3 1/0:101:61:2,59:0,39:39,61:0.604:1,1:23.4:1:28.1:1:0.51939:0:59.4:122:0.604:0:1.3 +11 100922451 . T A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00908;SOR=0.32668;LSEQ=CACTGAAAATCAGAAAACAT;RSEQ=AATAAATAATACAGCCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:51:0,51:0,33:33,51:0.6071:1,1:22.5:1:31.5:1:1:0:60:102:0.6071:0:1.8 0/1:36:12:1,11:0,24:24,12:0.3333:1,2:38:1:31.3:1:0.33333:0:60:24:0.3333:0:1.8 +11 100922568 . C A 106 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCATCCATCACTCATTCATG;RSEQ=AACACCCATTTAATAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:1,10:0.9091:0,0:24.4:1:32:1:1:0:54:20:0.9091:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:43:0:30:0:1:0:60:2:1:0:1 +11 100933092 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15944;SOR=Inf;LSEQ=TATATTGTAGTTAATTTACT;RSEQ=CATAGAGTGTTTTATTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:252,6:258,0:0:1,0:24.5:1:32.4:1:1:0:60:63.5:1:0:0.1 0/1:172:2:2,0:168,2:170,2:0.0116:1,0:31.5:1:29.5:1:1:0:60:4:0.0118:0:1 +11 100933412 . C A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.20095;LSEQ=GCTTTCATTTGGAACGCCCA;RSEQ=TGGCTGTGGGAGAGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1331:115:49,66:517,697:1214,115:0.0864:2,2:27.2:1:30.4:1:1:1.00:60:114:0.0864:0:1.1 0/1:1236:213:101,112:449,574:1023,213:0.1723:2,2:25:1:29.6:1:0.36357:1.15:60:426:0.1733:0:1.1 +11 100933494 . G GA 64 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.2613;SOR=2.87347;LSEQ=AATTTTCGACCTACAGAGAA;RSEQ=AAAAAAAAGAAATTCATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:2:1,1:77,358:435,2:0.0046:2,2:19:1:29.5:1:0.32546:4.63:60:4:0.0046:0:0.5 0/1:383:5:2,3:88,289:377,5:0.0131:2,2:19.6:1:27.6:1:0.33668:2.18:60:10:0.0134:0.0078:0.4 +11 100933598 . G GAATGA 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.14371;LSEQ=TATGCATTTTAGCATCAATC;RSEQ=AATGAAATAGAATAAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:65:0,65:0,12:12,65:0.8442:0,1:28.6:1:31.6:1:1:0:59.5:130:0.8442:0.0909:0.2 0/1:37:16:1,15:0,21:21,16:0.4324:1,1:18.3:1:30.7:1:0.43243:0:59.7:32:0.4324:0.1081:0.1 +11 100962200 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCAGCAAAGCCTAGACTCC;RSEQ=ACACATGTTACTTAATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:22.3:1:30.3:1:1:0:60:6:0.375:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:33:0:33:0:1:0:60:2:1:0:1 +11 100998019 . T A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAAGGGAGGCAACTGCCCC;RSEQ=GTGCTGTGTCCCGCTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:24,7:31,2:0.0606:2,2:33:1:32:0:0.43182:3.27323:60:4:0.0606:0:1 0/0:15:0:0,0:14,1:15,0:0:1,0:23.5:1:31.8:1:1:0:60:30:1:0:0.3 +11 100998076 . T A 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05544;SOR=2.29816;LSEQ=CGGGGAGCGCAGCGGTGCGC;RSEQ=GGGGCTGGGGCTGAGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:11:11,0:128,9:137,11:0.0743:2,0:13.3:1:32.3:1:1:0:60:22:0.0753:0:1 0/1:96:15:13,2:73,7:80,15:0.1563:2,2:26.8:1:30:1:0.62994:1.59535:60:30:0.1579:0:1.1 +11 100998105 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0;SOR=0.28087;LSEQ=GGCTGAGGGTTGGCGGCCGC;RSEQ=GCCGCCAACGGAACCGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:348:202:161,41:115,31:146,202:0.5805:2,2:23.4:1:31.6:1:0.89351:1.06:60:49.5:0.5773:0:1.1 0/1:272:76:59,17:146,50:196,76:0.2794:2,2:21.5:1:29.9:1:0.6406:1.19:60:37:0.2761:0:1.2 +11 100998107 . C T 55 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.00749;SOR=Inf;LSEQ=CTGAGGGTTGGCGGCCGCCG;RSEQ=CGCCAACGGAACCGCTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:0:0,0:282,78:360,0:0:2,0:24.2:1:32:1:1:0:60:59:1:0:0.7 0/1:288:6:1,5:210,72:282,6:0.0208:2,2:7.7:1:21.5:1:0.00586:14.42888:60:2:0.0142:0:1.8 +11 100998285 . CCGG C 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.28461;SOR=2.54414;LSEQ=GGTAGAGCGCGGGGGCCGCC;RSEQ=CGGCGGCGGCAGAGGCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:2:1,1:140,355:495,2:0.004:2,2:14:1:30.5:1:0.48733:2.53:60:4:0.0041:0.002:0.5 0/1:491:5:1,4:159,323:482,5:0.0102:2,2:31.6:1:31.4:1:1:1.96666:60:10:0.0104:0:0.2 +11 100998330 . G A 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.60589;SOR=0.45064;LSEQ=TGGAGGGCAGGCCGTCCCGC;RSEQ=GGAGCAGGCAGCCGCTCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:36,79:115,2:0.0171:2,2:38:0:32.5:1:0.53434:2.18:60:4:0.0174:0:1.5 0/0:129:1:1,0:44,84:128,1:0.0078:2,0:1:0:23:0:0.34884:0:60:2:0.0078:0:1 +11 100998343 . C T 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92639;LSEQ=GTCCCGCGGGAGCAGGCAGC;RSEQ=GCTCGCGCCCGGCGCCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:36,38:74,2:0.026:2,0:1:0:26:0:0.49474:0:60:4:0.027:0:1 0/1:83:2:1,1:38,42:80,2:0.0241:2,2:20:0:32:1:1:1.10:60:4:0.0244:0:1.5 +11 100998362 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28546;SOR=0;LSEQ=CCGCTCGCGCCCGGCGCCTT;RSEQ=CAGGGCGGCGGCGCGAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:3:1,2:159,43:202,3:0.0146:2,2:9:1:28.3:1:0.12198:7.29895:60:6:0.0149:0:1 0/0:130:0:0,0:94,34:128,0:0:2,0:1:0:16:0:1:0:60:0:0:0:1 +11 100998374 . C T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.14748;SOR=0;LSEQ=GGCGCCTTGCAGGGCGGCGG;RSEQ=GCGAACGGGCCCTGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:4:2,2:235,72:307,4:0.0129:2,2:8:1:28.3:1:0.24077:3.24847:60:8:0.0129:0:1.3 0/0:217:0:0,0:150,65:215,0:0:2,0:16:1:30.8:1:1:0:60:42:1:0:0.3 +11 100998375 . G T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08527;SOR=6.0993;LSEQ=GCGCCTTGCAGGGCGGCGGC;RSEQ=CGAACGGGCCCTGCTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:1:0,1:255,83:338,1:0.0029:2,0:1:0:26:0:0.24779:0:60:2:0.003:0:1 0/1:225:4:1,3:156,64:220,4:0.0178:2,2:13.3:1:27.8:1:0.08116:7.23994:60:8:0.0179:0:1.3 +11 100998389 . C T 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78169;LSEQ=GGCGGCGCGAACGGGCCCTG;RSEQ=TGGGGCGGCGCGCCCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:5:3,2:350,128:478,5:0.0104:2,2:28.8:1:31:1:0.61462:1.82031:60:10:0.0106:0:1 0/0:370:3:0,3:246,121:367,3:0.0081:2,0:1:0:26:1:0.03703:0:60:6:0.0083:0:1 +11 100998623 . G A 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27692;LSEQ=GAGCGCGCGGAGGCCTCCGC;RSEQ=CCTTCCTCCTCCTCCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1577:889:455,434:337,346:683,889:0.5637:2,2:24.3:1:30.1:1:0.4766:1.08:59.9:73.083:0.5633:0:1.1 0/1:1340:353:169,184:479,507:986,353:0.2634:2,2:23.2:1:29.5:1:0.85237:1.02862:60:706:0.2668:0:1.2 +11 100998762 . C G 240 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CGACCGGGGTGGACGAGGCA;RSEQ=AGGGTGAACTCCGCGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1713:0:0,0:843,867:1710,0:0:2,0:25.5:1:32.2:1:1:0:60:67.4:0.9982:0:0.2 0/1:1437:213:111,102:621,598:1219,213:0.1482:2,2:23.8:1:31.1:1:0.7668:1.05:59.8:212:0.1496:0:1.2 +11 100998771 . C G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.18786;LSEQ=TGGACGAGGCACAGGGTGAA;RSEQ=TCCGCGGCGGGGCAAAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1660:140:66,74:720,798:1518,140:0.0843:2,2:25.4:1:32.7:1:1:1.01161:60:69:0.0844:0:1.2 0/1:1383:232:116,116:576,569:1145,232:0.1678:2,2:23.1:1:31.4:1:0.94272:1.01229:60:115:0.1685:0:1.1 +11 100999013 . T C 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGGGACCAGGGCGACGCC;RSEQ=CCTGCTGCCGCCCCCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1556:0:0,0:794,760:1554,0:0:2,0:23.7:1:31.1:1:1:0:59.9:54.5:1:0:0.2 0/1:1205:74:40,34:575,556:1131,74:0.0614:2,2:25.2:1:30:1:0.63219:1.14:59.9:23.667:0.0598:0:1.2 +11 100999043 . G T 213 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01018;LSEQ=GCCCCCGGCGGGACAGCCGC;RSEQ=GCTCCTCCTCCAGCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1549:112:56,56:765,669:1434,112:0.0723:2,2:23.7:1:31.3:1:0.55548:1.1434:60:55:0.0718:0:1.1 0/0:1262:1:0,1:657,603:1260,1:8e-04:2,0:1:0:25:0:0.47898:0:60:2:8e-04:0:1 +11 100999190 . G A 224 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=272.48889;LSEQ=TTCACTGGGGCCCCGGACCA;RSEQ=TGAGGGCTCTCAGAGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1527:1:1,0:771,755:1526,1:7e-04:2,0:1:0:25:0:1:0:60:2:7e-04:0:1 0/1:1239:187:90,97:520,531:1051,187:0.1509:2,2:24.9:1:29.8:1:0.75134:1.05543:59.9:61.333:0.1502:0:1.2 +11 100999194 . G T 208 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGGCCCCGGACCAGTGA;RSEQ=GGCTCTCAGAGGCCGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1510:120:60,60:700,688:1388,120:0.0795:2,2:27.6:1:30.2:1:1:1.01743:60:16.143:0.0766:0:1.3 0/0:1234:0:0,0:605,628:1233,0:0:2,0:23.2:1:30.5:1:1:0:60:55.045:0.9992:0:0.3 +11 100999838 . A AG 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.23961;LSEQ=TTTTCTCCTCCCCCGTCTCC;RSEQ=GGAGGAGGGAAAAGGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:990:916:275,641:33,40:73,916:0.9253:2,2:24:1:31.4:1:0.0086:1.92168:59.9:64.429:0.9309:0.1505:0.1 1/0:761:569:169,400:94,94:188,569:0.7477:2,2:27.1:1:30.5:1:0:2.36397:60:188.667:0.7547:0.021:0.1 +11 101102103 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGGTCAATGGGACCGGGC;RSEQ=CCACAGAGCAGGGGGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:28:1:30.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 101102948 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5045;SOR=0;LSEQ=TGGCTGTCATGGGACCTAGA;RSEQ=AGGGGAGAAGCCGTGTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:17,3:20,2:0.0909:2,2:47:1:33.5:1:0.33766:5.04987:22:4:0.0909:0:1 0/0:15:0:0,0:10,5:15,0:0:2,0:37.1:1:29.1:1:1:0:36.8:30:1:0:0.1 +11 101347908 . G T 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCCAACCTTTCCTTAGACT;RSEQ=TGTAAAGATCTAGGATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:6,25:31,0:0:2,0:27.9:1:32.5:1:1:0:60:62:1:0:0 1/0:25:14:6,8:2,9:11,14:0.56:2,2:24.4:1:29.5:1:0.23368:3.22:60:28:0.56:0:1.1 +11 101981196 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTCTCAGTCGGGCGCAGCCG;RSEQ=CGCCAGGGAAAAGAAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:17:1:27:1:1:1:60:4:0.5:0:1 +11 101981277 . T C 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGGGAAAGGCAACGAGC;RSEQ=GTCCGGCCTCCGTCAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:22.3:1:30.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:26:0:33:0:1:0:60:2:1:0:1 +11 101981532 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50096;SOR=Inf;LSEQ=GCCGGGGCGTCCGGGCGTAG;RSEQ=CCTCGCTCGCCTGGGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:69,35:104,0:0:2,0:23.8:1:31.9:1:1:0:60:51:1:0:0.2 0/1:122:2:1,1:76,44:120,2:0.0164:2,2:23.5:1:26:1:1:1.71909:60:4:0.0172:0:2 +11 101981543 . C T 123 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=18.21756;LSEQ=CGGGCGTAGCCCTCGCTCGC;RSEQ=TGGGTCAGGGGGTGCGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:0,1:85,52:137,1:0.0072:2,0:1:0:29:0:0.38406:0:60:2:0.0074:0:1 0/1:144:17:11,6:74,53:127,17:0.1181:2,2:27.7:1:30.1:1:0.7939:1.31:60:34:0.1206:0:1.3 +11 101981552 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11932;SOR=Inf;LSEQ=CCCTCGCTCGCCTGGGTCAG;RSEQ=GGGTGCGCGTCGGGGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:93,72:165,0:0:2,0:24:1:31:1:1:0:60:81.5:1:0:0.3 0/1:161:3:2,1:87,71:158,3:0.0186:2,2:18.3:1:23.3:1:1:1.63:60:2:0.0128:0:2 +11 101981563 . CG C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=CTGGGTCAGGGGGTGCGCGT;RSEQ=GGGGAGGCAGAAGCCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:101,83:184,2:0.0108:2,2:19.5:1:30.5:1:1:1.21557:60:4:0.0109:0:0 0/0:180:0:0,0:93,87:180,0:0:2,0:28:1:29:1:1:0:60:59:1:0:0.3 +11 101981571 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22771;SOR=0;LSEQ=GGGGGTGCGCGTCGGGGGAG;RSEQ=CAGAAGCCATGGATCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:102,90:192,2:0.0103:2,2:24.5:1:30:1:1:1.1326:60:4:0.0105:0:1.5 0/0:212:0:0,0:105,106:211,0:0:2,0:24.9:1:30.1:1:1:0:59.5:51.75:0.9952:0:0.3 +11 101981599 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11329;SOR=Inf;LSEQ=CATGGATCCCGGGCAGCAGC;RSEQ=GCCGCCTCAACCGGCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:100,124:224,0:0:2,0:26:1:30.3:1:1:0:58.8:111:1:0:0.3 0/1:211:3:2,1:91,117:208,3:0.0142:2,2:17:1:25.7:1:0.58407:2.56:58.3:6:0.015:0:1.3 +11 101981600 . G T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05331;SOR=Inf;LSEQ=ATGGATCCCGGGCAGCAGCC;RSEQ=CCGCCTCAACCGGCCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:97,123:220,0:0:2,0:26.5:1:30.9:1:1:0:58.8:35.667:1:0:0.3 0/1:205:4:2,2:87,114:201,4:0.0195:2,2:29.3:1:31:1:1:1.31:34:8:0.0202:0:1.5 +11 101981623 . G A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12734;SOR=0;LSEQ=GCCTCAACCGGCCCCCCAGG;RSEQ=CCAAGGGCAGCCGCCTTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:4:1,3:71,104:175,4:0.0223:2,2:17.5:1:31.8:1:0.64951:2.04066:60:8:0.0229:0:1 0/0:153:0:0,0:61,92:153,0:0:2,0:25.5:1:31.2:1:1:0:58:37.25:1:0:0.4 +11 101981648 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.24648;SOR=Inf;LSEQ=GGGCAGCCGCCTTCGCAGCC;RSEQ=CCGCAGGGGCAGGGCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:36,68:104,0:0:2,0:21.7:1:31.3:1:1:0:59.9:33.667:1:0:0.3 0/1:106:3:2,1:41,62:103,3:0.0283:2,2:27.7:1:27:1:0.5647:2.99:55:6:0.0286:0:1.7 +11 101981681 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2357;SOR=Inf;LSEQ=GGCCCGCCGTCCGGACCCGG;RSEQ=CAACCGGCACCCGCGGCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:98,35:133,0:0:2,0:11.4:1:32.1:1:1:0:60:132:1:0:0.2 0/1:126:2:1,1:86,38:124,2:0.0159:2,2:13.5:1:30.5:1:0.52495:2.24694:60:4:0.016:0:1 +11 101981687 . G C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49839;SOR=0;LSEQ=CCGTCCGGACCCGGGCAACC;RSEQ=GCACCCGCGGCGACCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:120,34:154,2:0.0128:2,2:8:1:29.5:1:0.3995:3.49292:60:4:0.0131:0:1 0/0:155:0:0,0:110,44:154,0:0:2,0:13.7:1:29.6:1:1:0:60:50.333:0.9934:0:0.2 +11 101981695 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61847;SOR=0.48365;LSEQ=ACCCGGGCAACCGGCACCCG;RSEQ=GGCGACCCAGGCGGCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:135,32:167,2:0.0118:2,2:27:1:29:1:0.35334:4.1697:60:4:0.0119:0:1 0/0:174:1:0,1:128,44:172,1:0.0057:2,0:1:0:23:0:0.26012:0:60:2:0.0058:0:1 +11 101981950 . CG C 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.68657;SOR=0.52018;LSEQ=CCGTCGGGCGGGCCTCAGAC;RSEQ=GGGGGGCGCTCGGGAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:4:0,4:72,270:342,4:0.0115:2,0:33.5:1:32.8:1:0.58397:0:60:8:0.0116:0:0 0/0:332:2:0,2:83,247:330,2:0.006:2,0:33.5:1:32:1:1:0:60:4:0.0061:0:0.5 +11 101981959 . G A 43 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.08162;LSEQ=GGGCCTCAGACCGGGGGGGC;RSEQ=CTCGGGAGCCGCGGCCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:47,244:291,3:0.0102:2,2:21:1:29.3:1:0.07312:10.25:60:6:0.0104:0:1 0/1:272:3:2,1:49,220:269,3:0.011:2,2:18.7:1:27.7:1:0.09123:8.88:60:6:0.0114:0:1 +11 101982041 . T TGGA 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.05027;SOR=0.40429;LSEQ=GTGGGGGTCCCGAGGCGAAG;RSEQ=GGAACTGGAGTCGTCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:53:1,52:0,19:19,53:0.7361:1,1:24.3:1:30.9:1:1:0:59.9:106:0.7361:0.1806:0.3 1/0:36:19:0,19:0,17:17,19:0.5278:1,1:17.5:1:30.7:1:1:0:60:38:0.5278:0.25:0 +11 101982250 . GA G 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGAAGGAAGGGGGTGGG;RSEQ=AAAGTCGGGCCTGGGCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:24.3:1:33.7:1:1:0:60:6:1:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 101984718 . A G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01456;SOR=5.14418;LSEQ=ATATAATATTAAAAGTATCC;RSEQ=TTTGAAAACCTGTGTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:12:12,0:29,0:29,12:0.2927:1,0:25.3:1:31.5:1:1:0:57.8:24:0.2927:0:1.1 1/0:16:11:11,0:4,1:5,11:0.6875:2,0:24.7:1:30.5:1:0.3125:0:60:22:0.6875:0:1.2 +11 101985302 . C T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00202;SOR=9.44239;LSEQ=GTTTGGTATGACCTAAATAC;RSEQ=TTTGTTAGTATGGGTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:0,27:27,3:0.1:1,0:11:1:31.7:1:1:0:60:6:0.1034:0:1 1/0:19:10:0,10:0,9:9,10:0.5263:0,0:19.2:1:30.5:1:1:0:60:20:0.5263:0:1 +11 102019959 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18958;SOR=Inf;LSEQ=GCACATTTAGATAGGAGATC;RSEQ=CCAGCCATTGGAGTCAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:144,33:177,0:0:2,0:25.3:1:30.6:1:1:0:59.8:176:1:0:0.1 0/1:137:2:2,0:110,25:135,2:0.0146:2,0:25.5:1:30:1:1:0:60:4:0.0146:0:1 +11 102019970 . G T 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25142;SOR=0;LSEQ=TAGGAGATCACCAGCCATTG;RSEQ=AGTCAATCTGCAACTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:165,51:216,3:0.0137:2,2:12.7:1:20.3:1:0.14605:6.40079:57.7:2:0.0093:0:3.3 0/0:192:0:0,0:146,46:192,0:0:2,0:21.9:1:30.3:1:1:0:60:47:1:0:0.1 +11 102020070 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=14.03163;LSEQ=ATGGTTTGTACAGGGAGATG;RSEQ=AATAAGATGGGTATGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:66:27,39:184,252:436,66:0.1312:2,2:22.8:1:30.2:1:0.89404:1.05458:60:65:0.1308:0:1.1 1/0:444:302:143,159:62,80:142,302:0.6802:2,2:25.9:1:29.2:1:0.47691:1.16:60:99.667:0.6811:0:1.1 +11 102020234 . G A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=36.0863;LSEQ=GAGGGGAAAGACTAACATCA;RSEQ=TTATGTTTAAGGGAAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:0,3:0,22:22,3:0.12:1,0:15:1:33.3:1:1:0:60:6:0.12:0:1 1/1:20:17:0,17:0,3:3,17:0.85:0,1:25.2:1:30.3:1:1:0:60:34:0.85:0:1 +11 102033146 . C T 64 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10827;SOR=5.54202;LSEQ=ATAAGAATTGTTTTTGGAAC;RSEQ=TGGTATTTGTTTCCTAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:1:0,1:325,179:504,1:0.002:2,0:1:0:25:0:0.35644:0:60:2:0.002:0:1 0/1:459:5:1,4:285,169:454,5:0.0109:2,2:5:1:27.6:1:0.06939:6.71865:60:10:0.0111:0:1.8 +11 102033351 . G A 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21346;SOR=Inf;LSEQ=TGGAGTAATGCTTACGCATT;RSEQ=GTAAAAGTTGATGTGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:22,194:216,0:0:2,0:23.6:1:31.6:1:1:0:59.9:53:1:0:0.1 0/1:186:2:1,1:32,152:184,2:0.0108:2,2:11.5:1:22.5:1:0.32415:4.69:60:4:0.0108:0:1 +11 102056589 . A G 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29788;SOR=0;LSEQ=TTAGTGGAGAAGAAGCAGGT;RSEQ=TATAGGTTTACCTTTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:4,0:27,1:28,4:0.125:1,0:33.3:1:33.5:1:1:0:60:8:0.1333:0:1.3 0/0:14:0:0,0:13,1:14,0:0:1,0:24.7:1:26.7:1:1:0:60:13:1:0:0 +11 102056690 . C CT 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14249;SOR=0;LSEQ=TAAATTAGTACCCCCTCCCA;RSEQ=TTTTTTTTAGGTGCACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:4:3,1:183,2:185,4:0.0211:1,2:33:1:32.8:1:0.06248:27.88466:60:8:0.0217:0:0.3 0/0:137:0:0,0:130,5:135,0:0:1,0:27.4:1:31.6:1:1:0:59.4:44:1:0:0.5 +11 102056907 . AT A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0032;SOR=Inf;LSEQ=TTAGATGCTTTTGGTTGCTA;RSEQ=TTTTTTTGTAAATATACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:136,352:488,0:0:2,0:23.3:1:30.3:1:1:0:60:60:1:0:0.1 0/1:468:8:4,4:140,320:460,8:0.0171:2,2:28:1:30.6:1:0.25795:2.28:59.4:16:0.0172:0:0.3 +11 102057068 . C A 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00188;SOR=0.07796;LSEQ=GAATCAGATTTTTAGGGCTC;RSEQ=TCAGGTTGGGGTGGGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:0,13:0,6:6,13:0.6842:0,1:23.6:1:32.8:1:1:0:58.2:26:0.7222:0:1.2 0/1:15:2:0,2:1,12:13,2:0.1333:1,0:7:1:30:1:1:0:60:4:0.1333:0:1 +11 102076600 . A AT 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.02849;SOR=0.33242;LSEQ=TCACTAGTTTTTTAGGACAG;RSEQ=TTTTTTTTTTCTTTTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:17:13,4:176,36:212,17:0.0742:2,2:30.8:1:30.1:1:0.50762:1.50128:59.7:16:0.0734:0.0044:1.1 0/1:193:5:5,0:141,47:188,5:0.0259:2,0:22.8:1:30.6:1:0.33761:0:60:10:0.0265:0:0 +11 102077200 . G A 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11111;SOR=0;LSEQ=TTATTAATAACTTACGTGGC;RSEQ=GGATACACCAATATGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:19.9:1:30:1:1:0:60:16:1:0:1.1 0/0:1:0:0,0:0,1:1,0:0:0,0:44:0:32:0:1:0:60:2:1:0:0 +11 102080228 . G A 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTAAAGTAATTTTTATCC;RSEQ=TCTTATTTTTTACTCTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:648:0:0,0:359,288:647,0:0:2,0:24.3:1:30.3:1:1:0:60:37.059:0.9984:0:0.2 0/1:654:28:14,14:336,289:625,28:0.0428:2,2:25.1:1:28.4:1:0.70363:1.16236:59.5:27:0.0417:0:1.3 +11 102080325 . GA G 216 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.01023;SOR=0.63844;LSEQ=TATCTGATGTTTTAGCACTG;RSEQ=AAAAAAAAAAAAAAGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:112:21,91:80,108:188,112:0.3068:2,2:32.5:1:31.8:1:3e-05:3.19778:59.8:55:0.3073:0:0.7 0/1:336:74:24,50:75,142:217,74:0.2202:2,2:31.6:1:30.1:1:0.77784:1.10003:59.8:23.667:0.2185:0:0.6 +11 102094001 . A G 42 d5;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=19.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACAAAAAAAAAAAAAAAA;RSEQ=AAGAAGAATTTTTTTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:19.7:1:27:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 102094424 . C T 182 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=31.03953;LSEQ=CAAAATCCAGTGTCTTCTCC;RSEQ=GGGATGTCTCAGGAATTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:855:3:1,2:434,417:851,3:0.0035:2,2:28.3:1:30:1:0.61764:2.0798:42.7:6:0.0036:0:1 0/1:740:73:37,36:307,360:667,73:0.0986:2,2:25.8:1:29.5:1:0.46089:1.20:47.6:72:0.0977:0:1.1 +11 102094548 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27388;SOR=0;LSEQ=CTTTAAAATCATTCTGCTTA;RSEQ=TGCTTGTAATAGGCTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:3:1,2:20,171:191,3:0.0155:2,2:31.3:1:25.3:1:0.2922:4.22:60:2:0.0104:0:3.3 0/0:133:0:0,0:19,114:133,0:0:2,0:21.9:1:31.4:1:1:0:60:266:1:0:0.1 +11 102094585 . CA C 33 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.23506;SOR=4.42025;LSEQ=TTTGGAACATCTGTGTGGGC;RSEQ=AAAACCATAGCTGTAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:1:0,1:4,101:105,1:0.0094:1,0:18:0:34:0:1:0:60:2:0.0097:0:0 0/1:49:2:0,2:0,47:47,2:0.0408:1,0:21:1:33:0:1:0:60:4:0.0408:0:0 +11 102098001 . G C 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GAGCTGCCAGCTTCAATTAG;RSEQ=ATTAACTTGTCTATTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:5,8:0.6154:0,0:25:1:33.9:1:1:0:60:16:0.6154:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:21.5:1:32.5:1:1:0:60:4:1:0:0 +11 102098113 . A C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04571;SOR=Inf;LSEQ=ACTAATCCTCTTTGAGAATT;RSEQ=TGTTGCTGCTCAGCAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:104,2:106,0:0:1,0:23.4:1:28.4:1:1:0:60:25.5:1:0:0.1 0/1:60:3:3,0:57,0:57,3:0.05:1,0:27.3:1:32.3:1:1:0:60:6:0.0508:0:1.3 +11 102098343 . G A 55 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07045;SOR=0;LSEQ=TTTATTCCTCTTAGTAACCT;RSEQ=ACTTAACAGTGGGATATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:5:4,1:143,341:484,5:0.0102:2,2:11.2:1:23.8:1:0.03031:9.49:60:4:0.0083:0:1.8 0/0:387:0:0,0:127,260:387,0:0:2,0:23:1:30.5:1:1:0:60:76.4:1:0:0.3 +11 102098354 . G C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.06981;LSEQ=TAGTAACCTGACTTAACAGT;RSEQ=GGATATGTTATCACCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:403:345:85,260:10,48:58,345:0.8561:2,2:22.1:1:30.3:1:0.24585:1.57:60:171.5:0.8575:0:1.1 0/1:301:88:29,59:61,151:212,88:0.2924:2,2:24.5:1:29.3:1:0.49096:1.22:60:87:0.291:0:1.1 +11 102098365 . T A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06976;SOR=Inf;LSEQ=CTTAACAGTGGGATATGTTA;RSEQ=CACCAGGTCTCATAAGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:61,262:323,0:0:2,0:22.4:1:30.3:1:1:0:60:79.75:1:0:0.9 0/1:227:3:2,1:59,165:224,3:0.0132:2,2:14.7:1:22:1:0.17661:5.54:60:2:0.009:0:1.3 +11 102100039 . G C 58 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TATATTTAAGGCCAAGGTAG;RSEQ=TCTATACCACTCATGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:29:1:29.3:1:1:0:60:3:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 102100367 . C A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09225;SOR=Inf;LSEQ=CCTGTGCATTTCTCTGTGCT;RSEQ=ATATGATACAGCCCTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:249,64:313,0:0:2,0:20.4:1:31.9:1:1:0:60:312:1:0:0.1 0/1:259:3:2,1:200,56:256,3:0.0116:2,2:24:1:21.7:1:0.52715:1.78111:60:2:0.0078:0:2.7 +11 102195124 . A G 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCATAGAAATAAAAATAAT;RSEQ=AAAAATTTTTCATTTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:180,1:181,0:0:1,0:23.3:1:28.7:1:1:0:59.6:59.333:1:0:0.1 0/1:126:17:17,0:108,1:109,17:0.1349:1,1:20.4:1:31.4:1:1:0:60:34:0.136:0:1.1 +11 102196116 . TA T 121 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.28341;SOR=0.56912;LSEQ=AAGAAACTGAATCTGCTAAT;RSEQ=AAAAAAATATATTTCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:933:14:4,10:422,497:919,14:0.015:2,2:35.9:1:31.9:1:0.28056:2.12109:60:28:0.0152:0:0 0/0:931:8:4,4:416,507:923,8:0.0086:2,2:27.3:1:31.6:1:1:1.22:60:16:0.0087:0:0 +11 102197189 . G A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03646;SOR=Inf;LSEQ=CAAGTGTGGGTTTTTATCAC;RSEQ=TGGGTAAGAAACTTAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:86,139:225,0:0:2,0:25.4:1:31.2:1:1:0:60:74:1:0:0.1 0/1:283:6:5,1:114,163:277,6:0.0212:2,2:10.8:1:26.2:1:0.08583:7.10:60:12:0.0214:0:1 +11 102197221 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19346;SOR=0;LSEQ=CTTAATGTACTAACTAAAAT;RSEQ=TCAGCTTCAAAAAGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:19,91:110,2:0.0179:2,2:18.5:1:28.5:1:0.32658:4.69:60:4:0.0179:0:1 0/0:142:0:0,0:33,109:142,0:0:2,0:21.8:1:28.8:1:1:0:60:70:1:0:0.1 +11 102197235 . GT G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.18664;SOR=0;LSEQ=TAAAATATCAGCTTCAAAAA;RSEQ=TTTTTACACTCTCCTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:6,64:70,2:0.0278:2,2:21:1:29.5:1:0.18623:9.95:60:4:0.0282:0.0139:0.5 0/0:94:0:0,0:10,84:94,0:0:2,0:23:1:29.3:1:1:0:60:93:1:0:0 +11 102199589 . TTA T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=11.000;MSILEN=2;SSF=0.23632;SOR=1.2992;LSEQ=GATAAGATTTCTATTTTAAT;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:69:55,14:121,17:138,69:0.3301:2,2:21.9:1:30.9:1:0.14981:1.8063:58.9:22:0.322:0.0718:1.1 0/1:169:66:50,16:80,18:98,66:0.3905:2,2:21.4:1:29.7:1:0.43301:1.41907:59:65:0.3892:0.1124:1.5 +11 102199609 . ATA TTTT 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.25873;SOR=0;LSEQ=TTATATATATATATATATAT;RSEQ=TTTTTTTTTTCTGCAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:3:2,1:188,61:249,3:0.0115:2,2:30.3:1:32.7:1:0.57307:1.53807:60:6:0.0119:0:2 0/0:207:0:0,0:144,56:200,0:0:2,0:24.2:1:27:1:1:0:58.8:14.385:0.9689:0:1.4 +11 102199610 . TA T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.82432;SOR=0.87496;LSEQ=TATATATATATATATATATA;RSEQ=TTTTTTTTTTCTGCAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:13:8,5:96,34:130,13:0.0489:2,2:26.5:1:31.8:1:0.34201:1.75695:60:26:0.0884:0:0 0/1:186:8:5,3:15,3:18,8:0.043:2,2:29.6:1:29.4:1:0.33013:2.86039:57.3:16:0.0473:0:0.8 +11 102199611 . A AT 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.13483;SOR=0.31106;LSEQ=ATATATATATATATATATAT;RSEQ=TTTTTTTTTTCTGCAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:9:9,0:96,34:130,9:0.0338:2,0:32.3:1:31.4:1:0.11272:0:58.9:18:0.0612:0:0.3 0/1:186:2:1,1:15,3:18,2:0.0108:2,2:31:1:25:1:0.36842:4.47215:60:4:0.0118:0:1 +11 102199792 . AT A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.21978;SOR=Inf;LSEQ=TTATAATTTACGATGAATGC;RSEQ=TTTCAAATATACTGTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:3,146:149,0:0:1,0:23.1:1:30.8:1:1:0:60:48.667:1:0:0 0/1:132:2:1,1:7,123:130,2:0.0152:2,2:18:1:27:1:0.11797:16.50:60:4:0.0153:0.0076:0.5 +11 102202053 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17063;SOR=Inf;LSEQ=TGAAAAATATACTCATCTAG;RSEQ=ATATCTGAAAATATACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:12,199:211,0:0:2,0:25:1:32.6:1:1:0:60:210:1:0:0 0/1:149:2:0,2:12,135:147,2:0.0134:2,0:12.5:1:31:1:1:0:60:4:0.0135:0:1 +11 102206417 . T C 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=AAGACAGGGTATTGCTATGT;RSEQ=GCCCAGTCTGGTCTCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:34.8:1:32.8:1:1:0:60:10:0.625:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:29:1:31:0:1:0:60:4:1:0:0 +11 102206585 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51828;SOR=0;LSEQ=CCTAGCAATCAACATCAATG;RSEQ=CTTACTGATTACGAATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:106,4:110,2:0.0179:1,2:20.5:1:29.5:1:0.08768:23.81438:60:4:0.0183:0:1 0/0:74:0:0,0:74,0:74,0:0:1,0:22.6:1:31.3:1:1:0:60:36:1:0:0.1 +11 102206592 . G T 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16886;SOR=Inf;LSEQ=ATCAACATCAATGCCTTACT;RSEQ=ATTACGAATTAAAGATAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:119,5:124,0:0:1,0:25.5:1:32.9:1:1:0:60:123:1:0:0.1 0/1:87:2:2,0:85,0:85,2:0.023:1,0:6:1:31:1:1:0:60:4:0.0233:0:1 +11 102207024 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=7.42449;LSEQ=CTCTTATTAATAATTTATGA;RSEQ=TACTGAAAATAATTCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:54:1,53:3,66:69,54:0.439:1,1:21.2:1:30.9:1:0.63022:2.39349:58.8:26:0.4333:0:1 1/1:103:88:3,85:2,13:15,88:0.8544:2,1:22.8:1:30:1:0.15292:4.26662:58.5:87:0.8614:0:1 +11 102207318 . C CA 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39095;SOR=0.32327;LSEQ=TTGGGTGACAGACTCTGTCT;RSEQ=AAAAAAAAATCAATCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:4:3,1:63,5:68,4:0.0556:2,2:20.5:1:30.5:1:0.29945:4.06382:60:8:0.0556:0:0 0/1:54:1:1,0:50,3:53,1:0.0185:2,0:13:0:31:0:1:0:60:2:0.0189:0:0 +11 102207593 . C T 141 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=26.65506;LSEQ=TTTATTTTCTTAGTTTTTCA;RSEQ=TGAAGAAGCAAACTGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:905:1:0,1:444,457:901,1:0.0011:2,0:1:0:25:0:1:0:60:2:0.0011:0:1 0/1:872:25:14,11:433,414:847,25:0.0287:2,2:22.4:1:30.4:1:0.68814:1.22:60:50:0.0289:0:1.1 +11 102207851 . G A 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.99144;LSEQ=TGAAGAAGAACCAAAACATC;RSEQ=TCTAAACTTTAGAATTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:915:346:107,239:184,384:568,346:0.3781:2,2:24.6:1:31:1:0.66107:1.07024:59.9:172:0.3805:0:1.1 1/0:883:693:224,469:65,122:187,693:0.7848:2,2:23.4:1:29.8:1:0.53983:1.11538:60:172.25:0.7883:0:1.1 +11 102220662 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50996;SOR=0;LSEQ=GAGTATAATGGAAGATAGCA;RSEQ=GATCTTGTCAGATTGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:158,2:160,2:0.0123:1,0:20:1:29.5:1:1:0:60:4:0.0124:0:1 0/0:119:0:0,0:118,1:119,0:0:1,0:23:1:31.8:1:1:0:60:238:1:0:0.1 +11 102221242 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49837;SOR=Inf;LSEQ=GGACCTGGAGATAGGGTAGC;RSEQ=TGCTTTGCCTGTGGTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:100,43:143,0:0:2,0:22:1:31.3:1:1:0:60:34.75:1:0:0.1 0/1:147:2:1,1:103,42:145,2:0.0136:2,2:38:1:29:1:0.50089:2.43545:60:4:0.0138:0:1 +11 102221559 . C CT 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.12468;LSEQ=ACGTGTTTTCAATATTTAGT;RSEQ=TTTTTTTTCCTGAAGGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:665:7:4,3:488,168:656,7:0.0105:2,2:23.3:1:30.3:1:0.38203:2.17565:60:14:0.0107:0.003:0 0/1:592:7:5,2:421,164:585,7:0.0118:2,2:26.3:1:28.7:1:1:1.02678:60:14:0.012:0:0 +11 102221882 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06359;SOR=Inf;LSEQ=TACTTTTGTAAGTCAGTTAC;RSEQ=AGTATGACCGTACATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:0,40:40,0:0:1,0:23.7:1:31.3:1:1:0:60:39:1:0:0.1 0/1:14:2:1,1:0,12:12,2:0.1429:0,2:8.5:1:32:0:0.14286:0:60:4:0.1429:0:1 +11 102248406 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49245;SOR=Inf;LSEQ=TGATTGATACCATTTTGGTT;RSEQ=AAGGAAATGCTGCGGCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:28.1:1:30.1:1:1:0:60:38:1:0:0.1 0/1:23:2:1,1:10,11:21,2:0.087:2,2:9:0:33:1:1:1.10:60:4:0.087:0:1.5 +11 102248667 . C CT 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.64792;SOR=0.49037;LSEQ=AACCAACATGAACTATTACC;RSEQ=TTTTTTTTTAATGAAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:3,0:55,2:57,3:0.05:1,0:21.7:1:34:0:1:0:60:6:0.0508:0:0 0/1:40:1:1,0:38,1:39,1:0.025:1,0:31:0:32:0:1:0:60:2:0.025:0:0 +11 102248722 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22274;SOR=Inf;LSEQ=AGTTATTTTTTGTTATTAGG;RSEQ=CTGTCACTGGAAGAACAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:150,43:193,0:0:2,0:20.6:1:29.9:1:1:0:60:95.5:1:0:0.1 0/1:173:2:1,1:126,45:171,2:0.0116:2,2:34.5:1:30:1:0.46223:2.78037:60:4:0.0116:0:1 +11 102248747 . A G 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11826;SOR=Inf;LSEQ=CACTGGAAGAACAATTGAGG;RSEQ=GGTTGCAAGAAGAACGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:174,104:278,0:0:2,0:26.2:1:30.5:1:1:0:60:68.5:1:0:0.1 0/1:269:3:2,1:165,101:266,3:0.0112:2,2:27.7:1:25:1:1:1.22:52.7:2:0.0076:0:3.3 +11 102248753 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12065;SOR=Inf;LSEQ=AAGAACAATTGAGGAGGTTG;RSEQ=AAGAAGAACGAACTTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:181,121:302,0:0:2,0:27:1:32.2:1:1:0:60:99.667:1:0:0.1 0/1:296:3:1,2:170,123:293,3:0.0101:2,2:21.3:1:25.3:1:0.57537:2.75478:60:6:0.0103:0:1.7 +11 102671697 . C T 81 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01669;SOR=11.53145;LSEQ=TCCGGACTATTTCCAGGCAG;RSEQ=CAGATTATTTCCGTGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:7,9:16,1:0.0588:2,0:19:0:32:0:1:0:60:2:0.0625:0:1 0/1:16:7:3,4:4,4:8,7:0.4375:2,2:28.1:1:28.9:1:1:1.30792:60:14:0.4375:0:1.1 +11 102916090 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2438;SOR=Inf;LSEQ=GAAAGGTGATATTGTAGACA;RSEQ=CAAGGGAATAGGTTGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:28,33:61,0:0:2,0:24.9:1:29.6:1:1:0:59.3:14.25:1:0:0.1 0/1:60:2:1,1:31,27:58,2:0.0333:2,2:9:0:31:0:1:1.1455:60:4:0.0339:0:1 +11 102916105 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24436;SOR=Inf;LSEQ=AGACATCAAGGGAATAGGTT;RSEQ=AAAAAGGAGTGCCCACAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:31,36:67,0:0:2,0:28.4:1:32.2:1:1:0:59.4:134:1:0:0.1 0/1:66:2:1,1:35,29:64,2:0.0303:2,2:8:1:30:1:1:1.20344:60:4:0.0303:0:1 +11 105610204 . GA TG 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2205;SOR=Inf;LSEQ=AACACTGAAAGTACTTAATT;RSEQ=TATATAATTAAAGTGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:84,86:170,0:0:2,0:25.5:1:31.9:1:1:0:59.7:84:1:0:0.7 0/1:151:2:1,1:71,77:148,2:0.0132:2,2:27:1:32.3:1:1:1.08:60:4:0.0132:0:1 +11 105610205 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00273;SOR=2.03124;LSEQ=ACACTGAAAGTACTTAATTG;RSEQ=TATATAATTAAAGTGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:172:95:45,50:39,38:77,95:0.5523:2,2:24.9:1:31.7:1:0.75925:1.13948:60:94:0.5595:0:1.1 1/0:151:108:50,58:22,19:41,108:0.7152:2,2:24.3:1:30.8:1:0.4659:1.34048:60:216:0.7347:0:1.2 +11 105610267 . T C 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=Inf;LSEQ=AACTTGTCATTTATGGTGAT;RSEQ=AGCTTCAGTAACTTTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:34,72:106,0:0:2,0:24.9:1:29.3:1:1:0:60:212:1:0:0.4 0/1:106:2:1,1:38,66:104,2:0.0189:2,2:6:0:26:1:1:1.73:60:4:0.0189:0:2 +11 105830380 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18803;SOR=Inf;LSEQ=TGCACCCTTTATGGAGAGAC;RSEQ=TTGTGATCATCTGGAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:29.8:1:29.6:1:1:0:60:14:1:0:0 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:41:0:31.5:1:1:1:60:4:0.1667:0:1.5 +11 105831145 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCACAGCCGGTGTGTTG;RSEQ=GCTGTGGGGACAAGTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:14,12:0,0:0,26:1:0,2:26.7:1:30.7:1:1:0:53.9:25:1:0:1.2 1/1:19:19:11,8:0,0:0,19:1:0,2:30.2:1:30.5:1:1:0:54.4:38:1:0:1.1 +11 105831347 . CA GG 67 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCCCCAAGGAGCTGAAA;RSEQ=GCTTCGACAGCAGGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:15:1:29.2:1:1:0:60:10:1:0.6:0.6 1/1:1:1:0,1:0,0:0,1:1:0,0:19:0:32:0:1:0:60:2:1:0:1 +11 105831672 . A G 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGTCATGCCAGCCTTCTAG;RSEQ=CAATTTTGATGAGAGAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:33.5:1:29.5:1:1:0:60:4:1:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:32.5:1:33:1:1:1.7321:60:4:0.4:0:1 +11 106361902 . T C 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TGTTGGTGCTGCTGTTGTTG;RSEQ=TGCTGCTGTTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:102,99:201,0:0:2,0:28.5:1:30:1:1:0:59.7:200:1:0:0.2 0/1:251:26:13,13:120,104:224,26:0.1036:2,2:34.3:1:32.2:1:0.83623:1.15318:54:52:0.1048:0:1.2 +11 106361916 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.19267;SOR=0;LSEQ=TTGTTGTTGCTGCTGTTGTT;RSEQ=CTGCTGCTGTTGTTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:94,104:198,2:0.01:2,2:19:1:29:1:1:1.11:60:4:0.0102:0:1 0/0:255:0:0,0:119,136:255,0:0:2,0:28.8:1:31.2:1:1:0:59.1:41.5:1:0:0.3 +11 106361974 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50187;SOR=Inf;LSEQ=TAAAATTTTTTCAGTTATTG;RSEQ=ATTTTTTTTCAGCCGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:19,60:79,0:0:2,0:24:1:31.5:1:1:0:60:38.5:1:0:0.2 0/1:96:2:1,1:28,66:94,2:0.0208:2,2:8.5:1:25:1:0.51513:2.33:60:4:0.0213:0:1 +11 106361988 . C T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.18508;LSEQ=TTATTGCATTTTTTTTCAGC;RSEQ=GAAAAGCTTCAATTGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:8:1,7:9,46:55,8:0.127:2,2:25.4:1:31:1:1:1.36327:60:16:0.1311:0:1 1/0:66:34:6,28:6,25:31,34:0.5152:2,2:29:1:29.8:1:1:1.11804:60:68:0.5231:0:1 +11 107025440 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.47826;SOR=Inf;LSEQ=ATGATAAGTAATGTCAGATC;RSEQ=TTCAGTCACATTCATGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:11,0:0:2,0:22.6:1:29.5:1:1:0:60:22:1:0:0 0/1:12:2:1,1:3,7:10,2:0.1667:2,2:11.5:1:27.5:1:1:2.16:54:4:0.1667:0:1 +11 108098299 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50088;SOR=0;LSEQ=ATATACATATACATATATAT;RSEQ=CCTATATGTATTTTTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:109,23:132,2:0.0148:2,2:13:0:34:0:0.32724:4.66061:60:4:0.0149:0:1 0/0:116:0:0,0:95,21:116,0:0:2,0:22.6:1:27.8:1:1:0:60:57:1:0:0.1 +11 108098301 . C T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.22113;SOR=Inf;LSEQ=ATACATATACATATATATAC;RSEQ=TATATGTATTTTTTTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:112,26:138,0:0:2,0:23.5:1:31.3:1:1:0:60:137:1:0:0.1 0/1:123:2:1,1:98,23:121,2:0.0163:2,2:16.5:1:23:1:0.35346:4.19239:60:4:0.0165:0:1 +11 108098309 . A AT 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.48321;SOR=1.88672;LSEQ=ACATATATATACCTATATGT;RSEQ=TTTTTTTTACAGACAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:3:2,1:132,37:169,3:0.0174:2,2:13:1:28.4:1:0.5295:1.77689:60:6:0.0176:0.0116:0.3 0/1:154:5:3,2:116,33:149,5:0.0325:2,2:21.6:1:28.7:1:0.31869:2.32793:60:10:0.0331:0.013:0.2 +11 108098459 . TAA T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00258;LSEQ=AATTCAATTTTTCCTTGAAA;RSEQ=GTGTGATTAGTAACCCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:324:172:85,87:80,72:152,172:0.5309:2,2:25.7:1:32.6:1:0.57936:1.1368:60:344:0.5325:0.071:0.1 1/0:365:194:97,97:75,96:171,194:0.5315:2,2:24.9:1:31.3:1:0.24959:1.28:59.8:388:0.5315:0.0959:0.1 +11 108098576 . C G 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTAGATCGGCATTCAGATT;RSEQ=CAAACAAGGAAAATATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:149,209:358,0:0:2,0:25.1:1:31.5:1:1:0:59.9:118.333:1:0:0.1 0/1:383:27:14,13:168,188:356,27:0.0705:2,2:23.8:1:30.8:1:0.69226:1.20:60:54:0.0711:0:1.1 +11 108098647 . AT A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.20115;SOR=0;LSEQ=AAATTTATTTTACTGTCTTT;RSEQ=TTTTCTCTTTCATATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:23,117:140,2:0.0141:2,2:36.5:1:31.5:1:0.31046:5.00:60:4:0.0143:0:0 0/0:174:0:0,0:52,120:172,0:0:2,0:25.1:1:29.4:1:1:0:60:56.333:0.9883:0:0.1 +11 108099845 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21141;SOR=Inf;LSEQ=TGATGGCATGAACAGCTTTT;RSEQ=AAATTATTATAATTTAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:71,13:84,0:0:2,0:25.5:1:32.5:1:1:0:60:83:1:0:0.1 0/1:72:2:1,1:55,15:70,2:0.0278:2,2:25:1:32.5:1:0.3975:3.58204:60:4:0.0286:0:1 +11 108099886 . G A 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50071;SOR=Inf;LSEQ=TTCAACGAGTTTCTGAAATT;RSEQ=CATTTTGTTTTCTTGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:112,42:154,0:0:2,0:23:1:32.5:1:1:0:60:308:1:0:0.1 0/1:176:2:1,1:119,54:173,2:0.0114:2,2:14:0:26.5:1:0.53103:2.19277:60:4:0.0114:0:1 +11 108100105 . G GT 131 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.21496;SOR=0.6115;LSEQ=AACAGATTACTGTCGCGTGA;RSEQ=TTTTTTTTTTTTTTCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:25:2,23:12,20:32,25:0.3425:2,2:33.6:1:28.4:1:0.01322:6.68696:59.8:11.5:0.3382:0:1.9 0/1:83:20:1,19:10,39:49,20:0.241:2,1:31:1:30.2:1:0.15701:4.78873:60:40:0.2778:0:1.4 +11 108106168 . C T 32 v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTTAATTACAAAAGCAG;RSEQ=CATAAACAATAAGTAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:8,0:8,2:0.2:0,2:20:0:32:0:0.2:0:60:4:0.2222:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108106443 . T A 114 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00113;SOR=12.83217;LSEQ=CTCTTAAATTATATCATGGA;RSEQ=ACAGTGAAAGATTCATCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:1:1,0:239,143:382,1:0.0026:2,0:20:0:32:0:1:0:60:2:0.0026:0:1 0/1:430:14:6,8:259,157:416,14:0.0326:2,2:30.1:1:30:1:0.16681:2.19539:60:28:0.0326:0:1.1 +11 108106635 . G A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.02404;SOR=Inf;LSEQ=CCAAAGAAAGCACTCTGTCT;RSEQ=TATCTGTCTATATCCCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:15,129:144,0:0:2,0:21.6:1:32.4:1:1:0:59.8:143:1:0:0.1 0/1:132:5:1,4:22,105:127,5:0.0379:2,2:25.2:1:30.6:1:1:1.19:60:10:0.0379:0:1 +11 108106782 . C T 90 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAGGTGCCTGATATCAGAGC;RSEQ=GGAATTACAGTTGAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:26.3:1:30.3:1:1:0:60:16:1:0:1 1/0:4:3:1,2:0,1:1,3:0.75:0,2:15.7:1:29:1:1:0:60:6:0.75:0:1 +11 108114506 . A G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50549;SOR=0;LSEQ=TCCTGTCTTAAAGGCATTTT;RSEQ=TATAAGATAAAATTAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:28.7:1:33:1:1:0:60:6:0.3:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:9:1:29.5:1:1:0:60:8:1:0:0 +11 108114840 . T C 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTTCCAAGGCTATTCAGTG;RSEQ=GCGAGGTAATCTAATCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:202,336:538,0:0:2,0:25.7:1:30.3:1:1:0:60:178.333:1:0:0.1 0/1:674:27:12,15:275,371:646,27:0.0401:2,2:23:1:30.1:1:0.84536:1.08:60:54:0.0402:0:1.4 +11 108115360 . AT A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.07181;SOR=3.01604;LSEQ=CAGTGTGAAGTAATGCTGTG;RSEQ=TTTTTTTTTTAATGAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:39:37,2:11,0:11,39:0.6964:0,2:22.6:1:31.9:1:1:0:58.8:78:0.6964:0.1429:0.3 1/1:32:28:28,0:4,0:4,28:0.875:0,1:28:1:30.9:1:1:0:60:56:0.875:0.0938:0.2 +11 108115419 . G GT 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54506;SOR=0.75036;LSEQ=TGTTTGAAAATTAGGGTTTT;RSEQ=TTTTTTTTTCTTTCAGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:17:14,3:132,12:144,17:0.1056:2,2:19.7:1:29.8:1:0.19886:2.34083:60:34:0.1069:0.0373:0.4 0/1:123:10:8,2:97,13:110,10:0.0813:2,2:17.8:1:27.4:1:0.61164:1.85382:60:9:0.0744:0.0244:0 +11 108115451 . C T 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAGCATACCACTTCATAA;RSEQ=TGTTCAGTTTGTACAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:207,57:264,0:0:2,0:24.9:1:31.8:1:1:0:60:25.4:1:0:0.1 0/1:259:27:19,8:169,63:232,27:0.1042:2,2:22:1:30.5:1:0.82072:1.12894:60:54:0.1071:0:1.1 +11 108115456 . C T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05962;SOR=0;LSEQ=CATACCACTTCATAACTGTT;RSEQ=AGTTTGTACAGTTTGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:4:1,3:211,61:272,4:0.0145:2,2:11.5:1:28.8:1:0.04002:10.2621:60:8:0.0151:0:1 0/0:281:0:0,0:198,83:281,0:0:2,0:24.9:1:30.6:1:1:0:60:55.2:1:0:0.2 +11 108115594 . C T 128 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.05218;LSEQ=AGACTTTGGCTGTCAACTTT;RSEQ=GAATTCGAGTGTGTGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:856:18:11,7:411,427:838,18:0.021:2,2:25.4:1:30.8:1:0.34829:1.63:58.7:17:0.0201:0:1 0/0:894:1:0,1:444,448:892,1:0.0011:2,0:1:0:25:0:1:0:60:2:0.0011:0:1 +11 108115778 . T G 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06091;SOR=Inf;LSEQ=AAAGGAAATGTTTACTGTTT;RSEQ=GAATTTGCTTCTTCATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:42,148:190,0:0:2,0:24.6:1:30.7:1:1:0:60:94:1:0:0.1 0/1:193:5:1,4:55,133:188,5:0.0259:2,2:16.2:1:30.8:1:1:1.65029:60:10:0.026:0:1 +11 108117335 . C T 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACACTAGTTGAAGGAACT;RSEQ=GTAATATTTTTCTCTTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:29.7:1:32.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108117897 . A AT 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.12246;LSEQ=CATTTAGAAATTTCCTGTTA;RSEQ=TTTTTTTTTTAAACTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:0,3:15,122:137,3:0.0214:2,0:20:1:29.7:1:1:0:51.7:6:0.0217:0:1.7 0/1:125:3:0,3:15,106:121,3:0.024:2,0:21.3:1:31:0:1:0:60:6:0.0244:0:0 +11 108119677 . C T 43 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21441;SOR=4.07974;LSEQ=CAGGTTTTTAATGAAGATAC;RSEQ=AGATCCTTGGAGATTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:1:0,1:281,95:376,1:0.0026:2,0:1:0:24:0:0.25464:0:60:2:0.0028:0:1 0/1:373:4:1,3:248,120:368,4:0.0107:2,2:9:1:21.8:1:0.10754:6.16783:60:3:0.0084:0:2 +11 108121410 . C CT 163 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.17867;SOR=0.60113;LSEQ=GGAATAGTTTTCAAATTATC;RSEQ=TTTTTTTTTTTTTTTAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:32:31,1:48,1:49,32:0.3299:1,1:29.9:1:32.6:1:1:1.53975:58.8:64:0.3368:0:0.9 0/1:79:18:17,1:51,2:53,18:0.2278:1,1:26.4:1:31.2:1:1:1.4907:59.9:36:0.2368:0:1.7 +11 108121846 . GAC G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.50469;SOR=0;LSEQ=CTTACAGATAAACACACACA;RSEQ=ACACACACACTCACATATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:0,2:10,117:127,2:0.0155:2,0:22:1:32:0:1:0:60:4:0.0159:0:1.5 0/0:102:0:0,0:10,92:102,0:0:2,0:23.3:1:29.1:1:1:0:59.8:101:1:0:0 +11 108122592 . C G 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGCTGTTTGACTTTGGCA;RSEQ=TGACCACCAGTATAGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:0:0,0:395,319:714,0:0:2,0:25.9:1:32.4:1:1:0:60:78.333:1:0:0.1 0/1:729:27:14,13:395,305:700,27:0.037:2,2:30.8:1:31.9:1:0.69471:1.20226:60:54:0.0374:0:1.1 +11 108122659 . G T 138 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=6.3397;LSEQ=AAATATGTGTGAAGTAAATA;RSEQ=AAGCTTTTCTTTAAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:712:4:2,2:318,388:706,4:0.0056:2,2:20.5:1:29.8:1:1:1.22:60:8:0.0057:0:1 0/1:809:28:13,15:350,431:781,28:0.0346:2,2:27.3:1:28.9:1:1:1.07:60:56:0.035:0:1.1 +11 108122786 . G GT 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24858;SOR=0;LSEQ=AAGTTCATTAGCATGCTGCT;RSEQ=TTTTTTTTGTTTGTTTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:3:1,2:57,158:215,3:0.0136:2,2:29.3:1:30.7:1:1:1.38:58.3:6:0.0138:0:1 0/0:211:0:0,0:62,147:209,0:0:2,0:25.4:1:31.5:1:1:0:60:208:0.9952:0:0.1 +11 108122828 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5007;SOR=0;LSEQ=GGCTCTCTCCACTTATTTGA;RSEQ=GCCAGATGGCTTTATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:8,98:106,2:0.0185:2,2:34:1:29:1:0.16044:11.61:60:4:0.0189:0:1 0/0:92:0:0,0:16,76:92,0:0:2,0:22.2:1:29.5:1:1:0:60:45:1:0:0.1 +11 108123189 . C A 58 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGATAAAGGAATGGAGTC;RSEQ=CTCGTCCACTTAACCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:11:1:29:1:1:0:52.5:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108123390 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20814;SOR=Inf;LSEQ=CTCCTTAAATTGTCCTTTTA;RSEQ=ATATTAAGAAATTTAGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:27,1:28,0:0:1,0:25.9:1:32.8:1:1:0:60:27:1:0:0.2 0/1:24:2:1,1:22,0:22,2:0.0833:1,2:29:0:27.5:1:0.08333:0:60:4:0.087:0:1 +11 108123515 . TA T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12371;SOR=Inf;LSEQ=TTACATGGCTTTTGGTCTTC;RSEQ=AGTGAAGCTTTTTGTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:180,71:251,0:0:2,0:24.9:1:29.2:1:1:0:60:502:1:0:0.1 0/1:259:4:1,3:175,80:255,4:0.0154:2,2:8.5:1:28.5:1:0.09831:6.5112:60:8:0.0156:0.0077:0.3 +11 108123719 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49846;SOR=Inf;LSEQ=TAATTTTAGCTGGGTAGTAG;RSEQ=TGCATCTTAATAATTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:2,83:85,0:0:1,0:22.6:1:33.2:1:1:0:60:84:1:0:0 0/1:94:2:1,1:3,89:92,2:0.0213:1,2:22.5:1:27.5:1:0.08373:25.83:60:4:0.022:0:1 +11 108124299 . G A 97 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAATTTGCCTTTGAGATT;RSEQ=TAACTTGTATTTTTTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:0,12:1:0,0:23.6:1:27.1:1:1:0:58.2:11:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108127010 . C T 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCTTGGCTGCTACTGTTA;RSEQ=ATGGGTGTAATAGCTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:901:0:0,0:414,487:901,0:0:2,0:25.7:1:31.9:1:1:0:60:52:1:0:0.1 0/1:848:28:11,17:381,439:820,28:0.033:2,2:21.7:1:28.8:1:0.56412:1.34081:60:56:0.0334:0:1.1 +11 108127089 . A C 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00192;SOR=Inf;LSEQ=TAGGAGAATTTATACTAATA;RSEQ=AGTTTCGGATAAATTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:39,213:252,0:0:2,0:24.4:1:31.1:1:1:0:60:49.4:1:0:0.1 0/1:273:10:1,9:84,176:260,10:0.0366:2,2:29.6:1:32.1:1:0.17854:4.2785:60:20:0.0372:0:1.8 +11 108127101 . A C 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00086;SOR=Inf;LSEQ=TACTAATAAAGTTTCGGATA;RSEQ=ATTTGAATGAAATGTATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:32,177:209,0:0:2,0:23.6:1:31.1:1:1:0:60:103.5:1:0:0.1 0/1:215:11:2,9:61,143:204,11:0.0512:2,2:22.4:1:31.4:1:0.51477:1.91452:60:22:0.0514:0:2 +11 108127288 . T C 116 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTCTGGGGTACATGATG;RSEQ=AGAGCATGCAGGTTTGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:0,13:1:0,1:18.5:1:31.5:1:1:0:56.9:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108128397 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1973;SOR=Inf;LSEQ=TTCTCTGTCACCCAGGCTGG;RSEQ=GTGCAGTGGGATTGTCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:8,114:122,0:0:2,0:25.4:1:32.2:1:1:0:59.7:29.5:1:0:0 0/1:98:2:1,1:11,85:96,2:0.0204:2,2:25:1:27.5:1:0.23101:7.44:60:4:0.0204:0:1 +11 108129657 . A G 248 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00592;LSEQ=TAGAGAAAACACTGTCTGCC;RSEQ=AGAATAATTGTTTTTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:292:291:229,62:0,0:0,291:0.9966:0,2:22.8:1:30.4:1:1:0:60:144.5:0.9966:0:1.1 1/0:233:147:107,40:55,31:86,147:0.6309:2,2:23:1:29.1:1:0.1848:1.50:60:146:0.6348:0:1.1 +11 108137775 . T A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00724;SOR=0;LSEQ=TCAGGTGATCCACCTGGCTC;RSEQ=GCCTCCCAAATTGCTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:74:74,0:0,0:0,74:1:0,1:26.3:1:30.8:1:1:0:55.5:148:1:0:1.1 1/1:32:28:27,1:4,0:4,28:0.875:0,1:21.9:1:30.2:1:1:0:58.4:56:0.875:0:1 +11 108138045 . C T 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGTTAGTGATGCAAACGAA;RSEQ=CTGGAGAGAGCCAAAGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:283,443:726,0:0:2,0:26.1:1:31.9:1:1:0:60:144.2:0.9972:0:0.1 0/1:713:30:12,18:291,392:683,30:0.0421:2,2:28.4:1:28.9:1:0.85175:1.11332:60:29:0.0412:0:1.2 +11 108138214 . A AT 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01831;LSEQ=GTTCCTTTCTTATATACTTT;RSEQ=TTTTTTTTTTATTTTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:0,2:3,52:55,2:0.0351:2,0:36.5:1:32:0:1:0:60:4:0.0357:0:0 0/1:28:1:0,1:1,26:27,1:0.0357:1,0:44:0:26:0:1:0:60:2:0.0357:0:0 +11 108138923 . G GT 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATGATCATTTGTCTAAGG;RSEQ=TTTTTTTTTCTCATATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:13,0:13,2:0.1333:1,0:30.5:1:28.5:1:1:0:60:4:0.1429:0:0 0/0:3:0:0,0:3,0:3,0:0:0,0:31:1:31.7:1:1:0:60:6:1:0:0.3 +11 108139091 . C T 52 v3;p8;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01084;SOR=Inf;LSEQ=GTTAATATGACTATATATGG;RSEQ=TGTTGTGCCCTTCTCTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:211,73:284,0:0:2,0:21.8:1:32.2:1:1:0:59.8:70:1:0:0.1 0/1:195:5:0,5:141,49:190,5:0.0256:2,0:7.8:1:22.6:1:0.00142:0:60:4:0.0207:0:1.2 +11 108139183 . A G 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATCTGTCAAAGCAAGATCT;RSEQ=CTTTTCTTAGACATGCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:0:0,0:441,329:770,0:0:2,0:24.4:1:28.9:1:1:0:60:153:0.9987:0:0.1 0/1:629:28:16,12:323,276:599,28:0.0445:2,2:26.4:1:31:1:0.84694:1.14:60:56:0.0448:0:1.1 +11 108141677 . T C 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.75725;LSEQ=GTGATCTGCCTGCTTCAGCC;RSEQ=CCCAAAGTGCTGGGATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:2,0:121,0:121,2:0.0163:1,0:30:1:32:1:1:0:46.5:4:0.0163:0:1 0/1:81:1:1,0:79,1:80,1:0.0123:1,0:38:0:27:0:1:0:28:2:0.0123:0:2 +11 108141701 . G T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00312;SOR=2.00676;LSEQ=AAAGTGCTGGGATTACAGGT;RSEQ=TGAGCCACTGCACCCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:70:63,7:101,12:113,70:0.3825:2,2:21.6:1:30.8:1:1:1.07:53.9:69:0.3791:0:1.1 1/0:137:76:67,9:53,8:61,76:0.5547:2,2:26.8:1:29.4:1:1:1.12:54.7:75:0.5556:0:1.1 +11 108141940 . G A 33 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.24691;LSEQ=TAACTGATGTGTTCTGTTAA;RSEQ=CTTATAAAGTTGAACTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:3:0,3:173,178:351,3:0.0084:2,0:4.7:1:13.3:1:0.24826:0:51.7:0:0:0:3.3 0/1:286:3:0,3:146,136:282,3:0.0105:2,0:6.3:1:21:1:0.11473:0:60:2:0.0081:0:1.3 +11 108142186 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3456;SOR=3.41587;LSEQ=CTTTTGCTATCTGTGGATAC;RSEQ=AATGCAAGTTTTGTATCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:1:1,0:84,232:316,1:0.0032:2,0:1:0:27:0:0.26814:0:60:2:0.0032:0:1 0/1:280:3:2,1:74,203:277,3:0.0107:2,2:18:1:27.3:1:0.18005:5.45:60:6:0.0109:0:1 +11 108142191 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10243;SOR=Inf;LSEQ=GCTATCTGTGGATACGAATG;RSEQ=AAGTTTTGTATCCACATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:69,221:290,0:0:2,0:24.4:1:32.2:1:1:0:59.9:95.667:1:0:0.1 0/1:256:3:1,2:63,190:253,3:0.0117:2,2:14.7:1:26.7:1:1:1.51:60:6:0.0118:0:1 +11 108143182 . C T 235 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACATATTGGAAGTAACTTA;RSEQ=AATAACCTTTCAGTGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:179:179:155,24:0,0:0,179:1:0,2:23.2:1:31.5:1:1:0:59.9:178:1:0:1.1 1/0:156:124:111,13:27,5:32,124:0.7949:2,2:21.8:1:29.9:1:0.53355:1.58:60:123:0.7935:0:1.1 +11 108143456 . C G 256 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTTTTCCCGTAGGCTGATC;RSEQ=TTATTCAAAATGGGCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1029:305:172,133:394,327:721,305:0.2964:2,2:25.3:1:31.1:1:0.631:1.07:59.8:100.667:0.2967:0:1.1 0/0:925:0:0,0:500,423:923,0:0:2,0:8:0:15:0:1:0:60:0:0:0:1 +11 108148332 . T C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGCCCCTCACAGCATAG;RSEQ=CCCTCACGGCTTCCCTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:8:0:26:0:1:0:49:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:32.5:1:1:0:47.5:4:1:0:1 +11 108150207 . CT C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19778;LSEQ=TTTGTTTGTTTGTTTGCTTG;RSEQ=TGTTTTAAGATTGTTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:191:127,64:141,66:207,191:0.4799:2,2:25.2:1:32.6:1:0.74916:1.07639:60:382:0.486:0.0779:0.1 0/1:383:59:34,25:219,105:324,59:0.154:2,2:28:1:31.4:1:0.13859:1.53187:59.7:118:0.1549:0.0052:0.1 +11 108150405 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16275;SOR=Inf;LSEQ=ATCCCATAAATTACTTCACC;RSEQ=AGTTTGGTATAAGAGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:8,114:122,0:0:2,0:23.4:1:31.7:1:1:0:60:121:1:0:0 0/1:83:2:1,1:8,73:81,2:0.0241:2,2:10:1:31.5:1:0.20629:8.66:60:4:0.0241:0:1 +11 108151269 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGTGTGTGTGTGATAC;RSEQ=GGTATACAATGTGAAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:39.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108151707 . T TA 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=0;SOR=0.14483;LSEQ=TTTACATTACATTTTTTTTT;RSEQ=AATTTCTTTTTAAGTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:149:140:106,34:5,0:5,140:0.9396:0,2:24.7:1:28.7:1:0.59127:0:60:45.667:0.9448:0.2953:0.4 1/0:162:112:79,33:34,6:40,112:0.6914:2,2:23.8:1:27.7:1:0.09185:2.35502:60:55:0.6875:0.1728:0.3 +11 108151729 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10628;SOR=0;LSEQ=ATTTCTTTTTAAGTCCCATA;RSEQ=TGCTGAGAACCCTGAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:2,1:179,71:250,3:0.0119:2,2:23.3:1:24.3:1:1:1.25939:56.3:2:0.0081:0:3.3 0/0:280:0:0,0:192,88:280,0:0:2,0:23.5:1:31.1:1:1:0:60:39:1:0:0.2 +11 108151839 . T G 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGCGAAAAACAGGCTTTG;RSEQ=TTGCCCTGTGTAAATCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:0:0,0:257,267:524,0:0:2,0:26.1:1:30.1:1:1:0:59.9:73.857:1:0:0.1 0/1:564:35:16,19:241,287:528,35:0.0621:2,2:20.9:1:30.4:1:1:1.00:60:34:0.0608:0:1.1 +11 108151929 . CT C 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24873;SOR=0;LSEQ=AGTATTTTATTAGAAGCTTC;RSEQ=TAGGTCACTGTGAAATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:2,1:35,140:175,3:0.0169:2,2:21.3:1:29.3:1:0.11002:7.87:60:6:0.0171:0.0056:0 0/0:166:0:0,0:41,125:166,0:0:2,0:20.9:1:29.3:1:1:0:60:82:1:0:0.1 +11 108153361 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18185;SOR=Inf;LSEQ=GTTGTTTCTAGGTCCTACTC;RSEQ=AAATAATATTAACAAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:133,20:153,0:0:2,0:23:1:32.1:1:1:0:59.9:75.5:0.9934:0:0.1 0/1:115:2:1,1:100,13:113,2:0.0174:2,2:24:1:28:1:0.2296:7.44943:60:4:0.0175:0:1 +11 108153392 . A AT 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.1159;SOR=0;LSEQ=AACAAGCATTTAAATGATTT;RSEQ=TTTTTTTCATTTTTCTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:232,60:292,3:0.0102:2,2:16:1:27:1:0.11296:7.66002:60:6:0.0102:0.0068:0.7 0/0:309:0:0,0:229,79:308,0:0:2,0:20.7:1:28.1:1:1:0:60:101.667:0.9967:0:0.1 +11 108154931 . A T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.2186;SOR=Inf;LSEQ=AAAAGTTATATATAACCTGT;RSEQ=TTTTAAATTTTTCTATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:139,21:160,0:0:2,0:22.8:1:28.6:1:1:0:59.9:39:1:0:0.1 0/1:141:2:1,1:114,25:139,2:0.0142:2,2:5:0:31:1:0.33587:4.49103:60:4:0.0143:0:1.5 +11 108155333 . A G 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00905;SOR=Inf;LSEQ=TGTGGTAATCATTATCTAGC;RSEQ=TAGCCAACCCATGAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:0,64:64,0:0:1,0:26.5:1:31.4:1:1:0:59.7:128:1:0:0.3 0/1:43:5:0,5:0,38:38,5:0.1163:1,0:23.4:1:31.4:1:1:0:60:10:0.119:0:1 +11 108155397 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06401;SOR=0;LSEQ=TCTGATTGGCTTTTAACTAA;RSEQ=TAGAAATGTTTTAAATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:0,28:0,0:0,28:1:0,1:24.5:1:31.7:1:1:0:57.8:56:1:0:1.3 1/1:10:8:1,7:0,2:2,8:0.8:0,2:22.5:1:30.5:1:1:0:60:16:0.8:0:1 +11 108158134 . T C 124 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11111;SOR=0;LSEQ=ATTTTCATACTTTTTCCTCT;RSEQ=AGTCTACAGGTTGGCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:15,1:0,0:0,16:1:0,1:25.5:1:31.1:1:1:0:60:15:1:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:45:0:30:0:1:0:60:2:0.5:0:1 +11 108160242 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14662;SOR=Inf;LSEQ=TATAAAATGTGTAGGTATTC;RSEQ=AATATTTGAAGAAAAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:98,14:112,0:0:2,0:22.6:1:30.9:1:1:0:59.8:111:1:0:0 0/1:70:2:1,1:60,8:68,2:0.0286:2,2:21:1:28.5:1:0.24224:7.12928:60:4:0.029:0:1 +11 108160632 . C T 150 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACAAAGACTCACTCTGTC;RSEQ=GCCCAGGCTGGGTGCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:29:0,29:1,25:26,29:0.5273:1,1:25.1:1:31:1:0.47273:0:59.3:58:0.537:0:1.1 0/0:46:0:0,0:0,46:46,0:0:1,0:9:0:16:0:1:0:60:0:0:0:2 +11 108163323 . G GT 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.25992;SOR=0.6096;LSEQ=AGAACTTACTGGTTGTTGTT;RSEQ=TTTTTTTTTCTCCCTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:20:16,4:269,77:346,20:0.0546:2,2:27.6:1:30:1:1:1.14:59.8:40:0.0551:0.0109:0.2 0/1:294:10:9,1:221,60:281,10:0.034:2,2:28.8:1:28:1:0.69378:2.44:59.6:9:0.031:0:1.2 +11 108163733 . A G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTATCTACTGTGCTGAAGT;RSEQ=GAGAGGTAGTCAAAACTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:3,6:0,0:0,9:1:0,2:20:1:30.3:1:1:0:59.6:18:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:31:1:29:1:1:0:60:4:1:0:1 +11 108165219 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCACGCCTGTAATCCCAG;RSEQ=GCTTTGGAAGGCTAAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108165406 . GC AG 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=0.17439;LSEQ=GAACCGGGGAGGCGGAGGTA;RSEQ=AGTGAGCCTTGATAGCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:0,0:0,7:0.875:0,0:30.6:1:33.5:0:1:0:60:14:1:0:1.1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19:1:29.3:1:1:0:60:4:0.5:0:1.5 +11 108165542 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20915;SOR=Inf;LSEQ=CCTTGATTAGTAGTAATAGA;RSEQ=ACATGAGTCAGTGTCTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:123,1:124,0:0:1,0:22.5:1:32.9:1:1:0:60:16.714:1:0:0.1 0/1:105:2:1,1:100,3:103,2:0.019:1,2:10.5:1:28.5:1:0.07509:28.9907:60:4:0.0196:0:1.5 +11 108165634 . A G 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCAATACGTGTTAAAAGCA;RSEQ=GTTACATTTTCTCTTTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:640:0:0,0:416,223:639,0:0:2,0:24.9:1:30.8:1:1:0:60:105.5:0.9984:0:0.1 0/1:668:24:13,11:366,278:644,24:0.0359:2,2:25.4:1:29.3:1:0.83575:1.11382:60:11:0.0331:0:1 +11 108170042 . CT C 34 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGGTTGATTCTCTCTCT;RSEQ=TTTTTTTTTTTTCTTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:33.5:1:34:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108170271 . G A 154 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=TGACCTCAGGTGATCCGCCC;RSEQ=CCTCTGTCTCCCAAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:32,1:0,0:0,33:1:0,1:23.8:1:30.6:1:1:0:39.7:66:1:0:1.1 1/0:12:6:6,0:6,0:6,6:0.5:0,0:26.7:1:28.5:1:1:0:38.7:5:0.4545:0:1.3 +11 108170373 . T G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00349;SOR=Inf;LSEQ=CAGCATTATAGTTTTGAAAT;RSEQ=AGAAAATTTCAGTTTTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:136,7:143,0:0:1,0:24.7:1:31.3:1:1:0:59.9:142:1:0:0.1 0/1:118:7:5,2:101,10:111,7:0.0593:2,2:18.9:1:30.6:1:0.14949:3.96569:60:14:0.0593:0:1 +11 108172385 . C T 64 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.03162;SOR=Inf;LSEQ=TTTTTTTCAGTGTCAAAGTT;RSEQ=GATCAGCAGCTGTTACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:354,199:553,0:0:2,0:23.5:1:31.1:1:1:0:59.9:54.3:1:0:0.1 0/1:600:6:2,4:355,239:594,6:0.01:2,2:6.8:1:24.8:1:0.22865:2.96528:60:5:0.0084:0:1.3 +11 108172526 . G T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05974;SOR=Inf;LSEQ=CAAGAAAAAAGGTCTCTTAA;RSEQ=TAATAAATGTTTATTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:103,280:383,0:0:2,0:25.3:1:32.3:1:1:0:60:53.714:1:0:0.1 0/1:376:4:2,2:109,260:369,4:0.0106:2,2:20.3:1:30.3:1:0.58555:2.38:60:8:0.0108:0:1.3 +11 108173801 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19639;SOR=Inf;LSEQ=TAATTCCTTGTTTATGACCT;RSEQ=TTTATCTAAAGAGTGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:26,142:168,0:0:2,0:23:1:32.5:1:1:0:60:336:0.9941:0:0.1 0/1:135:2:1,1:22,111:133,2:0.0148:2,2:31.5:1:29.5:1:0.31277:4.96:60:4:0.015:0:1 +11 108175462 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14714;LSEQ=TTCATGATATTTTACTCCAA;RSEQ=ATACAAATGAATCATGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:271:154,117:149,123:272,271:0.4982:2,2:24.6:1:30.4:1:0.66597:1.09:59.9:53.2:0.4935:0:1.1 0/1:613:78:40,38:280,255:535,78:0.1272:2,2:25.8:1:29.4:1:0.90372:1.04308:60:77:0.1266:0:1.1 +11 108175681 . A G 51 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.061;SOR=Inf;LSEQ=CACTTTACAGGATTAAATCT;RSEQ=TAACCTCTAAATTTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:1,76:77,0:0:1,0:23.8:1:32:1:1:0:60:76:1:0:0.1 0/1:51:3:0,3:1,47:48,3:0.0588:1,0:7.7:1:32.7:1:1:0:60:6:0.0588:0:1 +11 108178575 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.51228;SOR=Inf;LSEQ=TAAACAAGAAGGAAGAAGGT;RSEQ=TGTAAGCAAGAATGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:102,39:141,0:0:2,0:24.9:1:32.5:1:1:0:60:140:1:0:0.1 0/1:197:2:1,1:136,58:194,2:0.0102:2,2:28:0:28:1:0.51251:2.33343:60:4:0.0102:0:1 +11 108178730 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24019;SOR=Inf;LSEQ=AGGTAATGTAATGAGTGTTG;RSEQ=TTCTTACGTTTAGGATCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:60,133:193,0:0:2,0:25.6:1:32.6:1:1:0:60:63.333:1:0:0.2 0/1:186:2:1,1:48,136:184,2:0.0108:2,2:18:1:28:1:0.45853:2.81:60:4:0.0109:0:1 +11 108178767 . T C 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CTAGAGTGTAACTTGTTAAC;RSEQ=ATCGGCTGAATTTTAACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:13,92:105,0:0:2,0:21:1:29:1:1:0:60:210:0.9906:0:0.1 0/1:75:10:1,9:8,57:65,10:0.1333:2,2:24.5:1:31.2:1:1:1.25948:60:20:0.1333:0:1 +11 108181094 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50057;SOR=Inf;LSEQ=ATTAATGTTGGCATTGTCTC;RSEQ=ATAAGGGTATATAGTAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:15,102:117,0:0:2,0:23.8:1:31.2:1:1:0:60:234:1:0:0 0/1:135:2:1,1:28,105:133,2:0.0148:2,2:21.5:1:29.5:1:0.38474:3.70:60:4:0.015:0:1 +11 108181123 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49618;SOR=0;LSEQ=ATATAGTAAAGATTTATTTT;RSEQ=CCTCCTGTTCCCCATTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:2,62:64,2:0.0303:1,2:23.5:1:29:1:0.08951:25.52:60:4:0.0308:0:1 0/0:65:0:0,0:2,63:65,0:0:1,0:24.1:1:31.7:1:1:0:60:31.5:1:0:0.2 +11 108181511 . A C 35 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTGATTTATTTCTGTGACTA;RSEQ=TTAAGTTTCATTTCTTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:12.5:1:35:0:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:33:1:27.5:1:1:0:60:4:1:0:0 +11 108183167 . A G 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGAAGAAGGAAGCCAGA;RSEQ=TACAACTATTTCTAGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:546:546:280,266:0,0:0,546:1:0,2:26.3:1:32.8:1:1:0:59.9:135.5:1:0:1.1 1/1:548:548:279,269:0,0:0,548:1:0,2:26.6:1:31.2:1:1:0:59.9:108.6:1:0:1.1 +11 108183413 . ACT A 118 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.05;SOR=0;LSEQ=AGACTTGAGTTCTAATACTG;RSEQ=CTGCCACTTCTTGAGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:1,11:0,0:0,12:1:0,2:25.1:1:33.1:1:1:0:59.6:24:1:0.25:0.1 1/0:4:2:0,2:0,2:2,2:0.5:0,0:26:1:31:1:1:0:60:4:0.5:0.25:0 +11 108186258 . G A 30 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AACTTTTAAAAAATTTTTCA;RSEQ=TAGTTCTAAACTGTGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31:1:30.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:29:0:1:0:60:2:1:0:1 +11 108186653 . T C 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TACTAGGTAAATTGCATTTT;RSEQ=CTAAACAACGGTATAGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:255,201:456,0:0:2,0:23.6:1:30.8:1:1:0:59.9:151:1:0:0.1 0/1:506:17:9,8:239,250:489,17:0.0336:2,2:20.5:1:30.9:1:0.8083:1.18:60:34:0.0337:0:1.4 +11 108186662 . C A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06221;SOR=Inf;LSEQ=AATTGCATTTTTCTAAACAA;RSEQ=GGTATAGTAATTCTGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:0:0,0:260,207:467,0:0:2,0:22.7:1:31.2:1:1:0:59.9:232.5:0.9957:0:0.1 0/1:492:5:4,1:254,233:487,5:0.0102:2,2:8.8:1:25.2:1:0.37544:3.66:60:10:0.0103:0:1 +11 108186956 . T C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06639;SOR=Inf;LSEQ=AGAGATAAGACTAGAACTTA;RSEQ=CTGTTTTTCAGAGGATTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:2,69:71,0:0:1,0:22.3:1:30.4:1:1:0:60:70:1:0:0.1 0/1:50:3:1,2:1,46:47,3:0.06:1,2:23.7:1:32.7:1:0.11755:18.99:60:6:0.0625:0:1 +11 108187830 . T AA 30 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=ACTACCATACCCAGCTATTT;RSEQ=AAAAAAAAAAAAAAATTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19:1:30.5:1:1:0:60:4:1:0.5:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:11:1:30.7:1:1:0:48.5:4:0.6667:0.3333:1 +11 108188342 . TTATATA T 103 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=19.000;MSILEN=2;SSF=0.0315;SOR=0;LSEQ=TGAATATAACAGGAGTTGTT;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:12:0,12:0,36:36,12:0.2069:1,0:37.5:1:28.9:1:1:0:42.3:24:0.2069:0.0172:1.1 0/0:19:0:0,0:0,12:12,0:0:0,0:15.1:1:26.8:1:1:0:53.8:11:0.6111:0:0.8 +11 108188377 . T C 88 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=17.000;MSILEN=2;SSF=0.0031;SOR=10.82888;LSEQ=TATATATATATATATATATA;RSEQ=ATACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:0,22:22,2:0.0714:1,0:13.5:1:32.5:1:1:0:45:4:0.0833:0:2 0/1:17:8:0,8:0,9:9,8:0.4706:0,0:26.6:1:29.5:1:1:0:36.1:7:0.4375:0:3.1 +11 108188379 . T C 103 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0.02895;SOR=4.41395;LSEQ=TATATATATATATATATATA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:0,8:0,16:16,8:0.2857:1,0:28.9:1:32.6:1:1:0:39.4:16:0.3333:0:1.5 1/0:17:11:0,11:0,6:6,11:0.6471:0,0:27:1:29.9:1:1:0:35.8:10:0.625:0:2.6 +11 108188462 . T A 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06061;SOR=0;LSEQ=TATATATATATAAAAAAATA;RSEQ=ATAGTAGATGTTGCAAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:24.2:1:32:1:1:0:60:12:0.75:0:1.5 0/0:3:0:0,0:0,3:3,0:0:0,0:19:1:29:1:1:0:60:6:1:0:0.7 +11 108192159 . G T 132 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.84695;LSEQ=TTTCTCAAGGTATGTAATTC;RSEQ=TATGACTTTGTTATCCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:568:1:0,1:195,372:567,1:0.0018:2,0:9:0:32:0:1:0:60:2:0.0018:0:1 0/1:646:24:10,14:234,387:621,24:0.0372:2,2:33.8:1:28.9:1:0.67478:1.18:60:23:0.0362:0:1.3 +11 108193671 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12795;SOR=0;LSEQ=AGTCTGGCAGGATGACAAAG;RSEQ=AAAGTGTTTTGGGTCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:5,13:18,2:0.1:2,2:27:1:32:1:0.52105:2.46:60:4:0.1:0:1 0/0:35:0:0,0:17,18:35,0:0:2,0:23.3:1:28:1:1:0:60:70:1:0:0.1 +11 108195976 . GT G 173 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.073;SOR=0.52207;LSEQ=TAAGTTCCAGAACTTACATA;RSEQ=TTTTTTTTTTTTTTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:41:37,4:53,5:58,41:0.3504:2,2:22.3:1:32.3:1:1:1.14435:59.4:40:0.3509:0.0855:0.7 0/1:73:16:12,4:40,5:45,16:0.2192:2,2:23.9:1:32.4:1:0.22409:2.61718:56.3:32:0.2254:0:1.7 +11 108196509 . G C 142 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08696;SOR=0;LSEQ=GTTATAAAATGAGAAGATAC;RSEQ=TAACTTACTATATTGATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:6,15:0,0:0,21:1:0,2:23.3:1:32.5:1:1:0:59.4:42:1:0:1.1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:14:0:33:0:1:0:60:2:0.5:0:1 +11 108196712 . CATT C 221 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0;SOR=0.07772;LSEQ=TGAATGGTAGTTGCTGCTTT;RSEQ=ATTATTATTATTCATGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:119:105,14:4,0:4,119:0.9597:0,2:26.6:1:32.1:1:1:0:59.9:58.5:0.975:0.129:0.1 1/0:99:64:52,12:32,3:35,64:0.6465:2,2:23.9:1:30.7:1:0.24503:2.44155:59.9:128:0.6465:0.1111:0.1 +11 108196957 . G GT 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.80009;SOR=0.85793;LSEQ=TGCCAGCTGTGCAGCGGTTT;RSEQ=TTTTTTTTATTGGCTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:8:1,7:112,236:348,8:0.0225:2,2:32.6:1:27.6:1:0.44402:3.31354:60:7:0.02:0:0.8 0/1:362:7:1,6:138,216:354,7:0.0193:2,2:33.1:1:30:1:0.25687:3.82221:60:14:0.0198:0:0 +11 108196973 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.30998;LSEQ=GTTTGTTTTTTTTATTGGCT;RSEQ=GATTAGTGTTTTACTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:77,211:288,3:0.0103:2,2:27.7:1:25.3:1:0.18015:5.44:60:2:0.007:0:1.3 0/1:297:4:3,1:97,196:293,4:0.0135:2,2:1.8:1:23.5:1:0.11261:6.02:60:8:0.0137:0:1 +11 108196975 . A G 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11981;SOR=0;LSEQ=TTGTTTTTTTTATTGGCTGG;RSEQ=TTAGTGTTTTACTGTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:73,206:279,3:0.0106:2,2:13.7:1:26.3:1:1:1.41:60:2:0.0072:0:2.7 0/0:289:0:0,0:97,192:289,0:0:2,0:22.9:1:29:1:1:0:60:35.125:1:0:0.2 +11 108198249 . C CT 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50705;SOR=0;LSEQ=CAAAAGCAGATGAGGAAAAA;RSEQ=TTTTTTTTTCCCACCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:2,0:48,1:49,2:0.0392:1,0:13.5:1:34:0:1:0:60:4:0.0392:0:0 0/0:37:0:0,0:37,0:37,0:0:1,0:19:1:31.9:1:1:0:60:74:1:0:0 +11 108198297 . T TC 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.03299;SOR=Inf;LSEQ=ACATTTTTAACCTGCTTTTT;RSEQ=CCCCGTACATGAAGGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:128,10:138,0:0:2,0:23.5:1:31.4:1:1:0:59.8:137:1:0:0 0/1:104:4:4,0:87,13:100,4:0.0385:2,0:23:1:32:1:1:0:60:8:0.0385:0.0096:0 +11 108198313 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17308;SOR=Inf;LSEQ=TTTTTCCCCGTACATGAAGG;RSEQ=CAGTTGGGTACAGTCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:169,24:193,0:0:2,0:24.5:1:31.7:1:1:0:60:47.25:1:0:0.1 0/1:138:2:1,1:116,20:136,2:0.0145:2,2:31.5:1:27.5:1:0.28213:5.68462:60:4:0.0146:0:1 +11 108199583 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCGTCCTGGGCCACATG;RSEQ=GGCCCATGGGCCGTGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:3,0:22,0:22,3:0.12:1,0:31.7:1:30.7:1:1:0:58:6:0.12:0:1.7 0/0:7:0:0,0:7,0:7,0:0:0,0:33.3:1:31:1:1:0:60:14:1:0:0.1 +11 108200142 . T G 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=11.000;MSILEN=1;SSF=0.14328;SOR=0.13275;LSEQ=TTTCGGTTTTTGTTTTTTGT;RSEQ=TTTTTTTTTGAGACAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:1,16:0,1:1,17:0.9444:0,1:20.3:1:32.2:1:1:0:59.2:16:0.9412:0:1 1/0:6:4:1,3:0,2:2,4:0.6667:0,2:16.5:1:32.8:1:1:0:60:8:0.6667:0:1 +11 108201207 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51078;SOR=0;LSEQ=AAAAACTTAGACATAAGCCC;RSEQ=TTGATGTCAGGAATCGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:9,111:120,2:0.0164:2,2:20.5:1:30.5:1:0.15784:11.75:60:4:0.0165:0:1 0/0:88:0:0,0:15,73:88,0:0:2,0:22.8:1:31.6:1:1:0:60:176:1:0:0.1 +11 108201215 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17084;SOR=Inf;LSEQ=AGACATAAGCCCCTTGATGT;RSEQ=AGGAATCGTGTATACCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:8,102:110,0:0:2,0:24.2:1:32.3:1:1:0:60:109:1:0:0.1 0/1:78:2:1,1:13,63:76,2:0.0256:2,2:30:1:27.5:1:0.32867:4.71:60:4:0.0256:0:1 +11 108202154 . C CT 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.77947;SOR=0.74614;LSEQ=CTTGTTTCTTAATTTTGTGT;RSEQ=TTTTTTTTAATGGTAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:8:6,2:193,48:241,8:0.0321:2,2:29.1:1:31.5:1:0.66315:1.33857:60:16:0.0327:0.004:0.1 0/1:207:5:2,3:149,53:202,5:0.0242:2,2:29.6:1:30.6:1:0.12371:4.18173:57:10:0.0243:0:0.6 +11 108203501 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12475;SOR=Inf;LSEQ=ATTAATAGGATCGAACAGAG;RSEQ=CTGCAAATAGAATAATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:244,129:373,0:0:2,0:24.4:1:31.4:1:1:0:60:40.444:1:0:0.1 0/1:397:4:2,2:239,153:392,4:0.0101:2,2:36:1:27.5:1:0.64614:1.56022:60:8:0.0103:0:1 +11 108203632 . G GT 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.3768;SOR=0.27877;LSEQ=TGGAAGACTCAGAGAAGTAT;RSEQ=TTTTTTTTAAAGAAGAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:4:1,3:63,193:256,4:0.0153:2,2:32.8:1:30.8:1:1:1.02:60:8:0.0156:0.0038:0 0/0:232:1:0,1:54,177:231,1:0.0043:2,0:45:0:32:0:1:0:60:2:0.0043:0:0 +11 108203640 . T A 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCAGAGAAGTATGTTTTTTT;RSEQ=AAAGAAGAAACGTTACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:49,172:221,0:0:2,0:23.4:1:29.1:1:1:0:59.9:109.5:1:0:0.1 0/1:200:15:4,11:39,146:185,15:0.075:2,2:23.4:1:29.1:1:0.74332:1.36:60:30:0.075:0:1.2 +11 108203769 . G A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTATATCTGATGGCTTCA;RSEQ=CATTCCCTGGTTACTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:0,16:0,0:0,16:1:0,1:20.6:1:30.8:1:1:0:60:32:1:0:1.2 1/1:9:9:1,8:0,0:0,9:1:0,2:16.8:1:28.1:1:1:0:60:18:1:0:1.2 +11 108204456 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGCTTTGACTCTGAGCT;RSEQ=CATAGTGGCCAAAGCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:34,1:35,2:0.0541:1,2:10:0:31:1:0.10661:24.39295:60:4:0.0571:0:1 0/0:17:0:0,0:17,0:17,0:0:1,0:24.2:1:30.2:1:1:0:60:16:1:0:0.2 +11 108204557 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50747;SOR=0;LSEQ=TCTGCTGACTATTCCTGCTT;RSEQ=ACCTTCAATGCTGTTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:139,59:198,2:0.01:2,2:15.5:1:26:1:0.51106:2.34463:60:4:0.0101:0:1.5 0/0:153:0:0,0:118,35:153,0:0:2,0:23.8:1:31.3:1:1:0:60:75.5:1:0:0.1 +11 108204717 . A AT 107 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00436;SOR=10.54262;LSEQ=TAATTTGCAATTAACTCTTG;RSEQ=TTTTTTTTAAACTAAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:0,1:64,144:208,1:0.0048:2,0:27:0:11:0:1:0:60:0:0:0:0 0/1:248:12:4,8:87,149:236,12:0.0484:2,2:27.3:1:30.1:1:1:1.16711:60:24:0.05:0:0 +11 108204881 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AAAATACTCAAAAGCTTCTC;RSEQ=TGCTTTCTTTTCCATTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:12.4:1:31.8:1:1:0:60:4:1:0:0 1/0:5:3:0,3:0,2:2,3:0.6:0,0:28:1:28.3:1:1:0:60:6:0.6:0:1 +11 108204945 . GT G 28 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTATGAAGGTCTATAGACT;RSEQ=TACTTTCATTGGCCAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:28.5:1:1:0:60:4:1:0:0 1/1:1:1:0,1:0,0:0,1:1:0,0:20:0:26:0:1:0:60:2:1:0:0 +11 108205329 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGAAATGTAGCTGTATC;RSEQ=TGTGGATTAACTGCTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:32:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108205383 . G A 55 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAGGTGATTTCGCTGAAT;RSEQ=TTTCCTTAAAATGCCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:18.3:1:27.5:1:1:0:60:8:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 108205659 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18842;SOR=Inf;LSEQ=CTTTAAGTGCAAATAGTGTA;RSEQ=CTGACCTATTATCAATCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:162,29:191,0:0:2,0:23.1:1:31.1:1:1:0:60:62.667:1:0:0.1 0/1:147:2:1,1:114,31:145,2:0.0136:2,2:25.5:1:27.5:1:0.38915:3.63573:60:4:0.0137:0:1 +11 108205861 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11324;SOR=Inf;LSEQ=GCCTTCCCTTCTCTGGCTTA;RSEQ=CCCTTAGAGTTTTAGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:69,200:269,0:0:2,0:23.2:1:32.3:1:1:0:60:43.833:0.9962:0:0.1 0/1:255:3:2,1:73,179:252,3:0.0118:2,2:13.3:1:26.3:1:0.20762:4.87:60:6:0.0118:0:1 +11 108205865 . T C 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11678;SOR=Inf;LSEQ=TCCCTTCTCTGGCTTAGCCC;RSEQ=TAGAGTTTTAGTGATGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:58,193:251,0:0:2,0:22.7:1:30.5:1:1:0:60:40.833:1:0:0.1 0/1:241:3:1,2:62,176:238,3:0.0124:2,2:24:1:25:1:1:1.42:60:2:0.0085:0:1.3 +11 108205919 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07542;SOR=Inf;LSEQ=TTTTCTTTCTGCTTTATTTG;RSEQ=GATTTTGTCTTTATTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:1,81:82,0:0:1,0:25:1:31.5:1:1:0:60:40:1:0:0.1 0/1:61:3:0,3:1,57:58,3:0.0492:1,0:23:1:31.3:1:1:0:60:6:0.05:0:1 +11 108206747 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1974;SOR=Inf;LSEQ=TAAAAGATGCCATTTGGTTG;RSEQ=GTGAAGTGGCTCATGCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:19,193:212,0:0:2,0:23:1:31.7:1:1:0:59.9:105:1:0:0 0/1:170:2:1,1:17,151:168,2:0.0118:2,2:13.5:1:27.5:1:0.20111:8.66:60:4:0.0118:0:1 +11 108206868 . TA T 75 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.26213;SOR=0;LSEQ=ACCCCATCTTGACAAAAAGT;RSEQ=AAAAAAAAAAAAAAGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:10,6:0.375:0,0:21.7:1:29.2:1:1:0:59.3:12:0.375:0.0625:0.5 0/0:5:0:0,0:1,4:5,0:0:2,0:20.8:1:28.4:1:1:0:57.6:10:1:0:0.2 +11 108213851 . GA G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50517;SOR=0;LSEQ=GAGAAATATTAATACAACTT;RSEQ=AAAAAAATGCTTTGCACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:2,0:79,1:80,2:0.0244:1,0:31.5:1:34:0:1:0:60:4:0.025:0:0 0/0:63:0:0,0:63,0:63,0:0:1,0:24:1:28.6:1:1:0:59.7:126:1:0:0 +11 108218196 . T C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=0;LSEQ=AATATAAGAGACAGATAAAT;RSEQ=GAAGCAGTAAATATTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:76:0,76:0,0:0,76:1:0,1:21.4:1:30.4:1:1:0:60:75:1:0:1.1 1/1:54:44:0,44:1,9:10,44:0.8148:2,1:23.8:1:30.2:1:0.18519:0:60:88:0.8148:0:1 +11 108224677 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20376;SOR=Inf;LSEQ=CATGGGCTGGGCATGGTTCT;RSEQ=TGCACCTGTAATCCCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:10,117:127,0:0:2,0:21.3:1:30.6:1:1:0:60:126:1:0:0.7 0/1:105:2:1,1:7,96:103,2:0.019:2,2:18.5:1:30:1:0.14725:12.89:60:4:0.0192:0:1.5 +11 108224696 . TG CA 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03284;SOR=Inf;LSEQ=TTTGCACCTGTAATCCCAGC;RSEQ=CTCAAGAGGCTGAAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:1,86:87,0:0:1,0:22.7:1:28.7:1:1:0:59.9:174:1:0:1.1 0/1:66:4:0,4:1,61:62,4:0.0606:1,0:9.3:1:31.1:1:1:0:60:8:0.0606:0.0303:0.5 +11 108224697 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17384;SOR=0;LSEQ=TTGCACCTGTAATCCCAGCT;RSEQ=CTCAAGAGGCTGAAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:86:86:1,85:0,0:0,86:1:0,1:22.6:1:30.3:1:1:0:59.9:85:1:0:1.1 1/1:62:60:1,59:0,0:0,60:0.9677:0,1:23.8:1:29.6:1:1:0:60:120:1:0:1 +11 108224757 . A T 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00094;SOR=0;LSEQ=GTTTGAGTCCAGCCTAGGCA;RSEQ=TACAGCAAGACCCTGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:1,12:0,12:12,13:0.52:0,1:20.6:1:31.7:1:1:0:59.5:26:0.52:0:2 0/0:14:0:0,0:0,14:14,0:0:1,0:15.4:1:31.3:1:1:0:58.5:28:1:0:1 +11 108224791 . CACACAA C 86 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=21.000;MSILEN=2;SSF=0.00126;SOR=0;LSEQ=TGTATCTAAAAAAATACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:7:1,6:0,0:0,7:1:0,2:19.4:1:30.7:1:1:0:50.3:14:1:0.7143:1.7 0/0:5:0:0,0:0,5:5,0:0:0,0:26.2:1:30.8:1:1:0:49.4:10:1:0:1.4 +11 108224797 . A C 50 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAAAATACACACACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:0,3:0,1:1,3:0.75:0,0:31:1:32:1:1:0:42.3:6:0.75:0:2 +11 108225473 . G A 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=0;LSEQ=ACTACACATGAGAGTATACA;RSEQ=ATAAAGATACGTTGACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:13:9,4:218,58:276,13:0.0447:2,2:18.7:1:30.4:1:0.48654:1.66714:60:26:0.045:0:2.1 0/0:266:0:0,0:192,73:265,0:0:2,0:22:1:31.1:1:1:0:60:87.333:1:0:0.8 +11 108225483 . C T 261 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01127;LSEQ=AGAGTATACAGATAAAGATA;RSEQ=GTTGACAACATTGGTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:356:354:270,84:1,1:2,354:0.9944:2,2:23.7:1:30.9:1:0.42103:3.20:60:353:0.9972:0:1.1 1/0:319:212:144,68:77,30:107,212:0.6646:2,2:23.5:1:29.7:1:0.52104:1.21131:60:52:0.6603:0:1.1 +11 108225628 . AT A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.03968;SOR=Inf;LSEQ=TATTTTATAAGGAAGACTTT;RSEQ=TTTTTTTCTTACCAGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:119,290:409,0:0:2,0:22.6:1:30.5:1:1:0:60:80.8:0.9975:0:0.5 0/1:332:4:1,3:98,230:328,4:0.012:2,2:16:1:29.8:1:1:1.27734:60:8:0.0121:0.006:1 +11 108225661 . A G 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCAGGTAGACTGTGTATCTC;RSEQ=TCAGGAAGTCACTGATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:206:206:33,173:0,0:0,206:1:0,2:22.3:1:31.9:1:1:0:60:205:1:0:1.1 1/0:149:119:23,96:5,25:30,119:0.7987:2,2:22.8:1:31.2:1:1:1.20:60:238:0.8041:0:1 +11 108235681 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10109;SOR=Inf;LSEQ=AGGAAACATGAAGTGTGCAT;RSEQ=ATGTTTGTTCCCCTCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:74,0:74,0:0:1,0:24.5:1:33:1:1:0:59.6:148:1:0:0.1 0/1:35:2:1,1:33,0:33,2:0.0571:1,2:37:1:29:1:0.05714:0:60:4:0.0571:0:1 +11 108235730 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50948;SOR=0;LSEQ=CATGTGACTGGCTTATTTGT;RSEQ=TGATACTGGTTCTACTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:136,18:154,2:0.0127:2,2:13.5:1:32:1:0.22945:7.38177:60:4:0.0131:0:1 0/0:116:0:0,0:96,20:116,0:0:2,0:22:1:27.7:1:1:0:60:115:1:0:0.1 +11 108235739 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50258;SOR=0;LSEQ=GGCTTATTTGTATGATACTG;RSEQ=TTCTACTGTTTCTAAGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:148,31:179,2:0.011:2,2:25:1:28.5:1:0.32314:4.7149:60:4:0.0114:0:1 0/0:151:0:0,0:116,34:150,0:0:2,0:21.7:1:30.8:1:1:0:60:300:1:0:0.1 +11 108235752 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20123;SOR=Inf;LSEQ=GATACTGGTTCTACTGTTTC;RSEQ=AAGTATGTGATTAAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:184,60:244,0:0:2,0:21.5:1:30.7:1:1:0:59.9:47.8:1:0:0.1 0/1:199:2:1,1:148,49:197,2:0.0101:2,2:19:1:32.5:1:0.44033:3.00013:60:4:0.0101:0:1 +11 110097796 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22509;SOR=Inf;LSEQ=TGCTAGACTTGAATTTCATA;RSEQ=ACTTTTCAATATATATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:123,98:221,0:0:2,0:25.4:1:32.5:1:1:0:60:109.5:1:0:1.2 0/1:200:2:1,1:108,90:198,2:0.01:2,2:10:0:30.5:1:1:1.1989:60:4:0.0102:0:1.5 +11 110097811 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=0.1381;LSEQ=TCATAGACTTTTCAATATAT;RSEQ=TAAAAGGAAAGTGAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:237:187:98,89:26,23:49,187:0.789:2,2:25:1:32.4:1:1:1.02651:60:374:0.789:0:1.7 0/1:218:74:36,38:75,68:143,74:0.3394:2,2:24.7:1:31.1:1:0.66781:1.1634:60:73:0.3395:0:1.8 +11 110097851 . A G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13491;LSEQ=GAGATAGATATTCCCTTATG;RSEQ=TTCTGAAAAACACGATTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:219:178:70,108:15,25:40,178:0.8128:2,2:27.7:1:31.8:1:0.85981:1.08:59.9:88:0.8148:0:1.7 0/1:220:81:34,47:59,80:139,81:0.3682:2,2:27.5:1:31.3:1:1:1.0194:60:80:0.367:0:1.7 +11 110644532 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.71895;SOR=1.07511;LSEQ=GTGCCATATCTTCTCATAGG;RSEQ=GCAGGCAATAGCATTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:105:44,61:110,109:219,105:0.3241:2,2:24.8:1:31:1:0.1911:1.39762:59.7:104:0.326:0:1 0/1:244:83:39,44:78,83:161,83:0.3402:2,2:26.3:1:29.8:1:0.89264:1.05996:59.7:40.5:0.3418:0:1.3 +11 110665848 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16507;SOR=Inf;LSEQ=AAAAGTTCATAGCATTGAAA;RSEQ=AGATTGAGAAATTGTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:169,86:255,0:0:2,0:25.7:1:30.4:1:1:0:60:510:1:0:0.1 0/1:175:2:1,1:107,66:173,2:0.0114:2,2:17.5:1:30:1:1:1.61651:60:4:0.0115:0:1 +11 110665914 . A G 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.51337;LSEQ=GCACACACAGCTTAAAAGTT;RSEQ=TGAATCTGTGTAATTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:34:13,21:132,157:289,34:0.1053:2,2:27.4:1:31.7:1:0.46854:1.35689:60:33:0.1025:0:1.4 1/0:255:147:66,81:50,58:108,147:0.5765:2,2:27.1:1:31.1:1:0.89883:1.05774:60:48:0.5737:0:1.4 +11 110665974 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=12.42914;LSEQ=TAAATATAACACTTTTTTTC;RSEQ=CTTGAATGAAAAATTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:17:2,15:33,88:121,17:0.1232:2,2:23.1:1:32:1:0.23798:2.79565:60:34:0.1232:0:1.8 1/0:130:83:27,56:12,35:47,83:0.6385:2,2:20.5:1:30.1:1:0.43296:1.40:60:40.5:0.6378:0:1.7 +11 110697305 . C G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.28683;LSEQ=CCATGTGCTGGAATGCTGAT;RSEQ=CTTAACCATGTTGCCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:28:13,15:187,195:382,28:0.0683:2,2:21.6:1:31.7:1:0.84655:1.10623:60:27:0.0667:0:1.1 0/1:354:175:80,95:92,87:179,175:0.4944:2,2:24.7:1:30.9:1:0.28997:1.25493:60:57.333:0.4928:0:1.1 +11 110697444 . G A 120 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=13.26791;LSEQ=TTTAGCACTGTGTATCCACC;RSEQ=GTAGTCACTTCCCTCCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:1,46:47,2:0.04:1,0:37:1:30:0:1:0:60:4:0.0426:0:1 0/1:47:17:2,15:1,29:30,17:0.3617:1,2:26.6:1:29.6:1:0.54394:3.75:60:16:0.3478:0:1.1 +11 111273583 . TTAA T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=0;SOR=0.13058;LSEQ=TGTTTTCAGCCAAGACCAAA;RSEQ=TAATAATAATAATAATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:56:51,5:21,1:22,56:0.6829:1,2:29.8:1:30.9:1:0.66968:2.04254:60:17.667:0.6709:0.0122:0.1 0/1:60:13:12,1:38,7:45,13:0.2167:2,1:26.3:1:30.6:1:0.66855:2.19:60:26:0.2203:0.0333:0 +11 111273686 . T A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08082;LSEQ=AAGAATTTCAATGGAACTGA;RSEQ=CACCGCTTTGCAGAGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:398:364:189,175:14,19:33,364:0.9146:2,2:26.4:1:30:1:0.3639:1.46:60:181:0.9141:0:1.1 0/1:419:194:99,95:121,104:225,194:0.463:2,2:25.5:1:29:1:0.62397:1.11616:60:47.5:0.4612:0:1.1 +11 111734964 . C A 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81392;LSEQ=AACCCACGAACTGGCCCGGC;RSEQ=CTCACGTGCACCATGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:30,22:52,2:0.037:2,2:12.5:1:26.5:1:1:1.35569:60:4:0.0377:0:1 0/1:66:2:1,1:41,23:64,2:0.0303:2,2:24.5:1:27.5:1:1:1.76614:60:4:0.0313:0:1 +11 111734995 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49776;SOR=Inf;LSEQ=CCATGTCTGGCTCCTCCAGC;RSEQ=TTGCCGCTATGAAGAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:38,35:73,0:0:2,0:26.7:1:30.7:1:1:0:59.9:72:1:0:0.2 0/1:80:2:1,1:41,37:78,2:0.025:2,2:47:1:30:1:1:1.10668:51.5:4:0.0253:0:1 +11 111956184 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09405;SOR=0;LSEQ=CATAACTCCATGAAGTGATG;RSEQ=ACCTAAAAGGAAAGAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:3:1,2:18,166:184,3:0.016:2,2:31.3:1:28.7:1:0.27622:4.55:47.3:6:0.0161:0:1 0/0:223:0:0,0:28,195:223,0:0:2,0:27:1:31.6:1:1:0:44.5:222:1:0:0.1 +11 111956291 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19821;SOR=Inf;LSEQ=ACAAAACCATTCTTTAAATC;RSEQ=ACCACGGAGTCACTTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:2,36:38,0:0:2,0:16.8:1:31.7:1:1:0:60:76:1:0:0 0/1:31:2:0,2:0,29:29,2:0.0645:1,0:26.5:1:32:0:1:0:60:4:0.0645:0:1 +11 111956989 . C A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAGTGGGGTGACGGCGA;RSEQ=ACCAAAACCCACAGTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:41.3:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 111957494 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22136;SOR=Inf;LSEQ=GACAGCTGTGTTTGCGCATG;RSEQ=GCGACGGGTGTGCACCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:156,1:157,0:0:1,0:22.2:1:32.8:1:1:0:60:51.333:1:0:0 0/1:140:2:2,0:134,4:138,2:0.0143:1,0:39:1:29:1:1:0:60:4:0.0146:0:1 +11 111957551 . G T 69 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03232;SOR=Inf;LSEQ=CCCAGCATTTCCTCTTCCCT;RSEQ=TTTTCTTTCGTCGTCGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:0:0,0:373,124:497,0:0:2,0:22.7:1:32.2:1:1:0:60:123.25:1:0:0.1 0/1:557:6:1,5:378,173:551,6:0.0108:2,2:5.5:1:26.7:1:0.01421:10.87459:60:12:0.0109:0:1 +11 111957665 . G A 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGCTGAGTGCCGTTTGC;RSEQ=GTGCCCTAGGAGGCCGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1193:0:0,0:583,610:1193,0:0:2,0:25.2:1:30.1:1:1:0:56.7:40.138:1:0:0.1 0/1:1314:90:39,51:582,642:1224,90:0.0685:2,2:26.7:1:30:1:0.44658:1.18532:57.7:89:0.0685:0:1.1 +11 111957819 . G T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03045;SOR=0.56019;LSEQ=TCACAGCAATGACCACTGTA;RSEQ=TCTAGGGGTCCAGATGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:143:81:1,80:1,61:62,81:0.5664:1,1:25.2:1:31:1:1:1.30895:60:162:0.5745:0:1.1 0/1:109:46:0,46:2,61:63,46:0.422:1,1:22.9:1:28.9:1:0.50765:0:60:22:0.4112:0:1.2 +11 111959562 . A G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATGTGTGTTTCTCACATC;RSEQ=ACTTTTATGAATCTGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:559:0:0,0:386,172:558,0:0:2,0:23.8:1:30.4:1:1:0:58.6:54.8:0.9982:0:0.1 0/1:607:31:23,8:387,187:574,31:0.0511:2,2:22.9:1:29.7:1:0.55484:1.39:57.7:62:0.0519:0:1.6 +11 111959625 . C T 146 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=28.61553;LSEQ=GCATCTCTCCACTGGACTAG;RSEQ=GAGAGGGTTGTCAGTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:1:0,1:301,250:551,1:0.0018:2,0:4:0:32:0:0.45471:0:60:2:0.0019:0:1 0/1:627:31:18,13:326,270:596,31:0.0494:2,2:30.9:1:29.6:1:0.85353:1.15:43.7:62:0.0501:0:1.6 +11 111959859 . T C 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.04677;SOR=Inf;LSEQ=TTGTTGAAAACTTTAAAATA;RSEQ=ATATAAAATATGTATATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:0,71:71,0:0:1,0:25.7:1:28.2:1:1:0:59.9:16.75:1:0:0 0/1:41:3:0,3:0,38:38,3:0.0732:1,0:39:1:27.3:1:1:0:60:2:0.05:0:1 +11 111965497 . T C 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAATTTCACTGTGGTTTTT;RSEQ=ATTGATGTTATGATTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:0:0,0:483,249:732,0:0:2,0:24.2:1:29.7:1:1:0:59.3:65.545:1:0:0.1 0/1:755:35:23,12:454,265:719,35:0.0464:2,2:23.9:1:30.4:1:0.85837:1.12:58.7:70:0.0468:0:1.1 +11 113282222 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18491;SOR=Inf;LSEQ=CATGCCCTCTCACCCAGGGC;RSEQ=GCCACCTACCTGCTCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:137,89:226,0:0:2,0:26.9:1:31.1:1:1:0:60:225:1:0:0.4 0/1:171:2:1,1:97,72:169,2:0.0117:2,2:37:1:29.5:1:1:1.34483:60:4:0.0117:0:1 +11 113282275 . C A 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TGCACTTTTTCCAGGACCTC;RSEQ=TGCACAGGTGTGATATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:144,166:310,0:0:2,0:24.7:1:32:1:1:0:59.7:76.5:1:0:0.8 0/1:243:46:21,25:97,100:197,46:0.1893:2,2:24.6:1:27.8:1:0.74385:1.15408:60:14.333:0.1807:0:1.1 +11 113282295 . T G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10128;LSEQ=CTGCACAGGTGTGATATTTA;RSEQ=CCTGGAAGCAATGTGTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:271:254:113,141:5,11:16,254:0.9373:2,2:26.3:1:32.5:1:0.43679:1.76:59.8:62.5:0.9398:0:1.2 1/0:218:131:58,73:37,50:87,131:0.6009:2,2:26.9:1:31.4:1:0.88918:1.07:60:262:0.6093:0:1.1 +11 113282319 . A G 33 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59699;SOR=2.34951;LSEQ=GGAAGCAATGTGTACATGGA;RSEQ=TGCCCTACAGGCACAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:1,0:81,145:226,1:0.0044:2,0:10:0:14:0:0.36123:0:60:0:0:0:7 0/1:194:2:1,1:80,112:192,2:0.0103:2,2:10:0:33.5:1:1:1.40:60:4:0.0105:0:2.5 +11 113282324 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20888;SOR=Inf;LSEQ=CAATGTGTACATGGAATGCC;RSEQ=TACAGGCACAGGAGGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:76,142:218,0:0:2,0:25.8:1:32.5:1:1:0:60:108:1:0:0.9 0/1:184:2:1,1:76,106:182,2:0.0109:2,2:16:0:31:0:1:1.39:60:4:0.0111:0:1.5 +11 113282396 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.023;SOR=Inf;LSEQ=GGCCACAGAGCTGAGCCCCT;RSEQ=TGGACTGCAGCAGAGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:6,77:83,0:0:2,0:25.7:1:31.4:1:1:0:60:82:1:0:0.1 0/1:34:3:0,3:6,25:31,3:0.0882:2,0:10:1:32:1:1:0:60:6:0.0882:0:1 +11 113283499 . G T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGGGACGGGTCGGGGAGA;RSEQ=TCAGCTGGTGGTGGCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:20:0:33:0:1:0:60:2:1:0:0 +11 113872373 . T A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACGTCAGCACTGCATCGC;RSEQ=GTCTGACAGCTCTCACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:18,14:0,0:0,32:1:0,2:24.3:1:30.3:1:1:0:60:31:1:0:1.3 1/1:20:20:14,6:0,0:0,20:1:0,2:20.4:1:29.7:1:1:0:60:40:1:0:1.2 +11 113872478 . C A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04862;SOR=5.88717;LSEQ=TCCCGTCTTGGCATCTGATT;RSEQ=TCAGAGGACCTGGAATAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:2,5:7,4:0.3636:2,0:23.5:1:31:1:0.49091:0:60:8:0.4:0:1.8 1/0:14:11:1,10:0,3:3,11:0.7857:0,2:25:1:30.5:1:1:0:60:22:0.7857:0:1.1 +11 115127176 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTGCTGGCCCTGTTCT;RSEQ=AGTCACTGGAGTCAGCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:34,2:0.0556:2,2:21:0:31.5:1:1:1.26:60:4:0.0571:0:1 0/0:17:0:0,0:7,10:17,0:0:2,0:27.7:1:31.6:1:1:0:60:34:1:0:0 +11 116658823 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49491;SOR=0;LSEQ=AAAAAGCCGCAGACTCCGGG;RSEQ=ACTCGGGGAACAATGTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:24,2:0.0769:2,2:28.5:1:31:1:1:1:60:4:0.08:0:1.5 0/0:21:0:0,0:12,9:21,0:0:2,0:26.1:1:31.8:1:1:0:60:42:1:0:0.2 +11 116728931 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51163;SOR=0;LSEQ=GCGCTCTGTCATGCTCTGTC;RSEQ=CCCAAGGCTGGGAGCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:2,0:122,2:124,2:0.0159:1,0:10.5:1:32:1:1:0:60:4:0.016:0:1 0/0:90:0:0,0:85,5:90,0:0:2,0:26.9:1:30.7:1:1:0:60:89:1:0:0.1 +11 116729013 . TTGC T 85 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.2029;SOR=2.67337;LSEQ=TATTCTTGCTGTTGCTGCTG;RSEQ=TGCTGCTGCTGCCGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:3:2,1:223,206:429,3:0.0069:2,2:36:1:31.7:1:1:1.85:60:6:0.007:0:0 0/1:381:7:3,4:189,185:374,7:0.0184:2,2:30.1:1:30.6:1:0.72223:1.36106:60:14:0.0185:0:0.6 +11 117049938 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50529;SOR=0;LSEQ=GTCCTGTCTCCTGTCGCCGC;RSEQ=GCCGCCGCCACCACCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:24,2:0.0769:2,2:19.5:1:30:1:1:1:60:4:0.0833:0:1 0/0:18:0:0,0:10,8:18,0:0:2,0:28.3:1:29.2:1:1:0:60:17:1:0:0.2 +11 117226726 . G GCAGCAA 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.09117;SOR=0;LSEQ=TGACTTGGAGAGCAGCAGCA;RSEQ=CAGCAGCAGCAACAGCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:14,7:21,2:0.087:2,2:37.5:1:32.9:1:1:1.93655:55:4:0.087:0:0.5 0/0:52:0:0,0:22,30:52,0:0:2,0:29.8:1:31.3:1:1:0:59.8:25:1:0:0.3 +11 117226746 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAGCAGCAGCAACAGCAAC;RSEQ=TGGCCTCACACCTGGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:22,0:0:2,0:26.1:1:31.8:1:1:0:59.5:44:1:0:0 0/1:49:2:1,1:19,28:47,2:0.0408:2,2:18.5:1:28:1:1:1.46:60:4:0.0417:0:1.5 +11 117226849 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=GGGTATGGCTCAGTCAGACT;RSEQ=GGGTCTCAGAGATCAACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:40:1:32:0:1:0:60:4:0.2857:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:29.3:1:31.2:1:1:0:60:12:1:0:0.2 +11 118307175 . GC G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.51052;SOR=0;LSEQ=GCCCCCCCCTCCGCCTCCCC;RSEQ=CCCCCTGTGTTGTCGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:50,28:78,2:0.025:2,2:23.5:1:31:1:1:1.77202:60:4:0.0256:0:0 0/0:57:0:0,0:37,20:57,0:0:2,0:18.7:1:29.8:1:1:0:59.2:56:1:0:0.8 +11 118307282 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.49474;SOR=Inf;LSEQ=GACCCGGGACCACCGGGGGC;RSEQ=GCGGCGGCGGGGGGCGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:9,36:45,0:0:2,0:16.6:1:31.4:1:1:0:60:90:1:0:0.1 0/1:47:2:1,1:16,29:45,2:0.0426:2,2:16:0:32:0:1:1.79:60:4:0.0435:0:1.5 +11 118307284 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.49412;SOR=Inf;LSEQ=CCCGGGACCACCGGGGGCGG;RSEQ=GGCGGCGGGGGGCGCCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:9,34:43,0:0:2,0:15.3:1:30.5:1:1:0:60:86:1:0:0.1 0/1:43:2:1,1:14,27:41,2:0.0465:2,2:19:1:27:1:1:1.90:60:4:0.0465:0:1 +11 118307391 . C T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.44582;LSEQ=TGGCGGCCCCGGGGCGCCCC;RSEQ=CTCCCCCCCGGCTGTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:20,4:24,1:0.04:2,0:1:0:27:0:0.2:0:60:2:0.0435:0:1 0/1:35:2:1,1:25,8:33,2:0.0571:2,2:6.5:1:27:1:0.45378:3.00458:60:4:0.0571:0:1 +11 118307409 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5099;SOR=Inf;LSEQ=CCCCTCCCCCCCGGCTGTGG;RSEQ=GGCCGCGGCGGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:72,13:85,0:0:2,0:11.7:1:32.5:1:1:0:60:41.5:0.9881:0:0.2 0/1:118:2:1,1:93,23:116,2:0.0169:2,2:22:0:31.5:1:0.3668:3.97957:60:4:0.0174:0:1.5 +11 118307413 . CGCG C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.5109;SOR=1.38883;LSEQ=TCCCCCCCGGCTGTGGCGGC;RSEQ=GCGGCGGCGGCGGGAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:8:7,1:97,16:113,8:0.0645:2,2:13.5:1:32.5:1:1:1.15:59.4:16:0.065:0.0161:0.3 0/1:160:14:10,4:119,27:146,14:0.0875:2,2:14.9:1:29.8:1:0.47591:1.75581:60:13:0.0833:0.0125:0.4 +11 118307703 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53179;SOR=0;LSEQ=GTCCGGGGTCTCGACCCTCT;RSEQ=CGGAGCCCCCTCCCCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:42,151:193,2:0.0103:2,2:10:0:32.5:1:0.39329:3.56:60:4:0.0104:0:1.5 0/0:115:0:0,0:34,80:114,0:0:2,0:23.1:1:31.3:1:1:0:60:113:0.9912:0:0.1 +11 118307774 . A T 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.31207;SOR=0;LSEQ=GGACCATCTCGGGGTCCCTG;RSEQ=CCCGGGGCGAATGGCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:2,42:44,4:0.0833:1,0:28:1:27.5:1:1:0:60:3:0.0667:0:1.5 0/0:20:0:0,0:0,20:20,0:0:1,0:28:1:29.6:1:1:0:60:40:1:0:0.1 +11 118308285 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCAAGCAGACCGATCCTCC;RSEQ=CCATCCCGCCCTACCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:7:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:27.5:1:1:0:60:4:1:0:1 +11 118339693 . TTTTA T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=5.000;MSILEN=4;SSF=0.50693;SOR=0;LSEQ=GGCTGATGAGCTAGACTTCT;RSEQ=TTTATTTATTTATTTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:0,91:91,2:0.0215:1,0:44.5:1:28.5:1:1:0:60:4:0.0215:0:0 0/0:70:0:0,0:1,69:70,0:0:1,0:22.5:1:29.9:1:1:0:57.7:140:1:0:0.1 +11 118341921 . A G 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGATTGAAGAGCAGCGT;RSEQ=TTCAAATTTGTTCAAAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:37.7:1:33:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 118342292 . C T 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.45642;LSEQ=TTGAACTCAGTACAAAATGG;RSEQ=CAGTGCTAAGTTATATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:2,0:146,29:175,2:0.0113:2,0:44:1:28.5:1:1:0:60:4:0.0115:0:1 0/1:122:2:1,1:97,23:120,2:0.0164:2,2:17.5:1:27:1:0.35605:4.14982:60:4:0.0164:0:1 +11 118342294 . A G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5182;SOR=0;LSEQ=GAACTCAGTACAAAATGGCC;RSEQ=GTGCTAAGTTATATTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:154,31:185,2:0.0107:2,2:17.5:1:28.5:1:0.31373:4.90546:60:4:0.0109:0:1 0/0:125:0:0,0:100,25:125,0:0:2,0:22.4:1:29.6:1:1:0:60:250:1:0:0.1 +11 118342310 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19109;SOR=Inf;LSEQ=GGCCAGTGCTAAGTTATATT;RSEQ=AGCTTAGTTAAAACCTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:188,56:244,0:0:2,0:23.5:1:32:1:1:0:59.8:121:1:0:0.1 0/1:190:2:1,1:145,43:188,2:0.0105:2,2:18:1:29:1:0.41047:3.34498:60:4:0.0106:0:1 +11 118342819 . T G 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=ACAGAAAGGATAAAGACCCC;RSEQ=TCGGGTCTCCTCATTAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:888:18:10,8:431,437:868,18:0.0203:2,2:25.1:1:31.4:1:0.64287:1.27:60:36:0.0206:0:1 0/0:710:0:0,0:347,361:708,0:0:2,0:23.9:1:29.6:1:1:0:60:63.364:0.9986:0:0.2 +11 118344493 . TAG T 84 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.2055;SOR=2.6255;LSEQ=AGCGTGGAGAAGGACAAGAG;RSEQ=AGAGAGAGACCGGGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:745:3:1,2:491,250:741,3:0.004:2,2:27:1:27.7:1:0.26616:3.92017:60:6:0.0041:0.0013:0.3 0/1:666:7:4,3:417,242:659,7:0.0105:2,2:25.9:1:30.1:1:0.71209:1.29182:60:14:0.0106:0:0.1 +11 118347812 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51722;SOR=0;LSEQ=GGTCCTCTGAAAAACAGATG;RSEQ=CAAGAGGGGATTAAATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:82,104:186,2:0.0106:2,2:16.5:1:28.5:1:1:1.27:60:4:0.0108:0:1 0/0:127:0:0,0:65,62:127,0:0:2,0:21.4:1:31.3:1:1:0:60:254:1:0:0.1 +11 118347839 . T C 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27211;SOR=0;LSEQ=GGGATTAAATACATGAGGAT;RSEQ=TTATTAGAAGAAATGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:123,115:238,3:0.0124:2,2:22.7:1:25.7:1:1:1.87:60:2:0.0085:0:1.7 0/0:168:0:0,0:97,71:168,0:0:2,0:21.9:1:29.5:1:1:0:60:83:1:0:0.1 +11 118347943 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50302;SOR=0;LSEQ=ACCCCCATGAAGGAGCAGGG;RSEQ=AAGGAAGGCAGAATCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:18,104:122,2:0.0161:2,2:29:1:30.5:1:0.28403:5.65:60:4:0.0163:0:1 0/0:101:0:0,0:23,78:101,0:0:2,0:17.7:1:30.2:1:1:0:60:202:1:0:0 +11 118348712 . C T 79 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22132;SOR=2.38398;LSEQ=AATTGCTGGCTCAGAAGATG;RSEQ=TGAACCTCTTGCTCCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:597:3:0,3:376,218:594,3:0.005:2,0:1:0:21.7:1:0.05029:0:60:2:0.0034:0:1.3 0/1:588:7:3,4:362,219:581,7:0.0119:2,2:14.1:1:28.3:1:0.4354:2.20089:60:14:0.0121:0:1.1 +11 118350811 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14938;SOR=Inf;LSEQ=ATACAGATTCACTGATTGTT;RSEQ=CAGACAAAATGAACACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:200,49:249,0:0:2,0:25.7:1:32.6:1:1:0:60:82:1:0:0.1 0/1:158:2:1,1:118,38:156,2:0.0127:2,2:40:1:29:1:0.43393:3.07797:60:4:0.0127:0:1 +11 118351035 . CT C 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.52458;SOR=1.54548;LSEQ=ACACCCAGTAGAAGAGAATA;RSEQ=TTTTTTTTTAAAGTACAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:5:1,4:19,159:178,5:0.0273:2,2:27.6:1:34.4:1:0.44317:2.08:59:10:0.0282:0:0.2 0/1:120:5:1,4:22,91:113,5:0.0417:2,2:18:1:30.6:1:1:1.03:60:10:0.0417:0.0083:0.2 +11 118351046 . A T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.6854;LSEQ=AAGAGAATACTTTTTTTTTT;RSEQ=AAGTACAACTCTTTCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:5:0,5:11,131:142,5:0.034:2,0:14.6:1:30.4:1:1:0:57.6:10:0.034:0:3 0/1:85:2:0,2:8,75:83,2:0.0235:2,0:21:1:29.5:1:1:0:60:4:0.0238:0:1.5 +11 118354750 . T A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.03254;SOR=Inf;LSEQ=AAGCAAGACCCAGTCTCTTT;RSEQ=AAAAAAAAATTCAAAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,0:48,0:0:1,0:18.1:1:31.4:1:1:0:60:47:0.9792:0:0.1 0/1:24:3:3,0:21,0:21,3:0.125:1,0:18:1:29:0:1:0:60:6:0.125:0:1 +11 118355063 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23437;SOR=Inf;LSEQ=GTGATCATAAAGTATATTGA;RSEQ=TGTCAAAGACTTTAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:37,165:202,0:0:2,0:22:1:32.6:1:1:0:60:66.333:1:0:0.1 0/1:191:2:1,1:43,146:189,2:0.0105:2,2:39:1:30:1:0.4086:3.37:60:4:0.0106:0:1 +11 118355642 . A C 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCTTGACTTCTGTTCCTAT;RSEQ=ACACCCAGGGTGGTTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1008:0:0,0:481,525:1006,0:0:2,0:25.9:1:29.3:1:1:0:60:58.176:0.998:0:0.1 0/1:839:63:31,32:378,396:774,63:0.0751:2,2:25.2:1:30.8:1:1:1.01:59.7:62:0.075:0:1.1 +11 118355770 . T C 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51279;SOR=0;LSEQ=AATTACTATAGTCTGTTTTG;RSEQ=TGGTATTTAGCAGGTACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:0,2:5,147:152,2:0.013:1,0:17.5:1:35:0:1:0:60:4:0.013:0:1 0/0:109:0:0,0:8,101:109,0:0:2,0:24.6:1:30:1:1:0:60:108:1:0:0 +11 118359161 . G A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07824;SOR=0;LSEQ=AGTACTCTGAATCTCCCGCA;RSEQ=TGTCCAATACTGTACTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:27,0:0,0:0,27:1:0,1:19.3:1:31.3:1:1:0:59.2:54:1:0:1 1/1:11:9:9,0:2,0:2,9:0.8182:0,0:22.9:1:29:1:1:0:60:18:0.8182:0:1.1 +11 118359261 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25531;SOR=0;LSEQ=AACCCAAAGTATATAAGAAG;RSEQ=GTATGGTTGATTATGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:2,1:135,11:146,3:0.0201:2,2:18.3:1:30.3:1:0.22406:5.99104:60:6:0.0203:0:1 0/0:121:0:0,0:109,12:121,0:0:2,0:24.5:1:30.9:1:1:0:60:120:1:0:0.1 +11 118360465 . G T 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01842;SOR=Inf;LSEQ=GTAATAGGTGTTGGGTGAAG;RSEQ=TAATATGATGCTTATCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:357,98:455,0:0:2,0:23.2:1:31.6:1:1:0:60:64:1:0:0.1 0/1:374:5:3,2:276,93:369,5:0.0134:2,2:12.8:1:24.2:1:0.6046:1.97445:60:4:0.0109:0:1 +11 118360822 . A T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0342;SOR=Inf;LSEQ=AAAACAAGAAATTCCTATTG;RSEQ=ATTTCTTTTCTTCTTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:205,74:279,0:0:2,0:21.7:1:30.3:1:1:0:60:68.75:1:0:0.1 0/1:212:4:1,3:158,50:208,4:0.0189:2,2:8.5:1:23.5:1:0.04911:9.35479:60:8:0.0189:0:1.3 +11 118361882 . C T 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37326;SOR=3.89937;LSEQ=CACGGGTATGTGAGCCAAAG;RSEQ=ACTGCTGTAAACTTTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:0,1:228,67:295,1:0.0034:2,0:1:0:12:0:0.22973:0:60:0:0:0:1 0/1:306:4:1,3:202,100:302,4:0.0131:2,2:11.3:1:25.8:1:0.11257:6.02256:59.5:8:0.0133:0:1 +11 118362385 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19092;SOR=Inf;LSEQ=ATGGCTTTATAGTAAGTTCA;RSEQ=TGGAATAGTTTCCTCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:184,37:221,0:0:2,0:22.7:1:32.7:1:1:0:59.9:54.25:1:0:1 0/1:172:2:1,1:143,27:170,2:0.0116:2,2:8.5:1:28:1:0.29988:5.21913:60:4:0.0118:0:1.5 +11 118362393 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19195;SOR=Inf;LSEQ=ATAGTAAGTTCAGTGGAATA;RSEQ=TTTCCTCTTCTTCCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:206,46:252,0:0:2,0:22.6:1:33.2:1:1:0:59.9:125:1:0:1 0/1:197:2:1,1:160,35:195,2:0.0102:2,2:12.5:1:28:1:0.33285:4.52157:60:4:0.0103:0:2 +11 118362414 . T C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TTTCCTCTTCTTCCTCTCTC;RSEQ=CATTCTTCAGAGGACCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:370:289,81:0,0:0,370:1:0,2:23.2:1:31.4:1:1:0:59.9:60.667:1:0:1.1 1/1:300:271:203,68:20,8:28,271:0.9033:2,2:24.1:1:30.1:1:0.65441:1.19:60:44.167:0.9075:0:1.1 +11 118362869 . T C 98 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAATGAGAAATTTGGACTT;RSEQ=ATACTCTGAAGGTGATAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:25.3:1:29.6:1:1:0:57.2:9:1:0:1.2 1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:33:0:1:0:60:2:1:0:1 +11 118363418 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAAAAAGAAGAAGAACC;RSEQ=CATGGATCACTTTACCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:27.7:1:31.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 118363424 . A C 56 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAGAAGAACCGCATGG;RSEQ=TCACTTTACCTCAGAGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:20:1:28:1:1:0:51.3:3:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 118364071 . G C 33 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=ATATTTAGAAATGTCACGTG;RSEQ=CTTTAGATACCTAAAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:0,2:3,76:79,2:0.0247:1,0:7:1:33:0:1:0:60:4:0.0247:0:1 0/0:64:0:0,0:0,64:64,0:0:1,0:23.2:1:31.9:1:1:0:59.6:63:1:0:0.1 +11 118365162 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51975;SOR=0;LSEQ=AATGCTTACCTATAAGTAAT;RSEQ=ACCCTGTGAATACAATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:41,135:176,2:0.0112:2,2:33.5:1:32:1:0.41725:3.27:60:4:0.0114:0:1 0/0:117:0:0,0:15,102:117,0:0:2,0:21.3:1:28.5:1:1:0:60:116:1:0:0.2 +11 118365163 . A T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51834;SOR=0;LSEQ=ATGCTTACCTATAAGTAATT;RSEQ=CCCTGTGAATACAATGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:41,131:172,2:0.0115:2,2:23.5:1:32.5:1:0.42555:3.17:60:4:0.0115:0:1 0/0:116:0:0,0:15,101:116,0:0:2,0:20.9:1:29.6:1:1:0:60:232:1:0:0.2 +11 118365168 . G A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TACCTATAAGTAATTACCCT;RSEQ=TGAATACAATGAACTTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:38,125:163,0:0:2,0:24.2:1:32.3:1:1:0:59.8:162:1:0:0.1 0/1:103:11:1,10:14,78:92,11:0.1068:2,2:15.1:1:30.6:1:1:1.78626:60:22:0.1078:0:1.1 +11 118365263 . C T 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CCCTGATTCTTTGAGAGGAA;RSEQ=TTGGTGAGGTTGCCAGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:83,20:103,0:0:2,0:25.7:1:32:1:1:0:60:19.6:1:0:0.2 0/1:55:9:6,3:39,7:46,9:0.1636:2,2:34.1:1:31.3:1:0.33983:2.72289:60:18:0.1667:0:1 +11 118365319 . C G 41 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2728;SOR=0;LSEQ=TGGTGGCCTGAAATTATCCT;RSEQ=GTATTAACAGAGAAGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:2,1:186,49:235,3:0.0126:2,2:6.7:1:26:1:0.50878:1.89188:60:2:0.0086:0:1 0/0:165:0:0,0:127,37:164,0:0:2,0:22.5:1:30.4:1:1:0:60:81:1:0:0.1 +11 118366327 . G T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50933;SOR=0;LSEQ=GTGAATGGCTCCTACATGGG;RSEQ=CAACAGGTGATATCAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:146,10:156,2:0.0127:2,2:13:1:25.5:1:0.13481:13.96849:60:4:0.0131:0:1 0/0:117:0:0,0:103,14:117,0:0:2,0:20:1:30.2:1:1:0:60:38:1:0:0.1 +11 118366362 . T A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11149;SOR=Inf;LSEQ=AAGAATTTATTTTATACAGT;RSEQ=CTAGGTATACTGTAGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:238,81:319,0:0:2,0:23.6:1:30.8:1:1:0:59.9:105.333:1:0:0.1 0/1:297:3:2,1:215,78:293,3:0.0101:2,2:14.7:1:22:1:1:1.37661:60:2:0.0069:0:1.7 +11 118367110 . G A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03505;SOR=Inf;LSEQ=CTTTGCAACACAGGGCCCTA;RSEQ=TTAATACATACTCCAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:0:0,0:124,350:474,0:0:2,0:24.2:1:32.2:1:1:0:60:58.25:1:0:0.1 0/1:363:4:3,1:102,257:359,4:0.011:2,2:8.3:1:25.5:1:0.07469:7.51:60:8:0.0111:0:1 +11 118368665 . A G 160 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=42.46474;LSEQ=TTATAGGATGCTGGTCGTTT;RSEQ=CTATATATTGGCCAAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:1:1,0:370,230:600,1:0.0017:2,0:44:0:15:0:1:0:60:0:0:0:3 0/1:528:35:21,14:293,198:491,35:0.0663:2,2:22.1:1:31.3:1:1:1.01:59.3:34:0.0654:0:1.1 +11 118368822 . T G 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGTAAATTTTATGAAAGAGA;RSEQ=TCCCTCTCAGTTTCCAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:26,174:200,0:0:2,0:23.4:1:30.3:1:1:0:60:32.333:1:0:0.1 0/1:185:16:4,12:33,135:168,16:0.0865:2,2:26.2:1:31.4:1:0.53308:1.36:60:32:0.0879:0:1 +11 118370615 . C G 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=ACTGTGAAGATAAGCTCTTT;RSEQ=CTATTGGATATCAGTAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:15:8,7:208,288:496,15:0.0293:2,2:28.2:1:32.3:1:0.43201:1.58:60:30:0.0299:0:1.1 0/0:530:0:0,0:229,301:530,0:0:2,0:24.9:1:30.2:1:1:0:60:52:1:0:0.1 +11 118372187 . G GA 60 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.67946;SOR=1.85242;LSEQ=GAGTGAGACTGTGTCTCAAA;RSEQ=AAAAAAAAAAAAAGATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:3,1:14,1:15,4:0.1905:1,2:24.5:1:30.3:1:0.38596:4.1833:60:8:0.2105:0.0476:0.3 0/1:13:4:2,2:8,1:9,4:0.3077:2,2:17.5:1:30:1:0.2028:6.5151:58.8:8:0.3333:0.0769:0.5 +11 118372452 . C G 222 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCATCACCAGACCGACCT;RSEQ=CTCATTCACAAACCTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1401:119:69,50:677,600:1277,119:0.0849:2,2:25.4:1:32.2:1:0.33682:1.22:59.9:118:0.0856:0:1.1 0/0:1404:0:0,0:737,664:1401,0:0:2,0:24.8:1:30.4:1:1:0:60:86.563:0.9978:0:0.2 +11 118373018 . AAT A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.66616;SOR=1.21393;LSEQ=TAGATTTCCAGTTACCTATA;RSEQ=ATATATATATATAGTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:15:15,0:157,7:164,15:0.0838:1,1:28.1:1:31.5:1:1:0:60:30:0.0843:0.0056:0.1 0/1:100:10:10,0:87,2:89,10:0.1:1,0:26.3:1:31.1:1:1:0:60:20:0.1031:0:0 +11 118373861 . C T 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=45.66524;LSEQ=AACAGATCATCCATTATCAA;RSEQ=GAACATATGGGATCTAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:636:1:0,1:334,301:635,1:0.0016:2,0:1:0:25:0:0.47484:0:60:2:0.0016:0:1 0/1:550:37:22,15:276,237:513,37:0.0673:2,2:25.4:1:30.1:1:0.60899:1.26:60:74:0.0676:0:1 +11 118377394 . T A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26521;SOR=0;LSEQ=AATACTAGCTAGGCTGGGTC;RSEQ=GTGGGATTTCATGTTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:36,230:266,3:0.0112:2,2:12:1:31.7:1:0.05325:12.57:60:6:0.0113:0:1.3 0/0:199:0:0,0:29,170:199,0:0:2,0:21.8:1:29.7:1:1:0:59.8:198:1:0:0.1 +11 118379970 . T A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10254;SOR=Inf;LSEQ=TATCAATGCTAAAAGGATTA;RSEQ=GAGAATCACCCACTTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:80,253:333,0:0:2,0:22.4:1:30.4:1:1:0:60:36:1:0:0.2 0/1:294:3:2,1:77,214:291,3:0.0102:2,2:10:1:23.3:1:0.17687:5.52:60:2:0.0069:0:2.7 +11 118380007 . T TA 115 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11173;SOR=2.16769;LSEQ=ACCTACTTATTTTCTACATT;RSEQ=AAAAAAAAAAATCTAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:9:0,9:9,126:135,9:0.0616:2,0:31.8:1:31.8:1:1:0:60:18:0.0643:0:1.6 0/1:104:13:1,12:5,85:90,13:0.125:2,1:24.5:1:31.3:1:0.56456:1.41:60:26:0.1313:0:0.4 +11 118380850 . A G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05193;SOR=Inf;LSEQ=GAAGGTGAGTGGATTAAATC;RSEQ=GGTTGACCCATCAGCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:116,271:387,0:0:2,0:23.8:1:31.5:1:1:0:59.9:95.75:1:0:0.1 0/1:355:4:2,2:119,232:351,4:0.0113:2,2:16.5:1:31:1:0.60794:1.95:60:8:0.0115:0:1.3 +11 118382820 . GA G 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.52828;LSEQ=TAAGGCAGAGTTGATTCTGT;RSEQ=AAAAAAAATCAGTTAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:3:0,3:21,172:193,3:0.0153:2,0:23.7:1:33.7:1:1:0:60:6:0.0156:0:0 0/0:123:1:0,1:14,108:122,1:0.0081:2,0:38:0:31:0:1:0:60:2:0.0081:0:0 +11 118390255 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12748;SOR=Inf;LSEQ=CCTCTGGCAGAGTGACTATA;RSEQ=CATAGGCATTTCTGTAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:219,34:253,0:0:2,0:24.2:1:32.9:1:1:0:60:41.167:1:0:0.1 0/1:141:2:1,1:123,16:139,2:0.0142:2,2:32:1:28:1:0.22736:7.48819:60:4:0.0145:0:1 +11 118390798 . G A 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.14458;LSEQ=CGGTAAGTCTTGAGTGGGGA;RSEQ=CAGTCATTAGAAACTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:2:1,1:232,445:677,2:0.0029:2,2:16.5:1:29:1:1:1.92:60:4:0.003:0:1 0/1:641:24:10,14:238,379:617,24:0.0374:2,2:28.6:1:29.3:1:0.83178:1.14:59.3:48:0.0379:0:1.5 +11 118391365 . CA C 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.3055;SOR=4.20628;LSEQ=GACAGAGCGAAACTCCATCT;RSEQ=AAAAAAAAAGGGGGGCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:25,1:26,1:0.037:1,0:23:0:34:0:1:0:60:2:0.0385:0:1 0/1:21:3:3,0:17,1:18,3:0.1429:1,0:10.3:1:30.8:1:1:0:60:6:0.15:0.0476:0 +11 118391375 . A G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=0.05454;LSEQ=AACTCCATCTCAAAAAAAAA;RSEQ=GGGGGGCGCTCATTTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:32:31,1:0,0:0,32:0.9143:0,1:18.5:1:33.1:1:1:0:57.1:31:0.9394:0:1.1 0/1:31:11:11,0:18,1:19,11:0.3548:1,0:15.5:1:31.3:1:1:0:55.7:22:0.3793:0:1 +11 118391456 . T A 31 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49853;SOR=0;LSEQ=TTGTCTCTAGGAACCTTCGA;RSEQ=TCAAGACTCAAAACATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:123,46:169,2:0.0117:2,2:7:0:31.5:1:0.47534:2.65605:60:4:0.0118:0:1.5 0/0:170:0:0,0:122,48:170,0:0:2,0:24.2:1:29.6:1:1:0:60:41.5:1:0:0.1 +11 118392935 . C A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07569;SOR=Inf;LSEQ=TGCAAGGAGGCGGGGCCATC;RSEQ=AAAGCAACGCTGAAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:73,253:326,0:0:2,0:23.3:1:32.1:1:1:0:60:64.2:1:0:0.1 0/1:240:3:1,2:61,176:237,3:0.0125:2,2:28.7:1:23.7:1:1:1.44:60:2:0.0085:0:2.7 +11 118432275 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20964;SOR=Inf;LSEQ=CAAGCTCCCTCAGAGCTCAG;RSEQ=AGCAGGCTGCTGAGAGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:8,21:29,0:0:2,0:24.6:1:31.8:1:1:0:50.8:58:1:0:0.1 0/1:25:2:1,1:8,15:23,2:0.08:2,2:30.5:1:29.5:1:1:1.83:29.5:4:0.08:0:2 +11 118432279 . A G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03845;SOR=Inf;LSEQ=CTCCCTCAGAGCTCAGGAGC;RSEQ=GGCTGCTGAGAGCTAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:6,21:27,0:0:2,0:25.4:1:32:1:1:0:50.1:54:1:0:0.1 0/1:23:4:2,2:6,13:19,4:0.1739:2,2:22.3:1:31.5:1:0.58893:2.09:30:8:0.1739:0:1.5 +11 118432350 . G GA 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGATAAACATATGGACA;RSEQ=AAAAAAAAAAGATTTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:18.5:1:33:0:1:0:60:4:0.1818:0:0 0/0:3:0:0,0:1,2:3,0:0:2,0:19.3:1:31:1:1:0:40.3:6:1:0:0.7 +11 119077003 . C T 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCCTCCGCCCGGATAGCCGG;RSEQ=GGCGGCGGCGGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:2,1:3,6:0.6667:2,2:29.3:1:28.8:1:1:2.24:60:5:0.625:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 119077091 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07006;SOR=Inf;LSEQ=TCGCTCGCAGTCGAGCCGAG;RSEQ=CGGCGGACCCGCCTGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:230,58:288,0:0:2,0:25.8:1:31.9:1:1:0:60:47:1:0:0.2 0/1:203:3:1,2:157,43:200,3:0.0148:2,2:13.3:1:25.3:1:0.1242:7.20733:60:6:0.0149:0:1.3 +11 119077232 . GCAC G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.60018;SOR=0.85156;LSEQ=ATGAAGGACGCCTTCCAGCC;RSEQ=CACCACCACCACCACCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:32:20,12:463,402:865,32:0.0355:2,2:29:1:32.1:1:0.36894:1.45:59.8:64:0.0363:0.0011:0.2 0/1:921:28:14,14:473,414:887,28:0.0304:2,2:34.2:1:31.6:1:0.84794:1.14234:60:56:0.0311:0.0011:0 +11 119140830 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTTTAGTGTAATAGTAT;RSEQ=TATATCATCTGTATCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:28.5:1:1:0:60:4:1:0:1.5 +11 119144148 . G T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTATTTTTCTTTTCTT;RSEQ=TTTTGCAGCAAGGTTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:19.7:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 119144402 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCCAAAGGCATGCACC;RSEQ=TGGCTCCTGGTCCCCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:29,1:0,0:0,30:1:0,1:22.2:1:29.7:1:1:0:60:60:1:0:1 1/1:13:13:12,1:0,0:0,13:1:0,1:25.5:1:29.5:1:1:0:60:26:1:0:1.2 +11 119144809 . A T 55 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76367;LSEQ=AGCTTTTTTTTTTTTTTTTT;RSEQ=AATAACATTTGGGGTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:4:1,3:6,112:118,4:0.0325:2,2:15.3:1:27.5:1:0.21291:6.03:56.3:8:0.0331:0:2.3 0/1:120:3:1,2:8,107:115,3:0.025:2,2:12:1:27.3:1:0.21348:6.47:56.7:6:0.0254:0:2 +11 119144869 . CA C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50128;SOR=0;LSEQ=ATTCATTTTAGGAACTATGC;RSEQ=AAAAAAAGATTAAAACTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:0,37:37,2:0.0513:1,0:32:1:32.5:1:1:0:60:4:0.0513:0:0 0/0:30:0:0,0:1,29:30,0:0:1,0:27:1:30.8:1:1:0:59.5:60:1:0:0.5 +11 119145274 . A G 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TTTCAGTTTGTTGTTGTTCA;RSEQ=CCCCACTACTGTTAATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:11,2:6,0:6,13:0.6842:0,2:29.2:1:30:1:1:0:60:5.5:0.6471:0:1.8 0/0:2:0:0,0:2,0:2,0:0:0,0:15.5:1:30.5:1:1:0:60:4:1:0:0 +11 119145463 . GT G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.37596;SOR=1.40774;LSEQ=ATGAACTGAGAGTTGGTGTT;RSEQ=TTTTTTTTTTTCTCATTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:16:14,2:242,49:291,16:0.051:2,2:21:1:32.3:1:1:1.42:59.5:32:0.051:0.0096:0.6 0/1:256:18:13,5:188,49:237,18:0.0703:2,2:19.6:1:31.1:1:0.54842:1.4732:59.4:36:0.072:0.0234:0.3 +11 119145705 . G GT 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.16087;LSEQ=GATTTATTCTTCTGAATTTC;RSEQ=TTATCTTGAGACTTCTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:260:155:29,126:21,83:104,155:0.5962:2,2:20.8:1:30:1:0.87256:1.09889:60:154:0.5969:0.1423:0 0/1:277:53:10,43:54,170:224,53:0.1913:2,2:25.8:1:29.3:1:0.47284:1.36443:60:106:0.1927:0.0325:0.1 +11 119146659 . G C 273 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTTGCCTTGCCTTCCACC;RSEQ=TAATACCAGCATAATCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:432:432:341,91:0,0:0,432:1:0,2:25.2:1:31.2:1:1:0:60:38.273:1:0:1.1 1/0:387:217:160,57:122,47:169,217:0.5607:2,2:24.1:1:29.7:1:0.8172:1.08:60:35.167:0.5538:0:1.1 +11 119148322 . AT A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.7544;SOR=1.35719;LSEQ=AAGTATTATTTTTTGGAAGT;RSEQ=TTTTTTTTTGAAGTAAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:7:7,0:97,2:99,7:0.066:1,0:26.9:1:31.6:1:1:0:60:14:0.066:0:0 0/1:57:5:5,0:50,2:52,5:0.0877:1,0:20.2:1:31.8:1:1:0:60:10:0.0877:0:0.2 +11 119148573 . G T 272 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00163;LSEQ=AGGTGAGTTTTGTTTCACAT;RSEQ=ATAACCATATCACTGGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:638:637:231,406:0,0:0,637:0.9984:0,2:25.4:1:29.3:1:1:0:59.9:211.333:0.9984:0:1.1 1/0:598:306:108,198:107,183:290,306:0.5117:2,2:23.4:1:28.4:1:0.73295:1.07182:60:612:0.5126:0:1.1 +11 119148851 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17414;SOR=Inf;LSEQ=AGTTATTTATTCAACTAATA;RSEQ=TCTTTTAATTTTTTTTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:208,58:266,0:0:2,0:22.8:1:33.1:1:1:0:60:87.667:1:0:0.1 0/1:191:2:1,1:144,45:189,2:0.0105:2,2:26:0:31.5:1:0.42463:3.17599:60:4:0.0106:0:1 +11 119148859 . AT A 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.41054;SOR=2.64693;LSEQ=ATTCAACTAATAGTCTTTTA;RSEQ=TTTTTTTAATCAAAGGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:2:2,0:220,77:297,2:0.0067:2,0:31:1:33:0:1:0:60:4:0.0067:0:0 0/1:228:4:3,1:167,57:224,4:0.0175:2,2:28.5:1:29:1:1:1.02:58.8:8:0.0175:0.0044:0.3 +11 119149126 . CT C 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.99864;LSEQ=GGGTTAGGTTTAAACTTTTA;RSEQ=TTTTTTTGATCTCTAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:4:1,3:179,65:244,4:0.0161:2,2:22.8:1:34.5:1:0.06394:8.17895:60:8:0.0161:0:0 0/1:187:3:3,0:135,49:184,3:0.016:2,0:20:1:31:1:0.56809:0:60:6:0.0163:0:0 +11 119149355 . TATG T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.36701;SOR=0.61131;LSEQ=AGGGAGCTCCCTCCCCAAAT;RSEQ=ATGATGATGATGATGAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:13:5,8:161,294:455,13:0.0278:2,2:28.2:1:31.5:1:0.77789:1.14:60:26:0.0285:0.0043:0 0/1:408:7:2,5:139,261:400,7:0.0172:2,2:24.6:1:26.9:1:1:1.33053:57.9:6:0.0148:0.0025:0.6 +11 119149481 . T A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.27661;SOR=0;LSEQ=TGAGTTGTCTTCTAAAGCCG;RSEQ=AAAACACTTAACGATATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:2,1:27,140:167,3:0.0176:2,2:19.3:1:28:1:0.0757:10.15:60:6:0.0178:0:1.3 0/0:114:0:0,0:27,87:114,0:0:2,0:21:1:27.7:1:1:0:60:56:1:0:0.1 +11 119155618 . G T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.15376;LSEQ=TGCCATCCACAGCTTTAGGA;RSEQ=AGTTGAAAGATGCCATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:296:192:164,28:88,16:104,192:0.6486:2,2:23.3:1:31.1:1:0.86525:1.06:60:191:0.6497:0:1.1 0/1:245:54:48,6:155,36:191,54:0.2204:2,2:25.5:1:29.6:1:0.2228:1.85:59.7:108:0.2231:0:1 +11 119155649 . G C 165 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCATTTCCCCAAACGAAA;RSEQ=TAATCTGTTAAATTTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:572:0:0,0:407,164:571,0:0:2,0:23:1:32.6:1:1:0:60:62.444:0.9982:0:0.4 0/1:540:45:30,15:339,155:494,45:0.0833:2,2:24.5:1:30.2:1:0.86705:1.09336:60:21.5:0.081:0:1.3 +11 119156346 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50621;SOR=0;LSEQ=CCAGGCACAGTGGCTCATGT;RSEQ=TGTAATCCCAGCAATTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:15,129:144,2:0.0137:2,2:30.5:1:30:0:0.20784:8.36:60:4:0.014:0:1 0/0:113:0:0,0:17,96:113,0:0:2,0:22.9:1:31.5:1:1:0:59.9:226:1:0:0.1 +11 119157009 . C CA 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGTGAAACTTTGTCT;RSEQ=AAAAAAAAAATGTGTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:31:1:1:0:43:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 119167825 . G A 23 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13068;SOR=Inf;LSEQ=ACCTGCTTGGCTTGCTACCT;RSEQ=CACATACTGTTATCCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:18,186:204,0:0:2,0:23.5:1:32.3:1:1:0:60:50:1:0:0 0/1:116:2:1,1:8,106:114,2:0.0172:2,2:7.5:1:23.5:1:0.14978:12.55:60:4:0.0174:0:1 +11 119168007 . T A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17063;SOR=Inf;LSEQ=TTAACATTTATTAGTGATAT;RSEQ=GGCAAAACGAGAAGATGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:160,24:184,0:0:2,0:22.3:1:31.4:1:1:0:59.7:183:1:0:0.1 0/1:130:2:1,1:109,19:128,2:0.0154:2,2:29:0:28:1:0.28503:5.61724:60:4:0.0154:0:1 +11 119168330 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17293;SOR=Inf;LSEQ=GGTACGTGCCACCATGCCCG;RSEQ=CTAATTTTTGTATTTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:33,0:0:1,0:24.2:1:31.3:1:1:0:46.9:15.5:1:0:0.3 0/1:24:2:0,2:1,21:22,2:0.0833:1,0:17:1:30.5:1:1:0:60:4:0.0833:0:1 +11 119168370 . G A 107 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57143;SOR=0.3808;LSEQ=TAGAGACGGGGTTTCACTAT;RSEQ=TTGGCCAGGCTGGCCTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:0,11:0,7:7,11:0.5789:0,0:20.6:1:31.2:1:1:0:33.5:22:0.5789:0:1 0/1:3:1:0,1:0,1:1,1:0.3333:0,0:47:0:30:0:1:0:21:2:0.3333:0:1 +11 119169032 . C T 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00169;SOR=14.07352;LSEQ=ATGTATTAGAAGATGAAGTG;RSEQ=GTCAGAAGAAGATAACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:0,1:305,126:431,1:0.0023:2,0:1:0:29:0:0.29398:0:60:2:0.0023:0:1 0/1:347:11:9,2:221,115:336,11:0.0317:2,2:22.8:1:28.5:1:0.346:2.34:60:10:0.0293:0:1.1 +11 119170148 . G T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09668;SOR=Inf;LSEQ=ATTAGCACATTTTTATTGCT;RSEQ=TTGTTAAATGAGGATTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:169,9:178,0:0:2,0:21.1:1:32.8:1:1:0:60:177:1:0:0 0/1:152:3:1,2:138,11:149,3:0.0197:2,2:9:1:21.7:1:0.01939:23.76087:60:2:0.0134:0:1.7 +11 119342538 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTACCCGGCAGGACTCAGG;RSEQ=CACCCAGCCATACCCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:29.5:1:1:0:60:4:1:0:1 +11 119343746 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1705;SOR=Inf;LSEQ=CGTGCTGGTGGTGTCGGGAG;RSEQ=GAAGGCAGGGAACAAGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:23,36:59,0:0:2,0:25.6:1:30.7:1:1:0:60:58:1:0:0.2 0/1:42:2:1,1:13,27:40,2:0.0476:2,2:33.5:1:29.5:1:1:2.04:60:4:0.0476:0:1 +11 119841508 . A G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACTGCAGTGCCGCTGGA;RSEQ=TCAGCGCGGAGCAGTTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:14,11:0,0:0,25:1:0,2:25.6:1:33.2:1:1:0:60:50:1:0:2.2 1/1:39:39:18,21:0,0:0,39:1:0,2:28.1:1:31.7:1:1:0:60:78:1:0:2.1 +11 119841515 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18984;LSEQ=CAGTGCCGCTGGAATCAGCG;RSEQ=GGAGCAGTTAGTTCTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:22:12,10:2,1:3,22:0.88:2,2:26.9:1:29.8:1:1:1.63407:60:44:0.88:0:2.3 1/1:39:35:16,19:2,2:4,35:0.8974:2,2:30.9:1:29.2:1:1:1.18225:60:70:0.8974:0:2.2 +11 119841603 . G C 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TCCAAGGCTGTATTAGCAGG;RSEQ=GGCTGTCAATCTCCAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:17:1:27.3:1:1:0:60:6:0.5:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:29:1:32:0:1:0:60:4:1:0:0 +11 120490037 . G T 27 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATACCCCCATTGCATCTTG;RSEQ=AAGTAACTAACTTGTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:27:1:1:0:52:4:1:0:1 +11 120490585 . CT C 113 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.15944;SOR=1.97095;LSEQ=TTACCCAGTCTCTGCTATTT;RSEQ=TTTTTTTTTTTTAATACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:12:11,1:37,4:41,12:0.2143:2,2:29.8:1:32.8:1:1:1.19:59.6:24:0.2143:0.0357:0.4 0/1:37:13:11,2:20,0:20,13:0.3514:1,2:21.5:1:30.7:1:0.14773:0:59.7:26:0.3514:0.0811:0.5 +11 120490614 . TA T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50599;SOR=0;LSEQ=TTTTTAATACTGAAAAGAGT;RSEQ=ACAGTGTATTATAATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:67,19:86,2:0.0227:2,2:19.5:1:29.5:1:0.40491:3.46244:60:4:0.0227:0:0.5 0/0:67:0:0,0:54,13:67,0:0:2,0:22.3:1:27.1:1:1:0:59.9:21.333:1:0:0.2 +11 120490713 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.3301;SOR=1.26233;LSEQ=AATTGGGAGTTTGGGAATCT;RSEQ=GGTGGAGCTGTTAGCGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:78:36,42:40,53:93,78:0.4535:2,2:23.9:1:30.4:1:0.75774:1.13:60:38:0.4497:0:1.1 1/0:170:87:37,50:39,44:83,87:0.5118:2,2:25.5:1:29.7:1:0.64374:1.19651:60:174:0.5148:0:1 +11 120490857 . G T 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.79492;LSEQ=ACTCAACATGGCTTTATCAT;RSEQ=CCTGATGTTAATGCATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:130,67:197,2:0.0101:2,2:8:0:32.5:1:1:1.93344:60:4:0.0103:0:1 0/0:125:1:0,1:88,36:124,1:0.008:2,0:1:0:22:0:0.296:0:60:2:0.0082:0:1 +11 120490870 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17895;SOR=Inf;LSEQ=TTATCATGCCTGATGTTAAT;RSEQ=CATGTTCTCTTTTTACAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:161,77:238,0:0:2,0:23.7:1:32.5:1:1:0:58.8:237:1:0:0.1 0/1:175:2:1,1:120,53:173,2:0.0114:2,2:6.5:1:27:1:0.52315:2.25245:38:4:0.0115:0:1.5 +11 120491113 . C T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04363;SOR=0.24496;LSEQ=CATGTACTGCCCCGTAGCTA;RSEQ=CATAACCCAGTCCCCATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:18:0,18:2,21:23,18:0.439:2,1:25.9:1:30.5:1:0.49512:0:60:17:0.4359:0:1.1 0/1:19:3:0,3:0,16:16,3:0.1579:1,0:17:1:29.7:1:1:0:60:6:0.1579:0:1 +11 121232665 . T C 32 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01099;SOR=0;LSEQ=CCCAGCATTCTGACATTAGC;RSEQ=TCAAAACTGCTCGTAGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:32:1:1:0:25:4:1:0:1.5 0/0:12:0:0,0:4,8:12,0:0:2,0:35.5:1:29.7:1:1:0:30.8:24:1:0:1 +11 121232674 . G A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGACATTAGCTTCAAAACT;RSEQ=CTCGTAGACATTCATCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:21:0:34:1:1:0:25:4:1:0:1.5 0/1:12:2:0,2:4,6:10,2:0.1667:2,0:28.5:1:30.5:1:0.51515:0:33:4:0.1667:0:1 +11 121232681 . G A 95 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=TAGCTTCAAAACTGCTCGTA;RSEQ=ACATTCATCACTGTTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:14:0:34:1:1:0:25:4:1:0:1.5 1/1:12:10:4,6:0,2:2,10:0.8333:0,2:19.2:1:28.8:1:0.51515:0:30.4:20:0.8333:0:1 +11 121232811 . A G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCAATTGGTACTCTTCCAC;RSEQ=ATCCCTCCTGTGATACAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:12,21:0,0:0,33:1:0,2:28.7:1:32.2:1:1:0:32.6:66:1:0:1.2 0/1:164:29:9,20:68,67:135,29:0.1768:2,2:29.3:1:30.4:1:0.06702:2.24452:33:28:0.175:0:1.3 +11 121233279 . T C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.12046;LSEQ=CCTGTACCTTTAATGTCTGC;RSEQ=GCTATGAAACCAAGTATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:44:13,31:1,7:8,44:0.8462:2,2:38.4:1:30.3:1:0.42338:2.89:31.1:21:0.84:0:1.2 0/1:61:24:8,16:10,27:37,24:0.3934:2,2:36.7:1:29.5:1:0.7745:1.34:28.8:23:0.3898:0:1.1 +11 121233315 . C A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49508;SOR=0;LSEQ=ATGTTTTCATGGCGCATTAG;RSEQ=ACAGTTTGGTAGATTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:8,23:31,2:0.0606:2,2:7.5:1:29.5:1:0.47727:2.77:35:4:0.0606:0:2 0/0:28:0:0,0:9,19:28,0:0:2,0:6.5:1:30.9:1:1:0:43.7:56:1:0:0.5 +11 121233586 . G C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07831;LSEQ=CTTCATCCGTTCCAAATCAC;RSEQ=ATTGTAACGACGTCTGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:360:323:69,254:11,25:36,323:0.8972:2,2:29.1:1:31.2:1:0.20996:1.6173:45.5:39.375:0.9:0:1.1 0/1:284:115:30,85:42,127:169,115:0.4049:2,2:28.7:1:30.9:1:0.88962:1.07:45.1:230:0.4064:0:1.1 +11 121233618 . CAAT C 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTCTGCTTGAGATGCTCTTG;RSEQ=AATGTCTCCAAGATGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:86,382:468,0:0:2,0:30.3:1:31.1:1:1:0:45.1:116:1:0:0.8 0/1:374:15:3,12:79,280:359,15:0.0401:2,2:27.3:1:31.9:1:1:1.12822:40.2:30:0.0402:0.0027:0.1 +11 121777266 . T TA 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCATATACTACTCAGTT;RSEQ=GACTACTTTTATTTTGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:42:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:28:1:1:0:60:4:1:0:1 +11 121779353 . A G 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18473;SOR=Inf;LSEQ=CCTCACTTGCCAAAGGAAGC;RSEQ=GGGGTGGGAAGATGGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:95,37:132,0:0:2,0:22.5:1:30:1:1:0:59.7:32:1:0:0.1 0/1:100:2:1,1:74,23:97,2:0.02:2,2:6.5:1:30.5:1:0.42795:3.17085:60:4:0.0204:0:1 +11 121779422 . A G 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATTGTGCACATGCTGCTA;RSEQ=GTGCCCAGTGGCACCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:136,131:267,0:0:2,0:26.4:1:31:1:1:0:59.9:65.75:1:0:0.7 0/1:260:17:10,7:127,115:242,17:0.0654:2,2:25.2:1:30.6:1:0.80241:1.29:60:34:0.0659:0:1.1 +11 121779467 . T C 255 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03707;LSEQ=CTTTTACATTATTAATTACC;RSEQ=TGAAATTCAGCCACATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:250:239:103,136:3,7:10,239:0.956:2,2:24:1:32.4:1:0.52387:1.76:60:238:0.9558:0:1.1 0/1:234:104:47,57:58,71:129,104:0.4444:2,2:24.2:1:30.7:1:1:1.01:59.9:103:0.444:0:1.2 +11 121779484 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24825;SOR=Inf;LSEQ=ACCTTGAAATTCAGCCACAT;RSEQ=GTCCCTCTGCCTGCCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:78,125:203,0:0:2,0:25.1:1:31.8:1:1:0:60:100.5:0.995:0:1 0/1:208:3:1,2:81,124:205,3:0.0144:2,2:30:1:27.7:1:1:1.30483:60:6:0.0146:0:2.3 +11 121779497 . G A 39 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62311;SOR=2.90476;LSEQ=GCCACATGGTCCCTCTGCCT;RSEQ=CCTGGACCAGTGCTTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:1:1,0:60,107:167,1:0.006:2,0:1:0:25:0:0.3631:0:55:2:0.006:0:2 0/1:175:3:2,1:67,105:172,3:0.0171:2,2:5.3:1:25:1:0.56265:3.11:60:6:0.0173:0:1.3 +11 121779543 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.27689;LSEQ=GCCATTGGAAACTGACTGTG;RSEQ=TCCAAGAGCCCCCAAGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:4:1,3:22,58:80,4:0.0476:2,2:23:1:29:1:1:1.13623:60:8:0.0482:0:1 0/1:88:32:7,25:15,41:56,32:0.3636:2,2:28.5:1:29.4:1:0.7986:1.30272:60:64:0.3678:0:1 +11 121779664 . T C 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00588;SOR=0;LSEQ=GGCTTTATGCATTTATCTCT;RSEQ=GGTTCCAGGCACAGCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,1:1,13:0.9286:0,1:17:1:31.1:1:1:0:60:26:0.9286:0:1.4 0/0:3:0:0,0:0,3:3,0:0:0,0:32.3:1:26.3:1:1:0:60:2:1:0:0.7 +11 121779687 . A G 76 pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.375;SOR=0;LSEQ=TTCCAGGCACAGCTTTGCAT;RSEQ=TATATGTGTATACGTACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:18.6:1:33:1:1:0:60:10:1:0:2 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:8:0:33:0:1:0:60:4:0.6667:0:1 +11 121939883 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23582;SOR=Inf;LSEQ=TGTTACCGTCCACCTTTTCT;RSEQ=TGATCACTGAGACAAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:121,31:152,0:0:2,0:21.8:1:32.3:1:1:0:60:75:1:0:0.1 0/1:144:2:1,1:108,34:142,2:0.0139:2,2:14:0:28.5:1:0.42832:3.14522:60:4:0.0139:0:1.5 +11 121939976 . A G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.48605;LSEQ=ACTGCCTCTTTTATGACCAC;RSEQ=TTCTCCATCTTAACAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:417:191:107,84:119,106:225,191:0.458:2,2:28:1:30.9:1:0.55409:1.13:60:46.75:0.455:0:1.1 0/1:433:126:67,59:159,148:307,126:0.291:2,2:25.7:1:30.1:1:0.83259:1.06:60:252:0.2937:0:1.1 +11 121940064 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21329;SOR=Inf;LSEQ=TTGTTTAAAATTGCCCACTG;RSEQ=ATACAGCCATTGTAAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:52,156:208,0:0:2,0:25:1:31.6:1:1:0:60:40.6:1:0:0.2 0/1:179:2:1,1:51,125:176,2:0.0112:2,2:18.5:1:26:1:0.5001:2.44:60:4:0.0114:0:1 +11 121940113 . TA T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.18608;SOR=0.31546;LSEQ=AGGTGGGAAAATATCAGACT;RSEQ=AAAAAAAAAGCCTAGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:8:0,8:1,54:55,8:0.127:1,0:32:1:32.4:1:1:0:60:16:0.1356:0:0.3 0/1:46:2:0,2:1,43:44,2:0.0435:1,0:18:1:32:0:1:0:60:4:0.0444:0:0 +11 123605723 . GA G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.2291;SOR=2.35757;LSEQ=TCACACAACACTTGGCATTT;RSEQ=AAAAAAAAAAATCATTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:16,0:11,0:11,16:0.5714:0,1:19.5:1:32.2:1:1:0:60:32:0.5714:0.1429:0.1 1/0:21:16:15,1:3,0:3,16:0.7619:0,1:26.2:1:31.9:1:1:0:60:32:0.7619:0.0952:0.3 +11 123605822 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TACAATACTAATTATTTATC;RSEQ=AGACAAAGCTTTCCAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:132,40:172,2:0.0115:2,2:11.5:1:28:0:0.41678:3.27181:60:4:0.0116:0:1 0/0:137:0:0,0:106,31:137,0:0:2,0:22.6:1:30.1:1:1:0:60:136:1:0:0.1 +11 123605937 . C T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.25871;LSEQ=CTTAAAAGTTTGAGAACCGA;RSEQ=GTCCAGTGAAGTAGACTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:212:105,107:118,131:249,212:0.4599:2,2:26.4:1:30.9:1:0.70846:1.09:60:105:0.4605:0:1.1 1/0:491:385:192,193:53,53:106,385:0.7841:2,2:25.5:1:29.4:1:1:1.0052:60:76:0.7835:0:1.1 +11 123606029 . A C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08647;LSEQ=ATCCTACAACGTATGCATTG;RSEQ=CAGAAGAGTTCCTGCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:83:18,65:27,71:98,83:0.4586:2,2:24.5:1:32.1:1:0.39244:1.37084:60:166:0.4611:0:1 0/1:177:12:3,9:42,123:165,12:0.0678:2,2:19.1:1:31.2:1:1:1.02426:60:24:0.0686:0:1.2 +11 123855651 . C G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01445;SOR=Inf;LSEQ=GGTTATGACCGCCCCTCCCC;RSEQ=CAGGAACTCAGCAGGCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:11,1:12,0:0:2,0:33.8:1:32.3:1:1:0:60:24:1:0:0.2 1/0:8:4:4,0:4,0:4,4:0.5:0,0:23:1:31:1:1:0:60:8:0.5:0:1 +11 123855790 . GA G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50129;SOR=0;LSEQ=ATGAGTTGCACAGTTCCATG;RSEQ=AAAAGCATGGTTTCCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:26,34:60,2:0.0323:2,2:33.5:1:32.5:1:1:1.30:60:4:0.0323:0:0 0/0:50:0:0,0:24,26:50,0:0:2,0:28.5:1:29.7:1:1:0:60:100:1:0:0.1 +11 123856980 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAAATCTGGCTCTCATA;RSEQ=GAGCTTAGTAGCTTGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 125496956 . G T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTCCATGCCCACAAAT;RSEQ=GCTTCTCAGGGTTTAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:19.1:1:31.5:1:1:0:59.6:22:1:0:1.2 1/1:7:7:0,7:0,0:0,7:1:0,0:11.9:1:29.4:1:1:0:60:14:1:0:1.4 +11 125497145 . G A 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATCGCATCTACCCCATA;RSEQ=GAGCTTAGGACAGTCAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:25.5:1:31.5:1:1:0:51.5:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 125497342 . A G 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=TGTATTTCACATTTTAGAAA;RSEQ=GAGTAGTGTGTGTTGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:6,0:23,1:24,6:0.2:1,0:23.8:1:34.2:1:1:0:60:12:0.2069:0:1 0/1:5:1:1,0:4,0:4,1:0.2:0,0:2:0:28:0:1:0:60:2:0.2:0:1 +11 125497461 . G T 56 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.37158;SOR=3.91191;LSEQ=AATCTTTGGAAGTTTTAGAA;RSEQ=AAATGGAATTCTGTAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:1:0,1:103,57:160,1:0.0062:2,0:1:0:23:0:0.36025:0:60:2:0.0063:0:1 0/1:167:4:1,3:101,62:163,4:0.024:2,2:5.5:1:28:1:0.30016:4.84127:60:8:0.0241:0:1.5 +11 125497466 . G T 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGAAGTTTTAGAAGAAAT;RSEQ=GAATTCTGTAATGTTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:106,62:168,0:0:2,0:25.8:1:31.9:1:1:0:60:83:1:0:0.1 0/1:183:70:44,26:67,46:113,70:0.3825:2,2:22.4:1:29.1:1:0.64437:1.16:60:69:0.3791:0:1.1 +11 125498872 . G C 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.59564;LSEQ=TAAGAGGAAGCAGAGGCTTT;RSEQ=AAGTCATGGCTTGCATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:38.5:1:33.5:1:1:0:60:4:0.2857:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:20.5:1:28.5:1:1:0:60:4:0.4:0:1 +11 125499052 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49852;SOR=Inf;LSEQ=GCACATTTGTAAATGTCTAA;RSEQ=CTTCAAATTAAGAAGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:142,26:168,0:0:2,0:24.8:1:33.4:1:1:0:60:167:1:0:0.3 0/1:169:2:2,0:130,37:167,2:0.0118:2,0:23.5:1:31.5:1:1:0:60:4:0.0119:0:1.5 +11 125499059 . A T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.23893;SOR=0;LSEQ=TGTAAATGTCTAAGCTTCAA;RSEQ=TTAAGAAGCTATGTGGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:153,31:184,2:0.0108:2,2:17:0:32:1:0.31526:4.87369:60:4:0.0109:0:1.5 0/0:194:0:0,0:141,53:194,0:0:2,0:23.5:1:29.2:1:1:0:60:96:1:0:0.4 +11 125499063 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00182;SOR=2.09372;LSEQ=AATGTCTAAGCTTCAAATTA;RSEQ=GAAGCTATGTGGTTGCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:36:30,6:139,30:169,36:0.1756:2,2:25.8:1:32.4:1:1:1.08:60:35:0.1716:0:1.3 0/1:204:63:44,19:102,39:141,63:0.3088:2,2:24.4:1:30.4:1:0.73865:1.12868:60:62:0.3069:0:1.1 +11 125502981 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21163;SOR=Inf;LSEQ=ACACCAGTGATTTTTTTTCA;RSEQ=TAAAACTTAATTCCTGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:143,9:152,0:0:2,0:25.7:1:33.6:1:1:0:60:151:1:0:0.1 0/1:130:2:2,0:116,12:128,2:0.0154:2,0:18:1:32:0:1:0:60:4:0.0156:0:1 +11 125505095 . C G 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02064;SOR=Inf;LSEQ=AACTCCTGGGCTCAAGCAGT;RSEQ=CTTCTGCCTCAGCCTCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:19.8:1:32.9:1:1:0:50.1:26:1:0:0.2 1/0:6:3:3,0:3,0:3,3:0.5:0,0:29:1:33.3:1:1:0:60:6:0.5:0:1.3 +11 125505377 . G GA 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58485;SOR=1.15117;LSEQ=AGGAGTATTCTGACTGGAAA;RSEQ=AAAAAAAAACATACCTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:39:21,18:442,400:842,39:0.0442:2,2:28.8:1:30.5:1:1:1.06:59.9:78:0.0452:0:0.2 0/1:969:49:25,24:470,440:910,49:0.0506:2,2:30.2:1:29.1:1:1:1.02543:59.6:48:0.0506:0:0.3 +11 125505504 . C CT 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.82014;SOR=0.89267;LSEQ=GCTATTTGAATTTTTTCTTA;RSEQ=TTTTTTTTTTGTTTTAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:10:1,9:28,206:234,10:0.0405:2,2:29.6:1:31.4:1:1:1.22236:59.5:20:0.0418:0:0.2 0/1:248:9:1,8:32,204:236,9:0.0363:2,2:29.6:1:29.2:1:1:1.25383:60:18:0.039:0:0.1 +11 125507219 . C CTT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.1161;SOR=Inf;LSEQ=GTAATTTAGTAGCTTTAATT;RSEQ=TTTCTCTTCCCCAGGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:59,0:59,0:0:1,0:22.9:1:33.1:1:1:0:60:118:1:0:0.1 0/1:31:2:2,0:29,0:29,2:0.0645:1,0:8.5:1:31.1:1:1:0:60:4:0.0645:0.0323:0 +11 125507256 . G C 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17585;SOR=Inf;LSEQ=ATAATATTTAGACATAAGTA;RSEQ=GCTAACAGAAAATGTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:113,4:117,0:0:1,0:23.5:1:33.6:1:1:0:60:116:1:0:0.2 0/1:85:2:1,1:75,8:83,2:0.0235:2,2:7:1:27:1:0.20168:8.89809:60:4:0.0235:0:1 +11 125507277 . T C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.34503;SOR=1.36275;LSEQ=GCTAACAGAAAATGTGTTTC;RSEQ=TACCTCAAGCCATAGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:26:24,2:139,26:165,26:0.1361:2,2:20.5:1:32.2:1:0.37997:2.24:60:52:0.1368:0:1 0/1:130:23:20,3:81,26:107,23:0.1769:2,2:26:1:30.5:1:0.28428:2.13:60:46:0.1783:0:1 +11 125507402 . CA C 96 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.14965;SOR=2.74618;LSEQ=AGAATTACCATTCCAGACAT;RSEQ=AAAAAGATAGATGGTACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:3:1,2:272,307:579,3:0.0052:2,2:29.7:1:32:1:1:1.77031:60:6:0.0052:0:0 0/1:641:9:4,5:316,316:632,9:0.014:2,2:26.6:1:30.6:1:1:1.24956:60:18:0.0143:0.0016:0 +11 125507588 . TTTTG T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16173;SOR=Inf;LSEQ=AGAAAAAAATACAGAAATAA;RSEQ=TTTATTAATAATTATAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:1,25:26,0:0:1,0:18.4:1:29.5:1:1:0:60:12:1:0:0.2 0/1:18:2:0,2:0,16:16,2:0.1111:1,0:27:1:30:1:1:0:60:4:0.125:0.0556:1.5 +11 125513857 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.09863;SOR=Inf;LSEQ=CCCCATGAAGAATAATACAT;RSEQ=TATGTGTTTTTTCATAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:95,245:340,0:0:2,0:22.8:1:32.4:1:1:0:60:84:1:0:0.1 0/1:293:3:2,1:68,218:286,3:0.0102:2,2:17.7:1:29:1:0.14659:6.36:60:6:0.0103:0:1 +11 125514274 . T A 159 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=118.09797;LSEQ=AACTTTTAAATCACATGTAT;RSEQ=CTTTTTTGGTCAAGGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:1:1,0:48,97:145,1:0.0068:2,0:45:0:28:0:0.33562:0:60:2:0.0069:0:1 0/1:102:46:25,21:23,33:56,46:0.451:2,2:22:1:28.8:1:0.23234:1.70:60:92:0.451:0:1.1 +11 125514323 . A G 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15427;SOR=0;LSEQ=GGGAGGCCTTCATGCAAAAT;RSEQ=ATTTTAAGTCAGACTAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:4:4,0:109,54:163,4:0.024:2,0:25:1:33.5:1:0.30579:0:60:8:0.0244:0:1 0/0:110:0:0,0:87,23:110,0:0:2,0:24:1:28.1:1:1:0:60:109:1:0:0.3 +11 125514573 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10629;LSEQ=TTTTCATTATACCTTTTCCT;RSEQ=AAGAAGAATTTAAATATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:298:244:59,185:14,40:54,244:0.8188:2,2:23.5:1:30:1:0.86129:1.0971:60:47.8:0.8185:0:1 0/1:306:99:28,71:66,141:207,99:0.3235:2,2:23.7:1:28.9:1:0.5967:1.18627:60:48.5:0.3191:0:1.1 +11 125514591 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4998;SOR=0;LSEQ=CTGAAGAAGAATTTAAATAT;RSEQ=TGAGTAAAAGCTATCATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:30,169:199,2:0.01:2,2:18.5:1:34.5:1:0.28532:5.56:60:4:0.0102:0:2 0/0:183:0:0,0:45,138:183,0:0:2,0:25.3:1:29.5:1:1:0:60:182:1:0:0.4 +11 125516454 . CA C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTGTGAAATGATTTTTC;RSEQ=AAGCACCTGTACCATTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:32:1:1:0:60:4:1:0:1 +11 125516476 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCACCTGTACCATTTTAC;RSEQ=TTCCCATCAGTAATGTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:29:1:1:0:60:4:1:0:1 +11 125523456 . C CTG 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=1.20624;LSEQ=CTTGGCTATTGTGAATAATG;RSEQ=TGTAGGGTTGCAAATTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:17,0:17,4:0.1905:1,0:25.5:1:31.1:1:1:0:60:8:0.1905:0.0476:0.3 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:13.5:1:32.5:1:1:0:60:4:0.25:0.1111:0 +11 125525195 . A G 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4898;SOR=0;LSEQ=ATATTGTGAGCAGCCAGAAG;RSEQ=TTTGGCTTCCTGCCACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:500:500:223,277:0,0:0,500:1:0,2:25.1:1:31.7:1:1:0:60:70.429:1:0:1.1 1/1:480:479:208,271:1,0:1,479:0.9979:0,2:25.5:1:30.6:1:0.43542:0:60:78.833:0.9979:0:1.1 +11 125525262 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18889;SOR=Inf;LSEQ=GGTGAATATAGTGCTGCTAT;RSEQ=TTGACATTATTCTTCCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:58,169:227,0:0:2,0:22.2:1:32.2:1:1:0:59.9:112.5:1:0:0.6 0/1:175:2:1,1:44,128:172,2:0.0114:2,2:24.5:1:31.5:1:0.45147:2.89:60:4:0.0116:0:3 +11 125525277 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51461;SOR=0;LSEQ=GCTATGTTGACATTATTCTT;RSEQ=CTAGAGAAGATTATCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:32,136:168,2:0.0118:2,2:8.5:1:27.5:1:0.35148:4.20:60:4:0.012:0:2 0/0:118:0:0,0:27,91:118,0:0:2,0:22:1:30.8:1:1:0:60:236:1:0:0.5 +11 126528035 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACCCAAATGCTGCCATGT;RSEQ=TGTAGTGGTAATGCTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 126528388 . G T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60106;SOR=2.28765;LSEQ=TGAATGTTCACCACTGCAGT;RSEQ=CCCTCATTTAGCCTAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:0,1:130,42:172,1:0.0058:2,0:1:0:25:0:0.24855:0:60:2:0.0059:0:1 0/1:152:2:1,1:111,39:150,2:0.0132:2,2:18:1:25:1:0.45835:2.82298:60:4:0.0133:0:1 +11 126528497 . C G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=1.76839;LSEQ=TCTTTTATACTTTGCCAGCC;RSEQ=TACATTGCTGGATATACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:218:103,115:123,128:251,218:0.4648:2,2:24.4:1:31.2:1:0.71197:1.07273:60:108:0.4635:0:1.1 1/0:378:229:106,123:66,79:145,229:0.6058:2,2:25.9:1:30.4:1:0.91543:1.03:60:228:0.608:0:1.1 +11 126528579 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=TCGTTAAGACTTTTTCTTTG;RSEQ=CTTTAAGGTGCCATATCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:48,137:185,2:0.0107:2,2:23:1:27.5:1:0.45644:2.84:60:4:0.0109:0:1.5 0/0:141:0:0,0:38,103:141,0:0:2,0:23.3:1:29:1:1:0:60:282:1:0:0.3 +11 126529001 . G C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGAAAACTACAGAAAAT;RSEQ=ATACATTTTCCCTCTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:14.5:1:34:0:1:0:45:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 126595573 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12722;SOR=Inf;LSEQ=GCACTGCTGCAGGCTGGACC;RSEQ=TGAGCCCGCTCTGCCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:31,24:55,0:0:2,0:24:1:31.7:1:1:0:60:110:1:0:0.7 0/1:31:2:1,1:15,14:29,2:0.0645:2,2:25.5:1:31:1:1:1.06901:60:4:0.0667:0:2 +11 126595594 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17335;SOR=Inf;LSEQ=TGAGCCCGCTCTGCCCTCGC;RSEQ=GCAAGGCTGCTGCTGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:46,36:82,0:0:2,0:23.2:1:31:1:1:0:59.8:40:1:0:1 0/1:59:2:1,1:33,24:57,2:0.0339:2,2:29.5:1:28:1:1:1.36746:60:4:0.0351:0:2 +11 126595633 . A C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0163;SOR=0;LSEQ=TGGATGTGCGGGGCTGGTGG;RSEQ=GCTCTGTGGCCTGGGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:92:92:43,49:0,0:0,92:1:0,2:26.6:1:31.1:1:1:0:60:45:1:0:1.2 1/1:74:69:33,36:2,3:5,69:0.9324:2,2:25.3:1:30.4:1:1:1.37:59.3:138:0.9324:0:1.4 +11 126595635 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03772;SOR=Inf;LSEQ=GATGTGCGGGGCTGGTGGAG;RSEQ=TCTGTGGCCTGGGTCCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:43,49:92,0:0:2,0:26:1:32.6:1:1:0:60:29.667:1:0:1.2 0/1:74:4:2,2:32,38:70,4:0.0541:2,2:27.3:1:30.5:1:1:1.18:58:8:0.0548:0:3.3 +11 126595642 . G C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04069;SOR=Inf;LSEQ=GGGGCTGGTGGAGCTCTGTG;RSEQ=CCTGGGTCCAGTCTGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:39,43:82,0:0:2,0:26.4:1:31.5:1:1:0:60:19.5:0.975:0:1.2 0/1:70:4:2,2:31,35:66,4:0.0571:2,2:23.8:1:31.5:1:1:1.13:58:8:0.0571:0:3.3 +11 126595646 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50622;SOR=0;LSEQ=CTGGTGGAGCTCTGTGGCCT;RSEQ=GGTCCAGTCTGCACAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:37,42:79,2:0.0244:2,2:29.5:1:29.5:1:1:1.13:60:4:0.0253:0:2 0/0:62:0:0,0:30,32:62,0:0:2,0:23.2:1:30.4:1:1:0:60:124:1:0:1.2 +11 126595819 . T C 54 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTAACTTTCACCCCCAG;RSEQ=TTCTCTGGTGATGTAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:23:1:34.3:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:1:0:31:0:1:0:60:2:1:0:1 +11 127528679 . T A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10992;SOR=Inf;LSEQ=CAGTCAACAATCCATATAGT;RSEQ=GTGTGCCACCGCCGCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:41,46:87,0:0:2,0:27.8:1:30.6:1:1:0:60:86:1:0:0.1 0/1:81:3:2,1:40,38:78,3:0.037:2,2:16.7:1:26:1:1:1.89:60:6:0.0375:0:1 +11 127528695 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.49724;SOR=0;LSEQ=TAGTTGTGTGCCACCGCCGC;RSEQ=GCCTCCTGCTCCTTCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:38,48:86,2:0.0227:2,2:9.5:1:30.5:1:1:1.26:60:4:0.023:0:1 0/0:85:0:0,0:42,43:85,0:0:2,0:29.1:1:29.6:1:1:0:60:84:1:0:0.3 +11 127528712 . GCTC G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.49693;SOR=Inf;LSEQ=CGCCGCCTCCTGCTCCTTCT;RSEQ=CTCCTCCTCCTTCTTCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:32,49:81,0:0:2,0:28.7:1:33.2:1:1:0:60:162:1:0:0.2 0/1:82:2:1,1:34,46:80,2:0.0244:2,2:28.5:1:32:1:1:1.35:60:4:0.0253:0:0.5 +11 127795759 . G T 24 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05983;LSEQ=ATCAGTAATAACATTCTGTA;RSEQ=ATAGCTAGACCCCACTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:104,55:159,2:0.0124:2,2:32.5:1:28.5:1:1:1.88301:60:4:0.0125:0:1 0/1:152:2:0,2:99,51:150,2:0.0132:2,0:1:0:24:1:0.12008:0:60:4:0.0133:0:1 +11 127795770 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49882;SOR=Inf;LSEQ=CATTCTGTAGATAGCTAGAC;RSEQ=CCACTCCATTGATATTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:117,73:190,0:0:2,0:24.2:1:30.8:1:1:0:60:46.5:1:0:0.3 0/1:196:2:1,1:126,68:194,2:0.0102:2,2:19:0:30.5:1:1:1.84682:60:4:0.0104:0:1 +11 127795846 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67147;SOR=0.91935;LSEQ=GGCTAGTATAGTATTCCTAA;RSEQ=CTATTTTTCCCGTTATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:116:57,59:70,76:146,116:0.4427:2,2:24.7:1:31.7:1:0.90116:1.05:60:232:0.4514:0:1 0/1:308:130:61,69:86,92:178,130:0.4221:2,2:26.8:1:30.6:1:0.81838:1.05716:60:260:0.4235:0:1.1 +11 127795857 . C T 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTCCTAATCTATTTTTCC;RSEQ=GTTATAGAAAATTAGATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:116,139:255,0:0:2,0:24.1:1:30.3:1:1:0:59.9:84:1:0:0.5 0/1:283:20:12,8:119,143:262,20:0.0707:2,2:21.2:1:29.2:1:0.24816:1.80:60:40:0.0709:0:1.1 +11 127797395 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGAGTAGCTGGGACTA;RSEQ=AGGCGCCAGCCAACACGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:28.5:1:1:0:27:4:1:0:1.5 +11 128571043 . A G 109 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47619;SOR=0.33027;LSEQ=TGTTGATTAAATATGGCATT;RSEQ=GGGGAGGGAGGAGAAACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:10,0:3,0:3,10:0.7692:0,0:21.7:1:33.1:1:1:0:60:20:0.7692:0:2 1/0:2:1:1,0:1,0:1,1:0.5:0,0:4:0:30:0:1:0:60:2:0.5:0:2 +11 128571080 . T C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19486;SOR=0.31249;LSEQ=CTCTATTTCACCAGATGACA;RSEQ=AAAACTGTGATTATCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:20,0:4,0:4,20:0.8333:0,1:23.2:1:32.2:1:1:0:60:40:0.8696:0:1.6 1/0:10:6:6,0:4,0:4,6:0.6:0,0:22:1:33.5:1:1:0:60:12:0.6:0:1.2 +11 128571179 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49786;SOR=0;LSEQ=CCTGGGCTACAATTTTAGTT;RSEQ=CTTTTGAGAATGAGTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:94,15:109,2:0.018:2,2:33:1:30:0:0.26863:6.09988:60:4:0.0183:0:1 0/0:107:0:0,0:84,23:107,0:0:2,0:23.1:1:30.6:1:1:0:59.9:214:1:0:0.3 +11 128571224 . GA G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.28877;LSEQ=GTGCTTGAGAGGAGAAAAAA;RSEQ=AAAAAAAAAGTCTCTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:298:221:154,67:48,22:70,221:0.7416:2,2:22.2:1:32.6:1:0.88225:1.05:59.8:442:0.7466:0.1611:1 0/1:285:129:89,40:100,55:155,129:0.4526:2,2:26.7:1:31.3:1:0.45055:1.22:60:258:0.4574:0:1 +11 128571257 . A G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.29382;LSEQ=CTCTCTAAAACTCAAATCAA;RSEQ=TTTCTGTGGGCCTTCAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:461:365:221,144:56,40:96,365:0.7918:2,2:25.6:1:32.8:1:0.72595:1.10:59.8:59.833:0.7907:0:1.1 1/0:476:251:149,102:122,103:225,251:0.5273:2,2:25.9:1:31.6:1:0.26724:1.23:60:124.5:0.5309:0:1.2 +11 128571294 . A G 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00373;SOR=Inf;LSEQ=GACAAGTCTGACATTCTTCC;RSEQ=TGAGTTGGCTGGGCCGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:239,246:485,0:0:2,0:27.7:1:30.6:1:1:0:59.9:68.286:1:0:0.7 0/1:483:8:4,4:228,246:474,8:0.0166:2,2:16.3:1:30.5:1:1:1.08:60:16:0.0168:0:1.8 +11 128680191 . A G 33 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGCAAGCAGAAAGGCA;RSEQ=ATCAACAATGACATAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:5:1:33:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 128680394 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18357;SOR=Inf;LSEQ=TGGCAATTCCTCCTGGAGCT;RSEQ=CTCTCCGACAGCGCCAACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:24,2:26,0:0:2,0:20.9:1:32.9:1:1:0:60:52:1:0:0.2 0/1:20:2:1,1:15,3:18,2:0.1:2,2:23:1:27:1:0.36842:4.47215:60:4:0.1:0:1 +11 128680448 . G C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51064;SOR=0;LSEQ=TGGGAGGGGACCAACGGGGA;RSEQ=TTCAAAATGACGGACCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:45,21:66,2:0.0294:2,2:42:1:33.5:1:0.54565:2.11677:60:4:0.0294:0:1 0/0:48:0:0,0:30,18:48,0:0:2,0:24.7:1:31.4:1:1:0:60:96:1:0:0.2 +11 128680462 . AC A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51284;SOR=0;LSEQ=CGGGGAGTTCAAAATGACGG;RSEQ=CCCGATGAGGTGGCCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:44,32:76,2:0.0256:2,2:34.5:1:30.5:1:1:1.36929:60:4:0.0263:0:0 0/0:54:0:0,0:32,22:54,0:0:2,0:27.5:1:30.4:1:1:0:60:53:1:0:0.2 +11 128682606 . G T 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGCTGGTCTATCCAGACT;RSEQ=GTCTGTGAGATTTAACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:50:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:28:1:1:0:60:4:1:0:1 +11 129529524 . G T 111 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.0049;SOR=0;LSEQ=ATCAATGAATCCAGGAGCTG;RSEQ=TTTTTTGAAAAAAATCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:5,9:0,0:0,14:1:0,2:22.7:1:29.4:1:1:0:52.6:28:1:0:1.1 0/1:4:1:1,0:1,2:3,1:0.25:2,0:25:0:25:0:1:0:60:2:0.25:0:1 +11 130715999 . G T 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28821;SOR=3.69083;LSEQ=ATTAACCTCATTCTTATGGA;RSEQ=CTCCCTTTAAAATATTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:1,0:93,2:95,1:0.0104:1,0:48:0:14:0:1:0:50:0:0:0:2 0/1:53:2:2,0:49,2:51,2:0.0377:1,0:41:1:32:1:1:0:60:4:0.0392:0:1 +11 130716055 . T C 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17872;SOR=Inf;LSEQ=AAACCAGACTCGGCAATAAA;RSEQ=GTAAAACCCAAGTCCCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:189,52:241,0:0:2,0:23:1:30.8:1:1:0:60:240:1:0:0.1 0/1:177:2:1,1:128,47:175,2:0.0113:2,2:24:1:25.5:1:0.46995:2.70539:60:4:0.0114:0:1 +11 130716157 . C T 211 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=78.16748;LSEQ=AAAATCCTCTGATTCTATTG;RSEQ=ATAATCTCCAAAAGCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:784:4:1,3:410,369:779,4:0.0051:2,2:30:1:28:1:0.35097:3.32862:60:8:0.0052:0:1 0/1:601:172:95,77:220,208:428,172:0.2862:2,2:25.4:1:28.5:1:0.41668:1.17:60:344:0.2905:0:1.2 +11 130716235 . C A 44 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04057;SOR=Inf;LSEQ=TCCCTGTTTAGTAGAGTCCC;RSEQ=ATTTCCAATTTAGGACTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:133,311:444,0:0:2,0:25.3:1:31.7:1:1:0:60:62.429:1:0:0.1 0/1:363:4:3,1:128,231:359,4:0.011:2,2:7:1:22.3:1:0.13584:5.39:60:3:0.0084:0:1.8 +11 130716312 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17849;SOR=Inf;LSEQ=AGATAAGGTCAAGGAGAAGG;RSEQ=CTTACATTATGTCAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:2,93:95,0:0:1,0:24.2:1:31.5:1:1:0:59.9:30.667:1:0:0.5 0/1:70:2:0,2:2,66:68,2:0.0286:1,0:19:1:30.5:1:1:0:60:4:0.029:0:1.5 +11 130716344 . T C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21125;SOR=0.42476;LSEQ=TCAGCCCCATTATCTGAGCT;RSEQ=GAGAGCCTCCCTTGGCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:59:53:2,51:0,6:6,53:0.8983:0,1:22.6:1:30.5:1:1:0:60:52:0.8966:0:1.1 1/0:33:26:2,24:0,7:7,26:0.7879:0,2:20.5:1:29.7:1:1:0:60:52:0.7879:0:1.1 +11 131050894 . G C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10717;LSEQ=AATATACTACTCCGTCTGAT;RSEQ=GAAAGAATGGCCTCATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:251:235:119,116:8,7:15,235:0.9363:2,2:25.9:1:30.8:1:1:1.11356:60:46:0.935:0:1.2 1/0:213:130:69,61:38,42:80,130:0.6103:2,2:26.1:1:29.7:1:0.47842:1.25:60:129:0.6085:0:1.1 +11 131085743 . T A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00976;SOR=17.54038;LSEQ=TCATTCCTCTTTCCCCAGCA;RSEQ=TGCAAGAGGCCACCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:5,3:8,3:0.2727:2,2:14.7:1:30.3:1:1:1.18:60:6:0.2727:0:1 1/1:9:8:5,3:1,0:1,8:0.8889:0,2:14.8:1:28.4:1:1:0:60:16:0.8889:0:1.1 +11 131085828 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCCTAGCCAATGGTTCC;RSEQ=GGAAAAACACAAGAGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:6,11:17,2:0.1053:2,2:40.5:1:30.5:1:1:1.77:60:4:0.1053:0:1.5 0/0:3:0:0,0:0,3:3,0:0:0,0:25.3:1:29.7:1:1:0:60:6:1:0:2 +11 131085891 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGGCCTGTTTACCACTCTG;RSEQ=GTGGTGAGCGGGGAGGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:23.3:1:31:1:1:0:60:14:0.875:0:1.9 1/1:2:2:0,2:0,0:0,2:1:0,0:34.5:1:31:0:1:0:60:4:1:0:3 +11 131085910 . T C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCGTGGTGAGCGGGGAGGAC;RSEQ=ATTCTGCCTAACTAGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:20:1:33.2:1:1:0:60:10:0.8333:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:15.5:1:31:1:1:0:60:4:1:0:3 +11 131086171 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGTCTGCATCCTGCAAT;RSEQ=GTTTTGAACTCATTAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 131904413 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAAGTGGGCAACTGGATA;RSEQ=TGGCAGATGGGTTTACATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:36.3:1:30.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +11 131904754 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14084;SOR=Inf;LSEQ=AGTTGCTAAATCCCTGTGCT;RSEQ=ATCAAAAATGTTCCCACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:110,24:134,0:0:2,0:24.3:1:32.3:1:1:0:60:66:1:0:0.1 0/1:81:2:1,1:65,14:79,2:0.0247:2,2:31:1:28.5:1:0.33796:4.51981:60:4:0.0247:0:1 +11 131904861 . A T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.88682;SOR=0.97433;LSEQ=CATATTTCTGGTCTCCTAGC;RSEQ=TCTTGATTATTCAGTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:182:89,93:120,122:242,182:0.4282:2,2:26.5:1:31:1:0.92197:1.02776:59.9:59.667:0.4272:0:1.1 0/1:384:162:79,83:115,107:222,162:0.4219:2,2:24.8:1:30.1:1:0.60563:1.12883:59.5:161:0.4226:0:1.1 +11 131904927 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10123;SOR=Inf;LSEQ=GTTTTTCTTCCCATGGTTTT;RSEQ=ATTAACAAAAAATAATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:71,165:236,0:0:2,0:23.3:1:32.1:1:1:0:59.9:46.2:1:0:0.4 0/1:207:3:2,1:78,126:204,3:0.0145:2,2:14.7:1:25.7:1:0.56067:3.21:60:6:0.0148:0:1.3 +11 131904958 . T A 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00625;SOR=Inf;LSEQ=AATAATCTGTTTTGCTGTTG;RSEQ=TTGCTTTGAGTAACTGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:25,98:123,0:0:2,0:23.6:1:30.3:1:1:0:60:246:1:0:0.3 0/1:95:6:1,5:20,69:89,6:0.0632:2,2:21.7:1:29.7:1:1:1.44411:60:12:0.0638:0:1 +11 131905008 . T C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18061;SOR=0.38761;LSEQ=CTGAGAGAAATTTAAAATGT;RSEQ=CCTTTCTAAAAAACCGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:47:0,47:0,4:4,47:0.9216:0,1:23.7:1:31:1:1:0:60:46:0.92:0:1.1 1/1:33:27:0,27:0,6:6,27:0.8182:0,1:22.6:1:30.8:1:1:0:60:54:0.8182:0:1.3 +11 131905556 . G A 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AGTGGGAGGGGTGTGTGTGT;RSEQ=TGTATGTGTGTGTGCCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:3:0:32:1:1:0:51.5:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:30.5:1:1:0:60:4:1:0:1.5 +11 132534870 . A G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00044;SOR=1.59847;LSEQ=TGCAACGGGTTGACTTTGAA;RSEQ=TCTGACATAACATGACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:486:265:124,141:96,125:221,265:0.5453:2,2:26.3:1:32.5:1:0.46577:1.14:59.8:87.333:0.5436:0:1.1 1/0:461:303:134,169:74,84:158,303:0.6573:2,2:26.1:1:31.6:1:0.62259:1.1108:60:606:0.6573:0:1.1 +11 132534934 . G A 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07302;SOR=0;LSEQ=ACAGTGCCACACTAACACCA;RSEQ=CTGGAGGGGAGATGTCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:5:4,1:71,202:273,5:0.018:2,2:17:1:27.8:1:0.01978:11.27:60:10:0.0184:0:1.2 0/0:211:0:0,0:72,139:211,0:0:2,0:22.4:1:31.1:1:1:0:60:104.5:1:0:0.5 +11 132534972 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18487;SOR=Inf;LSEQ=CATTAATACATAGGAAGGGT;RSEQ=CATGCCCACGTGTGTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:17,99:116,0:0:2,0:25.2:1:31.8:1:1:0:59.8:28:1:0:0.2 0/1:88:2:1,1:17,69:86,2:0.0227:2,2:39:1:28:1:0.36912:3.97:60:4:0.0233:0:1 +11 133495417 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20009;SOR=Inf;LSEQ=CCATGATGAGTGACAATCAT;RSEQ=CTATTTTATACTAATATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:136,3:139,0:0:1,0:26:1:32.6:1:1:0:60:45.333:1:0:0 0/1:113:2:1,1:103,8:111,2:0.0177:2,2:10:1:27.5:1:0.1536:12.19759:60:4:0.0182:0:1 +11 133495458 . C T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76153;LSEQ=TGTACACCAAGCTATTTCAT;RSEQ=GGCTGCAATAAATTCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:1,2:233,57:290,3:0.0102:2,2:14.7:1:28.3:1:0.10432:8.09327:60:6:0.0103:0:1 0/0:256:2:1,1:171,83:254,2:0.0078:2,2:20.5:1:28:1:0.54945:2.05398:60:4:0.0079:0:1 +11 133495556 . G C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.77201;LSEQ=GAAGCCTCCCAAGGAACTTT;RSEQ=AGGGAAATTGTAGCCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:739:53:25,28:334,350:684,53:0.0717:2,2:24.6:1:32.1:1:0.88691:1.06874:60:106:0.0724:0:1.1 0/1:620:267:134,133:176,174:350,267:0.4306:2,2:24.9:1:30.9:1:1:1.00394:60:52.4:0.4295:0:1.2 +11 133495639 . C A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.08412;SOR=Inf;LSEQ=CCACTTCACCATACTTCCTC;RSEQ=CCCAGCCCCTACATGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:109,259:368,0:0:2,0:23.7:1:30.7:1:1:0:60:35.8:1:0:0.2 0/1:288:3:2,1:96,188:284,3:0.0104:2,2:5:1:26:1:0.26941:3.90:60:6:0.0106:0:1 +11 133495676 . C T 143 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=4.76265;LSEQ=TTCCATTAAACTGTGATTCC;RSEQ=TTGGAAATAGGCTTAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:12:1,11:19,181:200,12:0.0566:2,2:21.7:1:30.5:1:1:1.15391:60:24:0.0569:0:1.4 0/1:121:27:1,26:16,78:94,27:0.2231:2,1:23.1:1:30.1:1:0.11544:5.28443:60:54:0.225:0:1.3 +11 133495735 . G C 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00562;SOR=5.88046;LSEQ=TATTCCCTGTCATAATGCTT;RSEQ=TCTCAATAGATACTTATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:0,4:1,71:72,4:0.0526:1,0:16.3:1:33.3:1:1:0:60:8:0.0541:0:2.3 0/1:32:8:0,8:0,24:24,8:0.25:1,0:20.8:1:32:1:1:0:60:16:0.25:0:1.9 +12 401969 . C A 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTTCTGTGCTGCGCACACAG;RSEQ=ATTCTCATCATCAGACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1678:41:19,22:795,839:1634,41:0.0244:2,2:27:1:29:1:0.8746:1.09709:60:9.25:0.0222:0:1.2 0/0:1130:0:0,0:552,577:1129,0:0:2,0:24.8:1:31.3:1:1:0:60:111.9:0.9991:0:0.1 +12 404988 . CA C 97 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53982;SOR=0.52744;LSEQ=AAAAATACCATAAAACAAAG;RSEQ=AAAAAAATTAAAACTATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:8:1,7:128,378:506,8:0.0156:2,2:28.1:1:32.6:1:0.6861:2.36739:60:16:0.0159:0:0.1 0/0:363:3:0,3:116,243:359,3:0.0083:2,0:30.7:1:33.3:1:0.55418:0:60:6:0.0083:0:0 +12 405043 . G A 127 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.04226;LSEQ=CAAAGCAAATATTGAGACTA;RSEQ=CCCCCCATCCCCCAATACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:20:1,19:4,132:136,20:0.1274:1,1:25.4:1:29.4:1:0.50124:1.73:60:40:0.137:0:1.1 0/1:106:14:1,13:5,87:92,14:0.1321:2,1:26.4:1:29.2:1:0.582:1.33:60:28:0.1359:0:1.3 +12 406292 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62615;SOR=1.06372;LSEQ=ATGTGGGTCACCACCTCCTC;RSEQ=GATTTGATGGGAATCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1613:216:109,107:697,699:1396,216:0.1339:2,2:25.8:1:30.9:1:0.94173:1.02:60:42.2:0.1325:0:1.2 0/1:885:125:58,67:384,375:759,125:0.1412:2,2:26.7:1:29.6:1:0.44008:1.18267:60:124:0.1417:0:1.1 +12 406427 . G C 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TTTAACTTATTTTATGACAA;RSEQ=GCCCAAAATGGAGGCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:29:2,27:17,231:248,29:0.1047:2,2:24:1:30.3:1:1:1.01:60:58:0.1062:0:1.1 0/0:135:0:0,0:16,119:135,0:0:2,0:25:1:30.2:1:1:0:60:44:1:0:0.1 +12 416059 . T A 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.81067;LSEQ=TCAATAGCTTTTTTTTTTTT;RSEQ=AAACAAACCCAATGATCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:7:5,2:412,144:556,7:0.0124:2,2:26.7:1:27:1:1:1.14414:58.4:6:0.011:0:1.7 0/1:396:4:2,2:270,122:392,4:0.0101:2,2:33.5:1:27.8:1:0.59243:2.20824:58.8:8:0.0104:0:1.8 +12 416764 . C A 195 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTTCATCTGTGGCTAGAGC;RSEQ=TGCCGCGCTCTATCTTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1193:85:45,40:607,500:1107,85:0.0712:2,2:25.2:1:30.5:1:0.7361:1.07904:60:41.5:0.0709:0:1.1 0/0:806:0:0,0:427,379:806,0:0:2,0:24.2:1:30.8:1:1:0:60:114.143:1:0:0.1 +12 416952 . CT C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.97017;LSEQ=TTTAGCTTGCCAGCTGGATC;RSEQ=TTTTTTTGGGAACTTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1155:17:9,8:540,597:1137,17:0.0147:2,2:25.9:1:33.4:1:0.80775:1.24:60:34:0.0148:9e-04:0.2 0/1:840:12:5,7:432,396:828,12:0.0143:2,2:24.9:1:31.2:1:0.56622:1.52649:59.6:24:0.0144:0:0.7 +12 418777 . G T 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10627;SOR=3.81155;LSEQ=TATGGAAAAGACAATTTTGG;RSEQ=AAAAGAGCAGAATACTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:5:5,0:65,0:65,5:0.0714:1,0:17.6:1:30:1:1:0:54.2:10:0.0725:0:1 0/1:13:3:3,0:10,0:10,3:0.2308:0,0:12.3:1:31:0:1:0:60:6:0.2308:0:1 +12 418916 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=1.97867;LSEQ=CTGTGAGTCTGCTAATATCT;RSEQ=TACAGAGTTTTGTATTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:851:94:73,21:582,175:757,94:0.1105:2,2:22.1:1:30.8:1:1:1.05:60:188:0.1115:0:1.1 0/1:522:103:71,32:296,123:419,103:0.1973:2,2:22:1:30.2:1:0.71982:1.08445:60:206:0.1985:0:1 +12 419624 . T C 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCAGGCAACATGATGAAA;RSEQ=CCCATCTCCACCAAAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:27:1:33.5:1:1:0:53.5:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 420274 . G A 44 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.02729;SOR=Inf;LSEQ=ACAATTTGAGTTCTCTTATG;RSEQ=GGTTTGGCAATATACTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:65,238:303,0:0:2,0:25.2:1:31.1:1:1:0:60:59.6:1:0:0.1 0/1:209:4:3,1:53,151:204,4:0.0191:2,2:6.8:1:22:1:0.06046:8.44:60:3:0.0146:0:1.5 +12 421994 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTGTGAGAGAATGTCAT;RSEQ=CCACATATTGCTAGCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:23,1:24,2:0.0769:1,0:21:1:34.5:1:1:0:60:4:0.0769:0:1 0/0:10:0:0,0:9,1:10,0:0:2,0:19.6:1:27.7:1:1:0:60:20:1:0:0 +12 427077 . G A 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53924;SOR=0;LSEQ=GGGAGAGAGGAGAATCTCCC;RSEQ=GTTTCCTTCAGGCCCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:6,0:14,0:14,6:0.3:1,0:19.7:1:30.2:1:1:0:60:12:0.3:0:2 0/0:3:0:0,0:3,0:3,0:0:0,0:19.7:1:28.7:1:1:0:60:6:1:0:0 +12 427165 . CA C 132 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.01111;SOR=2.88767;LSEQ=ATACATTAAAATCCTAAACG;RSEQ=AAAAAAAAAAAAGTCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:17:17,0:91,2:93,17:0.1504:1,1:30.6:1:33.4:1:1:0:56.1:34:0.1504:0.0177:1 0/1:50:17:17,0:29,0:29,17:0.34:1,1:29.7:1:32.5:1:1:0:58.8:34:0.3542:0:0.4 +12 427575 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00018;SOR=1.80747;LSEQ=AAGAATCTGGGGTTTCATCC;RSEQ=TCATGGCCTCCTGAGCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:872:84:26,58:294,493:787,84:0.0963:2,2:26.5:1:31.2:1:0.28438:1.32989:60:41:0.0951:0:1.1 0/1:625:101:43,58:209,312:521,101:0.1616:2,2:26.8:1:30.3:1:0.65896:1.11:60:49.5:0.1602:0:1.1 +12 427687 . T A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.28523;SOR=0;LSEQ=TTAAAACATACAAAAGAGTA;RSEQ=GAAATAGACATAGTCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:3:1,2:5,133:138,3:0.0213:1,2:16:1:31.3:1:0.12314:12.59:60:6:0.0221:0:1.3 0/0:89:0:0,0:2,87:89,0:0:1,0:21.8:1:30:1:1:0:60:88:1:0:0.1 +12 430050 . G GA 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.43376;SOR=1.3807;LSEQ=ATAGCAGCATATATGTGAGA;RSEQ=AAAAAAAAAATCAGAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:20:20,0:175,7:182,20:0.0976:1,1:25.6:1:30.9:1:1:0:59.8:40:0.098:0.0195:0.5 0/1:100:13:13,0:87,0:87,13:0.13:1,1:24.6:1:28:1:1:0:60:12:0.1224:0.03:0.3 +12 431504 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.16184;SOR=Inf;LSEQ=TCAAAGATAATGTACGGCTT;RSEQ=ACAGGCCGGATAAAATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:190,43:233,0:0:2,0:21.8:1:31.9:1:1:0:60:45.6:0.9956:0:0.1 0/1:158:2:1,1:123,33:156,2:0.0127:2,2:17:1:25:1:0.38515:3.68723:60:4:0.013:0:1 +12 431510 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16307;SOR=Inf;LSEQ=ATAATGTACGGCTTCACAGG;RSEQ=CGGATAAAATTTTGGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:209,56:265,0:0:2,0:21.7:1:31.9:1:1:0:60:87.333:1:0:0.1 0/1:180:2:1,1:135,43:178,2:0.0111:2,2:36:1:29:1:0.43017:3.11533:60:4:0.0113:0:2 +12 431517 . A C 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=3e-04;SOR=Inf;LSEQ=ACGGCTTCACAGGCCGGATA;RSEQ=AATTTTGGTTTTTACTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:237,77:314,0:0:2,0:21.5:1:30.6:1:1:0:60:313:1:0:0.1 0/1:219:9:8,1:147,63:210,9:0.0411:2,2:25:1:30.8:1:0.28948:3.41:60:18:0.0421:0:1 +12 431586 . T A 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTCTTCTTAGGTTTACCTG;RSEQ=GTTTCTGCTTTTTGCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:463,257:720,0:0:2,0:24.9:1:30.2:1:1:0:59.9:89:1:0:0.1 0/1:542:32:20,12:306,203:509,32:0.059:2,2:23.6:1:28.8:1:0.85395:1.11:60:31:0.0578:0:1.1 +12 432200 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10783;SOR=0.59762;LSEQ=ACTAAAACAAAGCCTCTTTT;RSEQ=AAGTGACAATCAATTCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:34:29,5:387,154:541,34:0.059:2,2:18.4:1:30.8:1:0.11201:2.31:60:10.333:0.0546:0:1.2 0/1:443:16:11,5:303,123:426,16:0.0361:2,2:27.1:1:31.3:1:0.78539:1.11943:60:32:0.0364:0:1.1 +12 432368 . G A 47 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16277;SOR=2.76207;LSEQ=GAGGTCTTCTAATGGGTAGC;RSEQ=ATATCTACAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:3:2,1:177,349:526,3:0.0057:2,2:18:1:17.3:1:0.26559:3.93:57.7:0.5:0.002:0:3 0/1:322:5:4,1:125,192:317,5:0.0155:2,2:13.8:1:20.6:1:0.16159:6.11:52.2:1.5:0.0103:0:2.6 +12 432406 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26841;SOR=1.41852;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AAAACAGAAATAAAAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:25:24,1:3,156:159,25:0.1359:1,1:6.9:1:28.4:1:0:990.10:53:7.333:0.1236:0:2.5 0/1:126:23:22,1:0,102:102,23:0.1825:1,1:6.1:1:26.1:1:0:0:53.9:6.667:0.1653:0:3.7 +12 432411 . C A 75 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12436;SOR=2.28993;LSEQ=AAAAAAAAAAAAAAAGAAAA;RSEQ=AGAAATAAAAACCTCAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:7:7,0:3,161:164,7:0.0409:1,0:4.6:1:25.6:1:0:0:54.6:14:0.0409:0:3.4 0/1:112:10:9,1:0,102:102,10:0.0893:1,2:5.4:1:22.6:1:0:0:57.2:4:0.0734:0:4.5 +12 432413 . G A 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.83059;LSEQ=AAAAAAAAAAAAAGAAAACA;RSEQ=AAATAAAAACCTCAAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:2,0:3,163:166,2:0.0119:1,0:9.5:1:27:1:0.00071:0:43.5:4:0.0121:0:5 0/0:101:1:1,0:0,100:100,1:0.0099:1,0:4:0:23:0:0.0099:0:52:2:0.0102:0:5 +12 432654 . T A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06091;SOR=2.70084;LSEQ=TCAAGCCTAGAAGTAGACAG;RSEQ=GAAGTTTAGAAGTCCAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:11:9,2:67,5:72,11:0.1325:2,2:27.2:1:29.2:1:0.23126:2.92489:60:10:0.1266:0:2.4 0/1:34:10:10,0:24,0:24,10:0.2941:1,0:27.9:1:29.6:1:1:0:60:20:0.2941:0:2.1 +12 432666 . G C 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00804;SOR=3.32368;LSEQ=GTAGACAGTGAAGTTTAGAA;RSEQ=TCCAGAGTAAAGGAGTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:12:10,2:88,8:96,12:0.1111:2,2:23.1:1:32.5:1:0.30691:2.17968:60:24:0.1121:0:1.8 0/1:44:13:13,0:31,0:31,13:0.2955:1,1:28.5:1:32.8:1:1:0:60:26:0.2955:0:1.8 +12 433026 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13157;SOR=Inf;LSEQ=CTTAAGTTACTACATTTTTT;RSEQ=CTATAGACAAATCTCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:5,153:158,0:0:1,0:24.8:1:29.8:1:1:0:60:30.6:0.9935:0:0.1 0/1:91:2:1,1:9,80:89,2:0.022:2,2:11.5:1:28:1:0.20879:8.48:60:4:0.0225:0:1 +12 433151 . A G 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATTAAAGTTTGGTATCT;RSEQ=AGGATGCACATTTGAGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:0,15:15,3:0.1667:1,2:27:1:34:0:0.16667:0:60:6:0.1765:0:1.3 0/0:5:0:0,0:0,5:5,0:0:0,0:16.8:1:31.8:1:1:0:60:10:1:0:0 +12 437579 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAAGTATTCTAAATCCCA;RSEQ=CCTTGGGGTTAGTCCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:40.5:1:32:0:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 437591 . G T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCCCAGCCTTGGGGTTA;RSEQ=TCCATCCTTCCTATTCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:40:1:33:0:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 438242 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15622;SOR=Inf;LSEQ=AACTCGCTTATAACATATCC;RSEQ=AGCACAGAACCACTACTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:41,226:267,0:0:2,0:23.3:1:31.8:1:1:0:60:65.75:1:0:0.1 0/1:175:2:1,1:35,138:173,2:0.0114:2,2:12:1:28:1:0.37005:3.90:60:4:0.0117:0:1 +12 442584 . C CA 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.79448;SOR=1.2017;LSEQ=AACAGAGCAAGACCCTGTTT;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:8:7,1:338,67:405,8:0.0192:2,2:28.9:1:32:1:1:1.39:56.9:16:0.0197:0:0.4 0/1:304:7:4,3:241,55:296,7:0.023:2,2:20:1:28.9:1:0.13124:3.26924:57.7:14:0.0233:0.0033:0.6 +12 442620 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=4;SSF=0.00011;SOR=1.68562;LSEQ=AGAAAAAACAAACAAACAAA;RSEQ=AAACAACTGAAGGAAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1039:111:79,32:641,287:928,111:0.1068:2,2:25.9:1:30.5:1:0.74405:1.11:59.9:110:0.1079:0:1.2 0/1:858:144:101,43:440,273:713,144:0.1678:2,2:24.8:1:29:1:0.05863:1.46:59.7:71:0.1673:0:1.1 +12 443372 . G C 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=TAATCCACTAGACTTTAGTA;RSEQ=AGTTCATGCATGCTGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:339,108:447,0:0:2,0:24.1:1:32.8:1:1:0:60:73.5:0.9955:0:0 0/1:261:9:7,2:187,65:252,9:0.0345:2,2:18.1:1:31.2:1:1:1.22:60:18:0.0349:0:1.1 +12 459805 . C A 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=ACCTCTTCTTCTGGCAGAAT;RSEQ=TTTCTCCGCCCATCCTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1657:24:15,9:872,759:1631,24:0.0145:2,2:22.8:1:29.5:1:0.41612:1.45:58.9:48:0.0146:0:1.1 0/0:1086:0:0,0:574,512:1086,0:0:2,0:25.5:1:30.9:1:1:0:60:82.538:1:0:0.2 +12 459955 . G GA 93 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.77612;SOR=0.7136;LSEQ=GTGGGAACCATCTACACAGG;RSEQ=AAAAAAAAGATGACAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:810:9:5,4:239,561:800,9:0.0111:2,2:29.8:1:29.6:1:0.13834:2.93:60:18:0.0112:0.0012:0.3 0/0:503:4:0,4:167,332:499,4:0.008:2,0:28:1:30:1:0.30697:0:60:8:0.008:0:0.3 +12 459976 . T A 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01877;SOR=Inf;LSEQ=AAAAAAAAGATGACAAATTA;RSEQ=TAAACCACTATAACTATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:542:0:0,0:114,426:540,0:0:2,0:22.1:1:30.3:1:1:0:59.9:53:0.9981:0:0.1 0/1:320:4:3,1:82,234:316,4:0.0125:2,2:11.8:1:22.3:1:0.05886:8.49:60:3:0.0096:0:1.5 +12 460226 . C T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTAGGAAATCAAGGAGGAA;RSEQ=AAGGAAATGTAAACAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:0,14:1,1:2,14:0.875:2,1:16:1:28.2:1:0.125:0:55:28:0.9333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:28.5:1:1:0:60:4:1:0:1 +12 461598 . C A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12024;LSEQ=TTCCCTAGGTAAAGTAAATC;RSEQ=AGTCAACCCTAGACAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:135:117:1,116:0,18:18,117:0.8667:1,1:28.1:1:32.1:1:1:0:60:234:0.8731:0:1.5 1/1:58:51:0,51:0,7:7,51:0.8793:0,1:24.5:1:30.7:1:1:0:60:50:0.8772:0:1.5 +12 461637 . C T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4425;SOR=0.59168;LSEQ=AAACAAATATCAGCTACTTA;RSEQ=AATACCGTATCAGGAAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:68:1,67:0,5:5,68:0.9315:0,1:21.9:1:29.2:1:1:0:60:67:0.9306:0:1.9 1/1:27:24:0,24:0,3:3,24:0.8889:0,1:25:1:28.3:1:1:0:60:48:0.8889:0:2 +12 461807 . A G 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCTAGGGATGCCTAAC;RSEQ=TTCTTGGCATACCCAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:36.2:1:30.3:1:1:0:55.5:5:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 463405 . T TA 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.09527;SOR=0.62426;LSEQ=AAACATAGAGATCAACCTGT;RSEQ=AAAAAAAAAATAAATGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:856:44:10,34:255,552:807,44:0.0514:2,2:30.2:1:29.9:1:0.24512:1.56989:59.9:21:0.05:0.0035:0.1 0/1:642:21:8,13:213,405:618,21:0.0327:2,2:28:1:29.2:1:0.81625:1.17:59.5:42:0.0334:0:0.3 +12 463460 . G C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATAATAAATTTTTACCA;RSEQ=GAACTCCTTAGCTGAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:16,261:277,0:0:2,0:23.8:1:31.7:1:1:0:59.8:68.25:1:0:0.1 0/1:168:16:2,14:8,144:152,16:0.0952:2,2:16.3:1:29:1:0.2437:2.55:60:15:0.0915:0:1.1 +12 463930 . C CA 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAACAGCAAGACTCCGTCT;RSEQ=AAAAAAAAAAGGAAAGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:31:1:32:1:1:0:46.3:6:0.75:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 464254 . T C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27289;SOR=0.75263;LSEQ=TAAACACATACCATGATATA;RSEQ=CAGGATAGAAAGTGCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:401:355:295,60:35,11:46,355:0.8853:2,2:22:1:32.1:1:0.30276:1.54:59.9:117.333:0.8866:0:1.1 1/1:245:209:172,37:30,5:35,209:0.8531:2,2:22.7:1:31.3:1:0.80956:1.28941:60:208:0.8595:0:1.1 +12 464481 . C A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55418;SOR=0;LSEQ=AGCTTACTATGGACCAGACA;RSEQ=TATTTAAAATTATTTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:2,1:25,273:298,3:0.01:2,2:8.3:1:22.3:1:0.02202:21.31:60:2:0.0069:0:1 0/0:146:0:0,0:14,132:146,0:0:2,0:40:0:17:0:1:0:60:0:0:0:1 +12 465673 . C G 213 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATCTGAAGTTTCTTCAGTT;RSEQ=CGTGTTTCTACTCACATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1195:98:38,60:436,661:1097,98:0.082:2,2:27:1:32.3:1:0.91433:1.04145:60:196:0.0832:0:1.2 0/0:932:0:0,0:384,547:931,0:0:2,0:25.2:1:30.1:1:1:0:60:83.636:0.9989:0:0.1 +12 466176 . A G 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCGAATGGCCAGACACA;RSEQ=TGGCTCACACCTGTAATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:31:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:31.5:1:1:0:49:4:1:0:1.5 +12 476972 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGATCAAGGCTGCAGC;RSEQ=AGCCATGATCACACCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 493157 . C T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16864;SOR=5.49748;LSEQ=ATTTGATATTCCTAAATTCA;RSEQ=AAGCCTGTGCTCTAATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:1:0,1:375,122:497,1:0.002:2,0:1:0:27:0:0.24699:0:60:2:0.002:0:1 0/1:365:4:1,3:257,104:361,4:0.011:2,2:9.3:1:26:1:0.07749:7.36756:60:8:0.0111:0:1 +12 493443 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00577;SOR=0.23242;LSEQ=GGCCTGTTAGGAACCCAGCC;RSEQ=CACAGCAGGAGGTGAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:75:0,75:0,7:7,75:0.9146:0,1:24.9:1:32.3:1:1:0:60:24:0.9114:0:1.1 1/0:38:27:1,26:0,11:11,27:0.7105:0,1:28:1:32:1:1:0:60:54:0.7105:0:1 +12 495217 . G T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0448;SOR=0.39455;LSEQ=AATTATTCCCTTAAAGGGGG;RSEQ=TTTTGCCACAAATCATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:151:140:4,136:0,11:11,140:0.9272:0,1:23.6:1:29.8:1:1:0:60:22.333:0.9241:0:1.1 1/1:84:70:3,67:0,14:14,70:0.8333:1,1:21.6:1:30:1:1:0:60:140:0.8333:0:1 +12 495652 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCAATAAACAATCATTTC;RSEQ=TTACACTTATTTCCACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:32:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 497910 . T G 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48392;SOR=2.0153;LSEQ=AAGAGACACCACTTTCTCGC;RSEQ=TTCAGACGTGTCTACATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:50:50,0:7,0:7,50:0.8772:0,1:26.8:1:29.1:1:1:0:60:15.667:0.8704:0:1.2 1/1:31:29:28,1:2,0:2,29:0.9355:0,1:20.5:1:30.3:1:1:0:60:58:0.9355:0:1.2 +12 497958 . T G 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00217;SOR=Inf;LSEQ=AAGAAACCGAGGCAAAAACA;RSEQ=CCAGAAACAGGCTCCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:149,1:150,0:0:1,0:22.7:1:31.6:1:1:0:59.8:74:1:0:0.2 0/1:110:7:6,1:101,2:103,7:0.0636:1,2:36.1:1:31.7:1:0.18056:8.0519:60:14:0.066:0:1.6 +12 500430 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTTGAGACCAGCCTGGC;RSEQ=AACATGGTGAAATCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:30.5:1:1:0:36:4:1:0:1 +12 1022352 . A G 156 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00034;SOR=0.05909;LSEQ=TCTGTCCAGAGCCTCTCCCT;RSEQ=CTAGAGTGATGGACAAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:25:25,0:42,0:42,25:0.3731:1,1:23.1:1:33.7:1:1:0:57.4:50:0.3731:0:1 0/1:30:1:1,0:29,0:29,1:0.0333:1,0:21:0:27:0:1:0:60:2:0.0333:0:1 +12 1022452 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21594;LSEQ=CAGAATGAAGCAAGATAAAT;RSEQ=GCAATGACGTTCATTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:294:205:191,14:80,9:89,205:0.6973:2,2:22.8:1:31.3:1:0.34979:1.53:58.2:204:0.7034:0:1.1 0/1:169:56:50,6:98,15:113,56:0.3314:2,2:23.9:1:30.5:1:0.80543:1.27:57.9:112:0.3353:0:1 +12 1022453 . G A 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=38.59166;LSEQ=AGAATGAAGCAAGATAAATC;RSEQ=CAATGACGTTCATTCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:1:1,0:271,25:296,1:0.0034:2,0:22:0:14:0:1:0:32:0:0:0:8 0/1:173:20:15,5:135,18:153,20:0.1156:2,2:21.4:1:28.1:1:0.15136:2.48306:57.9:19:0.1105:0:1.2 +12 1022569 . A C 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AGCCTCAGTTAAGATGGATC;RSEQ=TATTTCCTTTTCTTCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1192:0:0,0:574,616:1190,0:0:2,0:25.1:1:30.6:1:1:0:59.8:118:0.9983:0:0.1 0/1:948:22:14,8:444,479:923,22:0.0232:2,2:32.4:1:29.6:1:0.19531:1.89:44.6:21:0.0223:0:1.4 +12 1022679 . A G 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAAAATAAACTGACAGCTA;RSEQ=TGATTTCTGGATTATATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:42,267:309,0:0:2,0:22.1:1:31.2:1:1:0:59.8:60.8:1:0:0.1 0/1:222:66:16,50:39,117:156,66:0.2973:2,2:18.2:1:31.8:1:1:1.04148:60:132:0.2973:0:1 +12 1023218 . G T 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCTGGGTCTGCTCTAGAC;RSEQ=AGGGCTTGACCACACCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:895:0:0,0:352,541:893,0:0:2,0:25.3:1:31.1:1:1:0:59.9:62.786:0.9977:0:0.1 0/1:602:45:20,25:234,322:556,45:0.0748:2,2:21:1:28.9:1:0.75641:1.10:57:90:0.0756:0:1.2 +12 1023273 . T A 48 v3;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01283;SOR=Inf;LSEQ=CACAGCCCACTTTTCAGAGT;RSEQ=GTCTTCAAGAGTCTCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:0:0,0:152,356:508,0:0:2,0:25.1:1:30.4:1:1:0:60:55.444:0.996:0:0.1 0/1:369:5:5,0:133,230:363,5:0.0136:2,0:8.6:1:20.8:1:0.00708:0:60:4:0.0111:0:1.2 +12 1023348 . C G 34 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11574;SOR=Inf;LSEQ=AAGTATTCTCACAGAAAGCA;RSEQ=TGGAAAAACTGGCCCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:28,132:160,0:0:2,0:25.5:1:33:1:1:0:59.7:25.667:1:0:0.2 0/1:83:2:1,1:15,66:81,2:0.0241:2,2:29:1:34:0:0.35028:4.29:60:4:0.025:0:1 +12 1023503 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11345;SOR=Inf;LSEQ=GAACCCCCTCAACAAAACCA;RSEQ=ACGAAAATGAGGATTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:220,33:253,0:0:2,0:21.6:1:32.2:1:1:0:59.9:49.6:1:0:0.1 0/1:129:2:1,1:106,21:127,2:0.0155:2,2:17.5:1:27:1:0.31311:4.9549:60:4:0.0156:0:2.5 +12 1023997 . TA T 60 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTGTCTGGCTCGCTTGT;RSEQ=ACAGCCATAACCCTTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:35.3:1:30.3:1:1:0:60:8:1:0:0 1/1:1:1:0,1:0,0:0,1:1:0,0:40:0:30:0:1:0:60:2:1:0:0 +12 1025332 . C T 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGAAACGGGAAAATGTA;RSEQ=AGCAGATTTAAATATCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:62,3:0,0:0,65:1:0,1:22.1:1:31.5:1:1:0:59.4:64:1:0:1.1 1/1:18:18:18,0:0,0:0,18:1:0,1:22.6:1:30.4:1:1:0:60:36:1:0:1.2 +12 1025475 . C T 67 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.336;SOR=2.10048;LSEQ=GCTACACTTCCTCCTGCAGA;RSEQ=GCCTCCCAGGGCCCTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:4:1,3:508,250:758,4:0.0052:2,2:6:1:29:1:0.10936:6.08073:60:8:0.0053:0:1.3 0/1:547:6:2,4:353,188:541,6:0.011:2,2:11.7:1:26.3:1:0.19088:3.74596:59.5:5:0.0093:0:1 +12 1026061 . G A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15662;SOR=Inf;LSEQ=TTCTCCCTGACTCACAGATT;RSEQ=CGATTCCTGGAAAATCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:14,228:242,0:0:2,0:23.8:1:32.3:1:1:0:59.8:39.333:1:0:0.1 0/1:159:2:1,1:9,148:157,2:0.0126:2,2:7:1:26.5:1:0.1222:15.65:60:4:0.0126:0:1 +12 1026078 . G A 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56177;SOR=3.1907;LSEQ=ATTGCGATTCCTGGAAAATC;RSEQ=CATTTGACATCCTCCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:1:0,1:2,179:181,1:0.0055:1,0:15:0:32:0:1:0:60:2:0.0056:0:1 0/1:115:2:1,1:3,110:113,2:0.0174:1,2:23:0:31.5:1:0.06865:31.90:60:4:0.0177:0:1 +12 1034704 . GA G 92 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00465;SOR=11.51266;LSEQ=CAAAACTCCTAAGGGCAAGA;RSEQ=AAAAAAGGTGAAACAGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1129:1:0,1:407,719:1126,1:9e-04:2,0:18:0:34:0:1:0:60:2:9e-04:0:0 0/1:791:8:3,5:304,479:783,8:0.0101:2,2:30.4:1:30.9:1:1:1.05769:60:16:0.0102:0:0 +12 1034742 . G A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02119;SOR=Inf;LSEQ=GGTTAAGAATTGTTACACAT;RSEQ=AATATCAGAGAATAGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:0:0,0:145,488:633,0:0:2,0:22.7:1:32.1:1:1:0:60:78.125:1:0:0.1 0/1:392:4:3,1:101,285:386,4:0.0102:2,2:10:1:25.8:1:0.05971:8.41:60:8:0.0103:0:1 +12 1034788 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10631;SOR=Inf;LSEQ=TTTGTACAGGTTGCTTCTCA;RSEQ=GAGCAGCAGAGGAAGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:5,242:247,0:0:1,0:23.6:1:31.6:1:1:0:60:122.5:1:0:0.1 0/1:120:2:1,1:4,114:118,2:0.0167:1,2:8.5:1:27.5:1:0.08193:25.60:60:4:0.0169:0:1 +12 1034943 . C T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGAGTATGAAAAGATTA;RSEQ=GGCGCCATTCACAAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:14,5:0.2632:1,0:22:1:31.2:1:1:0:60:10:0.2632:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:23.5:1:32:0:1:0:60:4:1:0:0 +12 1035947 . C A 67 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCGTGACTGTGTAACTA;RSEQ=GTTAACTATGCTACCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:25.3:1:26.3:1:1:0:57.7:5:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:3:0:28:0:1:0:60:2:1:0:1 +12 1036042 . C T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=AGTAGGAGTGGGAAGGCCTC;RSEQ=GGCACACATGACTGAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:30.3:1:33:1:1:0:55:6:0.3:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:16:1:30.8:1:1:0:60:8:1:0:0.8 +12 1036239 . C CA 57 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.43341;SOR=2.26413;LSEQ=TGTGGATGTGTTACCTCTTC;RSEQ=AAAAAAAATCGAAATCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:3:3,0:329,57:386,3:0.0077:2,0:8.7:1:31.9:1:1:0:60:6:0.0079:0.0051:0 0/1:231:4:3,1:183,44:227,4:0.0173:2,2:34:1:28.8:1:0.58232:1.38421:60:8:0.0179:0:0 +12 1036481 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13205;SOR=Inf;LSEQ=ACGAGAGCGGCAGGCGTGCC;RSEQ=CAACTCCCCTGTTCCTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:53,293:346,0:0:2,0:23.7:1:30:1:1:0:60:114.333:1:0:0.1 0/1:198:2:1,1:41,155:196,2:0.0101:2,2:28:1:28.5:1:0.3801:3.75:60:4:0.0104:0:1 +12 1036498 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11172;SOR=Inf;LSEQ=GCCACAACTCCCCTGTTCCT;RSEQ=AAGCAGCAGGGTTCAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:17,226:243,0:0:2,0:25.9:1:32.4:1:1:0:60:47.6:1:0:0.1 0/1:123:2:1,1:17,104:121,2:0.0163:2,2:13.5:1:27:1:0.27229:5.97:60:4:0.0164:0:1 +12 1036562 . AG A 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00135;SOR=0;LSEQ=GCTACAGGGGCACGGGCAGA;RSEQ=GCTGGGTGAGAATCCATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:21:0,21:0,52:52,21:0.2877:1,1:22.7:1:32.8:1:1:0:60:42:0.2877:0.0685:0.2 0/0:26:0:0,0:0,26:26,0:0:1,0:20.9:1:29.8:1:1:0:60:25:1:0:0.3 +12 1036626 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGCCTGGACATGTGCCTG;RSEQ=GGTCAAGGTGTCAAGACGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:0,19:0,0:0,19:0.95:0,1:22.2:1:28.1:1:1:0:60:8.5:0.9444:0:1.5 1/1:8:8:1,7:0,0:0,8:1:0,2:30.4:1:30.1:1:1:0:60:16:1:0:1.1 +12 1038602 . AT CA 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACAACTTATTAACAAAAC;RSEQ=ATTTTTGTTTTCATCAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:0,0:0,5:0.8333:0,0:20.6:1:30.9:1:1:0:56.6:10:1:0.1667:0.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 1038742 . A G 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=CCAAAAAATACATCCTTTGC;RSEQ=ACAATTTTTATATATGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:11,0:10,0:10,11:0.5238:0,0:21.7:1:30.3:1:1:0:60:22:0.5238:0:1.1 0/0:2:0:0,0:2,0:2,0:0:0,0:39:1:29.5:1:1:0:60:4:1:0:0 +12 1038766 . C G 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53613;SOR=0;LSEQ=ATTTTTATATATGGTGAAAA;RSEQ=TTTTAGGTGTCAGCTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:12,0:21,0:21,12:0.3636:1,0:19.6:1:32.8:1:1:0:60:24:0.3636:0:1.2 0/0:3:0:0,0:3,0:3,0:0:0,0:27.3:1:31:1:1:0:60:6:1:0:0 +12 1038854 . C T 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00159;SOR=0;LSEQ=AGAGTATTTGAATTCCACCA;RSEQ=TCTAGGGAACGCTGGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:24:24,0:140,2:142,24:0.1446:1,1:24.3:1:31.4:1:1:0:60:48:0.1463:0:1.1 0/0:51:0:0,0:48,3:51,0:0:2,0:22:1:32:1:1:0:60:102:1:0:0.1 +12 1038978 . C CT 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.24413;LSEQ=GGCAGCAGGTCTACTCCATC;RSEQ=CCTCACCTTCAGCTGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1021:252:140,112:395,373:768,252:0.2468:2,2:27.2:1:30.9:1:0.27575:1.18:59.9:35:0.2448:0.0264:0.1 0/1:770:57:27,30:391,321:712,57:0.074:2,2:26.8:1:29.3:1:0.27329:1.35286:59.7:56:0.0739:0.0156:0.1 +12 1039099 . G A 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05468;SOR=7.43547;LSEQ=AAGAGGACACTGACCGCTGG;RSEQ=CCACAACCATTCCTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:1:1,0:217,249:466,1:0.0021:2,0:46:0:16:0:0.46681:0:60:0:0:0:1 0/1:254:4:3,1:102,148:250,4:0.0157:2,2:21.5:1:28:1:0.30958:4.33:60:8:0.0159:0:1 +12 1039105 . A G 105 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=19.74845;LSEQ=ACACTGACCGCTGGGCCACA;RSEQ=CCATTCCTCCTGCTGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:1:0,1:215,233:448,1:0.0022:2,0:22:0:13:0:1:0:60:0:0:0:1 0/1:236:10:5,5:94,132:226,10:0.0424:2,2:25:1:31.7:1:0.74586:1.40:60:20:0.0431:0:1 +12 1039335 . A G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAACAAATGTTTTTAAGG;RSEQ=AAAGCTGTGTTAATTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:916:0:0,0:313,603:916,0:0:2,0:25:1:30.6:1:1:0:60:113.5:1:0:0.1 0/1:652:31:13,18:233,388:621,31:0.0475:2,2:28.5:1:29.8:1:0.70481:1.20:60:30:0.0464:0:1.2 +12 1039439 . G A 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55067;SOR=0;LSEQ=GTCCTTAAACATTCTTCTCG;RSEQ=GAGGCTGAGGTGGGAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:0,2:0,89:89,2:0.022:1,0:18.5:1:34:0:1:0:60:4:0.0227:0:1 0/0:46:0:0,0:1,45:46,0:0:1,0:21:1:29.9:1:1:0:59.8:22:1:0:0.1 +12 1040143 . TA T 92 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.52273;SOR=0;LSEQ=CAAGACCCTGTCTTTAAAAA;RSEQ=AAAAAAAAAAAAGATGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:7,0:10,0:10,7:0.3684:0,0:27:1:32.8:1:1:0:60:14:0.3684:0.0526:0 0/0:3:0:0,0:3,0:3,0:0:0,0:11.7:1:29:1:1:0:56.7:6:1:0:0 +12 1040219 . G A 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=37.17724;LSEQ=GACCATGCCCAGGCCCCTTC;RSEQ=GATGAGAATGAAGTCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:1:1,0:73,0:73,1:0.0135:1,0:16:0:30:0:1:0:60:2:0.0135:0:2 0/1:17:6:6,0:10,1:11,6:0.3529:2,0:38.2:1:30.3:1:1:0:60:12:0.3529:0:1.2 +12 1040307 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.268;SOR=3.90453;LSEQ=GCAGACTTCCGAATCCCTGA;RSEQ=GACCCAGAGAGGGAACTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:0,1:255,31:286,1:0.0035:2,0:1:0:28:0:0.1115:0:60:2:0.0035:0:3 0/1:148:2:1,1:125,21:146,2:0.0135:2,2:21:1:29:1:0.27606:5.83878:60:4:0.0135:0:1.5 +12 1040373 . T C 304 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGCCTGCTTTCCAGGCACA;RSEQ=GAATTCTCCTACCTTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:800:800:539,261:0,0:0,800:1:0,2:26:1:31.6:1:1:0:59.9:159:1:0:1.1 1/0:528:321:199,122:130,77:207,321:0.608:2,2:27.1:1:30.3:1:0.92674:1.03499:60:44.857:0.605:0:1.1 +12 1041951 . C G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11526;SOR=Inf;LSEQ=TACTAGGTACTGCCCCCGCA;RSEQ=GCACCGCGTCAACGTACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:69,1:70,0:0:1,0:27.3:1:32.3:1:1:0:59.6:69:0.9857:0:0 0/1:37:2:2,0:31,4:35,2:0.0541:2,0:14.5:1:33:0:1:0:50:4:0.0541:0:2 +12 1041953 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.0401;SOR=Inf;LSEQ=CTAGGTACTGCCCCCGCACG;RSEQ=ACCGCGTCAACGTACTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:72,1:73,0:0:1,0:27.4:1:32:1:1:0:59.5:23.333:1:0:0 0/1:39:3:3,0:32,4:36,3:0.0769:2,0:11.3:1:31:0:1:0:51.7:6:0.0769:0:1.7 +12 1041961 . CAACGTACTAGGTACTGCTCACACACGTACTAGGTA C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=59;MSI=3.000;MSILEN=1;SSF=0.85806;SOR=0.92034;LSEQ=TGCCCCCGCACGCACCGCGT;RSEQ=AACGTACTAGGTACTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:51:50,1:42,1:43,51:0.5426:1,1:15.3:1:32.1:1:1:1.19:59.7:102:0.5484:0.2447:0.1 1/0:46:24:23,1:19,3:22,24:0.5217:2,1:22.3:1:31.7:1:0.33643:3.54:59:48:0.5333:0.1522:0.2 +12 1042103 . C T 138 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=18.99295;LSEQ=TGCCCTAACTTTACTCACTT;RSEQ=ACCTCATTCTTTCCCGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:760:2:0,2:510,248:758,2:0.0026:2,0:1:0:23:1:0.10792:0:60:4:0.0027:0:1 0/1:523:25:18,7:316,182:498,25:0.0478:2,2:21:1:29.8:1:0.52284:1.48:60:50:0.0483:0:1.3 +12 1042261 . G GA 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.76553;SOR=0.90426;LSEQ=CTCTATATAAATAAAAAGCG;RSEQ=AAAAAAAAAACAACCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:29:7,22:91,345:436,29:0.0614:2,2:27:1:30.7:1:0.64244:1.21:60:58:0.0652:0:0.1 0/1:340:19:3,16:80,234:314,19:0.0559:2,2:30.1:1:30:1:0.42447:1.82054:60:38:0.0579:0:0.1 +12 1042283 . G A 34 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.6416;SOR=0.4542;LSEQ=AAAAAAAAACAACCCTCAAA;RSEQ=AATGTTTAAAGTAAAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:2,1:34,264:298,3:0.01:2,2:7.7:1:21.7:1:0.03869:15.25:60:2:0.007:0:1.3 0/0:220:1:1,0:32,187:219,1:0.0045:2,0:1:0:25:0:0.15:0:60:2:0.0048:0:1 +12 1043521 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTGTAATTCCAGCTACT;RSEQ=GGGAGGCTGAGGTAGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:32:1:1:0:42:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 1820080 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51531;SOR=0;LSEQ=TGACAAGGAGTTTAAAAATA;RSEQ=GGGCCTGAAGGCGAGTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:2,0:21,7:28,2:0.0667:2,0:29.5:1:31:1:1:0:57.5:4:0.0667:0:1.5 0/0:19:0:0,0:12,7:19,0:0:2,0:18.4:1:29.9:1:1:0:55.1:38:1:0:0.3 +12 2017413 . C G 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CGGCGCGGAGAGGCGTGAGG;RSEQ=CGACGTTTGATGACAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:9,0:0:2,0:29.4:1:32.1:1:1:0:60:18:1:0:0.1 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:5.5:1:31:1:1:1:60:4:0.3333:0:1 +12 2017754 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTCCACACGACCGGGTTCA;RSEQ=ACCTGAACACCCCCCAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:28.5:1:30:0:1:0:46.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 2018088 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=GCCAACTCCCACGCCAGGTT;RSEQ=CTGCACCCCACACCCGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:26.6:1:32.2:1:1:0:51.4:10:1:0:0.4 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:28:1:1:0:60:4:1:0:2.5 +12 2018124 . T C 41 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GGCTCCTCCTCACGACACTG;RSEQ=GGCCCGCGCTGGCCTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:3,1:0.25:2,0:47:0:27:0:1:0:60:2:0.25:0:2 1/1:3:3:1,2:0,0:0,3:1:0,2:22.3:1:26.3:1:1:0:60:6:1:0:2.7 +12 2018272 . C G 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTCACCTAACTGTCCAAGAC;RSEQ=ACTGCCTTCCTCACCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:22.5:1:31.5:1:1:0:60:4:1:0:0.5 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:17:0:32:0:1:0:60:4:1:0:1.5 +12 2018280 . T G 31 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGTCCAAGACCACTGCCT;RSEQ=CCTCACCAGCCTCTGGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:50:0:30:0:1:0:60:2:1:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:5.5:1:31.5:1:1:1.7321:55.5:4:0.5:0:1 +12 2018987 . A G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCAGTGGATCGCCACCCT;RSEQ=CGCCGCCACCCTATGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:36:1:32.5:1:1:0:60:4:1:0:1 +12 2403450 . G C 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23368;SOR=Inf;LSEQ=CGAGAAGACATGGCAGCGGT;RSEQ=GTGGGTCCTGGCAGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:13,26:39,0:0:2,0:25.4:1:31.4:1:1:0:60:78:1:0:0.1 0/1:37:2:0,2:14,21:35,2:0.0541:2,0:6.5:1:31.5:1:0.51652:0:60:4:0.0541:0:1 +12 3001081 . C A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AAAATAAAATAAAATAAAAT;RSEQ=AATCAGTCAATCAATTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:2,3:0.6:0,2:14.3:1:28.7:1:1:0:60:6:0.6:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:19:1:32:0:1:0:60:4:1:0:1.5 +12 3001202 . C A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56854;SOR=1.62419;LSEQ=TTCCAAACTCCTGTGTTGGG;RSEQ=CACTGAGCTCGCTAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:5,0:22,3:25,5:0.1613:2,0:14.8:1:30.6:1:1:0:60:10:0.1786:0:2.2 0/1:46:11:11,0:31,4:35,11:0.2391:2,0:25.5:1:29:1:0.55881:0:60:22:0.25:0:2.3 +12 3001213 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55116;SOR=Inf;LSEQ=TGTGTTGGGCCACTGAGCTC;RSEQ=CTAGCCTGGGCAACGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:31,3:34,0:0:2,0:23.6:1:29.8:1:1:0:59.6:33:1:0:1.3 0/1:68:2:1,1:56,10:66,2:0.0294:2,2:27:1:28:1:0.29939:5.38694:60:4:0.0303:0:1.5 +12 3001248 . T TA 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=4e-05;SOR=0.27095;LSEQ=GCAGTGACATCCTGTCACCT;RSEQ=AAAAAAAAAATGATTTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:32:25,7:25,8:33,32:0.4384:2,2:30.1:1:28.2:1:1:1.14:59.5:15:0.4225:0:2.2 0/1:167:29:20,9:83,37:120,29:0.1737:2,2:23.5:1:27.9:1:1:1.0094:59.7:28:0.1697:0:2 +12 3001268 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.197;LSEQ=TAAAAAAAAAATGATTTGAC;RSEQ=TGTAAGTATTTAGTTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:112:72:52,20:27,13:40,72:0.6429:2,2:25:1:29.7:1:0.66724:1.25:59.5:17:0.6355:0:2.7 0/1:211:55:38,17:103,53:156,55:0.2607:2,2:26.3:1:28.7:1:0.7408:1.15:59.8:17.333:0.2537:0:2.6 +12 3001275 . T G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19653;LSEQ=AAAATGATTTGACGTGTAAG;RSEQ=ATTTAGTTTGATATTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:122:78:55,23:31,13:44,78:0.6393:2,2:25.2:1:31.6:1:1:1.00:59.7:77:0.6364:0:2.6 0/1:237:61:40,21:116,60:176,61:0.2574:2,2:27:1:29.9:1:1:1.01494:59.8:60:0.2575:0:2.6 +12 3001344 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20697;LSEQ=TTTTTAAAAATTGTCACAAA;RSEQ=TTGTTGGGGGTAAAGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:156:89,67:51,40:91,156:0.6316:2,2:26:1:30.5:1:0.89477:1.04:60:77:0.6286:0:1.6 0/1:482:126:71,55:195,159:354,126:0.2614:2,2:23.4:1:29.3:1:0.83517:1.05:60:30.5:0.2552:0:1.4 +12 3001424 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28288;SOR=Inf;LSEQ=TGCACTCTGAAATTTGTTCA;RSEQ=TGTGCTTTTTTTTTTCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:48,107:155,0:0:2,0:23.6:1:32:1:1:0:60:21.143:1:0:0.5 0/1:243:3:1,2:76,164:240,3:0.0123:2,2:24.7:1:24:1:1:1.08:60:2:0.0087:0:2 +12 3001429 . C CT 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.69584;SOR=0.83734;LSEQ=TCTGAAATTTGTTCACTGTG;RSEQ=TTTTTTTTTTCCCAAGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:13:3,10:38,95:133,13:0.0872:2,2:22.3:1:29.5:1:1:1.33089:59.8:12:0.0845:0.0067:0.8 0/1:216:16:4,12:55,143:198,16:0.0741:2,2:26.7:1:27.5:1:1:1.15309:58.8:7:0.0693:0:0.8 +12 3001493 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00952;SOR=0.30141;LSEQ=GTAAGTGGTAGAGGAGATAA;RSEQ=GTTAGTATTCAGCATCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:22:0,22:1,16:17,22:0.5641:1,1:26.3:1:32.2:1:0.4359:0:60:44:0.5789:0:1.5 0/1:54:15:0,15:1,38:39,15:0.2778:1,1:24.9:1:28.4:1:1:0:60:6.5:0.25:0:1.7 +12 3001523 . C A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25903;SOR=0.45705;LSEQ=CAGCATCTCTGGTTGAATTC;RSEQ=GAAAATATTTGTTCAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:0,12:1,11:12,12:0.5:2,0:26.1:1:32.6:1:1:0:60:24:0.5:0:1.8 0/1:29:9:0,9:1,19:20,9:0.3103:1,0:28.4:1:31.6:1:1:0:60:18:0.3103:0:2 +12 3001616 . AT A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGTTTGATATGACTCAG;RSEQ=TTTTTGGGGAAAAAAAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:12:1:31.5:1:1:0:60:4:0.2857:0.125:2 0/0:3:0:0,0:0,3:3,0:0:0,0:22.3:1:28.3:1:1:0:60:6:1:0:1.7 +12 3001627 . A G 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGACTCAGATTTTTTGGGG;RSEQ=AAAAAAAACGGGATGCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:12.5:1:24.5:1:1:0:60:4:0.3333:0:2 0/0:2:0:0,0:0,2:2,0:0:0,0:21:1:30.5:1:1:0:60:4:1:0:0 +12 3001716 . T G 29 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGACGGAGTCTCTCTCTG;RSEQ=CGCCAGGCGGTAGTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:7.5:1:29.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 3361739 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24976;SOR=Inf;LSEQ=CACATGCGGGGAGCCTGCCG;RSEQ=TAGCTGGGCCTGGGCCGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:54,29:83,0:0:2,0:23.1:1:31.5:1:1:0:60:15.6:1:0:0.2 0/1:96:3:1,2:59,34:93,3:0.0313:2,2:12.3:1:29.3:1:0.55403:3.42401:60:6:0.0316:0:1 +12 3361743 . C G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22543;SOR=0;LSEQ=TGCGGGGAGCCTGCCGCTAG;RSEQ=TGGGCCTGGGCCGACTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:57,31:88,2:0.0222:2,2:34:1:32:1:1:1.82563:60:4:0.0227:0:1 0/0:99:0:0,0:62,37:99,0:0:2,0:24:1:31.1:1:1:0:60:98:1:0:0.1 +12 3361750 . TGG T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49841;SOR=Inf;LSEQ=AGCCTGCCGCTAGCTGGGCC;RSEQ=GCCGACTCTTGCAAGATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:67,42:109,0:0:2,0:23.6:1:30.8:1:1:0:60:17.167:1:0:0.1 0/1:117:2:1,1:69,45:114,2:0.0171:2,2:21.5:1:30:1:1:1.52748:60:4:0.0172:0:0 +12 3361755 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49937;SOR=Inf;LSEQ=GCCGCTAGCTGGGCCTGGGC;RSEQ=GACTCTTGCAAGATCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:69,46:115,0:0:2,0:24.3:1:29.6:1:1:0:60:22:1:0:0.2 0/1:128:2:1,1:75,51:126,2:0.0156:2,2:24.5:1:31:0:1:1.46602:60:4:0.0157:0:1 +12 3361756 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49935;SOR=Inf;LSEQ=CCGCTAGCTGGGCCTGGGCC;RSEQ=ACTCTTGCAAGATCCTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:71,47:118,0:0:2,0:24.3:1:30:1:1:0:60:38.333:1:0:0.2 0/1:131:2:1,1:75,53:128,2:0.0153:2,2:13:0:32:1:1:1.41122:60:4:0.0153:0:1.5 +12 3361799 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21375;SOR=0;LSEQ=ATCACAGCCGGAGTCAGCTG;RSEQ=TGGTTTGGGAAGCCTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:69,86:155,2:0.0127:2,2:43.5:1:33.5:1:1:1.24:60:4:0.0131:0:1 0/0:182:0:0,0:91,91:182,0:0:2,0:26.5:1:29.2:1:1:0:60:90:1:0:0.2 +12 3361806 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50116;SOR=Inf;LSEQ=CCGGAGTCAGCTGTTGGTTT;RSEQ=GGAAGCCTTCCCTGGTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:62,90:152,0:0:2,0:27.2:1:31.4:1:1:0:60:75:1:0:0.1 0/1:176:2:1,1:84,90:174,2:0.0114:2,2:22:0:31.5:1:1:1.07:60:4:0.0117:0:1 +12 4383036 . C T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42528;SOR=0.44157;LSEQ=CACCACCCAATCCTCGCCTC;RSEQ=CTTCTGCTCCACCTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:14,0:5,1:6,14:0.7:2,1:29.1:1:32.5:1:0.3:0:60:28:0.7:0:1 1/0:10:5:5,0:4,1:5,5:0.5:2,0:18.4:1:31.6:1:1:0:60:10:0.5:0:1 +12 4383158 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.71495;LSEQ=AAAACAAAAACAGAAAAACC;RSEQ=TTTTCCAGGCCGGGGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:217:181,36:0,0:0,217:0.9954:0,2:21.9:1:31.4:1:1:0:60:35.167:0.9953:0:1.1 1/1:156:155:119,36:0,0:0,155:0.9936:0,2:20.9:1:30.4:1:1:0:60:30:0.9934:0:1.2 +12 4383246 . G T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01924;SOR=Inf;LSEQ=AGGTGGACCCGGTCCGCAGG;RSEQ=CCGTGCGGGACCGCAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:334,230:564,0:0:2,0:24.9:1:31.3:1:1:0:59.9:55.4:0.9946:0:0.2 0/1:473:5:2,3:257,211:468,5:0.0106:2,2:27.4:1:27.8:1:0.66228:1.82466:60:10:0.0108:0:1 +12 4383433 . A G 38 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08573;SOR=Inf;LSEQ=GGTGGCGCTCGCCAGGAGCC;RSEQ=GGACCCCTCCGGATGCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:78,258:336,0:0:2,0:24:1:31.7:1:1:0:60:111:1:0:0.1 0/1:266:3:2,1:74,189:263,3:0.0113:2,2:6.7:1:24.3:1:0.19726:5.07:60:2:0.0076:0:2.7 +12 4383448 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18074;SOR=Inf;LSEQ=GAGCCAGGACCCCTCCGGAT;RSEQ=CTCGGGTCCCCGGCCGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:46,217:263,0:0:2,0:22.1:1:32.2:1:1:0:60:51.6:1:0:0.1 0/1:195:2:1,1:39,154:193,2:0.0103:2,2:26.5:1:29:1:0.36902:3.91:60:4:0.0104:0:1 +12 4384964 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13904;SOR=Inf;LSEQ=TTATAGGATCCCTGGGAATA;RSEQ=CAAAGCACTGATGGGCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:18,3:21,0:0:2,0:19.8:1:31.3:1:1:0:59:20:1:0:0.1 0/1:13:2:1,1:9,2:11,2:0.1538:2,2:18:1:28.5:1:0.42308:3.87298:60:4:0.1538:0:1 +12 4385055 . C CA 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.6505;SOR=0.37357;LSEQ=CTGGTCCCCTCCCCCTCCCA;RSEQ=AAAAAAAAATTAATTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:4:4,0:127,4:131,4:0.0296:1,0:15.8:1:28:1:1:0:60:3:0.0234:0.0148:0 0/1:89:1:1,0:88,0:88,1:0.0112:1,0:23:0:24:0:1:0:60:2:0.0112:0:0 +12 4385068 . A AT 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.56938;SOR=2.92171;LSEQ=CCTCCCACAAAAAAAAATTA;RSEQ=TTTTTTTTGTTTCGATAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:1:1,0:206,3:209,1:0.0047:1,0:34:0:28:0:1:0:60:2:0.005:0:0 0/1:146:2:2,0:144,0:144,2:0.0137:1,0:20.5:1:31.2:1:1:0:60:4:0.0141:0.0068:0.5 +12 4388084 . C G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88685;SOR=1.02425;LSEQ=TTCATTGCTCTGTGTGCCAC;RSEQ=GGTAAGATGAGGCTTGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:439:223:71,152:66,148:214,223:0.508:2,2:26:1:31.2:1:0.83721:1.05:59.9:222:0.5115:0:1.1 1/0:358:184:65,119:53,121:174,184:0.514:2,2:25.6:1:30:1:0.36853:1.25:60:368:0.5169:0:1.1 +12 4388271 . C T 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29412;SOR=4.3679;LSEQ=TTATCTGAGCTTTATATATT;RSEQ=GCTTTCTCTGCTAAACTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:0,8:8,5:0.3846:0,0:17.4:1:31.2:1:1:0:60:10:0.3846:0:1 1/0:4:3:0,3:0,1:1,3:0.75:0,0:33.3:1:31.7:1:1:0:60:6:0.75:0:1 +12 4397766 . G C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14031;SOR=0.37274;LSEQ=TCTGTGCATTCATTGTGTGC;RSEQ=CTTAGATAAGCTGTCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:24,0:22,0:22,24:0.5217:1,1:23.3:1:32.5:1:1:0:59.8:48:0.5217:0:1 0/1:14:4:3,1:9,1:10,4:0.2857:2,2:17.5:1:31.5:1:0.50549:2.73861:60:8:0.3077:0:1 +12 4408673 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCAGAAAGCATCTGGT;RSEQ=GGCCCCTTGATTACCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:33:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 4409270 . TA T 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.70658;SOR=0.61813;LSEQ=TTGTGTTTTAGGGTGAAACT;RSEQ=AAAAAAAAATTCTGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:5:0,5:2,92:94,5:0.0505:1,0:37.6:1:32.2:1:1:0:60:10:0.051:0:0 0/1:63:2:0,2:2,59:61,2:0.0317:1,0:29.5:1:32:0:1:0:60:4:0.0328:0:0 +12 4411343 . CT C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGTCTCACTCCCAGGGAC;RSEQ=TTTTGGTCATGGAGGCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:29.5:1:1:0:60:4:1:0:0 +12 4554413 . C T 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGGGTTCTCCTCGTGGGT;RSEQ=CCGCTGATCCGGCCGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:559:0:0,0:335,224:559,0:0:2,0:26.4:1:31.3:1:1:0:60:49.818:1:0:0.1 0/1:501:93:57,36:239,169:408,93:0.1856:2,2:21.8:1:28.5:1:0.64262:1.12:59.8:22.25:0.1816:0:1.2 +12 4554548 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=0;LSEQ=GCAATCTCTCCAGCTAGCCC;RSEQ=GCGCGAGACCTGGACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:234:20,214:0,0:0,234:1:0,2:21.6:1:29.9:1:1:0:60:45.8:1:0:1.1 1/1:189:178:22,156:2,9:11,178:0.9418:2,2:22:1:29.5:1:0.6341:1.57137:59.8:177:0.9415:0:1.1 +12 4554630 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04966;SOR=Inf;LSEQ=GGGTGCCTGCAGGCGAGGGC;RSEQ=CCACCATGCCCACTAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:0,61:61,0:0:1,0:27.3:1:29.9:1:1:0:60:29.5:1:0:0.3 0/1:18:2:0,2:1,15:16,2:0.1111:1,0:23.5:1:33.5:1:1:0:60:4:0.1111:0:1 +12 4946467 . T G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTACATCTCTTCATCAC;RSEQ=ATCCTTTGTAATAAACCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 4947235 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.18367;SOR=Inf;LSEQ=GGAGGGATGGGGTGGTTATC;RSEQ=TCATCTGACTGCCTTCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:134,36:170,0:0:2,0:23.6:1:30.7:1:1:0:59.9:169:1:0:0.1 0/1:128:2:1,1:100,26:126,2:0.0156:2,2:16:1:30:1:0.37869:3.79308:60:4:0.016:0:1.5 +12 4947259 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25582;SOR=0;LSEQ=TCTGACTGCCTTCGGCTGCA;RSEQ=GGTCTCATAAGTTCCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:3:2,1:174,77:251,3:0.0118:2,2:19.3:1:29.7:1:1:1.12931:60:6:0.0121:0:2 0/0:208:0:0,0:143,65:208,0:0:2,0:24.9:1:31.1:1:1:0:60:103:1:0:0.5 +12 4947332 . A G 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01108;LSEQ=CCCTCTCCCAGAGCTTAAGA;RSEQ=CCCCTTCCTCAGACGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:497:496:250,246:1,0:1,496:0.998:0,2:26.6:1:32.5:1:1:0:60:61:0.998:0:1.5 1/1:421:356:172,184:35,29:64,356:0.8456:2,2:26.1:1:31.3:1:0.41542:1.29031:59.9:70.2:0.8438:0:1.5 +12 4947385 . C T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06712;LSEQ=GGAACACTGTCTCTTTTGTT;RSEQ=TTGGGATGTCCTCCATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:328:323:99,224:1,2:3,323:0.9848:2,2:24.5:1:30.3:1:1:1.13087:60:45.143:0.9875:0:1.7 1/1:234:190:58,132:19,24:43,190:0.812:2,2:24.9:1:29.3:1:0.10596:1.79696:60:46.5:0.8087:0:1.8 +12 4947423 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14146;SOR=Inf;LSEQ=AAAATTTCAGAGCTGCCTGG;RSEQ=AATCAAGTTGAGTGGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:24,151:175,0:0:2,0:24:1:32.2:1:1:0:60:86.5:1:0:1.2 0/1:106:2:0,2:22,82:104,2:0.0189:2,0:34:1:29:1:1:0:60:4:0.019:0:2 +12 4947496 . G A 150 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=AAAGCTTTGCCTGCAGCCTC;RSEQ=TGGCTCCTGGCTTGTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:0,28:0,0:0,28:1:0,1:23.1:1:31.3:1:1:0:60:27:1:0:1 1/0:19:10:0,10:0,9:9,10:0.5263:0,0:33.5:1:28.6:1:1:0:60:9:0.5294:0:1.4 +12 6775800 . TA T 28 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGAAATCTGCCATGATT;RSEQ=AAAAAAAAAAAAAAAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:28.5:1:1:0:45:4:1:0:4 +12 6777069 . TTGC T 89 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=41;MSI=14.000;MSILEN=3;SSF=0.12413;SOR=0.23505;LSEQ=TGGAAGTGTGGTGGTGGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:4,4:5,2:7,8:0.5:2,2:27:1:29.8:1:0.60839:2.34872:54.4:16:0.5:0:0.5 0/1:11:2:1,1:4,2:6,2:0.1818:2,2:36.5:1:31:0:1:1.8258:60:4:0.2:0:1 +12 6887493 . A ACCGGAG 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=23;MSI=4.000;MSILEN=6;SSF=0.24631;SOR=0;LSEQ=ATAGAGGAGCTGGAGCAAGA;RSEQ=CCGGAGCCGGAGCCGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:8,6:14,3:0.1765:2,2:26.3:1:31.3:1:0.57647:2.51691:60:6:0.1875:0:0 0/0:12:0:0,0:7,5:12,0:0:2,0:23.6:1:28.9:1:1:0:60:24:1:0:0.1 +12 6988887 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=CCTGGGGACAGAGAACAGTG;RSEQ=CTGCCCCATGGCTAGCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:10,0:0:2,0:23.3:1:31.8:1:1:0:60:20:1:0:0 0/1:5:2:1,1:3,0:3,2:0.4:0,2:16:1:27.5:1:0.4:0:60:4:0.4:0:1 +12 7023774 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48649;SOR=0;LSEQ=CTCTCTCAGCGCCGCCGTCG;RSEQ=CACCGCCACCGCCACCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:37:0:31.5:1:1:1.11803:60:4:0.1053:0:2.5 0/0:18:0:0,0:11,7:18,0:0:2,0:21.7:1:31.3:1:1:0:60:36:1:0:0.3 +12 7023804 . T G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03293;SOR=0.175;LSEQ=CGCCACCGCCACTACCACCG;RSEQ=CTGAGTCTGCAGTCCCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:5,5:3,3:6,10:0.625:2,2:27:1:32.2:1:1:1:60:20:0.625:0:1.5 0/1:14:3:2,1:6,5:11,3:0.2143:2,2:26:1:30.3:1:1:1.61:60:6:0.2308:0:1.7 +12 7023866 . T C 68 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AGCCCCTGTGGCCCCCTCCC;RSEQ=TCGCCGCGGCGCCCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:19.8:1:34.3:1:1:0:60:8:1:0:1.5 0/1:5:2:1,1:1,2:3,2:0.4:2,2:19:1:30.5:1:1:1.73:60:4:0.4:0:2 +12 7024304 . G T 31 d5;v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGGAGAGATGGAAGAAGT;RSEQ=GGGATCTGTCGAGGCGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:10.5:1:32:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:31.5:1:1:0:60:4:1:0:1 +12 7044647 . A AG 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATGATTTTATGCAAGAG;RSEQ=GCCCCAAATCTCAGGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12:1:32.5:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 7045844 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21369;SOR=Inf;LSEQ=CTACTGGGGCCCAGTCCACC;RSEQ=CCCACCCACCAGTCTCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:25,0:0:2,0:28:1:30.3:1:1:0:59.9:50:1:0:0 0/1:22:2:1,1:14,6:20,2:0.0909:2,2:22:1:27.5:1:1:2.2361:60:4:0.0909:0:1 +12 7045891 . ACAGCAGCAGCAGCAG A 133 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=15.000;MSILEN=3;SSF=0.00827;SOR=0.25279;LSEQ=CATCACCACCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:18:11,7:10,9:19,18:0.439:2,2:31:1:32.1:1:0.74314:1.40:57.7:36:0.439:0.0488:0.1 0/1:43:7:3,4:13,12:25,7:0.1628:2,2:32.3:1:30.7:1:1:1.42793:52.4:14:0.1628:0:0.4 +12 7061466 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCTCCCCTCCCTGCACC;RSEQ=GCTGGGGCTCTCAATGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 8200060 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTCAAAAAACAAAAAAC;RSEQ=GAAGGAAGAGGAGATAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:31:1:1:0:43.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 8200557 . ACAG A 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.34974;SOR=4.25161;LSEQ=CAGCAGCCACCGCCACCTCA;RSEQ=CAGCAGCAGCAGCAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:14,10:24,1:0.04:2,0:41:0:35:0:0.44:0:60:2:0.0417:0:0 0/1:26:4:2,2:11,11:22,4:0.1538:2,2:27.3:1:31.3:1:1:1:58.8:8:0.1538:0:0.3 +12 8679272 . A C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22857;SOR=0;LSEQ=TTATTATCCATCTTCTATAG;RSEQ=TTACTTCTATCAATTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:6,0:6,3:0.3333:0,2:22.7:1:32.3:1:0.33333:0:49:6:0.3333:0:1 0/0:6:0:0,0:5,1:6,0:0:2,0:19.5:1:29:1:1:0:60:12:1:0:0.5 +12 8679478 . TTTG T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.26744;SOR=0;LSEQ=GGGGCTTTTGTGGGGGCCCT;RSEQ=TTGTTGTTGTTGATGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:3,0:19,29:48,3:0.0588:2,0:14.3:1:26.3:1:0.07395:0:40.7:6:0.0588:0.0392:0.7 0/0:35:0:0,0:15,20:35,0:0:2,0:23.1:1:30:1:1:0:54.6:70:1:0:0.1 +12 8679767 . T C 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32763;SOR=2.08494;LSEQ=TGTTGAAGGGTCTCACCCAG;RSEQ=TGGGTGGCACAGGGAGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:3,2:10,3:13,5:0.2778:2,2:20:1:33:1:0.58275:2.11727:60:10:0.2941:0:1.6 0/1:20:9:4,5:6,5:11,9:0.45:2,2:21.7:1:29.9:1:1:1.46966:46.9:18:0.4737:0:1.2 +12 8679821 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23077;SOR=0;LSEQ=AGCCCTTTGTCCCTTGGTGG;RSEQ=GAGGGTGTGTTTTGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:17,2:0.1053:2,2:26.5:1:29.5:1:1:1.77272:60:4:0.1053:0:2.5 0/0:20:0:0,0:10,10:20,0:0:2,0:25.7:1:29.3:1:1:0:53.1:19:1:0:0.6 +12 8680419 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49091;SOR=0;LSEQ=GGATGCTAGGCCCCGGTGGC;RSEQ=TGCGTTTGTGAGTGGGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:22,2:0.0833:2,2:27.5:1:31:1:1:1:60:4:0.0833:0:1.5 0/0:21:0:0,0:12,9:21,0:0:2,0:26:1:30:1:1:0:60:20:1:0:0.3 +12 8948830 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCGCCTCCCAGGTTCAT;RSEQ=CCATTCTCCTGCCCCAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:1:31.5:1:1:0:29:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 9085099 . G A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=3.38757;LSEQ=ATGAATTTACTTTTAATTTA;RSEQ=AATGATTATTATTCTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:15:1:31.5:1:1:0:60:4:0.3333:0:2 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:13.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 +12 9085143 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07143;SOR=Inf;LSEQ=TTTTCTCTCTGTTGTATTCT;RSEQ=GGATTGTTCCTATAGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:15,0:0:1,0:24.3:1:33.2:1:1:0:47:30:1:0:0.1 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:45.5:1:30.5:1:0.33333:0:60:4:0.3333:0:1.5 +12 9392975 . C G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05361;SOR=0.09959;LSEQ=GGGGATAAAAAAGAAAGCGA;RSEQ=AGTTCAGGGACTCTGGCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:2,0:2,6:0.75:0,2:15:1:33.7:1:1:0:28.2:12:0.75:0:1 0/1:10:2:0,2:5,3:8,2:0.2:2,0:17:1:26.5:1:0.44444:0:30.5:4:0.2:0:1 +12 9847990 . C T 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGCCACCCGATGGAAGATT;RSEQ=GATGGACATGGACATGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:123,136:259,0:0:2,0:27:1:30.9:1:1:0:47.1:63.75:1:0:0.1 0/1:270:37:16,21:109,124:233,37:0.137:2,2:21.4:1:29.6:1:0.72564:1.15312:54.2:74:0.1391:0:1.1 +12 9848024 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49756;SOR=0;LSEQ=ATGAGCCCCCTGAGGCCCCA;RSEQ=AACTATCTTTTCAGTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:40,61:101,2:0.0194:2,2:22:1:31.5:1:1:1.52:28:4:0.0198:0:1 0/0:102:0:0,0:47,55:102,0:0:2,0:5:0:16:0:1:0:42:0:0:0:2 +12 9848109 . TA T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05092;SOR=0;LSEQ=AAAATGAGACCAGTTATCTT;RSEQ=AGAACGGTCAGCTCAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:4:1,3:73,53:126,4:0.0308:2,2:22.8:1:28.3:1:0.31422:4.08913:30:8:0.0308:0.0154:1.8 0/0:142:0:0,0:73,69:142,0:0:2,0:28:1:28.5:1:1:0:28.4:70:1:0:0.1 +12 9848119 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2279;SOR=0;LSEQ=CAGTTATCTTTAAGAACGGT;RSEQ=AGCTCAGGGGCTGGTGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:84,57:141,2:0.014:2,2:23:1:28.5:1:1:1.46956:25.5:4:0.0143:0:1 0/0:156:0:0,0:83,73:156,0:0:2,0:27.3:1:30.6:1:1:0:28.2:38:1:0:0.1 +12 9848179 . C T 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00085;SOR=Inf;LSEQ=GAAGCAGAGGCCATGAATGA;RSEQ=GAAGGCAGTCCAATTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:77,52:129,0:0:2,0:18.6:1:30.9:1:1:0:31.5:42:1:0:0.1 0/1:139:11:8,3:77,51:128,11:0.0791:2,2:9.9:1:30.3:1:0.52871:1.76:29.2:22:0.0797:0:1 +12 9848203 . A T 21 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23851;SOR=Inf;LSEQ=GGCAGTCCAATTAAAGTAAC;RSEQ=CTGGCAACTTTGAAAATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:116,71:187,0:0:2,0:20.7:1:30:1:1:0:33.8:45.75:1:0:0.1 0/1:179:2:0,2:112,65:177,2:0.0112:2,0:5.5:1:21.5:1:0.13879:0:40.5:4:0.0113:0:1 +12 9848208 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49872;SOR=0;LSEQ=TCCAATTAAAGTAACACTGG;RSEQ=AACTTTGAAAATGTCTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:2,0:115,76:191,2:0.0104:2,0:23:1:31:1:0.52008:0:21.5:4:0.0104:0:1 0/0:190:0:0,0:118,72:190,0:0:2,0:23.5:1:31.4:1:1:0:34.2:189:1:0:0.2 +12 9848411 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50012;SOR=Inf;LSEQ=TATCTGGAAAGCAGTCTGCC;RSEQ=CTGGAGGTGGGCAGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:57,56:113,0:0:2,0:20.4:1:31.3:1:1:0:52.2:36.667:1:0:0.7 0/1:129:2:1,1:63,64:127,2:0.0155:2,2:32.5:1:31.5:1:1:1.02:44.5:4:0.0161:0:1 +12 9848438 . CTT C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01123;SOR=0.45927;LSEQ=GTGGGCAGAAAAAAGTAAAA;RSEQ=GCTGCTGCTGCTGATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:35:22,13:22,16:38,35:0.2593:2,2:21.5:1:32.1:1:0.81128:1.23:58.7:70:0.2593:0.0444:0.2 0/1:152:21:13,8:49,32:81,21:0.1382:2,2:31.3:1:31.8:1:1:1.06:59.6:42:0.14:0:0 +12 9848439 . T TTGCTGC 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=6.000;MSILEN=3;SSF=0;SOR=0.03995;LSEQ=TGGGCAGAAAAAAGTAAAAC;RSEQ=TGCTGCTGCTGCTGATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:34:25,9:22,16:38,34:0.2519:2,2:34:1:32.3:1:0.21701:2.00:59.6:68:0.2519:0.0074:1.8 0/1:152:2:2,0:49,32:81,2:0.0132:2,0:29:1:32.7:0:0.52042:0:60:4:0.0133:0:2 +12 9848454 . A C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0;SOR=4.87865;LSEQ=AAAACTTGCTGCTGCTGCTG;RSEQ=TGATGATGATGATGAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:35:23,12:71,37:108,35:0.2448:2,2:23.3:1:33.1:1:1:1.00117:53:70:0.2448:0:2.1 1/0:158:97:65,32:39,20:59,97:0.6139:2,2:26.3:1:31.5:1:1:1.04:54.2:194:0.6258:0:1.7 +12 9848467 . T A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0;SOR=0.10783;LSEQ=GCTGCTGATGATGATGATGA;RSEQ=GAAGATGATGATGATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:31:23,8:84,45:129,31:0.1938:2,2:26.3:1:29.8:1:0.39944:1.54:58.2:30:0.1923:0:2.1 0/1:199:5:4,1:125,69:194,5:0.0251:2,2:39.4:1:29.4:1:0.65859:2.20:52:10:0.0256:0:2.6 +12 9848470 . A T 150 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGATGATGATGATGATGA;RSEQ=GATGATGATGATGATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:32:24,8:85,49:134,32:0.1928:2,2:23.4:1:30:1:0.30017:1.72:58.9:15:0.1899:0:2.2 0/0:201:0:0,0:124,70:194,0:0:2,0:23.4:1:29.6:1:1:0:46.3:63.667:1:0:0.8 +12 9848473 . T A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.09613;SOR=0;LSEQ=GATGATGATGATGATGAAGA;RSEQ=GATGATGATGATGATGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:2,1:104,56:160,3:0.0182:2,2:18.3:1:32.7:1:1:1.08:53.3:6:0.0188:0:3 0/0:194:0:0,0:124,70:194,0:0:2,0:25:1:29.5:1:1:0:46.1:37.8:1:0:0.9 +12 9848648 . A G 99 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02683;SOR=0.10923;LSEQ=AAAAACAGGAAAAATCTCCT;RSEQ=AAACACCAAAAGGATCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:2,6:0,15:15,8:0.3478:1,2:20.8:1:33.1:1:0.11067:0:24.1:16:0.3478:0:1 0/1:19:1:0,1:1,17:18,1:0.0526:1,0:30:0:32:0:1:0:22:2:0.0526:0:1 +12 10646574 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CAGACACCCTATACAGGAGT;RSEQ=ATCCTACTGGTGTCAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:23.1:1:34:1:1:0:57.4:14:1:0:0.4 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:10:1:28:1:1:1:60:4:0.4:0:1 +12 10646752 . G C 74 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAACCCTACAGAAGAGGGA;RSEQ=CTGACCATTGAAAGAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:0,5:1:0,2:22.4:1:32:1:1:0:36.4:10:1:0:1.2 +12 10646985 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAGCAAGGGCACATAAC;RSEQ=GGATAGAGGATGAAATGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:23.5:1:31:0:1:0:60:4:1:0:1 +12 11664166 . CT C 86 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.55635;SOR=0.64784;LSEQ=CACACAACTTTTTCTGGGGC;RSEQ=TTTTTTGGGGGAGGTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:7:3,4:289,357:646,7:0.0107:2,2:25.6:1:30.8:1:1:1.07926:60:14:0.0108:0.0031:1.4 0/0:574:4:2,2:245,321:566,4:0.007:2,2:26.5:1:31:1:1:1.31:60:8:0.0071:0.0017:1 +12 11664178 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=1.68137;LSEQ=TCTGGGGCCTTTTTTTGGGG;RSEQ=AGGTGGGCAGGCTACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:593:329:135,194:118,144:262,329:0.5548:2,2:25.9:1:30.2:1:0.35753:1.17724:60:22.5:0.5497:0:1.1 1/0:514:348:140,208:70,95:165,348:0.677:2,2:27.2:1:28.9:1:0.70071:1.09454:60:37.667:0.674:0:1.2 +12 11802929 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50282;SOR=Inf;LSEQ=CGCTCCAGACCCCCGGGGCG;RSEQ=CTGCCGGGAGAGATGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:51,1:52,0:0:1,0:24.2:1:31.8:1:1:0:60:51:1:0:0.1 0/1:66:2:1,1:59,4:63,2:0.0303:2,2:21:1:29.5:1:0.14904:13.30416:60:4:0.0313:0:1 +12 11802997 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12877;SOR=Inf;LSEQ=CTGGCCGTGGAGCCTTTCTG;RSEQ=GTTGGGGAGAGGAAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:221,106:327,0:0:2,0:27.5:1:31.4:1:1:0:59.8:53.5:1:0:0.1 0/1:384:4:1,3:246,134:380,4:0.0104:2,2:25.5:1:25:1:0.13185:5.48249:60:3:0.0079:0:1.8 +12 11803168 . C A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62337;SOR=2.93678;LSEQ=CAGGGCAGTCGTGCTGGGCT;RSEQ=CTCAGAGCAGGCTGTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:1,0:49,159:208,1:0.0048:2,0:1:0:23:0:0.23923:0:60:2:0.0049:0:1 0/1:215:3:2,1:56,156:212,3:0.014:2,2:9:1:27.7:1:0.17778:5.52:60:6:0.0144:0:1.3 +12 11803220 . A C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAGGAAATTATTTGGGGCG;RSEQ=GAGGGAAAGAGATGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:71:0,71:0,0:0,71:1:0,1:25.2:1:29.8:1:1:0:60:70:1:0:2 1/1:58:58:0,58:0,0:0,58:1:0,1:28.1:1:29.8:1:1:0:60:116:1:0:2 +12 11803228 . A G 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTATTTGGGGCGAGAGGGAA;RSEQ=GAGATGCAGCTCGCGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:67:0,67:0,0:0,67:1:0,1:24.2:1:31.4:1:1:0:60:32.5:1:0:2 1/1:54:54:0,54:0,0:0,54:1:0,1:27.3:1:30.8:1:1:0:60:53:1:0:2.1 +12 11803278 . T TC 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.56239;SOR=1.45474;LSEQ=CTTTAGCGTAACCTTGCTAC;RSEQ=CCCCCCCACCGCCGAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:15:0,15:0,10:10,15:0.5769:0,1:29.2:1:31.9:1:1:0:60:30:0.6:0.0385:1.5 1/0:21:14:1,13:0,7:7,14:0.6667:0,1:23.9:1:31.4:1:1:0:60:28:0.6667:0.0476:1.7 +12 11803303 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49275;SOR=0;LSEQ=CCCACCGCCGAGCCCCTGCC;RSEQ=GCTCCTCGGCCCCCACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:29.5:1:32:0:1:0:60:4:0.1429:0:2 0/0:10:0:0,0:1,9:10,0:0:2,0:21.4:1:28.9:1:1:0:60:9:1:0:1.1 +12 11904983 . A G 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATATTGCTACAGAAGAGAAA;RSEQ=CATGGCTTTAATATAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:44:0:36:0:1:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:33.5:1:1:0:60:4:1:0:1.5 +12 11905187 . T C 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.54017;SOR=0;LSEQ=GATGGCAGAGTTTTGTTATA;RSEQ=AGCCCCAAGGCTAGGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:27,0:27,3:0.1:1,0:19:1:34.3:1:1:0:60:6:0.1:0:1 0/0:14:0:0,0:13,1:14,0:0:1,0:18.1:1:30.3:1:1:0:60:28:1:0:0.2 +12 11905349 . T C 64 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01226;SOR=Inf;LSEQ=CCAAGCTTTCATTGTCTCTC;RSEQ=CCCCCTCCCCTCTTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:286,192:478,0:0:2,0:24.8:1:30.3:1:1:0:60:33.143:1:0:0.1 0/1:445:6:3,3:278,161:439,6:0.0135:2,2:25.2:1:24.8:1:0.67403:1.7244:57:2:0.0093:0:1.7 +12 11905554 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=AGGGACAGAGGATTGATGGC;RSEQ=TGGGGCGGGGGTGGCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:26,125:151,2:0.0131:2,2:30:0:32.5:1:0.32276:4.74:60:4:0.0134:0:2.5 0/0:120:0:0,0:20,100:120,0:0:2,0:23.4:1:30.7:1:1:0:60:39:1:0:0.2 +12 11905560 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01896;SOR=Inf;LSEQ=AGAGGATTGATGGCGTGGGG;RSEQ=GGGGGTGGCAGGCAGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:19,102:121,0:0:2,0:25.5:1:29.8:1:1:0:60:39.333:1:0:0.1 0/1:102:5:1,4:15,82:97,5:0.049:2,2:29.2:1:28.2:1:0.58188:1.36:60:10:0.05:0:1 +12 11905568 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50945;SOR=0;LSEQ=GATGGCGTGGGGCGGGGGTG;RSEQ=CAGGCAGTGGGCTCCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:17,97:114,2:0.0172:2,2:16:0:32:0:0.28741:5.57:60:4:0.0177:0:2.5 0/0:85:0:0,0:8,77:85,0:0:2,0:25:1:31.3:1:1:0:60:27.333:1:0:0.2 +12 11905668 . G A 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACACCCCCCTACCCCCA;RSEQ=ATACCTTTGAAAAATTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:0,22:0,0:0,22:1:0,1:25:1:31.2:1:1:0:60:21:1:0:1.1 1/1:7:7:0,7:0,0:0,7:1:0,0:18.6:1:30.7:1:1:0:57.4:14:1:0:1 +12 11905742 . TA T 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCTGACTATGACATGT;RSEQ=AAAAAAAAAGAAACCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:26:1:31:1:1:0:60:4:0.2222:0.1111:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 11992035 . C A 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50105;SOR=0;LSEQ=AGCTGTCTAACTGACAAGAC;RSEQ=TTTCTCTCTTTCTTTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:2,0:173,16:189,2:0.0105:2,0:6.5:1:27:1:1:0:49.5:4:0.0107:0:4 0/0:166:0:0,0:141,24:165,0:0:2,0:21.3:1:30.1:1:1:0:60:40.25:0.9938:0:0.1 +12 11992168 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00046;SOR=1.83391;LSEQ=AGGCCAATTGACAGCAACAC;RSEQ=TTTGAAATGAATGGCAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:827:60:29,31:379,388:767,60:0.0726:2,2:23.1:1:30.7:1:0.89409:1.04413:60:59:0.0721:0:1.2 0/1:741:93:43,50:321,327:648,93:0.1255:2,2:25.5:1:30.4:1:0.58037:1.14125:60:92:0.1255:0:1.2 +12 12006277 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19241;SOR=Inf;LSEQ=ATTGTATCTTTGGCACCGTG;RSEQ=CAGGCACTTAGCTGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:179,20:199,0:0:2,0:23.9:1:32:1:1:0:59.5:27.429:1:0:0 0/1:156:2:1,1:131,23:154,2:0.0128:2,2:31:1:27:1:0.28486:5.59704:60:4:0.013:0:1 +12 12006544 . G A 231 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01033;LSEQ=CTGAGGTTTAGACAAATCCA;RSEQ=GAAGTTTAATTGTTAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:999:170:83,87:421,406:827,170:0.1702:2,2:21.5:1:31.2:1:0.6738:1.08682:60:41.5:0.1692:0:1.1 0/0:948:2:2,0:476,469:945,2:0.0021:2,0:16.5:1:27.5:1:0.49952:0:60:4:0.0021:0:1 +12 12006736 . G T 188 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=26.42372;LSEQ=ATATAGTAGGCACCGTAAAG;RSEQ=TGTGGTGGAAGGGTCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1677:4:0,4:841,830:1671,4:0.0024:2,0:1.5:1:22.8:1:0.06124:0:60:3:0.0018:0:1.8 0/1:1480:88:39,49:669,723:1392,88:0.0595:2,2:28.1:1:29.2:1:0.51117:1.16245:60:87:0.0596:0:1.1 +12 12007114 . T A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11833;SOR=Inf;LSEQ=GTAAGGAGTGTGCAACTAGA;RSEQ=CCCGCGCATGCACAGTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:139,114:253,0:0:2,0:26.1:1:30.8:1:1:0:59.3:62.25:1:0:0.1 0/1:245:3:1,2:128,114:242,3:0.0122:2,2:19:1:24:1:0.60444:2.23844:60:2:0.0083:0:1.7 +12 12007343 . G C 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=14.37056;LSEQ=ACCTGGAGGTTGGGGACCCC;RSEQ=CCTTAGAAATCCAGCAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1020:164:102,62:534,321:855,164:0.1608:2,2:24.9:1:31.1:1:1:1.01117:59.4:81:0.1599:0:1.1 1/0:857:629:401,228:131,94:225,629:0.734:2,2:24.7:1:30.1:1:0.14956:1.26:59.5:56.182:0.7357:0:1.1 +12 12007720 . G GA 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.85715;SOR=0.96683;LSEQ=TAAAAGTTGGAAGAAGGAAA;RSEQ=AAAAAAAAACCCAAATCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1884:67:40,27:973,832:1805,67:0.0356:2,2:29.8:1:29.9:1:0.38351:1.27:60:21.333:0.0346:0.0011:0.3 0/1:1743:60:31,29:864,807:1671,60:0.0344:2,2:23.3:1:29.9:1:1:1.00156:59.8:120:0.0348:0.0029:0.4 +12 12007893 . C G 322 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04372;LSEQ=ATTTAATTTAGGCCCTGGAC;RSEQ=TAGTTCCAGAATAGGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1515:1234:489,745:116,161:277,1234:0.8145:2,2:26.7:1:31.4:1:0.49802:1.09762:59.9:175.286:0.8169:0:1.1 0/1:1635:263:115,148:612,755:1367,263:0.1609:2,2:23.8:1:30.4:1:0.7866:1.04319:60:64.75:0.1607:0:1.2 +12 12007996 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23947;SOR=0;LSEQ=TCCCAGCACTTTGAGAGGCC;RSEQ=AGGCGGGCGGATCACGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:23,125:148,2:0.0133:2,2:16.5:1:30.5:1:0.2953:5.34:30.5:4:0.0136:0:3.5 0/0:156:0:0,0:37,119:156,0:0:2,0:18.2:1:30.2:1:1:0:47:51:1:0:0.1 +12 12007997 . A C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49832;SOR=Inf;LSEQ=CCCAGCACTTTGAGAGGCCG;RSEQ=GGCGGGCGGATCACGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:23,123:146,0:0:2,0:18.8:1:32.5:1:1:0:45.6:292:1:0:0.1 0/1:148:2:1,1:32,114:146,2:0.0135:2,2:23.5:1:28.5:1:0.39741:3.52:52.5:4:0.0137:0:1 +12 12008218 . C T 105 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00261;SOR=7.5943;LSEQ=CCACTGCACTCCAGCCTGGG;RSEQ=GACAGAGCGAGACTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:2:1,1:303,121:424,2:0.0047:2,2:22.5:1:29:1:0.49123:2.49797:46.5:4:0.0047:0:1 0/1:376:13:7,6:262,101:363,13:0.0346:2,2:15.2:1:28.6:1:0.20709:2.21816:56.1:26:0.0349:0:1 +12 12008864 . G A 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08727;LSEQ=AAGCTTGACATTAAGGCAAG;RSEQ=AATATATTACCTAGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1836:1145:594,551:325,362:687,1145:0.6236:2,2:24.7:1:30.4:1:0.05995:1.20:60:51.045:0.6215:0:1.1 0/1:1727:218:111,107:778,727:1505,218:0.1262:2,2:24.3:1:28.9:1:0.88474:1.03158:60:42.6:0.1249:0:1.2 +12 12008944 . AT A 138 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.54032;SOR=1.25874;LSEQ=CTCTTAGTCTTTCTCTCATT;RSEQ=TTTTTTTGTTAATCTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2049:19:13,6:1036,990:2026,19:0.0093:2,2:23.8:1:30.4:1:0.16781:2.07:60:38:0.0093:0.0034:0.7 0/1:2061:24:14,10:1023,1014:2037,24:0.0116:2,2:22.1:1:30.3:1:0.53905:1.39:60:48:0.0117:0.0029:0.1 +12 12009529 . A G 324 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13822;LSEQ=TCCTCCTGCCTTTCAGCTAT;RSEQ=TGGTGCCCTTGATGACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1674:1048:527,521:325,300:625,1048:0.626:2,2:25.5:1:32.3:1:0.5113:1.07094:60:79.615:0.6258:0:1.1 0/1:1411:265:138,127:550,594:1144,265:0.1878:2,2:24:1:31.6:1:0.24699:1.17:59.9:264:0.1879:0:1.2 +12 12009741 . A G 254 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATATGTTAACATACAGAAAG;RSEQ=TCTGGTTCTGAAAAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1523:267:132,135:647,604:1251,267:0.1753:2,2:26.2:1:31.6:1:0.501:1.09547:60:43.5:0.1765:0:1.1 0/0:1380:0:0,0:698,682:1380,0:0:2,0:24.9:1:29:1:1:0:60:54.2:1:0:0.1 +12 12009751 . G GA 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.7638;SOR=0.93336;LSEQ=ATACAGAAAGATCTGGTTCT;RSEQ=AAAAAAAAATCTGTCAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1564:56:26,30:779,719:1498,56:0.0358:2,2:28.8:1:30.3:1:0.41798:1.24995:59.6:55:0.0356:0.0051:0.2 0/1:1403:47:22,25:698,656:1354,47:0.0335:2,2:28.2:1:29.7:1:0.55507:1.20895:60:94:0.0338:7e-04:0.1 +12 12009874 . G A 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11224;LSEQ=CCAAGATGACACATGTTGCT;RSEQ=CCAACTTGGCATAGGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2265:1376:742,634:471,416:887,1376:0.6075:2,2:26.1:1:29:1:0.72983:1.03:59.9:79.941:0.6075:0:1.1 0/1:1940:287:143,144:823,827:1650,287:0.1479:2,2:25.9:1:28.1:1:1:1.00212:59.7:94.667:0.1481:0:1.1 +12 12010056 . G A 315 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.08008;LSEQ=CCTTGTGATTTCACCTCGTC;RSEQ=TGGCCACAAACTTAACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1885:1210:599,611:333,339:672,1210:0.6419:2,2:24.4:1:30.8:1:1:1.00198:59.9:92.077:0.6432:0:1.1 0/1:1626:204:107,97:701,721:1422,204:0.1255:2,2:24.7:1:29.8:1:0.41096:1.13:60:101:0.1252:0:1.1 +12 12010544 . G T 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10282;LSEQ=GACAGTGACACAGGGCTCCA;RSEQ=CAATAAGTAAGCCAGGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1793:1160:611,549:333,295:628,1160:0.647:2,2:25.7:1:30.6:1:0.92095:1.01426:60:88.231:0.6469:0:1.1 0/1:1540:244:133,111:678,617:1295,244:0.1584:2,2:24.3:1:29.1:1:0.57617:1.09:59.9:47.8:0.1573:0:1.1 +12 12010736 . C T 324 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.80427;LSEQ=TAAGGGCTAAGTTTCTCATT;RSEQ=CTCTGGCTCTGTCTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1886:1530:771,759:182,170:352,1530:0.8112:2,2:24.3:1:30.7:1:0.67917:1.05392:60:108.286:0.8129:0:1.1 1/1:1562:1472:762,710:42,43:85,1472:0.9424:2,2:24.1:1:29.3:1:0.738:1.10:59.9:91:0.9442:0:1.1 +12 12011325 . A AAT 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0;SOR=6.84439;LSEQ=TTTTGGGTTTTATCCCCTTA;RSEQ=ATATATATATATATTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1209:111:61,50:533,548:1081,111:0.0918:2,2:30:1:30.6:1:0.27379:1.25:59.8:110:0.0927:0:1 0/1:958:392:207,185:277,247:524,392:0.4092:2,2:26.4:1:29.3:1:1:1.00227:59.6:784:0.4126:0.0783:0.9 +12 12011338 . AT A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.86956;SOR=0.89824;LSEQ=CCCCTTAAATATATATATAT;RSEQ=TTTTTTTTAATTGTCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1194:22:9,13:586,581:1167,22:0.0184:2,2:21.4:1:30.5:1:0.40024:1.45641:59.8:21:0.0178:0.0042:0 0/1:965:16:10,6:480,452:932,16:0.0166:2,2:17.1:1:28.9:1:0.45484:1.57:57.5:32:0.0168:0.0083:0.7 +12 12011340 . T A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0;SOR=5.95817;LSEQ=CCTTAAATATATATATATAT;RSEQ=TTTTTTTAATTGTCATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1199:187:95,92:502,509:1011,187:0.156:2,2:22.3:1:29.5:1:0.81139:1.05:59.6:45.75:0.1543:0:1.1 1/0:948:497:253,244:232,213:445,497:0.5243:2,2:21.1:1:28.2:1:0.74412:1.05037:59.6:44.182:0.5237:0:1.2 +12 12011342 . T A 119 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=9.000;MSILEN=1;SSF=3e-05;SOR=7.05712;LSEQ=TTAAATATATATATATATTT;RSEQ=TTTTTAATTGTCATTTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1215:4:2,2:608,603:1211,4:0.0033:2,2:24:1:28.3:1:1:1.00829:58.8:8:0.0033:0:2 0/1:965:22:12,10:485,458:943,22:0.0228:2,2:14.9:1:26.7:1:0.83158:1.13:58.6:44:0.0229:0:2.1 +12 12011520 . G A 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.42248;LSEQ=AGGGAGAAGGAGCAAGATCC;RSEQ=GATTTCTCAAACGTTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1669:268:133,135:668,733:1401,268:0.1606:2,2:24.1:1:31.4:1:0.59357:1.08:60:133:0.161:0:1.1 1/0:1409:827:404,423:299,283:582,827:0.5869:2,2:24.3:1:30:1:0.35809:1.10615:59.9:205.75:0.587:0:1.1 +12 12011764 . TGAG T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=3.86719;LSEQ=AACATGGAAATCGCAAGTGA;RSEQ=GAGAACTTTCAAGCATCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1479:27:18,9:603,605:1208,27:0.0183:2,2:11.3:1:28.8:1:0.11816:2.01:59.3:12.5:0.0173:0.0135:1.3 0/1:1341:90:45,45:239,236:475,90:0.0671:2,2:8:1:28:1:1:1.01269:59.6:89:0.0668:0.0559:1.2 +12 12011768 . GAGAA AG 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=7.724;LSEQ=ACATGGAAATCGCAAGTGAT;RSEQ=CTTTCAAGCATCGAAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1479:222:113,109:603,605:1208,222:0.1501:2,2:25.3:1:32.3:1:0.82668:1.04:59.8:73:0.1517:0.0311:0.3 1/0:1341:774:387,387:239,236:475,774:0.5772:2,2:27.3:1:30.9:1:0.95353:1.0127:59.8:1548:0.5806:0.0388:0.2 +12 12011772 . A G 240 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCGCAAGTGATGAGGAGA;RSEQ=CTTTCAAGCATCGAAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1245:0:0,0:613,594:1207,0:0:2,0:24.4:1:30.2:1:1:0:60:85.214:0.9983:0:0.1 0/1:578:236:114,122:170,169:339,236:0.4083:2,2:15.1:1:30.5:1:0.67252:1.07637:59.8:38.333:0.4078:0:1.1 +12 12012053 . G C 232 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=40.000;MSILEN=1;SSF=0.0614;SOR=0.42181;LSEQ=AGATGAGGTATATGAATCTG;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:207:199:58,141:0,6:6,199:0.9614:0,2:10.8:1:30.4:1:0.18701:0:59.3:7.652:0.9944:0:1.4 1/1:195:178:85,93:9,5:14,178:0.9128:2,2:12.2:1:29.3:1:0.2753:1.96257:59.1:15.182:0.9278:0:1.3 +12 12012363 . C T 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18837;SOR=0.21451;LSEQ=GGGATTACAAGCATGAGCCA;RSEQ=CACACCCGGCCTGAATCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:4:1,3:286,84:370,4:0.0107:2,2:19.3:1:28.8:1:0.0407:10.1313:59.5:8:0.0108:0:1.8 0/0:433:1:0,1:310,122:432,1:0.0023:2,0:1:0:23:0:0.28406:0:60:2:0.0023:0:1 +12 12012681 . T C 315 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.71134;LSEQ=TTTCATAAATATTTGTAGTG;RSEQ=AGGCGCCCTGAAAATAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1417:468:263,205:523,425:948,468:0.3303:2,2:25.3:1:32.6:1:0.73324:1.04:59.9:92.6:0.3295:0:1.1 1/0:1367:1050:553,497:165,150:315,1050:0.7681:2,2:24.7:1:31.4:1:0.94875:1.01:60:104:0.7675:0:1.1 +12 12012801 . A G 330 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03837;LSEQ=GTGTGGCAGGTCCTGCTTAC;RSEQ=TTACTGCCAAATTTGTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1589:1585:741,844:3,0:3,1585:0.9975:0,2:24.8:1:31.1:1:0.10262:0:59.9:98.063:0.9981:0:1.1 1/1:1490:1398:667,731:51,40:91,1398:0.9383:2,2:25.1:1:30.4:1:0.1305:1.39701:60:278.6:0.9387:0:1.1 +12 12013189 . A G 319 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.27846;LSEQ=GATTCTCTAGTCTTGCTGGA;RSEQ=TCGTGTTGATGACTGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1637:303:147,156:686,646:1332,303:0.1851:2,2:25.6:1:32.3:1:0.37288:1.12685:60:59.6:0.1856:0:1.1 1/0:1656:1244:610,634:204,205:409,1244:0.7512:2,2:24.8:1:31.1:1:0.77588:1.03427:60:68.111:0.7494:0:1.1 +12 12013292 . G A 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.45802;LSEQ=ACAGAGCCAGAGAGCATGCC;RSEQ=GCACGTATATGCGTGCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1505:271:133,138:623,610:1233,271:0.1801:2,2:25.3:1:31:1:0.68754:1.0597:60:32.875:0.1794:0:1.1 1/0:1370:1024:506,518:187,157:344,1024:0.7474:2,2:23.6:1:29.9:1:0.11934:1.21915:60:145.286:0.7506:0:1.1 +12 12013498 . C CA 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.31472;LSEQ=GACAGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAACAAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:782:304:182,122:204,181:385,304:0.3887:2,2:28.6:1:31.2:1:0.07571:1.32:57.8:608:0.407:0:0.6 0/1:726:121:67,54:302,260:562,121:0.1667:2,2:27.6:1:30:1:0.76376:1.07:57.5:242:0.1774:0:0.8 +12 12013572 . G A 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.75811;LSEQ=CTTAGAATAGCCAAGCATTC;RSEQ=GTAAATGTTATTCATTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1589:1267:686,581:172,141:313,1267:0.7974:2,2:26.2:1:31.2:1:0.80036:1.03313:59.8:73.529:0.7997:0:1.6 1/1:1482:1357:726,631:63,59:122,1357:0.9157:2,2:25.3:1:29.6:1:0.70565:1.08:59.9:40.121:0.9169:0:1.3 +12 12013612 . G A 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05221;LSEQ=ATGATTCAATATTTCTGGCT;RSEQ=TTATTTGGTTGTTTCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1773:1436:757,679:173,164:337,1436:0.8099:2,2:24.7:1:29.6:1:0.67156:1.06:60:64.273:0.8094:0:1.5 0/1:1843:335:174,161:784,722:1506,335:0.1818:2,2:23.7:1:28.5:1:1:1.00474:60:54.833:0.1799:0:1.6 +12 12013626 . T TC 260 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.0077;LSEQ=CTGGCTGTTATTTGGTTGTT;RSEQ=CCCCCCCTCTGTTTGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1777:308:155,153:763,702:1465,308:0.1733:2,2:27.2:1:31.5:1:0.61586:1.07281:59.8:50.333:0.1729:0.0214:1 0/0:1863:3:3,0:925,932:1857,3:0.0016:2,0:42.3:1:31.7:1:0.12399:0:60:6:0.0016:0:0.3 +12 12013985 . C A 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=16.90481;LSEQ=CACTGCTTGCATTTTATGTC;RSEQ=CCTTGCAGTATCTGGCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2007:322:161,161:835,847:1682,322:0.1604:2,2:25.4:1:30.1:1:0.9515:1.01:59.9:79.5:0.1609:0:1.1 1/0:1664:1271:652,619:188,201:389,1271:0.7638:2,2:24.7:1:29.1:1:0.32465:1.13:60:114.545:0.766:0:1.1 +12 12014424 . G A 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.88935;LSEQ=TTGCATCTGTCTGGGCCCTC;RSEQ=GCCTATTACAGGAGGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1344:253:109,144:534,557:1091,253:0.1882:2,2:23.6:1:31.1:1:0.09423:1.26632:59.9:62.25:0.1869:0:1.1 1/0:1211:889:411,478:147,169:316,889:0.7341:2,2:23.5:1:29.7:1:0.94769:1.01161:60:67.385:0.7337:0:1.1 +12 12014774 . T C 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCAGGCCTTATACATGAT;RSEQ=GAGAGGATTACCCAAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1924:0:0,0:888,1035:1923,0:0:2,0:24.5:1:30.6:1:1:0:60:95.15:0.9995:0:0.1 0/1:1760:66:31,35:812,882:1694,66:0.0375:2,2:24:1:30.3:1:0.9007:1.03941:60:132:0.0378:0:1.9 +12 12014808 . T C 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACAGACCTAATTGACTTA;RSEQ=TGGAAATCCAATCCTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1738:0:0,0:785,952:1737,0:0:2,0:25.2:1:30.8:1:1:0:60:85.85:1:0:0.1 0/1:1728:60:29,31:792,873:1665,60:0.0347:2,2:24.2:1:31:1:1:1.03:60:29:0.034:0:2 +12 12015401 . G A 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=13.68344;LSEQ=TTATTATCTCACTTTTCTGG;RSEQ=GGCTAGAAGTCCAAGGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1375:253:127,126:586,535:1121,253:0.184:2,2:23.4:1:31:1:0.57758:1.08664:60:62.25:0.1844:0:1.1 1/0:1104:834:434,400:134,132:266,834:0.7554:2,2:25:1:29.2:1:0.6726:1.07:59.6:42.895:0.7546:0:1.1 +12 12015706 . G T 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08959;LSEQ=ACATCCTGAGGGTACTAGGG;RSEQ=TTAGGACTTCAACTTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1028:668:400,268:195,164:359,668:0.6498:2,2:24:1:29.6:1:0.09744:1.25:59.8:40.75:0.6488:0:1.1 0/1:815:116:65,51:398,301:699,116:0.1423:2,2:23.4:1:28.6:1:0.91944:1.03744:59.9:37.667:0.1402:0:1.1 +12 12015905 . A G 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11392;LSEQ=AGAGGGAGAAAGTGAAACCC;RSEQ=GTGGACTGAGGCTTGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1804:1165:592,573:344,293:637,1165:0.6458:2,2:24.8:1:30.6:1:0.20007:1.1363:60:128.444:0.6469:0:1.1 0/1:1664:286:139,147:705,669:1374,286:0.1719:2,2:24.8:1:29.7:1:0.43543:1.11439:60:56.2:0.1718:0:1.2 +12 12016007 . C T 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGTGGGCTTAGGGAAAGCA;RSEQ=GGTGGTGGAAATGTGATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1847:0:0,0:924,922:1846,0:0:2,0:24.3:1:32.2:1:1:0:60:72.84:1:0:1.2 0/1:1811:87:49,38:901,822:1723,87:0.048:2,2:22.2:1:29.7:1:0.50972:1.18:59.9:42.5:0.0474:0:1.2 +12 12016008 . G A 337 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02253;LSEQ=CGTGGGCTTAGGGAAAGCAC;RSEQ=GTGGTGGAAATGTGATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1842:1838:922,916:0,0:0,1838:0.9978:0,2:24.5:1:31.1:1:1:0:60:53.059:0.9983:0:1.2 1/1:1814:1654:857,797:89,68:157,1654:0.9118:2,2:24.3:1:29.7:1:0.27712:1.21706:59.9:46.257:0.9111:0:1.6 +12 12016045 . C T 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.22578;LSEQ=CCTGGTGTGTGAGATGCAAA;RSEQ=TTGATCTTAGCCTTTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1938:289:142,147:798,850:1648,289:0.1491:2,2:25.4:1:30.7:1:0.84831:1.03:60:40.286:0.1474:0:1.8 1/0:2019:1377:691,686:322,317:639,1377:0.682:2,2:24:1:29.6:1:0.96183:1.00842:59.9:85.063:0.6815:0:1.7 +12 12016089 . C T 221 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00641;LSEQ=TGGAAACTTATCGGTCAAAA;RSEQ=TTTCACTAAAGGCAGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1859:138:66,72:822,897:1719,138:0.0742:2,2:25.1:1:31.2:1:1:1.00:59.9:276:0.075:0:1.3 0/0:1949:1:0,1:934,1011:1945,1:5e-04:2,0:1:0:28:0:1:0:60:2:5e-04:0:2 +12 12016183 . G T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.00577;LSEQ=GGGTCAAATTTTTATGAATT;RSEQ=TAAGTAGAGAAACTTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1548:271:147,124:637,640:1277,271:0.1751:2,2:22.9:1:31:1:0.20398:1.19:59.9:270:0.1754:0:1.1 0/1:1473:677:336,341:391,405:796,677:0.4596:2,2:24:1:29.7:1:0.87538:1.02:60:337.5:0.4601:0:1.1 +12 12016373 . G A 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=66.40448;LSEQ=ACACTTCCAACCAGAATGAC;RSEQ=GTTCCCTGCCAGTCCTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1850:1:0,1:924,922:1846,1:5e-04:2,0:7:0:21:0:0.49973:0:60:2:5e-04:0:1 0/1:1758:61:26,35:801,893:1694,61:0.0347:2,2:23.2:1:30.1:1:0.51537:1.20734:60:122:0.0349:0:1.1 +12 12016807 . G A 148 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=36.76667;LSEQ=AGACTGAAACAAAGCTTGCA;RSEQ=GGTCTCATTGCAGGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1256:1:1,0:706,546:1252,1:8e-04:2,0:1:0:29:0:1:0:60:2:8e-04:0:1 0/1:1054:30:17,13:583,440:1023,30:0.0285:2,2:22.6:1:30.3:1:1:1.01323:60:60:0.0288:0:1.3 +12 12017285 . T C 334 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28789;SOR=0.39817;LSEQ=CCGTTTTGAAATTTATAAGA;RSEQ=GGGAAATGGATTCAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1672:1670:833,837:0,2:2,1670:0.9988:0,2:25.4:1:31.2:1:0.49971:0:60:91.778:0.9988:0:1.1 1/1:1667:1662:806,856:0,2:2,1662:0.997:0,2:25.2:1:30.4:1:0.50019:0:59.9:109.8:0.997:0:1.1 +12 12017687 . TA T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=2.01346;LSEQ=GCAAGGTTAATTAAGCACTT;RSEQ=AAAAAAAAAAAGCTTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1402:194:92,102:608,578:1186,194:0.1384:2,2:27.4:1:31.4:1:0.35273:1.16611:59.7:388:0.1407:0.0143:0.2 0/1:1248:305:155,150:450,441:891,305:0.2444:2,2:26:1:30.3:1:0.94715:1.01:59.8:610:0.249:0.0264:0.2 +12 12017753 . A G 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGTAAAGAGAATTGTGTA;RSEQ=TGAATCACCATGTACCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1898:0:0,0:1056,840:1896,0:0:2,0:25.3:1:30.6:1:1:0:59.9:69.222:0.9989:0:0.2 0/1:1932:60:29,31:1019,852:1871,60:0.0311:2,2:23.8:1:31:1:0.35966:1.27832:59.9:19:0.0301:0:1.2 +12 12017875 . T C 197 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTACAGCAAATCTCAGATA;RSEQ=ATAATTTCCCTTGTAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1013:0:0,0:303,708:1011,0:0:2,0:24.5:1:29.3:1:1:0:59.2:125.375:0.998:0:0.2 0/1:1046:78:25,53:345,623:968,78:0.0746:2,2:21.3:1:31.5:1:0.62263:1.17386:58.4:156:0.0751:0:1.1 +12 12018042 . A G 106 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACTACAAAAAATTAGCC;RSEQ=GGCATGGTGGCGGGCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:2,9:0,0:0,11:1:0,2:14.7:1:30.9:1:1:0:24.3:22:1:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:13:0:32:0:1:0:25:2:1:0:1 +12 12018349 . T C 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATAAATGTTTTTTACAGTT;RSEQ=GGATCAGAATCCAAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1490:0:0,0:702,788:1490,0:0:2,0:25.8:1:30.8:1:1:0:60:113.615:1:0:0.2 0/1:1555:52:25,27:691,808:1499,52:0.0334:2,2:23.6:1:29.9:1:0.7794:1.08:60:104:0.0335:0:1.1 +12 12018392 . C T 242 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01442;LSEQ=TATACATTGCAGATGGTTAA;RSEQ=GTATCTCTTAAGTTTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1444:242:120,122:576,626:1202,242:0.1676:2,2:23.4:1:30.6:1:0.6724:1.07:60:79.667:0.1678:0:1.1 0/0:1384:4:0,4:634,746:1380,4:0.0029:2,0:1:0:24.8:1:0.12973:0:60:8:0.0029:0:1 +12 12018911 . T C 207 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTATTCTACTCTGTTTTTT;RSEQ=CTATATTCTCCTTCTTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1759:90:45,45:888,781:1669,90:0.0512:2,2:22.9:1:31.9:1:0.58848:1.13692:59.7:180:0.0517:0:1.1 0/0:1565:0:0,0:804,760:1564,0:0:2,0:23.1:1:29.2:1:1:0:60:119.308:0.9994:0:0.1 +12 12019055 . G A 191 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=30.00922;LSEQ=CCCTTTCTTCTCTCATCTCC;RSEQ=TTCTGCTATTAAGTCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2349:3:2,1:1107,1237:2344,3:0.0013:2,2:4:1:23.3:1:0.6054:2.23:60:2:9e-04:0:3.3 0/1:2218:82:43,39:1038,1094:2132,82:0.037:2,2:24.7:1:30.1:1:0.57381:1.16:59.4:164:0.0374:0:1.1 +12 12019081 . G A 214 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=84.33696;LSEQ=CTATTAAGTCCATCTAGTCC;RSEQ=GTCTTTCATTTCAGATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2111:2:1,1:984,1122:2106,2:9e-04:2,2:8:1:29:1:1:1.14:60:4:0.001:0:1 0/1:1970:146:70,76:857,963:1820,146:0.0741:2,2:25.7:1:29.9:1:0.86346:1.03:60:72:0.0739:0:1.1 +12 12019132 . C CT 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.09092;SOR=0.69074;LSEQ=TTATAGAATCTTTATTTTGC;RSEQ=TTTTTTTTTAATTCCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1673:55:21,34:814,798:1612,55:0.0329:2,2:23.7:1:30.3:1:0.07599:1.65101:59.8:26.5:0.0323:0.0042:0.2 0/1:1613:37:19,18:768,808:1576,37:0.0229:2,2:18.9:1:28.3:1:0.86816:1.11:59.9:36:0.0227:0.0043:0.3 +12 12019755 . GG AT 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGGCACTTGGGCTATTC;RSEQ=TAATCAGACAAGAATTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1807:0:0,0:875,927:1802,0:0:2,0:25.2:1:30.6:1:1:0:60:119.133:0.9972:0:0.1 0/1:1618:54:24,30:761,797:1558,54:0.0334:2,2:25.4:1:29.4:1:0.58072:1.19341:60:108:0.0338:0.0019:1 +12 12019756 . G T 199 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=27.55807;LSEQ=CCTGGCACTTGGGCTATTCG;RSEQ=TAATCAGACAAGAATTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1823:5:0,5:885,930:1815,5:0.0027:2,0:1:0:24.6:1:0.06263:0:60:4:0.0022:0:1.2 0/1:1603:113:58,55:700,735:1435,113:0.0705:2,2:26.4:1:29.2:1:0.62596:1.11:60:112:0.0732:0:1.2 +12 12020114 . C T 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=26.33353;LSEQ=TATGGTTTCTTTCATTTCTA;RSEQ=CCGTAAGAAGGTTAGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1809:294:160,134:803,706:1509,294:0.1625:2,2:25.2:1:30.8:1:0.7494:1.05:60:41:0.1611:0:1.6 1/1:1603:1341:703,638:139,122:261,1341:0.8366:2,2:24.6:1:29.1:1:0.83905:1.03399:60:45.241:0.8357:0:1.5 +12 12020170 . C T 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=11.17484;LSEQ=TATTGTTGAACTGAAATTGC;RSEQ=CCTTTCCTTGTTTAGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1959:330:177,153:834,792:1626,330:0.1685:2,2:24.3:1:30.9:1:0.46855:1.10:60:109:0.17:0:1.5 1/0:1832:1271:649,622:288,271:559,1271:0.6938:2,2:25.4:1:29.3:1:0.87899:1.01851:60:104.917:0.6948:0:1.5 +12 12021412 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19194;SOR=Inf;LSEQ=GACAAAGTTTTGCTCTGTCA;RSEQ=CCAGGCTGGAGTGCAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:60,82:142,0:0:2,0:23.2:1:28.9:1:1:0:38.9:6.1:1:0:1 0/1:112:2:1,1:31,79:110,2:0.0179:2,2:24.5:1:28:1:0.49163:2.52:51:4:0.0227:0:3.5 +12 12021474 . C T 113 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=23.09955;LSEQ=CTCCACCTCCTGGGTTCAAG;RSEQ=GATTCTCATGTCTCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:0,1:114,64:178,1:0.0056:2,0:16:0:31:0:0.36313:0:31:2:0.0062:0:1 0/1:121:14:9,5:73,33:106,14:0.1157:2,2:17.6:1:29.7:1:0.76411:1.22676:46.1:28:0.125:0:1.3 +12 12021657 . T C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=8.97961;LSEQ=ACTCCTAGAGTTAGAGAATA;RSEQ=GAAAATTTTAGTTGTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1156:180:104,76:599,377:976,180:0.1557:2,2:25:1:31.2:1:0.3623:1.16093:60:179:0.1569:0:1.1 1/0:1034:645:377,268:222,166:388,645:0.6238:2,2:24.8:1:30.3:1:0.69679:1.05:60:70.667:0.6223:0:1.1 +12 12021980 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54746;SOR=0;LSEQ=GGAGACCCAGACCATCCTGG;RSEQ=TAACACGGTGAAACCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:0,2:16,124:140,2:0.0141:2,0:39:1:31.5:1:1:0:47.5:4:0.0147:0:1 0/0:74:0:0,0:3,71:74,0:0:1,0:24.2:1:31.3:1:1:0:40.2:23.667:1:0:0.1 +12 12022012 . TA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCCATCTCTACTAAAAA;RSEQ=AAAAAAATTAGCCGAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:0,2:31,72:103,2:0.019:2,0:13.5:1:31.5:1:1:0:26.5:4:0.0198:0:0.5 0/0:39:0:0,0:6,33:39,0:0:2,0:24:1:30.3:1:1:0:34.6:78:1:0:0.1 +12 12022098 . A T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=5.61024;LSEQ=GAGAATGGCATGAACCCGGG;RSEQ=GGCAGAGCTTGCAGTGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:15:12,3:35,4:39,15:0.2778:2,2:18.9:1:30.5:1:0.38231:2.15219:34:30:0.2885:0:1 1/0:48:33:31,2:15,0:15,33:0.6875:1,2:15.9:1:30.5:1:1:0:25.9:66:0.6875:0:1 +12 12022128 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2419;SOR=0;LSEQ=TGCAGTGAGCCGAGATCGTG;RSEQ=CACTGCACTCCAGCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:2,0:95,9:104,2:0.0189:2,0:20.5:1:30.5:1:1:0:40:4:0.0196:0:1 0/0:109:0:0,0:106,3:109,0:0:1,0:23.1:1:32.2:1:1:0:38.4:108:1:0:0.6 +12 12022175 . G GA 200 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.00907;SOR=1.52759;LSEQ=GTGAGACTCCATCTCAAACA;RSEQ=AAAAAAAAAAAAAATATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:93:74,19:216,66:282,93:0.2268:2,2:28.5:1:30.8:1:0.66846:1.19:56.4:186:0.2507:0:1 0/1:407:126:96,30:170,47:217,126:0.3096:2,2:27.7:1:28.8:1:0.68785:1.12991:55.4:252:0.3325:0:0.7 +12 12022496 . T C 207 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACCCCGAGCAGCGGCCCC;RSEQ=CCGGTCCCCCCTGGACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1450:0:0,0:612,837:1449,0:0:2,0:23.9:1:30.5:1:1:0:60:37.132:0.9993:0:0.3 0/1:1422:117:57,60:589,712:1301,117:0.0823:2,2:24:1:30.2:1:0.4983:1.15:59.8:38:0.0823:0:1.2 +12 12022533 . C T 271 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACATGATCCGCCGCCTCTC;RSEQ=CCGGCTGAGAGAGCTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1239:474:201,273:334,430:764,474:0.3826:2,2:23.7:1:30.6:1:0.67962:1.05496:60:58.25:0.3835:0:1.2 0/0:1147:0:0,0:526,619:1145,0:0:2,0:23.8:1:30.1:1:1:0:60:70.563:0.9982:0:0.2 +12 12023023 . C G 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=21.84;LSEQ=TAGGCGCCCTCCAAGGCTCT;RSEQ=TGAGGGCAATTGGAGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:609:99:46,53:224,285:509,99:0.1626:2,2:20.7:1:32.5:1:0.65996:1.10:60:198:0.1639:0:1.1 1/1:531:430:204,226:51,50:101,430:0.8098:2,2:23.3:1:31.3:1:0.58243:1.12974:59.9:106.5:0.8099:0:1.1 +12 12023373 . G T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41602;SOR=2.47277;LSEQ=GGAGAGGAAAACAGGATTAT;RSEQ=GTATTGGAGGCAGGTGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:2:0,2:165,152:317,2:0.0063:2,0:10.5:1:21:1:0.23227:0:60:1:0.0032:0:1.5 0/1:260:4:3,1:131,125:256,4:0.0154:2,2:31.5:1:30.5:1:0.62281:2.85:60:8:0.0155:0:1 +12 12023773 . C A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.89;LSEQ=GATATAAGGCAGAATGAAGT;RSEQ=AGCCCCATTTCCCATTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:60:33,27:172,153:325,60:0.1558:2,2:25.6:1:30.4:1:0.78031:1.09:60:120:0.1571:0:1 1/0:327:260:140,120:35,32:67,260:0.7951:2,2:22.9:1:28.5:1:0.8909:1.07:60:85.667:0.7957:0:1.2 +12 12023843 . C A 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTCTGCCAGAGTAATAAAG;RSEQ=GCTGTAGAAGCAAAGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:0:0,0:304,240:544,0:0:2,0:24.1:1:31.4:1:1:0:59.9:271:0.9982:0:0.2 0/1:483:19:10,9:252,212:464,19:0.0393:2,2:28.9:1:28.8:1:1:1.06964:60:38:0.0396:0:1.3 +12 12023844 . G A 133 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=28.29782;LSEQ=GTCTGCCAGAGTAATAAAGC;RSEQ=CTGTAGAAGCAAAGCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:548:1:1,0:306,241:547,1:0.0018:2,0:1:0:26:0:1:0:60:2:0.0018:0:1 0/1:487:24:11,13:251,212:463,24:0.0493:2,2:21.9:1:29.1:1:0.52974:1.39825:60:48:0.0494:0:1.5 +12 12023941 . C T 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.61184;LSEQ=TACTGAAGTGACTGTGCTTT;RSEQ=GATAGTGGGAAGGAGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:90:38,52:186,244:430,90:0.1724:2,2:23.5:1:30.3:1:0.90707:1.04307:60:29:0.1699:0:1.1 1/0:490:347:155,192:61,81:142,347:0.7082:2,2:24.5:1:29.4:1:0.76396:1.07:60:114.667:0.7122:0:1.1 +12 12024162 . GC G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=TTTTTTTTCCACACTCTGTT;RSEQ=CCAGGCTGGAGTGCAGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:36,134:170,0:0:2,0:20.9:1:30.4:1:1:0:51.2:20.25:1:0:1.2 0/1:186:2:1,1:57,125:182,2:0.0108:2,2:25.5:1:31:1:0.53225:2.18:51:4:0.0114:0:0 +12 12024270 . C A 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16429;SOR=Inf;LSEQ=GTAGCTGCGACTACAGGCGC;RSEQ=CGCCACCATGCCCGGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:12,21:33,0:0:2,0:23.1:1:29.6:1:1:0:35.8:7.25:1:0:0.5 0/1:23:2:1,1:8,13:21,2:0.087:2,2:5:0:29:1:1:1.59:52.5:4:0.0909:0:1.5 +12 12024284 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=14.01283;LSEQ=AGGCGCCCGCCACCATGCCC;RSEQ=GCTAATTTTTTTCATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:13,11:24,3:0.1111:2,2:34.3:1:27:1:0.59556:2.29077:25.7:2:0.087:0:1 1/0:23:15:8,7:2,6:8,15:0.6522:2,2:28.4:1:29.9:1:0.37879:3.25:28.9:14:0.6364:0:1.1 +12 12024412 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24834;SOR=Inf;LSEQ=AGGATTACAGGCGTGAGCCA;RSEQ=CGCGCCTGGCCGGTACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:153,42:195,0:0:2,0:24.9:1:31.9:1:1:0:58.8:64:1:0:0.2 0/1:202:3:1,2:146,53:199,3:0.0149:2,2:13:1:25.7:1:0.18068:5.45406:60:6:0.0149:0:1 +12 12024543 . C A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06194;SOR=Inf;LSEQ=TACATCAGGGATGTTGAATC;RSEQ=AGAAAATAAAATGGCAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:171,248:419,0:0:2,0:25.9:1:31.9:1:1:0:59.9:82.8:1:0:0.1 0/1:433:5:4,1:177,250:427,5:0.0115:2,2:22.6:1:21:1:0.16623:5.63:60:1.5:0.0071:0:2.4 +12 12025110 . A G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=7.56461;LSEQ=TGTGGAAGGGTCATTTGTAC;RSEQ=GGGGAAACCACAGAGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:94:42,52:237,248:485,94:0.1623:2,2:27.3:1:30.7:1:0.4993:1.18283:60:46:0.1603:0:1.2 1/0:447:266:127,139:86,92:178,266:0.5951:2,2:25.7:1:29.7:1:0.92303:1.02306:59.9:265:0.5968:0:1.1 +12 12025234 . G A 120 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=7.33123;LSEQ=TGGCTGCTGTCCATAGTGCT;RSEQ=CCCTCGTGGGCCTGGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:458:3:2,1:272,182:454,3:0.0066:2,2:12.7:1:28:1:1:1.34:60:6:0.0067:0:1.3 0/1:433:20:10,10:223,190:413,20:0.0462:2,2:22.7:1:27.8:1:0.81981:1.17325:60:40:0.0467:0:1.2 +12 12025363 . A C 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.06549;LSEQ=CACATGGTTTAGACTTGAGG;RSEQ=GTTATTTTTCCCTTATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:644:520:201,319:53,69:122,520:0.8075:2,2:26.8:1:30.5:1:0.35507:1.21866:59.9:51:0.8108:0:1.1 0/1:721:155:73,82:267,292:559,155:0.215:2,2:25.4:1:30.1:1:0.92766:1.02708:59.9:154:0.2255:0:1.2 +12 12025428 . CTTTTTTTTTTT C 226 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=21.000;MSILEN=1;SSF=0;SOR=0.1656;LSEQ=AGTCTCTTAAAATTATATTA;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:114:22,92:19,53:72,114:0.5616:2,2:28.1:1:33.1:1:0.27925:1.49574:59.3:113:0.5622:0.0197:0.6 0/1:218:38:11,27:46,109:155,38:0.1743:2,2:31.1:1:30.8:1:1:1.03568:59.5:37:0.1796:0.0092:0.6 +12 12025712 . G T 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63142;SOR=0.41234;LSEQ=ATTGCTGGGATTACAGGCAT;RSEQ=AACCACTGCACCCAGCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:1,2:120,28:148,3:0.0199:2,2:16:1:27.3:1:0.1008:8.3986:60:6:0.02:0:1 0/0:121:1:0,1:94,26:120,1:0.0083:2,0:1:0:21:0:0.22314:0:60:2:0.0085:0:1 +12 12025714 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5058;SOR=0;LSEQ=TGCTGGGATTACAGGCATGA;RSEQ=CCACTGCACCCAGCCTATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:120,32:152,2:0.0129:2,2:15:0:34.5:1:0.38375:3.70832:60:4:0.013:0:3.5 0/0:121:0:0,0:93,27:120,0:0:2,0:23:1:28.8:1:1:0:57.8:39:0.9915:0:0.1 +12 12025719 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50533;SOR=0;LSEQ=GGATTACAGGCATGAACCAC;RSEQ=GCACCCAGCCTATACTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:132,42:174,2:0.0114:2,2:20:0:32.5:1:0.43:3.11802:60:4:0.0116:0:3.5 0/0:139:0:0,0:102,37:139,0:0:2,0:22.3:1:29.6:1:1:0:58.1:45.333:1:0:0.1 +12 12025722 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5028;SOR=0;LSEQ=TTACAGGCATGAACCACTGC;RSEQ=CCCAGCCTATACTACTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:137,43:180,2:0.0109:2,2:23:0:33:1:0.42608:3.1611:60:4:0.011:0:3.5 0/0:152:0:0,0:110,41:151,0:0:2,0:21.9:1:28.9:1:1:0:58.4:302:0.9934:0:0.1 +12 12025753 . A T 43 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05767;SOR=Inf;LSEQ=ACTACTATTTTTTTCATCTC;RSEQ=TTCCCCAATATCAGTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:216,104:320,0:0:2,0:24.4:1:30.6:1:1:0:60:39:1:0:0.1 0/1:309:4:1,3:190,115:305,4:0.0129:2,2:6.8:1:21.8:1:0.15745:4.93106:60:3:0.01:0:1.3 +12 12025940 . C T 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAATATTCATGTAAAATAA;RSEQ=CCTGGGGCCTAGATCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:0:0,0:263,235:498,0:0:2,0:25.1:1:31.5:1:1:0:59.8:54.333:1:0:0.1 0/1:499:37:23,14:237,225:462,37:0.0741:2,2:27.8:1:29.5:1:0.23319:1.56:60:74:0.0754:0:1.1 +12 12026415 . CAGCTGTTAGATGAGAAAACTTAGTTCCTTAAAGCTTTTCAAATGAGCACAGCACAAAAAGAAATGAAGGTGCTGCTGAATGTCAAACTGATGAGTACTATAGCTGGAGGGTATAGATGGAAATAGTACTCATGAATGTGGATCACAAAATGAAGCTAAATTCTTACTATTCAGATATGATTTGTTCAGGTGCCCTAGAATTTATGCATTTGGACACCTTCTGTGTATAAGGCACTGTTCTGCATTCTTGATGGGGTGGGGACAGCCTCAGAGAGGTATAAGACACAGTCTTTATCATGAAAGAGCTGAGCACAGTTAACTATAAAAGCGAAGCACATGACATGTATCTTAGAAGGGCTCCTGTTAAGTACCACAGGAGGTCAGAGTAGGGATGTCAGGGCAAGCTACATGGAGGGCTGGCTTTTAGCTGGGCTTGGATGAATGCTTAGAATGTGGACAAGTGGAGATTAGAGAAAAACAGGTCATTCCAGATGGAGAAAACTTACCAGGAGCAAAGCAAGATAAGGCTCGGTGTATTTTTTCTATTTCAGGTAGAAATGTAAATCTACAAGTTGAGATCTATTGAGGTCATTTAAAAATCTATCATTTTTCAGGCTGGGTACTGTGGCTCACGCCTGTAATCCCAGTACTTTGGAAGGCCAAGGCTGGCAGATCACCTGAGGTCAGGATTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCATCTCTATCAAAAAA C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.08875;LSEQ=GCCTTTAAATCTCCGTAAAG;RSEQ=TACAAAAATTCGTCGGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:146:110:20,90:13,23:36,110:0.7534:2,2:23.9:1:32.7:1:0.03763:2.52495:52.3:109:0.7569:0.1301:0.7 0/1:203:43:8,35:59,101:160,43:0.2118:2,2:21.2:1:31:1:0.02804:2.54495:40:86:0.2129:0.0345:0.5 +12 12026417 . G A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51977;SOR=Inf;LSEQ=CTTTAAATCTCCGTAAAGCA;RSEQ=CTGTTAGATGAGAAAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:13,23:36,0:0:2,0:22.2:1:32.4:1:1:0:60:72:1:0:0 0/1:193:2:1,1:57,98:155,2:0.0104:2,2:6.5:1:29:1:1:1.71:60:4:0.0127:0:1 +12 12026437 . A G 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51458;SOR=Inf;LSEQ=GCTGTTAGATGAGAAAACTT;RSEQ=GTTCCTTAAAGCTTTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:12,20:32,0:0:2,0:26.8:1:29.9:1:1:0:60:15:1:0:0.1 0/1:177:2:1,1:60,79:139,2:0.0113:2,2:7:0:33:1:1:1.31:60:4:0.0143:0:1 +12 12026524 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50496;SOR=Inf;LSEQ=GATGAGTACTATAGCTGGAG;RSEQ=GTATAGATGGAAATAGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:23,21:44,0:0:2,0:21:1:31.2:1:1:0:60:88:1:0:0.1 0/1:170:2:1,1:61,71:132,2:0.0118:2,2:6.5:1:28:1:1:1.16:60:4:0.0152:0:1.5 +12 12026529 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21052;SOR=0;LSEQ=GTACTATAGCTGGAGGGTAT;RSEQ=GATGGAAATAGTACTCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:23,21:44,2:0.0146:2,2:18:1:27.5:1:1:1.09307:60:4:0.0444:0:1 0/0:161:0:0,0:59,66:125,0:0:2,0:27.2:1:28.9:1:1:0:60:61.5:1:0:0.1 +12 12026792 . AG A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08024;SOR=0;LSEQ=CTCCTGTTAAGTACCACAGG;RSEQ=GTCAGAGTAGGGATGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:47,34:81,2:0.0115:2,2:29.5:1:33:1:1:1.37686:60:4:0.0244:0:0 0/0:439:0:0,0:251,152:403,0:0:2,0:25.6:1:31:1:1:0:60:79.6:1:0:0.1 +12 12026871 . A G 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0034;SOR=Inf;LSEQ=GATGAATGCTTAGAATGTGG;RSEQ=CAAGTGGAGATTAGAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:63,57:120,0:0:2,0:24.8:1:30.4:1:1:0:60:119:1:0:0.1 0/1:567:20:9,11:257,254:511,20:0.0353:2,2:22.9:1:30.1:1:0.65712:1.23616:60:40:0.0382:0:1.1 +12 12027101 . G C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=7.60198;LSEQ=TGGCAGATCACCTGAGGTCA;RSEQ=GATTTCGAGACCAGCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:11:1,10:0,0:0,11:0.1078:0,2:23.4:1:30.7:1:1:0:49.9:22:1:0:1.5 0/1:83:40:2,38:0,7:7,40:0.4819:0,2:25.1:1:28.8:1:1:0:43.1:80:0.8511:0:1.7 +12 12027136 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=8.76253;LSEQ=CCTGGCCAACATGGTGAAAC;RSEQ=CCATCTCTATCAAAAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:7:0,7:0,0:0,7:0.0714:0,0:23.7:1:30.6:1:1:0:43.1:14:1:0:2.1 0/1:64:26:0,26:0,2:2,26:0.4063:0,1:25.5:1:28:1:1:0:36:12:0.9231:0:2.2 +12 12027175 . G T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0156;SOR=0;LSEQ=ACAAAAATTCGTCGGGCATG;RSEQ=TGGTGCACACCTGTAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:78:78:8,70:0,0:0,78:1:0,2:23.4:1:30.5:1:1:0:52.7:77:1:0:1.1 1/1:27:24:0,24:0,3:3,24:0.8889:0,1:21.2:1:30:1:1:0:44.4:48:0.8889:0:1.5 +12 12027310 . CA C 66 MSI12;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGTGATACTCTGTCT;RSEQ=AAAAAAAAAAAAATGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:1,3:2,5:7,4:0.3077:2,2:29.8:1:33.3:1:1:1.18052:43.8:8:0.3077:0:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 12027342 . A G 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.17582;SOR=7.29544;LSEQ=AAATGTGTGTGTATATATAT;RSEQ=TGTGTGTATATATATACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:2,7:9,2:0.1818:2,0:31.5:1:33:1:0.10909:0:53.5:4:0.2222:0:2 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:23:1:33.5:1:1:0:46:4:0.6667:0:3 +12 12027372 . GTA G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATATATACACACACATATAT;RSEQ=TATATATATGCGTATGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:5,2:1,1:2,7:0.875:2,2:22.7:1:32.6:1:1:2.24:40.7:14:0.875:0.125:3.1 1/1:6:6:6,0:0,0:0,6:1:0,0:31:1:32.5:1:1:0:38.2:12:1:0:2.3 +12 12027405 . C T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGTATGTATATATACACACA;RSEQ=ACGTGTATGTGCGTGTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1:0,2:35.3:1:30:1:1:0:33.7:12:1:0:4.3 1/1:7:7:7,0:0,0:0,7:1:0,0:23.4:1:29.9:1:1:0:36.3:14:1:0:2.3 +12 12027407 . C T 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTATATATACACACACA;RSEQ=GTGTATGTGCGTGTGTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1:0,2:34.7:1:30.2:1:1:0:33.7:12:1:0:4.3 1/1:7:7:7,0:0,0:0,7:1:0,0:21.4:1:30:1:1:0:36.3:14:1:0:2.3 +12 12027429 . C CACGTGTGTGCGCGTGTGTATGTGTATATATGTGTGT 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.00216;SOR=Inf;LSEQ=TGTATGTGCGTGTGTACACA;RSEQ=ATATGTGTATGTGCGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:6,0:0:2,0:18:1:31:1:1:0:33.7:12:1:0:4.3 1/1:5:5:5,0:0,0:0,5:1:0,0:26.6:1:27.6:1:1:0:32.4:10:1:1:2 +12 12027431 . TATGTGTA CGTGTG 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01515;SOR=0;LSEQ=TATGTGCGTGTGTACACACA;RSEQ=TGTGCGTGTGTACACACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:23.4:1:29.9:1:1:0:29.2:10:0.8333:0.1667:3 0/0:5:0:0,0:5,0:5,0:0:0,0:1:0:27.4:1:1:0:32.4:10:1:0:2 +12 12027447 . T C 61 d5;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACATATGTGTATGTGCGTG;RSEQ=GTACACACATATATGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:10:0:30.8:1:1:0:27.3:8:1:0:5.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 12027457 . TA CACGTGTGTGCGCGTGTG 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TATGTGCGTGTGTACACACA;RSEQ=TATGTGTATGTGCGTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:21:1:29.7:1:1:0:25.5:4:0.5:0.5:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 12027586 . A ATG 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTGTGTGTGTATATACACAT;RSEQ=TGTGTGTATATGTATATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,0:1,2:0.5:0,0:32:1:30.3:1:1:0:44:4:0.5:0:1 +12 12027594 . A G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.02767;SOR=Inf;LSEQ=GTATATACACATATGTGTGT;RSEQ=TATGTATATATGTGTGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:16,0:0:1,0:7.4:1:29.8:1:1:0:31:32:1:0:1.1 0/1:8:3:3,0:4,0:4,3:0.375:0,0:21.7:1:30.3:1:1:0:49.3:6:0.4286:0:1 +12 12027596 . A G 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.09091;SOR=0.12397;LSEQ=ATATACACATATGTGTGTAT;RSEQ=TGTATATATGTGTGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:15,0:1,0:1,15:0.9375:0,1:8.1:1:33.7:1:1:0:30.3:30:0.9375:0:1.1 1/0:8:5:5,0:2,0:2,5:0.625:0,0:5.2:1:31.2:1:1:0:30.2:10:0.7143:0:1 +12 12027618 . G GTA 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.12207;SOR=0.13234;LSEQ=GTATATATGTGTGTATATAT;RSEQ=TATATGTGTGTATATATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:55:47,8:1,0:1,55:0.9821:0,2:15.4:1:30.2:1:1:0:46.7:110:0.9821:0.4286:0.4 1/1:16:14:14,0:1,0:1,14:0.875:0,1:21.6:1:30:1:1:0:37.9:28:0.875:0:0.5 +12 12027664 . GTA G 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.1613;SOR=0;LSEQ=GTATATGTGTATATATATGT;RSEQ=TATATATATGAAATTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:5:3,2:152,82:234,5:0.0209:2,2:28.6:1:32.4:1:1:1.23463:59:10:0.021:0:0.2 0/0:148:0:0,0:93,55:148,0:0:2,0:25.4:1:28.4:1:1:0:57.7:73:1:0:0.2 +12 12027745 . A C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49206;SOR=0.76771;LSEQ=CATACCATTAAGATACATGC;RSEQ=GAATTGTTCTCACTCATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:21:10,11:101,144:245,21:0.0787:2,2:26.1:1:30.9:1:0.64691:1.29:57.2:42:0.0787:0:1 0/1:244:15:5,10:98,131:229,15:0.0615:2,2:30.8:1:29.7:1:0.59359:1.4938:51.7:30:0.0615:0:1 +12 12027759 . T A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12132;SOR=0;LSEQ=ACATGCAGAATTGTTCTCAC;RSEQ=CATAGGTGGGAATTGAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:3,0:72,126:198,3:0.0149:2,0:10.3:1:21.3:1:0.05065:0:60:2:0.0105:0:1.3 0/0:204:0:0,0:83,121:204,0:0:2,0:25.2:1:28.8:1:1:0:53.7:203:1:0:0.2 +12 12027797 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49657;SOR=Inf;LSEQ=CAATGAGAACACATGGACAC;RSEQ=GGAAGGGGAACATCACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:9,58:67,0:0:2,0:22.5:1:32.1:1:1:0:38.6:32.5:1:0:0.2 0/1:70:2:1,1:13,55:68,2:0.0286:2,2:8.5:1:29:1:0.36232:4.11:52.5:4:0.029:0:1 +12 12027966 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50801;SOR=0;LSEQ=TTGTGCACATGTACCCTAAA;RSEQ=CTTAAAGTATAATTAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:131,25:156,2:0.0126:2,2:24.5:1:32:1:0.30291:5.15794:60:4:0.013:0:1.5 0/0:120:0:0,0:103,17:120,0:0:2,0:21.9:1:30.1:1:1:0:52.2:119:1:0:0.1 +12 12027980 . TA T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=5.72335;LSEQ=CCTAAAACTTAAAGTATAAT;RSEQ=AAAAAAAAAGATACATGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:52:44,8:164,46:210,52:0.1948:2,2:21.9:1:30.6:1:0.34355:1.54:54.8:51:0.1947:0.0562:0 1/0:196:114:92,22:65,15:80,114:0.5816:2,2:22.7:1:30:1:1:1.03605:54.8:113:0.5795:0.1327:0.1 +12 12028142 . A C 136 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=34.08331;LSEQ=AGCTTATTTTTAAAGGTGTC;RSEQ=CTTACTTTGCAAAGGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:1:0,1:367,387:754,1:0.0013:2,0:24:0:11:0:1:0:60:0:0:0:2 0/1:670:29:13,16:279,361:640,29:0.0433:2,2:25.7:1:28.1:1:1:1.05:60:8.667:0.0393:0:1 +12 12028157 . G T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.87271;LSEQ=GTGTCACTTACTTTGCAAAG;RSEQ=ATAAGGAGAACTGTTATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:689:101:44,57:287,301:588,101:0.1466:2,2:25:1:29.1:1:0.33467:1.23482:60:100:0.1464:0:1.1 1/0:622:337:144,193:117,168:285,337:0.5418:2,2:24.6:1:27.9:1:0.68424:1.07:60:83.25:0.5406:0:1.1 +12 12028566 . A AG 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGACTTGATTTCAAAGGT;RSEQ=GAAGGGCCTTTTACAGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:206,216:422,0:0:2,0:24.6:1:30.1:1:1:0:60:139.667:0.9976:0:0.1 0/1:377:34:13,21:164,179:343,34:0.0902:2,2:28.1:1:30.4:1:0.36808:1.4785:60:68:0.0912:0.0106:0.1 +12 12028629 . T G 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00046;SOR=Inf;LSEQ=CAAGAGTCTAGCCTCGAGCT;RSEQ=CTGTTCAGTGTTTTTCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:207,199:406,0:0:2,0:24.8:1:30.6:1:1:0:59.9:57:1:0:0.1 0/1:356:10:6,4:181,165:346,10:0.0281:2,2:27.8:1:31.1:1:0.75363:1.37:60:20:0.0283:0:1.1 +12 12028735 . G GT 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.06931;SOR=6.91571;LSEQ=GCCAAATCCAGCCACCATGC;RSEQ=TTTTTTTTAAATCAAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:1:1,0:225,247:472,1:0.0021:2,0:33:0:32:0:0.4778:0:60:2:0.0021:0:0 0/1:484:7:3,4:236,240:476,7:0.0145:2,2:23.1:1:29.6:1:1:1.31038:60:14:0.0146:0.0041:0.3 +12 12029748 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGAGGCTATCGCTGGTCA;RSEQ=TTGGGTCATTAATCCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:478:477:279,198:0,0:0,477:0.9979:0,2:24.6:1:30.3:1:1:0:59.9:52:0.9979:0:1.2 1/1:358:358:190,168:0,0:0,358:1:0,2:25.8:1:29.5:1:1:0:60:70.6:1:0:1.2 +12 12029765 . A G 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGTTGGGTCATTAATCCT;RSEQ=CAGCAGGCAAGACACAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:78:45,33:251,203:454,78:0.1463:2,2:21.7:1:32.1:1:0.7131:1.10:60:156:0.1477:0:1.8 0/0:431:0:0,0:232,199:431,0:0:2,0:22.8:1:27.8:1:1:0:59.9:70.833:1:0:0.8 +12 12030052 . A C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49942;SOR=Inf;LSEQ=ATATATACAAAGATTCAATT;RSEQ=GGGAAGCCTCTGAAGTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:325:323:172,151:0,0:0,323:0.9938:0,2:23.3:1:31.1:1:1:0:60:79.75:0.9969:0:1.5 1/1:312:312:168,144:0,0:0,312:1:0,2:23.8:1:30.1:1:1:0:60:103:1:0:1.6 +12 12030117 . A G 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47787;SOR=0;LSEQ=GAGAAAGCAGTTTGAGGCTT;RSEQ=TCCTCAGGGGCTTCAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:460:460:282,178:0,0:0,460:1:0,2:24.9:1:32.4:1:1:0:59.8:91:1:0:1.4 1/1:421:420:250,170:0,0:0,420:0.9976:0,2:25.2:1:31.2:1:1:0:60:69:0.9976:0:1.8 +12 12030123 . A G 213 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGTTTGAGGCTTATCCTC;RSEQ=GGGGCTTCAAGGACTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:289,202:491,0:0:2,0:24.4:1:31.1:1:1:0:59.9:121.75:1:0:1.2 0/1:435:158:94,64:152,125:277,158:0.3632:2,2:23.1:1:29.2:1:0.36674:1.21:59.9:51.667:0.3605:0:2.2 +12 12030306 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGCTAAAAGACCTCGTAAA;RSEQ=GAGAAGTGTGAAGGGATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:286:235:124,111:27,24:51,235:0.8217:2,2:27.2:1:31.8:1:1:1.00703:59.8:28.375:0.8225:0:1.4 1/1:322:322:156,166:0,0:0,322:1:0,2:26.5:1:30.3:1:1:0:59.6:34.778:1:0:1.4 +12 12030352 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12067;SOR=Inf;LSEQ=AGTGCTGGGGGCAAGTCTCA;RSEQ=CCCTCGGCCTTTGTTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:155,148:303,0:0:2,0:24.3:1:31.8:1:1:0:59.9:29.3:1:0:0.6 0/1:297:3:2,1:153,140:293,3:0.0101:2,2:9.7:1:26:1:1:1.83:60:6:0.0103:0:1.7 +12 12030834 . TC T 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00757;SOR=0;LSEQ=TTAATTGCTACGTGTCACTG;RSEQ=CCCCCCTGCCTCACTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:8:3,5:167,209:376,8:0.0208:2,2:30.6:1:31.9:1:1:1.33076:60:16:0.0213:0:0.1 0/0:373:0:0,0:168,203:371,0:0:2,0:23.6:1:30.3:1:1:0:59.8:52:0.9945:0:0.2 +12 12030905 . G A 50 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26302;SOR=0;LSEQ=GTGTGGGAGCTGTGGGTACA;RSEQ=CCAGCACAACTGCCTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:1,2:87,124:211,3:0.014:2,2:22:0:32:0:1:1.40109:60:6:0.0142:0:1 0/0:161:0:0,0:64,97:161,0:0:2,0:23.6:1:31.2:1:1:0:60:39.25:1:0:0.1 +12 12030945 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17111;SOR=Inf;LSEQ=AGCCACGCAGGGCACTGACA;RSEQ=GGAAGGCCTGTGTGGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:86,133:219,0:0:2,0:26:1:31.9:1:1:0:59.9:72:1:0:0.1 0/1:155:2:1,1:62,91:153,2:0.0129:2,2:23.5:1:31:0:1:1.46:60:4:0.0129:0:1 +12 12031015 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.509;SOR=0;LSEQ=CCTTGGAGATTTACTTTTGT;RSEQ=CTCCTGCTTCCCCTCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:90,102:192,2:0.0103:2,2:32:1:31.5:1:1:1.13:60:4:0.0105:0:1 0/0:145:0:0,0:75,69:144,0:0:2,0:22.8:1:31.4:1:1:0:60:143:0.9931:0:0.1 +12 12031080 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25502;SOR=0;LSEQ=GAGGGGATGAATAAGATGAG;RSEQ=ACTGGGGAGGGGAGGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:1,2:118,96:214,3:0.0138:2,2:19.3:1:26:1:0.59034:2.44837:60:6:0.0144:0:1 0/0:179:0:0,0:110,69:179,0:0:2,0:24.1:1:31.4:1:1:0:60:88.5:1:0:0.1 +12 12031265 . G A 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGAGTGGAAAATAATAGAA;RSEQ=GGGCTTGAGGAGACTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:61:35,26:187,134:321,61:0.1597:2,2:27.9:1:30.2:1:0.88862:1.0366:60:19.333:0.1538:0:1.1 0/0:396:0:0,0:214,182:396,0:0:2,0:24.6:1:30.6:1:1:0:60:78.2:1:0:0.2 +12 12031465 . A C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3437;LSEQ=TTTCGGATACCGGTGTTTCC;RSEQ=AGCCTTCTCCACACCTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:399:263:159,104:77,59:136,263:0.6591:2,2:24.8:1:31.9:1:0.51928:1.17:60:130.5:0.6574:0:1.1 0/1:371:148:81,67:125,97:222,148:0.3989:2,2:23.2:1:30.5:1:0.83092:1.06574:60:73:0.4022:0:1.1 +12 12031758 . AG A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=2e-04;SOR=0.33331;LSEQ=ATCTAGAATAGAGGAGGAGG;RSEQ=GGGAAAAAAAAAAAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:43:18,25:191,178:369,43:0.1026:2,2:28.4:1:31.1:1:0.25993:1.48887:58.6:20.5:0.1041:0.0119:1.1 0/1:409:15:10,5:192,194:386,15:0.0367:2,2:27.2:1:29.9:1:0.29267:2.02:57.9:30:0.0402:0.0073:1.8 +12 12031762 . G AA 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.01558;SOR=1.68357;LSEQ=AGAATAGAGGAGGAGGAGGG;RSEQ=AAAAAAAAAAAAAACAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:41:16,25:172,143:315,41:0.1012:2,2:29.3:1:29.4:1:0.06822:1.87601:55.3:12.667:0.1011:0:2.6 0/1:395:63:28,35:123,93:216,63:0.1595:2,2:26.8:1:28.8:1:0.08627:1.65017:54.1:62:0.1636:0:2.6 +12 12031783 . G A 139 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=9.76986;LSEQ=AAAAAAAAAAAAAACAAGCA;RSEQ=CAGATGGCCCCCTGAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:5:4,1:174,227:401,5:0.0122:2,2:20.2:1:15:1:0.17326:5.20:53:0.25:0.0028:0:3.8 0/1:408:44:22,22:149,212:361,44:0.1078:2,2:23.4:1:25.6:1:0.33214:1.42:55.8:4.5:0.1026:0:2.7 +12 12031894 . G C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13565;LSEQ=TTGCTTACTATATTGTAAGA;RSEQ=ATTCAGCAGCATCCCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:245:169:65,104:34,41:75,169:0.6898:2,2:24.7:1:32.4:1:0.32585:1.32525:59.9:168:0.6914:0:1.2 0/1:182:42:20,22:62,78:140,42:0.2308:2,2:22.1:1:31.5:1:0.72651:1.14:60:41:0.2278:0:1 +12 12032028 . C CT 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08749;SOR=0.4244;LSEQ=TTTGTAAAGCTTAGTAGCAA;RSEQ=TTTTTTTTTCATATGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:423:17:7,10:218,185:403,17:0.0402:2,2:28:1:29.6:1:0.32893:1.68129:58.5:34:0.0406:0.0024:0.7 0/1:344:6:3,3:173,162:335,6:0.0174:2,2:28.5:1:28.2:1:1:1.06766:60:12:0.0175:0.0029:0.3 +12 12032858 . C T 59 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71105;SOR=1.52883;LSEQ=GCTGAAAAATTCCAGGTGAG;RSEQ=CGTGGCAACAACCTCTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:3:1,2:226,225:451,3:0.0066:2,2:31.3:1:29:1:1:2.00591:60:6:0.007:0:1 0/1:398:4:2,2:199,195:394,4:0.0101:2,2:31.3:1:29.8:1:1:1.02046:60:8:0.0102:0:1 +12 12032986 . GG AA 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7639;SOR=1.32299;LSEQ=TAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAAAAATCTATTGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:5:5,0:122,117:239,5:0.0199:2,0:8.2:1:31.1:1:0.06099:0:53:10:0.023:0:1.6 0/1:229:6:6,0:106,111:217,6:0.0262:2,0:8.2:1:28.6:1:0.02918:0:56.7:12:0.0302:0:1.2 +12 12032996 . T A 41 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42892;SOR=2.24608;LSEQ=AAAAAAAAAAGGAAAAAAAA;RSEQ=CTATTGTGTGGTCAGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:2:2,0:174,133:307,2:0.0065:2,0:15:1:12:1:0.50809:0:42:0:0:0:5 0/1:277:4:4,0:147,126:273,4:0.0144:2,0:9.3:1:20.5:1:0.1284:0:56.3:3:0.012:0:3 +12 12033441 . AT A 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTGCAGGTTAAGCCCTTAC;RSEQ=TGGAGAAATGGTCTGGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:487:0:0,0:212,274:486,0:0:2,0:24.4:1:30.3:1:1:0:60:39.5:1:0:0.1 0/1:400:40:22,18:173,187:360,40:0.1:2,2:25.4:1:30:1:0.41104:1.32:59.9:39:0.1005:0.0175:0.3 +12 12033536 . C T 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGAAACATGCAGTGAAAA;RSEQ=GCCCATGCTTGTGGTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:205,220:425,0:0:2,0:24.3:1:31.1:1:1:0:59.9:59.714:1:0:0.4 0/1:379:34:15,19:151,193:344,34:0.0897:2,2:26:1:30.1:1:1:1.01:60:68:0.0904:0:1.9 +12 12033570 . C G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.329;LSEQ=GTTAGAGAACTGTCCGCTTT;RSEQ=TTTTTGCTCTACAGTAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:173:91,82:97,91:188,173:0.4792:2,2:24.1:1:32:1:0.91606:1.04:60:33.6:0.4773:0:1.2 0/1:293:68:36,32:107,117:224,68:0.2321:2,2:25.9:1:31.7:1:0.49031:1.23:60:136:0.2345:0:1.4 +12 12033609 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09174;SOR=Inf;LSEQ=CTTCTGAGTGGAGTGCCTTC;RSEQ=GCCTAGAGTCAAGAGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:186,167:353,0:0:2,0:27.1:1:30.5:1:1:0:60:116.667:1:0:0.4 0/1:291:3:1,2:151,137:288,3:0.0103:2,2:19.3:1:27:1:0.60756:2.19859:60:6:0.0104:0:1.7 +12 12033871 . C T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.48193;LSEQ=TCGTCCTGATTTACTGGCTT;RSEQ=TTTTCCCCCTAGAGATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1210:570:248,322:287,344:631,570:0.4711:2,2:26:1:30.5:1:0.52257:1.08317:60:80.429:0.4707:0:1.2 0/1:1189:357:161,196:366,459:825,357:0.3003:2,2:26:1:29.7:1:0.84843:1.03:59.7:70.4:0.2988:0:1.2 +12 12033974 . C A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29137;LSEQ=CCCAAACCCCTGGGCTCAAG;RSEQ=AATTCTCCCACCTCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:97:8,89:9,93:102,97:0.485:2,2:26.5:1:31.3:1:1:1.07618:59.7:96:0.4898:0:1 0/1:163:35:1,34:4,124:128,35:0.2147:1,1:24.3:1:30.4:1:1:1.09617:59.9:70:0.2174:0:1 +12 12034171 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24898;SOR=Inf;LSEQ=TATAATTATAAGCCACCACA;RSEQ=CCAACCCTAATTTACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:175,113:288,0:0:2,0:24.5:1:31.6:1:1:0:59.9:47:1:0:0.1 0/1:299:3:1,2:181,114:295,3:0.01:2,2:9:1:28.3:1:0.56241:3.16287:60:6:0.0102:0:1 +12 12034259 . G T 131 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=22.22017;LSEQ=AGATTATGGAAAATTAAAAT;RSEQ=TGTCTGCCATTTGATAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:1:0,1:318,231:549,1:0.0018:2,0:1:0:14:0:0.42182:0:60:0:0:0:1 0/1:539:21:15,6:285,233:518,21:0.039:2,2:21.5:1:30:1:0.1795:2.04:60:20:0.0377:0:1.3 +12 12034818 . T C 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATTATTCTCAGTCTGCAG;RSEQ=AGGACACTGATTTCTCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:172,227:399,0:0:2,0:24.9:1:28.7:1:1:0:59.9:56:0.9949:0:0.1 0/1:394:19:11,8:151,223:374,19:0.0482:2,2:23.8:1:31.4:1:0.15422:2.03:60:38:0.0487:0:1.2 +12 12034979 . G C 187 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=82.76675;LSEQ=TTGTTAGAATGGGGTTCAAA;RSEQ=TCCAGGACTATGGTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:624:1:0,1:343,280:623,1:0.0016:2,0:13:0:14:0:0.45032:0:60:0:0:0:2 0/1:536:63:36,27:244,228:472,63:0.1175:2,2:25.8:1:31.3:1:0.42453:1.25:60:126:0.1189:0:1.1 +12 12035282 . C G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15778;LSEQ=CCTAAGATTTTATAAACATA;RSEQ=ACCCATTAACGAGTTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:152:74,78:95,83:178,152:0.4606:2,2:23.4:1:32.7:1:0.43967:1.20575:59.9:151:0.459:0:1.1 0/1:304:36:19,17:139,127:266,36:0.1184:2,2:25.2:1:31.5:1:1:1.02:60:72:0.1184:0:1.1 +12 12035459 . C T 50 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.43552;SOR=2.16769;LSEQ=CTATAAAATAGGAATAGCAA;RSEQ=AGCACCTGCCTCATAAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:2:0,2:240,182:422,2:0.0047:2,0:1:0:23:1:0.18774:0:60:4:0.0048:0:1 0/1:393:4:1,3:221,168:389,4:0.0102:2,2:6.8:1:25.3:1:0.32146:3.93341:60:8:0.0103:0:1 +12 12035482 . G A 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCTGCCTCATAAGGCGGC;RSEQ=TAAGGGTCAGATGTAACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:309,228:537,0:0:2,0:23.9:1:30.9:1:1:0:60:133.25:0.9981:0:0.1 0/1:433:18:12,6:229,186:415,18:0.0416:2,2:20.8:1:30.8:1:0.46842:1.62:60:36:0.0421:0:1.1 +12 12035649 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0202;SOR=0.68068;LSEQ=CCACTTCATAAGTGAGGCAA;RSEQ=AGAACCTCAGGAAGATTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:112:55,57:273,249:522,112:0.1767:2,2:24.9:1:29.8:1:0.60253:1.13602:60:55:0.1768:0:1.1 0/1:573:73:41,32:251,249:500,73:0.1274:2,2:24.7:1:28.6:1:0.3811:1.27:60:72:0.1274:0:1.1 +12 12035664 . A G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.5264;LSEQ=GGCAACAGAACCTCAGGAAG;RSEQ=TTAAGAAGCGTGTCCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:629:475:237,238:77,77:154,475:0.7552:2,2:25.6:1:31.4:1:1:1.00421:59.9:46.5:0.7536:0:1.6 1/0:598:370:187,183:115,112:227,370:0.6187:2,2:25.5:1:30.6:1:1:1.00481:59.9:40.111:0.6182:0:1.6 +12 12035698 . T TC 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.56783;LSEQ=CCAGGGTGGCCCAACTGAAT;RSEQ=CCCCTTGTAAATATACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:612:433:198,235:88,91:179,433:0.7075:2,2:26.1:1:31.4:1:0.47641:1.14748:59.7:85.6:0.7074:0.1111:1.6 1/0:579:335:160,175:112,130:242,335:0.5786:2,2:25.4:1:30.2:1:0.73605:1.06:59.9:82.75:0.5838:0.0915:1.6 +12 12035714 . C T 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=5e-05;SOR=0.58596;LSEQ=GAATTCCCCTTGTAAATATA;RSEQ=CCCCAGAGAAGGGTGTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:559:409:186,223:73,75:148,409:0.7317:2,2:24.6:1:30.5:1:0.44257:1.16663:59.7:44.444:0.7299:0:1.6 1/0:509:313:145,168:88,106:194,313:0.6149:2,2:25.8:1:29:1:0.85485:1.04:59.9:51.167:0.6128:0:1.6 +12 12036197 . A C 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00104;SOR=Inf;LSEQ=AGAACAAGGGGAAGGTGTAC;RSEQ=TCATGTCTTCTTCTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:67,144:211,0:0:2,0:19.7:1:30:1:1:0:58.1:13.067:1:0:1.1 0/1:238:11:6,5:80,147:227,11:0.0462:2,2:24.1:1:28.5:1:0.21135:2.20:58.5:10:0.0437:0:2.4 +12 12036213 . T C 201 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=35.000;MSILEN=1;SSF=0.02249;SOR=0.47411;LSEQ=GTACATCATGTCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:87:29,58:3,10:13,87:0.7982:2,2:13.4:1:31.3:1:0.54143:1.66:58.3:13.5:0.8901:0:2.1 1/0:109:71:29,42:5,4:9,71:0.6514:2,2:13.3:1:27:1:0.48417:1.7966:57.5:4.917:0.831:0:2.3 +12 12036301 . T C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.144;SOR=Inf;LSEQ=GCAGTGGTGCGATCTCGACT;RSEQ=ACTGCAACTTCCACCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:27:7,20:0,5:5,27:0.8438:0,2:26.9:1:32.3:1:0.56028:0:45.2:26:0.8387:0:1.3 1/1:21:21:2,19:0,0:0,21:1:0,2:16.7:1:27.5:1:1:0:47:3.2:1:0:2 +12 12036529 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00454;SOR=0.68946;LSEQ=GTGAGCCACCACGCCCGGCC;RSEQ=TGTCTTCTCTTTTAATTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:506:350:226,124:94,57:151,350:0.6917:2,2:22.6:1:30.2:1:0.68528:1.10:56:37.889:0.6861:0:1.1 1/0:550:334:219,115:133,81:214,334:0.6073:2,2:23.3:1:29.6:1:0.465:1.16:56.5:65.8:0.6048:0:1.1 +12 12036821 . T C 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCAGAGTCACCAAGCCACA;RSEQ=AGTTTTTCTTTTCCCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:989:0:0,0:579,409:988,0:0:2,0:25.3:1:29.9:1:1:0:60:81.333:0.999:0:0.1 0/1:934:49:26,23:493,391:884,49:0.0525:2,2:26.4:1:31.7:1:0.76836:1.11525:60:98:0.0529:0:1.2 +12 12037081 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=0.29888;LSEQ=CCGTCTTTCACATGGGTTCT;RSEQ=CCCAGGTTTAAGTTTGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:611:44:19,25:283,283:566,44:0.072:2,2:25.5:1:29.3:1:0.43528:1.3152:60:88:0.0732:0:1.2 0/1:574:13:6,7:273,287:560,13:0.0226:2,2:27.8:1:28.3:1:1:1.10955:60:26:0.023:0:1 +12 12037089 . T C 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACATGGGTTCTGCCCAGGT;RSEQ=TAAGTTTGGGTCACGACCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:292,310:602,0:0:2,0:25.2:1:30.6:1:1:0:60:99.333:1:0:0.2 0/1:574:39:20,19:265,269:534,39:0.0679:2,2:24.7:1:30.7:1:0.8696:1.07:59.9:38:0.0676:0:1.3 +12 12037178 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3659;SOR=1.30222;LSEQ=GGATCATCTCTGAGGCCTCC;RSEQ=GTGGGTCAAAGGTCACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:27:14,13:234,227:461,27:0.0553:2,2:26.4:1:30.9:1:1:1.04:60:26:0.0541:0:1.1 0/1:522:37:16,21:252,233:485,37:0.0709:2,2:23.4:1:29.7:1:0.31284:1.41857:60:36:0.0702:0:1.2 +12 12037318 . C G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00098;SOR=1.62778;LSEQ=TGGATTCTTTTTTGATTCTT;RSEQ=TGGTTAGTGCCTCAACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1122:80:49,31:606,435:1041,80:0.0713:2,2:24.8:1:32.4:1:0.63888:1.13:60:160:0.0719:0:1 0/1:1224:136:74,62:612,475:1087,136:0.1111:2,2:21.8:1:31.3:1:0.7142:1.07942:60:44.333:0.1098:0:1.1 +12 12039518 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCAGGTGTGTATGTACG;RSEQ=GATGAGTCATGATGTAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 12043677 . C G 67 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90182;LSEQ=CCCTAGTCTTTTTAAATAAG;RSEQ=ATTTTACCACTTTTTAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:4,0:36,0:36,4:0.1:1,0:12.8:1:33.5:1:1:0:60:8:0.1:0:1 0/1:11:1:1,0:9,1:10,1:0.0909:2,0:39:0:31:0:1:0:60:2:0.0909:0:2 +12 12044195 . T C 62 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGAATTCTGGCGGAGGGCA;RSEQ=GAGCCTGGGACTCCATGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:15.8:1:31:1:1:0:58.8:8:0.5:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:36:0:30:0:1:0:60:2:0.5:0:1 +12 12268134 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23959;SOR=0;LSEQ=TTTGCAGTGTTTCCCCATTC;RSEQ=TGAGATTGCCTTTCCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:2,0:166,7:173,2:0.0114:1,0:20.5:1:31.5:1:1:0:60:4:0.0116:0:1.5 0/0:182:0:0,0:164,18:182,0:0:2,0:1:0:17:0:1:0:60:0:0:0:1 +12 12268230 . A G 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTCTGTTTTCCTTCTAGG;RSEQ=AAAAGAATGGGAGGAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:0:0,0:403,351:754,0:0:2,0:25.9:1:30.3:1:1:0:60:74.4:1:0:0.1 0/1:929:38:23,15:467,421:888,38:0.0409:2,2:25.6:1:29.7:1:0.40746:1.38:60:18:0.0396:0:1.3 +12 12268329 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12425;SOR=Inf;LSEQ=ACTTGGTTTCCCTTTAATTG;RSEQ=TATTTGGGCTCAAATACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:105,278:383,0:0:2,0:24.2:1:31.7:1:1:0:60:62.833:1:0:0.1 0/1:396:4:2,2:113,279:392,4:0.0101:2,2:19.5:1:29.3:1:0.58309:2.46:60:8:0.0103:0:1 +12 12268526 . C T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52857;SOR=Inf;LSEQ=TTATAAGCTAATTTAAGATC;RSEQ=TGGAAAAGAGGGAAGTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:0,9:0,3:3,9:0.75:0,0:28:1:29.8:1:1:0:60:8:0.7273:0:1.3 1/1:4:4:0,4:0,0:0,4:1:0,0:24.5:1:30.8:1:1:0:60:8:1:0:1.8 +12 12308013 . T C 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=CGTGATGCACGCCTGTAAAC;RSEQ=CAGCTACTCAGGAGGCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:43:1:32.3:1:1:0:49.7:6:0.6:0:1.7 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:42.5:1:31:1:1:0:60:4:0.6667:0:1 +12 12308074 . G A 111 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00288;SOR=0.066;LSEQ=TGGGAGGCGGATGTTGCAGT;RSEQ=AGCCAAGATCACGCCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:14,0:14,0:14,14:0.5:1,1:19.1:1:29.4:1:1:0:42.4:28:0.5:0:2.1 0/1:17:1:1,0:16,0:16,1:0.0588:1,0:13:0:29:0:1:0:49:2:0.0588:0:2 +12 12308087 . G A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=0.08927;LSEQ=TTGCAGTGAGCCAAGATCAC;RSEQ=CCACTTTACTCCAGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:17:17,0:16,0:16,17:0.5152:1,1:25.5:1:31.5:1:1:0:47.2:34:0.5152:0:1.8 0/1:24:2:2,0:22,0:22,2:0.0833:1,0:17:1:31:0:1:0:51.5:4:0.0833:0:2 +12 12308115 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49541;SOR=0;LSEQ=ACTCCAGCCTGGGTGACAGT;RSEQ=TGAGACTCTGTCTCAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:48,5:53,2:0.0364:2,2:17:1:29.5:1:0.20808:8.85505:60:4:0.0364:0:2 0/0:55:0:0,0:44,11:55,0:0:2,0:20.7:1:31.4:1:1:0:59.6:110:1:0:0.1 +12 12308124 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49687;SOR=Inf;LSEQ=TGGGTGACAGTGTGAGACTC;RSEQ=GTCTCAAACAAACAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:57,17:74,0:0:2,0:20.6:1:31:1:1:0:57.5:73:1:0:0.5 0/1:77:2:1,1:50,25:75,2:0.026:2,2:29.5:1:30.5:1:1:1.98074:57:4:0.026:0:1.5 +12 12308128 . T TCAAA 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=7.000;MSILEN=4;SSF=0.00174;SOR=Inf;LSEQ=TGACAGTGTGAGACTCTGTC;RSEQ=CAAACAAACAAACAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:59,20:79,0:0:2,0:20.8:1:30.6:1:1:0:57.5:25.333:1:0:0.4 0/1:89:10:6,4:52,27:79,10:0.1124:2,2:18.5:1:29:1:0.73421:1.28022:57.9:20:0.1124:0.0449:0.9 +12 12308149 . C T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23704;SOR=Inf;LSEQ=CAAACAAACAAACAAACAAA;RSEQ=AAAAAGTCTTTCAGCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:77,50:127,0:0:2,0:21.8:1:31.5:1:1:0:55.8:30.75:1:0:0.3 0/1:121:2:1,1:64,55:119,2:0.0165:2,2:13:0:27:1:1:1.16217:48:4:0.0165:0:2 +12 12308159 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49829;SOR=Inf;LSEQ=AACAAACAAACAAAAAGTCT;RSEQ=TCAGCCAGAACTGCCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:82,62:144,0:0:2,0:24.8:1:30.4:1:1:0:53.4:47:1:0:0.3 0/1:146:2:1,1:73,71:144,2:0.0137:2,2:29.5:1:28:1:1:1.02798:52:4:0.0137:0:1.5 +12 12308181 . C T 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCCAGAACTGCCATCTTC;RSEQ=AGTAATTTGCCAAAATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:80,76:156,0:0:2,0:31.7:1:31.6:1:1:0:51:38:1:0:0.2 0/1:166:23:11,12:68,73:141,23:0.1386:2,2:31.4:1:29:1:1:1.01609:48.7:46:0.1402:0:1.2 +12 12308216 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49819;SOR=Inf;LSEQ=ATGATGAACACAAAGGGAAA;RSEQ=AGGAGAGGCACCCGATACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:57,81:138,0:0:2,0:22.6:1:32.2:1:1:0:50.7:137:1:0:0.1 0/1:139:2:1,1:60,76:136,2:0.0144:2,2:20:0:30.5:1:1:1.26:30:4:0.0145:0:1.5 +12 12308391 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.24805;SOR=0;LSEQ=CAAAACTGGAAGGGTCTACA;RSEQ=TGTTACCCAGCATGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:94,96:190,2:0.0104:2,2:34.5:1:31.5:1:1:1.02:23:4:0.0105:0:1 0/0:193:0:0,0:91,102:193,0:0:2,0:29.2:1:29.8:1:1:0:56.1:95.5:1:0:0.2 +12 12308441 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21741;SOR=Inf;LSEQ=TAAACAAAAAAGTTAAGGGC;RSEQ=AGATTCTTGCCAACAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:25,66:91,0:0:2,0:22.5:1:30.3:1:1:0:57.7:29.333:1:0:0.1 0/1:80:2:1,1:22,56:78,2:0.025:2,2:15.5:1:28:1:0.49494:2.51:32.5:4:0.026:0:1.5 +12 12308503 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23684;SOR=Inf;LSEQ=AAGCACGCTAAGAGCCGAGA;RSEQ=AGCTTCCTAAAGGAAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:1,28:29,0:0:1,0:22.3:1:29:1:1:0:60:58:1:0:0 0/1:28:2:0,2:2,24:26,2:0.0714:2,0:22.5:1:33.5:1:1:0:60:4:0.0714:0:1 +12 12308741 . TA T 33 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAAGACTTCTGGACTGT;RSEQ=AAAAAAAAAAAAAGGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:21.5:1:33:0:1:0:54.5:4:1:0:0.5 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:26:0:1:0:60:2:1:0:0 +12 12767452 . G A 40 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACTGTTGCCCAGGCTGG;RSEQ=GTGCGTTGGTGTGATCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:33.7:1:25.7:1:1:0:52:2:1:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 12767856 . A G 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GGCTGGAGTGCAGTGGCACG;RSEQ=TCTCAGCTCACTGCAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:32:1:32.2:1:1:0:44.6:10:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:41:0:33:0:1:0:59:2:1:0:0 +12 12864389 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGGAAAGAGAGTGGCGG;RSEQ=TTCTGAGGGGGTCACATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:32:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 12865175 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.22475;SOR=Inf;LSEQ=GAACTCTGCCCATCTCCCCA;RSEQ=ATCCCACTGGATGAACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:10,198:208,0:0:1,0:24.4:1:32.8:1:1:0:60:103:1:0:0 0/1:188:2:1,1:13,173:186,2:0.0106:2,2:19:1:25.5:1:0.14376:12.86:60:4:0.0109:0:1 +12 12867300 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTGGGGCTGCAGAACTT;RSEQ=GGTGAGAGCGCTGCATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:29:1:1:0:60:4:1:0:1 +12 12869972 . G T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCGGGGCTTAGGCGCCGC;RSEQ=GCGAACCCGCCAACGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 12870695 . T C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00288;SOR=0.08137;LSEQ=CTTCCGAGAGGGGTTCGGGC;RSEQ=GCGTAGGGGCGCTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:50:40,10:0,1:1,50:0.9804:0,2:23.8:1:31:1:0.21569:0:60:49:1:0:1.2 1/1:60:48:37,11:8,4:12,48:0.8:2,2:25.8:1:29.9:1:0.47249:1.67:60:47:0.7966:0:1.2 +12 12870726 . G GT 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20345;SOR=0;LSEQ=GCTTTGTTTTGTTCGGTTTT;RSEQ=TTTTTTTGAGAGTGCGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:90,26:116,2:0.0169:2,2:20:0:28:1:0.40678:3.41555:60:4:0.0169:0:0 0/0:143:0:0,0:99,44:143,0:0:2,0:23.4:1:31.2:1:1:0:59.9:70.5:1:0:0.5 +12 12870750 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50469;SOR=Inf;LSEQ=TTTTGAGAGTGCGAGAGAGG;RSEQ=GGTCGTGCAGACCCGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:113,35:148,0:0:2,0:28.6:1:32.1:1:1:0:60:48.333:1:0:0.4 0/1:185:2:1,1:124,59:183,2:0.0108:2,2:39.5:1:28.5:1:0.54465:2.09254:60:4:0.011:0:1 +12 12870758 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50357;SOR=Inf;LSEQ=GTGCGAGAGAGGCGGTCGTG;RSEQ=AGACCCGGGAGAAAGATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:119,42:161,0:0:2,0:27.3:1:32.5:1:1:0:60:79.5:1:0:0.3 0/1:199:2:1,1:129,68:197,2:0.0101:2,2:26:1:29:1:1:1.89062:60:4:0.0102:0:1 +12 12871099 . T G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0126;SOR=0.6436;LSEQ=GGCGCAGGAGAGCCAGGATG;RSEQ=CAGCGGGAGCCGCCCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:99:40,59:117,173:290,99:0.2545:2,2:28.2:1:32.3:1:1:1.00:60:198:0.2565:0:1.2 0/1:411:74:31,43:133,203:336,74:0.18:2,2:22.6:1:30.2:1:0.79337:1.10:59.8:17.5:0.1754:0:1.2 +12 12871104 . G A 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19299;SOR=0.22046;LSEQ=AGGAGAGCCAGGATGTCAGC;RSEQ=GGAGCCGCCCGGCGGCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:4:3,1:142,218:360,4:0.011:2,2:27.3:1:25:1:0.30563:4.59:60:3:0.0083:0:2 0/0:410:1:1,0:170,238:408,1:0.0024:2,0:1:0:24:0:0.41809:0:60:2:0.0025:0:2 +12 12871147 . C A 45 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05086;SOR=0;LSEQ=AATTGGGGCTCCGGCTAACT;RSEQ=TGAGGACACGCATTTGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:4:2,2:118,187:305,4:0.0129:2,2:17.8:1:22.5:1:0.64328:1.58:60:3:0.0099:0:3.3 0/0:340:0:0,0:140,199:339,0:0:2,0:25.6:1:31.1:1:1:0:60:83.75:0.997:0:0.3 +12 12871188 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24951;SOR=Inf;LSEQ=ACCCAAAGACTGATCCGTCG;RSEQ=ACAGCCAGACGGGGTTAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:72,148:220,0:0:2,0:26.4:1:31.7:1:1:0:60:109:0.9909:0:0.2 0/1:240:3:2,1:93,144:237,3:0.0125:2,2:10.7:1:25.7:1:0.5641:3.08:60:6:0.0126:0:1.3 +12 12871220 . A G 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21716;SOR=Inf;LSEQ=GGGTTAGCGGAGCAATGCGC;RSEQ=GGAATAAGGAAGCGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:44,117:161,0:0:2,0:24.4:1:32:1:1:0:60:322:1:0:0.2 0/1:141:2:1,1:39,100:139,2:0.0142:2,2:34:0:30.5:1:0.48835:2.54:60:4:0.0144:0:1.5 +12 12872961 . G T 39 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63605;SOR=2.31679;LSEQ=AAAAATTTTAAAATAACAGG;RSEQ=ATTAAGGTGAGATTCAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:0,1:130,41:171,1:0.0058:2,0:20:0:11:0:0.24419:0:60:0:0:0:2 0/1:224:3:1,2:153,67:220,3:0.0134:2,2:17:1:25:1:0.22686:4.53237:60:6:0.0136:0:1 +12 12873124 . G GCAGC 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAAGCAACCTTAACATGC;RSEQ=CAGCCCTTGTTGGTTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:104,173:277,0:0:2,0:24.1:1:31.3:1:1:0:59.7:68.25:1:0:0.1 0/1:319:96:36,60:96,126:222,96:0.3009:2,2:24.4:1:30.8:1:0.38608:1.26889:59.5:192:0.3048:0.0564:0.2 +12 12873211 . A T 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02984;SOR=0;LSEQ=TTTGATCTGGCCCTGTTCTG;RSEQ=CATGCAATGAGGCATTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:6:1,5:1,65:66,6:0.0833:1,2:23.2:1:30.8:1:0.1608:11.96:60:12:0.0833:0:1.7 0/0:63:0:0,0:4,59:63,0:0:2,0:23:1:29.3:1:1:0:60:62:1:0:0.4 +12 12873233 . G C 190 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGCAATGAGGCATTTGTAG;RSEQ=ATTTAGTAATATTGCTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:51:0,51:0,0:0,51:1:0,1:25.2:1:33.5:1:1:0:60:102:1:0:1.1 0/1:40:19:0,19:0,21:21,19:0.475:1,1:24.4:1:32.1:1:1:0:60:38:0.475:0:1.1 +12 12873653 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTATCCCTGGCCTCTCACA;RSEQ=TAGATGCCAGCAGTATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:44:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 12874136 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23032;SOR=Inf;LSEQ=CTAAAATTTTAGGCACTCTT;RSEQ=AATGATCTGCCTCTAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:96,40:136,0:0:2,0:20:1:29.2:1:1:0:59.8:272:1:0:0.1 0/1:126:2:1,1:92,32:124,2:0.0159:2,2:13.5:1:28.5:1:0.45676:2.84645:60:4:0.0161:0:1 +12 12874159 . TG T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49904;SOR=0;LSEQ=TGATCTGCCTCTAAAAGCGT;RSEQ=GATGTAGCATTATGCAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:124,72:196,2:0.0101:2,2:26:1:31.5:1:1:1.71719:60:4:0.0102:0:1 0/0:188:0:0,0:119,68:187,0:0:2,0:24:1:30.7:1:1:0:60:92.5:0.9946:0:0.1 +12 12874329 . G A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24802;SOR=Inf;LSEQ=CTTGCTTTGATTTACAGCAA;RSEQ=TAGATAAATATTTGACTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:54,120:174,0:0:2,0:25:1:32.5:1:1:0:60:57:1:0:0.1 0/1:179:3:2,1:56,120:176,3:0.0168:2,2:21.7:1:23:1:0.24562:4.25:60:2:0.0112:0:3.3 +12 13685698 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50324;SOR=Inf;LSEQ=GAAAAATTGTGTACTTGTTG;RSEQ=TTTCATAGGGAGAATGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:123,42:165,0:0:2,0:22.1:1:29.6:1:1:0:60:22.571:1:0:0.1 0/1:200:2:1,1:146,52:198,2:0.01:2,2:23:1:29.5:1:0.46075:2.79059:60:4:0.0102:0:1 +12 13685700 . T C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20553;SOR=0;LSEQ=AAAATTGTGTACTTGTTGAT;RSEQ=TCATAGGGAGAATGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:129,42:171,2:0.0116:2,2:16:1:27.5:1:0.43642:3.04717:60:4:0.0117:0:1 0/0:208:0:0,0:150,58:208,0:0:2,0:22.1:1:29.6:1:1:0:60:68.333:1:0:0.1 +12 13685707 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18012;SOR=0;LSEQ=TGTACTTGTTGATTTCATAG;RSEQ=GAGAATGGGGAGGGACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:137,51:188,2:0.0105:2,2:14:0:32:0:0.47352:2.67001:60:4:0.0108:0:1.5 0/0:257:0:0,0:173,84:257,0:0:2,0:21.8:1:29.8:1:1:0:60:35.714:1:0:0.1 +12 13685730 . C T 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3077;SOR=0.22215;LSEQ=GAATGGGGAGGGACACAGTG;RSEQ=AAGCAGAGTGGGGAGATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:3:1,2:160,86:246,3:0.012:2,2:15.3:1:27.3:1:0.28561:3.70019:60:6:0.0123:0:1 0/0:371:1:0,1:223,147:370,1:0.0027:2,0:1:0:26:0:0.39892:0:60:2:0.0027:0:1 +12 13685742 . G A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0142;SOR=Inf;LSEQ=ACACAGTGCAAGCAGAGTGG;RSEQ=GAGATCAAATTGTAGAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:167,105:272,0:0:2,0:28.3:1:31:1:1:0:59.9:53.4:1:0:0.4 0/1:424:9:5,4:242,173:415,9:0.0212:2,2:24.2:1:29.3:1:1:1.11877:60:18:0.0214:0:1 +12 13685816 . T C 247 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATTTCCTCAGGCATGTCGG;RSEQ=GCAATAAGATGTCAGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:265:265:111,154:0,0:0,265:1:0,2:25.7:1:30.7:1:1:0:60:87.333:1:0:1.1 1/0:364:255:111,144:53,55:108,255:0.7005:2,2:22.7:1:29.6:1:0.35716:1.24934:60:62.75:0.6992:0:1.1 +12 13685894 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51644;SOR=Inf;LSEQ=GTTTTGTGGGTTCATGCAAT;RSEQ=CATTTCTTGCTGGTAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:35,91:126,0:0:2,0:25.4:1:31.9:1:1:0:60:252:1:0:0.4 0/1:185:2:1,1:52,130:182,2:0.0108:2,2:41:0:31:0:0.49424:2.49:60:4:0.011:0:1.5 +12 13720021 . A T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13355;SOR=0;LSEQ=ACCCATAAAGCAATGTCGGA;RSEQ=CTGCCAATAGAAAAGGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:42,2:44,2:0.0435:1,2:20:0:32.5:1:0.12754:17.3476:60:4:0.0435:0:1.5 0/0:79:0:0,0:66,13:79,0:0:2,0:21.8:1:29.4:1:1:0:60:38.5:1:0:0.3 +12 13720043 . G A 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TGCCAATAGAAAAGGTGTTC;RSEQ=CAGATGAAGGTGATGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:63,12:75,0:0:2,0:21.4:1:30.1:1:1:0:60:150:1:0:0.1 0/1:123:23:17,6:64,35:99,23:0.187:2,2:26.6:1:29.5:1:0.46929:1.54:60:46:0.1917:0:1.2 +12 13720074 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30245;SOR=Inf;LSEQ=TGATGAGGCTGAGAGCCATG;RSEQ=CCGCCCCCAACATGTAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:84,48:132,0:0:2,0:26.6:1:31.4:1:1:0:60:65:1:0:0.1 0/1:211:4:2,2:120,87:207,4:0.019:2,2:21.3:1:28.5:1:1:1.37715:60:8:0.019:0:1 +12 13720095 . A G 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29544;SOR=Inf;LSEQ=CCGCCCCCAACATGTAGAAG;RSEQ=CCCCTGCCATGTTGTCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:94,66:160,0:0:2,0:29.4:1:29.7:1:1:0:60:79:1:0:0.1 0/1:267:3:1,2:146,117:263,3:0.0112:2,2:17.7:1:24.7:1:0.58828:2.48732:60:2:0.0075:0:1 +12 13720163 . A G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17805;SOR=0;LSEQ=TTCTCATTGTGACAAATGCC;RSEQ=GTGAGCCAGAGAGCTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:33,75:108,2:0.0182:2,2:21:1:28.5:1:0.5246:2.25:60:4:0.0185:0:1 0/0:150:0:0,0:54,96:150,0:0:2,0:24.6:1:29.5:1:1:0:60:149:1:0:0.1 +12 13720168 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50484;SOR=Inf;LSEQ=ATTGTGACAAATGCCAGTGA;RSEQ=CCAGAGAGCTTCCAGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:32,73:105,0:0:2,0:22.7:1:32.2:1:1:0:60:104:1:0:0.1 0/1:133:2:1,1:44,87:131,2:0.015:2,2:32:1:28:1:1:1.97:60:4:0.0153:0:1 +12 13720272 . A G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=AGAGAAAAGGGAGAAAGAGG;RSEQ=GTATTGAGCAAGAAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,0:0,13:0.9286:0,1:24:1:32.2:1:1:0:60:26:1:0:1.2 1/1:14:14:0,14:0,0:0,14:1:0,1:16.8:1:30.9:1:1:0:60:28:1:0:1.1 +12 13761586 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13759;SOR=0;LSEQ=CCACATATTCCTCTTGGATC;RSEQ=TGAAGGCAGCTAAGTTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:66,41:107,2:0.0183:2,2:35.5:1:30.5:1:1:1.60242:60:4:0.0185:0:1 0/0:184:0:0,0:113,71:184,0:0:2,0:25.5:1:29.7:1:1:0:59.8:183:1:0:0.1 +12 13764741 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.52274;SOR=Inf;LSEQ=GCCACGGCTGAGACGATGAG;RSEQ=AGCATCACAAACATCATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:28,37:65,0:0:2,0:25.8:1:32.5:1:1:0:60:64:1:0:0.5 0/1:103:2:1,1:51,50:101,2:0.0194:2,2:40:0:30:0:1:1.01981:60:4:0.0194:0:2.5 +12 13764774 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.85579;SOR=1.10444;LSEQ=ATCATCACCCATACGTCAGC;RSEQ=CTGAATGGCTCTGAGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:19:7,12:13,21:34,19:0.3519:2,2:29.5:1:29.4:1:1:1.06006:60:38:0.3654:0:1.2 0/1:80:30:12,18:22,28:50,30:0.375:2,2:17.1:1:28.7:1:0.81698:1.17616:60:29:0.3671:0:1.3 +12 13764791 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=AGCGCTGAATGGCTCTGAGG;RSEQ=AGGGAAAAAAGCAGTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:12,22:34,2:0.0556:2,2:27.5:1:28:1:1:1.80:60:4:0.0588:0:2 0/0:55:0:0,0:21,34:55,0:0:2,0:21.8:1:29.4:1:1:0:60:110:1:0:0.4 +12 13764855 . T G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48538;SOR=Inf;LSEQ=ATTCGAATTAATTCACATAT;RSEQ=CATTTCATATTTTAGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:28.1:1:29.6:1:1:0:60:16:1:0:0.5 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:29.5:1:30:1:1:0:60:4:0.1818:0:1 +12 13767996 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21739;SOR=0;LSEQ=TGCTCCTTTTTTCCTTATTT;RSEQ=ACTTCCCCATCCATACGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:9,3:0.25:0,0:31:1:31.7:1:1:0:60:6:0.25:0:1 0/0:11:0:0,0:11,0:11,0:0:0,0:21.2:1:30.5:1:1:0:60:22:1:0:0.2 +12 13768136 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12303;SOR=0;LSEQ=AAGGGCACAGAGAAGTCGAC;RSEQ=ACCTCCGATCGTTCCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:35,44:79,2:0.0247:2,2:44.5:1:28.5:1:1:1.25:60:4:0.0253:0:1 0/0:149:0:0,0:69,80:149,0:0:2,0:29:1:30.5:1:1:0:60:73.5:1:0:0.2 +12 13768146 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11692;SOR=0;LSEQ=AGAAGTCGACCACCTCCGAT;RSEQ=GTTCCTCATTGATGGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:32,46:78,2:0.025:2,2:19:1:29.5:1:1:1.43:60:4:0.0256:0:1 0/0:153:0:0,0:66,86:152,0:0:2,0:28.5:1:29.5:1:1:0:60:75:0.9934:0:0.1 +12 13768161 . G C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53761;SOR=Inf;LSEQ=CCGATCGTTCCTCATTGATG;RSEQ=TGAGTGAGCCCACTGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:29,50:79,0:0:2,0:27.2:1:32.1:1:1:0:60:78:1:0:0.2 0/1:141:2:1,1:49,90:139,2:0.0142:2,2:31:1:26:1:1:1.83:60:4:0.0146:0:1.5 +12 13768354 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATGCATAAAGTGAGCA;RSEQ=GTTTTAAACTTATATTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:31.5:1:27:1:1:0:60:4:1:0:1.5 +12 16089876 . T C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCCTGTCCTGTCTTGTCC;RSEQ=GTCCCGTCCTGTCCTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:16,12:0,0:0,28:1:0,2:6:1:30.8:1:1:0:55.4:56:1:0:1.4 1/1:11:11:5,6:0,0:0,11:1:0,2:5:0:26.5:1:1:0:53:4.5:1:0:1.3 +12 16089886 . T C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGTCTTGTCCTGTCCCGTCC;RSEQ=GTCCTGCCCTGCCCTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:16,17:0,0:0,33:1:0,2:14.5:1:30.2:1:1:0:56.1:66:1:0:1.4 1/1:11:11:5,6:0,0:0,11:1:0,2:15:0:26.7:1:1:0:53:10:1:0:1.3 +12 16394674 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CTGAAAGGCTCCCAGCACAA;RSEQ=TTGGAAGTTTCTGTTACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:15,0:0:1,0:28.9:1:32.3:1:1:0:60:30:1:0:0.1 0/1:21:2:1,1:19,0:19,2:0.0952:1,2:8:1:28.5:1:0.09524:0:60:4:0.1053:0:1.5 +12 16394763 . GTTAAC G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08242;LSEQ=AATCACAGACACAGAAATAT;RSEQ=TTAATAATGTGGCAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:108:95:68,27:10,3:13,95:0.8796:2,2:28.5:1:32.2:1:1:1.32029:59.9:190:0.8796:0.0833:0.3 0/1:94:35:25,10:40,19:59,35:0.3723:2,2:25.6:1:31.4:1:0.81882:1.19:60:70:0.3763:0.0319:0.5 +12 16394823 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=TGAAGCAATATTAATATATT;RSEQ=CCTAATCTTAGAAAAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:93,83:176,0:0:2,0:24.9:1:32.4:1:1:0:59.9:352:1:0:1.3 0/1:182:2:1,1:104,76:180,2:0.011:2,2:26:0:32:1:1:1.36601:60:4:0.011:0:2.5 +12 16394848 . G T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05685;LSEQ=ATCTTAGAAAAGGCTGCAGT;RSEQ=TCTTGAAAGCTTGAAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:190:166:79,87:9,15:24,166:0.8737:2,2:25.9:1:30.7:1:0.38883:1.51:60:165:0.873:0:2.3 0/1:214:60:28,32:77,77:154,60:0.2804:2,2:24.6:1:29.5:1:0.76102:1.14214:60:120:0.283:0:2.4 +12 16394883 . G C 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05986;LSEQ=AATCATTTCTGCCTCTGCCT;RSEQ=AAGTTCTGAAATCATCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:153:133:52,81:6,13:19,133:0.8693:2,2:29.6:1:32.1:1:0.61932:1.39:60:43.333:0.8667:0:2.8 0/1:177:50:18,32:52,75:127,50:0.2825:2,2:28.1:1:31.4:1:0.61026:1.23115:59.2:100:0.2825:0:2.7 +12 16394899 . C T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05462;LSEQ=GCCTGAAGTTCTGAAATCAT;RSEQ=GCCCTGTAAAATTTTAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:141:123:44,79:5,13:18,123:0.8723:2,2:24.1:1:30.6:1:0.60297:1.44:60:60.5:0.8705:0:2.8 0/1:156:42:15,27:40,74:114,42:0.2692:2,2:24.5:1:29.4:1:1:1.03:59:84:0.2692:0:2.8 +12 16753352 . C T 41 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGGCAGCGCCATAACCAA;RSEQ=TGCCTGAGTGTGCAGGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:14.7:1:26:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 16753737 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50432;SOR=0;LSEQ=TAGAAGATACCGGTCCTTGA;RSEQ=CTTTCGGTTGCAGCCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:38,145:183,2:0.0108:2,2:25.5:1:27:1:0.37808:3.78:60:4:0.0112:0:1 0/0:149:0:0,0:41,107:148,0:0:2,0:22:1:28.2:1:1:0:59.9:48.333:1:0:0.1 +12 16753747 . G A 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGGTCCTTGATCTTTCGGTT;RSEQ=CAGCCAGCACAACCTTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:25:7,18:17,112:129,25:0.1623:2,2:22.4:1:29.2:1:0.07376:2.54:60:50:0.1689:0:1 0/0:112:0:0,0:22,89:111,0:0:2,0:23.1:1:31.6:1:1:0:60:222:1:0:0.1 +12 16753965 . A G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGAAACAAAAAGTCTCA;RSEQ=ACTTTATCAAGTGCTTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:15.7:1:32.7:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 17903151 . C A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0247;SOR=0;LSEQ=ATTTAACAGCTTACTATGTG;RSEQ=CACATTTTCTGAGAGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:34:34,0:0,0:0,34:1:0,1:23.1:1:30.6:1:1:0:60:68:1:0:1.1 1/1:15:12:12,0:3,0:3,12:0.8:0,0:19:1:28.5:1:1:0:60:24:0.8:0:1.6 +12 17903230 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49793;SOR=Inf;LSEQ=CAATAGAAACGATTCGTATC;RSEQ=CACTTTGAAAATGAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:88,30:118,0:0:2,0:22.8:1:30.3:1:1:0:60:117:1:0:0.2 0/1:120:2:1,1:94,24:118,2:0.0167:2,2:35:1:32:1:0.37465:3.85789:60:4:0.0168:0:1 +12 17903235 . T A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49807;SOR=0;LSEQ=GAAACGATTCGTATCACACT;RSEQ=TGAAAATGAAAACAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:97,31:128,2:0.0154:2,2:29:0:31.5:1:0.43315:3.0953:60:4:0.0161:0:1 0/0:129:0:0,0:99,30:129,0:0:2,0:22.2:1:30.2:1:1:0:60:128:1:0:0.1 +12 17903260 . C T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09258;SOR=0;LSEQ=AATGAAAACAAACAAAGACA;RSEQ=TGAGAGGTTAAATAACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:1,2:127,61:188,3:0.0157:2,2:14.3:1:23.3:1:0.25342:4.13006:60:2:0.0107:0:3 0/0:230:0:0,0:156,74:230,0:0:2,0:24.5:1:31.3:1:1:0:60:114:1:0:0.3 +12 17903344 . G A 243 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02777;LSEQ=TAAAATGTGTGAATTAAAAG;RSEQ=AAAGATACAAGCATTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:314:311:153,158:1,1:2,311:0.9904:2,2:25.8:1:30.4:1:1:1.03258:60:76.75:0.9935:0:1.2 1/0:449:333:163,170:56,58:114,333:0.7416:2,2:24.6:1:29.1:1:1:1.00697:59.9:82.25:0.7393:0:1.3 +12 17903404 . T A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25303;SOR=Inf;LSEQ=TGTCAGATGATTCTCTGCAA;RSEQ=GTTTGACCATAGGTACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:80,159:239,0:0:2,0:26.5:1:30.3:1:1:0:60:58.75:1:0:1.3 0/1:279:3:2,1:95,181:276,3:0.0108:2,2:10.7:1:27:1:0.27783:3.79:60:6:0.0108:0:1.3 +12 17903428 . T G 242 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGACCATAGGTACAAAACTA;RSEQ=TGGATAATCTTATGCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:170:170:38,132:0,0:0,170:1:0,2:24.9:1:32.7:1:1:0:60:169:1:0:1.3 1/0:176:135:41,94:12,28:40,135:0.767:2,2:22.5:1:31.2:1:1:1.02:60:134:0.7657:0:1.5 +12 17903475 . C T 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATTGAAATGAGGAAATTTT;RSEQ=GAAACCTTTCTGCTATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:3,66:69,0:0:1,0:23.1:1:30.2:1:1:0:60:138:1:0:0.8 1/0:55:30:2,28:1,24:25,30:0.5455:1,2:18.1:1:29.3:1:1:1.70:60:60:0.5455:0:1.7 +12 18192630 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5254;SOR=0;LSEQ=AGGCTTCTGAAAGCAGACAA;RSEQ=GCCTTTCAAATTCTTATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:12,9:21,2:0.087:2,2:8:0:32.5:1:1:1.31655:28:4:0.0909:0:2 0/0:13:0:0,0:10,3:13,0:0:2,0:22.8:1:30.8:1:1:0:40.8:26:1:0:0 +12 18192679 . T C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.51417;SOR=0;LSEQ=GAGTTGGGCAACATGGCTTC;RSEQ=CCCCTTCCTAGGTCCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:44:0:31.5:1:1:1.19087:28:4:0.0833:0:2 0/0:15:0:0,0:6,9:15,0:0:2,0:30.4:1:28.8:1:1:0:44.4:30:1:0:0 +12 18397905 . C G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGTGGCTCCAAGCAAGTTCT;RSEQ=TGTTCCCTCTTAGTCTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:30:1:33.3:1:1:0:60:6:0.6:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:10:0:33:0:1:0:60:2:1:0:0 +12 18398027 . A T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74388;SOR=1.35408;LSEQ=ACTGAAAAATACTTTAAGAG;RSEQ=TTACGTGGGCATCTGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:8,0:20,0:20,8:0.2857:1,0:33.3:1:29.3:1:1:0:60:16:0.2857:0:2 0/1:17:6:6,0:11,0:11,6:0.3529:0,0:17.2:1:30.5:1:1:0:60:12:0.375:0:1.8 +12 18398063 . A G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTTAGAAGCCTCAATTG;RSEQ=GGAATTATTGTGAGTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:43,1:0,0:0,44:1:0,1:24:1:31.5:1:1:0:60:43:1:0:1.3 1/1:36:36:36,0:0,0:0,36:1:0,1:26.9:1:31.2:1:1:0:60:72:1:0:1.2 +12 18398236 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32249;SOR=1.17034;LSEQ=CCAATTTTAACTCAGTCAGC;RSEQ=CTGCATTTTACACATTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:114:45,69:136,189:325,114:0.2597:2,2:25.6:1:29.6:1:0.74022:1.10309:60:56:0.2593:0:1.1 0/1:426:124:57,67:132,170:302,124:0.2911:2,2:23.1:1:28.8:1:0.66949:1.10:60:61:0.2891:0:1.1 +12 18398330 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21136;SOR=Inf;LSEQ=TTTACTTACATCTCAATATT;RSEQ=TATCATAAAATTGTTAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:19,85:104,0:0:2,0:24.8:1:30.9:1:1:0:60:208:1:0:0 0/1:89:2:1,1:11,75:86,2:0.0225:2,2:11:0:33:0:0.25549:6.57:60:4:0.0227:0:1.5 +12 18398431 . G GA 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.30451;SOR=3.41678;LSEQ=CCCAAGAGTGATTTGGGAGG;RSEQ=AAAAAAATCTACTGTATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:0,5:0,18:18,5:0.2174:1,0:34.2:1:33:0:1:0:60:10:0.2174:0:0 1/0:6:3:0,3:0,3:3,3:0.5:0,0:33.7:1:32:1:1:0:60:6:0.5:0:0 +12 18406957 . AG A 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=2e-05;SOR=4.13673;LSEQ=AACCTGAGTAAGAAAAAAAA;RSEQ=ATGCATCCTAAGAGCCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:16:12,4:75,20:95,16:0.1441:2,2:22.4:1:30.9:1:0.74609:1.24739:60:32:0.1509:0.027:0.3 0/1:97:40:31,9:45,12:57,40:0.4124:2,2:25.2:1:29.7:1:1:1.08775:60:80:0.4124:0.1237:0.6 +12 18406979 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58226;SOR=2.60501;LSEQ=ATGCATCCTAAGAGCCTAGT;RSEQ=CTTAAAGTGGAGAAACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:144,47:191,1:0.0052:2,0:13:0:27:0:0.25:0:60:2:0.0053:0:1 0/1:149:2:1,1:116,31:147,2:0.0134:2,2:36:1:27.5:1:0.38455:3.69909:60:4:0.0135:0:1.5 +12 18407043 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.3873;LSEQ=TTGAGAATAGAAGAATATAT;RSEQ=TTTTTCTTATTTTATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:76:50,26:186,126:312,76:0.1954:2,2:25.3:1:28.9:1:0.3603:1.30:60:75:0.1943:0:1.8 0/1:354:130:79,51:144,78:222,130:0.3672:2,2:19.7:1:28:1:0.49192:1.19121:60:64:0.3647:0:1.9 +12 18407074 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.08093;LSEQ=TTTATTTTTAAAGAGTTAGA;RSEQ=GAATTTAAAAACCAACCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:101:60,41:217,184:401,101:0.2012:2,2:25:1:32.5:1:0.37135:1.24:60:202:0.2028:0:1.6 0/1:529:182:99,83:193,154:347,182:0.344:2,2:27.3:1:31:1:0.85401:1.05057:60:181:0.3441:0:1.7 +12 18434981 . G T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10669;SOR=0;LSEQ=TTATCAAGGAGATATTTGGA;RSEQ=CAGAGTCAACCCTCTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:167,78:245,3:0.012:2,2:10.7:1:23.3:1:0.24409:4.25444:60:2:0.0081:0:2 0/0:276:0:0,0:182,94:276,0:0:2,0:24.4:1:31:1:1:0:60:54.2:1:0:0.1 +12 18435398 . GCCC G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=6e-05;SOR=1.68943;LSEQ=TAAAGAATGCTCCTGGGGAA;RSEQ=CATAGGAAAACATCATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:645:137:67,70:252,252:504,137:0.2124:2,2:25:1:32.7:1:0.84754:1.04472:59.8:274:0.2164:0.0388:0.6 0/1:626:196:83,113:213,216:429,196:0.3131:2,2:25.6:1:31.2:1:0.10096:1.34189:60:195:0.3166:0.0495:0.5 +12 18435452 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.8429;LSEQ=CAGATTCAGTATTTTAGCTC;RSEQ=ATCATTCACAAGTTTGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:636:140:66,74:227,269:496,140:0.2201:2,2:27:1:29.7:1:0.77434:1.06:59.8:45.667:0.2185:0:1.1 0/1:558:191:87,104:171,194:365,191:0.3423:2,2:25.5:1:28.8:1:0.78875:1.05361:60:382:0.3441:0:1.1 +12 18439648 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05875;SOR=Inf;LSEQ=TTTTCTATGTGTAAATATTA;RSEQ=TTCAATTTTTAAAAAATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:44,0:0:1,0:24.9:1:32.8:1:1:0:60:88:1:0:0 0/1:29:3:3,0:25,1:26,3:0.1034:1,0:30.7:1:30.3:1:1:0:60:6:0.1034:0:1 +12 18443729 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59323;SOR=2.40689;LSEQ=AATTACATTGTGGGCAATAT;RSEQ=TTTTAAACTGTGTCTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:162,25:187,1:0.0053:2,0:16:0:32:0:0.1383:0:60:2:0.0054:0:1 0/1:157:2:1,1:124,31:155,2:0.0127:2,2:26.5:1:28:1:0.36714:3.95285:60:4:0.0131:0:1 +12 18443809 . C A 120 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=20.04176;LSEQ=AATCAGAGAAAGATATCATG;RSEQ=AGCTGATGTTAATTTCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:1:1,0:371,269:640,1:0.0016:2,0:1:0:29:0:1:0:60:2:0.0016:0:1 0/1:592:18:12,6:318,254:572,18:0.0304:2,2:24.2:1:28.9:1:0.47117:1.60:60:36:0.0308:0:1.1 +12 18443955 . C A 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTATGCCATGTGGTAAGCAA;RSEQ=CTTGCAAATAAGTCTACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:125,281:406,0:0:2,0:26.1:1:31.4:1:1:0:60:66.667:1:0:0.1 0/1:346:15:5,10:121,209:330,15:0.0434:2,2:24.7:1:28.7:1:1:1.15744:60:30:0.0439:0:1.1 +12 18444144 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTTTCTTCAAGAAGTAT;RSEQ=TTCACATAGCTCACCCGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:0,14:14,3:0.1765:1,0:29.3:1:29:1:1:0:60:6:0.1765:0:1.7 0/0:2:0:0,0:0,2:2,0:0:0,0:20:1:33:0:1:0:60:4:1:0:0 +12 18444163 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCACATAGCTCACCCGA;RSEQ=AATATTTTATCTTCCTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:8,2:0.2:0,0:44.5:1:33:0:1:0:60:4:0.2:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:29:0:1:0:60:2:1:0:0 +12 18446881 . C T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCAGAAATTCTGCATTTTTG;RSEQ=ACAAATGACCAGCTACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:0:0,0:367,310:677,0:0:2,0:27.1:1:32:1:1:0:60:44.133:1:0:0.1 0/1:623:21:11,10:323,278:601,21:0.0337:2,2:19.5:1:26.5:1:1:1.05618:60:42:0.0342:0:1 +12 18446924 . T G 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00571;SOR=Inf;LSEQ=AAGATCATATTCTAAGTGTA;RSEQ=GTGGCTCTGAAGAATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:657:0:0,0:267,388:655,0:0:2,0:25.5:1:30.6:1:1:0:60:130:0.9985:0:0.1 0/1:605:7:3,4:254,344:598,7:0.0116:2,2:20.1:1:28.6:1:1:1.02:60:6:0.01:0:1.1 +12 18466738 . TCACA T 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=12.000;MSILEN=2;SSF=0.03064;SOR=3.19153;LSEQ=AATATGTAATGCATATATAT;RSEQ=CACACACACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:12:12,0:39,0:39,12:0.2069:1,0:24.3:1:33.7:1:1:0:59.6:24:0.2105:0.0172:0.1 0/1:24:11:11,0:11,0:11,11:0.4583:0,0:25.1:1:31:1:1:0:57.6:22:0.4583:0.0833:0.7 +12 18467005 . C T 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTATCTCGAAAGGTAAGA;RSEQ=TTTCTTAGCATTGGTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:769:0:0,0:292,477:769,0:0:2,0:25.5:1:32.6:1:1:0:60:75.9:1:0:0.1 0/1:505:40:14,26:174,291:465,40:0.0792:2,2:25.6:1:30:1:0.86522:1.11025:60:80:0.0795:0:1.1 +12 18467122 . T C 200 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AATACATGTTTATTTAAATA;RSEQ=ATTCATTGAAACATGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:67:1,66:0,36:36,67:0.6505:1,1:23.4:1:33:1:1:0:59.4:134:0.6505:0:1 0/0:51:0:0,0:0,51:51,0:0:1,0:20.8:1:28.5:1:1:0:60:102:1:0:0.2 +12 18473690 . C G 34 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03968;SOR=Inf;LSEQ=TCTTTCAGGTTTATTCTCAA;RSEQ=AAAAGCCAAGCTTTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:22,0:0:1,0:27.8:1:32.3:1:1:0:60:44:1:0:0 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:38.5:1:34:0:1:0:60:4:0.3333:0:1 +12 18473729 . T C 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTACTTTTGAAAAGGCTTA;RSEQ=ATAGTTAAGGAGAGCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:2,0:46,0:46,2:0.0417:1,0:26:0:34:0:1:0:60:4:0.0417:0:1 0/0:13:0:0,0:13,0:13,0:0:1,0:23.2:1:31.7:1:1:0:60:26:1:0:0.2 +12 18473881 . T G 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03952;LSEQ=ACTCAATAAATATTAATATA;RSEQ=TCTGCTGTCTACAGCATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:659:444:289,155:136,79:215,444:0.6737:2,2:24.4:1:32.7:1:0.66471:1.08:60:110:0.6728:0:1.1 0/1:452:34:22,12:264,154:418,34:0.0752:2,2:25:1:31.1:1:1:1.07:60:68:0.0754:0:1.1 +12 18473928 . T C 218 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACAGTCAGTTTTATCTGAA;RSEQ=CAACTTCTAGAATTTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1011:0:0,0:512,499:1011,0:0:2,0:27.1:1:30.3:1:1:0:60:37.885:1:0:0.5 0/1:705:145:69,76:279,281:560,145:0.2057:2,2:28.8:1:30.5:1:0.64242:1.09347:60:47.333:0.2023:0:1.1 +12 18477895 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10751;SOR=Inf;LSEQ=ATGGGCAAAACAATTTGTGA;RSEQ=AAATGTTTGTGCTAAAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:0:0,0:280,90:370,0:0:2,0:24.5:1:30.8:1:1:0:59.9:740:1:0:0.1 0/1:181:2:1,1:137,42:179,2:0.011:2,2:26:1:30:1:0.41971:3.23548:60:4:0.011:0:1 +12 18477900 . G T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11379;SOR=5.95238;LSEQ=CAAAACAATTTGTGATAAAT;RSEQ=TTTGTGCTAAAGGTAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:1:1,0:304,102:406,1:0.0025:2,0:20:0:32:0:1:0:60:2:0.0025:0:1 0/1:207:3:3,0:150,54:204,3:0.0145:2,0:12.7:1:26.3:1:0.56902:0:60:6:0.0145:0:1 +12 18478126 . A T 104 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02117;SOR=2.78025;LSEQ=GCAAATTTTGAAGATGACAA;RSEQ=AATGAATAAAACAGAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:10:0,10:9,212:221,10:0.0433:1,0:23:1:29.4:1:1:0:60:20:0.0442:0:1 0/1:116:13:0,13:8,95:103,13:0.1121:2,1:25.4:1:28.2:1:0.59456:0:60:26:0.1121:0:1.1 +12 18496149 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53383;SOR=0;LSEQ=ATGATGCCAAGAAATATTTT;RSEQ=TTGTTTTACCATGACAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:132,37:169,2:0.0117:2,2:11:1:29:1:0.39608:3.5334:60:4:0.0118:0:1 0/0:99:0:0,0:82,17:99,0:0:2,0:23.5:1:31.4:1:1:0:60:98:1:0:0.1 +12 18496249 . A AT 69 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.29544;SOR=2.26968;LSEQ=AATAACAAGTATAATTTTAC;RSEQ=TTTTTTTTCAGAATTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:3:1,2:284,268:552,3:0.0054:2,2:35:1:31:1:0.61441:2.11662:60:6:0.0055:0:0 0/1:410:5:3,2:207,198:405,5:0.0122:2,2:34.4:1:29.8:1:1:1.43:60:10:0.0124:0:0.4 +12 18499636 . C T 226 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=197.42577;LSEQ=TACCAGCTAATCAATGTCTA;RSEQ=TGTAACAGCTTTTATGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1767:2:1,1:875,887:1762,2:0.0011:2,2:12.5:1:27.5:1:1:1.01:60:4:0.0011:0:1 0/1:1131:207:110,97:454,465:919,207:0.183:2,2:28:1:29.4:1:0.3561:1.16:60:68:0.1821:0:1.1 +12 18499777 . C G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40258;SOR=0;LSEQ=ACCTGGGTGCACAGGTGAGT;RSEQ=GTGGTGAGTTTTTCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:463:463:110,353:0,0:0,463:1:0,2:26.2:1:31.6:1:1:0:59.9:76.167:1:0:1.1 1/1:312:311:98,213:0,0:0,311:0.9968:0,2:24.3:1:30.5:1:1:0:59.7:50.833:0.9967:0:1.1 +12 18514467 . G GA 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCTGTCTGGCTTCCCACT;RSEQ=AAAAAAAAAAACCTTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:31:1:28:1:1:0:60:4:0.6667:0:0 +12 18515791 . AT A 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.15416;SOR=3.51397;LSEQ=AATATTCCAGACAAGAAATT;RSEQ=TTTTTTTCTTGGTCAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:2:1,1:220,378:598,2:0.0033:2,2:26.5:1:31:1:1:1.72:60:4:0.0034:0:0 0/1:516:6:4,2:200,310:510,6:0.0116:2,2:36.7:1:32.2:1:0.21942:3.09:60:12:0.0117:0:0.2 +12 18515907 . T TA 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01345;SOR=Inf;LSEQ=TAAAAGCAAGGGATGTAATT;RSEQ=AAAAAAAATATGCTGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:1,81:82,0:0:1,0:25.9:1:28.8:1:1:0:60:164:1:0:0.1 0/1:62:5:0,5:2,55:57,5:0.0806:1,0:31.8:1:27.2:1:1:0:60:4:0.0656:0:0 +12 18524061 . T G 148 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATTATAAGAACATTTTCAT;RSEQ=AAAATATCAGTACAATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:24:17,7:262,85:347,24:0.0647:2,2:26.5:1:32.4:1:0.62703:1.26836:60:48:0.0652:0:1 0/0:303:0:0,0:217,86:303,0:0:2,0:24.1:1:29.1:1:1:0:60:74.75:1:0:0.1 +12 18534672 . CTG C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.88078;SOR=0.92946;LSEQ=CCTCATGAAGTGACTCCTGT;RSEQ=TGTGTGTGTGTGTTGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:446:26:20,6:326,92:418,26:0.0583:2,2:20.9:1:32.1:1:0.81247:1.0629:60:52:0.0596:0.0135:0 0/1:386:21:16,5:272,90:362,21:0.0544:2,2:20.7:1:31.1:1:1:1.06:60:42:0.0563:0.013:0 +12 18534866 . C A 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGCAAGTATTGGTTGATA;RSEQ=GTAGTTTGTTGTCAATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:29,215:244,0:0:2,0:24:1:30.2:1:1:0:60:47.8:0.9917:0:0.1 0/1:242:56:10,46:44,141:185,56:0.2314:2,2:21.8:1:30:1:0.46448:1.43341:60:55:0.2282:0:1 +12 18544512 . G A 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02778;SOR=Inf;LSEQ=CTCAACCTTCCTTCCAGGAG;RSEQ=TAGAAAGTTGTTTTAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:24.9:1:31.3:1:1:0:58.6:14:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:30:0:1:0:60:4:1:0:1.5 +12 18552446 . A C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08812;SOR=2.28085;LSEQ=TGATGAAATAACCTATGAAA;RSEQ=TATCCGAAGAAGGTAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:10:9,1:70,1:71,10:0.1235:1,2:17.2:1:32:1:0.23302:7.43114:60:20:0.1266:0:1 0/1:45:11:11,0:33,1:34,11:0.2444:1,0:21.1:1:31.5:1:1:0:60:22:0.2444:0:1 +12 18552467 . T TA 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0852;SOR=2.18879;LSEQ=TATCCGAAGAAGGTAAAAGA;RSEQ=GTTTTTGAAAGTAAACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:12:11,1:94,1:95,12:0.1121:1,2:24.2:1:29:1:0.21266:8.2242:60:24:0.1132:0.028:0.7 0/1:69:15:14,1:53,1:54,15:0.2174:1,1:20.5:1:27.6:1:0.39003:3.69192:60:30:0.2174:0.0435:0.7 +12 18573787 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49971;SOR=Inf;LSEQ=TTTTACCTTATGCACTGGGG;RSEQ=TAGAATTCATTCTCTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:101,5:106,0:0:1,0:25.6:1:31.2:1:1:0:60:34.333:1:0:0.1 0/1:120:2:1,1:107,11:118,2:0.0167:2,2:15.5:1:28:1:0.19076:9.35658:60:4:0.0174:0:1 +12 18573810 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5081;SOR=Inf;LSEQ=GAATTCATTCTCTGTTCTCC;RSEQ=TGACATGTCTTATGCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:131,19:150,0:0:2,0:23.5:1:31.2:1:1:0:60:49:1:0:0.1 0/1:198:2:1,1:155,41:196,2:0.0101:2,2:9:1:27.5:1:0.3801:3.74735:60:4:0.0102:0:1 +12 18574172 . A T 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.15636;SOR=4.47754;LSEQ=CATTAATTCCAAAAAGGAAA;RSEQ=TTTTTTAAAAATGATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:11,3:0.2143:0,0:31:1:29.3:1:1:0:60:6:0.2308:0:2 1/0:7:4:0,4:1,2:3,4:0.5714:2,0:32.8:1:30.5:1:0.42857:0:60:8:0.5714:0:2.8 +12 18574178 . T A 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.12193;SOR=6.4865;LSEQ=TTCCAAAAAGGAAAATTTTT;RSEQ=AAAAATGATTTCATTTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:11,3:0.2143:0,0:32.7:1:29.7:1:1:0:60:6:0.2143:0:2 1/0:6:4:0,4:1,1:2,4:0.6667:2,0:26.8:1:26.3:1:0.33333:0:60:3:0.6:0:2.8 +12 18576730 . C T 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=5.79268;LSEQ=TTTTGTTATTAGTCATATAC;RSEQ=GACTCATAAAATCATCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:6:6,0:51,0:51,6:0.1053:1,0:32.3:1:33.2:1:1:0:60:12:0.1071:0:1 0/1:39:16:15,1:23,0:23,16:0.4103:1,1:26:1:30:1:0.41026:0:60:32:0.4103:0:1.2 +12 18576807 . C G 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00116;SOR=Inf;LSEQ=TTCTCTAGTCTTTTCTCAAG;RSEQ=CTCTGAAGTCCCTCTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:194,35:229,0:0:2,0:23.6:1:31.9:1:1:0:60:37.167:1:0:0.1 0/1:266:11:8,3:214,40:254,11:0.0414:2,2:19.8:1:30.9:1:0.39371:1.99987:60:22:0.0423:0:1.2 +12 18576994 . C T 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09249;SOR=0;LSEQ=GTAAGATTAACTAAATCAGG;RSEQ=AAGGATGCCTTTTTAATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:1,2:65,215:280,3:0.0105:2,2:24:1:27:1:0.55062:1.65:55.7:6:0.0108:0:3.3 0/0:344:0:0,0:93,250:343,0:0:2,0:24.2:1:30.9:1:1:0:60:33.3:1:0:0.2 +12 18577002 . C G 124 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00033;SOR=14.84178;LSEQ=AACTAAATCAGGCAAGGATG;RSEQ=CTTTTTAATTGCCACCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:0,1:51,202:253,1:0.0039:2,0:46:0:30:0:1:0:60:2:0.004:0:1 0/1:289:16:4,12:71,200:271,16:0.0554:2,2:28.4:1:31.1:1:1:1.06477:60:32:0.0559:0:1.1 +12 18641326 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACTTACTGTTCCGGCTGGA;RSEQ=GTGGTTTAAAAAATTAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:55,1:0,0:0,56:1:0,1:20.7:1:32.1:1:1:0:59.4:17.667:1:0:1 1/1:74:74:69,5:0,0:0,74:1:0,2:21:1:31.8:1:1:0:60:148:1:0:1.1 +12 18641364 . TTC T 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTACATACAAGAATTTTT;RSEQ=TCTCTCTTTCCTTCAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:118,30:148,0:0:2,0:24.7:1:30.5:1:1:0:59.5:28.6:1:0:0.4 0/1:185:21:16,5:124,40:164,21:0.1135:2,2:23.8:1:29:1:1:1.03:60:42:0.1148:0.0216:0.4 +12 18644191 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13904;SOR=Inf;LSEQ=CATGCCTTAGTTTCCCATTT;RSEQ=TCCAACATGCCCTATTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:19,1:20,0:0:1,0:28.2:1:30.9:1:1:0:60:9:1:0:1.1 0/1:13:2:1,1:10,1:11,2:0.1538:2,2:24.5:1:28:1:0.29487:7.41607:60:4:0.1538:0:2 +12 18644222 . G C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06574;SOR=0;LSEQ=CCTATTGTCTTTAGCCCACT;RSEQ=TCTTCTCATGCCTGAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:30,1:0,0:0,31:1:0,1:24.8:1:31.1:1:1:0:59.8:14.5:1:0:1.3 1/1:22:19:17,2:3,0:3,19:0.8636:0,2:26.8:1:31.1:1:1:0:60:38:0.8636:0:1.2 +12 18648812 . G A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5453;SOR=0;LSEQ=AAGTAAAGGCTCCAGTTGAT;RSEQ=GACTAAATTTTTTAAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:16,0:16,4:0.2:1,0:24.3:1:27.5:1:1:0:60:8:0.2222:0:1 0/0:7:0:0,0:7,0:7,0:0:0,0:18:1:31:1:1:0:60:14:1:0:0.1 +12 18648909 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50068;SOR=Inf;LSEQ=ACAACAAAGTCTGCAAGGGG;RSEQ=TATGATTTTGGGGAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:117,17:134,0:0:2,0:22.1:1:32:1:1:0:60:43.667:1:0:0.1 0/1:154:2:1,1:131,21:152,2:0.013:2,2:11.5:1:25:0:0.26611:6.11791:60:4:0.0133:0:1 +12 18648919 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25318;SOR=Inf;LSEQ=CTGCAAGGGGCTATGATTTT;RSEQ=GGGAAAAGGTTTGCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:132,25:157,0:0:2,0:22.5:1:31.9:1:1:0:60:51.333:1:0:0.1 0/1:186:3:1,2:149,34:183,3:0.0161:2,2:15:1:27:1:0.09632:8.61851:60:6:0.0163:0:1 +12 18648928 . G T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13647;SOR=Inf;LSEQ=GCTATGATTTTGGGGAAAAG;RSEQ=TTTGCTTTTTGGGGATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:143,40:183,0:0:2,0:23:1:31.2:1:1:0:60:44.75:1:0:0.1 0/1:239:4:2,2:177,58:235,4:0.0167:2,2:8.3:1:26.3:1:0.2626:3.03442:60:8:0.0169:0:1 +12 18649057 . C T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48787;SOR=1.10806;LSEQ=TACTTTCATCAATGCTAATC;RSEQ=GATGGGCAAAAACATCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:110:57,53:156,196:352,110:0.2381:2,2:26.3:1:31.4:1:0.18888:1.35:60:220:0.2397:0:1.1 0/1:692:178:92,86:230,283:513,178:0.2572:2,2:24.1:1:29.9:1:0.11749:1.32:60:177:0.258:0:1.1 +12 18649158 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50382;SOR=Inf;LSEQ=GATTTATTACTCACAAAAAG;RSEQ=AATTGTTGTGGCTATTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:12,110:122,0:0:2,0:23.6:1:31.2:1:1:0:59.6:60:1:0:0.1 0/1:151:2:1,1:13,136:149,2:0.0132:2,2:8:1:27.5:1:0.1774:10.12:60:4:0.0137:0:1 +12 18650325 . C A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.84709;LSEQ=AACAACATTCCAAGCAGCAC;RSEQ=TCTAATTTGATGGTTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:42:1:31.5:1:1:0:60:4:0.2857:0:1 0/1:4:1:1,0:2,1:3,1:0.25:2,0:7:0:30:0:1:0:60:2:0.25:0:1 +12 18655952 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTCTCTGTTCATCATCAA;RSEQ=ATTGGCTTGCTACCATAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:14:1:33:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 18656122 . AGTAGT TTTTCTGGATTACCCAGAATA 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.1222;SOR=Inf;LSEQ=GAAAAGGAAAGGGGTAATCC;RSEQ=GCTGGAAGCTATTGTTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:47,1:48,0:0:1,0:25.6:1:31.1:1:1:0:60:47:1:0:0.2 0/1:56:4:3,1:50,2:52,4:0.0714:1,2:26.3:1:30.5:1:0.20274:7.69123:59.5:8:0.0727:0.0536:1 +12 18656174 . G C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01682;SOR=0.47715;LSEQ=CTAAGGCTCCCTCATCTTGT;RSEQ=ATGAAGGAATTGTCTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:32:29,3:82,24:106,32:0.2319:2,2:26.5:1:32.4:1:0.12837:2.81:60:64:0.2353:0:1.8 0/1:191:24:20,4:129,37:166,24:0.1257:2,2:25.5:1:31.1:1:0.79061:1.43:60:48:0.127:0:1.8 +12 18656225 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24062;SOR=0.80855;LSEQ=TCTCTACCAGGATTGGTGCA;RSEQ=ATGGTACCTGATGCTGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:69:46,23:152,95:247,69:0.2184:2,2:21.9:1:30.4:1:0.48321:1.25:60:138:0.2204:0:1.4 0/1:494:91:51,40:233,168:401,91:0.1842:2,2:23.8:1:29.6:1:0.72585:1.08758:60:182:0.1869:0:1.3 +12 18658178 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15606;SOR=0;LSEQ=CCTCTGATGCTAATGCATTT;RSEQ=CTCATTTTTTGTTGTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:155,27:182,2:0.0109:2,2:24.5:1:29:0:0.2819:5.65551:60:4:0.0109:0:1 0/0:281:0:0,0:213,68:281,0:0:2,0:20:1:31.3:1:1:0:60:280:1:0:0.1 +12 18690977 . A G 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0;LSEQ=GAAGGAAATTTATCTATTAC;RSEQ=GTAGAGAAAAAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:13:13,0:41,0:41,13:0.2407:1,1:24.9:1:29:1:1:0:60:12:0.2264:0:1.3 0/0:51:0:0,0:51,0:51,0:0:1,0:18.1:1:29.7:1:1:0:60:102:1:0:0.1 +12 18690983 . G GA 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.02181;LSEQ=AATTTATCTATTACAGTAGA;RSEQ=AAAAAAAAAAGAAAATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:7:7,0:61,0:61,7:0.1014:1,0:23.4:1:32:0:1:0:60:14:0.1045:0:0.6 0/1:58:6:6,0:52,0:52,6:0.1034:1,0:17.5:1:29.9:1:1:0:60:12:0.1034:0.0517:0 +12 18691017 . G A 100 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00734;SOR=9.83756;LSEQ=AATTCAAATGAAAATAAGTC;RSEQ=TTATAACTGCTGATTTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:1,0:131,20:151,1:0.0066:2,0:29:0:13:0:1:0:60:0:0:0:4 0/1:179:11:10,1:141,27:168,11:0.0615:2,2:19.1:1:29:1:1:1.91:60:10:0.0568:0:1.3 +12 18691253 . C T 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=ACCTGCTGGAAATGGTAAGT;RSEQ=CCTTGGGAAAAAAAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:38,154:192,0:0:2,0:23.4:1:31.2:1:1:0:59.9:31:1:0:0.1 0/1:264:19:3,16:61,184:245,19:0.072:2,2:24.7:1:28.6:1:0.57834:1.7648:60:38:0.072:0:1.2 +12 18691260 . G GA 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.3291;SOR=0.57278;LSEQ=GGAAATGGTAAGTCCCTTGG;RSEQ=AAAAAAAAACAAAAATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:10:2,8:30,128:158,10:0.0595:2,2:31.5:1:31.1:1:1:1.07:60:20:0.0629:0:0.1 0/1:229:8:1,7:51,170:221,8:0.0349:2,2:18.5:1:27:1:0.68639:2.09434:59.4:3:0.0269:0.0131:0.1 +12 18699424 . C A 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50414;SOR=Inf;LSEQ=AATGTACGCAGACACATGTT;RSEQ=CACAGTGGAGATGATTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:26,136:162,0:0:2,0:21.9:1:31.2:1:1:0:59.9:39.5:1:0:0.1 0/1:200:2:1,1:39,159:198,2:0.01:2,2:8.5:1:22.5:1:0.3608:4.04:60:4:0.0103:0:1 +12 18715593 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25595;SOR=Inf;LSEQ=CATAAATGAAATGAGTAGAT;RSEQ=CAGAGGAGTGTCACTCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:157,54:211,0:0:2,0:24:1:32.4:1:1:0:59.8:69.333:1:0:0.1 0/1:258:3:1,2:192,63:255,3:0.0116:2,2:20.7:1:27.3:1:0.15734:6.04239:60:6:0.0117:0:1 +12 18715673 . A G 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00052;SOR=Inf;LSEQ=CTGGAGTGTTTCCCTGTTAA;RSEQ=TTGAATAACTTGATCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:275,180:455,0:0:2,0:25.4:1:30.6:1:1:0:59.9:226.5:1:0:0.1 0/1:777:17:10,7:440,317:757,17:0.0219:2,2:27.3:1:31.3:1:1:1.03:60:34:0.0222:0:1 +12 18715728 . T G 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCCATAAGCCCTGCCAAA;RSEQ=CTACTTCACAGACTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:45:21,24:238,247:485,45:0.0847:2,2:27.7:1:32.5:1:0.87633:1.10101:60:90:0.0856:0:1 0/0:945:0:0,0:468,476:944,0:0:2,0:25:1:29:1:1:0:60:71.615:0.9989:0:0.1 +12 18715842 . G A 144 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=22.0115;LSEQ=GTAATGTAAGTTTAAAGTCC;RSEQ=TCATCTTGACTTACGTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:0,1:77,179:256,1:0.0039:2,0:24:0:33:0:1:0:60:2:0.004:0:1 0/1:378:30:11,19:104,244:348,30:0.0794:2,2:27.5:1:29.4:1:0.41755:1.36:60:60:0.0806:0:1.1 +12 18716461 . G A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07192;SOR=0;LSEQ=CTGTCCTTTTACATTGTTTT;RSEQ=CCTTCAGTACTTGTCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:49,164:213,3:0.0139:2,2:16.3:1:24:1:0.13958:6.62:60:6:0.014:0:1 0/0:302:0:0,0:88,214:302,0:0:2,0:23.3:1:30.8:1:1:0:60:59.4:1:0:0.1 +12 18719837 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06686;SOR=0;LSEQ=ACAATCTTAAGATGAAAAGG;RSEQ=CAGTTTTCAAACTAATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:0,3:190,70:260,3:0.0114:2,0:13:1:26:1:0.02075:0:60:6:0.0118:0:1 0/0:385:0:0,0:268,117:385,0:0:2,0:24:1:30.7:1:1:0:60:37.5:1:0:0.1 +12 18719891 . A G 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTTAAAACAGGTTTCCTC;RSEQ=TTGGTGGCACCTACCTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:296,223:519,0:0:2,0:24.4:1:30.7:1:1:0:60:73.143:1:0:0.1 0/1:829:32:17,15:442,354:796,32:0.0386:2,2:29.6:1:30.3:1:0.85682:1.10156:60:64:0.0392:0:1.1 +12 18719938 . G T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00853;SOR=0;LSEQ=CAGATCACAGAAGATTCAGA;RSEQ=ATCTAAATCATTACATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:5:2,3:203,270:473,5:0.0104:2,2:14.8:1:27.4:1:1:1.12746:60:10:0.0106:0:1 0/0:760:0:0,0:337,420:757,0:0:2,0:26.4:1:30.6:1:1:0:60:74.7:0.9973:0:0.2 +12 18719972 . T G 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGGAACAGATATTAAATG;RSEQ=ATCACATGAAGTTACAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:119,249:368,0:0:2,0:24.2:1:28.8:1:1:0:60:736:0.9946:0:0.1 0/1:544:45:16,29:172,326:498,45:0.0827:2,2:24.9:1:31:1:0.87157:1.05:60:90:0.0833:0:1.2 +12 18720023 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.516;SOR=Inf;LSEQ=TTAATTTTTCTATTTTTACA;RSEQ=AAAACATCAACTATTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:14,114:128,0:0:2,0:23.8:1:28.4:1:1:0:60:20.333:1:0:0.3 0/1:187:2:1,1:33,151:184,2:0.0107:2,2:35:1:33:1:0.33298:4.52:60:4:0.0108:0:2 +12 18720057 . T C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00482;SOR=0.29863;LSEQ=TTTTATATTTTATTCGTGAG;RSEQ=GTGGTGGTTTATGTCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:23:1,22:1,33:34,23:0.4035:1,1:14.2:1:29.3:1:1:1.49:60:22:0.3929:0:1.1 0/1:72:12:1,11:2,58:60,12:0.1667:1,2:21.7:1:30.1:1:0.42622:2.59:60:24:0.1667:0:1 +12 18747387 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18415;LSEQ=AATGAATAGCAGTAACAAAT;RSEQ=TAAGAAATAAAGAAATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:47:40,7:62,9:71,47:0.395:2,2:24.3:1:32.7:1:0.7871:1.20361:60:94:0.395:0:1.2 0/1:150:16:14,2:113,21:134,16:0.1067:2,2:27.6:1:31.9:1:1:1.30:60:32:0.1074:0:1.1 +12 18747528 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.4889;LSEQ=GTAAATTTGTCATTATATTA;RSEQ=GTACAGTGATTTTCAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:84:24,60:54,112:166,84:0.336:2,2:26.9:1:30.3:1:0.56536:1.20447:60:41:0.3347:0:1 0/1:434:86:40,46:135,213:348,86:0.1982:2,2:24.2:1:29.4:1:0.21978:1.37:60:172:0.1986:0:1.1 +12 18762113 . G A 45 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=AGGTTCACTGATTTCTAAAG;RSEQ=CCACACTTTTAATCTCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:34:1:28.7:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:25:0:18:0:1:0:60:0:0:0:0 +12 18762450 . A C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.28226;LSEQ=TTTCCAACTGAACTCACTGA;RSEQ=ATTCTATTCTTTTATCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:162:97,65:167,107:274,162:0.3716:2,2:26:1:32.1:1:0.83982:1.04572:60:80:0.3721:0:1.1 0/1:602:86:52,34:303,212:515,86:0.1429:2,2:30:1:31.3:1:0.81352:1.07:60:85:0.1426:0:1.2 +12 18793300 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50231;SOR=Inf;LSEQ=TTTGGTCTGGATATTTAGTA;RSEQ=CTCTGTATTTGTTTTCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:135,30:165,0:0:2,0:21.2:1:33.1:1:1:0:59.8:330:1:0:0.1 0/1:196:2:1,1:149,45:194,2:0.0102:2,2:5:1:27:1:0.41523:3.28587:60:4:0.0102:0:1 +12 18793583 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03185;SOR=Inf;LSEQ=AAAATTTGCAGTAATTGGCA;RSEQ=CATTATTTCATAAAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:2,92:94,0:0:1,0:21.3:1:33:1:1:0:60:188:0.9895:0:0.1 0/1:71:4:1,3:2,65:67,4:0.0563:1,2:27.3:1:28.8:1:0.16184:9.97:60:8:0.0571:0:1 +12 18800501 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATTTATGGGGTATAAAA;RSEQ=GTGAAGTATATTTAAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:20.3:1:30.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 18800755 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50444;SOR=Inf;LSEQ=TTAAAAGCAATACTCAAAAA;RSEQ=GAGATGTATTTAAGCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:104,10:114,0:0:2,0:24.8:1:30.2:1:1:0:59.6:56:1:0:0.1 0/1:143:2:1,1:127,14:141,2:0.014:2,2:20:1:30:1:0.19945:8.79957:60:4:0.0143:0:1 +12 18800840 . G T 72 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04741;SOR=Inf;LSEQ=ATGAAGTCACAGAGCTCCAA;RSEQ=GACATGTCTTAATGCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:263,162:425,0:0:2,0:25.7:1:32.4:1:1:0:60:211.5:1:0:0.1 0/1:670:7:1,6:372,291:663,7:0.0104:2,2:5.9:1:26:1:0.0484:7.65016:60:14:0.0105:0:1.1 +12 18800989 . CA C 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTATGAACATATGCATTATT;RSEQ=TTAACTACTTGTATTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:55,166:221,0:0:2,0:22.7:1:30.7:1:1:0:60:43.2:1:0:0.6 0/1:259:44:12,32:63,152:215,44:0.1699:2,2:23.3:1:30.2:1:0.85685:1.10486:60:43:0.1693:0.0386:0.6 +12 18801017 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00344;SOR=0;LSEQ=ACTTGTATTTTTTTCACTTC;RSEQ=GGGCCTCTGAATCACATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:136:136:17,119:0,0:0,136:1:0,2:23.5:1:29.8:1:1:0:59.8:67:1:0:1.1 1/1:140:131:26,105:0,0:0,131:0.9357:0,2:20.6:1:29.2:1:1:0:60:64.5:0.9348:0:1.1 +12 18801024 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24472;SOR=0;LSEQ=TTTTTTTCACTTCTGGGCCT;RSEQ=TGAATCACATAAGTAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:11,103:114,2:0.0171:2,2:29.5:1:31:1:0.197:9.01:60:4:0.0174:0:2 0/0:119:0:0,0:23,96:119,0:0:2,0:20.8:1:30.9:1:1:0:60:58.5:1:0:1 +12 20290640 . G GT 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28587;SOR=Inf;LSEQ=TCAGCACATTAAAAAATTTA;RSEQ=TTTTTTTTAGGATTACATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:62,51:113,0:0:2,0:22.8:1:32.3:1:1:0:60:226:1:0:0.5 0/1:179:3:1,2:99,77:176,3:0.0168:2,2:13.7:1:24.7:1:0.58396:2.55808:60:6:0.0168:0.0112:0.7 +12 20290667 . C G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00489;SOR=1.9266;LSEQ=TTAGGATTACATTCAATGTA;RSEQ=TTTCTGATAAATTCATTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:50:22,28:41,38:79,50:0.3846:2,2:24.2:1:32.3:1:0.47003:1.36981:60:24:0.378:0:1.4 1/0:203:111:55,56:51,41:92,111:0.5468:2,2:26.9:1:30.7:1:0.48054:1.26503:60:54.5:0.5423:0:1.2 +12 20290713 . GA G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5117;SOR=Inf;LSEQ=GAGTATCCTCATAAAGAGAG;RSEQ=AAATTACTGTAATCTGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:40,69:109,0:0:2,0:25.9:1:30.7:1:1:0:60:53.5:1:0:0.6 0/1:152:2:1,1:60,89:149,2:0.0132:2,2:29:1:31.5:1:1:1.48:60:4:0.0135:0:1 +12 20290733 . A G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=0.24331;LSEQ=GAAAATTACTGTAATCTGAT;RSEQ=ACTGTACTTTTACATATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:24:9,15:20,37:57,24:0.2963:2,2:21.3:1:32:1:1:1.11:60:48:0.2963:0:1.8 0/1:130:12:4,8:45,73:118,12:0.0923:2,2:16.9:1:31.2:1:1:1.23093:60:24:0.093:0:2 +12 20290761 . T G 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00301;SOR=Inf;LSEQ=TTTTACATATCCAGCATCAC;RSEQ=TGAGGGGAGCCCAAATATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:8,35:43,0:0:2,0:22.8:1:30.8:1:1:0:60:86:1:0:0.3 0/1:66:12:4,8:12,42:54,12:0.1818:2,2:24.3:1:31.2:1:0.4646:1.73:60:24:0.1846:0:1.3 +12 21591785 . G C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16494;SOR=0.48884;LSEQ=TGATGCAGGCACCGTATTAA;RSEQ=GGCTGAGTGTTCAACTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:20:19,1:9,0:9,20:0.6897:0,1:24.2:1:31.9:1:1:0:60:40:0.6897:0:2.3 1/0:54:28:27,1:26,0:26,28:0.5185:1,1:25.7:1:32.6:1:1:0:60:56:0.5185:0:2.5 +12 21591814 . GTA G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0.72837;SOR=1.17825;LSEQ=GTTCAACTATGAACAGCATG;RSEQ=TATACCATGCTGGGGACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:27:26,1:25,1:26,27:0.5094:1,1:25.6:1:31.6:1:1:1.04:60:54:0.5094:0.0755:2.3 1/0:89:49:47,2:37,3:40,49:0.5506:2,1:24.9:1:30.6:1:0.65378:1.89:60:48:0.5455:0.1124:2.3 +12 21591828 . G A 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27858;SOR=1.4511;LSEQ=AGCATGGTATATACCATGCT;RSEQ=GGGACTCACAGCCTGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:30:28,2:32,2:34,30:0.4688:2,2:26.9:1:27.9:1:1:1.14047:59.8:29:0.4603:0:2.5 1/0:121:68:60,8:44,8:52,68:0.562:2,2:21.2:1:28.1:1:0.59695:1.36:59.6:136:0.562:0:2.5 +12 21591837 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53431;SOR=Inf;LSEQ=TATACCATGCTGGGGACTCA;RSEQ=AGCCTGCTGGAAGAGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:70,14:84,0:0:2,0:23:1:31.4:1:1:0:59.9:20:1:0:1.2 0/1:146:2:1,1:118,26:144,2:0.0137:2,2:9.5:1:27:1:0.3367:4.47247:60:4:0.0138:0:1.5 +12 21591847 . G A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01964;SOR=1.78252;LSEQ=TGGGGACTCACAGCCTGCTG;RSEQ=AAGAGACAATATTACAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:50:40,10:43,10:53,50:0.4854:2,2:22.1:1:30:1:1:1.07423:59.9:100:0.495:0:2.3 1/0:196:123:94,29:51,22:73,123:0.6276:2,2:18.9:1:28.7:1:0.31794:1.40:59.8:246:0.6308:0:2.3 +12 21591921 . T G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00389;SOR=1.5245;LSEQ=TTAGAGGTGCCTGTGGAGTA;RSEQ=GTAGGGAGTGAATTAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:317:173:88,85:68,75:143,173:0.5457:2,2:27.8:1:32.5:1:0.57366:1.14:60:172:0.5548:0:1.3 1/0:558:361:192,169:94,103:197,361:0.647:2,2:26.9:1:30.7:1:0.24934:1.24:59.9:71.2:0.6508:0:1.3 +12 21591985 . T C 18 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6183;SOR=0.54993;LSEQ=AGGTATTTTTAAAATCTCAT;RSEQ=ATGAAAGAATGAGTGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:34,106:140,2:0.0141:2,0:17:1:30.5:1:0.06293:0:60:4:0.0146:0:1.5 0/0:257:2:1,1:74,180:254,2:0.0078:2,2:18.5:1:18:1:0.50092:2.42:60:1:0.0039:0:1 +12 21592011 . A T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1252;SOR=0;LSEQ=AGAATGAGTGAAAGTTTACC;RSEQ=AGTATTCAAGAAAAGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:9,70:79,2:0.0247:2,2:6.5:1:29.5:1:0.23302:7.43:60:4:0.0247:0:2 0/0:147:0:0,0:24,123:147,0:0:2,0:22.2:1:30.2:1:1:0:60:294:1:0:0.3 +12 21592094 . G T 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02751;LSEQ=CTTAAAGCATAGATCATAAG;RSEQ=AGTCTTAGCATGCTGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:3,7:0.7:0,0:18:1:29.7:1:1:0:60:14:0.7:0:1 1/0:17:12:0,12:0,5:5,12:0.7059:0,0:16.2:1:28.6:1:1:0:60:24:0.7059:0:1 +12 21600406 . G C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23412;SOR=2.86676;LSEQ=GCATTTGAATGAATCAGAGT;RSEQ=CTTCCCGTTACCATTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:42:1:29.2:1:1:0:60:4:0.4444:0:2.2 1/0:16:12:12,0:4,0:4,12:0.75:0,0:30.3:1:31.3:1:1:0:58.9:24:0.75:0:2 +12 21600443 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.008;SOR=4.2707;LSEQ=GAAAAATATCCCACATGCAG;RSEQ=GCATGTCTGCCTTCTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:13,0:13,0:13,13:0.5:1,1:15.9:1:30.9:1:1:0:60:12:0.48:0:1.5 1/1:43:35:35,0:8,0:8,35:0.814:0,1:19.5:1:31.7:1:1:0:59.6:70:0.814:0:1.4 +12 21600496 . GT G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5515;SOR=Inf;LSEQ=ACATTTTTGTTTTTTTAACA;RSEQ=TTATTATAATTTCTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:70,22:92,0:0:2,0:24.2:1:29:1:1:0:60:17.4:1:0:0.1 0/1:181:2:2,0:135,44:179,2:0.011:2,0:10:1:32:1:1:0:60:4:0.0112:0.0055:0 +12 21600639 . T G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45368;SOR=1.26997;LSEQ=TATGTAAAATACATGCATAC;RSEQ=GCCAGGCGCGGTGGCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:35:7,28:7,23:30,35:0.5385:2,2:24.2:1:31.2:1:0.77087:1.21369:56.1:70:0.5385:0:1.1 1/0:149:89:17,72:13,46:59,89:0.5973:2,2:23.8:1:30.3:1:0.6809:1.19545:56.3:178:0.5973:0:1.1 +12 21600649 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55284;SOR=Inf;LSEQ=ACATGCATACTGCCAGGCGC;RSEQ=GTGGCTCACACCTGTAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:8,42:50,0:0:2,0:21.5:1:31.4:1:1:0:57:100:1:0:0.7 0/1:111:3:2,1:18,90:108,3:0.027:2,2:11.7:1:27:1:0.08309:9.69:51:2:0.0185:0:2.7 +12 21600737 . G A 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.72239;SOR=1.48036;LSEQ=GAGACCGTCCTGGCTAACAC;RSEQ=GTGAAATCCCGTCTCTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:8,8:0.5:0,0:25.3:1:31.5:1:1:0:35.9:16:0.5714:0:1 1/0:15:9:0,9:1,4:5,9:0.6:2,0:32.2:1:31.2:1:0.35714:0:32.4:18:0.6429:0:1 +12 21600865 . T C 81 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08492;SOR=Inf;LSEQ=CCCGGGAGATTGCAGTGAGC;RSEQ=GAGATCACGCCGCTGCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:32:1:32:1:1:0:47.8:8:1:0:0 1/0:10:6:6,0:4,0:4,6:0.6:0,0:6.5:1:31.7:1:1:0:32.7:12:0.6:0:1.8 +12 21600915 . T TA 111 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.18293;SOR=2.28045;LSEQ=CGACAGAGCGAGACTCCATC;RSEQ=AAAAAAAAAAAAAACACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:3,2:13,4:17,5:0.2083:2,2:21.2:1:31.4:1:0.58533:2.08426:45.6:10:0.2273:0.0417:1.8 0/1:45:17:10,7:13,10:23,17:0.3778:2,2:28.5:1:27.2:1:1:1.10:43.4:16:0.4103:0:1.7 +12 21600952 . CG TA 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=0;LSEQ=CATGCGTACTTTTGATAGCA;RSEQ=TGTGAAGGTATCTCTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:7:5,2:21,16:37,7:0.1522:2,2:29:1:28.8:1:0.68165:1.88:51.6:6:0.1622:0:1.3 0/0:89:0:0,0:44,43:87,0:0:2,0:26.3:1:29.3:1:1:0:45.2:8.667:1:0:1.3 +12 21600953 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00013;SOR=Inf;LSEQ=ATGCGTACTTTTGATAGCAC;RSEQ=TGTGAAGGTATCTCTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:38:22,16:1,0:1,38:0.8261:0,2:26.8:1:29.1:1:1:0:48:18:1:0:1.7 1/1:88:88:44,44:0,0:0,88:1:0,2:27.1:1:28.5:1:1:0:46.3:21:1:0:1.3 +12 21600970 . T TA 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.11264;SOR=0;LSEQ=CACGTGTGAAGGTATCTCTC;RSEQ=AAAATTGACCTCATTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:26,19:45,2:0.0408:2,2:32.5:1:29:0:1:1.35916:26:4:0.0455:0:2 0/0:96:0:0,0:45,51:96,0:0:2,0:27.6:1:28.2:1:1:0:48.7:11:1:0:1.1 +12 21601106 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09318;SOR=0;LSEQ=GATGATATCAATTTCACATA;RSEQ=CTGGCATCAGGGCCTTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:96,62:158,2:0.0125:2,2:34:1:30.5:1:1:1.54398:34:4:0.0126:0:1 0/0:363:0:0,0:199,164:363,0:0:2,0:27.5:1:30.8:1:1:0:56.8:89.75:1:0:0.2 +12 21601137 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09675;SOR=0;LSEQ=GGCCTTCACAGCCACCATAG;RSEQ=TTTTCTCTTCCCCATCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:81,84:165,2:0.0119:2,2:7:1:29:1:1:1.04:60:4:0.0121:0:1 0/0:371:0:0,0:162,208:370,0:0:2,0:26.3:1:30.6:1:1:0:56.8:36:0.9972:0:0.2 +12 21601160 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0403;SOR=0;LSEQ=TTCTCTTCCCCATCCATTTT;RSEQ=TTCTTATGAAATGCTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:2,1:54,88:142,3:0.0207:2,2:20.3:1:27.7:1:0.55933:3.23:47.7:6:0.021:0:1 0/0:276:0:0,0:104,172:276,0:0:2,0:24.9:1:31:1:1:0:57.8:68:1:0:0.2 +12 22968378 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20347;LSEQ=GACCTCTTCCTATGTCATGC;RSEQ=AATTCAATGCTATATTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:243:160:74,86:40,43:83,160:0.6584:2,2:26.4:1:30.6:1:0.78784:1.08073:60:79:0.6639:0:1.1 0/1:409:115:50,65:140,154:294,115:0.2812:2,2:25.3:1:29.2:1:0.50842:1.18133:60:114:0.2808:0:1.1 +12 22968455 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51971;SOR=Inf;LSEQ=TCTAAGCCTTGGTTTTCTAA;RSEQ=CCATAAAATGGAGTGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:18,79:97,0:0:2,0:24.2:1:32.4:1:1:0:60:96:1:0:0.4 0/1:148:2:1,1:37,109:146,2:0.0135:2,2:33:1:29.5:1:0.44889:2.92:60:4:0.0136:0:1 +12 23617055 . G T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGTGTGACCCATGGACACAA;RSEQ=GAAGAGCAGTGTGATGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:25.5:1:29:1:1:1:50:4:0.5:0:1 0/0:3:0:0,0:2,1:3,0:0:2,0:27.7:1:31.3:1:1:0:60:6:1:0:0.3 +12 23617764 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16304;SOR=Inf;LSEQ=TGAGGAATCTGGGCAGCCCA;RSEQ=ATGAGTGGGTTTCCCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:14,0:0:2,0:33.7:1:32.5:1:1:0:46.1:28:1:0:0.2 0/1:10:2:1,1:5,3:8,2:0.2:2,2:42:1:28.5:1:1:1.58108:55.5:4:0.2:0:1 +12 23617776 . T TC 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16923;SOR=Inf;LSEQ=GCAGCCCAGATGAGTGGGTT;RSEQ=CCCCCCAGCAAAACACACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:15,0:0:2,0:31.9:1:30.4:1:1:0:47.1:30:1:0:0.2 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:38:1:29.5:1:1:1.22474:45:4:0.1818:0:0 +12 23618113 . G A 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02778;SOR=0;LSEQ=AAGAAAAACAAGCAGAAAGT;RSEQ=ACAACAACAGCATCAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:26.3:1:29.9:1:1:0:57:14:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:25:1:21.5:1:1:0:54.5:1:1:0:1.5 +12 24796145 . AAGAG A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGGGCTGTGAAAGAAAGA;RSEQ=AGGGAGGAGAGAAAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:29.5:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 25362465 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAACTGCATGCACCAAAA;RSEQ=CCCCAAGACAGAAATCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:13,1:0,0:0,14:1:0,1:26.7:1:30.4:1:1:0:32.4:28:1:0:1.1 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:27.5:1:1:0:25:4:1:0:1 +12 25362552 . A C 147 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=7e-04;SOR=0.05055;LSEQ=CTCTGGGAATACTGGCACTT;RSEQ=GAGGAAAAAAAAACTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:23:23,0:0,0:0,23:0.9583:0,1:30.3:1:32.6:1:1:0:56.5:46:0.9583:0:1.1 1/0:23:12:12,0:9,2:11,12:0.5217:2,0:24.8:1:31.5:1:0.21739:0:57.9:24:0.5217:0:1 +12 25362556 . G GA 34 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39224;SOR=2.28916;LSEQ=GGGAATACTGGCACTTAGAG;RSEQ=AAAAAAAAACTTCCACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:30,0:30,2:0.0606:1,0:22:1:30.9:1:1:0:60:4:0.0625:0.0303:0.5 0/1:23:3:2,1:19,1:20,3:0.1304:1,2:33:1:22:1:0.24901:7.95767:60:2:0.0909:0:1 +12 25362777 . A G 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTTTTCTTCTTTTTACC;RSEQ=TCTTTGCTCATCTTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:662:0:0,0:308,354:662,0:0:2,0:25.1:1:30.5:1:1:0:59.9:59.182:1:0:0.1 0/1:532:67:33,34:235,230:465,67:0.1259:2,2:25.6:1:30.4:1:0.89634:1.05262:60:66:0.1277:0:1.1 +12 25362854 . C T 127 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=15.37897;LSEQ=ATCATCAACACCCTGAAATA;RSEQ=ATAAAAAGTATTAAAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:2:1,1:129,272:401,2:0.005:2,2:23:1:13:1:0.54165:2.10:60:0:0:0:2.5 0/1:322:23:9,14:101,198:299,23:0.0714:2,2:22.2:1:28.1:1:0.65042:1.26:60:46:0.0721:0:1 +12 25368084 . T C 95 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAACTTTTCCCTTAAAAA;RSEQ=AAAGGTAAATATCAGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:28.6:1:34.1:1:1:0:56.4:14:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 25368462 . C T 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.57264;LSEQ=AATCTGTATTGTCGGATCTC;RSEQ=CTCACCAATGTATAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:981:979:430,549:0,0:0,979:0.998:0,2:25.5:1:30.7:1:1:0:60:64.267:0.999:0:1.1 1/1:771:770:329,441:0,0:0,770:0.9987:0,2:24.8:1:29:1:1:0:59.9:76:0.9987:0:1.1 +12 25369027 . C T 29 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGAACCTTGAGTTTTAT;RSEQ=TTAAATTTTAACACCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:5.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 25378026 . G A 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAAAATGCATTAAATGA;RSEQ=TAACAGAATTTCTGTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:30.8:1:31.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 25378224 . ATATATATATATATATATATATATA T 80 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=22;MSI=24.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGTTGCCCTGTTCTTTAT;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:0,0:0,6:0.6667:0,0:17.7:1:31:1:1:0:60:12:0.6667:0.6667:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 25378456 . T C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TATTGTTTTATTTCCTAGTA;RSEQ=AGCATAATTGAGAGAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:188,9:197,0:0:1,0:23.7:1:31.5:1:1:0:60:64.667:1:0:0.1 0/1:110:12:12,0:94,4:98,12:0.1091:1,0:23.3:1:32.6:1:1:0:60:24:0.1091:0:1 +12 25378716 . G GA 69 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.52632;SOR=1.55177;LSEQ=TTAATTTGTTCTCTGGGAAA;RSEQ=AAAAAAAAGTTATAGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:5:2,3:159,461:620,5:0.008:2,2:6.2:1:29.7:1:0.60753:1.93:60:10:0.0081:0.0064:0.6 0/1:405:5:1,4:131,269:400,5:0.0123:2,2:29:1:29.8:1:1:1.94516:60:10:0.0125:0.0025:0 +12 25379793 . C T 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGCTATACACACGATTG;RSEQ=TTTTAAGACTGTTAAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:31.7:1:29:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 25380071 . T G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=TAAACATTATTTAAAAATTT;RSEQ=TATTAAATATTATATGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:131,3:134,0:0:1,0:23.7:1:31.6:1:1:0:60:66:1:0:0.1 0/1:69:8:8,0:61,0:61,8:0.1159:1,0:22.4:1:31.6:1:1:0:60:16:0.1159:0:1 +12 25398018 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03704;SOR=Inf;LSEQ=GAACATCATGGACCCTGACA;RSEQ=ACTCCCAAGGAAAGTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:43,1:44,0:0:1,0:24.5:1:31.2:1:1:0:60:43:1:0:0.1 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:15:1:31:0:1:0:60:4:0.1818:0:1 +12 25398280 . G A 76 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13636;SOR=2.54064;LSEQ=GTCAAGGCACTCTTGCCTAC;RSEQ=CCACCAGCTCCAACTACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1015:4:4,0:463,548:1011,4:0.0039:2,0:1:0:27:1:0.0445:0:47.5:8:0.004:0:1 0/1:703:7:5,2:323,372:695,7:0.01:2,2:12.1:1:27.3:1:0.26107:2.88:53.9:14:0.0101:0:1 +12 25398285 . C A 208 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GGCACTCTTGCCTACGCCAC;RSEQ=AGCTCCAACTACCACAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:113:49,64:384,490:874,113:0.1144:2,2:25.5:1:30.5:1:0.92017:1.02355:49.3:36.667:0.1125:0:1.1 0/0:664:0:0,0:288,376:664,0:0:2,0:24.7:1:30.7:1:1:0:59.3:220.333:1:0:0.1 +12 25398346 . T A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0568;SOR=Inf;LSEQ=AGGCCTTATAATAAAAATAA;RSEQ=GAAAATGTGACTATATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:98,328:426,0:0:2,0:24.5:1:30.4:1:1:0:59.9:52.25:1:0:0.2 0/1:267:3:1,2:74,190:264,3:0.0112:2,2:12.3:1:25:1:1:1.28:55.3:2:0.0077:0:3 +12 26410050 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=5.000;MSILEN=3;SSF=0.54332;SOR=0;LSEQ=AGGTGACAACAGCAGCAGCA;RSEQ=CAACAACAACAACAAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:31,26:57,2:0.0339:2,2:27:1:32.5:1:1:1.18874:44.5:4:0.0339:0:1 0/0:31:0:0,0:17,14:31,0:0:2,0:25.6:1:29.6:1:1:0:50.4:62:1:0:0.1 +12 26410211 . A G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1369;SOR=0;LSEQ=CTCCTCCAAATGATTGCAGT;RSEQ=TCTCTCCATCAAGGGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:23,17:0,0:0,40:1:0,2:32.4:1:32.2:1:1:0:43.2:39:1:0:1.1 1/1:24:22:13,9:1,1:2,22:0.9167:2,2:19:1:30.7:1:1:1.42:39.6:21:0.913:0:1.3 +12 26412198 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATGAATCCAAAAGCTAG;RSEQ=AGAAGAGAAGAAATAAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:14:1:29:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 27330424 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5414;SOR=0;LSEQ=AATACAATAATTACATGGCA;RSEQ=TGCTTGATAATTCTGTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:115,19:134,2:0.0147:2,2:39:1:30:1:0.27342:5.925:60:4:0.0148:0:1 0/0:74:0:0,0:60,14:74,0:0:2,0:21.6:1:31:1:1:0:60:36:1:0:0.2 +12 27330516 . T C 231 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCAGAAAAAGGAGACTTA;RSEQ=TTCTGCTAAGACGCAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:211,198:409,0:0:2,0:26.6:1:30.6:1:1:0:60:80.8:1:0:0.1 1/0:279:159:79,80:60,60:120,159:0.5699:2,2:26.2:1:31.6:1:1:1.01261:60:158:0.5745:0:1.2 +12 27330606 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53192;SOR=0;LSEQ=ACATGTAGCTATCAACCAAA;RSEQ=TTTGAGCAGAAAACTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:27,131:158,2:0.0125:2,2:18.5:1:29:1:0.32028:4.78:60:4:0.0126:0:1 0/0:94:0:0,0:22,72:94,0:0:2,0:23.4:1:31:1:1:0:60:188:1:0:0.3 +12 27578740 . G A 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00256;SOR=0;LSEQ=TCTAGAGAGTCAACCATCAT;RSEQ=AATTATAAGGTTCTATTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:13,0:12,0:12,13:0.52:0,1:30.8:1:29.2:1:1:0:60:26:0.52:0:1 0/0:11:0:0,0:11,0:11,0:0:0,0:17.6:1:31.3:1:1:0:60:22:1:0:0.1 +12 27578843 . C T 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69651;LSEQ=TCTTTTCCCCTTCAAGGATG;RSEQ=CTTTAAAGTTTATTTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:148,50:198,2:0.01:2,2:25.5:1:27.5:1:0.44593:2.9406:60:4:0.0102:0:1 0/0:144:1:0,1:95,48:143,1:0.0069:2,0:1:0:23:0:0.34028:0:60:2:0.007:0:2 +12 27578846 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17615;SOR=Inf;LSEQ=TTTCCCCTTCAAGGATGCCT;RSEQ=TAAAGTTTATTTTAATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:157,58:215,0:0:2,0:22.2:1:30.2:1:1:0:59.8:29.714:1:0:0.2 0/1:156:2:1,1:103,51:154,2:0.0128:2,2:25.5:1:32.5:1:1:2.00984:60:4:0.0129:0:2 +12 27578912 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.84815;LSEQ=GGGAAGGCAAAATAAGCAGT;RSEQ=GGTTCTTTCCAGGTCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:48:21,27:193,187:380,48:0.1119:2,2:27.8:1:31.9:1:0.44401:1.32609:59.9:96:0.1127:0:1.1 1/1:368:295:150,145:35,38:73,295:0.8016:2,2:28:1:30.8:1:0.696:1.12:60:72.75:0.7995:0:1.1 +12 27578968 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19885;SOR=Inf;LSEQ=TTAGCCAGGCTGTGATACAT;RSEQ=CTCAACCTTGGGTTGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:73,155:228,0:0:2,0:22.9:1:31.9:1:1:0:60:56:1:0:0.2 0/1:184:2:1,1:59,123:182,2:0.0109:2,2:8.5:1:27.5:1:0.54704:2.08:60:4:0.0111:0:1 +12 27580442 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51923;SOR=Inf;LSEQ=GGCCTCAGGAGGCCTACCTA;RSEQ=TTATTTTGCCTACCCTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:15,0:0:2,0:19.1:1:33:1:1:0:57.9:30:1:0:0.5 0/1:25:2:1,1:13,10:23,2:0.08:2,2:13.5:1:27.5:1:1:1.28628:60:4:0.08:0:1 +12 27705987 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAAGGAAGTGCACGCAG;RSEQ=GGCCTAGGAGAAGATTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:3,16:0,0:0,19:1:0,2:26.1:1:31.8:1:1:0:60:38:1:0:1.1 1/1:11:11:3,8:0,0:0,11:1:0,2:15.9:1:30.5:1:1:0:60:22:1:0:1 +12 27706244 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGTCCAGCTGGGCCGGG;RSEQ=ATGGTGCTCACCCACACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 28073093 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.30178;SOR=0;LSEQ=CATGCAGCTTTCTGAGTTCC;RSEQ=GTGTCCCTAGATTTATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:195,87:282,3:0.0105:2,2:45.3:1:26:1:1:1.12023:60:2:0.0072:0:2 0/0:165:0:0,0:110,55:165,0:0:2,0:24:1:30:1:1:0:60:330:1:0:0.2 +12 28073101 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1349;SOR=Inf;LSEQ=TTTCTGAGTTCCTGTGTCCC;RSEQ=AGATTTATGATGTGCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:211,112:323,0:0:2,0:27.1:1:30.5:1:1:0:60:52.833:1:0:0.4 0/1:188:2:1,1:117,69:186,2:0.0106:2,2:24.5:1:29.5:1:1:1.6906:60:4:0.0106:0:1.5 +12 28073172 . T A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32813;LSEQ=CATTTGAAGGAGAAATGATC;RSEQ=AGAGATTTGTGCTGGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:387:280:128,152:50,56:106,280:0.7235:2,2:26.2:1:30.4:1:0.81973:1.06009:60:45.667:0.723:0:1.1 0/1:286:132:60,72:69,85:154,132:0.4615:2,2:26.2:1:30:1:1:1.03:59.8:264:0.4615:0:1.1 +12 28073457 . G C 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTCCTATGCCCTGTCCCC;RSEQ=CTATTTCAGCACTCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:13.5:1:33:0:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:17:0:32:0:1:0:60:2:1:0:1 +12 29426005 . T C 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=3.76419;LSEQ=CCTGATGCCAGTAGGATTGC;RSEQ=CCTGTATAGAGTGTCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:3,2:0.4:0,2:14:1:29:1:0.4:0:60:4:0.4:0:1 1/0:4:3:2,1:1,0:1,3:0.75:0,2:6.3:1:28.7:1:1:0:37:6:0.75:0:1.3 +12 29426031 . T G 64 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.44461;LSEQ=ATAGAGTGTCTGACAACCCC;RSEQ=GTAGGAAGGTCTCACCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:3,2:5,4:0.4444:2,2:19.5:1:32:1:0.52381:3.76419:50.8:8:0.4444:0:1.3 0/1:4:1:1,0:2,1:3,1:0.25:2,0:47:0:26:0:1:0:60:2:0.25:0:2 +12 29426387 . C T 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4408;SOR=0.45138;LSEQ=CAGTGTGTGTGTGGCTGCCA;RSEQ=GGTGTGTAGGGCTGTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:3,4:7,8:0.5333:2,2:29.5:1:29.9:1:1:1.23147:60:16:0.5333:0:1.1 0/1:12:4:2,2:4,4:8,4:0.3333:2,2:20:1:30:1:1:1:57.5:8:0.3333:0:1.3 +12 29426859 . C A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCTCTCAGGTGGGCCAC;RSEQ=GCACCACACTGCTCTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:44:0:32.5:1:1:1:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 29811355 . A C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GTTCCAGTAGGCCAGACTCC;RSEQ=TTCCACTCGTTCACAGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:7.3:1:29.3:1:1:0:60:6:1:0:0.7 1/0:4:2:1,1:2,0:2,2:0.5:0,2:18.5:1:30.5:1:1:0:60:4:0.5:0:1 +12 29811514 . A G 26 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=ACTTGTTTGTTTATAACAAC;RSEQ=CCAACAGCAGCTGGGTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:16,2:0.1111:2,2:33:0:26:1:1:1:60:4:0.1111:0:1.5 0/0:11:0:0,0:7,4:11,0:0:2,0:21.8:1:27:1:1:0:60:10:1:0:0 +12 29811614 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19615;SOR=0;LSEQ=AACCATTCCCTTGATGTCAA;RSEQ=AATATCACCTTTCTTATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,9:16,2:0.1111:2,2:25.5:1:29.5:1:1:1.27:53:4:0.1111:0:1.5 0/0:22:0:0,0:9,13:22,0:0:2,0:24.4:1:32.1:1:1:0:60:44:1:0:0.2 +12 30533133 . A T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGGCTCTGTGTCAGGGA;RSEQ=ATCAGAGTTCTGTCCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:30.5:1:1:0:28:4:1:0:1.5 +12 30848675 . C T 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17222;SOR=0;LSEQ=CAGCCTCCTCTTCCGCGACC;RSEQ=CTGGATTACCTCACACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:6,3:14,13:27,9:0.25:2,2:18.8:1:31.8:1:0.70027:1.83:60:18:0.25:0:1.7 0/0:10:0:0,0:5,5:10,0:0:2,0:20.7:1:30.1:1:1:0:60:20:1:0:0.3 +12 30848763 . CT C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.2029;SOR=Inf;LSEQ=CTCCGCGCCCCCTGTCCTCC;RSEQ=TTTTCCCCCCCACAACTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:8,16:24,0:0:2,0:19.2:1:28.5:1:1:0:59.6:7:1:0:0.6 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:44:1:31:1:1:1.10554:60:4:0.0952:0:0 +12 31932814 . A C 119 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01992;SOR=0.10853;LSEQ=ATCCCCTCGGAGGGTTTTAC;RSEQ=AACATTTACAATTTTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:14,0:19,0:19,14:0.4242:1,1:12.4:1:31.5:1:1:0:60:28:0.4242:0:1 0/1:14:1:1,0:12,1:13,1:0.0714:1,0:6:0:32:0:1:0:60:2:0.0769:0:1 +12 31932960 . C T 55 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06833;SOR=Inf;LSEQ=TTTTGATCTTGTGATTCATG;RSEQ=CAGGGTCATGATGTCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:250,127:377,0:0:2,0:24.9:1:31.8:1:1:0:60:61.833:1:0:0.1 0/1:463:5:1,4:288,170:458,5:0.0108:2,2:12.8:1:23.8:1:0.06867:6.74957:60:4:0.0087:0:1 +12 31933059 . A G 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTACCAATACCTGCATCCT;RSEQ=TAAGTGTTTTGCAATACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:769:0:0,0:384,385:769,0:0:2,0:25.6:1:29.3:1:1:0:60:75.9:1:0:0.1 0/1:890:43:20,23:406,440:846,43:0.0483:2,2:24.4:1:30.7:1:0.8769:1.06109:60:42:0.0478:0:1.2 +12 31933213 . C T 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.07299;LSEQ=CTTTACTGTGGGTTCTGGTA;RSEQ=GCCAAAGAAGGCAGTACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:21:0,21:1,61:62,21:0.253:1,1:29.1:1:31.2:1:1:0:60:42:0.253:0:1 0/1:45:12:0,12:1,32:33,12:0.2667:1,0:27.3:1:29.6:1:1:0:60:24:0.2727:0:1.1 +12 31938381 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03577;SOR=Inf;LSEQ=ATTCAAAGTAAAAATCATGT;RSEQ=TGCATGACGAACTGTATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:62,1:63,0:0:1,0:28.8:1:32.5:1:1:0:60:62:1:0:0 0/1:50:4:4,0:46,0:46,4:0.08:1,0:10.5:1:25:1:1:0:60:3:0.0625:0:1 +12 31944567 . T G 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCACTTTTCGCATTCATCC;RSEQ=GAGTGAAAGATGGAATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:77,3:80,0:0:1,0:23.9:1:31.4:1:1:0:35.6:25.667:1:0:0.1 0/1:63:17:16,1:43,3:46,17:0.2698:2,1:22.8:1:29.5:1:1:1.11:31.9:34:0.2742:0:1.1 +12 31944691 . A C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18132;LSEQ=ATGCCATAAAAACTGCCTTC;RSEQ=CTTAAGCTCTCTCTCCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:50:40,10:56,50:106,50:0.3205:2,2:8.9:1:29.9:1:0.00138:3.54:40.4:49:0.3182:0:1.1 0/1:204:16:10,6:97,91:188,16:0.0784:2,2:10.9:1:28.2:1:0.44523:1.56:45.1:32:0.0796:0:1.1 +12 31944710 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2529;SOR=0.23927;LSEQ=CACTTAAGCTCTCTCTCCCC;RSEQ=TATCCGGCGAGCCAACTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:2,0:10,23:33,2:0.0571:2,0:8.5:1:28.5:1:0.11092:0:60:4:0.0588:0:1 0/1:71:1:1,0:25,45:70,1:0.0141:2,0:1:0:24:0:0.3662:0:60:2:0.0141:0:1 +12 31945622 . G T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCATTTCAATCCCACCTCC;RSEQ=TCACAAAGCATTCTTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:30:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 31950904 . AT A 41 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGTAAATCCTTTGTGGG;RSEQ=TTTTTTACATACTATAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:17.7:1:26.2:1:1:0:57:6:0.75:0.5:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 31950931 . A G 40 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATACTATAACCATTCAT;RSEQ=CATTCAACACATATTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:27.3:1:25.7:1:1:0:57:2:0.6667:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 31957141 . TA T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50222;SOR=0;LSEQ=AGTGGAAGCCAGTGTCTCTA;RSEQ=ATGAAGGTTGTAGAGAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:52,1:53,2:0.0357:1,2:24:1:30.5:1:0.07205:37.11322:60:4:0.0385:0:0 0/0:44:0:0,0:44,0:44,0:0:1,0:26.3:1:27.1:1:1:0:60:43:1:0:0.1 +12 31957306 . A G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.30163;LSEQ=TAGTGCAAAACTTCAGAATA;RSEQ=ATAAAAGTTGACTTCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:830:550:312,238:158,120:278,550:0.6627:2,2:26.9:1:32.6:1:1:1.00438:60:274:0.665:0:2.3 0/1:1046:389:217,172:344,309:653,389:0.3719:2,2:25.8:1:30.9:1:0.33604:1.13:60:76.8:0.371:0:2.1 +12 31957321 . C T 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28826;LSEQ=GAATAAATAAAAGTTGACTT;RSEQ=AGTAACACATGGGTATCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:898:605:325,280:153,140:293,605:0.6737:2,2:26.7:1:29.8:1:0.72141:1.06:60:604:0.6771:0:2.4 0/1:1169:436:234,202:368,365:733,436:0.373:2,2:25.5:1:28.5:1:0.27609:1.15:60:144.333:0.3736:0:2.1 +12 31957372 . CT C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.26246;SOR=1.66833;LSEQ=TTCCCTCCCATTTACTGCAT;RSEQ=TTTTTTTGATCTTTGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:810:9:2,7:367,431:798,9:0.0111:2,2:20.4:1:34.2:1:0.19165:2.97658:59.4:18:0.0112:0.0012:1.1 0/1:1141:21:10,11:528,591:1119,21:0.0184:2,2:27.5:1:31.2:1:1:1.02:60:42:0.0185:0.0026:0.4 +12 31957381 . G A 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09951;LSEQ=ATTTACTGCATCTTTTTTTT;RSEQ=ATCTTTGGTGCTCTCACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:752:531:233,298:92,128:220,531:0.7061:2,2:23.8:1:29.7:1:0.62784:1.09:60:105.2:0.7079:0:1.9 0/1:1064:205:93,112:392,464:856,205:0.1927:2,2:24.9:1:28.8:1:0.93788:1.01741:59.9:410:0.1949:0:1.8 +12 31957584 . G A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05883;SOR=5.19189;LSEQ=TTATTAGCTTTTAGTACTGC;RSEQ=GGAGATTTTTTTTTTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:1,8:0,21:21,9:0.3:1,2:11.8:1:30.1:1:0.3:0:60:8:0.2857:0:1 1/0:10:7:0,7:0,3:3,7:0.7:0,0:19.9:1:31.3:1:1:0:60:14:0.7778:0:1 +12 31957589 . A AT 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05645;SOR=Inf;LSEQ=AGCTTTTAGTACTGCGGGAG;RSEQ=TTTTTTTTTTCAAGAGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,23:23,0:0:1,0:21.3:1:31.3:1:1:0:57.1:22:1:0:0.3 0/1:8:2:0,2:0,6:6,2:0.25:0,0:32.5:1:30:1:1:0:60:4:0.25:0:0.5 +12 32411399 . A G 50 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTCTCTCCGTGTGTGGA;RSEQ=ACGAGAGATCTAAGAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:15.3:1:32:1:1:0:43.7:6:1:0:1.7 1/1:1:1:1,0:0,0:0,1:1:0,0:38:0:34:0:1:0:44:2:1:0:1 +12 32411442 . G C 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22797;SOR=0;LSEQ=ACACAAGACAAAGAGATAAA;RSEQ=AGAAGACAGCTGGGCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:4,1:5,4:0.4444:2,0:27:1:34.3:1:1:0:42.3:8:0.4444:0:2.3 0/0:4:0:0,0:4,0:4,0:0:0,0:8.3:1:32.5:1:1:0:53.8:8:1:0:0.8 +12 32411481 . C T 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0419;SOR=0;LSEQ=GGGGACCACTACCACCAAGA;RSEQ=GCAGAGACCAGTAATGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:5,1:6,8:0.5714:2,0:24.8:1:32.4:1:0.42857:0:48.5:16:0.5714:0:2.3 0/0:6:0:0,0:6,0:6,0:0:0,0:27.3:1:32.3:1:1:0:48:12:1:0:1.3 +12 32411515 . G A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0309;SOR=Inf;LSEQ=ATGGCCCCGAATGGTTGGGC;RSEQ=TGCTGATATTTATCGTATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:17,3:20,0:0:2,0:21:1:30.2:1:1:0:46.7:40:1:0:1.1 0/1:16:4:4,0:12,0:12,4:0.25:0,0:30:1:31.3:1:1:0:32.3:8:0.25:0:2.8 +12 32411529 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10986;SOR=Inf;LSEQ=TTGGGCGTGCTGATATTTAT;RSEQ=GTATACAAGACAACGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:18,7:25,0:0:2,0:21.6:1:31.6:1:1:0:39.4:50:1:0:0.9 0/1:25:4:4,0:16,5:21,4:0.16:2,0:28.8:1:32:1:0.54941:0:32.3:8:0.16:0:2.8 +12 32411544 . G A 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00033;SOR=0.08437;LSEQ=TTTATCGTATACAAGACAAC;RSEQ=GGGCAGGGTAAGGAGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:10,6:7,1:8,16:0.6667:2,2:30.3:1:30.4:1:0.35215:3.98153:38.8:32:0.6667:0:1.3 0/1:22:3:3,0:14,5:19,3:0.1364:2,0:31:1:30:1:1:0:26:6:0.1429:0:3 +12 32412038 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGGCGTAAGAGAGGGC;RSEQ=CACCTCTTGCCTTCTTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:32:1:1:0:36:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 33147320 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGCTGTGGTCAGCACTCTC;RSEQ=CTGCTGGAAATGCTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:9,18:27,0:0:2,0:25.4:1:31.2:1:1:0:60:54:1:0:0.1 0/1:55:2:1,1:18,33:51,2:0.0364:2,2:28.5:1:30:0:1:1.81:60:4:0.0364:0:1 +12 33147332 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACTCTCCCTGCTGGAAAT;RSEQ=CTTTCTTTGAGCTTTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:7,15:22,0:0:2,0:25.8:1:32.1:1:1:0:60:44:1:0:0 0/1:47:2:1,1:16,29:45,2:0.0426:2,2:5.5:1:28:1:1:1.79:60:4:0.0435:0:1 +12 38600022 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19802;SOR=0;LSEQ=AGTATGGTTCTGCTACATTT;RSEQ=AGTAGAACGCTTACCTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:100,34:134,2:0.0147:2,2:23:1:26:1:0.44989:2.91357:30:4:0.0148:0:1 0/0:169:0:0,0:127,42:169,0:0:2,0:25.4:1:31.1:1:1:0:40.3:338:1:0:0.1 +12 38600037 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1954;SOR=0;LSEQ=CATTTCAGTAGAACGCTTAC;RSEQ=TGAACAGATATAACATAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:123,49:172,2:0.0115:2,2:18:0:32.5:1:0.49332:2.49507:23:4:0.0116:0:1.5 0/0:219:0:0,0:153,66:219,0:0:2,0:26:1:30.6:1:1:0:36.1:438:1:0:0.1 +12 38600104 . G A 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20149;SOR=0;LSEQ=TTCAGAGCTGCCTTCAGTAT;RSEQ=ATTATCTAGCAAGTTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:2,0:82,46:128,2:0.0154:2,0:7.5:1:26.5:1:0.53918:0:21.5:4:0.0156:0:1 0/0:159:0:0,0:90,69:159,0:0:2,0:13.2:1:29.7:1:1:0:24.1:38.75:1:0:0.2 +12 38600143 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21196;SOR=0;LSEQ=CATTATAGCTATGGTTTGCT;RSEQ=TACAAATTGAGTATTGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:103,96:199,2:0.01:2,2:32.5:1:29:1:1:1.07251:42:4:0.0101:0:1.5 0/0:235:0:0,0:104,130:234,0:0:2,0:25.9:1:30.8:1:1:0:43.6:116:1:0:0.1 +12 38600255 . T C 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19973;SOR=Inf;LSEQ=AGAGAGATGAAACCAACTGA;RSEQ=CTAAACACACAAACAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:16,96:112,0:0:2,0:25.5:1:30.1:1:1:0:58.6:55:1:0:0.2 0/1:91:2:1,1:9,80:89,2:0.022:2,2:6.5:1:26:1:0.20879:8.48:60:4:0.0222:0:1 +12 38600903 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23923;SOR=0;LSEQ=GTCATGTTGATCCATTCCTG;RSEQ=AGAGAGTCTGTGTCAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:71,96:167,2:0.0118:2,2:28.5:1:31.5:1:1:1.35:26.5:4:0.0118:0:1 0/0:176:0:0,0:90,86:176,0:0:2,0:25.5:1:28.6:1:1:0:47.1:175:1:0:0.1 +12 38601013 . T G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00135;SOR=0.56335;LSEQ=GCCTAAACACAAAATTTTCA;RSEQ=GTAAAGCATGAATTAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:96:33,63:74,126:200,96:0.3243:2,2:24.1:1:32.1:1:0.69951:1.12078:37.5:192:0.3276:0:1.1 0/1:362:77:27,50:106,177:283,77:0.2127:2,2:23.7:1:30.6:1:0.79024:1.10867:37.7:76:0.2105:0:1.1 +12 38601111 . A T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03471;SOR=0;LSEQ=TACAAGAAATGTAAAAAAAC;RSEQ=CATTAAAATCAACCCCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:0,7:0,28:28,7:0.2:1,0:33.3:1:26.9:1:1:0:54.7:6:0.1765:0:1.1 0/0:25:0:0,0:2,23:25,0:0:2,0:25.5:1:29.1:1:1:0:55.7:50:1:0:0 +12 40763955 . G A 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAATAACAATTCAGAATCTG;RSEQ=CTGCTTAAAGGCACCTACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:272,258:530,0:0:2,0:25.6:1:31.5:1:1:0:60:57.889:1:0:0.7 0/1:428:28:15,13:211,187:398,28:0.0654:2,2:27.5:1:27:1:1:1.02:60:13:0.0621:0:1.2 +12 40763973 . C G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.04926;SOR=0.77115;LSEQ=TGGCTGCTTAAAGGCACCTA;RSEQ=GTACGTGGTTCTTTCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:540:341:153,188:102,95:197,341:0.6315:2,2:25.4:1:31.9:1:0.1284:1.3186:60:67.2:0.6304:0:1.1 1/0:441:251:124,127:98,90:188,251:0.5692:2,2:25.3:1:30.5:1:0.62968:1.11495:60:61.75:0.5704:0:1.2 +12 40764063 . G A 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21925;SOR=Inf;LSEQ=AGGGAGGCACCTGACCCAAA;RSEQ=GCCTGCTGTCTGAACACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:40,140:180,0:0:2,0:24.7:1:31.3:1:1:0:60:59:1:0:0.3 0/1:159:2:1,1:41,116:157,2:0.0126:2,2:11:1:22.5:1:0.45976:2.81:60:4:0.0129:0:1.5 +12 43130905 . G A 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25359;SOR=0;LSEQ=GTTTTCTGGCATGAAACATA;RSEQ=TTTTATTTGTTTTCAGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:8,0:10,0:10,8:0.4444:0,0:32.4:1:30.4:1:1:0:60:16:0.4444:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:10.3:1:32.5:1:1:0:60:8:1:0:0.3 +12 43130986 . C G 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00073;SOR=Inf;LSEQ=AATTTTTTTTCTTAGGCTTA;RSEQ=GCGTCCCCTCTAATGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:38,0:0:1,0:18.3:1:32.7:1:1:0:60:76:1:0:0.1 0/1:35:9:8,1:23,3:26,9:0.2571:2,2:26.8:1:31.8:1:1:1.04:60:18:0.2571:0:1.1 +12 43131131 . T C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=5.49478;LSEQ=ATACAAATTGTTGAGAATAA;RSEQ=ATCTATGTGAGCAATCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:59:23,36:49,71:120,59:0.3296:2,2:26.5:1:32.3:1:0.8719:1.07973:60:118:0.3315:0:1.1 1/0:234:171:71,100:30,33:63,171:0.7308:2,2:28.1:1:31.1:1:0.45764:1.27903:60:342:0.7308:0:1.1 +12 43131140 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17664;SOR=0;LSEQ=GTTGAGAATAATATCTATGT;RSEQ=AGCAATCACATTGGCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:60,97:157,2:0.0125:2,2:14.5:1:28.5:1:1:1.61:60:4:0.0126:0:2 0/0:220:0:0,0:92,128:220,0:0:2,0:28.2:1:30.4:1:1:0:60:109:1:0:0.8 +12 43131208 . T C 149 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.0116;LSEQ=TAGATCGGGTATGTATTCTT;RSEQ=TGGAGTTATCAAATATAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:24:4,20:0,10:10,24:0.7059:0,2:22.1:1:32.5:1:0.29576:0:60:23:0.697:0:1.2 0/1:40:1:0,1:3,36:39,1:0.025:2,0:19:0:33:0:1:0:60:2:0.025:0:2 +12 43954690 . C T 59 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCATTGGTTCTCACAAAG;RSEQ=GTGCTTCTCTGAATGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:18.3:1:28.3:1:1:0:60:6:1:0:1 1/1:4:4:3,1:0,0:0,4:1:0,2:22.5:1:29.8:1:1:0:54:8:1:0:1 +12 43954956 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.56437;LSEQ=CTTGTGGGGCACTCTTTTTT;RSEQ=AACAGTATCTATTCCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:1:0,1:37,68:105,1:0.0094:2,0:14:0:30:0:1:0:60:2:0.0095:0:1 0/1:136:2:1,1:51,83:134,2:0.0147:2,2:39.5:1:29:1:1:1.62:60:4:0.0152:0:1.5 +12 43955005 . C T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13083;SOR=0;LSEQ=ATATCACCTTTCTTATAGAT;RSEQ=CGCATATATGTGGCCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:7,21:0,0:0,28:1:0,2:16.3:1:31.3:1:1:0:37.5:56:1:0:1.1 1/1:38:34:9,25:2,2:4,34:0.8947:2,2:20.5:1:28.8:1:0.56411:2.69323:34.8:68:0.8947:0:1 +12 46121662 . T A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCCTGGGTTGTCAGGA;RSEQ=CTTCCTAGCCACAACCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:27:1:1:0:60:4:1:0:1.5 +12 46123143 . G A 79 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCATCGGCTCGCCTTGCCC;RSEQ=TCGCCCGCTCGCGCGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:4,3:0,0:0,7:1:0,2:32.7:1:28.3:1:1:0:60:14:1:0:1.1 +12 46123558 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1199;SOR=0;LSEQ=GGCTCTGGTAGGAAGCGCTG;RSEQ=GAGCGGGGGGCGCTTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:147,38:185,2:0.0106:2,2:24.5:1:30:0:0.3745:3.83147:60:4:0.0108:0:1 0/0:354:0:0,0:262,92:354,0:0:2,0:23.9:1:30.2:1:1:0:60:87.5:1:0:0.1 +12 46123788 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1563;SOR=0;LSEQ=CCGCCCGGGCCGGGCACGGG;RSEQ=TCCCGGCTGACAAGTGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:0,2:85,92:177,2:0.0112:2,0:21:1:28.5:1:0.49846:0:60:4:0.0114:0:1 0/0:273:0:0,0:147,124:271,0:0:2,0:23.2:1:30.7:1:1:0:60:66.75:1:0:0.1 +12 46123810 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05472;SOR=0;LSEQ=CCCGGCTGACAAGTGCGGGG;RSEQ=TTTTTCTCTCCCGCAGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:1,2:116,76:192,3:0.0154:2,2:12.3:1:28:1:0.56502:3.03496:60:6:0.0156:0:1.3 0/0:317:0:0,0:198,119:317,0:0:2,0:25:1:31:1:1:0:60:34.222:1:0:0.1 +12 46123959 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10079;SOR=0;LSEQ=TTGTATTTCCCTCTCGCTGG;RSEQ=CTCCTCCAAAAAGTCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:48,124:172,2:0.0115:2,2:27:1:29:1:0.48508:2.57:60:4:0.0115:0:1 0/0:373:0:0,0:125,248:373,0:0:2,0:22.5:1:30.2:1:1:0:60:40.444:1:0:0.1 +12 46123990 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52432;SOR=Inf;LSEQ=AAGTCTCCTTTGACCCCGGA;RSEQ=TGGGCGCTTGGGGCTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:11,92:103,0:0:2,0:23.8:1:32.3:1:1:0:60:206:1:0:0.1 0/1:164:2:1,1:28,133:161,2:0.0122:2,2:7.5:1:27:1:0.32508:4.68:60:4:0.0125:0:1.5 +12 46124911 . A T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51217;SOR=Inf;LSEQ=GATGCCTTAGGTATCTACAG;RSEQ=TCTCTGTAGAATGGGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:131,8:139,0:0:2,0:22.6:1:30:1:1:0:60:22.167:1:0:0.1 0/1:194:2:1,1:174,18:192,2:0.0103:2,2:12:1:24.5:1:0.18674:9.43585:60:4:0.0104:0:1 +12 46204991 . CA C 66 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=1.04727;LSEQ=GACAGAGCGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAGAACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:24.8:1:33.4:1:1:0:53.8:8:0.3636:0.0909:0 0/1:8:3:3,0:5,0:5,3:0.375:0,0:25.3:1:32.3:1:1:0:52:6:0.375:0:0 +12 46205132 . T C 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30149;SOR=Inf;LSEQ=TTAGAAAAGGAAAACAAATA;RSEQ=GTGGTGAGAGTTAAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:128,16:144,0:0:2,0:22.2:1:30.9:1:1:0:60:71:1:0:0.1 0/1:257:4:2,2:209,44:253,4:0.0156:2,2:19:1:28.8:1:0.1481:4.70875:60:8:0.0157:0:1 +12 46208438 . A G 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0063;SOR=0;LSEQ=CAAAACTCCATCTCAAAAAA;RSEQ=TAATAAACTTCCCTCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:2,11:0.8462:0,0:28.4:1:33.6:1:1:0:60:22:0.8462:0:1.1 0/0:4:0:0,0:4,0:4,0:0:0,0:10.3:1:30.5:1:1:0:60:8:1:0:0.3 +12 46208593 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12493;SOR=0;LSEQ=GAATTTTTAATTCGCCAAAT;RSEQ=ATTATAATAAATTGGTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:2,0:121,59:180,2:0.011:2,0:25.5:1:33:0:1:0:60:4:0.011:0:1 0/0:332:0:0,0:213,119:332,0:0:2,0:26.7:1:31.2:1:1:0:56.8:65.4:1:0:0.1 +12 46208631 . C A 30 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67524;SOR=0.58632;LSEQ=CTTTCACTGTTATCTGAACT;RSEQ=CCAAATGAAGCAGACTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:3:2,1:126,96:222,3:0.0133:2,2:11:1:27:1:1:1.52:48:6:0.0134:0:1 0/0:382:3:3,0:224,155:379,3:0.0079:2,0:16:1:19.3:1:0.27475:0:50.7:2:0.0053:0:3 +12 46208668 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0477;SOR=0;LSEQ=TTGCTGTTAATGTATGCAGT;RSEQ=TCCTGTCAAATGAAAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:109,128:237,3:0.0125:2,2:11.7:1:28.3:1:1:1.6995:60:6:0.0127:0:1 0/0:420:0:0,0:209,211:420,0:0:2,0:24:1:30.5:1:1:0:59.7:104:1:0:0.1 +12 46209382 . TTG T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=11.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGCATCCTACTTAAAGAGA;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:28.5:1:1:0:60:4:1:0:0 +12 46211214 . T A 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AATGATGGCCAAATGGTATG;RSEQ=ACATTTTGGTATTTTAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:21:1:29.5:1:0.33333:0:60:4:0.3333:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:9:0:30:0:1:0:60:2:1:0:1 +12 46211353 . T TTA 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.23913;SOR=0;LSEQ=TATATTATATTTTATATATA;RSEQ=TATATATATATATTTAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:32,0:32,2:0.0588:1,0:7.5:1:29.9:1:1:0:60:4:0.0606:0.0294:0.5 0/0:35:0:0,0:33,2:35,0:0:2,0:24.8:1:30.3:1:1:0:60:70:1:0:0.2 +12 46211396 . T C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03904;SOR=0.504;LSEQ=TGTTCTGTATTCAAGGGATA;RSEQ=TCACCATAAAGGTATCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:28:20,8:72,10:82,28:0.2545:2,2:20.8:1:31.8:1:0.07198:2.84761:60:27:0.2477:0:1.1 0/1:157:23:19,4:108,26:134,23:0.1465:2,2:24:1:31.1:1:1:1.14:60:46:0.1474:0:1 +12 46211435 . AT A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.16249;SOR=Inf;LSEQ=ATCTTTGATATACTTAAGGT;RSEQ=TTTTTTTCTTTGTTAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:177,64:241,0:0:2,0:24.7:1:31.4:1:1:0:60:482:1:0:0.2 0/1:371:5:4,1:246,120:366,5:0.0135:2,2:15.8:1:30.3:1:1:1.95:60:10:0.0137:0.0054:0.4 +12 46211714 . G GT 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.483;SOR=1.36061;LSEQ=TATATAATTCTTCTGTAAAA;RSEQ=TTTTTTTTTTAAGGTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:13:3,10:27,148:175,13:0.0684:2,2:26.5:1:30.4:1:0.4397:1.64:60:26:0.0695:0:0 0/1:253:23:4,19:43,176:219,23:0.0909:2,2:27.6:1:28.8:1:1:1.15982:60:22:0.0898:0.0079:0.3 +12 46215128 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50024;SOR=Inf;LSEQ=TAGTTTTGTTGTTTTTCCAA;RSEQ=CCTATTATTAAATAATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:72,0:72,0:0:1,0:23.9:1:33.7:1:1:0:60:144:1:0:0.9 0/1:85:2:2,0:77,6:83,2:0.0235:2,0:22.5:1:29:1:1:0:60:4:0.0235:0:1 +12 46215147 . A C 74 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.40552;SOR=3.4664;LSEQ=AGCCTATTATTAAATAATTA;RSEQ=TTGAAAGAATTTATTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:1,0:90,4:94,1:0.0105:1,0:45:0:12:0:1:0:60:0:0:0:5 0/1:140:5:4,1:118,17:135,5:0.0357:2,2:20.2:1:32:1:0.50287:1.72709:60:10:0.0365:0:1 +12 46215163 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08642;LSEQ=ATTAATTGAAAGAATTTATT;RSEQ=CATTTTATTGAATGTACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:134:121:107,14:9,4:13,121:0.903:2,2:23.9:1:28.4:1:0.07521:3.35:60:39.333:0.9008:0:1.1 0/1:196:87:69,18:89,18:107,87:0.4439:2,2:22.2:1:27.4:1:0.57829:1.28814:59.8:42.5:0.4404:0:1.1 +12 46215315 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55696;SOR=Inf;LSEQ=GATTCATTGAGTTACATGCA;RSEQ=CTAAGCCAACAATAGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:31,123:154,0:0:2,0:24:1:32.5:1:1:0:60:76:1:0:0.1 0/1:268:3:1,2:67,198:265,3:0.0112:2,2:11.3:1:27.7:1:1:1.48:60:6:0.0114:0:1 +12 46215342 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54044;SOR=Inf;LSEQ=CAACAATAGATCAGTGGTTG;RSEQ=TTATTTAATATACATAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:11,73:84,0:0:2,0:23.4:1:32.8:1:1:0:60:41:1:0:0.1 0/1:153:2:0,2:21,130:151,2:0.0131:2,0:30.5:1:28.5:1:1:0:55.5:4:0.0132:0:4.5 +12 46230031 . C T 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATGGGGTCTCACTCTTC;RSEQ=GCCCAGGCTGGAGTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:14.3:1:32.5:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 46230789 . G A 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06872;SOR=Inf;LSEQ=GCTGAGGTAAGCATGTGACT;RSEQ=TACCTTAAACTAGTTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:60,205:265,0:0:2,0:23.5:1:32.2:1:1:0:59.8:52:1:0:0.2 0/1:329:5:4,1:83,241:324,5:0.0152:2,2:8.2:1:24.6:1:0.01848:11.51:60:10:0.0154:0:1 +12 46231546 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16021;SOR=0;LSEQ=TGAGTAAAAGTGTTTAATAT;RSEQ=GTACTGTACAAAACCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:42,110:152,2:0.013:2,2:32.5:1:30.5:1:0.48179:2.60:60:4:0.0134:0:1 0/0:230:0:0,0:58,172:230,0:0:2,0:22.1:1:30.4:1:1:0:60:229:1:0:0.1 +12 46240570 . T TA 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.65104;SOR=2.5233;LSEQ=GTTAATGGGTTCAATATCCA;RSEQ=AAAAAAAAGTATGGCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:1,0:69,7:76,1:0.013:2,0:30:0:25:0:1:0:60:2:0.0135:0:1 0/1:124:4:3,1:106,14:120,4:0.0323:2,2:35.5:1:28:1:0.40698:2.49808:60:8:0.0323:0:0 +12 46240594 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12511;SOR=0;LSEQ=AAAAAGTATGGCAAATAGTG;RSEQ=CTAACTTTTAAGAAATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:99,21:120,2:0.0164:2,2:43.5:1:30.5:1:0.32936:4.62913:60:4:0.0167:0:1.5 0/0:222:0:0,0:169,53:222,0:0:2,0:22.6:1:28.7:1:1:0:60:444:1:0:0.1 +12 46240638 . G T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01393;SOR=0;LSEQ=CTAATGTATTTTTTTCTTTA;RSEQ=CTTCCAGAGCAGTTGTAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:4:2,2:174,81:255,4:0.0154:2,2:28:1:27:1:0.59529:2.14124:60:3:0.0118:0:1 0/0:492:0:0,0:311,181:492,0:0:2,0:23.2:1:31.5:1:1:0:60:163:1:0:0.1 +12 46240657 . C T 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09891;SOR=Inf;LSEQ=AGCTTCCAGAGCAGTTGTAG;RSEQ=GCAGCATGTTGCTCCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:190,121:311,0:0:2,0:26.3:1:31.3:1:1:0:60:76.75:1:0:0.1 0/1:591:6:2,4:341,244:585,6:0.0102:2,2:17.5:1:26.8:1:0.2438:2.79024:60:12:0.0103:0:1 +12 46240661 . G T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01321;SOR=0;LSEQ=TCCAGAGCAGTTGTAGCGCA;RSEQ=CATGTTGCTCCACCTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:4:2,2:190,125:315,4:0.0125:2,2:27.8:1:31.5:1:0.65167:1.51791:60:8:0.0127:0:1.3 0/0:619:0:0,0:362,257:619,0:0:2,0:25.4:1:31.3:1:1:0:60:87.429:1:0:0.1 +12 46240772 . G GA 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.16642;SOR=Inf;LSEQ=CTTGGGAGGAGTAAAGCAAA;RSEQ=AAAAAAAGGAAATGTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:46,135:181,0:0:2,0:23.7:1:32.2:1:1:0:59.9:180:1:0:0.1 0/1:329:5:3,2:87,237:324,5:0.0152:2,2:23.2:1:27.4:1:0.12826:4.07:60:10:0.0153:0.003:0.2 +12 46242781 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12681;SOR=0;LSEQ=CCATAGTTCTTTAAATAAAG;RSEQ=CCATTTACGTCACTTACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:30,104:134,2:0.0147:2,2:40:1:31:1:0.40523:3.43:60:4:0.0149:0:1 0/0:245:0:0,0:67,178:245,0:0:2,0:23.1:1:28.2:1:1:0:60:48:1:0:0.1 +12 46242790 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13944;LSEQ=TTTAAATAAAGTCCATTTAC;RSEQ=TCACTTACAACATCTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:1:0,1:19,91:110,1:0.009:2,0:25:0:27:0:1:0:60:2:0.0091:0:1 0/1:195:2:1,1:46,147:193,2:0.0103:2,2:10:1:27.5:1:0.4249:3.17:60:4:0.0104:0:1 +12 46243742 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53221;SOR=Inf;LSEQ=TAATTTCTTAAAACTATTTT;RSEQ=TCTTAAGTAAAATAATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:53,14:67,0:0:2,0:23.1:1:32.2:1:1:0:60:21.333:1:0:0.1 0/1:115:2:1,1:93,20:113,2:0.0174:2,2:22.5:1:27.5:1:0.33318:4.56229:60:4:0.0177:0:1 +12 46243835 . A T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10606;SOR=0.16161;LSEQ=TCAGGAATCCCTCATGGATC;RSEQ=CAAACCATAGGAAACCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:1,2:161,74:235,3:0.0126:2,2:8.7:1:28:1:0.23979:4.32166:60:6:0.0128:0:1 0/0:487:1:0,1:306,180:486,1:0.0021:2,0:1:0:23:0:0.37166:0:60:2:0.0021:0:1 +12 46246569 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.093;SOR=0;LSEQ=GCTGCAGCGCAACAATGGTT;RSEQ=CTGTGCCAGCAGGAGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:71,121:192,2:0.0103:2,2:31:1:28:1:1:1.70:60:4:0.0104:0:1 0/0:441:0:0,0:179,262:441,0:0:2,0:23.6:1:31.3:1:1:0:60:219.5:1:0:0.1 +12 46254499 . CAT C 158 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.00181;SOR=0.34887;LSEQ=ATGGTAGAAATGTATAACAA;RSEQ=AATCAAATTTATAAGACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:30:27,3:81,3:84,30:0.2632:1,2:19.6:1:32.2:1:0.18559:2.96569:60:60:0.2655:0.0789:0 0/1:154:17:16,1:127,10:137,17:0.1104:2,1:22.1:1:30.4:1:1:1.26:60:34:0.1118:0.026:0.1 +12 46254505 . C G 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=GAAATGTATAACAACATAAT;RSEQ=AAATTTATAAGACTATACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:11:11,0:98,10:108,11:0.0924:2,0:29.1:1:32.8:1:0.59561:0:59.1:22:0.0932:0:1.1 0/0:177:0:0,0:157,19:176,0:0:2,0:21.8:1:30.3:1:1:0:59.9:24.143:1:0:0.1 +12 46285536 . A T 33 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2563;SOR=Inf;LSEQ=AATATACTTGAATACATCCA;RSEQ=GTGTCTACTACTTTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:160,55:215,0:0:2,0:25.3:1:30.8:1:1:0:60:214:1:0:0.1 0/1:264:3:0,3:183,78:261,3:0.0114:2,0:6:1:21.3:1:0.02814:0:60:2:0.0077:0:1 +12 46286262 . C CAT 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTCATATCTTGTCATTAT;RSEQ=ATATATATATATATACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:32.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 46287120 . G T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5053;SOR=Inf;LSEQ=TTAAAATAACCAGCTTAAAG;RSEQ=GGTTGGCAGGGTGGTCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:73,2:75,0:0:1,0:24.2:1:31.6:1:1:0:59.7:150:1:0:0.1 0/1:97:2:2,0:92,2:94,2:0.0206:1,0:5.5:1:29:1:1:0:60:4:0.022:0:1 +12 46287390 . C CT 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.08904;SOR=Inf;LSEQ=GTATGATTTAGATCTTTATT;RSEQ=TTTTTTTTCCTTTCTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:152,151:303,0:0:2,0:23.7:1:32.4:1:1:0:59.9:59.6:1:0:0 0/1:505:6:2,4:266,232:498,6:0.0119:2,2:20.8:1:28:1:0.42567:2.28944:60:12:0.012:0.004:0.5 +12 46287550 . A G 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTGAATTTAGTTTATTTT;RSEQ=TTTTTACATATAAGTTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:13:3,10:25,88:113,13:0.1032:2,2:29.5:1:29.3:1:1:1.06:59:5.5:0.0894:0:1.2 0/0:210:0:0,0:61,149:210,0:0:2,0:22.5:1:29.2:1:1:0:60:104:1:0:0.1 +12 46298916 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50179;SOR=Inf;LSEQ=GTCAGCCACATTTCACATAC;RSEQ=GTTACTGAAGAAAGCACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:38,130:168,0:0:2,0:24.1:1:30.6:1:1:0:60:32.6:1:0:0.1 0/1:197:2:1,1:36,159:195,2:0.0102:2,2:23:1:26:0:0.34114:4.37:60:4:0.0103:0:1 +12 46298934 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49961;SOR=Inf;LSEQ=ACTGTTACTGAAGAAAGCAC;RSEQ=AAGTCTTAATGGAACAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:16,98:114,0:0:2,0:23.1:1:32.6:1:1:0:60:113:1:0:0.1 0/1:128:2:1,1:11,115:126,2:0.0156:2,2:8.5:1:29:1:0.17938:10.05:60:4:0.0159:0:1 +12 46515942 . C CT 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.05636;SOR=3.19211;LSEQ=AGAATGAACCAATGGACTTA;RSEQ=GACTTACATTACGAACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:5:5,0:61,2:63,5:0.0735:1,0:37.4:1:32.6:1:1:0:60:10:0.0758:0:0.2 0/1:54:11:11,0:43,0:43,11:0.2037:1,0:23.9:1:31:1:1:0:60:22:0.2037:0.037:0 +12 46516045 . A G 222 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCTCTACATGCAAAATA;RSEQ=CATTGTTACATGTGCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:322,178:500,0:0:2,0:24:1:30:1:1:0:60:70.429:1:0:0.1 0/1:678:141:88,53:340,195:535,141:0.208:2,2:23.9:1:31.2:1:0.8444:1.05003:60:69.5:0.2087:0:1.4 +12 46516129 . C A 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.02311;LSEQ=ATGTTAACTGGCAGGGACTA;RSEQ=GTAATTATGGGACTAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:698:40:18,22:295,363:658,40:0.0573:2,2:25:1:31:1:1:1.01:60:19:0.0555:0:1.1 1/0:943:518:240,278:182,242:424,518:0.5493:2,2:24.1:1:29.6:1:0.32331:1.15:60:171.667:0.552:0:1.2 +12 46516197 . G A 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATTTTTATGAAAGACAAAAT;RSEQ=AAAAGGGACACAATGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:62,233:295,0:0:2,0:24.2:1:32.1:1:1:0:60:294:1:0:0.1 0/1:305:18:5,13:55,231:286,18:0.059:2,2:29:1:29.9:1:0.36629:1.61:60:36:0.059:0:1.5 +12 46955238 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14634;SOR=0;LSEQ=GCTCAGAAGATATCACTAAA;RSEQ=AAGCCGAACACGGTGGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:73,125:198,2:0.01:2,2:12:0:31.5:1:1:1.71:42:4:0.0102:0:1 0/0:322:0:0,0:129,193:322,0:0:2,0:21:1:30.4:1:1:0:57.2:63.4:1:0:0.2 +12 46955268 . T C 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2757;SOR=Inf;LSEQ=ACGGTGGTGCATGCCTATAG;RSEQ=CCCAGCTATTCAGGAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:16,74:90,0:0:2,0:21.2:1:29.7:1:1:0:56.5:21.5:1:0:0.2 0/1:134:3:0,3:32,97:129,3:0.0224:2,0:8.7:1:25.7:1:1:0:60:2:0.0152:0:1 +12 46955302 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49833;SOR=Inf;LSEQ=GAGGCCAAGACGGGAGGATT;RSEQ=CTTGAGCCCAGGAATTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:0,42:42,0:0:1,0:30.7:1:32.7:1:1:0:49.2:41:1:0:0.1 0/1:50:2:0,2:0,48:48,2:0.04:1,0:25:1:31:0:1:0:49.5:4:0.04:0:1 +12 46955381 . CA C 30 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=AAAACAAAACAAAAAACAAC;RSEQ=AAAAAAAAAAAAATAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,3:3,2:0.3333:0,0:37.5:1:30.5:1:1:0:29:4:0.3333:0:0.5 0/0:9:0:0,0:0,9:9,0:0:0,0:36.6:1:31.8:1:1:0:34.8:18:1:0:0.3 +12 49027335 . C T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=2.61246;LSEQ=TTGACCCTTGCCATACCCTC;RSEQ=GTGTTACAGAAATCATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:10.2:1:31.8:1:1:0:60:10:0.7143:0:1 1/1:8:7:6,1:1,0:1,7:0.875:0,2:27:1:29.9:1:1:0:60:6:0.8571:0:1.6 +12 49027446 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTGTTGCTGTCGCTGCTG;RSEQ=TGCTGTCGCTGCTGCTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:15,17:32,0:0:2,0:25.2:1:29.7:1:1:0:60:64:1:0:0.2 0/1:72:2:1,1:35,34:69,2:0.0278:2,2:48:0:32:1:1:1.029:60:4:0.029:0:1 +12 49208028 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49479;SOR=Inf;LSEQ=GTCTCCATGAAGGGGGGTCC;RSEQ=TCTCTCCCCGCCCCAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:14,28:42,0:0:2,0:26:1:30.6:1:1:0:60:20:1:0:0 0/1:45:2:1,1:20,23:43,2:0.0444:2,2:16:0:31:0:1:1.15:60:4:0.0455:0:1.5 +12 49209368 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGCGGGCGTGGGGCGAGG;RSEQ=CAGGCGTGCAGGCGGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:21:1:29.5:1:1:1:60:4:0.5:0:1 +12 49413580 . T TA 28 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGTTGAGGAAGCAGCTT;RSEQ=AAAAAAAAAAAATCTCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:28.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 49413694 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCCTCCAGCAGGCCCGC;RSEQ=CGTCCACCACCACCAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:26.5:1:29:1:1:1:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 49415492 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.22353;SOR=Inf;LSEQ=GGCTCTGGCTGCTACCTCTC;RSEQ=TCCCCCTCATCCCTTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:174,44:218,0:0:2,0:22.6:1:31.8:1:1:0:59.9:108:1:0:0.1 0/1:196:2:1,1:149,45:194,2:0.0102:2,2:40:1:31.5:1:0.41523:3.28587:60:4:0.0103:0:1 +12 49415498 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10908;SOR=Inf;LSEQ=GGCTGCTACCTCTCTTCCCC;RSEQ=TCATCCCTTTCAGGGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:193,54:247,0:0:2,0:22.8:1:31.5:1:1:0:59.9:60.75:1:0:0.1 0/1:227:3:2,1:164,59:223,3:0.0132:2,2:8.3:1:27.3:1:1:1.38766:60:6:0.0133:0:1.3 +12 49415513 . G T 59 v3;p8;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03102;SOR=Inf;LSEQ=TCCCCCTCATCCCTTTCAGG;RSEQ=AAGAGGTTGTGGGTAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:233,80:313,0:0:2,0:24.1:1:31.6:1:1:0:59.9:155.5:1:0:0.1 0/1:335:6:0,6:221,107:328,6:0.0179:2,0:5.3:1:23.2:1:0.00137:0:60:12:0.0182:0:1 +12 49416046 . TC T 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.4162;LSEQ=GGGACCACTAAATCCCTCCT;RSEQ=CTCGTCATCTCTCACCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1200:519:274,245:327,354:681,519:0.4325:2,2:29.6:1:32.8:1:0.10318:1.21:60:1038:0.435:0.0175:0.2 0/1:1242:299:150,149:496,447:943,299:0.2407:2,2:26.3:1:30.5:1:0.4659:1.10213:59.8:298:0.2425:0.0362:0.2 +12 49416292 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52549;SOR=0;LSEQ=CCCACCACAGCTTTCCTCCT;RSEQ=CTCTCCTGTGACCAATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:141,37:178,2:0.0111:2,2:26:1:30.5:1:0.37858:3.77366:60:4:0.0114:0:1 0/0:112:0:0,0:93,19:112,0:0:2,0:23.6:1:31.7:1:1:0:60:55:1:0:0.1 +12 49416696 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22005;SOR=Inf;LSEQ=CCATGACAAGACAGCTCTCC;RSEQ=TCAGACCAAGTACATACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:45,174:219,0:0:2,0:21.8:1:32.5:1:1:0:59.9:42.8:1:0:0.1 0/1:194:2:1,1:42,150:192,2:0.0103:2,2:21:1:28.5:1:0.39506:3.54:60:4:0.0105:0:1 +12 49418267 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53668;SOR=0;LSEQ=TCCCCATTTTCTCCACGGGA;RSEQ=CTCTGATCTGTATCCTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:129,9:138,2:0.0143:2,2:21.5:1:30.5:1:0.13823:13.65041:60:4:0.0145:0:1 0/0:79:0:0,0:69,10:79,0:0:2,0:25.5:1:29.2:1:1:0:60:78:1:0:0.1 +12 49418291 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18264;SOR=Inf;LSEQ=TGATCTGTATCCTAAATCCT;RSEQ=ATAATGGGACCAGAGGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:164,38:202,0:0:2,0:24.2:1:32:1:1:0:60:66.333:0.995:0:0.1 0/1:152:2:1,1:123,27:150,2:0.0132:2,2:11.5:1:27:1:0.33548:4.49163:60:4:0.0133:0:1 +12 49418435 . A C 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCATGAGTGGCAGCTCCAT;RSEQ=AGGGGGTGGCGCCCATAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:0:0,0:283,305:588,0:0:2,0:25.2:1:29.6:1:1:0:60:195:1:0:0.1 0/1:511:40:20,20:215,255:470,40:0.0783:2,2:25.4:1:30.9:1:0.62364:1.19:60:39:0.0778:0:1.1 +12 49418727 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0849;SOR=Inf;LSEQ=CTCAATGATGCGATTCCACA;RSEQ=GGCTAAGAAGCAGGGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:106,260:366,0:0:2,0:25.7:1:30.5:1:1:0:60:182:1:0:0.1 0/1:288:3:1,2:70,214:284,3:0.0104:2,2:32.7:1:28.7:1:0.57517:1.53:60:6:0.0107:0:1.3 +12 49418788 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12971;SOR=Inf;LSEQ=TCTGCTCACTGACCTCCAGT;RSEQ=CCTAACCCCAATCCAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:14,145:159,0:0:2,0:22.4:1:30.7:1:1:0:59.9:21.714:1:0:0.2 0/1:90:2:1,1:12,76:88,2:0.0222:2,2:21.5:1:28:1:0.26941:6.12:60:4:0.0227:0:1 +12 49419677 . G C 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTAGGTTGGGTGAGGCA;RSEQ=ATGATAGTCTCAGAACTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:13.5:1:34:0:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 49421160 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17497;SOR=Inf;LSEQ=TCCTCATCTAACTAGCTCCC;RSEQ=CCTTCCCCTCACCCATATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:25,169:194,0:0:2,0:22.5:1:29.9:1:1:0:59.8:37.8:1:0:0.7 0/1:140:2:1,1:20,118:138,2:0.0143:2,2:20.5:1:27:1:0.27842:5.78:60:4:0.0149:0:1.5 +12 49421179 . G C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTTCCCCTCACCCATAT;RSEQ=CCACCCTCCCAAAAGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:135:135:7,128:0,0:0,135:1:0,2:25.6:1:31.6:1:1:0:59.7:134:1:0:1.1 1/1:93:93:5,88:0,0:0,93:1:0,2:24.7:1:30.3:1:1:0:59.9:30:1:0:1.1 +12 49421241 . CT C 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.13819;LSEQ=CCTCTTTTTTCTTTTCTTTT;RSEQ=TTTTTTTTTGAGACACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:0,2:7,50:57,2:0.0339:2,0:42.5:1:33.5:1:1:0:60:4:0.0351:0:0 0/1:26:1:0,1:1,24:25,1:0.0385:1,0:49:0:34:0:1:0:60:2:0.0385:0:0 +12 49421368 . G A 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04564;SOR=0;LSEQ=TCAGCCTTTCGAGTAGCTGG;RSEQ=ATTACAGGCACGCACCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:15:12,3:9,3:12,15:0.5556:2,2:30.5:1:31.1:1:1:1.32:59.4:30:0.5556:0:1.1 0/0:5:0:0,0:4,1:5,0:0:2,0:28:1:32.6:1:1:0:56.4:10:1:0:0 +12 49421427 . G A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=TTTTTGTTTTTAGTAGAGAC;RSEQ=GGGTTTCGCCATGTTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:76,1:77,0:0:1,0:22.9:1:30.2:1:1:0:55.3:37.5:1:0:0.2 0/1:45:8:8,0:37,0:37,8:0.1778:1,0:27.4:1:30.1:1:1:0:48.6:16:0.1905:0:1 +12 49421535 . C T 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18065;SOR=3.26326;LSEQ=ATGTGAGCCACCGCGCCTGG;RSEQ=CGGCAGCCCCTTTTTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:2:1,1:317,132:449,2:0.0044:2,2:19.5:1:28.5:1:0.5033:2.39626:60:4:0.0045:0:2.5 0/1:488:7:2,5:321,160:481,7:0.0143:2,2:12.1:1:25.9:1:0.04686:4.99783:60:14:0.0147:0:1.1 +12 49422007 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1956;SOR=Inf;LSEQ=TACCAGCTGGGTGGGGACAA;RSEQ=GACACCTAGAACCCACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:4,124:128,0:0:1,0:23.2:1:31.7:1:1:0:60:41.667:1:0:0.2 0/1:102:2:0,2:4,96:100,2:0.0196:1,0:11:1:31:0:1:0:60:4:0.0202:0:1 +12 49422033 . T G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04833;SOR=Inf;LSEQ=CTAGAACCCACTCCCCAGGG;RSEQ=AGTTCTATCCTATGTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:2,87:89,0:0:1,0:24.9:1:28.1:1:1:0:60:43.5:1:0:0.3 0/1:52:3:0,3:0,49:49,3:0.0577:1,0:19.3:1:32.3:1:1:0:60:6:0.0588:0:1 +12 49422094 . A G 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63785;SOR=0.4721;LSEQ=CTCACAGCAGCCTTTCCCAA;RSEQ=CTGCTGTGGGCACTGACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:1,22:1,14:15,23:0.5897:1,1:24:1:33.4:1:1:1.55221:60:46:0.6053:0:1.1 0/1:5:2:0,2:0,3:3,2:0.4:0,0:36.5:1:33.5:1:1:0:60:4:0.4:0:1 +12 49422519 . T C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20613;SOR=Inf;LSEQ=TAGGTACTCAGTACATGTGC;RSEQ=TGAACGACTACATTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:169,18:187,0:0:2,0:24.7:1:31.9:1:1:0:60:36.4:1:0:0.1 0/1:156:2:1,1:138,16:154,2:0.0128:2,2:23.5:1:26:1:0.2067:8.3964:60:4:0.0128:0:1 +12 49422795 . G A 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGCCTCTCCCCCAGCTTC;RSEQ=GACAACCCAGGTGAACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:258,257:515,0:0:2,0:22.8:1:30.4:1:1:0:60:45.818:1:0:0.1 0/1:431:41:20,21:190,200:390,41:0.0951:2,2:25.5:1:30.2:1:1:1.00:60:82:0.0967:0:1.1 +12 49422826 . A G 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGAACTGGGCCTGGCCCAC;RSEQ=TCCAGAGTAGCACATACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:562:0:0,0:313,249:562,0:0:2,0:25.5:1:30.6:1:1:0:60:79.286:1:0:0.1 0/1:465:25:13,12:232,206:438,25:0.0538:2,2:20.8:1:29.7:1:1:1.03951:58.6:50:0.0545:0:1.9 +12 49422857 . C T 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACATACCTGGGATGCTGGC;RSEQ=CGAGGAATGAGGGGGATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:750:0:0,0:413,337:750,0:0:2,0:25.2:1:30.8:1:1:0:60:34.714:1:0:0.1 0/1:626:38:18,20:312,276:588,38:0.0607:2,2:25.9:1:29:1:0.50774:1.25557:60:76:0.0616:0:1.6 +12 49423300 . G A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09823;SOR=Inf;LSEQ=AGAAAAGTCAGGTGAGGGTG;RSEQ=CCAGGGCTGATGGTACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:66,241:307,0:0:2,0:23:1:31.8:1:1:0:60:22.615:1:0:0.2 0/1:264:3:2,1:65,195:260,3:0.0114:2,2:7.3:1:27.7:1:0.16056:5.95:60:6:0.0114:0:1 +12 49423328 . AT A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50542;SOR=0;LSEQ=TGATGGTACCTTCTCCCAAT;RSEQ=TTTAGGCCTAATTAGCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:19,136:155,2:0.0126:2,2:14.5:1:26:1:0.23926:7.00:60:4:0.013:0.0063:1.5 0/0:125:0:0,0:21,103:124,0:0:2,0:25.7:1:29.6:1:1:0:60:248:0.992:0:0.1 +12 49423925 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16312;SOR=Inf;LSEQ=AAATCAGTCCTGAAAGGGCC;RSEQ=TTCCTACCTCAGGTGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:167,2:169,0:0:1,0:23.6:1:31.3:1:1:0:60:55.333:1:0:0.1 0/1:115:2:1,1:113,0:113,2:0.0174:1,2:38.5:1:30.5:1:0.01739:0:60:4:0.0177:0:1 +12 49424230 . G A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02543;SOR=Inf;LSEQ=TACTCAGGTTATTCTGAGGG;RSEQ=TGGGGGGTGGGGTGTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:185,147:332,0:0:2,0:19.3:1:29.4:1:1:0:58.7:7.737:1:0:0.8 0/1:311:5:5,0:174,131:305,5:0.0161:2,0:13:1:21:1:0.07556:0:60:1.5:0.011:0:1.6 +12 49424259 . G T 57 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19478;SOR=4.49078;LSEQ=GGGGTGTTGTGTGCAAGATG;RSEQ=CATAGGGAGACTGATATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:1:0,1:193,167:360,1:0.0028:2,0:18:0:14:0:0.46537:0:60:0:0:0:2 0/1:324:4:2,2:168,151:319,4:0.0123:2,2:27.8:1:28.8:1:1:1.11221:60:8:0.0132:0:1.3 +12 49424534 . G A 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGATAGCAGGCTCCGTTAG;RSEQ=GGCAGCAGGGACAGCTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:827:0:0,0:383,444:827,0:0:2,0:26.4:1:31.3:1:1:0:60:67.917:1:0:0.2 0/1:670:32:12,20:296,342:638,32:0.0478:2,2:26.7:1:30:1:0.36686:1.44172:60:31:0.047:0:1.1 +12 49424616 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.3349;LSEQ=ATCGCTGTCTTGCACAGCTG;RSEQ=GGGACAGGGTGCCCCCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:562:281:167,114:168,112:280,281:0.5:2,2:22.5:1:30.9:1:0.93146:1.02392:60:34.125:0.4946:0:1.1 0/1:379:95:62,33:155,129:284,95:0.2507:2,2:24.3:1:28.8:1:0.07327:1.56:60:46.5:0.248:0:1 +12 49424873 . TTCTG T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0.00649;SOR=0.5186;LSEQ=CTCCTCAGAGCCCTCATCTC;RSEQ=TCTGACCCAGGCTCACTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:63:24,39:185,292:477,63:0.1165:2,2:25.4:1:30.9:1:1:1.02949:59.7:30.5:0.1144:0.0129:0.1 0/1:391:25:9,16:122,244:366,25:0.0639:2,2:21.9:1:29.9:1:0.82782:1.12:59.6:50:0.0656:0.0102:0.1 +12 49425823 . AGCT A 98 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.29497;SOR=1.9312;LSEQ=GCTGCATGAGGAGTGCCTGT;RSEQ=GCTGCTGCTGCTGAGGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:672:6:6,0:379,287:666,6:0.0089:2,0:27.3:1:33.5:1:0.04066:0:60:12:0.0091:0.0015:0.3 0/1:526:9:7,2:291,223:514,9:0.0171:2,2:22.4:1:31.2:1:0.3119:2.68:60:18:0.0173:0.0019:0 +12 49425978 . T C 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.47048;LSEQ=GGTCCTGGTTTGGGAGGTTG;RSEQ=GGCCCTGTATTATTTTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1406:520:231,289:390,491:881,520:0.3698:2,2:25.2:1:31:1:0.95568:1.01:59.9:73.286:0.3688:0:1.2 0/1:1188:257:121,136:446,484:930,257:0.2163:2,2:24.3:1:30:1:0.83253:1.0357:59.9:41.833:0.2138:0:1.2 +12 49426156 . G A 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07304;SOR=4.2508;LSEQ=GCCCATGGCTTCCTCCACCT;RSEQ=CTGTGTGGAGCAGGCTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:2:2,0:317,252:569,2:0.0035:2,0:11:1:18.5:1:0.50602:0:60:1:0.0018:0:2 0/1:407:6:6,0:216,185:401,6:0.0147:2,0:18.3:1:26:1:0.03396:0:60:12:0.015:0:1.5 +12 49426176 . TTGC T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.01152;SOR=Inf;LSEQ=GCTGTGTGGAGCAGGCTAAC;RSEQ=TGCTGCTGTTGTCCTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:584:0:0,0:357,227:584,0:0:2,0:24.4:1:30.6:1:1:0:60:82.429:1:0:0.1 0/1:407:5:3,2:242,160:402,5:0.0123:2,2:22:1:30.2:1:1:1.00831:60:10:0.0124:0.0025:0.4 +12 49426460 . A G 205 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=148.14282;LSEQ=ACCCAGGGCTCCAGGGCTAG;RSEQ=AAAGTGTTGAAGAGGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1362:1:0,1:729,630:1359,1:7e-04:2,0:2:0:16:0:0.46397:0:60:0:0:0:1 0/1:1150:113:60,53:538,497:1035,113:0.0983:2,2:24.7:1:30.2:1:0.84332:1.05:60:55.5:0.0975:0:1.3 +12 49426669 . AGCT A 78 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.33825;SOR=2.0559;LSEQ=GTTGCTGCTGCTGTTGTTGA;RSEQ=GCTGCTGCTGTTGCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:4:1,3:187,446:633,4:0.0063:2,2:25.3:1:30.5:1:1:1.25739:60:8:0.0064:0.0016:0.3 0/1:469:6:2,4:123,339:462,6:0.0128:2,2:19.7:1:30.2:1:0.66013:1.38:60:12:0.0131:0.0064:1.3 +12 49426729 . AGCT A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.84071;SOR=0.87057;LSEQ=GAAGTTGCTGTTGCTGTTGT;RSEQ=GCTGCTGCTGCTGCTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:16:6,10:187,226:413,16:0.0371:2,2:30.8:1:33.7:1:0.61529:1.37804:60:32:0.0381:0.0023:0 0/1:308:10:4,6:141,155:296,10:0.0325:2,2:27.9:1:29.3:1:0.75328:1.36315:58.9:9:0.0296:0:0.5 +12 49426771 . AGCT A 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=1;SOR=1.01392;LSEQ=GAAGTTGCTGTTGCTGTTGC;RSEQ=GCTGCTGCTGCTGAAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:12:6,6:273,200:473,12:0.0247:2,2:25.8:1:30.9:1:0.76891:1.36409:60:11:0.023:0.0062:0.2 0/1:319:8:5,3:179,131:310,8:0.0251:2,2:30.4:1:32:1:1:1.22:60:16:0.0254:0:0 +12 49426905 . TTGC T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.13008;SOR=1.68824;LSEQ=CCTTGCTGTTGGTGCTGTTG;RSEQ=TGCTGCTGCTGCTGGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:775:15:5,10:357,401:758,15:0.0194:2,2:25.3:1:30.8:1:0.31183:1.77927:60:30:0.0197:0:0.1 0/1:651:21:9,12:311,315:626,21:0.0323:2,2:26.5:1:29.2:1:0.65872:1.31584:57.6:42:0.0331:0.0046:0.4 +12 49426945 . A G 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGACCAGCCTGTGTCCC;RSEQ=TAAGGCCCTGACCCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:324,396:720,0:0:2,0:24.6:1:30.7:1:1:0:59.9:89:1:0:0.2 0/1:578:18:7,11:248,311:559,18:0.0311:2,2:23.8:1:30.2:1:0.81048:1.25262:60:36:0.0319:0:1.2 +12 49427265 . TTGC T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.79886;SOR=1.18932;LSEQ=AGAAGGTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:9:3,6:230,341:571,9:0.0155:2,2:25.4:1:30.1:1:0.74656:1.3483:60:18:0.0156:0.0034:0 0/1:381:7:5,2:168,206:374,7:0.0184:2,2:19.6:1:28.5:1:0.25253:3.06:60:14:0.0185:0.0052:0 +12 49427652 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12619;SOR=0.83123;LSEQ=AGAGCCAGCACAGCTGAGTG;RSEQ=TGTTGCTGTTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:270:149,121:193,171:364,270:0.4259:2,2:23.8:1:29.4:1:0.62894:1.09:59.8:37.571:0.4249:0:1.2 0/1:569:217:118,99:196,155:351,217:0.3814:2,2:23.2:1:28.6:1:0.7945:1.06078:59.6:53.25:0.3824:0:1.2 +12 49427664 . TTGC T 90 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=0.91959;LSEQ=GCTGAGTGCTGTTGCTGTTG;RSEQ=TGCTGCTGCTGCTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:7:4,3:369,325:694,7:0.01:2,2:23.4:1:32.1:1:1:1.17:60:14:0.0101:0.0014:0.9 0/0:652:6:3,3:337,309:646,6:0.0092:2,2:36.8:1:30.2:1:1:1.09046:60:12:0.0093:0:0.7 +12 49427679 . C T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=3;SSF=0.01381;SOR=2.50341;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGTTGTTGCTGCTGCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:10:6,4:406,352:758,10:0.013:2,2:29.2:1:30.4:1:0.75887:1.30:60:20:0.0132:0:1.9 0/1:719:23:13,10:359,337:696,23:0.032:2,2:25.5:1:28:1:0.67705:1.22:60:22:0.031:0:1.4 +12 49427789 . C T 125 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=3e-05;SOR=8.83423;LSEQ=GGTCAGGCTGGGGCATGCTC;RSEQ=CCCCATGCCAACCCTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:895:3:1,2:494,397:891,3:0.0034:2,2:15.3:1:23.7:1:0.58897:2.48618:60:2:0.0023:0:1.7 0/1:727:21:11,10:389,316:705,21:0.0289:2,2:15.9:1:28.5:1:0.82688:1.11893:60:42:0.0294:0:1 +12 49427919 . T C 195 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=130.38932;LSEQ=AGCTTCTCAGCATCAGCTTC;RSEQ=GGGAACTCACGGCCAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1242:1:0,1:584,655:1239,1:8e-04:2,0:7:0:8:0:1:0:60:0:0:0:5 0/1:998:95:47,48:443,459:902,95:0.0952:2,2:26.2:1:29.8:1:1:1.01:60:46.5:0.0943:0:1.2 +12 49428239 . G T 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01626;SOR=8.91072;LSEQ=GGGTTGGGACGAGGCTGGGA;RSEQ=GGATCACCAGCACTCCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:864:1:0,1:458,403:861,1:0.0012:2,0:1:0:29:0:0.46868:0:60:2:0.0012:0:1 0/1:782:8:3,5:397,377:774,8:0.0102:2,2:21.3:1:26.3:1:0.49649:1.75383:60:7:0.0091:0:1.3 +12 49428717 . G A 173 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01971;LSEQ=TCTGCAGCAAATTTGTCCAG;RSEQ=TCTGGAGAGGGGAGAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:747:57:23,34:229,461:690,57:0.0763:2,2:28.5:1:29.8:1:0.30771:1.36:60:13.25:0.0724:0:1.3 0/0:616:1:1,0:238,377:615,1:0.0016:2,0:1:0:23:0:0.38799:0:60:2:0.0017:0:1 +12 49428748 . C A 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01115;SOR=Inf;LSEQ=GGAGAACCAAGTGAGCTGGG;RSEQ=TATGGGGCCAATGCTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:143,373:516,0:0:2,0:24.3:1:32.8:1:1:0:60:56.333:1:0:0.2 0/1:356:5:4,1:105,246:351,5:0.014:2,2:11:1:24.6:1:0.03218:9.31:60:10:0.0141:0:1.2 +12 49428841 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53593;SOR=0;LSEQ=AATGGCACGGCAAGGCAGAA;RSEQ=GACCACTGAATTAGGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:0,80:80,2:0.0244:1,0:32.5:1:32:1:1:0:60:4:0.0256:0:1.5 0/0:46:0:0,0:3,43:46,0:0:2,0:22.5:1:30.6:1:1:0:60:45:1:0:0.2 +12 49430855 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07339;SOR=Inf;LSEQ=CTAGCCTCAGTGCCCATTTA;RSEQ=GGATAACAATAATCACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:154,14:168,0:0:2,0:24:1:33:1:1:0:60:41:1:0:0.1 0/1:122:3:1,2:99,20:119,3:0.0246:2,2:16:1:26:1:0.08346:9.61997:60:6:0.0248:0:1 +12 49431301 . G A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.07126;SOR=Inf;LSEQ=CAGTAGGGAATGCTGCTGCT;RSEQ=CTGTTGCTGCTGCTGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:161,192:353,0:0:2,0:23:1:32.4:1:1:0:59.9:69.6:1:0:0.1 0/1:251:3:3,0:109,139:248,3:0.012:2,0:11.7:1:20.3:1:0.08752:0:60:2:0.0081:0:1.3 +12 49431305 . TTGC T 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0.85739;LSEQ=AGGGAATGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGGGCAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:5:3,2:159,181:340,5:0.0145:2,2:19.8:1:29.6:1:0.6688:1.70:60:10:0.0147:0.0087:0.2 0/1:241:3:1,2:106,130:236,3:0.0124:2,2:31.7:1:27.3:1:1:1.62757:60:6:0.0127:0:0 +12 49431654 . C T 215 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01494;LSEQ=CCATCCGGGTATCCCGGCTG;RSEQ=CCATCATGCTCTGTCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:914:148:81,67:411,355:766,148:0.1619:2,2:24.8:1:29.9:1:0.85721:1.04:59.9:36:0.1609:0:1.2 0/0:696:2:0,2:370,323:693,2:0.0029:2,0:1:0:23.5:1:0.21832:0:60:4:0.0029:0:1 +12 49432840 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09706;SOR=Inf;LSEQ=GCAAGAACATGGGCTTAGGG;RSEQ=AGTGAGGAAGGATAGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:59,99:158,0:0:2,0:23.8:1:32.8:1:1:0:59.3:51.667:1:0:0.1 0/1:72:2:1,1:16,54:70,2:0.0278:2,2:35.5:1:26.5:1:0.41901:3.30:60:4:0.0282:0:1 +12 49433005 . C T 78 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0865;SOR=4.44264;LSEQ=GGAACCTCCTGGAGCCTCAC;RSEQ=GGCTGTTCACATCCATAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:725:2:0,2:434,288:722,2:0.0028:2,0:1:0:25:0:0.16011:0:60:4:0.0028:0:1 0/1:576:7:1,6:332,237:569,7:0.0122:2,2:5.9:1:27.9:1:0.04551:8.37784:60:14:0.0123:0:1 +12 49433406 . C CA 81 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.50081;SOR=0.50657;LSEQ=TCGTAGTCGCTGGCGCTATG;RSEQ=AAAAAAAAGAGAAGAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:7:5,2:275,120:395,7:0.0174:2,2:8.7:1:28.9:1:1:1.09:60:14:0.0181:0.0124:1 0/0:225:2:2,0:136,87:223,2:0.0089:2,0:40:1:30.5:1:0.52357:0:60:4:0.0091:0:0 +12 49434074 . C A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.53729;SOR=1.09022;LSEQ=GCGGGCAGGGCTGCTGGGAA;RSEQ=CCCCCAGCCCCCAGCGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:239:138,101:186,133:319,239:0.426:2,2:23.4:1:30.2:1:0.93098:1.0235:59.7:78.667:0.4245:0:1.1 0/1:351:157:80,77:105,89:194,157:0.4473:2,2:24.9:1:29:1:0.59149:1.13512:60:156:0.4509:0:1.1 +12 49435057 . G T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.04005;SOR=Inf;LSEQ=AGGCACTTGGGCGGGCACCT;RSEQ=GGGTGGGAGCTTGAGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:241,233:474,0:0:2,0:24.3:1:31.5:1:1:0:60:93.8:1:0:0.1 0/1:386:4:2,2:182,199:381,4:0.0104:2,2:17:1:31.3:1:1:1.09:60:8:0.0105:0:1.3 +12 49435814 . C T 150 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=15.3363;LSEQ=GTCAGAGAAGACTTGGCAGG;RSEQ=GACTCCTCCACCTGCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:854:3:1,2:411,439:850,3:0.0035:2,2:13.7:1:26.7:1:1:1.87111:60:6:0.0036:0:1 0/1:662:34:18,16:303,324:627,34:0.0514:2,2:21.5:1:29.6:1:0.60334:1.20:60:68:0.0525:0:1.1 +12 49436066 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02262;SOR=Inf;LSEQ=TGCCACCTGAGCCCGTCCAG;RSEQ=GGCTGTCGGGCTCACCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:72,295:367,0:0:2,0:24.3:1:31.5:1:1:0:60:121.333:1:0:0.1 0/1:234:4:2,2:60,170:230,4:0.0171:2,2:25.5:1:29.3:1:0.28643:2.82:60:8:0.0173:0:1.3 +12 49436153 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28621;SOR=0;LSEQ=AGTCACAGGGCGCAGGGATG;RSEQ=CAAGTCCCACCCCAGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:2,1:44,62:106,3:0.0275:2,2:18:1:31.3:1:0.57207:2.79:60:6:0.0286:0:1 0/0:68:0:0,0:28,40:68,0:0:2,0:23.9:1:30.9:1:1:0:60:21.667:1:0:0.1 +12 49436229 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2902;SOR=0;LSEQ=AGAGGAGGGTCACTAACAAG;RSEQ=GAATGGGGAGGAGCAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:199,33:232,3:0.0128:2,2:12.3:1:29.3:1:0.37563:2.99531:60:6:0.0133:0:1 0/0:145:0:0,0:135,10:145,0:0:2,0:22.3:1:30.7:1:1:0:60:35.25:1:0:0.1 +12 49436235 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56348;SOR=3.13604;LSEQ=GGGTCACTAACAAGGGAATG;RSEQ=GGAGGAGCAGGGGAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:1,0:225,36:261,1:0.0038:2,0:30:0:12:0:1:0:60:0:0:0:2 0/1:168:2:1,1:152,14:166,2:0.0119:2,2:12:1:28.5:1:0.17109:10.52356:60:4:0.0122:0:1 +12 49436248 . G A 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGAATGGGGAGGAGCAGGG;RSEQ=AAGTGCTGCAGGAGTCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:46:41,5:226,54:280,46:0.1411:2,2:23.7:1:29.9:1:0.21623:1.96:60:22:0.1406:0:1.1 0/0:239:0:0,0:198,41:239,0:0:2,0:22.3:1:30.6:1:1:0:60:78.667:1:0:0.1 +12 49436724 . A G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43195;LSEQ=TCAGGTGACACCACAGGTCT;RSEQ=CAAATGATCATGGCCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:160:67,93:79,108:187,160:0.4611:2,2:24.4:1:32.4:1:1:1.0153:59.7:39:0.4561:0:1.1 0/1:230:62:28,34:65,103:168,62:0.2696:2,2:24.5:1:31.6:1:0.44923:1.30:60:124:0.2696:0:1 +12 49437399 . T G 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=GTTGGATTCTCTCACACCAC;RSEQ=CACTCCCACATAACTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:785:0:0,0:503,282:785,0:0:2,0:24.2:1:31.1:1:1:0:60:59.385:1:0:0.1 0/1:655:46:32,14:366,241:607,46:0.0702:2,2:30.5:1:29:1:0.2725:1.50:60:22:0.0681:0:1.1 +12 49438164 . C T 174 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=85.54658;LSEQ=CGCACCACCCCACCACCCCA;RSEQ=AACCCCATCCCAGGACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1221:1:0,1:641,579:1220,1:8e-04:2,0:1:0:24:0:0.47502:0:60:2:8e-04:0:1 0/1:1067:70:40,30:556,441:997,70:0.0656:2,2:23.3:1:28.4:1:0.90108:1.06:60:69:0.0653:0:1.2 +12 49438347 . T C 113 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00011;SOR=19.17564;LSEQ=ATGGAGGCAAATCAGAACTA;RSEQ=AGGCCCTTTTAACCTTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:1:0,1:66,239:305,1:0.0033:2,0:33:0:15:0:1:0:60:0:0:0:3 0/1:202:12:0,12:28,161:189,12:0.0594:2,0:23.7:1:31.6:1:0.38025:0:60:24:0.06:0:1 +12 49438415 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04454;SOR=Inf;LSEQ=TGCCTCAGAGCCACTTAGAC;RSEQ=AGACAGCAGTGCTTAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:162,62:224,0:0:2,0:24.6:1:31:1:1:0:59.7:55:1:0:0.2 0/1:124:3:2,1:93,28:121,3:0.0242:2,2:30.7:1:29:1:0.55368:1.6531:60:6:0.0248:0:1 +12 49438490 . C A 222 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACTCCCAGAGTCACGCTCC;RSEQ=CCTACTCTGCCGCTCCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:611:181:127,54:281,148:429,181:0.2962:2,2:25.7:1:29.7:1:0.30034:1.24:60:44.25:0.2945:0:1.1 0/0:556:0:0,0:359,196:555,0:0:2,0:23.3:1:29.9:1:1:0:60:38.643:0.9982:0:0.2 +12 49438500 . C T 81 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1826;SOR=0.31211;LSEQ=GTCACGCTCCCCCTACTCTG;RSEQ=CGCTCCCTAAGATTCCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:699:7:2,5:440,252:692,7:0.01:2,2:21:1:29.1:1:0.10699:4.35559:60:14:0.0102:0:1 0/0:636:2:0,2:385,248:633,2:0.0031:2,0:12:1:23.5:1:0.15462:0:60:4:0.0032:0:1 +12 49438794 . G A 49 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37558;SOR=0.2741;LSEQ=TCCCTGGATGGAAGCCCCAG;RSEQ=GAAACCAGAACTGCAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:4:2,2:42,202:244,4:0.0161:2,2:17.8:1:24.5:1:0.14578:4.77:60:3:0.0123:0:1.5 0/0:225:1:1,0:43,181:224,1:0.0044:2,0:1:0:22:0:0.19556:0:60:2:0.0046:0:1 +12 49438807 . G A 26 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5848;SOR=2.55536;LSEQ=GCCCCAGGGAAACCAGAACT;RSEQ=CAAGTTTCAACCTATGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:1,0:19,177:196,1:0.0051:2,0:1:0:23:0:0.10152:0:60:2:0.0052:0:1 0/1:155:2:1,1:16,137:153,2:0.0129:2,2:7.5:1:26.5:1:0.20796:8.34:60:4:0.0131:0:1 +12 49439376 . A G 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAAAGCTTGCAATGTGCC;RSEQ=AGCTTGTGCCACTGCACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:31.2:1:30.8:1:1:0:29.6:10:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 49439521 . A G 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27492;SOR=0.58313;LSEQ=CATTGCCCGGGAAGCTGGAG;RSEQ=CCTTGGTTCTAGGCATAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:29:29,0:37,0:37,29:0.4394:1,1:23.7:1:31.9:1:1:0:60:58:0.4394:0:1 0/1:32:10:10,0:22,0:22,10:0.3125:1,0:15.7:1:30.3:1:1:0:60:20:0.3125:0:1.1 +12 49439659 . C T 297 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9716;LSEQ=GAGCTAGACTAGATGATGTC;RSEQ=GACGTCTGGTCTGGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:706:704:443,261:0,1:1,704:0.9972:0,2:26.3:1:31.5:1:0.37163:0:60:351:1:0:1.1 1/1:686:684:391,293:0,0:0,684:0.9971:0,2:26.1:1:30:1:1:0:59.9:113:0.9971:0:1.1 +12 49440635 . AT A 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.13196;SOR=0.19569;LSEQ=AAGAGGTAGAACTTCTTTTT;RSEQ=TTTTTTTTGGAGATGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:6:2,4:8,151:159,6:0.0364:2,2:26.3:1:30.3:1:0.04367:9.14:60:12:0.0375:0.0061:0.3 0/0:137:1:0,1:26,110:136,1:0.0073:2,0:40:0:33:0:1:0:60:2:0.0075:0:0 +12 49441376 . AT A 100 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTCAGCTAATTTTTGTT;RSEQ=TTTTTAGAAGAGACGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:1,9:0.9:0,0:22:1:31.8:1:1:0:56.8:18:0.9:0.3:0.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 49441898 . T A 42 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41322;SOR=2.56762;LSEQ=TGTCCAACTAGATCTCCCCA;RSEQ=CCCACTCAGATCCAGTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:2:1,1:103,342:445,2:0.0045:2,2:13:1:14:0:0.41159:3.31:60:0:0:0:1 0/1:351:4:3,1:90,257:347,4:0.0114:2,2:6.8:1:21.3:1:0.05855:8.50:60:3:0.0089:0:1 +12 49441959 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.1435;SOR=Inf;LSEQ=TTGCGACCAGAGTCAGGAAC;RSEQ=CCATCCCACAGCGTTAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:6,126:132,0:0:1,0:24.3:1:31.3:1:1:0:60:65:1:0:0.2 0/1:81:2:1,1:1,78:79,2:0.0247:1,2:35.5:1:29:1:0.04907:55.56:60:4:0.026:0:2 +12 49442356 . C CA 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.92943;SOR=1.03023;LSEQ=TCTCATTAGCTGGGTATCCC;RSEQ=AAAGTAGGTCCAGTTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:127:119,8:171,21:192,127:0.3981:2,2:28.1:1:30.2:1:0.17054:1.82:60:62.5:0.3968:0.0094:0.1 0/1:227:92:80,12:118,17:135,92:0.4053:2,2:23.7:1:29.8:1:1:1.04102:59.8:184:0.4126:0.1057:0.1 +12 49442511 . TTCC T 101 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.19543;SOR=2.17301;LSEQ=TGCATGGTGTCATCATCTTC;RSEQ=TCCTCCTCCTTACTGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:930:5:2,3:377,544:921,5:0.0054:2,2:14:1:32.3:1:1:1.03948:60:10:0.0055:0.0032:0 0/1:861:10:4,6:345,502:847,10:0.0116:2,2:17.4:1:30.5:1:1:1.03084:53:20:0.0118:0.0058:1.7 +12 49442561 . CAG C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AATGTCAGCAACCTGATGGG;RSEQ=AGAGTTATGGAAAGTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:0:0,0:137,366:503,0:0:2,0:23.1:1:31.5:1:1:0:59.9:61.875:1:0:0.1 0/1:382:42:11,31:95,244:339,42:0.1099:2,2:23.9:1:31.5:1:0.85746:1.09699:60:84:0.1111:0.0052:0.3 +12 49442788 . A G 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05421;SOR=Inf;LSEQ=GACATAGCCAGACAGGCCCT;RSEQ=GACGAGCAGGCAGGTAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:185,17:202,0:0:2,0:26.1:1:28.5:1:1:0:60:66.333:1:0:0.5 0/1:124:3:2,1:105,16:121,3:0.0242:2,2:21.7:1:23:1:0.35998:3.23613:60:2:0.0165:0:2 +12 49442813 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25388;LSEQ=AGCAGGCAGGTAGGCAAGCA;RSEQ=GCAAGGGACTGGCAGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:135:107,28:137,31:168,135:0.4426:2,2:22.9:1:31.2:1:0.66262:1.15591:60:66.5:0.4448:0:1.1 0/1:221:37:29,8:140,44:184,37:0.1674:2,2:24.5:1:30.2:1:0.83508:1.14:60:74:0.1713:0:1.2 +12 49443136 . GA G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49462;SOR=Inf;LSEQ=GAGTCCCACTCAGGGCAAGG;RSEQ=AAAGGCCAAACTCCCAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:5,42:47,0:0:2,0:23.6:1:30.5:1:1:0:60:46:1:0:0.2 0/1:47:2:1,1:1,44:45,2:0.0426:1,2:21.5:1:29.5:1:0.08418:31.47:60:4:0.0435:0.0213:0 +12 49443666 . AC A 90 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.07391;SOR=3.28417;LSEQ=AACTCCATGGACAGGGAGCC;RSEQ=CCCCCTCCGGGTCTGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:947:3:0,3:447,497:944,3:0.0032:2,0:31.3:1:33:0:0.25156:0:60:6:0.0032:0:0 0/1:774:8:3,5:376,390:766,8:0.0103:2,2:22.5:1:30.3:1:0.72561:1.60587:60:16:0.0105:0.0026:0.6 +12 49444545 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.10886;SOR=0.78503;LSEQ=GGTGGGGCCGCAGCTGTGAT;RSEQ=ATGGGTGAGAGTGGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:165:63,102:97,122:219,165:0.4297:2,2:24.9:1:29.8:1:0.25077:1.28642:59.7:54:0.4286:0:1.2 0/1:401:149:58,91:109,143:252,149:0.3716:2,2:28.2:1:28.9:1:0.404:1.19539:59.9:28.8:0.3673:0:1.3 +12 49444932 . CG C 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.21748;SOR=0.20272;LSEQ=ACAGATGCGATTCCTCAGGC;RSEQ=GGGGGACAGGCATGGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:5:3,2:212,282:494,5:0.01:2,2:25.2:1:32.2:1:0.6561:1.99:60:10:0.0101:0:0.2 0/0:492:1:0,1:218,270:488,1:0.002:2,0:17:0:30:0:1:0:60:2:0.0021:0:1 +12 49445028 . G A 131 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=10.87633;LSEQ=CAGGCACAGGAGACAGGTGC;RSEQ=GCTCCTCAGTCTGGGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:2:2,0:304,249:553,2:0.0036:2,0:1:0:26:0:0.50438:0:60:4:0.0037:0:1 0/1:554:21:8,13:297,236:533,21:0.0379:2,2:22.5:1:29.9:1:0.12233:2.0424:60:20:0.0372:0:1.1 +12 49445780 . G A 206 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=75.35248;LSEQ=GCTTCAGGTGGCGGGGAAGT;RSEQ=GGCAATTCCTCAGGTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1920:2:1,1:921,996:1917,2:0.001:2,2:4.5:1:20.5:1:1:1.08:60:1:5e-04:0:1 0/1:1934:141:67,74:863,925:1788,141:0.0729:2,2:22.8:1:28.9:1:0.93029:1.03044:60:282:0.0737:0:1.2 +12 49446040 . C T 198 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=62.40225;LSEQ=TGCCTCAGGAAGTGGGGATG;RSEQ=GGGCAATTCCTCAGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1423:2:0,2:731,690:1421,2:0.0014:2,0:1:0:25.5:1:0.23631:0:60:4:0.0014:0:1 0/1:1460:118:56,62:672,668:1340,118:0.0808:2,2:24.2:1:28.9:1:0.63134:1.11369:59.6:117:0.0817:0:1.3 +12 49447715 . A T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32358;SOR=3.87753;LSEQ=AGTACAAAAATCCAAGGCAC;RSEQ=TTTGGTCTCTCATTTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:0,1:174,70:244,1:0.0041:2,0:1:0:26:0:0.2898:0:60:2:0.0041:0:1 0/1:192:3:0,3:145,44:189,3:0.0156:2,0:12.7:1:21:1:0.01396:0:57.7:2:0.0108:0:2.7 +12 49447863 . G A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01587;SOR=Inf;LSEQ=GCAGGGGAAGTGGTAAAGCC;RSEQ=TGGACATCCAGGTGAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:0:0,0:240,257:497,0:0:2,0:24.6:1:31.1:1:1:0:60:123.25:1:0:0.1 0/1:540:7:3,4:242,290:532,7:0.013:2,2:23.1:1:30.6:1:1:1.1124:60:14:0.0132:0:1.4 +12 49448463 . C T 175 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=70.0353;LSEQ=CAAATGGCAACTCAAAGCGC;RSEQ=GTAGCTCCCGCTGCCCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:882:1:0,1:378,503:881,1:0.0011:2,0:2:0:28:0:1:0:60:2:0.0012:0:1 0/1:895:66:27,39:408,421:829,66:0.0737:2,2:23:1:29:1:0.20312:1.39931:60:32:0.0726:0:1.1 +12 49448590 . G A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0459;SOR=Inf;LSEQ=CCCAGCAACCCCATGATCTG;RSEQ=CATGCCCATGCTTCCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:158,229:387,0:0:2,0:24.9:1:31.8:1:1:0:60:47.375:1:0:0.1 0/1:335:4:3,1:129,202:331,4:0.0119:2,2:14.5:1:26.3:1:0.30426:4.68:60:8:0.0122:0:1.3 +12 50412621 . AT A 33 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAACCTGTTCTCTTGTCC;RSEQ=TTTTTTTTTTTTAATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,0:3,2:0.3333:0,0:44:1:33:0:1:0:60:4:0.3333:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:32:0:1:0:60:2:1:0:0 +12 50412911 . C A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.24554;LSEQ=CCTCTGGTTCCTCCCCTTCC;RSEQ=ACAGCATAATCACTAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:611:570:300,270:21,19:40,570:0.9329:2,2:27.1:1:30.4:1:1:1.01:59.9:50.818:0.9317:0:1.1 1/0:763:590:289,301:90,81:171,590:0.7733:2,2:27.2:1:29.3:1:0.43466:1.15702:60:58:0.7733:0:1.2 +12 50412969 . C G 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTATCTACCATACCCACCC;RSEQ=CTTATCACTTGCAGGTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:162,269:431,0:0:2,0:24.8:1:31.1:1:1:0:60:85.2:1:0:1 0/1:525:45:22,23:177,303:480,45:0.0857:2,2:28.6:1:30.3:1:0.14729:1.64:60:90:0.0865:0:2 +12 50413015 . T G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACTTCAATTGCACTCCCT;RSEQ=CCTCCAGTCCTTCCCCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:217:217:52,165:0,0:0,217:1:0,2:24.5:1:32.1:1:1:0:60:53.25:1:0:1.1 1/1:250:250:67,183:0,0:0,250:1:0,2:22.5:1:31:1:1:0:60:61.5:1:0:1.2 +12 50413034 . C A 97 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01599;SOR=0.1107;LSEQ=TTCCTCCAGTCCTTCCCCTA;RSEQ=TGCTTCAGGCAGTTGCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:8:0,8:19,129:148,8:0.0513:2,0:24:1:32.4:1:0.59685:0:60:16:0.0513:0:2.1 0/0:169:1:1,0:29,139:168,1:0.0059:2,0:1:0:24:0:0.17751:0:60:2:0.0059:0:2 +12 50479374 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49936;SOR=0;LSEQ=CGCGGGCCGGGGGCGGGGCC;RSEQ=AGCGGGGACATGGGAGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:51,137:188,2:0.0105:2,2:39.5:1:30.5:1:0.47352:2.67:60:4:0.0108:0:3 0/0:176:0:0,0:48,128:176,0:0:2,0:25:1:29.6:1:1:0:59.7:34.2:1:0:0.3 +12 50479408 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50582;SOR=0;LSEQ=GAGTGACAGGGGTGGGGGGA;RSEQ=AAGTAGGAGGGACTCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:5,96:101,2:0.0192:1,2:16:1:29:1:0.11365:17.61:60:4:0.0211:0:3 0/0:80:0:0,0:6,74:80,0:0:2,0:21.8:1:29.6:1:1:0:60:10.429:1:0:0.5 +12 50479935 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.07888;LSEQ=GACATCTCTGGGTCCTCTCC;RSEQ=CTCTGTAGAGACCAGGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:39:24,15:477,338:815,39:0.0457:2,2:26.2:1:31.7:1:0.74247:1.13:60:78:0.046:0:1.1 0/1:825:106:58,48:402,317:719,106:0.1285:2,2:25.1:1:29.1:1:0.83462:1.04947:59.9:105:0.1288:0:1.1 +12 50480150 . AGAGG A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=4.000;MSILEN=4;SSF=0.21839;SOR=0.48298;LSEQ=AAGTAAGATGATCCTGGGGC;RSEQ=GAGGGAGGGAGGGAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:11:2,9:101,243:344,11:0.0309:2,2:30.9:1:32.8:1:0.52099:1.86751:60:22:0.0314:0:0.1 0/1:396:6:1,5:138,252:390,6:0.0152:2,2:34.5:1:30.2:1:0.66972:2.7324:60:12:0.0153:0:0 +12 50480262 . T TTGGTGGTGGTGGTGGTGGTGG 132 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=14.000;MSILEN=3;SSF=0.00821;SOR=0.26504;LSEQ=GAACTCATCCTTGAGAATGC;RSEQ=TGGTGGTGGTGGTGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:19:13,6:13,27:40,19:0.2043:2,2:25.4:1:31.3:1:0.0126:4.38:58.7:38:0.2159:0.129:0.1 0/1:79:5:4,1:18,20:38,5:0.0633:2,2:42.2:1:25.6:1:0.34487:4.31:52:10:0.0649:0:0.6 +12 50480308 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21056;SOR=Inf;LSEQ=TCTTTGAGAGAAGCTTTGCA;RSEQ=TCCCTTCACATTACTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:117,31:148,0:0:2,0:21.3:1:33.1:1:1:0:59.4:147:1:0:0.1 0/1:126:2:1,1:97,27:124,2:0.0159:2,2:31.5:1:30:1:0.39644:3.54575:57.5:4:0.016:0:1 +12 50480699 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20333;SOR=Inf;LSEQ=TAGGCAGAGAGCCAAAGGAG;RSEQ=GGACCCAGGAACCTTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:26,167:193,0:0:2,0:21.8:1:31.5:1:1:0:59.9:47.25:1:0:0.2 0/1:159:2:1,1:27,130:157,2:0.0126:2,2:13:0:31.5:1:0.32211:4.75:60:4:0.0126:0:2 +12 50482211 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15497;LSEQ=AGATATTTTTTGAGTTTTTT;RSEQ=CCATTGTTGTTGGGGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:118:79:77,2:38,1:39,79:0.6695:1,1:22.3:1:31.6:1:1:1.01:59.6:25.333:0.6609:0:1.1 0/1:97:23:22,1:71,3:74,23:0.2371:1,1:22.3:1:30.9:1:1:1.07494:60:46:0.2396:0:1.2 +12 50482230 . CT C 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.57541;SOR=2.75615;LSEQ=TTCCATTGTTGTTGGGGTTC;RSEQ=TTTTCATAGGATTTTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:1,0:170,17:187,1:0.0053:2,0:12:0:34:0:1:0:60:2:0.0054:0:0 0/1:138:2:1,1:125,11:136,2:0.0145:2,2:23.5:1:32.5:1:0.16693:10.92357:60:4:0.0145:0:0 +12 50482247 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19109;SOR=Inf;LSEQ=TTCCTTTTTCATAGGATTTT;RSEQ=TCTTGGGAAGTTTCTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:206,38:244,0:0:2,0:24.1:1:32.2:1:1:0:60:243:1:0:0.3 0/1:190:2:1,1:142,46:188,2:0.0105:2,2:31:1:28.5:1:0.43453:3.06455:60:4:0.0107:0:1.5 +12 50482261 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09287;SOR=Inf;LSEQ=GATTTTGTCTTGGGAAGTTT;RSEQ=TTCTGGCCTTTCCTAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:248,77:325,0:0:2,0:24.7:1:31.9:1:1:0:60:45.429:1:0:0.3 0/1:270:3:1,2:173,94:267,3:0.0111:2,2:12:1:29.7:1:0.28862:3.66211:60:6:0.0114:0:1 +12 50483610 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24838;SOR=Inf;LSEQ=AGTCATTACAGAAGCTCTTC;RSEQ=CTCCCACCCCAGCTCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:205,27:232,0:0:2,0:21.7:1:31.4:1:1:0:60:45.4:1:0:0.1 0/1:232:3:1,2:189,40:229,3:0.0129:2,2:20:1:26:1:0.08522:9.31246:60:6:0.0129:0:1 +12 50484013 . G A 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTCATCCCCTATACTTTG;RSEQ=TTCCCTGCAGCCTCCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:779:0:0,0:468,310:778,0:0:2,0:26.1:1:31.6:1:1:0:60:54.571:0.9987:0:0.1 0/1:784:59:38,21:406,318:724,59:0.0753:2,2:23.7:1:29:1:0.22256:1.42:59.7:118:0.0769:0:1.1 +12 50484405 . C T 190 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTGGGAGGCAGTGCTGTGC;RSEQ=GGAGCTGCCTTGTGCCGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:72:15,57:56,206:262,72:0.2149:2,2:26.2:1:30.8:1:1:1.03291:59.9:35:0.2121:0:1.2 0/0:352:0:0,0:112,239:351,0:0:2,0:21.3:1:28.9:1:1:0:59.9:57.5:0.9971:0:0.1 +12 50484460 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=GTCAAATTTTCAGGAATTTT;RSEQ=CAAACAGGTTGTTAAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:2,112:114,2:0.0171:1,0:19:1:32:0:1:0:60:4:0.0174:0:1 0/0:107:0:0,0:5,102:107,0:0:1,0:25.1:1:31.9:1:1:0:59.9:106:1:0:0 +12 50484603 . G A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACATTTTATTGTATTTGT;RSEQ=CTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:7:1:29:1:1:0:60:4:0.4:0:1.5 0/0:2:0:0,0:0,2:2,0:0:0,0:10.5:1:30.5:1:1:0:60:4:1:0:0.5 +12 50485350 . G T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACAGGCGTGAGCCACCGC;RSEQ=CCCGGCCTTTTGTTTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:30.5:1:1:0:60:4:1:0:1 +12 50488458 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12662;SOR=Inf;LSEQ=TCAAAATACGGTGACACCCA;RSEQ=TATATGTCAGGTACTGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:1,123:124,0:0:1,0:22.9:1:32.4:1:1:0:59.7:61:1:0:0.1 0/1:69:2:0,2:1,66:67,2:0.029:1,0:11:1:27.5:1:1:0:60:4:0.0299:0:1.5 +12 50488547 . G A 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90182;LSEQ=TCTCAACAGCACTGAGCCTC;RSEQ=GTTTCTGATTTGTGGAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:0,4:0,36:36,4:0.1:1,0:23.8:1:32.3:1:1:0:60:8:0.1053:0:1 0/1:11:1:0,1:0,10:10,1:0.0909:0,0:4:0:31:0:1:0:60:2:0.0909:0:1 +12 50490554 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19705;SOR=Inf;LSEQ=TAGGTTGGAAGTGGCATGTG;RSEQ=AGTTGTCAGGCACCACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:142,29:171,0:0:2,0:21.8:1:31.2:1:1:0:60:41.75:1:0:0.1 0/1:137:2:1,1:110,25:135,2:0.0146:2,2:30:1:27:1:0.34468:4.33413:60:4:0.0148:0:1 +12 50492873 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09705;SOR=Inf;LSEQ=TATCTGCCTTGGTCTTGCTT;RSEQ=GGGCGTTCCAGGGGATGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:53,261:314,0:0:2,0:22.5:1:31.2:1:1:0:60:61.8:1:0:0.1 0/1:268:3:1,2:63,202:265,3:0.0112:2,2:14.7:1:29:1:0.56051:1.60:60:6:0.0115:0:1 +12 50492911 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50232;SOR=0;LSEQ=CTGTTGGTTCAAGGACAACA;RSEQ=CAGAATGAAGAGGGTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:3,145:148,2:0.0133:1,2:15.5:1:29:1:0.0528:42.03:60:4:0.0134:0:1 0/0:125:0:0,0:6,119:125,0:0:1,0:25.8:1:30.7:1:1:0:60:40.667:1:0:0.1 +12 51491761 . G A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCGAGATCACACCACC;RSEQ=CACAACAGCCTGGGCGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:31:0:1:0:53:4:1:0:1 +12 51493260 . CA C 32 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:2,0:2,2:0.3333:0,0:19:1:32.5:1:1:0:47:4:0.3333:0.1667:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:19:0:31:0:1:0:60:2:1:0:0 +12 51493439 . G T 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10225;SOR=0;LSEQ=TGTGTCCAGAACAACCTACC;RSEQ=AAGAAAGTACCATTTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:3:1,2:89,39:128,3:0.0229:2,2:5:1:27.7:1:0.23067:4.50517:60:6:0.0234:0:1 0/0:148:0:0,0:103,45:148,0:0:2,0:21.9:1:29.4:1:1:0:60:147:1:0:0.1 +12 51493511 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26971;SOR=Inf;LSEQ=TGCTGTTGTTGCTGCTCCCT;RSEQ=AACTGCAGTGATTCCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:87,121:208,0:0:2,0:27.5:1:32.2:1:1:0:59.7:103:1:0:0.1 0/1:292:3:2,1:127,162:289,3:0.0103:2,2:25.7:1:29:1:0.58529:2.54:53:6:0.0104:0:1 +12 51493543 . T A 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.4628;LSEQ=TTCCTGACAAACATAAATGG;RSEQ=TAACCTTGGACGCACCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:1:1,0:40,94:134,1:0.0074:2,0:1:0:25:0:0.3037:0:60:2:0.0074:0:1 0/1:185:2:1,1:60,123:183,2:0.0108:2,2:14.5:1:24.5:1:0.55194:2.04:60:4:0.011:0:1 +12 52401452 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16844;SOR=Inf;LSEQ=AAGGTCCGAGAGCCCCCGGT;RSEQ=GGAGAAGCGGGCCGGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:22,6:28,0:0:2,0:20.4:1:31.4:1:1:0:60:27:1:0:0.1 0/1:20:2:2,0:12,6:18,2:0.1:2,0:11:1:26:1:1:0:60:4:0.1:0:1 +12 52401505 . G C 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50695;SOR=0;LSEQ=TTCTCACTCTGAGGAAGTGC;RSEQ=TGGGGAGCCGCTGACTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:32,31:63,2:0.0308:2,2:16:0:34:1:1:1.03176:60:4:0.0308:0:1.5 0/0:48:0:0,0:25,23:48,0:0:2,0:27.6:1:30.5:1:1:0:60:96:1:0:0.2 +12 52906415 . C A 98 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00109;SOR=0.02184;LSEQ=TTACTCTCCAGCCTGGGCAA;RSEQ=AATAGCAAAACTCTGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:1,9:0.9:0,0:26.3:1:31:1:1:0:41.1:18:0.9:0:2.4 0/1:9:1:1,0:8,0:8,1:0.1111:0,0:18:0:31:0:1:0:22:2:0.125:0:2 +12 52906434 . G A 60 p8;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=0.01542;SOR=0;LSEQ=ACAATAGCAAAACTCTGTAG;RSEQ=AAAAAAAAAAAAAACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:9,0:9,4:0.3077:0,2:6.3:1:30:1:0.07692:0:53:8:0.3333:0:4.5 0/0:21:0:0,0:12,2:14,0:0:2,0:16.6:1:29.5:1:1:0:46.8:6:0.6316:0:1.1 +12 52906449 . C A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00019;SOR=0.12734;LSEQ=TGTAGGAAAAAAAAAAAAAA;RSEQ=AAAAAACCAGAGTGCTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:29:17,12:4,0:4,29:0.8529:0,2:9.7:1:28.5:1:0.27126:0:53.2:13.5:0.871:0:3.5 0/1:36:15:11,4:14,7:21,15:0.4167:2,2:10.9:1:28.4:1:0.72877:1.36:47.4:14:0.4375:0:2.7 +12 52906524 . CA TG 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0716;LSEQ=GCTGCTGTTGCTCCTGTTGC;RSEQ=CCGCTGCCGCTGCCTATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:143:113:46,67:15,11:26,113:0.7902:2,2:30.2:1:31.7:1:0.12974:1.97619:59.9:226:0.8129:0.007:2.4 0/1:100:21:12,9:36,43:79,21:0.21:2,2:30:1:30.6:1:0.46193:1.59:59.2:42:0.2121:0:2.3 +12 52906525 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=17.65784;LSEQ=CTGCTGTTGCTCCTGTTGCC;RSEQ=CCGCTGCCGCTGCCTATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:7:5,2:13,10:23,7:0.049:2,2:19.9:1:27.7:1:0.66932:1.88:60:6:0.2069:0:2.6 0/1:98:47:18,29:14,14:28,47:0.4796:2,2:27.3:1:29.9:1:0.34494:1.60068:59.9:22.5:0.6164:0:1.4 +12 52906534 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15133;SOR=Inf;LSEQ=CTCCTGTTGCCACCGCTGCC;RSEQ=CTGCCTATGCCTCTGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:61,78:139,0:0:2,0:27.6:1:30.9:1:1:0:59.9:278:1:0:2.1 0/1:89:2:1,1:36,50:86,2:0.0225:2,2:17.5:1:27.5:1:1:1.38:60:4:0.0233:0:1 +12 52906536 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0;SOR=0.07438;LSEQ=CCTGTTGCCACCGCTGCCGC;RSEQ=GCCTATGCCTCTGTTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:137:111:46,65:13,12:25,111:0.8102:2,2:27.3:1:29.8:1:0.37655:1.52589:60:222:0.8102:0:2.5 0/1:84:20:11,9:23,41:64,20:0.2381:2,2:26.9:1:29.9:1:0.19144:2.16:59.2:40:0.2381:0:2.5 +12 52906545 . C T 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16033;SOR=0;LSEQ=ACCGCTGCCGCTGCCTATGC;RSEQ=TCTGTTACCAGAAAAGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:5:1,4:53,70:123,5:0.0388:2,2:31:1:31.6:1:0.39615:3.00602:60:10:0.0394:0:1 0/0:75:0:0,0:30,45:75,0:0:2,0:24.3:1:31.1:1:1:0:59.8:150:1:0:1.2 +12 52906586 . G A 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0059;SOR=0.23455;LSEQ=TCATCCTCCGGGTTATAGGA;RSEQ=AAAACACACATGGCACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:37:2,35:0,8:8,37:0.8222:0,2:21:1:31.2:1:1:0:60:36:0.8372:0:2.5 1/0:33:17:2,15:4,12:16,17:0.5152:2,2:20.1:1:30.3:1:0.39832:2.4317:60:34:0.5152:0:2.2 +12 52906763 . G C 53 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.25;SOR=0;LSEQ=CCACAAGAAAGATAGAGAGA;RSEQ=AGAGAGAAACCTGAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:8.3:1:34:1:1:0:60:6:1:0:1.3 0/0:1:0:0,0:0,1:1,0:0:0,0:44:0:33:0:1:0:60:2:1:0:0 +12 52921215 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=27.71131;LSEQ=TCAGCAGAGGCCTCAACCTC;RSEQ=GGATAGTCTGTGAAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:53:37,16:173,99:272,53:0.1631:2,2:26:1:31.3:1:0.4349:1.32:60:52:0.1615:0:1.9 1/1:213:180:111,69:19,14:33,180:0.8451:2,2:27.6:1:29.6:1:0.69995:1.18:60:59:0.8429:0:1.8 +12 52921279 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=21.94958;LSEQ=ACTCAGCAGTCAGTATACCA;RSEQ=AACATCTTCCAGCAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:76:33,43:170,205:375,76:0.1685:2,2:28.1:1:31.9:1:0.80117:1.08034:60:37:0.1667:0:2.4 1/1:323:264:125,139:29,30:59,264:0.8173:2,2:26.1:1:31.4:1:0.88555:1.07468:59.8:87:0.8156:0:2.3 +12 52921294 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=19.77311;LSEQ=TACCATAACATCTTCCAGCA;RSEQ=CCCCAAGAGAGAGGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:74:28,46:146,199:345,74:0.1766:2,2:26.5:1:30.5:1:0.51732:1.20478:60:148:0.1779:0:2.3 1/1:274:222:99,123:24,27:51,222:0.8102:2,2:27.2:1:28.9:1:0.7575:1.10397:59.8:110:0.8118:0:2.3 +12 52921297 . C A 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATAACATCTTCCAGCAGCC;RSEQ=CAAGAGAGAGGGACCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:34:12,22:155,219:374,34:0.0833:2,2:29.7:1:30.2:1:0.58583:1.29675:60:68:0.0848:0:1.2 0/0:272:0:0,0:121,151:272,0:0:2,0:26.6:1:30.1:1:1:0:59.8:67:1:0:1.8 +12 52921334 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14361;SOR=Inf;LSEQ=CTGCCCTGGAGTATAGACAG;RSEQ=GGAGGTGCCCTTGGAGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:76,167:243,0:0:2,0:23.6:1:31.1:1:1:0:60:120.5:0.9918:0:0.5 0/1:150:2:1,1:43,105:148,2:0.0133:2,2:14:1:27:1:0.50201:2.43:60:4:0.0133:0:2 +12 53030453 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.50212;SOR=0;LSEQ=ATCTTTTCCCAGCAGCAGCA;RSEQ=CAGCAACAGCAACAGCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:75,62:137,2:0.0144:2,2:28:1:31.5:1:1:1.20801:60:4:0.0144:0:1 0/0:116:0:0,0:59,57:116,0:0:2,0:27.5:1:29.4:1:1:0:59:115:1:0:0.2 +12 53030489 . C T 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CACGGGTATCATGTATTGCC;RSEQ=GATTATTGTGTTTCACAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:18:7,11:35,54:89,18:0.1682:2,2:27.6:1:29.8:1:1:1.01835:60:17:0.1635:0:1 0/0:92:0:0,0:39,53:92,0:0:2,0:26.6:1:29.5:1:1:0:60:91:1:0:0.3 +12 53030543 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24578;SOR=3.87584;LSEQ=AAAGATAATCTCCTTTAATC;RSEQ=CCACAACAGTACTATGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:35:1,34:0,6:6,35:0.8537:0,1:25.1:1:31.6:1:1:0:60:34:0.85:0:1.1 1/1:24:23:2,21:0,1:1,23:0.9583:0,2:22.2:1:31:1:1:0:60:46:0.9583:0:1 +12 53129862 . T C 34 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTGCCCCCTGTCACGGCA;RSEQ=AGGCCGCAGCAGCACTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28.5:1:34:0:1:0:44.5:4:1:0:1.5 1/1:1:1:0,1:0,0:0,1:1:0,0:33:0:34:0:1:0:60:2:1:0:1 +12 53130248 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28215;SOR=0;LSEQ=CTGACATTGGCCTCATTTTT;RSEQ=CTTCACCAGATCCAAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:1,2:141,40:181,3:0.0163:2,2:12:1:28.3:1:0.13094:6.95219:60:6:0.0168:0:1 0/0:119:0:0,0:87,32:119,0:0:2,0:25.4:1:30.1:1:1:0:60:58.5:1:0:0.2 +12 53130297 . G T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08243;SOR=Inf;LSEQ=TTAGGCTCCCTACAATGGAT;RSEQ=GGCTGCTTCCTACTGGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:201,152:353,0:0:2,0:25:1:31.4:1:1:0:59.8:38.222:1:0:0.4 0/1:273:3:0,3:164,106:270,3:0.011:2,0:16:1:21.3:1:0.06259:0:60:2:0.0075:0:2.7 +12 53130344 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.10162;LSEQ=CAAACATCAGGGCATTTGCT;RSEQ=TAATTAGGTGATTTTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:213:97,116:117,134:251,213:0.4591:2,2:24.3:1:30:1:0.85196:1.04409:59.9:212:0.4599:0:1.1 1/0:337:216:103,113:64,56:120,216:0.6409:2,2:27.9:1:28.4:1:0.36265:1.25296:60:42.2:0.6355:0:1.1 +12 53130451 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13771;SOR=Inf;LSEQ=AAATATTCACAGGAGACCTT;RSEQ=TCTCAGTTAATTGTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:20,91:111,0:0:2,0:20.5:1:32.1:1:1:0:60:110:1:0:0.1 0/1:66:2:1,1:7,57:64,2:0.0303:2,2:21.5:1:26.5:1:0.22937:7.68:60:4:0.0303:0:1 +12 53130531 . T C 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21603;SOR=4.82289;LSEQ=CATCCACTGCGGTGGGGTCC;RSEQ=CGGGATGCAGGGGCCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:23:1,22:0,19:19,23:0.5476:1,1:24.7:1:32.4:1:1:0:60:46:0.5476:0:1 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:22.7:1:31.7:1:1:0:58.3:12:0.8571:0:1 +12 53130533 . G A 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACTGCGGTGGGGTCCTC;RSEQ=GGATGCAGGGGCCATCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:0,5:1,33:34,5:0.1282:1,0:34.2:1:33.4:1:1:0:60:10:0.1282:0:1 0/0:7:0:0,0:0,7:7,0:0:0,0:19.6:1:32.1:1:1:0:58.6:14:1:0:0.9 +12 53607024 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGCTCCTCCAGGTCCATG;RSEQ=GGTCTATGGGGACAAGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:1 0/1:10:2:1,1:2,6:8,2:0.2:2,2:21.5:1:29.5:1:1:2.65:60:4:0.2222:0:1.5 +12 53609418 . C A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50209;SOR=Inf;LSEQ=CCCCCGTCTGCCCACTCCCA;RSEQ=CACGTACACACCTTGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:33,24:57,0:0:2,0:24.6:1:31.6:1:1:0:59.8:114:1:0:0.2 0/1:71:2:1,1:38,31:69,2:0.0282:2,2:14:0:27.5:1:1:1.22227:60:4:0.029:0:1 +12 53609436 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22289;SOR=0;LSEQ=CACCACGTACACACCTTGCA;RSEQ=CCTTCACAAGAGCTGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:34,28:62,2:0.0313:2,2:28:1:28.5:1:1:1.21058:60:4:0.0317:0:1 0/0:71:0:0,0:41,30:71,0:0:2,0:32.2:1:31.3:1:1:0:60:70:1:0:0.2 +12 53858379 . CT C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.51087;SOR=0;LSEQ=TGAAATCTGCCACTAGGTAA;RSEQ=TTTTTTTTTAATTCACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:13,0:13,2:0.1333:1,0:14.5:1:34:0:1:0:60:4:0.1333:0:0 0/0:9:0:0,0:9,0:9,0:0:0,0:26.2:1:30:1:1:0:60:18:1:0:0 +12 53858460 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50153;SOR=Inf;LSEQ=GGAAAAAGGAAAAAAATAAA;RSEQ=AACTTTTTTTGTGTGAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:45,10:55,0:0:2,0:16.9:1:31.4:1:1:0:60:17.333:1:0:0.1 0/1:68:2:1,1:55,11:66,2:0.0294:2,2:21.5:1:28:1:0.32397:4.83054:60:4:0.0303:0:1 +12 53858463 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=7.000;MSILEN=1;SSF=1;SOR=1.55053;LSEQ=AAAAGGAAAAAAATAAACAA;RSEQ=TTTTTTTGTGTGAATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:1:1,0:44,12:56,1:0.0175:2,0:17:0:20:0:1:0:60:2:0.0182:0:2 0/1:74:2:1,1:57,15:72,2:0.027:2,2:23:1:28.5:1:0.388:3.71165:60:4:0.027:0:1 +12 53858514 . TG T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51072;SOR=Inf;LSEQ=AGGTGCCGGATTGACAGCCC;RSEQ=GAGACTGAAATCCTCTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:70,56:126,0:0:2,0:29.6:1:31.1:1:1:0:59.4:24.2:1:0:0.1 0/1:173:2:1,1:93,78:171,2:0.0116:2,2:44:1:31:1:1:1.19109:60:4:0.012:0:0 +12 53858548 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51465;SOR=Inf;LSEQ=CTCTATTTATCCACAGGACA;RSEQ=GTACAGCACAGGCAGCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:45,67:112,0:0:2,0:26.6:1:31.4:1:1:0:60:36.333:1:0:0.1 0/1:163:2:1,1:69,92:161,2:0.0123:2,2:26:1:28.5:1:1:1.33:60:4:0.0124:0:1 +12 53877562 . C T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTTCACCTAGGGCCATAA;RSEQ=AGATCTCAGTCTCAGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:29:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:29:1:1:0:60:4:1:0:1 +12 53878882 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24151;SOR=Inf;LSEQ=TGAAACCATCTGGGCAACTG;RSEQ=AGGGCACGGGCAGATGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:75,29:104,0:0:2,0:22.4:1:31:1:1:0:60:25:1:0:0.2 0/1:101:2:1,1:68,31:99,2:0.0198:2,2:36:0:31:1:0.53545:2.17486:60:4:0.02:0:1.5 +12 53878911 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23719;SOR=0;LSEQ=GGCAGATGGAGACTGTTGCT;RSEQ=CCCACACCCCAGATAATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:96,62:158,2:0.0125:2,2:42.5:1:31.5:1:1:1.54398:60:4:0.0129:0:1.5 0/0:168:0:0,0:97,71:168,0:0:2,0:24.7:1:29:1:1:0:60:55:1:0:0.1 +12 53878931 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49885;SOR=0;LSEQ=TCCCACACCCCAGATAATGG;RSEQ=TGAGGAATCTACGTCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:102,89:191,2:0.0104:2,2:32.5:1:29.5:1:1:1.14525:60:4:0.0108:0:1 0/0:186:0:0,0:97,89:186,0:0:2,0:28.5:1:31.3:1:1:0:60:92:1:0:0.2 +12 53879009 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50103;SOR=0;LSEQ=GCCAAAGGACCTAGGGATGA;RSEQ=GGGACATCACTTGTGCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:11,60:71,2:0.0274:2,2:15.5:1:30.5:1:0.30365:5.27:60:4:0.0278:0:1.5 0/0:60:0:0,0:10,50:60,0:0:2,0:21.7:1:29.8:1:1:0:60:29:1:0:0.2 +12 54338916 . G T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.05782;SOR=Inf;LSEQ=GTTCATCACCAAAGAGAAGC;RSEQ=CCGGCGCATCTCCGCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:222,73:295,0:0:2,0:22.7:1:29.9:1:1:0:60:31.778:1:0:0.1 0/1:187:3:1,2:120,64:184,3:0.016:2,2:11:1:23.7:1:0.28468:3.72213:60:6:0.0165:0:1 +12 54339029 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.15368;SOR=Inf;LSEQ=AATCGAAAGCGCCTCATCTC;RSEQ=ACTCCACCTGACCACCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:38,183:221,0:0:2,0:24.2:1:32.5:1:1:0:59.9:109.5:1:0:0.3 0/1:143:2:1,1:35,106:141,2:0.014:2,2:26:1:29:1:0.44145:3.00:60:4:0.0141:0:1 +12 54339052 . C A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.28516;SOR=1.35622;LSEQ=TCCACCTGACCACCCACCCG;RSEQ=TGCTTGCCCCATCTATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:66:4,62:4,78:82,66:0.4459:1,2:23.4:1:31.4:1:1:1.26:60:132:0.449:0:1 1/0:90:47:6,41:2,41:43,47:0.5222:1,2:22.6:1:29.6:1:0.27046:2.97:59.8:46:0.5169:0:1.1 +12 54340765 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGCTCTATTGCCCCAGAG;RSEQ=GCCCCGAATACCTTCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:48.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 54943389 . CGCG C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.48988;SOR=0;LSEQ=AGGAGGCGGCTCTGGCAGCG;RSEQ=GCGGCGGCGGCGGTAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:29:1:32.5:1:1:1.10554:60:4:0.0952:0:0.5 0/0:18:0:0,0:8,10:18,0:0:2,0:31.6:1:29.3:1:1:0:60:17:1:0:0.5 +12 55213743 . AA GG 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTCATTTAGAAACCTC;RSEQ=GCAGAGGGTTTGGAGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:28.5:1:1:0:60:4:1:0:1 +12 55215117 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTACAGAGGTTTCTTC;RSEQ=ACAATATAGTGTGTCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:35,0:0,0:0,35:1:0,1:22.2:1:31.4:1:1:0:59.1:34:1:0:1.1 1/1:15:15:15,0:0,0:0,15:1:0,1:18.3:1:31.1:1:1:0:60:30:1:0:1.1 +12 55215314 . C A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00149;SOR=1.5711;LSEQ=AAGAAGACGGACCATAGGAA;RSEQ=TTCCAGGATAATGTTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:121:56,65:168,202:370,121:0.2459:2,2:25.2:1:30.7:1:0.91637:1.04:59.9:120:0.2459:0:1.4 0/1:478:162:66,96:146,170:316,162:0.3389:2,2:23.8:1:30.1:1:0.28494:1.24861:60:324:0.3411:0:1.4 +12 55215378 . G A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGACCGAAGTTGTGAGA;RSEQ=TTGCCATGATGGTGAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:234:69,165:0,0:0,234:1:0,2:25.7:1:30.8:1:1:0:60:57.5:1:0:1.4 1/1:235:235:74,161:0,0:0,235:1:0,2:24.8:1:29.7:1:1:0:60:57.75:1:0:1.4 +12 55215401 . T G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08469;SOR=1.63034;LSEQ=GCCATGATGGTGAGGGCTGA;RSEQ=AGCAGGACAGTCACATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:33:6,27:33,103:136,33:0.1953:2,2:24.9:1:32.2:1:0.64524:1.43882:60:66:0.1976:0:2.3 0/1:148:42:13,29:27,79:106,42:0.2838:2,2:24:1:31:1:0.54059:1.31:60:84:0.2857:0:2.2 +12 55215403 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22519;SOR=Inf;LSEQ=CATGATGGTGAGGGCTGATA;RSEQ=CAGGACAGTCACATTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:38,122:160,0:0:2,0:22.9:1:32.5:1:1:0:60:52.333:1:0:1.2 0/1:145:2:1,1:37,106:143,2:0.0138:2,2:25:1:29:1:0.4568:2.84:60:4:0.014:0:2 +12 55215404 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22209;SOR=Inf;LSEQ=ATGATGGTGAGGGCTGATAG;RSEQ=AGGACAGTCACATTAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:38,123:161,0:0:2,0:22.2:1:32.6:1:1:0:60:322:1:0:1.2 0/1:144:2:1,1:37,105:142,2:0.0139:2,2:12:0:31:1:0.4595:2.81:60:4:0.014:0:3.5 +12 55215754 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTAGGCTGCATCCTGCTG;RSEQ=CACGGCATCTTCCACCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:31:1:31.7:1:1:0:51.7:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 55427158 . A C 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05131;SOR=0;LSEQ=AGTGATTGAGTAAAAGCTAA;RSEQ=AGATGAGGCAAAAATCGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:7:7,0:95,3:98,7:0.0667:1,0:24.4:1:31.4:1:1:0:60:14:0.068:0:1 0/0:58:0:0,0:55,3:58,0:0:2,0:21.6:1:29.3:1:1:0:60:28:1:0:0.1 +12 55427311 . A T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27273;LSEQ=TAGGCAATGATCTTATTCTC;RSEQ=AGAGACAACTACTCTAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:306:126,180:61,71:132,306:0.6986:2,2:26.5:1:29.7:1:0.34467:1.22678:60:60.2:0.7:0:1.1 0/1:429:166:76,90:130,133:263,166:0.3869:2,2:25.8:1:28.5:1:0.48819:1.1571:60:332:0.3915:0:1.1 +12 55427394 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22896;SOR=Inf;LSEQ=ATTTTACTGTAAATCAAATT;RSEQ=AGGAATTATGCTATTCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:49,138:187,0:0:2,0:24.9:1:32.3:1:1:0:59.8:374:0.9947:0:0.3 0/1:173:2:1,1:45,126:171,2:0.0116:2,2:34:1:29:0:0.46223:2.78:60:4:0.0118:0:1 +12 55427428 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=TTCCTAGAATTGTACAATTG;RSEQ=CCCTTTTCCTTCCTCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:12,76:88,2:0.0222:2,2:14:1:29:1:0.26941:6.12:60:4:0.0225:0:1 0/0:81:0:0,0:6,75:81,0:0:2,0:22.9:1:30.3:1:1:0:60:39.5:1:0:0.1 +12 55807417 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18947;SOR=Inf;LSEQ=TGGATCTGTGTGTAGGTGGC;RSEQ=GAGCTAATAAGTGTCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:11,0:0:0,0:30:1:30.7:1:1:0:39.5:22:1:0:0 0/1:9:2:1,1:0,7:7,2:0.2222:0,2:35:1:30:1:0.22222:0:41.5:4:0.2222:0:1 +12 56383796 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18367;SOR=Inf;LSEQ=AGTTTGAGATCTGGGACACA;RSEQ=CTGGGCAGGAGCGATATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:42,48:90,0:0:2,0:29.2:1:33:1:1:0:60:180:1:0:0.1 0/1:68:2:1,1:33,32:65,2:0.0294:2,2:25.5:1:28:1:1:1.03078:60:4:0.0303:0:1 +12 56421196 . AAACAACAAC A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=8.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCTCCCATCTAATAATTAAA;RSEQ=AACAACAACAACAACAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:28.3:1:1:0:60:4:1:0.5:0 +12 56421614 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23775;SOR=Inf;LSEQ=GTGCCTCCTTCACCCAGAAG;RSEQ=GGAACCTGCTGCGCCACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:58,35:93,0:0:2,0:23.8:1:30.6:1:1:0:60:45.5:1:0:0.2 0/1:89:2:1,1:55,32:87,2:0.0225:2,2:31.5:1:28.5:1:1:1.70775:60:4:0.0233:0:1 +12 56421720 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50511;SOR=Inf;LSEQ=TGCACTCACTGGTCACCTCC;RSEQ=CACACACTCAGGTCAGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:7,31:38,0:0:2,0:22.8:1:30.7:1:1:0:60:37:1:0:0.1 0/1:51:2:1,1:12,37:49,2:0.0392:2,2:21:1:27.5:1:0.44863:3.00:60:4:0.04:0:1 +12 56422162 . A C 32 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTAAAAATACAAAAAAAA;RSEQ=AAAAATTAGCCGGGCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:32:1:1:0:31:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 56473808 . T C 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=GTCCGAGGCTCCGCAATCCC;RSEQ=ACTCCAGCCTCGCGCGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:28.6:1:32.2:1:1:0:60:10:1:0:1.4 0/1:5:1:1,0:4,0:4,1:0.2:0,0:9:0:24:0:1:0:60:2:0.2:0:1 +12 56473874 . CCT C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=0.72668;SOR=0.63347;LSEQ=TCCCTCTGCGTTCCTCCCTC;RSEQ=CTCTCTCTCTCTCTCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:11,0:11,8:0.4211:0,0:14.4:1:30.1:1:1:0:59.4:16:0.4211:0.2632:1.5 0/1:16:5:5,0:10,1:11,5:0.3125:2,0:13:1:30.2:1:1:0:56:10:0.3125:0.1875:0.8 +12 56473994 . G T 29 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.5663;LSEQ=GCCGCAGCAGCCACCAATTC;RSEQ=CCAGCGGTTCAGGTGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:157,16:173,2:0.0114:2,2:7.5:1:29.5:1:0.18535:9.5498:60:4:0.0116:0:1 0/0:154:1:1,0:129,24:153,1:0.0065:2,0:8:0:32:0:1:0:60:2:0.0066:0:1 +12 56473999 . C T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.56754;LSEQ=AGCAGCCACCAATTCGCCAG;RSEQ=GGTTCAGGTGGCTCTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:162,25:187,2:0.0106:2,2:18.5:1:28.5:1:0.25684:6.37375:60:4:0.0108:0:1 0/0:166:1:1,0:130,35:165,1:0.006:2,0:46:0:27:0:1:0:60:2:0.0061:0:1 +12 56474006 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22582;SOR=Inf;LSEQ=ACCAATTCGCCAGCGGTTCA;RSEQ=GTGGCTCTTGCCTCGATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:183,34:217,0:0:2,0:24.5:1:32.7:1:1:0:59.9:107.5:1:0:0.2 0/1:197:2:1,1:150,45:195,2:0.0102:2,2:15:1:27.5:1:0.41339:3.30784:60:4:0.0104:0:1 +12 56474379 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05812;SOR=0.09823;LSEQ=GGACCCTCACGCCACCCTTC;RSEQ=CCAGAGCGTCGCCGACCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:19:1,18:0,1:1,19:0.95:0,1:29.2:1:30.5:1:1:0:60:18:0.9474:0:1.2 1/0:8:5:0,5:0,3:3,5:0.625:0,0:15.8:1:31.4:1:1:0:60:10:0.625:0:1 +12 56474480 . A G 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=TGCAGGGAGGGGAGCAGGGA;RSEQ=CTTCATTCTGTAAACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:23.9:1:31.1:1:1:0:59.4:6:0.8571:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:8:0:31:0:1:0:60:2:1:0:0 +12 56477694 . A T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38143;LSEQ=CTCCTTCCTGCAGGTTAGTG;RSEQ=GCCCACCCTCCTTCCTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:561:382:121,261:57,122:179,382:0.6809:2,2:25.8:1:30.2:1:1:1.00778:60:190:0.6859:0:1.1 0/1:573:257:90,167:110,203:313,257:0.4485:2,2:26.1:1:29.1:1:1:1.00546:60:127.5:0.4529:0:1.1 +12 56478002 . A C 73 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGATGAGGAAGGGGCCCT;RSEQ=CTGGTATGAGGCACTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:12.4:1:31.8:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 56478607 . G A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53586;SOR=0.63275;LSEQ=GCACTATTGTACTCCAGCCT;RSEQ=GGCAACAAGAGCGTAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:9,0:24,0:24,9:0.2727:1,0:22.4:1:27.1:1:1:0:55.6:18:0.2727:0:1.7 0/1:21:4:3,1:17,0:17,4:0.1905:1,2:28.5:1:26.5:1:0.19048:0:60:8:0.1905:0:1 +12 56478639 . TA T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.64202;SOR=0.4654;LSEQ=CGTAACTCCGTCTCAAATTT;RSEQ=AAAAAAAGAAAAAAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:3,0:75,0:75,3:0.0385:1,0:15.3:1:30.2:1:1:0:58.7:6:0.0385:0.0128:1 0/1:55:1:1,0:53,1:54,1:0.0182:1,0:17:0:32:0:1:0:60:2:0.0182:0:0 +12 56478658 . A C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=8e-05;SOR=0.30682;LSEQ=TTAAAAAAAAGAAAAAAAGA;RSEQ=AGGAAAGAAAGAAGGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:119:78:78,0:40,0:40,78:0.6555:1,1:23.5:1:32.2:1:1:0:59.9:38:0.6667:0:1 0/1:79:29:28,1:48,2:50,29:0.3671:1,1:25.4:1:31.8:1:1:1.16:60:28:0.359:0:1.1 +12 56480269 . C T 42 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.36245;SOR=3.15973;LSEQ=GTGGAGAGGTAAGGAAGAGG;RSEQ=GTTCCGCTGCGGCCCTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:0,1:199,68:267,1:0.0037:2,0:1:0:25:0:0.25746:0:60:2:0.0038:0:1 0/1:256:3:1,2:193,60:253,3:0.0117:2,2:6.3:1:27:1:0.14643:6.37421:60:6:0.0122:0:1 +12 56480474 . C A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCAAGATTGCTCCCCAGTC;RSEQ=CACCAAACCAGAGTGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:123,286:409,0:0:2,0:25.3:1:30.9:1:1:0:59.9:44.444:1:0:0.1 0/1:345:36:13,23:106,202:308,36:0.1043:2,2:28.2:1:28.3:1:0.85438:1.08:60:72:0.1062:0:1.1 +12 56480583 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04922;LSEQ=TGACTCAGCAGCCCACCAGG;RSEQ=CAGACCATTCCAGTCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:52:1,51:0,3:3,52:0.9455:0,1:22.2:1:29.8:1:1:0:59.4:51:0.9444:0:1.2 0/1:29:13:0,13:0,16:16,13:0.4483:1,1:22.5:1:30.3:1:1:0:60:26:0.4483:0:1 +12 56480648 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05848;SOR=Inf;LSEQ=TTCAAGAAAAGGAGCAGGCC;RSEQ=AGCATGGTGGCTCATGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:1,13:14,0:0:1,0:19.9:1:31.7:1:1:0:60:28:1:0:0.8 0/1:5:2:0,2:0,3:3,2:0.4:0,0:12:1:29:1:1:0:60:4:0.4:0:1 +12 56480920 . C CAAA 25 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=21.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:25:1:25.8:1:0.33333:0:38:4:1:0.3333:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 56481264 . G T 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.38373;SOR=0.30048;LSEQ=CCCTGGCTTTTTGCTTCCCG;RSEQ=GATTGAGGTGCCTGTGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:4:2,2:195,34:229,4:0.0172:2,2:23.5:1:31.3:1:0.11389:5.66842:60:8:0.0176:0:1 0/0:192:1:0,1:153,38:191,1:0.0052:2,0:1:0:23:0:0.20312:0:60:2:0.0053:0:1 +12 56482180 . T G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13387;LSEQ=TGAAGAGACTTTTGAATCTA;RSEQ=AGGGCAGCACTTAAGGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:121:110:92,18:10,1:11,110:0.9091:2,2:25.7:1:33.2:1:1:1.94759:59.8:54:0.9231:0:1.1 1/0:58:33:30,3:22,3:25,33:0.569:2,2:26.1:1:31:1:1:1.36:60:15.5:0.5536:0:1.2 +12 56482227 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16059;SOR=Inf;LSEQ=GGCAGATGGGGACAAATCCA;RSEQ=TGCAGAGCTGGAGGGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:216,27:243,0:0:2,0:23.9:1:33.3:1:1:0:59.9:80:1:0:0.4 0/1:163:2:1,1:136,24:160,2:0.0123:2,2:29:1:28:1:0.28564:5.57262:60:4:0.0125:0:1.5 +12 56486447 . G T 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.34035;SOR=3.50779;LSEQ=TTAGTGGAGAATGATATTTA;RSEQ=AAACCAAATGCTGAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:0,1:219,26:245,1:0.0041:2,0:12:0:11:0:0.10976:0:60:0:0:0:2 0/1:212:3:2,1:170,39:209,3:0.0142:2,2:20.3:1:22.7:1:0.46773:2.16965:60:2:0.0095:0:2.3 +12 56486473 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05763;SOR=Inf;LSEQ=AAATGCTGAGGCTGGGTGTG;RSEQ=TCATTGCCATTGAGTTATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:287,107:394,0:0:2,0:23:1:32.1:1:1:0:60:42.778:1:0:0.1 0/1:380:4:3,1:268,108:376,4:0.0105:2,2:36.8:1:29.3:1:1:1.21:60:8:0.0107:0:2 +12 56487077 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18151;SOR=Inf;LSEQ=CTAACATGAATCCTTTGAAT;RSEQ=GTTAATGTTCCCTTAGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:156,71:227,0:0:2,0:24.7:1:29.4:1:1:0:59.9:74.667:1:0:0.1 0/1:169:2:1,1:128,39:167,2:0.0118:2,2:22:1:29:1:0.41843:3.25338:60:4:0.012:0:1 +12 56487201 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59977;SOR=1.10358;LSEQ=TTCCGATCCCTGAAGGAAAT;RSEQ=AGTGCTGGGCGTATCTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:75:38,37:187,185:372,75:0.1678:2,2:24.8:1:32.3:1:1:1.02:60:150:0.1689:0:1 0/1:456:83:37,46:177,196:373,83:0.182:2,2:19.8:1:30.1:1:0.71548:1.12244:60:26.667:0.1782:0:1.1 +12 56487296 . G A 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21806;SOR=4.76988;LSEQ=TCGGGGGCCTACGGAAGAGC;RSEQ=ACTAGACATCAAGCATAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:1:1,0:156,230:386,1:0.0026:2,0:21:0:14:0:0.40568:0:60:0:0:0:2 0/1:410:5:4,1:180,224:404,5:0.0122:2,2:8.8:1:26.2:1:0.179:4.96:60:10:0.0125:0:1 +12 56487359 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50136;SOR=Inf;LSEQ=GGGAAAGGGTCTGCTAGGTG;RSEQ=TGAGAATAGGGAGTCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:53,108:161,0:0:2,0:23.8:1:32.2:1:1:0:60:79.5:1:0:0.2 0/1:187:2:1,1:58,127:185,2:0.0107:2,2:34:0:31:1:0.53263:2.18:60:4:0.0108:0:1 +12 56487853 . AC A 109 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.13554;SOR=0.43547;LSEQ=AAGGTCAGGACTTGGAAGTG;RSEQ=CCCCCCCTCCCTTTATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:915:11:7,4:496,404:900,11:0.012:2,2:29.5:1:31.7:1:0.76271:1.42:60:22:0.0123:0.0011:0.1 0/0:949:5:3,2:517,422:939,5:0.0053:2,2:24.8:1:30.6:1:1:1.22:60:10:0.0053:0.0011:0.2 +12 56487860 . CCT C 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=GGACTTGGAAGTGACCCCCC;RSEQ=CCCTTTATTCCCCACTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:955:0:0,0:514,440:954,0:0:2,0:24.6:1:32.1:1:1:0:60:105:1:0:0.2 0/1:998:13:7,6:531,448:979,13:0.013:2,2:22.3:1:30.1:1:1:1.01593:58.1:26:0.0133:0:0.8 +12 56487861 . CT C 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTTGGAAGTGACCCCCCC;RSEQ=CCCTTTATTCCCCACTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:959:0:0,0:514,444:958,0:0:2,0:24.5:1:30.5:1:1:0:60:28.938:1:0:0.2 0/1:1002:28:14,14:517,439:956,28:0.0279:2,2:27:1:30:1:0.70376:1.17748:59.4:27:0.0285:0.008:1.1 +12 56488913 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00095;SOR=3.30436;LSEQ=GGAGGTGGAGGCCATGTCTT;RSEQ=GGATCAGCTCTGGGCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:34:31,3:59,1:60,34:0.3617:1,2:26.6:1:28.4:1:0.13295:5.60123:60:68:0.3656:0:1 1/0:52:34:32,2:17,1:18,34:0.6538:1,2:24.3:1:27.9:1:1:1.06128:60:68:0.6538:0:1 +12 56488937 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18058;SOR=Inf;LSEQ=TCAGCTCTGGGCTCCAGGAT;RSEQ=GGATGCCACGGTAAGTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:119,17:136,0:0:2,0:24:1:32:1:1:0:60:67:1:0:0.2 0/1:101:2:1,1:84,15:99,2:0.0198:2,2:20:1:29:1:0.29307:5.45444:60:4:0.02:0:1 +12 56488953 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.20991;SOR=Inf;LSEQ=GGATGGGATGCCACGGTAAG;RSEQ=TCTGAAACAAGCTTTTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:158,33:191,0:0:2,0:22.9:1:29.9:1:1:0:60:190:1:0:0.2 0/1:162:2:1,1:124,36:160,2:0.0123:2,2:21.5:1:28:1:0.40572:3.41116:60:4:0.0123:0:1 +12 56488985 . G T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05701;SOR=Inf;LSEQ=CTTTTATATGTTAGGCTGTT;RSEQ=AAATTGAGCCTCTGCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:253,96:349,0:0:2,0:24.2:1:32.6:1:1:0:59.9:173.5:1:0:0.1 0/1:335:4:2,2:231,100:331,4:0.0119:2,2:15.8:1:23.5:1:0.58815:2.30358:53.3:3:0.0091:0:2 +12 56489401 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23953;SOR=Inf;LSEQ=AAGTATAGTTGACATTTGTA;RSEQ=GGAAGATGCAAACCCAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:151,54:205,0:0:2,0:25.5:1:30.7:1:1:0:59.9:101.5:1:0:0.1 0/1:197:2:1,1:145,50:195,2:0.0102:2,2:11.5:1:32.5:1:0.45172:2.88131:60:4:0.0104:0:1 +12 56489421 . TA T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2489;SOR=Inf;LSEQ=AGGAAGATGCAAACCCAGGA;RSEQ=ATGTTGGGTTTCTATATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:181,75:256,0:0:2,0:25.7:1:29:1:1:0:59.9:84.333:1:0:0.1 0/1:267:3:1,2:182,82:264,3:0.0112:2,2:18.7:1:27.7:1:0.23375:4.41147:60:6:0.0116:0.0037:0.3 +12 56489429 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=GCAAACCCAGGATAATGTTG;RSEQ=GTTTCTATATATCCCATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:203,94:297,0:0:2,0:24.1:1:31.3:1:1:0:59.9:73.25:1:0:0.1 0/1:300:3:1,2:203,94:297,3:0.01:2,2:20.7:1:29:1:0.24087:4.2959:60:6:0.0102:0:1 +12 56489613 . T C 217 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGTACTTAGCTTACTTTTG;RSEQ=TTTTTCTTTTCTTTTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:97:33,64:119,211:330,97:0.2272:2,2:24.2:1:33:1:0.80948:1.09358:60:96:0.227:0:1.1 0/0:444:0:0,0:156,288:444,0:0:2,0:25.6:1:29.1:1:1:0:60:73:1:0:0.2 +12 56490760 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.05188;SOR=Inf;LSEQ=TGGGGGTGGGGGGGCCTGGG;RSEQ=TGGCTGTGCACATGCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:151,81:232,0:0:2,0:23.6:1:32.2:1:1:0:59.8:37.667:1:0:0.2 0/1:139:3:2,1:94,42:136,3:0.0216:2,2:27.7:1:28.3:1:1:1.11812:60:6:0.0221:0:1 +12 56491480 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14685;SOR=Inf;LSEQ=AAAGGTTGGGGACCACTGCT;RSEQ=AGAGGTACCTTCAAGATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:127,9:136,0:0:2,0:21.9:1:32.5:1:1:0:60:135:1:0:0.1 0/1:85:2:1,1:80,3:83,2:0.0235:1,2:21.5:1:25:1:0.09244:23.23849:60:4:0.0253:0:1 +12 56491758 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24551;SOR=Inf;LSEQ=AAGGGTAAGGAGGCGGGGGT;RSEQ=GAGTGAAGCATGGGGATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:40,156:196,0:0:2,0:24.4:1:31.4:1:1:0:59.8:64.333:1:0:0.2 0/1:193:2:1,1:48,143:191,2:0.0104:2,2:19.5:1:27.5:1:0.4443:2.96:60:4:0.0105:0:1 +12 56491880 . T G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02479;SOR=6.35728;LSEQ=TTAGTTCAGAGGGCAACAAA;RSEQ=AAAATAATGATCAAGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:1,4:2,15:17,5:0.2273:2,2:22.8:1:34:1:1:1.82:60:10:0.2273:0:1 1/0:12:8:1,7:0,4:4,8:0.6667:0,2:22.1:1:32:1:1:0:60:16:0.6667:0:1.3 +12 56492032 . CA C 53 MAF0.05;MSI12;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0.6037;LSEQ=CCCCGTCTCTACTAAATATA;RSEQ=AAAAAAAAAAAAATTAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:4,0:4,3:0.3:0,0:29.7:1:34:0:1:0:42.7:6:0.3:0:1.3 0/1:5:1:1,0:0,0:0,1:0.2:0,0:18:0:31:0:1:0:48:2:0.2:0:0 +12 56492721 . C CT 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.60552;SOR=2.22676;LSEQ=GCTGAGCCCAACCATTTTCT;RSEQ=TTTTTTTCTTTTTTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:0,1:30,148:178,1:0.0054:2,0:43:0:32:0:1:0:36:2:0.0061:0:4 0/1:166:2:0,2:30,130:160,2:0.012:2,0:16.5:1:30.5:1:1:0:46.5:4:0.0141:0:2 +12 56492729 . C T 40 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.3955;SOR=0.533;LSEQ=CAACCATTTTCTCTTTTTTT;RSEQ=TTTTTTTTTCTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:9:0,9:20,117:137,9:0.0604:2,0:25.2:1:12.8:1:0.61113:0:43.6:0.125:0.0081:0:3.3 0/1:121:4:0,4:22,94:116,4:0.0331:2,0:26:1:25.3:1:1:0:41:3:0.03:0:3.3 +12 56493381 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26733;SOR=0;LSEQ=GTGTGAGCCACCGCGCCCGG;RSEQ=CATGGAATGTATTCTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:3:1,2:195,38:233,3:0.0127:2,2:23.3:1:29.7:1:0.07525:10.10548:51.7:6:0.0128:0:1 0/0:171:0:0,0:139,32:171,0:0:2,0:22.4:1:31.5:1:1:0:57.5:84.5:1:0:0.1 +12 56493822 . A C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.43454;LSEQ=CGGCCACGTGGGGTAAGACA;RSEQ=CTTCTAATTACCCAACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:145:60,85:172,215:387,145:0.272:2,2:24:1:31.8:1:0.55657:1.13307:60:47.333:0.2694:0:1.1 1/0:537:302:117,185:109,125:234,302:0.5624:2,2:23.9:1:30.7:1:0.07781:1.37794:60:150:0.5629:0:1.2 +12 56494812 . C T 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39916;SOR=3.00412;LSEQ=TTCCTCATCATGTAAATTTC;RSEQ=TTGCATTATTTTCTGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:1:0,1:171,81:252,1:0.004:2,0:1:0:25:0:0.32411:0:60:2:0.004:0:1 0/1:339:4:1,3:229,106:335,4:0.0118:2,2:11.5:1:26.8:1:0.09961:6.44278:60:8:0.0119:0:1.3 +12 56494872 . C T 144 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=10.97532;LSEQ=CAGTTTCTGGGAGCAGTGAA;RSEQ=GGTGCCCCCGTCCAGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:2:0,2:261,209:470,2:0.0042:2,0:1:0:25.5:1:0.19931:0:60:4:0.0043:0:1 0/1:582:26:14,12:286,268:554,26:0.0447:2,2:25.2:1:30.8:1:0.84397:1.09:60:52:0.0451:0:1.2 +12 56494991 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.87936;LSEQ=GAGAAAGTGTCAATGTGTAG;RSEQ=AGCCGGAGCAGGAGCCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:155:91,64:239,180:419,155:0.27:2,2:22.7:1:30.4:1:0.77559:1.07:59.9:154:0.273:0:1.1 1/0:593:306:159,147:158,128:286,306:0.516:2,2:23.7:1:29:1:0.45819:1.14096:60:75.5:0.5198:0:1.1 +12 56494998 . A T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.02745;SOR=1.41346;LSEQ=TGTCAATGTGTAGGAGCCGG;RSEQ=GCAGGAGCCGGAGCCCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:89:52,37:310,223:533,89:0.1429:2,2:23.1:1:30:1:1:1.01:60:88:0.1436:0:1.2 0/1:624:119:62,57:275,229:504,119:0.1907:2,2:24.7:1:29.1:1:0.68269:1.10385:60:118:0.1934:0:1.1 +12 56495306 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13489;SOR=0.85111;LSEQ=TACCTAGCCTTTCTTCTCAA;RSEQ=CCCCAGGTACTCCCTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1051:230:125,105:470,351:821,230:0.2188:2,2:26.4:1:30.4:1:0.45204:1.12466:59.8:45:0.2166:0:1.1 0/1:1096:211:114,97:476,409:885,211:0.1925:2,2:27.5:1:29.2:1:1:1.01:59.9:104.5:0.1921:0:1.2 +12 56495877 . C T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21534;SOR=Inf;LSEQ=ACTCAGGGAGCATTTAATGG;RSEQ=AGCTAGTGCCTTTAGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:13,110:123,0:0:2,0:24.3:1:32.8:1:1:0:60:122:1:0:0.1 0/1:107:2:1,1:18,87:105,2:0.0187:2,2:7:1:29:0:0.32499:4.73:60:4:0.0192:0:1 +12 57486033 . A C 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=2.42298;LSEQ=GGACCCCACAGGAGAGGAGG;RSEQ=GGCCCCGGGCATTCCTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1316:312:171,141:529,473:1002,312:0.2371:2,2:24.3:1:31:1:0.55893:1.08:59.9:51:0.2378:0:1.1 0/1:1222:525:287,238:376,320:696,525:0.4296:2,2:23.4:1:30.5:1:0.86183:1.03:59.9:86.5:0.4318:0:1.1 +12 57486176 . G C 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGGGTGTGAGGAGGTCTG;RSEQ=TGAGGCAGCGGGGAAGTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1766:0:0,0:864,899:1763,0:0:2,0:24.9:1:31.8:1:1:0:60:52.424:0.9988:0:0.2 0/1:1963:63:31,32:937,958:1895,63:0.0321:2,2:24.4:1:31.7:1:1:1.00963:60:126:0.0326:0:1.2 +12 57486278 . G A 180 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=77.28782;LSEQ=TTCTGCATGAGGGACAACAC;RSEQ=CTCTTATTACGGAGAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1475:1:1,0:704,768:1472,1:7e-04:2,0:15:0:26:0:0.47862:0:60:2:7e-04:0:1 0/1:1484:74:39,35:689,721:1410,74:0.0499:2,2:23.5:1:29:1:0.55215:1.17:60:73:0.0498:0:1.2 +12 57486647 . A G 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.57657;LSEQ=GCTGGGTTCTGTGCTCTGCC;RSEQ=GTCGAGTGGCCCTCGTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1517:706:347,359:407,401:808,706:0.4654:2,2:24.5:1:30.4:1:0.64319:1.05:59.9:63.182:0.4668:0:1.2 1/0:1668:965:491,474:359,343:702,965:0.5785:2,2:26.2:1:29.8:1:0.92104:1.0104:59.9:95.5:0.5784:0:1.1 +12 57487340 . G A 74 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15095;SOR=3.63398;LSEQ=CGTCTCCCACGACCGCGTGG;RSEQ=CCGCCTCAGCCCCTGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:2:1,1:245,199:444,2:0.0045:2,2:21.5:1:31:0:1:1.23057:60:4:0.0045:0:1 0/1:372:6:3,3:194,172:366,6:0.0161:2,2:22.7:1:28.7:1:1:1.12754:60:12:0.0164:0:1.7 +12 57487729 . T G 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.63597;LSEQ=AGCAGGCTAGGAGTTGTGGG;RSEQ=ATGGGGATGGGGATGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1800:782:372,410:489,526:1015,782:0.4344:2,2:24.1:1:31.6:1:0.81189:1.02462:59.8:64.167:0.4355:0:1.3 1/0:1810:1008:471,537:383,413:796,1008:0.5569:2,2:24.3:1:30.4:1:0.569:1.05726:59.9:71:0.5569:0:1.3 +12 57487777 . G C 201 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGAGGAGCCCAAAGCAGT;RSEQ=ATGCTTTGTGTGTGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1436:0:0,0:669,765:1434,0:0:2,0:25:1:32.2:1:1:0:60:109.308:0.9986:0:0.6 0/1:1325:91:39,52:572,657:1229,91:0.0687:2,2:24.3:1:30.9:1:0.51517:1.1607:60:182:0.0695:0:1.1 +12 57487814 . A C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.18465;LSEQ=AGGGGGAAGAGGGAGTGGGC;RSEQ=GGCGGAGGGCCGGGCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1358:573:261,312:358,422:780,573:0.4219:2,2:24.7:1:30.2:1:0.91213:1.0141:60:39.929:0.4181:0:1.3 1/0:1164:814:390,424:169,178:347,814:0.6993:2,2:24.1:1:29.3:1:0.8474:1.03219:59.9:73:0.6983:0:1.3 +12 57488293 . A T 242 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=115.64009;LSEQ=AATTCAATAAACCTAAACTG;RSEQ=GCCCATCTTCACAGCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1950:3:0,3:1000,946:1946,3:0.0015:2,0:3:1:27.7:1:0.11525:0:60:6:0.0016:0:1 0/1:2022:306:151,155:850,865:1715,306:0.1513:2,2:23.6:1:29.4:1:0.9506:1.00869:59.9:152:0.1526:0:1.2 +12 57488303 . C T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31126;SOR=0.851;LSEQ=ACCTAAACTGAGCCCATCTT;RSEQ=ACAGCTTTCTTTGCCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1924:89:45,44:936,899:1835,89:0.0463:2,2:20.6:1:29.4:1:1:1.01801:59.9:88:0.0462:0:1.1 0/1:2094:83:38,45:1002,1003:2005,83:0.0396:2,2:21.6:1:28.4:1:0.50203:1.18293:60:166:0.04:0:1.2 +12 57496677 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50992;SOR=0;LSEQ=GTTGTCTTGGTTGCCATGGA;RSEQ=GATGACCACCAGGGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:14,22:36,2:0.0526:2,2:43:0:32:0:1:1.55:60:4:0.0526:0:1.5 0/0:26:0:0,0:11,15:26,0:0:2,0:25.6:1:28.4:1:1:0:59.5:25:1:0:0.3 +12 57674222 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.5224;SOR=Inf;LSEQ=AGTTGCTGCTGCTGCTGCTG;RSEQ=TGTTGCTGCTGGGCAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:23,0:0:2,0:26.4:1:33.3:1:1:0:52.7:46:1:0:0.2 0/1:38:2:1,1:17,19:36,2:0.0526:2,2:40.5:1:26:1:1:1.11:60:4:0.0526:0:1 +12 57674241 . CA C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13788;SOR=0;LSEQ=GCTGTTGCTGCTGGGCAGTA;RSEQ=AGGGAGAAGCCCCCGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:18,2:0.1:2,2:10.5:1:31:1:1:1:51:4:0.1:0.05:0.5 0/0:33:0:0,0:13,20:33,0:0:2,0:22.9:1:30.2:1:1:0:60:66:1:0:0.2 +12 57856933 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGAAGATCCCCAGAGTACA;RSEQ=AGACTACAAGACTGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:34.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 57857000 . G A 47 d5;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTCCCCTCACTCAGCGA;RSEQ=TGATGCTTTTTTTGTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:6:1:30:1:1:0:47.3:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 57857354 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10501;SOR=0.6624;LSEQ=TGTCTTAGAGGGGTGGGGGA;RSEQ=ACCAGGGATGTTCTGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:117:117,0:47,1:48,117:0.7091:1,1:23:1:32.4:1:0.29091:0:60:116:0.7073:0:1.1 1/0:128:79:79,0:48,1:49,79:0.6172:1,1:26.6:1:32.1:1:0.38281:0:60:78:0.6142:0:1.1 +12 57857647 . G T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02205;SOR=Inf;LSEQ=TGGGCCCACCCCCACCCCAT;RSEQ=CCAGTTTCCTATCTACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:167,288:455,0:0:2,0:23:1:32:1:1:0:60:36.917:0.9955:0:0.1 0/1:288:4:2,2:93,189:282,4:0.0139:2,2:31.3:1:26.5:1:0.60215:2.03:60:3:0.0112:0:2.5 +12 57858015 . GA TG 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01888;SOR=Inf;LSEQ=AGCACCATCAAGAAGTCACA;RSEQ=TGGGGCCGGGCGCGGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:3,98:101,0:0:1,0:22.4:1:32.5:1:1:0:60:49.5:1:0:0.1 0/1:61:4:0,4:1,56:57,4:0.0656:1,0:16.8:1:30:1:1:0:60:8:0.0678:0.0164:0.8 +12 57858414 . A G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29037;LSEQ=GGTTAGGTGCATGGAGAGAC;RSEQ=TGCCCCTTTACCATATCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:748:540:407,133:152,55:207,540:0.7219:2,2:22.8:1:29.9:1:0.57372:1.11:60:59:0.7234:0:1.1 0/1:696:299:224,75:275,120:395,299:0.4296:2,2:21.8:1:29.3:1:0.12602:1.30:60:98.667:0.4296:0:1.1 +12 57858421 . T C 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCATGGAGAGACATGCCCC;RSEQ=TTACCATATCCGTCTCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:840:0:0,0:597,243:840,0:0:2,0:23.2:1:31:1:1:0:60:59:1:0:0.7 0/1:815:54:39,15:517,244:761,54:0.0663:2,2:22.8:1:29.8:1:0.54947:1.23:60:26:0.0645:0:1.1 +12 57858835 . G A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.39952;LSEQ=TTCCAGAAATCCTCCAAATA;RSEQ=CCCAATCCTTCCTGAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:779:549:401,148:162,65:227,549:0.7047:2,2:23.1:1:29.8:1:0.65873:1.09:60:53.9:0.7027:0:1.1 0/1:707:345:250,95:260,102:362,345:0.488:2,2:22.9:1:28.8:1:0.86701:1.03:60:56.5:0.4864:0:1.1 +12 57859058 . T C 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGAGAGTCCCCATATTGC;RSEQ=ACCTGATTTCCCTCAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1243:0:0,0:498,745:1243,0:0:2,0:26.2:1:29.5:1:1:0:59.9:68.056:1:0:0.2 0/1:1260:57:23,34:516,687:1203,57:0.0452:2,2:26:1:31.1:1:0.7846:1.11018:60:56:0.0448:0:1.2 +12 57859431 . G A 316 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26139;LSEQ=CTGGTTGGCAAGTGCCGGGA;RSEQ=GAACCCTTGGAAGGTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1585:1160:580,580:210,214:424,1160:0.7319:2,2:24.5:1:31.1:1:0.90964:1.02:60:104.455:0.7323:0:1.2 0/1:1612:671:334,337:453,485:938,671:0.4163:2,2:24:1:29.8:1:0.5781:1.06:59.9:166.75:0.4174:0:1.2 +12 57859783 . G A 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03757;SOR=Inf;LSEQ=GTGGGACATGGTGGAATCCG;RSEQ=CTGAGGGCAGGAGGTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:89,321:410,0:0:2,0:23.4:1:32:1:1:0:59.8:50.25:1:0:0.1 0/1:324:4:2,2:67,253:320,4:0.0123:2,2:8:1:24.5:1:0.20013:3.76:60:8:0.0125:0:1.3 +12 57859932 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2938;LSEQ=TTCCTCCTTGAGGTGGAGTC;RSEQ=TGGAAGAGGAACAGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:362:267:228,39:83,12:95,267:0.7376:2,2:23.7:1:30.5:1:0.73256:1.1826:59.9:52.4:0.7339:0:1.1 0/1:259:117:106,11:128,14:142,117:0.4517:2,2:24.6:1:29.4:1:1:1.05:59.7:57.5:0.4475:0:1.1 +12 57860046 . C T 208 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=21.31045;LSEQ=ATCAACAGCGAGCACATCCA;RSEQ=GGGGAGCGGAAGGAGTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1446:7:2,5:762,676:1438,7:0.0048:2,2:10.6:1:29.4:1:0.2647:2.81613:60:14:0.0049:0:1 0/1:1426:134:65,69:652,638:1290,134:0.094:2,2:23.5:1:29.5:1:0.71669:1.08475:60:133:0.0942:0:1.1 +12 57860293 . T C 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.015;SOR=0;LSEQ=CCATAAACAAATATTAAAAA;RSEQ=AATGTTTGTGTGACTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:10:0,10:3,144:147,10:0.0637:1,0:14.1:1:32.8:1:1:0:60:20:0.0645:0:1 0/0:96:0:0,0:4,92:96,0:0:1,0:22.2:1:28:1:1:0:60:47:1:0:0.1 +12 57860665 . C T 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTGCACTCCAGCCTGGG;RSEQ=GACAGAGCAAAACTCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:24.3:1:30:1:1:0:38.3:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 57860826 . T C 109 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGCCCGTTCCCCCAAGA;RSEQ=GACCCCATCTTGGGACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:13,0:3,0:3,13:0.8125:0,1:30.9:1:29.6:1:1:0:60:12:0.8:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 57860972 . T C 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0027;SOR=Inf;LSEQ=TCTTGCCTGCCCTTGTCCCC;RSEQ=AGTTTTGGGAATTCTCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:150,2:152,0:0:1,0:25.7:1:31.6:1:1:0:59.8:15.889:1:0:0.2 0/1:93:6:6,0:86,1:87,6:0.0645:1,0:30.5:1:27.8:1:1:0:60:5:0.0556:0:1 +12 57861484 . A G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77905;SOR=0.82047;LSEQ=CTAACCTCTAACCAGCCAAA;RSEQ=GGCTAACCTAAAAGATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:57:16,41:4,16:20,57:0.7403:2,2:22.5:1:30.6:1:0.5652:1.55:58.6:10.4:0.7324:0:1.3 1/0:20:14:0,14:1,5:6,14:0.7:2,1:22.4:1:30.9:1:0.3:0:60:28:0.7:0:1.1 +12 57861785 . T C 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TCCACTCAACAGAAGCCGTA;RSEQ=GTATGTAAGCTCCCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1655:0:0,0:865,789:1654,0:0:2,0:26:1:30.7:1:1:0:60:77.762:1:0:0.1 0/1:1604:108:58,50:790,704:1494,108:0.0673:2,2:25.2:1:30:1:0.9206:1.03:60:107:0.0676:0:1.1 +12 57863084 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54113;SOR=0;LSEQ=TGCTCCCCCATCTCTTACCT;RSEQ=CTTAGCCCTTTCTACACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:154,5:159,2:0.0124:1,0:33:1:32:1:1:0:60:4:0.0126:0:1 0/0:88:0:0,0:87,1:88,0:0:1,0:24.4:1:31.3:1:1:0:59.7:43:1:0:0 +12 57865284 . C T 198 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01996;LSEQ=GCAGGGAAGATGCCCCCGCC;RSEQ=AGGAACCTTCCTACCAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1566:93:45,48:759,713:1472,93:0.0594:2,2:24.1:1:30.3:1:0.59337:1.13539:60:92:0.0596:0:1.1 0/0:1591:2:0,2:815,773:1588,2:0.0013:2,0:1:0:23:1:0.23742:0:53.5:4:0.0013:0:1.5 +12 57865321 . G A 314 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25812;LSEQ=GAGTCCCAAGTTTCTGGGGG;RSEQ=TTCCCAGGTTAGCCCAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1675:1262:645,617:189,217:406,1262:0.7534:2,2:24.9:1:30.5:1:0.12337:1.20:60:69.111:0.7535:0:1.1 0/1:1851:816:420,396:508,525:1033,816:0.4408:2,2:24.2:1:29.2:1:0.34891:1.10:59.9:61.769:0.4419:0:1.2 +12 57865821 . G C 332 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.59076;LSEQ=GATCCCTACCTGGGGAAACA;RSEQ=AATTCCTCAACTCTAGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1620:1221:585,636:174,222:396,1221:0.7537:2,2:25.3:1:32.4:1:0.18268:1.17:60:110:0.7544:0:1.1 1/0:1721:1108:526,582:295,316:611,1108:0.6438:2,2:24.2:1:31.3:1:0.76229:1.03293:60:84.231:0.6453:0:1.2 +12 57865928 . A C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTGGGGGAGCTGCAGTCCC;RSEQ=TGCACAAGATGCCCCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:429:429:73,356:0,0:0,429:1:0,2:23.5:1:32.8:1:1:0:60:213.5:1:0:1.1 1/1:366:347:67,280:5,14:19,347:0.9481:2,2:22.8:1:30.7:1:0.55118:1.49073:60:37.556:0.9468:0:1.1 +12 57865994 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13775;SOR=Inf;LSEQ=TATAGTCTGTATACGTTTTG;RSEQ=GGAGAAATTTGATAATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:3,129:132,0:0:1,0:23.7:1:32.3:1:1:0:60:43:0.9923:0:0.7 0/1:79:2:1,1:2,75:77,2:0.0253:1,2:23.5:1:31:0:0.07498:30.85:60:4:0.0263:0:1.5 +12 57982794 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GGACCACTGCCACCAAGACG;RSEQ=GGAGACCGATAGTGGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:25.2:1:32.2:1:1:0:60:10:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:20:1:27:1:1:0:60:4:0.6667:0:1 +12 57983043 . C A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28205;SOR=0.16243;LSEQ=TTTCACTATTTCTTCTACCG;RSEQ=TATCTACTAAGAACTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:1,6:1,0:1,7:0.875:0,2:16.3:1:31.3:1:0.25:0:33.3:14:0.875:0:1 1/0:8:4:1,3:0,4:4,4:0.5:0,2:32.8:1:30.8:1:1:0:37.8:8:0.5:0:1 +12 58142216 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57132;SOR=2.86454;LSEQ=AAAGATGGAGGAGGACCCTC;RSEQ=ATAGCCTCAGAGATAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:1:0,1:182,22:204,1:0.0049:2,0:1:0:24:0:0.1122:0:60:2:0.0051:0:2 0/1:144:2:1,1:117,25:142,2:0.0139:2,2:15.5:1:28:1:0.32955:4.60871:60:4:0.0139:0:1 +12 58142488 . T TTTC 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.02523;SOR=Inf;LSEQ=TGGGATGAGCTTTCTTCTTT;RSEQ=TTCTTTTTTTTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:10,199:209,0:0:1,0:20.1:1:30.5:1:1:0:56.1:25.125:1:0:0.7 0/1:140:4:0,4:6,130:136,4:0.0286:1,0:19.5:1:31.1:1:1:0:60:8:0.0294:0.0071:0 +12 58142854 . C A 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00617;SOR=0.47131;LSEQ=AGCTGTAATAAAAACTACAG;RSEQ=CCATCTACCAACCAAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:72:71,1:91,3:94,72:0.4337:1,1:25.2:1:30.4:1:0.63379:2.33:59.6:144:0.439:0:1.1 0/1:102:27:25,2:72,3:75,27:0.2647:1,2:26.4:1:28.9:1:0.606:1.90631:60:54:0.2647:0:1 +12 58143030 . TG T 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00433;SOR=Inf;LSEQ=CTGCACTGGGCGGGGCCCTC;RSEQ=GGGGGAAAGGCTCCACGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:796:0:0,0:362,432:794,0:0:2,0:23.8:1:31.6:1:1:0:60:98.25:0.9975:0:0.1 0/1:680:7:4,3:324,349:673,7:0.0103:2,2:18.9:1:28:1:0.71664:1.44:60:14:0.0104:0.0044:0.3 +12 58143349 . C T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26357;SOR=0;LSEQ=ATATCTTAGTTGAATGGTTA;RSEQ=TGCTTAGTGGCTCAAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:44,235:279,3:0.0106:2,2:30.7:1:29.3:1:0.4076:2.66:60:6:0.0108:0:1 0/0:212:0:0,0:51,161:212,0:0:2,0:22.4:1:31.4:1:1:0:60:105:1:0:0.1 +12 58143486 . T TA 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGACCTTGTCTCTTTTTT;RSEQ=AAAAAAAAAGAAATGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:0,22:22,2:0.0833:1,0:8.5:1:32:1:1:0:60:4:0.087:0.0417:0.5 0/0:10:0:0,0:0,10:10,0:0:0,0:26.5:1:27.4:1:1:0:60:20:1:0:0 +12 58143777 . TA T 29 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGACAGAGCAAGACTCCATC;RSEQ=AAAAAAAAAAAAGCCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:34.5:1:29.5:1:0.33333:0:49:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 58144349 . C CA 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.36388;SOR=0.49073;LSEQ=AACACAGCAAGCCCTGGTCT;RSEQ=AAAAAAAAAGAATGGGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:8:7,1:165,27:192,8:0.04:2,2:17.8:1:29.9:1:1:1.14:60:16:0.041:0.01:0.6 0/1:150:3:2,1:118,28:146,3:0.02:2,2:18:1:29.3:1:0.48019:2.09441:60:6:0.0201:0.0067:0.3 +12 58144359 . G T 190 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCCTGGTCTCAAAAAAAAA;RSEQ=AATGGGCAAGGTATGGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:91:74,17:135,27:162,91:0.3597:2,2:22.8:1:29.2:1:0.73074:1.14801:60:12:0.3457:0:1.1 0/0:198:0:0,0:151,46:197,0:0:2,0:20.7:1:30.9:1:1:0:60:196:1:0:0.1 +12 58144665 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36948;LSEQ=TACGGGCAATCACTCTCCTA;RSEQ=TCCCAACCAGAACCCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:216:135,81:159,93:252,216:0.4615:2,2:22.6:1:30.7:1:0.92372:1.02576:60:42.2:0.4577:0:1.1 0/1:387:93:61,32:184,110:294,93:0.2403:2,2:24.4:1:29.6:1:0.62369:1.14:60:92:0.2421:0:1.1 +12 58145156 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.05442;SOR=0.75808;LSEQ=TAAATGCTCACTTTTCAATC;RSEQ=CCTTTAACCCAACATGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:228:65,163:90,204:294,228:0.4351:2,2:23:1:30.3:1:0.62995:1.10612:59.8:37:0.437:0:1.1 0/1:331:122:34,88:61,148:209,122:0.3686:2,2:24.4:1:29:1:0.89984:1.06659:60:60:0.3681:0:1.1 +12 58145598 . C CA 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.81144;LSEQ=TGCAGCAACAAAGGGACTCC;RSEQ=AAAAAAAAAGCGCAAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:0,2:2,92:94,2:0.0208:1,0:32:1:31.5:1:1:0:60:4:0.0222:0:0 0/1:59:1:0,1:3,55:58,1:0.0169:2,0:41:0:33:0:1:0:60:2:0.0175:0:0 +12 58638231 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATGGAGTTGTTTAGAAAC;RSEQ=TGGAGTTGTTTGTTTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:11,15:0,0:0,26:1:0,2:25.3:1:30.4:1:1:0:58.5:52:1:0:1.1 1/1:17:17:9,8:0,0:0,17:1:0,2:21.7:1:30.1:1:1:0:56.2:34:1:0:1.3 +12 58638253 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03759;SOR=Inf;LSEQ=GGAGTTGTTTGTTTGGCCAC;RSEQ=TATATGTGAATTTCTAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:26,0:0:2,0:27.2:1:30.9:1:1:0:58.5:25:1:0:0.9 0/1:22:4:2,2:7,10:17,4:0.1818:2,2:28.5:1:29.8:1:1:1.40:47:8:0.1818:0:2 +12 58638327 . C T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.12281;SOR=Inf;LSEQ=GTTCAAAAAGGAATGCCCCA;RSEQ=TAATGCTGCCATGGCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:25,0:0:2,0:23.2:1:32.8:1:1:0:59.6:50:1:0:0.2 0/1:14:2:2,0:5,7:12,2:0.1429:2,0:7:1:30:1:0.46154:0:60:4:0.1429:0:2 +12 58638335 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAATGCCCCACTAATGCT;RSEQ=CCATGGCAAAACCGGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:22:1:28:1:1:1.11:59:4:0.0952:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:22.4:1:31.5:1:1:0:60:20:1:0:0.5 +12 58638348 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11084;SOR=Inf;LSEQ=TAATGCTGCCATGGCAAAAC;RSEQ=GGAACACTCTATAGTGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:19,0:0:2,0:28.7:1:30.6:1:1:0:59.9:38:1:0:0.2 0/1:10:2:2,0:4,4:8,2:0.2:2,0:28:1:32:0:0.46667:0:60:4:0.2:0:2 +12 58639786 . G A 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCCCCCCACCTAGTCCT;RSEQ=AAGACATAAGGTGCTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:9:1:26.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 58814924 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1464;SOR=Inf;LSEQ=TATTGCCTTATTTAGTAGAT;RSEQ=TTTTGTACGTTGTGTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:201,108:309,0:0:2,0:25.3:1:32.6:1:1:0:59.9:618:1:0:0.9 0/1:192:2:1,1:123,67:190,2:0.0104:2,2:16.5:1:27.5:1:1:1.82974:60:4:0.0105:0:1.5 +12 58814968 . A G 281 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGACATCATCCCAAATGCT;RSEQ=TCAATGTCAAAATGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:429:429:227,202:0,0:0,429:1:0,2:25.6:1:32.2:1:1:0:60:84.8:1:0:1.1 1/0:259:164:88,76:53,41:94,164:0.6332:2,2:25.9:1:30.9:1:0.69823:1.11593:60:53.667:0.6289:0:1.1 +12 58814990 . A G 82 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01454;SOR=9.80928;LSEQ=CAATGTCAAAATGACAGAAA;RSEQ=GGATGTAGAGCGTCCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:1:0,1:212,234:446,1:0.0022:2,0:28:0:34:0:1:0:60:2:0.0023:0:3 0/1:278:6:3,3:126,145:271,6:0.0216:2,2:19.2:1:31.8:1:1:1.15:60:12:0.0219:0:1.3 +12 58815319 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TAAAAAAATGAAAGCAAACA;RSEQ=CAAATAAAACAACATATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:39:1:33.5:1:1:0:54:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 59868733 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTATGAGATGCCACCCAG;RSEQ=GTTTATAGGAAAAGGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:15,10:25,2:0.0741:2,2:36:1:31.5:1:1:1.47706:45:4:0.0741:0:1 0/0:9:0:0,0:6,3:9,0:0:2,0:18.8:1:27.8:1:1:0:60:8:1:0:0 +12 59868991 . T C 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACCAAGGACCCCTGGAC;RSEQ=GACCCACTGGCCCTTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:30:1:29:1:1:1:35:4:0.5:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:6:0:32:0:1:0:28:2:1:0:0 +12 60263226 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6636;SOR=0.9173;LSEQ=ACTTCTCAGAATTCCATTCA;RSEQ=CTAAGCATTCTGGGCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:137:74,63:81,68:149,137:0.479:2,2:24.4:1:32.8:1:1:1.01406:59.7:274:0.479:0:1.1 0/1:247:113:66,47:73,61:134,113:0.4575:2,2:26.6:1:30.9:1:0.6068:1.17:60:112:0.4553:0:1.1 +12 60263339 . A G 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=TTTTTAATGCACAAATGGAA;RSEQ=GAACCATGATGTTAGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:10,69:79,0:0:2,0:23.1:1:32.2:1:1:0:60:158:1:0:0.1 0/1:73:11:1,10:12,50:62,11:0.1507:2,2:21.2:1:28.8:1:0.67596:2.37692:60:10:0.1389:0:1.3 +12 60263362 . CA C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.22492;SOR=Inf;LSEQ=ACCATGATGTTAGTGCCTTG;RSEQ=AAAAAAGGTAGGCCACTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:1,45:46,0:0:1,0:28.7:1:31.6:1:1:0:60:92:1:0:0.1 0/1:42:2:0,2:3,37:40,2:0.0476:2,0:19.5:1:33:0:1:0:60:4:0.0476:0:0.5 +12 61873046 . G A 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CCACAACTAATATAAGTCAC;RSEQ=TCTTCACATAGTAAATATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:18:9,9:165,159:324,18:0.0525:2,2:21.3:1:30.9:1:1:1.03764:60:36:0.0529:0:2.7 0/0:332:0:0,0:183,149:332,0:0:2,0:27.3:1:29.9:1:1:0:60:109.667:1:0:1.5 +12 61873055 . T C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97162;LSEQ=ATATAAGTCACGTCTTCACA;RSEQ=AGTAAATATCAGGAATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:353:352:175,177:0,0:0,352:0.9972:0,2:26.5:1:32.1:1:1:0:59.9:57.667:0.9971:0:1.3 1/1:343:342:190,152:0,0:0,342:0.9971:0,2:26.8:1:31.2:1:1:0:60:84.5:0.9971:0:1.6 +12 61873087 . A G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0;SOR=4.66378;LSEQ=GGAATGGAGTATGCAAAAAC;RSEQ=TGTAAATATTCATAATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:78:32,46:116,157:273,78:0.2222:2,2:28.3:1:31.1:1:0.89672:1.06194:60:77:0.2219:0:2.1 1/0:327:187:85,102:64,76:140,187:0.5719:2,2:25.5:1:30.1:1:1:1.0105:60:92.5:0.5728:0:1.9 +12 61873147 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24803;SOR=0;LSEQ=ACAGTTTAGAAAGTAATTTT;RSEQ=CATTTATTTTTTACATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:2,1:44,107:151,3:0.0195:2,2:11.7:1:28.3:1:0.2127:4.81:60:6:0.0196:0:1 0/0:146:0:0,0:41,105:146,0:0:2,0:25.7:1:31.6:1:1:0:60:145:1:0:0.5 +12 61873411 . T C 70 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCAATACATTAAAGGTA;RSEQ=TCAAAAGTTAGACCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:15:1:35.3:1:1:0:58.8:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 62168965 . G T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGGATGTGGAGCAACAA;RSEQ=AACTCTCATTCATTGCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:27.5:1:1:0:60:4:1:0:1 +12 62169686 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGCAGGAACTTCCATA;RSEQ=TTCAGTAATATGCCAAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:0,8:1:0,2:30.1:1:32:1:1:0:60:16:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:10.5:1:31:1:1:0:60:4:1:0:1 +12 62169944 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50598;SOR=0;LSEQ=TTGTAAACAGACAATTTAAG;RSEQ=GCATGATTCTTGCCAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:26,70:96,2:0.0204:2,2:24.5:1:28.5:1:0.47717:2.66:60:4:0.0206:0:1 0/0:75:0:0,0:24,51:75,0:0:2,0:22.1:1:29.5:1:1:0:59.7:17.75:1:0:0.4 +12 62169948 . T C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13589;SOR=0.59283;LSEQ=AAACAGACAATTTAAGGGCA;RSEQ=GATTCTTGCCAAAAGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:39:8,31:14,39:53,39:0.4239:2,2:21.7:1:29.7:1:0.62341:1.3861:60:38:0.4176:0:1 0/1:66:20:4,16:15,31:46,20:0.303:2,2:20.5:1:29.3:1:0.38276:1.91725:59.1:19:0.2969:0:1.2 +12 62290554 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52434;SOR=0;LSEQ=TGTCACATTGTCAACCAAAT;RSEQ=CTAAATATATATTCTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:95,31:126,2:0.0156:2,2:28.5:1:27.5:1:0.43898:3.03204:60:4:0.0156:0:1 0/0:80:0:0,0:58,22:80,0:0:2,0:24.1:1:30.1:1:1:0:60:19:1:0:0.4 +12 62290583 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15828;SOR=Inf;LSEQ=ATATTCTGATTTCTAAGAGA;RSEQ=CCTGGAACCTAAATTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:121,75:196,0:0:2,0:25.3:1:31.7:1:1:0:60:64.333:1:0:0.4 0/1:130:2:0,2:74,54:128,2:0.0154:2,0:12.5:1:27.5:1:0.18366:0:60:4:0.0157:0:4 +12 62290629 . T C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.9145;LSEQ=GATGTAACTGCTTGCATTAT;RSEQ=TATGATGTTTCCTTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:63:30,33:85,101:186,63:0.253:2,2:22.7:1:32.3:1:0.88388:1.08:60:126:0.254:0:1.9 1/0:187:117:54,63:31,39:70,117:0.6257:2,2:24.2:1:31.1:1:0.87967:1.08:60:116:0.627:0:1.8 +12 62290646 . T A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57867;SOR=2.68383;LSEQ=TATTTATGATGTTTCCTTTC;RSEQ=TTTGCCTGCCATCAAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:1,0:96,129:225,1:0.0044:2,0:1:0:27:0:0.4292:0:60:2:0.0044:0:1 0/1:170:2:1,1:72,95:167,2:0.0118:2,2:18.5:1:29.5:1:1:1.32:60:4:0.0118:0:3 +12 62290651 . C G 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.07004;SOR=0;LSEQ=ATGATGTTTCCTTTCTTTTG;RSEQ=CTGCCATCAAGCTATTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:5:2,3:86,122:208,5:0.0235:2,2:18.4:1:31:1:1:1.05711:60:10:0.0236:0:3.6 0/0:167:0:0,0:70,97:167,0:0:2,0:26.7:1:30.7:1:1:0:60:82.5:1:0:1.2 +12 62290656 . C T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=4.44311;LSEQ=GTTTCCTTTCTTTTGCCTGC;RSEQ=ATCAAGCTATTTGTGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:45:14,31:65,90:155,45:0.225:2,2:25.1:1:29.5:1:0.22687:1.59555:60:90:0.2261:0:2.2 1/0:163:92:36,56:28,42:70,92:0.5644:2,2:27.9:1:28.6:1:1:1.03683:60:184:0.5679:0:1.9 +12 62290662 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09643;SOR=Inf;LSEQ=TTTCTTTTGCCTGCCATCAA;RSEQ=CTATTTGTGATACAAATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:68,115:183,0:0:2,0:25.8:1:32.7:1:1:0:60:182:1:0:0.6 0/1:156:3:3,0:61,92:153,3:0.0192:2,0:9.3:1:27.3:1:0.06713:0:60:6:0.0196:0:1.3 +12 62290742 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00021;SOR=0.08292;LSEQ=TAGATAATATCTTATCTCTA;RSEQ=TGAGGGTCCAGATGATCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:20:3,17:0,20:20,20:0.5:1,2:22.3:1:32.9:1:0.23077:0:60:40:0.5:0:1.3 0/1:27:2:0,2:4,21:25,2:0.0741:2,0:16.5:1:33:0:1:0:60:4:0.0741:0:1 +12 62290795 . C T 84 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39211;SOR=0.25813;LSEQ=TTCATGCAATATTACTTTTC;RSEQ=ATATTATTTGATACATATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:0,8:0,18:18,8:0.3077:1,0:28:1:28.3:1:1:0:60:16:0.32:0:1.5 0/1:10:1:0,1:0,9:9,1:0.1:0,0:19:0:29:0:1:0:60:2:0.1:0:1 +12 62755589 . T A 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCAAAATGTTTTCTAAAAG;RSEQ=TTACCATTTACTTCTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:0:0,0:350,243:593,0:0:2,0:25.7:1:29.9:1:1:0:60:117.6:0.9983:0:0.5 0/1:395:91:54,37:169,135:304,91:0.2304:2,2:23.6:1:28.7:1:0.54888:1.17:60:90:0.2314:0:1.1 +12 62755631 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.4978;LSEQ=TGATTTATAAACTATTCTGG;RSEQ=CAGGGGAGAGGGTCAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:629:389:182,207:112,128:240,389:0.6184:2,2:26.3:1:29.9:1:1:1.00:59.9:76.8:0.6204:0:1.1 0/1:457:204:91,113:114,139:253,204:0.4464:2,2:25.8:1:28.8:1:0.92498:1.01838:60:101:0.4459:0:1.1 +12 63294744 . T G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12237;SOR=Inf;LSEQ=TTTCCGAGTCACATCTGAGA;RSEQ=CTCACCCTCTCTAAACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:213,50:263,0:0:2,0:23.1:1:30.7:1:1:0:60:51.6:1:0:0.1 0/1:142:2:2,0:99,41:140,2:0.0141:2,0:19.5:1:29.5:1:1:0:60:4:0.0141:0:1 +12 63294746 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04193;SOR=Inf;LSEQ=TCCGAGTCACATCTGAGATC;RSEQ=CACCCTCTCTAAACTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:217,61:278,0:0:2,0:22.9:1:31.3:1:1:0:60:38.714:1:0:0.1 0/1:149:3:2,1:104,42:146,3:0.0201:2,2:45:1:31.3:1:1:1.2362:60:6:0.0203:0:1 +12 63294859 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00678;SOR=0.68155;LSEQ=TCCGCCTCTATTTCCATGTA;RSEQ=CCGGATACATTTTTGCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:516:294:129,165:89,131:220,294:0.5698:2,2:24.8:1:30:1:0.47093:1.15:60:97:0.5717:0:1.1 0/1:350:166:81,85:83,101:184,166:0.4743:2,2:24.2:1:28.7:1:0.52069:1.16:60:82:0.4824:0:1.1 +12 63295001 . T C 138 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00562;SOR=0.09488;LSEQ=CTGATACCATATGTTCCCAG;RSEQ=GGGCAACAGCCAATCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:23:1,22:1,44:45,23:0.3382:1,1:26.3:1:30.7:1:1:1.98:60:46:0.3382:0:1 0/1:22:1:0,1:1,20:21,1:0.0455:1,0:3:0:26:0:1:0:60:2:0.0455:0:1 +12 65379265 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.61987;LSEQ=TCTGACAAGGCATTTCATAA;RSEQ=CTTCACCCAAGCACCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:13:9,4:139,69:208,13:0.0588:2,2:22.8:1:29.8:1:1:1.12:60:26:0.0588:0:1.4 0/1:178:40:25,15:88,49:137,40:0.2247:2,2:27.9:1:29.3:1:0.85333:1.07709:60:80:0.2286:0:1 +12 65379373 . G C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.7449;SOR=0.94404;LSEQ=AGACATGTTCTTTATACAAA;RSEQ=CAGCCTGCTACAGCTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:305:164:77,87:58,83:141,164:0.5377:2,2:24.7:1:31.9:1:0.35516:1.27:60:328:0.5395:0:1.1 1/0:300:157:73,84:66,74:140,157:0.5233:2,2:26.7:1:30.2:1:1:1.02621:60:156:0.5324:0:1.1 +12 65379582 . CT C 34 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=ATAATCTTGTAAGTTTTGGG;RSEQ=TTTTTTTTTTTTTGCCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,9:9,0:0:0,0:17.4:1:27.8:1:1:0:60:8:0.8:0:1.4 0/1:5:2:0,2:0,3:3,2:0.4:0,0:41:1:34:0:1:0:60:4:0.4:0:0 +12 66431045 . AC A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18976;SOR=Inf;LSEQ=CAAAGGGAAAGAAGACAGGC;RSEQ=CCAATATATGTTCTCTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:60,43:103,0:0:2,0:26.4:1:32.1:1:1:0:47.2:102:1:0:0.1 0/1:80:2:1,1:34,44:78,2:0.025:2,2:13:1:28.5:1:1:1.29:36:4:0.0253:0.0125:0.5 +12 66431148 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23025;SOR=Inf;LSEQ=TATTGTAGATGTAAGAGAAT;RSEQ=GGTACTTTTCAAAAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:120,80:200,0:0:2,0:23.3:1:31.7:1:1:0:47.2:49:1:0:0.1 0/1:185:2:1,1:110,73:183,2:0.0108:2,2:23.5:1:28:1:1:1.50338:45.5:4:0.0109:0:1 +12 66431273 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.18232;SOR=Inf;LSEQ=AGGGCAAGATTCTTGTCAAG;RSEQ=GAATTAACGTGCATATTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:16,88:104,0:0:2,0:23.2:1:31.7:1:1:0:42.4:208:1:0:0.1 0/1:78:2:1,1:13,63:76,2:0.0256:2,2:12:1:30.5:1:0.32867:4.71:29.5:4:0.026:0:1 +12 66943027 . T C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00404;SOR=0.38362;LSEQ=AGGGAATTATAATGGGGTGG;RSEQ=GAGCATCAGCTTGTGGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:42:42,0:40,5:45,42:0.4828:2,1:17.8:1:33.3:1:0.05609:0:60:84:0.4884:0:1.2 0/1:80:21:21,0:55,4:59,21:0.2625:2,1:28.8:1:32:1:0.56835:0:60:42:0.2692:0:1.2 +12 66943069 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10038;SOR=Inf;LSEQ=AGAATTATTGCTGGACGGTG;RSEQ=AGAAGCAAAATGATAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:163,42:205,0:0:2,0:25.5:1:31.9:1:1:0:60:33.167:1:0:0.6 0/1:179:3:1,2:131,45:176,3:0.0168:2,2:17.7:1:28:1:0.16906:5.75275:60:6:0.017:0:1.3 +12 66943117 . T C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32933;LSEQ=CTGAACAGGAGCAGACAGAG;RSEQ=TATTTCCCTAAGCTTACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:188:113,75:120,85:205,188:0.4784:2,2:24.4:1:32.4:1:0.75896:1.07:59.9:61.667:0.4768:0:1.6 0/1:410:95:50,45:182,133:315,95:0.2317:2,2:25.8:1:30.9:1:0.40917:1.23094:60:46.5:0.2285:0:1.6 +12 66943175 . A G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.47556;LSEQ=ATGCCTTAGTAAGGGGAATT;RSEQ=GGGCACGCACCAGAATACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:233:99,134:109,127:236,233:0.4968:2,2:27.2:1:31.5:1:0.45738:1.16132:59.9:76.667:0.4946:0:1.5 0/1:476:152:65,87:154,169:323,152:0.3193:2,2:24.6:1:30.5:1:0.32557:1.21915:60:304:0.322:0:1.4 +12 66943230 . T A 57 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06283;SOR=0;LSEQ=TACTACTATTGAAAAAAATA;RSEQ=TATTGCTCATACTACAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:5:4,1:90,199:289,5:0.017:2,2:6:1:24.8:1:0.03758:8.78:60:4:0.0138:0:1.8 0/0:267:0:0,0:87,180:267,0:0:2,0:24.4:1:29.4:1:1:0:60:88:1:0:0.3 +12 66943257 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49926;SOR=0;LSEQ=TCATACTACAGTTTTATCTG;RSEQ=ATATTACTTTTGGTGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:39,140:179,2:0.011:2,2:12.5:1:29.5:1:0.39411:3.56:60:4:0.0111:0:1 0/0:168:0:0,0:41,127:168,0:0:2,0:23.3:1:27.6:1:1:0:59.9:55:1:0:0.2 +12 66943270 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.5028;SOR=0;LSEQ=TTATCTGTATATTACTTTTG;RSEQ=TGGTGCCACTAGGAAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:22,117:139,2:0.0142:2,2:11.5:1:29:1:0.30061:5.22:60:4:0.0145:0:1.5 0/0:116:0:0,0:18,97:115,0:0:2,0:25:1:31.4:1:1:0:59.9:114:1:0:0.1 +12 66943275 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19331;SOR=Inf;LSEQ=TGTATATTACTTTTGGTGGT;RSEQ=CCACTAGGAAGTTTATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:18,119:137,0:0:2,0:22.7:1:32:1:1:0:60:33.25:1:0:0.1 0/1:108:2:1,1:15,91:106,2:0.0185:2,2:18:1:27:1:0.27553:5.91:60:4:0.0189:0:1 +12 68307522 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.31658;LSEQ=TTATATCTCTATTCAGTCTC;RSEQ=TTTCTGATGCCCCCAACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:195:173:89,84:12,10:22,173:0.8872:2,2:26.5:1:30.7:1:0.82427:1.13186:59.8:85.5:0.886:0:1.1 1/0:195:139:74,65:29,27:56,139:0.7128:2,2:25:1:29.5:1:0.87518:1.06:60:138:0.7113:0:1.1 +12 68307536 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24814;SOR=0;LSEQ=AGTCTCGTTTCTGATGCCCC;RSEQ=AACATACTCCATCAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:1,2:95,103:198,3:0.0149:2,2:21.3:1:29.7:1:1:1.83927:60:6:0.0151:0:2 0/0:199:0:0,0:103,96:199,0:0:2,0:24.5:1:30.4:1:1:0:60:98.5:1:0:0.7 +12 68307594 . T C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.91089;LSEQ=TGAGGACAGAGTTAAAGCTT;RSEQ=CCCTAGGATCATGTGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:0,1:34,80:114,1:0.0087:2,0:42:0:12:0:1:0:60:0:0:0:2 0/1:121:2:1,1:37,81:118,2:0.0165:2,2:20.5:1:29:1:0.53487:2.17:60:4:0.0167:0:2.5 +12 68316282 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAGACGTTTAATTTCCAAA;RSEQ=TGTACAAGAGGGGAATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:28.5:1:1:0:60:4:1:0:2 +12 68316304 . C G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACAAGAGGGGAATGTTTT;RSEQ=AAATCCTGTTTCACAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:46.5:1:32:1:1:0:60:4:1:0:2 +12 68616970 . G T 94 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38577;SOR=0.29539;LSEQ=TTTACCCCAGGGCATAAACT;RSEQ=CACAGCTTGTAAGACAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:8,0:16,0:16,8:0.3333:1,0:20.4:1:31.5:1:1:0:60:16:0.3333:0:1.8 0/1:8:1:1,0:7,0:7,1:0.125:0,0:9:0:32:0:1:0:60:2:0.125:0:2 +12 68617021 . C G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30674;SOR=1.6056;LSEQ=TGATAGGCTTGAGGTGGGAG;RSEQ=AGGGAAGAAGGAAAGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:31:31,0:40,0:40,31:0.4366:1,1:23.7:1:30.7:1:1:0:60:9.333:0.4242:0:1.3 1/0:36:20:20,0:15,1:16,20:0.5556:1,1:20:1:29.4:1:0.44444:0:60:9:0.5294:0:1.1 +12 68617104 . C T 51 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05731;SOR=Inf;LSEQ=TATTTGGCCACAGGAGGGAG;RSEQ=CAGACCCTTTGGGAAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:235,63:298,0:0:2,0:23.7:1:31.7:1:1:0:60:73.5:1:0:0.2 0/1:287:4:1,3:218,65:283,4:0.0139:2,2:5:1:25.5:1:0.04259:9.95724:60:8:0.0144:0:1.3 +12 68617219 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=1.56308;LSEQ=CCAGAGTTCCTAGACATATC;RSEQ=AGGTTTCCTAAGCTTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:220:97,123:205,253:458,220:0.324:2,2:24.7:1:29.6:1:0.93424:1.02743:60:43:0.3214:0:1.1 0/1:775:332:147,185:215,227:442,332:0.4284:2,2:23.4:1:28.4:1:0.24448:1.1917:60:65.4:0.4269:0:1.1 +12 69201797 . C G 50 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACACCCCCACCCCGCCTCA;RSEQ=AGCCCGCCGCGCCCGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:39.3:1:32:1:1:0:60:6:1:0:1.7 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:31:1:1:0:56:4:1:0:1.5 +12 69202164 . A G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10913;LSEQ=CTGGCCCGGAGAGTGGAATG;RSEQ=TCCCCGAGGCCCAGGGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:159:118:95,23:31,10:41,118:0.7421:2,2:23.6:1:31.3:1:0.50881:1.33:60:38.333:0.7372:0:1.1 0/1:97:23:19,4:58,16:74,23:0.2371:2,2:18:1:30:1:0.77463:1.31:60:10.5:0.2234:0:1 +12 69202171 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.53681;SOR=0;LSEQ=GGAGAGTGGAATGATCCCCG;RSEQ=GGCCCAGGGCGTCGTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:147,40:187,2:0.0106:2,2:27.5:1:30.5:1:0.38771:3.64261:60:4:0.0107:0:2.5 0/0:107:0:0,0:85,22:107,0:0:2,0:23.1:1:28.6:1:1:0:60:106:1:0:0.3 +12 69202255 . C A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03015;SOR=Inf;LSEQ=GACTCCAAGCGCGAAAACCC;RSEQ=GGATGGTGAGGAGCAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:541:0:0,0:281,257:538,0:0:2,0:26:1:30.3:1:1:0:60:52.8:0.9944:0:0.4 0/1:388:4:2,2:201,181:382,4:0.0103:2,2:22.3:1:30.5:1:1:1.11019:60:8:0.0105:0:1 +12 69202326 . C T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08351;LSEQ=CTGGGCTCTGACGGTGTCCC;RSEQ=TCTATCGCTGGTTCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:404:330:122,208:31,41:72,330:0.8168:2,2:23.7:1:30.8:1:0.3505:1.28823:60:109:0.8175:0:1.1 0/1:281:76:30,46:81,122:203,76:0.2705:2,2:26.7:1:29.6:1:1:1.01797:60:37:0.2681:0:1.2 +12 69202580 . T G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=CCGGGGGCTGCGGGGCCGCT;RSEQ=CGGCGCGGGAGGTCCGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,5:8,0:0:2,0:32.9:1:28.5:1:1:0:60:7:1:0:0.3 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:21.5:1:33:0:1:0:60:4:0.6667:0:2.5 +12 69202810 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=TCCCAGCTGTGTTCAGTGGC;RSEQ=ATTGGAGGGTAGACCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:54,2:56,0:0:1,0:22.7:1:30.4:1:1:0:60:112:1:0:0.2 0/1:20:2:1,1:16,2:18,2:0.1:2,2:9:1:27:1:0.28421:6.73285:60:4:0.1:0:1 +12 69202867 . G C 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00483;SOR=0;LSEQ=CTTTTTCTCTGCTGATCCAG;RSEQ=TAAGCACCGACTTGCTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:13:13,0:118,2:120,13:0.0977:1,1:27.7:1:30.9:1:1:0:60:12:0.0923:0:1 0/0:75:0:0,0:73,2:75,0:0:1,0:21.9:1:31.3:1:1:0:60:150:1:0:0.1 +12 69202888 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15817;SOR=Inf;LSEQ=TAAGCACCGACTTGCTTGTA;RSEQ=CTTTAGTTTTAACTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:177,7:184,0:0:1,0:24.6:1:33:1:1:0:60:35.8:1:0:0.2 0/1:122:2:1,1:110,10:120,2:0.0164:2,2:10.5:1:28:1:0.17288:10.53577:60:4:0.0164:0:1 +12 69202971 . C CT 76 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54144;SOR=1.67605;LSEQ=ATTTCCAGTTTTCATCGTGT;RSEQ=TTTTTTTTCCTTGTAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:821:5:2,3:530,286:816,5:0.0061:2,2:36.6:1:31.6:1:0.35122:2.77602:60:10:0.0062:0:0 0/1:590:6:3,3:356,228:584,6:0.0102:2,2:19:1:29.5:1:0.68341:1.56014:60:12:0.0102:0.0034:0.3 +12 69203312 . G A 119 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0797;SOR=0.07842;LSEQ=CCATTACATTGTTAAGCGTG;RSEQ=TTGAAGTTACGTTTGTTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:1,15:0,2:2,16:0.8889:0,1:21.9:1:29.8:1:1:0:60:7:0.875:0:1.3 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:40:0:27:0:1:0:60:2:0.3333:0:1 +12 69203524 . T A 77 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGCGTACCCACATATA;RSEQ=TTACATTTGAATTTAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:23.3:1:30:1:1:0:58.7:5:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 69207162 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.59054;SOR=0.71865;LSEQ=GCTCTTTTGGATTGGATACT;RSEQ=TCTGTGATCACAACTGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:67:67,0:14,0:14,67:0.8272:1,1:23.1:1:29.4:1:1:0:60:134:0.8272:0:1 1/0:31:24:22,2:7,0:7,24:0.7742:0,2:27.5:1:28.4:1:1:0:58.7:48:0.7742:0:1.1 +12 69207194 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07044;SOR=Inf;LSEQ=AACTGATACTTGATGATTCC;RSEQ=TGATACTTGCATAATGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:136,1:137,0:0:1,0:28.6:1:30.8:1:1:0:60:136:1:0:0.6 0/1:50:2:2,0:47,1:48,2:0.04:1,0:18.5:1:27.5:1:1:0:60:4:0.0408:0:1.5 +12 69207561 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13959;SOR=Inf;LSEQ=GTTTGGACTATATTTTAAAG;RSEQ=TGAAAATTCTAATTATACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:0,31:31,0:0:1,0:23:1:33.8:1:1:0:60:62:1:0:0.1 0/1:19:2:0,2:1,16:17,2:0.1053:1,0:22.5:1:31:0:1:0:60:4:0.1053:0:1 +12 69210757 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08338;SOR=Inf;LSEQ=GTTTAGTCCATTGTAAAAAG;RSEQ=CATCTGGGCTAACATTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:77,262:339,0:0:2,0:24.3:1:31.1:1:1:0:59.9:47.429:1:0:0.1 0/1:264:3:1,2:73,187:260,3:0.0114:2,2:35.3:1:28.7:1:1:1.28:60:6:0.0117:0:1 +12 69210789 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13024;SOR=Inf;LSEQ=ACATTTCAGTTCACCTCTAC;RSEQ=CTCATTCACTTTTGTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:16,185:201,0:0:2,0:24.5:1:31.5:1:1:0:59.9:200:1:0:0 0/1:114:2:1,1:12,100:112,2:0.0175:2,2:22:1:29.5:1:0.21596:8.05:60:4:0.0179:0:1 +12 69211456 . C T 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGAATCACTTGAACCAGG;RSEQ=AGGTGGAGGTTGTGGTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21:0:30:0:1:0:48:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 69214011 . G T 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.552;SOR=0;LSEQ=TGTGCAGTAGTTCATACTAA;RSEQ=TATGTATGTAGAAGTCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:2,0:120,3:123,2:0.016:1,0:7:1:27.5:1:1:0:60:4:0.0163:0:1 0/0:63:0:0,0:62,1:63,0:0:1,0:24.5:1:32:1:1:0:59.9:126:1:0:0.1 +12 69214081 . AT A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.32008;SOR=0.76875;LSEQ=TAAAATGTACATCTCTTGTT;RSEQ=TTTTTTTTTTTCTGTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:50:36,14:302,84:386,50:0.1124:2,2:23.7:1:31.3:1:0.36736:1.397:59.9:24:0.1086:0.0225:0.3 0/1:282:25:17,8:182,72:254,25:0.0887:2,2:24:1:29:1:0.81691:1.18875:60:24:0.086:0.0248:0.1 +12 69214691 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACATGTATATATACATGG;RSEQ=TAAGTCAATAAGTGTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:26.5:1:30:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 69218038 . T G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=19.27491;LSEQ=TTTAATGTTTATTGAAAGGT;RSEQ=AAATTGCATAAGGGTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:7:7,0:147,10:157,7:0.0427:2,0:23.7:1:32.6:1:1:0:60:14:0.044:0:1 0/1:88:41:39,2:40,7:47,41:0.4659:2,1:25.8:1:31.3:1:0.16622:3.37:60:40:0.4651:0:1.2 +12 69218083 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07746;SOR=Inf;LSEQ=ACTGATAGCATATCTACTGA;RSEQ=TAGCGCCCCGCCGCCCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:244,79:323,0:0:2,0:26.7:1:33:1:1:0:60:160.5:1:0:0.2 0/1:241:3:1,2:166,72:238,3:0.0124:2,2:12.7:1:27.3:1:0.22391:4.57829:60:6:0.0127:0:1 +12 69218090 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08848;SOR=Inf;LSEQ=GCATATCTACTGAGTAGCGC;RSEQ=CCGCCGCCCCCCGCCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:278,94:372,0:0:2,0:25.4:1:30.6:1:1:0:59.9:40.333:1:0:0.2 0/1:300:3:1,2:195,102:297,3:0.01:2,2:8.3:1:29.7:1:0.27651:3.80497:60:6:0.0101:0:1 +12 69218096 . G A 58 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.47555;SOR=1.74221;LSEQ=CTACTGAGTAGCGCCCCGCC;RSEQ=CCCCCCGCCCACCACCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:3:1,2:292,116:408,3:0.0073:2,2:34:1:30.7:1:0.19932:5.01157:60:6:0.0074:0:1 0/1:316:4:2,2:200,112:312,4:0.0127:2,2:21.8:1:29:1:0.6215:1.78216:60:8:0.0132:0:1.3 +12 69218525 . CT C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16911;SOR=Inf;LSEQ=AGACTTAATTAAATTGTTCC;RSEQ=TTTTTTGGTTGAGATGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:2,129:131,0:0:1,0:23.6:1:30.6:1:1:0:59.7:130:1:0:0 0/1:92:2:0,2:4,86:90,2:0.0217:1,0:17:0:33:0:1:0:60:4:0.0217:0:0.5 +12 69222357 . C A 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07327;SOR=0.16568;LSEQ=GAGCAAGACCCTTTCTCAGA;RSEQ=AATAAATAAATAAACAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:26:26,0:4,0:4,26:0.8667:0,1:17.7:1:31.1:1:1:0:60:52:0.8667:0:1.1 1/0:6:3:3,0:3,0:3,3:0.5:0,0:9:1:29.7:1:1:0:60:6:0.5:0:1 +12 69222464 . C G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12648;LSEQ=TTGAACTAATTTTATTGAAA;RSEQ=TAAGTTTCTGTACAAATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:165:155,10:30,0:30,165:0.8418:1,2:21.8:1:33.1:1:0.36564:0:60:54:0.8438:0:1.1 0/1:80:32:30,2:45,3:48,32:0.4:2,2:25.8:1:31.6:1:1:1:60:64:0.4051:0:1 +12 69222528 . A AT 60 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.43433;SOR=2.25326;LSEQ=AAATCACAGTACAGCAATTT;RSEQ=TTTTTTTTCCTTACATATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:3:3,0:388,155:543,3:0.0055:2,0:24.3:1:31:1:0.56197:0:60:6:0.0056:0:0.3 0/1:325:4:3,1:215,106:321,4:0.0123:2,2:21:1:30:1:1:1.48:60:8:0.0124:0:0 +12 69222809 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGAATGTACATGTGTCTTA;RSEQ=GAGATTGATAGAAAACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:3,221:224,0:0:1,0:24.5:1:30.6:1:1:0:60:111:1:0:0 0/1:95:10:0,10:1,84:85,10:0.1053:1,0:21.6:1:29.8:1:1:0:60:20:0.1064:0:1.1 +12 69229553 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15115;SOR=Inf;LSEQ=CAGGGATGAGTTAGGAAACA;RSEQ=ATACAGAGGTCAAGAGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:148,10:158,0:0:2,0:23.8:1:33.4:1:1:0:60:78:1:0:0.1 0/1:101:2:1,1:93,6:99,2:0.0198:2,2:19:1:24.5:1:0.13446:14.42391:60:4:0.0198:0:1 +12 69230189 . G T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19706;SOR=0.19028;LSEQ=TATTTAATATCTCCATATTA;RSEQ=TTATTTATGAAGTAAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:11,1:2,0:2,12:0.8571:0,2:25.4:1:30.8:1:1:0:60:24:0.8571:0:1.3 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19.5:1:28.5:1:1:0:60:4:0.5:0:1 +12 69230735 . C CT 49 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TTTAGGTGCTGGAATTTGAA;RSEQ=TTTTTTTTTTTTTTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,3:3,3:0.4286:0,0:16.7:1:31:1:1:0:53:6:0.6:0.1429:4.3 0/0:2:0:0,0:0,1:1,0:0:0,0:12:1:33:0:1:0:60:2:0.5:0:0 +12 69232879 . ATAAC A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10672;SOR=0.26584;LSEQ=AATTTCCAGTATACCAATAT;RSEQ=TAACTATAGTCCTCATGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:25:24,1:7,1:8,25:0.7576:2,1:20.2:1:31.7:1:0.43182:3.27:59.6:50:0.7813:0.1212:0 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:19:1:31.6:1:1:0:60:8:0.4444:0.1111:0 +12 69233067 . G A 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00786;SOR=Inf;LSEQ=ATTGAAGGACTATTGGAAAT;RSEQ=CACTTCATGCAATGAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:772:0:0,0:491,281:772,0:0:2,0:24.5:1:32.1:1:1:0:60:69.182:1:0:0.1 0/1:474:5:3,2:296,172:468,5:0.0105:2,2:27:1:27.4:1:1:1.14694:60:10:0.0106:0:1 +12 69233215 . A G 195 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=124.5168;LSEQ=GAAAACTCAACACAAGCTGA;RSEQ=GAGGGCTTTGATGTTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1396:1:0,1:652,743:1395,1:7e-04:2,0:18:0:31:0:1:0:60:2:7e-04:0:1 0/1:975:80:38,42:420,475:895,80:0.0821:2,2:23.1:1:30.9:1:1:1.02:60:160:0.0828:0:1.2 +12 71002542 . G T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATTTAATGCAATGGAAGC;RSEQ=TAAACCACATCACTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:28:1:1:0:60:4:1:0:1 +12 72825422 . GT G 98 MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.04952;SOR=0.1084;LSEQ=GCCAATAACAGGAAGAAGAG;RSEQ=TTTTTTTTTTTTGAGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:5,4:6,5:11,9:0.45:2,2:14.9:1:31.1:1:1:1.04:55.2:18:0.45:0.25:0.2 0/1:13:1:0,1:7,5:12,1:0.0769:2,0:34:0:30:0:0.46154:0:39:2:0.0769:0:4 +12 72825540 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48667;SOR=0;LSEQ=TTACATGTTTTACATGGATA;RSEQ=CACACAGGTTGATGTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:32:1:30:1:1:1.36624:60:4:0.1429:0:1 0/0:11:0:0,0:3,8:11,0:0:2,0:29.8:1:32:1:1:0:60:22:1:0:0.1 +12 72825619 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=CCAATAGCTGCTCTCAGGAA;RSEQ=CACAGATGTTTTGAAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:27:1:32.8:1:1:0:60:20:1:0:0 0/1:10:2:1,1:6,2:8,2:0.2:2,2:18:1:27:1:1:2.64575:60:4:0.2:0:1 +12 72825701 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2139;SOR=0;LSEQ=ATCAGAAGTTCAGTGGACTT;RSEQ=TGATAACAAATTTCACGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:14,2:0.125:2,2:27.5:1:30:0:1:1.30929:49:4:0.125:0:1 0/0:18:0:0,0:10,8:18,0:0:2,0:17.4:1:31.6:1:1:0:60:36:1:0:0.1 +12 73053766 . G A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14194;SOR=Inf;LSEQ=ACCAAGATGAGGAGACCGGT;RSEQ=GTGGCCCCAAATGGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:18,1:19,0:0:1,0:24:1:32.3:1:1:0:55.5:18:1:0:0.1 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:16:0:29:0:1:0:54.5:4:0.1667:0:1 +12 73053894 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50467;SOR=0;LSEQ=GATCATGGGACAGGGGGCCC;RSEQ=TCCCTTTTAGGTAGCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:18,27:45,2:0.0426:2,2:12.5:1:31.5:1:1:1.49:25:4:0.0426:0:1.5 0/0:35:0:0,0:16,18:34,0:0:2,0:13.7:1:29.1:1:1:0:27:68:0.9714:0:0.1 +12 73729972 . CA C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.52;SOR=Inf;LSEQ=TCTGGCACATATTTGGAGTT;RSEQ=AAAAATGGTAGTTATGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:9,0:0:2,0:22.6:1:30.3:1:1:0:60:18:1:0:0 0/1:16:2:1,1:6,8:14,2:0.125:2,2:18.5:1:29:1:1:1.31:60:4:0.125:0:0 +12 73931078 . A G 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGCAACCAAGTTATCCAG;RSEQ=TTCTGTCATTAGGGCTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:25:0:32:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:28.5:1:1:0:60:4:1:0:1 +12 76424463 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=6;SSF=0.44444;SOR=0;LSEQ=GAGTGTGGATGTGGATGTGG;RSEQ=TGCGGATACGGGTGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:19.5:1:30:0:1:1.7321:60:4:0.4:0:2 0/0:4:0:0,0:2,2:4,0:0:2,0:29.8:1:29.3:1:1:0:60:8:1:0:0.3 +12 76424896 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50583;SOR=Inf;LSEQ=TGGGTTGGGACGGCTCGGCC;RSEQ=GCCCCTGCCCGGGCTGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:24,16:40,0:0:2,0:23.5:1:30.2:1:1:0:59.2:80:1:0:0.2 0/1:54:2:1,1:29,23:52,2:0.037:2,2:38.5:1:30:1:1:1.25542:60:4:0.0385:0:1 +12 76424910 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2387;SOR=Inf;LSEQ=TCGGCCGGCCCCTGCCCGGG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:32,24:56,0:0:2,0:22.4:1:31.6:1:1:0:59.4:55:1:0:0.2 0/1:54:2:1,1:26,26:52,2:0.037:2,2:17.5:1:28.5:1:1:1:60:4:0.037:0:1 +12 76424916 . TTGC T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.1184;SOR=0;LSEQ=GGCCCCTGCCCGGGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:4:2,2:28,26:54,4:0.0714:2,2:16.8:1:30.8:1:1:1.07552:58.8:8:0.0714:0.0357:0.5 0/0:54:0:0,0:25,29:54,0:0:2,0:29.2:1:29.4:1:1:0:59.6:108:1:0:0.3 +12 76424928 . C T 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.2344;SOR=Inf;LSEQ=GGCTGTTGTTGCTGCTGCTG;RSEQ=TGCTGCTGTTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:29,28:57,0:0:2,0:27.8:1:32.5:1:1:0:59.2:56:1:0:0.2 0/1:54:2:1,1:22,30:52,2:0.037:2,2:7:0:26.5:1:1:1.36:60:4:0.0377:0:2 +12 76424931 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.23021;SOR=Inf;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:30,28:58,0:0:2,0:27.7:1:32.2:1:1:0:59.2:28:1:0:0.2 0/1:54:2:1,1:22,30:52,2:0.037:2,2:34:1:30:1:1:1.36:60:4:0.037:0:1.5 +12 76424937 . TTGC T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.82696;SOR=1.11257;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:44:21,23:4,6:10,44:0.7586:2,2:31.5:1:31.3:1:0.73634:1.36:59.9:88:0.7586:0.069:0.1 1/0:54:42:15,27:6,4:10,42:0.7778:2,2:34:1:29.7:1:0.28183:2.64613:59.5:84:0.7778:0:0.3 +12 76424952 . C G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.10252;SOR=Inf;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TGGTGTTGCAGCTGCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:22,27:49,0:0:2,0:32.5:1:32.4:1:1:0:59.9:23.5:1:0:0.1 0/1:45:3:2,1:14,28:42,3:0.0667:2,2:19.3:1:28.7:1:0.28471:3.87:60:6:0.0682:0:2 +12 77053902 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCACTTAAAAAAAAAAAT;RSEQ=GTGTCTCCTAAGTTAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:19:1:31.5:1:0.33333:0:41.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 77054134 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49934;SOR=Inf;LSEQ=GTCAGGCTTTTAGCTTGTAA;RSEQ=AACAGTAAACCCTTTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:71,48:119,0:0:2,0:23.8:1:32.1:1:1:0:47.6:118:1:0:0.1 0/1:133:2:1,1:76,55:131,2:0.015:2,2:32:1:28:1:1:1.37839:52:4:0.0154:0:1 +12 77054179 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19775;SOR=0;LSEQ=CCGCCATCTTCCAGTAATTC;RSEQ=CCAAAATGACGAACACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:43,54:97,2:0.0202:2,2:16:1:31:1:1:1.25:57:4:0.0206:0:1 0/0:123:0:0,0:58,65:123,0:0:2,0:28.3:1:29.6:1:1:0:41.7:19.5:1:0:0.1 +12 77054235 . G T 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0368;LSEQ=ACCCCATATATGTTCTCTAG;RSEQ=CCTTTTAGAAAACATGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:25:11,14:9,10:19,25:0.5682:2,2:39.8:1:31.2:1:1:1.14192:22.3:50:0.5682:0:1.1 0/1:45:2:1,1:16,27:43,2:0.0444:2,2:34.5:1:29.5:1:1:1.67:20:4:0.0444:0:1 +12 77054292 . AG A 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATATGCGAATCTATAAGAA;RSEQ=GTGATATTGTAGACATCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:17,0:0:2,0:12.1:1:31.8:1:1:0:25.7:34:1:0:0.6 1/0:22:16:6,10:4,2:6,16:0.7273:2,2:11.2:1:30.5:1:0.34763:3.14794:32:32:0.7273:0.3182:0.1 +12 77781871 . G A 269 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00678;LSEQ=TCCTGTAGTGTGAAGAACAG;RSEQ=TGTTCTACGGCCTAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:474:472:227,245:1,1:2,472:0.9958:2,2:24.7:1:30.3:1:1:1.0791:60:93.4:0.9957:0:1.1 1/0:464:285:150,135:84,94:178,285:0.6142:2,2:24.6:1:28.7:1:0.29329:1.24:60:56:0.61:0:1.2 +12 77814031 . T C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.41555;SOR=0.77069;LSEQ=AGTCAGGAAATATTTTTTAT;RSEQ=ACCAAGCATTTTGAATATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:38:19,19:93,104:197,38:0.1617:2,2:29.5:1:32.4:1:0.85951:1.12:60:76:0.1624:0:1.1 0/1:201:26:11,15:88,87:175,26:0.1294:2,2:29.1:1:30:1:0.53039:1.37711:60:52:0.1294:0:1 +12 77814083 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51552;SOR=0;LSEQ=ACATATTAATACAATGAGTA;RSEQ=GTAAAACTATAGATGTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:72,122:194,2:0.0102:2,2:13:1:27:1:1:1.69:60:4:0.0105:0:1 0/0:135:0:0,0:52,83:135,0:0:2,0:24.8:1:30.2:1:1:0:60:44:1:0:0.2 +12 78288587 . C T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.65944;SOR=0.58664;LSEQ=CTGACATGCAAGAATGTGGA;RSEQ=TCAGTGTAGACAGATCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:8,7:0.4667:0,0:27.6:1:32.9:1:1:0:60:14:0.4667:0:1 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:50:0:31:1:1:0:60:4:0.3333:0:1 +12 78288719 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50228;SOR=0;LSEQ=AATACAGCATCTTTGGAGAG;RSEQ=TTCATCCAGTTCACTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:139,56:195,2:0.0102:2,2:33:1:30.5:1:0.49601:2.46912:60:4:0.0103:0:1 0/0:166:0:0,0:112,54:166,0:0:2,0:25.1:1:31:1:1:0:60:82:1:0:0.2 +12 78288720 . T C 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0912;SOR=Inf;LSEQ=ATACAGCATCTTTGGAGAGC;RSEQ=TCATCCAGTTCACTACTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:144,60:204,0:0:2,0:24.4:1:31.3:1:1:0:60:101:1:0:0.2 0/1:168:3:1,2:113,52:165,3:0.0179:2,2:22.7:1:24.7:1:0.24212:4.30428:60:2:0.0124:0:1 +12 78288811 . T C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.68778;SOR=1.07113;LSEQ=CCATCTGCAGAGGAGTAACT;RSEQ=ATTAAAATATTAGTAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:136:52,84:92,102:194,136:0.4109:2,2:23.1:1:32.1:1:0.1145:1.45533:60:135:0.4128:0:1.1 0/1:304:130:57,73:83,91:174,130:0.4276:2,2:26.5:1:31.1:1:0.56121:1.16751:60:260:0.4333:0:1.1 +12 78288910 . GA G 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.02947;SOR=0;LSEQ=AAAGGACAGGAGTGTTTCTT;RSEQ=AAAAAAAAATTCTCACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:6:2,4:9,66:75,6:0.0741:2,2:19.2:1:33.1:1:0.18577:3.58:60:12:0.075:0.0123:0.2 0/0:73:0:0,0:15,58:73,0:0:2,0:24.2:1:30:1:1:0:60:146:1:0:0.2 +12 81101931 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49938;SOR=Inf;LSEQ=TCAGCTATATTGAGCGGCTG;RSEQ=AGGACCTGCTGCACCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:12,19:31,0:0:2,0:23.1:1:31.3:1:1:0:60:30:1:0:0.2 0/1:39:2:1,1:17,20:37,2:0.0513:2,2:24:1:26.5:1:1:1.17:60:4:0.0513:0:1 +12 81110990 . G A 28 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AAGCAGAGCTGCAGGGCTCA;RSEQ=ATGAGGACGAGCACGTGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:2,2:0.5:2,0:6:1:28.5:1:1:0:60:4:0.5:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:4.5:1:28:1:1:0:60:4:1:0:0.5 +12 81111172 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50511;SOR=0;LSEQ=GAAACCCTCAAGAGGTGTAC;RSEQ=ACGACCAACCCCAACCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:37,12:49,2:0.0392:2,2:38.5:1:30.5:1:0.44863:3.00212:60:4:0.0408:0:1 0/0:38:0:0,0:26,12:38,0:0:2,0:22:1:30.4:1:1:0:60:76:1:0:0.2 +12 81111256 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19522;SOR=Inf;LSEQ=GAGAGCCTGCAGGAGTTGCT;RSEQ=AGAGAGCAGGTGGAGAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:21,39:60,0:0:2,0:22.6:1:32.4:1:1:0:60:120:1:0:0.1 0/1:48:2:1,1:18,28:46,2:0.0417:2,2:21:1:27.5:1:1:1.54:60:4:0.0426:0:1 +12 81163925 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49646;SOR=Inf;LSEQ=TGCCAGTCCGAGACAGCCTT;RSEQ=CTTCTCACAGGAATTATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:57,11:68,0:0:2,0:19.5:1:31.1:1:1:0:60:136:1:0:0.2 0/1:70:2:1,1:58,10:68,2:0.0286:2,2:26:1:30:1:0.29151:5.57762:60:4:0.0286:0:1 +12 81163991 . G T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04548;SOR=Inf;LSEQ=TCTCCATGGCTTTTCTAGAG;RSEQ=AAACCTAACAGTGTGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:142,101:243,0:0:2,0:27.5:1:31.5:1:1:0:60:47.6:1:0:0.8 0/1:210:4:2,2:119,87:206,4:0.019:2,2:16:1:26.3:1:1:1.36573:60:8:0.0192:0:1.3 +12 81164017 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.40462;LSEQ=TAACAGTGTGGGTTTATCAA;RSEQ=CATTTTGACAAGACTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:270:222:115,107:25,22:47,222:0.8222:2,2:28.9:1:31.7:1:0.87393:1.05712:60:221:0.8216:0:1.1 1/0:261:170:87,83:49,42:91,170:0.6513:2,2:27.6:1:30.6:1:0.69838:1.11257:60:55.667:0.6498:0:1.2 +12 81164078 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49849;SOR=Inf;LSEQ=AATAAAAATTATGAACAAAG;RSEQ=AAGTGTAGTAAATCTGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:47,113:160,0:0:2,0:25.3:1:30.6:1:1:0:60:39:1:0:0.5 0/1:163:2:1,1:59,102:161,2:0.0123:2,2:25:1:29:1:1:1.72:60:4:0.0123:0:1.5 +12 81164095 . C A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=AAGAAAGTGTAGTAAATCTG;RSEQ=TAATAGAAAAACTGACTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:28,95:123,2:0.016:2,2:9:1:26.5:1:0.41161:3.35:60:4:0.0161:0:3 0/0:117:0:0,0:37,80:117,0:0:2,0:21.2:1:30.6:1:1:0:60:28.25:1:0:0.4 +12 81164122 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5106;SOR=0;LSEQ=AAAAACTGACTATGCCTTGT;RSEQ=GGAAAATTTTTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:6,64:70,2:0.0278:2,2:11.5:1:31.5:1:0.18623:9.95:60:4:0.0294:0:1 0/0:51:0:0,0:6,45:51,0:0:2,0:26.9:1:30.3:1:1:0:60:102:1:0:0.1 +12 81164213 . A G 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61297;SOR=0.37275;LSEQ=AAATTGTTCAATTTTTAAGC;RSEQ=GGTCCATTGTTATGATTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:23:1:32.4:1:1:0:60:14:0.875:0:1.3 1/0:14:10:0,10:0,4:4,10:0.7143:0,0:23.7:1:30.6:1:1:0:60:20:0.7143:0:1.1 +12 81164375 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTGTTTGTTTGTTTTT;RSEQ=TCCCATCATTTTCGGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:9:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 81205188 . A ATATGTG 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.48571;SOR=Inf;LSEQ=GTATATTCATATATACATAT;RSEQ=TGTGTGTGTGTATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:25.2:1:28:1:1:0:60:12:1:0:0.2 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:7.5:1:28.5:1:1:0:42:4:0.2222:0.1111:3 +12 81205196 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.26316;SOR=Inf;LSEQ=ATATATACATATATGTGTGT;RSEQ=TGTATATATATATATATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:24.6:1:31.9:1:1:0:60:14:1:0:0.1 0/1:12:3:3,0:9,0:9,3:0.25:0,0:12.7:1:29:0:1:0:48:6:0.2727:0:2.3 +12 81205319 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51662;SOR=Inf;LSEQ=ATTAGCAATTGCTGCTGCTG;RSEQ=CGACGCCTGGCTGTTCGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:11,16:27,0:0:2,0:26.3:1:31.6:1:1:0:60:54:1:0:0 0/1:42:2:1,1:16,24:40,2:0.0476:2,2:24:1:27.5:1:1:1.49:60:4:0.0488:0:1 +12 82298329 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCAAAGCACTGGAATAG;RSEQ=CAGTTTATCTACTTCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:28:1:1:0:55:4:1:0:2.5 +12 82298338 . C T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGGAATAGCCAGTTTAT;RSEQ=TACTTCATTATCCTACTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:26.5:1:1:0:55:4:1:0:2.5 +12 82298472 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCAAAACCGCTCAGGC;RSEQ=TAGACCTCCTCACTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:6,2:0.25:2,2:20.5:1:33:1:0.46429:3.87298:36.5:4:0.2857:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:16.7:1:29.7:1:1:0:45.3:6:1:0:1 +12 82298568 . A G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14974;SOR=0.39858;LSEQ=CAGGGATAGTATGAGACACC;RSEQ=CCCAGCGTTTACAGGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:10:7,3:19,3:22,10:0.3125:2,2:16.1:1:28.9:1:0.34615:2.62113:36.3:9:0.2903:0:1 0/1:33:5:3,2:20,8:28,5:0.1515:2,2:27.8:1:30.2:1:0.6269:1.63932:42.6:10:0.1515:0:1 +12 82298589 . G GC 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=0;LSEQ=CCCAGCGTTTACAGGAAAAG;RSEQ=CTTGTGAAATCAGACAACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:11:6,5:28,10:38,11:0.2245:2,2:27.7:1:32.1:1:0.27541:2.28948:34.6:22:0.2245:0.0204:0.8 0/0:62:0:0,0:37,24:61,0:0:2,0:19.6:1:30.7:1:1:0:43.9:122:0.9839:0:0.2 +12 82298604 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49759;SOR=Inf;LSEQ=AAAAGGCTTGTGAAATCAGA;RSEQ=AACGCCTTTCAAACTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:38,24:62,0:0:2,0:24.9:1:32.3:1:1:0:38:124:1:0:0.3 0/1:69:2:1,1:41,26:67,2:0.029:2,2:40.5:1:28:1:1:1.56615:51:4:0.029:0:1 +12 82764072 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06776;SOR=Inf;LSEQ=TGATGGCCTCGATCCTAGAG;RSEQ=AAACAGATTTGACAAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:13,0:0:2,0:23:1:31.2:1:1:0:43.8:26:1:0:0.4 0/1:10:3:2,1:5,2:7,3:0.3:2,2:12.7:1:29:1:1:1.22183:45.7:6:0.3:0:1.3 +12 82764479 . TTCTA T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGTTTTTTCTTTACTAT;RSEQ=TCTTTTTCTCTCTTTGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:30.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 82764823 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGCATGTAGGATTAAATGA;RSEQ=CACACTTACTATCTGTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:29:1:1:0:23:4:1:0:2 +12 83193586 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACAACAGAGGTCTTGCC;RSEQ=ATGAATCCCTCAGAGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:24:1:34:0:1:0:60:4:0.4:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:9:1:31.5:1:1:0:60:4:1:0:0 +12 87754814 . G C 53 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTTTTGCATTTGCTGAG;RSEQ=AGTCTTTTACTTCCAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:34.7:1:34:0:1:0:54.7:6:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:24:0:27:0:1:0:23:2:1:0:1 +12 87756302 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCATTTATATTCCTCT;RSEQ=TAAACTGGTTATTCTAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32.5:1:1:0:34:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 87756513 . C T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49059;SOR=Inf;LSEQ=CATTTGGAGGAGAAGAGGCA;RSEQ=TCTGACTTTTTGGGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:20,0:0:2,0:27.2:1:33.6:1:1:0:58.1:40:1:0:0.1 0/1:23:2:1,1:11,10:21,2:0.087:2,2:5.5:1:28:1:1:1.09544:46.5:4:0.087:0:1 +12 87756606 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19821;SOR=Inf;LSEQ=TTTGAAGCTGCTGACCCTTG;RSEQ=ATGGGGTTTTTGTGGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:38,0:0:2,0:26:1:31.2:1:1:0:55.7:37:1:0:0.4 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:28:0:31.5:1:1:1.07:60:4:0.0645:0:1 +12 87756803 . GC G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5013;SOR=Inf;LSEQ=TTCAAGGAGGCTGGAGAGCA;RSEQ=AAAAATGGGCACCTGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,14:23,0:0:2,0:21.2:1:32.1:1:1:0:57.3:46:0.9583:0:0.4 0/1:32:2:1,1:14,16:30,2:0.0625:2,2:10.5:1:31.5:1:1:1.14:26:4:0.0625:0:0 +12 87756834 . G A 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=0;LSEQ=CACCTGCTCCTTCTTCTGGG;RSEQ=ACTTCTGACCTCTAGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,2:3,6:0.6667:2,2:28:1:30:1:1:1.85:60:12:0.6667:0:1.2 0/0:18:0:0,0:7,11:18,0:0:2,0:18.2:1:29.8:1:1:0:60:36:1:0:0.2 +12 87757148 . G A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAACCTGAGCCTCTAGCC;RSEQ=AAGTTATTGGAGATCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:0,8:1:0,2:24.5:1:28.4:1:1:0:60:7:1:0:1.1 1/1:4:4:2,2:0,0:0,4:1:0,2:24.5:1:26.5:1:1:0:60:3:1:0:1.3 +12 87757324 . A G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAGGGGAAAAGCACAGACC;RSEQ=GAGCTATAGCAATGGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:4,5:0,0:0,9:1:0,2:21.8:1:30:1:1:0:48.2:18:1:0:1 1/1:15:15:6,9:0,0:0,15:1:0,2:25.1:1:30.3:1:1:0:50.5:30:1:0:1.1 +12 87757467 . A G 51 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGCAGCTGGTGCTGGTC;RSEQ=CCCCTCCCCAGAGGAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:13.3:1:32.3:1:1:0:60:6:1:0:1 +12 87757632 . G C 69 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAGAAAAAGCACAGTTT;RSEQ=CCCCGCTGGGTGGCACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:8:0:34:0:1:0:60:2:1:0:1 1/1:5:5:1,4:0,0:0,5:1:0,2:21.4:1:30:1:1:0:60:10:1:0:1 +12 87757684 . T G 48 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTGGATGGGGGAAGGGG;RSEQ=TTCCCCTTCCCCATGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:16:1:31.3:1:1:0:60:6:1:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:32:1:30.7:1:1:0:60:6:1:0:1 +12 87815751 . AA GC 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCCTGTAAACACTGGGCA;RSEQ=ATCTCATACTATCCCTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:23:8,15:0,1:1,23:0.9583:0,2:26:1:32.7:1:1:0:27.3:46:0.9583:0.0833:1 1/1:19:19:6,13:0,0:0,19:1:0,2:20.3:1:32.4:1:1:0:23.2:38:1:0.2105:0.9 +12 90837982 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGAAGCCTTTTCCTGTAA;RSEQ=TGCCAGGCAGCATCTCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:2,15:17,2:0.1053:2,2:36:0:34.5:1:0.29825:6.32:23:4:0.1053:0:1.5 0/0:8:0:0,0:2,6:8,0:0:2,0:27.8:1:30.4:1:1:0:32.9:16:1:0:0.1 +12 91237913 . A T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2048;SOR=Inf;LSEQ=TAGAAACACTGATTTAAAAA;RSEQ=TCAGAATTGAGGAACTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:112,87:199,0:0:2,0:25.9:1:30.7:1:1:0:60:198:1:0:0.5 0/1:165:2:1,1:92,71:163,2:0.0121:2,2:30:0:30.5:1:1:1.29371:60:4:0.0123:0:1.5 +12 91237920 . T A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-04;SOR=0.45116;LSEQ=ACTGATTTAAAAAATCAGAA;RSEQ=TGAGGAACTAATGAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:77:41,36:70,60:130,77:0.372:2,2:25.2:1:30.5:1:1:1.02428:60:76:0.3689:0:1.1 0/1:171:36:20,16:71,64:135,36:0.2105:2,2:25.3:1:28.8:1:0.85144:1.13:60:35:0.2071:0:1 +12 91237933 . GA G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.20914;SOR=Inf;LSEQ=ATCAGAATTGAGGAACTAAT;RSEQ=AAAGGTGGAATACAGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:104,109:213,0:0:2,0:25.7:1:30.4:1:1:0:60:70:1:0:0.5 0/1:180:2:1,1:91,87:178,2:0.0111:2,2:24:0:31:1:1:1.04573:60:4:0.0112:0:0.5 +12 91237962 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49978;SOR=0;LSEQ=GAATACAGAGGAAATATTCA;RSEQ=CATATATTAAATCATCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:74,103:177,2:0.0112:2,2:28:1:29:1:1:1.39:60:4:0.0113:0:1 0/0:162:0:0,0:70,92:162,0:0:2,0:24.7:1:28.8:1:1:0:60:53:1:0:0.2 +12 91237979 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49963;SOR=0;LSEQ=TCATCATATATTAAATCATC;RSEQ=CAAGAGCATCCTGTGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:56,92:148,2:0.0133:2,2:28.5:1:30:1:1:1.64:60:4:0.0136:0:2 0/0:135:0:0,0:52,83:135,0:0:2,0:26.5:1:28.9:1:1:0:60:134:1:0:0.2 +12 91238015 . G A 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAAAAAAATACATCATAAG;RSEQ=ATATGAGCTAACTGTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:18:5,13:9,44:53,18:0.2535:2,2:20.1:1:30.5:1:0.32418:1.86:60:36:0.2535:0:1.1 0/0:88:0:0,0:26,62:88,0:0:2,0:24.4:1:30.6:1:1:0:60:176:1:0:0.1 +12 91742514 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ACCAAGAGGAGGCATCAGGG;RSEQ=TAAGAGGCGATTCTGGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:24.5:1:29:1:1:0:60:4:0.4:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:2:0:30:0:1:0:60:2:0.3333:0:3 +12 91742590 . G A 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.7086;SOR=0.69934;LSEQ=AGGTGATCAGACACTACATG;RSEQ=GGAATGGTTGGGAATGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:3,2:12,3:15,5:0.25:2,2:23.8:1:31.8:1:0.55979:2.52201:60:10:0.25:0:2 0/1:16:3:3,0:9,4:13,3:0.1875:2,0:15.3:1:27:1:0.52857:0:60:6:0.1875:0:2.3 +12 91742612 . A C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22092;SOR=0;LSEQ=GAATGGTTGGGAATGAGGAA;RSEQ=CTGCTCAGATATACAGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:20,11:0,0:0,31:1:0,2:23.5:1:32:1:1:0:60:62:1:0:1.2 1/1:28:26:16,10:1,1:2,26:0.9286:2,2:25:1:31:1:1:1.57:60:52:0.9286:0:1.4 +12 92562048 . A G 44 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59006;SOR=0.28733;LSEQ=AGGAAGACAAGAATTCATAA;RSEQ=GGAAAAGATTAAAACATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:8,1:9,3:0.25:2,0:48.3:1:28:1:1:0:60:2:0.1818:0:1 0/1:12:1:1,0:9,2:11,1:0.0833:2,0:20:0:33:0:1:0:60:2:0.0833:0:1 +12 92787049 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=Inf;LSEQ=TGAGAAAGGAGGACTTTGCA;RSEQ=CTTCTTAGGGGAAGAGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:10,1:11,0:0:2,0:18.9:1:31.8:1:1:0:38.5:22:1:0:0.9 0/1:13:2:2,0:11,0:11,2:0.1538:0,0:37:0:32:0:1:0:30:4:0.1538:0:1 +12 92787053 . C T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1107;SOR=0.22314;LSEQ=AAAGGAGGACTTTGCACCTT;RSEQ=TTAGGGGAAGAGTGTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:8,1:3,0:3,9:0.75:0,2:21.1:1:29:1:1:0:37.8:8:0.7273:0:1.2 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:32:1:31.2:1:1:0:28:10:0.3846:0:1 +12 92787216 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20131;SOR=0;LSEQ=TCCCCTTTCTAGTTCCCATG;RSEQ=CAGCCATCTTGTGATTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:23,52:75,2:0.026:2,2:23.5:1:31:1:0.52905:2.23:52:4:0.026:0:1 0/0:94:0:0,0:31,63:94,0:0:2,0:24.9:1:28.3:1:1:0:40.7:46:1:0:0.1 +12 92820481 . T A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20808;SOR=0;LSEQ=TAGGAGGATTGGCTCAGTCA;RSEQ=CTTGGCTGAGGCTCATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:30.5:1:31:1:1:0:60:8:0.5:0:1.5 0/0:4:0:0,0:4,0:4,0:0:0,0:19.3:1:31.8:1:1:0:60:8:1:0:0 +12 92820493 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGTCATCTTGGCTGAGG;RSEQ=TCATGAAACCAGGTGTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:31:1:29:1:1:0:60:4:0.1667:0:2 0/0:5:0:0,0:5,0:5,0:0:0,0:21.4:1:33.6:1:1:0:60:10:1:0:0 +12 92820605 . T G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13437;SOR=Inf;LSEQ=TTTGATGGTAGAAGGTATTT;RSEQ=GGGACTATTCCATTTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:103,4:107,0:0:1,0:24.4:1:31.5:1:1:0:60:214:0.9907:0:0.1 0/1:63:2:1,1:59,2:61,2:0.0317:1,2:14.5:1:31.5:1:0.0937:24.29032:60:4:0.0317:0:2 +12 92820633 . T C 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00122;SOR=Inf;LSEQ=TTCCATTTGAAATGAGAAGG;RSEQ=ACCTGACATTCTTTGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:147,31:178,0:0:2,0:23.1:1:29.7:1:1:0:60:88:1:0:0.1 0/1:139:8:7,1:99,32:131,8:0.0576:2,2:14.3:1:32.5:1:0.68004:2.25:60:16:0.0584:0:1 +12 92820637 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50547;SOR=0;LSEQ=ATTTGAAATGAGAAGGTACC;RSEQ=GACATTCTTTGAATTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:151,37:188,2:0.0105:2,2:32.5:1:31.5:1:0.36085:4.04034:60:4:0.0106:0:1 0/0:150:0:0,0:113,37:150,0:0:2,0:20.3:1:29.6:1:1:0:60:49:1:0:0.2 +12 92820752 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02435;SOR=1.49463;LSEQ=TTATCTAACTCATTCTCACT;RSEQ=CTTATTCCATGATGAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:71:30,41:179,208:387,71:0.155:2,2:24.9:1:30.8:1:0.6046:1.17571:60:16.75:0.1502:0:1.1 0/1:432:93:49,44:154,185:339,93:0.2153:2,2:28.5:1:30.1:1:0.24129:1.34:60:45.5:0.2131:0:1.2 +12 92820790 . ATTG A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.07858;SOR=3.34081;LSEQ=TGACATAAATGAGGTTTTTT;RSEQ=TTGTTGTTGTTGTTTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:0,3:97,192:289,3:0.0103:2,0:24.7:1:28.7:1:0.55326:0:60:6:0.0103:0.0034:0.7 0/1:268:9:3,6:103,156:259,9:0.0336:2,2:29.9:1:30.9:1:1:1.31919:60:18:0.034:0:0.2 +12 92820822 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50666;SOR=0;LSEQ=GTTGTTTTCTGGACACAAGG;RSEQ=AAGGTAGCTACCTGGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:33,136:169,2:0.0117:2,2:27:1:31:1:0.35906:4.07:60:4:0.012:0:1 0/0:132:0:0,0:34,98:132,0:0:2,0:21.9:1:31.4:1:1:0:60:264:1:0:0.2 +12 92821133 . A T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGAAGCTAAACTGAGAA;RSEQ=TCTTGCAAATCATTGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:26.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 92821237 . G GGA 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGGCAGGGAGAGTTGAT;RSEQ=GGGGGGGCGGGGTTCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:48:0:31.5:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:31.3:1:1:0:60:4:1:0:1 +12 92821245 . C T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGAGTTGATGGGGGGGG;RSEQ=GGGGTTCACACATCTTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:39:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:31:1:1:0:60:4:1:0:1 +12 93919072 . C T 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTAGCCAGGTGTGGTGG;RSEQ=GGGTGCCTGTAATCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:13.5:1:32:0:1:0:52.5:4:0.6667:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:46:0:15:0:1:0:23:0:0:0:5 +12 93919097 . C T 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGTAATCCCAGCTACTC;RSEQ=GGAGGTTGAGGCAGGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:13:1:30.7:1:1:0:49.7:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:21:0:32:0:1:0:23:2:1:0:5 +12 93919227 . G A 87 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.78496;SOR=0.78601;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAGAAAAATTAGGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:8:7,1:29,20:49,8:0.1333:2,2:11.6:1:29:1:0.23567:4.72:35.6:16:0.1702:0:3 0/1:65:7:7,0:24,33:57,7:0.1077:2,0:19:1:21.3:1:0.00423:0:36.7:1.333:0.0769:0:4.3 +12 93919243 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1929;SOR=0;LSEQ=AAAAGAAAAGAAAAATTAGG;RSEQ=GCCATAATGTTCTTCCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:59,28:87,2:0.0225:2,2:20:0:31.5:1:0.54801:2.08802:45.5:4:0.023:0:2.5 0/0:113:0:0,0:63,50:113,0:0:2,0:20.6:1:30:1:1:0:57.8:36.667:1:0:1.8 +12 93919278 . C A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25174;SOR=Inf;LSEQ=CCATCAATAAAATTTGTTTC;RSEQ=CACGTGGAAATGCACAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:99,62:161,0:0:2,0:27:1:30.9:1:1:0:59.4:25.833:1:0:2.4 0/1:186:3:2,1:94,89:183,3:0.0161:2,2:10:1:23:1:1:1.89:55.3:2:0.0111:0:3.3 +12 93919282 . G A 220 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0312;LSEQ=CAATAAAATTTGTTTCCCAC;RSEQ=TGGAAATGCACAACCATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:161:159:98,61:2,0:2,159:0.9876:0,2:28:1:30.2:1:0.5264:0:59.7:30.8:0.9872:0:2.5 1/0:194:138:72,66:29,26:55,138:0.7113:2,2:27.6:1:28.8:1:1:1.02232:59.3:22:0.7021:0:2.6 +12 93919285 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20206;SOR=0;LSEQ=TAAAATTTGTTTCCCACGTG;RSEQ=AAATGCACAACCATGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:101,60:161,2:0.0123:2,2:23:1:29:1:1:1.67765:60:4:0.0127:0:3.5 0/0:199:0:0,0:104,95:199,0:0:2,0:26.9:1:29.8:1:1:0:59.4:27.429:1:0:1.9 +12 93919297 . C G 226 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04562;LSEQ=CCCACGTGGAAATGCACAAC;RSEQ=ATGGGGCATTTTTACTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:182:179:108,71:2,0:2,179:0.9835:0,2:27.1:1:30.3:1:0.52056:0:59.9:43.75:0.9831:0:2.5 1/0:215:157:84,73:32,26:58,157:0.7302:2,2:26.1:1:28.7:1:0.87815:1.06923:59.9:21.429:0.7246:0:2.6 +12 93919335 . T A 32 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2505;SOR=Inf;LSEQ=TCTGAGTGGCCACATGGGGG;RSEQ=GCTGAGTCGAAAGGCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:103,93:196,0:0:2,0:24.8:1:30.1:1:1:0:60:392:1:0:2.5 0/1:219:3:3,0:112,104:216,3:0.0137:2,0:6:1:20.7:1:0.24846:0:60:2:0.0093:0:3.7 +12 93919341 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21962;SOR=0;LSEQ=TGGCCACATGGGGGTGCTGA;RSEQ=TCGAAAGGCACATTTAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:95,94:189,2:0.0105:2,0:9:1:30:1:0.49738:0:60:4:0.0105:0:4 0/0:216:0:0,0:107,109:216,0:0:2,0:10:0:14:0:1:0:60:0:0:0:5 +12 93919355 . T A 228 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03473;LSEQ=TGCTGAGTCGAAAGGCACAT;RSEQ=TAACAACGTGTTGTTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:197:195:89,106:0,2:2,195:0.9898:0,2:23.6:1:30:1:0.50212:0:60:194:0.9898:0:2.9 1/0:214:165:80,85:23,26:49,165:0.771:2,2:22.3:1:28.6:1:0.87202:1.06:60:54:0.7714:0:3 +12 93919390 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0.21263;LSEQ=TACTGTGAGCAAGGCTATTC;RSEQ=GGGATGCGTTTTGCTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:179:170:67,103:4,5:9,170:0.9497:2,2:24.5:1:31.1:1:0.74193:1.22839:60:84:0.9492:0:3.1 1/1:175:140:67,73:16,19:35,140:0.8:2,2:25.8:1:29.4:1:0.85194:1.09:60:69:0.7977:0:3.1 +12 93919397 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24046;SOR=0;LSEQ=AGCAAGGCTATTCGGGGATG;RSEQ=GTTTTGCTATGCATCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:66,98:164,2:0.012:2,2:23.5:1:32:0:1:1.48:59:4:0.0123:0:4.5 0/0:172:0:0,0:77,95:172,0:0:2,0:26.6:1:29.8:1:1:0:60:56.333:1:0:2.5 +12 93919402 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49855;SOR=Inf;LSEQ=GGCTATTCGGGGATGCGTTT;RSEQ=GCTATGCATCCCCCCAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:65,98:163,0:0:2,0:26.1:1:30.6:1:1:0:60:80.5:1:0:2.9 0/1:167:2:1,1:74,91:165,2:0.012:2,2:19:1:29.5:1:1:1.23:60:4:0.012:0:3.5 +12 93919408 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.19916;LSEQ=TCGGGGATGCGTTTTGCTAT;RSEQ=CATCCCCCCAAAATCCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:158:149:60,89:5,4:9,149:0.943:2,2:26.5:1:29.3:1:0.48926:1.84668:60:148:0.9427:0:3.2 1/0:167:128:60,68:16,22:38,128:0.7665:2,2:27.6:1:27.7:1:0.71142:1.21:60:31:0.7654:0:3.2 +12 93919441 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=0.22961;LSEQ=ATCCCAATACATGCAGTAAT;RSEQ=AAGATGATTAATATAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:146:136:50,86:6,4:10,136:0.9315:2,2:23.8:1:31.9:1:0.18294:2.56246:60:33:0.9296:0:2.9 1/0:152:115:48,67:15,22:37,115:0.7566:2,2:23.9:1:30.7:1:1:1.05:60:114:0.755:0:2.9 +12 93919495 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00289;SOR=0.21844;LSEQ=TGACTCTGTCTTTTTCATGG;RSEQ=GAATTTCCTCCCCAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:77:24,53:3,2:5,77:0.939:2,2:26:1:31.1:1:0.32502:3.25935:60:76:0.95:0:1.9 1/0:78:60:21,39:7,11:18,60:0.7692:2,2:29.5:1:29.6:1:0.78484:1.17925:60:59:0.7662:0:1.7 +12 93919724 . G T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTTAGGAAACAGCAAA;RSEQ=CCCTATAAAAGGAATAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:46.5:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 95539120 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53613;SOR=Inf;LSEQ=GATTCTGTACTGGTCAGGTT;RSEQ=CTGAATCTTTTCTTAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:12,0:0:2,0:20.7:1:29.8:1:1:0:58.8:11:1:0:0.2 0/1:23:2:1,1:13,8:21,2:0.087:2,2:23.5:1:29:1:1:1.58984:60:4:0.087:0:1 +12 95843385 . T A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1079;SOR=Inf;LSEQ=CTCATACTATCCCTGACTGA;RSEQ=TAGTGTAAAAACAACACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:2,17:19,0:0:2,0:28.4:1:30.5:1:1:0:52.1:38:1:0:0.1 0/1:21:4:1,3:4,13:17,4:0.1905:2,2:19.8:1:26.3:1:1:1.08:48:3:0.15:0:1 +12 97487531 . C T 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6044;SOR=0.42404;LSEQ=TTGTCTACAGTAGACCAGTC;RSEQ=GAGATATTTGGAAAAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:15.7:1:33.7:1:1:0:60:6:0.3333:0:1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:33:0:33:0:1:0:60:2:0.1667:0:1 +12 97487633 . G T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02771;LSEQ=CACAGAAGTACTGCAGGACT;RSEQ=ACTTACAGGGTAAAAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:55:54,1:4,1:5,55:0.9167:2,1:30.6:1:31.6:1:0.16102:12.19:59.8:110:0.9167:0:1 0/1:36:8:8,0:28,0:28,8:0.2222:1,0:33.8:1:31.1:1:1:0:60:16:0.2222:0:1 +12 97487819 . GT G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.25927;SOR=1.51666;LSEQ=TGGCATGTTTAGGGATACGT;RSEQ=TTTTTTTTTTGTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:16:9,7:238,285:523,16:0.0294:2,2:29.5:1:31.4:1:0.45104:1.54:60:32:0.0295:0:0.4 0/1:546:24:11,13:242,278:520,24:0.044:2,2:26.5:1:30.3:1:1:1.02873:60:48:0.0449:0:0.3 +12 97487825 . T TTTG 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTAGGGATACGTGTTTTT;RSEQ=TTTTTGTTTTTTTTTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:218,272:490,0:0:2,0:21.7:1:30.4:1:1:0:55.9:121.5:1:0:1.4 0/1:515:21:10,11:220,273:493,21:0.0408:2,2:21.7:1:30.2:1:0.82538:1.13:60:42:0.0411:0.0117:0.1 +12 97487829 . TTG GT 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGGATACGTGTTTTTTTTT;RSEQ=TTTTTTTTTTGTAACTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:20:9,11:203,262:465,20:0.0407:2,2:8.2:1:28.4:1:1:1.06:60:40:0.041:0.0367:0.2 0/0:494:0:0,0:206,275:481,0:0:2,0:21.4:1:29.1:1:1:0:58.3:67.714:0.9793:0:1 +12 97487831 . G GT 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.00087;LSEQ=GGATACGTGTTTTTTTTTTT;RSEQ=TTTTTTTTTTGTAACTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:36:5,31:109,175:284,36:0.0788:2,2:17.9:1:31.2:1:0.00303:3.84844:53.1:72:0.1272:0:0.9 0/1:482:38:14,24:147,207:354,38:0.0788:2,2:22.8:1:28.9:1:0.60768:1.21679:56.1:76:0.0962:0.0021:1.2 +12 97487833 . T G 87 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.00607;SOR=10.97783;LSEQ=ATACGTGTTTTTTTTTTTGT;RSEQ=TTTTTTTTGTAACTTTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:1:0,1:196,266:462,1:0.0022:2,0:5:0:33:0:1:0:60:2:0.0022:0:2 0/1:473:11:6,5:191,270:461,11:0.0233:2,2:7.5:1:25.3:1:0.53805:1.69:60:1.75:0.015:0:2.3 +12 97487836 . T TG 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0;SOR=0.09837;LSEQ=CGTGTTTTTTTTTTTGTTTT;RSEQ=TTTTTGTAACTTTAACTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:126:41,85:145,177:322,126:0.2775:2,2:22.5:1:28.6:1:0.01884:1.69637:54.2:3.667:0.2357:0.0529:1.3 0/1:468:17:6,11:188,262:450,17:0.0363:2,2:24.3:1:32.5:1:0.80288:1.31477:60:34:0.0366:0.0064:0.3 +12 97487948 . G A 25 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20457;SOR=Inf;LSEQ=AAAGAACAGATGGTCACAGT;RSEQ=TACAAAAAGGTCTACCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:7,82:89,0:0:2,0:21.5:1:32.2:1:1:0:60:43.5:1:0:0 0/1:74:2:1,1:11,61:72,2:0.027:2,2:6:0:25.5:1:0.29989:5.35:60:4:0.0274:0:1 +12 98095696 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.57135;LSEQ=GCTTGGCCAAACTTTAATCA;RSEQ=GCTTCTGAACCATTTCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:19,23:42,2:0.0455:2,2:34:1:29.5:1:1:1.21:60:4:0.0465:0:1.5 0/1:38:1:0,1:24,13:37,1:0.0263:2,0:1:0:26:0:0.36842:0:60:2:0.0278:0:1 +12 100536318 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09677;SOR=Inf;LSEQ=GAAGCCGCAGGCTGACTCCA;RSEQ=TGCGGGCTGGGGTGGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:21,0:0:2,0:21.5:1:32.8:1:1:0:60:42:1:0:0.1 0/1:10:2:1,1:5,3:8,2:0.2:2,2:36:1:28.5:1:1:1.58108:60:4:0.2:0:1 +12 100967441 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48768;SOR=Inf;LSEQ=TCGAAACAGGCGGCGGCCAG;RSEQ=GGCTACTGACCCTGAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:13,0:0:2,0:26.7:1:31:1:1:0:60:26:1:0:0 0/1:16:2:1,1:10,4:14,2:0.125:2,2:31:0:28.5:1:1:2.34522:60:4:0.125:0:1 +12 100967543 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.48667;SOR=0;LSEQ=GAGTTGTCGCCCCGCTGGGA;RSEQ=AAGTGACCCTCCTGCGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:3,9:12,2:0.1429:2,2:18:1:28.5:1:0.50549:2.74:60:4:0.1429:0:1 0/0:11:0:0,0:2,9:11,0:0:2,0:25.3:1:29.6:1:1:0:60:10:1:0:0 +12 101083978 . G A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48846;SOR=Inf;LSEQ=TTTAGCAAGATGAATTCCAG;RSEQ=TGATTCGTATGTAACCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:22.6:1:31.3:1:1:0:60:18:1:0:0 0/1:21:2:1,1:5,14:19,2:0.0952:2,2:5.5:1:25:1:0.5:2.65:60:4:0.0952:0:1.5 +12 102796005 . G GAT 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=0.04329;SOR=Inf;LSEQ=TCTTGAGAGGCAGGGACTAA;RSEQ=ATATATATATATATATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:17,0:0:1,0:17.5:1:32.8:1:1:0:58.4:34:1:0:0.8 0/1:5:2:2,0:3,0:3,2:0.4:0,0:8:1:30:1:1:0:50:4:0.4:0.2:0.5 +12 102796022 . A AT 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.39665;LSEQ=TAAGATATATATATATATAT;RSEQ=TTTTTTTTTTCTTTTCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:15,1:16,2:0.1053:1,0:15.5:1:29.9:1:1:0:60:4:0.1111:0.0526:1 0/1:7:1:1,0:6,0:6,1:0.1429:0,0:50:0:28:0:1:0:60:2:0.1429:0:0 +12 102796024 . TT A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.53962;SOR=0;LSEQ=AGATATATATATATATATAT;RSEQ=TTTTTTTCTTTTCTATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:3,0:14,1:15,3:0.1579:1,0:16.7:1:28.6:1:1:0:60:6:0.1667:0.0526:0.7 0/0:7:0:0,0:7,0:7,0:0:0,0:27.9:1:29.9:1:1:0:56.9:14:1:0:0.1 +12 102796522 . G C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71096;SOR=0.67777;LSEQ=GACAGGCCCTTAGTACTTTT;RSEQ=CCAAACCTCACTCAGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:29:1,28:0,6:6,29:0.8286:0,1:27.4:1:31.8:1:1:0:60:58:0.8529:0:1.1 1/0:17:13:0,13:0,4:4,13:0.7647:0,1:18.8:1:30.9:1:1:0:60:26:0.7647:0:1.1 +12 102811349 . AT A 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.12774;LSEQ=TTGCCTCTTTTATAATTTTT;RSEQ=TTTTTTTTTTCATTTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:17,0:17,3:0.15:1,0:8.3:1:31.4:1:1:0:60:6:0.15:0.1:0 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:15:0:32:0:1:0:60:2:0.1667:0:0 +12 102811559 . A ATCATCCTTGCCTCTGTCTGATCTCTATTTTCCTCTTATTGCACACTTTCCTCAACCACACCCACCTCT 82 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=2.000;MSILEN=1;SSF=0.00056;SOR=Inf;LSEQ=TTGCTGTCTGCTCCTCTCTC;RSEQ=TCATCCTTGCCTCTGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:921:0:0,0:589,331:920,0:0:2,0:24.7:1:30.3:1:1:0:60:47.421:1:0:0.1 0/1:832:10:2,8:508,314:822,10:0.012:2,2:15.4:1:24.8:1:0.01665:6.45753:60:9:0.011:0.012:0.7 +12 102813524 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51255;SOR=0;LSEQ=TGCAATCTGCTTTCTTCAGT;RSEQ=TTCCACCCAGCTCCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:27,159:186,2:0.0106:2,2:8:1:29:1:0.27637:5.80:60:4:0.0109:0:1 0/0:134:0:0,0:19,115:134,0:0:2,0:21.9:1:30.9:1:1:0:60:25.8:1:0:0.2 +12 102869354 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60032;SOR=0.43475;LSEQ=AGTTATTCACACACTCCCTG;RSEQ=GGTTGTAAATCCACAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:157,40:197,2:0.0101:2,2:22.5:1:29:1:0.37044:3.88917:60:4:0.0103:0:1 0/0:228:1:0,1:154,73:227,1:0.0044:2,0:1:0:23:0:0.32456:0:60:2:0.0044:0:1 +12 102869479 . G A 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21947;SOR=4.63989;LSEQ=GCATCCACCAGCTCAGCCCC;RSEQ=CAGAGCGTCTCCGGTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:0,1:203,205:408,1:0.0024:2,0:19:0:32:0:1:0:60:2:0.0025:0:1 0/1:444:5:3,2:219,219:438,5:0.0113:2,2:23:1:28.2:1:1:1.50:60:10:0.0114:0:1 +12 102869600 . G T 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GCCCAAGAAACAGAGGGAGG;RSEQ=TCAGGTTTCCTCCTTGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:104,200:304,0:0:2,0:25.8:1:31.4:1:1:0:59.9:32.778:1:0:0.2 0/1:272:14:5,9:92,165:257,14:0.0515:2,2:20.7:1:29.2:1:1:1.00362:60:28:0.052:0:1 +12 102869603 . A G 38 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6651;SOR=1.77361;LSEQ=CAAGAAACAGAGGGAGGGTC;RSEQ=GGTTTCCTCCTTGATCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:2:1,1:98,192:290,2:0.0068:2,2:33:1:29.5:1:1:1.95:60:4:0.0069:0:1 0/1:248:3:2,1:80,165:245,3:0.0121:2,2:6.3:1:24:1:0.25477:4.10:60:2:0.0081:0:1 +12 102869641 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28811;SOR=3.66927;LSEQ=TTGCAAGGGGAGTGGGGTGG;RSEQ=ACAGAAGTGCATTGACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:33,133:166,1:0.006:2,0:50:0:30:0:1:0:60:2:0.0061:0:1 0/1:92:2:1,1:18,72:90,2:0.0217:2,2:14.5:1:27:1:0.37219:3.92:60:4:0.0225:0:1 +12 102871775 . CT C 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAATAGATTTCTCTTTTT;RSEQ=TTTTTTTTTTTTTTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:40.5:1:31:0:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 102872095 . G GA 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.5107;SOR=0;LSEQ=AGAAAGACATGAGAAAAAAA;RSEQ=AAAAAAAAATCAGAAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:2,0:62,0:62,2:0.0313:1,0:11.5:1:32:0:1:0:60:4:0.0323:0:0 0/0:45:0:0,0:43,2:45,0:0:1,0:25.3:1:31.5:1:1:0:59.2:21.5:1:0:0.2 +12 102872155 . C CT 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.0022;SOR=0.45673;LSEQ=AAACCCAAATTTTAAAAGTT;RSEQ=TTTTTTTTTTAATCTTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:191:150:139,11:27,1:28,150:0.7853:1,2:25.5:1:32.3:1:0.69421:2.12946:59.7:300:0.7853:0.0942:0.3 1/0:128:80:72,8:37,4:41,80:0.625:2,2:23.4:1:30.2:1:1:1.02755:60:79:0.632:0.125:0.2 +12 104974951 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03297;SOR=Inf;LSEQ=GGATGCTTCTTGCATCCTTA;RSEQ=CCTTGAGGACTTTGGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:11,0:11,0:0:0,0:24.2:1:32.2:1:1:0:60:22:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:12.5:1:30:1:1:0:60:4:0.6667:0:2 +12 104975016 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04779;SOR=Inf;LSEQ=TAGCTTCAGGGTGTTGACTT;RSEQ=CATTAGCTTCTGCTGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:20,1:21,0:0:1,0:25.3:1:32.3:1:1:0:60:42:1:0:0 0/1:13:3:2,1:10,0:10,3:0.2308:0,2:32:1:28:1:0.23077:0:60:6:0.2308:0:1.7 +12 104975209 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00015;SOR=2.32287;LSEQ=GAGAAAGCTTGATAATTGAG;RSEQ=AAAATTTATCCCTATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:36:15,21:91,122:213,36:0.1446:2,2:23.2:1:30.8:1:1:1.04409:60:72:0.1469:0:1.1 0/1:287:81:37,44:93,113:206,81:0.2822:2,2:26.5:1:29.2:1:1:1.02:60:26:0.2746:0:1.1 +12 104975323 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03869;SOR=Inf;LSEQ=ATTGTCGAGTGACTGGAAAC;RSEQ=GTTGATTTAAAGGAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:5,37:42,0:0:2,0:24.6:1:30:1:1:0:60:41:1:0:0.1 0/1:35:4:0,4:3,28:31,4:0.1143:2,0:14.5:1:30.3:1:1:0:60:8:0.1143:0:1 +12 105192655 . C T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18108;SOR=0.50466;LSEQ=AGTGACTAGGCTTGTTTGTA;RSEQ=GGGAAGTATTGTCAAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:57:33,24:7,4:11,57:0.8382:2,2:28.3:1:30.5:1:1:1.26829:60:56:0.8358:0:1 1/0:54:39:23,16:8,7:15,39:0.7222:2,2:25.1:1:29.9:1:0.76485:1.25:60:78:0.7222:0:1.1 +12 106214220 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25614;SOR=0;LSEQ=CCTCTTGTCCTCACTCTTGG;RSEQ=AGTTTCTTCTCTGGTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:3:1,2:113,67:180,3:0.0164:2,2:17:1:28:1:0.55766:3.35:60:6:0.0166:0:1.3 0/0:148:0:0,0:99,48:147,0:0:2,0:24.6:1:31.3:1:1:0:60:72.5:0.9932:0:0.3 +12 106214293 . G A 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAAAGAGAGATCAAATCT;RSEQ=TGGAGACCCTTGCTCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:112,135:247,0:0:2,0:26.6:1:32.1:1:1:0:60:60.75:1:0:0.2 0/1:218:50:27,23:83,85:168,50:0.2294:2,2:25.9:1:28.7:1:0.6301:1.20:60:100:0.2315:0:1.1 +12 106214315 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23326;SOR=Inf;LSEQ=GGAGACCCTTGCTCTTTGAG;RSEQ=ACCTTGCCTGCAGCCCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:82,123:205,0:0:2,0:26.2:1:32.1:1:1:0:60:50.25:1:0:0.1 0/1:192:2:1,1:77,113:190,2:0.0104:2,2:35:1:28:1:1:1.46:60:4:0.0105:0:1 +12 106214318 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22937;SOR=Inf;LSEQ=GACCCTTGCTCTTTGAGCAC;RSEQ=TTGCCTGCAGCCCTTAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:82,122:204,0:0:2,0:25.4:1:32.1:1:1:0:60:203:1:0:0.1 0/1:188:2:1,1:75,111:186,2:0.0106:2,2:26:1:29:1:1:1.48:60:4:0.0109:0:1 +12 106214322 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50054;SOR=0;LSEQ=CTTGCTCTTTGAGCACCTTG;RSEQ=CTGCAGCCCTTAAGCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:79,119:198,2:0.01:2,2:25.5:1:29.5:1:1:1.50:60:4:0.0103:0:1 0/0:177:0:0,0:72,104:176,0:0:2,0:23.3:1:30.5:1:1:0:60:87:0.9943:0:0.3 +12 106214325 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50063;SOR=0;LSEQ=GCTCTTTGAGCACCTTGCCT;RSEQ=CAGCCCTTAAGCTGACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:73,118:191,2:0.0104:2,2:30.5:1:28.5:1:1:1.61:60:4:0.0105:0:1 0/0:170:0:0,0:68,102:170,0:0:2,0:23:1:30.8:1:1:0:60:41.5:1:0:0.3 +12 106589370 . C T 73 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTACTTGCTGCTCCTTAA;RSEQ=GGGAGGGTGTGGGCAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:22.4:1:31.8:1:1:0:60:10:0.7143:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:29:0:1:0:60:2:1:0:1 +12 106589658 . C G 218 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TGCAAACCAGCCGAGAAGCG;RSEQ=AGCATGACCAAGATCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:172,151:323,0:0:2,0:24.6:1:32.1:1:1:0:59.9:322:1:0:0.1 1/0:287:163:88,75:67,57:124,163:0.5679:2,2:27.2:1:29.7:1:1:1.00179:59.9:22.286:0.5591:0:1.2 +12 106589663 . T G 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00463;SOR=Inf;LSEQ=ACCAGCCGAGAAGCGCAGCA;RSEQ=GACCAAGATCAACAATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:166,161:327,0:0:2,0:25:1:30.7:1:1:0:59.9:162.5:1:0:0.1 0/1:286:7:4,3:146,132:278,7:0.0245:2,2:22.1:1:29.6:1:1:1.20:60:6:0.0214:0:1.1 +12 106589765 . G A 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20982;SOR=Inf;LSEQ=CCCAAGTCCTTGTTTGACTT;RSEQ=CTGTGCAACTTACAGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:28,98:126,0:0:2,0:20.4:1:32.2:1:1:0:60:62:1:0:0.1 0/1:107:2:1,1:21,84:105,2:0.0187:2,2:8:1:22.5:1:0.37048:3.93:60:4:0.0194:0:1.5 +12 107194087 . A G 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAGCTTTTACTCATGGC;RSEQ=GAAGGCAAAGCTGGAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:32:1:1:0:60:4:1:0:1 +12 107194580 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13153;SOR=0.32598;LSEQ=AAGTAAGGAAATTCCAAAGA;RSEQ=ATTGTATATAGGAAAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:15,0:23,1:24,15:0.3846:1,1:26.5:1:29.8:1:1:0:60:14:0.3684:0:1.1 0/1:18:3:3,0:14,1:15,3:0.1667:1,0:6:1:25.3:1:1:0:60:2:0.1176:0:1 +12 107194707 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24847;SOR=0;LSEQ=GTGACAGTGTTCATCTTGCA;RSEQ=CCTTGCCTAGTGTACTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:1,2:146,93:239,3:0.0124:2,2:15:1:30.7:1:0.56301:3.12467:60:6:0.0126:0:1.3 0/0:239:0:0,0:147,92:239,0:0:2,0:25.7:1:31.3:1:1:0:60:478:1:0:0.2 +12 107194776 . T G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51683;SOR=0.89303;LSEQ=CCCTAAAGATTAAATGAGTA;RSEQ=TGTTCTCTCATTTGGTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:299:157:67,90:51,91:142,157:0.5251:2,2:24.5:1:32.4:1:0.23889:1.33:60:156:0.5235:0:1.1 0/1:310:154:71,83:69,87:156,154:0.4968:2,2:26.7:1:31.2:1:0.8195:1.08:60:153:0.5:0:1.1 +12 107194826 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2453;SOR=0;LSEQ=AAACAAATGAAGATACCGCT;RSEQ=TATTTGCCAACATACTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:58,124:182,2:0.0109:2,2:19.5:1:27:1:0.53968:2.13:60:4:0.0109:0:2 0/0:187:0:0,0:62,125:187,0:0:2,0:25.4:1:31.5:1:1:0:59.8:186:1:0:0.4 +12 107194832 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23711;SOR=0;LSEQ=ATGAAGATACCGCTGTATTT;RSEQ=CCAACATACTAACTTTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:44,113:157,2:0.0126:2,2:41:1:30:0:0.48722:2.55:60:4:0.0128:0:1 0/0:167:0:0,0:50,117:167,0:0:2,0:1:0:12:0:1:0:60:0:0:0:1 +12 107194904 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50054;SOR=0;LSEQ=ACAGGGCTTTCTGAAAAATA;RSEQ=GCTTAAGTAGTAAAAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:4,36:40,2:0.0476:2,2:14.5:1:30.5:1:0.22648:8.16:60:4:0.0488:0:1 0/0:33:0:0,0:2,31:33,0:0:2,0:24.8:1:30.8:1:1:0:60:66:1:0:0 +12 108602855 . C G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05095;LSEQ=AGGTTTTGTCCTTCCTACTC;RSEQ=CAGAGCCAGAGCAAGCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:69:62,7:20,3:23,69:0.75:2,2:26:1:29.8:1:0.70662:1.32:60:68:0.764:0:1.1 0/1:77:10:10,0:50,17:67,10:0.1299:2,0:30.6:1:30.3:1:0.10568:0:60:20:0.1316:0:1 +12 108602871 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22258;SOR=Inf;LSEQ=ACTCCCAGAGCCAGAGCAAG;RSEQ=AATGCTCTTTTCATTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:95,22:117,0:0:2,0:22.4:1:31.8:1:1:0:60:116:1:0:0.6 0/1:105:2:1,1:73,30:103,2:0.019:2,2:13.5:1:28:1:0.50531:2.41012:60:4:0.0192:0:2.5 +12 108602874 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2194;SOR=Inf;LSEQ=CCCAGAGCCAGAGCAAGCAA;RSEQ=GCTCTTTTCATTTGTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:98,24:122,0:0:2,0:22.4:1:30.5:1:1:0:60:39.667:1:0:0.6 0/1:108:2:1,1:73,33:106,2:0.0185:2,2:16.5:1:30:1:0.53254:2.19426:60:4:0.0187:0:2.5 +12 108602893 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20425;SOR=Inf;LSEQ=ATGCTCTTTTCATTTGTTTA;RSEQ=AGAGTGGGGTAGCCACTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:128,63:191,0:0:2,0:20.7:1:32:1:1:0:60:382:1:0:0.7 0/1:158:2:1,1:100,56:156,2:0.0127:2,2:15.5:1:25:1:1:1.77872:60:4:0.0127:0:1 +12 108602970 . C A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13653;LSEQ=ATTTCAAAAAAACTTGAAAA;RSEQ=CTTGCAGTGCCTGGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:347:261:117,144:36,50:86,261:0.7522:2,2:25.5:1:29.8:1:0.70743:1.13:60:51.2:0.7485:0:1.8 0/1:308:90:42,48:103,115:218,90:0.2922:2,2:29:1:29.1:1:1:1.02353:60:89:0.2918:0:1.7 +12 108603016 . A G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17103;LSEQ=TAGGAATAAATATTTCCTTG;RSEQ=TGAATGTGTGAGCTCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:215:168:64,104:16,31:47,168:0.7814:2,2:26:1:31.7:1:0.73315:1.19:60:41:0.7773:0:2.5 0/1:193:73:29,44:48,72:120,73:0.3782:2,2:25:1:31:1:1:1.01144:60:146:0.3822:0:2 +12 108603024 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49959;SOR=0;LSEQ=AATATTTCCTTGATGAATGT;RSEQ=TGAGCTCATTTTTGTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:66,122:188,2:0.0105:2,2:28.5:1:32.5:1:1:1.84:60:4:0.0109:0:3 0/0:174:0:0,0:64,109:173,0:0:2,0:24.5:1:31.2:1:1:0:60:56.667:0.9942:0:0.8 +12 108603028 . G A 28 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60289;SOR=2.2622;LSEQ=TTTCCTTGATGAATGTGTGA;RSEQ=CTCATTTTTGTCTTCTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:1,0:62,116:178,1:0.0056:2,0:1:0:26:0:0.35196:0:60:2:0.0057:0:3 0/1:159:2:1,1:56,101:157,2:0.0126:2,2:18:0:28.5:1:1:1.80:60:4:0.0127:0:1.5 +12 108603041 . T C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0793;LSEQ=TGTGTGAGCTCATTTTTGTC;RSEQ=TCTCTCGAAGGGGTGTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:150:119:42,77:10,21:31,119:0.7933:2,2:21.9:1:31.9:1:0.83418:1.14:60:38.667:0.7891:0:2.6 0/1:134:31:12,19:30,73:103,31:0.2313:2,2:23.8:1:31.2:1:0.37796:1.53:60:62:0.2331:0:2.5 +12 109003754 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18354;SOR=0;LSEQ=CCAGGGTGAGCATTAACTGG;RSEQ=ACCGACTGTGTGCCAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:5,10:15,2:0.1176:2,2:29.5:1:30:1:1:1.91:60:4:0.1176:0:1.5 0/0:22:0:0,0:9,13:22,0:0:2,0:27.6:1:30.9:1:1:0:60:44:1:0:0.1 +12 109004229 . G C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTGAATATCTGGGGGCA;RSEQ=GGCTGCAGAGTGGGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:29:1:1:0:60:4:1:0:1 +12 109592181 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CACAGTGGCGACCTCTGACT;RSEQ=ACATTTTAAATTTCCCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:21,25:46,0:0:2,0:24.1:1:31.9:1:1:0:60:92:1:0:0.1 0/1:101:2:1,1:47,52:99,2:0.0198:2,2:9:0:31:1:1:1.11:60:4:0.0198:0:1.5 +12 109592193 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11109;SOR=0;LSEQ=CTCTGACTCACATTTTAAAT;RSEQ=TCCCATATTTTCCACCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:15,22:37,2:0.0513:2,2:23:1:32:1:1:1.45:60:4:0.0526:0:1 0/0:77:0:0,0:37,40:77,0:0:2,0:22.8:1:30.1:1:1:0:60:76:1:0:0.3 +12 109960852 . TC T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50587;SOR=0;LSEQ=TCGCCTCTGTGTCCTTTCCC;RSEQ=CCTCACCTCTGACAGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:132,66:198,2:0.01:2,2:8.5:1:26.5:1:1:1.99258:60:4:0.0103:0.005:0.5 0/0:157:0:0,0:106,51:157,0:0:2,0:21.7:1:30.2:1:1:0:60:156:1:0:0.1 +12 109960962 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06472;SOR=0.78237;LSEQ=CCTTACGGTCCTCTGACAGG;RSEQ=GTCATCAAGTCCGAGTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:495:268:129,139:113,111:224,268:0.5414:2,2:24.7:1:30.7:1:0.65097:1.09673:59.9:52.6:0.5445:0:1.2 0/1:427:205:99,106:108,113:221,205:0.4801:2,2:26.8:1:30.5:1:0.92295:1.02328:60:410:0.4812:0:1.1 +12 109961122 . C T 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26167;SOR=0.4372;LSEQ=CTGTCTTCCTCTCGCCAGCC;RSEQ=ATTCCCCACATAAAAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:13:0,13:1,37:38,13:0.2549:1,1:23.6:1:28.5:1:1:0:60:26:0.2549:0:1.2 0/1:31:4:0,4:1,26:27,4:0.129:1,0:19.5:1:29.5:1:1:0:60:8:0.129:0:1 +12 111855461 . A T 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGAGATGGGCTTTCACC;RSEQ=TGTTGCCCAGGCTGGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:25.5:1:34:0:1:0:29.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 111855854 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13997;SOR=Inf;LSEQ=TCTGCTGTGGTGCCCGGTGT;RSEQ=TAATGGGGCCTACACCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:284,27:311,0:0:2,0:21.2:1:32.5:1:1:0:60:50.833:0.9967:0:0.1 0/1:187:2:1,1:166,19:185,2:0.0107:2,2:11.5:1:28:1:0.20298:8.53933:60:4:0.0108:0:1 +12 111856247 . G A 54 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18936;SOR=4.63262;LSEQ=GCCGTGGGCCCCCAGCCAAG;RSEQ=CCGAGGCGTCCCCGGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:1:1,0:100,230:330,1:0.003:2,0:1:0:25:0:0.30514:0:60:2:0.0031:0:1 0/1:290:4:3,1:102,184:286,4:0.0138:2,2:6.5:1:27:1:0.13671:5.38:60:8:0.0142:0:1.3 +12 111856273 . C T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24561;SOR=0;LSEQ=GCGTCCCCGGAGCCAGGCCC;RSEQ=GGCCCCGCCGCCCCTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:54,84:138,2:0.0142:2,2:29:0:33:1:1:1.55:60:4:0.0144:0:2.5 0/0:143:0:0,0:70,73:143,0:0:2,0:20.7:1:29.8:1:1:0:60:46.667:1:0:0.4 +12 111856282 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.10008;SOR=0;LSEQ=GAGCCAGGCCCCGGCCCCGC;RSEQ=GCCCCTGGCCTGCCCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:1,2:64,51:115,3:0.0254:2,2:13.7:1:30.3:1:0.58699:2.49063:60:6:0.0259:0:2 0/0:135:0:0,0:75,60:135,0:0:2,0:21:1:30.1:1:1:0:60:134:1:0:0.4 +12 111856294 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50442;SOR=Inf;LSEQ=GGCCCCGCCGCCCCTGGCCT;RSEQ=CCCAAGGCCCGCAGCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:82,56:138,0:0:2,0:20:1:32.6:1:1:0:60:45:1:0:0.3 0/1:172:2:1,1:97,71:168,2:0.0116:2,2:31.5:1:28.5:1:1:1.36363:60:4:0.0116:0:1 +12 111856296 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50191;SOR=Inf;LSEQ=CCCCGCCGCCCCTGGCCTGC;RSEQ=CAAGGCCCGCAGCTCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:85,57:142,0:0:2,0:19.8:1:31.6:1:1:0:59.9:46.333:1:0:0.3 0/1:168:2:1,1:97,69:166,2:0.0119:2,2:31:0:31.5:1:1:1.40287:60:4:0.0119:0:1.5 +12 111856309 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24282;SOR=Inf;LSEQ=GGCCTGCCCAAGGCCCGCAG;RSEQ=TCTGAGGAGCTGGCCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:112,81:193,0:0:2,0:17.5:1:32.9:1:1:0:59.9:95.5:1:0:0.3 0/1:188:2:1,1:102,84:186,2:0.0106:2,2:19.5:1:27:1:1:1.21302:60:4:0.0107:0:1 +12 111856329 . C T 53 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.70631;SOR=1.63071;LSEQ=CTCTGAGGAGCTGGCCCCGC;RSEQ=GCGGCCGCCCGGGCCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:0,3:155,107:262,3:0.0113:2,0:1:0:28:1:0.07038:0:60:6:0.0115:0:1 0/1:218:4:2,2:114,100:214,4:0.0183:2,2:27.8:1:26.5:1:1:1.13931:60:3:0.0142:0:1.5 +12 111856596 . G A 64 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09728;SOR=6.07335;LSEQ=CTCCATGGACAGCGGGGCAC;RSEQ=CTGGCAGCGCGGGAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:1:1,0:285,288:573,1:0.0017:2,0:1:0:32:0:0.49826:0:60:2:0.0018:0:1 0/1:476:5:4,1:224,245:469,5:0.0105:2,2:10:1:27.8:1:0.20026:4.36:60:10:0.0107:0:1 +12 111856604 . C T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09605;SOR=6.15241;LSEQ=ACAGCGGGGCACGCTGGCAG;RSEQ=GCGGGAGGCTGGCGCTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:1:0,1:315,279:594,1:0.0017:2,0:36:0:33:0:0.47059:0:60:2:0.0017:0:1 0/1:487:5:1,4:244,237:481,5:0.0103:2,2:9.8:1:25.8:1:0.21301:4.10736:60:10:0.0104:0:1 +12 111856738 . T A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=4e-04;SOR=1.77296;LSEQ=TGCGCCCTTCGCCTTCACCC;RSEQ=GGGGAGAGCGCGGGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:95:35,60:133,295:428,95:0.1813:2,2:22.1:1:30.7:1:0.27702:1.29:60:46.5:0.182:0:1.1 0/1:390:110:45,65:104,175:279,110:0.2821:2,2:20.8:1:28.6:1:0.56279:1.16:60:35.667:0.2816:0:1.2 +12 111856750 . G A 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06212;SOR=Inf;LSEQ=CTTCACCCTGGGGAGAGCGC;RSEQ=GGCTGGGGAGGTGTGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:98,328:426,0:0:2,0:23.4:1:30.5:1:1:0:60:84.2:1:0:0.3 0/1:281:3:2,1:79,199:278,3:0.0107:2,2:6.7:1:27:1:0.20044:5.00:60:6:0.0109:0:1.3 +12 111884415 . T C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00647;SOR=3.1341;LSEQ=GAAGGCACCCTGGACCTCAC;RSEQ=ACAGGCTCAGAGCCTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:15:15,0:99,1:100,15:0.1304:1,1:28.7:1:31.7:1:1:0:60:30:0.1327:0:1 0/1:56:18:17,1:37,1:38,18:0.3214:1,1:19.5:1:31.7:1:0.54351:2.14358:57.9:36:0.3273:0:1.1 +12 111884449 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17467;SOR=Inf;LSEQ=CTGCCCAGCAACACCATGGA;RSEQ=ACTCTCTCTAAAAGGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:170,2:172,0:0:1,0:23.4:1:31.4:1:1:0:59.7:85:1:0:0.2 0/1:124:2:2,0:117,5:122,2:0.0161:1,0:12:1:29.5:1:1:0:60:4:0.0161:0:1 +12 111884608 . T C 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.42582;LSEQ=CCAGCATCCAGGAGGTCCGG;RSEQ=GGTGCACACGGCTTGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1586:905:474,431:364,315:679,905:0.5706:2,2:24.9:1:30.9:1:0.64726:1.05073:60:89.5:0.5708:0:1.1 1/0:1352:885:446,439:240,225:465,885:0.6546:2,2:24.7:1:30.1:1:0.68862:1.04992:60:48.167:0.6529:0:1.2 +12 111885351 . ATGGGG A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=5.000;MSILEN=5;SSF=0;SOR=1.93889;LSEQ=TTTCAGGGGATAGCCAAGGT;RSEQ=TGGGGTGGGGTGGGGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1236:191:107,84:621,287:908,191:0.1545:2,2:35.6:1:27.8:1:0.00134:1.69787:59:3.659:0.1508:8e-04:0.9 0/1:982:257:129,128:388,274:662,257:0.2617:2,2:35.9:1:25.4:1:0.02183:1.40453:59.3:2.295:0.2204:0.0143:1.2 +12 112036753 . GGCT G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=9.000;MSILEN=3;SSF=0.44;SOR=0;LSEQ=CATTGGCAGCCGCGGGCGGC;RSEQ=GCTGCTGCTGCTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:8,6:0,0:0,14:1:0,2:32.5:1:32.5:1:1:0:51.4:28:1:0:1 1/1:11:10:6,4:1,1:2,10:0.9091:2,2:31.2:1:29.6:1:1:1.45:52.7:9:0.9:0.1818:1.4 +12 112036797 . C T 122 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=3;SSF=0.7075;SOR=1.67486;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:7,7:3,2:5,14:0.7368:2,2:24.4:1:30.9:1:1:1.46843:48.1:28:0.7778:0:1.2 1/1:23:19:11,8:2,2:4,19:0.8261:2,2:21.5:1:28.9:1:1:1.36:49.6:38:0.8261:0:1.1 +12 112037526 . A G 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCCGGATCCGCCTTCCTC;RSEQ=AGGCGGGTCTGCCCTTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 112856810 . G T 43 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63423;SOR=2.36613;LSEQ=CGGCCGGCTGGCTCTGCCCC;RSEQ=CGTCCGGTCCCGAGCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:150,42:192,1:0.0052:2,0:1:0:25:0:0.2228:0:60:2:0.0053:0:1 0/1:246:3:1,2:191,52:243,3:0.0122:2,2:7:1:27.7:1:0.12222:7.26668:60:6:0.0123:0:1.3 +12 112856954 . G C 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGAGCCCCGAGGGGCCCGGC;RSEQ=CGGGCCTCGGCCCGGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:101,211:312,0:0:2,0:24.1:1:31.5:1:1:0:60:61.4:0.9935:0:0.2 0/1:383:26:10,16:131,225:356,26:0.0679:2,2:26.3:1:30.3:1:0.83694:1.07:59.8:52:0.0688:0:1.8 +12 112856963 . G A 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24926;SOR=0.30879;LSEQ=AGGGGCCCGGCGCGGGCCTC;RSEQ=GCCCGGCCACCGCCGCGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:5:4,1:76,169:245,5:0.02:2,2:9.2:1:28:1:0.03747:8.81:60:10:0.0202:0:1 0/0:320:2:2,0:109,209:318,2:0.0063:2,0:1:0:24.5:1:0.11961:0:60:4:0.0063:0:1 +12 112856983 . C A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=GGCCCGGCCACCGCCGCGTT;RSEQ=GGTTAGCCCCGTCCGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:23,105:128,0:0:2,0:16.9:1:31.1:1:1:0:60:256:1:0:0.2 0/1:160:13:4,9:36,110:146,13:0.0813:2,2:18.4:1:28.6:1:0.73899:1.36:60:26:0.0813:0:2.2 +12 112884001 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61244;SOR=0.46785;LSEQ=TTTCTACTCTGCTCATAATG;RSEQ=GTCTTAGCTGTGTTGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:131,9:140,2:0.0141:2,2:17.5:1:30:1:0.13635:13.86122:60:4:0.0142:0:1 0/0:151:1:1,0:139,11:150,1:0.0066:2,0:41:0:32:0:1:0:60:2:0.0067:0:1 +12 112884145 . G T 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07798;SOR=5.90804;LSEQ=GTTGACAAGAGGAGTTGATG;RSEQ=CAGTTTTTTGGCAAGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:1:0,1:256,289:545,1:0.0018:2,0:1:0:28:0:1:0:27:2:0.0019:0:1 0/1:652:7:4,3:310,335:645,7:0.0107:2,2:19.6:1:25.1:1:0.71625:1.44:39:6:0.0093:0:1 +12 112887890 . C CA 29 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGAGCGAAACTCCATCT;RSEQ=AAAAAAAAAAAAAAAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,0:4,2:0.2857:0,0:21:1:29.5:1:1:0:52.5:4:0.2857:0.1429:0 0/0:2:0:0,0:2,0:2,0:0:0,0:20.5:1:31.5:1:1:0:57.5:4:1:0:0.5 +12 112888054 . G T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25113;SOR=Inf;LSEQ=TAAAATCCGACGTGGAAGAT;RSEQ=AGATCTGATTTTACTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:142,31:173,0:0:2,0:21.9:1:32.6:1:1:0:59.8:346:1:0:0.1 0/1:197:3:1,2:158,36:194,3:0.0152:2,2:13:1:23.7:1:0.0958:8.63933:60:6:0.0152:0:1 +12 112888372 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50069;SOR=0;LSEQ=TCCCTTGTGCCCTGAGTGTC;RSEQ=GAAATGCATGACGGTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:21,142:163,2:0.0121:2,2:26.5:1:30.5:1:0.24959:6.63:60:4:0.0123:0:1 0/0:144:0:0,0:27,117:144,0:0:2,0:21.9:1:30.6:1:1:0:60:143:1:0:0.1 +12 112891235 . T A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12156;SOR=Inf;LSEQ=GTCTGGCAAGATGTTACCTT;RSEQ=GGGTGATTTTTCTGCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:39,179:218,0:0:2,0:26.4:1:30.5:1:1:0:60:53.5:1:0:0.1 0/1:215:3:2,1:45,167:212,3:0.014:2,2:13.3:1:20.7:1:0.12111:7.33:60:2:0.0093:0:1 +12 112891241 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.23337;SOR=Inf;LSEQ=CAAGATGTTACCTTTGGGTG;RSEQ=TTTTCTGCTGACAGAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:31,160:191,0:0:2,0:27.1:1:30.4:1:1:0:60:46.75:1:0:0.1 0/1:179:2:1,1:34,143:177,2:0.0112:2,2:10.5:1:28:1:0.35371:4.16:60:4:0.0112:0.0056:0.5 +12 112891260 . A G 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.25179;SOR=0;LSEQ=GATTTTTCTGCTGACAGAAG;RSEQ=CAGACACCATTACATTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:2,1:7,135:142,3:0.0207:1,2:17:1:24.7:1:0.01001:35.47:60:2:0.0142:0:1 0/0:124:0:0,0:14,110:124,0:0:2,0:22.8:1:29.4:1:1:0:60:123:1:0:0 +12 112892552 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.56825;LSEQ=AATCCTAATAGAGAATTTTG;RSEQ=AAACATACAGAGGTAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:4,98:102,2:0.0192:1,0:26:1:30:0:1:0:60:4:0.0196:0:1 0/1:91:1:0,1:8,81:89,1:0.011:2,0:1:0:31:0:1:0:60:2:0.0111:0:1 +12 112915336 . G GT 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.72962;SOR=1.32655;LSEQ=CTGGGCTTTAATTTTTATGT;RSEQ=TTTTTTTTTCAATCATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:4:4,0:159,3:162,4:0.0241:1,0:22.3:1:29.6:1:1:0:60:8:0.0241:0.006:0 0/1:126:4:4,0:117,5:122,4:0.0317:1,0:20.5:1:30.7:1:1:0:60:8:0.0323:0.0079:0 +12 112915434 . C T 154 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=18.85922;LSEQ=CAGTCCAGGACTTATGTGAC;RSEQ=GTGGTCTCTTTTTCTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:2:0,2:459,340:799,2:0.0025:2,0:1:0:26.5:1:0.18199:0:52:4:0.0025:0:1 0/1:820:37:21,16:460,323:783,37:0.0451:2,2:26.8:1:29.7:1:0.86498:1.08496:59:17.5:0.0434:0:1.1 +12 112919869 . C A 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TAACTTTCTTTTTTTCTGAT;RSEQ=TCTTCCAGAGTAAATGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:252,93:345,0:0:2,0:27.8:1:32.3:1:1:0:50.2:68:1:0:0.1 0/1:305:20:13,7:201,84:285,20:0.0656:2,2:31.2:1:28.5:1:0.61737:1.28739:51.6:19:0.0633:0:1.2 +12 112924509 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18058;SOR=Inf;LSEQ=AGGGCTTGCTTTTACCTACC;RSEQ=ACTCCTAGCTCTTTAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:19,116:135,0:0:2,0:23:1:32.5:1:1:0:60:66.5:0.9925:0:0.1 0/1:101:2:1,1:14,85:99,2:0.0198:2,2:26.5:1:26:1:0.27624:5.90:60:4:0.0202:0:1 +12 112924520 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16378;SOR=Inf;LSEQ=TTACCTACCCACTCCTAGCT;RSEQ=TTTAACTGTAGGAAGAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:10,104:114,0:0:2,0:21:1:33.2:1:1:0:60:113:1:0:0.1 0/1:78:2:1,1:6,70:76,2:0.0256:2,2:16.5:1:25:1:0.17249:10.88:60:4:0.026:0:1 +12 112924706 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26058;SOR=Inf;LSEQ=CTGAGTCCACCAGAAGTTGT;RSEQ=CATTAAACAACTTCATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:21,16:37,0:0:2,0:23:1:32.4:1:1:0:59.2:74:1:0:0.1 0/1:51:3:2,1:31,17:48,3:0.0588:2,2:24:1:28:1:1:1.09:57:6:0.0588:0:1 +12 112924732 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50394;SOR=Inf;LSEQ=AACAACTTCATCCTGGCTCT;RSEQ=CAGTTTCTCCTTATTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:34,22:56,0:0:2,0:25.4:1:32.7:1:1:0:59.5:112:1:0:0.1 0/1:72:2:1,1:37,33:70,2:0.0278:2,2:36:0:28:1:1:1.11943:55:4:0.0278:0:1 +12 112924762 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19201;SOR=0;LSEQ=CTTATTCTTCATGATGTTTG;RSEQ=TTTGTAGCTGTTGACTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:28,29:57,2:0.0339:2,2:19.5:1:29:1:1:1.04:57.5:4:0.0345:0:1 0/0:75:0:0,0:35,40:75,0:0:2,0:28.6:1:31.2:1:1:0:59.7:150:1:0:0.2 +12 112927003 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20407;SOR=Inf;LSEQ=CCAGCCTGAGGGCTGGCATG;RSEQ=GGATTCTCATTCTCTTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:39,157:196,0:0:2,0:25.1:1:30.2:1:1:0:59.2:64.333:1:0:0.1 0/1:162:2:1,1:34,126:160,2:0.0123:2,2:24:1:27.5:1:0.38647:3.67:57.5:4:0.0124:0:1 +12 112938755 . CCAGAGTG C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGGTCTTGTTGCCCAGG;RSEQ=CAGTGGTGCGATCATAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 112939836 . A AT 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.11322;LSEQ=TATTCTCAACCCGTCTATCA;RSEQ=TTTTTTTTTCTTTCTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:2,0:87,0:87,2:0.0222:1,0:28:1:33:0:1:0:60:4:0.023:0:0 0/1:81:2:2,0:79,0:79,2:0.0247:1,0:8.5:1:30.5:1:1:0:60:4:0.025:0.0123:0.5 +12 112939853 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00068;SOR=0.30219;LSEQ=TCAATTTTTTTTTCTTTCTC;RSEQ=CTCTTTTTTCTTTTTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:37:35,2:82,0:82,37:0.3083:1,2:20.8:1:32.3:1:0.09486:0:59.2:74:0.3162:0:1.1 0/1:110:13:13,0:96,1:97,13:0.1182:1,1:31.2:1:29.2:1:1:0:60:12:0.1143:0:1.1 +12 112939880 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24301;SOR=Inf;LSEQ=TTTCTTTTTTTGGGCAAAAT;RSEQ=CCTTTTTTGCTTTTTATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:168,30:198,0:0:2,0:23:1:28.1:1:1:0:59.7:32:1:0:0.3 0/1:193:2:1,1:164,26:190,2:0.0104:2,2:28:1:30:1:0.26211:6.20863:60:4:0.011:0:1 +12 112939889 . G T 45 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.24908;SOR=Inf;LSEQ=TTGGGCAAAATACCTTTTTT;RSEQ=CTTTTTATCCCCTTAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:199,40:239,0:0:2,0:22.8:1:32:1:1:0:59.8:28.875:1:0:0.3 0/1:253:3:2,1:195,54:249,3:0.0119:2,2:6.7:1:28.7:1:0.52385:1.80066:60:6:0.0125:0:1.3 +12 113097659 . G A 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.43671;LSEQ=ATCTGTCTGCATCATTCTTC;RSEQ=GGTGCCCCTTTGCTTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:5,11:16,2:0.1111:2,0:31.5:1:25:1:1:0:60:1:0.0667:0:1.5 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:43.5:1:29.5:1:1:1.18:60:4:0.1538:0:1 +12 115109672 . C A 141 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02338;LSEQ=GGACGCGCTGCGGGACCTGT;RSEQ=CGGCTTGGCTTCCAAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:37:21,16:400,362:762,37:0.0463:2,2:23.2:1:27.2:1:0.73647:1.19:60:17.5:0.0446:0:1.2 0/0:885:1:1,0:463,421:884,1:0.0011:2,0:1:0:21:0:1:0:60:2:0.0011:0:1 +12 115109963 . G A 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.193;SOR=4.53581;LSEQ=GATGGAGTAGGGGCTGTAGC;RSEQ=CAGCCGCGGGCGCATGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:1:0,1:251,192:443,1:0.0023:2,0:18:0:26:0:0.43468:0:60:2:0.0023:0:1 0/1:394:4:3,1:213,177:390,4:0.0102:2,2:23.5:1:28:1:0.6301:2.49:60:8:0.0104:0:1.8 +12 115110038 . C T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06263;SOR=0;LSEQ=GGAGGCTGCCGCAGAGGAGG;RSEQ=GGCCGCCGCTGCGGCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:5:2,3:219,248:467,5:0.0106:2,2:15:1:26.4:1:1:1.32382:60:4:0.0087:0:1.4 0/0:439:0:0,0:218,220:438,0:0:2,0:24.3:1:29.5:1:1:0:60:61.571:0.9977:0:0.2 +12 115110078 . C T 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=0;LSEQ=TACGTGTAGGGGTAAGGGAA;RSEQ=AGGCTTCCGAAAGGGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:14:7,7:156,241:397,14:0.0341:2,2:20.3:1:30.5:1:0.42078:1.54:60:28:0.0347:0:1.2 0/0:357:0:0,0:141,216:357,0:0:2,0:26.3:1:31:1:1:0:60:38.667:1:0:0.2 +12 115110222 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08831;SOR=Inf;LSEQ=CCATGAATCCCTGGTATGTT;RSEQ=TGTTGTTGTTGTTGTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:39,0:0:1,0:20.2:1:30:1:1:0:58.8:3.875:1:0:0.8 0/1:17:2:1,1:1,14:15,2:0.1176:1,2:24:1:26.5:1:0.22794:10.25:52:4:0.125:0:4 +12 115110241 . GT G 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.62202;SOR=1.68152;LSEQ=TCTGTTGTTGTTGTTGTTGT;RSEQ=TTTTTTTTTTGGGGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:0,14:14,3:0.1429:1,0:32.3:1:33.3:1:1:0:60:6:0.1667:0:0.7 0/1:9:2:1,1:0,7:7,2:0.2222:0,2:31:0:32:1:0.22222:0:52:4:0.25:0:4 +12 115112258 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4989;SOR=Inf;LSEQ=AGGCCAGGCAGGGGGCCCTG;RSEQ=GCCAGGTGCGCGGCGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:34,151:185,0:0:2,0:19.1:1:31.7:1:1:0:60:45.25:1:0:0.2 0/1:193:2:1,1:50,141:191,2:0.0104:2,2:11:1:30:1:0.45968:2.80:60:4:0.0105:0:1 +12 115112260 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23569;SOR=0;LSEQ=GCCAGGCAGGGGGCCCTGGG;RSEQ=CAGGTGCGCGGCGGCCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:30,144:174,2:0.0114:2,2:22.5:1:28.5:1:0.32208:4.74:60:4:0.0118:0:1 0/0:186:0:0,0:48,137:185,0:0:2,0:21:1:30.5:1:1:0:60:25.429:0.9944:0:0.2 +12 115112273 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50405;SOR=Inf;LSEQ=CCCTGGGCCAGGTGCGCGGC;RSEQ=GCCGCGTCCGTCTGCACCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:18,86:104,0:0:2,0:19.4:1:31.9:1:1:0:60:208:1:0:0.1 0/1:130:2:1,1:35,93:128,2:0.0154:2,2:29:1:31:0:0.47871:2.63:60:4:0.0155:0:1 +12 115112274 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50433;SOR=Inf;LSEQ=CCTGGGCCAGGTGCGCGGCG;RSEQ=CCGCGTCCGTCTGCACCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:19,82:101,0:0:2,0:19.3:1:33:1:1:0:60:202:1:0:0.1 0/1:127:2:1,1:34,90:124,2:0.0157:2,2:27.5:1:27.5:1:0.48:2.62:60:4:0.0161:0:1 +12 115112315 . G T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01105;SOR=0.24201;LSEQ=AGCGGCGCGAAGGCCTCCTT;RSEQ=CCCGGGAGCGCGCGCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:18:12,6:63,29:92,18:0.1636:2,2:20.1:1:31.6:1:1:1.08538:60:36:0.1651:0:1.2 0/1:89:4:2,2:63,22:85,4:0.0449:2,2:9.3:1:26:1:0.29336:2.824:60:3:0.0345:0:3 +12 115112565 . G T 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00654;SOR=Inf;LSEQ=TGGTGGTGGAGATCTTGGCC;RSEQ=CGTCGCAGGCCTCGGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:0:0,0:214,318:532,0:0:2,0:24.6:1:30.8:1:1:0:60:34.467:0.9981:0:0.1 0/1:510:7:3,4:228,273:501,7:0.0137:2,2:11.3:1:28.9:1:1:1.11329:60:14:0.014:0:1 +12 115112986 . C T 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCAGATTTCACATGCAT;RSEQ=TCCCCATTCGATTGCAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:28.8:1:31.5:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 115114036 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.57853;LSEQ=GCTTTTAAAGGGCAAGTGCC;RSEQ=TGGTTGGTGCCCCATCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:81:72,9:157,14:171,81:0.3202:2,2:22.3:1:32:1:0.4858:1.39986:60:80:0.3213:0:1.1 1/0:153:84:75,9:62,7:69,84:0.549:2,2:26.5:1:30.7:1:1:1.06246:60:83:0.5533:0:1.1 +12 115117029 . G T 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAGGACAAAGCCCAAGAG;RSEQ=GGGGGAGGAGTGGGTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:42.5:1:31:0:1:0:60:4:0.4:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:38:0:32:0:1:0:60:2:1:0:1 +12 115117337 . G A 219 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTGGTATGCAGTCACAGC;RSEQ=ATGAATTCAGTTTCGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:152:89,63:407,344:751,152:0.1683:2,2:25.2:1:30.3:1:0.37148:1.19:60:304:0.1698:0:1.1 0/0:1097:0:0,0:586,510:1096,0:0:2,0:26:1:29.8:1:1:0:60:77.286:0.9991:0:0.2 +12 115117564 . G A 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15131;SOR=5.07115;LSEQ=TCCCCACCGCAGGGTACCAC;RSEQ=CTTGTACCGAGCCCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:1:0,1:70,73:143,1:0.0069:2,0:42:0:32:0:1:0:60:2:0.007:0:1 0/1:87:3:3,0:42,42:84,3:0.0345:2,0:19:1:30.7:1:0.24218:0:60:6:0.0345:0:1.7 +12 115117604 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15585;SOR=Inf;LSEQ=CTTGGAGTACCCCCTGGGTA;RSEQ=GTTTCGCTCCACAGATGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:134,40:174,0:0:2,0:22.1:1:32.2:1:1:0:60:173:1:0:0.1 0/1:114:2:1,1:88,24:112,2:0.0175:2,2:13.5:1:26:0:0.39202:3.61257:60:4:0.0177:0:1.5 +12 115117664 . GC G 77 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.73094;SOR=0.69074;LSEQ=TGCTCCTCAGTTGCCAAAGG;RSEQ=CCCCCCCACCCTCACCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:5:3,2:306,152:458,5:0.0108:2,2:15:1:33.2:1:1:1.34127:52.2:10:0.0112:0.0022:1.4 0/0:401:3:2,1:249,146:395,3:0.0075:2,2:23.7:1:30.3:1:1:1.17:60:6:0.0077:0.0025:0.3 +12 115118579 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21412;SOR=Inf;LSEQ=ACAAGTTTGCTATGCTTAGG;RSEQ=AGAAGCAAAGGAGAAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:154,37:191,0:0:2,0:25.2:1:31.7:1:1:0:60:37.2:1:0:0.3 0/1:165:2:1,1:130,33:163,2:0.0121:2,2:16.5:1:26:0:0.37066:3.89593:60:4:0.0122:0:1 +12 115118589 . G A 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATGCTTAGGGAGAAGCAAA;RSEQ=GAGAAGTCTGGGCTGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:35:26,9:152,38:190,35:0.1556:2,2:25.7:1:31.1:1:0.49752:1.38248:60:70:0.157:0:1 0/0:203:0:0,0:158,45:203,0:0:2,0:24.3:1:31.6:1:1:0:60:100.5:1:0:0.1 +12 115118997 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=2.8451;LSEQ=AAAAGAAAGATAAACCACCC;RSEQ=TAATCTTGGGTTTGATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:35:6,29:7,64:71,35:0.3302:2,2:21.9:1:31.2:1:0.34801:1.88:60:70:0.3365:0:1.1 1/0:94:55:5,50:6,33:39,55:0.5851:2,2:20.7:1:30.3:1:0.5165:1.80627:60:54:0.587:0:1 +12 115120322 . CT C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTCTTGCAGTAGAGTGC;RSEQ=TTTTTTTTTTTCTTTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,0:7,2:0.2:0,0:26.5:1:34:0:1:0:60:4:0.2222:0:0 0/0:3:0:0,0:2,1:3,0:0:2,0:5.3:1:28.3:1:1:0:60:6:1:0:0.3 +12 115121027 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06321;SOR=Inf;LSEQ=CACTCCAGGCGGGGCGCTGG;RSEQ=CTCCAGCCGGGGACAAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:114,239:353,0:0:2,0:24.5:1:31.6:1:1:0:59.8:57.833:1:0:0.1 0/1:390:5:4,1:151,234:385,5:0.0128:2,2:14.6:1:25.4:1:0.08371:6.17:60:10:0.0131:0:1 +12 115121189 . G A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.67683;LSEQ=GCACTTCAAAGGGAGGAGGG;RSEQ=AAGTGTCTTTTGGAGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:12,6:0.3333:0,0:21.5:1:31:1:1:0:60:12:0.3333:0:1.2 0/1:8:2:0,2:1,5:6,2:0.25:2,0:13.5:1:32:0:1:0:60:4:0.25:0:1 +12 115121203 . A G 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46619;LSEQ=GGAGGGGAAGTGTCTTTTGG;RSEQ=GAATGGGAGGCCGCTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:31.5:1:30:1:1:0:60:4:0.1538:0:1 0/1:5:1:0,1:1,3:4,1:0.2:2,0:12:0:32:0:1:0:60:2:0.2:0:1 +12 117193175 . T A 22 d5;v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATAGCCCAGAGGTCTTTT;RSEQ=TTTTTTTTTTTTTAACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:49:0:26:0:1:0:42:2:1:0:4 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:27:1:22.5:1:0.33333:0:51.5:4:0.6667:0:3 +12 117193323 . C G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCAGGTACCTTTCTCTTC;RSEQ=GCTTCTTTCTTTTTCTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:13.2:1:31:1:1:0:23.5:12:1:0:1 1/1:8:7:6,1:1,0:1,7:0.875:0,2:17.7:1:30.6:1:1:0:21.1:14:0.875:0:1.1 +12 117193507 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.50847;SOR=Inf;LSEQ=AGACTCTTCCAGTTTTGCCA;RSEQ=GGTAACACTTACGGGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:6,25:31,0:0:2,0:24.1:1:29.4:1:1:0:26.6:62:1:0:0.1 0/1:44:2:1,1:8,34:42,2:0.0455:2,2:25.5:1:27.5:1:0.37104:4.07:22:4:0.0455:0:1.5 +12 117549739 . A C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.73172;SOR=1.48323;LSEQ=CTGACTCAGCAGAGCTCAGA;RSEQ=CCTACTCTCCGCTGACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:2,3:3,7:10,5:0.3333:2,2:26.6:1:31.6:1:1:1.51:60:10:0.3333:0:1.2 0/1:21:9:6,3:6,6:12,9:0.4286:2,2:30.8:1:31.8:1:0.66049:1.93:60:18:0.45:0:1.4 +12 117683444 . T C 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.76457;LSEQ=TGACTGTAGTGAACGTTGTA;RSEQ=GTGAAATGTGTGCCACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:1,3:4,4:0.5:2,2:28:1:31.8:1:1:1:60:8:0.5:0:2 0/1:7:3:0,3:1,3:4,3:0.4286:2,0:20:1:21.7:1:1:0:60:2:0.3333:0:2 +12 117683447 . G A 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.18452;LSEQ=CTGTAGTGAACGTTGTATGT;RSEQ=AAATGTGTGCCACACCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:1,2:3,5:0.625:2,2:20.4:1:31.6:1:1:1.8258:60:10:0.625:0:1.8 1/0:6:4:1,3:0,2:2,4:0.6667:0,2:16:1:26.5:1:1:0:60:8:0.6667:0:1.8 +12 117838703 . T A 77 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0068;SOR=17.95587;LSEQ=GAATATATTTGAAACTCCAC;RSEQ=TGCACCTAGGAGAAAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:13,1:14,1:0.0667:1,0:4:0:32:0:1:0:60:2:0.0667:0:1 1/0:10:6:6,0:4,0:4,6:0.6:0,0:42.8:1:29.8:1:1:0:60:12:0.6:0:1 +12 117838835 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23236;SOR=Inf;LSEQ=CCTATGCTGAGACTGTTTCC;RSEQ=ATGGACATGGCAATGATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:111,26:137,0:0:2,0:24.4:1:30.6:1:1:0:60:136:1:0:0.1 0/1:128:2:1,1:92,34:126,2:0.0156:2,2:35.5:1:29:1:0.47367:2.6814:60:4:0.0157:0:1.5 +12 117838844 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23147;SOR=Inf;LSEQ=AGACTGTTTCCAATGGACAT;RSEQ=GCAATGATTTGCTCTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:121,37:158,0:0:2,0:24.3:1:31.6:1:1:0:60:51.667:1:0:0.1 0/1:147:2:1,1:104,41:145,2:0.0136:2,2:23:1:27.5:1:0.49119:2.51824:60:4:0.0137:0:1 +12 117838846 . CA T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23413;SOR=Inf;LSEQ=ACTGTTTCCAATGGACATGG;RSEQ=ATGATTTGCTCTGTGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:123,44:167,0:0:2,0:23.7:1:31.8:1:1:0:60:40.75:0.9939:0:0.2 0/1:158:2:1,1:112,44:156,2:0.0127:2,2:37.5:1:27.5:1:0.4898:2.52823:52.5:4:0.013:0:1.5 +12 117838929 . T C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.30722;LSEQ=AAGGGTCATTACCAAGTTCT;RSEQ=GTCCACATAGCCTCTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:128:64,64:82,108:190,128:0.4025:2,2:25.6:1:30.8:1:0.25206:1.32:59.9:63:0.4013:0:1.1 1/0:317:193:87,106:58,66:124,193:0.6088:2,2:25.5:1:29.5:1:0.81757:1.07048:59.9:47.25:0.6058:0:1.1 +12 117870842 . G T 60 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10007;SOR=0;LSEQ=TCTAAGAATCCATAAGTAAT;RSEQ=AAAATACATGGATATGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:4,6:10,4:0.2857:2,2:6:1:30:1:1:1.46:60:8:0.2857:0:1 0/0:12:0:0,0:4,8:12,0:0:2,0:21.2:1:29.8:1:1:0:60:24:1:0:0.1 +12 118034656 . G T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89003;SOR=1.06824;LSEQ=GGAGGAAGAGCAAGCACCAT;RSEQ=CTCACTATAGCTTTGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:138:70:70,0:68,0:68,70:0.5072:1,1:23.9:1:31.2:1:1:0:60:69:0.5036:0:1.1 1/0:84:44:41,3:38,2:40,44:0.5238:2,2:24.1:1:30.5:1:1:1.38487:60:88:0.5301:0:1.1 +12 118034737 . C T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGCAGATAAACACTTCATAT;RSEQ=TTCCCTTCAAGTTACTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:354,162:516,0:0:2,0:24.3:1:32.5:1:1:0:59.8:128:1:0:0.1 0/1:422:15:7,8:278,129:407,15:0.0355:2,2:28.5:1:29.6:1:0.09416:2.45712:60:30:0.0361:0:1 +12 118035029 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54615;SOR=0;LSEQ=TTTAGTCACTGTGGTAGACT;RSEQ=AATAATGCCCCAGCCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:7,83:90,2:0.0217:2,2:23.5:1:27:1:0.16722:11.16:60:4:0.0217:0:1 0/0:48:0:0,0:0,48:48,0:0:1,0:25.8:1:31.5:1:1:0:60:96:1:0:0.1 +12 118035090 . T C 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31303;SOR=3.29503;LSEQ=GCTGGAATCAGTGACTGTTA;RSEQ=TAGGTTTGTGTGAAAGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:7:0,7:0,24:24,7:0.2258:1,0:20.6:1:32:1:1:0:60:14:0.2333:0:1 1/0:6:3:0,3:0,3:3,3:0.5:0,0:25.3:1:33.3:1:1:0:60:6:0.5:0:1 +12 119594500 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=CTCCCGCAGCCCTAGTCCGG;RSEQ=CTCCCGCAGCCGGAGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:51,39:90,0:0:2,0:25:1:30.7:1:1:0:60:21.5:1:0:0.2 0/1:99:2:1,1:52,45:97,2:0.0202:2,2:18.5:1:31:1:1:1.15386:60:4:0.0211:0:1 +12 119594501 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=TCCCGCAGCCCTAGTCCGGG;RSEQ=TCCCGCAGCCGGAGCCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:51,39:90,0:0:2,0:25.4:1:32.3:1:1:0:60:89:0.9889:0:0.2 0/1:99:2:1,1:52,45:97,2:0.0202:2,2:19:1:29:1:1:1.15386:60:4:0.0213:0:1 +12 119594521 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.21155;SOR=0;LSEQ=CTCCCGCAGCCGGAGCCGGA;RSEQ=CAGGAGCCGGAGCCGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:53,46:99,2:0.0198:2,2:17:1:29:1:1:1.15055:60:4:0.0206:0:1 0/0:118:0:0,0:62,56:118,0:0:2,0:25.9:1:31:1:1:0:59.4:38.333:1:0:0.3 +12 120534993 . G T 64 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02048;SOR=8.81258;LSEQ=GTCCCCCGAGGAACCTCCGT;RSEQ=GGCCTCGGGCTGGGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:763:1:0,1:597,165:762,1:0.0013:2,0:1:0:25:0:0.21756:0:60:2:0.0013:0:1 0/1:524:6:3,3:391,127:518,6:0.0115:2,2:14.3:1:24.8:1:0.16528:3.07052:60:5:0.0097:0:1 +12 120535169 . G A 182 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=89.51553;LSEQ=AGGACCAGCTCCGTGATGCA;RSEQ=TTGAACATCTGTGGAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1331:1:1,0:558,772:1330,1:8e-04:2,0:1:0:26:0:0.41998:0:60:2:8e-04:0:1 0/1:1077:68:26,42:421,588:1009,68:0.0631:2,2:22.7:1:30:1:0.61269:1.15642:60:136:0.0638:0:1.2 +12 120535238 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13736;SOR=5.32781;LSEQ=CAGGAGGCCCCTGCTGGCCT;RSEQ=CACGGCTGCCTCCCCGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:1:0,1:80,429:509,1:0.002:2,0:34:0:32:0:1:0:60:2:0.002:0:1 0/1:289:3:1,2:59,227:286,3:0.0104:2,2:27.3:1:27.3:1:0.50384:1.92:60:6:0.0106:0:1 +12 120535242 . G A 132 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=38.23069;LSEQ=AGGCCCCTGCTGGCCTGCAC;RSEQ=GCTGCCTCCCCGCCTTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:1:0,1:64,408:472,1:0.0021:2,0:17:0:34:0:1:0:60:2:0.0021:0:1 0/1:266:20:4,16:46,200:246,20:0.0752:2,2:20.2:1:30.6:1:0.77469:1.09:60:40:0.076:0:1 +12 120536571 . C T 156 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=12.74395;LSEQ=GGCCAGCAGCATGGAGAAGG;RSEQ=GGCCACGGGTGTGTGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:734:5:2,3:566,163:729,5:0.0068:2,2:7.8:1:28.4:1:0.07929:5.19327:60:10:0.0069:0:1 0/1:559:45:28,17:371,143:514,45:0.0805:2,2:21.2:1:28.5:1:0.17:1.5738:59.6:44:0.0799:0:1.2 +12 120536777 . C T 138 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=18.91428;LSEQ=GTCAGCGCAGCCCTGAGGGG;RSEQ=GCAGCCGGCTGCCTCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1336:2:1,1:660,672:1332,2:0.0015:2,2:15.5:1:28.5:1:1:1.02:60:4:0.0015:0:1 0/1:942:26:17,9:450,465:915,26:0.0276:2,2:24.3:1:29.4:1:0.11458:1.95:60:52:0.0279:0:1.1 +12 120536783 . C T 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGCCCTGAGGGGCGCAGC;RSEQ=GGCTGCCTCTCTCCCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1308:0:0,0:655,653:1308,0:0:2,0:24.1:1:30.5:1:1:0:59.9:99.615:1:0:0.1 0/1:929:67:34,33:429,432:861,67:0.0721:2,2:24.7:1:29.6:1:0.89976:1.04:60:134:0.0727:0:1.2 +12 120536820 . G A 183 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=118.81924;LSEQ=CCCAACCCCGACCCGGCCCT;RSEQ=AGTGCAGCCTCACCTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1392:1:1,0:721,669:1390,1:7e-04:2,0:1:0:24:0:1:0:60:2:7e-04:0:1 0/1:1028:81:45,36:488,458:946,81:0.0788:2,2:22.7:1:28.9:1:0.56267:1.17:60:162:0.0799:0:1.1 +12 120537042 . C G 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCTGCCCACGTCAGGACA;RSEQ=TGACCCGGAAAAGGTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:31,307:338,0:0:2,0:22.9:1:33:1:1:0:60:47.286:1:0:0.1 0/1:232:38:5,33:29,165:194,38:0.1638:2,2:22:1:30.8:1:1:1.15928:59.9:37:0.1623:0:1.3 +12 120537079 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54511;SOR=0;LSEQ=AGGGTGGCCCTGGAGCCTGG;RSEQ=CTCTCACTCAGCCTCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:0,2:3,170:173,2:0.0114:1,0:26:1:32:0:1:0:60:4:0.0116:0:1 0/0:93:0:0,0:1,92:93,0:0:1,0:21.3:1:31.8:1:1:0:60:30:1:0:0.3 +12 120537094 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00279;SOR=Inf;LSEQ=CCTGGGCTCTCACTCAGCCT;RSEQ=GGCAGATGCCCCCGAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:3,136:139,0:0:1,0:25:1:30.2:1:1:0:59.8:45.333:1:0:0.2 0/1:64:5:0,5:1,58:59,5:0.0781:1,0:13:1:29.6:1:1:0:59.4:10:0.0781:0:2.6 +12 120541567 . G T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00475;SOR=Inf;LSEQ=TCCACCATGACCAGGCACCG;RSEQ=TCGCTCAACTGTGTCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:792:0:0,0:573,219:792,0:0:2,0:22.3:1:30.9:1:1:0:59.9:30.68:1:0:0.6 0/1:553:6:3,3:388,159:547,6:0.0108:2,2:11.8:1:22.2:1:0.36539:2.4358:60:5:0.0092:0:2.8 +12 120541570 . G A 224 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01219;LSEQ=ACCATGACCAGGCACCGGTC;RSEQ=CTCAACTGTGTCCACAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:184:141,43:455,198:653,184:0.2196:2,2:22.3:1:29.8:1:0.07962:1.43:60:25.286:0.2153:0:2 0/0:586:2:1,1:401,181:582,2:0.0034:2,2:17:1:31.5:1:0.52653:2.21217:60:4:0.0035:0:1 +12 120541597 . G A 239 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00704;LSEQ=TGTGTCCACAGGTCAGTGGC;RSEQ=CGGGTTGGGTGGGAGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1232:276:178,98:578,374:952,276:0.224:2,2:25.4:1:29.5:1:0.26181:1.18:60:22:0.2198:0:1.7 0/0:987:2:2,0:594,388:982,2:0.002:2,0:11:1:23:1:0.52186:0:60:1:0.001:0:1.5 +12 120541599 . G A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTCCACAGGTCAGTGGCGC;RSEQ=GGTTGGGTGGGAGTGGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1277:0:0,0:775,499:1274,0:0:2,0:25.2:1:30.1:1:1:0:60:56.909:0.9976:0:0.5 0/1:1043:28:18,10:607,406:1013,28:0.0268:2,2:20.5:1:30.4:1:0.6998:1.20:60:56:0.0272:0:1.2 +12 120546136 . G A 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGTTCCCAACATCAGGCA;RSEQ=AGGCAACTCTGTTTGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:252,38:290,0:0:2,0:23.2:1:32.6:1:1:0:59.9:31.222:1:0:0.1 0/1:196:18:14,4:149,29:178,18:0.0918:2,2:20:1:30.9:1:0.51281:1.4648:60:36:0.0938:0:2.1 +12 120546145 . C G 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AACATCAGGCAGAGGCAACT;RSEQ=TGTTTGGTGCCAGGGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:289,70:359,0:0:2,0:22.1:1:32.2:1:1:0:60:118.667:1:0:0.1 0/1:234:34:26,8:157,43:200,34:0.1453:2,2:23.2:1:31.7:1:0.82298:1.12285:60:68:0.1485:0:1.6 +12 120546378 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03161;SOR=Inf;LSEQ=GTCCCAACTCTTAAGAAGCT;RSEQ=GGTGGGACCCAGCTCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:2,171:173,0:0:1,0:25.6:1:29.9:1:1:0:60:27.833:1:0:0.1 0/1:81:3:0,3:0,78:78,3:0.037:1,0:31:1:31.3:1:1:0:60:6:0.0375:0:1 +12 120554361 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49248;SOR=0;LSEQ=CGAGGCCCCCGCGGGCCGCG;RSEQ=CCGGCAGGGCCCGCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:21,7:28,2:0.0667:2,2:10.5:1:29:1:0.46897:2.87249:60:4:0.0667:0:1 0/0:27:0:0,0:21,6:27,0:0:2,0:4.3:1:30.6:1:1:0:60:54:1:0:0.4 +12 120554466 . G A 240 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00243;LSEQ=CCGGGCCATGGCGGGCGGGG;RSEQ=CGGTGCGCGCGGGCGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:291:170,121:224,169:393,291:0.423:2,2:27.1:1:29.4:1:0.75437:1.06:60:35.375:0.4268:0:1.2 0/0:560:1:1,0:299,257:556,1:0.0018:2,0:1:0:25:0:1:0:60:2:0.0018:0:1 +12 120554510 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07029;SOR=Inf;LSEQ=CGGTACTGGCCTCGCGATCC;RSEQ=CAGCTCCCTTCGGGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:159,248:407,0:0:2,0:23.4:1:30.6:1:1:0:60:36:1:0:0.5 0/1:287:3:2,1:106,178:284,3:0.0105:2,2:26.3:1:29.7:1:0.55871:3.34:60:6:0.0107:0:1 +12 120554520 . T C 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCGCGATCCGCAGCTCCCT;RSEQ=CGGGCTGCTCCGGCAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:107,236:343,0:0:2,0:22.9:1:29.6:1:1:0:60:33.3:0.9911:0:0.4 0/1:251:16:5,11:77,158:235,16:0.0637:2,2:22.1:1:30.7:1:1:1.07186:60:32:0.0645:0:1.3 +12 120554596 . CCCT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52989;SOR=0;LSEQ=GAAACACCTCCCTCCGCTCC;RSEQ=CCTCCTCCTCAGCAGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:0,2:5,63:68,2:0.0286:2,0:26:1:31:1:1:0:60:4:0.0294:0.0143:0 0/0:41:0:0,0:5,36:41,0:0:2,0:19.5:1:30.4:1:1:0:59.6:40:1:0:0.1 +12 121416596 . C T 62 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03091;SOR=Inf;LSEQ=TTTCTAAACTGAGCCAGCTG;RSEQ=AGACGGAGCTCCTGGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:586:0:0,0:331,254:585,0:0:2,0:24.1:1:32.3:1:1:0:60:82.571:1:0:1 0/1:599:6:2,4:312,280:592,6:0.01:2,2:6.7:1:24.2:1:0.43049:2.22569:60:5:0.0085:0:2.3 +12 121416622 . C G 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32621;LSEQ=GAGCTCCTGGCGGCCCTGCT;RSEQ=GAGTCAGGGCTGAGCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:626:436:252,184:102,87:189,436:0.6965:2,2:25:1:31.8:1:0.38096:1.17:60:108:0.6979:0:1.9 0/1:610:261:130,131:182,167:349,261:0.4279:2,2:24.2:1:30.5:1:0.62337:1.09803:60:86:0.4293:0:1.9 +12 121416650 . A C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29247;LSEQ=GGCTGAGCAAAGAGGCACTG;RSEQ=TCCAGGCACTGGGTGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:663:457:237,220:111,95:206,457:0.6893:2,2:25.8:1:32.4:1:0.67453:1.08447:60:44.7:0.6888:0:1.9 0/1:623:245:128,117:193,181:374,245:0.3933:2,2:25.8:1:31.3:1:0.93446:1.03:59.9:80.667:0.3948:0:1.9 +12 121416988 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22698;SOR=0.68744;LSEQ=CCCTTCTGAGTTGAGTCCCC;RSEQ=TGACCTTCAGCCTTTAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:63:0,63:1,38:39,63:0.6058:1,1:24.7:1:32.3:1:0.38235:0:60:62:0.62:0:1.1 1/0:76:39:2,37:1,36:37,39:0.5132:1,2:23:1:31.6:1:1:1.93:60:38:0.5067:0:1.2 +12 121417829 . C A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCCCTCCCCAGCGGCTC;RSEQ=CTGACCTCCACCCTACAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:33:0:32:0:1:1:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 121426478 . C T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99058;LSEQ=CATAAATGACCATACCTCAC;RSEQ=GTCCCTGAGTCTATGTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:19:18,1:23,0:23,19:0.4524:1,1:28.3:1:32.5:1:0.45238:0:60:38:0.4634:0:1.3 0/1:20:9:9,0:11,0:11,9:0.45:0,0:23.7:1:30.1:1:1:0:60:18:0.45:0:1.6 +12 121426545 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.39149;SOR=0;LSEQ=TGCACAGTCCCCACCCTCAG;RSEQ=GTTGACAAGGTTCCAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:143:143:134,9:0,0:0,143:1:0,2:23.3:1:30:1:1:0:60:22.833:1:0:1.5 1/1:92:91:84,7:0,0:0,91:0.9891:0,2:20.6:1:28.9:1:1:0:60:29.333:1:0:1.5 +12 121426594 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.81868;SOR=0.95575;LSEQ=CAGCCCCACCTATGGGGAGA;RSEQ=ACAGCCCTTGCTGAGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:357:182:142,40:134,40:174,182:0.5098:2,2:24:1:30.5:1:0.89903:1.06:60:90:0.5158:0:1.4 0/1:329:164:117,47:114,51:165,164:0.4985:2,2:23.2:1:29.4:1:0.71789:1.11:60:40:0.4923:0:1.3 +12 121426869 . G A 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24943;SOR=0;LSEQ=CTACCCCGCATCTTCCCTGG;RSEQ=AGGGCCCAGGACTCTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:2,1:77,213:290,3:0.0102:2,2:16.7:1:22:1:0.17795:5.49:60:2:0.007:0:1.3 0/0:275:0:0,0:60,215:275,0:0:2,0:22:1:30.4:1:1:0:60:54:1:0:0.1 +12 121426901 . G C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14884;SOR=0.55293;LSEQ=CTCTCCCCTAACTCATAGGT;RSEQ=GGGGCTGGAAGCTTCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:27:7,20:13,136:149,27:0.1534:2,2:18.9:1:30:1:0.01756:3.62:60:26:0.152:0:1.1 0/1:110:10:1,9:7,93:100,10:0.0909:2,2:29.7:1:30.2:1:0.5458:1.47:60:20:0.0917:0:1 +12 121426907 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53636;SOR=0;LSEQ=CCTAACTCATAGGTGGGGGC;RSEQ=GGAAGCTTCACCATCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:14,148:162,2:0.0122:2,2:30:1:30:1:0.17507:10.25:60:4:0.0127:0:1 0/0:93:0:0,0:5,88:93,0:0:2,0:24.4:1:30.2:1:1:0:60:186:1:0:0.1 +12 121428455 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATAGGAAAGGGAGGAAAG;RSEQ=TAGGAAAGGGAGGAAAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38.5:1:28:1:1:0:30.5:4:1:0:1.5 +12 121431225 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50658;SOR=1.45281;LSEQ=GTAAGCTCCTCTGGTTCAGC;RSEQ=CCATGGCAATGAGAAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:16:16,0:45,0:45,16:0.2623:1,1:20.7:1:29.7:1:1:0:60:32:0.2623:0:1.5 0/1:41:14:14,0:25,2:27,14:0.3415:2,1:25.1:1:29.4:1:0.53902:0:60:28:0.3415:0:1.6 +12 121431272 . T A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00063;SOR=0.36749;LSEQ=CAAGGTCAGGGGAATGGACG;RSEQ=GGGAAGGTGAGAGTGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:60:60,0:84,7:91,60:0.3974:2,1:24.9:1:29.9:1:0.04227:0:60:29:0.3946:0:1.2 0/1:108:21:19,2:76,11:87,21:0.1944:2,2:23.5:1:29.4:1:1:1.37:60:42:0.1944:0:1.1 +12 121431300 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.46319;LSEQ=TGAGAGTGGCCAGTACCCCA;RSEQ=TCACGGCTTTCTGTGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:61:46,15:159,30:189,61:0.244:2,2:22.4:1:30.6:1:0.12911:1.72406:60:60:0.2439:0:1.2 0/1:212:94:73,21:92,25:117,94:0.4434:2,2:22.1:1:29.4:1:0.86851:1.05832:60:46:0.4402:0:1.1 +12 121431569 . G T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11794;SOR=Inf;LSEQ=GCTGCGGCAAGGCCAGGGAA;RSEQ=GGGAAGGTGACTCTAGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:54,185:239,0:0:2,0:22.6:1:31.3:1:1:0:60:33.143:1:0:0.1 0/1:231:3:1,2:65,162:227,3:0.013:2,2:35.3:1:24.7:1:1:1.24:60:2:0.0089:0:2.7 +12 121431590 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20027;SOR=Inf;LSEQ=GGGAAGGTGACTCTAGGTCC;RSEQ=GTAAAAGGCTGTCCAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:19,131:150,0:0:2,0:23.7:1:30.8:1:1:0:60:74:1:0:0.1 0/1:122:2:1,1:20,100:120,2:0.0164:2,2:13.5:1:27:1:0.31581:4.90:60:4:0.0168:0:1 +12 121432114 . CG C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.81091;SOR=0.8595;LSEQ=CTGGCCATGGACACGTACAG;RSEQ=GGCCCCCCCCAGGGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:738:9:5,4:328,399:727,9:0.0122:2,2:26.8:1:30.9:1:0.73853:1.52:59.4:18:0.0127:0.0027:0.2 0/1:762:8:2,6:346,407:753,8:0.0105:2,2:26.4:1:31.1:1:0.30085:2.54744:60:16:0.0106:0:0.4 +12 121432117 . G CC 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.19186;SOR=0.59158;LSEQ=GCCATGGACACGTACAGCGG;RSEQ=CCCCCCCCAGGGCCAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:737:18:5,13:323,390:713,18:0.0244:2,2:30.8:1:30.1:1:0.15722:2.15119:58.6:36:0.0251:0:1.2 0/1:754:11:6,5:336,403:739,11:0.0146:2,2:24.5:1:31:1:0.56013:1.44:60:22:0.0148:0:1.2 +12 121432154 . G A 151 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=19.83641;LSEQ=GCCCGGGACCTGCGCTGCCC;RSEQ=CTCACAGCTCCCCTGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:2:1,1:276,368:644,2:0.0031:2,2:1.5:1:27.5:1:1:1.33:60:4:0.0032:0:1.5 0/1:655:38:18,20:277,340:617,38:0.058:2,2:19.9:1:28.9:1:0.86689:1.10:60:76:0.0605:0:1.2 +12 121432302 . T G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.87726;SOR=1.05946;LSEQ=TCACCTAAACCTCTTTGCAC;RSEQ=TCAGTTTGGTTCCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:39:0,39:0,60:60,39:0.3939:1,1:26.3:1:32.7:1:1:0:59.1:78:0.3939:0:1 0/1:76:31:2,29:2,43:45,31:0.4079:1,2:24.8:1:31.8:1:1:1.47:60:62:0.4133:0:1.1 +12 121433453 . C G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCACTGTGTTCACACAA;RSEQ=TCCATCCATTCCACTCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:32.5:1:1:0:60:4:1:0:1.5 +12 121433844 . A G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14987;SOR=Inf;LSEQ=GTATAGCACTAGGCAGTGGG;RSEQ=GGAATGGAGCTAATAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:18,0:5,0:5,18:0.7826:0,1:26.6:1:29.6:1:1:0:58.9:8:0.7619:0:1.6 1/1:11:11:8,3:0,0:0,11:1:0,2:18.4:1:30.5:1:1:0:60:22:1:0:1.1 +12 121434630 . C CTCATTCAT 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=6.000;MSILEN=4;SSF=0.29799;SOR=0.87805;LSEQ=AGCTGGAAGAGCCACTGGGA;RSEQ=TCATTCATTCATTCATACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:621:357:189,168:125,132:257,357:0.5749:2,2:24.9:1:31.2:1:0.32617:1.19:59.8:356:0.5742:0.1675:0.1 1/0:479:260:130,130:97,114:211,260:0.5428:2,2:24.2:1:29.9:1:0.40482:1.17:59.6:259:0.5476:0.1712:0.2 +12 121434833 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.43062;LSEQ=AAATTACAGCAGGGTAAGGG;RSEQ=GACTGATGTTTTCTAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:189:53,136:149,336:485,189:0.2804:2,2:22.5:1:31.3:1:0.51382:1.13767:60:62:0.281:0:1.1 0/1:635:309:103,206:101,224:325,309:0.4866:2,2:22:1:29.1:1:0.55272:1.11:60:27.091:0.4838:0:1.2 +12 121435221 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15285;SOR=Inf;LSEQ=GGTGCCCTTGGGAGGTCTTG;RSEQ=GCAGGGGTGGGATATAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:130,24:154,0:0:2,0:22.1:1:30.5:1:1:0:60:29.8:1:0:0.2 0/1:100:2:1,1:76,21:97,2:0.02:2,2:15.5:1:28.5:1:0.39683:3.55875:60:4:0.0208:0:1 +12 121435342 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.68665;LSEQ=TGGGCAGCAGCCTGACCACC;RSEQ=TGCAGCCCGTCCAGTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:719:187:97,90:309,222:531,187:0.2601:2,2:25.2:1:31.2:1:0.14505:1.29097:60:61.333:0.2592:0:1.3 0/1:743:361:192,169:198,183:381,361:0.4859:2,2:26.3:1:29.4:1:0.76879:1.05:59.8:35.1:0.4808:0:1.4 +12 121435427 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.23123;LSEQ=GCAGAGCCATGTGACCCAGA;RSEQ=CCCCTTCATGGCCACCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:735:179:101,78:286,269:555,179:0.2435:2,2:24.5:1:30.3:1:0.26412:1.22:60:358:0.2472:0:1.8 0/1:660:276:145,131:219,165:384,276:0.4182:2,2:23.1:1:28.5:1:0.26714:1.19878:60:45:0.4173:0:1.8 +12 121435475 . G A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.99349;LSEQ=GCAGAGCCCCCACGGTGAGC;RSEQ=CCCTGTGCCCCACACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:883:229:130,99:337,316:653,229:0.2593:2,2:24.3:1:30.3:1:0.1912:1.23:60:228:0.2609:0:1.5 0/1:895:368:209,159:291,230:521,368:0.4112:2,2:25.7:1:29.2:1:0.78417:1.04:59.8:121.667:0.4148:0:1.5 +12 121435587 . G T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.87575;LSEQ=TGTGTCTCTGGGACAAGTGT;RSEQ=TTTCCGTGATTGAGGGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1299:378:175,203:449,471:920,378:0.291:2,2:26.7:1:30.3:1:0.42703:1.10573:59.9:46.25:0.2884:0:1.1 0/1:1370:596:284,312:377,395:772,596:0.435:2,2:25.7:1:29.6:1:0.70255:1.04852:59.9:84.143:0.4347:0:1.2 +12 121435778 . C T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03945;SOR=0;LSEQ=ATGAATTTCTAAAATCTATT;RSEQ=AGATTTTAGAAAGGTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:0,7:0,53:53,7:0.1167:1,0:20.1:1:27.4:1:1:0:58.9:6:0.1053:0:1.6 0/0:41:0:0,0:0,41:41,0:0:1,0:21.9:1:32.4:1:1:0:59.6:82:1:0:0.1 +12 121437114 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.50268;LSEQ=GTGGCCCAGTACACCCACAC;RSEQ=GGCCTGCTCCCGCAGACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:944:136:75,61:453,354:807,136:0.1441:2,2:26:1:31:1:0.85218:1.04077:60:135:0.1469:0:1.2 0/1:872:68:38,30:449,354:803,68:0.078:2,2:23.4:1:29.4:1:1:1.00134:60:67:0.0783:0:1.2 +12 121437221 . T C 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99683;LSEQ=CAGGCCTGCTGGCCCTCCCT;RSEQ=GGCCTGTGACAGAGCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1112:873:428,445:109,126:235,873:0.7851:2,2:24.2:1:30.7:1:0.50826:1.11:59.9:66.154:0.7854:0:1.2 1/0:1151:903:458,445:130,117:247,903:0.7845:2,2:25:1:29.7:1:0.61551:1.07948:60:89.3:0.7847:0:1.2 +12 121437382 . A G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16006;LSEQ=TCCCCAGCCAGGACCCTGCC;RSEQ=GCATCCAGCACCTGCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:674:670:241,429:1,0:1,670:0.9941:0,2:25.2:1:30.4:1:0.36066:0:59.9:50.538:0.997:0:1.2 1/1:586:583:226,357:1,0:1,583:0.9949:0,2:24.6:1:29.5:1:0.3887:0:59.9:52:0.9948:0:1.2 +12 121437474 . C T 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCCTTACTGTCCCTGCCC;RSEQ=CTTCCATGTTGGTCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:16,157:173,0:0:2,0:23.8:1:31.2:1:1:0:60:33.6:1:0:0.3 0/1:147:17:4,13:24,106:130,17:0.1156:2,2:29.2:1:27.8:1:0.74203:1.36:60:7.5:0.1064:0:1.2 +12 121438382 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCTGTTGCTGGCAGCTC;RSEQ=GGGGAGTGAATTCTGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:28.5:1:1:0:60:4:1:0:1.5 +12 121438709 . G GTT 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53281;SOR=1.68065;LSEQ=CTGGCTGGGAGGCTCCCTTT;RSEQ=AAGAACCGAGGGTAGAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:39:39,0:11,0:11,39:0.78:0,1:23.2:1:30.7:1:1:0:59.7:78:0.78:0.26:0.1 1/1:21:18:17,1:3,0:3,18:0.8571:0,1:25.3:1:30.3:1:1:0:60:36:0.8571:0.2381:0 +12 121438776 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17286;SOR=Inf;LSEQ=GTGATCCAGGAGGTGTGGCC;RSEQ=TGCCTCCCCATCCTGAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:163,26:189,0:0:2,0:25.6:1:30.9:1:1:0:59.9:26:1:0:0.3 0/1:135:2:1,1:115,18:133,2:0.0148:2,2:9.5:1:27:1:0.26258:6.24548:60:4:0.015:0:1.5 +12 121438844 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.38901;LSEQ=GTGGGTGCCTGGTGGGTGGC;RSEQ=AGCAGCCTTGTTTGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:542:140:104,36:266,136:402,140:0.2583:2,2:23.9:1:31.7:1:0.09138:1.48:60:69:0.2579:0:1.2 0/1:493:224:152,72:175,93:268,224:0.4544:2,2:26.7:1:30.5:1:0.56628:1.12:60:73.667:0.4576:0:1.2 +12 121439192 . G T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49085;SOR=0.53438;LSEQ=ACCCGTGGAGGCTGCTCGGG;RSEQ=TGCACAGGAGGGGGTCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:0,9:0,13:13,9:0.4091:1,0:24:1:30.2:1:1:0:60:18:0.4091:0:1.1 0/1:15:4:0,4:0,11:11,4:0.2667:0,0:32.3:1:31.3:1:1:0:60:8:0.2857:0:1 +12 122849392 . A C 132 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TCTCTAGGCCTTTTAGAAAA;RSEQ=ATGGAGTTGCTCCTTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:3,17:0,0:0,20:1:0,2:21.7:1:30.6:1:1:0:40.3:40:1:0:1 0/1:27:10:0,10:2,15:17,10:0.3704:2,0:16.4:1:30.7:1:0.51567:0:47.5:20:0.3704:0:1.1 +12 122849912 . G T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17592;SOR=0;LSEQ=TCTACAATGTTACCCAGCAT;RSEQ=CTGTTGGCATTGTTGTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:72,109:181,2:0.0109:2,2:7:0:32.5:1:1:1.51:31.5:4:0.0109:0:1.5 0/0:254:0:0,0:99,154:253,0:0:2,0:24.5:1:31.1:1:1:0:46.6:125.5:0.996:0:0.1 +12 122974253 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.15733;LSEQ=AGGCAGATAACCAGAAAGAT;RSEQ=AAAAATATATAGTTTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:170:122:61,61:27,21:48,122:0.7176:2,2:25.1:1:29.6:1:0.49862:1.28381:60:244:0.7262:0:1 0/1:274:78:37,41:93,99:192,78:0.2847:2,2:26.6:1:28.4:1:0.89395:1.04081:60:77:0.2862:0:1.1 +12 122974288 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28727;SOR=Inf;LSEQ=TTACATTACTGGTCAATATT;RSEQ=ATAATATAACCCTCACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:53,73:126,0:0:2,0:25.7:1:32:1:1:0:60:62:1:0:0.6 0/1:201:3:1,2:82,116:198,3:0.0149:2,2:22.7:1:29.7:1:1:1.41145:60:6:0.0153:0:1.3 +12 122974833 . G C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAAGTCTGAGCCACAAG;RSEQ=TAAAAGAACGCTGTGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:12.5:1:29:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 124159885 . A T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=Inf;LSEQ=GCCGATGTAGAGGGCTCTGC;RSEQ=GTGATGAGTGCTACTGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:20.5:1:31.7:1:1:0:60:30:1:0:0.1 1/0:8:6:4,2:2,0:2,6:0.75:0,2:32.5:1:29.7:1:1:0:60:12:0.75:0:1 +12 124160021 . C G 34 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GTTACCTGGAGACTCCTTTA;RSEQ=TGCCGCTTCCCTTATTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:22.3:1:34.3:1:1:0:60:6:1:0:0 1/0:4:2:0,2:0,2:2,2:0.5:0,0:38.5:1:34:0:1:0:60:4:0.5:0:1 +12 124786017 . T A 29 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTTCCTGGGGGCAGGTGTGG;RSEQ=CTGTCCTGTCTGCCCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42:0:29.5:1:1:0:60:4:1:0:2.5 0/0:1:0:0,0:0,1:1,0:0:0,0:27:0:31:0:1:0:60:2:1:0:0 +12 124786053 . C T 29 d5;v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCCAGTGCTCGGCCTCCCTG;RSEQ=GGGGCACGGTACATGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:29:0:1:0:60:4:1:0:2.5 0/0:1:0:0,0:0,1:1,0:0:0,0:38:0:32:0:1:0:60:2:1:0:0 +12 124786741 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=GACCCTCTTTCCAAATAAGG;RSEQ=GACAGTTGCAGGTACCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:10,2:0.1667:2,2:26:1:29.5:1:1:2.16:60:4:0.1667:0:1 0/0:7:0:0,0:2,5:7,0:0:2,0:15.7:1:29.7:1:1:0:60:14:1:0:0 +12 124787795 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGTGGGCTATGGCCTGTGCA;RSEQ=CAGCCAGGAAGGTGGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 124885756 . CAA C 29 d5;v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=14.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACAGAACAAGACCCTGTCT;RSEQ=AAAAAAAAAAAAGAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:5:0:32:0:1:0:41:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:29.5:1:1:0:58:4:1:0:1.5 +12 124887026 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14194;SOR=Inf;LSEQ=CTCCTTTTCCTTCTCCTTCT;RSEQ=ATCTTTCTCCTCCTGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:19,0:0:2,0:27.1:1:32.8:1:1:0:57.5:38:1:0:0.3 0/1:12:2:1,1:8,2:10,2:0.1667:2,2:5:1:26:1:0.45455:3.4638:57.5:4:0.1818:0:1.5 +12 124887058 . G GGCT 106 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=37;MSI=13.000;MSILEN=3;SSF=0.14533;SOR=2.57341;LSEQ=CCTGGCTGCTGCGGGGCATG;RSEQ=GCTGCTGCTGCTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:11:6,5:11,8:19,11:0.3438:2,2:15.1:1:30.4:1:1:1.14063:51.6:22:0.3438:0.1563:0.5 1/0:19:11:6,5:6,2:8,11:0.5789:2,2:22.1:1:30.7:1:0.63325:2.38223:56.9:22:0.6111:0.0526:0.3 +12 124913905 . TG T 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTGTTGTGGCATCTGGA;RSEQ=GGGGAGCGCCAGGGCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:0:32.5:1:1:0:60:4:1:0:0.5 +12 124915134 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACCCCGGGCCCTGACGTCG;RSEQ=GGGCCCTGGGCTCAGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:40:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:28:1:1:0:60:4:1:0:1 +12 124915344 . G A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01515;SOR=Inf;LSEQ=ACTTCTGCTCCTGGGAGAGC;RSEQ=CAGGGGGCACTGCGGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:10,0:0:2,0:29.6:1:31.6:1:1:0:60:20:1:0:0.2 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:31.5:1:1:0:60:4:1:0:1 +12 124915431 . T C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGCAGACACACAGGTGCG;RSEQ=GCGCACACACACAAAGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:43.5:1:32:0:1:0:60:4:0.6667:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:32:1:1:0:60:4:1:0:1.5 +12 125257551 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGCCACGCAGGGGCGA;RSEQ=GCAGGCCGAGCAGGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 125658603 . C T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.41961;SOR=2.0742;LSEQ=GACATAACAGCCATCACCAA;RSEQ=CCCATTGTATAAATGGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:2,2:9,8:17,4:0.1905:2,2:16:1:31:1:1:1.1187:60:8:0.1905:0:1.3 0/1:12:4:2,2:6,2:8,4:0.3333:2,2:34.5:1:30.3:1:0.54747:2.71347:60:8:0.3636:0:1.5 +12 125658628 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15455;SOR=Inf;LSEQ=TTGTATAAATGGTGAAACTG;RSEQ=GGCTCAGAGAGGCTGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:27,0:0:2,0:28.9:1:32:1:1:0:60:54:1:0:0.3 0/1:18:2:1,1:10,6:16,2:0.1111:2,2:36.5:1:29.5:1:1:1.61828:60:4:0.1111:0:2 +12 127625632 . TAA T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTATCTTTATTTGTT;RSEQ=AGTCTGTTTTGTCAGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:33.5:1:1:0:20:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 127626655 . G A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTTCAGCTGTTGATACTTCG;RSEQ=TATGCTTCACAAAGTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:27:1:30.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:29:1:1:0:60:4:1:0:1 +12 127627037 . C A 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=GGTTTTTGAGGCTGCTGACC;RSEQ=TTGGATGGGGTTTTTATGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:6,2:0.25:2,2:18.5:1:31:1:0.46429:3.87298:56:4:0.25:0:1 0/0:13:0:0,0:7,6:13,0:0:2,0:28:1:30.8:1:1:0:33.8:26:1:0:0.8 +12 127627056 . C G 96 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00548;SOR=23.99965;LSEQ=CCTTGGATGGGGTTTTTATG;RSEQ=GGGCCTTTTTGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:24.5:1:29.5:1:1:2.23609:32.5:4:0.2222:0:1 1/1:10:9:5,4:0,1:1,9:0.9:0,2:37.8:1:30.4:1:1:0:32.1:18:0.9:0:1.1 +12 127627064 . TTTG T 87 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.06978;SOR=7.02745;LSEQ=GGGGTTTTTATGCGGGCCTT;RSEQ=TTGTTGTTGTTGTTGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:6,2:0.25:2,2:24.5:1:29.5:1:1:1.8258:32.5:4:0.25:0:1 1/0:11:8:4,4:1,2:3,8:0.7273:2,2:33:1:29.2:1:1:1.88:34.8:16:0.7273:0.0909:1 +12 127627596 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11905;SOR=Inf;LSEQ=TTCTGCAGGGAAGCCCCGCC;RSEQ=ACTGAAGAAGGATGGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:18,0:0:2,0:25.1:1:31.6:1:1:0:57.4:36:1:0:0.1 0/1:10:2:1,1:5,3:8,2:0.2:2,2:45:1:29.5:1:1:1.58108:60:4:0.2:0:1 +12 127627683 . TC T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05641;SOR=Inf;LSEQ=GCGTTGAGCTGTGGGACAAG;RSEQ=TTGGGACCAAGCTGTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:16,0:0:2,0:25.3:1:33.3:1:1:0:60:32:1:0:0.1 0/1:11:3:1,2:3,5:8,3:0.2727:2,2:26:1:27.7:1:1:1.18052:60:6:0.2727:0:0 +12 127627843 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=CCCTCCCCCATGAGGCTAAA;RSEQ=GGCTTAGAGAGCAGGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:0,6:6,2:0.25:0,2:26:1:31:1:0.25:0:60:4:0.25:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:24.3:1:32:1:1:0:60:8:1:0:0.3 +12 127628242 . CTTTTTTTT C 30 d5;v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=19.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTATTATGTTTTTCTTTT;RSEQ=TTTTTTTTTTTGGAGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:12.3:1:30.3:1:1:0:60:6:1:0:0 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:27.5:1:30:1:1:1.41418:43.5:4:0.2857:0:0 +12 128101812 . A T 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21651;SOR=0.42049;LSEQ=ACACTAACAAGTCAGGGATA;RSEQ=CAGGAGACACCATCCAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:10,3:13,9:0.4091:2,0:29.9:1:32.2:1:0.24026:0:55.4:18:0.4091:0:1.1 0/1:27:6:5,1:20,1:21,6:0.2222:1,2:33:1:29.8:1:0.40171:3.74166:57.5:12:0.2308:0:1 +12 128101865 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21919;SOR=0;LSEQ=TCTTCTGAAATCAGACAATG;RSEQ=CTTTCAAACTCTTATACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:28,11:39,2:0.0488:2,2:20:1:29.5:1:0.50488:2.48023:44:4:0.05:0:1.5 0/0:46:0:0,0:23,23:46,0:0:2,0:33.8:1:29.6:1:1:0:37.7:14.333:1:0:0.2 +12 129468836 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21041;SOR=Inf;LSEQ=CAGCATTGTCCTTGCTTCAA;RSEQ=TTTTAGGATGTCTGAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:22,1:23,0:0:1,0:21.2:1:32.8:1:1:0:60:46:1:0:0.3 0/1:20:2:1,1:18,0:18,2:0.1:1,2:23.5:1:27:1:0.1:0:60:4:0.1:0:1 +12 129468880 . A AT 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06005;SOR=Inf;LSEQ=CTTTCATGTTTTCAACCATC;RSEQ=TTTTTTTAATGGCACAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:50,11:61,0:0:2,0:24.1:1:30.7:1:1:0:60:60:1:0:0.1 0/1:70:5:4,1:47,18:65,5:0.0714:2,2:33.4:1:30.6:1:1:1.52:56:10:0.0714:0:0 +12 129468945 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52003;SOR=Inf;LSEQ=CCTCAAATTAAACTCCTTAA;RSEQ=CTCTGATGCCCTGGGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:62,54:116,0:0:2,0:25.7:1:29.8:1:1:0:59.5:232:1:0:0.1 0/1:177:2:1,1:90,84:174,2:0.0113:2,2:10.5:1:27.5:1:1:1.07098:60:4:0.0116:0:1 +12 129468954 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51861;SOR=Inf;LSEQ=AAACTCCTTAAACTCTGATG;RSEQ=CCTGGGGATGAGAACAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:58,57:115,0:0:2,0:24.6:1:31.6:1:1:0:59.5:114:1:0:0.1 0/1:173:2:1,1:83,88:171,2:0.0116:2,2:49.5:1:29.5:1:1:1.06:59.5:4:0.0118:0:1 +12 129468990 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51098;SOR=Inf;LSEQ=AACTAGCTTGGATCTCGTGC;RSEQ=GTGTAATTCAATGTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:35,55:90,0:0:2,0:26.3:1:31.1:1:1:0:60:180:1:0:0 0/1:125:2:1,1:44,79:123,2:0.016:2,2:32.5:1:31.5:1:1:1.79:60:4:0.0163:0:1 +12 129468991 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.51055;SOR=Inf;LSEQ=ACTAGCTTGGATCTCGTGCC;RSEQ=TGTAATTCAATGTTTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:35,54:89,0:0:2,0:26.4:1:31.9:1:1:0:60:178:1:0:0 0/1:123:2:1,1:43,78:121,2:0.0163:2,2:39:1:31:1:1:1.80:60:4:0.0164:0:1 +12 130908927 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11109;SOR=0;LSEQ=ACGCTGCTCTGCCGGGTCAG;RSEQ=GTCCGCCGCCGGGCCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:14,16:30,2:0.0625:2,2:30:1:32:0:1:1.14:60:4:0.0667:0:1.5 0/0:63:0:0,0:33,30:63,0:0:2,0:26.7:1:30.5:1:1:0:60:62:1:0:0.3 +12 130908945 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11108;SOR=0;LSEQ=AGCGTCCGCCGCCGGGCCAG;RSEQ=AGCGGCCTCGGGCCCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:11,15:26,2:0.0714:2,2:22.5:1:31:1:1:1.35:60:4:0.0741:0:1.5 0/0:55:0:0,0:26,29:55,0:0:2,0:25.9:1:32:1:1:0:60:110:1:0:0.3 +12 130908949 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCGCCGCCGGGCCAGCAGC;RSEQ=GCCTCGGGCCCCTCCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:23,0:0:2,0:27.5:1:29.3:1:1:0:60:10.5:1:0:0.3 0/1:51:2:1,1:23,26:49,2:0.0392:2,2:25:0:29.5:1:1:1.13:60:4:0.04:0:2 +12 130962191 . C A 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.67919;SOR=1.63158;LSEQ=ATACGATCTCATGCTAAATG;RSEQ=TTAGAGAAATGGCATCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:7,1:8,3:0.2727:2,0:25:1:31.7:1:1:0:60:6:0.2727:0:1 0/1:13:5:5,0:7,1:8,5:0.3846:2,0:30.2:1:29:1:1:0:60:10:0.3846:0:1 +12 130962254 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19918;SOR=0;LSEQ=CTCTGCTAATAAACTCTGGA;RSEQ=GAGAAACGCTGCTCCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:20,18:38,2:0.05:2,2:8:0:32.5:1:1:1.10818:60:4:0.05:0:1.5 0/0:49:0:0,0:24,25:49,0:0:2,0:27.4:1:30.1:1:1:0:60:15.333:1:0:0.3 +12 131517730 . T G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGCCCGAGCTCTTTTT;RSEQ=TGTGCGGGCAGGGCCGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:30.5:1:1:0:60:4:1:0:1 +12 131518875 . C T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.26092;LSEQ=TGAATGGAATGCTCTTCCCC;RSEQ=GGGTCCCCGCATGGTTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:5,2:5,3:8,7:0.4667:2,2:37:1:32.3:1:1:1.46:60:14:0.4667:0:1 1/0:19:10:4,6:5,4:9,10:0.5263:2,2:20.7:1:28.8:1:0.65628:1.81296:60:20:0.5263:0:1.3 +12 131518981 . T A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16619;SOR=3.21651;LSEQ=TCGCCACATCAGCTGGCTCC;RSEQ=TTTCTTTCCTGGAAGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:1,3:4,8:12,4:0.25:2,2:29:1:30.3:1:1:1.46398:60:8:0.25:0:1 1/0:19:10:4,6:4,5:9,10:0.5263:2,2:15:1:28.8:1:1:1.18851:60:20:0.5263:0:1.1 +12 131534668 . G C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.09565;SOR=Inf;LSEQ=TGCAGGAAGCTGGGAATTCA;RSEQ=TGTGTCCTCCTGGGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:22.3:1:33.2:1:1:0:60:26:1:0:0.1 0/1:12:3:3,0:9,0:9,3:0.25:0,0:24.7:1:33:1:1:0:60:6:0.25:0:1.3 +12 131534763 . G GTCA 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=8.000;MSILEN=3;SSF=0.05799;SOR=0.4675;LSEQ=TTGAAATCACCATCGTCATC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:40:19,21:17,9:26,40:0.6061:2,2:34.3:1:31.1:1:0.20761:2.06433:58.6:80:0.6061:0.0152:0.1 0/1:48:20:10,10:13,15:28,20:0.4167:2,2:30.2:1:29.8:1:1:1.15:58.1:40:0.4167:0.0208:0.1 +12 131621997 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGGGCCTGGCACCTGCC;RSEQ=TGTACTTGGCTGGGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 131622735 . T C 89 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=TGGTCGCTCACGAGCAGCTC;RSEQ=GCCCGCACCTCCAACGCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:35:0:32.5:1:1:1:60:4:0.5:0:1 1/1:8:8:4,4:0,0:0,8:1:0,2:26.8:1:29.9:1:1:0:60:16:1:0:1.4 +12 131944873 . C CT 66 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.41421;LSEQ=CACCCACCCCTGCTCCTCCC;RSEQ=GCCCTCTCCATTAATCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:22.5:1:33.4:1:1:0:60:8:0.5714:0.1429:0 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:13:0:31:0:1:0:60:2:0.3333:0:4 +12 131944995 . C A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15936;LSEQ=AAAGGGAATTAATTTATTCT;RSEQ=AAGCCAAATATAAATCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:50:47,3:13,1:14,50:0.7813:1,2:23.1:1:28.6:1:1:1.20:60:24:0.7742:0:1.7 0/1:53:19:17,2:34,0:34,19:0.3585:1,2:20.9:1:28.2:1:0.12409:0:60:38:0.3585:0:1.7 +12 131945052 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24661;SOR=0;LSEQ=TCTTAGATTACTCATCTCCT;RSEQ=GTATCTTTTCCACCAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:142,39:181,2:0.0109:2,2:20.5:1:30:1:0.39032:3.60751:60:4:0.011:0:3 0/0:185:0:0,0:134,51:185,0:0:2,0:25.8:1:30.9:1:1:0:60:91.5:1:0:0.8 +12 131945067 . A G 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27088;LSEQ=CTCCTGGTATCTTTTCCACC;RSEQ=GGACGAGTGAATGAGCGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:226:171:127,44:35,18:53,171:0.7566:2,2:23.9:1:30.1:1:0.29171:1.48:60:41.75:0.7626:0:1.8 0/1:241:110:70,40:91,39:130,110:0.4564:2,2:24.3:1:29.4:1:0.33533:1.33171:60:220:0.4641:0:1.7 +12 131945098 . G A 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=ATGAGCGAACCTAAGTGTGG;RSEQ=TGCACAGAGTGTCACCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:201,144:345,0:0:2,0:23.8:1:31.5:1:1:0:60:85.25:0.9971:0:1.2 0/1:365:14:7,7:201,149:350,14:0.0384:2,2:22.8:1:29.2:1:0.59379:1.34785:60:28:0.0387:0:2.6 +12 131945101 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02628;SOR=0;LSEQ=AGCGAACCTAAGTGTGGGTG;RSEQ=ACAGAGTGTCACCATATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:5:2,3:203,149:352,5:0.014:2,2:20:1:26:1:0.6544:2.03951:60:4:0.0113:0:1.2 0/0:380:0:0,0:214,166:380,0:0:2,0:23.5:1:31.1:1:1:0:60:94:1:0:0.8 +12 131945129 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26452;LSEQ=GTCACCATATTCTGGAACTC;RSEQ=AGTTGTGTTTGGGTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:426:326:164,162:45,53:98,326:0.7653:2,2:27.5:1:31:1:0.48995:1.19:59.9:325:0.7665:0:1.4 0/1:482:223:115,108:129,130:259,223:0.4627:2,2:26.5:1:29.9:1:0.71551:1.07:59.9:222:0.4664:0:1.5 +12 131945207 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24044;SOR=Inf;LSEQ=CTGTGCCAGGCAGAGCTAAT;RSEQ=TCCATGCATTTCACAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:53,145:198,0:0:2,0:22.4:1:32.5:1:1:0:60:197:1:0:0.4 0/1:191:2:1,1:53,135:188,2:0.0105:2,2:36.5:1:29:1:0.48872:2.53:60:4:0.0106:0:1 +12 131945210 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2293;SOR=Inf;LSEQ=TGCCAGGCAGAGCTAATGTC;RSEQ=ATGCATTTCACAAACACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:49,142:191,0:0:2,0:21.6:1:32:1:1:0:60:94.5:1:0:0.4 0/1:176:2:1,1:47,127:174,2:0.0114:2,2:17:1:27:1:0.47221:2.68:60:4:0.0115:0:2 +12 131945403 . A G 81 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAATGACAGGCAAAGAAA;RSEQ=TAAACCCTATAAATTTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:22.7:1:31.7:1:1:0:60:12:0.8571:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 132001302 . AG TT 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05779;SOR=0;LSEQ=TTCTTCTGTACTTATAAGAA;RSEQ=ATCAAAGACTTTAAGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:1,4:5,3:0.375:2,0:20.7:1:29:1:1:0:45.3:6:0.375:0:1 0/0:11:0:0,0:1,10:11,0:0:2,0:23.2:1:29.2:1:1:0:51.5:22:1:0:0.1 +12 132547073 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.23469;SOR=0;LSEQ=ATTTCCAGCTTCTCAGGCAG;RSEQ=AGCAGCAGCAGCAGCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:15,7:22,2:0.0833:2,2:28:1:30.5:1:1:2.07024:60:4:0.0833:0:1 0/0:25:0:0,0:14,11:25,0:0:2,0:26:1:31.6:1:1:0:53.2:50:1:0:0.4 +12 132547087 . G A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=1.6756;LSEQ=AGGCAGCAGCAGCAGCAGCA;RSEQ=CAACAACAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:13,9:22,1:0.0435:2,0:22:0:32:0:1:0:50:2:0.0526:0:2 0/1:28:2:1,1:12,14:26,2:0.0714:2,2:10.5:1:31:0:1:1.16:54.5:4:0.0741:0:2 +12 132547093 . A G 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07321;SOR=Inf;LSEQ=CAGCAGCAGCAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,5:17,0:0:2,0:39.4:1:27.8:1:1:0:53.9:7.5:0.7895:0:0.5 0/1:31:5:3,2:12,13:25,5:0.1613:2,2:9:1:31.8:1:1:1.60:37.4:10:0.1613:0:1.6 +12 132547162 . G A 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00292;SOR=0.06371;LSEQ=CAGCAGCAGCAACAGACGAC;RSEQ=ACGACCTCTCAGGTGCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:5,3:6,7:13,8:0.381:2,2:27.8:1:30.5:1:0.65944:1.88:57.4:16:0.381:0:1 0/1:28:1:0,1:10,17:27,1:0.0357:2,0:9:0:32:0:1:0:45:2:0.0357:0:3 +12 132547192 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14194;SOR=Inf;LSEQ=CAGGTGCAAGTTCCACAGAT;RSEQ=CAGGGCCAGGCCCAGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:19,0:0:2,0:29.3:1:31.5:1:1:0:59.8:38:1:0:0.4 0/1:12:2:1,1:2,8:10,2:0.1667:2,2:33:1:26:0:0.45455:3.46:60:4:0.1667:0:1.5 +12 132827994 . A T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATCCGCTTTCCGGGGAGGGG;RSEQ=GCGGCTGCTCTCGTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:22:1:29.5:1:1:1.7321:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 132829434 . CA C 30 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=CAACAACAGCGAAACTGCCT;RSEQ=AAAAAAAAAAAAGACACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:20:1:30.8:1:1:0:29:4:0.2857:0.1429:2.5 0/0:7:0:0,0:6,1:7,0:0:2,0:17.1:1:29.7:1:1:0:43.1:14:1:0:1 +12 132834097 . C A 27 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATGCCCTCATCCCCACGCC;RSEQ=TCGTCCCCACGCCCTCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:27:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:34.5:1:29.5:1:1:0:60:4:1:0:0 +12 132834622 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACCCACCCTGACCAAGG;RSEQ=CTCACCCCTGCTGGGGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:19,12:31,2:0.0606:2,2:33:0:32:0:1:1.56069:60:4:0.0667:0:1.5 0/0:16:0:0,0:7,9:16,0:0:2,0:21.2:1:30.2:1:1:0:60:32:1:0:0.1 +12 132834744 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11077;SOR=Inf;LSEQ=GGGTCCATAAGAGGTCAGCT;RSEQ=TGTCCACCACGGGGCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,12:17,0:0:2,0:25.2:1:28.8:1:1:0:60:16:1:0:0.1 0/1:9:2:0,2:3,4:7,2:0.2222:2,0:24.5:1:30:1:0.5:0:60:4:0.2222:0:1.5 +12 132836476 . A G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGGGTGGACAGGGGTGG;RSEQ=TCCTGGCCCTGGTGCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:33.5:1:1:0:39.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 132836492 . A G 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGATCCTGGCCCTGGTGC;RSEQ=GGGAACACCCTGAGCATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:41:0:32.5:1:1:0:39.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 132836505 . A T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTGCAGGGAACACCCTG;RSEQ=GCATTGTGGGTGCGGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:30:1:1:0:39.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 132836516 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACCCTGAGCATTGTGGG;RSEQ=GCGGGGCCTGCCTGGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:31:1:1:0:39.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 133132275 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51049;SOR=0;LSEQ=TGACTCCGGCATCCCTGGCT;RSEQ=GTGGTTGCATTGCTCCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:38,44:82,2:0.0238:2,2:23:1:29.5:1:1:1.16:60:4:0.0247:0:1.5 0/0:60:0:0,0:26,34:60,0:0:2,0:25.2:1:31.4:1:1:0:60:120:1:0:0.3 +12 133132329 . G C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=0.66254;SOR=0.56365;LSEQ=GTCCTCACATGGCCCCTCCT;RSEQ=TGTGTGTGTCTTTGTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:27:4,23:2,7:9,27:0.75:2,2:21.4:1:33.6:1:0.62698:1.61846:60:54:0.75:0:1.1 1/0:8:5:2,3:1,2:3,5:0.625:2,2:28.8:1:31.4:1:1:1.29:60:10:0.625:0:1 +12 133200748 . T C 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CGGGTTAGGGTCTGGATTCC;RSEQ=GGGGAAACCAGCCCACAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:41.5:1:30.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:26:0:30:0:1:0:60:2:1:0:0 +12 133201204 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20284;SOR=Inf;LSEQ=TCAGGGTGGTCAGTGGTCTG;RSEQ=TCACTGGAAGCACGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:167,13:180,0:0:2,0:25.5:1:31.7:1:1:0:59.8:89:1:0:0.1 0/1:148:2:1,1:123,23:146,2:0.0135:2,2:13:1:27:1:0.29895:5.25658:60:4:0.0137:0:4 +12 133201443 . GAGGCCAAGG C 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACCCCAGTCCACTCAGAGAG;RSEQ=AGGCCAGGCTGAGCCGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:0:0,0:341,299:640,0:0:2,0:24:1:30.7:1:1:0:60:31:1:0:0.1 0/1:572:24:15,9:300,243:543,24:0.042:2,2:29:1:31.2:1:0.53481:1.35:60:48:0.0429:0.0035:0.1 +12 133201452 . G C 71 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00993;SOR=Inf;LSEQ=CACTCAGAGAGGAGGCCAAG;RSEQ=AGGCCAGGCTGAGCCGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:0:0,0:349,307:656,0:0:2,0:24.8:1:31.7:1:1:0:60:81:0.9954:0:0.1 0/1:573:6:2,4:315,252:567,6:0.0105:2,2:7.3:1:27.5:1:0.41508:2.49608:59.2:5:0.009:0:2 +12 133201947 . T C 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACCTTCCTGTGGCCGAGCTG;RSEQ=GCAACTCCCTCTTCCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:1,2:3,5:0.625:2,2:30.8:1:32:1:0.46429:5.78:53.8:10:0.625:0:1.6 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:29:1:1:0:60:4:1:0:1.5 +12 133202004 . C T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82509;LSEQ=TGGGAGTGTCTGCCTCCTTC;RSEQ=GCTAGAACGAAGCACCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:10,1:8,1:9,11:0.55:2,2:16.1:1:32.2:1:1:1.24:60:22:0.55:0:1.3 1/0:4:2:1,1:2,0:2,2:0.5:0,2:16.5:1:30.5:1:1:0:60:4:0.5:0:1.5 +12 133202131 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50035;SOR=0;LSEQ=AGGCCCCTTGGAAGACACCA;RSEQ=GGCGTGCCTCAGGACCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:125,5:130,2:0.0152:1,2:25.5:1:29:1:0.08917:22.91347:60:4:0.0154:0:1.5 0/0:115:0:0,0:105,10:115,0:0:2,0:21.6:1:31.7:1:1:0:60:114:1:0:0.2 +12 133202215 . G A 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29643;LSEQ=TCCAGGGCACACGGGCAGGC;RSEQ=GCATGCACGACTCACCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:681:447:270,177:127,105:232,447:0.6564:2,2:26.7:1:30.9:1:0.16338:1.26:60:73.5:0.6592:0:1.1 0/1:620:224:131,93:225,167:392,224:0.3613:2,2:24.8:1:29.7:1:0.79987:1.05:60:111:0.3633:0:1.1 +12 133202428 . G A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06486;SOR=0.64272;LSEQ=TGCCATGGGCAGGATCTCAG;RSEQ=AGAGGAAGGGGCTGTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:174:93:14,79:14,66:80,93:0.5345:2,2:23.6:1:30.9:1:0.68398:1.19572:60:30:0.5294:0:1.1 0/1:132:56:11,45:16,60:76,56:0.4242:2,2:24.6:1:29.8:1:1:1.09016:60:112:0.4341:0:1.1 +12 133202626 . G A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2874;SOR=0;LSEQ=TGACCCACAGAGCTGGAGCT;RSEQ=CAGAAGCCCTCAAGACACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:2,1:156,39:195,3:0.0152:2,2:21.7:1:22.3:1:0.49383:1.99173:60:2:0.0104:0:1.7 0/0:124:0:0,0:105,19:124,0:0:2,0:23.9:1:31.6:1:1:0:59.9:61:1:0:0 +12 133202907 . C A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0162;SOR=Inf;LSEQ=GTGTCCAGGGACAGCACCTG;RSEQ=AGAGACCACAGCCCACATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:109,256:365,0:0:2,0:24.5:1:32.3:1:1:0:60:59.833:1:0:0.1 0/1:287:5:3,2:97,185:282,5:0.0174:2,2:12.4:1:26.4:1:0.34632:2.85:60:10:0.0175:0:1.2 +12 133208511 . G C 51 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGGCCCTCTCCCTTCTC;RSEQ=GGTCGGCTGGCAGCAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:24.7:1:32.7:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:49:0:33:0:1:0:60:2:1:0:1 +12 133208611 . A G 73 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=TGGCTGCATGTGACAGGGAC;RSEQ=TGATAAATGTTGGTGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:18:1:29:1:1:0:43.5:4:0.6667:0:1 1/1:5:5:3,2:0,0:0,5:1:0,2:19.8:1:31.8:1:1:0:60:10:1:0:1 +12 133208739 . A G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.79104;SOR=0.78758;LSEQ=AGCCTCATCCTGCATTCATT;RSEQ=ACATCCTTACCATGCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:26:26,0:16,1:17,26:0.6047:1,1:19.3:1:31.7:1:0.39535:0:60:12:0.5854:0:1.3 1/0:22:12:10,2:10,0:10,12:0.5455:0,2:19.3:1:32:1:0.48052:0:60:24:0.5455:0:1.1 +12 133208752 . T A 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.077;SOR=0;LSEQ=ATTCATTAACATCCTTACCA;RSEQ=GCACAGGTATGTCGGTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:5:5,0:41,1:42,5:0.1064:1,0:23:1:30.2:1:1:0:60:10:0.1087:0:1 0/0:32:0:0,0:31,1:32,0:0:1,0:20:1:31:1:1:0:60:64:1:0:0.4 +12 133208886 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.00094;SOR=0.64532;LSEQ=GTGTCCTCTCCTCACACGCA;RSEQ=GCTGGCACTCTCACCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:466:308:203,105:96,62:158,308:0.6609:2,2:25.7:1:30.9:1:0.30763:1.25:60:76:0.658:0:1.3 1/0:535:298:189,109:153,83:236,298:0.557:2,2:24:1:29.4:1:0.78546:1.06296:59.9:36.25:0.5524:0:1.3 +12 133208979 . T C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2638;SOR=0.88939;LSEQ=GGGAGGACAGGAAACATCTC;RSEQ=GAGAGCTCAGTGGAGTTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:809:540:265,275:137,130:267,540:0.6675:2,2:24.5:1:30.6:1:0.60053:1.09349:59.9:76.143:0.6696:0:1.2 1/0:908:582:286,296:153,173:326,582:0.641:2,2:25:1:29.6:1:0.53394:1.09:60:63.667:0.6395:0:1.2 +12 133209593 . T C 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74487;SOR=1.32326;LSEQ=CTCGCTGACACCTGAGTTCA;RSEQ=TGTCAGAGAGAAAACTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:0,12:0,12:12,12:0.5:0,0:28.1:1:33.9:1:1:0:60:24:0.5217:0:1.3 1/0:14:8:0,8:0,6:6,8:0.5714:0,0:24.1:1:31.9:1:1:0:60:16:0.5714:0:1 +12 133209653 . C T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGCCTCTCACTGGGTAGCG;RSEQ=GTGAAAGACAGCTCCCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:17.3:1:31.5:1:1:0:60:8:0.5:0:2.5 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:28:0:1:0:60:2:1:0:0 +12 133209660 . G A 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACTGGGTAGCGCGTGAAA;RSEQ=ACAGCTCCCAACACAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:20.3:1:31.7:1:1:0:60:6:0.375:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 133210659 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13759;SOR=Inf;LSEQ=CCAACTGCTGGGCAGGCTCC;RSEQ=CCCGATCTGATTTTCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:143,2:145,0:0:1,0:22.8:1:29.9:1:1:0:59.8:71.5:1:0:0 0/1:86:2:1,1:79,5:84,2:0.0233:2,2:32.5:1:28.5:1:0.13543:14.51227:60:4:0.0233:0:2 +12 133210985 . C T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01183;SOR=0.67911;LSEQ=CTGTAACACATGAGACAACG;RSEQ=GGCTGTGTTTGCACCATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:379:269:62,207:27,82:109,269:0.7098:2,2:25.4:1:30.4:1:0.78911:1.09905:59.9:88.667:0.7112:0:1.2 1/0:391:244:80,164:44,102:146,244:0.624:2,2:25.1:1:29:1:0.65338:1.13:60:47.8:0.6224:0:1.2 +12 133211059 . T C 157 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCCTCCAACCTGGGTCCA;RSEQ=CTGCCCCGTTTGACCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:31:0,31:0,61:61,31:0.337:1,1:23.9:1:31.7:1:1:0:60:30:0.3333:0:1.5 0/0:71:0:0,0:1,70:71,0:0:1,0:22.2:1:29.2:1:1:0:60:142:1:0:0.4 +12 133212382 . G A 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=GTGCAGTGTCTGCTGCTCAC;RSEQ=GCCAGGCCCGCCGGGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:113,2:115,0:0:1,0:25:1:29.9:1:1:0:60:27.75:1:0:0.1 0/1:91:10:9,1:80,1:81,10:0.1099:1,2:17.1:1:30.6:1:0.20879:8.48355:60:20:0.1124:0:1.2 +12 133212393 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50032;SOR=0;LSEQ=GCTGCTCACGGCCAGGCCCG;RSEQ=CGGGGCCCTGAGCACTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:2,0:124,6:130,2:0.015:1,0:26:1:29:1:1:0:60:4:0.0154:0:1 0/0:116:0:0,0:106,10:116,0:0:2,0:22.1:1:31.7:1:1:0:60:232:1:0:0.1 +12 133212582 . G A 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=TCGAGAGAAAGAAATTGTCA;RSEQ=AGAATGGAAGGTCTCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:527:0:0,0:220,306:526,0:0:2,0:24.8:1:32.4:1:1:0:60:130.5:1:0:0.1 0/1:670:20:11,9:290,359:649,20:0.0299:2,2:22.8:1:28.4:1:0.37228:1.51:60:40:0.0302:0:1.1 +12 133212692 . T C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40899;SOR=0.73267;LSEQ=TATTTCCCCTTGTATCTATC;RSEQ=GTACCCTCCACTTACTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:101:71:1,70:2,28:30,71:0.703:2,1:23.1:1:30.7:1:0.20969:4.90895:60:70:0.7:0:1.2 1/0:71:45:0,45:1,25:26,45:0.6338:1,1:19.3:1:29.8:1:0.3662:0:59.8:90:0.6338:0:1.2 +12 133212737 . C T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40974;SOR=1.65961;LSEQ=AATTTGAAAGTTCATTCAGA;RSEQ=CACATCATCCCTCAGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:22:1,21:0,17:17,22:0.5641:1,1:26:1:30.4:1:1:0:60:21:0.5526:0:1.8 1/0:19:13:0,13:0,6:6,13:0.6842:0,1:31.5:1:28.4:1:1:0:60:12:0.6667:0:1.8 +12 133214441 . C T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.73374;SOR=1.59958;LSEQ=CTGCTACCGCGCACAGGTGG;RSEQ=GGTAACCCCCTTTTCACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:17:15,2:10,0:10,17:0.6296:0,2:13.1:1:29:1:0.51567:0:60:16:0.64:0:2.5 1/0:15:11:10,1:4,0:4,11:0.7333:0,2:26.1:1:29.5:1:1:0:60:22:0.7333:0:1.4 +12 133214517 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.26206;SOR=0.6912;LSEQ=CGACCTCCCAGCCCACCCAG;RSEQ=AGGAGAGCTGGCACCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:68:63,5:33,1:34,68:0.6667:1,2:24.6:1:29.9:1:0.66071:2.59855:60:67:0.6634:0:2.3 1/0:69:40:35,5:23,6:29,40:0.5797:2,2:28.9:1:28.9:1:0.50728:1.81:60:80:0.5882:0:2.1 +12 133214522 . G C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54565;SOR=0.81987;LSEQ=TCCCAGCCCACCCAGGAGGA;RSEQ=AGCTGGCACCTCAGGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:72:65,7:36,1:37,72:0.6606:1,2:24.3:1:31.6:1:0.2611:3.83989:60:35:0.6542:0:2.2 1/0:83:51:45,6:26,6:32,51:0.6145:2,2:24.5:1:31.3:1:0.52285:1.72:60:102:0.622:0:1.8 +12 133214754 . G A 35 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.36264;SOR=0.31672;LSEQ=CAAGTTGAGAGTCCGTGGTG;RSEQ=AGACGCCACAGTCATGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:76,218:294,3:0.0101:2,2:11.7:1:22.3:1:0.16975:5.70:60:2:0.0069:0:1.3 0/0:312:1:1,0:85,226:311,1:0.0032:2,0:1:0:22:0:0.27564:0:60:2:0.0032:0:1 +12 133214768 . A G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55805;SOR=0.87525;LSEQ=GTGGTGGAGACGCCACAGTC;RSEQ=TGGAGAGCCAGAGGGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:154:29,125:18,59:77,154:0.6667:2,2:22.6:1:31.8:1:0.48838:1.31338:60:153:0.6711:0:1.1 1/0:231:147:29,118:17,67:84,147:0.6364:2,2:23.2:1:30.7:1:1:1.0323:60:72.5:0.6332:0:1.1 +12 133215534 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07429;SOR=Inf;LSEQ=TCTCTGCAGGATGTGCAGGC;RSEQ=ACGCTGCAGCAGCAGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:35,1:36,0:0:1,0:24.1:1:30.4:1:1:0:60:72:1:0:0.1 0/1:14:2:1,1:12,0:12,2:0.1429:0,2:26:1:29.5:1:0.14286:0:60:4:0.1429:0:1 +12 133215853 . T A 53 v3;p8;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0125;SOR=Inf;LSEQ=GTGGTACTGGGTGATCTCCT;RSEQ=CACCCAGCCCACGACCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:212,391:603,0:0:2,0:24:1:30.3:1:1:0:60:66:1:0:0.1 0/1:563:6:6,0:206,351:557,6:0.0107:2,0:6.7:1:20.8:1:0.00273:0:59.7:5:0.0091:0:2 +12 133216124 . T TCCCTCAACACAA 59 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=CTTGTTCAGGCTTCACCGCA;RSEQ=CCCAAACTCTGTGTGTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,2:2,4:0.5714:0,0:19.3:1:29.8:1:1:0:60:8:0.5714:0.2857:0 1/0:2:1:0,1:0,1:1,1:0.5:0,0:40:0:31.4:0:1:0:60:2:0.5:0:0 +12 133218493 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.17299;SOR=Inf;LSEQ=GCCAGCTCCAGCACCACCAG;RSEQ=CCCCTGGGCCTGACTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:35,128:163,0:0:2,0:22.2:1:30.7:1:1:0:60:22.286:0.9873:0:0.2 0/1:118:2:1,1:19,96:115,2:0.0169:2,2:19:1:27:1:0.31388:4.95:60:4:0.0172:0:2 +12 133218724 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=0.55928;LSEQ=TCACAGAATGGCAGAAACAC;RSEQ=AGCCAGGTCTCATGGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:360:241:167,74:81,37:118,241:0.6694:2,2:25.1:1:30.5:1:0.90379:1.03:60:39.167:0.6714:0:1.1 1/0:356:189:121,68:106,61:167,189:0.5309:2,2:25.2:1:29:1:1:1.02:60:62:0.5269:0:1.1 +12 133219582 . C A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02747;SOR=Inf;LSEQ=GGGCATCTGGTTGCTGCGCA;RSEQ=CTAGACCAACGCAGGCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:136,327:463,0:0:2,0:24.3:1:31.5:1:1:0:60:45.3:1:0:0.2 0/1:442:5:3,2:136,301:437,5:0.0113:2,2:16:1:27.8:1:0.18158:3.31:60:10:0.0115:0:1 +12 133219602 . G A 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20159;SOR=4.33292;LSEQ=CCTAGACCAACGCAGGCCAC;RSEQ=TCAGCCTCCCCCTGCGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:1:1,0:84,246:330,1:0.003:2,0:1:0:27:0:0.2568:0:60:2:0.0031:0:1 0/1:308:4:2,2:91,213:304,4:0.013:2,2:21:1:30:1:0.58689:2.33:60:8:0.0132:0:1.3 +12 133219609 . T C 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.13436;LSEQ=CAACGCAGGCCACGTCAGCC;RSEQ=CCCCCTGCGCAGGAGGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:1,2:69,226:295,3:0.0101:2,2:30.3:1:24.7:1:0.55352:1.63:60:2:0.007:0:1.7 0/1:263:3:0,3:74,186:260,3:0.0114:2,0:23.7:1:32:0:0.56139:0:60:6:0.0116:0:1 +12 133219800 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12019;SOR=0;LSEQ=ATGTGCTGCCATGGAGGGCC;RSEQ=AGGACTCACAGTGTCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:1,2:182,82:264,3:0.0112:2,2:23.7:1:28.7:1:0.23375:4.41147:60:6:0.0115:0:2.3 0/0:273:0:0,0:191,82:273,0:0:2,0:24.5:1:30.8:1:1:0:60:135.5:1:0:0.6 +12 133219831 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=0.6083;LSEQ=GTGTCCAGCACAAAGACGGA;RSEQ=GCCCTGCGCTGTGAGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:412:276:171,105:82,54:136,276:0.6699:2,2:25.3:1:31.2:1:0.74804:1.07:60:91:0.6757:0:1.2 1/0:411:227:138,89:116,67:183,227:0.5523:2,2:23.5:1:30.2:1:0.61012:1.11629:60:55.75:0.552:0:1.2 +12 133219989 . A T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=ATGGGCGGCTGGTGCAGGCC;RSEQ=TACCTGGTTCCAGGTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:656:0:0,0:350,306:656,0:0:2,0:23.8:1:30.8:1:1:0:60:108.333:1:0:0.1 0/1:610:12:6,6:316,282:598,12:0.0197:2,2:26.4:1:30.2:1:1:1.12036:60:24:0.0199:0:1.1 +12 133220098 . CCA C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.57239;SOR=1.27097;LSEQ=CCTCACCAGCTGTTTATTGA;RSEQ=CACACACACAGCCCAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:952:12:7,5:453,486:939,12:0.0126:2,2:30:1:32.9:1:0.56835:1.50:60:24:0.0128:0:0.1 0/1:1002:16:8,8:480,504:984,16:0.016:2,2:27.2:1:31.8:1:1:1.05:59.7:32:0.0162:0.003:0.3 +12 133220142 . G A 77 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22482;SOR=2.66881;LSEQ=CCAGGGCCCGGAACAGTAAC;RSEQ=GAACCTGGAAGAATCGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:3:3,0:299,427:726,3:0.0041:2,0:1.7:1:27:0:0.07068:0:60:6:0.0042:0:1 0/1:734:8:7,1:327,399:726,8:0.0109:2,2:7.1:1:25.8:1:0.02646:8.52:60:16:0.011:0:1.1 +12 133220168 . G A 46 v3;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02348;SOR=Inf;LSEQ=TGGAAGAATCGGGCAGACAG;RSEQ=CCGGCAAGGGCTGGATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:0:0,0:168,345:513,0:0:2,0:24.1:1:31.4:1:1:0:60:56:1:0:0.1 0/1:461:5:5,0:164,292:456,5:0.0108:2,0:10.8:1:20:1:0.00637:0:60:1.5:0.0066:0:1 +12 133220206 . C T 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00041;SOR=Inf;LSEQ=GTGGGGGCTCTGGCTGCCCA;RSEQ=GTGACTTCTGCCCGGGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:36,225:261,0:0:2,0:23.1:1:30.3:1:1:0:60:42.5:1:0:0.1 0/1:193:9:0,9:26,158:184,9:0.0466:2,0:21.2:1:30:1:0.61165:0:60:18:0.0469:0:1 +12 133220230 . T G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.00021;SOR=Inf;LSEQ=ACTTCTGCCCGGGATGTGGC;RSEQ=GTGCCCCTGCAGCTGCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:18,161:179,0:0:2,0:21.9:1:30.8:1:1:0:60:58.667:1:0:0.1 0/1:119:9:0,9:8,102:110,9:0.0756:2,0:23.6:1:30.3:1:1:0:60:18:0.0776:0:1.2 +12 133220321 . T A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49426;SOR=0.78175;LSEQ=ACCTGTGGGAACGAGTCCAC;RSEQ=GTCGCTGCTGTTCCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:79:55,24:24,11:35,79:0.693:2,2:27.1:1:31.5:1:1:1.05:59.9:158:0.693:0:1.1 1/0:58:37:30,7:16,5:21,37:0.6379:2,2:24.1:1:30.4:1:0.74089:1.33:60:74:0.6379:0:1.1 +12 133220380 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08474;SOR=Inf;LSEQ=CTTTCCTCCATACCACCCTG;RSEQ=TGGAGCCTCCCCCAGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:190,73:263,0:0:2,0:22.6:1:32.3:1:1:0:59.9:51.6:1:0:0.3 0/1:207:3:2,1:148,56:204,3:0.0145:2,2:23.7:1:28.7:1:1:1.31955:60:6:0.0147:0:1.3 +12 133220454 . G A 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=23.88604;LSEQ=ATACGCCCTCGATGTCTGGC;RSEQ=CTGACAGCTCAGCGTTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:1:1,0:265,238:503,1:0.002:2,0:1:0:25:0:1:0:60:2:0.002:0:2 0/1:640:29:14,15:335,275:610,29:0.0453:2,2:27:1:28.4:1:0.56803:1.30464:60:58:0.0456:0:1.2 +12 133220526 . T C 215 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACTGAATACTCATAGAGA;RSEQ=TGTAGACCATGTTGGAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:0:0,0:209,291:500,0:0:2,0:26.2:1:30.4:1:1:0:59.9:61.5:0.996:0:0.1 0/1:537:125:55,70:185,226:411,125:0.2328:2,2:24.1:1:30.9:1:0.91824:1.04177:60:61.5:0.2316:0:1.2 +12 133220600 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49986;SOR=Inf;LSEQ=GATGATCTCGTCACTGGGCG;RSEQ=AAGTGGTAATGTCTGTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:42,129:171,0:0:2,0:22.7:1:28.7:1:1:0:60:170:1:0:0.2 0/1:189:2:1,1:46,140:186,2:0.0106:2,2:43:1:31.5:1:0.4385:3.02:60:4:0.0109:0:1 +12 133220652 . A AG 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3497;SOR=0.66902;LSEQ=CACACGCTATTCGGAGTCCT;RSEQ=GACTTCTGGTGCCCCTAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:39:0,39:1,25:26,39:0.6:1,1:22.2:1:31:1:0.4:0:60:38:0.5938:0.1538:0.6 1/0:52:26:0,26:1,25:26,26:0.5:1,1:20.8:1:29.4:1:1:0:60:52:0.5:0.1923:0.7 +12 133220670 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09691;LSEQ=CTAGACTTCTGGTGCCCCTA;RSEQ=CGACGGGGTACACCCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:29:0,29:0,23:23,29:0.5577:1,1:20.9:1:28.9:1:1:0:60:58:0.58:0:1 1/0:31:18:0,18:0,13:13,18:0.5806:1,1:24.7:1:28.8:1:1:0:60:36:0.5806:0:1.1 +12 133224393 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTCCCACCTGTTCTCTG;RSEQ=GGTCTCGATGCCTCTGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:32:1:1:0:60:4:1:0:2 +12 133224410 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGTCTCGATGCCTCTG;RSEQ=GTCCGCTTTCCTCTTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:31:0:1:0:60:4:1:0:2 +12 133225446 . G T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00607;SOR=0.61894;LSEQ=GAGATGGAGGCTGGAGGCCA;RSEQ=GCTAGATCATGGGAAAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:213:175,38:80,18:98,213:0.6827:2,2:23:1:30.8:1:1:1.04:59.9:41.6:0.6797:0:1.1 1/0:275:157:122,35:89,28:117,157:0.5709:2,2:24.8:1:29.7:1:0.77301:1.10:59.9:77.5:0.572:0:1.1 +12 133225670 . C A 51 v3;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.05633;SOR=Inf;LSEQ=CTCGCTGATCTGAAAGGCCA;RSEQ=ACGGACATACAGCACATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:109,241:350,0:0:2,0:24.8:1:31.9:1:1:0:60:42.75:1:0:0.1 0/1:334:4:4,0:98,232:330,4:0.012:2,0:10.3:1:25.5:1:0.00834:0:60:8:0.0122:0:1 +12 133225705 . C T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26364;SOR=0;LSEQ=CATCACAGGACACACTGGAA;RSEQ=CCACAGACGGGGCCACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:3:1,2:63,165:228,3:0.013:2,2:20.3:1:24.3:1:1:1.31:60:2:0.009:0:1 0/0:173:0:0,0:53,120:173,0:0:2,0:22.9:1:30.4:1:1:0:60:56.667:1:0:0.1 +12 133225713 . C T 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.002;SOR=Inf;LSEQ=GACACACTGGAACCCACAGA;RSEQ=GGGGCCACCTTCCAGGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:60,143:203,0:0:2,0:22.5:1:30.4:1:1:0:60:39.6:1:0:0.2 0/1:145:7:2,5:43,95:138,7:0.0483:2,2:19.7:1:30.1:1:1:1.13063:60:14:0.0493:0:1.1 +12 133225753 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51587;SOR=0;LSEQ=CTTGCAGCTCCCAGCACAGG;RSEQ=CCTTAGGCCTCCCTACGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:67,79:146,2:0.0135:2,2:41:0:31.5:1:1:1.18:60:4:0.0144:0:1 0/0:101:0:0,0:52,49:101,0:0:2,0:21.3:1:31.1:1:1:0:60:49.5:1:0:0.1 +12 133225761 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51463;SOR=0;LSEQ=TCCCAGCACAGGGCCTTAGG;RSEQ=CTCCCTACGATGGGCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:70,74:144,2:0.0137:2,2:42:0:31:1:1:1.06:60:4:0.0144:0:1 0/0:101:0:0,0:61,40:101,0:0:2,0:21.7:1:31.6:1:1:0:60:100:1:0:0.1 +12 133226159 . T C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03395;SOR=0.70695;LSEQ=TGAGATGGGAATGCCCGCCA;RSEQ=GACTTTCTCACAAGCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:373:249:126,123:57,65:122,249:0.6676:2,2:23.4:1:30.8:1:0.50842:1.17:59.9:48.8:0.6667:0:1.7 1/0:283:166:74,92:53,63:116,166:0.5866:2,2:22:1:30.4:1:0.90339:1.04577:60:82:0.5857:0:1.6 +12 133226196 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00652;SOR=0.64429;LSEQ=GCCTCCCTAGGGGTCAGGAC;RSEQ=CATCTCGGGCTCCCTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:382:252:138,114:80,49:129,252:0.6597:2,2:24.8:1:30.4:1:0.19021:1.34765:59.9:83:0.664:0:1.7 1/0:290:161:113,48:70,59:129,161:0.5552:2,2:23.4:1:29.6:1:0.00695:1.98:60:79.5:0.5559:0:1.5 +12 133226249 . G T 75 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03696;SOR=0.1392;LSEQ=CAGAGACAGACAGTATCACA;RSEQ=CTGTGTGCCTTACCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:7:1,6:378,239:617,7:0.0112:2,2:11.3:1:26.9:1:0.01651:9.45822:60:14:0.0116:0:1.1 0/0:635:1:0,1:402,232:634,1:0.0016:2,0:1:0:23:0:0.36693:0:60:2:0.0016:0:1 +12 133233705 . T C 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13067;SOR=0;LSEQ=GATCCCGCCCAGCCCAGCCT;RSEQ=GGGGCCCCACCGTCACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:462:462:320,142:0,0:0,462:1:0,2:24.1:1:31.3:1:1:0:59.9:91.4:1:0:1.1 1/1:556:552:366,186:0,3:3,552:0.9928:0,2:25.2:1:29.9:1:0.03908:0:60:45:0.9926:0:1.1 +12 133234389 . CAT C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.2504;SOR=0.75467;LSEQ=AAAACATAATCCAACTCAGA;RSEQ=ATTCTGCTCTGTCTAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:164:107:85,22:47,10:57,107:0.6524:2,2:22.5:1:32:1:0.68492:1.21504:59.8:106:0.6503:0.122:0.1 1/0:157:92:71,21:50,15:65,92:0.586:2,2:24.5:1:31:1:1:1.01:59.9:91:0.5833:0.1019:0 +12 133234741 . C CGTGT 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.63022;SOR=0.50206;LSEQ=TCCTCGGGGAGTAACACGTG;RSEQ=GTATGTGTAAACACGTGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:4,11:0.7333:0,0:20.9:1:31.7:1:1:0:60:22:0.7333:0.1333:0 1/0:7:4:1,3:0,3:3,4:0.5714:0,2:9:1:28.5:1:1:0:60:8:0.5714:0.4286:0.5 +12 133235577 . A C 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTGCTTTTTTCTCCAA;RSEQ=GTGGTTTCAAACTGTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:35.3:1:33.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 133235789 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00109;SOR=0.36147;LSEQ=GCCCTCACCTCTCTGTGATG;RSEQ=GGGGAGCCCTCACCTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:90:68,22:19,5:24,90:0.7895:2,2:25.7:1:31.2:1:0.79361:1.2273:59.1:29:0.7838:0:1.3 1/0:101:58:45,13:31,12:43,58:0.5743:2,2:25.7:1:30.4:1:0.64198:1.34:58.8:57:0.5816:0:1.2 +12 133235817 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11574;SOR=0;LSEQ=CCTCACCTCTCCGTGACGGA;RSEQ=GGAGCCCTCACCTGTCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:2,1:118,33:151,3:0.0194:2,2:21.3:1:25.7:1:0.52951:1.78013:60:2:0.0136:0:3 0/0:162:0:0,0:123,39:162,0:0:2,0:1:0:16:0:1:0:60:0:0:0:1 +12 133235824 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49884;SOR=Inf;LSEQ=TCTCCGTGACGGAGGGAGCC;RSEQ=TCACCTGTCCGTGATGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:136,37:173,0:0:2,0:23.5:1:31.4:1:1:0:59.9:42.25:1:0:0.6 0/1:181:2:1,1:134,45:179,2:0.011:2,2:27.5:1:28.5:1:0.44475:2.95614:60:4:0.0113:0:1 +12 133235831 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24686;SOR=0;LSEQ=GACGGAGGGAGCCCTCACCT;RSEQ=TCCGTGATGGGAGGAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:153,43:196,2:0.0101:2,2:32:0:32.5:1:0.39594:3.52874:60:4:0.0109:0:1.5 0/0:200:0:0,0:147,53:200,0:0:2,0:22.6:1:30.9:1:1:0:59.6:21.222:1:0:0.5 +12 133236000 . C T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.66215;LSEQ=CGCTTTGCTGTGCTGATGGA;RSEQ=GTAGACTTCTGCTCCCCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:703:471:221,250:112,120:232,471:0.67:2,2:24.7:1:30.4:1:0.7485:1.0557:59.9:38.25:0.6701:0:1.2 1/0:886:508:242,266:187,190:377,508:0.5734:2,2:25.4:1:29.5:1:0.58663:1.08172:60:45.182:0.5713:0:1.2 +12 133236030 . C T 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCCCCGTAATCTTCCAG;RSEQ=TTCCGAGACATGGAACGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:0:0,0:266,349:615,0:0:2,0:24.5:1:32.6:1:1:0:59.9:67.333:1:0:0.7 0/1:799:39:16,23:340,419:759,39:0.0488:2,2:22.4:1:29.2:1:0.7419:1.16624:60:38:0.0478:0:1.7 +12 133236094 . G A 63 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03299;SOR=Inf;LSEQ=CAGAGTCAGGCATGTTGGCT;RSEQ=CCTAGAGAAAGACAATGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:123,254:377,0:0:2,0:24.3:1:32.1:1:1:0:60:61.833:1:0:0.2 0/1:434:6:5,1:155,272:427,6:0.0138:2,2:10:1:24.5:1:0.02773:8.74:60:12:0.014:0:1.3 +12 133237514 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49875;SOR=0;LSEQ=TCCCCTTCTTGCTTCATCCT;RSEQ=CATCCCTCAGAGCAGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:161,37:198,2:0.01:2,2:39:0:32:1:0.34467:4.30703:60:4:0.0103:0:1 0/0:199:0:0,0:153,46:199,0:0:2,0:21.3:1:29.9:1:1:0:60:98.5:1:0:0.1 +12 133237555 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04536;SOR=0;LSEQ=GGTGGAGGGTAGGCCTTTAC;RSEQ=TTGCTGTACAGCACGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:4:2,2:278,112:390,4:0.0102:2,2:8.8:1:25.8:1:0.58273:2.47563:60:3:0.0079:0:1.5 0/0:458:0:0,0:310,147:457,0:0:2,0:14:0:18:0:1:0:60:0:0:0:2 +12 133237827 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21263;SOR=Inf;LSEQ=AGCTGTGCCTCATCCTCTCT;RSEQ=CCCGCCTCTTCCCTTTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:11,138:149,0:0:2,0:25.4:1:32.3:1:1:0:59.7:28.8:1:0:0.3 0/1:128:2:1,1:2,124:126,2:0.0156:1,2:28.5:1:26.5:1:0.04651:50.84:60:4:0.0161:0:1.5 +12 133237831 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50207;SOR=0;LSEQ=GTGCCTCATCCTCTCTGCCC;RSEQ=CCTCTTCCCTTTCCAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:8,129:137,2:0.0143:2,2:40:1:29:1:0.12574:15.26:60:4:0.0148:0:1 0/0:117:0:0,0:3,114:117,0:0:1,0:25.5:1:32:1:1:0:59.6:234:1:0:0.2 +12 133238026 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2328;SOR=Inf;LSEQ=CCAGGTCTGTTTCTATCCTG;RSEQ=CTCCTGATCCAACCTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:156,14:170,0:0:2,0:24.5:1:31.1:1:1:0:59.9:27.333:1:0:0.5 0/1:159:2:1,1:142,15:157,2:0.0126:2,2:16:1:30.5:1:0.1917:9.19828:60:4:0.0128:0:2 +12 133238040 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11359;SOR=Inf;LSEQ=ATCCTGGCTCCTGATCCAAC;RSEQ=TCCTTTCTGGGCTAAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:193,37:230,0:0:2,0:23.1:1:31.1:1:1:0:60:31.857:1:0:0.5 0/1:217:3:1,2:177,37:214,3:0.0138:2,2:13.7:1:27.3:1:0.08397:9.41755:60:6:0.014:0:2 +12 133238076 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08532;SOR=0.78453;LSEQ=ATTTAATCTATCTCAATCCA;RSEQ=GTCCTTTCTAAAGCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:422:259:186,73:114,49:163,259:0.6137:2,2:22.5:1:31.4:1:0.74091:1.09:60:63.75:0.6159:0:1.1 1/0:447:248:167,81:135,64:199,248:0.5548:2,2:25.9:1:30.3:1:0.91942:1.02306:59.9:48.6:0.5535:0:1.1 +12 133238275 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06282;SOR=Inf;LSEQ=CATTGGTGAAGCCTTCCTGA;RSEQ=AAACAAGAGTGAAGAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:132,275:407,0:0:2,0:23.4:1:32.2:1:1:0:60:49.875:1:0:0.1 0/1:442:5:4,1:134,302:436,5:0.0113:2,2:14.8:1:26.4:1:0.03511:8.97:60:10:0.0115:0:1.4 +12 133238313 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23761;SOR=0;LSEQ=GGGCAGCTTCACTCATGATG;RSEQ=CCCAAACCTGGAAACCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:25,158:183,2:0.0108:2,2:23.5:1:29.5:1:0.26199:6.22:60:4:0.0109:0:1 0/0:194:0:0,0:39,155:194,0:0:2,0:22.7:1:30.8:1:1:0:60:37.8:1:0:0.1 +12 133240181 . A G 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGAGAGAAGAGGGGCT;RSEQ=TGGTGGGAAATGGGAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:29:1:33.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 133240781 . CACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT C 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.04738;SOR=0;LSEQ=GTGAGTTCCCCTTTCCTTTT;RSEQ=GCCCAGTGTGTGGCCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:7:2,5:43,64:107,7:0.0262:2,2:43.6:1:32.4:1:0.70187:1.67252:24.9:14:0.027:0:0 0/0:165:0:0,0:26,60:86,0:0:2,0:22.3:1:29.1:1:1:0:54.5:85:0.528:0:0.1 +12 133240782 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05981;SOR=0.68507;LSEQ=TGAGTTCCCCTTTCCTTTTC;RSEQ=CCCAGTGTGTGGCCTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:267:153:46,107:43,64:107,153:0.573:2,2:23.5:1:31.2:1:0.11093:1.56005:51.4:24.5:0.5676:0:1.2 0/1:165:79:24,55:26,60:86,79:0.4788:2,2:23.1:1:30.5:1:1:1.01:53.5:25.333:0.472:0:1.2 +12 133241144 . C A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02573;SOR=Inf;LSEQ=GGAGGAGGAAAGGAGAGATG;RSEQ=GACAGGGACAAGGGAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:4,106:110,0:0:1,0:24.5:1:30.5:1:1:0:60:54:1:0:0.1 0/1:75:4:0,4:3,68:71,4:0.0533:1,0:19.8:1:29.5:1:1:0:60:8:0.0556:0:1 +12 133241785 . A G 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19911;SOR=Inf;LSEQ=CCTCCAACATTCCTTGAATC;RSEQ=GATGAACGGCCCTCCATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:114,7:121,0:0:2,0:23.9:1:30.3:1:1:0:60:39.333:1:0:0.1 0/1:98:2:1,1:91,5:96,2:0.0204:2,2:16:0:28:1:0.11929:16.70476:60:4:0.0204:0:1 +12 133241792 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60443;SOR=2.23919;LSEQ=CATTCCTTGAATCAGATGAA;RSEQ=GGCCCTCCATGCACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:1,0:127,10:137,1:0.0072:2,0:38:0:33:0:1:0:60:2:0.0074:0:1 0/1:124:2:1,1:110,12:122,2:0.0161:2,2:24.5:1:29.5:1:0.19945:8.84796:60:4:0.0164:0:1 +12 133242073 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10727;SOR=Inf;LSEQ=CATGGAGCACCTCACAGATT;RSEQ=TTCCATTTCACATTCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:48,215:263,0:0:2,0:24.9:1:33.1:1:1:0:60:130.5:0.9962:0:0.2 0/1:240:3:1,2:46,190:236,3:0.0125:2,2:16.7:1:29:1:0.48315:2.06:60:6:0.0126:0:1.3 +12 133242140 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11276;SOR=0.52731;LSEQ=TTGAAAATTTTCAAATCTAT;RSEQ=GAAAACCTAAAAAACCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:53:1,52:0,22:22,53:0.7067:1,1:23.3:1:31.6:1:1:0:60:52:0.7123:0:1.2 1/0:43:24:0,24:0,19:19,24:0.5581:1,1:22.8:1:31.6:1:1:0:60:48:0.5581:0:1 +12 133243788 . T A 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAACAATAGGCGAAGGCAG;RSEQ=TGGGTTCGTAAAACTTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:14.2:1:29.7:1:1:0:57:12:0.8571:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +12 133243817 . C T 66 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAAACTTGATGTACTCAAA;RSEQ=GGCCAGCCAGCTGTAGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:36:1:33.3:1:1:0:60:8:0.8:0:1.8 1/1:1:1:1,0:0,0:0,1:1:0,0:2:0:29:0:1:0:60:2:1:0:1 +12 133244013 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11857;SOR=Inf;LSEQ=CAGAGGATCCCAGGCAAGGA;RSEQ=CCAAGAGTGCCCACTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:175,29:204,0:0:2,0:24.1:1:32.7:1:1:0:60:50:1:0:0.1 0/1:198:3:2,1:165,30:195,3:0.0152:2,2:21.7:1:29.3:1:0.4017:2.73094:60:6:0.0154:0:1.3 +12 133244668 . CA C 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=GACAGAGTGAGACCTCATTT;RSEQ=AAAAAAAAAAGAAAGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:3,0:3,5:0.5:0,0:28:1:32:1:1:0:60:10:0.5556:0:0 0/0:3:0:0,0:3,0:3,0:0:0,0:16.7:1:30.7:1:1:0:60:6:1:0:0.3 +12 133245149 . A G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31775;SOR=0.83994;LSEQ=AGACACACCGGCTTCCCACC;RSEQ=AGTGGAGAAAGGCGGCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:333:205:124,81:67,60:127,205:0.6156:2,2:22:1:30.8:1:0.17239:1.37:60:67.333:0.6196:0:1.1 1/0:272:156:95,61:76,39:115,156:0.5735:2,2:22.6:1:29.7:1:0.44497:1.25024:60:77:0.5856:0:1.1 +12 133245556 . G A 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62399;SOR=2.88805;LSEQ=AGCGAAACTCAGTAGAGGCT;RSEQ=GTGACCAAGCTTGCCTCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:1:1,0:64,206:270,1:0.0037:2,0:1:0:23:0:0.23985:0:60:2:0.0037:0:1 0/1:283:3:2,1:75,205:280,3:0.0106:2,2:10.3:1:21:1:0.18084:5.43:60:6:0.0108:0:1 +12 133245584 . C G 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22239;SOR=Inf;LSEQ=AGCTTGCCTCGTGTGCAGTT;RSEQ=ACCAACCCCTTTTAGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:28,144:172,0:0:2,0:23.9:1:32.3:1:1:0:59.8:85:1:0:0.1 0/1:154:2:1,1:31,121:152,2:0.013:2,2:7.5:1:28.5:1:0.37348:3.86:60:4:0.0132:0:1.5 +12 133245594 . T C 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.60505;LSEQ=GTGTGCAGTTCACCAACCCC;RSEQ=TTTAGACATTCAGGAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:19,131:150,2:0.0131:2,2:23:1:30.5:1:0.2466:6.74:60:4:0.0132:0:1 0/0:126:1:0,1:23,102:125,1:0.0079:2,0:37:0:29:0:1:0:60:2:0.008:0:1 +12 133248977 . G A 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15811;LSEQ=TAGCCTGCCTCAGGTTTGAC;RSEQ=CTGTGGCTGCACGTGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:26,119:145,2:0.0135:2,2:8:1:28.5:1:0.33464:4.51:60:4:0.0137:0:1 0/1:128:2:1,1:25,101:126,2:0.0156:2,2:7.5:1:29:1:0.36626:3.98:60:4:0.0159:0:1 +12 133249017 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10946;SOR=0.54429;LSEQ=GTTGTGCCCGAGAAAGCTCC;RSEQ=GAAGGACTCATGTGCACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:90:62:13,49:4,24:28,62:0.6889:2,2:21.1:1:32.2:1:0.56788:1.58:59.6:124:0.6889:0:1.1 1/0:55:30:5,25:3,22:25,30:0.5455:2,2:24:1:30.2:1:0.71527:1.46:60:29:0.5577:0:1.1 +12 133249139 . T A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76702;SOR=0.93611;LSEQ=TGGGGAGAAGGGGCTTTATT;RSEQ=CAGCCCCTGCAGCTTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:223:139:114,25:69,15:84,139:0.6233:2,2:24.2:1:28.6:1:1:1.00873:60:278:0.6233:0:1 1/0:209:127:100,27:63,19:82,127:0.6077:2,2:21.7:1:28.3:1:0.73621:1.12:60:126:0.6058:0:1.1 +12 133250017 . C A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01971;SOR=Inf;LSEQ=CGTGTGTCCCGGAGACACAG;RSEQ=CTGCTGGGTGGAGCGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:96,40:136,0:0:2,0:25:1:32.5:1:1:0:59.8:272:1:0:0.1 0/1:83:4:3,1:54,24:78,4:0.0482:2,2:19.5:1:29.8:1:1:1.33:60:8:0.0482:0:1.3 +12 133250118 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00502;SOR=0.65099;LSEQ=GCTCCGTGGCCATCTGGATG;RSEQ=GTGCACACGGCAGCAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:398:262:174,88:90,46:136,262:0.6583:2,2:25.3:1:29.6:1:1:1.01:59.9:51.4:0.6607:0:1.1 1/0:338:188:118,70:94,55:149,188:0.5562:2,2:24.8:1:28.9:1:1:1.01383:60:36.6:0.5562:0:1.1 +12 133250128 . G T 41 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19969;SOR=4.37469;LSEQ=CATCTGGATGCGTGCACACG;RSEQ=CAGCAGGGGCAGCCGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:1:0,1:281,155:436,1:0.0023:2,0:1:0:28:0:0.35698:0:60:2:0.0023:0:1 0/1:402:4:1,3:248,148:396,4:0.01:2,2:5.3:1:20.8:1:0.1531:5.00682:60:3:0.0076:0:2 +12 133250359 . T C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2614;SOR=0;LSEQ=GCCCGGGAACCCCTGAGAAC;RSEQ=GGCAAAACTGGGCACCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:47,194:241,3:0.0123:2,2:32.7:1:31.7:1:0.48325:2.06:60:6:0.0127:0:1 0/0:187:0:0,0:37,150:187,0:0:2,0:22.3:1:29.4:1:1:0:60:45.75:1:0:0.2 +12 133250442 . A G 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0946;SOR=0.44004;LSEQ=CAAGGCCCCACATGGTGTAG;RSEQ=CACCTTGTGAAAACCCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:48:0,48:0,16:16,48:0.75:1,1:21.9:1:31.1:1:1:0:59.5:15:0.7377:0:1.1 1/0:30:17:1,16:0,13:13,17:0.5667:1,1:26.2:1:31.9:1:1:0:60:34:0.5667:0:1 +12 133250550 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=CCTCGCCTTCCTCCCATCCT;RSEQ=AGCAGAGTTTGTGGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:1,11:12,0:0:2,0:22.7:1:32.1:1:1:0:56.2:11:1:0:1.3 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:41:1:28.5:1:1:0:60:4:0.6667:0:2 +12 133250569 . T G 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50909;SOR=Inf;LSEQ=TCAGCAGAGTTTGTGGCCTC;RSEQ=CCGACGGGCGCCCCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:3,6:0.6667:0,0:25.7:1:29.3:1:1:0:60:5:0.625:0:2.2 1/1:3:3:1,2:0,0:0,3:1:0,2:38.3:1:31.3:1:1:0:60:6:1:0:2 +12 133252176 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1572;SOR=Inf;LSEQ=CCTTTCTCCATTCCTCCCTC;RSEQ=GACCCAGGGAGGAACCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:99,158:257,0:0:2,0:23.7:1:30.8:1:1:0:60:18.769:1:0:0.1 0/1:170:2:0,2:47,121:168,2:0.0118:2,0:26:1:31:1:1:0:60:4:0.0125:0:1 +12 133252462 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0766;SOR=Inf;LSEQ=TTCTCTTCTTCAAGCTATTC;RSEQ=AAATTCCTCTCCCAAAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:41,150:191,0:0:2,0:25.4:1:32.1:1:1:0:60:46.75:1:0:0.1 0/1:142:3:1,2:20,119:139,3:0.0211:2,2:16:1:29:1:0.38358:2.94:60:6:0.0213:0:1 +12 133252556 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01098;SOR=0.47533;LSEQ=TCTGGCAGAAAAGACGGTCA;RSEQ=ACCCTGAGAACAAAGCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:125:86:68,18:25,14:39,86:0.688:2,2:24.7:1:32.5:1:0.08225:2.10:60:85:0.6911:0:1.2 1/0:92:47:41,6:36,9:45,47:0.5109:2,2:26:1:31.6:1:0.40587:1.70:60:46:0.5055:0:1.2 +12 133252796 . C G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.18603;LSEQ=GGTGATGAGGTAGCCCTAGC;RSEQ=AAGTTCATTAGCAATCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:114:30,84:74,165:239,114:0.3211:2,2:23.3:1:31.3:1:0.38542:1.25496:60:113:0.321:0:1.1 1/0:394:237:74,163:51,103:154,237:0.6015:2,2:26:1:29.8:1:0.73952:1.09041:60:46.4:0.601:0:1.1 +12 133252947 . T C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.55378;SOR=1.60358;LSEQ=TCCTGAGAAGAGACGCTCTG;RSEQ=GTGTGGATTCCCACTCGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:13:9,4:16,20:36,13:0.2653:2,2:15.5:1:32:1:0.19633:2.75:60:26:0.2708:0:1.2 0/1:19:7:4,3:4,8:12,7:0.3684:2,2:25.6:1:29.3:1:0.37652:2.53:60:6:0.3333:0:1.9 +12 133253286 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2367;SOR=Inf;LSEQ=CAAGCTCTAAACTCCCCATT;RSEQ=GGCCTCCCTGAACACCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:24,176:200,0:0:2,0:23.5:1:31.6:1:1:0:59.9:99:1:0:0.3 0/1:190:2:1,1:35,153:188,2:0.0105:2,2:21.5:1:30.5:1:0.34386:4.32:60:4:0.0106:0:1.5 +12 133253310 . A G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59375;SOR=0.86163;LSEQ=CTCCCTGAACACCCACCCCC;RSEQ=GCCTGCTCTACCTCCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:52:4,48:2,73:75,52:0.4094:1,2:22.7:1:30.3:1:0.22593:3.01:60:25:0.4132:0:1.1 0/1:107:40:2,38:6,61:67,40:0.3738:2,2:26.8:1:30.7:1:0.70726:1.85884:60:39:0.3786:0:1 +12 133253995 . G A 148 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=31.60927;LSEQ=GGGTGATTTCTACCGGAAAA;RSEQ=CATTTCCTCGGTATCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:681:1:1,0:318,362:680,1:0.0015:2,0:1:0:26:0:0.46843:0:60:2:0.0015:0:1 0/1:742:33:14,19:312,397:709,33:0.0445:2,2:26:1:29.5:1:1:1.0665:60:32:0.0438:0:1.3 +12 133254042 . C T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06184;SOR=Inf;LSEQ=CAATGAGCCTGCAAAACACA;RSEQ=AGTGTGCTAACTAGAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:193,275:468,0:0:2,0:24.9:1:32.1:1:1:0:60:45.8:1:0:0.3 0/1:471:5:2,3:198,267:465,5:0.0106:2,2:16.4:1:27.4:1:1:1.11214:60:10:0.0107:0:1.8 +12 133254083 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24951;SOR=1.19631;LSEQ=ACATCCAGGAAAGTCTATTC;RSEQ=TCTGTGGATTCACCCATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:133:67,66:118,113:231,133:0.3644:2,2:24.9:1:32.5:1:0.91367:1.02859:60:43.333:0.3631:0:1.1 0/1:349:142:82,60:118,88:206,142:0.4069:2,2:21.2:1:30.8:1:1:1.02:60:70:0.407:0:1.2 +12 133256349 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20262;SOR=Inf;LSEQ=AAGAGTTGGCGACTTCAAGG;RSEQ=ACCTTGTCCAACTCTGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:46,56:102,0:0:2,0:26.3:1:32.5:1:1:0:59.6:101:1:0:0.1 0/1:84:2:2,0:23,59:82,2:0.0238:2,0:25.5:1:29:1:0.08606:0:60:4:0.0241:0:1 +12 133256904 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55591;SOR=0.83505;LSEQ=CTCCTATATCCCATGAACAG;RSEQ=CTAGGGCCAGGGTAGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:37:8,29:10,61:71,37:0.3426:2,2:32.5:1:28.9:1:0.41509:1.67:60:11.333:0.3269:0:1.4 0/1:99:30:7,23:11,58:69,30:0.303:2,2:23.6:1:28.5:1:0.40429:1.60:60:60:0.3125:0:1.1 +12 133256988 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0177;SOR=Inf;LSEQ=GGGCAAGAATCTGAAAGACA;RSEQ=GCTACTTCTCACCATTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:35,16:51,0:0:2,0:22.9:1:31.8:1:1:0:60:50:1:0:0.3 0/1:19:3:1,2:7,9:16,3:0.1579:2,2:27.7:1:29.3:1:1:1.52085:60:6:0.1667:0:1 +12 133257837 . C A 142 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02545;LSEQ=CCGTTCCAGGCGCTTGAGTG;RSEQ=CGAAACTGAGGAAGTGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:28:10,18:203,251:454,28:0.0579:2,2:22.7:1:29.7:1:0.43438:1.45467:60:56:0.0587:0:1 0/0:642:1:1,0:283,357:640,1:0.0016:2,0:1:0:22:0:0.44306:0:60:2:0.0016:0:1 +12 133257887 . C T 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00826;SOR=9.41074;LSEQ=TGAGTGAAAGAAGGGAACCC;RSEQ=GTGCTTAATTTGTAATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:1:0,1:87,250:337,1:0.003:2,0:42:0:32:0:1:0:60:2:0.003:0:1 0/1:404:11:3,8:132,261:393,11:0.0272:2,2:15.8:1:28.5:1:0.75795:1.34772:60:22:0.0276:0:1 +12 133257929 . C CT 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCTGCTGCTTCTTTTTTT;RSEQ=TTTTTTTTCTTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:18,148:166,0:0:2,0:20.9:1:33.7:1:1:0:58.7:82:1:0:0.1 0/1:172:20:4,16:27,125:152,20:0.1163:2,2:23.9:1:29.8:1:0.76196:1.16:59:40:0.1183:0:0.3 +12 133257938 . C CT 77 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.28253;SOR=2.98965;LSEQ=CTTCTTTTTTTCTTTTTTTT;RSEQ=TTTTTTTTTGAGACGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:12,128:140,2:0.0141:2,2:25:1:30:1:0.17531:10.29:53.5:4:0.0144:0.007:0.5 0/1:146:6:3,3:24,116:140,6:0.0411:2,2:7.7:1:29.9:1:0.07705:4.76:60:12:0.0423:0.0274:0.5 +12 133257999 . GGCTCA G 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06834;LSEQ=GAGTGCAGTGGTGTGATCTC;RSEQ=CTGCAAGCTCCGCCTCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:0,4:0,10:10,4:0.2857:0,0:23.3:1:33.4:1:1:0:40.3:8:0.2857:0.1429:0 0/1:10:3:0,3:0,7:7,3:0.3:0,0:11:1:30.5:1:1:0:36.7:6:0.3:0.2:0 +12 133263743 . A C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGCGGGCGGCTGCGGGA;RSEQ=CCGGGCCTCCCTCCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:11,4:0,0:0,15:1:0,2:12.1:1:32.4:1:1:0:60:30:1:0:1.5 1/1:21:21:16,5:0,0:0,21:1:0,2:16.7:1:31:1:1:0:60:42:1:0:1.8 +12 133263819 . C T 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12303;SOR=Inf;LSEQ=CCGGAGGGCCGGCCCGAGAG;RSEQ=CTCAGGAGGGCGCCCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:196,90:286,0:0:2,0:22.8:1:31.9:1:1:0:60:25:1:0:0.6 0/1:284:3:1,2:186,95:281,3:0.0106:2,2:5.3:1:25.3:1:0.26952:3.89553:60:6:0.0108:0:1.3 +12 133263825 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=1.9804;LSEQ=GGCCGGCCCGAGAGCCTCAG;RSEQ=AGGGCGCCCCTCACCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:95:64,31:151,75:226,95:0.296:2,2:22.4:1:30.3:1:1:1.03:59.9:30.667:0.2958:0:1.4 0/1:341:155:103,52:118,68:186,155:0.4545:2,2:23.4:1:29:1:0.5714:1.14:60:37.75:0.4562:0:1.3 +12 133263950 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24905;SOR=Inf;LSEQ=GGGGAGAAATTTGGCGCGCT;RSEQ=CCACCCAGACTCGCGAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:94,172:266,0:0:2,0:24.1:1:30.6:1:1:0:60:19.462:1:0:0.2 0/1:279:3:1,2:95,180:275,3:0.0108:2,2:29.7:1:23.3:1:1:1.05536:60:2:0.0075:0:2.3 +13 20847593 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54884;SOR=Inf;LSEQ=CTCCTAGAGTACCTTCGCCC;RSEQ=TTTCTCCAGGCTGACTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:35,32:67,0:0:2,0:29.5:1:32.6:1:1:0:60:134:1:0:1.1 0/1:130:2:1,1:65,61:126,2:0.0154:2,2:22:1:28:1:1:1.06508:60:4:0.0155:0:2 +13 20847602 . G C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34314;SOR=Inf;LSEQ=TACCTTCGCCCCTTTCTCCA;RSEQ=GCTGACTCCTCCTTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:69:34,35:0,0:0,69:0.9857:0,2:29.3:1:31.2:1:1:0:60:138:0.9857:0:1.1 1/1:134:134:66,68:0,0:0,134:1:0,2:25:1:30.1:1:1:0:59.8:133:1:0:1.3 +13 20847634 . A C 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01154;SOR=Inf;LSEQ=CTTTGCAAGCCCTATCCTGC;RSEQ=ACCCTGATTGTCGCTGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:27,35:62,0:0:2,0:26.2:1:29.9:1:1:0:60:61:1:0:0.9 0/1:93:9:3,6:35,49:84,9:0.0968:2,2:29.4:1:29.1:1:0.73303:1.42327:60:8:0.087:0:2.1 +13 21004618 . A G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=4.70489;LSEQ=CACTCAGGCTGCCATGACCC;RSEQ=TGAAGAGGGACAACCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:21:19,2:44,6:50,21:0.2958:2,2:20.8:1:29.3:1:1:1.29:60:20:0.2899:0:1.1 1/0:72:48:42,6:20,4:24,48:0.6667:2,2:26.9:1:29.6:1:0.72208:1.39:60:96:0.6667:0:1.1 +13 21004660 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23105;SOR=0;LSEQ=AGGGTGGACATCGTGAGTCA;RSEQ=CAGAACTACCAGAGCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:104,50:154,2:0.0128:2,2:25:0:31.5:1:0.54839:2.06944:60:4:0.0129:0:1 0/0:168:0:0,0:113,55:168,0:0:2,0:23.2:1:31.3:1:1:0:60:167:1:0:0.6 +13 21004678 . C T 44 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25001;SOR=Inf;LSEQ=CAGCAGAACTACCAGAGCAG;RSEQ=CCAACTCACCCCTCCGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:115,74:189,0:0:2,0:26:1:31.9:1:1:0:60:93.5:1:0:0.4 0/1:209:3:2,1:130,75:205,3:0.0144:2,2:27:0:28.3:1:1:1.15:60:6:0.0147:0:1.3 +13 21004709 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24879;SOR=Inf;LSEQ=CCTCCGCCTGCCCTCCTCCA;RSEQ=CAGCAAAAGGAAACACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:159,121:280,0:0:2,0:25.4:1:32.7:1:1:0:60:92.333:1:0:0.4 0/1:287:3:3,0:157,127:284,3:0.0105:2,0:17:1:26:1:0.25733:0:60:6:0.0107:0:1 +13 21004738 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.14755;LSEQ=GGAAACACCAGAGTCCTCCA;RSEQ=GGCTCTTGCAATGGAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:93:42,51:120,113:233,93:0.2853:2,2:26.7:1:30.4:1:0.32767:1.28849:59.8:45.5:0.2826:0:1.4 1/0:351:219:106,113:71,61:132,219:0.6239:2,2:26:1:30.1:1:0.3781:1.24003:60:72:0.6243:0:1.4 +13 21004758 . T C 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGCTCTTGCAATGGAGAGT;RSEQ=CTTTGTGTACACCTCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:18:8,10:147,156:303,18:0.0561:2,2:24.4:1:31.7:1:0.81122:1.17729:60:36:0.057:0:1.7 0/0:359:0:0,0:168,191:359,0:0:2,0:26.1:1:28.9:1:1:0:59.9:70.8:1:0:1.1 +13 21004816 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCCAAACCCTTCCTTGA;RSEQ=TGGGCTCACACCTTTCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:183:183:60,123:0,0:0,183:1:0,2:25.5:1:30.4:1:1:0:59.6:35.6:1:0:1.4 1/1:175:175:61,114:0,0:0,175:1:0,2:23.1:1:29.7:1:1:0:60:174:1:0:1.7 +13 21004828 . C T 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50068;SOR=0;LSEQ=TTCCTTGAGTGGGCTCACAC;RSEQ=TTTCATATTGGAGAAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:40,112:152,2:0.013:2,2:7:0:33:1:0.46286:2.78:60:4:0.0134:0:3.5 0/0:134:0:0,0:38,96:134,0:0:2,0:21.6:1:31.1:1:1:0:60:268:1:0:1.7 +13 21004834 . T G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.98654;LSEQ=GAGTGGGCTCACACCTTTCA;RSEQ=ATTGGAGAAAGCAAGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:25:8,17:28,86:114,25:0.1799:2,2:19.7:1:32.6:1:0.45606:1.44:58.5:50:0.1838:0:2.5 1/0:108:69:16,53:12,27:39,69:0.6389:2,2:23.4:1:30.8:1:0.4934:1.46675:60:138:0.6389:0:2.1 +13 21006781 . C T 33 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTTGTCTTCAAAGCTTC;RSEQ=TCCCAGCCCACCACCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:15:0:33:1:1:1:60:4:0.5:0:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:42:0:30:0:1:0:60:2:1:0:0 +13 21006784 . C A 32 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTCTTCAAAGCTTCCTC;RSEQ=CAGCCCACCACCCCCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:18:0:32:0:1:1:60:4:0.5:0:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:45:0:26:0:1:0:60:2:1:0:0 +13 21549384 . G A 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=11.01031;LSEQ=GGGTGGGCCTTCAGGTCATC;RSEQ=GCCCCATTCCGCCCCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:2:1,1:114,274:388,2:0.0051:2,2:18.5:1:21.5:1:0.50333:2.40:60:1:0.0026:0:1 0/1:502:27:10,17:168,306:474,27:0.0538:2,2:22:1:29.4:1:0.83943:1.07:60:54:0.0549:0:1.1 +13 21549395 . G A 48 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17074;SOR=0.18668;LSEQ=CAGGTCATCGGCCCCATTCC;RSEQ=CCCCAGGCGGTGGTCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:4:2,2:88,228:316,4:0.0125:2,2:15.3:1:24:1:0.31497:2.58:60:3:0.0096:0:1.8 0/0:425:1:0,1:138,286:424,1:0.0024:2,0:8:0:30:0:1:0:60:2:0.0024:0:1 +13 21549485 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2419;SOR=Inf;LSEQ=CTGGGCTGGAATGTGGAGCG;RSEQ=GTTCTCCCAGTTGATCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:17,92:109,0:0:2,0:21.7:1:30.5:1:1:0:60:108:1:0:0.1 0/1:106:2:1,1:29,75:104,2:0.0189:2,2:31.5:1:29.5:1:0.48787:2.56:60:4:0.019:0:1 +13 21553234 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTAGTGGGATTACAGGCA;RSEQ=GAGCCACTGCGCCTGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:27.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 21553971 . C T 165 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCACTCAATCCCTACACAGG;RSEQ=ATGAATTCTCCTCCGAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:125,314:439,0:0:2,0:23.6:1:31.9:1:1:0:60:47.778:0.9977:0:0.1 0/1:507:64:19,45:147,295:442,64:0.1262:2,2:22.8:1:27.5:1:0.66951:1.17986:60:128:0.128:0:1.2 +13 21554217 . A T 64 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTTAGCAAATAGTTACT;RSEQ=GCCAGAATTTTATGTTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:22.6:1:27.6:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 21555544 . CT GA 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.45294;LSEQ=GAAAGCTAGAGCCAGCGAGA;RSEQ=CAGCTCACGTCTGAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:76:56,20:151,43:194,76:0.2794:2,2:24:1:31.2:1:0.52269:1.25303:60:152:0.2879:0.0147:2 0/1:289:141:101,40:108,39:147,141:0.4879:2,2:23.6:1:29.8:1:0.79195:1.09637:60:282:0.4896:0.0381:2 +13 21555545 . T A 58 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21724;SOR=4.79068;LSEQ=AAAGCTAGAGCCAGCGAGAC;RSEQ=CAGCTCACGTCTGAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:1,0:152,43:195,1:0.0037:2,0:36:0:29:0:1:0:60:2:0.0053:0:3 0/1:283:5:2,3:107,41:148,5:0.0177:2,2:7.8:1:25:1:0.14347:3.87387:60:4:0.0267:0:2.2 +13 21555554 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.17322;LSEQ=GCCAGCGAGACTCAGCTCAC;RSEQ=TCTGAAGGGAAGGAGACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:95:68,27:159,55:214,95:0.3074:2,2:23.3:1:30.6:1:0.67566:1.14733:60:94:0.3082:0:1.9 0/1:346:170:116,54:120,56:176,170:0.4913:2,2:24.3:1:29.2:1:1:1.00:60:33:0.4896:0:2 +13 21557174 . TA T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCTGAAATCCACTACCT;RSEQ=AAAAAAAATGCATATCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:2,0:27,0:27,2:0.069:1,0:23:1:33:0:1:0:60:4:0.069:0:0 0/0:14:0:0,0:14,0:14,0:0:1,0:20.6:1:27.3:1:1:0:60:13:1:0:0.3 +13 21557284 . G T 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63023;LSEQ=AAATGATTAGGAGCCACTAG;RSEQ=ATGGGAAATTTAGTTGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:162,17:179,2:0.011:2,2:8.5:1:27.5:1:0.1895:9.28947:60:4:0.0111:0:1 0/0:144:1:0,1:118,25:143,1:0.0069:2,0:1:0:22:0:0.18056:0:60:2:0.0071:0:1 +13 21557960 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19739;SOR=Inf;LSEQ=TCCAGCCTGTGTAGAAGGAA;RSEQ=AGGAAGGAGGAAGAATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:27,165:192,0:0:2,0:24.4:1:31.3:1:1:0:60:191:1:0:0.1 0/1:154:2:1,1:22,130:152,2:0.013:2,2:37:1:31:1:0.27723:5.80:60:4:0.0131:0:1 +13 21558264 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATTTTTAGTAGAAACAG;RSEQ=GTTTCATCATGTTGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:27:1:1:0:44:4:1:0:1 +13 21562371 . C T 143 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=33.47284;LSEQ=AGCAGGTGCTTCGGGTAGGG;RSEQ=GGAGGCGGGCACCTCCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:1:0,1:132,285:417,1:0.0024:2,0:1:0:25:0:1:0:60:2:0.0024:0:1 0/1:403:30:9,21:142,229:371,30:0.0744:2,2:25.5:1:29.2:1:0.43645:1.4456:60:60:0.0754:0:1.1 +13 21562506 . C G 30 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.54295;LSEQ=GCGGGGGCGGGGGCGGGGGC;RSEQ=GGGGCAGGCGCGGGCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:7,9:16,2:0.1111:2,0:7:1:30.5:1:0.49673:0:60:4:0.1176:0:1.5 0/1:16:1:0,1:7,8:15,1:0.0625:2,0:1:0:30:0:1:0:60:2:0.0625:0:2 +13 21562608 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50384;SOR=Inf;LSEQ=ACCGGGTGCAAGATGTGCGC;RSEQ=GCCGTGACAGCCGTCACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:91,41:132,0:0:2,0:26.2:1:29.9:1:1:0:60:131:1:0:0.2 0/1:163:2:1,1:103,57:160,2:0.0123:2,2:27.5:1:27.5:1:1:1.79995:60:4:0.0126:0:1.5 +13 21562636 . G T 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.58572;SOR=0.39375;LSEQ=CAGCCGTCACGGTGTTGGGG;RSEQ=CGGGCAGGGAGGGCTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:109,67:176,2:0.0112:2,2:22:1:32:0:1:1.62219:60:4:0.0114:0:1 0/0:225:1:0,1:125,99:224,1:0.0044:2,0:1:0:25:0:0.44444:0:60:2:0.0046:0:1 +13 21562756 . G A 44 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24945;SOR=0;LSEQ=CCACGTGCGCGCGCGGCGGC;RSEQ=CCTCCAGGCCCGGCTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:2,1:185,85:270,3:0.011:2,2:5.7:1:28.3:1:1:1.08789:60:6:0.0112:0:1.7 0/0:255:0:0,0:161,94:255,0:0:2,0:23.3:1:29.8:1:1:0:60:126.5:1:0:0.4 +13 21562789 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02913;SOR=Inf;LSEQ=GCTTCTGCAGGGAGTCCCGG;RSEQ=GGGCCAGGGTGGCAGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:207,120:327,0:0:2,0:24.6:1:31:1:1:0:60:53.5:1:0:0.7 0/1:320:5:1,4:188,127:315,5:0.0156:2,2:8.8:1:25.8:1:0.16302:5.89078:60:10:0.0161:0:2 +13 21562832 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26008;SOR=1.18913;LSEQ=CTGCTGGACGGAGGTGCTGC;RSEQ=CAATTCATACAGGTCCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:541:426:252,174:68,47:115,426:0.7874:2,2:24.6:1:31:1:1:1.00:60:41.6:0.7909:0:1.2 1/1:573:467:262,205:58,48:106,467:0.815:2,2:26.6:1:29.3:1:0.82883:1.06:60:37.917:0.8213:0:1.2 +13 21562948 . G A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50623;LSEQ=GCACATGCAGCTGGTGGGCC;RSEQ=CGGGACCGGCCTGCTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:549:430:214,216:57,59:116,430:0.7832:2,2:24:1:29.8:1:0.91704:1.03:60:60.429:0.7833:0:1.1 1/0:642:415:204,211:116,108:224,415:0.6464:2,2:24.4:1:29.1:1:0.56188:1.11075:60:82:0.6457:0:1.2 +13 21563506 . C A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.34358;SOR=3.45142;LSEQ=ATCAGTGGGTTCTGGCACTT;RSEQ=CAGGCTGGTCCCCACTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:1:1,0:69,271:340,1:0.0029:2,0:1:0:24:0:0.20528:0:60:2:0.003:0:1 0/1:298:3:2,1:57,238:295,3:0.0101:2,2:8.3:1:26:1:0.1011:8.27:60:6:0.0102:0:1.3 +13 21563518 . C A 36 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25752;SOR=0;LSEQ=TGGCACTTCCAGGCTGGTCC;RSEQ=CACTCTAGCGCTGCCCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:32,249:281,3:0.0106:2,2:7:1:23:1:0.31062:3.86:60:2:0.0072:0:1 0/0:228:0:0,0:29,199:228,0:0:2,0:23:1:30.3:1:1:0:60:37:1:0:0.1 +13 21563642 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15837;SOR=Inf;LSEQ=AGGACCAGTTGCCCTAATGT;RSEQ=TTAGCAGAGTGGAGACAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:0,31:31,0:0:1,0:21.1:1:31.4:1:1:0:58.2:30:1:0:0.5 0/1:21:2:1,1:0,19:19,2:0.0952:1,2:34.5:1:30:1:0.09524:0:60:4:0.0952:0:1 +13 21563715 . C T 73 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGACTGCGTCCACATCC;RSEQ=GAGGTGCGTCCCTGCCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:5,7:0.5833:0,0:19.1:1:26.1:1:1:0:60:2.5:0.5:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 21565327 . C T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09659;SOR=Inf;LSEQ=CTGGCTCTGGCCAGGCCAGG;RSEQ=CAGGTTGGACCCCTCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:245,31:276,0:0:2,0:24.5:1:32:1:1:0:60:68:1:0:0 0/1:235:3:2,1:194,38:232,3:0.0128:2,2:10.3:1:22.3:1:0.4213:2.53915:60:2:0.0087:0:2 +13 21566131 . C A 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGGGGCCCATGGAGCCACAC;RSEQ=GGTCCAGGACAGGTAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28:1:32:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:19.5:1:30:1:1:0:60:4:1:0:0 +13 21619782 . A T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2038;SOR=0;LSEQ=CTGACTGCCCCAGCTGTCCC;RSEQ=TAGCTGCCTCTGCACATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:113,18:131,2:0.015:2,2:12.5:1:26:0:0.26623:6.13733:60:4:0.0154:0:1 0/0:161:0:0,0:130,31:161,0:0:2,0:23.8:1:29.5:1:1:0:60:322:1:0:0.1 +13 21620085 . T C 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=5.28364;LSEQ=ACCGAAGACTTGGATGGCTG;RSEQ=TTTAACCCCTCACGAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:841:454:192,262:170,217:387,454:0.5398:2,2:25.3:1:32.8:1:0.67512:1.06894:59.9:150.333:0.5401:0:1.1 1/1:951:819:374,445:60,69:129,819:0.8612:2,2:25.1:1:31.4:1:0.9243:1.03462:59.9:135.5:0.8612:0:1.2 +13 21620222 . T TA 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.51857;SOR=1.41136;LSEQ=TCTTAAAGTGTTTTATTATT;RSEQ=AAAAAAAAAAACTGTCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:11:0,11:4,75:79,11:0.1209:2,0:28.3:1:31:1:1:0:59.5:22:0.1222:0:0.1 0/1:86:14:0,14:2,68:70,14:0.1628:1,1:33.4:1:29.8:1:1:0:60:28:0.1647:0.0116:0 +13 22057796 . G A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGAAAAAAGAGGGGCTA;RSEQ=TTTTTCTTAGCCAGGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:19.2:1:30.8:1:1:0:60:10:1:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:16:1:30.7:1:1:0:60:6:1:0:1.3 +13 22057951 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50658;SOR=Inf;LSEQ=AAAGATATGTCTAAAGGCTG;RSEQ=TGTCTCCTCTTGGCAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:63,43:106,0:0:2,0:23.7:1:29.7:1:1:0:59.9:105:1:0:0.2 0/1:138:2:1,1:86,50:136,2:0.0145:2,2:22:1:29.5:1:1:1.71285:60:4:0.0146:0:1 +13 22058032 . G A 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.35163;LSEQ=CGACACGGCGTGCTTGGCCA;RSEQ=CTCCCCGGGCAGCAGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:1,0:33,57:90,1:0.011:2,0:1:0:26:0:0.37363:0:60:2:0.0111:0:1 0/1:135:2:2,0:47,85:132,2:0.0148:2,0:22.5:1:25:1:0.13197:0:40:4:0.0153:0:1 +13 22058168 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49762;SOR=Inf;LSEQ=TTAACGAATGGCCTTGGAAG;RSEQ=GATGCGGGTGTCGGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:69:47,22:0,0:0,69:0.9718:0,2:26.4:1:31.6:1:1:0:60:138:0.9718:0:1.1 1/1:64:64:45,19:0,0:0,64:1:0,2:22.4:1:30.5:1:1:0:59.9:63:1:0:1.1 +13 22058175 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4966;SOR=0;LSEQ=ATGGCCTTGGAAGAGATGCG;RSEQ=GTGTCGGGGTGGACCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:49,23:72,2:0.027:2,2:20.5:1:29.5:1:0.54646:2.1068:60:4:0.0278:0:2 0/0:73:0:0,0:50,23:73,0:0:2,0:23:1:31:1:1:0:59.7:146:1:0:1 +13 22058205 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18057;SOR=0;LSEQ=TGGACCTGCTTCAGCAGAGT;RSEQ=GCTCTCCTTGCGGCTGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:56,26:82,2:0.0238:2,2:37.5:1:30.5:1:0.54217:2.13242:60:4:0.0241:0:1.5 0/0:113:0:0,0:68,44:112,0:0:2,0:26.1:1:28.1:1:1:0:59.1:111:0.9911:0:0.6 +13 22058257 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50285;SOR=Inf;LSEQ=CCAACCTTCTGCGCCTTGGT;RSEQ=ACCGCCTTCTTGGAGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:61,66:127,0:0:2,0:24.6:1:31.7:1:1:0:59.5:62.5:1:0:0.2 0/1:154:2:1,1:71,81:152,2:0.013:2,2:14.5:1:27:1:1:1.14:60:4:0.0132:0:1 +13 22058292 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49896;SOR=0;LSEQ=GCCCTTCTTCAGGGAGGGAG;RSEQ=AGACTTGGCTGGCTCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:48,73:121,2:0.0163:2,2:22.5:1:27:1:1:1.52:60:4:0.0163:0:1.5 0/0:112:0:0,0:42,70:112,0:0:2,0:27.9:1:31.5:1:1:0:58.4:111:1:0:0.3 +13 22058311 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17342;SOR=Inf;LSEQ=GCAGACTTGGCTGGCTCAGG;RSEQ=ATCTTCAAACACCAGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:37,73:110,0:0:2,0:24.6:1:31.8:1:1:0:59.5:21:1:0:0.4 0/1:79:2:1,1:24,53:77,2:0.0253:2,2:36.5:1:29.5:1:0.53554:2.18:60:4:0.0256:0:1.5 +13 22058339 . G A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27126;SOR=0;LSEQ=AACACCAGAAGTATGTCCCT;RSEQ=ATGGTCTTTTTCACAAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:3:0,3:13,42:55,3:0.0517:2,0:22.7:1:31:1:1:0:60:6:0.0536:0:1.7 0/0:39:0:0,0:9,30:39,0:0:2,0:17.5:1:30.2:1:1:0:59.7:18.5:1:0:0.8 +13 22058353 . C T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCTGATGGTCTTTTTCA;RSEQ=AAGGATAACTGAGTAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:5,31:0,0:0,36:1:0,2:22.5:1:28.4:1:1:0:60:35:1:0:1.1 1/1:20:20:1,19:0,0:0,20:1:0,1:21:1:26.6:1:1:0:60:9:1:0:1.3 +13 24942750 . T G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTTGCTTTTCTGTTCTG;RSEQ=TCTGCTGATCTGTTTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14.5:1:32:1:1:0:53:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 24942936 . C A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41176;SOR=0;LSEQ=AACAGCTGGGCCCGGGGCAC;RSEQ=ACTACCATCAAAATGCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:0,10:1:0,0:30.7:1:30.6:1:1:0:39.3:20:1:0:2.1 1/1:7:6:5,1:1,0:1,6:0.8571:0,2:14.8:1:29.5:1:1:0:43:12:0.8571:0:2 +13 24942948 . A G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=CGGGGCACCACTACCATCAA;RSEQ=ATGCGGAGACCGGTAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:0,12:1:0,0:29.5:1:33.2:1:1:0:42.8:24:1:0:1.9 1/1:12:10:8,2:1,1:2,10:0.8333:2,2:16.5:1:31.1:1:0.45455:3.46:45.6:20:0.8333:0:1.6 +13 25693092 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATCATCCCCAGAACCACC;RSEQ=TGAGAGTGAGCCTGGTAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45:1:30.5:1:1:0:60:4:1:0:1 +13 25694006 . G C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACAAAGTATTGGCTGTGC;RSEQ=CCTGGCACTATCAGGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:1,1:0.5:0,0:34:0:28:0:1:0:60:2:0.5:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:47:1:29.5:1:1:0:60:4:1:0:1 +13 25694340 . A T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.75698;LSEQ=GCTCCTAATGACCTCATGAC;RSEQ=GCTGAATCTCCTGATCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:71:32,39:88,122:210,71:0.2527:2,2:26.6:1:31.5:1:0.67832:1.14:60:142:0.2563:0:1.2 0/1:321:155:64,91:77,87:164,155:0.4829:2,2:25.1:1:29.4:1:0.31303:1.25752:60:37.75:0.4794:0:1.1 +13 25694388 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22043;SOR=Inf;LSEQ=CAACACAGAGAAAGGAGAGA;RSEQ=ACCTAGGGTGTCTAGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:62,125:187,0:0:2,0:22.7:1:30.2:1:1:0:60:25.714:1:0:0.4 0/1:166:2:1,1:57,107:164,2:0.012:2,2:40:0:31:1:1:1.87:60:4:0.0122:0:1 +13 25694405 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49829;SOR=0;LSEQ=AGAAACCTAGGGTGTCTAGG;RSEQ=TGCAACTCAGGGACCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:32,95:127,2:0.0155:2,2:41:1:30.5:1:0.44767:2.94:60:4:0.0161:0:1 0/0:123:0:0,0:39,84:123,0:0:2,0:24:1:31.3:1:1:0:60:122:1:0:0.5 +13 25694435 . C A 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=GGGACCTGTGGCTCCTGCAC;RSEQ=AAGCATGTGAATCACCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:18,79:97,0:0:2,0:23.5:1:31.9:1:1:0:60:47.5:1:0:0.4 0/1:73:10:2,8:17,46:63,10:0.137:2,2:28.8:1:29.9:1:1:1.47092:60:20:0.1389:0:1.1 +13 25694482 . C A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02454;SOR=0.27779;LSEQ=TGGTTTCCTAAGAAAATCTG;RSEQ=CCTGTTCATGCATTATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:19:1,18:1,25:26,19:0.413:1,1:25.6:1:30.2:1:1:1.38:60:38:0.4318:0:1.1 0/1:31:5:0,5:4,22:26,5:0.1613:2,0:21.8:1:27.2:1:1:0:60:10:0.1667:0:1 +13 26828732 . GC G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.2192;SOR=0;LSEQ=CTTCCCCGGTCCCCACCCCT;RSEQ=CCCCCGGCCCCCCGACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:117,25:142,2:0.0139:2,2:36:1:29:0:0.32955:4.60871:60:4:0.0156:0:3.5 0/0:163:0:0,0:130,33:163,0:0:2,0:23.1:1:29.5:1:1:0:59.3:11.538:1:0:0.9 +13 26828746 . C T 91 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=8;SSF=0.35845;SOR=2.23979;LSEQ=ACCCCTGCCCCCCGGCCCCC;RSEQ=GACCCAGCTCTCCGGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:3:0,3:157,34:191,3:0.0155:2,0:1:0:25.7:1:0.00649:0:60:6:0.0162:0:1 0/1:235:8:7,1:174,53:227,8:0.034:2,2:9.3:1:30.4:1:0.68573:2.13:60:16:0.0343:0:1.1 +13 26828808 . C T 58 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07258;SOR=0.23447;LSEQ=GACTTTAAAGTGAAGCTGAG;RSEQ=AGCGAGCGGGAGCGGGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:6:2,4:309,180:489,6:0.0121:2,2:15.8:1:22.5:1:0.20143:3.42444:60:5:0.0104:0:1.8 0/0:698:2:1,1:406,290:696,2:0.0029:2,2:28:1:28.5:1:1:1.39929:60:4:0.0029:0:1 +13 26828973 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50267;SOR=Inf;LSEQ=GCAGGCCGAGGCAGGTAGCC;RSEQ=GGAGGGAGAGCGGGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:18,136:154,0:0:2,0:24.7:1:30.4:1:1:0:60:153:1:0:0.1 0/1:186:2:1,1:28,156:184,2:0.0108:2,2:23:0:31:1:0.28823:5.49:60:4:0.0109:0:2.5 +13 26828980 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50075;SOR=Inf;LSEQ=GAGGCAGGTAGCCCGGAGGG;RSEQ=GAGCGGGCCGCCGGGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:14,127:141,0:0:2,0:23.6:1:32:1:1:0:60:46:1:0:0.1 0/1:162:2:1,1:19,141:160,2:0.0123:2,2:16:0:32:0:0.23234:7.26:60:4:0.0123:0:2.5 +13 26829388 . G T 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTATTTTATTTGAGGAAA;RSEQ=GAAGGCAGCGAGTGAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:33:1:30:1:1:1.73:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 26911643 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20542;SOR=Inf;LSEQ=TATATTTATTTATATTTTAC;RSEQ=TTATAAAAATGCACATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:170,19:189,0:0:2,0:22.2:1:32.2:1:1:0:59.9:62:1:0:0.1 0/1:158:2:1,1:132,24:156,2:0.0127:2,2:12:0:31.5:1:0.29227:5.40934:60:4:0.0128:0:1 +13 26911849 . A G 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00357;SOR=Inf;LSEQ=CCAACTATATAAGGCTCTGT;RSEQ=TTGTATTTGTCATATTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:21,182:203,0:0:2,0:23.2:1:31.2:1:1:0:60:406:1:0:0.1 0/1:203:9:1,8:27,167:194,9:0.0443:2,2:27.7:1:32.3:1:1:1.29191:60:18:0.0446:0:1.1 +13 26922450 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAACGCAGGGGTCCCTGC;RSEQ=TCAGCACCGGTACGTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 26922759 . A C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATTTGTCTTCCTCAAAA;RSEQ=TGGTTTCTGATGCCAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:35:0:35:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:29:1:1:0:60:4:1:0:1.5 +13 26923073 . G A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00105;SOR=0;LSEQ=TTACTGAAGTATCCGTCTCA;RSEQ=AATTGTGTGGGTGCTTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:67:66,1:0,0:0,67:1:0,1:24.3:1:29.7:1:1:0:59.5:12.4:1:0:1.1 1/1:53:45:45,0:8,0:8,45:0.8491:0,1:26.6:1:29.5:1:1:0:60:21.5:0.8431:0:1.2 +13 26927833 . T C 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02043;SOR=Inf;LSEQ=ATTATACATCAAATTATCTT;RSEQ=TCCTTTTTTTAAGCTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:152,14:166,0:0:2,0:23.1:1:31:1:1:0:59.7:40.5:1:0:0.2 0/1:143:5:5,0:121,17:138,5:0.035:2,0:19:1:32:1:1:0:60:10:0.0355:0:1 +13 26928092 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0943;SOR=Inf;LSEQ=TTTCTAGTCGTCTGTAGATA;RSEQ=CAGTGCTATATGTAGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:9,149:158,0:0:2,0:26.4:1:31.3:1:1:0:60:51.667:1:0:0.1 0/1:133:3:1,2:14,116:130,3:0.0226:2,2:15:1:29:1:0.30365:4.07:60:6:0.0231:0:2 +13 26929683 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACTTGAACGCAGGAAGC;RSEQ=GAGGTTGCAGTGAGCCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:29.5:1:1:0:52:4:1:0:1 +13 26957049 . TA T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.23953;SOR=Inf;LSEQ=GTCACAGTGTAGCACTTTTT;RSEQ=AAACTTTTGCAGGCAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:50,155:205,0:0:2,0:23.1:1:30.3:1:1:0:59.9:101.5:1:0:0.1 0/1:197:2:1,1:63,132:195,2:0.0102:2,2:35:1:31:1:0.54532:2.09:60:4:0.0103:0:0 +13 26959325 . A AT 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05197;SOR=2.16489;LSEQ=AAAATCATTTACTTAGCATG;RSEQ=TTTTTTTTTTATTATTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:10:9,1:192,30:222,10:0.0431:2,2:24.6:1:31:1:1:1.40:60:20:0.0452:0:0 0/1:281:25:17,8:210,45:255,25:0.089:2,2:25.9:1:29.9:1:0.10501:2.18868:60:50:0.0909:0.0071:0.1 +13 26959593 . T G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02562;SOR=0.33454;LSEQ=TTATAAAAGTAAGAGCAGAC;RSEQ=GAGTGTGATGGCTCATGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:22:0,22:0,30:30,22:0.4231:1,1:29.7:1:31:1:1:0:60:21:0.4118:0:1 0/1:41:8:0,8:2,31:33,8:0.1951:2,0:25.1:1:31.5:1:1:0:60:16:0.1951:0:1.3 +13 26967477 . C CT 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.63607;SOR=1.1381;LSEQ=TTCCTTGCCTATTTTTCTTT;RSEQ=TTTTTTTTTTTCTTTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:37:28,9:268,82:350,37:0.093:2,2:27.2:1:32.1:1:0.84152:1.05039:58.1:74:0.1:0:1.1 0/1:402:42:32,10:267,87:354,42:0.1045:2,2:28.5:1:30:1:1:1.04:58.7:84:0.1151:0:0.4 +13 26967849 . C T 128 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13636;SOR=0;LSEQ=ATGGAAATATTTATGGGTTT;RSEQ=CTGAATTTCAGGACTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:1,18:0,0:0,19:1:0,1:18.5:1:30.2:1:1:0:58.7:38:1:0:1.2 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:13.5:1:26.5:1:1:0:60:4:0.6667:0:1 +13 26971195 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15686;SOR=Inf;LSEQ=TTCAATATATATTTTATATC;RSEQ=GTTATGATCAAAATAATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:126,12:138,0:0:2,0:24:1:30.2:1:1:0:60:68:1:0:0.1 0/1:91:2:2,0:83,6:89,2:0.022:2,0:45:1:29.5:1:1:0:60:4:0.022:0:1 +13 26971442 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2251;SOR=Inf;LSEQ=TGAGGCTTTTTTGGATCAAT;RSEQ=TATGTGGTTACTTAGCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:16,164:180,0:0:2,0:23.1:1:30.3:1:1:0:60:89:1:0:0 0/1:163:2:1,1:18,143:161,2:0.0123:2,2:28.5:1:29:1:0.22018:7.76:60:4:0.0124:0:1 +13 26974562 . G A 263 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAACTGTGAGAAGCAATACC;RSEQ=TCATGTTTGTATGATTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:405:405:305,100:0,0:0,405:1:0,2:24.7:1:30.4:1:1:0:59.9:56.857:1:0:1.1 1/0:469:356:246,110:77,36:113,356:0.7591:2,2:25.7:1:29.5:1:0.90723:1.05:60:70.2:0.7614:0:1.1 +13 26975608 . CCAG C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.73989;SOR=0.86713;LSEQ=GTTTAACCAATTGAGAAGAA;RSEQ=CAGCAGCAGCAGGGCAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:699:19:12,7:464,216:680,19:0.0272:2,2:25.3:1:32.4:1:0.62489:1.25263:60:38:0.0275:0.0043:0.1 0/1:761:18:13,5:485,256:741,18:0.0237:2,2:21.6:1:31.1:1:0.62485:1.37:60:36:0.0238:0.0026:0.1 +13 27793359 . T C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12694;SOR=Inf;LSEQ=GACAATGCCTTTCAAACTCT;RSEQ=ATAACAACCTCTGGAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:28,29:57,0:0:2,0:26.6:1:29.4:1:1:0:40.7:27.5:1:0:0.2 0/1:70:4:3,1:30,36:66,4:0.0571:2,2:43.5:1:30.8:1:0.33683:3.54:38.5:8:0.058:0:1.3 +13 27793370 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50761;SOR=Inf;LSEQ=TCAAACTCTTATAACAACCT;RSEQ=TGGAGTTGAGCAACATGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:25,28:53,0:0:2,0:26.4:1:33:1:1:0:39.2:106:1:0:0.2 0/1:72:2:1,1:29,41:70,2:0.0278:2,2:18:1:32:0:1:1.41:58.5:4:0.0282:0:1.5 +13 27793387 . G C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.5186;SOR=Inf;LSEQ=CCTCTGGAGTTGAGCAACAT;RSEQ=GCTTCTCCCCTTTCTAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:18,24:42,0:0:2,0:23.2:1:31.5:1:1:0:35.9:84:1:0:0.2 0/1:65:2:1,1:25,38:63,2:0.0308:2,2:23:0:32:1:1:1.51:35:4:0.0323:0:1 +13 27793407 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52465;SOR=Inf;LSEQ=GGCTTCTCCCCTTTCTAGGT;RSEQ=CCGTGGCAGCCATCTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:27,0:0:2,0:24.7:1:31.4:1:1:0:32:54:1:0:0.1 0/1:45:2:1,1:15,28:43,2:0.0444:2,2:5.5:1:27.5:1:1:1.84:27.5:4:0.0455:0:1 +13 27793546 . G A 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATGAGCTCAATTAACA;RSEQ=CTTCTACCAAGGACCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:31.5:1:30.3:1:1:0:33:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 27825902 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GCAGCGTGCGCCGGGTCGGG;RSEQ=CTGGGCCGTGGGCTGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:22.7:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 27827811 . C T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTTTGCAGTTCTCACTT;RSEQ=GCTACTGAAATGTGAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:0,9:1:0,0:25.8:1:31.8:1:1:0:60:18:1:0:1.1 1/1:8:8:8,0:0,0:0,8:1:0,0:27:1:31.9:1:1:0:60:16:1:0:1 +13 27827942 . G A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23449;SOR=0;LSEQ=CACAAAGGGAAAGAGGAGAG;RSEQ=CACCCGATATATGTTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:2,0:19,18:37,2:0.0513:2,0:6:1:30:1:0.48988:0:50.5:4:0.0541:0:1 0/0:41:0:0,0:19,22:41,0:0:2,0:24.6:1:30.5:1:1:0:40:40:1:0:0.1 +13 27828041 . A G 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.58204;SOR=0.31051;LSEQ=TTTGTGTTCTGTTGTGTTCA;RSEQ=CATGTGTTGTAGTTCATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:7,3:0.3:0,0:24:1:34:1:1:0:60:6:0.3:0:1 0/1:9:1:0,1:1,7:8,1:0.1111:2,0:10:0:33:0:1:0:60:2:0.1111:0:1 +13 27829310 . G A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAATCTTAGAATACTTT;RSEQ=CAGTTACTTAAAGTCAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:52,0:0,0:0,52:1:0,1:28.7:1:28.7:1:1:0:60:51:1:0:1.1 1/1:48:48:47,1:0,0:0,48:1:0,1:22.7:1:28:1:1:0:60:96:1:0:1 +13 27829381 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.51285;SOR=Inf;LSEQ=CATTGGTTTCTTTAATAGGG;RSEQ=ATGGGTACTGTTCAAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:96,31:127,0:0:2,0:31.5:1:30.1:1:1:0:45.8:62.5:1:0:0.3 0/1:179:2:1,1:122,55:177,2:0.0112:2,2:24:1:28.5:1:0.52903:2.20732:49:4:0.0114:0:1.5 +13 27829408 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27004;SOR=Inf;LSEQ=ACTGTTCAAAAAGGAATGCC;RSEQ=CACAAGTGTTACCATGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:80,33:113,0:0:2,0:31.9:1:30.3:1:1:0:42.1:27.25:1:0:0.2 0/1:162:3:1,2:101,57:158,3:0.0185:2,2:23.7:1:26.3:1:0.5548:3.5148:28.3:6:0.019:0:1.3 +13 27829460 . G A 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.90619;LSEQ=TCTACAATGTTACCCAGCAT;RSEQ=CTGTTGGCATTGTTGTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:1,0:26,82:108,1:0.0092:2,0:1:0:25:0:0.24771:0:21:2:0.0094:0:1 0/1:115:2:1,1:26,87:113,2:0.0174:2,2:5.5:1:28.5:1:0.41602:3.30:40.5:4:0.0177:0:1 +13 28270502 . G A 61 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26573;SOR=6.78852;LSEQ=TGAAATAAGATGGAATATTC;RSEQ=TAACAAACTATTTAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:5,1:6,1:0.1429:2,0:35:0:32:0:1:0:50:2:0.1429:0:2 1/0:7:4:2,2:3,0:3,4:0.5714:0,2:18.8:1:30.5:1:0.42857:0:53:8:0.5714:0:1.8 +13 28270520 . T A 24 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58204;SOR=2.44724;LSEQ=TCGTAACAAACTATTTAAAT;RSEQ=ATTTTCTTAAAGAGACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:7,2:9,1:0.1:2,0:17:0:30:0:1:0:50:2:0.1111:0:2 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:11:1:24:1:1:2.23609:46:4:0.2222:0:2.5 +13 28270611 . C T 127 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55906;SOR=0;LSEQ=TTCTTCACATAATTGATGAA;RSEQ=GTGGTTTCCACTTTGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:33:1:31.4:1:1:0:42.8:10:1:0:1 1/0:28:21:13,8:4,3:7,21:0.75:2,2:27:1:29:1:1:1.21:43.1:42:0.75:0:1 +13 28270714 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00024;SOR=0.03884;LSEQ=CTTTTGGTGTTTCAGTTTTT;RSEQ=TCTCTTTTTGAAGGATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:8,5:0,2:2,13:0.8667:0,2:18.2:1:31.4:1:0.2:0:55.7:12:0.8571:0:1.2 0/1:17:3:1,2:5,9:14,3:0.1765:2,2:15.7:1:29.3:1:1:1.10434:59.7:6:0.1765:0:1.7 +13 28270899 . A C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16949;SOR=Inf;LSEQ=TCTTCTTCTTCTTCATCAGC;RSEQ=GCAACTTTTTTCTGTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:23,12:35,0:0:2,0:23:1:31.3:1:1:0:59.5:34:1:0:0.1 0/1:25:2:1,1:14,9:23,2:0.08:2,2:23:1:32:1:1:1.52748:60:4:0.08:0:1 +13 28270918 . A C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09061;SOR=Inf;LSEQ=CAGCAACTTTTTTCTGTGAA;RSEQ=TCTTGCTACCACCTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:25,13:38,0:0:2,0:26.2:1:31.4:1:1:0:59.6:76:1:0:0.3 0/1:32:3:1,2:19,10:29,3:0.0938:2,2:41.7:1:33:1:0.54032:3.63479:60:6:0.0938:0:1.7 +13 28270984 . T A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02369;SOR=Inf;LSEQ=AGAGTTTTACAACCTCCTCC;RSEQ=TTTCATCTTCTGACTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:78,20:98,0:0:2,0:22.2:1:32:1:1:0:57.9:196:1:0:1.1 0/1:90:5:4,1:59,26:85,5:0.0556:2,2:22:1:31:1:1:1.75:57:10:0.0562:0:1.2 +13 28270989 . A C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.26814;LSEQ=TTTACAACCTCCTCCTTTTC;RSEQ=TCTTCTGACTCTGCATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:60:48,12:31,7:38,60:0.6122:2,2:21.2:1:32:1:1:1.10597:58.3:120:0.6122:0:1.5 0/1:98:29:21,8:48,21:69,29:0.2959:2,2:26.6:1:31.6:1:1:1.15:58.1:58:0.299:0:1.3 +13 28271025 . G C 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24282;SOR=1.33007;LSEQ=TCTTCCTCTACAGCTACTAC;RSEQ=TGCTGTCCACTATTATGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:53:30,23:79,39:118,53:0.3099:2,2:24:1:31.8:1:0.22938:1.54882:57.5:106:0.3099:0:1.1 0/1:155:58:34,24:61,36:97,58:0.3742:2,2:21.1:1:30.4:1:0.61318:1.19468:57.1:116:0.3742:0:1.1 +13 28271052 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.224;SOR=Inf;LSEQ=CCACTATTATGCACTGGCCC;RSEQ=GAACCACACTTCAGTCGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:118,94:212,0:0:2,0:26.7:1:31.1:1:1:0:59.2:424:1:0:1.2 0/1:191:2:1,1:98,91:189,2:0.0105:2,2:30.5:1:27.5:1:1:1.07648:52:4:0.0105:0:1.5 +13 28271064 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2252;SOR=Inf;LSEQ=ACTGGCCCTGAACCACACTT;RSEQ=AGTCGTAAAAGCACAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:124,98:222,0:0:2,0:27.8:1:31.7:1:1:0:58.9:73:1:0:1.2 0/1:201:2:1,1:96,103:199,2:0.01:2,2:41:1:30.5:1:1:1.07:60:4:0.0101:0:1.5 +13 28271068 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17827;LSEQ=GCCCTGAACCACACTTCAGT;RSEQ=GTAAAAGCACAGGTGGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:227:159:91,68:32,36:68,159:0.7004:2,2:27.6:1:30.4:1:0.19085:1.50:58.7:52:0.6964:0:1.5 0/1:208:61:29,32:69,78:147,61:0.2933:2,2:24.5:1:29.3:1:1:1.02:57.4:122:0.2961:0:1.5 +13 28271142 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16602;LSEQ=GCAAACATTTTCAAAGTTGC;RSEQ=GGTGTTACTTTAATTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:134:97:32,65:15,22:37,97:0.7239:2,2:24.4:1:30.9:1:0.425:1.38145:56.5:47.5:0.7197:0:1.8 0/1:126:38:12,26:35,53:88,38:0.3016:2,2:23.9:1:28.9:1:0.42725:1.42681:56.5:37:0.3033:0:1.9 +13 28271189 . C T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=0.23423;LSEQ=ATAATTCATTGCCTCTGCTT;RSEQ=AACAATGTGCAATTTATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:46:12,34:5,15:20,46:0.697:2,2:23.8:1:29.4:1:1:1.06:59.6:45:0.6923:0:1.8 0/1:49:17:3,14:6,26:32,17:0.3469:2,2:18.7:1:26.8:1:1:1.07532:59.4:16:0.3333:0:1.8 +13 28271317 . T C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06416;SOR=2.5369;LSEQ=CTGGGGCCTCAGGGGGCTCA;RSEQ=TTCCATGTCCACCAAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:9:3,6:15,23:38,9:0.1915:2,2:24.4:1:33.7:1:1:1.29714:57.2:18:0.2045:0:1 0/1:45:17:7,10:13,15:28,17:0.3778:2,2:27.1:1:31.2:1:0.76669:1.23224:55.3:34:0.3778:0:1.1 +13 28271536 . T C 28 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATATGGGCCTGCAGTTT;RSEQ=CTTTTTTGGTTGTATCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:5.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28589267 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03536;SOR=0.74239;LSEQ=CTGTACCTTTCTGATTTCAA;RSEQ=CAAATTACAGTCTGACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:155:112,43:143,72:215,155:0.4178:2,2:24.6:1:30.9:1:0.25636:1.31:60:50.667:0.4153:0:1.1 0/1:518:180:119,61:213,125:338,180:0.3475:2,2:25.1:1:29.1:1:0.50216:1.14:60:89:0.347:0:1.1 +13 28589495 . C G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=16.00648;LSEQ=GATCTGCCATGTGCCAGACA;RSEQ=TGTTGCAGGCACACGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:4:0,4:23,76:99,4:0.0388:2,0:26:1:33:1:0.57259:0:60:8:0.0392:0:2 0/1:96:38:1,37:4,54:58,38:0.3958:2,1:20.6:1:31.8:1:0.64512:2.716:60:76:0.4043:0:1.7 +13 28589509 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.94789;LSEQ=CAGACACTGTTGCAGGCACA;RSEQ=GGGCTGCGGCTGGGAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:4:0,4:26,51:77,4:0.0494:2,0:12:1:31.3:1:0.29993:0:60:8:0.05:0:2 0/1:75:29:3,26:6,40:46,29:0.3867:2,2:22:1:30.7:1:1:1.29557:60:58:0.3919:0:1.9 +13 28589662 . C G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10413;LSEQ=TGTTGGGGGGAGGGGTGGGG;RSEQ=GGCACCGAGAGAGCAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:238:235:179,56:0,0:0,235:0.9874:0,2:23.7:1:30.5:1:1:0:59.8:25.111:0.9956:0:1.2 1/1:393:350:249,101:27,11:38,350:0.8906:2,2:23.3:1:29.2:1:1:1.00:60:22.333:0.891:0:1.2 +13 28589905 . G T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50078;SOR=Inf;LSEQ=GACATGACTTCTTTTCTTTT;RSEQ=TATTAAGATGAAATGCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:18,132:150,0:0:2,0:24.4:1:32.7:1:1:0:60:149:1:0:0.1 0/1:172:2:1,1:14,154:168,2:0.0116:2,2:7:1:29:1:0.16916:10.66:60:4:0.0118:0:1 +13 28592165 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATAAATATTCATTAATTC;RSEQ=TATTTAAGTATTTAGCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28592546 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00166;SOR=1.66884;LSEQ=GTGAGTGCAGTTGTTTACCA;RSEQ=GATAACGACACAACACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:89:72,17:180,58:238,89:0.2722:2,2:21.7:1:31.6:1:0.37584:1.36:60:178:0.2738:0:1.2 0/1:411:158:116,42:169,84:253,158:0.3844:2,2:24.7:1:30.9:1:0.18692:1.37:60:157:0.3839:0:1.1 +13 28592796 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4973;SOR=Inf;LSEQ=GGAGTGCAATCTTTCTTCTA;RSEQ=ACTCAACTTCAGTAGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:4,88:92,0:0:1,0:24.2:1:32.6:1:1:0:60:45:1:0:0.1 0/1:93:2:1,1:8,83:91,2:0.0215:2,2:14:1:25:1:0.18513:9.84:60:4:0.0217:0:1 +13 28593787 . T C 38 d5;MAF0.05;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTTACCCCAGGTCTGCAACC;RSEQ=GCCTCCTCCTCCTGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:41.3:1:24.3:1:1:0:60:2:1:0:2.3 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:18:0:31:0:1:0:60:2:0.3333:0:1 +13 28597427 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49968;SOR=Inf;LSEQ=TAAAATAAACAAGAAAACAT;RSEQ=TATAAGCACATCTTTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:159,23:182,0:0:2,0:22.2:1:29:1:1:0:60:90:1:0:0.1 0/1:199:2:2,0:165,32:197,2:0.0101:2,0:25.5:1:33.5:1:1:0:60:4:0.0103:0:1 +13 28597447 . ATC A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1037;LSEQ=ATATAAGCACATCTTTTCAA;RSEQ=TTTTTTTTGGTTTGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:256:173:133,40:60,18:78,173:0.6758:2,2:24.7:1:31.4:1:1:1.0025:59.9:346:0.6758:0.1445:0.1 0/1:322:57:46,11:210,54:264,57:0.177:2,2:26.6:1:30.5:1:1:1.08:59.9:114:0.1792:0.0217:0.1 +13 28597839 . G A 64 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=0.33854;LSEQ=TTGGAACTGCTTTGATGACC;RSEQ=ATGACCTCCTGATTGATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:27.3:1:32:1:1:0:60:8:0.4444:0:1 0/1:5:1:0,1:1,3:4,1:0.2:2,0:30:0:32:0:1:0:60:2:0.2:0:1 +13 28598825 . T C 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90412;LSEQ=AAAATAGTCCTCAGTGTTTA;RSEQ=TAGTTGAATGTTGACATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:9,6:0.4:0,0:20.3:1:31.8:1:1:0:60:12:0.4:0:1 0/1:8:3:3,0:5,0:5,3:0.375:0,0:21.3:1:33.3:1:1:0:60:6:0.375:0:1 +13 28599112 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23838;SOR=Inf;LSEQ=TTTTGTTTTTTCATTATTTA;RSEQ=ATTATTCTTCTCAGCAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:44,141:185,0:0:2,0:23:1:32.4:1:1:0:60:184:1:0:0.1 0/1:177:2:1,1:46,129:175,2:0.0113:2,2:39.5:1:28.5:1:0.46167:2.79:60:4:0.0114:0:1 +13 28601389 . TAC T 207 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAATTGGTCCTGAAATAGT;RSEQ=AGTTTCAATTATAGGCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:93:23,70:64,148:212,93:0.3049:2,2:25.6:1:31.7:1:0.40864:1.31494:59.9:186:0.3079:0.0525:0.1 0/0:397:0:0,0:132,265:397,0:0:2,0:24.8:1:28.3:1:1:0:60:78.4:1:0:0.1 +13 28601621 . C T 50 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTTTTGTATGTGTGGCCTCA;RSEQ=CAATACCACTGGCCTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:1,0:1,3:0.75:0,0:21:1:32:0:0.25:0:60:6:0.75:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:30:0:32:0:1:0:60:2:1:0:0 +13 28601651 . T C 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCTCCTGGATTCTCCAG;RSEQ=TGGCAACTGAAAGTAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:3,2:0.4:0,2:20.5:1:31.5:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28601994 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTAACCACTCTCACCAC;RSEQ=CCTGTGCACCAGCTTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:28.5:1:32.5:1:1:0:45:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28602216 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49957;SOR=Inf;LSEQ=ACTGTGACTGAGAAAAGACA;RSEQ=AGAATTAAAAAGAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:134,10:144,0:0:2,0:21.7:1:30.7:1:1:0:60:47:1:0:0.4 0/1:159:2:1,1:139,17:156,2:0.0126:2,2:24.5:1:29:1:0.21551:7.97426:60:4:0.0127:0:1 +13 28602226 . AAG A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=11.000;MSILEN=2;SSF=0.75895;SOR=1.08395;LSEQ=AGAAAAGACAAAGAATTAAA;RSEQ=AGAGAGAGAGAGAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:178:91:77,14:17,1:18,91:0.5112:1,2:24.4:1:31:1:0.45757:3.06754:60:182:0.5141:0.0787:0.1 1/0:207:110:90,20:10,1:11,110:0.5314:2,2:23.7:1:29.8:1:0.68712:2.21047:59.9:220:0.5366:0.087:0.2 +13 28602256 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48204;SOR=0.89432;LSEQ=GAGAGAGAGAGAGCAAACAT;RSEQ=CTCTTTGTCATCAAGCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:114:83,31:161,65:226,114:0.3353:2,2:22.9:1:30.7:1:0.79959:1.08:59.9:37:0.3343:0:1.1 0/1:415:129:91,38:194,91:285,129:0.3108:2,2:23.6:1:29.6:1:0.64805:1.12:59.9:128:0.3168:0:1.1 +13 28602604 . T C 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.46553;LSEQ=AGCACTTTGGGAGGCCGAGG;RSEQ=GGGTGGATCACTTGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:0,9:9,4:0.3077:0,0:21:1:31.5:1:1:0:45:8:0.3077:0:1 0/1:5:2:0,2:0,3:3,2:0.4:0,0:10.5:1:32:0:1:0:51.5:4:0.4:0:1 +13 28607517 . T C 40 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCCTATAAAAACTAAA;RSEQ=AGGCCTGGCACAGTGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:18.7:1:25.7:1:1:0:58.7:2:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28607710 . G C 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGAGGAGCCTGAGCCCAG;RSEQ=GGGTGGAGGCTGCAGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:42.5:1:32.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28607916 . T A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36055;SOR=0.75055;LSEQ=CCATTTTTAGCCTTGAAACA;RSEQ=GGCAAACAGTAACCATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:45:44,1:31,2:33,45:0.5769:2,1:20.2:1:30.3:1:0.57056:2.80:59.6:21.5:0.5658:0:1.5 1/0:93:47:46,1:45,1:46,47:0.5054:1,1:21:1:29.6:1:1:1.02:60:94:0.5109:0:1.5 +13 28607989 . T G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=0.53651;LSEQ=AACTGTGCCTCCCATTTTTG;RSEQ=GCATCTTTGTTGCTGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:390:260:182,78:87,43:130,260:0.6667:2,2:25.4:1:31.2:1:0.56247:1.15:60:85.667:0.6658:0:1.2 1/0:516:267:175,92:161,88:249,267:0.5174:2,2:25.5:1:30.2:1:0.85369:1.04:60:65.75:0.5157:0:1.2 +13 28608459 . T C 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTGTACTTGTGACAAAT;RSEQ=AGCAGGGTTAAAACGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:244,218:462,0:0:2,0:26.9:1:29.8:1:1:0:59.9:230:1:0:0.1 0/1:752:32:16,16:385,335:720,32:0.0426:2,2:26.2:1:31.1:1:0.7207:1.14904:60:64:0.0427:0:1.2 +13 28608709 . G A 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02795;SOR=0;LSEQ=CCCACAGACAATCAGGCAAT;RSEQ=TCCCTGTAAAGGATACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:0,11:0,12:12,11:0.4783:0,0:22.4:1:31:1:1:0:60:22:0.4783:0:1 0/0:8:0:0,0:0,8:8,0:0:0,0:20.6:1:32.5:1:1:0:60:16:1:0:0.3 +13 28608811 . T G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACAAGAATTACATCTGG;RSEQ=CCAGGCACGATGGCTCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:35:1:32.3:1:1:0:51.7:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28609396 . T C 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.63707;SOR=2.00059;LSEQ=TCCATGGAGATTCACCACAC;RSEQ=GGGAGTTTCTGCTTCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:5,6:0.5455:0,0:18.3:1:32:1:1:0:60:12:0.5455:0:2 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:20.4:1:32.4:1:1:0:60:10:0.7143:0:2 +13 28609399 . G C 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.52862;LSEQ=ATGGAGATTCACCACACTGG;RSEQ=AGTTTCTGCTTCTCCCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:5,8:0.6154:0,0:15.3:1:32.1:1:1:0:60:16:0.6154:0:1.9 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:22.4:1:33.2:1:1:0:60:10:0.7143:0:2 +13 28609813 . G GA 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.87263;SOR=1.07541;LSEQ=GTGATCTCTTCTGTGCAGCT;RSEQ=AAAAAAAAAATAGCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:17:7,10:117,216:333,17:0.0478:2,2:28:1:31.1:1:0.61145:1.29:60:34:0.0494:0:1.2 0/1:469:24:10,14:165,275:440,24:0.0512:2,2:27.6:1:28.5:1:0.6717:1.19:59.2:23:0.0516:0.0021:0.9 +13 28609825 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38576;LSEQ=GTGCAGCTGAAAAAAAAAAT;RSEQ=GCAAAGAATTTAGACAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:314:216:66,150:32,66:98,216:0.6879:2,2:23.5:1:31.6:1:0.79276:1.10158:60:107:0.6926:0:1.7 0/1:392:180:57,123:67,144:211,180:0.4592:2,2:22:1:29.9:1:1:1.00401:59.7:21.5:0.4526:0:1.7 +13 28609846 . A T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37445;LSEQ=GCAAAGAATTTAGACAGGTG;RSEQ=GCTGTCATCAGATTGGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:221:151:34,117:19,51:70,151:0.6833:2,2:22.5:1:30.2:1:0.49938:1.2805:60:302:0.6895:0:1.9 0/1:242:108:16,92:33,101:134,108:0.4463:2,2:22.5:1:29.2:1:0.07629:1.87391:59.6:107:0.4534:0:2.1 +13 28609991 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13894;SOR=0.73642;LSEQ=AAATATTTCATCATTTCCTC;RSEQ=TAAACTGTATTCATGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:202:126:108,18:62,14:76,126:0.6238:2,2:23.3:1:31.6:1:0.43452:1.35:60:62:0.6231:0:2 1/0:222:122:105,17:82,18:100,122:0.5495:2,2:21.3:1:30.5:1:0.46118:1.35:60:121:0.5576:0:2.1 +13 28609997 . T C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05163;SOR=0.69094;LSEQ=TTCATCATTTCCTCTTAAAC;RSEQ=GTATTCATGAAAGAGTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:221:140:121,19:65,16:81,140:0.6335:2,2:23.7:1:31.3:1:0.25348:1.56:60:45.667:0.6343:0:1.9 1/0:261:142:116,26:93,26:119,142:0.5441:2,2:21.3:1:29.9:1:0.53469:1.25:60:70:0.5469:0:1.9 +13 28610183 . A G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.40739;LSEQ=CGAGCACTTGAGGTTTCCCT;RSEQ=TAGAAAAGAACGTGTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:349:234:64,170:34,81:115,234:0.6705:2,2:24.9:1:32.3:1:0.70441:1.11461:60:77:0.6676:0:1.1 0/1:521:236:80,156:96,188:284,236:0.453:2,2:24.6:1:31.3:1:1:1.00:60:472:0.4538:0:1.1 +13 28610219 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17634;SOR=0;LSEQ=GAAATAAGCTCACTGGCTGG;RSEQ=CATAGTGGTTCACTCCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:30,135:165,2:0.012:2,2:17:1:26.5:1:0.33771:4.44:60:4:0.0121:0:2 0/0:230:0:0,0:47,183:230,0:0:2,0:20.7:1:31.2:1:1:0:60:229:1:0:0.5 +13 28610355 . T A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26923;SOR=0;LSEQ=TAATAAAATAAAATAAGCTC;RSEQ=TGGAGTATGGTACTTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:0,19:1:0,1:22.7:1:31.3:1:1:0:59.5:18:1:0:1 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:13.7:1:29.8:1:1:0:58:12:0.8571:0:1.3 +13 28611149 . A G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.45755;SOR=2.19472;LSEQ=AAAATAACATAAAAAATAAA;RSEQ=AGATATATGATCAATGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:6,0:6,8:0.5714:0,0:20.4:1:33.9:1:1:0:60:16:0.5714:0:1 1/0:20:15:15,0:5,0:5,15:0.75:0,1:23:1:32.5:1:1:0:60:30:0.75:0:1.1 +13 28611186 . G C 138 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02753;LSEQ=CCAGTAGATATGAGAGTAAA;RSEQ=TTTCAAAACACTTCAGCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:20:20,0:25,0:25,20:0.4444:1,1:23.9:1:32:1:1:0:60:19:0.4318:0:2 0/1:48:1:1,0:47,0:47,1:0.0208:1,0:19:0:34:0:1:0:60:2:0.0208:0:3 +13 28611215 . GT G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=13.67538;LSEQ=CACTTCAGCGTACAAAAACA;RSEQ=TTTGTAGTAGCCCTTCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:4:4,0:33,0:33,4:0.0556:1,0:13.8:1:31.8:1:1:0:60:8:0.0597:0.0417:1.3 0/1:80:36:36,0:41,1:42,36:0.45:1,1:25.8:1:30.7:1:1:0:60:72:0.4675:0.1125:0.1 +13 28611219 . TGT GC 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGCGTACAAAAACAGTTT;RSEQ=AGTAGCCCTTCTAAGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:31:31,0:33,0:33,31:0.4306:1,1:26.8:1:31.5:1:1:0:60:30:0.4478:0.0972:0.8 0/0:80:0:0,0:41,1:42,0:0:1,0:25.3:1:28.2:1:1:0:60:20:0.5195:0:0.2 +13 28611450 . G A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09302;SOR=0;LSEQ=TTGAAAAAGAATTAAAGACA;RSEQ=ATTTAGCCCAATTGCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:3,0:82,199:281,3:0.0105:2,0:8.7:1:24.3:1:0.02615:0:52.7:2:0.0071:0:3 0/0:344:0:0,0:107,237:344,0:0:2,0:22.5:1:30.8:1:1:0:60:343:1:0:0.1 +13 28611480 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21677;SOR=Inf;LSEQ=AATTGCTACAGGAGATGCTG;RSEQ=AACTAATGACAGTGTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:32,166:198,0:0:2,0:21.1:1:31.9:1:1:0:60:38.6:1:0:0.1 0/1:173:2:1,1:39,131:170,2:0.0116:2,2:25.5:1:27:1:0.41208:3.33:60:4:0.0116:0:1 +13 28611489 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.219;SOR=Inf;LSEQ=AGGAGATGCTGCAACTAATG;RSEQ=CAGTGTGCATGGGAGGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:18,144:162,0:0:2,0:22:1:30.1:1:1:0:60:161:1:0:0.1 0/1:143:2:1,1:27,114:141,2:0.014:2,2:21:1:29:1:0.35438:4.16:60:4:0.0141:0:1 +13 28611669 . C T 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAGATTTCAGGTCCCTT;RSEQ=CAAATCACTGACTCAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:22.6:1:27.8:1:1:0:60:10:1:0:1.6 1/1:2:2:0,2:0,0:0,2:1:0,0:20.5:1:29:0:1:0:60:4:1:0:1 +13 28611710 . A G 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATTTTAAGATGATCACC;RSEQ=TGTGAGTCATATGCCCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:24.7:1:34.3:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28622356 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=6.98223;LSEQ=AAACTGTCCTTCTCAAGGGC;RSEQ=ACAAGCAAGGAGAATTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:47:37,10:69,19:88,47:0.3481:2,2:22.6:1:30.6:1:1:1.02:60:94:0.3534:0:1 1/0:176:139:105,34:30,6:36,139:0.7898:2,2:24.7:1:29.5:1:0.37971:1.61494:60:68.5:0.7874:0:1.1 +13 28623180 . A T 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACTAGTATTTATTGTCC;RSEQ=TTTTGTGTCAGGCTCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:13.3:1:32.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28623588 . G A 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.37032;SOR=0.39994;LSEQ=CAAGTGTAGTATCCGGTGTC;RSEQ=TTTCTTGCCACTGATGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:144,148:292,3:0.0101:2,2:19.3:1:27.7:1:0.61991:2.05:60:6:0.0102:0:1 0/0:491:2:1,1:240,248:488,2:0.0041:2,2:3:1:26:1:1:1.03:60:4:0.0041:0:1 +13 28623699 . G T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22131;LSEQ=GTTTTAATAAAACAGAGTTT;RSEQ=CATTTAATGTTTTCAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:294:184:120,64:66,44:110,184:0.6259:2,2:22.5:1:30.6:1:0.38379:1.25:60:368:0.6259:0:1.5 0/1:456:123:69,54:197,135:332,123:0.2697:2,2:21.9:1:29:1:0.59243:1.14169:60:60.5:0.2677:0:1.6 +13 28623759 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21637;LSEQ=CTGCATTTTCAGAATACAAA;RSEQ=TTGTCCTATTACCTCCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:527:310:180,130:122,94:216,310:0.5882:2,2:27:1:30.7:1:0.72098:1.07:59.9:102.333:0.587:0:1.3 0/1:797:188:96,92:323,286:609,188:0.2359:2,2:25.7:1:29.3:1:0.67632:1.08221:60:61.667:0.2366:0:1.4 +13 28623938 . G GA 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.30951;LSEQ=GATGAAAACATCCCAAGTGA;RSEQ=AAAAAAAAAGTGATTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:84:18,66:16,78:94,84:0.4541:2,2:28.2:1:30.9:1:0.56718:1.33:59.8:83:0.4486:0.0324:0.2 0/1:191:39:9,30:38,109:147,39:0.2042:2,2:27.3:1:28.9:1:0.83709:1.16119:60:78:0.2097:0.0052:0.1 +13 28624294 . G A 244 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=104.82043;LSEQ=TGGCACAGCACCTTATGTCC;RSEQ=TCCCAAATAATTCATGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:836:3:3,0:398,435:833,3:0.0036:2,0:21.3:1:29.3:1:0.10993:0:60:6:0.0036:0:1.3 0/1:1108:304:150,154:400,403:803,304:0.2744:2,2:25.4:1:29.6:1:0.89308:1.01901:59.9:75:0.2745:0:1.2 +13 28624374 . G T 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTACAGCTGCAATTAGAAAA;RSEQ=AAGTACCATTTGGCTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:92,259:351,0:0:2,0:23.9:1:32.4:1:1:0:60:174.5:1:0:0.1 0/1:490:24:7,17:153,313:466,24:0.049:2,2:20.7:1:28:1:0.82542:1.1867:60:48:0.0495:0:1.1 +13 28624407 . AC A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01109;SOR=Inf;LSEQ=GCTAAACAAGTTTTAAAATT;RSEQ=AAATGAATGCTCAAGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:22,153:175,0:0:2,0:22.9:1:32.4:1:1:0:59.8:86.5:1:0:0.1 0/1:228:8:1,7:39,181:220,8:0.0351:2,2:31.6:1:30.6:1:1:1.50589:60:16:0.0356:0:0 +13 28624587 . C T 97 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11739;SOR=0.13795;LSEQ=CACTAAGGAGAATTACATAA;RSEQ=AAAACAGTTTAAAATTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:4,11:0.7333:0,0:22.7:1:28.3:1:1:0:57.3:22:0.7333:0:1.9 0/1:4:1:0,1:1,2:3,1:0.25:2,0:16:0:29:0:1:0:60:2:0.25:0:1 +13 28626325 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCACAACCTTTGCCTCCC;RSEQ=GGTTCAAGAGATTCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:27:1:29:1:1:0:48:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28631647 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.21491;SOR=0;LSEQ=TTTTGGAAAATGTGTGAAAC;RSEQ=AAAAACAAAATTTCATAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:14,115:129,2:0.0153:2,2:28.5:1:32.5:1:0.21668:7.97:60:4:0.0154:0:1 0/0:151:0:0,0:15,135:150,0:0:2,0:19.8:1:28.2:1:1:0:60:149:0.9933:0:0 +13 28635285 . G A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGATCATCTGAGGTCAG;RSEQ=AGTTCGAAGCCAGCCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:36:0:30:0:1:0:52:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:27:1:1:0:60:4:1:0:1 +13 28635909 . C CA 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.22257;SOR=0.5705;LSEQ=CAGAGAGAGACCCTGACTCA;RSEQ=AAAAAAAAAAGGTTTACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:15:13,2:109,16:125,15:0.1064:2,2:21:1:28.7:1:1:1.04773:57.9:14:0.1053:0.0426:0.6 0/1:189:12:9,3:152,23:175,12:0.0635:2,2:16.3:1:29.3:1:0.22266:2.19117:60:24:0.0659:0.0265:0 +13 28636084 . G A 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69777;SOR=1.40362;LSEQ=CAGGAAATGTTCCCTGGGGC;RSEQ=TCGACCAGCACTTGCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:607:604:291,313:1,0:1,604:0.9951:0,2:24.7:1:30.7:1:0.48264:0:60:74.5:0.9967:0:1.1 1/1:851:848:399,449:0,0:0,848:0.9965:0,2:24:1:29.6:1:1:0:60:120.143:1:0:1.1 +13 28636312 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09802;LSEQ=ATGCATGCTGACACACTGCA;RSEQ=GCAACACCCACACAAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:44:1,43:0,21:21,44:0.6769:1,1:25.9:1:30.8:1:1:0:60:88:0.6769:0:1.5 0/1:36:6:0,6:2,28:30,6:0.1667:2,0:25.5:1:29.3:1:1:0:60:12:0.1714:0:1.8 +13 28636354 . C T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04875;SOR=0.24106;LSEQ=ACCCACTGAGAACACGTTGC;RSEQ=GACTGAAGGTCCTATTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:21:0,21:0,11:11,21:0.6563:0,1:24.1:1:31.5:1:1:0:60:42:0.6563:0:2 0/1:13:4:0,4:0,9:9,4:0.3077:0,0:27.5:1:27.3:1:1:0:60:8:0.3077:0:2.3 +13 28636446 . G A 83 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTACGGACTGTCATGGCGT;RSEQ=TGTCCCCCTACCTCTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:19.4:1:29.9:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28644510 . C A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTGGTACCAGATGTGAGG;RSEQ=CATAATATACTTAAATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:58:58,0:0,0:0,58:1:0,1:23.4:1:30.2:1:1:0:60:57:1:0:1.1 1/1:44:44:44,0:0,0:0,44:1:0,1:25.3:1:29.1:1:1:0:60:88:1:0:1 +13 28644538 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20448;SOR=0;LSEQ=TACTTAAATACATAAAGAGA;RSEQ=GCCCATTTAGCCATGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:83,3:86,2:0.0227:1,2:23.5:1:31:1:0.08934:24.1044:60:4:0.0233:0:1.5 0/0:106:0:0,0:100,6:106,0:0:2,0:20:1:30:1:1:0:60:105:1:0:0.5 +13 28644563 . A G 33 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61354;SOR=0.47044;LSEQ=ATTTAGCCATGGTAGGCTTC;RSEQ=ATAACTTACAAATTACGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:148,37:185,2:0.0107:2,2:12:0:33:1:0.36599:3.96033:60:4:0.0107:0:1.5 0/0:198:1:1,0:160,37:197,1:0.0051:2,0:20:0:31:0:1:0:60:2:0.0051:0:1 +13 28644610 . A C 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAAAACAGCTAAAGGTATA;RSEQ=TTTTAATGTTACTTTACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:39:24,15:234,125:359,39:0.098:2,2:24.8:1:32.5:1:0.72449:1.16952:60:38:0.0964:0:1.1 0/0:513:0:0,0:311,201:512,0:0:2,0:25.1:1:29.4:1:1:0:60:127:0.998:0:0.1 +13 28644830 . A G 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=Inf;LSEQ=ATTTATCTTGCAACCAAACA;RSEQ=CAAAACAAAGTGTAATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:2,54:56,0:0:1,0:27.3:1:30.6:1:1:0:60:55:1:0:0 0/1:43:13:0,13:1,29:30,13:0.3023:1,1:22:1:30.5:1:1:0:60:12:0.2927:0:1.3 +13 28644885 . T C 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02158;SOR=Inf;LSEQ=ATGAAAGTATGTAGGAAATT;RSEQ=GATTTTATGCAAGTTTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:0,20:20,0:0:1,0:27.2:1:31.7:1:1:0:60:40:1:0:0 0/1:14:4:0,4:0,10:10,4:0.2857:0,0:40.3:1:28.8:1:1:0:60:8:0.2857:0:1.3 +13 28645341 . A T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTAGTAGAGACGGGGT;RSEQ=TCGCCACGTTAGCCAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:29:0:1:0:21.5:4:1:0:1 +13 28674453 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12884;SOR=Inf;LSEQ=GTGGGCGAGTCCGGAGGGCG;RSEQ=GAAAGAGGGGAGGGGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:11,0:11,0:0:0,0:29.5:1:33.6:1:1:0:60:22:1:0:0 0/1:19:5:3,2:12,2:14,5:0.2632:2,2:24.2:1:28.2:1:0.27219:3.66084:60:10:0.2632:0:1 +13 28674526 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50714;SOR=Inf;LSEQ=CGAGGCGGCTGGGCCGGAGG;RSEQ=GGCGCGCGCCCGGGTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:32,37:69,0:0:2,0:27.9:1:29.7:1:1:0:60:33.5:1:0:0.1 0/1:92:2:1,1:40,50:90,2:0.0217:2,2:17:1:28.5:1:1:1.25:60:4:0.0222:0:1 +13 28674528 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.18135;SOR=0;LSEQ=AGGCGGCTGGGCCGGAGGAG;RSEQ=CGCGCGCCCGGGTCCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:30,36:66,2:0.0294:2,2:21:1:30:1:1:1.20:60:4:0.0303:0:2 0/0:91:0:0,0:41,50:91,0:0:2,0:28.3:1:29.9:1:1:0:60:44.5:1:0:0.2 +13 28674533 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.08503;SOR=0;LSEQ=GCTGGGCCGGAGGAGGCGCG;RSEQ=GCCCGGGTCCACACTGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:3:1,2:31,40:71,3:0.0405:2,2:17.7:1:27.7:1:1:1.5412:60:6:0.0435:0:2 0/0:93:0:0,0:41,52:93,0:0:2,0:30.2:1:29.1:1:1:0:60:45.5:1:0:0.2 +13 28674558 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=1.28541;LSEQ=GGGTCCACACTGCGGGGTGG;RSEQ=GGCTGAGGGACCGCGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:0,1:44,57:101,1:0.0098:2,0:1:0:25:0:1:0:60:2:0.0101:0:3 0/1:159:2:1,1:73,84:157,2:0.0126:2,2:42.5:1:28.5:1:1:1.15:60:4:0.0126:0:1 +13 28674579 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51559;SOR=Inf;LSEQ=GGCTGAGGGACCGCGAGGGG;RSEQ=TGCGAGCGAGCGAGCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:52,71:123,0:0:2,0:22.3:1:32.8:1:1:0:59.8:60.5:1:0:0.5 0/1:179:2:1,1:79,98:177,2:0.0112:2,2:9.5:1:28.5:1:1:1.24:60:4:0.0113:0:1 +13 28674580 . TGCGA T 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.51408;SOR=Inf;LSEQ=GCTGAGGGACCGCGAGGGGC;RSEQ=GCGAGCGAGCGGGGCCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:52,71:123,0:0:2,0:22.3:1:32.5:1:1:0:59.8:60.5:1:0:0.5 0/1:176:2:1,1:75,99:174,2:0.0114:2,2:36:0:33:1:1:1.32:60:4:0.0116:0:0 +13 28674589 . G T 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.16473;SOR=0.17552;LSEQ=CCGCGAGGGGCTGCGAGCGA;RSEQ=CGAGCGGGGCCTTACCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:4:2,2:49,69:118,4:0.0328:2,2:31:1:32.8:1:1:1.40:60:8:0.0333:0:1.5 0/0:170:1:0,1:74,94:168,1:0.0059:2,0:1:0:22:0:1:0:60:2:0.006:0:1 +13 28674591 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.51307;SOR=Inf;LSEQ=GCGAGGGGCTGCGAGCGAGC;RSEQ=AGCGGGGCCTTACCGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:50,68:118,0:0:2,0:22.4:1:31.2:1:1:0:60:236:1:0:0.5 0/1:167:2:1,1:73,92:165,2:0.012:2,2:20.5:1:27:1:1:1.26:60:4:0.012:0:2.5 +13 28674611 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51533;SOR=Inf;LSEQ=GAGCGGGGCCTTACCGAGCA;RSEQ=CGGCAGCTGGCCGCCGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:43,53:96,0:0:2,0:23.9:1:32.7:1:1:0:60:47:1:0:0.6 0/1:140:2:1,1:63,74:137,2:0.0143:2,2:39.5:1:26.5:1:1:1.17:60:4:0.0145:0:2 +13 28674618 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51529;SOR=Inf;LSEQ=GCCTTACCGAGCAGCGGCAG;RSEQ=TGGCCGCCGTCGCGCGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:39,43:82,0:0:2,0:25.8:1:32.7:1:1:0:60:40:1:0:0.7 0/1:120:2:1,1:56,61:117,2:0.0167:2,2:28.5:1:29.5:1:1:1.09:60:4:0.0168:0:1 +13 28674626 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16615;SOR=0;LSEQ=GAGCAGCGGCAGCTGGCCGC;RSEQ=GTCGCGCGCCAACGCCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:32,36:68,2:0.0286:2,2:37:0:32.5:1:1:1.12:60:4:0.0299:0:1.5 0/0:101:0:0,0:50,51:101,0:0:2,0:23.2:1:29.8:1:1:0:60:49.5:1:0:0.5 +13 28674628 . T C 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00388;SOR=0.31859;LSEQ=GCAGCGGCAGCTGGCCGCCG;RSEQ=CGCGCGCCAACGCCGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:23:10,13:23,24:47,23:0.3286:2,2:26:1:31.2:1:0.79989:1.24193:60:22:0.3188:0:1.5 0/1:97:13:7,6:41,42:83,13:0.134:2,2:27.8:1:31.7:1:1:1.19:60:26:0.1383:0:1.3 +13 28674630 . G A 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.57039;SOR=0.34962;LSEQ=AGCGGCAGCTGGCCGCCGTC;RSEQ=CGCGCCAACGCCGGCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:31,35:66,2:0.0294:2,2:15:0:32.5:1:1:1.13:60:4:0.0308:0:1.5 0/1:96:1:1,0:47,48:95,1:0.0104:2,0:1:0:27:0:1:0:60:2:0.0109:0:1 +13 28674704 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGCCCTGCGATGCCGCCT;RSEQ=GAGCGGCGCGCCTCGCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:18,0:0:2,0:27.3:1:30.6:1:1:0:60:17:1:0:0.3 0/1:38:2:1,1:20,16:36,2:0.0526:2,2:8.5:1:30:0:1:1.24262:60:4:0.0541:0:1.5 +13 28674713 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.09512;SOR=0;LSEQ=CGATGCCGCCTGGAGCGGCG;RSEQ=GCCTCGCGCTGCAGGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:29.5:1:29.5:1:1:1.18321:60:4:0.1538:0:1 0/0:28:0:0,0:15,11:26,0:0:2,0:31.5:1:30:1:1:0:60:52:0.9286:0:0.2 +13 28877146 . CA C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.25657;SOR=0;LSEQ=GGAGTTACATTCTTGTTAGT;RSEQ=AAAAAAAAAAAGCACTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:3,0:26,2:28,3:0.0938:2,0:23.3:1:31.9:1:1:0:60:6:0.0968:0.0313:0 0/0:23:0:0,0:22,0:22,0:0:1,0:22.7:1:29.4:1:1:0:57.1:21:0.9545:0:0.8 +13 28877518 . AG A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.12245;SOR=Inf;LSEQ=CTCTCAAGCTAAAGAAAGAA;RSEQ=GAAAGAAATCAAATATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:51,170:221,0:0:2,0:22.8:1:31.6:1:1:0:60:109.5:1:0:0.1 0/1:219:3:2,1:66,150:216,3:0.0137:2,2:18:1:27.3:1:0.22824:4.51:60:6:0.0137:0.0046:0.3 +13 28877629 . A AC 102 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.32927;SOR=0.48206;LSEQ=CTAGAGTTCATGGTTTTGGA;RSEQ=CCCCCCCCCCCTCAATTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:0,11:1,11:12,11:0.4583:2,0:27.7:1:29.5:1:1:0:59.5:10:0.4545:0.0417:1.2 0/1:14:4:1,3:0,10:10,4:0.2857:0,2:27.8:1:22.7:1:0.28571:0:60:1:0.1667:0.0714:0.5 +13 28880609 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAAGATTTTCTGCATG;RSEQ=TTTCCCCAGAGCTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:2,0:27,0:27,2:0.069:1,0:23:1:32.5:1:1:0:60:4:0.0714:0:1 0/0:13:0:0,0:12,1:13,0:0:1,0:20.2:1:28.5:1:1:0:60:26:1:0:0.2 +13 28881158 . G A 90 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATACATTTAGGCAAAAGGG;RSEQ=AAATGGCAAGTAACAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:27.7:1:32.1:1:1:0:60:14:1:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:20:0:32:0:1:0:60:2:1:0:1 +13 28881375 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCCCCCAGCCCTTGGTCATG;RSEQ=TCTCCAGCAATTAGACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:44:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:18:0:31:1:1:0:60:4:1:0:1.5 +13 28881464 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTAATACGGCATGTTCCA;RSEQ=TAAGTGGATCCCACGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:36:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28882948 . G A 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0.27013;LSEQ=CTGAAGAAGGGGTCTATCGG;RSEQ=GTGCACTAGGTACCTTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:629:607:373,234:12,8:20,607:0.965:2,2:24.9:1:30.5:1:1:1.06:60:36.938:0.9673:0:1.1 1/1:625:551:332,219:43,26:69,551:0.8816:2,2:25.4:1:28.7:1:0.79476:1.09081:59.9:49.091:0.8795:0:1.1 +13 28883061 . G A 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2103;LSEQ=ATGAACTTGAAAGCATTTAC;RSEQ=TATCTAATGAAGAAACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:495:477:151,326:6,12:18,477:0.9636:2,2:25.2:1:30.9:1:1:1.0793:46.8:94.4:0.9633:0:1.1 1/1:545:462:163,299:31,52:83,462:0.8477:2,2:24.9:1:29.6:1:0.71064:1.09338:46.5:76:0.8476:0:1.1 +13 28883337 . A G 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATCAGAGAATGCCAGAC;RSEQ=TAGGAGAGACTGGAGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:30.7:1:33.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28885408 . C A 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCAACAATAGCCTTCTT;RSEQ=CAAAATGTATACTAAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:12:1:28.7:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28885452 . C T 97 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGTAAAGTGCTATTATGC;RSEQ=TTAAGCCTCCTTTTAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:7,1:1,0:1,8:0.8889:0,2:25.8:1:32.6:1:1:0:60:16:0.8889:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:23:0:32:0:1:0:60:2:1:0:1 +13 28885589 . ATCTT A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=4.000;MSILEN=4;SSF=0.20126;SOR=Inf;LSEQ=TATGGGTGGTGATCAACATA;RSEQ=TCTTTCTTTCTTTCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:51,0:51,0:0:1,0:23.9:1:31.9:1:1:0:55.1:102:1:0:0.5 0/1:42:2:2,0:40,0:40,2:0.0476:1,0:40.5:1:32:0:1:0:60:4:0.0476:0:0.5 +13 28885593 . TTCTTTCTTTCTTTCTC T 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.0029;SOR=0;LSEQ=GGTGGTGATCAACATAATCT;RSEQ=TCTTTCTTTCTTTCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:9:9,0:42,0:42,9:0.1765:1,0:29.2:1:32.3:1:1:0:46.7:18:0.1765:0.0196:1 0/0:46:0:0,0:46,0:46,0:0:1,0:23.2:1:31.4:1:1:0:58.3:92:1:0:0.5 +13 28885672 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03246;LSEQ=TTCTCTTTCGTCTTTCTTTC;RSEQ=TTCTTTTTTTTGTTGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:249:246:205,41:0,0:0,246:0.988:0,2:24.1:1:32.1:1:1:0:59.1:245:0.9919:0:1.1 1/1:257:254:200,54:0,0:0,254:0.9883:0,2:22.8:1:30.1:1:1:0:59.7:83.667:0.9882:0:1.1 +13 28885675 . C CT 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.62358;SOR=2.99446;LSEQ=TCTTTCGTCTTTCTTTCCTT;RSEQ=TTTTTTTTGTTGGAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:1,0:213,45:258,1:0.0038:2,0:13:0:34:0:1:0:60:2:0.004:0:1 0/1:264:3:1,2:203,55:258,3:0.0114:2,2:11.7:1:28.7:1:0.12114:7.30616:60:6:0.0116:0.0038:1 +13 28885997 . TAC T 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.81251;LSEQ=TTTGAGAAGATAATTCTGTA;RSEQ=ACACACACACACCCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:4:2,2:76,75:151,4:0.0258:2,2:36.5:1:31.5:1:1:1.01325:60:8:0.026:0:0 0/1:95:2:2,0:46,46:92,2:0.0211:2,0:30:1:29.5:1:0.49485:0:60:4:0.0213:0:0 +13 28886013 . CT C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.1401;SOR=Inf;LSEQ=TGTATACACACACACACACC;RSEQ=TTTTTTAAACTTCTGATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:104,64:168,0:0:2,0:23.3:1:31.8:1:1:0:59.7:83:1:0:0.4 0/1:101:2:2,0:65,34:99,2:0.0198:2,0:33:1:32.5:1:0.54891:0:60:4:0.0204:0:0 +13 28886032 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16132;SOR=Inf;LSEQ=CCTTTTTTTAAACTTCTGAT;RSEQ=TCAGCTATTATATTAATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:132,49:181,0:0:2,0:25.8:1:32.4:1:1:0:59.9:44.25:1:0:0.7 0/1:122:2:1,1:97,23:120,2:0.0164:2,2:21.5:1:29:1:0.35605:4.14982:60:4:0.0168:0:1.5 +13 28886056 . T TA 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.74304;SOR=0.84885;LSEQ=GCTATTATATTAATAGCTCT;RSEQ=AAAAAAAAAACAAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:24:16,8:176,60:236,24:0.0923:2,2:25:1:28.8:1:0.46461:1.46435:59.5:48:0.0927:0.0231:1 0/1:214:17:14,3:152,44:196,17:0.0794:2,2:22.9:1:27.6:1:0.76964:1.35:60:16:0.0755:0.0047:1.1 +13 28886113 . A G 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26407;SOR=2.8277;LSEQ=TTCAAAGGCATTTTGATGTA;RSEQ=ATAAATTTAGTTTTACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:680:675:413,262:0,1:1,675:0.9926:0,2:27.2:1:32.7:1:0.38905:0:54:66.5:0.9985:0:1.1 1/1:766:764:457,307:1,0:1,764:0.9974:0,2:26.3:1:30.8:1:1:0:53.9:46.75:0.9987:0:1.2 +13 28886388 . A G 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28955;SOR=5.18096;LSEQ=ATTTTTAGGTTTGGGTTTAT;RSEQ=GCACCAGCACTTAAAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:1:0,1:0,39:39,1:0.025:1,0:16:0:33:0:1:0:60:2:0.027:0:1 0/1:25:3:0,3:1,21:22,3:0.12:1,0:22.7:1:32.3:1:1:0:60:6:0.12:0:1 +13 28891487 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34437;SOR=0;LSEQ=CCCAGCATATCTGGGCCTGA;RSEQ=GGGCTGAGGGGAGCATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:99:99:99,0:0,0:0,99:1:0,1:22.8:1:32.3:1:1:0:60:32:1:0:1.1 1/1:52:51:50,1:0,0:0,51:0.9808:0,1:23:1:31.6:1:1:0:60:102:0.9808:0:1.2 +13 28891815 . C A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17795;SOR=Inf;LSEQ=GAGGGGACAATTCAGTGTTT;RSEQ=TTTCCTCCCTTTAAAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:2,170:172,0:0:1,0:24.1:1:33.6:1:1:0:60:85:1:0:0.1 0/1:126:2:1,1:7,116:123,2:0.0159:2,2:20:0:29.5:1:0.12439:15.56:60:4:0.016:0:1.5 +13 28893377 . A C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATCATATAAAGCCCTTTT;RSEQ=CAGTAGAGGGCAGACATGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:29,0:29,2:0.0645:1,0:24.5:1:33:0:1:0:60:4:0.0645:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:22.7:1:27.3:1:1:0:60:12:1:0:0 +13 28893484 . T C 237 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTTCTAATCTAAAGGCTGTC;RSEQ=AACCAAAGGACATTCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:188:188:146,42:0,0:0,188:1:0,2:22.6:1:31.4:1:1:0:60:93:1:0:1.1 1/0:188:136:105,31:44,7:51,136:0.7234:2,2:24.9:1:30.2:1:0.22155:1.85017:60:135:0.7258:0:1 +13 28893526 . G T 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12541;SOR=5.60293;LSEQ=AGATGCAGACATTTATTTCT;RSEQ=GGCTGTTTGATTTCTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:0,1:247,143:390,1:0.0026:2,0:1:0:15:0:0.36829:0:60:0:0:0:3 0/1:424:6:2,4:253,165:418,6:0.0142:2,2:15:1:27.5:1:0.22181:3.05844:60:12:0.0144:0:1 +13 28893642 . A G 185 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=72.00504;LSEQ=ATTTTGTCAAAGATAGATTC;RSEQ=GGAGCCATCCATTTCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:509:1:0,1:207,301:508,1:0.002:2,0:18:0:27:0:1:0:60:2:0.002:0:1 0/1:603:75:34,41:233,295:528,75:0.1244:2,2:24.8:1:29.8:1:0.90131:1.05:59.3:74:0.1242:0:1.1 +13 28893719 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49872;SOR=Inf;LSEQ=AGAAGGGCATGAAAACAAAG;RSEQ=ACATTCAACCCGAGTGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:31,158:189,0:0:2,0:23.8:1:32.3:1:1:0:60:46.25:1:0:0.1 0/1:192:2:1,1:47,143:190,2:0.0104:2,2:17.5:1:30:1:0.43848:3.02:60:4:0.0105:0:2 +13 28895524 . G C 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGGGACTACAGCTGAGGAA;RSEQ=TGTAAATATTTACCAAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:191,23:214,0:0:2,0:23.4:1:33.1:1:1:0:60:70.333:0.9953:0:0.1 0/1:231:27:23,4:163,41:204,27:0.1169:2,2:21.5:1:31.6:1:0.61415:1.44:60:26:0.1145:0:1.1 +13 28901505 . C T 44 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08397;SOR=Inf;LSEQ=GTTTTAAGTTTAATCATTAA;RSEQ=AACACAATACAGGTTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:236,22:258,0:0:2,0:23.2:1:32.5:1:1:0:60:257:1:0:0.1 0/1:202:3:1,2:181,18:199,3:0.0149:2,2:5:1:28.3:1:0.02639:19.44549:60:6:0.0149:0:1 +13 28901750 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50048;SOR=Inf;LSEQ=CCAGTCAGCCATTTGCCAGC;RSEQ=TTCAGCCTGCCTGAGAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:21,148:169,0:0:2,0:24.7:1:32.8:1:1:0:60:83.5:1:0:0.1 0/1:191:2:1,1:32,157:189,2:0.0105:2,2:45:1:30:1:0.31645:4.85:60:4:0.0106:0:2 +13 28901759 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21734;SOR=0;LSEQ=CATTTGCCAGCCTTCAGCCT;RSEQ=CCTGAGAAACCTCAAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:13,120:133,2:0.0148:2,2:14.5:1:31:1:0.19735:8.93:60:4:0.0148:0:1 0/0:154:0:0,0:25,129:154,0:0:2,0:24.1:1:31.6:1:1:0:60:37.5:1:0:0.1 +13 28903707 . G T 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45145;SOR=0.40202;LSEQ=GGCAGAGAACTGTTCTCCCA;RSEQ=CCTGTGCAGGGGGAGACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:5:2,3:328,148:476,5:0.0104:2,2:13:1:29.6:1:0.18091:3.31513:60:10:0.0105:0:1.2 0/0:476:2:0,2:311,163:474,2:0.0042:2,0:1:0:25:0:0.11968:0:60:4:0.0043:0:1 +13 28903895 . G A 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCAAGGAAGAGTCAGGGC;RSEQ=ACAGGACAATGGGGCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:96,298:394,0:0:2,0:24.2:1:31.4:1:1:0:59.9:196:1:0:0.1 0/1:373:22:3,19:94,257:351,22:0.059:2,2:29.5:1:30.8:1:0.21596:2.31221:60:44:0.0595:0:1.1 +13 28904316 . G T 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGGGCAGAATGGCTACT;RSEQ=TTGTAAACATCTTTGCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:21:1:31.5:1:1:0:53.5:8:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28912726 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAGTGAAACTTAAATGA;RSEQ=TCCCCTAGGGCTTTCTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:30.5:1:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28912964 . G C 44 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAATGCCTCTCTCTCCGCC;RSEQ=CCCTTCACTTACCACTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:12.3:1:28:1:1:0:56.7:6:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:32:0:1:0:49:4:1:0:1.5 +13 28913463 . C A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11153;SOR=Inf;LSEQ=AAATAAAGAGATCTCAAAGT;RSEQ=ATCGAGAAGAAAACAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:65,241:306,0:0:2,0:22.7:1:32.3:1:1:0:60:101:1:0:0.1 0/1:285:3:2,1:77,205:282,3:0.0105:2,2:6:1:25.7:1:0.18696:5.29:60:6:0.0106:0:1 +13 28913502 . G A 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18338;SOR=4.8023;LSEQ=TTACAAATCCTAGATATTCC;RSEQ=TTAACATCCACTGTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:1:0,1:13,121:134,1:0.0074:2,0:27:0:14:0:1:0:60:0:0:0:6 0/1:115:4:0,4:8,102:110,4:0.0348:2,0:22.3:1:30.5:1:1:0:60:8:0.0351:0:1.8 +13 28919218 . T G 33 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCAAAGTGCTGGGATTACAG;RSEQ=CATGTACCACCGTGCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:40:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:33:1:1:0:27:4:1:0:4 +13 28919223 . TA AG 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTGCTGGGATTACAGTCATG;RSEQ=CCACCGTGCCCAGTCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:25:1:31.5:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:32.5:1:1:0:27:4:1:0:3 +13 28919330 . G A 86 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31818;SOR=0.14907;LSEQ=AGACTCTATTAACATATTTT;RSEQ=TATCAAAAATACCTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:1,9:0.9:0,0:20.3:1:27.4:1:1:0:59.9:18:0.9:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:26:0:30:0:1:0:60:2:0.5:0:1 +13 28919462 . T C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02173;SOR=0;LSEQ=TGTGTTCACCAGGTCAGAGA;RSEQ=AGGAATGAGAGGGAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:81:79,2:0,0:0,81:1:0,1:25.8:1:32.8:1:1:0:60:162:1:0:1 1/1:52:48:48,0:4,0:4,48:0.9231:0,1:23.2:1:31.9:1:1:0:60:96:0.9412:0:1.1 +13 28919696 . G A 57 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.03365;SOR=Inf;LSEQ=TTGTCCGAGGTTCCTGGAGA;RSEQ=AAAAAAAATCACAATAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:128,296:424,0:0:2,0:25.4:1:32.3:1:1:0:60:83.8:0.9929:0:0.1 0/1:500:6:5,1:174,318:492,6:0.012:2,2:5.2:1:22.3:1:0.02451:9.10:60:2:0.0081:0:1.8 +13 28931455 . G A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=TTCTGGGAACGACTTCTCCC;RSEQ=CAGACACTGTGTTCGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:6:1:29.5:1:1:0:60:4:0.1818:0:1 0/0:6:0:0,0:5,1:6,0:0:2,0:14.5:1:28.8:1:1:0:60:12:1:0:0.2 +13 28931611 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49825;SOR=Inf;LSEQ=GACTGGAGCAGGCAGCAGGA;RSEQ=ACTGGGAGGTGGAAAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:121,21:142,0:0:2,0:25.3:1:32.6:1:1:0:60:46.333:1:0:0.1 0/1:143:2:1,1:116,25:141,2:0.014:2,2:7.5:1:28:1:0.33163:4.56949:60:4:0.0141:0:1 +13 28942716 . TATG T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.52511;SOR=0.80156;LSEQ=ATGATGATAATGATGATAGC;RSEQ=ATGATGATGATGATGACGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:504:21:13,8:377,105:482,21:0.0417:2,2:24.5:1:30.5:1:0.10513:2.20541:60:42:0.0423:0.0119:0.2 0/1:594:20:15,5:402,171:573,20:0.0337:2,2:25.3:1:30.2:1:0.80513:1.28:60:40:0.0342:0.0017:0 +13 28942736 . CGAT C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0;SOR=4.00077;LSEQ=TATGATGATGATGATGATGA;RSEQ=GATGATGATGATGACAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:753:12:8,4:476,262:738,12:0.0159:2,2:28.3:1:31.5:1:1:1.10:60:24:0.0161:0.0027:0.1 0/1:969:59:30,29:552,355:907,59:0.0609:2,2:24.9:1:29.7:1:0.13303:1.5024:59.5:28.5:0.0596:0.0072:0.4 +13 28943002 . C T 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.36441;SOR=2.57642;LSEQ=CAGGTGCCCACCACCATACC;RSEQ=GGCTAATTTTTGTGTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:0,16:16,2:0.1111:1,0:12:1:32:1:1:0:38:4:0.1111:0:1.5 0/1:12:3:0,3:0,9:9,3:0.25:0,0:29:1:31:0:1:0:22.3:6:0.25:0:1 +13 28958893 . A AT 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03213;SOR=Inf;LSEQ=TTGCTATCAGCATGAACCAG;RSEQ=TCCCAGTGTTTGGGGCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:94,2:96,0:0:1,0:25.5:1:30.5:1:1:0:60:47:1:0:0.2 0/1:72:4:4,0:66,2:68,4:0.0556:1,0:29:1:31.5:1:1:0:60:8:0.0571:0.0139:0.5 +13 28958955 . C A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00512;SOR=1.74125;LSEQ=ACTGGAAGCAGGTGACGGGA;RSEQ=TGTTAAGGGAAAGGGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:50:38,12:206,72:278,50:0.1524:2,2:21.2:1:30.3:1:0.86149:1.11:60:49:0.1541:0:1 0/1:352:84:65,19:193,73:266,84:0.2386:2,2:20.3:1:28.7:1:0.47721:1.29:60:27:0.2382:0:1.1 +13 28959273 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51521;SOR=0;LSEQ=AGAAACAGCAAAACTCAACT;RSEQ=TTAGGTTTCATTTTCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:1,77:78,2:0.025:1,2:24:1:30.5:1:0.04968:54.82:60:4:0.025:0:1 0/0:54:0:0,0:2,52:54,0:0:1,0:23.5:1:30.4:1:1:0:60:53:1:0:0 +13 28963676 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92922;LSEQ=CCCCCCGGAGCAGCCCCCTC;RSEQ=GCCTGAATGGGGGGCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:23:22,1:8,0:8,23:0.7419:0,1:24.8:1:30.2:1:1:0:60:22:0.7333:0:1 1/0:11:8:8,0:3,0:3,8:0.7273:0,0:25.5:1:29.9:1:1:0:60:16:0.7273:0:1.1 +13 28963702 . G A 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=1.19131;LSEQ=AATGGGGGGCCCAGAGCTGG;RSEQ=GCCCGGGGGTCTCATTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:6:6,0:41,2:43,6:0.1224:1,0:32.3:1:30.8:1:1:0:60:12:0.125:0:1 0/1:21:3:3,0:17,1:18,3:0.1429:1,0:21.7:1:29.7:1:1:0:60:6:0.15:0:1 +13 28964198 . C T 128 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=0.14334;LSEQ=AGTTTCAGGTCCTCTCCTTC;RSEQ=GTCGGCATTTTTTCCAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:18:6,12:179,295:474,18:0.0366:2,2:28.1:1:30.7:1:0.8076:1.21306:60:36:0.0369:0:1.2 0/0:555:3:1,2:238,314:552,3:0.0054:2,2:22.7:1:25.7:1:1:1.51483:60:6:0.0055:0:1 +13 28964325 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07053;LSEQ=AAAGATCTTAAGAATTGTTC;RSEQ=TGCACAAATTATCTCAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:63:2,61:0,5:5,63:0.9265:0,1:22.7:1:31:1:1:0:59:30.5:0.9242:0:1.1 0/1:56:26:0,26:0,30:30,26:0.4643:1,1:22.7:1:30.7:1:1:0:60:52:0.4643:0:1 +13 28970917 . C T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05352;SOR=0;LSEQ=AGAATACAGGGAAATAACTC;RSEQ=TTACGAGATCCGATGAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:37,1:0,0:0,38:1:0,1:22.4:1:33.4:1:1:0:60:76:1:0:1 1/1:24:21:21,0:3,0:3,21:0.875:0,1:22.1:1:30.8:1:1:0:60:42:0.875:0:1 +13 28970996 . TA T 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.75373;SOR=0.74336;LSEQ=GTTTGACAATTCTATGGAAT;RSEQ=AAAAAAAATCACTCAAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:6:6,0:133,4:137,6:0.042:1,0:21.3:1:31.7:1:1:0:60:12:0.0423:0.007:0 0/1:127:4:4,0:112,11:123,4:0.0315:2,0:23:1:31.2:1:1:0:60:8:0.0317:0.0079:0 +13 28971220 . G A 194 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02893;LSEQ=AGCCATCTGCAAAAGAAAAG;RSEQ=AAACTTTAGCTAGCAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:76:17,59:43,162:205,76:0.2705:2,2:24:1:31.1:1:0.86998:1.09:60:152:0.2714:0:1.1 0/1:284:3:3,0:78,202:280,3:0.0106:2,0:1:0:24:1:0.02283:0:60:6:0.0107:0:1 +13 28973703 . C T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGACCTGTGTAGGTAAC;RSEQ=TGGGAATGGCCGTGGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:25.3:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28979545 . C T 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCAGTGATTCTCAATCCC;RSEQ=GTTAGGTACTGGAATCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 28979837 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.367;SOR=0.32264;LSEQ=TGAACATTTAAATTACTTCT;RSEQ=GTGCCAATAAACCTAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:219,37:256,3:0.0116:2,2:13.7:1:28.7:1:0.37998:2.94221:60:6:0.0118:0:1.3 0/0:266:1:1,0:191,74:265,1:0.0038:2,0:43:0:29:0:1:0:60:2:0.0038:0:1 +13 28980036 . T TA 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.76642;SOR=1.13966;LSEQ=GGAACAAAAGTCACACCTAT;RSEQ=AAAAAAAAAAGTTGTCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:22:6,16:69,216:285,22:0.0712:2,2:23.3:1:29.3:1:0.79732:1.17:59.8:21:0.0705:0.0032:0.7 0/1:336:27:8,19:83,222:305,27:0.0804:2,2:30:1:29.4:1:0.82279:1.13:60:54:0.0831:0:0 +13 28980065 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=Inf;LSEQ=AAGTTGTCACAATGTGGCTT;RSEQ=ACAGCATGGTTCAGTCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:23,155:178,0:0:2,0:22.6:1:28.8:1:1:0:59.7:88:1:0:0.2 0/1:193:2:1,1:26,164:190,2:0.0104:2,2:9:1:27.5:1:0.26211:6.21:60:4:0.0104:0:1 +13 28980150 . A AG 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.48303;LSEQ=AGTCACAAATTTTATGTGTG;RSEQ=TCTTCTTTTCCTTAGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:44:0,44:0,1:1,44:0.9778:0,1:24.2:1:32.6:1:1:0:60:43:0.9773:0.2:0.1 1/1:22:21:0,21:0,1:1,21:0.9545:0,1:19.7:1:32:1:1:0:60:42:0.9545:0.2273:0 +13 29001208 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50898;SOR=Inf;LSEQ=ATATACAGTACATCCCACAT;RSEQ=CAGATTCCCATCTGCGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:95,18:113,0:0:2,0:21.7:1:31.9:1:1:0:60:36.667:1:0:0.1 0/1:152:2:2,0:128,22:150,2:0.0132:2,0:24:1:31.5:1:1:0:60:4:0.0132:0:1 +13 29001476 . G A 29 v3;p8;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59918;SOR=0.43164;LSEQ=CTGGAAAGGAGATGAAGAAC;RSEQ=GGACAGAAGTCAAGAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:44,149:193,2:0.0103:2,2:6:0:29.5:1:0.4092:3.36:60:4:0.0104:0:1 0/0:225:1:1,0:59,165:224,1:0.0044:2,0:1:0:27:0:0.26667:0:60:2:0.0045:0:1 +13 29001586 . T A 28 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15;SOR=Inf;LSEQ=ACAAGAAACAAAAAAACAAA;RSEQ=AAACCCTCCTATTTGTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:6,28:34,0:0:2,0:26.8:1:28:1:1:0:60:16:1:0:0.2 0/1:22:2:1,1:0,20:20,2:0.0909:1,2:5:0:28.5:1:0.09091:0:60:4:0.0952:0:0 +13 29001721 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCGCCTATGGAATACAA;RSEQ=AAACAAACACGAGATTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:32,7:39,2:0.0488:2,0:24.5:1:31:1:1:0:60:4:0.0488:0:2.5 0/0:19:0:0,0:19,0:19,0:0:1,0:24.5:1:32.1:1:1:0:60:38:1:0:0 +13 29001807 . G T 26 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00509;LSEQ=ATTTTGCTATCTTTGATGTT;RSEQ=TTACGCTGATTTTTGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:181,16:197,2:0.0101:2,2:25:1:28:1:0.16395:11.00534:60:4:0.0102:0:1 0/1:198:2:1,1:172,23:195,2:0.0101:2,2:1.5:1:26:1:0.22936:7.34332:60:4:0.0102:0:1 +13 29002081 . TA T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21703;SOR=Inf;LSEQ=GTGGTTAAAAACATGATCAG;RSEQ=AGTCATTTCACACGGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:38,185:223,0:0:2,0:22.5:1:30.5:1:1:0:60:110.5:1:0:0.1 0/1:195:2:0,2:34,159:193,2:0.0103:2,0:13:1:28:1:1:0:60:4:0.0105:0.0051:3 +13 29002098 . C A 32 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32379;SOR=3.86074;LSEQ=CAGTAAGTCATTTCACACGG;RSEQ=CTCTCAATATCACTTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:1:1,0:16,143:159,1:0.0063:2,0:1:0:25:0:0.10625:0:60:2:0.0064:0:1 0/1:126:3:1,2:15,108:123,3:0.0238:2,2:14.7:1:20.3:1:0.33696:3.54:60:2:0.0161:0:1.3 +13 29004064 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.19501;SOR=Inf;LSEQ=AGAATCTACAGAGTTCTGAG;RSEQ=TCTCTGGGGCTGTCTGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:54,1:55,0:0:1,0:27.2:1:32.6:1:1:0:60:110:1:0:0.1 0/1:44:2:2,0:41,1:42,2:0.0455:1,0:16:1:30.5:1:1:0:60:4:0.0476:0:1 +13 29004123 . G C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06198;SOR=Inf;LSEQ=TCAGGAATTCGAGTCATTAG;RSEQ=CTCTTGCAGCTTCCCACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:152,25:177,0:0:2,0:24.1:1:31.5:1:1:0:60:58:1:0:0 0/1:193:5:4,1:150,37:187,5:0.0259:2,2:24.6:1:31.8:1:1:1.01344:60:10:0.0263:0:1 +13 29012114 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATACATAACATTTTTCA;RSEQ=GATTTCAGTTCTTTCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:11,0:11,3:0.2:0,0:20.7:1:30:1:1:0:60:6:0.2143:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:30:1:28.8:1:1:0:57.5:3:1:0:0.3 +13 29012584 . G A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5131;SOR=0;LSEQ=GTAGGCATTGCCACAGTCAC;RSEQ=TCATTCTCCCTTAATGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:0,2:0,47:47,2:0.0408:1,0:26:1:33:0:1:0:60:4:0.0417:0:1 0/0:33:0:0,0:1,32:33,0:0:1,0:19.2:1:30.4:1:1:0:60:66:1:0:0 +13 29041007 . A T 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGACTCATTTGCAAAGCAA;RSEQ=AGCAAACAGAATGTAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:160,49:209,0:0:2,0:24.5:1:30.3:1:1:0:60:40.8:1:0:0.1 0/1:232:21:19,2:150,61:211,21:0.0905:2,2:22.1:1:30.5:1:0.07106:3.85:60:42:0.0925:0:1.1 +13 29041544 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53231;SOR=0;LSEQ=AAGCTGGATGCCTATGGTTT;RSEQ=CACTTTGCAGATCACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:2,0:92,11:103,2:0.019:2,0:18:1:30:0:1:0:60:4:0.0194:0:1 0/0:61:0:0,0:60,1:61,0:0:1,0:7:0:14:0:1:0:60:0:0:0:7 +13 29041581 . C A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04583;SOR=Inf;LSEQ=GGAGATCACTGAGGTCCCTA;RSEQ=CTTTTTACTCTGCCAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:164,34:198,0:0:2,0:23.1:1:32.1:1:1:0:60:65:1:0:0.1 0/1:172:4:4,0:137,31:168,4:0.0233:2,0:29.3:1:30.5:1:1:0:60:8:0.0241:0:1 +13 29041776 . T C 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00092;SOR=Inf;LSEQ=TGAAAAACAAATTTTTAAAA;RSEQ=GTATTATTTGTAAATTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:60,215:275,0:0:2,0:22.5:1:30.7:1:1:0:60:90.667:1:0:0.1 0/1:291:11:2,9:67,213:280,11:0.0378:2,2:21:1:30.3:1:1:1.41392:60:22:0.0381:0:1.7 +13 29041794 . T C 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01572;SOR=Inf;LSEQ=AATGTATTATTTGTAAATTG;RSEQ=CTTCTTACCTTTTTTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:17,153:170,0:0:2,0:25.1:1:30.6:1:1:0:60:84:1:0:0.1 0/1:190:7:0,7:28,154:182,7:0.0368:2,0:23.9:1:31.3:1:0.59648:0:60:14:0.0372:0:2.3 +13 29041826 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10797;SOR=Inf;LSEQ=TTTTTAAGTTATCTTTCCAT;RSEQ=AAGGTGAGTTTTTCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:3,85:88,0:0:1,0:24.5:1:32.5:1:1:0:60:43:1:0:0.1 0/1:81:3:0,3:4,74:78,3:0.037:2,0:30.3:1:30.7:1:1:0:60:6:0.0375:0:2.7 +13 29068175 . A C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CACGGACTGGACCGCGCACC;RSEQ=CGCCTGCTCCCGGCAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:32.5:1:1:0:60:4:1:0:1.5 +13 29069018 . C A 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05108;SOR=0;LSEQ=CTGCTCGCCCGGTGCCCGCG;RSEQ=TCCCCGCGGCCAACGACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:4:3,1:41,145:186,4:0.0211:2,2:24.8:1:26.5:1:0.03934:10.44:60:3:0.016:0:2.8 0/0:208:0:0,0:62,146:208,0:0:2,0:24.7:1:31.7:1:1:0:60:103:1:0:0.2 +13 29069024 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49905;SOR=Inf;LSEQ=GCCCGGTGCCCGCGCTCCCC;RSEQ=CGGCCAACGACCCGGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:33,129:162,0:0:2,0:22.9:1:31.9:1:1:0:60:53:0.9938:0:0.3 0/1:174:2:1,1:48,124:172,2:0.0115:2,2:18.5:1:28:1:0.48508:2.57:60:4:0.0117:0:1 +13 29069039 . G A 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02556;SOR=0.17709;LSEQ=TCCCCGCGGCCAACGACCCG;RSEQ=CCGCCAGAGTCCGTCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:9:3,6:18,73:91,9:0.09:2,2:15.8:1:29.7:1:0.39198:2.01:60:18:0.0909:0:1.1 0/1:117:2:1,1:30,85:115,2:0.0171:2,2:7.5:1:26.5:1:0.46139:2.80:60:4:0.0175:0:1 +13 29678908 . AT A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03905;SOR=0;LSEQ=CCATAGCTTTTCAAAAAAAT;RSEQ=TTACATTGAAAGAGGGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:4:3,1:144,148:292,4:0.0135:2,2:22:1:27.5:1:0.36908:3.07:60:8:0.0137:0.0068:2.3 0/0:368:0:0,0:174,194:368,0:0:2,0:23.9:1:29.3:1:1:0:60:60.333:1:0:0.9 +13 29678920 . A G 258 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04742;LSEQ=AAAAAAATATTTACATTGAA;RSEQ=GAGGGAACGTAATTTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:290:281:133,148:3,6:9,281:0.969:2,2:24.2:1:31.8:1:0.5087:1.79:60:55.2:0.9684:0:1.7 1/0:339:202:91,111:64,72:136,202:0.5959:2,2:24.4:1:30.6:1:0.73932:1.08399:60:49.5:0.5928:0:1.8 +13 29678955 . G A 238 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.034;LSEQ=TTCTAACTTAGAAATTAAGC;RSEQ=TAAACTTAACATATCGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:226:220:82,138:1,5:6,220:0.9735:2,2:26.8:1:30.7:1:0.41831:2.96:60:109:0.9732:0:1.8 1/0:271:150:56,94:50,70:120,150:0.5535:2,2:24.9:1:29.4:1:0.53088:1.19816:60:49:0.5485:0:2 +13 29678976 . G T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25026;SOR=Inf;LSEQ=TAAACTTAACATATCGGTCT;RSEQ=ACCCAGGATGTGGCTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:56,128:184,0:0:2,0:25.3:1:32.1:1:1:0:60:368:1:0:1.6 0/1:205:3:1,2:73,129:202,3:0.0146:2,2:43:1:23.7:1:1:1.13113:60:2:0.0099:0:1.3 +13 29678997 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12419;SOR=Inf;LSEQ=ACCCAGGATGTGGCTCCTTA;RSEQ=TTCTTTTATAATGTTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:32,101:133,0:0:2,0:24.3:1:32.6:1:1:0:60:132:1:0:1.2 0/1:147:4:2,2:41,102:143,4:0.0272:2,2:30.8:1:29.8:1:0.58063:2.47:60:8:0.0274:0:2.3 +13 29679002 . T C 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24903;SOR=Inf;LSEQ=GGATGTGGCTCCTTAGTTCT;RSEQ=TTATAATGTTCAGAGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:24,94:118,0:0:2,0:24.9:1:30.7:1:1:0:60:117:1:0:1.1 0/1:131:3:1,2:38,90:128,3:0.0229:2,2:13.3:1:24:1:1:1.18:60:2:0.0154:0:2 +13 29679010 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49768;SOR=Inf;LSEQ=CTCCTTAGTTCTTTTATAAT;RSEQ=TTCAGAGATGAAAAAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:22,83:105,0:0:2,0:23.6:1:32.1:1:1:0:60:51.5:1:0:1 0/1:107:2:1,1:30,75:105,2:0.0187:2,2:7.5:1:27.5:1:0.49744:2.48:60:4:0.019:0:1 +13 29679113 . A G 128 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05263;SOR=0;LSEQ=AGTGTCGGAAACATACTATT;RSEQ=CCTAATGTGTATAGGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:0,15:1:0,1:26.3:1:32.8:1:1:0:58.6:30:1:0:1.5 1/0:5:3:0,3:0,2:2,3:0.6:0,0:7.7:1:26.3:1:1:0:60:2:0.5:0:1.3 +13 29679161 . G A 100 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=AATCAGAAAATCTGAAATTC;RSEQ=AAATGCTCCAAAACCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:25.6:1:31.8:1:1:0:60:18:1:0:2.1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:40:0:33:0:1:0:60:2:0.3333:0:2 +13 29679209 . T C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GAACACTGACACGATGCCCA;RSEQ=GGGAAATAGTCACTGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:21.7:1:31.3:1:1:0:60:6:1:0:1.7 0/0:2:0:0,0:0,2:2,0:0:0,0:36.5:1:29.5:1:1:0:60:4:1:0:0 +13 30073814 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTTTTATATCCTTAGCTTG;RSEQ=CATCTCAGGCAGGAACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:10,0:0:2,0:19.7:1:31.1:1:1:0:60:20:1:0:0.1 0/1:26:2:1,1:8,16:24,2:0.0769:2,2:9:0:30.5:1:1:1.94:60:4:0.0769:0:1.5 +13 30440094 . G T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12401;SOR=Inf;LSEQ=TCTCATCCTCCCAGGGGATG;RSEQ=CCTACTGCCCTCCTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:186,129:315,0:0:2,0:26.7:1:31.7:1:1:0:59.2:314:1:0:0.1 0/1:325:4:2,2:203,118:321,4:0.0123:2,2:18.8:1:28.8:1:0.62792:1.71725:60:8:0.0125:0:1 +13 30440177 . G A 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00131;SOR=Inf;LSEQ=TGAAGCGGTCCACAGAGCTA;RSEQ=AGAGGCAATTTTCAGTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:119,184:303,0:0:2,0:27.3:1:32.3:1:1:0:59.8:100:0.9934:0:0.1 0/1:364:11:8,3:151,200:351,11:0.0302:2,2:30.3:1:29:1:0.06529:3.52:60:22:0.0306:0:1.2 +13 30440216 . G A 49 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12586;SOR=Inf;LSEQ=GAGAGTCTAGGCATTTCCCT;RSEQ=GCTTCTCCACACATCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:45,141:186,0:0:2,0:23.6:1:31.2:1:1:0:59.8:25.571:1:0:0.1 0/1:210:4:3,1:56,148:204,4:0.019:2,2:7.5:1:24.8:1:0.06994:7.84:60:8:0.0197:0:1 +13 32183909 . G A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11097;SOR=3.10858;LSEQ=GGTATAAGAATTTGAAAGGC;RSEQ=TTGTCTGATTTCAGAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:4,4:6,8:14,8:0.3636:2,2:31.5:1:29.8:1:1:1.32:24.4:16:0.381:0:1.8 1/0:17:11:4,7:3,3:6,11:0.6471:2,2:21.9:1:28.8:1:0.64367:1.692:23.2:10:0.625:0:1.5 +13 32183944 . C T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCTTTCCTGTAAACGC;RSEQ=GGGCAGCATCTCATACTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:0,11:1:0,2:32.4:1:27.5:1:1:0:23.1:4.5:1:0:1.5 1/1:7:7:1,6:0,0:0,7:1:0,2:35.1:1:29.3:1:1:0:24:6:1:0:1.7 +13 32507296 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23097;SOR=0;LSEQ=CTGACCTCCCTAATAGGATA;RSEQ=CATTTCATCAAGGTGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:73,6:79,2:0.0247:2,2:23:1:31.5:1:0.16636:11.34129:60:4:0.0253:0:1 0/0:87:0:0,0:79,8:87,0:0:2,0:24.4:1:32.3:1:1:0:60:86:1:0:0 +13 32507426 . T C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00064;SOR=1.73359;LSEQ=TTGTTAACTTTTGGTTGTTT;RSEQ=CTGTCTAGTTTGAGGACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:86:39,47:147,157:304,86:0.2205:2,2:27.9:1:31.5:1:0.62749:1.12802:60:85:0.2214:0:1.1 0/1:404:133:63,70:123,148:271,133:0.3292:2,2:25.7:1:30.3:1:0.75035:1.08:60:132:0.33:0:1.1 +13 32507524 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23579;SOR=Inf;LSEQ=TATGCCAGAAGAGTGAAAAT;RSEQ=TATTTCTTTATTTGCCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:12,104:116,0:0:2,0:22.7:1:30.9:1:1:0:60:115:1:0:0.1 0/1:110:2:1,1:22,86:108,2:0.0182:2,2:25:1:30:1:0.37598:3.85:60:4:0.0183:0:1 +13 32507566 . AT A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05325;SOR=3.65225;LSEQ=AAATTGCAATTATAAAGACA;RSEQ=TCATTTAGCTTATATCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:41:0,41:1,12:13,41:0.7593:1,1:23.3:1:31.4:1:0.24074:0:60:82:0.7593:0.1667:0.1 1/1:38:35:0,35:0,3:3,35:0.9211:0,1:23.5:1:30.9:1:1:0:60:70:0.9211:0.1053:0 +13 32507665 . G A 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCATATGCGTTGGTTAC;RSEQ=TAGCATGAAGACCTATTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:38:1:32:1:1:0:60:12:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:15:1:28:1:1:0:60:4:1:0:1 +13 32747122 . C T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.76462;LSEQ=AAAGTAAATGTTTGAAAATT;RSEQ=GATTCAATAGTATCCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:76:32,44:123,127:250,76:0.2331:2,2:26.2:1:30.6:1:0.29638:1.33052:60:75:0.2351:0:1.1 1/0:410:219:108,111:97,93:190,219:0.5341:2,2:24.6:1:29.8:1:0.76642:1.0718:60:438:0.5381:0:1.1 +13 32747212 . C G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0632;LSEQ=GTGTAATACCAAGTGGTATA;RSEQ=ATGAAAGGAGTTGTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:50:9,41:18,56:74,50:0.4032:2,2:23.9:1:32.3:1:0.50735:1.45988:60:100:0.4032:0:1 0/1:148:6:2,4:34,108:142,6:0.0405:2,2:20.3:1:31:1:0.63336:1.58:60:12:0.0411:0:1 +13 32890572 . G A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.62364;LSEQ=TTTGCAGACTTATTTACCAA;RSEQ=CATTGGAGGAATATCGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:17:11,6:266,190:456,17:0.0359:2,2:24.3:1:28.8:1:0.80287:1.31:60:16:0.0342:0:1.1 0/1:513:61:39,22:253,199:452,61:0.1189:2,2:24:1:29.1:1:0.27156:1.39:60:122:0.1206:0:1.1 +13 32890587 . C T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=ACCAAGCATTGGAGGAATAT;RSEQ=GTAGGTAAAAATGCCTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:292,245:537,0:0:2,0:25.9:1:31.1:1:1:0:60:133.25:1:0:0.1 0/1:560:16:11,5:291,253:544,16:0.0286:2,2:23.9:1:29.1:1:0.31033:1.91:60:32:0.029:0:1 +13 32890716 . TA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.24046;SOR=0;LSEQ=TACACCGAGAAAGTGTTTTC;RSEQ=AAAAATGCTTGCTAAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:25,139:164,2:0.012:2,2:26.5:1:31:1:0.28952:5.47:60:4:0.0122:0:0 0/0:172:0:0,0:28,144:172,0:0:2,0:24.3:1:29.8:1:1:0:60:344:1:0:0.1 +13 32893197 . AT A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.67514;SOR=0.79505;LSEQ=CTGGTTAAAACTAAGGTGGG;RSEQ=TTTTTTTTTAAATAGATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:12:10,2:168,40:208,12:0.0543:2,2:19.8:1:30.8:1:1:1.19:60:24:0.0556:0.0136:0.3 0/1:275:12:8,4:201,62:263,12:0.0436:2,2:28.1:1:28.5:1:0.49008:1.61781:60:11:0.0404:0.0036:0.4 +13 32893214 . A T 33 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66303;SOR=0.5505;LSEQ=GGGATTTTTTTTTTAAATAG;RSEQ=TTTAGGACCAATAAGTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:218,79:297,3:0.01:2,2:13:1:21.3:1:1:1.37816:60:2:0.0071:0:3.3 0/0:362:2:0,2:248,111:359,2:0.0055:2,0:1:0:27:0:0.09738:0:60:4:0.0057:0:1 +13 32893514 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49894;SOR=0;LSEQ=ACTACAAACTAGGAATTTAG;RSEQ=CAAACCTGTGTTAAAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:38,131:169,2:0.0117:2,2:10:1:29:1:0.40516:3.42:60:4:0.0118:0:1 0/0:161:0:0,0:43,118:161,0:0:2,0:25.1:1:30.9:1:1:0:60:52.667:1:0:0.1 +13 32893527 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22243;SOR=Inf;LSEQ=AATTTAGGCAAACCTGTGTT;RSEQ=AAATCTTAGCTCATTCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:25,110:135,0:0:2,0:24:1:31:1:1:0:60:270:1:0:0 0/1:121:2:1,1:29,90:119,2:0.0165:2,2:35.5:1:31:1:0.43595:3.07:60:4:0.0165:0:1 +13 32893584 . CT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.5082;SOR=0;LSEQ=CAAATCAGTCTCTCTGGCCT;RSEQ=TTTTCCTCACTCGAAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:0,34:34,2:0.0556:1,0:8:1:31:1:1:0:60:4:0.0571:0.0278:0.5 0/0:25:0:0,0:1,24:25,0:0:1,0:26.9:1:29.7:1:1:0:60:50:1:0:0.1 +13 32893791 . A G 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTAAACTATATTTCTGCA;RSEQ=GCTATCACAGAGGACAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:22.2:1:32.8:1:1:0:52.6:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32899115 . C G 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18754;SOR=Inf;LSEQ=TCCCTATACATTCTCATTCC;RSEQ=AGTATAGAGGAGACTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:104,4:108,0:0:1,0:24.6:1:30.6:1:1:0:60:17:1:0:0.1 0/1:83:2:1,1:78,3:81,2:0.0241:1,2:7.5:1:28.5:1:0.09462:22.66097:60:4:0.0241:0:3 +13 32899388 . A C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0674;LSEQ=TACATATATTTGTTCTATAA;RSEQ=GATGAATCTGATTTTTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:49:3,46:3,51:54,49:0.4757:2,2:25.1:1:30.1:1:1:1.11:59.9:98:0.4757:0:1.2 0/1:158:9:1,8:12,137:149,9:0.057:2,2:21.6:1:30.3:1:0.54796:1.42:60:18:0.057:0:1 +13 32899468 . G T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02155;SOR=Inf;LSEQ=TTTAAATAATCTTTTAGGTT;RSEQ=AGTCCTTTAATAGAATAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:23,0:0:1,0:22.8:1:33.4:1:1:0:59.8:46:1:0:0.4 0/1:22:5:0,5:0,17:17,5:0.2273:1,0:18.8:1:28.2:1:1:0:60:10:0.2273:0:1 +13 32900149 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08577;LSEQ=TAGTATTCCAACAATTTATA;RSEQ=GAATGAGAATCTTCTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:63:52,11:61,11:72,63:0.4599:2,2:21.5:1:32:1:0.81698:1.17168:60:62:0.4627:0:1.1 0/1:163:11:10,1:122,30:152,11:0.0675:2,2:18.4:1:30.9:1:0.69192:2.45:60:22:0.0692:0:1 +13 32900933 . T A 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02754;SOR=0;LSEQ=GGAATAAATACAAATACATT;RSEQ=AGTGGTAGTCCAGTGGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:1,12:0,12:12,13:0.52:0,1:28:1:30.8:1:1:0:60:26:0.52:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:31.2:1:27.8:1:1:0:53.7:12:1:0:0 +13 32902941 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTTATCCAGAAGTCCTAC;RSEQ=CACAGTAAAGTTTGTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:30:1:1:0:60:4:1:0:1 +13 32903685 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08322;SOR=0.73325;LSEQ=TGCTAACAATTTTGGAATGC;RSEQ=TTGTTAAATTATTTATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:117:33,84:35,118:153,117:0.4317:2,2:22.7:1:31.1:1:0.32586:1.32:59.8:234:0.4317:0:1.1 0/1:288:103:29,74:64,121:185,103:0.3576:2,2:20.9:1:29.8:1:0.29412:1.34828:60:102:0.3579:0:1.1 +13 32905207 . G A 52 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.40908;SOR=3.5011;LSEQ=GAACTACAGGTTTTTTTGTT;RSEQ=TTGTTGTTTTGATTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:1:0,1:87,175:262,1:0.0038:2,0:18:0:29:0:1:0:60:2:0.0042:0:1 0/1:380:5:3,2:138,237:375,5:0.0132:2,2:11.8:1:22.8:1:0.3645:2.57:55.2:4:0.0111:0:2.4 +13 32905219 . AT A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00884;SOR=2.71092;LSEQ=TTTTTGTTGTTGTTGTTTTG;RSEQ=TTTTTTTTTTTGAGGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:9:3,6:46,129:175,9:0.0486:2,2:24.4:1:32.2:1:0.7019:1.40:60:18:0.0497:0.0054:0.6 0/1:287:35:11,24:80,162:242,35:0.122:2,2:29.5:1:30.8:1:1:1.07716:59.9:70:0.1224:0:0.4 +13 32905245 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.45079;LSEQ=TTTTTTTGAGGTGGAGTCTT;RSEQ=CTCTGTCACCCGTGATCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:1,0:16,77:93,1:0.0106:2,0:1:0:12:0:0.18085:0:60:0:0:0:1 0/1:130:2:1,1:23,105:128,2:0.0154:2,2:17:1:27.5:1:0.33631:4.49:60:4:0.0159:0:1.5 +13 32905265 . G A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTGTCACCCGTGATCTC;RSEQ=GTTTACCGCAACCTCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:68:1,67:0,0:0,68:1:0,1:21.1:1:31.9:1:1:0:59.1:67:1:0:1.3 1/1:81:81:3,78:0,0:0,81:1:0,1:22.8:1:30.6:1:1:0:59.4:39.5:1:0:1.3 +13 32906480 . A C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08838;LSEQ=ACATTGGAAAGTCAATGCCA;RSEQ=ATGTCCTAGAAGATGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:274:134,140:201,195:396,274:0.409:2,2:24.6:1:32:1:0.69443:1.0768:59.9:90.333:0.4087:0:1.1 0/1:730:42:18,24:334,353:687,42:0.0575:2,2:25.2:1:31.6:1:0.52625:1.26117:60:84:0.0583:0:1.1 +13 32906729 . A C 230 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTAGATTCAAATGTAGCA;RSEQ=ATCAGAAGCCCTTTGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:805:0:0,0:471,334:805,0:0:2,0:24.6:1:30.3:1:1:0:60:60.923:1:0:0.1 0/1:890:166:101,65:411,313:724,166:0.1865:2,2:24.1:1:31.3:1:0.38408:1.18:60:165:0.1864:0:1.1 +13 32906980 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.11044;LSEQ=ATTTCTAGCCTACCAAAATC;RSEQ=GAGAAGCCATTAAATGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:117:58,59:109,83:192,117:0.3786:2,2:25.1:1:30.8:1:0.24015:1.33462:59.8:116:0.3803:0:1.1 0/1:350:22:12,10:172,156:328,22:0.0629:2,2:23.3:1:29.2:1:1:1.09:60:44:0.063:0:1.1 +13 32907420 . GA G 77 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.76698;SOR=1.30358;LSEQ=TGATGAAACATCTTATAAAG;RSEQ=AAAAAAATACCGAAAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:4:2,2:272,218:490,4:0.0081:2,2:25.8:1:31:1:1:1.24714:60:8:0.0082:0.002:0.3 0/1:666:7:4,3:364,293:657,7:0.0105:2,2:15.9:1:27.7:1:1:1.07:60:14:0.0106:0.003:0.3 +13 32907535 . CT C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.78612;SOR=1.08105;LSEQ=GCTGATTCAGGTACCTCTGT;RSEQ=TTTTTTTTTTGTAAATAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:27:8,19:97,222:319,27:0.0771:2,2:30:1:33.1:1:1:1.03762:60:54:0.0806:0:0 0/1:374:31:10,21:101,237:338,31:0.0829:2,2:31.7:1:31.2:1:0.83837:1.12:60:62:0.0864:0:0.2 +13 32907767 . C T 39 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGTTTTATTTTAAGTTC;RSEQ=GGGGTACATGTGCAGGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:40:1:25:1:1:0:52.7:2:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32910056 . T G 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGAGACTGTCTCATTCTG;RSEQ=TACCTAGTCTGGAGTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:42.5:1:31.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32910328 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5691;SOR=0.88878;LSEQ=GTGCCCAAACACTACCTTTT;RSEQ=AACTTAGTGAAAAATATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:85:82,3:125,9:134,85:0.3881:2,1:23.1:1:33:1:0.37615:1.96:59.6:170:0.3917:0:1.1 0/1:258:93:82,11:145,20:165,93:0.3605:2,2:22:1:30.8:1:1:1.03:59.3:186:0.3605:0:1.1 +13 32910351 . G T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10265;LSEQ=CTTAGTGAAAAATATTTAGT;RSEQ=AATGTGATTGATGGTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:182:151,31:172,25:197,182:0.4802:2,2:23.3:1:30.6:1:0.24924:1.41115:60:90:0.4813:0:1.1 0/1:440:38:27,11:306,96:402,38:0.0864:2,2:22:1:28.7:1:0.55259:1.2978:60:76:0.087:0:1.1 +13 32910721 . T C 307 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09989;LSEQ=GCATGTCACCCAGTACAACA;RSEQ=TCAAAAGTGGAATACAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1597:675:340,335:462,459:921,675:0.4227:2,2:26.9:1:32.7:1:0.9596:1.01:60:83.375:0.4243:0:1.1 0/1:1865:127:65,62:842,895:1737,127:0.0681:2,2:24.8:1:31.3:1:0.58181:1.11:60:41.333:0.0673:0:1.1 +13 32911463 . A G 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0883;LSEQ=AAAAAAATAATGATTACATG;RSEQ=ACAAATGGGCAGGACTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1553:689:353,336:472,390:862,689:0.4437:2,2:23.5:1:31.8:1:0.18304:1.15186:60:75.556:0.4442:0:1.1 0/1:1780:117:62,55:859,801:1660,117:0.0657:2,2:21.5:1:30.2:1:0.84834:1.05:60:116:0.0661:0:1.2 +13 32911888 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.21649;LSEQ=GAATTTACTCAGTTTAGAAA;RSEQ=CCAAGCTACATATTGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1578:65:35,30:738,772:1510,65:0.0412:2,2:25.8:1:32.9:1:0.44964:1.22:60:64:0.0411:0:1.2 0/1:1731:317:159,158:704,708:1412,317:0.1831:2,2:24.8:1:31.5:1:0.95047:1.01:59.9:316:0.1836:0:1.1 +13 32912299 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=1.72711;LSEQ=AGTAAATGTCATGATTCTGT;RSEQ=GTTTCAATGTTTAAGATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1405:129:59,70:609,665:1274,129:0.0918:2,2:23.8:1:31.2:1:0.71155:1.08644:60:128:0.0919:0:1.1 0/1:1547:230:120,110:631,685:1316,230:0.1487:2,2:27.1:1:29.9:1:0.25284:1.18:60:56.5:0.147:0:1.1 +13 32912582 . A C 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TATTTACTGATCAGCACAAC;RSEQ=TATGTCTTAAATTATCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1568:0:0,0:785,782:1567,0:0:2,0:24.6:1:30.8:1:1:0:60:70.227:0.9994:0:0.2 0/1:1854:54:22,32:913,883:1796,54:0.0291:2,2:23.9:1:31:1:0.16735:1.50362:60:108:0.0294:0:1.1 +13 32912885 . G A 127 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.08569;LSEQ=ATAACTTTTCCTTAAATTCT;RSEQ=AATTACATTCTGACATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1573:21:10,11:763,788:1551,21:0.0134:2,2:21:1:29:1:1:1.06509:60:20:0.0128:0:1.1 0/0:1728:2:1,1:855,869:1724,2:0.0012:2,2:16:1:27:1:1:1.02:60:4:0.0012:0:1 +13 32913055 . A G 344 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09951;SOR=0.33793;LSEQ=AAGATCAAAGAACCTACTCT;RSEQ=TTGGGTTTTCATACAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1756:1753:864,889:0,0:0,1753:0.9983:0,2:24.4:1:32.4:1:1:0:60:145.083:0.9983:0:1.1 1/1:1984:1974:929,1045:3,0:3,1974:0.995:0,2:23.5:1:31.5:1:0.10459:0:60:140:0.9954:0:1.1 +13 32913562 . A C 188 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=54.19072;LSEQ=ACTTCATTACTTGAAGCAAA;RSEQ=AAATGGCTTAGAGAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1594:1:1,0:771,822:1593,1:6e-04:2,0:27:0:13:0:0.48432:0:60:0:0:0:4 0/1:1914:63:32,31:909,939:1848,63:0.0329:2,2:25.1:1:31.5:1:0.89817:1.07:59.3:126:0.0331:0:1.2 +13 32915005 . G C 337 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.13533;SOR=0.19931;LSEQ=TTGGTATTAGGAACCAAAGT;RSEQ=TCACTTGTTGAGAACATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1628:1627:789,838:0,0:0,1627:0.9994:0,2:25.4:1:32.8:1:1:0:59.9:100.688:0.9994:0:1.1 1/1:1951:1945:989,956:0,0:0,1945:0.9969:0,2:24.4:1:30.9:1:1:0:60:175.818:0.9969:0:1.1 +13 32915410 . CAATT C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=3.86076;LSEQ=CAGTAGACTTGGTATGCTAA;RSEQ=AAGAGTGTTATAAACTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1097:49:19,30:370,677:1047,49:0.0447:2,2:29.5:1:32.7:1:0.64814:1.16:58.7:98:0.0451:0.0018:0.1 0/1:1157:177:65,112:381,599:980,177:0.153:2,2:24:1:30.9:1:0.61534:1.09592:60:354:0.1542:0.0225:0 +13 32915524 . C A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=4.75745;LSEQ=TTCGTATACAGATTTGATAT;RSEQ=TTGGTATACAGATTCGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:7:0,7:2,140:142,7:0.047:1,0:19.6:1:31.9:1:1:0:60:14:0.0476:0:1 0/1:110:21:0,21:1,88:89,21:0.1909:1,1:17.5:1:30:1:1:0:60:20:0.1852:0:1.1 +13 32915806 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTCAGGAGATCGAGACC;RSEQ=TCCCGGCTAAAACGGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:24:1:34.5:1:1:0:39:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32916789 . A G 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGCTCCTAGGCTGCAAACCT;RSEQ=TACAGCATGTTACTGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:8:0:27:0:1:0:60:2:1:0:0 +13 32918941 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08578;SOR=0.37638;LSEQ=ACCTCTTTATACTCTTAAAA;RSEQ=TTACTGAGGACCTAAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:22:0,22:0,30:30,22:0.4231:1,1:23.8:1:32.2:1:1:0:60:21:0.42:0:1.6 0/1:28:6:0,6:0,22:22,6:0.2143:1,0:35.5:1:33.5:1:1:0:60:12:0.2143:0:1.7 +13 32918967 . G A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34993;SOR=0.45134;LSEQ=GAGGACCTAAAAGAGCATTT;RSEQ=TTTATGTGGAATATATCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:15:0,15:0,20:20,15:0.4286:1,1:20:1:31.8:1:1:0:60:30:0.4286:0:1.9 0/1:16:4:0,4:0,12:12,4:0.25:0,0:27.3:1:32.3:1:1:0:60:8:0.25:0:2 +13 32920844 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAACATTTATTGAGCATC;RSEQ=GTTACATTCACTGAAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:67:66,1:0,0:0,67:1:0,1:23.8:1:31.6:1:1:0:59.9:134:1:0:1 1/1:44:44:44,0:0,0:0,44:1:0,1:21:1:30.8:1:1:0:60:43:1:0:1.1 +13 32921098 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50564;SOR=0;LSEQ=AAAGTCTCGTTTTTATAAAT;RSEQ=AACATTTCTAAAAATAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:25,140:165,2:0.012:2,2:33:1:28.5:1:0.28793:5.51:60:4:0.0121:0:1 0/0:131:0:0,0:19,112:131,0:0:2,0:25.4:1:30.8:1:1:0:60:262:1:0:0.1 +13 32921146 . C T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01693;SOR=Inf;LSEQ=GTTAAGAAGTTAACACTTCC;RSEQ=GTTTTATAAAATTTATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:0,63:63,0:0:1,0:22.4:1:30.2:1:1:0:60:126:1:0:0 0/1:52:5:0,5:0,47:47,5:0.0962:1,0:15:1:30.8:1:1:0:60:10:0.0962:0:1 +13 32921148 . T TTTTATAAAA 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=4.000;MSILEN=1;SSF=0.09138;SOR=0.31915;LSEQ=TAAGAAGTTAACACTTCCCG;RSEQ=TTTATAAAATTTATAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:11:0,11:0,51:51,11:0.1774:1,0:30.5:1:31:1:1:0:60:22:0.1774:0.0161:0 0/1:47:3:0,3:0,44:44,3:0.0638:1,0:31.3:1:29.4:1:1:0:60:6:0.0652:0:0 +13 32921362 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTTTTATCTCTCCTCTC;RSEQ=AAACCTTTAAAAAAGTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:38:1:32:1:1:0:49:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32928936 . A G 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=TGAGGGTCTGCAACAAAGGC;RSEQ=TATTCCTAAATATTTATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:339,45:384,0:0:2,0:21.8:1:30.6:1:1:0:60:127:1:0:0.1 0/1:360:14:11,3:274,72:346,14:0.0389:2,2:23.1:1:30.8:1:1:1.03777:60:28:0.039:0:1.1 +13 32929232 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=5.77441;LSEQ=CCACCTTTTAAAACTAAATC;RSEQ=CATTTTCACAGAGTTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1542:72:36,36:723,747:1470,72:0.0467:2,2:23.8:1:31.1:1:0.90453:1.03:59.8:71:0.0465:0:1.2 0/1:1891:417:207,210:739,731:1470,417:0.2205:2,2:23.8:1:30.1:1:0.8246:1.02559:60:138:0.2196:0:1.1 +13 32929387 . T C 336 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31751;SOR=2.33434;LSEQ=AAACAACTCCAATCAAGCAG;RSEQ=AGCTGTAACTTTCACAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1457:1451:712,739:0,0:0,1451:0.9959:0,2:25.2:1:32.3:1:1:0:60:110.615:0.9965:0:1.2 1/1:1697:1694:857,837:0,2:2,1694:0.9982:0,2:26.3:1:31.4:1:0.24457:0:60:168.4:0.9982:0:1.1 +13 32929478 . C T 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06881;LSEQ=GCCTTTCAGTTAGATATTTC;RSEQ=GTTGTTAAATAATGTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1177:589:229,360:238,348:586,589:0.5004:2,2:26.8:1:31.1:1:0.55157:1.07507:59.9:146.25:0.5004:0:1.2 0/1:1444:93:38,55:582,766:1348,93:0.0644:2,2:27.4:1:29.2:1:0.7455:1.09966:60:45.5:0.0634:0:1.2 +13 32930673 . C T 209 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00967;LSEQ=CAGTCTGTATCTTGCAAAAA;RSEQ=ATCCACTCTGCCTCGAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:133:64,69:205,235:440,133:0.2321:2,2:26.3:1:29.7:1:0.76702:1.06:60:132:0.2316:0:1.1 0/0:688:2:1,1:331,355:686,2:0.0029:2,2:15:0:24:1:1:1.07:60:4:0.003:0:1.5 +13 32930936 . G A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTAGGCCTGCCTCATCCT;RSEQ=CTAAAGTGATCTGTGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:0,18:0,0:0,18:1:0,1:27.6:1:28.8:1:1:0:60:8:1:0:1.5 1/1:3:3:0,3:0,0:0,3:1:0,0:22.3:1:31.3:1:1:0:60:6:1:0:1 +13 32931817 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50027;SOR=Inf;LSEQ=GGTTTGTTATAATTGTTTTT;RSEQ=TTGTGTGATACATGTTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:119,13:132,0:0:2,0:21.6:1:28.9:1:1:0:59.8:264:1:0:0.1 0/1:150:2:1,1:130,18:148,2:0.0133:2,2:33:1:31.5:1:0.23803:7.05649:60:4:0.0134:0:1 +13 32936646 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.1632;LSEQ=TTTTTATGATAATATTCTAC;RSEQ=TTTATTTGTTCAGGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:314:285:195,90:19,10:29,285:0.9076:2,2:24.4:1:31.8:1:0.83462:1.14:60:70.25:0.9094:0:1.1 1/0:403:248:166,82:97,58:155,248:0.6154:2,2:25.6:1:30.4:1:0.39085:1.21:60:40.333:0.6111:0:1.1 +13 32936865 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09986;SOR=0;LSEQ=TTACATTACGTAATCATATA;RSEQ=GGCAGTATGGTTAAGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:81,213:294,3:0.0101:2,2:30:1:26:1:1:1.31:60:2:0.0068:0:2.3 0/0:342:0:0,0:116,225:341,0:0:2,0:24:1:29.9:1:1:0:60:67.2:0.997:0:0.1 +13 32943782 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAGTGGCACAATCTCGG;RSEQ=TCACTGCACCCTCTGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:32:1:29:1:1:0:52:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32944098 . G A 60 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATTTGCTTTTTGTATTA;RSEQ=CCATAATCATTCTCAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:27.5:1:30:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32944777 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52162;SOR=0;LSEQ=TTGTTTGAGATGGAGTTTCG;RSEQ=TCTCTTGCCCAGGCTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:0,2:8,95:103,2:0.019:2,0:28:1:30.5:1:1:0:60:4:0.0196:0:1 0/0:67:0:0,0:1,66:67,0:0:1,0:21.8:1:32.3:1:1:0:58.3:134:1:0:0 +13 32945021 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4978;SOR=0;LSEQ=ATTACAGATGTGAGCCACTG;RSEQ=GCCTGGCCTGATACAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:2,0:92,20:112,2:0.0175:2,0:31.5:1:31.5:1:1:0:60:4:0.0175:0:1 0/0:114:0:0,0:98,16:114,0:0:2,0:22.9:1:29.4:1:1:0:59.8:56:1:0:0.1 +13 32945054 . A T 43 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0494;SOR=Inf;LSEQ=ACAATTAACTTGAATGTTAT;RSEQ=TATGTGACTTTTTTGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:177,59:236,0:0:2,0:22.7:1:28.9:1:1:0:60:46.2:1:0:0.1 0/1:212:4:1,3:152,56:208,4:0.0189:2,2:7:1:21.8:1:0.06637:8.04905:56.3:3:0.0143:0:3.3 +13 32945537 . A T 27 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTATGCCTGGAACTAGG;RSEQ=CCTATTGTGGTGTCAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:30.5:1:27:0:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32950727 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.10432;SOR=Inf;LSEQ=TTTAAATCTCCCTTCTTTGG;RSEQ=TGTTTTATGCTTGGTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:173,17:190,0:0:2,0:26.7:1:30.9:1:1:0:59.7:22.75:1:0:0.2 0/1:170:3:2,1:138,29:167,3:0.0176:2,2:26:1:25.7:1:0.44361:2.36392:60:2:0.0119:0:1.7 +13 32953182 . A G 61 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41667;SOR=Inf;LSEQ=TATTTCTCAAAATAATGAGC;RSEQ=TTCAGATATTAGCCATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:30.5:1:30.5:1:1:0:60:8:0.3636:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:42:0:32:0:1:0:60:2:1:0:1 +13 32953388 . T C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11855;LSEQ=TTGTCCTGTTTAAAGCCATC;RSEQ=AGTTACAATAGATGGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:285:257,28:22,2:24,285:0.9194:2,2:24.1:1:31.5:1:1:1.19778:60:94:0.9186:0:1.1 1/0:251:144:129,15:88,19:107,144:0.5737:2,2:23.5:1:30.5:1:0.09762:1.85:60:143:0.5743:0:1.1 +13 32953550 . G A 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCAGTTGGAAATTAGGAAG;RSEQ=CCATGGAATCTGCTGAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1565:0:0,0:765,799:1564,0:0:2,0:25:1:31.7:1:1:0:59.9:81.316:0.9994:0:0.1 0/1:1675:107:56,51:798,770:1568,107:0.0639:2,2:22.4:1:28.8:1:0.84169:1.06:60:106:0.0641:0:1.1 +13 32954022 . C CA 107 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09308;SOR=0.40777;LSEQ=TAACATACAGTTAGCAGCGA;RSEQ=AAAAAAAACTCAGTATCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:12:7,5:309,299:608,12:0.0194:2,2:14:1:30.1:1:0.77272:1.35:59.2:24:0.0196:0.0145:0.3 0/0:752:6:4,2:380,363:743,6:0.008:2,2:26.8:1:30.5:1:0.68685:1.91:59.3:12:0.008:0:1.2 +13 32954302 . A AT 76 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.75293;SOR=1.44501;LSEQ=GGTAATGCACAATATAGTTA;RSEQ=TTTTTTTTATTGATTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:4:1,3:85,313:398,4:0.0099:2,2:22:1:30.3:1:1:1.23:60:8:0.0101:0:0 0/1:420:6:2,4:114,299:413,6:0.0143:2,2:20.8:1:29.5:1:0.67058:1.31:60:12:0.0145:0.0048:0.2 +13 32954357 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50814;SOR=0;LSEQ=TTTAAAATCTCTTATGATTA;RSEQ=TTGGAGCTACCAGTTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:6,128:134,2:0.0147:1,2:28:1:31:1:0.10065:19.83:60:4:0.0147:0:1 0/0:102:0:0,0:5,97:102,0:0:1,0:22.4:1:31.8:1:1:0:59.9:204:1:0:0 +13 32954561 . G A 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTTTTCTTACTATTTCT;RSEQ=GTGTATGTGTTTATCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:23:1:30:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:32:0:1:0:60:2:1:0:0 +13 32968591 . G A 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAATGTGTGCGTATACCT;RSEQ=CTTCCACATGACCTCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:36:1:29.2:1:1:0:60:12:0.75:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:27:0:29:0:1:0:60:2:1:0:2 +13 32968607 . A G 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.37796;LSEQ=ACCTGCTTCCACATGACCTC;RSEQ=GTAAAAGAATGTGTTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:39:1:30.2:1:1:0:60:12:0.75:0:2 1/0:2:1:1,0:1,0:1,1:0.5:0,0:43:0:29:0:1:0:60:2:0.5:0:2 +13 32968790 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49937;SOR=Inf;LSEQ=TTAAAATTCATCTAACACAT;RSEQ=TATAATAACATTCTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:145,22:167,0:0:2,0:24.5:1:32:1:1:0:59.8:82.5:1:0:0.1 0/1:181:2:1,1:149,30:179,2:0.011:2,2:30:1:29:1:0.314:4.90237:60:4:0.0112:0:1.5 +13 32968793 . T C 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATTCATCTAACACATCTA;RSEQ=AATAACATTCTTTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:18:13,5:137,28:165,18:0.0984:2,2:22.9:1:32.7:1:0.32836:1.87439:57.9:36:0.0994:0:1.1 0/0:205:0:0,0:166,39:205,0:0:2,0:23:1:29.2:1:1:0:60:101.5:1:0:0.2 +13 32969137 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49846;SOR=Inf;LSEQ=TTTGACAGTCCAGTATCAAG;RSEQ=AAATAGCTTTTATACAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:5,157:162,0:0:1,0:25.3:1:32.5:1:1:0:60:324:1:0:0 0/1:163:2:1,1:14,147:161,2:0.0123:2,2:30:1:27:1:0.1761:10.18:60:4:0.0123:0:1 +13 32969248 . A G 34 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32341;LSEQ=GGAATGGGGAAATGACAGCA;RSEQ=CTAGAAAGAGAAGAATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:28.5:1:34:0:1:0:60:4:0.0909:0:1 0/1:17:2:0,2:0,15:15,2:0.1176:1,0:29:1:34:0:1:0:60:4:0.1176:0:1 +13 32970736 . G C 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAGCCCCAATCTTCCA;RSEQ=CTTCAATCCAGATCATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:38:1:33:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 32970928 . C CT 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.51472;SOR=0;LSEQ=CACATTTAGGGTTTTTCATT;RSEQ=TTTTTTGGTCCAAACTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:2,0:60,2:62,2:0.0313:1,0:27:1:34:0:1:0:60:4:0.0328:0:0 0/0:43:0:0,0:43,0:43,0:0:1,0:22.6:1:31.1:1:1:0:59.8:86:1:0:0.3 +13 32970980 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21126;SOR=Inf;LSEQ=TAAAGGAAATACTTTTGGAA;RSEQ=CATAAATATGTGGGTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:140,24:164,0:0:2,0:24.1:1:30.6:1:1:0:60:328:1:0:0.1 0/1:140:2:1,1:109,29:138,2:0.0143:2,2:16.5:1:29.5:1:0.38386:3.71257:60:4:0.0144:0:1 +13 32971425 . T C 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTGAAAAGTGTTTTTTG;RSEQ=CATTTATTTCACTGTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:18.7:1:31:1:1:0:60:12:1:0:1 1/1:4:4:0,4:0,0:0,4:1:0,0:30.5:1:32.3:1:1:0:56.3:8:1:0:1 +13 32972745 . C GAATTATATCT 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=Inf;LSEQ=GAAAAACAATTTATATCTGT;RSEQ=AGTGAATCCACTAGGACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:0:0,0:256,254:510,0:0:2,0:23.6:1:29.8:1:1:0:59.9:101:1:0:0.1 0/1:622:25:14,11:305,290:595,25:0.0402:2,2:24.5:1:29.9:1:0.68716:1.21:59.6:50:0.0408:0.0129:1.1 +13 32972914 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16455;SOR=0;LSEQ=AAAAATATATCTAAGCATTT;RSEQ=CAAAGGCGACAATAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:53,125:178,2:0.0111:2,2:45.5:1:29.5:1:0.51117:2.35:60:4:0.0113:0:1.5 0/0:263:0:0,0:86,177:263,0:0:2,0:23.9:1:31.4:1:1:0:60:86.667:1:0:0.1 +13 32973012 . A C 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02681;SOR=4.74152;LSEQ=TACTTATGTTGCACAATGAG;RSEQ=AAAGAAATTAGTTTCAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:0,3:0,34:34,3:0.0811:1,0:23:1:33.3:1:1:0:60:6:0.0811:0:2 0/1:30:9:0,9:0,21:21,9:0.3:1,0:33.7:1:31:1:1:0:60:18:0.3:0:1 +13 33833810 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.21952;LSEQ=AGGAAATCGCCAAAAAGTGA;RSEQ=AATACGCTTGCTTGAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:566:180:79,101:176,210:386,180:0.318:2,2:26:1:29.8:1:0.7176:1.07133:60:360:0.3214:0:1.1 1/0:627:319:140,179:146,162:308,319:0.5088:2,2:26.1:1:28.6:1:0.3792:1.15203:59.9:105.333:0.5089:0:1.1 +13 33834013 . G C 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54972;SOR=0;LSEQ=AATTCCCACATGTCATGGGA;RSEQ=GGACCTGCTACTCAGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:20,3:0.1304:1,0:29:1:30:1:1:0:60:6:0.1304:0:1 0/0:8:0:0,0:0,8:8,0:0:0,0:7:0:11:0:1:0:50:0:0:0:4 +13 34298817 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTGCATCTTTGCTGTGG;RSEQ=GCAAGCTAAAAATTTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:15:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 34298900 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGACATATTTGCTAAACA;RSEQ=ATATGTCAAATGTCTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:22.5:1:31.5:1:1:0:60:4:0.4:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:21:0:31:0:1:0:60:2:1:0:1 +13 34298947 . A C 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAAAGAACATGACTAATT;RSEQ=AGGAAGATTATTTCCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:32.8:1:29.8:1:1:0:60:3:0.75:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:19:1:29.5:1:1:0:60:4:1:0:1 +13 34299233 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.58782;LSEQ=AAGTTTATTTGCCATTGTTC;RSEQ=CCCAGTCTTTAGCACGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:84:37,47:151,183:334,84:0.201:2,2:27.1:1:30.6:1:0.9026:1.04804:60:27:0.1985:0:1.1 1/0:470:252:115,137:104,114:218,252:0.5362:2,2:26.1:1:30.1:1:0.71083:1.08661:59.6:83:0.5343:0:1.1 +13 34299330 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.65991;LSEQ=TATGTCTTAGTTCCTCATGT;RSEQ=CTTTCTTGTGGAAGGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:13,95:108,2:0.0182:2,2:25.5:1:29.5:1:0.23937:7.08:60:4:0.0185:0:1 0/1:83:1:0,1:12,70:82,1:0.012:2,0:11:0:30:0:1:0:60:2:0.012:0:1 +13 34348208 . A G 71 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACATCTAATTTGCTTCTAA;RSEQ=ATGCAAGATTGAATAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:37:1:35.5:1:1:0:57:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 34348415 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.49669;SOR=Inf;LSEQ=CCAGGCAAGCATGCCCCTAG;RSEQ=ATAGGAGAGGCCACATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:58,7:65,0:0:2,0:26.2:1:31.8:1:1:0:60:130:1:0:0 0/1:69:2:1,1:65,2:67,2:0.029:1,2:17.5:1:28.5:1:0.08568:26.73959:60:4:0.0299:0:1 +13 34348532 . A G 263 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCAATGGGGTAAGTTGGGAA;RSEQ=AGGACGCTCTCTACTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:261:261:124,137:0,0:0,261:1:0,2:27:1:32.8:1:1:0:60:260:1:0:1.2 0/1:408:180:89,91:113,114:227,180:0.4412:2,2:26.5:1:30.8:1:1:1.01347:60:89:0.4406:0:1.3 +13 34348548 . T A 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15349;SOR=Inf;LSEQ=GGAAAAGGACGCTCTCTACT;RSEQ=TCAGGATCCTATGGTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:120,140:260,0:0:2,0:24.3:1:30.5:1:1:0:60:85.667:1:0:1.2 0/1:390:4:3,1:177,209:386,4:0.0103:2,2:12.8:1:22.5:1:0.339:3.53:60:3:0.0079:0:2 +13 34348601 . T C 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAAGGCTCCCAGAGGTGC;RSEQ=GCTTGCTTGCTGATATACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:45,100:145,0:0:2,0:26.4:1:30.9:1:1:0:60:290:1:0:1.2 0/1:200:49:18,31:45,106:151,49:0.245:2,2:22.6:1:29.3:1:0.38014:1.37:60:98:0.2462:0:1.8 +13 34348610 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.16742;SOR=0;LSEQ=CCCAGAGGTGCTGCTTGCTT;RSEQ=CTGATATACAACCTGCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:30,89:119,2:0.0165:2,2:14.5:1:29.5:1:0.44835:2.93:60:4:0.0167:0:3 0/0:174:0:0,0:50,124:174,0:0:2,0:22.8:1:31.3:1:1:0:60:86:1:0:1.4 +13 34348618 . A C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGCTTGCTTGCTGATAT;RSEQ=CAACCTGCTTGTCACTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:115:115:26,89:0,0:0,115:1:0,2:23.5:1:31.4:1:1:0:60:114:1:0:1.3 1/1:153:153:38,115:0,0:0,153:1:0,2:21.9:1:30.5:1:1:0:60:75.5:1:0:1.4 +13 34348632 . A T 30 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19633;SOR=0;LSEQ=TGATATACAACCTGCTTGTC;RSEQ=CTGGGCTTGGTTGGAAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:16,74:90,2:0.0217:2,2:5:0:30:1:0.33708:4.52:60:4:0.022:0:1 0/0:115:0:0,0:18,97:115,0:0:2,0:22.3:1:28.8:1:1:0:60:37.333:1:0:1.2 +13 34348725 . A G 49 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08966;SOR=Inf;LSEQ=AGAAACTGCCAATAAAAATA;RSEQ=TAACAGCAGGCTGGGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:0,16:16,0:0:1,0:20.3:1:32.8:1:1:0:58.2:32:1:0:1 0/1:14:3:0,3:0,11:11,3:0.2143:0,0:7.7:1:31:1:1:0:60:6:0.2308:0:1 +13 34348737 . T C 96 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02941;SOR=0;LSEQ=TAAAAATAATAACAGCAGGC;RSEQ=GGGCGCGGTGGCTCACGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:20.6:1:30.4:1:1:0:56.8:18:1:0:1.8 1/0:8:4:0,4:0,3:3,4:0.5:0,0:19:1:24:1:1:0:59.8:3:0.5:0:1.8 +13 34348744 . G A 93 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=AATAACAGCAGGCTGGGCGC;RSEQ=GTGGCTCACGCCTGTAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:18.6:1:33.4:1:1:0:55.9:14:1:0:2 1/0:6:3:0,3:0,3:3,3:0.5:0,0:17.3:1:30.3:1:1:0:59.7:6:0.6:0:2 +13 35153749 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53846;SOR=Inf;LSEQ=TTAGCATGATCCATCCACAA;RSEQ=CCAAGGAATGCCAAAGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:18,0:0:2,0:23.7:1:32.5:1:1:0:56:36:1:0:0.2 0/1:34:2:1,1:17,15:32,2:0.0588:2,2:32.5:1:27.5:1:1:1.12916:60:4:0.0588:0:1 +13 35153868 . G A 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTACCAATGTCTTGTTTTC;RSEQ=GATTTCCAGCCTCCAGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,1:1,2:0.5:0,0:16:1:33:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:10:0:32:0:1:0:60:2:1:0:2 +13 35155046 . A G 25 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTAGAATGGTAGGGATC;RSEQ=GAGGGAGTCACTTCTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:25:1:1:0:60:4:1:0:1.5 +13 35516626 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=Inf;LSEQ=CGCGGGGGGCGGGCCGGGCC;RSEQ=GACAGACCGGGAGAGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:10,0:0:2,0:20.2:1:31:1:1:0:60:20:1:0:0.1 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:30:0:28.5:1:1:1.4491:60:4:0.1667:0:1 +13 41032399 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49913;SOR=Inf;LSEQ=TGTAGGGGGGAAGAAGGTTG;RSEQ=TGGTGTCCTTGCTCACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:94,49:143,0:0:2,0:21.6:1:31.4:1:1:0:60:142:1:0:0.8 0/1:155:2:1,1:96,57:153,2:0.0129:2,2:22.5:1:27:1:1:1.67823:60:4:0.0131:0:2.5 +13 41032426 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2185;SOR=0;LSEQ=CCTTGCTCACTGGGACAGTC;RSEQ=CCCAGGGGACACGAGACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:91,69:160,2:0.0123:2,2:21:1:29.5:1:1:1.31655:60:4:0.0125:0:1 0/0:184:0:0,0:101,82:183,0:0:2,0:27.1:1:29.9:1:1:0:60:60:1:0:0.4 +13 41032432 . G C 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCACTGGGACAGTCGCCCAG;RSEQ=GGACACGAGACATATACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:56:31,25:61,52:113,56:0.3294:2,2:31.9:1:30.9:1:1:1.06:60:55:0.3293:0:2 0/0:191:0:0,0:101,89:190,0:0:2,0:27.3:1:29.8:1:1:0:60:46.5:0.9947:0:0.4 +13 41032438 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20508;SOR=0;LSEQ=GGACAGTCGCCCAGGGGACA;RSEQ=GAGACATATACAGCCAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:93,75:168,2:0.0117:2,2:45:1:31:1:1:1.23841:60:4:0.0118:0:3 0/0:206:0:0,0:107,99:206,0:0:2,0:26:1:29.8:1:1:0:60:50.5:1:0:0.5 +13 41032459 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.35825;LSEQ=GAGACATATACAGCCAGTCT;RSEQ=CTTGTGCCTACCAGGGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:179:117:54,63:34,27:61,117:0.6536:2,2:26.1:1:30.5:1:0.26945:1.46592:60:234:0.661:0:1.6 0/1:221:89:45,44:60,72:132,89:0.4027:2,2:22.4:1:28.5:1:0.49371:1.23:59.9:28.667:0.3963:0:1.1 +13 41032473 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20508;SOR=0;LSEQ=CAGTCTCCTTGTGCCTACCA;RSEQ=GGTCTGGCAGCCCATTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:76,93:169,2:0.0117:2,2:27:1:32.5:1:1:1.22:60:4:0.012:0:3 0/0:206:0:0,0:88,118:206,0:0:2,0:25.6:1:30.5:1:1:0:60:67.667:1:0:0.5 +13 41032524 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24463;SOR=Inf;LSEQ=CCCAGCAAATTAGGGGTTGG;RSEQ=TAAGCAGCTGTGGAGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:33,84:117,0:0:2,0:23.6:1:31.7:1:1:0:60:116:1:0:0.5 0/1:115:2:1,1:33,80:113,2:0.0174:2,2:39.5:1:31:0:0.50572:2.40:60:4:0.0174:0:1.5 +13 41032536 . G T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49724;SOR=0;LSEQ=GGGGTTGGGTAAGCAGCTGT;RSEQ=GAGCCTTTTACTTCAGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:17,71:88,2:0.0222:2,2:14:0:29:1:0.3618:4.09:60:4:0.0227:0:2 0/0:88:0:0,0:23,64:87,0:0:2,0:24:1:30.7:1:1:0:60:42.5:1:0:0.4 +13 41032542 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49761;SOR=0;LSEQ=GGGTAAGCAGCTGTGGAGCC;RSEQ=TTTACTTCAGGGATCTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:0,2:17,66:83,2:0.0235:2,0:38.5:1:32.5:1:1:0:60:4:0.0244:0:1 0/0:79:0:0,0:18,61:79,0:0:2,0:22.2:1:29.9:1:1:0:60:78:1:0:0.3 +13 41032620 . GCA G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=1;SOR=0.87141;LSEQ=ACATGAGCACGTGCACGCAT;RSEQ=CACACACACACACACACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:1,5:0,12:12,6:0.3158:0,2:29.8:1:34:0:0.33333:0:60:12:0.3158:0:0 0/1:7:2:0,2:0,3:3,2:0.2857:0,0:42:1:32.5:1:1:0:60:4:0.3333:0:0 +13 41133502 . G T 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52068;SOR=0;LSEQ=AAAACTGTAAGCTGCAAAAA;RSEQ=GACAGAGAATGAATGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:93,0:93,2:0.0211:1,2:6:0:33:1:0.02105:0:60:4:0.0213:0:1 0/0:61:0:0,0:58,3:61,0:0:1,0:23.9:1:31.5:1:1:0:59.7:60:1:0:0.1 +13 41161770 . G A 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12884;SOR=0;LSEQ=TCCATCTATACCTAAAGCAC;RSEQ=GCTCAAGTGCTTGGAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:10,1:14,0:14,11:0.44:1,2:23.6:1:30.2:1:0.44:0:60:22:0.44:0:1.6 0/0:5:0:0,0:5,0:5,0:0:0,0:25.8:1:31.2:1:1:0:60:10:1:0:0 +13 41161979 . C G 194 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGTGTTCACAGTAGCCTCT;RSEQ=CCCACCTTTTAAAAGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1029:68:48,20:647,313:960,68:0.0661:2,2:26.9:1:32:1:0.68778:1.16:60:67:0.0654:0:1.1 0/0:1138:0:0,0:712,426:1138,0:0:2,0:25.4:1:30.1:1:1:0:60:102.455:1:0:0.2 +13 41162086 . G A 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTAAGGCCTTTCATGTGAAA;RSEQ=AGAGTCAATGCACTAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1623:0:0,0:747,874:1621,0:0:2,0:24.2:1:32.7:1:1:0:59.9:123.692:0.9988:0:0.1 0/1:1802:64:31,33:813,925:1738,64:0.0355:2,2:21.4:1:29.8:1:0.80015:1.07:60:128:0.0358:0:1.2 +13 41162225 . C T 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=80.91724;LSEQ=AGCCCAGGATAGAAAGGATT;RSEQ=AATTCAATTAACAGAACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:1:0,1:3,187:190,1:0.0052:1,0:38:0:30:0:1:0:60:2:0.0053:0:1 0/1:123:37:1,36:1,85:86,37:0.3008:1,1:20.1:1:28:1:0.51286:2.34:60:74:0.3008:0:1 +13 41183050 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGATGGATCCTAGAGAT;RSEQ=GGTGGGAAGGGGGTACGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:33:1:1:0:60:4:1:0:1.5 +13 41185309 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.21528;LSEQ=ATATATTCTCAGAACAATGA;RSEQ=TTTTGTTCTACCCTGTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:343:249:46,203:12,82:94,249:0.7259:2,2:23.1:1:31.1:1:0.25866:1.55:60:248:0.7273:0:1.1 0/1:353:128:32,96:48,177:225,128:0.3626:2,2:24.3:1:29.5:1:0.43088:1.23:60:41.667:0.3592:0:1.1 +13 41218947 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07272;SOR=0;LSEQ=TCCTTTTACTAATGTTAAGA;RSEQ=ACTTCTCCATCCAGTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:3:2,1:236,50:286,3:0.0104:2,2:15.7:1:24:1:0.44273:2.35109:60:2:0.007:0:1 0/0:402:0:0,0:320,82:402,0:0:2,0:21.4:1:31.4:1:1:0:60:401:1:0:0.1 +13 41219125 . G A 179 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=64.27757;LSEQ=ACTAAACCAGACTACTGCTG;RSEQ=CGACAGAGTCGAGACAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:693:1:1,0:268,424:692,1:0.0014:2,0:1:0:26:0:0.38817:0:60:2:0.0015:0:1 0/1:905:77:28,49:325,502:827,77:0.0851:2,2:26.7:1:28.7:1:0.71429:1.13278:60:76:0.085:0:1 +13 41239549 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16198;SOR=Inf;LSEQ=CGCGCACGCACACCTACTGC;RSEQ=GTCCCCGACCGGACCCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:70,2:72,0:0:1,0:21.8:1:31:1:1:0:60:35:1:0:0.2 0/1:49:2:1,1:47,0:47,2:0.0408:1,2:10.5:1:30.5:1:0.04082:0:60:4:0.0408:0:1 +13 41239928 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19844;SOR=0;LSEQ=GCCCCGCGAGCGGCCCAGCG;RSEQ=CGGCGGGGGGCACCGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:32,136:168,2:0.0118:2,2:12.5:1:27.5:1:0.35148:4.20:60:4:0.0122:0:1 0/0:211:0:0,0:60,148:208,0:0:2,0:14.6:1:31.3:1:1:0:60:68.333:0.9856:0:0.3 +13 41239932 . CG C 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1.52175;LSEQ=CGCGAGCGGCCCAGCGGCGG;RSEQ=GGGGGCACCGGCGGGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:1:0,1:21,104:125,1:0.0078:2,0:10:0:33:0:1:0:60:2:0.0078:0:0 0/1:170:2:1,1:44,123:167,2:0.0118:2,2:28.5:1:32.5:1:0.46281:2.78:60:4:0.012:0:0.5 +13 41239943 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50693;SOR=Inf;LSEQ=CAGCGGCGGCGGGGGGCACC;RSEQ=GCGGGTGCTGCGACAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:13,56:69,0:0:2,0:11.4:1:31:1:1:0:59.7:33.5:0.9853:0:0.2 0/1:93:2:1,1:27,63:90,2:0.0215:2,2:11.5:1:29.5:1:0.51839:2.31:60:4:0.022:0:1.5 +13 41240087 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19905;SOR=0;LSEQ=CCACCGCCGCCGCCACGGAG;RSEQ=CGGGCGCCTGCGGGAAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:61,39:100,2:0.0196:2,2:34.5:1:32:0:1:1.55699:60:4:0.0198:0:1.5 0/0:126:0:0,0:76,50:126,0:0:2,0:15.8:1:30.8:1:1:0:59.9:62:1:0:0.3 +13 41240157 . C T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58048;SOR=0.37821;LSEQ=CATGAAGTCGGCGCTGACAG;RSEQ=GGCAGCCGAGGCCGAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:78,88:166,2:0.0119:2,2:33.5:1:31.5:1:1:1.13:60:4:0.0121:0:1.5 0/0:221:1:0,1:107,112:219,1:0.0045:2,0:1:0:30:0:1:0:45:2:0.0046:0:1 +13 41240180 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51503;SOR=Inf;LSEQ=CAGCCGAGGCCGAGGGCAGG;RSEQ=CCGCCGCGGCGTCGGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:61,67:128,0:0:2,0:17.9:1:31.8:1:1:0:60:41.667:1:0:0.2 0/1:185:2:1,1:84,99:183,2:0.0108:2,2:24:0:31:1:1:1.18:60:4:0.0111:0:2.5 +13 41240375 . G A 83 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2377;SOR=2.32631;LSEQ=CCCCCGCCCCTCCCCCAGCC;RSEQ=CAGGAGAGCCAAGAGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:3:2,1:257,409:666,3:0.0045:2,2:3:1:21:1:0.56288:3.18:60:0.5:0.0015:0:1 0/1:771:8:4,4:324,439:763,8:0.0104:2,2:24.8:1:27.9:1:0.72873:1.35:60:7:0.0093:0:1.3 +13 41240379 . G A 154 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=45.39553;LSEQ=CGCCCCTCCCCCAGCCGCAG;RSEQ=AGAGCCAAGAGGGGGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:645:1:1,0:234,408:642,1:0.0016:2,0:1:0:26:0:0.36547:0:60:2:0.0016:0:1 0/1:728:48:22,26:273,407:680,48:0.0659:2,2:23.6:1:27.7:1:0.45022:1.26:60:15:0.0629:0:1.1 +13 41240855 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCGCGGCCAATGGGCATG;RSEQ=GGCACCGCCGCCCGGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:27:1:1:0:60:4:1:0:2.5 +13 41240899 . G T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCGCCGGGCTGGGTGGG;RSEQ=CCCGGTTTTCCACGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:1:28:1:1:0:60:4:1:0:2.5 +13 41862213 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23009;SOR=0;LSEQ=GCAAGACTCACAAGGGAGAA;RSEQ=CATATTAAAAATATGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:0,2:81,65:146,2:0.0135:2,0:19.5:1:28.5:1:0.20325:0:60:4:0.0139:0:1 0/0:160:0:0,0:87,73:160,0:0:2,0:19.3:1:31.3:1:1:0:60:39:1:0:0.1 +13 41862285 . T A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.867;SOR=1.08247;LSEQ=AATCTTCTTGTCCAGATGTA;RSEQ=CCCATAAGCCCAGATTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:17:8,9:113,114:227,17:0.0697:2,2:28.1:1:30.6:1:1:1.11463:59.3:34:0.072:0:1.1 0/1:280:21:10,11:133,125:258,21:0.075:2,2:30:1:29.8:1:0.82194:1.16974:57.7:42:0.0761:0:1.1 +13 41862317 . T C 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00779;SOR=Inf;LSEQ=AGATTCACTGGCTTTCCATC;RSEQ=ACCTTAACATTGGCAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:74,122:196,0:0:2,0:26.5:1:29.4:1:1:0:59.9:31.667:1:0:0.1 0/1:216:8:4,4:90,118:208,8:0.037:2,2:26.1:1:31.5:1:0.73043:1.31:57.8:16:0.0374:0:1 +13 41862325 . C A 28 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8364;LSEQ=TGGCTTTCCATCTACCTTAA;RSEQ=ATTGGCAGCAGAATAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:1,0:67,116:183,1:0.0054:2,0:1:0:27:0:0.36957:0:60:2:0.0055:0:1 0/1:201:2:1,1:84,115:199,2:0.01:2,2:10:0:28:1:1:1.37:60:4:0.0101:0:1 +13 41862553 . C G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60839;SOR=0.46982;LSEQ=AGGTGCATGGCTGCAGGTGG;RSEQ=AGGGGATGGGGTGCCAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:39:1:33.2:1:1:0:60:12:0.75:0:1 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:19:1:30.8:1:1:0:60:8:0.5714:0:1.3 +13 42178299 . C T 45 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43766;SOR=0.46715;LSEQ=CCCTGAAGCTCAGAGCCAAC;RSEQ=TGGCAGTGTCCTGGTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:4:0,4:152,127:279,4:0.0141:2,0:10.3:1:22.8:1:0.04478:0:60:3:0.0108:0:2.5 0/0:301:2:0,2:163,136:299,2:0.0066:2,0:18:1:19:1:0.20937:0:60:1:0.0034:0:2 +13 42178332 . A C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=8.92624;LSEQ=GGTGCTCTCAATGTCCAGGG;RSEQ=AAGGAACACTTGTCAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:28:12,16:129,166:295,28:0.0864:2,2:27.5:1:32.4:1:1:1.03604:60:56:0.0889:0:1.1 0/1:303:139:65,74:79,84:163,139:0.4587:2,2:26.1:1:31.3:1:0.81748:1.07045:60:138:0.457:0:1.1 +13 42178403 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23395;SOR=Inf;LSEQ=TATCATGTTGTTCACATATA;RSEQ=TTTATATAAAATCTTATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:53,129:182,0:0:2,0:22.9:1:32.3:1:1:0:59.9:90:1:0:0.2 0/1:171:2:1,1:53,115:168,2:0.0117:2,2:20:1:27.5:1:0.53568:2.16:60:4:0.0118:0:1.5 +13 42178450 . A AT 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.25234;SOR=0;LSEQ=TCCTAAATAACTGCATATAG;RSEQ=TTTTTTTTAAAGTACATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:0,3:5,52:57,3:0.05:2,0:30.7:1:30:1:1:0:60:6:0.0508:0:0 0/0:48:0:0,0:5,43:48,0:0:2,0:21.5:1:30.5:1:1:0:59.8:47:1:0:0 +13 42830030 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24935;SOR=Inf;LSEQ=GAAGGTTGCTGCAAAATTGG;RSEQ=TGCACGTACAGGCTTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:217,41:258,0:0:2,0:25.1:1:32.6:1:1:0:52.4:128:1:0:0.1 0/1:275:3:1,2:201,71:272,3:0.0109:2,2:17:1:27.7:1:0.17298:5.61898:43.3:6:0.0109:0:1 +13 42830444 . T A 25 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59796;SOR=2.33402;LSEQ=CTTTACAGAAAACTGCGTGG;RSEQ=GGGAATCCAGGCCAATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:1,0:104,96:200,1:0.005:2,0:2:0:28:0:1:0:45:2:0.005:0:1 0/1:173:2:1,1:87,84:171,2:0.0116:2,2:5.5:1:25:0:1:1.03551:44.5:4:0.0116:0:1 +13 42830686 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49818;SOR=0;LSEQ=AGTGATTTAAGTAAATTTAT;RSEQ=ATGAAAATAAACGTGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:20,109:129,2:0.0153:2,2:18.5:1:32:1:0.29595:5.34:60:4:0.0154:0:1 0/0:127:0:0,0:25,102:127,0:0:2,0:24.2:1:29.9:1:1:0:60:254:1:0:0 +13 43549586 . C T 26 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGATTAGTTCTTTCATCAG;RSEQ=ACAACTCATTGCCTCTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:26:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:45:0:30:0:1:0:60:2:1:0:1 +13 43549782 . G A 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67662;SOR=0.51406;LSEQ=AAAAGTGCTGCTTCTTTCAG;RSEQ=TGGAGGTAATCCCACACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:21.3:1:30.7:1:1:0:60:12:0.4286:0:1 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:19.3:1:29:1:1:0:60:6:0.2727:0:1 +13 43549921 . AAC A 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.02926;SOR=0.19329;LSEQ=ATGATGTATTTCTTCACTTA;RSEQ=ACACACACACACATAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:9:5,4:166,76:242,9:0.0359:2,2:15.9:1:30.2:1:0.47185:1.74321:59.4:18:0.036:0.0159:0.1 0/0:281:2:0,2:183,90:273,2:0.0071:2,0:23:1:32:0:0.11111:0:60:4:0.0071:0:0 +13 43549923 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.25142;SOR=Inf;LSEQ=GATGTATTTCTTCACTTAAA;RSEQ=ACACACACACACATAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:171,77:248,0:0:2,0:23.4:1:31.8:1:1:0:60:81.667:1:0:0.1 0/1:286:3:2,1:185,91:276,3:0.0105:2,2:32.7:1:24:1:1:1.01643:60:2:0.0072:0:1.7 +13 43549952 . C CA 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01285;SOR=1.5019;LSEQ=ACACATAAGTAAAAGCCACA;RSEQ=AAAAAAAAGTTAGCAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:80:44,36:166,98:264,80:0.2319:2,2:30.1:1:29.5:1:0.23902:1.38452:59.9:25.667:0.2292:0.0145:0.4 0/1:439:137:81,56:170,123:293,137:0.3121:2,2:29.9:1:30:1:0.83464:1.05:59.8:136:0.3134:0:0.4 +13 43550021 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00012;SOR=1.80933;LSEQ=TATGAAGTACAATATTGTAG;RSEQ=GACTCACCATCTTTAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:341:193:87,106:64,83:147,193:0.566:2,2:26.9:1:30.9:1:0.82587:1.06:60:47.25:0.5625:0:1.1 1/0:400:281:130,151:48,71:119,281:0.7025:2,2:25.5:1:29.7:1:0.32205:1.27:60:45.833:0.7033:0:1.1 +13 43550043 . CA C 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.10567;SOR=0.17702;LSEQ=ACTCACCATCTTTAAGAGGC;RSEQ=AAAACCAATGATGGGACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:5:2,3:112,190:302,5:0.0163:2,2:30:1:32.8:1:1:1.13:60:10:0.0164:0.0033:0.8 0/0:343:1:0,1:125,217:342,1:0.0029:2,0:50:0:30:0:1:0:60:2:0.0029:0:0 +13 43550089 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49854;SOR=0;LSEQ=GAGATGGAGACCAACTGGTA;RSEQ=GTATACTTACAAAATGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:41,129:170,2:0.0116:2,2:16:0:32.5:1:0.42982:3.12:60:4:0.0118:0:1.5 0/0:172:0:0,0:39,133:172,0:0:2,0:24.6:1:30.6:1:1:0:60:171:1:0:0.6 +13 43550139 . C A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11877;SOR=2.21108;LSEQ=TCCTCAGTAAAAATAACTGT;RSEQ=AGAAATTCATATTTTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:36:1,35:0,19:19,36:0.6545:1,1:25.8:1:31.5:1:1:0:60:72:0.6545:0:1 1/1:47:38:1,37:0,9:9,38:0.8085:0,1:22.6:1:30.7:1:1:0:60:76:0.8085:0:1.1 +13 43550243 . A G 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26316;SOR=0;LSEQ=ACTGTTTCACAGACACTGGC;RSEQ=GAAGACATGAAATTCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:0,7:0,9:9,7:0.4375:0,0:29.3:1:31.4:1:1:0:60:14:0.4375:0:2 0/0:3:0:0,0:1,2:3,0:0:2,0:18:1:31:1:1:0:60:6:1:0:0 +13 43550270 . T A 104 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAAATTCCTGGATCAGAG;RSEQ=CAAAGACTTTATTACTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:26.2:1:31.4:1:1:0:60:20:1:0:1.9 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 43603669 . CT C 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.81998;LSEQ=TTTGTAAACAATTTTGGTGC;RSEQ=TTTTTTTTTTCCCCAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:6,1:20,0:20,7:0.2593:1,2:23.7:1:32.7:1:0.25926:0:60:14:0.2593:0.0741:0 0/1:18:4:4,0:14,0:14,4:0.2222:1,0:26.3:1:30.4:1:1:0:60:8:0.2222:0.0556:0 +13 43603680 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17857;SOR=Inf;LSEQ=TTTTGGTGCCTTTTTTTTTT;RSEQ=CCCCAGCTGTAGCAGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:27,1:28,0:0:1,0:28.1:1:31.3:1:1:0:59.6:27:1:0:0.5 0/1:21:2:2,0:19,0:19,2:0.0952:1,0:42.5:1:30.5:1:1:0:60:4:0.0952:0:1 +13 43603871 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.67016;LSEQ=GACATGGCCCATTTGTTGAT;RSEQ=TGCTGGCATTATTTAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:46:16,30:103,141:244,46:0.1586:2,2:23.9:1:29.2:1:0.41486:1.36822:60:14.333:0.153:0:1.3 0/1:364:122:50,72:101,140:241,122:0.3352:2,2:24.9:1:29.5:1:0.91046:1.03876:59.9:121:0.338:0:1.1 +13 43603878 . C A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07141;SOR=Inf;LSEQ=CCCATTTGTTGATCTGCTGG;RSEQ=ATTATTTAAATAATGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:103,161:264,0:0:2,0:24.2:1:32:1:1:0:59.9:43:1:0:0.3 0/1:340:5:4,1:129,206:335,5:0.0147:2,2:24.6:1:27:1:0.07889:6.35:60:10:0.0148:0:1.2 +13 43604158 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAGATAAATGAGACTAT;RSEQ=CCTCTTTGACTTTTGTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:35:1:29:0:1:0:41:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 46174403 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07;SOR=Inf;LSEQ=CAATTGAAGAGTGGTGACAA;RSEQ=AATTCTTTGCTTGACCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:18,0:0:2,0:22.4:1:32.8:1:1:0:60:36:1:0:0.1 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:12.5:1:29:1:1:3.1622:60:4:0.2857:0:1 +13 46174493 . A AT 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=GTAAAATCCAGTTTCATTTT;RSEQ=TTTTTTTTTTATTTTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:4,15:19,2:0.0952:2,2:45.5:1:30:1:0.42857:3.46:60:4:0.0952:0:1 0/0:21:0:0,0:10,11:21,0:0:2,0:25.3:1:28:1:1:0:59.9:42:1:0:0 +13 46407969 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.20715;SOR=0;LSEQ=GCATGGCGATGACTCACCCT;RSEQ=GCCTTCTTGCCCACAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:45,22:67,2:0.029:2,2:33.5:1:31.5:1:1:2.02266:60:4:0.029:0:1 0/0:82:0:0,0:52,30:82,0:0:2,0:24:1:30.5:1:1:0:60:19.5:1:0:0.4 +13 46408024 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19735;SOR=0;LSEQ=GAAGAGCTCAGCCAGGCTTT;RSEQ=AACAATCAATCAGGAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:64,60:124,2:0.0159:2,2:25.5:1:27.5:1:1:1.06615:60:4:0.0161:0:1 0/0:157:0:0,0:80,77:157,0:0:2,0:23.7:1:28.5:1:1:0:60:77.5:1:0:1.1 +13 46408037 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=18.73136;LSEQ=AGGCTTTTAACAATCAATCA;RSEQ=GAGTTTTCCTGAGGCGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:11:5,6:56,67:123,11:0.0821:2,2:24.6:1:31.8:1:1:1.00296:60:22:0.0853:0:1.7 1/0:159:100:45,55:31,27:58,100:0.6289:2,2:27.3:1:29.8:1:0.32581:1.40024:60:49:0.6242:0:1.7 +13 46408045 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22045;SOR=0;LSEQ=AACAATCAATCAGGAGTTTT;RSEQ=CTGAGGCGTCTGCACAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:57,83:140,2:0.014:2,2:20.5:1:27.5:1:1:1.45:60:4:0.0144:0:1 0/0:161:0:0,0:75,86:161,0:0:2,0:25.7:1:30.3:1:1:0:60:79.5:1:0:1.2 +13 46408057 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49854;SOR=Inf;LSEQ=GGAGTTTTCCTGAGGCGTCT;RSEQ=CACAGACTTTTGGCTGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:62,77:139,0:0:2,0:27.1:1:31.9:1:1:0:59.9:45.333:1:0:0.3 0/1:146:2:1,1:64,80:144,2:0.0137:2,2:39:1:28.5:1:1:1.25:60:4:0.0137:0:3 +13 46408073 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=25.95169;LSEQ=GTCTGCACAGACTTTTGGCT;RSEQ=GTCTTCTCAGAAGCTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:9:4,5:52,70:122,9:0.0687:2,2:27:1:30.1:1:1:1.08:60:18:0.0709:0:2 1/0:115:76:31,45:16,23:39,76:0.6609:2,2:27.6:1:28.6:1:1:1.00973:60:37:0.6607:0:2 +13 46751970 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50244;SOR=Inf;LSEQ=CAGTCAAGTGTACAGAGGGG;RSEQ=TGACTACTGATGCTGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:17,0:0:2,0:24.1:1:31.9:1:1:0:59.1:34:1:0:0.5 0/1:24:2:1,1:14,8:22,2:0.0833:2,2:27:1:29.5:1:1:1.70775:60:4:0.0833:0:2 +13 46751989 . C T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.05738;SOR=0.19373;LSEQ=GCTGACTACTGATGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:3,3:5,9:14,6:0.3:2,2:21.2:1:30.5:1:0.64241:1.75:60:12:0.3158:0:1 0/1:27:2:1,1:14,11:25,2:0.0741:2,2:34.5:1:28.5:1:1:1.2613:60:4:0.0741:0:2 +13 46752000 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.16522;SOR=0;LSEQ=ATGCTGTTGCTGCTGCTGCT;RSEQ=CTGCTGATGGTGATGATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:6,11:17,2:0.1053:2,2:28.5:1:28:1:1:1.77:60:4:0.1053:0:1 0/0:27:0:0,0:15,12:27,0:0:2,0:33:1:31.5:1:1:0:60:54:1:0:0.2 +13 46752059 . T TA 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.59993;LSEQ=ATGACACAGAATAATTTGTT;RSEQ=ATAAAAGCACTTATCATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:1,1:2,4:0.6667:2,0:28.3:1:32.1:1:0.33333:0:60:8:0.6667:0.1667:0 1/0:13:7:2,5:3,3:6,7:0.5385:2,2:13.7:1:29.1:1:0.59207:2.32357:60:14:0.5385:0.2308:0 +13 46833150 . A C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.06328;LSEQ=TTTGAGTAAAGCACACATTT;RSEQ=CTGAGGCCTACATTTTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:73:41,32:129,127:256,73:0.2219:2,2:25.6:1:31.7:1:0.42669:1.26:60:146:0.226:0:1.9 0/1:402:149:67,82:131,120:251,149:0.3706:2,2:25.2:1:30.1:1:0.17925:1.33508:60:48.667:0.3687:0:1.9 +13 46833167 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=1.88403;LSEQ=TTTACTGAGGCCTACATTTT;RSEQ=GTTCCTAAGGTTTTGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:70:37,33:114,133:247,70:0.2201:2,2:27.3:1:30.5:1:0.3447:1.31:60:69:0.2219:0:2 0/1:380:132:58,74:116,132:248,132:0.3474:2,2:26.9:1:29.5:1:0.6655:1.12087:60:264:0.3511:0:2 +13 46833227 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=TGTGAGGCAGCATGGAGGCA;RSEQ=GAAAGCTCAGCTTCTGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:48,114:162,0:0:2,0:24.9:1:31.6:1:1:0:60:161:1:0:0.5 0/1:175:2:1,1:55,118:173,2:0.0114:2,2:24.5:1:26.5:1:0.53885:2.14:60:4:0.0115:0:1.5 +13 46833228 . G A 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.88868;LSEQ=GTGAGGCAGCATGGAGGCAG;RSEQ=AAAGCTCAGCTTCTGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:1,0:45,113:158,1:0.0063:2,0:1:0:28:0:0.28931:0:60:2:0.0063:0:1 0/1:169:2:1,1:53,114:167,2:0.0118:2,2:7.5:1:27.5:1:0.53825:2.14:60:4:0.012:0:1.5 +13 48095708 . G A 49 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCATTTGGGGTTCCATTC;RSEQ=TAAGACCATCAGTAGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:6:0:33:0:1:0:60:2:1:0:1 1/0:5:3:2,1:2,0:2,3:0.6:0,2:21:1:31.3:1:1:0:52:6:0.6:0:1 +13 48095852 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15726;SOR=0;LSEQ=AAGCCATGTTGCCCAACTCC;RSEQ=GAGGTTGGTATAAGAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:4,7:11,2:0.1538:2,2:28:1:31.5:1:1:1.67:24:4:0.1538:0:1 0/0:19:0:0,0:9,10:19,0:0:2,0:33.7:1:29.7:1:1:0:28.1:38:1:0:0.5 +13 48095922 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGTAAATGCTGGGTGGC;RSEQ=TCTCGTATGATCCCTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:19.9:1:33.1:1:1:0:40.7:14:1:0:1.1 1/1:18:18:5,13:0,0:0,18:1:0,2:18.9:1:31.7:1:1:0:40.2:36:1:0:1.1 +13 48877985 . G T 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.06114;SOR=6.48543;LSEQ=GACGGGGCGTGCCCCGACGT;RSEQ=CGCGCGCGTCGTCCTCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:0,1:239,151:390,1:0.0026:2,0:1:0:25:0:0.38875:0:60:2:0.0026:0:1 0/1:367:6:3,3:216,145:361,6:0.0163:2,2:15.7:1:25.5:1:0.68859:1.48796:60:5:0.0139:0:1.7 +13 48878084 . CGCCGCCGCT C 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCGAAAAACGGCCGCCAC;RSEQ=GCCGCCGCGGAACCCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:232,314:546,0:0:2,0:21.3:1:31.1:1:1:0:59.9:33.125:0.987:0:0.3 0/1:703:71:40,31:287,342:629,71:0.101:2,2:28.7:1:30.7:1:0.10261:1.54:59.6:142:0.103:0.0057:0.3 +13 48878114 . ACCG A 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.2193;SOR=2.85222;LSEQ=GCCGCCGCGGAACCCCCGGC;RSEQ=CCGCCGCCGCCCCCTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:2:0,2:190,188:378,2:0.0052:2,0:8.5:1:33:1:0.49868:0:60:4:0.0054:0.0026:1 0/1:608:9:4,5:316,282:598,9:0.0148:2,2:33:1:31.1:1:0.74173:1.39992:60:18:0.015:0.0016:0.2 +13 48878251 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51361;SOR=Inf;LSEQ=GGGTGTGCGTAGGGCGGGCG;RSEQ=CAAGGCGGCTCGGCGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:14,66:80,0:0:2,0:20.3:1:31.6:1:1:0:60:39:1:0:0.7 0/1:115:2:1,1:21,92:113,2:0.0174:2,2:28:1:27.5:1:0.34737:4.30:60:4:0.0187:0:1.5 +13 48878271 . T C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGCGGCTCGGCGGGGA;RSEQ=CCGTCCTCGCCAGGGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:4,34:0,0:0,38:1:0,2:18.2:1:31.4:1:1:0:60:18:1:0:1.4 1/1:57:57:4,53:0,0:0,57:1:0,2:17:1:31.5:1:1:0:60:114:1:0:1.3 +13 48878292 . G A 117 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10673;SOR=0;LSEQ=CCGTCCTCGCCAGGGGCCGG;RSEQ=TCCCGGCGGGAGGAGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:1,12:0,0:0,13:1:0,1:18.4:1:31.8:1:1:0:60:26:1:0:2.1 1/0:16:12:0,12:0,4:4,12:0.75:0,0:10.3:1:30.4:1:1:0:60:24:0.75:0:2.2 +13 48878344 . C A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCGCCACGGCGGAGCGTCTG;RSEQ=AGAATGGTGACAGGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:9:1:30.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:31.5:1:1:0:60:4:1:0:1.5 +13 48881154 . G C 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TTCCTTCACAGAAGTGTTTT;RSEQ=CTGCTTTGAAGTATATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:29.4:1:32.7:1:1:0:60:14:0.7778:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:7:0:32:0:1:0:60:2:1:0:1 +13 48881570 . A AT 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.15669;SOR=2.60774;LSEQ=TTTTCTTAAAACGTTTTGAA;RSEQ=TTTTTTTTTCTCATTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:74,215:289,3:0.0103:2,2:34.7:1:31:1:1:1.45:60:6:0.0105:0:0 0/1:341:9:2,7:93,239:332,9:0.0264:2,2:30.3:1:29.8:1:1:1.36073:60:18:0.0269:0:0.1 +13 48916172 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTGTATACTATATACTA;RSEQ=GCCAAAGGCTTTATAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:35.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 48916672 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24781;SOR=Inf;LSEQ=AATCAGTTATAATACAGTTT;RSEQ=AACATAGTATCCAGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:147,25:172,0:0:2,0:23.7:1:30.7:1:1:0:60:56.333:1:0:0.1 0/1:171:2:1,1:132,37:169,2:0.0117:2,2:15:1:29:1:0.39608:3.5334:60:4:0.0118:0:1 +13 48916895 . C T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00248;LSEQ=GCCTCTGCCATAAAAGGAAA;RSEQ=GAATTCTGGATTTTCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:8:2,6:28,145:173,8:0.0442:2,2:16.9:1:30.9:1:0.62115:1.72:60:16:0.0442:0:1 0/1:158:7:0,7:32,118:150,7:0.0443:2,0:29.4:1:28.1:1:0.34593:0:60:14:0.0446:0:1.3 +13 48916904 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20571;SOR=Inf;LSEQ=ATAAAAGGAAACGAATTCTG;RSEQ=ATTTTCCTCTCAATAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:17,133:150,0:0:2,0:22.3:1:32.7:1:1:0:60:300:1:0:0.1 0/1:125:2:1,1:15,107:122,2:0.016:2,2:13:1:27.5:1:0.24233:6.94:60:4:0.0163:0:1 +13 48919167 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23035;SOR=0;LSEQ=GATTTGAAAACGAAATAACA;RSEQ=AAATTTTTAAGGTTACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:136,36:172,2:0.0115:2,2:20:1:29:1:0.38104:3.74018:60:4:0.0116:0:1 0/0:188:0:0,0:142,46:188,0:0:2,0:23.5:1:31.2:1:1:0:60:61.667:1:0:0.1 +13 48919358 . T G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTAAACATTTTATTAGG;RSEQ=TTACACTCTGATTTTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:273:273:73,200:0,0:0,273:1:0,2:24.2:1:31.7:1:1:0:60:53.6:1:0:1.1 1/1:290:289:97,192:0,0:0,289:0.9966:0,2:24.1:1:30.7:1:1:0:60:143.5:0.9965:0:1.1 +13 48919381 . A G 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01453;SOR=Inf;LSEQ=ACACTCTGATTTTTTATGTC;RSEQ=TTGTTCACAATTAGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:34,155:189,0:0:2,0:22.5:1:30.9:1:1:0:59.9:62:1:0:1 0/1:187:6:2,4:42,139:181,6:0.0321:2,2:23.2:1:30.8:1:0.62699:1.65:60:12:0.0323:0:2 +13 48919455 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18365;SOR=Inf;LSEQ=GTATTAATTCTTAGACTTGT;RSEQ=CCTTTTAATGTTAGCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:1,53:54,0:0:1,0:24.8:1:31.7:1:1:0:59.8:53:1:0:0.3 0/1:41:2:0,2:2,37:39,2:0.0488:2,0:35.5:1:28:1:1:0:60:4:0.0488:0:1 +13 48921884 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00027;SOR=0;LSEQ=TATACTTCTTAAAAGAAGAT;RSEQ=AATAAAGCATGAGAAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:184:184:144,40:0,0:0,184:1:0,2:21.8:1:32.4:1:1:0:60:183:1:0:1.1 1/1:254:239:174,65:10,5:15,239:0.9409:2,2:23.9:1:31:1:0.56497:1.34:59.9:78.667:0.9402:0:1.1 +13 48921934 . A T 55 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.16782;SOR=0.17979;LSEQ=CTAAATTACGAAAAAATGTT;RSEQ=AAAAGTCATAATGTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:1,3:232,155:387,4:0.0102:2,2:13.3:1:27.8:1:0.30755:4.47361:60:8:0.0103:0:1.3 0/0:540:1:0,1:299,240:539,1:0.0019:2,0:1:0:24:0:0.4463:0:60:2:0.0019:0:1 +13 48922031 . TA T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.38014;SOR=0.54054;LSEQ=ACAGAATGTTATTTTTCACT;RSEQ=AAAAAAAAGATTTTTATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:7:1,6:79,175:254,7:0.0268:2,2:24.6:1:31.7:1:0.67946:2.70035:60:14:0.0268:0:0 0/1:341:5:0,5:122,214:336,5:0.0147:2,0:32.4:1:28.8:1:0.16458:0:60:10:0.0148:0:0 +13 48922078 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51035;SOR=Inf;LSEQ=CTCAAACATCTTGATAGTTA;RSEQ=GGTTAGTTTGATCGATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:2,82:84,0:0:1,0:24.5:1:31.8:1:1:0:59.6:168:1:0:0 0/1:116:2:0,2:12,102:114,2:0.0172:2,0:10:1:31:0:1:0:60:4:0.0174:0:1 +13 48922984 . A AT 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.03875;LSEQ=TTATGCATTTAACTAAGGTC;RSEQ=TTTTTTTTTTAATGCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:8:7,1:56,0:56,8:0.1231:1,2:24:1:31.6:1:0.125:0:60:16:0.1231:0:0.1 0/1:55:7:6,1:48,0:48,7:0.1273:1,2:20.3:1:29.7:1:0.12727:0:60:14:0.1273:0.0364:0.3 +13 48923061 . G GT 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.1844;LSEQ=TTCAGTGATACATTTTTCCT;RSEQ=TTTTTTTTCTGCTTTCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:196,91:287,3:0.0103:2,2:14:1:28.7:1:1:1.07664:60:6:0.0106:0.0069:0.7 0/1:327:4:4,0:214,109:323,4:0.0122:2,0:28.5:1:30.5:1:0.30545:0:60:8:0.0123:0:0 +13 48923200 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19418;SOR=0;LSEQ=AAATGCTAATATTTCAAATG;RSEQ=AATAATTAAATTGGCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:33,127:160,2:0.0123:2,2:20:1:29.5:1:0.37673:3.81:60:4:0.0124:0:1 0/0:205:0:0,0:48,157:205,0:0:2,0:21.8:1:27.8:1:1:0:60:204:1:0:0.1 +13 48934140 . A AT 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08328;SOR=0.57837;LSEQ=AACTTTCTTTAAAAATGTAC;RSEQ=TTTTTTTTTCAGGGGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:24:15,9:171,70:241,24:0.0902:2,2:24.1:1:31.4:1:0.48262:1.46348:59.1:48:0.0916:0.0075:0.5 0/1:369:20:10,10:233,116:349,20:0.0542:2,2:22.4:1:28.8:1:0.14707:2.00459:60:40:0.0549:0.019:0.4 +13 48934316 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23219;SOR=0;LSEQ=TCATTCAGCAGTTGCTTATT;RSEQ=AATGTCTAGTGGGTACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:20,118:138,2:0.0143:2,2:15:1:28:1:0.27842:5.78:60:4:0.0144:0:1 0/0:150:0:0,0:34,116:150,0:0:2,0:22.1:1:30.4:1:1:0:60:49:1:0:0.1 +13 48934329 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23579;SOR=Inf;LSEQ=GCTTATTGAATGTCTAGTGG;RSEQ=TACCAAACATGGTTCTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:12,104:116,0:0:2,0:21.9:1:32.1:1:1:0:60:115:1:0:0.1 0/1:110:2:1,1:15,93:108,2:0.0182:2,2:21:1:27:1:0.27089:6.04:60:4:0.0185:0:1 +13 48938897 . TA T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.21831;SOR=Inf;LSEQ=TCTAAGAAAATAATAAAAAA;RSEQ=AAAAAGTTATACACAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:61,0:0:1,0:17.8:1:28.8:1:1:0:60:29.5:1:0:0.1 0/1:54:2:2,0:52,0:52,2:0.037:1,0:15:0:32:0:1:0:60:4:0.037:0:0 +13 48939018 . C T 51 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01465;SOR=0;LSEQ=TAATGATCATGTTGTAACTT;RSEQ=ATCTTTTTCAGGTGAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:5:1,4:217,150:367,5:0.0134:2,2:5:1:22:1:0.16451:5.76167:60:4:0.011:0:1.8 0/0:491:0:0,0:280,211:491,0:0:2,0:24.2:1:30.9:1:1:0:60:162.667:1:0:0.1 +13 48939204 . A AT 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.68764;SOR=0.58741;LSEQ=ATCAATTTACTGTGTATCAC;RSEQ=TTTTTTTTTTGCCCAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:4:0,4:1,61:62,4:0.0606:1,0:34.8:1:31.8:1:1:0:60:8:0.0625:0:0 0/1:55:2:0,2:3,50:53,2:0.0364:2,0:37.5:1:30:1:1:0:60:4:0.0385:0:0 +13 48941548 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22999;SOR=0;LSEQ=ATGTATATTATACAAAAATT;RSEQ=TTTAATGAAATCTGTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:139,18:157,2:0.0126:2,2:9:1:28:1:0.22538:7.54319:60:4:0.0127:0:1 0/0:172:0:0,0:146,26:172,0:0:2,0:21.3:1:30.7:1:1:0:60:171:1:0:0.1 +13 48942787 . G A 39 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.21827;LSEQ=ATTATAATTTTGTTATTCAT;RSEQ=GCTTTATAGTGTTTCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:2:2,0:42,179:221,2:0.009:2,0:1:0:23.5:1:0.03822:0:60:4:0.0093:0:1 0/1:275:3:2,1:56,216:272,3:0.0109:2,2:22:1:24.7:1:0.11363:7.64:60:6:0.011:0:1 +13 48943142 . C CA 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGCGAAACTCCGTCT;RSEQ=AAAAAAAAAATGTGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:34.5:1:32:1:1:0:48:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 48947469 . G T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACATTTAACTTGGGAGAT;RSEQ=GAAAACATTTCATTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:144:144:117,27:0,0:0,144:1:0,2:19.5:1:31.3:1:1:0:60:288:1:0:1.1 1/1:137:137:109,28:0,0:0,137:1:0,2:20.8:1:29.6:1:1:0:60:136:1:0:1.1 +13 48950990 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50526;SOR=Inf;LSEQ=AAAAGTCATATATTATGGAG;RSEQ=AGAAAATATTAATTCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:89,12:101,0:0:2,0:23.5:1:32.5:1:1:0:60:32.667:1:0:0.1 0/1:129:2:1,1:102,25:127,2:0.0155:2,2:32.5:1:28.5:1:0.36374:4.02033:60:4:0.0156:0:1.5 +13 48951025 . A G 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00859;SOR=Inf;LSEQ=CTGATTACACAGTATCCTCG;RSEQ=CATTGATTTCTGTTTTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:170,58:228,0:0:2,0:23.7:1:30.3:1:1:0:60:75:1:0:0.1 0/1:265:8:5,3:175,82:257,8:0.0302:2,2:32.8:1:30.8:1:0.71405:1.2792:60:16:0.0304:0:1.1 +13 48951239 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24184;SOR=Inf;LSEQ=AAAGCAGCATCTTTCCAGTT;RSEQ=GTATAAATACTCTAACAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:13,126:139,0:0:2,0:24.3:1:30:1:1:0:59.8:68.5:1:0:0.1 0/1:135:2:0,2:7,126:133,2:0.0148:2,0:42:0:30.5:1:1:0:60:4:0.015:0:2.5 +13 48953655 . C CA 140 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.54336;SOR=0.75216;LSEQ=AAAACAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAAATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:20:20,0:14,1:15,20:0.4878:1,1:30.9:1:31.1:1:0.42857:0:60:40:0.4878:0:0.2 0/1:60:25:25,0:22,1:23,25:0.4167:1,1:28:1:30.2:1:0.47917:0:59.8:50:0.4167:0:0.5 +13 48953730 . C T 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19667;SOR=0.28111;LSEQ=TTCTTTTTGTTTGTTTGTAG;RSEQ=GATACAAACTTGGAGTTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:4:1,3:176,117:293,4:0.0135:2,2:12:1:28:1:0.30674:4.49061:60:8:0.0141:0:1 0/0:524:2:0,2:308,213:521,2:0.0038:2,0:1:0:23.5:1:0.16853:0:60:4:0.0039:0:1.5 +13 48953840 . G A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.44637;LSEQ=GGGCGCGGTGGCTCACGCCT;RSEQ=CAATCCCAGCACTTTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:1:1,0:29,110:139,1:0.0071:2,0:1:0:23:0:0.21429:0:60:2:0.0072:0:1 0/1:194:2:1,1:42,150:192,2:0.0103:2,2:26.5:1:26:1:0.39506:3.54:58.5:4:0.0105:0:1 +13 48954021 . G C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36111;SOR=0;LSEQ=CAGGAGAATCCCTTGAACCA;RSEQ=GGAGGTGGAGGTTGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:17,6:0,0:0,23:1:0,2:27.3:1:28.3:1:1:0:54.5:4.75:1:0:1.2 1/1:13:12:11,1:0,0:0,12:0.9231:0,2:24.7:1:31.5:1:1:0:55.5:24:0.9231:0:1.4 +13 48954126 . G T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88342;LSEQ=AAAAAAAAAAAAAATTCAAT;RSEQ=CTGACACAAATAAGGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:112,23:135,2:0.0145:2,2:4.5:1:28.5:1:0.32074:4.78833:60:4:0.0171:0:1 0/1:234:3:1,2:163,66:229,3:0.0128:2,2:22.3:1:21.3:1:0.20625:4.90039:47.3:2:0.0103:0:5.3 +13 48954131 . C T 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16193;SOR=Inf;LSEQ=AAAAAAAAATTCAATGCTGA;RSEQ=ACAAATAAGGTTTCAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:137,34:171,0:0:2,0:15.2:1:27.6:1:1:0:58.4:2.638:1:0:1.2 0/1:273:5:1,4:184,78:262,5:0.0183:2,2:9:1:20:1:0.03222:9.35114:52.4:4:0.0205:0:2.2 +13 48954175 . A T 168 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.85087;LSEQ=ACTTCTTTTTTTTTTTTTAA;RSEQ=TTATCTGTTTCAGGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:507:5:2,3:297,205:502,5:0.0099:2,2:13.2:1:21.8:1:0.40504:2.1698:58.2:1.5:0.0066:0:3.4 0/1:777:63:33,30:371,343:714,63:0.0811:2,2:26.7:1:28.2:1:1:1.02:59.1:14.75:0.0836:0:1.4 +13 48954282 . CT C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.30885;SOR=0.76749;LSEQ=AGAAGTAAGTATTTTATAAT;RSEQ=TTTTTTTTTTCCTTTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:35:15,20:115,180:295,35:0.1054:2,2:24.7:1:32.5:1:0.71563:1.17:59.7:70:0.107:0.009:0.1 0/1:398:33:14,19:136,228:364,33:0.0829:2,2:28.9:1:31.3:1:0.57798:1.23:60:66:0.0855:0:0.3 +13 48954329 . A T 51 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22994;SOR=4.15497;LSEQ=TGAATGACAACATTTTTCAT;RSEQ=TGTCTTTATTGGCGTGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:1:0,1:164,203:367,1:0.0027:2,0:1:0:26:0:1:0:60:2:0.0028:0:1 0/1:446:5:2,3:203,238:441,5:0.0112:2,2:11.6:1:22:1:1:1.27871:60:1.5:0.0072:0:2.4 +13 48954450 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49925;SOR=Inf;LSEQ=TGGTGTGTTTCTTTGGTCGG;RSEQ=GGAGAGGGATAGTGTGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:9,90:99,0:0:2,0:23.3:1:30.7:1:1:0:60:18.8:1:0:0.1 0/1:111:2:1,1:14,95:109,2:0.018:2,2:9:1:28.5:1:0.25307:6.59:60:4:0.0183:0:1 +13 48955201 . T A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGAAAAACACAGATTTGC;RSEQ=TACACTCAAAATTGGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:27.3:1:31:1:1:0:57:14:1:0:1.3 1/1:2:2:2,0:0,0:0,2:1:0,0:20.5:1:28.5:1:1:0:60:4:1:0:1.5 +13 48955363 . CT C 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.42612;SOR=0.63896;LSEQ=TAATATTTCATAAATAGTTA;RSEQ=TTTTTTTTTCATTTTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:8:7,1:93,15:108,8:0.069:2,2:33.1:1:32.9:1:1:1.13:60:16:0.069:0:0 0/1:133:6:6,0:112,15:127,6:0.0451:2,0:22.2:1:33:0:1:0:54.7:12:0.0458:0:0.3 +13 48955407 . C T 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67671;SOR=0.62229;LSEQ=TACATCTCAGAATCTTGATT;RSEQ=TGGAACAGATTTGTCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:1,2:188,74:262,3:0.0113:2,2:8.7:1:21.7:1:0.19858:5.04497:60:2:0.0077:0:1 0/0:284:2:0,2:215,67:282,2:0.007:2,0:3:1:26.5:1:0.05838:0:60:4:0.0074:0:1 +13 48955445 . C T 51 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22149;SOR=4.50549;LSEQ=TCCCATGGATTCTGAATGTG;RSEQ=TTAATTTAAAAGCCTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:1:0,1:248,168:416,1:0.0024:2,0:1:0:26:0:0.40528:0:60:2:0.0024:0:1 0/1:466:5:0,5:272,189:461,5:0.0107:2,0:7.2:1:22:1:0.01213:0:60:4:0.0088:0:1.6 +13 48955623 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.10678;SOR=Inf;LSEQ=AATTCATTCATGTGCATATG;RSEQ=CTAACAAATTATTGTTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:40,145:185,0:0:2,0:25.6:1:32.1:1:1:0:59.9:184:1:0:0.3 0/1:168:3:1,2:42,123:165,3:0.0179:2,2:23.7:1:25.3:1:1:1.46:60:6:0.0183:0:1.3 +13 48955659 . C CAA 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.74215;SOR=1.45686;LSEQ=TAGTGAGAGGTGTTTCTTAA;RSEQ=ATCTACCTCAAGAACATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:5:0,5:2,90:92,5:0.0515:1,0:29:1:32:1:1:0:60:10:0.0521:0.0103:0.8 0/1:68:5:0,5:3,60:63,5:0.0735:1,0:15.2:1:31.3:1:1:0:60:10:0.0758:0.0441:0.4 +13 48955676 . T A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.40517;SOR=0;LSEQ=TAACATCTACCTCAAGAACA;RSEQ=ATAGGGAATTTAATGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:69:2,67:0,0:0,69:1:0,1:23.3:1:32:1:1:0:60:138:1:0:1 1/1:47:46:0,46:0,1:1,46:0.9787:0,1:21.9:1:30.6:1:1:0:59.3:92:0.9787:0:1 +13 49026852 . C T 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTCTCTCCACTTTCTT;RSEQ=GTTTTTTTTCTGTCTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:24.5:1:32.8:1:1:0:53:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 49027044 . A T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22873;SOR=Inf;LSEQ=GCCTAAAATTCATAGTACTT;RSEQ=CCATGTCAAACAATATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:147,15:162,0:0:2,0:24.1:1:28.8:1:1:0:60:324:1:0:0.1 0/1:149:2:1,1:128,18:146,2:0.0134:2,2:6:1:27:1:0.24104:6.94841:60:4:0.0135:0:1 +13 49033747 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00696;SOR=0;LSEQ=AACAGCATTATAATTAGAGC;RSEQ=ATTTCATGATTTGAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:218:180,38:0,0:0,218:1:0,2:23:1:30.4:1:1:0:60:217:1:0:1.1 1/1:214:207:172,35:7,0:7,207:0.9673:0,2:23.2:1:29.7:1:0.60219:0:60:102.5:0.967:0:1.1 +13 49034008 . T A 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36573;SOR=3.11601;LSEQ=TCACCTTCTCTCCTCCCTAC;RSEQ=TACTTGTTAACTGATTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:1,0:56,251:307,1:0.0032:2,0:1:0:26:0:0.18506:0:60:2:0.0033:0:1 0/1:300:3:2,1:86,211:297,3:0.01:2,2:8:1:22:1:0.20679:4.88:53:2:0.007:0:1 +13 49034022 . A AT 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.21126;LSEQ=CCCTACTTACTTGTTAACTG;RSEQ=TTCTTTCTTTCTTTCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:235:220:29,191:4,11:15,220:0.9362:2,2:27.2:1:30.8:1:0.23797:2.38362:55.9:54:0.9351:0.1362:0.1 1/0:188:142:26,116:12,32:44,142:0.7553:2,2:32.1:1:29.4:1:0.20491:1.66802:54.8:27.4:0.7611:0.0053:0.1 +13 49034073 . C CT 86 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=15.000;MSILEN=4;SSF=0.30776;SOR=0.41836;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TTTCTTTCTTTCTTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:7:0,7:0,26:26,7:0.2121:1,0:7.4:1:30.9:1:1:0:44.4:14:0.2188:0.1212:0.3 0/1:30:3:0,3:0,27:27,3:0.1:1,0:9.7:1:31:1:1:0:45:6:0.1034:0.0333:0.7 +13 49034077 . C CT 62 p8;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=14.000;MSILEN=4;SSF=0.1039;SOR=0;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TTTCTTTCTTTTTCTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:0,4:0,14:14,4:0.2222:1,0:5:1:31.3:1:1:0:33.8:8:0.2222:0.1667:0 0/0:17:0:0,0:0,17:17,0:0:1,0:7.5:1:32.5:1:1:0:32.6:34:1:0:0.4 +13 49037825 . G T 154 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02587;LSEQ=TTTTTTAAGAACAAAACCAT;RSEQ=TAATAAAATTCTGACTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:34:25,9:199,58:257,34:0.1168:2,2:20.8:1:30.3:1:0.66496:1.23426:60:33:0.1158:0:1 0/0:294:1:1,0:216,77:293,1:0.0034:2,0:27:0:32:0:1:0:60:2:0.0034:0:1 +13 49038039 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15972;SOR=Inf;LSEQ=ACATAACATAGGTAATTCAT;RSEQ=TGATCTCATTTATTCATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:19,156:175,0:0:2,0:23.3:1:30.5:1:1:0:60:86.5:1:0:0.1 0/1:117:2:1,1:14,101:115,2:0.0171:2,2:32:1:30.5:1:0.24094:7.00:60:4:0.0171:0:1 +13 49038459 . A T 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTGTGGAAAGTGAGTTG;RSEQ=GGGGTATTTTTCCCATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:20.5:1:30.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:27.5:1:1:0:60:4:1:0:1 +13 49047529 . G C 236 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTGGTGAATCATTCGGGGT;RSEQ=AGTATTTTCTTTCTATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:158:63,95:89,140:229,158:0.4062:2,2:27.3:1:32.4:1:0.9157:1.04:60:157:0.4067:0:1.1 0/0:508:0:0,0:217,290:507,0:0:2,0:25.9:1:30.7:1:1:0:60:100.4:0.998:0:0.1 +13 49050784 . C T 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02688;SOR=Inf;LSEQ=CTATAACTTGAGGTTGCTAA;RSEQ=TATGAAACACTGGCATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:74,13:87,0:0:2,0:23.3:1:32.3:1:1:0:59.7:174:1:0:0 0/1:84:5:4,1:66,13:79,5:0.0595:2,2:25.8:1:30:1:1:1.26538:60:10:0.0595:0:1 +13 49051012 . C T 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGAATGTTTTCCAGTAGC;RSEQ=GAGATGGTCATCTGGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:160:160:38,122:0,0:0,160:1:0,2:25:1:31:1:1:0:60:320:1:0:1.1 1/1:165:165:43,122:0,0:0,165:1:0,2:23.3:1:29.4:1:1:0:60:40.25:1:0:1.1 +13 49051029 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22923;SOR=Inf;LSEQ=AGCCGAGATGGTCATCTGGG;RSEQ=AATCCAGAGTCTCAGCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:22,107:129,0:0:2,0:22.2:1:31.8:1:1:0:60:63.5:1:0:0.9 0/1:119:2:0,2:20,97:117,2:0.0168:2,0:28:1:29.5:1:1:0:60:4:0.0171:0:2 +13 49051428 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20112;SOR=Inf;LSEQ=ATCGAAAGCATCATAGTTAC;RSEQ=GGAAATTTGAGTTTTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:145,61:206,0:0:2,0:25.7:1:31.3:1:1:0:60:67.667:1:0:0.1 0/1:168:2:1,1:130,36:166,2:0.0119:2,2:23:1:27.5:1:0.393:3.57536:60:4:0.0119:0:1 +13 49051481 . T A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.8477;SOR=0.88903;LSEQ=TGAAATGTTTTGCATTTTTT;RSEQ=AATCTGCAGTAAACATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:14:9,5:183,144:327,14:0.0409:2,2:19.5:1:29.2:1:0.59405:1.41:60:28:0.0414:0:1.3 0/1:383:14:9,5:211,158:369,14:0.0366:2,2:27.3:1:28.2:1:0.78454:1.35:60:28:0.037:0:1.1 +13 49051605 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50012;SOR=Inf;LSEQ=TACACTGCAAGAAGTCTTTT;RSEQ=GTTATATAAAAGAATGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:33,141:174,0:0:2,0:22.9:1:30.6:1:1:0:60:173:1:0:0.1 0/1:194:2:0,2:47,144:191,2:0.0103:2,0:19:1:31.5:1:1:0:60:4:0.0104:0:1 +13 49051632 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49771;SOR=Inf;LSEQ=TAAAAGAATGTATAATTTCT;RSEQ=CAGTTGGCAGGTTTGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:13,80:93,0:0:2,0:22.2:1:29.9:1:1:0:60:30:1:0:0 0/1:98:2:1,1:16,80:96,2:0.0204:2,2:22.5:1:26:1:0.31833:4.88:60:4:0.0206:0:1 +13 49051848 . G A 79 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCAGAACTACAAAGAGGA;RSEQ=CTATTTGGGAGTGTTAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:25.3:1:30.8:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 49054037 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49958;SOR=Inf;LSEQ=TGCTTTTGCAAGGTCCTGAG;RSEQ=GCCATCAGTTTGACATGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:119,23:142,0:0:2,0:25.7:1:31.5:1:1:0:60:70:1:0:0.1 0/1:157:2:2,0:130,25:155,2:0.0127:2,0:20.5:1:30.5:1:1:0:60:4:0.013:0:1 +13 49054056 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24875;SOR=Inf;LSEQ=GCGCCATCAGTTTGACATGA;RSEQ=CATAATATATATGGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:163,68:231,0:0:2,0:22:1:32.3:1:1:0:59.9:45.2:1:0:0.1 0/1:241:3:2,1:175,63:238,3:0.0124:2,2:11:1:27.3:1:1:1.38686:60:6:0.0126:0:1 +13 49054299 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51237;SOR=0;LSEQ=CTTTCCCAGGTTCTGTTTAT;RSEQ=GCCACATTTAATATCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:0,2:10,100:110,2:0.0179:2,0:24.5:1:26:1:1:0:60:4:0.0183:0:1 0/0:79:0:0,0:4,75:79,0:0:2,0:21.6:1:30.4:1:1:0:59.8:38.5:1:0:0.1 +13 50950167 . C A 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01318;SOR=Inf;LSEQ=CAGAATCCAGACCAAAGTCA;RSEQ=GGTGAACTGGCATGAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:12,0:0:2,0:19.3:1:31.1:1:1:0:60:24:1:0:1 0/1:22:9:6,3:8,5:13,9:0.4091:2,2:26.6:1:30.2:1:1:1.24:60:18:0.4091:0:2.1 +13 50950203 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACAACAACAACAGCAGC;RSEQ=GCAGCAGCAGCAACAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:10,9:0,0:0,19:1:0,2:32.2:1:31.9:1:1:0:59.8:38:1:0:1.1 1/1:36:36:20,16:0,0:0,36:1:0,2:31.4:1:30.5:1:1:0:58.6:72:1:0:1.5 +13 50950213 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.54413;SOR=Inf;LSEQ=CAACAGCAGCGGCAGCAGCA;RSEQ=CAACAATATAGACACATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:20,0:0:2,0:30.4:1:33.5:1:1:0:59.8:40:1:0:1.1 0/1:39:2:1,1:19,18:37,2:0.0513:2,2:28:1:27.5:1:1:1.05412:60:4:0.0513:0:2 +13 51448137 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TTTTTGCTGAAGACAGGCCA;RSEQ=GGTGATCAGACATCACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:20:1:30.8:1:1:0:60:8:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:18:0:31.5:1:1:1:60:4:0.5:0:1 +13 51448230 . C A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ATCAGATATTGAGGATGGGA;RSEQ=CACTTGCTAAACCAACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:5.5:1:29.5:1:1:2.44949:32:4:0.3333:0:1.5 0/0:4:0:0,0:3,1:4,0:0:2,0:31.3:1:31.5:1:1:0:60:8:1:0:0 +13 51449467 . G A 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71669;SOR=0.72259;LSEQ=ATCTGCAGTTGCCAAGCTGG;RSEQ=AACTCAGGAGAGCCAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:5,2:4,6:10,7:0.4118:2,2:21.1:1:30:1:0.33484:3.46:59.6:14:0.4118:0:1.1 0/1:12:4:2,2:4,4:8,4:0.3333:2,2:40.8:1:29:1:1:1:60:8:0.3636:0:1 +13 51449485 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48308;SOR=0;LSEQ=GGGAACTCAGGAGAGCCAAG;RSEQ=GTGTAAGTTCTAATCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:4,8:12,2:0.1429:2,2:37.5:1:29.5:1:1:1.90:60:4:0.1429:0:1 0/0:12:0:0,0:5,7:12,0:0:2,0:18.5:1:30.7:1:1:0:60:24:1:0:0.6 +13 51775024 . T A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50232;SOR=0;LSEQ=GAGTAATAGCAAGATGGCTG;RSEQ=CACGGGGCCTAGAAAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:75,58:133,2:0.0148:2,2:12:0:32:0:1:1.29061:60:4:0.0149:0:1 0/0:112:0:0,0:66,46:112,0:0:2,0:22.1:1:28.3:1:1:0:52.8:55:1:0:0.2 +13 51775043 . GA G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=GTCACGGGGCCTAGAAAGGG;RSEQ=AAAGGCATGTCGCCCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:92,79:171,2:0.0115:2,2:36:1:33:1:1:1.16353:49.5:4:0.0118:0:0 0/0:168:0:0,0:90,77:167,0:0:2,0:23.8:1:28.6:1:1:0:53.2:40.75:1:0:0.2 +13 51775049 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24784;SOR=Inf;LSEQ=GGGCCTAGAAAGGGGAAAAG;RSEQ=CATGTCGCCCAACTCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:93,81:174,0:0:2,0:29.2:1:31.8:1:1:0:55.2:173:1:0:0.2 0/1:173:2:1,1:90,81:171,2:0.0116:2,2:25:1:26:1:1:1.11043:60:4:0.0119:0:1 +13 51775062 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24829;SOR=Inf;LSEQ=GGAAAAGGCATGTCGCCCAA;RSEQ=TCCAGAGGTTGGTATAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:89,88:177,0:0:2,0:31.8:1:32.6:1:1:0:56.4:58:1:0:0.2 0/1:185:3:1,2:88,94:182,3:0.0162:2,2:29:1:26:1:1:1.86625:52:2:0.011:0:2.3 +13 51775082 . G GT 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.02852;SOR=Inf;LSEQ=CTCCAGAGGTTGGTATAAGA;RSEQ=TTTGAAGGGCATTGTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:74,95:169,0:0:2,0:28.5:1:32.9:1:1:0:56.6:338:1:0:0.3 0/1:165:5:2,3:69,91:160,5:0.0303:2,2:24.6:1:29:1:1:1.13646:49.6:10:0.0307:0.0121:0.2 +13 51775127 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01956;SOR=0.35043;LSEQ=GAAGCTTTTTTCTGTAAACG;RSEQ=CGGGTAGTGTCTCATACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:19:6,13:10,26:36,19:0.3455:2,2:23.2:1:28.8:1:0.76517:1.20:58.9:18:0.3333:0:1.3 0/1:71:11:3,8:17,43:60,11:0.1549:2,2:17.6:1:29.1:1:1:1.05349:59.8:22:0.1594:0:1 +13 51775149 . C T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.60191;SOR=1.3439;LSEQ=GGGTAGTGTCTCATACTATC;RSEQ=CTGACTGGTTAGTGTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:10:1,9:3,24:27,10:0.2703:2,2:16.8:1:30.8:1:1:1.1215:42.2:20:0.2703:0:1 0/1:30:10:1,9:2,18:20,10:0.3333:2,2:19.3:1:28.7:1:1:1:45.3:20:0.3571:0:1 +13 54073225 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTAAGGAGTGGGAAGACGAG;RSEQ=ACAAAAAATTGTGAATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 54073461 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49836;SOR=Inf;LSEQ=TCTCTGTACAGAGTGACTAT;RSEQ=TCAGACCCATTGAAGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:85,62:147,0:0:2,0:25:1:32:1:1:0:60:72.5:1:0:0.8 0/1:150:2:2,0:82,66:148,2:0.0133:2,0:15.5:1:25.5:1:0.50389:0:60:4:0.0135:0:1 +13 54073469 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.36615;LSEQ=CAGAGTGACTATGTCAGACC;RSEQ=ATTGAAGGGTCCACTTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:114:64,50:18,22:40,114:0.7403:2,2:23.4:1:30.1:1:0.27027:1.56:60:228:0.7403:0:1.2 1/0:153:78:39,39:44,31:75,78:0.5098:2,2:26:1:29.2:1:0.33105:1.41607:60:156:0.5098:0:1.3 +13 54073555 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14909;LSEQ=TTAAAAGATTATAAGGAAAA;RSEQ=CAATAAAAATATGTTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:59:11,48:3,13:16,59:0.7867:2,2:23.7:1:33.1:1:1:1.0069:60:118:0.7867:0:1.3 0/1:74:26:9,17:13,35:48,26:0.3514:2,2:21.3:1:31:1:0.59638:1.42:60:52:0.3562:0:1.3 +13 54891366 . GCACCTTCTTAGGGGAAGAGTGTTGTTTTTACACTAACCAGT G 45 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.53981;LSEQ=TGTTGAGAAAGGAGGATTCT;RSEQ=CAGGGATAGTACGAGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:1,3:0.75:0,2:13.7:1:31.1:1:1:0:27:6:0.75:0.75:0 1/0:5:3:2,1:2,0:2,3:0.6:0,2:17:1:28.8:1:1:0:24:6:0.6:0.6:0 +13 55384564 . T G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTCCCAAATTAATGTTCT;RSEQ=TTTAGTGAGCACCTGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:194:194:135,59:0,0:0,194:1:0,2:22.9:1:32:1:1:0:60:63.667:1:0:1.3 1/1:234:201:126,75:20,13:33,201:0.859:2,2:24.1:1:31.2:1:0.84767:1.09:60:200:0.8621:0:1.3 +13 55384646 . A C 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19389;LSEQ=TGACTCTGAAGGTTGTTCGC;RSEQ=TGCTGTTACCAAATCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:328:150,178:24,18:42,328:0.8865:2,2:28.2:1:31.8:1:0.18994:1.58023:59.9:45.857:0.8867:0:1.2 1/0:354:213:103,110:65,76:141,213:0.6017:2,2:24.6:1:30.8:1:0.74444:1.09:60:212:0.6127:0:1.3 +13 55384686 . T A 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.25229;SOR=0;LSEQ=TGTATTTCAGCTCCAGCATC;RSEQ=TCAATTTCATAAAGGATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:101,196:297,3:0.01:2,2:9.3:1:26.3:1:0.27198:3.86:60:6:0.0101:0:1.7 0/0:261:0:0,0:100,161:261,0:0:2,0:27.4:1:29.2:1:1:0:60:51.2:1:0:0.5 +13 65163931 . A G 93 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0172;SOR=9.4511;LSEQ=TGCTTTTACTAAGTGCTTTC;RSEQ=AAAAATAGAATCATAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:12,14:26,1:0.037:2,0:1:0:30:0:1:0:60:2:0.037:0:1 0/1:33:9:4,5:10,14:24,9:0.2727:2,2:17.6:1:29.4:1:1:1.12:60:18:0.2727:0:1.1 +13 67591492 . T C 182 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GTTTCACTTTAAGTGAATTA;RSEQ=ACCATCACTTTTGGGAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:48:47,1:0,0:0,48:1:0,1:21.5:1:32.6:1:1:0:60:47:1:0:1.6 0/1:16:7:7,0:8,1:9,7:0.4375:2,0:16.9:1:31.7:1:1:0:60:14:0.4375:0:1 +13 67591561 . CA TG 163 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGGCATTGATATTCCCTAA;RSEQ=GTTTAAAATACCCCTGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:35:35,0:68,1:69,35:0.3365:1,1:23.3:1:31.8:1:1:0:60:70:0.3365:0.0385:1.4 0/0:64:0:0,0:63,1:64,0:0:1,0:25.8:1:31.7:1:1:0:60:128:1:0:0.2 +13 67591727 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04527;LSEQ=TTTTGTCTCAAACATGAAAG;RSEQ=GAAATAGGATAAATGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:279:256:77,179:4,16:20,256:0.9176:2,2:22.5:1:31.2:1:0.44845:1.72:60:127:0.917:0:1.1 0/1:273:91:37,54:65,117:182,91:0.3333:2,2:21.8:1:29.6:1:0.42954:1.23:60:44.5:0.3296:0:1.1 +13 67591752 . A C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24759;SOR=0;LSEQ=TAGGATAAATGATATTTTAA;RSEQ=CATTTTTACTATTTTAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:29,124:153,2:0.0129:2,2:16.5:1:29:0:0.35065:4.22:60:4:0.0129:0:2 0/0:156:0:0,0:38,118:156,0:0:2,0:24.2:1:29.2:1:1:0:60:312:1:0:0.4 +13 67591966 . A G 67 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CAAAAATTTTAAACATTTTT;RSEQ=CTGTACACAGAGAAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:12.5:1:33.5:1:1:0:60:8:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:7:0:31:0:1:0:60:2:1:0:0 +13 68406117 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49479;SOR=Inf;LSEQ=CTTCCACTTTGGGAAGGGAA;RSEQ=CACTTTTTCTATACTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:42,0:0:2,0:22.1:1:32:1:1:0:60:84:1:0:0.2 0/1:45:2:1,1:24,19:43,2:0.0444:2,2:27:1:27.5:1:1:1.25655:60:4:0.0455:0:1 +13 68406186 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23287;SOR=Inf;LSEQ=ACTTGGTTCTTTTGGTGTTT;RSEQ=AGGAGTTCTTTCCCGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:39,13:52,0:0:2,0:24.3:1:30:1:1:0:60:51:1:0:0.3 0/1:49:2:2,0:33,14:47,2:0.0408:2,0:22:1:31.5:1:1:0:60:4:0.0408:0:1 +13 68406205 . T A 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00044;SOR=0;LSEQ=TTAGGAGTTCTTTCCCGTTT;RSEQ=TTGTAGGATTTTTGTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:10:8,2:37,16:53,10:0.1587:2,2:28.5:1:28.2:1:0.71026:1.72:60:20:0.1724:0:1 0/0:68:0:0,0:49,19:68,0:0:2,0:23:1:29.7:1:1:0:59.9:33:1:0:0.2 +13 68406302 . A G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=0.20586;LSEQ=ATTTTTGGCTGGAGTATCTC;RSEQ=TATAGATTTCTTCACTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:35:16,19:18,17:35,35:0.5:2,2:13.7:1:30.9:1:0.81123:1.25323:36.2:70:0.5072:0:1.9 0/1:71:12:5,7:30,29:59,12:0.169:2,2:16.7:1:31.1:1:0.75305:1.44076:36.8:24:0.169:0:2.1 +13 68406306 . A G 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=0.24918;LSEQ=TTGGCTGGAGTATCTCATAT;RSEQ=GATTTCTTCACTGGCGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:35:17,18:20,17:37,35:0.4861:2,2:13.9:1:31.5:1:0.81375:1.24186:37.5:70:0.493:0:1.9 0/1:74:14:6,8:29,31:60,14:0.1892:2,2:14:1:31.2:1:0.77318:1.2436:39.7:28:0.1892:0:1.9 +13 68406623 . T A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31407;SOR=0.23833;LSEQ=AAAGCCCCCAAGGGAAACCA;RSEQ=TGGATGTACAGGCATTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:115,174:289,3:0.0103:2,2:8:1:29.7:1:0.56627:3.01:54:6:0.0106:0:1.3 0/0:406:1:1,0:173,232:405,1:0.0025:2,0:1:0:24:0:0.42857:0:60:2:0.0025:0:1 +13 68406678 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51389;SOR=Inf;LSEQ=ACTTTAATTGGAATCCCTTC;RSEQ=TAATTCATGGCCTCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:33,84:117,0:0:2,0:21.7:1:31.6:1:1:0:60:234:0.9832:0:0.1 0/1:170:2:1,1:58,110:168,2:0.0118:2,2:32.5:1:28.5:1:1:1.89:60:4:0.0118:0:1 +13 68406761 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20299;LSEQ=CGTTCTTAAAGATAACTGGT;RSEQ=CTCATTTTCATCATTATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:40:22,18:31,33:64,40:0.3846:2,2:23.3:1:29.5:1:0.55043:1.30:36.9:80:0.3883:0:1.1 0/1:143:16:6,10:68,59:127,16:0.1119:2,2:25.8:1:28.3:1:0.29128:1.91218:41.7:15:0.1071:0:1.1 +13 68406770 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51048;SOR=Inf;LSEQ=AGATAACTGGTGCTCATTTT;RSEQ=ATCATTATCCACCTTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:56,48:104,0:0:2,0:26.3:1:32.4:1:1:0:37.6:51:1:0:0.5 0/1:143:2:1,1:73,68:141,2:0.014:2,2:11:1:28:1:1:1.07297:52:4:0.0141:0:1 +13 68406783 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50532;SOR=Inf;LSEQ=TCATTTTCATCATTATCCAC;RSEQ=TTAAAGTGATCATCTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:61,48:109,0:0:2,0:25.4:1:32.4:1:1:0:38.4:108:1:0:0.4 0/1:139:2:1,1:77,60:137,2:0.0144:2,2:7:0:31.5:1:1:1.281:52.5:4:0.0147:0:1.5 +13 68406829 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19667;SOR=0;LSEQ=TTAGTTCACTACTGAAAAGA;RSEQ=AATTCTAGGGCCTCAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:85,41:126,2:0.0156:2,2:34.5:1:33:1:0.55032:2.06041:35:4:0.0156:0:1.5 0/0:160:0:0,0:100,60:160,0:0:2,0:21.6:1:28.7:1:1:0:49.1:320:1:0:0.2 +13 68406834 . C A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50787;SOR=Inf;LSEQ=TCACTACTGAAAAGATAATT;RSEQ=TAGGGCCTCAGGGGGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:85,43:128,0:0:2,0:26.2:1:32.3:1:1:0:53.4:41.667:1:0:0.2 0/1:169:2:1,1:107,60:167,2:0.0118:2,2:25.5:1:24:1:1:1.77681:34.5:4:0.012:0:1.5 +13 68406850 . G C 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07239;SOR=Inf;LSEQ=AATTCTAGGGCCTCAGGGGG;RSEQ=ACATGTCCATGTCCATCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:102,57:159,0:0:2,0:23.8:1:31.5:1:1:0:56.8:318:1:0:0.1 0/1:209:5:3,2:132,72:204,5:0.0239:2,2:26.4:1:31:1:1:1.221:53.4:10:0.0244:0:1 +13 68930918 . G T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=AATGGTAGGGACATGGGATA;RSEQ=TTCAATACCAGTGGTACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:2,1:132,103:235,3:0.0126:2,2:26.7:1:31.3:1:1:1.56:60:6:0.0127:0:1.3 0/0:262:0:0,0:139,123:262,0:0:2,0:24.1:1:30.8:1:1:0:60:86.333:1:0:0.4 +13 68930985 . G T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43808;SOR=1.14602;LSEQ=AAATAAATACATGCTTCCCA;RSEQ=AATAAAGTTTACAGGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:259:135:64,71:61,63:124,135:0.5212:2,2:24.3:1:29.1:1:0.80419:1.07386:60:44:0.5217:0:1.1 1/0:281:156:75,81:56,69:125,156:0.5552:2,2:23.9:1:28:1:0.63093:1.14:60:25:0.5455:0:1.1 +13 68931132 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23178;SOR=Inf;LSEQ=CAAAGCTGGCTAGTAATTGA;RSEQ=GAACACAGCCTGAAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:1,34:35,0:0:1,0:24.3:1:30.4:1:1:0:60:34:1:0:0.1 0/1:33:2:1,1:1,30:31,2:0.0606:1,2:23:1:27:1:0.11932:21.57:60:4:0.0606:0:1 +13 71158022 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTTCAGGAAATGTAATG;RSEQ=TTTCTACATTGCACTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:27.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 71158340 . C T 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.69203;SOR=1.71453;LSEQ=CCAGCCCAGCTTGCCAATGG;RSEQ=GGACTCAAACGCCGCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:2:0,2:196,142:338,2:0.0059:2,0:1:0:26:1:0.17866:0:60:4:0.006:0:1 0/1:398:4:1,3:212,182:394,4:0.0101:2,2:12.5:1:26.5:1:0.34157:3.48432:35.5:8:0.0102:0:1.3 +13 71158400 . G A 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01589;SOR=0;LSEQ=CAGACCACCGTGTTCAGTTT;RSEQ=TATTTTCGATTGAGAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:5:3,2:118,200:318,5:0.0155:2,2:11.6:1:26.6:1:0.36716:2.53:36:10:0.0157:0:1 0/0:414:0:0,0:151,263:414,0:0:2,0:23.3:1:31:1:1:0:49.4:102.5:1:0:0.2 +13 72248871 . T TAATAGAGTGCTCCATTCAAGTTTGAAAACTA 83 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACGGCAGGCACAGGAAAC;RSEQ=AATAAATTGCATGATGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:41.3:1:29.7:1:1:0:54:14:1:1:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 72249107 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23782;SOR=0;LSEQ=GTGTTCGCAGCCGCCACCGC;RSEQ=CTGCCGTCGCTCTCCAACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:2,0:48,0:48,2:0.04:1,0:28.5:1:29.5:1:1:0:57:4:0.0408:0:4 0/0:52:0:0,0:46,6:52,0:0:2,0:34.4:1:28.1:1:1:0:52.2:16.333:1:0:0.2 +13 72249162 . A AG 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17235;SOR=0;LSEQ=GCTCGCCGAGCTCCAGCCGA;RSEQ=GAGAAGGGGGGTAAGTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:19,0:0,0:0,19:1:0,1:7.1:1:30:1:1:0:34.5:38:1:0.6316:0.1 1/1:14:12:10,2:1,1:2,12:0.8571:2,2:6.6:1:28.2:1:0.3956:4.28:33.8:24:0.8571:0.7143:0.3 +13 72249324 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50226;SOR=0;LSEQ=AAGAAACCTCATCGTAACAG;RSEQ=CCTGGTACTGTGGCGCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:88,69:157,2:0.0126:2,2:26.5:1:30.5:1:1:1.27339:45.5:4:0.0128:0:1.5 0/0:133:0:0,0:76,57:133,0:0:2,0:23.2:1:30.8:1:1:0:46.7:43.333:1:0:0.2 +13 72249333 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20031;SOR=Inf;LSEQ=CATCGTAACAGGCCTGGTAC;RSEQ=GTGGCGCTCCGTGAAGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:103,84:187,0:0:2,0:25.9:1:31.2:1:1:0:45.5:92.5:1:0:0.1 0/1:152:2:1,1:81,69:150,2:0.0132:2,2:21:0:32:0:1:1.17267:43:4:0.0132:0:1 +13 72249338 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58586;SOR=2.53538;LSEQ=TAACAGGCCTGGTACTGTGG;RSEQ=GCTCCGTGAAGTTAGACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:0,1:107,90:197,1:0.0051:2,0:18:0:14:0:0.4596:0:60:0:0:0:1 0/1:157:2:2,0:84,71:155,2:0.0127:2,0:30.5:1:30.5:1:0.50139:0:36.5:4:0.0128:0:1.5 +13 72249375 . ACTT A 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTTATCAGAAGTCCACTGA;RSEQ=CTGATTCGCAGACTTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:137,117:254,0:0:2,0:26.9:1:33:1:1:0:40.5:253:1:0:0.1 0/1:187:19:10,9:87,81:168,19:0.1016:2,2:29.9:1:31.5:1:1:1.03:36.9:38:0.1022:0.0107:0.2 +13 72249638 . C CA 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.24895;SOR=0;LSEQ=GATGGGAAACATTTCATTCT;RSEQ=AAAAAAAAAATTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:1,2:16,124:140,3:0.021:2,2:41.7:1:23.7:1:0.31788:3.82:27.7:2:0.0148:0:0.3 0/0:130:0:0,0:23,106:129,0:0:2,0:34.9:1:30.8:1:1:0:32:20.5:1:0:0.4 +13 72249647 . AAT A 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.2163;SOR=0.21321;LSEQ=CATTTCATTCTCAAAAAAAA;RSEQ=TTTTTTTTTTCTCTTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:5:0,5:17,122:139,5:0.0347:2,0:35.6:1:33:1:1:0:33.2:10:0.0352:0:0.6 0/0:132:1:1,0:21,108:129,1:0.0076:2,0:35:0:32:0:0.16923:0:35:2:0.0079:0:0 +13 72249648 . AT A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.0613;SOR=1.75664;LSEQ=ATTTCATTCTCAAAAAAAAA;RSEQ=TTTTTTTTTTCTCTTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:144:105:11,94:2,9:11,105:0.7292:2,2:34.6:1:31.7:1:0.35611:1.88633:33.2:104:0.7536:0.0139:0.1 1/1:132:109:18,91:3,12:15,109:0.8258:2,2:34.2:1:30.3:1:0.71821:1.26136:31.4:53.5:0.8359:0.0833:0.3 +13 72249649 . T A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.77206;SOR=0.77125;LSEQ=TTTCATTCTCAAAAAAAAAA;RSEQ=TTTTTTTTTTCTCTTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:7:1,6:2,9:11,7:0.0486:2,2:32.1:1:31.1:1:1:1.3127:25.3:14:0.0507:0:1.3 0/1:132:5:0,5:3,12:15,5:0.0379:2,0:30:1:32:0:0.53947:0:28.2:10:0.0391:0:1 +13 72278395 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50096;SOR=Inf;LSEQ=ACATAGAGTTGATCCTTTGG;RSEQ=CACGAATATGCAAATCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:30,8:38,0:0:2,0:25:1:32.5:1:1:0:60:76:1:0:0.1 0/1:48:2:1,1:31,15:46,2:0.0417:2,2:32:0:31:1:1:2.03311:60:4:0.0417:0:1 +13 72278445 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24774;SOR=Inf;LSEQ=TGTAGACATCAAGAGAATGC;RSEQ=TACTGTTCAAAAAGGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:58,35:93,0:0:2,0:23.5:1:30.9:1:1:0:60:186:1:0:0.1 0/1:102:3:1,2:53,46:99,3:0.0294:2,2:17:1:27.3:1:0.59995:2.28605:60:6:0.0294:0:1 +13 72278472 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49932;SOR=Inf;LSEQ=TCAAAAAGGAATGCTCCACA;RSEQ=GTGTTACCATGGCAAAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:75,50:125,0:0:2,0:25.6:1:32.2:1:1:0:60:250:1:0:0.1 0/1:138:2:1,1:72,63:135,2:0.0145:2,2:17:1:28.5:1:1:1.14174:46.5:4:0.0148:0:1 +13 72278495 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23623;SOR=Inf;LSEQ=GTTACCATGGCAAAACTGGA;RSEQ=GAGTCTACCATGTTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:71,67:138,0:0:2,0:27.5:1:31.1:1:1:0:59.9:276:1:0:0.2 0/1:131:2:1,1:63,66:129,2:0.0153:2,2:17:1:28.5:1:1:1.05:26.5:4:0.0154:0:2 +13 72278579 . G A 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02016;SOR=0.3033;LSEQ=TGCAAAGAGAATTAATGTGC;RSEQ=TACTGAGTATATGAAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:51:28:3,25:3,20:23,28:0.549:2,2:21.9:1:32:1:1:1.2445:60:56:0.549:0:1.1 0/1:30:8:2,6:2,20:22,8:0.2667:2,2:26.1:1:29:1:0.28352:3.18:60:16:0.2667:0:1.1 +13 73277800 . C T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATATTCTGGCCTTTCGGC;RSEQ=GGAACCGCCATCTTCCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:0,8:1:0,2:21.9:1:31.9:1:1:0:49.3:16:1:0:1.1 1/1:7:7:6,1:0,0:0,7:1:0,2:21.1:1:30.6:1:1:0:53.7:14:1:0:1 +13 73277913 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17037;SOR=0;LSEQ=ACATGGAGTTGTCCCTTTGG;RSEQ=CACGTATATGCGAAATCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:13,8:21,2:0.087:2,2:11:0:32:0:1:1.58984:60:4:0.087:0:1.5 0/0:32:0:0,0:17,15:32,0:0:2,0:28.2:1:31.4:1:1:0:57.3:64:1:0:0.1 +13 73333369 . T A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTGCCTTTCTACCAA;RSEQ=TCCCAAACATTCACAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 73334081 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4998;SOR=0;LSEQ=GAATACATCTCAACCTCATC;RSEQ=TCCCCTTCCCCACTGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:7,105:112,2:0.0175:2,2:19.5:1:30:1:0.136:14.10:60:4:0.0177:0:1 0/0:100:0:0,0:9,91:100,0:0:2,0:22.7:1:31.2:1:1:0:59.8:49:1:0:0.1 +13 73334603 . C T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25182;SOR=0;LSEQ=AAACAGAAATAACTACGTCC;RSEQ=TTCTTTGACAAAATATGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:212,49:261,3:0.0114:2,2:8.3:1:24.7:1:0.09644:8.55153:60:6:0.0114:0:2 0/0:231:0:0,0:171,60:231,0:0:2,0:23.1:1:30.6:1:1:0:60:114.5:1:0:0.1 +13 73335383 . G T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13694;LSEQ=TTTTCTGGCATGTATTTGGA;RSEQ=ATCAGGATAAATTCTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:49:47,2:46,1:47,49:0.5104:1,1:25.2:1:31.5:1:1:1.94429:59.9:98:0.5104:0:1.1 0/1:97:12:12,0:82,2:84,12:0.1237:1,0:22.9:1:31.2:1:1:0:60:24:0.1263:0:1.1 +13 73335469 . G A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAAAGAAAAAGTGCCCCCC;RSEQ=GAAAAGAAAACAAACATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:0:0,0:367,198:565,0:0:2,0:26.6:1:30.1:1:1:0:59.9:55.5:1:0:0.2 0/1:638:21:13,8:381,233:614,21:0.0329:2,2:25.2:1:29.8:1:1:1.00626:60:20:0.0319:0:1.1 +13 73335767 . C T 99 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0071;SOR=9.91728;LSEQ=TTCATTTTTTCTAGCAGTAT;RSEQ=GACAAAAGGCAAATACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:1:0,1:229,153:382,1:0.0026:2,0:1:0:26:0:0.40209:0:60:2:0.0026:0:1 0/1:436:11:6,5:249,175:424,11:0.0252:2,2:19.5:1:28.9:1:0.76734:1.18524:60:22:0.0257:0:1.2 +13 73337440 . C CA 62 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.68087;SOR=1.75093;LSEQ=GTGACAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAACCAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:2,0:30,0:30,2:0.0625:1,0:31:1:30:1:1:0:58.5:4:0.0645:0:0 0/1:38:4:4,0:34,0:34,4:0.1053:1,0:25.3:1:31.3:1:1:0:60:8:0.1053:0:0 +13 73337683 . AT A 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.37899;SOR=0.51715;LSEQ=GTTCAGAAAATTCCTCATGA;RSEQ=TTTTTTTGCAACAGAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:7:4,3:228,293:521,7:0.0133:2,2:17.3:1:31.7:1:0.70479:1.71:60:14:0.0134:0.0076:0.9 0/0:725:5:0,5:332,387:719,5:0.0069:2,0:26.4:1:29.6:1:0.06593:0:60:10:0.007:0:0 +13 73338175 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCACACTCCTGTAGTCCC;RSEQ=GCTACTTGAGAGGCTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:31:1:1:0:57.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 73338276 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAGGCTGGGTGACAGAG;RSEQ=AAGACTCTGTGTCAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25.5:1:29.5:1:1:0:56.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 73340242 . AAAGAC A 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00066;SOR=Inf;LSEQ=TATAGTCAAGCAAGCCAATA;RSEQ=AAAAGTATAGAAATTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:43,182:225,0:0:2,0:22.5:1:31:1:1:0:59.9:36.5:1:0:0.1 0/1:268:12:2,10:53,203:256,12:0.0448:2,2:17.6:1:30.6:1:1:1.30421:59.6:24:0.0451:0.0187:0.1 +13 73343039 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17157;LSEQ=CTCAACTGAGCTTCAGCATA;RSEQ=GTCAGAGATGCCTAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:355:323:66,257:6,26:32,323:0.9099:2,2:24.2:1:30.7:1:1:1.11:60:106.667:0.9091:0:1.1 1/0:401:254:67,187:34,113:147,254:0.6334:2,2:24.9:1:29.8:1:0.55073:1.19:60:253:0.6341:0:1.1 +13 73344848 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58935;SOR=0.48705;LSEQ=GTTTATATCTCAGGTACTTA;RSEQ=ATGTATATGTTTTTTCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:19,0:3,0:3,19:0.8636:0,1:24.3:1:30.9:1:1:0:60:18:0.8571:0:1 1/0:8:6:5,1:2,0:2,6:0.75:0,2:23:1:28.3:1:1:0:60:12:0.8571:0:1 +13 73345369 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=TTCTCAAATAACATTAATTA;RSEQ=ACAAGGAAAGAAAAGAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:7,154:161,2:0.0123:1,2:8.5:1:32.5:1:0.09604:20.64:60:4:0.0126:0:1 0/0:150:0:0,0:18,132:150,0:0:2,0:22.4:1:30:1:1:0:60:74:1:0:0.1 +13 73345443 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00349;SOR=Inf;LSEQ=GTCAAATAAAAGGTTTGTTT;RSEQ=TATAAAAGCACTTATACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:2,41:43,0:0:1,0:20.9:1:33.7:1:1:0:60:86:1:0:0.1 0/1:30:6:0,6:0,24:24,6:0.2:1,0:12.2:1:26.5:1:1:0:60:5:0.1786:0:1.7 +13 73345851 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.21057;SOR=Inf;LSEQ=TTAAAGCCACATTATTCCAT;RSEQ=TATTTTTCTTAGCTAATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:95,7:102,0:0:2,0:23.7:1:32.5:1:1:0:60:204:1:0:0.1 0/1:87:2:1,1:82,3:85,2:0.023:1,2:22.5:1:31.5:1:0.09035:23.81577:60:4:0.023:0:1 +13 73345995 . G A 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03244;SOR=Inf;LSEQ=TTGATCCAAGGCATTTCCTG;RSEQ=CCTAATAAAATGGCTCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:242,279:521,0:0:2,0:26.9:1:31.4:1:1:0:59.9:39.077:1:0:0.1 0/1:586:6:5,1:265,315:580,6:0.0102:2,2:20.2:1:21.7:1:0.09975:5.93:60:2:0.007:0:2.2 +13 73346089 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22473;SOR=Inf;LSEQ=CTTGACTGGGTAAATGTACC;RSEQ=AATGGAGTTTTAATAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:31,116:147,0:0:2,0:21.4:1:28.9:1:1:0:59.8:48:1:0:0.1 0/1:133:2:1,1:29,102:131,2:0.015:2,2:23:1:28:1:0.40157:3.47:60:4:0.0153:0:1 +13 73346722 . GA G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50276;SOR=0;LSEQ=CTATACCCAACAAAATGCAG;RSEQ=AAAGAGGGCCCGTGGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:2,0:65,6:71,2:0.0274:2,0:29.5:1:32.5:1:1:0:60:4:0.0282:0:0 0/0:58:0:0,0:58,0:58,0:0:1,0:26.4:1:29.2:1:1:0:59.3:57:1:0:0.1 +13 73347990 . C CA 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.44306;SOR=2.0854;LSEQ=TTAGGAATAAAGATTTTACA;RSEQ=AAAAAAAATCTGAGGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:2:0,2:140,168:308,2:0.0064:2,0:39:1:32:0:0.50308:0:60:4:0.0066:0:0 0/1:300:4:2,2:129,166:295,4:0.0133:2,2:23.3:1:29.5:1:1:1.29:60:8:0.0134:0.0033:0 +13 73348372 . A C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27931;SOR=0;LSEQ=AAGAACATGCATGCCAAACC;RSEQ=AACCACAGACATTCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:0,3:0,16:16,3:0.1579:1,0:24:1:33.7:1:1:0:60:6:0.1579:0:1 0/0:11:0:0,0:0,11:11,0:0:0,0:23:1:30.9:1:1:0:60:22:1:0:0.2 +13 73349225 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=0.29244;LSEQ=AAACCATGTGTATGACATGC;RSEQ=TTAAATATACAGAACTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:110:62:61,1:46,1:47,62:0.5636:1,1:25.7:1:31.2:1:1:1.32:60:61:0.5648:0:1 0/1:66:18:17,1:48,0:48,18:0.2727:1,1:23.5:1:29.6:1:0.27273:0:60:17:0.2615:0:1.3 +13 73349321 . C CA 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.85748;SOR=0.93216;LSEQ=ATAATACAAAGCTACACAGA;RSEQ=AAAAAAAAATCCTGCTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:15:9,6:345,215:560,15:0.026:2,2:24.3:1:31.7:1:1:1.06964:59:30:0.0262:0.0035:0.7 0/1:658:16:10,6:397,244:641,16:0.0243:2,2:29.3:1:29.6:1:1:1.02:60:32:0.025:0.0015:0.4 +13 73349359 . G C 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.9592;SOR=1.00656;LSEQ=AGATTCATACCATTCGTTCT;RSEQ=TCTCTTCTTCTTTCTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:306:165,141:224,176:400,306:0.4334:2,2:27.1:1:32.7:1:0.59374:1.08747:60:50:0.4317:0:1.1 0/1:862:375:211,164:273,212:485,375:0.435:2,2:27.8:1:31:1:1:1.00089:60:124:0.4382:0:1.1 +13 73349527 . C T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00022;SOR=Inf;LSEQ=AGATTATCTGTTTAAAACAA;RSEQ=AGAGGGCACGTGCCCAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:58,196:254,0:0:2,0:23.7:1:32.6:1:1:0:59.9:253:0.9961:0:0.1 0/1:265:13:5,8:71,181:252,13:0.0491:2,2:22.5:1:28.5:1:0.52942:1.59:60:26:0.05:0:1 +13 73349918 . CA C 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.81051;LSEQ=CTGACAAATTGTGAGCACTG;RSEQ=AAAAAAAAAAGAAAAAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:3,1:26,2:28,4:0.125:2,2:35.5:1:32:1:0.33952:4.04395:60:8:0.125:0:0.8 0/1:29:3:3,0:22,3:25,3:0.1034:2,0:18.3:1:31.5:1:1:0:60:6:0.1071:0.0345:0.3 +13 73349930 . G A 30 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.79251;LSEQ=GAGCACTGCAAAAAAAAAAA;RSEQ=AAAAAAGTTACTATTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:2,0:46,3:49,2:0.0392:2,0:7.5:1:30.5:1:1:0:51.5:4:0.0435:0:1.5 0/1:32:1:1,0:28,3:31,1:0.0313:2,0:7:0:25:0:1:0:57:2:0.0345:0:1 +13 73350079 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22086;LSEQ=TTGCCTCTTTATTTTCTTCA;RSEQ=TGTCGCCATGAATCCATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:550:233:155,78:190,127:317,233:0.4236:2,2:24.9:1:32.7:1:0.12933:1.33:59.9:232:0.4241:0:1.1 0/1:681:95:58,37:328,258:586,95:0.1395:2,2:26.4:1:30.5:1:0.37374:1.23:60:22.75:0.1348:0:1.1 +13 73350257 . C T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00717;SOR=Inf;LSEQ=AAGAAGCAAACCAAAAGATG;RSEQ=CGCTAATAAGTCTTCTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:31,135:166,0:0:2,0:26.3:1:31.3:1:1:0:59.8:40.5:1:0:0.1 0/1:167:8:2,6:36,122:158,8:0.0479:2,2:14.3:1:29:1:1:1.13:60:16:0.0485:0:1.4 +13 73351707 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.516;SOR=Inf;LSEQ=AAAATGGATAGTCTTGTTTG;RSEQ=GACAGTATACACGTCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:14,113:127,0:0:2,0:22:1:30.4:1:1:0:60:126:0.9921:0:0.1 0/1:187:2:0,2:25,160:185,2:0.0107:2,0:26:1:31.5:1:1:0:60:4:0.0107:0:1 +13 73352630 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24228;SOR=Inf;LSEQ=AGAAAAAGTCAATGGTATAT;RSEQ=TTTTCTCTTGAATGTATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:0,46:46,0:0:1,0:25.1:1:33.6:1:1:0:60:45:1:0:0 0/1:48:3:0,3:1,44:45,3:0.0625:1,0:12.3:1:29.7:1:1:0:60:6:0.0625:0:1 +13 73353348 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTACTGCAACCTCTACC;RSEQ=CCGGGTTCAAGTGATCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29.5:1:1:0:48.5:4:1:0:3.5 +13 73354335 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGCCTGGCATAGTGGTGC;RSEQ=TGACTGTAATCCCAGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:31:1:1:0:28:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 73354919 . G C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23465;SOR=Inf;LSEQ=AATGTCATAAATTACTCACA;RSEQ=GAACCCTCTCCCGAATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:112,12:124,0:0:2,0:25:1:32.9:1:1:0:60:40.333:1:0:0.1 0/1:117:2:1,1:104,11:115,2:0.0171:2,2:15:0:32.5:1:0.1954:9.09546:60:4:0.0174:0:1 +13 73354930 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49833;SOR=Inf;LSEQ=TTACTCACAGGAACCCTCTC;RSEQ=CGAATTTTGCTAATCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:128,21:149,0:0:2,0:24.9:1:31.3:1:1:0:60:148:1:0:0 0/1:150:2:1,1:128,20:148,2:0.0133:2,2:29:1:30:1:0.26121:6.27012:60:4:0.0133:0:1 +13 73355574 . A G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00711;SOR=Inf;LSEQ=AACTAAATTTTTTAAAGCAC;RSEQ=AGGAAAAGAACCTCGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:37,75:112,0:0:2,0:24.6:1:31.1:1:1:0:60:55:1:0:0.1 0/1:90:6:1,5:19,65:84,6:0.0667:2,2:20.3:1:29.5:1:1:1.45592:60:5:0.0568:0:1 +13 73355673 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49966;SOR=Inf;LSEQ=CAAAGACCCGCCTCCCTGGG;RSEQ=CTCAGTTTCCCTGTCATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:124,32:156,0:0:2,0:23:1:31.8:1:1:0:59.9:38:1:0:0.1 0/1:172:2:1,1:130,40:170,2:0.0116:2,2:15.5:1:28.5:1:0.42098:3.22243:60:4:0.0116:0:1 +13 73355679 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50139;SOR=Inf;LSEQ=CCCGCCTCCCTGGGCCTCAG;RSEQ=TTCCCTGTCATACCCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:132,35:167,0:0:2,0:23.1:1:29.7:1:1:0:59.9:40.75:1:0:0.1 0/1:195:2:1,1:145,48:193,2:0.0103:2,2:23:1:32.5:1:0.44039:3.00014:60:4:0.0104:0:1 +13 73356410 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAACCTTGTGCTTCCGAC;RSEQ=GGAGACGCCTTTGGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:47:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 75628825 . GACA G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.38801;SOR=0.5376;LSEQ=ACAGCTATTTAAAGGAATCA;RSEQ=ACAACCAAGGTAGCCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:14,0:13,0:13,14:0.5185:1,1:25.1:1:34.1:1:1:0:60:28:0.5185:0.1111:0.1 0/1:22:8:8,0:13,1:14,8:0.3636:1,0:31.5:1:32.7:1:1:0:60:16:0.3636:0.0455:0.3 +13 75629027 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03114;SOR=0.71752;LSEQ=AAAATTTGGATTCAGAACTC;RSEQ=CAAGCCAACCAGAAATTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:129:64,65:103,84:187,129:0.4082:2,2:26.6:1:30.8:1:0.36042:1.24447:60:42:0.4078:0:1.1 0/1:426:141:68,73:134,150:284,141:0.331:2,2:26.7:1:28.8:1:0.91787:1.04:60:34.25:0.327:0:1.1 +13 75629056 . A G 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07363;SOR=0;LSEQ=CCAGAAATTGAGGAACCAAA;RSEQ=TCAAGGGGAAAACAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:130,165:295,3:0.01:2,2:26.3:1:27:1:1:1.57345:60:2:0.0068:0:2 0/0:413:0:0,0:176,236:412,0:0:2,0:26.1:1:29.8:1:1:0:60:81.4:1:0:0.4 +13 75629119 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49835;SOR=0;LSEQ=TTAGGAATGGGCTGAATGGA;RSEQ=CAAGAAGTAGAAAAAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:34,116:150,2:0.0132:2,2:16.5:1:29:1:0.40868:3.38:60:4:0.0136:0:1 0/0:151:0:0,0:44,107:151,0:0:2,0:22.6:1:31.5:1:1:0:60:150:1:0:0.2 +13 75629124 . A C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24721;SOR=Inf;LSEQ=AATGGGCTGAATGGAGCAAG;RSEQ=AGTAGAAAAAGTCAGCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:27,107:134,0:0:2,0:23.5:1:30.4:1:1:0:60:32.5:1:0:0.1 0/1:134:2:1,1:36,96:132,2:0.0149:2,2:17:1:27.5:1:0.4775:2.64:60:4:0.0152:0:1.5 +13 75909122 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1467;SOR=0;LSEQ=ATATATAACCCATCTCCACA;RSEQ=TGGCCACTGCACAGACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:70,21:91,2:0.0215:2,2:18.5:1:29.5:1:0.41912:3.27985:60:4:0.022:0:1.5 0/0:149:0:0,0:104,45:149,0:0:2,0:24.9:1:29.2:1:1:0:60:73.5:1:0:0.3 +13 75909125 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5228;SOR=Inf;LSEQ=TATAACCCATCTCCACAATG;RSEQ=CCACTGCACAGACACTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:73,25:98,0:0:2,0:23.9:1:31.7:1:1:0:60:48:1:0:0.4 0/1:154:2:1,1:104,48:152,2:0.013:2,2:20.5:1:27:0:0.53654:2.15477:57.5:4:0.0133:0:1 +13 75909164 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.53238;SOR=Inf;LSEQ=CCTCATCCCACCCAGGCTGT;RSEQ=CCACTCCCTGCTGGGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:78,40:118,0:0:2,0:26.8:1:32:1:1:0:60:38.333:1:0:0.7 0/1:201:2:1,1:112,87:199,2:0.01:2,2:18:1:27:1:1:1.28571:60:4:0.0103:0:1.5 +13 75909166 . C CA 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00097;SOR=0.40265;LSEQ=TCATCCCACCCAGGCTGTGC;RSEQ=ACTCCCTGCTGGGGCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:128:108:71,37:12,8:20,108:0.8438:2,2:25:1:29.9:1:0.61936:1.28:60:35:0.84:0.1641:0.9 1/0:225:154:85,69:38,32:70,154:0.6844:2,2:23.6:1:29.2:1:1:1.04:59.8:308:0.6875:0.1689:0.8 +13 75909196 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32121;LSEQ=TGGGGCTGCCACCCCAACAC;RSEQ=TGCACATCCTCAGCCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:150:123:63,60:13,14:27,123:0.82:2,2:25.2:1:29.8:1:0.8335:1.13:60:29.75:0.8151:0:1.2 1/0:241:143:70,73:49,48:97,143:0.5934:2,2:24:1:29.8:1:0.89542:1.06429:59.8:70.5:0.6026:0:1.2 +13 75909238 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18078;SOR=0;LSEQ=GGCACCCATCCCTGTGAATG;RSEQ=TCGCTCCCCTCCACTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:62,80:142,2:0.0139:2,2:31.5:1:29.5:1:1:1.29:60:4:0.0143:0:2 0/0:194:0:0,0:79,115:194,0:0:2,0:25.6:1:31.5:1:1:0:59.9:96:1:0:0.6 +13 75909241 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18703;SOR=0;LSEQ=ACCCATCCCTGTGAATGCTC;RSEQ=CTCCCCTCCACTGTGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:60,81:141,2:0.014:2,2:24:0:32:1:1:1.35:60:4:0.0142:0:1.5 0/0:187:0:0,0:74,113:187,0:0:2,0:25.8:1:30.4:1:1:0:59.9:92.5:1:0:0.5 +13 75909256 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51027;SOR=Inf;LSEQ=TGCTCGCTCCCCTCCACTGT;RSEQ=GCTCTGACACCCGCACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:49,79:128,0:0:2,0:24.9:1:31.7:1:1:0:59.8:127:0.9922:0:0.7 0/1:176:2:1,1:65,109:174,2:0.0114:2,2:19.5:1:28.5:1:1:1.67:60:4:0.0114:0:1 +13 75909295 . G T 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.82886;LSEQ=GGCCTTCCCTCTGCCAGTAT;RSEQ=CTGCCTCCTACAACCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:24,53:77,2:0.0253:2,2:6:1:29.5:1:0.53554:2.18:60:4:0.026:0:1 0/1:95:2:1,1:23,70:93,2:0.0211:2,2:26:1:28:1:0.44345:3.00:60:4:0.0213:0:1 +13 76833565 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50178;SOR=Inf;LSEQ=GAAGGGTTGGTCTTGTCTTA;RSEQ=GAGTGGCAGAGGTGAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:96,13:109,0:0:2,0:21.9:1:30.3:1:1:0:59.8:53.5:1:0:0.1 0/1:130:2:1,1:103,25:128,2:0.0154:2,2:32.5:1:31.5:1:0.36124:4.05956:60:4:0.0156:0:1 +13 76833573 . A T 52 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.06544;SOR=Inf;LSEQ=GGTCTTGTCTTAAGAGTGGC;RSEQ=GAGGTGAAAGAAAATCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:104,20:124,0:0:2,0:23:1:30.7:1:1:0:59.8:248:1:0:0.1 0/1:149:5:2,3:114,30:144,5:0.0336:2,2:7.2:1:22.4:1:0.07235:5.61133:60:1.5:0.0204:0:1.2 +13 76833590 . C T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25577;SOR=Inf;LSEQ=GGCAGAGGTGAAAGAAAATC;RSEQ=ACGTATAATGAATCTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:127,51:178,0:0:2,0:24.2:1:31.7:1:1:0:59.9:177:1:0:0.1 0/1:218:3:1,2:157,58:215,3:0.0138:2,2:17.3:1:20.7:1:0.18431:5.36417:60:2:0.0094:0:1 +13 76833621 . G T 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCTGTGGAGTTCAAACCT;RSEQ=CATTGTTCAACCTGTGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:194,123:317,0:0:2,0:25.2:1:32.1:1:1:0:59.9:78.25:0.9968:0:0.2 0/1:374:29:19,10:210,135:345,29:0.0775:2,2:28.1:1:29.3:1:0.69474:1.22:60:58:0.0784:0:1.1 +13 76833684 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.34137;LSEQ=GCATCCTGGCAGTATACAAA;RSEQ=CTTGCTACCCTGTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:83:39,44:164,182:346,83:0.1935:2,2:25:1:32.7:1:1:1.01659:59.8:82:0.1948:0:1.1 0/1:575:256:122,134:148,170:318,256:0.4452:2,2:24.7:1:31.1:1:0.80127:1.05:60:127:0.4464:0:1.1 +13 76833862 . G T 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44765;SOR=0.46068;LSEQ=TTATTGGACATTTATTGTTT;RSEQ=CAATGCACAGTTTCAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:0,6:0,19:19,6:0.24:1,0:29.3:1:30.7:1:1:0:60:12:0.24:0:1 0/1:16:2:0,2:0,14:14,2:0.125:1,0:12:1:26:1:1:0:60:4:0.125:0:1 +13 78503715 . T G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATCTTAGTTCTTCTGAAG;RSEQ=TTAGATGCTGGTTCATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:0,9:1:0,2:31.9:1:32.6:1:1:0:60:18:1:0:2.2 1/1:7:7:6,1:0,0:0,7:1:0,2:8.7:1:31:1:1:0:60:14:1:0:1.9 +13 78503731 . T C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GAAGTTTAGATGCTGGTTCA;RSEQ=GCCCTGAAAACCCATTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:0,12:1:0,2:28.1:1:30.7:1:1:0:60:11:1:0:1.9 1/1:8:7:6,1:1,0:1,7:0.875:0,2:17.1:1:33.1:1:1:0:60:14:0.875:0:1.9 +13 78503873 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21778;SOR=0;LSEQ=TCTGGGAAAGAGGAGAGCAT;RSEQ=GACTTCAGGAACGCTGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:78,64:142,2:0.0139:2,2:27.5:1:30:1:1:1.21706:60:4:0.014:0:1 0/0:164:0:0,0:89,75:164,0:0:2,0:24.7:1:30.8:1:1:0:60:53.667:1:0:0.2 +13 78503886 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50006;SOR=Inf;LSEQ=AGAGCATGGACTTCAGGAAC;RSEQ=CTGACTCCTGGCCATTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:76,71:147,0:0:2,0:28.6:1:31:1:1:0:60:146:1:0:0.3 0/1:165:2:1,1:81,82:163,2:0.0121:2,2:35:1:28.5:1:1:1.01:60:4:0.0123:0:1 +13 78503966 . A G 171 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00368;SOR=0.11855;LSEQ=ATCCTCTGGGTAAAAGAAAG;RSEQ=GTAAGAATAGTGTCTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:45:9,36:0,2:2,45:0.9574:0,2:21.1:1:31.3:1:1:0:60:90:0.9574:0:1.1 1/0:36:26:1,25:1,9:10,26:0.7222:2,1:23.4:1:30.5:1:0.48413:2.68742:60:52:0.7222:0:1.3 +13 78504047 . T C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTGCGTGGAATACAGTGA;RSEQ=TGTCTAGGAAATGTCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:23.3:1:34.2:1:1:0:60:22:1:0:1.4 1/1:8:8:0,8:0,0:0,8:1:0,0:24.1:1:32.1:1:1:0:60:16:1:0:1.4 +13 79333573 . CA C 32 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAAGGTGAGACACCATCT;RSEQ=AAAAAAAAAAAAAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:32.5:1:1:0:54.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 79335274 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01412;SOR=Inf;LSEQ=TTTATAAAAGCATAGCCTTT;RSEQ=GGCCAGAACCACCATCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:27,20:47,0:0:2,0:25.8:1:30.7:1:1:0:60:46:1:0:0.2 0/1:37:5:3,2:17,15:32,5:0.1351:2,2:29.2:1:28.2:1:1:1.31:56.8:10:0.1351:0:1.6 +13 79335295 . A G 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19394;SOR=Inf;LSEQ=GGCCAGAACCACCATCTTCC;RSEQ=GTAAATCGCCAAAATGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:30,24:54,0:0:2,0:27.7:1:31.2:1:1:0:60:108:1:0:0.1 0/1:43:2:1,1:20,21:41,2:0.0465:2,2:24.5:1:24.5:1:1:1.05:60:4:0.0465:0:1 +13 79335305 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50011;SOR=0;LSEQ=ACCATCTTCCAGTAAATCGC;RSEQ=AAAATGATAAACAAAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:26,26:52,2:0.037:2,2:23:1:28.5:1:1:1:60:4:0.0377:0:1 0/0:44:0:0,0:21,23:44,0:0:2,0:29:1:30.5:1:1:0:58.9:21:1:0:0.5 +13 79335332 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49608;SOR=0;LSEQ=ATAAACAAAAGGGAAAGAGG;RSEQ=GAGGCACCCAATATATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:22,26:48,2:0.04:2,2:20.5:1:30:1:1:1.18:60:4:0.04:0:1 0/0:45:0:0,0:20,25:45,0:0:2,0:18.8:1:29.4:1:1:0:58.8:90:1:0:0.4 +13 79335334 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22649;SOR=Inf;LSEQ=AAACAAAAGGGAAAGAGGAG;RSEQ=GGCACCCAATATATGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:49,0:0:2,0:22.8:1:30.7:1:1:0:60:48:1:0:0.2 0/1:45:2:1,1:19,24:43,2:0.0444:2,2:16:0:31.5:1:1:1.26:52:4:0.0455:0:2.5 +13 79335796 . TA T 42 d5;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATTCATGGCATAATAGGTGT;RSEQ=AAAAAAAAAAAAGACCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:21:1:26.7:1:1:0:51:2:0.5:0.25:0 0/0:2:0:0,0:1,1:2,0:0:2,0:3:0:28.5:1:1:0:48:4:1:0:0.5 +13 80561254 . G T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00377;SOR=5.23198;LSEQ=TTGATTTTTCAGTTTGTTCA;RSEQ=GTTTGACTTCTTAGAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:10:10,0:24,0:24,10:0.2941:1,0:25.6:1:32.3:1:1:0:60:20:0.303:0:1 1/0:26:18:18,0:8,0:8,18:0.6923:0,1:23.9:1:30.2:1:1:0:60:17:0.68:0:1 +13 80561304 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49735;SOR=0;LSEQ=TCTAAGCTCCTTACATGCCA;RSEQ=AACAAAGGCAGAAGTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:65,7:72,2:0.027:2,0:17.5:1:29.5:1:1:0:60:4:0.0278:0:1.5 0/0:68:0:0,0:61,7:68,0:0:2,0:25.7:1:31.2:1:1:0:60:67:1:0:0.7 +13 80561354 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18697;SOR=0;LSEQ=TTAAAATATTCACATTTATC;RSEQ=GCAGTATCTGTGGAGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:130,46:176,2:0.0112:2,2:27.5:1:29:1:0.45947:2.80659:60:4:0.0114:0:1 0/0:233:0:0,0:168,65:233,0:0:2,0:20.3:1:30.1:1:1:0:60:115.5:1:0:1 +13 80561367 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.01433;LSEQ=ATTTATCTGCAGTATCTGTG;RSEQ=AGTCCCATCAATTTTGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:73:52,21:110,50:160,73:0.3133:2,2:21:1:30.4:1:0.76027:1.12:60:146:0.3188:0:1.7 1/0:295:191:123,68:68,36:104,191:0.6475:2,2:22.7:1:28.9:1:0.89903:1.04412:60:94.5:0.6473:0:1.6 +13 80561434 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.03037;SOR=0;LSEQ=GGATTTTCCCATTTTGCAAA;RSEQ=AAAAAAAAGATCATCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:4:2,2:191,186:377,4:0.0105:2,2:17.5:1:25.8:1:1:1.02682:60:3:0.0079:0:2.8 0/0:531:0:0,0:249,281:530,0:0:2,0:25.3:1:30.6:1:1:0:60:105:0.9981:0:1 +13 80561436 . A T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=3.92917;LSEQ=ATTTTCCCATTTTGCAAAGA;RSEQ=AAAAAAGATCATCGGGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:128:62,66:130,124:254,128:0.3351:2,2:25:1:29.8:1:0.66487:1.1157:60:256:0.336:0:1.4 1/0:528:351:164,187:81,96:177,351:0.6648:2,2:24.8:1:28.3:1:0.85373:1.04:60:350:0.6641:0:1.4 +13 85271335 . T C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00199;SOR=0.20922;LSEQ=AAATAAAATAAATAGACTAC;RSEQ=AGCTAGACTAGTAAAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:21:5,16:4,8:12,21:0.6364:2,2:20:1:31.9:1:0.69046:1.5767:58.1:42:0.6563:0:1.1 0/1:38:10:4,6:10,18:28,10:0.2632:2,2:25.9:1:30.4:1:1:1.19:59.8:20:0.2703:0:1 +13 87971222 . G A 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTCATTAAATAGCACAGT;RSEQ=GAAATGTGGAAGCGATCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:153,38:191,0:0:2,0:23.1:1:32.2:1:1:0:60:190:1:0:0.1 0/1:160:22:16,6:112,26:138,22:0.1375:2,2:24.4:1:28.4:1:0.39126:1.61004:60:44:0.1384:0:1 +13 87971336 . C T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.38877;LSEQ=TCTTCATAATGAGATGGGCC;RSEQ=TTTCCTCTTAGAAGAGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:494:315:148,167:89,89:178,315:0.6377:2,2:26.6:1:30.9:1:0.5735:1.1281:60:104:0.638:0:1.1 0/1:500:203:94,109:138,158:296,203:0.406:2,2:25.3:1:29.6:1:1:1.01277:60:66.667:0.4065:0:1.1 +13 87971354 . A T 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTTTCCTCTTAGAAGAGT;RSEQ=GTCACAAGTTGAAAGTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:0:0,0:202,270:472,0:0:2,0:26.7:1:30.3:1:1:0:60:93.4:1:0:0.6 0/1:443:36:13,23:184,223:407,36:0.0813:2,2:27.8:1:29.9:1:0.38193:1.45859:60:72:0.082:0:1.1 +13 88542298 . AT A 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.571;LSEQ=CAGTTAAGAATACTCACCTC;RSEQ=TTTTTTTTTATCTCAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:18,0:18,2:0.1:1,0:9:1:32.5:1:1:0:60:4:0.1:0.05:0 0/1:17:1:1,0:13,3:16,1:0.0588:2,0:30:0:32:0:1:0:60:2:0.0625:0:0 +13 88542455 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.06356;LSEQ=AATGGTTATAGGGCACCGCA;RSEQ=TGTATGTGAGAGCATAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:46:26,20:166,121:287,46:0.1377:2,2:30:1:33.3:1:0.87363:1.05512:60:92:0.1407:0:1.1 0/1:304:100:55,45:115,89:204,100:0.3289:2,2:25.7:1:31:1:0.90221:1.05699:60:99:0.3333:0:1.1 +13 88542881 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61673;SOR=0.47958;LSEQ=GTGGGACAATTTCTTTTCAG;RSEQ=AGGTGACAGGCAGTCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:0,2:46,63:109,2:0.018:2,0:31.5:1:29:1:0.51024:0:60:4:0.0185:0:1.5 0/0:115:1:0,1:51,63:114,1:0.0087:2,0:42:0:27:0:1:0:60:2:0.009:0:1 +13 88542916 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49704;SOR=Inf;LSEQ=CATCAGATAGCAACTAGTTT;RSEQ=ATAGAGGCTCATTTGCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:28,57:85,0:0:2,0:25.7:1:32.1:1:1:0:59.7:170:1:0:0.1 0/1:85:2:1,1:28,55:83,2:0.0235:2,2:10.5:1:26.5:1:1:1.95:60:4:0.0235:0:1 +13 88543077 . AG A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49574;SOR=Inf;LSEQ=GAAACCAAGGGCTCTGTCAC;RSEQ=GGGGAGACAGAGTGGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:39,0:0:2,0:20.7:1:32.4:1:1:0:59.5:78:1:0:0.1 0/1:44:2:1,1:30,12:42,2:0.0455:2,2:16:1:28.5:1:0.50846:2.44164:60:4:0.0476:0:0 +13 88543179 . C T 29 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2369;SOR=0;LSEQ=CTGAGTCTTCCAGAAGGCAT;RSEQ=GTGCAGTGAGCAGTGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:47,34:81,2:0.0241:2,2:7:0:29:1:1:1.37686:60:4:0.0241:0:1 0/0:87:0:0,0:53,34:87,0:0:2,0:25.3:1:29.4:1:1:0:59.6:20.75:1:0:0.1 +13 88543183 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24267;SOR=Inf;LSEQ=GTCTTCCAGAAGGCATCGTG;RSEQ=AGTGAGCAGTGGGGAATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:52,34:86,0:0:2,0:23.8:1:32.2:1:1:0:59.7:42:1:0:0.1 0/1:84:2:2,0:49,33:82,2:0.0238:2,0:21:1:27.5:1:0.51721:0:60:4:0.0247:0:1 +13 88543265 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50366;SOR=Inf;LSEQ=TCAATAGAGCTGGGTGGCTG;RSEQ=AGCAGTCTTCGGGGACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:86,70:156,0:0:2,0:26.2:1:30.4:1:1:0:59.2:77:1:0:0.1 0/1:191:2:1,1:99,90:189,2:0.0105:2,2:35:0:32.5:1:1:1.09945:60:4:0.0105:0:1.5 +13 88543278 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18919;SOR=0;LSEQ=GTGGCTGAAGCAGTCTTCGG;RSEQ=GACCAGGAGAAGCCTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:79,75:154,2:0.0128:2,2:25.5:1:29.5:1:1:1.053:60:4:0.013:0:1 0/0:202:0:0,0:99,103:202,0:0:2,0:28.1:1:30.3:1:1:0:58.8:49.5:1:0:0.2 +13 88543282 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50738;SOR=Inf;LSEQ=CTGAAGCAGTCTTCGGGGAC;RSEQ=AGGAGAAGCCTGGAGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:76,78:154,0:0:2,0:27.4:1:31.6:1:1:0:59.2:308:1:0:0.1 0/1:201:2:1,1:96,103:199,2:0.01:2,2:24.5:1:30.5:1:1:1.07:53:4:0.0101:0:1.5 +13 88543512 . C T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4997;SOR=0;LSEQ=ATTTGGGGAATGGGTTTTTT;RSEQ=TCCACTGCCCTTATCTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:119,74:193,2:0.0103:2,2:6.5:1:28.5:1:1:1.60399:60:4:0.0104:0:1 0/0:178:0:0,0:112,66:178,0:0:2,0:22.8:1:30.5:1:1:0:60:177:1:0:0.2 +13 88543630 . C T 47 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02783;SOR=Inf;LSEQ=TTTTTTTTTTTTCTTTGCAT;RSEQ=AAGGTGCCAGGACCTCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:162,123:285,0:0:2,0:21:1:30.4:1:1:0:59.5:8.194:1:0:0.5 0/1:279:5:3,2:149,122:271,5:0.0179:2,2:5.8:1:20.4:1:1:1.23:60:1.5:0.0121:0:1.4 +13 88543770 . G A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02586;SOR=Inf;LSEQ=GGAATAACACCCAAAGAGCA;RSEQ=TTATCTTCTTGAATTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:141,180:321,0:0:2,0:25.4:1:32.7:1:1:0:59.9:320:1:0:0.1 0/1:300:5:2,3:134,161:295,5:0.0167:2,2:8.2:1:30:1:1:1.24754:60:10:0.0168:0:1.2 +13 88543882 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52798;SOR=0;LSEQ=CTATGATGCCAGAGAAGGAA;RSEQ=AACTATTCTTGCTGCCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:48,87:135,2:0.0146:2,2:16:1:33:1:1:1.80:60:4:0.0149:0:1 0/0:83:0:0,0:27,56:83,0:0:2,0:19.5:1:29.7:1:1:0:60:82:1:0:0.1 +13 88544037 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17616;SOR=Inf;LSEQ=TTTTTTTCCATGGCCTCATG;RSEQ=TCCACACAAATTTGTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:76,27:103,0:0:2,0:26.3:1:30:1:1:0:59.8:33.333:1:0:0.2 0/1:75:2:1,1:49,24:73,2:0.0267:2,2:16.5:1:30:1:1:2.02078:60:4:0.0267:0:1 +13 88544040 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.16872;SOR=Inf;LSEQ=TTTTCCATGGCCTCATGTTC;RSEQ=ACACAAATTTGTTCCAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:78,26:104,0:0:2,0:26.2:1:31.7:1:1:0:59.8:103:1:0:0.2 0/1:73:2:2,0:49,22:71,2:0.0274:2,0:23.5:1:26.5:1:1:0:60:4:0.0278:0:3 +13 88544233 . G A 49 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10916;SOR=5.50882;LSEQ=ATGAAGTGCCACATGTCTCT;RSEQ=GATCAATTCCTTAACATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:1:1,0:154,239:393,1:0.0025:2,0:1:0:24:0:0.3934:0:49:2:0.0026:0:1 0/1:361:5:4,1:139,217:356,5:0.0139:2,2:5:1:21.4:1:0.08262:6.21:48.8:4:0.0113:0:1 +13 88544358 . G A 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCCAGTCAGCCACTGAGAA;RSEQ=CGATTGCCATCCCACACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:83,105:188,0:0:2,0:26.5:1:32.3:1:1:0:60:187:1:0:0.1 0/1:166:17:9,8:78,71:149,17:0.1024:2,2:25.5:1:30.2:1:1:1.02:60:34:0.103:0:1.1 +13 88544427 . C A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.66858;SOR=1.70228;LSEQ=CAGTGGTGGCCTGTACACTG;RSEQ=TAGACCAGAGAGCTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:53,88:141,2:0.014:2,2:1:0:29:1:1:1.65:60:4:0.0143:0:1 0/1:127:3:2,1:54,70:124,3:0.0236:2,2:25:1:26.7:1:0.58257:2.57:60:6:0.0244:0:1 +13 88544519 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23931;SOR=Inf;LSEQ=CTTTTCCCTTCATTACCAGT;RSEQ=TACACTACTGTTTCTATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:60,70:130,0:0:2,0:25.6:1:32.1:1:1:0:59.9:64:1:0:0.1 0/1:125:2:1,1:69,54:123,2:0.016:2,2:27:1:29.5:1:1:1.27524:60:4:0.0163:0:1 +13 88544588 . A G 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49869;SOR=0;LSEQ=TTCACCATGATTTCCCTGAC;RSEQ=GCAGCAACACCTGGTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:90,93:183,2:0.0108:2,2:30.5:1:26:1:1:1.03:60:4:0.011:0:1 0/0:181:0:0,0:92,89:181,0:0:2,0:26.3:1:29.6:1:1:0:60:35.2:1:0:0.1 +13 88544636 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50051;SOR=Inf;LSEQ=GTATATAATATGAGCCTTTG;RSEQ=TTTTCGTGTAACTCGATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:62,69:131,0:0:2,0:23.7:1:30.6:1:1:0:60:64.5:1:0:0.1 0/1:150:2:1,1:64,84:148,2:0.0133:2,2:27:1:28.5:1:1:1.31:60:4:0.0134:0:0 +13 88544720 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50905;SOR=Inf;LSEQ=TCAGGTGTTTTGTAGGGATA;RSEQ=TAAAGAAATTCATGGCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:27,44:71,0:0:2,0:25:1:32:1:1:0:60:34.5:1:0:0.2 0/1:97:2:2,0:38,57:95,2:0.0206:2,0:19:1:25:1:0.16753:0:60:4:0.0208:0:1 +13 88544737 . A T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12605;SOR=Inf;LSEQ=ATAGTAAAGAAATTCATGGC;RSEQ=TATTCACCAGAATTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:28,36:64,0:0:2,0:23.9:1:30.1:1:1:0:60:15:1:0:0.2 0/1:77:4:2,2:33,40:73,4:0.0519:2,2:22:1:30:1:1:1.21:60:8:0.0519:0:1 +13 88544795 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20858;SOR=Inf;LSEQ=AAAACTGATGTTTCAACAGT;RSEQ=GGTGAACCTACTTCCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:45,46:91,0:0:2,0:24.5:1:31.7:1:1:0:60:44.5:1:0:0.1 0/1:77:2:1,1:36,39:75,2:0.026:2,2:28:1:28.5:1:1:1.08:60:4:0.0267:0:1 +13 88544803 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21082;SOR=Inf;LSEQ=TGTTTCAACAGTGGGTGAAC;RSEQ=TACTTCCTCTTCACTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:48,48:96,0:0:2,0:25.7:1:32.2:1:1:0:60:192:1:0:0.2 0/1:82:2:1,1:42,38:80,2:0.0244:2,2:18:0:32:0:1:1.10391:42.5:4:0.0247:0:1 +13 88545032 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4987;SOR=Inf;LSEQ=TTCTGGGTTGTGTTCTTTTA;RSEQ=TTTGTTAATGATGAACTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:98,50:148,0:0:2,0:27.2:1:32.1:1:1:0:59.7:23.667:1:0:0.2 0/1:156:2:1,1:94,60:154,2:0.0128:2,2:30:0:30.5:1:1:1.56196:60:4:0.013:0:1.5 +13 88545081 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21129;SOR=0;LSEQ=GGACACTTGAAGGTGGTTTC;RSEQ=ATTGTATTACACCCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:94,84:178,2:0.0111:2,2:47:0:32:1:1:1.11835:58:4:0.0111:0:1 0/0:211:0:0,0:98,113:211,0:0:2,0:24.4:1:28.4:1:1:0:59.5:41.2:1:0:0.1 +13 88545085 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21762;SOR=0;LSEQ=ACTTGAAGGTGGTTTCTATT;RSEQ=TATTACACCCTTCTCCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:92,91:183,2:0.0108:2,2:8.5:1:32:1:1:1.01093:60:4:0.0109:0:1 0/0:211:0:0,0:99,112:211,0:0:2,0:24.9:1:31.2:1:1:0:59.4:69.333:1:0:0.1 +13 88545141 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6195;SOR=2.05601;LSEQ=CATTACATGCAACAAGGCTT;RSEQ=TCAGTGTACTTTCAACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:62,109:171,1:0.0058:2,0:1:0:23:0:0.36628:0:60:2:0.0058:0:1 0/1:168:2:1,1:69,97:166,2:0.0119:2,2:30.5:1:28.5:1:1:1.40:59:4:0.012:0:1 +13 88545143 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24334;SOR=Inf;LSEQ=TTACATGCAACAAGGCTTGT;RSEQ=AGTGTACTTTCAACATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:61,109:170,0:0:2,0:28:1:32.3:1:1:0:59.9:55.667:1:0:0.1 0/1:166:2:1,1:67,97:164,2:0.012:2,2:30.5:1:27:1:1:1.44:45:4:0.0123:0:1 +13 88545378 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0437;SOR=Inf;LSEQ=ATTCTTGCAACAACTGTCAA;RSEQ=AGTAATTCTACCTTGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,9:21,0:0:2,0:25.1:1:33.2:1:1:0:56.7:42:1:0:0 0/1:13:3:2,1:8,2:10,3:0.2308:2,2:13.7:1:29.7:1:1:1.88511:60:6:0.2308:0:1 +13 88545458 . C T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32879;SOR=3.70854;LSEQ=GCTTAAAAAGAGATAACTAG;RSEQ=TGTTCTCTGCTCTGATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:44,16:60,1:0.0164:2,0:1:0:27:0:0.27869:0:60:2:0.0172:0:1 0/1:51:3:1,2:31,17:48,3:0.0588:2,2:14.3:1:29:1:0.54747:3.55085:60:6:0.0588:0:1.3 +13 88545493 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24136;SOR=0;LSEQ=ATTCTTCATCATTCTCTGAC;RSEQ=TTGATGGGGAAGAATTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:47,22:69,2:0.0282:2,2:20.5:1:31.5:1:0.54608:2.11156:60:4:0.029:0:1.5 0/0:73:0:0,0:43,30:73,0:0:2,0:28.4:1:29.8:1:1:0:60:72:1:0:0.4 +13 88545521 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50473;SOR=Inf;LSEQ=GGAAGAATTCTCTGGTGGGG;RSEQ=TTCTGAGAGCTGAGTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:37,24:61,0:0:2,0:24.6:1:32.6:1:1:0:60:60:1:0:0.2 0/1:79:2:1,1:43,34:77,2:0.0253:2,2:18:1:27:1:1:1.26091:60:4:0.0256:0:2 +13 88545547 . A G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=6.34583;LSEQ=AGAGCTGAGTCAAGACCTCT;RSEQ=TGGCTGCCACTTCCTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:7:4,3:36,19:55,7:0.1129:2,2:17.4:1:32.1:1:0.69093:1.41267:60:14:0.1129:0:1 0/1:80:36:18,18:25,19:44,36:0.45:2,2:24.8:1:30.1:1:0.6532:1.31125:60:17:0.4416:0:1.1 +13 88546181 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19304;SOR=Inf;LSEQ=ATCTATTGTAGTCCATGGAT;RSEQ=CTGACTTGGGGACATTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:93,85:178,0:0:2,0:28.2:1:30.5:1:1:0:60:58.333:1:0:0.1 0/1:140:2:1,1:72,66:138,2:0.0143:2,2:37.5:1:32:1:1:1.09022:60:4:0.0147:0:1.5 +13 88546266 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20292;SOR=Inf;LSEQ=CCTCTGGGGTCTCTTGATTT;RSEQ=CTTTATAACCTCCAAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:30,56:86,0:0:2,0:23.3:1:31.7:1:1:0:60:85:1:0:0 0/1:71:2:1,1:27,42:69,2:0.0282:2,2:29.5:1:27:1:1:1.55:60:4:0.0286:0:1 +13 88546371 . G A 26 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.60911;LSEQ=TTTCTCTTCTTGCAACTAGT;RSEQ=CATTCACCAAAGTTGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:74,50:124,2:0.0159:2,2:24:1:26.5:1:1:1.47525:60:4:0.0159:0:1 0/0:103:1:1,0:61,41:102,1:0.0097:2,0:37:0:28:0:1:0:60:2:0.0099:0:1 +13 88546432 . C CT 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.23173;SOR=0.42139;LSEQ=CCTCATATTGCTTTCATTTC;RSEQ=TTTTTTTTTCAAAGTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:8:6,2:142,33:175,8:0.0435:2,2:27.4:1:30.7:1:0.64988:1.43123:57.5:16:0.0442:0.0054:0.8 0/1:160:3:3,0:124,33:157,3:0.0188:2,0:35:1:31.3:1:1:0:60:6:0.0192:0:0 +13 88546805 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24879;SOR=Inf;LSEQ=GGCAAAATGTATATAGCACT;RSEQ=TGGACCACAAACCCATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:127,154:281,0:0:2,0:23.9:1:32.4:1:1:0:60:69.25:1:0:0.1 0/1:288:3:2,1:119,166:285,3:0.0104:2,2:22.3:1:26.7:1:0.57431:2.78:60:6:0.0106:0:1 +13 88546844 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21034;SOR=Inf;LSEQ=GAGACAGTGCCATAGGGCTC;RSEQ=GGCCATTTGGGAGGAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:59,134:193,0:0:2,0:23.2:1:31.3:1:1:0:59.9:192:1:0:0.1 0/1:164:2:1,1:51,111:162,2:0.0122:2,2:20:1:28.5:1:0.53494:2.17:60:4:0.0122:0:1 +13 88546965 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17065;SOR=Inf;LSEQ=GTTGTTGGTCTAAGATAGTA;RSEQ=CAAAGAGCTCTTCTTGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:48,55:103,0:0:2,0:27.5:1:32:1:1:0:60:102:1:0:0.2 0/1:73:2:1,1:34,37:71,2:0.0274:2,2:32.5:1:28.5:1:1:1.09:60:4:0.0278:0:1 +13 88546991 . AG A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=4.50032;LSEQ=AGCTCTTCTTGGACTGGAAT;RSEQ=CACCAGGAACCTTTGTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:10:4,6:45,49:94,10:0.0952:2,2:16.8:1:30.6:1:0.74585:1.37336:60:20:0.098:0.0381:0 0/1:68:22:9,13:25,21:46,22:0.3235:2,2:26.5:1:32.1:1:0.43722:1.70578:60:44:0.3284:0.0441:0.2 +13 88547033 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.519;SOR=0;LSEQ=TCTGGGGTCTTACCCAGGGC;RSEQ=TTGGCATGAAGTTGCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:50,40:90,2:0.0217:2,2:25.5:1:29.5:1:1:1.24694:60:4:0.0227:0:1 0/0:60:0:0,0:35,25:60,0:0:2,0:24.3:1:30.6:1:1:0:60:59:1:0:0.1 +13 88547421 . A T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.594;SOR=2.39341;LSEQ=TGGCAGTTGTTCTTTGTGGC;RSEQ=AAGGAGCACACACAATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:1:0,1:68,100:168,1:0.0059:2,0:1:0:24:0:1:0:60:2:0.006:0:1 0/1:142:2:0,2:56,84:140,2:0.0141:2,0:13:1:25:1:0.51893:0:60:4:0.0142:0:1 +13 88547636 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20184;SOR=Inf;LSEQ=TCTTGGCTCTTACTTTTGAT;RSEQ=AAAGAGGGATTTTGTACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:66,67:133,0:0:2,0:29.2:1:29.2:1:1:0:59.7:65.5:1:0:0.2 0/1:109:2:1,1:57,50:107,2:0.0183:2,2:33:1:32:0:1:1.13863:60:4:0.0183:0:1 +13 88547685 . T TG 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=6.67761;LSEQ=CCTCTATATTAAGAAGAATG;RSEQ=GGTGTCTTGCATTGGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:15:6,9:24,47:71,15:0.1744:2,2:21.3:1:32.1:1:0.76707:1.30:60:30:0.1765:0.0349:0.1 1/0:85:50:22,28:12,22:34,50:0.5882:2,2:24:1:30.8:1:0.5001:1.43:59.8:100:0.5882:0.0941:0.1 +13 88547915 . G T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24861;SOR=Inf;LSEQ=GGTTCTGAAAAGAAACCTCA;RSEQ=TCCTATCCAAATTCATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:187,83:270,0:0:2,0:23.5:1:32.7:1:1:0:59.9:53:1:0:0.1 0/1:270:3:2,1:172,95:267,3:0.0111:2,2:26.3:1:31.3:1:1:1.10:60:6:0.0113:0:1 +13 88548165 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52442;SOR=0;LSEQ=AAGCCTTGTGTGGCAGGACC;RSEQ=AGACATAGCTGCAGGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:1,100:101,2:0.0194:1,2:43.5:1:31:1:0.03864:71.17:60:4:0.0196:0:1 0/0:64:0:0,0:4,60:64,0:0:2,0:24.9:1:31.5:1:1:0:60:63:1:0:0 +13 90822777 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49673;SOR=0;LSEQ=ATGCCTAGCCCAGTAGAAAT;RSEQ=GTATGGACTAAATGGATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:2,0:57,5:62,2:0.0313:2,0:14:1:32.5:1:1:0:60:4:0.0317:0:1 0/0:59:0:0,0:52,7:59,0:0:2,0:24.1:1:31.4:1:1:0:60:58:1:0:0.1 +13 90822829 . G T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63076;SOR=2.46141;LSEQ=TTTCTCTTCTATCACATAGT;RSEQ=TTTGGGCTTGAGAAGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:1:0,1:120,42:162,1:0.0061:2,0:1:0:30:0:0.2638:0:60:2:0.0063:0:1 0/1:200:3:1,2:136,61:197,3:0.015:2,2:16.3:1:28:1:0.23395:4.42203:60:6:0.015:0:1.7 +13 90822835 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19332;SOR=0;LSEQ=TTCTATCACATAGTGTTTGG;RSEQ=CTTGAGAAGGGACTGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:124,44:168,2:0.0118:2,2:21:1:29:1:0.46049:2.79791:60:4:0.012:0:1 0/0:216:0:0,0:143,73:216,0:0:2,0:25:1:30.6:1:1:0:60:107:1:0:0.4 +13 90822837 . TTG T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25955;SOR=Inf;LSEQ=CTATCACATAGTGTTTGGGC;RSEQ=AGAAGGGACTGTCACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:129,49:178,0:0:2,0:24.2:1:30.8:1:1:0:60:177:1:0:0.7 0/1:228:3:1,2:147,78:225,3:0.0132:2,2:15:1:24.7:1:0.28205:3.74625:60:6:0.0133:0.0088:1.3 +13 90822839 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19524;SOR=0;LSEQ=ATCACATAGTGTTTGGGCTT;RSEQ=AGAAGGGACTGTCACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:130,48:178,2:0.011:2,2:11.5:1:28.5:1:0.47145:2.69085:60:4:0.0112:0:3 0/0:228:0:0,0:146,79:225,0:0:2,0:25.6:1:31.1:1:1:0:60:111.5:1:0:0.5 +13 90822845 . G T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58385;SOR=0.38813;LSEQ=TAGTGTTTGGGCTTGAGAAG;RSEQ=GACTGTCACCCTGACTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:134,55:189,2:0.0105:2,2:8:1:30:1:0.50152:2.42352:60:4:0.0106:0:1 0/0:245:1:0,1:156,88:244,1:0.0041:2,0:1:0:22:0:0.36327:0:60:2:0.0041:0:5 +13 90822855 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25886;SOR=Inf;LSEQ=GCTTGAGAAGGGACTGTCAC;RSEQ=CTGACTGGGACTGCATTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:149,81:230,0:0:2,0:23.9:1:31.2:1:1:0:60:56.5:1:0:1 0/1:291:3:1,2:174,114:288,3:0.0103:2,2:11.3:1:26.7:1:0.56551:3.04078:60:6:0.0103:0:2.3 +13 90822896 . G C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=0.55127;LSEQ=CATATATATTCTGCAAAAGC;RSEQ=CTGACATGACTGTGCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:350:203:107,96:83,64:147,203:0.58:2,2:26.8:1:31.1:1:0.51527:1.16305:60:100.5:0.5776:0:2.1 0/1:412:178:93,85:120,114:234,178:0.432:2,2:25.7:1:30.2:1:0.92075:1.04:59.7:177:0.436:0:2.1 +13 90822912 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00073;SOR=0.60912;LSEQ=AAGCGCTGACATGACTGTGC;RSEQ=AAAACTAAGTTAGTGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:353:202:100,102:79,70:149,202:0.5722:2,2:28.2:1:31.3:1:0.51932:1.15068:60:32.667:0.5681:0:2.1 0/1:430:193:94,99:120,117:237,193:0.4488:2,2:25:1:30.4:1:0.69927:1.08:59.7:47.25:0.4458:0:2 +13 90823086 . AT A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.25339;SOR=0;LSEQ=GTGCAGGTAAATGCTTAAAT;RSEQ=TTTTTTTTTTTGAGACGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:2,25:27,3:0.1:2,0:21:1:33.3:1:1:0:52.7:6:0.1071:0:0 0/0:22:0:0,0:1,20:21,0:0:1,0:26.1:1:29.6:1:1:0:60:20:0.9524:0:0.1 +13 92901774 . A G 110 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=21.48473;LSEQ=AGCAGAAGTCAGAACTGGCT;RSEQ=AGAATTTATTTATGTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:2,0:49,3:52,2:0.037:2,0:28.5:1:34:0:1:0:21:4:0.0385:0:1 0/1:28:13:13,0:15,0:15,13:0.4643:1,1:18.1:1:29.8:1:1:0:40.6:26:0.4643:0:1.5 +13 92901900 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.0629;SOR=Inf;LSEQ=CTGAAAATTTTTAGTGGGGG;RSEQ=GTTGATGGCATGCTCAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:195,191:386,0:0:2,0:24.9:1:30.5:1:1:0:59.5:28.692:1:0:0.2 0/1:421:5:1,4:213,203:416,5:0.0119:2,2:15.8:1:25.4:1:0.20895:4.18418:52:4:0.0096:0:1.4 +13 92901901 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.06283;SOR=Inf;LSEQ=TGAAAATTTTTAGTGGGGGG;RSEQ=TTGATGGCATGCTCAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:196,192:388,0:0:2,0:24.8:1:31.2:1:1:0:59.5:37.8:1:0:0.2 0/1:422:5:4,1:212,203:415,5:0.0118:2,2:16.8:1:25.2:1:0.37304:3.82:55.6:4:0.0096:0:2 +13 92901914 . T G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=23.06425;LSEQ=TGGGGGGGTTGATGGCATGC;RSEQ=CAATGGTTTAGTATATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:9:5,4:170,204:374,9:0.0235:2,2:24:1:29.1:1:0.73748:1.50:53.1:8:0.0212:0:2.9 0/1:397:142:71,71:123,132:255,142:0.3577:2,2:31.1:1:30.4:1:0.75421:1.07:49.3:284:0.3622:0:2.2 +13 92901926 . T G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=23.1593;LSEQ=TGGCATGCTCAATGGTTTAG;RSEQ=ATATTTGAGTTAGTGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:8:4,4:156,200:356,8:0.0219:2,2:17.9:1:29.9:1:0.7346:1.28:52.3:7:0.0197:0:2.4 0/1:395:135:66,69:117,141:258,135:0.3418:2,2:28.2:1:30.2:1:0.52417:1.15:47.2:134:0.3436:0:2.4 +13 92901981 . G A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=19.93792;LSEQ=GTGAGTAGAGAATGCAGAGC;RSEQ=GACCAGGCAATTCAGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:4:1,3:73,161:234,4:0.0168:2,2:27.5:1:30.8:1:1:1.35864:40.8:8:0.0171:0:4 0/1:188:48:10,38:52,88:140,48:0.2553:2,2:27.3:1:29.5:1:0.04977:2.23647:40.9:47:0.2513:0:3.3 +13 92901984 . C G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=23.70023;LSEQ=AGTAGAGAATGCAGAGCGGA;RSEQ=CAGGCAATTCAGGAATCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:0,3:66,157:223,3:0.0133:2,0:23.7:1:25:1:0.55777:0:38.3:2:0.009:0:5 0/1:177:43:8,35:50,84:134,43:0.2429:2,2:30.3:1:30.1:1:0.02538:2.59116:42.2:20.5:0.2426:0:3.3 +13 92901995 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50421;SOR=0;LSEQ=CAGAGCGGACCAGGCAATTC;RSEQ=GGAATCTATGTTGGTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:46,133:179,2:0.011:2,2:36.5:1:30:1:0.45298:2.87:60:4:0.0111:0:1 0/0:146:0:0,0:43,103:146,0:0:2,0:26.1:1:29.7:1:1:0:56.4:292:1:0:0.9 +13 92902025 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=19.2763;LSEQ=GTTGGTTGTTTAATTGCTTC;RSEQ=GTTTTGTCAACATCTTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:4:0,4:16,98:114,4:0.0339:2,0:17.3:1:28.5:1:1:0:53.5:8:0.0345:0:3.3 0/1:86:35:5,30:9,42:51,35:0.407:2,2:24.5:1:29.2:1:0.77226:1.28202:54.5:34:0.4048:0:2.6 +13 93770081 . C G 52 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.87089;LSEQ=AAGTAGCCCATATTCAATCT;RSEQ=TTTTGTTATATAGTACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:21:1:33:1:1:0:60:6:0.3333:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:46:0:31:0:1:0:60:2:0.5:0:1 +13 93770238 . TAC T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.00688;SOR=Inf;LSEQ=TATATGCATATATATATGTA;RSEQ=ACACACACATATATATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:100,11:111,0:0:2,0:24:1:29:1:1:0:59.9:110:1:0:0.2 0/1:113:8:6,2:95,10:105,8:0.0708:2,2:22.9:1:30.1:1:0.20173:3.1202:60:16:0.0714:0.0088:0.4 +13 93770333 . A G 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06044;SOR=1.26957;LSEQ=AGAGTGGAGGAAAAATGGCA;RSEQ=TGGGTCACAGTAATTACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:192:99,93:137,121:258,192:0.4257:2,2:27.4:1:32.6:1:0.77507:1.06345:60:95:0.4241:0:1.2 0/1:596:289:148,141:157,150:307,289:0.4849:2,2:25.8:1:31.5:1:1:1.00:60:95.333:0.4839:0:1.2 +13 93770390 . C T 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGTACTATTCTTAAAATAA;RSEQ=CATAGGGCTTTGGTTATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:102,187:289,0:0:2,0:24.7:1:31.5:1:1:0:60:95.333:1:0:0.4 0/1:397:33:13,20:140,223:363,33:0.0831:2,2:26.1:1:28.7:1:1:1.04:60:66:0.0842:0:1.8 +13 95364018 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54257;SOR=0;LSEQ=GCCGCCCAGGCCGTAGGGCA;RSEQ=CGGGAAGGCGAACTTGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:60,4:64,2:0.0303:2,0:13.5:1:32:0:1:0:60:4:0.0308:0:1.5 0/0:35:0:0,0:35,0:35,0:0:1,0:21.4:1:32.4:1:1:0:60:70:1:0:0.8 +13 95364046 . C G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15965;SOR=1.52077;LSEQ=GCGAACTTGTCCTTCTTGAG;RSEQ=AGCGTCTTGGGCTTGCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:55:49,6:61,4:65,55:0.4583:2,2:24.1:1:32:1:0.50973:1.85758:60:110:0.4583:0:1.1 1/0:87:49:44,5:32,6:38,49:0.5632:2,2:22.5:1:30.1:1:0.52295:1.64:60:23.5:0.5529:0:1.2 +13 95364090 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10837;SOR=Inf;LSEQ=CCGGTACTTGTAGTCGGGGT;RSEQ=CTCCTTCATGTGCATGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:202,57:259,0:0:2,0:25.4:1:32.5:1:1:0:59.9:85.333:1:0:0.3 0/1:237:3:2,1:164,70:234,3:0.0127:2,2:29:1:27.7:1:1:1.1706:60:6:0.0128:0:1.7 +13 95364307 . C A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.10439;SOR=Inf;LSEQ=TCCACCGGCTTGGACATGCT;RSEQ=TCGCCCTGCCGCGGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:28,198:226,0:0:2,0:23.7:1:32.9:1:1:0:59.9:112:1:0:0.4 0/1:203:3:2,1:40,160:200,3:0.0148:2,2:5.7:1:27.7:1:0.10927:7.89:60:6:0.0149:0:1.7 +13 95364334 . GCCT G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50446;SOR=0;LSEQ=TGCCGCGGCTGCAGCCCGCC;RSEQ=CCCGGGCCCTCGCCCTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:4,114:118,2:0.0167:1,2:13.5:1:34:0:0.08193:25.60:60:4:0.0169:0:0 0/0:95:0:0,0:6,89:95,0:0:2,0:26.1:1:31:1:1:0:60:190:1:0:0.8 +13 95364337 . T G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.31577;SOR=1.36675;LSEQ=CGCGGCTGCAGCCCGCCGCC;RSEQ=CCCGGGCCCTCGCCCTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:115:66:0,66:3,44:47,66:0.5739:2,1:26.5:1:32.8:1:0.06925:0:60:65:0.5856:0:1.1 1/0:91:59:3,56:2,30:32,59:0.6484:2,2:24.7:1:31.6:1:1:1.24135:60:58:0.6591:0:1.3 +13 95413053 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19481;SOR=Inf;LSEQ=ACTTGTTTGTTTACAATGAT;RSEQ=CCAACAGCATGCTAGGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:14,17:31,0:0:2,0:27.1:1:32.5:1:1:0:58.8:62:1:0:0 0/1:25:2:1,1:10,13:23,2:0.08:2,2:30:1:28.5:1:1:1.29:44.5:4:0.0833:0:1 +13 95413146 . G C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=TGGACAGTACCCATTCCCTT;RSEQ=GTGTCTACATTATCGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:3,7:10,3:0.2143:2,2:19.3:1:31:1:1:1.15:60:6:0.2143:0:1 0/0:5:0:0,0:3,2:5,0:0:2,0:25.4:1:30.2:1:1:0:60:10:1:0:0 +13 95413279 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=GTTCGTCATTTTATCAAATT;RSEQ=CTGGAAGCTGGGAGTTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:7,0:0:2,0:12.4:1:29.6:1:1:0:60:14:1:0:0.3 0/1:5:2:1,1:1,2:3,2:0.4:2,2:12.5:1:27:1:1:1.73:60:4:0.4:0:1 +13 96897256 . T A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02347;SOR=0.5384;LSEQ=ACAGCATGTACAAAATATTA;RSEQ=TTTTAATCTGTTTCAGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:66:39,27:25,11:36,66:0.6471:2,2:25.6:1:30.8:1:0.39217:1.56652:60:132:0.6471:0:1.1 0/1:127:63:39,24:35,29:64,63:0.4961:2,2:23.8:1:29.5:1:0.47306:1.34:60:62:0.496:0:1.2 +13 96897357 . A G 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49607;SOR=0;LSEQ=TTGTGTGTCATTACTAAATC;RSEQ=TCCCAGATGATTGAAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:12,49:61,2:0.0317:2,2:5.5:1:30:1:0.37276:3.96:60:4:0.0323:0:1.5 0/0:61:0:0,0:16,45:61,0:0:2,0:26.7:1:29.6:1:1:0:60:60:1:0:0 +13 99176306 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCCCGTCCACACCCAG;RSEQ=CCCAAAGCAGGCAGGGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:27.5:1:1:0:60:4:1:0:1 +13 99177868 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAGCCGGGCTCGCCACCCC;RSEQ=GTATAGGCAGGAGGATCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:48.5:1:19.5:1:1:0:60:1:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:28:1:1:0:60:4:1:0:1.5 +13 99177963 . C T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCCTCGAGCCCCACAAGC;RSEQ=GCCTCACACTGATGAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:21:1:32.5:1:1:0:60:8:0.5714:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:39:0:32:0:1:0:60:2:1:0:0 +13 99178276 . G A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41291;SOR=1.14596;LSEQ=GAAGGACAGGCTTTGGTTGG;RSEQ=TAAGTCAGGGTTGGTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:328:232:135,97:49,47:96,232:0.7073:2,2:26.1:1:30.4:1:0.27135:1.33:59.9:57:0.7081:0:1.1 1/0:426:313:164,149:62,51:113,313:0.7347:2,2:25.2:1:28.8:1:0.66182:1.10424:60:38.125:0.7332:0:1.1 +13 99178332 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13716;SOR=Inf;LSEQ=TGAGGGATGGTGGCTGGAGT;RSEQ=CGGTGGAGGGAGGAGCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:115,172:287,0:0:2,0:26.8:1:31.7:1:1:0:59.9:94.667:1:0:0.5 0/1:375:4:3,1:165,206:371,4:0.0107:2,2:23:1:25.3:1:0.32928:3.73:60:8:0.0108:0:1.8 +13 99178385 . C T 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGAAAGGGGCTTTCGAAA;RSEQ=AGGTCCGTCTTTGCTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:10,99:109,0:0:2,0:21.9:1:33:1:1:0:59.8:218:1:0:0.1 0/1:129:23:3,20:16,90:106,23:0.1783:2,2:21.7:1:28:1:1:1.18368:60:46:0.1811:0:1.1 +13 99565179 . T C 33 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTATGAACCCCCAAACA;RSEQ=CCAGAAACAAAAAAGCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 99566435 . G A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42598;LSEQ=ATCATACTGCATGAGTACAC;RSEQ=TCACCTCGTAATCAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:406:262:129,133:80,64:144,262:0.6453:2,2:27.6:1:31:1:0.25376:1.28794:60:130:0.65:0:1.1 0/1:385:168:89,79:101,114:215,168:0.4364:2,2:27:1:29.8:1:0.25847:1.27:59.9:83:0.4368:0:1.1 +13 99566465 . G T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.12448;SOR=0;LSEQ=AATCAGGTCAGAAAAAGAGA;RSEQ=AGGTAATCACAATGTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:4:2,2:157,195:352,4:0.0112:2,2:25:1:30:1:1:1.24:60:8:0.0113:0:2 0/0:337:0:0,0:142,195:337,0:0:2,0:24.1:1:30.7:1:1:0:60:111.333:1:0:0.5 +13 102276430 . G T 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGGATTCCTGGAGATAT;RSEQ=CTTAGATGTTTACTAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:18:1:31:1:1:0:55:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 102276717 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16293;SOR=1.29418;LSEQ=CATTTATGTTTTATGCCCCA;RSEQ=TAACTACACTTCCTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:320:223:125,98:50,47:97,223:0.6969:2,2:26.3:1:32.6:1:0.4662:1.20:60:73.333:0.7029:0:1.6 1/0:338:253:149,104:45,40:85,253:0.7485:2,2:26.2:1:31.3:1:0.37547:1.27:60:125.5:0.747:0:1.6 +13 102276769 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01033;SOR=1.47875;LSEQ=GAGCCTTGAAGTGTTCACCT;RSEQ=AAAGCATTTTAAAATAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:355:211:99,112:66,77:143,211:0.5944:2,2:26.1:1:29.3:1:0.91382:1.03:59.9:34.167:0.5908:0:1.6 1/0:415:284:136,148:62,67:129,284:0.6843:2,2:26.1:1:28.3:1:1:1.00701:60:55.8:0.6822:0:1.6 +13 102276854 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2225;SOR=Inf;LSEQ=AGGACTCAGGATACAGATTG;RSEQ=CCTGGGGTTGCTCATGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:45,108:153,0:0:2,0:24.3:1:29.9:1:1:0:60:152:1:0:0.2 0/1:138:2:1,1:34,102:136,2:0.0145:2,2:33.5:1:29.5:1:0.4443:2.97:60:4:0.0145:0:1 +13 103337240 . A G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01383;SOR=0.47507;LSEQ=TTAGCTTGACAAATTCCACA;RSEQ=GAAAGTATATTGGGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:44:41,3:54,7:61,44:0.419:2,2:23:1:33.1:1:0.51476:1.76:60:88:0.419:0:1 0/1:110:28:25,3:69,13:82,28:0.2545:2,2:20.1:1:31.8:1:0.75701:1.56:60:56:0.2545:0:1 +13 103337266 . G T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60163;SOR=0.43836;LSEQ=TATATTGGGATTTTTACAAT;RSEQ=ATTTCACGTAAGCTGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:136,53:189,2:0.0105:2,2:24:1:28.5:1:0.48658:2.5515:60:4:0.0105:0:1 0/0:217:1:1,0:155,61:216,1:0.0046:2,0:2:0:28:0:1:0:60:2:0.0046:0:1 +13 103337294 . G T 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65904;SOR=0.52356;LSEQ=GTAAGCTGTTGATCAATTTG;RSEQ=AGAAAACTGACATATTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:1,2:190,105:295,3:0.0101:2,2:30.7:1:27.7:1:0.29353:3.60263:60:6:0.0103:0:1 0/0:378:2:0,2:228,148:376,2:0.0053:2,0:1:0:23:1:0.15684:0:60:4:0.0053:0:1 +13 103337357 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34796;LSEQ=GATGTCTCCCCATTTACTTA;RSEQ=GTTAGTTTTAATTTGTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:205:101,104:90,102:192,205:0.5164:2,2:25.6:1:30.9:1:0.68783:1.10:60:67.333:0.5127:0:1.1 0/1:569:154:80,74:215,195:410,154:0.2707:2,2:26.3:1:30.1:1:0.9249:1.01984:60:50.333:0.2692:0:1.2 +13 103337590 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08669;SOR=Inf;LSEQ=CAATAATTTCACTGTGGATC;RSEQ=CCTGCAGTTCCAGGGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:10,0:0:0,0:25.1:1:32.6:1:1:0:60:20:1:0:0.1 0/1:9:3:0,3:2,4:6,3:0.3333:2,0:31:1:30.3:1:0.5:0:60:6:0.3333:0:1 +13 103498375 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=CAACGGCCATTCTCTGGACC;RSEQ=GTCTTTCTTCCGGGAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:8,1:9,0:0:2,0:21.7:1:31.9:1:1:0:60:18:1:0:0.1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:19:1:32:0:1:0:60:4:0.6667:0:1 +13 103498470 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50662;SOR=0;LSEQ=ATTAGTGCCGTCCCCCACTG;RSEQ=AAAACCGTGGCTTCTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:2,0:82,1:83,2:0.0235:1,0:14.5:1:32:0:1:0:60:4:0.0244:0:1 0/0:64:0:0,0:63,1:64,0:0:1,0:21:1:31.1:1:1:0:60:128:1:0:0 +13 103498545 . C T 130 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=24.35945;LSEQ=CTTCCTCCCGGGGTCCTAGG;RSEQ=GGCGGTGCAGTCCGTCGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:1:0,1:292,48:340,1:0.0029:2,0:1:0:25:0:0.1437:0:60:2:0.003:0:1 0/1:388:26:17,9:266,96:362,26:0.067:2,2:24:1:27.7:1:0.36702:1.46536:60:25:0.066:0:1.1 +13 103504270 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GATTTTAAAATGCAGTATGT;RSEQ=AATAGGGGTAACAAGAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:19,0:0:1,0:25.1:1:31.8:1:1:0:60:38:1:0:0.1 0/1:13:2:2,0:11,0:11,2:0.1538:0,0:10:1:29:0:1:0:60:4:0.1538:0:1 +13 103504331 . T C 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15072;SOR=0;LSEQ=TAGGTAGATCCCATGAGAGC;RSEQ=AAATGTTTTTCAATTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:4:4,0:47,0:47,4:0.0784:1,0:17.5:1:31:1:1:0:60:8:0.0816:0:1 0/0:33:0:0,0:33,0:33,0:0:1,0:22.6:1:30.5:1:1:0:60:66:1:0:0.1 +13 103504399 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18436;SOR=Inf;LSEQ=ACGTTTGGATAATATCAGTT;RSEQ=TTAGGAAATTGAAGTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:185,19:204,0:0:2,0:24.6:1:28.5:1:1:0:60:67:1:0:0.1 0/1:154:2:1,1:131,21:152,2:0.013:2,2:18:1:31:1:0.26611:6.11791:60:4:0.0134:0:2 +13 103504409 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20152;SOR=Inf;LSEQ=AATATCAGTTATTAGGAAAT;RSEQ=GAAGTTGTGAGGATGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:207,33:240,0:0:2,0:24.3:1:31.1:1:1:0:60:119:1:0:0.1 0/1:196:2:1,1:160,34:194,2:0.0102:2,2:28:1:29.5:1:0.32601:4.65267:60:4:0.0103:0:2 +13 103504517 . T C 283 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGGAGTCCGGGATCGCCA;RSEQ=GGGAACTCAATAGAAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:947:0:0,0:519,428:947,0:0:2,0:25.3:1:30.6:1:1:0:60:93.7:1:0:0.1 1/0:1166:670:366,304:264,228:492,670:0.5746:2,2:25.5:1:30.2:1:0.76588:1.04:60:166.5:0.5761:0:1.1 +13 103506235 . T A 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04922;SOR=0;LSEQ=AGCAAAAGGCAAGAGGAAAA;RSEQ=TATAGTCGTGTTAGAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:4:3,1:140,219:359,4:0.011:2,2:15:1:28:1:0.30447:4.67:60:8:0.0112:0:1 0/0:406:0:0,0:146,260:406,0:0:2,0:27.3:1:29.5:1:1:0:60:49.75:1:0:0.2 +13 103506362 . AT A 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=2.03913;LSEQ=AATGAGACAAGTAGGCTGCC;RSEQ=TTTGACCTGGTAATTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:32:3,29:0,3:3,32:0.9143:0,2:28:1:31.6:1:1:0:60:64:0.9143:0.1143:0 1/1:23:22:3,19:0,1:1,22:0.9565:0,2:22.7:1:30.3:1:1:0:60:44:0.9565:0.2174:0.1 +13 103506509 . A C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGGTGAGCAGCCCCGCCA;RSEQ=GGTTCCTTCCTTTCTCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:78:78:71,7:0,0:0,78:1:0,2:27.5:1:32.3:1:1:0:59.6:156:1:0:1 1/1:58:58:58,0:0,0:0,58:1:0,1:22.8:1:31.9:1:1:0:60:57:1:0:1.1 +13 103506587 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13987;SOR=Inf;LSEQ=CAGGTCAGGTCCCTGTTCAC;RSEQ=ATCCTGAGCAGGGTCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:191,81:272,0:0:2,0:24.7:1:31.6:1:1:0:60:67:1:0:0.2 0/1:365:4:1,3:252,109:361,4:0.011:2,2:16:1:26:1:0.08781:6.8953:60:8:0.0112:0:1 +13 103507049 . G A 36 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGCTGCTTTTCAATCCA;RSEQ=TATGGTCTCTCTCACCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:8.3:1:23:1:1:0:60:2:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 103507111 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATTCTTGTTGCTAAATC;RSEQ=AGCAGACGCTTTGCACGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:29:1:34:0:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 103508356 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25019;SOR=Inf;LSEQ=ATACAAGTATTTTTGTAAGG;RSEQ=GTCCTTAAAAATCATAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:157,68:225,0:0:2,0:25:1:31.1:1:1:0:59.9:36.5:1:0:0.3 0/1:248:3:1,2:166,79:245,3:0.0121:2,2:15:1:29:1:0.24941:4.17592:60:6:0.0122:0:1.3 +13 103508378 . C T 169 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01699;LSEQ=TCCTTAAAAATCATAGATAT;RSEQ=GTAAAAGTATGTTTGACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:46:30,16:157,108:265,46:0.1474:2,2:25.8:1:30.6:1:0.51548:1.29:60:92:0.1498:0:1.1 0/0:343:1:1,0:206,136:342,1:0.0029:2,0:16:0:32:0:1:0:60:2:0.0029:0:1 +13 103508537 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21178;SOR=0;LSEQ=ATGAAAATGAATATTAATGA;RSEQ=GTATATCAAACTGTGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:4,61:65,2:0.0299:2,2:7.5:1:29:1:0.14473:13.75:60:4:0.0308:0:1.5 0/0:78:0:0,0:6,71:77,0:0:2,0:18:1:30.2:1:1:0:60:154:0.9872:0:0 +13 103510556 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22601;SOR=Inf;LSEQ=TTATATAAACATAATACATA;RSEQ=CCTTAATGTTGAATAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:75,5:80,0:0:2,0:26.9:1:31.5:1:1:0:60:79:1:0:0.1 0/1:73:2:1,1:62,9:71,2:0.0274:2,2:8.5:1:28.5:1:0.25685:6.58787:60:4:0.0274:0:1.5 +13 103510559 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2266;SOR=Inf;LSEQ=TATAAACATAATACATATCC;RSEQ=TAATGTTGAATAGAACTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:77,5:82,0:0:2,0:27.7:1:32.1:1:1:0:60:81:1:0:0.1 0/1:75:2:1,1:64,9:73,2:0.0267:2,2:21.5:1:33:1:0.25045:6.79808:60:4:0.027:0:1 +13 103510604 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25462;SOR=Inf;LSEQ=TGAAATGTAAATTTCATGGT;RSEQ=CTGTGATTTTATCTTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:150,36:186,0:0:2,0:23.1:1:32:1:1:0:60:61:1:0:0.1 0/1:224:3:1,2:154,65:219,3:0.0134:2,2:23.7:1:29:1:0.21713:4.70089:60:6:0.0136:0:1.7 +13 103510896 . C T 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAGTAAACAGCATTTCTA;RSEQ=ATCTCAGATTCTAAGAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:1,47:48,0:0:1,0:22.6:1:32.8:1:1:0:59.8:47:1:0:0.1 1/0:24:16:0,16:0,8:8,16:0.6667:0,1:19.8:1:28:1:1:0:60:32:0.6667:0:1 +13 103510997 . T C 115 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCGAGACTAGGTCTTTT;RSEQ=TCCTGGTCTTTGTTCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:22.7:1:34.8:1:1:0:60:20:1:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:12:0:33:0:1:0:60:2:1:0:1 +13 103513578 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CGAACTCCTGACCTCCGGTG;RSEQ=TCCACCCATCTCGGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:32:0:1:0:41.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 103514091 . T C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACCATCATTTATATATT;RSEQ=ACATTAAAAAATCAAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:279:279:74,205:0,0:0,279:1:0,2:24:1:32.2:1:1:0:59.9:138.5:1:0:1.1 1/1:272:272:71,201:0,0:0,272:1:0,2:23.4:1:31.3:1:1:0:59.9:67:1:0:1.1 +13 103518769 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTTTCCTTTACCACCTTC;RSEQ=TCAGACCCCTGGGGGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:245:245:74,171:0,0:0,245:1:0,2:23.6:1:32.2:1:1:0:59.9:39.833:1:0:1.2 1/1:288:288:81,207:0,0:0,288:1:0,2:23:1:30.9:1:1:0:60:95:1:0:1.2 +13 103518782 . G T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22098;SOR=0;LSEQ=CACCTTCTTCAGACCCCTGG;RSEQ=GGAATGCACTGCATGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:49,141:190,2:0.0104:2,2:39:0:30:1:0.45402:2.86:60:4:0.0107:0:2 0/0:217:0:0,0:52,165:217,0:0:2,0:23.5:1:29.9:1:1:0:60:35.167:1:0:1.2 +13 103518784 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22209;SOR=0;LSEQ=CCTTCTTCAGACCCCTGGGG;RSEQ=AATGCACTGCATGAAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:48,135:183,2:0.0108:2,2:34:1:30.5:1:0.46063:2.79:60:4:0.011:0:2 0/0:207:0:0,0:48,159:207,0:0:2,0:23.7:1:30.2:1:1:0:60:68:1:0:1.2 +13 103518844 . C T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00604;SOR=0.39444;LSEQ=TGCTCAGGGCCTGGTGATGC;RSEQ=GTTCCCTGGGGGTCACTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:91:52:22,30:20,19:39,52:0.5714:2,2:24.7:1:31.9:1:0.40594:1.42964:60:51:0.5795:0:1.4 0/1:67:23:5,18:14,30:44,23:0.3433:2,2:20.5:1:29.5:1:0.56892:1.66747:60:22:0.3385:0:1.7 +13 103518918 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20141;SOR=Inf;LSEQ=TGAAGTGGTAGGCACTGCTC;RSEQ=CCCTGTGCTCAGGGCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:104,44:148,0:0:2,0:22.8:1:30.7:1:1:0:60:36:1:0:0.2 0/1:121:2:1,1:88,31:119,2:0.0165:2,2:31:1:25:0:0.46061:2.80983:60:4:0.0169:0:1.5 +13 103518945 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23083;SOR=Inf;LSEQ=GCTCAGGGCCTGGCGGTGCC;RSEQ=TTCCCTGGGCGTCACTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:130,75:205,0:0:2,0:25:1:31.6:1:1:0:60:33.167:1:0:0.1 0/1:191:2:2,0:129,60:189,2:0.0105:2,0:31:1:27:0:1:0:60:4:0.0106:0:1 +13 103518970 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24892;SOR=Inf;LSEQ=CTGGGCGTCACTGTGTACCC;RSEQ=TCACTCTGCAGGAACTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:163,100:263,0:0:2,0:25.3:1:31.8:1:1:0:60:86.667:1:0:0.1 0/1:275:3:1,2:176,96:272,3:0.0109:2,2:23.7:1:29:1:0.28975:3.64841:60:6:0.0112:0:1 +13 103518989 . T A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.109;SOR=0;LSEQ=CCTCACTCTGCAGGAACTCC;RSEQ=GCGCCTGTTCGGCATTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:172,115:287,3:0.0103:2,2:10:1:23:1:1:1.34:60:2:0.0071:0:1 0/0:316:0:0,0:189,127:316,0:0:2,0:25:1:29.9:1:1:0:60:44.143:1:0:0.2 +13 103519251 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00756;SOR=Inf;LSEQ=ATTTACCTTCAGAGTTTGTC;RSEQ=TAGGAAGTTTTCTTTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:18,119:137,0:0:2,0:22.3:1:33:1:1:0:60:67.5:1:0:0.1 0/1:151:8:2,6:19,124:143,8:0.053:2,2:13.1:1:30.1:1:0.30781:2.16:60:16:0.0537:0:1.1 +13 103519256 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23389;SOR=0;LSEQ=CCTTCAGAGTTTGTCCTAGG;RSEQ=AGTTTTCTTTCCAAGGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:15,109:124,2:0.0159:2,2:17:1:30.5:1:0.23873:7.07:60:4:0.016:0:1 0/0:134:0:0,0:14,120:134,0:0:2,0:25.2:1:30.4:1:1:0:60:133:1:0:0.1 +13 103519771 . G A 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTTGGGAAAGGCTTTACTC;RSEQ=TGTAACTTCAAGGCAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:29.8:1:27:1:1:0:60:3:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 103520764 . G A 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGTTTTCCATTTTCTAGA;RSEQ=ATGATGAAATCAGAGTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:0,35:0,0:0,35:1:0,1:21:1:31.3:1:1:0:59.6:34:1:0:1.1 1/1:8:8:0,8:0,0:0,8:1:0,0:31:1:31.4:1:1:0:60:16:1:0:1 +13 103524611 . GA G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.06054;LSEQ=AATCCTCATGACACCAAAGT;RSEQ=AAAAAAAATTACGGACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:15:10,5:426,327:753,15:0.0195:2,2:34.5:1:31.8:1:0.60039:1.53:60:14:0.0186:0:0.4 0/1:870:18:8,10:478,372:850,18:0.0207:2,2:25.6:1:29.5:1:0.34532:1.60527:59.4:17:0.0199:0.0046:0.3 +13 103524762 . C T 227 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAGAGAATATCCTTTGCTT;RSEQ=TTAAAAGAGAAGGAAACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:121,284:405,0:0:2,0:22.9:1:32.6:1:1:0:60:134:0.995:0:0.1 1/0:426:217:62,155:66,143:209,217:0.5094:2,2:25:1:29.3:1:0.52685:1.15346:60:216:0.5082:0:1.1 +13 103524795 . T A 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24851;SOR=0;LSEQ=GAAACACCTTGTCAAATATG;RSEQ=GTTTGGTTTAAAACTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:1,2:38,194:232,3:0.0128:2,2:17.3:1:20.7:1:0.4213:2.54:60:2:0.0086:0:1.3 0/0:229:0:0,0:42,187:229,0:0:2,0:22.4:1:29.3:1:1:0:60:228:1:0:0.5 +13 103525564 . G T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14186;SOR=Inf;LSEQ=GACCTTTTTATTTGTCACTT;RSEQ=TTTAAATATCTTTCAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:189,70:259,0:0:2,0:21.3:1:32.4:1:1:0:60:85.333:1:0:0.1 0/1:354:4:2,2:250,100:350,4:0.0113:2,2:21.5:1:24.5:1:0.3271:2.49262:60:3:0.0085:0:2.5 +13 103525883 . C A 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.03727;SOR=0;LSEQ=CTTCATTTTCTATGATCACT;RSEQ=TTAGGGCTGAACTTTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:0,7:7,4:0.3636:0,0:22.3:1:29.8:1:1:0:60:8:0.3636:0:1.3 0/0:12:0:0,0:0,12:12,0:0:0,0:19.6:1:31.7:1:1:0:57.3:24:1:0:0.1 +13 103527121 . C T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTCGTGATCCACCCACCT;RSEQ=GGCCTCCCAGAGTGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:24:1:30.7:1:1:0:36:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 103527149 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTGCTGGGGTTACAGG;RSEQ=GTGAGCCACCATGCCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:31:1:1:0:30.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 103527528 . A C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00603;SOR=Inf;LSEQ=GGAGAGAACTGGGTTTTGGG;RSEQ=GATAATGAATTAATATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:40,0:40,0:0:1,0:24.5:1:30.5:1:1:0:59.1:39:1:0:0.1 0/1:17:4:4,0:13,0:13,4:0.2353:1,0:26.8:1:31.8:1:1:0:60:8:0.2353:0:1.3 +13 103527849 . G C 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.66003;SOR=1.89581;LSEQ=AGCTACTTGATAAGGCAAAA;RSEQ=GAAAAACCCAGAAGAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:589:586:255,331:0,0:0,586:0.9949:0,2:26.4:1:31.1:1:1:0:59.9:96.667:0.9949:0:1.2 1/1:743:741:348,393:0,0:0,741:0.9973:0,2:26:1:30.3:1:1:0:59.9:246:0.9973:0:1.2 +13 103527930 . G C 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGCTTTCAGATTCTAAA;RSEQ=GAAAGAATACATGCGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:460:460:229,231:0,0:0,460:1:0,2:28.1:1:31.2:1:1:0:59.9:114:1:0:1.3 1/1:564:563:249,314:0,0:0,563:0.9982:0,2:26:1:30.3:1:1:0:60:186.667:0.9982:0:1.3 +13 103528002 . G C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19211;LSEQ=CTGATGGATCTTCAAGTGAA;RSEQ=ATGCTGAAAGTTCATCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:110:47,63:104,125:229,110:0.3245:2,2:27.5:1:31.5:1:0.72635:1.11488:60:17.333:0.3142:0:1.3 0/1:427:36:18,18:180,211:391,36:0.0843:2,2:23.5:1:31.6:1:0.72778:1.17:60:72:0.0847:0:1.4 +13 103528235 . A G 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.24818;SOR=0;LSEQ=AAACTAAGACGTGCGAGGGG;RSEQ=AGAAAAAGGAAAACCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:1,2:16,70:86,3:0.0337:2,2:35:1:26.3:1:0.47483:2.16:60:2:0.0227:0:1.3 0/0:79:0:0,0:16,63:79,0:0:2,0:26.3:1:30.1:1:1:0:60:158:1:0:0.1 +13 103528250 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22515;SOR=Inf;LSEQ=AGGGGAAGAAAAAGGAAAAC;RSEQ=TAATTAAAAAATATGTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:13,54:67,0:0:2,0:22.8:1:33.1:1:1:0:60:134:1:0:0.2 0/1:61:2:1,1:10,49:59,2:0.0328:2,2:18:1:31.5:1:0.3306:4.72:60:4:0.0333:0:1 +13 103528337 . G A 82 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGTAATAAAATTAACTGGT;RSEQ=GCACGGTCTTTGTATTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:3,7:0.7:0,0:18.1:1:29.3:1:1:0:56.7:6:0.6667:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:49:0:29:0:1:0:60:2:1:0:1 +13 103529284 . A G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCAGCAGTCTTTGAACG;RSEQ=CTCCTAGATGTGTTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:32.5:1:1:0:60:4:1:0:1 +13 104189681 . G A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15882;SOR=0.17679;LSEQ=GGGATTTTTCCATTTGCAAG;RSEQ=CTCTTGAAATATTTTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:2,10:0.8333:0,0:30.2:1:28.9:1:1:0:60:20:0.8333:0:1 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:22.3:1:30.3:1:1:0:60:8:0.4444:0:1 +13 104189781 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50376;SOR=Inf;LSEQ=TGGTTTTGATGAATTTGCTG;RSEQ=GATCCAGGAGTGTTCAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:47,35:82,0:0:2,0:28.4:1:31.6:1:1:0:60:81:1:0:0 0/1:103:2:1,1:54,47:101,2:0.0194:2,2:27:0:31:0:1:1.14738:60:4:0.0194:0:1 +13 104377661 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGGCAAAAGAATAATT;RSEQ=TAAAATTAAGAGGATTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:37:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 104377856 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTAACTAATATGGATCCT;RSEQ=TAAATTGTGTGAATGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:9.5:1:33:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 104378073 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20046;SOR=0;LSEQ=TTTGACACATTTGTAAAACC;RSEQ=TCGCTCTTTGGGACTACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:88,24:112,2:0.0175:2,2:14:1:29.5:1:0.39202:3.61257:60:4:0.0183:0:1 0/0:140:0:0,0:102,38:140,0:0:2,0:22.3:1:29.6:1:1:0:60:139:1:0:0.1 +13 104378182 . G C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2383;LSEQ=GTTCACTGGCTCCTTACTTC;RSEQ=TCAGTCCCATTGCTTGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:340:222:106,116:61,55:116,222:0.6529:2,2:27:1:32.1:1:0.42379:1.21302:60:221:0.6558:0:1.1 0/1:385:119:62,57:125,141:266,119:0.3091:2,2:26.7:1:30.7:1:0.37849:1.23:60:118:0.3089:0:1.1 +13 104378270 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49965;SOR=Inf;LSEQ=CCTACTTGGTTATCTCAAGC;RSEQ=ACAGCTGCTCCTAGTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:32,100:132,0:0:2,0:24:1:29.5:1:1:0:59.8:131:1:0:0.3 0/1:147:2:1,1:39,106:145,2:0.0136:2,2:13:1:30:1:0.47153:2.70:60:4:0.0138:0:1 +13 104378280 . C G 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49897;SOR=Inf;LSEQ=TATCTCAAGCTACAGCTGCT;RSEQ=CTAGTTGGTGCCTCCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:23,85:108,0:0:2,0:22.2:1:31.8:1:1:0:59.7:107:1:0:0.1 0/1:119:2:1,1:26,91:117,2:0.0168:2,2:7:0:32:1:0.40379:3.45:60:4:0.0169:0:1.5 +13 104378348 . A C 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71446;SOR=0.6111;LSEQ=GGAGACTCATGCCTGAACTC;RSEQ=ACTTCTCTATGTCTAGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:0,6:0,23:23,6:0.2069:1,0:28:1:32.5:1:1:0:60:12:0.2069:0:1.7 0/1:22:3:0,3:1,18:19,3:0.1364:1,0:26:1:33.7:1:1:0:60:6:0.1364:0:1.3 +13 104378382 . A G 131 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00174;SOR=0.03601;LSEQ=TAGGTAGTGTCCACATGCAG;RSEQ=TATTGATATAATGTATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:0,3:3,17:0.85:0,1:22.1:1:32.1:1:1:0:60:34:0.85:0:1.3 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:33:0:34:0:1:0:60:2:0.1429:0:2 +13 104378499 . G A 51 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.40825;LSEQ=TTATATTGGATGTTATCTAA;RSEQ=GAAGAGGCTTTCAATTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:35:1:32.3:1:1:0:60:6:1:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:28:0:32:0:1:0:60:2:0.5:0:1 +13 105247235 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22414;SOR=Inf;LSEQ=GAAACTGAAGAGAGAAGCCA;RSEQ=AAATATCAAGAAGATGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:15,0:0:2,0:22.4:1:32.9:1:1:0:60:30:1:0:0 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:16:0:31:1:1:1.36624:60:4:0.1429:0:1.5 +13 106236098 . G A 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGAATATCTTAGCCTACA;RSEQ=AAGTGAAGTGAACCAAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:191,185:376,0:0:2,0:24.9:1:32.3:1:1:0:60:61.667:1:0:0.1 0/1:345:84:45,39:129,132:261,84:0.2435:2,2:28.5:1:29.9:1:0.53239:1.18:60:168:0.2463:0:1.1 +13 106236146 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24951;SOR=0;LSEQ=GAACCTGATCTGCCGGAGCA;RSEQ=AATATCCAACTGAGTCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:1,2:111,184:295,3:0.0101:2,2:18.7:1:29:1:1:1.20574:60:6:0.0102:0:1 0/0:279:0:0,0:112,167:279,0:0:2,0:25.3:1:30.6:1:1:0:60:68.75:1:0:0.3 +13 106826378 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01752;SOR=0.66614;LSEQ=TTATGCTTCATCCTACGGCA;RSEQ=GTATATAAAAAAGAAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:103:55,48:106,107:213,103:0.3249:2,2:24.1:1:30.6:1:0.55114:1.16:60:50.5:0.3217:0:1.4 0/1:375:91:39,52:143,139:282,91:0.2427:2,2:22.8:1:28.8:1:0.22786:1.37053:60:29.333:0.2398:0:1.1 +13 106826430 . G T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.09997;LSEQ=ACAATTGTGGGTTGTTTCAC;RSEQ=TTTCAGTGAAAGGAGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:61:20,41:84,130:214,61:0.2218:2,2:27.4:1:30.7:1:0.37419:1.32329:60:122:0.2243:0:1.5 0/1:326:9:4,5:123,194:317,9:0.0276:2,2:32.2:1:29.6:1:0.74007:1.26:60:18:0.0278:0:1.2 +13 106826445 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.25308;SOR=Inf;LSEQ=TTCACGTTTCAGTGAAAGGA;RSEQ=AGAAGACACAAGAATGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:77,152:229,0:0:2,0:27:1:32.4:1:1:0:60:113.5:0.9956:0:0.5 0/1:269:3:1,2:94,171:265,3:0.0112:2,2:25.3:1:27.3:1:1:1.09904:60:6:0.0113:0:1 +13 108490042 . A G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43478;SOR=0;LSEQ=CACCAGCTGCGCAGACTCCC;RSEQ=GGAGTCAGCGTGACATCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:14,12:0,0:0,26:1:0,2:27.4:1:30.2:1:1:0:60:52:1:0:1.1 1/1:20:19:10,9:1,0:1,19:0.95:0,2:23.8:1:27.7:1:1:0:60:18:0.9474:0:1.2 +13 109078075 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGGCTCACTGCAACCTC;RSEQ=GCCTCCCAGGTTCAAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44:1:30.5:1:1:0:33:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 109078371 . A C 65 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACCTCCCAAAGTCCTCAT;RSEQ=CTCCTAATACCATCATCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:26.3:1:32.8:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:26:0:32:0:1:0:60:2:1:0:1 +13 109078699 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28906;LSEQ=ACATTAACCTAAGAAAAGTT;RSEQ=TCTTCTAATGTAAGTGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:443:269:125,144:76,97:173,269:0.6072:2,2:25.9:1:29.4:1:0.62545:1.11:60:52.8:0.6097:0:1.1 0/1:457:141:67,74:143,173:316,141:0.3085:2,2:25.2:1:28.8:1:0.68497:1.10:60:282:0.3099:0:1.1 +13 110408608 . C T 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.08478;LSEQ=AGCGTCTTCTTTTAATGATA;RSEQ=TCTCTGACATGTGACATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:419:400:250,150:14,4:18,400:0.9547:2,2:25.1:1:30.8:1:0.22066:2.09668:59.9:79:0.9587:0:1.1 1/0:431:276:164,112:87,68:155,276:0.6404:2,2:23.7:1:29.9:1:0.54193:1.14:59.8:137:0.6462:0:1.1 +13 110408755 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21603;SOR=Inf;LSEQ=AACCCACAGCTAGGACCTGG;RSEQ=TCATTTTCATAAACTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:30,178:208,0:0:2,0:22.7:1:32.3:1:1:0:60:207:0.9952:0:0.1 0/1:182:2:1,1:44,136:180,2:0.011:2,2:24.5:1:28:1:0.4344:3.07:60:4:0.0112:0:1 +13 110408810 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22387;SOR=Inf;LSEQ=ACATGTATTCATTCTGTTTT;RSEQ=CAGAGGTGAGTTCAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:2,52:54,0:0:1,0:21.1:1:31.6:1:1:0:60:26:1:0:0.1 0/1:49:2:0,2:1,46:47,2:0.0408:1,0:18.5:1:30:0:1:0:60:4:0.0417:0:1 +13 110414458 . C T 84 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05639;SOR=0.23025;LSEQ=TGTATAAATTTTACAGTGCA;RSEQ=GGCTACAGCAGATTGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:8:3,5:267,121:388,8:0.0202:2,2:17:1:28.3:1:0.11641:3.66418:60:16:0.0204:0:1 0/0:424:2:0,2:263,159:422,2:0.0047:2,0:1:0:26.5:1:0.14363:0:60:4:0.0047:0:1 +13 110414506 . G C 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=TGTACACGGTTCTTTTCTGA;RSEQ=TGTTATTGTTAAAAACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:0:0,0:396,325:721,0:0:2,0:26.1:1:32.5:1:1:0:60:54.462:1:0:0.1 0/1:797:17:7,10:437,342:779,17:0.0213:2,2:20.9:1:31.2:1:0.22933:1.82398:60:34:0.0216:0:1 +13 110414665 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60582;SOR=2.22378;LSEQ=CAAAAAGTTCCAAGAATTGC;RSEQ=GGTGGACCCTTTCTTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:0,1:25,190:215,1:0.0046:2,0:18:0:15:0:1:0:54:0:0:0:7 0/1:195:2:1,1:32,161:193,2:0.0103:2,2:12.5:1:27:1:0.31055:4.97:60:4:0.0104:0:1 +13 110414685 . A G 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12803;LSEQ=GGGTGGACCCTTTCTTTTAA;RSEQ=TTATGAAATGTTAGACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:56:3,53:3,80:83,56:0.4029:1,2:23.3:1:31.7:1:0.68485:1.50:60:27:0.3971:0:1.1 0/1:114:9:2,7:10,95:105,9:0.0789:2,2:18.3:1:32.4:1:0.24065:2.68:60:18:0.0804:0:1.1 +13 110419164 . T C 66 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTCATCCACCTTGGCTC;RSEQ=GACTCCCCTGCATGTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:32:1:33.3:1:1:0:57.8:8:1:0:1.3 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:29:1:1:0:58:4:1:0:1 +13 110419354 . C A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGATCTTGTAGACATTTTC;RSEQ=AATGCTCATGGGCTGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:159,3:162,0:0:1,0:26.1:1:31.8:1:1:0:60:161:1:0:0.7 0/1:96:15:15,0:80,1:81,15:0.1563:1,1:28.9:1:30.3:1:1:0:60:30:0.1596:0:1.1 +13 110419392 . G A 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGAGCCTCACACACCAGAG;RSEQ=ACCCAGATCTGCGAAATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:258,14:272,0:0:2,0:24.6:1:31.3:1:1:0:60:29.222:1:0:1 0/1:208:15:13,2:180,13:193,15:0.0721:2,2:29.2:1:29.6:1:0.29526:2.11992:60:30:0.0743:0:1 +13 110419404 . C T 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00977;LSEQ=CACCAGAGGACCCAGATCTG;RSEQ=GAAATGCTTTGGTCAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:322:309:277,32:12,1:13,309:0.9596:1,2:23.8:1:29.9:1:1:1.38503:60:37.625:0.9586:0:1.1 0/1:274:51:43,8:190,33:223,51:0.1861:2,2:23.4:1:28:1:0.83032:1.07091:60:16:0.1798:0:1.2 +13 110419621 . G A 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGCTCCTGTCCAGGCGG;RSEQ=CCACACCGGGAATGTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:0:0,0:133,399:532,0:0:2,0:25.7:1:31.8:1:1:0:60:34.467:1:0:0.1 0/1:434:36:9,27:109,289:398,36:0.0829:2,2:22:1:29.3:1:0.84685:1.13117:60:72:0.0843:0:1.3 +13 110419697 . G C 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=AGGAGAAGGAGGTGTGGAAG;RSEQ=AGAAAATACCCAGCAACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:4,151:155,0:0:1,0:24:1:32.6:1:1:0:59.9:76.5:1:0:0.2 0/1:101:12:1,11:3,86:89,12:0.1188:1,2:22.2:1:32:1:0.40199:2.57:60:24:0.1188:0:1.6 +13 110428702 . A G 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0119;SOR=0;LSEQ=GACAGAGTTTCCAAGGCTTC;RSEQ=CCTTTACCCATTCAAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:27:1:27.2:1:1:0:54.7:5:1:0:2.2 0/0:3:0:0,0:2,1:3,0:0:2,0:35.3:1:28:1:1:0:60:6:1:0:0.3 +13 110428923 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01497;LSEQ=ATAACACACAGAAGCATCTT;RSEQ=CATTATTTGCACCTACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:170:155,15:49,12:61,170:0.7359:2,2:25.6:1:28.8:1:0.03485:2.52:59.7:84:0.7336:0:1.1 0/1:177:7:7,0:151,19:170,7:0.0395:2,0:26.7:1:28.6:1:1:0:60:14:0.0407:0:1.1 +13 110428933 . C A 120 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=28.40884;LSEQ=GAAGCATCTTGCATTATTTG;RSEQ=ACCTACAGAGCAAAATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:1,0:225,44:269,1:0.0037:2,0:20:0:15:0:1:0:60:0:0:0:4 0/1:198:19:16,3:153,26:179,19:0.096:2,2:23.6:1:28.4:1:1:1.10282:60:38:0.0969:0:1.1 +13 110429191 . G A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47788;SOR=0;LSEQ=GAGTCAGAATAACCACTGCA;RSEQ=TCTTGAAGAACCCACTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:177:177:6,171:0,0:0,177:1:0,1:23.9:1:31.4:1:1:0:59.4:58:1:0:1.1 1/1:162:161:10,151:0,0:0,161:0.9938:0,2:25.4:1:30.8:1:1:0:60:160:1:0:1.1 +13 110434028 . G C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGGACGGACCCACGCA;RSEQ=CCGGATGAAGACAGTCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:15:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 110434223 . A G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=6.93152;LSEQ=GTTCCTGGCAAGTTCTCTGA;RSEQ=GGAAGAGAACAGGGCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:15:14,1:41,0:41,15:0.2679:1,1:15.2:1:33.9:1:0.26786:0:60:30:0.2727:0:1.2 1/0:36:26:25,1:10,0:10,26:0.7222:0,1:23:1:31.5:1:1:0:60:52:0.7222:0:1.2 +13 110434295 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19205;SOR=Inf;LSEQ=GCTGTCGGCTTCTGGGTCAA;RSEQ=GTCCCCAAAAAGTGGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:206,10:216,0:0:1,0:23.7:1:32.6:1:1:0:60:26:1:0:0.2 0/1:169:2:1,1:154,13:167,2:0.0118:2,2:13:1:27.5:1:0.15927:11.4525:60:4:0.012:0:2 +13 110434310 . G A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=12.23539;LSEQ=GTCAAGGTCCCCAAAAAGTG;RSEQ=GAGCAGTGAAACCCAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:7:7,0:247,22:269,7:0.0254:2,0:35.1:1:28.9:1:1:0:60:14:0.0261:0:1.1 0/1:227:55:43,12:150,22:172,55:0.2423:2,2:21.3:1:28.7:1:0.12777:1.8968:60:54:0.2389:0:1.1 +13 110434577 . AGCG A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.71029;SOR=0.85421;LSEQ=TCTTGTCTCCCGGCTGAGGA;RSEQ=GCGGCGGCGGCGGCTGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:550:16:8,8:314,217:531,16:0.0291:2,2:32:1:32.1:1:0.60735:1.44598:60:32:0.0298:0.0018:0.3 0/1:521:13:8,5:275,233:508,13:0.025:2,2:34.2:1:31.2:1:0.77967:1.35:60:26:0.0255:0.0019:0.5 +13 110434713 . C T 86 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01546;SOR=9.11336;LSEQ=TCCACCGCTCCCAGGACAAC;RSEQ=GACCAAGCCCCCGGGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:813:1:1,0:404,407:811,1:0.0012:2,0:40:0:32:0:0.49877:0:60:2:0.0012:0:1 0/1:720:8:3,5:365,346:711,8:0.0111:2,2:22.1:1:28.9:1:0.49608:1.75682:60:16:0.0113:0:1.3 +13 110435231 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=2.12502;LSEQ=AGGACAACGATGAGGCGGCG;RSEQ=CCGGGCCCTGGGCGGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:101:32,69:105,240:345,101:0.2254:2,2:27.5:1:29.3:1:0.80735:1.06:60:32.667:0.2227:0:1.1 0/1:442:169:64,105:97,176:273,169:0.3824:2,2:25.4:1:28.1:1:0.68424:1.11:60:32.8:0.3796:0:1.2 +13 110435280 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19831;SOR=Inf;LSEQ=GGCGGGGGGCAGGCGGTACA;RSEQ=CTCCCCCGGGGCCGGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:96,150:246,0:0:2,0:16.7:1:33.1:1:1:0:60:122:1:0:0.4 0/1:198:2:2,0:80,116:196,2:0.0101:2,0:25.5:1:27:1:0.17028:0:60:4:0.0102:0:1.5 +13 110435292 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10062;SOR=Inf;LSEQ=GCGGTACAGCTCCCCCGGGG;RSEQ=CGGCGGCGGTGGCGGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:131,122:253,0:0:2,0:17.7:1:31.9:1:1:0:60:49.6:1:0:0.4 0/1:221:3:1,2:126,92:218,3:0.0136:2,2:19:1:28.3:1:0.5762:2.72673:60:6:0.0138:0:1 +13 110435302 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=11.90858;LSEQ=TCCCCCGGGGCCGGCGGCGG;RSEQ=GGCGGCGGCTGCAGAGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:11:7,4:171,95:266,11:0.0397:2,2:26.6:1:31.6:1:1:1.02849:60:22:0.0404:0:1.5 0/1:266:88:57,31:110,66:176,88:0.3308:2,2:18.3:1:31.3:1:0.78698:1.10:59.7:176:0.3346:0:1.6 +13 110435308 . C T 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=19.97933;LSEQ=GGGGCCGGCGGCGGTGGCGG;RSEQ=GGCTGCAGAGACGACGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:2:1,1:191,95:286,2:0.0069:2,2:17.5:1:19:1:1:2.00532:60:1:0.0035:0:1.5 0/1:301:37:24,13:169,95:264,37:0.1229:2,2:18.9:1:28:1:1:1.04:60:36:0.1208:0:2 +13 110435472 . C T 127 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=20.43668;LSEQ=GAAGTCGAGGTTCATGTAGT;RSEQ=GGAGAGCGGAGACCGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:487:1:1,0:199,287:486,1:0.0021:2,0:29:0:12:0:0.41068:0:60:0:0:0:1 0/1:470:19:9,10:174,275:449,19:0.0404:2,2:27.5:1:29.9:1:0.47808:1.42:60:38:0.0409:0:1.2 +13 110435526 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1924;SOR=Inf;LSEQ=GGTGCCCGGGGTGCCTGAGC;RSEQ=CAGCGACGAGGCCGGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:55,176:231,0:0:2,0:23:1:30.9:1:1:0:60:37.5:1:0:0.1 0/1:181:2:1,1:48,131:179,2:0.011:2,2:34.5:1:28.5:1:0.46924:2.71:60:4:0.0112:0:1 +13 110435527 . C A 28 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58605;SOR=2.53362;LSEQ=GTGCCCGGGGTGCCTGAGCC;RSEQ=AGCGACGAGGCCGGGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:0,1:53,172:225,1:0.0044:2,0:1:0:27:0:1:0:60:2:0.0045:0:7 0/1:180:2:1,1:49,129:178,2:0.0111:2,2:10:0:28:1:0.47952:2.62:60:4:0.0114:0:1 +13 110435541 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17709;SOR=Inf;LSEQ=TGAGCCCAGCGACGAGGCCG;RSEQ=GCTGCTGGCGGACAAGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:60,143:203,0:0:2,0:23.3:1:31.7:1:1:0:60:100.5:1:0:0.1 0/1:148:2:1,1:48,98:146,2:0.0135:2,2:8:1:28.5:1:1:2.03:60:4:0.0136:0:1 +13 110435560 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59452;SOR=2.3857;LSEQ=GGGCTGCTGGCGGACAAGAG;RSEQ=GAGGAGGACGAGGCCGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:1:0,1:73,103:176,1:0.0056:2,0:1:0:26:0:1:0:60:2:0.0057:0:1 0/1:150:2:1,1:61,87:148,2:0.0133:2,2:13:1:27.5:1:1:1.42:60:4:0.0135:0:1 +13 110435585 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23405;SOR=Inf;LSEQ=AGGACGAGGCCGCCGACGCC;RSEQ=GCAGGGGAGGCGCGGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:110,89:199,0:0:2,0:22.8:1:31.4:1:1:0:60:65.333:1:0:0.2 0/1:187:2:1,1:102,83:185,2:0.0107:2,2:20:1:30.5:1:1:1.22755:60:4:0.0108:0:1 +13 110435596 . C T 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05683;SOR=Inf;LSEQ=GCCGACGCCAGCAGGGGAGG;RSEQ=GCGGGCGGCGACAGGCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:123,84:207,0:0:2,0:23.7:1:31.1:1:1:0:60:50.75:1:0:0.3 0/1:199:4:2,2:113,82:195,4:0.0201:2,2:16.3:1:24:1:1:1.37577:60:3:0.0153:0:1 +13 110435602 . C T 90 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06208;SOR=4.5948;LSEQ=GCCAGCAGGGGAGGCGCGGG;RSEQ=GGCGACAGGCGGGCCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:2:0,2:133,78:211,2:0.0094:2,0:9.5:1:30:1:0.13996:0:60:4:0.0096:0:1 0/1:215:9:4,5:124,82:206,9:0.0419:2,2:25:1:28.6:1:0.49022:1.88452:58.1:8:0.0377:0:2.1 +13 110435668 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12704;SOR=Inf;LSEQ=TCGCCGGGGCTCTTGGGCTC;RSEQ=GGTGGCAGTGGGTACTCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:142,158:300,0:0:2,0:25.2:1:30.3:1:1:0:60:74:1:0:0.2 0/1:342:4:1,3:174,164:338,4:0.0117:2,2:14.5:1:29:1:0.36142:3.17312:60:8:0.0119:0:1 +13 110435756 . C G 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00074;SOR=Inf;LSEQ=TCACCGCCCGGCCGCGCTGG;RSEQ=CCAAGAAGCCCTCCGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:48,81:129,0:0:2,0:19.6:1:31.7:1:1:0:60:42:1:0:0.3 0/1:164:13:5,8:52,99:151,13:0.0793:2,2:24:1:32.1:1:0.76854:1.19:60:26:0.0807:0:2 +13 110435766 . C T 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=GCCGCGCTGGCCCAAGAAGC;RSEQ=CTCCGGGCGGCCGCCGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:51,73:124,0:0:2,0:20:1:31.6:1:1:0:60:123:1:0:0.2 0/1:159:13:6,7:51,95:146,13:0.0818:2,2:24.5:1:30.3:1:0.54736:1.59:60:26:0.0818:0:1.9 +13 110435789 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49833;SOR=Inf;LSEQ=CCGGGCGGCCGCCGCTAGGC;RSEQ=GCACGGGCGAAGGCACTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:75,65:140,0:0:2,0:22.8:1:31.1:1:1:0:60:139:1:0:0.2 0/1:144:2:1,1:70,72:142,2:0.0139:2,2:25.5:1:31:0:1:1.03:60:4:0.0143:0:1 +13 110435790 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24737;SOR=Inf;LSEQ=CGGGCGGCCGCCGCTAGGCC;RSEQ=CACGGGCGAAGGCACTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:77,65:142,0:0:2,0:22.8:1:31.3:1:1:0:60:46.333:1:0:0.2 0/1:143:3:2,1:70,70:140,3:0.021:2,2:24:1:30.7:1:1:1.99:60:6:0.0216:0:1 +13 110435794 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49831;SOR=Inf;LSEQ=CGGCCGCCGCTAGGCCGCAC;RSEQ=GGCGAAGGCACTACAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:81,64:145,0:0:2,0:23.9:1:30.9:1:1:0:60:71.5:1:0:0.2 0/1:147:2:1,1:76,69:145,2:0.0136:2,2:39.5:1:30.5:1:1:1.10072:60:4:0.0139:0:1.5 +13 110435800 . A T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24287;SOR=0;LSEQ=CCGCTAGGCCGCACGGGCGA;RSEQ=GGCACTACAGGGTGAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:91,62:153,2:0.0129:2,2:24:0:32.5:1:1:1.46399:60:4:0.013:0:1 0/0:159:0:0,0:88,71:159,0:0:2,0:22.8:1:30.1:1:1:0:59.9:52:1:0:0.4 +13 110435821 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23531;SOR=Inf;LSEQ=GGCACTACAGGGTGAGGGGG;RSEQ=TGCGTGGGGCCGGCCCCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:105,59:164,0:0:2,0:27.8:1:32.5:1:1:0:60:40:1:0:0.2 0/1:155:2:1,1:88,65:153,2:0.0129:2,2:16:1:31:0:1:1.35115:60:4:0.0132:0:1.5 +13 110435831 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49864;SOR=0;LSEQ=GGTGAGGGGGCTGCGTGGGG;RSEQ=CGGCCCCGAAGGCGCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:108,49:157,2:0.0126:2,2:40:0:31:1:0.53141:2.19205:60:4:0.0129:0:1 0/0:152:0:0,0:91,61:152,0:0:2,0:24.4:1:31.1:1:1:0:59.9:49.667:1:0:0.3 +13 110435889 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19596;SOR=Inf;LSEQ=CGTGGCCTGAGGCTCCAGAC;RSEQ=CTCCTCCTCCAGGATGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:123,69:192,0:0:2,0:23.8:1:30.2:1:1:0:60:37.4:1:0:0.9 0/1:153:2:1,1:86,65:151,2:0.0131:2,2:18:1:27:1:1:1.32061:60:4:0.0135:0:1 +13 110435914 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.00738;LSEQ=TCCTCCAGGATGCGCCCCAC;RSEQ=GGGGAGCTCATGAGCACGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:170:104,66:33,20:53,170:0.7589:2,2:26.9:1:30.2:1:1:1.04691:59.9:20.25:0.7535:0:1.2 0/1:179:4:3,1:97,78:175,4:0.0223:2,2:20:1:28:1:0.63124:2.40:60:3:0.0172:0:1 +13 110435953 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.09417;LSEQ=TACTGGTCGCTGTCCCCGCC;RSEQ=CAGGTGTAGGGGGCCTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:76:50,26:151,71:222,76:0.255:2,2:22.9:1:30.7:1:0.77702:1.10554:59.9:37:0.2543:0:1.3 1/0:231:147:91,56:52,32:84,147:0.6364:2,2:25.7:1:30.1:1:1:1:60:48:0.6372:0:1.2 +13 110436031 . G T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.03126;SOR=Inf;LSEQ=CCCCTGAGCGGCTCCCCGCC;RSEQ=GGGTGCAGGGCTGCGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:0:0,0:351,201:552,0:0:2,0:24.9:1:30:1:1:0:60:60.333:1:0:0.2 0/1:586:6:1,5:348,232:580,6:0.0102:2,2:16.2:1:27.3:1:0.04224:7.4755:60:12:0.0103:0:1 +13 110436232 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.47116;LSEQ=CTGGCCTTGTAGCCGCCCCC;RSEQ=CTCGCCGGGAATGTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:133:36,97:74,234:308,133:0.3016:2,2:23.3:1:29.2:1:0.549:1.17:60:18:0.2958:0:1.2 1/0:490:323:108,215:59,108:167,323:0.6592:2,2:22.5:1:29.1:1:0.68844:1.08735:59.9:160.5:0.6605:0:1.2 +13 110436287 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4994;SOR=Inf;LSEQ=GTGCTGGCCCCGCAGGCCCC;RSEQ=CAGAAGGCACGGCGGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:44,104:148,0:0:2,0:18.5:1:32.4:1:1:0:60:147:1:0:0.3 0/1:162:2:1,1:63,97:160,2:0.0123:2,2:11:1:27:1:1:1.54:60:4:0.0127:0:1.5 +13 110436312 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=3;SSF=0.62357;SOR=2.83387;LSEQ=AGGCACGGCGGCGGCGGCGG;RSEQ=GGCGGCGGCCCTGGGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:1:0,1:113,49:162,1:0.0061:2,0:1:0:26:0:0.30675:0:60:2:0.0064:0:1 0/1:174:3:0,3:120,51:171,3:0.0172:2,0:17.7:1:26.3:1:0.02874:0:60:6:0.0176:0:1.7 +13 110436315 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.49878;SOR=Inf;LSEQ=CACGGCGGCGGCGGCGGCGG;RSEQ=GGCGGCCCTGGGCTGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:129,53:182,0:0:2,0:16.9:1:31.7:1:1:0:60:90:1:0:0.2 0/1:188:2:1,1:128,58:186,2:0.0106:2,2:21.5:1:27.5:1:0.53032:2.19668:60:4:0.011:0:1 +13 110436667 . C T 170 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=81.50094;LSEQ=CGCTGCCGGGCTGGCGTGGT;RSEQ=AGGGAGTAGGTCCTCTTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:1:0,1:434,359:793,1:0.0013:2,0:1:0:23:0:0.4534:0:60:2:0.0013:0:1 0/1:664:62:33,29:315,287:602,62:0.0934:2,2:25.5:1:28.7:1:1:1.04:60:124:0.0944:0:1.1 +13 110436790 . ACCG A 100 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.02451;SOR=0.12788;LSEQ=GTCATGTACCCGTAGAACTC;RSEQ=CCGCCGCCGCCGTCTCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:9:4,5:367,461:828,9:0.0107:2,2:20.4:1:31.8:1:1:1.00:60:18:0.0109:0.0036:0.3 0/0:722:1:1,0:336,379:715,1:0.0014:2,0:25:0:27:0:0.47067:0:60:2:0.0014:0:0 +13 110436793 . G A 95 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.06486;SOR=2.92062;LSEQ=ATGTACCCGTAGAACTCACC;RSEQ=CCGCCGCCGCCGTCTCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:834:4:2,2:365,458:823,4:0.0048:2,2:14.5:1:29:1:1:1.25:60:8:0.0049:0:1 0/1:720:10:6,4:333,373:706,10:0.0139:2,2:27.4:1:28.7:1:0.52959:1.68:60:20:0.0142:0:1.3 +13 110436914 . C T 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37574;SOR=0.27455;LSEQ=ACTCGTCCAGGGACATGAAG;RSEQ=CGGGGTCGCTGGGGGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:4:1,3:54,198:252,4:0.0156:2,2:18.3:1:26:1:1:1.22:60:3:0.0122:0:2 0/0:231:1:0,1:58,172:230,1:0.0043:2,0:1:0:24:0:1:0:60:2:0.0045:0:1 +13 110436922 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20641;SOR=Inf;LSEQ=AGGGACATGAAGCCGGGGTC;RSEQ=CTGGGGGAGCCCGAGGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:48,176:224,0:0:2,0:24.3:1:31.5:1:1:0:60:36.333:1:0:0.2 0/1:187:2:1,1:46,139:185,2:0.0107:2,2:24.5:1:29:1:0.44052:3.00:60:4:0.0112:0:1 +13 110436986 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22547;SOR=Inf;LSEQ=GGCCGGGGCCGTGGTGCAGC;RSEQ=GATGCGGCAGAGGCGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:9,38:47,0:0:2,0:12.8:1:32.3:1:1:0:60:94:1:0:0.3 0/1:43:2:1,1:12,29:41,2:0.0465:2,2:17:0:31.5:1:0.51827:2.36:60:4:0.0465:0:1.5 +13 110436991 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18045;SOR=Inf;LSEQ=GGGCCGTGGTGCAGCGGATG;RSEQ=GGCAGAGGCGGGTGCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:11,33:44,0:0:2,0:11.3:1:30.6:1:1:0:60:43:1:0:0.4 0/1:33:2:1,1:8,22:30,2:0.0606:2,2:12:1:27:1:0.48992:2.65:60:4:0.0606:0:1 +13 110437024 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12783;SOR=Inf;LSEQ=TGCGGGCCGGGCGGCGGCGG;RSEQ=TAGGAGCCCGAGCCGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:32,21:53,0:0:2,0:17.5:1:31.7:1:1:0:59.1:52:1:0:0.6 0/1:30:2:1,1:16,12:28,2:0.0667:2,2:20.5:1:30:0:1:1.32044:60:4:0.0667:0:1 +13 110437035 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCGGCGGGTAGGAGCCCG;RSEQ=GCCGTGGCCGCTGCTGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:41,28:69,2:0.0282:2,2:24.5:1:31:1:1:1.45623:60:4:0.0299:0:1.5 0/0:35:0:0,0:20,15:35,0:0:2,0:22.9:1:27.2:1:1:0:60:6:1:0:0.6 +13 110437072 . G T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.54398;LSEQ=GACGACAGGGAGCCGGGGCT;RSEQ=GTGGCGGCGGGCGGCGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:45,45:90,2:0.0217:2,2:43:1:30.5:1:1:1:60:4:0.023:0:1 0/1:84:1:0,1:42,41:83,1:0.0119:2,0:1:0:24:0:1:0:60:2:0.0123:0:1 +13 110437076 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49714;SOR=0;LSEQ=ACAGGGAGCCGGGGCTGGTG;RSEQ=CGGCGGGCGGCGAGTGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:43,42:85,2:0.023:2,2:40.5:1:30.5:1:1:1.02354:60:4:0.0247:0:1 0/0:85:0:0,0:42,43:85,0:0:2,0:24.3:1:30.4:1:1:0:59.9:27.333:1:0:0.4 +13 110437087 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23097;SOR=0;LSEQ=GGGCTGGTGGCGGCGGGCGG;RSEQ=GAGTGCGCCACGGGCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:40,39:79,2:0.0247:2,2:43:1:30.5:1:1:1.02533:60:4:0.025:0:1 0/0:87:0:0,0:43,44:87,0:0:2,0:25.9:1:28.6:1:1:0:59.9:8.667:1:0:0.4 +13 110437165 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48308;SOR=Inf;LSEQ=AGCAGCGCCACCTTGCTCCC;RSEQ=CGGCCGCCGCAGCCGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:12,0:0:2,0:25.6:1:32:1:1:0:60:24:1:0:0.3 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:9:0:27.5:1:1:1.37:60:4:0.1538:0:1 +13 110437366 . G C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49843;SOR=Inf;LSEQ=GGCGGGGTGGCGGCCAGGCT;RSEQ=TCGGTGCGCGAGCGGCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:98,37:135,0:0:2,0:14.2:1:32.6:1:1:0:59.9:134:0.9926:0:0.2 0/1:142:2:1,1:93,47:140,2:0.0141:2,2:5:1:29:1:1:1.96856:60:4:0.0143:0:1 +13 110437374 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24084;SOR=Inf;LSEQ=GGCGGCCAGGCTGTCGGTGC;RSEQ=CGAGCGGCGCACCAGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:133,46:179,0:0:2,0:17.4:1:31.2:1:1:0:59.9:178:1:0:0.2 0/1:173:2:1,1:114,57:171,2:0.0116:2,2:24:1:26.5:1:1:1.99142:60:4:0.0118:0:1 +13 110437376 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62302;SOR=0.33602;LSEQ=CGGCCAGGCTGTCGGTGCGC;RSEQ=AGCGGCGCACCAGGCCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:3:1,2:139,46:185,3:0.016:2,2:10.3:1:29:1:0.16077:5.97234:60:6:0.016:0:1.3 0/0:185:1:0,1:123,61:184,1:0.0054:2,0:1:0:22:0:0.33514:0:60:2:0.0056:0:1 +13 110437379 . C T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24829;SOR=0;LSEQ=CCAGGCTGTCGGTGCGCGAG;RSEQ=GGCGCACCAGGCCCGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:1,2:148,51:199,3:0.0148:2,2:11:1:22:1:0.16902:5.74266:60:2:0.0101:0:2.3 0/0:197:0:0,0:132,65:197,0:0:2,0:22.1:1:31.1:1:1:0:60:196:1:0:0.3 +13 110437497 . G A 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00611;SOR=Inf;LSEQ=CGATTGGCTCTTACTGCGCG;RSEQ=CCGGAACTCGAAGAGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:661:0:0,0:365,295:660,0:0:2,0:25.5:1:31.4:1:1:0:60:40.25:1:0:0.2 0/1:620:7:4,3:311,302:613,7:0.0113:2,2:21.4:1:29.3:1:1:1.29:60:14:0.0115:0:1 +13 110437862 . G A 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3864;SOR=0.30662;LSEQ=CCAGCCCGTAGCTGTCCTCG;RSEQ=CCCCGGCGGCGCCGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:4:3,1:36,221:257,4:0.0153:2,2:14.3:1:27:1:0.01117:18.07:60:8:0.0154:0:1 0/0:211:1:1,0:28,181:209,1:0.0047:2,0:1:0:22:0:0.1381:0:60:2:0.0049:0:1 +13 110437871 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2196;SOR=Inf;LSEQ=AGCTGTCCTCGGCCCCGGCG;RSEQ=CGCCGGCAGAGCCGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:19,163:182,0:0:2,0:21.9:1:33.2:1:1:0:60:364:1:0:0.1 0/1:161:2:1,1:17,142:159,2:0.0124:2,2:9:1:27.5:1:0.21172:8.15:60:4:0.0126:0:1 +13 110437958 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.49896;SOR=0;LSEQ=GGGGCGCGTCTCCGGCGGCC;RSEQ=CGCGGCCCTCGCTGACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:98,25:123,2:0.0159:2,2:17:0:32:0:0.37406:3.86344:60:4:0.0165:0:1.5 0/0:115:0:0,0:93,20:113,0:0:2,0:15.7:1:29.3:1:1:0:60:21.6:0.9818:0:0.1 +13 110437991 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.11235;SOR=0;LSEQ=TGACCAGGTCGGTGAGCGCG;RSEQ=GGTACCAGCCCTCCTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:1,2:204,84:288,3:0.0103:2,2:15.7:1:26.3:1:0.20951:4.82702:60:6:0.0107:0:1 0/0:311:0:0,0:208,103:311,0:0:2,0:26.1:1:30.5:1:1:0:60:43.429:1:0:0.2 +13 110438203 . C T 43 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67449;SOR=1.6298;LSEQ=AGCCGCGGCGGTTGCGGCGC;RSEQ=GACCCCCCGCCCGCCGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:0,2:56,142:198,2:0.01:2,0:1:0:25.5:1:1:0:60:4:0.0102:0:1 0/1:185:3:0,3:61,121:182,3:0.0162:2,0:7:1:27.3:1:0.55194:0:60:6:0.0169:0:1.7 +13 110438216 . G A 28 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.61086;SOR=0.46345;LSEQ=GCGGCGCCGACCCCCCGCCC;RSEQ=CCGTCGCCTCGTCGCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:54,106:160,2:0.0123:2,2:7.5:1:28.5:1:1:1.95:60:4:0.0127:0:1 0/0:174:1:1,0:75,98:173,1:0.0057:2,0:1:0:24:0:0.43678:0:60:2:0.006:0:1 +13 110438218 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49926;SOR=Inf;LSEQ=GGCGCCGACCCCCCGCCCGC;RSEQ=GTCGCCTCGTCGCCGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:57,105:162,0:0:2,0:13:1:30.8:1:1:0:59.9:80:1:0:0.2 0/1:175:2:0,2:76,97:173,2:0.0114:2,0:8:1:28:1:0.50581:0:60:4:0.0118:0:1 +13 110438226 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49988;SOR=Inf;LSEQ=CCCCCCGCCCGCCGTCGCCT;RSEQ=GTCGCCGCCCGCGCCGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:64,84:148,0:0:2,0:12.8:1:30.7:1:1:0:59.9:147:1:0:0.2 0/1:165:2:1,1:76,86:162,2:0.0121:2,2:11.5:1:29.5:1:1:1.13:60:4:0.0123:0:1.5 +13 110438241 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24806;SOR=Inf;LSEQ=CGCCTCGTCGCCGCCCGCGC;RSEQ=GGGTCCGCGCAGCACGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:80,52:132,0:0:2,0:20.1:1:30.5:1:1:0:59.9:65:1:0:0.2 0/1:141:3:1,2:79,59:138,3:0.0213:2,2:33.3:1:28.3:1:0.57849:2.65947:60:6:0.0217:0:1 +13 110438293 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24104;SOR=0;LSEQ=CCATGCTTCTGCTTGCGCAG;RSEQ=TAGCCGCACTTGCGCACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:91,84:175,2:0.0113:2,2:35.5:1:31:1:1:1.08283:60:4:0.0114:0:1.5 0/0:183:0:0,0:94,88:182,0:0:2,0:27.3:1:30:1:1:0:59.9:21.75:1:0:0.3 +13 110438296 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24811;SOR=Inf;LSEQ=TGCTTCTGCTTGCGCAGGTA;RSEQ=CCGCACTTGCGCACGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:91,85:176,0:0:2,0:27.2:1:32.4:1:1:0:60:175:1:0:0.1 0/1:182:3:1,2:92,87:179,3:0.0165:2,2:17:1:26.7:1:0.61473:2.10653:60:6:0.0169:0:1 +13 110438338 . G A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.21284;SOR=Inf;LSEQ=TTGTTGTTGTTGTTGTTGTT;RSEQ=TTGAGGTTGGGGCCGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:33,75:108,0:0:2,0:22.3:1:32.2:1:1:0:60:53:1:0:0.1 0/1:93:2:1,1:31,60:91,2:0.0215:2,2:5.5:1:25:1:1:1.92:60:4:0.0217:0:1.5 +13 110438392 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51613;SOR=0;LSEQ=GGCGGCCCGTGCCGCGGCGG;RSEQ=CTCGCCATCGCGGGCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:2,16:18,2:0.1:2,2:12:1:28.5:1:0.28421:6.73:60:4:0.1053:0:1 0/0:12:0:0,0:2,10:12,0:0:2,0:6:0:19:0:1:0:60:0:0:0:5 +13 110438877 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.23077;SOR=Inf;LSEQ=TGCTGCTGGTGTTGCTGCTG;RSEQ=TGCTGCCAACGGCGACCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:20,0:0:2,0:27:1:31.7:1:1:0:60:19:1:0:0.4 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:20.5:1:30:1:1:1.11803:52:4:0.1053:0:1.5 +13 110439354 . C T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGGGCTTGAGCTTCCGC;RSEQ=GGGGAGGGGGCGCCGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 111118948 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03452;SOR=0.19517;LSEQ=TGGCTGATTGCTGTGGTTCA;RSEQ=TCTGAAAGTAAACAAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:12:10,2:26,5:31,12:0.2791:2,2:18.8:1:31.4:1:1:1.03904:60:24:0.2791:0:1.1 0/1:29:2:2,0:20,7:27,2:0.069:2,0:14.5:1:30.5:1:1:0:60:4:0.069:0:1 +13 111119004 . A G 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50173;SOR=0;LSEQ=ATAATTCATTTTGAAATCGC;RSEQ=GGCTATCTCCATTGCTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:91,38:129,2:0.0153:2,2:38:0:30.5:1:0.5084:2.37681:60:4:0.0156:0:1 0/0:110:0:0,0:72,37:109,0:0:2,0:26:1:30.1:1:1:0:60:108:0.9908:0:0.7 +13 111119009 . A T 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59134;SOR=2.43409;LSEQ=TCATTTTGAAATCGCAGGCT;RSEQ=TCTCCATTGCTGGCAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:0,1:97,41:138,1:0.0072:2,0:1:0:27:0:0.30216:0:60:2:0.0072:0:1 0/1:115:2:1,1:73,40:113,2:0.0174:2,2:22:0:32:1:1:1.81481:60:4:0.0175:0:1.5 +13 111119019 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50425;SOR=0;LSEQ=ATCGCAGGCTATCTCCATTG;RSEQ=TGGCAGATGCTTCCAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:103,52:155,2:0.0127:2,2:30.5:1:29:1:1:1.97156:60:4:0.0129:0:1 0/0:126:0:0,0:79,47:126,0:0:2,0:26.8:1:31.6:1:1:0:60:125:1:0:0.7 +13 111119052 . C G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.21545;LSEQ=CCAGACAAAAGAAAAGCATC;RSEQ=ACACTGACTTGCAGGGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:38:25,13:83,59:142,38:0.2111:2,2:29.7:1:30.4:1:0.45989:1.36:60:76:0.2135:0:1.9 1/0:160:85:51,34:47,28:75,85:0.5313:2,2:21.2:1:29.2:1:0.74773:1.11826:60:170:0.5313:0:1.9 +13 111119077 . A G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.02952;LSEQ=TGACTTGCAGGGTAGCAGCC;RSEQ=GATTAACTCGGTTTGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:46:25,21:77,68:145,46:0.2408:2,2:22.3:1:31:1:1:1.05:60:92:0.2421:0:1.8 0/1:165:81:43,38:44,40:84,81:0.4909:2,2:25.8:1:29.6:1:1:1.03:60:162:0.4939:0:2.1 +13 111119136 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20226;SOR=0;LSEQ=AGGGAATCAATTGTTTGCCA;RSEQ=CACAGTGCCAGTTTTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:38,88:126,2:0.0156:2,2:37.5:1:30.5:1:0.51821:2.30:60:4:0.0159:0:1 0/0:156:0:0,0:60,96:156,0:0:2,0:25.3:1:31.6:1:1:0:59.8:155:1:0:0.8 +13 111119146 . A T 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTTTGCCAGCACAGTGCC;RSEQ=GTTTTTATTTGACTAGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:32,83:115,0:0:2,0:26.3:1:31.3:1:1:0:60:114:1:0:0.2 0/1:140:56:21,35:27,57:84,56:0.4:2,2:26.2:1:29.2:1:0.58661:1.26:59.5:112:0.4029:0:1.6 +13 111119152 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50076;SOR=Inf;LSEQ=GCCAGCACAGTGCCAGTTTT;RSEQ=ATTTGACTAGACTGGCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:28,82:110,0:0:2,0:26.2:1:28.7:1:1:0:60:220:1:0:0.2 0/1:128:2:1,1:41,84:125,2:0.0156:2,2:26:1:32:1:1:2.04:60:4:0.0159:0:1 +13 111119957 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGTGAGAAAGAGTCTGGG;RSEQ=GCCCTTCACAGAGCCCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:32:1:1:0:60:4:1:0:1.5 +13 111415092 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTCTCACAAAGTGTGCTTC;RSEQ=CTGGGTGGAGCAGGCTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:19.5:1:30.5:1:1:1:44:4:0.3333:0:1.5 0/0:2:0:0,0:2,0:2,0:0:0,0:13.5:1:31.5:1:1:0:40:4:1:0:0 +13 111415746 . A T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTACATAAGGGACGTCA;RSEQ=ATAAGTGGGATCAGACAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:48:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 111588789 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCTAACAGAGGAGGAAGAAG;RSEQ=TAAGATTAACTCCCTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:11:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 111588868 . C T 87 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTACAGACCGAATGAAAA;RSEQ=ATCCAGGAGAAAGAGTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:22.9:1:31.3:1:1:0:57.4:14:0.7778:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +13 111588967 . T C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01539;SOR=0;LSEQ=ACAAATTAAAGACGAACTAT;RSEQ=GAGCTGGGTACTCGGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:45:44,1:0,0:0,45:1:0,1:26.4:1:31.8:1:1:0:59.2:21.5:1:0:1.4 1/1:26:22:22,0:4,0:4,22:0.8462:0,1:22.3:1:31:1:1:0:60:44:0.8462:0:1 +13 111589079 . C T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25548;SOR=0;LSEQ=CAGGTCGTCGCGTCGGGCTC;RSEQ=TGGGATTTGGCGGCAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:243,52:295,3:0.0101:2,2:17.7:1:25.7:1:0.4455:2.32811:60:2:0.0069:0:1.7 0/0:246:0:0,0:193,53:246,0:0:2,0:21.8:1:30.4:1:1:0:60:122:1:0:0.3 +13 111589152 . G A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71343;SOR=1.04325;LSEQ=CTGAGTGGAGTACACCAAGA;RSEQ=CGGGCGCACCTCTTGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:747:332:187,145:228,187:415,332:0.4444:2,2:26.9:1:29.8:1:0.71169:1.06:45.2:82:0.445:0:1.6 0/1:721:328:182,146:203,188:391,328:0.4549:2,2:27.6:1:29.2:1:0.36782:1.15:44.9:53.667:0.4542:0:1.6 +13 111589204 . G C 306 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01104;LSEQ=AGCATCCCCAAGGACTCGCT;RSEQ=CGGATGGCCATCATGGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:850:847:422,425:1,0:1,847:0.9965:0,2:26.4:1:31.5:1:0.49882:0:44.7:46.056:0.9964:0:1.5 1/0:756:572:274,298:91,92:183,572:0.7566:2,2:25:1:30.1:1:0.67195:1.07566:44.1:43:0.7564:0:1.6 +13 111589278 . G A 290 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00474;LSEQ=GTACCACTTCTCCTGCTTGC;RSEQ=GAAGGTGGGCCACTCCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:623:622:278,344:0,0:0,622:0.9984:0,2:24.1:1:31.3:1:1:0:53.3:87.857:0.9984:0:1.4 1/0:615:459:223,236:79,74:153,459:0.7463:2,2:24.3:1:29.7:1:0.51531:1.12958:52.4:64.571:0.7459:0:1.4 +13 111589587 . G C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00154;SOR=1.70246;LSEQ=TTGACCCCTGGTACCACCCA;RSEQ=GCTGCTTTGTCAAGAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:596:72:35,37:258,265:523,72:0.1208:2,2:24.2:1:30.2:1:1:1.02918:51.6:35:0.1199:0:1.1 0/1:522:99:50,49:216,207:423,99:0.1897:2,2:26.2:1:30.3:1:1:1.02257:47.6:198:0.1919:0:1.1 +13 111589752 . G A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAGGCGATGAGGTGGATGGA;RSEQ=TGGATGAAGTGGCCAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:585:0:0,0:300,285:585,0:0:2,0:26.3:1:33:1:1:0:58.8:194:1:0:0.1 0/1:516:15:7,8:262,239:501,15:0.0291:2,2:23.6:1:30.3:1:0.79487:1.25229:59.1:30:0.0293:0:1 +13 111590028 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03383;SOR=0.61568;LSEQ=AGCTGGTCTTCAAGAGCGAC;RSEQ=CTTATTACTGCACCGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:54:26,28:189,186:375,54:0.1259:2,2:26.5:1:30.6:1:0.77299:1.09406:54.6:26:0.1226:0:1.1 0/1:430:35:17,18:198,197:395,35:0.0814:2,2:26.7:1:30.7:1:1:1.06408:57.7:70:0.0818:0:1.1 +13 111590169 . C T 228 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAAAGCAGGACCGTATATT;RSEQ=CCCCCAGAAACCAGTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:191:191:90,101:0,0:0,191:1:0,2:23.3:1:30.2:1:1:0:60:26.286:1:0:1.1 1/0:176:99:55,44:42,35:77,99:0.5625:2,2:23.7:1:29.6:1:1:1.04:60:48.5:0.5607:0:1.1 +13 111590176 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49962;SOR=0;LSEQ=AGGACCGTATATTCCCCCCA;RSEQ=AAACCAGTGACCCAGTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:88,93:181,2:0.0109:2,2:21.5:1:29.5:1:1:1.06:60:4:0.0113:0:2 0/0:167:0:0,0:95,72:167,0:0:2,0:27:1:31.5:1:1:0:60:166:1:0:0.6 +13 111590409 . AAAG A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=1;SOR=0.98052;LSEQ=AGCACTAAAGAGGAGGTGGA;RSEQ=AAGAAGAAGAAGATGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:13:5,8:202,259:461,13:0.0274:2,2:25.4:1:30.6:1:0.78287:1.2473:60:26:0.028:0.0021:0.1 0/1:446:12:5,7:175,258:433,12:0.0269:2,2:24:1:29:1:1:1.05:60:24:0.027:0.0022:0.2 +13 111590550 . A G 295 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGTCCCCCTGGGGGGCAGA;RSEQ=GTGAAGGCAGAGCCTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:595:595:301,294:0,0:0,595:1:0,2:23.8:1:32.1:1:1:0:37:73.375:1:0:1.1 1/0:596:420:228,192:90,85:175,420:0.7047:2,2:23.9:1:30.7:1:0.5293:1.12:36.5:59:0.7024:0:1.1 +13 111590610 . CA C 107 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.34619;SOR=1.6809;LSEQ=AAGTCAGGAGCTGTGCTCTC;RSEQ=AAAAAAGCAAGGGCCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1170:7:4,3:560,599:1159,7:0.006:2,2:21.1:1:30.9:1:0.71778:1.43:44.7:14:0.0061:9e-04:0.1 0/1:1098:11:6,5:541,546:1087,11:0.01:2,2:26.3:1:31.2:1:0.77256:1.21:50:22:0.0101:0.0018:0.2 +13 111590720 . ACT A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.956;SOR=0.9895;LSEQ=TCCTGACTCTGGTCTGGAAC;RSEQ=CTGCACATGTTCTGGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:925:241:122,119:358,325:683,241:0.2605:2,2:25.3:1:32.3:1:0.65317:1.07436:56:240:0.2629:0.0422:0.1 0/1:793:205:102,103:304,283:587,205:0.2585:2,2:22.4:1:30.7:1:0.62713:1.08462:53.1:410:0.2632:0.0555:0.1 +13 111590727 . A G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=0.67229;LSEQ=TCTGGTCTGGAACACTCTGC;RSEQ=CATGTTCTGGAGAAAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:908:300:160,140:311,296:607,300:0.3304:2,2:16.9:1:30.4:1:0.57243:1.09:43:29:0.3262:0:2 0/1:787:196:96,100:312,278:590,196:0.249:2,2:16.9:1:30.6:1:0.36456:1.16883:42.9:97:0.2497:0:2 +13 111590733 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.6364;LSEQ=CTGGAACACTCTGCACATGT;RSEQ=CTGGAGAAAGGTGGGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:898:274:145,129:319,303:622,274:0.3051:2,2:12.3:1:31.1:1:0.6639:1.07:43.6:23.909:0.3006:0:2.1 0/1:806:176:85,91:326,304:630,176:0.2184:2,2:12.5:1:30.4:1:0.44326:1.14787:43.4:28.333:0.2174:0:2.1 +13 111590803 . T A 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02885;SOR=0;LSEQ=TCGTTAAAGGAACCAACTCC;RSEQ=ATTACAAGCTGAAGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:3,2:205,288:493,5:0.01:2,2:9:1:25.2:1:0.6538:2.10:59:4:0.0081:0:1 0/0:512:0:0,0:224,286:510,0:0:2,0:24.7:1:28.6:1:1:0:59.9:71.857:1:0:0.1 +13 111590930 . C T 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGTCCAAGGAGGACACCA;RSEQ=TGAACACTTCATGAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:409:409:226,183:0,0:0,409:1:0,2:25.4:1:30.7:1:1:0:54.7:101.25:1:0:1.1 1/0:366:257:144,113:60,48:108,257:0.7022:2,2:21:1:29.6:1:1:1.02:55.8:84.667:0.6997:0:1.1 +13 111591170 . G A 285 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00669;LSEQ=CCATGGTGGGGTGTGAGATC;RSEQ=ACCTTCAGATGCCCTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:608:606:285,321:0,0:0,606:0.9967:0,2:23.4:1:30.9:1:1:0:55.6:201:0.9983:0:1.1 1/0:571:382:187,195:93,96:189,382:0.669:2,2:22.9:1:29.5:1:1:1.01018:55.5:94.5:0.6714:0:1.1 +13 111591265 . G A 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.57611;LSEQ=TGGTGTCCCAGGGCAGCAGC;RSEQ=ACTCTCAGATCCTGGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:37:18,19:199,219:418,37:0.0813:2,2:26.4:1:30.3:1:1:1.04:49.9:74:0.0824:0:1.9 0/1:452:84:41,43:170,198:368,84:0.1858:2,2:21.6:1:29.3:1:0.71663:1.11:47.5:83:0.1865:0:1.7 +13 111591283 . T C 287 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.0163;LSEQ=GCGACTCTCAGATCCTGGAT;RSEQ=TCTCAAATCGCTTTTACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:458:455:215,240:1,0:1,455:0.9934:0,2:24.2:1:32.6:1:0.47368:0:41.2:55.875:1:0:1.2 1/0:416:296:143,153:57,63:120,296:0.7115:2,2:26.3:1:31:1:0.91399:1.03:38.9:97.667:0.7129:0:1.3 +13 111592184 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24857;SOR=0;LSEQ=CGGTGACTCTGGTATTAATT;RSEQ=ACCCTAAGCGCTTCTGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:1,2:42,155:197,3:0.015:2,2:15.7:1:30.7:1:0.51827:1.84:60:6:0.0152:0:1 0/0:190:0:0,0:39,151:190,0:0:2,0:20.3:1:31.1:1:1:0:59.9:94:1:0:0.1 +13 111592285 . A G 184 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00016;SOR=0;LSEQ=GATTTTGCAGAAATGCATTA;RSEQ=AAGCTTTTTCCCAAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:3,49:0,0:0,52:1:0,2:25.7:1:32.3:1:1:0:60:104:1:0:1.1 1/0:13:8:0,8:1,4:5,8:0.6154:2,0:26.4:1:31.4:1:0.38462:0:60:16:0.6154:0:1.1 +13 111840700 . T G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAAACTGAGATAACAGA;RSEQ=GCTTGTTGTTTGGGCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:29.5:1:32.5:1:1:1:60:4:0.5:0:1 +13 112722084 . G T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.51746;SOR=0;LSEQ=GCGGGGGCGGAGGCGGGGGC;RSEQ=GCGGCGGCGGCGGGGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:69,5:74,2:0.0263:2,2:5:0:32.5:1:0.15263:12.68865:60:4:0.0267:0:1 0/0:50:0:0,0:45,5:50,0:0:2,0:10.9:1:29.8:1:1:0:60:24:1:0:0.1 +13 112722172 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08027;SOR=Inf;LSEQ=GTGGTCCCGCGGGCAGCGGC;RSEQ=CAAGATGGCCCAGGAGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:266,110:376,0:0:2,0:17.1:1:29.7:1:1:0:40.4:40.778:0.9973:0:0.1 0/1:287:3:2,1:181,100:281,3:0.0105:2,2:29:1:28.7:1:1:1.10:33.3:6:0.0105:0:1.3 +13 112722356 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20462;SOR=Inf;LSEQ=CCGCGCCGCAAGACCAAGAC;RSEQ=CTGCTCAAGAAGGACAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:47,178:225,0:0:2,0:24.9:1:31.5:1:1:0:60:55.25:0.991:0:0.2 0/1:188:2:1,1:44,142:186,2:0.0106:2,2:5.5:1:28:1:0.4224:3.20:60:4:0.0108:0:1 +13 112722387 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11048;SOR=0.32337;LSEQ=AGGACAAGTACTCGCTGGCC;RSEQ=GCGGGCTCCTGGCGGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:14:0,14:5,82:87,14:0.1386:2,1:25.1:1:33.6:1:1:0:60:28:0.1386:0:1.1 0/1:61:3:0,3:5,52:57,3:0.0492:2,0:34.7:1:32.3:1:1:0:60:6:0.0508:0:1 +13 114443604 . GCA G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.49734;SOR=0;LSEQ=ACACACAGGTGCACACATGC;RSEQ=CACACACACACCTCTACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:12,13:25,2:0.0741:2,2:29:0:34.5:1:1:1.08:60:4:0.0741:0:0 0/0:21:0:0,0:10,11:21,0:0:2,0:33.4:1:30.3:1:1:0:58.6:20:1:0:0.7 +13 114826465 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCCCCACAGCCGGCAGA;RSEQ=GGAGCCCCCCACAGCCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:27.5:1:1:0:38.5:4:1:0:1 +13 114828023 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=GTGCAGCAATAGACATCACA;RSEQ=CCCACGTCCGCACGCAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:18,2:0.1:2,2:23:1:29.5:1:1:1.23603:60:4:0.1:0:1 0/0:16:0:0,0:8,8:16,0:0:2,0:28.3:1:30.6:1:1:0:57.4:32:1:0:0.6 +13 114828045 . G A 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00201;SOR=Inf;LSEQ=CCACGTCCGCACGCAGACTC;RSEQ=GACACGCGTGCTCACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:20.7:1:31.4:1:1:0:52.7:30:1:0:0.4 1/0:11:6:3,3:2,3:5,6:0.5455:2,2:22.8:1:31.3:1:1:1.45:53:12:0.5455:0:1.3 +13 114828075 . C T 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=GCTCACAGCCCACGTCCGCA;RSEQ=GCAGACTCAGACACGCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:22.8:1:30.1:1:1:0:43.1:20:1:0:0.5 0/1:5:2:0,2:0,3:3,2:0.4:0,0:5:1:31:0:1:0:40:4:0.4:0:2 +14 19890214 . T C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCACCACGTCCCGGGATGG;RSEQ=GGGCGTCGGGTGGGAGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:47:0:32:0:1:0:22:2:0.5:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:31:1:1:0:22:4:1:0:1 +14 20084416 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16418;SOR=Inf;LSEQ=CATGATTTCAGTGATGTCCT;RSEQ=AGAGGGAAACGCAGATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:51,98:149,0:0:2,0:12.7:1:31.2:1:1:0:27.5:36.25:1:0:0.1 0/1:102:2:1,1:34,66:100,2:0.0196:2,2:15.5:1:26.5:1:1:1.93:60:4:0.0198:0:1.5 +14 20084445 . A T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29633;SOR=3.56101;LSEQ=ACGCAGATACACCTGTCAGG;RSEQ=AATATATGGATCAGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:1:1,0:119,197:316,1:0.0032:2,0:29:0:12:0:0.37855:0:22:0:0:0:1 0/1:179:2:1,1:70,107:177,2:0.0112:2,2:33.5:1:26.5:1:1:1.52:21.5:4:0.0112:0:1 +14 20085023 . C A 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=1.64517;LSEQ=TTGACTGATACCAATACTCA;RSEQ=TTTGTAGATATAATGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:815:480:242,238:172,163:335,480:0.589:2,2:31.6:1:30.8:1:0.83092:1.03774:24.7:52.333:0.5866:0:1.1 1/0:450:316:159,157:76,58:134,316:0.7022:2,2:30.1:1:30:1:0.2178:1.29311:24.6:104.333:0.7018:0:1.1 +14 20085849 . G C 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ATCCGCCCGCCTCGGCCTCC;RSEQ=AAAGTGCTGGGTAAATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:1,4:0.8:0,2:30.8:1:30.5:1:1:0:41.8:8:0.8:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:11:1:28:1:1:0:60:4:1:0:0 +14 20086227 . GGT G 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.28094;SOR=0;LSEQ=AGTAATCTTACATGACTGAA;RSEQ=GTGTGTGTGGGGGGGTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:3:2,1:70,28:98,3:0.0297:2,2:15:1:30.6:1:1:1.24717:37.3:6:0.0297:0.0099:0 0/0:65:0:0,0:42,22:64,0:0:2,0:8.3:1:30.3:1:1:0:34.2:63:0.9844:0:1.3 +14 20086236 . GT G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.29206;SOR=0.47151;LSEQ=ACATGACTGAAGGTGTGTGT;RSEQ=GGGGGGGTATGACTTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:12:7,5:35,19:54,12:0.0822:2,2:23.1:1:32.3:1:0.74523:1.31017:38.6:24:0.0828:0:2 0/1:99:4:2,2:31,22:53,4:0.0404:2,2:22.5:1:31:1:1:1.40047:40.8:8:0.0408:0:1.8 +14 20086237 . T G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.06848;SOR=0.60916;LSEQ=CATGACTGAAGGTGTGTGTG;RSEQ=GGGGGGGTATGACTTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:146:80:53,27:35,19:54,80:0.5479:2,2:17.8:1:31.6:1:1:1.07:32.3:160:0.5517:0:1.9 0/1:99:42:25,17:31,22:53,42:0.4242:2,2:15.9:1:30.6:1:1:1.04:30:84:0.4286:0:2.1 +14 20086239 . G T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.30578;SOR=4.53243;LSEQ=TGACTGAAGGTGTGTGTGTG;RSEQ=GGGGGTATGACTTCAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:0,1:101,57:158,1:0.0063:2,0:1:0:26:0:0.36478:0:23:2:0.0064:0:3 0/1:107:3:1,2:62,42:104,3:0.028:2,2:17.3:1:27.7:1:0.56706:2.9224:35.7:6:0.028:0:1.3 +14 20086240 . G T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.2185;SOR=1.35639;LSEQ=GACTGAAGGTGTGTGTGTGG;RSEQ=GGGGTATGACTTCAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:62:38,24:67,37:104,62:0.3735:2,2:19.4:1:29.7:1:0.74032:1.14274:30.1:61:0.372:0:2 0/1:114:51:30,21:37,26:63,51:0.4474:2,2:15.9:1:28.8:1:1:1.00:28.7:50:0.4425:0:2 +14 20086244 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23479;SOR=0.51038;LSEQ=GAAGGTGTGTGTGTGGGGGG;RSEQ=TATGACTTCAGAAAAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:14:7,7:104,69:173,14:0.0745:2,2:24.1:1:30.3:1:0.57369:1.50382:35.3:28:0.0753:0:2.3 0/1:127:5:3,2:69,51:120,5:0.0394:2,2:23:1:29.6:1:1:1.11:36.6:10:0.0397:0:1.8 +14 20086290 . T C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23221;SOR=0.49929;LSEQ=GTTTCTCTTTTCTCCACCAT;RSEQ=CTATAGGAATAAGATGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:14:7,7:104,69:173,14:0.0749:2,2:23.9:1:32.4:1:0.57369:1.50382:35.3:28:0.0761:0:2.3 0/1:129:5:2,3:71,53:124,5:0.0388:2,2:26:1:31.6:1:0.652:1.9985:31.4:10:0.0388:0:1.8 +14 20347304 . A G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29167;SOR=0;LSEQ=GTAGTTGGATTGATAGTAAA;RSEQ=TTCTGTGGCTGATAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:0,17:1:0,1:25.3:1:34:1:1:0:57.8:34:1:0:1 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:11.2:1:32.5:1:1:0:60:12:0.8571:0:1.2 +14 20347432 . T G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09705;SOR=1.68841;LSEQ=TGGTACCTCTGCATGTTATA;RSEQ=AAACACTTAAAAATCTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:75:64,11:92,8:100,75:0.4286:2,2:22.1:1:31.9:1:0.21948:1.96874:60:17.75:0.4226:0:1.2 1/0:59:33:26,7:22,4:26,33:0.5593:2,2:20.1:1:31.6:1:0.73968:1.4711:60:66:0.5593:0:1.1 +14 20347539 . T C 192 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=120.41479;LSEQ=TTCACCAAGGATAACTGCAG;RSEQ=GACATGGCCATGGACTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:687:2:1,1:357,328:685,2:0.0029:2,2:27.5:1:29.5:1:1:1.08827:60:4:0.003:0:2 0/1:325:85:49,36:124,116:240,85:0.2615:2,2:25.6:1:30.1:1:0.37702:1.27:59.4:84:0.2609:0:1.8 +14 20347564 . A C 186 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=79.05085;LSEQ=TGGCCATGGACTCGTTAAGC;RSEQ=ATAGTAAGGATGGTGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:668:3:1,2:295,369:664,3:0.0045:2,2:25.3:1:26.3:1:1:1.59784:60:2:0.003:0:2 0/1:311:82:37,45:96,133:229,82:0.2637:2,2:24.4:1:29.4:1:0.69655:1.14:59.4:19.5:0.2566:0:1.9 +14 20347644 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09513;SOR=Inf;LSEQ=GAGAATACAAGATAAGCAGG;RSEQ=AAGTATAATTTTAAGTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:58,192:250,0:0:2,0:23.3:1:32:1:1:0:59.8:61.5:1:0:0 0/1:112:2:1,1:23,87:110,2:0.0179:2,2:6:0:31.5:1:0.38417:3.72:60:4:0.0183:0:2 +14 20893115 . T A 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TAGGCACAGGAGACAAGTGA;RSEQ=ACCTAGAGTCCCACACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:27:17,10:239,117:356,27:0.0705:2,2:22.2:1:30.2:1:0.67461:1.201:60:54:0.0712:0:1.2 0/0:213:0:0,0:143,70:213,0:0:2,0:25.1:1:28.6:1:1:0:60:41.6:1:0:0.1 +14 20893219 . T G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=8.34454;LSEQ=ATAAGAGAGATATCAGAAAT;RSEQ=TCACCCTCACCAGCAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:584:91:32,59:214,279:493,91:0.1558:2,2:25.9:1:32.3:1:0.16572:1.41338:60:182:0.1574:0:1.1 1/0:402:244:109,135:79,79:158,244:0.607:2,2:26.2:1:31.4:1:0.30767:1.23786:60:488:0.6085:0:1.1 +14 20893275 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17724;SOR=Inf;LSEQ=GTTGGGGGAGCTATTAGAGA;RSEQ=CATCTAGAACACCTTGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:61,212:273,0:0:2,0:22.7:1:32.3:1:1:0:60:44.5:1:0:0.3 0/1:199:2:1,1:66,131:197,2:0.0101:2,2:22:1:25.5:1:1:1.98:60:4:0.0102:0:1 +14 20893369 . C T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07669;SOR=2.93554;LSEQ=GTCTTGCCAGGTCACCACCA;RSEQ=GGCTGCCCAATCTGTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:44:0,44:1,17:18,44:0.7097:1,1:23.7:1:30.3:1:0.29032:0:60:43:0.7049:0:1 1/1:33:29:0,29:1,3:4,29:0.8788:2,1:28:1:29.9:1:0.12121:0:60:28:0.875:0:1.1 +14 20969716 . C T 77 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTCCATGGTACATGTAC;RSEQ=ATGGTTTGCTTAATGCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,1:2,5:0.7143:2,0:18.8:1:33.4:1:0.28571:0:60:10:0.8333:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 20969733 . A G 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCATGGTTTGCTTAATGC;RSEQ=TCACCCATTGAAGAACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1:0,2:35.2:1:31.8:1:1:0:60:12:1:0:1.8 1/1:2:2:2,0:0,0:0,2:1:0,0:5.5:1:30:1:1:0:60:4:1:0:1 +14 21336860 . A AT 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CATGCCTGGCTTATTTTTGT;RSEQ=TTTTTAGTACAGACGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:25.8:1:33.2:1:1:0:36.2:10:1:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:2:0:24:0:1:0:22:2:1:0:0 +14 21337266 . T G 296 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00382;LSEQ=GAGCTGGTTTTAGAAACAGG;RSEQ=GGAGATCACCGAGTCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:744:742:341,401:0,0:0,742:0.9973:0,2:27.2:1:31.1:1:1:0:59.9:81.444:0.9973:0:1.1 1/0:480:281:137,144:97,101:198,281:0.5854:2,2:26.7:1:30.2:1:1:1.00945:59.9:139.5:0.5837:0:1.1 +14 21337344 . A G 33 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55898;SOR=3.37126;LSEQ=AATGTCTAAAATACAGCAAA;RSEQ=GAGAAGGCATTCGAATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:1:1,0:86,230:316,1:0.0032:2,0:21:0:14:0:0.27445:0:60:0:0:0:4 0/1:189:2:1,1:54,133:187,2:0.0106:2,2:23:1:33:1:0.49842:2.45:60:4:0.0107:0:1.5 +14 21337644 . G A 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCGTGTGCCACTACGCCC;RSEQ=GCTAATTTTTGTATTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:31:0:1:0:32.5:4:1:0:3 1/1:1:1:0,1:0,0:0,1:1:0,0:15:0:32:0:1:0:54:2:1:0:2 +14 22394783 . T C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTCAACATTCCTATCCA;RSEQ=GAAGTGATCATTATTTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:25.7:1:32:1:1:0:52.7:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 22395250 . A T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.41946;SOR=1.16237;LSEQ=TTTCGTATGTTTTTATTCAG;RSEQ=AAAATGATATTTTTTCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:329:193:91,102:61,74:135,193:0.5866:2,2:25.3:1:28.7:1:0.73708:1.08:59.9:192:0.589:0:1.1 1/0:212:132:59,73:39,41:80,132:0.6226:2,2:25.4:1:28.3:1:0.57338:1.17602:60:131:0.6238:0:1.1 +14 22395264 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.15298;SOR=Inf;LSEQ=ATTCAGAAAAATGATATTTT;RSEQ=TCTAATTGTAAAGGATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:124,171:295,0:0:2,0:26.1:1:30.6:1:1:0:60:294:1:0:0.7 0/1:190:2:1,1:76,112:188,2:0.0105:2,2:9:1:27:1:1:1.47:60:4:0.0106:0:1.5 +14 22395357 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32811;SOR=1.50952;LSEQ=GTATATAACTGTTCCCACAC;RSEQ=TTCATCTATATATATGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:87:52:4,48:2,33:35,52:0.5977:2,2:25.6:1:31.3:1:1:1.37:60:51:0.593:0:2 1/0:39:27:5,22:2,10:12,27:0.6923:2,2:22.2:1:29.7:1:1:1.13:60:26:0.6842:0:2 +14 22395359 . T C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41934;SOR=1.48328;LSEQ=ATATAACTGTTCCCACACGT;RSEQ=CATCTATATATATGCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:49:4,45:2,33:35,49:0.5833:2,2:26.3:1:31.9:1:1:1.46:60:98:0.5833:0:2 1/0:37:25:4,21:2,10:12,25:0.6757:2,2:22.9:1:30.4:1:1:1.04861:60:50:0.6757:0:2 +14 22395405 . A T 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33085;SOR=0;LSEQ=AAATTATCTTTTATATATTC;RSEQ=TTTTTACTGATATTCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:7:0,7:0,36:36,7:0.1628:1,0:18:1:31:1:1:0:54.4:14:0.1628:0:1.6 0/0:9:0:0,0:0,9:9,0:0:0,0:26.9:1:31.9:1:1:0:60:18:1:0:1.6 +14 22395437 . C T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCCAGTACAAACAAATG;RSEQ=TATTTAAAAATCATCTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:19,5:0.2083:1,0:28.6:1:31:1:1:0:52.2:10:0.2083:0:1.8 0/0:4:0:0,0:0,4:4,0:0:0,0:17:1:32:1:1:0:60:8:1:0:1 +14 22592304 . G A 116 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00068;SOR=0.056;LSEQ=CTGGTGGCAAGTGAGGAGGA;RSEQ=GGTAGCATTCACCTAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:4,10:6,12:18,14:0.4375:2,2:17.9:1:30.6:1:1:1.24135:60:28:0.4375:0:1 0/1:25:1:1,0:10,14:24,1:0.04:2,0:9:0:31:0:0.44:0:60:2:0.04:0:1 +14 22592311 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21647;SOR=Inf;LSEQ=CAAGTGAGGAGGAGGGTAGC;RSEQ=TTCACCTAGAGCAAAATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:6,21:27,0:0:2,0:24.1:1:30.6:1:1:0:60:26:1:0:0.4 0/1:24:2:1,1:10,12:22,2:0.0833:2,2:18.5:1:32:1:1:1.19:60:4:0.0833:0:1 +14 23549896 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.4902;SOR=Inf;LSEQ=TCTTCCTCCTCCTCCTCCTC;RSEQ=TCTTCTTCCTCCTCTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:26,0:0:2,0:26.8:1:32.3:1:1:0:60:25:1:0:0.2 0/1:26:2:1,1:12,12:24,2:0.0769:2,2:27:0:31.5:1:1:1:60:4:0.0769:0:1 +14 23574095 . GGCA G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=11.000;MSILEN=3;SSF=1;SOR=1.08739;LSEQ=CAACCCTGAGGACTAGTGGC;RSEQ=GCAGCAGCAGCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:3,8:5,4:9,11:0.55:2,2:38.3:1:32.8:1:0.36185:3.12593:60:22:0.5789:0:1.1 1/0:7:4:1,3:2,0:2,4:0.5714:0,2:18.3:1:29.5:1:0.4:0:60:8:0.5714:0.1429:1.3 +14 23574116 . A G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=3;SSF=0.34968;SOR=4.32204;LSEQ=GCAGCAGCAGCAGCAGCAGC;RSEQ=GCAGCAGCAGCATCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:3,8:5,5:10,11:0.5238:2,2:33.6:1:30.2:1:0.387:2.54034:60:10:0.5:0:1.1 1/1:6:5:2,3:1,0:1,5:0.8333:0,2:30:1:30.6:1:1:0:60:10:0.8333:0:1.2 +14 23586789 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.30819;SOR=4.4708;LSEQ=TCTAGCTCCTGGGTGAGCTG;RSEQ=TCCACGCGGCTGCGGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:1,0:305,58:363,1:0.0027:2,0:42:0:14:0:1:0:60:0:0:0:6 0/1:246:3:1,2:196,47:243,3:0.0122:2,2:18.3:1:28.3:1:0.10204:8.23893:60:6:0.0123:0:1 +14 23586796 . C T 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39398;SOR=2.26069;LSEQ=CCTGGGTGAGCTGCTCCACG;RSEQ=GGCTGCGGAGGCGCTCGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:2:0,2:333,91:424,2:0.0047:2,0:1:0:25.5:1:0.04726:0:60:4:0.0048:0:1 0/1:284:3:1,2:210,71:281,3:0.0106:2,2:7.7:1:26:1:0.16326:5.87016:60:6:0.0106:0:1 +14 23586802 . C T 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01809;LSEQ=TGAGCTGCTCCACGCGGCTG;RSEQ=GGAGGCGCTCGTTCTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:6:2,4:364,113:477,6:0.0124:2,2:10:1:24.7:1:0.03274:6.41097:60:5:0.0105:0:1.8 0/1:317:4:1,3:225,88:313,4:0.0126:2,2:12.5:1:23.3:1:0.07298:7.61416:60:3:0.0096:0:1.3 +14 23586970 . C T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62421;SOR=1.75548;LSEQ=TCTTGCCCTTGTGTAAGGGG;RSEQ=CAGCCGGGGAGGGCGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:2:0,2:25,251:276,2:0.0072:2,0:24:1:19.5:1:1:0:60:1:0.0037:0:3.5 0/1:159:2:0,2:11,146:157,2:0.0126:2,0:16:1:25:1:1:0:60:4:0.0128:0:1 +14 23586985 . G A 36 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.65367;LSEQ=AGGGGCCAGCCGGGGAGGGC;RSEQ=CCTTCAGGAGGGGACTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:0,3:1,187:188,3:0.0157:1,0:18.7:1:23.3:1:1:0:60:2:0.0107:0:1.3 0/1:97:1:0,1:1,95:96,1:0.0103:1,0:22:0:31:0:1:0:60:2:0.0104:0:2 +14 23587046 . A C 133 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01173;SOR=0.10491;LSEQ=AGGGGCCTGGAGGGGAAGGC;RSEQ=CGGAGAGACGGAGAGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:19:0,19:1,58:59,19:0.2436:1,1:20.2:1:31.4:1:1:0:60:18:0.2368:0:1.2 0/1:31:1:0,1:3,27:30,1:0.0323:2,0:8:0:32:0:1:0:60:2:0.0323:0:1 +14 23587231 . G A 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGATGCACAGGGTCCTCT;RSEQ=CTTGAGACCAAAACTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:1,7:8,2:0.2:2,0:11.5:1:30:1:1:0:60:4:0.2:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 23652004 . G A 100 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13442;SOR=0.19129;LSEQ=CCACAGGCACTGACCAATCC;RSEQ=ATCTCTTTCTTCAGGGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:9,0:19,1:20,9:0.3103:1,0:32.2:1:31.7:1:1:0:60:18:0.3214:0:1 0/1:13:1:1,0:11,1:12,1:0.0769:2,0:16:0:31:0:1:0:60:2:0.0833:0:1 +14 23652305 . A C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.06001;LSEQ=TATTCCTACTCCGCATTCAC;RSEQ=CTTTCTGGTCACTCGCGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1339:523:258,265:413,403:816,523:0.3906:2,2:26.9:1:31.3:1:0.65444:1.05255:59.6:36.357:0.3943:0:1.2 0/1:1189:44:22,22:591,554:1145,44:0.037:2,2:20.7:1:27.9:1:0.87857:1.0667:57:6.333:0.0333:0:2 +14 23652384 . C A 35 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.14419;LSEQ=AAAAGGCCAGGGGAGACATA;RSEQ=ATTTAAATATAAAAATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:672:6:6,0:241,423:664,6:0.0089:2,0:33:1:13.7:1:0.00241:0:45.2:0:0:0:6.3 0/1:490:5:3,2:179,305:484,5:0.0102:2,2:24.2:1:23.8:1:0.36607:2.55:57.4:4:0.0084:0:3.2 +14 23652708 . T A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.55769;LSEQ=AGATCTGGTTTCCACCTGCT;RSEQ=TGGGTTTCTTTTCCCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:0,19:1,4:5,19:0.7917:2,1:29:1:31.7:1:0.20833:0:60:38:0.7917:0:1.1 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:18.7:1:29.3:1:1:0:60:12:0.8571:0:1 +14 23764410 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51083;SOR=0;LSEQ=ACTGGAGGGCGAAGAAACCT;RSEQ=GTCATTACAGGCCTGGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:62,50:112,2:0.0175:2,2:29.5:1:30.5:1:1:1.23764:55:4:0.0187:0:1.5 0/0:82:0:0,0:42,40:82,0:0:2,0:27.7:1:28.7:1:1:0:58.7:10.714:1:0:0.5 +14 23764564 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGTGCAGCTTAGTGGT;RSEQ=CTTTGCAGGAGGCAAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:125,45:170,2:0.0116:2,2:25.5:1:28:1:0.4645:2.75839:60:4:0.012:0:1 0/0:81:0:0,0:57,24:81,0:0:2,0:22.3:1:31.2:1:1:0:60:80:1:0:0.1 +14 23764577 . C T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98505;LSEQ=TAGTGGTGCTTTGCAGGAGG;RSEQ=AAGCAAAGCCTATCTGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:145,52:197,2:0.0101:2,2:29:1:28:1:0.46272:2.77154:60:4:0.0103:0:1 0/0:101:1:0,1:73,27:100,1:0.0099:2,0:19:0:29:0:0.27723:0:60:2:0.0102:0:1 +14 23764732 . TA T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.54825;SOR=1.5715;LSEQ=GATGGGGGAAACTTCATTCT;RSEQ=AAAAAAAAAAGTCTCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:6:0,6:34,123:157,6:0.0364:2,0:27.8:1:31.2:1:0.34549:0:60:12:0.0366:0:0.7 0/1:107:6:1,5:28,71:99,6:0.0561:2,2:23.8:1:30:1:1:1.96093:60:12:0.0571:0:0 +14 23764745 . T G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16387;SOR=Inf;LSEQ=TCATTCTTAAAAAAAAAAAG;RSEQ=CTCTGCTTCCTGTCATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:19,117:136,0:0:2,0:23.6:1:29.6:1:1:0:60:135:1:0:0.4 0/1:93:2:1,1:24,67:91,2:0.0215:2,2:39.5:1:30.5:1:0.46751:2.76:60:4:0.023:0:1 +14 23764770 . C G 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=GCTTCCTGTCATTGGTAGTT;RSEQ=TGAATGTTAGATATTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:20:2,18:3,69:72,20:0.2174:1,2:31.3:1:33.5:1:0.29708:2.52:59.8:40:0.2198:0:1.2 0/0:52:0:0,0:6,46:52,0:0:2,0:24.8:1:31.2:1:1:0:60:16.333:1:0:0.3 +14 23764788 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGAATGTTAGATATTTT;RSEQ=TCCCCATGGGGTCAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:5,75:80,2:0.0244:2,2:18:1:33:1:0.14182:13.78:60:4:0.0253:0:1.5 0/0:33:0:0,0:4,29:33,0:0:2,0:24.7:1:30.4:1:1:0:60:66:1:0:0.3 +14 23851325 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.01171;SOR=Inf;LSEQ=CTGGCAAGAGGGAGAAGTGT;RSEQ=TGGGGACAAATCCCTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:35,33:68,0:0:2,0:29.1:1:32.1:1:1:0:60:67:1:0:0.2 0/1:21:3:1,2:8,10:18,3:0.1429:2,2:25.3:1:30.3:1:1:1.56568:60:6:0.1429:0:1.7 +14 23851400 . C T 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCAGGGCCCCAGGGATC;RSEQ=TGTGGTCCCACGTTAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:14,2:0.125:1,0:7.5:1:32:0:1:0:60:4:0.125:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:29.3:1:31.3:1:1:0:60:6:1:0:0 +14 23992742 . T G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.39457;SOR=0.67093;LSEQ=GGCTGCTAAGAGGCCCTCAC;RSEQ=GCTGCCCCCAGTGCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:23:21,2:23,1:24,23:0.4894:1,2:24.5:1:29.7:1:0.60851:2.15523:60:46:0.4894:0:1.2 0/1:41:16:14,2:22,3:25,16:0.3902:2,2:20.8:1:29.6:1:1:1.0464:60:32:0.3902:0:1 +14 23992764 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21325;SOR=Inf;LSEQ=CTGCCCCCAGTGCTCCCAGC;RSEQ=GCTGTCCCCTGTAGTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:55,26:81,0:0:2,0:21.6:1:30.2:1:1:0:60:80:1:0:0.4 0/1:70:2:1,1:46,22:68,2:0.0286:2,2:19:1:28:1:1:2.06711:60:4:0.029:0:1 +14 23992778 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20171;SOR=Inf;LSEQ=CCCAGCGGCTGTCCCCTGTA;RSEQ=TTTGGCCTTCTTTTCCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:69,42:111,0:0:2,0:23:1:32.4:1:1:0:60:36:1:0:0.3 0/1:91:2:1,1:52,37:89,2:0.022:2,2:21:1:28:1:1:1.40004:60:4:0.0222:0:1 +14 24002092 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53209;SOR=0;LSEQ=CAGCCACCTCCTTCCATTCA;RSEQ=CTTCCGGGAGGCTCCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:19,109:128,2:0.0154:2,2:10.5:1:26.5:1:0.28503:5.62:60:4:0.0155:0:1 0/0:76:0:0,0:12,63:75,0:0:2,0:22:1:31.7:1:1:0:60:150:1:0:0.1 +14 24002880 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11243;SOR=Inf;LSEQ=CCGCGGAGGGTGGGAGTGAT;RSEQ=CCTCTGGTGGACTTCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:214,11:225,0:0:1,0:22.4:1:32.4:1:1:0:60:74:1:0:0.1 0/1:114:2:1,1:99,13:112,2:0.0175:2,2:12:1:31:1:0.23149:7.37604:60:4:0.0177:0:1 +14 24002887 . G T 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTGGGAGTGATGCCTCTG;RSEQ=TGGACTTCCCTGCCCACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:222,25:247,0:0:2,0:22.6:1:31:1:1:0:60:29.875:1:0:0.1 0/1:130:19:13,6:95,16:111,19:0.1462:2,2:24.8:1:28.9:1:0.09299:2.71415:60:38:0.1496:0:1.2 +14 24002902 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11471;SOR=Inf;LSEQ=CTCTGGTGGACTTCCCTGCC;RSEQ=ACCAGGGCCCGCCTGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:242,87:329,0:0:2,0:22.8:1:30.8:1:1:0:60:31.9:1:0:0.1 0/1:169:2:1,1:118,49:167,2:0.0118:2,2:15:1:27.5:1:0.50542:2.39406:60:4:0.012:0:1.5 +14 24003268 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.07029;SOR=Inf;LSEQ=AGGGGCTGGGGTGTAGTCAT;RSEQ=AGCTAGGCGATAGGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:3,173:176,0:0:1,0:23.7:1:32.4:1:1:0:60:34.2:1:0:0.1 0/1:64:2:1,1:2,60:62,2:0.0313:1,2:35.5:1:29.5:1:0.09226:24.70:60:4:0.0313:0:1 +14 24153786 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1455;SOR=Inf;LSEQ=GGTAGAGAAGATATAATTTG;RSEQ=TGACGTGGGATGTGAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:17,0:0:2,0:24.6:1:32.8:1:1:0:60:34:1:0:0.2 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:36.5:1:27.5:1:1:1.22474:60:4:0.2:0:1.5 +14 24324170 . C T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTATTAATTTACAGTGACC;RSEQ=ATGATCCTGTTTTGATCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:21.3:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 24324349 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52193;SOR=0;LSEQ=TAGAGATATTAAATGATTAG;RSEQ=CTTATTTGGTAAATTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:24,18:42,2:0.0455:2,2:16.5:1:29.5:1:1:1.32452:60:4:0.0465:0:2.5 0/0:27:0:0,0:15,12:27,0:0:2,0:19.7:1:31.1:1:1:0:60:54:1:0:0.1 +14 24324391 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GGAACACTGTCAAATGATGA;RSEQ=TGATGCTAGATCTTCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:36,30:66,2:0.0294:2,2:29:0:32.5:1:1:1.19677:60:4:0.0294:0:2.5 0/0:43:0:0,0:20,23:43,0:0:2,0:29.4:1:31.4:1:1:0:60:86:1:0:0.1 +14 24851624 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=ATACATCTAGAAAGACCCTG;RSEQ=TTCCAAATAATGTCACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:10,2:0.1667:2,2:38.5:1:33:1:1:2.16:60:4:0.1667:0:1 0/0:9:0:0,0:4,5:9,0:0:2,0:17:1:28.6:1:1:0:60:18:1:0:0.1 +14 25195504 . C CAA 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CATCTTTTGGAGGCTCCCAT;RSEQ=AAAAAAAAAACATAATAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:23.7:1:29.8:1:1:1.73:46:6:0.6:0.2:0.3 0/0:2:0:0,0:2,0:2,0:0:0,0:36.5:1:31:1:1:0:60:4:1:0:0 +14 25195808 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01494;SOR=Inf;LSEQ=GTGTCCCAGTCCCGGAATGC;RSEQ=CAGATTCTTATGGCCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:11,14:25,0:0:2,0:23:1:31.8:1:1:0:60:50:1:0:0 0/1:15:4:2,2:5,6:11,4:0.2667:2,2:24.5:1:28.3:1:1:1.19:60:8:0.2857:0:1 +14 25196787 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.49296;SOR=0;LSEQ=GATGAGAAAGAACCAATGAA;RSEQ=AAATGCTGAAAACCCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:13,21:34,2:0.0556:2,2:36:0:34.5:1:1:1.59:27:4:0.0571:0:2.5 0/0:36:0:0,0:16,20:36,0:0:2,0:29.1:1:30.4:1:1:0:52.7:35:1:0:0.2 +14 25196793 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49296;SOR=0;LSEQ=AAAGAACCAATGAAAAAATG;RSEQ=TGAAAACCCAAAAGGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:13,21:34,2:0.0556:2,2:30:0:32.5:1:1:1.59:27:4:0.0556:0:2.5 0/0:36:0:0,0:16,20:36,0:0:2,0:27:1:32.3:1:1:0:52.7:72:1:0:0.2 +14 25197223 . T C 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAAGAAATCTGGGACTT;RSEQ=GTAAAAAGACCAAACCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:50:0:30:0:1:0:51:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:28:1:1:0:60:4:1:0:1 +14 25438138 . A G 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14529;SOR=Inf;LSEQ=TCTTGCACAACACTTTCAAA;RSEQ=TACAGATTAGCTTCCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:146,60:206,0:0:2,0:23.8:1:29.6:1:1:0:60:17.727:1:0:0.3 0/1:128:2:1,1:85,41:126,2:0.0156:2,2:5.5:1:30:1:0.55032:2.06041:60:4:0.0161:0:1 +14 25438143 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14101;SOR=Inf;LSEQ=CACAACACTTTCAAAATACA;RSEQ=ATTAGCTTCCCCACCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:161,65:226,0:0:2,0:23.7:1:32.3:1:1:0:60:44.2:1:0:0.3 0/1:137:2:1,1:90,45:135,2:0.0146:2,2:21.5:1:27:1:1:1.98916:60:4:0.0149:0:1 +14 25438186 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGTGCTGCATTAGAACCAGG;RSEQ=CATCTGTACTTTGAGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:263,179:442,0:0:2,0:26.4:1:31.4:1:1:0:60:25:0.9953:0:0.4 0/1:249:11:9,2:134,104:238,11:0.0442:2,2:19.9:1:29.2:1:0.12325:3.48:58.5:22:0.0449:0:1.8 +14 25438196 . T C 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGAACCAGGCCATCTGTAC;RSEQ=TTGAGAAATTCTAGAGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:40:24,16:253,179:432,40:0.0847:2,2:31.8:1:31.9:1:1:1.06:60:80:0.0862:0:1.6 0/0:264:0:0,0:146,118:264,0:0:2,0:25.3:1:29.7:1:1:0:59.9:65:1:0:0.5 +14 25438250 . A G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.56031;SOR=1.09929;LSEQ=CTAGGGCTGCCAATCACTGA;RSEQ=ATAAAGGGCAGTATTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:243:120,123:132,150:282,243:0.4629:2,2:24:1:32.1:1:0.59932:1.11:59.9:47.6:0.4595:0:1.2 0/1:296:144:65,79:74,78:152,144:0.4865:2,2:27.9:1:30.1:1:0.56181:1.1525:60:19.571:0.4757:0:1.1 +14 25438321 . T A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10907;SOR=Inf;LSEQ=TCCATGGGTATCTATTTACA;RSEQ=AAATTATTTCATCAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:88,203:291,0:0:2,0:23:1:28.9:1:1:0:60:57.2:1:0:0.3 0/1:144:2:1,1:53,89:142,2:0.0139:2,2:5:0:31.5:1:1:1.67:60:4:0.014:0:1 +14 27035112 . A G 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.46853;LSEQ=TTCATACAGAAAAAAATATA;RSEQ=TGATTCAGAAAAGTGATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:294:124,170:48,55:103,294:0.7406:2,2:26.5:1:32.6:1:0.4884:1.19593:60:97:0.7386:0:1.1 1/0:306:175:82,93:59,71:130,175:0.5719:2,2:25.4:1:31.1:1:0.81721:1.06:60:86.5:0.571:0:1.2 +14 27035196 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14793;SOR=Inf;LSEQ=ATGATGCAATTGAAAGATAG;RSEQ=CAGGAGTATGTTTCATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:45,143:188,0:0:2,0:24.6:1:31.8:1:1:0:59.8:61.667:1:0:0.3 0/1:118:2:1,1:36,80:116,2:0.0169:2,2:35:0:30.5:1:0.53064:2.21:60:4:0.0171:0:1.5 +14 27035215 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52205;SOR=0;LSEQ=GGCAGGAGTATGTTTCATGG;RSEQ=AAACAAAGGGATGAAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:21,110:131,2:0.015:2,2:23.5:1:29.5:1:0.30451:5.14:60:4:0.0153:0:1 0/0:85:0:0,0:20,65:85,0:0:2,0:23.6:1:31.7:1:1:0:60:170:1:0:0.1 +14 27036114 . C T 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGAAATCAATCCTTAGA;RSEQ=AAACATTCAATTTTTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:45:0:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 29235537 . C G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCCCACTCTTCCCACTACCA;RSEQ=CACCACCCCCGCTTTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:34.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 29237128 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50419;SOR=0;LSEQ=ACGAGTTCATCATGAAGAAC;RSEQ=TCCCTTACTACCGCGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:98,46:144,2:0.0137:2,2:43:0:33.5:1:0.54171:2.11842:60:4:0.0137:0:1 0/0:117:0:0,0:75,42:117,0:0:2,0:22.2:1:29.6:1:1:0:60:116:1:0:0.2 +14 29237161 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19369;SOR=Inf;LSEQ=GCGAGAACAAGCAGGGCTGG;RSEQ=AGAACTCCATCCGCCACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:114,93:207,0:0:2,0:28:1:32.1:1:1:0:60:68:1:0:0.2 0/1:164:2:1,1:87,75:162,2:0.0122:2,2:14.5:1:26:1:1:1.15895:60:4:0.0123:0:1.5 +14 29237172 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1961;SOR=Inf;LSEQ=CAGGGCTGGCAGAACTCCAT;RSEQ=CGCCACAATCTGTCCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:106,106:212,0:0:2,0:28.7:1:31.7:1:1:0:60:69.667:1:0:0.2 0/1:169:2:1,1:85,82:167,2:0.0118:2,2:18:0:30:1:1:1.03638:60:4:0.012:0:1.5 +14 29237182 . C A 30 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59464;SOR=2.38511;LSEQ=AGAACTCCATCCGCCACAAT;RSEQ=TGTCCCTCAACAAGTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:1,0:93,109:202,1:0.0049:2,0:1:0:23:0:0.46305:0:60:2:0.005:0:1 0/1:171:2:1,1:79,90:169,2:0.0117:2,2:5:0:30:0:1:1.14:60:4:0.0117:0:1.5 +14 29237224 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18313;SOR=Inf;LSEQ=TGAAGGTGCCGCGCCACTAC;RSEQ=ACGACCCGGGCAAGGGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:45,84:129,0:0:2,0:21.8:1:31.1:1:1:0:60:42:1:0:0.2 0/1:97:2:1,1:33,62:95,2:0.0206:2,2:25.5:1:27.5:1:1:1.87:60:4:0.0208:0:1 +14 29237265 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53824;SOR=0;LSEQ=TACTGGATGCTGGACCCGTC;RSEQ=AGCGACGACGTGTTCATCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:10,52:62,2:0.0313:2,2:13:0:32:1:0.31647:5.01:60:4:0.0317:0:1.5 0/0:35:0:0,0:6,29:35,0:0:2,0:20.2:1:30.7:1:1:0:60:70:1:0:0.2 +14 29237270 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.11874;SOR=Inf;LSEQ=GATGCTGGACCCGTCGAGCG;RSEQ=CGACGTGTTCATCGGCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:10,48:58,0:0:2,0:23.7:1:29.6:1:1:0:60:57:1:0:0.1 0/1:31:2:1,1:4,25:29,2:0.0645:2,2:10.5:1:29:1:0.30108:5.70:60:4:0.0645:0:1.5 +14 31375248 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1762;SOR=Inf;LSEQ=GGCTTGGACTCTGGAATCAG;RSEQ=TGATGCAGTACTTTACCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:177,96:273,0:0:2,0:25.7:1:32.7:1:1:0:59.9:135.5:1:0:0.2 0/1:198:2:1,1:117,79:196,2:0.0101:2,2:21.5:1:27.5:1:1:1.47797:60:4:0.0103:0:1 +14 31375294 . CT C 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06297;SOR=Inf;LSEQ=GCCTGAGCAGCAATTTCTCT;RSEQ=TTAACATACTAAATTAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:204,188:392,0:0:2,0:25.2:1:30.9:1:1:0:60:48:1:0:0.4 0/1:260:3:2,1:135,122:257,3:0.0115:2,2:17.3:1:29.3:1:1:1.80:59.3:6:0.0116:0.0038:1.3 +14 31375322 . A T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01365;SOR=1.48348;LSEQ=TACTAAATTAAACTAGCCAG;RSEQ=TCAATGCACAATTAGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:166:77,89:114,125:239,166:0.4099:2,2:25.5:1:29.7:1:0.8398:1.05396:60:54.333:0.4116:0:1.1 1/0:262:133:63,70:67,62:129,133:0.5076:2,2:25.5:1:28.8:1:0.53673:1.19987:60:65.5:0.5097:0:1.1 +14 31581199 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=6;SSF=0.50736;SOR=0;LSEQ=TCTGTCTCAAAAAAACAAAA;RSEQ=CAAAAACAAAAACAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:129,38:167,2:0.0118:2,2:17:1:32:1:0.40934:3.36384:60:4:0.012:0:1 0/0:129:0:0,0:99,30:129,0:0:2,0:20.2:1:29.4:1:1:0:57:258:1:0:0.1 +14 31581306 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18561;SOR=Inf;LSEQ=GGGGCATTCCTTTTTGAACA;RSEQ=TACCCATTCCCTTAATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:77,139:216,0:0:2,0:22.8:1:32.1:1:1:0:58.2:53:1:0:0.1 0/1:164:2:1,1:51,111:162,2:0.0122:2,2:18:1:25.5:1:0.53494:2.17:60:4:0.0123:0:2 +14 32175558 . G T 69 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55808;SOR=3.3264;LSEQ=GTTAGTTGAGCTCATTTGGG;RSEQ=TTCCATTTGTAAGATCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:9.5:1:28.5:1:0.4:0:36.5:4:0.4:0:1 1/0:7:5:3,2:2,0:2,5:0.7143:0,2:20.2:1:30:1:1:0:33.6:10:0.8333:0:1.2 +14 32175775 . C T 26 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05637;SOR=19.04025;LSEQ=AAGCCTTTTCCTGTAAATGC;RSEQ=GGGTGGCATCTTCTACTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:0,1:3,11:14,1:0.0667:2,0:37:0:32:0:1:0:24:2:0.0667:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:13.5:1:26.5:1:1:0:38.5:4:0.6667:0:1 +14 33106799 . A T 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGTAGTGACAAGGGGT;RSEQ=GATTGGTATAATGAACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:20.3:1:33:0:1:0:60:6:0.75:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 33106864 . G A 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGAAGAGAGCTGATATA;RSEQ=AGGCAGGGATTAGAGTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:13.7:1:30:1:1:0:60:6:0.2727:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 33106926 . G T 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAGTGCATTAACAATGAGAT;RSEQ=AGGGTGGAGAGTGGGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:25,0:25,5:0.1667:1,0:10.6:1:28.2:1:1:0:60:4:0.1379:0:1.6 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:37:0:33:0:1:0:60:2:0.1667:0:1 +14 33107026 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=3.76423;LSEQ=AAATATGATAATGGGAGTTG;RSEQ=TTGCAGAATGGTGTAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:53:51,2:93,1:94,53:0.3605:1,1:22.1:1:32:1:0.29491:3.61335:60:106:0.363:0:1.4 1/0:69:47:45,2:21,1:22,47:0.6812:1,1:26.3:1:30.7:1:1:1.07:60:94:0.6812:0:1.7 +14 33107053 . C T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.62504;LSEQ=AATGGTGTAGGTCATCGGAA;RSEQ=TGAGGAAGCCAAGAAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:25:23,2:186,25:211,25:0.1059:2,2:21.8:1:30.9:1:0.74807:1.54:60:50:0.1073:0:1.6 0/1:138:49:39,10:78,10:88,49:0.3551:2,2:23.5:1:29.1:1:0.20627:1.98932:60:23.5:0.3507:0:1.5 +14 33107172 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.94254;LSEQ=GATCCCAGGGCAAGTGCCAT;RSEQ=ATCTTCAACCAATGAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:248:119,129:271,354:625,248:0.2841:2,2:27.7:1:32.1:1:0.22755:1.20:60:496:0.2864:0:1.1 0/1:565:246:116,130:144,175:319,246:0.4354:2,2:25.9:1:31:1:0.67061:1.08:60:245:0.4367:0:1.1 +14 33107318 . G A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17002;SOR=1.93619;LSEQ=ACTGTCTTGTGCATATTATG;RSEQ=TGAGTGGAGAGAGGAAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:19:0,19:0,45:45,19:0.2969:1,1:24.3:1:29.6:1:1:0:60:5.333:0.2667:0:1.7 0/1:31:14:0,14:0,17:17,14:0.4516:1,1:31:1:31.6:1:1:0:60:28:0.4516:0:1 +14 33107381 . AG A 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.45285;SOR=2.67506;LSEQ=AAGGGCTAGTGGGGATGTCA;RSEQ=GGGGAATATGAGCTGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:0,17:17,3:0.15:1,0:38.3:1:34:0:1:0:60:6:0.1579:0:0 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:30:0:26:0:1:0:60:2:0.3333:0:0 +14 33941242 . C A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0485;SOR=Inf;LSEQ=GTCACTGTCTCCCTCTCTGC;RSEQ=CTCATGGAGCTTGTATTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:22,0:0:2,0:32.7:1:30.1:1:1:0:60:21:1:0:0.2 0/1:21:4:2,2:8,9:17,4:0.1905:2,2:33.8:1:28:1:1:1.12:60:8:0.1905:0:1 +14 33941280 . G A 45 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60435;SOR=0.38068;LSEQ=CTAGCTGGAGGAGAGAACAA;RSEQ=CAAGTAAACTATATGTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:3,8:11,3:0.2143:2,2:9:1:29:1:1:1.31:60:6:0.2143:0:1 0/1:11:1:0,1:3,7:10,1:0.0909:2,0:15:0:31:0:1:0:60:2:0.0909:0:1 +14 33960172 . TGCA T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.15749;SOR=0;LSEQ=GCAAAAATACAATTTTTCAC;RSEQ=GCAGCAGCAGCAGCAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:5:3,2:29,17:46,5:0.098:2,2:31.4:1:32.6:1:1:1.13435:60:10:0.098:0:0 0/0:27:0:0,0:17,10:27,0:0:2,0:28:1:31.5:1:1:0:60:54:1:0:0.1 +14 34552277 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52273;SOR=Inf;LSEQ=ATGATGTTTGTGTTCCCAGA;RSEQ=CAAATGGTTCTTTTAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:8,4:12,0:0:2,0:20.2:1:29.2:1:1:0:60:5:1:0:0.1 0/1:21:2:1,1:12,7:19,2:0.0952:2,2:39:1:28.5:1:1:1.66897:60:4:0.0952:0:1 +14 34769895 . G A 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGGATCTACGGCCACCACCA;RSEQ=GAGCCAAGAAGAGGCAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:32:0:33:0:1:0:60:2:1:0:0 +14 34770002 . G A 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTAAAGTGAGAGAATAA;RSEQ=TTTATGTGGTTTAAGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:30:1:1:0:44:4:1:0:1.5 1/1:1:1:0,1:0,0:0,1:1:0,0:31:0:29:0:1:0:60:2:1:0:1 +14 34771783 . G T 91 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTCAGTCTGGTTTCCTG;RSEQ=GACGCTTGTCACCACTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:5,3:2,1:3,8:0.7273:2,2:26.4:1:30.5:1:1:1.18052:60:16:0.7273:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 35871093 . C T 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00543;SOR=0.45138;LSEQ=CACAATAAGACGTTTTGGGC;RSEQ=AGGCAGTGTGCAGTGTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:362:291:282,9:66,4:70,291:0.8039:2,1:24.2:1:32.2:1:0.28882:1.89:59.8:96:0.8045:0:1.1 1/0:74:48:47,1:26,0:26,48:0.6486:1,1:26.4:1:31.2:1:1:0:60:96:0.6486:0:1.1 +14 35871135 . TTTC T 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAGTACACCCTTTAAATTT;RSEQ=TTCTTTTTTCTTTTTTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1013:0:0,0:857,156:1013,0:0:2,0:20.5:1:30.9:1:1:0:59.9:52.316:1:0:0.7 0/1:281:23:18,5:216,42:258,23:0.0819:2,2:14.6:1:29.8:1:0.55797:1.42657:59.1:46:0.0827:0.0356:0.3 +14 35871168 . C CT 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.27374;SOR=1.45341;LSEQ=CTTTTTTTAGAAAAATAAAA;RSEQ=TTTTTTTTTGTACAAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1818:30:24,6:1338,445:1783,30:0.0165:2,2:27.6:1:32:1:0.67186:1.33:59.5:60:0.0168:0.0022:0.7 0/1:546:13:6,7:369,164:533,13:0.0238:2,2:28.5:1:28.7:1:0.12498:2.61982:60:26:0.024:0.0037:0.5 +14 35871217 . G A 346 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.35026;LSEQ=TGTTCTTTCAGCCCCTTTGC;RSEQ=CTCATAACGTCAGACGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3712:3025:1771,1254:385,298:683,3025:0.8149:2,2:26.3:1:30:1:0.30298:1.09:59.9:53.018:0.8166:0:1.1 1/0:1126:683:375,308:247,194:441,683:0.6066:2,2:26.3:1:29:1:0.75872:1.0457:60:55.917:0.6089:0:1.1 +14 35871292 . G A 166 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=55.41352;LSEQ=AACAAGGGGAAAAAAGACAC;RSEQ=TTAAGCTTCCGGAGCGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3092:3:3,0:1168,1920:3088,3:0.001:2,0:1:0:26:1:0.05429:0:60:6:0.001:0:1.7 0/1:939:48:21,27:360,531:891,48:0.0511:2,2:24.5:1:29.8:1:0.65346:1.15:60:47:0.0506:0:1.4 +14 35871407 . A G 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13022;SOR=0.60252;LSEQ=AATGAACTTTACAGGCTGAG;RSEQ=GAGTTTGCCTTTAATGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:554:511:98,413:8,32:40,511:0.9224:2,2:24:1:31.6:1:0.83732:1.05348:59.6:45.455:0.9242:0:1.1 1/1:106:93:11,82:2,10:12,93:0.8774:2,2:21.4:1:30.8:1:0.64195:1.48457:59.9:30:0.8824:0:1 +14 35871430 . T TTTAAAAAAGAGTAAGCTA 185 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00012;SOR=0;LSEQ=GTTTGCCTTTAATGCTTCTC;RSEQ=TTAAAAAAAGAGGGGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:72:54,18:139,321:460,72:0.1351:2,2:9.1:1:30.1:1:0:6.90:58.4:71:0.1365:0.1351:0.3 0/0:70:0:0,0:19,51:70,0:0:2,0:17.6:1:30.2:1:1:0:59.6:69:1:0:0.8 +14 35871441 . A AGTAAGCTATTAAAAAAAGG 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=0.00296;SOR=0.46462;LSEQ=ATGCTTCTCTTTAAAAAAAG;RSEQ=GGGGGGGCAGGTACATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:497:308:182,126:16,34:50,308:0.6197:2,2:25.5:1:31.3:1:4e-04:3.06:59.2:153:0.6309:0.1972:0.6 0/1:72:31:23,8:11,29:40,31:0.4306:2,2:22.4:1:31:1:0.00012:7.33:58.9:62:0.4306:0.1667:0.4 +14 35871960 . G A 159 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=82.19869;LSEQ=AGCCTGACTCAGTGCGTCGG;RSEQ=GGCAGGAAGCACCAACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4493:2:1,1:2540,1943:4483,2:4e-04:2,2:11:1:16:1:1:1.30717:60:0:0:0:2 0/1:1330:47:24,23:694,585:1279,47:0.0353:2,2:22.6:1:28.7:1:0.766:1.13678:60:22.5:0.0343:0:1.1 +14 35872068 . G A 200 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=68.63829;LSEQ=AGTGTAGACACGTGTGGCCT;RSEQ=GAAGAACAAAAGGAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4465:6:6,0:1735,2720:4455,6:0.0013:2,0:1.3:1:24.5:1:0.00351:0:60:12:0.0014:0:1 0/1:1442:122:53,69:552,767:1319,122:0.0846:2,2:23.8:1:28.9:1:0.77385:1.07:60:121:0.0845:0:1.2 +14 35872094 . C T 127 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=66.07867;LSEQ=ACAAAAGGAAAAAAGTATAA;RSEQ=CACCTGTTTCAACCCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3123:1:0,1:1070,2046:3116,1:3e-04:2,0:27:0:15:0:1:0:60:0:0:0:3 0/1:964:20:6,14:337,605:942,20:0.0207:2,2:20.6:1:29.5:1:0.64674:1.29939:60:40:0.0211:0:1.2 +14 35872221 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02166;SOR=Inf;LSEQ=AGGCATCCAATAGGCACTTT;RSEQ=CACACATATTTTCTCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:878:0:0,0:541,337:878,0:0:2,0:23.7:1:32.6:1:1:0:59.9:37.174:1:0:0.1 0/1:152:2:0,2:95,55:150,2:0.0132:2,0:21.5:1:27.5:1:0.13907:0:60:4:0.0133:0:1 +14 35872307 . C T 125 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.03071;LSEQ=GCCCACCTGCCCCTTCTCCA;RSEQ=GTCACCTGCCCTCCGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2475:3:0,3:1695,777:2472,3:0.0012:2,0:1:0:26:0:0.03122:0:60:6:0.0012:0:1 0/1:644:19:14,5:431,194:625,19:0.0295:2,2:20.8:1:29.5:1:0.80366:1.26:60:38:0.0298:0:1.1 +14 35872765 . G A 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTTCACTCTCTAGGATGTG;RSEQ=GCTGATGTGAAGTAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:0:0,0:628,134:762,0:0:2,0:24:1:31.4:1:1:0:59.9:37.1:1:0:0.9 0/1:151:9:8,1:123,19:142,9:0.0596:2,2:27.6:1:29.9:1:1:1.23:60:18:0.0616:0:1 +14 35872792 . A G 328 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11868;LSEQ=GTGAAGTAAAAGGTGAGGGT;RSEQ=AATAGTGCTCAGTGGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1076:1049:960,89:23,4:27,1049:0.9749:2,2:23.9:1:32.7:1:0.28341:1.87:59.9:94.364:0.9746:0:1.1 1/1:252:207:197,10:41,1:42,207:0.8214:1,1:24.5:1:31.8:1:0.69615:2.07633:60:68:0.8259:0:1.1 +14 35872835 . ACT A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.83467;SOR=0.96212;LSEQ=TTCAGAAAGGATCTGGGGTG;RSEQ=CTGCTACATCAGCTACGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2282:264:209,55:1532,483:2015,264:0.1157:2,2:25.1:1:32.2:1:0.28094:1.20:59.9:528:0.117:0.0245:0.5 0/1:653:73:49,24:428,152:580,73:0.1118:2,2:22.9:1:30.3:1:0.2624:1.37845:59.9:72:0.1113:0.0276:0.3 +14 35872920 . G T 233 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01114;LSEQ=TGCAGGTTGTTCTGGAAGTT;RSEQ=AGGAAGGCCAGGTCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5599:257:124,133:2686,2653:5339,257:0.0459:2,2:24.3:1:29.2:1:0.52382:1.08589:60:84.667:0.0458:0:1.2 0/0:1870:1:0,1:969,900:1869,1:5e-04:2,0:1:0:22:0:0.48182:0:60:2:5e-04:0:1 +14 35872926 . G A 222 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=145.83518;LSEQ=TTGTTCTGGAAGTTGAGGAA;RSEQ=GCCAGGTCTCCCTTCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5796:4:4,0:2886,2895:5781,4:7e-04:2,0:10.5:1:24.5:1:0.06222:0:60:3:5e-04:0:2.3 0/1:1897:174:90,84:869,853:1722,174:0.0917:2,2:24:1:29.9:1:0.81144:1.05:59.9:348:0.0926:0:1.1 +14 35873369 . T TG 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCCGGCCTAGAGGACGGGTC;RSEQ=GGGGGGAGGGGGCGTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:32.5:1:1:0:60:4:1:0:0.5 0/0:2:0:0,0:1,1:2,0:0:2,0:2:1:27:0:1:0:60:4:1:0:0 +14 35873544 . C T 52 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84684;LSEQ=TGGTCCCCCGGCTCGGGCTC;RSEQ=AGGCCCGGCGCCTCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:4:1,3:314,28:342,4:0.0116:2,2:7.8:1:26.3:1:0.00247:32.80297:60:8:0.0117:0:1 0/0:102:1:1,0:88,13:101,1:0.0098:2,0:14:0:32:0:1:0:60:2:0.0099:0:1 +14 35873553 . C T 47 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14779;SOR=3.26372;LSEQ=GGCTCGGGCTCCAGGCCCGG;RSEQ=GCCTCCCACCCCCAGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:3:1,2:444,63:507,3:0.0059:2,2:19.3:1:29:1:0.0441:13.95925:60:6:0.0061:0:1 0/1:158:3:2,1:130,25:155,3:0.019:2,2:16.3:1:29.7:1:0.41909:2.57937:60:6:0.0194:0:1 +14 35873567 . A T 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=93.12626;LSEQ=GCCCGGCGCCTCCCACCCCC;RSEQ=GGCCGCGCGCGTCCCGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:856:1:0,1:690,159:849,1:0.0012:2,0:1:0:26:0:0.18824:0:60:2:0.0012:0:1 0/1:274:27:22,5:181,64:245,27:0.0985:2,2:21.1:1:29:1:0.48877:1.55:60:12.5:0.0951:0:1.6 +14 35873570 . C T 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00376;SOR=Inf;LSEQ=CGGCGCCTCCCACCCCCAGG;RSEQ=CGCGCGCGTCCCGCCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:916:0:0,0:732,184:916,0:0:2,0:22:1:32.2:1:1:0:60:31.714:1:0:0.3 0/1:303:4:2,2:224,75:299,4:0.0132:2,2:11.5:1:27:1:0.26803:2.97367:60:8:0.0136:0:1 +14 35873770 . G A 373 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11795;LSEQ=AGGCCGCTGTCGTGGCGGTC;RSEQ=TCCAGTAGCCGCTCCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5061:4463:1896,2567:255,331:586,4463:0.8818:2,2:24.9:1:30.8:1:0.65689:1.04306:59.9:68.734:0.8835:0:1.2 0/1:1816:850:373,477:434,532:966,850:0.4681:2,2:23.8:1:29.6:1:0.6703:1.04325:59.9:43.737:0.4674:0:1.2 +14 35873840 . G A 78 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00488;SOR=4.68166;LSEQ=ACTCCTGGGGGCGCTCGGCC;RSEQ=CCTGGAACATGGCGCGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2016:6:6,0:539,1470:2009,6:0.003:2,0:1:0:26.2:1:0.00038:0:60:12:0.003:0:2 0/1:580:8:5,3:178,394:572,8:0.0138:2,2:9.6:1:26.1:1:0.11663:3.68:60:16:0.014:0:1.5 +14 35873905 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCTGGGCCGCGGGCTGCGCG;RSEQ=TGCTTCCTCGCTGGGGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:16,69:85,2:0.023:2,2:26:1:31:1:0.35445:4.21:60:4:0.0233:0:1 0/0:19:0:0,0:3,16:19,0:0:2,0:12.6:1:32.6:1:1:0:60:38:1:0:0.1 +14 35873907 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCCGCGGGCTGCGCGCT;RSEQ=CTTCCTCGCTGGGGCGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:18,64:82,2:0.0235:2,2:37.5:1:28.5:1:0.40333:3.49:60:4:0.0238:0:1 0/0:16:0:0,0:2,14:16,0:0:2,0:12.9:1:32.6:1:1:0:60:32:1:0:0.1 +14 35888950 . G T 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAGTGAGTGCAGAGGCCCG;RSEQ=AGAAGGATGCACCTTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:40,27:67,2:0.029:2,2:7.5:1:27.5:1:1:1.47282:60:4:0.0294:0:2.5 0/0:15:0:0,0:7,8:15,0:0:2,0:21.5:1:29.7:1:1:0:60:30:1:0:0.8 +14 35888987 . A G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGACAGCAGGGAGTCAGC;RSEQ=TGGGGGAAGTCGTGTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:100:51,49:0,0:0,100:1:0,2:25.5:1:31.3:1:1:0:59.1:200:1:0:1.2 1/1:14:14:6,8:0,0:0,14:1:0,2:27.8:1:30.9:1:1:0:60:28:1:0:1.2 +14 36417741 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAATCACAGGCCGGAGGA;RSEQ=ATGGAGGGTAATCACAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16.5:1:30:1:1:0:20:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 36418423 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAGGCTGGAGGATATGGAG;RSEQ=GTAATCACAGGCCGGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29.5:1:1:0:32.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 36492295 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCTTTCCTGTTTTCAG;RSEQ=AGTATAAAGAAGATTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:26,33:59,2:0.0328:2,2:27.5:1:31:1:1:1.26:60:4:0.0333:0:2 0/0:15:0:0,0:7,8:15,0:0:2,0:24.8:1:31.4:1:1:0:60:30:1:0:0.1 +14 36558077 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.31011;LSEQ=TAGCCCCACCCTTATTTAAG;RSEQ=ACACAGTTGGAAGAAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3896:138:56,82:1724,2029:3753,138:0.0354:2,2:25.3:1:32.6:1:0.2242:1.2441:60:137:0.0357:0:2.5 0/1:566:242:112,130:156,168:324,242:0.4276:2,2:26.2:1:31.1:1:0.67136:1.07766:60:241:0.4296:0:2.6 +14 36558089 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=18.71936;LSEQ=TATTTAAGTACACAGTTGGA;RSEQ=GAAGGTCTGTAATACTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3655:120:47,73:1554,1978:3532,120:0.0328:2,2:27:1:31.8:1:0.30505:1.22019:60:39:0.0326:0:2.8 0/1:535:208:92,116:147,178:325,208:0.3888:2,2:27.2:1:30.6:1:0.85845:1.04122:60:207:0.392:0:2.9 +14 36558104 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=46.17337;LSEQ=TTGGAAGAAGGTCTGTAATA;RSEQ=TGCATTTAACTCGCTACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3286:103:37,66:1293,1885:3178,103:0.0313:2,2:27.4:1:30.7:1:0.35978:1.22349:60:102:0.0315:0:2.8 1/0:477:286:117,169:80,110:190,286:0.5996:2,2:25.7:1:29.6:1:0.84936:1.05037:60:572:0.6008:0:2.3 +14 36558246 . G C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.33996;LSEQ=TGATTAGAGTGATGCTTTTT;RSEQ=TTAGGAAAGGGTGAAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:9:0,9:1,262:263,9:0.0331:1,0:24.8:1:34.3:1:1:0:60:18:0.0335:0:1.8 0/1:33:11:0,11:1,21:22,11:0.3333:1,0:29.3:1:32.8:1:1:0:60:22:0.3333:0:1.9 +14 36558266 . A T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.26553;LSEQ=GTTAGGAAAGGGTGAAAGTC;RSEQ=CTGCTATAAGCCATGTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:6:0,6:1,175:176,6:0.033:1,0:21.2:1:31.5:1:1:0:60:12:0.0331:0:2.2 0/1:23:9:0,9:2,12:14,9:0.3913:2,0:19.6:1:29.2:1:0.50198:0:60:18:0.3913:0:2.1 +14 36983065 . A C 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGGCCAGGGTGGGGAGC;RSEQ=GCTTTGGGATGCTAAACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:25.6:1:30.6:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 36983623 . A G 137 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCGGATGGAGCCAGCGT;RSEQ=ATTGATGGCAAGAAAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:20,1:0,0:0,21:1:0,1:25.3:1:31.3:1:1:0:60:20:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 36983798 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATGATAAGGCCGAGGGT;RSEQ=CCACAGCCTACTAAAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:257:257:255,2:0,0:0,257:1:0,1:24.2:1:28.5:1:1:0:59.6:50.4:1:0:1.1 1/1:15:15:14,1:0,0:0,15:1:0,1:20.9:1:28.7:1:1:0:60:30:1:0:1 +14 36983940 . C A 43 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01342;SOR=9.67496;LSEQ=CTGGGGCAGGTTAAGCGAAG;RSEQ=TCCAATTCCGTGGGATCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2368:3:2,1:1889,476:2365,3:0.0013:2,2:21.7:1:16.3:1:0.49091:1.98365:60:0.5:4e-04:0:3.3 0/1:247:3:2,1:180,63:243,3:0.0121:2,2:25.3:1:27.7:1:1:1.42634:60:6:0.0124:0:1.3 +14 36984074 . C T 163 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=26.52886;LSEQ=CACAGCTGACCATTCCAACG;RSEQ=AAGTGGTCAAATTTGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8337:16:1,15:4152,4162:8314,16:0.0019:2,1:3.9:1:23.9:1:0.00051:14.96365:60:7:0.0017:0:1.5 0/1:1338:65:29,36:636,635:1271,65:0.0486:2,2:24.2:1:27.2:1:0.44601:1.24313:60:20.667:0.047:0:1.2 +14 36984376 . G T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGCTCTTGGTGGGGGAGC;RSEQ=GGAGAGAGGGATTGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:114:113:2,111:0,1:1,113:0.9912:0,1:27.5:1:30.4:1:1:0:59.2:112:1:0:2.7 1/1:3:3:0,3:0,0:0,3:1:0,0:33.3:1:27.7:1:1:0:60:6:1:0:2.3 +14 36984383 . A G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGGTGGGGGAGCGGGAGAG;RSEQ=GGGATTGGGAAGAGATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:111:110:2,108:0,0:0,110:0.991:0,1:27.1:1:31.5:1:1:0:59.5:35.667:0.9907:0:2.8 1/1:3:3:0,3:0,0:0,3:1:0,0:31:1:30:1:1:0:60:6:1:0:2.3 +14 36984399 . T C 190 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29043;SOR=0.18119;LSEQ=AGAGAGGGATTGGGAAGAGA;RSEQ=GCAGACGAATAACGAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:100:85:2,83:0,15:15,85:0.85:1,1:24.4:1:29.7:1:1:0:59.3:84:0.8485:0:2.9 1/0:2:1:0,1:0,1:1,1:0.5:0,0:27:0:31:0:1:0:60:2:0.5:0:3 +14 36984603 . A AG 119 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGGCAAGGGTGACCCGGA;RSEQ=GGGCTACAGCCCATCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:1,13:0,2:2,14:0.875:0,1:24.8:1:31.4:1:1:0:60:28:0.875:0.1875:0 1/1:1:1:1,0:0,0:0,1:1:0,0:29:0:34:0:1:0:60:2:1:0:0 +14 36986190 . A AC 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.03704;SOR=0;LSEQ=TTGAATCACCAAAAAAAGAC;RSEQ=CCCCAAAGCTGTTTTATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:44:39,5:9,0:9,44:0.8302:0,2:23.2:1:32.8:1:0.57425:0:59.1:88:0.8302:0.1132:0.4 0/0:2:0:0,0:2,0:2,0:0:0,0:31:1:31.5:1:1:0:41:4:1:0:0 +14 36986218 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGTTTTATGCCCTTCTCT;RSEQ=CTTAAAGATTCCTTGAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:2,0:87,5:92,2:0.0213:2,0:20:1:30:1:1:0:60:4:0.0217:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:19:1:28.8:1:1:0:52.4:4:1:0:0.4 +14 36986265 . C CT 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.07542;SOR=0.32907;LSEQ=GCTTGGTTGTTTTTCATTTT;RSEQ=TTTTTTTAAAAAAAAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:145:142,3:88,5:93,145:0.6042:2,1:22:1:32:1:0.26795:2.68:57.4:35.25:0.613:0.1583:0.6 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:18.5:1:30.6:1:1:0:55.8:8:0.3333:0.0833:0 +14 36986272 . T TTA 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.37433;SOR=0;LSEQ=TGTTTTTCATTTTCTTTTTT;RSEQ=AAAAAAAAAAACCCACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:30:30,0:228,7:235,30:0.1128:1,1:19.1:1:30:1:1:0:57.2:60:0.1163:0.0301:0.6 0/0:12:0:0,0:12,0:12,0:0:0,0:28.3:1:30.9:1:1:0:58.6:24:1:0:0.7 +14 36986273 . A T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.00342;SOR=6.04237;LSEQ=GTTTTTCATTTTCTTTTTTT;RSEQ=AAAAAAAAAACCCACAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:66:64,2:194,5:199,66:0.2472:1,1:19.7:1:30.8:1:1:1.21161:59.4:32:0.249:0:1.2 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:32.3:1:31.5:1:1:0:60:16:0.6667:0:1 +14 36986296 . A AG 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00373;SOR=Inf;LSEQ=AAAAAAAACCCACAAATTTT;RSEQ=GGGGGGGAAAAAAAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:0:0,0:348,6:354,0:0:1,0:24.6:1:26:1:1:0:58.4:5.103:0.9966:0:0.6 0/1:24:2:2,0:22,0:22,2:0.0833:1,0:8:1:30.5:1:1:0:60:4:0.0909:0.0417:1 +14 36986300 . GGGGAAAA TGGGGGGGGG 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.10708;SOR=0.5164;LSEQ=AAAAAAACCCACAAATTTTA;RSEQ=AAAGAAAGACGTCCAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:370:232:228,4:103,3:106,232:0.627:1,1:28.4:1:31.4:1:0.68227:1.66:58.8:115:0.6497:0:0.4 0/1:28:13:13,0:15,0:15,13:0.4643:1,1:15.3:1:30.7:1:1:0:60:26:0.4643:0.1786:0.1 +14 36986304 . AAAA GGGGGG 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACAAATTTTAGGGGGGG;RSEQ=AAAGAAAGACGTCCAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:6:6,0:103,3:106,6:0.0162:1,0:40.5:1:28.4:1:1:0:48.5:12:0.0169:0:1.8 0/0:28:0:0,0:15,0:15,0:0:1,0:21.3:1:32:1:1:0:58.9:30:0.5357:0:0.5 +14 36986307 . AAAAG G 83 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.42806;SOR=2.0563;LSEQ=ACAAATTTTAGGGGGGGAAA;RSEQ=AAGACGTCCAGCAGTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:6:6,0:64,5:69,6:0.0176:2,0:12:0:32.4:1:1:0:59.2:12:0.0811:0:1.2 0/1:28:1:1,0:19,0:19,1:0.0357:1,0:12:0:31.5:0:1:0:60:2:0.0526:0:1 +14 36986598 . G A 88 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0958;SOR=2.71147;LSEQ=GCAGCGCCGCGGGGCTGGCG;RSEQ=CGTGGTGCGCCAGGTCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2621:10:8,2:593,2016:2609,10:0.0038:2,2:12:1:26.5:1:0.00021:13.58:60:20:0.0039:0:1 0/1:389:4:3,1:122,263:385,4:0.0103:2,2:9.5:1:23.3:1:0.09961:6.43:60:3:0.0078:0:1.5 +14 36986634 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03951;SOR=14.79045;LSEQ=CCGGAGACTGGCCTGCGCTG;RSEQ=CTGGCTGGTGGCCCGGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1211:1:0,1:191,1018:1209,1:8e-04:2,0:19:0:32:0:1:0:60:2:8e-04:0:1 0/1:165:2:1,1:43,120:163,2:0.0121:2,2:14:1:29.5:1:0.46341:2.77:60:4:0.0123:0:1 +14 36986669 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00071;SOR=Inf;LSEQ=GGGTGTGCGCCAAGGCCGGC;RSEQ=CCACCGCTGCCCACGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:77,196:273,0:0:2,0:17:1:31.9:1:1:0:60:90:0.9963:0:0.3 0/1:28:3:2,1:6,19:25,3:0.1071:2,2:19.7:1:29:1:0.18803:5.84:60:6:0.1111:0:1.3 +14 36986678 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGCCGGCGCCACCGCT;RSEQ=CCCACGGAGATGGCCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:65,107:172,2:0.0115:2,2:15.5:1:31:1:1:1.64:60:4:0.0117:0:1.5 0/0:17:0:0,0:6,11:17,0:0:2,0:22.5:1:32.4:1:1:0:60:34:1:0:0.4 +14 36986682 . A G 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCGGCGCCACCGCTGCCC;RSEQ=CGGAGATGGCCGCTGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:62,96:158,2:0.0125:2,2:5:1:30:1:1:1.54:60:4:0.0127:0:2.5 0/0:16:0:0,0:6,10:16,0:0:2,0:19.9:1:30.1:1:1:0:60:32:1:0:0.4 +14 36986692 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00768;SOR=Inf;LSEQ=ACCGCTGCCCACGGAGATGG;RSEQ=CGCTGCCGCCGCCTGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:52,77:129,0:0:2,0:14.9:1:31.7:1:1:0:59.7:63.5:0.9922:0:0.4 0/1:13:2:1,1:4,7:11,2:0.1538:2,2:23:1:30.5:1:1:1.67:60:4:0.1538:0:1 +14 36986695 . C T 24 v3;p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCCCACGGAGATGGCCG;RSEQ=TGCCGCCGCCTGCGCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:48,66:114,2:0.0172:2,2:6.5:1:24.5:1:1:1.37:60:4:0.0175:0:1.5 0/0:11:0:0,0:5,6:11,0:0:2,0:12.4:1:31.2:1:1:0:60:22:1:0:0.6 +14 36986706 . T C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGGCCGCTGCCGCCGCC;RSEQ=GCGCGGCCTGCGCCTGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:35,35:70,2:0.0278:2,2:40:0:31.5:1:1:1:60:4:0.0286:0:1.5 0/0:9:0:0,0:5,4:9,0:0:2,0:7.3:1:29:1:1:0:60:18:1:0:0.7 +14 36986741 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01273;SOR=Inf;LSEQ=TGGTGCTGCGCCTGCTGCTG;RSEQ=GCGTGGCCTTGTAGGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:109,60:169,0:0:2,0:20:1:31.4:1:1:0:60:32.8:1:0:0.3 0/1:22:2:1,1:13,7:20,2:0.0909:2,2:24:0:31:0:1:1.80284:60:4:0.0909:0:1.5 +14 36986818 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05176;SOR=9.16406;LSEQ=GCCGTCTTTCACCAGGACCG;RSEQ=CACCGCCACGCGTCGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:2:1,1:442,284:726,2:0.0027:2,2:26:1:28.5:1:1:1.55531:60:4:0.0028:0:2 0/1:81:2:1,1:52,27:79,2:0.0247:2,2:13:1:30.5:1:1:1.90939:60:4:0.025:0:1 +14 36986850 . G T 57 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13116;SOR=3.95435;LSEQ=GTCGCGGCGACTGCTGCTGA;RSEQ=CCTGTTGCTGCTGCGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1589:5:3,2:1171,411:1582,5:0.0031:2,2:21.2:1:24.8:1:0.60986:1.89846:60:4:0.0026:0:2.2 0/1:162:2:1,1:116,44:160,2:0.0123:2,2:15.5:1:28.5:1:0.47964:2.61812:60:4:0.0125:0:1.5 +14 36986866 . G T 51 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00274;SOR=12.08059;LSEQ=CTGAGCCTGTTGCTGCTGCG;RSEQ=GCACCCGGTGCCCCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2001:3:1,2:1460,536:1996,3:0.0015:2,2:15.3:1:28.3:1:0.17818:5.44226:60:6:0.0015:0:1.3 0/1:224:4:1,3:157,63:220,4:0.0179:2,2:21.8:1:25.5:1:0.07786:7.40055:60:8:0.0182:0:1.3 +14 36986888 . CCCG C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.06619;SOR=2.00177;LSEQ=CACCCGGTGCCCCCGCCGCC;RSEQ=CCGCCGCCGCTGTCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2838:38:25,13:2000,794:2794,38:0.0134:2,2:30.5:1:31.2:1:0.46953:1.30971:59.9:76:0.0137:0.0011:0.3 0/1:378:10:5,5:240,126:366,10:0.0265:2,2:26.9:1:27.8:1:0.32712:1.90135:60:9:0.0243:0.0026:0.3 +14 36987119 . C A 31 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00725;SOR=14.47772;LSEQ=AGCACCCGGCGCTTCCTGCG;RSEQ=GGCGCGCTTGGCAGCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2603:2:2,0:1127,1467:2594,2:8e-04:2,0:1:0:27:1:0.18904:0:60:4:8e-04:0:1 0/1:272:3:3,0:111,156:267,3:0.011:2,0:7:1:20:1:0.07412:0:60:2:0.0075:0:1.3 +14 36987198 . C T 36 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01787;SOR=8.61365;LSEQ=CCATGCCGCTCATGTTCATG;RSEQ=CGCTCGCCGGGCCCATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2402:3:2,1:952,1445:2397,3:0.0012:2,2:14.3:1:32:0:0.56687:3.03:60:6:0.0013:0:1 0/1:281:3:1,2:128,150:278,3:0.0107:2,2:13.3:1:23.3:1:1:1.70355:60:2:0.0074:0:2.7 +14 36987253 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01131;SOR=Inf;LSEQ=CGACAAACGCACAGCGTCGG;RSEQ=CGGGGCCAGGCCGAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1382:0:0,0:411,969:1380,0:0:2,0:24.7:1:31.3:1:1:0:60:52.077:0.9985:0:0.2 0/1:165:2:1,1:64,99:163,2:0.0121:2,2:33:1:29:1:1:1.54:60:4:0.0123:0:1.5 +14 36987283 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01019;SOR=Inf;LSEQ=GCCGAGCCAGGCCACCCCTG;RSEQ=TTTCCGCGCCATTGGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:797:0:0,0:131,665:796,0:0:2,0:23.2:1:30.2:1:1:0:59.9:65.333:0.9987:0:0.2 0/1:90:2:1,1:25,62:87,2:0.0222:2,2:9:1:30:1:0.50128:2.45:60:4:0.0225:0:1 +14 36988175 . G A 313 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCCCGCGGCCCCGCAGTGG;RSEQ=GCGGCCTCACTTACTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1726:1414:960,454:211,99:310,1414:0.8192:2,2:23.8:1:30:1:1:1.00793:60:25.679:0.8159:0:1.3 0/0:235:0:0,0:143,92:235,0:0:2,0:24.1:1:29.4:1:1:0:59.9:38.167:1:0:0.3 +14 36988274 . G A 60 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.047;SOR=4.95742;LSEQ=GGTGTCCTGGTACGGCGGCA;RSEQ=CTCGCTCATGTTGCCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2230:5:5,0:1025,1198:2223,5:0.0022:2,0:1:0:26.2:1:0.02101:0:60:10:0.0023:0:1.2 0/1:272:3:2,1:125,144:269,3:0.011:2,2:22.3:1:31.7:1:0.60028:2.30:60:6:0.0111:0:1.3 +14 36988279 . C A 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01139;SOR=12.12028;LSEQ=CCTGGTACGGCGGCAGCTCG;RSEQ=TCATGTTGCCCAGGTTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2180:2:2,0:987,1186:2173,2:9e-04:2,0:1:0:28:0:0.20665:0:60:4:9e-04:0:1 0/1:272:3:2,1:118,150:268,3:0.011:2,2:6.7:1:26.3:1:0.58573:2.53:60:6:0.0114:0:1.3 +14 36988331 . G A 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00413;SOR=26.05194;LSEQ=CCCCACGGCGGAGTGCGAGA;RSEQ=CTGGGGCACCCCCGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1692:1:1,0:615,1075:1690,1:6e-04:2,0:1:0:27:0:0.36428:0:60:2:6e-04:0:1 0/1:197:3:2,1:71,123:194,3:0.0152:2,2:17.3:1:29.3:1:0.55638:3.44:60:6:0.0157:0:1 +14 36988345 . G A 67 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22198;SOR=2.61304;LSEQ=GCGAGAGCTGGGGCACCCCC;RSEQ=CCGCCGTCATGTGGTAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1563:7:5,2:519,1036:1555,7:0.0045:2,2:8.6:1:23.9:1:0.04614:4.98:60:2.5:0.0033:0:1.1 0/1:172:2:1,1:64,105:169,2:0.0116:2,2:6.5:1:27:1:1:1.64:60:4:0.0119:0:1 +14 36988369 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00786;SOR=Inf;LSEQ=CCGTCATGTGGTAGGCGGCG;RSEQ=TGACGGCGCCGTGGTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1434:0:0,0:585,847:1432,0:0:2,0:22:1:31.7:1:1:0:60:64.091:0.9993:0:0.1 0/1:140:2:1,1:58,79:137,2:0.0143:2,2:15.5:1:33.5:1:1:1.36:60:4:0.0145:0:1 +14 36988419 . C T 96 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03335;SOR=3.3551;LSEQ=TGCTGCATGGCCGCTGTTGG;RSEQ=GGTGCCGCCTGGCCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2566:12:5,7:1720,832:2552,12:0.0047:2,2:11.4:1:26.9:1:0.06858:2.89291:59.4:11:0.0044:0:1.5 0/1:322:5:2,3:213,103:316,5:0.0155:2,2:14.8:1:25.2:1:0.33643:3.08993:60:4:0.0126:0:1.2 +14 36988598 . GA G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.60357;SOR=1.1614;LSEQ=GGAGGAGGAAGGAAGAGGAG;RSEQ=AAAAAAAGGGAGAGGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5117:61:27,34:1993,3055:5048,61:0.0119:2,2:30.2:1:32:1:0.51038:1.22:59.9:122:0.0122:4e-04:0.1 0/1:796:11:4,7:319,464:783,11:0.0138:2,2:22.6:1:30.2:1:1:1.20283:60:22:0.0143:0.0013:0.2 +14 36988635 . C CT 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.26469;SOR=1.41391;LSEQ=GGGAAGGCGAAGCCTCGCTG;RSEQ=TTTTTTTTTCTCCCTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2517:63:12,51:590,1854:2444,63:0.025:2,2:26.4:1:30.9:1:0.45468:1.35231:59.6:62:0.0253:0:0.2 0/1:314:11:2,9:70,232:302,11:0.035:2,2:29.1:1:27.2:1:1:1.35652:60:10:0.0332:0:0.3 +14 36989078 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00533;SOR=Inf;LSEQ=AACCGAGAGCGGGGAGGGCA;RSEQ=GAGGTGGGGTGGGGGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:457,31:488,0:0:2,0:23.6:1:33.1:1:1:0:59.8:68.714:1:0:0.2 0/1:39:2:2,0:31,6:37,2:0.0513:2,0:17.5:1:30.5:1:1:0:60:4:0.0513:0:1 +14 36989188 . C T 76 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00072;SOR=6.79498;LSEQ=AGTGGAACCACTTTCCAATT;RSEQ=GGTCGGGGTTCCCCGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4003:8:0,8:2792,1203:3995,8:0.002:2,0:1:0:25.6:1:7e-05:0:60:16:0.002:0:1 0/1:521:7:1,6:329,185:514,7:0.0134:2,2:5.7:1:25.3:1:0.01118:10.62402:60:6:0.0119:0:1.3 +14 36989596 . A G 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11754;SOR=17.32762;LSEQ=ACAACCCGCCCCCGCAGCTC;RSEQ=GGGGTTTTTCAGTGGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:4:0,4:2,75:77,4:0.0494:1,0:20.5:1:32.8:1:1:0:60:8:0.0513:0:1.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:1:0:29:0:1:0:60:2:0.5:0:1 +14 36989638 . A C 158 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCTAACACGCCTCCCCC;RSEQ=AGGTCTTCCCCCCCCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:32:1,31:0,2:2,32:0.8:0,1:18.8:1:31.7:1:1:0:58.1:31:0.8611:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 36989645 . TCCCC T 127 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGCCTCCCCCAAGGTCT;RSEQ=CCCCCCCCCCACCCCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:18:0,18:2,7:9,18:0.6207:2,1:29.8:1:30.5:1:0.10256:0:56.6:36:0.7826:0.1379:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 36990890 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00051;SOR=Inf;LSEQ=CCTCCGCCCTCCCACCTGCG;RSEQ=CCGCGTTTTTGTGCGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:709,19:728,0:0:1,0:25:1:32.4:1:1:0:59.8:59.667:1:0:0.1 0/1:64:3:3,0:60,1:61,3:0.0469:1,0:21.7:1:29.7:1:1:0:60:6:0.0469:0:1 +14 36990941 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01155;SOR=Inf;LSEQ=CTGGGGAGGCCACCCTACGT;RSEQ=TGCGCAGGGAGACGCGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1615:0:0,0:1335,280:1615,0:0:2,0:23.7:1:30.7:1:1:0:59.9:61.115:1:0:0.1 0/1:195:2:1,1:153,40:193,2:0.0103:2,2:18.5:1:27:1:0.37716:3.79039:60:4:0.0104:0:1 +14 36990957 . G T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01165;SOR=12.00896;LSEQ=ACGTTTGCGCAGGGAGACGC;RSEQ=CTCGCCGCTGGTGTTGCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2200:2:1,1:1642,551:2193,2:9e-04:2,2:3:0:31.5:1:0.4398:2.97822:60:4:9e-04:0:1.5 0/1:277:3:1,2:188,86:274,3:0.0108:2,2:20.3:1:27.3:1:0.23779:4.34632:60:6:0.0111:0:1 +14 36991229 . C T 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGTGGGTTTCCCAGTCAC;RSEQ=CAGCTTCTTTCTCTCACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1317:0:0,0:26,1290:1316,0:0:1,0:25.2:1:31.5:1:1:0:59.9:44.379:1:0:0.1 0/1:140:9:0,9:2,129:131,9:0.0643:1,0:24.4:1:29.1:1:1:0:60:18:0.0672:0:1.1 +14 37050384 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01153;SOR=Inf;LSEQ=CTGCCAGGTCAGGCGACTCC;RSEQ=CCGCCCCTGGAGCGCGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:769:0:0,0:544,225:769,0:0:2,0:22.1:1:30.3:1:1:0:60:84.444:1:0:0.1 0/1:93:2:1,1:55,36:91,2:0.0215:2,2:18:0:27.5:1:1:1.52059:60:4:0.0217:0:1 +14 37050396 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.01237;SOR=Inf;LSEQ=GCGACTCCGCCGCCCCTGGA;RSEQ=CGCGAGCGCGCTTCAGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:899:0:0,0:593,304:897,0:0:2,0:24.7:1:32.5:1:1:0:59.9:55.063:0.9989:0:0.1 0/1:113:2:1,1:64,45:109,2:0.0177:2,2:21.5:1:27.5:1:1:1.4176:60:4:0.0177:0:1 +14 37050436 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01271;SOR=Inf;LSEQ=GTAGCGATGATTCTGGAACC;RSEQ=GATCTTGACCTGCGTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1326:0:0,0:743,583:1326,0:0:2,0:27.9:1:31:1:1:0:59:50:1:0:0.2 0/1:169:2:1,1:86,81:167,2:0.0118:2,2:30.5:1:28:1:1:1.06138:60:4:0.0123:0:1 +14 37052721 . C G 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCCCATAGCCTCAACGGCA;RSEQ=TCTCACTGCCTGGGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:34.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 37127253 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.1;SOR=Inf;LSEQ=CCAGCGGTCCAGGGCGGACC;RSEQ=TCCCTCGCCCTGGGCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:17.3:1:31.7:1:1:0:60:6:1:0:0.7 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:27.5:1:1:0:60:4:1:0:1 +14 37128564 . C A 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTCGTCTCTCGGTCGGT;RSEQ=TCAGCGGGTCGCTGACTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 38054959 . AGT A 108 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.69986;SOR=0.44766;LSEQ=CAAATGTACTCCTTTTTAAA;RSEQ=GTGTGTGTGTTGGGGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:963:10:10,0:951,2:953,10:0.0104:1,0:21.1:1:32.6:1:1:0:54.5:20:0.0107:0:1.5 0/0:214:1:1,0:212,1:213,1:0.0047:1,0:28:0:27:0:1:0:60:2:0.0048:0:0 +14 38054972 . T TG 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00332;SOR=0.59582;LSEQ=TTTTAAAAGTGTGTGTGTGT;RSEQ=GGGGGGGGGGGCGGGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:990:284:284,0:599,10:609,284:0.2869:1,1:31.3:1:32.9:1:0.03572:0:58.7:70:0.3118:0:1.7 0/1:238:46:42,4:165,3:168,46:0.1933:1,2:28.3:1:30.3:1:0.03994:5.18356:59:14.333:0.1991:0.0378:1.8 +14 38054994 . G T 73 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34942;SOR=1.51768;LSEQ=GGGGGGGGGGCGGGGGGATT;RSEQ=GCTAAGGAGGTTTCCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2093:21:9,12:1258,811:2069,21:0.01:2,2:16:1:16.7:1:0.11599:2.06752:56.2:0.313:0.0027:0:3.4 0/1:528:8:3,5:304,214:518,8:0.0152:2,2:19.1:1:21.4:1:0.28689:2.36369:60:1.667:0.0105:0:2.1 +14 38055101 . A G 344 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.50224;LSEQ=CTTGGTTTCAGAAATTAAAT;RSEQ=AAGAGAAAAGAAAAAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2196:1819:655,1164:132,245:377,1819:0.8283:2,2:23.8:1:31.8:1:0.72377:1.04:60:57.677:0.8266:0:1.8 1/0:575:407:158,249:64,104:168,407:0.7078:2,2:25.3:1:30.3:1:0.92503:1.03:59.8:49.875:0.7037:0:1.7 +14 38055123 . G C 326 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.44826;LSEQ=AGAGAAAAGAAAAAGCCCCT;RSEQ=ATGTGTAATCTTGAAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1411:1121:267,854:86,200:286,1121:0.7945:2,2:23.1:1:32.2:1:0.03242:1.37504:60:100.909:0.7963:0:2.2 1/0:377:239:69,170:39,96:135,239:0.634:2,2:23.2:1:30.9:1:1:1.0009:59.8:78.667:0.631:0:2.2 +14 38055177 . C T 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1328;LSEQ=AAAAGTTAAACCAAGGCAAC;RSEQ=TCACACTTAAATTCTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:479:391:6,385:0,88:88,391:0.8163:1,1:23.4:1:30.3:1:0.5982:0:59.9:38.1:0.8141:0:2.2 0/1:100:37:0,37:1,62:63,37:0.37:1,1:24.3:1:29.6:1:1:0:60:74:0.3737:0:2.4 +14 38055445 . C T 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAGGGGGAGGAGTGCT;RSEQ=ACTCTCACCATGTGCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:21.6:1:27:1:1:0:56.4:14:0.875:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 38058065 . C T 192 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=88.59001;LSEQ=GTTGGGATTGGAAGCTTTTT;RSEQ=CTCTCTTTGGGACTTTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3658:5:1,4:1675,1975:3650,5:0.0014:2,2:16.4:1:28.2:1:0.38323:3.39132:60:10:0.0014:0:1 0/1:970:105:48,57:404,460:864,105:0.1082:2,2:26.8:1:28.7:1:0.91756:1.0429:59.9:51.5:0.1083:0:1.1 +14 38058622 . AC A 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAATGCAAAATAGCGGCT;RSEQ=CCTAAAATGTCCTGTCGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:26.3:1:31.3:1:1:0:60:8:0.8:0:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 38060427 . T A 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTTGCACTGGGGGAAAGGT;RSEQ=GTGCATGAAAAATGAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:821:0:0,0:801,20:821,0:0:1,0:26:1:31.4:1:1:0:59.9:90.222:1:0:0.1 0/1:154:7:7,0:143,4:147,7:0.0455:1,0:21.4:1:29:0:1:0:60:14:0.0458:0:1.1 +14 38060646 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00079;SOR=1.62602;LSEQ=GGGCTGAGGGCTCGATGGGG;RSEQ=TCCTGGTGGTCACCGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5409:188:85,103:2586,2633:5219,188:0.0348:2,2:25.5:1:30.2:1:0.2655:1.19009:60:93:0.0351:0:1.1 0/1:1392:77:37,40:655,658:1313,77:0.0553:2,2:22.8:1:28.7:1:0.8149:1.07607:60:37.5:0.0549:0:1.2 +14 38060768 . G A 232 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05847;LSEQ=TTATGCTGCTGCTCCGAGGA;RSEQ=GACATGAGGTTGTTGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7224:172:93,79:3566,3481:7047,172:0.0238:2,2:25.2:1:31.3:1:0.39614:1.15:59.3:85:0.0238:0:1.1 0/0:2107:3:3,0:1062,1039:2101,3:0.0014:2,0:1:0:26.7:1:0.24976:0:53.3:6:0.0014:0:1 +14 38061106 . T A 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00869;SOR=0;LSEQ=AGAGGCGCCAGAGGGGTCCT;RSEQ=GCGGCTCTCAGGGCCGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:753:28:20,8:378,346:724,28:0.0372:2,2:22:1:30.1:1:0.05362:2.29:60:56:0.0377:0:1.3 0/0:155:0:0,0:81,74:155,0:0:2,0:19.5:1:29.7:1:1:0:60:50.667:1:0:0.1 +14 38061137 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02646;SOR=Inf;LSEQ=GGGCCGCCCTTGGCGCCGCT;RSEQ=CCCCCGCTTCCGCTCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:785:0:0,0:628,156:784,0:0:2,0:23.2:1:32.5:1:1:0:59.9:48:0.9987:0:0.1 0/1:153:2:2,0:116,35:151,2:0.0131:2,0:17.5:1:29.5:1:1:0:60:4:0.0133:0:1 +14 38061649 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00162;SOR=Inf;LSEQ=CTGCTGCGCACCCATGGCGC;RSEQ=CATGCCGCTCGGGCTCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:959:0:0,0:599,360:959,0:0:2,0:23.6:1:31.1:1:1:0:60:49.474:1:0:0.2 0/1:242:4:0,4:134,104:238,4:0.0165:2,0:10.8:1:25.3:1:0.03845:0:60:8:0.0169:0:1 +14 38061742 . C T 319 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0.63947;LSEQ=CGAGCCCCCCGGCATGCCGG;RSEQ=TACTGCGCCGGGACTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2069:1650:1236,414:307,107:414,1650:0.7975:2,2:23.2:1:29.9:1:0.752:1.04:60:102.125:0.799:0:1.1 1/0:496:355:249,106:99,42:141,355:0.7157:2,2:20.6:1:28.8:1:1:1.00344:60:58.167:0.7166:0:1.1 +14 38062062 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACCCGGGGCAAATGGCTAA;RSEQ=CGCCCTCCCCAGACCGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:0,2:2,194:196,2:0.0101:1,0:25:1:31:1:1:0:60:4:0.0102:0:1 0/0:15:0:0,0:0,15:15,0:0:1,0:19.5:1:32:1:1:0:60:30:1:0:0.1 +14 38062506 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TAAGTTTTGGAAAAATAAAA;RSEQ=TAAAAGTAGATCCATAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:32.5:1:34:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:29:1:1:0:60:4:1:0:1 +14 38064009 . G C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44611;SOR=2.92363;LSEQ=CGAGAAGGCGCCCCCGGCCC;RSEQ=CCTGCCTGCCTTGCCTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:61:57,4:9,1:10,61:0.8592:2,2:8:1:31.3:1:0.54307:1.57:60:60:0.8571:0:1.2 1/1:19:18:16,2:1,0:1,18:0.9474:0,2:8.5:1:31.1:1:1:0:60:36:0.9474:0:1.3 +14 38064215 . G C 369 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38615;LSEQ=CAATACAACCATCCAGCCCT;RSEQ=TGCGAAGCGACGGGCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3109:2502:785,1717:194,405:599,2502:0.8048:2,2:24.7:1:32.7:1:0.65966:1.04771:60:74.818:0.8061:0:1.1 1/0:767:471:158,313:105,185:290,471:0.6141:2,2:25.6:1:30.9:1:0.48024:1.12418:59.9:46.1:0.6122:0:1.2 +14 38064738 . G T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTAGGGAAAGAGGGAAAT;RSEQ=GGGAGGGAGGGGGTGTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:25:1:28.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 38068148 . C A 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=40.76028;LSEQ=CGCGGGCCCCCACCCCCCAC;RSEQ=CAGATAAGAAGCTTAAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2569:7:7,0:256,2305:2561,7:0.0027:2,0:1:0:26.9:1:0:0:60:14:0.0029:0:1.1 0/1:618:62:28,34:55,500:555,62:0.1003:2,2:28.1:1:29.1:1:0:7.44:60:30:0.1024:0:1.1 +14 38068225 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03152;SOR=Inf;LSEQ=AGACCTGTGGTCGTTAACGC;RSEQ=GTTCAAAGCCGACCCCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:0:0,0:10,751:761,0:0:1,0:23.9:1:31.2:1:1:0:60:39.053:0.9987:0:0.3 0/1:165:2:0,2:1,161:162,2:0.0121:1,0:27.5:1:31:1:1:0:60:4:0.0126:0:1.5 +14 38068315 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGTCACACGTGCGTGTG;RSEQ=CTGGCCTTCGCAGGTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:0,2:2,153:155,2:0.0127:1,0:9.5:1:31.5:1:1:0:60:4:0.0136:0:1 0/0:24:0:0,0:1,23:24,0:0:1,0:19.5:1:31.5:1:1:0:58.6:48:1:0:0.5 +14 38345849 . A G 313 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0445;LSEQ=AGTCTGAAGTTTTTCTACAG;RSEQ=GTATATTTATCACCATAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1266:1080:470,610:84,100:184,1080:0.8531:2,2:25.3:1:31.1:1:0.62979:1.09014:60:66.5:0.8539:0:1.1 0/1:410:84:30,54:145,181:326,84:0.2049:2,2:23.3:1:29.7:1:0.17373:1.44072:60:20:0.2:0:1.1 +14 38882673 . T A 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=0;LSEQ=AAAGACCTCATCCAAAGGTC;RSEQ=GCATCCTCAAAGACTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:7,3:2,3:5,10:0.6667:2,2:27.6:1:31.9:1:0.32867:3.20:41.3:20:0.6667:0:1.1 0/0:2:0:0,0:1,1:2,0:0:2,0:35:0:32:0:1:0:46:4:1:0:0.5 +14 38882750 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02222;SOR=Inf;LSEQ=AAAATGCTGAAAACCCAAAA;RSEQ=GCCAGAGTGCCTCTTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,5:7,0:0:2,0:18.3:1:32:1:1:0:38.4:14:0.875:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:28.5:1:1:0:25:4:1:0:1.5 +14 38910644 . G C 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=TAAGAGTCTATGCCATAGGA;RSEQ=GTACCATGGGAGTTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:12.8:1:33.4:1:1:0:60:10:0.7143:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:30:0:1:0:60:2:1:0:0 +14 38910766 . TAG T 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03652;SOR=0;LSEQ=CAGAGCCATCTTAAGGTTTA;RSEQ=AGTCTCAGTGAGCTCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:7,9:1,5:6,16:0.7273:2,2:21.6:1:31.7:1:0.35116:3.68:60:32:0.7273:0.1364:0 0/0:3:0:0,0:1,2:3,0:0:2,0:14.7:1:30.3:1:1:0:60:6:1:0:0 +14 38912633 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTACACTCCTTCCAATGG;RSEQ=GTATAAGCATTCCCTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 38937149 . A C 52 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGCTGGCTGCTGACCTTC;RSEQ=CACAAGGAGCTCAAATGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:21:1:33:1:1:0:57.7:6:1:0:1.3 1/1:2:2:2,0:0,0:0,2:1:0,0:9:1:31:1:1:0:60:4:1:0:2.5 +14 39630513 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAACCTATACACATTTA;RSEQ=TTATCAACTCTAGTTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:8,1:9,2:0.1818:2,0:42:1:33:1:1:0:60:4:0.1818:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:22:0:32:0:1:0:60:2:1:0:0 +14 39630822 . A T 317 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26267;LSEQ=GCCTTCACTTAAGCTCGCTC;RSEQ=CTCCGTGTCTGGCGAGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1271:1200:673,527:41,29:70,1200:0.9441:2,2:26.9:1:31:1:0.71171:1.10696:59.3:56.143:0.944:0:1.1 1/1:549:448:239,209:53,47:100,448:0.816:2,2:26.9:1:29.2:1:1:1.01:59:39.727:0.8168:0:1.1 +14 39630971 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08111;SOR=Inf;LSEQ=CACTAGCCTCCTGCAGCACC;RSEQ=CAATGACTGTGCTCTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:241,260:501,0:0:2,0:22.3:1:31.1:1:1:0:60:44.545:1:0:0.1 0/1:200:2:1,1:102,96:198,2:0.01:2,2:23.5:1:27:1:1:1.06221:60:4:0.0103:0:1 +14 39631046 . A G 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02709;SOR=Inf;LSEQ=TCACCAACCTCTAGAAAGGC;RSEQ=GCTTCCAGATGAGAAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:608:0:0,0:249,359:608,0:0:2,0:25.9:1:31:1:1:0:60:75:1:0:0.1 0/1:262:3:1,2:112,147:259,3:0.0115:2,2:20.3:1:25.7:1:1:1.52146:60:2:0.0079:0:1 +14 46730763 . T C 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07886;SOR=7.25322;LSEQ=ATTTTATAACACTATAAATG;RSEQ=ATTTTAGGGATTTGAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:1,0:27,3:30,1:0.0323:2,0:9:0:28:0:1:0:60:2:0.0333:0:1 0/1:25:5:5,0:18,1:19,5:0.2:1,0:31.6:1:31.2:1:1:0:60:10:0.2083:0:2 +14 46730797 . G T 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=26.25534;LSEQ=GAGGTTTTATTGTTTCTTTT;RSEQ=CCTTTCTTACATTTTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:1:1,0:58,14:72,1:0.0137:2,0:6:0:34:0:1:0:60:2:0.0139:0:1 0/1:59:16:13,3:31,12:43,16:0.2712:2,2:17.1:1:27.6:1:0.7376:1.66:60:15:0.2586:0:1.4 +14 46730800 . T C 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTTTTATTGTTTCTTTTGCC;RSEQ=TTCTTACATTTTAATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:62,16:78,0:0:2,0:24:1:32.2:1:1:0:59.7:77:1:0:0.2 0/1:61:13:8,5:37,11:48,13:0.2131:2,2:19.4:1:29.8:1:0.2968:2.07417:60:26:0.2131:0:1.1 +14 46730802 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=TTTATTGTTTCTTTTGCCTT;RSEQ=CTTACATTTTAATATATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:64,15:79,2:0.0247:2,2:23:1:28.5:1:0.35802:4.16333:60:4:0.0263:0:1 0/0:64:0:0,0:47,17:64,0:0:2,0:21.3:1:28.9:1:1:0:60:128:1:0:0.6 +14 46730842 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50434;SOR=0;LSEQ=TTTGGAAATCTTGACTGTAA;RSEQ=CACTATCTGAAAATAAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:105,43:148,2:0.0133:2,2:25:1:29:1:0.50201:2.42544:60:4:0.0137:0:1 0/0:120:0:0,0:70,50:120,0:0:2,0:26.9:1:31.5:1:1:0:60:119:1:0:0.6 +14 46730851 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.1951;SOR=Inf;LSEQ=CTTGACTGTAAGCACTATCT;RSEQ=AAAATAAAGTTGAAAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:113,57:170,0:0:2,0:25.8:1:32:1:1:0:59.9:55.667:1:0:0.2 0/1:135:2:1,1:78,55:133,2:0.0148:2,2:8.5:1:27.5:1:1:1.41442:60:4:0.0149:0:1 +14 46730853 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20214;SOR=Inf;LSEQ=TGACTGTAAGCACTATCTGA;RSEQ=AATAAAGTTGAAAATATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:113,59:172,0:0:2,0:25.9:1:29.9:1:1:0:59.9:27.667:1:0:0.2 0/1:141:2:1,1:81,58:139,2:0.0142:2,2:40.5:1:31:1:1:1.39317:60:4:0.0143:0:1 +14 46730899 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=8.88467;LSEQ=TCTTTGGTGAGTAAATAATA;RSEQ=CAATTAATACCACTTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:25:15,10:110,109:219,25:0.1025:2,2:21.1:1:31.4:1:0.40285:1.48:60:50:0.1037:0:1.1 1/0:204:103:53,50:49,52:101,103:0.5049:2,2:23.7:1:30.3:1:0.77951:1.12:60:33.333:0.5025:0:1.1 +14 46730999 . CAGTGAGT GAGG 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15196;SOR=Inf;LSEQ=CCAGAAGGGGCAAATCCAAG;RSEQ=AAGTGGTAGAAACAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:19,70:89,0:0:2,0:22.2:1:31.9:1:1:0:60:43.5:0.9886:0:0.1 0/1:58:2:1,1:14,42:56,2:0.0345:2,2:10:1:28:1:0.45372:2.93:60:4:0.0351:0.0172:0 +14 46731001 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15603;SOR=Inf;LSEQ=AGAAGGGGCAAATCCAAGCA;RSEQ=TGAGTAAGTGGTAGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:17,68:85,0:0:2,0:22.3:1:32.5:1:1:0:60:84:1:0:0.1 0/1:56:2:1,1:12,41:53,2:0.0357:2,2:37:1:30.5:1:0.4202:3.32:60:4:0.0364:0:1 +14 46732517 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGCGATTTTGGTTATC;RSEQ=TGAGTTGAACCTTCATTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:29.5:1:1:0:60:4:1:0:1.5 +14 46853609 . C G 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.27494;SOR=2.71757;LSEQ=AAGACGCAGAAACAGTATTG;RSEQ=CCCCAAAGGGCTGGGCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:8,0:10,0:10,8:0.4444:0,0:29:1:32.4:1:1:0:59.4:16:0.4444:0:2 1/0:13:9:8,1:4,0:4,9:0.6923:0,2:24.8:1:28.2:1:1:0:57.3:8:0.6667:0:2.3 +14 46853617 . G T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16619;SOR=3.21651;LSEQ=GAAACAGTATTGCCCCCAAA;RSEQ=GGCTGGGCGTGCTGATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:9:9,0:12,0:12,9:0.4286:0,0:32.2:1:32.4:1:1:0:59.1:18:0.4286:0:1.9 1/0:14:10:8,2:4,0:4,10:0.7143:0,2:21.8:1:28.4:1:1:0:57.6:9:0.6923:0:2.2 +14 46853709 . A T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15173;SOR=0;LSEQ=TTGATAAGGTCAAGCAAGTC;RSEQ=CGTGATCATGGGACAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:4:2,2:26,36:62,4:0.0606:2,2:16.5:1:29.8:1:1:1.38:40.5:8:0.0635:0:1.3 0/0:43:0:0,0:19,24:43,0:0:2,0:24.3:1:28.6:1:1:0:35.4:42:1:0:0.2 +14 46853878 . G A 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=ACTTCAAAGAGGAACCAGGA;RSEQ=TATGGGAGGAACGTGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:3,1:4,1:0.2:2,0:30:0:33:0:0.4:0:29:2:0.2:0:1 1/1:3:3:0,3:0,0:0,3:1:0,0:14.7:1:32:0:1:0:47.3:6:1:0:1 +14 47138865 . A C 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72707;LSEQ=CCTGGGTCTCCAGCTAGCCA;RSEQ=CTGCAGATCTTGAAACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:15,11:26,2:0.0714:2,0:16:1:31:1:0.50529:0:60:4:0.0741:0:1.5 0/1:19:1:1,0:10,8:18,1:0.0526:2,0:11:0:33:0:1:0:60:2:0.0526:0:1 +14 48351255 . A C 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATAAGTAGGCAGTAGT;RSEQ=AGAGATATGGAGATCAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:35.7:1:31.7:1:1:0:60:6:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 48351280 . T A 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATATGGAGATCAACTATAGA;RSEQ=GAGATGAGTCATGGCCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:17:1:30.3:1:1:0:60:6:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 48351622 . G T 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43416;LSEQ=CACTTGAAAAACATCATGTC;RSEQ=TGGTAAAAGAGAAAGTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:437:355:161,194:38,44:82,355:0.8124:2,2:25.6:1:30.8:1:0.90245:1.04058:60:43.375:0.8107:0:1.2 1/0:400:261:112,149:60,79:139,261:0.6525:2,2:26.8:1:29.4:1:1:1.01037:60:86:0.6548:0:1.1 +14 48351664 . A G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1862;LSEQ=ATTTTTTCCAGTGGAAGAAA;RSEQ=TGTGGATTTTATCAAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:46:21,25:78,174:252,46:0.1544:2,2:28.5:1:33:1:0.06138:1.87:60:92:0.1549:0:1.8 0/1:244:8:4,4:70,166:236,8:0.0328:2,2:14.4:1:32.8:1:0.24946:2.36:60:16:0.0331:0:2.1 +14 48577206 . G A 34 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGAACCACTTGACTTCA;RSEQ=GAAGAATGAGATTTTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:31:1:34:0:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:8:0:31:0:1:0:60:2:1:0:0 +14 49042424 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51234;SOR=0;LSEQ=TTTGAAGGGATTTTTGTGTC;RSEQ=CTATGTCCTTCAGTTCTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:17,13:30,2:0.0625:2,2:31.5:1:29.5:1:1:1.29665:37.5:4:0.0625:0:1 0/0:21:0:0,0:12,9:21,0:0:2,0:26.5:1:30:1:1:0:46.9:42:1:0:0.1 +14 49557446 . C T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=1.63931;LSEQ=GATCCAATGAGTTTTTGGAC;RSEQ=CAGCTTGTAGGTCCCTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:733:371:172,199:160,199:359,371:0.5061:2,2:27:1:30.7:1:0.6558:1.07:60:91.75:0.5069:0:1.5 1/0:571:358:165,193:100,113:213,358:0.627:2,2:25.3:1:28.9:1:0.86251:1.03509:60:70.6:0.6326:0:1.4 +14 49557507 . T A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04557;SOR=0.11876;LSEQ=ATATATACCCTGGCCTGTGG;RSEQ=ATAGGGGCATTATGGTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:381:380:107,273:0,0:0,380:0.9974:0,2:24.1:1:30.6:1:1:0:60:37:1:0:1.4 1/1:276:270:91,179:2,4:6,270:0.9783:2,2:23.7:1:29:1:1:1.02:60:37.571:0.9777:0:1.5 +14 49557539 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16328;SOR=Inf;LSEQ=ATGGTAGAAAGAGCTTAGTA;RSEQ=AAACCACTAAAATGACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:40,179:219,0:0:2,0:23.6:1:32.2:1:1:0:60:35.5:1:0:1 0/1:149:2:1,1:34,113:147,2:0.0134:2,2:13.5:1:28.5:1:0.41584:3.29:60:4:0.0135:0:1.5 +14 49557544 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15882;SOR=Inf;LSEQ=AGAAAGAGCTTAGTAGAAAC;RSEQ=ACTAAAATGACCTCCCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:32,171:203,0:0:2,0:23.2:1:32.2:1:1:0:60:49.75:1:0:0.9 0/1:135:2:1,1:28,105:133,2:0.0148:2,2:23.5:1:27:1:0.38474:3.70:60:4:0.0149:0:2 +14 49557562 . G T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13052;SOR=Inf;LSEQ=ACCACTAAAATGACCTCCCA;RSEQ=TAATATTATCTCTGACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:18,142:160,0:0:2,0:21.5:1:31.7:1:1:0:60:21.857:1:0:0.8 0/1:91:2:1,1:10,79:89,2:0.022:2,2:6.5:1:29:1:0.22833:7.58:60:4:0.0225:0:2 +14 49557672 . C A 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53924;SOR=0;LSEQ=CTCCATCAGCCAGAAATAGC;RSEQ=AGTCTCATTGGATCATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:0,4:0,14:14,4:0.2222:1,0:25.8:1:29.8:1:1:0:60:8:0.2222:0:1.3 0/0:6:0:0,0:0,6:6,0:0:0,0:24.5:1:32:1:1:0:60:12:1:0:0.3 +14 49557843 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAAAGGGTAAAAATAAAA;RSEQ=TGGCCATTTAAACCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:20.5:1:33:1:1:0:52:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 50232682 . C CG 25 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGTCTCCAGGTACCCA;RSEQ=GGGGCTTGGAACTATACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:25:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 50234258 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=TGGTTACGGCTTCGGAAACG;RSEQ=TTTTCAAGCCAACTCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:17,13:30,2:0.0625:2,2:32.5:1:29.5:1:1:1.29665:60:4:0.0625:0:1 0/0:32:0:0,0:17,15:32,0:0:2,0:27.5:1:30.7:1:1:0:60:64:1:0:0.2 +14 50234786 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTGAGCGGCAGCCTCGC;RSEQ=TCCGGAGCTCGGCGGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29.5:1:1:0:60:4:1:0:1 +14 50455087 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12899;LSEQ=TCACGATCCTGTGTGCAGAA;RSEQ=GCTATTGTGGAAAGCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:428:304:136,168:52,72:124,304:0.7103:2,2:25.3:1:30.5:1:0.66775:1.12:60:59.8:0.7069:0:1.1 0/1:413:99:47,52:150,164:314,99:0.2397:2,2:24.3:1:30.1:1:1:1.01191:60:198:0.2432:0:1.1 +14 50456628 . G TTT 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=TTCCACATTGATTTAAATTG;RSEQ=TTTTTTTGCTTTTATGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:30.3:1:1:0:60:4:1:0.5:1.5 +14 50550133 . C CTCTG 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTCTATCCAGCCAATCTCT;RSEQ=TCTGTCTTTCTCTCTCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16:1:34.6:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 50550946 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21578;SOR=Inf;LSEQ=GGATCTCTGGATGGTATTTA;RSEQ=CAAACAGAAATACAGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:140,60:200,0:0:2,0:23.2:1:32.7:1:1:0:60:99:1:0:0.2 0/1:174:2:1,1:120,52:172,2:0.0115:2,2:11.5:1:27:1:0.51764:2.29535:60:4:0.0116:0:1.5 +14 50551034 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.34506;LSEQ=AAATATGTCCCACATACTGC;RSEQ=TGGGGTACATTTAAGACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:407:228:106,122:82,95:177,228:0.5602:2,2:25.1:1:30.9:1:1:1.01:60:44.6:0.5617:0:1.1 1/0:407:305:152,153:48,51:99,305:0.7494:2,2:25.4:1:30.2:1:0.81829:1.06:60:75.25:0.7525:0:1.1 +14 51598192 . T G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATCCAGCACTTTCAGAG;RSEQ=CCGAGGTGGGCAGAGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 51598375 . C T 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02564;SOR=Inf;LSEQ=CAGGGACAGAATTCAGATCT;RSEQ=CCTGGGCCTGAGCCTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:12.2:1:29:1:1:0:57.2:10:1:0:0.2 1/0:10:7:4,3:0,2:2,7:0.7:0,2:19.7:1:30.9:1:0.44444:0:47.4:14:0.7:0:1.1 +14 51598580 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20588;SOR=Inf;LSEQ=CCCAACTGGGTGAGACCCTC;RSEQ=AACATGGGTTGTCAGACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:39.4:1:32:1:1:0:47.6:18:1:0:0.2 0/1:8:2:1,1:2,4:6,2:0.25:2,2:16:1:28.5:1:1:1.83:60:4:0.25:0:1.5 +14 51598610 . A G 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=TGTCAGACACCATATACAGG;RSEQ=GCAATCCTAGTGGCATCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:25:1:30:1:1:2.24:52.5:4:0.2222:0:1 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:40:1:31:1:0.33333:0:58.5:4:0.6667:0:1.5 +14 51598843 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02419;SOR=Inf;LSEQ=AACAATAGCATCATCAACAA;RSEQ=AACAAAAACAACAAAAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:22,0:0:2,0:22.6:1:29.7:1:1:0:59.4:44:1:0:0.1 0/1:10:3:1,2:4,3:7,3:0.3:2,2:21.7:1:29.7:1:1:2.41422:58.3:6:0.3:0:1 +14 51598867 . CA C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.01217;SOR=Inf;LSEQ=AAAAACAACAAAAAGACCCC;RSEQ=AAAAACCCCATCCAAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:25,0:0:2,0:34.2:1:30.3:1:1:0:56.6:24:1:0:0.4 0/1:14:4:2,2:6,4:10,4:0.2857:2,2:31.8:1:30.8:1:1:1.45647:57.8:8:0.2857:0:0.8 +14 51598912 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=AGCCTCAAAGACTGAAACAA;RSEQ=ACCAACTCACAAAGACGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:8,13:21,0:0:2,0:18.3:1:30.9:1:1:0:58.7:20:1:0:0.4 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:21.5:1:28:1:1:1:60:4:0.1429:0:1 +14 51605639 . A G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCTGCATTTAGAGGCTG;RSEQ=TAAAGGTTACAGTACAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:23.3:1:32.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 51606001 . C G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67944;SOR=0.93008;LSEQ=AGGACTTTGATTCTGTCTTG;RSEQ=TCCTCCCTTCAGCACTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:146:75,71:91,92:183,146:0.4438:2,2:27.9:1:31.6:1:0.82452:1.07:60:47.667:0.4387:0:1.2 0/1:270:115:57,58:76,79:155,115:0.4259:2,2:25.3:1:30.9:1:1:1.02:60:114:0.4318:0:1.1 +14 51606027 . G A 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25208;SOR=0;LSEQ=CCTTCAGCACTTGACCACTG;RSEQ=GGTGTGACTTCTGTTGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:118,170:288,3:0.0103:2,2:5.3:1:27.3:1:0.5709:2.87:60:6:0.0105:0:1 0/0:254:0:0,0:104,150:254,0:0:2,0:26.7:1:30:1:1:0:60:41.333:1:0:0.4 +14 51606336 . A T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAAGCAAAGAACTGAATG;RSEQ=TGTGCAACTACTTTCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:31:1:1:0:42:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 52143744 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTTACTTGCTTTTTTCC;RSEQ=TAATGTTGTTTTTTGAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 52145105 . T C 65 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGAGACTTTTGCAGAAA;RSEQ=TATTTTGTGGACAGTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:12.5:1:32.8:1:1:0:60:8:1:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:18.3:1:33:0:1:0:60:6:1:0:1 +14 52145244 . T C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03366;SOR=0.32405;LSEQ=TGACCAACGCTGACTCCCAT;RSEQ=GTGGGGGAAAAGTGTGTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:20:9,11:15,17:32,20:0.3846:2,2:24.8:1:31.2:1:1:1.07686:60:40:0.3922:0:1.2 0/1:36:6:2,4:14,16:30,6:0.1667:2,2:24.2:1:30.3:1:0.67224:1.72372:60:12:0.1667:0:1.2 +14 52640477 . C G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00034;SOR=4.90022;LSEQ=ATAAAGTTTTGATAAACCAT;RSEQ=CAATGCCTATCTGCCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:6:5,1:107,15:122,6:0.0469:2,2:25.3:1:31:1:0.55889:1.42221:60:12:0.0469:0:1.2 0/1:123:24:22,2:83,16:99,24:0.1951:2,2:23.8:1:31:1:0.5214:2.11:60:23:0.1933:0:1.4 +14 52640520 . AAG A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.28231;SOR=0.82846;LSEQ=CCCCCAAAAAAAGAAAAAGA;RSEQ=AAGGGCAGTGATATTAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:128:85,43:129,56:185,128:0.4076:2,2:23.2:1:30.8:1:0.53922:1.16476:59.8:256:0.4116:0.0764:1 0/1:303:110:71,39:124,69:193,110:0.363:2,2:23.6:1:29.9:1:1:1.01:60:220:0.3654:0.0528:1.1 +14 52640564 . C A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00513;SOR=0.68374;LSEQ=CTTTCTAAATATATTTAAGC;RSEQ=TCGTTTAAAGGAAGTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:205:113,92:148,133:281,205:0.4209:2,2:27.8:1:30.8:1:0.64524:1.10:59.9:204:0.4224:0:1.1 0/1:473:157:85,72:165,149:314,157:0.3319:2,2:28.8:1:29.2:1:0.76948:1.07:60:51.333:0.3341:0:1.2 +14 52640760 . ACTA T 111 MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=42;MSI=15.000;MSILEN=3;SSF=0.01294;SOR=0.08388;LSEQ=CAGAGCTAGCCAAAATGCTT;RSEQ=CTACTACTACTACTACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:0,11:0,10:10,11:0.44:0,0:22.7:1:32.2:1:1:0:60:22:0.4583:0.12:0.6 0/1:17:1:0,1:0,16:16,1:0.0588:1,0:44:0:32.8:0:1:0:60:2:0.0588:0:1 +14 52640795 . T C 70 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=3;SSF=0.6004;SOR=0.39896;LSEQ=ACTACTACTACTACTACTAC;RSEQ=ACTACTAAAATCTTCCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:0,4:0,6:6,4:0.4:0,0:23.3:1:35:0:1:0:55.5:8:0.4444:0:2.8 0/1:5:1:0,1:0,4:4,1:0.2:0,0:23:0:34:0:1:0:60:2:0.2:0:2 +14 54776972 . C A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=TGGAGGACTGAATTAAGATT;RSEQ=CACTCGGGCTGGAGGTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:8,2:0.2:2,2:43.5:1:25:1:1:1.58108:60:4:0.2:0:1 0/0:7:0:0,0:4,3:7,0:0:2,0:28.1:1:31.3:1:1:0:60:14:1:0:0.1 +14 54908166 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16429;SOR=Inf;LSEQ=ACCGCCACCGCTACCGCCGC;RSEQ=GCGCCAGCCCTCTCAGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:25,8:33,0:0:2,0:13.7:1:30.5:1:1:0:60:66:1:0:0.1 0/1:23:2:1,1:18,3:21,2:0.087:2,2:18:1:28:1:0.32411:5.33862:60:4:0.087:0:1 +14 55397563 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15485;SOR=Inf;LSEQ=TTCATTTCTCTGGGATAAAT;RSEQ=CCCAAGAGGGCAATTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:47,0:0:2,0:27.9:1:31.7:1:1:0:58.1:46:1:0:0.2 0/1:31:2:1,1:11,17:28,2:0.0645:2,2:39.5:1:30:1:1:1.52:60:4:0.0645:0:1 +14 55397566 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15892;SOR=Inf;LSEQ=ATTTCTCTGGGATAAATGCC;RSEQ=AAGAGGGCAATTGCTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:24,22:46,0:0:2,0:28.2:1:31.2:1:1:0:58.1:45:1:0:0.2 0/1:31:2:1,1:12,17:29,2:0.0645:2,2:31:1:30.5:1:1:1.40:60:4:0.0645:0:1 +14 55878636 . G C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGAAGGGGGGCTGGGAT;RSEQ=CCGGCGAGCCCCCGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 55880341 . G C 51 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TCCATTGGTTCTAAGTGCTT;RSEQ=TCTGGGTGGAGCAGGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:29:1:32.7:1:1:0:56.3:6:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:16:0:33:0:1:0:60:2:1:0:0 +14 55880730 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.47007;SOR=0.82917;LSEQ=CCATCTTTTCTAAAAGGCCT;RSEQ=GAGAACATGTATCAGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:136:69:48,21:38,29:67,69:0.5074:2,2:24.2:1:31.9:1:0.1549:1.74:47.9:138:0.5111:0:1.1 0/1:139:64:37,27:51,24:75,64:0.4604:2,2:21.9:1:30.3:1:0.22285:1.54569:44.8:31:0.4526:0:1.3 +14 55880744 . A G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22479;SOR=0;LSEQ=AGGCCTAGAGAACATGTATC;RSEQ=GGTGCCTCACCTCTTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:104,64:168,2:0.0118:2,2:8:0:32.5:1:1:1.62012:60:4:0.0118:0:1 0/0:188:0:0,0:120,68:188,0:0:2,0:22.5:1:29.6:1:1:0:51.4:61.667:1:0:0.6 +14 55880745 . G T 45 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24922;SOR=Inf;LSEQ=GGCCTAGAGAACATGTATCA;RSEQ=GTGCCTCACCTCTTTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:104,67:171,0:0:2,0:23.1:1:32:1:1:0:53.7:56:1:0:0.5 0/1:186:3:1,2:116,66:182,3:0.0161:2,2:5:1:29:1:0.55554:3.49026:52:6:0.0164:0:1 +14 55880810 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24864;SOR=Inf;LSEQ=CTGGAAGATGGCCCTTCCGG;RSEQ=TAAAAGGAAACGCATTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:104,119:223,0:0:2,0:27.1:1:32.7:1:1:0:59:222:1:0:0.2 0/1:232:3:2,1:112,117:229,3:0.0129:2,2:23.7:1:27.7:1:0.61694:2.08:50.7:6:0.0129:0:1.7 +14 55880918 . A G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20739;SOR=0.48296;LSEQ=TCAGTTTTTAAAATAACACA;RSEQ=AAGGAGTCATTTTGAATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:22:0,22:0,14:14,22:0.6111:1,1:24.5:1:31.8:1:1:0:60:44:0.6286:0:1 0/1:28:12:0,12:0,16:16,12:0.4286:1,0:15.8:1:30.2:1:1:0:60:24:0.4286:0:1.3 +14 57024413 . T A 25 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14106;SOR=Inf;LSEQ=GTCATGTAACGAGCGGCCCT;RSEQ=CCAAGTTCTAACAACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:44,20:64,0:0:2,0:19.3:1:30.4:1:1:0:60:63:1:0:0.1 0/1:39:2:1,1:24,13:37,2:0.0513:2,2:13:0:25:1:1:1.81575:60:4:0.0513:0:1 +14 57141318 . T G 62 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTACTGAAGGAGAACTTG;RSEQ=GGGTCAGTGTGGATGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:5,0:5,5:0.5:0,2:26.4:1:26.8:1:1:0:55:4:0.4444:0:2.4 1/1:1:1:1,0:0,0:0,1:1:0,0:39:0:31:0:1:0:60:2:1:0:1 +14 57141401 . G A 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31484;SOR=0;LSEQ=AGGAACAGGTGAAGGAAACA;RSEQ=CTTTCAGACACAAGTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:11,0:32,0:32,11:0.2558:1,0:23.3:1:30:1:1:0:60:10:0.2439:0:1.1 0/0:6:0:0,0:5,1:6,0:0:2,0:27.5:1:31.8:1:1:0:60:12:1:0:0.2 +14 57141480 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12432;SOR=Inf;LSEQ=AACAGGTAAAGCAGGGGAAG;RSEQ=CCTTTTGTGAAGCAGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:128,40:168,0:0:2,0:21.5:1:31.8:1:1:0:60:41:1:0:0.2 0/1:92:2:1,1:73,17:90,2:0.0217:2,2:8:0:30.5:1:0.35475:4.20162:60:4:0.022:0:1.5 +14 57141489 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52029;SOR=0;LSEQ=AGCAGGGGAAGCCCTTTTGT;RSEQ=AAGCAGAGATACAGAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:145,44:189,2:0.0105:2,2:15.5:1:28.5:1:0.41664:3.26983:60:4:0.0105:0:1 0/0:125:0:0,0:94,31:125,0:0:2,0:22.3:1:31.4:1:1:0:60:61.5:1:0:0.2 +14 57141493 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15928;SOR=Inf;LSEQ=GGGGAAGCCCTTTTGTGAAG;RSEQ=AGAGATACAGAAAGATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:151,50:201,0:0:2,0:24.6:1:32:1:1:0:60:39.2:1:0:0.1 0/1:134:2:1,1:96,36:132,2:0.0149:2,2:36.5:1:29.5:1:0.4775:2.64405:60:4:0.0152:0:1 +14 57141496 . A T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2731;SOR=0;LSEQ=GAAGCCCTTTTGTGAAGCAG;RSEQ=GATACAGAAAGATGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:2,1:155,52:207,3:0.0143:2,2:34.3:1:29.3:1:1:1.4873:60:6:0.0146:0:1 0/0:145:0:0,0:104,41:145,0:0:2,0:23.2:1:29.2:1:1:0:60:144:1:0:0.2 +14 57141603 . C T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2916;LSEQ=CCAGGTTAGGCACAGCTGGG;RSEQ=TTGGCTTCAGGCTATTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:438:304:126,178:57,76:133,304:0.6941:2,2:24:1:29.9:1:0.83325:1.05937:59.7:100.333:0.6968:0:1.6 0/1:352:140:69,71:107,105:212,140:0.3977:2,2:24.7:1:28.9:1:0.9133:1.04847:60:69:0.3977:0:1.7 +14 57141647 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22042;LSEQ=TCTCATTTCCTGGGATTGGC;RSEQ=GAGCAGGATGTCTTTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:281:213:66,147:20,48:68,213:0.758:2,2:26.6:1:30.6:1:0.88041:1.08:59.8:41.6:0.7564:0:1.8 0/1:260:106:41,65:61,93:154,106:0.4077:2,2:25:1:29.5:1:0.89786:1.03972:59.8:34.333:0.4104:0:1.8 +14 57141681 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49969;SOR=0;LSEQ=TTCTCATTGCCATGACAGAA;RSEQ=CCAAGAGGGAAAACCCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:33,132:165,2:0.012:2,2:37:1:30:1:0.36671:3.96:60:4:0.0121:0:2 0/0:151:0:0,0:41,109:150,0:0:2,0:24.6:1:31.5:1:1:0:60:49:0.9932:0:0.6 +14 57141867 . G T 44 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.48571;SOR=0.15605;LSEQ=GGGCTTCGAACTTTATAAGA;RSEQ=AGTGGAAGCAACATGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:41:1:28.3:1:1:0:60:6:0.75:0:1.7 0/1:4:1:0,1:0,3:3,1:0.25:0,0:16:0:29:0:1:0:60:2:0.25:0:1 +14 57141908 . G T 32 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGAACATATGGGTTTGG;RSEQ=GTATTCAGCGTTACCTAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:7:1:32:0:1:0:60:4:0.6667:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:16:0:25:0:1:0:60:2:1:0:0 +14 57255538 . C CA 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50465;SOR=0;LSEQ=TTATGGTTTCTTTGACTGTT;RSEQ=AAAAAAAGATACAGAATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:86,46:132,2:0.0148:2,2:30.5:1:29.5:1:1:1.86036:60:4:0.0149:0:0 0/0:107:0:0,0:66,41:107,0:0:2,0:28:1:30.4:1:1:0:60:34.667:1:0:0.3 +14 57255551 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50404;SOR=0;LSEQ=GACTGTTCAAAAAAAGATAC;RSEQ=GAATAGATGTGACAAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:86,60:146,2:0.0135:2,2:16:1:31:1:1:1.42975:60:4:0.0137:0:1 0/0:119:0:0,0:74,45:119,0:0:2,0:28.6:1:29.7:1:1:0:60:238:1:0:0.3 +14 57255601 . A G 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAAATGAATTTAGCCATGC;RSEQ=GTTATGCTACATATGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:88,89:177,0:0:2,0:24.4:1:31.2:1:1:0:60:176:1:0:0.1 0/1:145:49:22,27:44,52:96,49:0.3379:2,2:21.5:1:28.9:1:1:1.03821:60:98:0.3427:0:1.1 +14 57255604 . T C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23785;SOR=0.40304;LSEQ=AATGAATTTAGCCATGCAGT;RSEQ=ATGCTACATATGTAGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:9:4,5:80,84:164,9:0.052:2,2:19.9:1:31.4:1:1:1.18928:60:18:0.052:0:1.1 0/1:139:3:1,2:62,74:136,3:0.0216:2,2:41.3:1:31:1:1:1.66972:60:6:0.0216:0:1.3 +14 57255651 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.50697;SOR=0;LSEQ=GTATATAATATTATATCATC;RSEQ=CTCTTCTTGAATTCTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:50,83:133,2:0.0148:2,2:32:1:30.5:1:1:1.65:60:4:0.0149:0:1 0/0:103:0:0,0:39,64:103,0:0:2,0:26.6:1:29.4:1:1:0:60:206:1:0:0.4 +14 57542776 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21212;SOR=Inf;LSEQ=ACGCTGACTCCTGACTCTAG;RSEQ=TTATTTGTTCAGTAGGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:24,0:0:2,0:24.2:1:30.5:1:1:0:60:23:1:0:0.2 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:27:0:30.5:1:1:1.10554:60:4:0.1:0:1 +14 57732994 . T G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=6.69807;LSEQ=AAAGATACTTCCCGTGACTC;RSEQ=TACTACAACCTAGATGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:28:14,14:298,229:527,28:0.0505:2,2:27.5:1:30:1:0.55961:1.30067:60:13:0.0474:0:2.5 0/1:468:123:69,54:193,151:344,123:0.2628:2,2:24.6:1:30.1:1:1:1.00029:59.8:60.5:0.2613:0:2.7 +14 57733016 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.80745;LSEQ=ACTACAACCTAGATGCTATG;RSEQ=CAGTAGTTACAGGAAACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:600:30:12,18:297,273:570,30:0.05:2,2:24.4:1:30.5:1:0.26063:1.63053:60:60:0.0505:0:2.7 0/1:496:131:68,63:191,174:365,131:0.2641:2,2:26.4:1:28.2:1:1:1.01696:59.9:25.2:0.2598:0:2.8 +14 57733023 . T C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3306;SOR=1.15054;LSEQ=CCTAGATGCTATGGCAGTAG;RSEQ=TACAGGAAACTGAGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:598:438:222,216:75,84:159,438:0.7324:2,2:26.7:1:32.7:1:0.46016:1.15:60:61.571:0.7342:0:1.2 1/0:498:378:199,179:60,59:119,378:0.759:2,2:26.5:1:31:1:0.67552:1.09:59.9:53:0.7556:0:1.7 +14 57733423 . TTA T 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATGTATGTTATATATACG;RSEQ=TATATATATATGTGTATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:34:1:31.7:1:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 59555994 . G A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01764;SOR=5.90054;LSEQ=TGAACACTACCTGCTCACCA;RSEQ=GTGCAAGGAACTGATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:6:5,1:31,0:31,6:0.1622:1,2:23.8:1:29.3:1:0.16216:0:60:12:0.1667:0:1 1/0:11:6:6,0:5,0:5,6:0.5455:0,0:15.7:1:27.8:1:1:0:60:5:0.5:0:1.2 +14 59556100 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5173;SOR=0;LSEQ=GCACAACATCCCCTGGCAGG;RSEQ=CCACTTGCAGTCCAGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:155,37:192,2:0.0103:2,2:34:1:29.5:1:0.3542:4.14702:60:4:0.0108:0:1 0/0:131:0:0,0:106,25:131,0:0:2,0:23.6:1:31.1:1:1:0:60:64.5:1:0:0.2 +14 59556112 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58435;SOR=2.56526;LSEQ=CTGGCAGGCCCACTTGCAGT;RSEQ=CAGTCTGGCAACATGGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:1:1,0:163,53:216,1:0.0046:2,0:18:0:11:0:1:0:60:0:0:0:3 0/1:170:2:1,1:123,45:168,2:0.0118:2,2:29.5:1:27.5:1:0.46913:2.71443:60:4:0.0121:0:1.5 +14 59556134 . C T 39 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32051;SOR=3.97053;LSEQ=AGTCTGGCAACATGGTCATG;RSEQ=AGACAGAGTGAAAGGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:1:0,1:212,113:325,1:0.0031:2,0:1:0:25:0:0.34969:0:60:2:0.0031:0:1 0/1:248:3:1,2:156,89:245,3:0.0121:2,2:9.7:1:24.7:1:0.55629:3.48713:60:6:0.0121:0:1.7 +14 59556157 . A T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.40892;LSEQ=ACAGAGTGAAAGGGCTTTTA;RSEQ=GATTTAAAGTCAAGAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:22:9,13:261,181:442,22:0.0474:2,2:23.1:1:30.6:1:0.12038:2.07954:60:44:0.0485:0:2 0/1:344:62:38,24:156,126:282,62:0.1802:2,2:25.8:1:29.8:1:0.40085:1.28:60:124:0.1813:0:1.7 +14 59556205 . G C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.51516;LSEQ=CAGTGCAGAAGACAGGAGAT;RSEQ=TCACCTAATCGTTTTAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:118:62,56:245,243:488,118:0.1941:2,2:27.8:1:32.8:1:0.68215:1.10:60:117:0.195:0:1.4 1/0:427:261:125,136:80,86:166,261:0.6112:2,2:26.8:1:30.9:1:1:1.01207:60:51.2:0.6095:0:1.3 +14 59556269 . G A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30503;SOR=4.69268;LSEQ=TTTCTGTAAGTCAAGGCCTA;RSEQ=CCAACTGGCTTAGGCGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:1:1,0:102,254:356,1:0.0028:2,0:47:0:32:0:0.28852:0:60:2:0.0028:0:1 0/1:230:3:2,1:81,146:227,3:0.013:2,2:10:1:26.3:1:0.29585:3.58:60:6:0.013:0:1.7 +14 59556292 . A ATCATTCAT 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=5.000;MSILEN=4;SSF=0;SOR=4.13846;LSEQ=AACTGGCTTAGGCGTGGTTC;RSEQ=TCATTCATTCATTCACTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:20:2,18:39,164:203,20:0.0866:2,2:31.8:1:31.3:1:0.5434:2.1342:59.3:40:0.087:0.013:0.4 0/1:138:39:9,30:25,55:80,39:0.2826:2,2:23.8:1:28.9:1:0.39484:1.51002:59.9:78:0.2826:0.1014:0.4 +14 59556318 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09997;SOR=Inf;LSEQ=CATTCATTCACTTATGAATG;RSEQ=CATGCTTTTTAGCCCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:6,126:132,0:0:1,0:25.4:1:30.6:1:1:0:60:264:1:0:0.1 0/1:62:2:1,1:5,55:60,2:0.0323:2,2:13.5:1:28:1:0.18562:10.13:60:4:0.0323:0:1 +14 59556354 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=22.41285;LSEQ=TTTCTGCAGTATATAATGAA;RSEQ=AGTAGAACCAAGTTCACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:8:0,8:0,56:56,8:0.125:1,0:14.3:1:33.1:1:1:0:60:16:0.127:0:1 1/0:22:17:0,17:0,5:5,17:0.7727:0,1:18.6:1:31.7:1:1:0:59.7:34:0.7727:0:1.1 +14 59556404 . A G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02809;SOR=0.11467;LSEQ=GTGCTTGTTTTGGGATATCT;RSEQ=TATAAAAGCAAGACTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:0,16:0,5:5,16:0.7619:0,1:20.9:1:31.6:1:1:0:60:32:0.7619:0:1.1 0/1:8:2:0,2:1,5:6,2:0.25:2,0:28.5:1:33:0:1:0:60:4:0.25:0:1.5 +14 61655082 . A C 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00057;SOR=Inf;LSEQ=CTCAGCTTCTGCCCCCGCCC;RSEQ=CAGCCTGCAAACCGAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:20,8:28,0:0:2,0:22:1:30.2:1:1:0:60:56:1:0:0 0/1:14:6:3,3:8,0:8,6:0.4286:0,2:27.7:1:30.2:1:0.05495:0:60:12:0.4286:0:1.3 +14 61655194 . GC G 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01765;SOR=Inf;LSEQ=GGCAGCGGCTCGGGCAGGCG;RSEQ=CTTGTGGCTCCGCAACCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,17:26,0:0:2,0:25.8:1:31.5:1:1:0:60:52:1:0:0.1 0/1:23:5:2,3:5,13:18,5:0.2174:2,2:24.2:1:31.8:1:0.62139:1.69:60:10:0.2174:0.087:0.4 +14 61799651 . G T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50265;SOR=0;LSEQ=CTGTGGTCCTTCCGGTGTCA;RSEQ=AGTTTTGTGGTTCTGGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:136,27:163,2:0.0121:2,2:46:0:30:0:0.31146:4.96456:60:4:0.0121:0:1 0/0:137:0:0,0:106,31:137,0:0:2,0:20.5:1:30.5:1:1:0:60:33.25:1:0:0.1 +14 61799771 . C G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.40662;LSEQ=TCTGAAATTATTTTGGGAAG;RSEQ=GCACCCAAAAGTCATACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:111:54,57:145,188:333,111:0.25:2,2:28.3:1:31.2:1:0.37869:1.23:60:222:0.2528:0:1.1 1/0:365:260:122,138:47,57:104,260:0.7123:2,2:24.6:1:30:1:0.81637:1.07:60:42.333:0.7155:0:1.1 +14 61799782 . G T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06918;SOR=0;LSEQ=TTTGGGAAGCGCACCCAAAA;RSEQ=TCATACGTGTATTAGCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:5:2,3:195,252:447,5:0.011:2,2:19.4:1:29.8:1:1:1.16032:60:10:0.0111:0:1.8 0/0:364:0:0,0:161,203:364,0:0:2,0:24.5:1:31.4:1:1:0:60:728:1:0:0.7 +14 61799788 . C T 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGCGCACCCAAAAGTCATA;RSEQ=GTGTATTAGCCTAATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:58:20,38:159,224:383,58:0.1315:2,2:25.7:1:30.5:1:0.38945:1.34776:60:57:0.1323:0:1.1 0/0:352:0:0,0:155,197:352,0:0:2,0:24.6:1:30:1:1:0:60:87:1:0:0.7 +14 61799843 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1786;SOR=Inf;LSEQ=TATTTATTTGCAAGCTGTGG;RSEQ=CCTCTTAGATGCTTTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:74,189:263,0:0:2,0:25.4:1:31.9:1:1:0:60:86.667:1:0:0.3 0/1:193:2:1,1:59,132:191,2:0.0104:2,2:14.5:1:28:1:0.52623:2.23:60:4:0.0104:0:1.5 +14 61799920 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=5.85898;LSEQ=AGAGCAGATTCCATCTAAAT;RSEQ=AGTGCTTTTGAAACTGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:18:0,18:1,41:42,18:0.3:1,1:21.7:1:29.6:1:1:0:60:36:0.3051:0:1.1 1/0:25:18:0,18:0,7:7,18:0.72:0,1:25.8:1:27.9:1:1:0:60:36:0.72:0:1 +14 61800094 . G A 66 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGGACACAGGACCTCAG;RSEQ=TTGAGAAACCTCAGTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:18.8:1:33.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 61884484 . G A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00323;SOR=Inf;LSEQ=TTTAAAAAAAGAAAGAAAGA;RSEQ=GAGCCTGTAGTGTGATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:113,3:116,0:0:1,0:21.5:1:33.5:1:1:0:59.9:115:1:0:0.1 0/1:56:5:5,0:49,2:51,5:0.0893:1,0:24.6:1:29.6:1:1:0:60:10:0.0893:0:1.2 +14 61884632 . T C 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGATGAGGAAGCCACACA;RSEQ=GGGTTATTTCTCTACTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:0:0,0:297,354:651,0:0:2,0:24.9:1:30.3:1:1:0:60:53.25:1:0:0.1 0/1:479:73:34,39:200,206:406,73:0.1524:2,2:24:1:30.2:1:0.70413:1.1134:60:146:0.1537:0:1.9 +14 61884646 . A G 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACACATGGGTTATTTCTCT;RSEQ=CTGAAAGGGTAGAGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:253,348:601,0:0:2,0:25.5:1:29:1:1:0:60:74.125:1:0:0.1 0/1:441:83:40,43:160,198:358,83:0.1882:2,2:23.5:1:31.7:1:0.62486:1.15:60:82:0.1872:0:1.9 +14 61884724 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17723;SOR=Inf;LSEQ=GTGTCTTTTGCCATCTCAAA;RSEQ=GCCAGCTGTTTATTGAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:54,195:249,0:0:2,0:23.6:1:31.9:1:1:0:59.9:123.5:0.992:0:0.1 0/1:183:2:1,1:49,132:181,2:0.0109:2,2:35:0:31:0:0.47289:2.68:60:4:0.011:0:1.5 +14 62805991 . A G 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAATTTAAGGGCCTTTTCT;RSEQ=TCTTGACTCTTCCTGACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:19.5:1:29.5:1:1:0:60:3:0.5:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:1:0:29:0:1:0:60:2:1:0:2 +14 62907490 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49194;SOR=0;LSEQ=GAAAAAGGAGATATTGCATA;RSEQ=TGGTGACTGGACCCTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:16,2:0.1111:2,2:6.5:1:29:1:1:1.62:60:4:0.1111:0:1 0/0:14:0:0,0:5,9:14,0:0:2,0:21.9:1:30.8:1:1:0:60:28:1:0:0.1 +14 62907565 . A G 53 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTTGCAGCAGCAGCAAA;RSEQ=ACCCAGGAATGGTAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:19.7:1:34:0:1:0:60:6:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:18:1:32.5:1:1:0:60:4:1:0:1.5 +14 63589720 . GC G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16859;SOR=Inf;LSEQ=CAAAAGATAGAAAGGCCCAT;RSEQ=CCCGGGTCCACAACCACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:178,61:239,0:0:2,0:23:1:31.8:1:1:0:59.8:46.8:1:0:0.1 0/1:167:2:1,1:118,47:165,2:0.012:2,2:27:1:30.4:1:0.49347:2.49486:60:4:0.0123:0.006:0 +14 63589724 . C T 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00164;SOR=Inf;LSEQ=AGATAGAAAGGCCCATGCCC;RSEQ=GGGTCCACAACCACCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:190,65:255,0:0:2,0:23.1:1:30.9:1:1:0:59.8:84:1:0:0.1 0/1:173:7:5,2:117,49:166,7:0.0405:2,2:18.9:1:30.6:1:1:1.05:60:14:0.0414:0:1 +14 63589734 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16179;SOR=Inf;LSEQ=GCCCATGCCCCGGGTCCACA;RSEQ=CCACCAGCTTTGCTGGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:211,84:295,0:0:2,0:24.8:1:30.1:1:1:0:59.8:72.75:1:0:0.1 0/1:199:2:1,1:134,62:196,2:0.0101:2,2:23:1:31:1:0.53623:2.1521:60:4:0.0103:0:1 +14 63589819 . G T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGGCTACATGTTTGGTAAAG;RSEQ=GATCTATTTCGCTGACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:591:0:0,0:338,253:591,0:0:2,0:24.4:1:31.1:1:1:0:59.2:48.25:1:0:0.1 0/1:383:12:6,6:206,165:371,12:0.0313:2,2:30.3:1:29.3:1:0.77292:1.24775:59.4:24:0.0316:0:1.1 +14 63589829 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGGTAAAGGGATCTATTT;RSEQ=GCTGACATGGCCTCCAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:0:0,0:326,263:589,0:0:2,0:26.2:1:31.2:1:1:0:59.1:146.25:1:0:0.1 0/1:404:19:10,9:212,173:385,19:0.047:2,2:23.8:1:29.3:1:1:1.10262:49.8:38:0.0474:0:1.1 +14 63590051 . G T 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02454;SOR=Inf;LSEQ=ATGGTGCAGAGGTTCCTCTT;RSEQ=GGACTGGGATTTCATCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:0:0,0:268,290:558,0:0:2,0:25:1:31.7:1:1:0:59.5:68.75:1:0:0.1 0/1:367:4:1,3:187,173:360,4:0.0109:2,2:15:1:22.8:1:0.35715:3.23319:51.5:3:0.0083:0:1 +14 64619727 . A G 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=ATCTCCATACCCCAAACCCA;RSEQ=CAGAGTATCTGGCATTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:54,6:60,0:0:2,0:24.2:1:30.8:1:1:0:60:120:1:0:0.2 0/1:51:10:9,1:34,7:41,10:0.1961:2,2:26.4:1:29.9:1:1:1.83:60:9:0.18:0:1.3 +14 64619788 . C T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00177;SOR=0.40697;LSEQ=CAGTGATGAAGCAGTGTCTC;RSEQ=ATGTACAGGGAGATGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:47:34,13:85,39:124,47:0.2749:2,2:24.4:1:31.2:1:0.71149:1.20:60:46:0.2722:0:1.6 0/1:165:22:14,8:85,58:143,22:0.1333:2,2:21:1:29.8:1:0.81711:1.19:60:44:0.1358:0:1.7 +14 64619793 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49961;SOR=0;LSEQ=ATGAAGCAGTGTCTCCATGT;RSEQ=CAGGGAGATGCCTCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:128,55:183,2:0.0108:2,2:35.5:1:32:1:0.51492:2.31542:60:4:0.011:0:1.5 0/0:169:0:0,0:100,68:168,0:0:2,0:24.3:1:28.4:1:1:0:59.8:336:0.9941:0:0.5 +14 64619797 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49982;SOR=0;LSEQ=AGCAGTGTCTCCATGTACAG;RSEQ=GAGATGCCTCAGGGAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:134,60:194,2:0.0102:2,2:25.5:1:32.5:1:0.52669:2.22324:60:4:0.0104:0:1 0/0:178:0:0,0:104,74:178,0:0:2,0:23.9:1:30.5:1:1:0:59.8:356:1:0:0.5 +14 64619850 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41644;LSEQ=ATGTAGCCTCTATGAGCTAG;RSEQ=AGCATAGTCAGCTCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:273:137:70,67:69,66:135,137:0.5018:2,2:26.6:1:30.6:1:1:1.00065:59.7:67.5:0.4982:0:1.2 0/1:227:67:35,32:83,77:160,67:0.2952:2,2:24.3:1:29:1:1:1.01:60:66:0.292:0:1.2 +14 64619878 . A C 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00917;SOR=Inf;LSEQ=TCAGCTCCAGGAGGACTCTA;RSEQ=AGTTTGGAAGAAACACTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:110,155:265,0:0:2,0:26:1:30.6:1:1:0:59.8:264:1:0:0.5 0/1:226:6:3,3:107,113:220,6:0.0265:2,2:22.5:1:31.3:1:1:1.06:60:12:0.0271:0:1.2 +14 64619897 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21029;SOR=Inf;LSEQ=AAAGTTTGGAAGAAACACTA;RSEQ=ATGGTGTTGAAGAGAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:80,152:232,0:0:2,0:25.6:1:32.3:1:1:0:59.8:464:1:0:0.5 0/1:197:2:1,1:88,107:195,2:0.0102:2,2:22.5:1:29:1:1:1.21:60:4:0.0103:0:1.5 +14 64619929 . A C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2235;SOR=Inf;LSEQ=GAGAGAGTATAAAGGAAGAA;RSEQ=GGGTGCAAGACATCTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:40,110:150,0:0:2,0:22.6:1:31.9:1:1:0:59.9:300:1:0:0.3 0/1:135:2:1,1:47,85:132,2:0.0148:2,2:30:1:28.5:1:1:1.80:60:4:0.015:0:1 +14 64699816 . C T 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.32198;LSEQ=ACTGGAGTTCACGCTTCAGC;RSEQ=TGTGACCTCTGTGGGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:20.5:1:30.5:1:1:0:60:4:0.6667:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:14:0:32:0:1:0:60:2:0.3333:0:1 +14 64699990 . TG T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53187;SOR=0;LSEQ=TCCAGCAGCAGGTCATACAC;RSEQ=GGACCACATTTTTGCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:28,26:54,2:0.0357:2,2:31.5:1:31:1:1:1.07547:60:4:0.0364:0:0 0/0:32:0:0,0:16,16:32,0:0:2,0:32.8:1:30.7:1:1:0:60:64:1:0:0.2 +14 64700009 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53026;SOR=0;LSEQ=CTGGGACCACATTTTTGCAC;RSEQ=TCATGTTGAGCAGATGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:24,26:50,2:0.0385:2,2:15.5:1:32.5:1:1:1.08:60:4:0.0385:0:1 0/0:30:0:0,0:13,16:29,0:0:2,0:26.7:1:28.8:1:1:0:60:28:0.9655:0:0.1 +14 65009431 . AGCG A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.13664;SOR=Inf;LSEQ=AAGGTGGTCCTGGCGGCGGC;RSEQ=GCGGCGGCGGTTCAGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:23,0:0:2,0:26:1:33.1:1:1:0:60:46:1:0:0.1 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:26.5:1:31:1:1:1:60:4:0.1429:0:0.5 +14 65471386 . C CT 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCTTTTTCTTTCTTTTT;RSEQ=TTTTTTTTTTTGAGACAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:31.5:1:1:0:51:4:1:0:0 +14 65473196 . G A 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90046;LSEQ=GAGAACGAGCTCTCTTAAAT;RSEQ=TAATGGTATCCTTGGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:0,7:0,22:22,7:0.2414:1,0:16.1:1:32.6:1:1:0:60:14:0.2414:0:1 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:28.5:1:32.5:1:1:0:60:4:0.2222:0:1 +14 65473875 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAATATAAGGCTGAAG;RSEQ=CAAACATCACCATCATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 65543062 . AT A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5355;SOR=0;LSEQ=GCTTCTACGTAAAAATAAAA;RSEQ=TTAAAAAAAAAAGGGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:2,0:152,2:154,2:0.0128:1,0:15.5:1:28.5:1:1:0:60:4:0.0134:0.0064:0.5 0/0:89:0:0,0:83,6:89,0:0:2,0:21.9:1:30.1:1:1:0:59.8:43.5:1:0:0.3 +14 65543065 . TA T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58909;SOR=1.47735;LSEQ=TCTACGTAAAAATAAAAATT;RSEQ=AAAAAAAAAGGGAGAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:9:9,0:153,2:155,9:0.0545:1,0:14.2:1:31.8:1:1:0:59.4:18:0.0549:0.0182:0.6 0/1:89:7:6,1:77,5:82,7:0.0787:2,2:20.6:1:29.9:1:0.39742:2.52895:60:14:0.0805:0.0225:0.3 +14 65543076 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1365;SOR=Inf;LSEQ=ATAAAAATTTAAAAAAAAAA;RSEQ=GGAGAAAGAGAAAAATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:189,3:192,0:0:1,0:22.6:1:33.2:1:1:0:59.8:47:1:0:0.6 0/1:113:2:1,1:105,6:111,2:0.0177:2,2:23:0:30.5:1:0.12058:16.27862:60:4:0.0182:0:1.5 +14 65543102 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00067;SOR=0.46279;LSEQ=AAGAGAAAAATAAAGAGTCT;RSEQ=TTAAATGGTTCTGAGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:89:79,10:184,17:201,89:0.3058:2,2:27.5:1:29.9:1:0.51192:1.36854:59.7:11.714:0.2929:0:1.3 0/1:201:34:27,7:140,27:167,34:0.1692:2,2:21.2:1:29.5:1:0.61528:1.3422:60:33:0.1692:0:1.1 +14 65543920 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATAGCCCCTACATGCAG;RSEQ=CTGCCTGGCCCAGTAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:2,0:59,4:63,2:0.0308:2,0:17.5:1:31.5:1:1:0:60:4:0.0308:0:1 0/0:31:0:0,0:28,3:31,0:0:2,0:16.6:1:30.6:1:1:0:60:30:1:0:0.1 +14 65544275 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12284;SOR=Inf;LSEQ=GAACACCTGGAGTCTCTGGT;RSEQ=CTTACACAGCACATTCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:2,162:164,0:0:1,0:24.6:1:30.8:1:1:0:60:328:1:0:0.1 0/1:89:2:1,1:2,85:87,2:0.0225:1,2:9:0:33:0:0.06665:34.90:60:4:0.0225:0:1 +14 65544367 . C A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50783;SOR=1.66609;LSEQ=CTGCAGGCAGAGCACCTGAG;RSEQ=CCCAAGAAGGGGAGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:13:8,5:31,17:48,13:0.2131:2,2:31:1:30.3:1:1:1.13723:60:26:0.2167:0:1.2 0/1:16:5:3,2:8,3:11,5:0.3125:2,2:20:1:30:1:1:1.71205:60:10:0.3333:0:1 +14 65544450 . C T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TTCCACTGTCTCCTCACTGG;RSEQ=GCCTCAGGTCCTTCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:122,30:152,0:0:2,0:25.1:1:31.6:1:1:0:60:29.4:1:0:0.1 0/1:110:11:8,3:76,22:98,11:0.1:2,2:29.5:1:28.1:1:0.71217:1.29221:60:22:0.1028:0:1.3 +14 65544475 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17254;SOR=Inf;LSEQ=CAGGTCCTTCCTCAGGACGG;RSEQ=TCTAACACTCAGTTACTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:185,62:247,0:0:2,0:24.7:1:32.2:1:1:0:60:60.75:1:0:0.1 0/1:176:2:1,1:116,58:174,2:0.0114:2,2:25:1:27.5:1:1:1.99157:60:4:0.0118:0:2 +14 65544558 . C T 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1781;SOR=5.00823;LSEQ=CATGACTGGCTCTGACTCTG;RSEQ=AGGCCCAGGTGCCAAAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:465:1:0,1:311,153:464,1:0.0022:2,0:1:0:12:0:0.33118:0:60:0:0:0:3 0/1:374:4:1,3:233,137:370,4:0.0107:2,2:11:1:24.5:1:0.14967:5.07997:60:8:0.0108:0:1.3 +14 65544815 . G A 186 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCAATCCAGGCAGTGAGG;RSEQ=AACCTGGCCTGCAGCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:72:7,65:15,120:135,72:0.3462:2,2:23.4:1:30.3:1:0.81758:1.15993:60:144:0.3478:0:1.1 0/0:121:0:0,0:21,100:121,0:0:2,0:22.8:1:30.1:1:1:0:60:120:1:0:0.1 +14 65544917 . ATTTATTTT A 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=7.000;MSILEN=1;SSF=0.57728;SOR=0;LSEQ=ACTGTAGGCTTTATTTATTT;RSEQ=TTTATTTTTTTGAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:1,4:0,40:40,5:0.1111:1,2:27.8:1:32.6:1:0.11111:0:59.2:10:0.1111:0:0 0/0:13:0:0,0:0,13:13,0:0:1,0:22.2:1:30.5:1:1:0:59.1:26:1:0:0.2 +14 65545076 . C T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATTATAGGTGTGCGCCACCA;RSEQ=GCCCATCTAATTTTTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:22.3:1:32:0:1:0:46:6:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:47:1:30.5:1:1:0:60:4:1:0:1 +14 65550816 . T A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00051;SOR=0.44382;LSEQ=CATTTTGCTGATTACCAGGG;RSEQ=AAGGCAGAGCTATCAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:82:68,14:116,25:141,82:0.3677:2,2:24:1:31:1:1:1.05:60:164:0.3677:0:1.1 0/1:166:34:25,9:103,29:132,34:0.2048:2,2:20.6:1:28.9:1:0.6478:1.27668:60:68:0.2048:0:1 +14 65551042 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11293;SOR=Inf;LSEQ=TAAATAAACATGTGGAAAAG;RSEQ=AATTAATTTCACAAGTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:66,229:295,0:0:2,0:23.9:1:32.4:1:1:0:59.9:146.5:1:0:0.1 0/1:277:3:2,1:77,197:274,3:0.0108:2,2:12.7:1:24:1:0.19666:5.08:60:6:0.0109:0:1 +14 65551114 . CA C 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.53169;SOR=1.57155;LSEQ=CTGAATTAGTTACCCTCTTC;RSEQ=AAAAAAAAAATTCCAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:0,5:0,49:49,5:0.0909:1,0:22.6:1:32.4:1:1:0:60:10:0.0943:0:0 0/1:44:6:0,6:1,37:38,6:0.1364:1,0:21.2:1:31.1:1:1:0:60:12:0.1364:0.0227:0 +14 65560024 . TA T 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAGTGCTCATTTACAA;RSEQ=AAGTATTAACTTTGAACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:30.3:1:30.7:1:1:0:60:6:0.6:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 65568176 . G T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24896;SOR=Inf;LSEQ=AGTTTACTACAATATTAAAA;RSEQ=TAATAGTACGATCTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:172,50:222,0:0:2,0:23.1:1:32.7:1:1:0:60:54.5:1:0:0.4 0/1:235:3:0,3:172,60:232,3:0.0128:2,0:10.7:1:20.3:1:0.0186:0:58.3:2:0.0086:0:3.7 +14 65568208 . CA C 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.01584;SOR=Inf;LSEQ=TCTCTTTTTCTCTCTGACCC;RSEQ=AAAAGGAATAGAACTGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:261,191:452,0:0:2,0:23.6:1:30.2:1:1:0:60:49.222:1:0:0.5 0/1:491:7:4,3:280,203:483,7:0.0143:2,2:29.3:1:31.7:1:1:1.03443:60:14:0.0145:0.002:0.3 +14 65568215 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.52534;LSEQ=TTCTCTCTGACCCCAAAAAG;RSEQ=AATAGAACTGAACGGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:182:102,80:166,125:291,182:0.384:2,2:24.2:1:30.3:1:0.84915:1.04151:60:59.667:0.3833:0:1.1 0/1:507:125:73,52:214,168:382,125:0.2465:2,2:25:1:28.6:1:0.6782:1.10:59.8:61.5:0.244:0:1.1 +14 65568285 . C A 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GCAGATTGAAACCTCGGTTG;RSEQ=TCTTCCTGGAATAAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:29:12,17:145,250:395,29:0.0684:2,2:21:1:29.9:1:0.69118:1.22:60:28:0.068:0:1.2 0/0:432:0:0,0:160,270:430,0:0:2,0:23:1:30.7:1:1:0:59.8:22.889:1:0:0.3 +14 65568304 . GA G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.24821;SOR=0.66665;LSEQ=GCTCTTCCTGGAATAAGAGA;RSEQ=AAAAAAAAAATAGAAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:24:7,17:79,178:257,24:0.0848:2,2:27:1:31.1:1:1:1.07757:59.6:48:0.0863:0.0035:0.1 0/1:258:15:6,9:68,172:240,15:0.0581:2,2:26.5:1:30.4:1:0.38125:1.68:60:30:0.0595:0.0039:0.1 +14 65568563 . C T 68 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCTCCCTGCAGACCCAG;RSEQ=TCGGGCATCTAGGCACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:3,5:0.625:2,2:13.6:1:29.6:1:1:2.60168:58.2:10:0.625:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 65569147 . A G 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27342;SOR=0;LSEQ=TCACCGACAACAACAAGCCG;RSEQ=GTCCCCCCCACACACACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:23,265:288,3:0.0103:2,2:20:1:32.7:1:0.2283:5.69:60:6:0.0105:0:1 0/0:202:0:0,0:20,182:202,0:0:2,0:23.1:1:30.3:1:1:0:59.9:32.667:1:0:0.1 +14 65569163 . ACACT A 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=5.000;MSILEN=4;SSF=0.00344;SOR=Inf;LSEQ=GCCGAGTCCCCCCCACACAC;RSEQ=CACTCACTCACTCACTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:6,212:218,0:0:1,0:24.1:1:32.9:1:1:0:60:53.5:1:0:0.2 0/1:141:6:0,6:6,129:135,6:0.0426:1,0:36:1:31.8:1:1:0:60:12:0.0435:0:0 +14 65569195 . TCA T 41 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.64449;SOR=0.47075;LSEQ=TCACTCACTCGCTCTCTCAC;RSEQ=CACACACACACAACACGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:3:0,3:5,109:114,3:0.0256:1,0:21.3:1:26:1:1:0:60:2:0.0177:0.0085:0 0/1:82:1:0,1:5,76:81,1:0.0122:2,0:49:0:30:0:1:0:60:2:0.0123:0:0 +14 65733333 . CT C 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTTTATAGTCTAGAGGT;RSEQ=TTTTTTTTTTTTTAACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:32.5:1:31:1:1:0:42:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 65733748 . C T 61 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.19284;LSEQ=TACGATATCACCTTTCTTTC;RSEQ=TTCTTTCTTTCTTTCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:4,5:9,2:0.1818:2,2:18:1:29.5:1:1:1.22:60:4:0.1818:0:1 0/1:19:4:2,2:7,8:15,4:0.2105:2,2:27.3:1:30.5:1:1:1.13:56.3:8:0.2105:0:1 +14 65734370 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49918;SOR=Inf;LSEQ=CTAAAGGGCCTAGAGAACAT;RSEQ=TATCGGGTGCCTCTCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:118,65:183,0:0:2,0:13.4:1:28.4:1:1:0:36.7:90.5:1:0:0.1 0/1:195:2:1,1:117,75:192,2:0.0103:2,2:16.5:1:29:1:1:1.55626:28.5:4:0.0103:0:1 +14 65734376 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25057;SOR=Inf;LSEQ=GGCCTAGAGAACATATATCG;RSEQ=GTGCCTCTCCTCTTTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:132,87:219,0:0:2,0:13.7:1:30.2:1:1:0:36.2:30.286:1:0:0.1 0/1:244:3:1,2:144,97:241,3:0.0123:2,2:13.7:1:28.7:1:0.56781:2.95574:24:6:0.0124:0:1 +14 65734491 . T A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0134;SOR=0.41902;LSEQ=TAGGCAGAGGCAGAAATGGA;RSEQ=ATCAGGGCCTGCTCAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:29:5,24:32,120:152,29:0.1602:2,2:22.9:1:29.7:1:0.80338:1.27831:58.3:13.5:0.1543:0:1 0/1:176:13:2,11:26,137:163,13:0.0739:2,2:22.5:1:29.4:1:1:1.04356:59.1:26:0.0751:0:1.1 +14 65734498 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23299;SOR=Inf;LSEQ=AGGCAGAAATGGATATCAGG;RSEQ=CCTGCTCAAGGGCACATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:19,123:142,0:0:2,0:24.6:1:31.7:1:1:0:59.8:34.5:1:0:0.3 0/1:133:2:0,2:10,121:131,2:0.015:2,0:16:1:31:0:1:0:60:4:0.0154:0:1 +14 65734529 . GGT G 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.52071;SOR=0;LSEQ=GGCACATGGATGTGTTGGCG;RSEQ=GTGTGTGTGTCGTGGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:0,2:2,88:90,2:0.0217:1,0:28.5:1:33.5:1:1:0:60:4:0.0217:0:0.5 0/0:59:0:0,0:2,57:59,0:0:1,0:17:0:14:0:1:0:60:0:0:0:5 +14 65734600 . G A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03339;SOR=5.24205;LSEQ=GCGAAGTGGAGAGAGAAGAG;RSEQ=ATATGGGAGTGAACAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:4:0,4:0,35:35,4:0.1026:1,0:15.3:1:31.5:1:1:0:60:8:0.1081:0:1 0/1:13:5:1,4:0,8:8,5:0.3846:0,2:17:1:30.4:1:0.38462:0:60:10:0.3846:0:1.2 +14 65935016 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11031;SOR=Inf;LSEQ=CATGTTTACTAAAAGGCCTA;RSEQ=AGAACATATATCGGGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:108,45:153,0:0:2,0:21.3:1:32.5:1:1:0:57.9:152:1:0:0.1 0/1:142:3:1,2:82,57:139,3:0.0211:2,2:16.7:1:27.3:1:0.57024:2.85578:60:6:0.0217:0:1 +14 65935096 . C A 48 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09469;SOR=Inf;LSEQ=TGGAAGATGGTGGTTCCGGC;RSEQ=GAAAGGTTGGATTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:134,143:277,0:0:2,0:23:1:27.6:1:1:0:56.6:7.394:1:0:0.7 0/1:233:3:2,1:117,113:230,3:0.0129:2,2:5.7:1:30.7:1:1:1.93:50.7:6:0.0144:0:1.3 +14 65935102 . G GT 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00882;SOR=Inf;LSEQ=ATGGTGGTTCCGGCCGAAAG;RSEQ=TTGGATTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:120,134:254,0:0:2,0:21.5:1:29.4:1:1:0:56.7:9.16:1:0:0.8 0/1:215:6:0,6:106,102:208,6:0.0279:2,0:15.7:1:25.1:1:0.02912:0:54.3:12:0.0306:0.0047:3.3 +14 65935103 . T A 32 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09026;SOR=Inf;LSEQ=TGGTGGTTCCGGCCGAAAGG;RSEQ=TGGATTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:118,133:251,0:0:2,0:21.1:1:26.1:1:1:0:56.7:4.229:1:0:0.8 0/1:206:3:3,0:100,103:203,3:0.0146:2,0:5.3:1:20.7:1:0.24634:0:60:2:0.0113:0:1.3 +14 65935106 . GA TT 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58389;SOR=2.57517;LSEQ=TGGTTCCGGCCGAAAGGTTG;RSEQ=TTTTTTTTTTTTTTTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:0,1:110,116:226,1:0.0043:2,0:9:0:26:0:1:0:60:2:0.0049:0:1 0/1:181:2:0,2:92,83:175,2:0.011:2,0:25:1:28.5:0:0.2292:0:60:4:0.0122:0:2 +14 65995797 . C T 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01705;SOR=Inf;LSEQ=TCTTTTTTCTCAATTTTCCT;RSEQ=TCATATGACATAACCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:122,87:209,0:0:2,0:27.8:1:32.6:1:1:0:60:68.667:0.9952:0:0.1 0/1:169:5:2,3:88,76:164,5:0.0296:2,2:23.6:1:28.6:1:0.66555:1.73118:60:10:0.0299:0:1.2 +14 65995849 . T A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06742;SOR=Inf;LSEQ=GCACATTGATTCTAATCATC;RSEQ=GTTTTCCTTCATTTTGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:68,101:169,0:0:2,0:24.5:1:30.6:1:1:0:60:168:1:0:0.1 0/1:117:3:2,1:43,71:114,3:0.0256:2,2:15.7:1:25.7:1:0.55784:3.27:60:6:0.0259:0:1 +14 68181468 . G A 74 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGATATAAGTTGAAAAGA;RSEQ=ACTAAGGGATTTTTGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:26.2:1:32:1:1:0:60:10:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:46:0:33:0:1:0:60:2:1:0:1 +14 68290372 . T G 208 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATTTAACATTTTTATTGA;RSEQ=AAGTTTTATGCACAAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:119,343:462,0:0:2,0:23:1:29:1:1:0:60:56.75:0.9978:0:0.1 0/1:391:125:37,88:79,186:265,125:0.3197:2,2:24.2:1:30:1:1:1.01015:60:40.667:0.3177:0:1.3 +14 68290426 . T C 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCTCTTAAACTTGAAATA;RSEQ=GAAAATGTAGGCTTACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:6,166:172,0:0:1,0:23.4:1:30.8:1:1:0:60:171:1:0:0.1 0/1:109:29:0,29:6,74:80,29:0.2661:2,1:18.4:1:30.2:1:0.33863:0:60:28:0.2593:0:2.1 +14 68290442 . CA C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53815;SOR=0;LSEQ=AATATGAAAATGTAGGCTTA;RSEQ=AAAAAAAGATAAATGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:0,2:3,125:128,2:0.0153:1,0:31:1:33.5:1:1:0:60:4:0.0159:0:0 0/0:73:0:0,0:1,72:73,0:0:1,0:22.9:1:29.9:1:1:0:60:35.5:1:0:0.5 +14 68290464 . G A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AAAAAAAGATAAATGATGGT;RSEQ=CTTTTCCATAGGCTAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:1,95:96,0:0:1,0:27.2:1:32.3:1:1:0:60:31:1:0:0.1 0/1:40:7:0,7:1,32:33,7:0.175:1,0:28.4:1:31:1:1:0:60:14:0.175:0:2.4 +14 68290520 . T G 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01056;SOR=Inf;LSEQ=TTGGGTGCATTTCCAACTGC;RSEQ=ATTTCATTTACCCAAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:39,0:0:1,0:22.6:1:27.3:1:1:0:59.1:12:1:0:0.4 0/1:12:3:0,3:1,8:9,3:0.25:2,0:15:1:29.3:1:1:0:60:6:0.25:0:1.7 +14 68291907 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=CACAAGTGTAGCGCTCATAC;RSEQ=CACCTGGATTGGATGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:9,0:0:0,0:34.3:1:29.8:1:1:0:53.2:18:1:0:0.1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:25.5:1:30:1:1:0:60:4:0.6667:0:2 +14 68292097 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16381;SOR=Inf;LSEQ=TTATACTTTTGTCTACATAA;RSEQ=CAGTATCAATTGAAGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:234,29:263,0:0:2,0:22.7:1:33.3:1:1:0:59.9:262:1:0:0 0/1:180:2:1,1:154,24:178,2:0.0111:2,2:13.5:1:24.5:1:0.25916:6.30741:60:4:0.0112:0:1 +14 68301767 . G GA 210 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=55.30664;LSEQ=TTTGAATATATATAGAGGTT;RSEQ=AAAAAAAACTTAATCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:581:5:3,2:393,183:576,5:0.0086:2,2:29:1:29.1:1:0.6557:1.43079:60:10:0.0087:0.0017:0 0/1:517:168:95,73:215,128:343,168:0.325:2,2:24:1:28.5:1:0.21015:1.29003:59.9:41:0.3222:0.0542:0.1 +14 68301990 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17073;SOR=Inf;LSEQ=GAAAAAGTTTAGTTAAAAAA;RSEQ=ATAAATTATTTCTGGAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:3,117:120,0:0:1,0:21.9:1:32.7:1:1:0:60:59:1:0:0.1 0/1:85:2:1,1:2,81:83,2:0.0235:1,2:33.5:1:28.5:1:0.06975:33.24:60:4:0.0235:0:1 +14 68331675 . A T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.8232;SOR=1.13612;LSEQ=GCTTGTGATGTTTATCTAAA;RSEQ=AACTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:120:120,0:0,6:6,120:0.916:0,1:29.8:1:29.7:1:0:0:50.4:59:0.9593:0:1.2 1/1:134:124:121,3:0,1:1,124:0.9254:0,1:30.6:1:28.4:1:0.032:0:48.3:23.8:0.9297:0:1.1 +14 68331956 . GCCTT TCC 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24832;SOR=0;LSEQ=ATTTACCACCCCTCCCCCTT;RSEQ=TTTTTTTTTTTTGAGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:3:0,3:0,76:76,3:0.0375:1,0:20:1:22.2:1:1:0:46.7:2:0.0345:0.025:3 0/0:70:0:0,0:2,64:66,0:0:1,0:18.9:1:27:1:1:0:56.6:2.474:0.9792:0:1 +14 68352497 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17578;SOR=Inf;LSEQ=TCTATTGATAAGGCTTAGGA;RSEQ=TTTCTCAAGTAAAATTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:180,16:196,0:0:2,0:24.4:1:33.1:1:1:0:60:64.333:1:0:0.1 0/1:142:2:1,1:123,17:140,2:0.0141:2,2:21:1:28.5:1:0.23824:7.05987:60:4:0.0141:0:1 +14 68352528 . C T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08487;SOR=Inf;LSEQ=AAAATTAATTAGAGATTCAG;RSEQ=AATGTGGCTTTAAGTAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:278,97:375,0:0:2,0:21.7:1:31.6:1:1:0:60:33.091:1:0:0.1 0/1:295:3:1,2:213,78:291,3:0.0102:2,2:20.7:1:20.7:1:0.18091:5.42404:60:2:0.0068:0:1.7 +14 68352905 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03695;SOR=Inf;LSEQ=TTAAATGAATAAAATGTTCT;RSEQ=TATTTAATTAATTAAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:1,22:23,0:0:1,0:22.9:1:32.6:1:1:0:60:46:1:0:0 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:12.5:1:30.5:1:0.33333:0:60:4:0.3333:0:1.5 +14 68353893 . A G 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAGAGGCATCCTCCTTGA;RSEQ=GTATTTGGCTGAGGAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:826:0:0,0:360,465:825,0:0:2,0:26.9:1:31.2:1:1:0:60:90.667:0.9988:0:0.1 0/1:707:33:15,18:297,376:673,33:0.0467:2,2:22.7:1:31:1:1:1.05:60:66:0.0473:0:1.1 +14 68354012 . TAG T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.17631;SOR=Inf;LSEQ=ATGGTATCAAATAATAAAAT;RSEQ=AGGAAAATGTAAAACAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:30,142:172,0:0:2,0:24.3:1:31.8:1:1:0:59.9:85:1:0:0 0/1:125:2:1,1:32,91:123,2:0.016:2,2:28.5:1:32:0:0.45987:2.82:60:4:0.0161:0:0 +14 68354015 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51059;SOR=0;LSEQ=GTATCAAATAATAAAATTAG;RSEQ=GGAAAATGTAAAACAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:28,136:164,2:0.012:2,2:20.5:1:30.5:1:0.31975:4.79:60:4:0.0123:0:1 0/0:121:0:0,0:30,91:121,0:0:2,0:24.1:1:30.1:1:1:0:60:59.5:1:0:0.1 +14 68679132 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51284;SOR=0;LSEQ=ACTCAGAGCCTTACATAGAG;RSEQ=TGTTAGCAGCAGCAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:54,40:94,2:0.0208:2,2:46.5:1:30.5:1:1:1.34571:60:4:0.0211:0:1 0/0:67:0:0,0:38,29:67,0:0:2,0:24.4:1:31.2:1:1:0:60:66:1:0:0.1 +14 68679150 . A T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15566;SOR=Inf;LSEQ=AGCTGTTAGCAGCAGCAACA;RSEQ=CAGCAGCACCAGCAGCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:64,58:122,0:0:2,0:27:1:30.5:1:1:0:60:244:1:0:0.1 0/1:80:2:1,1:41,37:78,2:0.025:2,2:6:1:28:1:1:1.10668:60:4:0.0253:0:1 +14 68757735 . G T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGTTTCTCCACATTGGCAA;RSEQ=GCTGGTCTCAAACTCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:48:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:28.5:1:1:0:54.5:4:1:0:1 +14 68818292 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43071;LSEQ=GGTACATTGACTAAGAGAGC;RSEQ=CATTACAGGAGAGTGGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:2,11:0.8462:0,0:24.4:1:31.2:1:1:0:60:22:0.8462:0:1.1 1/1:9:8:8,0:1,0:1,8:0.8889:0,0:24.4:1:30.3:1:1:0:60:16:0.8889:0:1.1 +14 68818383 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49875;SOR=0;LSEQ=AGGCATTGATTAGAGGAGAG;RSEQ=GCTCTATGGAGAGGAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:61,36:97,2:0.0202:2,2:19:1:29.5:1:1:1.68496:60:4:0.0204:0:1.5 0/0:89:0:0,0:51,38:89,0:0:2,0:23.6:1:30.2:1:1:0:60:21.25:1:0:0.3 +14 68818394 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49758;SOR=Inf;LSEQ=AGAGGAGAGCGCTCTATGGA;RSEQ=AGGAGTCAGCGTGGACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:61,43:104,0:0:2,0:31.2:1:33.2:1:1:0:60:208:1:0:0.1 0/1:104:2:1,1:56,46:102,2:0.0192:2,2:21.5:1:29:0:1:1.21507:60:4:0.0194:0:1 +14 68818442 . G T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=AAGAGTGAGGGAATGTGCGG;RSEQ=ATTAGACCACAGTCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:33,44:77,0:0:2,0:20.6:1:31.2:1:1:0:60:76:1:0:0.1 0/1:86:2:1,1:39,45:84,2:0.0233:2,2:38:0:27.5:1:1:1.15:60:4:0.0233:0:1 +14 68818450 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49849;SOR=Inf;LSEQ=GGGAATGTGCGGGATTAGAC;RSEQ=ACAGTCAGGGAGCAGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:26,39:65,0:0:2,0:20.2:1:31.5:1:1:0:60:130:1:0:0.1 0/1:74:2:1,1:33,39:72,2:0.027:2,2:30.5:1:30.5:1:1:1.18:60:4:0.027:0:1 +14 68878038 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38862;SOR=1.38457;LSEQ=TGGTAATGAACTGAGCCTCC;RSEQ=AGTACTCTCTGGACTACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:21:20,1:100,4:104,21:0.168:1,1:21.8:1:30:1:1:1.24762:60:42:0.168:0:1 0/1:96:21:21,0:72,3:75,21:0.2188:1,1:23.1:1:28.3:1:1:0:60:20:0.2128:0:1.1 +14 68878369 . C A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00096;SOR=4.93741;LSEQ=CCAGCAGCAGCTATTAGGGC;RSEQ=TAAAGAAACCAGCATTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:7:0,7:1,65:66,7:0.0959:1,0:31.7:1:29.7:1:1:0:57.4:14:0.0972:0:1 0/1:49:17:0,17:1,31:32,17:0.3469:1,1:26.7:1:30.3:1:1:0:60:34:0.3542:0:1.1 +14 68878582 . A G 43 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=TTTGTTGAGGACTAATTTGT;RSEQ=TATGAATTAAATAATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:26.3:1:27.3:1:1:0:50.3:2:0.6667:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:29:0:1:0:60:2:1:0:0 +14 68934690 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00998;SOR=4.08535;LSEQ=ACAGAATAGTTGGAATAAGC;RSEQ=TACAGCCTTTTAAGGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:23:23,0:40,1:41,23:0.3594:1,1:29:1:30.4:1:1:0:60:46:0.3594:0:1.2 1/0:20:14:14,0:6,0:6,14:0.7:0,1:20.7:1:29:1:1:0:60:28:0.7:0:1 +14 68934769 . A T 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.67391;SOR=1.71242;LSEQ=AAAATGGTTTTTTTTTTTTT;RSEQ=AATAAGCCTTGTGACTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:3,0:194,5:199,3:0.0149:1,0:21.3:1:32.7:1:1:0:60:6:0.0151:0:1.3 0/1:119:3:3,0:112,4:116,3:0.0252:1,0:35.7:1:30.3:1:1:0:60:6:0.0273:0:2.3 +14 68935112 . G A 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00491;SOR=5.59798;LSEQ=GGCCAGTGATATTTACCCTA;RSEQ=TGAGAGCAAGAGAGCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:5:0,5:2,80:82,5:0.0575:1,0:15.4:1:31.2:1:1:0:60:10:0.0588:0:1 0/1:31:8:0,8:0,23:23,8:0.2581:1,0:31.8:1:31.3:1:1:0:60:16:0.2581:0:1 +14 68944245 . T C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00061;SOR=5.49177;LSEQ=GCCAGTGGCTCTGTGGGCAA;RSEQ=ACGTATGAAAGAGGACTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:6:6,0:101,1:102,6:0.0556:1,0:19.7:1:31.3:1:1:0:60:12:0.0566:0:1 0/1:65:16:15,1:48,1:49,16:0.2462:1,1:20.6:1:31.9:1:0.43462:3.13049:60:32:0.2462:0:1.1 +14 68944321 . AT A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.73238;SOR=1.06231;LSEQ=AGTTAGTGCATTTCATAACA;RSEQ=TTTTTTTTTTCAAACTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:577:91:75,16:425,59:484,91:0.1577:2,2:22.5:1:30.5:1:0.17468:1.53545:57.5:21.75:0.1545:0.0416:1.1 0/1:446:74:64,10:302,65:367,74:0.1659:2,2:23.9:1:29.9:1:0.4973:1.38:57.5:23.667:0.1632:0.0381:1.1 +14 68944693 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACCAGGCACCTCAAAG;RSEQ=GGTTTAACCACATTAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:0,18:18,2:0.1:1,0:24:1:32:0:1:0:60:4:0.1053:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:13.5:1:29.5:1:1:0:60:4:1:0:0.5 +14 68963082 . T C 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTCCTCTCTGCAGCAG;RSEQ=GTTCCCCAGATATGCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:39:1:33:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:26:0:31:0:1:0:60:2:1:0:0 +14 68963737 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19544;SOR=Inf;LSEQ=GGGGGCATGAACTTTTTTCC;RSEQ=CATAACTTCAATAAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:192,32:224,0:0:2,0:22.4:1:31:1:1:0:59.9:23.889:1:0:1 0/1:178:2:1,1:150,26:176,2:0.0112:2,2:25:1:28:1:0.28109:5.68028:60:4:0.0114:0:2 +14 68963746 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14673;LSEQ=AACTTTTTTCCCCATAACTT;RSEQ=AATAAACAACAGTTTTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:269:229:191,38:31,9:40,229:0.8513:2,2:22:1:30.4:1:0.36999:1.46:60:75.333:0.8561:0:1.1 0/1:213:97:81,16:91,25:116,97:0.4554:2,2:23.4:1:29.2:1:0.38664:1.39:60:47.5:0.4545:0:1.1 +14 68963946 . G A 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30393;SOR=4.76378;LSEQ=TATTGGGAAAGAGTCTTGTG;RSEQ=TGAAACACCCATCGTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:1:1,0:47,235:282,1:0.0035:2,0:1:0:25:0:0.16961:0:60:2:0.0036:0:1 0/1:180:3:1,2:22,155:177,3:0.0167:2,2:14.3:1:22.7:1:0.33807:3.49:60:2:0.0113:0:1.3 +14 69059620 . G GATCT 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTCATTCTTATGGTCTGA;RSEQ=ATCAGGAAGGTCCATGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:30:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 69060959 . GGA G 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGTGAGTGAGGCGGTGGG;RSEQ=GAGAGAGAGGAAAAGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:2,1:58,2:60,3:0.0476:1,2:29.3:1:32.3:1:0.13827:12.89309:60:6:0.0508:0:0 0/0:15:0:0,0:14,1:15,0:0:1,0:21.1:1:29.3:1:1:0:60:14:1:0:0.1 +14 69061064 . G A 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTTTGCACATGTCTACC;RSEQ=TTATGTACATTCCTATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:344,45:389,0:0:2,0:23.3:1:30:1:1:0:60:54.571:1:0:0 0/1:246:26:22,4:203,17:220,26:0.1057:2,2:22.6:1:29.7:1:0.25319:2.16241:60:52:0.1061:0:1.1 +14 69061259 . C G 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGCTCCAGAAATCCTCC;RSEQ=ACCTCAGCCTCCTGAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:76:0,76:1,150:151,76:0.3348:1,1:26:1:32.8:1:1:0:60:152:0.3393:0:1.1 0/0:143:0:0,0:2,141:143,0:0:1,0:24.7:1:31.8:1:1:0:59.9:70.5:1:0:0.1 +14 69117298 . G A 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08954;SOR=0;LSEQ=TAAAATCAGACCAGAACCTG;RSEQ=GGATGAGCCAAGAAATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:7:7,0:48,1:49,7:0.125:1,0:31.7:1:30.1:1:1:0:60:14:0.1273:0:1 0/0:28:0:0,0:28,0:28,0:0:1,0:24.5:1:30.6:1:1:0:60:27:1:0:0.4 +14 69117377 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13024;SOR=Inf;LSEQ=GTTTAAAGTAGCATCTAATT;RSEQ=AAAACAACTAGTTTCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:198,3:201,0:0:1,0:26.3:1:32.2:1:1:0:60:66:1:0:1 0/1:114:2:2,0:110,2:112,2:0.0175:1,0:18:1:29:1:1:0:60:4:0.0175:0:1 +14 69117387 . A G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07619;LSEQ=GCATCTAATTCAAAACAACT;RSEQ=GTTTCTCAGAGGGCTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:242:218:210,8:24,0:24,218:0.9008:1,1:25.6:1:32.8:1:1:0:60:217:0.9004:0:1.1 0/1:145:59:54,5:81,4:85,59:0.4069:1,2:23.5:1:31.8:1:0.4873:1.86654:60:118:0.4097:0:1 +14 69117450 . T C 207 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGATGAATCCTCTCAAAA;RSEQ=AGGAAAAGCTAGGTTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:733:88:60,28:412,233:645,88:0.1201:2,2:23.7:1:32.1:1:0.47737:1.21:60:87:0.1202:0:1.8 0/0:526:0:0,0:332,194:526,0:0:2,0:23.6:1:29:1:1:0:60:525:1:0:0.4 +14 69117512 . T C 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14194;LSEQ=ACACAGAATTTTGGCACATT;RSEQ=GCATATCTGGTTTCTCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1195:1006:510,496:89,98:187,1006:0.8418:2,2:26.6:1:31.2:1:0.47368:1.13:60:124.75:0.8415:0:1.2 0/1:937:403:203,200:269,264:533,403:0.4301:2,2:27:1:29.8:1:1:1.00388:59.9:200.5:0.4303:0:1.1 +14 69117751 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04113;SOR=0;LSEQ=CTGGGTTAACAGTACAGTAA;RSEQ=TGAAGTTTCTAAATATGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:0,36:0,0:0,36:1:0,1:23.3:1:30.8:1:1:0:60:72:1:0:1.1 1/1:20:17:0,17:0,3:3,17:0.85:0,1:25.7:1:30.1:1:1:0:60:34:0.85:0:1 +14 69118621 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTGAATCATCCCGGAAC;RSEQ=GTCTTGGTGCTGTGGTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 69798284 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGGTGAGTTCTGCTCCC;RSEQ=GGGGTGGGGCTGTAGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:28.5:1:1:0:60:4:1:0:1 +14 70439711 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27899;SOR=0;LSEQ=CTTGGCCATGGGAGTCAAGG;RSEQ=CCCTGGGAGTGAGTCAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:2,1:11,8:19,3:0.1364:2,2:32.7:1:31.7:1:1:1.43:60:6:0.1429:0:1.3 0/0:13:0:0,0:8,5:13,0:0:2,0:22.4:1:30.8:1:1:0:60:26:1:0:0.1 +14 70439776 . A G 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06213;SOR=0;LSEQ=TTCCCCAGAGGTGATTATTG;RSEQ=CCAAGGAGGAGAGAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:2,5:6,6:12,7:0.3684:2,2:22.4:1:31.1:1:0.63325:2.38223:60:14:0.3889:0:1.3 0/0:9:0:0,0:4,5:9,0:0:2,0:27.8:1:28.8:1:1:0:60:18:1:0:0 +14 71133586 . A T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49677;SOR=0;LSEQ=GATGGTGATGATGATGATGA;RSEQ=GATGATGATGAAGAGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:10,6:16,2:0.1111:2,2:28.5:1:32:0:1:1.61828:60:4:0.1111:0:1.5 0/0:13:0:0,0:8,5:13,0:0:2,0:25.2:1:28.4:1:1:0:60:26:1:0:0.1 +14 71133607 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50758;SOR=0;LSEQ=GATGATGATGAAGAGATGAT;RSEQ=ATTGCCTCTGGTAGCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:18,2:0.1:2,2:18:1:27:0:1:1.54:60:4:0.1:0:1 0/0:13:0:0,0:7,6:13,0:0:2,0:29.6:1:30.1:1:1:0:60:26:1:0:0.1 +14 71133638 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GTAGCTTATTCCTAAGGCTG;RSEQ=CTACAACAAAGTCCCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:11,2:0.1538:2,2:24:1:30:1:1:2.45:60:4:0.1538:0:1 0/0:7:0:0,0:3,4:7,0:0:2,0:22.9:1:32.1:1:1:0:60:14:1:0:0.1 +14 73128902 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51278;SOR=0;LSEQ=CACTTACCACATCCAACTCG;RSEQ=AGAAATAAAAATACCTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:138,43:181,2:0.0109:2,2:28:1:30.5:1:0.42407:3.18409:60:4:0.0109:0:1 0/0:130:0:0,0:98,31:129,0:0:2,0:24.9:1:31.8:1:1:0:60:128:0.9922:0:0.3 +14 73128962 . G T 42 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04438;SOR=Inf;LSEQ=TTAAAAAGCCTGAGAGAGCA;RSEQ=AGTTGATCTTTATTTTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:217,182:399,0:0:2,0:25.7:1:32.6:1:1:0:60:198.5:1:0:0.5 0/1:340:4:1,3:179,157:336,4:0.0118:2,2:11:1:21.3:1:0.34582:3.40895:60:3:0.0089:0:1.5 +14 73128983 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.41225;LSEQ=AGTTGATCTTTATTTTCTTA;RSEQ=TTAAAATGTGGGGCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:177:85,92:117,121:238,177:0.4255:2,2:27.5:1:32.7:1:0.843:1.04649:60:354:0.4255:0:1.1 1/0:343:220:104,116:59,64:123,220:0.6414:2,2:27.9:1:30.8:1:0.91073:1.02817:59.9:54:0.6372:0:1.2 +14 73129086 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12959;SOR=Inf;LSEQ=CAAAATTGCGCTTAACTTTT;RSEQ=AAGTAGGAGGTACTTTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:17,103:120,0:0:2,0:24.5:1:32.1:1:1:0:60:240:1:0:0.1 0/1:68:2:1,1:10,56:66,2:0.0294:2,2:25.5:1:27.5:1:0.29939:5.39:60:4:0.0294:0:1 +14 73129120 . C A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00126;SOR=4.86973;LSEQ=TTTAAACAAAAATACTGTGC;RSEQ=ATGTCAGCACTTTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:16:1,15:2,51:53,16:0.2319:1,1:32.6:1:31.8:1:0.55289:1.69:60:32:0.2319:0:1 1/0:25:15:0,15:0,10:10,15:0.6:0,1:30.4:1:31.1:1:1:0:60:30:0.625:0:1 +14 73208742 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCACACAGACTTCGTCCC;RSEQ=CAGTCCCTGCTCCTTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:1:31:1:1:0:60:4:1:0:2 +14 74204636 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGATTACAGGCGTGCAG;RSEQ=ACCACACCTGGCTAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:16.5:1:34.5:1:1:0:59:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 74205878 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23153;SOR=0;LSEQ=GGTTGCTGCGAGGGTTGCTG;RSEQ=GGCATGGAATAGAAGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:9,4:13,3:0.1875:2,2:25.3:1:31:1:1:1.11662:60:6:0.1875:0:1.3 0/0:13:0:0,0:8,5:13,0:0:2,0:19.7:1:30.5:1:1:0:60:26:1:0:0.2 +14 74207345 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGGCAGCAAAAGCCACA;RSEQ=TGGCTCCCCTCTCCTCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 75181614 . G A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAACCTAAAAAGAAAGAAAA;RSEQ=AAGGATCCCAGCGCATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:29:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:25.5:1:29.5:1:1:0:60:4:1:0:0 +14 75182937 . G A 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAGTGGTCACCATAGCA;RSEQ=TGACCATGTTTAATGAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:9.5:1:33:0:1:0:60:4:1:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:34:0:32:0:1:0:60:2:0.5:0:1 +14 75189967 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09344;SOR=Inf;LSEQ=TCTTAATGTGAATTTTTTTC;RSEQ=CTGGCAGGTATCCCATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:28,14:42,0:0:2,0:21:1:30.8:1:1:0:60:41:1:0:0.1 0/1:19:2:2,0:13,4:17,2:0.1053:2,0:44.5:1:31.5:1:1:0:60:4:0.1053:0:1 +14 75189968 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAATGTGAATTTTTTTCC;RSEQ=TGGCAGGTATCCCATGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:27,13:40,2:0.0476:2,2:10:1:29.5:1:1:2.03815:59:4:0.0476:0:1 0/0:19:0:0,0:15,4:19,0:0:2,0:26.3:1:30.5:1:1:0:59.9:38:1:0:0.3 +14 75190034 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2027;SOR=Inf;LSEQ=AGAAATTGGGGCAGAAGTAT;RSEQ=GAGTGGCTCTAAGGTAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:26,32:58,0:0:2,0:27.6:1:31.2:1:1:0:60:116:1:0:0.1 0/1:48:2:1,1:21,25:46,2:0.0417:2,2:42.5:1:29.5:1:1:1.19:45.5:4:0.0417:0:1.5 +14 75322327 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.8737;LSEQ=GAAAGTAAATCTGTGGCTCA;RSEQ=AGAGACTTCGGTATTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:134:62,72:165,171:336,134:0.2851:2,2:25.8:1:32.5:1:0.60995:1.12027:60:43.667:0.2829:0:1.1 1/0:456:277:138,139:83,96:179,277:0.6075:2,2:25.1:1:30.6:1:0.50238:1.15:59.9:33.625:0.6018:0:1.2 +14 76119531 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5312;SOR=0;LSEQ=GTTAGGGAGGGAATAGGATC;RSEQ=GAATGCACATCAGAAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:22,10:32,2:0.0588:2,2:12:1:29:1:1:2.1448:60:4:0.0606:0:1 0/0:19:0:0,0:14,5:19,0:0:2,0:24:1:29.3:1:1:0:60:38:1:0:0 +14 76119728 . C T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.59564;LSEQ=AGGCCAAGGTGGGTGGATCA;RSEQ=GAGGTCAGGAGTTCGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:25.5:1:32:0:1:0:60:4:0.2857:0:1.5 0/1:5:2:0,2:0,3:3,2:0.4:0,0:13:0:31:0:1:0:45:4:0.4:0:1 +14 76996321 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAGTGCTGGGATTACAGG;RSEQ=GTGAGCCACCACACACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:0:32:0:1:0:37:4:1:0:1.5 +14 76998511 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTCCCGGCATGACTTCTG;RSEQ=GTAAACCTGCCAGTTCCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:29:1:1:0:60:4:1:0:1 +14 77427469 . G C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20662;LSEQ=GGGTGGGGGTCTCTGTCCTA;RSEQ=CATTTGGTTGCAGCACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:267:157,110:37,33:70,267:0.7899:2,2:25:1:31.3:1:0.41563:1.27:59.7:32.375:0.792:0:1.4 0/1:355:155:84,71:112,87:199,155:0.4366:2,2:25.5:1:30.4:1:0.74673:1.08786:59.3:30:0.4348:0:1.6 +14 77427556 . T A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11868;SOR=Inf;LSEQ=CACACCTTCACACCGAAATG;RSEQ=GCTCCATTCCCTTTGCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:88,179:267,0:0:2,0:24.5:1:29:1:1:0:59:11.714:1:0:0.7 0/1:259:3:2,1:85,170:255,3:0.0116:2,2:16.7:1:22.3:1:0.26359:3.98:48:2:0.0082:0:3 +14 77427558 . C A 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12427;SOR=0;LSEQ=CACCTTCACACCGAAATGTG;RSEQ=TCCATTCCCTTTGCTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:4:2,2:82,178:260,4:0.0152:2,2:26.3:1:32:0:0.59413:2.16:60:8:0.0166:0:2 0/0:248:0:0,0:79,169:248,0:0:2,0:23.9:1:30.2:1:1:0:58.7:15.533:1:0:0.5 +14 77427574 . A AT 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.86809;LSEQ=TGTGCTCCATTCCCTTTGCT;RSEQ=TTTTTTTTTCTTTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:7:4,3:40,116:156,7:0.0409:2,2:27.3:1:30:1:0.0858:3.83:56.9:14:0.0519:0:0.6 0/1:168:6:2,4:44,109:153,6:0.0357:2,2:18.2:1:30:1:1:1.24:60:12:0.0435:0:0 +14 77427579 . T TTTTTC 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=0.01421;SOR=Inf;LSEQ=TCCATTCCCTTTGCTATTTT;RSEQ=TTTTCTTTTCTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:32,114:146,0:0:2,0:21.2:1:30.6:1:1:0:56.9:72:1:0:1 0/1:144:6:0,6:39,97:136,6:0.0417:2,0:16.8:1:29.6:1:0.1881:0:53:12:0.0423:0.0208:1.2 +14 77493590 . G C 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=AGTCGCGCGGTGTGGCTGCT;RSEQ=CTTCCCAGGCTCACCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:20:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:29.5:1:1:0:60:4:1:0:1.5 +14 77493760 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.2287;SOR=0;LSEQ=ATCAACGTGGTTGAGCTGTT;RSEQ=TTGCTGCTGCTGCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:19,18:37,2:0.0513:2,2:37:0:31:0:1:1.05412:42:4:0.0513:0:2.5 0/0:42:0:0,0:20,22:42,0:0:2,0:27.7:1:30.6:1:1:0:54:41:1:0:0.7 +14 77493761 . TTGCTGC T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=10.000;MSILEN=3;SSF=0.19611;SOR=1.79687;LSEQ=TCAACGTGGTTGAGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:13:5,8:16,12:28,13:0.3171:2,2:26.9:1:31.1:1:0.32642:2.09362:57:26:0.3171:0.0488:0.2 0/1:46:21:7,14:12,11:23,21:0.4565:2,2:27.9:1:28.8:1:0.23867:2.14268:55.7:42:0.4565:0.087:0.2 +14 77493788 . CTGCTGT TTGC 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=10.000;MSILEN=3;SSF=0.00031;SOR=0.1961;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:26:12,14:8,11:19,26:0.5778:2,2:36:1:31.8:1:1:1.17:49.8:52:0.5778:0:1.6 0/1:48:10:2,8:12,19:31,10:0.2083:2,2:28.6:1:30.8:1:0.44737:2.47411:45.5:20:0.2128:0.0208:0.9 +14 77493797 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.49561;SOR=Inf;LSEQ=TGCTGCTGCTGCTGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:21,25:46,0:0:2,0:31.8:1:33:1:1:0:52.2:45:1:0:1.1 0/1:50:2:0,2:18,30:48,2:0.04:2,0:24.5:1:27:1:0.5298:0:50.5:4:0.0408:0:1.5 +14 77493815 . T C 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.02074;SOR=0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGTTGCGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:3,2:19,25:44,5:0.102:2,2:19.2:1:33.6:1:0.64567:1.95:40:10:0.102:0:2 0/0:55:0:0,0:20,35:55,0:0:2,0:22.7:1:29.1:1:1:0:53.4:26.5:1:0:0.7 +14 77493860 . C T 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.11067;SOR=0;LSEQ=GCGGCGGCCGCCGCTGCTGC;RSEQ=GCCGCCGCCGCCGCTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,3:5,2:0.25:2,2:39:1:32.5:1:1:1.41:60:4:0.2857:0:2 0/0:15:0:0,0:4,10:14,0:0:2,0:10.3:1:29.1:1:1:0:58.9:28:1:0:0.9 +14 77493875 . T C 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=GCTGCCGCCGCCGCCGCCGC;RSEQ=TCCTTAGCCGACAGGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:24:1:34:1:1:0:60:4:1:0:2 0/1:5:2:1,1:1,2:3,2:0.4:2,2:18.5:1:28.5:1:1:1.73:60:4:0.5:0:2 +14 78149694 . C G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13116;SOR=Inf;LSEQ=TTCTTTTTCTGATCATTTTA;RSEQ=TACACGTTTCAGGAAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:8,0:0:2,0:23.3:1:32.3:1:1:0:38.4:16:1:0:0.6 0/1:13:4:2,2:5,4:9,4:0.3077:2,2:25.5:1:30.8:1:1:1.22862:40.8:8:0.3077:0:1 +14 78149834 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49275;SOR=Inf;LSEQ=GCTGGGGAACACTGTAGACT;RSEQ=TTCCAGTTTTGCCATGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:34,0:0:2,0:29.2:1:31.9:1:1:0:58.6:33:1:0:0.1 0/1:35:2:1,1:16,17:33,2:0.0571:2,2:28.5:1:29:1:1:1.06:60:4:0.0571:0:1 +14 78150099 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAATTTTTGTATTTTTAGTA;RSEQ=AGACAGGGTTTCCCCATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:28.5:1:1:0:49:4:1:0:1 +14 78150227 . C T 66 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19394;SOR=0;LSEQ=GTCCAGCTGACAATATCATC;RSEQ=CTCTTACAGATGCGCATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:16.8:1:33:1:1:0:60:8:1:0:1.3 0/1:7:3:2,1:3,1:4,3:0.4286:2,2:29:1:29.7:1:1:1.41418:60:6:0.4286:0:1 +14 78150336 . C T 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01238;SOR=0;LSEQ=CCCTTTGTCTTCGTCATTTT;RSEQ=GCAAATTACTGGAAGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:11:7,4:3,2:5,11:0.6875:2,2:24.7:1:30.7:1:1:1.16:55.1:22:0.6875:0:1.2 0/0:6:0:0,0:3,3:6,0:0:2,0:31.3:1:29.5:1:1:0:60:12:1:0:0 +14 78514879 . CT C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53512;SOR=0;LSEQ=TGGTGGTTTTCTGTCTCTTT;RSEQ=TGGTGAGTTTCTCTAAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:28,35:63,2:0.0303:2,2:28.5:1:34.5:1:1:1.25:60:4:0.0313:0:0 0/0:37:0:0,0:16,21:37,0:0:2,0:19.3:1:29.1:1:1:0:60:36:1:0:0.2 +14 78514913 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.53131;SOR=0;LSEQ=CTAAAGCGGCAGTTCTCAAA;RSEQ=TGTGGTGTGCATCAGGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:5,22:27,2:0.069:2,2:10:1:27:0:0.37685:4.11:60:4:0.069:0:1 0/0:16:0:0,0:5,11:16,0:0:2,0:18.3:1:30.1:1:1:0:60:32:1:0:0.1 +14 78628632 . T C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GAGGGTGCAGATGGCAGTGG;RSEQ=GGTGAGGAGGCAGCGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:10,17:27,2:0.069:2,2:21:1:27.5:1:1:1.67:60:4:0.0714:0:1 0/0:6:0:0,0:2,4:6,0:0:2,0:34:1:27.2:1:1:0:60:5:1:0:0.3 +14 78958326 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1908;SOR=Inf;LSEQ=GGTGCTGAGATTCGGATTCC;RSEQ=CCTCTGCTGCTTACCATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:17,12:29,0:0:2,0:27.3:1:31:1:1:0:60:58:1:0:0.1 0/1:23:2:1,1:13,8:21,2:0.087:2,2:32:1:29.5:1:1:1.58984:60:4:0.087:0:1 +14 78958489 . G A 53 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGATATGACATACATTAT;RSEQ=GGTCTATCACATGATAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:34.3:1:34:0:1:0:60:6:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:14:1:30.5:1:1:0:60:4:1:0:1 +14 80471794 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17586;SOR=Inf;LSEQ=CCTATGTGCTGTCTATATCT;RSEQ=ACATATGATAGTGTTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:157,85:242,0:0:2,0:24.2:1:31.7:1:1:0:60:33.571:0.9958:0:0.3 0/1:176:2:1,1:112,62:174,2:0.0114:2,2:18:0:30.5:1:1:1.79994:60:4:0.0114:0:1 +14 80471852 . A G 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTTTCTACTCAAACATTCC;RSEQ=TGAACTCACTCCCCAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:55:27,28:184,164:348,55:0.1365:2,2:28.9:1:30.8:1:0.66375:1.16306:60:110:0.1389:0:1.5 0/0:333:0:0,0:168,165:333,0:0:2,0:25.9:1:29.4:1:1:0:60:46.571:1:0:0.7 +14 80471876 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.07193;LSEQ=ACTCACTCCCCAGTGAGGAA;RSEQ=ATGGAGGCAAAAGCGAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:160:74,86:131,130:261,160:0.38:2,2:25.8:1:30.6:1:0.48214:1.17066:60:159:0.3831:0:1.1 1/0:318:178:85,93:67,73:140,178:0.5597:2,2:25.5:1:29.6:1:1:1.00418:60:356:0.5615:0:1.1 +14 80471918 . T C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.42223;LSEQ=CCTTCATTTGTCCATAAGAA;RSEQ=ATTGATTTGTTTATGCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:121:47,74:53,100:153,121:0.4416:2,2:25.3:1:32.5:1:0.52793:1.20:60:242:0.4449:0:1.2 0/1:220:55:24,31:63,102:165,55:0.25:2,2:22.1:1:31.1:1:0.52529:1.25:59.5:110:0.2523:0:1.2 +14 80472006 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=6.56947;LSEQ=TTTCATGGAAACTAGAGTGT;RSEQ=ACAGCCAAGGCTGGAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:15:1,14:2,56:58,15:0.2055:1,1:20.6:1:32:1:0.50389:1.98:60:30:0.2055:0:1 1/0:41:26:2,24:1,14:15,26:0.6341:1,2:23.8:1:30.7:1:1:1.16:60:52:0.6341:0:1 +14 80952019 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCAATTAAATAAGATTTGG;RSEQ=ACATAATAGGTCCACAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:2,0:167,7:174,2:0.0113:1,0:15:1:31:1:1:0:60:4:0.0116:0:1 0/0:70:0:0,0:67,3:70,0:0:1,0:26.9:1:31.5:1:1:0:60:34:1:0:0.7 +14 80952038 . A G 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACATAATAGGTCCACAAG;RSEQ=ATTTAGCAATGAATGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:224,35:259,0:0:2,0:23.9:1:30.5:1:1:0:60:128.5:1:0:0.4 0/1:109:10:9,1:87,12:99,10:0.0917:2,2:20.2:1:30.1:1:1:1.24:60:20:0.0943:0:2.8 +14 80952091 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=6.70708;LSEQ=TTGAATTAAGGGAAATAATG;RSEQ=TTTCTCGAGTGGAAGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:105:66,39:322,198:520,105:0.1677:2,2:27.2:1:32.6:1:0.9124:1.04:59.9:104:0.168:0:3 1/0:365:210:133,77:85,70:155,210:0.5753:2,2:24.5:1:31.4:1:0.10666:1.42:60:104:0.5762:0:3 +14 80952097 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.05337;LSEQ=TAAGGGAAATAATGTTTTCT;RSEQ=GAGTGGAAGGCCACTAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:114:69,45:338,221:559,114:0.1691:2,2:27:1:30.6:1:1:1.00:60:113:0.1694:0:3 1/0:400:236:144,92:88,76:164,236:0.59:2,2:25.2:1:29.8:1:0.15046:1.35:60:117:0.5879:0:2.8 +14 80952108 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.45719;LSEQ=ATGTTTTCTCGAGTGGAAGG;RSEQ=CACTAGTGCTGAGGAAACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:756:126:71,55:347,283:630,126:0.1667:2,2:26.7:1:29.9:1:0.84458:1.05:60:62:0.168:0:2.8 0/1:441:208:123,85:123,109:232,208:0.4717:2,2:27.5:1:28.9:1:0.21193:1.28:60:207:0.4737:0:2.8 +14 80952410 . A G 45 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26667;SOR=Inf;LSEQ=TTTAACTGTTGCAATTAGCT;RSEQ=GAAGGGTGGGGAATCCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:11,3:0.2143:0,0:23.3:1:29:1:1:0:60:6:0.2143:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:17:0:32:0:1:0:60:2:1:0:1 +14 81376407 . G T 16 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.39215;LSEQ=TACCTCACCAGATACCAAAT;RSEQ=ATGATCCTATTTTCCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:108,69:177,2:0.0112:2,2:21:0:31.5:1:1:1.56112:60:4:0.0112:0:1.5 0/1:129:2:0,2:79,48:127,2:0.0155:2,0:19:1:16:1:0.14838:0:60:1:0.0079:0:1.5 +14 81376490 . T C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=2.74611;LSEQ=TAATATAATGTATATTAATA;RSEQ=CTCACTTGATATAAATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:70:32,38:108,108:216,70:0.2448:2,2:27.1:1:31.7:1:0.58315:1.18678:60:69:0.2447:0:1.1 0/1:210:99:46,53:60,51:111,99:0.4714:2,2:22.9:1:31:1:0.33322:1.35351:60:48.5:0.4686:0:1.2 +14 81376511 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17096;SOR=Inf;LSEQ=CTCACTTGATATAAATGCAT;RSEQ=ATTTAAAGATTAGGTCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:132,151:283,0:0:2,0:24.9:1:32.1:1:1:0:60:93.333:1:0:0.3 0/1:200:2:1,1:92,106:198,2:0.01:2,2:25.5:1:28:1:1:1.15:60:4:0.0102:0:1 +14 81422178 . C A 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACGCATCCCCAGCTTACCG;RSEQ=CCAGTACGCAGACTCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:846:0:0,0:365,481:846,0:0:2,0:25.3:1:31.7:1:1:0:60:83.6:1:0:0.2 0/1:760:70:29,41:305,385:690,70:0.0921:2,2:24.6:1:28.5:1:0.70556:1.11983:60:22.333:0.0897:0:1.2 +14 81422220 . A C 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCCGGGAGAGATCAGGGT;RSEQ=GGACCCAGAGATCAAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:161,324:485,0:0:2,0:24.2:1:30.6:1:1:0:60:160.667:1:0:0.2 0/1:419:28:12,16:145,246:391,28:0.0668:2,2:25.6:1:30:1:0.54983:1.27:60:56:0.0676:0:1.1 +14 81422257 . G C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23665;SOR=0.74528;LSEQ=GGCATCTGCAGAGGTGGCCC;RSEQ=AAGTGCACAAAAGCAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:60:8,52:32,152:184,60:0.2459:2,2:24.2:1:32.9:1:0.55003:1.36676:60:120:0.2459:0:1.1 0/1:174:34:8,26:26,114:140,34:0.1954:2,2:21.2:1:31:1:0.48095:1.35:60:33:0.1953:0:1.1 +14 81422286 . C G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00096;SOR=Inf;LSEQ=AAAAGCAGCTCAATAACAGC;RSEQ=CGAAGTAGTGTGTGAGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:8,138:146,0:0:2,0:22:1:31.2:1:1:0:60:35.5:1:0:0.2 0/1:89:7:1,6:4,78:82,7:0.0787:1,2:23.6:1:30.6:1:0.34264:3.18:60:14:0.0805:0:1.1 +14 81528412 . T A 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACTGTCATGCTTTTTAAT;RSEQ=ATGTGTTTTTATAATTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:278,36:314,0:0:2,0:24.3:1:30.9:1:1:0:60:77.5:1:0:0.1 0/1:228:36:27,9:153,39:192,36:0.1579:2,2:21.8:1:27.8:1:0.51035:1.30607:60:72:0.1593:0:1 +14 81534271 . C CTA 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=14.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAACATTCCACAGGGTGACA;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:28:1:31:1:1:0:60:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 81534440 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=0.10165;LSEQ=ACAAGATCTGAAAAAAAAAG;RSEQ=AGTAAGTAATTTTAACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:61:61,0:12,0:12,61:0.8356:0,1:24.9:1:32.3:1:1:0:59.6:29.5:0.831:0:1 0/1:24:8:8,0:16,0:16,8:0.3333:1,0:23.1:1:32.1:1:1:0:60:16:0.3333:0:1.3 +14 81534709 . A T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00776;SOR=Inf;LSEQ=GTGCAGCATAGACCTAAGCC;RSEQ=CAACCACTCTTGACTGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:145,328:473,0:0:2,0:24.9:1:30.1:1:1:0:59.9:235.5:1:0:0.1 0/1:290:5:2,3:90,194:284,5:0.0172:2,2:11.4:1:28.4:1:0.65491:1.44:60:10:0.0174:0:1.4 +14 81536844 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCGGGCATGGTGGTGTGT;RSEQ=CCTGTAATCCCAGCTACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:31.5:1:1:0:32.5:4:1:0:1 +14 81554209 . G T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30228;SOR=0;LSEQ=TGCATATTTTTCTCATGAAC;RSEQ=TTTGTTAAAACTGATTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:4:2,2:321,37:358,4:0.011:2,2:14.8:1:29.5:1:0.05907:8.57345:60:8:0.0111:0:1 0/0:215:0:0,0:193,21:214,0:0:2,0:21.7:1:30:1:1:0:60:213:0.9953:0:0.1 +14 81554592 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=Inf;LSEQ=CAGAGACCTGCTCCAAGAAA;RSEQ=AGGAGGGAGAAAATGCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:1,25:26,0:0:1,0:23.6:1:31.7:1:1:0:60:25:1:0:0.3 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:20.2:1:29.2:1:1:0:60:10:0.5556:0:1.2 +14 81557084 . G A 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATAATTTTTTCCAATTAAAC;RSEQ=AGAAAATCACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:24.7:1:30.3:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 81558806 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTTATTTAAGTGCATATG;RSEQ=GCAGCAAGACCCCTGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:280,69:349,0:0:2,0:24.9:1:31.9:1:1:0:60:57.167:1:0:0.1 0/1:232:23:19,4:159,49:208,23:0.0991:2,2:23.7:1:29.4:1:0.60945:1.46:60:46:0.1004:0:1.1 +14 81558965 . A G 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGACACTGTGAGTATTACC;RSEQ=GTTCTACTCCCTCCATCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:0:0,0:242,441:683,0:0:2,0:25.4:1:31.4:1:1:0:59.9:84.375:1:0:0.1 0/1:583:87:33,54:194,302:496,87:0.1492:2,2:23.8:1:29.4:1:0.90529:1.05109:59.8:42.5:0.1473:0:1.2 +14 81559160 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03226;SOR=Inf;LSEQ=GGTAACAAGACAAGAGGATT;RSEQ=CATTACGGCAGTGGTTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:0,25:25,0:0:1,0:22.6:1:32:1:1:0:60:50:1:0:0.1 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:32.5:1:28:1:0.33333:0:60:4:0.3333:0:1 +14 81562582 . A T 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAAAAACATACGCATTC;RSEQ=GATGAATGTCTTTCAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:34:1:32:1:0.33333:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 81562808 . A G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00283;SOR=Inf;LSEQ=GGGCATTCAAACTGAGAAAT;RSEQ=TTATCTTGTTTCCAACAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:95,1:96,0:0:1,0:23.5:1:28.9:1:1:0:59.7:192:1:0:0.1 0/1:45:5:5,0:40,0:40,5:0.1111:1,0:23.4:1:33:1:1:0:60:10:0.1111:0:1.2 +14 81562876 . C A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00443;SOR=Inf;LSEQ=CATATGTGGGACCTGAAAAA;RSEQ=CTTTATGTACATTTATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:298,49:347,0:0:2,0:23:1:32.1:1:1:0:60:85.75:1:0:0 0/1:239:6:4,2:198,34:232,6:0.0251:2,2:14.2:1:27.7:1:0.22524:2.89388:60:12:0.0255:0:1 +14 81562998 . T C 215 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTAGGAAGCTGTACAACAA;RSEQ=GGCTTTACTTCAGTCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1221:0:0,0:583,637:1220,0:0:2,0:24.3:1:30.6:1:1:0:60:109.909:0.9992:0:0.1 0/1:954:147:67,80:378,429:807,147:0.1541:2,2:24.4:1:30:1:0.7882:1.05205:60:146:0.154:0:1.2 +14 81563195 . G A 139 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01278;SOR=0;LSEQ=AACATGGAAATGAGGTCAAG;RSEQ=AACTTGGCAGGGGCCCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:0,20:1,82:83,20:0.1942:1,1:19.8:1:32.2:1:1:0:60:40:0.198:0:1.1 0/0:25:0:0,0:0,25:25,0:0:1,0:26.2:1:31.3:1:1:0:60:50:1:0:0 +14 81563267 . G GGTGT 69 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=17.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTCCAAAGCTTTTCTCCCT;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,14:14,5:0.2083:1,0:45:1:30:1:1:0:57:10:0.2174:0:0.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 81573148 . G C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATACAAAAATTAGTCAG;RSEQ=CATGATGGCGATCGCCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29:1:1:0:37.5:4:1:0:1 +14 81574283 . T A 48 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.25;SOR=0;LSEQ=CTCTGACAGTCCTCAGCATC;RSEQ=CTCACCACCCTCACCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:15.3:1:30.3:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:39:0:27:0:1:0:60:2:1:0:0 +14 81574429 . G A 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAAAAATACAGTTGCCACTG;RSEQ=CCTGAAAAATAGGGAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:3,8:0.7273:0,0:18.6:1:27.5:1:1:0:60:3:0.6667:0:1.4 0/0:1:0:0,0:0,1:1,0:0:0,0:22:0:34:0:1:0:60:2:1:0:0 +14 81574687 . T TTCTC 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=8.000;MSILEN=2;SSF=1e-05;SOR=0.42724;LSEQ=TCTTAAAATCACCTAATTCA;RSEQ=TCTCTCTCTCTCTTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:328:240:213,27:62,3:65,240:0.7317:1,2:22.1:1:31.9:1:0.15728:2.61314:59.9:480:0.7339:0.2073:0.1 1/0:212:114:102,12:76,13:89,114:0.5377:2,2:27.8:1:30.4:1:0.39743:1.45:59.9:228:0.5403:0.0189:0.1 +14 81574816 . G C 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGAGTAAGACATACAAAA;RSEQ=AATATTTTAGTCTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:886:0:0,0:446,430:876,0:0:2,0:22.7:1:31:1:1:0:58.3:9.683:0.9987:0:0.4 0/1:793:21:14,7:388,370:758,21:0.0265:2,2:20.5:1:30:1:0.18808:1.91:60:20:0.0282:0:1.1 +14 81574828 . C CT 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.11546;SOR=0.55247;LSEQ=ATACAAAAGAATATTTTAGT;RSEQ=TTTTTTTTTCTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:825:22:11,11:430,344:774,22:0.0267:2,2:24.9:1:30.7:1:0.66653:1.24964:55.6:21:0.029:0:0.5 0/1:738:11:7,4:388,307:695,11:0.0149:2,2:21.4:1:30.2:1:0.76309:1.38:57.7:22:0.017:0:0.5 +14 81574845 . T TTTTTTTCTTTTTAC 247 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0;SOR=0.55962;LSEQ=AGTCTTTTTTTTTCTTTTTT;RSEQ=TTTTTTGGAATAAATGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1062:313:195,118:159,200:359,313:0.2947:2,2:20.4:1:29.9:1:0:2.08:58.5:312:0.3679:0.113:0.4 0/1:818:155:89,66:175,183:358,155:0.1895:2,2:24.1:1:28.9:1:0.0836:1.41:57.8:310:0.2385:0.055:0.4 +14 81574959 . A G 324 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33701;LSEQ=TTTTCCTGGCTGTATAGGCT;RSEQ=CCTCTTGGAAGAAAGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1352:1155:485,670:83,113:196,1155:0.8543:2,2:25.1:1:31.9:1:0.93774:1.01468:60:38.828:0.8517:0:1.5 1/0:1068:709:284,425:159,199:358,709:0.6639:2,2:23.4:1:31.1:1:0.18826:1.19547:60:87.625:0.6632:0:1.5 +14 81575005 . C A 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29348;LSEQ=TTGAGACTCAGAAGGCCCCA;RSEQ=GCTCCAGTATGCCATCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:824:707:214,493:42,75:117,707:0.858:2,2:24.1:1:31.2:1:0.2361:1.28963:59.9:43.188:0.8563:0:1.8 1/0:607:388:139,249:83,135:218,388:0.6392:2,2:24.9:1:29.9:1:0.59882:1.10118:60:76.6:0.6394:0:1.8 +14 81575078 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55667;SOR=0;LSEQ=CTCACAGAGGCTCTGTTCAT;RSEQ=GAGCAGCTGCTGTTTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:19,217:236,3:0.0126:2,2:13:1:24:1:0.23151:5.63:60:2:0.0087:0:1.7 0/0:137:0:0,0:18,119:137,0:0:2,0:22.4:1:30.7:1:1:0:59.7:136:1:0:0.5 +14 81575419 . T C 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTTGGTTTTGCCTCAG;RSEQ=TTAGAATCTCATCATTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:24:1:32.8:1:1:0:53:10:0.8333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 81606214 . A G 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGAAGAAAATCAGAGGGT;RSEQ=AGTGGCAGGGACCCGGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:659:0:0,0:206,451:657,0:0:2,0:24.2:1:30.1:1:1:0:59.8:130.4:0.9985:0:0.1 0/1:565:41:13,28:190,334:524,41:0.0726:2,2:23.2:1:31:1:0.61535:1.22478:60:82:0.0739:0:1 +14 81608950 . CT C 32 v3;MSI12;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGTTTTAAACAAGCATT;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,0:4,2:0.2857:0,0:20:1:32.9:1:1:0:56.5:4:0.2857:0.1429:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 81609779 . G A 166 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=21.38007;LSEQ=ATGTGCAACCTGGCCTTTGC;RSEQ=GATTTCTGCATGGGGATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:985:3:3,0:403,579:982,3:0.003:2,0:1:0:27:1:0.06972:0:60:6:0.0031:0:1 0/1:782:48:18,30:343,391:734,48:0.0614:2,2:26:1:29.8:1:0.23432:1.46136:60:23:0.0601:0:1.1 +14 81610105 . T A 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=22.57702;LSEQ=TAGCTATGCCAAAGTCAGTA;RSEQ=CTGCCTGCCCATGGACACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1003:2:2,0:475,526:1001,2:0.002:2,0:1:0:29:0:0.22592:0:60:4:0.002:0:1 0/1:810:35:14,21:391,383:774,35:0.0432:2,2:21.8:1:29.4:1:0.23229:1.53052:60:70:0.0441:0:1.3 +14 81610583 . G C 330 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01128;LSEQ=GTTCAAAAGGTTACCCACGA;RSEQ=ATGAGGCAGGGTCTCCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1218:1215:614,601:0,0:0,1215:0.9975:0,2:24.6:1:32.3:1:1:0:60:120.5:0.9983:0:1.1 1/1:967:793:433,360:83,90:173,793:0.8201:2,2:24.2:1:31.3:1:0.12991:1.30:60:98.125:0.8211:0:1.2 +14 81610634 . C G 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTATGAACTGATTGAAAA;RSEQ=TCCCATCTAACCCCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1234:0:0,0:561,673:1234,0:0:2,0:25.2:1:32.6:1:1:0:60:87.143:1:0:0.6 0/1:1057:48:23,25:488,518:1006,48:0.0454:2,2:25.5:1:31.8:1:1:1.02399:60:96:0.0456:0:1.6 +14 81610715 . C A 122 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=27.93219;LSEQ=TAAGTTAACACTACACTACT;RSEQ=ACAATGGTAGGGGAACTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:1:1,0:172,469:641,1:0.0016:2,0:1:0:23:0:0.26947:0:60:2:0.0016:0:1 0/1:502:21:8,13:152,329:481,21:0.0418:2,2:25:1:27.8:1:0.63276:1.33:60:9.5:0.0382:0:1.6 +14 81610869 . C A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01552;SOR=Inf;LSEQ=TGGAGAGTGATTAGTATTAA;RSEQ=CTAATCATTGCCCCCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:36,0:0:1,0:27.5:1:30.5:1:1:0:59.1:11:1:0:0.4 0/1:13:3:0,3:1,9:10,3:0.2308:2,0:18.3:1:31:1:1:0:60:6:0.2308:0:1.3 +14 81610942 . C T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGAAATCAAAATAATCTA;RSEQ=ACTATCTAGAAGACTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:28.5:1:28.4:1:1:0:60:20:1:0:1 1/1:4:4:0,4:0,0:0,4:1:0,0:12.3:1:28.8:1:1:0:60:8:1:0:1.3 +14 82491812 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05495;SOR=0;LSEQ=CACTCACCATCTCACTTGGC;RSEQ=AGGGGGAGGGGGTTCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:2,1:3,3:0.5:2,0:25.7:1:29.3:1:0.4:0:60:6:0.5:0:1 0/0:8:0:0,0:3,5:8,0:0:2,0:31.4:1:30.8:1:1:0:60:16:1:0:0 +14 83401758 . A G 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.9379;SOR=1.01624;LSEQ=GAGAAAAGTAAGACAGAAAG;RSEQ=AATTTTGTGCCTTTAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:482:363:149,214:54,65:119,363:0.7531:2,2:26.2:1:31.4:1:0.45413:1.19274:59.9:50.857:0.7511:0:1.1 1/0:410:310:140,170:43,57:100,310:0.7561:2,2:27.2:1:30.2:1:0.72976:1.09:60:102.333:0.7562:0:1.2 +14 83401847 . A T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01357;SOR=2.60306;LSEQ=TTTTAAACTATATTTTCCAA;RSEQ=CACAAGCTATTTAATAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:14:2,12:5,75:80,14:0.1489:2,2:16.1:1:30.2:1:0.27864:2.47:60:28:0.1489:0:1.7 0/1:70:22:2,20:5,43:48,22:0.3143:2,2:19.3:1:28.3:1:1:1.16037:60:44:0.3188:0:1.7 +14 83401883 . T A 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26679;SOR=1.70344;LSEQ=AGAATTACCTTCAACAATAG;RSEQ=TGATTAAAAACAAAGTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:28:0,28:0,22:22,28:0.56:1,1:26.3:1:31.9:1:1:0:60:56:0.56:0:1.2 1/0:35:24:0,24:0,11:11,24:0.6857:0,1:29.1:1:30.7:1:1:0:60:48:0.6857:0:1.4 +14 83401953 . TGAGAG CT 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=2;SSF=0.60647;SOR=2.96045;LSEQ=TAGTGTGTATAATATGGATA;RSEQ=AGAGAGAGAGAGAGAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:0,9:0,3:3,9:0.6923:0,0:24.2:1:32.1:1:1:0:60:18:0.75:0.1538:0.6 1/1:8:7:0,7:0,1:1,7:0.875:0,0:26.6:1:31.7:1:1:0:59.9:14:0.875:0.25:0.6 +14 84027719 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GGGAATCTGCTGAAGCCTAC;RSEQ=GAACCCCTTGCGGGAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:28:1:29.5:1:1:0:60:12:1:0:0 0/1:6:2:0,2:2,2:4,2:0.3333:2,0:27:1:31:0:0.46667:0:60:4:0.3333:0:1 +14 84028114 . A G 33 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCCTGAGCCCCTAGGA;RSEQ=GGAGGGGTGGCCACAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:7.5:1:33:0:1:1:48:4:0.5:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:22:0:33:0:1:0:60:2:1:0:0 +14 84782145 . C G 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05359;SOR=0;LSEQ=AGAGGGGTGGACATGACAAA;RSEQ=GGCTGCCTCACCTGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:6,3:9,6:0.375:2,2:24.5:1:30.8:1:1:1:60:5:0.3333:0:1.2 0/0:11:0:0,0:6,5:11,0:0:2,0:19:1:30.4:1:1:0:60:22:1:0:0.1 +14 85172722 . G A 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTTTCTGGTTTTAAT;RSEQ=CACATCACTAATGCTAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:15.5:1:27.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 85173181 . G C 215 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGGTAGACAACAGTTATT;RSEQ=TTTTGTTAGTAGGAACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:258,181:439,0:0:2,0:25.5:1:32.2:1:1:0:60:218.5:1:0:0.2 0/1:379:129:77,52:153,97:250,129:0.3404:2,2:25.3:1:30.8:1:0.82456:1.06502:59.5:63.5:0.3378:0:1.2 +14 85173227 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0;SOR=2.34571;LSEQ=GCTAGCTAGATGATCAAACA;RSEQ=ACACATGCCCAGATTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:545:91:41,50:215,239:454,91:0.167:2,2:26.2:1:32.3:1:0.73061:1.09685:60:90:0.1667:0:1.2 0/1:450:144:71,73:150,156:306,144:0.32:2,2:26.1:1:31:1:1:1.01:60:47:0.3176:0:1.2 +14 85173316 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15156;SOR=Inf;LSEQ=AATTTCCTTTAAAATTTCCC;RSEQ=TTCTTTCCCTGTATTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:47,153:200,0:0:2,0:23:1:30.4:1:1:0:60:39:1:0:1.1 0/1:128:2:1,1:22,104:126,2:0.0156:2,2:16.5:1:30:1:0.32825:4.65:60:4:0.016:0:1.5 +14 85173319 . C A 229 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00771;LSEQ=TTCCTTTAAAATTTCCCTTT;RSEQ=TTTCCCTGTATTTTTAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:192:191:41,150:0,1:1,191:0.9948:0,2:22.4:1:30.3:1:1:0:60:30.833:1:0:1.1 1/0:118:70:11,59:7,41:48,70:0.5932:2,2:20.6:1:29.6:1:1:1.09:60:34:0.5913:0:1.2 +14 85173327 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.13497;SOR=Inf;LSEQ=AAATTTCCCTTTCTTTCCCT;RSEQ=TATTTTTAATTGGCATTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:29,132:161,0:0:2,0:22.4:1:32.3:1:1:0:60:79.5:1:0:1.1 0/1:94:2:1,1:12,80:92,2:0.0213:2,2:16:1:27:1:0.25875:6.44:60:4:0.0213:0:2 +14 85955817 . G T 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.51228;LSEQ=AGATGACTCCAGTCTCAGCT;RSEQ=CCATCTGACCACATTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:14,4:0.2222:1,0:42.3:1:32.3:1:1:0:60:8:0.2222:0:1 0/1:8:1:1,0:7,0:7,1:0.125:0,0:1:0:30:0:1:0:60:2:0.125:0:1 +14 87812897 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54999;SOR=0;LSEQ=TTAATAAAAAGAAACGGTTT;RSEQ=CTGGCCCTTAGCTTTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:156,25:181,2:0.0109:2,2:22:1:28.5:1:0.26464:6.13842:60:4:0.011:0:1 0/0:94:0:0,0:81,13:94,0:0:2,0:23.5:1:30.4:1:1:0:60:30.333:1:0:0 +14 87812927 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14211;SOR=Inf;LSEQ=AGCTTTGTGGAACAAAACAT;RSEQ=CTAGAGAGAAACAAAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:202,93:295,0:0:2,0:26.3:1:32.1:1:1:0:59.9:72.75:1:0:0.2 0/1:179:2:1,1:125,52:177,2:0.0112:2,2:25.5:1:26.5:1:0.50568:2.39058:60:4:0.0112:0:1 +14 87813007 . A T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.42527;LSEQ=GAAACCTCAGGTACTCCTGA;RSEQ=GACTCAGTTAAAAATAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:260:122,138:144,142:286,260:0.4762:2,2:27:1:30.7:1:0.44121:1.14679:60:129:0.4743:0:1.9 1/1:337:270:133,137:40,25:65,270:0.8012:2,2:26:1:29.6:1:0.09672:1.64566:60:66.5:0.8036:0:1.9 +14 87813031 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=5.688;LSEQ=TCAGTTAAAAATAGAATATG;RSEQ=GAGGATGTAAGTGTGCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:254:113,141:128,147:275,254:0.4792:2,2:24:1:31:1:0.66265:1.08634:60:83.667:0.4772:0:1.9 1/1:331:278:132,146:27,25:52,278:0.8399:2,2:24:1:29.2:1:0.65048:1.1939:60:45.333:0.8369:0:1.8 +14 87813148 . T A 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04426;SOR=0;LSEQ=TACAGAAAGCCCTAGGTCTC;RSEQ=GGTTTGGGGCTTTCCTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:7:1,6:13,105:118,7:0.056:2,2:21.9:1:33.3:1:0.57407:1.34:60:14:0.0588:0:1.1 0/0:80:0:0,0:14,66:80,0:0:2,0:21.2:1:29.9:1:1:0:60:160:1:0:0.2 +14 87813214 . G A 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08817;SOR=0;LSEQ=CTGCATAACCTACCAATTCA;RSEQ=GAATGCCTCTTTGGCATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:7:0,7:0,37:37,7:0.1591:1,0:18.7:1:32:1:1:0:60:14:0.1591:0:1.6 0/0:20:0:0,0:0,20:20,0:0:1,0:20.7:1:29.8:1:1:0:60:19:1:0:0.1 +14 87813312 . A C 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=CTTGTAGTATCATCCATCCA;RSEQ=GTTCTTGCCATGGGCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:15:1:29.2:1:1:0:57.2:10:0.7143:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:32:0:1:0:60:2:1:0:0 +14 87813714 . G A 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTTCTACAGCCTCCCTGAG;RSEQ=CATTTCAGAGCCTAGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:30.5:1:1:0:60:4:1:0:1.5 +14 88360375 . C T 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=GCTGACTCCCCCAAGTCTAC;RSEQ=GTGTTTTGTTCCTGGGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:3,9:10,12:22,12:0.3529:2,2:27.8:1:30.3:1:0.29195:2.43465:60:24:0.3529:0:2 0/0:30:0:0,0:13,17:30,0:0:2,0:30.3:1:29.6:1:1:0:60:60:1:0:0.1 +14 88360384 . T A 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=CCCAAGTCTACCGTGTTTTG;RSEQ=TCCTGGGTTATCTTTGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:2,9:6,7:13,11:0.4583:2,2:24.2:1:29.2:1:0.2108:3.64266:60:22:0.4583:0:2.1 0/0:26:0:0,0:12,14:26,0:0:2,0:28.6:1:28.8:1:1:0:60:52:1:0:0 +14 90358295 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.49858;SOR=Inf;LSEQ=CGCCGAGTGCTACCGCCGCG;RSEQ=GCTGCAGCTGCGGGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:9,2:11,0:0:2,0:28.4:1:31.9:1:1:0:53.5:22:1:0:0.1 0/1:16:2:1,1:12,2:14,2:0.125:2,2:13:0:31.5:1:0.35:5.09912:60:4:0.125:0:1.5 +14 92132168 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCGCAGTGAGCCTGGGC;RSEQ=ACAGAACAAGACTCCGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:29.5:1:1:0:45.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 92134321 . C T 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=AGATGGTCTTACAAATGGAA;RSEQ=CCCAAATGAGCTCAACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:32:1:1:0:21:4:1:0:1 0/1:6:1:0,1:2,3:5,1:0.1667:2,0:24:0:29:0:1:0:21:2:0.1667:0:1 +14 92391945 . C A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCTGGGAGCCAGTCTC;RSEQ=CCCATGGCAGGAAAACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:29:1:1:0:60:4:1:0:1.5 +14 92392303 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AGGGTGTGCTGGAGGTGAGT;RSEQ=CTGGGAGACTGAGTGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:21,0:0:2,0:30.6:1:32.1:1:1:0:60:42:1:0:0.2 0/1:28:2:1,1:12,14:26,2:0.0714:2,2:22.5:1:29.5:1:1:1.16:60:4:0.0714:0:1 +14 95556508 . CA C 34 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAAAGCTGACATAAACT;RSEQ=AAAAAAAAAAAACAAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:14.5:1:34:0:1:0:52.5:4:0.6667:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 95556644 . A C 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15053;SOR=0;LSEQ=GCGCAAAAAACTAAAACTAC;RSEQ=ATTAGTTCCAAAATTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:6,0:20,0:20,6:0.2308:1,0:31.3:1:32.3:1:1:0:55.7:12:0.24:0:1 0/0:11:0:0,0:11,0:11,0:0:0,0:14.9:1:29.8:1:1:0:58.3:22:1:0:0 +14 95556747 . A T 225 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=0.01594;LSEQ=TCAATTCATTCCACTCACTA;RSEQ=CAACTTTAAGTCTTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:155:154:153,1:1,0:1,154:0.9935:0,1:24.9:1:31.1:1:1:0:59.7:37.5:1:0:1.1 1/0:120:85:82,3:31,4:35,85:0.7083:2,1:23.5:1:30.4:1:0.19182:3.48:60:170:0.7143:0:1.1 +14 95556765 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21238;SOR=Inf;LSEQ=TAACAACTTTAAGTCTTCCT;RSEQ=TCCGATTTAAATAATTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:199,11:210,0:0:2,0:23:1:31:1:1:0:59.7:51.5:1:0:0.8 0/1:180:2:1,1:159,19:178,2:0.0111:2,2:12.5:1:30.5:1:0.21043:8.18141:60:4:0.0114:0:2 +14 95556791 . AT A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.74211;SOR=1.39791;LSEQ=TTTAAATAATTTTCCCCTTA;RSEQ=TTTTTTTGTTTTGTTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:4:3,1:330,56:386,4:0.0103:2,2:17.8:1:32.5:1:0.46989:1.96014:60:8:0.0103:0.0026:0.5 0/1:350:5:4,1:268,77:345,5:0.0143:2,2:22.2:1:30.4:1:1:1.15:56.4:10:0.0144:0.0029:0.2 +14 95557284 . A G 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACAGTGTAAATATTTTTC;RSEQ=GAATCATTAGTTTACAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:216,55:271,0:0:2,0:22:1:30.7:1:1:0:59.9:270:1:0:0 0/1:207:21:16,5:153,33:186,21:0.1014:2,2:24.6:1:28.7:1:0.55132:1.44602:60:42:0.1029:0:1 +14 95559858 . A G 49 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATTTCTGATCCATTTAAAAA;RSEQ=GGAAGGATAAGCTACACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:25.7:1:31:1:1:0:60:6:0.75:0:1.3 0/0:2:0:0,0:2,0:2,0:0:0,0:17:1:24:1:1:0:60:4:1:0:0 +14 95560444 . G A 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCATAAAGGTGCTTGGTTAT;RSEQ=AGGTAGTCCAAAATCGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:26:9,17:168,268:436,26:0.0563:2,2:18:1:29.8:1:0.83618:1.18362:60:52:0.057:0:1 0/0:385:0:0,0:157,226:383,0:0:2,0:24.5:1:30.8:1:1:0:60:382:0.9948:0:0.1 +14 95560556 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14216;SOR=Inf;LSEQ=TTTACACTATCCCCACATAG;RSEQ=AACTGATCCCCAAATCCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:11,122:133,0:0:2,0:24:1:32.7:1:1:0:59.8:132:1:0:0.1 0/1:81:2:1,1:12,67:79,2:0.0247:2,2:18:1:28.5:1:0.29691:5.40:60:4:0.0253:0:1 +14 95562347 . G A 123 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=8.02573;LSEQ=TCTTCAAACAACCATATTCC;RSEQ=AGTCTTTCAATACAGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:924:3:3,0:436,485:921,3:0.0032:2,0:1:0:27:1:0.10686:0:60:6:0.0033:0:1 0/1:745:19:11,8:331,394:725,19:0.0255:2,2:20.7:1:29.1:1:0.35354:1.64:60:38:0.0257:0:1.2 +14 95562735 . C T 85 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03808;SOR=3.93605;LSEQ=AGGATCCAGATAGCACATTG;RSEQ=ATCCCAAGAGCTGTAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:972:3:0,3:496,473:969,3:0.0031:2,0:1:0:25.7:1:0.11706:0:60:6:0.0031:0:1 0/1:747:9:4,5:386,352:738,9:0.012:2,2:24.7:1:27:1:0.74356:1.37015:60:18:0.0123:0:1 +14 95562999 . C A 181 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GCTCTCCTCCTCCTCATCCT;RSEQ=CTCCTCGTAATCCTCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1043:82:36,46:417,543:960,82:0.0786:2,2:25.2:1:28.6:1:1:1.02:60:164:0.0795:0:1.1 0/0:796:0:0,0:352,442:794,0:0:2,0:25.1:1:30.2:1:1:0:59.8:55.714:0.9987:0:0.2 +14 95566068 . TACACACACACAC T 199 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=20.000;MSILEN=2;SSF=0;SOR=0.0864;LSEQ=GAAAAGTAAATCCCTCCAGT;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:86:75,11:48,0:48,86:0.2945:1,2:29.8:1:31.1:1:0.00759:0:58.7:85:0.2972:0.0308:1.3 0/1:173:6:6,0:39,0:39,6:0.0347:1,0:29.3:1:31.7:1:1:0:60:12:0.0357:0:1 +14 95566108 . C A 265 MSI12 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0;SOR=0.01252;LSEQ=CACACACACACACACACACA;RSEQ=AAACTTACCATTTCATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:465:463:341,122:0,1:1,463:0.9957:0,2:24.8:1:30:1:0.26509:0:59:45.3:0.9956:0:1.3 1/0:361:268:190,78:56,33:89,268:0.7424:2,2:24.5:1:29:1:0.18624:1.43:58.9:43.667:0.7507:0:1.4 +14 95569500 . C T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57302;SOR=0;LSEQ=TGTAAAGCAATACTCATCAA;RSEQ=TGCCAGGTAGTTCTGCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:5,0:35,0:35,5:0.125:1,0:28:1:32.8:1:1:0:60:10:0.125:0:1 0/0:8:0:0,0:8,0:8,0:0:0,0:22.6:1:31.5:1:1:0:60:16:1:0:0.1 +14 95571390 . C A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17574;SOR=Inf;LSEQ=ATGATCTGTGTTCTTTCTGG;RSEQ=TGACTGCACAGGCATACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:203,54:257,0:0:2,0:27.5:1:32.5:1:1:0:60:84.667:1:0:0.1 0/1:186:2:1,1:134,50:184,2:0.0108:2,2:5.5:1:29:1:0.47428:2.66348:60:4:0.011:0:1 +14 95571416 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09668;SOR=Inf;LSEQ=GCACAGGCATACCTAAAATC;RSEQ=GCAGGAAGTGATCTGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:242,81:323,0:0:2,0:25.5:1:30.7:1:1:0:60:63.6:1:0:0.1 0/1:275:3:1,2:194,78:272,3:0.0109:2,2:9:1:26:1:0.2037:4.94097:60:6:0.011:0:1 +14 95571635 . G GA 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.213;SOR=0.71553;LSEQ=TACAAAGCGCACACACAAAA;RSEQ=AAAAAAAAAAAGACCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:52:5,47:71,283:354,52:0.1218:2,2:26:1:30.1:1:0.08603:2.35429:58.8:25:0.1433:0.0117:0.7 0/1:266:24:3,21:45,184:229,24:0.0902:2,2:30:1:30:1:0.58476:1.70873:59.6:48:0.1048:0:0.3 +14 95572298 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15634;SOR=Inf;LSEQ=TCCACGGGTGGGCAGGGGGA;RSEQ=AGTGAACCTCTGCATGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:207,43:250,0:0:2,0:23.5:1:32.5:1:1:0:60:82.333:1:0:0.1 0/1:164:2:1,1:131,30:161,2:0.0122:2,2:40:1:30.5:1:0.34515:4.31203:60:4:0.0123:0:1 +14 95572302 . G C 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15437;SOR=Inf;LSEQ=CGGGTGGGCAGGGGGACAGT;RSEQ=AACCTCTGCATGTCTAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:232,50:282,0:0:2,0:22.6:1:32.5:1:1:0:60:69.5:1:0:0.1 0/1:183:2:1,1:146,35:181,2:0.0109:2,2:10:0:29:1:0.35561:4.12715:60:4:0.011:0:1 +14 95572575 . C CA 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25451;SOR=0;LSEQ=CGATATCTAAAAAAGAAAAA;RSEQ=AAAAAAACAATCAGTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:49,243:292,3:0.0102:2,2:8.3:1:27:1:0.07837:9.80:60:6:0.0103:0.0068:0.3 0/0:247:0:0,0:59,188:247,0:0:2,0:22.8:1:31.1:1:1:0:60:122.5:1:0:0.1 +14 95573590 . A ATT 28 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=ATTCCCATGTGAATAAGTGA;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:44:0:33:0:1:0:60:2:0.1667:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:28.5:1:1:0:57:4:1:0:0 +14 95573883 . G A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGCGTGAGCCACCGTGCCC;RSEQ=ACCTAGTGCATCTTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:315,128:443,0:0:2,0:22.4:1:30.2:1:1:0:56.9:62.286:0.9977:0:0.1 0/1:327:16:11,5:224,87:311,16:0.0489:2,2:26.5:1:28.6:1:0.77893:1.16972:56.5:32:0.0494:0:1 +14 95574226 . G T 61 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07733;SOR=4.11548;LSEQ=TTTTTTCTTACCAACATTAA;RSEQ=AGGTAGAACACAGTATGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:2:1,1:451,318:769,2:0.0026:2,2:26:1:28:1:1:1.41756:60:4:0.0026:0:1 0/1:566:6:1,5:320,240:560,6:0.0106:2,2:12.2:1:23.7:1:0.08992:6.64636:60:12:0.0107:0:1 +14 95577966 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAGGCAAAGTCTATTTT;RSEQ=GCATCCATATATTCCAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:0,2:2,67:69,2:0.0282:1,0:22.5:1:28:1:1:0:60:4:0.0294:0:1 0/0:26:0:0,0:0,26:26,0:0:1,0:16.1:1:31.4:1:1:0:60:52:1:0:0.1 +14 95578448 . CT C 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02599;SOR=0;LSEQ=TCTATAAAGTCCTCTATATG;RSEQ=TTTTTTTTACAATGGTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:8:8,0:243,76:319,8:0.0244:2,0:21.5:1:31.7:1:0.20568:0:59.4:16:0.0246:0.0091:0.1 0/0:206:0:0,0:151,55:206,0:0:2,0:21.2:1:29.9:1:1:0:60:412:1:0:0.2 +14 95578673 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08715;SOR=Inf;LSEQ=TATGAAACCACTGCCCCAAC;RSEQ=TTTTTAAAGTTCAATTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:23,205:228,0:0:2,0:21.6:1:31.2:1:1:0:60:113:1:0:0.5 0/1:96:2:1,1:20,74:94,2:0.0208:2,2:21.5:1:29.5:1:0.39145:3.64:60:4:0.0211:0:1 +14 95578675 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.09131;LSEQ=TGAAACCACTGCCCCAACAT;RSEQ=TTTAAAGTTCAATTTACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:95:8,87:12,113:125,95:0.4318:2,2:21.4:1:33:1:0.81696:1.15412:60:46.5:0.4306:0:1.1 0/1:93:6:1,5:18,69:87,6:0.0645:2,2:27.3:1:31.3:1:1:1.30087:60:12:0.0645:0:1 +14 95579370 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.1806;SOR=Inf;LSEQ=TGCAAGTCTTAGAAAAGCTG;RSEQ=AAAAATCCACTAATGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:188,39:227,0:0:2,0:23.6:1:30.4:1:1:0:59.8:112.5:1:0:0.1 0/1:169:2:1,1:134,33:167,2:0.0118:2,2:13.5:1:30:1:0.36285:4.01535:60:4:0.0119:0:1 +14 95579653 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGTCATGTGCCTCTTC;RSEQ=CCTCTACTGAATTTGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:0,2:0,81:81,2:0.0241:1,0:37.5:1:30.5:1:1:0:60:4:0.025:0:1 0/0:37:0:0,0:1,36:37,0:0:1,0:20.4:1:31.2:1:1:0:60:74:1:0:0 +14 95581506 . C G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAAAGAAAATCTTATACTTG;RSEQ=TCTTTTGTCTCTGAATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:24.5:1:30:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 95581843 . T TA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTTTTTGCCTTTTGATT;RSEQ=AAAAAAAAATGAAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:2,0:38,0:38,2:0.05:1,0:21.5:1:30:0:1:0:60:4:0.0526:0:0 0/0:10:0:0,0:9,1:10,0:0:2,0:22.2:1:30.2:1:1:0:60:20:1:0:0.2 +14 95581961 . G A 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGGTTTAGACTTAAACTGT;RSEQ=CAACATTCCCAGGTTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:305,66:371,0:0:2,0:22.8:1:32.2:1:1:0:60:122.667:1:0:0.1 0/1:249:13:11,2:182,53:235,13:0.0522:2,2:26.6:1:27.4:1:0.73873:1.60:60:26:0.0528:0:1.1 +14 95582395 . GAC G 78 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=16.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACTGTACCGTGCCTACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:1,5:4,11:15,6:0.2857:2,2:18.2:1:30.5:1:1:1.77078:53.2:12:0.2857:0.1429:1.2 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:31:0:1:0:60:2:1:0:0 +14 95582544 . A C 98 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.89443;LSEQ=ATTTCCCAGACGTTCATCCC;RSEQ=AATAACATATGTGATGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:6,3:6,2:8,9:0.5294:2,2:24:1:31:1:1:1.46472:55:8:0.5:0:1.3 1/0:2:1:1,0:1,0:1,1:0.5:0,0:37:0:31:0:1:0:60:2:0.5:0:1 +14 95582735 . G T 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65396;SOR=0.40076;LSEQ=ATACAAAGAATAACAAAGAA;RSEQ=CCACATTAATTTTTTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:4:1,3:292,65:357,4:0.0111:2,2:11.5:1:25:1:0.02227:13.33991:60:3:0.0085:0:1 0/0:224:1:0,1:178,44:222,1:0.0045:2,0:1:0:22:0:0.20179:0:60:2:0.0045:0:1 +14 95582744 . A AT 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.22271;SOR=3.04485;LSEQ=ATAACAAAGAAGCCACATTA;RSEQ=TTTTTTTTCCCAATCTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:2:2,0:333,97:430,2:0.0046:2,0:18:1:32:1:1:0:60:4:0.0047:0.0023:0.5 0/1:286:4:2,2:210,71:281,4:0.014:2,2:23.8:1:29:1:0.27142:2.94417:60:8:0.0141:0.007:0 +14 95583035 . G GA 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.3176;SOR=0.61169;LSEQ=TCGAAATTTCCTAAGTACCT;RSEQ=AAAAAAAAAATCCACCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:19:8,11:82,285:367,19:0.0481:2,2:30.9:1:29.1:1:0.05521:2.52:60:18:0.049:0.0051:0.4 0/1:267:8:1,7:79,178:257,8:0.03:2,2:33.4:1:29.3:1:0.44183:3.09656:60:16:0.0311:0:0.1 +14 95583060 . C A 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27475;SOR=0;LSEQ=AAAAAATCCACCAAGAAAAG;RSEQ=ACTTCTAAGAAAATTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:2,1:37,238:275,3:0.0108:2,2:12.7:1:22:1:0.05258:12.66:60:2:0.0076:0:2.7 0/0:191:0:0,0:37,154:191,0:0:2,0:22.9:1:31.1:1:1:0:60:46.75:1:0:0.1 +14 95583087 . CA C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.16031;SOR=Inf;LSEQ=AAGAAAATTTCTAAAATGAA;RSEQ=AAAAAAATTAGTAAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:10,145:155,0:0:2,0:24.4:1:30.2:1:1:0:60:24.833:1:0:0.3 0/1:104:2:0,2:6,96:102,2:0.0192:2,0:18:1:29.5:1:1:0:60:4:0.0196:0:1.5 +14 95583900 . C T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0804;SOR=0;LSEQ=AAAAAGGGAGACCCTATGGG;RSEQ=ACTTTGTCTGTATATGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:5:2,3:230,48:278,5:0.0177:2,2:12:1:27:1:0.04236:7.11288:60:10:0.0179:0:1 0/0:199:0:0,0:150,49:199,0:0:2,0:23.5:1:31.3:1:1:0:60:65.333:1:0:0.1 +14 95590985 . G A 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGTCCCAGAACTACCAATAC;RSEQ=GCACGACAGTCTGATAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:126,361:487,0:0:2,0:25.7:1:31:1:1:0:59.9:80.167:1:0:0.1 0/1:332:13:5,8:102,217:319,13:0.0392:2,2:27.7:1:30.3:1:0.76285:1.33:60:26:0.0393:0:1.1 +14 95591009 . C CA 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.95075;LSEQ=CGACAGTCTGATAGTATCTA;RSEQ=AAAAAAAAGAAAAGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:6:0,6:67,250:317,6:0.0185:2,0:8:1:30.4:1:0.35112:0:60:12:0.0189:0.0123:0.3 0/1:227:4:1,3:58,165:223,4:0.0176:2,2:25.5:1:23.3:1:1:1.05429:60:3:0.0134:0.0044:0.3 +14 95591070 . G A 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGTAGCATTTTCATGTGGG;RSEQ=TTTAACTGGGATTTCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:33:1,32:1,46:47,33:0.4125:1,1:26.8:1:31.4:1:1:1.43:60:66:0.4177:0:1.3 0/0:48:0:0,0:3,45:48,0:0:2,0:22.4:1:31.4:1:1:0:60:96:1:0:0.1 +14 95593174 . G A 38 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.27702;LSEQ=AAAAGCAAAAAAAAAAAAAA;RSEQ=GGAATAGATACTAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:1,2:1,139:140,3:0.021:1,2:12.7:1:24:1:0.04166:56.85:60:2:0.0172:0:2 0/1:75:2:0,2:4,69:73,2:0.0267:2,0:10.5:1:22.5:1:1:0:47.5:1:0.0154:0:3.5 +14 95595654 . T C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72973;SOR=0.64391;LSEQ=ATTCTTGAACTCACAGGTAA;RSEQ=GGTACTTATAGAGAATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:24:24,0:23,0:23,24:0.5106:1,1:21.9:1:32.9:1:1:0:60:48:0.5106:0:1.1 0/1:10:4:4,0:5,1:6,4:0.4:2,0:17.8:1:32.8:1:1:0:60:8:0.4:0:1 +14 95595739 . C T 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.29635;SOR=3.57154;LSEQ=GTACTCTCTGCAAGGTACTA;RSEQ=AAAAACACCAAAGACTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:1,0:172,11:183,1:0.0054:2,0:11:0:32:0:1:0:60:2:0.0056:0:2 0/1:104:2:1,1:94,8:102,2:0.0192:2,2:6:1:28.5:1:0.16636:11.13707:60:4:0.0196:0:1 +14 95596279 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1254;LSEQ=TATTCATTCATTCATACACT;RSEQ=CAGCCAAACTCCCAATATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:53:52,1:64,3:67,53:0.438:1,1:23.4:1:29:1:0.6291:2.42:59.7:106:0.438:0:1 0/1:68:6:6,0:60,2:62,6:0.0882:1,0:27:1:27.5:1:1:0:60:12:0.0882:0:1.2 +14 95596304 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10713;SOR=Inf;LSEQ=CAAACTCCCAATATTGATAA;RSEQ=TAATATTATTGCTTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:176,10:186,0:0:2,0:24:1:32.7:1:1:0:59.9:372:1:0:0.3 0/1:91:2:1,1:84,5:89,2:0.022:2,2:23.5:1:28:1:0.12821:15.42515:60:4:0.0222:0:1 +14 95596542 . C A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02787;SOR=Inf;LSEQ=ATGAGAACCTAAAATAAAAT;RSEQ=AACATCAGTAAACAAACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:127,321:448,0:0:2,0:24:1:32:1:1:0:60:63:1:0:0.1 0/1:311:4:3,1:103,204:307,4:0.0129:2,2:10.8:1:26:1:0.11644:5.91:60:8:0.0129:0:1 +14 95598045 . T C 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TTGGCTCTCTGGACTACTAA;RSEQ=GATTAACAGTCTACAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:9,178:187,0:0:1,0:25.1:1:30.5:1:1:0:59.9:61.333:1:0:0.1 0/1:104:10:0,10:2,92:94,10:0.0962:1,0:19.4:1:30.5:1:1:0:60:20:0.098:0:1 +14 95598665 . G C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27947;SOR=Inf;LSEQ=CATTCAAAAGAAATACAGAA;RSEQ=CAGAACATTTAAGAGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:23,0:16,0:16,23:0.5897:1,1:28.3:1:32.1:1:1:0:60:22:0.5789:0:1.1 1/1:4:4:4,0:0,0:0,4:1:0,0:25.8:1:30.8:1:1:0:60:8:1:0:1 +14 95599049 . T G 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.28405;SOR=0;LSEQ=AAAAAAAAGTTATGCACTTC;RSEQ=TACCTAAGTACAAAATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:61,223:284,3:0.0104:2,2:17.3:1:24.3:1:0.51956:1.82:58.7:2:0.007:0:3.3 0/0:185:0:0,0:48,136:184,0:0:2,0:20.5:1:29.4:1:1:0:60:91:0.9945:0:0.1 +14 95600006 . G C 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25497;SOR=Inf;LSEQ=AGGATCATTTTAGGAGTCAA;RSEQ=CATTCTGTACCTTACCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:0,10:0,7:7,10:0.5882:0,0:28:1:32.5:1:1:0:60:20:0.625:0:1 1/1:4:4:0,4:0,0:0,4:1:0,0:21.3:1:31.3:1:1:0:60:8:1:0:1 +14 95600072 . T G 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAATGAATCAAGCAACT;RSEQ=CACAAAGAGATGTACATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:46:1:33.7:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 96640647 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.08867;SOR=Inf;LSEQ=GGCAGATGGCATTTGAGCGG;RSEQ=GGGCTGCGTGAGCTCCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:20,0:0:2,0:22.5:1:31.8:1:1:0:60:40:1:0:0.1 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:22:1:29.5:1:1:1.29:60:4:0.2222:0:0 +14 98238063 . TA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=GCACTATTGCTTGATTGTAG;RSEQ=ACAGACCTGATTTGTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:10,5:15,2:0.1176:2,2:29:1:31:1:1:1.91491:60:4:0.1176:0:0 0/0:17:0:0,0:10,6:16,0:0:2,0:23.8:1:28.3:1:1:0:60:32:0.9412:0:0.4 +14 98238140 . G T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.13004;LSEQ=CTGACTCAGGACTGTGGCTT;RSEQ=TTTGGTGAATGAAACAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:17:8,9:8,13:21,17:0.4474:2,2:20.3:1:30:1:0.74297:1.43:60:34:0.4474:0:1.2 0/1:23:11:4,7:5,7:12,11:0.4783:2,2:21.8:1:29.5:1:1:1.23792:60:22:0.5:0:1.3 +14 98830005 . A C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.6171;LSEQ=GCATGATTAGAAGTAAAGGA;RSEQ=TCCAAGATGGTACAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:34:18,16:217,231:448,34:0.0705:2,2:24.1:1:32.3:1:0.72252:1.20:60:33:0.0688:0:1 0/1:311:146:65,81:82,83:165,146:0.4695:2,2:23.9:1:31.2:1:0.36567:1.23031:60:292:0.474:0:1.3 +14 98830038 . C T 141 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=56.16962;LSEQ=CAAGGTCAAAATGGAGTGAG;RSEQ=CAGATTTCTGTGGCCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:1:0,1:165,235:400,1:0.0025:2,0:45:0:25:0:1:0:60:2:0.0025:0:8 0/1:251:31:15,16:90,130:220,31:0.1235:2,2:28.1:1:28.5:1:0.44299:1.35:60:62:0.1255:0:1.8 +14 98830090 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10598;SOR=Inf;LSEQ=TGTCCAGGAGGACAAGCCGA;RSEQ=CCACATTGAATTGTAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:43,159:202,0:0:2,0:24.5:1:31:1:1:0:60:39.4:1:0:0.2 0/1:98:2:1,1:22,73:95,2:0.0204:2,2:35.5:1:28.5:1:0.41989:3.27:60:4:0.0208:0:1 +14 98830132 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08859;SOR=Inf;LSEQ=GAATTGTGTAAGTCAAAGAG;RSEQ=AATAAGGAGTGTTACAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:4,101:105,0:0:1,0:22.2:1:31.8:1:1:0:59.7:34:1:0:0.1 0/1:45:2:1,1:3,40:43,2:0.0444:2,2:31:1:28.5:1:0.17172:11.69:60:4:0.0455:0:1 +14 99364299 . A G 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=GTAAATATTTTAGCTTTGCA;RSEQ=GCCCAGTGGTCCCTGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:23,0:0:2,0:28.7:1:31.8:1:1:0:60:46:1:0:0.2 0/1:26:10:5,5:8,8:16,10:0.3846:2,2:25.5:1:30.1:1:1:1:60:20:0.3846:0:1.2 +14 100615989 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.51919;SOR=0;LSEQ=TGCACCAGCACCAGCACCAG;RSEQ=ACCGCCCACTTGAGGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:12,20:32,2:0.0588:2,2:27.5:1:30.5:1:1:1.64:60:4:0.0606:0:1.5 0/0:21:0:0,0:9,12:21,0:0:2,0:26.7:1:30.6:1:1:0:60:20:1:0:0.3 +14 101529758 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=5;SSF=0.50307;SOR=0;LSEQ=AGTTCTACGGTCAGTGGGGT;RSEQ=TGGTCTTTCAGGACAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:60,68:128,2:0.0154:2,2:35.5:1:30:0:1:1.13:60:4:0.0155:0:1 0/0:106:0:0,0:45,61:106,0:0:2,0:26.4:1:30.8:1:1:0:60:52:1:0:0.1 +14 101529781 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51564;SOR=0;LSEQ=GTCTTTCAGGACAGTTGCTT;RSEQ=TGTGAACTCAGAAAATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:46,61:107,2:0.0183:2,2:30:1:29.5:1:1:1.32:60:4:0.0185:0:1 0/0:74:0:0,0:30,44:74,0:0:2,0:20.5:1:30.7:1:1:0:60:148:1:0:0.1 +14 101875648 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGAGGCCCCTCCTGGCGT;RSEQ=GCCATAAAAGCCACAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:14,2:0.125:2,2:29.5:1:31:1:1:1:60:4:0.125:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 +14 102309693 . C T 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATCAACTGTTAGAGATA;RSEQ=GAAATAAGATGGAACATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:32.5:1:1:0:60:4:1:0:1 +14 102901263 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07143;SOR=Inf;LSEQ=CTCTGGCATGCTGTCACTGA;RSEQ=GATGACACAGGTCAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:12,3:15,0:0:2,0:22.6:1:30.2:1:1:0:60:14:1:0:0.1 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:28.5:1:29:1:1:2.44949:60:4:0.3333:0:1 +14 103269755 . C A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50004;SOR=1.96266;LSEQ=CCCTGGGTCTTGGGCAGTTA;RSEQ=CTTCCGTGTGTCTCAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:1,10:1,10:11,11:0.5:2,2:23.1:1:30.7:1:1:1:60:22:0.5:0:1 1/0:15:10:2,8:0,5:5,10:0.6667:0,2:25.8:1:28.8:1:0.52381:0:60:20:0.6667:0:1 +14 103613192 . A C 28 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGGGCTGGGCGGCACAG;RSEQ=GGCTTGTACGCATAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:28.5:1:1:0:60:4:1:0:1 +14 103614902 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49854;SOR=0;LSEQ=AGATAACAAAGCCCTTTCAG;RSEQ=CGGAACCGCCGTTTTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:18,13:31,2:0.0606:2,2:14.5:1:32:0:1:1.37079:32.5:4:0.0606:0:2 0/0:26:0:0,0:14,12:26,0:0:2,0:29.7:1:30.2:1:1:0:49.4:25:1:0:0.6 +14 103614968 . G A 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46158;SOR=2.53072;LSEQ=GGGAAAGAGGAGAGGCACCC;RSEQ=ATGTATGTTCTCCAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:30:15,15:5,2:7,30:0.8108:2,2:25.7:1:31.3:1:0.41646:2.4409:43.1:60:0.8108:0:1.1 1/1:24:22:11,11:0,2:2,22:0.9167:0,2:25.3:1:30.3:1:0.48188:0:42.7:44:0.9167:0:1.1 +14 103615117 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18201;SOR=Inf;LSEQ=GTGTCACCATGGCAAAGCTG;RSEQ=AAGAGTCTACGATGTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:67,60:127,0:0:2,0:30.3:1:31.4:1:1:0:57.3:41.333:1:0:0.1 0/1:95:2:1,1:48,45:93,2:0.0211:2,2:35.5:1:27:1:1:1.06598:40:4:0.0211:0:1 +14 103615319 . T G 83 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=GGTACCTGGGCCGGGCACTG;RSEQ=GGCTCACGCCTGTAATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:31.4:1:29.6:1:1:0:57.9:6:1:0:1 1/0:4:3:1,2:0,1:1,3:0.75:0,2:38.3:1:31.3:1:1:0:58:6:0.75:0:1 +14 103615399 . A G 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGTTCGAGACCAGCCTG;RSEQ=CCAACATGGTGAAAACTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:20:1:28:1:1:0:37:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 103707780 . G A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01372;SOR=0.14574;LSEQ=TACATTGGTTCTTTAAAATG;RSEQ=CATCAGTGCCTTTTGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:11:8,3:22,11:33,11:0.25:2,2:28.4:1:31.2:1:1:1.32:60:22:0.25:0:1.1 0/1:44:2:1,1:25,17:42,2:0.0455:2,2:22.5:1:27.5:1:1:1.45743:60:4:0.0455:0:1 +14 103707824 . C G 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24453;SOR=0;LSEQ=CGCCATCTTCCAGGAATTCG;RSEQ=CAAAATGATGAATGCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:36,30:66,2:0.0294:2,2:22:0:31:1:1:1.19677:60:4:0.0299:0:1.5 0/0:69:0:0,0:33,36:69,0:0:2,0:29.3:1:30.4:1:1:0:60:68:1:0:0.2 +14 103707879 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15146;SOR=Inf;LSEQ=ACCCGGTACATGTTCTCCAG;RSEQ=CGTTTTGGAAAACATGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:51,0:0:2,0:25.4:1:32.1:1:1:0:59.5:102:1:0:0.5 0/1:33:2:1,1:10,21:31,2:0.0606:2,2:41.5:1:28.5:1:1:2.05:59:4:0.0606:0:2 +14 103707881 . G A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02936;SOR=0.22477;LSEQ=CCGGTACATGTTCTCCAGGC;RSEQ=TTTTGGAAAACATGGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:16:9,7:16,16:32,16:0.3265:2,2:22.4:1:31.1:1:0.76481:1.28:60:32:0.3333:0:1.1 0/1:31:3:2,1:8,20:28,3:0.0968:2,2:37.3:1:29.7:1:0.23693:4.71:59.3:6:0.0968:0:1.7 +14 103707954 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51518;SOR=0;LSEQ=AAAGGTGACACTGTAGACAT;RSEQ=AAGAGAATGGGAACTGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:45,23:68,2:0.0286:2,2:26:0:31.5:1:1:1.93656:52:4:0.0286:0:1.5 0/0:47:0:0,0:32,14:46,0:0:2,0:24:1:31.8:1:1:0:59.5:92:0.9787:0:0.1 +14 103708015 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50029;SOR=0;LSEQ=TCACCATGGCAAAGCTGGAA;RSEQ=AGTCTACAGTGTTCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:55,64:119,2:0.0165:2,2:39.5:1:30.5:1:1:1.16:32.5:4:0.0167:0:1 0/0:105:0:0,0:56,49:105,0:0:2,0:28.9:1:30.8:1:1:0:57.2:210:1:0:0.1 +14 103708044 . G C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18589;SOR=Inf;LSEQ=GTGTTCCCCAGCATGCTGTT;RSEQ=GCATTGCTGTAGACAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:53,73:126,0:0:2,0:23.2:1:31.2:1:1:0:56.5:30.5:1:0:0.1 0/1:96:2:1,1:39,55:94,2:0.0208:2,2:46:0:30:1:1:1.41:43:4:0.0208:0:1.5 +14 103708045 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18929;SOR=Inf;LSEQ=TGTTCCCCAGCATGCTGTTG;RSEQ=CATTGCTGTAGACAAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:53,71:124,0:0:2,0:23:1:31.7:1:1:0:56.4:123:1:0:0.1 0/1:96:2:1,1:39,55:94,2:0.0208:2,2:37.5:1:28.5:1:1:1.41:41:4:0.0211:0:1 +14 103708279 . G A 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20808;SOR=0;LSEQ=GGGAAGGAGCCTGAACTGCT;RSEQ=GAACCTATTCCCTATGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:0,4:4,4:0.5:0,2:38:1:30.8:1:1:0:45:8:0.5:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:34.5:1:32:1:1:0:60:8:1:0:0 +14 104146361 . A G 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31118;LSEQ=GGTCAGAAACAAGAGCTTAC;RSEQ=TGGCTGCTCTCTTGATGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:317:274:128,146:22,20:42,274:0.8644:2,2:24.7:1:31:1:0.51136:1.25378:60:136:0.8662:0:1.4 1/0:283:188:82,106:43,52:95,188:0.6643:2,2:24.7:1:30.1:1:0.8012:1.0687:60:61.667:0.6631:0:1.3 +14 104146367 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10786;SOR=Inf;LSEQ=AAACAAGAGCTTACATGGCT;RSEQ=CTCTCTTGATGTCCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:134,161:295,0:0:2,0:26.3:1:32:1:1:0:60:58:1:0:1.2 0/1:269:3:2,1:118,148:266,3:0.0112:2,2:25:1:26.7:1:0.58757:2.50:60:6:0.0113:0:2.7 +14 104146409 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22625;SOR=Inf;LSEQ=GTCCTGAGCGTCCTGCATTT;RSEQ=CCCTGAGAGGGCGTCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:75,135:210,0:0:2,0:25.3:1:31.5:1:1:0:59.9:51.5:1:0:1.2 0/1:191:2:1,1:67,122:189,2:0.0105:2,2:19.5:1:28:1:1:1.81:60:4:0.0105:0:3 +14 104146421 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33982;LSEQ=CTGCATTTCCCCTGAGAGGG;RSEQ=GTCCAGATCTTTGGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:177:113:37,76:20,44:64,113:0.6384:2,2:22.7:1:30.1:1:0.86856:1.07:59.8:112:0.6364:0:1.7 0/1:155:58:15,43:33,64:97,58:0.3742:2,2:23.3:1:29.6:1:0.3697:1.47445:59.9:116:0.3742:0:1.5 +14 104146611 . AT A 67 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAATTTTTTAGCACATGG;RSEQ=TTTTTTTTTTTTTTTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,8:8,5:0.3125:0,0:22.2:1:29:1:1:0:60:4:0.2857:0.0625:0 0/0:2:0:0,0:0,1:1,0:0:0,0:6:0:31:0:1:0:60:2:0.5:0:0 +14 104540660 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00501;SOR=0.15989;LSEQ=GTTCCTGTTTAAAACAGTAT;RSEQ=TACTAAAAAACCCAAGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:25:25,0:6,1:7,25:0.7813:2,1:29.8:1:28.7:1:0.21875:0:60:24:0.8:0:1 0/1:17:6:6,0:11,0:11,6:0.3529:0,0:19.2:1:29:1:1:0:60:12:0.3529:0:1.2 +14 104540796 . G T 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08474;SOR=0;LSEQ=GCATGTGGTCGTGTATATTT;RSEQ=CTTCCAGGCTATTTATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:5:2,3:277,155:432,5:0.0114:2,2:24.8:1:29:1:0.35706:2.67423:60:10:0.0116:0:1.2 0/0:297:0:0,0:179,118:297,0:0:2,0:25.8:1:31.2:1:1:0:60:73.25:1:0:0.3 +14 104540855 . T C 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00018;SOR=0.58612;LSEQ=TAACTTAACCAAAACCTACT;RSEQ=TCTACTCTGAAAAGTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:489:297:139,158:88,104:192,297:0.6074:2,2:25:1:32.3:1:0.85308:1.04:60:296:0.6091:0:1.1 0/1:345:164:72,92:83,98:181,164:0.4754:2,2:25.2:1:30.6:1:0.74576:1.08195:60:81:0.4751:0:1.1 +14 104540915 . C T 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11561;SOR=3.98546;LSEQ=ACAGGCAGTATCTCAATAAT;RSEQ=GGAATTCAGGTAACAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:2:1,1:51,181:232,2:0.0085:2,2:23:1:29.5:1:0.3958:3.52:60:4:0.0086:0:1 0/1:150:5:1,4:38,106:144,5:0.0333:2,2:16.2:1:30:1:1:1.43073:60:10:0.034:0:2.2 +14 104541169 . G T 61 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTACATTCATTTGAAAAG;RSEQ=CTTTTTAAGCAAGAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:17.5:1:30.8:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 104575466 . C T 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTGGGCCGGCCGGTCCC;RSEQ=GTCCCTGTGCACAGGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:28:1:1:0:60:4:1:0:2 +14 104576448 . G A 59 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGAGGCCAGGACGACTCC;RSEQ=AGGGACCCAAAAAGGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:15.5:1:32:0:1:0:60:4:1:0:1 1/1:4:4:2,2:0,0:0,4:1:0,2:28:1:29.8:1:1:0:60:8:1:0:1 +14 104579210 . C G 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGGTGGGGTGCATGGA;RSEQ=GTGACTTGGCCAAGTGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:9:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:30:1:1:0:60:4:1:0:1 +14 105236277 . GA TT 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGAGGCCCAGGGCCCCAGA;RSEQ=GATGACAGATAGCTGGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:30:1:30.7:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 105236532 . CA C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.09855;SOR=Inf;LSEQ=GGAGGGTGCTGCCCACAGCA;RSEQ=AAAACGTCTTTCCATCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:164,1:165,0:0:1,0:25:1:31.2:1:1:0:60:330:1:0:0.1 0/1:76:2:1,1:74,0:74,2:0.0263:1,2:31:1:31:1:0.02632:0:60:4:0.0263:0:0 +14 105236553 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09541;SOR=Inf;LSEQ=AAAAACGTCTTTCCATCTGG;RSEQ=CTCGAGAGGACAGCGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:237,8:245,0:0:1,0:24:1:31.5:1:1:0:59.8:39.833:1:0:0.1 0/1:110:2:2,0:103,5:108,2:0.0182:1,0:10.5:1:31:0:1:0:60:4:0.0183:0:1 +14 105236847 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.29101;SOR=3.61989;LSEQ=TAGGAAGCCAACCTCTTAAA;RSEQ=CACGGCCAGCACGCTGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:1:1,0:61,291:352,1:0.0028:2,0:13:0:15:0:0.17564:0:60:0:0:0:1 0/1:196:2:1,1:41,152:193,2:0.0102:2,2:30:1:29.5:1:0.38525:3.68:60:4:0.0106:0:1 +14 105236856 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55489;SOR=0;LSEQ=AACCTCTTAAAGCACGGCCA;RSEQ=CACGCTGCCATACTGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:1,2:50,236:286,3:0.0103:2,2:14.3:1:32:0:0.44273:2.35:60:6:0.0106:0:1.3 0/0:156:0:0,0:29,125:154,0:0:2,0:23.6:1:31.3:1:1:0:60:153:1:0:0.1 +14 105237004 . CA C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.09224;SOR=Inf;LSEQ=GATTTTAAAACATCTGAAGC;RSEQ=AAAAAGCTGAACACTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:349,35:384,0:0:2,0:24.8:1:30.7:1:1:0:59.8:53.857:1:0:0.1 0/1:168:2:1,1:154,12:166,2:0.0119:2,2:11.5:1:30:1:0.1492:12.36995:60:4:0.0121:0.006:0.5 +14 105237401 . A G 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09636;SOR=9.46398;LSEQ=GAGACAACCCTCAACAGCTG;RSEQ=GACGCAAAGCTGCCCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:0,31:31,1:0.0313:1,0:36:0:8:0:1:0:60:0:0:0:2 0/1:8:2:0,2:0,6:6,2:0.25:0,0:23.5:1:29:1:1:0:60:4:0.25:0:1 +14 105238591 . CCTGAG C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.97628;LSEQ=TACCAGGACTGCAGCAGGCT;RSEQ=GTGAGGGCGAGTGTGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:97:84,13:172,16:188,97:0.3392:2,2:24.2:1:31.6:1:0.21735:1.6606:59.9:194:0.3428:0.0839:1 1/0:119:72:56,16:41,6:47,72:0.605:2,2:19.4:1:29.9:1:0.23301:1.94196:59.9:144:0.605:0.1849:1.3 +14 105238604 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.54847;LSEQ=GCAGGCTCCTGAGGTGAGGG;RSEQ=GAGTGTGTGGGAAATCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:122:100,22:208,37:245,122:0.3324:2,2:21.8:1:29:1:0.54642:1.236:59.9:29.5:0.3296:0:1.1 1/0:159:89:67,22:55,15:70,89:0.5597:2,2:18.7:1:27.8:1:0.70688:1.20258:59.9:28.667:0.5513:0:1.4 +14 105238624 . C T 39 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11838;SOR=5.81302;LSEQ=CGAGTGTGTGGGAAATCTGG;RSEQ=GAGCGTGCCACGTGCATGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:506:1:0,1:380,125:505,1:0.002:2,0:1:0:26:0:0.24901:0:60:2:0.002:0:1 0/1:263:3:1,2:178,82:260,3:0.0114:2,2:11:1:24.7:1:0.23997:4.3147:60:6:0.0118:0:2 +14 105238636 . G C 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATCTGGCGAGCGTGCCAC;RSEQ=TGCATGCGTGAGTGTGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:711:0:0,0:490,219:709,0:0:2,0:23.1:1:30.3:1:1:0:59.9:63.455:0.9986:0:0.3 0/1:348:59:40,19:189,99:288,59:0.1695:2,2:23.2:1:30.6:1:0.88021:1.10:60:118:0.173:0:1.7 +14 105238643 . C T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09566;SOR=4.10009;LSEQ=GCGAGCGTGCCACGTGCATG;RSEQ=GTGAGTGTGGATATGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:780:2:0,2:523,255:778,2:0.0026:2,0:1:0:25:0:0.10828:0:60:4:0.0026:0:1 0/1:383:4:2,2:244,135:379,4:0.0104:2,2:23:1:29.3:1:0.61955:1.80436:60:8:0.0106:0:1.5 +14 105238820 . G C 183 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAACAAGGCCACAGTGTCG;RSEQ=TACCGCCACCTGCCCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:48:13,35:170,403:573,48:0.0772:2,2:23.4:1:32.8:1:0.86918:1.13548:60:96:0.0782:0:1.1 0/0:343:0:0,0:111,231:342,0:0:2,0:25.9:1:30.9:1:1:0:60:170:0.9971:0:0.2 +14 105239144 . C T 105 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=27.81468;LSEQ=GAGGTGCCAGGACCGCCTGG;RSEQ=GCAGGGGCAGGTGCAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:0,1:273,35:308,1:0.0032:2,0:1:0:25:0:0.1165:0:60:2:0.0033:0:1 0/1:144:12:10,2:109,23:132,12:0.0833:2,2:22.2:1:29.5:1:1:1.05:60:24:0.0857:0:1.1 +14 105239146 . C G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.51027;LSEQ=GGTGCCAGGACCGCCTGGCG;RSEQ=AGGGGCAGGTGCAGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:109:94,15:191,23:214,109:0.3375:2,2:23:1:31.5:1:0.46662:1.32392:59.2:35.333:0.3376:0:1.9 1/0:146:82:69,13:52,12:64,82:0.5616:2,2:25.4:1:30.3:1:0.66398:1.22:60:40:0.5556:0:1.9 +14 105239192 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.12018;LSEQ=GGGGATGGAGGTGTAGCCTG;RSEQ=AGCTGGGATGGGCGGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:229:157,72:332,127:459,229:0.3328:2,2:25.3:1:31.8:1:0.32665:1.19852:59.7:31.714:0.3274:0:1.5 1/0:394:240:164,76:102,52:154,240:0.6091:2,2:22.9:1:31.3:1:0.66125:1.10:59.6:79:0.6108:0:1.5 +14 105239465 . AG A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.03412;SOR=Inf;LSEQ=ATGGGCAGGACTCGGCATCA;RSEQ=GGGTGTCCGGGACACTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:176,423:599,0:0:2,0:23.1:1:31.8:1:1:0:59.9:53.455:0.9983:0:0.1 0/1:290:3:2,1:75,212:287,3:0.0103:2,2:22:1:27.7:1:0.17311:5.61:60:6:0.0106:0.0034:0.3 +14 105239531 . C T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33836;SOR=3.06919;LSEQ=ACAGAGAGGACACAGCATTG;RSEQ=GTGTGCTCAGGACGTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:2:0,2:338,201:539,2:0.0037:2,0:26:1:30.5:1:0.14036:0:60:4:0.0038:0:1.5 0/1:267:3:1,2:183,81:264,3:0.0112:2,2:22.7:1:27.3:1:0.22891:4.49004:60:6:0.0114:0:1 +14 105239894 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72347;SOR=0.95248;LSEQ=CGGTCCTCGGAGAACACACG;RSEQ=TCCCGGGACAGGTGGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:984:277:115,162:326,381:707,277:0.2815:2,2:25.5:1:29.9:1:0.20012:1.20511:59.9:54.4:0.2816:0:1.1 0/1:563:153:76,77:182,227:409,153:0.2718:2,2:27.9:1:29.2:1:0.29602:1.23:59.6:152:0.2729:0:1.2 +14 105240530 . T C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATCACACTGCCCCACACCA;RSEQ=ACACCCCCACATCACACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:31:3,28:0,0:0,31:0.9688:0,2:24.3:1:31.8:1:1:0:60:30:1:0:1.7 1/1:10:10:1,9:0,0:0,10:1:0,2:25.7:1:32.7:1:1:0:59.5:20:1:0:1.7 +14 105241021 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGCCTCCTGGAGCCTCG;RSEQ=CAGAGTGCAAGGAAGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:18,1:19,2:0.0952:1,2:36.5:1:29.5:1:0.18571:13.07671:60:4:0.0952:0:1 0/0:5:0:0,0:4,1:5,0:0:2,0:15.2:1:31.2:1:1:0:60:10:1:0:0 +14 105241103 . C G 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACAGCCCCTAGCCCACA;RSEQ=TGGGCACCTCCACAGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:4,0:66,3:69,4:0.0548:1,0:35.3:1:33:1:1:0:60:8:0.0556:0:1.3 0/0:17:0:0,0:15,2:17,0:0:2,0:24.5:1:31.3:1:1:0:60:16:1:0:0.2 +14 105241155 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1013;SOR=Inf;LSEQ=AGGCCTGTCTCACCAGCGGC;RSEQ=GAGTCCACGGTGTGTAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:141,10:151,0:0:2,0:20:1:29.1:1:1:0:59.9:24.167:1:0:0.2 0/1:71:2:1,1:61,8:69,2:0.0282:2,2:23.5:1:32:1:0.23903:7.24626:60:4:0.0282:0:1 +14 105241182 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11002;SOR=Inf;LSEQ=ACGGTGTGTAAAGCCCTCAC;RSEQ=TGCCCAAGAAGACAGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:224,47:271,0:0:2,0:22.5:1:30:1:1:0:59.9:44.167:1:0:0.2 0/1:135:2:1,1:102,31:133,2:0.0148:2,2:28.5:1:31.5:1:0.41924:3.25432:60:4:0.015:0:1 +14 105241378 . C T 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07752;LSEQ=GTGAGCTGCCACCCCGCACC;RSEQ=TCATCTCCACCCTGCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1568:399:193,206:605,562:1167,399:0.2545:2,2:23.3:1:31:1:0.2461:1.14892:59.9:48.875:0.2534:0:1.1 0/1:815:21:9,12:398,392:790,21:0.0258:2,2:22.4:1:28.3:1:0.51665:1.35323:60:42:0.0262:0:1 +14 105241607 . G A 216 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCCCAGCTGGTCGGCATGC;RSEQ=TGGGGTGGCATGAGGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:128:26,102:64,273:337,128:0.2753:2,2:22.6:1:30.9:1:0.7929:1.09:60:41.667:0.2717:0:1.1 0/0:225:0:0,0:45,179:224,0:0:2,0:21:1:30.5:1:1:0:60:31:0.9954:0:0.2 +14 105242072 . TCTC T 118 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.07723;SOR=1.98315;LSEQ=TGAGCCCGACCGGAAGTCCA;RSEQ=CTCCTCCTCCTGCTTCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2124:13:7,6:1061,1048:2109,13:0.0061:2,2:30.1:1:33.3:1:1:1.15:60:26:0.0062:9e-04:0 0/1:1243:15:8,7:594,634:1228,15:0.0121:2,2:26.9:1:30.3:1:0.79765:1.22:60:30:0.0122:0.0016:0.2 +14 105242228 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.71359;LSEQ=GCCAGCCTCACAAGCGTGGT;RSEQ=CCACAGCTGTCGGGGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:75:2,73:6,176:182,75:0.2918:1,1:22.2:1:31.7:1:1:1.24329:59.7:74:0.296:0:1.1 1/0:104:63:1,62:0,41:41,63:0.6058:1,1:21.8:1:31.4:1:1:0:60:126:0.63:0:1.1 +14 105242374 . G A 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53924;SOR=0;LSEQ=AGGACTCTGTCCCCACAACC;RSEQ=GACTCCAACCCCCAGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:14,5:0.2632:1,0:26.8:1:31.2:1:1:0:60:10:0.2632:0:1.2 0/0:4:0:0,0:1,3:4,0:0:2,0:26:1:30.5:1:1:0:60:8:1:0:0.5 +14 105242826 . C T 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05819;SOR=0;LSEQ=CCTCAGTTTCCCCACCCAAA;RSEQ=CCCACAGGCAGGACTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:11:10,1:47,1:48,11:0.1864:1,2:30.3:1:31.5:1:0.34074:4.52871:60:22:0.1864:0:1 0/0:18:0:0,0:16,2:18,0:0:2,0:24.1:1:32.6:1:1:0:60:36:1:0:0.5 +14 105242831 . C T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20778;SOR=1.88835;LSEQ=GTTTCCCCACCCAAACCCCA;RSEQ=AGGCAGGACTGGGCCAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:19:18,1:46,1:47,19:0.2879:1,1:19.6:1:30.2:1:0.49604:2.5143:60:38:0.2879:0:1.2 0/1:23:10:9,1:12,1:13,10:0.4348:1,2:19.6:1:29.7:1:1:1.31655:60:20:0.4348:0:1 +14 105242966 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01171;SOR=1.42057;LSEQ=AAGCGCTGGGGCTGCCCAAG;RSEQ=GCCTGGCCTGGCCGCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:662:235:171,64:303,123:426,235:0.355:2,2:24.9:1:31.6:1:0.71832:1.08:60:77.333:0.3575:0:1.1 0/1:319:140:98,42:119,60:179,140:0.4389:2,2:26:1:29.8:1:0.54619:1.18:60:45.667:0.4363:0:1.1 +14 105243148 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04296;SOR=Inf;LSEQ=TGTCTGCGTGCATCCCCCTG;RSEQ=CCCTCCCAGGGCCCTCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:159,392:551,0:0:2,0:23.4:1:31.3:1:1:0:59.9:77.714:1:0:0.2 0/1:298:3:1,2:91,203:294,3:0.0101:2,2:10:1:23.3:1:1:1.11:60:2:0.0069:0:2.3 +14 105243151 . C A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35241;SOR=2.75508;LSEQ=CTGCGTGCATCCCCCTGCCC;RSEQ=TCCCAGGGCCCTCACCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:2:1,1:147,379:526,2:0.0038:2,2:7:1:30:1:0.48242:2.57:60:4:0.0038:0:1 0/1:289:3:2,1:86,199:285,3:0.0104:2,2:14.7:1:26.3:1:0.22217:4.60:60:6:0.0108:0:1 +14 105243199 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10664;SOR=Inf;LSEQ=TGCACCAGCCAGCTCCCCTT;RSEQ=CATACCACCCACCAGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:14,218:232,0:0:2,0:23.2:1:32.3:1:1:0:60:37.667:1:0:0.3 0/1:113:2:1,1:14,97:111,2:0.0177:2,2:10.5:1:28.5:1:0.24889:6.73:60:4:0.0182:0:1 +14 105243220 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13585;SOR=1.59791;LSEQ=CATACCACCCACCAGGTCCT;RSEQ=GGAAGCCCCATCTCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:54:2,52:1,105:106,54:0.3375:1,1:20.1:1:31.7:1:0.26345:4.00:60:26:0.3399:0:1 0/1:69:31:1,30:3,35:38,31:0.4493:2,1:26.9:1:30.5:1:0.62187:2.53941:60:30:0.4478:0:1.2 +14 105244329 . C T 31 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGCCCACTGCCCCGGAAC;RSEQ=GTTCCCCGGAGAAAAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:6.5:1:31:1:1:1:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 105244349 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTCCCCGGAGAAAAGCCC;RSEQ=GGACAGAGGCCCAGCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:32:0:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 105246024 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=CCCTGCCCAGCCGGCCTCGG;RSEQ=CTCGGGACTCAGCCCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:6,0:0:2,0:33.7:1:28.3:1:1:0:59:5:1:0:0.7 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:6:0:31:0:1:3.1622:60:4:0.2857:0:2 +14 105246056 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=GCCCAGAGACCCCGGCCCAG;RSEQ=CAGCCTCGGCCTCGGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:7,0:0:2,0:24:1:32.3:1:1:0:59.1:14:1:0:0.7 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:38:0:30.5:1:1:1.29098:60:4:0.2222:0:2 +14 105246325 . T A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.91668;SOR=1.02847;LSEQ=GTTGCTTGCCAGCCCAGGAC;RSEQ=TGGAGGCTCCAGGGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:100:92,8:182,14:196,100:0.3378:2,2:24.8:1:30.2:1:0.81684:1.12995:60:200:0.3413:0:1.3 0/1:154:53:49,4:95,6:101,53:0.3442:2,2:22.3:1:29.6:1:0.73735:1.29026:59.7:106:0.3442:0:1.3 +14 105246407 . G A 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.53748;LSEQ=CCCAAATCTGAATCCCGAGA;RSEQ=GCCAAGGGGATACTTACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1310:419:250,169:515,376:891,419:0.3198:2,2:26.7:1:31:1:0.54806:1.08:60:58.857:0.3189:0:1.2 0/1:818:165:96,69:368,285:653,165:0.2017:2,2:24.9:1:29.6:1:0.72519:1.08:59.8:164:0.2037:0:1.3 +14 105246681 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12731;SOR=Inf;LSEQ=GAGTCCCAGGGGGCAGGCGC;RSEQ=GTACGGGAGCTGTTTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:0,73:73,0:0:1,0:19.8:1:31.3:1:1:0:60:35.5:1:0:0 0/1:41:2:0,2:2,37:39,2:0.0488:2,0:21.5:1:32.5:1:1:0:60:4:0.0488:0:1 +14 105246692 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15309;SOR=Inf;LSEQ=GGCAGGCGCGGTACGGGAGC;RSEQ=GTTTCTTAGGGCCAGCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:0,49:49,0:0:1,0:22.6:1:31.1:1:1:0:60:98:1:0:0 0/1:32:2:0,2:2,28:30,2:0.0625:2,0:11:1:30.5:1:1:0:60:4:0.0625:0:1 +14 105247366 . A G 29 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCAGGTACACGGGAAC;RSEQ=TTCTCCCTCAAGTTTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +14 105258801 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0402;SOR=Inf;LSEQ=AAGACATGGGGCCCAGGACA;RSEQ=TCACCCTAGGCCAGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:253,8:261,0:0:1,0:24:1:32.7:1:1:0:60:86:1:0:0.3 0/1:137:3:2,1:131,3:134,3:0.0219:1,2:13:1:28.3:1:0.08567:20.00289:60:6:0.0221:0:1.3 +14 105258892 . CA TG 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03284;SOR=1.23659;LSEQ=GACCCTGGGGCTACTACCCC;RSEQ=TCTCTCCCTCCCCAGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1176:356:213,143:478,338:816,356:0.3027:2,2:27.4:1:31.8:1:0.69895:1.05:59.9:712:0.3058:0.0094:1.1 0/1:770:269:155,114:271,225:496,269:0.3494:2,2:25.3:1:30.5:1:0.44651:1.13:60:538:0.3539:0.0429:1 +14 105258893 . A G 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.56463;LSEQ=ACCCTGGGGCTACTACCCCC;RSEQ=TCTCTCCCTCCCCAGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1183:632:371,261:120,84:204,632:0.5342:2,2:25.2:1:30.5:1:1:1.005:59.9:62.2:0.7549:0:1.1 0/1:743:292:164,128:112,101:213,292:0.393:2,2:25.2:1:29.9:1:0.46915:1.16:60:47.667:0.5755:0:1.2 +14 105259002 . G A 71 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0608;SOR=4.83662;LSEQ=GTGCCCGAGGCTCCCGCGAC;RSEQ=CTCACGCGCTCCTCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:2:1,1:262,537:799,2:0.0025:2,2:8:1:26.5:1:0.54915:2.05:60:4:0.0025:0:1 0/1:501:6:4,2:167,328:495,6:0.012:2,2:5:1:27.5:1:0.18727:3.92:60:12:0.0122:0:1.7 +14 105259042 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10136;SOR=Inf;LSEQ=CTGGCGCTCCCCGAGCCCAG;RSEQ=TGGCCTGGCCACAGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:52,373:425,0:0:2,0:25:1:32.7:1:1:0:60:29.357:1:0:0.1 0/1:199:2:1,1:25,171:196,2:0.0101:2,2:33:1:29.5:1:0.24596:6.73:60:4:0.0101:0:1 +14 105615026 . A G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGTCCATCTCAGGGTGAT;RSEQ=AGGGGCCCACAGGGGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:35:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:32:0:1:0:60:4:1:0:1.5 +14 105617042 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05949;SOR=0.39453;LSEQ=GCAGGGGCTGCTGGCACACT;RSEQ=GTCTCGTTCCAGCTCGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:7,8:10,14:24,15:0.3846:2,2:21.9:1:31.1:1:1:1.22:60:30:0.3947:0:1.1 0/1:51:10:4,6:18,23:41,10:0.1961:2,2:29.8:1:29.3:1:1:1.17025:60:20:0.1961:0:1.1 +14 105800258 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACACGCACCTGCCTGTG;RSEQ=CTCACCCGGGCTAAAATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:27:1:1:0:60:4:1:0:1.5 +14 105801668 . G A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCCTGGAGTGGCTGTGAC;RSEQ=CTGTGGCCGGCGCCTGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:31:0:1:0:37.5:4:1:0:1.5 +14 105801780 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16393;SOR=Inf;LSEQ=TGTGGCCGGCGCCTGGCGTG;RSEQ=CTCTGACGCTGTGGCCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:22,14:36,0:0:2,0:19.8:1:31.3:1:1:0:51.1:72:1:0:0.1 0/1:25:2:1,1:14,9:23,2:0.08:2,2:13.5:1:28:1:1:1.52748:60:4:0.0833:0:1.5 +14 105801859 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5023;SOR=0;LSEQ=GTTCCTTCCCCTATTCTGGG;RSEQ=CAGGTGGGGACCACCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:18,16:34,2:0.0556:2,2:11:1:27.5:1:1:1.12132:60:4:0.0571:0:1 0/0:27:0:0,0:14,13:27,0:0:2,0:19.7:1:30.1:1:1:0:59.6:26:1:0:0.1 +14 105905995 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05472;SOR=Inf;LSEQ=GTCCCCACCAGTGGACACAT;RSEQ=GTTCCAGCAGAGAGTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:113,70:183,0:0:2,0:24.6:1:31.7:1:1:0:59.9:90.5:1:0:0.5 0/1:113:3:1,2:66,44:110,3:0.0265:2,2:14.7:1:28:1:0.56561:2.97064:60:6:0.0268:0:1 +14 105906059 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14361;SOR=Inf;LSEQ=CTCTCTGTGCCTGCCTGCAG;RSEQ=GCTCCTGAGCCCCCGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:84,102:186,0:0:2,0:27.9:1:30.6:1:1:0:59.7:22.25:1:0:1 0/1:114:2:1,1:46,66:112,2:0.0175:2,2:16.5:1:30:1:1:1.43:60:4:0.0179:0:1 +14 105906063 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52855;SOR=0;LSEQ=CTGTGCCTGCCTGCAGGGCT;RSEQ=CTGAGCCCCCGATCCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:76,102:178,2:0.0111:2,2:43:1:30.5:1:1:1.34:60:4:0.0114:0:2 0/0:109:0:0,0:43,66:109,0:0:2,0:26.4:1:30.3:1:1:0:60:218:1:0:0.7 +14 105906073 . C T 225 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0192;LSEQ=CTGCAGGGCTCCTGAGCCCC;RSEQ=GATCCCCTGGAGCCAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:162:160:62,98:0,0:0,160:0.9877:0,2:25.6:1:30.8:1:1:0:59.9:52.333:0.9874:0:1.2 1/0:98:59:23,36:12,26:38,59:0.602:2,2:27.5:1:29.7:1:0.52009:1.38:60:118:0.6082:0:1.2 +15 20487945 . T C 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCTCTCTGCGCCTGCGC;RSEQ=GGCGCTGTGCGCCTTTGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:26.5:1:1:0:33:4:1:0:2 +15 20487948 . C T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTCTGCGCCTGCGCTGG;RSEQ=GCTGTGCGCCTTTGCGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:26.5:1:1:0:33:4:1:0:2 +15 20488202 . G A 45 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAGCACAGACCTTGGGA;RSEQ=CACTGCATCGCTTTGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:31:0:32:0:1:0:55:2:1:0:1 1/1:3:3:1,2:0,0:0,3:1:0,2:24.3:1:29:1:1:0:45.7:6:1:0:1.3 +15 20488870 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17669;LSEQ=TGGGACTGCTGGGTATAACC;RSEQ=TGCTGTGGACTGCTGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:104:46,58:206,252:458,104:0.1851:2,2:15.8:1:31.1:1:0.91341:1.03066:29.2:103:0.1859:0:1.1 0/1:623:24:14,10:297,300:597,24:0.0385:2,2:13.3:1:28.9:1:0.53316:1.41:27.5:48:0.039:0:1.1 +15 20489155 . T C 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21569;SOR=Inf;LSEQ=ATGGGGTTTTGCCATGTTGC;RSEQ=CACGCTGGTCTTGAACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:5,2:5,3:8,7:0.4667:2,2:21.4:1:29.1:1:1:1.46:29.7:6:0.4286:0:1.1 1/1:3:3:3,0:0,0:0,3:1:0,0:17.3:1:31.3:1:1:0:31.3:6:1:0:1.3 +15 20489199 . C T 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41224;SOR=2.24222;LSEQ=CTCAAGTGATCCTCCTGCCT;RSEQ=GGCCTCCCAAAGTGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:2,1:16,7:23,3:0.1111:2,2:26.7:1:32.3:1:1:1.13688:20.7:6:0.125:0:1.3 0/1:18:4:4,0:12,2:14,4:0.2222:2,0:22.3:1:32:0:1:0:20.8:8:0.2222:0:1 +15 20489490 . A T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=Inf;LSEQ=AGTCTGGGCAGAAGTCTCAG;RSEQ=GAAAGGTATGAATATGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1235:0:0,0:530,704:1234,0:0:2,0:21.2:1:31:1:1:0:27.1:136.111:0.9992:0:0.1 0/1:1493:17:7,10:674,802:1476,17:0.0114:2,2:13.4:1:28.4:1:0.80927:1.20042:21.5:16:0.0109:0:1 +15 20489800 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGAGGGTTAGGTATAAT;RSEQ=TAAACAAGTGCCTTGTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:1,2:2,26:28,3:0.0968:2,2:43.3:1:29.3:1:0.27119:5.85:49.7:6:0.0968:0:1 0/0:6:0:0,0:1,5:6,0:0:2,0:18.3:1:31:1:1:0:32.8:12:1:0:0.2 +15 20489987 . A G 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AAAATTAAATGTCAAATAAC;RSEQ=TAACATAGGTAATTGTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:3,2:5,5:0.5:2,0:24.8:1:32.2:1:0.16667:0:53.8:10:0.5:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 20490242 . G A 28 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11662;LSEQ=TTAGTTTGACCTTGAGTCTA;RSEQ=CAACAAGAGAGGGAACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:9,0:9,2:0.1818:0,2:13:0:28:1:0.18182:0:60:4:0.1818:0:1 0/1:5:1:1,0:4,0:4,1:0.2:0,0:7:0:29:0:1:0:60:2:0.2:0:1 +15 20490501 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=3.96809;LSEQ=GATTTGCCCAATTGTTGCTT;RSEQ=AGCTCTGGACCTTGTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:175:121:61,60:30,24:54,121:0.6914:2,2:6.4:1:28.6:1:0.62354:1.22805:23.1:59.5:0.6879:0:1 1/1:139:125:71,54:7,7:14,125:0.8993:2,2:6.6:1:28:1:0.77778:1.31:23.5:250:0.8993:0:1.1 +15 20490520 . G T 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGCTCTGGACCTTGTCAA;RSEQ=AAGTTGTTGGTAGTGGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:182,239:421,0:0:2,0:16.9:1:32:1:1:0:31.8:83.2:1:0:0.4 0/1:438:28:14,14:205,205:410,28:0.0639:2,2:12.8:1:27.7:1:1:1:39.8:56:0.0642:0:1.3 +15 20490549 . GT G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=3.16517;LSEQ=GGTAGTGGATCCAAAGGCAT;RSEQ=TTTACAACAGAAGAAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:50:24,26:312,408:720,50:0.0649:2,2:37:1:32.4:1:0.55692:1.21:28.1:100:0.0656:0:0.3 0/1:893:161:83,78:346,386:732,161:0.1803:2,2:32.7:1:32:1:0.33877:1.19:28.5:322:0.1819:0:0.3 +15 20490611 . T C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17431;LSEQ=GGGTGTGGGACAGTGCCTGC;RSEQ=AGCATAAAATACATGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:80:26,54:162,239:401,80:0.1663:2,2:17.9:1:31.7:1:0.21033:1.40681:31.1:79:0.1653:0:1 0/1:596:20:4,16:246,330:576,20:0.0336:2,2:19.6:1:31.8:1:0.06277:2.97703:27.8:40:0.0341:0:1.3 +15 20490624 . A T 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01698;SOR=Inf;LSEQ=TGCCTGCTAGCATAAAATAC;RSEQ=TGGGAAGCCCTGCTGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:132,241:373,0:0:2,0:11.9:1:30.2:1:1:0:28.9:92.25:1:0:0.2 0/1:432:7:0,7:155,270:425,7:0.0162:2,0:10.9:1:29.3:1:0.05317:0:25:14:0.0163:0:1.7 +15 20495201 . GA G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.77022;SOR=1.18204;LSEQ=TGGACTCCTGTGGGAAGGTA;RSEQ=GGGGGGCAACACATAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:9:8,1:20,1:21,9:0.2195:1,2:36.2:1:32.7:1:0.51724:2.41524:30.2:18:0.225:0:0 0/1:24:6:5,1:17,0:17,6:0.25:1,2:24.2:1:30.2:1:0.26087:0:39.8:12:0.3:0:0.2 +15 20495202 . A AG 107 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.04316;SOR=0.12157;LSEQ=GGACTCCTGTGGGAAGGTAG;RSEQ=GGGGGGCAACACATAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:11:9,2:20,1:21,11:0.2683:1,2:26.6:1:31.2:1:0.26613:4.22133:32.1:22:0.275:0.0732:0.2 0/1:24:1:1,0:17,0:17,1:0.0417:1,0:32:0:33:0:1:0:26:2:0.05:0:0 +15 20495371 . A T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14323;SOR=Inf;LSEQ=TTAATTCCCTCACAGGATGA;RSEQ=GACATGAAGAGAAAGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:60,36:96,0:0:2,0:9:1:30.6:1:1:0:49.3:95:1:0:0.1 0/1:135:4:1,3:83,47:130,4:0.0296:2,2:9:1:26.5:1:0.14615:5.23154:52.5:8:0.0301:0:1 +15 20495408 . G A 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.83318;SOR=0.87865;LSEQ=TTCAAGATCTTCTGTGTGAG;RSEQ=AAAATGAATCCACAGCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:10:4,6:109,103:212,10:0.045:2,2:18.4:1:31.2:1:0.53313:1.5841:20.5:20:0.0457:0:1.1 0/1:377:15:7,8:186,176:362,15:0.0398:2,2:18.9:1:28.6:1:0.79576:1.20719:24.2:30:0.0402:0:1.2 +15 20495453 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.44537;LSEQ=AGGTTCTAGCCCAGGTATTC;RSEQ=TATTCCTGATGATCACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:10:6,4:89,88:177,10:0.0535:2,2:18.4:1:28.5:1:0.74741:1.48:29.3:9:0.0489:0:1 0/1:301:105:62,43:92,104:196,105:0.3488:2,2:22.5:1:29.5:1:0.05301:1.63:24.5:210:0.35:0:1.1 +15 20495645 . A C 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18452;LSEQ=ATATGTTTAATATCTAACAC;RSEQ=TAATAGACAGATAAGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:32.4:1:34.4:1:1:0:22:10:0.625:0:1 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:29.8:1:33.5:1:1:0:22:8:0.6667:0:1 +15 20496657 . C T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15526;SOR=0.43548;LSEQ=AGGGTGCCGAGACCACAAAG;RSEQ=GCCCGGCTGTGTGTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:8:4,4:24,21:45,8:0.1509:2,2:32.8:1:30.5:1:1:1.13997:33.1:16:0.1538:0:1.4 0/1:84:6:3,3:39,39:78,6:0.0714:2,2:29.3:1:28.2:1:1:1:30.8:12:0.0723:0:1.3 +15 20496770 . T C 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3356;SOR=3.57365;LSEQ=AGTCTGTTTTTTATAGTGTG;RSEQ=ATTTTAATTATGGAAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:1:0,1:7,52:59,1:0.0167:2,0:35:0:34:0:1:0:22:2:0.0169:0:1 0/1:52:3:0,3:7,42:49,3:0.0577:2,0:43.7:1:32.3:1:1:0:25:6:0.0577:0:1 +15 20498452 . C T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCTGGAGTGCAATGGTG;RSEQ=GATCTCGGCTCACTGCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:30:1:1:0:40.5:4:1:0:1 +15 21136727 . T A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00342;SOR=Inf;LSEQ=CTTTAATTGTGTAAGATTTC;RSEQ=TACAGTGCAAATAATTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:3,36:39,0:0:2,0:27.5:1:28.9:1:1:0:25:38:1:0:0.1 0/1:14:4:0,4:0,10:10,4:0.2857:0,0:39:1:30.3:1:1:0:22:8:0.2857:0:1 +15 21137284 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATAGACAAAAGAGAAAG;RSEQ=ATTCAAAGTACTTTAGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:12,34:46,2:0.0417:2,2:22:0:32.5:1:0.47252:2.76:60:4:0.0426:0:1 0/0:19:0:0,0:5,14:19,0:0:2,0:8.1:1:30.9:1:1:0:58.4:38:1:0:0.2 +15 21141162 . A G 74 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01786;SOR=Inf;LSEQ=AGCATACAATAACTCACAAG;RSEQ=GTTTTCTCCTTTAATCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:18.3:1:30:1:1:0:20.7:6:1:0:1.7 1/1:5:5:0,5:0,0:0,5:1:0,0:17.2:1:32.2:1:1:0:20.2:10:1:0:1.2 +15 21936715 . G A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.88119;LSEQ=ACATCGATTTAAGAAATCCC;RSEQ=AAATATTGGGGAAAGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:8,0:7,0:7,8:0.5333:0,0:23.3:1:32:1:1:0:42.8:16:0.5333:0:1.8 1/0:4:2:2,0:2,0:2,2:0.5:0,0:17:1:31:0:1:0:42.5:4:0.5:0:2 +15 21936770 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6238;SOR=0.73066;LSEQ=TCTGGGATTCCATTAGTTGC;RSEQ=ATTAGGCACAAGGCCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:22:17,5:15,5:20,22:0.5238:2,2:22.9:1:32:1:1:1.13:47.4:44:0.5238:0:1.5 0/1:27:12:10,2:12,3:15,12:0.4444:2,2:30.8:1:29.8:1:1:1.24:51:11:0.4231:0:1.3 +15 21936839 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50444;SOR=0;LSEQ=CCTTCTACCATCTCAGTAGC;RSEQ=ATGATACCCAGAGACCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:58,15:73,2:0.0267:2,2:24:1:30:1:0.38342:3.77602:46:4:0.027:0:1.5 0/0:58:0:0,0:45,13:58,0:0:2,0:24.9:1:30.8:1:1:0:54.1:116:1:0:0.5 +15 21936861 . T C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65083;SOR=0.77148;LSEQ=TGATACCCAGAGACCATACA;RSEQ=TGACTTTAGGGCCATAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:13:7,6:67,12:79,13:0.1413:2,2:32.2:1:33.3:1:0.01794:4.6764:48.9:26:0.1429:0:1.6 0/1:80:9:7,2:54,17:71,9:0.1125:2,2:24.8:1:31.2:1:1:1.10:43.9:18:0.1139:0:1.8 +15 21936913 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26414;SOR=0.74757;LSEQ=CACTTCTGGTGCCATCCAGT;RSEQ=TGGCGTTCTGACCACGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:45:27,18:104,72:176,45:0.2036:2,2:24.4:1:32.7:1:1:1.04:37.4:90:0.2055:0:1.5 0/1:212:34:19,15:105,73:178,34:0.1604:2,2:23.8:1:31.8:1:0.84965:1.13486:36.5:68:0.1611:0:1.6 +15 21936925 . C T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.69575;LSEQ=CATCCAGTATGGCGTTCTGA;RSEQ=CACGGTACTGCGTTTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:4:2,2:126,106:232,4:0.0169:2,2:24:1:29.8:1:1:1.1878:46.5:8:0.0172:0:1.3 0/1:224:35:17,18:108,81:189,35:0.1563:2,2:30.2:1:28.3:1:0.36071:1.40954:39.5:70:0.1591:0:1.4 +15 21936929 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05006;SOR=Inf;LSEQ=CAGTATGGCGTTCTGACCAC;RSEQ=GTACTGCGTTTGCTCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:134,115:249,0:0:2,0:28.2:1:30.2:1:1:0:45.4:82:1:0:0.4 0/1:225:4:2,2:120,100:220,4:0.0178:2,2:29:1:28.3:1:1:1.19901:40.5:8:0.0182:0:1.5 +15 21936992 . C T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01325;SOR=1.87092;LSEQ=CCAAAGTCAGTGAGCTTAAC;RSEQ=GATCCTTCCATTCCCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:48:16,32:32,88:120,48:0.2857:2,2:25.5:1:31:1:0.45032:1.37:47.3:96:0.2892:0:1.4 0/1:126:54:15,39:20,52:72,54:0.4286:2,2:22.1:1:29.4:1:1:1:45.2:108:0.432:0:1.6 +15 21937097 . G A 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.7154;SOR=0.67944;LSEQ=AAACTCTCTCTGCATACAGC;RSEQ=GCAATCTGTGCTTCATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:2,3:8,19:27,5:0.1563:2,2:32.4:1:32.4:1:0.63675:1.56:46.4:10:0.1563:0:1 0/1:27:3:1,2:7,17:24,3:0.1111:2,2:19.7:1:29.3:1:1:1.21:46.3:6:0.12:0:1 +15 21937168 . C T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59993;LSEQ=CCCCCTAGCAAGGTATTCCA;RSEQ=GACCACAAACAATTCATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:1,3:2,5:7,4:0.3636:2,2:4.8:1:30.3:1:1:1.18052:50.8:8:0.3636:0:1 0/1:8:2:0,2:1,5:6,2:0.25:2,0:45.5:1:29:1:1:0:32.5:4:0.2857:0:1 +15 21937819 . G C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34156;SOR=0.27909;LSEQ=TTGAGGTCTGTAGTAATCGA;RSEQ=CCCAGTGTTCTGGCATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:25.6:1:33.4:1:1:0:59:10:0.625:0:1 0/1:10:3:2,1:5,2:7,3:0.3:2,2:23.3:1:31:1:1:1.22183:23:6:0.3:0:1.3 +15 21938163 . T G 28 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCCCCAGGTGAGGCAAG;RSEQ=TCCCCACCCCAGTGAGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:28:1:1:0:49:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 22136743 . TATATATATAA T 30 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=TATATATATATATATATATA;RSEQ=ATAAATAATATATAGAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31.5:1:30.5:1:1:0:23.5:4:1:0:0.5 0/0:1:0:0,0:1,0:1,0:0:0,0:44:0:25:0:1:0:34:2:1:0:0 +15 23699447 . A T 49 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTGTGTGGCTCCTCTTA;RSEQ=GTAATACTCTGCTTCGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:40:1:32.5:1:1:0:47.5:4:1:0:2 1/1:3:3:2,1:0,0:0,3:1:0,2:23:1:31.3:1:1:0:49.3:6:1:0:1.7 +15 23699462 . C G 50 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTAAGTAATACTCTGCTT;RSEQ=GTCCATATAAGCAGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:46:1:32:1:1:0:47.5:4:1:0:2 1/1:3:3:3,0:0,0:0,3:1:0,0:23.7:1:32:1:1:0:36.3:6:1:0:1.7 +15 23699616 . G T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.59083;SOR=2.43877;LSEQ=GATTGAAACATTTTAGCGGC;RSEQ=GGGTGCGGGGGTTGATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:1:0,1:75,34:109,1:0.0091:2,0:1:0:26:0:0.31818:0:47:2:0.0093:0:1 0/1:91:2:1,1:59,30:89,2:0.022:2,2:19.5:1:31.5:1:1:1.95108:57.5:4:0.022:0:1 +15 23699713 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02935;SOR=0;LSEQ=AGAGAGTGCGTAGCAGAGCA;RSEQ=GCAATTCAGGAATCTATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:27,79:0,0:0,106:1:0,2:20.7:1:31.4:1:1:0:52.4:105:1:0:1.2 1/1:111:105:34,71:3,3:6,105:0.9459:2,2:21.7:1:31:1:0.39832:2.07331:50.9:210:0.9459:0:1.1 +15 23699735 . G GTTGT 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.82932;LSEQ=CAATTCAGGAATCTATGTTG;RSEQ=TTAATTACTTTTGTTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:57:9,48:1,3:4,57:0.9344:2,2:22.5:1:31:1:0.52113:1.75818:49.5:114:0.9344:0.2951:1 1/1:64:59:15,44:2,3:5,59:0.9219:2,2:16.2:1:29.9:1:0.60231:1.93273:49.5:118:0.9219:0.4219:1 +15 25903846 . G A 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ACACACAGGTGGAGATGCAG;RSEQ=GGGCAGCCAGCGGGCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:33.5:1:30:1:1:1:60:4:0.5:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:42.5:1:30.5:1:1:0:60:4:1:0:0 +15 25904406 . AC A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAACAAAAACAAAAAA;RSEQ=AAAAGAAAAGAAATTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:32.5:1:1:0:48.5:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 25904539 . G A 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTCTACTCCTGCAGCCT;RSEQ=GTGTGTAGCGCCCACTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:25:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:34:0:31:1:1:0:60:4:1:0:1.5 +15 25905150 . A G 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56923;SOR=0.38278;LSEQ=GCCCGGGAAGCCTGGGCGCC;RSEQ=GGAACCCCAGAACACCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:4,3:0,1:1,7:0.875:0,2:22.1:1:26.6:1:1:0:60:6:0.8571:0:1.1 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:10.8:1:29.2:1:1:1.41418:60:10:0.7143:0:1 +15 26216159 . G T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53877;SOR=0;LSEQ=GCAAGGGTTGACTGGCCAGC;RSEQ=GGGAGATGAGGCTGGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:21,0:21,3:0.125:1,0:40.7:1:33:1:1:0:60:6:0.1304:0:1.3 0/0:10:0:0,0:10,0:10,0:0:0,0:22.2:1:30.7:1:1:0:60:20:1:0:0.6 +15 26216249 . T G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.24999;LSEQ=ACTTTTTGGATGAAGGCCAG;RSEQ=AACATAGAAGAGATTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:19:17,2:82,12:94,19:0.1681:2,2:23.2:1:30.9:1:1:1.24:60:18:0.1636:0:1.2 1/0:63:44:38,6:17,2:19,44:0.6984:2,2:21.9:1:29:1:1:1.33614:60:43:0.6935:0:1.1 +15 26216271 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55957;SOR=3.29309;LSEQ=ACATAGAAGAGATTTTCTGG;RSEQ=AGAAGCCATAGACTGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:1,0:137,35:172,1:0.0058:2,0:12:0:15:0:1:0:60:0:0:0:2 0/1:106:2:1,1:76,28:104,2:0.0189:2,2:26.5:1:27.5:1:0.47421:2.68457:60:4:0.019:0:1 +15 26216370 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=11.079;LSEQ=AAAAATTGTTGAGATTTACG;RSEQ=GTGGCTATTCATAGCATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:501:86:43,43:215,199:414,86:0.1717:2,2:28:1:29.8:1:0.81274:1.08023:60:42:0.1714:0:1.7 1/0:304:212:104,108:45,47:92,212:0.6974:2,2:25.9:1:29:1:1:1.01:60:52:0.6933:0:1.7 +15 26216374 . G C 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTGTTGAGATTTACGCGTG;RSEQ=CTATTCATAGCATGACCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:252,239:491,0:0:2,0:27.1:1:31.3:1:1:0:60:27.882:0.9979:0:0.4 0/1:296:35:16,19:124,133:257,35:0.1182:2,2:26.2:1:30.2:1:0.85766:1.10676:60:34:0.1172:0:1 +15 26216409 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.67476;LSEQ=ACCGTCATCCATCTCTTACT;RSEQ=GGAATGTTCAGAAGGCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:68:26,42:131,195:326,68:0.1726:2,2:24.1:1:30.7:1:0.78723:1.08501:60:136:0.1757:0:1.9 1/0:224:150:57,93:25,49:74,150:0.6696:2,2:24.7:1:29.5:1:0.55897:1.20:60:149:0.6712:0:1.8 +15 26216422 . A AG 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=TCTTACTCGGAATGTTCAGA;RSEQ=GGCATAGCCTCTCAGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:130,212:342,0:0:2,0:24.5:1:31:1:1:0:60:84.5:1:0:0.4 0/1:203:7:3,4:67,129:196,7:0.0345:2,2:31.4:1:29:1:0.69427:1.44:60:14:0.0345:0:1.6 +15 26216430 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.14193;SOR=Inf;LSEQ=GGAATGTTCAGAAGGCATAG;RSEQ=CTCTCAGACATTCTTCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:97,195:292,0:0:2,0:25.2:1:31.3:1:1:0:60:145:1:0:0.4 0/1:177:2:1,1:57,118:175,2:0.0113:2,2:36.5:1:30:1:0.54924:2.06:60:4:0.0114:0:2 +15 26216553 . A G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00499;SOR=21.31864;LSEQ=ATGAGGGGGCTCACTCATCC;RSEQ=CGGAAAGTGGCCATAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:7:0,7:0,41:41,7:0.1458:1,0:24.4:1:34.1:1:1:0:60:14:0.1489:0:2.7 1/1:5:4:1,3:1,0:1,4:0.8:0,2:7:1:32.3:1:0.4:0:60:8:0.8:0:2.3 +15 26216557 . A G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02937;SOR=13.19036;LSEQ=GGGGGCTCACTCATCCACGG;RSEQ=AAGTGGCCATAAAAGGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:0,8:0,38:38,8:0.1739:1,0:19.4:1:33.1:1:1:0:60:16:0.1739:0:2.6 1/0:4:3:1,2:1,0:1,3:0.75:0,2:7:1:30:1:1:0:60:6:0.75:0:2.7 +15 26216566 . A G 86 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31585;SOR=5.1687;LSEQ=CTCATCCACGGAAAGTGGCC;RSEQ=TAAAAGGGATATTTTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:0,6:0,33:33,6:0.1538:1,0:18.7:1:33.3:1:1:0:60:12:0.1538:0:2.8 1/0:2:1:0,1:1,0:1,1:0.5:0,0:24:0:33:0:1:0:60:2:0.5:0:3 +15 26933094 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15954;SOR=Inf;LSEQ=GAATCTTAGTAACTTTCATC;RSEQ=TTTCCAGAGCACGCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:92,14:106,0:0:2,0:24.6:1:32.3:1:1:0:60:212:1:0:0 0/1:71:2:1,1:61,8:69,2:0.0282:2,2:34.5:1:33:1:0.23903:7.24626:60:4:0.0282:0:2 +15 26933113 . T C 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05293;SOR=Inf;LSEQ=CTTTTCCAGAGCACGCTTTT;RSEQ=GAGTCCAGTGGACAACCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:128,35:163,0:0:2,0:23.7:1:31.1:1:1:0:60:326:1:0:0.1 0/1:99:3:2,1:73,23:96,3:0.0303:2,2:22:1:28.7:1:0.56949:1.57878:60:6:0.0306:0:1 +15 26933228 . G C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=1.76387;LSEQ=TTTCTTCATTTCATAATGAC;RSEQ=ACAAGACTGGTCATTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:114:52,62:138,149:287,114:0.2843:2,2:25.5:1:31.3:1:0.65948:1.10401:60:113:0.2839:0:1.7 0/1:279:115:50,65:76,87:163,115:0.4122:2,2:23.7:1:30.6:1:0.62628:1.13511:60:37.333:0.4103:0:1.6 +15 26933242 . T C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69965;SOR=0.91255;LSEQ=AATGACGACAAGACTGGTCA;RSEQ=TTGAGTGGAAAGCTCAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:87:34,53:131,159:290,87:0.2296:2,2:25.7:1:32.2:1:0.32724:1.28346:59.9:86:0.2293:0:2 0/1:262:56:24,32:87,117:204,56:0.2137:2,2:24:1:30.6:1:1:1.01:60:27:0.2093:0:2.1 +15 26933734 . C T 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAGGTGTGTCACCGATG;RSEQ=TATTTGTGGAGTTTCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:30:1:30.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 31862323 . C T 28 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=ACCCCGCCCTTCATTGAACA;RSEQ=ATGTGGCAGATTGGCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:28:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:1 +15 31863093 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22868;SOR=Inf;LSEQ=GGCACTCTGATTCCCGACTC;RSEQ=GAGAGTCAGTGGGCTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:30,0:0:2,0:25.6:1:31.2:1:1:0:60:60:1:0:0.4 0/1:28:2:1,1:14,12:26,2:0.0714:2,2:34.5:1:28.5:1:1:1.16024:60:4:0.0714:0:1 +15 31863103 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.20814;SOR=0;LSEQ=TTCCCGACTCTGAGAGTCAG;RSEQ=GGGCTTGTAACGGCAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:10,12:22,2:0.0833:2,2:19.5:1:33.5:1:1:1.19:60:4:0.087:0:1 0/0:28:0:0,0:15,13:28,0:0:2,0:22.6:1:28.3:1:1:0:60:27:1:0:0.1 +15 32220788 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49951;SOR=Inf;LSEQ=TCACTTAGGAACGAATATGA;RSEQ=TGGAACTCATTCATGTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:56,44:100,0:0:2,0:27.6:1:31:1:1:0:56.3:200:1:0:0.1 0/1:113:2:1,1:65,46:111,2:0.0177:2,2:37.5:1:32.5:1:1:1.40862:59:4:0.0177:0:1.5 +15 32220789 . TG T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21979;SOR=0;LSEQ=CACTTAGGAACGAATATGAT;RSEQ=GAACTCATTCATGTTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:56,44:100,2:0.0196:2,2:15.5:1:32.5:1:1:1.26969:23.5:4:0.0196:0:0.5 0/0:115:0:0,0:67,48:115,0:0:2,0:26.4:1:30.7:1:1:0:58.9:230:1:0:0.1 +15 32220854 . A G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00348;SOR=Inf;LSEQ=CAGATCCACCTACACTAAAA;RSEQ=TGACCCTAAAGTAAATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:34,49:83,0:0:2,0:26.1:1:30.8:1:1:0:59.1:82:1:0:0.1 0/1:92:9:4,5:29,54:83,9:0.0978:2,2:22.9:1:31:1:0.71703:1.48:51.3:18:0.1:0:1.1 +15 33009478 . A T 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07211;SOR=9.12257;LSEQ=AGCCTTGACTTTTGACGGTC;RSEQ=TTTAGTTTTATTCTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:17,0:17,1:0.0556:1,0:29:0:29:0:1:0:60:2:0.0588:0:1 0/1:8:3:2,1:5,0:5,3:0.375:0,2:25.7:1:31.3:1:0.375:0:60:6:0.375:0:2 +15 33009574 . C G 206 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCTTGGCGGGCGAGGAGAG;RSEQ=AGGGTGTCATGTTGGCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:92:92:91,1:0,0:0,92:1:0,1:22.4:1:31.7:1:1:0:60:91:1:0:1.1 0/1:45:20:19,1:24,1:25,20:0.4444:1,1:24:1:30.7:1:1:1.25655:60:40:0.4444:0:1.1 +15 33009607 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53456;SOR=0;LSEQ=TGGCGACAGGCTCCTGCTGG;RSEQ=GGCCAGCGAGCCCGCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:2,0:151,7:158,2:0.0125:1,0:20.5:1:32:0:1:0:60:4:0.0127:0:1.5 0/0:92:0:0,0:88,4:92,0:0:1,0:22.9:1:31.9:1:1:0:60:91:1:0:0.4 +15 33009934 . GA G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16145;SOR=Inf;LSEQ=TTCCCTCTCCAACGGGAGCG;RSEQ=AAATGTGATTTGCTGTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:3,96:99,0:0:1,0:22.3:1:31.3:1:1:0:60:48.5:1:0:0.2 0/1:67:2:1,1:4,61:65,2:0.0299:2,2:11:0:32.5:1:0.14473:13.75:60:4:0.0299:0:0.5 +15 33010736 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCCGCCAGAGCGCAGGA;RSEQ=CATCCGGACCTGCTAGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:27:1:1:0:60:4:1:0:1 +15 33015206 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07281;LSEQ=ATGCAGCTTAATTTAATTTA;RSEQ=TGATATGAGTAGGCCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:102:4,98:1,25:26,102:0.7969:1,1:22.4:1:31.6:1:1:1.02:59.9:50:0.8:0:1 0/1:73:16:2,14:2,55:57,16:0.2192:1,2:16.9:1:29.8:1:0.20696:3.83:60:32:0.2192:0:1.2 +15 33022582 . A T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=Inf;LSEQ=TAAGTGAACGTAATACAAAG;RSEQ=CAAATGTGGTTGGTGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:10:1:28.5:1:1:0:44.5:4:0.1818:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:1:0:30:0:1:0:60:2:1:0:1 +15 33023486 . C A 281 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=1695.49744;LSEQ=AGCATGTCCTAGGAATGCAG;RSEQ=CCCAGGAAGTCCCAGACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2038:1:1,0:925,1109:2034,1:5e-04:2,0:1:0:26:0:0.45504:0:60:2:5e-04:0:1 0/1:1856:847:396,451:458,546:1004,847:0.4564:2,2:25:1:28.9:1:0.63995:1.05:59.7:140.167:0.4586:0:1.2 +15 33023670 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=15.85917;LSEQ=AGTCTCTGCTAGAGAGCACT;RSEQ=CCTATTTTGTAAACATATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:16:0,16:0,103:103,16:0.1333:1,1:18.3:1:30.4:1:1:0:60:32:0.1379:0:1.6 1/0:49:35:0,35:0,14:14,35:0.7143:1,1:18.5:1:29.1:1:1:0:60:34:0.7083:0:1.5 +15 33023685 . A C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=13.29664;LSEQ=GCACTCCCTATTTTGTAAAC;RSEQ=TATCTGCTTTAATGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:10:0,10:0,73:73,10:0.1205:1,0:23.8:1:31.7:1:1:0:60:9:0.1154:0:2.1 1/0:26:17:0,17:0,9:9,17:0.6538:0,1:25.2:1:32.7:1:1:0:60:34:0.6538:0:2 +15 33023951 . T C 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCTCTTCTTAAGTTGA;RSEQ=AGTGACTATGTCAGTCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:18:1:34.5:1:1:0:60:4:0.25:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 33026667 . A T 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATTATGTATTATGTCTGCTT;RSEQ=AATCATTTAAAAACGGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:366,135:501,0:0:2,0:22:1:29.1:1:1:0:60:166:1:0:0.1 0/1:504:18:10,8:324,162:486,18:0.0357:2,2:26.4:1:28.7:1:0.32235:1.59846:60:36:0.0361:0:1.3 +15 33026886 . T C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1639;SOR=Inf;LSEQ=CTGTGTGTGTGAGCGTGCGT;RSEQ=TGTGTTTGGTAGTGTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:23,210:233,0:0:2,0:24.5:1:30.6:1:1:0:60:115.5:1:0:0.1 0/1:159:2:1,1:14,143:157,2:0.0126:2,2:5.5:1:29:1:0.18032:9.90:60:4:0.0128:0:1 +15 33027179 . T A 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACACAGAAATGATAATA;RSEQ=CTTCATTTCAGGGTGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:30.2:1:30.3:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 33033059 . A T 33 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33352;SOR=3.64513;LSEQ=CTTAAGGAAAATTCTTATGG;RSEQ=CTTAGCTTGAGTTTCAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:0,1:244,75:319,1:0.0031:2,0:1:0:26:0:0.2375:0:60:2:0.0032:0:1 0/1:265:3:1,2:186,76:262,3:0.0113:2,2:7:1:21:1:0.20793:4.86117:60:2:0.0077:0:1 +15 33033107 . A G 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAATCAATCATGGTGGCCA;RSEQ=ACGGAATGAGCATTCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:608:0:0,0:376,232:608,0:0:2,0:24.6:1:30.5:1:1:0:59.9:151:1:0:0.1 0/1:520:49:32,17:290,181:471,49:0.0942:2,2:30.9:1:31.5:1:0.64609:1.17:59.2:98:0.0955:0:1.1 +15 33033236 . GA G 112 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19053;SOR=0.41658;LSEQ=GGGATAGGGGGAAAGTAGTT;RSEQ=AAAAAAATAGTTGTAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:11:3,8:139,344:483,11:0.0223:2,2:33.4:1:32.4:1:1:1.07736:60:22:0.0224:0:0.1 0/0:426:4:2,2:144,278:422,4:0.0094:2,2:39.3:1:30.3:1:0.60942:1.93:60:8:0.0095:0:0 +15 33035271 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22807;SOR=Inf;LSEQ=ACGACCAACTGAATGAAAAG;RSEQ=CAATCTATGGAACAGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:77,22:99,0:0:2,0:22.4:1:31.8:1:1:0:60:198:1:0:0.7 0/1:91:2:1,1:65,24:89,2:0.022:2,2:42.5:1:29:1:0.47619:2.67395:60:4:0.0233:0:2 +15 33035284 . C G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.34683;LSEQ=TGAAAAGGCAATCTATGGAA;RSEQ=AGAAGACACGGGGTGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:133:88:66,22:27,18:45,88:0.6617:2,2:22.9:1:33:1:0.10907:1.99:60:176:0.6617:0:1.1 1/1:108:100:67,33:4,3:7,100:0.9259:2,2:24.1:1:30.8:1:0.68544:1.52:60:99:0.9252:0:1.1 +15 33035342 . G A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00898;SOR=Inf;LSEQ=CAGAATGCTCATTCCATTTG;RSEQ=CCACCATGATTGGTTTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:82,100:182,0:0:2,0:27.2:1:31.7:1:1:0:59.9:90:1:0:0.4 0/1:155:6:4,2:63,86:149,6:0.0387:2,2:22.2:1:25.8:1:0.40373:2.71:56.8:5:0.0329:0:1.2 +15 33035503 . C A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATATCTGCTGGCAGCCAC;RSEQ=TTTCCCAGGTATATGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:8,2:0.2:0,0:32.5:1:33:0:1:0:60:4:0.2:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:8.5:1:32.5:1:1:0:60:4:1:0:0 +15 34638342 . G T 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTGCTACACCCCGTCAAA;RSEQ=GTATCACACTTGGGGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:818:0:0,0:465,353:818,0:0:2,0:25.6:1:32.1:1:1:0:59.9:73.364:1:0:0.1 0/1:739:19:9,10:373,345:718,19:0.0257:2,2:15.8:1:29.5:1:0.81719:1.20099:60:38:0.0261:0:1.1 +15 34638544 . G A 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.24575;LSEQ=GTGGTGGGAGAGAGGATCAG;RSEQ=GGTATGTGTCTTAGGACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:703:497:251,246:114,91:205,497:0.707:2,2:25:1:30.7:1:0.24484:1.22743:60:40.417:0.7039:0:1.1 0/1:656:244:119,125:204,207:411,244:0.372:2,2:25.6:1:29.1:1:0.87165:1.03516:60:29.5:0.3682:0:1.2 +15 34638784 . T G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0905;SOR=Inf;LSEQ=AACTAGGCTGGAATGTATTA;RSEQ=AAACTGCCTCTGCTTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:40,176:216,0:0:2,0:21.8:1:29.3:1:1:0:58.9:71:1:0:0.2 0/1:177:3:1,2:39,133:172,3:0.0169:2,2:27:1:30.7:1:0.54327:1.70:57:6:0.0172:0:1.3 +15 34638841 . A G 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GCCTGTAATCCCAGCACTTT;RSEQ=GGAGGTCGAGGCGGGTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:1,0:1,8:0.8889:0,0:17.9:1:32.9:1:0.11111:0:38.6:16:0.8889:0:4 1/1:12:12:0,12:0,0:0,12:1:0,0:19:1:30.5:1:1:0:34.7:11:1:0:4.3 +15 34638843 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTGTAATCCCAGCACTTTAG;RSEQ=AGGTCGAGGCGGGTGGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:1,0:1,8:0.8889:0,0:15.9:1:32:1:0.11111:0:38.6:16:0.8889:0:4 1/1:12:12:0,12:0,0:0,12:1:0,0:17:1:31.7:1:1:0:34.7:24:1:0:4.3 +15 34638847 . TC CT 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42105;SOR=Inf;LSEQ=AATCCCAGCACTTTAGGAGG;RSEQ=GAGGCGGGTGGATTACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:1,0:1,7:0.875:0,0:12.6:1:33.5:1:0.125:0:35.6:14:0.875:0:3.3 1/1:11:11:0,11:0,0:0,11:1:0,0:13.5:1:31.4:1:1:0:32.8:22:1:0:3.4 +15 34639015 . C T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.52725;SOR=1.64477;LSEQ=AATCACTTGAACCCAGGAGG;RSEQ=GGAGGTTGCAGTGAGCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:8,0:12,0:12,8:0.4:0,0:20:1:29:1:1:0:48.3:16:0.4211:0:1.4 1/0:19:10:10,0:7,0:7,10:0.5263:0,0:28.2:1:27.7:1:1:0:39.5:9:0.6:0:1.8 +15 34639360 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.212;SOR=Inf;LSEQ=GGGGTGTGGTGGCTCACACC;RSEQ=GTTATCTCTGCACTTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:35,173:208,0:0:2,0:20.7:1:31:1:1:0:59.9:28.714:1:0:0.1 0/1:178:2:1,1:38,138:176,2:0.0112:2,2:28:1:30:1:0.39116:3.60:60:4:0.0115:0:1.5 +15 34639365 . T A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20736;SOR=Inf;LSEQ=GTGGTGGCTCACACCAGTTA;RSEQ=CTCTGCACTTTGGAAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:27,153:180,0:0:2,0:22.1:1:29.9:1:1:0:59.9:29:1:0:0 0/1:151:2:1,1:27,122:149,2:0.0132:2,2:9:1:24.5:1:0.33748:4.46:60:4:0.0134:0:1.5 +15 34640054 . AAAAAAT A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=6.000;MSILEN=6;SSF=0.00088;SOR=0.58462;LSEQ=ACAGAGCGAGACTCCATCTC;RSEQ=AAAAATAAAAATAAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:416:329:210,119:82,0:82,329:0.7909:1,2:25:1:31.1:1:0:0:52.3:328:0.7961:0.0601:0.1 1/0:414:285:171,114:112,15:127,285:0.6884:2,2:26.5:1:29.9:1:0:4.96063:52.4:284:0.6927:0:0.1 +15 34640060 . TAAAAA T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.06251;SOR=Inf;LSEQ=CGAGACTCCATCTCAAAAAA;RSEQ=TAAAAATAAAAATAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:0:0,0:295,129:424,0:0:2,0:22.8:1:30:1:1:0:48.8:69.667:0.9905:0:0.1 0/1:460:5:1,4:301,154:455,5:0.0109:2,2:13.4:1:27:1:0.04953:7.78314:54.8:10:0.011:0.0065:1 +15 34640218 . C T 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03516;LSEQ=CATGAAACCTAGTGCCGCCC;RSEQ=GTCTCCATCCCCTGCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:404:403:31,372:0,1:1,403:0.9975:0,2:24.5:1:30.5:1:1:0:60:56.571:0.9975:0:1.1 1/1:348:325:31,294:4,18:22,325:0.9339:2,2:20.9:1:29.8:1:0.25896:2.10172:60:324:0.9337:0:1.1 +15 34640378 . T C 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCACTGTTGGTGACAGGGGA;RSEQ=GGGGGCCCTTGCCTCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:22:1,21:0,0:0,22:0.9565:0,1:18:1:29.4:1:1:0:60:21:0.9545:0:1.2 1/1:12:12:1,11:0,0:0,12:1:0,2:25.1:1:29.6:1:1:0:60:24:1:0:1.3 +15 35384456 . A T 98 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0.23368;SOR=0.31102;LSEQ=TAACTTAGTTGCATGTCTGT;RSEQ=AAAAAAAAAAAAATATTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:9,0:2,0:2,9:0.5294:0,0:21.1:1:31:1:1:0:60:18:0.5294:0:1.1 0/1:8:2:2,0:2,0:2,2:0.25:0,0:10:1:31.5:1:1:0:60:4:0.2857:0:1 +15 35384578 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50484;SOR=0;LSEQ=ACACGTCCATTACTTCGGGG;RSEQ=CTTTGGTGGATTTTTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:2,0:130,1:131,2:0.015:1,0:30:0:31.5:1:1:0:60:4:0.0155:0:1 0/0:105:0:0,0:102,3:105,0:0:1,0:24.3:1:31:1:1:0:60:16.5:1:0:0.2 +15 35384660 . C T 75 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00433;SOR=Inf;LSEQ=AGGTCTCCCGCGGGCGTCAG;RSEQ=AGGGGCGGCGGCGGGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:0:0,0:359,233:592,0:0:2,0:24.2:1:32:1:1:0:59.9:52.818:0.9983:0:0.2 0/1:673:9:2,7:392,272:664,9:0.0134:2,2:10.7:1:23.9:1:0.03782:5.03268:58.9:8:0.012:0:1 +15 35384908 . C A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28173;SOR=0.83293;LSEQ=TGTTGAGGTGCAGGAACACT;RSEQ=TGATGAATTTTTTGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:339:233:147,86:68,37:105,233:0.6873:2,2:24:1:29.3:1:0.80773:1.075:57.8:45.6:0.6847:0:1.1 1/0:317:205:132,73:68,43:111,205:0.6467:2,2:23.9:1:28.4:1:0.62543:1.14:58.3:67.333:0.6495:0:1.1 +15 35385071 . C T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07123;LSEQ=GCTGTGATTGACTTGAACAA;RSEQ=CGTTGGTTTAACGGACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:699:283:145,138:197,214:411,283:0.4049:2,2:26.5:1:30.7:1:0.39666:1.14:47.8:93.333:0.4058:0:1.1 0/1:802:37:17,20:359,405:764,37:0.0461:2,2:26.7:1:29:1:1:1.0428:46.7:36:0.0453:0:1.1 +15 35385244 . G A 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12625;SOR=5.52206;LSEQ=GGAGCTGTGTGGGCAGCGTC;RSEQ=CAAGAAGCATAGATCAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:1:1,0:189,212:401,1:0.0025:2,0:1:0:28:0:0.47264:0:33:2:0.0025:0:1 0/1:441:6:3,3:196,238:434,6:0.0136:2,2:20.7:1:27.2:1:1:1.21:41.7:5:0.0115:0:1.2 +15 35385293 . T C 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGAGCGTCATTCTCGGTC;RSEQ=GGAGACCGTGGTCATGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:212,146:358,0:0:2,0:26.3:1:30.9:1:1:0:59.5:31.545:1:0:0.5 0/1:363:26:9,17:176,161:337,26:0.0716:2,2:24.6:1:29.8:1:0.10361:2.06085:54.8:25:0.0708:0:1.2 +15 35385338 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=6;SSF=0.00789;SOR=0.70583;LSEQ=GGTGGCGGTGGCGGTGGCGG;RSEQ=GGCCCAGGCGGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:493:312:176,136:96,85:181,312:0.6329:2,2:22.3:1:30.4:1:0.51099:1.15:52.5:33.667:0.6352:0:1.2 1/0:492:270:157,113:122,87:209,270:0.5488:2,2:22.6:1:29.6:1:1:1.00928:51.4:23.545:0.5418:0:1.2 +15 35385342 . CCAGGC GGTGGCGGCGGCCCA 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=3;SSF=0.00749;SOR=Inf;LSEQ=GCGGTGGCGGTGGCGGTGGC;RSEQ=GGCGGCGGCGGACGGGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:276,225:501,0:0:2,0:22:1:30.3:1:1:0:53.6:30.313:1:0:0.8 0/1:498:7:5,2:287,204:491,7:0.0141:2,2:20:1:29:1:0.7051:1.78:47.9:14:0.0143:0.012:1.1 +15 35385344 . AGGC A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.06037;SOR=1.69536;LSEQ=GGTGGCGGTGGCGGTGGCCC;RSEQ=GGCGGCGGCGGACGGGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:22:12,10:245,224:469,22:0.0447:2,2:31.5:1:32.2:1:1:1.10:48.6:21:0.0438:0.002:0.7 0/1:503:37:20,17:272,193:465,37:0.0736:2,2:30.3:1:30.6:1:0.6076:1.19749:45:74:0.0751:0:0.6 +15 35385419 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23343;SOR=Inf;LSEQ=TCTGGGCGATTCTGAGCCAT;RSEQ=CCATTTTTACCTTACGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:88,119:207,0:0:2,0:12:1:31.9:1:1:0:37.4:50.75:1:0:0.7 0/1:194:2:2,0:96,96:192,2:0.0103:2,0:12:1:24.5:1:0.49746:0:44:4:0.0105:0:1.5 +15 35385420 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23792;SOR=Inf;LSEQ=CTGGGCGATTCTGAGCCATG;RSEQ=CATTTTTACCTTACGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:84,115:199,0:0:2,0:11.8:1:31.1:1:1:0:36.6:38.8:1:0:0.7 0/1:190:2:1,1:94,94:188,2:0.0105:2,2:23.5:1:27:1:1:1:22.5:4:0.0109:0:1 +15 35385434 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.88117;SOR=0.91472;LSEQ=GCCATGCCATTTTTACCTTA;RSEQ=GTCTGCTAGAAAGTGTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:32:12,20:23,55:78,32:0.2883:2,2:9.1:1:29.4:1:0.4999:1.43:32.1:31:0.2925:0:1.5 0/1:111:30:13,17:32,48:80,30:0.2703:2,2:10.5:1:28:1:0.82877:1.15:30:14:0.2617:0:1.6 +15 35385567 . TA T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.01129;SOR=5.01207;LSEQ=AAATTTGTAGTGATAACAGT;RSEQ=AAAAAAAAAAGATTCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:4:0,4:0,58:58,4:0.0635:1,0:34.5:1:29.8:1:1:0:59.8:8:0.0635:0:0.3 0/1:35:9:2,7:0,26:26,9:0.2571:1,2:27.3:1:30.6:1:0.0605:0:60:18:0.2647:0:0 +15 35385596 . T C 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01875;SOR=0;LSEQ=AAAGATTCTCCATAAATAGG;RSEQ=CGGGCGCGGTGCCTCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:10:0,10:0,21:21,10:0.3226:1,0:15.2:1:30.6:1:1:0:55.9:9:0.3103:0:1 0/0:15:0:0,0:0,15:15,0:0:1,0:20.2:1:27.6:1:1:0:58.5:14:1:0:0.4 +15 36871957 . C T 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCAAGCAGGCGAGGACC;RSEQ=GGGCCTGTGCCGCTTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:19.3:1:32.3:1:1:0:60:8:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 36872369 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=0;LSEQ=CGGTGAGTTCATGGCAGCCT;RSEQ=CCAAGGCCTTGCAATTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:127:116,11:0,0:0,127:1:0,2:27.2:1:32.4:1:1:0:60:126:1:0:1.1 1/1:158:145:121,24:9,4:13,145:0.9177:2,2:23.4:1:30:1:0.24874:2.23:60:35.25:0.9276:0:1.1 +15 36872487 . G C 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01712;LSEQ=CAGAGGTTAATTGACAGATA;RSEQ=TAGGAATGAATGATGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:663:662:367,295:0,1:1,662:0.9985:0,2:26.4:1:32.3:1:0.44646:0:60:65.2:0.9985:0:1.6 1/1:813:747:393,354:33,29:62,747:0.9188:2,2:26.1:1:31:1:1:1.02498:60:48.8:0.9184:0:1.5 +15 36872498 . T A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.3981;LSEQ=TGACAGATAGTAGGAATGAA;RSEQ=GATGGGTGGGAATATGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:673:370:197,173:156,147:303,370:0.5498:2,2:27.3:1:30.9:1:0.69817:1.07:60:91.5:0.5487:0:2 0/1:838:274:139,135:286,276:562,274:0.327:2,2:25.9:1:29.4:1:1:1.00641:60:53.8:0.3276:0:2.1 +15 36872595 . C T 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39137;SOR=0.31721;LSEQ=AAGGGAGCATAGAGGTAAAG;RSEQ=GGCTTCATACTGTTTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:4:1,3:81,242:323,4:0.0122:2,2:23.8:1:30.8:1:1:1.00412:60:8:0.0125:0:1 0/0:256:1:0,1:59,195:254,1:0.0039:2,0:23:0:31:0:1:0:60:2:0.0039:0:1 +15 36872619 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51538;SOR=0;LSEQ=TTCATACTGTTTGACTGTGG;RSEQ=TTGTACTGTTAACTGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:27,161:188,2:0.0105:2,2:20:1:28.5:1:0.27368:5.87:60:4:0.0106:0:1 0/0:131:0:0,0:18,113:131,0:0:2,0:20.2:1:31.9:1:1:0:60:130:1:0:0.1 +15 36872642 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15587;SOR=Inf;LSEQ=GTACTGTTAACTGTGGAATT;RSEQ=AGTGACCTCAAGGGTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:3,102:105,0:0:1,0:21.5:1:31.2:1:1:0:60:51.5:1:0:0.1 0/1:69:2:1,1:4,63:67,2:0.029:2,2:9.5:1:30:1:0.14066:14.19:60:4:0.029:0:1 +15 38456417 . C T 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTGGGTTTAATTATGAG;RSEQ=CTTTCTTTAACAGTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:26.3:1:32:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 38456861 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.24375;LSEQ=AGCAGTAACACCTAGTCAAA;RSEQ=AGGTTGCAGCCAGAAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:256:120,136:133,158:291,256:0.4672:2,2:26.8:1:29.2:1:0.79707:1.05:60:41.667:0.4655:0:1.2 1/0:567:376:182,194:90,100:190,376:0.6631:2,2:26.3:1:28.3:1:0.85872:1.04:60:74.2:0.6637:0:1.2 +15 38457016 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02107;SOR=Inf;LSEQ=GGATCAGGGATCGGAACCAT;RSEQ=CTTGAATTCCAGCATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:1,42:43,0:0:1,0:26.3:1:33.1:1:1:0:60:42:1:0:1 0/1:28:4:0,4:0,24:24,4:0.1429:1,0:26.5:1:27.8:1:1:0:60:8:0.1429:0:2.5 +15 38457024 . T C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58467;SOR=1.40643;LSEQ=GATCGGAACCATGCTTGAAT;RSEQ=CCAGCATAAAAAAAGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:21:0,21:1,15:16,21:0.5676:1,1:28.9:1:32.9:1:0.43243:0:60:42:0.5833:0:1.6 1/0:20:13:0,13:0,7:7,13:0.65:0,1:15.1:1:30.8:1:1:0:60:26:0.65:0:1.1 +15 38457041 . G A 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01832;SOR=0;LSEQ=AATTCCAGCATAAAAAAAGA;RSEQ=CACAAATCAGAAACACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:0,12:1,18:19,12:0.3871:1,0:24.3:1:29.9:1:1:0:60:11:0.3667:0:2 0/0:11:0:0,0:0,11:11,0:0:0,0:21.7:1:31:1:1:0:60:22:1:0:1.5 +15 39564293 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29586;LSEQ=ATTTCATGGAAATTTTTTCA;RSEQ=CAGGCTATAAATTCCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:131:69,62:101,114:215,131:0.3775:2,2:27.5:1:30.2:1:0.32:1.26:60:262:0.3808:0:1.1 0/1:316:48:22,26:134,129:263,48:0.1519:2,2:28.1:1:29.2:1:0.53401:1.22681:60:47:0.1506:0:1.1 +15 39564351 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09022;SOR=Inf;LSEQ=GACATTATGTTCTATACCTT;RSEQ=TCCACTCCCCTGATTATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:98,143:241,0:0:2,0:24.7:1:32.3:1:1:0:60:119.5:1:0:0.3 0/1:197:3:2,1:65,129:194,3:0.0152:2,2:21.3:1:25.3:1:0.26722:3.94:60:6:0.0153:0:1 +15 40243559 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03948;SOR=3.80123;LSEQ=GAGCCACCACGCCCGACCCA;RSEQ=AGTGGATTCTTAAGCACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:3,4:9,3:12,7:0.35:2,2:24.1:1:28.4:1:0.32609:3.68811:57.7:14:0.3684:0:1.3 1/0:28:19:12,7:7,2:9,19:0.6786:2,2:25.8:1:28.9:1:0.67003:1.99246:59.7:38:0.6786:0:1.1 +15 40243698 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17273;SOR=0;LSEQ=AACCAGATAGGCCTCACTTG;RSEQ=CTTCTGCAAAGCACCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:34:1:29:1:1:1.12:58.5:4:0.1053:0:1 0/0:26:0:0,0:13,13:26,0:0:2,0:23.4:1:31.3:1:1:0:52.3:52:1:0:0.1 +15 40328575 . G C 288 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTTGTTGCTGCTGTTGTTG;RSEQ=TGCTGTTGCTGCTGCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:486:482:214,268:1,1:2,482:0.9918:2,2:25.7:1:32.4:1:1:1.25174:53.4:39.167:0.9937:0:1.2 0/0:609:0:0,0:10,14:24,0:0:2,0:24:1:30.7:1:1:0:57:23:0.8846:0:0.1 +15 40328665 . G A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33448;SOR=0.66302;LSEQ=CTTTTTGTCTCTCTTCTTCA;RSEQ=CCCATCCATGTTAGCTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:49:0,49:0,17:17,49:0.7424:1,1:17.9:1:29.1:1:1:0:38.5:23.5:0.7581:0:1.3 1/0:61:40:2,38:0,21:21,40:0.6557:1,2:19.9:1:29.5:1:0.54098:0:35.7:80:0.6557:0:1.3 +15 40329033 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAGGAAGACGGTATTAGC;RSEQ=TTGAAATTCACACCCTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:8.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 40626252 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1707;SOR=Inf;LSEQ=CCAGAACAGCTCCCGCCCAG;RSEQ=ACAGCCCAGATCTGCCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,7:22,0:0:2,0:24.8:1:30.5:1:1:0:60:44:1:0:0 0/1:16:2:1,1:9,5:14,2:0.125:2,2:12:1:32.5:1:1:1.73197:60:4:0.125:0:1 +15 40626319 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51373;SOR=0;LSEQ=TGGCAGTCTCCGTCGCCTAC;RSEQ=GGCTGGATTACTGGTAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:12,17:29,2:0.0645:2,2:17.5:1:31:1:1:1.40:60:4:0.0645:0:1.5 0/0:20:0:0,0:7,13:20,0:0:2,0:26.8:1:29.2:1:1:0:60:40:1:0:0.3 +15 40627784 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TGACTCCCCCTTCGGCCCCT;RSEQ=TGGGGATGCCAGGGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:33:0:30:0:1:0:56:2:1:0:6 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:1 +15 40949823 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21771;SOR=Inf;LSEQ=TGTCCATGCCTTCTCCCAGT;RSEQ=TCTGGTGGTTTGCTGGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:13,15:28,0:0:2,0:29.9:1:30.3:1:1:0:60:13:1:0:0.1 0/1:25:2:1,1:14,9:23,2:0.08:2,2:36:1:28.5:1:1:1.52748:60:4:0.08:0:1 +15 40990288 . C T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAACTTTGTGCCTGTTGA;RSEQ=CAACCTCTCTCCTTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:0:30.5:1:1:0:60:4:1:0:1 +15 40991153 . A G 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00125;SOR=Inf;LSEQ=ACTACCAAGGTCAAGACCCA;RSEQ=ATTAGACTTTTCAGAAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:1,106:107,0:0:1,0:24.4:1:31.3:1:1:0:60:52.5:1:0:0.1 0/1:70:7:0,7:1,62:63,7:0.1:1,0:15.4:1:31.3:1:1:0:60:14:0.1014:0:1 +15 40993120 . T TC 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.51405;SOR=0;LSEQ=CCTGGAACCAACTTCCCATC;RSEQ=CCCCCCGCCCCCCCAAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:38,0:38,2:0.0488:1,0:14:1:26:1:1:0:60:4:0.0513:0.0244:2.5 0/0:27:0:0,0:26,1:27,0:0:1,0:27.9:1:31.3:1:1:0:60:54:1:0:0.2 +15 40993435 . T A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13527;SOR=Inf;LSEQ=TTAACCTAGGGAGGCATTAG;RSEQ=GGGAATAGTACAAAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:87,190:277,0:0:2,0:24.2:1:29.6:1:1:0:59.9:26.7:1:0:0.1 0/1:355:4:3,1:122,229:351,4:0.0113:2,2:13.8:1:25.5:1:0.12722:5.60:60:8:0.0114:0:1.3 +15 40993451 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25775;SOR=Inf;LSEQ=TTAGTGGGAATAGTACAAAA;RSEQ=GGAATGTAGTGAAAGACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:45,162:207,0:0:2,0:23.7:1:31.7:1:1:0:60:414:1:0:0.1 0/1:259:3:2,1:72,184:256,3:0.0116:2,2:19.3:1:28:1:0.19723:5.07:60:6:0.0117:0:1 +15 40993559 . C CT 46 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.06545;LSEQ=TTCTTCTTTTCTTTTCTTTT;RSEQ=TTTTTTTTTTCTTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:1,2:2,28:30,3:0.0857:2,2:23.7:1:29.1:1:0.25587:6.29:59.3:6:0.1034:0.0286:0.3 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:29:1:31:0:1:0:60:4:0.1:0:0.5 +15 40993710 . C T 59 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63287;SOR=1.91506;LSEQ=AGCCTCCCAAGTAGCTGGGA;RSEQ=TACACTACAGGCACATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:29.5:1:30:1:1:0:60:4:0.2857:0:1 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:38.8:1:29.8:1:1:0:60:8:0.4444:0:1 +15 40993966 . T A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0796;SOR=Inf;LSEQ=CCTTGAAGTTTTATGTAGTA;RSEQ=AAAGCAGATTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:116,101:217,0:0:2,0:19.7:1:28.6:1:1:0:58.7:17.083:1:0:0.7 0/1:306:5:3,2:177,123:300,5:0.0163:2,2:13.6:1:21:1:1:1.04:55:1.5:0.0108:0:2.8 +15 40994067 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24492;SOR=Inf;LSEQ=TCTTGGTCTACTGCACCCTC;RSEQ=GCCTCTCAGGTTCAAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:0,27:27,0:0:1,0:19.9:1:23.1:1:1:0:51.5:3.5:1:0:0.5 0/1:33:3:0,3:0,30:30,3:0.0909:1,0:14.7:1:29.7:1:1:0:43.3:6:0.1071:0:1 +15 40998302 . TA T 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTCTTTTTTCTTTATATA;RSEQ=TTTTTTTGCCATCAAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:200,44:244,0:0:2,0:23.2:1:28.9:1:1:0:60:80.333:1:0:0.2 0/1:212:26:22,4:150,34:184,26:0.1226:2,2:25.1:1:30.5:1:1:1.25:60:52:0.125:0.0236:0 +15 40998305 . T A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=4.81467;LSEQ=TCTTTTTTCTTTATATATAT;RSEQ=TTTTTGCCATCAAGATCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:45:41,4:165,42:207,45:0.1779:2,2:25.7:1:28.9:1:0.08854:2.60:60:44:0.1753:0:1 1/0:225:115:93,22:87,23:110,115:0.5111:2,2:23.2:1:27.3:1:0.74245:1.12:60:22:0.5:0:1.1 +15 40998342 . T G 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTGTGGTAAGGAATATTA;RSEQ=TTTGTTGATTTAATATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:311,152:463,0:0:2,0:25.4:1:30.9:1:1:0:60:91.6:1:0:0.2 0/1:497:42:32,10:303,152:455,42:0.0845:2,2:21.9:1:31.7:1:0.23182:1.60:60:84:0.0857:0:1 +15 40998563 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20572;SOR=Inf;LSEQ=AGGTTATAAAACAAAACTGA;RSEQ=ATATTTGTGTAGCATTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:18,184:202,0:0:2,0:24.9:1:31.4:1:1:0:59.8:201:1:0:0 0/1:169:2:1,1:18,149:167,2:0.0118:2,2:9.5:1:29.5:1:0.21281:8.08:60:4:0.012:0:1 +15 41001187 . T G 201 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTACAGTTTCTACATGTTTG;RSEQ=ATTATGCTAAGAGTTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:665:0:0,0:418,247:665,0:0:2,0:25.7:1:29.1:1:1:0:59.9:82.125:1:0:0.1 0/1:717:97:61,36:372,248:620,97:0.1353:2,2:24.1:1:30.5:1:0.65556:1.13:60:96:0.1345:0:1.2 +15 41001354 . T C 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08488;SOR=Inf;LSEQ=GCTAATCAAATAAGCAAGCA;RSEQ=TACTTCATTCCTGCTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:55,245:300,0:0:2,0:23.1:1:30.4:1:1:0:60:74:0.9966:0:0.1 0/1:237:3:1,2:46,188:234,3:0.0127:2,2:26:1:29.3:1:0.48638:2.04:60:6:0.0128:0:1.3 +15 41001367 . G A 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07774;SOR=Inf;LSEQ=GCAAGCATTACTTCATTCCT;RSEQ=CTATTTGCAAGCATCTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:28,203:231,0:0:2,0:23.2:1:32.2:1:1:0:60:76:1:0:0.1 0/1:173:3:1,2:25,145:170,3:0.0173:2,2:16.7:1:20:1:0.3884:2.88:60:2:0.0118:0:1 +15 41003463 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACAAACAAACAAAAACA;RSEQ=ACAATTAAAAATATTAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 41011311 . G A 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14861;SOR=6.81287;LSEQ=TGTCACCCAGGCTAGAGTGC;RSEQ=GTGGCGTGATCTCAGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:1,5:0,9:9,6:0.4:0,2:25.5:1:32:1:0.4:0:39.5:12:0.4:0:1.2 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:29.8:1:28.8:1:1:0:36.6:10:0.8333:0:2 +15 41020653 . GA G 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAAGACTCCGTCTCAAA;RSEQ=AAAAAAAAAAAGAATGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:25.3:1:35.3:1:1:0:54.7:6:0.3333:0:0.3 0/0:1:0:0,0:1,0:1,0:0:0,0:2:0:31:0:1:0:60:2:1:0:1 +15 41021123 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51403;SOR=0;LSEQ=TAGTAGTTTGAATTAGAAAT;RSEQ=AGGAGGTTTAAGTATAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:0,2:0,136:136,2:0.0145:1,0:27:1:34:0:1:0:60:4:0.0145:0:1 0/0:96:0:0,0:2,94:96,0:0:1,0:23.2:1:31:1:1:0:60:95:1:0:0.1 +15 41021570 . CAAAA C 61 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=25.000;MSILEN=1;SSF=0.06178;SOR=8.38866;LSEQ=GACAGAGCTAGACTCCATCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:1,0:11,1:12,1:0.0588:2,0:12:0:34:0:1:0:44:2:0.0588:0:5 0/1:11:4:4,0:5,0:5,4:0.3636:0,0:7.8:1:30.9:1:1:0:55:8:0.3636:0.1818:3.3 +15 41021635 . TG T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50584;SOR=0;LSEQ=ATGAATATGAGATTTTAGGG;RSEQ=GTAAGGAAGGGACCAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:140,37:177,2:0.0111:2,2:23.5:1:29.5:1:0.38045:3.74709:60:4:0.0116:0.0056:0.5 0/0:141:0:0,0:119,22:141,0:0:2,0:23.5:1:31.1:1:1:0:59.3:34.25:1:0:0.3 +15 41021973 . TG T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21012;SOR=Inf;LSEQ=ATTAGTTATTCGTTATTTTG;RSEQ=GGGGAAAGTGGTGGCAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:160,58:218,0:0:2,0:22.7:1:32.4:1:1:0:60:71.667:1:0:0.1 0/1:185:2:1,1:129,54:183,2:0.0108:2,2:37:1:30:1:0.50734:2.37625:60:4:0.011:0:0 +15 41022006 . G T 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18837;SOR=4.66082;LSEQ=TGGCAGCATTAAGGCTTTTG;RSEQ=AGTGTCTATGGCCACAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:1:0,1:250,103:353,1:0.0028:2,0:1:0:23:0:0.29379:0:60:2:0.0029:0:1 0/1:308:4:1,3:205,97:302,4:0.013:2,2:12.3:1:24.5:1:0.10394:6.29946:60:8:0.0132:0:1 +15 41023027 . T G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCATGCCCGGCCTAAATTT;RSEQ=TCTTTTTTTAATGTTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:12,0:12,3:0.2:0,0:20:1:33:1:1:0:60:6:0.2:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:8.3:1:29.3:1:1:0:60:6:1:0:0 +15 41023425 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09759;SOR=Inf;LSEQ=CTTAAGTGCTGCAGCCTAAT;RSEQ=AGAGTGCACTGCTCCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:65,228:293,0:0:2,0:23.1:1:31.7:1:1:0:60:57.6:1:0:0.1 0/1:251:3:1,2:60,188:248,3:0.012:2,2:35.3:1:22.7:1:0.56792:1.56:60:2:0.0081:0:1.3 +15 41794852 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCTTCCCTTCTGGGCCA;RSEQ=GCTGGGCGGGGCCCTGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:31.5:1:1:0:60:4:1:0:1 +15 41796991 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=CAGGAATCTGTCTTGGATGT;RSEQ=AAGATGCCCTCCAGGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:40.7:1:32.2:1:1:0:60:12:1:0:0 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:39:1:28:1:1:1.29098:60:4:0.2222:0:1 +15 41798217 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0769;SOR=0;LSEQ=CAGGGCTCTGCAGGAAGACA;RSEQ=GTTGGAAGGGAGTGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:7,11:18,3:0.1429:2,0:31.7:1:31.7:1:0.52105:0:60:6:0.15:0:1 0/0:27:0:0,0:11,15:26,0:0:2,0:24:1:28.8:1:1:0:60:52:0.963:0:0.2 +15 41804302 . G T 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22367;SOR=0;LSEQ=GCGCCGCCCCATCCCCACTG;RSEQ=CTGCGCTCACTCCGGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:68,31:99,2:0.0198:2,2:6.5:1:27.5:1:0.53545:2.17486:60:4:0.0202:0:1 0/0:112:0:0,0:66,46:112,0:0:2,0:24.7:1:29.9:1:1:0:60:36.333:1:0:0.2 +15 41804336 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49805;SOR=Inf;LSEQ=GGGACAGGCGTCCTCTCCCT;RSEQ=CTGCCCCACCAGGATGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:57,69:126,0:0:2,0:28.6:1:32:1:1:0:60:62:1:0:0.2 0/1:128:2:1,1:56,70:126,2:0.0156:2,2:26:1:28:1:1:1.25:60:4:0.0159:0:1 +15 41804342 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23922;SOR=Inf;LSEQ=GGCGTCCTCTCCCTGCTGCC;RSEQ=CACCAGGATGTACAGCGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:56,73:129,0:0:2,0:28.2:1:30.7:1:1:0:60:24.8:1:0:0.2 0/1:124:2:1,1:52,70:122,2:0.0161:2,2:21.5:1:27:1:1:1.34:60:4:0.0164:0:1 +15 41849048 . G GGAAGAA 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=7.000;MSILEN=3;SSF=0.30952;SOR=0.18569;LSEQ=GGAAGGGGAAGAGAGGGAGA;RSEQ=GAAGAAGAAGAAGAAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:29:29,0:0,0:0,29:0.9667:0,1:26.5:1:30.7:1:1:0:59.7:28:0.9655:0.1667:0.1 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:26.6:1:29.9:1:1:0:60:10:0.8333:0.1667:0 +15 41849686 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20568;SOR=Inf;LSEQ=CAGTATGTAATACCTGTAGA;RSEQ=CAGTTAGTAACTTTTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:4,93:97,0:0:1,0:20.5:1:30.8:1:1:0:36.6:194:1:0:0.1 0/1:81:2:0,2:6,73:79,2:0.0247:2,0:16.5:1:31:0:1:0:21:4:0.0247:0:1.5 +15 41863181 . G A 30 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=GAGGGTCACTTGGGAGGAAG;RSEQ=TTGGCAGGGAGCAGAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:36:1:30.5:1:1:0:60:4:0.6667:0:1 0/1:4:1:1,0:3,0:3,1:0.25:0,0:3:0:28:0:1:0:60:2:0.25:0:1 +15 41865488 . C T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGCAGAAGGCTGACTCTCTC;RSEQ=CTCAATGCCCCTTGTAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:22,5:27,0:0:2,0:28:1:31.3:1:1:0:60:54:1:0:0.1 1/0:18:10:7,3:5,3:8,10:0.5556:2,2:23.5:1:29.2:1:1:1.37:60:20:0.5556:0:1 +15 41865510 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22817;SOR=Inf;LSEQ=TCAATGCCCCTTGTAGGCTG;RSEQ=CAGAGGACATGACAGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:29,12:41,0:0:2,0:26.5:1:30.6:1:1:0:60:40:1:0:0.1 0/1:38:2:1,1:22,14:36,2:0.0526:2,2:15:1:30.5:1:1:1.55221:60:4:0.0526:0:1 +15 41865525 . G T 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.02666;SOR=Inf;LSEQ=GGCTGGCAGAGGACATGACA;RSEQ=TGTGTGTGGCTGACTTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:31,18:49,0:0:2,0:25.4:1:32.8:1:1:0:60:98:1:0:0.1 0/1:50:6:5,1:27,17:44,6:0.12:2,2:11.2:1:31.5:1:0.39907:3.09:60:12:0.12:0:1 +15 41867443 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAGGGAAATCTTGAGTA;RSEQ=ACAAGCCAGGCCCTGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 41961003 . G GT 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.57834;SOR=1.44287;LSEQ=AAGGGTGTTTTTTGTTTTTG;RSEQ=TTTTTTTTTGCTTGTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:6:5,1:220,9:229,6:0.0255:1,2:27:1:30.5:1:0.23187:4.82321:60:12:0.0259:0.0043:0 0/1:192:7:5,2:179,6:185,7:0.0365:1,2:22.1:1:25.2:1:0.02882:11.51991:60:2.5:0.0267:0.0052:0.7 +15 41961017 . G T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25231;SOR=0;LSEQ=TTTTTGGTTTTTTTTTGCTT;RSEQ=TTTCTTAGGATGGGAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:2,1:273,23:296,3:0.01:2,2:22.7:1:23.7:1:0.22268:5.86556:60:2:0.0069:0:2.7 0/0:260:0:0,0:236,24:260,0:0:2,0:23.8:1:31.1:1:1:0:60:25:1:0:0.1 +15 41962213 . G A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=AAGATTGAGATGGGCCAGGT;RSEQ=TTGGATTTAACATCTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:68,326:394,0:0:2,0:26:1:32.1:1:1:0:60:97.5:1:0:0.1 0/1:356:11:2,9:64,281:345,11:0.0309:2,2:22.1:1:29.5:1:1:1.02485:60:22:0.0313:0:1.1 +15 41989730 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCAAGCCATTCTCGTGCC;RSEQ=CAGCCTCACGAGTAGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:27:1:1:0:50:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 41991315 . A T 304 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00947;LSEQ=AATTGATAGAAGATTTGAAG;RSEQ=CTTTGCGGCACAAGCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1226:1223:597,626:1,1:2,1223:0.9976:2,2:26.3:1:29.7:1:1:1.04855:60:57.238:0.9983:0:1.1 1/0:1432:1137:568,569:144,147:291,1137:0.794:2,2:26:1:28.4:1:0.89563:1.02:59.9:58.842:0.7935:0:1.1 +15 41991376 . CT C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.55811;SOR=1.22539;LSEQ=AGGTAATAGACTAGCGACTT;RSEQ=TTTTTTTTGTTTTCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:734:21:7,14:226,487:713,21:0.0286:2,2:30.4:1:33.1:1:0.81722:1.08:59.1:42:0.0288:0.0014:0.9 0/1:775:27:10,17:255,490:745,27:0.0348:2,2:24.1:1:30.5:1:0.83704:1.13:59.1:54:0.0352:0.0065:0.7 +15 41991391 . CT C 218 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTTCTTTTTTTTTGTTTT;RSEQ=TTTTTTCTTTCTTCCCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:576:0:0,0:146,429:575,0:0:2,0:22.1:1:30.7:1:1:0:60:94.833:0.9982:0:0.5 0/1:601:131:28,103:151,318:469,131:0.218:2,2:27.1:1:31.1:1:0.01746:1.74522:60:130:0.217:0.0083:0.4 +15 41999771 . C A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1705;SOR=Inf;LSEQ=ACCTTAAATTGAATCTGCTA;RSEQ=AGTTTGTTTTTTTCATTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:57,2:59,0:0:1,0:23.7:1:32.3:1:1:0:60:58:1:0:0.1 0/1:42:2:1,1:37,2:39,2:0.0476:2,2:23:1:24.5:1:0.14268:15.3059:60:4:0.0476:0:1 +15 41999827 . A AC 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.51296;SOR=0;LSEQ=CTCCTTTCTCTCTCGACCTT;RSEQ=CCCCCCCGCCATCTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:2,0:177,3:180,2:0.011:1,0:25:1:34.5:1:1:0:60:4:0.0114:0:1.5 0/0:129:0:0,0:121,8:129,0:0:2,0:23.5:1:27.8:1:1:0:60:128:1:0:0.1 +15 42003382 . ACAG A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03388;SOR=0.56421;LSEQ=CAGATTAGTTTGCGGCAGGC;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1302:35:18,17:686,579:1265,35:0.0269:2,2:22.4:1:31.9:1:0.86378:1.11888:59.9:70:0.0273:0.0069:0.2 0/1:1499:23:12,11:781,691:1472,23:0.0153:2,2:20.3:1:31.2:1:1:1.03605:59.7:46:0.0156:0.0047:0.3 +15 42004962 . G C 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AGACCATACACTCTCTATAG;RSEQ=AGTTACTGAACTCTGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:0,9:1:0,0:21.8:1:32.7:1:1:0:54.4:18:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:41:0:31:0:1:0:60:2:1:0:0 +15 42005039 . T C 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCGTTCCAGTGAAACTT;RSEQ=ATGACACAGGCTGGATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:24:1:33.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 42005145 . G A 23 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCCATCCTTGATAGTTTT;RSEQ=CCCATAATTGTCTGTACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:2,0:48,0:48,2:0.04:1,0:13:1:23.5:1:1:0:60:4:0.0455:0:1 0/0:14:0:0,0:12,2:14,0:0:2,0:32.4:1:30.7:1:1:0:57.9:13:1:0:0.4 +15 42005772 . A G 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTAGAATAATACAACCT;RSEQ=CCTTAATCCCGATCAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:0,118:118,0:0:1,0:21.9:1:30.3:1:1:0:60:58:1:0:0.1 0/1:80:18:0,18:1,61:62,18:0.225:1,1:19.9:1:31.4:1:1:0:60:36:0.225:0:1.1 +15 42006104 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCAAAAAGACCCTCTG;RSEQ=TCATGGTTGGAGATTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:13:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 42021512 . T C 221 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTTCAGCAGCAAACTTCA;RSEQ=GTCATTCTAGCCCTGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1642:0:0,0:759,882:1641,0:0:2,0:25.4:1:30.7:1:1:0:60:77.143:0.9994:0:0.2 0/1:1681:166:72,94:728,784:1512,166:0.0988:2,2:27.1:1:30.1:1:0.25262:1.21216:60:82:0.0983:0:1.2 +15 42026363 . C T 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATCTTCCCACCTCGGCCT;RSEQ=TCGGAATGCTGGGATTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:28.6:1:30.8:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 42026764 . C T 314 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0096;LSEQ=TTAAAACAACTCACCTGTGA;RSEQ=TTGGAGGATGATTCTGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1288:1285:605,680:1,0:1,1285:0.9977:0,2:25.7:1:30.5:1:0.47123:0:59.9:63.25:1:0:1.1 1/1:1323:1064:517,547:121,136:257,1064:0.8042:2,2:26.2:1:29.4:1:0.67698:1.06:59.9:58.111:0.8028:0:1.1 +15 42026894 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=CATCAATTCAGAATATGTCT;RSEQ=CCTACCCTGTTTCAAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:2,169:171,0:0:1,0:25.1:1:32.9:1:1:0:59.8:170:1:0:0 0/1:143:2:0,2:4,137:141,2:0.014:1,0:17.5:1:30:0:1:0:60:4:0.0144:0:1 +15 42028295 . G GT 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.63657;SOR=0.43859;LSEQ=AAGAACGTGAGAATGTGACA;RSEQ=TTTTTTTTCAGAGTTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:3:3,0:118,0:118,3:0.0248:1,0:36:1:31:0:1:0:60:6:0.0248:0:0.3 0/1:91:1:1,0:89,1:90,1:0.011:1,0:18:0:30:0:1:0:60:2:0.011:0:0 +15 42028354 . C A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=9.95618;LSEQ=AAATAATCTTTCAACTTTTT;RSEQ=TTTTTTATTATTATTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:102:82,20:256,71:327,102:0.2378:2,2:20.7:1:29.1:1:0.78151:1.14:59.7:204:0.24:0:1.1 1/0:387:293:207,86:64,30:94,293:0.7571:2,2:21.5:1:27.9:1:0.6981:1.13:60:145.5:0.7558:0:1.1 +15 42030102 . T C 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGAGAATCATTTGAACC;RSEQ=GGGAGGTGGAGGTTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:28:1:1:0:26:4:1:0:1 +15 42032383 . C G 313 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11554;LSEQ=AGAATCTGAAGGCGTTTGTC;RSEQ=CAGCAAAACGGCCAATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1535:1143:548,595:174,212:386,1143:0.7446:2,2:23.7:1:30.9:1:0.34569:1.12:59.9:50.955:0.7434:0:1.1 0/1:1775:447:220,227:622,701:1323,447:0.2518:2,2:24.9:1:30:1:0.44325:1.09:59.9:48.667:0.2514:0:1.2 +15 42032503 . G A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0824;SOR=Inf;LSEQ=ATTAGAGAAATATGTACTTT;RSEQ=GCATTATTCTTATTCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:2,254:256,0:0:1,0:22.8:1:31.4:1:1:0:60:50.2:1:0:0.1 0/1:199:3:1,2:3,193:196,3:0.0151:1,2:9.3:1:23:1:0.05939:29.43:60:2:0.0102:0:1 +15 42032655 . T C 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04348;SOR=0;LSEQ=TATTTTTTAATAACACTGAC;RSEQ=TGAAGGCAAGTTTTATAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:3,19:0,0:0,22:1:0,2:25.3:1:32.9:1:1:0:60:44:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:29:0:27:0:1:0:60:2:1:0:0 +15 42034002 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACTGCAGCATCCACCTCC;RSEQ=GGGTTCAAACCATTCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:31.5:1:1:0:42:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 42034594 . G GA 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.50578;SOR=0;LSEQ=AGAAACTCCATCTTAAAAAA;RSEQ=AAAAAAAAGAAATTGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:72,0:72,2:0.027:1,0:10:1:28.3:1:1:0:55:4:0.0278:0.0135:0 0/0:56:0:0,0:56,0:56,0:0:1,0:23.4:1:32.3:1:1:0:59.8:112:1:0:0.1 +15 42035713 . C A 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAATACTAAAAAACATTA;RSEQ=AATGGAAGTGGTGGCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:30.8:1:30.8:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 42041712 . G A 322 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.01219;LSEQ=GTTGCTTCCCTTCAGATGAA;RSEQ=AGAGAATCTCAGAATCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1418:1412:652,760:1,0:1,1412:0.9958:0,2:23.9:1:30.8:1:0.46214:0:59.9:87.25:0.9964:0:1.1 1/0:1398:1036:520,516:174,187:361,1036:0.7411:2,2:24.7:1:29.9:1:0.54119:1.08:60:128.5:0.7422:0:1.1 +15 42043067 . G A 129 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17957;SOR=0.1619;LSEQ=TGGGGGATAGGTGCTTGAGA;RSEQ=TCCCTACCGAGTTAGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:17:2,15:0,5:5,17:0.7727:0,2:25.8:1:31.8:1:1:0:60:34:0.7727:0:1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:22:0:28:0:1:0:60:2:0.3333:0:1 +15 42046568 . A G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0175;LSEQ=TGGTTTTATAAGGGGAACAA;RSEQ=CATTTGAAAAGTTTAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:233:222,11:0,0:0,233:0.9957:0,1:24.6:1:33.1:1:1:0:59.8:57.25:0.9957:0:1.2 1/1:182:146:136,10:35,1:36,146:0.8022:1,2:24.8:1:31.7:1:0.69539:2.56348:59.9:72:0.8045:0:1 +15 42046575 . A T 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00081;SOR=0;LSEQ=ATAAGGGGAACAAACATTTG;RSEQ=AAAGTTTAGGTGTGCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:13:11,2:235,17:252,13:0.0491:2,2:18.3:1:30.4:1:0.23672:2.50094:60:26:0.0504:0:2.2 0/0:214:0:0,0:194,20:214,0:0:2,0:23:1:28.9:1:1:0:60:213:1:0:0.7 +15 42049890 . A AC 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCACACCTTGGGAAAAAGAA;RSEQ=CTGGTTGTAATTTGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:46:43,3:174,17:191,46:0.1933:2,2:26.4:1:32.5:1:0.77232:1.40:59.9:45:0.1923:0.0336:0.2 0/0:215:0:0,0:182,33:215,0:0:2,0:23.3:1:29.7:1:1:0:60:430:1:0:0.1 +15 42050095 . T A 46 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37347;SOR=0.25167;LSEQ=TAAAATTGTTAACATTTATC;RSEQ=TAGGGTTGAAACAACATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:4:2,2:105,291:396,4:0.01:2,2:11.8:1:23.3:1:0.29114:2.76:60:3:0.0076:0:1.3 0/0:395:1:1,0:110,284:394,1:0.0025:2,0:1:0:23:0:0.28101:0:60:2:0.0026:0:1 +15 42052933 . AT A 134 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.09549;SOR=0.34358;LSEQ=AGGTTTTCATTGAAAGTCAG;RSEQ=TTTTTTTTTTTTCTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:19:0,19:0,13:13,19:0.5429:1,1:27.7:1:31.7:1:1:0:54.5:38:0.5429:0:0.2 0/1:21:6:0,6:0,12:12,6:0.2857:0,0:25.8:1:30.3:1:1:0:58.7:12:0.3:0.0476:0.3 +15 42053846 . G GT 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.75469;LSEQ=CTCTTAAGATGTCAGATTAA;RSEQ=TTTTTTTTCATTAGAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:182,5:187,2:0.0106:1,0:36.5:1:32:0:1:0:60:4:0.0107:0:0 0/0:125:1:1,0:121,3:124,1:0.008:1,0:10:0:29:0:1:0:60:2:0.008:0:0 +15 42057318 . G A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12413;SOR=0;LSEQ=AGTTATCCCTAACATCTCAC;RSEQ=GTGACCAAGGAAGGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:4:3,1:73,322:395,4:0.01:2,2:10.3:1:27.8:1:0.02306:13.11:60:8:0.0101:0:1 0/0:391:0:0,0:96,295:391,0:0:2,0:23.1:1:29.7:1:1:0:60:54.857:1:0:0.1 +15 42057362 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16741;SOR=Inf;LSEQ=TGTTCTGTAATGATAAAGAG;RSEQ=TATTCTGTTGGCATTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:2,198:200,0:0:1,0:26.1:1:33.3:1:1:0:59.8:49:1:0:0.1 0/1:139:2:0,2:5,132:137,2:0.0144:1,0:42.5:1:31.5:1:1:0:60:4:0.0147:0:1 +15 42057369 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51975;SOR=0;LSEQ=TAATGATAAAGAGCTATTCT;RSEQ=TTGGCATTTGCCTTGGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:0,2:1,172:173,2:0.0114:1,0:8:1:31.5:1:1:0:60:4:0.0115:0:1 0/0:115:0:0,0:4,111:115,0:0:1,0:21.7:1:31.9:1:1:0:60:114:1:0:0.1 +15 42057370 . T C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1536;SOR=Inf;LSEQ=AATGATAAAGAGCTATTCTG;RSEQ=TGGCATTTGCCTTGGTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:1,172:173,0:0:1,0:26.6:1:30.9:1:1:0:59.8:172:1:0:0.1 0/1:112:2:1,1:3,107:110,2:0.0179:1,2:33:0:30.5:1:0.07046:31.02:60:4:0.0179:0:1.5 +15 42057373 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14664;SOR=Inf;LSEQ=GATAAAGAGCTATTCTGTTG;RSEQ=CATTTGCCTTGGTAAGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:1,169:170,0:0:1,0:25.8:1:32.6:1:1:0:59.8:41.5:1:0:0.1 0/1:106:2:0,2:5,99:104,2:0.0189:1,0:26.5:1:31:1:1:0:60:4:0.0189:0:1 +15 42058105 . C T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=AGAGTGCTGAATTTAGACTA;RSEQ=AAATCCCTAAGATGGTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:168,1:169,0:0:1,0:26.2:1:33:1:1:0:59.9:168:1:0:0.1 0/1:100:10:10,0:85,5:90,10:0.1:2,0:24.9:1:31.8:1:1:0:60:20:0.101:0:1 +15 42059521 . A T 286 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.015;LSEQ=GCCAGGCTGTGAGGGGAAAT;RSEQ=GATCTCACCTCCTTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:694:691:172,519:0,2:2,691:0.9957:0,2:23.7:1:30.4:1:1:0:60:68.1:1:0:1.1 1/0:604:468:116,352:34,102:136,468:0.7748:2,2:21.7:1:29.5:1:1:1.01148:60:92.6:0.7768:0:1.1 +15 42059612 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15639;SOR=Inf;LSEQ=TGCAGTGGATAATGATGGGA;RSEQ=AAAGGGGGTAGGGTGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:1,119:120,0:0:1,0:24.9:1:32.3:1:1:0:59.6:39:1:0:0.2 0/1:79:2:1,1:3,74:77,2:0.0253:1,2:23:1:30:0:0.09932:21.51:60:4:0.026:0:1 +15 42607721 . G A 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAGGATGCAGAGAAATTG;RSEQ=AACATTGCTGGTGGAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:29.5:1:1:0:57.5:4:1:0:1 +15 42608498 . A G 106 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGAAAACAGCTGGGCCC;RSEQ=GGGGACCACTACCACCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:12,1:0,0:0,13:1:0,1:16.8:1:28.8:1:1:0:25.8:26:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:31:0:1:0:20:2:1:0:1 +15 42608677 . A G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTCCCTTTTAGGCAGCC;RSEQ=AAGCAGAGAGGGAAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:45:17,28:0,0:0,45:1:0,2:25.1:1:31:1:1:0:40.7:44:1:0:1.8 1/1:41:41:18,23:0,0:0,41:1:0,2:25.9:1:29.9:1:1:0:36.6:82:1:0:1.6 +15 42608712 . G A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCATTTTCTTCTATGC;RSEQ=TTTTCTTCTATGCACTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:5,25:0,0:0,30:1:0,2:24.4:1:30.8:1:1:0:50.6:60:1:0:2.3 1/1:26:26:5,21:0,0:0,26:1:0,2:19.4:1:29.8:1:1:0:48.9:52:1:0:2.3 +15 42608758 . T C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCAAGGACTTTAAGACTT;RSEQ=CACTATTTATTCTACCGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:1,17:0,0:0,18:1:0,1:25:1:30.7:1:1:0:47.9:17:1:0:2.6 1/1:15:15:2,13:0,0:0,15:1:0,2:30.5:1:31.2:1:1:0:44.2:30:1:0:2.3 +15 42608793 . A C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCGCTATCTACTATGAACTT;RSEQ=AAAGAGAAACATGAAAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:23.1:1:33:1:1:0:40.3:14:0.875:0:2.6 1/1:10:10:1,9:0,0:0,10:1:0,2:21.5:1:32.6:1:1:0:42.1:20:1:0:2.3 +15 45003317 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGATCTTAATCTTCTGGG;RSEQ=TTCCGTTTTCTCGAATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:21.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 45003364 . T G 57 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCGAGCAGTTAACTGGC;RSEQ=GGGGCACCATTAGCAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:29.3:1:28.8:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 45003619 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49981;SOR=Inf;LSEQ=CTCTCTCTAACCTGGCACTG;RSEQ=GTCGCTGGCTTGGAGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:116,1:117,0:0:1,0:26.2:1:32.9:1:1:0:60:234:1:0:0.1 0/1:132:2:1,1:126,4:130,2:0.0152:1,2:11:1:28.5:1:0.0746:28.29628:60:4:0.0153:0:1 +15 45005933 . T G 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTTAATATGTTCTTATTA;RSEQ=TAGAAGCTCAGATGCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:241,61:302,0:0:2,0:22:1:31.1:1:1:0:59.9:150:1:0:0.1 0/1:315:54:39,15:199,62:261,54:0.1714:2,2:20.9:1:31.8:1:0.60183:1.23368:60:108:0.172:0:1.2 +15 45007543 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50088;SOR=Inf;LSEQ=AAATGTAAACACTTGGTGCC;RSEQ=GATATAGCTTGACACCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:86,11:97,0:0:2,0:24.1:1:31.8:1:1:0:60:47.5:1:0:0.1 0/1:114:2:1,1:99,13:112,2:0.0175:2,2:25.5:1:31.5:1:0.23149:7.37604:60:4:0.0175:0:1 +15 45007947 . G A 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23068;SOR=0;LSEQ=CTGAAAGTTGTGTATGAGTA;RSEQ=TCATATCATAAAGCTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:21,142:163,2:0.0121:2,2:6.5:1:31:1:0.24959:6.63:60:4:0.0123:0:1 0/0:178:0:0,0:38,140:178,0:0:2,0:24.2:1:31.7:1:1:0:60:177:1:0:0.1 +15 45008414 . G A 120 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=4e-05;SOR=19.11658;LSEQ=TGTATTCATGGGTAGGAACA;RSEQ=CAGCCTATTCTGCCAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:1,0:144,20:164,1:0.0061:2,0:23:0:32:0:1:0:60:2:0.0062:0:1 0/1:162:17:15,2:126,19:145,17:0.1049:2,2:31.3:1:29.4:1:1:1.13:60:34:0.1063:0:1 +15 45008498 . C CT 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.6358;SOR=0.76502;LSEQ=AAGTAAAACTTAATGTCTTC;RSEQ=TTTTTTTTCTCCACTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:9:3,6:322,257:579,9:0.0153:2,2:30.2:1:31.7:1:0.31123:2.502:60:18:0.0155:0:0.2 0/1:766:9:6,3:420,336:756,9:0.0117:2,2:20.6:1:27.4:1:0.73828:1.60:58.6:8:0.0106:0.0039:1.1 +15 45008608 . T A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.13524;SOR=Inf;LSEQ=TCACTGTCCTGAGGACTATT;RSEQ=ATAGACAGCTCTAACATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:62,223:285,0:0:2,0:23.9:1:28.8:1:1:0:59.9:94:1:0:0.1 0/1:365:4:3,1:105,256:361,4:0.011:2,2:16.3:1:26.5:1:0.07949:7.27:60:8:0.011:0:1.8 +15 45010012 . G C 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCCACAGGTAGCTCTAG;RSEQ=AGGGCTGGCAACTTAGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:508:0:0,0:311,196:507,0:0:2,0:24.6:1:31.4:1:1:0:60:125.75:0.998:0:0.1 0/1:622:26:16,10:363,232:595,26:0.0418:2,2:28.5:1:31.1:1:1:1.02:60:52:0.0423:0:1 +15 45010022 . A G 219 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGCTCTAGGAGGGCTGGC;RSEQ=ACTTAGAGGTGGGGAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:0:0,0:334,229:563,0:0:2,0:24.9:1:30.2:1:1:0:60:50.182:1:0:0.1 0/1:709:188:106,82:304,216:520,188:0.2652:2,2:25.6:1:29.1:1:0.66662:1.08862:60:36.6:0.2633:0:1.1 +15 45154900 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19255;SOR=0;LSEQ=AATAGCAAGATGGCTGTCAC;RSEQ=GGACCTAGAAAGGGGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:18,11:29,2:0.0645:2,2:15:1:29.5:1:1:1.60957:29.5:4:0.0645:0:1 0/0:39:0:0,0:22,17:39,0:0:2,0:19.3:1:29.1:1:1:0:32.8:78:1:0:0.3 +15 45466409 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGTCAGGATTACTCAGAC;RSEQ=TGAGGGCAGATGTTTTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:30.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 45466432 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCAGATGTTTTATTGAA;RSEQ=TTTAATCCCCACCCCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:32.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 45467512 . CG C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTGGCAGGCGGGACTCC;RSEQ=GGGCCAGGGGGCCCCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:37.5:1:32:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 45467540 . C G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGCCCCCTCACCTTCCG;RSEQ=GGTGGCCCCATCCTCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:26.7:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 45468594 . A T 46 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04159;SOR=Inf;LSEQ=GTGGCCTCCTGTACCACTTC;RSEQ=GGTCACACAAGTCACATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:243,162:405,0:0:2,0:26.1:1:30.5:1:1:0:60:39.5:1:0:0.6 0/1:335:4:1,3:189,142:331,4:0.0119:2,2:6.3:1:23.3:1:0.31978:3.97734:60:3:0.0091:0:1.5 +15 45468626 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.27645;LSEQ=TCACATCTGCTTCTCCAAAA;RSEQ=GACTATTGGAAAGGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:418:275:147,128:73,70:143,275:0.6579:2,2:25.3:1:30.6:1:0.68004:1.10:59.7:67.75:0.661:0:1.2 1/1:366:298:137,161:30,38:68,298:0.8142:2,2:26.9:1:30:1:0.78932:1.08:60:148:0.8177:0:1.1 +15 45470189 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61708;SOR=0.48044;LSEQ=TTCAGGTCTCACAGGTCACA;RSEQ=CTGCTTCTCCAAAATGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:58,56:114,2:0.0172:2,2:40:1:29.5:1:1:1.03541:60:4:0.0179:0:1 0/0:120:1:1,0:57,61:118,1:0.0083:2,0:1:0:24:0:0.48739:0:60:2:0.0085:0:1 +15 45470200 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24205;SOR=0;LSEQ=CAGGTCACAGCTGCTTCTCC;RSEQ=AAATGACTCTGAAAGGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:47,59:106,2:0.0185:2,2:32:1:32:0:1:1.25:60:4:0.0187:0:1 0/0:111:0:0,0:47,64:111,0:0:2,0:28.1:1:29.8:1:1:0:59.9:110:1:0:0.1 +15 45507632 . CCGT C 142 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04316;SOR=0.08502;LSEQ=TCGAGTTGTGTTTGCAGCCG;RSEQ=CGCTGCCGCGCCGCCGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:22:19,3:1,0:1,22:0.9565:0,2:25.5:1:32:1:1:0:60:44:1:0.1739:0 1/0:8:5:5,0:2,1:3,5:0.625:2,0:30:1:32.4:1:0.375:0:60:10:0.625:0:0.2 +15 45507789 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49814;SOR=0;LSEQ=CAAACTGGACGGTGGTAAAG;RSEQ=ACCAGGAAGCAACTGGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:44,41:85,2:0.023:2,2:9.5:1:28:1:1:1.07227:60:4:0.0233:0:1.5 0/0:79:0:0,0:43,36:79,0:0:2,0:26.3:1:31.1:1:1:0:60:38.5:1:0:0.1 +15 45507792 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=0;LSEQ=ACTGGACGGTGGTAAAGCAC;RSEQ=AGGAAGCAACTGGCTACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:42,42:84,2:0.0233:2,2:22.5:1:28:1:1:1:60:4:0.0241:0:1.5 0/0:80:0:0,0:45,35:80,0:0:2,0:25.3:1:30.5:1:1:0:60:79:1:0:0.1 +15 45507889 . C A 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24322;SOR=0;LSEQ=GGCCTGGTACTGTGGCACTC;RSEQ=GTGAAATTAGGCGTTATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:60,65:125,2:0.0157:2,2:16:0:30.5:1:1:1.08:38:4:0.0159:0:1.5 0/0:130:0:0,0:63,67:130,0:0:2,0:29.7:1:30.1:1:1:0:58.9:129:1:0:0.1 +15 45507947 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.5022;SOR=0;LSEQ=TCGCAAACTCCCCTTCCGGC;RSEQ=TCTGGTGAGAGAAATTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:40,50:90,2:0.0217:2,2:5.5:1:29.5:1:1:1.25:60:4:0.022:0:1.5 0/0:75:0:0,0:39,34:73,0:0:2,0:22.8:1:29.8:1:1:0:59.9:35.5:0.9726:0:0.2 +15 45508034 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50915;SOR=0;LSEQ=AGGAGTCAAGTAAGGCCTAT;RSEQ=TTGTTGGCCTTTTTGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:60,18:78,2:0.025:2,2:35:1:28.5:1:0.42089:3.27133:56:4:0.025:0:1 0/0:58:0:0,0:47,11:58,0:0:2,0:25.5:1:30.9:1:1:0:59.7:28:1:0:0.1 +15 45508100 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.23266;SOR=0;LSEQ=AGCATGTAACAGTTATGCCA;RSEQ=AAGATATCCAGCTAGCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:104,79:183,2:0.0108:2,2:37.5:1:33.5:1:1:1.31446:60:4:0.0112:0:1.5 0/0:198:0:0,0:106,92:198,0:0:2,0:27.6:1:29.6:1:1:0:51.4:197:1:0:0.2 +15 45508137 . G A 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36177;SOR=0.31559;LSEQ=ACTCCGCACACGTGGAGAAC;RSEQ=TGCTTAAGAATCCACTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:3:2,1:94,110:204,3:0.0145:2,2:23.7:1:28.3:1:0.59773:2.33:41.3:6:0.015:0:1.3 0/0:217:1:1,0:94,122:216,1:0.0046:2,0:50:0:28:0:0.43779:0:28:2:0.0047:0:1 +15 45508175 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50274;SOR=0;LSEQ=TGATGGGAAACATTTCATTC;RSEQ=CAAAAAAAAAAATTATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:51,96:147,2:0.0134:2,2:17.5:1:28.5:1:1:1.87:28:4:0.0143:0:2.5 0/0:123:0:0,0:40,83:123,0:0:2,0:23.1:1:28.1:1:1:0:37.5:16.571:1:0:0.2 +15 45508176 . CA C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.50001;SOR=1.38609;LSEQ=GATGGGAAACATTTCATTCT;RSEQ=AAAAAAAAAATTATCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:10:1,9:51,84:135,10:0.069:2,2:32.1:1:31.8:1:0.09588:5.4181:39.6:20:0.0694:0:0.1 0/1:118:11:4,7:33,74:107,11:0.0932:2,2:27:1:30.9:1:0.73881:1.28:32.9:22:0.0957:0:0.4 +15 45508183 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.50328;SOR=0;LSEQ=AACATTTCATTCTCAAAAAA;RSEQ=AAAATTATCTTATTCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:38,87:125,2:0.0157:2,2:9.5:1:30.5:1:0.52156:2.27:28:4:0.0157:0:2.5 0/0:103:0:0,0:27,76:103,0:0:2,0:23.8:1:30.5:1:1:0:38.3:206:1:0:0.2 +15 45508196 . T A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69116;LSEQ=CAAAAAAAAAAATTATCTTA;RSEQ=TCCTGTTATTGGTAGTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:29,80:109,2:0.018:2,2:25:1:28:1:0.46929:2.73:46:4:0.0182:0:1 0/1:80:1:1,0:17,62:79,1:0.0125:2,0:1:0:23:0:0.225:0:20:2:0.013:0:1 +15 45508233 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14673;SOR=Inf;LSEQ=TCTGAACATTAGATTTTTTT;RSEQ=CCCCCATGGGGTCAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:8,54:62,0:0:2,0:23.5:1:30.1:1:1:0:55.5:19.667:1:0:0.1 0/1:39:2:0,2:6,31:37,2:0.0513:2,0:22:1:32.5:1:1:0:60:4:0.0513:0:1 +15 45929970 . T C 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=GTTGCCTGTGTCTAGCTTTG;RSEQ=TAATCCGATGTGTTGTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:27.3:1:28.3:1:1:0:60:2:0.5:0:1 0/0:7:0:0,0:1,6:7,0:0:2,0:26.1:1:28:1:1:0:60:14:1:0:0.1 +15 47969373 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4955;SOR=0;LSEQ=CTACAGACTGGTACCAGTCT;RSEQ=CGACCTGGAGGTTGGGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:19,2:0.0952:2,2:23:0:32.5:1:1:1.66897:60:4:0.0952:0:1.5 0/0:16:0:0,0:9,7:16,0:0:2,0:23.1:1:31.2:1:1:0:60:32:1:0:0.1 +15 47969386 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18018;SOR=Inf;LSEQ=CCAGTCTGCGACCTGGAGGT;RSEQ=GGGACCCCTGTTGTAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:21,0:0:2,0:27.2:1:31.6:1:1:0:60:42:1:0:0.1 0/1:16:2:1,1:7,7:14,2:0.125:2,2:21.5:1:29:1:1:1:60:4:0.125:0:0 +15 48073099 . C A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACCCTGGGAACACTGAAAA;RSEQ=ACATTGATTACATTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:29:1:1:0:60:4:1:0:1.5 +15 48073424 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGTCTAACAACTATTTG;RSEQ=TTTTGTTCACATCTGATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:12.5:1:30:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 48073651 . T C 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55194;SOR=0;LSEQ=GTGGCAAAAGGCATGGGGAA;RSEQ=GTGGCATGTTTGGAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:107,14:121,2:0.0163:2,2:15.5:1:24.5:1:0.22991:7.41827:60:4:0.0165:0:1.5 0/0:62:0:0,0:54,8:62,0:0:2,0:23:1:30:1:1:0:60:61:1:0:0.6 +15 48073702 . T C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0111;SOR=1.66026;LSEQ=CTGAGGTCTTATATTTCCCT;RSEQ=AGGAGAGAAGGTAGCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:268:148:99,49:82,38:120,148:0.5522:2,2:23.8:1:31.9:1:0.8957:1.06776:60:73:0.5551:0:1.5 1/0:183:123:79,44:42,17:59,123:0.6721:2,2:26.3:1:30.4:1:0.40364:1.37365:60:40:0.6667:0:1.5 +15 48073768 . G C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00259;SOR=1.56691;LSEQ=ACAGGCTTTCATTGGGAAAG;RSEQ=AGAAAGAGAATGAAGGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:410:215:99,116:96,96:192,215:0.5244:2,2:25.9:1:32.3:1:0.4288:1.17126:60:70.667:0.5274:0:1.3 1/0:352:223:109,114:64,65:129,223:0.6335:2,2:25.5:1:31.4:1:0.91227:1.02971:59.9:110.5:0.6332:0:1.5 +15 48073801 . G A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AAGGATCTTAGAAACTAAAC;RSEQ=GGAGTGTCAGAATACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:157,222:379,0:0:2,0:27.5:1:30.6:1:1:0:60:74.8:0.9947:0:0.5 0/1:328:14:5,9:137,177:314,14:0.0427:2,2:25.7:1:30.1:1:0.59633:1.39185:60:28:0.0429:0:1.8 +15 48073820 . G A 39 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.31883;SOR=4.02296;LSEQ=CGGGAGTGTCAGAATACCCT;RSEQ=AAAACTTCTCTAAGAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:1:1,0:125,211:336,1:0.003:2,0:1:0:26:0:0.37389:0:60:2:0.003:0:2 0/1:253:3:2,1:98,152:250,3:0.0119:2,2:5.3:1:25:1:0.56403:3.09:60:6:0.012:0:2 +15 48073862 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51129;SOR=0;LSEQ=AACTAGTTGAAAGACAGAAG;RSEQ=GCATGTAGAGAACATTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:33,122:155,2:0.0127:2,2:20.5:1:30:1:0.38731:3.66:60:4:0.0127:0:1.5 0/0:114:0:0,0:33,81:114,0:0:2,0:21.5:1:30:1:1:0:60:27.5:1:0:0.2 +15 48073867 . G A 29 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56881;SOR=2.92425;LSEQ=GTTGAAAGACAGAAGGGCAT;RSEQ=TAGAGAACATTCTGCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:1,0:28,113:141,1:0.007:2,0:1:0:27:0:0.20423:0:60:2:0.007:0:2 0/1:98:2:1,1:24,72:96,2:0.0204:2,2:5:1:29:0:0.44709:2.96:60:4:0.0206:0:1 +15 48073968 . T A 93 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20927;SOR=0.20881;LSEQ=TCATGCTTAGCTGGACTCTT;RSEQ=GATAAAAGTTGAAGGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:0,14:14,7:0.3333:1,0:28.6:1:33.4:1:1:0:60:14:0.3333:0:1 0/1:11:1:0,1:1,9:10,1:0.0909:2,0:5:0:30:0:1:0:60:2:0.1:0:2 +15 48074071 . A C 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GACTAGTAAGCTAGGTACCT;RSEQ=AGTGTTTCTACATACTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:29.7:1:34.3:1:1:0:60:6:0.5:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:11.3:1:31.7:1:1:0:60:6:1:0:0 +15 48633020 . T C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24894;SOR=0;LSEQ=AATATTTGCAAGACTGCTGC;RSEQ=TAACAATGTCAGCGTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:190,106:296,3:0.01:2,2:14:1:31.7:1:0.29651:3.56885:60:6:0.0101:0:1.7 0/0:290:0:0,0:185,105:290,0:0:2,0:25.8:1:29.9:1:1:0:60:71.5:1:0:0.3 +15 48633092 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06653;SOR=0.75069;LSEQ=ATTTTTATTTATGACTCAAT;RSEQ=GTATTTCAATCTGGGTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:374:221:105,116:70,83:153,221:0.5909:2,2:27:1:30.4:1:0.75285:1.07:60:220:0.5946:0:1.4 1/0:323:168:69,99:74,80:154,168:0.5201:2,2:24.4:1:29.5:1:0.21856:1.32598:60:83:0.522:0:1.4 +15 48633153 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=0.47417;LSEQ=AAAACCTTTAAAACCCAAAT;RSEQ=GTAATTTTCTCCTAGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:124:48,76:38,62:100,124:0.5536:2,2:25.6:1:30.8:1:1:1.03:60:248:0.5561:0:1.6 0/1:219:81:31,50:44,94:138,81:0.3699:2,2:26.1:1:29.4:1:0.37717:1.32:60:162:0.3733:0:1.6 +15 48633174 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=GTAATTTTCTCCTAGTCTTT;RSEQ=TGGCAAGTGTGCCGTGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:62,106:168,2:0.0118:2,2:14.5:1:27.5:1:1:1.70:60:4:0.012:0:1.5 0/0:157:0:0,0:52,105:157,0:0:2,0:25.7:1:29.5:1:1:0:60:314:1:0:0.6 +15 48633243 . A G 32 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1591;SOR=Inf;LSEQ=CTGCCAGCTTAAAATAGGAA;RSEQ=TGGTCGCCATTTGATAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:0,55:55,0:0:1,0:26.1:1:31.8:1:1:0:60:110:1:0:0.1 0/1:37:2:0,2:0,35:35,2:0.0541:1,0:5:1:32:1:1:0:60:4:0.0556:0:1 +15 50243260 . G GT 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGTGGTCTGAGAGACT;RSEQ=TTTTTTTGTGATTTCAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:30.3:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 50244547 . T C 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11084;SOR=0.26467;LSEQ=CCAATCAATCATAGGTTTGG;RSEQ=GTTTTTATGAAGTCCCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:3,3:6,5:0.4545:2,2:26.6:1:29.8:1:1:1.44544:60:10:0.4545:0:1 0/1:23:4:1,3:10,9:19,4:0.1739:2,2:27:1:31:1:0.59006:3.17098:60:8:0.1905:0:1.3 +15 50244675 . A G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATATCCTTTCTTCTGTTT;RSEQ=GTCAATTCGGCTGTTGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:18.5:1:33:0:0.33333:0:43:4:0.6667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:35:0:32:0:1:0:60:2:1:0:0 +15 50245053 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=TTGTCTCATTTTGGTCTTTG;RSEQ=GGCTGCTGACCCTTGGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:21,16:37,0:0:2,0:22.3:1:30.5:1:1:0:54.4:36:1:0:0.2 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:41.5:1:27:1:1:1.40151:58:4:0.1053:0:1 +15 50245089 . C CTTTTGT 101 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=5.000;MSILEN=1;SSF=0.07212;SOR=0.14667;LSEQ=GATGGGGTTTTTGTGGGGGC;RSEQ=TTTTGTTGTTGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:3,6:13,14:27,9:0.25:2,2:29.2:1:32.1:1:0.70027:1.82595:54.7:18:0.25:0:0 0/1:22:1:1,0:10,11:21,1:0.0455:2,0:34:0:31.2:0:1:0:42:2:0.0476:0:0 +15 50245683 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50226;SOR=Inf;LSEQ=AGACCTGAAGAGGCCCTCTG;RSEQ=CCGCAGACTACCACAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:22,0:0:2,0:26.3:1:32:1:1:0:57.5:44:1:0:0.5 0/1:30:2:1,1:13,15:28,2:0.0667:2,2:27.5:1:27:1:1:1.15:52.5:4:0.0667:0:5 +15 50245685 . C T 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00521;SOR=0;LSEQ=ACCTGAAGAGGCCCTCTGGC;RSEQ=GCAGACTACCACAGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:2,4:10,8:18,6:0.25:2,2:22.8:1:31.3:1:0.64041:2.40592:60:12:0.25:0:1.2 0/0:30:0:0,0:14,16:30,0:0:2,0:31:1:29.8:1:1:0:59.5:60:1:0:0.6 +15 50245701 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51711;SOR=Inf;LSEQ=TGGCCGCAGACTACCACAGC;RSEQ=AGTGTGTTGAGCTGTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:18,0:0:2,0:19.9:1:32.7:1:1:0:59.3:36:1:0:0.5 0/1:29:2:1,1:11,16:27,2:0.069:2,2:9.5:1:25.5:1:1:1.44:52.5:4:0.069:0:5 +15 50245712 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49245;SOR=Inf;LSEQ=TACCACAGCCAGTGTGTTGA;RSEQ=CTGTGGGGACAAGTCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,10:18,0:0:2,0:14.7:1:33.2:1:1:0:60:36:0.9474:0:0.4 0/1:23:2:1,1:9,12:21,2:0.087:2,2:30:1:29.5:1:1:1.32:60:4:0.087:0:1 +15 50245985 . C T 47 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22222;SOR=0.13854;LSEQ=AGCTGAGAATGTGCACATTC;RSEQ=GGAGTTGGGATGCTAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:2,0:2,3:0.6:0,2:16.3:1:30:1:0.4:0:60:6:0.6:0:1 0/1:7:1:0,1:3,3:6,1:0.1429:2,0:50:0:31:0:1:0:60:2:0.1429:0:1 +15 52311700 . C T 58 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCCTCCATTGTGTGTGA;RSEQ=CCTCCGGCGGCTGCCGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:33.8:1:29.3:1:1:0:60:8:1:0:1 +15 52312068 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12821;SOR=0;LSEQ=CTCGCCTTACTGGCACGCTG;RSEQ=CTTTCGAAATGCTCCCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:5,3:8,2:0.2:2,2:10:1:28.5:1:1:1.58108:60:4:0.2:0:1 0/0:17:0:0,0:10,7:17,0:0:2,0:22.5:1:31.2:1:1:0:60:34:1:0:0.1 +15 52312203 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAGAGCCCTGAAGTCCGCC;RSEQ=AAGTTTTGAGTCTTGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:18:1:30.5:1:1:0:60:4:1:0:0 0/1:15:2:1,1:4,9:13,2:0.1333:2,2:11.5:1:29:1:1:2.12:60:4:0.1429:0:1 +15 53253417 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2139;SOR=Inf;LSEQ=TGTTGGGGCTGTCTTAATGG;RSEQ=CCATTGTCAAAGGGCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:18,0:0:2,0:20.4:1:29.7:1:1:0:60:17:1:0:0.8 0/1:16:2:1,1:9,5:14,2:0.125:2,2:18:1:27:1:1:1.73197:60:4:0.125:0:2 +15 53253466 . A G 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.57522;SOR=2.67662;LSEQ=GAACAACAGCAGCAGCAGCA;RSEQ=CAACAACAACCACAACGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:25:11,14:1,1:2,25:0.9259:2,2:29.5:1:33.6:1:1:1.2613:57.2:50:0.9259:0:1.2 1/1:35:34:15,19:1,0:1,34:0.9714:0,2:28.8:1:31.7:1:0.45714:0:57.7:68:0.9714:0:1.2 +15 53613642 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49884;SOR=Inf;LSEQ=GTGACAAAGATTCTTTGCTT;RSEQ=ATCAAACTTTAGTCAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:82,52:134,0:0:2,0:27.3:1:32.2:1:1:0:58.8:268:1:0:0.1 0/1:144:2:1,1:82,60:142,2:0.0139:2,2:18.5:1:27.5:1:1:1.36364:59.5:4:0.014:0:1 +15 53613659 . G T 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50247;SOR=Inf;LSEQ=CTTGATCAAACTTTAGTCAG;RSEQ=CTCCTGAACCTTCTCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:84,70:154,0:0:2,0:28.7:1:31.7:1:1:0:58.6:308:1:0:0.1 0/1:184:2:0,2:93,89:182,2:0.0109:2,0:5.5:1:24:1:0.24323:0:60:4:0.0111:0:1 +15 53613677 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25209;SOR=Inf;LSEQ=AGGCTCCTGAACCTTCTCCT;RSEQ=GGCCCATCTGTGCATTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:86,82:168,0:0:2,0:27.2:1:31.6:1:1:0:58.5:167:1:0:0.1 0/1:195:3:2,1:92,100:192,3:0.0154:2,2:10.3:1:26.3:1:0.6099:2.17:40.7:6:0.0157:0:1 +15 53613961 . T C 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCATGCTATATTCAGAG;RSEQ=TGTGGCTTATATCTCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:34:1:30:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 53613980 . C G 58 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGTGGCTTATATCTCTCT;RSEQ=ACACTGCAAAATTCTATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:40.3:1:29:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 54532000 . A G 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00357;SOR=Inf;LSEQ=TGCCATGTAATATTTTGAGT;RSEQ=TAGTTTGGGCACAAGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:58,5:63,0:0:2,0:23.6:1:29.2:1:1:0:60:126:1:0:0 0/1:43:6:5,1:34,3:37,6:0.1395:2,2:24.5:1:31.8:1:0.46483:2.21301:60:12:0.1429:0:1.5 +15 54532057 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.25148;SOR=0;LSEQ=GTAGGAGAAAGCTGCATATT;RSEQ=CTTGCTGAATCTCAAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:3:1,2:102,47:149,3:0.0197:2,2:14:1:28:1:0.24321:4.2943:60:6:0.0199:0:1.3 0/0:131:0:0,0:92,39:131,0:0:2,0:22:1:31.3:1:1:0:60:130:1:0:0.3 +15 54532082 . T C 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAATCTCAAAGCATCTAG;RSEQ=CTTCTTTTGAGTAAATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:115,83:198,0:0:2,0:24:1:30.1:1:1:0:60:197:1:0:0.3 0/1:191:23:14,9:101,67:168,23:0.1204:2,2:22.4:1:30:1:1:1.03:60:22:0.1164:0:1.8 +15 54532120 . T C 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03063;SOR=Inf;LSEQ=ATAAAGTCTGAAGAATTTTA;RSEQ=TGATAAACTCCTACACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:113,130:243,0:0:2,0:26.3:1:30.6:1:1:0:60:80:1:0:0.5 0/1:256:6:4,2:125,125:250,6:0.0234:2,2:21.7:1:28.7:1:0.68384:1.99:60:5:0.0196:0:2.3 +15 54532140 . A T 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01013;LSEQ=TTGATAAACTCCTACACTGT;RSEQ=CCTTTCTTATGTTTTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:96:41,55:65,80:145,96:0.3983:2,2:28.1:1:30.2:1:0.79162:1.08955:60:47:0.3983:0:1.1 0/1:262:105:51,54:66,91:157,105:0.4008:2,2:26.3:1:29:1:0.31268:1.30:60:104:0.4:0:1.3 +15 54532164 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10412;SOR=0;LSEQ=TTCTTATGTTTTAAAACATG;RSEQ=TATTTGATTTGAACTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:1,2:73,124:197,3:0.015:2,2:22.3:1:29.3:1:1:1.17651:60:6:0.0151:0:1 0/0:224:0:0,0:87,135:222,0:0:2,0:26.5:1:31.1:1:1:0:60:221:0.991:0:0.5 +15 54609467 . C T 186 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=113.21845;LSEQ=ATGTTAGCACTAATGATAAA;RSEQ=GTGTGGTGAAGATTGTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:1:1,0:219,257:476,1:0.0021:2,0:44:0:33:0:0.46122:0:60:2:0.0021:0:1 0/1:410:79:36,43:155,175:330,79:0.1927:2,2:27.5:1:29.6:1:0.90023:1.05782:60:158:0.1955:0:1.3 +15 54609538 . T A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25993;SOR=0.79043;LSEQ=CATGACGTTTCCTGAATTAT;RSEQ=CAAATTTTCACATATAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:220:115:28,87:25,80:105,115:0.5227:2,2:24.4:1:29.6:1:1:1.03:60:230:0.5227:0:1 0/1:166:77:22,55:27,62:89,77:0.4639:2,2:25.4:1:28.5:1:0.86529:1.08815:60:76:0.4606:0:1.2 +15 55966241 . T G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGGGTGGGGAAGCCTAG;RSEQ=ATTCTACAGTTATAACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:35.5:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 55966445 . G C 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02268;SOR=Inf;LSEQ=AAGAGTTCAGATGGGTTCTA;RSEQ=AGTTAGCTTCTCTGTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:37,0:37,0:0:1,0:27.5:1:32.9:1:1:0:59.5:36:1:0:0.1 0/1:25:4:4,0:20,1:21,4:0.16:1,0:27.8:1:32.5:1:1:0:52.5:8:0.16:0:1 +15 55966487 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59162;SOR=2.4132;LSEQ=AACCTTGTTCTACCATGTAC;RSEQ=ACTCTGTGATCTTGACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:1:1,0:59,3:62,1:0.0159:1,0:4:0:28:0:1:0:60:2:0.0164:0:2 0/1:53:2:1,1:49,2:51,2:0.0377:1,2:42.5:1:30:1:0.11103:20.20728:60:4:0.0377:0:1 +15 55966523 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24233;SOR=Inf;LSEQ=CCAAATTAACCTCTCTTACC;RSEQ=AGGTTTCTTCAGACACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:90,25:115,0:0:2,0:22.4:1:30.5:1:1:0:59.8:37.333:1:0:0 0/1:112:2:1,1:88,22:110,2:0.0179:2,2:11.5:1:28.5:1:0.37001:3.93424:60:4:0.0179:0:1 +15 55966642 . C A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.43718;SOR=0.84942;LSEQ=GAACAGACCTCACACACACA;RSEQ=AAAATCTATCTTTATTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:67:31,36:155,169:324,67:0.1709:2,2:21.7:1:30.3:1:0.89328:1.06495:60:32.5:0.1711:0:1.1 0/1:396:59:32,27:175,159:334,59:0.149:2,2:23.1:1:29.4:1:0.88769:1.08:60:58:0.1491:0:1.3 +15 55966688 . C A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10274;SOR=0;LSEQ=TTCACCTTAGACATGCATAA;RSEQ=AGAGGTTGTTAATAGCAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:107,187:294,3:0.0101:2,2:24.3:1:29.7:1:0.55672:3.48:60:6:0.0103:0:1.7 0/0:336:0:0,0:147,189:336,0:0:2,0:25.7:1:31.3:1:1:0:60:83:1:0:0.3 +15 56872926 . T C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.19206;LSEQ=CACATCTTTGATGAGCTTCC;RSEQ=TTGTAACAAAATTCTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:15:15,0:2,0:2,15:0.8824:0,1:30.2:1:32.2:1:1:0:60:30:0.8824:0:1 1/1:10:9:9,0:1,0:1,9:0.9:0,0:23.9:1:29.6:1:1:0:60:8:0.8889:0:1.1 +15 56873003 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49692;SOR=Inf;LSEQ=GTGAGCCTCAATAGACAGAT;RSEQ=TGTCCTCTTATAATAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:50,14:64,0:0:2,0:21.1:1:32:1:1:0:60:128:1:0:0.1 0/1:69:2:1,1:48,19:67,2:0.029:2,2:17.5:1:29:1:0.49872:2.48788:60:4:0.029:0:1.5 +15 56873061 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=TATGGGAAGCATTGTCAATT;RSEQ=ATAAGTGATGCTAGATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:51,60:111,0:0:2,0:30.6:1:32.3:1:1:0:60:222:1:0:0.1 0/1:122:2:1,1:61,59:120,2:0.0164:2,2:41.5:1:28.5:1:1:1.03362:60:4:0.0164:0:1 +15 59161828 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51157;SOR=Inf;LSEQ=ATGGAGTAAACCTTTCGGCC;RSEQ=GAACCGCCATCTTCCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:79,63:142,0:0:2,0:30:1:30:1:1:0:45:70:0.9929:0:0.1 0/1:198:2:1,1:103,93:196,2:0.0101:2,2:40.5:1:30:1:1:1.10695:54:4:0.0103:0:1 +15 59161834 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17942;SOR=0;LSEQ=TAAACCTTTCGGCCGGAACC;RSEQ=CCATCTTCCAGTAATTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:76,67:143,2:0.0137:2,2:34:1:30:1:1:1.13334:60:4:0.0139:0:1 0/0:198:0:0,0:99,99:198,0:0:2,0:11:0:16:0:1:0:31:0:0:0:1 +15 59161897 . A T 18 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.83805;LSEQ=AGGGGAGAGGCACCCAATAT;RSEQ=TGTTCTCTAGGTCTTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:32,71:103,2:0.019:2,2:12.5:1:29:1:0.53187:2.20:23.5:4:0.0202:0:1 0/1:125:2:0,2:41,82:123,2:0.016:2,0:10:1:18.5:1:1:0:24:1:0.0085:0:4.5 +15 59162013 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51276;SOR=Inf;LSEQ=GGTACTGTTCAAAAAGGAAT;RSEQ=CCCCACAAGTGTTACCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:33,29:62,0:0:2,0:25.2:1:28.7:1:1:0:41.4:61:1:0:0.1 0/1:89:2:1,1:50,37:87,2:0.0225:2,2:9.5:1:29.5:1:1:1.3467:52.5:4:0.0225:0:1 +15 59162117 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49254;SOR=0;LSEQ=AAGGGCAAGATTCTTGCCAA;RSEQ=AGAATTAATGTGTGTATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:7,25:32,2:0.0588:2,2:20.5:1:31.5:1:0.42068:3.41:25.5:4:0.0588:0:1 0/0:33:0:0,0:9,24:33,0:0:2,0:19.9:1:31.2:1:1:0:36.2:66:1:0:0 +15 59341646 . A G 48 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGCAGTTCAGGCTCCTGTCC;RSEQ=TTGGTTCTCACAAAGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:33:0:1:0:60:2:1:0:0 1/0:4:3:2,1:0,1:1,3:0.75:0,2:31.3:1:30.7:1:1:0:60:6:0.75:0:1 +15 59342553 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48663;SOR=Inf;LSEQ=GCCCTAGAGAACAAATTGGA;RSEQ=GTGCCTCTTCTTTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:16,0:0:2,0:24:1:31.9:1:1:0:57.8:32:1:0:0.3 0/1:18:2:1,1:7,9:16,2:0.1111:2,2:20:0:32:1:1:1.27:60:4:0.1111:0:1 +15 59502492 . TTGTACATTGAC T 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATTCAATAACAACTTCCAT;RSEQ=ATTTTACTCATATCCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:96:45,51:105,113:218,96:0.3057:2,2:27.2:1:31:1:0.90252:1.05295:59.7:192:0.3097:0.0446:0.2 0/0:484:0:0,0:242,242:484,0:0:2,0:24.8:1:29.4:1:1:0:59.9:95.8:1:0:0.3 +15 59502497 . C A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23985;LSEQ=AATAACAACTTCCATTTGTA;RSEQ=ATTGACATTTTACTCATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:295:149:73,76:30,34:64,149:0.5051:2,2:25.2:1:30.6:1:0.88123:1.09:60:73.5:0.7033:0:1.1 0/1:489:96:48,48:195,198:393,96:0.1963:2,2:26.9:1:30:1:1:1.02:60:192:0.1983:0:1.1 +15 59502520 . CAT C 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACATTTTACTCATATCCA;RSEQ=GTTCATATTTACTGCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:148,167:315,0:0:2,0:25.3:1:30.8:1:1:0:59.9:44:1:0:0.5 0/1:471:40:19,21:199,231:430,40:0.0849:2,2:24.3:1:31.2:1:1:1.05:60:80:0.0862:0.0106:0.9 +15 59502553 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15539;SOR=Inf;LSEQ=ACTGCCAGAATAAAGCCGTA;RSEQ=TGTTCTCTTTTCACACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:86,148:234,0:0:2,0:25.8:1:33.1:1:1:0:59.9:468:0.9957:0:0.4 0/1:356:4:2,2:138,214:352,4:0.0112:2,2:26.5:1:29:1:0.6476:1.55:60:8:0.0113:0:2 +15 59817922 . A G 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49254;SOR=Inf;LSEQ=TTGCCATGGTAACATTTGTG;RSEQ=GGTATTCCTTTTTGAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:33,0:0:2,0:20.7:1:31:1:1:0:59.2:66:1:0:0.1 0/1:34:2:1,1:15,17:32,2:0.0588:2,2:7.5:1:27:1:1:1.13:60:4:0.0606:0:1 +15 59845063 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18366;SOR=0;LSEQ=ATCTTGCCCTTAACTGTTTG;RSEQ=TTACAACAATGCCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:33,15:48,2:0.04:2,2:33.5:1:30.5:1:0.54204:2.16222:37:4:0.0408:0:1.5 0/0:66:0:0,0:40,26:66,0:0:2,0:27.4:1:29.2:1:1:0:47.3:132:1:0:0.2 +15 59845138 . G A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.11803;LSEQ=CGTGGTAACACTTGTGGGGC;RSEQ=TTCCTTTTTGAACAGTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:24:10,14:3,8:11,24:0.6857:2,2:13.7:1:30.2:1:0.47758:1.87:28.8:48:0.6857:0:1 0/1:55:11:4,7:15,29:44,11:0.2:2,2:11.3:1:28.9:1:1:1.10:31.5:10:0.1852:0:1 +15 59845326 . C T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01405;SOR=0;LSEQ=TGGAAGATGGCGGTTCCCGC;RSEQ=GAAAGGCGCCTTAGTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:0,4:2,4:6,4:0.4:2,0:24.8:1:29.8:1:0.46667:0:52.3:8:0.4:0:2 0/0:16:0:0,0:5,11:16,0:0:2,0:22.8:1:28.7:1:1:0:59.7:32:1:0:0.3 +15 60297406 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50046;SOR=Inf;LSEQ=CGCGGCGGCCGGACCAGCCA;RSEQ=GCAAGGGCAGCTTCTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:20,0:0:2,0:21.9:1:31.1:1:1:0:58.1:19:1:0:0.1 0/1:27:2:1,1:14,11:25,2:0.0741:2,2:8:1:30:1:1:1.2613:60:4:0.0741:0:1 +15 60297427 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50588;SOR=Inf;LSEQ=GCAAGGGCAGCTTCTGGGCG;RSEQ=TGCACCCAAGCTGCGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:14,0:0:2,0:25.8:1:31.1:1:1:0:60:13:1:0:0.1 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:27:1:28:1:1:1.11:55.5:4:0.0952:0:1 +15 60297536 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GCCCAGCAAGCCAGCCGACG;RSEQ=GGCGCAGTACCTGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:6,0:0:0,0:32.7:1:30.5:1:1:0:60:12:1:0:0 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:29:1:27.5:1:1:2.45:60:4:0.3333:0:1 +15 60297613 . CCCG C 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=GCACGCACCTGCCACAGATG;RSEQ=CCGCCGCCTACAACTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:35.5:1:33:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:0.5 +15 61656824 . A G 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=GAATAGGGCCTGTTTAACAA;RSEQ=GTACTTTGTCCTTTGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:3,3:0.5:2,2:10.3:1:34:1:1:3.11:55:6:0.5:0:1 0/0:6:0:0,0:3,3:6,0:0:2,0:22.3:1:29.3:1:1:0:55.7:12:1:0:0.2 +15 61657223 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05455;SOR=Inf;LSEQ=ATGGGTGCCGCCCTTCCCCC;RSEQ=CCCATGAAGCTTAGTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:13.9:1:31.8:1:1:0:60:16:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:38.5:1:28:1:1:0:58.5:4:0.6667:0:1 +15 62266250 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01314;SOR=0.58734;LSEQ=AGTGATCTAGAACTTATAAG;RSEQ=CTAACATATAAGAAAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:104:49,55:35,26:61,104:0.6303:2,2:26.2:1:30.2:1:0.25886:1.50717:60:51:0.6335:0:1.1 1/0:224:112:60,52:54,58:112,112:0.5:2,2:27.5:1:28.9:1:0.50406:1.24:60:111:0.5023:0:1.1 +15 62374593 . C T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=GGACAGCCAGATATCAACTG;RSEQ=TACACAAATGAAATAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:20.5:1:29.5:1:1:0:60:4:0.4:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:31:1:31:0:1:0:57:4:0.5:0:1 +15 62374729 . A G 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCACAAAATTGATGAAC;RSEQ=TGGCCTCCACTTTGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:16,11:0,0:0,27:1:0,2:28.9:1:31.3:1:1:0:58.3:54:1:0:1.1 1/1:35:35:17,18:0,0:0,35:1:0,2:25.9:1:30.1:1:1:0:56.7:70:1:0:1.3 +15 62374877 . T C 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22857;SOR=0;LSEQ=ACCTTTTAATCTTGTGTTGA;RSEQ=GGTTTTGAGTCTTTTCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:4,5:9,3:0.25:2,2:37:1:30.7:1:1:1.53983:60:6:0.25:0:1 0/0:9:0:0,0:3,6:9,0:0:2,0:25.1:1:28.6:1:1:0:60:18:1:0:0.6 +15 62374915 . T C 64 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30245;SOR=4.19343;LSEQ=ACTCTGATTTTGTTGTTTTG;RSEQ=ATTTTGGGTTGAAATACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:23:1:32:1:1:2.24:60:4:0.2222:0:1.5 1/0:7:4:1,3:2,1:3,4:0.5714:2,2:24:1:32:1:0.48571:4.4496:60:8:0.5714:0:1.3 +15 62374942 . T A 28 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.62174;LSEQ=GGTTGAAATACCTCCTGTAG;RSEQ=TTTCTTCCCTGAAGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:1,5:6,2:0.25:2,0:17:1:28.5:1:0.10714:0:60:4:0.25:0:1.5 0/1:6:1:0,1:3,2:5,1:0.1667:2,0:29:0:32:0:1:0:60:2:0.1667:0:2 +15 62375036 . T G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.70357;SOR=1.76214;LSEQ=CCATCCTTTGTCAGCAGCAC;RSEQ=TTTTACTTTTTTCTGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:4,3:5,4:9,7:0.4375:2,2:20.4:1:31.1:1:1:1.06:58.1:14:0.4375:0:1.9 1/0:12:7:4,3:2,3:5,7:0.5833:2,2:20.9:1:31.1:1:1:1.89:55.3:14:0.5833:0:1.3 +15 62375068 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=TCTGTGGAAGCTTGCTACCA;RSEQ=CTGCAGGGGCAGATCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:13,0:0:2,0:40.2:1:31.4:1:1:0:59:12:1:0:1 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:35:1:28.5:1:1:1.18:60:4:0.1538:0:2 +15 62375236 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51446;SOR=0;LSEQ=TGGGTGGTGTTATTTCAAAG;RSEQ=CCCAAAGGGAAACTGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:22,20:42,2:0.0455:2,2:17:1:30.5:1:1:1.09762:60:4:0.0455:0:1 0/0:29:0:0,0:15,14:29,0:0:2,0:26.7:1:31:1:1:0:60:58:1:0:0.1 +15 62375334 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51111;SOR=0;LSEQ=ATTATCTCTGCTTCAACAAC;RSEQ=TGCAATTCATCCTTTGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:11,20:31,2:0.0606:2,2:33.5:1:32.5:1:1:1.78:60:4:0.0606:0:1 0/0:22:0:0,0:8,13:21,0:0:2,0:27.1:1:30.3:1:1:0:60:42:0.9545:0:0.3 +15 62375389 . C T 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04885;SOR=4.21228;LSEQ=TGGTTCTTAAAGATAACTGG;RSEQ=GCTCATTTGTATCATTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:4,3:3,8:11,7:0.3889:2,2:23.7:1:30.3:1:0.3322:3.29:60:14:0.3889:0:1 1/0:19:14:8,6:1,4:5,14:0.7368:2,2:25.3:1:30.1:1:0.30341:4.89:60:28:0.7368:0:1.1 +15 62375453 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23153;SOR=0;LSEQ=ACCCTTTAGCTCGCAACTGA;RSEQ=AAGATAGTTCTGGGCCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:11,2:13,3:0.1875:2,2:12.7:1:28.7:1:0.48929:2.54679:60:6:0.1875:0:1.3 0/0:13:0:0,0:7,6:13,0:0:2,0:18.7:1:29.9:1:1:0:60:26:1:0:0.5 +15 62375494 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15385;SOR=Inf;LSEQ=GAGGCTTAAGTACATGTCCA;RSEQ=CAAATCTTCCATAGGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:24,0:0:2,0:27.7:1:30.3:1:1:0:60:48:1:0:0.1 0/1:16:2:1,1:7,7:14,2:0.125:2,2:11:1:31.5:1:1:1:60:4:0.125:0:1 +15 63054439 . C G 264 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00358;LSEQ=ATTCACTCATGTCTTCGACC;RSEQ=TGACTTTGATTTCTCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:394:393:188,205:1,0:1,393:0.9975:0,2:25.2:1:30.7:1:0.4797:0:60:77.6:1:0:1.1 1/0:420:245:109,136:78,94:172,245:0.5833:2,2:25.8:1:30.3:1:0.92038:1.03526:59.9:121.5:0.5855:0:1.1 +15 63766676 . C T 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CACCTGGGATCCTTGCTGCT;RSEQ=TGGGAAAGATAAACTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:165,173:338,0:0:2,0:26.6:1:32.4:1:1:0:60:41.25:1:0:0.1 0/1:419:56:26,30:193,170:363,56:0.1337:2,2:24.1:1:28.8:1:0.3896:1.3091:60:17.667:0.1286:0:1.2 +15 63766778 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23287;SOR=0;LSEQ=GGACTTTTAGACTTGGAAGA;RSEQ=ATCTTGGTGGAAAAAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:24,106:130,2:0.0152:2,2:15:1:28.5:1:0.34409:4.35:60:4:0.0154:0:2 0/0:141:0:0,0:29,112:141,0:0:2,0:21.3:1:30.5:1:1:0:60:69.5:1:0:0.1 +15 63766788 . GA G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=ACTTGGAAGAGATCTTGGTG;RSEQ=AAAAAAGGAAGGGAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:18,97:115,2:0.0171:2,0:23:1:34:0:1:0:60:4:0.0174:0:0 0/0:104:0:0,0:17,87:104,0:0:2,0:21.9:1:29.4:1:1:0:60:33.667:1:0:0.1 +15 63995032 . T C 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATTTAGCTGGCCGGGCA;RSEQ=GGTGGCTCACGCCTGTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:21.8:1:32:1:1:0:56:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 63995328 . G A 42 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22213;LSEQ=CAAAAAAAAAAAAAAAAAAA;RSEQ=AGTAAATTTAGCTTTGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:3,0:91,39:130,3:0.0221:2,0:13.7:1:20.3:1:0.55527:0:41.3:2:0.019:0:3.3 0/1:149:4:3,1:88,54:142,4:0.0268:2,2:12.5:1:21:1:1:1.83:41.8:3:0.0256:0:2.5 +15 63995339 . G T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58939;SOR=0.40428;LSEQ=AAAAAAAAAGAGTAAATTTA;RSEQ=CTTTGATGCCTCTGAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:0,2:132,56:188,2:0.0105:2,0:17:1:28.5:1:0.09206:0:60:4:0.0114:0:1 0/0:234:1:0,1:156,74:230,1:0.0043:2,0:1:0:25:0:0.32468:0:60:2:0.0047:0:2 +15 63995347 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25654;SOR=Inf;LSEQ=AGAGTAAATTTAGCTTTGAT;RSEQ=CCTCTGAAAAGCTGAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:169,71:240,0:0:2,0:22.1:1:31.7:1:1:0:58.7:17.462:1:0:1 0/1:295:3:2,1:190,100:290,3:0.0102:2,2:21.7:1:24:1:1:1.05:47.3:2:0.0073:0:2.7 +15 63995423 . C T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCCTACATATTCACTTTCT;RSEQ=AGACCAAGGGCTTAGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:476:476:231,245:0,0:0,476:1:0,2:24.7:1:29.2:1:1:0:60:94.2:1:0:1.1 1/1:616:531:279,252:37,47:84,531:0.862:2,2:23.2:1:28.4:1:0.15965:1.41:60:131.75:0.8625:0:1.1 +15 64923588 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52241;SOR=Inf;LSEQ=AATGCCAACAGCGTGCTGGG;RSEQ=GACACTGTAGACTCTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:39,34:73,0:0:2,0:29.3:1:31.3:1:1:0:57.7:146:1:0:0.1 0/1:115:2:1,1:60,53:113,2:0.0174:2,2:36.5:1:30:1:1:1.13085:54.5:4:0.018:0:1.5 +15 64923740 . CT C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49291;SOR=0;LSEQ=CTTCATATTTTCTTTTCTTT;RSEQ=TTTTTTTTAGACGGAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:6,18:24,2:0.0769:2,2:38:1:32:1:0.47385:2.85:58.5:4:0.0769:0:0 0/0:22:0:0,0:5,15:20,0:0:2,0:17.2:1:29.9:1:1:0:51.7:40:0.9091:0:0.3 +15 66679601 . G C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.27696;LSEQ=CGGCCCGGACTTGGTCCTGC;RSEQ=CAGCGGGCGCGGGGCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:119:98,21:137,25:162,119:0.422:2,2:23.3:1:31.2:1:0.62826:1.1736:53.9:38.667:0.4173:0:1.1 0/1:280:47:35,12:189,43:232,47:0.1679:2,2:18.3:1:30.7:1:0.31425:1.50458:55.2:94:0.1691:0:1.3 +15 66679602 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24872;SOR=0;LSEQ=GGCCCGGACTTGGTCCTGCG;RSEQ=AGCGGGCGCGGGGCAGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:1,2:239,48:287,3:0.0103:2,2:17.3:1:27.3:1:0.07795:9.83407:49.3:6:0.0105:0:1 0/0:287:0:0,0:228,59:287,0:0:2,0:20:0:14:0:1:0:38:0:0:0:4 +15 66679649 . T TC 207 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAGCGAGAGGTGCTGCCC;RSEQ=CCCCCCGGAGTTGGAAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:756:0:0,0:510,242:752,0:0:2,0:24.4:1:31:1:1:0:56.7:31.696:0.9959:0:0.4 0/1:826:115:71,44:436,271:707,115:0.1392:2,2:28.1:1:30.3:1:1:1.00:51.9:230:0.1425:0.0048:0.2 +15 66679684 . A G 206 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGCGCGTTACCCGGGTCCA;RSEQ=AATGCCCAAGAAGAAGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1040:76:46,30:551,412:963,76:0.0731:2,2:27.6:1:33:1:0.63056:1.15:51.9:75:0.0734:0:1.1 0/0:1239:0:0,0:663,575:1238,0:0:2,0:24.4:1:29.5:1:1:0:58.2:60.9:0.9992:0:0.3 +15 66679819 . G C 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGCTGGGGAGGCCCGAGCC;RSEQ=GGGAGCAGGAGCGCGCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:121,303:424,0:0:2,0:24.1:1:30.8:1:1:0:60:105:0.9976:0:0.1 0/1:399:33:10,23:126,240:366,33:0.0827:2,2:28.8:1:29.8:1:0.70466:1.2069:59.8:66:0.0831:0:1 +15 66679850 . TG T 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCGCGCCAGGCTCCGATC;RSEQ=GTTTGTCACGTACGTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:32,217:249,0:0:2,0:23.7:1:31.4:1:1:0:60:34.571:1:0:0.1 0/1:206:24:4,20:26,156:182,24:0.1165:2,2:18.1:1:30.9:1:0.75922:1.20:59.8:48:0.1182:0.0388:0.9 +15 66694155 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50335;SOR=Inf;LSEQ=GATTCCATGGGAATGGAGGG;RSEQ=CGTGGCAGGAAGAGAGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:109,15:124,0:0:2,0:24.5:1:31.8:1:1:0:60:248:1:0:0.1 0/1:152:2:1,1:131,19:150,2:0.0132:2,2:7:1:26.5:1:0.2466:6.74443:60:4:0.0133:0:1 +15 66694161 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49938;SOR=Inf;LSEQ=ATGGGAATGGAGGGGCGTGG;RSEQ=AGGAAGAGAGCACGGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:135,26:161,0:0:2,0:21.5:1:32.2:1:1:0:60:52.667:1:0:0 0/1:175:2:1,1:146,27:173,2:0.0114:2,2:13:1:27:1:0.29517:5.32823:60:4:0.0116:0:1 +15 66694351 . C A 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30534;SOR=0.21361;LSEQ=ATCACATGCAAATTTTTCTT;RSEQ=CTTTCTGATCATTTTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:80,186:266,3:0.0112:2,2:13:1:28.3:1:0.22119:4.62:60:6:0.0112:0:1 0/0:417:1:1,0:150,266:416,1:0.0024:2,0:1:0:23:0:0.36211:0:60:2:0.0024:0:1 +15 66694420 . A T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00394;SOR=Inf;LSEQ=ATTTTGAAGTTTTATAAATG;RSEQ=TGTGGTTACTACATTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:2,69:71,0:0:1,0:31.2:1:31.6:1:1:0:59.6:70:1:0:0.3 0/1:84:9:1,8:1,74:75,9:0.1071:1,2:18.9:1:28.7:1:0.20396:8.78:60:18:0.1084:0:1.7 +15 66694431 . A G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02656;SOR=2.36522;LSEQ=TTATAAATGATGTGGTTACT;RSEQ=CATTGTTCCATTGTGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:18:0,18:0,49:49,18:0.2687:1,1:26.7:1:33.2:1:1:0:58.4:36:0.2687:0:1 0/1:60:28:0,28:0,32:32,28:0.4667:1,1:21.4:1:30.9:1:1:0:60:56:0.4667:0:1.2 +15 66694558 . A C 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTAACATCTGTCATCTCT;RSEQ=CACAACTAGCAGGAATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:23.7:1:32.3:1:1:0:60:12:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:33:1:32.5:1:1:0:60:4:1:0:1 +15 66727325 . C G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00818;SOR=Inf;LSEQ=ACTTCTTTGGGTTGACTTCT;RSEQ=TGGTGACAGTATTGACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:159,49:208,0:0:2,0:24.5:1:32.1:1:1:0:60:40.6:1:0:0.1 0/1:236:8:7,1:165,62:227,8:0.0339:2,2:13.6:1:32.8:1:0.68556:2.62:60:16:0.0345:0:1.1 +15 66727597 . G C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=1.99907;LSEQ=TGAGTTTGCCTTGATTAACA;RSEQ=GTAATTGGATTATTTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:74:16,58:33,159:192,74:0.2772:2,2:21:1:29.3:1:0.48021:1.33:60:36:0.2748:0:1.1 0/1:357:155:38,117:50,152:202,155:0.4342:2,2:22.7:1:29.8:1:1:1.01278:60:76.5:0.4334:0:1.1 +15 66727632 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23912;SOR=Inf;LSEQ=TCTCAGGGTACTTAGAAGCC;RSEQ=GGGGACCAGGGTAGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:7,144:151,0:0:1,0:28.6:1:29.9:1:1:0:59.6:17.875:1:0:0.4 0/1:145:2:1,1:18,125:143,2:0.0138:2,2:27.5:1:32:1:0.24569:6.79:60:4:0.0146:0:1 +15 66727689 . A ATTT 116 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=18.000;MSILEN=1;SSF=0.00333;SOR=5.5907;LSEQ=TACCTTTTTGTGCTGTTTGA;RSEQ=TTTTTTTTTTTTTTTAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:0,4:1,21:22,4:0.0833:1,0:34.8:1:30.9:1:1:0:52.5:8:0.0889:0:2 0/1:41:14:0,14:2,16:18,14:0.3415:2,1:23.6:1:30.5:1:0.49194:0:55.1:28:0.3415:0.0244:1.5 +15 66728951 . A C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00238;SOR=0.2217;LSEQ=CATTTCTTGGTTGAGCAGAA;RSEQ=CTTGTTTGTAACAACTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:26:25,1:33,3:36,26:0.4194:2,1:21.9:1:32.9:1:0.63296:2.25:60:25:0.4098:0:1.1 0/1:44:6:6,0:36,2:38,6:0.1364:2,0:14:1:31.5:1:1:0:60:12:0.1364:0:1 +15 66729250 . C A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23947;SOR=0;LSEQ=GGTATGTGACACCCTCTCAG;RSEQ=CTCTGGAGCAATGGCCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:30,164:194,2:0.0102:2,2:5:1:28.5:1:0.29199:5.39:60:4:0.0106:0:1 0/0:204:0:0,0:46,158:204,0:0:2,0:23.1:1:30.6:1:1:0:60:67:1:0:0.1 +15 66735551 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCCTGCCTCAGCCACAGC;RSEQ=GAAAGTTATCACTTGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:148:118,30:0,0:0,148:1:0,2:20.9:1:32:1:1:0:56:296:1:0:1.1 1/1:155:136:105,31:16,3:19,136:0.8774:2,2:23.4:1:30.3:1:0.76725:1.57047:57.1:135:0.8766:0:1.1 +15 66735925 . C CAG 95 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGTGTGTCTTGAAAAA;RSEQ=GGGCCAGGCACAGTGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:27.4:1:31.7:1:1:0:55.8:16:1:0.25:0.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 66736741 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAGCCGGGGGTGGTAGCG;RSEQ=ATGCCCGTAATCCCAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:8:1:32.5:1:1:0:30.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 66773935 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCAGAACAAAGGGCCTT;RSEQ=GTGTACAGTGTTTGCAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:34,0:34,2:0.0556:1,2:10:0:32.5:1:0.05556:0:60:4:0.0606:0:1.5 0/0:11:0:0,0:10,1:11,0:0:2,0:22.4:1:32.1:1:1:0:60:22:1:0:0.2 +15 66773975 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0486;SOR=0.38307;LSEQ=CAAGGGCTGCCTCTGATGGC;RSEQ=GACGGGGGTGTGGTCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:23:23,0:35,1:36,23:0.3898:1,1:26.9:1:29.5:1:1:0:60:10.5:0.375:0:1.2 0/1:41:8:8,0:30,3:33,8:0.1951:2,0:20.6:1:30.5:1:1:0:60:16:0.1951:0:1 +15 66774285 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23005;SOR=Inf;LSEQ=GAGGAGCCCAGTGGGTGCCT;RSEQ=TCCTGTGGAGCCAGAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:22,176:198,0:0:2,0:23.3:1:30.7:1:1:0:60:65:1:0:0.1 0/1:183:2:1,1:30,151:181,2:0.0109:2,2:32:1:31.5:1:0.31087:4.97:60:4:0.0111:0:1 +15 66774559 . A G 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCAGGATGCTCAGATAT;RSEQ=ATCCACCCCAAACTACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:18.5:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 66779698 . C T 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAGAAAACACCCAGGTGGC;RSEQ=GGGTGCAGTGGTTCACGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:52:12,40:33,150:183,52:0.2203:2,2:21.4:1:30.3:1:0.42772:1.36:56.6:51:0.2237:0:1.2 0/0:248:0:0,0:57,190:247,0:0:2,0:21.6:1:29.3:1:1:0:58.5:122.5:0.9959:0:0.1 +15 66779707 . T A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24838;SOR=0;LSEQ=ACCCAGGTGGCCGGGTGCAG;RSEQ=GGTTCACGCCTGTAATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:2,1:29,166:195,3:0.0152:2,2:10:1:28.7:1:0.06447:11.22:60:6:0.0155:0:1.7 0/0:190:0:0,0:29,160:189,0:0:2,0:22.7:1:29.2:1:1:0:57.9:62:1:0:0.1 +15 66781452 . T TA 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.65691;LSEQ=TTGGACTGCAGAGAAGACTT;RSEQ=AAAAAAAAGTAGCACTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:148,16:164,2:0.012:2,2:38:1:30.5:1:0.19489:9.00409:60:4:0.0121:0:0 0/0:126:1:1,0:107,18:125,1:0.0079:2,0:11:0:27:0:1:0:60:2:0.008:0:0 +15 66781718 . C T 26 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57404;SOR=2.79181;LSEQ=TTCTGCAGGCAGAGTTTTGC;RSEQ=CTTTACCCTCCCGTCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:0,1:15,187:202,1:0.0049:2,0:26:0:14:0:1:0:60:0:0:0:2 0/1:147:2:1,1:10,135:145,2:0.0136:2,2:7:1:26.5:1:0.14453:12.92:60:4:0.014:0:1 +15 66781887 . G A 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1733;SOR=Inf;LSEQ=ACCTTAGTTTAACTCAGCAA;RSEQ=AATGTATTAACTTACTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:53,15:68,0:0:2,0:21.6:1:33:1:1:0:60:136:1:0:0.1 0/1:49:2:1,1:45,2:47,2:0.0408:1,2:6:0:32.5:1:0.1199:18.56672:60:4:0.0426:0:1 +15 66781953 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49959;SOR=Inf;LSEQ=GGATGAATCAAGCCCAGGCA;RSEQ=TCCTCGGCCTCTAGTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:152,21:173,0:0:2,0:25.7:1:30.2:1:1:0:60:33.6:1:0:0.1 0/1:189:2:1,1:156,31:187,2:0.0106:2,2:25:1:31.5:1:0.31071:4.96899:60:4:0.0108:0:1.5 +15 66782048 . C T 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCTTACCTTGTCTTTCTT;RSEQ=CTTTAAGCTTAATAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:110:60,50:288,246:534,110:0.1708:2,2:23.7:1:30.2:1:0.91678:1.02:60:35.667:0.1709:0:1.2 0/0:819:0:0,0:431,388:819,0:0:2,0:25.1:1:30.2:1:1:0:60:57.5:1:0:0.2 +15 66782192 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21673;SOR=0;LSEQ=CAGTACTTCCAGAGCCCATT;RSEQ=ATTCCCTGCCCACTGTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:18,146:164,2:0.012:2,2:14.5:1:28:1:0.21643:7.92:60:4:0.012:0:1 0/0:190:0:0,0:27,163:190,0:0:2,0:21.5:1:31.3:1:1:0:60:189:1:0:0.1 +15 66782260 . C G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05784;SOR=Inf;LSEQ=AAACACCAGTCTCCTTTGCT;RSEQ=TCCCATCAGTTTAAGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:0,65:65,0:0:1,0:25.9:1:33.3:1:1:0:59.9:31.5:1:0:0.3 0/1:42:3:0,3:2,37:39,3:0.0714:2,0:19:1:32.7:1:1:0:60:6:0.0714:0:1 +15 66783025 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21703;SOR=Inf;LSEQ=CGCTTTTGGGCCTCCTTCCC;RSEQ=TGCCTGTCTCTGTTCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:1,89:90,0:0:1,0:24.8:1:32.1:1:1:0:52.3:89:1:0:0.1 0/1:79:2:1,1:2,75:77,2:0.0253:1,2:32.5:1:28:1:0.07498:30.85:29.5:4:0.0256:0:1.5 +15 67358478 . G A 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGCGCTCCTCGCCGCCCGC;RSEQ=CGCCCTCCCCAGCCATGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:224,40:264,0:0:2,0:25:1:30.7:1:1:0:60:65:1:0:0.1 0/1:251:44:34,10:163,44:207,44:0.1753:2,2:23.6:1:28.5:1:0.84095:1.08919:59.3:13.667:0.1673:0:1.1 +15 67358480 . G T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12393;SOR=0;LSEQ=GCGCTCCTCGCCGCCCGCGC;RSEQ=CCCTCCCCAGCCATGTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:4:2,2:231,43:274,4:0.0144:2,2:17.5:1:30:1:0.12406:5.32294:60:8:0.0146:0:1 0/0:267:0:0,0:208,59:267,0:0:2,0:23.8:1:29.8:1:1:0:59.9:88:1:0:0.4 +15 67430223 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGTCCTCCCTTTGGATTTCT;RSEQ=CTGTCTGGGTGTTGCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:92:92:90,2:0,0:0,92:1:0,1:24.8:1:32.4:1:1:0:60:91:1:0:1.1 1/1:56:56:56,0:0,0:0,56:1:0,1:23.1:1:29.8:1:1:0:60:13:1:0:1.1 +15 67430489 . C T 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.10447;SOR=0;LSEQ=CTCTTTCTTGAACTCGTCTC;RSEQ=CCACCCGTCCACAGGGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:2,1:44,165:209,3:0.0142:2,2:28.3:1:26.7:1:0.11944:7.40:60:2:0.0098:0:2 0/0:237:0:0,0:66,170:236,0:0:2,0:23.5:1:30:1:1:0:60:235:0.9958:0:0.2 +15 67430538 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23161;SOR=Inf;LSEQ=GATCTGTCAGAGTTTCTCCG;RSEQ=GCTTCTCTTTCTCTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:1,89:90,0:0:1,0:23.6:1:30.9:1:1:0:60:44:1:0:0.1 0/1:84:2:1,1:4,78:82,2:0.0238:1,2:25:1:26:1:0.11618:17.55:60:4:0.0241:0:1 +15 67430552 . T C 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0217;SOR=9.71314;LSEQ=TCTCCGGGCTTCTCTTTCTC;RSEQ=GGGTGGGGATGTGGACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:0,1:0,76:76,1:0.013:1,0:35:0:10:0:1:0:60:0:0:0:1 0/1:61:7:0,7:3,51:54,7:0.1148:2,0:20.6:1:28:1:1:0:60:14:0.1148:0:1 +15 67430733 . T C 93 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTGCCATCGCAGTGGAT;RSEQ=TGCGGAAGAGGGTTCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:17.3:1:33.3:1:1:0:60:14:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 67432161 . A C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGAAGCTGTGCTTGGAA;RSEQ=GTGAATGTGTTTAGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 67455276 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCATTGTGTGTAATTGT;RSEQ=GGTTTCTGTGATGATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:2,2:0.5:0,2:28.5:1:31.5:1:1:0:60:4:0.5:0:1 +15 67457335 . A G 317 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01429;LSEQ=CTGCACAGCCACCACGAGCT;RSEQ=CGGGCCATGGAGCTGTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:931:926:468,458:0,0:0,926:0.9946:0,2:25.9:1:32.2:1:1:0:60:101.889:0.9967:0:1.2 1/0:884:641:323,318:120,123:243,641:0.7251:2,2:25.7:1:31.2:1:0.82133:1.04:60:63.1:0.7278:0:1.2 +15 67457480 . T TC 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGCCAGGGGTCATCACCTC;RSEQ=CCCCGGCTCCCCATCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:39:25,14:42,89:131,39:0.0975:2,2:10.6:1:29.1:1:0.00064:3.75:58.7:12:0.0916:0.07:1.3 0/0:217:0:0,0:82,135:217,0:0:2,0:21:1:28.9:1:1:0:59.8:30:1:0:0.7 +15 67457485 . G CC 247 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=AGGGGTCATCACCTCTCCCC;RSEQ=GCTCCCCATCCCCCCGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:400:230:74,156:42,89:131,230:0.575:2,2:28.3:1:31.6:1:1:1.01:59.8:229:0.5827:0.0375:1.1 0/0:217:0:0,0:82,135:217,0:0:2,0:21:1:28.9:1:1:0:59.8:30:1:0:0.7 +15 67457698 . A G 151 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=31.91396;LSEQ=ACACTAACTTCCCCGCAGGC;RSEQ=TCGAGCCCCAGAGCAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1017:1:0,1:443,573:1016,1:0.001:2,0:16:0:32:0:1:0:60:2:0.001:0:1 0/1:1017:31:12,19:448,537:985,31:0.0305:2,2:29.5:1:30.6:1:0.58321:1.32056:60:62:0.031:0:1.1 +15 67457805 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.52317;SOR=0;LSEQ=GTCCTGTGGCCCCAATCTCT;RSEQ=CCCCCTGGCCGTCCCCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:0,2:4,194:198,2:0.01:1,0:31.5:1:32:0:1:0:60:4:0.0102:0:1 0/0:128:0:0,0:0,128:128,0:0:1,0:20.6:1:31.8:1:1:0:59.7:24.6:1:0:0.2 +15 67458805 . G A 80 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGGACGCCTCCCTGGAGG;RSEQ=GGTGGGGCTTAACCCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:0,0:0,7:0.875:0,0:29.6:1:28.7:1:1:0:56.1:14:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 67458930 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05585;LSEQ=AAAGGCAGTTATGATCCAAG;RSEQ=GGGAGTCAGAGGTGGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:65:63,2:4,1:5,65:0.9155:2,1:25.9:1:30.5:1:0.20205:7.40:60:130:0.9286:0:1 0/1:30:11:10,1:19,0:19,11:0.3667:1,2:25.9:1:29.5:1:0.36667:0:60:22:0.3667:0:1.2 +15 67458957 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGGTGGACAGGGGCGAG;RSEQ=ACAACAGAACCAAGAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:121,4:125,2:0.0157:1,0:14:1:27.5:1:1:0:60:4:0.0161:0:1.5 0/0:63:0:0,0:62,1:63,0:0:1,0:21.3:1:30.5:1:1:0:60:30.5:1:0:0.3 +15 67459245 . TCATCCCTTC T 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=2.000;MSILEN=1;SSF=0.00255;SOR=Inf;LSEQ=CTGATTAGCAGCTGGTGGGT;RSEQ=CATCCCTTCCTCTTCGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:50,288:338,0:0:2,0:24.8:1:32.6:1:1:0:60:111.667:1:0:0.1 0/1:254:7:2,5:70,177:247,7:0.0276:2,2:26:1:31.6:1:1:1.01:60:14:0.0277:0:0 +15 67459280 . TC T 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53466;SOR=0;LSEQ=CTTCCTCTTCGCCCTCTCCC;RSEQ=CCTCCCTTCTATCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:16,173:189,2:0.0105:2,0:7:1:32:1:1:0:60:4:0.0105:0.0052:1 0/0:110:0:0,0:18,92:110,0:0:2,0:23.7:1:30.5:1:1:0:60:109:1:0:0 +15 67462798 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20534;SOR=Inf;LSEQ=GGGTTTTCTTTCTGCTGTGT;RSEQ=GGCTACCCCTCCTTGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:183,30:213,0:0:2,0:23:1:32.3:1:1:0:60:52.25:1:0:0.1 0/1:177:2:1,1:149,26:175,2:0.0113:2,2:18:1:29:1:0.28255:5.64254:60:4:0.0115:0:0 +15 67463026 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50478;SOR=0;LSEQ=TGTGGGGAGGGGGCCCTGAA;RSEQ=GTAAGGCTCTCCCCCGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:20,156:176,2:0.0112:2,2:16.5:1:29.5:1:0.22262:7.64:60:4:0.0116:0:1 0/0:142:0:0,0:14,128:142,0:0:2,0:24.3:1:30.4:1:1:0:60:46.333:1:0:0.1 +15 67473310 . C CTAAA 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=10.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=CGGGGCAGGGCCTTTATGAG;RSEQ=TAAATAAATAAATAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:33.2:1:31.8:1:1:0:60:10:0.7143:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:28:1:1:0:60:4:1:0:0 +15 67473790 . C T 245 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGCTGACACGGAGACACAT;RSEQ=GGTATGGGGTGGCTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:259:95,164:137,236:373,259:0.4098:2,2:24.1:1:30.6:1:1:1.00214:59.5:63.75:0.414:0:1.3 0/0:586:0:0,0:237,346:583,0:0:2,0:24:1:29.6:1:1:0:59.6:63.778:0.9948:0:0.4 +15 67473814 . GC G 77 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.31715;SOR=2.30869;LSEQ=ATGGGGTGGCTCCATTCCCC;RSEQ=CCCCCCACCCTGCCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:3:1,2:126,303:429,3:0.0069:2,2:20:1:31.3:1:1:1.20:60:6:0.0079:0:1 0/1:379:6:3,3:130,241:371,6:0.0158:2,2:22.3:1:29.8:1:0.42981:1.85:60:12:0.019:0:0.3 +15 67473822 . A C 79 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32861;SOR=1.39738;LSEQ=GCTCCATTCCCCGCCCCCCC;RSEQ=CCCTGCCCCTGCCACTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:18:17,1:7,287:294,18:0.0577:1,1:8.3:1:22.4:1:0:621.12:60:3.5:0.0468:0:2.7 0/1:279:22:22,0:24,231:255,22:0.0789:2,1:9.7:1:17.9:1:0:0:59.5:1.2:0.0463:0:2.7 +15 67473823 . C A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02213;SOR=Inf;LSEQ=CTCCATTCCCCGCCCCCCCA;RSEQ=CCTGCCCCTGCCACTCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:19,285:304,0:0:2,0:23.2:1:31:1:1:0:60:42.429:1:0:0.5 0/1:268:5:4,1:37,226:263,5:0.0187:2,2:10.2:1:20.8:1:0.00214:23.93:60:1.5:0.012:0:1.2 +15 67473827 . G C 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.32629;SOR=3.80973;LSEQ=ATTCCCCGCCCCCCCACCCT;RSEQ=CCCCTGCCACTCTATCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:1:1,0:6,269:275,1:0.0036:1,0:35:0:15:0:0.02536:0:60:0:0:0:6 0/1:219:3:1,2:18,195:213,3:0.0137:2,2:11.7:1:24.3:1:0.24238:5.34:60:2:0.0099:0:2 +15 67476756 . C T 47 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CGCCTGGCCCCCATCCCTAT;RSEQ=GTAGAGACAAACGAAGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:8.3:1:30:1:1:0:60:6:1:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:25:0:32:0:1:0:54:2:1:0:0 +15 67476768 . C T 52 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATCCCTATCGTAGAGACAAA;RSEQ=GAAGACTCAGAGGGTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:15.3:1:33:1:1:0:60:6:1:0:2 1/0:2:1:1,0:1,0:1,1:0.5:0,0:2:0:28:0:1:0:60:2:0.5:0:1 +15 67476952 . G T 211 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01447;LSEQ=CCGTTTGCCTGGGGAAGCTG;RSEQ=CAGTCACTGGGAGCAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:133:132,1:6,0:6,133:0.9568:0,1:24:1:30:1:1:0:60:132:0.9565:0:1.9 0/1:72:17:17,0:55,0:55,17:0.2361:1,1:20.7:1:29.5:1:1:0:60:34:0.2429:0:2 +15 67476970 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02003;LSEQ=TGGCAGTCACTGGGAGCAGC;RSEQ=CTGCTGTTCTGCCTCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:156:147:141,6:8,1:9,147:0.9423:2,1:26.1:1:31.3:1:0.34587:2.91:60:35.75:0.9408:0:1.9 0/1:132:32:29,3:93,7:100,32:0.2424:2,2:19.9:1:30.8:1:0.70422:1.37085:60:64:0.2443:0:1.6 +15 67479505 . C A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAGTGAGGAGATGGGTT;RSEQ=AAGGGGAGGGACTGGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:37,2:39,2:0.0488:2,0:7:1:28.5:1:1:0:60:4:0.0526:0:1.5 0/0:8:0:0,0:8,0:8,0:0:0,0:29.9:1:31.1:1:1:0:60:16:1:0:0.4 +15 67479678 . A AG 216 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGCCACTTCCATCCCCAC;RSEQ=GCCCTGTTTCTGTGTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:787:99:66,33:418,265:683,99:0.1258:2,2:29.6:1:32.6:1:0.32028:1.27:60:98:0.1284:0.0038:0.1 0/0:708:0:0,0:419,288:707,0:0:2,0:25.1:1:29.7:1:1:0:59.9:77.556:0.9986:0:0.2 +15 67479911 . G T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16342;SOR=Inf;LSEQ=TGACTCTGGACAGCAGAGCA;RSEQ=GCAGGGCTCCTCAGAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:54,238:292,0:0:2,0:24.1:1:31.7:1:1:0:60:145:0.9966:0:0.1 0/1:200:2:1,1:37,161:198,2:0.01:2,2:7:1:29:1:0.34467:4.31:60:4:0.0102:0:1 +15 67482591 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08584;SOR=Inf;LSEQ=CCTGGGTAGAGGAGTTTGGC;RSEQ=GGGTAGTTTCAGCAAGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:75,1:76,0:0:1,0:26.7:1:31.1:1:1:0:59.6:37:1:0:0.1 0/1:32:2:2,0:28,2:30,2:0.0625:2,0:26:1:32:0:1:0:60:4:0.0625:0:1 +15 67482696 . AC GT 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGCTTTCTGACTTGTGTA;RSEQ=CCCCTGGAGATTTTTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:0:0,0:360,135:495,0:0:2,0:22.9:1:29.9:1:1:0:59.9:48.5:1:0:0.2 0/1:404:21:17,4:268,109:377,21:0.052:2,2:17.8:1:30.1:1:0.45737:1.73:60:42:0.0529:0.0124:0.8 +15 67483276 . C T 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGTTCACCTTGGAAGGG;RSEQ=GTTCTAGGTAGGAAGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:34.7:1:30:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 69264924 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89676;LSEQ=GGGTTGCTGGCAAGCTTTGG;RSEQ=ATTCCTTGGTTTATAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:32,37:69,2:0.0282:2,2:31.5:1:28:1:1:1.15:60:4:0.0282:0:1 0/1:79:2:1,1:34,43:77,2:0.0253:2,2:24.5:1:30.5:1:1:1.26:60:4:0.0253:0:1 +15 69264941 . A G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21212;SOR=0;LSEQ=TGGCATTCCTTGGTTTATAG;RSEQ=AACATCACCCTGATCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:22,32:54,2:0.0357:2,2:25:0:32.5:1:1:1.44:60:4:0.0385:0:1.5 0/0:65:0:0,0:26,39:65,0:0:2,0:23.7:1:27.9:1:1:0:59.2:12:1:0:0.2 +15 69265832 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAATGGTGCAATCTCGG;RSEQ=TCACTGCAAGCTCCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:0:31:1:1:0:24:4:1:0:1.5 +15 70348128 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGCATCTAGATTCTCGT;RSEQ=GACAATTAGAGGACTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:29:1:1:0:60:4:1:0:1.5 +15 70349888 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52923;SOR=0;LSEQ=GGTGGGATGTTGTGGAGGCC;RSEQ=GCGTAGGCGCCAGGACTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:15,2:0.1176:2,2:16:0:32:1:1:1.46:60:4:0.1176:0:1.5 0/0:9:0:0,0:5,4:9,0:0:2,0:30.1:1:30.6:1:1:0:60:18:1:0:0 +15 70351649 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTCCCTGCTCAGGCTG;RSEQ=CAGTAATACTAGAACAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:30.5:1:1:0:60:4:1:0:1 +15 71891715 . G A 27 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACACAGAGCCCACTTCCT;RSEQ=TCTAACTATTTTTTCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24:1:27:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:29:0:1:0:60:2:1:0:1 +15 71892037 . T G 70 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09657;SOR=4.77762;LSEQ=GATGAGGAGCATTTTATAAA;RSEQ=TAAGAGCTGTTCCCTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:2,0:65,1:66,2:0.0294:1,0:14.5:1:32:1:1:0:60:4:0.0308:0:1.5 0/1:39:5:5,0:34,0:34,5:0.1282:1,0:17.6:1:30.4:1:1:0:60:10:0.1282:0:1.6 +15 71892101 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3056;SOR=1.59295;LSEQ=TGGCAGTGGGCCAGGAGGAA;RSEQ=GTGTGTGCATTCAAGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:10:6,4:157,45:202,10:0.0472:2,2:23.5:1:30.1:1:0.24458:2.31493:60:20:0.0483:0:1.6 0/1:205:15:11,4:142,48:190,15:0.0732:2,2:24.3:1:29.8:1:1:1.07538:60:30:0.0739:0:1.5 +15 71892119 . C T 55 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21708;SOR=4.84336;LSEQ=AACGTGTGTGCATTCAAGGG;RSEQ=AAATGTCATCTCTCTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:1:0,1:200,99:299,1:0.0033:2,0:1:0:23:0:0.33333:0:60:2:0.0034:0:1 0/1:313:5:1,4:203,105:308,5:0.016:2,2:9.4:1:23.8:1:0.05163:7.68286:60:10:0.0162:0:1 +15 71892168 . C G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15006;SOR=1.67532;LSEQ=AGGCCCACTTTGAGCCGAAA;RSEQ=ACTGGGAGCCGCATAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:14:6,8:249,228:477,14:0.0285:2,2:18.4:1:32.7:1:0.59139:1.45502:60:28:0.0292:0:1.9 0/1:577:27:14,13:298,249:547,27:0.0468:2,2:29.9:1:30.7:1:0.84451:1.1111:60:26:0.0455:0:1.8 +15 71892215 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13366;LSEQ=TCTTCCCCACAATGCCCCCC;RSEQ=GTATGGGAAGCTCCTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:455:350:146,204:49,56:105,350:0.7692:2,2:25.9:1:30.2:1:0.37117:1.22205:60:30.818:0.767:0:1.2 0/1:507:156:69,87:163,188:351,156:0.3077:2,2:25:1:29.1:1:0.69944:1.09301:60:25:0.3049:0:1.3 +15 71892532 . T A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCTGTGCAAGACTTACTCAC;RSEQ=CAGAAAGCTCTGTATTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:14:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 71950355 . C T 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00144;SOR=6.46031;LSEQ=GACGTCTGTCCCATCTTTGG;RSEQ=GACTCTCATTCATTCTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:2,1:142,20:162,3:0.0182:2,2:24.3:1:29.7:1:0.33706:3.50896:60:6:0.0183:0:1.3 0/1:121:13:10,3:85,23:108,13:0.1074:2,2:16.8:1:29.6:1:1:1.10774:60:26:0.1074:0:1 +15 71950447 . C A 120 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=16.27164;LSEQ=TCTCCACTCTAGGTAAGGCC;RSEQ=GCTCCACACTGCAGTCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:1:1,0:229,261:490,1:0.002:2,0:1:0:26:0:0.46843:0:60:2:0.0021:0:2 0/1:499:16:9,7:243,237:480,16:0.0321:2,2:22.1:1:30.1:1:0.8008:1.25:60:32:0.0324:0:2.6 +15 71950471 . C T 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACACTGCAGTCATTGTTA;RSEQ=CACCGAAAAGCAAGTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:0:0,0:189,256:445,0:0:2,0:26.4:1:31.5:1:1:0:60:62.571:1:0:0.1 0/1:448:60:26,34:182,206:388,60:0.1339:2,2:26.1:1:28.3:1:0.67711:1.15497:59.8:19:0.1298:0:1.7 +15 71950475 . C T 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=ACTGCAGTCATTGTTACCAC;RSEQ=GAAAAGCAAGTCTGAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:178,248:426,0:0:2,0:26.8:1:30.3:1:1:0:60:70:0.9976:0:0.1 0/1:430:16:7,9:191,223:414,16:0.0372:2,2:27.7:1:29.4:1:1:1.10094:60:32:0.0376:0:3 +15 71950538 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50416;SOR=0;LSEQ=TGGGGGTTGCTGATGCCATA;RSEQ=GATGAAAATCTAATTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:43,131:174,2:0.0114:2,2:38:1:32:1:0.43857:3.02:60:4:0.0114:0:1 0/0:142:0:0,0:25,116:141,0:0:2,0:24.1:1:30.3:1:1:0:60:282:1:0:0.2 +15 71950542 . GA G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5061;SOR=0;LSEQ=GGTTGCTGATGCCATAGGAT;RSEQ=AAATCTAATTCTTCAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:34,116:150,2:0.0132:2,2:26:1:32.5:1:0.40868:3.38:60:4:0.0132:0:0 0/0:118:0:0,0:18,100:118,0:0:2,0:26:1:29.9:1:1:0:60:117:1:0:0.2 +15 72427055 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49895;SOR=0;LSEQ=TTGGAAAAAACATGGAGTTG;RSEQ=TCCTTTGGCCATGTATATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:27,13:40,2:0.0476:2,2:21.5:1:31.5:1:1:2.03815:58.5:4:0.0476:0:1 0/0:34:0:0,0:18,16:34,0:0:2,0:26.5:1:29.3:1:1:0:57.2:68:1:0:0.1 +15 72427143 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20031;SOR=Inf;LSEQ=GTTCAAAAAGGAATGTCCCA;RSEQ=AAGTGTTACCATGGCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:68,40:108,0:0:2,0:24.1:1:32.1:1:1:0:59.9:35:1:0:0.1 0/1:88:2:1,1:53,33:86,2:0.0227:2,2:23.5:1:30:1:1:1.59707:60:4:0.023:0:1.5 +15 72427149 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1929;SOR=Inf;LSEQ=AAAGGAATGTCCCAGAAGTG;RSEQ=TACCATGGCAAAACTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:69,44:113,0:0:2,0:26.1:1:29.8:1:1:0:59.9:112:1:0:0.1 0/1:89:2:1,1:55,32:87,2:0.0225:2,2:23:0:33.5:1:1:1.70775:60:4:0.0227:0:1.5 +15 72427153 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50199;SOR=0;LSEQ=GAATGTCCCAGAAGTGTTAC;RSEQ=ATGGCAAAACTGGAAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:64,44:108,2:0.0182:2,2:42:1:29:1:1:1.44946:55.5:4:0.0183:0:1 0/0:91:0:0,0:56,35:91,0:0:2,0:30.4:1:30.8:1:1:0:59.1:90:1:0:0.1 +15 72427442 . A G 29 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGAGTCTGGCTCTGTC;RSEQ=CCCAGGCTGGAATGCAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 73191863 . T C 126 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06267;SOR=0;LSEQ=ACCAGCTTTTTCTATACTTG;RSEQ=TTGCATTTTTGCTTTAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:10,5:0,0:0,15:1:0,2:28.2:1:33.3:1:1:0:39.7:30:1:0:1.1 1/0:22:16:7,9:6,0:6,16:0.7273:0,2:29.1:1:31.6:1:0.04608:0:34.6:32:0.7273:0:1.2 +15 73191920 . G GT 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.14546;SOR=0.47422;LSEQ=CCCTTTTGGTGTTTTAGGAG;RSEQ=TTTTTTTTTTTCCTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:13,3:3,3:6,16:0.5714:2,2:30.8:1:30.9:1:0.28286:4.00:48.9:32:0.5714:0:0.8 0/1:39:15:9,6:14,9:23,15:0.3846:2,2:31.3:1:30.5:1:1:1.03607:45.7:30:0.3947:0:0.6 +15 73192251 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27433;SOR=0;LSEQ=TGATTCTGCAGCTTCCTCCA;RSEQ=AGCTACTAAGTGCTGTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:3:1,2:129,90:219,3:0.0135:2,2:11:1:28.3:1:0.57118:2.85306:53.7:6:0.0136:0:1 0/0:152:0:0,0:89,63:152,0:0:2,0:26.6:1:31.2:1:1:0:57.2:75:1:0:0.1 +15 73192349 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09391;SOR=Inf;LSEQ=CAAAGTCCCCAAGGGAAACC;RSEQ=TTGACTGTACAGACATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:100,128:228,0:0:2,0:25.1:1:31.6:1:1:0:59.2:227:1:0:0.1 0/1:191:3:2,1:87,101:188,3:0.0157:2,2:16.3:1:30:1:0.59896:2.31:50.7:6:0.0159:0:1.3 +15 73192415 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21907;SOR=Inf;LSEQ=GACTGTCTTCATAATTCATT;RSEQ=TTTCTGCTTCAACAATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:82,97:179,0:0:2,0:24.3:1:32.3:1:1:0:59.6:178:1:0:0.1 0/1:158:2:1,1:67,89:156,2:0.0127:2,2:8.5:1:26:1:1:1.33:42:4:0.0129:0:1 +15 73192458 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49901;SOR=0;LSEQ=TTCATCCTTTGCACCAGCTC;RSEQ=TAAACTGACTGTTCCTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:73,114:187,2:0.0106:2,2:35:1:28.5:1:1:1.56:49:4:0.0106:0:1 0/0:179:0:0,0:75,104:179,0:0:2,0:28.9:1:31.2:1:1:0:53.9:88.5:1:0:0.2 +15 73192681 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49929;SOR=0;LSEQ=GCTCCAGAGAACAGCCATGC;RSEQ=GGATGGAATCACACCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:5,15:20,2:0.0909:2,2:36.5:1:30:1:0.48052:2.83:60:4:0.0909:0:1 0/0:16:0:0,0:4,12:16,0:0:2,0:23.5:1:30.1:1:1:0:60:32:1:0:0.1 +15 73454308 . T G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=TGTTTTAGGAAGTTTGTTTG;RSEQ=TTTTTTTTCTCCTGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:8,7:0,0:0,15:1:0,2:22.8:1:30.9:1:1:0:60:14:1:0:1.1 1/1:16:14:8,6:1,1:2,14:0.875:2,2:25.8:1:31.1:1:1:1.31:60:28:0.875:0:1.1 +15 73454432 . A T 34 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23734;SOR=Inf;LSEQ=CATACAGATTTCTTCAGTGG;RSEQ=GCTTATTCTTGTCTCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:27,0:0:2,0:23.2:1:29.9:1:1:0:60:12.5:1:0:0.2 0/1:29:3:0,3:12,14:26,3:0.1034:2,0:5.7:1:21.7:1:0.24631:0:60:2:0.0769:0:1 +15 73455034 . T C 94 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=CAGATGTGAGTCATCATGCC;RSEQ=GGCCAGTTGCCAGTATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:22.4:1:31.6:1:1:0:60:10:1:0:1.4 1/0:12:9:7,2:1,2:3,9:0.75:2,2:18.6:1:29.8:1:0.23636:5.73:60:18:0.75:0:1.2 +15 73991904 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08956;SOR=Inf;LSEQ=GAGAACCTTTGGAGACAAAG;RSEQ=CCTTGCGTCCTCTTTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:277,75:352,0:0:2,0:22.2:1:30.9:1:1:0:60:26.077:1:0:0.1 0/1:286:3:1,2:218,65:283,3:0.0105:2,2:8.7:1:27.7:1:0.13792:6.65026:60:6:0.0106:0:1.3 +15 73992124 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08606;SOR=Inf;LSEQ=TGGCAGTTGGGGAGGGGGTG;RSEQ=CCACGCCTGTTAGGGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:43,315:358,0:0:2,0:23.9:1:31.3:1:1:0:60:38.778:1:0:0.1 0/1:284:3:1,2:46,233:279,3:0.0106:2,2:31:1:26.7:1:0.42253:2.52:60:6:0.0111:0:1 +15 73994122 . G GA 59 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATTCTCTCTCCTCCAGA;RSEQ=AAACCACTATTGACATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:25.3:1:29.8:1:1:0:60:8:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 73994523 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.53933;SOR=0;LSEQ=AGGGCCTGGGGTTAGCAGGG;RSEQ=CAGGGAGCGGGACTAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:160,20:180,2:0.011:2,2:9:1:26:1:0.21802:7.83134:60:4:0.0114:0:1 0/0:101:0:0,0:83,17:100,0:0:2,0:24.1:1:30.3:1:1:0:60:49:0.9899:0:0.2 +15 73994543 . G T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15686;SOR=Inf;LSEQ=GCAGGGAGCGGGACTAGGGA;RSEQ=GCCCACCCCTCCTCAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:212,48:260,0:0:2,0:23.5:1:32.4:1:1:0:60:27.889:1:0:0.1 0/1:171:2:1,1:117,52:169,2:0.0117:2,2:7:1:29:1:0.52508:2.23821:60:4:0.0118:0:1 +15 73994806 . C T 142 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=33.53936;LSEQ=CAACCGCACGGCCCTCTTCC;RSEQ=GGACCTGCTGGCACAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:1:0,1:241,255:496,1:0.002:2,0:8:0:33:0:1:0:60:2:0.002:0:1 0/1:458:29:14,15:189,237:426,29:0.0633:2,2:25.1:1:29.4:1:0.70328:1.17:50.4:28:0.0622:0:1.3 +15 73994847 . C A 69 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02254;SOR=Inf;LSEQ=ACGCATCCCTGAGGCTGCAG;RSEQ=GCGTGCGTGTGGCGGACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:64,79:143,0:0:2,0:10.8:1:30.4:1:1:0:33.4:34.75:1:0:0.2 0/1:128:5:2,3:54,69:123,5:0.0391:2,2:7.4:1:30:1:1:1.17246:30.2:10:0.0394:0:1.8 +15 73994910 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.16268;SOR=Inf;LSEQ=GCATCCGGGATTTCGGCAGC;RSEQ=CTGCCGTCAGCCTGCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:41,84:125,0:0:2,0:11.8:1:30.4:1:1:0:26.3:40.667:1:0:0.2 0/1:85:2:1,1:25,58:83,2:0.0235:2,2:22:1:31:0:0.52073:2.29:21:4:0.0235:0:1 +15 73995273 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49499;SOR=0;LSEQ=ACTGGCAACGTGACCACGTC;RSEQ=CAGATGGCCAACGAGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:23,6:29,2:0.0645:2,2:9.5:1:28.5:1:0.40645:3.62563:60:4:0.0667:0:1 0/0:26:0:0,0:20,6:26,0:0:2,0:5.7:1:30.2:1:1:0:60:52:1:0:0.1 +15 73995378 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08453;SOR=Inf;LSEQ=GTGCGCAACCCCGTGCTGCA;RSEQ=CAGGATGCGCACAGCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:113,244:357,0:0:2,0:28.9:1:32.4:1:1:0:43.4:70.4:1:0:0.1 0/1:281:3:2,1:99,179:278,3:0.0107:2,2:8:1:26:1:0.294:3.60:60:6:0.0108:0:1 +15 73995386 . C T 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00062;SOR=Inf;LSEQ=CCCCGTGCTGCAGCAGGATG;RSEQ=GCACAGCTCTGTCACCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:106,250:356,0:0:2,0:29.3:1:30.2:1:1:0:43.2:31.364:1:0:0.1 0/1:284:9:4,5:90,185:275,9:0.0317:2,2:29.4:1:30.6:1:0.48457:1.64:48.4:18:0.0323:0:1 +15 73995431 . G T 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00401;SOR=Inf;LSEQ=CCAGAGAAGCCCCACAGGTT;RSEQ=CTTTGCTTAAATGTCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:67,184:251,0:0:2,0:24.7:1:32.4:1:1:0:57.7:82.667:0.996:0:0.1 0/1:213:7:2,5:72,134:206,7:0.0329:2,2:27.1:1:28.4:1:1:1.34151:54.6:14:0.0333:0:1.1 +15 73995930 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.50921;SOR=0;LSEQ=ATTGATGGGGGAAGAGTTTG;RSEQ=GGGACTCGGGTGGTAGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:151,35:186,2:0.0106:2,2:16:1:30:1:0.34714:4.26801:60:4:0.0108:0:1 0/0:140:0:0,0:107,32:139,0:0:2,0:24.8:1:30.4:1:1:0:60:45.333:0.9927:0:0.1 +15 73995991 . C T 123 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=22.59767;LSEQ=CCACCCTGCCCCTCTGACCC;RSEQ=GCCCCCAGGAGCCGTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:1:0,1:326,165:491,1:0.002:2,0:1:0:26:0:0.3374:0:60:2:0.0021:0:1 0/1:431:19:11,8:253,159:412,19:0.0441:2,2:19.7:1:29.1:1:0.81171:1.15683:60:18:0.0424:0:1.2 +15 73996066 . G A 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGCACCGATGCCACCCTGC;RSEQ=CTGCTCCTTCTCCCCCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:731:0:0,0:416,314:730,0:0:2,0:24.4:1:30.8:1:1:0:46.3:80.111:0.9986:0:0.1 0/1:710:43:29,14:364,302:666,43:0.0606:2,2:23.7:1:29.1:1:0.11465:1.72:47:86:0.061:0:1.7 +15 73996101 . G A 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGAGCCTGGCTTCAGCCTG;RSEQ=CACAGCTCAACCTCATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:887:0:0,0:476,410:886,0:0:2,0:24.5:1:31.4:1:1:0:43.6:45.632:0.9988:0:0.1 0/1:844:61:34,27:416,366:782,61:0.0723:2,2:23.9:1:28.3:1:0.79015:1.11:48.8:60:0.0719:0:1.5 +15 73996359 . G A 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=GTGAGCACCAGGAGGGCGAC;RSEQ=CCTTCCCCTTGGTTCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:83,192:275,0:0:2,0:31.3:1:31.2:1:1:0:31:44.833:1:0:0.1 0/1:195:10:4,6:52,133:185,10:0.0513:2,2:25.4:1:29.5:1:0.47681:1.70:24.2:20:0.0524:0:1.2 +15 73996364 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00029;SOR=Inf;LSEQ=CACCAGGAGGGCGACGCCTT;RSEQ=CCCTTGGTTCACCCTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:95,203:298,0:0:2,0:30.6:1:31.4:1:1:0:30.6:58.6:1:0:0.1 0/1:207:9:5,4:55,143:198,9:0.0435:2,2:33.4:1:28.7:1:0.12486:3.23:27.3:8:0.039:0:1.1 +15 73996391 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06277;SOR=Inf;LSEQ=GTTCACCCTCCATTCCCTCT;RSEQ=CAGCCCACCCTCTGCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:130,243:373,0:0:2,0:24.3:1:32.3:1:1:0:29.4:92.25:1:0:0.1 0/1:247:3:1,2:85,158:243,3:0.0121:2,2:31.7:1:23.3:1:1:1.07564:27.7:2:0.0082:0:2.7 +15 73996462 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16117;SOR=Inf;LSEQ=TGTACTCAGCCCCATGCATC;RSEQ=TTTCCTCCCCTGCCATTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:68,54:122,0:0:2,0:22.1:1:31:1:1:0:26:121:0.9918:0:0.1 0/1:83:2:1,1:50,31:81,2:0.0241:2,2:9:1:29.6:1:1:1.60324:20:4:0.0244:0.012:0.5 +15 73996739 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49919;SOR=0;LSEQ=CCTGCGGGTGGTGCTGGGTG;RSEQ=GAATGGCACCTACAGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:85,114:199,2:0.01:2,2:22.5:1:31:0:1:1.34:23:4:0.0101:0:1.5 0/0:189:0:0,0:80,109:189,0:0:2,0:27.7:1:29.8:1:1:0:40:188:1:0:0.2 +15 73996766 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10691;SOR=Inf;LSEQ=CACCTACAGCTGCCTGGTGC;RSEQ=CAACCCCGTGCTGCAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:88,181:269,0:0:2,0:26.9:1:30.6:1:1:0:43.1:32.625:1:0:0.1 0/1:244:3:2,1:91,149:240,3:0.0123:2,2:25.3:1:28.3:1:0.56001:3.26:45.3:6:0.0124:0:1 +15 73996790 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09617;SOR=Inf;LSEQ=CCCCGTGCTGCAGCAGGATG;RSEQ=GCACGGCTCTGTCACCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:55,204:259,0:0:2,0:30.2:1:30:1:1:0:42.5:36:1:0:0.2 0/1:220:3:0,3:65,152:217,3:0.0136:2,0:9:1:28.3:1:0.55684:0:47.3:6:0.0139:0:1 +15 73996842 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1915;SOR=Inf;LSEQ=AGATGAACAGCTGGGGAAGG;RSEQ=CGGAGCGAGTAACTCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:21,138:159,0:0:2,0:22.8:1:29.9:1:1:0:58.8:52:1:0:0.1 0/1:125:2:1,1:26,97:123,2:0.016:2,2:41:0:32.5:1:0.38671:3.68:60:4:0.0161:0:1 +15 74000503 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01838;SOR=Inf;LSEQ=TGTCCACATCAGCCAGGGTT;RSEQ=TATCAGGGTTTGGGGAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:53,1:54,0:0:1,0:27.6:1:32.5:1:1:0:60:53:1:0:0.9 0/1:33:4:4,0:27,2:29,4:0.1212:2,0:21:1:29.3:1:1:0:60:8:0.1212:0:1 +15 74000506 . T G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00325;SOR=0.27874;LSEQ=CCACATCAGCCAGGGTTGTA;RSEQ=CAGGGTTTGGGGAGTGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:44:43,1:13,0:13,44:0.7586:1,1:25.9:1:33.5:1:1:0:60:88:0.7586:0:1.1 0/1:41:19:18,1:21,1:22,19:0.4634:1,1:15.6:1:31.6:1:1:1.16227:60:38:0.4872:0:1.2 +15 74000729 . G C 196 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=CTGTGGGTGACCGTGGGGCT;RSEQ=TCTGTCTGTCTCATTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1339:0:0,0:694,643:1337,0:0:2,0:25.8:1:32.3:1:1:0:60:101.846:0.9992:0:0.2 0/1:1293:89:46,43:644,553:1197,89:0.0688:2,2:27.6:1:30.4:1:0.74149:1.08854:60:43.5:0.0686:0:1.3 +15 74000839 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3371;LSEQ=GTGTGTGTGTATGTGTGTGC;RSEQ=TGCGCATGCACACTTATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:574:433:102,331:31,110:141,433:0.7544:2,2:23.9:1:30.8:1:0.7318:1.09:60:143.333:0.7544:0:1.1 1/0:478:243:60,183:62,173:235,243:0.5084:2,2:22.6:1:29.6:1:0.67633:1.09286:60:120.5:0.5074:0:1.1 +15 74001902 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25132;SOR=0;LSEQ=CACTCAGGCCCTGTTCACCA;RSEQ=CTTCCTGCACTCTCAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:183,71:254,3:0.0116:2,2:12.3:1:30:1:0.19518:5.11663:60:6:0.0118:0:1 0/0:228:0:0,0:166,62:228,0:0:2,0:22.8:1:31.5:1:1:0:60:113:1:0:0.1 +15 74001993 . T C 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCTTGCCTTTGCAGGAGC;RSEQ=GAGGACCAGGATGGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:759:0:0,0:412,346:758,0:0:2,0:26.5:1:31.1:1:1:0:60:83.222:0.9987:0:0.1 0/1:761:48:26,22:365,347:712,48:0.0631:2,2:27.1:1:29.4:1:0.76617:1.12:60:47:0.0627:0:2.1 +15 74002006 . G A 164 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=57.68213;LSEQ=CAGGAGCTGAGGACCAGGAT;RSEQ=GGGAGGGAGAAGGCTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:761:1:1,0:392,367:759,1:0.0013:2,0:1:0:24:0:1:0:60:2:0.0013:0:1 0/1:750:53:28,25:342,355:697,53:0.0707:2,2:22.5:1:28.7:1:0.66962:1.16:60:106:0.0711:0:2 +15 74002854 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGAGAGGCAGGTTTCC;RSEQ=CTGAGCCATTTGGGATGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:36.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 74003518 . A C 168 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=51.15379;LSEQ=TGACAGCAAAGAAGGTAAAG;RSEQ=CACCTGGGCTTGAGGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1037:1:1,0:446,590:1036,1:0.001:2,0:9:0:13:0:0.43105:0:60:0:0:0:6 0/1:891:42:18,24:372,477:849,42:0.0471:2,2:27:1:31.3:1:1:1.03979:60:84:0.0477:0:1.2 +15 74003533 . G A 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=58.28406;LSEQ=TAAAGACACCTGGGCTTGAG;RSEQ=TTGTGTCTGTGTATGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:964:1:1,0:399,564:963,1:0.001:2,0:24:0:12:0:0.41494:0:60:0:0:0:2 0/1:787:45:20,25:310,432:742,45:0.0572:2,2:22.3:1:28.7:1:0.75704:1.11:60:21.5:0.0555:0:1.2 +15 74003625 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15393;SOR=Inf;LSEQ=GACCTGAGGCCCCCTCTGCA;RSEQ=AAGAGCAGCCTCAACTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:34,195:229,0:0:2,0:21.3:1:32.5:1:1:0:60:75.333:0.9956:0:0.1 0/1:149:2:1,1:35,111:146,2:0.0134:2,2:22:1:30.5:1:0.42857:3.14:60:4:0.0135:0:1 +15 74005132 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11307;SOR=Inf;LSEQ=GCCGTGGTCAGCACGGGGGC;RSEQ=GTCCGTTGGGCTGCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:145,6:151,0:0:1,0:25.1:1:31.6:1:1:0:59.9:49.333:1:0:0.1 0/1:77:2:2,0:69,6:75,2:0.026:2,0:23:1:32:0:1:0:60:4:0.0267:0:1 +15 74005246 . CT C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.97647;LSEQ=ATCTAATGCTTTTCCCTTCC;RSEQ=TTTTTTTCTTCCCATCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:797:9:6,3:417,370:787,9:0.0113:2,2:18.9:1:32.4:1:0.51314:1.77:60:18:0.0115:0.0025:0.2 0/1:816:9:4,5:444,362:806,9:0.011:2,2:26:1:28:1:0.73854:1.53232:60:8:0.01:0.0025:0.2 +15 74005600 . C T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTTCTTAGGGACACAGTA;RSEQ=ACTGACCACATCACCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:0,11:0,1:1,11:0.9167:0,0:23.9:1:29:1:1:0:60:22:0.9167:0:1.1 1/1:4:4:1,3:0,0:0,4:1:0,2:26:1:29.3:1:1:0:60:8:1:0:1.3 +15 74567019 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12217;SOR=Inf;LSEQ=AGAAAATTAAGAACCAATCA;RSEQ=CAGGCTGTCCCAAGGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:122,143:265,0:0:2,0:27.4:1:32.6:1:1:0:60:65.25:1:0:0.7 0/1:262:3:2,1:120,139:259,3:0.0115:2,2:12.3:1:26.7:1:0.5994:2.31:60:6:0.0116:0:2.3 +15 74567025 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78969;SOR=0.94733;LSEQ=TTAAGAACCAATCAGCAGGC;RSEQ=GTCCCAAGGGGCAAGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:268:162:74,88:49,57:106,162:0.6045:2,2:24.8:1:30.7:1:1:1.02221:60:161:0.603:0:1.1 1/0:257:152:66,86:49,56:105,152:0.5914:2,2:26.6:1:29.4:1:0.61249:1.13957:60:75:0.5906:0:1.2 +15 74567036 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2485;SOR=0;LSEQ=TCAGCAGGCTGTCCCAAGGG;RSEQ=CAAGAGGCACTGCCTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:2,1:105,142:247,3:0.012:2,2:13.7:1:32:0:0.57778:2.69:60:6:0.0121:0:2.3 0/0:250:0:0,0:106,144:250,0:0:2,0:25.2:1:30.1:1:1:0:60:30.25:1:0:0.7 +15 74567042 . G A 101 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00524;SOR=10.66054;LSEQ=GGCTGTCCCAAGGGGCAAGA;RSEQ=GCACTGCCTGCTTTAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:1,0:97,147:244,1:0.0041:2,0:12:0:19:0:0.4:0:60:0:0:0:1 0/1:239:10:4,6:96,133:229,10:0.0418:2,2:33.9:1:30.6:1:1:1.08237:60:20:0.0424:0:1.1 +15 74567043 . G A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11811;SOR=Inf;LSEQ=GCTGTCCCAAGGGGCAAGAG;RSEQ=CACTGCCTGCTTTAATGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:98,147:245,0:0:2,0:24.2:1:31.8:1:1:0:60:48:1:0:0.7 0/1:237:3:2,1:98,136:234,3:0.0127:2,2:35.7:1:23:1:0.57474:2.76:60:2:0.0087:0:2 +15 74567061 . A G 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12227;SOR=Inf;LSEQ=AGGCACTGCCTGCTTTAATG;RSEQ=GTGTGCCCCCTCCCACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:70,136:206,0:0:2,0:23.5:1:30.9:1:1:0:60:40.2:1:0:0.6 0/1:204:3:1,2:75,126:201,3:0.0147:2,2:14:1:29.3:1:1:1.18952:60:6:0.0155:0:2 +15 74567064 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49873;SOR=Inf;LSEQ=CACTGCCTGCTTTAATGAGT;RSEQ=TGCCCCCTCCCACCCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:61,136:197,0:0:2,0:23.7:1:32.1:1:1:0:59.9:196:1:0:0.6 0/1:197:2:1,1:72,123:195,2:0.0102:2,2:15.5:1:27.5:1:1:1.70:60:4:0.0105:0:2 +15 74567129 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22658;SOR=Inf;LSEQ=TAACTAGTCTGGGTAGGAGA;RSEQ=GTGCCACTCACTACAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:6,65:71,0:0:2,0:24.1:1:31.7:1:1:0:59.9:142:1:0:0.1 0/1:65:2:1,1:12,51:63,2:0.0308:2,2:26:1:30.5:1:0.3625:4.12:60:4:0.0313:0:1 +15 75094100 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=Inf;LSEQ=TGCATCGAGACCTGGCTGCC;RSEQ=GCAATGTGCTGGTGTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:68,63:131,0:0:2,0:26.7:1:30.7:1:1:0:58.4:130:1:0:0.1 0/1:145:2:1,1:75,68:143,2:0.0138:2,2:30.5:1:30.5:1:1:1.10219:60:4:0.0139:0:1.5 +15 75094101 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22437;SOR=0;LSEQ=GCATCGAGACCTGGCTGCCC;RSEQ=CAATGTGCTGGTGTCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:67,62:129,2:0.0153:2,2:11:1:30:1:1:1.07998:60:4:0.0154:0:1 0/0:145:0:0,0:76,69:145,0:0:2,0:28:1:30.5:1:1:0:59.4:144:1:0:0.1 +15 75095483 . T C 40 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCCTTGTGAGATGGAAT;RSEQ=GTAATAAACCACGCCATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:21:1:25.3:1:1:0:60:2:1:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 76023637 . A G 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=2;SSF=0.72456;SOR=1.54299;LSEQ=AGACCCACACCTTACTCTAC;RSEQ=CACACACACCTGGTACCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:14,14:28,5:0.1515:2,2:37.6:1:32:1:1:1.48182:35.6:10:0.1515:0:1.2 0/1:23:5:2,3:11,6:17,5:0.2174:2,2:14.8:1:30:1:0.60902:2.61967:60:10:0.2174:0:1.4 +15 76023673 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49209;SOR=0;LSEQ=CCACCACTGCCTTCAAACAC;RSEQ=CTGCCCCATCCCTCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:13,16:29,2:0.0645:2,2:16:0:32:0:1:1.22:36:4:0.0645:0:1.5 0/0:29:0:0,0:14,15:29,0:0:2,0:30.2:1:29.1:1:1:0:57.8:28:1:0:0.6 +15 76023721 . T C 117 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.04564;SOR=0;LSEQ=TCATCTCATGCACAGATACG;RSEQ=GCCCACCCAGGCTCACTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:0,15:1:0,2:23.5:1:30.1:1:1:0:57.1:14:1:0:1.1 1/0:17:12:5,7:0,5:5,12:0.7059:0,2:15.3:1:30.1:1:0.24451:0:60:24:0.7059:0:1.4 +15 77033879 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19656;SOR=0;LSEQ=TCAACTGTAAATATTTAGGA;RSEQ=GGAGATAAAAATAAACTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:2,0:89,68:157,2:0.0126:2,0:30.5:1:32:1:0.50736:0:60:4:0.0127:0:1 0/0:199:0:0,0:113,86:199,0:0:2,0:26.1:1:30.7:1:1:0:60:198:1:0:0.3 +15 77033880 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19848;SOR=0;LSEQ=CAACTGTAAATATTTAGGAG;RSEQ=GAGATAAAAATAAACTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:92,68:160,2:0.0123:2,2:38:0:31.5:1:1:1.35037:60:4:0.0124:0:1 0/0:201:0:0,0:111,88:199,0:0:2,0:25.8:1:29.7:1:1:0:60:27.429:0.9897:0:0.3 +15 77033898 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25743;SOR=Inf;LSEQ=AGGGAGATAAAAATAAACTG;RSEQ=TGGCAGCTGCAATGGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:82,71:153,0:0:2,0:25.2:1:31.8:1:1:0:59.8:75.5:1:0:0.1 0/1:192:3:3,0:102,87:189,3:0.0156:2,0:14:1:26.3:1:0.2527:0:60:6:0.0159:0:1 +15 77033900 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2023;SOR=0;LSEQ=GGAGATAAAAATAAACTGGT;RSEQ=GCAGCTGCAATGGAAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:0,2:83,70:153,2:0.0129:2,0:23:1:29.5:1:0.21416:0:60:4:0.0132:0:1 0/0:189:0:0,0:102,87:189,0:0:2,0:26.6:1:30.9:1:1:0:60:93.5:1:0:0.3 +15 77033934 . G A 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=4.38387;LSEQ=AAAATGTAGCTGCCTACAGA;RSEQ=TTAGAGAACTGCAGGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:10:4,6:81,74:155,10:0.0606:2,2:25.3:1:32:1:0.52571:1.63698:60:20:0.061:0:1 0/1:199:44:20,24:79,76:155,44:0.2211:2,2:22.4:1:29.4:1:0.60892:1.24598:60:88:0.2211:0:1.2 +15 77033958 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24239;SOR=0;LSEQ=GAGAACTGCAGGTGTATGTA;RSEQ=ACATAGGACTCCAAAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:79,96:175,2:0.0113:2,2:35.5:1:31:1:1:1.21:60:4:0.0114:0:1 0/0:182:0:0,0:85,97:182,0:0:2,0:27.1:1:28.5:1:1:0:60:181:1:0:0.4 +15 77034023 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49744;SOR=Inf;LSEQ=TCTGGCTGATACACAAAAAG;RSEQ=TGTCAAGAAGAGATTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:21,74:95,0:0:2,0:22.6:1:29.7:1:1:0:60:18:1:0:0 0/1:97:2:1,1:30,65:95,2:0.0206:2,2:24.5:1:29:1:0.5393:2.15:60:4:0.0211:0:1.5 +15 77034175 . G A 62 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GATAAAGGAGATGGTGAGCT;RSEQ=ATGAGTTCCACTCAATACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:22:1:31:1:1:0:53.5:8:0.5714:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:49:0:29:0:1:0:60:2:1:0:1 +15 78163623 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTTGAGGGGGGCTCCTG;RSEQ=TCACCTCCCCACCCCATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:35.5:1:32:0:1:0:35.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 78164594 . T C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.02508;SOR=Inf;LSEQ=CGCCAGTGAGCCTGGGTGGG;RSEQ=GCATATCTGTGCAGGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:86,4:90,0:0:1,0:24.1:1:29.6:1:1:0:60:44:1:0:0.4 0/1:61:4:4,0:52,5:57,4:0.0656:2,0:17:1:33:1:1:0:60:8:0.0667:0:2 +15 78164597 . A G 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03538;SOR=8.17609;LSEQ=CAGTGAGCCTGGGTGGGTGC;RSEQ=TATCTGTGCAGGAGATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:1,0:92,4:96,1:0.0103:1,0:46:0:30:0:1:0:59:2:0.011:0:1 0/1:63:5:4,1:53,5:58,5:0.0794:2,2:16.6:1:30.2:1:0.4043:2.59415:60:10:0.082:0:1.8 +15 78164645 . TG T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.26521;SOR=0;LSEQ=GAGAGAGGGACGGGGTGGGG;RSEQ=GGGGGAGTAAGAGGTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:178,88:266,3:0.0112:2,2:17:1:32.3:1:1:1.01133:60:6:0.0115:0.0037:1.3 0/0:199:0:0,0:130,68:198,0:0:2,0:23:1:31:1:1:0:60:197:1:0:0.5 +15 78164649 . G T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.31766;SOR=4.05633;LSEQ=GAGGGACGGGGTGGGGTGGG;RSEQ=GGAGTAAGAGGTGTGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:1:0,1:184,98:282,1:0.0035:2,0:1:0:26:0:0.34982:0:60:2:0.0036:0:1 0/1:211:3:1,2:134,74:208,3:0.0142:2,2:15.7:1:27.3:1:0.29482:3.59843:60:6:0.0145:0:1.3 +15 78164706 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.39196;LSEQ=GTGCGCATGTGTGGTATAAG;RSEQ=GTGGGTCGCGTCTGCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:83:47,36:230,181:411,83:0.167:2,2:21:1:30.9:1:1:1.03:60:40.5:0.167:0:1.3 0/1:444:144:77,67:160,139:299,144:0.3243:2,2:24.6:1:29.9:1:1:1.00158:60:71:0.3279:0:1.2 +15 78164773 . GGT G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1e-05;SOR=6.46297;LSEQ=TGAAGGCAGTGGTGGTACCA;RSEQ=GTGTGTGTGTGGAGTAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:5:1,4:131,204:335,5:0.0147:2,2:27.4:1:28.1:1:0.65232:2.56253:48:4:0.012:0.0029:1.2 0/1:364:32:11,21:139,193:332,32:0.0879:2,2:30.6:1:31.1:1:0.45673:1.37377:48.8:31:0.0868:0:0.2 +15 78164805 . T C 232 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.027;LSEQ=TGGAGTAAGGTGTGGGTCTG;RSEQ=GCATTTGTGTGTGTGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:215:213:47,166:0,0:0,213:0.9907:0,2:21.5:1:30.1:1:1:0:49.9:41.6:0.9905:0:1.1 1/0:189:140:44,96:15,34:49,140:0.7407:2,2:21.5:1:29.1:1:1:1.04:45.4:27:0.7377:0:1.2 +15 78164810 . T TTG 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.2226;SOR=Inf;LSEQ=TAAGGTGTGGGTCTGTGCAT;RSEQ=TGTGTGTGTGTCTTGCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:42,150:192,0:0:2,0:21.2:1:30.1:1:1:0:48.5:47:1:0:1.1 0/1:172:2:1,1:51,119:170,2:0.0116:2,2:34:1:30.5:1:0.51448:2.32:45:4:0.012:0:1.5 +15 78164840 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0523;SOR=Inf;LSEQ=GTCTTGCTCCACGTGTGTGC;RSEQ=GTAAGGGACATGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:4,74:78,0:0:2,0:26.7:1:31.7:1:1:0:39.2:156:1:0:1 0/1:73:4:0,4:14,55:69,4:0.0548:2,0:30.3:1:30.8:1:1:0:33.8:8:0.0556:0:1.8 +15 79155088 . C T 45 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGAAAGCCATGTGCAGA;RSEQ=GAAGGCAGAAACTGGGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:13:1:29:1:1:0:60:6:1:0:1 +15 79155946 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49484;SOR=Inf;LSEQ=TGAACAGTACCCATTCCCTT;RSEQ=ATGTCTACAATATCACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:14,23:37,0:0:2,0:7.9:1:32:1:1:0:21.3:74:1:0:0.1 0/1:41:2:1,1:19,20:39,2:0.0488:2,2:6.5:1:27:1:1:1.05:23:4:0.05:0:1 +15 80448068 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50603;SOR=Inf;LSEQ=CACACAAGACAAGGGGGGCA;RSEQ=GGTAGGGAGGGTGAGTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:34,21:55,0:0:2,0:24.3:1:31.9:1:1:0:53.4:26.5:1:0:0.2 0/1:73:2:1,1:42,29:71,2:0.0274:2,2:15:1:29:1:1:1.44076:50:4:0.0274:0:1 +15 81411834 . C T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57576;SOR=2.74155;LSEQ=AAATTAACAGATTTTAATAA;RSEQ=GTTATATAATTTTTGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:2,1:3,4:0.5714:2,0:17:1:32.3:1:0.42857:0:60:8:0.5714:0:1.5 1/1:5:4:4,0:0,1:1,4:0.8:0,0:16.3:1:30:1:0.2:0:60:8:0.8:0:1.5 +15 81411917 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49306;SOR=Inf;LSEQ=CAGCACCACTTACCATTTGG;RSEQ=AATGGCTCCCATACAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:23,0:0:2,0:27.1:1:31.6:1:1:0:60:46:1:0:0.7 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:28:1:26.5:1:1:1.0801:60:4:0.0741:0:2 +15 81411922 . G C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03058;SOR=6.00757;LSEQ=CCACTTACCATTTGGCAATG;RSEQ=CTCCCATACAATTTACCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:6,8:3,4:7,14:0.6667:2,2:30.7:1:30.6:1:1:1:60:28:0.7:0:1.1 1/1:27:25:13,12:1,1:2,25:0.9259:2,2:34.9:1:30.7:1:1:1.08:60:50:0.9259:0:1.3 +15 86582918 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49153;SOR=Inf;LSEQ=TCTTCACTTCACCAAACTTT;RSEQ=GTCAGGATCCTGAACCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:29,0:0:2,0:26:1:28.9:1:1:0:60:28:1:0:0.2 0/1:30:2:1,1:17,11:28,2:0.0667:2,2:8.5:1:29:1:1:1.52251:60:4:0.0667:0:1.5 +15 86582925 . A C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25622;SOR=Inf;LSEQ=TTCACCAAACTTTAGTCAGG;RSEQ=TCCTGAACCTTCTCCAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:20,12:32,0:0:2,0:26:1:30.3:1:1:0:60:64:1:0:0.2 0/1:43:3:2,1:22,17:39,3:0.0698:2,2:28:1:31.7:1:1:1.53:60:6:0.0714:0:1 +15 86583133 . A G 91 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02564;SOR=0;LSEQ=AGCCAGAATCCCCCTTACCC;RSEQ=TGAGGATGTTCCCTCTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:2,6:0,0:0,8:1:0,2:28.1:1:30.5:1:1:0:60:16:1:0:1.8 0/1:7:3:1,2:1,3:4,3:0.4286:2,2:41.7:1:31.3:1:1:1.41:60:6:0.4286:0:2 +15 87255595 . C CT 134 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.83232;SOR=1.11509;LSEQ=GATTACAGAGACGATGTGTA;RSEQ=TTTTTTTTTTTTTAATTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:18:17,1:47,0:47,18:0.2609:1,1:21.6:1:32.2:1:0.27692:0:58.9:36:0.2647:0.087:1.2 0/1:46:13:12,1:33,0:33,13:0.2826:1,1:21.5:1:31.1:1:0.28261:0:59.2:26:0.2826:0.0217:0.8 +15 87255699 . C T 72 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0143;SOR=Inf;LSEQ=GAGATTAGGCAATTGGGCTT;RSEQ=AAAGTGGAATATGAAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:239,158:397,0:0:2,0:25.1:1:31.9:1:1:0:60:65.167:1:0:0.8 0/1:388:6:2,4:219,162:381,6:0.0155:2,2:5.8:1:28:1:0.40879:2.69681:57.3:12:0.0157:0:1.7 +15 87255720 . A C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00113;SOR=0.64548;LSEQ=AAAGTGGAATATGAAACTTA;RSEQ=TGTGGCTAAGTGATGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:452:249:139,110:100,102:202,249:0.5509:2,2:24.3:1:32.4:1:0.1857:1.29:59.9:61.25:0.5543:0:1.1 0/1:455:201:108,93:142,112:254,201:0.4418:2,2:27.2:1:30.9:1:0.7044:1.09155:59.9:66:0.443:0:1.2 +15 87255748 . A C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.10142;SOR=0.80231;LSEQ=AAGTGATGCACTTGGGTAGA;RSEQ=ATAATGCCCAGGCTAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:200:92,108:128,132:260,200:0.4338:2,2:27.4:1:32.3:1:0.51086:1.13802:60:199:0.4374:0:1.1 0/1:507:193:91,102:157,156:313,193:0.3807:2,2:27.7:1:31.4:1:0.52288:1.12779:60:192:0.3802:0:1.1 +15 87255833 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2416;SOR=Inf;LSEQ=TCCGCCTGTACTCTGAGAAT;RSEQ=AACATTTACATTTTGGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:45,150:195,0:0:2,0:24.9:1:32:1:1:0:59.8:64:1:0:0.2 0/1:189:2:1,1:50,137:187,2:0.0106:2,2:18:1:26.5:1:0.46792:2.72:60:4:0.0107:0:2 +15 87255983 . C T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39451;SOR=0.34745;LSEQ=CAAGGCATCTGGTCCAATTC;RSEQ=GGACTCATTAAGTAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:0,9:0,9:9,9:0.5:0,0:13.6:1:28.8:1:1:0:60:8:0.4706:0:1.1 0/1:8:2:0,2:1,5:6,2:0.25:2,0:17:1:28.5:1:1:0:60:4:0.25:0:1.5 +15 88125886 . GT G 51 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCCCTAAAATTGGAGGG;RSEQ=TTTTTTTTTTTTTTGGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:21.7:1:32.7:1:1:0:60:6:0.375:0.125:0.3 0/0:2:0:0,0:2,0:2,0:0:0,0:24:1:31.5:1:1:0:60:4:1:0:3 +15 88125977 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49643;SOR=Inf;LSEQ=GCAATGCACCTGTTTGGTGT;RSEQ=TGGCACTCAGGAGATACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:49,2:51,0:0:1,0:25.1:1:32.1:1:1:0:60:50:0.9804:0:0 0/1:57:2:2,0:52,3:55,2:0.0351:2,0:31.5:1:32.5:1:1:0:60:4:0.0351:0:1 +15 88126035 . G T 49 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12329;SOR=Inf;LSEQ=AACTAGATCTAGACAGCCAT;RSEQ=GGAAAAGAACAACAGGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:139,49:188,0:0:2,0:24.6:1:32.3:1:1:0:60:187:1:0:0.2 0/1:195:4:1,3:142,49:191,4:0.0205:2,2:6.3:1:24.8:1:0.05874:8.57858:60:3:0.0157:0:1 +15 88126117 . G T 202 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00403;LSEQ=AATGCTACCTCTGGGAATCG;RSEQ=ATCATTCAGGAAAAGACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:130:66,64:94,100:194,130:0.3976:2,2:25.9:1:28.8:1:0.73413:1.10:59.7:64:0.4:0:1.2 0/0:379:1:0,1:173,204:377,1:0.0026:2,0:44:0:30:0:1:0:60:2:0.0027:0:1 +15 88126129 . A C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=1.99372;LSEQ=GGGAATCGGATCATTCAGGA;RSEQ=AAGACACCGGCTGCTCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:74:34,40:119,130:249,74:0.2284:2,2:25.4:1:31.7:1:0.79253:1.07665:60:36:0.2271:0:1.2 0/1:377:140:65,75:99,138:237,140:0.3714:2,2:24.5:1:31.1:1:0.39146:1.21:60:69:0.373:0:1.2 +15 88126191 . C T 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGACAAAAAGAATCCTGC;RSEQ=GGAAGCTGATTAGGCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:53,115:168,0:0:2,0:22.9:1:30.2:1:1:0:59.8:55:1:0:0.4 0/1:170:35:12,23:45,90:135,35:0.2059:2,2:22.6:1:29.6:1:1:1.04:60:70:0.2108:0:1.1 +15 88126196 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24278;SOR=Inf;LSEQ=CAAAAAGAATCCTGCCGGAA;RSEQ=CTGATTAGGCCAGACAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:40,117:157,0:0:2,0:22:1:32.2:1:1:0:60:77.5:1:0:0.4 0/1:153:2:1,1:50,100:150,2:0.0131:2,2:21.5:1:28.5:1:1:1.99:60:4:0.0132:0:1 +15 88126197 . C A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=AAAAAGAATCCTGCCGGAAG;RSEQ=TGATTAGGCCAGACAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:40,117:157,0:0:2,0:21.6:1:32.3:1:1:0:60:30.4:1:0:0.4 0/1:150:12:3,9:46,92:138,12:0.08:2,2:26:1:29.7:1:0.75166:1.49621:60:24:0.0805:0:1.1 +15 88126291 . A C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0336;SOR=3.46417;LSEQ=TTCAGAGAAAAGGAGGCACC;RSEQ=TTGATATAAATAACACTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:16:0,16:0,20:20,16:0.4444:1,1:13.4:1:33.4:1:1:0:60:32:0.4444:0:1.1 1/0:23:17:1,16:0,6:6,17:0.7391:0,1:20.5:1:32:1:1:0:60:34:0.7391:0:1.1 +15 88311418 . C A 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.47868;LSEQ=TTTCCCCCCAGCAAAGCACA;RSEQ=CCCCTCCACCAAGGACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:9,6:15,2:0.1176:2,0:39.5:1:31:1:0.51471:0:58.5:4:0.1176:0:1.5 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:39:1:29:1:1:1.4491:60:4:0.1667:0:1.5 +15 88311747 . T C 51 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AATAAACAAACAGAAAGCAA;RSEQ=AATAGCATCAACAACAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:6,2:0.25:2,2:37.5:1:32.5:1:1:1.83:50.5:4:0.25:0:2 0/1:12:3:1,2:2,7:9,3:0.25:2,2:26:1:32.3:1:1:1.66:53:6:0.25:0:1.7 +15 88311755 . T TCAA 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=0.57471;LSEQ=AACAGAAAGCAATAATAGCA;RSEQ=CAACAACAACAAAAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:40:1:32.3:1:1:1.41:50.5:4:0.2857:0:2 0/1:11:2:1,1:2,7:9,2:0.1818:2,2:36.5:1:29.5:1:0.49091:3.06:49.5:4:0.1818:0:2 +15 88311773 . A G 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.61991;SOR=2.00863;LSEQ=CATCAACAACAACAAAAAAA;RSEQ=ACCCCACAAAAACCCTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:1,2:3,5:0.625:2,2:24.2:1:32:1:1:1.29:56.2:10:0.625:0:1.4 1/0:9:7:2,5:1,1:2,7:0.7778:2,2:28:1:29.1:1:1:2.23609:57:14:0.7778:0:1.4 +15 88419947 . AAT A 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=11.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAGATAGTTAGATATATA;RSEQ=ATATATATATATATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:3,1:13,0:13,4:0.2353:1,2:14:1:32.3:1:0.23529:0:60:8:0.25:0:0.3 0/0:3:0:0,0:3,0:3,0:0:0,0:21.3:1:30.3:1:1:0:60:6:1:0:0.7 +15 88420004 . C CT 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.77654;LSEQ=TACAGGGTTTTTTTTTCTTT;RSEQ=TTTTTTTTTCCTTTTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:2,0:46,1:47,2:0.04:1,0:40:1:33.5:1:1:0:60:4:0.0426:0:0.5 0/1:32:1:1,0:30,1:31,1:0.0313:1,0:34:0:32:0:1:0:60:2:0.0323:0:1 +15 88420286 . G A 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06953;SOR=7.02268;LSEQ=CAGCACCCCAGCATGACATC;RSEQ=TACACCTCTTTGGGGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:1:1,0:288,406:694,1:0.0014:2,0:1:0:25:0:0.41583:0:60:2:0.0015:0:1 0/1:698:7:6,1:291,400:691,7:0.01:2,2:9.7:1:25.1:1:0.046:8.23:60:6:0.0087:0:1.3 +15 88423051 . C T 61 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGTTCACACATGACTCTA;RSEQ=CAGTTATAAAACTGGTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:32.8:1:30.5:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 88423336 . A AT 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.79138;SOR=1.14349;LSEQ=ACCACATTTCCTACAGTTCC;RSEQ=TTTTTTTTTTCCTACTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:12:12,0:101,1:102,12:0.1043:1,0:26.6:1:32.1:1:1:0:60:24:0.1071:0.0261:0.3 0/1:51:6:6,0:44,1:45,6:0.1176:1,0:24.5:1:29.7:1:1:0:55:12:0.1176:0:0.2 +15 88423463 . C T 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.22457;LSEQ=CTGAGATAGCTCTTATGAGC;RSEQ=CTCCCCCAATCAAGATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:835:664:421,243:101,69:170,664:0.7952:2,2:24.9:1:30.9:1:0.37447:1.18:60:46.429:0.7956:0:1.1 0/1:668:311:187,124:217,139:356,311:0.4656:2,2:25.9:1:29.2:1:0.87385:1.03517:60:37.875:0.4647:0:1.1 +15 88423710 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21162;SOR=Inf;LSEQ=GTGACCAGATGGCCAGAATG;RSEQ=GTGTTATCTGTCTGCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:13,193:206,0:0:2,0:23.8:1:32.2:1:1:0:60:102:1:0:0.1 0/1:176:2:1,1:26,148:174,2:0.0114:2,2:27:1:28.5:1:0.28403:5.60:60:4:0.0115:0:1 +15 88428702 . C A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.19167;LSEQ=ATACTTGAAATAGAACAATA;RSEQ=GGGAGAGTTACTCTATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:113:90:90,0:21,0:21,90:0.7965:1,1:22.4:1:30.8:1:1:0:60:89:0.7946:0:1 0/1:47:20:20,0:27,0:27,20:0.4255:1,1:25.5:1:28.7:1:1:0:60:9:0.4:0:1.1 +15 88428899 . T TA 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01079;SOR=1.92186;LSEQ=TGGGACAATGAACTATTCAT;RSEQ=AAAAAAAATACGCTTAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1755:24:11,13:907,824:1731,24:0.0137:2,2:29.9:1:29.9:1:0.54407:1.30066:60:48:0.0138:0.0023:0 0/1:1772:46:22,24:874,849:1723,46:0.026:2,2:27.8:1:29:1:0.76583:1.12296:60:92:0.0262:0.0017:0.2 +15 88429076 . A G 223 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACACATGTTCAAGAAGCC;RSEQ=TCAAGAATAAGATTTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:118:118:0,118:0,0:0,118:1:0,1:23.8:1:32.5:1:1:0:60:28.5:1:0:1.1 1/0:55:31:1,30:0,24:24,31:0.5636:1,1:21.7:1:31.5:1:1:0:60:62:0.5741:0:1 +15 88429142 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06633;SOR=Inf;LSEQ=TTGCATGGCAAAAGACAACA;RSEQ=AAGCATAGCTAAAAGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,35:35,0:0:1,0:27.3:1:28.5:1:1:0:58.4:70:0.9722:0:0.5 0/1:13:2:0,2:0,11:11,2:0.1538:0,0:29.5:1:33.5:1:1:0:60:4:0.1538:0:1 +15 88459632 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14625;SOR=Inf;LSEQ=CTCCACAGGAGTAGAGAGAC;RSEQ=TGAATGACTCAACACCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:105,4:109,0:0:1,0:21.3:1:29.8:1:1:0:60:53.5:1:0:0.1 0/1:68:2:2,0:66,0:66,2:0.0294:1,0:17.5:1:27.5:1:1:0:60:4:0.0294:0:1 +15 88459695 . A T 57 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18661;SOR=4.71286;LSEQ=TCCTCTCCTTTCCCGAGGAC;RSEQ=GAATCCAATATAAGCATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:1:0,1:279,100:379,1:0.0026:2,0:1:0:26:0:0.26579:0:60:2:0.0027:0:1 0/1:325:4:1,3:234,87:321,4:0.0123:2,2:5:1:28.5:1:0.0661:8.00848:60:8:0.0124:0:1 +15 88459998 . CT C 65 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.64239;SOR=1.94933;LSEQ=TACCTATGAAAAGCACAAGG;RSEQ=TTTTTTTTTTTTAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:0,4:0,16:16,4:0.2:1,0:32:1:32.8:1:1:0:60:8:0.2:0:0.3 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:34:1:32.7:1:1:0:60:6:0.375:0:0 +15 88472228 . G T 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16588;SOR=0;LSEQ=TGTCCAAGAAGAAAGAAGGA;RSEQ=TGGGCAATTGAGAACATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:6:6,0:35,0:35,6:0.1463:1,0:27.7:1:32.5:1:1:0:60:12:0.15:0:1 0/0:17:0:0,0:17,0:17,0:0:1,0:16.6:1:32.5:1:1:0:60:34:1:0:0.1 +15 88472341 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08201;SOR=Inf;LSEQ=ATGTGTGTGCCAGAGTGACA;RSEQ=GGTTAATGGACAATGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:195,38:233,0:0:2,0:24.7:1:32.9:1:1:0:60:76.667:1:0:0.1 0/1:180:3:2,1:143,34:177,3:0.0167:2,2:18:1:28:1:0.47938:2.09245:60:6:0.0167:0:1 +15 88472655 . G T 226 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACAAGGATCATTGCATCTG;RSEQ=CCCATGGGCCCTGCAAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:195:52,143:91,208:299,195:0.3947:2,2:23.7:1:29.8:1:0.41699:1.20268:60:47.75:0.3979:0:1.1 0/0:375:0:0,0:112,262:374,0:0:2,0:24.1:1:31:1:1:0:59.9:40.556:0.9973:0:0.2 +15 88472697 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12327;SOR=Inf;LSEQ=TGGGGAGAAGAGAGGGGGCA;RSEQ=AGAGAAATCAGGAGATCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:53,226:279,0:0:2,0:24.3:1:32.2:1:1:0:59.9:54.8:0.9964:0:0.4 0/1:152:2:1,1:28,122:150,2:0.0132:2,2:29.5:1:27:1:0.3462:4.30:60:4:0.0132:0:1 +15 88472729 . T A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATCAAGGAGAAAGGCCT;RSEQ=CCTGGGTCCCTGCCCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:9,142:151,2:0.0131:2,2:9:1:26.5:1:0.12685:15.02:60:4:0.0132:0:1 0/0:73:0:0,0:7,66:73,0:0:2,0:24.6:1:28.9:1:1:0:60:146:1:0:0.1 +15 88476518 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53165;SOR=0;LSEQ=ACACACCACTGGGTTACCAA;RSEQ=AAATATGAATCTAAATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:1,73:74,2:0.0263:1,2:17.5:1:33.5:1:0.05228:51.98:60:4:0.0267:0:1.5 0/0:44:0:0,0:0,44:44,0:0:1,0:20.3:1:27.3:1:1:0:60:43:1:0:0.1 +15 88483456 . T C 49 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCCTCCTTAATCAGCC;RSEQ=GCTCTACAACAGCTCAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:44.7:1:31.3:1:1:0:50:6:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:28:1:1:0:60:4:1:0:1 +15 88485503 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCTGACGACCGCTCCTC;RSEQ=CAAGCCACAGGCTGCAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 88522524 . A G 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07325;SOR=Inf;LSEQ=TAGAGCTTCCAACCTCTCAG;RSEQ=GGGCCCAGCCTACCAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:300,117:417,0:0:2,0:24.3:1:30.4:1:1:0:60:103.25:1:0:0.1 0/1:301:3:2,1:214,84:298,3:0.01:2,2:31:1:26:1:1:1.27277:60:2:0.0068:0:1 +15 88522711 . G GA 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.99967;LSEQ=AAACCTATAAAAAACAAAAA;RSEQ=AAAAAAAAACAGAAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:28:8,20:98,292:390,28:0.0665:2,2:26:1:30.4:1:0.65778:1.19:60:56:0.0698:0:0.1 0/1:376:25:10,15:99,248:347,25:0.0665:2,2:23.7:1:27.8:1:0.25605:1.67:58.2:24:0.067:0.008:0.6 +15 88522723 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.03696;SOR=Inf;LSEQ=AACAAAAAGAAAAAAAAACA;RSEQ=AAAAAAGCAAAATAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:64,285:349,0:0:2,0:22.9:1:31.9:1:1:0:59.9:28.083:1:0:0.2 0/1:274:4:3,1:63,206:269,4:0.0146:2,2:8:1:27:1:0.04502:9.70:60:8:0.0148:0:1 +15 88523033 . G T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGAAAGGAGGAGACCCT;RSEQ=ACGATGAGCTGAGGGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:33:1:30:0:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 88523035 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAAGGAGGAGACCCTGA;RSEQ=GATGAGCTGAGGGGTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:31:1:32.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 88524624 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10317;SOR=Inf;LSEQ=GCAGACATGGGGGAATTAAT;RSEQ=GTCAGTATTAAACCCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:56,261:317,0:0:2,0:25.5:1:31.8:1:1:0:60:157.5:1:0:0.1 0/1:281:3:2,1:69,209:278,3:0.0107:2,2:15.3:1:26:1:0.15826:6.01:60:6:0.0108:0:1 +15 88524788 . A G 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03324;SOR=0;LSEQ=ATCTAGATCCTAAGAATCTC;RSEQ=CCCTGGCATTATAGAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:12,8:0.4:0,0:23.1:1:33.9:1:1:0:60:16:0.4:0:1 0/0:9:0:0,0:0,9:9,0:0:0,0:29.6:1:30.2:1:1:0:60:18:1:0:0 +15 88576090 . G A 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=26.02466;LSEQ=TTCCATCCCAGTACTTACAC;RSEQ=TGTCCGGCTTGTGGCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:875:2:1,1:476,396:872,2:0.0023:2,2:21:1:14.5:1:1:1.20176:60:0:0:0:1 0/1:870:49:23,26:450,370:820,49:0.0563:2,2:27.9:1:29.6:1:0.30324:1.37433:60:48:0.0558:0:1.2 +15 88576185 . G C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01024;SOR=0.75861;LSEQ=ATGACCACAGTGTCGGGCCC;RSEQ=GCATCCAGTGACGAGGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:674:386:160,226:117,169:286,386:0.5727:2,2:25.6:1:30.3:1:0.93685:1.02:60:63.333:0.5723:0:1.2 1/0:732:369:164,205:164,195:359,369:0.5041:2,2:24.4:1:29.2:1:0.76589:1.05118:60:40:0.5028:0:1.1 +15 88576215 . G A 194 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=99.96749;LSEQ=GACGAGGGCGTGGTGATGCC;RSEQ=TGGTTGATGTGGTGCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:1:1,0:245,358:603,1:0.0017:2,0:1:0:31:0:0.40728:0:54:2:0.0017:0:2 0/1:681:97:48,49:251,333:584,97:0.1424:2,2:25.2:1:29.4:1:0.26927:1.30:59.3:23.25:0.1386:0:1.3 +15 88576339 . T A 22 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50074;SOR=0;LSEQ=CCGGCCAGTTTCCAGCCCTG;RSEQ=CCACAGACAACCCCCAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:12,93:105,2:0.0187:2,2:21.5:1:22.5:1:0.22924:7.49:60:4:0.019:0:1 0/0:91:0:0,0:12,79:91,0:0:2,0:26.8:1:28.6:1:1:0:60:90:1:0:0.1 +15 88576408 . TATATATATATATATAT C 104 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=24;MSI=20.000;MSILEN=2;SSF=0.0129;SOR=0;LSEQ=TTTACTTTTGGGGGGTGTGT;RSEQ=ATATATATATATATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:0,11:0,7:7,11:0.4783:0,0:15.6:1:30.3:1:1:0:54.2:10:0.4762:0.3043:0.7 0/0:10:0:0,0:0,6:6,0:0:0,0:7:1:28.8:1:1:0:60:12:0.6:0:0 +15 88610388 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5016;SOR=0;LSEQ=CCTTCCCTTGGATCAGTTCC;RSEQ=TGCAACACGTGGTGCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:109,49:158,2:0.0125:2,2:10:1:28:1:0.52869:2.21225:60:4:0.0127:0:2 0/0:136:0:0,0:89,47:136,0:0:2,0:26.4:1:29.6:1:1:0:60:135:1:0:0.4 +15 88610457 . C T 244 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02238;LSEQ=GAGTTGTACAGACTCCCACA;RSEQ=GCCATTTTTTTTCACTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:247:244:115,129:0,0:0,244:0.9879:0,2:26.7:1:30.8:1:1:0:60:60:0.9877:0:1.2 1/0:267:172:83,89:39,50:89,172:0.6442:2,2:28.7:1:29.6:1:0.51544:1.19:60:56.333:0.645:0:1.1 +15 88610461 . A AT 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.27037;SOR=0.36838;LSEQ=TGTACAGACTCCCACACGCC;RSEQ=TTTTTTTTCACTTCCTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:5:3,2:109,128:237,5:0.0205:2,2:27:1:32:1:0.66483:1.76:60:10:0.0208:0:1.2 0/0:262:2:1,1:117,140:257,2:0.0076:2,2:30:1:29.5:1:1:1.20:60:4:0.0078:0:1 +15 88612019 . A G 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGCAAGAAGGGCAAGGAGGG;RSEQ=GCAGATTTTGGGGCTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:27.5:1:1:0:60:4:1:0:1.5 +15 88669128 . G A 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAACTTCAAAAACAAGA;RSEQ=GAAAACCGTGTCCTCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:29:1:26.8:1:1:0:59.5:3:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 88669163 . T C 73 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACTAGGAGTCCCTTTAC;RSEQ=CACCCGTAATGAAAATAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:23.4:1:31.8:1:1:0:59.6:10:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 88669382 . G C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGAGTTTCCATCAGTACCA;RSEQ=TTAGACCCCATGACCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:144:144:143,1:0,0:0,144:1:0,1:23.3:1:32.6:1:1:0:60:47:1:0:1.1 1/1:99:80:78,2:19,0:19,80:0.8081:1,1:24.5:1:32.1:1:1:0:60:160:0.8081:0:1.1 +15 88669644 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16724;SOR=Inf;LSEQ=GAGAGTCAGCAACAATCACA;RSEQ=AAAACCCAATTTCCTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:42,241:283,0:0:2,0:22.8:1:32.1:1:1:0:59.9:39.429:0.9964:0:0.1 0/1:197:2:1,1:39,156:195,2:0.0102:2,2:11.5:1:27.5:1:0.36569:3.96:60:4:0.0102:0:1 +15 88670278 . C CT 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.18709;SOR=1.87042;LSEQ=GAACGTAGTTCAATTCATTA;RSEQ=TTTTTTTTTTCAAAGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:8:8,0:112,8:120,8:0.0625:2,0:22.1:1:32.1:1:1:0:60:16:0.0625:0.0078:0 0/1:126:14:13,1:107,4:111,14:0.1111:1,1:20.7:1:30.3:1:0.45353:2.04251:60:28:0.1111:0.0317:0.3 +15 88670293 . G C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49939;SOR=Inf;LSEQ=CATTACTTTTTTTTTTCAAA;RSEQ=TTTCAAGTAAGATAATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:137,17:154,0:0:2,0:24.1:1:32.7:1:1:0:60:37.5:1:0:0.1 0/1:168:2:1,1:148,18:166,2:0.0119:2,2:15:0:30:1:0.214:8.02946:60:4:0.012:0:1 +15 88671809 . C T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.74137;LSEQ=TACCCTTCATTTCCCTTTCA;RSEQ=AGTTCACTCAGATGCCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:105,9:114,2:0.0172:2,2:20.5:1:31.5:1:0.16567:11.12085:60:4:0.0175:0:1 0/1:78:1:0,1:72,5:77,1:0.0128:2,0:1:0:22:0:0.07692:0:60:2:0.013:0:1 +15 88677817 . G A 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGATCAGGTCATTCATCC;RSEQ=TTAAATGGAGGGTTAAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:15.5:1:27.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 88678680 . T C 204 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACACAGAGTCTACCACCTCC;RSEQ=GCAGTAGCCTTCCAGCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:110:110:11,99:0,0:0,110:1:0,2:21.1:1:30.2:1:1:0:60:109:1:0:1.1 1/0:75:57:10,47:4,14:18,57:0.76:2,2:22.1:1:29.5:1:0.73146:1.33734:60:114:0.76:0:1.1 +15 88679065 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04282;SOR=Inf;LSEQ=CCCTGACAACACCTTGGCCC;RSEQ=TCTCCAGCCTCCTATGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:207,68:275,0:0:2,0:25.3:1:31.4:1:1:0:60:90.667:1:0:0.1 0/1:231:4:1,3:158,69:227,4:0.0173:2,2:13.3:1:25.8:1:0.09094:6.80696:60:8:0.0173:0:1 +15 88679324 . C A 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30594;SOR=4.60159;LSEQ=TAGCTTCTACAAGGATGGCT;RSEQ=TGCTACCTAATCCCCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:1:1,0:38,262:300,1:0.0033:2,0:1:0:23:0:0.12957:0:60:2:0.0034:0:1 0/1:198:3:2,1:38,157:195,3:0.0152:2,2:11.3:1:23.3:1:0.10447:8.14:60:6:0.0153:0:1.7 +15 88679785 . G A 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01794;LSEQ=CCATTGCAAGTGATAACAGC;RSEQ=TTGTCACCCTCTCGTACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:961:960:413,547:1,0:1,960:0.999:0,2:24.8:1:30.8:1:0.4308:0:59.9:67.571:1:0:1.1 1/1:709:670:306,364:20,17:37,670:0.945:2,2:25.3:1:29.8:1:0.39734:1.39878:60:82.75:0.9457:0:1.2 +15 88680100 . G A 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGGTGGGGGCAGTGCTTA;RSEQ=GGAATGCATTTCTGGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:0,8:1:0,2:24.8:1:32.8:1:1:0:60:16:1:0:1 1/1:3:3:1,2:0,0:0,3:1:0,2:29.3:1:27.7:1:1:0:60:6:1:0:1 +15 88680645 . G T 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.00109;SOR=Inf;LSEQ=ACTCACTCACCACACTGACT;RSEQ=ATGTTCATGCGGAAGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:952:0:0,0:522,430:952,0:0:2,0:25.8:1:32.1:1:1:0:60:67:1:0:0.4 0/1:844:9:5,4:461,373:834,9:0.0107:2,2:18.4:1:30.3:1:1:1.01:60:18:0.0108:0:1.7 +15 88680684 . G A 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.84286;LSEQ=GGAAGCTGGGAGCCATCAGC;RSEQ=TTGATGCAGTAGAGGTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1104:367:190,177:373,363:736,367:0.3324:2,2:24.6:1:30.8:1:0.74953:1.04:60:121.333:0.3321:0:1.2 0/1:1005:481:252,229:262,260:522,481:0.4786:2,2:25.7:1:29.7:1:0.48764:1.09:60:159.333:0.4794:0:1.2 +15 88680943 . G T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGAAGTGGAAAAATCCTT;RSEQ=TAAGTCCATAAATTGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:2,50:52,0:0:1,0:25.9:1:32.9:1:1:0:59.6:104:1:0:0.3 1/0:15:9:0,9:0,6:6,9:0.6:0,0:20.4:1:31:1:1:0:60:18:0.6:0:1.1 +15 88680987 . T A 124 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAATAAACTCATTTTTT;RSEQ=AAAAAAAGAAATCCAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:0,14:1:0,1:25.6:1:32.8:1:1:0:60:28:1:0:1.1 1/1:2:2:0,2:0,0:0,2:1:0,0:3.5:1:28.5:1:1:0:60:4:1:0:1.5 +15 88690725 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14477;SOR=Inf;LSEQ=TAATCATTTCACTGGAGCCT;RSEQ=GCTTTGTTTTCCTTCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:10,152:162,0:0:2,0:24.7:1:31.4:1:1:0:59.7:39.5:1:0:0.1 0/1:100:2:1,1:14,84:98,2:0.02:2,2:26.5:1:28.5:1:0.27879:5.83:59.5:4:0.0202:0:1 +15 88726253 . G C 30 d5;v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCTTCTTGCAACCCCCCCCC;RSEQ=CCCCCCGCCAGTCCTAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:7:0:30:1:1:0:47.5:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:47:0:30:0:1:0:60:2:1:0:0 +15 88726405 . G A 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12797;SOR=0;LSEQ=GAAAGTGAACACACTTGGGT;RSEQ=TCAGGAGACTGACTCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:23.2:1:26.8:1:1:0:60:12:0.4286:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:27.8:1:31.2:1:1:0:60:10:1:0:0 +15 88726569 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1674;SOR=Inf;LSEQ=CTGGAGGCAAAAAGCCAGGT;RSEQ=TAGACCTCAGGTCTCCGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:221,44:265,0:0:2,0:25.7:1:32.1:1:1:0:60:65.25:1:0:0.6 0/1:184:2:1,1:146,35:181,2:0.0109:2,2:19.5:1:27:1:0.35561:4.12715:60:4:0.011:0:1.5 +15 88726586 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17436;LSEQ=GGTCTAGACCTCAGGTCTCC;RSEQ=GTTTCACTGCCCCAAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:340:190:150,40:111,39:150,190:0.5588:2,2:25.9:1:30.5:1:0.30267:1.32:59.9:94:0.5595:0:1.1 0/1:266:48:37,11:158,60:218,48:0.1805:2,2:22.5:1:29.8:1:0.59132:1.28:60:96:0.1825:0:1 +15 88726814 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28232;SOR=0;LSEQ=GGGGGTGAGGCTAAGGCTGG;RSEQ=CCTGCAGCCGCCCTGTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:1,2:7,130:137,3:0.0214:2,2:33:1:28.7:1:0.16292:8.93:60:6:0.0221:0:1 0/0:90:0:0,0:6,84:90,0:0:2,0:22.9:1:30.7:1:1:0:60:29:1:0:0.1 +15 88727336 . C G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01628;SOR=0.45213;LSEQ=CCAACTCTACCAAAAGAAGA;RSEQ=CTGGGGGAGAAAGCACGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:97:57:55,2:39,1:40,57:0.5876:1,1:25.6:1:33.6:1:1:1.41327:60:114:0.5876:0:1 0/1:64:25:23,2:38,1:39,25:0.3906:1,2:26.1:1:30.2:1:0.55537:3.24132:60:11.5:0.371:0:1.4 +15 88727443 . C T 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=15.8991;LSEQ=GGGAAAGGCCTCTCTGTGGC;RSEQ=GGGTGTACTCACAGCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:578:2:1,1:330,245:575,2:0.0035:2,2:13.5:1:30.5:1:1:1.34622:60:4:0.0035:0:1 0/1:630:33:18,15:342,255:597,33:0.0524:2,2:24.7:1:28.9:1:0.85698:1.11745:60:15.5:0.0502:0:1 +15 88727612 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24849;SOR=Inf;LSEQ=AGCCACAGAGACCTGGCTTT;RSEQ=ATCCCCGATGAGCTAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:14,125:139,0:0:2,0:24:1:32.7:1:1:0:59.9:138:1:0:0.1 0/1:150:3:1,2:19,128:147,3:0.02:2,2:15:1:27.7:1:0.35106:3.33:60:6:0.02:0:1 +15 88727751 . A T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20156;SOR=0.26942;LSEQ=GAATTAACTGGATTCATTGG;RSEQ=TCCAAGTTCCTGGCCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:7,11:0.6111:0,0:34:1:29.8:1:1:0:60:22:0.6471:0:1.1 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:23:1:28:1:1:0:60:4:0.2857:0:1 +15 88799100 . C T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01661;SOR=Inf;LSEQ=CAGGAGGGAGACGCAGAGCG;RSEQ=GGGGGAGGCAGGCTGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:0:0,0:425,164:589,0:0:2,0:25.6:1:31.8:1:1:0:60:97.167:1:0:0.1 0/1:466:5:2,3:294,167:461,5:0.0107:2,2:17.2:1:27.4:1:0.35978:2.63491:60:10:0.0108:0:1 +15 88799443 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21676;SOR=Inf;LSEQ=AGAGGGGGGTGGGGTGGGGG;RSEQ=AGTGGGGAGAGCAGGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:11,55:66,0:0:2,0:12.7:1:30:1:1:0:56.6:10:1:0:1.7 0/1:58:2:1,1:12,42:54,2:0.0345:2,2:9:0:30:1:0.41364:3.40:60:4:0.0392:0:1.5 +15 88799446 . T G 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.24928;SOR=0;LSEQ=GGGGGGTGGGGTGGGGGGAG;RSEQ=GGGGAGAGCAGGGGGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:0,3:10,48:58,3:0.0492:2,0:27.3:1:23.3:1:1:0:35.3:2:0.0377:0:6 0/0:51:0:0,0:11,40:51,0:0:2,0:21:0:10:0:1:0:26:0:0:0:4 +15 88799494 . A G 36 p8;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGGCGAGGGAGGGGGGA;RSEQ=GGGGGAGGGGGGGCCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:2,0:2,3:0.5:0,0:7.7:1:23.3:1:0.1:0:60:2:0.6667:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 90627426 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17192;SOR=Inf;LSEQ=GAGGGGCTGTGAGGCTCACC;RSEQ=TCTGCCGCGCTCAGGAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:181,23:204,0:0:2,0:27.9:1:31.9:1:1:0:59.9:203:1:0:0.1 0/1:145:2:1,1:123,20:143,2:0.0138:2,2:29.5:1:28:1:0.26954:6.02616:60:4:0.0142:0:1 +15 90627616 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32607;LSEQ=AGCACCACTCACATCAGGGG;RSEQ=GGCTCCAGGCCTTGCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:399:263:83,180:38,98:136,263:0.6591:2,2:23:1:30.2:1:0.4918:1.19:59.9:51.6:0.6565:0:1.1 0/1:396:153:53,100:73,170:243,153:0.3864:2,2:24.3:1:29.8:1:0.37574:1.23:60:50:0.3836:0:1.1 +15 90628537 . G A 189 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=43.47788;LSEQ=TCCCGATAGTGGCGGGTGAC;RSEQ=GTCCCATGAGCGGCCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1339:3:3,0:668,660:1328,3:0.0022:2,0:26.7:1:19.3:1:0.24949:0:60:0.5:9e-04:0:4 0/1:1302:116:58,58:614,559:1173,116:0.0891:2,2:24.2:1:27.7:1:0.69692:1.09831:59.9:8.667:0.0929:0:1.4 +15 90628591 . G A 212 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=56.6019;LSEQ=CCATCAGGGCAGACCAGGAC;RSEQ=GACGTCATCAGGCCAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1404:3:3,0:659,740:1399,3:0.0021:2,0:4.3:1:22.3:1:0.10502:0:60:2:0.0015:0:2 0/1:1358:147:66,81:577,630:1207,147:0.1082:2,2:27.7:1:29.5:1:0.54074:1.12393:60:20:0.1115:0:1.9 +15 90628594 . C T 192 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=36.11691;LSEQ=TCAGGGCAGACCAGGACGGA;RSEQ=GTCATCAGGCCAAGGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1408:3:1,2:660,743:1403,3:0.0021:2,2:30.7:1:25.3:1:1:1.77588:60:2:0.0015:0:1 0/1:1355:97:44,53:596,660:1256,97:0.0716:2,2:29.4:1:29.1:1:0.75181:1.08764:59.8:18.4:0.074:0:2.1 +15 90628777 . T C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01022;SOR=Inf;LSEQ=AGGACAGGGACTGTTCCAGG;RSEQ=CTCTTCACCCTCCTGTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:1,102:103,0:0:1,0:25.2:1:30.1:1:1:0:59.5:102:0.9903:0:0.1 0/1:50:4:0,4:1,45:46,4:0.08:1,0:21.5:1:30.5:1:1:0:60:8:0.0816:0:1 +15 90630560 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04107;SOR=Inf;LSEQ=CAGGTTGGGGATCCCTCCCT;RSEQ=AGCCTCGGAGCTGAGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:207,204:411,0:0:2,0:22.8:1:32.1:1:1:0:60:67.5:1:0:0.1 0/1:338:4:1,3:160,174:334,4:0.0118:2,2:11.3:1:26.5:1:0.62446:2.75094:60:3:0.0091:0:1.3 +15 90630832 . G A 39 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35536;SOR=3.25958;LSEQ=AGGGGGAGAGACAGGGCCCT;RSEQ=GCGTGGTGCCCTAGCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:1:1,0:35,172:207,1:0.0048:2,0:1:0:23:0:0.17308:0:60:2:0.0049:0:1 0/1:193:3:2,1:33,157:190,3:0.0155:2,2:10.7:1:24.7:1:0.08524:9.35:60:6:0.0158:0:1 +15 90630859 . C T 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00284;SOR=Inf;LSEQ=TGCCCTAGCCTGGCGATTGC;RSEQ=GGCAACCTCCCACCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:8,106:114,0:0:2,0:23:1:30.2:1:1:0:60:228:1:0:0.3 0/1:90:7:1,6:7,76:83,7:0.0778:2,2:27.4:1:28.6:1:0.49116:1.79:60:14:0.0787:0:1.6 +15 90630892 . C A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0325;SOR=0.40163;LSEQ=CCTCCCAGGGCAAGGCCCAG;RSEQ=TCTCCAGGAACGGTACCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:35:0,35:1,26:27,35:0.5645:1,1:23.9:1:32.1:1:0.43548:0:60:70:0.5645:0:1 0/1:47:16:1,15:0,31:31,16:0.3404:1,1:29.9:1:29.7:1:0.34043:0:60:32:0.3404:0:1.3 +15 90631247 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01818;SOR=Inf;LSEQ=GCATTGGAGCTGGAACTGGG;RSEQ=ATAAAGAGGCATTCTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:20.8:1:27.1:1:1:0:60:3.5:1:0:1.4 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:28:1:1:0:60:4:1:0:1 +15 90631255 . G A 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=GCTGGAACTGGGGATAAAGA;RSEQ=GCATTCTCTTCTGATAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:0,2:2,6:0.75:0,2:22.8:1:27.3:1:0.42857:0:60:5:0.7143:0:2.2 0/0:2:0:0,0:1,1:2,0:0:2,0:26.5:1:29.5:1:1:0:60:4:1:0:1 +15 90631491 . C A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04088;SOR=Inf;LSEQ=CCATTTCTGCCTCTTTGTGG;RSEQ=CTAAGAATGAGGCCATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:116,7:123,0:0:2,0:26.8:1:32.6:1:1:0:59.7:40:1:0:0 0/1:102:4:4,0:93,5:98,4:0.0392:2,0:27.3:1:30.3:1:1:0:60:8:0.0412:0:1 +15 90631540 . G T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12427;SOR=0;LSEQ=GAAAGCCACGAGACAGAGAT;RSEQ=AAGAGACAAGCTGGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:4:2,2:249,104:353,4:0.0112:2,2:21.8:1:30.3:1:0.58521:2.38765:60:8:0.0114:0:1 0/0:343:0:0,0:245,96:341,0:0:2,0:22.8:1:31:1:1:0:60:67.2:1:0:0.2 +15 90631774 . C T 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTAGGCGAGGAGCTCCAGT;RSEQ=GGGGGGTGCCCAGGTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:0:0,0:263,213:476,0:0:2,0:23.7:1:31.1:1:1:0:59.8:94.2:0.9979:0:0.1 0/1:390:31:18,13:175,183:358,31:0.0795:2,2:22.8:1:29.8:1:0.35418:1.45:60:62:0.0801:0:1 +15 90632057 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49835;SOR=0;LSEQ=TGAACCCCAAGCAACAACAC;RSEQ=GCCAGACGGGGGTCCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:8,142:150,2:0.0132:2,2:24:1:29.5:1:0.11528:16.79:60:4:0.0132:0:1 0/0:152:0:0,0:18,134:152,0:0:2,0:19.3:1:30.2:1:1:0:60:49.667:1:0:0.1 +15 90633317 . TTCC T 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTGACCACATCAGCATTACC;RSEQ=TCCTCCTCCTCCTCCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:46:1:32:1:1:0:60:8:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 90633416 . A G 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=TGGCCTGGGAGATGGAAGAC;RSEQ=TGGATTCTGTTCTCAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:3,7:0.7:0,0:16.3:1:27.4:1:1:0:60:14:0.7:0:1.4 0/0:1:0:0,0:1,0:1,0:0:0,0:6:0:31:0:1:0:60:2:1:0:0 +15 90633685 . G T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12408;SOR=Inf;LSEQ=GAAGCCTGTGACCCTCCCTG;RSEQ=CCCGCCCACCTCCACACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:275,121:396,0:0:2,0:25.2:1:31.1:1:1:0:60:23.75:1:0:0.1 0/1:400:4:3,1:250,144:394,4:0.01:2,2:31.5:1:25.5:1:1:1.73:60:3:0.0077:0:2 +15 90633954 . G A 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26003;SOR=0;LSEQ=AAGGGCAGGATAAGAAGTCT;RSEQ=CAGGCCATGGCAGGGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:2,1:5,110:115,3:0.0254:1,2:8.7:1:26:1:0.00886:39.29:60:6:0.0261:0:1 0/0:90:0:0,0:4,85:89,0:0:1,0:20.4:1:31.7:1:1:0:60:178:0.9889:0:0.1 +15 90634287 . GCA G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAACCTTTGTCCCATGAAC;RSEQ=CACACAGTGTGGGGCCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:16:1:34.5:1:0.33333:0:60:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 90634599 . C T 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02206;SOR=0.16518;LSEQ=GGGGACAGGCCCCCGCCTGA;RSEQ=GACTTCTGAACAATTAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:22:22,0:4,0:4,22:0.8462:0,1:24.7:1:30.8:1:1:0:60:21:0.84:0:1.1 0/1:13:6:6,0:7,0:7,6:0.4615:0,0:17:1:28.3:1:1:0:60:5:0.4167:0:2.2 +15 90634678 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1852;SOR=Inf;LSEQ=AGAGCTGCTGCTGCCTACCA;RSEQ=GACAACGGGGGGGTCCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:132,5:137,0:0:1,0:25.1:1:33.5:1:1:0:60:136:1:0:0.2 0/1:104:2:1,1:99,3:102,2:0.0192:1,2:17:1:31.5:1:0.0758:28.74616:60:4:0.0192:0:1 +15 90634684 . CG C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.20014;SOR=0.71201;LSEQ=GCTGCTGCCTACCAGGACAA;RSEQ=GGGGGGTCCTAGGGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:159:111:106,5:42,3:45,111:0.6981:2,1:24.9:1:32.3:1:0.69075:1.51:59.9:222:0.707:0.1132:0.1 1/0:119:74:68,6:44,1:45,74:0.6218:1,2:26.4:1:31.5:1:0.25142:3.84738:59.9:148:0.6325:0.0924:0.2 +15 90634941 . A G 236 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.02628;LSEQ=GAGGGGGGCCCTCTCCTCCC;RSEQ=GCCAGGCCCGCCCTTCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:202:200:32,168:0,0:0,200:0.9901:0,2:24.3:1:30.9:1:1:0:60:39:0.9949:0:1.1 1/0:195:141:31,110:11,43:54,141:0.7231:2,2:22.6:1:29.9:1:0.84858:1.10:60:140:0.7292:0:1.1 +15 90634994 . GC G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00011;SOR=0.16907;LSEQ=AGAAAGCCAGGGCTCCAGCT;RSEQ=CCGGTGTCCACTCCCCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:27:0,27:0,39:39,27:0.4091:1,1:24.3:1:31.6:1:1:0:60:54:0.4154:0.0303:0.6 0/1:58:6:0,6:0,52:52,6:0.1034:1,0:21.8:1:32:1:1:0:60:12:0.1034:0.0345:0.8 +15 90645546 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49968;SOR=Inf;LSEQ=CTTGCGAGGTGGGGGCTGTC;RSEQ=GGGCCGCCGGCGCCCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:121,61:182,0:0:2,0:21.2:1:31.1:1:1:0:59.7:59.667:1:0:0.2 0/1:199:2:1,1:125,72:197,2:0.0101:2,2:23:1:31.5:1:1:1.73098:60:4:0.0102:0:1 +15 90645566 . C T 44 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25235;SOR=Inf;LSEQ=AGGGCCGCCGGCGCCCAGGC;RSEQ=GGCCGCGAGCCTGAGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:142,100:242,0:0:2,0:24.8:1:30.7:1:1:0:59.9:241:1:0:0.2 0/1:279:3:1,2:161,115:276,3:0.0108:2,2:5.3:1:28.3:1:0.57389:2.7897:58.3:6:0.0108:0:1.3 +15 90645573 . G T 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37902;SOR=3.50149;LSEQ=CCGGCGCCCAGGCCGGCCGC;RSEQ=AGCCTGAGGCTCTGCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:1:0,1:157,114:271,1:0.0037:2,0:1:0:23:0:0.42279:0:60:2:0.0038:0:1 0/1:313:4:1,3:171,138:309,4:0.0128:2,2:21.8:1:25.3:1:0.33048:3.70281:60:8:0.0128:0:1 +15 90645593 . C T 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.41763;SOR=0.40947;LSEQ=GAGCCTGAGGCTCTGCAGAG;RSEQ=GAGCGCACGACCCGCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:4:1,3:171,148:319,4:0.0124:2,2:19.8:1:28.8:1:0.34318:3.45387:60:8:0.0127:0:1 0/0:392:2:0,2:203,187:390,2:0.0051:2,0:1:0:25.5:1:0.23182:0:60:4:0.0052:0:1 +15 90645601 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06853;SOR=Inf;LSEQ=GGCTCTGCAGAGCGAGCGCA;RSEQ=GACCCGCAGGTAGCCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:169,160:329,0:0:2,0:27.1:1:30.6:1:1:0:59.9:40.125:1:0:0.2 0/1:406:5:2,3:199,202:401,5:0.0123:2,2:32:1:29.4:1:1:1.47631:60:10:0.0126:0:1.6 +15 90645618 . G T 57 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17162;SOR=0.18846;LSEQ=GCACGACCCGCAGGTAGCCG;RSEQ=CCATCCCAAGCTGGAGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:4:1,3:148,168:316,4:0.0125:2,2:5.5:1:28.8:1:0.62622:2.63548:60:8:0.0128:0:1.3 0/0:421:1:0,1:195,222:417,1:0.0024:2,0:1:0:23:0:1:0:60:2:0.0024:0:1 +15 91290552 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18887;SOR=0;LSEQ=TGAATCAAGTCCTTCCTCCC;RSEQ=TCAAAAAACATTGTGATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:130,22:152,2:0.0129:2,2:36.5:1:30:1:0.27723:5.80143:60:4:0.0129:0:1 0/0:201:0:0,0:160,41:201,0:0:2,0:26.8:1:30.3:1:1:0:60:66:1:0:0.1 +15 91290600 . T C 73 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.13396;SOR=0.28188;LSEQ=TACCTAACTCCACTGATTTC;RSEQ=TTTTCCCTCACTTTTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:5:3,2:237,155:392,5:0.0126:2,2:23.4:1:31.8:1:1:1.01931:60:10:0.0126:0:1 0/0:559:2:1,1:338,218:556,2:0.0036:2,2:7.5:1:30.5:1:1:1.54915:60:4:0.0036:0:1 +15 91292543 . T C 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.11371;SOR=0;LSEQ=AAAAATTAGTTTTGTAGAGT;RSEQ=GGGGGGTTTCTTAAAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:124,29:153,3:0.0191:2,2:20:1:25.7:1:0.47552:2.12527:60:2:0.0132:0:2 0/0:166:0:0,0:119,47:166,0:0:2,0:22.9:1:29.1:1:1:0:60:26.667:1:0:0.1 +15 91292544 . G T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.62371;SOR=2.81205;LSEQ=AAAATTAGTTTTGTAGAGTT;RSEQ=GGGGGTTTCTTAAAATGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:0,1:127,30:157,1:0.0063:2,0:22:0:14:0:0.1962:0:60:0:0:0:1 0/1:170:3:1,2:119,48:167,3:0.0176:2,2:30.3:1:28.3:1:0.2071:4.90482:60:6:0.0182:0:1 +15 91292908 . A G 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCCGGGATACTGCTCTCA;RSEQ=GAAATTAGAATTTAGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:0:0,0:235,276:511,0:0:2,0:23.6:1:31.3:1:1:0:60:55.778:1:0:0.1 0/1:546:25:11,14:251,269:520,25:0.0458:2,2:25.3:1:31.4:1:0.68882:1.18719:60:50:0.046:0:1.1 +15 91292969 . G A 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCAATGATTGGGATGATAT;RSEQ=GATGACTTTGATACTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:26:15,11:238,254:492,26:0.0502:2,2:21.3:1:30.7:1:0.42263:1.45:60:52:0.051:0:1.2 0/0:541:0:0,0:275,264:539,0:0:2,0:25:1:30.7:1:1:0:60:133.75:0.9963:0:0.1 +15 91293298 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2273;SOR=0;LSEQ=TCATTTGGAAGATGAAAGAG;RSEQ=TAACAATTATTTTATCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:33,104:137,2:0.0144:2,2:20.5:1:27:1:0.43072:3.12:60:4:0.0146:0:1.5 0/0:152:0:0,0:41,109:150,0:0:2,0:22.4:1:30.8:1:1:0:59.8:49:0.9866:0:0.2 +15 91294897 . T C 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTAAAGGGAGAGGATCCA;RSEQ=ACAAAGTGGTGTGATTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:67,0:67,0:0:1,0:23.1:1:32.1:1:1:0:59.8:66:1:0:0 0/1:60:25:25,0:35,0:35,25:0.4167:1,1:28.7:1:31.9:1:1:0:60:50:0.4167:0:1 +15 91295363 . C T 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54629;SOR=0;LSEQ=TTGCATTCTAAAGATGAAGT;RSEQ=CCATTATGATTAATTACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:0,7:1,14:15,7:0.3182:1,0:27.4:1:30.6:1:1:0:58.3:14:0.3182:0:1.9 0/0:4:0:0,0:0,4:4,0:0:0,0:16.5:1:31.5:1:1:0:60:8:1:0:0 +15 91295410 . A ATT 49 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACAATTTTAGGTAGCTG;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:24.3:1:31.5:1:1:0:56:6:0.4286:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 91297987 . A T 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05445;SOR=Inf;LSEQ=TAAGGGTTTCAAAATTATAC;RSEQ=TTTATTGAGTCTAGCCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:200,67:267,0:0:2,0:24.2:1:30.2:1:1:0:59.9:88:1:0:0.1 0/1:251:4:2,2:170,77:247,4:0.0159:2,2:9.3:1:23:1:0.59225:2.20015:60:3:0.0122:0:1.8 +15 91298024 . AT A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.63628;SOR=1.35875;LSEQ=TATAGTATGATTGGCTTAAC;RSEQ=TTTTTTTATTTGCAGTACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:7:3,4:288,173:461,7:0.015:2,2:30.9:1:31.5:1:0.43432:2.21572:60:14:0.0151:0.0021:0 0/1:544:11:5,6:306,226:532,11:0.0202:2,2:31.6:1:29.7:1:0.54136:1.62327:60:22:0.0204:0.0018:0.2 +15 91303269 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07395;SOR=Inf;LSEQ=GACTTAAGCAATCCTCCTGC;RSEQ=TTGGCCTCCCCAAAGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:29,0:0:1,0:24:1:29.8:1:1:0:59.2:8.667:1:0:0.4 0/1:22:3:3,0:19,0:19,3:0.1364:1,0:11.3:1:29.7:1:1:0:60:6:0.1429:0:1.3 +15 91303325 . CT C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.096;SOR=1.80586;LSEQ=GCCACCATGCCTAGCCAAGA;RSEQ=TTTTTTTTTTTCCCTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:15:12,3:71,12:83,15:0.1485:2,2:17.2:1:30.9:1:0.69602:1.4727:59.3:14:0.1443:0.0594:0.6 0/1:125:30:24,6:74,14:88,30:0.24:2,2:17.7:1:30.2:1:0.58437:1.31819:59.8:14:0.2276:0.072:0.2 +15 91303355 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16731;SOR=0;LSEQ=TTTCCCTCAAAGAAAAATAT;RSEQ=AACAACATAATTATTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:133,41:174,2:0.0113:2,2:9:1:30.5:1:0.42136:3.21707:60:4:0.012:0:1 0/0:255:0:0,0:181,74:255,0:0:2,0:22.5:1:28:1:1:0:59.8:16:1:0:0.3 +15 91303814 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.49858;SOR=Inf;LSEQ=TTAATACGTTGTTCTCTTTT;RSEQ=TCTCTTCAGAAGGAAACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:129,24:153,0:0:2,0:22:1:32.2:1:1:0:59.4:29.6:1:0:0.1 0/1:159:2:1,1:126,31:157,2:0.0126:2,2:26.5:1:27.5:1:0.36303:4.01635:60:4:0.0127:0:1 +15 91303818 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.49896;SOR=Inf;LSEQ=TACGTTGTTCTCTTTTCTCT;RSEQ=TTCAGAAGGAAACTTCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:135,29:164,0:0:2,0:22.5:1:32.4:1:1:0:59.4:53.667:0.9938:0:0.1 0/1:175:2:1,1:138,35:173,2:0.0114:2,2:26:1:27.5:1:0.37005:3.90177:60:4:0.0116:0:1 +15 91304138 . G GA 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00892;SOR=2.29475;LSEQ=GGCTGAAACACCAAGACTAG;RSEQ=AAAAAAAAATGAAAGCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:14:6,8:314,374:688,14:0.0198:2,2:28.4:1:31:1:1:1.11923:60:28:0.0201:0:0.1 0/1:811:36:16,20:361,409:770,36:0.0444:2,2:30.4:1:29.8:1:0.86489:1.10314:60:72:0.0455:0.0025:0.3 +15 91306067 . A C 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02695;SOR=Inf;LSEQ=ACTTGTAGGGAAGGAAAGCC;RSEQ=GTAAAGAGTTTAAGAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:32,0:32,0:0:1,0:23:1:31:1:1:0:60:64:1:0:0.1 0/1:37:6:6,0:30,1:31,6:0.1622:1,0:22.3:1:31.7:1:1:0:60:12:0.1714:0:1 +15 91308699 . C G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22437;SOR=0;LSEQ=AGAAACAATTAAATTTCAGT;RSEQ=CTCTGGATAACCTTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:15,132:147,2:0.0134:2,2:31:1:29:0:0.20388:8.55:60:4:0.0136:0:1.5 0/0:165:0:0,0:21,143:164,0:0:2,0:23.6:1:30.8:1:1:0:60:81:0.9939:0:0.1 +15 91308705 . G C 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06419;SOR=Inf;LSEQ=AATTAAATTTCAGTCCTCTG;RSEQ=ATAACCTTTTTATTAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:13,114:127,0:0:2,0:22.1:1:31.9:1:1:0:60:62.5:1:0:0.1 0/1:149:5:0,5:17,127:144,5:0.0336:2,0:22:1:32.2:1:1:0:60:10:0.0342:0:1.4 +15 91308728 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.80625;LSEQ=AACCTTTTTATTAAATAGTT;RSEQ=GTGATTTGTAAAAAATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:1:0,1:3,65:68,1:0.0145:1,0:23:0:28:0:1:0:60:2:0.0147:0:1 0/1:77:2:0,2:3,72:75,2:0.026:1,0:21:1:30.5:1:1:0:60:4:0.0263:0:2 +15 91310275 . T A 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12415;SOR=Inf;LSEQ=TTTGTATTTATATCATTATT;RSEQ=TAAAATATATTAAAGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:119,247:366,0:0:2,0:23.6:1:30.6:1:1:0:60:365:1:0:0.1 0/1:377:4:3,1:108,265:373,4:0.0106:2,2:7:1:25:1:0.07846:7.32:60:8:0.0107:0:1 +15 91310290 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24863;SOR=Inf;LSEQ=TTATTTTAAAATATATTAAA;RSEQ=ACCACTAGAATACATATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:61,202:263,0:0:2,0:21.9:1:32.5:1:1:0:60:262:1:0:0 0/1:267:3:1,2:52,212:264,3:0.0112:2,2:20.7:1:29:1:0.48656:2.03:60:6:0.0113:0:1 +15 91312313 . G A 203 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=204.56313;LSEQ=TTTGAAGACCACAGAATCAT;RSEQ=AGGTGATGTGTTTCAGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:1,0:244,65:309,1:0.0032:2,0:40:0:13:0:1:0:60:0:0:0:1 0/1:373:149:113,36:160,63:223,149:0.3995:2,2:24.2:1:28.2:1:0.40406:1.24:60:148:0.4011:0:1.1 +15 91312650 . A AT 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17399;SOR=1.54992;LSEQ=CAAGTAGTCTGAAAAGCAGT;RSEQ=TTTTTTTTTCCAACTAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:16:10,6:355,272:627,16:0.0249:2,2:28.1:1:30.2:1:0.7998:1.28:60:15:0.0237:0.0047:0.2 0/1:762:29:14,15:424,307:731,29:0.0381:2,2:29.1:1:29.5:1:0.34009:1.47895:59.8:28:0.0371:0:0.2 +15 91312823 . T C 215 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CTCAGACCTCAGGTGTAAGT;RSEQ=GTTGCACGTCACGTATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:0:0,0:132,303:435,0:0:2,0:24:1:30.5:1:1:0:60:61.143:0.9977:0:0.1 0/1:409:171:57,114:82,153:235,171:0.4181:2,2:23.5:1:29.1:1:0.75198:1.07168:60:41.75:0.4154:0:1.2 +15 91312859 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21443;SOR=Inf;LSEQ=TTTGAGAACCCTGGGGCAGT;RSEQ=ACTGCCAGAGCTGCTACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:38,191:229,0:0:2,0:22.2:1:32.1:1:1:0:60:113.5:1:0:0.1 0/1:198:2:1,1:39,156:195,2:0.0101:2,2:31:0:31:1:0.36569:3.96:60:4:0.0102:0:1 +15 91325622 . A C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAGACTCTGTCTCAAAA;RSEQ=AAAACAAAACAAAACAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:21.7:1:32:1:1:0:46:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 91325922 . C T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCATGACCTAATTATCTC;RSEQ=CGGAGGCTCCAACTCCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:37,2:39,0:0:2,0:26.9:1:31.2:1:1:0:60:78:1:0:0.1 0/1:31:14:13,1:17,0:17,14:0.4516:1,1:20.4:1:30.4:1:0.45161:0:60:28:0.4667:0:1.1 +15 91326099 . C T 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGAAATACTATGTATTAC;RSEQ=GAAAAAGCCTAAAAAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:0:0,0:324,276:600,0:0:2,0:24.4:1:30.5:1:1:0:60:65.667:1:0:0.1 0/1:670:21:13,8:338,309:647,21:0.0313:2,2:25.9:1:29.7:1:0.50648:1.48:60:20:0.0305:0:1.1 +15 91328376 . C G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01434;SOR=Inf;LSEQ=AGCATATAACCAAACATGCA;RSEQ=ATGTAGAATGCAAACTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:8,111:119,0:0:2,0:24:1:33:1:1:0:59.8:58.5:1:0:0 0/1:122:7:2,5:14,101:115,7:0.0574:2,2:12.3:1:30.6:1:0.2287:2.85:60:14:0.0579:0:1 +15 91333714 . CATATT C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00151;SOR=Inf;LSEQ=AAGTTATCAGTATAAAAACT;RSEQ=AGTTATACTAAATAGTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:29,0:0:1,0:20.9:1:29.6:1:1:0:60:28:1:0:0.1 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:12.8:1:31.6:1:1:0:60:10:0.3846:0.0769:0 +15 91334179 . G A 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGTTTTCCTTAAATAATC;RSEQ=TAGAAAAATAGAGGAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:0,45:45,0:0:1,0:25.5:1:32.4:1:1:0:59.4:44:1:0:0 0/1:38:18:0,18:0,20:20,18:0.4737:1,1:27.3:1:30.2:1:1:0:60:36:0.4737:0:1.2 +15 91334258 . T A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00312;SOR=Inf;LSEQ=AAAAGTGGTAAGTGCTTATT;RSEQ=TGTAAAACTCAAATGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:17,0:0:1,0:20.9:1:30:1:1:0:58:34:1:0:0 1/0:10:5:0,5:1,4:5,5:0.5:2,0:15.8:1:30.4:1:1:0:60:10:0.5:0:1.6 +15 91337479 . G A 246 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=476.91975;LSEQ=CATTACTGTGAAAATATAAC;RSEQ=GAATGCAGGAGAATACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:623:1:0,1:333,289:622,1:0.0016:2,0:7:0:17:0:0.46549:0:60:0:0:0:3 0/1:702:303:154,149:206,192:398,303:0.4316:2,2:24.8:1:29.9:1:0.81935:1.03805:60:100:0.4317:0:1.1 +15 91337623 . AT A 172 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=76.69193;LSEQ=TTAAAATTCTTTATAATTAA;RSEQ=TTTTTTTCTCTTACTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:0,1:14,113:127,1:0.0078:2,0:33:0:33:0:1:0:60:2:0.0079:0:0 0/1:132:50:8,42:10,72:82,50:0.3788:2,2:25.9:1:30.6:1:0.6046:1.37:60:100:0.3906:0.0303:0.1 +15 91341599 . T G 213 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTTGAATGTTTGAGTTAC;RSEQ=TCAATTGAAATTGAACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:65,197:262,0:0:2,0:22.9:1:30.5:1:1:0:60:51.4:1:0:0.1 0/1:277:125:39,86:46,106:152,125:0.4513:2,2:23.7:1:30.7:1:0.89631:1.04:59.9:250:0.4562:0:1.1 +15 91346630 . C CA 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14547;SOR=2.91678;LSEQ=ACAGAAATGAGTGTCTGTGC;RSEQ=GGGGTTTGTGATCTATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:23:21,2:13,0:13,23:0.6389:1,2:23:1:31.7:1:0.5254:0:60:46:0.6389:0.1667:0 1/1:25:21:21,0:4,0:4,21:0.84:0,1:26.4:1:28.3:1:1:0:60:20:0.8333:0.28:0.1 +15 91346700 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1416;SOR=Inf;LSEQ=TTAGCCTCTTCTATTTGAGG;RSEQ=TGATGATATACGTACATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:140,10:150,0:0:2,0:23.5:1:31.6:1:1:0:60:74:1:0:0.1 0/1:91:2:1,1:82,7:89,2:0.022:2,2:6.5:1:26:1:0.16899:11.02463:60:4:0.023:0:1 +15 91346923 . C A 224 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGATGCTCGGAAATAAAGC;RSEQ=CAAACTGTACTAAATGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:0:0,0:207,339:546,0:0:2,0:26.6:1:31.1:1:1:0:60:67.25:1:0:0.1 0/1:547:199:81,118:140,206:346,199:0.3638:2,2:26.8:1:29.4:1:1:1.01:60:98.5:0.3662:0:1.1 +15 91347135 . C A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00102;SOR=Inf;LSEQ=TCAACCCAAGTAATATGACA;RSEQ=CTGTCAAAAGTAATTTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:6,14:20,0:0:2,0:21:1:30.5:1:1:0:60:9:1:0:0.5 1/0:12:6:2,4:2,4:6,6:0.5:2,2:15.2:1:30.3:1:1:1:60:12:0.5:0:1 +15 91347297 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51889;SOR=0;LSEQ=ACTATCTGCATGACAGAATA;RSEQ=AATTGCCCCCCAAAAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:72,9:81,2:0.0241:2,2:10:1:30:1:0.22774:7.64189:60:4:0.0244:0:2 0/0:54:0:0,0:52,2:54,0:0:1,0:25.2:1:32.5:1:1:0:60:108:1:0:0.8 +15 91347302 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.83733;SOR=1.11127;LSEQ=CTGCATGACAGAATAGAATT;RSEQ=CCCCCCAAAAATGCAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:73:63,10:17,2:19,73:0.7935:2,2:21:1:28.8:1:1:1.34507:60:72:0.8:0:1.1 1/1:58:47:46,1:10,1:11,47:0.8103:2,1:26.3:1:28.3:1:0.34604:4.43:60:94:0.8103:0:1 +15 91347755 . A G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGCTGGAGTGCTGTGGC;RSEQ=TGATCATGACTCACTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:31:1:32.8:1:1:0:57.6:10:1:0:2 1/1:8:7:1,6:0,1:1,7:0.875:0,2:16.4:1:31.7:1:1:0:59:14:0.875:0:1.1 +15 91347784 . C T 64 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ACTCACTGCAGCCTCAACCT;RSEQ=CTGGGCTCAAGTGATCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:34:1:32:0:1:0:57:8:1:0:2 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:25:0:30:0:1:0:55:2:0.3333:0:2 +15 91351930 . G A 45 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AGTAACAATTTGGTTATGCC;RSEQ=TCTAGGGTGGGGTGTACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:29:1:28.7:1:1:0:60:6:0.75:0:1.7 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:29:0:1:0:60:2:1:0:0 +15 91352248 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13816;SOR=Inf;LSEQ=TACAAAATTGGCCTGTGTTC;RSEQ=CAGTACCCTGCAGTTAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:60,0:0:1,0:29:1:32.1:1:1:0:60:120:1:0:0 0/1:36:2:2,0:34,0:34,2:0.0556:1,0:29.5:1:31.5:1:1:0:60:4:0.0556:0:1 +15 91352501 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10944;SOR=0;LSEQ=CATCGCCAGGTTAGTACACA;RSEQ=CCATGTGTGTTCTCTAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:80,216:296,3:0.01:2,2:27:1:25.3:1:1:1.35:60:2:0.0068:0:2 0/0:325:0:0,0:87,237:324,0:0:2,0:23.2:1:31.3:1:1:0:60:80:0.9969:0:0.1 +15 91352774 . A G 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGATCAGAGCCCTGGGT;RSEQ=CCAGTTCCAGATCTGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:38.2:1:32.2:1:1:0:60:10:0.7143:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 91354377 . TA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.24482;SOR=0;LSEQ=GCGTGTCTCTTCATATACAC;RSEQ=AAAACACGTGGACCAGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:132,33:165,2:0.012:2,2:48:1:31.5:1:0.36671:3.95564:60:4:0.0123:0:0 0/0:170:0:0,0:127,43:170,0:0:2,0:23.6:1:27.7:1:1:0:60:84:1:0:0.1 +15 91354494 . G A 116 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=14.41667;LSEQ=GAGGCCCCGGAAGAAGTGCC;RSEQ=CTGAGGAGCTCGACGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:1:1,0:239,211:450,1:0.0022:2,0:1:0:29:0:1:0:60:2:0.0022:0:1 0/1:548:17:9,8:288,243:531,17:0.031:2,2:24.3:1:28.4:1:1:1.05343:60:16:0.0295:0:1.6 +15 91354505 . C T 236 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=375.1691;LSEQ=AGAAGTGCCGCTGAGGAGCT;RSEQ=GACGAGGAAATACCCGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:1:0,1:242,210:452,1:0.0022:2,0:1:0:26:0:0.46578:0:60:2:0.0022:0:1 0/1:576:261:144,117:168,144:312,261:0.4531:2,2:23.7:1:29.4:1:0.8006:1.05:60:260:0.4577:0:1.1 +15 91354520 . C T 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCTCGACGAGGAAATACC;RSEQ=GTATCTTCCCACTACTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:271,192:463,0:0:2,0:23.2:1:30.5:1:1:0:60:65.143:1:0:0.1 0/1:602:36:21,15:311,251:562,36:0.0598:2,2:22.9:1:30.5:1:0.86295:1.13:60:72:0.0609:0:1.2 +15 91354521 . G A 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.12306;LSEQ=AGCTCGACGAGGAAATACCC;RSEQ=TATCTTCCCACTACTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:465:1:1,0:273,191:464,1:0.0022:2,0:1:0:25:0:1:0:60:2:0.0022:0:1 0/1:606:37:18,19:319,249:568,37:0.0611:2,2:23.1:1:29.5:1:0.39677:1.3516:60:74:0.0619:0:1.4 +15 91357029 . G C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCCTTTCCACCGACCCAGT;RSEQ=TGCTCCCCGGATTGAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:31.5:1:1:0:60:4:1:0:1.5 +15 91358271 . G GGAA 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=3.0731;LSEQ=TAGCTCTGTGCAGGTTGAGA;RSEQ=GAAGGTCATTCATTTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:69:64,5:54,7:61,69:0.5308:2,2:30:1:31.2:1:0.54633:1.65:60:68:0.5271:0:0.2 1/0:202:157:128,29:39,5:44,157:0.7772:2,2:21.3:1:29.5:1:0.36372:1.76272:59.7:314:0.7811:0.2079:0.1 +15 91359755 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGTGACGTTACTCAGGAG;RSEQ=GTGTAGCTGGGGAGACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 91792303 . C T 84 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATACATCTACGTTTTCACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:3,4:5,4:9,7:0.35:2,2:23.3:1:30:1:1:1.61372:59.9:14:0.4375:0:1.1 0/0:2:0:0,0:1,0:1,0:0:0,0:28:0:34:0:1:0:60:2:1:0:0 +15 91792337 . CAT C 33 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=19.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACACACACACACACACACA;RSEQ=GTTTATGATCTGGCTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,5:5,2:0.3333:0,0:27.5:1:33:1:1:0:59.5:4:0.3333:0.1667:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:32:0:1:0:60:2:1:0:0 +15 92757222 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50187;SOR=0;LSEQ=ACAACGCCTTTCAAACTCTT;RSEQ=TACCAACTTCTGGAGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:29,27:56,2:0.0345:2,2:26:1:31:1:1:1.07272:36:4:0.0364:0:1 0/0:46:0:0,0:25,21:46,0:0:2,0:30.5:1:29.4:1:1:0:56.5:45:1:0:0.2 +15 92829095 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20744;SOR=0;LSEQ=CATGTATGTGGACATGAGCC;RSEQ=CCTGAGGCCCCAGAACTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:70,64:134,2:0.0147:2,2:37.5:1:29.5:1:1:1.09302:54.5:4:0.015:0:1 0/0:162:0:0,0:94,68:162,0:0:2,0:27.7:1:29.8:1:1:0:41.4:31.4:1:0:0.1 +15 92829116 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50223;SOR=Inf;LSEQ=CCTGAGGCCCCAGAACTATC;RSEQ=TTTCGGTTGTGAACTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:80,74:154,0:0:2,0:27.3:1:30.9:1:1:0:42.3:29.8:1:0:0.1 0/1:183:2:1,1:98,83:181,2:0.0109:2,2:42:1:31.5:1:1:1.17964:32.5:4:0.0112:0:1 +15 92829136 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49876;SOR=Inf;LSEQ=TTTTCGGTTGTGAACTAAAG;RSEQ=CCGACAAAGATTACCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:86,72:158,0:0:2,0:25.6:1:31.4:1:1:0:43.1:18.75:1:0:0.2 0/1:166:2:1,1:88,75:163,2:0.012:2,2:32:1:27.5:1:1:1.17219:32:4:0.0124:0:1 +15 92829186 . G T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24803;SOR=0;LSEQ=AATGATGAAAATGGACACCA;RSEQ=TTATTTTTAAGAACAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:3:1,2:97,90:187,3:0.0158:2,2:26:1:25:1:0.61137:2.14715:60:2:0.0107:0:2 0/0:188:0:0,0:88,100:188,0:0:2,0:24.3:1:31.2:1:1:0:56.8:187:1:0:0.1 +15 92829220 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24271;SOR=Inf;LSEQ=CAGTCAGTTTAGGGGCGGGT;RSEQ=CAAAGGATGAATTGGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:89,101:190,0:0:2,0:27:1:32.3:1:1:0:56.3:380:1:0:0.2 0/1:185:2:1,1:81,102:183,2:0.0108:2,2:30.5:1:28:1:1:1.26:48:4:0.011:0:1 +15 92829291 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49874;SOR=0;LSEQ=GTCCAATTAAAGTAACACTG;RSEQ=CAACTTTGAAAATGTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:58,45:103,2:0.019:2,2:19:1:28.5:1:1:1.28574:40:4:0.0194:0:1 0/0:95:0:0,0:51,44:95,0:0:2,0:24.4:1:30.9:1:1:0:35.3:190:1:0:0.1 +15 92829320 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23271;SOR=Inf;LSEQ=AAAATGTCTGTACAGCCAAC;RSEQ=GTTTCCCTTGGGGACTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:83,42:125,0:0:2,0:20.5:1:30.2:1:1:0:38.5:61.5:1:0:0.1 0/1:117:2:1,1:71,44:115,2:0.0171:2,2:13:1:31:0:1:1.60674:22:4:0.0171:0:1 +15 92829336 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24735;SOR=Inf;LSEQ=CAACGGTTTCCCTTGGGGAC;RSEQ=CTGAAATAACACCACCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:90,52:142,0:0:2,0:22.6:1:31:1:1:0:37.3:46.333:1:0:0.1 0/1:141:2:1,1:85,54:139,2:0.0142:2,2:23:1:27.5:1:1:1.56879:35:4:0.0145:0:1 +15 92829382 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2438;SOR=Inf;LSEQ=ACGGTTGAAGTGTGGTTCAG;RSEQ=GCCAGTGCATATTAGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:81,61:142,0:0:2,0:29.7:1:31.2:1:1:0:34.7:141:1:0:0.2 0/1:139:2:1,1:75,62:137,2:0.0144:2,2:17:1:29:1:1:1.20801:55.5:4:0.0149:0:1 +15 92829452 . G A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0.09258;LSEQ=GAGTCAGAAGACGAAGAGGA;RSEQ=GAGGATGTGAGACTCTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:67:27,40:39,51:90,67:0.4268:2,2:25.2:1:31.2:1:0.74546:1.132:39.6:32.5:0.4194:0:1.1 0/1:125:8:5,3:51,66:117,8:0.064:2,2:18.6:1:30:1:0.46517:2.14:45:16:0.064:0:1 +15 92829541 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49854;SOR=Inf;LSEQ=GAAACAAGTAAAACTTGCTG;RSEQ=TGATGAAGATGATGGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:69,92:161,0:0:2,0:24.9:1:32.3:1:1:0:50.1:79.5:1:0:0.2 0/1:165:2:1,1:76,87:163,2:0.0121:2,2:32:1:31:0:1:1.14:54.5:4:0.0122:0:1 +15 92829554 . T C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99215;LSEQ=CTTGCTGCTGATGAAGATGA;RSEQ=GGTGATGATGATTTTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:19:8,11:45,69:114,19:0.1429:2,2:28.2:1:31.2:1:1:1.11:52.8:38:0.1439:0:1.2 0/1:148:21:10,11:57,70:127,21:0.1419:2,2:21.2:1:29.2:1:0.81792:1.12:51.2:42:0.1458:0:1 +15 92829629 . CA C 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.60285;SOR=0.44298;LSEQ=TCTATACAAGATACTCCAGC;RSEQ=AAAAATGCACAAAAGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:31,59:90,2:0.0217:2,2:18.5:1:31.8:1:1:1.89:55:4:0.022:0.0109:0 0/0:103:1:0,1:45,57:102,1:0.0097:2,0:24:0:31:0:1:0:23:2:0.01:0:0 +15 92829642 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49948;SOR=Inf;LSEQ=CTCCAGCCAAAAAATGCACA;RSEQ=AAGTCAAATCAGAATAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:28,54:82,0:0:2,0:28.4:1:30.8:1:1:0:58:40:1:0:0.1 0/1:94:2:2,0:40,52:92,2:0.0213:2,0:21.5:1:31:1:0.19698:0:52.5:4:0.0215:0:1 +15 92830133 . TA T 50 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTTAAAGTATAATAATAA;RSEQ=AAAAAAAAAAGAAAAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0,3:0.75:0,2:24:1:31.7:1:1:0:57.3:6:0.75:0:0.3 1/1:1:1:0,1:0,0:0,1:1:0,0:41:0:28:0:1:0:60:2:1:0:0 +15 93545831 . G T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.49452;LSEQ=TAGGACAGGTGAGAGAAATC;RSEQ=GCATTTACATGTAAATACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:97:73,24:49,8:57,97:0.6299:2,2:24.6:1:31.9:1:0.15014:2.00507:60:194:0.6299:0:1.1 1/1:140:131:101,30:5,4:9,131:0.9357:2,2:22:1:30.2:1:0.22053:2.67:60:130:0.9353:0:1.1 +15 93545934 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00055;SOR=1.72427;LSEQ=GTTTGAGTCAAAAACAAATA;RSEQ=TAGCAAGAGTTATTGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:171:78,93:60,84:144,171:0.5429:2,2:23.1:1:32.5:1:0.49608:1.17:60:84.5:0.5452:0:1.1 1/0:372:250:110,140:61,60:121,250:0.672:2,2:25.9:1:31.2:1:0.26741:1.29302:59.8:61.5:0.6758:0:1.1 +15 94590208 . T C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGTTTCTTTGCTCCGAA;RSEQ=GCTGACTTCATTTTAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:33:1:1:0:60:4:1:0:1 +15 94590782 . G GTATTTATT 55 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=8.000;MSILEN=4;SSF=0.04762;SOR=Inf;LSEQ=AACACAGTCCAAATTGAGAG;RSEQ=TATTTATTTATTTATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:29.3:1:32.5:1:1:0:60:8:1:0:0 1/1:5:4:4,0:1,0:1,4:0.8:0,0:26.8:1:27.7:1:1:0:59.5:8:0.8:0.4:0 +15 94590949 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21922;SOR=Inf;LSEQ=GAGCAGCATGTTTGTATATC;RSEQ=GGGACTTCTCTTCCAAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:102,36:138,0:0:2,0:24.4:1:30.6:1:1:0:60:33.5:1:0:0.3 0/1:122:2:1,1:86,34:120,2:0.0164:2,2:30.5:1:28:1:0.49316:2.50748:60:4:0.0172:0:1 +15 94590966 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61943;SOR=2.05669;LSEQ=ATCAGGGACTTCTCTTCCAA;RSEQ=CTGTGGAAGCAATTGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:121,48:169,1:0.0059:2,0:1:0:26:0:0.28824:0:60:2:0.0061:0:2 0/1:166:2:1,1:103,61:164,2:0.012:2,2:10.5:1:28.5:1:1:1.68289:60:4:0.0123:0:2 +15 94590975 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22331;SOR=Inf;LSEQ=TTCTCTTCCAAGCTGTGGAA;RSEQ=CAATTGGTGTGCCCATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:136,61:197,0:0:2,0:25.8:1:32.5:1:1:0:60:38.4:1:0:0.4 0/1:177:2:1,1:102,73:175,2:0.0113:2,2:27:1:27.5:1:1:1.39455:60:4:0.0118:0:2 +15 94590981 . G T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36368;SOR=3.14281;LSEQ=TCCAAGCTGTGGAAGCAATT;RSEQ=GTGTGCCCATAATTGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:0,1:139,70:209,1:0.0048:2,0:9:0:15:0:0.3381:0:60:0:0:0:4 0/1:202:3:1,2:116,83:199,3:0.0149:2,2:12:1:28:1:0.57381:2.78101:60:6:0.0153:0:1.7 +15 94591032 . T G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.37684;SOR=1.17718;LSEQ=TGTCCAAGAAGCCTGGTTCT;RSEQ=ATTTTGAGAGATAAAGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:155:79,76:66,51:117,155:0.5699:2,2:25.2:1:32:1:0.3923:1.24396:60:76.5:0.5667:0:1.1 1/0:256:156:78,78:46,54:100,156:0.6094:2,2:24.7:1:30.6:1:0.60835:1.17:59.9:77:0.6063:0:1.2 +15 94591097 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50329;SOR=0;LSEQ=TGGAGATGGGATAAAATTGG;RSEQ=GGCTCCCTGGAGGCCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:53,124:177,2:0.0112:2,2:43.5:1:30:1:0.51353:2.33:60:4:0.0116:0:1 0/0:147:0:0,0:51,96:147,0:0:2,0:24.6:1:29.3:1:1:0:60:48:1:0:0.7 +15 94591107 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20751;SOR=Inf;LSEQ=ATAAAATTGGAGGCTCCCTG;RSEQ=AGGCCTGGTGGGAAGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:37,113:150,0:0:2,0:21.6:1:31.5:1:1:0:60:49:1:0:0.6 0/1:126:2:1,1:36,88:124,2:0.0159:2,2:18:1:25.5:1:0.50273:2.42:60:4:0.0163:0:2 +15 94591144 . A G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.065;SOR=2.05533;LSEQ=TGATCTGAAAATTGTGATCA;RSEQ=ATTTTTTGCCCCATTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:37:4,33:2,34:36,37:0.5068:2,2:21.8:1:30.6:1:0.6741:2.04:60:8.25:0.4783:0:1.2 1/0:50:34:6,28:2,14:16,34:0.68:2,2:21.3:1:30.4:1:1:1.49:60:68:0.68:0:1.1 +15 94711926 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52801;SOR=Inf;LSEQ=TTGTGCACTATCCATGCCAA;RSEQ=TGTGTAACAATTATGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:31,31:62,0:0:2,0:23.3:1:31.1:1:1:0:60:124:1:0:0.1 0/1:103:2:1,1:55,46:101,2:0.0194:2,2:8:0:33:0:1:1.19357:60:4:0.0194:0:2 +15 94711951 . G A 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAACAATTATGCCAAAAGTC;RSEQ=TCCAGCTAGCACATCTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:30,34:64,0:0:2,0:28.1:1:31:1:1:0:60:63:1:0:0.1 1/1:106:88:44,44:10,8:18,88:0.8302:2,2:31.2:1:29.7:1:0.79731:1.24737:59.5:87:0.8286:0:1.1 +15 94711966 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53714;SOR=Inf;LSEQ=AAGTCGTCCAGCTAGCACAT;RSEQ=TCATACGTAGAGAAGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:27,34:61,0:0:2,0:28.3:1:32.6:1:1:0:60:60:1:0:0.1 0/1:109:2:1,1:50,57:107,2:0.0183:2,2:13.5:1:27.5:1:1:1.14:60:4:0.0187:0:1 +15 94711987 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13838;SOR=0;LSEQ=TCATACGTAGAGAAGGTCCT;RSEQ=AAGAATCCTCTATGATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:17,36:53,2:0.0364:2,2:27.5:1:29:1:1:2.09:60:4:0.0364:0:1 0/0:92:0:0,0:39,53:92,0:0:2,0:24.7:1:28:1:1:0:60:45:1:0:0.9 +15 95084911 . C T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02108;SOR=Inf;LSEQ=TGTCCTGACTTACTAAGATA;RSEQ=TGAGATGTCTACAGGGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:56,0:56,0:0:1,0:25:1:32.6:1:1:0:60:55:1:0:0.2 0/1:36:4:4,0:32,0:32,4:0.1111:1,0:28.8:1:31.3:1:1:0:60:8:0.1212:0:1 +15 95084941 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49725;SOR=0;LSEQ=TACAGGGCTAGGTAGGATTT;RSEQ=GAATACATATGGCTAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:73,3:76,2:0.0253:1,2:22:1:30.5:1:0.10057:21.21721:60:4:0.0256:0:1 0/0:74:0:0,0:71,3:74,0:0:1,0:20.4:1:31.6:1:1:0:60:73:1:0:0.3 +15 95084954 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23895;SOR=Inf;LSEQ=AGGATTTGGAATACATATGG;RSEQ=TAGAAATTTTAATTGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:96,7:103,0:0:2,0:21.8:1:32.4:1:1:0:60:102:1:0:0.1 0/1:99:2:1,1:87,10:97,2:0.0202:2,2:23.5:1:28:1:0.21088:8.34147:60:4:0.0206:0:1.5 +15 95085045 . TC T 96 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06345;SOR=0.24577;LSEQ=TAATCAAGCGGATTTTGGCA;RSEQ=CCCCCCTTTTTTAAAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:493:8:3,5:265,220:485,8:0.0162:2,2:19.3:1:32.1:1:0.47843:2.00473:60:16:0.0167:0.0061:0.9 0/0:496:2:2,0:260,234:494,2:0.004:2,0:47:1:28.5:1:0.50059:0:60:4:0.0041:0:1 +15 95085074 . T C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.28691;LSEQ=TTTTTAAAAGTTTTATCTTA;RSEQ=ATCCTCTGCCCCATTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:503:317:164,153:89,95:184,317:0.6302:2,2:26.6:1:32.2:1:0.51658:1.14:60:78.25:0.631:0:1.1 0/1:509:167:85,82:167,172:339,167:0.3281:2,2:25:1:31.1:1:0.77686:1.07:60:166:0.3287:0:1.1 +15 95085088 . T C 205 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=57.81662;LSEQ=ATCTTATATCCTCTGCCCCA;RSEQ=TTTCAAGACCATTCATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:2:1,1:229,243:472,2:0.0042:2,2:35.5:1:31.5:1:1:1.06:60:4:0.0043:0:1 0/1:461:91:45,46:170,199:369,91:0.1974:2,2:24.6:1:31.6:1:0.63911:1.14:60:182:0.1983:0:1.2 +15 95085160 . G A 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05477;SOR=6.93728;LSEQ=GTGCTTAAACAGACACCATC;RSEQ=CATGGTTTCAGGCACATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:43,144:187,1:0.0053:2,0:27:0:32:0:1:0:60:2:0.0054:0:1 0/1:167:6:2,4:42,117:159,6:0.0359:2,2:23.8:1:27.7:1:0.65786:1.39:60:5:0.0305:0:1.2 +15 95085372 . T C 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCAGAAATGCAAACTAAA;RSEQ=TGACCAATTATCAATGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:32:1:33.5:1:1:0:58:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 95792165 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58224;SOR=2.60696;LSEQ=CAACCCCACTTCTAGGGAGG;RSEQ=AAGGGGGCGCACTTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:1:1,0:173,40:213,1:0.0047:2,0:5:0:30:0:1:0:60:2:0.0048:0:1 0/1:165:2:1,1:124,39:163,2:0.0121:2,2:47:1:28.5:1:0.4272:3.15212:60:4:0.0123:0:1 +15 95792273 . C G 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0975;LSEQ=GATTCCAGCTACTTCTGGTT;RSEQ=TCGGTCCTGGTTTTACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:560:529:249,280:17,14:31,529:0.9446:2,2:25.4:1:31.9:1:0.46106:1.36469:59.9:87.167:0.944:0:1.1 1/0:588:367:190,177:107,114:221,367:0.6241:2,2:25:1:31.1:1:0.44442:1.14:60:90.75:0.6291:0:1.1 +15 97474261 . T C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAGTTTCCTTCAAGAGTC;RSEQ=TCCTGTCTGGAGTCCTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:0,7:1:0,2:17.9:1:31.3:1:1:0:60:14:1:0:2 1/1:5:5:3,2:0,0:0,5:1:0,2:18:1:31.6:1:1:0:60:10:1:0:2.2 +15 97474303 . G GC 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.73799;SOR=0.64449;LSEQ=GTCTATGTTTCTTACCAGCA;RSEQ=CCCCCCACTGCACCCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:4,5:6,3:9,9:0.5:2,2:26.3:1:32.3:1:0.63719:2.37182:60:18:0.5:0.1111:2 0/1:18:7:4,3:7,4:11,7:0.3889:2,2:32.1:1:30.1:1:1:1.29262:60:14:0.3889:0:2.1 +15 97474330 . G C 141 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00204;SOR=0;LSEQ=ACTGCACCCTGACTCCTGCT;RSEQ=TTTTCTTATGCCTGTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:11,8:0,0:0,19:1:0,2:25.6:1:33.3:1:1:0:60:38:1:0:2.2 1/0:23:14:8,6:4,5:9,14:0.6087:2,2:30.3:1:30:1:0.68017:1.63:60:13:0.5909:0:2.2 +15 97474355 . T C 117 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01047;SOR=0;LSEQ=CTTATGCCTGTCCATGTGCC;RSEQ=TCCTTTAAAGATTCTGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:7,7:0,0:0,14:1:0,2:20.9:1:30.9:1:1:0:60:13:1:0:2.2 1/0:18:11:5,6:3,4:7,11:0.6111:2,2:17.5:1:30.5:1:1:1.10:60:22:0.6111:0:2.2 +15 97475636 . TA T 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAGGCAATCATCTGATCT;RSEQ=AAAAAAAAAAGTCTAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:29.7:1:33:0:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 97475981 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24385;SOR=0;LSEQ=TACAACCAAGAAAAATAAGT;RSEQ=GTGAGGACAAGGGCCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:143,35:178,2:0.0111:2,2:25:1:28.5:1:0.36089:4.04263:60:4:0.0112:0:1 0/0:184:0:0,0:127,57:184,0:0:2,0:24.2:1:29.4:1:1:0:60:35.8:1:0:0.1 +15 97476082 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34694;SOR=1.14727;LSEQ=CAGTGGATTATCCTTGGAAT;RSEQ=GACTTACCTCTGGGCTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:154:66,88:114,146:260,154:0.372:2,2:28.5:1:31:1:0.91834:1.04101:60:153:0.3714:0:1.1 0/1:388:157:72,85:109,119:228,157:0.4046:2,2:27.5:1:29.6:1:0.75553:1.08113:59.8:77.5:0.4036:0:1.2 +15 97476200 . C CA 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05926;SOR=0.46243;LSEQ=TTTAACAAATGTCTTCATTA;RSEQ=AAAAAAAACCCTGAAATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:58:2,56:3,10:13,58:0.7838:2,1:29.9:1:31.1:1:0.03959:8.02043:59.6:28:0.7778:0:0.4 1/0:64:40:2,38:1,21:22,40:0.625:1,2:28.3:1:31.4:1:1:1.10:59.9:80:0.6349:0.0156:0.1 +15 97476271 . T C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.59931;LSEQ=TTAAAGATGCGTTGATTTGA;RSEQ=TCTACTAGGAAAGCAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:0,7:7,8:0.5333:0,0:24.9:1:34.1:1:1:0:60:16:0.5333:0:1.3 0/1:5:2:0,2:0,3:3,2:0.4:0,0:13:1:31.5:1:1:0:60:4:0.4:0:1 +15 98674720 . C T 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TACTTTGTGCTTCCTGAGAT;RSEQ=TCCTCCTAAATGAACAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:80,4:84,0:0:1,0:23:1:31.8:1:1:0:60:41:1:0:0.6 0/1:70:12:10,2:55,3:58,12:0.1714:2,2:22.3:1:30:1:0.20075:3.5742:60:24:0.1739:0:1.1 +15 98674754 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=ACAACTTGCATCCAAACCTT;RSEQ=CTTTCAATGTCATCTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:127,32:159,0:0:2,0:22.5:1:31.9:1:1:0:60:78.5:1:0:0.7 0/1:161:2:1,1:118,41:159,2:0.0124:2,2:21.5:1:27.5:1:0.45489:2.8556:60:4:0.0126:0:2 +15 98674766 . A G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02531;SOR=0.61689;LSEQ=CAAACCTTCCTTTCAATGTC;RSEQ=TCTTCTGGGGAAGCCCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:76:61,15:94,30:124,76:0.38:2,2:24.3:1:30.6:1:0.49102:1.30:59.9:152:0.3838:0:2.2 0/1:197:54:36,18:105,38:143,54:0.2741:2,2:22.3:1:29.9:1:0.37825:1.37928:60:53:0.2718:0:2.1 +15 98674786 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00326;SOR=0.58432;LSEQ=ATCTTCTGGGGAAGCCCAAC;RSEQ=ACTAGAGCTATGAAGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:112:77,35:111,60:171,112:0.3958:2,2:24.5:1:30.2:1:0.52256:1.19:59.9:36.333:0.3893:0:2.1 0/1:282:78:46,32:130,73:203,78:0.2766:2,2:23.9:1:29.4:1:0.49147:1.23786:60:38:0.2734:0:2.2 +15 98674828 . C T 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=56.26436;LSEQ=TCATTGACTTCAGATCCATT;RSEQ=CTGCTCTACAATTTTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:1:0,1:217,183:400,1:0.0025:2,0:38:0:28:0:0.45885:0:60:2:0.0025:0:1 0/1:397:49:30,19:188,160:348,49:0.1234:2,2:29.1:1:28.8:1:0.36192:1.34:60:98:0.1247:0:1.1 +15 98674857 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.50785;LSEQ=CAATTTTGCTTCCTAAATAT;RSEQ=GCACAAATGTGTCTCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:178:90,88:103,124:227,178:0.4395:2,2:25.1:1:31:1:0.31723:1.23:60:177:0.4392:0:1.5 0/1:397:113:56,57:138,146:284,113:0.2846:2,2:24.7:1:29.4:1:0.91155:1.04:60:226:0.2861:0:1.4 +15 98674903 . A T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11875;SOR=0;LSEQ=AGCCCACTGTTTCTGAGTTC;RSEQ=GAACCTCATCCTTTCCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:109,179:288,3:0.0103:2,2:14.7:1:28:1:0.56007:3.27:60:2:0.007:0:2.3 0/0:300:0:0,0:109,191:300,0:0:2,0:24.8:1:30:1:1:0:60:149:1:0:0.4 +15 99192744 . C T 90 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.87077;SOR=0.90644;LSEQ=TCCTTTCATTTCCTTTTTTT;RSEQ=TTTTCTTTTCTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:20:2,18:206,20:226,20:0.081:2,2:9:1:22.3:1:0:88.95283:46.8:1.857:0.0591:0:3.9 0/1:284:21:0,21:230,33:263,21:0.0739:2,1:10.6:1:20.7:1:0:0:46.3:1.1:0.0449:0:4.2 +15 99192745 . TTTTC T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.06448;SOR=Inf;LSEQ=CCTTTCATTTCCTTTTTTTC;RSEQ=TTTTCTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:215,41:256,0:0:2,0:22:1:30.1:1:1:0:53.8:24.6:1:0:1.3 0/1:296:5:5,0:232,57:289,5:0.0169:2,0:30.2:1:27.1:1:0.58705:0:44:4:0.0141:0.0068:1.2 +15 99226021 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17423;SOR=Inf;LSEQ=TCCTGATTAGGTGATCCACC;RSEQ=GCCTCTGCCTCCCAAAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:94,3:97,0:0:1,0:25.7:1:30.7:1:1:0:49.6:31.333:1:0:0.1 0/1:70:2:1,1:62,6:68,2:0.0286:2,2:11.5:1:26.5:1:0.1913:9.64366:54.5:4:0.029:0:1 +15 99226148 . C G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.92147;LSEQ=CAGTGGTTATACTTTTCTTG;RSEQ=TATGCATTTAAGTTGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:491:291:161,130:104,95:199,291:0.5927:2,2:26.2:1:31.8:1:0.51927:1.13:59.9:71.75:0.5942:0:1.1 1/1:473:383:206,177:52,36:88,383:0.8097:2,2:25.7:1:30.8:1:0.40657:1.24053:60:75.6:0.8094:0:1.1 +15 99226256 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49958;SOR=0;LSEQ=CAGTGTATCTCGTGTGCACT;RSEQ=CTAGATATTCTGATCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:37,154:191,2:0.0104:2,2:17.5:1:29.5:1:0.35584:4.12:60:4:0.0104:0:1 0/0:177:0:0,0:38,139:177,0:0:2,0:20.7:1:31.2:1:1:0:60:87.5:1:0:0.1 +15 99227648 . T G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGGGGAGGTGGGGGGTG;RSEQ=GGGCGGATGAATATAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:23:0:28:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:32:0:1:0:60:4:1:0:1 +15 99250709 . A G 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25981;SOR=0;LSEQ=AATAATACAGGATTCCTGAA;RSEQ=ACCAACTGTATTATTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:2,1:154,20:174,3:0.0169:2,2:22.3:1:28.7:1:0.31695:3.80442:60:2:0.0116:0:1.3 0/0:137:0:0,0:120,17:137,0:0:2,0:21.1:1:29.3:1:1:0:60:26.4:1:0:0.1 +15 99250711 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19349;SOR=Inf;LSEQ=TAATACAGGATTCCTGAAAA;RSEQ=CAACTGTATTATTGTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:160,24:184,0:0:2,0:21.9:1:32.1:1:1:0:60:60.333:1:0:0.1 0/1:145:2:1,1:125,18:143,2:0.0138:2,2:17.5:1:27.5:1:0.24569:6.7853:60:4:0.014:0:1 +15 99250753 . C T 116 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=19.36544;LSEQ=AATAGTTTAAAAATTATTTC;RSEQ=TTCTAACTGAGACGTTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:1:1,0:288,116:404,1:0.0025:2,0:47:0:16:0:1:0:60:0:0:0:4 0/1:349:16:11,5:232,101:333,16:0.0458:2,2:18.6:1:29.2:1:1:1.04397:60:32:0.0461:0:1.2 +15 99251356 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=10.04005;LSEQ=AGTAAGAATGATGCTGACTG;RSEQ=TGCTTTCTCTCTGCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:17:2,15:105,229:334,17:0.0484:2,2:27.5:1:31.5:1:0.10719:3.42971:60:34:0.049:0:1.1 0/1:363:123:42,81:88,152:240,123:0.3388:2,2:23.7:1:29.2:1:0.64591:1.1162:60:122:0.3398:0:1.1 +15 99251389 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00168;SOR=Inf;LSEQ=GCCTCTCTCTCTCCTCTCCT;RSEQ=CTCCTTGACCTCCCTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:37,175:212,0:0:2,0:23:1:31.3:1:1:0:60:34.333:1:0:0.2 0/1:177:8:3,5:37,131:168,8:0.0452:2,2:22.1:1:30.3:1:0.38409:2.11:60:16:0.0462:0:1 +15 99251417 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51349;SOR=0;LSEQ=ACCTCCCTTCTCTTCTGAGT;RSEQ=CACGAGTTCCGCTGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:6,118:124,2:0.0159:1,2:25.5:1:30.5:1:0.10844:18.28:60:4:0.0163:0:1 0/0:88:0:0,0:8,80:88,0:0:2,0:22.7:1:31.8:1:1:0:60:176:1:0:0.3 +15 99434357 . G A 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28007;SOR=0;LSEQ=GACTGAACTTTAAAGATATC;RSEQ=ACTCTCTGCAGGTCTAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:13,0:13,6:0.3158:1,0:15.8:1:28.5:1:1:0:60:5:0.2778:0:1.5 0/0:5:0:0,0:5,0:5,0:0:0,0:18.8:1:30:1:1:0:60:10:1:0:0 +15 99434457 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1285;SOR=Inf;LSEQ=ATGAGTGATCTGGTGCTGGT;RSEQ=GTAGCAGTGAATGACCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:83,2:85,0:0:1,0:25.5:1:32.4:1:1:0:60:41.5:1:0:0.2 0/1:48:2:1,1:42,4:46,2:0.0417:2,2:21:1:27.5:1:0.19947:9.50264:60:4:0.0417:0:1 +15 99434514 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50022;SOR=0;LSEQ=CCAGAGAAGGCGGTGCCTCC;RSEQ=CTGCCCGGTCTCATCTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:143,39:182,2:0.0109:2,2:5.5:1:29.5:1:0.38845:3.63358:60:4:0.0112:0:1 0/0:164:0:0,0:128,36:164,0:0:2,0:23.9:1:30.5:1:1:0:60:328:1:0:0.1 +15 99434816 . C A 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTTTGTGATCCACGACGG;RSEQ=GAGTGCATGCAGGAGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:0:0,0:220,353:573,0:0:2,0:25.4:1:30.7:1:1:0:59.9:62.667:0.9982:0:0.1 0/1:626:21:8,13:254,351:605,21:0.0335:2,2:24.6:1:29.2:1:0.82401:1.17561:60:42:0.0338:0:1.1 +15 99434906 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23275;SOR=Inf;LSEQ=GTGGTCACTACCCGCCCCAC;RSEQ=TCACCCGCCACCCTAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:39,160:199,0:0:2,0:22.6:1:32.4:1:1:0:60:38.8:1:0:0.1 0/1:186:2:1,1:43,140:183,2:0.0108:2,2:35:1:29.5:1:0.42009:3.23:60:4:0.0109:0:1 +15 99435582 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGAGGTCAGAGTTTGAGA;RSEQ=CAGCCTGGCCAACGTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:30:0:1:0:31.5:4:1:0:1 +15 99439963 . A AT 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.362;SOR=0.72834;LSEQ=CTCAATTATGTGTGTTTTTG;RSEQ=TTTTTTTTTTCTTCTTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:30:22,8:296,82:378,30:0.0733:2,2:21.6:1:29.1:1:0.49904:1.31171:59.5:14:0.0702:0.022:0.4 0/1:312:17:10,7:215,79:294,17:0.0545:2,2:18.7:1:29.1:1:0.26231:1.90076:60:34:0.0557:0.0192:0.3 +15 99451887 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12434;SOR=Inf;LSEQ=ACTGTGGCCAAGGGCAGGTG;RSEQ=GCTAACATCGATTTCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:267,98:365,0:0:2,0:23.3:1:31.6:1:1:0:60:90.25:1:0:0.1 0/1:381:4:1,3:253,124:377,4:0.0105:2,2:20.8:1:26:1:0.10994:6.0903:60:3:0.008:0:1 +15 99452153 . G A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08241;SOR=Inf;LSEQ=GTGACAGCATCCAAAACACC;RSEQ=TGGGCCCAACCATCATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:107,272:379,0:0:2,0:24.9:1:31.4:1:1:0:60:125.333:1:0:0.1 0/1:293:3:2,1:97,193:290,3:0.0102:2,2:12.3:1:21.3:1:0.2646:3.96:60:2:0.0069:0:2 +15 99454245 . A G 43 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGAAGAAAGATAAGTTC;RSEQ=CCTCGTTCACTGAAGTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:13.7:1:27.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99454363 . A G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30567;SOR=Inf;LSEQ=ACAAAGGATGGAGCCCTTGG;RSEQ=GCTCTGCATAGTGAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:27:26,1:5,0:5,27:0.8438:0,1:27:1:32.1:1:1:0:58.5:54:0.8438:0:1 1/1:11:11:10,1:0,0:0,11:1:0,2:19.3:1:29.4:1:1:0:60:10:1:0:1.1 +15 99454620 . GC G 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00095;SOR=Inf;LSEQ=ATAACCTGGCACCGGTACCG;RSEQ=CCCCTGACTACAGGGATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1051:0:0,0:519,531:1050,0:0:2,0:24.7:1:31.4:1:1:0:60:44.652:0.999:0:0.2 0/1:1067:11:4,7:524,531:1055,11:0.0103:2,2:25.9:1:30.2:1:0.5469:1.72606:60:22:0.0105:0.0028:0.5 +15 99454795 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54819;SOR=0;LSEQ=GAGTCCCCAGGGAGAGCCAC;RSEQ=CCAAACATCCCTACTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:2,95:97,2:0.0202:1,0:17.5:1:28.5:1:1:0:60:4:0.0208:0:1 0/0:51:0:0,0:1,50:51,0:0:1,0:24.7:1:31.5:1:1:0:60:50:1:0:0.2 +15 99454924 . G A 111 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTTTAGTGAGTGATTAGAG;RSEQ=TGTTTGAATAAAATAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:21.6:1:32.2:1:1:0:56.7:22:1:0:1.4 1/1:1:1:0,1:0,0:0,1:1:0,0:40:0:31:0:1:0:60:2:1:0:1 +15 99454962 . C T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAAAATGGGGAAAGCTTG;RSEQ=TTTTTCCAGAATTAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25.5:1:29:1:1:0:60:4:0.6667:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:33:0:1:0:60:2:1:0:1 +15 99456175 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14916;SOR=Inf;LSEQ=TATTTGTTTATTTAGACCTC;RSEQ=CATTATAGAAAGTGTGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:138,9:147,0:0:2,0:23.3:1:32:1:1:0:59.9:146:1:0:0.4 0/1:93:2:1,1:83,8:91,2:0.0215:2,2:15:1:27.5:1:0.18513:9.84041:60:4:0.022:0:1 +15 99456198 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50154;SOR=0;LSEQ=TTATAGAAAGTGTGACATGC;RSEQ=GGGCCTCTGGGGAAGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:2,0:172,24:196,2:0.0101:2,0:24:1:30:1:1:0:60:4:0.0102:0:2 0/0:170:0:0,0:135,35:170,0:0:2,0:23.1:1:29.9:1:1:0:60:340:1:0:0.4 +15 99456253 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21637;LSEQ=TCAGAGCCCCGAACTTTCTC;RSEQ=GAACTTAATTGTCTTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:434:333:230,103:69,32:101,333:0.7673:2,2:24.2:1:31:1:0.90268:1.04:59.9:332:0.7685:0:1.1 0/1:452:188:112,76:160,103:263,188:0.4159:2,2:25.9:1:29.8:1:0.84529:1.05395:60:61.667:0.4129:0:1.1 +15 99456553 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09916;SOR=1.39592;LSEQ=CCCAGCATCCACACTTCTTC;RSEQ=CAAGCTCACTGGCCTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:245:155:36,119:16,74:90,155:0.6327:2,2:22.3:1:29.6:1:0.33597:1.40:59.9:37.75:0.6266:0:1.1 1/0:235:166:48,118:21,48:69,166:0.7064:2,2:23.1:1:28.7:1:0.87531:1.07518:60:82:0.71:0:1.2 +15 99456562 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1044;SOR=Inf;LSEQ=CACACTTCTTCGCAAGCTCA;RSEQ=TGGCCTTGCTTGTACCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:38,180:218,0:0:2,0:21.9:1:32.7:1:1:0:59.9:53.5:1:0:0.7 0/1:195:3:1,2:47,145:192,3:0.0154:2,2:9:1:25.7:1:0.57377:1.54:60:2:0.0105:0:3.7 +15 99458718 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACACACAGACTCTCCAG;RSEQ=CCCCTTTCCACTTCCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19:1:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99459642 . C T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGGGATTACAGGCATGCAC;RSEQ=ACCATGCCCAGCTAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:2,2:6,5:11,4:0.2667:2,2:31:1:31.8:1:1:1.18545:36:8:0.2667:0:1 0/0:3:0:0,0:2,1:3,0:0:2,0:23.3:1:32:1:1:0:40.3:6:1:0:0 +15 99459832 . AT A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.20418;SOR=Inf;LSEQ=TAAAGGTACTGAGAGCTATT;RSEQ=TTTTCCTTACAAGCATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:194,48:242,0:0:2,0:21.3:1:31.1:1:1:0:60:120:1:0:0.1 0/1:200:2:1,1:146,52:198,2:0.01:2,2:37.5:1:31:1:0.46075:2.79059:60:4:0.0101:0:0.5 +15 99460184 . G T 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GCCTTTCTCCCCACCAGGTA;RSEQ=TGTGTAAGTCAGCAGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:35:2,33:8,111:119,35:0.2273:2,2:25:1:30.5:1:1:1.1879:60:34:0.2267:0:1.1 0/0:121:0:0,0:4,117:121,0:0:1,0:23.7:1:31.5:1:1:0:60:59.5:1:0:0.2 +15 99465274 . C T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=0.14963;LSEQ=CTAAGGGGGCTCAATAGCTC;RSEQ=TTCTATTCCACGGTTAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:36:33,3:46,4:50,36:0.4186:2,2:24:1:32:1:1:1.04494:60:72:0.4186:0:1.1 0/1:52:5:3,2:45,2:47,5:0.0962:1,2:34.8:1:30.8:1:0.04168:13.36202:60:10:0.1:0:1.2 +15 99465285 . C T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70931;SOR=1.21943;LSEQ=CAATAGCTCCTTCTATTCCA;RSEQ=GGTTAAGATTCTTCTGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:22:20,2:71,8:79,22:0.2178:2,2:21.8:1:31.8:1:1:1.13:60:44:0.22:0:1.3 0/1:67:17:17,0:44,6:50,17:0.2537:2,1:23.9:1:30.4:1:0.32522:0:60:16:0.2424:0:1 +15 99465306 . T C 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.17428;SOR=Inf;LSEQ=GGTTAAGATTCTTCTGTTAC;RSEQ=CTTACTCAAGTCATAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:131,19:150,0:0:2,0:23.8:1:32.2:1:1:0:60:149:1:0:0.5 0/1:108:2:1,1:92,14:106,2:0.0185:2,2:5.5:1:27.5:1:0.25961:6.38302:60:4:0.0187:0:1.5 +15 99465473 . C T 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGACACCTACAACATCAC;RSEQ=GACCCGGAAGAGCTGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1047:0:0,0:502,544:1046,0:0:2,0:25:1:30.4:1:1:0:60:68.733:0.999:0:0.1 0/1:1136:53:24,29:515,568:1083,53:0.0467:2,2:23.3:1:29.5:1:0.77963:1.09547:60:106:0.0474:0:1.1 +15 99465709 . T A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60441;SOR=2.24043;LSEQ=CCACCTTCCTCACAACCTAG;RSEQ=GGAGAAGATGTGTTTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:1:1,0:35,119:154,1:0.0064:2,0:1:0:27:0:0.23226:0:60:2:0.0066:0:2 0/1:140:2:1,1:34,104:138,2:0.0143:2,2:16:1:28:1:0.43885:3.03:60:4:0.0145:0:2 +15 99465886 . C T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AGCTTGGTCTCTCCATAGAA;RSEQ=GTGCTGGGAGCAGGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:28:1:30.8:1:1:0:60:8:0.5:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:15:1:29.5:1:1:0:60:4:1:0:0 +15 99466085 . C T 34 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAAGATCAACTCCTGGAG;RSEQ=AGCCTCTGGTCTTGCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:34.7:1:22:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99466969 . C G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0089;SOR=0.08391;LSEQ=CCTGCCCGCGTGGATGGGGG;RSEQ=GTTATTCTCAGTGTACGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:73:73,0:0,0:0,73:0.9865:0,1:21.6:1:31.9:1:1:0:58.8:72:0.9863:0:1.4 1/1:42:36:33,3:6,0:6,36:0.8571:0,2:24.9:1:29.7:1:1:0:58.4:17:0.85:0:1.3 +15 99467239 . G T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00913;SOR=Inf;LSEQ=TAAAATACGGATCACAAGTT;RSEQ=AGGTAGGACTGGGGCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:217,382:599,0:0:2,0:25:1:31.8:1:1:0:60:73.875:1:0:0.1 0/1:507:6:3,3:193,307:500,6:0.0118:2,2:23.5:1:27.8:1:0.68128:1.59:60:12:0.0119:0:1 +15 99467303 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51039;SOR=0;LSEQ=CCATTGACAGCATATGCTAC;RSEQ=TGACTGCACAGGTTACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:19,170:189,2:0.0105:2,2:14:1:27.5:1:0.19895:8.75:58:4:0.0108:0:4.5 0/0:140:0:0,0:21,119:140,0:0:2,0:24.8:1:31.7:1:1:0:60:280:1:0:0.1 +15 99467708 . T C 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00024;SOR=Inf;LSEQ=TAGTTGGCAGGCCCCAGATT;RSEQ=CTCCTGCATTCATGGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:198,48:246,0:0:2,0:22.7:1:30.7:1:1:0:60:81:1:0:0.1 0/1:222:11:8,3:151,60:211,11:0.0495:2,2:18:1:29.5:1:1:1.06:60:22:0.0507:0:1.3 +15 99467930 . G A 202 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00961;LSEQ=AAAAGTAAGGCTTGTGGAGG;RSEQ=AGAAGAAACGTGGTAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:99:29,70:115,292:407,99:0.1953:2,2:25.2:1:30.6:1:0.90121:1.05:60:32:0.1932:0:1.1 0/0:431:1:1,0:144,286:430,1:0.0023:2,0:1:0:22:0:0.33643:0:60:2:0.0024:0:1 +15 99467934 . A C 219 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=292.08309;LSEQ=GTAAGGCTTGTGGAGGGAGA;RSEQ=GAAACGTGGTAAAACTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:1:1,0:129,347:476,1:0.0021:2,0:43:0:27:0:0.27254:0:60:2:0.0021:0:2 0/1:396:151:58,93:69,176:245,151:0.3813:2,2:24.8:1:30.3:1:0.03587:1.59:60:74.5:0.3791:0:1.2 +15 99467942 . GGT G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.4666;LSEQ=TGTGGAGGGAGAAGAAACGT;RSEQ=AAAACTGAAAGCAGGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:135:32,103:59,188:247,135:0.3525:2,2:25.9:1:31.8:1:1:1.01011:60:134:0.3536:0.0548:0.1 0/1:336:68:19,49:84,184:268,68:0.2024:2,2:22.2:1:30.3:1:0.65975:1.17675:59.9:136:0.2048:0.0327:0.1 +15 99468159 . GA G 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATCCGAGCCTCTCCTTT;RSEQ=GGTTGTGTAACCACTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:8.5:1:28:1:1:0:47:4:0.2222:0.1111:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99472170 . G A 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTATTTTAAATTGTCT;RSEQ=TGGAACTATCTCAAAGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:15.5:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99472734 . T C 262 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0;SOR=0.00651;LSEQ=CTGAATGTGAAGAAATGAAA;RSEQ=GAGCAAATTGTTCACCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:301:297:233,64:2,1:3,297:0.9867:2,2:25.3:1:31.9:1:0.52067:1.82:60:98:0.9899:0:1.1 0/1:226:73:54,19:124,29:153,73:0.323:2,2:28.5:1:30.4:1:0.22868:1.50168:60:23.333:0.3153:0:1.1 +15 99473361 . C T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60668;SOR=2.21236;LSEQ=TCCCCATTCTGTTCTGATAC;RSEQ=GTGTGAGAGAGGATAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:0,1:179,36:215,1:0.0046:2,0:1:0:25:0:0.1713:0:60:2:0.0047:0:1 0/1:196:2:1,1:165,29:194,2:0.0102:2,2:19:1:25.5:1:0.28336:5.61102:60:4:0.0104:0:1 +15 99473512 . G A 60 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72542;SOR=1.65135;LSEQ=CTGTATGCCTCTGTGAACCC;RSEQ=GAGTACTTCAGCGCTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:461:3:3,0:153,305:458,3:0.0065:2,0:1:0:27:1:0.03826:0:60:6:0.0065:0:1.3 0/1:467:5:4,1:163,298:461,5:0.0107:2,2:17.6:1:26:1:0.05783:7.28:60:10:0.0108:0:1.4 +15 99473606 . A G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04434;SOR=2.92392;LSEQ=AGCTTTCAGGAGGGTTGCTA;RSEQ=TTTGGGAAAGGAAGGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:0,6:5,95:100,6:0.0566:2,0:28:1:32:1:1:0:60:12:0.0577:0:1 0/1:80:12:0,12:5,63:68,12:0.15:2,0:34.4:1:29.8:1:1:0:60:11:0.1392:0:1.4 +15 99473685 . C CT 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.36407;SOR=0.29207;LSEQ=TCATTAATATTTCTTTCTTT;RSEQ=TTTTTTTTTTTAATCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:1,3:0,17:17,4:0.1905:1,2:21.8:1:32.5:1:0.19048:0:60:8:0.2105:0:0 0/1:16:1:0,1:0,15:15,1:0.0625:1,0:42:0:27:0:1:0:60:2:0.0714:0:0 +15 99473878 . ATGC A 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTAACATCTAGTCAGAGGAT;RSEQ=TGCAGCTGACAAAACAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:32.5:1:1:0:60:4:1:0:0 +15 99477722 . G A 42 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTTTTTTTCAAAAATGT;RSEQ=TTTTTATGTGATGAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:19.7:1:27:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99477911 . T G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCATGTGGAAAGTTGACA;RSEQ=CAAGCCATGCCATCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:68:68:68,0:0,0:0,68:1:0,1:23:1:33.3:1:1:0:59.7:136:1:0:1.1 1/1:31:31:30,1:0,0:0,31:1:0,1:26:1:32.3:1:1:0:60:62:1:0:1 +15 99478225 . G A 272 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GAGGCCGCAAGCATGCGTGA;RSEQ=AGGATTGAGTTTCTCAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:465:465:154,311:0,0:0,465:1:0,2:24.5:1:30.7:1:1:0:59.8:115.25:1:0:1.1 0/1:515:155:60,95:131,229:360,155:0.301:2,2:24.7:1:29.3:1:0.62044:1.10:60:50.667:0.298:0:1.2 +15 99478451 . C G 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGACCCCTGTGCTCAGAC;RSEQ=AGGCCGCAGCACCACAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:135,17:152,0:0:2,0:23.2:1:31.2:1:1:0:60:37:1:0:0.8 0/1:127:18:16,2:98,11:109,18:0.1417:2,2:26.8:1:29.2:1:1:1.11269:60:36:0.1429:0:1.8 +15 99478493 . T C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AGTTCCAGACAACACAGGCA;RSEQ=CAGCAAGGGCCACCTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:269:269:201,68:0,0:0,269:1:0,2:24.5:1:31.7:1:1:0:59.9:66.25:1:0:1.1 1/1:282:264:194,70:13,5:18,264:0.9362:2,2:23.9:1:30.8:1:1:1.07:60:65:0.9386:0:1.2 +15 99478505 . A AC 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=0.19604;LSEQ=CACAGGCATCAGCAAGGGCC;RSEQ=CCTGACCCTCTGAGTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:291:285:205,80:6,0:6,285:0.9794:0,2:27.7:1:31.8:1:0.19294:0:59.8:56:0.979:0.0412:1 1/1:319:288:208,80:20,9:29,288:0.9028:2,2:27.2:1:30.7:1:0.67113:1.17:59.9:40.143:0.9035:0.0376:1 +15 99478713 . T C 265 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00415;LSEQ=GCCTGCTCTCTTTTCCTTTA;RSEQ=AATCTCCCTGCAAGGAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:306:63,243:1,2:3,306:0.9871:2,2:24.3:1:32.1:1:0.50282:1.92363:60:60.2:0.9901:0:1 0/1:252:60:12,48:48,142:190,60:0.2381:2,2:25.9:1:31.7:1:0.4892:1.35055:60:120:0.2429:0:1.2 +15 99478966 . C T 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCTGCCAAGCCAGGCCAG;RSEQ=GCCACTCCCTCCCCGAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:21.4:1:31.4:1:1:0:59.6:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99479013 . T C 43 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCCACTCCAGTAGCTATCT;RSEQ=CTCTGCTAACTTCTCGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:23:1:27.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99481953 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAATTTATAACGATGCT;RSEQ=TTATGGGAAATAAAATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14.5:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 99482380 . G GA 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.97486;LSEQ=CCTCGAAAGAAATTGGCATG;RSEQ=AAAAAAAAAATCCAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:7:6,1:155,19:174,7:0.0387:2,2:20.7:1:30.8:1:0.56588:1.35707:60:14:0.0393:0.011:0.9 0/1:159:6:5,1:133,19:152,6:0.0377:2,2:23.2:1:27.5:1:0.56227:1.39666:59.3:5:0.0321:0:1.7 +15 99482702 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12879;SOR=Inf;LSEQ=AGTGTGTCCCTTGAGTGCAC;RSEQ=GACTCCTTCTTGGGAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:0,92:92,0:0:1,0:26.6:1:31.3:1:1:0:60:22:1:0:0.1 0/1:52:2:0,2:3,47:50,2:0.0385:2,0:36.5:1:31:1:1:0:60:4:0.0385:0:1 +15 99485931 . T A 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09023;SOR=0;LSEQ=GAATCAAATTGTAAATATAT;RSEQ=AAAAGTGGAGATTGCTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:10,0:7,0:7,10:0.5882:0,0:24.5:1:28.6:1:1:0:60:20:0.5882:0:1.1 0/0:4:0:0,0:3,1:4,0:0:2,0:30:1:31.3:1:1:0:60:8:1:0:0.3 +15 99491644 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14672;SOR=Inf;LSEQ=CAACAGAGGGAGGATGATAT;RSEQ=CCGCACTTAGCCCAGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:90,1:91,0:0:1,0:23.8:1:32.9:1:1:0:60:182:1:0:0.1 0/1:57:2:2,0:55,0:55,2:0.0351:1,0:31:1:31:1:1:0:60:4:0.0351:0:1 +15 99491660 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51563;SOR=0;LSEQ=ATATCCCGCACTTAGCCCAG;RSEQ=GCCTGGCTCGCTGTCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:2,0:116,1:117,2:0.0168:1,0:21.5:1:31.5:1:1:0:60:4:0.0171:0:1 0/0:81:0:0,0:80,1:81,0:0:1,0:23.2:1:31:1:1:0:60:80:1:0:0.1 +15 99492045 . G A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72939;SOR=0.88125;LSEQ=GCCATTCTCTCTGGTCCTGC;RSEQ=CCTCCCTTGCCAGGCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:46:1,45:0,26:26,46:0.6301:1,1:20.6:1:29.7:1:1:0:60:22:0.6197:0:1.1 1/0:65:39:3,36:0,26:26,39:0.6:1,2:24.4:1:29.6:1:0.26875:0:60:38:0.5938:0:1.6 +15 99492061 . G A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCGCCTCCCTTGCCAGGC;RSEQ=TGGCTAAGAGGTTTGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:1,59:60,0:0:1,0:22:1:32.1:1:1:0:60:59:1:0:0.6 0/1:46:18:0,18:2,26:28,18:0.3913:2,1:20.7:1:31.2:1:0.51304:0:60:36:0.4:0:1.9 +15 99500055 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTTTGGGTTTTGTACC;RSEQ=TGGTGGTTCTGGGTTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:17,1:18,2:0.1:1,0:34:1:30:1:1:0:60:4:0.1111:0:3 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:30:0:1:0:60:2:1:0:0 +15 99500064 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTTTGTACCGTGGTGGTT;RSEQ=TGGGTTCTGGGGGAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:18,1:19,2:0.0952:1,0:34:1:30:1:1:0:60:4:0.0952:0:3 0/0:4:0:0,0:4,0:4,0:0:0,0:5.8:1:30.5:1:1:0:60:8:1:0:0.5 +15 99500074 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGGTGGTTCTGGGTTCTG;RSEQ=GGGAAGAGAATGGAACCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:22,1:23,2:0.08:1,0:29.5:1:28.5:1:1:0:60:4:0.0833:0:3 0/0:5:0:0,0:5,0:5,0:0:0,0:13:1:32:1:1:0:60:10:1:0:0.4 +15 99500197 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16218;SOR=Inf;LSEQ=CAGTGCTCCCGCCGTACGCT;RSEQ=GTATGCGGGAAACCACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:191,7:198,0:0:1,0:22:1:30.5:1:1:0:60:17:1:0:0.4 0/1:134:2:1,1:125,7:132,2:0.0149:2,2:21.5:1:28:1:0.11626:16.76993:60:4:0.015:0:2 +15 99500256 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00748;SOR=0.69384;LSEQ=CTGGCCATGTGCGCCCTCCC;RSEQ=GTTTGGACCCCCTCCCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:197:141,56:221,101:322,197:0.3796:2,2:28.4:1:30.5:1:0.49242:1.15:60:48.25:0.3784:0:1.1 0/1:480:143:98,45:213,123:336,143:0.2979:2,2:23.9:1:29.3:1:0.297:1.26:60:46.667:0.2941:0:1.2 +15 99500636 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01585;SOR=Inf;LSEQ=ACGGGGGCCGCAAGAACGAG;RSEQ=GGGCCTTGCCGCTGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:200,328:528,0:0:2,0:24.7:1:30.1:1:1:0:60:43:1:0:0.2 0/1:411:5:2,3:172,234:406,5:0.0122:2,2:12.6:1:29:1:1:1.10233:60:10:0.0123:0:1.6 +15 99500673 . C A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09214;SOR=Inf;LSEQ=CCAGTCTTCGACCTGCTGAT;RSEQ=CTTGGATCCTGAATCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:88,241:329,0:0:2,0:27.5:1:31.2:1:1:0:60:26.417:1:0:0.1 0/1:272:3:2,1:90,179:269,3:0.011:2,2:19.3:1:21:1:0.26501:3.96:60:2:0.0076:0:3.3 +15 99500676 . TG T 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66056;SOR=1.86684;LSEQ=GTCTTCGACCTGCTGATCCT;RSEQ=GATCCTGAATCTGTGCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:2:2,0:77,232:309,2:0.0064:2,0:1:1:27.5:1:0.06391:0:60:6:0.0046:0.0074:1 0/1:251:3:2,1:78,170:248,3:0.012:2,2:21.7:1:28.7:1:0.23905:4.33:60:6:0.0121:0.004:0 +15 99500693 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20392;SOR=Inf;LSEQ=CCTTGGATCCTGAATCTGTG;RSEQ=AAACAGTAACGTGTGCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:44,191:235,0:0:2,0:23.8:1:32.6:1:1:0:60:57.75:1:0:0.1 0/1:194:2:1,1:53,139:192,2:0.0103:2,2:19:1:27.5:1:0.48026:2.61:60:4:0.0105:0:2 +15 99500720 . C G 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50037;SOR=0;LSEQ=TAACGTGTGCGCACGCGCAG;RSEQ=GGGGTGGGGGGGGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:14,102:116,2:0.0169:2,0:13:1:27.5:1:1:0:48.5:4:0.0174:0:3 0/0:102:0:0,0:16,84:100,0:0:2,0:42:0:8:0:1:0:60:0:0:0:3 +15 99500725 . T G 47 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.12934;SOR=0;LSEQ=TGTGCGCACGCGCAGCGGGG;RSEQ=GGGGGGGGAGAGAGAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:4:0,4:12,95:107,4:0.0357:2,0:11.5:1:23.5:1:1:0:52.5:3:0.028:0:2.3 0/0:91:0:0,0:14,76:90,0:0:2,0:47:0:9:0:1:0:60:0:0:0:3 +15 99500734 . A G 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.62075;SOR=0.34965;LSEQ=GCGCAGCGGGGTGGGGGGGG;RSEQ=GAGAGAGTTTTAACAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:0,3:3,70:73,3:0.039:1,0:20.3:1:30.7:1:1:0:60:6:0.04:0:2.3 0/1:72:1:0,1:7,64:71,1:0.0139:2,0:45:0:33:0:1:0:60:2:0.0141:0:3 +15 99835432 . TTGC T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.4929;SOR=Inf;LSEQ=TGTATGTGTTTTTGTTGCTG;RSEQ=TGCTGCTGCTGCTGTTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:29,0:0:2,0:27:1:31.5:1:1:0:60:58:1:0:0.2 0/1:32:2:1,1:14,16:30,2:0.0625:2,2:17:0:32:0:1:1.14:60:4:0.0625:0:0.5 +15 99835492 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11095;SOR=Inf;LSEQ=TTTACGTATTGCTTTTCCCT;RSEQ=CACCTGGCATCAAAACTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:8,17:25,0:0:2,0:21.8:1:28.2:1:1:0:60:24:1:0:0.1 0/1:13:2:1,1:1,10:11,2:0.1538:2,2:16.5:1:33:0:0.29487:7.42:60:4:0.1538:0:1 +15 99835541 . C G 34 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03846;SOR=Inf;LSEQ=TGTCATAGAACATATTTAAA;RSEQ=TAATTTTCTCCCAATGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:10,0:0:0,0:25.8:1:34.1:1:1:0:60:20:1:0:0 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:47:1:34:0:1:0:60:4:0.6667:0:1 +15 99856834 . A G 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=GAAGGCCTGTTTTTGCTTAT;RSEQ=GGGAAGAAAGTAGAGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:115,114:229,0:0:2,0:26:1:29.5:1:1:0:59.9:37.167:1:0:0.4 0/1:311:15:6,9:153,143:296,15:0.0482:2,2:27.7:1:31.3:1:0.43474:1.60246:60:30:0.0485:0:1.1 +15 99856849 . G A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42416;SOR=1.17001;LSEQ=CTTATAGGGAAGAAAGTAGA;RSEQ=AATTAATGGATGATAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:83:36,47:72,82:154,83:0.3502:2,2:29.4:1:30.9:1:0.68225:1.14568:59.9:166:0.3656:0:1.2 0/1:318:123:59,64:97,98:195,123:0.3868:2,2:28:1:29.6:1:0.81802:1.07343:60:60.5:0.3967:0:1.2 +15 99856920 . TAAA T 168 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=18.000;MSILEN=1;SSF=0.25446;SOR=0.74666;LSEQ=GGATTTAAATAGAAAACTCT;RSEQ=AAAAAAAAAAAAAAACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:50:12,38:20,18:38,50:0.4237:2,2:30.6:1:30.3:1:0.00748:3.46468:59.3:100:0.4274:0:0.5 0/1:144:51:10,41:22,20:42,51:0.3542:2,2:31.2:1:29.7:1:0.00112:4.43047:59.3:102:0.3592:0.0069:0.8 +15 99857022 . G A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46819;SOR=0.5095;LSEQ=CCCTGGCGGATACAAGCTTG;RSEQ=ACACCAGGGAAGGTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:0,7:0,14:14,7:0.3333:1,0:35.4:1:31:1:1:0:60:14:0.3333:0:1 0/1:15:3:1,2:0,12:12,3:0.2:0,2:12:1:29:1:0.2:0:60:6:0.2:0:1.3 +15 99861491 . G A 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0728;SOR=2.11802;LSEQ=GGCAATATTTATTTGCTTAC;RSEQ=TGACTTCTGACATGCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:17:15,2:39,2:41,17:0.2931:1,2:26.1:1:31.4:1:0.57287:2.55162:60:34:0.2982:0:1.1 0/1:49:23:21,2:25,1:26,23:0.4694:1,2:20.2:1:30.3:1:0.59428:2.34:60:46:0.4792:0:1 +15 99861539 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22191;SOR=Inf;LSEQ=TAGTTATGTTATTGTATAGT;RSEQ=TAAGTTATGCATGTTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:131,29:160,0:0:2,0:23.7:1:32.3:1:1:0:60:52.333:1:0:0.2 0/1:143:2:1,1:108,33:141,2:0.014:2,2:26.5:1:27.5:1:0.42027:3.23912:60:4:0.0143:0:1.5 +15 99861618 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.26612;LSEQ=ACACACAAATTTGAAAATGC;RSEQ=TAAGAGACTGGGGCTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:134:74,60:147,130:277,134:0.3252:2,2:26.7:1:30.7:1:0.75165:1.09:60:66:0.3243:0:1.1 1/0:471:246:129,117:119,106:225,246:0.5223:2,2:27.2:1:29.7:1:0.92669:1.01818:60:492:0.5223:0:1.1 +15 99861641 . T G 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAGACTGGGGCTATTTAGC;RSEQ=TGTGGGCAGCTGGCGTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:77:35,42:155,203:358,77:0.177:2,2:25.4:1:30.9:1:0.80025:1.09:60:154:0.182:0:1.1 0/0:493:0:0,0:233,260:493,0:0:2,0:26.3:1:29.6:1:1:0:60:81.167:1:0:0.6 +15 99861714 . TA T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20481;SOR=Inf;LSEQ=TGCATTCACAGAGATAATTA;RSEQ=AGACATTAAGGAAAACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:33,143:176,0:0:2,0:22.2:1:30.6:1:1:0:60:87:1:0:0.2 0/1:146:2:1,1:31,113:144,2:0.0137:2,2:22.5:1:29.5:1:0.3915:3.60:60:4:0.0139:0.0068:0 +15 99945673 . C G 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00041;SOR=0;LSEQ=GAGAAGGCCCAGGAATCTGA;RSEQ=TAAAGTTTGGTCAAGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:4,5:1,0:1,9:0.9:0,2:17.1:1:31.4:1:1:0:60:18:0.9:0:1.2 0/0:8:0:0,0:3,5:8,0:0:2,0:26.3:1:30.6:1:1:0:60:16:1:0:0.1 +15 101020987 . G A 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1448;SOR=0.16952;LSEQ=TAAAGAGTTCTTATCTTTTC;RSEQ=AGATACATGCTAAAATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:2,0:2,8:0.8:0,0:24.6:1:31:1:1:0:60:16:0.8:0:1.6 0/1:8:3:3,0:5,0:5,3:0.375:0,0:31.7:1:30.7:1:1:0:60:6:0.375:0:1.3 +15 101021060 . C G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAACCTATCTGTGGTAGG;RSEQ=GAGAGGTGTAGTGGGGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:21,10:0,0:0,31:1:0,2:21.8:1:30.9:1:1:0:60:62:1:0:1.2 1/1:36:36:25,11:0,0:0,36:1:0,2:21.7:1:30.2:1:1:0:60:72:1:0:1.1 +15 101021087 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51263;SOR=Inf;LSEQ=TGTAGTGGGGATAGAGAGGA;RSEQ=ATAGGATTGGCCTTGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:26,18:44,0:0:2,0:26.1:1:32.5:1:1:0:60:88:1:0:0.9 0/1:64:2:1,1:36,26:62,2:0.0313:2,2:29:1:28.5:1:1:1.37745:60:4:0.0317:0:1.5 +15 101022693 . A C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGGAGAGCCCTTTCTCC;RSEQ=ACACTGAGGAGTTCTCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 101094127 . T C 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=ACACACACAAATGGAGGAAA;RSEQ=CCCGAGAGCATCTCGAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:24.5:1:34:0:1:0:56.5:8:0.6667:0:3 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:25.5:1:34:0:1:0:60:4:0.6667:0:2.5 +15 101094130 . C T 90 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3;SOR=0;LSEQ=CACACAAATGGAGGAAATCC;RSEQ=GAGAGCATCTCGAATATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:30.6:1:32.1:1:1:0:58:14:1:0:2.1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:28.5:1:32.5:1:1:0:60:4:0.6667:0:2.5 +15 101094174 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.40739;LSEQ=GCTGAGGGCCCACCAGTCCA;RSEQ=AGCCCTTCCGTGACCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:7,0:5,0:5,7:0.5833:0,0:27:1:31.6:1:1:0:56.7:14:0.5833:0:2.1 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:18.9:1:32.1:1:1:0:60:16:0.6667:0:1.3 +15 101094335 . C G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27061;LSEQ=TGTTCTCCGGCTTCAAGTCC;RSEQ=TGTAGATGATCTCCTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:53:29,24:28,27:55,53:0.4907:2,2:27.5:1:31.4:1:0.7047:1.16:46.8:106:0.4907:0:2 0/1:136:28:12,16:56,52:108,28:0.2059:2,2:30.3:1:30.7:1:0.52517:1.43207:44.9:56:0.2105:0:2 +15 101094336 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50455;SOR=Inf;LSEQ=GTTCTCCGGCTTCAAGTCCC;RSEQ=GTAGATGATCTCCTTAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:56,52:108,0:0:2,0:26:1:30.4:1:1:0:47.8:216:1:0:1.5 0/1:136:2:1,1:67,67:134,2:0.0147:2,2:42:1:30.5:1:1:1:40:4:0.0152:0:2 +15 101094342 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50224;SOR=Inf;LSEQ=CGGCTTCAAGTCCCTGTAGA;RSEQ=GATCTCCTTAGAGTGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:53,54:107,0:0:2,0:26.7:1:30.8:1:1:0:48.4:214:1:0:1.5 0/1:129:2:1,1:62,65:127,2:0.0155:2,2:45.5:1:28.5:1:1:1.05:26:4:0.0157:0:2 +15 101094352 . A G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCCTGTAGATGATCTCCTT;RSEQ=GAGTGCAGGATGGCACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:49,57:0,0:0,106:1:0,2:27.1:1:31.4:1:1:0:48.2:105:1:0:1.6 1/1:129:129:59,70:0,0:0,129:1:0,2:27.2:1:30.6:1:1:0:47.3:128:1:0:1.4 +15 101094354 . A G 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50328;SOR=Inf;LSEQ=CCTGTAGATGATCTCCTTAG;RSEQ=GTGCAGGATGGCACAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:47,56:103,0:0:2,0:27.8:1:30.7:1:1:0:47.9:102:1:0:1.6 0/1:127:2:1,1:58,67:125,2:0.0157:2,2:8:0:30:1:1:1.15:60:4:0.0159:0:2.5 +15 101094364 . G A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61997;SOR=0.75493;LSEQ=ATCTCCTTAGAGTGCAGGAT;RSEQ=GCACAGATGATCTCTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:9:3,6:43,52:95,9:0.0865:2,2:18.6:1:30.9:1:0.72785:1.64614:48.4:18:0.0865:0:1.9 0/1:120:8:4,4:49,63:112,8:0.0667:2,2:22:1:29.4:1:0.73075:1.28:49.1:16:0.069:0:1.9 +15 101094365 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50108;SOR=Inf;LSEQ=TCTCCTTAGAGTGCAGGATG;RSEQ=CACAGATGATCTCTGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:45,56:101,0:0:2,0:27:1:31.3:1:1:0:49:49.5:1:0:1.5 0/1:119:2:1,1:52,65:117,2:0.0168:2,2:26.5:1:27:1:1:1.25:46:4:0.0171:0:2 +15 101094376 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.2251;SOR=0;LSEQ=TGCAGGATGGCACAGATGAT;RSEQ=TCTGCAGAGTAGAAGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:39,57:96,2:0.0204:2,2:23.5:1:30.5:1:1:1.46:45:4:0.0204:0:3.5 0/0:108:0:0,0:44,64:108,0:0:2,0:27:1:30.5:1:1:0:50.4:35:1:0:1.3 +15 101094448 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51153;SOR=0;LSEQ=CCCGGAACATACTCCATGAG;RSEQ=CTGCAGAGGAAGCGCTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:9,29:38,2:0.05:2,2:36.5:1:29.5:1:0.44231:3.11:60:4:0.0526:0:1 0/0:27:0:0,0:4,23:27,0:0:2,0:25.6:1:30.5:1:1:0:60:26:1:0:0.2 +15 101094476 . G A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14272;SOR=0.24552;LSEQ=GGAAGCGCTAGTCATGCCCC;RSEQ=TCCAGCACAGCCTGATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:1,10:1,12:13,11:0.4583:1,2:20.5:1:29.7:1:1:1.19:55.4:10:0.4348:0:1 0/1:12:2:0,2:0,10:10,2:0.1667:0,0:42:1:33:0:1:0:60:4:0.1667:0:1 +15 101592369 . C G 66 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGCTTTCCATTTTGGAGG;RSEQ=CTTGATAGGCCCAACTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:33.5:1:33.3:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:14:0:32:0:1:0:60:2:1:0:1 +15 101592629 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49862;SOR=0;LSEQ=GCTGACTCCTGTCTGTAGCC;RSEQ=TAGCGCTGAGCTCCCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:86,77:163,2:0.0121:2,2:38.5:1:31.5:1:1:1.11613:51:4:0.0123:0:1 0/0:159:0:0,0:90,69:159,0:0:2,0:29.1:1:30.1:1:1:0:53.3:52:1:0:0.3 +15 101592692 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23423;LSEQ=CAAACGCTGACTCCTGTCTG;RSEQ=AGCCCTAGCGCTGAGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:70:10,60:10,34:44,70:0.614:2,2:24:1:32.2:1:0.31328:1.75565:57.8:34:0.6071:0:1.2 0/1:100:27:6,21:21,52:73,27:0.27:2,2:21.4:1:31:1:0.61662:1.40876:58.7:54:0.2755:0:1.3 +15 101592701 . C A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09221;SOR=Inf;LSEQ=ACTCCTGTCTGTAGCCCTAG;RSEQ=GCTGAGCCTTGGACCCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:13,78:91,0:0:2,0:23.7:1:30.3:1:1:0:56.2:90:1:0:0.8 0/1:76:3:1,2:12,61:73,3:0.0395:2,2:31.7:1:26:1:0.43512:2.50:52:6:0.0395:0:1 +15 101592773 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.02437;SOR=0.25011;LSEQ=TAACCCAAGATCATAACTAG;RSEQ=GAGAGAATCGGGGAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:17:0,17:0,11:11,17:0.6071:0,1:31.1:1:32.4:1:1:0:60:34:0.6071:0:2.5 0/1:22:6:0,6:1,15:16,6:0.2727:1,0:21:1:30.5:1:1:0:60:12:0.2727:0:2.7 +15 101592783 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0177;SOR=0.20412;LSEQ=TCATAACTAGAGAGAGAATC;RSEQ=GGGAGGAAATAGGAAACGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:16:1,15:0,10:10,16:0.5926:0,1:27.6:1:32.8:1:1:0:60:32:0.5926:0:2.6 0/1:18:4:0,4:1,13:14,4:0.2222:1,0:30.3:1:31.5:1:1:0:60:8:0.2222:0:3 +15 101592831 . G A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53007;SOR=0.31868;LSEQ=AGAAGAAAACTTCCAAAGGG;RSEQ=TCCTTTCTCTACGGCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:1,6:0,2:2,7:0.7778:0,2:19:1:31.4:1:1:0:60:14:0.7778:0:2.9 1/0:4:2:0,2:0,2:2,2:0.5:0,0:5:1:31:1:1:0:60:4:0.5:0:3 +15 101592856 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTCTACGGCCACCACTTC;RSEQ=GTGGGGTTCACCCTGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:33:1:31:1:1:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +15 101593086 . A T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCCCAGGACCCACCCGCATC;RSEQ=GGGCGGGGGGGATGTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:30.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:28:0:1:0:60:2:1:0:0 +16 114974 . G A 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.51609;SOR=0;LSEQ=TAGCCAGGGTGGCTTCTTGC;RSEQ=CTGCAGGCTGCTCGTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:46,14:60,2:0.0323:2,2:10:0:30:1:0.42834:3.20861:60:4:0.0323:0:1 0/0:41:0:0,0:33,8:41,0:0:2,0:20.1:1:29.7:1:1:0:60:82:1:0:0.2 +16 115021 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50159;SOR=0;LSEQ=GGGCCTCACTCATGGTTCCT;RSEQ=GCAGAGCAAGGCAGGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:67,48:115,2:0.0171:2,2:39.5:1:29.5:1:1:1.39177:60:4:0.0171:0:1 0/0:98:0:0,0:61,37:98,0:0:2,0:25.4:1:30.2:1:1:0:60:31.667:1:0:0.5 +16 115041 . C T 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAGAGCAAGGCAGGCCTG;RSEQ=GGGGCATGGTGTGTTATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:71,63:134,0:0:2,0:27:1:30.8:1:1:0:60:43.667:1:0:0.2 0/1:128:26:13,13:58,44:102,26:0.2031:2,2:21.2:1:28.7:1:0.6591:1.3153:60:52:0.2031:0:2 +16 115072 . A C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGTTATTCAATAATGACAA;RSEQ=GCTGACATCTGAAGATTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:83,80:163,0:0:2,0:24.7:1:31.2:1:1:0:60:80.5:0.9938:0:0.2 0/1:153:47:22,25:55,51:106,47:0.3072:2,2:27.6:1:30.5:1:0.60198:1.22385:60:94:0.3092:0:1.6 +16 337750 . C G 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATCCGGGCCTGGGCCCCA;RSEQ=CCAGACCTGGGTACGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:16.5:1:32:1:1:0:52.5:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 337871 . T C 83 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAGGGACCTCGGCTGCC;RSEQ=CACTTGGGCTGGGCCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:12,6:0.3333:0,0:31:1:32.2:1:1:0:60:12:0.3333:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 338322 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17858;SOR=Inf;LSEQ=GAGGCCTGTGGCAGGGGACG;RSEQ=CGTGTCCACACCCCATCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:7,199:206,0:0:1,0:24.2:1:32.2:1:1:0:59.8:67.667:0.9951:0:0.2 0/1:152:2:1,1:9,141:150,2:0.0132:2,2:27.5:1:29.5:1:0.12766:14.91:60:4:0.0135:0:1 +16 338332 . A AC 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21436;SOR=0.68;LSEQ=GCAGGGGACGGCGTGTCCAC;RSEQ=CCCCATCCCGAGGAGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:47:1,46:1,132:133,47:0.2611:1,1:22.7:1:30.6:1:0.45512:2.85:59.9:22.5:0.2586:0.0556:0.1 0/1:124:24:1,23:3,97:100,24:0.1935:1,1:23.6:1:30.5:1:0.58201:1.40:60:48:0.2034:0.0242:0 +16 338366 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52999;SOR=0;LSEQ=AGCCTCCTGTCCATGCCCCA;RSEQ=GGCCCCCACTGCATGTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:0,2:1,105:106,2:0.0185:1,0:28.5:1:31.5:1:1:0:60:4:0.019:0:1 0/0:64:0:0,0:1,63:64,0:0:1,0:22.4:1:29.3:1:1:0:59.9:63:1:0:0.1 +16 339082 . CT C 32 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCGGAAGCCCTTTTTCTT;RSEQ=TTTTTTTTTTTTGGGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:39.5:1:32.5:1:1:0:57.5:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 339291 . G C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.81657;SOR=0.82747;LSEQ=GCCCAGGCTGGTCTCGAACT;RSEQ=CTGAGCTGAGGCAATCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:24:24,0:57,0:57,24:0.2963:1,1:24:1:31.1:1:1:0:40.3:11:0.2821:0:1.5 0/1:31:8:8,0:23,0:23,8:0.2581:1,0:22.8:1:29.9:1:1:0:40.4:16:0.2581:0:1.1 +16 339415 . G T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.12714;LSEQ=CCACATACTCGTGCGGGGAG;RSEQ=GGGCACCCCAGCCCTCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:667:214:148,66:312,138:450,214:0.3208:2,2:25.1:1:29.6:1:1:1.00821:60:34.667:0.318:0:1.1 0/1:495:28:14,14:294,173:467,28:0.0566:2,2:22.4:1:28.4:1:0.22776:1.69745:60:27:0.0556:0:1.1 +16 339665 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.18192;SOR=Inf;LSEQ=ACTGAGGTCCCACAGGGTCC;RSEQ=TCCTGCTGGCCTCAGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:13,227:240,0:0:2,0:23.8:1:33.4:1:1:0:59.9:79:1:0:0.4 0/1:179:2:1,1:19,158:177,2:0.0112:2,2:18.5:1:28:1:0.21154:8.13:60:4:0.0113:0:1 +16 339670 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17638;SOR=Inf;LSEQ=GGTCCCACAGGGTCCCTCCT;RSEQ=CTGGCCTCAGGCTGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:7,205:212,0:0:1,0:25.2:1:32.8:1:1:0:59.9:105:1:0:0.4 0/1:154:2:1,1:9,143:152,2:0.013:2,2:12:1:28:1:0.12605:15.13:60:4:0.013:0:1 +16 339672 . T C 180 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00291;SOR=0.43599;LSEQ=TCCCACAGGGTCCCTCCTGC;RSEQ=GGCCTCAGGCTGCCAGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:59:1,58:6,148:154,59:0.277:1,1:27.3:1:30.7:1:0.67624:2.3437:60:118:0.2783:0:1.3 0/1:147:21:0,21:7,119:126,21:0.1429:2,1:21.6:1:29.9:1:0.59372:0:60:42:0.1438:0:1.2 +16 339727 . C T 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCAGGGGTGAGCAGCACCC;RSEQ=ATTCAAACACCTGGGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:30:1,29:0,63:63,30:0.3226:1,1:21.8:1:28.3:1:0.32258:0:59.9:14:0.3146:0:1.7 0/0:43:0:0,0:0,43:43,0:0:1,0:20.1:1:31.9:1:1:0:60:42:1:0:0.3 +16 341078 . T C 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28531;SOR=0;LSEQ=TCTCCTGCCACAGCTGCTTC;RSEQ=GAGCGTGGTACCCGAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:2,1:244,6:250,3:0.0119:1,2:31.3:1:29.3:1:0.08104:19.385:60:6:0.0119:0:1 0/0:161:0:0,0:153,7:160,0:0:1,0:23.7:1:30.3:1:1:0:60:52.333:0.9937:0:0.3 +16 341109 . C T 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.41008;SOR=0.29333;LSEQ=CCCGAGCTCAAGCCCCGGGA;RSEQ=GGCGGCTCTACGATGGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:5:1,4:365,114:479,5:0.0103:2,2:8:1:25.2:1:0.01376:12.72483:60:4:0.0084:0:1.2 0/0:328:1:1,0:229,98:327,1:0.003:2,0:42:0:28:0:1:0:60:2:0.0032:0:2 +16 341120 . C T 142 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.16105;LSEQ=GCCCCGGGACGGCGGCTCTA;RSEQ=GATGGGACCTGGCTTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:623:2:1,1:434,187:621,2:0.0032:2,2:39.5:1:30:1:0.51281:2.31737:60:4:0.0032:0:1 0/1:426:32:20,12:255,139:394,32:0.0751:2,2:22.4:1:28.4:1:0.8484:1.10047:60:64:0.0758:0:1.1 +16 341362 . G A 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14234;SOR=0;LSEQ=AGCCCTGGGGAGGGAGCCTC;RSEQ=ACCAATGCTGCTGCGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:4:3,1:73,216:289,4:0.0137:2,2:19.3:1:28.8:1:0.05497:8.80:60:8:0.0139:0:1 0/0:213:0:0,0:67,146:213,0:0:2,0:21.3:1:29.6:1:1:0:60:52.25:1:0:0.1 +16 341476 . T C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49594;SOR=1.64964;LSEQ=GTCCCCTCCTAGGCCTGCCT;RSEQ=GGTGGTACCCGATACTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:12:0,12:1,27:28,12:0.3:1,0:24.3:1:29.8:1:1:0:60:24:0.3077:0:1.2 0/1:12:5:0,5:0,7:7,5:0.4167:0,0:18.8:1:30.6:1:1:0:60:10:0.4167:0:1.4 +16 341500 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.03448;SOR=Inf;LSEQ=GGTACCCGATACTGCAGCGC;RSEQ=CCCCACATTCATGATCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,24:24,0:0:1,0:21.2:1:33.2:1:1:0:60:48:1:0:0.3 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:30.5:1:31.5:1:1:0:60:4:0.3333:0:2 +16 343369 . TG T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAAGGGCCCAGTATGGC;RSEQ=GGGGACACCCAGAGGGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:2,0:120,3:123,2:0.016:1,0:10:1:32.5:1:1:0:60:4:0.0161:0.008:3 0/0:48:0:0,0:46,2:48,0:0:1,0:24:1:32.2:1:1:0:60:96:1:0:0.1 +16 343905 . T C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7376;SOR=0.67566;LSEQ=AAAAACATCCCGGCCAGGCA;RSEQ=GGTGGCTCACACCTGTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:0,11:0,32:32,11:0.2558:1,0:23.5:1:29.9:1:1:0:60:22:0.2619:0:1.1 0/1:16:3:0,3:1,12:13,3:0.1875:1,0:17.3:1:28.7:1:1:0:60:6:0.1875:0:1 +16 346986 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.14342;SOR=Inf;LSEQ=CACACACTGAAGCTGCACAC;RSEQ=CTGAGACTGTGCGGAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:288,36:324,0:0:2,0:25.9:1:30.4:1:1:0:60:53:1:0:0.1 0/1:198:2:1,1:169,27:196,2:0.0101:2,2:32.5:1:27:1:0.26345:6.16464:60:4:0.0102:0:1 +16 347063 . C T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05996;SOR=0.62449;LSEQ=GCGGGGTGCTCACCCGTGGC;RSEQ=GGTCCTGCGGTGCCTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1115:50:30,20:597,468:1065,50:0.0448:2,2:23.7:1:31.2:1:0.6625:1.18:60:100:0.0455:0:1.1 0/1:913:26:13,13:509,376:885,26:0.0285:2,2:21.3:1:29.2:1:0.54704:1.35325:60:52:0.0289:0:1.1 +16 347184 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07881;LSEQ=CTGGCGCTCTTCCCCGACTC;RSEQ=GCCTTCTTGGCATTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:244:96,148:265,407:672,244:0.2661:2,2:25.7:1:30.5:1:1:1.00378:60:243:0.2703:0:1.1 0/1:829:23:9,14:347,457:804,23:0.0277:2,2:24.5:1:29.4:1:0.83184:1.1809:60:46:0.0282:0:1.2 +16 347257 . G T 104 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00167;SOR=14.007;LSEQ=AAGAGCTGCGAGTCGCCCTG;RSEQ=CCTCCGGTGGCCGAGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:1:0,1:74,275:349,1:0.0028:2,0:26:0:17:0:1:0:60:0:0:0:1 0/1:285:11:3,8:77,195:272,11:0.0386:2,2:26.5:1:30.2:1:1:1.0528:60:22:0.0396:0:1.5 +16 347326 . G A 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGCATCTGTAAGGCTCCC;RSEQ=TGGTGCAGCCGCCGCCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:36:0,36:2,71:73,36:0.3303:1,1:21.3:1:30.7:1:1:0:60:17:0.3208:0:1.2 0/0:43:0:0,0:1,42:43,0:0:1,0:17.8:1:31.4:1:1:0:60:42:1:0:0.2 +16 347668 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16921;SOR=Inf;LSEQ=TGAGGAGGTTCTGGCCTTCT;RSEQ=CAGGGACACAGCCTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:212,41:253,0:0:2,0:23.5:1:32.5:1:1:0:60:62.25:1:0:0.1 0/1:178:2:1,1:140,36:176,2:0.0112:2,2:27.5:1:30.5:1:0.37345:3.84965:60:4:0.0113:0:1 +16 348222 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3008;LSEQ=CACGGCCCTGGGGGCCCTGA;RSEQ=GATGGATCGCCGTCCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:615:169:80,89:185,261:446,169:0.2748:2,2:28.1:1:30.7:1:0.20227:1.27:60:55.333:0.2753:0:1.2 0/1:450:46:20,26:171,233:404,46:0.1022:2,2:26.9:1:29.9:1:0.87639:1.05:60:45:0.1011:0:1.4 +16 348417 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.08615;SOR=Inf;LSEQ=CTGAGGATGGAGAGGCAGGA;RSEQ=GGGGCATAGACAGAAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:0,18:18,0:0:1,0:25.7:1:30.1:1:1:0:60:36:1:0:0.1 0/1:8:2:0,2:0,6:6,2:0.25:0,0:37:1:28:1:1:0:60:4:0.25:0:2.5 +16 354143 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04876;SOR=Inf;LSEQ=CCCATCTTGAGCTGGGGCTC;RSEQ=GCTGCAGAGAAAGGGGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:37,0:37,0:0:1,0:22.2:1:29.9:1:1:0:60:74:1:0:0 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:42:1:31:1:1:0:60:4:0.1818:0:1 +16 354244 . C T 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.40726;SOR=0.34872;LSEQ=TGAAGAACATCAGGACATCC;RSEQ=GGCGGCAAGAAAACAGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:4:1,3:135,50:185,4:0.0212:2,2:8.5:1:28.3:1:0.06756:7.99598:60:8:0.0213:0:1.3 0/0:134:1:0,1:101,32:133,1:0.0075:2,0:1:0:25:0:0.24627:0:60:2:0.0075:0:1 +16 354287 . C T 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGACGCGGAGCGCGACAC;RSEQ=GACGCGGCCCACTCACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:255,108:363,0:0:2,0:26.1:1:31.2:1:1:0:60:362:1:0:0.1 0/1:286:40:29,11:165,81:246,40:0.1399:2,2:24.5:1:30.1:1:0.58582:1.29:60:80:0.1444:0:1.2 +16 354312 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02209;SOR=Inf;LSEQ=CGGCCCACTCACCATGCGCA;RSEQ=GCGCTTCAGCCGCTCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:308,146:454,0:0:2,0:25.6:1:31.4:1:1:0:60:112.5:1:0:0.1 0/1:399:5:3,2:253,141:394,5:0.0125:2,2:31.6:1:29.6:1:1:1.19566:60:10:0.0128:0:1.2 +16 354493 . C T 158 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=63.25937;LSEQ=TTGAAAGGTCACAGGCTAAA;RSEQ=ATTTCTTTGTGAAGGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:1:0,1:78,276:354,1:0.0028:2,0:41:0:11:0:1:0:60:0:0:0:5 0/1:355:54:13,41:78,223:301,54:0.1521:2,2:25.4:1:27.5:1:0.86646:1.10285:60:108:0.1538:0:1.3 +16 358161 . C A 41 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=CCTGTCTGTGCCTGCCGCCT;RSEQ=TGTTGGCTTTCATCTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:17.5:1:29.5:1:1:0:60:4:1:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:13.3:1:26.3:1:1:0:60:6:1:0:1 +16 359953 . A G 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.68725;LSEQ=GGGAGGACGATGGGCTGAGG;RSEQ=CCGCAAAGCCGGTACTTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1129:500:270,230:345,282:627,500:0.4429:2,2:26.2:1:31.6:1:0.76343:1.04215:59.8:82.333:0.4427:0:1.1 1/0:1049:601:332,269:241,204:445,601:0.5729:2,2:25.6:1:30.7:1:0.75353:1.04:59.9:53.636:0.5712:0:1.2 +16 360144 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14956;SOR=Inf;LSEQ=CCGTGCCAATAGAGCTCCTG;RSEQ=CCCCGACCGCCGGTCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:32,213:245,0:0:2,0:21.5:1:32.1:1:1:0:60:48:1:0:0.1 0/1:155:2:1,1:24,128:152,2:0.0129:2,2:21:1:27:1:0.29921:5.25:60:4:0.0131:0:1 +16 360149 . G A 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01556;SOR=0;LSEQ=CCAATAGAGCTCCTGGCCCC;RSEQ=ACCGCCGGTCAGCAGGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:10:1,9:23,187:210,10:0.0455:2,2:18.4:1:30.9:1:1:1.10648:60:20:0.0457:0:1 0/0:129:0:0,0:17,112:129,0:0:2,0:23.2:1:30.3:1:1:0:60:42:1:0:0.1 +16 360303 . T C 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40351;SOR=3.42835;LSEQ=CCCAGGTGCCCAGCCACGCG;RSEQ=CTTCCTAGCTGGTATTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:0,15:15,2:0.1176:1,0:41.5:1:30:1:1:0:60:4:0.1176:0:2 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:40:0:31:0:1:0:60:2:0.3333:0:2 +16 360317 . A G 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42208;SOR=3.20798;LSEQ=CACGCGTCTTCCTAGCTGGT;RSEQ=TTTACTGGGCACCTCCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:14,2:0.125:1,0:44:1:31.5:1:1:0:60:4:0.1333:0:2 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:26:0:34:0:1:0:60:2:0.3333:0:2 +16 364762 . G C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5159;SOR=0;LSEQ=TTCACATTTTCATGTTATCT;RSEQ=AATATCTCAATGTATTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:9,127:136,2:0.0145:2,2:18:1:28.5:1:0.14017:13.44:60:4:0.0146:0:1 0/0:94:0:0,0:11,83:94,0:0:2,0:21.2:1:30.7:1:1:0:60:93:1:0:0.1 +16 396070 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50385;SOR=0;LSEQ=GGTGTGGGTTAACGCCCGCC;RSEQ=CATCAGCACCTTTCCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:145,22:167,2:0.0118:2,2:12.5:1:29:1:0.25437:6.46823:60:4:0.012:0:1 0/0:137:0:0,0:108,29:137,0:0:2,0:20.2:1:29.6:1:1:0:60:67.5:1:0:0.1 +16 396077 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50052;SOR=0;LSEQ=GTTAACGCCCGCCTCATCAG;RSEQ=ACCTTTCCCTGGCTTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:155,31:186,2:0.0106:2,2:16.5:1:29.5:1:0.31221:4.93722:60:4:0.0108:0:1 0/0:166:0:0,0:124,41:165,0:0:2,0:20.2:1:31:1:1:0:60:40.25:0.9938:0:0.2 +16 396106 . C T 39 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.07042;LSEQ=CTGGCTTGTTCTCCAGCTCT;RSEQ=GGAGGTGAGTACAGAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:1,2:192,81:273,3:0.0109:2,2:22.7:1:30:1:0.21599:4.71046:60:6:0.0109:0:1 0/1:258:3:0,3:162,93:255,3:0.0116:2,0:1:0:25:1:0.0505:0:60:6:0.0118:0:1 +16 396234 . G A 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCTTCTGAGGGAGTCTTCC;RSEQ=GGGGGAGCAGCGTCTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:32:17,15:450,310:760,32:0.0403:2,2:26.1:1:30.3:1:0.58275:1.28041:60:31:0.0394:0:1.9 0/0:707:0:0,0:391,316:707,0:0:2,0:23.6:1:29.6:1:1:0:60:234.667:1:0:0.6 +16 396264 . A G 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=0.69347;LSEQ=GCGTCTCTGCCATCGTCCTC;RSEQ=TCCATGTCCTGGTCACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1011:662:370,292:203,144:347,662:0.6548:2,2:24.2:1:30.8:1:0.46187:1.11242:60:81.75:0.656:0:1.2 1/0:933:530:298,232:216,185:401,530:0.5681:2,2:24.7:1:30.2:1:0.50581:1.10:60:131.5:0.568:0:1.1 +16 397044 . G T 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTGGGACTCTGCGTCAA;RSEQ=GAACAATGAGCGCTGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:97,270:367,0:0:2,0:23.3:1:31.5:1:1:0:60:44.875:1:0:0.1 0/1:320:65:21,44:81,174:255,65:0.2031:2,2:24.4:1:29.5:1:1:1.03:60:64:0.2025:0:1.1 +16 397060 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.103;SOR=Inf;LSEQ=TCAAGGAACAATGAGCGCTG;RSEQ=ACCCTAATACATCAGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:59,213:272,0:0:2,0:23.3:1:32.1:1:1:0:60:89.667:1:0:0.1 0/1:241:3:2,1:59,179:238,3:0.0124:2,2:14.7:1:25.7:1:0.15859:6.01:60:6:0.0125:0:1 +16 397764 . CT C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGATAATCATGGGTCAC;RSEQ=TCAGCCCCATCGACCGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:45:1:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 447416 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCTGGGGTCCGACTCCCCC;RSEQ=GAGGCCTCGGGGCGCGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:31.5:1:1:0:60:4:1:0:1 +16 737793 . G A 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.45385;LSEQ=GGGGCTGGCCCATGAGGTGC;RSEQ=CCCTCAGAACAGCTGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:28.5:1:32.5:1:1:0:60:4:0.4:0:1 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:17.3:1:31:0:1:0:60:6:0.4286:0:1 +16 737939 . C A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.64518;LSEQ=CTGGGCCCGGGAGCAGGACA;RSEQ=CACGTGATTTGTAACACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:1,0:13,16:29,1:0.0333:2,0:1:0:31:0:0.46667:0:40:2:0.0357:0:1 0/1:37:2:1,1:16,19:35,2:0.0541:2,2:27.5:1:31.5:1:1:1.18:60:4:0.0541:0:1 +16 1032133 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17753;SOR=Inf;LSEQ=TCCCGGCCTGCATCCGCGAC;RSEQ=CCGTGTCGCAGGTGCTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:32,14:46,0:0:2,0:25.7:1:30.5:1:1:0:60:92:1:0:0.1 0/1:34:2:1,1:20,12:32,2:0.0588:2,2:15:0:31.5:1:1:1.64076:60:4:0.0606:0:1.5 +16 1032162 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16954;SOR=Inf;LSEQ=CAGGTGCTCAAGGGCTACGA;RSEQ=TGGAGTCTGGTGCCCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:48,27:75,0:0:2,0:26.7:1:32.2:1:1:0:60:74:1:0:0.2 0/1:53:2:1,1:30,21:51,2:0.0377:2,2:42:1:27.5:1:1:1.41877:60:4:0.0392:0:1 +16 1032176 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51502;SOR=0;LSEQ=CTACGACTGGAGTCTGGTGC;RSEQ=CATGCCGGTGCGCGGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:48,27:75,2:0.026:2,2:31.5:1:30:1:1:1.76374:60:4:0.0267:0:1 0/0:52:0:0,0:31,21:52,0:0:2,0:28.8:1:30.1:1:1:0:60:25:1:0:0.4 +16 1032187 . CGCG C 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.71059;SOR=1.60247;LSEQ=GTCTGGTGCCCATGCCGGTG;RSEQ=GCGGCGGCGGCGGCGCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:4:2,2:44,30:74,4:0.0513:2,2:10.8:1:32.5:1:1:1.45929:60:8:0.0519:0.0385:1 0/1:50:4:3,1:27,19:46,4:0.08:2,2:32.8:1:33:1:0.64112:2.08:60:8:0.08:0:0.3 +16 1032294 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50504;SOR=0;LSEQ=CGCAAGCTGGCCGACCAGTA;RSEQ=CCGCACCTGCACAACGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:89,78:167,2:0.0118:2,2:32.5:1:31:1:1:1.14013:55:4:0.0123:0:1.5 0/0:134:0:0,0:67,67:134,0:0:2,0:29.1:1:30.7:1:1:0:58.4:32.5:1:0:0.3 +16 1032336 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50887;SOR=0;LSEQ=CTCAGCAAGACGCTGGGCAA;RSEQ=CTGTGGCGGTGAGTGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:58,79:137,2:0.0143:2,2:32:1:30.5:1:1:1.36:60:4:0.0145:0:1 0/0:104:0:0,0:42,61:103,0:0:2,0:24.9:1:31.3:1:1:0:58.4:102:1:0:0.3 +16 1032339 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16649;SOR=Inf;LSEQ=AGCAAGACGCTGGGCAAGCT;RSEQ=TGGCGGTGAGTGCCGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:59,81:140,0:0:2,0:26.2:1:32.5:1:1:0:59.4:280:1:0:0.2 0/1:97:2:1,1:36,59:95,2:0.0206:2,2:9.5:1:28:1:1:1.63:60:4:0.0213:0:1 +16 1032343 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15752;SOR=Inf;LSEQ=AGACGCTGGGCAAGCTGTGG;RSEQ=GGTGAGTGCCGGCGCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:56,80:136,0:0:2,0:24.7:1:30.6:1:1:0:59.4:67:1:0:0.2 0/1:90:2:1,1:32,56:88,2:0.0222:2,2:8.5:1:28:1:1:1.74:37:4:0.023:0:1.5 +16 1032357 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11654;SOR=Inf;LSEQ=CTGTGGCGGTGAGTGCCGGC;RSEQ=CCCCGGGGGCGGGGTTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:41,68:109,0:0:2,0:20.8:1:31:1:1:0:60:53.5:1:0:0.1 0/1:57:2:1,1:18,37:55,2:0.0351:2,2:12:1:30:1:1:2.03:60:4:0.0364:0:1 +16 1033669 . G A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12995;SOR=Inf;LSEQ=CGGTTCCCCCTGTGGTGTGT;RSEQ=CCTGCGCCGAGGGCACAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:98,4:102,0:0:1,0:25.5:1:32.2:1:1:0:60:33:1:0:0 0/1:58:2:2,0:54,2:56,2:0.0345:1,0:15:0:29:0:1:0:60:4:0.0351:0:1 +16 1033698 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14609;SOR=Inf;LSEQ=GAGGGCACAGTGGGCGCCCT;RSEQ=GCCATCCCTGCCTCTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:156,42:198,0:0:2,0:22.7:1:32:1:1:0:60:38.6:1:0:0.1 0/1:123:2:1,1:100,21:121,2:0.0163:2,2:14:0:31.5:1:0.32694:4.67566:60:4:0.0163:0:1.5 +16 1033701 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15155;SOR=Inf;LSEQ=GGCACAGTGGGCGCCCTGGC;RSEQ=ATCCCTGCCTCTGCCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:163,48:211,0:0:2,0:22.7:1:31.4:1:1:0:60:51.75:1:0:0.1 0/1:135:2:1,1:106,27:133,2:0.0148:2,2:17:1:27:1:0.37302:3.87333:60:4:0.0149:0:1.5 +16 1033737 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08605;SOR=Inf;LSEQ=CTGTGCTGCAGCTTGCTGAG;RSEQ=GAGAGCGAGAAGCGGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:226,151:377,0:0:2,0:24.7:1:31.1:1:1:0:59.6:74.4:1:0:0.1 0/1:299:3:1,2:180,116:296,3:0.01:2,2:10.3:1:24.3:1:0.56418:3.09151:53.7:2:0.0068:0:3.3 +16 1033841 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16162;SOR=Inf;LSEQ=GCCACGGCGCAGGAAGAGCG;RSEQ=CAAAGCCGGCCACAGCGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:81,186:267,0:0:2,0:22.2:1:31:1:1:0:59.9:32.375:1:0:0.1 0/1:180:2:1,1:53,125:178,2:0.0111:2,2:9:1:25.5:1:0.51117:2.35:60:4:0.0116:0:2.5 +16 1034954 . T C 48 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGAGCCGGGCCAGGCCTA;RSEQ=GGGGGCGCCTACTTCCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:2,3:0.6:2,2:26.3:1:30.7:1:1:1.73:60:6:0.6:0:1 +16 1034977 . G A 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGCCTACTTCCACGCCG;RSEQ=GGCGTCCCCCGTGTGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:6:1:28.5:1:1:1:60:4:0.5:0:1 +16 1035069 . C T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGCCGCACATCAAGACGGAG;RSEQ=AGCCGAGCCCCGGCCACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:7,0:0:2,0:28.7:1:31.7:1:1:0:60:14:1:0:0.4 0/1:16:2:1,1:8,6:14,2:0.125:2,2:37:0:29.5:1:1:1.30929:60:4:0.125:0:1.5 +16 1035074 . G T 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07609;SOR=0;LSEQ=CACATCAAGACGGAGCAGCC;RSEQ=AGCCCCGGCCACTACGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:25.5:1:29.5:1:1:3.1622:60:4:0.2857:0:1 0/0:17:0:0,0:9,8:17,0:0:2,0:31.4:1:29.5:1:1:0:60:34:1:0:0.5 +16 1035077 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCAAGACGGAGCAGCCGAG;RSEQ=CCCGGCCACTACGGCGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:7,0:0:2,0:29.9:1:30.3:1:1:0:60:14:1:0:0.4 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:35:0:31:0:1:1.13389:60:4:0.1176:0:1.5 +16 1035107 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACGGCGACCAGCCCCGAGG;RSEQ=TCGCCCGACTACGGTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:26.1:1:29.9:1:1:0:60:6:1:0:0.4 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:28:1:28.5:1:1:1.55:60:4:0.1333:0:1 +16 1601287 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04565;SOR=1.70117;LSEQ=ACACAATGACCACGGCTGGC;RSEQ=GGGGTGGGCAGGTGCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:41:20,21:49,51:100,41:0.2908:2,2:27.6:1:30.3:1:1:1.00876:60:82:0.295:0:1.8 0/1:141:58:29,29:44,38:82,58:0.4113:2,2:27.3:1:30.1:1:0.73239:1.15668:60:57:0.4161:0:1.6 +16 1601299 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24397;SOR=0;LSEQ=CGGCTGGCAGGGGTGGGCAG;RSEQ=TGCAACTCTAAGCCGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:66,75:141,2:0.014:2,2:24:1:28:1:1:1.14:60:4:0.0143:0:2 0/0:146:0:0,0:74,72:146,0:0:2,0:26.4:1:30.4:1:1:0:60:35.5:1:0:0.7 +16 1601321 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24327;SOR=Inf;LSEQ=GCAACTCTAAGCCGAGGCCC;RSEQ=AAGGATCAGCAGCAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:62,69:131,0:0:2,0:27.1:1:30.3:1:1:0:60:20.833:1:0:0.7 0/1:128:2:1,1:57,67:124,2:0.0156:2,2:40.5:1:29:0:1:1.17:60:4:0.016:0:1 +16 1601331 . C A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.88889;SOR=1.07467;LSEQ=GCCGAGGCCCGAAGGATCAG;RSEQ=AGCAGGAGGGGCCCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:37:17,20:37,49:86,37:0.3008:2,2:26.4:1:30.4:1:0.84375:1.12:60:36:0.2975:0:1.8 0/1:117:37:16,21:34,46:80,37:0.3162:2,2:22.3:1:28:1:1:1.03:60:11.333:0.3036:0:1.8 +16 1601458 . A G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCCCCAGGGTGGCAGA;RSEQ=GGGCGGCCGCAGGTAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:0,12:1:0,0:28.4:1:31.4:1:1:0:60:24:1:0:1.2 1/1:6:6:0,6:0,0:0,6:1:0,0:13.8:1:32:0:1:0:60:12:1:0:2.2 +16 1968638 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50714;SOR=0;LSEQ=AGGCCCTGGCTCGCTTGACT;RSEQ=CGGCATCTTCACCTCTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:17,14:31,2:0.0606:2,2:24.5:1:27.5:1:1:1.20712:60:4:0.0625:0:1 0/0:23:0:0,0:11,12:23,0:0:2,0:23.3:1:30.3:1:1:0:60:22:1:0:0.3 +16 1986839 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGCTAAAACACTGAAA;RSEQ=AAACTGGCCCAGCCCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:10,1:11,2:0.1538:2,0:34:1:27.5:1:1:0:35.5:4:0.1538:0:7 0/0:6:0:0,0:6,0:6,0:0:0,0:22.3:1:33:0:1:0:60:12:1:0:0 +16 1986945 . T C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51937;SOR=0;LSEQ=GGCACCTCTTCTCTCTCGCT;RSEQ=TTGTTGCAAGGATACGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:113,34:147,2:0.0134:2,2:13:0:31.5:1:0.41584:3.29014:60:4:0.0137:0:1 0/0:98:0:0,0:72,26:98,0:0:2,0:20:1:29.4:1:1:0:60:48:1:0:0.3 +16 1986949 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16508;SOR=Inf;LSEQ=CCTCTTCTCTCTCGCTTTTG;RSEQ=TGCAAGGATACGCTGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:118,42:160,0:0:2,0:22:1:30.3:1:1:0:60:159:1:0:0.3 0/1:110:2:1,1:78,30:108,2:0.0182:2,2:17:1:32:1:0.48607:2.57407:60:4:0.0183:0:1 +16 1986980 . C G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00176;SOR=0.46684;LSEQ=CGCTGCGGCCTTCTGTAAGT;RSEQ=CCCCTAATAAATGCTCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:66:44,22:114,78:192,66:0.2558:2,2:22.6:1:32:1:0.30955:1.37:60:65:0.2549:0:1.5 0/1:210:29:18,11:109,71:180,29:0.1381:2,2:26:1:31.4:1:1:1.07:60:28:0.1359:0:1.4 +16 1987049 . C A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=AGTTCAGATCCCAACTGGCC;RSEQ=CATCTTGCAATGCTTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:94,136:230,0:0:2,0:24.8:1:30.9:1:1:0:60:31.857:1:0:0.5 0/1:261:15:7,8:111,135:246,15:0.0575:2,2:37.5:1:29.3:1:1:1.06:60:30:0.0591:0:2.4 +16 1987058 . A G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37054;SOR=0.80996;LSEQ=CCCAACTGGCCCCATCTTGC;RSEQ=ATGCTTTGGGGCCATCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:53:20,33:58,93:151,53:0.2598:2,2:22.8:1:30.7:1:1:1.02889:60:52:0.2562:0:1.5 0/1:235:52:24,28:84,99:183,52:0.2213:2,2:25.8:1:29.5:1:1:1.01:60:104:0.2261:0:1.7 +16 1987179 . C T 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00675;SOR=0;LSEQ=ATCCACTCCCACATGCTCCC;RSEQ=GGATTTCTGTGGGTATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:8:1,7:1,31:32,8:0.2:1,2:24.9:1:29:1:0.3641:4.21:60:7:0.1795:0:1.3 0/0:33:0:0,0:3,30:33,0:0:2,0:20.4:1:29.5:1:1:0:60:66:1:0:0.1 +16 1987238 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTGGAGCCTTGTTCCGT;RSEQ=CCCTCCAGGGCCTGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:0,13:13,2:0.1333:1,2:9.5:1:27.5:1:0.13333:0:60:4:0.1429:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:25.2:1:32.8:1:1:0:60:12:1:0:0 +16 2098815 . G A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25167;SOR=0;LSEQ=TGCAGAGAAGGCTGGGTTTG;RSEQ=TCTTGCACCAGGTTCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:29,187:216,3:0.0137:2,2:12.7:1:24.3:1:0.35864:3.20:60:2:0.0094:0:2.3 0/0:191:0:0,0:44,147:191,0:0:2,0:21:1:30.8:1:1:0:60:94.5:1:0:0.1 +16 2100311 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57954;SOR=2.66396;LSEQ=AGTCTCTAGTCTGGAAAATG;RSEQ=AGTGGGAGTCTTTAGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:1,0:182,33:215,1:0.0046:2,0:10:0:30:0:1:0:60:2:0.0047:0:1 0/1:163:2:1,1:136,25:161,2:0.0123:2,2:20.5:1:26.5:1:0.2944:5.35403:60:4:0.0126:0:2 +16 2100342 . C T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65684;SOR=1.97532;LSEQ=TTTAGGTGGTTTGTGACTTG;RSEQ=AGTTAAGGAGACCGTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:2:1,1:248,104:352,2:0.0056:2,2:21:1:21.5:1:0.50583:2.37803:60:1:0.0029:0:2.5 0/1:270:3:2,1:193,74:267,3:0.0111:2,2:9.7:1:27:1:1:1.30272:60:6:0.0113:0:1 +16 2100548 . G A 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25986;SOR=0;LSEQ=ACTATTCAGAGCCTGAGTTT;RSEQ=CTTTTTTTAGGAACATGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:43,209:252,3:0.0116:2,2:21.3:1:26.3:1:0.08132:9.59:60:6:0.0124:0:1 0/0:202:0:0,0:37,163:200,0:0:2,0:25.6:1:30.5:1:1:0:59.7:11.5:1:0:0.3 +16 2102486 . T A 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCTGGCTAAGTTTTGTA;RSEQ=TTTTTGTCGTGACAGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:6:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:29.5:1:1:0:60:4:1:0:1.5 +16 2103242 . C T 135 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=43.79641;LSEQ=GGCTCTCAGTCACAAGCCCC;RSEQ=GTTGTTCCTCCCTGTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:1:0,1:160,21:181,1:0.0055:2,0:1:0:26:0:0.12088:0:60:2:0.0056:0:1 0/1:112:22:20,2:75,15:90,22:0.1964:2,2:19.9:1:30.4:1:0.51728:1.99:60:21:0.1909:0:1 +16 2103261 . C T 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGTTGTTCCTCCCTGTCCT;RSEQ=CGCTCACGGCACTGCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:193,42:235,0:0:2,0:23.6:1:31.6:1:1:0:59.9:77.333:1:0:0.1 0/1:159:14:11,3:118,27:145,14:0.0881:2,2:21.1:1:28.1:1:0.72906:1.19056:60:13:0.0839:0:1.1 +16 2103266 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16363;SOR=Inf;LSEQ=GTTCCTCCCTGTCCTCCGCT;RSEQ=ACGGCACTGCTCCAGTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:204,47:251,0:0:2,0:24.1:1:31.5:1:1:0:59.9:34.857:1:0:0.1 0/1:171:2:1,1:134,35:169,2:0.0117:2,2:18.5:1:28.5:1:0.37771:3.78908:60:4:0.012:0:1 +16 2103485 . C T 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=GGCGACGCTGGGATGGGTGA;RSEQ=GTCAGGCTGCCCACTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:64,190:254,0:0:2,0:24.3:1:29.8:1:1:0:60:30.75:1:0:0.2 0/1:159:8:1,7:39,111:150,8:0.0503:2,2:18.9:1:29.5:1:0.68052:2.44826:60:16:0.0516:0:1.3 +16 2104217 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1704;SOR=Inf;LSEQ=CCAGGGCTGGAGTCCGGGTG;RSEQ=CCCTGCACTTCAGGGACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:208,26:234,0:0:2,0:22.3:1:32.1:1:1:0:59.7:77:1:0:0.1 0/1:165:2:1,1:138,25:163,2:0.0121:2,2:15:1:27:1:0.29113:5.43247:60:4:0.0123:0:1 +16 2105055 . A G 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACGTCTCCTCCGAGCC;RSEQ=CTCTCTGCTGGGGGTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:3,0:3,5:0.625:0,2:33.8:1:31.2:1:1:0:48.4:10:0.7143:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 2105280 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCTGTCTGTTGCTGCCG;RSEQ=GGGACTGATGATGGGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:2,0:91,2:93,2:0.0211:1,0:25.5:1:30.5:1:1:0:60:4:0.0215:0:1 0/0:32:0:0,0:31,1:32,0:0:1,0:19.2:1:30.5:1:1:0:60:64:1:0:0.3 +16 2105335 . C G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.82036;SOR=0.929;LSEQ=TTGGACACACTGTCCTGCGG;RSEQ=GGGAGGGGGAGGTGAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:68:59,9:146,14:160,68:0.2982:2,2:20.7:1:30.8:1:0.33879:1.58734:59.7:67:0.3032:0:1.2 0/1:159:45:35,10:99,15:114,45:0.283:2,2:24:1:30.5:1:0.22509:1.87758:60:90:0.2866:0:1.6 +16 2105400 . C T 202 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=198.87799;LSEQ=AACTGCCGCCGCTTCTCCCC;RSEQ=AGCTGACTTTGTCCTGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:790:1:0,1:499,289:788,1:0.0013:2,0:1:0:26:0:0.36755:0:60:2:0.0013:0:1 0/1:590:119:78,41:289,181:470,119:0.2017:2,2:25.8:1:29.3:1:0.4591:1.19:60:238:0.2038:0:1.3 +16 2105555 . G A 35 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92823;LSEQ=GAGATCCTGTTCTGATAATG;RSEQ=TCCTAAGTTCAGCTCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:39,244:283,3:0.0105:2,2:10.7:1:22.3:1:0.05483:12.32:60:2:0.0072:0:3 0/0:206:2:1,1:40,163:203,2:0.0097:2,2:37:1:30:0:0.36078:4.04:60:4:0.0099:0:1 +16 2106113 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.072;SOR=Inf;LSEQ=TGAGCCATGCGTGTTATTGA;RSEQ=GTCATAGAGTGACTAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:321,58:379,0:0:2,0:23.5:1:32.1:1:1:0:60:125.333:1:0:0.1 0/1:271:3:2,1:222,46:268,3:0.0111:2,2:24.3:1:29.7:1:0.4366:2.40299:60:6:0.0112:0:1.3 +16 2106362 . C G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.002;SOR=Inf;LSEQ=GTAGCCCTGGGCAAGCTGCT;RSEQ=GGTCTCTCTGAGCCTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:11,188:199,0:0:2,0:24.5:1:30.2:1:1:0:59.9:65.333:1:0:0.1 0/1:112:6:0,6:2,104:106,6:0.0536:1,0:30.3:1:29.5:1:1:0:60:12:0.0545:0:1.2 +16 2106547 . C A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10307;SOR=Inf;LSEQ=ATGGCAGCGGGGAGAGGTGG;RSEQ=AGCGCAGGCTGAAGGAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:193,28:221,0:0:2,0:24.5:1:32.2:1:1:0:60:43.2:1:0:0.1 0/1:105:2:1,1:90,13:103,2:0.019:2,2:9:0:27:1:0.25:6.70931:60:4:0.0194:0:1 +16 2106864 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55382;SOR=0;LSEQ=GAATGGTTGTCTGATTCTTG;RSEQ=GGTGGCCAGACAATGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:3:0,3:26,170:196,3:0.0151:2,0:34:1:29.7:1:1:0:60:6:0.0152:0:2.3 0/0:105:0:0,0:4,100:104,0:0:1,0:27.1:1:30.5:1:1:0:60:33.667:0.9902:0:0.1 +16 2107033 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14732;SOR=Inf;LSEQ=TATAGGGCAGCAGCCAGGCG;RSEQ=GGCCAGCAGCGGGACTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:223,78:301,0:0:2,0:22.2:1:30.9:1:1:0:60:42:1:0:0.1 0/1:188:2:1,1:145,41:186,2:0.0106:2,2:17:1:28:1:0.39783:3.50607:60:4:0.0108:0:1 +16 2107200 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30496;SOR=4.71977;LSEQ=GTGAGTGTGGTGGGTGGGGC;RSEQ=CAGGGCAGTGGAGGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:1:1,0:137,294:431,1:0.0023:2,0:1:0:26:0:0.31944:0:60:2:0.0024:0:2 0/1:277:3:2,1:101,173:274,3:0.0108:2,2:9.3:1:27:1:0.55758:3.41:60:6:0.0113:0:1 +16 2107322 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01255;SOR=Inf;LSEQ=GAGGCTGCCACTAGAGCGAG;RSEQ=CCCATGACTTCTAGGATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:3,63:66,0:0:1,0:23.7:1:32.5:1:1:0:59.6:32:1:0:0 0/1:21:3:0,3:1,17:18,3:0.1429:1,0:25.3:1:30.3:1:1:0:60:6:0.1579:0:1 +16 2108627 . G GC 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.66881;SOR=0.44141;LSEQ=CCTTCCCCAGCGGTGCTCCT;RSEQ=CCCCCCCCAAGCACAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:5:5,0:142,1:143,5:0.0338:1,0:20.8:1:31.3:1:1:0:60:10:0.0342:0.0068:0.2 0/1:66:1:1,0:64,1:65,1:0.0152:1,0:45:0:32:0:1:0:60:2:0.0152:0:0 +16 2108678 . C T 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00342;SOR=Inf;LSEQ=GCTGCAGGAGCCTCGGCAAC;RSEQ=TCACACATCCATGGCGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:297,90:387,0:0:2,0:21.6:1:31.5:1:1:0:59.9:128:1:0:0.1 0/1:248:6:2,4:181,61:242,6:0.0242:2,2:13.2:1:27:1:0.04233:5.88235:60:12:0.0246:0:1.2 +16 2108920 . T C 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03438;SOR=Inf;LSEQ=GCTGGCAGGAACGGGAGAGC;RSEQ=CCCCTCACGCCTGCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:124,275:399,0:0:2,0:22.8:1:30.3:1:1:0:60:27.5:0.9974:0:0.1 0/1:304:4:2,2:107,193:300,4:0.0132:2,2:22.5:1:28.3:1:0.61982:1.80:60:8:0.0138:0:1.8 +16 2109252 . G C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCTCGAATTCCTGACCT;RSEQ=AAGTGATCCACCCATCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:41.5:1:34:0:1:0:23.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 2110571 . C G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66402;SOR=0.85849;LSEQ=AACGTGTGGTGGGCACTGCG;RSEQ=GCTCAGGCGTGCTACTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:99:93,6:47,2:49,99:0.6689:1,2:22.9:1:31.1:1:1:1.51216:59.7:32:0.6621:0:1.1 1/0:82:52:48,4:24,5:29,52:0.6341:2,2:21.8:1:29.4:1:0.27005:2.47:60:16.333:0.6282:0:1.1 +16 2110573 . C T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11965;SOR=Inf;LSEQ=CGTGTGGTGGGCACTGCGCG;RSEQ=TCAGGCGTGCTACTCTCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:146,10:156,0:0:2,0:22.5:1:32.6:1:1:0:59.8:77:1:0:0.7 0/1:83:2:1,1:73,8:81,2:0.0241:2,2:37:0:29.5:1:0.20629:8.66381:60:4:0.0247:0:1.5 +16 2110575 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11382;SOR=Inf;LSEQ=TGTGGTGGGCACTGCGCGCT;RSEQ=AGGCGTGCTACTCTCGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:154,10:164,0:0:2,0:22.3:1:32.3:1:1:0:59.8:53.667:1:0:0.7 0/1:84:2:1,1:72,10:82,2:0.0238:2,2:13.5:1:26.5:1:0.24613:6.91238:60:4:0.0238:0:2 +16 2110577 . G T 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54145;SOR=0;LSEQ=TGGTGGGCACTGCGCGCTCA;RSEQ=GCGTGCTACTCTCGGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:154,9:163,2:0.0121:2,2:7.5:1:32.5:1:0.11789:16.28546:60:4:0.0122:0:2 0/0:90:0:0,0:78,12:90,0:0:2,0:23:1:31.2:1:1:0:60:44:1:0:0.8 +16 2110583 . C A 29 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90752;LSEQ=GCACTGCGCGCTCAGGCGTG;RSEQ=TACTCTCGGTCCCAAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:166,10:176,2:0.0112:2,2:29:0:29:1:0.1201:15.86783:60:4:0.0113:0:2 0/1:98:1:1,0:81,16:97,1:0.0102:2,0:28:0:30:0:1:0:60:2:0.0105:0:2 +16 2110608 . G A 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCGGTCCCAAGGGTGACTG;RSEQ=GAGGGCGTCCCACAGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:228,38:266,0:0:2,0:24.8:1:31.5:1:1:0:59.9:132:1:0:0.4 0/1:179:19:15,4:125,35:160,19:0.1061:2,2:23:1:28.2:1:1:1.05:60:18:0.1017:0:1.1 +16 2110795 . G A 231 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00592;LSEQ=TCTGCTGAACATCATCGAAC;RSEQ=GCTCCTTCAGCAGCTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:904:173:71,102:331,400:731,173:0.1914:2,2:26.3:1:31.2:1:0.34947:1.18858:60:85.5:0.1926:0:1.1 0/0:716:1:1,0:318,397:715,1:0.0014:2,0:37:0:25:0:0.44553:0:60:2:0.0014:0:1 +16 2111735 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25453;SOR=4.13201;LSEQ=CGGCCTCAGAGGGCTGGGGG;RSEQ=GTCTGTCCCCATGCGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:1,0:91,3:94,1:0.0105:1,0:7:0:32:0:1:0:60:2:0.0108:0:1 0/1:47:2:2,0:44,1:45,2:0.0426:1,0:29.5:1:29:1:1:0:60:4:0.0435:0:1 +16 2111779 . T C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90489;SOR=0.96549;LSEQ=CGGCCTGAGAGGGCTGAGGG;RSEQ=GTCTCCATGCGGTGGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:193:120:111,9:66,7:73,120:0.6218:2,2:23.2:1:31.7:1:0.60215:1.31:60:39:0.6223:0:1 1/0:119:73:67,6:44,2:46,73:0.6134:1,2:24.8:1:31.1:1:0.48278:1.9599:60:35.5:0.6121:0:1.2 +16 2112382 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15649;SOR=Inf;LSEQ=TTGTGTCTGGGCTGTGGGCT;RSEQ=CAGGCTGTGAGGCGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:170,8:178,0:0:1,0:25.2:1:32.3:1:1:0:59.8:34.6:1:0:0.1 0/1:117:2:2,0:111,4:115,2:0.0171:1,0:26:1:28:1:1:0:60:4:0.0171:0:1 +16 2112384 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1613;SOR=Inf;LSEQ=GTGTCTGGGCTGTGGGCTGC;RSEQ=GGCTGTGAGGCGGCTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:175,9:184,0:0:1,0:25.1:1:30.3:1:1:0:59.8:29.667:1:0:0.1 0/1:124:2:1,1:119,3:122,2:0.0161:1,2:19:1:31:1:0.06373:34.50252:60:4:0.0163:0:1 +16 2112668 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15283;SOR=Inf;LSEQ=GTCTCTGTCTGGGGCCCACC;RSEQ=GGGCTGGGTCTCAGGATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:50,239:289,0:0:2,0:22.1:1:30.2:1:1:0:60:71.25:1:0:0.1 0/1:186:2:1,1:29,153:182,2:0.0108:2,2:40.5:1:31:1:0.30025:5.20:60:4:0.011:0:1 +16 2113135 . G A 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65517;SOR=2.04942;LSEQ=TCTGTTGTGCACGTGCTCCC;RSEQ=CAGAGCCGGGCTCTGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:2:0,2:70,328:398,2:0.005:2,0:41:1:30:1:1:0:60:4:0.0052:0:1 0/1:294:3:2,1:63,228:291,3:0.0102:2,2:5:1:26.3:1:0.12404:7.17:60:6:0.0103:0:1.7 +16 2114407 . C T 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACACACACCACTTCAACAG;RSEQ=CTGCTGGACATCATCGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:767:0:0,0:305,462:767,0:0:2,0:26:1:31.5:1:1:0:60:41.611:1:0:0.1 0/1:630:84:35,49:235,311:546,84:0.1333:2,2:25.4:1:27.7:1:0.90581:1.0578:60:15.8:0.1274:0:1.2 +16 2115413 . CAAAAAAAAAAAAAAA C 183 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=24.000;MSILEN=1;SSF=0.00029;SOR=0.26631;LSEQ=GACAGAGCAAGACTCGATCT;RSEQ=AAAAAAAAAGGTGTTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:52:50,2:39,1:40,52:0.4444:1,1:29.1:1:32.2:1:1:1.55277:52.6:25:0.4545:0:0.1 0/1:63:11:10,1:25,6:31,11:0.1746:2,2:24.8:1:30.3:1:0.65361:2.36:54.7:22:0.1864:0.0317:0 +16 2115481 . C T 192 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=208.66288;LSEQ=TCACGGCTGCTGACTCAGAA;RSEQ=CATGAGCCTGTGTGTAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:787:1:0,1:498,287:785,1:0.0013:2,0:1:0:27:0:0.36641:0:60:2:0.0013:0:1 0/1:528:111:68,43:254,163:417,111:0.2102:2,2:26.5:1:28.3:1:1:1.01:59.8:11.333:0.2:0:1.3 +16 2115506 . C T 174 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=48.35918;LSEQ=AGCCTGTGTGTAAGTCCTGG;RSEQ=CTTCTCTTCAAAGGTGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1017:2:1,1:581,431:1012,2:0.002:2,2:6:1:30:1:1:1.34761:60:4:0.002:0:1 0/1:747:65:42,23:374,306:680,65:0.087:2,2:28.5:1:28.9:1:0.15131:1.49:60:130:0.0894:0:1.3 +16 2115712 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1401;SOR=Inf;LSEQ=AGCTGCATCTGCGTTGTGTT;RSEQ=GAGTCTGTTCCCCAGCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:33,247:280,0:0:2,0:23.2:1:31.5:1:1:0:60:55:1:0:0.1 0/1:168:2:1,1:33,133:166,2:0.0119:2,2:9.5:1:29:1:0.36477:3.99:60:4:0.0123:0:1 +16 2115819 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75613;SOR=0.73727;LSEQ=TCTTGTGGAGGGATGGATGC;RSEQ=AGAGGCCCCGTTGTACGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:30:1,29:0,10:10,30:0.7317:0,1:23.2:1:31.8:1:1:0:60:29:0.7632:0:1.2 1/0:18:12:0,12:0,6:6,12:0.6667:0,0:31.9:1:30.6:1:1:0:60:11:0.6471:0:1.5 +16 2120402 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.36269;LSEQ=TCCGGGACAAGGGTGCTGTC;RSEQ=TAGGACTGCGTTTTCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:434:226:158,68:141,66:207,226:0.5207:2,2:22.9:1:31.7:1:0.75499:1.09:59.7:112:0.5234:0:1.1 0/1:301:85:61,24:145,71:216,85:0.2824:2,2:23.2:1:30.2:1:0.49203:1.24:59.9:84:0.28:0:1.2 +16 2120643 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17767;SOR=Inf;LSEQ=CAGGTATCCCCGTCTCGGCA;RSEQ=GTGTGGTTCCTGGAAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:17,146:163,0:0:2,0:22.6:1:31.6:1:1:0:60:162:1:0:0.1 0/1:120:2:1,1:19,99:118,2:0.0167:2,2:29.5:1:32:0:0.30672:5.10:60:4:0.0168:0:1.5 +16 2120663 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16629;SOR=Inf;LSEQ=GGTGTGGTTCCTGGAAGCTG;RSEQ=AGAGACGGCCCCAGGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:6,108:114,0:0:2,0:22.7:1:32.5:1:1:0:60:113:1:0:0.1 0/1:79:2:1,1:7,70:77,2:0.0253:2,2:19.5:1:26.5:1:0.19344:9.42:60:4:0.0253:0:1 +16 2121725 . C T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06846;SOR=Inf;LSEQ=GTCCCAGGGTTGGGAAGAGC;RSEQ=AAGTCTGTTCCGTTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:416:0:0,0:241,175:416,0:0:2,0:23.1:1:31.4:1:1:0:60:45.222:1:0:0.1 0/1:289:3:1,2:178,108:286,3:0.0104:2,2:25.7:1:22.3:1:0.55984:3.2823:60:2:0.007:0:1 +16 2121961 . C A 49 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04398;SOR=Inf;LSEQ=TGGGGCCGGGCAGGGACCAT;RSEQ=CGTCCCACGTTGGGCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:127,204:331,0:0:2,0:26:1:31.4:1:1:0:59.9:35.778:1:0:0.2 0/1:282:4:3,1:114,164:278,4:0.0142:2,2:7.5:1:24.8:1:0.31058:4.29:60:8:0.0146:0:1 +16 2121994 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08779;SOR=Inf;LSEQ=GGCCAGGAGGACAGGGAGCT;RSEQ=CCACCTGCCTGCTGGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:73,137:210,0:0:2,0:23.4:1:31.6:1:1:0:60:29:1:0:0.1 0/1:169:3:2,1:61,105:166,3:0.0178:2,2:15.7:1:27.3:1:0.55635:3.42:60:6:0.0182:0:1 +16 2122005 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.16428;SOR=Inf;LSEQ=CAGGGAGCTGCCACCTGCCT;RSEQ=CTGGGCCTCCCTCCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:64,126:190,0:0:2,0:22.2:1:31.8:1:1:0:60:46.5:1:0:0.1 0/1:130:2:1,1:42,86:128,2:0.0154:2,2:27.5:1:26.5:1:1:2.04:60:4:0.0159:0:1 +16 2122139 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13298;SOR=Inf;LSEQ=GCTGAGAACAGGGCTCCATA;RSEQ=CCCTTGACGCTGTGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:168,28:196,0:0:2,0:24.4:1:32.9:1:1:0:59.8:31.667:1:0:0.1 0/1:113:2:2,0:97,14:111,2:0.0177:2,0:26.5:1:28:1:1:0:60:4:0.0179:0:1 +16 2122476 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGGCTCGGGCTCCATTTC;RSEQ=CTCAAACTCAGCTGCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:2,85:87,2:0.0225:1,2:28.5:1:31:1:0.06665:34.90:60:4:0.023:0:1 0/0:43:0:0,0:0,43:43,0:0:1,0:24:1:31.2:1:1:0:60:42:1:0:0.1 +16 2122708 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACTCCGAAAGGGAGGCC;RSEQ=TTCCTGGGAGGGAGGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:2,0:80,8:88,2:0.0222:2,0:20.5:1:29.5:1:1:0:60:4:0.0222:0:1 0/0:34:0:0,0:34,0:34,0:0:1,0:20.9:1:30.7:1:1:0:60:68:1:0:0.1 +16 2123009 . G A 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02475;SOR=9.04358;LSEQ=GAGGTCAGAGCAGGACAGGC;RSEQ=AGCTTGATGGGGCCTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:1:1,0:160,341:501,1:0.002:2,0:1:0:27:0:0.32072:0:60:2:0.002:0:1 0/1:394:7:5,2:132,255:387,7:0.0178:2,2:9.6:1:25.4:1:0.05251:4.81:60:6:0.0156:0:1.1 +16 2123028 . A G 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07035;SOR=Inf;LSEQ=CGAGCTTGATGGGGCCTGGG;RSEQ=TTCGAGGGCCTGGCCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:98,295:393,0:0:2,0:23.8:1:30.6:1:1:0:60:48.125:1:0:0.1 0/1:278:3:1,2:75,200:275,3:0.0108:2,2:18.7:1:24:1:1:1.33:53:2:0.0075:0:2.7 +16 2124115 . C T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18693;SOR=Inf;LSEQ=CTAAGCCTCGGCTGTTCTCC;RSEQ=GGTGGAGCACTCGAGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:103,4:107,0:0:1,0:24.3:1:31.2:1:1:0:60:34.667:1:0:0.1 0/1:82:2:1,1:73,7:80,2:0.0244:2,2:6:1:28:1:0.18669:9.82164:60:4:0.0247:0:1 +16 2124148 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07833;SOR=Inf;LSEQ=GAGGTTGGCGAGGGGTAGGC;RSEQ=AGGCTGCCTCTGCTGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:201,33:234,0:0:2,0:21.7:1:30.8:1:1:0:60:233:1:0:0.1 0/1:176:3:2,1:130,42:172,3:0.017:2,2:20.7:1:24.3:1:0.57327:1.54337:60:2:0.0118:0:2 +16 2124170 . G T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06174;SOR=Inf;LSEQ=GGCTGCCTCTGCTGCAAGCG;RSEQ=GTGGGGCCTGAGGTGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:298,83:381,0:0:2,0:23.2:1:31.2:1:1:0:60:37.1:1:0:0.1 0/1:250:3:2,1:173,74:247,3:0.012:2,2:16:1:20.3:1:1:1.16815:60:2:0.0083:0:2.7 +16 2124176 . G T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30771;SOR=4.50692;LSEQ=CTCTGCTGCAAGCGGGTGGG;RSEQ=CCTGAGGTGTCCTGTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:1:1,0:316,92:408,1:0.0024:2,0:24:0:32:0:1:0:60:2:0.0025:0:1 0/1:274:3:1,2:186,84:270,3:0.0109:2,2:16.3:1:26.7:1:0.2343:4.40175:60:6:0.0112:0:1 +16 2124431 . G A 44 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15704;SOR=4.91235;LSEQ=CGCATGCACCCGAGAGGTTC;RSEQ=GGCTGTGTAACCTGTGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:1:1,0:104,344:448,1:0.0022:2,0:1:0:29:0:0.23385:0:60:2:0.0023:0:1 0/1:276:3:2,1:73,200:273,3:0.0109:2,2:5.7:1:28.3:1:0.1804:5.44:60:6:0.0111:0:1.3 +16 2125687 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54798;SOR=0;LSEQ=GCCACGTCCGTGTGGCCGTG;RSEQ=CCTTCTCTCCTCTGCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:145,5:150,2:0.0132:1,2:9:1:28.5:1:0.07764:26.56453:60:4:0.0134:0:1 0/0:79:0:0,0:77,2:79,0:0:1,0:22.3:1:31:1:1:0:60:158:1:0:0.1 +16 2125769 . G A 132 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=42.53398;LSEQ=AGGCGCTGCACGGGACCCCG;RSEQ=CTCCCCTGACCACCCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:747:1:1,0:517,227:744,1:0.0013:2,0:12:0:20:0:1:0:60:2:0.0014:0:1 0/1:444:24:16,8:278,140:418,24:0.0541:2,2:22.3:1:29:1:1:1.01:60:48:0.0549:0:1.1 +16 2125788 . C T 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTCCCCTGACCACCCTCT;RSEQ=CATTACCGCAGCTCTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:945:0:0,0:588,357:945,0:0:2,0:25.6:1:31.7:1:1:0:60:71.692:1:0:0.1 0/1:650:108:67,41:337,205:542,108:0.1662:2,2:21.9:1:29:1:1:1.00596:60:53:0.1661:0:1.5 +16 2125834 . T C 180 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=45.34544;LSEQ=CCGCACCTCTACAGGAACTT;RSEQ=GCCGCGGAGCAGTATGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1414:2:0,2:741,671:1412,2:0.0014:2,0:17.5:1:19:1:0.22636:0:60:1:7e-04:0:1.5 0/1:1094:66:36,30:545,482:1027,66:0.0603:2,2:25.8:1:29.9:1:0.8989:1.06:60:65:0.0604:0:1.7 +16 2125937 . C G 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCTCCCAGCCGTGGCCCC;RSEQ=GCTAGGCCTTGCGGCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:778:0:0,0:312,464:776,0:0:2,0:24.1:1:30.2:1:1:0:59.9:50.733:0.9974:0:0.1 0/1:540:84:30,54:168,286:454,84:0.1556:2,2:23.7:1:29.4:1:0.90214:1.05724:59.9:41:0.1536:0:1.3 +16 2126322 . C T 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0916;SOR=Inf;LSEQ=GCGCTGGGGGCTCTGCTGGG;RSEQ=AGCCTGCAGGGCTTTGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:78,66:144,0:0:2,0:25.3:1:32.4:1:1:0:59.6:35:1:0:0.1 0/1:63:2:1,1:24,37:61,2:0.0317:2,2:34:0:26.5:1:1:1.53:60:4:0.0328:0:1 +16 2126452 . A G 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGAGGGCCTCCAGCCCCC;RSEQ=TTGCCACCCCTCACTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:0:0,0:430,217:647,0:0:2,0:23.9:1:30.5:1:1:0:60:106.833:1:0:0.1 0/1:489:31:20,11:294,163:457,31:0.0634:2,2:23.7:1:29.9:1:1:1.01:60:62:0.0642:0:1.1 +16 2127762 . G A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGGTGGGGGGCACGGACCCT;RSEQ=GAGCTTGGCCCCGTGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:0:0,0:81,283:364,0:0:2,0:23.6:1:31.5:1:1:0:60:71.8:1:0:0.1 0/1:225:12:3,9:54,159:213,12:0.0533:2,2:31.2:1:30.3:1:1:1.01879:60:24:0.0541:0:1 +16 2127944 . G T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=CGCATCCCCAGGCCCCCTCG;RSEQ=GGTGCCGCTCCGAGAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:1,3:0,6:6,4:0.4:0,2:22:1:26.3:1:0.4:0:50.5:3:0.3333:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:28.5:1:32:0:1:0:60:4:1:0:0 +16 2128670 . C T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGCTTGCCGGAGGCAGCCTG;RSEQ=GGGCAGAATGCAATCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:43.5:1:34:0:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:50:0:30:1:1:0:60:4:0.6667:0:1 +16 2128935 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12909;SOR=Inf;LSEQ=TGGGGTCTTTCCGAGCGAGG;RSEQ=CCTCAGCCGTGCATGCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:73,1:74,0:0:1,0:23.6:1:30:1:1:0:60:148:1:0:0.1 0/1:42:2:1,1:37,3:40,2:0.0476:2,2:31.5:1:32:1:0.18351:10.82458:60:4:0.0476:0:1 +16 2129003 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17646;SOR=Inf;LSEQ=CGGCCCGCCCTACCTGGCAC;RSEQ=CTGACCCTGGTCACGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:177,56:233,0:0:2,0:23.1:1:30.9:1:1:0:60:45.6:0.9956:0:0.2 0/1:170:2:1,1:120,48:168,2:0.0118:2,2:8.5:1:27.5:1:0.4946:2.48466:60:4:0.012:0:1 +16 2129455 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06058;SOR=Inf;LSEQ=TGCACCTTCCTTTCCTCCGC;RSEQ=CCTGCCAGCCTCGACACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:197,221:418,0:0:2,0:23.8:1:31:1:1:0:60:37:1:0:0.2 0/1:272:3:2,1:124,144:268,3:0.011:2,2:9.3:1:24.3:1:0.59901:2.32:60:6:0.0112:0:1.7 +16 2129482 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38554;SOR=2.33791;LSEQ=AGCCTCGACACCGGCTGTCC;RSEQ=GAGCCCAGGCCCACGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:2:0,2:216,196:412,2:0.0048:2,0:21.5:1:19.5:1:0.22813:0:60:1:0.0025:0:1.5 0/1:267:3:1,2:142,121:263,3:0.0112:2,2:22.7:1:28.3:1:0.59736:2.33979:60:6:0.0115:0:1 +16 2129489 . A G 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.06317;SOR=Inf;LSEQ=ACACCGGCTGTCCCGAGCCC;RSEQ=GGCCCACGTGGCACCCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:227,190:417,0:0:2,0:23.9:1:31.1:1:1:0:60:45.333:1:0:0.1 0/1:277:3:2,1:153,121:274,3:0.0108:2,2:30.7:1:21.3:1:1:1.58:60:2:0.0073:0:1.3 +16 2129494 . C A 37 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06808;SOR=Inf;LSEQ=GGCTGTCCCGAGCCCAGGCC;RSEQ=ACGTGGCACCCTCGTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:236,187:423,0:0:2,0:24.1:1:31.5:1:1:0:60:51.875:0.9928:0:0.1 0/1:295:3:2,1:165,125:290,3:0.0102:2,2:7.7:1:23.7:1:1:1.51:60:2:0.0068:0:2.7 +16 2129518 . G T 64 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01477;SOR=Inf;LSEQ=TGGCACCCTCGTACCAGCCT;RSEQ=GGGACTAAGTCCACCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:0:0,0:323,217:540,0:0:2,0:24.2:1:31.8:1:1:0:60:66.5:1:0:0.1 0/1:410:5:2,3:237,168:405,5:0.0122:2,2:5.4:1:27.8:1:0.65336:2.11216:60:10:0.0124:0:1.2 +16 2130395 . G A 47 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1666;SOR=5.6643;LSEQ=ACAGGTACTGGGCGGGGCTG;RSEQ=CCTGAGCGCCATCTTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:1:1,0:171,368:539,1:0.0019:2,0:1:0:25:0:0.31852:0:60:2:0.0019:0:1 0/1:384:4:3,1:147,231:378,4:0.0104:2,2:7.3:1:23.5:1:0.30431:4.70:60:3:0.008:0:1.3 +16 2130492 . G GT 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.40809;SOR=1.65222;LSEQ=GATATTTGGGGGTAACTTTT;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:10:0,10:0,115:115,10:0.0794:1,0:23.3:1:31.1:1:1:0:60:20:0.082:0:0 0/1:56:7:0,7:2,44:46,7:0.125:1,0:16.3:1:29.2:1:1:0:56.3:14:0.1296:0.0357:0.6 +16 2131766 . G A 85 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10614;SOR=2.50558;LSEQ=CGGTGCCGGCAGCCAGCACG;RSEQ=CCAAACCCCCTCCTCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1140:5:3,2:489,644:1133,5:0.0044:2,2:14.4:1:30.8:1:0.65736:1.97:60:10:0.0045:0:1 0/1:824:9:6,3:363,450:813,9:0.0109:2,2:23.3:1:27:1:0.31248:2.48:60:18:0.0111:0:1.6 +16 2132552 . C T 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24935;SOR=0.23433;LSEQ=GGCTGCAGAGCGCCACTCTG;RSEQ=CTCATAGGTGCTGTGCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:6:2,4:105,333:438,6:0.0135:2,2:25:1:30.2:1:0.63426:1.58:60:12:0.0138:0:1.3 0/0:313:1:0,1:92,220:312,1:0.0032:2,0:16:0:30:0:1:0:60:2:0.0032:0:1 +16 2132583 . G A 198 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGTGCTCGTCGCCTCATCC;RSEQ=CCCACCCCCATGGTCCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:94:16,78:20,136:156,94:0.3745:2,2:25.6:1:30.3:1:0.35981:1.39:60:188:0.379:0:1.1 0/0:152:0:0,0:29,122:151,0:0:2,0:20.7:1:30.4:1:1:0:60:24.167:1:0:0.1 +16 2133637 . C T 43 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72822;SOR=1.35756;LSEQ=AGGCTGGTTCTCGGAGGCCA;RSEQ=GTCAGGGCCAGGGCCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:4:1,3:283,62:345,4:0.0115:2,2:2:1:28.5:1:0.02153:13.54713:60:8:0.0116:0:1.3 0/1:258:4:1,3:204,50:254,4:0.0155:2,2:9.8:1:21.8:1:0.02825:12.08016:60:3:0.0118:0:1 +16 2133640 . C G 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGTTCTCGGAGGCCACGT;RSEQ=AGGGCCAGGGCCTGGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:304,74:378,0:0:2,0:21.3:1:31.8:1:1:0:60:62:1:0:0.1 0/1:284:19:15,4:205,59:264,19:0.0669:2,2:17.7:1:31.2:1:1:1.08:60:38:0.0676:0:1.4 +16 2134075 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCACAGCTGGTGGCAGTGCT;RSEQ=CTGCGTCAACGGGCGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:2,0:66,11:77,2:0.0253:2,0:49:0:32:1:1:0:60:4:0.0253:0:1 0/0:33:0:0,0:30,3:33,0:0:2,0:24.6:1:30.9:1:1:0:60:15.5:1:0:0.5 +16 2134095 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08979;SOR=Inf;LSEQ=GCTGCGTCAACGGGCGGGGG;RSEQ=CGTAGCCTGGTGCTCGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:95,9:104,0:0:2,0:23.5:1:32.4:1:1:0:60:103:1:0:0.1 0/1:45:2:1,1:41,1:42,2:0.0444:1,2:33:1:29.5:1:0.08985:29.33286:60:4:0.0488:0:1 +16 2134721 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28002;SOR=0;LSEQ=CAGGCATCAACCCCAGGTGG;RSEQ=CCTCTTGCTTCCGGGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:91,194:285,3:0.0104:2,2:13.3:1:28.7:1:0.24467:4.24:60:6:0.0108:0:1.3 0/0:190:0:0,0:67,123:190,0:0:2,0:22.5:1:30.8:1:1:0:60:62.333:1:0:0.2 +16 2134797 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07989;SOR=Inf;LSEQ=ACTTGCCCCAGGCCGAGCGG;RSEQ=CTGGGGTGGGGTCCTCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:151,66:217,0:0:2,0:24.2:1:31.5:1:1:0:60:26.125:1:0:0.3 0/1:86:2:1,1:45,39:84,2:0.0233:2,2:10:1:28:1:1:1.15192:60:4:0.0233:0:1 +16 2134850 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25783;SOR=4.03883;LSEQ=TGGCTGGAACCCCTGGGAGG;RSEQ=CGGTGGAGTGGGAGATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:1:1,0:266,45:311,1:0.0032:2,0:1:0:25:0:1:0:60:2:0.0033:0:1 0/1:156:2:1,1:129,25:154,2:0.0128:2,2:28.5:1:27.5:1:0.30645:5.07951:60:4:0.0132:0:2.5 +16 2134851 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1088;SOR=Inf;LSEQ=GGCTGGAACCCCTGGGAGGG;RSEQ=GGTGGAGTGGGAGATGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:274,46:320,0:0:2,0:25.3:1:31.7:1:1:0:59.9:34.556:1:0:0.5 0/1:158:2:2,0:129,27:156,2:0.0127:2,0:33:1:30.5:1:1:0:60:4:0.0132:0:1 +16 2134852 . G A 208 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGGAACCCCTGGGAGGGC;RSEQ=GTGGAGTGGGAGATGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:112:100,12:193,35:228,112:0.3294:2,2:23.6:1:30.6:1:0.31586:1.51:60:36.333:0.3313:0:1.1 0/0:170:0:0,0:140,29:169,0:0:2,0:22.1:1:30:1:1:0:60:338:1:0:0.2 +16 2134868 . G T 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05598;SOR=7.36082;LSEQ=GGGCGGTGGAGTGGGAGATG;RSEQ=CCAGGCTCTGTGTTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:1:0,1:366,98:464,1:0.0021:2,0:17:0:27:0:0.2129:0:60:2:0.0022:0:1 0/1:256:4:1,3:198,54:252,4:0.0156:2,2:12:1:23.3:1:0.03557:10.86168:60:8:0.0158:0:2.5 +16 2135048 . CT C 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGGCGTGGCCTCCCTCTC;RSEQ=GCATCCGCTGGAGCTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:825:0:0,0:335,488:823,0:0:2,0:24.8:1:31:1:1:0:60:101.875:0.9988:0:0.1 0/1:658:20:10,10:269,365:634,20:0.0304:2,2:19.4:1:29.6:1:0.50172:1.36:59.8:19:0.0293:0.0106:0.1 +16 2135056 . G A 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04878;SOR=7.61955;LSEQ=GGCCTCCCTCTCCTGCATCC;RSEQ=CTGGAGCTGTGTGGCTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:736:1:1,0:301,433:734,1:0.0014:2,0:1:0:25:0:0.41088:0:60:2:0.0014:0:1 0/1:584:6:5,1:244,334:578,6:0.0103:2,2:9.2:1:25.7:1:0.08854:6.82:60:12:0.0104:0:1.2 +16 2135059 . G A 70 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14878;SOR=3.82227;LSEQ=CTCCCTCTCCTGCATCCGCT;RSEQ=GAGCTGTGTGGCTCGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:706:2:2,0:280,424:704,2:0.0028:2,0:2:1:24:0:0.15921:0:60:4:0.0029:0:1 0/1:558:6:4,2:227,324:551,6:0.0108:2,2:5.2:1:27.2:1:0.23837:2.85:60:12:0.0108:0:1.3 +16 2135073 . C T 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCGCTGGAGCTGTGTGGCT;RSEQ=GGGTGAATGGTGGGGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:596:0:0,0:215,380:595,0:0:2,0:24.6:1:30.5:1:1:0:60:73.375:0.9983:0:0.1 0/1:409:21:6,15:154,234:388,21:0.0513:2,2:20.9:1:26.8:1:0.36495:1.64341:60:9.5:0.0476:0:1.1 +16 2135157 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0206;SOR=Inf;LSEQ=AAGCTCCCTGTGGCAGCCTG;RSEQ=CGTGACCGGCCTGGGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:230,142:372,0:0:2,0:23.8:1:32:1:1:0:60:92:1:0:0.1 0/1:229:4:2,2:129,96:225,4:0.0175:2,2:21.8:1:29.5:1:1:1.34198:60:8:0.0177:0:1 +16 2135390 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13541;SOR=Inf;LSEQ=CCTCAGCCTGCAGTGGGTAG;RSEQ=GAGTCTGGGCCCCCAACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:28,203:231,0:0:2,0:23.5:1:30.9:1:1:0:59.9:45.2:1:0:0.2 0/1:135:2:1,1:29,104:133,2:0.0148:2,2:29:1:28:1:0.39635:3.54:60:4:0.0148:0:1 +16 2135429 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCACAGAGCTCAACACTG;RSEQ=CGGGTCCCCTACAGCATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:0,2:0,118:118,2:0.0167:1,0:36:1:30.5:1:1:0:60:4:0.0169:0:1 0/0:41:0:0,0:1,40:41,0:0:1,0:25.1:1:30.5:1:1:0:60:82:1:0:0.1 +16 2136155 . C G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11986;SOR=Inf;LSEQ=CTGCGGGGCAGGGCCCGGCC;RSEQ=GGGAGTGATGCCACCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:199,55:254,0:0:2,0:23.7:1:30.8:1:1:0:60:62.5:1:0:0.1 0/1:135:2:1,1:89,44:133,2:0.0148:2,2:27:0:31.5:1:1:2.01139:60:4:0.015:0:1.5 +16 2136455 . C T 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATCCAGTCCTGCTACCCCA;RSEQ=GCCCTGGGGCATGGCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:38:4,34:28,158:186,38:0.1696:2,2:25.6:1:29.8:1:0.61401:1.50378:60:76:0.1704:0:1.1 0/0:118:0:0,0:14,104:118,0:0:2,0:23.3:1:29.3:1:1:0:60:58:1:0:0.1 +16 2136558 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGATGGGGCTGGTGGC;RSEQ=TTGCGTCCCAAAGCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:45,39:84,2:0.0233:2,2:23.5:1:33:0:1:1.15192:60:4:0.0241:0:1 0/0:25:0:0,0:11,14:25,0:0:2,0:17.8:1:31.1:1:1:0:60:50:1:0:0.4 +16 2136624 . T C 143 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=104.1546;LSEQ=CCAGGCACCAGAGGACGTGG;RSEQ=CCCCGCAGGCCCCCAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:1,0:144,14:158,1:0.0063:2,0:25:0:28:0:1:0:60:2:0.0065:0:2 0/1:62:25:21,4:36,1:37,25:0.4032:1,2:21:1:30.9:1:0.1479:6.65145:60:50:0.4032:0:1 +16 2136663 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11556;SOR=Inf;LSEQ=CCCCTGGAGTAATCAGGAGG;RSEQ=GCCCCAGTGCAAGGCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:270,63:333,0:0:2,0:23:1:30.2:1:1:0:60:165.5:1:0:0.2 0/1:172:2:1,1:138,32:170,2:0.0116:2,2:13.5:1:29:1:0.34782:4.26202:60:4:0.0118:0:1.5 +16 2138197 . TAGTG T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGCCCAGGTGCCACCTGA;RSEQ=AGCTCACCCCCTGCCTACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:992:0:0,0:500,488:988,0:0:2,0:24.3:1:29.9:1:1:0:60:69.571:0.9969:0:0.1 0/1:710:23:9,14:367,318:685,23:0.0324:2,2:25:1:29.4:1:0.20461:1.79375:60:46:0.033:0.007:0.2 +16 2138218 . A C 242 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTGAGCTCACCCCCTGCCT;RSEQ=CGTCCCCAGATGGCCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1093:0:0,0:536,557:1093,0:0:2,0:25.3:1:29.1:1:1:0:60:120.444:1:0:0.1 0/1:852:277:158,119:306,267:573,277:0.3251:2,2:24.8:1:29.9:1:0.33965:1.16:60:20.308:0.3162:0:1.6 +16 2138269 . T C 249 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCCGCTCCAACCCCACCGA;RSEQ=ATCTACCCCTCCAAGTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1160:0:0,0:547,613:1160,0:0:2,0:26.5:1:29.4:1:1:0:59.9:49.435:1:0:0.2 0/1:942:261:123,138:324,357:681,261:0.2771:2,2:27.2:1:31.1:1:0.94192:1.01823:60:86:0.2783:0:1.6 +16 2138398 . C T 208 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.30197;LSEQ=GGGCGGGTGTGTGGGCAGAG;RSEQ=GGTTGCCACGCCTCCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:758:6:2,4:467,285:752,6:0.0079:2,2:9.3:1:28.2:1:0.20882:3.27191:60:12:0.0081:0:1.5 0/1:467:152:92,60:187,128:315,152:0.3255:2,2:25.1:1:28.7:1:0.84082:1.05:60:75:0.324:0:2 +16 2138422 . C G 241 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCACGCCTCCCAGACTTA;RSEQ=TGCCCAAGCCGCCTCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1005:0:0,0:591,413:1004,0:0:2,0:24.8:1:32.5:1:1:0:60:82.667:0.999:0:0.1 0/1:720:223:127,96:300,194:494,223:0.3097:2,2:23:1:31:1:0.36614:1.16866:60:73.333:0.3077:0:1.7 +16 2138584 . G C 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGAAGCGCCTCATCTCCTC;RSEQ=GTGGAGGACTTCACCGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:849:0:0,0:297,548:845,0:0:2,0:24.2:1:30.4:1:1:0:60:55.333:0.9976:0:0.1 0/1:639:32:14,18:230,377:607,32:0.0501:2,2:24.7:1:29.7:1:0.57634:1.27:58.4:64:0.0506:0:1.2 +16 2138670 . TAA T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00142;SOR=Inf;LSEQ=TTGCCTGTCAGTGAAATAAA;RSEQ=AGTCCTGACCCCAGTGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:24,204:228,0:0:2,0:23:1:30.9:1:1:0:59.7:75:1:0:0.1 0/1:150:7:1,6:24,119:143,7:0.0467:2,2:23.1:1:31.1:1:1:1.20863:60:14:0.0467:0:0.1 +16 2138738 . T C 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03798;SOR=Inf;LSEQ=GACAGCTCTTTTATTGACTT;RSEQ=GTCTGCTTGGTGCGGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:0,77:77,0:0:1,0:19.4:1:30.7:1:1:0:58.7:37.5:1:0:0.2 0/1:40:3:1,2:1,36:37,3:0.075:1,2:16.7:1:21.3:1:0.14615:14.90:60:2:0.0526:0:2 +16 2199788 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCAGCCTTTCAGAGGCA;RSEQ=ACGCTGGGTGTCCAGCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:29:1:1:0:60:4:1:0:1 +16 2200882 . A G 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGCAGGAGCTCAGGCTGA;RSEQ=GGAGGTGGCACAGGTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 2213760 . G GT 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.04673;SOR=2.56114;LSEQ=TGCCTGAGCCGGGGCTGGTG;RSEQ=TGGAAGGCTGCTGCGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:15:15,0:79,2:81,15:0.1563:1,1:27.9:1:30.4:1:1:0:60:14:0.1522:0.0104:0 0/1:34:11:11,0:23,0:23,11:0.3235:1,0:18.4:1:27.8:1:1:0:60:10:0.303:0.1471:0.4 +16 2213800 . G C 123 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.54384;LSEQ=CCCCACGGTGCCCCACAGCA;RSEQ=GTCTGCACACTTGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:1,0:174,6:180,1:0.0055:1,0:13:0:31:0:1:0:60:2:0.0056:0:1 0/1:93:14:14,0:77,2:79,14:0.1505:1,1:21.4:1:32.4:1:1:0:60:28:0.1538:0:1.3 +16 2213819 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11281;SOR=Inf;LSEQ=AGGTCTGCACACTTGCAGCA;RSEQ=CCCGTCTGACTCACAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:236,26:262,0:0:2,0:23:1:33.1:1:1:0:60:64.5:1:0:0.1 0/1:133:2:1,1:120,11:131,2:0.015:2,2:27:1:30:1:0.17293:10.4882:60:4:0.0156:0:1.5 +16 2214127 . T TG 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.09063;LSEQ=GGGGTCTCAGGGGAGCTCGG;RSEQ=GGGGGGGGGTGTGGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:11:1,10:8,200:208,11:0.048:1,2:32.4:1:32.2:1:0.3767:2.48:56.9:22:0.0553:0:1.1 0/1:115:6:0,6:3,102:105,6:0.0522:1,0:27.8:1:29.5:1:1:0:57.3:12:0.0606:0:0.7 +16 2214137 . T A 23 v3;pSTD;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09681;SOR=Inf;LSEQ=GGGAGCTCGGTGGGGGGGGG;RSEQ=GTGGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:8,197:205,0:0:1,0:27.1:1:29.6:1:1:0:58:13.643:1:0:0.8 0/1:94:2:1,1:2,90:92,2:0.0213:1,2:30:0:23:1:0.06314:36.94:60:4:0.0222:0:1.5 +16 2214162 . C T 114 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GCGCGCGCGCGCGCGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:5,96:101,0:0:1,0:19.7:1:28.9:1:1:0:57.6:32.667:1:0:0.8 0/1:48:14:0,14:4,18:22,14:0.2917:2,1:7.1:1:30:1:0.14118:0:58.9:28:0.3889:0:1.2 +16 2215659 . CT GC 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.0506;SOR=0;LSEQ=GCGTGTGAGTGCTGCGTGGC;RSEQ=GGCCTGGTCGCATGGTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:11:11,0:30,1:31,11:0.2619:1,0:8.8:1:32.1:1:1:0:42.2:22:0.2619:0.0714:1.3 0/0:15:0:0,0:14,1:15,0:0:1,0:22:1:31.3:1:1:0:42.5:30:1:0:0.2 +16 2215686 . T G 52 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55134;SOR=0;LSEQ=GGTCGCATGGTTAAGCGTGT;RSEQ=AGCGCTGCGTGGCGCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:3:3,0:94,4:98,3:0.0297:1,0:6:1:33.3:1:1:0:31.3:6:0.0313:0:2.3 0/0:48:0:0,0:45,3:48,0:0:2,0:21.9:1:29.7:1:1:0:53.8:11:1:0:0.1 +16 2215689 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.55143;SOR=0;LSEQ=CGCATGGTTAAGCGTGTTAG;RSEQ=GCTGCGTGGCGCGGCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:3:3,0:99,4:103,3:0.0283:1,0:9:1:32:0:1:0:31.3:6:0.0316:0:2.3 0/0:51:0:0,0:48,3:51,0:0:2,0:22.6:1:30.4:1:1:0:54.2:9.2:1:0:0.1 +16 2215780 . G A 55 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01168;SOR=Inf;LSEQ=AAGTGTGTGAGTGCTGCGTG;RSEQ=CCTGGCCTGGTCGCGTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:620:0:0,0:493,126:619,0:0:2,0:23.1:1:31.1:1:1:0:59.7:60.9:0.9984:0:0.1 0/1:434:5:3,2:313,116:429,5:0.0115:2,2:21.2:1:24:1:0.61637:1.79608:54.8:4:0.0095:0:1.4 +16 2216073 . G C 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96151;LSEQ=GGCGCGGGCAGCCTCACACC;RSEQ=CAGCCTGTGTCCTCACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:157:79:2,77:1,77:78,79:0.5032:1,1:24.4:1:30.7:1:1:1.99:60:25.333:0.5067:0:1.1 0/1:75:37:1,36:3,34:37,37:0.4933:2,1:21.7:1:30.6:1:0.61451:3.13091:60:74:0.5:0:1.1 +16 2217903 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGGCACTGGTTTGACCTT;RSEQ=AGAGGGAACCCAAGCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:2,0:107,2:109,2:0.018:1,0:23:1:32:1:1:0:60:4:0.0183:0:1 0/0:45:0:0,0:43,2:45,0:0:1,0:23.5:1:31.4:1:1:0:60:44:1:0:0 +16 2217925 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55333;SOR=0;LSEQ=GAGGGAACCCAAGCTTCCCC;RSEQ=GTGCCATCCCTGCATGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:2,1:149,3:152,3:0.0194:1,2:19.3:1:29.7:1:0.07592:22.73218:60:6:0.0195:0:1 0/0:72:0:0,0:70,2:72,0:0:1,0:24.4:1:30.9:1:1:0:60:144:1:0:0 +16 2218260 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11676;SOR=Inf;LSEQ=TCCCAGGAGGAGTTGACAGT;RSEQ=AGCTGGTGAGGCACAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:12,355:367,0:0:1,0:25.2:1:32.2:1:1:0:60:44.875:1:0:0.1 0/1:191:2:1,1:15,174:189,2:0.0105:2,2:18:1:26.5:1:0.16093:11.26:60:4:0.0105:0:1 +16 2218359 . G A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCTCCTGTGGCTGGACT;RSEQ=TGGGTGGCAGGGGGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:0,3:1,53:54,3:0.0526:1,0:34:1:33:0:1:0:60:6:0.0526:0:1 0/0:12:0:0,0:0,12:12,0:0:0,0:11.3:1:31.9:1:1:0:60:24:1:0:0.1 +16 2220401 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08942;SOR=Inf;LSEQ=GAGCGGGCAGCCCAGCACCC;RSEQ=GGCCCAGGCCGCCCAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:40,1:41,0:0:1,0:21.3:1:31.5:1:1:0:60:82:1:0:0.1 0/1:18:2:2,0:16,0:16,2:0.1111:1,0:15:1:28:1:1:0:56:4:0.1111:0:1 +16 2220713 . CGAG C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.35255;SOR=0.61362;LSEQ=CGCTCCACATTCTCACTGCC;RSEQ=GAGGAGGAGGAGCCGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:726:12:3,9:255,458:713,12:0.0165:2,2:23.2:1:31.9:1:0.55337:1.66922:59.1:24:0.0169:0:0.7 0/1:588:6:2,4:214,367:581,6:0.0102:2,2:22.7:1:30.6:1:1:1.16594:60:12:0.0103:0.0017:0.3 +16 2220787 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5209;SOR=0;LSEQ=GGGCTGTCACCGCAGCCGTG;RSEQ=CACGGAGGCACCTTCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:0,2:6,169:175,2:0.0113:1,0:22.5:1:32:0:1:0:60:4:0.0115:0:1 0/0:115:0:0,0:5,109:114,0:0:1,0:22.3:1:31.9:1:1:0:60:113:0.9912:0:0.1 +16 2221157 . T C 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00378;SOR=13.17546;LSEQ=CCTCTCTCAGGACGTGACCC;RSEQ=GTCCTCAGAGGACAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:1,0:196,5:201,1:0.005:1,0:8:0:34:0:1:0:60:2:0.005:0:1 0/1:113:7:6,1:100,6:106,7:0.0619:2,2:14.4:1:30.1:1:0.36898:2.74094:60:14:0.0619:0:1 +16 2221642 . C T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=GGCCCAGGCCTGACGCCGAC;RSEQ=GTGCCCATGGCTGCCGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:747:0:0,0:271,476:747,0:0:2,0:25.5:1:29.9:1:1:0:60:61.25:1:0:0.2 0/1:576:12:4,8:207,354:561,12:0.0208:2,2:19.5:1:29.4:1:1:1.16921:60:24:0.0211:0:1 +16 2222286 . C T 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTTCATCCACTGCCGGCA;RSEQ=GGCTGCCGGGTAGCGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1094:0:0,0:476,618:1094,0:0:2,0:24.5:1:30.7:1:1:0:59.9:63.353:1:0:0.2 0/1:854:84:41,43:352,416:768,84:0.0984:2,2:22.9:1:29.5:1:0.64537:1.13:60:83:0.0983:0:1.1 +16 2222668 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12362;SOR=Inf;LSEQ=CACAGGCTCCGCTGAGAGCT;RSEQ=CCCGCTTGCTGGTCCCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:11,202:213,0:0:2,0:23.2:1:32.4:1:1:0:59.2:52.25:1:0:0.4 0/1:116:2:1,1:7,106:113,2:0.0172:2,2:20.5:1:27.5:1:0.13486:14.24:60:4:0.0177:0:1 +16 2223000 . T C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00713;SOR=Inf;LSEQ=GCGGGGGTGACGTGATGGGA;RSEQ=CTCACTTGTGAAGCAGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:44,2:46,0:0:1,0:21.3:1:31.7:1:1:0:60:45:1:0:0.2 0/1:12:3:3,0:9,0:9,3:0.25:0,0:24.7:1:33.3:1:1:0:60:6:0.25:0:1 +16 2223578 . G A 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00179;SOR=Inf;LSEQ=GAGCGGGCGGGGCTGGAGGG;RSEQ=CTGGGTTGTGAGACCCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:223,326:549,0:0:2,0:25.3:1:31.6:1:1:0:60:35.6:1:0:0.2 0/1:377:7:4,3:145,225:370,7:0.0186:2,2:21.9:1:28.4:1:0.44149:2.06:59.3:14:0.0189:0:1 +16 2223629 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1195;SOR=Inf;LSEQ=CCCCGGCAGGGAGGCCTCCC;RSEQ=TGGCCTTGCCTACACTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:130,169:299,0:0:2,0:23.1:1:32.2:1:1:0:60:41.714:1:0:0.1 0/1:159:2:1,1:47,110:157,2:0.0126:2,2:22:1:31.5:1:0.51397:2.33:60:4:0.0129:0:1 +16 2223859 . C CT 84 Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33446;SOR=1.60673;LSEQ=TGAGTATGGACCCGCCGTGG;RSEQ=TCCCGCCCACCCTCCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1228:8:8,0:551,666:1217,8:0.0065:2,0:25.8:1:25.5:1:0.00183:0:48:1.667:0.0042:0:2.9 0/1:863:9:9,0:379,473:852,9:0.0104:2,0:24.4:1:26.6:1:0.00073:0:54.4:8:0.0096:0:3.7 +16 2223872 . T C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.51328;SOR=0.93197;LSEQ=GCCGTGGCTCCCGCCCACCC;RSEQ=CCCCCCCGGGCCCCAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1141:364:360,4:90,637:727,364:0.319:2,1:16.7:1:19.8:1:0:636.94:53.8:1.459:0.2446:0:3.7 0/1:770:234:232,2:66,439:505,234:0.3039:2,1:16.3:1:20.4:1:0:751.88:53.6:1.69:0.239:0:3.7 +16 2224467 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00285;SOR=Inf;LSEQ=CCTATAGGGCACCCTCCACC;RSEQ=GGAGCAGCACTGTTTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:1,97:98,0:0:1,0:21.5:1:30:1:1:0:59.6:48:1:0:0.1 0/1:46:5:0,5:1,40:41,5:0.1087:1,0:12.4:1:29.6:1:1:0:60:10:0.1087:0:1 +16 2225040 . C T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23974;SOR=2.83228;LSEQ=CTGATGGCTGGCATGGACCT;RSEQ=GGGCCCTGCCAGGGCGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:2:0,2:352,155:507,2:0.0039:2,0:1:0:21:1:0.09472:0:60:1:0.002:0:1 0/1:363:4:1,3:245,114:359,4:0.011:2,2:17.8:1:29:1:0.10035:6.41189:60:8:0.0111:0:1.8 +16 2225064 . C T 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08657;SOR=4.43007;LSEQ=CCCTGCCAGGGCGGTGTCAG;RSEQ=ATGGACACAGCTTCTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:747:2:0,2:454,291:745,2:0.0027:2,0:23.5:1:19.5:1:0.15353:0:60:1:0.0013:0:1.5 0/1:595:7:3,4:360,228:588,7:0.0118:2,2:21.6:1:28:1:0.4401:2.10256:58.7:14:0.012:0:1.1 +16 2225666 . A G 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09778;SOR=Inf;LSEQ=GCCACAGGGCCTTGCCTCCT;RSEQ=CCAGCACTTCCCAGGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:118,204:322,0:0:2,0:23.5:1:29.6:1:1:0:59.9:321:1:0:0.1 0/1:147:2:1,1:47,98:145,2:0.0136:2,2:8:0:29.5:1:0.54795:2.07:60:4:0.0139:0:1 +16 2225823 . G A 220 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGGACCAACTGGCCCAC;RSEQ=ATTACTCATAGATCTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1189:0:0,0:644,544:1188,0:0:2,0:26.9:1:31.1:1:1:0:59.9:147.5:0.9992:0:0.1 0/1:876:170:95,75:387,317:704,170:0.1941:2,2:27:1:29.8:1:0.86378:1.04:60:169:0.1945:0:1.2 +16 2225987 . CTG C 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CATCTGGGTGCAAGGCCAGA;RSEQ=TGGCCCCGTCTCCCCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:0:0,0:335,347:682,0:0:2,0:23.2:1:31.3:1:1:0:60:112.667:0.9985:0:0.1 0/1:441:18:9,9:196,226:422,18:0.0408:2,2:20.6:1:30.9:1:0.8128:1.15:60:36:0.0411:0.0091:0.2 +16 2226435 . G A 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGGGCTGCACAGGATGGAGC;RSEQ=GGGGTGGGGACGAGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:299,250:549,0:0:2,0:23.1:1:30.5:1:1:0:59.9:67.625:1:0:0.1 0/1:304:11:8,3:156,137:293,11:0.0362:2,2:24.7:1:29.2:1:0.23431:2.34:60:22:0.037:0:1.2 +16 2226437 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04257;SOR=Inf;LSEQ=GGCTGCACAGGATGGAGCGG;RSEQ=GGTGGGGACGAGGAGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:548:0:0,0:306,242:548,0:0:2,0:23.1:1:31.2:1:1:0:59.9:48.818:1:0:0.1 0/1:295:3:2,1:161,131:292,3:0.0102:2,2:12.7:1:22.7:1:1:1.62:60:2:0.0069:0:1 +16 2226763 . C G 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18678;SOR=0;LSEQ=TCTACTCGGCACTGTCCTTG;RSEQ=TGCCCAGCCCCTCTCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:7:0,7:0,58:58,7:0.1077:1,0:29.7:1:33.1:1:1:0:60:14:0.1077:0:1 0/0:21:0:0,0:0,21:21,0:0:1,0:19.1:1:31.7:1:1:0:60:42:1:0:0.1 +16 2227368 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GCACGCCGGGACGCCACCTC;RSEQ=GCCAGCCGCCTCCACCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:40.3:1:32:1:1:0:60:8:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:42:1:28.5:1:1:0:60:4:1:0:2.5 +16 2587734 . G A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GACAGCTCGCCCCCTGCCCC;RSEQ=CCCAGCCCCGCCCAGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:28:1:25.5:1:1:0:60:4:1:0:1.5 +16 2588026 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.51919;SOR=Inf;LSEQ=CAGGATGAGGGCGGCCATTG;RSEQ=TGGGGCTCCGCTTCGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:17,0:0:2,0:27.9:1:33.2:1:1:0:60:34:1:0:0.3 0/1:28:2:1,1:14,12:26,2:0.0714:2,2:16:1:26.5:1:1:1.16024:60:4:0.0741:0:1 +16 2588050 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.49438;SOR=0;LSEQ=GGCTCCGCTTCGGGGAGGAG;RSEQ=ACGCTGAGGAGGCGCCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:22,21:43,2:0.0444:2,2:34.5:1:28:1:1:1.04655:60:4:0.0455:0:1 0/0:45:0:0,0:22,22:44,0:0:2,0:21.5:1:30.2:1:1:0:60:43:0.9773:0:0.3 +16 2588078 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64824;LSEQ=GGAGGCGCCGAGCCGCGCAG;RSEQ=GCTGCGGGGGAGGCGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:30,32:62,2:0.0313:2,2:20:1:29:1:1:1.07:60:4:0.0313:0:2 0/1:49:1:0,1:24,24:48,1:0.0204:2,0:1:0:23:0:1:0:60:2:0.0208:0:1 +16 2588090 . G T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1894;SOR=Inf;LSEQ=CCGCGCAGCGCTGCGGGGGA;RSEQ=GCGCCCGCGCCGACGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:41,44:85,0:0:2,0:21.7:1:31.6:1:1:0:59.8:27.333:1:0:0.4 0/1:66:2:1,1:35,29:64,2:0.0303:2,2:7:0:31.5:1:1:1.20344:60:4:0.0308:0:1.5 +16 2588092 . C T 26 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.2482;LSEQ=GCGCAGCGCTGCGGGGGAGG;RSEQ=GCCCGCGCCGACGCGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:41,44:85,2:0.023:2,2:41:1:30.5:1:1:1.07:60:4:0.0244:0:1 0/1:70:2:0,2:35,32:67,2:0.0286:2,0:1:0:26.5:1:0.23913:0:60:4:0.0299:0:1 +16 2588101 . C A 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50368;SOR=0;LSEQ=TGCGGGGGAGGCGCCCGCGC;RSEQ=GACGCGGGGCCCATGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:57,54:111,2:0.0172:2,2:7.5:1:31:1:1:1.05507:52:4:0.0182:0:1.5 0/0:93:0:0,0:46,45:91,0:0:2,0:17.7:1:29.3:1:1:0:60:44.5:0.978:0:0.4 +16 2588131 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21961;SOR=0;LSEQ=CCCATGGCCAGGACCACCAG;RSEQ=CAGCTGGTGAGCGCGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:85,88:173,2:0.0114:2,2:16.5:1:30:1:1:1.04:60:4:0.0117:0:1 0/0:199:0:0,0:99,100:199,0:0:2,0:21.7:1:31:1:1:0:59.8:38.8:1:0:0.4 +16 2588135 . C T 49 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09019;SOR=0;LSEQ=TGGCCAGGACCACCAGCCAG;RSEQ=TGGTGAGCGCGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:1,2:84,88:172,3:0.0171:2,2:7.7:1:31:1:1:1.90232:60:6:0.0174:0:1.3 0/0:214:0:0,0:107,107:214,0:0:2,0:22.3:1:31.3:1:1:0:59.9:29.571:1:0:0.5 +16 2588146 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.50409;SOR=Inf;LSEQ=ACCAGCCAGCTGGTGAGCGC;RSEQ=CGGCGGCGGACTGGACGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:80,83:163,0:0:2,0:29.7:1:31:1:1:0:60:31.6:1:0:0.4 0/1:201:2:1,1:100,98:198,2:0.01:2,2:24:0:27:1:1:1.02031:60:4:0.0103:0:1.5 +16 2588178 . C A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13546;SOR=Inf;LSEQ=TGGACGCGCCGGTTTGTTAC;RSEQ=CTGCCGGGTCCGGCGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:69,71:140,0:0:2,0:21.3:1:31.3:1:1:0:59.8:34:1:0:0.3 0/1:182:4:3,1:88,90:178,4:0.022:2,2:11.8:1:28:1:0.62082:3.05:60:8:0.0226:0:1.5 +16 2588189 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50008;SOR=Inf;LSEQ=GTTTGTTACCCTGCCGGGTC;RSEQ=GGCGGCCGCCCGGGTCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:57,58:115,0:0:2,0:18:1:30.5:1:1:0:59.7:56.5:1:0:0.3 0/1:131:2:1,1:61,67:128,2:0.0153:2,2:31.5:1:28:1:1:1.10:60:4:0.0156:0:1 +16 2588206 . C A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12624;SOR=Inf;LSEQ=GTCCGGCGGCCGCCCGGGTC;RSEQ=GGCGAGGCGGGGCGGCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:24,30:54,0:0:2,0:18.1:1:29.7:1:1:0:58.6:26:1:0:0.3 0/1:66:4:3,1:29,33:62,4:0.0606:2,2:19.5:1:28:1:0.34823:3.36:60:8:0.0606:0:1.3 +16 2627491 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGCTCACGGAGAAGTCC;RSEQ=CCTGTAAGAGGTAACCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:16.5:1:28.5:1:1:1:60:4:0.3333:0:1.5 +16 2635850 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGCAGCAGCCAGGGCCTG;RSEQ=GTCTGGAGGCACGGAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:27:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:28.5:1:1:0:60:4:1:0:1 +16 2636625 . G T 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1376;SOR=0;LSEQ=GGGAGGGGCTGGGGTTTTAG;RSEQ=ACCTTAGAGGCAAGTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:4:2,2:175,51:226,4:0.0174:2,2:22.5:1:24.3:1:0.22805:3.40811:60:3:0.0136:0:2.5 0/0:174:0:0,0:124,50:174,0:0:2,0:22.9:1:30.3:1:1:0:60:42.5:1:0:0.2 +16 2645703 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0843;SOR=Inf;LSEQ=GCTCTGTGAGGGGCAGGCCG;RSEQ=GGCTATGGGGAGTTCGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:257,67:324,0:0:2,0:23.4:1:29.6:1:1:0:60:28.455:1:0:0.1 0/1:254:3:2,1:191,59:250,3:0.0118:2,2:33.7:1:31.7:1:0.55772:1.6152:60:6:0.0122:0:1 +16 2645879 . G A 77 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12962;SOR=2.95534;LSEQ=GTCAGTGGTCCCGCTGCTCC;RSEQ=CACGGACACCTGCATCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:3:3,0:184,323:507,3:0.0059:2,0:1:0:27.7:1:0.04879:0:60:6:0.006:0:1 0/1:465:8:6,2:176,281:457,8:0.0172:2,2:13.5:1:25.9:1:0.06139:4.77:60:16:0.0174:0:1 +16 2645965 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.87509;SOR=1.08645;LSEQ=CCATCTCTTGATTTTCATCA;RSEQ=ACATCATCTCTAGATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:59:1,58:1,70:71,59:0.4538:1,1:24:1:31.4:1:1:1.21:60:118:0.4574:0:1.1 0/1:59:28:1,27:2,29:31,28:0.4746:2,1:23.4:1:31.4:1:1:1.84327:60:56:0.4746:0:1.1 +16 2647348 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50404;SOR=0;LSEQ=ACCACGTGGGAAGCAGCCAC;RSEQ=GGCCTTGGCCAGAGGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:26,120:146,2:0.0135:2,2:37:1:31:1:0.3326:4.55:60:4:0.0138:0:1 0/0:119:0:0,0:24,95:119,0:0:2,0:23.9:1:30:1:1:0:60:38.667:1:0:0.1 +16 2647826 . G A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57264;SOR=2.82679;LSEQ=ACCTGCCCCAGCGCGGCTTG;RSEQ=CCGCCATCCGGGACGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:1:0,1:19,171:190,1:0.0052:2,0:1:0:27:0:1:0:60:2:0.0053:0:1 0/1:136:2:0,2:11,123:134,2:0.0147:2,0:32:1:31:0:1:0:60:4:0.0148:0:1 +16 2647876 . C T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.01146;SOR=Inf;LSEQ=GCCAGCCATCACAAGGGGAA;RSEQ=GCAGAGGCGGAAACCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:3,107:110,0:0:1,0:24.3:1:30.4:1:1:0:59.8:109:1:0:0.1 0/1:55:4:0,4:0,51:51,4:0.0727:1,0:23.5:1:31.5:1:1:0:60:8:0.0727:0:1 +16 2723242 . A G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00054;SOR=Inf;LSEQ=CGCAGGTAAGGCGGCACCCG;RSEQ=CCCTCGGGACCCCGGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:26,9:35,0:0:2,0:11.4:1:30:1:1:0:60:34:1:0:0.1 0/1:31:9:6,3:13,8:21,9:0.2903:2,2:15.8:1:29.7:1:1:1.22:60:8:0.2963:0:1.8 +16 2723255 . C T 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02956;SOR=8.16065;LSEQ=GCACCCGACCCTCGGGACCC;RSEQ=GGGCCGCCCCGCCTCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:0,1:35,16:51,1:0.0192:2,0:1:0:26:0:0.32692:0:60:2:0.0192:0:1 0/1:50:7:4,3:29,14:43,7:0.14:2,2:18.9:1:29.6:1:0.67685:1.53933:60:14:0.1489:0:1.9 +16 2723276 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.23573;SOR=Inf;LSEQ=GGGCCGCCCCGCCTCGCCGC;RSEQ=CGCTCACCAGCTAGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:50,30:80,0:0:2,0:28.6:1:30.8:1:1:0:60:39:1:0:0.6 0/1:76:2:2,0:47,27:74,2:0.0263:2,0:37:1:29.5:1:0.53579:0:60:4:0.0267:0:2 +16 2723303 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24108;SOR=Inf;LSEQ=CCAGCTAGGTGGTGGTCCTG;RSEQ=CTATGGGCCTCGCGTCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:55,44:99,0:0:2,0:28.5:1:31.1:1:1:0:60:32:1:0:0.7 0/1:96:2:1,1:55,39:94,2:0.0208:2,2:45.5:1:28.5:1:1:1.4051:60:4:0.0213:0:1.5 +16 2723305 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24126;SOR=Inf;LSEQ=AGCTAGGTGGTGGTCCTGGC;RSEQ=ATGGGCCTCGCGTCTGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:55,46:101,0:0:2,0:27.7:1:29.6:1:1:0:60:32.667:1:0:0.7 0/1:98:2:1,1:56,40:96,2:0.0204:2,2:13.5:1:29.5:1:1:1.39509:60:4:0.0208:0:1 +16 2723329 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23074;SOR=Inf;LSEQ=GGCCTCGCGTCTGCGCGGGC;RSEQ=CCTCCCCCGAAGCGCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:39,47:86,0:0:2,0:22.6:1:30.2:1:1:0:60:42:1:0:0.8 0/1:80:2:1,1:40,38:78,2:0.025:2,2:13:0:31.5:1:1:1.05198:60:4:0.025:0:4.5 +16 2723332 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23027;SOR=Inf;LSEQ=CTCGCGTCTGCGCGGGCGCC;RSEQ=CCCCCGAAGCGCTCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:36,46:82,0:0:2,0:22.4:1:29.7:1:1:0:60:19.5:0.975:0:0.9 0/1:78:2:1,1:36,39:75,2:0.0256:2,2:46.5:1:27.5:1:1:1.08:60:4:0.0256:0:4 +16 2723350 . C G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCTCCCCCGAAGCGCTCCGC;RSEQ=GCTCGGGGCCTCCTCAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:20,36:0,0:0,56:1:0,2:24.1:1:30.5:1:1:0:60:112:1:0:1.1 1/1:66:66:28,38:0,0:0,66:1:0,2:23.3:1:28.8:1:1:0:60:65:1:0:2 +16 2723368 . A C 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCCGCTCGGGGCCTCCTCAG;RSEQ=GTCCTCCTTCCCTAAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:5,29:34,0:0:2,0:26.8:1:32.4:1:1:0:60:68:1:0:1 1/0:52:29:10,19:4,17:21,29:0.5577:2,2:22.9:1:29.5:1:0.34084:2.20:60:58:0.58:0:3.1 +16 2723374 . C G 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CGGGGCCTCCTCAGAGTCCT;RSEQ=CTTCCCTAAGCTGAACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:5,26:31,0:0:2,0:26:1:32.5:1:1:0:60:62:1:0:1 0/1:44:17:5,12:7,20:27,17:0.3864:2,2:21.2:1:31.5:1:1:1.19:60:34:0.3953:0:3.2 +16 2723442 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=CGACGCCCCGCCCCCCGCGA;RSEQ=GCCCCCGCCCCCCGCGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:5,0:0:2,0:12.6:1:31.8:1:1:0:60:10:1:0:0.6 0/1:9:2:1,1:1,6:7,2:0.2222:2,2:8:1:29.5:1:0.41667:4.58:60:4:0.2222:0:3 +16 2781843 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28491;LSEQ=AATGCACAGTCTTGCAGTGA;RSEQ=AGCAATGTCAGGGCAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:446:366:183,183:43,37:80,366:0.8206:2,2:26.9:1:29.8:1:0.62172:1.16177:60:51.286:0.8178:0:1.1 1/0:359:203:101,102:78,77:155,203:0.5655:2,2:26.8:1:28.7:1:1:1.02296:60:202:0.5642:0:1.1 +16 2781929 . G A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03866;SOR=Inf;LSEQ=ATCAGCGTTTGTCAGCTTAC;RSEQ=TCTGCATGTTTGAGCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:60,154:214,0:0:2,0:24.3:1:31.4:1:1:0:60:52.5:1:0:0.7 0/1:172:4:2,2:48,120:168,4:0.0233:2,2:15.5:1:24:1:0.58073:2.48:60:3:0.018:0:2 +16 2781959 . G C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00328;SOR=0.41441;LSEQ=TTGAGCATCTTTCTGTGAGT;RSEQ=TATGTAGGTTTATATGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:127:95:8,87:7,25:32,95:0.748:2,2:21.3:1:33.4:1:0.05693:3.0131:60:190:0.748:0:1 1/0:89:49:6,43:8,32:40,49:0.5506:2,2:21:1:31.9:1:0.38627:1.77975:60:98:0.5506:0:1.1 +16 3233415 . G C 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66992;SOR=0.61559;LSEQ=GACGTGGGGAAGCAGAGGCC;RSEQ=CTTGGGGCAGCAGAGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:6,5:0.4545:2,2:15.4:1:30:1:1:1.30:60:10:0.4545:0:1.2 0/1:9:3:1,2:1,5:6,3:0.3333:2,2:20:1:32.7:1:1:2.24:60:6:0.3333:0:1 +16 3233737 . C A 29 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCGCCACATACATTACT;RSEQ=CCCGCAATACCATGCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43:0:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 3498884 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49976;SOR=Inf;LSEQ=TGTTAGTGGAGAACGAGACT;RSEQ=TCCCAGTGTGCTGCCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:99,42:141,0:0:2,0:25:1:32.5:1:1:0:60:282:1:0:0.3 0/1:157:2:1,1:91,64:155,2:0.0127:2,2:21.5:1:28.5:1:1:1.4186:60:4:0.0132:0:1.5 +16 3498895 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=Inf;LSEQ=AACGAGACTCTCCCAGTGTG;RSEQ=TGCCCTGACCCTCTGAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:105,54:159,0:0:2,0:24.9:1:32.4:1:1:0:60:318:1:0:0.3 0/1:171:2:1,1:93,76:169,2:0.0117:2,2:14.5:1:28.5:1:1:1.22223:60:4:0.0118:0:1.5 +16 3498907 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49936;SOR=Inf;LSEQ=CCAGTGTGCTGCCCTGACCC;RSEQ=CTGAGATTGGTCTGTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:109,73:182,0:0:2,0:24.6:1:31:1:1:0:60:44.5:1:0:0.4 0/1:196:2:1,1:106,88:194,2:0.0102:2,2:34.5:1:29:1:1:1.20339:60:4:0.0103:0:1 +16 3498924 . T A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24832;SOR=Inf;LSEQ=CCCTCTGAGATTGGTCTGTG;RSEQ=AGCCACGTGGTGGTCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:119,98:217,0:0:2,0:23.9:1:29:1:1:0:60:107.5:1:0:0.4 0/1:220:3:2,1:115,102:217,3:0.0136:2,2:25.7:1:28.7:1:1:1.77:60:6:0.0137:0:2 +16 3498951 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7176;SOR=1.0835;LSEQ=GTGGTGGTCATCCTGTGCCA;RSEQ=CTCTGGTTTGGTTCTAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:98:54,44:64,71:135,98:0.4206:2,2:24.4:1:30.1:1:0.28862:1.36:60:48:0.4192:0:1.1 0/1:268:118:58,60:75,75:150,118:0.4403:2,2:22.9:1:28.8:1:0.90267:1.03437:60:58:0.4377:0:1.1 +16 3499000 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27012;SOR=Inf;LSEQ=AGTATCATCTGTGGTGATCC;RSEQ=TCTTACACACTTGCATCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:66,114:180,0:0:2,0:25.9:1:31:1:1:0:60:59:1:0:0.4 0/1:254:3:1,2:108,143:251,3:0.0118:2,2:38.7:1:28.7:1:1:1.50814:60:6:0.0119:0:1.3 +16 3499158 . A C 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56488;SOR=3.5981;LSEQ=TGAGGCGGGTAGATCTCTGG;RSEQ=GGTCAGGAGTTCGAGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:19.3:1:30.8:1:1:0:56.5:8:0.5:0:1 1/1:5:4:0,4:0,1:1,4:0.8:0,0:14.5:1:30.8:1:1:0:56.8:8:0.8:0:1.5 +16 3776413 . CCGCCCACCTCAGT C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGGGGCCAACGCTGAG;RSEQ=CGCCCACCTCAGTCTCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:33:1:34.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 3777496 . C A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=GGAAAAAAAAGAACCCCCCC;RSEQ=ACCCCCCCGCCAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:20.4:1:26.8:1:1:0:60:4:0.5714:0:2.6 0/0:3:0:0,0:3,0:3,0:0:0,0:7.3:1:32:0:1:0:43.3:6:1:0:0.3 +16 3777497 . A C 45 MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0.6871;LSEQ=GAAAAAAAAGAACCCCCCCC;RSEQ=CCCCCCCGCCAAAAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:8:0:29:1:1:0:50.7:6:0.375:0:1.3 0/1:4:1:1,0:3,0:3,1:0.25:0,0:8:0:30:0:1:0:35:2:0.5:0:1 +16 3777693 . A AG 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAGGTCCAAGAACATGAA;RSEQ=GGGAAAAGGTGATGCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1073:0:0,0:625,445:1070,0:0:2,0:25.6:1:30.9:1:1:0:60:75.429:0.9972:0:0.1 0/1:1071:37:20,17:575,458:1033,37:0.0345:2,2:30.1:1:30.8:1:0.86757:1.06706:60:36:0.0343:9e-04:0.1 +16 3778400 . TTGC T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.35087;SOR=1.61646;LSEQ=CCAGCCATGCCGGCACTCCC;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:7:7,0:361,205:566,7:0.0122:2,0:26.6:1:32.8:1:0.05393:0:60:14:0.0123:0.0017:0 0/1:561:11:8,3:370,179:549,11:0.0196:2,2:20.7:1:31:1:1:1.29:57.7:22:0.0199:0.0053:0.5 +16 3778427 . T C 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGCTGTTGCTGCTGTTG;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:0:0,0:461,269:730,0:0:2,0:24.9:1:30.3:1:1:0:59.6:242.333:1:0:0.1 0/1:731:41:24,17:417,273:690,41:0.0561:2,2:24.3:1:31.5:1:0.86991:1.08184:58.9:82:0.0564:0:1.2 +16 3778439 . TTGC T 97 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.47941;SOR=1.5277;LSEQ=TGCTGTTGTTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCAGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:853:7:5,2:510,336:846,7:0.0082:2,2:31.9:1:31.6:1:0.70947:1.65:60:14:0.0082:0:0 0/1:881:11:4,7:489,381:870,11:0.0125:2,2:20.3:1:28.3:1:0.22836:2.24402:60:22:0.0126:0.0045:0.2 +16 3778990 . G A 47 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12528;SOR=0;LSEQ=AAGGGGCGCCTGCTGCCACT;RSEQ=CCCGGGAGGCATGCTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:4:2,2:171,174:345,4:0.0114:2,2:13.5:1:23.8:1:1:1.02:60:3:0.0087:0:1 0/0:321:0:0,0:163,157:320,0:0:2,0:26.6:1:31:1:1:0:59.9:52.333:0.9968:0:0.2 +16 3778998 . G T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02457;SOR=Inf;LSEQ=CCTGCTGCCACTGCCCGGGA;RSEQ=GCATGCTGGGCATGACGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:180,188:368,0:0:2,0:22.3:1:31.9:1:1:0:59.9:51.571:1:0:0.2 0/1:337:5:3,2:163,169:332,5:0.0148:2,2:13.2:1:27.8:1:0.68105:1.55:60:10:0.015:0:1.2 +16 3779060 . G A 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCACATTCAGGCTCACGGG;RSEQ=GCCATCTGGCTCCCCGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:237,202:439,0:0:2,0:23.8:1:31:1:1:0:60:38.909:1:0:0.1 0/1:426:31:15,16:208,187:395,31:0.0728:2,2:24.6:1:30.1:1:0.71061:1.18597:60:62:0.074:0:1.3 +16 3779115 . T C 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCTGGGGGCATGCTGTTG;RSEQ=TGATGTTCACCCGGTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:596:0:0,0:304,292:596,0:0:2,0:25.7:1:29.9:1:1:0:60:65.222:1:0:0.2 0/1:595:38:19,19:284,272:556,38:0.0639:2,2:28.8:1:30.8:1:1:1.04406:60:37:0.0631:0:1.1 +16 3779135 . GTGC G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=1.04989;LSEQ=TTGATGTTCACCCGGTACAG;RSEQ=TGCTGCTGCTGGGCCTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:10:5,5:292,296:588,10:0.0167:2,2:28.5:1:32.4:1:1:1.01:59.5:20:0.0175:0.0017:0.2 0/1:571:10:6,4:280,281:561,10:0.0175:2,2:30.9:1:29.4:1:0.75173:1.50:60:9:0.0164:0.0035:0.5 +16 3779205 . G A 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.32012;SOR=3.98427;LSEQ=CTGCAGGAGGGGGCTGGGCC;RSEQ=GGGGTGGGGGGGCCGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:1:1,0:179,177:356,1:0.0028:2,0:1:0:25:0:1:0:60:2:0.0029:0:2 0/1:272:3:3,0:120,148:268,3:0.011:2,0:7.7:1:26.3:1:0.09225:0:60:6:0.0118:0:1.7 +16 3779222 . C T 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09362;SOR=6.31869;LSEQ=GCCGGGGGTGGGGGGGCCGG;RSEQ=ACCTGGCTGGTAGGCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:1:0,1:222,174:396,1:0.0025:2,0:1:0:26:0:0.44081:0:60:2:0.0026:0:1 0/1:320:5:4,1:159,156:315,5:0.0156:2,2:17:1:21.4:1:0.37151:3.91:56:1.5:0.01:0:2.8 +16 3779237 . C T 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09577;SOR=6.16757;LSEQ=GCCGGCACCTGGCTGGTAGG;RSEQ=TTCCCTGTGGACACCGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:1:0,1:273,188:461,1:0.0022:2,0:1:0:25:0:0.40909:0:60:2:0.0023:0:1 0/1:378:5:2,3:199,174:373,5:0.0132:2,2:19.4:1:24.6:1:0.66838:1.71306:60:4:0.011:0:2 +16 3779293 . C T 66 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01411;SOR=9.55147;LSEQ=GGCCACGCTGGGGAAGCCAG;RSEQ=TGGTGACATGCTCACGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:821:1:0,1:486,332:818,1:0.0012:2,0:1:0:25:0:0.40659:0:60:2:0.0013:0:1 0/1:694:8:4,4:403,281:684,8:0.0115:2,2:18.5:1:22:1:0.72319:1.43337:60:1.667:0.0075:0:1.9 +16 3780053 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03394;SOR=Inf;LSEQ=CCCGGACAGGGCGGGAGCAC;RSEQ=GACAAGATGGGATCATGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:3,39:42,0:0:2,0:23.8:1:31.7:1:1:0:60:84:1:0:0.2 0/1:10:2:1,1:0,8:8,2:0.2:0,2:25:1:31.5:1:0.2:0:60:4:0.2:0:1 +16 3781441 . C T 47 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12525;SOR=0;LSEQ=GGGGGGCAGGGTGTTGATGA;RSEQ=AGGCCCAGCGTGCAGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:4:1,3:105,227:332,4:0.0119:2,2:21.8:1:23.8:1:1:1.38643:60:3:0.009:0:1.8 0/0:308:0:0,0:99,209:308,0:0:2,0:26.2:1:31.3:1:1:0:60:50.333:1:0:0.2 +16 3781450 . C G 38 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11117;SOR=Inf;LSEQ=GGTGTTGATGACAGGCCCAG;RSEQ=GTGCAGGTGGATCACGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:89,209:298,0:0:2,0:24.1:1:30.4:1:1:0:59.9:36.25:1:0:0.2 0/1:277:3:1,2:86,187:273,3:0.0108:2,2:6.7:1:24.3:1:1:1.09:60:2:0.0074:0:1.7 +16 3781492 . C A 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.54999;LSEQ=GACCTGCAGGAGAGGAGGGG;RSEQ=TTTAGTCCCACACAAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:24,100:124,2:0.0159:2,2:21:1:27.5:1:0.35873:4.10:60:4:0.0161:0:1 0/0:114:1:1,0:27,85:112,1:0.0088:2,0:1:0:22:0:0.24779:0:60:2:0.009:0:1 +16 3781508 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50914;SOR=0;LSEQ=GGGGCTTTAGTCCCACACAA;RSEQ=GGACATGGCACCTCCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:19,84:103,2:0.019:2,2:38:1:31.5:1:0.34615:4.33:60:4:0.019:0:1 0/0:77:0:0,0:14,62:76,0:0:2,0:20.9:1:29.9:1:1:0:60:18:0.9863:0:0.2 +16 3781516 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14751;SOR=Inf;LSEQ=AGTCCCACACAAGGGACATG;RSEQ=CACCTCCAGTGGTGAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:16,73:89,0:0:2,0:22.4:1:32.6:1:1:0:59.7:178:1:0:0.1 0/1:56:2:1,1:7,47:54,2:0.0357:2,2:30.5:1:29.5:1:0.26753:6.35:60:4:0.0364:0:2 +16 3781952 . C G 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GACTGCCCTGCAACAACACG;RSEQ=AAGGCTGTGAGACCAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:0:0,0:151,344:495,0:0:2,0:25.2:1:31.7:1:1:0:59.9:26.5:0.9979:0:0.1 0/1:388:11:2,9:109,268:377,11:0.0284:2,2:26.3:1:29.8:1:0.73567:1.82774:60:22:0.0286:0:1.1 +16 3782011 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16201;SOR=Inf;LSEQ=CACGGACGCCCAGCTCCCAG;RSEQ=CCGTGGGCATCAGGAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:4,163:167,0:0:1,0:24:1:32.2:1:1:0:60:32.4:1:0:0.1 0/1:113:2:0,2:6,105:111,2:0.0177:2,0:21:1:29.5:1:1:0:60:4:0.0182:0:1 +16 3785911 . G A 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00108;SOR=Inf;LSEQ=CCTGTGCTGCAGGTGGTGTC;RSEQ=ACGTGCATGTGTGAACGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:122,0:122,0:0:1,0:24.4:1:30.4:1:1:0:59.7:121:1:0:0 0/1:94:8:7,1:84,2:86,8:0.0851:1,2:24:1:29.6:1:0.23652:5.7867:60:16:0.0851:0:1 +16 3786520 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15441;SOR=Inf;LSEQ=TTCTAAGTTCTCACTTTAGG;RSEQ=TTTTATTTTTCTGCTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:109,3:112,0:0:1,0:25.9:1:32.8:1:1:0:59.5:55:1:0:0.1 0/1:73:2:1,1:66,5:71,2:0.0274:2,2:38.5:1:26.5:1:0.15868:12.14098:60:4:0.0286:0:1 +16 3786557 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1703;SOR=Inf;LSEQ=TCTAATCCTCATAAGTGAAG;RSEQ=TAATTAACAAGTATGCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:217,10:227,0:0:1,0:23.9:1:31.7:1:1:0:59.8:112.5:1:0:0.2 0/1:160:2:1,1:151,7:158,2:0.0125:1,2:37.5:1:28.5:1:0.0978:20.24495:60:4:0.0127:0:1 +16 3786594 . C G 182 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAATGCAAGAAAAAGGCACA;RSEQ=AAATATCCTCCCCTCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:51:40,11:330,70:400,51:0.1126:2,2:26.9:1:32.1:1:0.44449:1.29563:60:50:0.1126:0:1.1 0/0:367:0:0,0:286,81:367,0:0:2,0:23.6:1:31.3:1:1:0:60:72.4:1:0:0.1 +16 3786862 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19012;SOR=Inf;LSEQ=GATGAACGTGCCAGTGAAAT;RSEQ=GGCCCTGCCTTTAAGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:23,204:227,0:0:2,0:24.3:1:30.3:1:1:0:59.8:74.667:1:0:0.1 0/1:176:2:1,1:23,150:173,2:0.0114:2,2:22.5:1:28.5:1:0.25616:6.41:60:4:0.0116:0:1 +16 3789523 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16785;SOR=Inf;LSEQ=TGGGACACTTAAGAGCCCTG;RSEQ=TCTATCCTAACACGGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:224,62:286,0:0:2,0:25.9:1:31.2:1:1:0:60:56.2:1:0:0.1 0/1:199:2:1,1:168,29:197,2:0.0101:2,2:23:1:31:0:0.27943:5.71271:60:4:0.0102:0:1 +16 3789537 . G A 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCTGGTCTATCCTAACAC;RSEQ=GCTCACTGAATGACACGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:256,101:357,0:0:2,0:25.8:1:29.7:1:1:0:60:28.75:1:0:0.1 0/1:267:43:35,8:172,52:224,43:0.161:2,2:26.1:1:30.1:1:0.68995:1.32:60:86:0.1629:0:1.1 +16 3790186 . G T 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35749;SOR=0.32196;LSEQ=AAACAGTATACTATAATATG;RSEQ=TATGTGGTCTCTCTCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:13:12,1:8,0:8,13:0.619:0,1:20.8:1:31.2:1:1:0:57.2:26:0.619:0:1.1 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:39:1:30:1:1:0:60:4:0.3333:0:1 +16 3790307 . T C 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03348;SOR=Inf;LSEQ=GCTGCAAAGTCTTGGAAGGA;RSEQ=GACCTCAAACTCAAGAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:101,4:105,0:0:1,0:20.2:1:31.6:1:1:0:59.8:210:1:0:0.1 0/1:80:4:4,0:74,2:76,4:0.05:1,0:15.8:1:32.5:1:1:0:60:8:0.05:0:1 +16 3790610 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19649;SOR=Inf;LSEQ=GCACTGCTGAGACAGTGACT;RSEQ=AGACTAGAGAATCCACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:19,219:238,0:0:2,0:25.5:1:32.5:1:1:0:59.8:118:1:0:0.1 0/1:190:2:1,1:23,165:188,2:0.0105:2,2:12.5:1:27.5:1:0.23726:7.04:60:4:0.0105:0:1.5 +16 3794705 . T G 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00073;SOR=0;LSEQ=ACATTCTTGCATTCTTACCC;RSEQ=CATGACTGGCCTGGCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:14:13,1:53,0:53,14:0.209:1,1:19.6:1:30.3:1:0.20896:0:60:28:0.209:0:1 0/0:43:0:0,0:41,2:43,0:0:1,0:17.5:1:31.2:1:1:0:60:86:1:0:0.1 +16 3795292 . G T 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.8318;LSEQ=ACTCACCCTGAAGGCCAAAT;RSEQ=ATGTCATAGTGCAGAACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:1:1,0:315,294:609,1:0.0016:2,0:4:0:30:0:1:0:60:2:0.0017:0:1 0/1:610:33:13,20:294,283:577,33:0.0541:2,2:22.7:1:28.8:1:0.21413:1.59703:60:66:0.0545:0:1.3 +16 3795363 . G A 159 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=58.08551;LSEQ=GCAATCAACGAAACTAGGAG;RSEQ=CAAAGAAGGCGCACTGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:1:1,0:177,288:465,1:0.0021:2,0:1:0:27:0:0.38197:0:60:2:0.0022:0:1 0/1:431:48:18,30:161,222:383,48:0.1114:2,2:28.6:1:28.6:1:0.64175:1.20818:59.3:47:0.1108:0:1.4 +16 3795409 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23235;SOR=Inf;LSEQ=ACGGAACCACAAGACCAGAG;RSEQ=CACTTGTAGAAGTCTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:42,167:209,0:0:2,0:22.1:1:29.8:1:1:0:59.7:68.667:1:0:0.1 0/1:195:2:1,1:48,144:192,2:0.0103:2,2:45:1:31.5:1:0.44234:2.98:60:4:0.0107:0:1 +16 3796147 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAATGCATACCTCCGAGGA;RSEQ=AGGCTGAAGGGACTGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 3801649 . T C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=AATGGCACCGGTACCTTCCT;RSEQ=ATAGTCATTGGTAAGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:242,71:313,0:0:2,0:24.6:1:30.1:1:1:0:59.9:51.167:1:0:0.1 0/1:303:14:11,3:208,81:289,14:0.0462:2,2:24.1:1:30.6:1:0.76439:1.43:60:28:0.0468:0:1 +16 3807171 . G A 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCGTGAGCCACCACACCC;RSEQ=GCCTGAAATTGGGCCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:16,0:28,0:28,16:0.3636:1,1:29.4:1:30.6:1:1:0:52.6:32:0.3636:0:1.1 0/0:63:0:0,0:58,4:62,0:0:2,0:24:1:29:1:1:0:57.9:61:1:0:0 +16 3807946 . C T 158 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0202;LSEQ=AGGCATTGTTGAACATGAGC;RSEQ=AGACGTCGTCCACGTACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:39:16,23:247,284:531,39:0.0684:2,2:24.9:1:29.9:1:0.61816:1.24973:60:78:0.0693:0:1.2 0/0:677:1:0,1:329,347:676,1:0.0015:2,0:2:0:22:0:1:0:60:2:0.0015:0:1 +16 3819388 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21851;SOR=Inf;LSEQ=GAAAGCACTGACTTCAGTAA;RSEQ=CAAGGTAACATAAATGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:32,193:225,0:0:2,0:24.8:1:32.6:1:1:0:60:55.25:1:0:0.1 0/1:198:2:1,1:32,163:195,2:0.0101:2,2:25.5:1:28:1:0.30768:5.03:60:4:0.0102:0:1 +16 3820552 . C T 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37347;SOR=3.85596;LSEQ=GAGTCTTGGCCCAAAAACAG;RSEQ=AGAGACAGAGAGGCTTACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:1:0,1:208,76:284,1:0.0035:2,0:1:0:22:0:0.27018:0:60:2:0.0036:0:1 0/1:298:4:2,2:199,94:293,4:0.0134:2,2:25.5:1:28.3:1:0.5971:2.11123:60:8:0.014:0:1 +16 3820667 . C T 162 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=48.18394;LSEQ=TGAACTGGGGTTTGAGGCTG;RSEQ=GGGGTCACCTGGGCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:1:0,1:372,319:691,1:0.0014:2,0:1:0:25:0:0.46243:0:60:2:0.0015:0:1 0/1:723:47:23,24:355,321:676,47:0.065:2,2:27.6:1:29.3:1:0.6534:1.15377:60:46:0.0652:0:1.1 +16 3820929 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25075;SOR=Inf;LSEQ=CTGGAGGGCAAGGTAGCTGG;RSEQ=TGGCCTGAGGCCCCAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:88,183:271,0:0:2,0:24.3:1:32.7:1:1:0:60:53.2:1:0:0.1 0/1:301:3:1,2:115,183:298,3:0.01:2,2:23:1:27.7:1:1:1.25588:60:6:0.01:0:1 +16 3820966 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24975;SOR=Inf;LSEQ=CATGTTGAGAGGGTTAGGAA;RSEQ=AGCAGCACCAGGCACCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:64,137:201,0:0:2,0:24.3:1:31.8:1:1:0:60:32.5:1:0:0.2 0/1:220:3:2,1:75,141:216,3:0.0136:2,2:16.3:1:27.3:1:0.283:3.74:60:6:0.0138:0:1 +16 3820999 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49824;SOR=Inf;LSEQ=CACCTGTCCCTACCAGAAAT;RSEQ=GACAGAGTATGGTAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:26,100:126,0:0:2,0:22.2:1:30.8:1:1:0:60:41:1:0:0.2 0/1:131:2:1,1:39,89:128,2:0.0153:2,2:16.5:1:28.5:1:0.52236:2.27:60:4:0.0153:0:1 +16 3821077 . A AT 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.05714;SOR=Inf;LSEQ=ATTAAATGTATGAAAAAAAA;RSEQ=TTTTTTTTTTTGAGACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:0,27:27,0:0:1,0:21.4:1:31.1:1:1:0:60:26:1:0:0.1 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:47.5:1:32:0:1:0:60:4:0.2222:0:0 +16 3823680 . G GA 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.65576;SOR=1.23083;LSEQ=AATTTCCACGAAGGAAGACA;RSEQ=AAAAAAAAAACCAAAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:12:12,0:125,10:135,12:0.0811:2,0:21.6:1:30.8:1:1:0:60:24:0.0822:0.027:0.2 0/1:102:10:9,1:79,9:88,10:0.098:2,2:24.5:1:29.4:1:1:1.03:60:20:0.101:0.0294:0.4 +16 3827492 . CA C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.60416;SOR=2.24458;LSEQ=AACTGAATTCTGCTTATCAG;RSEQ=AAAAGGAATGGAAAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:157,14:171,1:0.0058:2,0:14:0:34:0:1:0:60:2:0.0059:0:0 0/1:154:2:1,1:137,15:152,2:0.013:2,2:20:1:29.1:1:0.19761:8.87634:60:4:0.0132:0.0065:0 +16 3827553 . G A 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGGGGGAGAGGAAAAAACA;RSEQ=TGAAAGTTATGGCTGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:368,183:551,0:0:2,0:26.6:1:32.9:1:1:0:60:274.5:1:0:0.1 0/1:528:16:9,7:342,170:512,16:0.0303:2,2:19.3:1:30.3:1:0.42336:1.56334:60:32:0.0307:0:1.3 +16 3827931 . T C 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CATCAGATATTCTAATTCTC;RSEQ=GTTCTTAGAAATACACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:170,44:214,0:0:2,0:23:1:31.3:1:1:0:59.9:34.667:1:0:0.1 0/1:198:15:10,5:149,34:183,15:0.0758:2,2:21.3:1:27.9:1:0.18061:2.18078:60:14:0.0725:0:1.1 +16 3828172 . A G 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTCTCTGCTAATAAGTG;RSEQ=TAATATTCATCCTAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:158,330:488,0:0:2,0:24.9:1:30.8:1:1:0:60:53.222:1:0:0.1 0/1:488:35:12,23:152,301:453,35:0.0717:2,2:26:1:30.7:1:1:1.03:60:70:0.0728:0:1.2 +16 3828585 . G T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01539;SOR=Inf;LSEQ=CTTGGTCAGTGGCCTCAAGG;RSEQ=GAGGAGTCTGTCCCAACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:91,0:91,0:0:1,0:21.2:1:31.2:1:1:0:60:90:1:0:0.1 0/1:51:4:4,0:47,0:47,4:0.0784:1,0:17.5:1:25.8:1:1:0:60:3:0.0612:0:1.3 +16 3828847 . CT C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54089;SOR=0.81178;LSEQ=ATAACACATCTATCAAACTA;RSEQ=TTTTTTTTTCTTCTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:24:7,17:166,392:558,24:0.041:2,2:28.5:1:32.9:1:1:1.0284:59.8:48:0.0423:0.0017:0.1 0/1:596:20:8,12:200,375:575,20:0.0336:2,2:31:1:31.7:1:0.63877:1.25:60:40:0.0341:0:0.1 +16 3828861 . CT C 66 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.20425;LSEQ=AAACTACTTTTTTTTTTCTT;RSEQ=TTTTTTTAAAGACATGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:4:2,2:113,335:448,4:0.0088:2,2:23.8:1:30:1:0.26876:2.96:58.5:8:0.0089:0.0022:0.3 0/1:472:5:3,2:135,332:467,5:0.0106:2,2:20.4:1:28.8:1:0.152:3.68:59.2:10:0.0107:0.0021:0.4 +16 3830936 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24128;SOR=Inf;LSEQ=AAGTGACTCAAACACACTTT;RSEQ=TCTAGTAAGGTTCTTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:21,167:188,0:0:2,0:24.5:1:32.2:1:1:0:59.9:93:1:0:0.1 0/1:182:2:1,1:22,158:180,2:0.011:2,2:11:1:27.5:1:0.23739:7.05:60:4:0.011:0:1 +16 3831187 . T A 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTTGGACTGTCACTCAGA;RSEQ=CTGAAACAGGGTCTTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:0:0,0:301,158:459,0:0:2,0:26:1:30.7:1:1:0:59.9:75.5:1:0:0.1 0/1:543:39:25,14:319,184:503,39:0.0718:2,2:27:1:28.9:1:1:1.03:60:78:0.0726:0:1.9 +16 3831230 . G T 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=51.16288;LSEQ=GGCCCCCAGGGAAGTCGGAA;RSEQ=AGCTGATTCTGAAATCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:658:1:0,1:341,316:657,1:0.0015:2,0:1:0:23:0:0.48176:0:60:2:0.0015:0:1 0/1:788:57:29,28:367,364:731,57:0.0723:2,2:25.6:1:28.5:1:1:1.03:60:114:0.0738:0:1.7 +16 3832471 . A G 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.98026;LSEQ=GAAGTGGCACAGCAAGCAAC;RSEQ=AAAACATTGCTTCATTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:7,0:12,0:12,7:0.3684:0,0:15.4:1:30.1:1:1:0:60:14:0.3684:0:2 0/1:11:4:4,0:6,1:7,4:0.3636:2,0:6.3:1:30:1:1:0:60:8:0.3636:0:1 +16 3832939 . AACAG A 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.0566;SOR=0;LSEQ=CCAGGATGGCTATAACGACA;RSEQ=ACAGACAGACAAAAACGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:4:2,2:100,245:345,4:0.0114:2,2:13.3:1:28.8:1:0.58347:2.44:60:8:0.0115:0.0086:0.8 0/0:366:0:0,0:110,256:366,0:0:2,0:25:1:29:1:1:0:60:60:1:0:0.2 +16 3832959 . C A 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAGACAGACAGACAAAAA;RSEQ=GAGAGGTAAGTAAAAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:61,232:293,0:0:2,0:25.2:1:30.6:1:1:0:60:145.5:1:0:0.1 0/1:256:45:11,34:48,163:211,45:0.1758:2,2:24.7:1:30.3:1:0.84592:1.10:60:90:0.1765:0:1.2 +16 3833026 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1285;SOR=Inf;LSEQ=TGAGAAGCAAATACATTTCA;RSEQ=CAAAATACTACACATGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:0,85:85,0:0:1,0:24:1:30.6:1:1:0:60:84:1:0:0.1 0/1:48:2:0,2:2,44:46,2:0.0417:1,0:23.5:1:32:0:1:0:60:4:0.0435:0:2 +16 3833306 . A G 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCTGGGGACCAGCAGAC;RSEQ=CCTCTGAGATGAACAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:29:1:29:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 3843454 . C T 105 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00482;SOR=10.92242;LSEQ=TTTTTCATGGTTCGACAATG;RSEQ=GGGAGCGAGCAGGCCCGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:1:0,1:336,309:645,1:0.0015:2,0:35:0:28:0:0.47988:0:60:2:0.0016:0:1 0/1:780:13:8,5:393,374:767,13:0.0167:2,2:24.4:1:28.5:1:0.57983:1.52:60:26:0.0168:0:1 +16 3860539 . G A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00055;SOR=Inf;LSEQ=AGACTTTCACTGTGAGAATG;RSEQ=TAAAAATCCACAGACCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:237,59:296,0:0:2,0:21.9:1:31:1:1:0:60:31.889:0.9965:0:0.4 0/1:232:9:7,2:167,55:222,9:0.0388:2,2:27.8:1:29:1:1:1.15:60:18:0.0395:0:1 +16 3860550 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.0188;SOR=Inf;LSEQ=GTGAGAATGGTAAAAATCCA;RSEQ=AGACCACAGCACCCACCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:268,95:363,0:0:2,0:22.3:1:32:1:1:0:60:71.6:1:0:0.4 0/1:301:5:1,4:213,83:296,5:0.0166:2,2:8:1:25:1:0.02578:10.17732:60:10:0.0168:0:1 +16 3860554 . C T 218 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAATGGTAAAAATCCACAGA;RSEQ=CACAGCACCCACCGGAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:130:93,37:181,67:248,130:0.3439:2,2:23:1:31.1:1:0.80872:1.07458:60:260:0.3476:0:1.1 0/0:322:0:0,0:222,100:322,0:0:2,0:1:0:15:0:1:0:60:0:0:0:1 +16 3860640 . A G 212 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTGACTGAAGTATTCTTGAT;RSEQ=TCTGTAGGGAAGGTGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:989:0:0,0:544,445:989,0:0:2,0:25.7:1:29.5:1:1:0:60:51.053:1:0:0.2 0/1:943:105:59,46:463,372:835,105:0.1113:2,2:23.6:1:31.7:1:0.91729:1.03:60:210:0.1128:0:1.2 +16 3900184 . TG T 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51639;SOR=0;LSEQ=TTCCAAGCATGAGTGGCACG;RSEQ=GAGAGCCCAAGAGGAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:188,5:193,2:0.0103:1,2:22:0:34.5:1:0.06075:34.42571:60:4:0.0105:0:0.5 0/0:133:0:0,0:129,4:133,0:0:1,0:23.9:1:31.9:1:1:0:60:132:1:0:0 +16 3900218 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04656;SOR=Inf;LSEQ=GGAAAAACAGGAGTGGGCCA;RSEQ=GTGGTCCCATTTTACGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:268,83:351,0:0:2,0:23.2:1:31.2:1:1:0:60:57.5:1:0:0.2 0/1:306:4:2,2:228,74:302,4:0.0131:2,2:14.3:1:27.8:1:0.25825:3.06714:60:8:0.0133:0:1 +16 3901285 . G A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAACAAGACCGAAACACC;RSEQ=TCTCAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:17:1:32.3:1:1:0:37:6:0.6:0:2.7 0/0:1:0:0,0:0,1:1,0:0:0,0:5:0:33:0:1:0:26:2:1:0:0 +16 3929235 . GCACACACACA G 66 d5;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=14.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GACTAAAAACACACACGCGC;RSEQ=CACACACACACACACACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:29:1:33.4:1:1:0:55.3:8:1:0.25:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 3929738 . C T 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34191;SOR=3.48027;LSEQ=CCTGCTCCGAGCTCCCGGCT;RSEQ=GATCGGTATCCGCGACCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:0,1:247,39:286,1:0.0035:2,0:1:0:25:0:0.13937:0:60:2:0.0036:0:1 0/1:249:3:2,1:224,22:246,3:0.012:2,2:16.3:1:23:1:0.25322:5.03117:60:2:0.0082:0:2.3 +16 3929991 . C A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25889;SOR=Inf;LSEQ=CCCGGACGGGGGTCGGGGGC;RSEQ=CTGCCGGCTGCGAGGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:21,123:144,0:0:2,0:13.6:1:31.3:1:1:0:60:27.8:1:0:0.3 0/1:184:3:1,2:46,135:181,3:0.0163:2,2:16.7:1:23.7:1:1:1.46:60:2:0.0111:0:3 +16 3929992 . C A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07871;SOR=0;LSEQ=CCGGACGGGGGTCGGGGGCC;RSEQ=TGCCGGCTGCGAGGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:2,1:16,117:133,3:0.0221:2,2:8:1:22.7:1:0.04602:14.10:60:2:0.0148:0:1.3 0/0:180:0:0,0:46,134:180,0:0:2,0:12.4:1:31.7:1:1:0:60:360:1:0:0.3 +16 4013467 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCGTGGCCCAGAGAGAA;RSEQ=GTCTGCACTGGCTGTTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 4343926 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCTTTCCTGCTGTGCAG;RSEQ=TGCGGCCGCCAGCGCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:10,4:14,2:0.125:2,2:10:1:28.5:1:1:2.34522:60:4:0.125:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:32.7:1:32.8:1:1:0:60:12:1:0:0 +16 4344012 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49383;SOR=0;LSEQ=CAGCAGCAACAGACAGTGGT;RSEQ=CCAGTAACTCAGAGGCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:18,21:39,2:0.0488:2,2:22:1:29:1:1:1.16:60:4:0.05:0:1 0/0:40:0:0,0:18,22:40,0:0:2,0:35.1:1:31.8:1:1:0:59.8:80:1:0:0.3 +16 4344056 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=TGAGAAGCAAGACGAGAGGG;RSEQ=CAGGGCTGGGAAAGGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:10,18:28,0:0:2,0:23.5:1:31.4:1:1:0:60:27:1:0:0.1 0/1:28:2:1,1:10,16:26,2:0.0714:2,2:28.5:1:27:1:1:1.57:60:4:0.0714:0:1 +16 5415619 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00903;SOR=Inf;LSEQ=GGTGGAGGTTGCAGTGAGCC;RSEQ=ATATCGTGCACTGTACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:19.9:1:30.9:1:1:0:57.3:24:1:0:0 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:19.5:1:26.5:1:1:0:59.8:3:0.5:0:1 +16 5415716 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51873;SOR=Inf;LSEQ=GCTTTCCCTGGTGTGATTCC;RSEQ=TCCTGCATGGCTGTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:79,21:100,0:0:2,0:22.1:1:30:1:1:0:59.3:49:1:0:0.1 0/1:151:2:1,1:96,53:149,2:0.0132:2,2:40.5:1:29:1:1:1.8037:60:4:0.0135:0:1 +16 5415787 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26445;SOR=Inf;LSEQ=CTCTCCCACCTAAGTGCATG;RSEQ=TGCCACCCAATGGAAGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:69,80:149,0:0:2,0:26.3:1:32.7:1:1:0:59.4:148:1:0:0.1 0/1:201:3:1,2:84,114:198,3:0.0149:2,2:22.7:1:29:1:1:1.47095:52:6:0.0151:0:1.3 +16 5415791 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51143;SOR=Inf;LSEQ=CCCACCTAAGTGCATGCTGC;RSEQ=ACCCAATGGAAGATTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:64,80:144,0:0:2,0:25.8:1:31.5:1:1:0:59.4:47:1:0:0.1 0/1:199:2:1,1:83,114:197,2:0.0101:2,2:28.5:1:29:1:1:1.37:60:4:0.0103:0:1 +16 5415812 . G T 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50367;SOR=Inf;LSEQ=ACCCAATGGAAGATTCAGTG;RSEQ=ACATGGACATGAGCCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:46,73:119,0:0:2,0:22.3:1:31.7:1:1:0:59.8:58.5:1:0:0.1 0/1:147:2:1,1:52,92:144,2:0.0136:2,2:6:0:29.5:1:1:1.76:60:4:0.0138:0:1.5 +16 5415915 . A G 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06421;LSEQ=GGATAATGATGAAAAGGAGC;RSEQ=CCAGTTATCTTTAAGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:56:24,32:1,5:6,56:0.9032:2,2:22.8:1:31.7:1:0.38699:3.68:58.9:112:0.9032:0:1.1 0/1:49:18:7,11:12,19:31,18:0.3673:2,2:27.3:1:31.1:1:1:1.01:59.3:36:0.375:0:1.2 +16 5415928 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14386;SOR=Inf;LSEQ=AAGGAGCACCAGTTATCTTT;RSEQ=AGAATGGTCAGTTTAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:25,38:63,0:0:2,0:24.6:1:30.3:1:1:0:58:126:1:0:0.9 0/1:39:2:1,1:16,21:37,2:0.0513:2,2:20:1:28.5:1:1:1.30:60:4:0.0513:0:2 +16 5415971 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=9.2767;LSEQ=GTGTGAAGGATGAATCGTAC;RSEQ=TTGTGGAAGCAGAGGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:5:1,4:26,31:57,5:0.0806:2,2:21.6:1:31.4:1:0.37604:3.29782:59.4:10:0.0806:0:1.4 0/1:44:20:11,9:12,12:24,20:0.4545:2,2:23.5:1:30.9:1:0.77086:1.22:59.5:40:0.4545:0:1.3 +16 5416051 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00118;SOR=7.49252;LSEQ=TGAAAATGTCTGTACAGCAA;RSEQ=GGTTTCCCTTGGGGCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:1,2:14,14:28,3:0.0968:2,2:27.7:1:31:1:1:1.9571:59:6:0.1:0:1.3 0/1:51:23:11,12:15,13:28,23:0.451:2,2:29.2:1:30.7:1:0.78125:1.25305:54.2:46:0.451:0:1.3 +16 5416085 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24195;SOR=Inf;LSEQ=GCTTTGAAATCATACCACCA;RSEQ=TGCTCTTACGGTTGAAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:35,0:0:2,0:21.1:1:32.7:1:1:0:59.5:70:1:0:0.1 0/1:39:3:1,2:18,18:36,3:0.0769:2,2:8.3:1:27.3:1:1:1.96588:57.3:6:0.0769:0:1 +16 5416245 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49697;SOR=Inf;LSEQ=TGGAGGTGGTAGCATGGTTC;RSEQ=ACAGAAAAAAGTAAAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:39,43:82,0:0:2,0:26.2:1:31.2:1:1:0:59.1:40:1:0:0.3 0/1:83:2:1,1:50,31:81,2:0.0241:2,2:5.5:1:27.5:1:1:1.60324:60:4:0.0241:0:2.5 +16 5416256 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20184;SOR=0;LSEQ=GCATGGTTCCACAGAAAAAA;RSEQ=TAAAACTTGCTGCCGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:36,40:76,2:0.0256:2,2:31.5:1:30:1:1:1.11:58:4:0.0256:0:1 0/0:95:0:0,0:56,39:95,0:0:2,0:22.1:1:31.1:1:1:0:58.8:190:1:0:0.6 +16 5416308 . A G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.00235;SOR=4.06325;LSEQ=TCATGACGATTTTGATGATG;RSEQ=TGAAGATGATGATGATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:6:3,3:33,27:60,6:0.0909:2,2:41.2:1:32.2:1:1:1.21849:60:12:0.0909:0:1 0/1:86:25:11,14:30,31:61,25:0.2907:2,2:24:1:29.5:1:0.8126:1.22869:57.8:11.5:0.2805:0:1.5 +16 5416313 . G A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16087;LSEQ=ACGATTTTGATGATGATGAA;RSEQ=ATGATGATGATGATGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:56:34,22:7,4:11,56:0.8358:2,2:22.4:1:31:1:1:1.13025:59.9:112:0.8485:0:1 0/1:85:38:20,18:20,26:46,38:0.4471:2,2:27.2:1:29.7:1:0.51093:1.44:60:76:0.4578:0:1.1 +16 5416316 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.50579;SOR=Inf;LSEQ=ATTTTGATGATGATGAAGAT;RSEQ=ATGATGATGATGATTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:41,23:64,0:0:2,0:25.3:1:32.7:1:1:0:59.8:128:1:0:1 0/1:84:2:1,1:38,44:82,2:0.0238:2,2:27:0:30.5:1:1:1.16:60:4:0.0238:0:2.5 +16 5416332 . TTGA T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.25068;SOR=Inf;LSEQ=AGATGATGATGATGATGATT;RSEQ=TGATGATGATGATTTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:50,18:68,0:0:2,0:25.1:1:31.5:1:1:0:59.9:136:1:0:0.8 0/1:81:3:0,3:41,37:78,3:0.037:2,0:6.7:1:27:1:0.1158:0:60:6:0.038:0.0247:1 +16 5416410 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.1753;SOR=Inf;LSEQ=TATATATGAGATACTCCAGC;RSEQ=AAAAATGCACACAAGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:197,52:249,0:0:2,0:21.8:1:31.6:1:1:0:59.3:123.5:0.988:0:0.1 0/1:182:2:1,1:133,47:180,2:0.011:2,2:10:0:31.5:1:0.45899:2.81066:60:4:0.0111:0:1.5 +16 5416451 . A G 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=TCAAAATGAAAAGACTCAGA;RSEQ=CCATCATCAACACCAAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:0:0,0:283,183:466,0:0:2,0:26.5:1:30:1:1:0:59.4:232:1:0:0.2 0/1:402:12:8,4:229,160:389,12:0.0299:2,2:27.2:1:30.3:1:0.76823:1.40:54.5:11:0.028:0:2 +16 5416455 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=4.48254;LSEQ=AATGAAAAGACTCAGAACCA;RSEQ=CATCAACACCAAGATCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:41:27,14:267,185:452,41:0.0828:2,2:26.5:1:31.7:1:0.50648:1.34:53.4:82:0.0847:0:1 0/1:409:118:76,42:163,128:291,118:0.2885:2,2:27.8:1:30.5:1:0.12283:1.42:54.7:58:0.2886:0:1.3 +16 5416679 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13606;SOR=Inf;LSEQ=CCCGATCTCTGGCAGTGGAG;RSEQ=AAGTCTCTTTAAGAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:13,58:71,0:0:2,0:24.2:1:31.8:1:1:0:59.2:70:1:0:0 0/1:42:2:1,1:12,28:40,2:0.0476:2,2:19:1:25:1:0.52846:2.28:60:4:0.0488:0:1 +16 7032232 . G A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2028;SOR=6.5151;LSEQ=TGGTTGGCTATCAGGTACCC;RSEQ=GGGAGAAATGTAGCTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:7,1:8,1:0.1111:2,0:20:0:32:0:1:0:60:2:0.125:0:2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:24.5:1:31:0:1:0:60:4:0.5:0:2 +16 7032247 . T C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCCGGGGAGAAATGTAGC;RSEQ=GCTTTCAATTTGAAAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:0,10:1:0,2:27.7:1:30.9:1:1:0:60:20:1:0:1.2 1/1:6:6:6,0:0,0:0,6:1:0,0:17.8:1:30.2:1:1:0:60:12:1:0:1.3 +16 7032415 . T C 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21705;SOR=Inf;LSEQ=CAGAGTCAGGGCTCTGATCC;RSEQ=GGAGCATCAGTCATGTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:114,70:184,0:0:2,0:26.1:1:31.2:1:1:0:60:60.333:1:0:1.2 0/1:161:2:1,1:97,62:159,2:0.0124:2,2:27:0:28.5:1:1:1.55998:60:4:0.0124:0:2 +16 7032430 . G C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43939;SOR=0;LSEQ=GATCCTGGAGCATCAGTCAT;RSEQ=TCTACTTAAGTCCTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:222:222:124,98:0,0:0,222:1:0,2:25.4:1:32.3:1:1:0:59.9:110:1:0:1.3 1/1:174:173:98,75:0,0:0,173:0.9943:0,2:25.7:1:30.5:1:1:0:60:85.5:0.9942:0:2 +16 7032453 . AG CC 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=14.05132;LSEQ=TACTTAAGTCCTTTCATTGC;RSEQ=CGAGCTCCTTCTCATTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:18:9,9:103,111:214,18:0.0769:2,2:27.7:1:30.3:1:1:1.08:58.9:36:0.0796:0.0043:1.8 1/0:194:105:59,46:42,43:85,105:0.5412:2,2:25.5:1:29.7:1:0.38244:1.31:59.9:210:0.5556:0.0052:1.9 +16 7032454 . G C 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66263;SOR=1.81487;LSEQ=ACTTAAGTCCTTTCATTGCA;RSEQ=CGAGCTCCTTCTCATTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:2:2,0:99,112:211,2:0.0087:2,0:32.5:1:31.5:1:0.22367:0:60:4:0.0096:0:3 0/1:192:3:0,3:42,43:85,3:0.0156:2,0:15:1:22.3:1:0.24295:0:56.7:2:0.0233:0:2 +16 7032513 . C A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=0;LSEQ=GGTGGATCCTGGAGTAGTCT;RSEQ=AGACGGCCTCGCCCTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:39,100:139,2:0.0142:2,2:5:1:30:1:0.48835:2.54:60:4:0.0142:0:2 0/0:132:0:0,0:44,88:132,0:0:2,0:25.3:1:31:1:1:0:60:131:1:0:0.7 +16 7032523 . C T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05979;SOR=Inf;LSEQ=GGAGTAGTCTCAGACGGCCT;RSEQ=GCCCTCTGTTCATCATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:25,87:112,0:0:2,0:24.8:1:30.5:1:1:0:60:36.333:1:0:0.3 0/1:114:5:1,4:36,73:109,5:0.0439:2,2:28.8:1:30.2:1:1:1.96233:60:10:0.0442:0:1.6 +16 8382667 . T A 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.02375;SOR=0;LSEQ=AGTTTTATGTGCCTGCTCCA;RSEQ=AAAAAAAAGAAATGCGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:9,6:0.4:0,0:11.5:1:31.3:1:1:0:60:12:0.4:0:2 0/0:11:0:0,0:11,0:11,0:0:0,0:22.9:1:31.3:1:1:0:60:22:1:0:0.2 +16 8382737 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.17234;LSEQ=GCCCCGTTGTGACAGCTAGA;RSEQ=CCCCTGCGTTCTTCTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:61:58,3:16,0:16,61:0.7922:1,1:30.1:1:29.6:1:1:0:60:19.333:0.7838:0:1.2 0/1:56:22:21,1:33,1:34,22:0.3929:1,1:27.5:1:28.4:1:1:1.55834:60:21:0.3818:0:1.2 +16 8382825 . G T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24894;SOR=0;LSEQ=CCTCATCTCCCTCCATTTCA;RSEQ=AGAAGACCAAATAGCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:159,120:279,3:0.0106:2,2:23.7:1:23.7:1:0.58035:2.64095:60:2:0.0072:0:1.7 0/0:271:0:0,0:153,118:271,0:0:2,0:25.9:1:31.1:1:1:0:59.9:89.333:1:0:0.6 +16 8382863 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10191;SOR=Inf;LSEQ=ATTCCCAGGTTTGCCATCCT;RSEQ=GTAATTTGGCTTAGCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:159,172:331,0:0:2,0:26.7:1:31.7:1:1:0:59.9:109.333:1:0:1.5 0/1:292:3:1,2:142,147:289,3:0.0103:2,2:26:1:28.7:1:1:1.92778:60:6:0.0103:0:1 +16 8382864 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25019;LSEQ=TTCCCAGGTTTGCCATCCTG;RSEQ=TAATTTGGCTTAGCACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:146:68,78:91,95:186,146:0.4398:2,2:27.2:1:30.8:1:0.73999:1.09845:60:145:0.4421:0:2.3 0/1:293:48:23,25:122,123:245,48:0.1638:2,2:27:1:29.3:1:0.87511:1.07782:60:47:0.1626:0:2.4 +16 8382873 . C T 154 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=55.56721;LSEQ=TTGCCATCCTGGTAATTTGG;RSEQ=TTAGCACTTCCTCAGAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:0,1:154,173:327,1:0.003:2,0:1:0:28:0:1:0:60:2:0.0031:0:3 0/1:281:41:23,18:113,127:240,41:0.1459:2,2:24.9:1:28.9:1:0.31348:1.43:60:82:0.1459:0:1.9 +16 8382880 . C G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.34472;LSEQ=CCTGGTAATTTGGCTTAGCA;RSEQ=TTCCTCAGAGTGCTCAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:238:106,132:44,43:87,238:0.7301:2,2:26.2:1:32.8:1:0.37944:1.27328:59.9:476:0.7301:0:2.1 0/1:278:134:63,71:67,77:144,134:0.482:2,2:26.1:1:31.3:1:1:1.02:60:268:0.4838:0:2.1 +16 8382914 . C A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2544;SOR=0;LSEQ=TCAGAACATCCATTGCAGAC;RSEQ=CTGCTGAACCCAAAGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:2,1:94,165:259,3:0.0114:2,2:16.7:1:29.3:1:0.55632:3.49:60:6:0.0116:0:1.3 0/0:220:0:0,0:87,133:220,0:0:2,0:24.9:1:30.3:1:1:0:59.9:440:1:0:1 +16 8382920 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.24779;LSEQ=CATCCATTGCAGACCCTGCT;RSEQ=AACCCAAAGATGAGACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:239:166:59,107:25,48:73,166:0.6946:2,2:25.7:1:30:1:0.88394:1.06:60:332:0.6946:0:2.1 0/1:203:73:25,48:46,84:130,73:0.3596:2,2:22.3:1:28.7:1:1:1.05119:60:146:0.3596:0:2.1 +16 8383921 . G GCT 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCTCTCTCACTCTCTCTT;RSEQ=CTCTCTCTCTCTCTCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:32:1:1:0:60:4:1:0:0.5 +16 9855916 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAACCATGCTAGCCTTCG;RSEQ=CAGACAGATGGCATTGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 9856192 . C G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTCACAGACAGAAGATC;RSEQ=ACACTTAGATCTCGGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:30.5:1:1:0:60:4:1:0:1 +16 9858404 . G A 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.22579;LSEQ=GCTTTGGATTCTGTGCTCAC;RSEQ=GCCACCTCCACCGTGTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:814:3:1,2:435,375:810,3:0.0037:2,2:15:1:31.3:1:0.59934:2.31767:60:6:0.0038:0:1 0/1:789:60:32,28:396,333:729,60:0.076:2,2:24.9:1:29.4:1:0.89356:1.04051:60:29:0.0743:0:1.3 +16 9862556 . G T 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00584;SOR=0.15834;LSEQ=ATCTAAGTTTGCAACACCTG;RSEQ=CTTATGAATGCACAAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:37:37,0:4,1:5,37:0.881:2,1:21.2:1:30.5:1:0.11905:0:60:36:0.9:0:1.1 1/0:17:9:9,0:8,0:8,9:0.5294:0,0:16.6:1:29.8:1:1:0:60:18:0.5294:0:1 +16 9862646 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25192;SOR=0;LSEQ=AGACCCCACTGAGACATCAA;RSEQ=AACCCAAGCGCTTTTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:2,1:134,34:168,3:0.0175:2,2:13:1:32:1:0.49922:1.96142:60:6:0.0179:0:1 0/0:147:0:0,0:126,21:147,0:0:2,0:21.6:1:31.3:1:1:0:60:72.5:1:0:0.2 +16 9863193 . G T 23 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAATATAATATATATATA;RSEQ=AGAGAGAGTATAGCAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:22:1:23:1:1:0:60:4:0.2857:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:36:0:27:0:1:0:60:2:1:0:0 +16 9892300 . G A 141 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=25.64287;LSEQ=TAATTCAAGACTGCGGCATC;RSEQ=TAGATGAAAGCGTCCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:496:1:1,0:159,336:495,1:0.002:2,0:1:0:26:0:0.32258:0:60:2:0.002:0:1 0/1:527:26:7,19:181,319:500,26:0.0493:2,2:26.3:1:30.1:1:0.4051:1.5389:59.9:52:0.0499:0:1 +16 9893684 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTAATAAAATGCTTGAT;RSEQ=AATTTTTACATATGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:28.5:1:1:0:60:4:1:0:1 +16 9916049 . C T 26 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56494;SOR=3.07027;LSEQ=GGAGCAGATAGGAACTGAGG;RSEQ=ATGCCGAGAGTCAATTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:1:0,1:182,29:211,1:0.0047:2,0:18:0:11:0:0.14151:0:60:0:0:0:5 0/1:139:2:1,1:120,17:137,2:0.0144:2,2:6.5:1:26.5:1:0.24304:6.88827:60:4:0.0145:0:1 +16 9916204 . C G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.62258;LSEQ=TGCATGTAGGGATAGTTATT;RSEQ=CGAATGTTTCTCTCCGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:892:584:300,284:162,145:307,584:0.6547:2,2:24.9:1:32.3:1:0.72442:1.05756:60:115.8:0.6542:0:1.1 1/0:811:439:228,211:195,172:367,439:0.5413:2,2:25:1:31.2:1:0.77702:1.04916:59.9:47.778:0.5402:0:1.2 +16 9916303 . A AAG 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=3e-04;SOR=Inf;LSEQ=TGGAGAGAGAACGAGAAAGG;RSEQ=AGAGAGAGAGTAGGAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:141,350:491,0:0:2,0:25.5:1:30.6:1:1:0:60:53.556:1:0:0.1 0/1:397:10:4,6:115,270:385,10:0.0252:2,2:24.8:1:30.6:1:0.49675:1.56:60:20:0.0256:0:0.1 +16 9916317 . G A 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=25.47722;LSEQ=GAAAGGAAGAGAGAGAGTAG;RSEQ=AAAAGAAAGAGAAGGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:2:1,1:78,306:384,2:0.0052:2,2:11.5:1:30:1:0.36786:3.90:60:4:0.0052:0:1 0/1:290:34:7,27:61,195:256,34:0.1172:2,2:23.2:1:29.6:1:0.83025:1.20583:60:33:0.115:0:1 +16 9916342 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.56238;SOR=3.18404;LSEQ=GAAAGAGAAGGGAGGAGGGG;RSEQ=AGGAGAGAACAAATAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:0,1:23,242:265,1:0.0038:2,0:5:0:30:0:1:0:60:2:0.0038:0:1 0/1:168:2:1,1:25,141:166,2:0.0119:2,2:23:1:26.5:1:0.28636:5.55:60:4:0.012:0:1 +16 9923179 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1212;SOR=0.63652;LSEQ=CTTCTGGCTTTTGTGCATTC;RSEQ=AGTTGATGGATCTCAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:129:93:92,1:36,0:36,93:0.7209:1,1:24.1:1:30.6:1:1:0:60:30:0.72:0:1.1 1/0:103:64:64,0:39,0:39,64:0.6214:1,1:25.6:1:29.7:1:1:0:60:31:0.6139:0:1 +16 9923301 . C T 151 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=43.3348;LSEQ=TTTTTGTCACTGAGGCCGGT;RSEQ=ACTTGGTCCACAAATTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:752:1:0,1:442,309:751,1:0.0013:2,0:1:0:26:0:0.41223:0:60:2:0.0014:0:1 0/1:695:38:22,16:360,297:657,38:0.0547:2,2:24.7:1:28.9:1:0.74037:1.13:60:76:0.0552:0:1.2 +16 9927866 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20389;SOR=Inf;LSEQ=TTACAGGCGTGAGCCACCAT;RSEQ=CCTGGTCTAGAGTAATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:118,15:133,0:0:2,0:22.1:1:32.4:1:1:0:56.1:65.5:1:0:0 0/1:110:2:1,1:94,14:108,2:0.0182:2,2:8:1:27.5:1:0.25521:6.52103:48:4:0.0189:0:1 +16 9934691 . G A 196 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AGAGAGAGAGAACAACAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:61,61:122,0:0:2,0:15.3:1:29:1:1:0:55.8:4.304:0.8609:0:1.3 0/1:354:101:53,48:79,70:149,101:0.2853:2,2:12.9:1:29.5:1:1:1.02202:55:32.667:0.4336:0:1.8 +16 9935066 . T G 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00207;SOR=0.17609;LSEQ=CAGATGAGTAAACTGAAGTT;RSEQ=AAAAGGGGAAGTGGCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:73:1,72:0,6:6,73:0.9241:0,1:25.8:1:32.4:1:1:0:59.6:146:0.9241:0:1.1 1/0:31:21:0,21:0,9:9,21:0.6774:0,1:21:1:29.8:1:1:0:58.5:20:0.6897:0:1 +16 9943432 . G T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35323;SOR=0.50187;LSEQ=GGAATTAAATGAATGCAAGT;RSEQ=TGGCACATCTCTAGGAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:18:18,0:7,1:8,18:0.6923:2,1:24.4:1:30.9:1:0.30769:0:60:36:0.6923:0:1.4 1/0:19:10:9,1:9,0:9,10:0.5263:0,2:27:1:29.6:1:1:0:60:20:0.5556:0:1.1 +16 9943471 . T A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08336;SOR=Inf;LSEQ=TTATCTAAGTCTTTTTTAAA;RSEQ=TGATTATTGTATTATACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:57,1:58,0:0:1,0:24.1:1:31.1:1:1:0:60:18.333:1:0:0.4 0/1:46:3:3,0:41,2:43,3:0.0652:1,0:13.3:1:24.3:1:1:0:60:2:0.0444:0:2.3 +16 9943666 . C T 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.51626;LSEQ=TTCCTCACACACGTCTCGGT;RSEQ=AGGGGGTCTATGTCTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:725:506:274,232:114,105:219,506:0.6979:2,2:24.9:1:29.3:1:0.62702:1.09:60:35.143:0.6939:0:1.1 1/0:798:434:217,217:172,192:364,434:0.5439:2,2:24.3:1:28.4:1:0.47715:1.12:60:71.333:0.5473:0:1.2 +16 9943843 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10939;SOR=Inf;LSEQ=AGCACAAACACAAAGACACA;RSEQ=CTGTGCTTTCTTCCGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:76,222:298,0:0:2,0:25.4:1:32.2:1:1:0:60:36.25:0.9932:0:0.1 0/1:276:3:2,1:78,195:273,3:0.0109:2,2:26:1:29.7:1:0.20239:4.97:60:6:0.011:0:1 +16 9943995 . A G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.57174;LSEQ=ATAAAGAGAAAACAGAATAT;RSEQ=GGGCAGTTCTCCATCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:22:0,22:0,7:7,22:0.7586:0,1:18.4:1:31.6:1:1:0:60:44:0.7586:0:1.2 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:22:1:30.4:1:1:0:60:10:0.8333:0:1 +16 9944017 . G A 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=GGCAGTTCTCCATCCCAGCC;RSEQ=CCCTCATCCCCAGAGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,11:11,5:0.3125:0,0:17.2:1:29.8:1:1:0:60:10:0.3125:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:27.3:1:31.7:1:1:0:60:6:1:0:1 +16 9984523 . C T 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTCTATGATCATTGCTA;RSEQ=ATAGTCAACACTTATTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:32.3:1:33.3:1:1:0:52.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 9985492 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTAAACACAGATTTATG;RSEQ=CAAATGATACAAGGGACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:27.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 10033874 . TGA T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=12.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATAACTTATGGGGATTCCAC;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:29:1:1:0:50:4:1:0:0 +16 10273656 . C T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25824;SOR=0;LSEQ=GTGTACACCATTTTCAGAAA;RSEQ=AAGGCAAAAGGCATTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:10.8:1:28.8:1:1:0:60:4:0.4:0:1.8 0/0:3:0:0,0:2,1:3,0:0:2,0:11.3:1:33.3:1:1:0:60:6:1:0:0.3 +16 10273800 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19574;SOR=Inf;LSEQ=TCCGAAGACCTGCAGCAGCT;RSEQ=CCATGCAGCTGGTGGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:205,25:230,0:0:2,0:24.2:1:32:1:1:0:59.8:19.909:1:0:0.2 0/1:183:2:1,1:144,36:180,2:0.0109:2,2:21:1:25:1:0.36616:3.95925:60:4:0.0118:0:1 +16 10273821 . C T 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CCATGCAGCTGGTGGCTTCC;RSEQ=AGGTCCTGGCAGGGCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:20:16,4:254,62:316,20:0.0595:2,2:23.5:1:31.3:1:1:1.02412:60:19:0.0572:0:1.2 0/0:268:0:0,0:191,77:268,0:0:2,0:23.9:1:30.6:1:1:0:60:88.333:1:0:0.2 +16 10274208 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07533;SOR=Inf;LSEQ=CGCCGCCGCGCTCGGCGCCG;RSEQ=ACCGCGCCAGACCAGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:112,219:331,0:0:2,0:22.7:1:31.5:1:1:0:59.9:46.286:1:0:0.1 0/1:243:3:1,2:89,149:238,3:0.0123:2,2:27.7:1:22.3:1:1:1.19381:60:2:0.0084:0:1.3 +16 10274263 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15035;SOR=Inf;LSEQ=AGGGTCCAATAGCCCACTCT;RSEQ=CCCATAGTCGCCACTGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:60,135:195,0:0:2,0:24.8:1:32.3:1:1:0:60:64:1:0:0.1 0/1:124:2:1,1:38,84:122,2:0.0161:2,2:32.5:1:28.5:1:0.53186:2.20:60:4:0.0164:0:1 +16 10353107 . A G 92 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGAAGTTCTTAGAAGATAGC;RSEQ=GTAGAAGAAACAGTGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:0,8:1:0,2:12.9:1:30.9:1:1:0:27.6:16:1:0:1 1/0:4:3:3,0:1,0:1,3:0.75:0,0:19.7:1:31.3:1:1:0:26:6:0.75:0:1 +16 10353347 . T C 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69057;SOR=0.65808;LSEQ=CAGCCATTTGGAGCCACTAC;RSEQ=GGTCTCTGCGTCTTGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:0,4:0,13:13,4:0.2353:1,0:29.8:1:29:1:1:0:52.3:8:0.2353:0:2.5 0/1:18:3:1,2:1,14:15,3:0.1667:1,2:14:1:28.3:1:0.31373:5.92:60:6:0.1667:0:1 +16 10353357 . G A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08462;SOR=0;LSEQ=GAGCCACTACTGGTCTCTGC;RSEQ=TCTTGGTGGTAGTGGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:9,3:0.25:0,0:35.3:1:32.3:1:1:0:49.7:6:0.25:0:3 0/0:14:0:0,0:1,13:14,0:0:1,0:24.6:1:32.1:1:1:0:57.1:28:1:0:0.5 +16 10353379 . A G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37652;SOR=0.39596;LSEQ=CTTGGTGGTAGTGGTCCCCC;RSEQ=GGCCCAGCTGTTTTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:3,8:0.7273:0,0:18.6:1:31:1:1:0:56.1:16:0.7273:0:1.8 1/0:8:4:1,3:0,4:4,4:0.5:0,2:34.8:1:31.5:1:1:0:60:8:0.5:0:1 +16 11295290 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGCCTGTGCTGGACCCA;RSEQ=GTGGTGAGCTGAGGTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:29:1:1:0:60:4:1:0:1 +16 11343726 . T C 48 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCTGCGGCGTGGGATGC;RSEQ=GGACTCGCCCTGGGTGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:19.3:1:30.3:1:1:0:60:6:1:0:1.3 +16 11345651 . T TA 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.68817;SOR=1.87979;LSEQ=GACAGAGCAAGACTCTGTCT;RSEQ=AAAAAAAAAAAGAAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:7,0:8,0:8,7:0.4375:0,0:31.3:1:27:1:1:0:56.7:6:0.4:0:0.7 1/0:10:6:5,1:1,0:1,6:0.6:0,2:19.7:1:27.5:1:1:0:60:12:0.6:0.2:0.5 +16 11345660 . AAAG A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.17243;SOR=0;LSEQ=AGACTCTGTCTTAAAAAAAA;RSEQ=AAGAAGAAACCTGTCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:6,0:26,0:26,6:0.1935:1,0:12.8:1:29.5:1:1:0:60:12:0.1935:0.129:0.8 0/0:11:0:0,0:10,1:11,0:0:2,0:25.4:1:29.1:1:1:0:58.5:22:1:0:0.5 +16 11345699 . G C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78148;SOR=0.74129;LSEQ=TTGTTGTTTAGAGTGGGATG;RSEQ=ATTTGGTCCAAGTCCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:14:14,0:31,0:31,14:0.3111:1,1:29.4:1:28.1:1:1:0:58.8:2.5:0.2703:0:1.5 0/1:24:6:5,1:18,0:18,6:0.25:1,2:32.8:1:29.5:1:0.25:0:53.7:5:0.2174:0:1.8 +16 11345753 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17419;SOR=Inf;LSEQ=TGTGTGACCTTGAGTAGGTG;RSEQ=CTGCACTTGTCTGAGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:102,2:104,0:0:1,0:21.5:1:31.6:1:1:0:60:103:1:0:0.2 0/1:75:2:1,1:70,3:73,2:0.0267:1,2:27.5:1:30.5:1:0.1045:20.35111:60:4:0.027:0:1 +16 11345754 . C T 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=GTGTGACCTTGAGTAGGTGG;RSEQ=TGCACTTGTCTGAGCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:105,2:107,0:0:1,0:21.3:1:32.4:1:1:0:60:106:1:0:0.2 0/1:75:9:9,0:62,4:66,9:0.12:2,0:19.6:1:29.4:1:1:0:60:18:0.1233:0:1.1 +16 11346008 . A C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38021;LSEQ=AAACCCTCCTCTCACTTTTC;RSEQ=TTCTTGTAAATTGACGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:861:303:109,194:200,357:557,303:0.3519:2,2:24.6:1:32.5:1:1:1.00:60:150.5:0.3575:0:1.1 0/1:1064:182:75,107:354,527:881,182:0.1711:2,2:26.4:1:30.8:1:0.80386:1.04:59.8:90:0.1727:0:1.2 +16 11346074 . G A 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36545;SOR=3.11951;LSEQ=TTGAGAGAGAGACAGAATCT;RSEQ=CACCACCCGGGAAGCCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:1:1,0:39,209:248,1:0.004:2,0:1:0:24:0:0.16064:0:60:2:0.0041:0:2 0/1:241:3:2,1:49,188:237,3:0.0124:2,2:8.7:1:25.7:1:0.11506:7.58:60:6:0.0128:0:1 +16 11346107 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.18746;SOR=Inf;LSEQ=AGCCACATGGCGCTGGTGCG;RSEQ=GCGCACACACACAAACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:8,121:129,0:0:2,0:20.8:1:29.3:1:1:0:58.9:31.25:1:0:0.4 0/1:99:2:1,1:6,91:97,2:0.0202:2,2:5.5:1:26.5:1:0.13709:14.12:60:4:0.0202:0:1 +16 11346110 . G GCACA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=7.000;MSILEN=2;SSF=0.50531;SOR=0;LSEQ=CACATGGCGCTGGTGCGCGC;RSEQ=CACACACACAAACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:6,109:115,2:0.0169:2,0:17.5:1:30.5:1:1:0:47:4:0.0172:0.0085:1.5 0/0:92:0:0,0:4,87:91,0:0:1,0:22.3:1:30.8:1:1:0:58.7:17.2:0.9885:0:0.6 +16 11346111 . C CAG 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0.90358;LSEQ=ACATGGCGCTGGTGCGCGCG;RSEQ=ACACACACAAACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:7:0,7:5,105:110,7:0.0598:1,0:35.3:1:28.4:1:1:0:55.4:14:0.0609:0:1.3 0/1:92:5:0,5:4,83:87,5:0.0543:1,0:40:1:29.4:1:1:0:57.8:10:0.0556:0:1 +16 11346113 . C G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.36756;SOR=1.46438;LSEQ=ATGGCGCTGGTGCGCGCGCA;RSEQ=ACACACAAACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:19:0,19:3,88:91,19:0.1712:1,1:21:1:29.5:1:1:0:59.5:5.333:0.1524:0:1.7 0/1:86:20:1,19:1,65:66,20:0.2326:1,1:15.8:1:30.9:1:0.41313:3.36:59.5:19:0.2317:0:1.6 +16 11346412 . GA G 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCATACTTTTTTCAAAGGAG;RSEQ=AAAAAAACTGTAACATATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:11:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:28.4:1:1:0:60:4:1:0.5:1 +16 11346462 . T C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTAGCTGACCCCTCTTT;RSEQ=GAGGAGGACCTGTTTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:1:30:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:29:1:1:0:60:4:1:0:1 +16 11346732 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGTCCTGCTTTGCCTCT;RSEQ=GGAGCCCGTTTTCCCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42:1:32:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 11346782 . G T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCCAGCACAGCCACTGAGTG;RSEQ=TCACTAAGGGTCTGTGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9:1:29:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:18.5:1:31:1:1:0:60:4:1:0:0.5 +16 11346954 . AAAAAAG A 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=12.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GCAGGGGTGTGGCAAAAAAA;RSEQ=AAAAGAAAAGAAAAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:5,1:6,4:0.4:2,0:17.3:1:30.1:1:1:0:60:8:0.4:0.2:0 1/1:1:2:2,0:0,0:0,2:2:0,0:11:1:31:1:1:0:60:8:0.8365:0.6909:2 +16 11346955 . AAAAAG A 31 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CAGGGGTGTGGCAAAAAAAA;RSEQ=AAAAGAAAAGAAAAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:3,1:4,1:0.125:2,0:20:0:32:0:1:0:60:2:0.1667:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:14:1:31:1:1:0:60:4:1:0.5:1 +16 11346970 . G A 52 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AAAAAAAAAAGAAAAGAAAA;RSEQ=AAAAGAAAAGAAAAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:4,0:10,1:11,4:0.2667:2,0:5:1:26:1:1:0:57.3:3:0.25:0:2.8 0/0:2:0:0,0:2,0:2,0:0:0,0:23.5:1:25:1:1:0:60:1:1:0:1 +16 11347048 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93062;LSEQ=TTCCCTCCCACTTCACCTTA;RSEQ=TAAGGGATGAAATTGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:13:13,0:28,1:29,13:0.3095:1,1:29:1:31.5:1:1:0:59.2:26:0.3171:0:1.4 0/1:17:5:5,0:11,1:12,5:0.2941:2,0:23.8:1:33.6:1:1:0:60:10:0.2941:0:1 +16 11347138 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49843;SOR=0;LSEQ=CTACTTAATCCCCAAGACAG;RSEQ=CCTGGGCTGCTCTGACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:128,30:158,2:0.0125:2,2:17:0:32:0:0.35094:4.21365:60:4:0.0126:0:1.5 0/0:159:0:0,0:126,33:159,0:0:2,0:22:1:30.5:1:1:0:59.9:52:1:0:0.2 +16 11347168 . A G 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTCTGACTCTCTGACCATCA;RSEQ=GTTAATTTTATGTTGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:183,76:259,0:0:2,0:25.3:1:30.8:1:1:0:60:85.333:1:0:0.4 0/1:276:18:12,6:175,83:258,18:0.0652:2,2:23.7:1:31.8:1:1:1.05401:60:36:0.0669:0:1.2 +16 11347199 . A G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.20854;LSEQ=TGTTGTACTTTCAAGTCTGA;RSEQ=AAGTATTATTAAGCATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:143:89,54:157,96:253,143:0.3611:2,2:26.1:1:32.6:1:1:1.01:59.9:70.5:0.3606:0:1.1 0/1:456:48:31,17:252,155:407,48:0.1053:2,2:21.4:1:31.2:1:0.75556:1.12:60:96:0.1067:0:1.1 +16 11347311 . T C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59212;LSEQ=CCAGGCTGCTTAACCCTAAA;RSEQ=CTGAAAATGACTCAGTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:491:490:192,298:0,0:0,490:0.998:0,2:26:1:31.7:1:1:0:60:97:1:0:1.1 1/1:582:580:256,324:0,1:1,580:0.9966:0,2:26.4:1:30.8:1:1:0:60:289:1:0:1.1 +16 11348264 . AT A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACTCGCTAGAAAACTT;RSEQ=TTTTTTTTAAAAAAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:9.5:1:31.5:1:1:0:60:4:1:0.5:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 11348516 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14329;SOR=Inf;LSEQ=AGCACCAGGAGGGGGAGGAC;RSEQ=CCCTCAAGAGGTGAGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:31,1:32,0:0:1,0:20.7:1:31.2:1:1:0:60:31:1:0:0.3 0/1:20:2:2,0:18,0:18,2:0.1:1,0:19.5:1:32:0:1:0:60:4:0.1053:0:1 +16 11348658 . C T 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00994;SOR=Inf;LSEQ=CAAGTAATAACAAAATAACA;RSEQ=GGCATCCCAGTTAATGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:318,167:485,0:0:2,0:23.2:1:31:1:1:0:60:68.286:1:0:0.1 0/1:597:8:3,5:373,214:587,8:0.0134:2,2:9.9:1:28.1:1:0.1514:2.89951:60:16:0.0136:0:1.1 +16 11348825 . C A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62121;SOR=0.49107;LSEQ=CAGCTCCTGCAGCGGCCGCA;RSEQ=GCGGCGCTGGCGCAGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:32,114:146,2:0.0135:2,2:21:1:29:1:0.39741:3.52:60:4:0.0139:0:1 0/0:150:1:1,0:40,109:149,1:0.0067:2,0:1:0:29:0:0.27333:0:59:2:0.0068:0:1 +16 11348826 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49822;SOR=Inf;LSEQ=AGCTCCTGCAGCGGCCGCAC;RSEQ=CGGCGCTGGCGCAGCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:34,104:138,0:0:2,0:15.1:1:32.1:1:1:0:60:45:1:0:0.2 0/1:140:2:1,1:38,100:138,2:0.0143:2,2:6.5:1:27.5:1:0.48099:2.61:60:4:0.0143:0:1 +16 11348844 . G T 38 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24922;SOR=0;LSEQ=ACGCGGCGCTGGCGCAGCGG;RSEQ=GCCCCCAGCATGCGGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:3:1,2:47,44:91,3:0.0319:2,2:7.7:1:24.3:1:0.6129:2.11971:60:2:0.0222:0:2.3 0/0:82:0:0,0:42,39:81,0:0:2,0:12.7:1:30.6:1:1:0:60:26:0.9873:0:0.2 +16 11348857 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24815;SOR=0;LSEQ=GCAGCGGGGCCCCCAGCATG;RSEQ=GGCGCGGCGCCGCCACGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:1,2:63,27:90,3:0.0323:2,2:9:1:30:1:0.2284:4.5803:60:6:0.0333:0:1 0/0:83:0:0,0:67,16:83,0:0:2,0:18.6:1:31.8:1:1:0:60:166:1:0:0.1 +16 11348914 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09176;SOR=0;LSEQ=AGAGGCAGTCGAAGCTCTCG;RSEQ=GGCTGCCATCCAGGTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:191,88:279,3:0.0106:2,2:24:1:29.7:1:0.23971:4.31594:60:6:0.0108:0:1 0/0:342:0:0,0:214,128:342,0:0:2,0:24.6:1:30.1:1:1:0:60:67.4:1:0:0.2 +16 11348920 . C T 60 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18505;SOR=0.21002;LSEQ=AGTCGAAGCTCTCGCGGCTG;RSEQ=CATCCAGGTGAAAGCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:4:2,2:200,101:301,4:0.0131:2,2:21:1:30.3:1:0.60568:1.97548:60:8:0.0133:0:1 0/0:360:1:0,1:225,133:358,1:0.0028:2,0:7:0:30:0:0.37326:0:60:2:0.0028:0:1 +16 11349077 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10896;SOR=0;LSEQ=CAGCCGCTCGTGCGCCCCGT;RSEQ=CACGCTCAGGGGCCCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:128,168:296,3:0.01:2,2:27:1:27.3:1:1:1.52175:60:6:0.0103:0:2 0/0:327:0:0,0:144,183:327,0:0:2,0:23.9:1:31:1:1:0:60:53.5:1:0:0.2 +16 11349185 . CG C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21494;SOR=0;LSEQ=TGTGCGGAAGTGCGTGTCGC;RSEQ=GGGGCCGGGGCCGGGACCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:32,78:110,2:0.0179:2,2:23:1:30:1:0.50434:2.42:60:4:0.0179:0:0 0/0:129:0:0,0:42,86:128,0:0:2,0:15.7:1:30.4:1:1:0:60:127:0.9922:0:0.3 +16 11349191 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21808;SOR=0;LSEQ=GAAGTGCGTGTCGCCGGGGG;RSEQ=CGGGGCCGGGACCGCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:28,66:94,2:0.0208:2,2:19:0:32:0:0.51513:2.33:60:4:0.0211:0:1.5 0/0:109:0:0,0:34,75:109,0:0:2,0:13:1:31:1:1:0:60:108:1:0:0.3 +16 11349213 . CGGCCGCGGGCGCGCGGG C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=5.000;MSILEN=1;SSF=0.50268;SOR=0;LSEQ=GGGGCCGGGACCGCGGGGCA;RSEQ=GGCCGCGGGCGAGGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:67,25:92,2:0.0213:2,2:8:1:29.1:1:0.47884:2.6475:60:4:0.0213:0.0213:0 0/0:76:0:0,0:53,23:76,0:0:2,0:9.1:1:29.9:1:1:0:60:152:1:0:0.2 +16 11349252 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25101;SOR=Inf;LSEQ=GCCGCGGGCGAGGAGGAGGA;RSEQ=GAGGAGGAAGGTTCTGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:153,72:225,0:0:2,0:22.4:1:30.9:1:1:0:60:74:1:0:0.2 0/1:253:3:1,2:164,85:249,3:0.0119:2,2:21:1:31.7:1:0.27443:3.83652:57.3:6:0.0122:0:1.3 +16 11349302 . C T 63 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09072;SOR=0.15169;LSEQ=CTCTGCTGCTGTGGAGACTG;RSEQ=ATTGTCGGCTGCCACCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:5:2,3:232,169:401,5:0.0123:2,2:21:1:27.4:1:0.65431:2.05549:60:10:0.0126:0:1 0/0:532:1:0,1:299,232:531,1:0.0019:2,0:1:0:23:0:0.43797:0:60:2:0.0019:0:2 +16 11349403 . A C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4899;SOR=0;LSEQ=GCGCTGCGGGAGAGACAAAG;RSEQ=GGTGAGCTGGGGCGCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:101:101:14,87:0,0:0,101:1:0,2:24.3:1:30.2:1:1:0:60:49.5:1:0:1.1 1/1:97:96:8,88:0,0:0,96:0.9897:0,2:23.9:1:29.8:1:1:0:60:192:0.9897:0:1.1 +16 11349847 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCGCGGCCGCGACCCCAT;RSEQ=CTGCAGCCCCCGAGGCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 11350714 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17137;SOR=Inf;LSEQ=GGCGGCGCGGGCGCCTCCAC;RSEQ=CCGGCCCAGTTCCTCGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:153,19:172,0:0:2,0:21.8:1:31.2:1:1:0:59.9:85:1:0:0.2 0/1:122:2:2,0:105,15:120,2:0.0164:2,0:15:1:28.5:1:1:0:60:4:0.0168:0:1 +16 11350735 . C T 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20544;SOR=Inf;LSEQ=CCGGCCCAGTTCCTCGGAAA;RSEQ=TGGGCGGGGCCGGGCAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:192,39:231,0:0:2,0:25.1:1:32.1:1:1:0:59.9:37.5:1:0:0.2 0/1:192:2:1,1:154,36:190,2:0.0104:2,2:7:1:25.5:1:0.34909:4.23325:60:4:0.0106:0:1 +16 11350811 . CTG C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00516;SOR=1.34488;LSEQ=CTACCCGGCTGCGGAAGAAA;RSEQ=AGGCTGGGGAGGGGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:759:229:141,88:326,203:529,229:0.3017:2,2:25.4:1:32.1:1:1:1.00227:59.8:113.5:0.3059:0.0553:0.2 0/1:925:340:198,142:345,240:585,340:0.3676:2,2:23.2:1:31.1:1:0.83567:1.03092:59.7:339:0.3725:0.0822:0.2 +16 11350965 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0014;SOR=0.57542;LSEQ=GGTGCATTCTCAGACGTGAT;RSEQ=AATCCCCAAACCTGGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:123:17,106:36,167:203,123:0.3773:2,2:24.6:1:30.2:1:0.43905:1.34295:60:29.75:0.3719:0:1.1 0/1:329:85:14,71:49,194:243,85:0.2584:2,2:23.6:1:29.9:1:0.52424:1.27996:60:170:0.2623:0:1.1 +16 11350991 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=2.65552;LSEQ=CCAAACCTGGTTTCCTAGCC;RSEQ=TCCTCTCCCCCGACCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:54:1,53:7,132:139,54:0.2798:2,1:24.9:1:30.9:1:0.4463:2.79888:60:108:0.2813:0:1.2 1/0:177:90:6,84:4,83:87,90:0.5085:1,2:21.7:1:30.2:1:0.74705:1.48:59.7:89:0.5057:0:1 +16 11350995 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50079;SOR=0;LSEQ=ACCTGGTTTCCTAGCCCTCC;RSEQ=CTCCCCCGACCCCTTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:0,2:7,174:181,2:0.0109:1,0:11:1:31:1:1:0:60:4:0.0113:0:2 0/0:160:0:0,0:9,151:160,0:0:2,0:21.3:1:28.9:1:1:0:59.8:31:1:0:0.8 +16 11352604 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20858;SOR=Inf;LSEQ=GGGACCACAGGCCAGGGAAG;RSEQ=CACAGCAAGGGAGCAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:88,3:91,0:0:1,0:23.5:1:31.8:1:1:0:59.6:182:1:0:0 0/1:77:2:1,1:68,7:75,2:0.026:2,2:18.5:1:30.5:1:0.19822:9.15346:60:4:0.0274:0:1 +16 11352652 . G T 54 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12372;SOR=Inf;LSEQ=AAGGTACACTCAGCACACGT;RSEQ=GGTTCTCCTCACTGCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:180,45:225,0:0:2,0:24.3:1:31.7:1:1:0:60:44:1:0:0.1 0/1:235:4:1,3:172,58:230,4:0.017:2,2:6.8:1:27:1:0.05543:8.79585:60:8:0.0172:0:1 +16 11352793 . G C 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.062;LSEQ=TCCACCTTGTGGGCTGTTCT;RSEQ=CTGGAGGGCTGGGCACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:593:590:265,325:0,0:0,590:0.9949:0,2:23.5:1:31.2:1:1:0:60:64.556:0.9949:0:1.1 1/1:593:548:245,303:20,22:42,548:0.9241:2,2:25.3:1:30.1:1:0.7492:1.12408:60:90.333:0.9233:0:1.1 +16 11352843 . T A 59 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12414;SOR=0;LSEQ=AGCCAGGCAGTGCGAAACCC;RSEQ=GAGGGGCTCAGAGTGCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:4:2,2:68,222:290,4:0.0136:2,2:5.3:1:29.8:1:0.24098:3.25:60:8:0.0137:0:2.3 0/0:280:0:0,0:77,203:280,0:0:2,0:24.5:1:29.6:1:1:0:60:279:1:0:0.8 +16 11352930 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-04;SOR=0.12796;LSEQ=GCAAGTGACCTGTCCTCTTG;RSEQ=GACCTGATTTGCCCCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:21:0,21:0,45:45,21:0.3182:1,1:28.6:1:32.9:1:1:0:60:42:0.3387:0:2 0/1:54:3:0,3:5,46:51,3:0.0556:2,0:18.7:1:32:0:1:0:60:6:0.0556:0:2 +16 11352936 . G C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTGTCCTCTTGGGACCT;RSEQ=ATTTGCCCCAACTGCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:64:0,64:0,0:0,64:1:0,1:24.9:1:33.2:1:1:0:59.4:128:1:0:1.3 1/1:47:47:4,43:0,0:0,47:1:0,2:21.8:1:31.7:1:1:0:59.6:94:1:0:1.1 +16 11507019 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11053;SOR=Inf;LSEQ=AGGTTGGCAGTGCCCACCGA;RSEQ=GGACCTCAAAGGACAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:13,0:0:2,0:30.3:1:31.8:1:1:0:60:26:1:0:0.9 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:16:1:28:1:1:1.41418:60:4:0.2857:0:2 +16 11507025 . T C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52322;SOR=0.24759;LSEQ=GCAGTGCCCACCGAGGGACC;RSEQ=CAAAGGACAGCTGCAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:4,7:0,1:1,11:0.9167:0,2:30.5:1:30.8:1:1:0:60:22:0.9167:0:1.1 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:21.2:1:29.8:1:1:1.41:60:10:0.7143:0:1.4 +16 11508311 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACCAGGGCTGCCAGGTCCA;RSEQ=GCTGACTCCACTGTCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:46:26,20:0,0:0,46:0.9787:0,2:27.7:1:31.8:1:1:0:60:92:1:0:1.2 1/1:22:22:12,10:0,0:0,22:1:0,2:22.1:1:31:1:1:0:60:44:1:0:1.3 +16 13872875 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52284;SOR=Inf;LSEQ=CCTGGTTTCTGGTGGTTTGC;RSEQ=GGCCACCTTTGGCATTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:21,20:41,0:0:2,0:27.4:1:30.4:1:1:0:60:40:1:0:0.2 0/1:66:2:1,1:35,29:64,2:0.0303:2,2:26.5:1:29:1:1:1.20344:60:4:0.0303:0:1 +16 13872919 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14655;SOR=0;LSEQ=TTAATGAAGCATCTCTGCCT;RSEQ=CACCTTCACATAGAGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:8,24:32,2:0.0588:2,2:25.5:1:31.5:1:0.46524:2.89:60:4:0.0606:0:1 0/0:54:0:0,0:21,33:54,0:0:2,0:21.6:1:28.5:1:1:0:60:108:1:0:0 +16 14013631 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCCCCTTCCCTTGCTTTTT;RSEQ=GCAGCTTGAGGCTAGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:24:1:32.5:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:28.5:1:1:0:60:4:1:0:1 +16 14013666 . A C 35 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGGTGCCAGGGGATGTGGAA;RSEQ=CTCAAAAGAGACGTGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:18.5:1:35:0:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:31:0:1:0:60:2:1:0:1 +16 14013993 . T A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25119;LSEQ=AGGAGTCGGCTTCCTTCGGC;RSEQ=GCGTTCGGCTGCGACCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:367:219:154,65:97,51:148,219:0.5967:2,2:24.2:1:30.7:1:0.36078:1.24:60:108.5:0.5994:0:1.2 0/1:377:102:72,30:177,98:275,102:0.2706:2,2:24.7:1:29.5:1:0.27293:1.33:60:101:0.2708:0:1.1 +16 14014222 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5655;SOR=3.05907;LSEQ=GGTGCTCAACACGCAGCCGG;RSEQ=CGAGGAGGTGCGGCCGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:1:0,1:58,218:276,1:0.0036:2,0:43:0:31:0:1:0:60:2:0.0037:0:3 0/1:182:2:1,1:31,147:178,2:0.011:2,2:9.5:1:26.5:1:0.32477:4.68:60:4:0.0112:0:2 +16 14014240 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.23694;LSEQ=GGCCGAGGAGGTGCGGCCGC;RSEQ=CTGGCGCGGGAGTGAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:122:15,107:11,65:76,122:0.6131:2,2:26.4:1:30.6:1:0.67036:1.206:60:121:0.6142:0:1.1 0/1:125:34:4,30:9,82:91,34:0.272:2,2:24.3:1:29.6:1:0.74884:1.21:60:68:0.2764:0:1.1 +16 14020382 . C G 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=AATGAATGGCAATTACCTAC;RSEQ=TGTTCTGTAGTTTAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:237,72:309,0:0:2,0:24.9:1:31.8:1:1:0:60:76.25:0.9967:0:0.1 0/1:283:30:24,6:188,64:252,30:0.106:2,2:27.9:1:29.8:1:0.65656:1.36:60:60:0.1064:0:1 +16 14020660 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18157;SOR=Inf;LSEQ=GATGACATTATTTGTCATCT;RSEQ=TGTTTGTGAGATCTACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:22,178:200,0:0:2,0:24.3:1:30.7:1:1:0:60:199:1:0:0 0/1:149:2:1,1:16,130:146,2:0.0134:2,2:33.5:1:33:0:0.21723:7.91:60:4:0.0137:0:2 +16 14021276 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACAAAAATTAGCCAGG;RSEQ=GTGTTGGCACATGCCTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:31.5:1:1:0:21:4:1:0:1.5 +16 14021754 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11355;SOR=Inf;LSEQ=TTGAAAATGTTGTTGCTTTG;RSEQ=TTTTCATTTGTTTGTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:58,2:60,0:0:1,0:22.4:1:32.5:1:1:0:60:29:1:0:0.2 0/1:31:2:1,1:29,0:29,2:0.0645:1,2:7.5:1:27:1:0.06452:0:60:4:0.0645:0:1 +16 14024407 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72447;SOR=0.72805;LSEQ=AGCCACTTCCTTGAATAATG;RSEQ=TTGCAGTTTTTTTATTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:18:18,0:13,0:13,18:0.5806:1,1:21.4:1:28.6:1:1:0:60:17:0.5667:0:1.2 1/0:10:5:5,0:5,0:5,5:0.5:0,0:12.8:1:30:1:1:0:60:10:0.5:0:1 +16 14025892 . C A 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14255;SOR=5.30883;LSEQ=CAGATCACAGTAGTGGGAGG;RSEQ=GGTGTGGTTGGTAGGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:1:1,0:84,2:86,1:0.0115:1,0:2:0:15:0:1:0:60:0:0:0:3 0/1:51:3:3,0:48,0:48,3:0.0588:1,0:29:1:29.7:1:1:0:60:6:0.0588:0:1 +16 14026007 . G A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0263;LSEQ=ACTTTTTCTTTTAACTTTTC;RSEQ=TATTAGGTTGGCTGTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:486:485:278,207:0,0:0,485:0.9979:0,2:26.4:1:30.4:1:1:0:60:39.417:0.9979:0:1.1 1/1:508:471:283,188:18,16:34,471:0.9272:2,2:26.4:1:29.4:1:0.47033:1.34:59.9:57.875:0.9279:0:1.1 +16 14026361 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05556;SOR=Inf;LSEQ=TATACAGCATGGCAAGTCTT;RSEQ=CAGTCTATTGCCCAGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:0,21:21,0:0:1,0:28.6:1:30.8:1:1:0:60:9.5:1:0:0.1 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:35:1:28.5:1:1:0:60:4:0.2857:0:1 +16 14027947 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19918;SOR=Inf;LSEQ=AGAAAGCTTAAATAAATGGG;RSEQ=ATATGTACTGATGCTCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:49,0:0:1,0:22.7:1:32:1:1:0:60:15.333:1:0:0.1 0/1:40:2:1,1:38,0:38,2:0.05:1,2:13:0:30:1:0.05:0:60:4:0.0513:0:1.5 +16 14028026 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09842;SOR=0;LSEQ=TAAATATTATCACATAGAAT;RSEQ=AGATATTTTTATTTCTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:2,1:151,58:209,3:0.0142:2,2:18:1:28.7:1:1:1.30004:60:6:0.0142:0:1 0/0:246:0:0,0:167,78:245,0:0:2,0:24.1:1:30.8:1:1:0:60:60.25:0.9959:0:0.1 +16 14028199 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49992;SOR=0;LSEQ=AAACATTTGCTTCCAAAATC;RSEQ=ATCAAATGAGTCCTGATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:34,124:158,2:0.0125:2,2:24.5:1:30.5:1:0.39072:3.61:60:4:0.0127:0:1.5 0/0:143:0:0,0:35,107:142,0:0:2,0:23.5:1:28:1:1:0:60:70:0.9929:0:0.1 +16 14028861 . C T 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03594;SOR=0;LSEQ=ATTTGATCAATACCTAAGAC;RSEQ=CTTTTTAAATAGTTTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:7:7,0:32,0:32,7:0.1795:1,0:30.4:1:32.4:1:1:0:60:14:0.1795:0:1.6 0/0:28:0:0,0:28,0:28,0:0:1,0:22.3:1:31:1:1:0:60:56:1:0:0 +16 14029536 . G A 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12403;SOR=0;LSEQ=GATACGTGGTTCTTTATGAC;RSEQ=CAGAGCTAACCTTTGTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:4:3,1:107,187:294,4:0.0134:2,2:22:1:29:1:0.14393:5.21:60:8:0.0137:0:1.3 0/0:286:0:0,0:113,173:286,0:0:2,0:26:1:30.3:1:1:0:60:70.5:1:0:0.2 +16 14031520 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCTTAGTCAAATATTT;RSEQ=TTATTTGAGCGCTCTAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:205:204:190,14:0,0:0,204:0.9951:0,2:23.2:1:28.6:1:1:0:60:39.8:0.995:0:1.2 1/1:128:128:121,7:0,0:0,128:1:0,2:23.5:1:27.9:1:1:0:60:41.667:1:0:1.1 +16 14031530 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07128;SOR=Inf;LSEQ=TCAAATATTTGTTATTTGAG;RSEQ=GCTCTAGGTTGCTGATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:237,26:263,0:0:2,0:22.7:1:32.2:1:1:0:60:42.833:1:0:0.9 0/1:188:3:1,2:156,28:184,3:0.016:2,2:9.7:1:25:1:0.06747:10.90966:60:6:0.0161:0:1.3 +16 14031598 . C A 171 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=62.14163;LSEQ=AAAAATGCTGTTTTTCCAAC;RSEQ=TAAAAGTTCTGTCTTAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:757:1:1,0:432,321:753,1:0.0013:2,0:5:0:14:0:1:0:60:0:0:0:2 0/1:736:56:31,25:381,299:680,56:0.0761:2,2:25.5:1:29.6:1:1:1.02759:60:112:0.0764:0:1.2 +16 14038545 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27639;LSEQ=AAATCTAGAATTTTGAAATT;RSEQ=GTTTCAGAAGTGTTGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:359:186:136,50:121,52:173,186:0.5181:2,2:23.1:1:31.2:1:0.55855:1.17:60:92:0.5169:0:2 0/1:424:97:65,32:221,106:327,97:0.2288:2,2:22:1:29.7:1:0.90252:1.02637:60:96:0.228:0:1.9 +16 14038552 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22894;LSEQ=GAATTTTGAAATTTGTTTCA;RSEQ=AAGTGTTGACAATGTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:424:224:154,70:134,66:200,224:0.5283:2,2:22:1:30.2:1:0.75473:1.08:60:111:0.5298:0:1.9 0/1:476:97:62,35:246,130:376,97:0.2038:2,2:22.7:1:29.5:1:0.81156:1.06809:60:96:0.2038:0:1.9 +16 14038659 . T C 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTAGTAAGAGGCACAGCA;RSEQ=CTGCAGATGTTTCCACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:225,327:552,0:0:2,0:25.2:1:30.5:1:1:0:60:91:0.9982:0:0.1 0/1:607:29:13,16:237,340:577,29:0.0478:2,2:26.8:1:31.5:1:0.70279:1.17:60:58:0.0484:0:1.2 +16 14038727 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2444;SOR=Inf;LSEQ=TTGTCAGGCACCTCCATTGC;RSEQ=TGCAAAGGGGGCTGTGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:35,167:202,0:0:2,0:23.8:1:32.6:1:1:0:60:66.333:1:0:0.1 0/1:198:2:1,1:41,154:195,2:0.0101:2,2:10.5:1:28:1:0.3818:3.72:60:4:0.0103:0:1 +16 14038762 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.178;SOR=Inf;LSEQ=TGAAGTTCCAGAGTTACTCT;RSEQ=CCAAGGCTTGGTCTGTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:8,116:124,0:0:2,0:26.3:1:32.7:1:1:0:59.7:248:1:0:0.1 0/1:91:2:1,1:5,83:88,2:0.022:2,2:7.5:1:27.5:1:0.12959:15.24:60:4:0.022:0:1 +16 14041760 . C A 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTAGCAAGCCTTTCTCTCT;RSEQ=ACTTCCCGAGGTGCCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:19:9,10:290,350:640,19:0.0288:2,2:28.8:1:29.1:1:1:1.09:60:38:0.0288:0:1.1 0/0:751:0:0,0:357,392:749,0:0:2,0:24.6:1:30.9:1:1:0:59.9:123.833:0.9973:0:0.1 +16 14041958 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.258;LSEQ=CTGGCCATTACAGCAGATTC;RSEQ=GAAACCCTTCCCGAGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:579:309:157,152:141,128:269,309:0.5337:2,2:25.3:1:30.3:1:0.73875:1.06635:60:43.143:0.5355:0:1.1 0/1:584:133:70,63:228,221:449,133:0.2277:2,2:25.3:1:29.5:1:0.76717:1.08:59.7:32.25:0.2247:0:1.2 +16 14042077 . A G 189 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCACGTTAAGAACATCGCAG;RSEQ=ATTAGCAGCCCTGTCACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:61:26,35:269,323:592,61:0.0934:2,2:26.2:1:31.9:1:0.688:1.12089:59.5:122:0.0953:0:1.2 0/0:727:0:0,0:358,369:727,0:0:2,0:24.8:1:29.2:1:1:0:59.9:144.4:1:0:0.2 +16 16100560 . A G 30 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=CCAGCTGTGTGATACTGGAC;RSEQ=CAGTATTTAACCCTTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:30.5:1:31.5:1:1:0:60:4:1:0:1 1/0:4:2:2,0:1,0:1,2:0.5:0,0:32.5:1:30.5:1:1:0:60:4:0.6667:0:1.5 +16 16100673 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.30239;SOR=2.40636;LSEQ=ACTTAGAATAAAGCCTGGCA;RSEQ=ACAGAACTGCAGTTTGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:4,5:5,2:7,9:0.5625:2,2:31.3:1:31.3:1:0.35752:2.90271:60:18:0.5625:0:1.3 1/0:25:19:9,10:3,3:6,19:0.76:2,2:27.2:1:30.6:1:1:1.10643:58.9:38:0.76:0:1.7 +16 16100704 . T C 38 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.10694;SOR=0;LSEQ=AGTTTGGTTGTTATCCGTGG;RSEQ=GGTGGCGGTGGCGGTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:8,9:17,3:0.15:2,2:5.3:1:24.3:1:1:1.72884:52.7:2:0.1111:0:2.3 0/0:21:0:0,0:6,15:21,0:0:2,0:4:0:10:0:1:0:60:0:0:0:2 +16 16100728 . C T 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=6;SSF=0.43612;SOR=0.43704;LSEQ=GGCGGTGGCGGTGGCGGTGG;RSEQ=GGTGGCGGTGATGGTGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:2,3:7,8:15,5:0.25:2,2:24.8:1:31.4:1:1:1.29489:55.6:10:0.25:0:1.8 0/1:24:3:1,2:5,16:21,3:0.125:2,2:25.3:1:28:1:1:1.57:58.7:6:0.125:0:1.7 +16 16100739 . A G 84 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03946;SOR=9.39079;LSEQ=TGGCGGTGGCGGTGGCGGTG;RSEQ=TGGTGGTGGTGATGGTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:6,7:13,1:0.0714:2,0:8:0:34:0:1:0:60:2:0.0769:0:3 0/1:16:7:1,6:2,7:9,7:0.4375:2,2:8.9:1:30.1:1:1:1.659:57.1:6:0.4:0:2.7 +16 16100746 . T C 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.31677;SOR=3.88274;LSEQ=GGCGGTGGCGGTGATGGTGG;RSEQ=GGTGATGGTGGCGATGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:5,6:11,1:0.0833:2,0:1:0:32:0:1:0:60:2:0.0833:0:3 0/1:11:3:1,2:2,6:8,3:0.2727:2,2:8.7:1:31.3:1:1:1.44:53.3:6:0.2727:0:3.3 +16 16100769 . ATGATGGTGG A 24 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0.88119;LSEQ=TGATGGTGGCGATGGTGATG;RSEQ=TGATGGTGGTGATGGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:38.5:1:28:0:1:2.24:60:4:0.2222:0:0 0/1:10:2:1,1:2,6:8,2:0.2:2,2:24.5:1:24:1:1:2.65:60:4:0.2:0.1:0.5 +16 17380507 . T TATCATCATCATCCTC 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=39;MSI=2.600;MSILEN=1;SSF=0.00968;SOR=0;LSEQ=CAACAATCCCCATGGATAGG;RSEQ=ATCATCATCATCCTCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:4,4:6,3:9,8:0.4706:2,2:12.1:1:29.5:1:0.63719:1.91839:38.6:16:0.4706:0.4706:0.1 0/0:11:0:0,0:7,4:11,0:0:2,0:30.5:1:29.1:1:1:0:52.9:22:1:0:0.1 +16 17449069 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03352;SOR=0.23135;LSEQ=GAAGCCTCAGGTGCTGGCCA;RSEQ=AGCCACTGGTCTGCAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:5,11:3,7:10,16:0.6154:2,2:26.9:1:33:1:1:1.06:60:32:0.6154:0:1.1 0/1:19:5:2,3:7,7:14,5:0.2632:2,2:21.4:1:31.6:1:1:1.46843:60:10:0.2632:0:1.4 +16 18820808 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1951;SOR=0;LSEQ=TTGCATCACCACCGACTGTG;RSEQ=TGTGGCTTTGGATGCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:92,41:133,2:0.0148:2,2:31.5:1:29.5:1:0.52703:2.22908:60:4:0.0154:0:1 0/0:170:0:0,0:113,57:170,0:0:2,0:25.6:1:30.4:1:1:0:60:55.667:1:0:0.2 +16 18820818 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50659;SOR=Inf;LSEQ=ACCGACTGTGGTGTGGCTTT;RSEQ=GATGCCTGAGGCTGAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:100,48:148,0:0:2,0:24.3:1:32.1:1:1:0:59.8:296:1:0:0.1 0/1:191:2:1,1:120,69:189,2:0.0105:2,2:11.5:1:29:1:1:1.73376:60:4:0.0106:0:1 +16 20634775 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGGCCAGGGATTTGCCT;RSEQ=AGGTGTGCAGTGCGTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 20636814 . G A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05845;SOR=Inf;LSEQ=GCTGGGTGCTCCACCAAAGC;RSEQ=CTTTCAACCTCTGCAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:17,29:46,0:0:2,0:23.3:1:31.8:1:1:0:60:92:1:0:0.2 0/1:52:5:2,3:19,28:47,5:0.0962:2,2:20.8:1:28.6:1:1:1.01751:60:10:0.098:0:1 +16 23614688 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.506;SOR=0;LSEQ=AACAAGCAATCATTTTAAGT;RSEQ=TCATTCAGATATTCTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:2,0:75,6:81,2:0.0241:2,0:12.5:1:33:0:1:0:60:4:0.0247:0:1 0/0:63:0:0,0:62,1:63,0:0:1,0:25.9:1:31.7:1:1:0:60:126:1:0:0 +16 23614719 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19958;SOR=Inf;LSEQ=ATTCTCCTTTATATTTAAAA;RSEQ=TCCAAAAAATACTAAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:139,35:174,0:0:2,0:21:1:32.6:1:1:0:60:348:1:0:0.1 0/1:141:2:1,1:118,21:139,2:0.0142:2,2:5.5:1:27.5:1:0.28865:5.51315:60:4:0.0144:0:1 +16 23615041 . T A 60 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75949;SOR=1.38362;LSEQ=ATTACATATCCAAAAAACAA;RSEQ=TAAAAAAAAAAAAAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:0,5:13,114:127,5:0.0379:2,0:28:1:17.4:1:1:0:54.4:0.25:0.0102:0:2.2 0/1:116:6:1,5:12,96:108,6:0.0517:2,2:19.5:1:23.5:1:0.52479:1.59:54.8:2:0.0449:0:3.2 +16 23615042 . TA T 138 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.00152;SOR=3.03083;LSEQ=TTACATATCCAAAAAACAAT;RSEQ=AAAAAAAAAAAAAGGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:15:1,14:11,89:100,15:0.1181:2,1:29.7:1:30.9:1:1:1.72334:60:30:0.122:0:0.3 0/1:107:31:2,29:10,56:66,31:0.2897:2,2:27.6:1:28:1:0.32746:2.56766:59.3:9.333:0.28:0.0187:1 +16 23619235 . A C 182 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=53.31511;LSEQ=AGCATCACACCCACGCTGAG;RSEQ=GTCGTCTTAGGGTTAATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:715:1:1,0:372,342:714,1:0.0014:2,0:10:0:14:0:1:0:60:0:0:0:4 0/1:805:56:33,23:380,367:747,56:0.0696:2,2:25.8:1:31.4:1:0.26912:1.39:60:112:0.0705:0:1.1 +16 23619547 . C CT 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.51786;SOR=4.05684;LSEQ=TCTGGCTTCTTGTTCTTCTT;RSEQ=TTTTTTTTTTTAGAGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,9:9,1:0.1:0,0:22:0:32:0:1:0:60:2:0.1111:0:0 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:19:1:28.9:1:0.33333:0:60:4:0.3333:0.1667:0 +16 23624740 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTTGGGAGGCTGAGGCGGGT;RSEQ=GATCACCTGAGGTCAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:35:0:1:0:21:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:27.5:1:1:0:33.5:4:1:0:1 +16 23625138 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52995;SOR=0;LSEQ=CAGGTCCTACAGCCAGAAAA;RSEQ=TTACCAAGCAATCACTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:35,0:35,2:0.0541:1,2:39:1:29:0:0.05405:0:60:4:0.0541:0:1 0/0:21:0:0,0:21,0:21,0:0:1,0:20.8:1:30.3:1:1:0:60:42:1:0:0.4 +16 23625224 . T C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=3.1121;LSEQ=TATCCAATTTTGAAAAAAGA;RSEQ=GCCACGGGGAAGGTTTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:25:23,2:162,18:180,25:0.122:2,2:17.2:1:32.3:1:1:1.28:60:50:0.1238:0:1.1 0/1:162:49:41,8:100,13:113,49:0.3025:2,2:20.1:1:30.7:1:0.4479:1.49698:60:98:0.3043:0:1.6 +16 23625230 . G A 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTGAAAAAAGATGCCAC;RSEQ=GGGAAGGTTTGTTCATTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:212,33:245,0:0:2,0:21.7:1:30.3:1:1:0:60:121.5:1:0:0.2 0/1:192:30:23,7:136,26:162,30:0.1563:2,2:22.4:1:28.6:1:0.42778:1.58771:60:29:0.1526:0:2 +16 23625463 . A T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCTTCCAACAAACCAGT;RSEQ=TTCAGAAAATATTTTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:209:209:25,184:0,0:0,209:1:0,2:23.3:1:30.6:1:1:0:60:51.25:1:0:1.1 1/1:223:222:47,175:1,0:1,222:0.9955:0,2:22.1:1:29.1:1:0.21525:0:60:110:0.9955:0:1.1 +16 23632479 . C T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71197;LSEQ=AGGCAGAGGTTGCAGTGAGC;RSEQ=GAGATCATACCACTGTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:26.6:1:33.2:1:1:0:51.6:10:0.4167:0:1 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:23:1:32.3:1:1:0:48.7:6:0.3333:0:1 +16 23632614 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20024;SOR=Inf;LSEQ=TTATTTAATCTTCACAACAA;RSEQ=CCTGTAAAATTAGAGGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:166,26:192,0:0:2,0:21:1:32.5:1:1:0:59.9:95:1:0:0.1 0/1:156:2:1,1:131,23:154,2:0.0128:2,2:24:1:28.5:1:0.28486:5.59704:60:4:0.013:0:1 +16 23632906 . G GA 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.46688;SOR=2.12281;LSEQ=ATAAACTAACCTAATATCAG;RSEQ=AAAAAAAAATCTAACCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:0,3:2,71:73,3:0.0395:1,0:36:1:33:0:1:0:60:6:0.0417:0:0 0/1:62:5:0,5:1,55:56,5:0.0806:1,0:33.4:1:31.2:1:1:0:60:10:0.0847:0:0 +16 23634026 . A G 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCAGAGGTATTTCTAAC;RSEQ=TTTAAGGGACACACAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:41.5:1:31:0:1:0:42.5:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 23634496 . T A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24881;SOR=Inf;LSEQ=GGGTGATGTGAGGAGTAACC;RSEQ=TTTAATATTAAAGGACTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:54,195:249,0:0:2,0:20.7:1:30.6:1:1:0:59.5:30.125:1:0:0.4 0/1:259:3:1,2:64,190:254,3:0.0116:2,2:12:1:23.7:1:1:1.48:47:2:0.0082:0:1.7 +16 23635189 . AT A 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.30598;LSEQ=TCAGGGATGTCATTCTATTG;RSEQ=TTTTTTTTAAACAAATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:2,0:55,0:55,2:0.0351:1,0:27.5:1:33:0:1:0:60:4:0.0351:0:0 0/1:44:2:2,0:41,1:42,2:0.0455:1,0:33:1:30:1:1:0:60:4:0.0455:0:0 +16 23636063 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGTCTTGAACTCCTGAC;RSEQ=TCAGGTGATCCACCCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:31.5:1:1:0:43.5:4:1:0:1 +16 23637473 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50619;SOR=0;LSEQ=GTTCTGCCTTGCATGGTCAT;RSEQ=GCTCCCAATTTTGGTAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:150,19:169,2:0.0117:2,2:20.5:1:33.5:1:0.22085:7.72031:60:4:0.012:0:1 0/0:133:0:0,0:119,14:133,0:0:2,0:22.9:1:27.7:1:1:0:60:43.333:1:0:0.1 +16 23637824 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23964;SOR=Inf;LSEQ=TTCAATGAAACAGTAGGTAT;RSEQ=TAAAATTTAAGTCTTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:3,58:61,0:0:1,0:24.1:1:32.3:1:1:0:59.4:60:1:0:0 0/1:59:2:0,2:0,57:57,2:0.0339:1,0:32.5:1:32:0:1:0:60:4:0.0351:0:1 +16 23637843 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51163;SOR=0;LSEQ=TGTAAAATTTAAGTCTTATG;RSEQ=AGGTGAAAAGAAAGAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:0,2:2,47:49,2:0.0392:1,0:33:1:29.5:1:1:0:60:4:0.04:0:1 0/0:35:0:0,0:0,35:35,0:0:1,0:24.4:1:32:1:1:0:60:70:1:0:0.1 +16 23640442 . A T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22627;SOR=Inf;LSEQ=TAATAGTATTAAAGAACAAG;RSEQ=AGCTATATGACTGAATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:191,30:221,0:0:2,0:22.9:1:30.4:1:1:0:60:72.667:1:0:0.3 0/1:201:2:1,1:161,37:198,2:0.01:2,2:10:1:24:1:0.34467:4.30703:60:4:0.0101:0:1.5 +16 23640467 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29153;SOR=0.83878;LSEQ=ATATGACTGAATTCTTTTCA;RSEQ=TTCATTAAAGTTTTCATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:118:87,31:160,68:228,118:0.3401:2,2:21.4:1:30.6:1:0.5317:1.19:59.9:58:0.3382:0:1.1 0/1:348:105:74,31:166,76:242,105:0.3017:2,2:24.8:1:29.1:1:0.80056:1.09:60:34:0.2974:0:1.1 +16 23640630 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=AGTCACATCATTAGTCTACA;RSEQ=TTTATGTATAATGTCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:64,234:298,0:0:2,0:24.6:1:32.8:1:1:0:59.9:98.333:1:0:0.1 0/1:301:3:2,1:80,218:298,3:0.01:2,2:14.7:1:27:1:0.1813:5.41:60:6:0.0101:0:1 +16 23641461 . C G 203 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=87.76006;LSEQ=TAGAACAATAAGGTCCTCTT;RSEQ=TAAGTCCTCCATTTCTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:829:1:0,1:408,419:827,1:0.0012:2,0:30:0:13:0:1:0:60:0:0:0:2 0/1:938:90:47,43:408,439:847,90:0.0959:2,2:22.2:1:31.4:1:0.50631:1.18:60:180:0.0966:0:1.1 +16 23641859 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.17644;SOR=Inf;LSEQ=AGACAATCTGTTTCACTGAT;RSEQ=ACAAAGAGAATAGGATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:2,105:107,0:0:1,0:23.4:1:32.3:1:1:0:57.9:34.667:1:0:0.1 0/1:78:2:1,1:2,74:76,2:0.0256:1,2:23.5:1:28.5:1:0.07592:30.41:60:4:0.0263:0:2.5 +16 23646191 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.21334;LSEQ=ATCTTGATTTACCTTTCACT;RSEQ=GAATAAATAATTTTTCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:65:41,24:414,248:662,65:0.0892:2,2:26.1:1:31.9:1:1:1.02:60:130:0.0907:0:1.1 0/1:944:226:139,87:420,297:717,226:0.2394:2,2:26.2:1:30:1:0.48478:1.13:60:225:0.2432:0:1.1 +16 23647664 . G GA 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25133;SOR=Inf;LSEQ=TATTTTTAGGTTCTGAGGAG;RSEQ=AAAAAAATGTATATAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:61,197:258,0:0:2,0:23.4:1:31.7:1:1:0:60:50.6:0.9961:0:0 0/1:292:3:2,1:82,205:287,3:0.0103:2,2:12:1:26.3:1:0.20219:4.97:60:6:0.0103:0.0034:0.7 +16 23647706 . CA C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.501;SOR=0;LSEQ=ATTTTTCTTATAAAATAAAA;RSEQ=AAAAATACTCATTTTTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:11,98:109,2:0.018:2,2:14:1:30.5:1:0.20541:8.57:60:4:0.0182:0:0 0/0:94:0:0,0:11,83:94,0:0:2,0:20.2:1:30.5:1:1:0:60:188:1:0:0.1 +16 23647713 . T G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00051;SOR=Inf;LSEQ=TTATAAAATAAAACAAAAAA;RSEQ=ACTCATTTTTAACCTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:9,94:103,0:0:2,0:24.4:1:28.8:1:1:0:60:50.5:1:0:0 0/1:82:9:1,8:6,67:73,9:0.1098:2,2:22.7:1:31.1:1:0.57142:1.39:60:18:0.1098:0:1 +16 23647838 . A C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04549;SOR=Inf;LSEQ=TTTTTTAGGCTGTGAGTAGT;RSEQ=AGGTCACTGTTACCTTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:24,29:53,0:0:2,0:27.3:1:30.2:1:1:0:58.9:52:1:0:0.2 0/1:47:4:2,2:19,24:43,4:0.0851:2,2:12.8:1:30.8:1:1:1.26:60:8:0.087:0:1 +16 23649504 . G A 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36215;SOR=3.1638;LSEQ=AGTGGAAAGGTGGAGTCAGA;RSEQ=GGAAGGGATGCAGTGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:1,0:74,205:279,1:0.0036:2,0:1:0:28:0:0.26786:0:60:2:0.0036:0:1 0/1:268:3:2,1:77,188:265,3:0.0112:2,2:13.7:1:23.3:1:0.20849:4.85:60:2:0.0075:0:3 +16 23652268 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19268;SOR=Inf;LSEQ=ACGCCACCACGTGAGCACCA;RSEQ=GCTATTTCCACATTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:105,3:108,0:0:1,0:22.5:1:32.5:1:1:0:60:53:1:0:0 0/1:85:2:2,0:82,1:83,2:0.0235:1,0:22.5:1:31:1:1:0:60:4:0.0238:0:1 +16 23652330 . G T 52 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37318;SOR=0.24899;LSEQ=AGAGGAGGGGGTGGTCAGAT;RSEQ=ATACTGCTGCCCTCGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:4:1,3:268,72:340,4:0.0116:2,2:5:1:26.3:1:0.0338:11.05971:60:8:0.0119:0:1 0/0:343:1:0,1:270,72:342,1:0.0029:2,0:1:0:22:0:0.21283:0:60:2:0.003:0:1 +16 24788422 . AGCAGCCACAGCC A 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.0277;SOR=0.14918;LSEQ=GCAGCAGCAGCAGCCACAGC;RSEQ=GCAGCCGCAGCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:7,7:14,5:0.2632:2,2:35.4:1:31.2:1:1:1.46843:45.2:10:0.2632:0:0 0/1:41:2:2,0:14,25:39,2:0.0488:2,0:32.5:1:31:1:0.14634:0:43.5:4:0.05:0:0.5 +16 26319906 . A G 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GGTGCTTTATGCAACAGTGA;RSEQ=TTTGGTTGCCAGTTTAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:36:1:35.3:1:1:0:60:6:0.5:0:2 0/0:3:0:0,0:3,0:3,0:0:0,0:4:1:30.3:1:1:0:60:6:1:0:0.7 +16 26319948 . C A 63 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6169;SOR=0.34632;LSEQ=AGGTGTTGTTCTTCCATGAA;RSEQ=CCTTTCTGAGTCTTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:4,0:12,0:12,4:0.25:0,0:17.3:1:31.8:1:1:0:60:8:0.25:0:1.8 0/1:10:1:1,0:9,0:9,1:0.1:0,0:27:0:31:0:1:0:60:2:0.1:0:1 +16 26319949 . C A 46 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.32615;SOR=3.06658;LSEQ=GGTGTTGTTCTTCCATGAAC;RSEQ=CTTTCTGAGTCTTTTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:15,2:0.1176:1,0:6:1:29.5:1:1:0:60:4:0.1176:0:1.5 0/1:10:3:3,0:7,0:7,3:0.3:0,0:34.7:1:29.3:1:1:0:60:6:0.3:0:1 +16 26320124 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24836;SOR=Inf;LSEQ=CTCCACCGAGTTCCCTCGGG;RSEQ=CATCAGAGCAAACTGTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:122,104:226,0:0:2,0:26.2:1:31.5:1:1:0:60:74.333:1:0:0.4 0/1:228:3:2,1:116,109:225,3:0.0132:2,2:25.7:1:26.3:1:1:1.87:60:6:0.0135:0:1 +16 26320139 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25188;LSEQ=TCGGGGCATCAGAGCAAACT;RSEQ=TATTCCACAATCTAACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:91:45,46:79,80:159,91:0.3625:2,2:26:1:29.5:1:1:1.00941:59.8:182:0.364:0:1.1 0/1:256:32:18,14:110,114:224,32:0.125:2,2:25.3:1:28.1:1:0.57132:1.33:60:64:0.126:0:1.1 +16 26320217 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10729;SOR=0;LSEQ=AAAACAAAATGTTGGATGAA;RSEQ=CTTGTATATGCAGAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:2,1:41,91:132,3:0.0222:2,2:33:1:29.3:1:0.23795:4.38:60:6:0.0227:0:1 0/0:148:0:0,0:55,93:148,0:0:2,0:23.2:1:31.3:1:1:0:60:48.333:1:0:0.3 +16 26320274 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15652;SOR=Inf;LSEQ=AAGTGTGTTTGCACAATATC;RSEQ=ACCCCTTGCCTGAAACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:3,39:42,0:0:2,0:20.4:1:28.5:1:1:0:60:84:1:0:0.1 0/1:28:2:1,1:2,24:26,2:0.0714:2,2:17:1:29:1:0.20635:10.00:60:4:0.0741:0:1 +16 27356203 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCAGAGCCCACACGTGT;RSEQ=TCCCTGAGAACAACGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 27356359 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ATGGTGAGCAGGGCGGAGTG;RSEQ=GGCAGGGGTGGCTGGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:7:1:29:1:1:0:60:4:0.3333:0:1.5 0/0:4:0:0,0:2,1:3,0:0:2,0:25.3:1:33.3:1:1:0:60:6:1:0:0.3 +16 27356398 . C T 54 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=TGTTCCCACAGCTGCCTGGG;RSEQ=TGAGGGTGGGGTGGGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:3,0:3,4:0.5714:0,2:30.5:1:27.3:1:1:0:60:3:0.5:0:1.8 1/0:2:1:1,0:1,0:1,1:0.5:0,0:35:0:25:0:1:0:60:2:0.5:0:6 +16 27356584 . T G 185 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGTTTCCACCCCTGAACT;RSEQ=AAGTGCCCAGGAAGGCGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:56:43,13:70,40:110,56:0.3373:2,2:24.1:1:32:1:0.11282:1.88:60:27:0.3293:0:1.3 0/0:150:0:0,0:100,50:150,0:0:2,0:23.6:1:28.7:1:1:0:60:49:1:0:0.3 +16 27356585 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49953;SOR=0;LSEQ=CTGTTTCCACCCCTGAACTT;RSEQ=AGTGCCCAGGAAGGCGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:113,52:165,2:0.0119:2,2:16.5:1:34:0:0.53531:2.16202:60:4:0.012:0:2 0/0:153:0:0,0:102,50:152,0:0:2,0:23.9:1:27.8:1:1:0:60:29.4:0.9932:0:0.3 +16 27356590 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23655;SOR=Inf;LSEQ=TCCACCCCTGAACTTAAGTG;RSEQ=CCAGGAAGGCGTATTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:117,61:178,0:0:2,0:26.4:1:31.8:1:1:0:60:34.6:0.9943:0:0.6 0/1:170:2:1,1:109,59:168,2:0.0118:2,2:39.5:1:30:1:1:1.84045:60:4:0.0119:0:1.5 +16 27356606 . G T 48 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19009;SOR=0.21686;LSEQ=AGTGCCCAGGAAGGCGTATT;RSEQ=AGATGAGGTGTGCTTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:4:2,2:132,79:211,4:0.0186:2,2:7:1:24.3:1:0.63313:1.66666:60:3:0.0142:0:1 0/0:245:1:0,1:155,89:244,1:0.0041:2,0:1:0:24:0:0.36735:0:60:2:0.0041:0:2 +16 27356607 . A G 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12625;SOR=Inf;LSEQ=GTGCCCAGGAAGGCGTATTG;RSEQ=GATGAGGTGTGCTTGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:139,82:221,0:0:2,0:26.2:1:30.1:1:1:0:59.9:26.625:1:0:0.7 0/1:250:4:3,1:156,89:245,4:0.016:2,2:10.8:1:29.8:1:1:1.71:60:8:0.0165:0:3.8 +16 27356623 . C T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.67238;SOR=0.60167;LSEQ=ATTGAGATGAGGTGTGCTTG;RSEQ=TGGAAGGCATGCCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:1,2:155,111:266,3:0.0112:2,2:11.7:1:28.3:1:0.57415:2.78217:60:6:0.0114:0:2 0/0:297:2:1,1:174,121:295,2:0.0067:2,2:5:1:19:1:1:1.43619:60:1:0.0034:0:1.5 +16 27356635 . C T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10274;SOR=0;LSEQ=TGTGCTTGCTGGAAGGCATG;RSEQ=CTGCTGCTGATTGAAAACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:160,134:294,3:0.0101:2,2:17.7:1:22.3:1:1:1.67:60:2:0.0069:0:1 0/0:336:0:0,0:191,144:335,0:0:2,0:25.4:1:30.7:1:1:0:60:54.833:1:0:0.6 +16 27356667 . T G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38789;LSEQ=TGAAAACCGAACTGGGAACA;RSEQ=TCCTTCCATTCTGTGTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:321:226:107,119:40,55:95,226:0.704:2,2:25.6:1:32.3:1:0.46168:1.24:60:44.2:0.6994:0:1.2 0/1:367:176:92,84:101,90:191,176:0.4796:2,2:25.5:1:30.7:1:0.91705:1.02458:60:57.667:0.4779:0:1.4 +16 27356680 . G A 115 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.001;SOR=7.73725;LSEQ=GGGAACATTCCTTCCATTCT;RSEQ=TGTCCACTGGTCAGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:2:2,0:136,169:305,2:0.0065:2,0:21:1:27.5:1:0.20125:0:60:4:0.0066:0:2.5 0/1:372:18:10,8:176,178:354,18:0.0484:2,2:22.7:1:27.8:1:0.80988:1.26:60:36:0.0493:0:3.1 +16 27356689 . G C 109 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00133;SOR=13.24824;LSEQ=CCTTCCATTCTGTGTCCACT;RSEQ=GTCAGCTGCTGCGGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:1,0:129,170:299,1:0.0033:2,0:50:0:31:0:0.43333:0:60:2:0.0034:0:3 0/1:355:15:8,7:164,174:338,15:0.0423:2,2:26.8:1:28.1:1:0.79526:1.21:60:14:0.0403:0:3.2 +16 27356771 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50874;SOR=Inf;LSEQ=GAGTCCCTGCAGGAATCCCC;RSEQ=TTGAGCTTGCTGGGCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:10,72:82,0:0:2,0:26.4:1:32.7:1:1:0:60:40:1:0:0.1 0/1:111:2:1,1:25,84:109,2:0.018:2,2:10:1:29:1:0.41523:3.31:60:4:0.0185:0:1 +16 27358190 . G A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTCCTCTGTAAAGGTAG;RSEQ=GCTGTGGGCCACATCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 28883841 . C T 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36652;SOR=0.35477;LSEQ=GCCTCCTACCTCACCTCCCC;RSEQ=ATCCCGCCCTCAGCACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:2,3:2,3:5,5:0.5:2,2:17.6:1:28.4:1:1:1:60:10:0.5:0:1 0/1:8:2:1,1:4,2:6,2:0.25:2,2:32:1:27.5:1:1:1.8258:60:4:0.25:0:1 +16 30125840 . G C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAACTGGGGCCACCTGAG;RSEQ=TCCCGAGGCCCCGTGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:11:1:29:1:1:1:60:4:0.3333:0:1.5 +16 30128808 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11108;SOR=Inf;LSEQ=TCCTAGGTCTGGTGCCTCCT;RSEQ=AGGTGTGGGACTTAGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:35,26:61,0:0:2,0:24:1:33:1:1:0:60:122:1:0:0.2 0/1:31:2:1,1:18,11:29,2:0.0645:2,2:27:1:28.5:1:1:1.60957:60:4:0.0645:0:1 +16 30128929 . T C 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGTATCCCTGACTTGGACTC;RSEQ=CGAGAAATCTCACCTCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:0:0,0:380,91:471,0:0:2,0:24.8:1:31.5:1:1:0:59.9:93.2:1:0:0.1 0/1:438:25:21,4:313,100:413,25:0.0571:2,2:24.4:1:30.3:1:0.47014:1.68:60:24:0.055:0:1.2 +16 30129191 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13357;SOR=Inf;LSEQ=GGCCACCACCTCCAAGTTAG;RSEQ=TCCAACACCAGGCAGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:68,259:327,0:0:2,0:24.1:1:31:1:1:0:60:26.25:1:0:0.1 0/1:190:2:1,1:23,165:188,2:0.0105:2,2:9:1:29.5:1:0.23726:7.04:60:4:0.0108:0:1 +16 30129206 . G T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55444;SOR=0;LSEQ=GTTAGATCCAACACCAGGCA;RSEQ=AAGGCAGAGGCCTGGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:0,3:76,208:284,3:0.0105:2,0:26.7:1:23.3:1:0.56814:0:60:2:0.0072:0:1.3 0/0:151:0:0,0:33,118:151,0:0:2,0:24.2:1:31.2:1:1:0:59.9:302:1:0:0.1 +16 30129542 . CA GT 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=GCCTCTGCAGCCTAAGCAGT;RSEQ=CGCCCCCTTGTCTTTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:0:0,0:220,369:589,0:0:2,0:24.1:1:32.2:1:1:0:60:72.625:1:0:0.1 0/1:595:15:6,9:213,364:577,15:0.0252:2,2:28.5:1:31:1:0.79256:1.14:60:30:0.0255:0.0017:1.1 +16 30129559 . G A 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45236;SOR=0.41744;LSEQ=AGTCACGCCCCCTTGTCTTT;RSEQ=CCTCCACTGTTCCCTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:5:3,2:195,293:488,5:0.0101:2,2:15.6:1:28:1:0.39522:2.25:60:10:0.0104:0:1 0/0:471:2:1,1:193,276:469,2:0.0042:2,2:27.5:1:27:1:1:1.43:60:4:0.0043:0:1 +16 30129936 . C T 197 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00817;LSEQ=AGGAAAACAGGCTCTGAAGG;RSEQ=GAGGCTGCACACCTCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:91:7,84:14,150:164,91:0.3569:2,2:22.5:1:30.4:1:1:1.11953:60:90:0.3571:0:1.1 0/0:223:1:0,1:30,192:222,1:0.0045:2,0:21:0:31:0:1:0:60:2:0.0045:0:1 +16 30134265 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27355;SOR=0;LSEQ=TGCCTCCTCGGGACGCTCCG;RSEQ=GTCTCCACGTCCCGGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:282,13:295,3:0.0101:1,2:29.7:1:28.7:1:0.13485:10.60833:60:6:0.0104:0:1 0/0:206:0:0,0:195,10:205,0:0:1,0:25.4:1:31.3:1:1:0:60:40:1:0:0.3 +16 30134293 . GCCT G 99 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.01219;SOR=6.03997;LSEQ=CGTCCCGGAAAGCGCTCGGC;RSEQ=CCTCCTCCTCTCCCGCGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:556:2:1,1:431,122:553,2:0.0036:2,2:32:1:30.5:1:0.39444:3.52228:60:4:0.0037:0:0 0/1:421:9:5,4:296,115:411,9:0.0214:2,2:18.9:1:31.4:1:0.27945:2.05521:59.4:18:0.0221:0.0071:0.1 +16 30134312 . C G 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CGCCTCCTCCTCCTCTCCCG;RSEQ=GAAGCCCCCTCCCCTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:738:0:0,0:495,240:735,0:0:2,0:24.4:1:30.8:1:1:0:60:44.938:0.9958:0:0.5 0/1:613:63:38,25:354,194:548,63:0.1028:2,2:22.5:1:30:1:0.492:1.20011:60:62:0.103:0:1.4 +16 30134513 . AGCC A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.28236;SOR=1.7623;LSEQ=TCCCCGCCCCCGCCCCCCTG;RSEQ=GCCGCCGCCGCCATCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:8:3,5:163,509:672,8:0.0117:2,2:26.8:1:29.9:1:0.41148:1.87:60:16:0.0133:0.0029:0.6 0/1:686:14:5,9:194,475:669,14:0.0204:2,2:24.9:1:31.6:1:0.56262:1.36:58.9:28:0.0235:0:0.3 +16 30134541 . C A 44 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05159;SOR=Inf;LSEQ=CCGCCGCCATCTCCACTCCT;RSEQ=CCCTCCCACCGCCCTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:52,345:397,0:0:2,0:23.3:1:30.7:1:1:0:59.7:15.542:1:0:0.7 0/1:363:4:3,1:52,307:359,4:0.011:2,2:6.3:1:22:1:0.01184:17.48:60:3:0.0086:0:1 +16 30134583 . C T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.22848;SOR=Inf;LSEQ=CACGGCGGCCCCGCCCGAGG;RSEQ=CCCGCCCCTTCCCGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:1,88:89,0:0:1,0:18:1:32.1:1:1:0:60:43.5:1:0:0.3 0/1:82:2:0,2:2,78:80,2:0.0244:1,0:6:1:28.5:1:1:0:60:4:0.0256:0:1 +16 30134811 . C T 31 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCACCCTCCCCTCGATGG;RSEQ=GAAGCGGCCAGGGCGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:31.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 30134816 . C G 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCCCCTCGATGGCGAAG;RSEQ=GGCCAGGGCGTGACCTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:32:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 31009588 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATTGTGGCAAAATCTAC;RSEQ=TCGGTGAGATCAGAAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 31010999 . A G 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1888;LSEQ=AGCCAAGGATACCGATTCAG;RSEQ=GGCATTTGCTGGGCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:18:1:32:1:1:0:60:4:0.1429:0:1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:2:0:30:0:1:0:60:2:0.1667:0:1 +16 31011122 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10939;SOR=Inf;LSEQ=TTTTCTGGTGAACCTTCATG;RSEQ=TGGTGGAACCAGCAGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:85,47:132,0:0:2,0:25.8:1:32.2:1:1:0:60:65:1:0:0.3 0/1:122:3:1,2:84,35:119,3:0.0246:2,2:13.7:1:26.3:1:0.21806:4.73022:60:6:0.0246:0:1.7 +16 31011137 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24584;SOR=Inf;LSEQ=TCATGCTGGTGGAACCAGCA;RSEQ=GGCTCAGATGCAATTTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:92,59:151,0:0:2,0:25.5:1:31.9:1:1:0:60:29.2:1:0:0.4 0/1:149:2:1,1:91,56:147,2:0.0134:2,2:31.5:1:30:1:1:1.61945:60:4:0.0136:0:1 +16 31011183 . A G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=2e-05;SOR=2.37401;LSEQ=CCTTTCCCTCATTTCCTATC;RSEQ=TATATCTTTCTCCAAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:70:37,33:69,67:136,70:0.3398:2,2:27.3:1:30.5:1:0.88308:1.09:59.6:22.333:0.3333:0:1.1 1/0:218:120:69,51:47,51:98,120:0.5505:2,2:25.5:1:29.9:1:0.1743:1.47:60:59:0.5463:0:1.1 +16 31404827 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18659;SOR=0;LSEQ=CACTCTTATGAGGAGCTGAG;RSEQ=CAGGGGAGTGCTTCATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:13,3:16,2:0.1111:2,2:20:1:29:1:0.40523:3.89444:60:4:0.1111:0:1 0/0:23:0:0,0:16,7:23,0:0:2,0:13.5:1:30.3:1:1:0:60:46:1:0:0 +16 31406638 . CA C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACAGAGTGAGACTCCGT;RSEQ=AAAAAAAAAAGTCATGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:30:1:1:0:60:4:1:0:1 +16 31691894 . A G 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTTTGGAAACCACTCAACT;RSEQ=TACGCTGTGAGTAGTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:204,215:419,0:0:2,0:25.7:1:29.5:1:1:0:59.8:58.857:1:0:0.9 0/1:476:40:21,19:207,229:436,40:0.084:2,2:27.4:1:31.2:1:0.62072:1.22:59.6:80:0.086:0:1.1 +16 31691912 . C T 251 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTATACGCTGTGAGTAGTTT;RSEQ=AAAGGGCATTCGCATTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:383:383:170,213:0,0:0,383:1:0,2:25.3:1:29.3:1:1:0:59.9:53.714:1:0:1.1 0/1:428:209:88,121:99,120:219,209:0.4883:2,2:25.4:1:28.3:1:0.55895:1.13404:60:51.25:0.4869:0:1.2 +16 31692468 . T C 34 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TCATGATACAGAATTGTCTT;RSEQ=AAAAGATGACTTGGCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28.5:1:34:0:1:0:44:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 +16 32368345 . C T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15616;SOR=0.15947;LSEQ=GGCGCTTTGTGGTCTCGGCA;RSEQ=CCTCGGCTTCCCCTTCACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:11.5:1:28.5:1:1:1.40151:60:4:0.1111:0:1 0/1:56:1:0,1:32,23:55,1:0.0179:2,0:1:0:25:0:0.42857:0:60:2:0.0179:0:1 +16 32369541 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08067;SOR=0;LSEQ=CATCAGGAATACGAATACCT;RSEQ=GGCTAGAACCTGAGATAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:12.5:1:30.5:1:1:1.36624:60:4:0.1429:0:1.5 0/0:34:0:0,0:16,17:33,0:0:2,0:9.3:1:30.7:1:1:0:55.2:66:0.9706:0:0.3 +16 33365525 . G A 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.36985;SOR=0.36377;LSEQ=AGCAGCACACACAGCCGGGC;RSEQ=CTTTGTGGTCTCGGCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:2,5:2,2:4,7:0.6364:2,2:29.7:1:31.9:1:0.57576:2.28835:21.7:14:0.6364:0:1.3 0/1:8:3:1,2:4,1:5,3:0.375:2,2:28.7:1:29:1:0.46429:5.78427:21.3:6:0.375:0:1 +16 33365537 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=AGCCGGGCGCTTTGTGGTCT;RSEQ=GGCACCCTCGGCTTCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:36:0:32:1:1:1.87:20:4:0.1818:0:1 0/0:8:0:0,0:5,3:8,0:0:2,0:18.6:1:29:1:1:0:21.9:16:1:0:0.9 +16 33365544 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16374;SOR=Inf;LSEQ=CGCTTTGTGGTCTCGGCACC;RSEQ=TCGGCTTCCCCTTCACGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:11,0:0:2,0:17.2:1:33.9:1:1:0:21.3:22:1:0:1 0/1:8:2:1,1:3,2:5,2:0.25:2,2:26.5:1:29:1:1:1.41418:24:4:0.25:0:1.5 +16 33366647 . CAG TA 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00206;SOR=Inf;LSEQ=AATGTTAAGCAATTATTACT;RSEQ=GAAAATCTTGAATTTCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:191,23:214,0:0:2,0:22.8:1:32.1:1:1:0:43.6:70.333:1:0:0.1 0/1:241:10:9,1:194,35:229,10:0.0415:2,2:23.5:1:29.6:1:1:1.62:41.9:20:0.042:0.0041:1 +16 33371341 . CG C 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=GCAGGAGGATCACTTGAACC;RSEQ=GGGGGCAGAGGTTGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:28.2:1:32.8:1:1:0:41.4:10:0.4545:0:0 0/0:2:0:0,0:0,1:1,0:0:0,0:14:0:32:0:1:0:20:2:0.5:0:1 +16 33371424 . G GA 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.07016;SOR=0.28427;LSEQ=GAGAACCTGTCTCAAAAAAG;RSEQ=AAAAAAAAAACAGGTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:9:9,0:41,2:43,9:0.1731:1,0:17.7:1:31.7:1:1:0:52.7:18:0.1731:0.0769:0.4 0/1:54:3:3,0:43,2:45,3:0.0556:1,0:32:1:30:0:1:0:43:6:0.0652:0:1 +16 33371430 . AA T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.12296;SOR=Inf;LSEQ=CTGTCTCAAAAAAGGAAAAA;RSEQ=AAACAGGTTGTAACCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:52,2:54,0:0:1,0:15.6:1:31:1:1:0:58:108:0.9818:0:0.1 0/1:64:4:4,0:54,2:56,4:0.0625:1,0:21.8:1:31:1:1:0:60:8:0.0656:0.0313:0.5 +16 33371451 . T C 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAACAGGTTGTAACCCATC;RSEQ=GCCAAGATACTCCCCCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:90,9:99,0:0:2,0:22.5:1:32.3:1:1:0:58.7:48.5:1:0:0.3 0/1:134:29:26,3:97,8:105,29:0.2164:2,2:17.7:1:30.6:1:0.70319:1.39526:52.6:58:0.2214:0:2.8 +16 33371484 . T G 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCAATACATTAAAACAAT;RSEQ=AAACAGATTCAACAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:129,15:144,0:0:2,0:28.8:1:30.8:1:1:0:53.5:71:1:0:0.2 0/1:191:35:29,6:140,14:154,35:0.1832:2,2:34.8:1:29.1:1:0.21835:2.05959:49.5:6:0.163:0:2.7 +16 33371537 . T G 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26077;SOR=1.27319;LSEQ=CCTCTGTCTCATGTCTCTCA;RSEQ=GCAGCAGGGCTTCCCATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:47:38,9:107,44:151,47:0.2374:2,2:9.8:1:31.2:1:0.19284:1.73:34.9:94:0.2386:0:1 0/1:317:90:61,29:152,75:227,90:0.2839:2,2:8.6:1:29.4:1:1:1.04:36.7:44:0.2821:0:1.6 +16 33371626 . A T 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02011;SOR=Inf;LSEQ=TTAAGGCTTCTTCTGTCGTA;RSEQ=AACATGCCTTTGGATCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:250,207:457,0:0:2,0:30.9:1:30.4:1:1:0:36.8:90.4:1:0:0.1 0/1:870:11:5,6:449,409:858,11:0.0126:2,2:34.1:1:28.7:1:0.76521:1.31694:28.3:22:0.0128:0:1.2 +16 33371658 . C T 208 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATCCACTACCAACAACTT;RSEQ=TTGACAAGGTCCAGAGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:116,128:244,0:0:2,0:16.5:1:32.4:1:1:0:34.8:121:1:0:0.1 0/1:435:133:70,63:164,136:300,133:0.3057:2,2:17.7:1:29.6:1:0.754:1.08509:35.6:266:0.3086:0:1.1 +16 33372666 . C T 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00362;SOR=Inf;LSEQ=GAATACCACAAATTCTTAAC;RSEQ=CTTTCATATTCATACCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:0:0,0:359,188:547,0:0:2,0:26.7:1:31:1:1:0:49.4:90.167:1:0:0 0/1:766:11:9,2:467,288:755,11:0.0144:2,2:15.3:1:26.6:1:0.22208:2.77:43.7:10:0.0132:0:2.5 +16 33373312 . G T 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCAGTCCAACACAAACAA;RSEQ=AACTTCAGGAGCCAAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:587:22:11,11:345,220:565,22:0.0375:2,2:26.3:1:29.2:1:0.37409:1.56689:50.3:44:0.0382:0:1.1 0/0:1114:0:0,0:628,486:1114,0:0:2,0:26.7:1:30.8:1:1:0:50.3:60.889:1:0:0.2 +16 33373357 . C T 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTCCACATAAGGTTCTCA;RSEQ=GAGAGAGGTCTCTCCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:196,130:326,0:0:2,0:24.6:1:30.9:1:1:0:50:325:1:0:0.1 0/1:564:92:53,39:258,214:472,92:0.1631:2,2:15.9:1:29.6:1:0.6475:1.13:39.8:184:0.1646:0:1.2 +16 33375471 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTAAGGCCTTCATTGACC;RSEQ=AAAGGATAGTGGGTCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:29.5:1:1:0:55.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 33947334 . T A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTTCTCCTTATTATCAC;RSEQ=CTGCTCTCCTACTACATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:27:1:1:0:60:4:1:0:2 +16 33947339 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCCTTATTATCACTCTGC;RSEQ=CTCCTACTACATTCCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:28.5:1:1:0:60:4:1:0:2 +16 33948637 . TGTG T 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.16844;SOR=Inf;LSEQ=CCCAACCCCCGACTGGCGAC;RSEQ=GTGGTGGTGGTGGTGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:28,0:0:2,0:14.4:1:32.1:1:1:0:46:56:1:0:0.5 0/1:20:2:2,0:14,4:18,2:0.1:2,0:22.5:1:33:0:1:0:60:4:0.1:0:0 +16 33948656 . GT G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.49586;SOR=0;LSEQ=CTGTGGTGGTGGTGGTGGTG;RSEQ=TTTGTGTTCCAGCTTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:23,21:44,2:0.0435:2,2:30:1:30.5:1:1:1.09307:58.5:4:0.0444:0:0 0/0:41:0:0,0:25,16:41,0:0:2,0:17.6:1:27.8:1:1:0:51.6:19.5:1:0:1.9 +16 33948678 . CTGT C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.24476;SOR=Inf;LSEQ=TTTGTGTTCCAGCTTCTGTT;RSEQ=TGTTGTTGTTGTTGGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:35,34:69,0:0:2,0:25.7:1:30.9:1:1:0:50.5:33.5:1:0:1.3 0/1:71:3:2,1:37,31:68,3:0.0423:2,2:27.3:1:30.7:1:1:1.66:55:6:0.0435:0:0 +16 33948693 . TTGG T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.03872;SOR=0.23618;LSEQ=CTGTTCTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:10:6,4:31,33:64,10:0.1351:2,2:28.2:1:30.7:1:0.73552:1.59:28.2:20:0.1389:0:0.7 0/1:85:3:2,1:42,40:82,3:0.0353:2,2:30.3:1:29.3:1:1:1.89:47:6:0.0361:0.0118:1 +16 33948696 . G C 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTGTTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:21:9,12:21,21:42,21:0.2877:2,2:35.2:1:33.1:1:0.78947:1.32725:44.4:20:0.3279:0:4 0/0:85:0:0,0:24,28:52,0:0:2,0:25.7:1:31:1:1:0:57.5:104:1:0:0.2 +16 33948708 . C T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.8654;SOR=1.11289;LSEQ=TGTTGTTGGTGCTGCTGCTG;RSEQ=TGTTGCTGCTGCTGCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:22:11,11:23,26:49,22:0.3099:2,2:34.5:1:31.1:1:1:1.13:44:44:0.3235:0:4.1 0/1:90:30:18,12:28,32:60,30:0.3333:2,2:34.2:1:29.8:1:0.26868:1.70:41:29:0.3258:0:4.1 +16 33948711 . T C 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTTGGTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:21:11,10:23,27:50,21:0.2958:2,2:31.5:1:33.2:1:0.79516:1.29:43.3:20:0.2899:0:4.1 0/0:88:0:0,0:26,32:58,0:0:2,0:29.4:1:29.7:1:1:0:53.8:116:1:0:0.2 +16 33948720 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50619;SOR=Inf;LSEQ=TGCTGCTGCTGTTGCTGCTG;RSEQ=TGCTGGTGCTGTCGTCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:30,36:66,0:0:2,0:25.4:1:33.1:1:1:0:50:65:1:0:1.5 0/1:87:2:1,1:42,43:85,2:0.023:2,2:13:1:32:0:1:1.02:30.5:4:0.0233:0:4.5 +16 33948733 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.52085;SOR=Inf;LSEQ=GCTGCTGCTGCTGGTGCTGT;RSEQ=GTCGTTGTTTTGGTATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:23,28:51,0:0:2,0:22.7:1:30.9:1:1:0:52:50:1:0:1.7 0/1:80:2:1,1:37,41:78,2:0.025:2,2:20.5:1:31.5:1:1:1.11:38:4:0.025:0:2.5 +16 33948736 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51802;SOR=Inf;LSEQ=GCTGCTGCTGGTGCTGTCGT;RSEQ=GTTGTTTTGGTATTTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:21,26:47,0:0:2,0:21.9:1:31.3:1:1:0:51.4:46:1:0:1.8 0/1:72:2:1,1:32,38:70,2:0.0278:2,2:23.5:1:31.5:1:1:1.18:38:4:0.0282:0:2.5 +16 33948737 . G A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.83951;SOR=0.85756;LSEQ=CTGCTGCTGGTGCTGTCGTC;RSEQ=TTGTTTTGGTATTTTACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:8,8:12,16:28,16:0.3636:2,2:16.4:1:30.7:1:0.75677:1.32:44.6:15:0.3571:0:4.3 0/1:70:23:14,9:18,29:47,23:0.3286:2,2:11.7:1:28.5:1:0.12451:2.47:40.8:22:0.3188:0:4 +16 33948761 . A G 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.62735;SOR=0.58692;LSEQ=TTTTGGTATTTTACAGACTC;RSEQ=GGGGGTGTATGTGCTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:18,2:0.1:2,2:7.5:1:29.5:1:1:1.54:44.5:4:0.1:0:6.5 0/1:33:2:2,0:10,21:31,2:0.0606:2,0:6:0:31:0:0.125:0:47.5:4:0.0645:0:6.5 +16 33948854 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTTACCCACGTGGCGAAC;RSEQ=TTGTCTCTGACGGGCGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:36.5:1:32.5:1:1:0:60:4:1:0:0 0/1:5:2:1,1:0,3:3,2:0.4:0,2:17:0:31.5:1:0.4:0:26:4:0.4:0:3.5 +16 33948862 . T C 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CACGTGGCGAACGTTGTCTC;RSEQ=GACGGGCGATTTATTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:32:1:31:1:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:25:0:30.5:1:1:0:26:4:0.6667:0:3.5 +16 33948865 . C CG 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GTGGCGAACGTTGTCTCTGA;RSEQ=GGGCGATTTATTCATTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:29:1:31.5:1:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29:0:32:1:1:0:26:4:0.6667:0:3.5 +16 33948881 . T C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGACGGGCGATTTATTCAT;RSEQ=CCTCGTCCCCCTCTTACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:27:0:32:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:28.5:1:31.5:1:1:0:26:4:0.6667:0:3.5 +16 33949210 . A G 27 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTTGTGTTGCTCAGTTGCTC;RSEQ=GGCTGGTCTCAAACTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:33.5:1:27.5:1:1:0:22.5:4:1:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:44:0:33:0:1:0:60:2:1:0:0 +16 33957634 . AC GT 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTAATTATTTCCTGAGC;RSEQ=GCCCTTCCTCCTCCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:31:1:1:0:29.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 33958006 . C T 29 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=CTCTGCCGGTCTCTCTCTCT;RSEQ=TCTCTCTCTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:33:1:31.5:1:1:0:42.5:4:1:0:1.5 1/0:4:2:1,1:1,1:2,2:0.5:2,2:13:0:29.5:1:1:1:25:4:0.5:0:2.5 +16 33958061 . TG CA 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGTCTCTCTCTGTCCATCTC;RSEQ=TCTTTCTCTGTGTGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:23.5:1:31.5:1:1:0:45.5:4:1:0:1.5 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:10:1:30.8:1:1:0:25:4:0.6667:0.3333:2 +16 33958170 . GTGTCTGTT CTG 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GTAGGTCTCTCTCTCCCTGT;RSEQ=TTTTTTCTCTCTTTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:14:1:31.6:1:1:0:26.5:4:0.6667:0.3333:1.5 +16 33958191 . T C 51 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTGTTTTTTTTCTCTCT;RSEQ=TCTCTTTGCCTGTCTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:20:0:32:0:1:0:27:2:1:0:3 1/1:3:3:3,0:0,0:0,3:1:0,0:16.7:1:32.3:1:1:0:30.7:6:1:0:2 +16 33958242 . T C 60 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=TCTCTCTGTCTGTCTCTCTC;RSEQ=GCCTGTCTCTCTCTGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:1,1:0.5:0,0:28:0:29:0:1:0:20:2:0.5:0:4 1/0:6:4:3,1:2,0:2,4:0.6667:0,2:32.3:1:30.3:1:1:0:36:8:0.6667:0:2.8 +16 33958255 . C G 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.04762;SOR=0;LSEQ=CTCTCTCTGCCTGTCTCTCT;RSEQ=TGTGTCTGTCTTCTGTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:32:1:1:0:23.5:4:1:0:3.5 0/0:5:0:0,0:4,1:5,0:0:2,0:20:1:30.8:1:1:0:34.8:10:1:0:2.2 +16 33958270 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TCTCTCTGTGTCTGTCTTCT;RSEQ=TCTTACTGTCTTTCTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:23.5:1:26:1:1:0:23.5:1:1:0:3.5 1/0:4:2:1,1:2,0:2,2:0.5:0,2:9.5:1:27.5:1:1:0:41:4:0.5:0:2.5 +16 33958346 . G C 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTCTCTCTGTCTCTGTTTCT;RSEQ=TCTGTCTATCTCTGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:29.5:1:1:0:60:4:1:0:1 +16 33958581 . GTCTC G 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCTGTGTCTTTATCTGTCT;RSEQ=TCTCTCTCTTTCTGTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,2:4,3:0.6:2,2:14:1:34.7:1:1:1.81:39.3:6:0.6:0.4:1.7 0/0:1:0:0,0:1,0:1,0:0:0,0:10:0:31:0:1:0:60:2:1:0:0 +16 33958659 . GTC G 34 v3;pSTD;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=16.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTGTCTCTGTCTTT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:33:0:34:0:1:1.73:60:4:0.4:0:0.5 0/0:2:0:0,0:1,1:2,0:0:2,0:18:1:30.5:1:1:0:60:4:1:0:0.5 +16 33959025 . G C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAACTGTGACCGAGCCCT;RSEQ=TCCGTTCTGTCTCAAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:31:1:32.5:1:1:1:24:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 33959052 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTCAAATATGTATCTG;RSEQ=AAACACGTCTCTCCATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:36.5:1:29:1:1:1:30.5:4:0.5:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 34422819 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23279;SOR=Inf;LSEQ=AAGGAGTTCCATTGACAGCA;RSEQ=CACATCAGGGAATCAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:20,17:37,0:0:2,0:18.3:1:28.9:1:1:0:59.7:17.5:1:0:0.3 0/1:35:2:1,1:14,19:33,2:0.0571:2,2:31.5:1:29.5:1:1:1.35:60:4:0.0571:0:1 +16 34467290 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49619;SOR=Inf;LSEQ=ATGTGATGCTCTGCTTAGAA;RSEQ=CCTTGTGGTTCTTCAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:47,0:0:2,0:27:1:31.9:1:1:0:58.3:94:1:0:0.1 0/1:52:2:1,1:30,20:50,2:0.0385:2,2:23.5:1:29.5:1:1:1.48801:38:4:0.0385:0:2.5 +16 34467307 . C T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.5826;LSEQ=GAACCCTTGTGGTTCTTCAG;RSEQ=CAGGAGATGGAGAGAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:1:0,1:28,26:54,1:0.0182:2,0:48:0:30:0:0.49091:0:52:2:0.0185:0:1 0/1:70:2:1,1:40,28:68,2:0.0286:2,2:30:0:31:1:1:1.42114:38:4:0.029:0:2.5 +16 34467540 . A T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCAGTTTTTCCTCCTGT;RSEQ=TAGGGAGAGTGTTGGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 34469185 . T TG 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGGGACCCCAAGAGGCC;RSEQ=TGCCTTAATCTCCCCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:40:1:31.5:1:1:0:60:4:1:0:0.5 +16 34765942 . A G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCACAGCTCCAGGTAGAA;RSEQ=GGCAGGTGAGCCAAAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:0,9:1:0,2:29.7:1:31.3:1:1:0:58.2:18:1:0:1.3 1/1:4:4:3,1:0,0:0,4:1:0,2:22.5:1:27.3:1:1:0:57.3:3:1:0:1 +16 46389303 . A T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGATGTTTCCATTCGAGTTC;RSEQ=TTCTATTATTCCATTAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:17:0:33:0:1:0:28:2:1:0:2 0/1:5:2:1,1:1,2:3,2:0.4:2,2:10.5:1:31.5:1:1:1.73:42:4:0.4:0:2 +16 46389974 . C T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTTGATTCCATT;RSEQ=GATGATGATTACATTCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:40:1:32:0:1:0:35:4:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:41:1:31:1:1:2.44949:36:4:0.3333:0:2 +16 46389987 . A C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCGATGATGATTAC;RSEQ=TTCGAGTCCATACGATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:44.5:1:31:1:1:0:35:4:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:44.5:1:31:1:1:2.44949:36:4:0.3333:0:2 +16 46393218 . A T 48 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGATAATGATTACATCCG;RSEQ=GTCCATTCAGTGATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:29.7:1:30.7:1:1:0:21.3:6:1:0:1.3 +16 46395394 . A T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TTCAATTCTATGATGATTAC;RSEQ=TTGGATTCCATTCGTTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:1,4:0.8:0,2:15.5:1:33:1:1:0:60:8:0.8:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:11.5:1:31.5:1:1:0:60:4:1:0:0 +16 46403589 . TTCCATTCGAGGATGATTCCATTCGATTCCATTC T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CATTCGGTGATTTCATTAGA;RSEQ=GATGATTCCATTCAATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:29.5:1:1:0:20.5:4:1:1:1 +16 46403636 . A G 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATTCGATGATTCCATTC;RSEQ=ATTCCATTCGATGATGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:9.3:1:30:1:1:0:23.7:6:1:0:1.3 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:14:0:31:1:1:1.41418:20.5:4:0.2857:0:1 +16 46403685 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCATATGATCATTCCATTT;RSEQ=ATTTCATTCGATGATGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,3:7,0:0:2,0:29.4:1:32:1:1:0:30.6:14:1:0:1.6 0/1:20:2:1,1:12,6:18,2:0.1:2,2:15:0:30.5:1:1:1.92731:56:4:0.1:0:1.5 +16 46403709 . T G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08867;SOR=0;LSEQ=TCATTCGATGATGATTCCAT;RSEQ=CGATTCCATTCGACGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:32.5:1:31:1:1:1.29:25:4:0.2222:0:1 0/0:20:0:0,0:13,7:20,0:0:2,0:27.7:1:28.8:1:1:0:33.9:40:1:0:1.1 +16 46403716 . C G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12964;SOR=0.24578;LSEQ=ATGATGATTCCATTCGATTC;RSEQ=ATTCGACGATTCCATTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:3,4:1,1:2,7:0.7778:2,2:30.7:1:30.6:1:1:1.29098:35.7:14:0.7778:0:2.3 0/1:20:9:4,5:8,3:11,9:0.45:2,2:22.7:1:28.8:1:0.36185:3.12593:38:18:0.45:0:2 +16 46403720 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCGATTCCATT;RSEQ=GACGATTCCATTCTATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:29.1:1:30.4:1:1:0:33.3:18:1:0:2 0/1:20:2:1,1:10,8:18,2:0.1:2,2:33.5:1:28.5:1:1:1.23603:45:4:0.1:0:3 +16 46403769 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCGAGTCCATT;RSEQ=GATGATTCCATTCGAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:13.3:1:29.3:1:1:0:35:8:1:0:3 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:36.5:1:29.5:1:1:1.22474:25:4:0.1818:0:4.5 +16 46403773 . G C 33 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TCCATTCGAGTCCATTCGAT;RSEQ=ATTCCATTCGAGTCCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21:1:34:0:1:0:43:4:1:0:3.5 0/1:8:2:0,2:3,3:6,2:0.25:2,0:25:1:33:0:0.46429:0:37.5:4:0.25:0:3 +16 46403785 . G T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTCGATGATTCCATTCGA;RSEQ=TCCATTTAATGATTCCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:18:0:35:0:1:0:38:2:1:0:2 0/1:5:2:1,1:0,3:3,2:0.4:0,2:20.5:1:29:1:0.4:0:25:4:0.4:0:4.5 +16 46403791 . T G 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGATTCCATTCGAGTCCAT;RSEQ=TAATGATTCCATTGGGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:32:0:1:0:38:2:1:0:2 0/1:5:2:1,1:0,3:3,2:0.4:0,2:14.5:1:30:1:0.4:0:25:4:0.4:0:4.5 +16 46403793 . A G 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTCCATTCGAGTCCATTT;RSEQ=ATGATTCCATTGGGTTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:10:0:33:0:1:0:38:2:1:0:2 1/0:4:2:1,1:0,2:2,2:0.5:0,2:12.5:1:29.5:1:1:0:25:4:0.5:0:4.5 +16 46432638 . AA GC 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCATCATAGAAAGGAATC;RSEQ=AGGGAATCATCGAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:32.3:1:1:0:31.5:4:1:0:1 +16 46660689 . C T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.51595;LSEQ=GGATGGCCCCATTGGCACTG;RSEQ=GGTAGTAGCTCTGGGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:1:0,1:38,41:79,1:0.0125:2,0:1:0:25:0:1:0:44:2:0.0125:0:1 0/1:106:2:1,1:54,50:104,2:0.0189:2,2:17.5:1:31:0:1:1.07919:28:4:0.0196:0:1 +16 49346687 . TCGGTGC T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=2.000;MSILEN=1;SSF=0.08038;SOR=3.82508;LSEQ=TTGCAAACGCAGCGTGGCAC;RSEQ=CGGTGCCGGCATAAAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:3,3:9,6:15,6:0.2857:2,2:28.7:1:30.3:1:1:1.47083:60:12:0.2857:0:0.2 1/0:13:8:6,2:3,2:5,8:0.6154:2,2:32.5:1:31.6:1:1:1.89:60:16:0.6154:0:0 +16 52085593 . A G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.04744;LSEQ=CTCCTTTTTCTATGGGGAGA;RSEQ=AATTAATATCCAGGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:271:212:98,114:25,34:59,212:0.7823:2,2:25.3:1:32.8:1:0.6585:1.17:60:211:0.7815:0:1.1 0/1:311:45:23,22:125,141:266,45:0.1447:2,2:27.5:1:31.2:1:0.63148:1.18:60:90:0.1456:0:1 +16 52085683 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20617;SOR=0;LSEQ=GAAACACAGAAGGCTAAGGG;RSEQ=AGACAGGTCTGGTCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:17,68:85,2:0.023:2,2:10.5:1:28.5:1:0.37289:3.92:60:4:0.023:0:1.5 0/0:104:0:0,0:25,79:104,0:0:2,0:19.6:1:30.1:1:1:0:60:103:1:0:0.3 +16 52473512 . TTGC T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.48986;SOR=0;LSEQ=ATCTGTTGCATCTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:13,9:22,2:0.0833:2,2:23:1:26:1:1:1.42202:60:4:0.087:0.0417:2 0/0:22:0:0,0:12,10:22,0:0:2,0:29.5:1:28.5:1:1:0:60:21:1:0:0.3 +16 55216576 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49057;SOR=Inf;LSEQ=AGGGGAAAGTTGGATATAGA;RSEQ=AGGCATGCACACAGGTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:27,0:0:2,0:25.4:1:32.5:1:1:0:60:54:1:0:0 0/1:27:2:1,1:18,7:25,2:0.0741:2,2:19.5:1:27.5:1:0.51282:2.47127:60:4:0.0769:0:1 +16 55329102 . T A 54 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTCTTGCCCACACCCCAGG;RSEQ=CTCAGGAACTACCAAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:17.5:1:27:1:1:0:60:3:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:8:0:30:0:1:0:60:2:1:0:1 +16 55329381 . G GTCTCTCTGTC 123 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=16.000;MSILEN=2;SSF=0.77751;SOR=0.78961;LSEQ=ACCACAATCTCAACCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:14:14,0:11,0:11,14:0.56:0,1:20.8:1:32.4:1:1:0:53:28:0.56:0.36:0.9 1/0:24:12:11,1:11,0:11,12:0.5:0,2:18:1:31.4:1:1:0:49:24:0.5217:0.25:1.2 +16 55329465 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51029;SOR=0;LSEQ=TAGTTTTGTGTATTCTGTTT;RSEQ=TGCACCAGGACATTGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:134,12:146,2:0.0135:2,2:23:1:32:1:0.16851:10.76875:60:4:0.0138:0:1 0/0:108:0:0,0:92,16:108,0:0:2,0:21.2:1:31.8:1:1:0:59.6:107:1:0:0.2 +16 55329601 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18496;SOR=1.20082;LSEQ=CATTTACCAGTGAGTTAGGC;RSEQ=TCCGCACTCTTGGGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:516:227:98,129:124,165:289,227:0.4399:2,2:26.1:1:31.4:1:1:1.01:60:226:0.4414:0:1.1 0/1:412:200:96,104:91,121:212,200:0.4854:2,2:25.1:1:30.1:1:0.32291:1.23:60:65.667:0.484:0:1.1 +16 55329605 . G A 89 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00654;SOR=11.55364;LSEQ=TACCAGTGAGTTAGGCATCC;RSEQ=CACTCTTGGGAAACAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:1:1,0:211,292:503,1:0.002:2,0:13:0:32:0:0.42063:0:60:2:0.002:0:2 0/1:400:9:4,5:174,217:391,9:0.0225:2,2:23:1:28.1:1:1:1.0023:60:18:0.0226:0:2 +16 55329657 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26774;SOR=0;LSEQ=TTTAAATGAGCATTAATTAT;RSEQ=TCATTATTAGAAATGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:2,1:66,176:242,3:0.0122:2,2:27.7:1:27.7:1:0.18724:5.29:60:6:0.0123:0:1.3 0/0:177:0:0,0:55,122:177,0:0:2,0:23.2:1:31.2:1:1:0:60:176:1:0:0.4 +16 56226526 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50175;SOR=Inf;LSEQ=AGCACCATTGTGAAGCAGAT;RSEQ=AAGTAAGTCCCTGTGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:5,18:23,0:0:2,0:21.9:1:32.2:1:1:0:60:46:1:0:0.1 0/1:31:2:1,1:15,14:29,2:0.0645:2,2:19.5:1:27:1:1:1.06901:60:4:0.0667:0:1 +16 56226542 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=AGATGAAGTAAGTCCCTGTG;RSEQ=CATTGGGATTCGTACTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:3,12:15,0:0:2,0:28.3:1:32.7:1:1:0:60:30:1:0:0 0/1:28:2:1,1:12,14:26,2:0.0714:2,2:22.5:1:27:1:1:1.16:60:4:0.0714:0:1 +16 56781830 . C T 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGGTTTCCATTTCCTTA;RSEQ=CTGCTTTGAGTCTGTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:20.4:1:31.2:1:1:0:60:10:1:0:1.2 1/1:1:1:1,0:0,0:0,1:1:0,0:3:0:26:0:1:0:60:2:1:0:1 +16 56781965 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08245;SOR=Inf;LSEQ=GTTTTTTCACAGCCTGACTC;RSEQ=TTTTCTCTGTCAGGCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:31,0:0:1,0:23.1:1:30.7:1:1:0:60:30:1:0:0.1 0/1:13:2:2,0:11,0:11,2:0.1538:0,0:20.5:1:28:1:1:0:60:4:0.1667:0:1.5 +16 56791999 . T G 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAGAAAAAAAAAAAAGT;RSEQ=GGGGGGAGCTTGTGCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:25.3:1:30.3:1:1:0:57.5:8:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 56832302 . C T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00088;SOR=0.36714;LSEQ=TGTAGGTAGCATAGTAGATA;RSEQ=CATTATGGTTATTGTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:46:41,5:197,30:227,46:0.1685:2,2:21.7:1:31:1:0.8112:1.25:60:22:0.1667:0:1 0/1:217:15:13,2:175,27:202,15:0.0691:2,2:23.3:1:30.3:1:1:1.00:60:30:0.0701:0:1 +16 56832506 . G A 49 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72196;SOR=0.7286;LSEQ=TGAGGGCAAGAGGGCTGGGC;RSEQ=TGGTGGCTCACATCTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:4:3,1:103,266:369,4:0.0107:2,2:11.8:1:24.8:1:0.07116:7.70:60:3:0.0082:0:1.8 0/0:383:3:2,1:121,259:380,3:0.0078:2,2:17:1:25.7:1:0.24255:4.26:60:6:0.0079:0:1 +16 56839364 . G GT 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.12716;SOR=0.32812;LSEQ=TCTGTTGGGTCTTAAACCAT;RSEQ=TTTTTTTTGTTTTTTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:8:5,3:461,143:604,8:0.0131:2,2:20.5:1:29.6:1:0.40391:1.93197:60:16:0.0131:0.0049:0.4 0/0:695:3:2,1:487,205:692,3:0.0043:2,2:23.7:1:26:1:1:1.18748:60:6:0.0044:0:0 +16 56839439 . C T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20666;LSEQ=TTCGGCATGGCTGAGGAGTA;RSEQ=CATCGGGAGTCAATGTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1506:296:164,132:654,554:1208,296:0.1965:2,2:25.9:1:30.6:1:0.74482:1.05:60:97.667:0.1978:0:1.1 0/1:1684:81:45,36:837,762:1599,81:0.0481:2,2:24.8:1:29.6:1:0.64856:1.14:60:162:0.0487:0:1.1 +16 56852311 . A C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATGTACATTTCCAGAAA;RSEQ=AGTCATTGAGGTATTGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:0,9:1:0,2:24.2:1:32.4:1:1:0:60:18:1:0:1.2 1/1:2:2:2,0:0,0:0,2:1:0,0:38.5:1:33.5:1:1:0:60:4:1:0:1 +16 56852389 . T C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.29167;SOR=0.53284;LSEQ=ATCTCATGCCTGCTCTCTTC;RSEQ=CATGTGTTCATAGTAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:31:31,0:18,0:18,31:0.6327:1,1:24:1:31:1:1:0:60:30:0.6383:0:1.1 0/1:21:10:10,0:11,0:11,10:0.4762:0,0:31:1:30.2:1:1:0:60:20:0.4762:0:1 +16 56852494 . G T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24927;SOR=0;LSEQ=CACAGCTCTGTTAAAGACAA;RSEQ=AATATGTTTATGATGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:234,30:264,3:0.0112:2,2:33.3:1:25:1:0.31046:3.86829:60:2:0.0075:0:1.3 0/0:253:0:0,0:212,41:253,0:0:2,0:22.4:1:31.2:1:1:0:60:62.25:1:0:0.1 +16 56852644 . G A 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AACATCGAGATGGCCTATGC;RSEQ=CGGCAAGTGAGTGTGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1131:0:0,0:524,606:1130,0:0:2,0:24.5:1:30.9:1:1:0:60:58.474:0.9991:0:0.1 0/1:1325:50:23,27:616,656:1272,50:0.0377:2,2:27.4:1:28.5:1:0.77437:1.10224:60:24:0.0369:0:1.2 +16 56852822 . G T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00469;SOR=4.30841;LSEQ=GGAGAATTCTATCAAATAGG;RSEQ=TAATAGAATTACTCACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:9:1,8:0,48:48,9:0.1579:1,2:28.6:1:31.7:1:0.15789:0:60:18:0.1579:0:1 0/1:31:14:0,14:0,17:17,14:0.4516:1,1:16.6:1:29.9:1:1:0:60:28:0.4667:0:1 +16 56855192 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTTCTCCCCCTGGACCC;RSEQ=GCTGCTCCCGTTCCTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:28:1:32.3:1:1:0:52.7:6:0.3333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:42:0:30:0:1:0:60:2:1:0:0 +16 56855496 . C G 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05875;LSEQ=TGTGCTTCCGTCGCAGAGCT;RSEQ=GATGATAAGGTAGCACCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:808:803:371,432:0,0:0,803:0.9938:0,2:25.7:1:31.6:1:1:0:59.9:99.375:0.9938:0:1.2 1/1:1074:971:444,527:48,53:101,971:0.9041:2,2:26:1:30.8:1:0.75367:1.07488:59.9:137.714:0.9043:0:1.2 +16 56855549 . TC T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17021;LSEQ=TAGAAACCGGGGTCCAGTGT;RSEQ=CGATGGGCCTAGCAACTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:100:30,70:94,259:353,100:0.2203:2,2:26.1:1:30.8:1:0.52627:1.18:60:200:0.2242:0.0242:0.7 0/1:524:24:9,15:169,329:498,24:0.0458:2,2:24.6:1:28.8:1:0.8259:1.17:60:48:0.0465:0.0019:0.5 +16 56855616 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49883;SOR=0;LSEQ=GACACGCCATTCTGTGGAAT;RSEQ=AAATGTTAACTGTTCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:0,2:2,137:139,2:0.0142:1,0:39.5:1:28.5:1:1:0:60:4:0.0143:0:1 0/0:131:0:0,0:3,128:131,0:0:1,0:22.8:1:31:1:1:0:60:64.5:1:0:0 +16 56862766 . G T 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15566;SOR=4.9785;LSEQ=CATGTACTATTTCCTCTTCT;RSEQ=CATTGAGCTTGAAGTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:1:1,0:149,3:152,1:0.0065:1,0:34:0:13:0:1:0:60:0:0:0:3 0/1:94:3:3,0:88,3:91,3:0.0319:1,0:28.3:1:30.7:1:1:0:60:6:0.0319:0:1 +16 56863072 . C T 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACACCCCCAGAGCAGTTGCC;RSEQ=TCAGATGGGCATTTTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:121,407:528,0:0:2,0:22.2:1:32.2:1:1:0:59.9:51.8:1:0:0.1 0/1:543:27:8,19:142,373:515,27:0.0497:2,2:26:1:29.4:1:0.82663:1.11:60:54:0.05:0:1.1 +16 56863215 . C T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00629;SOR=Inf;LSEQ=GGTGATGGTGGACTCAGCTC;RSEQ=GGGTGGAGAAGAGTGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:3,32:35,0:0:2,0:23.1:1:30.4:1:1:0:60:70:1:0:0.2 0/1:22:5:0,5:0,17:17,5:0.2273:1,0:27:1:30.6:1:1:0:60:10:0.2273:0:1 +16 56863229 . T C 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03858;SOR=0;LSEQ=CAGCTCCGGGTGGAGAAGAG;RSEQ=GCATGGAGAAGATGTCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:0,7:0,23:23,7:0.2333:1,0:22.7:1:32:0:1:0:60:14:0.2333:0:1 0/0:17:0:0,0:0,17:17,0:0:1,0:17.7:1:29.5:1:1:0:60:34:1:0:0.3 +16 56864398 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=1.77733;LSEQ=CACATATGAAAGCAGTCAGC;RSEQ=TTTCCTTGTTTATTTTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:701:260:192,68:311,129:440,260:0.3709:2,2:23.5:1:31.4:1:0.38545:1.17:60:85.667:0.3698:0:1 1/0:764:391:264,127:252,121:373,391:0.5118:2,2:23.9:1:29.7:1:1:1.00188:60:47.875:0.5073:0:1.1 +16 56864618 . C T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.02373;LSEQ=GTATGGTGAATGAGGTGGCA;RSEQ=GCCCAGGGGCAGCCATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:122:41,81:281,478:759,122:0.1383:2,2:27.8:1:30.5:1:0.4806:1.16117:59.8:244:0.1402:0:1.1 0/1:871:342:124,218:205,324:529,342:0.3927:2,2:25.6:1:29.8:1:0.4748:1.11222:59.9:170:0.394:0:1.1 +16 56865608 . A G 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55872;SOR=3.31445;LSEQ=AAAGCGATGGTACCGAGGGG;RSEQ=GGGGATGGGGCAGAGACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:1,0:134,1:135,1:0.0074:1,0:26:0:13:0:1:0:60:0:0:0:2 0/1:83:2:2,0:81,0:81,2:0.0241:1,0:16:1:32:0:1:0:60:4:0.0244:0:1 +16 56865686 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06197;SOR=Inf;LSEQ=TATGTGTTTGGGACCTGGGA;RSEQ=GCTTTCAGATGCCCTTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:0:0,0:409,71:480,0:0:2,0:23.2:1:31.6:1:1:0:60:52.333:1:0:0.1 0/1:493:5:1,4:383,105:488,5:0.0101:2,2:10:1:26.2:1:0.00947:14.48762:60:10:0.0102:0:1 +16 56866054 . A AT 174 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=0.02565;LSEQ=GTTCCTCGTCTCCTGTCCCC;RSEQ=TTTTTTGTTGTGTAATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:49:20,29:88,87:175,49:0.2188:2,2:28.3:1:31:1:0.26107:1.46415:58.7:48:0.2192:0.0268:0.1 0/0:141:1:0,1:71,69:140,1:0.0071:2,0:12:0:31:0:0.49645:0:60:2:0.0072:0:0 +16 56866196 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.11893;LSEQ=ACCAATGCATGTGTTTCTCT;RSEQ=GGGGATTTAGTTGAACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1123:221:130,91:526,376:902,221:0.1968:2,2:24.8:1:31:1:0.93934:1.02:60:220:0.1984:0:1.2 0/1:1202:34:24,10:675,493:1168,34:0.0283:2,2:23.6:1:29.2:1:0.15959:1.75:60:33:0.0277:0:1.1 +16 56866502 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05251;SOR=0.32841;LSEQ=TAAGAAATACATAAAACTTA;RSEQ=ATGGTCATACACAATAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:33:2,31:0,13:13,33:0.7174:1,2:22.4:1:32.5:1:1:0:58.9:66:0.7174:0:1.1 0/1:20:9:1,8:0,11:11,9:0.45:0,2:22.8:1:33.1:1:0.45:0:60:18:0.45:0:1.1 +16 56866801 . G T 88 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTGAGTGACTTAACAGG;RSEQ=TAAAGGAGATAAACACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:0,8:1:0,2:21.5:1:29.6:1:1:0:56.5:16:1:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 56867101 . ATCTCC A 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=3.000;MSILEN=5;SSF=0.2258;SOR=1.76691;LSEQ=CTTCTTTCTAAGTTGGTTTT;RSEQ=TCTCCTCTCCTCTCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:8:4,4:519,267:786,8:0.0101:2,2:18.1:1:29.6:1:0.45533:1.94214:60:16:0.0102:0.005:0.3 0/1:962:17:8,9:585,358:943,17:0.0177:2,2:14.7:1:28.7:1:0.21751:1.83705:59:34:0.018:0.0073:0.4 +16 56867804 . C T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTTGGATTATGTTTTCA;RSEQ=TCAAAGACCAGCATATTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:23,0:0,0:0,23:1:0,1:21.2:1:31.4:1:1:0:57.4:46:1:0:1.4 1/1:5:5:5,0:0,0:0,5:1:0,0:24:1:30.4:1:1:0:60:10:1:0:1 +16 56868700 . A G 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.99614;LSEQ=GAAGTAGAAAGGTGAGTTAA;RSEQ=TGCATCCTTAGAGAAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1318:197:90,107:507,614:1121,197:0.1495:2,2:25.2:1:32.6:1:0.9382:1.02:60:64.667:0.1489:0:1.1 0/1:1563:645:293,352:421,496:917,645:0.4127:2,2:26:1:31.3:1:0.87705:1.0197:59.9:106.5:0.4123:0:1.2 +16 56869430 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACAGGCATTGTGCTGAG;RSEQ=GCTTTGCATAGTTTCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0,3:0.75:0,2:27.3:1:31:1:1:0:55:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 56871469 . TTTTATTGATTAC T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02213;SOR=0.59671;LSEQ=GGGCATTATATAGTTGTTCC;RSEQ=TTTATTGATTGCTTCCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:57:42,15:257,54:311,57:0.1549:2,2:27.8:1:31.5:1:0.13829:1.69697:59.6:114:0.157:0.019:0.1 0/1:406:40:28,12:285,80:365,40:0.0985:2,2:24.4:1:29.8:1:0.2393:1.52504:59.8:80:0.0993:0.0246:0.1 +16 56871762 . T C 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00044;SOR=0;LSEQ=ACAGCTTTCCAAAGTGGTTC;RSEQ=ACTAACTCACCATGCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:15:0,15:2,70:72,15:0.1724:1,1:26.3:1:32.3:1:1:0:60:30:0.1744:0:1 0/0:56:0:0,0:0,56:56,0:0:1,0:23.1:1:28.4:1:1:0:60:112:1:0:0 +16 56871781 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53663;SOR=0;LSEQ=CTACTAACTCACCATGCCAC;RSEQ=AGCACTGTGTGAGTTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:1,62:63,2:0.0308:1,2:12:1:29:1:0.06106:44.19:60:4:0.0308:0:1 0/0:36:0:0,0:0,36:36,0:0:1,0:21.5:1:32.2:1:1:0:60:72:1:0:0 +16 56872722 . C T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02784;SOR=0.29111;LSEQ=CCTGGCCTCAAGCAATCCTT;RSEQ=CGCCCCAGCCTCCCATGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:24:24,0:99,0:99,24:0.1951:1,1:31.5:1:30.8:1:1:0:58.7:23:0.1901:0:1.1 0/1:61:4:4,0:57,0:57,4:0.0656:1,0:21.8:1:30.5:1:1:0:60:8:0.0667:0:1 +16 56872730 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.54022;SOR=0;LSEQ=CAAGCAATCCTTCCGCCCCA;RSEQ=CCTCCCATGTAGCTGAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:140,0:140,2:0.0141:1,0:20:1:32:0:1:0:60:4:0.0143:0:1 0/0:78:0:0,0:78,0:78,0:0:1,0:22.4:1:32:1:1:0:60:77:1:0:0.1 +16 56872804 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03085;SOR=Inf;LSEQ=TAAATGCTATTCCACTGTTA;RSEQ=GGATTACACAGAAATTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:517:0:0,0:399,117:516,0:0:2,0:23:1:31.8:1:1:0:60:171:0.9981:0:0.3 0/1:528:6:1,5:384,138:522,6:0.0114:2,2:8.7:1:26.5:1:0.00648:13.83361:60:12:0.0115:0:1 +16 56872824 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15683;LSEQ=CGGATTACACAGAAATTCCT;RSEQ=ATACACTCTTACTACCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:169:106,63:383,184:567,169:0.2296:2,2:25.3:1:29.4:1:0.26558:1.23674:60:338:0.2312:0:1.1 0/1:807:36:24,12:485,285:770,36:0.0446:2,2:19.6:1:28.4:1:0.72609:1.18:60:72:0.0454:0:1.1 +16 56873495 . C T 230 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=75.00101;LSEQ=GTGGAAGAGAGAGTGGCTGC;RSEQ=TTCAGAAATTTCAGTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1410:3:1,2:643,764:1407,3:0.0021:2,2:24.3:1:30.7:1:1:1.68265:60:6:0.0021:0:1.3 0/1:1587:219:100,119:629,734:1363,219:0.138:2,2:24.4:1:29.6:1:0.94181:1.01976:60:72:0.1378:0:1.1 +16 56873613 . T TA 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.103;LSEQ=ACAGCTTTAAGAATTCTAGT;RSEQ=ACAGTAACTATCCAGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:49:1,48:8,183:191,49:0.2042:1,1:23:1:31.5:1:0.69047:2.09308:60:98:0.2059:0.0458:0 0/1:195:5:1,4:10,180:190,5:0.0256:2,2:13.4:1:28.1:1:0.2543:4.44:60:10:0.0259:0.0051:0 +16 56873789 . T C 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAGGTTTCTGGTTGATCTG;RSEQ=GAAGTCTGGTTTAATTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:8,7:0.4667:0,0:23.6:1:30.3:1:1:0:60:14:0.4667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:33:0:31:0:1:0:60:2:1:0:0 +16 56875548 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.23388;SOR=0;LSEQ=CCTGCCTGGAGCAGCCCACC;RSEQ=TCCCTCCATCTGTGGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:2,0:168,15:183,2:0.0108:2,0:29:1:33.5:1:1:0:60:4:0.0109:0:1 0/0:197:0:0,0:176,21:197,0:0:2,0:21.3:1:30.5:1:1:0:60:48.25:1:0:0.1 +16 56878714 . T TC 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.41458;SOR=0.55944;LSEQ=TTTTATTTTCTTTTTTTTTT;RSEQ=CTTTGAAATTTTGTTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:20:0,20:0,2:2,20:0.7143:0,1:26.2:1:29.8:1:1:0:60:9:0.72:0.1429:0.7 1/0:31:18:1,17:0,5:5,18:0.5806:0,1:23.2:1:29.9:1:1:0:59.5:17:0.5667:0.0645:0.7 +16 57429701 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20448;SOR=Inf;LSEQ=GCTGTCACGGGACCTAGAAA;RSEQ=GGGAGAAGCATGTCGCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:43,0:0:2,0:27.7:1:31.1:1:1:0:55.7:86:1:0:0.1 0/1:36:2:1,1:17,17:34,2:0.0556:2,2:32.5:1:30:1:1:1:24:4:0.0556:0:1 +16 57429734 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20556;SOR=Inf;LSEQ=TCGCCCAACTCCAGAAGTGG;RSEQ=TATAAGAGTTTGAAAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:22,22:44,0:0:2,0:30.1:1:32:1:1:0:54.7:43:1:0:0.1 0/1:37:2:1,1:16,19:35,2:0.0541:2,2:29:0:30:1:1:1.18:60:4:0.0541:0:1 +16 57429740 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20556;SOR=Inf;LSEQ=AACTCCAGAAGTGGGTATAA;RSEQ=AGTTTGAAAGGCATTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:21,23:44,0:0:2,0:26.5:1:32.9:1:1:0:54.7:88:1:0:0.1 0/1:37:2:1,1:16,19:35,2:0.0541:2,2:17.5:1:29:1:1:1.18:60:4:0.0541:0:1.5 +16 57429779 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16774;SOR=Inf;LSEQ=TGATTTCAGAAGCCTTTTCC;RSEQ=GTAAACACCGGGTGGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:18,0:0:2,0:19.6:1:30:1:1:0:46.4:36:1:0:0 0/1:13:2:1,1:4,7:11,2:0.1538:2,2:11.5:1:28:1:1:1.67:34:4:0.1538:0:1.5 +16 57698702 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18301;SOR=Inf;LSEQ=GTGAGGCGTGCGTGAAGCAA;RSEQ=AACTCCTGGAGCTACAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:10,0:0:2,0:24.6:1:34.7:1:1:0:60:20:1:0:0.4 0/1:8:2:1,1:4,2:6,2:0.25:2,2:16.5:1:27.5:1:1:1.8258:60:4:0.25:0:1 +16 58030634 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAGTTGGGGCACTTGTAGGG;RSEQ=TTCTCGCCTGTGTGTACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:27.5:1:33:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:29.5:1:1:0:60:4:1:0:1.5 +16 58032026 . G A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01686;SOR=0;LSEQ=TGCAGGAGGATGCCATAGAC;RSEQ=GCACAGCCCAGGGGGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:5,1:7,2:9,6:0.4:2,2:32.3:1:29.5:1:1:1.40:60:5:0.3571:0:1.2 0/0:14:0:0,0:10,4:14,0:0:2,0:22.9:1:30:1:1:0:60:28:1:0:0.1 +16 58032054 . C T 20 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.8876;LSEQ=CCAGGGGGTTCTCCGCCGTG;RSEQ=CCGGAGGCAGCGTGTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:27,12:39,2:0.0488:2,2:27.5:1:31:1:0.53902:2.20143:60:4:0.05:0:1.5 0/1:46:2:0,2:29,15:44,2:0.0435:2,0:1:0:20:1:0.1314:0:60:1:0.0222:0:1.5 +16 58032133 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20877;SOR=Inf;LSEQ=CGGTGGCTGTGGCTGCTGCG;RSEQ=CTGCGTCTGTGGCGGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:16,25:41,0:0:2,0:17.9:1:32:1:1:0:60:82:1:0:0.1 0/1:35:2:1,1:11,22:33,2:0.0571:2,2:21.5:1:27:1:1:1.96:60:4:0.0571:0:2 +16 58529615 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=16.54653;LSEQ=TCGTCCCCCAGTGGGAGCAA;RSEQ=GCGAGGATCAGTGTGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:11:6,5:104,106:210,11:0.0498:2,2:25.1:1:32.1:1:0.76807:1.22:60:22:0.0507:0:1.2 0/1:206:96:50,46:60,49:109,96:0.466:2,2:26.8:1:29.1:1:0.67668:1.12587:60:47:0.47:0:1.3 +16 58960831 . G A 138 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATACAGTAATTGACCAAGG;RSEQ=TACCAACTATTGTGCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:24:24,0:39,1:40,24:0.375:1,1:21.5:1:30.3:1:1:0:57.1:48:0.375:0:1.2 0/0:45:0:0,0:44,1:45,0:0:1,0:22.5:1:31:1:1:0:58.1:90:1:0:0 +16 58960901 . C T 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46243;LSEQ=TGTTTCCCACCAGCTGCTCC;RSEQ=AGCCCATGAATGAGTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:2:1,1:151,51:202,2:0.0098:2,2:20:1:29:1:0.44576:2.94175:60:4:0.0099:0:1 0/1:210:3:2,1:139,68:207,3:0.0143:2,2:18.7:1:29.7:1:1:1.02197:60:6:0.0146:0:1 +16 58960987 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12477;SOR=Inf;LSEQ=GATGATGACTTTGGCTTGAG;RSEQ=ACTCCCCAGTAGCCTTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:127,193:320,0:0:2,0:24.1:1:31.7:1:1:0:60:159:1:0:0.1 0/1:343:4:3,1:127,212:339,4:0.0117:2,2:11.5:1:27.3:1:0.15452:4.98:57:8:0.0119:0:1 +16 59584343 . G A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10373;LSEQ=TTACAAGGAAATGCACAGAT;RSEQ=AGCCTAGGTGAAGATTCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:31:15,16:18,18:36,31:0.4627:2,2:26:1:29.9:1:1:1.06563:58.5:62:0.4627:0:1.9 0/1:99:8:4,4:42,49:91,8:0.0808:2,2:24.4:1:29.3:1:1:1.16:60:16:0.0808:0:1.8 +16 59584360 . C T 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0833;LSEQ=GATGAGCCTAGGTGAAGATT;RSEQ=GATCTAAGGTTTTGACTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:25:10,15:13,18:31,25:0.4464:2,2:22.3:1:30.2:1:1:1.08178:58.8:24:0.4364:0:2 0/1:81:5:2,3:30,46:76,5:0.0617:2,2:32.4:1:30:1:1:1.02:60:10:0.0625:0:2 +16 59584685 . G A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGTTGACCAGCGACATTC;RSEQ=GCTGCAGTTTGTTTGGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 61579246 . A G 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACTAAAAAGCTTCTATACA;RSEQ=CAAAGGAAACAATCAATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:22:1:33.7:1:1:0:60:6:0.4286:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:8:0:32:0:1:0:60:2:1:0:1 +16 61579445 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=TTTAAAATGTTACATTAAAA;RSEQ=CGGAAGAAAAATATGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:122,10:132,2:0.0149:2,2:29.5:1:33:0:0.15801:11.68004:60:4:0.015:0:1.5 0/0:105:0:0,0:99,6:105,0:0:2,0:22.2:1:29:1:1:0:60:51.5:1:0:0.1 +16 61579446 . C T 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32201;SOR=3.90234;LSEQ=TTAAAATGTTACATTAAAAA;RSEQ=GGAAGAAAAATATGTAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:1,0:124,11:135,1:0.0073:2,0:16:0:33:0:1:0:60:2:0.0074:0:1 0/1:107:3:3,0:97,7:104,3:0.028:2,0:26.7:1:31:1:1:0:60:6:0.0286:0:1 +16 61579583 . C A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.77222;LSEQ=TTAGTCTTTGTTTTAATTAG;RSEQ=ATTACAAAAGAGAAACATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:121:49,72:117,180:297,121:0.2881:2,2:25.7:1:30.3:1:0.91228:1.05:60:39.333:0.2843:0:1.4 1/0:448:237:96,141:88,123:211,237:0.529:2,2:24.6:1:28.8:1:0.84753:1.05067:60:38.5:0.525:0:1.3 +16 61579609 . A G 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AAAAGAGAAACATCGCATAT;RSEQ=TTAGACATAATTTCTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:99,204:303,0:0:2,0:24.4:1:30.2:1:1:0:60:74.75:1:0:0.5 0/1:335:29:10,19:105,201:306,29:0.0866:2,2:23.3:1:30.9:1:1:1.01:60:58:0.0871:0:1.9 +16 61579618 . A G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29469;SOR=0.77531;LSEQ=ACATCGCATATATTAGACAT;RSEQ=ATTTCTAACCTCAGAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:47:13,34:67,157:224,47:0.1734:2,2:26.1:1:32.6:1:0.86107:1.11569:60:94:0.1754:0:2 0/1:286:40:12,28:78,168:246,40:0.1399:2,2:24.9:1:30.8:1:1:1.08304:60:39:0.1368:0:1.9 +16 61579666 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22357;SOR=0;LSEQ=CCTTAAGTTCCACAGTGAGC;RSEQ=CATGCTGAATTACTGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:22,94:116,2:0.0169:2,2:19.5:1:32:0:0.35318:4.20:60:4:0.0169:0:2 0/0:131:0:0,0:27,104:131,0:0:2,0:21.7:1:31.3:1:1:0:60:262:1:0:0.4 +16 63438484 . A T 34 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26087;SOR=Inf;LSEQ=TATATCTTCAGGTTACTTAA;RSEQ=AGTTTGCAAGTTCTCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:196,24:220,0:0:2,0:22.1:1:30.4:1:1:0:58.2:72.333:1:0:0.2 0/1:286:3:1,2:245,36:281,3:0.0105:2,2:5:1:21.7:1:0.04801:13.38498:60:6:0.0107:0:1.3 +16 63438539 . A ACTGTTGTTGCTGTTGCTG 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=2.000;MSILEN=3;SSF=0.87533;SOR=0.97536;LSEQ=GAGAAATCTGGTGTTGTGCC;RSEQ=CTGTTGTTGCTGTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:81:40,41:355,261:616,81:0.1151:2,2:19.8:1:31.1:1:0.18936:1.39346:44.8:162:0.1167:0.0866:0.1 0/1:933:105:57,48:486,341:827,105:0.1125:2,2:17.8:1:30.2:1:0.40156:1.19994:47.7:210:0.1136:0.089:0.1 +16 63438564 . C T 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.91767;SOR=1.02481;LSEQ=TGTTGCTGTTGCTGCTGTTG;RSEQ=TGCTGTTGTTGCTGCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:837:43:28,15:374,420:794,43:0.0514:2,2:15.2:1:30:1:0.02739:2.09:27.7:86:0.0526:0:2.3 0/1:1065:56:30,26:509,500:1009,56:0.0526:2,2:16.5:1:28.6:1:0.68211:1.13:29.6:112:0.0533:0:2.3 +16 63438579 . C T 97 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.82612;SOR=0.86187;LSEQ=TGTTGCTGCTGTTGTTGCTG;RSEQ=TGATGCTCCAAGAGTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:777:10:5,5:333,432:765,10:0.0129:2,2:3.7:1:30.1:1:0.75432:1.30:30.1:20:0.0131:0:3.4 0/1:990:11:8,3:445,532:977,11:0.0111:2,2:5.1:1:28.1:1:0.12453:3.18:25.9:22:0.0113:0:3.6 +16 63438619 . AT A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.24159;LSEQ=GCATGCATCTTATTTAGATT;RSEQ=TTTTACTTGTCTGAATTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:170:46,124:78,182:260,170:0.3944:2,2:22.5:1:31:1:0.58631:1.15489:59.8:169:0.3967:0.0603:0.1 0/1:545:74:17,57:148,322:470,74:0.1358:2,2:21.6:1:30:1:0.17329:1.53996:60:148:0.1378:0.0275:0 +16 63438640 . C A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0931;SOR=0;LSEQ=TTTTTACTTGTCTGAATTCA;RSEQ=CCTATTTCAAAATTATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:38,241:279,3:0.0106:2,2:13:1:22.7:1:0.05372:12.49:60:2:0.0072:0:2 0/0:339:0:0,0:50,289:339,0:0:2,0:24:0:11:0:1:0:60:0:0:0:7 +16 63438757 . A T 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65194;SOR=1.89315;LSEQ=TGCTTTATAAATTATTGTTA;RSEQ=ATCTTATTCTTCTGGTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:0,3:0,25:25,3:0.1071:1,0:6.3:1:29:1:1:0:60:6:0.1071:0:1.3 0/1:16:3:0,3:1,12:13,3:0.1875:1,0:29:1:28:1:1:0:60:6:0.2:0:1 +16 64648860 . C T 64 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.40518;SOR=0.41704;LSEQ=TTTTGTTTATTCTTTCTCAT;RSEQ=TTCATGAGTTCGTCTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:3,1:14,4:18,4:0.1818:2,2:8.5:1:32.3:1:1:1.15827:60:8:0.1905:0:1.3 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:3:0:30:1:1:1.19087:60:4:0.0909:0:1.5 +16 64649225 . G A 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=AGAGTCTCACCCAGTTGGGT;RSEQ=GCACAGGGAGCACTTCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:5,2:0.2857:2,0:19:1:34:0:1:0:53.5:4:0.2857:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:28.8:1:27.5:1:1:0:44:3:1:0:0.3 +16 64649649 . C T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GCTATCGAAATGAGTTGCCA;RSEQ=CCTTCCCCCACCCAGGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:23.8:1:31.8:1:1:0:60:8:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:20:0:30.5:1:1:1:60:4:0.5:0:1 +16 66648874 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=Inf;LSEQ=TGCTGTCGGGGACAAATCAA;RSEQ=AGCAGCAAAGCTTTGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:6,17:23,0:0:2,0:28.2:1:29:1:1:0:60:46:1:0:0.1 0/1:26:2:1,1:6,18:24,2:0.0769:2,2:24.5:1:32.5:1:0.47385:2.85:60:4:0.08:0:1 +16 66648879 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22429;SOR=0;LSEQ=TCGGGGACAAATCAATAGCA;RSEQ=CAAAGCTTTGGGGCCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:5,16:21,2:0.087:2,2:25.5:1:30.5:1:0.46245:3.01:60:4:0.087:0:1 0/0:25:0:0,0:7,18:25,0:0:2,0:27.6:1:31.2:1:1:0:60:24:1:0:0.1 +16 67063200 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCTGAAACAAAGGGAAG;RSEQ=GGGCGTCCGGGCGCCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:19.5:1:28:1:1:1:60:4:0.5:0:1.5 +16 67063247 . C T 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37078;SOR=0.25846;LSEQ=GTCAGTCGGTCAGCGCGGAG;RSEQ=CAGCCAGCGGGTGCCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:2,0:2,1:0.3333:0,0:1:0:25:0:0.33333:0:60:2:0.3333:0:1 0/1:19:2:1,1:12,5:17,2:0.1053:2,2:27.5:1:28:1:1:2.28037:60:4:0.1053:0:1.5 +16 67063287 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14807;SOR=0;LSEQ=CAAGCCCCGAGCGCGGCCGG;RSEQ=CGGCGCGGCCTCAGGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:116,42:158,2:0.0125:2,2:27.5:1:30.5:1:0.46651:2.74134:60:4:0.0127:0:1 0/0:255:0:0,0:183,72:255,0:0:2,0:19.5:1:31.3:1:1:0:60:62.75:1:0:0.2 +16 67063289 . G T 22 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15156;SOR=0;LSEQ=AGCCCCGAGCGCGGCCGGCC;RSEQ=GCGCGGCCTCAGGGCGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:129,48:177,2:0.0112:2,2:20:1:22.5:1:0.47367:2.67023:60:4:0.0112:0:1 0/0:280:0:0,0:198,82:280,0:0:2,0:43:0:18:0:1:0:60:0:0:0:2 +16 67063326 . C T 83 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.37867;SOR=2.09253;LSEQ=GGAAGATGCCGCGCGTCGTG;RSEQ=CCGACCAGAGAAGCAAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:3:1,2:304,165:469,3:0.0064:2,2:26:1:25:1:0.28654:3.67409:60:2:0.0043:0:1.3 0/1:681:9:3,6:413,259:672,9:0.0132:2,2:16.2:1:26.3:1:0.09775:3.18363:60:8:0.0119:0:1.3 +16 67063499 . G A 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0011;SOR=Inf;LSEQ=TCCCGGTCGGTGCGCCCGCG;RSEQ=AGGGGCAATCTCGCCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:46,58:104,0:0:2,0:17.5:1:32.7:1:1:0:60:103:1:0:0.1 0/1:96:9:4,5:32,55:87,9:0.0938:2,2:21.8:1:31:1:0.7243:1.37:60:18:0.0957:0:1.1 +16 67063546 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25457;SOR=Inf;LSEQ=CGCCCGCAGCCTCTGCTTGC;RSEQ=CTTATCGGCGCTGCGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:178,43:221,0:0:2,0:23:1:31.9:1:1:0:60:72.667:0.9954:0:0.1 0/1:266:3:1,2:200,61:261,3:0.0113:2,2:11:1:28:1:0.14257:6.49787:60:6:0.0115:0:1 +16 67063559 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0752;SOR=0;LSEQ=TGCTTGCCCTTATCGGCGCT;RSEQ=CGCTGGGAGGGCGGGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:1,2:213,64:277,3:0.0107:2,2:20.7:1:28.7:1:0.13946:6.59846:60:6:0.011:0:1 0/0:382:0:0,0:262,118:380,0:0:2,0:23.2:1:31.1:1:1:0:60:62.333:0.9947:0:0.2 +16 67063560 . C T 68 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70473;SOR=1.87174;LSEQ=GCTTGCCCTTATCGGCGCTG;RSEQ=GCTGGGAGGGCGGGCGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:2:1,1:218,69:287,2:0.0069:2,2:25:1:20.5:1:0.4264:3.14398:60:1:0.0036:0:1 0/1:388:5:3,2:262,121:383,5:0.0129:2,2:33.4:1:29.4:1:0.65401:1.44211:60:10:0.0131:0:1 +16 67063612 . G T 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATTTGGCTCCTGATTTCG;RSEQ=GCCGTCTTGCCTTGCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:0:0,0:373,281:654,0:0:2,0:24.4:1:30.7:1:1:0:59.9:31.7:1:0:0.2 0/1:869:81:42,39:434,354:788,81:0.0932:2,2:23.2:1:29.6:1:0.63946:1.13825:59.7:162:0.0945:0:1.2 +16 67070410 . G GT 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.47202;LSEQ=AAGAAAAATGATGAGTGCAT;RSEQ=TTTTTTTTTACTTTTAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:2,0:64,1:65,2:0.0299:1,0:9:1:27.6:1:1:0:60:4:0.0303:0.0149:0 0/1:46:2:2,0:44,0:44,2:0.0435:1,0:16:1:30.1:1:1:0:60:4:0.0435:0.0217:0 +16 67070442 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21914;SOR=Inf;LSEQ=TTTTAAGTATTCTCTGTGCT;RSEQ=CCTGGCTTAAGACATAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:113,8:121,0:0:2,0:25.4:1:32.5:1:1:0:59.8:39.333:1:0:0.1 0/1:107:2:1,1:101,4:105,2:0.0187:1,2:24:1:27.5:1:0.09169:22.69627:60:4:0.0194:0:1 +16 67070692 . T A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.28152;SOR=Inf;LSEQ=CTTTGCAATTTAAAATACTG;RSEQ=GGGTTGTTTTGTTAGAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:42,154:196,0:0:2,0:24.4:1:30.2:1:1:0:59.9:48:1:0:0.1 0/1:300:3:3,0:74,223:297,3:0.01:2,0:13:1:21:1:0.01642:0:60:2:0.0067:0:1 +16 67070698 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15764;SOR=0;LSEQ=AATTTAAAATACTGTGGGTT;RSEQ=TTTTGTTAGAGATTATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:29,144:173,2:0.0114:2,2:6:1:29.5:1:0.31429:4.90:60:4:0.0116:0:1 0/0:265:0:0,0:57,208:265,0:0:2,0:22.7:1:31.1:1:1:0:60:264:1:0:0.1 +16 67070721 . AT A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5077;SOR=Inf;LSEQ=TTGTTAGAGATTATCTGGTA;RSEQ=TTACATTTTAATAAAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:14,111:125,0:0:2,0:21.3:1:30.3:1:1:0:59.9:124:1:0:0 0/1:166:2:1,1:21,143:164,2:0.012:2,2:17:1:26.5:1:0.24819:6.68:60:4:0.0122:0.006:1.5 +16 67070808 . AT A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.23469;SOR=0;LSEQ=TGTTATAAGGATGTAATATA;RSEQ=TTTTTTTTTTTAATGGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:0,3:0,22:22,3:0.12:1,0:14.7:1:33:0:1:0:60:6:0.12:0:0 0/0:25:0:0,0:0,25:25,0:0:1,0:19.9:1:29.9:1:1:0:60:50:1:0:0.2 +16 67070862 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CCCAGGCTGGAGTGCAGTGG;RSEQ=GTGATGTTGGTTCACTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:25.3:1:30.7:1:1:0:53:6:0.5:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:25:1:28.5:1:1:0:50.3:8:1:0:0 +16 67100460 . CTCAA C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.23523;SOR=Inf;LSEQ=GGAGCACAGCGAAACTCCAT;RSEQ=TCAATCAGTCAATCATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:43,0:43,0:0:1,0:23.6:1:32.3:1:1:0:59:42:1:0:0 0/1:41:2:2,0:38,1:39,2:0.0488:1,0:24.5:1:32:0:1:0:60:4:0.0488:0:0 +16 67100529 . T C 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.2491;SOR=Inf;LSEQ=ATATAAGTAAGTTTAATCTT;RSEQ=TTATTTTCATGTGTCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:203,49:252,0:0:2,0:21.9:1:31.4:1:1:0:60:504:1:0:0.1 0/1:266:3:2,1:206,57:263,3:0.0113:2,2:28.3:1:26:1:0.52338:1.80236:60:2:0.0076:0:1 +16 67101184 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACTTTGGGAGGCTGAGG;RSEQ=AGACGGATCACCTGAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:22.5:1:27:1:1:0:46.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 67115910 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=TTCTGTATTTTTAGTAGAGA;RSEQ=GCGGTTTCACCATGTTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:25.7:1:26.3:1:1:0:37.7:2:0.5:0:2.3 0/0:3:0:0,0:3,0:3,0:0:0,0:25.3:1:24.7:1:1:0:38.3:2:1:0:4 +16 67116066 . AT A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.15851;SOR=0;LSEQ=AAACAAAACCCAAATATTGT;RSEQ=TTTTTTTATAAATCAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:2,0:124,24:148,2:0.0133:2,0:30.5:1:31:1:1:0:60:4:0.0139:0:0.5 0/0:226:0:0,0:186,40:226,0:0:2,0:21.6:1:29.2:1:1:0:58.6:31.286:1:0:0.8 +16 67116355 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25772;SOR=Inf;LSEQ=GTTGTACTCTCTGGCTTTGT;RSEQ=TTTATTAAATGTAATTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:1,75:76,0:0:1,0:25.4:1:32.3:1:1:0:60:37:1:0:0 0/1:98:3:0,3:0,95:95,3:0.0306:1,0:35.7:1:31:1:1:0:60:6:0.0309:0:1.3 +16 67132463 . G GT 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.0845;SOR=Inf;LSEQ=GTCAGACATAATTTTAATTG;RSEQ=TTTTTTTTTGCCTGTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:78,0:78,0:0:1,0:26.1:1:31.9:1:1:0:59.9:77:1:0:0.2 0/1:62:3:3,0:57,2:59,3:0.0484:1,0:21.3:1:29:1:1:0:60:6:0.0484:0:0 +16 67431239 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53623;SOR=Inf;LSEQ=CCCTCTCCCCAGCACAGCTG;RSEQ=CACCATCAGAGCCCAGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:16,0:0:2,0:22:1:31.7:1:1:0:60:32:1:0:0.1 0/1:30:2:1,1:18,10:28,2:0.0667:2,2:22.5:1:26.5:1:1:1.76317:60:4:0.0667:0:1 +16 67450281 . T TGGCTCC 86 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=42;MSI=8.000;MSILEN=6;SSF=0.01522;SOR=0.15118;LSEQ=GAGTCCTCGAGCTCTGGCTC;RSEQ=GGCTCCGGCTCCGGCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:5,3:13,16:29,8:0.2162:2,2:14.5:1:28.9:1:0.44703:2.01:60:7:0.1944:0.1351:0 0/1:51:2:1,1:27,22:49,2:0.0392:2,2:31.5:1:30.3:1:1:1.22232:60:4:0.0392:0:0 +16 67644775 . G A 79 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09321;SOR=5.44121;LSEQ=AAGCCATTGTGGAGGAGTCC;RSEQ=AAACTTTTATTAAAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:1:1,0:240,240:480,1:0.0021:2,0:1:0:16:0:1:0:60:0:0:0:1 0/1:713:8:7,1:339,366:705,8:0.0112:2,2:12.8:1:26.5:1:0.03323:7.54:60:16:0.0113:0:1.1 +16 67645883 . TGCAGTTACA T 214 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACATTCCAGTGTGAGCTT;RSEQ=CGTGTCCACGGCGTTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:111:66,45:227,170:397,111:0.2185:2,2:27.9:1:31.6:1:0.74457:1.10:59.9:110:0.2187:0.0177:0.1 0/0:723:0:0,0:406,317:723,0:0:2,0:25:1:31.5:1:1:0:60:102.286:1:0:0.1 +16 67650568 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50025;SOR=Inf;LSEQ=ATAGGGTTCCAGTCTCATAG;RSEQ=AGTTCTGTGCCACACATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:160,16:176,0:0:2,0:23.4:1:32.7:1:1:0:60:352:1:0:0.1 0/1:197:2:1,1:155,40:195,2:0.0102:2,2:10.5:1:27:1:0.37377:3.83978:60:4:0.0102:0:1 +16 67650676 . C T 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05524;SOR=4.10117;LSEQ=CCTCACAAGTGCCCAGACTG;RSEQ=GACATGGCCTTTGTGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:2:0,2:352,305:657,2:0.003:2,0:1:0:27.5:1:0.21664:0:60:4:0.0031:0:1 0/1:974:12:3,9:535,426:961,12:0.0123:2,2:11.5:1:27.5:1:0.04156:3.76278:60:24:0.0125:0:1.1 +16 67655537 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22079;SOR=Inf;LSEQ=AGTGAAAAAAATATTTTGAA;RSEQ=GATTTATATTTCGAAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:35,163:198,0:0:2,0:22.1:1:31.3:1:1:0:60:27.286:1:0:0.1 0/1:176:2:1,1:35,138:173,2:0.0114:2,2:39:1:29.5:1:0.37005:3.90:60:4:0.0116:0:1 +16 67655557 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61541;SOR=2.10063;LSEQ=GGATTTATATTTCGAAATAT;RSEQ=GGGATCAAAAATAACTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:0,1:13,105:118,1:0.0084:2,0:26:0:32:0:1:0:60:2:0.0085:0:1 0/1:114:2:1,1:16,96:112,2:0.0175:2,2:38.5:1:28:1:0.27713:5.85:60:4:0.0179:0:1 +16 67662204 . A T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22137;SOR=Inf;LSEQ=AATACCTGTTGGCCACATGC;RSEQ=TGCAGGTGGCAGCTGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:162,22:184,0:0:2,0:23.9:1:30.3:1:1:0:59.8:91:1:0:0.1 0/1:164:2:1,1:132,30:162,2:0.0122:2,2:5.5:1:27:1:0.34326:4.34482:60:4:0.0123:0:1.5 +16 67670472 . G GTA 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=11.000;MSILEN=2;SSF=0.79526;SOR=1.25236;LSEQ=AAAAAAAAAAGAAAGAAAGT;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:13:13,0:45,2:47,13:0.2031:1,1:26.3:1:28.2:1:1:0:53.8:12:0.2353:0:1.8 0/1:33:8:7,1:23,0:23,8:0.2424:1,2:14.6:1:29.5:1:0.25806:0:58.1:16:0.2667:0.1212:0.4 +16 67670521 . TA T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.22482;SOR=Inf;LSEQ=ACAAGACTTCAAATAATATA;RSEQ=ATTGTTTTCTTTCATCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:150,28:178,0:0:2,0:20.8:1:28:1:1:0:59.6:24.429:1:0:0.3 0/1:161:2:1,1:127,32:159,2:0.0124:2,2:13.5:1:28.5:1:0.36894:3.92351:60:4:0.0128:0:0 +16 67671804 . T G 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01015;SOR=Inf;LSEQ=CCTTGTGCGTCGCCAGGACT;RSEQ=CTCTGGGCTGTGTTTAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:58,181:239,0:0:2,0:24.4:1:30.5:1:1:0:60:118.5:1:0:0.1 0/1:299:8:2,6:86,205:291,8:0.0268:2,2:30.8:1:30.5:1:1:1.25759:60:16:0.027:0:1.1 +16 67876762 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50723;SOR=Inf;LSEQ=TGGGGCCGCGGCCGCCCGCC;RSEQ=CAGGCAGCAGCAGCAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:43,40:83,0:0:2,0:33.2:1:30.3:1:1:0:57.6:19.75:1:0:0.2 0/1:110:2:1,1:50,56:106,2:0.0182:2,2:16:1:25:1:1:1.12:58.5:4:0.0189:0:1 +16 67876778 . ACAG A 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.69742;SOR=0.71913;LSEQ=CGCCGCAGGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:3:2,1:41,43:84,3:0.0345:2,2:35.3:1:32:1:0.61623:2.08:52.3:6:0.0345:0:0 0/1:120:3:1,2:51,66:117,3:0.025:2,2:22.3:1:33:0:1:1.54008:60:6:0.0252:0:0 +16 67876820 . GCAA A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.55106;SOR=Inf;LSEQ=CAGCAACAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:16,34:50,0:0:2,0:26.1:1:32.3:1:1:0:51.4:49:1:0:0.1 0/1:99:2:1,1:40,57:97,2:0.0202:2,2:18:1:32:1:1:1.42:55:4:0.0204:0.0101:2 +16 67876875 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52565;SOR=Inf;LSEQ=CCTCACCCTCTGCCTCCACT;RSEQ=CCCAGACTGCCCAGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:2,21:23,0:0:2,0:25.4:1:33.1:1:1:0:54.2:46:1:0:0.1 0/1:39:2:1,1:15,22:37,2:0.0513:2,2:14.5:1:26.5:1:1:1.45:45:4:0.0513:0:1.5 +16 68732300 . C G 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19808;SOR=Inf;LSEQ=TACGGTGGCGGGGAGGACGA;RSEQ=TAGGCGGCCTGCCTGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:20,28:48,0:0:2,0:28.3:1:33.5:1:1:0:60:96:1:0:0.1 0/1:39:2:1,1:18,19:37,2:0.0513:2,2:17:0:30.5:1:1:1.05:60:4:0.0513:0:1.5 +16 68732304 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.18513;SOR=Inf;LSEQ=GTGGCGGGGAGGACGACTAG;RSEQ=CGGCCTGCCTGCAGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:19,28:47,0:0:2,0:27:1:32.4:1:1:0:60:94:1:0:0.1 0/1:36:2:1,1:16,18:34,2:0.0556:2,2:35:1:27.5:1:1:1.12:60:4:0.0556:0:1 +16 68732457 . G T 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTCTGACGTTAGAGTGGT;RSEQ=GCTTCCTTAGCCTTTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:32:0:1:0:60:4:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:20:1:30:0:1:0:60:4:1:0:1 +16 68771238 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49875;SOR=Inf;LSEQ=CCTGTGAGCTTGCGGAAGTC;RSEQ=GTTCAGACTCCAGCCCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:113,87:200,0:0:2,0:21.8:1:30.4:1:1:0:59.8:65.667:1:0:0.1 0/1:201:2:1,1:121,78:199,2:0.01:2,2:13:1:29:1:1:1.54774:60:4:0.0101:0:1 +16 68771347 . CGCT C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.48596;SOR=1.32791;LSEQ=TTGGAGCCGCAGCCTCTCGG;RSEQ=GCTGCTGCTGCTGCAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:14:9,5:253,170:423,14:0.032:2,2:27.9:1:32.3:1:0.78994:1.21:59.6:28:0.0326:0.0046:0.7 0/1:476:20:12,8:249,205:454,20:0.042:2,2:24.9:1:31.1:1:0.81909:1.23:58.5:40:0.0431:0.0063:1.2 +16 68771372 . C T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.30594;SOR=0.85777;LSEQ=CTGCTGCTGCTGCAGGTACC;RSEQ=CGGATCCCCTGACTTGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:463:346:193,153:64,53:117,346:0.7473:2,2:25.8:1:30.6:1:0.91435:1.04:59.5:42.25:0.7478:0:1.1 1/0:488:350:199,151:72,65:137,350:0.7172:2,2:24.7:1:29.1:1:0.41775:1.19:59.5:24:0.7119:0:1.2 +16 68771418 . C CGCCCCAGCCCCGT 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02049;SOR=1.37721;LSEQ=CATTCGGGCCGCAAGCTCCG;RSEQ=GCCCCAGCCCTGCGCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:422:224:77,147:93,98:191,224:0.5308:2,2:31.1:1:30.9:1:0.00367:1.80908:59.3:73.667:0.5338:0.064:0.6 1/0:458:279:123,156:83,91:174,279:0.6092:2,2:32.4:1:29.6:1:0.49732:1.15642:59.3:138.5:0.6128:0.0611:0.5 +16 68771431 . C T 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20107;SOR=0.23019;LSEQ=AGCTCCGCGCCCCAGCCCTG;RSEQ=GCCCCTTCCTCTCCCGTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:4:1,3:101,192:293,4:0.0134:2,2:23.8:1:26:1:1:1.57589:58.8:3:0.0103:0:2.5 0/0:321:1:0,1:127,193:320,1:0.0031:2,0:25:0:31:0:1:0:60:2:0.0032:0:2 +16 68771447 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09891;SOR=0;LSEQ=CCTGCGCCCCTTCCTCTCCC;RSEQ=TCGTCACCGCTTCCCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:3:2,1:67,159:226,3:0.0131:2,2:28.7:1:29.3:1:0.21655:4.71:58.3:6:0.0135:0:1 0/0:265:0:0,0:86,179:265,0:0:2,0:20.3:1:29.9:1:1:0:59.4:65.25:1:0:0.3 +16 68771547 . G C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.21989;SOR=0.46321;LSEQ=CCCCAGTGATGGGAGTGGGG;RSEQ=GTGGGTGGTGAGGGGCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:35:0,35:0,8:8,35:0.814:0,1:24.2:1:30.6:1:1:0:60:70:0.814:0:1.1 1/0:21:14:0,14:1,6:7,14:0.6667:2,1:26.1:1:29.9:1:0.33333:0:60:28:0.6667:0:1.1 +16 68771905 . A C 69 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGTCTAAGGAAAGTGGGGT;RSEQ=CTGGAGAATAAAGACATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:24.6:1:30:1:1:0:60:4:0.6667:0:1.4 1/1:1:1:1,0:0,0:0,1:1:0,0:32:0:32:0:1:0:60:2:1:0:1 +16 68772371 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2323;SOR=Inf;LSEQ=GGAGGGGTTGGAAAGGGGCC;RSEQ=AGAAATTGCACTCCCACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:25,169:194,0:0:2,0:24.4:1:31.6:1:1:0:60:47.5:1:0:0.1 0/1:181:2:1,1:44,135:179,2:0.011:2,2:11.5:1:27.5:1:0.43646:3.05:60:4:0.0114:0:1.5 +16 68835867 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24079;SOR=0;LSEQ=AATCCAGGTTTCTCAGCCTT;RSEQ=GTACCGTTGACATTTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:14,156:170,2:0.0116:2,2:11:1:28:1:0.16728:10.80:60:4:0.0117:0:1 0/0:178:0:0,0:24,154:178,0:0:2,0:21.3:1:30.2:1:1:0:60:34.6:1:0:0.1 +16 68835912 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05231;SOR=Inf;LSEQ=TGATTTTGTGTTGTAGGGGT;RSEQ=GTCCTGTGCACTGTGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:0,82:82,0:0:1,0:24.3:1:30.6:1:1:0:60:81:1:0:0.1 0/1:50:3:0,3:0,47:47,3:0.06:1,0:28.7:1:29.7:1:1:0:60:6:0.0612:0:1 +16 68842244 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21431;SOR=Inf;LSEQ=GCCCACAGAAGGCTGGGGAC;RSEQ=CTGTCTGGCTAGGTTGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:197,23:220,0:0:2,0:24.3:1:30.6:1:1:0:59.9:109:1:0:0.1 0/1:191:2:1,1:166,23:189,2:0.0105:2,2:17.5:1:31:1:0.2361:7.08652:60:4:0.0107:0:1 +16 68842797 . C A 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37295;SOR=3.91705;LSEQ=ACACCGGGGTAACATCCACC;RSEQ=AGGATTTTTTGGTCAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:1,0:68,197:265,1:0.0038:2,0:1:0:26:0:0.2594:0:60:2:0.0038:0:1 0/1:274:4:2,2:66,204:270,4:0.0146:2,2:23.8:1:25.3:1:0.25785:3.08:60:3:0.0112:0:1.8 +16 68842895 . G A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01212;SOR=0.15287;LSEQ=TGACCTGTTGCTAAGGAGAA;RSEQ=TGATGGGAGAACGTGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:16:0,16:0,36:36,16:0.3077:1,1:25.3:1:31.7:1:1:0:58.3:32:0.3077:0:1 0/1:32:2:0,2:2,28:30,2:0.0625:2,0:22.5:1:28.5:1:1:0:60:4:0.0625:0:1 +16 68844267 . G T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10694;SOR=0;LSEQ=ATATCCACTAATGAGAATCT;RSEQ=AATACTCAGAAAGACTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:78,201:279,3:0.0106:2,2:10.7:1:27.7:1:0.19483:5.12:60:6:0.0108:0:1 0/0:311:0:0,0:94,217:311,0:0:2,0:21.1:1:30.6:1:1:0:59.9:50.833:1:0:0.1 +16 68845894 . G AGA 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.31236;SOR=0.67476;LSEQ=TAAGCTTTGCATCTAAGCTT;RSEQ=TGCCCAGAGGTTCCGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:30:21,9:55,27:82,30:0.2679:2,2:19.6:1:30.5:1:0.82307:1.14:60:60:0.2679:0.0982:0.9 0/1:86:17:11,6:49,20:69,17:0.1977:2,2:21.4:1:29.3:1:0.76874:1.33176:60:16:0.1905:0.0581:1 +16 68846222 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21824;SOR=0;LSEQ=AGGTCTTTTGTTGTTCATGA;RSEQ=CTAAGTGTCACCACTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:36,151:187,2:0.0106:2,2:40:1:30:1:0.35405:4.15:60:4:0.0107:0:1 0/0:215:0:0,0:52,163:215,0:0:2,0:22.5:1:28.7:1:1:0:60:70.667:1:0:0.1 +16 68847433 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12399;SOR=0;LSEQ=TGGCAAGATGCAGAAACTGG;RSEQ=ATCCTCACAGCTGTTCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:4:1,3:90,248:338,4:0.0117:2,2:20.8:1:25.5:1:1:1.08844:60:3:0.0089:0:2.8 0/0:334:0:0,0:94,240:334,0:0:2,0:23:1:31.5:1:1:0:60:110.333:1:0:0.2 +16 68847443 . G C 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CAGAAACTGGCATCCTCACA;RSEQ=CTGTTCATACCCTTGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:67,227:294,0:0:2,0:23.2:1:32.3:1:1:0:59.9:41:0.9965:0:0.2 0/1:266:14:2,12:64,186:250,14:0.0526:2,2:25.9:1:30.4:1:0.52822:2.05979:60:28:0.0528:0:1.1 +16 68847463 . C CA 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50058;SOR=0;LSEQ=GCTGTTCATACCCTTGTCCC;RSEQ=TGGTATCTTCTTAGAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:19,163:182,2:0.0109:2,2:12:1:31:1:0.20611:8.39:60:4:0.0109:0.0054:0.5 0/0:162:0:0,0:24,138:162,0:0:2,0:20.3:1:31.1:1:1:0:60:53:1:0:0.2 +16 68847584 . T G 114 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.34446;SOR=0.26039;LSEQ=TGTAAGAAATCAAGAAACTG;RSEQ=GCTGTGTGTGGTGGCTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:0,13:0,13:13,13:0.5:1,1:21.2:1:31:1:1:0:59.8:12:0.48:0:1 0/1:5:1:0,1:0,4:4,1:0.2:0,0:12:0:32:0:1:0:60:2:0.2:0:1 +16 68853113 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49891;SOR=Inf;LSEQ=AACCATATAACTGAAGAAGC;RSEQ=CTTAAGCCGTTTTCAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:162,12:174,0:0:2,0:26.7:1:30:1:1:0:60:57:1:0:0.1 0/1:183:2:1,1:155,25:180,2:0.0109:2,2:14:0:30:0:0.26598:6.0992:60:4:0.0109:0:1.5 +16 68853671 . C T 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTACACATTATCGAACTC;RSEQ=GACTTCTAAGTGAGAACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:30.5:1:26.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 68855876 . G C 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12412;SOR=Inf;LSEQ=TTCATTACTGTTGCCAAGCT;RSEQ=CCACATTTTCTGTGTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:210,58:268,0:0:2,0:24.7:1:32.3:1:1:0:60:66:1:0:0.1 0/1:282:4:2,2:201,76:277,4:0.0142:2,2:25.8:1:31.3:1:0.30849:2.63413:60:8:0.0144:0:1.3 +16 68856168 . T A 40 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11206;SOR=0;LSEQ=TTTGGCAACTTTGCTCCAAC;RSEQ=GCCATGCTTCCCTTCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:3,0:72,209:281,3:0.0106:2,0:5.7:1:25.7:1:0.01788:0:60:6:0.0108:0:1.7 0/0:304:0:0,0:78,226:304,0:0:2,0:23.3:1:29.6:1:1:0:60:75:1:0:0.1 +16 68856782 . T A 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCTGGGTGCGATGGAAG;RSEQ=CACTCTGGCCCTGGAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:26:1:1:0:60:4:1:0:1 +16 68857191 . C A 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=9e-05;SOR=Inf;LSEQ=ATAAAACCCAAGCAGCTCTG;RSEQ=TCTCTTCACTCGGCTTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:59,2:61,0:0:1,0:26.2:1:31.9:1:1:0:60:11.2:1:0:0.4 0/1:44:10:10,0:34,0:34,10:0.2273:1,0:23.2:1:28.1:1:1:0:60:9:0.2432:0:1.1 +16 68857273 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.167;SOR=0;LSEQ=TTTATTTTCCTCCCCTGGTC;RSEQ=CATCATTTCTTTTTATTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:145,47:192,2:0.0103:2,2:21.5:1:28.5:1:0.43459:3.06319:60:4:0.0106:0:1 0/0:280:0:0,0:207,73:280,0:0:2,0:21.9:1:29.9:1:1:0:59.9:92.333:1:0:0.1 +16 68857289 . T C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17337;LSEQ=GGTCTCATCATTTCTTTTTA;RSEQ=TGCTTTCTCCAGCCCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:49:34,15:140,65:205,49:0.1929:2,2:23.3:1:33.1:1:1:1.05:60:98:0.1952:0:1 0/1:378:15:10,5:256,107:363,15:0.0397:2,2:26.3:1:32.9:1:0.7756:1.19565:59.1:30:0.0403:0:1 +16 68857441 . T C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.39518;LSEQ=TGTGACTGTGAAGGGGCCGC;RSEQ=GGCGTCTGTAGGAAGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:481:408:182,226:34,38:72,408:0.8482:2,2:23.8:1:30.3:1:0.70139:1.1108:59.9:67:0.8481:0:1.1 1/0:728:501:231,270:102,122:224,501:0.6882:2,2:26.7:1:29.5:1:0.93575:1.02:59.9:166:0.6898:0:1.1 +16 68857549 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18774;SOR=0;LSEQ=AGTAAGTCCAGCTGGCAAGT;RSEQ=ACTCAGCCTTTGACTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:29,140:169,2:0.0117:2,2:16.5:1:28.5:1:0.32095:4.76:60:4:0.0119:0:1.5 0/0:223:0:0,0:55,168:223,0:0:2,0:22.9:1:30.6:1:1:0:59.9:110.5:1:0:0.1 +16 68861656 . T C 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGCCCTGCTTGCCCCTC;RSEQ=GAGCTCTTCTCCATGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:27.5:1:1:0:60:4:1:0:1 +16 68862021 . C T 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12122;SOR=0;LSEQ=CTCTGTGATAGCTGCTGCTT;RSEQ=TGGCCTTCTTTATCTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:1,2:214,75:289,3:0.0102:2,2:13.3:1:21:1:0.17099:5.66554:60:2:0.007:0:1.3 0/0:298:0:0,0:220,78:298,0:0:2,0:22.7:1:30.7:1:1:0:60:297:1:0:0.1 +16 68862182 . A G 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAACGTTTATTACTATGATG;RSEQ=AGAAGGAGGCGGAGAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:18:8,10:177,283:460,18:0.0376:2,2:31.1:1:31.7:1:0.62828:1.28:60:36:0.0385:0:1 0/0:622:0:0,0:281,341:622,0:0:2,0:24.6:1:29.1:1:1:0:60:50.833:1:0:0.2 +16 68863752 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00027;SOR=0.17784;LSEQ=GCTCATCTCTAAGCTCAGGA;RSEQ=GAGTTGTGTCAAAAATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:21:0,21:1,91:92,21:0.1858:1,1:24.5:1:32:1:1:0:60:20:0.1802:0:1 0/1:129:5:0,5:2,122:124,5:0.0388:1,0:31.6:1:30.2:1:1:0:60:10:0.0397:0:1.2 +16 68863846 . C CT 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22222;SOR=Inf;LSEQ=GGAGCCCTGTTTTCCTTTTT;RSEQ=TTTTTTTTTCTTTTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:14,0:0:1,0:17:1:30.9:1:1:0:56.1:6:1:0:0 0/1:13:2:1,1:0,10:10,2:0.1538:0,2:18.5:1:30:1:0.16667:0:60:4:0.1818:0:0.5 +16 68863862 . C CT 32 v3;MAF0.05;MSI12;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.55;SOR=0.33678;LSEQ=TTTTCTTTTTTTTTCTTTTT;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:27.5:1:32:0:1:0:44:4:0.3333:0:0 0/1:9:1:0,1:1,7:8,1:0.1111:2,0:27:0:29:0:1:0:41:2:0.125:0:5 +16 68867145 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50985;SOR=Inf;LSEQ=CTTCTTGCCCCAGATGACAG;RSEQ=TGTGCCCTTCCTTTCACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:110,25:135,0:0:2,0:23.9:1:31.7:1:1:0:60:66.5:1:0:0.1 0/1:183:2:1,1:142,39:181,2:0.0109:2,2:31:1:28:1:0.39032:3.60751:60:4:0.0112:0:1 +16 68867397 . G A 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49912;SOR=0.55428;LSEQ=TGTACGGAGGCGGCGAGGAC;RSEQ=ACTAGGGGACTCGAGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:5:4,1:125,199:324,5:0.0152:2,2:13.4:1:27.6:1:0.07951:6.33:60:10:0.0154:0:1.4 0/0:472:4:3,1:187,281:468,4:0.0085:2,2:20.3:1:26:1:0.30748:4.49:56.3:3:0.0065:0:2.8 +16 68867427 . G A 32 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63578;SOR=2.32974;LSEQ=CTCGAGAGAGGCGGGCCCCA;RSEQ=ACCCATGTGCTGGGAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:1,0:67,150:217,1:0.0046:2,0:12:0:12:0:0.31193:0:60:0:0:0:2 0/1:282:3:3,0:82,197:279,3:0.0106:2,0:5:1:20.7:1:0.02671:0:60:2:0.0073:0:1.7 +16 68867456 . C T 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.15792;LSEQ=GCTGGGAAATGCAGAAATCA;RSEQ=GTTGCTGGTGGTTTTTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:23:4,19:16,76:92,23:0.2:2,2:20:1:31.1:1:1:1:60:46:0.2018:0:1.1 0/1:159:6:1,5:29,124:153,6:0.0377:2,2:22.2:1:31.2:1:1:1.16826:60:12:0.0387:0:1.2 +16 69726407 . G T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17143;SOR=0;LSEQ=CATCCACAGTCTGAAAACAC;RSEQ=TTATCTAATCAACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:19,2:0.0952:2,2:35:0:33:1:1:1.66897:60:4:0.1:0:1 0/0:29:0:0,0:18,11:29,0:0:2,0:30:1:30:1:1:0:59.1:58:1:0:0.2 +16 69726419 . ACAG A 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.61755;SOR=2.65986;LSEQ=GAAAACACGTTATCTAATCA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:1,0:16,11:27,1:0.0357:2,0:22:0:34:0:1:0:60:2:0.0357:0:0 0/1:33:3:2,1:17,13:30,3:0.0909:2,2:34:1:32.7:1:1:1.51:60:6:0.0909:0:0.3 +16 69727529 . ACAG A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.42619;SOR=1.69434;LSEQ=AGTAACTCTCCATCCCAGGA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:4:1,3:57,51:108,4:0.0357:2,2:30.8:1:32:1:0.35086:3.31952:60:8:0.0364:0:0 0/1:186:11:7,4:97,77:174,11:0.0591:2,2:27.6:1:32.8:1:0.75812:1.39:58.2:22:0.0591:0.0054:0.1 +16 69727536 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.13515;SOR=0;LSEQ=CTCCATCCCAGGAACAGCAG;RSEQ=AGCAGCAGCAACAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:62,58:120,2:0.0164:2,2:18.5:1:29:1:1:1.06835:60:4:0.0172:0:1.5 0/0:209:0:0,0:112,97:209,0:0:2,0:24.7:1:31.5:1:1:0:58.1:68.667:1:0:0.2 +16 69727565 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.12644;SOR=0;LSEQ=CAACAGCAGCAGCAACAGCA;RSEQ=CAGCAACAACAACAGAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:49,72:121,2:0.0163:2,2:41.5:1:31:1:1:1.46:60:4:0.0167:0:1 0/0:222:0:0,0:100,122:222,0:0:2,0:27.1:1:31.4:1:1:0:58.2:73:1:0:0.2 +16 69787697 . T A 27 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09259;SOR=0;LSEQ=CTCCTAAGCCAAGAGACAAT;RSEQ=CTTTAATTTTCTTTATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:10,13:23,2:0.08:2,2:48:0:27:1:1:1.29:60:4:0.087:0:1 0/0:56:0:0,0:24,32:56,0:0:2,0:26.8:1:28.8:1:1:0:59.6:55:1:0:0.2 +16 72821597 . G A 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=1;SOR=0.80984;LSEQ=GCCAGGCAGTGGTACGAGCC;RSEQ=CCGCCGCCGCCGCCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:56,233:289,3:0.0103:2,2:8.3:1:29:1:0.10169:8.24:60:6:0.0106:0:1.3 0/0:240:2:1,1:55,180:235,2:0.0083:2,2:2:1:26.5:1:0.41751:3.25:60:4:0.0085:0:1 +16 72821612 . G A 24 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=1;SOR=1.27839;LSEQ=GAGCCGCCGCCGCCGCCGCC;RSEQ=CCGCCACCGCCGCCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:47,127:174,2:0.0114:2,2:18:0:32:0:0.47221:2.68:60:4:0.0116:0:1.5 0/1:138:2:2,0:36,99:135,2:0.0145:2,0:1:0:24:1:0.07546:0:60:4:0.0149:0:1 +16 72821615 . G A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.00566;SOR=Inf;LSEQ=CCGCCGCCGCCGCCGCCGCC;RSEQ=CCACCGCCGCCGCCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:63,116:179,0:0:2,0:9.4:1:31.4:1:1:0:59.9:24.571:1:0:0.4 0/1:134:6:2,4:47,80:127,6:0.0448:2,2:11.3:1:30.2:1:1:1.17364:50.8:12:0.0465:0:2.2 +16 72821621 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=3;SSF=0.10909;SOR=0.4093;LSEQ=CCGCCGCCGCCGCCGCCACC;RSEQ=CCGCCGCCGCCGCCACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:16:2,14:97,80:177,16:0.0821:2,2:6.8:1:29.1:1:0.00124:8.40871:59.4:15:0.0789:0:2 0/1:142:5:3,2:71,65:136,5:0.0352:2,2:5:1:28.4:1:1:1.37:60:10:0.0365:0:1.4 +16 72821622 . C T 29 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.58031;SOR=2.64565;LSEQ=CGCCGCCGCCGCCGCCACCG;RSEQ=CGCCGCCGCCGCCACTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:102,93:195,1:0.0051:2,0:1:0:25:0:0.47959:0:60:2:0.0052:0:1 0/1:149:2:1,1:80,67:147,2:0.0134:2,2:6.5:1:29.5:1:1:1.1926:60:4:0.0137:0:1 +16 72821625 . C T 45 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.25087;SOR=0;LSEQ=CGCCGCCGCCGCCACCGCCG;RSEQ=CGCCGCCGCCACTGCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:1,2:107,74:181,3:0.0163:2,2:7.7:1:28.7:1:0.57007:2.87517:60:6:0.0168:0:1 0/0:162:0:0,0:95,66:161,0:0:2,0:8.2:1:31.3:1:1:0:59.4:79.5:1:0:0.4 +16 72821642 . ACCG A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=1.00051;LSEQ=CCGCCGCCGCCGCCACTGCC;RSEQ=CCGCCGCCGCCGGTGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:6:5,1:209,72:281,6:0.0208:2,2:22.3:1:33:1:1:1.72:60:12:0.0208:0:1.3 0/1:337:7:5,2:231,97:328,7:0.0208:2,2:16.3:1:31.1:1:1:1.05:60:14:0.0208:0:0.3 +16 72821645 . G A 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.76222;SOR=0.71129;LSEQ=CCGCCGCCGCCACTGCCACC;RSEQ=CCGCCGCCGCCGGTGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:6:4,2:221,74:295,6:0.0195:2,2:20.7:1:30.3:1:0.64451:1.49107:60:12:0.0203:0:1 0/1:359:5:4,1:240,106:346,5:0.0139:2,2:19.6:1:29.4:1:1:1.76:60:10:0.0145:0:1 +16 72821959 . CG C 126 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.01836;SOR=0.36214;LSEQ=TTTGTCTGGGGAAGGAGCCC;RSEQ=GGGGGGACTGGGGTTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1405:19:10,9:684,700:1384,19:0.0135:2,2:20.5:1:29.7:1:0.82093:1.14:60:38:0.0138:0.0036:0.4 0/0:1620:8:4,4:794,811:1605,8:0.0049:2,2:38.3:1:31.1:1:1:1.02:60:16:0.005:0:0.5 +16 72822008 . TTGC T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.28842;SOR=1.41542;LSEQ=GGCTGCTGCTGCTGCACTTT;RSEQ=TGCTGCTGCTGCTGTAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1075:17:13,4:492,563:1055,17:0.0158:2,2:30.1:1:31.2:1:0.02454:3.71:60:34:0.016:0:0.2 0/1:1214:27:13,14:562,624:1186,27:0.0222:2,2:27.9:1:29.1:1:1:1.03:59.8:54:0.0224:0.0025:0.2 +16 72822033 . CGCT C 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=1;SOR=0.99716;LSEQ=GCTGCTGCTGCTGTAGTTGC;RSEQ=GCTGCTGCTGCTGAATTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1069:15:7,8:543,508:1051,15:0.014:2,2:22.1:1:30.4:1:0.79739:1.22137:59.7:30:0.0142:0.0019:0.1 0/1:1072:15:5,10:509,544:1053,15:0.014:2,2:28.1:1:31.4:1:0.30349:1.87026:60:30:0.0142:0:0.1 +16 72822296 . G A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15814;LSEQ=GTGGGGTCCGAAGTCAACGC;RSEQ=GCCTGCAGGGCCTGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1798:337:185,152:774,684:1458,337:0.1874:2,2:24.5:1:30.8:1:0.58563:1.08:60:36.444:0.185:0:1.1 0/1:2132:75:39,36:1077,977:2054,75:0.0352:2,2:25.5:1:29.9:1:1:1.01755:60:150:0.0356:0:1.2 +16 72822563 . TTGC T 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.59315;SOR=0.8839;LSEQ=GGAGGCTGCTGCACCTGTGG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1437:49:24,25:661,721:1382,49:0.0341:2,2:28.6:1:30.8:1:0.88541:1.05:59.9:48:0.0342:7e-04:0.2 0/1:1355:41:20,21:624,650:1274,41:0.0303:2,2:26.7:1:29.8:1:1:1.00799:59.2:82:0.0311:0.003:0.2 +16 72822585 . T G 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=16.01814;LSEQ=GCTGCTGCTGCTGCTGCTGC;RSEQ=GGGGGGGTTGCTGAGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1396:4:4,0:671,716:1387,4:0.0029:2,0:31:1:9.8:1:0.0552:0:60:0:0:0:2.3 0/1:1363:60:32,28:630,666:1296,60:0.044:2,2:25.2:1:29.4:1:0.51045:1.21:60:59:0.045:0:1.1 +16 72827758 . T C 323 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0088;LSEQ=CGTTTCTGCCCAGGCCGATC;RSEQ=CCGCTGTCACCAGATTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1320:1315:699,616:1,0:1,1315:0.9962:0,2:24.5:1:31.2:1:1:0:59.9:45.964:0.9984:0:1.1 1/0:1460:1019:529,490:225,212:437,1019:0.6979:2,2:24.7:1:29.9:1:0.90892:1.02:59.9:49.95:0.6947:0:1.2 +16 72828383 . C T 246 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01444;LSEQ=TCTTGGCTTCATGCCAGTGA;RSEQ=GGGACCGGATATGAGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:269:133,136:530,562:1092,269:0.1974:2,2:23.8:1:30.5:1:0.83817:1.04:60:37.429:0.1948:0:1.1 0/0:1416:5:2,3:720,690:1410,5:0.0035:2,2:19.2:1:28.8:1:0.68089:1.56472:60:10:0.0036:0:1 +16 72829426 . C T 199 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=16.44993;LSEQ=CTGTAAGCCTGTGAGGGCAT;RSEQ=GGGGTACTGCAGGATGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1675:7:1,6:851,817:1668,7:0.0042:2,2:1.6:1:28.3:1:0.06534:6.24404:60:14:0.0042:0:1 0/1:1672:108:49,59:777,783:1560,108:0.0646:2,2:23.1:1:29.5:1:0.42613:1.19473:60:107:0.0646:0:1.1 +16 72830248 . C T 186 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=75.37706;LSEQ=AGCTGCGGGGGTAGCTGAGC;RSEQ=GGCAAGGTCTGCAGCGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:851:1:0,1:391,458:849,1:0.0012:2,0:19:0:15:0:1:0:60:0:0:0:1 0/1:895:73:37,36:391,430:821,73:0.0816:2,2:23.8:1:30.2:1:0.62703:1.13:60:146:0.0824:0:1.1 +16 72830539 . C G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16959;LSEQ=TGTTTGGCAAACCTCTCGAG;RSEQ=TGTTTGAAAGGAAAGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1827:283:140,143:747,793:1540,283:0.1549:2,2:24.2:1:31.7:1:0.79589:1.04:59.9:55.6:0.1543:0:1.2 0/1:1991:60:28,32:939,988:1927,60:0.0301:2,2:30.2:1:31.1:1:0.79403:1.0861:60:120:0.0307:0:1.2 +16 72831026 . T G 195 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0;SOR=39.88977;LSEQ=AGAGTTGGTTCTGCTGCTGC;RSEQ=GCGGCAAGATCTGCTGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1294:2:1,1:628,664:1292,2:0.0015:2,2:9.5:1:9:0:1:1.06:60:0:0:0:5 0/1:1495:87:42,45:696,711:1407,87:0.0582:2,2:24.2:1:30.3:1:0.9121:1.04881:60:86:0.058:0:1.2 +16 72831196 . GTGC G 126 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.73055;SOR=0.88449;LSEQ=ATGTAGAAAGGGAAGAGGAG;RSEQ=TGCTGCTGCTGTAGTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1623:17:10,7:837,768:1605,17:0.0105:2,2:18.1:1:31:1:0.6331:1.31:59.7:34:0.0106:0.0025:0.1 0/0:1725:16:8,8:868,839:1707,16:0.0093:2,2:35.6:1:31.6:1:1:1.03455:60:32:0.0094:0:0.3 +16 72832135 . T A 330 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01139;LSEQ=ACAATTATGGTATGGTCCTC;RSEQ=GCCAGAGTGGGGTCTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1529:1521:747,774:2,0:2,1521:0.9948:0,2:24.9:1:31.3:1:0.2417:0:59.9:100.4:0.9967:0:1.1 1/0:1539:1052:520,532:250,237:487,1052:0.6836:2,2:23.7:1:30.1:1:0.51082:1.07914:59.9:149.286:0.6843:0:1.2 +16 72832377 . G A 189 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04323;LSEQ=CAGGCTACACTGATTACAGC;RSEQ=GTACTTGTACACATGGCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1538:64:29,35:725,749:1474,64:0.0416:2,2:27.5:1:31.6:1:0.60999:1.16811:60:128:0.0421:0:1.1 0/0:1602:3:3,0:804,792:1596,3:0.0019:2,0:1:0:27.7:1:0.2496:0:60:6:0.0019:0:1 +16 72832609 . G A 77 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00402;SOR=Inf;LSEQ=TTCTTTCCCAGATCCTCTGA;RSEQ=GTTTCTGTTAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:753:0:0,0:245,507:752,0:0:2,0:23.9:1:31:1:1:0:59.5:17.8:1:0:0.6 0/1:812:9:5,4:299,504:803,9:0.0111:2,2:13.3:1:24.3:1:0.30678:2.11:56.6:3.5:0.0091:0:2.8 +16 72863486 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTACAGTATAATGTAGT;RSEQ=TAATAAAGAAGAATAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:75,1:76,2:0.0256:1,2:36.5:1:31:1:0.05095:53.38568:60:4:0.0267:0:1 0/0:33:0:0,0:33,0:33,0:0:1,0:19.8:1:27.3:1:1:0:60:66:1:0:0.1 +16 72863548 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26719;SOR=0;LSEQ=AAATCTCCCTCCCACTCATC;RSEQ=TTTTTCTGGGCAGACTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:2,1:190,2:192,3:0.0154:1,2:32.7:1:30.7:1:0.04568:41.95002:60:6:0.0155:0:1 0/0:141:0:0,0:137,4:141,0:0:1,0:23.4:1:30.8:1:1:0:59.8:69.5:1:0:0.1 +16 72923189 . A T 34 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTTGAGGCCACAAATTG;RSEQ=CTACTCTTAATACTGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:27.3:1:22:1:1:0:60:2:0.6667:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 72923450 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0115;SOR=0.28207;LSEQ=AGAAAAAAAGACAGAAAGGC;RSEQ=GGCAGGCAACAATCCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:34:34,0:26,1:27,34:0.5574:1,1:21.3:1:30.3:1:0.44262:0:59.7:16:0.5614:0:1.3 0/1:27:7:7,0:18,2:20,7:0.2593:2,0:24.7:1:30:1:1:0:60:14:0.2593:0:1 +16 72923905 . C T 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGCCTTGGGTAAGCCACT;RSEQ=GAAGCGGCCACTGGCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:0:0,0:226,443:669,0:0:2,0:23.4:1:30.5:1:1:0:60:132.8:0.9985:0:0.1 0/1:699:80:30,50:230,388:618,80:0.1144:2,2:23.4:1:29.4:1:1:1.01:60:160:0.1158:0:1.2 +16 72923990 . G A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00067;SOR=Inf;LSEQ=ACATCTCCACAGCCAAACAG;RSEQ=ACAGTCTTTGATATGGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:1,158:159,0:0:1,0:25.6:1:32.9:1:1:0:59.8:158:1:0:0.1 0/1:110:8:0,8:0,102:102,8:0.0727:1,0:11.5:1:29.1:1:1:0:60:16:0.0734:0:1.6 +16 72924122 . T C 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATGGGGGTGGTTCCCCCA;RSEQ=GCTGTTCTTGTGATACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:9,5:0.3571:0,0:24.8:1:31.2:1:1:0:60:10:0.3846:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:9.5:1:31.5:1:1:0:60:4:1:0:0 +16 72924395 . GT G 32 d5;v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTGTGAGATTCCTTAGAGG;RSEQ=TTTTTTTTTTTTTTCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:33.5:1:29.5:1:1:0:41:4:1:0:3.5 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:32:0:1:0:60:4:1:0:0.5 +16 72983981 . GA G 30 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCCGGGAAAGGAGAAATA;RSEQ=AAAAAAAAAAAAGGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:38.5:1:30.5:1:1:0:51.5:4:0.6667:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:2:0:30:0:1:0:60:2:1:0:0 +16 72984280 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=Inf;LSEQ=AGGCCATGCCAGAGACTGTC;RSEQ=GACTCCTCCCCAGTGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:180,15:195,0:0:2,0:23.5:1:31.1:1:1:0:59.9:96.5:1:0:0.1 0/1:197:3:1,2:176,18:194,3:0.0152:2,2:18:1:26:1:0.02771:18.90933:60:6:0.0154:0:1 +16 72984336 . GA G 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CAACCCCCTCCTTTCAGAAA;RSEQ=GCGCCTGAGCCATAAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:0:0,0:411,192:603,0:0:2,0:26:1:30.3:1:1:0:59.9:39.2:1:0:0.1 0/1:721:18:12,6:470,229:699,18:0.025:2,2:24.2:1:30.5:1:1:1.02619:60:36:0.0255:0.0055:0.1 +16 72984340 . G A 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCTCCTTTCAGAAAGAGC;RSEQ=CCTGAGCCATAAGGAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:637:0:0,0:430,207:637,0:0:2,0:25.9:1:30.4:1:1:0:59.9:44.5:1:0:0.2 0/1:759:46:32,14:473,240:713,46:0.0606:2,2:20.4:1:28.6:1:0.74813:1.16:60:22:0.0589:0:1.3 +16 72984595 . C A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33455;LSEQ=GCAGTGCAGCTGGAAGTTGG;RSEQ=CTTGAGCTGGGTGTTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1484:234:121,113:607,639:1246,234:0.1577:2,2:24.2:1:29.7:1:0.43324:1.13:59.8:32.429:0.1569:0:1.2 0/1:1867:110:54,56:848,904:1752,110:0.0589:2,2:22.7:1:29:1:0.92183:1.03:60:109:0.0593:0:1.2 +16 72984791 . G A 175 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=24.76506;LSEQ=TTGGTCTGGATGAAGCTCTC;RSEQ=CCCAGGTTCATCAGCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1193:2:2,0:578,613:1191,2:0.0017:2,0:1:0:28:1:0.23615:0:56.5:4:0.0017:0:1 0/1:1577:63:28,35:708,804:1512,63:0.0399:2,2:22.6:1:29.3:1:0.7969:1.10065:60:126:0.0406:0:1.1 +16 72984941 . T A 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20399;SOR=Inf;LSEQ=GCTGAGGCACCCCCCAGCCC;RSEQ=CCGCCACCCTCAACTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:16,208:224,0:0:2,0:23:1:29.8:1:1:0:60:31:1:0:0.1 0/1:185:2:1,1:22,161:183,2:0.0108:2,2:6:0:32:0:0.23378:7.18:60:4:0.011:0:3 +16 72985163 . C CT 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTTAATATTTCCTTTT;RSEQ=TTTTTTTTTTTCCCGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:20:1:29.7:1:1:0:57.3:6:0.3333:0.0909:0.7 0/0:2:0:0,0:0,2:2,0:0:0,0:8:1:32.5:1:1:0:60:4:1:0:0 +16 72990932 . A G 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCCCTAGTCCTCTTATTGA;RSEQ=ATGATTGCCTCAGCTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:19:1:33:1:1:0:60:4:0.4:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:26:0:1:0:60:2:1:0:1 +16 72991286 . C T 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.71846;LSEQ=CACCATTCTCCCTGGTTAAA;RSEQ=TCCTATCATGAAAACAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:241:168,73:260,125:385,241:0.385:2,2:24.5:1:30.6:1:0.5968:1.11:60:79.333:0.3857:0:1.2 1/0:653:488:329,159:113,52:165,488:0.7473:2,2:22:1:29.8:1:0.84755:1.05014:59.9:161.667:0.7473:0:1.2 +16 72991660 . C G 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.62867;LSEQ=GGTTTGGTTTTTGGTTTGGT;RSEQ=GGCGAGGGGGCCCCGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1094:416:166,250:302,370:672,416:0.3803:2,2:26:1:31.7:1:0.11519:1.229:59.9:58.429:0.3794:0:1.5 1/1:1288:1034:447,587:120,128:248,1034:0.8028:2,2:24.7:1:30.9:1:0.15458:1.23091:59.9:93:0.8042:0:1.5 +16 72991696 . TGCC T 119 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.00719;SOR=0.15522;LSEQ=CAGGAGCTACTGATATTGGC;RSEQ=GCCGCCGCCGCAGCCACCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:886:13:8,5:394,477:871,13:0.0147:2,2:22.4:1:32.2:1:0.2721:1.94:60:26:0.0149:0.0023:1.4 0/0:868:2:0,2:407,451:858,2:0.0023:2,0:18.5:1:27:1:0.50085:0:60:4:0.0023:0.0012:0.5 +16 72991712 . GCCA G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCTGCCGCCGCCGCCGCA;RSEQ=CCGCCGCCGCCGCCGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:864:0:0,0:430,432:862,0:0:2,0:22.9:1:31.6:1:1:0:59.9:44.368:0.9988:0:0.6 0/1:814:25:13,12:391,384:775,25:0.0307:2,2:27.6:1:31.7:1:1:1.06:58.2:50:0.0316:0:0.6 +16 72991715 . A G 255 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGCCGCCGCCGCCGCAGCC;RSEQ=CCGCCGCCGCCGCCGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:853:294:153,141:268,282:550,294:0.3447:2,2:22.1:1:31.1:1:0.38609:1.14:60:97:0.346:0:1.6 0/0:806:0:0,0:83,79:162,0:0:2,0:22.9:1:28.5:1:1:0:60:39.5:0.9814:0:0.2 +16 72992197 . G A 189 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=85.02676;LSEQ=GCGTGCTGGTGATGGGGAAC;RSEQ=AAGCCCCCATCGTCACCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1460:1:1,0:725,733:1458,1:7e-04:2,0:1:0:27:0:0.4976:0:60:2:7e-04:0:1 0/1:1706:94:48,46:829,779:1608,94:0.0551:2,2:25.6:1:28.9:1:1:1.01984:60:22.5:0.0535:0:1.2 +16 72992221 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.62227;LSEQ=CCCCCATCGTCACCCTCTGT;RSEQ=CTTTCATTTGGTTCTGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1468:219:116,103:634,612:1246,219:0.1492:2,2:24.7:1:29.1:1:0.60805:1.09:60:218:0.15:0:1.2 0/1:1830:180:91,89:860,788:1648,180:0.0984:2,2:22:1:28.3:1:0.69496:1.06732:60:179:0.0988:0:1.2 +16 72992269 . G A 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTCTTTATTGGCACTTTC;RSEQ=TCAGCGAAGTCCAGCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1589:0:0,0:820,765:1585,0:0:2,0:23.6:1:31:1:1:0:60:65.042:0.9981:0:0.2 0/1:1915:73:45,28:961,880:1841,73:0.0381:2,2:22.3:1:29.5:1:0.12124:1.47:59.9:146:0.0387:0:1.2 +16 72992443 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.31744;SOR=1.09957;LSEQ=TGGAGCACGTTAGGCATTAA;RSEQ=GGGGAGTTAGAAATGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1666:249:127,122:710,705:1415,249:0.1495:2,2:24:1:30.8:1:0.83679:1.03:59.9:48.8:0.1477:0:1.2 0/1:2044:331:170,161:860,839:1699,331:0.1619:2,2:22.5:1:30.1:1:0.81036:1.03:60:330:0.1626:0:1.2 +16 72992614 . TTCC T 108 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.83037;SOR=1.11009;LSEQ=TCTTCTTCCTCCTCCTCTTC;RSEQ=TCCTCCTCCTCCGCCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1105:10:5,5:516,577:1093,10:0.009:2,2:30.5:1:31.9:1:1:1.12:58.5:20:0.0094:0.0018:0.8 0/1:1096:11:5,6:503,580:1083,11:0.01:2,2:32.9:1:31.5:1:1:1.04066:60:22:0.0103:0:0.2 +16 72992667 . C G 155 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=29.2412;LSEQ=TTCCTCCTCCGCCTCCTCTT;RSEQ=GGCTGGCTCTACCTTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1213:1:0,1:665,547:1212,1:8e-04:2,0:30:0:33:0:0.45177:0:60:2:8e-04:0:1 0/1:1315:31:18,13:684,596:1280,31:0.0236:2,2:26.7:1:31.4:1:0.71646:1.21:60:62:0.0238:0:1.1 +16 72992763 . T G 209 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGCCCTCTGAGGATTTGG;RSEQ=AGGACTGGAAGCCAGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1383:0:0,0:676,705:1381,0:0:2,0:25.7:1:29.1:1:1:0:60:75.722:0.9985:0:0.2 0/1:1551:118:57,61:655,774:1429,118:0.0761:2,2:24:1:30.4:1:0.63156:1.10:59.9:117:0.0763:0:1.3 +16 72993586 . G C 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACTCCCACAGGCGCCCCC;RSEQ=CCCTGGGTCAGCTGGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1284:0:0,0:620,659:1279,0:0:2,0:24.9:1:30.9:1:1:0:60:57.136:0.996:0:0.2 0/1:1349:94:45,49:598,646:1244,94:0.0697:2,2:18.9:1:29.7:1:1:1.00798:59.8:30.333:0.0694:0:1.3 +16 72993622 . C T 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14556;LSEQ=CTCAGGCTCTCCACAATGTA;RSEQ=GCGGAGCCGTCCGGCTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1275:196:88,108:492,586:1078,196:0.1537:2,2:24.4:1:30.7:1:0.87626:1.03039:60:97:0.1546:0:1.3 0/1:1437:37:16,21:684,711:1395,37:0.0257:2,2:19.5:1:29.1:1:0.50983:1.26245:60:36:0.0255:0:1.3 +16 72993706 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1477;LSEQ=CCCTCCTCACCGGTGTCGCT;RSEQ=GCGCTCTCCTCTCTCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:193:92,101:586,551:1137,193:0.1449:2,2:22.8:1:30.2:1:0.35019:1.16742:60:63.333:0.1454:0:1.3 0/1:1516:37:17,20:716,763:1479,37:0.0244:2,2:22.1:1:28.5:1:0.86813:1.10391:60:74:0.0248:0:1.3 +16 72993708 . C T 193 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=48.62386;LSEQ=CTCCTCACCGGTGTCGCTGG;RSEQ=GCTCTCCTCTCTCAGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1331:2:1,1:679,648:1327,2:0.0015:2,2:17.5:1:29:1:1:1.04782:60:4:0.0015:0:1 0/1:1495:102:53,49:664,724:1388,102:0.0682:2,2:24.2:1:29:1:0.47257:1.18:60:50:0.0684:0:1.2 +16 72993831 . A C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.86369;LSEQ=CTCCTTGCTGGCGGGCTCGG;RSEQ=GGGGGGCCCGGCCGACGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1051:155:80,75:464,429:893,155:0.1475:2,2:24.8:1:31:1:1:1.01397:59.8:37.75:0.1486:0:1.3 0/1:1096:501:263,238:297,292:589,501:0.4571:2,2:24.8:1:30.1:1:0.50414:1.09:60:49.1:0.4615:0:1.2 +16 72993860 . G A 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14943;LSEQ=CGGCCGACGCGGTGCTCTCC;RSEQ=CGAGGCGCTCATTGAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:993:424:231,193:321,246:567,424:0.427:2,2:25.1:1:30.3:1:0.51849:1.09013:60:105:0.4312:0:1.1 0/1:1029:103:53,50:481,441:922,103:0.1001:2,2:24.3:1:28.7:1:0.91742:1.02894:60:19.6:0.0976:0:1.1 +16 72993925 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.64251;LSEQ=TGGCTCTCGCCTGTGGACTG;RSEQ=TCCATGCTACTGGGTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1423:229:118,111:599,594:1193,229:0.1609:2,2:25.9:1:29.7:1:0.71897:1.05:60:56.25:0.1606:0:1.3 0/1:1568:172:82,90:716,680:1396,172:0.1097:2,2:23.9:1:29.2:1:0.37533:1.15556:59.9:171:0.1105:0:1.1 +16 72994134 . AAG A 63 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.38512;SOR=0.30305;LSEQ=GGGAGGAGGGAGAGAGGGGA;RSEQ=AGAGAGAGAAAGGAAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:4:0,4:10,284:294,4:0.0134:1,0:26.8:1:31.8:1:1:0:60:8:0.0137:0.0034:0.5 0/0:244:1:0,1:16,227:243,1:0.0041:2,0:27:0:32:0:1:0:60:2:0.0042:0:0 +16 72994159 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52953;SOR=0;LSEQ=AGAGAGAAAGGAAAGAGGTT;RSEQ=GGAGGGCCGAGGCTGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:2,189:191,2:0.0104:1,2:26.5:1:30.5:1:0.03093:77.34:60:4:0.0108:0:1 0/0:116:0:0,0:0,116:116,0:0:1,0:22.3:1:30.8:1:1:0:60:57:1:0:0.3 +16 72994164 . G A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.8599;SOR=0.91664;LSEQ=GAAAGGAAAGAGGTTAGGAG;RSEQ=GCCGAGGCTGAGGTCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:25:0,25:3,141:144,25:0.1479:1,1:24:1:31.8:1:1:0:59.4:11.5:0.1438:0:1.3 0/1:102:14:0,14:0,88:88,14:0.1373:1,1:16.6:1:31.7:1:1:0:60:28:0.1429:0:1 +16 72994419 . T C 39 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGCCAGCATAGCTTCGA;RSEQ=GGGCCACAGTGGAGAACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:36.7:1:24.7:1:1:0:60:2:1:0:2.3 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:29.5:1:1:0:60:4:1:0:1 +16 72994891 . T C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCCTGTCTCCTCCACCCA;RSEQ=ACCAGTCAAGCTCCCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:36:0:27:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:31.5:1:1:0:60:4:1:0:2 +16 73350538 . A G 50 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGTCTTATACTTGTTGGG;RSEQ=ATCCCCCACTCCACTAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:11.7:1:32:1:1:0:50:6:1:0:1.3 1/1:2:2:2,0:0,0:0,2:1:0,0:33.5:1:31:1:1:0:60:4:1:0:1 +16 73350590 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACCTCAGCAAATTCTTGC;RSEQ=ATAAAATGCTTGATTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:7,1:8,2:0.2:2,2:19.5:1:32:1:0.37778:5.29155:60:4:0.2222:0:1 0/0:3:0:0,0:1,2:3,0:0:2,0:12.3:1:26.7:1:1:0:60:6:1:0:0.3 +16 73367952 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGATGCAATCAGACAGA;RSEQ=AAGAGGATGGGGTCAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:28:1:34:0:1:0:60:4:0.2857:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:36.3:1:32:1:1:0:60:6:1:0:0.3 +16 73367985 . C T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=TCAAGGACATGGCTTATGTG;RSEQ=TGAAAGAGGAAGGAGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:11,2:13,0:0:2,0:22.5:1:33:1:1:0:60:26:1:0:0.2 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:13:0:27.5:1:1:1.67325:60:4:0.1538:0:1 +16 74639138 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGACGCCTTTCCTCCTCTG;RSEQ=AGCATAAAACTGCCTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:28.5:1:1:0:60:4:1:0:1 +16 74640735 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17495;SOR=0;LSEQ=GGGAAAGGCGGCTGCGGCGG;RSEQ=TGAGGCTGCTGTTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:46,28:74,2:0.0263:2,2:42.5:1:29.5:1:1:1.63167:60:4:0.0274:0:1 0/0:105:0:0,0:59,46:105,0:0:2,0:24.3:1:30.7:1:1:0:59.5:104:1:0:0.2 +16 74640753 . TTGC T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.27717;SOR=Inf;LSEQ=GGCTGAGGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:48,37:85,0:0:2,0:26.7:1:30.2:1:1:0:59:41.5:1:0:0.2 0/1:128:3:2,1:66,59:125,3:0.0234:2,2:21.7:1:30.7:1:1:1.78:60:6:0.0236:0:0.7 +16 74640758 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51509;SOR=Inf;LSEQ=AGGCTGCTGTTGCTGTTGCT;RSEQ=CTGCTGCTGTTGCTGCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:48,37:85,0:0:2,0:26.4:1:31.6:1:1:0:59:27.333:1:0:0.2 0/1:124:2:1,1:63,59:122,2:0.0161:2,2:22:0:30.5:1:1:1.0672:60:4:0.0163:0:1.5 +16 74640810 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15034;SOR=0;LSEQ=TGAGGCAGCTGGGGCAGCTG;RSEQ=TGACCCGCCGGGCCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:12,34:46,2:0.0417:2,2:21.5:1:32:0:0.47252:2.76:60:4:0.0426:0:1 0/0:75:0:0,0:28,47:75,0:0:2,0:20.8:1:31:1:1:0:60:74:1:0:0.3 +16 74640828 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08062;SOR=0;LSEQ=TGCTGACCCGCCGGGCCGCC;RSEQ=CCTCCGGCCTGCCCTACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:2,1:7,26:33,3:0.0833:2,2:12:1:28.7:1:0.1479:6.91:60:6:0.0833:0:1 0/0:46:0:0,0:14,32:46,0:0:2,0:18.3:1:30.5:1:1:0:60:92:1:0:0.3 +16 74640849 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18659;SOR=Inf;LSEQ=CCTCCGGCCTGCCCTACGAA;RSEQ=GACACAAAGTTGGCCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:1,22:23,0:0:1,0:19.7:1:32.3:1:1:0:60:46:1:0:0 0/1:18:2:1,1:0,16:16,2:0.1111:1,2:5.5:1:27.5:1:0.11111:0:60:4:0.1111:0:1.5 +16 75226838 . T A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGCAACACAGCCCTTGGG;RSEQ=CACAGACCAGGCAGAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:22.5:1:30:1:1:0:60:4:1:0:0 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:23.5:1:28:1:1:0:60:4:0.2857:0:1.5 +16 78785550 . C T 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AAATAGAGTTTGATATTAAA;RSEQ=AATACTCCAAGAAAGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:125,83:208,0:0:2,0:25.1:1:32.1:1:1:0:60:103:1:0:0.6 0/1:342:19:11,8:182,139:321,19:0.0556:2,2:28.4:1:28.5:1:1:1.05:60:38:0.0567:0:2.1 +16 78785563 . A C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41881;LSEQ=TATTAAACAATACTCCAAGA;RSEQ=AGCCATTTCTGCAGAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:230:139:77,62:54,37:91,139:0.6043:2,2:24.2:1:32.2:1:0.58773:1.17432:60:68.5:0.6062:0:1.2 0/1:372:145:79,66:117,110:227,145:0.3898:2,2:24.7:1:30.9:1:0.59593:1.12:60:47.333:0.388:0:1.2 +16 78785618 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16648;SOR=0;LSEQ=CAGTTCCTTACCAACACGTA;RSEQ=ACATGTTGTGATGAAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:80,117:197,2:0.0101:2,2:24:1:28.5:1:1:1.46:60:4:0.0102:0:2.5 0/0:288:0:0,0:114,174:288,0:0:2,0:24.6:1:30.4:1:1:0:60:31:1:0:0.4 +16 78785640 . AAAGG A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=4.000;MSILEN=4;SSF=0.06824;SOR=Inf;LSEQ=CATGTTGTGATGAAAGAAGG;RSEQ=AAGGAAGGAAGGAGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:53,101:154,0:0:2,0:24.2:1:30.3:1:1:0:60:153:1:0:0.4 0/1:192:5:1,4:60,127:187,5:0.026:2,2:28.6:1:30.8:1:1:1.88428:59:10:0.0265:0:0.4 +16 78785685 . AAG A 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.51611;LSEQ=AAGAAGGAGGGAGGGAGGGA;RSEQ=AGAGAGAGAGAAAAGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:0,2:8,66:74,2:0.0263:2,0:31.5:1:32.5:1:1:0:60:4:0.027:0:0 0/1:73:1:0,1:9,63:72,1:0.0137:2,0:21:0:32:0:1:0:60:2:0.0137:0:0 +16 78785905 . T TAAG 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATTGGCATTTTTCTTTAAA;RSEQ=AAGGAGGAGGATGAGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:32.5:1:29.2:1:1:0:60:4:0.5:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 79008267 . T C 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=TAAACATCTTAATTGAACAG;RSEQ=ACGTGGGTTCTTCCCTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:33.8:1:29.5:1:1:0:60:8:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:31.5:1:33.5:1:1:0:60:4:1:0:1.5 +16 79008469 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16857;SOR=Inf;LSEQ=CCTTAAATATTGTGCAATGT;RSEQ=CAGGGAATTATTTCAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:95,22:117,0:0:2,0:22.2:1:32.5:1:1:0:60:116:1:0:0.1 0/1:82:2:1,1:58,22:80,2:0.0244:2,2:21:1:31:1:0.48479:2.60055:60:4:0.0244:0:2 +16 79008482 . T G 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAATGTGCAGGGAATTATT;RSEQ=CAGTTTTGTTTTTTATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:106,38:144,0:0:2,0:23.3:1:31:1:1:0:60:143:1:0:0.3 1/0:106:54:36,18:37,15:52,54:0.5094:2,2:25.5:1:31.5:1:0.67777:1.23089:60:108:0.5192:0:1.1 +16 79008499 . T G 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00039;SOR=Inf;LSEQ=ATTTCAGTTTTGTTTTTTAT;RSEQ=TAGCACAAACCTAAATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:130,68:198,0:0:2,0:24.2:1:30.8:1:1:0:60:98:1:0:0.5 0/1:146:9:7,2:84,53:137,9:0.0616:2,2:19.6:1:32.3:1:0.48372:2.20:60:18:0.0621:0:1.7 +16 79008502 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18334;SOR=Inf;LSEQ=TCAGTTTTGTTTTTTATTTA;RSEQ=CACAAACCTAAATATTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:135,74:209,0:0:2,0:24.4:1:32.9:1:1:0:60:208:1:0:0.6 0/1:157:2:1,1:95,60:155,2:0.0127:2,2:16.5:1:26:1:1:1.57849:60:4:0.0128:0:1.5 +16 79008568 . C T 239 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCTGTCCTGAAGAGGAGGA;RSEQ=AGATTATTCTGTGGCTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:295:295:141,154:0,0:0,295:1:0,2:26.8:1:29.2:1:1:0:60:58:1:0:1.1 0/1:255:106:53,53:77,72:149,106:0.4157:2,2:28.4:1:28.4:1:0.80076:1.06916:60:34.333:0.412:0:1.2 +16 79008612 . T C 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GGTGTTTACAGAGTTGCCAC;RSEQ=TTGCCAAACCCCAAGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:91,138:229,0:0:2,0:25.9:1:30.8:1:1:0:60:75.333:1:0:0.9 0/1:226:15:6,9:89,121:210,15:0.0664:2,2:31.7:1:30.5:1:1:1.10286:60:30:0.0664:0:1.8 +16 79008629 . C G 213 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTTTGCCAAACCCCAAGA;RSEQ=CCACACTTGGTCTCTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:62,121:183,0:0:2,0:24:1:31.9:1:1:0:60:182:1:0:0.7 1/0:181:107:39,68:25,48:73,107:0.5912:2,2:26.9:1:31.6:1:0.87413:1.10:60:106:0.5955:0:1.2 +16 79008692 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50858;SOR=0;LSEQ=TTCAGAATGGGATGTTTAGG;RSEQ=CGTAATCTTCTGAGACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:2,44:46,2:0.0417:1,2:25.5:1:30:1:0.12234:18.16:60:4:0.0417:0:1 0/0:34:0:0,0:1,33:34,0:0:1,0:22.9:1:32.2:1:1:0:60:68:1:0:0.6 +16 79109753 . A C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01063;SOR=3.24276;LSEQ=CTTATAACTATCTCAAAAAA;RSEQ=CATATTAAGTTATTTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:13:13,0:39,0:39,13:0.25:1,1:22.4:1:32.2:1:1:0:60:12:0.2353:0:1.3 1/0:44:23:22,1:21,0:21,23:0.5227:1,1:27.5:1:32.7:1:1:0:60:46:0.5227:0:1.1 +16 79109842 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.78114;LSEQ=TTAGTTAACATCTGCTCTAA;RSEQ=GTTGGATCATGTGTGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:71:46,25:152,69:221,71:0.2432:2,2:24:1:30.3:1:0.56064:1.19646:60:70:0.2414:0:1.2 0/1:307:145:98,47:95,67:162,145:0.4723:2,2:23.5:1:29.4:1:0.12414:1.47:59.9:71.5:0.4719:0:1.2 +16 79109859 . A G 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06037;SOR=0;LSEQ=TAACGTTGGATCATGTGTGG;RSEQ=GTCCCCAGTTTTCAACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:4:2,2:217,153:370,4:0.0107:2,2:17.8:1:26.5:1:1:1.41692:60:3:0.0082:0:1.5 0/0:380:0:0,0:212,167:379,0:0:2,0:25.3:1:28.6:1:1:0:60:33.455:0.9973:0:0.7 +16 79109935 . C T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.44385;LSEQ=TCTTACAGTATATGTAGAAC;RSEQ=ATTTTCTTGAAAATGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:71:27,44:98,160:258,71:0.2158:2,2:25.3:1:29.8:1:1:1.00:60:142:0.2185:0:1.1 1/0:325:179:67,112:58,88:146,179:0.5508:2,2:24.8:1:28.4:1:0.73119:1.10143:60:178:0.5511:0:1.2 +16 79167309 . T G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGATGTCAATATAAACTA;RSEQ=GACACACATTCATATTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28.5:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 79167548 . G A 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16111;LSEQ=AAGTGCTACTTTATATTTCT;RSEQ=CTGTCCTTGCCGGTGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:70:67,3:23,1:24,70:0.7447:1,1:24.4:1:28:1:1:1.02955:60:69:0.7419:0:2 0/1:82:26:24,2:52,4:56,26:0.3171:2,2:22.2:1:27.6:1:1:1.08226:60:52:0.3171:0:2 +16 79167560 . G C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16553;LSEQ=ATATTTCTGCTGTCCTTGCC;RSEQ=GTGGCCTGCACTGGGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:97:86,11:26,5:31,97:0.7578:2,2:21.1:1:31.4:1:0.53525:1.50:60:96:0.7559:0:1.8 0/1:112:38:33,5:63,10:73,38:0.3393:2,2:19.9:1:29.9:1:1:1.05:60:37:0.3333:0:1.7 +16 79167688 . A G 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.17982;LSEQ=TAACTAGGCGTATAGAATTG;RSEQ=GGGGAAATGCAGGATGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:495:391:192,199:47,56:103,391:0.7899:2,2:27.6:1:31.1:1:0.57997:1.15:60:54.857:0.7918:0:1.1 0/1:546:220:107,113:153,171:324,220:0.4029:2,2:26.8:1:30.2:1:0.79316:1.06:60:109:0.4067:0:1.1 +16 79167824 . T G 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01285;SOR=Inf;LSEQ=TGTCAGGGAAGAGATTAATA;RSEQ=AATACTCAGTGAATTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:2,55:57,0:0:1,0:24.1:1:29.1:1:1:0:60:56:1:0:0.1 0/1:57:7:0,7:2,48:50,7:0.1228:1,0:30.1:1:31.9:1:1:0:60:14:0.125:0:1.1 +16 79167945 . A G 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01786;SOR=0;LSEQ=AGAGTTTGTTTCTTCCTGCT;RSEQ=TGGCCATAGAGGTTTGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:20.2:1:33.4:1:1:0:60:10:1:0:1.2 0/0:3:0:0,0:0,3:3,0:0:0,0:19:1:30.7:1:1:0:60:6:1:0:0 +16 79168070 . AT A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATTGGGATTATCTTATG;RSEQ=TTTTTTTTCTCTTTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:43:1:33:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 79890072 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49826;SOR=Inf;LSEQ=TTGAAGAGTGTTTTCCAGCT;RSEQ=GTTTCCATTCTCCTCATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:18,0:0:2,0:19.6:1:31.1:1:1:0:60:36:1:0:0.1 0/1:24:2:1,1:14,8:22,2:0.0833:2,2:10:0:31.5:1:1:1.70775:60:4:0.087:0:1 +16 79979756 . A T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTATAAAACACTGCTCT;RSEQ=GCTAAGGGACCTAGTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:28:1:1:0:60:4:1:0:1 +16 79979968 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGCCTTAGGGCTGTCTC;RSEQ=CAGGTCTCCAGAGAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:22:1:32:1:1:0:43.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 79980350 . G T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25404;SOR=0;LSEQ=CCTGTGACATTTCCAACAAT;RSEQ=CAACACTATTTGGTAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:3:2,1:133,71:204,3:0.0145:2,2:24:1:23.3:1:1:1.07:60:2:0.0099:0:1.3 0/0:173:0:0,0:111,62:173,0:0:2,0:22.7:1:31.4:1:1:0:59.8:172:1:0:0.6 +16 79980354 . C T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21311;SOR=Inf;LSEQ=TGACATTTCCAACAATGCAA;RSEQ=ACTATTTGGTAAATATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:137,77:214,0:0:2,0:26.2:1:32.1:1:1:0:60:70.333:1:0:1 0/1:184:2:1,1:114,68:182,2:0.0109:2,2:6.5:1:28.5:1:1:1.67149:60:4:0.011:0:2.5 +16 79980355 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.21453;SOR=Inf;LSEQ=GACATTTCCAACAATGCAAC;RSEQ=CTATTTGGTAAATATTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:138,77:215,0:0:2,0:26.5:1:29.9:1:1:0:60:42:1:0:1 0/1:186:2:1,1:114,70:184,2:0.0108:2,2:26.5:1:28:1:1:1.62408:60:4:0.0109:0:1 +16 79980410 . A C 258 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00452;LSEQ=GGGATAAGAAATGACCTTTC;RSEQ=ATCTATATGGAGCAAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:288:287:153,134:1,0:1,287:0.9965:0,2:25.5:1:31.6:1:1:0:59.9:56.4:1:0:2.1 1/0:341:192:105,87:78,71:149,192:0.563:2,2:26.2:1:30.3:1:0.74266:1.10:59.8:47:0.5595:0:2.3 +16 79980425 . A T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24607;LSEQ=CTTTCAATCTATATGGAGCA;RSEQ=GTTAATTACTAAAAAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:299:239:123,116:30,30:60,239:0.7993:2,2:24.4:1:30.6:1:0.88566:1.06:59.9:78.667:0.8:0:2.5 0/1:360:178:92,86:94,88:182,178:0.4944:2,2:26.6:1:29.7:1:1:1.00:59.8:177:0.4958:0:2.6 +16 79980463 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28561;LSEQ=CAGCAATTGGTTGTAAAGGA;RSEQ=TGTTCTGCTGTCGTCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:256:203:83,120:19,34:53,203:0.793:2,2:27.4:1:30.6:1:0.53266:1.24:60:202:0.7922:0:2.3 1/0:320:167:72,95:67,86:153,167:0.5219:2,2:24.9:1:29.7:1:0.91062:1.02786:60:166:0.522:0:2.3 +16 79980525 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=0;LSEQ=GGTTATGAATTATCCTTGGA;RSEQ=GAAATATGGACACATGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:12,92:104,2:0.0189:2,2:13.5:1:31:1:0.23127:7.41:60:4:0.0189:0:1.5 0/0:106:0:0,0:25,81:106,0:0:2,0:22.6:1:30.2:1:1:0:60:212:1:0:0.5 +16 80160491 . A C 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54629;SOR=0;LSEQ=GGGGCACTTACTCCTAACAA;RSEQ=TTCACTCTAAAGACTTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:4,0:15,0:15,4:0.2105:1,0:11.5:1:27:1:1:0:60:3:0.1667:0:1.8 0/0:7:0:0,0:7,0:7,0:0:0,0:11.4:1:29.7:1:1:0:56.6:14:1:0:0.3 +16 80160551 . G A 164 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCCCTGTAACCTGCAAAG;RSEQ=GGAAGTAGCACCAGAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:42,0:0,0:0,42:1:0,1:22.5:1:30.5:1:1:0:60:41:1:0:1.3 0/1:25:6:6,0:19,0:19,6:0.24:1,0:26.2:1:28.7:1:1:0:56:12:0.24:0:1 +16 80160659 . G T 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0208;SOR=Inf;LSEQ=TTGTTGGCAGTTTATTTGAA;RSEQ=GCTCTTGTTTGTGAAATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:169,107:276,0:0:2,0:23.6:1:32.1:1:1:0:60:275:1:0:0.3 0/1:359:7:3,4:222,129:351,7:0.0195:2,2:8.3:1:28.9:1:0.43118:2.28899:60:14:0.0198:0:1.1 +16 80160745 . G C 264 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00177;LSEQ=TCTCTCATCTCTTTTCATCT;RSEQ=AAACACGATTATTATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:296:295:110,185:0,0:0,295:0.9966:0,2:24.6:1:32.2:1:1:0:60:97.333:0.9966:0:1.1 0/1:364:124:51,73:90,147:237,124:0.3407:2,2:23.9:1:30.9:1:0.57177:1.14:60:123:0.3417:0:1.1 +16 80160786 . TA T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.08968;SOR=0;LSEQ=TGCTTTTTGGTTCCAATTAT;RSEQ=AAAAAAAGATGAGCAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:0,3:31,108:139,3:0.0211:2,0:34.7:1:32:1:1:0:60:6:0.0213:0:1 0/0:174:0:0,0:49,125:174,0:0:2,0:22.6:1:29.2:1:1:0:60:86:1:0:0.4 +16 80160920 . C A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTAGGTGAGTGGAGTTGT;RSEQ=AGGGGATTGAGCCTCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:8,2:0.2:0,0:42.5:1:33:0:1:0:60:4:0.2:0:1.5 0/0:3:0:0,0:0,3:3,0:0:0,0:17:1:32:1:1:0:60:6:1:0:0 +16 80770070 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGTTCATCAGCTCCTGAA;RSEQ=CTAACTGCAAATGGTGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:27.5:1:1:0:60:4:1:0:1 +16 80771405 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08245;SOR=Inf;LSEQ=GCCACTGTATTAAACTGTAC;RSEQ=TTGCTCTAGGTACCGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:21,10:31,0:0:2,0:17.6:1:31.9:1:1:0:60:62:1:0:0.2 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:11.5:1:28:1:1:1.18321:60:4:0.1538:0:1 +16 80771438 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49521;SOR=0;LSEQ=CCGTGAGCATGGCTCTTCAT;RSEQ=CCAGCTGTTGCCTGGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:23,20:43,2:0.0444:2,2:31:1:29.5:1:1:1.14642:60:4:0.0444:0:1.5 0/0:41:0:0,0:23,18:41,0:0:2,0:23.9:1:27.4:1:1:0:60:40:1:0:0.2 +16 80771447 . TG T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21026;SOR=Inf;LSEQ=TGGCTCTTCATACCAGCTGT;RSEQ=CCTGGACTGTTGTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,23:49,0:0:2,0:31:1:31.4:1:1:0:59.8:11.25:1:0:0.2 0/1:42:2:1,1:22,18:40,2:0.0476:2,2:11.5:1:28.5:1:1:1.21636:60:4:0.0476:0:0 +16 81818459 . G C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCCAGGGCCTGGGGAGC;RSEQ=CCTTCACTCTAAGTCCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:28.5:1:1:0:60:4:1:0:1 +16 81819486 . C G 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGGTTCCTGAAGTTCATG;RSEQ=CCTGTTAACTAAACCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:185,8:193,0:0:1,0:23.8:1:32.8:1:1:0:60:63.333:1:0:0.1 0/1:193:33:32,1:158,2:160,33:0.171:1,1:23.3:1:30.7:1:0.43209:2.45404:60:66:0.1728:0:1.1 +16 81819768 . T C 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.78057;LSEQ=GTGGCCTGGAGCAAGACCGC;RSEQ=GACAAGATCGAGGGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1113:310:135,175:384,418:802,310:0.2785:2,2:23.7:1:30.2:1:0.20322:1.19067:60:61:0.2788:0:1.5 1/0:1516:785:373,412:354,375:729,785:0.5178:2,2:25:1:29.7:1:0.71862:1.0427:59.9:195.25:0.5193:0:1.5 +16 81819812 . T C 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTACTCGCTGGGTGGGGCAG;RSEQ=GTGGCCCGTCCTCTGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:775:0:0,0:296,479:775,0:0:2,0:24.3:1:30:1:1:0:60:95.875:1:0:0.6 0/1:1025:25:8,17:401,597:998,25:0.0244:2,2:23.2:1:30:1:0.53617:1.42687:60:24:0.0236:0:2.8 +16 81819820 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0029;SOR=1.38585;LSEQ=TGGGTGGGGCAGTGTGGCCC;RSEQ=TCCTCTGGGGCCCTGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:696:195:70,125:176,325:501,195:0.2802:2,2:24.5:1:30.8:1:0.86016:1.03:60:96.5:0.2805:0:1.7 0/1:896:314:115,199:214,368:582,314:0.3504:2,2:25.1:1:29.4:1:1:1.00628:60:51.333:0.3496:0:1.9 +16 81819853 . C T 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTGGCCTGAGCACCTGTCCA;RSEQ=CTTCCTGTCTTGTCATTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:80,327:407,0:0:2,0:24.9:1:31.3:1:1:0:59.9:49.875:1:0:0.4 0/1:494:19:4,15:97,378:475,19:0.0385:2,2:21.4:1:27.7:1:1:1.04:60:18:0.0376:0:1.8 +16 81887628 . G A 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGGGAAAAGGTCATCAA;RSEQ=GTCAAGGTCAACCGGACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:34:1:32:0:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81887820 . C T 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.28327;SOR=0;LSEQ=GGGTGAGCGGAAACCCCAAA;RSEQ=TCTTCAGACTCCAGGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:12,1:13,7:0.35:1,0:30.1:1:30.1:1:1:0:60:14:0.35:0:1.1 0/0:4:0:0,0:4,0:4,0:0:0,0:29:1:31:1:1:0:60:8:1:0:0.3 +16 81887903 . A G 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00101;SOR=0.11808;LSEQ=TCCATTTCCAGAAGGAGGGG;RSEQ=CACTGAGTCCAGACGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:24:24,0:61,2:63,24:0.2759:1,1:29.5:1:30.4:1:1:0:60:11:0.2619:0:3.1 0/1:47:2:2,0:43,2:45,2:0.0426:1,0:16.5:1:32:1:1:0:60:4:0.0444:0:2 +16 81887938 . T C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=0.33563;LSEQ=GCAGAGATAGCTTTGCGGGA;RSEQ=CCTGTTGGGGAAGGAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:56:55,1:98,0:98,56:0.3636:1,1:20.6:1:31.6:1:0.36364:0:60:27:0.3649:0:3.2 0/1:106:17:17,0:87,2:89,17:0.1604:1,1:16.8:1:32.9:1:1:0:60:34:0.165:0:2.4 +16 81887948 . G T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57048;SOR=2.88416;LSEQ=CTTTGCGGGATCCTGTTGGG;RSEQ=AAGGAAGGAGCCAGGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:1,0:177,1:178,1:0.0056:1,0:22:0:26:0:1:0:60:2:0.0056:0:4 0/1:125:2:2,0:121,2:123,2:0.016:1,0:30.5:1:30.5:1:1:0:60:4:0.0164:0:2.5 +16 81887957 . A C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=0.39784;LSEQ=ATCCTGTTGGGGAAGGAAGG;RSEQ=GCCAGGCTGTGCCTGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:70:69,1:122,2:124,70:0.3608:1,1:24.3:1:32.5:1:1:1.13:60:69:0.3613:0:3 0/1:153:28:28,0:119,6:125,28:0.183:1,1:23.8:1:32:1:0.59296:0:60:56:0.1854:0:1.9 +16 81887977 . G C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05421;LSEQ=AGCCAGGCTGTGCCTGGGCT;RSEQ=CAGTTGTGTGGCTGCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:107:96,11:141,17:158,107:0.4038:2,2:24.3:1:32.2:1:1:1.05:60:106:0.403:0:2.2 0/1:227:8:7,1:194,25:219,8:0.0352:2,2:24.1:1:31:1:1:1.10801:60:16:0.0357:0:2 +16 81888152 . A G 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.62233;LSEQ=GACTGCTGCTTCACCATCCT;RSEQ=TATGGCACTCAGTTCGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1217:388:188,200:404,424:828,388:0.3188:2,2:24.3:1:32:1:0.95094:1.01364:60:76.6:0.321:0:1.2 0/1:1410:318:149,169:511,580:1091,318:0.2255:2,2:22.8:1:31.1:1:1:1.00:60:52:0.2251:0:1.3 +16 81888237 . G C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.52386;LSEQ=CTCCTTCCCTGTGCCTTAGT;RSEQ=TCTTCCTGAAGAAGTTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:185:48,137:91,249:340,185:0.3517:2,2:24.1:1:32.6:1:0.91758:1.04301:60:36:0.3495:0:1.8 0/1:547:121:41,80:140,285:425,121:0.2212:2,2:24:1:30.9:1:0.91288:1.04:59.8:242:0.222:0:1.5 +16 81888274 . C A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.07271;LSEQ=CGCTAATAGCAGAATGCTCA;RSEQ=CCCTGCCTGCTCACTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:105:10,95:21,138:159,105:0.3977:2,2:26.4:1:29.8:1:0.43685:1.4437:60:34:0.3969:0:2 0/1:263:12:1,11:39,212:251,12:0.0456:2,2:21.2:1:29.6:1:0.69943:2.01927:60:24:0.0463:0:1.9 +16 81888279 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11706;SOR=Inf;LSEQ=ATAGCAGAATGCTCACCCCT;RSEQ=CCTGCTCACTGATGTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:26,210:236,0:0:2,0:25.2:1:32.3:1:1:0:60:46.2:1:0:0.8 0/1:227:3:1,2:32,192:224,3:0.0132:2,2:19.7:1:22.7:1:0.37721:2.98:60:2:0.0089:0:2 +16 81888344 . G A 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.43098;SOR=0.6866;LSEQ=CCCTGCCCCTTTCTAGCTGT;RSEQ=TGTCTTTAGGTGAGTGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:27:1,26:1,56:57,27:0.3214:1,1:22.6:1:31.4:1:0.54217:2.13:60:26:0.3133:0:1.7 0/1:49:12:1,11:1,36:37,12:0.2449:1,2:23.6:1:30:1:0.43367:3.18:57.8:24:0.2449:0:1.3 +16 81891432 . C G 92 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTGGACACATGACTGAA;RSEQ=CTGTCTTAGGTTCAGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:33:1:33:1:1:0:57.7:14:0.7:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81891475 . A G 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCATGTGTTAAATGGGAAT;RSEQ=TAATAGTACTTCCCTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:8,2:0.2:0,0:9:1:31:1:1:0:60:4:0.2:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81891694 . AAAGCAGG A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58523;SOR=1.51893;LSEQ=TGTGGCCCCATCTCAGACAA;RSEQ=TCCTAGGGCCATGACGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:17:17,0:26,0:26,17:0.3953:1,1:22.9:1:31.8:1:1:0:60:34:0.3953:0.093:0 1/0:20:10:10,0:9,1:10,10:0.5:2,0:28.1:1:31.2:1:1:0:60:20:0.5:0.05:0 +16 81891722 . GA G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01414;SOR=0.369;LSEQ=TCCTAGGGCCATGACGGTGT;RSEQ=AAGGGGATGCTTTCTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:34:34,0:43,0:43,34:0.4416:1,1:18:1:32.1:1:1:0:59.4:68:0.4416:0.1429:0.9 0/1:49:11:11,0:34,3:37,11:0.2245:2,0:16.7:1:32:1:1:0:60:22:0.2292:0.0612:0.1 +16 81891790 . C G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06394;LSEQ=GCTTCTCCCATCTTCGTGAT;RSEQ=TGTATGGGGCAGGGCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:86:80,6:182,12:194,86:0.3071:2,2:24.7:1:32.5:1:0.7956:1.13696:60:85:0.308:0:1.2 0/1:255:7:7,0:225,23:248,7:0.0275:2,0:28.1:1:30.9:1:1:0:60:14:0.028:0:1 +16 81891998 . G C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.91824;LSEQ=TGTTGATTTGCGTAGTTGCT;RSEQ=ATTCCTTTATTCTGCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:786:557:181,376:72,156:228,557:0.7087:2,2:24:1:32.1:1:0.86645:1.04:59.9:78.571:0.7152:0:1.2 1/1:822:744:264,480:27,50:77,744:0.9051:2,2:25:1:30.8:1:1:1.02:60:92:0.9064:0:1.3 +16 81892037 . AGG A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.62497;SOR=1.4398;LSEQ=CTTTAGCCAACATGGGCTAC;RSEQ=GGGGAAAAAAAAAAAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:7:4,3:43,314:357,7:0.019:2,2:14.1:1:32.7:1:0.00642:9.63:60:14:0.0197:0:2 0/1:369:10:2,8:59,299:358,10:0.0271:2,2:22.7:1:31.1:1:0.67397:1.27:60:20:0.0279:0:2 +16 81892042 . GGAAAAA AAAC 229 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0;SOR=2.14576;LSEQ=GCCAACATGGGCTACAGGGG;RSEQ=AAAAAAAAGGGACATTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:130:15,115:19,180:199,130:0.3846:2,2:23.6:1:31.5:1:0.58217:1.23:60:260:0.3951:0.0858:0.8 1/0:335:192:27,165:22,108:130,192:0.5731:2,2:22.1:1:30.2:1:0.5284:1.24398:60:191:0.577:0.1463:0.9 +16 81892472 . TA T 110 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTAGCTTTTTGGGGAT;RSEQ=AATGACTATCATCAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:10,1:0,0:0,11:1:0,2:29.2:1:31.9:1:1:0:56.5:22:1:0.0909:0.5 1/1:1:1:1,0:0,0:0,1:1:0,0:23:0:32:0:1:0:60:2:1:0:0 +16 81892498 . A T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTATCATCAGAAGGAATTG;RSEQ=CAATGTAAAGAAACCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:10,1:11,5:0.3125:2,0:27.8:1:30:1:1:0:60:10:0.3125:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:30:0:1:0:60:2:1:0:0 +16 81892708 . T A 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00405;SOR=0.70185;LSEQ=TCTCTCTTTCTTTTGTCTCA;RSEQ=ATTTCTTTCCAGTTGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:601:429:312,117:124,48:172,429:0.7138:2,2:23.5:1:30.6:1:0.91951:1.03:59.8:142:0.716:0:1.2 1/0:616:392:275,117:148,76:224,392:0.6364:2,2:23.9:1:29.4:1:0.32079:1.21:60:77.4:0.6386:0:1.1 +16 81892895 . C T 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=32.92637;LSEQ=ACTGCGTCCATTGTGATCTG;RSEQ=GGATGCCATGTTGGGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:1:0,1:0,162:162,1:0.0061:1,0:10:0:33:0:1:0:60:2:0.0062:0:1 0/1:153:26:2,24:2,124:126,26:0.1699:1,2:16.7:1:29.2:1:0.13577:5.08:60:25:0.1656:0:1.2 +16 81892901 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22174;SOR=Inf;LSEQ=TCCATTGTGATCTGCGGATG;RSEQ=CATGTTGGGTCCTGGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:0,150:150,0:0:1,0:24.5:1:32.1:1:1:0:59.8:149:1:0:0.3 0/1:134:2:0,2:3,129:132,2:0.0149:1,0:29:1:28:1:1:0:60:4:0.0152:0:1 +16 81892913 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10021;LSEQ=TGCGGATGCCATGTTGGGTC;RSEQ=TGGGGTTGAGGATGACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:37:0,37:0,91:91,37:0.2891:1,1:23.5:1:31.5:1:1:0:59.1:74:0.296:0:1.1 0/1:103:4:0,4:2,97:99,4:0.0388:1,0:26.8:1:29.5:1:1:0:60:8:0.0392:0:1.3 +16 81902583 . C G 115 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1872;SOR=0.17617;LSEQ=CCCTCCTTATTGGGGCATCA;RSEQ=CCTACCCTGTGAGTCTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:11,0:11,0:11,11:0.5:0,0:34.6:1:33.5:1:1:0:60:22:0.5:0:1.1 0/1:7:1:1,0:5,1:6,1:0.1429:2,0:39:0:32:0:1:0:60:2:0.1429:0:1 +16 81902600 . G C 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00922;SOR=8.3904;LSEQ=TCACCCTACCCTGTGAGTCT;RSEQ=CTATGTGACCCATGTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:27,0:27,3:0.1:1,0:8.3:1:34.3:1:1:0:60:6:0.1034:0:1 1/0:12:6:6,0:5,1:6,6:0.5:2,0:17.7:1:32.2:1:1:0:60:12:0.5455:0:1.3 +16 81902729 . GC G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23898;SOR=0.80139;LSEQ=ACCAGGCTCTCTCATAGAGG;RSEQ=TGCCTGAGGTGGGAACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:129:123,6:144,11:155,129:0.4542:2,1:23.7:1:31.6:1:0.45749:1.56:59.9:128:0.4571:0.0845:0.2 0/1:220:88:80,8:123,9:132,88:0.4:2,2:23.6:1:30.7:1:0.60957:1.36466:60:176:0.4037:0.0955:0 +16 81902746 . C G 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGCTGCCTGAGGTGGGAA;RSEQ=TGATGGGAGCAGCTAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:326,50:376,0:0:2,0:24.2:1:32.4:1:1:0:60:74.2:1:0:0.2 0/1:337:24:22,2:261,51:312,24:0.0712:2,2:23.9:1:31.4:1:0.39457:2.15:60:48:0.0719:0:2.5 +16 81902751 . G T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05403;SOR=Inf;LSEQ=TGCCTGAGGTGGGAACTGAT;RSEQ=GGAGCAGCTAAATCCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:344,68:412,0:0:2,0:24.1:1:32.2:1:1:0:60:81.4:1:0:0.2 0/1:386:4:1,3:316,66:382,4:0.0104:2,2:14.3:1:26:1:0.01919:14.21821:60:8:0.0104:0:1 +16 81902763 . A G 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACTGATGGGAGCAGCTAA;RSEQ=TCCTGTGCTGTTGAAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:0:0,0:399,119:518,0:0:2,0:24.2:1:30.2:1:1:0:60:46.091:1:0:0.3 0/1:524:38:29,9:363,122:485,38:0.0725:2,2:19.7:1:30.8:1:1:1.08:60:37:0.0721:0:2.6 +16 81902797 . A G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.17025;LSEQ=AAAACCCTCAAGGTGACAGA;RSEQ=CTGGGTCTCCCTCTTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:912:169:101,68:470,271:741,169:0.1853:2,2:25.1:1:32.5:1:0.37918:1.16745:60:55.333:0.1849:0:1.1 0/1:983:412:254,158:348,220:568,412:0.4191:2,2:24.6:1:31.2:1:0.94701:1.02:60:136.333:0.4199:0:1.2 +16 81902879 . C G 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTTTAAAGTGAGCAGTGC;RSEQ=AAGTTCCTTAAAGATAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1418:0:0,0:687,729:1416,0:0:2,0:24.3:1:31.8:1:1:0:60:107.923:0.9986:0:0.1 0/1:1611:77:33,44:753,778:1531,77:0.0478:2,2:21.7:1:29.7:1:0.29482:1.29028:60:76:0.0475:0:1.1 +16 81902990 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=0.46922;LSEQ=GTGGCTTGCCTTTGAGTTCC;RSEQ=TGGAATAGTGCACAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:74:11,63:41,231:272,74:0.2139:2,2:22.2:1:30.8:1:1:1.01649:60:73:0.2141:0:1.3 0/1:336:38:6,32:50,248:298,38:0.1131:2,2:22.8:1:30.3:1:1:1.07504:60:76:0.1145:0:1.2 +16 81903055 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=3.45871;LSEQ=AGTTCAGACAGAGGGATCAT;RSEQ=GACATATCTGAGGACCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:22:0,22:1,98:99,22:0.1803:1,1:24.1:1:33.2:1:1:0:60:44:0.1818:0:1.6 0/1:83:36:0,36:0,47:47,36:0.4337:1,1:22.9:1:30.8:1:1:0:60:35:0.4268:0:1.3 +16 81904375 . C TA 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=2e-05;SOR=2.56644;LSEQ=ATAGCATGCCATTTCTGAAA;RSEQ=AAAAATTATTCTATAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:48:46,2:154,16:170,48:0.2202:2,1:21.2:1:30.3:1:0.37432:2.38:59.7:96:0.2202:0.0826:1.1 0/1:183:77:71,6:96,10:106,77:0.4208:2,2:19.7:1:29.3:1:0.79486:1.23:59.9:154:0.4231:0.1475:1.1 +16 81904433 . TG T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.79021;LSEQ=GGTGGACATCAAAAATCATG;RSEQ=GTCACTTTTTTCATATTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:137:80,57:348,192:540,137:0.2024:2,2:25.9:1:32:1:0.19815:1.29088:59.9:274:0.2045:0.034:0.3 0/1:668:277:178,99:238,153:391,277:0.4147:2,2:26.6:1:31.2:1:0.41789:1.16:60:554:0.4184:0.0539:0.3 +16 81904674 . T C 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=9e-04;SOR=3.26354;LSEQ=GGAAACATAAATGAGAATGA;RSEQ=GAAAGCATACCATTTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:18:0,18:0,75:75,18:0.1935:1,1:23.9:1:30.8:1:1:0:60:36:0.1978:0:1.4 0/1:68:30:0,30:2,35:37,30:0.4412:2,1:19.6:1:29.8:1:0.49796:0:60:60:0.4412:0:1.4 +16 81904711 . T A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12159;SOR=2.34741;LSEQ=CATCCATTAGATTGGCAAAA;RSEQ=TCTTTAACCATGACAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:9:0,9:0,28:28,9:0.2432:1,0:26.6:1:31.1:1:1:0:60:18:0.2432:0:2.1 0/1:30:13:0,13:1,16:17,13:0.4333:1,1:24.8:1:30.5:1:1:0:60:26:0.4333:0:2 +16 81914000 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTTCTAGGACTCTACTC;RSEQ=GTAGAAAAACTGGCACAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:12.5:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81914303 . C A 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00642;SOR=0;LSEQ=GTGACTGCTTCTTGGGAATA;RSEQ=GACTGTGGAGGGAATGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:53,1:0,0:0,54:1:0,1:26.8:1:29.8:1:1:0:60:17:1:0:1.1 1/1:33:28:27,1:5,0:5,28:0.8485:0,1:19.4:1:30.6:1:1:0:60:56:0.8485:0:1.1 +16 81914486 . C CT 122 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16954;SOR=1.82662;LSEQ=TAAGTGACTTGTCTAAGGTT;RSEQ=TTTTTTTTGTGTGTGCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1239:8:4,4:702,528:1230,8:0.0065:2,2:23.5:1:28.8:1:0.73121:1.32922:60:7:0.0057:0.0016:0.4 0/1:1534:18:10,8:831,685:1516,18:0.0117:2,2:22.7:1:29.4:1:1:1.03:60:36:0.0118:0.0026:0.4 +16 81914583 . C T 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.22211;LSEQ=GGCAGCTCTTGTGTGTCGTT;RSEQ=GGGGCGGCTGTGCCGGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1001:754:299,455:82,162:244,754:0.7532:2,2:25.5:1:30.5:1:0.09572:1.30:60:61.833:0.7533:0:1.2 0/1:1191:481:200,281:277,433:710,481:0.4039:2,2:27.2:1:29.5:1:0.39894:1.11:60:79.167:0.4015:0:1.1 +16 81914619 . A C 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACCTCGGTGCCTGGTGCCC;RSEQ=GCCGGCCTCCAGGAGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:0:0,0:169,414:583,0:0:2,0:22.9:1:31.4:1:1:0:60:82.286:1:0:0.8 0/1:669:85:21,64:186,398:584,85:0.1271:2,2:23.4:1:29.4:1:0.2098:1.42355:60:170:0.1284:0:1.1 +16 81914851 . G GT 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TGAGATGTGACAGGTTAATA;RSEQ=TTTTTTTTTTTAATTACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:0,8:0,5:5,8:0.5714:0,0:22.3:1:29.5:1:1:0:58.3:16:0.5714:0:0.1 0/0:2:0:0,0:0,2:2,0:0:0,0:18:1:33.5:1:1:0:41:4:1:0:0 +16 81916638 . G A 118 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11928;SOR=0.17559;LSEQ=CTATTTTGGAGCAGCTAAAT;RSEQ=TAGACACCAGGGCCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:16:16,0:19,0:19,16:0.4571:1,1:15.3:1:29.7:1:1:0:60:32:0.4571:0:1.1 0/1:8:1:1,0:7,0:7,1:0.125:0,0:44:0:29:0:1:0:60:2:0.125:0:1 +16 81917099 . G T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.11666;LSEQ=GTCTTCATGGAACGATTGCA;RSEQ=TCTGCCAGATGCCAGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:26:0,26:2,65:67,26:0.2796:1,1:20.9:1:30.4:1:1:0:60:52:0.2889:0:1.2 0/1:70:3:0,3:2,65:67,3:0.0429:1,0:13.7:1:31.7:1:1:0:60:6:0.0441:0:1 +16 81917183 . G C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.43315;SOR=2.33278;LSEQ=CCTCATGTCGGGCCTCTTTT;RSEQ=AAGGCACACATTGAGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:0,10:0,12:12,10:0.4545:0,0:23.6:1:33.9:1:1:0:60:20:0.4762:0:1.3 1/0:9:6:0,6:0,3:3,6:0.6667:0,0:16.2:1:31.8:1:1:0:54:12:0.6667:0:1 +16 81922813 . C T 171 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.8609;LSEQ=ATCTGAACAAAGTCCGTGAG;RSEQ=GGATGACAAAGTTCATTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1352:2:0,2:736,614:1350,2:0.0015:2,0:1:0:26:0:0.20741:0:60:4:0.0015:0:1 0/1:1419:64:32,32:720,633:1353,64:0.0451:2,2:26.6:1:28.6:1:0.70091:1.13734:59.6:20.333:0.0436:0:1.1 +16 81923018 . GTTTCT G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=4.000;MSILEN=1;SSF=0.5355;SOR=0;LSEQ=CTGACTGGTTAGCTGGGATT;RSEQ=TTTCTTTTCTTTTCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:0,2:3,151:154,2:0.0128:1,0:25:1:32.5:1:1:0:60:4:0.0131:0.0064:0.5 0/0:89:0:0,0:3,86:89,0:0:1,0:19.5:1:30:1:1:0:60:88:1:0:0.1 +16 81924905 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12564;SOR=Inf;LSEQ=AAATATGTCGCTGCAGCCCA;RSEQ=TGCAGCCTGAGCCTTCGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:61,0:0:1,0:26.4:1:30.9:1:1:0:59.8:19.333:1:0:0.2 0/1:34:2:2,0:31,1:32,2:0.0588:1,0:35.5:1:31:1:1:0:60:4:0.0588:0:1 +16 81924989 . TC T 33 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.5919;SOR=2.42972;LSEQ=TCCCGCATCAGAGCTGTTCT;RSEQ=CCCCCTGGTGGGCGCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:1:1,0:190,17:207,1:0.0048:2,0:16:0:34:0:1:0:60:2:0.0049:0:0 0/1:172:2:2,0:153,17:170,2:0.0116:2,0:37:1:33:0:1:0:60:4:0.0117:0:0 +16 81924994 . C T 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.00086;SOR=Inf;LSEQ=CATCAGAGCTGTTCTTCCCC;RSEQ=CTGGTGGGCGCAGACCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:202,22:224,0:0:2,0:24:1:31.4:1:1:0:59.8:223:1:0:0.1 0/1:192:9:8,1:161,22:183,9:0.0469:2,2:23.8:1:30.4:1:1:1.09:60:18:0.0469:0:1.1 +16 81925026 . C T 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACCAGAAACAAGCAGACA;RSEQ=CATCCTGCCCGTCAACGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:309,110:419,0:0:2,0:23.9:1:31.8:1:1:0:59.9:51.375:1:0:0.1 0/1:391:25:19,6:272,93:365,25:0.0639:2,2:23.6:1:29.4:1:1:1.08:60:11.5:0.0594:0:1.4 +16 81925053 . G A 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCGTCAACGTGATGATTC;RSEQ=GTCTTCGTGTTTGACTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:0:0,0:434,236:670,0:0:2,0:24.8:1:30.2:1:1:0:60:50.538:1:0:0.1 0/1:669:26:19,7:407,234:641,26:0.0389:2,2:21.7:1:30:1:0.40666:1.56:60:52:0.0392:0:1.1 +16 81925437 . A G 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00393;SOR=18.76572;LSEQ=AAAAAGCTAGTAAAAACAAA;RSEQ=GTAACTTAGTTTATGTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:0,6:0,21:21,6:0.2222:1,0:29.2:1:28.3:1:1:0:60:5:0.2083:0:1 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:18:1:30.8:1:1:0:60:12:0.8571:0:1.2 +16 81926894 . A G 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCACCAACAGTTGTTGAAT;RSEQ=TCTGTTCTGTGCCTGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:28:1:30.5:1:1:0:60:4:0.4:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81927036 . TCTC T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACGTGCTTTGACCAACT;RSEQ=CTCAAAAGAACACGTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:8,2:0.2:0,0:39.5:1:34:0:1:0:60:4:0.2:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:8:0:32:0:1:0:60:2:1:0:0 +16 81927217 . G C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0.22164;LSEQ=CTCAGAGCTTTGGCGGCTCG;RSEQ=GCGGAGAAGTTCCCCCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:42:40,2:139,4:143,42:0.227:1,1:26.3:1:32:1:0.61988:1.73161:60:20:0.2235:0:1.2 0/1:115:7:7,0:107,1:108,7:0.0609:1,0:19.9:1:31.7:1:1:0:60:14:0.0625:0:1 +16 81927555 . C T 65 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.76152;SOR=0.70168;LSEQ=GTGTGATGTTTCTTTGTTTT;RSEQ=TTTTTTCTTTCTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:8:0,8:1,75:76,8:0.0941:1,0:25.9:1:21.8:1:1:0:51.8:1.667:0.0649:0:4 0/1:59:4:0,4:2,53:55,4:0.0678:1,0:21.5:1:20.3:1:1:0:48.8:1:0.0408:0:3.5 +16 81927562 . C T 77 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.77745;SOR=1.33306;LSEQ=GTTTCTTTGTTTTCTTTTTT;RSEQ=TTTCTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:8:0,8:1,53:54,8:0.127:1,0:22.6:1:25.8:1:1:0:49:3:0.1091:0:4.1 0/1:43:7:0,7:2,34:36,7:0.1628:2,0:29.4:1:17.1:1:1:0:53.1:0.4:0.0625:0:2.9 +16 81929158 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGGGCAACAGAGCGAGACT;RSEQ=TGTCTTAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:0,16:1:0,1:27.6:1:29.8:1:1:0:47.2:7:1:0:1.5 1/1:5:5:5,0:0,0:0,5:1:0,0:21.6:1:30.8:1:1:0:55.2:10:1:0:1.4 +16 81929164 . T TA 71 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.31069;SOR=3.23098;LSEQ=AACAGAGCGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAATGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:5,0:17,0:17,5:0.2273:1,0:21.8:1:30.8:1:1:0:47.2:10:0.2273:0.0909:1.6 1/0:6:3:3,0:3,0:3,3:0.5:0,0:18.7:1:29:0:1:0:60:6:0.5:0:1.3 +16 81929185 . A G 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAAAAAAAAAAATGAAAA;RSEQ=AAAAGCAGCATTGAAACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:47,0:47,0:0:1,0:16.7:1:30.1:1:1:0:55.4:14.667:1:0:0.7 1/0:17:9:9,0:7,1:8,9:0.5294:2,0:14.4:1:28.4:1:0.47059:0:57.8:3.5:0.4667:0:1.3 +16 81929379 . G A 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCTGTCAGTGAACACAC;RSEQ=TGGTATTGAGGCTGCCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1040:0:0,0:654,385:1039,0:0:2,0:25:1:30.6:1:1:0:60:78.923:1:0:0.2 0/1:1092:46:28,18:644,402:1046,46:0.0421:2,2:25.4:1:28.7:1:1:1.02984:60:10.5:0.0391:0:1.2 +16 81929488 . C T 304 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=332.21948;LSEQ=ACTACCAAGATCAAGTTTGA;RSEQ=GACGTCGTGCAGGCCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1736:9:1,8:842,884:1726,9:0.0052:2,2:15.6:1:26:1:0.03925:7.61322:60:8:0.0047:0:1.1 1/0:1862:1182:593,589:330,348:678,1182:0.6348:2,2:24:1:29.8:1:0.5632:1.06:59.9:130.333:0.6365:0:1.2 +16 81929527 . C G 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGACCACGCCTTTGTTAC;RSEQ=TCGAGGTCAGTTGGCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1569:0:0,0:730,839:1569,0:0:2,0:25.5:1:32:1:1:0:60:67.217:1:0:0.2 0/1:1764:60:31,29:817,882:1699,60:0.034:2,2:29.5:1:30.5:1:0.6015:1.15:60:59:0.0339:0:1.1 +16 81929641 . G A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=AGACACCTCCCTCCAAATGC;RSEQ=GGAAGGCCTGGGCCCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:6,230:236,0:0:1,0:23.3:1:31.2:1:1:0:60:46.2:1:0:0.1 0/1:214:11:0,11:2,201:203,11:0.0514:1,0:23.5:1:30.7:1:1:0:60:10:0.0481:0:1 +16 81930650 . G T 46 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=GTCTCTGTTGCAACTATTCA;RSEQ=CCCTGTTGCTGAAGTGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:13.8:1:30.3:1:1:0:60:8:1:0:0 1/0:6:3:2,1:2,1:3,3:0.5:2,2:42.7:1:29.3:1:1:1:60:6:0.5:0:1 +16 81933716 . C CAT 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATAAATGTATGCATGCACA;RSEQ=ATGCAAATTACATATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:18:1:32.2:1:1:0:60:6:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81934047 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.30593;LSEQ=TGAGTCCCAAGACTTGTGCC;RSEQ=TCACACCCAGGATGAGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:7:7,0:39,1:40,7:0.1489:1,0:20.1:1:30.6:1:1:0:54.3:14:0.1556:0:1 1/1:14:12:12,0:2,0:2,12:0.8571:0,0:24.1:1:32:1:1:0:60:24:0.8571:0:1.1 +16 81934130 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05189;SOR=Inf;LSEQ=CAGCGCCCGGTTTCTGTCGT;RSEQ=CCAGGGAGCTGCCCTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:185,10:195,0:0:2,0:24.9:1:32.4:1:1:0:60:194:1:0:0.1 0/1:117:3:2,1:112,2:114,3:0.0256:1,2:33.7:1:27:1:0.0756:24.79682:60:6:0.0259:0:1 +16 81934609 . T C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGAGATAATACTGGAAC;RSEQ=CATCTGGCTAGCTTGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:0,28:0,0:0,28:1:0,1:26.8:1:31.8:1:1:0:59.2:56:1:0:1.2 1/1:7:7:0,7:0,0:0,7:1:0,0:20:1:30.4:1:1:0:60:14:1:0:1 +16 81937556 . T G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACTTTGTACCATGCACT;RSEQ=GGCTAGGCGTGGTCATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:24:1:33.5:1:1:0:60:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81937565 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCATGCACTTGGCTAGGC;RSEQ=TGGTCATATGTATCTTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:33:1:31.5:1:1:0:60:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81937574 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGCTAGGCGTGGTCATA;RSEQ=GTATCTTCTTATTCAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:38.5:1:31.5:1:1:0:60:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81938677 . A T 39 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTTTTTTATTTTTGTAG;RSEQ=TACAGGGTTTTGCCATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:14.7:1:25:1:1:0:56.3:2:0.5:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81938720 . G T 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGCTGGTCTAGAACTCCT;RSEQ=AGCTCAAGTGATCTGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:36:1:32.4:1:1:0:59.6:10:0.7143:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:14:0:32:0:1:0:58:2:1:0:3 +16 81938787 . T C 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53924;SOR=Inf;LSEQ=TAGGTGTGAGCCACTGCGCC;RSEQ=GACCAGTATGGGCAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:14,0:6,0:6,14:0.7:0,1:25.3:1:31.5:1:1:0:59.9:28:0.7:0:2.1 1/1:4:4:4,0:0,0:0,4:1:0,0:22.8:1:30:1:1:0:59.5:8:1:0:2.3 +16 81938789 . A G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27982;SOR=Inf;LSEQ=GGTGTGAGCCACTGCGCCTG;RSEQ=CCAGTATGGGCAATTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:14:14,0:8,0:8,14:0.6364:0,1:26.3:1:31.6:1:1:0:59.9:28:0.6667:0:2 1/1:5:5:5,0:0,0:0,5:1:0,0:19.2:1:26.6:1:1:0:59.6:4:1:0:2 +16 81939150 . G C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.92749;LSEQ=CCCGTAGCCACTGCGGCCAC;RSEQ=CCCCTTGCAGCTGCTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:762:577:173,404:62,120:182,577:0.7572:2,2:25.4:1:30.7:1:0.31245:1.20623:60:40.214:0.7557:0:1.1 1/1:740:667:232,435:27,44:71,667:0.9014:2,2:23.4:1:30.1:1:0.6022:1.15034:60:221.333:0.9071:0:1.1 +16 81939157 . G T 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06704;SOR=0.56671;LSEQ=CCACTGCGGCCACGCCCCTT;RSEQ=CAGCTGCTTCTTGGAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:35:11,24:180,493:673,35:0.0494:2,2:20.5:1:31.3:1:0.55958:1.25:60:70:0.05:0:1.1 0/1:629:18:9,9:197,413:610,18:0.0286:2,2:21.4:1:29.1:1:0.12962:2.09:60:36:0.0292:0:1.1 +16 81939237 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09611;SOR=1.76802;LSEQ=TTAGTCAAGTGAGTTTTTGC;RSEQ=ATGTGAATTTACCTTCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:159:2,157:0,44:44,159:0.7833:1,1:25:1:28.9:1:1:0:60:52:0.78:0:1.3 1/1:111:96:1,95:0,15:15,96:0.8649:1,1:26.5:1:27.9:1:1:0:60:47:0.8624:0:1.4 +16 81939319 . A G 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33444;SOR=2.80432;LSEQ=TGTCGCCCAGGCTGGAGTGT;RSEQ=GTGGTGTGATTGCGGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:0,3:0,26:26,3:0.1034:1,0:33:1:33.3:1:1:0:60:6:0.1071:0:1 0/1:12:3:0,3:0,9:9,3:0.25:0,0:23.3:1:30:1:1:0:60:6:0.25:0:1 +16 81939404 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTCCCTGAGTCTCTGGGACC;RSEQ=CACGTGCGCACCACCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,1:1,9:0.9:0,0:24.8:1:33.3:1:1:0:59.7:18:0.9:0:2.1 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:31.5:1:1:0:60:4:1:0:1 +16 81939407 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGAGTCTCTGGGACCACA;RSEQ=GTGCGCACCACCATGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:7,3:0.3:0,0:24.7:1:31:1:1:0:59:6:0.3:0:2 0/0:2:0:0,0:0,2:2,0:0:0,0:27:1:28.5:1:1:0:60:4:1:0:1 +16 81939464 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAGAGATGGGATTTAGT;RSEQ=GTGTTGCCCAGGGTGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:26.5:1:33.5:1:1:0:60:4:0.6667:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81939466 . T C 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGATGGGATTTAGTCG;RSEQ=GTTGCCCAGGGTGATTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:17.3:1:30.3:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81939473 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGATTTAGTCGTGTTGCC;RSEQ=AGGGTGATTTCAAACTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:17.5:1:30:0:1:0:60:4:0.6667:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81940712 . A G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATGTAAGAAACCTGCAC;RSEQ=GTGTACACATGTACCCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:37.3:1:31.3:1:1:0:34.7:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81940867 . C A 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAAAGCTAAGAACTTAAC;RSEQ=CTGGTACTTTACAATAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:28.8:1:32:0:1:0:44.5:8:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81940910 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACTAAATTTCATCGGGG;RSEQ=AAAAAAAAAAGAAGTCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:28.5:1:29:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81941160 . A G 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10935;SOR=2.60977;LSEQ=TTGAATTCAGAGAATTCGCC;RSEQ=TAAATGTCTATGAAACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:6:6,0:117,1:118,6:0.0484:1,0:28.7:1:31.3:1:1:0:60:12:0.0488:0:1 0/1:85:10:10,0:74,1:75,10:0.1176:1,0:25.7:1:30.2:1:1:0:60:20:0.1176:0:1.4 +16 81941319 . C T 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.75817;LSEQ=CGGCACTACTGCGCCATTGC;RSEQ=GATGCCAAGCTGTCCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1103:802:398,404:151,145:296,802:0.7271:2,2:26.6:1:31.3:1:0.73386:1.05699:60:132.667:0.7303:0:1.1 1/1:1019:897:435,462:57,64:121,897:0.8803:2,2:26.5:1:29.7:1:0.84641:1.06:60:55.063:0.8801:0:1.2 +16 81941444 . C T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.8022;SOR=0.92501;LSEQ=CCCGAGGACCAGCCAGTCCC;RSEQ=GGGACCTCCTTCCCATGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:47:6,41:14,175:189,47:0.1975:2,2:23.9:1:30.6:1:0.24619:1.82:60:46:0.1983:0:1.1 0/1:178:33:5,28:13,131:144,33:0.1854:2,2:21.5:1:29.5:1:0.33668:1.79:60:66:0.1864:0:1.1 +16 81941493 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03319;SOR=Inf;LSEQ=GCCGGCTGGCAAGGGGATGC;RSEQ=CCGCTGAAGAAGCTGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:3,92:95,0:0:1,0:23.9:1:30.2:1:1:0:60:22.75:1:0:0.3 0/1:46:3:0,3:1,42:43,3:0.0652:1,0:26.3:1:31:1:1:0:60:6:0.0652:0:1.7 +16 81941530 . CCTGGCTGGCTTGTCTCTGATTGG C 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.32451;SOR=0;LSEQ=TGATACTCTGGGTACCATGT;RSEQ=CTGGCTGCCCCAGGTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:0,6:3,43:46,6:0.1154:2,0:26.5:1:32.3:1:1:0:60:12:0.1176:0.0192:0.3 0/0:15:0:0,0:3,12:15,0:0:2,0:23.1:1:30.5:1:1:0:60:14:1:0:0.3 +16 81941623 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00952;SOR=Inf;LSEQ=TCTCTAAAGTGCCTGATTGG;RSEQ=CTTAGATGGAGGCCGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:2,11:13,0:0:2,0:21.6:1:32.8:1:1:0:58.5:26:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:1:25:1:1:0:60:4:1:0:1 +16 81942028 . C G 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTGCGGCCCAGGATATAC;RSEQ=CCCTACAGAACTACATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1475:0:0,0:772,702:1474,0:0:2,0:24.8:1:31.1:1:1:0:60:48.133:0.9993:0:0.1 0/1:1421:104:55,49:708,606:1314,104:0.0732:2,2:23.4:1:29.7:1:0.91868:1.04085:60:33.667:0.0724:0:1.2 +16 81942175 . A G 202 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=43.33826;LSEQ=GGAGAGCGAGACCTTCCCCA;RSEQ=TGACTACACCCTGTCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1505:2:1,1:699,801:1500,2:0.0013:2,2:34:1:14.5:1:1:1.15:60:0:0:0:1 0/1:1558:85:34,51:681,789:1470,85:0.0546:2,2:24.3:1:31.6:1:0.26523:1.29446:60:170:0.0555:0:1.1 +16 81942401 . G T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGATTAATGAGATTTCA;RSEQ=GGCAATCTTTTAAAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:3:0,3:0,44:44,3:0.0638:1,0:27.3:1:25:1:1:0:60:2:0.0444:0:2.3 0/0:14:0:0,0:0,14:14,0:0:1,0:21.1:1:28.7:1:1:0:59.2:6:1:0:0.4 +16 81942936 . G C 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGATTTGTGAAAGTCTGTGA;RSEQ=GAAGGCTCTGATGCCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:49:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29:1:1:0:60:4:1:0:1 +16 81944404 . C T 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGAAGCTGGCCTGGTGGTT;RSEQ=AGCCGGGCCAGTCCCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:23,283:306,0:0:2,0:23.9:1:32.1:1:1:0:60:75.5:0.9967:0:0.1 0/1:268:28:2,26:24,216:240,28:0.1045:2,2:24.5:1:27.1:1:1:1.44268:60:56:0.1069:0:1.3 +16 81944804 . C A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAAAGCTGCAAAAATGT;RSEQ=CATTTCCGAGGAGGCCGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:44.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81945966 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTGTGAACCACTGTGCT;RSEQ=GGCCCAATGTATTATTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:3,0:14,0:14,3:0.1765:1,0:25.7:1:32:1:1:0:60:6:0.1765:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:25.6:1:32:0:1:0:60:10:1:0:0 +16 81946006 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTTGAAACAGACCCCTGG;RSEQ=GTCTTCCACTATTCTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:2,0:49,0:49,2:0.0392:1,0:28:1:30.5:1:1:0:60:4:0.04:0:1 0/0:20:0:0,0:18,2:20,0:0:2,0:23.5:1:30.4:1:1:0:60:19:1:0:0.1 +16 81946328 . G A 254 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00466;LSEQ=GCCATCACCTTCAGGTGGGT;RSEQ=CGAGGGTGGGAGGCACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1285:440:182,258:367,476:843,440:0.3424:2,2:25:1:29:1:0.47592:1.09289:60:72.333:0.3439:0:1.2 0/0:1240:3:3,0:556,681:1237,3:0.0024:2,0:1:0:23.3:1:0.09135:0:60:6:0.0025:0:1 +16 81946368 . A C 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCTACAGAGGGGCTTGGCA;RSEQ=GGACAGATGCGGAGAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:0:0,0:219,498:717,0:0:2,0:23.6:1:31.4:1:1:0:59.9:178.25:1:0:0.5 0/1:660:29:7,22:214,417:631,29:0.0439:2,2:23.4:1:30.1:1:0.31975:1.61181:60:58:0.0445:0:1.1 +16 81946423 . C T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=2.31051;LSEQ=TGGAGGCTCACCTGCAGTGC;RSEQ=CTGCCCCCCCAGCATCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:76:1,75:12,168:180,76:0.2969:2,1:23.5:1:30.8:1:0.11621:5.33422:60:152:0.304:0:1.4 0/1:176:87:5,82:6,83:89,87:0.4943:2,2:24.6:1:28.9:1:1:1.1844:60:86:0.5181:0:1.5 +16 81946471 . G T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05191;SOR=1.89305;LSEQ=CAACCACCACAGCAAAAGCC;RSEQ=CTGCGAGAATGTGCGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:37:0,37:1,79:80,37:0.3162:1,1:26:1:30.2:1:1:0:59.8:36:0.313:0:1.6 0/1:62:29:4,25:3,30:33,29:0.4677:2,2:22:1:29.3:1:0.69597:1.59:60:58:0.4754:0:2 +16 81946478 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54302;SOR=0;LSEQ=CACAGCAAAAGCCGCTGCGA;RSEQ=AATGTGCGCTCCTGCGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:0,2:1,98:99,2:0.0198:1,0:46.5:1:28.5:1:1:0:60:4:0.0204:0:2 0/0:54:0:0,0:7,47:54,0:0:2,0:21.8:1:30.6:1:1:0:60:26:1:0:1 +16 81946486 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01356;SOR=Inf;LSEQ=AAGCCGCTGCGAGAATGTGC;RSEQ=CTCCTGCGTGCCAGGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:0,82:82,0:0:1,0:26.7:1:33.2:1:1:0:59.9:164:1:0:0.6 0/1:44:4:1,3:5,35:40,4:0.0909:2,2:33:1:29.8:1:0.45625:2.28:60:8:0.093:0:2.3 +16 81946714 . T C 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCCAGGCCTGTGATGATA;RSEQ=AGATCTGGTTTCCTCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:43.7:1:33:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81946744 . T A 55 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCCTCCCAACTGCAGCTGC;RSEQ=GCCCAACCACCTCTAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:11:1:27.8:1:1:0:60:8:1:0:2.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81952767 . C G 52 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TAAAAGCAGGTGGTGGGACA;RSEQ=ATTTGGCCTACTCTTGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:31.7:1:33.3:1:1:0:54.3:6:0.2727:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:49:0:30:0:1:0:60:2:1:0:1 +16 81952775 . C G 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGTGGGACACATTTGGC;RSEQ=TACTCTTGACCTAGTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:18.8:1:29:1:1:0:60:8:0.3333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:41:0:28:0:1:0:60:2:1:0:1 +16 81952824 . T C 66 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00169;SOR=Inf;LSEQ=CCTAAAGTCAAGTCCTGTAG;RSEQ=TGGGGAGGAGAGGAAGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:16,1:17,2:0.1053:1,0:5.5:1:28.5:1:1:0:60:4:0.1053:0:1.5 1/1:4:4:4,0:0,0:0,4:1:0,0:16.5:1:33:0:1:0:60:8:1:0:1 +16 81952885 . C G 115 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26915;SOR=0.23101;LSEQ=CGGCCATATTTCTTCTGAGA;RSEQ=ACAGATTCTTCTAGATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:11:10,1:39,1:40,11:0.2157:1,2:26.1:1:33.5:1:0.38824:3.76588:60:22:0.22:0:1.2 0/1:17:1:1,0:16,0:16,1:0.0588:1,0:8:0:32:0:1:0:60:2:0.0588:0:1 +16 81952904 . G C 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.21473;SOR=4.8108;LSEQ=ACACAGATTCTTCTAGATCT;RSEQ=TTTTGAAAATACCCACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:1,0:70,1:71,1:0.0139:1,0:25:0:34:0:1:0:60:2:0.0141:0:1 0/1:31:2:2,0:29,0:29,2:0.0645:1,0:17.5:1:31.5:1:1:0:60:4:0.0645:0:1 +16 81952979 . C T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17504;SOR=Inf;LSEQ=CTATACCCTGTTTATTTACC;RSEQ=ACTTCTCTAAGGCTGGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:266,3:269,0:0:1,0:24.6:1:31.3:1:1:0:60:28.889:1:0:0.2 0/1:194:2:2,0:190,2:192,2:0.0103:1,0:6.5:1:30:1:1:0:60:4:0.0105:0:1 +16 81953023 . G T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01286;SOR=Inf;LSEQ=GGTTGTATCTAATCAGTAGG;RSEQ=TTTGTGTAAAAATTGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:0:0,0:489,100:589,0:0:2,0:21.7:1:31.4:1:1:0:60:52.545:1:0:0.8 0/1:555:6:3,3:434,114:548,6:0.0108:2,2:12.5:1:27.7:1:0.11198:3.79493:60:12:0.0111:0:2.3 +16 81953081 . T C 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03553;SOR=0.3067;LSEQ=TGTCAACCCTGTGTTCTTCC;RSEQ=GCTCCAGGGCTAGGGGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1247:1243:710,533:0,3:3,1243:0.9968:0,2:27.6:1:30.6:1:0.07935:0:59.9:112:0.9968:0:1.1 1/1:1444:1429:810,619:2,6:8,1429:0.9896:2,2:25.8:1:29.5:1:0.08478:3.92:60:63.955:0.9908:0:1.2 +16 81953368 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCTGAGTATTCACCATGT;RSEQ=TCTGATACTGCTGTAGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:254:253:0,253:0,0:0,253:0.9961:0,1:23.3:1:32.7:1:1:0:60:252:1:0:1.1 1/1:186:186:5,181:0,0:0,186:1:0,1:24.1:1:31.9:1:1:0:60:185:1:0:1 +16 81954359 . AG A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACAGCTCTCAGCGGGGT;RSEQ=GGGGAAGGCACTGGTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:10.5:1:32.5:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81954789 . C G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00041;SOR=1.47488;LSEQ=ATTATTCCATTTCTTTCTTT;RSEQ=TTTTTTTTTCCAGGAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:695:404:286,118:189,76:265,404:0.5813:2,2:23.3:1:32.2:1:0.93064:1.026:59.9:66.333:0.6012:0:1.1 1/0:759:510:346,164:144,77:221,510:0.6719:2,2:22.8:1:31.1:1:0.49381:1.13:60:71.857:0.6938:0:1.1 +16 81955177 . C T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11376;SOR=4.4393;LSEQ=AAATGTTTTTGGCTCGCTGA;RSEQ=AGAGCCTGTGGTGTTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:11:0,11:0,17:17,11:0.3929:1,0:27.9:1:26.3:1:1:0:60:10:0.3704:0:1.5 1/0:8:6:0,6:0,2:2,6:0.75:0,0:12.2:1:28.7:1:1:0:60:12:0.75:0:1 +16 81955238 . A G 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTTGCAGTGCAAATGCT;RSEQ=TCTCATATTCCCACCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:8,7:0.4667:0,0:26:1:33.6:1:1:0:60:14:0.4667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:10:0:32:0:1:0:60:2:1:0:1 +16 81955367 . A G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCCGGCAGAGGAAGAACC;RSEQ=CAGCGAATTTTCTGTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:29:1:32.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81956680 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGCTTGCTGAGCACCG;RSEQ=CACTGTGATGACAGTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:23:1:27.5:1:0.4:0:60:4:0.4:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:45:0:29:0:1:0:60:2:1:0:0 +16 81956810 . G C 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53044;SOR=0;LSEQ=AGCCTAACCCTAACCCCAGC;RSEQ=CTAAACCCTAGCCCCAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:11,0:11,5:0.3125:0,0:20.6:1:30.2:1:1:0:60:10:0.3333:0:1.4 0/0:3:0:0,0:3,0:3,0:0:0,0:26:1:28.3:1:1:0:60:6:1:0:0.3 +16 81956927 . C G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGGCTTTTTGGGGCCTT;RSEQ=GATCCTTTGCAATGCCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:77:77:76,1:0,0:0,77:1:0,1:25.1:1:32.9:1:1:0:60:154:1:0:1.2 1/1:45:45:44,1:0,0:0,45:1:0,1:23.1:1:31.5:1:1:0:60:90:1:0:1.3 +16 81956953 . C A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02834;SOR=Inf;LSEQ=TTTGCAATGCCAGTCCCTCT;RSEQ=CAGCAGATGACTTTGTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:116,4:120,0:0:1,0:24.4:1:32.5:1:1:0:60:240:1:0:0.7 0/1:85:4:3,1:79,2:81,4:0.0471:1,2:24.3:1:27.3:1:0.13617:12.09932:60:8:0.0482:0:1.8 +16 81956954 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02858;SOR=Inf;LSEQ=TTGCAATGCCAGTCCCTCTC;RSEQ=AGCAGATGACTTTGTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:117,4:121,0:0:1,0:24.5:1:31.4:1:1:0:60:39.333:1:0:0.7 0/1:86:4:4,0:79,3:82,4:0.0465:1,0:11.3:1:30.8:1:1:0:60:8:0.0465:0:1 +16 81956999 . A G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=Inf;LSEQ=CTGAAGCCTCCTGCTCCCCA;RSEQ=TGAGAAGAACCAAATGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:239,19:258,0:0:2,0:24.2:1:30.5:1:1:0:60:63.5:1:0:0.2 0/1:239:10:7,3:205,24:229,10:0.0418:2,2:11.1:1:28.4:1:0.09004:3.63049:60:9:0.0388:0:1.7 +16 81957227 . C T 213 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGAGTGGAGGCTGGGCTGCT;RSEQ=GGCAGGTGGGCTTGACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:133:44,89:224,392:616,133:0.1776:2,2:27.2:1:30.2:1:0.48721:1.1556:60:266:0.1807:0:1.1 0/0:774:0:0,0:284,490:774,0:0:2,0:24.8:1:29.4:1:1:0:60:63.5:1:0:0.2 +16 81957301 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50999;SOR=0;LSEQ=AGTCTGACCCCCTTTGTCAT;RSEQ=CTGGGCTGGCTTTGACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:10,174:184,2:0.0108:2,2:14:1:27:1:0.11508:16.64:60:4:0.0109:0:1.5 0/0:137:0:0,0:5,132:137,0:0:1,0:23.9:1:31:1:1:0:60:274:1:0:0.7 +16 81957303 . T G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.7202;SOR=1.09267;LSEQ=TCTGACCCCCTTTGTCATCC;RSEQ=GGGCTGGCTTTGACCTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:177:114:6,108:1,62:63,114:0.6441:1,2:25:1:31.2:1:0.42392:3.43:60:113:0.6457:0:1.1 1/0:134:89:3,86:2,43:45,89:0.6642:1,1:23.9:1:31:1:1:1.33031:60:178:0.6642:0:1.1 +16 81957349 . G T 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00978;SOR=0;LSEQ=AGTCCCTTCTTAGGAAGGTG;RSEQ=CTTGGTGCATGCTCTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:13:0,13:1,84:85,13:0.1327:1,1:21.6:1:29.8:1:1:0:59.8:12:0.1237:0:1.5 0/0:43:0:0,0:1,42:43,0:0:1,0:25.5:1:32:1:1:0:60:86:1:0:0.9 +16 81957386 . A T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.39242;SOR=1.87684;LSEQ=TTTGAGAAAATGGATAAACA;RSEQ=CAATATTAACAGGTATCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:37:0,37:0,20:20,37:0.6491:1,1:24.1:1:30.6:1:1:0:60:74:0.6491:0:1.3 1/0:18:14:0,14:0,4:4,14:0.7778:0,1:17.5:1:30.1:1:1:0:60:28:0.7778:0:1.4 +16 81957509 . T C 58 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTAATTGCTTTCCATGCAT;RSEQ=GTCTAACCAAATCTTCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:0,4:4,4:0.5:0,2:19.5:1:29.3:1:1:0:60:8:0.5:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:17:0:32:0:1:0:60:2:1:0:1 +16 81959952 . A G 64 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCCTGGCTGCGGAAAAT;RSEQ=GCTCAAGAGATGGGCAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:24.3:1:32:1:1:0:60:8:1:0:1.5 1/1:1:1:0,1:0,0:0,1:1:0,0:10:0:32:0:1:0:60:2:1:0:1 +16 81960200 . A G 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCACTCAGCTTATGTTA;RSEQ=TTTAGAGTCCTAATAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:31.7:1:31.7:1:1:0:60:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81960365 . C T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAAATTCACAACCTCCC;RSEQ=GAAATAGGGGTGAACTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:38.3:1:30.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81960480 . GC G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.07192;SOR=Inf;LSEQ=ATGTGATGGGGGTAAAATCA;RSEQ=CCCCAGTAACTCATTAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:43,2:45,0:0:1,0:26.2:1:32:1:1:0:60:90:1:0:1 0/1:17:2:1,1:14,1:15,2:0.1176:1,2:26:0:33.5:1:0.22794:10.24702:57.5:4:0.1176:0:1 +16 81960497 . A C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7855;SOR=0.8679;LSEQ=TCAGCCCCCAGTAACTCATT;RSEQ=GTAATTAAAAAATAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:73:60:59,1:13,0:13,60:0.8219:1,1:20.1:1:32.1:1:1:0:60:120:0.8219:0:1.1 1/1:30:24:22,2:5,1:6,24:0.8:2,2:16.9:1:30.7:1:0.50148:2.13:59.8:48:0.8:0:1.1 +16 81960958 . G C 117 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.14262;SOR=0.19396;LSEQ=ATTGAGATTGAGTTGTTGTG;RSEQ=GTGAGTTGCTGTGACAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:0,17:0,29:29,17:0.3696:1,1:20.6:1:28.8:1:1:0:60:16:0.3556:0:2 0/1:10:1:0,1:1,8:9,1:0.1:2,0:31:0:31:0:1:0:60:2:0.1111:0:1 +16 81961002 . T C 139 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24;SOR=0;LSEQ=CGTGTTTTAATCAGGTTGTG;RSEQ=TGGGCTTGGAAGGATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:1,18:0,5:5,19:0.7917:0,1:28.6:1:32.8:1:1:0:58.6:18:0.7826:0:2.9 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:31:0:1:0:60:2:1:0:0 +16 81961020 . C G 133 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTGGGCTTGGAAGGATTT;RSEQ=ATTATGCAGGAGAATTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:1,16:0,3:3,17:0.85:0,1:29.6:1:32.6:1:1:0:59:34:0.85:0:3.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81961022 . T A 126 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGGCTTGGAAGGATTTCA;RSEQ=TATGCAGGAGAATTCCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:1,17:0,2:2,18:0.9:0,1:27.4:1:30.4:1:1:0:59.1:17:0.8947:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81961260 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCCACTTTCAGCGTGCT;RSEQ=GCACTCCACCAAGGATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:33.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81961265 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTTCAGCGTGCTAGCAC;RSEQ=CCACCAAGGATGATATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:33:0:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81961639 . CTAAG C 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGTTCTGCCACCTCTC;RSEQ=CCCAGGATATTCTTCATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:19.3:1:33.3:1:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81961873 . G T 124 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAGTCTAGGATGTGTTT;RSEQ=GAAACCAGATCTGAGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:17,0:4,0:4,17:0.8095:0,1:29.6:1:30.5:1:1:0:58.8:16:0.8:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81962071 . A C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00203;SOR=0.52467;LSEQ=TTTTAAACAGTTCCACAGGC;RSEQ=GTATCTCTGCTAAACGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:246:230,16:48,2:50,246:0.8283:1,2:23.9:1:31.4:1:0.74719:1.66707:59.9:81:0.8265:0:1.1 1/0:254:182:168,14:62,9:71,182:0.7165:2,2:22.6:1:30.4:1:0.22859:1.74:60:59.667:0.716:0:1.1 +16 81962531 . T C 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53602;SOR=0;LSEQ=GGATCCATCTGTGTTTCCCA;RSEQ=GCGTTGCGAAGGAAAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:8:0,8:0,17:17,8:0.32:1,0:18.8:1:31.4:1:1:0:54:16:0.32:0:1.5 0/0:3:0:0,0:0,3:3,0:0:0,0:38.7:1:29.3:1:1:0:47.3:6:1:0:0 +16 81962574 . A C 80 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCAGCCTGGCTGAAATGC;RSEQ=GCGTGGAGTTGGGAGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:4,6:0.6:0,0:45.3:1:31:1:1:0:52:12:0.6:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81962621 . G C 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCCAGCTCTGCCTCTCT;RSEQ=TCGCTGTGAGACTACAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:16.5:1:31.5:1:1:0:60:4:0.3333:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81962627 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCTGCCTCTCTGTCGCT;RSEQ=TGAGACTACAGGCCTGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:18:1:29.5:1:1:0:45.5:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81964728 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTTTTTTTTTCCTGCAT;RSEQ=TTAAGTGTCCCTCTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:29.5:1:33.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81964977 . A G 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAGTAGACGTCCCCATC;RSEQ=GTGCTAACCGTGGTCATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:177,1:178,0:0:1,0:22.7:1:30.8:1:1:0:60:88:1:0:0.1 0/1:131:31:31,0:98,2:100,31:0.2366:1,1:21.2:1:29.6:1:1:0:60:62:0.2403:0:1 +16 81965344 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16966;SOR=Inf;LSEQ=GACTGTGGGTGGGTCCAGGC;RSEQ=GCAGGATGAGCAGGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:17,235:252,0:0:2,0:24.8:1:32.1:1:1:0:60:83:1:0:0.1 0/1:177:2:1,1:6,169:175,2:0.0113:1,2:25.5:1:28.5:1:0.07775:26.16:60:4:0.0114:0:1 +16 81965387 . A G 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54132;SOR=0;LSEQ=CTACTCAGAATTCAGGAAGG;RSEQ=GACCAGGTGGATTCAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:0,2:3,102:105,2:0.0187:1,0:33:1:26.5:1:1:0:60:4:0.019:0:3 0/0:58:0:0,0:2,56:58,0:0:1,0:25.9:1:30.3:1:1:0:60:28:1:0:0 +16 81968204 . T A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08272;SOR=Inf;LSEQ=ACTTCCTTTAGAGTCTGATA;RSEQ=TTTCAGAGGGGGCAGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:27,289:316,0:0:2,0:21.8:1:30.8:1:1:0:60:157:1:0:0.1 0/1:245:3:2,1:30,212:242,3:0.0122:2,2:12.3:1:26.7:1:0.04569:13.85:60:6:0.0123:0:1 +16 81968409 . G GGCT 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGACTCACAGTTCCACGT;RSEQ=GAGGAGGCCTCACAATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:9,3:0.25:0,0:27.3:1:31.7:1:1:0:56:6:0.25:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81968848 . T C 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGGCTGCTGGCATTCCT;RSEQ=GGCCTTCTCCTCTTCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:26.5:1:1:0:60:4:1:0:1 +16 81969436 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCTCCCAAGATCTTCTC;RSEQ=TACCCAAAACCATTCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:22:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81969515 . TA T 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.69895;LSEQ=GTTCAAGGATGGTGATAGTT;RSEQ=AAAAAAAAAGTAAATTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:11,0:11,2:0.1538:0,0:34:1:33:0:1:0:60:4:0.1538:0:0 0/1:9:1:1,0:8,0:8,1:0.1111:0,0:14:0:32:0:1:0:60:2:0.125:0:0 +16 81970188 . C G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20149;SOR=0.24525;LSEQ=ACCGAAGGCTGCTTGGCTTA;RSEQ=GCAGGCTTCGTGATTGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:34:0,34:0,2:2,34:0.9444:0,1:25.4:1:30.1:1:1:0:60:16:0.9412:0:1.2 1/1:10:8:0,8:0,2:2,8:0.8:0,0:21.5:1:31.3:1:1:0:58.9:16:0.8:0:1 +16 81970495 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACATTCTTTTTATAGCC;RSEQ=CATCGGATTCCACAGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:45.5:1:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81970766 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGCCAAACTGCCCTCCA;RSEQ=AGAGATCGTGGGCGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:20.5:1:29:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81971264 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16866;SOR=Inf;LSEQ=CAGCTGCCTCACATTAATTT;RSEQ=GGGAAAAGGTGAAATTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:159,1:160,0:0:1,0:24.7:1:33:1:1:0:60:320:1:0:0 0/1:112:2:1,1:107,3:110,2:0.0179:1,2:8:0:30.5:1:0.07046:31.01699:60:4:0.0182:0:1.5 +16 81971282 . A G 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58192;SOR=2.61454;LSEQ=TTGGGGAAAAGGTGAAATTC;RSEQ=TTCCCCACCTAGAAACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:215,13:228,1:0.0044:2,0:12:0:25:0:1:0:60:2:0.0044:0:1 0/1:176:2:1,1:160,14:174,2:0.0114:2,2:22:1:28.5:1:0.16364:11.07581:60:4:0.0114:0:1 +16 81971403 . T C 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.37731;LSEQ=CACGCATTGTTTTCTCTCAA;RSEQ=GGGCGCACGGGCTACGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1130:667:357,310:250,212:462,667:0.5903:2,2:24.4:1:31.2:1:0.85568:1.02398:60:132.4:0.5927:0:1.1 0/1:1247:439:239,200:439,366:805,439:0.352:2,2:25.9:1:30.2:1:1:1.00372:60:72.167:0.352:0:1.1 +16 81971560 . G A 55 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.73546;SOR=1.28251;LSEQ=GCCAGCCGCCCTCCCTGGGG;RSEQ=CTGGGCCGATGCTGTCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:4:3,1:115,342:457,4:0.0087:2,2:14.8:1:28.5:1:0.05342:8.87:60:8:0.0088:0:1 0/1:361:4:1,3:87,269:356,4:0.0111:2,2:12.5:1:27.8:1:1:1.03:60:8:0.0113:0:2.3 +16 81971567 . C T 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=15.42988;LSEQ=GCCCTCCCTGGGGGCTGGGC;RSEQ=GATGCTGTCTTGAGAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:2:1,1:89,316:405,2:0.0049:2,2:6:1:27.5:1:0.39379:3.54:60:4:0.0051:0:1 0/1:324:23:3,20:67,233:300,23:0.071:2,2:24:1:29.8:1:0.43189:1.91385:60:46:0.0726:0:1.2 +16 81971582 . A G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=3.38021;LSEQ=TGGGCCGATGCTGTCTTGAG;RSEQ=GCAGGGAACCCATGTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:62:10,52:27,214:241,62:0.2046:2,2:22.4:1:31.7:1:0.28336:1.52:59.9:61:0.204:0:1.2 0/1:219:102:12,90:10,107:117,102:0.4658:2,2:25:1:30.5:1:0.50198:1.42:60:204:0.4679:0:1.2 +16 81971625 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16531;SOR=Inf;LSEQ=GGCTGGTTGTCTTGTTTAAA;RSEQ=GATCCCCATTCAGGCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:3,132:135,0:0:1,0:25:1:30.2:1:1:0:59.9:44:1:0:0.5 0/1:93:2:1,1:2,89:91,2:0.0215:1,2:30.5:1:29.5:1:0.06381:36.54:60:4:0.0215:0:1 +16 81971657 . T C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.85253;SOR=1.12145;LSEQ=AGGCAGTGTTTGAGGATCTT;RSEQ=CTTTCTTACAGTACACTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:42:0,42:2,43:45,42:0.4828:1,1:24.8:1:30.9:1:0.49479:0:60:20:0.4706:0:1.4 1/0:43:22:1,21:1,20:21,22:0.5116:1,1:18.1:1:30.9:1:1:1.04883:60:44:0.5116:0:2.1 +16 81971677 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.45142;SOR=1.56231;LSEQ=TCTTTCTTACAGTACACTCC;RSEQ=GGGTCGTTCTGGGAGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:21:2,19:0,36:36,21:0.3684:1,2:26.4:1:32.3:1:0.13158:0:60:42:0.375:0:1.6 0/1:23:11:0,11:1,11:12,11:0.4783:2,0:23.5:1:29.5:1:1:0:60:10:0.4545:0:2.4 +16 81972268 . G A 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACTGCAGAAGGTTGCTCC;RSEQ=GCTTTTCCAGTGAATCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:134,4:138,0:0:1,0:23:1:30.2:1:1:0:60:137:1:0:0.9 0/1:90:13:13,0:76,1:77,13:0.1444:1,1:25.3:1:29.6:1:1:0:60:26:0.1461:0:1.8 +16 81972283 . T G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05423;SOR=0.62439;LSEQ=GCTCCGGCTTTTCCAGTGAA;RSEQ=CTAGGAAAATTAGGGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:187:119:118,1:65,3:68,119:0.6364:1,1:22.5:1:33.9:1:0.1374:5.40:60:238:0.6398:0:1.1 1/0:115:60:60,0:53,1:54,60:0.5217:1,1:26.1:1:32.4:1:0.47368:0:60:120:0.5217:0:1 +16 81972289 . A C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02163;SOR=1.79634;LSEQ=GCTTTTCCAGTGAATCTAGG;RSEQ=AAATTAGGGCTGGCATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:41:38,3:162,1:163,41:0.201:1,2:24.7:1:33:1:0.02625:12.56876:60:82:0.2103:0:1 0/1:138:43:41,2:95,0:95,43:0.3116:1,1:23.5:1:32.2:1:0.09553:0:60:86:0.3139:0:1.3 +16 81972496 . A G 215 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTGGAGCCGAGTATGACAAC;RSEQ=ACAAGTTCAAGACGACGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1731:0:0,0:806,924:1730,0:0:2,0:25.3:1:30.6:1:1:0:60:54.806:1:0:0.2 0/1:2031:147:67,80:929,951:1880,147:0.0724:2,2:23.7:1:30:1:0.39228:1.16632:60:146:0.0728:0:1.2 +16 81972902 . A G 60 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGATCAGCCTAACCTGGG;RSEQ=GATCTTAGCCCCTAGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:25.3:1:30:1:1:0:60:8:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 81973442 . T C 140 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.511;LSEQ=GAAGGATGCGGAGATTGTCT;RSEQ=ACCAGAAGGGGGCAGCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:1:1,0:324,41:365,1:0.0027:2,0:28:0:15:0:1:0:60:0:0:0:7 0/1:263:24:20,4:205,34:239,24:0.0913:2,2:25.1:1:30.6:1:0.7606:1.20498:60:48:0.0916:0:1 +16 81973474 . C A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02711;LSEQ=GCAGCTCCAATGTGGCCTCT;RSEQ=ATGAGCTTTGATCTCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:590:587:443,144:0,0:0,587:0.9949:0,2:23.8:1:28.7:1:1:0:60:44.154:0.9965:0:1.1 1/1:535:450:315,135:61,22:83,450:0.8411:2,2:24.1:1:27.8:1:0.60066:1.18797:60:39.909:0.8442:0:1.1 +16 81973773 . C G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07334;SOR=Inf;LSEQ=TTTCCTGGTTTGGATGGAAT;RSEQ=ACTGTAAAACCGATTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:2,121:123,0:0:1,0:24:1:32.6:1:1:0:60:246:0.9919:0:0.3 0/1:91:3:0,3:3,85:88,3:0.033:1,0:34.3:1:31.7:1:1:0:60:6:0.033:0:1.3 +16 81973788 . T C 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAATCACTGTAAAACCGAT;RSEQ=GGGTGGCTTGGAGAGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:0,99:99,0:0:1,0:24.3:1:30.3:1:1:0:60:32:1:0:0.4 0/1:62:19:0,19:2,41:43,19:0.3065:1,1:29.7:1:30.5:1:1:0:60:38:0.3065:0:1.3 +16 81973805 . A T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08403;SOR=0.3446;LSEQ=GATTGGGTGGCTTGGAGAGC;RSEQ=GGTGTACAGCCTGTCGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:18:0,18:0,60:60,18:0.2308:1,1:20.3:1:30.6:1:1:0:60:17:0.2237:0:1.1 0/1:43:4:0,4:2,37:39,4:0.093:2,0:22:1:29.5:1:1:0:60:8:0.0952:0:1 +16 81973807 . G GTGCA 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03002;SOR=0.20284;LSEQ=TTGGGTGGCTTGGAGAGCAG;RSEQ=TGTACAGCCTGTCGTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:16:0,16:0,61:61,16:0.2078:1,1:21.8:1:31.8:1:1:0:60:32:0.2133:0.0779:1.1 0/1:40:2:0,2:2,36:38,2:0.05:2,0:39:1:31.4:1:1:0:60:4:0.0513:0:1 +16 81973837 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07356;SOR=Inf;LSEQ=TGTCGTGTAGCACACAGGTG;RSEQ=GAGGAAGTGGGTGACAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:47,0:0:1,0:24.9:1:30.5:1:1:0:60:10.75:1:0:0.7 0/1:18:2:0,2:1,15:16,2:0.1111:1,0:19.5:1:32:0:1:0:60:4:0.1111:0:2 +16 81973841 . G C 131 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00118;SOR=0;LSEQ=GTGTAGCACACAGGTGGGAG;RSEQ=AAGTGGGTGACAGGGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:18:0,18:0,26:26,18:0.4091:1,1:22.1:1:31.6:1:1:0:60:17:0.3953:0:1.2 0/0:17:0:0,0:1,16:17,0:0:1,0:19.7:1:31.2:1:1:0:60:34:1:0:0.6 +16 81979657 . G C 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00692;SOR=Inf;LSEQ=TTCCACAAAGTCAGCCCCCA;RSEQ=CATGGGGCACTGACTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:138,2:140,0:0:1,0:23.7:1:33:1:1:0:60:27:1:0:0 0/1:111:6:6,0:103,2:105,6:0.0541:1,0:31:1:32.2:1:1:0:60:12:0.0545:0:1 +16 81979715 . C CA 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.27943;SOR=0.38425;LSEQ=TATGATCCCGAGGTAGCCTC;RSEQ=AAAAAAAATCTAAGGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:5:4,1:357,120:477,5:0.0104:2,2:15.4:1:31:1:1:1.34:60:10:0.0106:0.0021:0.6 0/0:499:2:2,0:342,154:496,2:0.004:2,0:24:1:31:0:1:0:60:4:0.0041:0:0 +16 81980019 . T C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0691;SOR=0.5322;LSEQ=ATACAAGAATTCCTTTTTGC;RSEQ=AATTCCCCAGAGTGTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:59:0,59:0,43:43,59:0.5784:1,1:23.5:1:32.3:1:1:0:60:58:0.58:0:1.1 0/1:57:24:0,24:3,30:33,24:0.4211:2,1:23.9:1:31.7:1:0.25564:0:60:48:0.4211:0:1.2 +16 81990505 . G T 249 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTAGGTCAGCCCCTCCACCT;RSEQ=CAAAAACTTTTGGGGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:959:316:114,202:238,403:641,316:0.3295:2,2:25.2:1:30:1:0.77583:1.04641:60:34.111:0.3273:0:1.1 0/0:1027:0:0,0:406,618:1024,0:0:2,0:25.4:1:31.3:1:1:0:60:77.769:0.997:0:0.2 +16 81990605 . GGGCATGGTGGCTCACAGGCCA G 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTCAGAAATCCTTGGCC;RSEQ=GGCATGGTGGCTCATGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:0,133:133,0:0:1,0:23.7:1:31.9:1:1:0:58.8:266:1:0:0 0/1:97:16:0,16:2,79:81,16:0.1649:1,1:28.1:1:31.6:1:1:0:48.8:32:0.1684:0.0103:0.1 +16 81991325 . G T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTACTCACATTATTCTCATT;RSEQ=AATCTTCATGTCAGCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:19:19,0:4,0:4,19:0.8261:0,1:23:1:31.8:1:1:0:60:38:0.8636:0:1.2 1/1:4:4:4,0:0,0:0,4:1:0,0:17.8:1:29.5:1:1:0:60:8:1:0:1 +16 81991638 . T C 210 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTGTAAGGGTATTGTGTGTG;RSEQ=GCGCATGTGTGTTTGCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1644:0:0,0:724,914:1638,0:0:2,0:25.6:1:30.3:1:1:0:59.9:147.909:0.9975:0:0.2 0/1:1687:120:54,66:743,818:1561,120:0.0711:2,2:23.2:1:30.5:1:0.63555:1.11008:59.6:119:0.0712:0:1.2 +16 81991864 . C G 105 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24381;SOR=0.22767;LSEQ=CATTTTTGGCCTCTCATGTT;RSEQ=CAAACCTCATTGAATAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:0,9:0,26:26,9:0.2571:1,0:31.8:1:33.2:1:1:0:60:18:0.2571:0:1.1 0/1:14:1:0,1:0,13:13,1:0.0714:1,0:17:0:34:0:1:0:60:2:0.0714:0:1 +16 82113356 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24287;SOR=0;LSEQ=GGAAAAGAAAAAGCTAGAAT;RSEQ=TAACACAAGGATTAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:121,32:153,2:0.0129:2,2:13:1:31.5:1:0.38157:3.739:60:4:0.0132:0:1 0/0:159:0:0,0:122,37:159,0:0:2,0:22.7:1:31.3:1:1:0:59.8:78.5:1:0:0.2 +16 82113471 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45919;SOR=1.12155;LSEQ=TGATATATCTTTGGCAAAAT;RSEQ=AATGTAATAGTAACTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:127:60,67:115,161:276,127:0.3144:2,2:25.1:1:29.4:1:0.33052:1.25:60:62.5:0.3125:0:1.1 0/1:424:144:66,78:130,149:279,144:0.3396:2,2:23.8:1:28.4:1:0.91822:1.03105:60:288:0.342:0:1.1 +16 82113555 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50162;SOR=0;LSEQ=AGCAAGGTGCATGGAGGGAG;RSEQ=GAAGCAGTCAGTCACTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:51,133:184,2:0.0108:2,2:35.5:1:30:1:0.48207:2.59:60:4:0.0109:0:1 0/0:159:0:0,0:40,119:159,0:0:2,0:24.8:1:29.8:1:1:0:60:78.5:1:0:0.2 +16 82468589 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21705;SOR=Inf;LSEQ=TACTCTTCAAAAGGGAATGC;RSEQ=CCACAAGTGTTACCATGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:129,55:184,0:0:2,0:22.8:1:31.5:1:1:0:59.1:183:1:0:0.1 0/1:161:2:1,1:105,54:159,2:0.0124:2,2:17:1:29.5:1:1:1.93591:60:4:0.0125:0:1 +16 82468627 . G A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=GCTAGACTGGGAGAGTCTAC;RSEQ=GTGTTCCCCAGCATGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:138,114:252,0:0:2,0:29.2:1:30.1:1:1:0:59.3:62:1:0:0.1 0/1:214:11:6,5:112,91:203,11:0.0514:2,2:29.5:1:30.5:1:1:1.02553:38.1:22:0.0529:0:1.7 +16 82468649 . G A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00223;SOR=Inf;LSEQ=TGTTCCCCAGCATGCTGTTG;RSEQ=CATTGCTGTAAACAACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:118,138:256,0:0:2,0:25.4:1:31.2:1:1:0:59.6:35.571:1:0:0.1 0/1:227:8:4,4:107,112:219,8:0.0352:2,2:20.5:1:28.6:1:1:1.05:36:16:0.0362:0:2 +16 82468709 . T TC 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.05941;SOR=Inf;LSEQ=ACTGGGAGAGTCTACAGTGT;RSEQ=CCCCCGCACGCTGTTGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:17,81:98,0:0:2,0:21.5:1:30.6:1:1:0:60:97:1:0:0.2 0/1:100:5:1,4:22,73:95,5:0.05:2,2:23.4:1:30.4:1:1:1.20333:60:10:0.0515:0:0 +16 82468718 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=GTCTACAGTGTTCCCCCGCA;RSEQ=GCTGTTGACATTGTTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:10,72:82,0:0:2,0:21.1:1:30:1:1:0:60:26.333:1:0:0.1 0/1:92:2:1,1:19,71:90,2:0.0217:2,2:16.5:1:30.5:1:0.38939:3.67:36:4:0.0217:0:3 +16 82468726 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24574;SOR=Inf;LSEQ=TGTTCCCCCGCACGCTGTTG;RSEQ=CATTGTTGTAAACAAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:11,60:71,0:0:2,0:21:1:30:1:1:0:60:34.5:1:0:0.2 0/1:76:3:1,2:15,58:73,3:0.0395:2,2:11.7:1:31:1:0.51323:1.91:35:6:0.0395:0:2.7 +16 82468755 . A T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13266;SOR=Inf;LSEQ=TAAACAAACAAGGGCAAGAT;RSEQ=CTTGCCAAGATAATTAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:5,37:42,0:0:2,0:25.7:1:30:1:1:0:59.9:84:1:0:0.1 0/1:56:4:1,3:9,43:52,4:0.0714:2,2:23.5:1:28.3:1:0.55571:1.58:41.5:8:0.0714:0:1.8 +16 82728685 . T C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00078;SOR=0.12416;LSEQ=GTGGGCAAAGTCCTGTCGGC;RSEQ=GGAGGAAGGGCATGTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:20:8,12:1,4:5,20:0.8:2,2:20.3:1:30.3:1:0.62055:2.57:60:40:0.8:0:1.1 0/1:28:9:5,4:7,12:19,9:0.3214:2,2:32.3:1:28.9:1:0.43188:2.08:60:18:0.3333:0:1.1 +16 83236502 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACACTGAAGACTCCAGA;RSEQ=GTGGGGAGGGATGGGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 83238012 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49812;SOR=Inf;LSEQ=ATAGCATGTGCCGGAGTCAG;RSEQ=GTTCAGTAAATGGTAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:40,37:77,0:0:2,0:29:1:30.3:1:1:0:59.7:154:1:0:0.2 0/1:85:2:1,1:38,45:83,2:0.0235:2,2:40.5:1:30:1:1:1.18:60:4:0.0238:0:1 +16 84245120 . A G 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGACCTCAGGGGATCCGCCC;RSEQ=CCGCAGCCTCCCAAAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:18:1:30.7:1:1:0:53:6:0.75:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:48:0:32:0:1:0:39:2:1:0:1 +16 84245226 . G A 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=TGGGATTCAACCTGTTTCCT;RSEQ=CTCCAGGGTGAACGCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:32,0:0:2,0:26.5:1:32.3:1:1:0:60:64:1:0:0 0/1:27:9:6,3:11,7:18,9:0.3333:2,2:27.6:1:27.9:1:1:1.26:60:18:0.3333:0:1.3 +16 84245230 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22186;SOR=Inf;LSEQ=ATTCAACCTGTTTCCTGCTC;RSEQ=AGGGTGAACGCTGACTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:32,0:0:2,0:27.9:1:31.7:1:1:0:60:64:1:0:0 0/1:29:2:1,1:17,10:27,2:0.069:2,2:14:1:29:1:1:1.66781:60:4:0.069:0:1 +16 84245323 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09023;SOR=Inf;LSEQ=ACTGCAGAACCAATAAGGCC;RSEQ=AAATCACATGCTTGGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:2,8:10,0:0:2,0:19.3:1:32.3:1:1:0:60:20:1:0:0 0/1:11:4:1,3:1,6:7,4:0.3636:2,2:12.8:1:28.8:1:1:1.87:60:8:0.3636:0:1.5 +16 84636456 . C CAA 29 pSTD;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.07;SOR=0;LSEQ=GGGCGACAGAGACTTCATCT;RSEQ=AAAAAAAAAAAAAAGTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,2:4,2:0.2857:2,2:14:0:29.3:1:1:1:60:4:0.3333:0:0 0/0:18:0:0,0:10,4:14,0:0:2,0:23.6:1:27.4:1:1:0:49.9:6:0.8:0:1.2 +16 84636489 . C A 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.01709;SOR=Inf;LSEQ=AAGTGCATGGAAAGGGAAGG;RSEQ=CAAAAAGGCAGTGTTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:22,0:0:2,0:19.7:1:30.5:1:1:0:59.1:21:1:0:0.2 0/1:34:8:4,4:11,15:26,8:0.2353:2,2:25.9:1:27.6:1:1:1.35:56.4:16:0.25:0:1.3 +16 84636781 . A G 48 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GTGGGGGCAGACTCGCAGCC;RSEQ=GTTTTCCTTCCCCGTGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:12.7:1:30.3:1:1:0:60:6:1:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:12:0:31:0:1:0:60:2:1:0:0 +16 84636803 . T C 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TTTTCCTTCCCCGTGGACTT;RSEQ=AACAACACTCCAGCCCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:1,3:0.75:0,2:25.3:1:34.3:1:1:0:60:6:0.75:0:1.7 0/0:3:0:0,0:2,1:3,0:0:2,0:21.7:1:29.3:1:1:0:60:6:1:0:0.3 +16 84637352 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAGGGCCTGTGGGGTTGGC;RSEQ=CATCATGCCTGGGGACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:28.5:1:1:0:60:4:1:0:1 +16 85214736 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24571;SOR=0;LSEQ=TCCGCAGCTGCCCACAGGGT;RSEQ=CGCTGGCCCCGGGATCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:50,35:85,2:0.023:2,2:22.5:1:28:1:1:1.42258:60:4:0.0233:0:1 0/0:88:0:0,0:53,35:88,0:0:2,0:22.9:1:30.2:1:1:0:60:176:1:0:0.2 +16 85214747 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4978;SOR=Inf;LSEQ=CCACAGGGTCCGCTGGCCCC;RSEQ=GGATCCTTCTGGGTCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:65,48:113,0:0:2,0:23:1:29.9:1:1:0:60:36.667:1:0:0.2 0/1:114:2:1,1:69,43:112,2:0.0175:2,2:29.5:1:28.5:1:1:1.59771:60:4:0.0175:0:1 +16 85214767 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50035;SOR=Inf;LSEQ=GGGATCCTTCTGGGTCTCAT;RSEQ=TGGGCTCCACGCTGACACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:90,63:153,0:0:2,0:27:1:32.6:1:1:0:60:50:1:0:0.2 0/1:173:2:1,1:99,72:171,2:0.0116:2,2:26:1:30.5:1:1:1.37241:60:4:0.0116:0:1 +16 85214786 . C A 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2013;SOR=0;LSEQ=TCTGGGCTCCACGCTGACAC;RSEQ=GGCTAACTTGGTGACCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:81,77:158,2:0.0125:2,2:45:0:29:0:1:1.05164:60:4:0.0126:0:1.5 0/0:196:0:0,0:101,95:196,0:0:2,0:26.2:1:29.9:1:1:0:59.7:195:1:0:0.2 +16 85338201 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.4949;SOR=Inf;LSEQ=CTGCATGGCAGCTGCCAAGC;RSEQ=GGGGGCGGGGGGGTGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:22,0:0:1,0:20.3:1:32.5:1:1:0:58.1:44:1:0:2 0/1:27:2:2,0:25,0:25,2:0.0741:1,0:15:1:32:0:1:0:60:4:0.0769:0:1 +16 85338207 . C CG 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01836;SOR=0.17312;LSEQ=GGCAGCTGCCAAGCCGGGGG;RSEQ=GGGGGGGTGGGGCATCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:11,0:11,9:0.4091:0,0:29.3:1:31.1:1:1:0:57.8:18:0.4091:0:3.2 0/1:29:3:3,0:24,0:24,3:0.1034:1,0:45.3:1:29.3:1:1:0:60:6:0.1071:0:1.7 +16 85338214 . GT G 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.56278;SOR=0.33462;LSEQ=GCCAAGCCGGGGGCGGGGGG;RSEQ=GGGGCATCCCTTTTGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:0,0:0,2:0.0741:0,0:22.5:1:33:0:1:0:60:4:0.0741:0:0 0/1:39:1:1,0:12,1:13,1:0.0256:1,0:29:0:32:0:1:0:60:2:0.0294:0:0 +16 85338215 . T G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00189;SOR=0.10682;LSEQ=CCAAGCCGGGGGCGGGGGGG;RSEQ=GGGGCATCCCTTTTGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:25:25,0:0,0:0,25:0.9259:0,1:24.4:1:31.9:1:1:0:58.3:50:0.9259:0:2.7 1/0:39:22:18,4:12,1:13,22:0.5641:1,2:17:1:28.9:1:0.62998:2.60115:55.9:21:0.6176:0:2 +16 85338232 . C T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0828;SOR=0;LSEQ=GGGTGGGGCATCCCTTTTGC;RSEQ=TTGAGTCCACCACCAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:2,1:35,14:49,3:0.0577:2,2:18.3:1:23:1:1:1.24447:53.3:2:0.0455:0:4 0/0:66:0:0,0:40,26:66,0:0:2,0:18.5:1:28.2:1:1:0:59.2:10:1:0:0.8 +16 85338253 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50478;SOR=Inf;LSEQ=TTGAGTCCACCACCAAACCT;RSEQ=GTGTCAGCTGAGAACGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:52,31:83,0:0:2,0:23:1:30.8:1:1:0:59.8:19.75:1:0:0.8 0/1:106:2:1,1:58,46:104,2:0.0189:2,2:18:0:30.5:1:1:1.25808:60:4:0.0192:0:1.5 +16 85338293 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19696;SOR=0;LSEQ=AAAGCCACCTGTTGGCAGCT;RSEQ=GGCCGTGATGTTCCTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:58,57:115,2:0.0171:2,2:15.5:1:27:1:1:1.0174:60:4:0.0171:0:1 0/0:146:0:0,0:74,72:146,0:0:2,0:27.3:1:30.9:1:1:0:59.8:145:1:0:0.4 +16 85338316 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18991;SOR=0;LSEQ=CCGTGATGTTCCTGCCTGAA;RSEQ=ATAAATAACACCTGCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:43,59:102,2:0.0192:2,2:35:1:30.5:1:1:1.37:60:4:0.0196:0:1 0/0:134:0:0,0:60,73:133,0:0:2,0:23.2:1:31:1:1:0:60:132:0.9925:0:0.3 +16 85338340 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50537;SOR=Inf;LSEQ=AATAACACCTGCAGAAGATG;RSEQ=CAGAGACAGGCCAGGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:24,38:62,0:0:2,0:25.8:1:31.9:1:1:0:60:61:1:0:0.3 0/1:81:2:1,1:32,47:79,2:0.0247:2,2:25.5:1:27.5:1:1:1.46:60:4:0.0253:0:1 +16 85338371 . C A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38515;SOR=1.52288;LSEQ=CCAGGGCCCTCTCGACTTCA;RSEQ=TGGGGATAAGACAGCGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:18:4,14:4,15:19,18:0.4865:2,2:23.3:1:31.2:1:1:1.07:60:36:0.4865:0:1 1/0:49:29:6,23:3,16:19,29:0.5918:2,2:23.6:1:29.3:1:1:1.38:60:28:0.5957:0:1 +16 85338398 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13564;SOR=0;LSEQ=TAAGACAGCGACCAGGCCGC;RSEQ=CTGCAGCCACAGAATGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:0,16:16,2:0.1111:1,2:19:0:33:0:0.11111:0:60:4:0.1111:0:1.5 0/0:30:0:0,0:1,29:30,0:0:1,0:21.8:1:29:1:1:0:60:60:1:0:0.6 +16 85490399 . T C 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01947;SOR=0;LSEQ=GCTGTGGCGACTCAGGGTCC;RSEQ=GGCGGGGAGAACCTGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:8,10:18,9:0.3333:2,2:20:1:27.4:1:1:1:60:8:0.32:0:1.1 0/0:13:0:0,0:4,9:13,0:0:2,0:28.2:1:29.7:1:1:0:60:26:1:0:0.1 +16 85741257 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GTTCTTGTTGGTGCTTATGG;RSEQ=AGGGGCATGTGTTTGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:33:1:32:1:1:0:60:10:1:0:0.2 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:25.5:1:29.5:1:1:0:60:4:0.3333:0:1 +16 85741351 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52288;SOR=Inf;LSEQ=CCAACAGCCAGGACCATGGC;RSEQ=CTCCCTTTCACCAGGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:26.2:1:30.6:1:1:0:60:29:1:0:0.1 0/1:49:2:1,1:26,21:47,2:0.0408:2,2:33.5:1:28.5:1:1:1.23267:60:4:0.0417:0:1 +16 85880256 . C G 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0364;SOR=Inf;LSEQ=TCACTCAGGCTGCCTGGACT;RSEQ=CTGGGTCTCCCCCTGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:38,0:0:1,0:27.5:1:32.1:1:1:0:60:37:1:0:0.4 0/1:31:4:4,0:27,0:27,4:0.129:1,0:25:1:33:1:1:0:60:8:0.1333:0:1.8 +16 85880315 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49826;SOR=0;LSEQ=TGCATGAAAAACAGATTTCA;RSEQ=GATTTCACTAAAATTGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:2,0:104,37:141,2:0.014:2,0:17.5:1:33:0:1:0:60:4:0.014:0:2.5 0/0:141:0:0,0:108,33:141,0:0:2,0:23.6:1:30.7:1:1:0:60:69.5:1:0:0.9 +16 85880339 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01274;SOR=0.60219;LSEQ=TTCACTAAAATTGGTTCGAG;RSEQ=CATCCTGTGTGTCCGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:218:160:111,49:36,22:58,160:0.7339:2,2:25.7:1:30.3:1:0.32928:1.38:60:320:0.7339:0:1.9 1/0:242:151:97,54:55,35:90,151:0.624:2,2:25.7:1:27.8:1:0.67957:1.14:60:36.75:0.6176:0:2 +16 85880399 . G C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00068;SOR=0.58249;LSEQ=GGGCGCAGGAGAAGGTGTGT;RSEQ=GGTCAGCAGGGTTCTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:353:259:132,127:45,48:93,259:0.7337:2,2:25.6:1:31:1:0.71741:1.11:59.9:258:0.735:0:2.2 1/0:414:255:122,133:81,78:159,255:0.6159:2,2:25.7:1:29.9:1:0.54606:1.13175:59.9:126.5:0.6141:0:2.2 +16 85880425 . A T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=3e-04;SOR=0.55105;LSEQ=GCAGGGTTCTCTGGGAAAGA;RSEQ=GACGGGAAGATGGCCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:327:242:118,124:37,48:85,242:0.7401:2,2:22.9:1:30.4:1:0.44955:1.23:60:47.4:0.7383:0:2.1 1/0:380:232:106,126:67,81:148,232:0.6105:2,2:25.8:1:29.7:1:1:1.02:59.8:115:0.615:0:2.1 +16 85880469 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24895;SOR=Inf;LSEQ=TGGCAGCCATGGGCCACCTG;RSEQ=CTCTTCACATTGAGCCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:78,138:216,0:0:2,0:25.7:1:29.7:1:1:0:60:53:1:0:1 0/1:229:3:1,2:83,143:226,3:0.0131:2,2:12:1:31.7:1:1:1.16013:60:6:0.0135:0:2 +16 85880496 . C T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49831;SOR=0;LSEQ=ACATTGAGCCTTGGAGCTGG;RSEQ=CAGCTAGAGGGCAGTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:41,102:143,2:0.0138:2,2:16:1:25.5:1:0.49684:2.47:60:4:0.0141:0:2.5 0/0:142:0:0,0:43,99:142,0:0:2,0:26.3:1:29.9:1:1:0:60:22.667:1:0:0.7 +16 85880505 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49813;SOR=Inf;LSEQ=CTTGGAGCTGGCCAGCTAGA;RSEQ=GGCAGTTGGGGAGAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:33,91:124,0:0:2,0:23:1:31.1:1:1:0:60:23.8:1:0:0.8 0/1:128:2:1,1:34,92:126,2:0.0156:2,2:46.5:1:31:1:0.47367:2.68:60:4:0.016:0:3 +16 85880551 . G C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01237;SOR=0.293;LSEQ=CACAAGAGAAGGCCGAGCTG;RSEQ=GAGGGAGGGTCTCTAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:47:3,44:1,6:7,47:0.8704:2,2:23.6:1:30:1:0.436:2.39206:60:22.5:0.8824:0:2 1/0:53:35:5,30:2,16:18,35:0.6604:2,2:23.3:1:29.3:1:1:1.33:60:34:0.6538:0:1.9 +16 85880560 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00712;SOR=0.2411;LSEQ=AGGCCGAGCTGGGAGGGAGG;RSEQ=TCTCTAAGGTGCGGTTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:38:2,36:0,6:6,38:0.8636:0,2:26.5:1:31.8:1:1:0:60:37:0.881:0:2.2 1/0:40:24:3,21:2,14:16,24:0.6:2,2:26.3:1:30.3:1:1:1:60:48:0.6154:0:2.1 +16 85880671 . C T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGATGTTCCAGAAGAGTGT;RSEQ=GTGAAGGAGCAAAGAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:18:1:32.3:1:1:0:60:8:0.4444:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:6:0:32:0:1:0:60:2:1:0:0 +16 85880822 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGGGAGGAGGCGGAGGAAG;RSEQ=GCACCTATGCTGCAGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:33:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 85880907 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGGCTCTGTGCGCTGCGC;RSEQ=GGGTGCCGGCCTGCTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:31.5:1:31.5:1:1:0:57:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36:0:31.5:1:1:0:60:4:1:0:1 +16 85936700 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1551;SOR=0;LSEQ=GTAGCATGTATCCAGGACTG;RSEQ=TTTGGGAGAATGAGGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:18,2:0.1:2,2:27:1:31:1:1:1.23603:60:4:0.1053:0:1 0/0:30:0:0,0:18,12:30,0:0:2,0:30.5:1:28.8:1:1:0:60:60:1:0:0 +16 85938125 . C A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCACGTCTCTGCCTGAC;RSEQ=GATGTTTGCAGTGGGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:27.5:1:1:0:60:4:1:0:1 +16 86248076 . C A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01928;SOR=Inf;LSEQ=CACACCAGCAGCATAGGTGT;RSEQ=CCCTGGGAGCCTGTTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:19,11:30,0:0:2,0:28.7:1:31.6:1:1:0:60:29:1:0:0.2 0/1:27:5:4,1:11,11:22,5:0.1852:2,2:20.6:1:27:1:0.34188:3.82:60:10:0.1923:0:1.4 +16 86248135 . C G 85 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13239;SOR=4.28645;LSEQ=ACCCCAGACCTGCTGAGTCA;RSEQ=AATCTGCACTTTGACAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:7,12:19,2:0.0952:2,2:44.5:1:34:1:1:1.67:60:4:0.0952:0:1 0/1:22:7:3,4:4,11:15,7:0.3182:2,2:27.3:1:30.6:1:0.63022:1.99:60:14:0.3333:0:1.3 +16 86437690 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20789;SOR=Inf;LSEQ=AAGCTGTGCCTGGAACCCCA;RSEQ=CGGAGTCTGCAGTGGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:34,0:0:2,0:26.7:1:32.5:1:1:0:60:68:1:0:0.1 0/1:29:2:1,1:14,13:27,2:0.069:2,2:12:0:31.5:1:1:1.07415:60:4:0.069:0:1 +16 86437767 . T C 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.22735;LSEQ=CATTATTTTTTCCTGGGTTT;RSEQ=TGTGGTTCGTCTACCTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:3,10:13,3:0.1875:2,2:26.3:1:33:1:1:1.61:60:6:0.2:0:1 0/1:9:2:1,1:1,6:7,2:0.2222:2,2:12.5:1:29:1:0.41667:4.58:60:4:0.25:0:1 +16 86437984 . G T 44 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCCGAGAAGCTGGGAT;RSEQ=ACAGGCGCACGCCACCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:33.3:1:28:1:1:0:38:6:1:0:1 +16 86544047 . C A 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CAGAGGTGCAGCCAGCCCCG;RSEQ=GCGCGCAGCCCCCTCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:25.2:1:30.6:1:1:0:60:10:0.8333:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:5:0:31:0:1:0:60:2:1:0:1 +16 86544473 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21392;SOR=Inf;LSEQ=AGAACTCCGTGCGCCACAAC;RSEQ=TCTCGCTCAACGAGTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:111,79:190,0:0:2,0:28:1:32.1:1:1:0:57.9:94:1:0:0.2 0/1:164:2:1,1:92,70:162,2:0.0122:2,2:26.5:1:30.5:1:1:1.31206:53:4:0.0125:0:1 +16 86544478 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21655;SOR=Inf;LSEQ=TCCGTGCGCCACAACCTCTC;RSEQ=CTCAACGAGTGCTTCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:108,81:189,0:0:2,0:28.6:1:30.8:1:1:0:57.2:62:1:0:0.2 0/1:165:2:1,1:92,71:163,2:0.0121:2,2:36.5:1:25.5:1:1:1.29371:60:4:0.0125:0:1 +16 86544479 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21655;SOR=Inf;LSEQ=CCGTGCGCCACAACCTCTCG;RSEQ=TCAACGAGTGCTTCATCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:108,81:189,0:0:2,0:28.7:1:32.6:1:1:0:57.2:62:1:0:0.2 0/1:165:2:1,1:92,71:163,2:0.0121:2,2:41.5:1:29.5:1:1:1.29371:44:4:0.0122:0:1.5 +16 86544504 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20487;SOR=Inf;LSEQ=CGAGTGCTTCATCAAGCTAC;RSEQ=CAAGGGCCTTGGGCGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:85,97:182,0:0:2,0:25.3:1:30.6:1:1:0:53.4:35.4:1:0:0.2 0/1:151:2:1,1:76,73:149,2:0.0132:2,2:23:1:27:1:1:1.04083:48:4:0.0134:0:1 +16 86544520 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08122;SOR=Inf;LSEQ=CTACCCAAGGGCCTTGGGCG;RSEQ=CCCGGCAAGGGCCACTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:60,84:144,0:0:2,0:23.7:1:31.1:1:1:0:49.8:71:1:0:0.1 0/1:111:3:2,1:51,57:108,3:0.027:2,2:17.3:1:26.7:1:0.60504:2.22:46.3:6:0.0286:0:1.3 +16 86544525 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58956;SOR=2.46393;LSEQ=CAAGGGCCTTGGGCGGCCCG;RSEQ=CAAGGGCCACTACTGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:1,0:56,80:136,1:0.0073:2,0:1:0:28:0:0.41606:0:60:2:0.0075:0:1 0/1:112:2:1,1:50,60:110,2:0.0179:2,2:20.5:1:27.5:1:1:1.20:48:4:0.0182:0:1 +16 86546145 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCTTCAACCCCGCCGGCAGT;RSEQ=GTAGCCTCTGAGGTTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:30:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:26:1:29.5:1:1:0:60:4:1:0:0.5 +16 86546173 . G A 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.1;SOR=0;LSEQ=CTGAGGTTGGGGGTGGTGGT;RSEQ=GCTGCCCTGGCGGTGACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:28.5:1:1:0:60:4:1:0:2 0/0:3:0:0,0:2,1:3,0:0:2,0:20.3:1:29.7:1:1:0:60:6:1:0:0.3 +16 86601049 . C T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=AGCTACGGCGGCATGGCCAG;RSEQ=CCCATGGGCGTCTATTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:22.6:1:27.8:1:1:0:55.8:4:0.4:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:20.8:1:31.8:1:1:0:60:8:1:0:0 +16 86601116 . TACC T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.05488;SOR=Inf;LSEQ=TGGGCCGCTCCTACGCGCCC;RSEQ=ACCACCACCAGCCCGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:27,4:31,0:0:2,0:21.6:1:26.8:1:1:0:60:9.333:1:0:0.1 0/1:10:2:1,1:8,0:8,2:0.2:0,2:17.5:1:27.3:1:0.2:0:60:4:0.2:0.1:0.5 +16 86601175 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50456;SOR=0;LSEQ=AAGCCGCCCTACAGCTACAT;RSEQ=GCGCTCATCACCATGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:44,12:56,2:0.0345:2,2:28:1:32:0:0.40109:3.56233:60:4:0.0345:0:1 0/0:44:0:0,0:36,8:44,0:0:2,0:22.9:1:30.3:1:1:0:52:88:1:0:0.1 +16 86601346 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24838;SOR=Inf;LSEQ=TGCTTCGTCAAGGTGCCCCG;RSEQ=GACGACAAGAAGCCCGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:68,158:226,0:0:2,0:30.5:1:30:1:1:0:35:36.667:1:0:0.1 0/1:229:3:1,2:85,141:226,3:0.0131:2,2:45:1:29:1:1:1.20467:29:6:0.0135:0:1 +16 86601431 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2081;SOR=Inf;LSEQ=AGAACGGCAGCTTCCTGCGG;RSEQ=GCCGGCGGCGCTTCAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:17,104:121,0:0:2,0:24.2:1:30.2:1:1:0:40.9:39.333:1:0:0.1 0/1:102:2:1,1:18,82:100,2:0.0196:2,2:12.5:1:30:1:0.33935:4.46:31:4:0.02:0:1 +16 86612584 . C A 37 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62319;SOR=0.33753;LSEQ=ATCATGGACCGCTTCCCCTT;RSEQ=TACCACGACAACCGGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:2,1:128,71:199,3:0.0149:2,2:37:1:23.7:1:1:1.11:41.7:2:0.01:0:2.3 0/0:198:1:1,0:122,75:197,1:0.0051:2,0:4:0:22:0:1:0:60:2:0.0051:0:1 +16 86612596 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24938;SOR=Inf;LSEQ=TTCCCCTTCTACCACGACAA;RSEQ=CGGCAGGGCTGGCAGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:141,85:226,0:0:2,0:26.4:1:31.6:1:1:0:56.7:74.333:1:0:0.1 0/1:243:3:2,1:140,100:240,3:0.0123:2,2:26:1:30.3:1:1:1.43:41:6:0.0124:0:1 +16 86612631 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09738;SOR=0;LSEQ=GAACAGCATCCGCCACAACC;RSEQ=CTCGCTCAACGACTGCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:3:1,2:145,141:286,3:0.0104:2,2:27.7:1:26:1:0.61981:2.05178:50.3:2:0.0073:0:1 0/0:338:0:0,0:173,165:338,0:0:2,0:28:1:29:1:1:0:55.7:41.25:1:0:0.2 +16 86612680 . G A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60477;SOR=0.44687;LSEQ=CCCCGCGAGAAAGGGCGGCC;RSEQ=GGCAAGGGCAGCTACTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:73,117:190,2:0.0104:2,2:26:1:30:1:1:1.60:53.5:4:0.0106:0:1 0/0:214:1:1,0:83,130:213,1:0.0047:2,0:1:0:22:0:0.39252:0:35:2:0.0047:0:1 +16 86612718 . T G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4977;SOR=Inf;LSEQ=GACGCTGGACCCCCGCTGCC;RSEQ=GGACATGTTTGAGAACGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:25,77:102,0:0:2,0:26.3:1:31:1:1:0:60:50:0.9901:0:0.1 0/1:106:2:1,1:23,80:103,2:0.0189:2,2:12.5:1:27.5:1:0.40659:3.43:60:4:0.0194:0:1 +16 86852074 . C A 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55181;SOR=3.1502;LSEQ=CCACCCCAGACACAGAGAAC;RSEQ=GGAATTTGCAGTTTAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:6,12:18,1:0.0526:2,0:1:0:26:0:0.36842:0:60:2:0.0526:0:1 0/1:13:2:1,1:0,11:11,2:0.1538:0,2:19:1:27.5:1:0.15385:0:60:4:0.1538:0:1.5 +16 86858299 . C A 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11765;SOR=0;LSEQ=TCCTGCCTTCCTGCAAGGGG;RSEQ=ATTGGGAAACTTACCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:6,16:22,2:0.0833:2,0:5.5:1:31.5:1:1:0:60:4:0.0833:0:1 0/0:45:0:0,0:17,28:45,0:0:2,0:19.1:1:30.5:1:1:0:60:21.5:1:0:0.1 +16 87032111 . T TTGC 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.33333;SOR=0;LSEQ=GAGGAGCTGGCTTGGGGTGG;RSEQ=TGCTGCTGCTGCAGCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:32.6:1:1:0:60:4:1:0.5:2 0/0:2:0:0,0:1,1:2,0:0:2,0:22:1:31:0:1:0:60:4:1:0:1 +16 87032133 . G A 28 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06667;SOR=0;LSEQ=GCTGCTGCTGCAGCCATGTT;RSEQ=TCATCACTGCTGCTGTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31.5:1:28.5:1:1:0:60:4:1:0:2 0/0:4:0:0,0:2,2:4,0:0:2,0:28.8:1:32.5:1:1:0:60:8:1:0:1 +16 87032181 . G T 68 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTGTTGTGTGCGTGTTG;RSEQ=CATTGTTGTGGCCACTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:24:0:26:0:1:0:60:2:1:0:2 1/1:5:5:3,2:0,0:0,5:1:0,2:22.2:1:29.6:1:1:0:60:10:1:0:1 +16 87032404 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20093;SOR=0;LSEQ=TGCTGTCCTTGTCACGCTGT;RSEQ=GTGGTGTTGTGGCTGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:17,27:44,2:0.0435:2,2:10:1:30:1:1:1.57:60:4:0.0435:0:1 0/0:56:0:0,0:25,31:56,0:0:2,0:25.4:1:28.6:1:1:0:60:27:1:0:0.2 +16 87727766 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.48864;SOR=0;LSEQ=GGGCAGAACTGGACCAGGAG;RSEQ=AGGAGGGGCAGCAGCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,9:16,2:0.1111:2,2:40:1:28.5:1:1:1.27:60:4:0.1176:0:1 0/0:15:0:0,0:6,9:15,0:0:2,0:23:1:30.6:1:1:0:60:30:1:0:0.1 +16 88086369 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCACCACCTTTACCATTA;RSEQ=CATCTCCATCATCATCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:27.5:1:1:0:60:4:1:0:1.5 +16 88086471 . C A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACCAACACAACCACCCTAA;RSEQ=AATCACTACCACCACCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:46:0:35:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:47.5:1:30.5:1:1:0:60:4:1:0:1 +16 89250710 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11712;SOR=Inf;LSEQ=ACAGCACGTCCTAGCTCCAG;RSEQ=TGTCCCGGGGGGAAGTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:49,0:0:1,0:24:1:32.8:1:1:0:59.8:48:1:0:0.1 0/1:26:2:1,1:24,0:24,2:0.0769:1,2:18.5:1:27.5:1:0.07692:0:60:4:0.0769:0:1.5 +16 89250778 . AC A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50663;SOR=0;LSEQ=GCCCAAAGCCCGTCCTTCCC;RSEQ=CCCACCTCGGTGGCTAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:92,34:126,2:0.0156:2,2:22.5:1:30.5:1:0.47367:2.6814:60:4:0.0159:0:0 0/0:98:0:0,0:75,23:98,0:0:2,0:24.6:1:30.5:1:1:0:60:31.667:1:0:0.1 +16 89250780 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50715;SOR=0;LSEQ=CCAAAGCCCGTCCTTCCCAC;RSEQ=CCACCTCGGTGGCTAAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:91,36:127,2:0.0155:2,2:12:1:28.5:1:0.49297:2.50706:60:4:0.0161:0:1 0/0:98:0:0,0:75,23:98,0:0:2,0:25:1:29.7:1:1:0:60:31.667:1:0:0.1 +16 89250882 . T C 207 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGTCCTGCCATATGTGG;RSEQ=CCCTCTAGCGGCACCTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:143,174:317,0:0:2,0:25.2:1:29.6:1:1:0:60:30.7:1:0:0.1 0/1:265:109:50,59:73,83:156,109:0.4113:2,2:27.8:1:30.6:1:0.90096:1.0377:59.9:35.333:0.4173:0:1.4 +16 89250885 . C T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08826;SOR=Inf;LSEQ=GGTCCTGCCATATGTGGTCC;RSEQ=TCTAGCGGCACCTTCGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:138,176:314,0:0:2,0:24.7:1:31.9:1:1:0:60:43.857:1:0:0.1 0/1:253:3:1,2:114,134:248,3:0.0119:2,2:14.7:1:22.7:1:1:1.69804:60:2:0.0082:0:2.7 +16 89250905 . G A 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22901;LSEQ=CTCTAGCGGCACCTTCGTGA;RSEQ=TACCGCTTCCCACAGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:2:2,0:98,143:241,2:0.0082:2,0:1:0:26:1:0.16835:0:60:4:0.0083:0:1 0/1:198:2:1,1:90,106:196,2:0.0101:2,2:14:0:31.5:1:1:1.18:54:4:0.0103:0:2.5 +16 89250922 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2121;SOR=Inf;LSEQ=TGAGTACCGCTTCCCACAGC;RSEQ=GGTGGGGCGGGGGCTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:69,119:188,0:0:2,0:24.7:1:31.3:1:1:0:60:93:1:0:0.1 0/1:161:2:1,1:71,88:159,2:0.0124:2,2:26:1:28.5:1:1:1.24:60:4:0.0128:0:1.5 +16 89250951 . T A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGGCTCTGGCCTACACAG;RSEQ=CACAGTGCGCGTCCTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:28,84:112,0:0:2,0:23.9:1:30.4:1:1:0:60:224:1:0:0.1 0/1:92:36:12,24:22,34:56,36:0.3913:2,2:26.4:1:28.4:1:0.65998:1.29051:60:72:0.3956:0:1.5 +16 89335023 . C T 45 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05295;SOR=0;LSEQ=CTGCCACTCCATCCTCTGCA;RSEQ=GGCGTTCAGGGCCGCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:4:0,4:106,181:287,4:0.0137:2,0:6:1:22.8:1:0.30033:0:53:3:0.0106:0:1.5 0/0:314:0:0,0:131,183:314,0:0:2,0:18.9:1:29.5:1:1:0:40.3:156:1:0:0.1 +16 89335122 . C A 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.41747;SOR=2.4481;LSEQ=GGAGGAGTGAAGGGAGAGCC;RSEQ=CAGACTCTGCCGACCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:2:1,1:117,307:424,2:0.0047:2,2:13:1:19:1:0.47774:2.62:60:1:0.0024:0:2.5 0/1:350:4:3,1:101,245:346,4:0.0114:2,2:8.3:1:26.5:1:0.08037:7.23:60:8:0.0116:0:1 +16 89337135 . C A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0258;SOR=Inf;LSEQ=AACTGGGCAGCGGCCTCCCC;RSEQ=CAGGCAGCGCAAAGGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:220,11:231,0:0:1,0:24:1:31.5:1:1:0:60:114.5:1:0:0.1 0/1:156:4:4,0:139,13:152,4:0.0256:2,0:32:1:30.3:1:1:0:60:8:0.0261:0:1 +16 89337143 . C A 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCGGCCTCCCCCCAGGCAG;RSEQ=GCAAAGGGGGTTGTCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:234,17:251,0:0:2,0:24.8:1:31.8:1:1:0:60:30.375:0.9959:0:0.1 0/1:192:33:27,6:138,21:159,33:0.1719:2,2:24.7:1:28.4:1:0.4212:1.45718:60:66:0.1746:0:1.1 +16 89337526 . G A 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00619;SOR=0;LSEQ=CTCCCTAAAATGCGCGTGGA;RSEQ=GCAGCTGGGCCTTTGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:19:0,19:1,17:18,19:0.5135:1,1:26.6:1:32.3:1:0.48649:0:59.7:18:0.5:0:1.2 0/0:9:0:0,0:0,9:9,0:0:0,0:20.3:1:29.2:1:1:0:60:8:1:0:0.8 +16 89341168 . C G 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTATCAAGGGGAGGGGAGG;RSEQ=GGGCAGGGTGCAGGCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:336,84:420,0:0:2,0:24.6:1:31.7:1:1:0:60:83:0.9952:0:0.1 0/1:350:43:35,8:236,68:304,43:0.1229:2,2:24.8:1:30.2:1:0.69528:1.26:60:42:0.1207:0:1.1 +16 89341311 . C T 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34692;SOR=3.39372;LSEQ=CTGGTTGGCGATGGTCCTGG;RSEQ=CGCCCGGCAGTGAACCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:1:0,1:131,192:323,1:0.0031:2,0:1:0:25:0:1:0:55:2:0.0032:0:1 0/1:288:3:1,2:124,161:285,3:0.0104:2,2:6.3:1:26.3:1:1:1.53816:40:6:0.0107:0:1 +16 89341429 . C T 130 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0;SOR=22.52578;LSEQ=TCCAGGCCCCACTGTCAACA;RSEQ=GACAGCCCCTGGGGCCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:1:0,1:295,302:597,1:0.0017:2,0:1:0:26:0:1:0:60:2:0.0017:0:1 0/1:551:20:11,9:264,267:531,20:0.0363:2,2:22.1:1:30.3:1:0.65737:1.24:60:40:0.0364:0:1.4 +16 89341682 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21206;SOR=Inf;LSEQ=TCTGGAGTTCACGGGGGTCC;RSEQ=GACTCAGCCTCCCCACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:36,143:179,0:0:2,0:20.2:1:30.2:1:1:0:59.8:358:0.9944:0:0.1 0/1:155:2:1,1:31,122:153,2:0.0129:2,2:9:1:26:1:0.37134:3.89:60:4:0.0132:0:1 +16 89341696 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50975;SOR=0;LSEQ=GGGTCCCGACTCAGCCTCCC;RSEQ=ACTCCTAGGAGCCTGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:16,121:137,2:0.0144:2,2:12:1:30:0:0.23042:7.37:60:4:0.0148:0:1 0/0:102:0:0,0:11,91:102,0:0:2,0:19.7:1:31.3:1:1:0:60:101:1:0:0.1 +16 89345122 . G A 28 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCAGGGGCAGGAGACACAG;RSEQ=GGGTGGCTCTCGTGAGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:29.5:1:28:1:1:0:57:4:1:0:4 0/0:2:0:0,0:1,1:2,0:0:2,0:38.5:1:29.5:1:1:0:60:4:1:0:0 +16 89345408 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00798;SOR=2.05193;LSEQ=TGGGACAAGACGGGCTGGAG;RSEQ=AAGCCGTGACTAGGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:263:212:184,28:43,8:51,212:0.8061:2,2:23:1:30:1:0.65199:1.22:60:34.333:0.8047:0:1.1 1/1:229:205:163,42:24,0:24,205:0.8952:1,2:22:1:29.2:1:0.00998:0:60:204:0.8987:0:1.1 +16 89345414 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25002;SOR=0;LSEQ=AAGACGGGCTGGAGGAAGCC;RSEQ=TGACTAGGGGCCCCAGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:243,49:292,3:0.0102:2,2:8.3:1:28:1:0.07837:9.79991:60:6:0.0103:0:1.3 0/0:271:0:0,0:216,55:271,0:0:2,0:21.9:1:30:1:1:0:60:270:1:0:0.8 +16 89345565 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62355;SOR=0.35349;LSEQ=ACTCGGCGTAGCACTGGGGC;RSEQ=CCTGCGGCGTGATACAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:3:2,1:79,86:165,3:0.0178:2,2:23:1:29.7:1:0.60962:2.17:21.3:6:0.0183:0:1.3 0/0:158:1:1,0:82,75:157,1:0.0063:2,0:1:0:26:0:1:0:20:2:0.0063:0:1 +16 89346073 . C T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10016;SOR=Inf;LSEQ=GGCACGGGAGGCCTCAGTGT;RSEQ=GTCCTCGGGGCCGGCACCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:69,74:143,0:0:2,0:13.4:1:29.7:1:1:0:33.4:22.833:1:0:0.2 0/1:125:3:1,2:60,62:122,3:0.024:2,2:11:1:24.7:1:1:1.92566:37:2:0.0161:0:1 +16 89346088 . C T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10636;SOR=Inf;LSEQ=AGTGTCGTCCTCGGGGCCGG;RSEQ=ACCGTCTGCGGCCTGAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:127,114:241,0:0:2,0:20.2:1:32.1:1:1:0:42.5:59.25:1:0:0.2 0/1:218:3:1,2:110,105:215,3:0.0138:2,2:13.7:1:24.7:1:0.61642:2.08837:46.7:6:0.0139:0:1 +16 89346157 . C T 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.05273;SOR=7.11919;LSEQ=AGGGGCACAGAGGGACGCGG;RSEQ=GGGGGGGCCTTCAGCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:645:1:0,1:336,306:642,1:0.0016:2,0:14:0:15:0:0.47745:0:60:0:0:0:1 0/1:548:6:2,4:280,259:539,6:0.0109:2,2:18.7:1:27.5:1:0.43592:2.15921:60:12:0.0113:0:1 +16 89346756 . A G 197 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGACTTGCAGTTGCTGAAG;RSEQ=AGGACTCCAGCCCGGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:995:0:0,0:467,527:994,0:0:2,0:25.2:1:30.5:1:1:0:59.9:44.182:0.999:0:0.2 0/1:1009:86:46,40:427,496:923,86:0.0852:2,2:26.9:1:30.7:1:0.21488:1.34:55.8:85:0.0859:0:1.2 +16 89349023 . C T 200 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.7561;LSEQ=CCCGGCTCCTGCCCTCGGTC;RSEQ=GTGAAGCTGTCAGAGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1588:4:0,4:843,741:1584,4:0.0025:2,0:1.3:1:27.8:1:0.04823:0:60:8:0.0025:0:1 0/1:1456:105:60,45:706,644:1350,105:0.0721:2,2:24.1:1:29.8:1:0.3621:1.22:59.5:210:0.073:0:1.2 +16 89349640 . C CT 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.79929;SOR=0.91093;LSEQ=CTCTTTGCCTTTCTTGTCAT;RSEQ=TTTTTTTTCAGAGAAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1780:31:15,16:885,864:1749,31:0.0174:2,2:23.3:1:30.5:1:0.85752:1.09252:47.7:30:0.017:0.0022:0.2 0/1:2014:32:14,18:1023,954:1977,32:0.0159:2,2:23.8:1:29.2:1:0.37961:1.37848:49.4:64:0.016:0.002:0.1 +16 89350038 . G A 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=1.45316;LSEQ=CCTTCAGCTCCTCCCGGTGC;RSEQ=CCTCCTCGGGCTTGGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1613:1294:665,629:155,159:314,1294:0.8022:2,2:25.2:1:30:1:0.5297:1.08:59.9:70.889:0.803:0:1.1 1/1:1648:1409:711,698:117,118:235,1409:0.855:2,2:23.9:1:29.1:1:0.88798:1.03:59.9:69.45:0.8553:0:1.2 +16 89350178 . G A 327 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.44627;LSEQ=GGGACACTTTTATGCTTTTC;RSEQ=GTCTGCTCTTTCCTCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1877:1500:754,746:193,180:373,1500:0.7991:2,2:25.4:1:31.2:1:0.64349:1.06085:59.8:82.333:0.8011:0:1.1 1/1:2038:1929:964,965:53,51:104,1929:0.9465:2,2:23.9:1:30:1:0.91987:1.04029:59.6:127.6:0.9471:0:1.2 +16 89350577 . C T 188 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=15.2486;LSEQ=TCTTCTTTAAAAATCTTCTC;RSEQ=TTCTCTTTTGAAATTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1585:5:1,4:843,737:1580,5:0.0032:2,2:10.4:1:28.2:1:0.19171:4.57088:38.8:10:0.0032:0:1 0/1:1759:81:50,31:881,796:1677,81:0.046:2,2:24.6:1:29.8:1:0.11157:1.46:39.5:162:0.0464:0:1.2 +16 89350597 . C G 246 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTCTCTTTTGAAATTTTGT;RSEQ=CTCTTTTAAATCATTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1731:191:105,86:786,751:1537,191:0.1103:2,2:28.3:1:32.5:1:0.31973:1.17:48.7:382:0.1118:0:1.1 0/0:1937:0:0,0:1010,925:1935,0:0:2,0:27:1:30.5:1:1:0:56.7:128:0.999:0:0.2 +16 89352149 . G A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00058;SOR=Inf;LSEQ=GGCTCTGCAGATGTGTCTGC;RSEQ=GGAAGGTTCCCACCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:29,289:318,0:0:2,0:22.9:1:31.5:1:1:0:59.6:105:1:0:0.1 0/1:210:8:0,8:28,174:202,8:0.0381:2,0:21.4:1:30.1:1:0.60108:0:60:16:0.0388:0:1.3 +16 89352678 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.00858;LSEQ=ATAACACGGCAGCCCCTTCC;RSEQ=AGAACCCTGGGGTTCGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:197:155:8,147:3,39:42,155:0.7868:2,2:22.9:1:31.2:1:0.70423:1.41076:60:76.5:0.7846:0:1.1 1/0:170:134:10,124:1,35:36,134:0.7882:1,2:20.9:1:30.6:1:0.46102:2.81:60:66:0.7904:0:1 +16 89352699 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50484;SOR=0;LSEQ=AGAACCCTGGGGTTCGACCC;RSEQ=AGAGCAGCCCCTCACGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:0,2:1,119:120,2:0.0164:1,0:24:1:29:0:1:0:60:4:0.0167:0:2 0/0:96:0:0,0:0,96:96,0:0:1,0:23.6:1:31:1:1:0:60:95:1:0:0.8 +16 89352777 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05909;SOR=Inf;LSEQ=GAGGCTCTGGGTGTGGTGGG;RSEQ=GAGGCTGTGGCTCCTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:1,41:42,0:0:1,0:26.3:1:30.1:1:1:0:59.3:41:1:0:0.2 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:17:1:30.5:1:1:0:60:4:0.1429:0:1 +16 89352786 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGGTGGGCGAGGCTGT;RSEQ=GCTCCTCTGTGGGAAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:0,34:34,2:0.0556:1,2:11.5:1:30:1:0.05556:0:60:4:0.0571:0:1 0/0:10:0:0,0:0,10:10,0:0:0,0:25.8:1:32.3:1:1:0:60:20:1:0:0.1 +16 89355278 . A G 189 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00153;SOR=0;LSEQ=TACTGTGGCACCTCGTTAGC;RSEQ=CGATCCATATCTAGCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:0,53:0,0:0,53:1:0,1:22.6:1:33:1:1:0:59.3:106:1:0:1.1 1/0:22:17:1,16:0,5:5,17:0.7727:0,1:18.6:1:31.6:1:1:0:60:34:0.7727:0:1.1 +16 89356582 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CCTGCAGAGCAGACGCGCAC;RSEQ=CCACGAGGCCACAGCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:7,0:0:2,0:32.1:1:31.7:1:1:0:54.3:14:1:0:1.1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:22:0:31.5:1:1:1:60:4:0.5:0:1 +16 89356864 . T G 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00833;SOR=0;LSEQ=GGCTCAGGGCTCCAATGGGG;RSEQ=GAGGCTCAGGGCTCCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:38.3:1:29.4:1:1:0:22.7:14:1:0:2 0/0:3:0:0,0:3,0:3,0:0:0,0:11.7:1:28.7:1:1:0:35:6:1:0:0 +16 89356882 . CGGGGGAGGCTCAGGGCTCCAATG C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=60;MSI=6.000;MSILEN=1;SSF=0.02248;SOR=0.1908;LSEQ=GGTGAGGCTCAGGGCTCCAG;RSEQ=GGGGGAGGCTCAGGGCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:16,0:7,1:8,16:0.6667:2,1:5.6:1:31.9:1:0.33333:0:34.1:32:0.6667:0.6667:0.1 0/1:15:4:4,0:8,3:11,4:0.2667:2,0:6.3:1:30.7:1:0.51648:0:31.8:8:0.2667:0.2667:0.8 +16 89356957 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17808;SOR=Inf;LSEQ=CTCAGGGCTCCAATGGGGGG;RSEQ=GGCTCAGGACTCCACTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:163,13:176,0:0:2,0:26.4:1:30.3:1:1:0:54.1:18.556:1:0:0.2 0/1:129:2:2,0:111,16:127,2:0.0155:2,0:36.5:1:31:1:1:0:59:4:0.0165:0:1 +16 89357823 . C G 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCTCGTTACCAGCCCCT;RSEQ=AAGTCTGCTAAGCCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:0,3:25,14:39,3:0.0714:2,0:28.7:1:32:1:0.05923:0:60:6:0.0732:0:1 0/0:9:0:0,0:7,2:9,0:0:2,0:18.7:1:31.2:1:1:0:60:18:1:0:0.2 +16 89360061 . G T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGCGGAGGGGAGGAGGCG;RSEQ=GGTGGTATTGGGGCTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:12:0:1:0:26:0:0:0:3 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:15.5:1:30:1:1:1.41418:47:4:0.2857:0:1 +16 89371407 . G A 162 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00576;SOR=0;LSEQ=AAGAGTGAAGCTCTCCAATC;RSEQ=GCCCCATGGGCCTGAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:38,3:0,0:0,41:1:0,2:25.2:1:30.4:1:1:0:60:40:1:0:1.1 1/0:10:7:7,0:3,0:3,7:0.7:0,0:21.6:1:30.9:1:1:0:60:14:0.7:0:1 +16 89371827 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCAAGATTTTGTTTCATAT;RSEQ=CCAGGAGAAGCGCATCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:198:198:5,193:0,0:0,198:1:0,1:24.3:1:30.4:1:1:0:60:98:1:0:1.8 1/1:149:124:6,118:3,22:25,124:0.8322:2,1:19.9:1:29.4:1:0.1754:2.65882:60:40.333:0.8288:0:1.8 +16 89371839 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TTTCATATGCCAGGAGAAGC;RSEQ=CATCTCTTATTTGGGCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:164:164:3,161:0,0:0,164:1:0,1:22.9:1:30.6:1:1:0:60:163:1:0:2 1/1:103:86:3,83:2,14:16,86:0.835:2,1:20.3:1:30.1:1:0.17395:3.87639:60:172:0.8431:0:2 +16 89371953 . G T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.21053;SOR=0;LSEQ=CGGGGTCGGGCTGTGGCTCA;RSEQ=CCCTGACTCTGGCCCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:0,30:0,0:0,30:1:0,1:22.4:1:30.6:1:1:0:60:60:1:0:1.1 1/1:8:7:0,7:0,1:1,7:0.875:0,0:28.1:1:30.1:1:1:0:60:14:0.875:0:1 +16 89372039 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGAGAAAGCAGAGGAGACA;RSEQ=ACACGCGCTACCTCTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:10:1:33:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 89382073 . G A 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGAGGAGCTTGGGACAGA;RSEQ=CAAGTGGGAGCAGACACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:32:0:1:0:60:4:1:0:1.5 +16 89383725 . T C 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22619;SOR=0.14055;LSEQ=CAGAGAAGGGTCAAGCACTT;RSEQ=GTAGTGGCAGAAAGGGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:17.6:1:31.4:1:1:0:59.2:10:0.8333:0:1.2 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:1:0:30:0:1:0:60:2:0.3333:0:1 +16 89384555 . G T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCTCTGCGACACACGGT;RSEQ=CGAGCGCACTTCTTCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 89653419 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12369;SOR=Inf;LSEQ=ACTGGCCTCAGTGTCCCTGG;RSEQ=GGGGGTGGACGCTGACTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:71,71:142,0:0:2,0:27.7:1:30.8:1:1:0:60:34.5:1:0:0.2 0/1:154:4:1,3:77,73:150,4:0.026:2,2:19.5:1:26.3:1:0.36359:3.14271:60:8:0.0263:0:1 +16 89653442 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36395;SOR=0.3186;LSEQ=GGGTGGACGCTGACTCCGCC;RSEQ=GCCGGAAGTTCCACAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:1,2:61,79:140,3:0.021:2,2:10.7:1:30:1:1:1.5398:60:6:0.0214:0:1 0/0:148:1:1,0:64,83:147,1:0.0068:2,0:1:0:27:0:0.43919:0:60:2:0.0068:0:1 +16 89653445 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24756;SOR=Inf;LSEQ=TGGACGCTGACTCCGCCGGC;RSEQ=GGAAGTTCCACAGGGTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:60,77:137,0:0:2,0:25.7:1:30.4:1:1:0:60:67.5:1:0:0.2 0/1:143:3:1,2:58,80:138,3:0.021:2,2:19:1:26.3:1:1:1.44633:56:2:0.0144:0:1 +16 89653446 . G A 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.96612;LSEQ=GGACGCTGACTCCGCCGGCC;RSEQ=GAAGTTCCACAGGGTGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:1,0:59,76:135,1:0.0074:2,0:1:0:25:0:0.44118:0:60:2:0.0074:0:1 0/1:139:2:1,1:57,80:137,2:0.0144:2,2:26:0:32.5:1:1:1.40:60:4:0.0145:0:1.5 +16 89653456 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49839;SOR=Inf;LSEQ=TCCGCCGGCCGGAAGTTCCA;RSEQ=AGGGTGTACTCCTTCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:50,72:122,0:0:2,0:24.7:1:32.3:1:1:0:60:60:1:0:0.2 0/1:129:2:1,1:49,78:127,2:0.0155:2,2:42:0:31:1:1:1.59:60:4:0.0159:0:1.5 +16 89653457 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49839;SOR=Inf;LSEQ=CCGCCGGCCGGAAGTTCCAC;RSEQ=GGGTGTACTCCTTCCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:50,72:122,0:0:2,0:24.3:1:31.4:1:1:0:60:121:1:0:0.2 0/1:129:2:1,1:49,78:127,2:0.0155:2,2:21.5:1:32:0:1:1.59:60:4:0.0156:0:2 +16 89653458 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23714;SOR=0;LSEQ=CGCCGGCCGGAAGTTCCACA;RSEQ=GGTGTACTCCTTCCTGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:49,71:120,2:0.0164:2,2:25.5:1:30:1:1:1.44:60:4:0.0167:0:1 0/0:128:0:0,0:49,79:128,0:0:2,0:24:1:30.7:1:1:0:59.8:127:1:0:0.4 +16 89653459 . G A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4985;SOR=Inf;LSEQ=GCCGGCCGGAAGTTCCACAG;RSEQ=GTGTACTCCTTCCTGGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:49,71:120,0:0:2,0:24:1:31.1:1:1:0:60:119:1:0:0.2 0/1:128:2:1,1:48,78:126,2:0.0156:2,2:5:0:31:1:1:1.62:60:4:0.0157:0:1.5 +16 89653520 . T C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01992;SOR=Inf;LSEQ=TCCACTTCACCGTGAGTCCA;RSEQ=GGCCCCGCCCCATGCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:2,27:29,0:0:2,0:23.5:1:31.1:1:1:0:59.9:58:1:0:0.5 0/1:19:4:0,4:0,15:15,4:0.2105:1,0:28.3:1:30.3:1:1:0:55.3:8:0.2105:0:1.5 +16 89653524 . C CCCGCCCCATG 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.0464;LSEQ=CTTCACCGTGAGTCCATGGC;RSEQ=CCGCCCCATGCCGCCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:0,3:1,21:22,3:0.12:1,0:20.3:1:32:1:1:0:59.3:6:0.12:0.08:0.7 0/1:16:2:0,2:0,14:14,2:0.125:1,0:26:1:31.9:1:1:0:60:4:0.1333:0.0625:0.5 +16 89653563 . G T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTCCGTGGCCCCGCCCC;RSEQ=CCCCGCCCCCTCAGTCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:1,10:0,0:0,11:1:0,2:16.4:1:28.1:1:1:0:50.5:4.5:1:0:1.5 1/1:4:4:0,4:0,0:0,4:1:0,0:23.5:1:26.3:1:1:0:49.3:3:1:0:1.5 +16 89653624 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGTCTGTGGCCCCGCCC;RSEQ=TCCCCGCCCCCTCAGTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:16:1:33:1:1:0:21.5:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 89804855 . C T 104 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00103;SOR=11.03216;LSEQ=CCCGCAAACGCTGAGTGACT;RSEQ=GGGGCCGGACAGTTCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:39,0:39,2:0.0488:1,0:28.5:1:33:0:1:0:60:4:0.0488:0:1 0/1:27:10:8,2:17,0:17,10:0.3704:1,2:25.5:1:31.4:1:0.12821:0:60:20:0.4:0:1.2 +16 89805218 . C T 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.25013;SOR=0;LSEQ=GAGTTGTATTGCCAGCCAGG;RSEQ=AGGCACATGGCCCAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:152,101:253,3:0.0117:2,2:18.7:1:26.7:1:0.56661:2.99682:60:6:0.0119:0:1 0/0:233:0:0,0:135,98:233,0:0:2,0:23.4:1:31.6:1:1:0:60:232:1:0:0.3 +16 89805261 . A G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.40544;LSEQ=TCAATTCTCATGTCCCCCAC;RSEQ=TGGCCCAAGGTGGGCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:111:62,49:172,123:295,111:0.2734:2,2:27.6:1:30.8:1:0.65431:1.10489:60:54.5:0.2732:0:1.1 0/1:406:193:114,79:124,87:211,193:0.4754:2,2:22.8:1:29.7:1:1:1.01:60:95.5:0.4775:0:1.1 +16 89805301 . G C 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=Inf;LSEQ=TGACGTTACCTCTGCCACGT;RSEQ=TGAGAAGCTCTTTTTCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:268,260:528,0:0:2,0:25.3:1:32.2:1:1:0:59.9:65:1:0:0.3 0/1:631:16:10,6:324,291:615,16:0.0254:2,2:23.8:1:30.1:1:0.46144:1.50:60:32:0.0255:0:1.6 +16 89805465 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17472;SOR=Inf;LSEQ=CCCATAGTCTGCATGCTGTG;RSEQ=CGGAACATTCTTTGGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:118,118:236,0:0:2,0:23.3:1:32:1:1:0:59.8:46.2:1:0:0.1 0/1:170:2:1,1:93,75:168,2:0.0118:2,2:5.5:1:27:1:1:1.23841:60:4:0.012:0:1 +16 89805977 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1385;SOR=1.27007;LSEQ=GAGGTCTGCAACACCAAGAA;RSEQ=TGGCTCAGGCAACTCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:101:35,66:93,181:274,101:0.2693:2,2:25.8:1:30.8:1:0.90282:1.03:60:202:0.2708:0:1.1 0/1:417:133:45,88:109,175:284,133:0.3189:2,2:24.4:1:29.7:1:0.38583:1.21746:60:65.5:0.3172:0:1.2 +16 89806018 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=ATCTCTGCCTATTATCAGTG;RSEQ=TGGGGACACCCCTGGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:41,151:192,0:0:2,0:22.8:1:32.8:1:1:0:60:47:1:0:0.3 0/1:192:2:1,1:52,138:190,2:0.0104:2,2:22:1:26.5:1:0.47693:2.64:60:4:0.0106:0:1.5 +16 89806347 . A T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.92509;SOR=1.03337;LSEQ=CGTTCTTAACCATTTGCAAG;RSEQ=TGCCTCTGAAAAGAGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:76:58,18:140,46:186,76:0.289:2,2:22.1:1:30.3:1:1:1.06:60:152:0.2912:0:1 0/1:284:84:65,19:149,51:200,84:0.2958:2,2:22.9:1:28.9:1:0.65329:1.17:60:168:0.2979:0:1.1 +16 89806445 . C T 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAGCCAGGATATCTTCCT;RSEQ=TTCTCTAAACACTCGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:668:0:0,0:344,323:667,0:0:2,0:25:1:32.3:1:1:0:60:59.636:0.9985:0:0.1 0/1:846:54:25,29:408,383:791,54:0.0638:2,2:26.3:1:29.9:1:0.48384:1.2354:60:108:0.0647:0:1.4 +16 89807044 . C CA 73 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.39986;SOR=2.33149;LSEQ=ACAGAGTGAGACCCCCATCT;RSEQ=AAAAAAAAAAAAAAAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:5,0:13,1:14,5:0.2174:1,0:9:1:31.6:1:1:0:52.2:10:0.2174:0.1739:1.4 0/1:10:4:4,0:6,0:6,4:0.4:0,0:7.5:1:30.7:1:1:0:56.3:8:0.4:0.2:2.8 +16 89807142 . G T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35775;SOR=3.225;LSEQ=CTGGAAACCCTGACTTGGAA;RSEQ=CTGGCTGCCTGGTGCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:1:0,1:179,42:221,1:0.0045:2,0:1:0:25:0:0.19369:0:60:2:0.0046:0:1 0/1:209:3:1,2:160,46:206,3:0.0144:2,2:28.7:1:27.3:1:0.13262:6.87246:60:6:0.0146:0:1.7 +16 89807147 . C T 38 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24882;SOR=0;LSEQ=AACCCTGACTTGGAAGCTGG;RSEQ=TGCCTGGTGCCCCTGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:3:1,2:187,53:240,3:0.0123:2,2:6:1:24.3:1:0.1293:6.98216:60:2:0.0083:0:2.3 0/0:232:0:0,0:172,60:232,0:0:2,0:23.1:1:31:1:1:0:60:115:1:0:0.1 +16 89807457 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19426;SOR=Inf;LSEQ=TAATTGAGAATTAATTACTA;RSEQ=TGGCTGGGTCATTTCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:26,0:0:1,0:22.3:1:33.2:1:1:0:58.6:52:1:0:0.2 0/1:21:2:1,1:1,18:19,2:0.0952:1,2:19.5:1:30:1:0.18571:13.08:60:4:0.0952:0:1.5 +16 89809061 . CA C 75 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=23.000;MSILEN=1;SSF=0.1235;SOR=0;LSEQ=CCCCGTCTCTACTAAAAATA;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:7,0:7,5:0.3571:0,0:11.4:1:32.7:1:1:0:43.8:10:0.3571:0.2143:2.6 0/0:7:0:0,0:7,0:7,0:0:0,0:3.4:1:29.9:1:1:0:53.1:14:1:0:3.6 +16 89809404 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49801;SOR=Inf;LSEQ=AACCATACAACCACGCCATA;RSEQ=AAACCAAGTCCTTATTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:7,113:120,0:0:2,0:23.8:1:32.4:1:1:0:60:119:1:0:0.1 0/1:123:2:1,1:12,109:121,2:0.0163:2,2:16.5:1:30.5:1:0.20099:8.77:60:4:0.0165:0:1 +16 89811196 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00134;SOR=5.23754;LSEQ=TGCCTCGGCCTCCCCAGTAG;RSEQ=TGGGATTACAGGCGCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:6:6,0:49,1:50,6:0.1034:1,0:26.3:1:28.8:1:1:0:57.7:5:0.0909:0:1.3 0/1:42:16:15,1:25,1:26,16:0.381:1,1:27.3:1:32.3:1:1:1.64563:57.4:32:0.381:0:1.1 +16 89811516 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.20028;SOR=Inf;LSEQ=AGCACACAGATGAGGGTGGC;RSEQ=GAGATGGACACACCTCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:37,192:229,0:0:2,0:21.2:1:30.5:1:1:0:60:56.25:1:0:0.2 0/1:186:2:1,1:24,160:184,2:0.0108:2,2:25:1:32:0:0.25138:6.55:60:4:0.011:0:1 +16 89811530 . C A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.17627;LSEQ=GGTGGCTGAGATGGACACAC;RSEQ=TCCGCTGCCCCAGCCATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:13,160:173,2:0.0114:2,2:23.5:1:21:1:0.15402:11.90:60:1:0.0058:0:1 0/1:149:2:1,1:13,134:147,2:0.0134:2,2:22.5:1:26.5:1:0.17967:9.97:60:4:0.0138:0:1 +16 89812582 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCTCTGCTCCGAAGTCC;RSEQ=AAGAAAGCATAGTCAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:33:1:29.5:1:1:0:54:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 89812778 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02419;SOR=Inf;LSEQ=CCTGCGGGTGCCATGGTGAC;RSEQ=GCGGTGGGGGCAGGGACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:22,0:0:1,0:28.5:1:30.9:1:1:0:59.7:44:1:0:0.1 0/1:10:3:3,0:7,0:7,3:0.3:0,0:33.7:1:30.7:1:1:0:60:6:0.3:0:1 +16 89812930 . G A 164 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=61.56097;LSEQ=CGTGCTGCAGAGATGCCAGA;RSEQ=GCAGCTGTGGAGTCTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:1:1,0:240,104:344,1:0.0029:2,0:40:0:15:0:1:0:60:0:0:0:2 0/1:315:48:36,12:181,86:267,48:0.1524:2,2:22.8:1:29.5:1:0.39785:1.42:60:23:0.1479:0:1.2 +16 89813156 . G T 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21182;SOR=4.12852;LSEQ=GGACCCACAACTAGTAGAGT;RSEQ=AAGGAACTCACAGGAAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:143,126:269,1:0.0037:2,0:1:0:24:0:0.47037:0:60:2:0.0037:0:1 0/1:264:4:2,2:148,112:260,4:0.0152:2,2:13:1:28:1:1:1.32:60:8:0.0155:0:1 +16 89813387 . A G 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09774;SOR=Inf;LSEQ=CTGCTGTGGATTCAGTTTTG;RSEQ=GAAAAACACTCGCTAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:32,153:185,0:0:2,0:19.7:1:31.9:1:1:0:60:184:1:0:0.1 0/1:159:3:1,2:31,125:156,3:0.0189:2,2:28.7:1:27.3:1:0.49286:2.01:60:6:0.019:0:1 +16 89814818 . T G 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57576;SOR=0.437;LSEQ=GTGTCAAAATCATTAAAACT;RSEQ=GAGGGAAACTAAAGGAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:27.4:1:32.2:1:1:0:60:10:0.7143:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:22.5:1:30.5:1:1:0:60:4:0.5:0:1 +16 89815049 . T C 173 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=23.32989;LSEQ=TGACAGATCGGACGGACACG;RSEQ=GCACACGGGGCACCTACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:2:1,1:312,205:517,2:0.0038:2,2:28:0:33:1:1:1.52064:60:4:0.0039:0:1 0/1:678:56:31,25:346,275:621,56:0.0826:2,2:26.4:1:29.8:1:1:1.01464:60:55:0.0821:0:1.1 +16 89815203 . G A 53 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1365;SOR=Inf;LSEQ=GAAGGGGCTGTATTGGTGGC;RSEQ=ACAGCACAGCGTACACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:72,185:257,0:0:2,0:26.1:1:31.6:1:1:0:60:84.667:1:0:0.1 0/1:334:4:3,1:116,213:329,4:0.012:2,2:7.3:1:26.5:1:0.13224:5.48:60:8:0.0123:0:1 +16 89815217 . C T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.12359;LSEQ=GGTGGCGACAGCACAGCGTA;RSEQ=ACTCTGCTCCTTCCCAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:11:2,9:58,149:207,11:0.0505:2,2:25.6:1:29.1:1:0.73127:1.74771:60:22:0.0516:0:1.2 0/1:228:80:24,56:51,97:148,80:0.3509:2,2:22.9:1:28.4:1:0.55577:1.22571:60:160:0.3556:0:1.2 +16 89816108 . C T 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2527;SOR=0.32085;LSEQ=GCTGCCCTGCCCAGGTGGTG;RSEQ=TGCCCTGCCCAGGTGGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:5:2,3:293,191:484,5:0.0102:2,2:10:1:30.6:1:0.3899:2.29703:60:10:0.0104:0:1.4 0/0:606:2:2,0:354,249:603,2:0.0033:2,0:25.5:1:30:1:0.51484:0:60:4:0.0034:0:1.5 +16 89818340 . G C 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51049;SOR=4.09114;LSEQ=AGGTGCCCGCCACCACGCCC;RSEQ=GCTAAATTTTTGTATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:12.3:1:30.3:1:1:0:53.7:6:0.3:0:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:29.5:1:28.5:1:1:0:38:4:0.6667:0:3 +16 89818422 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15938;SOR=Inf;LSEQ=TCTCCTGACTGTGTGATCCG;RSEQ=CTGCCTCGGCCTCCCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:78,1:79,0:0:1,0:24.5:1:32.9:1:1:0:50:158:1:0:0.3 0/1:53:2:1,1:51,0:51,2:0.0377:1,2:9.5:1:29.5:1:0.03774:0:55.5:4:0.0385:0:1 +16 89818491 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-04;SOR=1.85946;LSEQ=CCTGGCAATAAATATCTTAA;RSEQ=AGCACGCGGCTTAAATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:73:49,24:131,38:169,73:0.3017:2,2:24.1:1:32.6:1:0.10858:1.68473:57.9:146:0.3017:0:1.1 0/1:258:115:85,30:100,43:143,115:0.4457:2,2:22:1:31.6:1:0.49095:1.22:59.2:114:0.4436:0:1.2 +16 89818732 . C G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08126;SOR=0.42564;LSEQ=TGAGTGATGGCTGTGCTTCT;RSEQ=TGACAGTGTGACCCTCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:16:0,16:1,63:64,16:0.2:1,1:20.5:1:33.5:1:1:0:60:32:0.2025:0:1 0/1:94:9:0,9:3,82:85,9:0.0957:1,0:25.7:1:33.4:1:1:0:60:18:0.0957:0:1 +16 89825171 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22121;SOR=0;LSEQ=CTTCGTGGCCAGCGGTTCCC;RSEQ=ATAACCAGGGAATAGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:17,144:161,2:0.0123:2,2:22:1:29.5:1:0.20927:8.26:60:4:0.0126:0:1 0/0:183:0:0,0:29,154:183,0:0:2,0:21.8:1:31.5:1:1:0:60:366:1:0:0.1 +16 89828669 . C G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01144;SOR=Inf;LSEQ=CCTTCTTTCTAAGTATAAAA;RSEQ=GGCTATTTTAGTCTGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:11,0:0:0,0:31.6:1:31.2:1:1:0:60:22:1:0:0.1 1/0:7:4:0,4:1,2:3,4:0.5714:2,0:16:1:31.5:1:0.42857:0:60:8:0.5714:0:1 +16 89831149 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22802;SOR=0;LSEQ=CTAGACTCGAGACGAGGAGA;RSEQ=AGTCGGCACACACACACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:97,13:110,2:0.0179:2,2:7.5:1:29:1:0.23536:7.22608:60:4:0.0182:0:1 0/0:122:0:0,0:95,27:122,0:0:2,0:24.2:1:30.8:1:1:0:60:23.4:1:0:0.2 +16 89831155 . GCA G 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.34847;SOR=0.29732;LSEQ=TCGAGACGAGGAGACAGTCG;RSEQ=CACACACACCCTAGACTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:3:3,0:101,18:119,3:0.0246:2,0:27.3:1:30.3:1:1:0:60:6:0.0254:0:0 0/0:135:1:1,0:101,33:134,1:0.0074:2,0:42:0:29:0:1:0:60:2:0.0076:0:1 +16 89831510 . C A 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCCGGCCGTTTCTTCATTG;RSEQ=GCAAGTTTCACTGTGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:100,208:308,0:0:2,0:25.2:1:30.7:1:1:0:59.9:153:1:0:0.1 0/1:323:66:24,42:92,164:256,66:0.2043:2,2:27.6:1:29.4:1:1:1.02:60:65:0.2038:0:1.1 +16 89831549 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50144;SOR=0;LSEQ=GGCTGAGCAAATGCTCAGGT;RSEQ=GAAACAGACCATCAACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:16,138:154,2:0.0128:2,2:26.5:1:29.5:1:0.2067:8.40:60:4:0.013:0:1 0/0:133:0:0,0:27,106:133,0:0:2,0:19.6:1:30.7:1:1:0:60:65.5:1:0:0.3 +16 89833477 . C T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66848;SOR=0.58269;LSEQ=AAAGCGGCAGCAGACCTCGG;RSEQ=CTTCCGGTCCGAAAGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:1,2:178,49:227,3:0.013:2,2:11.3:1:28:1:0.12443:7.18216:60:6:0.0132:0:1 0/0:262:2:0,2:194,66:260,2:0.0076:2,0:1:0:23:1:0.06663:0:60:4:0.0077:0:1 +16 89833576 . G C 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ATAAGGCCTGGAGATAAGCA;RSEQ=CTGCACAAAGTATCTCGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:685:0:0,0:353,332:685,0:0:2,0:25.8:1:32.5:1:1:0:60:47.929:1:0:0.1 0/1:974:52:24,28:488,432:920,52:0.0534:2,2:26.2:1:30.6:1:0.39209:1.31752:60:104:0.0543:0:1.1 +16 89833715 . G C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1201;SOR=Inf;LSEQ=ATGAAGGAAAAAGTTACTTT;RSEQ=AATTTCATAAAACTGAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:4,111:115,0:0:1,0:23.3:1:31.9:1:1:0:60:37.333:1:0:0.1 0/1:113:3:0,3:4,106:110,3:0.0265:1,0:12:1:31.7:1:1:0:60:6:0.0275:0:1 +16 89833740 . C T 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21275;SOR=Inf;LSEQ=TCATAAAACTGAATTTAGTG;RSEQ=ATTCCGAACTGGATGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:0,73:73,0:0:1,0:23.7:1:32.7:1:1:0:60:72:1:0:0.1 0/1:63:2:1,1:1,60:61,2:0.0317:1,2:17:0:26.5:1:0.06298:42.79:60:4:0.0323:0:1 +16 89833774 . C G 102 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00264;SOR=9.62543;LSEQ=TGGCCTGAGCATTGGTCCTT;RSEQ=GTTTTTTGGTTCGTTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:0,34:34,2:0.0556:1,0:38.5:1:23.5:1:1:0:60:1:0.0286:0:1 0/1:27:10:1,9:1,16:17,10:0.3704:1,2:25:1:30.9:1:1:1.74:60:20:0.3704:0:1.1 +16 89836323 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.18443;LSEQ=CAGGGACAGGAAGGCCAGCA;RSEQ=CAGGTGCAGGAGGACCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:54:22,32:333,369:702,54:0.0713:2,2:22.4:1:30.6:1:0.39663:1.31217:59.6:53:0.0713:0:1.2 0/1:834:164:78,86:299,368:667,164:0.1966:2,2:26.1:1:28.7:1:0.541:1.12:60:22.429:0.1915:0:1.2 +16 89836436 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25407;SOR=0;LSEQ=GCACTCAGGCTCGGGCCCTG;RSEQ=AACGAGAATGAGGGTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:83,177:260,3:0.0114:2,2:32:1:27.7:1:1:1.07:60:6:0.0117:0:1.3 0/0:222:0:0,0:82,138:220,0:0:2,0:24.4:1:31:1:1:0:60:30.429:0.9907:0:0.3 +16 89836507 . T C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.82046;LSEQ=TCCAGGGCACTGAAGACGAA;RSEQ=TGAGAAGTAGCAGCCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:240:239:139,100:0,0:0,239:0.9958:0,2:21.2:1:32.3:1:1:0:60:33.143:1:0:1.1 1/1:197:196:126,70:0,1:1,196:0.9949:0,2:22.3:1:31.1:1:0.36041:0:60:38.2:0.9948:0:1.1 +16 89836718 . T A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13349;SOR=Inf;LSEQ=TAGCCATTCAGTCCTGCACA;RSEQ=CCCTCCAACAGCTAATCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:74,156:230,0:0:2,0:24.5:1:29.7:1:1:0:60:27.75:1:0:0.1 0/1:291:4:3,1:106,181:287,4:0.0137:2,2:13.3:1:26:1:0.14956:5.09:60:8:0.0143:0:1.5 +16 89836722 . T A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.25733;SOR=Inf;LSEQ=CATTCAGTCCTGCACATCCC;RSEQ=CCAACAGCTAATCCAACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:69,153:222,0:0:2,0:23.7:1:29.5:1:1:0:59.9:17.5:1:0:0.2 0/1:276:3:2,1:97,174:271,3:0.0109:2,2:5:1:27.7:1:0.2966:3.57:60:6:0.0112:0:1 +16 89836737 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50052;SOR=Inf;LSEQ=ATCCCTCCAACAGCTAATCC;RSEQ=ACCACCAGCGGCCGAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:41,137:178,0:0:2,0:22.2:1:30.2:1:1:0:59.9:21.25:1:0:0.2 0/1:201:2:1,1:62,136:198,2:0.01:2,2:21.5:1:28:1:0.53186:2.18:60:4:0.0104:0:1 +16 89836781 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=10.92106;LSEQ=CCAAGCTGTTCCCCAAAACA;RSEQ=TGGTCTTTCTGGAAGACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:5:1,4:25,68:93,5:0.051:2,2:14.2:1:31.6:1:1:1.46536:60:10:0.0515:0:1.4 0/1:102:38:6,32:15,49:64,38:0.3725:2,2:21:1:29.7:1:0.45112:1.62512:60:18:0.36:0:1.4 +16 89836863 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23513;SOR=Inf;LSEQ=TGATGAAACTCAGCATCGCC;RSEQ=CATGCTCCTGCGGAGACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:111,17:128,0:0:2,0:20:1:30:1:1:0:59.8:63:1:0:0.3 0/1:121:2:1,1:104,15:119,2:0.0165:2,2:13:1:30:1:0.24793:6.7441:60:4:0.0168:0:1 +16 89836865 . A G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=6.42012;LSEQ=ATGAAACTCAGCATCGCCGC;RSEQ=TGCTCCTGCGGAGACGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:8:8,0:107,18:125,8:0.0602:2,0:17.1:1:29.9:1:0.59748:0:60:16:0.0611:0:2.1 0/1:123:36:32,4:74,13:87,36:0.2927:2,2:21.7:1:30.7:1:0.77555:1.40:60:72:0.2927:0:2.1 +16 89836872 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.37292;LSEQ=TCAGCATCGCCGCATGCTCC;RSEQ=GCGGAGACGAGCTCATGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:8:8,0:115,19:134,8:0.0563:2,0:20.6:1:31.3:1:0.59768:0:60:16:0.0563:0:2.1 0/1:130:36:32,4:79,15:94,36:0.2769:2,2:25:1:30.9:1:0.58756:1.51:60:72:0.2813:0:2 +16 89836899 . T C 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGAGCTCATGAGTCCCTGG;RSEQ=CTGCAGACTTGGCCCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:164,38:202,0:0:2,0:26.1:1:29.9:1:1:0:59.9:100:1:0:0.2 0/1:210:45:35,10:126,39:165,45:0.2143:2,2:25.4:1:31.3:1:1:1.08:60:44:0.2126:0:1.1 +16 89836964 . G A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03599;SOR=Inf;LSEQ=CCACTCAGGGAGCTGCCCGC;RSEQ=CCTTCACCTCTCCGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:0:0,0:281,201:482,0:0:2,0:24.5:1:30.6:1:1:0:60:79.333:0.9979:0:0.1 0/1:596:6:2,4:332,258:590,6:0.0101:2,2:29.7:1:25.8:1:0.41269:2.56963:60:5:0.0085:0:1 +16 89838002 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.10659;SOR=0;LSEQ=GAGCAAGTCAAACAGAAATT;RSEQ=AGAGAAGGCTCCATGCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:179,39:218,3:0.0136:2,2:13.7:1:29.7:1:0.4523:2.28405:60:6:0.0136:0:1.3 0/0:244:0:0,0:188,56:244,0:0:2,0:20.6:1:30.6:1:1:0:60:39.667:1:0:0.3 +16 89838078 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=14.50172;LSEQ=CTGCTTTGTTCTGAGCCCCT;RSEQ=CACCTACCATGTGTTCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:737:25:13,12:404,307:711,25:0.0339:2,2:24.2:1:33:1:0.684:1.2144:60:50:0.034:0:1.1 0/1:921:311:171,140:345,264:609,311:0.3377:2,2:26.7:1:31.2:1:0.67357:1.06983:60:76.75:0.3381:0:1.1 +16 89838113 . C T 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCCGTGGCTCCAGTCTCGG;RSEQ=GTGTTGATGCTGAGCTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:0:0,0:420,381:801,0:0:2,0:25.1:1:31.1:1:1:0:60:199.25:1:0:0.2 0/1:980:34:18,16:487,458:945,34:0.0347:2,2:24.8:1:27.4:1:1:1.06:60:33:0.034:0:1.3 +16 89838275 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15385;LSEQ=GAACCCCGAAAGGAGGGATA;RSEQ=AGCTGCGGCCTAGAGAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:2:0,2:45,172:217,2:0.0091:2,0:31:1:29:1:1:0:60:4:0.0092:0:1.5 0/1:190:2:1,1:36,152:188,2:0.0105:2,2:25:1:27:1:0.35238:4.18:60:4:0.0107:0:1 +16 89839572 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17013;SOR=Inf;LSEQ=TTTAAACTACTGGACTACTA;RSEQ=GAAGACACACCAGCCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:141,5:146,0:0:1,0:25.2:1:33.9:1:1:0:59.9:145:1:0:0.1 0/1:103:2:1,1:94,7:101,2:0.0194:2,2:21:1:25.5:1:0.15001:12.628:60:4:0.0194:0:1 +16 89839581 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.18244;SOR=Inf;LSEQ=CTGGACTACTAGGAAGACAC;RSEQ=CCAGCCTGATGTCACTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:163,8:171,0:0:1,0:25.3:1:31.2:1:1:0:59.9:170:1:0:0.1 0/1:128:2:1,1:112,14:126,2:0.0156:2,2:14:1:28:1:0.22146:7.76299:60:4:0.0157:0:1 +16 89839915 . G A 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0312;SOR=0;LSEQ=AGCTGCTGTGTGTGGCAGAC;RSEQ=GAGGGACTGGGAGTCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:6:0,6:2,69:71,6:0.0769:1,0:33:1:32.7:1:1:0:60:12:0.0769:0:1 0/0:66:0:0,0:2,64:66,0:0:1,0:23.5:1:30.6:1:1:0:60:65:1:0:0.2 +16 89842029 . C G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=6.38224;LSEQ=CGGACCCTGTACCCAAAGCA;RSEQ=CGGCTTGAGCTGGCACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:7:7,0:84,2:86,7:0.0753:1,0:23.9:1:32.6:1:1:0:60:14:0.0753:0:1.1 0/1:93:32:32,0:57,4:61,32:0.3441:2,1:22.3:1:31.7:1:0.29468:0:60:31:0.337:0:1.1 +16 89842050 . A T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.49823;SOR=Inf;LSEQ=CGGCTTGAGCTGGCACAGCC;RSEQ=CCCCCGAGCTCACTCGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:128,13:141,0:0:2,0:24.1:1:30.4:1:1:0:60:34.25:1:0:0.1 0/1:142:2:1,1:122,18:140,2:0.0141:2,2:19:0:28.5:1:0.25052:6.62399:60:4:0.0142:0:1.5 +16 89842374 . T G 90 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00877;SOR=11.37732;LSEQ=AGCCTGTTTTTACAAAAAAA;RSEQ=ATTAAAAAATATATATAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:1:0,1:1,49:50,1:0.0196:1,0:15:0:34:0:1:0:60:2:0.02:0:1 0/1:37:7:0,7:0,30:30,7:0.1892:1,0:21.3:1:32.3:1:1:0:60:14:0.1944:0:1 +16 89845110 . A T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=22.95599;LSEQ=TATTTTACCAATAAAACACA;RSEQ=TAGTGGTCTAACAAATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:5:4,1:173,42:215,5:0.0227:2,2:30.2:1:31.4:1:1:1.02963:60:10:0.0233:0:1.2 0/1:229:80:56,24:109,40:149,80:0.3493:2,2:25.7:1:28.7:1:0.64471:1.16705:59.9:19:0.3439:0:1.7 +16 89845194 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.21037;LSEQ=GAAGTAGTCATCCCCTTCTA;RSEQ=CCGTTGCTGCATACCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:761:32:17,15:398,331:729,32:0.042:2,2:32.2:1:31.9:1:1:1.06085:60:15:0.0401:0:1.1 0/1:836:259:137,122:319,258:577,259:0.3098:2,2:24.3:1:31.1:1:0.54819:1.10093:60:50.8:0.3098:0:1.3 +16 89845455 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49972;SOR=0;LSEQ=TGCATCAGTCAGAGCAGCGA;RSEQ=AAGGCAATTCCCACAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:34,153:187,2:0.0105:2,2:11.5:1:28.5:1:0.33688:4.45:60:4:0.0105:0:1 0/0:173:0:0,0:26,147:173,0:0:2,0:24.4:1:30.7:1:1:0:60:56.667:1:0:0.1 +16 89845456 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23404;SOR=Inf;LSEQ=GCATCAGTCAGAGCAGCGAG;RSEQ=AGGCAATTCCCACAGACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:30,153:183,0:0:2,0:25.8:1:31.1:1:1:0:60:182:1:0:0.1 0/1:172:2:1,1:24,146:170,2:0.0116:2,2:29:1:32.5:1:0.2703:5.98:60:4:0.0118:0:1 +16 89846050 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02299;SOR=Inf;LSEQ=TAACGGCAGGATCCTCGATT;RSEQ=ACAGCCCTGACTCCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:24,1:25,0:0:1,0:24:1:32.2:1:1:0:59.3:50:1:0:0.2 0/1:5:2:2,0:3,0:3,2:0.4:0,0:17.5:1:32:0:1:0:60:4:0.4:0:1 +16 89846195 . A G 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.53521;LSEQ=CACCCTGCAGGCATCAGAGC;RSEQ=GAGTCTGCACATACTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:10:8,2:144,16:160,10:0.0588:2,2:20.9:1:31.2:1:0.2861:2.23596:60:20:0.0602:0:1 0/1:158:46:40,6:98,14:112,46:0.2911:2,2:25.3:1:29.7:1:1:1.04967:60:92:0.293:0:1.1 +16 89846203 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.12092;SOR=Inf;LSEQ=AGGCATCAGAGCAGAGTCTG;RSEQ=ACATACTGCAGGCATCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:161,22:183,0:0:2,0:23.8:1:31.7:1:1:0:60:25.143:0.9944:0:0.1 0/1:181:3:2,1:153,24:177,3:0.0166:2,2:19:1:28.3:1:0.36321:3.15816:60:6:0.0168:0:1 +16 89849480 . C T 247 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=117.64599;LSEQ=GAGGAGGGAGCGGTACTTGC;RSEQ=GGGAACCAGGGGTGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1111:3:0,3:495,612:1107,3:0.0027:2,0:8.7:1:29.7:1:0.2581:0:60:6:0.0027:0:1.7 0/1:1373:332:166,166:496,544:1040,332:0.2418:2,2:23.9:1:29.5:1:0.48794:1.10:59.9:54.333:0.2408:0:1.2 +16 89849539 . G A 75 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11516;SOR=3.54836;LSEQ=AGATAGCAGAGCGCAGCACC;RSEQ=TTAGTCTGGGAACTGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:651:2:2,0:215,434:649,2:0.0031:2,0:1:0:26.5:1:0.11077:0:60:4:0.0031:0:1 0/1:739:8:7,1:277,454:731,8:0.0108:2,2:5.5:1:25:1:0.00633:11.44:60:16:0.0109:0:1.4 +16 89849583 . C T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=6.99135;LSEQ=TCCAGGGAGGCCACAATTCA;RSEQ=TTCCAACATCCACAGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:13:3,10:32,212:244,13:0.0506:2,2:23.5:1:30.5:1:0.39539:1.98:60:26:0.051:0:1.5 0/1:272:74:14,60:36,162:198,74:0.2721:2,2:21.3:1:29:1:0.86225:1.05:60:73:0.2704:0:1.4 +16 89849629 . T A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=5.97856;LSEQ=AGAAACACAGCCCTTTACAG;RSEQ=CAGACTTATGAGTATGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:8:0,8:1,111:112,8:0.0667:1,0:24.8:1:31.1:1:1:0:60:16:0.0678:0:1.9 0/1:93:28:0,28:0,65:65,28:0.3011:1,1:26.7:1:30.6:1:1:0:60:56:0.3011:0:1.9 +16 89849735 . G A 50 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=6.40831;LSEQ=TTGGGAGGCTGAGGCGGGCA;RSEQ=ATCACGAGGTCAGGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:3,1:0.25:0,0:15:0:33:0:1:0:52:2:0.25:0:2 1/0:4:3:0,3:0,1:1,3:0.75:0,0:16:1:32:0:1:0:49:6:0.75:0:2 +16 89849740 . C T 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGGCTGAGGCGGGCAGATCA;RSEQ=GAGGTCAGGAGATGGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:10:0:32:0:1:0:52:2:0.5:0:2 1/1:3:3:0,3:0,0:0,3:1:0,0:11:1:30.3:1:1:0:49:6:1:0:2 +16 89851156 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50418;SOR=0;LSEQ=GGGAAGGGCCTGGCTGAGAG;RSEQ=CTCAGAGCAGATCTGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:2,0:151,5:156,2:0.0127:1,0:27:1:32:0:1:0:60:4:0.013:0:1 0/0:127:0:0,0:118,9:127,0:0:2,0:24.2:1:30.5:1:1:0:60:41.333:1:0:0.1 +16 89851445 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.50079;SOR=0;LSEQ=CCTAGGCAGTGTCCTGTGTG;RSEQ=AGAGAAGAGCGTGAAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:0,2:5,120:125,2:0.0157:1,0:24:1:27.5:1:1:0:56.5:4:0.0159:0:1 0/0:109:0:0,0:5,104:109,0:0:1,0:24.3:1:31.3:1:1:0:58.5:218:1:0:0.1 +16 89851575 . G A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGTCGGCCTCCTAAACA;RSEQ=AAAGGAAAAAAGAGAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:0,23:0,0:0,23:1:0,1:19.6:1:29.8:1:1:0:60:10.5:1:0:1.1 1/1:7:7:1,6:0,0:0,7:1:0,2:14.4:1:30.3:1:1:0:60:14:1:0:1 +16 89857622 . T C 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07258;SOR=8.68014;LSEQ=ACATGCAGAGGAAGATCCGC;RSEQ=GAGGCCCCGACAGGGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:22,0:22,1:0.0435:1,0:41:0:33:0:1:0:60:2:0.0476:0:1 0/1:10:3:3,0:6,1:7,3:0.3:2,0:36:1:30.3:1:1:0:60:6:0.3:0:1.3 +16 89857700 . A G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00077;SOR=5.64596;LSEQ=GGCCACTCGGCAAAGCTGAC;RSEQ=GCAAGGTTGCTCACTCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:5:5,0:73,1:74,5:0.0633:1,0:31.6:1:29.4:1:1:0:60:10:0.0649:0:1 0/1:61:17:16,1:44,0:44,17:0.2787:1,1:28.5:1:29.1:1:0.27869:0:60:16:0.2667:0:1.1 +16 89857755 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12357;SOR=Inf;LSEQ=TGGGGACAGCATGGTCCCCA;RSEQ=TCCCAGGCCTTCTGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:186,71:257,0:0:2,0:22.7:1:32:1:1:0:59.7:50.4:1:0:0.1 0/1:260:4:1,3:174,82:256,4:0.0154:2,2:12.5:1:25.5:1:0.10379:6.31758:60:8:0.0156:0:1 +16 89857964 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.55191;LSEQ=TCTAGTTAAGAACCATGACA;RSEQ=AGTCACAGCAAGGCAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:24:9,15:92,197:289,24:0.0767:2,2:23.3:1:32:1:0.65025:1.28:52.7:48:0.0777:0:1.4 0/1:391:138:46,92:94,158:252,138:0.3529:2,2:27.1:1:30.5:1:0.44249:1.18934:55.6:26.6:0.3491:0:1.3 +16 89858024 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.38151;LSEQ=TGAGTTATGCTGGGTGATCA;RSEQ=GTATTCCAGAAGGAGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:10:1,9:15,95:110,10:0.0833:2,2:26.5:1:32.2:1:1:1.41733:45.4:20:0.0833:0:1.8 0/1:106:35:1,34:12,59:71,35:0.3302:2,1:18.3:1:30.8:1:0.05611:6.82704:49.3:70:0.3333:0:1.9 +16 89858184 . A G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38;SOR=0;LSEQ=TGCTTATGGAAGCGTCTGAC;RSEQ=AAGAATGTTCCATCGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:23,8:0,0:0,31:1:0,2:23:1:30.9:1:1:0:58.3:62:1:0:1 1/1:19:18:16,2:0,0:0,18:0.9474:0,2:27.3:1:30.4:1:1:0:60:36:1:0:1.1 +16 89858277 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49843;SOR=Inf;LSEQ=CACAGTCAGCTGGGACTCTG;RSEQ=TGACACCCCCCTACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:136,13:149,0:0:2,0:25.1:1:32.3:1:1:0:60:36.25:1:0:0.1 0/1:153:2:1,1:135,16:151,2:0.0131:2,2:17:1:27.5:1:0.21053:8.21502:60:4:0.0132:0:1 +16 89858288 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.2103;SOR=0;LSEQ=GGGACTCTGCTGACACCCCC;RSEQ=TACACACACTCTTGACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:169,15:184,2:0.0108:2,2:23.5:1:29.5:1:0.16507:10.94143:60:4:0.0109:0:1 0/0:219:0:0,0:178,41:219,0:0:2,0:21.2:1:30.3:1:1:0:60:72:1:0:0.2 +16 89858505 . T C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.36847;LSEQ=AAAGCATCCGCTCCCTTCAA;RSEQ=ATCCAAGCAAACCAATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:22:6,16:79,245:324,22:0.0636:2,2:31.5:1:31:1:0.79875:1.16:60:10:0.0588:0:2.1 0/1:377:114:30,84:70,193:263,114:0.3024:2,2:23.5:1:31.3:1:1:1.0155:60:56:0.3019:0:1.6 +16 89858525 . C G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.42373;LSEQ=TATCCAAGCAAACCAATGTG;RSEQ=GACAGATGACCCCTCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:21:4,17:27,190:217,21:0.0882:2,2:23.4:1:30.7:1:0.49228:1.65:60:20:0.0858:0:2.1 0/1:233:70:10,60:25,138:163,70:0.3004:2,2:21.5:1:30.3:1:1:1.08658:60:69:0.304:0:2 +16 89858657 . C G 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20997;SOR=3.33229;LSEQ=CTCACAGTGGCCAGCACCTG;RSEQ=TTGGAGAGAATTCTCCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:6,13:19,2:0.0952:2,2:33:1:32.5:1:1:2.08:60:4:0.1:0:1 0/1:15:4:2,2:4,7:11,4:0.2667:2,2:28.3:1:30.3:1:1:1.68:60:8:0.2857:0:1 +16 89858759 . C T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=TGATGAGGACAGCCACATCT;RSEQ=ACCAGACATCCCTGAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:52,8:60,0:0:2,0:24.4:1:33:1:1:0:60:120:1:0:0.1 0/1:54:11:10,1:40,3:43,11:0.2037:2,2:27.7:1:30.6:1:1:1.32573:60:22:0.2037:0:1.1 +16 89858960 . A AG 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.1661;SOR=0;LSEQ=TGAACAGCATCAGATGCTGC;RSEQ=GGGGGAGAAACAGACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:60,138:198,2:0.01:2,2:30.5:1:32.5:1:0.51804:2.29:60:4:0.0101:0:0 0/0:290:0:0,0:95,195:290,0:0:2,0:24.9:1:30:1:1:0:60:57:1:0:0.2 +16 89858963 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17517;SOR=0;LSEQ=ACAGCATCAGATGCTGCAGG;RSEQ=GGAGAAACAGACAAAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:56,139:195,2:0.0102:2,2:12.5:1:29.5:1:0.49601:2.47:60:4:0.0104:0:1 0/0:273:0:0,0:85,188:273,0:0:2,0:25:1:30.5:1:1:0:60:135.5:1:0:0.2 +16 89859008 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00044;SOR=5.78811;LSEQ=TCAGAGATCAAAAAGTTGTG;RSEQ=GTTTTTGTTAAGGACCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:4:0,4:5,66:71,4:0.0533:2,0:32.5:1:32:1:1:0:53.8:8:0.0541:0:1 0/1:101:25:4,21:9,67:76,25:0.2475:2,2:19.4:1:29.4:1:0.73099:1.41:58.7:24:0.2424:0:1.1 +16 89859015 . GT G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00917;SOR=4.21183;LSEQ=TCAAAAAGTTGTGGGTTTTT;RSEQ=TAAGGACCAGCCCCACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:4:0,4:3,59:62,4:0.0606:1,0:36.5:1:32.8:1:1:0:53.8:8:0.0615:0:1 0/1:79:17:2,15:6,56:62,17:0.2152:2,2:21.9:1:31.2:1:1:1.24:58.1:34:0.2208:0.0253:1.1 +16 89860182 . TG GA 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTATTTTTTTGATGC;RSEQ=AGTCTCACTCTGTCACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:27.8:1:1:0:50.5:4:1:0:1 +16 89861243 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50049;SOR=Inf;LSEQ=AGGACACCCACTGGGCAGAC;RSEQ=ATGCCTGGGCCATCAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:39,19:58,0:0:2,0:24.7:1:30.4:1:1:0:60:116:1:0:0 0/1:70:2:1,1:39,29:68,2:0.0286:2,2:31:1:31:1:1:1.33905:60:4:0.029:0:1 +16 89862132 . G C 93 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00291;SOR=9.85376;LSEQ=TTTTCTTATAAAAATCTGTT;RSEQ=CTTTCAGGTAAAAGGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:41,0:41,2:0.0465:1,0:31:1:33.5:1:1:0:60:4:0.0476:0:1 0/1:24:8:7,1:16,0:16,8:0.3333:1,2:27.4:1:31.3:1:0.33333:0:60:16:0.3333:0:1 +16 89862155 . G C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06701;SOR=Inf;LSEQ=TTCAGGTAAAAGGATATTTA;RSEQ=TAACAATCTCAGGCATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:57,0:57,0:0:1,0:24.6:1:33.9:1:1:0:60:114:1:0:0.2 0/1:40:3:3,0:36,1:37,3:0.075:1,0:27.3:1:33.3:1:1:0:60:6:0.0769:0:2 +16 89862202 . C T 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTCTCTGGTTCAAGACAGA;RSEQ=GTAAAAGAGGTCCTAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:131,2:133,0:0:1,0:25.7:1:32.3:1:1:0:60:65.5:1:0:0.2 0/1:106:21:19,2:80,4:84,21:0.1981:1,2:23.1:1:29.1:1:0.34458:2.08751:60:20:0.1942:0:1.1 +16 89862212 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50707;SOR=0;LSEQ=TCAAGACAGACGTAAAAGAG;RSEQ=TCCTAGAATTCCTGGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:156,9:165,2:0.012:2,0:25:1:32:0:1:0:60:4:0.0121:0:1 0/0:128:0:0,0:119,9:128,0:0:2,0:23.7:1:30.6:1:1:0:60:63:1:0:0.3 +16 89862493 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=Inf;LSEQ=CACGCCACCCACCAATCCCA;RSEQ=CACAAACTGTGGCTCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:15,140:155,0:0:2,0:24.8:1:32.5:1:1:0:59.7:154:1:0:0.1 0/1:167:2:1,1:18,147:165,2:0.012:2,2:9.5:1:27:1:0.21521:7.98:60:4:0.012:0:1 +16 89862571 . T G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52893;SOR=0;LSEQ=AGGCCACTATAACCACAGAC;RSEQ=TGAAACTGAATCCAAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:1,37:38,2:0.05:1,0:19.5:1:34:0:1:0:60:4:0.0526:0:1 0/0:23:0:0,0:0,23:23,0:0:1,0:18.3:1:30.1:1:1:0:60:46:1:0:0 +16 89865242 . T C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17157;SOR=6.87863;LSEQ=GGCCAGCTCTAGAGCCTGAA;RSEQ=CACACCCAGGGAAGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:12,0:12,1:0.0769:0,0:12:0:34:0:1:0:60:2:0.0833:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:31:1:32:1:1:0:60:4:0.4:0:1 +16 89865380 . GA G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49832;SOR=Inf;LSEQ=TTCCGACCTCATCCTCACAG;RSEQ=AAAGGCTGACCAGAGCGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:125,18:143,0:0:2,0:25.2:1:30:1:1:0:60:46.667:1:0:0.1 0/1:146:2:1,1:125,19:144,2:0.0137:2,2:8.5:1:29.5:1:0.25602:6.43797:60:4:0.014:0.0068:0.5 +16 89865385 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=ACCTCATCCTCACAGGAAAA;RSEQ=GCTGACCAGAGCGTTCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:134,25:159,0:0:2,0:24.3:1:32.4:1:1:0:60:38.75:1:0:0.1 0/1:162:2:2,0:135,25:160,2:0.0123:2,0:34:1:32.5:1:1:0:60:4:0.0125:0:1 +16 89865404 . C A 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24974;SOR=Inf;LSEQ=AGGCTGACCAGAGCGTTCCC;RSEQ=GGGCTTTCCCATGGTCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:173,56:229,0:0:2,0:23.7:1:30.4:1:1:0:60:37.167:0.9955:0:0.2 0/1:250:3:2,1:177,69:246,3:0.012:2,2:36.7:1:24.7:1:1:1.28129:60:2:0.008:0:1.7 +16 89865408 . C T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25094;SOR=Inf;LSEQ=TGACCAGAGCGTTCCCCGGG;RSEQ=TTTCCCATGGTCGCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:181,61:242,0:0:2,0:24.1:1:31.8:1:1:0:60:25.889:1:0:0.2 0/1:271:3:1,2:189,79:268,3:0.0111:2,2:6.3:1:26:1:0.21367:4.75341:60:6:0.0112:0:1 +16 89865690 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.59955;SOR=0.43306;LSEQ=ATGTCAGCACACGGCGGCAG;RSEQ=CCACCAGAAACAATCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:0,2:32,114:146,2:0.0135:2,0:28:1:29:1:1:0:60:4:0.0138:0:1 0/0:170:1:0,1:40,129:169,1:0.0059:2,0:22:0:30:0:1:0:60:2:0.0061:0:1 +16 89866043 . T C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.13603;LSEQ=TCTCTGCAGTACATCAACCG;RSEQ=GACCTGTCAAAATAGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:617:35:14,21:275,307:582,35:0.0567:2,2:28.8:1:31.3:1:0.4864:1.34301:60:70:0.0575:0:1.1 0/1:722:217:102,115:236,269:505,217:0.3006:2,2:26.3:1:29.7:1:1:1.01:60:42.4:0.2994:0:1.1 +16 89866160 . A G 166 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=58.21667;LSEQ=AAGTAAAGAAACGGCACTTC;RSEQ=GGAGGCCGAGGCGGGCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:1,68:69,2:0.0278:1,0:16:1:33:0:1:0:60:4:0.0282:0:1 1/0:68:43:0,43:0,25:25,43:0.6324:1,1:23.3:1:30.6:1:1:0:55.7:42:0.6269:0:1.2 +16 89869466 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATGTTGCCAACACACA;RSEQ=AAATGATACATACTGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:26,0:26,2:0.0714:1,0:10:1:29.5:1:1:0:60:4:0.0714:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:26.7:1:32.2:1:1:0:60:12:1:0:0 +16 89869704 . T C 169 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.95061;LSEQ=GCTCCACAGTTCTTCTCAGA;RSEQ=CTGAGTTTTTCTGAAATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:1:0,1:335,434:769,1:0.0013:2,0:1:0:14:0:1:0:60:0:0:0:1 0/1:910:46:24,22:420,443:863,46:0.0505:2,2:24.4:1:30.6:1:0.65331:1.15:60:45:0.0504:0:1.5 +16 89869761 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=2.50415;LSEQ=GAACAAAATCTGAAAAACCA;RSEQ=AAAACCAAAGTTATTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:144:45,99:116,223:339,144:0.2981:2,2:22.9:1:32.3:1:0.59794:1.14408:60:143:0.2979:0:1.1 1/0:607:313:105,208:107,186:293,313:0.5157:2,2:24.4:1:31.3:1:0.44475:1.13933:60:43.714:0.5134:0:1.2 +16 89869803 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.17802;SOR=0;LSEQ=CATCATGGTCTCCAAGCAAC;RSEQ=GTGAATGGCACAGACCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:38,151:189,2:0.0105:2,2:32.5:1:29.5:1:0.36754:3.94:60:4:0.0106:0:1 0/0:261:0:0,0:56,205:261,0:0:2,0:23.3:1:29.4:1:1:0:60:51.2:1:0:0.6 +16 89871800 . G A 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01885;SOR=Inf;LSEQ=ACAGCATGCATGTCGGGATG;RSEQ=CTGGAGACACACACAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:0:0,0:208,306:514,0:0:2,0:24.7:1:31.7:1:1:0:60:63.25:1:0:0.2 0/1:632:7:5,2:265,359:624,7:0.0111:2,2:23:1:25.7:1:0.14405:3.38:60:6:0.0096:0:1.1 +16 89871879 . A AT 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.02891;LSEQ=GAGTTGAGCCATATGTCCCA;RSEQ=TTTTTTTTTTGAGACAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:8:0,8:18,128:146,8:0.0516:2,0:33.8:1:29.4:1:0.5972:0:60:16:0.0523:0:0.1 0/1:132:7:0,7:15,107:122,7:0.053:2,0:32.1:1:29.7:1:1:0:60:14:0.0547:0:0.4 +16 89872187 . G GTTGT 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTTCTTTGACTCATTAT;RSEQ=TTAACTTTCAAATATTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:29.5:1:30.8:1:1:0:60:4:0.4:0.2:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 89874477 . AG A 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGTCTCAAAAAAAAAAC;RSEQ=ACAAAAAGCAAACAAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:0,12:1:0,0:21.1:1:30.9:1:1:0:50.9:24:1:0.3333:4.8 1/1:7:7:7,0:0,0:0,7:1:0,0:22:1:31.1:1:1:0:48.4:14:1:0.2857:5.1 +16 89874486 . G A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAACAGACAAAAA;RSEQ=CAAACAAAACCAAAACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:25.1:1:31.5:1:1:0:50.5:22:1:0:5.3 1/1:7:7:7,0:0,0:0,7:1:0,0:25.4:1:30.9:1:1:0:48.4:14:1:0:5.1 +16 89874491 . C A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACAGACAAAAAGCAAA;RSEQ=AAAACCAAAACACCATAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:26.5:1:31.4:1:1:0:50.5:22:1:0:5.3 1/1:7:7:7,0:0,0:0,7:1:0,0:28.9:1:30.6:1:1:0:48.4:14:1:0:5.1 +16 89874494 . A C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGACAAAAAGCAAACAA;RSEQ=ACCAAAACACCATAAACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:27.4:1:33.4:1:1:0:50.5:22:1:0:5.3 1/1:8:8:8,0:0,0:0,8:1:0,0:26.6:1:32.6:1:1:0:49.9:16:1:0:5 +16 89874496 . CC AA 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACAAAAAGCAAACAAAA;RSEQ=AAAACACCATAAACGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:28.2:1:31.3:1:1:0:50.5:22:1:0:4.3 1/1:8:8:8,0:0,0:0,8:1:0,0:28.1:1:30.9:1:1:0:49.9:16:1:0:4 +16 89874559 . A C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.82136;SOR=0.80811;LSEQ=TCCTCCAGGTCTAGTCTAGT;RSEQ=TAAATATGCAATGCAATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:18:18,0:44,1:45,18:0.2857:1,1:27.7:1:32.1:1:1:0:59.6:17:0.2742:0:2.1 0/1:41:10:10,0:31,0:31,10:0.2439:1,0:23.4:1:30.5:1:1:0:60:20:0.2439:0:2.2 +16 89874624 . G T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46837;LSEQ=GCCAGAAATCAAACCCGTCT;RSEQ=ATTCTGGGCTTTGAAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:2:1,1:197,44:241,2:0.0082:2,2:1:0:27:1:0.3367:4.43848:60:4:0.0082:0:1 0/1:249:3:1,2:190,56:246,3:0.012:2,2:9.7:1:25.7:1:0.13633:6.71834:60:6:0.0121:0:1 +16 89874628 . C T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70243;SOR=0.9286;LSEQ=GAAATCAAACCCGTCTGATT;RSEQ=TGGGCTTTGAAATATAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:75:61,14:147,39:186,75:0.2874:2,2:24.3:1:30.7:1:0.73624:1.16:60:36.5:0.2852:0:1.1 0/1:279:76:55,21:152,49:201,76:0.2724:2,2:20.6:1:29.2:1:0.64237:1.18366:60:75:0.2778:0:1.2 +16 89874756 . G A 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.83352;LSEQ=GTACGTGAAGATGCCACACC;RSEQ=CTTCAAGCAACAAAGAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:2:2,0:193,330:523,2:0.0038:2,0:1:0:28.5:1:0.13751:0:60:4:0.0038:0:1 0/1:726:34:17,17:292,398:690,34:0.0468:2,2:27:1:28.6:1:0.38108:1.36:59.6:68:0.0482:0:1.3 +16 89874817 . AC A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.19995;SOR=0;LSEQ=ACAAAAACAAAAACAAAAAA;RSEQ=CCCCAGCATTCTGAGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:0,2:19,172:191,2:0.0104:2,0:25.5:1:29:1:1:0:60:4:0.0105:0.0052:3.5 0/0:238:0:0,0:39,199:238,0:0:2,0:22.1:1:30.7:1:1:0:60:237:1:0:0.1 +16 89874822 . C T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19791;SOR=0;LSEQ=AACAAAAACAAAAAAACCCC;RSEQ=AGCATTCTGAGTCCTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:15,159:174,2:0.0114:2,2:29.5:1:25.5:1:0.17403:10.30:60:4:0.0115:0:1.5 0/0:219:0:0,0:33,186:219,0:0:2,0:21.9:1:31.2:1:1:0:60:108.5:1:0:0.1 +16 89875033 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCTTCTCTCTTCCTAC;RSEQ=CACTGTAGCCTACTTCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:10.5:1:32:0:1:0:56.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 89875316 . CTA C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCCCCCTAACTCACACT;RSEQ=TTTTTTTTTTTTTGAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:34:0:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 89876261 . CAA C 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGCAAAACTCCATCT;RSEQ=AAAAAAAAAAAGATACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42:1:31.5:1:1:0:42.5:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +16 89876801 . AT A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAAAAAAATTACATAC;RSEQ=TTTTTTTTAATAGTTTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:31:1:1:0:60:4:1:0:0 +16 89877066 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58146;SOR=0.38124;LSEQ=TGCCTCCATCCAGATCAACA;RSEQ=AACATTGCCTGGAACACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:124,38:162,2:0.0122:2,2:30:1:29.5:1:0.42017:3.234:60:4:0.0122:0:1 0/0:214:1:0,1:151,62:213,1:0.0047:2,0:1:0:23:0:0.29439:0:60:2:0.0048:0:1 +16 89877076 . T A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19628;SOR=0;LSEQ=CAGATCAACAGAACATTGCC;RSEQ=GGAACACTGGAGAGTCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:139,52:191,2:0.0104:2,2:13:0:33.5:1:0.47485:2.65725:60:4:0.0105:0:1.5 0/0:242:0:0,0:166,76:242,0:0:2,0:24.9:1:29.9:1:1:0:60:79.667:1:0:0.2 +16 89877235 . A T 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAAGAGAGATTACATTTTTT;RSEQ=AAAAACAAATTACCTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:131,168:299,0:0:2,0:24.1:1:29.9:1:1:0:60:148.5:1:0:0.1 0/1:342:18:6,12:109,215:324,18:0.0526:2,2:26.8:1:28.3:1:1:1.01391:60:36:0.0528:0:1.1 +16 89877285 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20152;SOR=Inf;LSEQ=GCTATGTCCTATTTTCCCAA;RSEQ=CAGCTTAAAAGTAACAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:139,101:240,0:0:2,0:24.6:1:32:1:1:0:60:119:1:0:0.1 0/1:196:2:1,1:91,103:194,2:0.0102:2,2:13:1:29:1:1:1.13:60:4:0.0104:0:1 +16 89877546 . G C 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATCTAAAACCAAAGACTT;RSEQ=CTGTTTAAAATGCCTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:33,184:217,0:0:2,0:24:1:32.2:1:1:0:59.9:53.25:1:0:0 0/1:245:20:6,14:36,189:225,20:0.0816:2,2:18.3:1:30.4:1:0.12365:2.24:60:19:0.0788:0:1.2 +16 89877579 . CA C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.24651;SOR=Inf;LSEQ=CCTTATTTTAAGATGCAGCA;RSEQ=AAAAAAATTGCCTTTTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:3,104:107,0:0:1,0:23.7:1:31.4:1:1:0:59.8:214:1:0:0.1 0/1:108:3:0,3:3,102:105,3:0.0278:1,0:31.3:1:32.7:1:1:0:60:6:0.0283:0:0 +16 89877720 . C T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TTATACATTGGTATTTGTTA;RSEQ=GTTTCCCATGACACAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:0,7:7,5:0.4167:0,2:19.4:1:31.4:1:0.41667:0:59.4:10:0.4167:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:10:1:31:0:1:0:60:4:1:0:0 +16 89877929 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50266;SOR=Inf;LSEQ=AGGGATTTCCCAACATTCTG;RSEQ=CATGCACCTGGTGGGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:35,18:53,0:0:2,0:26.9:1:31.8:1:1:0:60:52:1:0:0.2 0/1:67:2:1,1:42,23:65,2:0.0299:2,2:36.5:1:26.5:1:1:1.8087:60:4:0.0308:0:1.5 +16 89877964 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49765;SOR=Inf;LSEQ=GCAGGTGCAGTCACAGCTGT;RSEQ=CTCAGTCCGCAGGCCACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:37,29:66,0:0:2,0:23.5:1:32:1:1:0:60:132:1:0:0.3 0/1:73:2:1,1:39,32:71,2:0.0274:2,2:29:1:28.5:1:1:1.21543:60:4:0.0278:0:1 +16 89877975 . A G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06148;SOR=0.4865;LSEQ=CACAGCTGTGCTCAGTCCGC;RSEQ=GGCCACCAAGTGGAACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:22:11,11:27,22:49,22:0.3099:2,2:26.5:1:28.8:1:0.79853:1.22372:60:21:0.3:0:1 0/1:84:15:8,7:36,33:69,15:0.1786:2,2:27.8:1:30:1:1:1.05:60:30:0.1786:0:1.3 +16 89878077 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49468;SOR=Inf;LSEQ=AAGTGAGAAACGGTGGGCAA;RSEQ=CTGGAAGCAGGCAATGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:5,35:40,0:0:2,0:25.8:1:31.1:1:1:0:59.4:80:0.9756:0:0 0/1:44:2:1,1:15,27:42,2:0.0455:2,2:15.5:1:27:1:1:1.77:60:4:0.0465:0:1 +16 89878134 . ATTTTT A 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=9.000;MSILEN=1;SSF=0.7241;SOR=0.73485;LSEQ=TTATTTGTCTTCCAAAATTA;RSEQ=TTTTGTTTTATTTTTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:0,6:0,8:8,6:0.4286:0,0:20.2:1:32.7:1:1:0:56:12:0.4286:0.0714:0 0/1:17:6:0,6:1,10:11,6:0.3529:2,0:23.5:1:30:1:1:0:60:12:0.3529:0.1176:0 +16 89880822 . C G 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1553;SOR=Inf;LSEQ=ACTACACACACCAGTGGAAA;RSEQ=CCATCGCCTGAGAAAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:49,1:50,0:0:1,0:23:1:32.2:1:1:0:59.8:100:1:0:0.1 0/1:78:4:4,0:71,3:74,4:0.0513:1,0:23.8:1:29:1:1:0:60:3:0.039:0:1 +16 89880844 . A G 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01918;SOR=Inf;LSEQ=CATCGCCTGAGAAAATTTAC;RSEQ=TTTCTACTTAATTTAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:99,4:103,0:0:1,0:19.7:1:31.2:1:1:0:59.9:102:1:0:0.1 0/1:132:7:7,0:112,11:123,7:0.053:2,0:21.7:1:29.6:1:1:0:60:14:0.0534:0:1 +16 89881076 . C A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AATTCAAGCTCCAGGCCAGG;RSEQ=GTAGTGGCTCACGCCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:54,176:230,0:0:2,0:23:1:30.2:1:1:0:57.7:56.5:0.9956:0:0.1 0/1:307:20:6,14:86,201:287,20:0.0651:2,2:25.1:1:30.2:1:1:1.00:59.9:40:0.0662:0:1.2 +16 89882191 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50042;SOR=Inf;LSEQ=GCCAGGCCACCGCGCCCGCC;RSEQ=CCTCGGGTGTTTTCTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:134,14:148,0:0:2,0:24.1:1:30.2:1:1:0:60:296:1:0:0.1 0/1:168:2:2,0:153,12:165,2:0.0119:2,0:20:1:30.5:1:1:0:60:4:0.0123:0:1 +16 89882928 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09031;SOR=0;LSEQ=ACGCCGCCCACTCCCGCGGC;RSEQ=TGCCGCGCCCACCTACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:1,2:124,75:199,3:0.0149:2,2:30.3:1:30:1:0.55907:3.28653:60:6:0.0151:0:1 0/0:247:0:0,0:140,107:247,0:0:2,0:22.9:1:30.4:1:1:0:60:34.286:1:0:0.4 +16 89882934 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.25392;SOR=Inf;LSEQ=CCCACTCCCGCGGCCTGCCG;RSEQ=GCCCACCTACCCAGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:137,95:232,0:0:2,0:22:1:31.1:1:1:0:60:45.4:1:0:0.2 0/1:275:3:1,2:152,120:272,3:0.0109:2,2:11.7:1:26:1:0.58622:2.52493:60:6:0.0112:0:1 +16 89883000 . G C 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTCCTGGCCCGAGGCGGA;RSEQ=TTCGGGACCCACGAGTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:219,201:420,0:0:2,0:26.6:1:32.6:1:1:0:60:83:0.9976:0:0.2 0/1:496:59:31,28:227,210:437,59:0.119:2,2:22.5:1:31.2:1:1:1.02:60:118:0.1207:0:1.2 +16 89883007 . A T 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCCGAGGCGGAGTTCGGG;RSEQ=CCCACGAGTCGGACATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:206,200:406,0:0:2,0:27.4:1:29.9:1:1:0:60:57:1:0:0.2 0/1:482:75:39,36:209,198:407,75:0.1556:2,2:27.2:1:28.3:1:1:1.03:60:24:0.1542:0:1.3 +16 89883047 . C A 44 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10307;SOR=0;LSEQ=CTTGGCGCCTACAGCCCCGG;RSEQ=GGCGGCTCCCTGCGCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:2,1:108,146:254,3:0.0117:2,2:5.3:1:28:1:0.57785:2.69:60:6:0.0118:0:1 0/0:290:0:0,0:125,164:289,0:0:2,0:25.6:1:29.7:1:1:0:60:47.167:1:0:0.4 +16 90001819 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GCCACCGTGTTCCGGGGCCG;RSEQ=ATGTCCATGAAGGAGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:7,1:8,2:0.2:2,2:22.5:1:32.5:1:0.37778:5.29155:25:4:0.2:0:1 0/0:6:0:0,0:5,1:6,0:0:2,0:20.7:1:31:1:1:0:31.5:12:1:0:0 +17 114669 . C A 231 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAATTCACAGTGGTCAATG;RSEQ=AAGACAAAACTCAGTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:129,164:293,0:0:2,0:27.7:1:32.4:1:1:0:60:586:1:0:0.1 1/0:376:250:112,138:61,65:126,250:0.6649:2,2:25.7:1:29:1:0.51302:1.15587:60:61.5:0.6613:0:1.1 +17 114710 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25593;SOR=Inf;LSEQ=TTACTAATGTACACATAACT;RSEQ=CAAAACATGAAAATGTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:66,130:196,0:0:2,0:23.1:1:32.3:1:1:0:59.9:195:1:0:0.1 0/1:240:3:2,1:80,157:237,3:0.0125:2,2:10.3:1:27.7:1:0.26954:3.90:60:6:0.0127:0:2 +17 953191 . C CA 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCCAACCAGCTTGGAAC;RSEQ=AAAATCACGAAAGAGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:25.5:1:32:0:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 953435 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50017;SOR=Inf;LSEQ=CAAACTCCTGGGGAAAGATG;RSEQ=GACAAAGGGCCCTGAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:76,77:153,0:0:2,0:25.9:1:31.1:1:1:0:60:75.5:1:0:0.4 0/1:172:2:1,1:84,84:168,2:0.0116:2,2:30.5:1:28.5:1:1:1:60:4:0.0119:0:2.5 +17 953456 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=2.37948;LSEQ=GACAAAGGGCCCTGAACCTC;RSEQ=GAAGCTGGGAGGCCTGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:58:24,34:51,61:112,58:0.3412:2,2:29.1:1:30.3:1:0.6286:1.18325:60:28:0.3373:0:1.2 1/0:190:105:50,55:40,45:85,105:0.5526:2,2:26.2:1:29.6:1:1:1.02:59.8:51.5:0.5538:0:1.2 +17 953482 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50113;SOR=Inf;LSEQ=TGGGAGGCCTGGCTTTCCGG;RSEQ=AGGTGCGTGCCTCAGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:60,93:153,0:0:2,0:27.4:1:32.4:1:1:0:60:152:1:0:0.5 0/1:177:2:1,1:77,98:175,2:0.0113:2,2:27.5:1:27.5:1:1:1.27:60:4:0.0115:0:2 +17 953491 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24992;SOR=Inf;LSEQ=TGGCTTTCCGGCAGGTGCGT;RSEQ=CCTCAGCTTTGCAAGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:55,86:141,0:0:2,0:25.3:1:32.1:1:1:0:60:27.2:1:0:0.4 0/1:158:3:2,1:60,95:155,3:0.019:2,2:32.3:1:29.3:1:0.56164:3.14:60:6:0.0191:0:1.3 +17 953660 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=AGAAGCCAGAGGAGCAGGGA;RSEQ=CAGAAAGGGGGGTGCAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:19.7:1:31.7:1:1:0:60:6:0.5:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:16.8:1:30.2:1:1:0:60:12:1:0:0 +17 986739 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25567;SOR=Inf;LSEQ=GCTCCTTGTCCCTCAGGGTG;RSEQ=CTATGTGGGGAGCGGCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:121,121:242,0:0:2,0:25:1:31.3:1:1:0:60:59.5:1:0:0.8 0/1:294:3:1,2:146,145:291,3:0.0102:2,2:24:1:28.7:1:1:2.00917:60:6:0.0103:0:2 +17 986742 . A G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.4736;LSEQ=CCTTGTCCCTCAGGGTGGCT;RSEQ=TGTGGGGAGCGGCCTACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:157:74,83:47,43:90,157:0.6356:2,2:25.2:1:32.1:1:0.5087:1.22494:60:156:0.6393:0:1.2 0/1:292:132:61,71:82,78:160,132:0.4521:2,2:24.3:1:31.2:1:0.41206:1.22277:60:264:0.4583:0:1.2 +17 986746 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25428;SOR=Inf;LSEQ=GTCCCTCAGGGTGGCTATGT;RSEQ=GGGAGCGGCCTACCTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:116,130:246,0:0:2,0:24.7:1:31.5:1:1:0:60:122:0.9959:0:0.7 0/1:294:3:1,2:142,149:291,3:0.0102:2,2:19.7:1:31.7:1:1:1.90202:55.7:6:0.0103:0:1.3 +17 986754 . G A 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13396;SOR=Inf;LSEQ=GGGTGGCTATGTGGGGAGCG;RSEQ=CCTACCTCTGAGATCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:113,132:245,0:0:2,0:25:1:31.6:1:1:0:60:80.667:1:0:0.7 0/1:310:4:3,1:145,161:306,4:0.0129:2,2:14:1:23:1:0.35135:3.32:60:3:0.0098:0:1.3 +17 1359199 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50978;SOR=Inf;LSEQ=GGCTGGGCGGGCGACGGTGG;RSEQ=ACCGGCGGGCGCGGGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:77,34:111,0:0:2,0:23.6:1:32.3:1:1:0:60:54.5:1:0:0.2 0/1:151:2:1,1:106,43:149,2:0.0132:2,2:6:1:26.5:1:0.49925:2.44842:60:4:0.0132:0:1 +17 1359204 . G T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76758;LSEQ=GGCGGGCGACGGTGGCACCG;RSEQ=CGGGCGCGGGCCGCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:0,2:83,42:125,2:0.0157:2,0:1:0:27:1:0.11824:0:60:4:0.0163:0:1 0/1:165:2:1,1:112,51:163,2:0.0121:2,2:15.5:1:30:1:0.5323:2.18459:60:4:0.0123:0:1 +17 1359205 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5061;SOR=Inf;LSEQ=GCGGGCGACGGTGGCACCGG;RSEQ=GGGCGCGGGCCGCTGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:85,45:130,0:0:2,0:24.3:1:30.7:1:1:0:60:20.667:1:0:0.2 0/1:167:2:1,1:113,52:165,2:0.012:2,2:5:1:28.5:1:0.53531:2.16202:60:4:0.0122:0:1.5 +17 1359206 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5047;SOR=Inf;LSEQ=CGGGCGACGGTGGCACCGGC;RSEQ=GGCGCGGGCCGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:88,46:134,0:0:2,0:24.3:1:29.9:1:1:0:60:43.667:1:0:0.2 0/1:168:2:1,1:113,51:164,2:0.0119:2,2:24:1:30.5:1:0.52968:2.204:60:4:0.0121:0:2 +17 1359227 . A T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.19159;SOR=0;LSEQ=GGCGCGGGCCGCTGCTGTTG;RSEQ=TGATGTAGTGGGAGACGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:119,71:190,2:0.0104:2,2:11:0:32:0:1:1.67128:60:4:0.0112:0:1.5 0/0:246:0:0,0:150,95:245,0:0:2,0:25.2:1:28.3:1:1:0:60:39.833:1:0:0.2 +17 1359363 . T G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.78849;SOR=1.18102;LSEQ=CGCCTCCTGCCGACTCAACC;RSEQ=CCCCCAGTACCAGCTACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:19:1,18:0,9:9,19:0.6786:0,1:22.2:1:31.4:1:1:0:60:38:0.6786:0:1 1/0:35:25:2,23:0,9:9,25:0.7143:0,2:26.1:1:32.3:1:1:0:60:50:0.7143:0:1.1 +17 1384066 . A G 28 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCGAAGAGTCTCCTCCTC;RSEQ=CCCCCCTCCAGCAGCTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:20:1:28:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:2:0:26:0:1:0:60:2:1:0:1 +17 1454506 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17066;SOR=Inf;LSEQ=GGGCAGCCAGATGGCTGACA;RSEQ=AGTAAAGCTTCTCTTGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:0,76:76,0:0:1,0:23.2:1:32.4:1:1:0:60:37:1:0:0.1 0/1:54:2:1,1:4,48:52,2:0.037:2,2:20:1:28:1:0.1782:10.84:60:4:0.0377:0:1 +17 1760942 . C G 62 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCCAAAGCCTCACCAAC;RSEQ=CACCCCCCACCCGGCCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:35.8:1:31:1:1:0:34:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 1761431 . T C 55 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06098;SOR=0;LSEQ=CTTCAGGCCTTTTCCTAGGT;RSEQ=CCACATCAAGTGTCGGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:10:0:34:0:1:0:24:2:1:0:2 0/1:81:4:2,2:40,37:77,4:0.0494:2,2:21.5:1:27.8:1:1:1.08002:22:8:0.05:0:2 +17 1761764 . C CT 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.19706;LSEQ=GGGTTCTGGTCTCTCTTTTT;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:99:24,75:32,75:107,99:0.45:2,2:26:1:29.6:1:0.43364:1.33146:50.5:15.5:0.4408:0.0091:0.3 0/1:325:45:17,28:83,188:271,45:0.1385:2,2:27:1:29.5:1:0.38729:1.37:54.4:90:0.1429:0.0062:0.5 +17 1762323 . G A 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCTATCTCAGCCTCCCA;RSEQ=GTAGCTAGGACTACAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:28:0:27:0:1:0:38:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:31.5:1:1:0:23.5:4:1:0:1 +17 3568401 . G A 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00404;SOR=0;LSEQ=TGCTGTGGCTTCTGTAGGTG;RSEQ=GAAGCCCGTCTCACAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:8,0:16,0:16,8:0.3333:1,0:29.3:1:30.1:1:1:0:60:16:0.3478:0:1.1 0/0:22:0:0,0:22,0:22,0:0:1,0:24.4:1:30.6:1:1:0:60:44:1:0:0.1 +17 3568479 . C A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.57663;LSEQ=GAGAGGAAGGGGTTTCCTTT;RSEQ=GGCCGGAACCGCCATCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:1,0:54,40:94,1:0.0105:2,0:25:0:11:0:1:0:35:0:0:0:5 0/1:121:2:1,1:69,50:119,2:0.0165:2,2:41.5:1:29:0:1:1.37625:59:4:0.0165:0:1 +17 3568499 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20065;SOR=0;LSEQ=CGGCCGGAACCGCCATCTTC;RSEQ=AGTAATTCGCCAAAATGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:50,41:91,2:0.0215:2,2:22:1:30:1:1:1.21689:50.5:4:0.0217:0:1.5 0/0:114:0:0,0:63,51:114,0:0:2,0:34.9:1:31.3:1:1:0:41.3:113:1:0:0.2 +17 3568508 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50689;SOR=Inf;LSEQ=CCGCCATCTTCCAGTAATTC;RSEQ=CCAAAATGACGAACACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:42,43:85,0:0:2,0:27.8:1:31:1:1:0:43.3:41.5:1:0:0.2 0/1:112:2:1,1:60,50:110,2:0.0179:2,2:24.5:1:27.5:1:1:1.19803:52:4:0.0179:0:1 +17 3568607 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24985;SOR=Inf;LSEQ=TTCCTTTGGCCACATATATG;RSEQ=GAATCTATAAGAAAGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:28,18:46,0:0:2,0:22.2:1:31.3:1:1:0:34.5:92:1:0:0.1 0/1:56:3:3,0:36,17:53,3:0.0536:2,0:24.7:1:29.7:1:0.54556:0:32:6:0.0545:0:1 +17 3958105 . T G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00859;SOR=0.10197;LSEQ=AGGGGCAAGCCTGGACTCAG;RSEQ=GAGACTGACCATGACCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:13:13,0:4,0:4,13:0.7647:0,1:20.9:1:32.6:1:1:0:60:26:0.7647:0:1.5 0/1:13:3:3,0:10,0:10,3:0.2308:0,0:18.7:1:29.7:1:1:0:60:6:0.2308:0:1.3 +17 3958194 . G A 198 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18238;LSEQ=GGCGGGATGGTGAAAGGTGC;RSEQ=TAGATTTGAGGTGTTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:139:89:85,4:47,3:50,89:0.6403:2,1:22:1:30.7:1:0.70198:1.35:60:43.5:0.635:0:1.1 0/1:164:40:39,1:113,11:124,40:0.2439:2,1:26.2:1:29.7:1:0.29666:3.77:60:39:0.2422:0:1.3 +17 3958212 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1895;SOR=0;LSEQ=GCGTAGATTTGAGGTGTTGA;RSEQ=GCAGAAGTGGGAAACCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:161,31:192,2:0.0103:2,2:18:1:29.5:1:0.3034:5.12774:60:4:0.0105:0:1.5 0/0:251:0:0,0:194,57:251,0:0:2,0:23.6:1:30.9:1:1:0:60:40.833:1:0:0.4 +17 3958282 . G T 190 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAAGAAAGTTTCTGGCTT;RSEQ=GGTACGTGGTTGGACGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:282,219:501,0:0:2,0:25.8:1:31.6:1:1:0:60:49.1:1:0:0.5 0/1:712:99:57,42:325,287:612,99:0.139:2,2:23.6:1:28.7:1:0.44761:1.20:60:32:0.1364:0:1.7 +17 3958341 . C T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26036;LSEQ=GAAACACTGCAAAAGGAGTA;RSEQ=TGTCCCTGGCACTTACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:472:300:127,173:75,96:171,300:0.6356:2,2:24.2:1:30.6:1:0.77197:1.06408:60:299:0.6389:0:1.1 0/1:673:210:96,114:209,252:461,210:0.312:2,2:24.2:1:29.5:1:0.93357:1.02:60:104:0.3123:0:1.3 +17 4540268 . G C 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=0;LSEQ=CACTGCAAGGCCTTCGAATA;RSEQ=AGACTTGGCGCATTTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:13:7,6:84,80:164,13:0.073:2,2:27.8:1:32.8:1:1:1.11:51.2:26:0.0743:0:2 0/0:195:0:0,0:93,102:195,0:0:2,0:27.1:1:30.4:1:1:0:45:31.5:1:0:0.5 +17 4540277 . C T 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31952;SOR=1.26337;LSEQ=GCCTTCGAATAGAGACTTGG;RSEQ=GCATTTCCTCCTTTCGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:53:25,28:70,64:134,53:0.2834:2,2:28.6:1:30.3:1:0.62669:1.22366:47.2:52:0.2873:0:1.3 0/1:195:65:32,33:61,69:130,65:0.3333:2,2:28.2:1:28.9:1:0.76373:1.10:47.7:64:0.3386:0:1.2 +17 4540306 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23798;SOR=Inf;LSEQ=TCCTTTCGCGTCTCCCAGGT;RSEQ=CCTTAGCCCAGTGCCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:86,113:199,0:0:2,0:26.6:1:32.2:1:1:0:47.5:48.75:0.9949:0:0.5 0/1:191:2:1,1:83,106:189,2:0.0105:2,2:13.5:1:27:1:1:1.28:60:4:0.0105:0:1.5 +17 4540313 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49865;SOR=Inf;LSEQ=GCGTCTCCCAGGTGCCTTAG;RSEQ=CCAGTGCCTTTGCAGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:79,107:186,0:0:2,0:27.4:1:32.2:1:1:0:48.7:372:1:0:0.5 0/1:186:2:1,1:78,106:184,2:0.0108:2,2:28:1:30:1:1:1.36:46.5:4:0.0111:0:3 +17 4540322 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23663;SOR=Inf;LSEQ=AGGTGCCTTAGCCCAGTGCC;RSEQ=TTGCAGATGGTGCTCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:73,107:180,0:0:2,0:26.3:1:30.8:1:1:0:50.5:59:1:0:0.4 0/1:171:2:1,1:69,100:169,2:0.0117:2,2:30:1:29.5:1:1:1.45:46:4:0.012:0:2 +17 4540328 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22188;SOR=Inf;LSEQ=CTTAGCCCAGTGCCTTTGCA;RSEQ=ATGGTGCTCAGTAAATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:67,102:169,0:0:2,0:26.3:1:32.6:1:1:0:52.1:83.5:1:0:0.4 0/1:151:2:1,1:59,90:149,2:0.0132:2,2:6.5:1:28:1:1:1.52:29:4:0.0135:0:1 +17 4540355 . G A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00197;SOR=Inf;LSEQ=CTCAGTAAATTTTGATAAGG;RSEQ=GCTGAGCTTTCTCAAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:38,78:116,0:0:2,0:24.2:1:30.6:1:1:0:58.3:37.667:1:0:0.3 0/1:102:8:2,6:33,61:94,8:0.0784:2,2:23.8:1:28.5:1:0.71176:1.61581:58.8:16:0.0825:0:1.3 +17 5828753 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22435;SOR=Inf;LSEQ=TCCCTTCTCCCTAAGCCCAC;RSEQ=TCATGACCACAGAGTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:32,13:45,0:0:2,0:22:1:32.1:1:1:0:60:90:1:0:0.1 0/1:41:2:1,1:25,14:39,2:0.0488:2,2:21:1:28:1:1:1.75924:60:4:0.0488:0:1 +17 5828945 . G T 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12727;SOR=11.0937;LSEQ=AAATAGTACTGAGTCCCTTT;RSEQ=TACCTTTACCCAGCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:0,8:8,1:0.1111:0,0:38:0:28:0:1:0:60:2:0.1111:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:8:1:28.5:1:1:0:60:4:0.6667:0:1 +17 6563456 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50161;SOR=0;LSEQ=AGCCCCTTATCGAAATGCAC;RSEQ=AAGCACCATCTTCAAAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:77,46:123,2:0.016:2,2:9.5:1:30:1:1:1.66666:33:4:0.0161:0:1.5 0/0:105:0:0,0:72,33:105,0:0:2,0:23:1:29.3:1:1:0:55.1:51.5:1:0:0.1 +17 6563475 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4987;SOR=0;LSEQ=CTAAGCACCATCTTCAAAGG;RSEQ=GCTGGGCTAAGGCACCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:88,64:152,2:0.0128:2,2:48:1:31.5:1:1:1.37209:55:4:0.0128:0:1 0/0:148:0:0,0:95,53:148,0:0:2,0:25.6:1:30.5:1:1:0:46.6:73:1:0:0.2 +17 6563487 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23832;SOR=0;LSEQ=TTCAAAGGCGCTGGGCTAAG;RSEQ=CACCAGGGAGACGCGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:99,75:174,2:0.0114:2,2:11:1:29.5:1:1:1.31788:51:4:0.0115:0:1 0/0:184:0:0,0:112,72:184,0:0:2,0:25.7:1:30.6:1:1:0:44.8:60.333:1:0:0.2 +17 6563489 . A C 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24904;SOR=Inf;LSEQ=CAAAGGCGCTGGGCTAAGGC;RSEQ=CCAGGGAGACGCGAAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:100,79:179,0:0:2,0:29.3:1:30.5:1:1:0:45:358:1:0:0.1 0/1:193:3:1,2:113,77:190,3:0.0155:2,2:26:1:26.3:1:0.56864:2.91862:33.3:2:0.0105:0:1 +17 6563566 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50489;SOR=Inf;LSEQ=GTAGCTGGAGAGACACATAG;RSEQ=GCTAGTCTGCAGAAGCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:42,76:118,0:0:2,0:23.9:1:30.8:1:1:0:50.6:117:1:0:0.1 0/1:149:2:1,1:51,96:147,2:0.0134:2,2:9:0:31:0:1:1.87:28:4:0.0137:0:1.5 +17 6846966 . GA G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.06479;SOR=0.39134;LSEQ=AAACTGAGTGAGTGTGGGAA;RSEQ=AAAAAAAAAAGATTCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:14:11,3:99,32:131,14:0.0959:2,2:25.2:1:31.9:1:1:1.18:59.6:13:0.0909:0.0205:0.4 0/1:151:6:5,1:109,35:144,6:0.0397:2,2:30.2:1:31.2:1:1:1.60:60:12:0.0403:0:0 +17 6846975 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=GAGTGTGGGAAGAAAAAAAA;RSEQ=AAGATTCCTTTGAGAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:122,46:168,0:0:2,0:24.5:1:30.5:1:1:0:59.9:83:1:0:0.2 0/1:176:2:1,1:130,44:174,2:0.0114:2,2:42.5:1:30.5:1:0.44708:2.93259:60:4:0.0115:0:1 +17 6846995 . C T 47 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34195;SOR=0.28742;LSEQ=AAAGATTCCTTTGAGAGATG;RSEQ=GCCTTTTGAGCATAATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:2,1:147,86:233,3:0.0127:2,2:6.7:1:29.7:1:1:1.17:60:6:0.0133:0:1.7 0/0:273:1:0,1:180,92:272,1:0.0037:2,0:1:0:24:0:0.34066:0:60:2:0.0038:0:2 +17 6847073 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-04;SOR=1.81421;LSEQ=TAATTCATTAATGGAGCAGC;RSEQ=GCATTACTCTAAACAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:105:46,59:94,129:223,105:0.3191:2,2:25.8:1:30.1:1:0.8114:1.07:60:25.25:0.3127:0:1.1 0/1:435:200:90,110:102,133:235,200:0.4598:2,2:27:1:29.1:1:0.77169:1.07:60:49:0.4548:0:1.1 +17 7216540 . G A 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCATACTCACTGAGTCGGA;RSEQ=AAGCCAGTCTGCTGGTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1013:0:0,0:526,486:1012,0:0:2,0:24.4:1:32.5:1:1:0:58.7:55.222:1:0:0.2 0/1:1487:65:36,29:746,674:1420,65:0.0437:2,2:27:1:28.9:1:0.70402:1.12:58.6:64:0.0436:0:1.1 +17 7217342 . G T 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCTTCATGATGCTGAAAT;RSEQ=GGAGGCTGTGACCTCCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:959:0:0,0:461,497:958,0:0:2,0:24.8:1:31.9:1:1:0:59.3:135.857:1:0:0.1 0/1:1119:66:30,36:510,542:1052,66:0.059:2,2:22.5:1:29.6:1:0.70372:1.12903:58.3:132:0.0597:0:1.1 +17 7217463 . T C 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.88856;LSEQ=TGCTGGTATGCAGCTGATGT;RSEQ=AGGGTGGTCAGGTCACTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:998:351:161,190:297,349:646,351:0.3517:2,2:26.4:1:32.1:1:1:1.00428:55:49.143:0.3514:0:1.2 1/0:1223:619:284,335:304,299:603,619:0.5061:2,2:27.1:1:30.7:1:0.12213:1.19912:54.4:67.778:0.5058:0:1.1 +17 7217497 . AG A 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTGGAGTGAAAGGAAGAC;RSEQ=GTCAAAGTCAAGGACAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:813:0:0,0:338,475:813,0:0:2,0:25:1:31.8:1:1:0:58.9:44.167:1:0:0.4 0/1:1035:34:16,18:465,532:997,34:0.0329:2,2:25.7:1:31.3:1:1:1.02:52.7:68:0.0331:0.0029:0.9 +17 7217944 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=0.52899;LSEQ=ATCAGGCAGAATGAAGAAGA;RSEQ=GCAGGGTAGTGAAAACAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:102:32,70:75,266:341,102:0.2302:2,2:23.9:1:31.2:1:0.06447:1.62:60:101:0.2306:0:1.1 0/1:520:71:21,50:114,335:449,71:0.1365:2,2:22.1:1:30.3:1:0.46782:1.23:59.7:142:0.1384:0:1.1 +17 7218443 . G A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24906;SOR=Inf;LSEQ=AGACCTCAGACGGGGCCTGC;RSEQ=GGGAGGCGGGCGCTCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:15,149:164,0:0:2,0:21.9:1:31.9:1:1:0:60:81:0.9939:0:0.1 0/1:179:3:1,2:26,150:176,3:0.0168:2,2:10:1:23.7:1:0.38953:2.86:60:2:0.0112:0:1 +17 7218670 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCTTCTCTGCGCTTTCT;RSEQ=AGCGGCTCCGACGCGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:28:1:1:0:60:4:1:0:1.5 +17 7481682 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51928;SOR=Inf;LSEQ=TCGGTCGAGGTGGACGGTTT;RSEQ=GCCGTAAAGGTGTGGCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:24,5:29,0:0:2,0:31.7:1:31.7:1:1:0:42.6:28:1:0:0.2 0/1:46:2:1,1:28,16:44,2:0.0435:2,2:36:1:29.5:1:1:1.72772:46:4:0.0435:0:1 +17 7492708 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23554;SOR=0;LSEQ=TGGCCTCCTCCACGAAGGGC;RSEQ=GCTTCTCGTCCTCGTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:62,44:106,2:0.0185:2,2:22:1:33.5:1:1:1.40451:60:4:0.0185:0:1 0/0:114:0:0,0:66,48:114,0:0:2,0:27.3:1:30.2:1:1:0:59.7:56:1:0:0.3 +17 7492728 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25015;SOR=Inf;LSEQ=CGCTTCTCGTCCTCGTCCAG;RSEQ=AGCTTCCACTGCGCGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:66,48:114,0:0:2,0:26.2:1:32.3:1:1:0:60:228:1:0:0.1 0/1:130:3:1,2:70,57:127,3:0.0231:2,2:25.3:1:26:1:0.59019:2.43955:60:6:0.0231:0:1 +17 7492804 . C T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49898;SOR=Inf;LSEQ=TCTGCTGCGCCATCTGGCGG;RSEQ=GCTGAGCGGAGCTCCACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:40,62:102,0:0:2,0:29.8:1:30.6:1:1:0:60:101:1:0:0.1 0/1:113:2:1,1:48,62:110,2:0.0177:2,2:7.5:1:28:1:1:1.29:60:4:0.0179:0:1.5 +17 7569510 . C A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05664;SOR=0;LSEQ=GATTCTCCTGCCTCAGCCTC;RSEQ=CGAGTAGCTGGGATTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:146,58:204,3:0.0144:2,2:11.7:1:21.3:1:0.20207:4.98914:59.3:2:0.0097:0:2.3 0/0:332:0:0,0:234,97:331,0:0:2,0:22.7:1:29.9:1:1:0:51:65.2:0.9969:0:0.1 +17 7569527 . C T 39 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16133;SOR=0.20707;LSEQ=CTCCCGAGTAGCTGGGATTA;RSEQ=AGGTGTGATCCACCGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:173,119:292,3:0.0102:2,2:8.7:1:24.7:1:0.57:2.89701:60:6:0.0104:0:1 0/0:472:1:0,1:287,184:471,1:0.0021:2,0:1:0:25:0:0.39195:0:60:2:0.0021:0:1 +17 7569534 . G T 44 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06431;SOR=0.14446;LSEQ=GTAGCTGGGATTACAGGTGT;RSEQ=ATCCACCGTGCCTGGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:4:0,4:177,128:305,4:0.0129:2,0:17:1:22:1:0.03243:0:57.3:3:0.01:0:2 0/0:530:1:0,1:316,213:529,1:0.0019:2,0:1:0:23:0:0.40377:0:60:2:0.0019:0:2 +17 7569698 . A C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.31172;LSEQ=TTTGAGTGGGAGGGTAGGGA;RSEQ=CATGTCTGCCATAGGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:76:0,76:0,38:38,76:0.6667:1,1:23.7:1:31.4:1:1:0:60:75:0.6637:0:1.1 0/1:128:49:1,48:1,77:78,49:0.3828:1,1:22.4:1:31:1:1:1.60:60:48:0.381:0:1.1 +17 7572869 . C T 54 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70518;SOR=1.78828;LSEQ=AGACCCAAAACCCAAAATGG;RSEQ=AGGGGAGGGAGAGATGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:2:0,2:191,51:242,2:0.0082:2,0:1:0:25:1:0.04648:0:60:4:0.0085:0:1 0/1:343:5:1,4:242,96:338,5:0.0146:2,2:8.8:1:23.4:1:0.02676:10.00876:60:10:0.0149:0:1.2 +17 7572873 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14306;SOR=Inf;LSEQ=CCAAAACCCAAAATGGCAGG;RSEQ=GAGGGAGAGATGGGGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:216,63:279,0:0:2,0:22.8:1:30.8:1:1:0:60:38.857:1:0:0.2 0/1:385:4:1,3:269,112:381,4:0.0104:2,2:16.3:1:25.3:1:0.08164:7.1641:60:8:0.0106:0:1 +17 7573085 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52495;SOR=Inf;LSEQ=GCCCCTTTTCCCTGACCAAT;RSEQ=CTTTGAAGGGCCTAAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:4,113:117,0:0:1,0:23.5:1:31.9:1:1:0:59.7:22.4:1:0:0.1 0/1:187:2:1,1:20,165:185,2:0.0107:2,2:25:1:27.5:1:0.21252:8.07:60:4:0.0108:0:1 +17 7573086 . C T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14396;SOR=0;LSEQ=CCCCTTTTCCCTGACCAATG;RSEQ=TTTGAAGGGCCTAAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:3,108:111,2:0.0177:1,2:5:1:30:1:0.06985:31.32:60:4:0.0182:0:1 0/0:184:0:0,0:21,163:184,0:0:2,0:21.2:1:31.5:1:1:0:60:91:1:0:0.1 +17 7573135 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49756;SOR=Inf;LSEQ=GAATTCAAATCAAGATGGTG;RSEQ=CCACACCCCATGCAAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:1,59:60,0:0:1,0:24.9:1:31.2:1:1:0:60:19:1:0:0.1 0/1:67:2:0,2:2,63:65,2:0.0299:1,0:23:1:28:1:1:0:60:4:0.0299:0:1 +17 7573889 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17414;SOR=0;LSEQ=GGCTTTCCAACCTAGGAAGG;RSEQ=AGGGGAGTAGGGCCAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:158,31:189,2:0.0105:2,2:32:1:27.5:1:0.30774:5.0325:60:4:0.0106:0:1 0/0:266:0:0,0:206,60:266,0:0:2,0:23.2:1:31.1:1:1:0:60:43.333:1:0:0.2 +17 7573894 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26938;SOR=Inf;LSEQ=TCCAACCTAGGAAGGCAGGG;RSEQ=AGTAGGGCCAGGAAGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:171,39:210,0:0:2,0:23.1:1:31.3:1:1:0:60:69:1:0:0.1 0/1:294:3:1,2:227,64:291,3:0.0102:2,2:9:1:27:1:0.12757:7.03148:60:6:0.0105:0:1.3 +17 7573897 . T A 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=AACCTAGGAAGGCAGGGGAG;RSEQ=AGGGCCAGGAAGGGGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:182,47:229,0:0:2,0:22.4:1:29.6:1:1:0:60:113.5:1:0:0.1 0/1:317:13:11,2:233,71:304,13:0.041:2,2:22.6:1:27.9:1:0.73966:1.67:60:12:0.0382:0:1.1 +17 7574074 . G A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08772;SOR=Inf;LSEQ=GAGAAGTAAGTATATACACA;RSEQ=TACCTGAGTTAAAAGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:100,212:312,0:0:2,0:24.6:1:32.1:1:1:0:60:51:1:0:0.2 0/1:503:6:4,2:155,342:497,6:0.0119:2,2:21.7:1:27.8:1:0.08274:4.40:60:12:0.012:0:1 +17 7576276 . T A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATCTCTACTAAAAAAAAAAA;RSEQ=AAATAAATAACAAAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:36:1:32.5:1:1:0:60:4:1:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:12:0:31:0:1:0:47.5:4:0.6667:0:3.5 +17 7576348 . C T 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01923;SOR=Inf;LSEQ=AGCTACTCAGTGGGCTGAGG;RSEQ=AGGAGAATCGCTTGAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:9,0:0:0,0:22.3:1:33:1:1:0:41.1:18:1:0:0.2 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:12.5:1:27.3:1:1:0:37.8:8:0.5714:0:2.3 +17 7576474 . T C 28 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.21804;LSEQ=AAAAAAAAAGCAGGCTAGGC;RSEQ=AAGCTATGATGTTCCTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:1:1,0:85,18:103,1:0.0096:2,0:14:0:15:0:1:0:60:0:0:0:1 0/1:171:2:1,1:140,28:168,2:0.0117:2,2:5:0:28.5:1:0.31291:4.93067:60:4:0.0121:0:2 +17 7576477 . G A 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52807;SOR=Inf;LSEQ=AAAAAAGCAGGCTAGGCTAA;RSEQ=CTATGATGTTCCTTAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:95,20:115,0:0:2,0:15.5:1:31.7:1:1:0:59.4:10.5:1:0:0.4 0/1:189:2:1,1:156,31:187,2:0.0106:2,2:8:0:26.5:1:0.31071:4.96899:60:4:0.0112:0:2 +17 7576478 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52992;SOR=Inf;LSEQ=AAAAAGCAGGCTAGGCTAAG;RSEQ=TATGATGTTCCTTAGATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:95,20:115,0:0:2,0:16.5:1:31.4:1:1:0:59.4:10.5:1:0:0.4 0/1:192:2:1,1:157,33:190,2:0.0104:2,2:16:1:25:0:0.32357:4.70203:53.5:4:0.0111:0:1.5 +17 7576501 . G A 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00099;SOR=Inf;LSEQ=TGATGTTCCTTAGATTAGGT;RSEQ=TATTAAATCCATTTTCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:142,45:187,0:0:2,0:26.1:1:31.4:1:1:0:59.7:12.357:1:0:0.2 0/1:344:16:13,3:234,91:325,16:0.0465:2,2:21.4:1:26.9:1:0.57111:1.68:58.8:32:0.0486:0:1.3 +17 7576841 . A G 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TCCACTTGATAAGAGGTCCC;RSEQ=AGACTTAGTACCTGAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:213,153:366,0:0:2,0:25.3:1:30.8:1:1:0:60:365:1:0:0.1 0/1:598:22:11,11:322,252:574,22:0.0368:2,2:23.1:1:28.8:1:0.66337:1.27724:60:21:0.0354:0:1.2 +17 7577407 . A C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03318;LSEQ=GTGGATGGGTAGTAGTATGG;RSEQ=AGAAATCGGTAAGAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:121:70:56,14:47,4:51,70:0.5785:2,2:22.3:1:33.1:1:0.07431:2.91375:60:140:0.5983:0:2 0/1:163:7:6,1:137,18:155,7:0.0429:2,2:22.7:1:31.3:1:0.58975:1.2665:60:14:0.0449:0:2 +17 7577427 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03018;LSEQ=AAGAAATCGGTAAGAGGTGG;RSEQ=CCCAGGGGTCAGAGGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:93:77,16:54,7:61,93:0.6039:2,2:24:1:30.3:1:0.36527:1.59825:60:92:0.6053:0:1.8 0/1:230:10:8,2:179,38:217,10:0.0435:2,2:25.2:1:28.3:1:0.69041:1.1767:60:20:0.0452:0:1.7 +17 7577709 . C T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1039;SOR=0;LSEQ=TTTTTTGAGATGGAATCTCG;RSEQ=TCTGTCGCCCAGGCTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:0,4:0,14:14,4:0.2222:1,0:28.5:1:31.3:1:1:0:33.8:8:0.2222:0:2.8 0/0:17:0:0,0:0,17:17,0:0:1,0:13.9:1:31.4:1:1:0:46.1:34:1:0:1.6 +17 7578115 . T C 254 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02627;LSEQ=AAGCCCCCCTACTGCTCACC;RSEQ=GGAGGGCCACTGACAACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:360:357:253,104:0,3:3,357:0.9917:0,2:24.3:1:30.5:1:0.02574:0:59.9:118:0.9916:0:1.1 1/0:511:387:277,110:84,40:124,387:0.7573:2,2:23.8:1:29.6:1:0.42888:1.20:60:54.286:0.757:0:1.1 +17 7578117 . G T 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16577;SOR=0.17409;LSEQ=GCCCCCCTACTGCTCACCTG;RSEQ=AGGGCCACTGACAACCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:4:1,3:262,112:374,4:0.0106:2,2:19.8:1:26.8:1:0.08582:6.97788:60:8:0.0109:0:1.5 0/0:539:1:0,1:377,161:538,1:0.0019:2,0:1:0:21:0:0.30056:0:60:2:0.0019:0:1 +17 7578210 . T C 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGGCACCACCACACTATG;RSEQ=CGAAAAGTGTTTCTGTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:723:0:0,0:358,364:722,0:0:2,0:25.1:1:30.1:1:1:0:60:89.25:0.9986:0:0.2 0/1:1197:84:38,46:537,573:1110,84:0.0702:2,2:24.6:1:30.6:1:0.65084:1.13435:60:41:0.069:0:1.3 +17 7578449 . C T 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0454;SOR=Inf;LSEQ=CTGTGACTGCTTGTAGATGG;RSEQ=CATGGCGCGGACGCGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:0:0,0:200,194:394,0:0:2,0:23.8:1:31.7:1:1:0:59.9:55.286:1:0:0.4 0/1:562:6:3,3:307,249:556,6:0.0107:2,2:16.2:1:28.3:1:1:1.23246:60:5:0.0091:0:1.2 +17 7578461 . C A 221 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GTAGATGGCCATGGCGCGGA;RSEQ=GCGGGTGCCGGGCGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:417:145:79,66:142,130:272,145:0.3477:2,2:20.9:1:30.9:1:0.68119:1.10:59.9:35.25:0.3447:0:1.2 0/0:626:0:0,0:343,281:624,0:0:2,0:23.5:1:30:1:1:0:59.9:61.4:0.9968:0:0.2 +17 7578640 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.50155;SOR=Inf;LSEQ=AGACGGCAGCAAAGAAACAA;RSEQ=CATGCGTAAGCACCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:3,66:69,0:0:1,0:28.2:1:29.9:1:1:0:60:138:1:0:1.2 0/1:84:2:0,2:1,81:82,2:0.0238:1,0:9:1:32:1:1:0:60:4:0.0247:0:1 +17 7578645 . C T 178 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=GCAGCAAAGAAACAAACATG;RSEQ=GTAAGCACCTCCTGCAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:3,62:0,0:0,65:1:0,1:28.4:1:29.6:1:1:0:60:15.25:1:0:1.2 1/0:70:55:1,54:0,15:15,55:0.7857:1,1:23.1:1:29.5:1:1:0:59.2:26.5:0.7794:0:1.3 +17 7578679 . A G 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.32171;SOR=3.84627;LSEQ=GCAACCCACTAGCGAGCTAG;RSEQ=GAGAGTTGGCGTCTACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:1:0,1:1,42:43,1:0.0227:1,0:18:0:15:0:1:0:24:0:0:0:6 0/1:36:3:0,3:0,33:33,3:0.0833:1,0:18:1:30:1:1:0:54.3:6:0.0968:0:3.3 +17 7578711 . CTTT C 64 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=18.000;MSILEN=1;SSF=0.44302;SOR=2.03983;LSEQ=TCTACACCTCAGGAGCTTTT;RSEQ=TTTTTTTTTTTTTTTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:0,3:0,8:8,3:0.1667:0,0:30.3:1:29.3:1:1:0:47.7:6:0.1765:0:2 0/1:17:5:0,5:0,10:10,5:0.2941:0,0:24.4:1:27.7:1:1:0:48.6:4:0.25:0.0588:1.8 +17 7578837 . A G 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCCACCTCAGCCTCCT;RSEQ=AGTGGCTGGGACTATAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:10.5:1:30.8:1:1:0:54.3:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 7579219 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=TGACAGGAAGCCAAAGGGTG;RSEQ=AGAGGAATCCCAAAGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:70,4:74,2:0.0263:2,2:21:1:31:1:0.12807:15.75751:60:4:0.0263:0:1 0/0:67:0:0,0:63,4:67,0:0:2,0:26.8:1:29.1:1:1:0:60:66:1:0:0 +17 7579258 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50359;SOR=Inf;LSEQ=CAAACAAAAGAAATGCAGGG;RSEQ=GATACGGCCAGGCATTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:129,23:152,0:0:2,0:23.5:1:31.4:1:1:0:60:151:1:0:0.1 0/1:186:2:1,1:148,35:183,2:0.0108:2,2:27:1:30.5:1:0.35217:4.18349:60:4:0.0109:0:1 +17 7579259 . G C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50448;SOR=Inf;LSEQ=AAACAAAAGAAATGCAGGGG;RSEQ=ATACGGCCAGGCATTGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:131,25:156,0:0:2,0:23.4:1:31.6:1:1:0:60:155:1:0:0.1 0/1:194:2:1,1:151,41:192,2:0.0103:2,2:5.5:1:29:1:0.387:3.65121:60:4:0.0107:0:1.5 +17 7579472 . G C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=2.28637;LSEQ=CTGCTGGTGCAGGGGCCACG;RSEQ=GGGGAGCAGCCTCTGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:156:83,73:123,133:256,156:0.3786:2,2:26.3:1:30.6:1:0.36067:1.23:60:51:0.3787:0:1.1 1/0:601:350:172,178:135,115:250,350:0.5824:2,2:24.5:1:29.6:1:0.24731:1.21446:60:37.889:0.577:0:1.2 +17 7579579 . C T 131 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=5e-04;SOR=8.23065;LSEQ=AAATCATCCATTGCTTGGGA;RSEQ=GGCAAGGGGGACTGTAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:2:0,2:216,182:398,2:0.005:2,0:1:0:26:0:0.21098:0:60:4:0.0051:0:1 0/1:557:22:9,13:279,255:534,22:0.0395:2,2:20.3:1:29.6:1:0.38477:1.57908:60:44:0.0401:0:1.1 +17 7579619 . G T 186 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.15014;LSEQ=GGGTGAAAAGAGCAGTCAGA;RSEQ=GACCAGGTCCTCAGCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:3:0,3:246,168:414,3:0.0072:2,0:1:0:25.7:1:0.06824:0:60:6:0.0074:0:1 0/1:592:82:43,39:300,210:510,82:0.1385:2,2:18.4:1:29.4:1:0.2809:1.29509:59:81:0.1387:0:1.1 +17 7579643 . CCCCCAGCCCTCCAGGT C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.34589;LSEQ=CAGGTCCTCAGCCCCCCAGC;RSEQ=CCCCAGCCCTCCAGGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:392:300:157,143:63,28:91,300:0.7653:2,2:29.5:1:31.1:1:0.00538:2.04571:59.4:59:0.7702:0.125:0.2 1/0:621:329:182,147:165,123:288,329:0.5298:2,2:28:1:30.5:1:0.62663:1.08335:59.5:328:0.5395:0.1079:0.3 +17 7579801 . G C 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.51338;LSEQ=TAGGGGGCTGGGGTTGGGGT;RSEQ=GGGGTGGTGGGCCTGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:232:114,118:183,203:386,232:0.3736:2,2:23.5:1:30.1:1:0.6787:1.07:59.9:32.143:0.3689:0:1.2 1/0:785:471:235,236:150,162:312,471:0.6:2,2:23.2:1:29.6:1:0.66143:1.08:60:66.286:0.5995:0:1.2 +17 7579960 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27692;SOR=Inf;LSEQ=GCTGCAAGAGGAAAAGTGGG;RSEQ=ATCCAGCATGAGACACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:58,145:203,0:0:2,0:23.6:1:31.6:1:1:0:60:39.6:1:0:0.1 0/1:301:3:1,2:88,209:297,3:0.01:2,2:21:1:27:1:1:1.19:60:6:0.0102:0:1 +17 7580002 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2291;SOR=Inf;LSEQ=ACCCTGGGTCACCTGGGCCT;RSEQ=CAGAGAAGGAACCCCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:18,98:116,0:0:2,0:24.2:1:31.8:1:1:0:60:37.667:1:0:0.1 0/1:107:2:1,1:7,97:104,2:0.0187:2,2:15.5:1:27:1:0.14591:13.03:60:4:0.019:0:1 +17 7580052 . C T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TGCCAGTGTCTGAGACAGCT;RSEQ=GGCTTCCTGTGGAGCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:2,48:50,0:0:1,0:26.8:1:30.1:1:1:0:60:49:1:0:0.1 0/1:46:12:0,12:1,33:34,12:0.2609:1,0:24.9:1:30.2:1:1:0:60:24:0.2609:0:1.1 +17 7580500 . C T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01571;LSEQ=CTTACTTCAGGTGATCGGCC;RSEQ=GCCTCAGCCTCCTAAAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:64:64,0:30,0:30,64:0.6737:1,1:27.1:1:32.9:1:1:0:59.1:128:0.6809:0:1 0/1:98:3:3,0:94,1:95,3:0.0306:1,0:18.7:1:30.3:1:1:0:53:6:0.0319:0:1.3 +17 7612635 . G A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11102;SOR=0;LSEQ=CATGTGTTGGCGGAGACGGC;RSEQ=GGCCAAGCCTTCGGAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:27:0:33:1:1:1.13389:60:4:0.1176:0:1.5 0/0:33:0:0,0:17,16:33,0:0:2,0:30.1:1:29.5:1:1:0:60:66:1:0:0.2 +17 7858597 . G GA 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.08991;LSEQ=TCTCAAGAAAAAAAAAAAAA;RSEQ=AAAAAAAAAGACAATATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:2,0:37,6:43,2:0.04:2,0:13.5:1:29.5:1:1:0:40.5:4:0.0513:0.02:2.5 0/1:46:2:2,0:40,4:44,2:0.0435:2,0:14.5:1:30:0:1:0:36:4:0.0556:0:0.5 +17 7858729 . CAAGTT C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00116;SOR=0.40798;LSEQ=GCTGTTGGCATTGTTGTAAA;RSEQ=AAGGGCAAGATTCTTGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:52:16,36:17,37:54,52:0.4906:2,2:23.3:1:31.7:1:1:1.03347:41.6:51:0.4857:0.066:0.4 0/1:128:36:7,29:29,63:92,36:0.2813:2,2:24.6:1:31.1:1:0.19613:1.89802:43.9:72:0.2813:0.0469:0.2 +17 7858774 . G A 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03422;SOR=0.37142;LSEQ=AGAGAATTAATGTGCGTATT;RSEQ=GGCACGTTAAGCACCTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:22:1,21:4,30:34,22:0.3929:2,1:25.9:1:32.9:1:0.63812:2.75541:48.9:44:0.3929:0:1 0/1:52:10:2,8:2,39:41,10:0.1923:1,2:22.9:1:30:1:0.16819:4.67:48:20:0.2041:0:1.1 +17 7858901 . A G 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54545;SOR=3.51553;LSEQ=AATGCCAGACTGCTCCACCC;RSEQ=GAGGGGTAAACACTGGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:18:1:33:1:1:0:60:6:0.5:0:2 1/1:5:4:0,4:0,1:1,4:0.8:0,0:19.5:1:30.3:1:1:0:60:8:0.8:0:1.5 +17 7858924 . C T 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGGTAAACACTGGTAAAGA;RSEQ=GCTCAGCCTCATTAGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:18.5:1:32.5:1:1:0:60:4:0.6667:0:2.5 1/1:1:1:0,1:0,0:0,1:1:0,0:46:0:27:0:1:0:60:2:1:0:3 +17 7948175 . C T 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=TTTGAGCACTGGCAGGAGGA;RSEQ=GCCTTCTTCGCCTCCCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:4,3:0.4286:2,2:20.3:1:30.3:1:1:1.81007:60:6:0.4286:0:1.3 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:7.5:1:29:1:1:0:48:4:0.6667:0:1.5 +17 7948942 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49673;SOR=Inf;LSEQ=ACCTGCTGCACTCACATCTG;RSEQ=TGCCTGAGGTCTTCACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:7,0:0:2,0:23.6:1:33.4:1:1:0:60:14:1:0:0.7 0/1:11:2:1,1:0,9:9,2:0.1818:0,2:22:1:28:1:0.18182:0:60:4:0.1818:0:1 +17 7975986 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49996;SOR=0;LSEQ=TTTTGTTTTTTTGTTTGTTT;RSEQ=GTGTTTTGGTCTCTGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:184,9:193,2:0.0103:1,2:25:1:29:1:0.10019:19.45504:60:4:0.0103:0:1 0/0:176:0:0,0:162,14:176,0:0:2,0:24.3:1:31.8:1:1:0:60:43:1:0:0.1 +17 7976291 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18308;SOR=Inf;LSEQ=GCGGGCAGAGAGCTCGACAG;RSEQ=TGGGACCAGGGCCGGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:66,170:236,0:0:2,0:22.8:1:32.5:1:1:0:59.9:38.333:1:0:0.1 0/1:177:2:1,1:51,123:174,2:0.0113:2,2:12.5:1:27.5:1:0.50481:2.40:60:4:0.0115:0:1 +17 7976310 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16871;SOR=Inf;LSEQ=GCTGGGACCAGGGCCGGCCA;RSEQ=CACCCCCTCCTCCTGCCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:43,126:169,0:0:2,0:25.6:1:32.6:1:1:0:59.8:168:0.9941:0:0.2 0/1:119:2:1,1:34,83:117,2:0.0168:2,2:42.5:1:27:0:0.50349:2.42:60:4:0.0171:0:1 +17 7976329 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51831;SOR=0;LSEQ=AGCACCCCCTCCTCCTGCCG;RSEQ=TGGCCCTGGCCCCTCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:40,100:140,2:0.014:2,2:34.5:1:31.5:1:0.49555:2.48:60:4:0.0144:0:1 0/0:95:0:0,0:30,65:95,0:0:2,0:24:1:31.6:1:1:0:59.3:46.5:1:0:0.2 +17 7976694 . C T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09563;SOR=Inf;LSEQ=GTACCTCAGGAGTTTCCTTC;RSEQ=ACCAGGTGCTGACCACCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:26,171:197,0:0:2,0:23.1:1:32.1:1:1:0:60:31.833:1:0:0.2 0/1:167:3:1,2:23,139:162,3:0.018:2,2:19:1:22:1:0.37792:2.99:60:2:0.0123:0:1.7 +17 7976707 . C A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50683;SOR=0;LSEQ=TTCCTTCCACCAGGTGCTGA;RSEQ=CACCCGCCCTCCAGTCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:18,135:153,2:0.0129:2,2:20:1:26:1:0.23083:7.33:60:4:0.0134:0:3 0/0:119:0:0,0:8,111:119,0:0:2,0:23.8:1:30.3:1:1:0:60:38.667:1:0:0.1 +17 7976917 . A T 184 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTTTGAGGTTGGGGCATGG;RSEQ=CGAAATTTAGAAGGTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:87:58,29:145,44:189,87:0.3152:2,2:24:1:28.7:1:0.10561:1.64468:59.9:28:0.3111:0:1.2 0/0:260:0:0,0:192,67:259,0:0:2,0:23.1:1:27.8:1:1:0:60:22.545:1:0:0.1 +17 7977105 . A G 258 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0157;LSEQ=GGGGGAAAAGCCCAGGCGAC;RSEQ=TCAGTCGTGCCCTGGTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:307:96,211:0,1:1,307:0.9903:0,2:25.2:1:31.3:1:1:0:60:152.5:0.9935:0:1.1 1/0:278:171:51,120:39,68:107,171:0.6151:2,2:21.1:1:30.6:1:0.29217:1.34797:60:170:0.6137:0:1.2 +17 7977139 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06991;SOR=Inf;LSEQ=GGTACTGGCTGCCCGGCAGA;RSEQ=GGCGCCACCATGCCCCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:17,160:177,0:0:2,0:23.7:1:31.7:1:1:0:60:354:1:0:0.9 0/1:125:3:2,1:20,102:122,3:0.024:2,2:19.7:1:25.3:1:0.07973:9.91:60:2:0.0163:0:1.7 +17 7977368 . C T 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCCTGGGGATGCCGCTC;RSEQ=GGTCCCAGACCTGGGGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:30:1:30:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 7978751 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.79772;SOR=1.17593;LSEQ=TGAGATGCCACTGCTCCAGG;RSEQ=GCCAGAGAAGAGCCTGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:18:17,1:32,1:33,18:0.3529:1,1:27.8:1:30.5:1:1:1.85775:60:36:0.36:0:1.3 0/1:23:9:9,0:13,1:14,9:0.3913:1,0:19.1:1:26.7:1:1:0:60:8:0.3636:0:1.4 +17 7978819 . T A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03563;SOR=0.53175;LSEQ=TCAGTCTACAATAAAATATG;RSEQ=TCTGATCCAGCCCAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:45:43,2:104,4:108,45:0.2922:1,1:26.4:1:30.1:1:1:1.20772:60:21.5:0.2848:0:1.2 0/1:128:23:21,2:94,11:105,23:0.1797:2,2:18.3:1:29.2:1:1:1.23:60:22:0.1746:0:1.4 +17 7978829 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19949;SOR=Inf;LSEQ=ATAAAATATGTTCTGATCCA;RSEQ=CCCAGGAGGGCCCTAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:192,18:210,0:0:2,0:22:1:33.3:1:1:0:59.9:69:1:0:0.3 0/1:170:2:1,1:147,21:168,2:0.0118:2,2:30:1:28.5:1:0.24274:6.86192:60:4:0.0121:0:1 +17 7978832 . C T 42 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62795;SOR=0.38882;LSEQ=AAATATGTTCTGATCCAGCC;RSEQ=AGGAGGGCCCTAGCAGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:1,2:194,19:213,3:0.0139:2,2:5.7:1:26.7:1:0.02553:19.77822:60:6:0.0141:0:1.7 0/0:184:1:0,1:155,28:183,1:0.0054:2,0:1:0:23:0:0.15761:0:60:2:0.0055:0:1 +17 7979075 . TC T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12885;SOR=0;LSEQ=CAGTTTGGATCCTCCTCCCC;RSEQ=CCACTCCTCAGCCAGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:4:3,1:90,255:345,4:0.0114:2,2:8.5:1:30.5:1:0.05948:8.44:60:8:0.0115:0.0057:0.5 0/0:298:0:0,0:79,219:298,0:0:2,0:22.9:1:30.1:1:1:0:60:48.667:1:0:0.2 +17 7979463 . A G 288 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATCCCAGGTTGTCCACCCT;RSEQ=AGAGCCACCCACTGCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:534:534:341,193:0,0:0,534:1:0,2:25.2:1:31.8:1:1:0:60:88:1:0:1.1 1/0:549:342:220,122:133,74:207,342:0.623:2,2:24.5:1:30.5:1:1:1.00:60:30.091:0.6222:0:1.1 +17 7979468 . C T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01276;SOR=0;LSEQ=CAGGTTGTCCACCCTAAGAG;RSEQ=CACCCACTGCTGTCCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:6:3,3:348,209:557,6:0.0107:2,2:20.3:1:29.2:1:0.67712:1.66343:60:12:0.0108:0:1.7 0/0:599:0:0,0:381,218:599,0:0:2,0:25.1:1:30.8:1:1:0:60:58.9:1:0:0.7 +17 7979721 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51169;SOR=0;LSEQ=TCCCTGGAACCCCTTCAGGT;RSEQ=CTCTAGGATCCCAGTAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:29,169:198,2:0.01:2,2:15.5:1:30.5:1:0.27814:5.75:60:4:0.0103:0:1 0/0:145:0:0,0:15,130:145,0:0:2,0:22.4:1:30.7:1:1:0:60:35.25:1:0:0.1 +17 7980013 . G T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00385;SOR=Inf;LSEQ=CTCATTGAGGAGAACGGCCC;RSEQ=GCCAATGCTGTTGATCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:325,273:598,0:0:2,0:25.5:1:29.9:1:1:0:59.9:45:0.9932:0:0.2 0/1:626:9:4,5:315,302:617,9:0.0144:2,2:27.8:1:28.7:1:0.74788:1.30325:60:18:0.0145:0:1.2 +17 7980112 . A G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04876;SOR=Inf;LSEQ=AGGGCTGAAGTGGCCCCCAA;RSEQ=GGAGCTCAGCTCCCCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:91,213:304,0:0:2,0:22.8:1:31:1:1:0:60:29.4:1:0:0.1 0/1:271:4:2,2:87,180:267,4:0.0148:2,2:12:1:30.8:1:0.59982:2.06:60:8:0.0149:0:1 +17 7980189 . TCCCCAGATGCC T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCAAGCCCTCTCTTGTGG;RSEQ=CCCCAGGCTGACTGGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:45,55:100,0:0:2,0:23.1:1:32:1:1:0:60:49:1:0:0 0/1:58:15:8,7:20,23:43,15:0.2586:2,2:26.9:1:29.6:1:0.76708:1.31:60:30:0.2632:0.0345:0.1 +17 7980530 . A C 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00109;SOR=Inf;LSEQ=AGCTAGGTGTGGTGAAAGAG;RSEQ=AAGGGTTGGGTGAGGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:100,253:353,0:0:2,0:25.3:1:30.7:1:1:0:60:69.6:1:0:0.2 0/1:398:11:5,6:118,267:385,11:0.0276:2,2:23.1:1:30.5:1:0.32792:1.88:60:22:0.0284:0:1.1 +17 7980902 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACTGAAATCAGCCTACG;RSEQ=TATTCCATTAAGGAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:32.5:1:27.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 7982693 . C T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13765;SOR=0;LSEQ=ACACAGAGGCTCAGCGGCAG;RSEQ=GCCGCCTGCAGCCCAGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:4:2,2:261,69:330,4:0.012:2,2:17.3:1:28.3:1:0.19954:3.7629:60:8:0.0121:0:1 0/0:254:0:0,0:177,77:254,0:0:2,0:23.3:1:30.4:1:1:0:60:126:1:0:0.1 +17 7982927 . C A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06801;SOR=Inf;LSEQ=CGTGACCCGCGCCGCAGGTG;RSEQ=ACAGGGCGCTGGCGACTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:78,311:389,0:0:2,0:23.7:1:32:1:1:0:59.9:31.417:1:0:0.1 0/1:270:3:2,1:56,211:267,3:0.0111:2,2:17.3:1:26:1:0.11753:7.46:60:6:0.0113:0:1 +17 7982976 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.1602;SOR=Inf;LSEQ=TGGGACGGGGACAGGGACGC;RSEQ=GGGTGCGGGCTTGCCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:66,167:233,0:0:2,0:23.4:1:30.9:1:1:0:59.9:45.6:1:0:0.2 0/1:156:2:1,1:66,88:154,2:0.0128:2,2:33.5:1:29:1:1:1.33:60:4:0.0131:0:1 +17 7983012 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61327;SOR=0.8072;LSEQ=TGGGACTGGCGCGGGCGCCG;RSEQ=AGGTGGGGAGAGACGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:25:12,13:119,80:199,25:0.1116:2,2:22.6:1:30.7:1:0.28645:1.6079:60:24:0.1076:0:1 0/1:163:15:13,2:103,45:148,15:0.092:2,2:27.8:1:26.8:1:0.23497:2.83:60:6.5:0.0813:0:1.1 +17 7983034 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08991;SOR=Inf;LSEQ=GGTGGGGAGAGACGGGGATG;RSEQ=CCGCGAGGGAGGCCGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:195,81:276,0:0:2,0:23.1:1:31.9:1:1:0:60:24.091:1:0:0.2 0/1:225:3:2,1:171,51:222,3:0.0133:2,2:23.3:1:23.3:1:0.54727:1.67212:60:2:0.0091:0:1.7 +17 7983379 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14914;SOR=Inf;LSEQ=GGAGGAAAACGAGGCCCCCA;RSEQ=CCTGGCGCTGAGCGGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:45,75:120,0:0:2,0:26.4:1:32.7:1:1:0:59.7:29:1:0:0.1 0/1:76:2:2,0:11,63:74,2:0.0263:2,0:27.5:1:30.5:1:0.02737:0:60:4:0.0267:0:1 +17 7983462 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50706;SOR=0;LSEQ=GCGCGCGCCTCGCTGCCTCT;RSEQ=CCGTCCCACTGCCCCGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:126,25:151,2:0.0131:2,2:7:1:29:1:0.31192:4.96183:60:4:0.0132:0:1 0/0:117:0:0,0:110,7:117,0:0:2,0:23.4:1:30.8:1:1:0:60:234:1:0:0.1 +17 7983507 . G T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03927;SOR=Inf;LSEQ=GGCCTGCCTAGCACGCCGGA;RSEQ=ACCGCCTGGCTCCCCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:257,124:381,0:0:2,0:23:1:32.5:1:1:0:60:41.333:1:0:0.1 0/1:308:4:1,3:211,93:304,4:0.013:2,2:10.5:1:26.5:1:0.09141:6.76021:60:8:0.013:0:1 +17 7983681 . G A 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGATGGGATTCCAGGAAGA;RSEQ=GCCTTCAGAGGGGCTGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:40:16,24:105,247:352,40:0.102:2,2:21.6:1:30.5:1:0.20731:1.57:60:39:0.101:0:1.1 0/0:359:0:0,0:116,243:359,0:0:2,0:23.6:1:30.5:1:1:0:60:88.75:1:0:0.2 +17 7983799 . A G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54101;SOR=0.75655;LSEQ=TCTGGGTCCCATGTCTCAAG;RSEQ=TCTTTGCATCTCTAGGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:26:7,19:8,26:34,26:0.4333:2,2:22.3:1:32.6:1:0.77299:1.19:60:25:0.4386:0:1 0/1:41:15:6,9:4,22:26,15:0.3659:2,2:15.1:1:31.4:1:0.13019:3.54:60:30:0.3659:0:1.1 +17 7983927 . GA G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23807;SOR=Inf;LSEQ=CGCCAAGGTTGGGGGAGAGG;RSEQ=AAGTTCTTGCAGGAGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:125,33:158,0:0:2,0:23.4:1:30.5:1:1:0:60:51.667:1:0:0.5 0/1:152:2:1,1:110,39:149,2:0.0132:2,2:38:1:29.5:1:0.46093:2.79766:60:4:0.0133:0:1 +17 7983969 . G C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01616;SOR=0.66189;LSEQ=GTTCTCCCGTCACTCACACG;RSEQ=ACTCACATGGGCCCCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:141:105,36:96,49:145,141:0.4896:2,2:24.3:1:32.5:1:0.15455:1.49:60:69.5:0.486:0:1.1 0/1:304:118:72,46:121,64:185,118:0.3882:2,2:22.4:1:30.9:1:0.46374:1.20713:60:28.5:0.3826:0:1.2 +17 7984157 . A C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.10576;LSEQ=CGGGGAGGAGGCAGGCGCCC;RSEQ=GGGGAAAACCATGGGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:157:91,66:301,224:525,157:0.2302:2,2:25.7:1:30.8:1:0.92682:1.03:60:156:0.2332:0:1.1 0/1:588:18:10,8:304,263:567,18:0.0306:2,2:21:1:27.8:1:1:1.08:60:8:0.0278:0:1.2 +17 7984479 . G A 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGTGCTCCAGGAGGACGG;RSEQ=GAGCGAGTCATCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:835:0:0,0:384,450:834,0:0:2,0:24.3:1:30.7:1:1:0:60:35.261:0.9988:0:0.2 0/1:870:30:13,17:388,451:839,30:0.0345:2,2:27.1:1:29.4:1:0.8529:1.12486:60:60:0.035:0:1.2 +17 7984529 . C T 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGGAGACCAAGGAGAGGA;RSEQ=TCAAGGGCTGACCCTTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:188,348:536,0:0:2,0:24.9:1:32.9:1:1:0:60:52.6:0.9981:0:0.1 0/1:513:42:17,25:184,285:469,42:0.0819:2,2:26:1:29.5:1:0.87053:1.05:60:41:0.0812:0:1.2 +17 7984552 . G A 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07294;SOR=0.1595;LSEQ=AAGGGCTGACCCTTGCCCCT;RSEQ=CCCACTTCAGGAAGCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:7:5,2:116,245:361,7:0.019:2,2:12.3:1:26:1:0.04118:5.25:60:14:0.0194:0:1 0/0:325:1:1,0:116,207:323,1:0.0031:2,0:1:0:22:0:0.36111:0:60:2:0.0032:0:1 +17 7984585 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19529;SOR=Inf;LSEQ=AGCAGGAGTTCAGCTTCTGT;RSEQ=CCCCAGGTCGTCTCTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:34,175:209,0:0:2,0:22.2:1:31.6:1:1:0:60:28.857:1:0:0.1 0/1:166:2:1,1:37,127:164,2:0.012:2,2:9:0:31:1:0.4065:3.40:60:4:0.0124:0:1 +17 7984600 . TG T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.14008;SOR=Inf;LSEQ=TCTGTGCCCCAGGTCGTCTC;RSEQ=GGGGGGCCCATGACCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:16,145:161,0:0:2,0:21.6:1:31.2:1:1:0:59.9:52.667:0.9937:0:0.1 0/1:98:2:0,2:9,87:96,2:0.0204:2,0:18.5:1:31.5:1:1:0:60:4:0.0206:0:1 +17 7989047 . G T 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54545;SOR=4.34109;LSEQ=GAGTCAGGGAGGACTGGAGA;RSEQ=GTAGCGGGGAGCGCACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:3,1:4,3:0.375:2,0:31.3:1:31.7:1:1:0:60:6:0.4286:0:1.3 1/0:4:3:3,0:1,0:1,3:0.75:0,0:21:1:31.3:1:1:0:60:6:0.75:0:1.3 +17 7989604 . T TC 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04238;SOR=Inf;LSEQ=GCTCCCAGGCCGCCCACCCC;RSEQ=CTGGCCCCTCACCTAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:4,95:99,0:0:1,0:26.1:1:30:1:1:0:60:32:1:0:0.1 0/1:54:3:0,3:5,46:51,3:0.0556:2,0:31.7:1:32.7:1:1:0:60:6:0.0577:0:0 +17 7989668 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18937;SOR=Inf;LSEQ=CTCCCTGGACTGACGGAGGG;RSEQ=CAGGATATTGACCTGATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,24:24,0:0:1,0:19.5:1:31:1:1:0:60:48:1:0:0 0/1:19:2:0,2:0,17:17,2:0.1053:1,0:38.5:1:32:1:1:0:60:4:0.1053:0:1 +17 7990437 . G A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03113;SOR=6.25546;LSEQ=CTGGGGAGCCCACTGCCTTC;RSEQ=GAGCTGTGCCTCAGCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:3,0:23,1:24,3:0.1111:1,0:34.7:1:30.7:1:1:0:60:6:0.12:0:1 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:28:1:30.6:1:1:0:60:10:0.5:0:1.2 +17 7990527 . GACACACAGAC G 63 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=4.000;MSILEN=2;SSF=0.4186;SOR=2.35947;LSEQ=ACCCCTCCCGGGGCCACAAA;RSEQ=ACACACAGACACACACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:2,0:94,2:96,2:0.0204:1,0:19:1:34:1:1:0:21:4:0.0206:0:2 0/1:85:4:4,0:79,2:81,4:0.0471:1,0:19.8:1:31.8:1:1:0:57.5:8:0.05:0.0118:2.5 +17 7990555 . G C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55684;SOR=1.20508;LSEQ=GACACACACAGACACACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:29:22,7:92,5:97,29:0.1908:2,2:18.4:1:30.9:1:0.00601:5.7451:40.1:28:0.2295:0:3.1 0/1:131:29:23,6:68,5:73,29:0.2214:2,2:19.2:1:31:1:0.07121:3.496:42.3:58:0.29:0:3.1 +17 7990575 . CAG GACACAC 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.36123;SOR=0.31482;LSEQ=ACAGACACACACACACACAC;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:3:3,0:189,49:238,3:0.012:2,0:36.7:1:31.6:1:1:0:32.7:6:0.0127:0:1 0/0:262:1:1,0:196,55:251,1:0.0038:2,0:19:0:31.9:0:1:0:41:2:0.0039:0:1 +17 7990719 . G A 179 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=56.11297;LSEQ=GAGTCCCGTGTTCCCGACAA;RSEQ=AGGTCGGTGCCTGTGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:791:1:0,1:341,449:790,1:0.0013:2,0:27:0:13:0:1:0:60:0:0:0:7 0/1:949:63:27,36:358,528:886,63:0.0664:2,2:24.2:1:30.1:1:0.693:1.11:59.7:126:0.0673:0:1.2 +17 7990787 . C T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10888;SOR=0;LSEQ=TCTTCAGGAGGCAAGAGGGG;RSEQ=ACTCAGTCCCAGACACCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:3:1,2:35,239:274,3:0.0108:2,2:24.7:1:25:1:0.34249:3.39:60:2:0.0074:0:1.3 0/0:302:0:0,0:66,236:302,0:0:2,0:22.6:1:31.4:1:1:0:60:59.4:1:0:0.1 +17 7990915 . A G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51706;SOR=0.53848;LSEQ=GGTGGCGAGGTGGGGTGACT;RSEQ=GGCCTGCCAGCCAAATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:0,13:0,19:19,13:0.4063:1,1:21.8:1:32.8:1:1:0:60:26:0.4194:0:1.2 0/1:15:4:0,4:2,9:11,4:0.2667:2,0:19:1:27.5:1:1:0:60:3:0.2143:0:1.3 +17 7990958 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=AAAGCTGCTGCCCTTGGTGG;RSEQ=CGGGGTGGGTGCCGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:14,0:0:1,0:18.3:1:29.9:1:1:0:60:13:1:0:0.4 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:18:1:26.5:1:1:2.45:60:4:0.3333:0:1 +17 7991330 . T G 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGGTGGGCGGGGGAGGG;RSEQ=AGGGGGAGGGGCACTAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:31:1:30:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 8107979 . G T 64 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00119;SOR=Inf;LSEQ=ATGCTCATCCCGGCTCCTCA;RSEQ=GGTGAGCCAGCTCTCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:2,0:19,0:19,2:0.0952:1,0:28:1:28:1:1:0:60:4:0.0952:0:1 1/1:4:4:3,1:0,0:0,4:1:0,2:29:1:32.3:1:1:0:60:8:1:0:1.3 +17 8108331 . A G 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06414;LSEQ=AGATGAGGTCCTGGGCTCCC;RSEQ=TGGGCACGGAAGCGGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:689:682:288,394:3,3:6,682:0.9898:2,2:25.8:1:31:1:0.70151:1.3674:59.8:51.462:0.9896:0:1.2 1/1:804:693:285,408:40,70:110,693:0.8619:2,2:25.6:1:30.5:1:0.40299:1.22:59.7:172.25:0.8634:0:2 +17 8108339 . G A 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=28.43536;LSEQ=TCCTGGGCTCCCATGGGCAC;RSEQ=GAAGCGGGGAACTTTAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:72:31,41:234,346:580,72:0.1099:2,2:24.9:1:31:1:0.7033:1.12:59.4:144:0.1116:0:2 1/0:760:592:243,349:60,105:165,592:0.7789:2,2:26.1:1:30:1:0.28283:1.22:59.8:97.667:0.7782:0:2.1 +17 8108765 . C T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACATAGGAACTCTCCTTTC;RSEQ=CTGCTGCCTGACGGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:44,214:258,0:0:2,0:22.8:1:31.3:1:1:0:59.9:128:0.9961:0:0.1 0/1:204:17:2,15:33,154:187,17:0.0833:2,2:22.3:1:28.6:1:0.74261:1.60385:60:34:0.0837:0:1.2 +17 8109598 . G A 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09491;SOR=9.51263;LSEQ=AGCTGGGATTACTGGCGTCC;RSEQ=CCACCATGGCCGGCTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:8,2:0.2:0,0:22:1:21:1:1:0:45.5:1:0.1111:0:2.5 1/0:4:3:3,0:1,0:1,3:0.75:0,0:17.3:1:30:1:1:0:60:6:0.75:0:1 +17 8110256 . GA G 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=1.33814;LSEQ=CCAAAGGCATAAAAGAGCTG;RSEQ=AAAGATGATAGGAGCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:2:1,1:77,164:241,2:0.0082:2,2:26:1:28:1:0.53984:2.12:60:4:0.0084:0:0 0/1:273:3:2,1:87,183:270,3:0.011:2,2:42.7:1:31.3:1:0.2487:4.18:60:6:0.0111:0:0 +17 8110260 . A T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09752;SOR=0;LSEQ=AGGCATAAAAGAGCTGGAAA;RSEQ=GATGATAGGAGCAAACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:3:1,2:70,154:224,3:0.0132:2,2:32.3:1:25:1:1:1.10:60:2:0.009:0:3 0/0:265:0:0,0:87,178:265,0:0:2,0:22.8:1:30:1:1:0:60:131.5:1:0:0.1 +17 8110286 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49839;SOR=0;LSEQ=TAGGAGCAAACTGGGGTCAG;RSEQ=CGTGGCCCAGGCCGGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:42,105:147,2:0.0134:2,2:32.5:1:30.5:1:0.49528:2.48:60:4:0.0136:0:1 0/0:145:0:0,0:36,109:145,0:0:2,0:21.1:1:29:1:1:0:60:47.333:1:0:0.2 +17 8110298 . C T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09391;SOR=Inf;LSEQ=GGGGTCAGACGTGGCCCAGG;RSEQ=CGGGGACACCAGGGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:33,93:126,0:0:2,0:24.2:1:31.4:1:1:0:60:41:1:0:0.1 0/1:106:3:1,2:24,79:103,3:0.0283:2,2:11.7:1:22.3:1:0.55774:1.64:59.3:2:0.0196:0:3 +17 8110437 . G T 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21458;SOR=Inf;LSEQ=TGGATGAAGTGGGGCTGAAT;RSEQ=AGGAGCTGGGGGTGAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:156,52:208,0:0:2,0:22.1:1:31.8:1:1:0:60:25:1:0:0.1 0/1:180:2:0,2:131,47:178,2:0.0111:2,0:5:1:25:1:0.073:0:60:4:0.0113:0:1 +17 8110764 . C A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=10.92396;LSEQ=TTTCTCTCTGCTTCCTCATC;RSEQ=CATCCTGTCCTCCGCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:39:21,18:140,122:262,39:0.1296:2,2:26.1:1:29.8:1:1:1.02:60:18.5:0.1271:0:1.2 1/0:295:183:96,87:65,47:112,183:0.6203:2,2:25.5:1:29.3:1:0.39934:1.25236:60:182:0.619:0:1.1 +17 8110765 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24874;SOR=Inf;LSEQ=TTCTCTCTGCTTCCTCATCC;RSEQ=ATCCTGTCCTCCGCCCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:160,138:298,0:0:2,0:25:1:32.1:1:1:0:59.9:98.333:1:0:0.3 0/1:299:3:1,2:163,133:296,3:0.01:2,2:25:1:27.3:1:0.59089:2.44394:60:6:0.0101:0:1 +17 8113163 . G GT 32 v3;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTATTTCTATTTGCTGTCTA;RSEQ=TTTTTTTTTTTTCAGGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:34:1:32:0:1:0:60:4:0.4:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:21:0:24:0:1:0:60:2:1:0:1 +17 8113186 . A G 89 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTTTTCAGGATATGG;RSEQ=TTGGGAATCATGGCCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:0,7:1:0,2:30.9:1:32:1:1:0:60:14:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:44:0:29:0:1:0:60:2:1:0:1 +17 8113380 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49857;SOR=Inf;LSEQ=ACTTGGGACCCGTACTTTGG;RSEQ=GCATAACGGGGAAGAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:150,9:159,0:0:2,0:23.4:1:30.3:1:1:0:60:38.75:1:0:0.1 0/1:164:2:2,0:143,16:159,2:0.0122:2,0:27:1:28:1:1:0:60:4:0.0127:0:1 +17 8113607 . AAG A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.32355;SOR=1.88177;LSEQ=AGCCGTGAGAAGCAGAGAAA;RSEQ=AGAGAGAGAGGGAGGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:5:2,3:78,249:327,5:0.015:2,2:18.8:1:31.8:1:0.59754:2.12:60:10:0.0152:0.006:0.4 0/1:430:12:5,7:130,288:418,12:0.0279:2,2:26.8:1:29.1:1:0.52928:1.58:58.3:24:0.0282:0.0023:0.3 +17 8113620 . G C 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07591;SOR=0;LSEQ=AGAGAAAAAGAGAGAGAGAG;RSEQ=GAGGGGTTGGACCGATCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:3:1,2:48,195:243,3:0.0121:2,2:36:1:23.3:1:0.488:2.02:60:2:0.0086:0:1.7 0/0:335:0:0,0:94,239:333,0:0:2,0:21.6:1:29:1:1:0:60:14.136:0.9968:0:0.2 +17 8383060 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAAGCAATCCCTTCTATGGG;RSEQ=AGAAGAAAGGCTCTGATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:71,4:75,2:0.026:2,2:11:1:28.5:1:0.12645:15.99265:60:4:0.0267:0:2 0/0:37:0:0,0:36,1:37,0:0:1,0:21.1:1:30.5:1:1:0:60:36:1:0:0.9 +17 8383105 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.22622;SOR=Inf;LSEQ=ATACTGCATTTGTTCTCTGG;RSEQ=AGCAAATTAGCATTTCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:122,34:156,0:0:2,0:25.7:1:32.4:1:1:0:60:51:1:0:1.2 0/1:142:2:1,1:110,30:140,2:0.0141:2,2:5.5:1:26.5:1:0.39017:3.62301:60:4:0.0145:0:2.5 +17 8383112 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGTTCTCTGGCAGCAAA;RSEQ=TAGCATTTCATGGGCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:174:173:126,47:0,1:1,173:0.9943:0,2:25.4:1:32.4:1:0.27586:0:60:85.5:0.9942:0:1.2 1/1:169:169:132,37:0,0:0,169:1:0,2:23.9:1:31.5:1:1:0:60:168:1:0:1.2 +17 8383199 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1473;SOR=0.79184;LSEQ=CCTAGGAAATCACGGGGCGC;RSEQ=GTCCTAAAGCCCAGCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:241:114,127:43,60:103,241:0.6986:2,2:27.4:1:31.1:1:0.40819:1.25:60:79.333:0.7021:0:1.6 1/0:445:288:150,138:79,78:157,288:0.6472:2,2:26.6:1:29.5:1:0.76614:1.07:60:56.6:0.6461:0:1.7 +17 8383253 . G C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57189;SOR=2.85803;LSEQ=GATGCCGTCTGTCCTCCCAG;RSEQ=CTCTGAATGCTCACAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:222:220:72,148:0,0:0,220:0.991:0,2:24.9:1:31.3:1:1:0:60:43:1:0:1.6 1/1:316:315:123,192:0,0:0,315:0.9968:0,2:24.4:1:30.4:1:1:0:60:104:0.9968:0:1.6 +17 8383262 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64124;SOR=2.20646;LSEQ=TGTCCTCCCAGGCTCTGAAT;RSEQ=CTCACAGCTCTTCTCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:1,0:58,135:193,1:0.0052:2,0:1:0:24:0:0.30412:0:60:2:0.0052:0:2 0/1:265:3:2,1:95,167:262,3:0.0113:2,2:29.3:1:27.7:1:0.55628:3.50:60:6:0.0115:0:2.3 +17 8383311 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23573;SOR=0;LSEQ=CAACTTCTGTGTCCCACTCT;RSEQ=GTTATATGTGTTCTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:5,69:74,2:0.0263:2,2:22.5:1:28:1:0.15263:12.69:60:4:0.0267:0:2 0/0:80:0:0,0:4,76:80,0:0:2,0:21.3:1:31:1:1:0:60:79:1:0:1 +17 8383344 . G GC 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.41795;SOR=1.68855;LSEQ=CTCTGCCCACGTGGTGGGGA;RSEQ=CCCCCCCGAAAGGGGCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:8:0,8:1,25:26,8:0.2353:1,0:17.6:1:31.5:1:1:0:59.4:16:0.2353:0.0882:0.3 0/1:32:11:0,11:0,20:20,11:0.3438:1,0:26.9:1:30.8:1:1:0:60:22:0.3438:0.0313:0 +17 8384077 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATCTCTCACCTGGACTG;RSEQ=TGGGTGGCCTCCCGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:27.5:1:1:0:60:4:1:0:1 +17 8693552 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50387;SOR=Inf;LSEQ=TCTGTTTAATTAACCTGAGG;RSEQ=CAGTGACTGTTTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:68,13:81,0:0:2,0:23:1:31.8:1:1:0:60:19.25:1:0:0.2 0/1:102:2:1,1:75,25:100,2:0.0196:2,2:11.5:1:27.5:1:0.44671:2.96126:60:4:0.0196:0:1 +17 8693563 . TTTG T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.12484;SOR=Inf;LSEQ=AACCTGAGGCCAGTGACTGT;RSEQ=TTGTTGTTGTTGTTTTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:83,27:110,0:0:2,0:21.6:1:30.6:1:1:0:60:109:1:0:0.3 0/1:126:4:3,1:88,34:122,4:0.0317:2,2:22.5:1:30:1:1:1.16:60:8:0.0323:0.0079:1 +17 8693585 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50118;SOR=Inf;LSEQ=TGTTGTTGTTGTTGTTTTAT;RSEQ=CATGAAATGTGACCAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:97,45:142,0:0:2,0:25.8:1:31.9:1:1:0:60:141:1:0:0.4 0/1:165:2:2,0:106,55:161,2:0.0121:2,0:16:1:29:0:0.5501:0:60:4:0.0122:0:1 +17 8693643 . T C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2909;SOR=1.21927;LSEQ=ATTTCAGAGGACAGCCCCTG;RSEQ=GACATTCGTCAGCTTATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:251:136:69,67:56,59:115,136:0.5418:2,2:26.4:1:30.8:1:0.80038:1.08:60:44.333:0.5407:0:1.1 1/0:276:163:82,81:60,52:112,163:0.5906:2,2:24.6:1:30.4:1:0.62456:1.13923:60:326:0.5927:0:1.1 +17 8693981 . T A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATCCCCACGCGTACATT;RSEQ=GAATTCTCAAAAGCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:40:1:33.5:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 8694016 . T C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCTCCAAAAGCATTGC;RSEQ=AATAAAAAATGTAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:14.3:1:32:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 9756002 . G T 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20629;SOR=4.5193;LSEQ=ATTTAATCTTGGTGTTGATG;RSEQ=TTTTGAGTCTTTTCCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:10,5:15,1:0.0625:2,0:29:0:32:0:0.375:0:60:2:0.0625:0:2 0/1:21:5:3,2:11,5:16,5:0.2381:2,2:31:1:26.2:1:1:1.43927:60:4:0.2:0:1.4 +17 9756083 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4878;SOR=Inf;LSEQ=ATTTCTCCACTGCTGCTTTT;RSEQ=CTTCAGTTTCCTCATCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:20,0:0:2,0:19.7:1:30.3:1:1:0:60:19:1:0:0.4 0/1:21:2:1,1:9,9:18,2:0.0952:2,2:15:0:32.5:1:1:1:60:4:0.0952:0:1 +17 9756171 . A T 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.78389;LSEQ=TCCATCAGCAGGAAGTTTTA;RSEQ=TTTTTTCTGTGGAAACTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:9,12:21,1:0.0455:2,0:1:0:25:0:1:0:46:2:0.0476:0:2 0/1:38:3:3,0:18,17:35,3:0.0789:2,0:17.3:1:32:0:0.23826:0:46.7:6:0.0833:0:2 +17 9756198 . T C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77978;SOR=1.19098;LSEQ=CTGTGGAAACTTGCTACCAC;RSEQ=TCCAGGGGCAGATTACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:4,7:5,3:8,11:0.5789:2,2:28.9:1:31.7:1:0.36985:2.74899:52.5:22:0.5789:0:1.2 1/0:37:23:12,11:6,8:14,23:0.6216:2,2:27.5:1:30.8:1:0.73743:1.44:50.1:22:0.6111:0:1.3 +17 9756374 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52425;SOR=Inf;LSEQ=AGCCCCCATGGAAACCATTG;RSEQ=CTGTACAGACATTTTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:22,0:0:2,0:23.1:1:31.5:1:1:0:59.5:21:1:0:0.1 0/1:37:2:1,1:18,17:35,2:0.0541:2,2:32.5:1:30:0:1:1.05721:59.5:4:0.0571:0:1 +17 10379676 . C A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03568;SOR=0.76422;LSEQ=CTTGAACCTGTTTTTCAAAA;RSEQ=TTCTATCTTGGTGACATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:448:232:114,118:106,110:216,232:0.5179:2,2:26.8:1:30.8:1:1:1.00:60:231:0.5214:0:1.1 0/1:548:247:116,131:153,148:301,247:0.4507:2,2:26.6:1:29.6:1:0.39099:1.16713:60:40.167:0.4455:0:1.2 +17 10379755 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23202;SOR=Inf;LSEQ=TCACCACTTACCCCTCCTGG;RSEQ=TGTCTACACCTTTCCTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:36,155:191,0:0:2,0:24.6:1:33.1:1:1:0:59.9:190:1:0:0.3 0/1:178:2:1,1:46,129:175,2:0.0112:2,2:27.5:1:27.5:1:0.46167:2.79:60:4:0.0113:0:1 +17 10552404 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17967;SOR=0;LSEQ=TGACTTTCCAATCCTAGGAC;RSEQ=AACCAAATCAGCAGCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:136,56:192,2:0.0103:2,2:14.5:1:28.5:1:0.50238:2.41602:60:4:0.0105:0:1.5 0/0:263:0:0,0:171,92:263,0:0:2,0:23.2:1:30.6:1:1:0:60:130.5:1:0:0.3 +17 10552409 . A T 31 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6433;SOR=2.16826;LSEQ=TTCCAATCCTAGGACCAACC;RSEQ=AATCAGCAGCATGTCTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:1:0,1:143,64:207,1:0.0048:2,0:1:0:23:0:0.3125:0:60:2:0.0048:0:2 0/1:289:3:0,3:180,106:286,3:0.0104:2,0:13.3:1:20:1:0.05273:0:60:2:0.007:0:1.3 +17 10552488 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08889;SOR=0.7872;LSEQ=GTTGGGGATCTCTTGACTGA;RSEQ=CATTCCTTTAACACTTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:403:261:131,130:74,68:142,261:0.6476:2,2:27.3:1:29.9:1:0.75472:1.07972:60:64.25:0.6441:0:1.2 1/0:526:311:163,148:101,114:215,311:0.5913:2,2:25.4:1:29.3:1:0.24893:1.24:60:622:0.5924:0:1.1 +17 10552622 . C T 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.71251;SOR=1.22482;LSEQ=TGGTATATGTGATTCTTCCA;RSEQ=AAAAGAACAAGCTCTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:45:3,42:4,19:23,45:0.6618:2,2:20.7:1:28.6:1:0.21572:2.89607:60:21.5:0.6515:0:1 1/0:68:48:2,46:1,19:20,48:0.7059:1,1:21.1:1:28.4:1:1:1.20698:60:96:0.7059:0:1.1 +17 10841682 . A G 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.87089;LSEQ=GGGAACTAGTGTTTGTGAGA;RSEQ=GAGAATGAACGTTGTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:11.7:1:34.3:1:1:0:60:6:0.3333:0:2.7 1/0:2:1:1,0:1,0:1,1:0.5:0,0:5:0:34:0:1:0:60:2:0.5:0:3 +17 10841701 . G T 48 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=2.73861;LSEQ=AAGAGAATGAACGTTGTTTG;RSEQ=AATATGTTGGTGTGAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:9,3:0.25:0,0:18:1:30.3:1:1:0:60:6:0.25:0:2.7 1/0:2:1:1,0:1,0:1,1:0.5:0,0:24:0:31:0:1:0:60:2:0.5:0:3 +17 10841749 . A G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02654;SOR=5.98999;LSEQ=GCACCTCTTCTTGAAGACCC;RSEQ=GTTGGAGAGAAGGTAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:2,3:12,4:16,5:0.2381:2,2:24.4:1:29.6:1:0.28001:4.14056:60:10:0.2381:0:1.8 1/0:12:8:6,2:3,1:4,8:0.6667:2,2:24.8:1:28.5:1:1:1:60:16:0.6667:0:1.6 +17 10841831 . G T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50166;SOR=Inf;LSEQ=TAAACTCTCTTAGAAAGTGG;RSEQ=GACAGCGGGGAAGTTGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:3,15:18,0:0:2,0:26.4:1:31.5:1:1:0:60:36:1:0:0.1 0/1:25:2:1,1:9,14:23,2:0.08:2,2:7:0:31:0:1:1.53:60:4:0.0833:0:2.5 +17 10841838 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4958;SOR=Inf;LSEQ=TCTTAGAAAGTGGGGACAGC;RSEQ=GGGAAGTTGGGTAATCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:2,13:15,0:0:2,0:28.3:1:32:1:1:0:60:30:1:0:0.1 0/1:20:2:1,1:7,11:18,2:0.1:2,2:30:1:29:1:1:1.54:60:4:0.1:0:1 +17 11396226 . C T 205 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=0;LSEQ=GCTTCTGCTCCTCTCTTCCC;RSEQ=TCCCCTGTCCCACAGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:77,5:0,0:0,82:1:0,2:23.3:1:32.4:1:1:0:60:164:1:0:1.3 1/0:82:50:47,3:30,2:32,50:0.6098:2,2:22.1:1:30.7:1:1:1.04:60:49:0.6049:0:1.4 +17 11396312 . T C 265 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGAACTTGGAGATTGGCCAT;RSEQ=TGTCACTAGGTGTCTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:285:285:158,127:0,0:0,285:1:0,2:25.2:1:32.6:1:1:0:60:284:1:0:1.6 1/0:361:249:143,106:54,58:112,249:0.6898:2,2:23.5:1:30.5:1:0.11081:1.45:60:61.25:0.6863:0:1.7 +17 11396377 . C T 255 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01723;LSEQ=GCCTCAACACTAACATTTAT;RSEQ=CAACTTTTCCATGGAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:328:326:167,159:0,0:0,326:0.9939:0,2:25.8:1:30.6:1:1:0:60:80.5:0.9969:0:1.5 1/0:391:288:131,157:46,57:103,288:0.7366:2,2:25.3:1:29:1:0.90861:1.03:59.9:71:0.7358:0:1.5 +17 11396420 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25032;SOR=Inf;LSEQ=AATGTTCTGGCTAATGTTTT;RSEQ=GCTAATGATTGCTGTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:81,130:211,0:0:2,0:26:1:31.4:1:1:0:59.9:41.2:1:0:0.8 0/1:234:3:2,1:89,142:231,3:0.0128:2,2:21:1:22.7:1:0.56174:3.17:60:6:0.013:0:2 +17 11396441 . C A 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60314;SOR=2.25891;LSEQ=GCTAATGATTGCTGTGAGTC;RSEQ=AGAGGACCTCCCTCATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:0,1:55,125:180,1:0.0055:2,0:6:0:14:0:1:0:60:0:0:0:2 0/1:161:2:1,1:52,106:158,2:0.0124:2,2:6:1:28:1:1:2.03:60:4:0.0126:0:1.5 +17 11396483 . A C 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00269;SOR=Inf;LSEQ=TAGCAGGACCACCTCCTGAC;RSEQ=ACTGTGACCACTTAGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:11,94:105,0:0:2,0:27.1:1:31.2:1:1:0:59.5:104:1:0:0.2 0/1:65:6:0,6:9,50:59,6:0.0923:2,0:25.3:1:29.7:1:0.58379:0:60:5:0.0794:0:1.2 +17 11396881 . G A 41 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTTTTGGTACCATGTG;RSEQ=ATACACGCGTGCGCGCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:32:1:26.3:1:1:0:60:2:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 11396889 . CGT C 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTACCATGTGGATACACG;RSEQ=GCGCGCGCACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:22.3:1:29.3:1:1:0:60:6:1:0.6667:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 11396900 . A G 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGATACACGCGTGCGCGCGC;RSEQ=CACACACACACACATACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:28.5:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 11914107 . T C 51 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCACCTCAGGCTTCTTCC;RSEQ=ACTGGTTCTCACGAAGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:38.7:1:32.3:1:1:0:60:6:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:32:0:1:0:60:4:1:0:1 +17 11914348 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50793;SOR=Inf;LSEQ=CAGCATGCTGGGGAACATTG;RSEQ=AGACTCTTCCAGTTTAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:24,28:52,0:0:2,0:31.6:1:28.3:1:1:0:32.3:51:1:0:0.2 0/1:71:2:1,1:33,36:69,2:0.0282:2,2:42.5:1:31.5:1:1:1.09:28.5:4:0.029:0:1 +17 11914391 . CT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.22769;SOR=0;LSEQ=GTGACACCTGTGGGGCATTC;RSEQ=TTTTGAACAGTACTCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:22,34:56,2:0.0345:2,2:13.5:1:31:1:1:1.53:44:4:0.0351:0:0 0/0:63:0:0,0:23,40:63,0:0:2,0:20.4:1:29.8:1:1:0:41.4:126:1:0:0.1 +17 11924199 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26377;SOR=Inf;LSEQ=GCCGCTCGGCTCTTCACTCC;RSEQ=AACAATGGCGGCTCCGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:33,0:0:2,0:20.9:1:31.5:1:1:0:60:32:1:0:0.3 0/1:47:3:1,2:21,23:44,3:0.0638:2,2:11.3:1:27:1:1:1.80368:60:6:0.0638:0:1.3 +17 11924222 . AGCG A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.09343;SOR=0;LSEQ=CAATGGCGGCTCCGAGCCCG;RSEQ=GCGGCGGCGGCTCCGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:0,2:13,15:28,2:0.0667:2,0:13:1:30.5:1:0.49195:0:60:4:0.0667:0.0333:0.5 0/0:67:0:0,0:32,35:67,0:0:2,0:21.7:1:31.7:1:1:0:59.6:21.333:1:0:0.5 +17 11924225 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.09987;SOR=0;LSEQ=TGGCGGCTCCGAGCCCGAGC;RSEQ=GCGGCGGCGGCTCCGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:13,15:28,2:0.0645:2,2:27.5:1:30:1:1:1.15:60:4:0.0667:0:1 0/0:66:0:0,0:32,34:66,0:0:2,0:22.1:1:30.6:1:1:0:59.5:132:1:0:0.5 +17 11924239 . CG C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14932;SOR=0;LSEQ=CCGAGCGGCGGCGGCGGCTC;RSEQ=GGGGCGGCAGCGGCAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:35,29:64,2:0.0303:2,2:12.5:1:33:0:1:1.20344:60:4:0.0323:0:1 0/0:104:0:0,0:54,49:103,0:0:2,0:14.9:1:29.2:1:1:0:59.7:24.75:0.99:0:0.5 +17 11924248 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=1;SOR=1.38246;LSEQ=GGCGGCGGCTCCGGGGGCGG;RSEQ=AGCGGCAGCGGCACCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:1:0,1:44,37:81,1:0.0122:2,0:1:0:24:0:0.46341:0:60:2:0.013:0:2 0/1:119:2:1,1:64,53:117,2:0.0168:2,2:9.5:1:26.5:1:1:1.20562:60:4:0.0172:0:1.5 +17 11924257 . C T 59 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16187;SOR=0.16776;LSEQ=TCCGGGGGCGGCAGCGGCAG;RSEQ=GGCACCCCCGGCCCCGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:4:1,3:56,44:100,4:0.0385:2,2:7.8:1:29.5:1:0.3257:3.77197:60:8:0.0392:0:1 0/0:151:1:0,1:85,65:150,1:0.0066:2,0:1:0:23:0:0.43709:0:60:2:0.0068:0:1 +17 11924279 . TC T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14744;SOR=0;LSEQ=GCACCCCCGGCCCCGTAGGG;RSEQ=CCCGGCGCCAGGCCACCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:106,77:183,2:0.0108:2,2:49.5:1:32.5:1:1:1.37419:60:4:0.0109:0:1 0/0:296:0:0,0:161,131:292,0:0:2,0:19.4:1:30.5:1:1:0:60:57.4:0.9897:0:0.4 +17 11924285 . G T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65302;SOR=2.57481;LSEQ=CCGGCCCCGTAGGGTCCCCG;RSEQ=CGCCAGGCCACCCGGCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:0,1:112,84:196,1:0.0051:2,0:1:0:28:0:0.43147:0:60:2:0.0052:0:1 0/1:308:4:1,3:167,137:304,4:0.013:2,2:8.8:1:26.3:1:0.33326:3.64257:60:8:0.0137:0:1.3 +17 11924302 . C T 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70934;SOR=1.64224;LSEQ=CCGGCGCCAGGCCACCCGGC;RSEQ=GTCAGCAGCATGCAGGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:2:1,1:142,117:259,2:0.0077:2,2:42:0:22:1:1:1.21277:60:1:0.0039:0:1.5 0/1:399:5:2,3:211,183:394,5:0.0125:2,2:30:1:28.2:1:0.66754:1.72713:60:10:0.0129:0:1 +17 11924308 . C A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.06012;SOR=0;LSEQ=CCAGGCCACCCGGCCGTCAG;RSEQ=AGCATGCAGGGTAAGGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:2,1:146,118:264,3:0.0112:2,2:16.3:1:22.3:1:1:1.61:60:2:0.0076:0:1 0/0:413:0:0,0:221,192:413,0:0:2,0:25.5:1:31.5:1:1:0:60:30.769:1:0:0.4 +17 11924335 . C T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.05912;SOR=0;LSEQ=CAGGGTAAGGAACGCGGCCG;RSEQ=GCCGAGATCCCAGCCCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:3:2,1:113,109:222,3:0.0133:2,2:18.3:1:24:1:1:1.92:60:2:0.0092:0:1.7 0/0:351:0:0,0:178,173:351,0:0:2,0:27.2:1:29.8:1:1:0:60:24.071:1:0:0.3 +17 11924367 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.18116;SOR=0;LSEQ=AGCCCCCTAGCGCGGCAACC;RSEQ=GCGTCGTCGCGGCCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:61,82:143,2:0.0138:2,2:12.5:1:30:1:1:1.34:60:4:0.014:0:1.5 0/0:195:0:0,0:82,110:192,0:0:2,0:21.7:1:28.8:1:1:0:60:37.4:0.9842:0:0.2 +17 11924373 . G A 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.39102;SOR=3.13736;LSEQ=CTAGCGCGGCAACCCGCGTC;RSEQ=TCGCGGCCTGCCCCAGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:1,0:47,75:122,1:0.0081:2,0:1:0:25:0:0.39024:0:60:2:0.0084:0:1 0/1:159:4:3,1:60,95:155,4:0.0252:2,2:13.3:1:26:1:0.30151:4.70:60:8:0.0258:0:1 +17 11935504 . TA T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.106;SOR=Inf;LSEQ=GTTTTATTCAAAATTTAATA;RSEQ=AAAATGCAATGTCATGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:228,96:324,0:0:2,0:22.8:1:29:1:1:0:60:80:0.9969:0:0.1 0/1:293:3:1,2:193,97:290,3:0.0102:2,2:7.7:1:26.3:1:0.2646:3.95918:60:6:0.0103:0.0068:0.7 +17 11958053 . A G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTATTTTTTCTTAGTTT;RSEQ=AGAAATTCCTCATTGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:39,0:0,0:0,39:1:0,1:22:1:32.4:1:1:0:59.1:38:1:0:1.2 1/1:20:20:20,0:0,0:0,20:1:0,1:17.5:1:31.5:1:1:0:60:40:1:0:1.1 +17 11958145 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49863;SOR=0;LSEQ=TGGTGTGACTTTCTTATGCC;RSEQ=TCAGAATAGTACCTGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:134,41:175,2:0.0113:2,2:25:1:30:1:0.4193:3.24116:60:4:0.0116:0:1 0/0:173:0:0,0:135,36:171,0:0:2,0:24:1:30:1:1:0:59.8:41.75:0.994:0:0.1 +17 11973193 . T A 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21782;SOR=0.20706;LSEQ=CTTACCTTTATTTTCCTGTC;RSEQ=AAGGAAGATTAGTCATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:5:4,1:205,254:459,5:0.0108:2,2:16:1:25.8:1:0.1796:4.94:60:4:0.0089:0:1 0/0:445:1:1,0:190,254:444,1:0.0022:2,0:1:0:27:0:0.42921:0:60:2:0.0023:0:1 +17 11973293 . A AGC 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.17745;SOR=1.96871;LSEQ=TGCTGAGGAGACAGTAAAAC;RSEQ=GCTTGGGGCGTTTTAGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:11:0,11:0,97:97,11:0.1019:1,0:28.3:1:31.2:1:1:0:53.8:22:0.1019:0.0185:0.6 0/1:71:13:0,13:2,56:58,13:0.1831:1,1:26:1:30.1:1:1:0:53.2:26:0.1857:0.0563:0.8 +17 11999052 . A T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20144;SOR=Inf;LSEQ=AGCTGACTAATGAATATCTA;RSEQ=TTGGGACAAATGAAGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:44,201:245,0:0:2,0:24.3:1:31.2:1:1:0:60:80.667:1:0:0.1 0/1:200:2:1,1:32,166:198,2:0.01:2,2:18:1:25:1:0.30347:5.12:60:4:0.0101:0:1 +17 11999147 . G A 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.36709;SOR=0;LSEQ=TATCTTAGTGTTTAACCATG;RSEQ=TAATTTACATATTAACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:50:1,49:0,0:0,50:1:0,1:24.8:1:32.2:1:1:0:59.8:100:1:0:1 1/1:29:28:1,27:0,1:1,28:0.9655:0,1:25:1:30.8:1:1:0:60:56:0.9655:0:1.1 +17 11999212 . TTG T 47 MAF0.05;MSI12;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=31;MSI=16.000;MSILEN=2;SSF=1;SOR=1.60994;LSEQ=GGGGTGAATCACACGTGTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:1,7:8,3:0.2308:2,2:33.7:1:30:1:0.49091:3.06:60:6:0.2308:0:0 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:41:0:30:0:1:0:60:2:0.3333:0:0 +17 12013376 . GA G 31 v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCTCAAAATAAAAAGG;RSEQ=AAAAAAAAAAGGAAATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:6.5:1:31:1:1:0:47:4:0.25:0.125:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 12016528 . G T 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22106;SOR=4.53086;LSEQ=GAAGAAGCTAATTGTATACT;RSEQ=AATGATATCTATGTCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:1:1,0:271,141:412,1:0.0024:2,0:40:0:13:0:1:0:60:0:0:0:3 0/1:459:5:3,2:288,166:454,5:0.0109:2,2:11.4:1:26.8:1:1:1.15625:54.4:4:0.0088:0:2.4 +17 12016736 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.5125;SOR=0;LSEQ=TGCACAGAGAGCCTGTGCTC;RSEQ=TTTGTGCTGGCCATTAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:14,154:168,2:0.0118:2,2:10.5:1:29:1:0.16916:10.66:60:4:0.012:0:1 0/0:121:0:0,0:16,105:121,0:0:2,0:25.1:1:29.5:1:1:0:60:59.5:1:0:0.1 +17 12028818 . G GA 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.23103;SOR=1.85512;LSEQ=CACTATGGTTTTAAGTTGCT;RSEQ=AAAAAAAAAAAGTATGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:9:0,9:1,95:96,9:0.0833:1,0:24.8:1:32.6:1:1:0:60:18:0.09:0:1.6 0/1:76:11:1,10:0,65:65,11:0.1447:1,2:31.9:1:29.5:1:0.14474:0:60:10:0.1449:0:0.3 +17 12032395 . C A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24815;SOR=Inf;LSEQ=TAGATTTTTTTGTGGCCCTT;RSEQ=CAGTGGGGAGTAGTAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:142,38:180,0:0:2,0:20.7:1:31.9:1:1:0:60:89:1:0:0.2 0/1:186:3:2,1:147,35:182,3:0.0161:2,2:25:1:20.7:1:0.47962:2.08983:60:2:0.011:0:3 +17 12042934 . T A 73 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23739;SOR=Inf;LSEQ=TTAATATTTTTTCTAATTTT;RSEQ=AACTAATCATCCTACACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:21:1:26.3:1:1:0:60:3:1:0:0.5 0/1:13:6:6,0:6,1:7,6:0.4615:2,0:25.3:1:28.3:1:1:0:60:12:0.4615:0:1 +17 12043099 . A T 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.24935;SOR=Inf;LSEQ=ATATTTCATCTGTGAAAAGA;RSEQ=AAATACTTAGGCAAATGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:202,62:264,0:0:2,0:24.7:1:30.5:1:1:0:60:131:1:0:0.1 0/1:281:3:1,2:205,73:278,3:0.0107:2,2:6:1:25.7:1:0.1747:5.57502:60:6:0.0107:0:1 +17 12043531 . A AG 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGAAAAAAATTAGTGAAA;RSEQ=TTTGTGTTTATTCTGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:20.6:1:32.1:1:1:0:60:10:1:0.2:0.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 12043573 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATTCATGCAAATTTAC;RSEQ=TCATATAGCCTATTCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:33:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 12044417 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49913;SOR=Inf;LSEQ=ATTGGAAAATGTTCAGTTTG;RSEQ=GCTGTCATACAAACTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:127,10:137,0:0:2,0:23.6:1:31.5:1:1:0:60:136:1:0:0.1 0/1:149:2:1,1:133,14:147,2:0.0134:2,2:9:1:26.5:1:0.19182:9.21231:60:4:0.0137:0:2 +17 13964644 . A T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=16.71238;LSEQ=TATCCTTTTTTGGATAGCTG;RSEQ=CATGATTCTAGTTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:6:5,1:64,20:84,6:0.0667:2,2:27.2:1:30.3:1:1:1.56:60:12:0.0667:0:1.2 1/0:82:45:31,14:26,11:37,45:0.5488:2,2:20.6:1:28.2:1:1:1.06657:60:44:0.5432:0:1 +17 13964744 . A C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=14.71047;LSEQ=TGAATGCATCAACCAGGATG;RSEQ=AATGAACAGACAACTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:15:8,7:83,85:168,15:0.082:2,2:26.8:1:32.6:1:0.79451:1.17:60:30:0.0829:0:1.1 1/0:223:127:63,64:47,49:96,127:0.5695:2,2:25.9:1:30.8:1:1:1.03:60:30.75:0.5616:0:1.1 +17 15935500 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49565;SOR=0;LSEQ=TGGGCTGGCTCTCCTGAAAA;RSEQ=TCTCAGGGAATAAGTCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:54,2:56,2:0.0345:1,2:15:1:28:0:0.10163:22.24886:60:4:0.0351:0:1 0/0:58:0:0,0:57,1:58,0:0:1,0:23.6:1:30.8:1:1:0:60:28:1:0:0.1 +17 15935574 . C T 108 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00423;SOR=10.60923;LSEQ=AACCACAAAAACTAGAGATC;RSEQ=CTCTCCTGCACCCTGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:0,1:185,79:264,1:0.0038:2,0:1:0:24:0:0.30189:0:60:2:0.0038:0:1 0/1:311:12:8,4:199,100:299,12:0.0386:2,2:24.7:1:30.3:1:1:1.01:60:24:0.0392:0:1.1 +17 15935837 . A C 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=GTTTTCATTGTCATGAACAT;RSEQ=ACTGGTATTTCATCCAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:44,158:202,0:0:2,0:23.4:1:30.6:1:1:0:60:100:1:0:0.1 0/1:229:13:3,10:54,162:216,13:0.0568:2,2:28:1:30.2:1:1:1.11061:60:12:0.0529:0:1.2 +17 15935842 . G T 46 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.36459;LSEQ=CATTGTCATGAACATAACTG;RSEQ=TATTTCATCCAATCCAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:34,149:183,2:0.0108:2,2:18.5:1:32:0:0.34342:4.33:60:4:0.011:0:2 0/1:204:3:1,2:47,153:200,3:0.0147:2,2:26.3:1:29.3:1:0.5569:1.62:60:6:0.0148:0:3 +17 15938342 . GA G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49789;SOR=Inf;LSEQ=ATGATTATATATTGCTAAAT;RSEQ=AAAAAAAGCAGAATGGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:1,115:116,0:0:1,0:23.2:1:31.2:1:1:0:60:57:1:0:0 0/1:118:2:0,2:2,114:116,2:0.0169:1,0:35:1:33:0:1:0:60:4:0.0172:0:0 +17 15942602 . CT C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.19195;SOR=Inf;LSEQ=CTGGGTAGGTTTTCAAAAAC;RSEQ=TTTTTAAGTAACGGAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:84,0:84,0:0:1,0:24.6:1:32.4:1:1:0:60:168:1:0:0 0/1:66:2:2,0:61,3:64,2:0.0303:1,0:11:1:30.8:1:1:0:60:4:0.0308:0.0152:0 +17 15943110 . C CT 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.91424;LSEQ=AGGACCCACCACACAGAGAC;RSEQ=TTTTTTTTTGGAGACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:0,2:2,40:42,2:0.0455:1,0:33:1:29.5:1:1:0:60:4:0.0455:0:0 0/1:24:1:0,1:1,22:23,1:0.0417:1,0:42:0:28:0:1:0:60:2:0.0435:0:1 +17 15943144 . A G 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66685;SOR=2.0749;LSEQ=ACAGAGTCTCTCTCTGTCGC;RSEQ=CCCAGGCTGGAGTGCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:1,6:0,9:9,7:0.4375:0,2:25.4:1:33:1:0.4375:0:53.4:14:0.4375:0:1 1/0:8:5:0,5:0,3:3,5:0.625:0,0:19.4:1:32:1:1:0:52.2:10:0.625:0:1 +17 15943331 . G C 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCTGATCTCGAATTCC;RSEQ=AACCTCAGGTGATCCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:19.7:1:30.7:1:1:1.73:39.7:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 15943672 . C T 42 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34271;SOR=3.46697;LSEQ=GCAGTCACTCCCCTGGTATA;RSEQ=AGTTGGTACTCAGTACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:1:1,0:263,82:345,1:0.0029:2,0:31:0:33:0:1:0:60:2:0.0029:0:1 0/1:301:3:1,2:223,75:298,3:0.01:2,2:6.7:1:27:1:0.16191:5.90344:60:6:0.01:0:1 +17 15943910 . T C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05763;SOR=1.98762;LSEQ=AAAATTAATCTTTTTATTTT;RSEQ=CATGATCTCAACCTTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:40:0,40:0,34:34,40:0.5405:1,1:24.5:1:31.5:1:1:0:60:39:0.5342:0:1.4 1/0:67:47:2,45:1,19:20,47:0.7015:1,1:23.4:1:29.8:1:1:1.18111:60:22.5:0.6923:0:1.2 +17 15943962 . AT A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11315;SOR=0;LSEQ=AGTGAAGATAAAATGGAAGT;RSEQ=TTTTTTTTTTTGAGACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:0,4:0,16:16,4:0.2:1,0:35.5:1:31.8:1:1:0:60:8:0.2:0:0.5 0/0:16:0:0,0:0,16:16,0:0:1,0:24.8:1:28.8:1:1:0:60:15:1:0:0.9 +17 15950172 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12759;SOR=Inf;LSEQ=GACAGATGTCCTGTAAAGAG;RSEQ=CTTCAAACTCAAGCATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:214,81:295,0:0:2,0:24.6:1:31.6:1:1:0:59.9:35.875:1:0:0.6 0/1:340:4:1,3:243,93:336,4:0.0118:2,2:8.3:1:25.3:1:0.0698:7.78397:60:8:0.0119:0:2.3 +17 15950198 . G A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=0.6207;LSEQ=AACTCAAGCATTACAGGAGA;RSEQ=GCAACACTGGAGATATCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:441:276:181,95:106,59:165,276:0.6259:2,2:24.3:1:30.7:1:0.83653:1.06:59.8:91:0.6276:0:1.1 1/0:540:275:185,90:163,100:263,275:0.5093:2,2:24.6:1:29.6:1:0.20754:1.26:59.9:90.667:0.5103:0:1.1 +17 15952093 . G C 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00145;SOR=Inf;LSEQ=TGAGAAAAACGGCAACAACT;RSEQ=AAGGAAATGTTAAAGCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:146,23:169,0:0:2,0:22.5:1:32.9:1:1:0:60:168:0.9941:0:0.1 0/1:138:8:6,2:108,22:130,8:0.058:2,2:20.8:1:30.6:1:0.62778:1.62968:60:16:0.058:0:1.3 +17 15952100 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20181;SOR=Inf;LSEQ=AACGGCAACAACTGAAGGAA;RSEQ=TGTTAAAGCATGAGCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:163,34:197,0:0:2,0:22.5:1:31.1:1:1:0:60:394:1:0:0.1 0/1:162:2:1,1:125,35:160,2:0.0123:2,2:18.5:1:29.5:1:0.39614:3.53531:60:4:0.0124:0:2 +17 15952588 . C A 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGCAGTGGCAGAAGCTG;RSEQ=GTCCTTGAGGCTCCGCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:30.3:1:32.3:1:1:0:60:8:0.8:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:27:1:1:0:60:4:1:0:1.5 +17 15960762 . C T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1183;SOR=Inf;LSEQ=TGAGAAACAAATTCCTTATC;RSEQ=TGTAGATATATTCCATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:98,14:112,0:0:2,0:22.8:1:31.5:1:1:0:60:36.333:1:0:0 0/1:109:3:1,2:92,14:106,3:0.0275:2,2:9:1:22:1:0.05583:12.60896:60:2:0.0185:0:2 +17 15961098 . CA C 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.77445;SOR=1.26334;LSEQ=TAAAATTCATTGAGTACTTG;RSEQ=AAAAAAAAATAGTATTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:5:1,4:40,107:147,5:0.0325:2,2:16.8:1:33.4:1:1:1.49179:60:10:0.0325:0.0065:0 0/1:172:7:0,7:39,126:165,7:0.0407:2,0:20.9:1:32.7:1:0.35254:0:60:14:0.0412:0:0 +17 15961518 . G GA 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.12216;SOR=Inf;LSEQ=GAACTTATCTTAATTTTGGA;RSEQ=AAAAAAAAAATTATTCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:8,32:40,0:0:2,0:25.4:1:32.8:1:1:0:60:80:1:0:0.1 0/1:22:2:0,2:6,13:19,2:0.0909:2,0:30:1:31:1:1:0:60:4:0.0909:0:0 +17 15961641 . T C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00604;SOR=Inf;LSEQ=AAAAAATAAAAAAGAATCGA;RSEQ=TGCTGTTTCTAAAGAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:87,9:96,0:0:2,0:25.4:1:31.4:1:1:0:60:192:1:0:0.1 0/1:56:5:5,0:51,0:51,5:0.0893:1,0:21.8:1:31.6:1:1:0:60:10:0.0893:0:1.2 +17 15961803 . TAAC T 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ACTTTCCGCTTGATTTGCCT;RSEQ=AACCTCTGGCTGATAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:961:0:0,0:523,437:960,0:0:2,0:25.7:1:29.4:1:1:0:60:72.846:1:0:0.1 0/1:1170:57:31,26:597,515:1112,57:0.0487:2,2:24.7:1:30.3:1:1:1.03:59.8:114:0.0493:0.0068:0.2 +17 15961951 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.90901;SOR=1.04412;LSEQ=CTTATTTCAAAACTAATCCC;RSEQ=GGAAAAGTTTCTGAAGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:83:8,75:6,51:57,83:0.5929:2,2:25:1:31.2:1:1:1.10216:60:82:0.5985:0:1.4 1/0:184:111:22,89:14,59:73,111:0.6033:2,2:22.4:1:29.7:1:1:1.04:60:36:0.6:0:1.5 +17 15961993 . T A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.62688;SOR=1.21507;LSEQ=GTTCTTCACACCTGTAGCAT;RSEQ=TTTTCAATTCTGATCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:43:1,42:0,31:31,43:0.5811:1,1:25.3:1:31.9:1:1:0:60:86:0.5811:0:1.8 1/0:86:54:2,52:0,32:32,54:0.6279:1,1:25.5:1:30.5:1:0.52722:0:60:108:0.6353:0:1.8 +17 15962121 . A G 68 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTAATCCCAGCACTTTGG;RSEQ=AGGCCGAGGCAGGTGGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,2:2,4:0.5714:0,0:17.8:1:34:0:1:0:49.8:8:0.6667:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:33:0:32:0:1:0:29:2:1:0:2 +17 15962151 . A G 32 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGTGGATCACCTGAGGTC;RSEQ=GGGGTTTGAGACCAGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:14.5:1:32.5:1:1:0:32.5:4:0.6667:0:1.5 1/1:1:1:0,1:0,0:0,1:1:0,0:3:0:30:0:1:0:29:2:1:0:2 +17 15965113 . G A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12639;SOR=Inf;LSEQ=CCATCTGGGGTGCAGAAGCT;RSEQ=CAGCATCCACAAGAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:106,201:307,0:0:2,0:24.8:1:32.5:1:1:0:59.8:152.5:0.9967:0:0.1 0/1:346:4:3,1:118,224:342,4:0.0116:2,2:14.5:1:24:1:0.12489:5.67:60:8:0.0117:0:1 +17 15965152 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49867;SOR=Inf;LSEQ=CCAGGGCATCCGCAGCAGTG;RSEQ=TGTAACGGGAGGCTGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:60,126:186,0:0:2,0:23.3:1:30:1:1:0:59.7:185:1:0:0.2 0/1:188:2:1,1:52,134:186,2:0.0106:2,2:47.5:1:31:1:0.48544:2.56:60:4:0.0109:0:1 +17 15965185 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2135;SOR=Inf;LSEQ=CTGGCAGGCCTTGGCTTATT;RSEQ=AAGGGCCCCCAGCAGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:29,88:117,0:0:2,0:26.2:1:32.2:1:1:0:59.8:38:1:0:0.2 0/1:101:2:1,1:24,75:99,2:0.0198:2,2:26:1:25.5:1:0.43564:3.08:60:4:0.0202:0:1 +17 15965268 . G A 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0013;SOR=Inf;LSEQ=CCATTTGCTGGGAATGTGGT;RSEQ=GGGAGATGGAAGGACAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:47,32:79,0:0:2,0:24.3:1:32.3:1:1:0:60:78:0.9873:0:0.1 0/1:42:6:4,2:25,11:36,6:0.1429:2,2:24:1:28.8:1:1:1.13284:60:12:0.1463:0:1.2 +17 15965366 . TA T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.07031;SOR=Inf;LSEQ=ACTATTGCAGTCACAAATTT;RSEQ=AAATGTATATGCAAGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:243,64:307,0:0:2,0:25.7:1:28.7:1:1:0:59.8:60.4:1:0:0.1 0/1:389:5:2,3:287,97:384,5:0.0129:2,2:12.2:1:26.6:1:0.10973:4.41705:60:10:0.0129:0.0077:0.6 +17 15965696 . AAAAC A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.2355;SOR=0.51062;LSEQ=ATACCTAAATAGAAAAAAGA;RSEQ=AAGATAAGAAACTTGATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:23:0,23:0,17:17,23:0.575:1,1:21.3:1:31.5:1:1:0:60:46:0.5897:0.125:0 0/1:32:13:0,13:1,18:19,13:0.4063:1,1:29.5:1:30.9:1:1:0:60:26:0.4194:0.0938:0.3 +17 15965863 . T G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTTCAATCTTGATTCCA;RSEQ=AAATAAAACAGCACCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:33.5:1:34:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 15967338 . C A 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCACAGTGTACAAGATTA;RSEQ=TAAGATGTGTCCAGAGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:320,82:402,0:0:2,0:24.1:1:32.3:1:1:0:59.9:79.4:0.9975:0:0.1 0/1:488:57:47,10:335,95:430,57:0.1168:2,2:23.3:1:29.8:1:0.49648:1.33:60:114:0.1173:0:1.1 +17 15968143 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.39502;SOR=0.88016;LSEQ=ATGTTGTAAAAATGTAAACA;RSEQ=GATGGTTCTATTAGAGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:389:239:177,62:108,42:150,239:0.6144:2,2:23.8:1:31.6:1:0.72418:1.11:60:118.5:0.6124:0:1.1 1/0:442:258:184,74:132,52:184,258:0.5837:2,2:24.4:1:30.4:1:1:1.02086:60:50.6:0.5803:0:1.1 +17 15968400 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=Inf;LSEQ=ACAGAACCATACATGACTTT;RSEQ=GATTTTGTCTATCTCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:16,134:150,0:0:2,0:23.7:1:31:1:1:0:60:29:1:0:0.1 0/1:163:2:1,1:16,145:161,2:0.0123:2,2:17:1:26:1:0.19829:8.82:60:4:0.0125:0:1 +17 15968549 . A C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91307;LSEQ=CTCAAAGTATGGGCAGATTA;RSEQ=AGAGAGCAAATTTGTAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:11:6,5:1,4:5,11:0.6875:2,2:27.6:1:32.6:1:0.30769:4.36:57.7:22:0.6875:0:1 1/0:6:4:1,3:1,1:2,4:0.6667:2,2:9.8:1:32.3:1:1:2.44949:60:8:0.6667:0:1 +17 15968673 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.194;SOR=0.53973;LSEQ=GGGCTAAAAAGTCTACGGGA;RSEQ=GAAGGATATAGTATTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:37:33,4:15,2:17,37:0.6852:2,2:25:1:30.3:1:1:1.10:59.9:36:0.6792:0:1.1 1/0:39:21:21,0:17,1:18,21:0.5385:1,1:20:1:29.7:1:0.46154:0:60:20:0.5263:0:1 +17 15970682 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAAGTTGAATCAGGTG;RSEQ=GGACTAGACAACTTCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:26.5:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 15973435 . A T 84 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64115;SOR=1.36827;LSEQ=AGGTTTTTTTTTTTTTTTTT;RSEQ=AATGCAATAAAAAGTATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:8:3,5:167,67:234,8:0.0331:2,2:9.8:1:19.5:1:0.05302:4.12601:54:1.667:0.0218:0:2.5 0/1:246:11:6,5:158,71:229,11:0.0447:2,2:21.7:1:24.5:1:0.33148:1.84937:59.1:4.5:0.038:0:2 +17 15973439 . G T 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21216;SOR=0.2426;LSEQ=TTTTTTTTTTTTTTTTAAAT;RSEQ=CAATAAAAAGTATCAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:4:2,2:193,79:272,4:0.0144:2,2:11.5:1:25.3:1:0.58334:2.4341:53:3:0.0119:0:2.5 0/0:284:1:0,1:195,86:281,1:0.0035:2,0:1:0:23:0:0.30851:0:60:2:0.0038:0:1 +17 15973844 . A T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00194;SOR=0.64068;LSEQ=ACTTTATTGGTGTGCCCTAA;RSEQ=GGGAAAGAAACAAACATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:371:225:67,158:47,98:145,225:0.6065:2,2:26.5:1:30.7:1:0.64485:1.1306:60:111.5:0.6093:0:1.1 0/1:451:224:68,156:70,157:227,224:0.4967:2,2:26.2:1:29.7:1:0.91899:1.02281:59.9:223:0.4978:0:1.1 +17 15974579 . GA G 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.45972;SOR=1.49988;LSEQ=CTCCAGCCTGGTCCACAGAG;RSEQ=AAAAAAAAAAAGGTACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:9:9,0:65,0:65,9:0.1216:1,0:22.4:1:32.1:1:1:0:60:18:0.1216:0.0135:0.3 0/1:58:10:10,0:46,1:47,10:0.1724:1,0:24.3:1:31:1:1:0:60:20:0.1754:0.0517:0.5 +17 15975029 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22042;SOR=Inf;LSEQ=TAATGCTGATGGTTGCACAA;RSEQ=AATGCCACGGAACTGTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:31,182:213,0:0:2,0:22.9:1:32.3:1:1:0:60:52.25:1:0:0 0/1:189:2:1,1:27,160:187,2:0.0106:2,2:12:1:28.5:1:0.27502:5.84:60:4:0.0108:0:1 +17 15975034 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.14493;LSEQ=CTGATGGTTGCACAACAATG;RSEQ=CACGGAACTGTGCACTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:0,2:24,173:197,2:0.0101:2,0:26.5:1:32:0:1:0:60:4:0.0102:0:1 0/1:174:2:0,2:21,150:171,2:0.0115:2,0:26:1:30.5:1:1:0:60:4:0.0118:0:1 +17 15976558 . T G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.47484;SOR=0.57408;LSEQ=CATTGTTATGTGCCACTTTA;RSEQ=ATACAGATATAAACTTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:17:17,0:6,0:6,17:0.7391:0,1:21.8:1:34:1:1:0:58.2:34:0.7391:0:1 1/0:13:8:8,0:4,1:5,8:0.6154:2,0:25.5:1:29.6:1:0.38462:0:60:7:0.5833:0:1 +17 15976663 . C T 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64871;LSEQ=GGTGGAAATGACAGAAATTG;RSEQ=ATACAACTTAATTCAACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:2,0:172,12:184,2:0.0108:2,0:21:1:32:0:1:0:60:4:0.0109:0:1 0/0:143:1:0,1:131,11:142,1:0.007:2,0:1:0:23:0:0.08392:0:60:2:0.007:0:1 +17 15976696 . T C 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCAACAATGCAAAATTACTA;RSEQ=ATAAAATAACATGTATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:0:0,0:282,86:368,0:0:2,0:22.8:1:30.6:1:1:0:60:121.667:1:0:0.1 0/1:325:24:18,6:220,81:301,24:0.0738:2,2:22.5:1:31.4:1:1:1.10:60:48:0.0743:0:1.1 +17 15976916 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10571;SOR=Inf;LSEQ=CAAACAAGACTTGCTCAGAC;RSEQ=GAGCACATGGTATACAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:42,220:262,0:0:2,0:23.6:1:30.8:1:1:0:59.9:64.5:1:0:0.1 0/1:236:3:2,1:40,193:233,3:0.0127:2,2:15.7:1:25.7:1:0.08253:9.51:60:6:0.0129:0:1 +17 15976952 . G T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22016;SOR=Inf;LSEQ=AATGTACAGTAAATAGGTTA;RSEQ=TTTCATAGTCTATCTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:8,117:125,0:0:2,0:24.2:1:32.7:1:1:0:59.7:124:1:0:0.2 0/1:111:2:1,1:12,97:109,2:0.018:2,2:7:0:31.5:1:0.22146:7.81:60:4:0.018:0:1.5 +17 15977005 . A T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11722;SOR=0.38666;LSEQ=TAAAACTTGTCTTAACCTAC;RSEQ=ATAAAATATGTGTAGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:27:0,27:0,18:18,27:0.6:1,1:22.1:1:28.2:1:1:0:60:26:0.619:0:1.3 0/1:22:8:0,8:1,13:14,8:0.3636:1,0:21.4:1:27.4:1:1:0:60:16:0.3636:0:1.5 +17 15977043 . C T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77542;LSEQ=GATTCATGAAAATATTTTCA;RSEQ=TCATTCAAATGTGTTTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:0,13:0,10:10,13:0.5652:0,1:22.8:1:30.6:1:1:0:59.7:26:0.5652:0:1.8 1/0:10:5:0,5:0,5:5,5:0.5:0,0:28:1:30.2:1:1:0:60:10:0.5:0:1.8 +17 15977132 . T C 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=AAATTAAGTCCCTTTCTGCA;RSEQ=GAAACTTACACAATAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:16.4:1:30.8:1:1:0:59.2:10:0.625:0:1.4 0/0:1:0:0,0:0,1:1,0:0:0,0:13:0:31:0:1:0:60:2:1:0:0 +17 15978663 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01449;SOR=Inf;LSEQ=CTGCGTTGTTAATTACTTTT;RSEQ=ATCGACTAAGCTGTTATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:34,0:34,0:0:1,0:18:1:32.4:1:1:0:59.8:68:1:0:0 0/1:12:3:2,1:9,0:9,3:0.25:0,2:20.7:1:30.7:1:0.25:0:60:6:0.25:0:1 +17 15983343 . G T 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCTGGTTGGAGTTCCCC;RSEQ=AGTTATACTTCCTTCTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:923:0:0,0:437,485:922,0:0:2,0:26.2:1:30.9:1:1:0:59.9:56.625:0.9989:0:0.2 0/1:1071:59:31,28:488,523:1011,59:0.0551:2,2:26.5:1:27.9:1:0.59247:1.19:60:18.667:0.0529:0:1.1 +17 15983458 . G A 197 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAAACAGCCCCTACTTGGGA;RSEQ=AGTACTCAACTAAGAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:82:10,72:6,113:119,82:0.408:2,2:24.8:1:31:1:0.10896:2.60:60:81:0.4091:0:1.1 0/0:190:0:0,0:17,173:190,0:0:2,0:24.7:1:30.9:1:1:0:60:380:1:0:0 +17 15984054 . CA C 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.97385;LSEQ=GGTGTTCCCTAAGAAAAAAA;RSEQ=AAAAAAAATTTAAAGATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:4:0,4:45,177:222,4:0.0176:2,0:20.3:1:32.8:1:0.58673:0:53.3:8:0.0179:0.0044:0.3 0/1:233:4:1,3:71,158:229,4:0.0172:2,2:29.3:1:31.8:1:1:1.34653:60:8:0.0174:0:0 +17 15984098 . G A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06244;SOR=Inf;LSEQ=AAACATTGTTTTTTTCACAA;RSEQ=GTCAATTTCACAAAGTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:4,75:79,0:0:2,0:24.7:1:30.8:1:1:0:59.7:18.75:1:0:0.2 0/1:92:5:0,5:10,77:87,5:0.0543:2,0:12.8:1:27.8:1:1:0:60:4:0.0449:0:1.2 +17 15989531 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22714;SOR=0;LSEQ=CTGACAAATCAGTGCGAGGA;RSEQ=GGAGGACAAGTTTTAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:156,40:196,2:0.0101:2,2:37:1:31.5:1:0.3721:3.86447:60:4:0.0102:0:1 0/0:218:0:0,0:176,42:218,0:0:2,0:21.5:1:31.2:1:1:0:60:53.5:1:0:0.1 +17 15994864 . T TCTCA 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTCAAGGACAGGACAACAAT;RSEQ=CTCACTCTGAAAATTCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:23:1:31.2:1:1:0:49.7:6:0.5:0.1667:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 15994888 . C T 80 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.37796;LSEQ=ACTCTGAAAATTCAGATGAA;RSEQ=GGAACATAAAGCATAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:9.8:1:31.3:1:1:0:54.8:12:0.75:0:1.2 1/0:2:1:1,0:1,0:1,1:0.5:0,0:16:0:21:0:1:0:60:2:0.5:0:1 +17 15995423 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10378;SOR=0;LSEQ=AACAACCAATGTAATAATTG;RSEQ=CATCTCTTAACAAGTAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:1,2:30,179:209,3:0.0142:2,2:11.3:1:27.3:1:0.37918:2.96:60:2:0.0096:0:1 0/0:238:0:0,0:43,195:238,0:0:2,0:21.6:1:30.3:1:1:0:60:33:1:0:0.1 +17 16001624 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09472;SOR=Inf;LSEQ=TTAAAGAACAGAAGAAATAT;RSEQ=TCTATAAAGGTCTCAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:160,31:191,0:0:2,0:24.9:1:32.5:1:1:0:59.6:190:1:0:0.1 0/1:161:3:3,0:129,29:158,3:0.0186:2,0:21:1:28:1:1:0:60:6:0.0188:0:1 +17 16004259 . A G 60 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCACTGCTGCCCTCCTC;RSEQ=GGCACAACAGTTATCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:22.8:1:30:1:1:0:51:8:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:30:0:32:0:1:0:60:2:1:0:1 +17 16004368 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1972;SOR=0.30168;LSEQ=ATATAGGAGAAATGTATAAT;RSEQ=TGTTTCATTAAAATGATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:14,0:4,0:4,14:0.7778:0,1:15.9:1:32.1:1:1:0:60:28:0.7778:0:1 1/0:8:4:4,0:4,0:4,4:0.5:0,0:17.5:1:28.3:1:1:0:60:8:0.5:0:1 +17 16004487 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51155;SOR=0;LSEQ=ATTTACATAGGAGACATGTC;RSEQ=GCAGCCAGCACCACCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:2,0:139,8:147,2:0.0134:2,0:9:1:33.5:1:1:0:60:4:0.0137:0:1 0/0:107:0:0,0:99,8:107,0:0:2,0:23.7:1:30.4:1:1:0:59.9:52.5:1:0:0.2 +17 16004537 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.97976;LSEQ=CCAACCAGCAGAGTAAGCAC;RSEQ=GGGAGGACTTATGGAACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:23:20,3:234,57:291,23:0.073:2,2:19.4:1:30:1:0.58701:1.62:60:46:0.0742:0:1.3 0/1:335:24:16,8:230,80:310,24:0.0716:2,2:26.5:1:29.7:1:0.47106:1.43583:60:48:0.0723:0:1 +17 16005187 . T C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36917;SOR=1.56084;LSEQ=AGGTGGTGATAGAAACCATG;RSEQ=TTGAAAGTAGTTGTTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:25:0,25:0,16:16,25:0.5952:1,1:21.3:1:33.5:1:1:0:60:24:0.6:0:1 1/0:43:30:4,26:1,12:13,30:0.6977:1,2:16.1:1:32.3:1:1:1.82:60:60:0.6977:0:1 +17 16012022 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61803;SOR=2.073;LSEQ=CTGTTTCCTCAATGAAGCAA;RSEQ=TCCTACACAGTCAAATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:169,20:189,1:0.0053:2,0:1:0:26:0:0.11053:0:60:2:0.0053:0:1 0/1:184:2:1,1:153,29:182,2:0.0109:2,2:11:1:28:1:0.30025:5.20423:60:4:0.0109:0:1 +17 16012296 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50103;SOR=0;LSEQ=AAATTCATTTCTGAAATAAT;RSEQ=TAGAACATTGATAAGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:0,2:2,69:71,2:0.0274:1,0:40:1:31:1:1:0:60:4:0.029:0:1 0/0:60:0:0,0:3,57:60,0:0:2,0:22.8:1:31.4:1:1:0:60:120:1:0:0 +17 16012311 . GCA G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.50204;SOR=0;LSEQ=ATAATGTAGAACATTGATAA;RSEQ=CACACACACACCAGACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:0,48:48,2:0.04:1,0:34.5:1:32.5:1:1:0:60:4:0.0408:0:0 0/0:39:0:0,0:2,37:39,0:0:2,0:25.4:1:32:1:1:0:60:78:1:0:0 +17 16012494 . A T 45 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACCACTATACATGTATAAA;RSEQ=AGCCAAAAATCACATACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:37.3:1:29:1:1:0:60:6:0.4286:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:10:0:29:0:1:0:28:2:1:0:1 +17 16021136 . AAAC A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.12364;SOR=Inf;LSEQ=ATAGAGTGAGACTCCATCTC;RSEQ=AACAACAACAACACTCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:195,50:245,0:0:2,0:23.3:1:30.5:1:1:0:59.8:121.5:0.9959:0:0.1 0/1:253:4:3,1:191,58:249,4:0.0158:2,2:27.3:1:30.1:1:1:1.0973:60:8:0.016:0.004:0 +17 16021611 . A G 52 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTATCTCTCACAGGGCT;RSEQ=GGACAACATTAGACACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:28:1:33:0:1:0:60:6:0.4286:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:39:0:33:0:1:0:60:2:1:0:1 +17 16022637 . A AT 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49913;SOR=0;LSEQ=CTCTTTGCCTTTTTGAAAGA;RSEQ=TTTTTTTTCCAATTAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:128,9:137,2:0.0143:2,2:16.5:1:30.5:1:0.13919:13.545:60:4:0.0144:0.0071:0 0/0:128:0:0,0:124,3:127,0:0:1,0:24.3:1:29.8:1:1:0:59.9:126:0.9921:0:0.1 +17 16024094 . T C 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GCCTCAATATTACACAGCCA;RSEQ=TAAAAAATAAAAATGGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:21:1:32:1:1:0:60:6:0.375:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:38:0:34:0:1:0:60:2:1:0:1 +17 16024701 . C CA 128 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.43487;SOR=0.71843;LSEQ=AAACTACCTAATCTCTCACT;RSEQ=AAAAAAAAAAAATTATCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:20:0,20:0,27:27,20:0.4167:1,1:29.1:1:30.7:1:1:0:59.9:19:0.4043:0:0.5 0/1:65:22:0,22:0,37:37,22:0.3385:1,1:30.5:1:28.8:1:1:0:60:10:0.339:0.0462:0.3 +17 16029445 . C CT 110 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.20142;SOR=0.57831;LSEQ=TTCATCTTTCTTTTCTTCTT;RSEQ=TTTTTTTTCTGTTTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:883:12:3,9:415,454:869,12:0.0136:2,2:21.3:1:30.8:1:0.14957:2.73926:60:24:0.0137:0.0057:0.2 0/0:1392:11:5,6:662,716:1378,11:0.0079:2,2:25.6:1:30.5:1:1:1.1094:60:22:0.008:0.0014:0.1 +17 16029600 . TA T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49818;SOR=Inf;LSEQ=TGTGATAAATTATGTCTATC;RSEQ=AAAAAATTTTAAATGATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:7,120:127,0:0:2,0:23:1:31:1:1:0:60:41.333:1:0:0.1 0/1:131:2:1,1:12,117:129,2:0.0153:2,2:19.5:1:30:1:0.18931:9.41:60:4:0.0155:0.0076:1 +17 16041149 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATGCTAATCTCTGCATC;RSEQ=TTCCAATTTTAGTATTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:5,1:6,2:0.25:2,0:33.5:1:32.5:1:1:0:60:4:0.25:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:19:1:26:0:1:0:60:4:1:0:0 +17 16041306 . C A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03226;LSEQ=TAGTTCTGTGTTCTGTGTTA;RSEQ=GATTTCTCTAATAATTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:44:42,2:23,1:24,44:0.6471:1,1:28.1:1:30.3:1:1:1.0938:60:43:0.6515:0:1.1 1/0:81:53:52,1:27,1:28,53:0.6543:1,1:24.5:1:29.8:1:1:1.91:60:106:0.6625:0:1.1 +17 16041592 . C A 34 p8;q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08044;SOR=0;LSEQ=AACAACTAAAAAAAAAAAAA;RSEQ=TTGGGAAAAGAAAGACTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:3,0:33,164:197,3:0.015:2,0:5.7:1:21.7:1:0.00544:0:60:2:0.0104:0:1.7 0/0:262:0:0,0:53,209:262,0:0:2,0:8:0:14:0:1:0:40:0:0:0:4 +17 16041636 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07536;SOR=0.54054;LSEQ=AGGCTGGGCGTGGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:44:3,41:1,24:25,44:0.6286:1,2:22.4:1:30.2:1:1:1.74:51.2:43:0.6232:0:1.2 0/1:86:41:0,41:1,43:44,41:0.4767:1,1:20.9:1:29.5:1:1:0:52.1:19.5:0.4699:0:1.3 +17 16041777 . C T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=GGGATGGTGGCACATGCCTG;RSEQ=AGTCCCACCTACTCAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:26.8:1:28.4:1:1:0:30.2:10:0.7143:0:2.2 0/0:1:0:0,0:0,1:1,0:0:0,0:13:0:33:0:1:0:60:2:1:0:0 +17 16041792 . A G 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGCAGTCCCACCTACTC;RSEQ=GGAAGCTGAGGCAGGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:17.8:1:31.4:1:1:0:30.2:10:0.7143:0:2.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 16042504 . G GA 88 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.23131;SOR=2.4083;LSEQ=ATTTGTTTCTCATTATTCTG;RSEQ=AAAAAAAATACAATTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:3:0,3:85,264:349,3:0.0085:2,0:14:1:32.3:1:1:0:60:6:0.0087:0.0028:0.7 0/1:394:8:4,4:116,270:386,8:0.0203:2,2:24.9:1:29.5:1:0.25341:2.32:60:16:0.0206:0.0025:0.3 +17 16046845 . A T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.26966;SOR=0.73294;LSEQ=TTCCCACATTTACATACAAA;RSEQ=AAACCCTTAGCTCCTACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:64:56,8:44,1:45,64:0.5872:1,2:19.6:1:30.9:1:0.07808:6.20555:60:128:0.5872:0:1.1 1/0:100:51:48,3:43,6:49,51:0.51:2,2:19.9:1:29.9:1:0.31341:2.22:60:102:0.51:0:1.1 +17 16047062 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50094;SOR=Inf;LSEQ=TAAAGACCTTATATAAAGAC;RSEQ=TATCAATTAAATTAACTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:23,149:172,0:0:2,0:23.3:1:31.2:1:1:0:59.9:85:1:0:0.1 0/1:197:2:0,2:31,163:194,2:0.0102:2,0:23.5:1:33:0:1:0:60:4:0.0103:0:1 +17 16047067 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23592;SOR=0;LSEQ=ACCTTATATAAAGACATATC;RSEQ=ATTAAATTAACTATAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:19,141:160,2:0.0123:2,2:22:1:29.5:1:0.23234:7.26:60:4:0.0126:0:1 0/0:171:0:0,0:21,150:171,0:0:2,0:22.6:1:30.1:1:1:0:60:84.5:1:0:0.1 +17 16047112 . CAAGTT C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=TCTGAATGGAACTTTTTAAC;RSEQ=AAGAGAAGAAACATAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:0,74:74,0:0:1,0:25.6:1:31.3:1:1:0:59.4:73:1:0:0.2 0/1:65:2:0,2:1,62:63,2:0.0308:1,0:18.5:1:33:0:1:0:60:4:0.0317:0:0 +17 16047179 . TTAA T 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.7369;SOR=1.47111;LSEQ=GTAATATGCTGTGTCACCTA;RSEQ=TAACAATTTAAATGTTACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:0,14:0,13:13,14:0.5185:1,1:20.1:1:30.2:1:1:0:60:28:0.5185:0.0741:0 1/0:13:8:1,7:0,5:5,8:0.6154:0,2:34.5:1:30:1:1:0:60:16:0.6154:0:0.1 +17 16049563 . C A 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00372;SOR=0;LSEQ=CTCCACTATTGTCCTATGAC;RSEQ=CTGCCAAATCCCCCTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:9:9,0:51,0:51,9:0.15:1,0:15:1:31.9:1:1:0:46.3:18:0.15:0:1.9 0/0:50:0:0,0:50,0:50,0:0:1,0:15.2:1:31.6:1:1:0:48.8:100:1:0:0.6 +17 16049626 . A T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00192;SOR=0.63837;LSEQ=TACATACTAAAAAAATTTTT;RSEQ=AAAAAAAGAAACAATAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:373:232:177,55:110,31:141,232:0.622:2,2:20.5:1:30.5:1:0.79999:1.10229:57.6:464:0.6253:0:1.1 1/0:453:232:173,59:167,54:221,232:0.5121:2,2:21.9:1:29.3:1:0.82866:1.0546:58.4:115:0.5122:0:1.1 +17 16049641 . TA T 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01289;SOR=0;LSEQ=TTTTTAAAAAAAAGAAACAA;RSEQ=AATATTTGAAGAAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:5:2,3:348,134:482,5:0.0103:2,2:20.2:1:29.4:1:0.13815:3.88273:60:10:0.0104:0.0041:0.6 0/0:673:0:0,0:468,205:673,0:0:2,0:23.4:1:28:1:1:0:59.7:167.25:1:0:0.5 +17 16050057 . C A 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11029;SOR=Inf;LSEQ=ACTAAGATCAACACATAGAG;RSEQ=ACAGGTTGGCTGGATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:11,0:0:0,0:23.3:1:32.5:1:1:0:60:22:1:0:0 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:5:0:30.5:1:0.33333:0:60:4:0.4:0:0 +17 16052381 . C T 51 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AGCTGAACCCTAGCTGACCC;RSEQ=GTTTCTAATAAAAGAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:19.3:1:32.3:1:1:0:57:6:0.75:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:6:0:31:0:1:0:60:2:1:0:0 +17 16056442 . C T 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.4564;SOR=1.95612;LSEQ=GGATTAAATAGCTGCTCAAG;RSEQ=AAAAACAAGCTCAGGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:11,0:6,0:6,11:0.6471:0,0:26.1:1:30.6:1:1:0:60:22:0.6471:0:1 1/0:14:11:11,0:3,0:3,11:0.7857:0,0:11.4:1:29.6:1:1:0:60:22:0.7857:0:1 +17 16056614 . TA T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.50367;SOR=0.81948;LSEQ=GAAAAACTACCACCAAAAAT;RSEQ=AAAAAAAAAATCACTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:30:19,11:273,122:395,30:0.0699:2,2:26.8:1:30.9:1:0.5422:1.29474:60:60:0.0713:0.0023:0.6 0/1:517:30:17,13:332,153:485,30:0.058:2,2:26.5:1:30.7:1:0.22619:1.65764:60:60:0.0587:0.0155:0 +17 16056741 . T C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08536;SOR=0;LSEQ=GACATTGTTGTATCATATAA;RSEQ=TAAAAATTACATTATCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:70,222:292,3:0.0101:2,2:32:1:33:1:0.14866:6.29:60:6:0.0103:0:1 0/0:375:0:0,0:104,269:373,0:0:2,0:23.2:1:29.2:1:1:0:60:92.25:0.9946:0:0.1 +17 16062400 . TA T 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AATTTTCATTAGATAGAGTT;RSEQ=AAAAAAAAAACTAAGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:4,6:0.6:0,0:27.2:1:32:1:1:0:60:12:0.6:0:0.3 1/0:5:3:0,3:0,2:2,3:0.6:0,0:19.3:1:31:1:1:0:60:6:0.6:0:0 +17 16068241 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12877;SOR=Inf;LSEQ=GGAAAACTCAAAAATATCTA;RSEQ=TGTAGGGAGACAAACATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:105,35:140,0:0:2,0:21:1:32.8:1:1:0:29.2:280:1:0:0.1 0/1:168:4:1,3:123,41:164,4:0.0238:2,2:15.5:1:26:1:0.05553:8.85747:26:8:0.024:0:1 +17 16068408 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50066;SOR=Inf;LSEQ=TTGAAGGTGAAGCATTTTGA;RSEQ=CATCTCCACATGGTTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:29,27:56,0:0:2,0:30.1:1:30:1:1:0:21.1:27:1:0:0.1 0/1:68:2:1,1:24,42:66,2:0.0294:2,2:27.5:1:28.5:1:1:1.73:24:4:0.0303:0:1 +17 16068446 . A T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51187;SOR=Inf;LSEQ=CCCGAAATTGGAGAGGATGG;RSEQ=GCTTCATGTTTGCCTCCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:35,54:89,0:0:2,0:23.3:1:31.7:1:1:0:23.7:178:1:0:0.2 0/1:125:2:1,1:55,68:123,2:0.016:2,2:30:0:29:0:1:1.23:20:4:0.0164:0:1 +17 16068463 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05493;SOR=0.25059;LSEQ=TGGAGCTTCATGTTTGCCTC;RSEQ=GAATGCTGGATCCTTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:8:4,4:31,50:81,8:0.0899:2,2:20.4:1:32.3:1:0.70692:1.60:20.5:16:0.0909:0:1.5 0/1:125:3:1,2:55,67:122,3:0.024:2,2:20.7:1:31.7:1:1:1.63555:20:6:0.0244:0:1.3 +17 16097430 . C T 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTCTTTATCTTGGCCCTCAC;RSEQ=CAAGACATGCCAAGTTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:22:1:34:0:1:0:33.3:8:0.8:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:49:0:33:0:1:0:60:2:1:0:0 +17 16097602 . T TAAG 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0.21111;SOR=0.4092;LSEQ=AAATCAGCATAAAGCCACAG;RSEQ=AAGACAGAAATAATTAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:15,1:8,0:8,16:0.6667:0,1:11.6:1:31.3:1:1:0:38.3:32:0.6667:0.2917:0.2 0/1:18:8:8,0:9,1:10,8:0.4444:2,0:15.8:1:30.4:1:1:0:36.9:16:0.4444:0.1111:0.3 +17 16097665 . TA T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.86805;SOR=1.1154;LSEQ=TGTAAATAGCTCTTGCAACT;RSEQ=AAAAAAAAAAAGATAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:22:22,0:88,2:90,22:0.188:1,1:25:1:32.1:1:1:0:54.5:44:0.188:0.0342:0.1 0/1:112:23:22,1:86,2:88,23:0.2054:1,1:20.1:1:30.1:1:0.50528:1.94075:52.2:46:0.2054:0.0625:0.3 +17 16097905 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17293;SOR=Inf;LSEQ=ATCAGTAAAGAAGTCCTCAC;RSEQ=AGACTGTGAGATCAATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:2,31:33,0:0:2,0:8.6:1:31.1:1:1:0:21.1:66:1:0:0.1 0/1:24:2:1,1:0,22:22,2:0.0833:1,2:13:0:31.5:1:0.08333:0:22:4:0.087:0:1 +17 16120448 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50761;SOR=Inf;LSEQ=CGGCGGGAGGGACTTAACAG;RSEQ=GGAACCCAACATTCCCCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:31,22:53,0:0:2,0:25.3:1:30.8:1:1:0:60:52:1:0:0.2 0/1:72:2:1,1:44,26:70,2:0.0278:2,2:17:0:31.5:1:1:1.67936:60:4:0.0282:0:1.5 +17 16120471 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14454;SOR=0;LSEQ=AACCCAACATTCCCCGGTGA;RSEQ=GTTTTCCAGCCGGAGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:33,25:58,2:0.0333:2,2:43:1:32:1:1:1.31382:60:4:0.0345:0:1 0/0:97:0:0,0:56,41:97,0:0:2,0:25.4:1:29.2:1:1:0:60:31.333:1:0:0.1 +17 17069105 . G A 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=GAGGAAAAGCTCAAAGACGT;RSEQ=ACCGTGAGGCTGGAGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:20.5:1:31.5:1:1:0:60:8:0.8:0:1 1/0:4:2:1,1:0,2:2,2:0.5:0,2:11:0:26.5:1:1:0:60:4:0.5:0:1.5 +17 17116952 . C A 163 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=53.56356;LSEQ=CAGCCATCCCTGTCTTTAGG;RSEQ=AGGTGTGTGTGACGGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:1:0,1:320,150:470,1:0.0021:2,0:48:0:15:0:0.32059:0:60:0:0:0:1 0/1:509:52:34,18:287,165:452,52:0.1022:2,2:25.3:1:28.6:1:0.87939:1.09:60:104:0.1042:0:1.2 +17 17118168 . T G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16372;SOR=Inf;LSEQ=TTGCAGTGGCGGACGTGGAG;RSEQ=TGGAACCCCGCCCCCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:63,1:64,0:0:1,0:26.7:1:29.5:1:1:0:60:9.667:1:0:0.2 0/1:44:2:2,0:38,4:42,2:0.0455:2,0:8:1:28:1:1:0:60:4:0.0465:0:1 +17 17118199 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21867;SOR=Inf;LSEQ=CCCCCAACCTCTTCTCTCGG;RSEQ=TCCTCCCTCAGTGGCCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:106,5:111,0:0:1,0:22.8:1:32.2:1:1:0:60:54.5:1:0:0.1 0/1:98:2:1,1:87,9:96,2:0.0204:2,2:22:1:26:1:0.19461:9.22316:60:4:0.0206:0:1 +17 17118442 . T C 227 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=199.46232;LSEQ=GGCAGAGCAAGGGCAGGCGT;RSEQ=AGCGCGGGGCGGGGGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:2:2,0:199,240:439,2:0.0045:2,0:15:1:32.5:1:0.20717:0:60:4:0.0046:0:1.5 0/1:365:174:77,97:85,106:191,174:0.4767:2,2:22.3:1:30.5:1:1:1.01014:60:33.8:0.4801:0:1.2 +17 17118689 . G A 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=0.30619;LSEQ=ATGCTCCTCACCTCCCCTGC;RSEQ=CTAGCCCACCGTGGGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:55:17,38:49,155:204,55:0.2115:2,2:24.9:1:29.7:1:0.30033:1.41:60:54:0.2151:0:1.1 0/1:264:20:7,13:74,170:244,20:0.0758:2,2:21.8:1:28.4:1:0.62447:1.24:60:9:0.0703:0:1.2 +17 17118786 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06701;SOR=Inf;LSEQ=AATGCTTTGGTATTTAAAAC;RSEQ=TTTCAGGTTATTCGTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:0,57:57,0:0:1,0:26.9:1:33.9:1:1:0:59.9:114:1:0:0 0/1:40:3:0,3:2,35:37,3:0.075:2,0:24.7:1:26.7:1:1:0:60:2:0.0513:0:1.3 +17 17119708 . TG T 86 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.33191;SOR=0.47577;LSEQ=ACGCACCTGAGGAGAGCACG;RSEQ=GGGGGGGATCTGCACGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:529:6:3,3:305,218:523,6:0.0113:2,2:27.3:1:33.3:1:0.69784:1.39816:60:12:0.0115:0:0.2 0/0:553:3:1,2:317,232:549,3:0.0054:2,2:22:1:31.7:1:0.57697:2.72782:60:6:0.0055:0:0.3 +17 17119871 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21289;SOR=Inf;LSEQ=CGAGGAAGCCCTCAGCCCCG;RSEQ=CCATCCATGCTCTACTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:16,141:157,0:0:2,0:26.3:1:32.2:1:1:0:60:38.25:1:0:0.1 0/1:135:2:1,1:23,110:133,2:0.0148:2,2:26.5:1:28:1:0.32504:4.70:60:4:0.0152:0:1.5 +17 17119875 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19915;SOR=Inf;LSEQ=GAAGCCCTCAGCCCCGGCCA;RSEQ=CCATGCTCTACTACCCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:14,137:151,0:0:2,0:26:1:30.4:1:1:0:60:150:1:0:0.1 0/1:123:2:1,1:19,102:121,2:0.0163:2,2:21:1:27:1:0.29988:5.26:60:4:0.0171:0:1 +17 17119903 . G A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00439;SOR=Inf;LSEQ=CTACTACCCAAACCCCACAC;RSEQ=CCTCCTGCAGCCCGGTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:4,96:100,0:0:1,0:25.1:1:32.3:1:1:0:60:32.333:1:0:0.2 0/1:53:5:0,5:1,47:48,5:0.0943:1,0:12.6:1:29:1:1:0:60:10:0.1:0:1.2 +17 17120204 . T C 164 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCACACGCATCCTTCTGA;RSEQ=GATTTAAACATCATCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:32,0:0,0:0,32:1:0,1:24.7:1:32.8:1:1:0:60:64:1:0:1 0/1:23:9:9,0:13,0:13,9:0.3913:1,0:25:1:31.3:1:1:0:60:18:0.4091:0:1 +17 17120300 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20959;SOR=Inf;LSEQ=GGTTCTGTGCTGGGCAGTCG;RSEQ=TGCACCTTGGCATCCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:165,30:195,0:0:2,0:20.4:1:31.3:1:1:0:59.8:47.75:0.9948:0:0.1 0/1:166:2:1,1:134,30:164,2:0.012:2,2:11:1:27.5:1:0.33954:4.41041:60:4:0.0121:0:1.5 +17 17120344 . C T 204 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCCAGGCACCAGGCCAATA;RSEQ=TGCCCTGCGCCGCACACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:241,166:407,0:0:2,0:26.1:1:32.4:1:1:0:59.9:66.833:1:0:0.2 0/1:433:121:76,45:182,130:312,121:0.2794:2,2:23.5:1:29.6:1:0.44522:1.21:60:120:0.2797:0:1.4 +17 17120352 . C T 170 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.85493;LSEQ=ACCAGGCCAATACTGCCCTG;RSEQ=GCCGCACACCTAAGGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:4:2,2:262,184:446,4:0.0089:2,2:28.8:1:31.3:1:1:1.42275:60:8:0.0091:0:1 0/1:506:56:34,22:260,190:450,56:0.1107:2,2:22.6:1:29.3:1:0.77427:1.13:59.9:112:0.1116:0:1.9 +17 17120353 . G A 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGGCCAATACTGCCCTGC;RSEQ=CCGCACACCTAAGGAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:267,189:456,0:0:2,0:26.8:1:30.6:1:1:0:59.9:37:1:0:0.2 0/1:509:34:20,14:273,202:475,34:0.0668:2,2:21.4:1:29.7:1:1:1.06:60:68:0.0675:0:1.3 +17 17120467 . C T 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31293;SOR=2.77497;LSEQ=CCCATGAGAACGTGCCAGGC;RSEQ=AGCATGCGGAAAGAAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:2:0,2:219,291:510,2:0.0039:2,0:10:1:27.5:1:0.50949:0:60:4:0.0039:0:1 0/1:651:7:3,4:286,357:643,7:0.0108:2,2:27:1:25.4:1:1:1.06807:60:6:0.0094:0:1.1 +17 17120550 . T C 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08096;SOR=0;LSEQ=TAGTAGAAATGGTTTTTCTC;RSEQ=CCCTTCCCATGAAGTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:1,2:18,118:136,3:0.0216:2,2:28.7:1:23.7:1:0.3588:3.24:60:2:0.0147:0:1.3 0/0:181:0:0,0:30,151:181,0:0:2,0:22.4:1:28.9:1:1:0:60:59.333:1:0:0.1 +17 17120668 . G C 141 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.01299;SOR=0;LSEQ=GGCCCAGGGTTAAAGGGGCA;RSEQ=AGAGAGAAGTTCCAGGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:0,19:1:0,1:26.2:1:33.2:1:1:0:57.9:38:1:0:1.5 0/1:3:1:0,1:0,1:1,1:0.3333:0,0:39:0:28:0:1:0:60:2:0.5:0:1 +17 17122223 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20042;SOR=Inf;LSEQ=CGAGGAGGCTGTCAGTCACT;RSEQ=CCTGCAGGGTTTTGAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:64,1:65,0:0:1,0:21.3:1:31.3:1:1:0:59.6:64:1:0:0.9 0/1:54:2:1,1:47,5:52,2:0.037:2,2:24.5:1:29:1:0.21174:8.67357:60:4:0.037:0:1.5 +17 17122261 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49945;SOR=0;LSEQ=GTGGAGGGTCCAGAGGCAAG;RSEQ=CGTGTGGGCAGGGACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:2,0:128,19:147,2:0.0134:2,0:33:1:28:1:1:0:60:4:0.014:0:4.5 0/0:135:0:0,0:102,33:135,0:0:2,0:21.2:1:30.2:1:1:0:60:26:1:0:1.1 +17 17122262 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5002;SOR=0;LSEQ=TGGAGGGTCCAGAGGCAAGG;RSEQ=GTGTGGGCAGGGACAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:133,19:152,2:0.013:2,2:25.5:1:30:1:0.24361:6.84793:60:4:0.0133:0:1.5 0/0:136:0:0,0:100,36:136,0:0:2,0:21.5:1:30.3:1:1:0:60:33:1:0:1.1 +17 17122274 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21123;SOR=Inf;LSEQ=AGGCAAGGCGTGTGGGCAGG;RSEQ=ACAGCCCATGACTGGCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:166,37:203,0:0:2,0:22.8:1:31.3:1:1:0:60:32.833:1:0:1.4 0/1:174:2:1,1:121,49:170,2:0.0115:2,2:19.5:1:28:1:0.4981:2.45466:60:4:0.0117:0:2 +17 17122279 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.216;SOR=Inf;LSEQ=AGGCGTGTGGGCAGGGACAG;RSEQ=CCATGACTGGCTCTCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:176,48:224,0:0:2,0:23.1:1:32:1:1:0:60:43.8:1:0:1.5 0/1:195:2:0,2:136,57:193,2:0.0103:2,0:19:1:27.5:1:0.09046:0:60:4:0.0104:0:2.5 +17 17122286 . C T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAGGGACAGCCCATGA;RSEQ=TGGCTCTCCTCCTGAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:248:248:187,61:0,0:0,248:1:0,2:24:1:31:1:1:0:60:81.667:1:0:1.5 1/1:233:233:165,68:0,0:0,233:1:0,2:22.9:1:29.8:1:1:0:60:232:1:0:1.3 +17 17122327 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18405;LSEQ=TGATGCGCTGTGCCCCTGCC;RSEQ=CCTACCTGCCTCATGTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:428:237:170,67:127,64:191,237:0.5537:2,2:25:1:30.1:1:0.24793:1.28:60:58.25:0.5534:0:1.5 0/1:431:80:52,28:233,117:350,80:0.1856:2,2:24.1:1:28.8:1:0.7943:1.07214:60:79:0.1863:0:1.7 +17 17122536 . T C 158 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=37.46202;LSEQ=TTCTAAATCTGCAAGACAGA;RSEQ=GACAAGGACAGTTACAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:584:1:0,1:184,398:582,1:0.0017:2,0:43:0:7:0:1:0:60:0:0:0:1 0/1:645:39:13,26:220,384:604,39:0.0605:2,2:22.9:1:29.9:1:0.73489:1.14563:60:38:0.0597:0:1.3 +17 17124556 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.172;SOR=Inf;LSEQ=GCACTTGGCTATCACAAAAT;RSEQ=GGGACGAGAAGCCTTTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:137,2:139,0:0:1,0:28:1:32.1:1:1:0:60:45.333:1:0:0.1 0/1:99:2:1,1:95,2:97,2:0.0202:1,2:38.5:1:28.5:1:0.05999:38.96618:60:4:0.0213:0:1 +17 17124625 . C T 206 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=230.09648;LSEQ=TGTGAATTTTCCCCACCTAG;RSEQ=TGGGGAACAGATTCTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:1:0,1:296,133:429,1:0.0023:2,0:1:0:26:0:0.31163:0:60:2:0.0024:0:1 0/1:420:147:103,44:182,91:273,147:0.35:2,2:23.5:1:28.7:1:0.51205:1.17:60:72.5:0.3502:0:1.1 +17 17124815 . C T 187 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=89.11608;LSEQ=GGTACCGCCCCACGGCCATC;RSEQ=GGGCCAAGGCCCCGGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:678:1:0,1:310,367:677,1:0.0015:2,0:1:0:27:0:1:0:60:2:0.0015:0:1 0/1:721:84:40,44:310,326:636,84:0.1165:2,2:24.4:1:29.4:1:0.90769:1.04596:60:41:0.115:0:1.1 +17 17125000 . G A 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59936;SOR=0.43279;LSEQ=AAGGAAAAAGCAAACCTGAC;RSEQ=CTCACCCAGCCCCTGATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:13,113:126,2:0.0156:2,2:22.5:1:27.5:1:0.20755:8.41:60:4:0.0161:0:1 0/0:147:1:0,1:8,138:146,1:0.0068:2,0:40:0:31:0:1:0:60:2:0.0068:0:1 +17 17125595 . A G 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00179;SOR=0;LSEQ=CAGGAAGAAGTGAGTTCCAC;RSEQ=TCAATATGTTTTCAGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1:0,1:23.3:1:30.1:1:1:0:57.5:26:1:0:1.1 0/0:3:0:0,0:3,0:3,0:0:0,0:19.3:1:30.7:1:1:0:60:6:1:0:0 +17 17125702 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08306;SOR=Inf;LSEQ=AGGCCAGTGCTCCTCACAGA;RSEQ=GCAGCAAGCAAACACGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:61,1:62,0:0:1,0:25.6:1:33.1:1:1:0:60:124:1:0:0.1 0/1:49:3:3,0:45,1:46,3:0.0612:1,0:38.7:1:28.7:1:1:0:60:6:0.0638:0:1 +17 17125752 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18757;SOR=0;LSEQ=CTCCCAAATCCATGGACAAG;RSEQ=CAACCAATGTATCGTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:119,30:149,2:0.0132:2,2:34.5:1:30:1:0.36954:3.91853:60:4:0.0135:0:1 0/0:197:0:0,0:159,38:197,0:0:2,0:21.9:1:31.2:1:1:0:60:64.667:1:0:0.1 +17 17125760 . T C 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07731;SOR=Inf;LSEQ=TCCATGGACAAGCCAACCAA;RSEQ=GTATCGTGACTGCTCTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:137,35:172,0:0:2,0:23.6:1:31.2:1:1:0:59.6:56.333:1:0:0.1 0/1:238:5:4,1:177,55:232,5:0.021:2,2:27.4:1:32:1:1:1.24:60:10:0.0214:0:1 +17 17125998 . G A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=0;LSEQ=GAAATGCAAAGGGAAGGGAT;RSEQ=GCCTCTTTAAGCCAAAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:75,196:271,3:0.0109:2,2:20:1:22.3:1:0.19156:5.19:60:2:0.0074:0:1 0/0:264:0:0,0:81,182:263,0:0:2,0:24.7:1:30.2:1:1:0:60:51.6:0.9961:0:0.2 +17 17126002 . T A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62352;SOR=3.01805;LSEQ=TGCAAAGGGAAGGGATGGCC;RSEQ=CTTTAAGCCAAAGCTGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:66,187:253,1:0.0039:2,0:1:0:30:0:0.26378:0:60:2:0.004:0:1 0/1:254:3:2,1:76,175:251,3:0.0118:2,2:17:1:27.7:1:0.22401:4.57:60:6:0.012:0:1.3 +17 17126041 . G A 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00533;SOR=Inf;LSEQ=AGCAGCTCGGACCCCTACTC;RSEQ=TTCACAGCCAACTCCAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:23,96:119,0:0:2,0:23.8:1:31.9:1:1:0:60:58.5:1:0:0 0/1:110:7:1,6:12,91:103,7:0.0636:2,2:18.4:1:30.1:1:1:1.26:60:14:0.0648:0:1 +17 17126736 . T TCTGC 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CATTTTCATATGGCTGCCGC;RSEQ=CTGCCTGCCAGGACGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:32.3:1:30.5:1:1:0:52.5:8:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 17126792 . C T 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTCCTGCAATGCACACA;RSEQ=CATGAGTAAGAAACAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:28.8:1:26.5:1:1:0:60:3:1:0:2.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 17127077 . G A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53816;SOR=0;LSEQ=TGGCCTGGGAGGCTCCTCAC;RSEQ=ACCTCCAGCTCTGAAGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:3,0:23,1:24,3:0.1111:1,0:37.7:1:31:1:1:0:60:6:0.1111:0:1 0/0:13:0:0,0:12,1:13,0:0:1,0:22.4:1:29.7:1:1:0:60:26:1:0:0.4 +17 17127100 . G C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14329;SOR=Inf;LSEQ=CTCCAGCTCTGAAGCCAAGA;RSEQ=ACTACAATTCACACAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:31,1:32,0:0:1,0:28:1:33.3:1:1:0:60:64:1:0:0.2 0/1:20:2:2,0:17,1:18,2:0.1:1,0:49:0:30:0:1:0:60:4:0.1:0:2.5 +17 17127155 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21741;SOR=Inf;LSEQ=AGGGGAAGACGCCACGCGGT;RSEQ=TCCAGGCCTCAACCTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:83,8:91,0:0:2,0:22.3:1:32.2:1:1:0:60:29.333:1:0:0.1 0/1:80:2:1,1:68,10:78,2:0.025:2,2:6.5:1:28:1:0.25759:6.53105:60:4:0.0253:0:1 +17 17127173 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.20154;SOR=Inf;LSEQ=GTCTCCAGGCCTCAACCTCA;RSEQ=CACAGAGCGGCTCATGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:118,25:143,0:0:2,0:23.2:1:33:1:1:0:60:34.75:1:0:0.1 0/1:117:2:1,1:91,24:115,2:0.0171:2,2:12.5:1:28.5:1:0.38314:3.73555:60:4:0.0171:0:1 +17 17127190 . C T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1943;SOR=Inf;LSEQ=TCAGCACAGAGCGGCTCATG;RSEQ=AGTGCAGGGCCCCCTGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:144,52:196,0:0:2,0:24.9:1:32.4:1:1:0:60:195:1:0:0.1 0/1:155:2:0,2:107,46:153,2:0.0129:2,0:14:1:24:1:0.09451:0:60:4:0.013:0:1 +17 17127199 . GC G 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.85336;LSEQ=AGCGGCTCATGCAGTGCAGG;RSEQ=CCCCTGCCGCCCCGGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:162,76:238,3:0.0124:2,2:16.7:1:32:1:1:1.0655:60:6:0.0126:0.0083:0.3 0/1:188:2:1,1:118,67:185,2:0.0106:2,2:24:1:29:1:1:1.7555:60:4:0.0109:0.0053:0.5 +17 17127471 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29555;LSEQ=GGCAGACCTGGAGGGACACC;RSEQ=GCGACTCAGACAGCCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:308:174:51,123:39,95:134,174:0.5649:2,2:26.2:1:31.3:1:1:1.01:60:57:0.5662:0:1.1 0/1:325:90:37,53:81,154:235,90:0.2769:2,2:24.4:1:29.4:1:0.30273:1.33:60:44:0.2759:0:1.2 +17 17127863 . A C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTCTTTCTTTCTTTCTTT;RSEQ=TTTGAGATGGAGTCTCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:33:0:1:0:60:4:1:0:1.5 +17 17129431 . A G 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCTGGCTCCGAGCCCACCC;RSEQ=GAGCACCTGGGAGCATGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:192,212:404,0:0:2,0:23.3:1:31:1:1:0:60:43.889:1:0:0.1 0/1:392:67:27,40:152,173:325,67:0.1709:2,2:20.5:1:29.3:1:0.34901:1.30078:60:66:0.171:0:1.2 +17 17131018 . T G 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGGCAATAAGAGCAAAAC;RSEQ=CTGTCTCAAAAAAAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:59,0:0:1,0:20.8:1:31.7:1:1:0:58:18.667:1:0:0.2 0/1:32:12:12,0:20,0:20,12:0.375:1,0:18.7:1:27.1:1:1:0:57.5:11:0.3548:0:1.1 +17 17131025 . CA C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.54878;SOR=0;LSEQ=ATAAGAGCAAAACTCTGTCT;RSEQ=AAAAAAACAAAACAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:3:3,0:60,1:61,3:0.0469:1,0:33:1:32.3:1:1:0:60:6:0.0484:0:0.7 0/0:33:0:0,0:33,0:33,0:0:1,0:21:1:29.9:1:1:0:59.5:66:1:0:0.5 +17 17131095 . G C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18173;SOR=Inf;LSEQ=AAGAACTGAAGGGCCCCTGA;RSEQ=AAGCAGTCTGTGTCACCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:207,9:216,0:0:1,0:25.5:1:32.7:1:1:0:59.7:29.857:1:0:0.2 0/1:161:2:1,1:150,9:159,2:0.0124:2,2:7.5:1:29.5:1:0.12073:15.85687:60:4:0.0125:0:1.5 +17 17131402 . C T 76 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.28784;SOR=2.92609;LSEQ=CCTCCGTGCAGAAGAGAGTG;RSEQ=GGGGGCCGTGGAGCTCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:2:2,0:210,362:572,2:0.0035:2,0:27:1:32:0:0.136:0:60:4:0.0035:0:1 0/1:592:6:3,3:227,359:586,6:0.0101:2,2:27.3:1:29.5:1:0.68204:1.58:60:12:0.0103:0:1 +17 17131869 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCCTCCACCCAATACATA;RSEQ=CTGCTTGGCACCTGCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:20.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 18215858 . G A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=CTGGTGGGACAAATTACAAC;RSEQ=ACATATGAGATCTGCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:4,0:4,1:0.2:0,0:40:0:31:0:1:0:60:2:0.2:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:15:0:31:0:1:0:60:4:0.4:0:1 +17 18216013 . C A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00662;SOR=2.05869;LSEQ=TGTACATAAAAATAAAAATT;RSEQ=TCTTTCCAAGAAAAGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:33:21,12:59,27:86,33:0.2773:2,2:18.3:1:28.6:1:0.66477:1.24628:60:66:0.2797:0:1 0/1:138:61:43,18:55,22:77,61:0.442:2,2:23.2:1:28:1:1:1.0462:60:122:0.4586:0:1.1 +17 18216100 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19452;SOR=1.51615;LSEQ=AACACAAAGGAAAAGAGGAC;RSEQ=AGGCATCTGATGTATGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:22:7,15:53,88:141,22:0.135:2,2:27.4:1:30.6:1:0.64416:1.28862:60:21:0.1296:0:1 0/1:188:36:13,23:58,94:152,36:0.1915:2,2:23.1:1:29.5:1:0.85106:1.09118:59.7:72:0.1935:0:1.1 +17 18216155 . G A 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50548;SOR=Inf;LSEQ=AAACATGGAGTTCGAGCTGG;RSEQ=CACGGTGGCTCACGCCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:4,37:41,0:0:2,0:21.1:1:32.6:1:1:0:60:82:1:0:0.1 0/1:55:2:1,1:4,49:53,2:0.0364:2,2:5:0:26.5:1:0.17508:11.07:60:4:0.037:0:1 +17 18216574 . A G 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20322;SOR=0;LSEQ=TTACATGGCAGAACTGGAAA;RSEQ=GTCTATGTTACCCAGCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:45,52:97,2:0.0202:2,2:26:0:30.5:1:1:1.15:60:4:0.0206:0:1 0/0:120:0:0,0:62,58:120,0:0:2,0:32.6:1:29.7:1:1:0:60:240:1:0:0.2 +17 18216745 . C A 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13193;SOR=0.15632;LSEQ=AGTCAAAGAGAAAGGGTTCA;RSEQ=CTGAAGTGCCAGCCTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:15.4:1:30:1:1:0:60:10:0.7143:0:1 0/1:8:2:0,2:0,6:6,2:0.25:0,0:35:1:31:1:1:0:60:4:0.25:0:1 +17 18575675 . T G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=0.32011;LSEQ=CTTGAAGTAGGGCACGCAAC;RSEQ=CACCATCCACTCGTAGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:32:25,7:63,45:108,32:0.2286:2,2:18.4:1:29.1:1:0.05984:2.54:42.5:31:0.2279:0:1 0/1:220:19:17,2:103,98:201,19:0.0864:2,2:19.7:1:27.8:1:0.00125:8.03:39.5:38:0.0905:0:1.1 +17 18575703 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53488;SOR=Inf;LSEQ=CACTCGTAGATCTGGGACAG;RSEQ=GTGAGCCGTCTGTCCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:51,46:97,0:0:2,0:26.1:1:30.3:1:1:0:49:47.5:1:0:0.2 0/1:169:2:1,1:79,88:167,2:0.0118:2,2:20.5:1:32:0:1:1.11:26:4:0.0123:0:1 +17 18575706 . G A 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12299;SOR=0;LSEQ=TCGTAGATCTGGGACAGAGT;RSEQ=AGCCGTCTGTCCGGGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:2,0:45,41:86,2:0.0227:2,0:18:1:24.5:1:0.4966:0:41:4:0.023:0:1 0/0:162:0:0,0:76,86:162,0:0:2,0:28.4:1:30.6:1:1:0:52.2:53:1:0:0.2 +17 19284152 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50444;SOR=0;LSEQ=GCTCGTGGCCTGTGCACCTC;RSEQ=CCCGCTGAACATCAGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:45,28:73,2:0.0267:2,2:29.5:1:32:0:1:1.59658:60:4:0.027:0:1 0/0:58:0:0,0:40,17:57,0:0:2,0:24.7:1:30.2:1:1:0:60:114:1:0:0.1 +17 19284156 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19509;SOR=Inf;LSEQ=GTGGCCTGTGCACCTCGCCC;RSEQ=CTGAACATCAGTACTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:48,31:79,0:0:2,0:25:1:31:1:1:0:60:158:1:0:0.1 0/1:63:2:1,1:41,20:61,2:0.0317:2,2:42:1:29.5:1:1:2.0249:60:4:0.0323:0:1 +17 19284257 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49697;SOR=Inf;LSEQ=TATACACAGGCTATTGACCT;RSEQ=TGGTCTGTGGGCTGCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:14,40:54,0:0:2,0:23.9:1:32.3:1:1:0:60:53:1:0:0.1 0/1:60:2:1,1:19,39:58,2:0.0333:2,2:33.5:1:27.5:1:1:2.03:60:4:0.0333:0:1 +17 19301452 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21256;SOR=Inf;LSEQ=AGCCTAGGAGAGTCGCCACT;RSEQ=TCCTCAGTCCTGATGTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:25,20:45,0:0:2,0:24.5:1:31.6:1:1:0:60:21.5:1:0:0.2 0/1:39:2:1,1:20,17:37,2:0.0513:2,2:27.5:1:32.5:1:1:1.17156:60:4:0.0513:0:1 +17 19301475 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.49568;SOR=0;LSEQ=CTCAGTCCTGATGTCCCTGG;RSEQ=CCGCCTGCCTTCTTTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:20,21:41,2:0.0465:2,2:39:1:29:1:1:1.05:60:4:0.0465:0:1 0/0:38:0:0,0:18,20:38,0:0:2,0:30.8:1:30.4:1:1:0:60:37:1:0:0.2 +17 21407795 . G T 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69057;SOR=0.52952;LSEQ=AAATCTCAATCCTCAGGCAG;RSEQ=GTCTGAAATAATCACAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:13,0:13,5:0.2778:1,0:26.6:1:31.6:1:1:0:58.2:10:0.2778:0:2.2 0/1:18:3:3,0:15,0:15,3:0.1667:1,0:31.3:1:31.3:1:1:0:55.3:6:0.1765:0:2.3 +17 21407854 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.04229;LSEQ=AGAAAACCCACCTTTCGGCC;RSEQ=GAACCGCCATCTTCCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:7,4:17,9:26,11:0.2973:2,2:29.6:1:30.5:1:1:1.07713:47.5:22:0.3143:0:2.4 0/1:49:15:9,6:19,15:34,15:0.3061:2,2:31.8:1:30.3:1:1:1.18:49.3:30:0.3061:0:2.2 +17 21407858 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.00264;LSEQ=AACCCACCTTTCGGCCGGAA;RSEQ=CGCCATCTTCCAGTAATTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:11:7,4:16,9:25,11:0.3056:2,2:30.5:1:30.3:1:1:1.01543:47.5:22:0.3056:0:2.4 0/1:49:15:9,6:19,15:34,15:0.3061:2,2:31.8:1:30.1:1:1:1.18:49.3:30:0.3125:0:2.2 +17 21407860 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50588;SOR=Inf;LSEQ=CCCACCTTTCGGCCGGAACC;RSEQ=CCATCTTCCAGTAATTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:23,13:36,0:0:2,0:34.4:1:30.1:1:1:0:52.1:35:1:0:0.8 0/1:49:2:1,1:27,20:47,2:0.0408:2,2:28:1:27:1:1:1.34163:60:4:0.0426:0:1 +17 21490090 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=5.16229;LSEQ=TTAAGAGCTTTGGAATGTAA;RSEQ=GAACCAATGTGGCATGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:16:14,2:33,18:51,16:0.2388:2,2:23.6:1:31.1:1:0.11914:3.75:55.5:32:0.2388:0:1.5 1/0:45:28:22,6:13,4:17,28:0.6222:2,2:25:1:29.7:1:1:1.13:52.9:56:0.6222:0:1.6 +17 21490163 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17192;SOR=Inf;LSEQ=GATGATAAACTTAATAAATG;RSEQ=TTGAATTTCGGAAGATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:82,50:132,0:0:2,0:26.4:1:32.3:1:1:0:43.2:131:1:0:0.5 0/1:94:2:1,1:63,29:92,2:0.0213:2,2:25.5:1:29:1:0.53878:2.15283:56:4:0.0217:0:1 +17 21490164 . T A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=3.31058;LSEQ=ATGATAAACTTAATAAATGC;RSEQ=TGAATTTCGGAAGATAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:29:22,7:60,43:103,29:0.2197:2,2:35:1:30.4:1:0.12826:2.24:33.7:58:0.2231:0:2.1 0/1:93:45:32,13:31,17:48,45:0.4839:2,2:34.6:1:29.7:1:0.51575:1.35:37.6:90:0.4891:0:2.1 +17 21490189 . G C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-04;SOR=3.1705;LSEQ=TTTCGGAAGATAATTTACAT;RSEQ=TCTCAGGATCAGTTACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:23:17,6:48,38:86,23:0.211:2,2:21.2:1:31.3:1:0.15265:2.23:28.7:46:0.215:0:2.1 0/1:76:35:25,10:25,16:41,35:0.4605:2,2:15.6:1:30:1:0.46731:1.59:32.6:70:0.4667:0:2.2 +17 21535775 . C T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53767;SOR=0;LSEQ=TTAAATATAAAAAGAAATGA;RSEQ=GCATTAATGTTTTCAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:4,0:11,1:12,4:0.25:2,0:20.8:1:28.5:1:1:0:23.3:8:0.25:0:1.3 0/0:4:0:0,0:4,0:4,0:0:0,0:37.5:1:32:1:1:0:22:8:1:0:0 +17 21536064 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14094;SOR=Inf;LSEQ=CATTCAGCACAGAACAAAGT;RSEQ=ATTATCCTCCTCACTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:28,61:89,0:0:2,0:21.7:1:30.9:1:1:0:24.2:88:1:0:0.1 0/1:54:2:1,1:15,37:52,2:0.037:2,2:8.5:1:26:1:0.50874:2.42:27.5:4:0.0385:0:1 +17 21536168 . G A 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15509;SOR=4.98148;LSEQ=TGTTTTTTGTGTTTTTCTTT;RSEQ=CTTTTCCTATTTAATACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:1:1,0:35,142:177,1:0.0056:2,0:30:0:30:0:0.20225:0:21:2:0.0058:0:1 0/1:109:3:1,2:26,79:105,3:0.0275:2,2:10.3:1:31:0:1:1.51:20.3:6:0.0278:0:2.7 +17 21536187 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.11939;SOR=Inf;LSEQ=TGCTTTTCCTATTTAATACA;RSEQ=ATGTTGGTAGAAACCACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:25,118:143,0:0:2,0:22.4:1:32:1:1:0:31.3:70.5:1:0:0.3 0/1:76:2:1,1:19,55:74,2:0.0263:2,2:31.5:1:29.5:1:0.45965:2.85:46.5:4:0.0274:0:2 +17 21536212 . A G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08463;SOR=2.13405;LSEQ=TGGTAGAAACCACCAAATTT;RSEQ=CCTTTTTTTTTAAGTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:16:1,15:8,63:71,16:0.1839:2,1:40.3:1:32.4:1:1:1.89282:21:32:0.1882:0:2.1 0/1:46:15:3,12:3,27:30,15:0.3261:2,2:39:1:30.9:1:0.38428:2.21:21.8:30:0.3409:0:2.3 +17 21536250 . G A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16135;SOR=1.98087;LSEQ=CAAGAGCTATTTACAAAGAC;RSEQ=AGGAACCAAAGGTTGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:1,15:1,27:28,16:0.3636:1,1:22.8:1:32.8:1:1:1.77:21:32:0.381:0:2.1 1/0:30:16:3,13:1,13:14,16:0.5333:1,2:15.3:1:30.5:1:0.60153:2.90:21.9:32:0.5333:0:2.4 +17 21544395 . T C 38 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24476;SOR=5.98921;LSEQ=TGAGAAATAAATTGTTTTTC;RSEQ=TGGTTTTATTCTCTAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:4,3:7,1:0.125:2,0:43:0:30:0:1:0:20:2:0.1429:0:1 1/0:6:3:3,0:3,0:3,3:0.5:0,0:42.7:1:24.3:1:1:0:20.3:2:0.4:0:1.3 +17 21544414 . G T 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30344;SOR=0.52939;LSEQ=CTTGGTTTTATTCTCTAAAG;RSEQ=ATCCAACATTTGGAGGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:21:14,7:6,5:11,21:0.6563:2,2:3.7:1:27.4:1:0.7026:1.64:20.8:42:0.6563:0:1 1/0:30:15:8,7:13,2:15,15:0.5:2,2:6.3:1:26.7:1:0.10865:5.35313:20.5:30:0.5:0:1.1 +17 21544462 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04261;SOR=Inf;LSEQ=CTCCATCCTCTCCAATTTCG;RSEQ=GGCAACCATGTGGAGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:25,14:39,0:0:2,0:41.4:1:31:1:1:0:26.2:38:1:0:0.7 0/1:34:4:2,2:20,10:30,4:0.1176:2,2:9.8:1:30.5:1:0.60152:1.95703:22:8:0.1212:0:1.8 +17 21544570 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05584;SOR=Inf;LSEQ=AAATTGCAAAAGTAGAACAG;RSEQ=AGATCCTTAAACTGAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:119,205:324,0:0:2,0:29.4:1:32.3:1:1:0:35.5:161:1:0:0.9 0/1:308:4:2,2:126,178:304,4:0.013:2,2:39.5:1:29.8:1:1:1.41:50.3:8:0.0132:0:2 +17 21544587 . A G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.43387;SOR=0.87833;LSEQ=CAGCAGATCCTTAAACTGAA;RSEQ=AAGAAACAAGTAAAAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:141:52,89:69,141:210,141:0.4017:2,2:34.5:1:32.7:1:0.49209:1.19:32.3:140:0.4011:0:1.4 0/1:337:125:46,79:83,129:212,125:0.3709:2,2:33.6:1:31.3:1:0.72815:1.10466:32.7:250:0.3731:0:1.4 +17 21544599 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.09779;LSEQ=AAACTGAAAAAGAAACAAGT;RSEQ=AAAGTCTTTGCTTATAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:115:31,84:84,156:240,115:0.3239:2,2:33.1:1:32:1:0.1465:1.45753:39.5:37.333:0.3191:0:1 0/1:336:15:6,9:116,205:321,15:0.0446:2,2:31.3:1:30.7:1:0.7875:1.18:39.6:30:0.0453:0:1.1 +17 21544646 . T C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54247;SOR=0.84605;LSEQ=AATGTGTGTTTTTCTCCCTA;RSEQ=AGAAGATATTTTTGAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:54:10,44:22,107:129,54:0.2951:2,2:16.9:1:32.4:1:0.83267:1.10:29.9:53:0.2928:0:2.1 0/1:153:40:13,27:27,86:113,40:0.2614:2,2:19.3:1:31.4:1:0.30094:1.53:30:39:0.2583:0:2.1 +17 21544674 . T A 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.43615;SOR=0.70622;LSEQ=ATTTTTGAGTTTTCCATATT;RSEQ=TGAAACTGTACATAAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:21:2,19:2,72:74,21:0.2211:1,2:17.1:1:31.4:1:0.21096:3.72:29:42:0.2258:0:1.8 0/1:72:12:0,12:3,57:60,12:0.1667:2,0:17.6:1:31.8:1:1:0:25.2:24:0.1667:0:2.2 +17 21809347 . G T 42 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.83796;LSEQ=TATGAAGTAACTGATCCTGA;RSEQ=AGATGTAAATTATCTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:152,137:289,3:0.0103:2,2:10:1:27:1:0.60645:2.21312:49.3:6:0.0104:0:2 0/0:232:2:1,1:123,107:230,2:0.0086:2,2:24.5:1:27.5:1:1:1.14884:49:4:0.0087:0:1 +17 21809394 . A T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01389;LSEQ=TGCATTTATGAAGTTTATCA;RSEQ=CTGAGTTTTCTGACACTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:371:370:172,198:0,1:1,370:0.9973:0,2:27.2:1:30.4:1:1:0:51.4:60.667:0.9973:0:1.2 1/1:318:266:127,139:27,25:52,266:0.8365:2,2:25:1:29:1:0.64979:1.18142:52.4:52.2:0.8365:0:1.2 +17 21809479 . A G 221 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07531;LSEQ=AAGCTCTTGAAGAACATTGA;RSEQ=AGAAACCAATGGCCTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:125:20,105:1,5:6,125:0.9542:2,2:25.8:1:31.8:1:1:1.04961:54.3:19.833:0.952:0:1.3 1/0:138:84:21,63:15,39:54,84:0.6087:2,2:21.6:1:30.6:1:0.84279:1.15264:57.3:83:0.6103:0:1.4 +17 22260014 . C T 55 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAGAAACTACTTTGTGA;RSEQ=GATTGCATTCAAGTCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:11.3:1:32.7:1:1:0:23.3:6:1:0:5 1/1:4:4:1,3:0,0:0,4:1:0,2:7.5:1:27.8:1:1:0:26:8:1:0:5 +17 22260036 . G T 65 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCATTCAAGTCACAGAG;RSEQ=TGAACATTCCCTTTCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:30.5:1:31.8:1:1:0:23.3:8:1:0:4.8 1/1:5:5:2,3:0,0:0,5:1:0,2:27.8:1:28:1:1:0:25:10:1:0:4.8 +17 22260051 . C G 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGGTGAACATTCCCTTT;RSEQ=AGAGAGCACTTTGGAAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:38.6:1:33.8:1:1:0:25.6:10:1:0:5.2 1/1:7:7:3,4:0,0:0,7:1:0,2:34.9:1:30.9:1:1:0:24.7:14:1:0:4.3 +17 22260053 . G C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGGTGAACATTCCCTTTCA;RSEQ=AGAGCACTTTGGAAACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:38.8:1:33.6:1:1:0:25.6:10:1:0:5.2 1/1:7:7:3,4:0,0:0,7:1:0,2:36.1:1:31.3:1:1:0:24.7:14:1:0:4.3 +17 22260060 . C G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCCCTTTCAGAGAGCA;RSEQ=TTTGGAAACTCTCTTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:0,6:1:0,2:29.8:1:33.5:1:1:0:26.3:12:1:0:5.3 1/1:8:8:4,4:0,0:0,8:1:0,2:33:1:31.5:1:1:0:24.4:16:1:0:4.5 +17 22260089 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=CTCTCTTTGTGTAGAATCTG;RSEQ=AAGTGGAGATATGGACCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:8,0:0:2,0:21.5:1:32.6:1:1:0:28.8:16:1:0:5.4 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:31:1:30.5:1:1:1.29:22:4:0.2222:0:5.5 +17 22260105 . CC AT 50 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=TCTGCAAGTGGAGATATGGA;RSEQ=GCTTTGAGGCCTATGGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:40.3:1:31.8:1:1:0:31.3:6:0.75:0:5.7 1/0:4:2:1,1:0,2:2,2:0.5:0,2:44:0:31:1:1:0:22:4:0.5:0:4.5 +17 22260116 . C A 49 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGATATGGACCGCTTTGAGG;RSEQ=CTATGGTAGTAAAGGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:38.7:1:31:1:1:0:31.3:6:0.75:0:5.7 1/1:2:2:1,1:0,0:0,2:1:0,2:34:0:31:0:1:0:22:4:1:0:4.5 +17 22260135 . C T 58 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTATGGTAGTAAAGGAAA;RSEQ=AGCTTCATATAAAAACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:22:1:29.3:1:1:0:34.3:8:1:0:5.3 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:30.5:1:1:0:22:4:1:0:4.5 +17 22260150 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAACAGCTTCATATAAAA;RSEQ=CTAGACAGCAGCATTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:13.5:1:31:1:1:0:29.5:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 26046862 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTACTTTATTATCCTACTAC;RSEQ=ACACACTCAAAGGATTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:27:1:1:0:46:4:1:0:1 +17 26047125 . C A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=0.07768;LSEQ=ACAACACCTTTCAAACTCTT;RSEQ=TACTAACCTCCGGAGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:22:13,9:3,4:7,22:0.7586:2,2:32.7:1:28.6:1:0.6665:1.88:38.2:44:0.7586:0:1.1 0/1:32:6:3,3:14,12:26,6:0.1875:2,2:35.2:1:29.8:1:1:1.16104:30.3:12:0.1935:0:1.2 +17 26368753 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGGGCGGGGCCTCGGCGG;RSEQ=TGGTTGCGCGTGTCCGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:34:0:1:0:60:2:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:41:1:29:1:1:0:60:4:0.6667:0:1 +17 26370249 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24541;SOR=0;LSEQ=AGCTCAGGTACAGGCTGCCG;RSEQ=AGCTGCTACAGTTAAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:91,42:133,2:0.0148:2,2:40:1:29:1:0.5372:2.1531:60:4:0.0153:0:1 0/0:137:0:0,0:86,51:137,0:0:2,0:23.6:1:31.1:1:1:0:60:67.5:1:0:0.2 +17 26370268 . G A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=GCAGCTGCTACAGTTAAGGC;RSEQ=CACCATCATCAGCACTCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:126,65:191,0:0:2,0:22.5:1:30.6:1:1:0:60:62.667:1:0:0.1 0/1:176:14:7,7:97,65:162,14:0.0795:2,2:24.1:1:27.9:1:0.57377:1.4888:60:28:0.0814:0:1.2 +17 26370299 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11293;SOR=Inf;LSEQ=AGCACTCGCATCATCCACAG;RSEQ=AGCAGCTGGATATTGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:148,115:263,0:0:2,0:26.7:1:32.3:1:1:0:60:51.6:1:0:0.1 0/1:248:3:2,1:138,107:245,3:0.0121:2,2:27:1:29.7:1:1:1.55:60:6:0.0121:0:1.7 +17 26370323 . A G 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12419;SOR=0;LSEQ=AGCTGGATATTGAGCCGGAT;RSEQ=GACCTATTGGATATGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:4:2,2:177,152:329,4:0.012:2,2:23.5:1:31.8:1:1:1.16394:60:8:0.0121:0:1 0/0:319:0:0,0:173,146:319,0:0:2,0:25.4:1:28.7:1:1:0:60:78.75:1:0:0.2 +17 26744227 . AG A 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGCACATGCACCATTAC;RSEQ=GTGGCTGGTGCCTGTAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:14:0:34:0:1:0:24:2:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29:1:33:0:1:0:60:4:0.6667:0:0 +17 26744523 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20801;SOR=0;LSEQ=GTGCTTAAGAATTAACTATG;RSEQ=TGGGAAACACTTCATTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:30,49:79,2:0.0247:2,2:22.5:1:29:1:1:1.62:60:4:0.0247:0:1 0/0:96:0:0,0:31,65:96,0:0:2,0:22.3:1:28.9:1:1:0:60:95:1:0:0.1 +17 26744679 . G A 101 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01099;SOR=0;LSEQ=GTTTTCCCATTTTCATCTGT;RSEQ=TATGAGTTTTTAGTATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:22.8:1:31.9:1:1:0:60:18:1:0:1 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:29.5:1:29:1:0.33333:0:60:4:0.3333:0:1 +17 27403067 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12216;SOR=Inf;LSEQ=TAGGAGGAGTCAGCGTTCTG;RSEQ=GGCAAGAACCACCTTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:63,63:126,0:0:2,0:28.1:1:31.2:1:1:0:60:125:1:0:0.2 0/1:129:4:2,2:60,65:125,4:0.031:2,2:38:1:30:1:1:1.08:60:8:0.031:0:1 +17 27403076 . C A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.49718;LSEQ=TCAGCGTTCTGCGGCAAGAA;RSEQ=CACCTTCTTAGCTTTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:56,61:117,2:0.0168:2,2:28.5:1:29.5:1:1:1.09:60:4:0.0172:0:1 0/0:119:1:1,0:52,66:118,1:0.0084:2,0:1:0:24:0:0.44538:0:60:2:0.0084:0:1 +17 27403092 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49874;SOR=0;LSEQ=AGAACCACCTTCTTAGCTTT;RSEQ=CCCAAGGTGGCAGTGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:43,58:101,2:0.0194:2,2:23.5:1:30.5:1:1:1.34:60:4:0.0196:0:1 0/0:93:0:0,0:37,55:92,0:0:2,0:26.7:1:28.9:1:1:0:60:91:0.9891:0:0.2 +17 28043426 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTAATTAGAGTGCTTAAT;RSEQ=TGCTCAATACACACATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:19.8:1:31.5:1:1:0:53.1:12:1:0:0 0/1:33:2:1,1:28,3:31,2:0.0606:2,2:32.5:1:27.5:1:0.23106:8.22492:58.5:4:0.0606:0:1 +17 28043488 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCAACTTGTGTACAACAAT;RSEQ=CCAGCAGCATGCTGGTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:33,20:53,0:0:2,0:19.8:1:30.8:1:1:0:51.1:25.5:1:0:0.2 0/1:117:2:1,1:68,46:114,2:0.0171:2,2:36.5:1:27:1:1:1.47313:60:4:0.0171:0:1 +17 28043492 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=ACTTGTGTACAACAATGCCA;RSEQ=CAGCATGCTGGTTAACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:33,21:54,0:0:2,0:21.6:1:32:1:1:0:50.8:53:1:0:0.2 0/1:123:2:1,1:70,51:121,2:0.0163:2,2:22:0:30.5:1:1:1.36894:60:4:0.0163:0:1 +17 28043556 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.536;SOR=Inf;LSEQ=GTAACACTTGTGGGGCATTC;RSEQ=TTTTTGAACAGTACCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:26,39:65,0:0:2,0:26.7:1:32.3:1:1:0:36.9:64:1:0:0.1 0/1:115:2:1,1:46,67:113,2:0.0174:2,2:28.5:1:30.5:1:1:1.45:23.5:4:0.0177:0:1 +17 28043667 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50639;SOR=Inf;LSEQ=TCTAAAAGACCTAGAGAACA;RSEQ=ATATCGGGTGCCTCTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:4,13:17,0:0:2,0:24:1:28.4:1:1:0:60:16:1:0:0.1 0/1:25:2:1,1:5,18:23,2:0.08:2,2:29.5:1:33:0:0.43:3.38:59:4:0.08:0:2 +17 29058863 . G A 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=GGCGCTTACTCTCCGGGGCC;RSEQ=CCCGGCGAGTAGCTGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:68,49:117,0:0:2,0:24.2:1:30.7:1:1:0:40.5:116:1:0:0.1 0/1:95:11:7,4:45,39:84,11:0.1158:2,2:24.2:1:29.1:1:0.74902:1.51:30.9:22:0.1183:0:1.2 +17 29058866 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20548;SOR=Inf;LSEQ=GCTTACTCTCCGGGGCCGCC;RSEQ=GGCGAGTAGCTGGCCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:71,49:120,0:0:2,0:25.2:1:30.3:1:1:0:39.7:119:1:0:0.1 0/1:100:2:1,1:53,45:98,2:0.02:2,2:8.5:1:28:1:1:1.17584:30.5:4:0.02:0:1 +17 29058972 . C T 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09547;LSEQ=AGCGCGGGGTCCGGGGGAGG;RSEQ=GGCTTCGGGGGTTCGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:4:1,3:211,86:297,4:0.0132:2,2:12.8:1:26.5:1:0.0791:7.30565:54:8:0.0139:0:1.3 0/1:414:6:2,4:263,145:408,6:0.0145:2,2:6.3:1:26.5:1:0.19419:3.6157:58:12:0.0151:0:1 +17 29059051 . GCCT G 108 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.62525;SOR=1.4205;LSEQ=GAGGCGGTGGCAGTTACTCG;RSEQ=CCTCCTCCTCCGCGGCGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:743:6:3,3:412,324:736,6:0.0081:2,2:19.5:1:32.8:1:1:1.27118:56:12:0.0083:0.0013:0.3 0/1:962:11:7,4:522,424:946,11:0.0114:2,2:24.9:1:31.4:1:0.76282:1.42:57.4:22:0.0116:0.001:0.3 +17 29086494 . CT C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.29795;SOR=1.34723;LSEQ=TTAAAATGATAAAATATTTC;RSEQ=TTTTTTTTTTTAGCTTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:34:24,10:69,51:120,34:0.2152:2,2:25.7:1:32.1:1:0.23315:1.77:43.6:68:0.2252:0.038:0.3 0/1:163:44:26,18:66,34:100,44:0.2699:2,2:23.9:1:30.8:1:0.45526:1.34105:42.4:43:0.2688:0.0613:0.4 +17 29086615 . TA T 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.69648;LSEQ=GCAAGATACCTTTGTGAATG;RSEQ=AAAAAAAAGTGGGGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:0,2:34,94:128,2:0.0154:2,0:15:1:27.5:1:1:0:21.5:4:0.0155:0.0077:0 0/1:186:2:1,1:60,124:184,2:0.0108:2,2:13:0:28:1:0.54955:2.06:23:4:0.0108:0:0 +17 29086657 . A G 123 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=11.53746;LSEQ=AGTGTAAATTTATAAAATTA;RSEQ=GTTTAATGGAAAAGATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:0,2:3,70:73,2:0.0267:1,0:20.5:1:32.5:1:1:0:25:4:0.027:0:1 0/1:70:17:1,16:2,51:53,17:0.2429:1,1:25.8:1:30.2:1:1:1.58:28.4:34:0.2429:0:1 +17 29095990 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50935;SOR=Inf;LSEQ=TTGAACCTAGTAACAGCCAC;RSEQ=TGGTGAAGTCTTACTCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:69,73:142,0:0:2,0:21.9:1:30.4:1:1:0:49.7:141:1:0:0.2 0/1:191:2:1,1:110,78:188,2:0.0105:2,2:8.5:1:28.5:1:1:1.40763:60:4:0.0105:0:1.5 +17 29096004 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16221;SOR=0;LSEQ=AGCCACATGGTGAAGTCTTA;RSEQ=TCGTTGCTATTTAGAGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:75,84:159,2:0.0124:2,0:25.5:1:31:1:0.49922:0:22.5:4:0.0125:0:1 0/0:238:0:0,0:135,103:238,0:0:2,0:28.1:1:31.2:1:1:0:54.4:237:1:0:0.1 +17 29096006 . C T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11553;SOR=0.43048;LSEQ=CCACATGGTGAAGTCTTACT;RSEQ=GTTGCTATTTAGAGTGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:9:0,9:75,79:154,9:0.0552:2,0:23.9:1:29.4:1:0.0039:0:24:18:0.0552:0:1 0/1:245:6:4,2:133,106:239,6:0.0245:2,2:13.8:1:28.7:1:0.69694:1.59:41:12:0.0249:0:1 +17 29096086 . A AT 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.07379;LSEQ=AAACCATGAAAATATTGGTA;RSEQ=TTTTTTTTTTTACTAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:5:1,4:20,66:86,5:0.0543:2,2:31:1:31.6:1:1:1.20968:36.6:10:0.0543:0:0 0/1:172:10:2,8:52,110:162,10:0.0581:2,2:41.1:1:30.7:1:0.72662:1.88473:23.8:20:0.0581:0:0.1 +17 29422537 . T G 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.33107;SOR=3.11347;LSEQ=AGAAGGGAAGGGGGGATAAG;RSEQ=GGGGGTGGCCAAGGCGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:0,2:1,60:61,2:0.0317:1,0:18.5:1:9.5:1:1:0:60:0:0:0:3.5 0/1:32:3:0,3:0,29:29,3:0.0938:1,0:19.3:1:22:1:1:0:60:2:0.0769:0:2.3 +17 29422861 . A T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTGTCTTATATACCCTC;RSEQ=ATAGGAGAACGATAACATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:27:1:1:0:60:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29423119 . T C 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACCGTGGTTCTGAAATA;RSEQ=CTTCCCCTTCCTTGATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29482701 . C T 79 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTGCTGGATAAAGAATT;RSEQ=TATTTTGTAGATAGAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1:0,2:23:1:30.8:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29482878 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08616;SOR=0.42172;LSEQ=AATCGGAGTTTGAGATGCAA;RSEQ=TATAGGTATCTGTGGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:36:34,2:12,1:13,36:0.7347:1,2:23.1:1:30:1:1:1.41:60:17:0.7234:0:1.1 1/0:28:15:15,0:13,0:13,15:0.5357:1,1:16.7:1:29:1:1:0:57.6:14:0.5185:0:1.2 +17 29482977 . G GT 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00742;SOR=2.15528;LSEQ=TAAGGATAAGCTGTTAACGT;RSEQ=TTTTTTTTTTCTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:21:18,3:230,47:277,21:0.0682:2,2:28.5:1:30.1:1:1:1.23:60:42:0.0712:0:0.2 0/1:308:42:33,9:206,54:260,42:0.1364:2,2:20.9:1:28.8:1:1:1.04027:59.8:84:0.1409:0.0357:0.1 +17 29482988 . C CT 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17763;SOR=0.51377;LSEQ=TGTTAACGTGTTTTTTTTTT;RSEQ=TTTTTTTTTCAGCTTCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:13:8,5:268,70:338,13:0.0361:2,2:22.8:1:31.2:1:0.16154:2.38562:60:26:0.0408:0.0056:0.2 0/1:371:7:5,2:256,100:356,7:0.0189:2,2:19:1:29.9:1:1:1.02393:60:14:0.0209:0.0081:0 +17 29483108 . C T 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=56.68797;LSEQ=AAGTTTTCTTTGGTTATAAG;RSEQ=GGCCTCACTACTATTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:1:0,1:300,419:719,1:0.0014:2,0:48:0:14:0:1:0:60:0:0:0:1 0/1:779:57:24,33:327,393:720,57:0.0732:2,2:24.7:1:28.5:1:0.67962:1.14389:60:56:0.0735:0:1.1 +17 29485963 . G C 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50133;SOR=0;LSEQ=TTTTAGTCTTTCACTTTTCA;RSEQ=ATGTGTGTTGATTGGTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:147,39:186,2:0.0106:2,2:5.5:1:32:0:0.38116:3.73461:60:4:0.0106:0:1 0/0:162:0:0,0:122,40:162,0:0:2,0:24.4:1:31.1:1:1:0:60:80:1:0:0.1 +17 29486152 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.166;LSEQ=TAGGCAGGCTTTGTGAATTT;RSEQ=ATCTTGAGAATGATCTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:257:226:68,158:5,26:31,226:0.8794:2,2:23.7:1:29.7:1:0.13723:2.23:60:44.2:0.877:0:1.1 1/0:289:158:52,106:48,82:130,158:0.5467:2,2:22:1:29.1:1:0.53438:1.19251:60:78:0.5474:0:1.1 +17 29486194 . C A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=CCCAAAGTACAGATGTGGAC;RSEQ=AAGAGGACAGTCCTATGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:7,115:122,2:0.0161:2,2:5.5:1:29:1:0.12536:15.43:60:4:0.0163:0:2 0/0:106:0:0,0:15,91:106,0:0:2,0:24:1:31.2:1:1:0:60:105:1:0:0.5 +17 29490132 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50137;SOR=0;LSEQ=TTTGTTCTGTGTGTGTGTTT;RSEQ=AAAATTTTCATAATAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:140,7:147,2:0.0134:1,2:26:1:28.5:1:0.10484:18.76643:60:4:0.0134:0:1.5 0/0:127:0:0,0:119,8:127,0:0:2,0:23.6:1:31.4:1:1:0:60:126:1:0:0 +17 29490382 . G A 63 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03312;SOR=Inf;LSEQ=CTTCAATGCAGTCTTTAGTC;RSEQ=CATTTCTACCAGGTTAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:0:0,0:180,322:502,0:0:2,0:26.6:1:31.1:1:1:0:59.9:49.2:1:0:0.1 0/1:580:6:5,1:220,354:574,6:0.0103:2,2:17.2:1:24.5:1:0.03493:8.02:60:5:0.0087:0:1.3 +17 29490992 . A G 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCTCCAGAAAGTGGACT;RSEQ=CATTTTAAATGTATGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:23:1:28.7:1:1:0:60:2:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29496756 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09947;SOR=Inf;LSEQ=GTATTTTTTTTAGAGATGAT;RSEQ=TCTTGCTATGTTGCCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:44,0:0:1,0:24.3:1:33.5:1:1:0:50.3:88:1:0:0.5 0/1:39:3:3,0:36,0:36,3:0.0769:1,0:22:1:29.3:1:1:0:47.7:6:0.0769:0:1 +17 29496819 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0.00085;SOR=0.35818;LSEQ=AGTGGTCCTCCTGCCTTGGC;RSEQ=TCCTGAAGTGCTGGGATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:91:68:67,1:23,0:23,68:0.7473:1,1:23.1:1:31.6:1:1:0:52.4:67:0.7444:0:1.1 1/0:115:59:56,3:52,4:56,59:0.513:2,2:25.3:1:30.6:1:0.71205:1.43:52.4:118:0.5175:0:1.1 +17 29496840 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50403;SOR=Inf;LSEQ=TCCTGAAGTGCTGGGATTAC;RSEQ=GGTGTGAGATACCACACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:118,21:139,0:0:2,0:21.5:1:30.7:1:1:0:56.1:68.5:1:0:0.5 0/1:172:2:1,1:139,31:170,2:0.0116:2,2:8:1:29.5:1:0.33837:4.42911:47.5:4:0.0118:0:1 +17 29496848 . G T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57859;SOR=0.37247;LSEQ=TGCTGGGATTACAGGTGTGA;RSEQ=ATACCACACCTGTCCCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:130,29:159,2:0.0124:2,2:16:1:28.5:1:0.3389:4.42434:60:4:0.0124:0:1.5 0/0:215:1:0,1:157,56:213,1:0.0047:2,0:1:0:23:0:0.26636:0:60:2:0.0047:0:1 +17 29508775 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19294;LSEQ=CCAGATGAATTTACAAAACT;RSEQ=TACCAGATCCCACAGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:897:732:328,404:71,89:160,732:0.8161:2,2:27.7:1:28.3:1:0.93032:1.02:59.6:9.765:0.8167:0:1.3 0/1:768:354:165,189:191,212:403,354:0.4609:2,2:27.2:1:27.5:1:0.88398:1.03196:59.7:10.8:0.4622:0:1.4 +17 29508876 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.52704;SOR=0;LSEQ=TGACATAAAAACCTATCATC;RSEQ=TTTTCCAAGTTATTTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:10,148:158,2:0.0125:2,2:12:1:29:1:0.13318:14.16:60:4:0.0132:0:1 0/0:98:0:0,0:1,97:98,0:0:1,0:23.1:1:31.6:1:1:0:59.3:48:1:0:0.6 +17 29509503 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08501;SOR=Inf;LSEQ=TTGTTCCTATCTAATAATGT;RSEQ=ATTTAATATATTTTTCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:234,68:302,0:0:2,0:25.5:1:32.1:1:1:0:60:99.667:1:0:0.1 0/1:238:3:0,3:176,59:235,3:0.0126:2,0:13.3:1:24.3:1:0.01705:0:60:6:0.0127:0:1 +17 29509791 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00224;SOR=0.24226;LSEQ=AAGCAAAGTATTTCAGGGAA;RSEQ=CATTTAAATGATCATTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:78:68:0,68:0,10:10,68:0.8718:0,1:22:1:30.9:1:1:0:59.8:67:0.8701:0:1.8 1/0:42:26:0,26:0,16:16,26:0.619:1,1:17.5:1:29.1:1:1:0:60:25:0.6098:0:1.7 +17 29509801 . G T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00407;SOR=0.23356;LSEQ=TTTCAGGGAACCATTTAAAT;RSEQ=ATCATTTTAGGTTTCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:57:0,57:0,10:10,57:0.8507:0,1:20.3:1:29.1:1:1:0:59.8:114:0.8636:0:1.9 1/0:30:17:0,17:0,13:13,17:0.5667:1,1:20.2:1:28.7:1:1:0:60:34:0.5667:0:2 +17 29509911 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACAAAGATTTAAAATAAT;RSEQ=CCTTAGTTTCATTCTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:8,2:0.2:0,0:13:1:31.5:1:1:0:60:4:0.2:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:4:0:31:0:1:0:60:2:1:0:0 +17 29527117 . G A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGCCAAGATCGTGCCTTT;RSEQ=TACTCCAGCCTGGGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:1,1:0.5:0,0:40:0:27:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:27.5:1:1:0:60:4:1:0:1 +17 29527250 . A AT 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.66729;SOR=0.65248;LSEQ=ATAAAGAAAATAGAAAAAGG;RSEQ=TTTTTTTTAAATTTGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:13,0:5,0:5,13:0.7222:0,1:26.9:1:30.3:1:1:0:38.4:12:0.75:0.0556:0.1 1/0:8:5:5,0:2,1:3,5:0.625:2,0:32:1:29.7:1:0.375:0:41.4:10:0.625:0.125:0 +17 29528325 . G GT 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.64556;SOR=0.75577;LSEQ=CAAGACCTTAAAAACTTAGT;RSEQ=TTTTTTTTTTAAACTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:17:12,5:105,63:168,17:0.0914:2,2:29.8:1:30.7:1:0.60456:1.44:43.5:34:0.0934:0.0054:0.2 0/1:85:6:6,0:56,23:79,6:0.0706:2,0:22.2:1:30.8:1:0.18385:0:43.3:12:0.0732:0.0235:0 +17 29528406 . C CT 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.27548;SOR=1.3714;LSEQ=TTTCTCATAGAAATAATCTG;RSEQ=TTTTTTTTTTCTTTTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:27:20,7:322,99:421,27:0.06:2,2:29.7:1:30.7:1:0.81565:1.13802:35:26:0.0588:0:0.1 0/1:385:31:24,7:265,84:349,31:0.0805:2,2:26.5:1:30.2:1:1:1.09:39.2:62:0.084:0:0.2 +17 29528744 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=GTTAATAAGATGCTTTGGAA;RSEQ=GATTAAATCTAAAACGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:17,0:0:1,0:26:1:33.9:1:1:0:60:34:1:0:0 1/0:4:2:1,1:0,2:2,2:0.5:0,2:21.5:1:28.5:1:1:0:59:4:0.5:0:1 +17 29532920 . T TA 29 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTGTAAAACATTAAACT;RSEQ=AAAAAAAAAAAAAGAAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:10.5:1:29:1:1:0:60:4:0.3333:0.1667:1 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:28:0:1:0:60:2:1:0:0 +17 29533434 . A AT 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.54107;LSEQ=TCTCACCTCCTTTCTATTGC;RSEQ=TTTTTTTTAGTGTCTTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:28,147:175,2:0.0113:2,2:30.5:1:30:1:0.30162:5.18:60:4:0.0116:0:1 0/0:163:1:0,1:27,135:162,1:0.0061:2,0:40:0:31:0:1:0:60:2:0.0062:0:0 +17 29533685 . CTTTTGAACAAAAATA C 82 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTTTTTTCTCCTTAAAA;RSEQ=TTTTGATTAGCCTCTCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:20:1:31.9:1:1:0:59:12:1:0.5:0.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29541061 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGAGTCTATGAAATACT;RSEQ=GTATGTATGTCTGGGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:30:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29541339 . A T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00082;SOR=0.11281;LSEQ=TACTATTGAGTGTTTCTACT;RSEQ=ATACCACACATTTGGTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:28:28,0:4,0:4,28:0.875:0,1:19.1:1:31.2:1:1:0:30.8:56:0.875:0:1.1 0/1:21:9:8,1:11,1:12,9:0.4286:2,2:17.3:1:30.2:1:1:1.35399:27.4:18:0.4286:0:1.1 +17 29541437 . T C 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=0.08173;LSEQ=AGCTATTATCCTGAGTCTTA;RSEQ=GTCTGATACCATGTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:42:40,2:3,0:3,42:0.9333:0,1:21.9:1:31:1:1:0:26:84:0.9333:0:1.1 1/0:23:12:11,1:11,0:11,12:0.5217:0,2:18.8:1:29.5:1:1:0:27.1:24:0.5217:0:1.1 +17 29544957 . CA C 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGCCATTGCACTCCGTTT;RSEQ=AAAAAAAAAAAAAAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:31:1:1:0:55.5:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29545987 . A AT 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00373;SOR=0.59848;LSEQ=TAATCTCTCTCGATTTATTT;RSEQ=TTTTTTTAATTGAAGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:259:179:143,36:63,14:77,179:0.6911:2,2:27.3:1:30.5:1:0.86369:1.13235:60:43.75:0.6944:0.0347:0.2 1/0:339:194:139,55:107,38:145,194:0.5723:2,2:22.6:1:29.2:1:0.71273:1.11381:59.9:63.667:0.5719:0.1327:0.1 +17 29546175 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13212;LSEQ=CCATGTTCTTGAAGGAAAGA;RSEQ=TGTAACTATGTACATTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:254:220:49,171:4,29:33,220:0.8661:2,2:24.1:1:33.2:1:0.25152:2.07:60:219:0.8656:0:1.1 0/1:274:126:33,93:44,103:147,126:0.4599:2,2:24.7:1:31.2:1:0.50366:1.20306:60:62:0.4627:0:1.2 +17 29546285 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06633;SOR=Inf;LSEQ=CTATACATTGTTTTATAAAA;RSEQ=TCCATGGAGAAAGAAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:2,34:36,0:0:2,0:22.8:1:33.1:1:1:0:60:35:1:0:0.2 0/1:13:2:1,1:0,11:11,2:0.1538:0,2:13.5:1:31:0:0.15385:0:60:4:0.1538:0:1 +17 29548953 . T A 34 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3271;SOR=3.78933;LSEQ=ATTTTGGGAGATTAGGTATA;RSEQ=GTACTTTTATTTTTTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:1:1,0:74,197:271,1:0.0037:2,0:1:0:26:0:0.27574:0:60:2:0.0037:0:1 0/1:217:3:2,1:52,162:214,3:0.0138:2,2:5.3:1:21.7:1:0.15364:6.17:60:2:0.0093:0:1.3 +17 29553332 . CGGAGAC TGGAG 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTGTGAGTTATTGTATG;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:2,0:137,2:139,2:0.0142:1,0:40:1:30.6:1:1:0:51:4:0.0149:0.0071:1 0/0:67:0:0,0:61,4:65,0:0:2,0:24.1:1:31.2:1:1:0:48.4:64:1:0:0.4 +17 29553336 . GAC G 183 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=39;MSI=20.000;MSILEN=2;SSF=0.00578;SOR=0.36099;LSEQ=TGTGAGTTATTGTATGCGGA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:43:43,0:79,2:81,43:0.2925:1,1:29.3:1:33.9:1:0.54327:0:52.3:20.5:0.2908:0:0.4 0/1:85:11:10,1:62,5:67,11:0.1294:2,2:18.4:1:32:1:1:1.23635:53.3:22:0.1294:0.0353:0.1 +17 29553485 . G A 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.29561;LSEQ=GGATGCAGCGGAACCCCCCC;RSEQ=ATTTGCCGACAAGCCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1475:161:88,73:696,615:1311,161:0.1092:2,2:27.3:1:30.2:1:0.73817:1.07:39.2:25.833:0.1073:0:1.2 0/1:1491:704:358,346:412,370:782,704:0.4722:2,2:27.5:1:29.5:1:0.49925:1.07614:38.8:49.286:0.4716:0:1.2 +17 29553719 . GT G 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02233;SOR=0;LSEQ=ACAGGTAAATGTGAATAGTG;RSEQ=TTTTTTTACTCAGTCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:5:2,3:69,229:298,5:0.0164:2,2:31.2:1:31.6:1:0.33392:2.21:44.2:10:0.0167:0:1 0/0:344:0:0,0:117,227:344,0:0:2,0:25.6:1:28.7:1:1:0:58.5:56.333:1:0:0.1 +17 29554158 . G T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12442;SOR=0;LSEQ=CTGCTCTTCCTACTCCTTTT;RSEQ=GGTGGAGCTTATCAGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:4:2,2:258,90:348,4:0.0114:2,2:18:1:30.8:1:0.2805:2.85647:32.8:8:0.0115:0:1 0/0:334:0:0,0:226,108:334,0:0:2,0:29:0:14:0:1:0:60:0:0:0:6 +17 29554732 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.07302;SOR=Inf;LSEQ=AAAGTAAACATATAGCTGTG;RSEQ=GAAGACTGATATTTAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:5,104:109,0:0:1,0:24.2:1:30.6:1:1:0:59.2:218:0.9909:0:0.1 0/1:80:3:1,2:1,76:77,3:0.0375:1,2:18.7:1:29.7:1:0.07405:31.23:60:6:0.0375:0:1.7 +17 29555960 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21058;SOR=Inf;LSEQ=TTTTGTACTTTTGTCATGGA;RSEQ=GAAATGTTGGATAAAGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:169,12:181,0:0:2,0:24.6:1:30.4:1:1:0:56.3:44.25:1:0:0.1 0/1:154:2:1,1:134,18:152,2:0.013:2,2:18.5:1:28:1:0.23224:7.27154:60:4:0.0132:0:1 +17 29555970 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22094;SOR=Inf;LSEQ=TTGTCATGGAAGAAATGTTG;RSEQ=ATAAAGCATAATTTGTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:179,20:199,0:0:2,0:26.4:1:31.3:1:1:0:56.3:32.167:1:0:0.1 0/1:177:2:1,1:145,30:175,2:0.0113:2,2:13.5:1:25:1:0.32043:4.77116:46.5:4:0.0114:0:1 +17 29555976 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24917;SOR=0;LSEQ=TGGAAGAAATGTTGGATAAA;RSEQ=CATAATTTGTCAAGTCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:3:1,2:187,31:218,3:0.0135:2,2:12.7:1:29:1:0.05901:11.83533:39.3:6:0.0137:0:1 0/0:208:0:0,0:165,43:208,0:0:2,0:22.5:1:31.3:1:1:0:55:416:1:0:0.1 +17 29556462 . GT G 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.68641;SOR=0.51545;LSEQ=TTGAAGAATACCATCAGCAA;RSEQ=TTTTTGACTCCCAAGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:4:2,2:78,266:344,4:0.0115:2,2:13.5:1:31:1:0.22753:3.40:60:8:0.0116:0.0029:0.3 0/0:336:2:1,1:100,234:334,2:0.006:2,2:25:1:31:1:0.51146:2.33:52.5:4:0.006:0:0 +17 29556703 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55088;SOR=0;LSEQ=ACGTGCCCTGTGTATGGGTA;RSEQ=GAGTGTCTGCGTATATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:2,0:109,15:124,2:0.0159:2,0:29.5:1:32:1:1:0:55.5:4:0.0164:0:1 0/0:64:0:0,0:61,3:64,0:0:1,0:24:1:31.6:1:1:0:60:63:1:0:0.1 +17 29556743 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13824;SOR=Inf;LSEQ=TATGCTTATTTGGCTCTATG;RSEQ=CTGTGGGTGCACTTACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:213,21:234,0:0:2,0:25.4:1:32.3:1:1:0:59.8:38:1:0:0.1 0/1:139:2:1,1:123,14:137,2:0.0144:2,2:23:1:26.5:1:0.20488:8.5204:60:4:0.0149:0:1 +17 29556837 . T C 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGGCAAATCATTAATGTA;RSEQ=TTGTTCTTTCTTTAGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:836:0:0,0:451,385:836,0:0:2,0:24.6:1:30.7:1:1:0:56.3:103.5:1:0:0.1 0/1:781:30:17,13:417,333:750,30:0.0384:2,2:26:1:32:1:1:1.04:47.7:60:0.0387:0:1.1 +17 29557205 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.09875;SOR=Inf;LSEQ=TTTAATTCGTTTTACTTGAT;RSEQ=ACTAAAGTATTTAGAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:205,37:242,0:0:2,0:24.5:1:32.7:1:1:0:59.9:120:1:0:0.1 0/1:209:3:2,1:173,33:206,3:0.0144:2,2:17:1:23:1:0.4146:2.60524:60:2:0.0097:0:1 +17 29557466 . A G 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=Inf;LSEQ=GTCCAATGAAGTACAGAAAA;RSEQ=GAGTAGATATGCGGTTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:7,169:176,0:0:1,0:25.8:1:32.6:1:1:0:49.6:87:1:0:0.1 0/1:124:11:0,11:4,109:113,11:0.0887:1,0:25.2:1:31:1:1:0:45.7:22:0.0887:0:1.3 +17 29558082 . T C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=3.96433;LSEQ=GTGTTTGAAATATGTAAAGA;RSEQ=GCTAATCTTTATTACTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:15:0,15:2,70:72,15:0.1724:1,1:25.3:1:31.6:1:1:0:54.7:30:0.1744:0:1 0/1:77:35:1,34:1,41:42,35:0.4545:1,1:25.4:1:29.7:1:1:1.20:56.3:70:0.4545:0:1.2 +17 29558293 . T G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCATTGTGTTGAATCTTT;RSEQ=TAAGAAATAATTGATTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:24.1:1:32.6:1:1:0:54:14:1:0:1 1/1:3:3:1,2:0,0:0,3:1:0,2:34.3:1:31.7:1:1:0:48.3:6:1:0:1 +17 29559092 . G T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.24816;SOR=0;LSEQ=TTTTTTTTTTTTTTTTCAGA;RSEQ=ATTTGGACCAGGCAAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:1,2:111,59:170,3:0.0168:2,2:28.7:1:23.3:1:0.28412:3.73244:33.3:2:0.0241:0:1.7 0/0:172:0:0,0:91,74:165,0:0:2,0:30.2:1:23.3:1:1:0:41.2:1.037:1:0:1.6 +17 29559109 . C A 45 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45058;SOR=0.49586;LSEQ=AGAGATTTGGACCAGGCAAG;RSEQ=ATGGAAGCAGTAGTTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:4:4,0:182,135:317,4:0.0124:2,0:24:1:22.8:1:0.14167:0:33.3:3:0.0123:0:4.5 0/0:324:2:2,0:165,156:321,2:0.0062:2,0:3.5:1:15:0:0.49903:0:60:0:0:0:2.5 +17 29559588 . G C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=4.43979;LSEQ=AGCCACCCTGGCTGATTATC;RSEQ=CGAGAGAGGAGAGAAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:18:18,0:69,7:76,18:0.1915:2,1:27.3:1:31.1:1:0.3394:0:59.2:17:0.1848:0:1.1 1/0:66:34:32,2:30,2:32,34:0.5152:2,2:25.6:1:30.8:1:1:1.07:60:33:0.5077:0:1 +17 29559932 . C A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.88314;LSEQ=GAAAGTTTCATATAGAAATA;RSEQ=AAAACCTAGAGAACTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:69:31,38:151,159:310,69:0.1821:2,2:20.2:1:31:1:0.5962:1.16366:46.3:68:0.1809:0:1.1 0/1:362:168:79,89:83,111:194,168:0.4641:2,2:21.5:1:30.1:1:0.45857:1.19:44.6:336:0.4667:0:1.1 +17 29560292 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50025;SOR=0;LSEQ=CATAGCAAATCCTTCAGAAT;RSEQ=TATTTGTTCAATAAATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:27,152:179,2:0.011:2,2:20.5:1:29:1:0.28619:5.55:44.5:4:0.0111:0:1 0/0:161:0:0,0:30,131:161,0:0:2,0:22.4:1:29.7:1:1:0:59.5:322:1:0:0.1 +17 29560296 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20902;SOR=Inf;LSEQ=GCAAATCCTTCAGAATATAT;RSEQ=TGTTCAATAAATGTTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:25,143:168,0:0:2,0:23.4:1:30:1:1:0:59.3:23:1:0:0.1 0/1:142:2:1,1:22,118:140,2:0.0141:2,2:12:1:26.5:1:0.29867:5.27:43.5:4:0.0142:0:1 +17 29563073 . T TTG 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.97113;LSEQ=TCACATAGAACCGCTGTTTT;RSEQ=TGTTTTTTTTTTTTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:56:12,44:123,337:460,56:0.1083:2,2:27.2:1:31.1:1:0.42633:1.33761:59.9:112:0.1105:0.0097:1.1 0/1:459:173:51,122:99,187:286,173:0.3769:2,2:25.7:1:30.5:1:0.26107:1.26579:59.6:172:0.3772:0.1198:1.2 +17 29563085 . T G 228 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0;SOR=4.39789;LSEQ=GCTGTTTTTTGTTTTTTTTT;RSEQ=TTTGTTTGTTTGTTTTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:66:13,53:76,301:377,66:0.149:2,2:22.2:1:31.8:1:1:1.02934:59.9:132:0.1503:0:1.1 0/1:372:162:40,122:66,144:210,162:0.4355:2,2:27.9:1:31.1:1:0.16574:1.39666:59.7:53:0.4321:0:1.1 +17 29575849 . CT C 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.21956;SOR=2.73279;LSEQ=TCCAGCCCTGTCAAAGTTGT;RSEQ=TTTTTTTTTTTATAGTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:4:4,0:36,2:38,4:0.093:2,0:10.5:1:31.9:1:1:0:60:8:0.0952:0.0698:0.3 0/1:18:4:4,0:13,1:14,4:0.2222:1,0:28.8:1:30.8:1:1:0:60:8:0.2222:0:0.3 +17 29585499 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09702;SOR=Inf;LSEQ=CCACCACCTAGAATCGAAAG;RSEQ=GGCTTGAAGTTAATGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:137,210:347,0:0:2,0:20.2:1:31.4:1:1:0:51.9:172.5:1:0:0.1 0/1:296:3:2,1:118,175:293,3:0.0101:2,2:8:1:26:1:0.56809:2.96:30.3:6:0.0103:0:1 +17 29585907 . T C 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17994;SOR=0;LSEQ=AGAAACACTACCTAAAATAA;RSEQ=TTATAGAATGAGGAATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:8,0:33,5:38,8:0.1739:2,0:25.1:1:31:1:0.5692:0:60:16:0.1739:0:1 0/0:13:0:0,0:13,0:13,0:0:1,0:31.1:1:29.4:1:1:0:60:12:1:0:0 +17 29586217 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50503;SOR=0;LSEQ=CGGTTTCACATAAATCCATG;RSEQ=ACCTGTTTTACATGAAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:12,128:140,2:0.0141:2,2:24:1:31:1:0.17531:10.29:47.5:4:0.0141:0:1 0/0:112:0:0,0:12,100:112,0:0:2,0:22.4:1:27.8:1:1:0:59.6:224:1:0:0.1 +17 29587277 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18367;SOR=Inf;LSEQ=CATTGTGTGAACAAGCCCTC;RSEQ=ATATTTGTAATCTTAGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:108,2:110,0:0:1,0:25.8:1:31.5:1:1:0:60:109:1:0:0.1 0/1:83:2:1,1:78,3:81,2:0.0241:1,2:28:1:27:1:0.09462:22.66097:60:4:0.0244:0:1 +17 29587341 . G C 182 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTAATTCAAACATAAGTCT;RSEQ=GGTGTATCTGGTGTTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:69:44,25:235,100:335,69:0.1708:2,2:23.2:1:29.8:1:0.31797:1.33429:59.8:22:0.1654:0:1.2 0/0:442:0:0,0:278,164:442,0:0:2,0:24.6:1:30.6:1:1:0:59.9:43.2:1:0:0.1 +17 29587561 . G T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07736;SOR=Inf;LSEQ=TTCCCAGTCATGGGGATAGT;RSEQ=AACACTCTCCGTTTAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:106,290:396,0:0:2,0:23.4:1:32.1:1:1:0:59.9:65:1:0:0.1 0/1:295:3:1,2:79,213:292,3:0.0102:2,2:8.7:1:21.7:1:1:1.35:60:2:0.0069:0:2 +17 29592095 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.10253;SOR=Inf;LSEQ=GAGTAATACCTTGAAATTTT;RSEQ=GGTGCATGTTGCCAAATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:50,2:52,0:0:1,0:26.4:1:31.8:1:1:0:55.4:104:1:0:0 0/1:25:2:1,1:23,0:23,2:0.08:1,2:16.5:1:26.5:1:0.08:0:44.5:4:0.08:0:1 +17 29652531 . A G 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTACCAGACTATTCGCCT;RSEQ=AGGAGTTTGGTGGGCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:27.7:1:31.7:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29652884 . T C 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTGCTGATATACCATGTC;RSEQ=TACTGACTTTAAAGCCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:806:0:0,0:480,324:804,0:0:2,0:24.9:1:31.3:1:1:0:60:133:0.9975:0:0.1 0/1:712:29:17,12:378,303:681,29:0.0407:2,2:24.8:1:30.7:1:0.84941:1.14:60:58:0.041:0:1.1 +17 29653293 . T C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.34779;LSEQ=AAGTTCCAGTCTGTGTTTTG;RSEQ=AAACGATTCATTGCTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:194:59,135:19,55:74,194:0.7212:2,2:23.9:1:32.2:1:0.54762:1.26:59.9:193:0.7228:0:1 0/1:260:123:39,84:45,92:137,123:0.4731:2,2:23.6:1:31.1:1:0.89467:1.05333:60:60.5:0.469:0:1.2 +17 29654876 . T A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18663;LSEQ=CGGTAGGTTTTTTAAAATTC;RSEQ=CTTCAGTTTGATTTGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:328:248:72,176:20,60:80,248:0.7561:2,2:25.7:1:30:1:0.56754:1.23:60:247:0.7554:0:1.1 0/1:257:94:31,63:48,115:163,94:0.3658:2,2:22.6:1:28.8:1:0.57652:1.18:60:93:0.3676:0:1.1 +17 29654913 . A T 46 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27878;SOR=0;LSEQ=GGTTTGTTGCTTTTAAAATG;RSEQ=GACCATTTAATGAATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:1,2:21,153:174,3:0.0169:2,2:6.3:1:29.3:1:0.33008:3.60:60:6:0.0174:0:2 0/0:117:0:0,0:11,106:117,0:0:2,0:23.1:1:30.1:1:1:0:60:116:1:0:0.5 +17 29654918 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52202;SOR=0;LSEQ=GTTGCTTTTAAAATGAGACC;RSEQ=TTTAATGAATTTTAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:16,141:157,2:0.0126:2,2:24.5:1:29:1:0.20301:8.58:60:4:0.0128:0:2 0/0:102:0:0,0:7,95:102,0:0:2,0:24.5:1:29.8:1:1:0:60:101:1:0:0.5 +17 29654974 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00022;SOR=0.16714;LSEQ=TGTAAATTGGAAGGTATGCA;RSEQ=TGTTGGTTAACCACTGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:38:0,38:0,10:10,38:0.7917:0,1:28.2:1:31.8:1:1:0:60:76:0.7917:0:1 0/1:34:13:0,13:0,21:21,13:0.3824:1,1:22.2:1:30.9:1:1:0:60:26:0.3824:0:1 +17 29655218 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAAGTCAAGTCAGATTATTG;RSEQ=TTTACAAAAGAAGGCCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:34.5:1:30:1:1:0:60:8:0.8:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:7:0:33:0:1:0:60:2:1:0:0 +17 29661923 . C T 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01678;SOR=8.79666;LSEQ=TCAAATCTAGTTCGTTTTTG;RSEQ=AAGCATAATGATGATGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:721:1:0,1:349,370:719,1:0.0014:2,0:1:0:26:0:1:0:60:2:0.0014:0:1 0/1:662:8:3,5:321,333:654,8:0.0121:2,2:14.3:1:26:1:0.72539:1.60547:59.5:16:0.0123:0:1.8 +17 29663172 . A C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82573;LSEQ=AATGAATATACTCATCCTTT;RSEQ=CTGGATATTTTATAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:11,0:1,0:1,11:0.9167:0,0:20.5:1:32.4:1:1:0:57.5:22:0.9167:0:1 1/1:10:9:9,0:1,0:1,9:0.9:0,0:33.8:1:29.2:1:1:0:60:8:0.8889:0:1.1 +17 29663322 . A T 40 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05293;SOR=Inf;LSEQ=TTAAATTGGTAGAGTGATTA;RSEQ=AAACATGTTATTTTCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:247,79:326,0:0:2,0:22.9:1:30.6:1:1:0:60:107.667:1:0:0.1 0/1:302:4:1,3:205,93:298,4:0.0132:2,2:9.8:1:20.3:1:0.09641:6.56823:60:3:0.0101:0:1.8 +17 29663614 . GT G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.21394;LSEQ=GCTAAAACTTTGAGTCCCAT;RSEQ=TTTTTTTTTTAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:69:47,22:241,102:343,69:0.1605:2,2:24.9:1:31.9:1:0.77389:1.10569:59.9:138:0.1616:0.0302:1.3 0/1:357:14:9,5:227,111:338,14:0.0392:2,2:31.6:1:32:1:0.77976:1.13571:60:28:0.0398:0:1.4 +17 29663623 . TTT AAA 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=0.06469;SOR=0;LSEQ=TTGAGTCCCATGTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:5:3,2:293,130:423,5:0.011:2,2:26.4:1:26.9:1:0.64614:1.50104:56:10:0.0111:0:2 0/0:395:0:0,0:249,137:386,0:0:2,0:23.3:1:29.1:1:1:0:59:76.2:0.9769:0:1.1 +17 29663624 . TT AA 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=0.45996;LSEQ=TGAGTCCCATGTTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:186:134,52:144,75:219,186:0.4106:2,2:27.8:1:29.7:1:0.19745:1.34:59.8:92:0.4532:0:1.3 0/1:400:97:67,30:179,109:288,97:0.2425:2,2:25.2:1:28.3:1:0.27128:1.36:59.3:96:0.2526:0:1.3 +17 29663625 . T A 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGTCCCATGTTTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:125:74,51:39,19:58,125:0.27:2,2:19.5:1:28.9:1:0.32978:1.412:59.9:40.667:0.5351:0:1.4 0/0:422:0:0,0:61,36:97,0:0:2,0:22.8:1:27.4:1:1:0:59.2:15.167:0.3033:0:0.6 +17 29664354 . C A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATTAAAAAGTAATATTTT;RSEQ=TGTCTTTACTTGTTCCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:239,45:284,0:0:2,0:22.2:1:32.2:1:1:0:60:55.8:0.9964:0:0.1 0/1:256:18:15,3:178,60:238,18:0.0703:2,2:28.2:1:28.3:1:0.57422:1.68:60:36:0.0711:0:1 +17 29664645 . T A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03596;SOR=Inf;LSEQ=ACTAAGTTAAAATCTTTTTT;RSEQ=AAAAATATGTTAATACTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:69,200:269,0:0:2,0:23.4:1:29.3:1:1:0:60:268:1:0:0.1 0/1:209:4:1,3:51,154:205,4:0.0191:2,2:18.5:1:27.8:1:1:1.01:60:8:0.0194:0:1.8 +17 29664671 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52935;SOR=0;LSEQ=TATGTTAATACTATATAGAA;RSEQ=AAATATTGGTTTATTGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:54,140:194,2:0.0102:2,2:5.5:1:28.5:1:0.48352:2.58:60:4:0.0104:0:1 0/0:118:0:0,0:24,93:117,0:0:2,0:23.6:1:30.8:1:1:0:60:38:0.9913:0:0.1 +17 29665081 . C T 54 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12177;SOR=0.1962;LSEQ=TCCATCCCTGCAACCAAGAG;RSEQ=TCTTGTTGTCTTTGGGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:5:0,5:274,206:480,5:0.0103:2,0:9.2:1:23.6:1:0.01517:0:60:4:0.0084:0:2 0/0:491:1:0,1:260,229:489,1:0.002:2,0:1:0:23:0:0.46939:0:60:2:0.0021:0:1 +17 29670190 . C G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6399;SOR=0.89402;LSEQ=TAGAATATTTTTATGAAGTA;RSEQ=TATTAAGAAACCAGAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:385:343:53,290:10,30:40,343:0.8909:2,2:24.1:1:32.2:1:0.17276:1.82048:59.9:48:0.8889:0:1.1 1/1:332:292:63,229:10,29:39,292:0.8795:2,2:22.4:1:31.2:1:0.5426:1.25253:60:145:0.8815:0:1.1 +17 29675744 . T TAA 27 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAAAGGGACATCTTTTCT;RSEQ=AAAAAAAAAAATGTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:17:1:27.8:1:1:0:46.5:4:0.6667:0.3333:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 29675862 . A G 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGGGAATAGAAGATCTGA;RSEQ=AGACTATCATGTTTTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:19.5:1:32:1:1:0:60:4:0.5:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:18:0:31:0:1:0:60:2:1:0:1 +17 29675878 . T G 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGAAAGACTATCATGTTTT;RSEQ=TAATTTTCCTCTTCCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:25:1:32.6:1:1:0:54.4:10:0.8333:0:1.6 1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:33:0:1:0:60:2:1:0:1 +17 29675971 . T A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01594;SOR=0.12774;LSEQ=TTATACATAATTAATTATTC;RSEQ=CATTCACATATGCATGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:27:27,0:4,0:4,27:0.871:0,1:23.5:1:30.1:1:1:0:58.5:54:0.871:0:1 0/1:9:4:3,1:5,0:5,4:0.4444:0,2:32.3:1:29.5:1:0.44444:0:60:8:0.5:0:1 +17 29676104 . CTTGT C 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=6.000;MSILEN=4;SSF=1;SOR=1.16146;LSEQ=GTTCAAAAAATTAATTCTTA;RSEQ=TTGTTTGTTTGTTTGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:4:3,1:180,44:224,4:0.0175:2,2:30:1:32.8:1:1:1.36161:60:8:0.0181:0.0044:0 0/1:246:5:4,1:180,61:241,5:0.0203:2,2:22.2:1:32.4:1:1:1.35:60:10:0.0208:0:0.2 +17 29679236 . C T 51 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17404;SOR=5.17693;LSEQ=ACGATGGTTGTATTTGTCAC;RSEQ=ATATTAATTGATTTTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:1:0,1:266,70:336,1:0.003:2,0:1:0:24:0:0.21068:0:60:2:0.003:0:2 0/1:263:4:1,3:199,60:259,4:0.0152:2,2:5.8:1:25.5:1:0.04382:9.83882:60:8:0.0155:0:1.3 +17 29679246 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19385;LSEQ=TATTTGTCACCATATTAATT;RSEQ=ATTTTTCTCTATTGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:398:308:232,76:69,20:89,308:0.7739:2,2:23.2:1:29:1:0.77885:1.12985:59.9:50.333:0.7724:0:1.1 0/1:339:135:100,35:149,55:204,135:0.3982:2,2:22.9:1:27.8:1:0.90022:1.05:60:66.5:0.397:0:1.1 +17 29679470 . T A 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12008;SOR=Inf;LSEQ=ATGTAGATTTTTTTTATTAT;RSEQ=TAAAAAAATAGATATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:75,230:305,0:0:2,0:24:1:30.4:1:1:0:59.8:100.667:1:0:0.1 0/1:298:3:2,1:75,220:295,3:0.0101:2,2:9:1:20:1:0.16485:5.82:60:2:0.0068:0:1.7 +17 29679587 . A C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13051;SOR=Inf;LSEQ=AAAAGAGAGTTTGATAGATC;RSEQ=GTTAAGCATTATAAGTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:1,37:38,0:0:1,0:26.9:1:32.1:1:1:0:59.1:37:1:0:0.4 0/1:22:2:0,2:2,18:20,2:0.0909:2,0:30.5:1:26.5:1:1:0:60:4:0.0909:0:1 +17 29683898 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.15276;SOR=Inf;LSEQ=CTACTAAAGAAAGCTGTTGA;RSEQ=TTTTAGAAGTAACATTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:251,35:286,0:0:2,0:23.1:1:30.2:1:1:0:60:34.75:1:0:0.1 0/1:184:2:1,1:159,23:182,2:0.0109:2,2:15.5:1:27:1:0.24448:6.7878:60:4:0.0109:0:3 +17 29683915 . G T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1483;SOR=0;LSEQ=TGAATTTTAGAAGTAACATT;RSEQ=AAATAGTTAGGTGAAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:4:2,2:308,78:386,4:0.0103:2,2:26.8:1:28.5:1:0.18795:3.93016:60:8:0.0103:0:1 0/0:271:0:0,0:212,59:271,0:0:2,0:23.7:1:30.9:1:1:0:60:53.2:1:0:0.1 +17 29684520 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15691;SOR=Inf;LSEQ=ATTTTAGCTTTGAGACAGTA;RSEQ=GTTTAATGAGGGTTAAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:2,107:109,0:0:1,0:25:1:32:1:1:0:60:108:1:0:0.5 0/1:72:2:0,2:1,69:70,2:0.0278:1,0:19:0:31:0:1:0:60:4:0.0278:0:1 +17 29684553 . C T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-04;SOR=0.20481;LSEQ=TTAAGATTAGTTTTGACCTA;RSEQ=TAGATCTATTAGAAAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:61:2,59:0,13:13,61:0.8243:1,1:25.6:1:30.6:1:1:0:60:29.5:0.8194:0:1 0/1:35:17:0,17:0,18:18,17:0.4857:1,1:21.8:1:29.9:1:1:0:60:34:0.4857:0:1.1 +17 29685481 . C CT 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.31058;SOR=0.52095;LSEQ=CTAAAATGTTCCTCTGTTGA;RSEQ=TTTTTTTTTCTTTTAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:11:7,4:254,62:316,11:0.0336:2,2:19.7:1:30.4:1:0.24196:2.33354:60:22:0.0341:0.0061:0.3 0/1:281:5:3,2:216,59:275,5:0.0178:2,2:16:1:28.4:1:0.29916:2.43117:60:10:0.0179:0.0071:0.4 +17 29687463 . T TA 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.46142;SOR=0.46864;LSEQ=GCTTCAGATGGGGATTTACT;RSEQ=AAAAAAAAGGAACTAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:5:3,2:247,42:289,5:0.017:2,2:18.8:1:30.4:1:0.16289:3.8939:60:10:0.0171:0:0.8 0/0:249:2:2,0:193,54:247,2:0.008:2,0:21:1:29:1:1:0:60:4:0.0081:0.004:2.5 +17 29687870 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51754;SOR=0;LSEQ=TTACCTTGTAACTGACTTGA;RSEQ=TTTTGTTATTCTATGAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:0,2:0,33:33,2:0.0571:1,0:9.5:1:29:1:1:0:60:4:0.0571:0:1 0/0:22:0:0,0:1,21:22,0:0:1,0:25.3:1:31.9:1:1:0:59:44:1:0:0 +17 29694054 . G C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00748;SOR=0.26585;LSEQ=AAAAATACATCTACAAAGTT;RSEQ=TAAGTTCTCTCATTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:55:54,1:18,0:18,55:0.7534:1,1:21.1:1:32.3:1:1:0:60:110:0.7534:0:2 0/1:27:12:12,0:15,0:15,12:0.4444:1,0:28.9:1:30.5:1:1:0:60:11:0.4231:0:2.1 +17 29694063 . C A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01786;SOR=0.34837;LSEQ=TCTACAAAGTTGTAAGTTCT;RSEQ=TCATTTATTTACCAACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:58:57,1:20,0:20,58:0.7436:1,1:24.5:1:28.8:1:1:0:60:116:0.7436:0:1.9 1/0:36:18:18,0:18,0:18,18:0.5:1,1:23.8:1:27.7:1:1:0:60:17:0.4857:0:1.7 +17 29700960 . A T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49982;SOR=Inf;LSEQ=TGTGTCCCCGTTGTTAAGCG;RSEQ=CACATGACTGCAATGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:98,18:116,0:0:2,0:22.8:1:30:1:1:0:60:37.667:1:0:0 0/1:131:2:1,1:104,25:129,2:0.0153:2,2:9.5:1:23.5:1:0.35878:4.09878:60:4:0.0157:0:1 +17 29700989 . G T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25849;SOR=Inf;LSEQ=TGCAATGAAATTCAGTCCTG;RSEQ=AAGGAAAAGAAGAAGTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:135,50:185,0:0:2,0:24.7:1:31.2:1:1:0:60:60.667:1:0:0.1 0/1:234:3:1,2:160,71:231,3:0.0128:2,2:16.3:1:25:1:0.2302:4.47473:60:6:0.0131:0:1 +17 29763096 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50639;SOR=Inf;LSEQ=TGCTGGGGGGGCCCTTCCTG;RSEQ=ATTGCTGAGCAGGAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:12,5:17,0:0:2,0:28.2:1:30.9:1:1:0:60:16:1:0:0.2 0/1:25:2:1,1:11,12:23,2:0.08:2,2:41.5:1:25:1:1:1.09:60:4:0.08:0:1 +17 30264207 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49946;SOR=Inf;LSEQ=CGAGCGGTTGGTATTGCAGG;RSEQ=GCTTGCTCTCCGGGGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:32,34:66,0:0:2,0:27.5:1:30.4:1:1:0:54.5:32:1:0:0.1 0/1:77:2:0,2:40,35:75,2:0.026:2,0:24.5:1:29:1:0.22761:0:48.5:4:0.0267:0:1.5 +17 30264257 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51075;SOR=Inf;LSEQ=GCTGGCGGGGGGAGGAGGCA;RSEQ=GAACCGCGATGGCGCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:27,38:65,0:0:2,0:26.3:1:32.4:1:1:0:46.3:64:1:0:0.2 0/1:91:2:1,1:43,46:89,2:0.022:2,2:20:1:26.5:1:1:1.07:44.5:4:0.022:0:1 +17 30264306 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53812;SOR=Inf;LSEQ=CGGTGGGGGAGGGGGCGGCT;RSEQ=GGGGCCCAGCGCGGGGTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:39,0:0:2,0:11:1:28.6:1:1:0:37.5:8.75:1:0:0.5 0/1:71:2:1,1:40,29:69,2:0.0282:2,2:5.5:1:27.5:1:1:1.37295:34:4:0.0299:0:1.5 +17 30264348 . C T 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07913;SOR=0.15864;LSEQ=GGGAGGCGGCTTCGGGGGTT;RSEQ=GGCGGCGGTGGCGGCGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:4:1,3:207,102:309,4:0.0128:2,2:16:1:28:1:0.11158:6.05131:57:8:0.0129:0:1.3 0/0:489:1:0,1:285,203:488,1:0.002:2,0:1:0:27:0:0.41718:0:60:2:0.0021:0:1 +17 30264425 . GCCT G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.6434;SOR=0.85345;LSEQ=GAGGGGGTGGCAGTTACTCG;RSEQ=CCTCCTCCTCCTCCGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:781:21:12,9:468,292:760,21:0.0269:2,2:29.4:1:31.7:1:0.65808:1.20176:52.1:42:0.0277:0.0013:0.4 0/1:955:22:14,8:527,405:932,22:0.023:2,2:28:1:32:1:0.66428:1.34:48:44:0.0237:0.001:0.4 +17 30267579 . T TA 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.6252;SOR=2.42328;LSEQ=AAAGTACTATTTCTCAAAAT;RSEQ=AAAAAAAAAAACGAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:1,26:27,1:0.0357:1,0:45:0:11:0:1:0:20:0:0:0:0 0/1:36:3:0,3:1,32:33,3:0.0833:1,0:24:1:27.7:1:1:0:20:6:0.0857:0:0 +17 30293164 . A T 43 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19594;SOR=4.46226;LSEQ=ATTTCCTTTTTTTTTTTTTT;RSEQ=GCTTGTCAGCTCATTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:1:1,0:232,196:428,1:0.0023:2,0:33:0:12:0:1:0:51:0:0:0:2 0/1:387:4:1,3:212,170:382,4:0.0103:2,2:9.3:1:21.5:1:0.32947:3.7292:54:3:0.0086:0:1.5 +17 30293221 . T A 60 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.21773;SOR=4.86062;LSEQ=TCTTCCACAAAAATGGTATG;RSEQ=ATTTAAAAGTAAATAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:1:1,0:242,235:477,1:0.0021:2,0:1:0:29:0:1:0:60:2:0.0021:0:1 0/1:495:5:4,1:249,241:490,5:0.0101:2,2:5.8:1:26:1:0.37308:3.86:46.4:10:0.0103:0:1 +17 30293261 . C A 39 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62711;SOR=2.62595;LSEQ=GGCATTTTAATAGCAAGATA;RSEQ=CTTTGTGAATGTAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:1:0,1:103,132:235,1:0.0042:2,0:40:0:12:0:1:0:20:0:0:0:2 0/1:271:3:2,1:113,155:268,3:0.0111:2,2:5.3:1:25:1:0.57617:2.73:47.7:6:0.0115:0:1 +17 30293398 . G T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.0179;SOR=Inf;LSEQ=ATTTGTTTTTGGTGGATGGG;RSEQ=GTGCAGAGTGAAGGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:0,32:32,0:0:1,0:26.4:1:31.9:1:1:0:58.6:31:1:0:0.1 0/1:20:4:0,4:1,15:16,4:0.2:1,0:18:1:31:1:1:0:43.3:8:0.2:0:1 +17 30300060 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23947;SOR=Inf;LSEQ=GAGTGAACTTTTGAGAAGTC;RSEQ=TACTGTGGGAAATCTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:82,2:84,0:0:1,0:21.6:1:32.9:1:1:0:25.1:41:1:0:0.1 0/1:81:2:2,0:78,1:79,2:0.0247:1,0:13.5:1:32:0:1:0:28:4:0.0247:0:1 +17 30302411 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28111;SOR=Inf;LSEQ=GTGATCATGGCCTATCTCCC;RSEQ=TGTTTCCTATAGCTGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:24,0:0:1,0:23.5:1:31.3:1:1:0:29.1:48:1:0:0 0/1:39:3:3,0:34,2:36,3:0.0769:2,0:30:1:29.7:1:1:0:21.7:6:0.0789:0:1 +17 30302597 . C T 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4953;SOR=Inf;LSEQ=AACCCGGAAATTTCCCGTCC;RSEQ=TTGCAGTTTCCAGTAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:33,9:42,0:0:2,0:7.2:1:32.1:1:1:0:60:84:1:0:0 0/1:46:2:2,0:34,10:44,2:0.0435:2,0:5:0:30:0:1:0:60:4:0.0435:0:1 +17 30302736 . AT A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.20589;SOR=0.55236;LSEQ=AACCAATGAAAATATTGGTA;RSEQ=TTTTTTTTTTACTAGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:15:1,14:55,103:158,15:0.0862:2,1:31.9:1:32.4:1:0.03927:7.42004:25.9:30:0.0888:0:0 0/1:182:9:3,6:52,118:170,9:0.0495:2,2:31.7:1:30.7:1:1:1.13:21.8:18:0.0506:0:0.1 +17 30302750 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49823;SOR=0;LSEQ=TTGGTAATTTTTTTTTTTAC;RSEQ=AGATTTTATCACTGGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:38,101:139,2:0.0142:2,2:17:1:29.5:1:0.47812:2.64:22:4:0.0148:0:1.5 0/0:139:0:0,0:38,101:139,0:0:2,0:26.4:1:28.3:1:1:0:47:68.5:1:0:0.1 +17 30315287 . A G 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00051;SOR=Inf;LSEQ=TTTTTTAATTTCTACAATTT;RSEQ=TTTGAATTCATTATCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:162,6:168,0:0:1,0:22.7:1:28.4:1:1:0:59.7:55:1:0:0.1 0/1:132:9:8,1:115,8:123,9:0.0682:2,2:18.3:1:30.7:1:0.48131:1.78695:60:8:0.0625:0:1.1 +17 30315470 . C T 229 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTAGAAATTCAGAGAGTCT;RSEQ=CATCAGGAAAACAAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:179:85,94:368,400:768,179:0.1888:2,2:26.4:1:30.7:1:0.93395:1.0174:60:358:0.191:0:1.1 0/0:1115:0:0,0:542,572:1114,0:0:2,0:26.1:1:30.4:1:1:0:60:84.692:1:0:0.1 +17 30320386 . G A 42 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13044;SOR=Inf;LSEQ=ACCCTTCTTAAAGTAATTAT;RSEQ=AAATGTATTTGTTTTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:82,229:311,0:0:2,0:23.4:1:32:1:1:0:60:50.833:1:0:0.1 0/1:375:4:3,1:109,259:368,4:0.0107:2,2:14:1:21:1:0.08339:7.09:60:3:0.0082:0:2 +17 30320860 . CT C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.0298;SOR=0.54036;LSEQ=ATGCGTAAATTGGAGATTTG;RSEQ=TTTTTTTTTTAATTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:38:29,9:208,66:274,38:0.121:2,2:27.6:1:32.8:1:1:1.02:60:76:0.1222:0.0096:0.2 0/1:318:22:16,6:212,81:293,22:0.0692:2,2:28.6:1:30.5:1:1:1.02:59.3:44:0.0701:0.0031:0.3 +17 30321113 . T G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.04336;SOR=Inf;LSEQ=ATCTATGTACCCACAAAAAT;RSEQ=TTTTAAATTAAAAAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:3,93:96,0:0:1,0:24:1:30.6:1:1:0:59.3:47:1:0:0.1 0/1:53:3:0,3:1,49:50,3:0.0566:1,0:23.7:1:32.3:1:1:0:60:6:0.0566:0:1 +17 30321131 . GA G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.10051;SOR=Inf;LSEQ=ATTTTTTAAATTAAAAAAGG;RSEQ=AAAAATATGCATTAAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:2,68:70,0:0:1,0:24:1:32:1:1:0:59.1:140:1:0:0.1 0/1:33:2:0,2:1,30:31,2:0.0606:1,0:26.5:1:28.5:1:1:0:60:4:0.0606:0:0 +17 30321556 . AT A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.28556;SOR=1.34172;LSEQ=TAGGATAGGATACTTAATAT;RSEQ=TTTTTTTTTTACATTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:27:21,6:211,51:262,27:0.0934:2,2:23.4:1:31.4:1:0.7993:1.18139:58.8:26:0.0909:0.0173:0.1 0/1:288:35:27,8:193,59:252,35:0.1215:2,2:20.7:1:29.4:1:1:1.03:60:70:0.1228:0.0208:0.2 +17 30321567 . T G 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACTTAATATATTTTTTTTTT;RSEQ=ACATTTTTGTTGCAGTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:264,77:341,0:0:2,0:22.6:1:30:1:1:0:59.7:36.889:0.997:0:0.2 0/1:326:16:14,2:221,89:310,16:0.0491:2,2:21.3:1:32:1:0.25183:2.81:59.9:32:0.0502:0:1.6 +17 30321762 . G C 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TAGGTAAAAAGGGCATATAA;RSEQ=AAAAGTTTAAGCTCTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:87,234:321,0:0:2,0:23.8:1:32:1:1:0:60:63.2:1:0:0.1 0/1:302:15:4,11:73,213:286,15:0.0497:2,2:18.9:1:32:1:1:1.06:60:30:0.0503:0:1.1 +17 30323737 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23779;SOR=Inf;LSEQ=ATATGTTGTATTTTTAGTTC;RSEQ=AAAACATTCTGTTTTTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:114,0:114,0:0:1,0:26.1:1:31.1:1:1:0:60:56:1:0:0.1 0/1:109:2:2,0:102,5:107,2:0.0183:1,0:25.5:1:31.5:1:1:0:60:4:0.0183:0:1 +17 30323950 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11375;SOR=0;LSEQ=TTATTCTTTATGGTCTTTTG;RSEQ=TGTTTCACATTCTAGAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:25,161:186,3:0.0159:2,2:9.7:1:30:1:0.36017:3.19:60:6:0.016:0:1.3 0/0:200:0:0,0:39,160:199,0:0:2,0:21.1:1:31.5:1:1:0:60:198:0.995:0:0.1 +17 30695964 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCGGGAGGCGGAGGTTG;RSEQ=GGTGAGCTGAGACCAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19:1:30.5:1:1:0:42.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 30696193 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.12426;SOR=0;LSEQ=TCTGGCAAAAGTAAATAGTT;RSEQ=GGATGTAAGGGTAAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:117,47:164,2:0.012:2,2:17:1:29:1:0.49595:2.47381:60:4:0.0123:0:1 0/0:304:0:0,0:189,114:303,0:0:2,0:24.8:1:30.4:1:1:0:60:49.5:0.9966:0:0.1 +17 30696292 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14397;LSEQ=CTGCATTCGAGTATTTAGCC;RSEQ=TGCGCTTATTTTTATTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:339:316:144,172:11,12:23,316:0.9322:2,2:24.7:1:30.8:1:0.83244:1.09461:59.9:157:0.9318:0:1.1 1/0:452:300:131,169:71,81:152,300:0.6637:2,2:25.3:1:29.3:1:0.54944:1.1305:60:49:0.6607:0:1.2 +17 30696296 . G A 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=30.15547;LSEQ=ATTCGAGTATTTAGCCCTGC;RSEQ=CTTATTTTTATTCCCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:1:1,0:154,180:334,1:0.003:2,0:13:0:33:0:0.46269:0:60:2:0.003:0:2 0/1:435:36:15,21:177,222:399,36:0.0828:2,2:24.5:1:29.1:1:0.86137:1.11591:60:72:0.0837:0:2 +17 30696372 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5107;SOR=Inf;LSEQ=TCTTCCTCGGCCAGGACAGG;RSEQ=CCCCATCGGTAATCCACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:35,94:129,0:0:2,0:22:1:31.8:1:1:0:60:128:1:0:0.4 0/1:177:2:1,1:52,123:175,2:0.0113:2,2:27.5:1:27:1:0.5104:2.35:60:4:0.0114:0:1 +17 31030528 . T G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGGTGGTATTGAACTCCTG;RSEQ=GCTAAAGTGATCCTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:21,1:0,0:0,22:1:0,1:24.4:1:30.9:1:1:0:59:21:1:0:1.1 1/1:14:14:14,0:0,0:0,14:1:0,1:22.1:1:31.6:1:1:0:60:28:1:0:1 +17 31030618 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50131;SOR=Inf;LSEQ=TATTGACGATTTTGATCTTG;RSEQ=CCTATGATTCCCTAGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:78,26:104,0:0:2,0:23.7:1:31.6:1:1:0:60:33.667:1:0:0.2 0/1:123:2:1,1:83,38:121,2:0.0163:2,2:11:1:27.5:1:0.53539:2.16902:60:4:0.0167:0:1 +17 31030620 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50148;SOR=Inf;LSEQ=TTGACGATTTTGATCTTGCC;RSEQ=TATGATTCCCTAGAATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:80,28:108,0:0:2,0:24:1:31.5:1:1:0:60:53:1:0:0.2 0/1:128:2:1,1:85,40:125,2:0.0156:2,2:24.5:1:28:1:0.54318:2.11128:60:4:0.0156:0:1 +17 31030716 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05001;LSEQ=TCATATCCCATTCCTCTTCC;RSEQ=AGACAACAAAATATTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:238:224:110,114:5,9:14,224:0.9412:2,2:26.9:1:30.7:1:0.41357:1.73:59.9:223:0.9409:0:1.1 0/1:298:132:65,67:78,87:165,132:0.443:2,2:26.2:1:29.3:1:0.81528:1.08:60:65:0.4498:0:1.1 +17 31030771 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50776;SOR=Inf;LSEQ=AATATTAGAGGATTATAAAT;RSEQ=TTTGTTATGCATTTGGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:35,94:129,0:0:2,0:23.3:1:32.4:1:1:0:60:63.5:1:0:0.7 0/1:170:2:1,1:54,114:168,2:0.0118:2,2:40.5:1:28.5:1:0.54368:2.10:60:4:0.0118:0:3 +17 31030783 . T G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50474;SOR=Inf;LSEQ=TTATAAATCTTTGTTATGCA;RSEQ=TTGGTACATTGTTTTCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:23,83:106,0:0:2,0:23.2:1:30.2:1:1:0:60:52:1:0:0.6 0/1:134:2:1,1:41,91:132,2:0.0149:2,2:45:0:32.5:1:0.53024:2.20:60:4:0.0152:0:1.5 +17 31030811 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=ATTGTTTTCATTAAAATTTG;RSEQ=CTAATTGTTAATTATTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:7,64:71,0:0:2,0:24.6:1:31.7:1:1:0:60:22.667:0.9855:0:0.2 0/1:81:2:1,1:18,60:78,2:0.0247:2,2:9:0:31:1:0.42089:3.27:60:4:0.0247:0:1 +17 31819598 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.82176;LSEQ=GGGTCACACCACCTTGTTGA;RSEQ=TGAACATACCTTTCCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:89:37,52:281,301:582,89:0.1319:2,2:27.2:1:31.1:1:0.25567:1.31149:60:178:0.1334:0:1.1 0/1:583:175:83,92:203,204:407,175:0.3002:2,2:25.6:1:29.7:1:0.6513:1.10281:60:174:0.301:0:1.1 +17 31819774 . A G 32 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16812;SOR=Inf;LSEQ=ACCATCTGTGATCCATGTAC;RSEQ=CATGTGACAGTGAACTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:41,0:0:1,0:24.4:1:29.8:1:1:0:59.3:40:1:0:0.1 0/1:29:2:1,1:1,26:27,2:0.069:1,2:7.5:1:32.5:1:0.13547:18.73:60:4:0.069:0:1 +17 31887973 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACCTTCCAAAATACCAC;RSEQ=TCGCCTCCCTGGTGTGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 31889916 . C T 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00057;SOR=15.25988;LSEQ=TAAACTGGGCCTGAGTGTCA;RSEQ=CCTCTTGATTCATTTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:1,0:224,166:390,1:0.0026:2,0:43:0:30:0:1:0:60:2:0.0026:0:2 0/1:292:11:5,6:159,122:281,11:0.0377:2,2:30:1:28.4:1:0.54302:1.56148:60:10:0.0348:0:1.6 +17 31889935 . G A 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41012;SOR=2.71248;LSEQ=ACCCTCTTGATTCATTTTCT;RSEQ=CACTCCCTTAGTATTTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:2:1,1:216,204:420,2:0.0047:2,2:40.5:1:28.5:1:1:1.05871:60:4:0.0048:0:1 0/1:314:4:2,2:160,150:310,4:0.0127:2,2:9.8:1:27.3:1:1:1.06641:60:8:0.0129:0:1.3 +17 31889954 . G A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.64873;SOR=1.07667;LSEQ=TGCACTCCCTTAGTATTTAG;RSEQ=CAACTTCCCTGCATACCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:419:231:104,127:86,100:186,231:0.5513:2,2:24.7:1:29.9:1:0.8434:1.05004:60:76:0.5534:0:1.1 1/0:302:172:83,89:61,68:129,172:0.5695:2,2:24:1:28.5:1:0.90743:1.04:59.9:56.333:0.5748:0:1.2 +17 31889971 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07259;SOR=Inf;LSEQ=TAGGCAACTTCCCTGCATAC;RSEQ=ACAGCCAGTTGCAGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:171,223:394,0:0:2,0:24.7:1:31.6:1:1:0:60:55.286:1:0:0.6 0/1:283:3:2,1:129,151:280,3:0.0106:2,2:13:1:27:1:0.59777:2.33:60:6:0.0107:0:1.7 +17 31890240 . G T 42 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATACTTCAGTTAGCACAG;RSEQ=ACAAGAAGGGAAATGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:13.3:1:26.7:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 31891106 . C A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGCACCGCGGCAGCCCC;RSEQ=CTGAGGAGGTGAGGCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:31.5:1:1:0:60:4:1:0:2.5 +17 31891149 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCCTGCACGGTCTTGCA;RSEQ=GGCTGAGATGAACCGGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:29.5:1:1:0:60:4:1:0:2.5 +17 32421391 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50273;SOR=0;LSEQ=TTCTAACTGAATCAGAACAT;RSEQ=AACTCAGGGTGCTCAAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:30,3:33,2:0.0571:2,2:21.5:1:30.5:1:0.21849:8.80417:60:4:0.0571:0:1 0/0:26:0:0,0:24,2:26,0:0:2,0:22.5:1:30.8:1:1:0:60:52:1:0:0.1 +17 32421433 . T C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51158;SOR=0;LSEQ=GACCTCACAGCCAGACAGGC;RSEQ=GCATCTCAAGCAGGCACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:50,29:79,2:0.0247:2,2:15.5:1:27.5:1:1:1.71195:60:4:0.025:0:1 0/0:57:0:0,0:35,22:57,0:0:2,0:26.5:1:29.7:1:1:0:60:56:1:0:0.2 +17 32421459 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17202;SOR=Inf;LSEQ=TCAAGCAGGCACATCTAACT;RSEQ=CTGCAGGACGCTGACTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:68,47:115,0:0:2,0:25.6:1:32.3:1:1:0:60:230:1:0:0.2 0/1:82:2:1,1:43,37:80,2:0.0244:2,2:26:1:29.5:1:1:1.16002:60:4:0.0247:0:1 +17 32421466 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17211;SOR=Inf;LSEQ=GGCACATCTAACTGCTGCAG;RSEQ=ACGCTGACTCCTCAATGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:64,58:122,0:0:2,0:26:1:31.4:1:1:0:60:121:1:0:0.2 0/1:87:2:1,1:43,42:85,2:0.023:2,2:39:0:30:0:1:1.02354:60:4:0.0233:0:1.5 +17 32421557 . A G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.53115;SOR=0;LSEQ=TACATGGGAAACCAAGGCAC;RSEQ=CAGTTACACAGTTAGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:1,36:37,2:0.0513:1,2:22:1:28:1:0.10121:25.81:60:4:0.0526:0:1 0/0:22:0:0,0:2,20:22,0:0:2,0:20.6:1:30.1:1:1:0:60:44:1:0:0 +17 32421636 . G A 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=2.31595;LSEQ=ACAGCACAAGTCACTTTGGA;RSEQ=ATCATGAAGCAATTGCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:34.3:1:30.8:1:1:0:60:8:0.4444:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:20.5:1:28:1:1:0:60:4:0.6667:0:1 +17 33428167 . G A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGAAGACATCTGTGGGTATG;RSEQ=AAACCACCCTCCAGGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:277,214:491,0:0:2,0:23.3:1:31.8:1:1:0:60:97.2:1:0:0.1 0/1:446:16:9,7:256,173:429,16:0.0359:2,2:24.1:1:28.6:1:0.79995:1.15056:60:32:0.0364:0:1.1 +17 33428445 . G A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35375;SOR=3.28333;LSEQ=AGAGGACATCGATTACTACC;RSEQ=CTTCATTTTACGGAGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:1:1,0:27,164:191,1:0.0052:2,0:1:0:25:0:0.14583:0:60:2:0.0052:0:1 0/1:177:3:2,1:37,137:174,3:0.0169:2,2:8:1:26:1:0.1226:7.29:60:6:0.0171:0:1 +17 33428487 . A G 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.79125;LSEQ=ACAGAGGCCTAGCACAGAGA;RSEQ=ATAACTTCCCCAAGGTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:5:1,4:1,78:79,5:0.0595:1,2:18.2:1:33.4:1:0.11618:17.55:60:10:0.0602:0:1.2 0/1:63:3:0,3:0,60:60,3:0.0476:1,0:12:1:32.3:1:1:0:60:6:0.05:0:1 +17 33430203 . G T 67 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01589;SOR=Inf;LSEQ=CACTTTGGGGTTCAGAAGCT;RSEQ=ACATTTAAGGGAAATAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:0:0,0:405,226:631,0:0:2,0:24.1:1:32.1:1:1:0:60:89.143:1:0:0.1 0/1:683:7:2,5:440,236:676,7:0.0102:2,2:7.3:1:24:1:0.10333:4.64997:60:6:0.0089:0:1 +17 33430316 . C T 186 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=29.15867;LSEQ=GGGCCAGGGTCTTCAGCTCT;RSEQ=GGGCCAGCTGCATCATCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1061:3:0,3:497,560:1057,3:0.0028:2,0:1:0:26.3:1:0.2522:0:60:6:0.0029:0:1 0/1:1086:83:34,49:449,554:1003,83:0.0764:2,2:24.1:1:29.3:1:0.56595:1.16786:60:166:0.0771:0:1.2 +17 33430327 . C A 194 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02951;LSEQ=TTCAGCTCTCGGGCCAGCTG;RSEQ=ATCATCAAGGCCAAGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:977:89:41,48:420,467:887,89:0.0911:2,2:26.6:1:30.1:1:0.82488:1.05287:60:21.25:0.0892:0:1.2 0/0:1018:3:3,0:442,572:1014,3:0.0029:2,0:1:0:23:1:0.08346:0:60:6:0.003:0:1.3 +17 33430714 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATCACAGAATGTCATCAGCA;RSEQ=CAATGTCTCCCTCGTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:0,2:1,52:53,2:0.0364:1,0:22.5:1:30.5:1:1:0:60:4:0.04:0:1 0/0:17:0:0,0:2,15:17,0:0:2,0:15.8:1:31.7:1:1:0:60:34:1:0:0 +17 33433487 . C T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.002;SOR=1.93146;LSEQ=CATGCACCACCTGGATCCTC;RSEQ=GGAGAGCTTCTGCCTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:36:15,21:200,282:482,36:0.0692:2,2:24.3:1:31.1:1:1:1.01:60:35:0.0689:0:1.2 0/1:549:69:29,40:216,262:478,69:0.1257:2,2:22.8:1:29.6:1:0.69807:1.13688:59.9:68:0.1252:0:1.1 +17 33433554 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=Inf;LSEQ=GATAAGAGGGAGTAGGGGGG;RSEQ=CAAGGTAAGGCTGAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:41,133:174,0:0:2,0:22.9:1:29.7:1:1:0:60:23.857:1:0:0.1 0/1:189:2:1,1:52,135:187,2:0.0106:2,2:33:1:30.5:1:0.48328:2.58:60:4:0.0108:0:1 +17 33433555 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49937;SOR=Inf;LSEQ=ATAAGAGGGAGTAGGGGGGT;RSEQ=AAGGTAAGGCTGAGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:40,133:173,0:0:2,0:22.5:1:32.1:1:1:0:60:27.833:1:0:0.1 0/1:187:2:1,1:51,134:185,2:0.0107:2,2:11.5:1:28.5:1:0.4799:2.61:60:4:0.0109:0:1 +17 33433820 . A G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43516;SOR=0.50813;LSEQ=GAGGGTTTCCTGGAAGAATC;RSEQ=GTGTGAGTAGCATCCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:28:24,4:5,2:7,28:0.8:2,2:25.1:1:29.2:1:0.57616:2.33:60:13:0.7879:0:1.4 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:23.3:1:29.3:1:1:0:60:16:0.7273:0:1 +17 33434190 . A G 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16409;SOR=Inf;LSEQ=ACACTTCAGAGAGGGTCCAG;RSEQ=TGGGAGCTCCCCACCAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:96,197:293,0:0:2,0:23.7:1:30.4:1:1:0:59.9:35.625:1:0:0.1 0/1:200:2:1,1:55,143:198,2:0.01:2,2:7.5:1:30:1:0.48261:2.59:60:4:0.0101:0:1 +17 33434276 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.15614;SOR=Inf;LSEQ=TCCTTATTACCCATCTTCTC;RSEQ=CTGTTGGGCTCTGAACCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:219,68:287,0:0:2,0:23.5:1:31.8:1:1:0:59.9:40:1:0:0.1 0/1:188:2:1,1:150,35:185,2:0.0106:2,2:32.5:1:29.5:1:0.3488:4.23984:60:4:0.0108:0:1 +17 33434519 . GA G 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0.97885;LSEQ=AGGTTAGGAGGAAGACAGGG;RSEQ=AAAGGTACCAAGAAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:1,2:37,194:231,3:0.0128:2,2:17.3:1:30.1:1:0.41382:2.61:60:6:0.0129:0.0043:0 0/1:239:3:0,3:56,179:235,3:0.0126:2,0:11.7:1:28:1:1:0:60:6:0.0128:0.0042:0.3 +17 33444110 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17623;SOR=Inf;LSEQ=CAATCGGCTTCCTGTTCACC;RSEQ=CTCCCTCCTTACCGTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:40,213:253,0:0:2,0:22.9:1:29.6:1:1:0:60:35.143:1:0:0.1 0/1:185:2:1,1:31,152:183,2:0.0108:2,2:29:1:28:1:0.3168:4.84:60:4:0.0109:0:1 +17 33445416 . TA T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.0059;SOR=0.26984;LSEQ=CCTTCCCATCCATTATTGGT;RSEQ=AAAAAAAAACCCCTCCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:24:24,0:267,7:274,24:0.0805:1,1:28.3:1:31.4:1:1:0:60:48:0.0814:0.0067:0.2 0/1:217:5:4,1:202,8:210,5:0.023:1,2:18.2:1:30.1:1:0.19416:6.19197:60:10:0.0234:0.0092:0 +17 33445549 . G A 189 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=58.9861;LSEQ=CCAGTGGACAGGATGGCAGT;RSEQ=GAGGTCTTCAGTTCCTCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1346:2:2,0:613,728:1341,2:0.0015:2,0:11.5:1:26.5:1:0.20951:0:60:4:0.0015:0:1 0/1:1312:106:59,47:585,621:1206,106:0.0808:2,2:20.9:1:28.2:1:0.18756:1.33:59.6:20.2:0.0783:0:1.3 +17 33817200 . C T 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCCGGGCTGCTGCAGCCA;RSEQ=CAGCGCTGGGACGAGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:153,268:421,0:0:2,0:24.2:1:31.7:1:1:0:59.8:37.273:1:0:0.1 0/1:374:19:7,12:155,198:353,19:0.0508:2,2:19.7:1:26.9:1:0.63878:1.34095:59.9:5.333:0.0438:0:1.1 +17 33817422 . A G 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.48175;LSEQ=GAAGTTCATTCAGCTCCTGA;RSEQ=CCAGTCACCCGATGGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:452:384:199,185:33,34:67,384:0.8496:2,2:27:1:32.3:1:0.79126:1.11:33.9:37.4:0.8481:0:1.1 1/0:409:299:155,144:61,48:109,299:0.7311:2,2:25.7:1:31.3:1:0.50188:1.18016:34.2:148.5:0.7333:0:1.1 +17 33817496 . G T 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TGCAAAATAGAAGGATTTAT;RSEQ=ATATCACCAAAGCTCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:0:0,0:244,285:529,0:0:2,0:25.6:1:32.3:1:1:0:43.2:175.333:1:0:1 0/1:478:13:5,8:225,239:464,13:0.0272:2,2:32.1:1:28.7:1:0.57898:1.505:43.2:26:0.0273:0:2.2 +17 33817525 . T C 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00282;SOR=0.13685;LSEQ=AAAGCTCTGAAAGGCATCCA;RSEQ=CTCATTAAGAAGAAGTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:475:473:231,242:0,1:1,473:0.9958:0,2:27.1:1:32:1:1:0:47.9:77.833:1:0:1.1 1/1:433:420:204,216:9,4:13,420:0.97:2,2:24.5:1:31.1:1:0.16701:2.3778:48.4:83:0.9696:0:1.2 +17 33817688 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17636;SOR=1.42481;LSEQ=TCCCAAGCTGCACGCTGGAC;RSEQ=TCAAACTATTAACCGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:31:16,15:278,250:528,31:0.0555:2,2:28:1:31.4:1:1:1.04244:59:62:0.0561:0:1.1 0/1:518:40:26,14:240,238:478,40:0.0772:2,2:24.4:1:30:1:0.09865:1.84:57.9:80:0.0781:0:1.1 +17 33817706 . G GATTC 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.00013;SOR=Inf;LSEQ=ACCTCAAACTATTAACCGAG;RSEQ=ATTCAGATCGTCAAAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:578:0:0,0:304,272:576,0:0:2,0:24.4:1:31.6:1:1:0:57.7:51.364:0.9982:0:0.2 0/1:526:12:8,4:279,235:514,12:0.0228:2,2:18.9:1:30.1:1:0.56:1.68:55.5:24:0.0232:0.0057:0 +17 33817716 . G A 143 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.97769;LSEQ=ATTAACCGAGGATTCAGATC;RSEQ=TCAAAGGTTAGCTTACGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:2:1,1:326,269:595,2:0.0033:2,2:30:1:29.5:1:1:1.2115:60:4:0.0034:0:1 0/1:545:31:15,16:283,231:514,31:0.0569:2,2:23.3:1:28.9:1:0.57799:1.30613:55.5:62:0.0572:0:1 +17 33818130 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33297;LSEQ=TGCCTCCCCTGCTGCAAGAT;RSEQ=ACCATTTGTGAACTTACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:562:433:193,240:56,73:129,433:0.7705:2,2:26:1:29.6:1:0.84049:1.05:59.5:53.125:0.7727:0:1.1 1/0:527:278:119,159:111,138:249,278:0.5275:2,2:25.4:1:28.8:1:0.72509:1.07457:59.9:91.667:0.5258:0:1.2 +17 33818293 . AT A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.25473;SOR=0;LSEQ=TGAACTCTCCTTAAAAACCA;RSEQ=TTTTTTAAATCATGGAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:3:2,1:43,156:199,3:0.0149:2,2:24:1:29:1:0.12533:7.16:53.3:6:0.015:0.005:0 0/0:167:0:0,0:46,121:167,0:0:2,0:24.4:1:29:1:1:0:59.6:54.667:1:0:0.1 +17 33818305 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18958;SOR=Inf;LSEQ=AAAAACCAATTTTTTTAAAT;RSEQ=ATGGAACCAGAACATATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:33,144:177,0:0:2,0:21.1:1:32.2:1:1:0:59.1:354:1:0:0.2 0/1:137:2:1,1:35,99:134,2:0.0146:2,2:25:1:27:1:0.46078:2.80:60:4:0.0146:0:2 +17 33818312 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18413;SOR=Inf;LSEQ=AATTTTTTTAAATCATGGAA;RSEQ=CAGAACATATGTCATGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:22,127:149,0:0:2,0:20.9:1:31.4:1:1:0:59.1:148:0.9933:0:0.1 0/1:114:2:1,1:23,89:112,2:0.0175:2,2:18:1:29:1:0.3782:3.81:60:4:0.0175:0:2 +17 34100256 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50062;SOR=Inf;LSEQ=AGGTGAGCCGGATGTCAGCG;RSEQ=GGCCTGTGGCTGGGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:25,23:48,0:0:2,0:28.9:1:31.3:1:1:0:60:47:1:0:0.3 0/1:59:2:1,1:29,28:57,2:0.0339:2,2:32.5:1:27.5:1:1:1.03511:60:4:0.0351:0:1 +17 34100284 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49438;SOR=Inf;LSEQ=GGCTGGGGCCTCCCAGAACT;RSEQ=CAGCGCTGAGACGTTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:17,28:45,0:0:2,0:25:1:31.8:1:1:0:60:90:1:0:0.3 0/1:45:2:1,1:18,25:43,2:0.0444:2,2:7.5:1:27.5:1:1:1.38:60:4:0.0444:0:1 +17 34100350 . G GC 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCGAACTGCCGGCTCCG;RSEQ=AGATGCTCAGGCCAGTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:0,14:1:0,1:24.1:1:33.4:1:1:0:60:28:1:0.1429:0.1 1/1:7:7:0,7:0,0:0,7:1:0,0:27.6:1:32.3:1:1:0:60:14:1:0:0.1 +17 36059034 . A AG 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCACATCCATGGCCTT;RSEQ=TCACACCCTGCCCACACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:34.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 36061130 . G A 47 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13979;SOR=0;LSEQ=GGCTGCAGGGCTGCCAGGCT;RSEQ=CCGGCCACACTGTTGATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:4:3,1:129,184:313,4:0.0126:2,2:16.3:1:23.5:1:0.31159:4.26:54.8:3:0.0096:0:1 0/0:236:0:0,0:107,129:236,0:0:2,0:26.9:1:30.9:1:1:0:60:58:1:0:0.2 +17 36061152 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16562;SOR=Inf;LSEQ=CGGCCACACTGTTGATGACA;RSEQ=GGACACTCTGTGCTTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:83,164:247,0:0:2,0:23.5:1:31.4:1:1:0:60:81.333:1:0:0.1 0/1:170:2:1,1:60,108:168,2:0.0118:2,2:10:0:31.5:1:1:1.79:60:4:0.012:0:1 +17 36061184 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12945;SOR=Inf;LSEQ=GCTTGGGAGGTGTTGAGGCC;RSEQ=GTGGGAGCAAGAGGAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:12,117:129,0:0:2,0:21.7:1:30.6:1:1:0:60:128:1:0:0.1 0/1:73:2:1,1:9,62:71,2:0.0274:2,2:20:1:28:1:0.25685:6.59:60:4:0.0274:0:1.5 +17 36061282 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.13382;SOR=5.95526;LSEQ=CTCAATGTCCCAGTCACCGG;RSEQ=CTGAGCCTGTTACACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:1:0,1:0,21:21,1:0.0455:1,0:17:0:32:0:1:0:60:2:0.0455:0:2 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:24.7:1:26.7:1:1:0:60:6:0.2308:0:2 +17 36061297 . C T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00165;SOR=Inf;LSEQ=ACCGGGCTGAGCCTGTTACA;RSEQ=AGGAGATTCCATGGGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:0,9:0,13:13,9:0.4091:1,0:17.3:1:29.7:1:1:0:60:18:0.4091:0:1.1 1/1:10:10:0,10:0,0:0,10:1:0,0:26.4:1:28.1:1:1:0:60:20:1:0:1.3 +17 36091780 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52119;SOR=0;LSEQ=CCAAGTTGGAGCCCAGGCCG;RSEQ=GGGCTTTGGAGGGGGACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:17,43:60,2:0.0323:2,2:20.5:1:33:1:0.49974:2.49:60:4:0.0339:0:2 0/0:39:0:0,0:10,28:38,0:0:2,0:24.8:1:29.3:1:1:0:60:76:1:0:0.1 +17 36093022 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTCAGCGGGGGCAGAGT;RSEQ=GACTGAACAGATCTGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:29.5:1:1:0:60:4:1:0:1.5 +17 36097661 . CA C 27 d5;v3;p8;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGTCTCTACTAAAAATAC;RSEQ=AAAAAAAAAAAAAATTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:7.5:1:27.4:1:1:0:21.5:4:0.6667:0.3333:0 +17 36099471 . C T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14387;SOR=Inf;LSEQ=TTTCTGACGTACCAGGTGTA;RSEQ=AGAGCGGCACGCTTCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:119,70:189,0:0:2,0:25:1:32:1:1:0:59.9:46.25:1:0:0.1 0/1:116:2:0,2:71,43:114,2:0.0172:2,0:21.5:1:24.5:1:0.14843:0:60:4:0.0182:0:1 +17 36099480 . A T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06704;SOR=Inf;LSEQ=TACCAGGTGTACAGAGCGGC;RSEQ=CGCTTCTGGGTCTTCATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:115,75:190,0:0:2,0:29:1:30:1:1:0:59.9:62.333:1:0:0.1 0/1:131:3:1,2:75,52:127,3:0.0229:2,2:13.3:1:25.3:1:0.56982:2.8611:60:6:0.0234:0:1.7 +17 36099518 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50659;SOR=0;LSEQ=AGGGGTGCCCTTGTTGAGAT;RSEQ=CTGGGAGAGGTGCGACTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:97,92:189,2:0.0105:2,2:30:1:31:1:1:1.05408:60:4:0.0106:0:1 0/0:148:0:0,0:75,73:148,0:0:2,0:23.1:1:30.7:1:1:0:60:36:1:0:0.2 +17 36099547 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50697;SOR=0;LSEQ=GGTGCGACTGGTTCAGGCCG;RSEQ=TGACATCGACCACCTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:51,82:133,2:0.0148:2,2:19:1:29.5:1:1:1.60:60:4:0.015:0:1 0/0:103:0:0,0:43,60:103,0:0:2,0:24.5:1:30.6:1:1:0:60:102:1:0:0.1 +17 36099858 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGAGGTTAGTGGGCAAAA;RSEQ=AGGACTTCCCATCTTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:19.5:1:31:1:1:0:55.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 36827523 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0119;SOR=Inf;LSEQ=AGGAGGAAAGTCCAAGAAGA;RSEQ=TATTTCATGCCCACCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:24.5:1:34.5:1:1:0:60:12:1:0:0 1/1:3:3:3,0:0,0:0,3:1:0,0:28:1:29.7:1:1:0:60:6:1:0:1 +17 37152094 . T C 50 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGCATGAGCCACTCAGC;RSEQ=GGCCATATATATATTTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:28:1:32:1:1:0:60:6:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:48:0:29:0:1:0:60:2:1:0:1 +17 37152369 . A G 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.35188;LSEQ=CTATTTCTCATCTTTTAGTG;RSEQ=CTGACCTAAAAATTTATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:816:680:341,339:72,63:135,680:0.8333:2,2:27.4:1:31.8:1:0.51089:1.13598:60:74.556:0.8356:0:1.1 1/0:833:531:246,285:142,157:299,531:0.6375:2,2:27.5:1:30.9:1:0.77214:1.04782:59.9:131.75:0.6388:0:1.1 +17 37152798 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAACCTGGTGTGCTTGGC;RSEQ=CCATGCCTGCCAGGGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:23.5:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 37618220 . C T 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00227;SOR=0;LSEQ=TGCCCTCCCCACCCCCTTCC;RSEQ=GGGGCGCTTTGGTGGGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:14:14,0:85,4:89,14:0.1359:1,1:21.7:1:32.6:1:1:0:60:28:0.1414:0:1 0/0:60:0:0,0:57,3:60,0:0:2,0:24.2:1:30:1:1:0:60:29:1:0:0.3 +17 37618266 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.22087;SOR=Inf;LSEQ=GGGGTTGGGGGGGTGGGTGG;RSEQ=GGTTGCTTTTTGGAGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:179,46:225,0:0:2,0:21.6:1:30.9:1:1:0:60:31.143:1:0:0.3 0/1:200:2:1,1:154,44:198,2:0.01:2,2:14.5:1:26.5:1:0.40025:3.47197:60:4:0.0104:0:1 +17 37618292 . C T 46 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.12443;SOR=0;LSEQ=CTTTTTGGAGTGCTGGGGAA;RSEQ=TTTTTTCCCTTCTTCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:4:1,3:253,116:369,4:0.0107:2,2:9.3:1:23.3:1:0.09764:6.5076:60:3:0.0083:0:1 0/0:355:0:0,0:246,109:355,0:0:2,0:23.2:1:30.8:1:1:0:60:43.375:1:0:0.3 +17 37619038 . G A 140 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=30.40839;LSEQ=AAACAAGATGATAGCCCCTC;RSEQ=GGAGCTTCTTATGGCCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:657:1:1,0:375,280:655,1:0.0015:2,0:1:0:26:0:1:0:60:2:0.0016:0:1 0/1:586:26:16,10:317,242:559,26:0.0444:2,2:21.8:1:29.8:1:0.68918:1.22:60:52:0.0452:0:1.2 +17 37619365 . C T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10707;SOR=0;LSEQ=TCTCTGAGTCGGAGTCCACT;RSEQ=CCCAGGTGAGCTATTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:80,154:234,3:0.0127:2,2:28:1:23:1:1:1.0388:60:2:0.0087:0:3.3 0/0:261:0:0,0:99,162:261,0:0:2,0:25.1:1:29.9:1:1:0:60:51.2:1:0:0.1 +17 37619376 . C A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11889;SOR=0;LSEQ=GAGTCCACTCCCCAGGTGAG;RSEQ=TATTTGTCTAACAGTCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:3:1,2:67,139:206,3:0.0144:2,2:37:1:25.7:1:1:1.04:60:2:0.0098:0:1.3 0/0:215:0:0,0:77,138:215,0:0:2,0:25:1:30.9:1:1:0:60:70.667:1:0:0.1 +17 37626963 . G A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.65066;LSEQ=ACATTTAGTCCTGTCTCCTT;RSEQ=GGGTGCCTCTTGATTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:28:28,0:2,0:2,28:0.9333:0,1:26.9:1:27.5:1:1:0:58.9:27:0.931:0:1.2 1/1:10:9:8,1:1,0:1,9:0.9:0,2:20.7:1:28.8:1:1:0:60:18:0.9:0:1.2 +17 37627072 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19282;SOR=Inf;LSEQ=CATAGTTTGTTTTATTGATC;RSEQ=GTTTTCCTCCATATACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:186,42:228,0:0:2,0:23.7:1:31.9:1:1:0:59.9:456:1:0:0.1 0/1:179:2:1,1:133,44:177,2:0.0112:2,2:33.5:1:30.5:1:0.44065:3.00017:60:4:0.0113:0:1 +17 37627115 . G T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05674;SOR=Inf;LSEQ=AGTCCATTCATTTAAAACTG;RSEQ=CTTTTTATTTTTCCAGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:264,154:418,0:0:2,0:26.3:1:31.4:1:1:0:60:45.444:1:0:0.1 0/1:400:4:1,3:251,145:396,4:0.01:2,2:22:1:26.8:1:0.14523:5.17163:60:8:0.0102:0:1 +17 37627387 . A G 163 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=23.01709;LSEQ=CCTAGAAAAGAGAACAGTTC;RSEQ=GTAGAGGCTAAGGATTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:855:2:1,1:433,420:853,2:0.0023:2,2:37.5:1:10.5:1:1:1.03092:60:0:0:0:1.5 0/1:878:45:24,21:410,422:832,45:0.0513:2,2:26.4:1:29.7:1:0.64763:1.18:60:90:0.0514:0:1.1 +17 37646589 . T C 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGATCACGCCACTGCATTC;RSEQ=AGCCTGGGCGACAGAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:21:1:32:1:1:0:46:10:0.8333:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:15.5:1:31.5:1:1:0:38.5:4:1:0:1 +17 37646619 . C CA 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.12644;SOR=Inf;LSEQ=GACAGAGTGATACTCTGTCT;RSEQ=AAAAAAAAAAGAAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:19,0:0:1,0:16.8:1:32:1:1:0:55.5:18:1:0:0.3 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:34.5:1:30:1:1:0:51.5:4:0.1818:0:0.5 +17 37646664 . AT A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.12013;SOR=Inf;LSEQ=ATCTTTAGTTGTGATTAATT;RSEQ=TTTTTTTTATGTTATAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:80,2:82,0:0:1,0:23.9:1:31.6:1:1:0:59.4:40:1:0:0.2 0/1:44:2:2,0:42,0:42,2:0.0455:1,0:17.5:1:30.9:1:1:0:60:4:0.0455:0.0227:0 +17 37646947 . C T 145 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03014;LSEQ=AGACTCTCCAGAACCAAAGG;RSEQ=AATCACACCACCTCAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:32:17,15:362,482:844,32:0.0365:2,2:27.3:1:29.1:1:0.27817:1.51:60:64:0.0369:0:1.1 0/0:877:1:0,1:395,481:876,1:0.0011:2,0:1:0:26:0:1:0:60:2:0.0012:0:1 +17 37648951 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50461;SOR=0;LSEQ=GGATTACAGGCATGAGCCAC;RSEQ=GCGCCCGGCCTTCATTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:101,10:111,2:0.0177:2,2:23:1:30:1:0.186:9.67754:52.5:4:0.018:0:1 0/0:89:0:0,0:74,14:88,0:0:2,0:23.2:1:29.4:1:1:0:54.7:28.333:0.9884:0:0.1 +17 37648954 . G A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01743;SOR=Inf;LSEQ=TTACAGGCATGAGCCACCGC;RSEQ=CCCGGCCTTCATTTTCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:114,12:126,0:0:2,0:22:1:30.1:1:1:0:53.9:125:1:0:0.1 0/1:103:5:4,1:80,18:98,5:0.0485:2,2:14.6:1:29.2:1:1:1.10996:53.6:10:0.0495:0:1 +17 37649178 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19504;SOR=Inf;LSEQ=AAAATTTTAGATGTCAGAAT;RSEQ=TTAACAATTTAGCAATACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:36,196:232,0:0:2,0:23.5:1:32.2:1:1:0:59.8:57:1:0:0.1 0/1:184:2:1,1:37,145:182,2:0.0109:2,2:14:1:26:1:0.37129:3.88:60:4:0.0109:0:1 +17 37649238 . TTTTG T 26 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=6.000;MSILEN=4;SSF=1;SOR=1.3957;LSEQ=CAAAAGTAAATTCTGAGGTG;RSEQ=TTTGTTTGTTTGTTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:0,2:1,62:63,2:0.0308:1,0:23.5:1:31.5:1:1:0:59:4:0.0313:0.0154:0 0/1:47:2:0,2:0,45:45,2:0.0426:1,0:40:1:26.5:1:1:0:57.5:4:0.0435:0:0 +17 37650304 . A G 68 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCAGGAAAGGGAATATA;RSEQ=AATTTCCTTTTTTGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:23.5:1:34:1:1:0:59.5:8:0.8:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 37650332 . A G 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTGTTTTTTTATTGAG;RSEQ=AGGAGTCTCACTCTGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:31.8:1:31.3:1:1:0:59.5:8:0.8:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 37650569 . G A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11652;SOR=0.15521;LSEQ=TTCCTAACCTCAGGTGATCC;RSEQ=CAGGCCTTGGCCTCCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:1,0:1,10:0.8333:0,0:26.5:1:31.6:1:1:0:55.5:20:0.9091:0:1.1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:30:1:23:1:1:0:60:4:0.4:0:1 +17 37650988 . C A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09315;SOR=Inf;LSEQ=TTTTACAGGGTAGACTGGTC;RSEQ=AATCTTTGCCTTTCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:45,234:279,0:0:2,0:22.9:1:31.1:1:1:0:58.5:9.333:0.996:0:0.4 0/1:234:3:2,1:48,183:231,3:0.0128:2,2:8.3:1:21:1:0.11621:7.54:49.3:2:0.0093:0:1.7 +17 37651002 . C CT 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.03117;LSEQ=CTGGTCCAATCTTTGCCTTT;RSEQ=TTTTTTTTTTTCTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:12:1,11:17,153:170,12:0.0638:2,2:22.2:1:31.3:1:1:1.22097:56.9:24:0.0828:0:0.8 0/1:137:9:1,8:17,105:122,9:0.0657:2,2:23.2:1:29.6:1:1:1.29288:58.3:18:0.0833:0:0.8 +17 37657460 . C CT 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1e-05;SOR=2.34817;LSEQ=GGCATTGTTATTTCAGCATT;RSEQ=TTTTTTTTTTCTTGCTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:59:45,14:216,66:282,59:0.1681:2,2:18.3:1:31.4:1:1:1.01813:59.7:118:0.173:0.0712:0.4 0/1:267:86:62,24:122,51:173,86:0.3221:2,2:27.4:1:30.6:1:0.88456:1.08:59.8:172:0.3258:0:0.4 +17 37657481 . AT A 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06456;SOR=0;LSEQ=TTTTTTTTTTCTTGCTTTTA;RSEQ=TTTTTTTCGTCTTTATGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:5:3,2:330,155:485,5:0.0102:2,2:35.2:1:31.4:1:0.65747:1.41832:60:10:0.0104:0.002:0 0/0:430:0:0,0:269,159:428,0:0:2,0:25.9:1:29.4:1:1:0:59.7:106:0.9953:0:0.3 +17 37657755 . A C 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=CTCTGACCTTTTTAGTTTCA;RSEQ=ATGGTTAATTGGTATTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:35,196:231,0:0:2,0:21.4:1:30.7:1:1:0:60:76:0.9956:0:0 0/1:195:11:0,11:32,152:184,11:0.0564:2,0:20:1:31.9:1:0.21667:0:60:22:0.057:0:1 +17 37665861 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22303;SOR=Inf;LSEQ=CAGAAGTTAAAATTTATTTT;RSEQ=GTAATTCCTTTACCCCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:150,26:176,0:0:2,0:23.3:1:31:1:1:0:60:87:1:0:0.1 0/1:158:2:1,1:123,33:156,2:0.0127:2,2:9.5:1:29.5:1:0.38515:3.68723:60:4:0.0127:0:1 +17 37666087 . T C 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00083;SOR=Inf;LSEQ=TTTTTTGAGGCAGGATCTTA;RSEQ=TCTGTTGCTCAGGCTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:17,124:141,0:0:2,0:24.3:1:30.9:1:1:0:60:282:1:0:0.1 0/1:148:11:4,7:22,115:137,11:0.0743:2,2:20.3:1:31.8:1:0.10342:2.96:60:22:0.0753:0:1.1 +17 37667944 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20414;SOR=Inf;LSEQ=TACTGTTGACTTGTACTTTG;RSEQ=TTTCTCTGTACACTGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:36,183:219,0:0:2,0:21.6:1:30.6:1:1:0:60:438:1:0:0 0/1:181:2:1,1:34,145:179,2:0.011:2,2:23.5:1:28:1:0.35021:4.22:60:4:0.011:0:1 +17 37669884 . G C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACCTCAGAGCAGTAGCAAA;RSEQ=TGTTGATTACATAATGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:33.5:1:1:0:60:4:1:0:1 +17 37671714 . G T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55084;LSEQ=GTTATTTCCTTAATTACAAT;RSEQ=GCATGATAGAAAAAGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:15:15,0:2,0:2,15:0.8824:0,1:22.6:1:31.9:1:1:0:60:30:0.8824:0:1 1/1:5:4:4,0:1,0:1,4:0.8:0,0:23.5:1:27.8:1:1:0:60:8:0.8:0:1 +17 37671910 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAATCCGACATATCAATAAT;RSEQ=TAAAAATTTTTTGAGACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:328:328:261,67:0,0:0,328:1:0,2:20.8:1:28.9:1:1:0:59.9:81:1:0:1.1 1/1:253:235:183,52:13,5:18,235:0.9289:2,2:22.6:1:28.1:1:0.56458:1.35:60:234:0.9286:0:1.1 +17 37673920 . T A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.022;SOR=Inf;LSEQ=AGTTTATCATGGCAACACAG;RSEQ=GTAGGAAAACATTTTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:0,79:79,0:0:1,0:24.2:1:30.2:1:1:0:59.1:38.5:1:0:0.2 0/1:51:4:0,4:0,47:47,4:0.0784:1,0:14.8:1:32:1:1:0:60:8:0.0784:0:1 +17 37675838 . CTT C 32 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAGCCACCATTGCACATC;RSEQ=TTTTTTTTTTTTTTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14.5:1:32.6:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 37676016 . A AAT 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTGCACCCAGCTAATTAAA;RSEQ=ATATATATATATTTGTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:33,0:33,2:0.0556:1,2:41.5:1:30.3:1:0.05714:0:60:4:0.0571:0:0.5 0/0:11:0:0,0:11,0:11,0:0:0,0:24.4:1:29.9:1:1:0:60:22:1:0:0 +17 37680096 . C T 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTATTTTTAGCAGAGAC;RSEQ=AGGTTTCACCATGTTGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:1:0:19:0:1:0:60:0:0:0:1 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:20:1:27.5:1:1:0:39.5:4:0.6667:0:1 +17 37680863 . G T 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0569;SOR=Inf;LSEQ=CCTTCCCATTTTAATCCTTT;RSEQ=CTCCTCCATTCATTCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:297,88:385,0:0:2,0:26.4:1:32.1:1:1:0:60:76:1:0:0.1 0/1:370:4:1,3:270,96:366,4:0.0108:2,2:18.8:1:27.3:1:0.06022:8.37951:60:8:0.0111:0:1 +17 37681332 . C T 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.73194;LSEQ=CATATGGTCCAGAAAGTCTA;RSEQ=AATAGATCATTTTCCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:2,5:0,5:5,7:0.5833:0,2:23.6:1:26.7:1:0.4697:0:56.1:6:0.5455:0:1.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:27:0:12:0:1:0:60:0:0:0:4 +17 37682001 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00372;SOR=Inf;LSEQ=TGAGGCATGAAAAAATGAGA;RSEQ=ATTTAAAATGAAATTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:70,0:70,0:0:1,0:25.6:1:32.2:1:1:0:59.6:34:1:0:0.1 0/1:36:5:5,0:31,0:31,5:0.1389:1,0:16.4:1:29:1:1:0:60:4:0.1143:0:1.8 +17 37682075 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08428;SOR=Inf;LSEQ=AGAAGGCAAAGGGCCCTTGG;RSEQ=CTATCTCATCGTCTTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:238,63:301,0:0:2,0:25.3:1:32.1:1:1:0:59.9:74.25:1:0:0.1 0/1:236:3:1,2:172,61:233,3:0.0127:2,2:8:1:23:1:0.17457:5.58969:60:2:0.0087:0:1 +17 37682200 . A G 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGCCAAACCGACCTGAGC;RSEQ=TCCCTCAAATGGCACAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:879:0:0,0:480,399:879,0:0:2,0:24.6:1:30.9:1:1:0:60:72.25:1:0:0.1 0/1:820:42:20,22:408,370:778,42:0.0512:2,2:22.9:1:31.5:1:0.63483:1.21268:60:84:0.052:0:1.3 +17 37682292 . G A 147 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=9.18394;LSEQ=CAATCCATCAGTGCCCTGAC;RSEQ=GAAGCTACTTCCCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:998:4:3,1:503,488:991,4:0.004:2,2:10.8:1:27.8:1:0.62446:2.91:60:8:0.0041:0:1 0/1:869:31:16,15:410,427:837,31:0.0357:2,2:24.6:1:29.7:1:0.85561:1.11:60:62:0.0362:0:1.2 +17 37682657 . A G 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CATTTTTTTTCCCCCACATC;RSEQ=ATGGCCTTGGTTTCAGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:4,121:125,0:0:1,0:22.3:1:30.9:1:1:0:59.7:19.833:1:0:0.1 0/1:78:10:1,9:3,65:68,10:0.1282:1,2:17.9:1:31.7:1:0.42907:2.37:60:20:0.1282:0:1.1 +17 37684407 . T A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCTTGAACTGCCGACCTC;RSEQ=GGTGATCCACCCGCCTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:29.5:1:1:0:35.5:4:1:0:1 +17 37686731 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.28281;SOR=0;LSEQ=TTGCAATTTTCTGATCCCAA;RSEQ=ATTTTATTCTTTATATATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:3,0:88,2:90,3:0.0323:1,0:27.3:1:31.7:1:1:0:60:6:0.033:0:1 0/0:59:0:0,0:57,2:59,0:0:1,0:21.5:1:32.4:1:1:0:59.5:58:1:0:0.1 +17 37686782 . C T 46 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12512;SOR=0;LSEQ=ATTGATATTTGTTTATGTTG;RSEQ=ACAGTGTGTGTGTTTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:4:2,2:220,32:252,4:0.0156:2,2:10.5:1:23.3:1:0.0866:6.78617:60:3:0.0119:0:1 0/0:233:0:0,0:194,38:232,0:0:2,0:23.7:1:31.4:1:1:0:60:115:1:0:0.1 +17 37687968 . A G 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAGTTTTGGGGTGGGGG;RSEQ=TTGTGTGTGGTTTCTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:38.2:1:32.8:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 37688375 . C T 30 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=10;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:15.5:1:30.5:1:1:1:32:4:0.5:0:3 +17 37688383 . C T 31 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTCTGTCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:31:1:1:0:32:4:1:0:3 +17 37688393 . C G 33 d5;v3;pSTD;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=17.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTGTCTCGCTTGCTCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:33.5:1:1:0:32:4:1:0:3 +17 37855686 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18794;SOR=Inf;LSEQ=ATCGCGCCATTGCTCTCCAG;RSEQ=CTGGGCAACAAGAGCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:140,7:147,0:0:1,0:23.7:1:32.4:1:1:0:55.1:35.75:1:0:0.7 0/1:113:2:1,1:109,2:111,2:0.0177:1,2:19:1:26.5:1:0.05262:44.70303:46:4:0.0185:0:1 +17 37855834 . C A 180 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=97.50925;LSEQ=TGCCCCGGGGGTCCTGGAAG;RSEQ=CACAAGGTAAACACAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1319:1:1,0:621,697:1318,1:8e-04:2,0:1:0:27:0:0.47157:0:60:2:8e-04:0:1 0/1:1102:76:34,42:468,558:1026,76:0.069:2,2:26.8:1:28.9:1:0.90555:1.03603:60:152:0.07:0:1.1 +17 37856472 . C T 63 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00672;SOR=Inf;LSEQ=GTCCAGCCGGAGCCATGGGG;RSEQ=CGGAGCCGCAGTGAGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:382,155:537,0:0:2,0:26.2:1:32.1:1:1:0:60:52.7:1:0:0.2 0/1:415:6:2,4:265,144:409,6:0.0145:2,2:22.8:1:24.5:1:0.19259:3.66835:58.8:5:0.0122:0:1.3 +17 37856502 . C T 74 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01162;SOR=6.1338;LSEQ=AGTGAGCACCATGGAGCTGG;RSEQ=GGCCTTGTGCCGCTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:840:2:1,1:533,304:837,2:0.0024:2,2:17.5:1:30.5:1:1:1.75197:60:4:0.0024:0:1 0/1:623:9:3,6:367,246:613,9:0.0144:2,2:25.7:1:23.6:1:0.16866:2.97845:60:3.5:0.0115:0:1.3 +17 37856512 . C T 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00668;SOR=11.40633;LSEQ=ATGGAGCTGGCGGCCTTGTG;RSEQ=CGCTGGGGGCTCCTCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:874:1:0,1:529,344:873,1:0.0011:2,0:1:0:16:0:0.39474:0:60:0:0:0:1 0/1:697:9:3,6:398,289:687,9:0.0129:2,2:13:1:26.3:1:0.17903:2.75034:60:18:0.0132:0:1.1 +17 37856623 . C A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.37888;SOR=2.40434;LSEQ=ACCCTGCCCTGTGGATGCCC;RSEQ=GCCGAGGTCCCGCGGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:2:2,0:94,264:358,2:0.0056:2,0:12:1:26.5:1:0.07057:0:60:4:0.0056:0:1 0/1:226:3:2,1:63,160:223,3:0.0133:2,2:17.3:1:27:1:0.19941:5.04:60:6:0.0136:0:1 +17 37856716 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGCTCAGGGCAGCCGGG;RSEQ=CCTGGGGCCCTCGGGCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:2,77:79,2:0.0247:1,2:29.5:1:28:1:0.07315:31.64:60:4:0.0256:0:1.5 0/0:26:0:0,0:0,26:26,0:0:1,0:21.5:1:30.9:1:1:0:60:52:1:0:0.1 +17 37861718 . T C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GAGTCTGTTGGGGGAGGAAG;RSEQ=GTGGGGAAGAGGAGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:1,1:0.5:0,0:35:0:34:0:1:0:60:2:0.5:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:31:0:1:0:60:4:1:0:2 +17 37861736 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AGTGTGGGGAAGAGGAGGGG;RSEQ=TGCAAGTGGGTGAGGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:31.7:1:32:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:28.5:1:1:0:60:4:1:0:2 +17 37863268 . G A 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGGCACAGACATGAAGCT;RSEQ=CGGCTCCCTGCCAGTCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:934:0:0,0:533,400:933,0:0:2,0:25.9:1:32:1:1:0:60:61.2:0.9989:0:0.1 0/1:713:50:27,23:363,299:662,50:0.0701:2,2:26.3:1:27.6:1:1:1.03415:60:49:0.0697:0:1.2 +17 37863426 . G A 64 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15961;SOR=0.22179;LSEQ=GGGCAACCCAGCCAGGCCCT;RSEQ=CCTCCAGCTGGGCTGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:7:5,2:227,443:670,7:0.0103:2,2:10.9:1:23.1:1:0.04999:4.87:60:6:0.009:0:1.1 0/0:433:1:1,0:151,280:431,1:0.0023:2,0:1:0:23:0:0.35185:0:60:2:0.0023:0:1 +17 37864853 . AG A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.03959;SOR=Inf;LSEQ=GACCAGGGCCACTGCTAACC;RSEQ=GGGGAGGCTTTGTGTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:16,159:175,0:0:2,0:22.6:1:31.7:1:1:0:60:174:0.9943:0:0.1 0/1:92:3:2,1:11,78:89,3:0.0326:2,2:10:1:27.7:1:0.05135:13.46:60:6:0.0326:0.0109:0 +17 37864895 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAATGGTGTCCCTTCTGG;RSEQ=CAGACGCAGGCAGAGCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:1,79:80,2:0.0244:1,2:10.5:1:29.5:1:0.04848:56.31:60:4:0.025:0:2.5 0/0:30:0:0,0:0,30:30,0:0:1,0:21.2:1:32.1:1:1:0:60:60:1:0:0.1 +17 37865725 . G A 53 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04945;SOR=7.5135;LSEQ=TGTAAGCCATGCCCCTCCCT;RSEQ=CTGCCTCTTCTCTCAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:1:1,0:268,447:715,1:0.0014:2,0:4:0:24:0:0.3757:0:60:2:0.0014:0:1 0/1:577:6:5,1:230,341:571,6:0.0104:2,2:7:1:20.8:1:0.04358:7.39:60:5:0.0088:0:1.7 +17 37865759 . G A 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70494;SOR=0.52312;LSEQ=CAGACAGCCTGACCCCAGCC;RSEQ=CAAACTCCCAACTTACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:5:2,3:103,322:425,5:0.0116:2,2:21.6:1:28.2:1:0.59965:2.08:60:10:0.0121:0:1.6 0/0:328:2:2,0:88,237:325,2:0.0061:2,0:1:0:25.5:1:0.07514:0:60:4:0.0062:0:1 +17 37865961 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05345;SOR=Inf;LSEQ=GGTCCCTCCCTTGCTGTGCA;RSEQ=TTGGCCTCGTGGCCTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:220,58:278,0:0:2,0:24.2:1:32.7:1:1:0:59.7:68.5:1:0:0.3 0/1:169:3:2,1:133,33:166,3:0.0178:2,2:21.3:1:24:1:0.49257:2.00525:60:2:0.0119:0:2.7 +17 37866005 . C T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.76154;LSEQ=GTTTGTGCCTCTCTCTGTTA;RSEQ=TAACCCGTCCTCTCGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:658:215:132,83:288,155:443,215:0.3267:2,2:23.2:1:30.7:1:0.38748:1.16804:59.9:52.75:0.3241:0:1.1 1/0:446:342:204,138:68,36:104,342:0.7668:2,2:23.1:1:29.8:1:0.30427:1.27708:60:341:0.7663:0:1.2 +17 37866232 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11212;SOR=Inf;LSEQ=TGGGAGGGGTGGGATAACAG;RSEQ=CTTGGGATGTCTCCCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:119,174:293,0:0:2,0:24.7:1:31.9:1:1:0:60:31.556:1:0:0.1 0/1:148:2:2,0:44,102:146,2:0.0135:2,0:25:1:31:0:0.09515:0:60:4:0.0137:0:1 +17 37866257 . G T 36 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08991;SOR=6.79734;LSEQ=GGATGTCTCCCCTGGGCCAG;RSEQ=TAGTCTCCCTAGAAGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:1:0,1:168,128:296,1:0.0034:2,0:19:0:14:0:0.43434:0:60:0:0:0:7 0/1:133:3:2,1:64,66:130,3:0.0226:2,2:6:1:23:1:0.6193:2.05:60:2:0.0152:0:1.7 +17 37866797 . G T 139 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGTTTGTTTCTGTAAATGG;RSEQ=AGCATATGGGGAGCACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:34:5,29:35,155:190,34:0.1504:2,2:24.6:1:27.5:1:0.80826:1.30817:60:33:0.15:0:1 0/0:149:0:0,0:27,122:149,0:0:2,0:20.8:1:30.4:1:1:0:60:148:1:0:0.2 +17 37868366 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06084;SOR=Inf;LSEQ=TGCGCATGCAGCCTGGCCCA;RSEQ=CCCACCCTGTCCTATCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:65,279:344,0:0:2,0:24.3:1:32.5:1:1:0:59.9:56.333:1:0:0.1 0/1:224:3:2,1:49,172:221,3:0.0134:2,2:20.3:1:26.7:1:0.13061:6.94:60:6:0.0136:0:1 +17 37868715 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.11067;LSEQ=TTGATGGGTAAGAGTGGGCA;RSEQ=GATGACCTGAGACAGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:157:44,113:113,268:381,157:0.2913:2,2:23.2:1:30.8:1:0.75477:1.08272:60:51.333:0.2884:0:1.1 1/0:416:282:99,183:43,90:133,282:0.6779:2,2:21.6:1:29.3:1:0.65756:1.13:60:281:0.6787:0:1.2 +17 37868786 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51659;SOR=0;LSEQ=GGCAGCATCTCTTGGGGATG;RSEQ=CAGGAGACAGAAGTGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:9,115:124,2:0.0159:2,2:23.5:1:28.5:1:0.15302:12.17:60:4:0.0164:0:1 0/0:85:0:0,0:9,76:85,0:0:2,0:24.8:1:31:1:1:0:60:41.5:1:0:0.4 +17 37871440 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15853;SOR=Inf;LSEQ=TCGATGGGCAAAGGGTTTGA;RSEQ=TGAAGGCATTCATGGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:263,31:294,0:0:2,0:20.4:1:32.7:1:1:0:60:35.75:1:0:0.1 0/1:195:2:1,1:159,34:193,2:0.0103:2,2:20.5:1:30:1:0.32752:4.62368:60:4:0.0105:0:1 +17 37871848 . G A 175 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCAGGGAGGAGTCCCTGTG;RSEQ=GAAGCTTTGGGCCTGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:49:19,30:134,222:356,49:0.121:2,2:26.1:1:31.2:1:0.87633:1.05:60:48:0.1209:0:1 0/0:228:0:0,0:64,164:228,0:0:2,0:24.1:1:30.2:1:1:0:60:31.571:1:0:0.2 +17 37871902 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12895;SOR=Inf;LSEQ=AGTAACCTTTCCATGAAAGT;RSEQ=TGCAGAGTGTGCTGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:208,131:339,0:0:2,0:22.6:1:32.9:1:1:0:60:338:0.9971:0:0.1 0/1:191:2:1,1:118,71:189,2:0.0105:2,2:17:1:27:1:1:1.6573:60:4:0.0106:0:1 +17 37871921 . TG T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06414;SOR=Inf;LSEQ=TCTGCAGAGTGTGCTGGGGA;RSEQ=GAGGAAGATGAGAATAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:264,141:405,0:0:2,0:23.8:1:31.9:1:1:0:60:56.857:0.9975:0:0.1 0/1:272:3:1,2:182,87:269,3:0.011:2,2:17:1:27.9:1:0.25028:4.15985:60:6:0.0112:0.0074:0.3 +17 37871951 . C T 105 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00022;SOR=16.97966;LSEQ=TGAGAATAGCCTTTGCTGAC;RSEQ=GGGAAGGGGTCCGTGGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:605:1:1,0:402,202:604,1:0.0017:2,0:36:0:31:0:1:0:60:2:0.0017:0:3 0/1:438:12:9,3:291,135:426,12:0.0274:2,2:31.3:1:29.3:1:0.76039:1.39:60:11:0.0255:0:1.2 +17 37872035 . G T 164 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=84.55406;LSEQ=CAAGGGCTGGGCATCAGCTG;RSEQ=CTGGGGCTGCGCTCACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1401:1:0,1:774,624:1398,1:7e-04:2,0:1:0:23:0:0.44675:0:60:2:7e-04:0:1 0/1:929:53:29,24:455,420:875,53:0.0571:2,2:27.3:1:28.7:1:0.77755:1.12:60:52:0.057:0:1.2 +17 37872206 . C T 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24897;SOR=2.73576;LSEQ=GAGTGTGGTAAGACAGGGAG;RSEQ=CCAGTGTGCGCACTCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:2:1,1:130,387:517,2:0.0038:2,2:32:1:30.5:1:0.44147:2.97:60:4:0.004:0:1 0/1:383:4:1,3:86,292:378,4:0.0104:2,2:26.3:1:24.8:1:1:1.13:60:3:0.008:0:1.5 +17 37872241 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15478;SOR=Inf;LSEQ=CCCCATCTGCCAGCACACAG;RSEQ=AGTGCCCAGGGGGCCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:26,260:286,0:0:2,0:24.1:1:32.7:1:1:0:60:285:1:0:0.2 0/1:186:2:0,2:20,164:184,2:0.0108:2,0:30:1:29:0:1:0:60:4:0.0109:0:1 +17 37872391 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCCTTGGCATCCTTCCC;RSEQ=CCCCCTCTGTTTCTGAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:47,23:70,2:0.0278:2,2:35:1:32:1:1:2.02168:60:4:0.0286:0:1 0/0:9:0:0,0:6,3:9,0:0:2,0:20.6:1:31:1:1:0:60:18:1:0:0 +17 37872475 . C T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55377;SOR=0;LSEQ=CCCTCCAGCCCACAGCCATG;RSEQ=CCACAGCCAGTTCCCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:2,1:150,26:176,3:0.0168:2,2:28:1:24:1:0.38953:2.86122:59:2:0.0116:0:2.7 0/0:83:0:0,0:66,17:83,0:0:2,0:21.9:1:31.4:1:1:0:60:166:1:0:0.2 +17 37872492 . G T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55608;SOR=0;LSEQ=ATGCCCACAGCCAGTTCCCT;RSEQ=GTTCACTTGGACCTGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:2,1:174,48:222,3:0.0133:2,2:27:1:24.7:1:0.52317:1.80695:60:2:0.0094:0:1 0/0:128:0:0,0:99,29:128,0:0:2,0:23.1:1:30.8:1:1:0:60:31:1:0:0.2 +17 37872512 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13744;SOR=Inf;LSEQ=GGTTCACTTGGACCTGGGGC;RSEQ=TCCCCTAAAAGTCCCCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:212,74:286,0:0:2,0:25.3:1:31.5:1:1:0:59.9:70.5:1:0:0.2 0/1:169:2:1,1:126,41:167,2:0.0118:2,2:28:0:30.5:1:0.43639:3.04831:60:4:0.0121:0:1.5 +17 37872907 . G T 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30407;SOR=4.78741;LSEQ=TGGAGGGGGGCAGCGAGGGG;RSEQ=ATTGCCAGGGACTTGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:1:0,1:83,277:360,1:0.0028:2,0:24:0:30:0:1:0:60:2:0.0029:0:1 0/1:228:3:1,2:65,158:223,3:0.0132:2,2:26.7:1:21.7:1:1:1.21:60:2:0.0092:0:1 +17 37872933 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12066;SOR=Inf;LSEQ=CAGGGACTTGGCAGGATGGC;RSEQ=AGATGCAGTAGGGTGTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:19,198:217,0:0:2,0:24.7:1:32:1:1:0:59.9:53.25:1:0:0.2 0/1:116:2:1,1:15,98:113,2:0.0172:2,2:25.5:1:27.5:1:0.25995:6.36:60:4:0.0175:0:2 +17 37873523 . C T 55 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01298;SOR=Inf;LSEQ=TAAGGGCCTGATCCTACTGC;RSEQ=CTGGGGGTGTCAGTGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:0:0,0:451,211:662,0:0:2,0:24.9:1:31.1:1:1:0:60:81.75:1:0:0.2 0/1:481:5:1,4:316,160:476,5:0.0104:2,2:5.8:1:24:1:0.04825:7.86585:60:4:0.0084:0:1 +17 37873562 . G GC 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.99146;LSEQ=GCCCCCCACAAATCTTTTCT;RSEQ=CCCCCCCCAGGAGGCTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1047:19:9,10:584,436:1020,19:0.0181:2,2:31.3:1:31.4:1:0.48424:1.48767:60:18:0.018:0.001:0.5 0/1:778:14:10,4:432,328:760,14:0.018:2,2:29.1:1:27.3:1:0.4148:1.90:57.9:3.667:0.0147:0.0039:0.9 +17 37873581 . C T 146 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=44.59995;LSEQ=TGCCCCCCCCAGGAGGCTGA;RSEQ=CAGTGTGTGGCCTGTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1172:1:0,1:635,535:1170,1:9e-04:2,0:1:0:26:0:0.45773:0:60:2:9e-04:0:1 0/1:952:35:21,14:510,406:916,35:0.0368:2,2:24.8:1:28.6:1:0.72936:1.19:60:34:0.0367:0:1.2 +17 37876179 . C G 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGGGAGGGGACCCCCTGA;RSEQ=ATATGTCCCTTCCCACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:76,304:380,0:0:2,0:23.9:1:31.9:1:1:0:60:53.286:1:0:0.1 0/1:240:15:4,11:54,171:225,15:0.0625:2,2:19:1:30.6:1:0.76219:1.15:60:30:0.0628:0:1.1 +17 37876208 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11909;SOR=Inf;LSEQ=CTTCCCACCCACTCTTCCAC;RSEQ=GTGGAACCTCCTGTCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:8,196:204,0:0:1,0:24:1:30.4:1:1:0:60:33:1:0:0.1 0/1:108:2:1,1:8,98:106,2:0.0185:2,2:37:1:29.5:1:0.16044:11.61:60:4:0.0185:0:1.5 +17 37879504 . CG C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18143;SOR=Inf;LSEQ=CCAAACACCTTCATGTCCCC;RSEQ=TGGGCCCCCTTTGTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:206,43:249,0:0:2,0:21.5:1:29.7:1:1:0:60:23.9:0.9958:0:0.3 0/1:186:2:1,1:152,32:184,2:0.0108:2,2:19:1:28:1:0.32415:4.69288:60:4:0.011:0.0054:2.5 +17 37879585 . A G 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CCCCCAGCCCTCTGACGTCC;RSEQ=TCATCTCTGCGGTGGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:0:0,0:353,275:628,0:0:2,0:23.7:1:30.4:1:1:0:60:47.308:1:0:0.5 0/1:551:33:17,16:261,256:517,33:0.0599:2,2:27.1:1:31.4:1:1:1.04:60:66:0.0607:0:2.1 +17 37879588 . A G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.76382;SOR=1.03887;LSEQ=CCAGCCCTCTGACGTCCATC;RSEQ=TCTCTGCGGTGGTTGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:637:229:123,106:231,177:408,229:0.3595:2,2:22.1:1:30.5:1:0.50658:1.1245:60:75.333:0.3622:0:1.2 0/1:562:207:109,98:170,185:355,207:0.3683:2,2:26.1:1:30:1:0.29447:1.21:60:50.75:0.3725:0:1.3 +17 37879762 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.6814;LSEQ=TGGGGTCTGCACCGGCCCCC;RSEQ=GCACTGACCCACCACCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:167:112,55:179,96:275,167:0.377:2,2:23.9:1:30.8:1:0.68067:1.09:59.9:54.667:0.3788:0:1.1 1/0:210:130:80,50:48,32:80,130:0.619:2,2:21.6:1:29.4:1:0.88449:1.07:60:260:0.6311:0:1.1 +17 37880106 . G T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16561;SOR=5.72033;LSEQ=GGACAAGTAATGATCTCCTG;RSEQ=AAGGCAGGTAGGATCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:1:0,1:286,61:347,1:0.0029:2,0:1:0:24:0:0.17816:0:60:2:0.0029:0:1 0/1:246:4:2,2:191,51:242,4:0.0163:2,2:18.8:1:27:1:0.2038:3.71909:60:8:0.0165:0:1 +17 37880725 . T C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCACCATGTTGGCCAGG;RSEQ=TGGTGTCAAACTCCTGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:16,1:17,3:0.15:1,0:12.3:1:34:0:1:0:22.3:6:0.1667:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:33.8:1:29.8:1:1:0:30.2:10:1:0:0.2 +17 37880997 . G GTGT 286 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGGAAGCATACGTGATGGCT;RSEQ=GTGTGGGCTCCCCATATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1440:624:314,310:419,389:808,624:0.4333:2,2:25.4:1:30.9:1:0.59401:1.06334:59.7:623:0.436:0.0778:0.2 0/0:1125:0:0,0:580,543:1123,0:0:2,0:26.2:1:30.8:1:1:0:59.9:79.214:0.9991:0:0.2 +17 37882611 . G GA 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.56698;SOR=0;LSEQ=AATAAAAAAGCAAACAAAAA;RSEQ=AAAAAAAAAATTAAAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:4:4,0:43,2:45,4:0.0816:1,0:24.5:1:30.5:1:1:0:60:8:0.0851:0:0 0/0:14:0:0,0:14,0:14,0:0:1,0:24.4:1:31.6:1:1:0:60:13:1:0:0.1 +17 37882982 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03757;SOR=Inf;LSEQ=TGCAGAGGGTGGGAAGGAGA;RSEQ=ATGAGTCCAGTATGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:232,322:554,0:0:2,0:23.3:1:32.7:1:1:0:59.9:78.143:1:0:0.1 0/1:280:3:1,2:113,164:277,3:0.0107:2,2:16:1:26:1:1:1.37653:60:6:0.0108:0:1 +17 37883441 . C T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12971;SOR=Inf;LSEQ=TCCACGGTGACTGTGTCATA;RSEQ=CCCAAAGGTGACCTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:275,51:326,0:0:2,0:23.2:1:32.1:1:1:0:59.9:53.333:1:0:0.1 0/1:184:2:1,1:155,27:182,2:0.0109:2,2:6:1:28.5:1:0.2819:5.65551:60:4:0.0109:0:1 +17 37884037 . C G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.19345;LSEQ=CTGGTGCCACTCTGGAAAGG;RSEQ=CCAAGACTCTCTCCCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1440:436:255,181:533,466:999,436:0.3028:2,2:25.4:1:31.6:1:0.07405:1.23:59.9:61.286:0.304:0:1.1 1/0:1016:656:363,293:183,170:353,656:0.6457:2,2:25.2:1:30.5:1:0.2902:1.15:59.9:49.462:0.6462:0:1.2 +17 37886420 . A T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATTCAGAGCACAGACTG;RSEQ=CCCAGCAGGTGTTCTGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 37922229 . C A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCACACCGATACACATCCAT;RSEQ=ACCTCCCCTTCCTTGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:31:1:31.5:1:1:0:60:4:1:0:0.5 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:28:1:28:1:1:1.29:60:4:0.2222:0:1.5 +17 37922259 . G A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCCTTGTTGATCACTTTGAC;RSEQ=GAGTCTCTTGGGCAGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:22:0:34:0:1:0:60:2:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:36.5:1:30:1:1:0:60:4:1:0:2 +17 38487414 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12977;SOR=Inf;LSEQ=CCGAGGAGGGGTGGTCTGAA;RSEQ=CCCACCAGAGCCCCCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:269,48:317,0:0:2,0:23.6:1:33.1:1:1:0:60:62.4:1:0:0.1 0/1:179:2:1,1:147,30:177,2:0.0112:2,2:15.5:1:31:1:0.31718:4.83676:60:4:0.0114:0:1 +17 38487501 . C T 175 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=97.44202;LSEQ=ACAGCAGCTCCTGCCCGACA;RSEQ=CTGGGGGCGGGCACCTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1018:1:0,1:626,390:1016,1:0.001:2,0:1:0:28:0:0.38446:0:60:2:0.001:0:1 0/1:765:67:39,28:412,286:698,67:0.0876:2,2:23:1:28.9:1:0.89729:1.03422:59.8:66:0.0874:0:1.2 +17 38497390 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACCCAAGCTAGGCCTTTC;RSEQ=TCCAGTGAAACGTGCATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:29,0:29,2:0.0645:1,2:44:0:32.5:1:0.06452:0:60:4:0.0645:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:15:1:29.7:1:1:0:60:6:1:0:0 +17 38497450 . G A 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20164;SOR=0;LSEQ=TAGTCCACTGGAAGGCACCA;RSEQ=CTCTTCCTTTTATCTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:9,0:78,1:79,9:0.1023:1,0:27.6:1:30.6:1:1:0:60:18:0.1023:0:1.1 0/0:21:0:0,0:20,1:21,0:0:1,0:24.5:1:31.8:1:1:0:60:42:1:0:0.1 +17 38497484 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCAGAGCTGGACAGTG;RSEQ=ACCAGGGGCCGGTACTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:157,3:160,2:0.0123:1,0:25:1:32:0:1:0:60:4:0.0126:0:1 0/0:51:0:0,0:48,3:51,0:0:2,0:23.8:1:31.8:1:1:0:60:102:1:0:0.1 +17 38497753 . G A 85 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12881;SOR=2.50616;LSEQ=CCCGCGCGACCCGGCCCTAC;RSEQ=CCTCCTGCCGCCGCTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1074:5:4,1:369,700:1069,5:0.0047:2,2:8.2:1:22.6:1:0.05212:7.57:60:4:0.0038:0:1 0/1:949:11:10,1:357,580:937,11:0.0116:2,2:6.3:1:24.8:1:5e-04:16.21:60:10:0.0107:0:1.2 +17 38497822 . C T 71 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.56264;SOR=1.63733;LSEQ=CCGGGCAGGGGGCTGGCGGG;RSEQ=GAGCCCCGCGGGCGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:645:5:1,4:374,266:640,5:0.0078:2,2:5:1:27.4:1:0.16692:5.61066:60:10:0.0079:0:1 0/1:554:7:2,5:312,235:547,7:0.0126:2,2:16.3:1:25.3:1:0.2483:3.31219:60:6:0.0111:0:1.3 +17 38497833 . G A 155 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02798;LSEQ=GCTGGCGGGCGAGCCCCGCG;RSEQ=GCGGGCTGGCGAGCGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:693:38:21,17:427,227:654,38:0.0548:2,2:28.3:1:29.7:1:0.22381:1.52185:60:11.667:0.0515:0:1.2 0/0:618:1:1,0:377,239:616,1:0.0016:2,0:1:0:27:0:1:0:57:2:0.0016:0:1 +17 38497884 . G A 200 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00818;LSEQ=AGCGGTGGGTGGGTCACTCG;RSEQ=AGGTGAGGCGCCGCCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:109:55,54:356,275:631,109:0.1467:2,2:24.7:1:29.6:1:0.25284:1.27058:60:26.25:0.1446:0:1.1 0/0:713:1:1,0:371,341:712,1:0.0014:2,0:1:0:23:0:1:0:60:2:0.0014:0:1 +17 38498810 . A AG 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGCGGGGACTTCAGGGC;RSEQ=GGGGGCGCCCCCTGCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:2,0:55,0:55,2:0.0351:1,0:22.5:1:35:0:1:0:60:4:0.0357:0:0 0/0:20:0:0,0:20,0:20,0:0:1,0:23.8:1:30.5:1:1:0:60:40:1:0:0.5 +17 38498899 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07606;SOR=Inf;LSEQ=CGGATGGCGCCGCCGGCTGA;RSEQ=TGACGGGGGCGGCGCGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:254,33:287,0:0:2,0:25.8:1:33.1:1:1:0:60:56.4:1:0:0.1 0/1:212:3:1,2:173,36:209,3:0.0142:2,2:8:1:26.3:1:0.08352:9.45639:60:6:0.0144:0:1.3 +17 38504241 . A G 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCCAGGCCGCCCAGGGGCA;RSEQ=GAGCTTTAGAATCAGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:24.4:1:33.8:1:1:0:60:10:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:26:0:34:0:1:0:60:2:1:0:1 +17 38504470 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.56122;SOR=3.23323;LSEQ=CTGCCAGCAGTGGTGAGGCT;RSEQ=GGAGAGGCTCTTAGGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:1:0,1:225,15:240,1:0.0041:2,0:1:0:25:0:0.06639:0:60:2:0.0042:0:1 0/1:150:2:2,0:140,8:148,2:0.0133:2,0:17:1:29.5:1:1:0:60:4:0.0135:0:1 +17 38505824 . C G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76096;LSEQ=GGGGAAGACTCCTGCCCATC;RSEQ=TGCAGTGTTGAGGCAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:6,2:6,0:6,8:0.5714:0,2:15.1:1:30.5:1:0.47253:0:60:16:0.5714:0:1.3 1/0:6:3:2,1:3,0:3,3:0.5:0,2:13.7:1:30:1:1:0:60:6:0.5:0:1.3 +17 38505991 . C T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.39069;SOR=2.2899;LSEQ=ACCGTAGCCAGGCACTGCTC;RSEQ=CACTGTGGGTGTGGACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:2:0,2:296,77:373,2:0.0053:2,0:1:0:26:0:0.04394:0:60:4:0.0054:0:1 0/1:247:3:1,2:180,64:244,3:0.0121:2,2:15:1:25.3:1:0.17492:5.57778:60:6:0.0125:0:1 +17 38506208 . G A 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04734;SOR=7.85486;LSEQ=TAGGGCAGGGGCCGAGTCCC;RSEQ=CCTCAGTTGGGGTCTCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:1:1,0:102,313:415,1:0.0024:2,0:1:0:25:0:0.2476:0:60:2:0.0025:0:1 0/1:323:6:4,2:87,230:317,6:0.0186:2,2:8.5:1:25.7:1:0.05519:5.26:60:12:0.0188:0:1 +17 38507948 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04148;SOR=Inf;LSEQ=GGGCCACAGCTGTGCTCATG;RSEQ=GGCTTCTGGGGCAGAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:41,0:41,0:0:1,0:21.1:1:31.7:1:1:0:59:82:1:0:0.1 0/1:11:2:1,1:7,2:9,2:0.1818:2,2:25.5:1:28.5:1:0.49091:3.05504:60:4:0.1818:0:1 +17 38508058 . C T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10984;SOR=Inf;LSEQ=TGTGTGCGCGTGCTTACAAG;RSEQ=CTGGGTGACCTCCTCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:226,7:233,0:0:1,0:24.3:1:32.8:1:1:0:59.9:115.5:1:0:0.1 0/1:116:2:2,0:107,7:114,2:0.0172:2,0:7.5:1:29.5:1:1:0:60:4:0.0175:0:1 +17 38508104 . G T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=AGCTCTCTGTCAGGCTGGGG;RSEQ=TGGACGAGGCCCTGAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:356,105:461,0:0:2,0:24.1:1:31.4:1:1:0:59.9:91.2:0.9978:0:0.1 0/1:306:11:9,2:210,85:295,11:0.0359:2,2:18.5:1:29.7:1:0.73433:1.82:60:22:0.0365:0:1.1 +17 38508416 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55496;SOR=0;LSEQ=CCCCTTCTTGTGCCAGGCAA;RSEQ=ATCTCTGCGTCCTTCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:3:0,3:115,159:274,3:0.0108:2,0:28.3:1:30:0:0.26895:0:60:6:0.0111:0:1.3 0/0:127:0:0,0:54,73:127,0:0:2,0:22.8:1:31.2:1:1:0:60:30.75:1:0:0.2 +17 38508756 . C T 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCTGCCTGCCTGGACAT;RSEQ=CTGGTGAGGGTCTGCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:685:0:0,0:228,457:685,0:0:2,0:23.5:1:31.5:1:1:0:60:75.111:1:0:0.1 0/1:504:21:6,15:156,326:482,21:0.0417:2,2:26.9:1:29:1:0.81505:1.19588:60:42:0.0422:0:1.2 +17 38510804 . C A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13198;SOR=5.48799;LSEQ=GCTGGGCTGGGACGGGGGTG;RSEQ=AGCCCTGGAGTCTCTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:1,0:22,184:206,1:0.0048:2,0:1:0:15:0:0.11111:0:60:0:0:0:1 0/1:115:3:2,1:14,98:112,3:0.0261:2,2:17:1:28:1:0.05038:13.43:60:6:0.027:0:1 +17 38511444 . GC G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.53456;SOR=0;LSEQ=TCCATGGCCTGGGCAGGCAC;RSEQ=CCCCCGGTGGCCGAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:148,10:158,2:0.0125:2,2:23.5:1:34:0:0.13318:14.16324:60:4:0.0127:0:0 0/0:92:0:0,0:79,13:92,0:0:2,0:25.2:1:31.8:1:1:0:59.8:184:1:0:0.2 +17 38511455 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15088;SOR=Inf;LSEQ=GGCAGGCACGCCCCCCGGTG;RSEQ=CCGAGGCTGGGGGTGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:168,17:185,0:0:2,0:24.5:1:31.4:1:1:0:59.9:29.833:1:0:0.1 0/1:118:2:1,1:94,22:116,2:0.0169:2,2:39.5:1:28:1:0.35318:4.20098:60:4:0.0174:0:1 +17 38511483 . C T 34 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30742;SOR=4.50882;LSEQ=TGGGGGTGCAGCTGTGTTCC;RSEQ=AGCTGCTCAGGGGGTGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:1:1,0:256,65:321,1:0.0031:2,0:23:0:15:0:1:0:60:0:0:0:8 0/1:216:3:1,2:164,49:213,3:0.0139:2,2:5:1:22:0:0.13958:6.61833:60:6:0.014:0:1 +17 38511722 . G A 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02802;SOR=Inf;LSEQ=GGCCCCCGACACCTGGCCCA;RSEQ=GCCCCCACATCCAAGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:69,287:356,0:0:2,0:25.6:1:31.4:1:1:0:59.9:88:1:0:0.1 0/1:248:4:2,2:58,184:242,4:0.0161:2,2:18:1:22:1:0.25054:3.15:60:8:0.0166:0:3 +17 38511741 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15502;SOR=Inf;LSEQ=AGGCCCCCACATCCAAGCCA;RSEQ=CACCCCATGTCTTTGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:30,231:261,0:0:2,0:24.6:1:32.4:1:1:0:59.7:42.5:1:0:0.1 0/1:170:2:1,1:27,141:168,2:0.0118:2,2:18.5:1:29:1:0.3031:5.15:60:4:0.0118:0:1 +17 38512197 . T C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08565;LSEQ=TTCCCACCTCGAGCCAGGCT;RSEQ=GCTGGGGCTGGGGGTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:145:119,26:162,34:196,145:0.4252:2,2:24.4:1:31.7:1:0.88674:1.04093:60:71.5:0.4231:0:1.1 0/1:219:13:11,2:164,42:206,13:0.0594:2,2:28.1:1:28.5:1:1:1.41:60:12:0.0556:0:1.5 +17 38512457 . C G 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCAGCTCCAACAGAAGCAG;RSEQ=CCGGCCACCCACTCCCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1138:41:15,26:488,606:1094,41:0.036:2,2:24.3:1:31.1:1:0.34009:1.39542:60:19.5:0.0349:0:2.2 0/0:857:0:0,0:396,458:854,0:0:2,0:25.3:1:30.5:1:1:0:59.9:36.13:0.9964:0:0.3 +17 38512461 . G T 158 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03168;LSEQ=GCTCCAACAGAAGCAGCCCG;RSEQ=CCACCCACTCCCCGTGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1134:40:14,26:495,597:1092,40:0.0353:2,2:25.8:1:29.7:1:0.25713:1.53927:60:39:0.0357:0:2.2 0/0:865:1:0,1:404,457:861,1:0.0012:2,0:6:0:29:0:1:0:60:2:0.0012:0:1 +17 38514723 . CAGAAA C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGGAAGGAAAGAAAGGA;RSEQ=GGAAAGAAAGAAAGAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:12:0:33:1:1:1:48.5:4:0.5:0:0 +17 39611498 . T C 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TGAACTCCAGGACTGGACGC;RSEQ=GAGCCTCAGACACCAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:23.5:1:33.3:1:1:0:60:8:0.8:0:1.3 0/0:2:0:0,0:2,0:2,0:0:0,0:16:1:32:0:1:0:60:4:1:0:0 +17 39611584 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.10145;SOR=Inf;LSEQ=TGCTCTTAGAGCAAAGCAAA;RSEQ=CTACCCATATGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:18,6:24,0:0:2,0:24:1:33.3:1:1:0:59.8:48:1:0:0.2 0/1:22:3:2,1:11,7:18,3:0.1364:2,2:29.3:1:29.7:1:1:1.26:60:6:0.1364:0:1 +17 39611602 . TTGC T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.00175;SOR=0.13444;LSEQ=AAGCTACCCATATGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:19:11,8:8,4:12,19:0.6333:2,2:27.3:1:30.4:1:0.71721:1.43716:59.7:38:0.6333:0.1:0.2 0/1:22:4:4,0:9,9:18,4:0.1818:2,0:25.5:1:31.8:1:0.11497:0:60:8:0.1818:0:0.3 +17 39611655 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5102;SOR=0;LSEQ=AAACTTGGGCTTCAGAATGG;RSEQ=TCCAAAATATGACTCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:11,17:28,2:0.0667:2,2:13.5:1:29:1:1:1.52:60:4:0.0667:0:1 0/0:20:0:0,0:9,11:20,0:0:2,0:21.9:1:30.9:1:1:0:60:40:1:0:0.2 +17 39874267 . T A 56 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=TCTCTACCCATCTTAGGTCC;RSEQ=CGGCTGGGGCTCTGTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:15.8:1:28.3:1:1:0:60:3:1:0:1.8 0/0:1:0:0,0:1,0:1,0:0:0,0:43:0:33:0:1:0:60:2:1:0:0 +17 39874283 . T A 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16667;SOR=0;LSEQ=GTCCTCGGCTGGGGCTCTGT;RSEQ=ATAAAAGACAGATTACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:24.8:1:29.6:1:1:0:60:10:1:0:1.6 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:32:0:1:0:60:2:1:0:0 +17 40353542 . GCA G 105 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=28;MSI=15.000;MSILEN=2;SSF=0.01548;SOR=4.48419;LSEQ=ACACCATAACGTGCAAACAC;RSEQ=CACACACACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:7:7,0:43,0:43,7:0.1346:1,0:21.4:1:33.6:1:1:0:57:14:0.1373:0.0192:0.1 0/1:24:10:10,0:14,0:14,10:0.4167:1,0:26.8:1:31.9:1:1:0:60:20:0.4167:0.0417:0.2 +17 40353722 . A G 195 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=47.69844;LSEQ=AAGAGTGATTCCTCTGGTGA;RSEQ=GATGAAGAAGCTGAAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1217:2:1,1:784,431:1215,2:0.0016:2,2:8.5:1:29.5:1:1:1.81798:60:4:0.0017:0:1 0/1:1097:80:50,30:616,398:1014,80:0.0729:2,2:21.4:1:30.9:1:0.81249:1.08:60:160:0.0743:0:1.1 +17 40354031 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07771;SOR=Inf;LSEQ=AACAACCATTCAAACAGCTG;RSEQ=CTGTACAGCAACTCAGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:10,131:141,0:0:2,0:25.6:1:31.9:1:1:0:59.8:22.5:1:0:0.2 0/1:55:2:1,1:1,52:53,2:0.0364:1,2:18.5:1:28:1:0.07205:37.12:60:4:0.037:0:1 +17 40354226 . G A 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0221;SOR=9.4963;LSEQ=TCTCCCTCCCAAAGGCCAGA;RSEQ=CCCGGGCCAGGGCTGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:1,0:190,7:197,1:0.0051:1,0:14:0:32:0:1:0:60:2:0.0052:0:1 0/1:108:5:5,0:101,2:103,5:0.0463:1,0:31.2:1:30.8:1:1:0:60:10:0.0481:0:1 +17 40354343 . A G 190 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=114.88209;LSEQ=CCTCCCCTGTGGACCCCCAC;RSEQ=AGAATGCCACCTACTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1534:1:0,1:921,607:1528,1:7e-04:2,0:41:0:15:0:0.39765:0:60:0:0:0:7 0/1:1218:85:49,36:641,490:1131,85:0.0698:2,2:24.6:1:29.7:1:0.9099:1.04:58.3:84:0.07:0:1.2 +17 40354558 . G T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGTATCTTTGTCTTTCTCAG;RSEQ=GTGTAGAAGGACAAAGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:101,225:326,0:0:2,0:24.2:1:31.5:1:1:0:58.7:45.571:1:0:0.1 0/1:154:10:3,7:24,120:144,10:0.0649:2,2:19.1:1:29.5:1:0.38141:2.13:57.5:20:0.0654:0:1.1 +17 40359479 . A G 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=GTAATTGTGTGGGTTTTCAC;RSEQ=CAAGAGAGATAACACACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:254,5:259,0:0:1,0:22.1:1:30.5:1:1:0:58.8:31.375:1:0:0.3 0/1:167:11:10,1:150,6:156,11:0.0659:1,2:25.5:1:30.6:1:0.38497:2.48037:58.6:22:0.0667:0:3.2 +17 40359505 . GCA G 253 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=36;MSI=19.000;MSILEN=2;SSF=8e-05;SOR=0.55771;LSEQ=GAGATAACACACGCAGGTAT;RSEQ=CACACACACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:435:229:196,33:95,6:101,229:0.5264:2,2:23.3:1:32.4:1:0.02731:2.65916:59.2:44.8:0.5333:0.1149:0.4 0/1:332:127:104,23:82,12:94,127:0.3825:2,2:23.3:1:31.3:1:0.35233:1.50846:58.5:41.333:0.3792:0.0693:0.6 +17 40363524 . CA C 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGCGAAACTCTGTCT;RSEQ=AAAAAAAAAAATGAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:3,0:3,3:0.5:0,2:37:1:32.7:1:1:0:53.3:6:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 40367850 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13835;SOR=Inf;LSEQ=GGATTTTGCTATGTTGGCCA;RSEQ=GCTGGTCTCGAACTCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:65,0:65,0:0:1,0:22.4:1:33.1:1:1:0:36.6:20.667:1:0:0.1 0/1:39:2:2,0:36,0:36,2:0.0513:1,0:42:1:31.5:1:1:0:37.5:4:0.0541:0:1 +17 40367917 . A G 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00175;SOR=Inf;LSEQ=CCCAAAGTGCTGGGATTACA;RSEQ=GTGTGAGTCACTGCACCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:164,0:164,0:0:1,0:21.7:1:30.3:1:1:0:51.1:53.667:1:0:0 0/1:139:8:8,0:128,3:131,8:0.0576:1,0:23.8:1:32.6:1:1:0:51.4:16:0.0584:0:1.6 +17 40367990 . G A 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATGAGATTCATGACACC;RSEQ=GCATTGATTTTGGGACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:775:0:0,0:567,207:774,0:0:2,0:24.9:1:30.1:1:1:0:60:50.6:0.9987:0:0.1 0/1:829:57:32,25:510,260:770,57:0.0688:2,2:24.9:1:29.5:1:0.14801:1.53167:59.8:56:0.0685:0:1.3 +17 40368183 . CT C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.75285;SOR=0.92809;LSEQ=TCAAGTTCTTCTCCTTCTCT;RSEQ=TTTTTTTTTTTCTTATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:413:58:4,54:51,289:340,58:0.1404:2,2:29.7:1:33.6:1:0.14682:2.37842:60:57:0.1516:0.0048:0.4 0/1:357:47:6,41:51,247:298,47:0.1317:2,2:28.2:1:30.6:1:0.53255:1.40961:59.9:22.5:0.1347:0.0056:0.6 +17 40368209 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.19206;SOR=Inf;LSEQ=TTTTTTTCTTATTATAACAA;RSEQ=ACTTTTATTTTCCAAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:9,247:256,0:0:1,0:20.8:1:32.4:1:1:0:59.2:50.2:0.996:0:0.8 0/1:201:2:1,1:16,182:198,2:0.01:2,2:25.5:1:28:1:0.16317:11.07:60:4:0.0101:0:1 +17 40369097 . T TA 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.04614;SOR=1.77405;LSEQ=AAGAAGAAGATGCTATGTGA;RSEQ=AAAAAAAAAATATTTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:23:21,2:299,32:331,23:0.0648:2,2:21.3:1:29.1:1:1:1.12:60:46:0.0655:0.0085:0.1 0/1:283:31:27,4:228,24:252,31:0.1095:2,2:20.3:1:28.1:1:0.52586:1.40552:59.8:62:0.1107:0.0389:0.1 +17 40369129 . CCA C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.61946;SOR=1.15564;LSEQ=ATTTTGTAACATAAAGTACA;RSEQ=CACACACACACGCACACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:828:34:26,8:583,211:794,34:0.0411:2,2:20.9:1:31.9:1:0.84323:1.18:60:68:0.0418:0.0097:0.1 0/1:721:34:26,8:489,197:686,34:0.0472:2,2:25.1:1:31.6:1:0.56624:1.31:59.7:33:0.0468:0:0.3 +17 40369149 . G A 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=6;SSF=0;SOR=52.85097;LSEQ=CCACACACACACACGCACAC;RSEQ=CACACGCAGAGCTGAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1031:1:0,1:700,330:1030,1:0.001:2,0:20:0:32:0:0.32105:0:60:2:0.001:0:1 0/1:1023:50:32,18:621,348:969,50:0.0489:2,2:28.9:1:28.7:1:1:1.00377:59.7:100:0.0502:0:1.1 +17 40369707 . C CT 44 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.19521;SOR=4.0916;LSEQ=GAAAACAGTTCCTAAGAGAA;RSEQ=TTTTTTTTTTTTTTTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:0,3:4,21:25,3:0.1034:2,0:14.3:1:28.3:1:1:0:48.7:6:0.12:0.0345:1.3 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:29:1:30:0:1:0:60:4:0.4:0:0 +17 40370235 . TG T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20439;SOR=1.44853;LSEQ=TGATGATGGTGGCCTTCACC;RSEQ=GGGGGGGTTCATGTGCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2021:23:10,13:1004,991:1995,23:0.0114:2,2:19.6:1:32.3:1:0.53707:1.31687:32.4:46:0.0116:0.0015:0.1 0/1:1707:28:17,11:829,849:1678,28:0.0164:2,2:16.8:1:29.7:1:0.25756:1.58:36.6:27:0.016:0.0047:0.1 +17 40370237 . G T 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=17.34296;LSEQ=ATGATGGTGGCCTTCACCTG;RSEQ=GGGGGGTTCATGTGCACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2018:8:0,8:1009,995:2004,8:0.004:2,0:2:1:26.3:1:0.00376:0:30.3:7:0.0035:0:1.1 0/1:1719:111:61,50:791,813:1604,111:0.0646:2,2:22.6:1:28.7:1:0.28045:1.25:32.2:222:0.0654:0:1.1 +17 40370345 . C T 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=48.93235;LSEQ=GGCTGCTTCTCAATGATGAA;RSEQ=GTGCTGCAGGGGACACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1837:2:0,2:776,1059:1835,2:0.0011:2,0:4.5:1:25.5:1:0.51177:0:48:4:0.0011:0:1 0/1:1558:79:30,49:655,822:1477,79:0.0507:2,2:32.1:1:28.8:1:0.29598:1.30128:32.9:25.333:0.0495:0:1.3 +17 40370565 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATGGGCTGCAGCCCAAGG;RSEQ=CATCTCTTGCAGTGTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:143,50:193,2:0.0103:2,2:23:1:30.5:1:0.45567:2.84171:55:4:0.0105:0:2 0/0:73:0:0,0:56,17:73,0:0:2,0:27:1:30.5:1:1:0:48.5:23.333:1:0:0.1 +17 40370908 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTCACACCTGCACGAGAG;RSEQ=CCCAAGGCCAACAGGAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:18.5:1:29.8:1:1:0:58.5:8:1:0:2.3 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:16.5:1:29.5:1:1:1.11803:20:4:0.1053:0:1.5 +17 40371805 . C T 72 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20034;SOR=2.79668;LSEQ=ACCTGCTTCTGCTGGAGGGC;RSEQ=GTCTCCCGGCTCAGACGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:622:3:0,3:285,334:619,3:0.0048:2,0:1.3:1:27:1:0.25404:0:46.7:6:0.0049:0:1.7 0/1:523:7:0,7:217,299:516,7:0.0134:2,0:5.4:1:25.7:1:0.04509:0:37.7:14:0.0137:0:1.1 +17 40371865 . A G 202 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=131.51296;LSEQ=AGCGGGCCAAACTGAGCTAG;RSEQ=GGAGGGGAGAGGAAACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1640:1:1,0:669,970:1639,1:6e-04:2,0:12:0:13:0:0.40854:0:24:0:0:0:2 0/1:1372:102:42,60:527,741:1268,102:0.0743:2,2:28.5:1:30.3:1:1:1.01599:40:101:0.0753:0:1.2 +17 40372009 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCTGACAGCCAGGGGGG;RSEQ=CAAGATGAATGGGTGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:7,144:151,2:0.0131:1,2:17.5:1:28.5:1:0.10217:19.32:60:4:0.0132:0:1 0/0:76:0:0,0:4,72:76,0:0:2,0:22:1:30.6:1:1:0:57.7:37:1:0:0.1 +17 40375268 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14449;SOR=Inf;LSEQ=GCACTGTCTTCAATGCAAAT;RSEQ=AGTCCCTGCTACTCAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:157,2:159,0:0:1,0:24.9:1:28.8:1:1:0:60:52:1:0:0.1 0/1:98:2:1,1:94,2:96,2:0.0204:1,2:23.5:1:30:1:0.06059:38.56166:60:4:0.0206:0:1 +17 40375335 . A G 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCTTTCTCCCAACCCCACC;RSEQ=GAGCTGCTTTCCAGTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:617:0:0,0:525,91:616,0:0:2,0:24.9:1:30.5:1:1:0:60:50.333:1:0:0.1 0/1:445:27:21,6:345,73:418,27:0.0607:2,2:26.1:1:29.6:1:0.6016:1.3493:60:54:0.0614:0:1.1 +17 40375716 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.08366;SOR=Inf;LSEQ=GGAGGAAAAGCAAACGTCAT;RSEQ=ATGAGACACAGGGTGGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:1,128:129,0:0:1,0:23:1:32.4:1:1:0:60:31.25:1:0:0.1 0/1:53:2:0,2:3,48:51,2:0.0377:2,0:26.5:1:30.5:1:1:0:60:4:0.0385:0:1 +17 40383886 . A G 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05072;SOR=Inf;LSEQ=AAAGAAAAAAAATTTTAAAT;RSEQ=CCTTTTTATGGATCACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:129,2:131,0:0:1,0:24.5:1:28.7:1:1:0:59.8:64.5:1:0:0.1 0/1:78:3:3,0:75,0:75,3:0.0385:1,0:31.7:1:33.3:1:1:0:60:6:0.039:0:1 +17 40384279 . A G 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TATTATTTATTTTTATTTTT;RSEQ=TTTTTTTGAGACAGTCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:0,110:110,0:0:1,0:17.3:1:31.6:1:1:0:59.6:109:1:0:0.1 0/1:76:10:0,10:1,65:66,10:0.1316:1,0:23.6:1:30.7:1:1:0:60:9:0.12:0:1 +17 40441357 . AG A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14408;SOR=Inf;LSEQ=TAGGTAGGCATGGCAAGGCC;RSEQ=GGGCAGGCCCGGTTCCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:292,21:313,0:0:2,0:23.4:1:33.2:1:1:0:59.9:61.6:1:0:0.1 0/1:192:2:1,1:171,19:190,2:0.0104:2,2:8.5:1:30.1:1:0.19797:8.79907:60:4:0.0104:0.0052:0 +17 40441819 . A G 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGTTTCCACTTTATTCC;RSEQ=GCTCCCTGACCTCCTTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:701:0:0,0:534,167:701,0:0:2,0:21.8:1:30.4:1:1:0:59.9:34.05:1:0:0.1 0/1:473:26:19,7:319,128:447,26:0.055:2,2:18.2:1:29.8:1:1:1.09:60:52:0.0557:0:1.2 +17 40444332 . G GT 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.32509;SOR=3.93338;LSEQ=CTCTCTGAGCCTCTGTTCCT;RSEQ=TTTTTTTTTCTTTTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:0,2:0,49:49,2:0.0392:1,0:35:1:32:0:1:0:60:4:0.0408:0:0 0/1:7:1:0,1:1,5:6,1:0.1429:2,0:23:0:31:0:1:0:60:2:0.1667:0:0 +17 40447401 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTGGACTTTGAAGGTGT;RSEQ=ACTATCTGCCGTTATCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:23:23,0:1,0:1,23:0.9583:0,1:21.6:1:33:1:1:0:58.3:46:0.9583:0:1.3 1/1:3:3:3,0:0,0:0,3:1:0,0:29:1:31.7:1:1:0:60:6:1:0:1.7 +17 40447500 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02655;SOR=Inf;LSEQ=CTTCTGATGCAAATGATCCT;RSEQ=CCTTCTTGCCCTAGTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:124,3:127,0:0:1,0:24.7:1:31.7:1:1:0:59.4:254:1:0:0.8 0/1:55:3:3,0:51,1:52,3:0.0545:1,0:24:1:32:1:1:0:60:6:0.0545:0:1 +17 40447558 . T C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.08817;LSEQ=GGTTTGGGGTTTGGGGTCTG;RSEQ=AGTATTGGTGTTTCCTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:271:242:214,28:27,0:27,242:0.893:1,2:21.9:1:32.2:1:0.08958:0:59.8:79.667:0.8985:0:1.1 0/1:154:65:57,8:73,15:88,65:0.4221:2,2:21.5:1:31.1:1:0.49641:1.46:60:64:0.4211:0:1.1 +17 40451643 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18458;LSEQ=CCCCTGGCTGTCAGGAACCC;RSEQ=GACTTGCTCTTGATGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:119:113,6:173,6:179,119:0.3993:1,2:22.7:1:32.6:1:0.5519:1.52868:54.4:38.667:0.3946:0:1.2 0/1:156:17:15,2:132,7:139,17:0.109:2,2:9.2:1:30.8:1:0.25474:2.49422:57.1:34:0.1097:0:1.1 +17 40451824 . G A 67 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10952;SOR=3.1333;LSEQ=GAGCGTCTGAGCCGGGAGAC;RSEQ=GCCCTCCAGCAGAAGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:3:3,0:382,329:711,3:0.0042:2,0:1.3:1:27.3:1:0.25357:0:40:6:0.0042:0:1 0/1:536:7:6,1:287,242:529,7:0.0131:2,2:8.7:1:24.1:1:0.13399:5.05:36.9:6:0.0113:0:1 +17 40452506 . T C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.34715;SOR=0.42534;LSEQ=CTGCTGTCCTGGGGGTGGGA;RSEQ=GGGGCTCGGGTGTGTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:12:6,6:30,41:71,12:0.1446:2,2:34.8:1:29.8:1:0.7552:1.36:21.8:11:0.1358:0:1.3 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:25.5:1:30:1:1:1.14834:21.5:4:0.0667:0:1.5 +17 40452675 . C A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=ACGGGAGCTGTGTCTTGGGG;RSEQ=CTGGCGTCTGTGAGGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:3.4:1:30.4:1:1:0:20.6:10:1:0:1.2 1/0:6:3:2,1:1,1:2,3:0.5:2,2:5.7:1:29.3:1:1:1.73:20:6:0.5:0:1.3 +17 40453240 . C T 65 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09984;SOR=3.55238;LSEQ=ACCACAGAGGGACTGAGAGC;RSEQ=CTTTCCCCTGCGCCAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:969:3:0,3:740,226:966,3:0.0031:2,0:1.3:1:26.7:1:0.01307:0:60:6:0.0032:0:1 0/1:641:7:2,5:464,170:634,7:0.0109:2,2:12:1:23.3:1:0.01849:6.79817:57.1:6:0.0095:0:1 +17 40453398 . TC T 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.76134;SOR=0.88981;LSEQ=AAGCTGAACGTGCACATGAA;RSEQ=CCCCCCAGGTGAAGGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2171:26:11,15:1016,1127:2143,26:0.012:2,2:25.9:1:30.7:1:0.69455:1.22921:32.2:52:0.0121:0.0028:0.2 0/1:1687:18:9,9:814,851:1665,18:0.0107:2,2:19.5:1:28.3:1:1:1.05:30:36:0.0108:0.003:0.4 +17 40454281 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAACAGAACTGGGCTGTCT;RSEQ=CTCGCCCAGCCCCTTGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:37.5:1:28.5:1:1:1:60:4:0.5:0:1 +17 40456499 . T G 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGCCCAGAGCTGAGTCCT;RSEQ=GTAAGCAGCCGCCATCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1283:0:0,0:610,673:1283,0:0:2,0:23.4:1:30.7:1:1:0:60:115.636:1:0:0.1 0/1:976:59:31,28:455,460:915,59:0.0605:2,2:23.5:1:31.3:1:0.68933:1.12:60:118:0.061:0:1.3 +17 40457074 . T C 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAAAAAGAAAAAAGT;RSEQ=GGGCATGGTGGCCTGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:4,6:10,2:0.1667:2,0:17:1:26.5:1:0.51515:0:60:4:0.1818:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:48:0:28:0:1:0:60:2:1:0:0 +17 40457140 . C A 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAGGAGGATCACTTGAG;RSEQ=CCAGGAGGTCAAGGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:8,2:0.2:2,2:24.5:1:29.5:1:1:1.58:56:4:0.2:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 40457246 . G C 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAGCAGATTGCGGCCATG;RSEQ=GTGGTGGGTCTTGCCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:16:1:34:1:1:0:41.7:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 40457510 . A G 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56597;SOR=3.02375;LSEQ=AGCCTGGGCAACAAGAGTGA;RSEQ=ACTCCATATCAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:1,0:170,0:170,1:0.0058:1,0:42:0:28:0:1:0:51:2:0.006:0:2 0/1:114:2:2,0:111,1:112,2:0.0175:1,0:20:1:31.5:1:1:0:40:4:0.0175:0:3.5 +17 40457520 . CA C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05471;SOR=1.77345;LSEQ=ACAAGAGTGAAACTCCATAT;RSEQ=AAAAAAAAAATACATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:25:25,0:216,2:218,25:0.1012:1,1:17.8:1:33.1:1:1:0:57.2:50:0.1012:0.0243:0.4 0/1:174:29:27,2:143,2:145,29:0.1667:1,2:20.6:1:31.2:1:0.12991:5.22074:58.9:58:0.1676:0.0402:0.2 +17 40457536 . T TA 114 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.83998;SOR=1.16345;LSEQ=ATATCAAAAAAAAAAATACA;RSEQ=AAAAAAAAATAAAGCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:14:13,1:321,29:350,14:0.0381:2,1:21.2:1:30.2:1:1:1.17:57.8:28:0.0406:0.0082:0.6 0/1:272:12:12,0:237,21:258,12:0.0441:2,0:20.1:1:29.1:1:0.6077:0:57.7:24:0.0474:0.011:0.1 +17 40458193 . TTG T 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.01301;SOR=0;LSEQ=TCTCTAGGTGTCTGTGTATC;RSEQ=TGTGTGTGTGAATATTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:9:4,5:622,126:748,9:0.0119:2,2:19.7:1:29.1:1:0.01009:6.1484:60:8:0.0108:0.0026:0.2 0/0:524:0:0,0:432,92:524,0:0:2,0:21.7:1:29.7:1:1:0:60:64.5:1:0:0.1 +17 40458684 . G GC 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12177;SOR=3.64978;LSEQ=CAAGAGCGAGATGACGGAGG;RSEQ=CCCAGGGCTGGGAGTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:0,5:0,50:50,5:0.0909:1,0:41.6:1:30:1:1:0:60:10:0.0943:0:0.2 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:32.3:1:31:1:1:0:60:6:0.2727:0:0 +17 40458742 . CT C 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGATGTGTTTGCTAATTTT;RSEQ=TTTTTTTTTTTAGAGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:7:0,7:0,26:26,7:0.2121:1,0:31.7:1:32:1:1:0:54.3:14:0.2121:0:0.4 0/0:3:0:0,0:0,3:3,0:0:0,0:11.3:1:30:1:1:0:60:6:1:0:0 +17 40459297 . T C 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=Inf;LSEQ=CACTTTATGGTCTGCTGGAG;RSEQ=GTGGTGGCAAGCAGGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:262,8:270,0:0:1,0:24.8:1:29.5:1:1:0:60:32.75:1:0:0.1 0/1:137:9:7,2:120,8:128,9:0.0657:2,2:27.6:1:31.9:1:0.13113:4.21058:60:18:0.0662:0:1.1 +17 40459562 . A G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=2.69988;LSEQ=GGCCAGCTGTGGGCGCAGAG;RSEQ=GACTGTGGCTGTGGCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1493:244:121,123:608,637:1245,244:0.1634:2,2:24.7:1:30.9:1:0.83397:1.03:60:26.111:0.1603:0:1.1 0/1:1216:420:211,209:395,397:792,420:0.3454:2,2:23.4:1:29.8:1:0.95187:1.01:60:37.182:0.3431:0:1.2 +17 40459737 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.03837;LSEQ=ACCATCGCCTGGAAGTTTGA;RSEQ=TCCCGTGAGTGCCCGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1778:278:124,154:730,768:1498,278:0.1564:2,2:26.2:1:30.7:1:0.21472:1.18037:60:54.6:0.156:0:1.2 0/1:1630:447:211,236:544,637:1181,447:0.2742:2,2:25.5:1:29.4:1:0.69689:1.05:59.8:54.875:0.273:0:1.2 +17 40460427 . C T 132 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.10126;LSEQ=ATAGACAAAGCCTTGGGCTG;RSEQ=GCCGTGGGGACTTCCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:1:0,1:61,355:416,1:0.0024:2,0:11:0:32:0:1:0:60:2:0.0024:0:1 0/1:304:23:3,20:42,238:280,23:0.0757:2,2:25.2:1:29.4:1:1:1.17587:60:46:0.0772:0:1.1 +17 40460428 . G A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25826;LSEQ=TAGACAAAGCCTTGGGCTGC;RSEQ=CCGTGGGGACTTCCCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:77:11,66:45,281:326,77:0.1906:2,2:22.1:1:30.3:1:0.85676:1.04:60:154:0.1969:0:1.1 0/1:297:17:3,14:41,239:280,17:0.0572:2,2:24.2:1:27:1:0.72503:1.25:59.2:16:0.055:0:1.4 +17 40460783 . GT G 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GCCCCAAATCCATTGGTTGG;RSEQ=TTGCTTGTTGATTCTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:11,4:15,2:0.1176:2,0:34.5:1:32:1:1:0:60:4:0.1176:0:0 1/1:1:1:1,0:0,0:0,1:1:0,0:32:0:32:0:1:0:60:2:1:0:0 +17 40460989 . A G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.64107;LSEQ=ATGTGAGCAGGAGGGAGACT;RSEQ=CATGGGGCGTGGGCTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:92:71,21:427,109:536,92:0.1463:2,2:22.1:1:32.3:1:0.57917:1.15837:60:184:0.147:0:2 0/1:478:149:117,32:247,81:328,149:0.3117:2,2:21.9:1:31.1:1:0.48676:1.20:60:48.667:0.312:0:2 +17 40461003 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=1.75591;LSEQ=GAGACTACATGGGGCGTGGG;RSEQ=TTCCACCCCACTTGGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:825:136:93,43:516,173:689,136:0.1648:2,2:21.3:1:30:1:0.13473:1.37852:59.9:135:0.1654:0:1.7 0/1:637:164:121,43:337,136:473,164:0.2575:2,2:23.3:1:28.8:1:0.61431:1.14:60:81:0.2576:0:1.8 +17 40461061 . A G 201 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCACCACTGTTCTTCCCTTG;RSEQ=CAGCTAAAGCTGTTGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1663:0:0,0:976,686:1662,0:0:2,0:26:1:30:1:1:0:50.9:68.25:0.9994:0:0.2 0/1:1421:92:54,38:741,587:1328,92:0.0647:2,2:30.7:1:30.9:1:0.66425:1.13:49.7:91:0.0651:0:1.4 +17 40461171 . C A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02439;SOR=Inf;LSEQ=CTCTTTCCTCCTCCCCCAGA;RSEQ=CCTGCCTCCCATCCTGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:541:0:0,0:130,411:541,0:0:2,0:32.1:1:31.2:1:1:0:39.9:134.25:1:0:0.1 0/1:355:4:2,2:95,256:351,4:0.0113:2,2:38.3:1:26:1:0.30104:2.69:32.3:3:0.0086:0:1.3 +17 40461250 . T A 91 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00017;SOR=20.80929;LSEQ=GCCCTGGGGAGGGAGTCCCC;RSEQ=CTCCTGTAGCTGGAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:1:0,1:114,355:469,1:0.0021:2,0:4:0:13:0:1:0:31:0:0:0:6 0/1:211:9:3,6:30,172:202,9:0.0427:2,2:19.1:1:28.8:1:0.15072:2.85:54.4:18:0.0443:0:1 +17 40461293 . C T 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGAGTGGGGCACTTTGTC;RSEQ=GTCTACACCCCGAGAAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:199,193:392,0:0:2,0:24:1:30.8:1:1:0:58.3:55:1:0:0.2 0/1:188:16:10,6:86,86:172,16:0.0851:2,2:19.8:1:30.9:1:0.43579:1.66:56.9:32:0.0856:0:1.1 +17 40461674 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00188;SOR=3.46317;LSEQ=AAGCTAGACATAGCAGGGTC;RSEQ=AGTCCTCACTCTAGTACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:15:0,15:5,97:102,15:0.1282:1,1:16.5:1:33:1:1:0:60:30:0.1327:0:1.1 0/1:56:19:1,18:1,36:37,19:0.3393:1,1:20.5:1:31.3:1:1:1.97:60:38:0.3393:0:1.3 +17 40462796 . TTGTG T 172 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=11.000;MSILEN=2;SSF=0.04095;SOR=0.55345;LSEQ=CTTTGCAGGCATGCATGTGC;RSEQ=TGTGTGTGTGTGTGTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:47:1,46:2,127:129,47:0.2461:1,1:35.5:1:31:1:1:1.38:59.8:94:0.2487:0:0.1 0/1:144:22:0,22:0,106:106,22:0.1528:1,1:36:1:29.9:1:1:0:59.8:44:0.1571:0.0069:0.1 +17 40462994 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGACCTATTCCTCCTG;RSEQ=GCCCCTCATCTGCTCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:8,2:0.2:0,0:22.5:1:32:1:1:0:60:4:0.2222:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:7:0:31:0:1:0:60:2:1:0:0 +17 40467625 . C T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16291;SOR=Inf;LSEQ=CCCAGATTGCTCAAAGATAG;RSEQ=AGAAGTAGGAGATTAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:181,0:181,0:0:1,0:25.7:1:32.4:1:1:0:59.9:59.333:1:0:0.1 0/1:123:2:1,1:116,4:120,2:0.0163:1,2:21:1:24:1:0.08061:26.05014:60:4:0.0163:0:1 +17 40467934 . C T 111 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03784;SOR=0.1384;LSEQ=CACTGCTATCCAATCTCCTG;RSEQ=CCCTTAAGGCCCAGGGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:12:0,12:15,343:358,12:0.0324:1,0:30.5:1:31.1:1:1:0:60:24:0.0335:0:1 0/0:217:1:0,1:12,204:216,1:0.0046:2,0:1:0:26:0:1:0:60:2:0.0047:0:1 +17 40467943 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.11567;SOR=Inf;LSEQ=CCAATCTCCTGCCCCTTAAG;RSEQ=CCCAGGGATGGTCAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:6,319:325,0:0:1,0:25.4:1:32.7:1:1:0:59.9:64:1:0:0.1 0/1:168:2:0,2:7,159:166,2:0.0119:1,0:45.5:1:29.5:1:1:0:60:4:0.012:0:1.5 +17 40467999 . G T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00214;SOR=Inf;LSEQ=TCCCTGGAGGACCCTGCCTC;RSEQ=GGAAGGGTCCTTTCTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:1,115:116,0:0:1,0:22.7:1:31.7:1:1:0:59.8:57:1:0:0.1 0/1:50:5:0,5:2,43:45,5:0.1:1,0:17:1:29.2:1:1:0:60:10:0.1:0:1 +17 40468009 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10228;SOR=Inf;LSEQ=ACCCTGCCTCGGGAAGGGTC;RSEQ=TTTCTCATTCCCACCTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:1,83:84,0:0:1,0:26.8:1:33.8:1:1:0:59.7:83:1:0:0.1 0/1:40:2:1,1:1,37:38,2:0.05:1,2:8.5:1:31.5:1:0.09872:26.51:60:4:0.05:0:1 +17 40468489 . G A 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGTGATCCACCCACCTC;RSEQ=GCCTCCCAAAGTGCTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:2,2:4,3:0.4286:2,0:30.3:1:31.7:1:0.42857:0:34.3:6:0.4286:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 40468747 . C T 57 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00957;SOR=Inf;LSEQ=TCGGTGTGTACATGTGAGAG;RSEQ=ATCACACAAAGGGGACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:0:0,0:427,147:574,0:0:2,0:24.4:1:32.3:1:1:0:60:142.5:1:0:0.1 0/1:493:6:1,5:364,122:486,6:0.0122:2,2:6.2:1:22.2:1:0.00513:14.82251:60:5:0.0103:0:1 +17 40468975 . GA G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.23858;SOR=0.71694;LSEQ=GGGGTTGACAAGACACAATG;RSEQ=AAAAAAAAAAAGAACAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:43:17,26:113,168:281,43:0.1311:2,2:27.2:1:30.9:1:1:1.02862:60:42:0.1321:0.0122:0.4 0/1:246:24:8,16:78,137:215,24:0.0976:2,2:30:1:30.7:1:0.8268:1.13811:60:48:0.0996:0:0.4 +17 40468994 . AAC A 103 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.07625;SOR=0.2521;LSEQ=GGAAAAAAAAAAAAGAACAA;RSEQ=ACACACACACAAGCCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:10:5,5:113,139:252,10:0.0379:2,2:19.2:1:31.1:1:0.75774:1.23:57.5:20:0.0394:0.0076:0.5 0/0:204:2:1,1:69,131:200,2:0.0098:2,2:29.5:1:30.5:1:1:1.89:60:4:0.0099:0:0 +17 40474864 . A G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32913;SOR=1.65717;LSEQ=AAACCAATCCTTCAGCTGGA;RSEQ=GGATTTAGAAGTCACGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:24:22,2:96,6:102,24:0.1905:2,2:26.8:1:33.4:1:0.6471:1.44978:60:48:0.1951:0:1.8 0/1:32:9:9,0:22,1:23,9:0.2813:1,0:16.9:1:32:1:1:0:60:18:0.2813:0:1.9 +17 40474880 . G C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31305;SOR=1.49599;LSEQ=TGGAAGGATTTAGAAGTCAC;RSEQ=CAAATGTGTTTTGCGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:27:25,2:104,5:109,27:0.1985:1,2:27.4:1:31.6:1:0.62537:1.65692:60:54:0.203:0:1.8 0/1:48:13:13,0:33,2:35,13:0.2708:2,1:22:1:32:1:1:0:60:26:0.2708:0:1.6 +17 40475650 . G GA 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=3.58151;LSEQ=ATTCACACCAGGTCCTGAAG;RSEQ=AAAGAAAAAGAGTCAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1502:244:109,135:588,666:1254,244:0.1625:2,2:24.2:1:30.5:1:0.52891:1.0934:59.9:121:0.1634:0.03:0.1 0/1:1517:622:290,332:431,460:891,622:0.41:2,2:26.3:1:29.1:1:0.53024:1.0726:59.8:55.545:0.4095:0.0481:0.1 +17 40476363 . G A 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TAAATAAATAAATAAAATAA;RSEQ=ACAAAAAAAACCAACTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:16.7:1:32:0:1:0:49:6:0.375:0:2.3 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:29:0:1:0:60:2:1:0:1 +17 40476667 . C G 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACATGGCCCAAATGAACAGC;RSEQ=CTATGGGCCGGATCCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:440,11:451,0:0:1,0:25.9:1:31.4:1:1:0:59.8:44.1:1:0:0.2 0/1:321:14:14,0:296,11:307,14:0.0436:1,1:23.9:1:28.5:1:1:0:60:13:0.0418:0:1.3 +17 40476701 . C G 116 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55706;SOR=0.86059;LSEQ=CCCTTTTCTGGGCGGGTGGG;RSEQ=GGGAGGGAGAAGGGGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:742:45:1,44:663,29:692,45:0.0606:1,1:17.3:1:21.2:1:0:986.71834:58.2:1.5:0.0389:0:3.2 0/1:608:32:0,32:542,29:571,32:0.0526:2,1:20.3:1:23.8:1:0:0:57.8:2.556:0.0398:0:3.5 +17 40477739 . T C 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTATAGGCGTCCGCCACCA;RSEQ=ACCCAGCTAATTTTTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:42:1:28.5:1:1:0:43:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41.5:1:32.5:1:1:0:45:4:1:0:1 +17 40481394 . AC A 241 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=144.45695;LSEQ=CTCTCTCCCTCAAGGAAAAC;RSEQ=CCCAGTTGTCTTTCATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1761:2:1,1:1001,756:1757,2:0.0011:2,2:34.5:1:31:1:1:1.32385:60:4:0.0012:0:0 0/1:1622:229:128,101:793,600:1393,229:0.1412:2,2:24.8:1:30.8:1:0.77389:1.04288:59.6:458:0.1426:0.0185:0.2 +17 40481529 . G C 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00033;SOR=0.73987;LSEQ=GGCTCTCCCTAGCCCTCTCC;RSEQ=GCAGCCAGAGGCCCTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1411:925:457,468:250,233:483,925:0.6556:2,2:24.4:1:30.8:1:0.43192:1.09871:60:461.5:0.6565:0:1.1 1/0:1086:635:304,331:214,235:449,635:0.5847:2,2:24.6:1:29.7:1:0.95086:1.01:60:56.727:0.5837:0:1.1 +17 40481902 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55736;SOR=3.48544;LSEQ=AAAAACCTCTGTGCTCCTGG;RSEQ=CATTTCTTTAAACTATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:1:1,0:49,269:318,1:0.0031:2,0:1:0:25:0:0.15674:0:60:2:0.0032:0:1 0/1:184:2:1,1:25,157:182,2:0.0109:2,2:39:1:30:1:0.2633:6.18:60:4:0.011:0:1 +17 40483403 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10688;SOR=Inf;LSEQ=TGAAGATCTCTGAATAAAGA;RSEQ=AGAGTCTCTAGTTCAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:223,25:248,0:0:2,0:24.4:1:32.5:1:1:0:59.8:496:1:0:0.1 0/1:225:3:2,1:193,29:222,3:0.0133:2,2:25:1:27.3:1:0.35038:3.30162:60:6:0.0134:0:1.3 +17 40483466 . C A 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTATTCCTCATTTGAAAAA;RSEQ=AGAGCTAAGATAGGAGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:773:0:0,0:452,318:770,0:0:2,0:25.3:1:32.1:1:1:0:59.9:109:0.9961:0:0.1 0/1:764:27:17,10:424,311:735,27:0.0353:2,2:25.3:1:29.5:1:0.69302:1.25:60:54:0.0354:0:1.2 +17 40485635 . C T 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCACCAACTCTACCCTCA;RSEQ=CCTAACAGTGTCCCTCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:0:0,0:436,174:610,0:0:2,0:23.1:1:31.4:1:1:0:60:45.923:1:0:0.1 0/1:558:44:34,10:356,158:514,44:0.0789:2,2:24.3:1:29.5:1:0.3074:1.51:60:43:0.078:0:1 +17 40489539 . G A 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=31.12752;LSEQ=TTCCAGTCAGCCAGCTCCTC;RSEQ=TCCGTGAGAGTTTTCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1783:4:4,0:885,893:1778,4:0.0022:2,0:1:0:24.3:1:0.06173:0:60:3:0.0017:0:1 0/1:1681:110:52,58:783,788:1571,110:0.0654:2,2:22.7:1:29.9:1:0.62297:1.10824:60:109:0.0657:0:1.2 +17 40489660 . C T 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CCTCAGACTGTCTCTAACCA;RSEQ=ATTCTTTAGTCAACTCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:774:37:13,24:299,436:735,37:0.0478:2,2:24.6:1:29.8:1:0.60735:1.26568:60:74:0.0485:0:1.1 0/0:697:0:0,0:266,429:695,0:0:2,0:21.8:1:31.4:1:1:0:60:172.75:0.9971:0:0.1 +17 40489741 . G C 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCTGAAATCCCGCAAGTGA;RSEQ=CGAGACACATGGGGGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:678:0:0,0:379,299:678,0:0:2,0:24.6:1:32.4:1:1:0:59.9:51.154:1:0:0.1 0/1:535:26:15,11:300,208:508,26:0.0486:2,2:22.1:1:31.4:1:1:1.05757:60:52:0.0491:0:1.1 +17 40489939 . T G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32447;SOR=1.30511;LSEQ=TGACCTGAGGGAATACTCCT;RSEQ=GACCTGAGGGAATACTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:44:15,29:65,154:219,44:0.166:2,2:16.2:1:31.3:1:0.59195:1.22:31.8:43:0.1686:0:1.2 0/1:189:39:14,25:44,104:148,39:0.2063:2,2:15.3:1:29.9:1:0.55965:1.32:31.4:38:0.2032:0:1.1 +17 40490539 . T G 65 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.46198;LSEQ=TGACCTGAGGGAATACTCCT;RSEQ=GACCTGAGGGAATACTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:4,2:6,4:0.4:2,0:6.3:1:32.8:1:0.46667:0:28.3:8:0.4444:0:2.3 1/0:6:3:2,1:3,0:3,3:0.5:0,2:3:1:29.7:1:1:0:35.7:6:0.5:0:2 +17 40490559 . G T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03443;LSEQ=TGACCTGAGGGAATACTCCT;RSEQ=GACCTGAGGGAATACTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:17:15,2:6,2:8,17:0.68:2,2:15:1:32.3:1:0.56996:2.40:31.1:34:0.68:0:1.3 1/0:16:11:10,1:3,2:5,11:0.6875:2,2:16.4:1:31.2:1:0.21429:5.76:30.8:22:0.6875:0:1.3 +17 40490643 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15394;SOR=Inf;LSEQ=AGGACCCGTACCTCCCTTGC;RSEQ=CCCCGCCCGCCTTAAGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:143,8:151,0:0:2,0:25.1:1:30.5:1:1:0:58.1:74.5:1:0:0.2 0/1:98:2:2,0:91,5:96,2:0.0204:2,0:29:1:31:0:1:0:60:4:0.0206:0:1 +17 40491110 . AT A 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.03807;SOR=8.77506;LSEQ=GGAGACCCCCATCTCTACAA;RSEQ=TTTTTTTTTTTAATTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:3,0:11,4:15,3:0.1667:2,0:29.3:1:33.3:1:1:0:60:6:0.1667:0:0 1/0:6:4:3,1:2,0:2,4:0.6667:0,2:21.3:1:30.7:1:1:0:49:8:0.6667:0.1667:0.5 +17 40491135 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02565;SOR=Inf;LSEQ=TTTTTTTTAATTAGCTGGGC;RSEQ=TGGTGGTGCATGCCTGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:29,2:31,0:0:2,0:15.7:1:28.2:1:1:0:59.6:30:1:0:0.2 0/1:14:3:2,1:11,0:11,3:0.2143:0,2:20.7:1:25.3:1:0.21429:0:45.3:2:0.1538:0:1 +17 40491301 . C T 62 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18406;SOR=0.31702;LSEQ=AAAAAAAAAATTAATGAAAG;RSEQ=TCCCTGCCCGAGGCTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:630:7:2,5:462,160:622,7:0.0111:2,2:12.1:1:22.4:1:0.01544:7.19275:58.3:2.5:0.0084:0:2.3 0/0:564:2:0,2:395,167:562,2:0.0035:2,0:1:0:23.5:1:0.08941:0:60:4:0.0037:0:1 +17 40497421 . C CT 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.55694;SOR=3.31355;LSEQ=ATTTTGGGGGGTGGAACTTT;RSEQ=TTTTTTTTTAGAGTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:1:1,0:66,6:72,1:0.0137:2,0:36:0:34:0:1:0:60:2:0.0137:0:0 0/1:45:2:2,0:40,3:43,2:0.0444:2,0:19.5:1:32:0:1:0:60:4:0.0444:0:0 +17 40497828 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00632;SOR=3.64473;LSEQ=AGAGCCTGGGTGAAGGCTCT;RSEQ=TGTCGGCGGGGGGCGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:8:0,8:0,59:59,8:0.1194:1,0:26.6:1:31:1:1:0:60:16:0.1231:0:2.5 0/1:51:17:1,16:0,34:34,17:0.3333:1,1:32.8:1:29.2:1:0.33333:0:60:16:0.3265:0:2.8 +17 40497835 . C G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00786;SOR=3.8565;LSEQ=GGGTGAAGGCTCTCTGTCGG;RSEQ=GGGGGGCGAAGGGGAGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:8:0,8:0,47:47,8:0.1455:1,0:27.1:1:26.1:1:1:0:60:3:0.12:0:2.8 0/1:40:16:1,15:0,24:24,16:0.4:1,1:32.3:1:30.8:1:0.4:0:60:15:0.3947:0:3.1 +17 40497839 . G C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00915;SOR=4.29815;LSEQ=GAAGGCTCTCTGTCGGCGGG;RSEQ=GGCGAAGGGGAGGTCGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:0,6:0,45:45,6:0.1176:1,0:28.3:1:31.7:1:1:0:60:12:0.1176:0:3 0/1:38:14:1,13:0,24:24,14:0.3684:1,1:31.8:1:29.7:1:0.36842:0:60:28:0.3684:0:3.2 +17 40497840 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.17952;SOR=Inf;LSEQ=AAGGCTCTCTGTCGGCGGGG;RSEQ=GCGAAGGGGAGGTCGTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:0,51:51,0:0:1,0:27.1:1:31.5:1:1:0:60:50:1:0:0.5 0/1:38:2:0,2:1,35:36,2:0.0526:1,0:8:1:32:1:1:0:60:4:0.0526:0:2.5 +17 40498944 . T C 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10967;SOR=6.88982;LSEQ=AGGCCAGGCATGGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:0,2:0,30:30,2:0.0625:1,0:32:1:32:0:1:0:53.5:4:0.0625:0:1 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:36.5:1:30:0:1:0:48:4:0.3333:0:1 +17 40500265 . C A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00087;SOR=3.56449;LSEQ=TTACAAGACCAAAGGGTGCC;RSEQ=CTTTATCTCCTGATCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:19:19,0:84,2:86,19:0.1792:1,1:26.3:1:31.1:1:1:0:60:38:0.1827:0:1.3 0/1:50:22:20,2:28,0:28,22:0.44:1,2:19.3:1:29:1:0.18857:0:60:21:0.4375:0:1.1 +17 40500283 . AT A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTTTATCTCCTGATCTC;RSEQ=TTTCCCCATCACCTGTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:2,0:142,3:145,2:0.0136:1,0:15:1:33.5:1:1:0:60:4:0.014:0:0 0/0:66:0:0,0:63,3:66,0:0:1,0:23.3:1:30.5:1:1:0:60:132:1:0:0.3 +17 40500343 . A G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00027;SOR=Inf;LSEQ=CAGCAAGGCATGACATTAAG;RSEQ=GTTCATGTCTCTTGACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:311,76:387,0:0:2,0:21.2:1:30.4:1:1:0:60:192.5:0.9948:0:0.1 0/1:264:9:6,3:203,50:253,9:0.0341:2,2:23.4:1:29.8:1:0.39208:2.02353:60:18:0.0347:0:1.1 +17 40501482 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAATGTAGAAATTGGATG;RSEQ=TTGGGGTTGGGGGACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 41091622 . C T 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=AATCTCTTGACCTCGTGATC;RSEQ=GCCTGCCTTGGCGTCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:9.5:1:34:0:1:0:60:4:0.5:0:1.5 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:21:1:32:0:1:0:49.5:4:0.6667:0:1 +17 41091721 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.52273;SOR=Inf;LSEQ=CAATTTACTTTAAGGTCATT;RSEQ=TTAGTGTAGGTGGATCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:14,7:21,0:0:2,0:32.4:1:30.9:1:1:0:60:42:1:0:0 0/1:35:2:1,1:20,13:33,2:0.0571:2,2:20:0:32.5:1:1:1.51907:50:4:0.0571:0:2.5 +17 41091772 . T C 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06537;SOR=0;LSEQ=TTTGACACCCTCTCTAAACA;RSEQ=GAATTTAGTTCAAATCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:1,2:11,14:25,3:0.1071:2,2:13:1:20.7:1:1:1.54711:47.7:2:0.0769:0:1 0/0:40:0:0,0:18,22:40,0:0:2,0:27.8:1:28.3:1:1:0:57.2:12.333:1:0:0.2 +17 41197274 . C A 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGGGTCTGACTCTCTGC;RSEQ=TTTGTGAACACAGGGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:35.5:1:29:1:1:0:60:4:0.4:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 41199788 . AT A 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.18069;SOR=4.90437;LSEQ=ACTGGAACTGTCACTTCATC;RSEQ=TTTTTTTGTTTGTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:0,1:41,253:294,1:0.0034:2,0:35:0:33:0:1:0:60:2:0.0034:0:0 0/1:244:4:1,3:43,197:240,4:0.0164:2,2:15.3:1:31.3:1:0.55106:1.52:60:8:0.0166:0.0082:0.8 +17 41199913 . T C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11251;SOR=3.46023;LSEQ=ATCCTTCCATCTCAGCCTCC;RSEQ=AAGTAGCTGGAACTACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:0,6:0,30:30,6:0.1667:1,0:35:1:33.3:1:1:0:54.8:12:0.1818:0:1 0/1:12:5:0,5:0,7:7,5:0.4167:0,0:24.4:1:30.6:1:1:0:49.8:10:0.4167:0:1 +17 41201364 . T C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65134;SOR=1.41067;LSEQ=GGACAATGGTCTTAAAATAG;RSEQ=AGGGGTATGGATTTTAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:8:0,8:1,67:68,8:0.1053:1,0:23.3:1:33.3:1:1:0:60:16:0.1053:0:1 0/1:14:2:0,2:1,11:12,2:0.1429:2,0:8.5:1:31.5:1:1:0:60:4:0.1429:0:1 +17 41202897 . GT G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.53846;SOR=0;LSEQ=GAGAAGGGGGACAAGGTATA;RSEQ=TTTTTTTTGCCATAGGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:32,0:32,2:0.0588:1,0:19:1:32.8:1:1:0:60:4:0.0588:0.0294:0 0/0:18:0:0,0:18,0:18,0:0:1,0:13.8:1:28.6:1:1:0:60:17:1:0:0.2 +17 41203325 . T A 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04977;SOR=13.25393;LSEQ=TCCAATGTCCAGAACACTAC;RSEQ=GGATTTCAGAAGATCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:34:1:32.3:1:1:0:60:6:0.2727:0:1 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:28.3:1:28.8:1:1:0:56.3:5:0.8333:0:1 +17 41215825 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.98913;LSEQ=CAAAAACCTTAGGTGTTAAA;RSEQ=GTTAGGTGTAAAAATGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:104:72,32:285,132:417,104:0.1996:2,2:24.6:1:30.3:1:0.90647:1.04:59.7:25:0.1961:0:1 0/1:422:140:88,52:185,97:282,140:0.3318:2,2:25.5:1:29.3:1:0.59002:1.12667:60:45.667:0.3285:0:1.2 +17 41216021 . G A 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00139;SOR=Inf;LSEQ=GTTGAAAACAAAATCAGGAA;RSEQ=TGCTGTCCTAAGAAGCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:45,239:284,0:0:2,0:22.3:1:32.3:1:1:0:60:70:1:0:0.1 0/1:185:7:1,6:40,138:178,7:0.0378:2,2:20.4:1:29.6:1:1:1.73461:60:14:0.0385:0:1 +17 41219549 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.84564;LSEQ=CCAAAGTGCTGCGATTACAG;RSEQ=CATGCGCCACCGTGCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:1,0:145,38:183,1:0.0054:2,0:13:0:25:0:1:0:39:2:0.0055:0:1 0/1:200:2:1,1:153,45:198,2:0.01:2,2:38.5:1:28:1:0.40799:3.37375:60:4:0.0102:0:2 +17 41219560 . C T 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=41.1943;LSEQ=CGATTACAGGCATGCGCCAC;RSEQ=GTGCCTCGCCTCATGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:169,63:232,1:0.0043:2,0:1:0:26:0:0.27468:0:60:2:0.0043:0:1 0/1:238:36:27,9:148,54:202,36:0.1513:2,2:20.8:1:30.3:1:1:1.09:58.2:35:0.1496:0:1.2 +17 41219780 . T C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.96555;LSEQ=CAGCTCAGAATACTAGTTAT;RSEQ=CCACCATGGCATATGTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:18:1,17:26,130:156,18:0.1034:2,1:21.9:1:30.9:1:0.31414:3.38345:60:36:0.104:0:1.6 0/1:162:51:9,42:23,88:111,51:0.3148:2,2:24.8:1:30.3:1:0.832:1.21822:60:50:0.3145:0:1.7 +17 41219790 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22949;SOR=Inf;LSEQ=TACTAGTTATTCCACCATGG;RSEQ=ATATGTTTACCTATGTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:19,124:143,0:0:2,0:24:1:31.8:1:1:0:59.8:27.6:1:0:0.4 0/1:132:2:1,1:23,107:130,2:0.0152:2,2:5:1:27.5:1:0.33171:4.58:60:4:0.0155:0:1 +17 41219804 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00041;SOR=3.9576;LSEQ=CCATGGCATATGTTTACCTA;RSEQ=GTAGCAATCCTGCACGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:11:0,11:5,86:91,11:0.1078:2,0:30.5:1:29:1:1:0:57.5:22:0.1089:0:2.5 0/1:83:27:3,24:3,53:56,27:0.3253:2,2:28.4:1:30:1:0.3852:2.19:60:54:0.3293:0:2.1 +17 41222723 . T C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33837;SOR=2.67059;LSEQ=ATAGCTTTTCCACTAATATT;RSEQ=AATAATTATTTTCTCAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:4,1:23,0:23,5:0.1786:1,2:21.4:1:33.4:1:0.17857:0:54.6:10:0.1852:0:1 0/1:8:3:3,0:5,0:5,3:0.375:0,0:27:1:31.3:1:1:0:60:6:0.375:0:1.3 +17 41222975 . C T 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GGGGTCAGGCCAGACACCAC;RSEQ=ATGGACATTCTTTTGTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1422:0:0,0:711,710:1421,0:0:2,0:24.6:1:31.9:1:1:0:60:128.182:1:0:0.1 0/1:1336:79:38,41:640,615:1255,79:0.0591:2,2:26.8:1:29:1:0.6439:1.12271:60:158:0.0597:0:1.2 +17 41223094 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.69872;LSEQ=AGTATGAGCAGCAGCTGGAC;RSEQ=CTGGGCAGATTCTGCAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:990:184:89,95:375,430:805,184:0.1859:2,2:25.1:1:31.2:1:0.68274:1.07:59.8:45:0.1848:0:1.1 0/1:873:244:122,122:289,340:629,244:0.2795:2,2:25.4:1:30:1:0.29092:1.18:60:33.857:0.2778:0:1.1 +17 41226488 . C A 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGAAGACTCCCAGAGCAA;RSEQ=TGTGCATGTACCACCTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:909:0:0,0:347,562:909,0:0:2,0:26:1:32.8:1:1:0:60:81.636:1:0:0.1 0/1:716:35:15,20:275,406:681,35:0.0489:2,2:28.3:1:29.7:1:0.86021:1.11:59.4:70:0.049:0:1.1 +17 41226601 . G C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=2.99294;LSEQ=TGAAAGGACAAATCATACTT;RSEQ=CTGGGCAGCCAAAGCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:29:5,24:13,133:146,29:0.1657:2,2:20.3:1:29.9:1:0.18589:2.12:59.9:13.5:0.1579:0:1.3 0/1:107:40:7,33:10,57:67,40:0.3738:2,2:23.8:1:29.9:1:0.78748:1.21:60:19:0.3619:0:1.4 +17 41226675 . A T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00496;SOR=4.9987;LSEQ=CTGGCAAAAAAGAGCCCGCA;RSEQ=GACAGCCTAGAAGTCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:7:0,7:1,35:36,7:0.1628:1,0:14.3:1:32.6:1:1:0:60:14:0.1628:0:1.9 1/0:24:12:1,11:0,12:12,12:0.5:0,2:13.1:1:27.9:1:1:0:60:11:0.5:0:1.9 +17 41226736 . GGGGTT G 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.47189;LSEQ=TCAGGGTTGACATATAACAT;RSEQ=GGGTTGGTCTGAGGCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:1,14:15,2:0.1176:1,0:20.5:1:33:0:1:0:60:4:0.1176:0:0 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:42:0:31:0:1:0:60:2:0.2:0:0 +17 41231216 . C CA 79 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.06589;SOR=0.16068;LSEQ=AAAAACAAAACAAAACAAAA;RSEQ=AAAAAAAATGAAAGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:6:4,2:365,70:435,6:0.0136:2,2:21.2:1:30.7:1:0.25453:2.59966:60:12:0.0137:0.0068:0 0/0:454:1:1,0:348,103:451,1:0.0022:2,0:30:0:32:0:1:0:60:2:0.0022:0:0 +17 41231221 . A C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=3.45001;LSEQ=CAAAACAAAACAAAACAAAA;RSEQ=AAATGAAAGGCAGAGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:72:59,13:341,79:420,72:0.1463:2,2:21.6:1:32.3:1:1:1.05:60:144:0.1472:0:1.1 0/1:492:183:131,52:234,73:307,183:0.372:2,2:20:1:31.2:1:0.28425:1.27175:60:90.5:0.3732:0:1.1 +17 41231516 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.4145;LSEQ=AAAACTGGAAAAGTCTACAA;RSEQ=GTGACCCAGCATGCTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:607:69:35,34:247,291:538,69:0.1137:2,2:31.2:1:30.5:1:0.52179:1.21:31.6:22:0.1104:0:1.1 0/1:596:141:59,82:218,237:455,141:0.2366:2,2:32.6:1:29.4:1:0.21091:1.27788:33.9:46:0.2327:0:1.2 +17 41234343 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23093;SOR=Inf;LSEQ=CATAAAATGTTGGAGCTAGG;RSEQ=CCTTACTCTTCAGAAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:173,34:207,0:0:2,0:24.1:1:30.1:1:1:0:60:68:1:0:0.1 0/1:192:2:1,1:152,38:190,2:0.0104:2,2:9.5:1:26.5:1:0.36584:3.96135:60:4:0.0106:0:2 +17 41234470 . A G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.39708;LSEQ=CGCAGGTCCTCAAGGGCAGA;RSEQ=GAGTCACTTATGATGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:895:147:79,68:404,342:746,147:0.1642:2,2:25.3:1:31.6:1:0.92814:1.01679:60:28.4:0.1619:0:1.1 0/1:821:263:132,131:289,268:557,263:0.3203:2,2:26.2:1:30.7:1:0.65422:1.07009:59.8:130.5:0.3258:0:1.1 +17 41234653 . G A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.90877;LSEQ=TGAGAAGCTTTCCATTAAAT;RSEQ=AAAATATATCATACAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:1,0:22,152:174,1:0.0057:2,0:1:0:25:0:0.13143:0:60:2:0.0058:0:1 0/1:184:2:1,1:32,150:182,2:0.0109:2,2:10:1:26.5:1:0.32733:4.63:60:4:0.011:0:1 +17 41242804 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14789;SOR=Inf;LSEQ=GGTAGTATGAGTTCCATCAA;RSEQ=GTGCTTACAGTCTAATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:44,0:0:1,0:22.8:1:33.1:1:1:0:60:43:1:0:0.1 0/1:28:2:2,0:25,1:26,2:0.0714:1,0:5:1:28:1:1:0:60:4:0.0714:0:1 +17 41242913 . C T 38 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6806;SOR=1.5633;LSEQ=GGGATACATACTACTGAATG;RSEQ=AAAGGACACCACACACACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:2:0,2:246,45:291,2:0.0068:2,0:1:0:23.5:1:0.02527:0:60:4:0.0069:0:1 0/1:282:3:1,2:217,62:279,3:0.0106:2,2:5:1:24:1:0.13011:6.93675:60:6:0.0107:0:1.7 +17 41242938 . GCA G 120 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.00219;SOR=7.48773;LSEQ=GACACCACACACACGCATGT;RSEQ=CACACACACACGCTTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:2:2,0:339,127:466,2:0.0043:2,0:37.5:1:32:1:1:0:60:4:0.0043:0:0 0/1:482:15:11,4:318,149:467,15:0.0311:2,2:26.3:1:30.9:1:0.78413:1.29:59.3:30:0.0314:0.0021:0.6 +17 41243108 . C A 31 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.35594;SOR=3.25208;LSEQ=ACTATAAACGCTGCAACTTG;RSEQ=TGTGTCTTTTTCTTCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:1:1,0:69,234:303,1:0.0033:2,0:1:0:25:0:0.23026:0:60:2:0.0033:0:1 0/1:282:3:2,1:67,212:279,3:0.0106:2,2:8.3:1:20:1:0.1493:6.28:60:2:0.0072:0:2.3 +17 41243190 . T G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00192;SOR=2.88551;LSEQ=ATTCCTTGCTTTGGGACACC;RSEQ=GGATTTGCTTTTATAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:22:15,7:49,48:97,22:0.1849:2,2:29:1:30.3:1:0.1597:2.09:58.8:44:0.188:0:1.1 0/1:68:27:7,20:15,26:41,27:0.3971:2,2:23.7:1:30.1:1:0.43276:1.63643:59:54:0.3971:0:1 +17 41244000 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.39097;LSEQ=GACTCCTGCTAAGCTCTCCT;RSEQ=TCTGGACGCTTTTGCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:119:55,64:265,289:554,119:0.1766:2,2:24.9:1:32.6:1:0.76251:1.06693:60:118:0.1766:0:1.1 0/1:640:217:115,102:221,202:423,217:0.3391:2,2:25.2:1:30.6:1:0.86757:1.03:60:42.4:0.3354:0:1.1 +17 41244435 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.5814;LSEQ=TAATATTGCTTGAGCTGGCT;RSEQ=CTTTAAAAACATTTTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:772:120:57,63:306,346:652,120:0.1554:2,2:24.2:1:31.1:1:0.92103:1.02:60:23:0.1517:0:1.1 0/1:720:232:111,121:218,269:487,232:0.3222:2,2:26.5:1:30.7:1:0.47134:1.13:60:115:0.3253:0:1.1 +17 41244880 . C G 182 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTTTGTTTCTTTAAGGACC;RSEQ=AGAGTGGGCAGAGAATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:56:33,23:277,269:546,56:0.0927:2,2:24.8:1:31.5:1:0.26351:1.39:60:112:0.0952:0:1.1 0/0:502:0:0,0:259,241:500,0:0:2,0:23.9:1:30.7:1:1:0:59.9:82.333:0.996:0:0.2 +17 41244936 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.14532;LSEQ=CATTTCCTGGATTTGAAAAC;RSEQ=GAGCAAATGACTGGCGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:110:54,56:263,253:516,110:0.1749:2,2:24.3:1:31.3:1:0.75327:1.07788:59.7:54:0.1734:0:1.1 0/1:630:197:99,98:237,196:433,197:0.3127:2,2:23.5:1:30:1:0.30262:1.19662:59.9:394:0.3137:0:1.1 +17 41245237 . A G 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.44971;LSEQ=ATAATCAGTACCAGGTACCA;RSEQ=TGAAATACTGCTACTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:887:159:77,82:339,387:726,159:0.1793:2,2:22.9:1:32.4:1:0.72597:1.07:60:158:0.1802:0:1.1 0/1:826:288:144,144:255,283:538,288:0.3487:2,2:25.2:1:31.5:1:0.51095:1.11:60:143:0.3501:0:1.1 +17 41245466 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.54056;LSEQ=TTCAGCTCTGGGAAAGTATC;RSEQ=CTGTCATGTCTTTTACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1130:172:98,74:514,442:956,172:0.1522:2,2:25.1:1:30:1:0.45518:1.14:60:85:0.1527:0:2.1 0/1:1117:350:202,148:431,334:765,350:0.3133:2,2:23.5:1:29.2:1:0.69611:1.06:60:174:0.3141:0:1.6 +17 41245471 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36535;SOR=1.11471;LSEQ=CTCTGGGAAAGTATCGCTGT;RSEQ=ATGTCTTTTACTTGTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1164:178:100,78:527,459:986,178:0.1529:2,2:24.6:1:29.4:1:0.51446:1.12:59.9:43.5:0.1517:0:2.1 0/1:1158:194:112,82:543,421:964,194:0.1675:2,2:23.5:1:28.8:1:0.75115:1.06:60:193:0.1681:0:2 +17 41245586 . C CT 116 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00106;SOR=0.07657;LSEQ=CTGACTGGCATTTGGTTGTA;RSEQ=TTTTTTTTCTTTATCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1020:14:4,10:426,577:1003,14:0.0137:2,2:23.3:1:30.6:1:0.41611:1.84471:60:28:0.0139:0.0029:0 0/0:940:1:1,0:392,543:935,1:0.0011:2,0:28:0:33:0:0.41987:0:60:2:0.0011:0:1 +17 41246481 . T C 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCTGAGCATGGCAGTTTC;RSEQ=GCTTATTCCATTCTTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:843:0:0,0:434,409:843,0:0:2,0:25.2:1:31.3:1:1:0:59.9:83.3:1:0:0.1 0/1:829:42:23,19:403,384:787,42:0.0507:2,2:25.1:1:29.6:1:0.75186:1.15:60:84:0.051:0:1 +17 41246902 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10659;SOR=0;LSEQ=AAATATACAAAAATAACAAG;RSEQ=TACTCAAAAACTGAATTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:2,1:65,208:273,3:0.0109:2,2:21.7:1:25.3:1:0.14714:6.35:60:2:0.0074:0:1.3 0/0:305:0:0,0:78,227:305,0:0:2,0:25.1:1:30.9:1:1:0:60:75.25:1:0:0.1 +17 41246925 . TA T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.10001;SOR=0;LSEQ=CTCAAAAACTGAATTGTCAT;RSEQ=AAAAAATACATACTTCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:3:1,2:21,139:160,3:0.0184:2,2:26:1:30.3:1:0.35459:3.27:60:6:0.0185:0:0.3 0/0:187:0:0,0:29,158:187,0:0:2,0:22.8:1:30.2:1:1:0:60:374:1:0:0.1 +17 41247604 . A C 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.54404;SOR=1.83231;LSEQ=GTGAGACCCCATCTCAAAAA;RSEQ=AAACAAACAAACAAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:16,1:17,3:0.15:1,0:25.3:1:31.7:1:1:0:55:6:0.1579:0:1.7 0/1:4:1:1,0:3,0:3,1:0.25:0,0:11:0:31:0:1:0:60:2:0.25:0:2 +17 41247620 . C CA 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.55739;SOR=0;LSEQ=AAAAAAAACAAACAAACAAA;RSEQ=AAAAAAAAAAACGAAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:4,0:23,1:24,4:0.1379:1,0:33.5:1:31:1:1:0:60:8:0.1481:0:0.5 0/0:8:0:0,0:8,0:8,0:0:0,0:19.1:1:30.8:1:1:0:59.9:16:1:0:1.8 +17 41248164 . C T 61 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01513;SOR=14.18671;LSEQ=AGCACTTTGGGAGGCTGAGG;RSEQ=GGGTGGACCACTTGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:0,17:17,2:0.1053:1,0:8.5:1:32.5:1:1:0:58.5:4:0.1111:0:1 1/0:6:4:1,3:0,2:2,4:0.6667:0,2:21.8:1:30.5:1:1:0:47.5:8:0.8:0:1.8 +17 41248166 . G A 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05929;SOR=Inf;LSEQ=CACTTTGGGAGGCTGAGGCG;RSEQ=GTGGACCACTTGAGGTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:17,0:0:1,0:26.8:1:30.6:1:1:0:46.6:16:1:0:0.1 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:6.5:1:31:1:0.33333:0:52.5:4:0.3333:0:2.5 +17 41249094 . A G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95446;LSEQ=CCGGATGATGAAAAAAATCT;RSEQ=TACACCAAATCCCAAGTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:13:13,0:31,0:31,13:0.2955:1,1:25.9:1:32.1:1:1:0:60:26:0.3023:0:1 0/1:28:8:8,0:20,0:20,8:0.2857:1,0:31.3:1:31.9:1:1:0:60:16:0.2963:0:1 +17 41249363 . TA T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.08352;SOR=1.50414;LSEQ=GTTTTCTTAATTAAAAGGGT;RSEQ=AAAAAATGTACTTGTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:42:5,37:31,135:166,42:0.2019:2,2:25.1:1:31.5:1:0.36705:1.69538:60:84:0.2019:0.0096:0.1 0/1:203:56:10,46:33,114:147,56:0.2759:2,2:24.8:1:30.5:1:0.56626:1.32977:59.9:55:0.2736:0.0148:0.1 +17 41251646 . T A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.0227;SOR=2.62708;LSEQ=GGAACTGCGTCTTTTACATT;RSEQ=TTTATAACTCACCATAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:17:17,0:74,1:75,17:0.1848:1,1:23.3:1:29.8:1:1:0:60:34:0.1848:0:1 0/1:48:18:16,2:30,0:30,18:0.375:1,2:19.2:1:27.1:1:0.13564:0:60:17:0.3617:0:1.3 +17 41251931 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21484;LSEQ=TAAAGAACAGTCAAGCAATT;RSEQ=TTGGCCAGTTCTGTGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:109:15,94:48,192:240,109:0.3123:2,2:26.7:1:31.6:1:0.17867:1.56476:60:218:0.3141:0:1 0/1:248:22:5,17:47,179:226,22:0.0887:2,2:24.3:1:29.6:1:0.78778:1.12:60:44:0.0902:0:1.2 +17 41256059 . A G 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.87896;LSEQ=GCTTCTAGCCTGGGCCACAG;RSEQ=GCAAGACTCCATCTCAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:0,2:143,9:152,2:0.013:2,0:18:1:24.5:1:0.00467:0:43.5:1:0.0067:0:2 0/1:175:2:1,1:145,28:173,2:0.0114:2,2:16:1:31:1:0.30476:5.10615:44:4:0.0117:0:1 +17 41256065 . A G 41 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6701;SOR=0.5923;LSEQ=AGCCTGGGCCACAGAGCAAG;RSEQ=CTCCATCTCAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:2,1:162,19:181,3:0.0163:2,2:6.7:1:26.3:1:0.29335:4.20866:56.7:2:0.0113:0:1 0/0:206:2:1,1:165,38:203,2:0.0097:2,2:21:1:24:1:0.34505:4.29905:43.5:1:0.005:0:1.5 +17 41256074 . CA C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.38865;SOR=0.7195;LSEQ=CACAGAGCAAGACTCCATCT;RSEQ=AAAAAAAAAAAGAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:20:16,4:173,37:210,20:0.0826:2,2:20.9:1:29.6:1:0.76262:1.16812:58.4:5.667:0.0717:0.0331:0.5 0/1:263:16:14,2:174,55:229,16:0.0608:2,2:28.3:1:30.3:1:0.37395:2.21:59.2:32:0.0615:0:0.4 +17 41256075 . AAAAAAAAAAAAG A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=3.94089;LSEQ=ACAGAGCAAGACTCCATCTC;RSEQ=AAAAAAAAAAGAAAAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:24:19,5:172,37:209,24:0.0988:2,2:28:1:30.9:1:0.77879:1.22222:47:48:0.1039:0:0.5 0/1:278:84:59,25:139,40:179,84:0.3022:2,2:27.2:1:29.7:1:0.22068:1.47026:45.8:41:0.3142:0.0144:0.3 +17 41256086 . AGAAAAAAAAAAGAAAAGAAG GAA 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.12465;SOR=Inf;LSEQ=CTCCATCTCAAAAAAAAAAA;RSEQ=AAGAAGAAGAAGAAGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:214,52:266,0:0:2,0:18.3:1:30.4:1:1:0:58:65.5:1:0:0.7 0/1:319:4:2,2:172,54:226,4:0.0125:2,2:26.8:1:29:1:0.24977:3.16549:47.8:8:0.0174:0:0 +17 41256087 . G GA 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.16881;SOR=0.54683;LSEQ=TCCATCTCAAAAAAAAAAAA;RSEQ=AAAAAAAAAAGAAAAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:17:14,3:211,59:270,17:0.0515:2,2:20.7:1:30:1:1:1.30:56.5:34:0.0746:0:1.2 0/1:347:10:8,2:168,59:227,10:0.0288:2,2:24.9:1:28.1:1:1:1.40:55.5:20:0.0532:0:1.3 +17 41256089 . AAAAAAAAAGAAAAG A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=3;SSF=0.23105;SOR=1.67006;LSEQ=CATCTCAAAAAAAAAAAAGA;RSEQ=AAGAAGAAGAAGAAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:9:5,4:286,90:376,9:0.0234:2,2:33.9:1:30.7:1:0.23056:2.53486:55.7:18:0.0236:0:0.3 0/1:416:16:12,4:273,122:395,16:0.0385:2,2:30.9:1:29.9:1:0.7849:1.34:56:32:0.0391:0:0.4 +17 41256100 . AAAG A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0;SOR=2.92282;LSEQ=AAAAAAAGAAAAAAAAAAGA;RSEQ=AAGAAGAAGAAGAAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:75:50,25:302,110:412,75:0.1509:2,2:21.8:1:30.6:1:0.2622:1.37181:53.3:74:0.1542:0.0302:0.4 0/1:532:182:111,71:220,109:329,182:0.3421:2,2:22.2:1:29.5:1:0.20871:1.29034:52.7:364:0.3604:0.0714:0.4 +17 41256318 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.17383;SOR=Inf;LSEQ=ACATTATGTTTGCAGTTAGA;RSEQ=AAAAATGTATGAATTATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:60,218:278,0:0:2,0:23.3:1:32.5:1:1:0:60:277:1:0:0.1 0/1:200:2:1,1:51,147:198,2:0.01:2,2:38.5:1:28:1:0.45337:2.86:60:4:0.0101:0:1 +17 41256860 . C T 56 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11793;SOR=5.2101;LSEQ=CATGGACAGCACTTGAGTGT;RSEQ=ATTCTTGGGATATTCAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:1:0,1:289,165:454,1:0.0022:2,0:1:0:25:0:0.36484:0:60:2:0.0022:0:1 0/1:440:5:1,4:270,164:434,5:0.0114:2,2:9.4:1:24.2:1:0.07325:6.55841:60:10:0.0115:0:1 +17 41257134 . T C 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21704;SOR=2.80915;LSEQ=CATCTGTATAAACCGTGTGA;RSEQ=GGCAGTGATTTAGTAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:0,4:0,26:26,4:0.1333:1,0:32.5:1:27.8:1:1:0:60:8:0.1333:0:1 0/1:13:4:0,4:1,8:9,4:0.3077:2,0:20.3:1:30:1:1:0:60:8:0.3077:0:1 +17 41267518 . CA C 84 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0.91151;LSEQ=GACAGAGCGAGACTTTGTCT;RSEQ=AAAAAAAAAAAAAAGATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:6,0:13,0:13,6:0.2857:1,0:17.2:1:32.7:1:1:0:58:12:0.2857:0.0952:0.2 0/1:15:4:4,0:9,0:9,4:0.2667:0,0:19.8:1:32:0:1:0:60:8:0.2667:0:0.5 +17 41267608 . G C 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03751;SOR=0;LSEQ=ACTATATACTCTCTGAGAAA;RSEQ=AATGAAATGGAGTTGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:6:6,0:152,2:154,6:0.0373:1,0:18.5:1:32.5:1:1:0:60:12:0.0387:0:1 0/0:124:0:0,0:121,3:124,0:0:1,0:25.1:1:31.5:1:1:0:60:30:1:0:0.1 +17 41267807 . AG A 96 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06582;SOR=3.05624;LSEQ=CAACTCCAGACTAGCAGGGT;RSEQ=GGGGGGAGAAAAAGAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:4:1,3:164,390:554,4:0.0072:2,2:18.3:1:31.1:1:1:1.26102:60:8:0.0073:0.0036:0.3 0/1:509:11:6,5:171,326:497,11:0.0216:2,2:7.4:1:27.9:1:0.20338:2.28:60:22:0.0217:0.0157:0.4 +17 41268206 . A C 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCTTTTGAATTCCTTCCTAG;RSEQ=ACTTTTTTTTGTTTACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:47:0:31:0:1:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:33.5:1:1:0:60:4:1:0:1 +17 41268208 . C CTT 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TTTTGAATTCCTTCCTAGAA;RSEQ=TTTTTTTTGTTTACTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,2:2,0:0:0,0:30:1:35:1:1:0:60:4:0.6667:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:31.5:1:1:0:60:4:1:0:1 +17 41276152 . C CAT 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.62365;SOR=0.33515;LSEQ=ACTTTAACACATTAGAAAAA;RSEQ=ATATATATATATCTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:0,3:62,209:271,3:0.0109:2,0:42.3:1:30.3:1:1:0:60:6:0.011:0:0 0/0:272:1:0,1:72,196:268,1:0.0037:2,0:29:0:30.5:0:1:0:60:2:0.0037:0:0 +17 41276247 . A G 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17908;SOR=2.28067;LSEQ=GATTTGGAAGGTTTTAGAAT;RSEQ=ATACAAACCAAAGAACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:9:0,9:0,34:34,9:0.2093:1,0:19.2:1:33:1:1:0:60:18:0.2143:0:1 0/1:29:11:1,10:0,18:18,11:0.3793:1,2:23.3:1:29:1:0.37931:0:60:10:0.3571:0:1.2 +17 41276348 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01786;SOR=Inf;LSEQ=TTCTGAATTTTTTCACATAT;RSEQ=GCTGCCAACCCCTTGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:17.2:1:29.6:1:1:0:60:10:1:0:0.2 1/1:3:3:0,3:0,0:0,3:1:0,0:32.3:1:30:1:1:0:41.7:6:1:0:1 +17 41412250 . A C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=4.91975;LSEQ=TACATACAAGACAAAGGGGG;RSEQ=AGAGTAAGGAGGGTGAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:12:6,6:63,34:97,12:0.1091:2,2:17.6:1:32.1:1:0.35091:1.84199:41.8:24:0.1154:0:1.2 0/1:82:31:18,13:29,21:50,31:0.378:2,2:16:1:31.1:1:1:1.00:46:62:0.3875:0:1.2 +17 41412258 . G T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26201;SOR=0;LSEQ=AGACAAAGGGGGAAGAGTAA;RSEQ=GAGGGTGAGACGTCCAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:3:1,2:77,48:125,3:0.0234:2,2:17.3:1:22:1:0.56016:3.17852:40.7:2:0.0159:0:1.3 0/0:96:0:0,0:59,37:96,0:0:2,0:21.8:1:30.5:1:1:0:48.7:95:1:0:0.5 +17 41412300 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18629;SOR=Inf;LSEQ=TTGATAAGCTCAAGCAAGTC;RSEQ=CATGATCATGGGACAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:77,83:160,0:0:2,0:28.1:1:30:1:1:0:45.7:79:1:0:0.3 0/1:122:2:1,1:60,60:120,2:0.0164:2,2:35:1:29.5:1:1:1:41:4:0.0168:0:1.5 +17 41412303 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.506;SOR=0;LSEQ=ATAAGCTCAAGCAAGTCACA;RSEQ=GATCATGGGACAGGGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:73,82:155,2:0.0127:2,2:13:0:33:1:1:1.12:60:4:0.0129:0:1 0/0:123:0:0,0:60,63:123,0:0:2,0:27.9:1:29.2:1:1:0:43.7:29.75:1:0:0.4 +17 41412324 . T G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51051;SOR=0;LSEQ=GATCATGGGACAGGGGGCCC;RSEQ=TCCCTTTTAGGTAGCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:51,81:132,2:0.0148:2,2:19:1:30.5:1:1:1.58:60:4:0.0154:0:1 0/0:98:0:0,0:42,56:98,0:0:2,0:24.4:1:29.5:1:1:0:40.5:97:1:0:0.2 +17 42083831 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1682;SOR=Inf;LSEQ=GGGTCAGAGAAAAGAGAGGT;RSEQ=CGTGGGGGTAGGGGGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:34,30:64,0:0:2,0:24.5:1:31:1:1:0:60:20.333:1:0:1.1 0/1:45:2:1,1:21,22:43,2:0.0444:2,2:22:0:30:1:1:1.05:60:4:0.0444:0:2.5 +17 42083840 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.50553;SOR=Inf;LSEQ=AAAAGAGAGGTCCGTGGGGG;RSEQ=AGGGGGGCAGTCCGTGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:68:36,32:0,0:0,68:0.9714:0,2:28.1:1:32.2:1:1:0:60:136:0.9714:0:1.2 1/1:53:53:26,27:0,0:0,53:1:0,2:27.3:1:31.9:1:1:0:60:106:1:0:1.3 +17 42083878 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49902;SOR=0;LSEQ=CGGCTGTGGGCCAGGCTCAC;RSEQ=CGCTGACTCCGGACACAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:33,38:71,2:0.0274:2,2:46.5:1:30.5:1:1:1.15:60:4:0.0278:0:2.5 0/0:63:0:0,0:28,35:63,0:0:2,0:24.8:1:30.5:1:1:0:59.6:126:1:0:1 +17 42084097 . C G 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGAGGGCGGTGGGCGGGC;RSEQ=GGGGACTGGGTCCCGGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:29:1:31.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:11:1:30.5:1:1:0:60:4:1:0:0.5 +17 42084276 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCAGTGTACTGGAAGGG;RSEQ=ACTCCGAAGGAATTAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:21:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 42084377 . G A 43 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAGGGAGGTGTTCGACC;RSEQ=GGAGAGATGGGCGGGGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:32:0:1:0:60:2:1:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:19.7:1:27.3:1:1:0:60:6:1:0:1.3 +17 43341917 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13558;SOR=Inf;LSEQ=GGCTGGCAGATCCCTGGGAA;RSEQ=GGCTGAGCCTGTGTTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:294,26:320,0:0:2,0:23.7:1:32.1:1:1:0:60:63:1:0:0.1 0/1:187:2:1,1:162,23:185,2:0.0107:2,2:9.5:1:27.5:1:0.24081:6.91631:60:4:0.0109:0:1 +17 43342141 . G C 345 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGGCTGCCCGTCTTTGGT;RSEQ=ACCAAGCTGAAGGCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1653:1653:793,860:0,0:0,1653:1:0,2:25.5:1:32.3:1:1:0:60:90.833:1:0:1.2 1/0:1397:866:420,446:253,274:527,866:0.6199:2,2:25.4:1:31:1:0.86842:1.02:60:77.727:0.6191:0:1.2 +17 43342306 . C A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=4.0501;LSEQ=TTCCACGGGACTCAGAGAAT;RSEQ=CCACCCGGCTCAAGTGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:20:3,17:24,130:154,20:0.1149:2,2:26.2:1:29.8:1:1:1.04591:60:40:0.1176:0:1 0/1:78:27:0,27:7,44:51,27:0.3462:2,1:20.9:1:30.3:1:0.08883:0:60:54:0.3462:0:1.1 +17 43342400 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07092;SOR=Inf;LSEQ=TGCTTTGAGGTCCTGGGGGA;RSEQ=GTTGAAGGCCAATTCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:164,44:208,0:0:2,0:25:1:32.1:1:1:0:60:40.6:1:0:0.1 0/1:76:2:2,0:66,8:74,2:0.0263:2,0:20:0:32:0:1:0:60:4:0.0263:0:1 +17 43342993 . C CG 72 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTGTATTTTTAGTAGAGA;RSEQ=GGGGTTTCACCATGTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:1,5:0,2:2,6:0.75:0,2:21.7:1:28.2:1:1:0:27.3:5:0.7143:0.125:0.2 1/1:1:1:0,1:0,0:0,1:1:0,0:17:0:32:0:1:0:32:2:1:0:0 +17 43343847 . G A 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCCCTCAATGGCTGTCTA;RSEQ=CTCCAGGCAGATCAGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:845:0:0,0:575,268:843,0:0:2,0:22.8:1:32.7:1:1:0:60:59.214:0.9976:0:0.1 0/1:681:36:23,13:425,217:642,36:0.0529:2,2:18.6:1:29.5:1:0.85668:1.10682:60:72:0.0539:0:1.4 +17 43343939 . C T 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=37.50479;LSEQ=GGGTGTCGGTGGGCCGCCCC;RSEQ=GGGCCAGCACCATGTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1818:4:1,3:946,862:1808,4:0.0022:2,2:17:1:30.5:1:0.3535:3.2904:60:8:0.0022:0:1 0/1:1492:114:61,53:706,666:1372,114:0.0764:2,2:23.7:1:29.6:1:0.69731:1.09:59.9:56:0.076:0:1.3 +17 43344073 . G A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=8.4533;LSEQ=AACAACAGGATTGGGTACGG;RSEQ=CTCAGGGCCCTGGGCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1356:118:46,72:531,707:1238,118:0.087:2,2:28.5:1:30.2:1:0.43679:1.17543:59.8:58:0.0873:0:1.1 0/1:1084:484:197,287:261,339:600,484:0.4465:2,2:27:1:28.7:1:0.3866:1.12153:60:95.8:0.4502:0:1.2 +17 43344420 . A C 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.31065;SOR=4.33259;LSEQ=GCCAGGGCCGGGAAAACCAC;RSEQ=CCCCTGGAGCCATGGCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:1:0,1:259,46:305,1:0.0032:2,0:46:0:13:0:0.15359:0:60:0:0:0:1 0/1:215:3:1,2:165,46:211,3:0.014:2,2:22.3:1:23:1:0.127:7.08677:60:2:0.0097:0:1 +17 43344458 . C A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCGGGGCCACAACCGACTCA;RSEQ=CTTCTCACTGTCATCCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:28:19,9:367,181:548,28:0.0486:2,2:24.8:1:29.5:1:1:1.04:60:56:0.0494:0:1.2 0/0:498:0:0,0:324,173:497,0:0:2,0:22.7:1:31.1:1:1:0:60:123.25:0.998:0:0.1 +17 43344637 . G A 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36663;SOR=2.54542;LSEQ=TGTTTTCAGGGGTTCTTCCT;RSEQ=CACAGTCGGTAGAAGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:2:2,0:193,256:449,2:0.0044:2,0:14.5:1:26:1:0.1864:0:60:4:0.0045:0:1 0/1:269:3:1,2:74,192:266,3:0.0112:2,2:14.3:1:30.3:1:1:1.30:60:6:0.0114:0:1.3 +17 43344809 . T C 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGTTCCTGCTCCGGGACGG;RSEQ=TGCTTTCCGCTCTGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1787:0:0,0:974,812:1786,0:0:2,0:24.3:1:30.2:1:1:0:60:161.364:1:0:0.1 0/1:1391:68:32,36:712,610:1322,68:0.0489:2,2:20.4:1:30.6:1:0.31874:1.31285:60:67:0.0484:0:1.1 +17 43347336 . C G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCCTGAGACTGGCATGG;RSEQ=TAGGGGGTGCAGTCTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:29:1:32.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 43347610 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01996;LSEQ=GCGCTGCCTCTGGGTCCAGG;RSEQ=GTGGCACTGTCGCAATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:109:109,0:17,0:17,109:0.8583:1,1:26.5:1:30.1:1:1:0:59.7:108:0.864:0:1.1 0/1:48:5:5,0:42,1:43,5:0.1042:1,0:27.6:1:29.2:1:1:0:60:10:0.1042:0:1.2 +17 43347965 . T A 158 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=30.71704;LSEQ=ACAACAGGTGAGGCCTGCCT;RSEQ=CCCTCATTTCCTGATACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:951:2:2,0:321,628:949,2:0.0021:2,0:1:0:26.5:1:0.11512:0:60:4:0.0022:0:1 0/1:805:49:19,30:287,469:756,49:0.0609:2,2:19.1:1:28.3:1:1:1.03:60:98:0.0623:0:1.3 +17 43348034 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14184;SOR=Inf;LSEQ=CCGGCCCCTGTTCCCGCTGT;RSEQ=CTGGGGTCTACCACAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:19,245:264,0:0:2,0:27.2:1:32.3:1:1:0:59.8:43:1:0:0.1 0/1:160:2:1,1:6,152:158,2:0.0125:1,2:8:1:26:1:0.08585:23.53:60:4:0.0129:0:1 +17 43348887 . G A 97 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCCAGCTAATTTTTAT;RSEQ=TTTTTGTAGAGATGGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:25.4:1:32.5:1:1:0:31.4:16:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 43350514 . G A 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGTGCTTCCAGCCAACC;RSEQ=TGCTCAGAGGCGCAGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:15.4:1:31:1:1:0:59.4:10:0.8333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 43350666 . A G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=11.57319;LSEQ=CCCTTCTCTTCCCTGTGTAC;RSEQ=GGAGCATCGACAATGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:7:7,0:39,0:39,7:0.1522:1,0:23.6:1:28:1:1:0:60:6:0.1364:0:1.3 1/0:16:11:9,2:5,0:5,11:0.6875:0,2:18.2:1:28.3:1:1:0:60:22:0.6875:0:1.1 +17 43350765 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.1553;SOR=Inf;LSEQ=GGTTGCGGGGCTTAAACACA;RSEQ=AGGTGGACCTAAGTGTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:249,7:256,0:0:1,0:25.6:1:32.4:1:1:0:59.8:84.333:1:0:0.1 0/1:167:2:1,1:161,4:165,2:0.012:1,2:18:1:27.5:1:0.05916:36.10823:60:4:0.012:0:1 +17 43350767 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06162;SOR=Inf;LSEQ=TTGCGGGGCTTAAACACACA;RSEQ=GTGGACCTAAGTGTTCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:258,7:265,0:0:1,0:25.4:1:33.2:1:1:0:59.9:43.167:1:0:0.1 0/1:174:3:3,0:166,5:171,3:0.0172:1,0:19.7:1:32:0:1:0:60:6:0.018:0:1 +17 43351127 . G C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.61907;LSEQ=TTAGTTTCATTAATCGTGGA;RSEQ=GAAGGGAGGAGGGTATCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1617:165:70,95:629,821:1450,165:0.102:2,2:26.8:1:30.8:1:0.86838:1.03974:60:54:0.1016:0:1.1 0/1:1355:395:170,225:439,519:958,395:0.2915:2,2:27.4:1:30.3:1:0.36754:1.11942:60:78:0.2921:0:1.2 +17 43351324 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTACAGTGCTTGGCTAA;RSEQ=GGGTTGGAGAACATCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:2,0:138,55:193,2:0.0102:2,0:11.5:1:29.5:1:1:0:60:4:0.0105:0:1 0/0:63:0:0,0:40,23:63,0:0:2,0:22.2:1:31:1:1:0:59.9:62:1:0:0.1 +17 43352041 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10011;SOR=Inf;LSEQ=CATCCTGTCAGCACCCTAGT;RSEQ=CTCCACACACAGAGGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:24,299:323,0:0:2,0:25:1:32.5:1:1:0:60:79.75:1:0:0.9 0/1:150:2:1,1:13,135:148,2:0.0133:2,2:19:1:26.5:1:0.17852:10.04:60:4:0.0133:0:1.5 +17 43352049 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=0.00891;LSEQ=CAGCACCCTAGTGCTCCACA;RSEQ=ACAGAGGCTGCTGCTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:267:14,253:1,28:29,267:0.899:1,2:24.4:1:28.4:1:1:1.55:60:52.4:0.8973:0:1.1 0/1:125:9:0,9:7,109:116,9:0.072:2,0:15.3:1:26.6:1:1:0:60:8:0.0656:0:1.1 +17 43352642 . T C 56 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCGGGAGATCAAGACCATC;RSEQ=TGGCCAACATGGCGAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:30:1:35.7:1:1:0:52.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 43353884 . CT C 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACTTAGACTGACTTAGAC;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:32:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 43362033 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCCTTCCAGTTCCAGCC;RSEQ=ACCTCAGGTGGCTAGTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:104,3:107,2:0.0183:1,0:14:1:26:1:1:0:60:4:0.0187:0:1 0/0:42:0:0,0:40,2:42,0:0:1,0:23.1:1:28.8:1:1:0:60:41:1:0:0.1 +17 43362093 . C T 40 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55558;SOR=0;LSEQ=TCAGACCCACGGCCACCCTG;RSEQ=GACTGTCCTGGACAGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:1,2:245,21:266,3:0.0112:2,2:6.3:1:25.7:1:0.01995:22.64625:60:2:0.0075:0:3 0/0:149:0:0,0:140,9:149,0:0:2,0:24.4:1:31.3:1:1:0:60:48.667:1:0:0.2 +17 43362475 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=GCGAAGGCAGGGATCTGAGC;RSEQ=GGGCAGCACCAGAGAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:4,111:115,0:0:1,0:21.3:1:30:1:1:0:60:27.75:1:0:0.1 0/1:41:6:2,4:3,32:35,6:0.1463:2,2:26.8:1:29.5:1:0.14759:5.02:60:12:0.1538:0:1.2 +17 43362479 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGGCAGGGATCTGAGCCGGG;RSEQ=AGCACCAGAGAGGGGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:0,2:4,99:103,2:0.019:1,0:6:1:29:1:1:0:60:4:0.0194:0:1 0/0:39:0:0,0:5,34:39,0:0:2,0:25.8:1:31.7:1:1:0:60:18.5:1:0:0.4 +17 43364293 . C CG 337 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23957;LSEQ=AGTTCTGATCGAGGCAGAGC;RSEQ=GCCGTAGGCCCTCGCCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2216:2148:1029,1119:23,32:55,2148:0.9693:2,2:23.1:1:30.5:1:0.41346:1.28:59.8:64.091:0.972:0.1904:0.2 1/1:1713:1513:736,777:95,98:193,1513:0.8832:2,2:25.4:1:29.9:1:0.93907:1.02338:59.9:93.563:0.8863:0.0981:0.2 +17 43364737 . C A 194 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=134.87605;LSEQ=GACTCTCGGACTGGCTGTCA;RSEQ=AAAAGGGACAGATTTGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1466:1:1,0:602,863:1465,1:7e-04:2,0:1:0:26:0:0.41132:0:60:2:7e-04:0:1 0/1:1185:100:45,55:476,609:1085,100:0.0844:2,2:24.8:1:29.2:1:0.83397:1.05:60:49:0.0839:0:1.1 +17 43364865 . G A 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=TCCTTGTGTGAATGCGGCAA;RSEQ=GTTTCTAAATCCCAAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:0,181:181,0:0:1,0:23.5:1:31.5:1:1:0:60:89.5:1:0:0.1 0/1:85:8:0,8:1,76:77,8:0.0941:1,0:31.9:1:31:1:1:0:60:16:0.0964:0:1.6 +17 43364882 . G GA 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01015;SOR=Inf;LSEQ=CAAGGTTTCTAAATCCCAAG;RSEQ=AACCTGTTTTCTCACTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:0,143:143,0:0:1,0:23.3:1:31.6:1:1:0:59.6:27.6:1:0:0.1 0/1:68:4:0,4:1,63:64,4:0.0588:1,0:35.5:1:30.8:1:1:0:60:8:0.0588:0:0 +17 43364914 . A G 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCACTTATCTCACTTATAAA;RSEQ=TGGGTTTGGTATTTTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:0,88:88,0:0:1,0:26.5:1:31.7:1:1:0:59.4:87:1:0:0.1 0/1:35:9:1,8:1,25:26,9:0.2571:1,2:19:1:32.6:1:0.45378:3.00:60:18:0.2571:0:1.4 +17 43365089 . C T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAGAGTCAGGGGAGCAGACA;RSEQ=GGTTCGCTCACTGCTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:33:1:31.5:1:1:0:59.3:8:0.8:0:2.8 0/0:1:0:0,0:0,1:1,0:0:0,0:40:0:27:0:1:0:60:2:1:0:0 +17 43365441 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAGCAGATCATGGCCTC;RSEQ=GCCACCCTCCCTTGGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 43366493 . G T 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01684;LSEQ=CCAGGAGCTGAACCACAGGT;RSEQ=CTGAGGGAGGGAGCCCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:3,0:238,3:241,3:0.0123:1,0:22.7:1:33:0:1:0:60:6:0.0127:0:1.3 0/1:160:2:1,1:156,2:158,2:0.0125:1,2:23:1:29:1:0.03726:63.88812:60:4:0.0127:0:1 +17 43367653 . T C 185 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00017;SOR=0;LSEQ=TCCAGTCACGATGGGCACAG;RSEQ=CTCCCCTTGCCACATCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:56,0:0,0:0,56:1:0,1:26.4:1:31.9:1:1:0:59.3:17.667:1:0:1 1/0:14:9:9,0:4,1:5,9:0.6429:2,0:18.1:1:29:1:0.35714:0:60:8:0.6154:0:1.1 +17 43369893 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGAGATTGCACCATTGCA;RSEQ=TCTCCAGCCTGAGTGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:32.5:1:1:0:57:4:1:0:1 +17 43369934 . G GA 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGACCCTGTCTCTAAAA;RSEQ=AAAAAAAAAGTCTAAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:27.5:1:1:0:57:4:1:0:1 +17 45356536 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24824;SOR=Inf;LSEQ=CACCCTCCCAGGAGAGGGAG;RSEQ=TAATTCAGCCAGCTCGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:119,84:203,0:0:2,0:22.9:1:31.5:1:1:0:59.9:66.667:1:0:0.4 0/1:207:3:1,2:125,79:204,3:0.0145:2,2:23.7:1:28.3:1:0.56218:3.14661:60:6:0.0147:0:1 +17 45356545 . C T 46 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35912;SOR=0.31196;LSEQ=AGGAGAGGGAGGTAATTCAG;RSEQ=CAGCTCGCAGGGCGCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:1,2:122,89:211,3:0.014:2,2:19.7:1:29.3:1:0.57607:2.72874:60:6:0.0144:0:2 0/0:227:1:0,1:134,92:226,1:0.0044:2,0:1:0:24:0:0.40969:0:60:2:0.0044:0:2 +17 45356559 . G T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10041;SOR=0;LSEQ=ATTCAGCCAGCTCGCAGGGC;RSEQ=CTGGCTGGAACCTCCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:1,2:124,105:229,3:0.0129:2,2:16.3:1:27.3:1:0.59635:2.35339:60:6:0.0132:0:1 0/0:266:0:0,0:148,117:265,0:0:2,0:25.6:1:29.8:1:1:0:60:131.5:0.9962:0:0.6 +17 45356561 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00466;SOR=1.68925;LSEQ=TCAGCCAGCTCGCAGGGCGC;RSEQ=GGCTGGAACCTCCCACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:76:40,36:90,72:162,76:0.3193:2,2:26.3:1:29.8:1:0.67807:1.12444:60:37:0.3162:0:1.2 0/1:269:119:70,49:83,67:150,119:0.4424:2,2:27:1:29:1:0.62056:1.15:60:38.667:0.4377:0:1.2 +17 45356654 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49959;SOR=Inf;LSEQ=ATCCGGTTTCCCTGGGAACT;RSEQ=AAACTTTAATATCCACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:49,127:176,0:0:2,0:25.8:1:32.1:1:1:0:60:175:1:0:0.1 0/1:192:2:1,1:66,124:190,2:0.0104:2,2:18:1:26:1:1:1.87:60:4:0.0106:0:1.5 +17 45356782 . T C 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63325;SOR=0.41977;LSEQ=GTATGTTGAGGTCACTGCCT;RSEQ=GGTGCTCTTCTGGAACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:6,6:0.5:0,0:23.8:1:30.7:1:1:0:60:12:0.5:0:1 0/1:7:2:1,1:0,5:5,2:0.2857:0,2:9:1:31.5:1:0.28571:0:60:4:0.2857:0:1 +17 46005528 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57291;SOR=2.80016;LSEQ=TCGAGGAGCAAAGTGAGCCC;RSEQ=TACCCCCCACCCCGATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:1:1,0:68,39:107,1:0.0093:2,0:41:0:17:0:1:0:60:0:0:0:8 0/1:78:2:1,1:45,31:76,2:0.0256:2,2:20.5:1:27.5:1:1:1.44451:60:4:0.026:0:1 +17 46005574 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4995;SOR=0;LSEQ=CAACACTGCCGGAGTCGCGT;RSEQ=ATGCCATGCCCCCTCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:61,77:138,2:0.0143:2,2:37.5:1:30.5:1:1:1.26:60:4:0.0147:0:1.5 0/0:126:0:0,0:61,65:126,0:0:2,0:28.9:1:30.6:1:1:0:60:24.2:1:0:0.4 +17 46005606 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50027;SOR=0;LSEQ=CCTCTCCTGCACCTCCCTGG;RSEQ=CCTGCCGGCCACTGTGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:33,74:107,2:0.0183:2,2:19:1:28:1:0.52854:2.22:60:4:0.0189:0:1 0/0:94:0:0,0:41,52:93,0:0:2,0:22.5:1:29.5:1:1:0:60:10.625:1:0:0.3 +17 46005613 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50464;SOR=0;LSEQ=TGCACCTCCCTGGCCCTGCC;RSEQ=GCCACTGTGGACGCCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:26,68:94,2:0.0208:2,2:34.5:1:32.5:1:0.48553:2.59:60:4:0.0211:0:1 0/0:75:0:0,0:31,44:75,0:0:2,0:1:0:16:0:1:0:60:0:0:0:1 +17 46801231 . G C 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01686;SOR=0;LSEQ=GAAATTATTTCGGGCCTGGA;RSEQ=CCCGCGTAGACGCGACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:10:0,10:3,191:194,10:0.049:1,0:28.6:1:30.1:1:1:0:60:9:0.0446:0:1 0/0:109:0:0,0:3,106:109,0:0:1,0:26.1:1:31.7:1:1:0:60:35.333:1:0:0 +17 46802314 . G T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29605;SOR=0;LSEQ=CCTTTTTCCTCTCTCCAAGG;RSEQ=GTCACCCCGCACCATGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:4:4,0:52,0:52,4:0.0714:1,0:12.8:1:30.5:1:1:0:56.5:8:0.0727:0:1 0/0:28:0:0,0:27,1:28,0:0:1,0:23:1:29.9:1:1:0:60:27:1:0:0.4 +17 46802329 . T C 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CAAGGGGTCACCCCGCACCA;RSEQ=GCCGCTCCCCCTCATCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:77,0:77,0:0:1,0:22.1:1:31.6:1:1:0:59.8:76:1:0:0.2 0/1:38:9:9,0:28,1:29,9:0.2368:1,0:22.6:1:31.3:1:1:0:60:18:0.2432:0:1 +17 46802412 . G A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05124;SOR=Inf;LSEQ=GTTCCGAAGTCGGCGAGGGA;RSEQ=GGGGTTTACTTGCCCGATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:310,19:329,0:0:2,0:20.6:1:32.9:1:1:0:60:46:0.9969:0:0.1 0/1:196:3:2,1:171,19:190,3:0.0153:2,2:6.7:1:27.3:1:0.28108:4.44137:60:6:0.0155:0:1 +17 46804582 . G C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACCCTGGCTTCCGGCTT;RSEQ=TTCTCTCACCACCGCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:1,47:48,2:0.04:1,2:44:0:33:1:0.07918:33.61:60:4:0.0417:0:1 0/0:11:0:0,0:3,8:11,0:0:2,0:15.2:1:31.3:1:1:0:60:22:1:0:0.2 +17 46804808 . T TAC 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCACTCCCAATACATGCGCA;RSEQ=ACACACACACACACACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:43:1:31.3:1:1:1.41418:60:4:0.3333:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:13:0:16:0:1:0:60:0:0:0:1 +17 46805221 . C T 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCAGACCTCCTTCAGAGT;RSEQ=CTAATAACCAAGGGAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:239,4:243,0:0:1,0:24:1:32.5:1:1:0:59.8:80:1:0:0.1 0/1:124:17:17,0:103,4:107,17:0.1371:1,1:29.4:1:30.6:1:1:0:60:34:0.1393:0:1.2 +17 46805272 . CCCT C 70 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.31922;SOR=1.996;LSEQ=TCCTCACCAGCTCCAAGTCT;RSEQ=CCTCCTCCTCCCAGGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:616:4:4,0:511,100:611,4:0.0065:2,0:21.5:1:32.8:1:1:0:60:8:0.0066:0.0032:0 0/1:388:5:3,2:308,75:383,5:0.0129:2,2:24.8:1:30.2:1:0.259:2.72888:60:10:0.0132:0.0026:0 +17 46805443 . A G 215 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=150.79767;LSEQ=CAGCCACCAGCGAGAGCCCA;RSEQ=GACTGGTAACTGTCCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2079:1:1,0:1054,1021:2075,1:5e-04:2,0:9:0:15:0:1:0:60:0:0:0:2 0/1:1802:122:61,61:837,841:1678,122:0.0677:2,2:21.7:1:31.1:1:1:1.00:60:244:0.0683:0:1.1 +17 46805590 . G A 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=61.40879;LSEQ=AAGGCAAACTCAGTGGGGCG;RSEQ=CTGGGGTACTCTTCCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1943:6:4,2:984,952:1936,6:0.0031:2,2:18.3:1:28:1:0.6873:1.93:60:12:0.0031:0:1.2 0/1:1787:286:149,137:790,709:1499,286:0.16:2,2:23.8:1:28.7:1:0.8972:1.0245:59.8:56.2:0.1598:0:1.2 +17 46806115 . G A 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGTCTTGACGCAAGAGAC;RSEQ=CAGGGGCCCGGGCACGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:0,2:4,62:66,2:0.0294:2,0:6:1:31:0:1:0:60:4:0.0299:0:1 0/0:8:0:0,0:0,8:8,0:0:0,0:25.9:1:29.8:1:1:0:60:16:1:0:0.1 +17 46812059 . G A 192 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=37.21853;LSEQ=AGGGAGGGAGGAGAAAGGGA;RSEQ=GAAGGGGGTCAAATATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1967:3:3,0:986,978:1964,3:0.0015:2,0:1:0:27.3:1:0.24964:0:60:6:0.0015:0:1 0/1:1692:91:41,50:775,825:1600,91:0.0538:2,2:23.1:1:29.6:1:0.59008:1.14551:60:90:0.0537:0:1.1 +17 47308105 . A G 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02324;SOR=Inf;LSEQ=GTCCCCTTTAAATGCCCGGG;RSEQ=GCCGGAGCCGGAGCCGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:22,18:40,0:0:2,0:25.6:1:29.1:1:1:0:60:7:1:0:0.2 0/1:17:3:1,2:7,7:14,3:0.1765:2,2:22.7:1:23:1:1:1.9219:60:2:0.1333:0:1.3 +17 47501674 . G T 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52862;SOR=0;LSEQ=TGGTGGAGCCGCTCTTAGTA;RSEQ=CTGTGTCTGCGTGGGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:2,0:23,10:33,2:0.0571:2,0:6.5:1:31.5:1:1:0:30.5:4:0.0606:0:1.5 0/0:20:0:0,0:14,6:20,0:0:2,0:7.6:1:31.5:1:1:0:28.1:40:1:0:0.1 +17 47501831 . C T 103 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00112;SOR=8.20524;LSEQ=AGCTCTAACATTAACAACAG;RSEQ=GCCACATACATCATCACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:2:0,2:215,147:362,2:0.0055:2,0:9.5:1:26:0:0.16689:0:21.5:4:0.0056:0:1 0/1:299:13:5,8:161,125:286,13:0.0435:2,2:7.8:1:28:1:0.25788:2.05583:24.8:26:0.0435:0:1.1 +17 47501902 . C T 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTGTCTCTAGCCAAAAG;RSEQ=GATCGAGGTCACTTCGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:877:0:0,0:469,405:874,0:0:2,0:30.8:1:31.3:1:1:0:27.6:217.5:0.9966:0:0.1 0/1:706:39:20,19:340,326:666,39:0.0552:2,2:27.6:1:29.6:1:1:1.01:29.3:78:0.0558:0:1.2 +17 47501985 . A C 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00385;SOR=Inf;LSEQ=TTTTTCTCATCTTCCCACAT;RSEQ=GGCTCAATACCATCCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:66,127:193,0:0:2,0:39.7:1:30.9:1:1:0:31.3:37.6:1:0:0.1 0/1:129:6:3,3:42,81:123,6:0.0465:2,2:36.3:1:31:1:0.41995:1.92:23.7:12:0.0476:0:1 +17 47502352 . T C 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.00589;SOR=Inf;LSEQ=TCCTTGGCCTCCCACAGTGC;RSEQ=GGGATTATAGGTATGACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:2,115:117,0:0:1,0:25.9:1:30.9:1:1:0:59.6:116:1:0:0.1 0/1:89:6:2,4:7,76:83,6:0.0674:2,2:24.3:1:27.5:1:0.11056:5.26:60:12:0.069:0:1 +17 47677367 . CT C 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAAAACTCAATGTCCTTT;RSEQ=TTTTTTTTTTTCCTTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:9,3:0.25:0,0:31.7:1:30.7:1:1:0:60:6:0.25:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:25:0:1:0:60:2:1:0:0 +17 47678020 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10823;SOR=Inf;LSEQ=ACAGAAGAACCCTTAATATG;RSEQ=ATAAGAATTTGCTTGTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:1,51:52,0:0:1,0:22.5:1:32.7:1:1:0:59.7:104:1:0:0.1 0/1:26:2:1,1:3,21:24,2:0.0769:2,2:25:1:28:1:0.28923:6.21:60:4:0.08:0:1 +17 47679378 . C A 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08899;SOR=6.8002;LSEQ=CTCCAGGGCATACTGTAAAA;RSEQ=ACAAGCACTGCTGTCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:1:1,0:157,335:492,1:0.002:2,0:1:0:25:0:0.32049:0:60:2:0.002:0:1 0/1:366:5:4,1:113,248:361,5:0.0137:2,2:12.8:1:26.8:1:0.03781:8.72:60:10:0.0138:0:1 +17 47679483 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGATACTTGAATAGAACT;RSEQ=CACAGACCATGAAAAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:0,2:0,84:84,2:0.0233:1,0:33.5:1:32:0:1:0:60:4:0.0235:0:1 0/0:24:0:0,0:0,24:24,0:0:1,0:25.9:1:32.5:1:1:0:58.5:48:1:0:0 +17 47685050 . T G 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10171;SOR=4.04942;LSEQ=GGATGATCAGCCTCATTTAA;RSEQ=AAGTCAATCTGCTTTACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:3,0:32,3:35,3:0.0789:2,0:34.7:1:34:1:1:0:60:6:0.0789:0:1 0/1:19:5:5,0:14,0:14,5:0.2632:1,0:22.8:1:32.4:1:1:0:60:10:0.2632:0:1 +17 47685200 . C G 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCATCTGACTCTAGATAC;RSEQ=TGGCTAAACAGACATGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:0:0,0:375,235:610,0:0:2,0:26:1:31.9:1:1:0:59.9:100.667:1:0:0.1 0/1:505:36:24,12:280,188:468,36:0.0713:2,2:28.5:1:28.9:1:0.48214:1.34:60:35:0.0697:0:1.1 +17 47685477 . AATAC A 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02254;SOR=0;LSEQ=AACAATAAGTAACTAATTAT;RSEQ=ATAAAGGAAAATAAGAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:0,12:0,22:22,12:0.3529:1,0:26.4:1:31.7:1:1:0:60:24:0.375:0.0294:0 0/0:11:0:0,0:0,11:11,0:0:0,0:21.8:1:31.1:1:1:0:60:22:1:0:0 +17 47688526 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12603;SOR=Inf;LSEQ=TACAAAGATATATTTAGCTG;RSEQ=AGTTTGTTTTGTAGTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:118,1:119,0:0:1,0:24.3:1:32.4:1:1:0:60:28.75:1:0:0.1 0/1:66:2:2,0:62,2:64,2:0.0303:1,0:12:1:29.5:1:1:0:60:4:0.0308:0:1 +17 47688864 . AT A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.08912;SOR=Inf;LSEQ=CCAAGCTTTTGTTACCAGGA;RSEQ=TTTTTTGCCAGCAGATAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:53,222:275,0:0:2,0:24.3:1:30.4:1:1:0:60:67.75:1:0:0.1 0/1:223:3:1,2:52,168:220,3:0.0135:2,2:30:1:31:1:0.55884:1.61:60:6:0.0138:0:0 +17 47688881 . T TAGAG 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0;SOR=5.82233;LSEQ=GGAATTTTTTTGCCAGCAGA;RSEQ=AGACGACTTTTACCTAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:40:5,35:18,159:177,40:0.1843:2,2:27.6:1:32:1:0.7756:1.26:60:80:0.1896:0.0369:0.1 1/0:151:86:12,74:12,53:65,86:0.5695:2,2:23.9:1:30.3:1:0.50431:1.39307:59.9:172:0.5733:0.1325:0.1 +17 47688929 . A G 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00246;SOR=Inf;LSEQ=ACATTCAGATACTAATATTA;RSEQ=TCATATTATCTTGAAACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:1,79:80,0:0:1,0:22.8:1:30.7:1:1:0:60:19:1:0:0.1 0/1:49:6:0,6:1,42:43,6:0.1224:1,0:29.3:1:32.2:1:1:0:59.2:12:0.1224:0:1.2 +17 47696481 . G GA 129 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00836;SOR=0.27634;LSEQ=CGTTGACTCTCTGGGGTGGG;RSEQ=AAAAAAAAAGTCATATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:639:21:9,12:308,309:617,21:0.0329:2,2:23.9:1:29.4:1:0.65837:1.32842:58.8:20:0.0321:0.0063:1.1 0/0:538:5:1,4:249,277:526,5:0.0093:2,2:27.8:1:31.6:1:0.37692:3.58805:60:10:0.0095:0:0 +17 47696586 . GA G 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAGAGTTGAACAAAGAGGA;RSEQ=ACATTTACCCATAGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:971:0:0,0:541,429:970,0:0:2,0:24.5:1:30.6:1:1:0:60:63.667:1:0:0.1 0/1:801:66:41,25:414,317:731,66:0.0824:2,2:28:1:31.7:1:0.43691:1.26:60:132:0.0837:0.0025:0 +17 47696740 . G A 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05647;SOR=6.79461;LSEQ=TAACCCTTTGGGGTTTACTC;RSEQ=CAAACACCTGTCCAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:653:1:1,0:214,436:650,1:0.0015:2,0:1:0:26:0:0.33026:0:60:2:0.0016:0:1 0/1:581:6:4,2:196,378:574,6:0.0103:2,2:10.7:1:27.7:1:0.18873:3.85:60:12:0.0107:0:1.2 +17 47696764 . G GA 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01152;LSEQ=ACACCTGTCCAAAACAGATA;RSEQ=AAAAAAAAAATGTCAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:34:5,29:86,272:358,34:0.0852:2,2:28.2:1:32:1:0.28889:1.83137:60:68:0.0888:0:0.1 0/1:360:31:10,21:82,241:323,31:0.0861:2,2:31.7:1:29.3:1:0.39731:1.40:59.4:62:0.0901:0.0056:0.2 +17 47696820 . G A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00013;SOR=6.19713;LSEQ=ACTGGAAATCAGACTCAAGA;RSEQ=AGGGAGATGTTTAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:5:0,5:1,137:138,5:0.035:1,0:22:1:30:1:1:0:60:10:0.035:0:1 0/1:103:19:1,18:3,81:84,19:0.1845:1,1:29.9:1:31.3:1:0.56359:1.49:60:38:0.1863:0:1.1 +17 47696903 . CT C 33 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16793;SOR=6.07129;LSEQ=GTTGGGAACAACTTTTTTCT;RSEQ=TTTTTTTTGAGACATGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:0,1:0,35:35,1:0.0278:1,0:38:0:34:0:1:0:60:2:0.0286:0:0 0/1:13:2:0,2:1,10:11,2:0.1538:2,0:30.5:1:33.5:1:1:0:60:4:0.1538:0:0.5 +17 47696933 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02463;SOR=Inf;LSEQ=GAGACATGGTCTTACTCTAT;RSEQ=GTCCAGGCTGGAGTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,24:24,0:0:1,0:21.4:1:30.2:1:1:0:59:48:1:0:0.5 0/1:5:2:0,2:0,3:3,2:0.4:0,0:28.5:1:31:1:1:0:60:4:0.4:0:1 +17 47700315 . G A 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02083;SOR=4.97896;LSEQ=CTATTGTTTGACCTGATAGA;RSEQ=GCTGGAAATTTTGTCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:0,3:2,55:57,3:0.05:1,0:31.3:1:25.3:1:1:0:60:2:0.0351:0:1.3 0/1:38:8:1,7:1,29:30,8:0.2105:1,2:15.1:1:30.1:1:0.38122:3.94:60:16:0.2105:0:1 +17 47700372 . A TT 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.06401;SOR=Inf;LSEQ=CTTACCACTGAGGTCCTAAA;RSEQ=TTTTTTTTTTTTTTCCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:28,0:0:1,0:20:1:31.9:1:1:0:59.4:56:1:0:0.5 0/1:10:2:1,1:0,8:8,2:0.2:0,2:11.5:1:27.5:1:0.2:0:60:4:0.2:0.1:1 +17 48978368 . C T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60839;SOR=0.35798;LSEQ=ACTGAGCCCGGGGCCCCCCA;RSEQ=GACACCCTCCCTGGAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:24.3:1:30:1:1:0:60:12:0.75:0:1 1/0:8:4:4,0:4,0:4,4:0.5:0,0:21.8:1:32:0:1:0:60:8:0.5:0:1 +17 50657476 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTACTTCATTATCCTACTAC;RSEQ=ACACACTCTCAAAGGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:28.5:1:1:0:34:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 50802094 . A G 35 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAGAGTCTTTAATGACC;RSEQ=GCTGATTTTTGTATTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:30.7:1:22.3:1:1:0:60:2:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 50802416 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50213;SOR=0;LSEQ=AATTTTAAGAGGAAATTCTG;RSEQ=AAACAATGATCTGGAGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:94,35:129,2:0.0153:2,2:18:1:27.5:1:0.47563:2.6622:60:4:0.0155:0:1 0/0:109:0:0,0:72,37:109,0:0:2,0:23:1:30.1:1:1:0:60:53.5:1:0:0.2 +17 50802507 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1641;LSEQ=GACATCTCCTCATACCAGGA;RSEQ=ATTTTACAGATGGAAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:245:186:78,108:26,32:58,186:0.7592:2,2:27.1:1:31.6:1:0.76158:1.12445:60:36.2:0.7542:0:1.1 0/1:203:69:32,37:63,71:134,69:0.3399:2,2:24.6:1:31.3:1:1:1.02585:60:138:0.3399:0:1.1 +17 50802634 . T C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.06086;LSEQ=GAAAGATACTAAAAACTCCA;RSEQ=GTACACAATCACAGAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:29:0,29:0,7:7,29:0.8056:0,1:28.2:1:30.4:1:1:0:60:58:0.8056:0:1.1 0/1:21:4:1,3:0,17:17,4:0.1905:1,2:16.8:1:31.3:1:0.19048:0:60:8:0.1905:0:1 +17 51930401 . G C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00341;SOR=6.56081;LSEQ=CAGCTGAGGCTGGCTTTTCC;RSEQ=CAGTGGGAGCCAGGGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:4,2:11,6:17,6:0.2609:2,2:18.5:1:31.2:1:1:1.09:49.5:12:0.2609:0:2.2 1/0:24:17:12,5:5,2:7,17:0.7083:2,2:26.4:1:30.8:1:1:1.03991:52.5:34:0.7083:0:2.1 +17 51930403 . A T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00474;SOR=5.77065;LSEQ=GCTGAGGCTGGCTTTTCCGC;RSEQ=GTGGGAGCCAGGGAGGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:4,2:11,6:17,6:0.2609:2,2:20.5:1:31.2:1:1:1.09:49.5:12:0.2609:0:2.2 1/0:25:17:12,5:6,2:8,17:0.68:2,2:27.4:1:30.5:1:1:1.23909:52.5:34:0.68:0:2.1 +17 51930483 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49463;SOR=Inf;LSEQ=CCAGCTGTGGTAGTCTGTGG;RSEQ=CAGAGTGCCTCTTCAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:15,20:35,0:0:2,0:27.9:1:31.5:1:1:0:48.2:70:1:0:0.3 0/1:39:2:1,1:13,24:37,2:0.0513:2,2:26.5:1:30:1:1:1.82:38:4:0.0513:0:1 +17 51931019 . T C 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20808;SOR=0;LSEQ=ACAGAAGACAGACCTGATTA;RSEQ=TGAAAGAAAAACAAGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:1,3:2,2:4,4:0.5:2,2:10:1:32.8:1:1:2.60168:60:8:0.5:0:1.3 0/0:4:0:0,0:0,4:4,0:0:0,0:34.5:1:31:1:1:0:60:8:1:0:0.3 +17 51931064 . A G 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.57651;LSEQ=ACAAGAACAGCATCATCAGC;RSEQ=TCATCAACAACGACAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:4,2:3,2:5,6:0.5455:2,2:27.3:1:30.3:1:1:1.30:60:12:0.5455:0:1 0/1:5:2:1,1:2,1:3,2:0.4:2,2:5:1:30:1:1:1.7321:60:4:0.4:0:1 +17 51931075 . C T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01373;SOR=0;LSEQ=ATCATCAGCATCATCAACAA;RSEQ=GACAACAACAACAACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:3,2:4,2:6,5:0.4545:2,2:35.4:1:30:1:1:1.29868:60:10:0.4545:0:1.6 0/0:12:0:0,0:6,6:12,0:0:2,0:10.6:1:30.2:1:1:0:56.3:24:1:0:0.6 +17 51931129 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26847;SOR=Inf;LSEQ=AGCCCACGCAAGGGTCAGCA;RSEQ=CCTCAAAGACCAAAACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:11,0:0:2,0:23.2:1:29.8:1:1:0:60:22:1:0:0.8 0/1:18:3:2,1:7,8:15,3:0.1667:2,2:22:1:31.3:1:1:2.18:49:6:0.1667:0:1.3 +17 52409334 . C T 69 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31561;SOR=0.2179;LSEQ=CACTAGCCCATCAGGGATAG;RSEQ=ATGAGATGCCACCTGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:3,2:5,1:6,5:0.4545:2,2:19.4:1:29.8:1:0.54545:2.97405:25.2:10:0.4545:0:1.2 0/1:7:1:0,1:5,1:6,1:0.1429:2,0:33:0:24:0:0.28571:0:21:2:0.1429:0:2 +17 52409443 . G C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGCTTCTCCCCTTTCTA;RSEQ=GTCCCATGACAGCCATCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:11,12:23,2:0.08:2,2:30.5:1:29.5:1:1:1.09:39:4:0.0833:0:1 0/0:10:0:0,0:4,6:10,0:0:2,0:23.4:1:30.8:1:1:0:53.2:20:1:0:0.2 +17 52595602 . CT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=AGGAGAAGAGGCGCTCTGGC;RSEQ=TTTGGGTTTTCAGCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:17:1:31:1:1:1.7321:60:4:0.4:0:0 0/0:3:0:0,0:2,1:3,0:0:2,0:19.3:1:26.7:1:1:0:60:6:1:0:0 +17 52596499 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23171;SOR=Inf;LSEQ=GCTCAAACAGGCTTACACAG;RSEQ=AGGAAATCACAGCTGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:5,16:21,0:0:2,0:25.3:1:33:1:1:0:60:42:1:0:0.2 0/1:20:2:1,1:6,12:18,2:0.1:2,2:25:1:28.5:1:1:1.93:60:4:0.1053:0:2 +17 52596616 . T C 86 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=CCAGGGTTGGGACGCTAGGC;RSEQ=CCAGTGGTGTGGGTTCGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:25.1:1:30.7:1:1:0:51.4:14:1:0:1 1/0:6:3:2,1:0,3:3,3:0.5:0,2:20.3:1:30:1:0.4:0:51:6:0.6:0:1 +17 53367223 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.9395;LSEQ=TCAGCTCTTAATCCTTCCTA;RSEQ=CACTTTGCATTCATTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:7:5,2:178,70:248,7:0.0273:2,2:29.9:1:28.7:1:1:1.01708:57:14:0.0285:0:1.1 0/1:211:71:51,20:100,40:140,71:0.3365:2,2:25.5:1:28.5:1:1:1.02:60:34.5:0.3382:0:1 +17 53367273 . G GA 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.95762;LSEQ=GCCTGTTTTCAGCCTAGTTA;RSEQ=AAAAAAAAAGGCCAGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:19:9,10:238,207:445,19:0.0405:2,2:26.7:1:30.9:1:0.64441:1.27683:59.7:38:0.0419:0.0085:0.7 0/1:386:15:10,5:199,170:369,15:0.0389:2,2:36.3:1:29.3:1:0.43112:1.71:60:30:0.04:0.0026:0.6 +17 53367300 . A G 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18377;LSEQ=AAAGGCCAGCCTCATTCATT;RSEQ=GAATTCTGCGTTCCCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:536:342:164,178:104,90:194,342:0.6381:2,2:26:1:31.6:1:0.24259:1.25366:59.9:37:0.6379:0:1.1 0/1:442:108:53,55:168,165:333,108:0.2443:2,2:26.5:1:30.9:1:0.8254:1.0565:59.9:107:0.2449:0:1.2 +17 53367453 . GAAAATGAAAAC AAAAAGAAAAT 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04376;SOR=0.42501;LSEQ=GATCTTTCTTCCTCAGTGCT;RSEQ=CAGACAAATAAGCACAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:32:0,32:0,19:19,32:0.5333:1,1:25.2:1:32:1:1:0:60:64:0.5333:0.1167:0.1 0/1:40:13:0,13:1,16:17,13:0.325:1,1:29.4:1:31.1:1:1:0:60:26:0.3421:0:0 +17 53367458 . T A 51 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33529;SOR=3.55531;LSEQ=TCTTCCTCAGTGCTGGAAAA;RSEQ=GAAAACCAGACAAATAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:0,1:0,16:16,1:0.0588:1,0:35:0:32:0:1:0:49:2:0.0588:0:8 0/1:16:3:0,3:0,13:13,3:0.1875:1,0:17.3:1:32.3:1:1:0:60:6:0.1875:0:1.3 +17 53367464 . C T 43 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66403;SOR=1.64705;LSEQ=TCAGTGCTGGAAAATGAAAA;RSEQ=CAGACAAATAAGCACAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:22.5:1:28.5:1:1:0:54.5:4:0.0909:0:4.5 0/1:21:3:0,3:0,18:18,3:0.1429:1,0:20.7:1:27.3:1:1:0:60:6:0.1429:0:2 +17 54123450 . A G 35 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGCCCAGCCGGTGGAA;RSEQ=CTAACAGCCCCAAAGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:36.5:1:35.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 54123623 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.18857;SOR=Inf;LSEQ=AAGCAGCAGCAACAGCAGCA;RSEQ=CAGCAGCGACTGGAGCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:28,0:0:2,0:29.3:1:32.4:1:1:0:59.5:27:1:0:0.4 0/1:22:2:1,1:10,10:20,2:0.0909:2,2:34.5:1:29.5:1:1:1:60:4:0.0952:0:1 +17 54123670 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGAAGAGGTAAAGGGA;RSEQ=GCTGAGGCTGCCGCATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:4,12:16,2:0.1111:2,2:26.5:1:30:1:0.4902:2.79:60:4:0.1111:0:1 0/0:7:0:0,0:3,4:7,0:0:2,0:13:1:30.1:1:1:0:60:14:1:0:0.3 +17 54445633 . T A 31 pSTD;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13735;LSEQ=AAACTTGAATAAACTGAAAA;RSEQ=GAACTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:0,3:22,110:132,3:0.0222:2,0:25.3:1:17:1:1:0:44.3:0:0:0:6.3 0/1:119:3:0,3:22,94:116,3:0.0252:2,0:26:0:20:0:1:0:31:6:0.0265:0:5.7 +17 54445635 . AACTT GAC 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21155;SOR=Inf;LSEQ=ACTTGAATAAACTGAAAATG;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:21,97:118,0:0:2,0:8.9:1:30.4:1:1:0:58.1:28.5:1:0:0.6 0/1:101:2:0,2:19,80:99,2:0.0198:2,0:19:1:31.2:1:1:0:37.5:4:0.0206:0.0099:1.5 +17 54445951 . C CT 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCCGGCTGAAAATGGAC;RSEQ=TTTTTTTTTAATGGCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:29:0:33:1:1:1.73:28:4:0.5:0:0 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:26:0:1:0:22:2:1:0:0 +17 55082412 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=TTTCGGTCTCTACCTACAAT;RSEQ=CTGTGTTTTGATTAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:24,0:0:2,0:29.2:1:32:1:1:0:60:23:1:0:0.1 0/1:20:2:1,1:8,10:18,2:0.1:2,2:24:1:27:1:1:1.24:60:4:0.1053:0:1 +17 55816722 . A G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.90908;SOR=1.05102;LSEQ=AGACTTCTCTCTGAAAATCT;RSEQ=AGCCTGCCAGGTTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:176:136,40:59,15:74,176:0.704:2,2:24.4:1:32.5:1:0.73972:1.15616:60:352:0.704:0:1.1 1/0:147:105:76,29:33,9:42,105:0.7143:2,2:24.8:1:30.7:1:0.53379:1.39604:60:51.5:0.7103:0:1.1 +17 55816832 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.65496;LSEQ=CCCTTTCTGAAACAAGACCC;RSEQ=TAGCTTCCCCTCTTTAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:640:93:41,52:257,290:547,93:0.1453:2,2:27.3:1:31.7:1:0.65348:1.12376:60:30:0.144:0:1.1 1/0:495:263:124,139:110,121:231,263:0.5313:2,2:24.6:1:30.8:1:0.92827:1.01903:60:130.5:0.5305:0:1.1 +17 55816867 . CTA TT 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=3.12576;LSEQ=TAGTTCTGCATCAAAAAAGT;RSEQ=AAACTTGGGCTGGCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:14:8,6:159,295:454,14:0.0298:2,2:22:1:30.4:1:0.09734:2.47:60:28:0.0302:0.0021:0.2 0/1:365:32:15,17:124,206:330,32:0.0877:2,2:24.7:1:29.4:1:0.34281:1.46:60:64:0.0882:0.011:0.3 +17 55816928 . T A 39 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0428;SOR=Inf;LSEQ=GATTGCAATCTCTTATAATT;RSEQ=AATATATTTCCTTTCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:20,151:171,0:0:2,0:23.8:1:28.5:1:1:0:60:33.2:1:0:0.1 0/1:93:3:2,1:9,81:90,3:0.0323:2,2:6:1:24.7:1:0.03603:16.88:60:6:0.0326:0:1 +17 56344972 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=GTGCGTCCTCAGCCAGGGAG;RSEQ=GAAGGGCAGGGCCCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:9,4:13,2:0.1333:2,2:8:1:28.5:1:1:2.12136:60:4:0.1333:0:1 0/0:12:0:0,0:7,5:12,0:0:2,0:17.7:1:29.7:1:1:0:60:24:1:0:0.1 +17 56432219 . T C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTGTTTGCTGTGGTCCTT;RSEQ=CCTTTCCCAGGAGCAGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:303,94:397,0:0:2,0:23.8:1:30.8:1:1:0:59.9:98.25:1:0:0.1 0/1:287:22:15,7:185,80:265,22:0.0767:2,2:15.8:1:30.1:1:1:1.07887:60:44:0.0772:0:1.2 +17 56432362 . C G 201 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAGCCTGTATTTAGAGAG;RSEQ=GGGGAGGAAAGAGGTCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:172,331:503,0:0:2,0:24.5:1:30.5:1:1:0:60:54.889:0.998:0:0.2 0/1:411:98:39,59:129,183:312,98:0.2384:2,2:26.1:1:30.5:1:0.8147:1.06627:60:97:0.2413:0:1.1 +17 56434481 . C G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21028;LSEQ=GCCAGGTTGGTCTTGAACTC;RSEQ=TGGCCTCAAGGGATCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:113:111,2:139,2:141,113:0.4431:1,1:26.8:1:30.3:1:1:1.25113:49:226:0.4449:0:1.1 0/1:98:14:14,0:82,2:84,14:0.1429:1,1:26.6:1:28.6:1:1:0:48.9:13:0.134:0:1.1 +17 56435080 . G C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.2364;LSEQ=ACCAAGGATATGCCACACTG;RSEQ=GGGTGTAATGGGGAAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:353:162,191:229,286:515,353:0.4044:2,2:26.1:1:31.1:1:0.72847:1.06:59.9:87.25:0.4035:0:1.1 0/1:579:80:37,43:229,269:498,80:0.1382:2,2:23.7:1:30.6:1:1:1.01:60:160:0.1396:0:1.2 +17 56435170 . CT C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00784;SOR=Inf;LSEQ=GCTCGGAGGGACCCCCCCGC;RSEQ=TTTCCTCTGTGGGTGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:614:0:0,0:263,351:614,0:0:2,0:24.8:1:30.7:1:1:0:59.9:33.111:1:0:0.2 0/1:377:5:1,4:162,210:372,5:0.0133:2,2:24.8:1:32.4:1:0.39457:3.07777:60:10:0.0134:0.0027:0 +17 56435257 . A G 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00178;SOR=Inf;LSEQ=GGCAGATGCTGGAGGCGTCA;RSEQ=CTGGGCCAGGGGCTGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:242,183:425,0:0:2,0:24.7:1:30.2:1:1:0:59.9:59.714:1:0:0.1 0/1:292:7:3,4:167,118:285,7:0.024:2,2:19.3:1:31.1:1:0.45676:1.88277:58:14:0.0245:0:2 +17 56435830 . C T 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0731;SOR=6.52956;LSEQ=TGTCAGGGGGCCTGGCCCGG;RSEQ=GTAGGGGCACTGGGCAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:1:0,1:340,301:641,1:0.0016:2,0:1:0:27:0:0.4704:0:60:2:0.0016:0:1 0/1:396:4:1,3:211,181:392,4:0.0101:2,2:11.8:1:25.8:1:0.34142:3.48699:60:3:0.0078:0:1.5 +17 56435885 . G T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.01681;LSEQ=GGTGGATTGGAGGTGGCTCA;RSEQ=TCCCCAGCCTTGTGCATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:810:121:57,64:351,338:689,121:0.1494:2,2:23.8:1:30.5:1:0.49033:1.16577:60:59.5:0.1499:0:1.1 0/1:558:146:76,70:206,205:411,146:0.2616:2,2:26:1:29.3:1:0.70095:1.08:60:145:0.2627:0:1.2 +17 56436109 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.53216;LSEQ=GGGCATGGCCGGGATGCTGG;RSEQ=GAATGAGGTGGAGTCTTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1542:193:96,97:674,673:1347,193:0.1252:2,2:26.1:1:29.9:1:1:1.01191:60:95.5:0.126:0:1.2 0/1:1131:80:38,42:531,520:1051,80:0.0707:2,2:25.7:1:29:1:0.64349:1.12852:59.9:160:0.0712:0:1.2 +17 56438301 . G A 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2338;LSEQ=AGGCTGTTCTCTGCTGAAGC;RSEQ=GATCCTGGGAAGAGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:919:346:145,201:246,324:570,346:0.3765:2,2:27.3:1:31.4:1:0.73079:1.05246:60:68.2:0.3764:0:1.1 0/1:631:78:33,45:241,312:553,78:0.1236:2,2:28.5:1:29.8:1:0.90306:1.05325:59.8:77:0.1242:0:1.2 +17 56438409 . G A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24496;SOR=4.23501;LSEQ=TCACTCAGGTAGATCACATG;RSEQ=CCAGTTGAACATCCTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:1:0,1:9,189:198,1:0.005:1,0:46:0:12:0:1:0:60:0:0:0:5 0/1:95:2:0,2:6,86:92,2:0.0211:2,0:39.5:1:31:0:1:0:60:4:0.0217:0:1 +17 56438433 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01185;SOR=Inf;LSEQ=GTTGAACATCCTTAGGAGTT;RSEQ=GTCTCCTCGGAGCTCATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:3,130:133,0:0:1,0:21.1:1:30.1:1:1:0:59.8:43.333:1:0:0.1 0/1:67:4:0,4:2,61:63,4:0.0597:1,0:15.8:1:29.3:1:1:0:60:8:0.0625:0:1 +17 56440474 . G A 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00013;SOR=0;LSEQ=GTAGGTGAGGCCCAAAGACG;RSEQ=GGGAAAACTTGCCCAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:27:27,0:131,4:135,27:0.1667:1,1:19.3:1:30.7:1:1:0:60:26:0.1635:0:2.7 0/0:61:0:0,0:60,1:61,0:0:1,0:26.8:1:31.3:1:1:0:60:122:1:0:0.3 +17 56440526 . G A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19645;LSEQ=GGATGAAGTTGGACTAGAGG;RSEQ=TTTCCAGGATCTCTCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:146:142,4:176,8:184,146:0.4424:1,1:23.3:1:30:1:0.55949:1.61:60:47.667:0.4414:0:2.1 0/1:171:23:21,2:140,8:148,23:0.1345:2,2:26.1:1:28.6:1:0.62601:1.66083:60:46:0.1353:0:2 +17 56440542 . G T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.68006;SOR=1.07222;LSEQ=GAGGGTTTCCAGGATCTCTC;RSEQ=CAGCTCCAGGAGTCTAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:182:160,22:210,33:243,182:0.4282:2,2:22.4:1:31.9:1:0.66491:1.14:60:90:0.4317:0:1.9 0/1:229:102:86,16:106,20:126,102:0.4454:2,2:22.1:1:29.9:1:1:1.01:60:101:0.4489:0:1.3 +17 56440642 . C T 189 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=0.03394;LSEQ=TCTAGTGTGCTTACCCAGGC;RSEQ=GGGGGCTCCTTCAGCTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1696:78:43,35:857,761:1618,78:0.046:2,2:24:1:30.1:1:0.72897:1.09:60:12:0.0434:0:1.1 0/0:1225:2:0,2:649,572:1221,2:0.0016:2,0:1:0:28.5:1:0.22007:0:60:4:0.0017:0:1 +17 56448220 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09147;SOR=Inf;LSEQ=GAGCACAGGGTCTTCTCACA;RSEQ=CCCAGAGCTGGGTGAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:218,71:289,0:0:2,0:23.3:1:32.9:1:1:0:60:47.167:1:0:0.1 0/1:238:3:2,1:180,55:235,3:0.0126:2,2:36.3:1:30.3:1:0.55456:1.63257:60:6:0.0126:0:1 +17 56448241 . C T 54 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.7104;SOR=1.54045;LSEQ=CCCAGAGCTGGGTGAAGCTC;RSEQ=GGGTGTGTGTAGGGCGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:3:0,3:291,122:413,3:0.0072:2,0:1:0:22.3:1:0.02667:0:60:2:0.005:0:1.3 0/1:363:4:1,3:245,114:359,4:0.011:2,2:17.8:1:27:1:0.10035:6.41189:60:8:0.0113:0:1 +17 56448297 . C T 165 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=16.39679;LSEQ=TAGCCAGTGACAGGCAGGGG;RSEQ=GGGGGGCCCGTCGAGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:800:4:0,4:455,341:796,4:0.005:2,0:1:0:25.5:1:0.03425:0:60:8:0.0052:0:1 0/1:682:52:33,19:336,293:629,52:0.0762:2,2:28.2:1:29:1:0.19276:1.51:60:51:0.0767:0:1.2 +17 56492800 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=2.83866;LSEQ=CAAGGGGATCACTCTGATAA;RSEQ=AGCTTTCTGTTCTGCTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1057:138:62,76:400,517:917,138:0.1306:2,2:25.5:1:32:1:0.78313:1.05:60:276:0.1323:0:1.1 0/1:1067:319:138,181:331,412:743,319:0.299:2,2:24.3:1:31.2:1:0.7362:1.0537:60:318:0.3:0:1.1 +17 56744028 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGAAAAACCACCTCCAT;RSEQ=ATCACAGTATTTCTCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:28:1:1:0:60:4:1:0:1 +17 56745294 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.16949;SOR=0;LSEQ=TTCTTTTCTTGTTTGCTTGG;RSEQ=CAAACCTTATTCAGGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:15,8:23,2:0.08:2,2:27:1:27.5:1:1:1.82581:60:4:0.08:0:2 0/0:35:0:0,0:22,13:35,0:0:2,0:19.3:1:29.7:1:1:0:58.9:16.5:1:0:0.8 +17 56769887 . G A 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAAAGCTGCAAGGCCCGGA;RSEQ=CCCCGTGCGGCCAGGCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:52,0:52,0:0:1,0:22.6:1:32.7:1:1:0:60:51:1:0:0 0/1:54:22:21,1:31,1:32,22:0.4074:1,1:23.1:1:29.5:1:1:1.46529:60:44:0.4151:0:1.3 +17 56769929 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21423;SOR=Inf;LSEQ=AGCCGGCCCCTTCCGCTTTA;RSEQ=GTCTGACGTCACGCCGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:124,17:141,0:0:2,0:22.6:1:32.4:1:1:0:60:140:1:0:0.1 0/1:122:2:1,1:102,18:120,2:0.0164:2,2:22.5:1:27.5:1:0.28831:5.54257:60:4:0.0165:0:1 +17 56769948 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24891;SOR=0;LSEQ=ACGTCTGACGTCACGCCGCA;RSEQ=GCCCCAGCGAGGGCGTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:3:1,2:162,40:202,3:0.0146:2,2:23.7:1:29:1:0.1073:7.98516:60:6:0.0149:0:1 0/0:192:0:0,0:147,45:192,0:0:2,0:21.8:1:30.7:1:1:0:59.9:191:1:0:0.5 +17 56769979 . C T 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GGGCGTGCGGAGTTTGGCTG;RSEQ=TCCGGGGTTAGCAGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:261,102:363,0:0:2,0:24.9:1:32.1:1:1:0:60:35.3:1:0:0.2 0/1:355:100:63,37:170,85:255,100:0.2817:2,2:22.9:1:28.8:1:0.53582:1.17406:59.8:99:0.2829:0:1.2 +17 56772255 . TA T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12677;SOR=0;LSEQ=ATGTTACACTTTTAAATCTC;RSEQ=AAATTAGGGTTCTTTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:4:2,2:191,92:283,4:0.0139:2,2:13.3:1:28.5:1:0.59944:2.07039:60:8:0.014:0.007:0.8 0/0:252:0:0,0:177,75:252,0:0:2,0:23.5:1:28.1:1:1:0:60:83:1:0:0.1 +17 56772522 . G A 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACAACAGAAATTTGTGGT;RSEQ=CACCAGGTGTTGGAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:0:0,0:171,352:523,0:0:2,0:24.5:1:31.7:1:1:0:60:36.357:0.998:0:0.1 0/1:455:39:12,27:171,245:416,39:0.0857:2,2:22:1:28:1:0.23495:1.56892:60:78:0.0878:0:1.3 +17 56773769 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTCACTGCACTCCAGCCT;RSEQ=GGCGACAGAGCGAGACTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:7,0:7,2:0.2222:0,2:9.5:1:31:1:0.22222:0:42:4:0.2222:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:23:0:33:0:1:0:60:2:1:0:0 +17 56773819 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.00923;SOR=Inf;LSEQ=ATAAATAAAATAAAATAAAA;RSEQ=ATCCTTAATCTTGGTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:23,0:23,0:0:1,0:18.8:1:31.1:1:1:0:59.9:22:1:0:0.4 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:37:1:33.5:1:1:0:60:4:0.6667:0:1 +17 56774577 . G T 30 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GTATAAGGACTTCCATATTG;RSEQ=TTTTCCAAAAACCAAAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:24:1:33.3:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:30:0:1:0:58:4:1:0:1 +17 56774920 . C CA 44 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAAAAAAAAAAAAAAAC;RSEQ=AAAAAAAAAAACCACGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,0:0,3:0.75:0,2:19.3:1:28.3:1:1:0:36.7:6:0.75:0:0.3 +17 56780459 . C G 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGTTAAAGAATTTTGTTAT;RSEQ=CAAAGGAGAACATTTTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:193,8:201,0:0:1,0:24.9:1:32.4:1:1:0:59.8:66:1:0:0.1 0/1:163:23:19,4:128,12:140,23:0.1411:2,2:24.6:1:31.7:1:0.24718:2.23177:60:46:0.1429:0:1 +17 56780540 . G T 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACAGGTAAAACTAATTAAGA;RSEQ=TGTTTTGTTGTTTCAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:867:0:0,0:490,377:867,0:0:2,0:26.4:1:32.8:1:1:0:60:107.375:1:0:0.1 0/1:767:57:33,24:401,308:709,57:0.0743:2,2:28.1:1:29.6:1:0.89017:1.06:60:114:0.0748:0:1.2 +17 56782275 . AT A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTTTAATTAATTAATTA;RSEQ=TTTTTTTTTGAGTCGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 56782297 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTTTGAGTCGCCCAG;RSEQ=CTGACTAACATGGCAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 56797788 . T A 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCTGTCTCAAAAAAAAAAA;RSEQ=AAAATAAAAAATAAAATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:2,2:0.5:2,0:20.5:1:32:0:1:0:60:4:0.5:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:8:0:30:0:1:0:60:2:1:0:1 +17 56797975 . A G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51913;SOR=0;LSEQ=TCCGGAGTAGCTGGGATTAC;RSEQ=GGTGCATGCCACCATGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:105,0:105,2:0.0187:1,2:18.5:1:28.5:1:0.01869:0:59:4:0.0189:0:1 0/0:70:0:0,0:70,0:70,0:0:1,0:23.9:1:29.6:1:1:0:43.9:22.333:1:0:0.1 +17 56797984 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17907;SOR=Inf;LSEQ=GCTGGGATTACAGGTGCATG;RSEQ=CACCATGTCTGGTTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:117,5:122,0:0:1,0:24.4:1:33.1:1:1:0:46.9:244:1:0:0.1 0/1:90:2:2,0:85,3:88,2:0.0222:1,0:12.5:1:28.5:1:1:0:52.5:4:0.0222:0:1 +17 56798207 . T C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1295;LSEQ=CAGATAAACATTTTAGTTTA;RSEQ=CACAGTTTTTCTTATCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:503:393:133,260:34,72:106,393:0.7813:2,2:24.8:1:31.7:1:0.81673:1.08:60:392:0.7809:0:1.1 0/1:475:150:51,99:111,212:323,150:0.3158:2,2:23.4:1:30.5:1:1:1.01634:60:300:0.3185:0:1.1 +17 56811731 . A T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2914;SOR=0;LSEQ=AATGGGAAAAATACCTAAAT;RSEQ=TGATTCTGTGAAAGTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:0,4:0,43:43,4:0.0851:1,0:18.8:1:31.8:1:1:0:60:8:0.0889:0:1 0/0:29:0:0,0:0,29:29,0:0:1,0:27:1:30.4:1:1:0:60:28:1:0:0.1 +17 58206139 . T C 285 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGCTGTTCAGGGATTCC;RSEQ=AGGGGGTCAACAGAGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:530:530:218,312:0,0:0,530:1:0,2:24.1:1:31.6:1:1:0:60:74.714:1:0:1.1 1/0:348:256:114,142:43,49:92,256:0.7356:2,2:24.9:1:30.6:1:0.71607:1.09281:59.9:63:0.7326:0:1.2 +17 58206188 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56083;SOR=3.26577;LSEQ=GGAGGCGGTCACTGGGGTAT;RSEQ=ACGGGGCCTCCTTGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:1:0,1:77,234:311,1:0.0032:2,0:27:0:11:0:1:0:60:0:0:0:5 0/1:192:2:0,2:60,130:190,2:0.0104:2,0:30:1:29.5:1:1:0:60:4:0.0105:0:2 +17 58206251 . C A 201 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAATATTTTGAAATAGCAA;RSEQ=AGACAGAAGAAAGCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:90:90:10,80:0,0:0,90:1:0,2:24:1:31:1:1:0:60:44:1:0:1.3 1/0:62:42:5,37:4,15:19,42:0.6774:2,2:24.4:1:30.3:1:0.44086:1.94964:60:84:0.6885:0:1.2 +17 58206314 . C T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22581;SOR=0;LSEQ=CCTCCAGCCCGGTGTCCCCC;RSEQ=ACCTCCCAGGGTCCCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:0,24:0,0:0,24:1:0,1:25.9:1:29:1:1:0:60:48:1:0:1.6 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:11.8:1:28.7:1:1:0:60:12:0.8571:0:1.8 +17 58393400 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=Inf;LSEQ=CAAACCTCCCTTCCAGCATC;RSEQ=GATATGGGACTTCAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:23.7:1:32:1:1:0:60:14:1:0:0 0/1:10:2:1,1:6,2:8,2:0.2:2,2:18:0:31.5:1:1:2.64575:60:4:0.2:0:1 +17 58393611 . C CA 70 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.24722;SOR=0.3636;LSEQ=GATGAGTAACATTTCATTCT;RSEQ=AAAAAAAAAAAAAAATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:4,8:12,5:0.2778:2,2:36.2:1:30.4:1:1:1.31:58:10:0.2941:0:0.8 0/1:25:3:2,1:7,14:21,3:0.12:2,2:31:1:28.7:1:0.5331:3.76:60:6:0.1429:0:0.7 +17 58677402 . C G 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCCAGCGGCGGGAGGAGG;RSEQ=AGCGCGGCCGTCGCAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:10,3:0,0:0,13:1:0,2:30.3:1:31.4:1:1:0:57.4:26:1:0:1.2 1/1:2:2:2,0:0,0:0,2:1:0,0:27:1:32.5:1:1:0:60:4:1:0:1 +17 58677659 . TC T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.11496;SOR=Inf;LSEQ=CCTTCTCCGGGTCCGCCCCC;RSEQ=CCCCTTCTCGGCGTCGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:222,9:231,0:0:1,0:22.8:1:32.3:1:1:0:60:37.5:1:0:0.2 0/1:119:2:1,1:114,3:117,2:0.0168:1,2:15:1:31.5:1:0.06637:33.03137:60:4:0.0169:0:0 +17 58678009 . T A 219 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00606;LSEQ=GCCCGAGAGGCTCGCGACCC;RSEQ=CTCCCGGACGCCGGGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:853:145:79,66:375,329:704,145:0.17:2,2:23.2:1:30.6:1:0.85499:1.05:60:144:0.1735:0:1.1 0/0:808:1:1,0:440,366:806,1:0.0012:2,0:1:0:24:0:1:0:60:2:0.0013:0:1 +17 58678443 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53051;SOR=0;LSEQ=CCTTGGGGAAGATAGGATTG;RSEQ=CGTCTCCCTGCAGCCTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:1,69:70,2:0.0278:1,0:27:1:30:1:1:0:60:4:0.0286:0:1 0/0:42:0:0,0:1,41:42,0:0:1,0:24.6:1:30.6:1:1:0:60:41:1:0:0.2 +17 58679806 . C T 31 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTTTTTTTTTAAGAGA;RSEQ=GGGCAGGGGCGGGGGACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:31.5:1:1:0:60:4:1:0:2 +17 58679831 . G A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGCGGGGGACGGGTGTG;RSEQ=GCCGCCTTACTTTGTTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:30.5:1:1:0:60:4:1:0:2 +17 58711077 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14357;SOR=Inf;LSEQ=AACAGGAATTTTGGCTTATG;RSEQ=ATCTTTGTATTTGAAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:109,0:109,0:0:1,0:23.9:1:32.8:1:1:0:60:53.5:1:0:0.1 0/1:67:2:2,0:62,3:65,2:0.0299:1,0:24:1:28:1:1:0:60:4:0.0303:0:3 +17 58725145 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.183;SOR=Inf;LSEQ=TTGAATGTTATCAAATGCTT;RSEQ=TCTGCGTCTATTGAGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:207,1:208,0:0:1,0:23.6:1:31.7:1:1:0:60:103:1:0:0.1 0/1:156:2:2,0:147,6:153,2:0.0128:1,0:8:1:32:0:1:0:60:4:0.0132:0:1 +17 58725241 . C A 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTTCTTGCTTTTTCTGCT;RSEQ=CCTTCCCCCAGGTGATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1220:0:0,0:737,480:1217,0:0:2,0:24.1:1:31.6:1:1:0:60:109.636:1:0:0.1 0/1:1024:53:33,20:572,396:968,53:0.0518:2,2:23.3:1:27.9:1:0.67001:1.14:60:52:0.0512:0:1.2 +17 58726474 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTCCCCCCAAGAGATG;RSEQ=GGTGTCACTATGTTGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29:1:1:0:60:4:1:0:1 +17 58733834 . GA G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.64201;SOR=0.74459;LSEQ=AAAAAAAAAAAAAGAGAAAA;RSEQ=AAAAAAAAAATTGGGAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:14:14,0:116,0:116,14:0.1077:1,1:23.8:1:32.5:1:1:0:58.4:28:0.112:0.0231:0.6 0/1:85:7:7,0:77,1:78,7:0.0824:1,0:19:1:31.5:1:1:0:60:14:0.0843:0.0235:0.6 +17 58740077 . G C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAAAATGCTTGTGACCAC;RSEQ=TGAATTTTCACCCACTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:32.3:1:32.3:1:1:0:60:6:0.2727:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:37:0:26:0:1:0:60:2:1:0:0 +17 59477796 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.52459;SOR=0;LSEQ=TGGGCCCGCACCCGCCCGCC;RSEQ=CGCATCTGCGCTCCCTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:97,34:131,2:0.015:2,2:37.5:1:31:1:0.45853:2.82635:60:4:0.0154:0:1.5 0/0:83:0:0,0:58,25:83,0:0:2,0:21.1:1:29.8:1:1:0:60:82:1:0:0.2 +17 59477818 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1438;SOR=Inf;LSEQ=GCATCTGCGCTCCCTCAAGA;RSEQ=CCTGGAGCCCGAGGACGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:154,76:230,0:0:2,0:26.1:1:32.6:1:1:0:60:31.857:1:0:0.2 0/1:141:2:1,1:92,47:139,2:0.0142:2,2:22.5:1:30.5:1:1:1.94751:60:4:0.0142:0:2.5 +17 59477832 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57196;SOR=2.85373;LSEQ=TCAAGAGCCTGGAGCCCGAG;RSEQ=ACGAGGTGGAGGACGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:1:0,1:175,101:276,1:0.0036:2,0:1:0:25:0:0.36823:0:60:2:0.0037:0:1 0/1:195:2:1,1:115,78:193,2:0.0103:2,2:45:1:28.5:1:1:1.47132:60:4:0.0104:0:1 +17 59477847 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2738;SOR=0;LSEQ=CCGAGGACGAGGTGGAGGAC;RSEQ=ACCCCAAGGTGACGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:175,122:297,3:0.01:2,2:33.7:1:27.3:1:1:1.39:60:2:0.0068:0:1 0/0:207:0:0,0:114,93:207,0:0:2,0:26.8:1:29.6:1:1:0:59.9:206:1:0:0.3 +17 59477856 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06553;SOR=Inf;LSEQ=AGGTGGAGGACGACCCCAAG;RSEQ=TGACGCTGGAGGCCAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:166,136:302,0:0:2,0:28.5:1:31.6:1:1:0:59.9:74.5:1:0:0.2 0/1:205:3:2,1:108,94:202,3:0.0146:2,2:25.7:1:26.7:1:1:1.74:60:6:0.015:0:2 +17 59477877 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14975;SOR=Inf;LSEQ=TGACGCTGGAGGCCAAGGAG;RSEQ=TGTGGGACCAGTTCCACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:119,140:259,0:0:2,0:26.4:1:32.6:1:1:0:60:518:1:0:0.1 0/1:164:2:1,1:76,85:161,2:0.0122:2,2:28:0:31.5:1:1:1.12:60:4:0.0123:0:1 +17 59477903 . C A 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00131;SOR=Inf;LSEQ=GACCAGTTCCACAAGCTAGG;RSEQ=ACGGAGATGGTCATCACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:63,106:169,0:0:2,0:23:1:31.5:1:1:0:60:32.8:1:0:0.1 0/1:110:7:2,5:37,66:103,7:0.0636:2,2:20.3:1:29.1:1:1:1.39742:60:14:0.0642:0:2.1 +17 59479113 . T C 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGCCAAGTATATCCTGCTGA;RSEQ=GGACATTGTAGCCGCTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:25:1:33.5:1:1:0:60:4:0.6667:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:24:1:30.7:1:1:0:60:6:1:0:3 +17 59480288 . CGATAGAGAGAGAGAGAGAGA C 63 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATGGGGAAGAGGAAGAAC;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:13.5:1:31.8:1:1:0:59:8:0.6667:0.6667:0.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 59480291 . T G 37 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGAAGAGGAAGAACCGA;RSEQ=AGAGAGAGAGAGAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:0,0:0,2:0.4:0,0:39.5:1:37.9:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 59480309 . GAGAGAGAGAGAGAGAGAGAGAGA G 34 v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAGAGAGAGAGAGAGAGA;RSEQ=AAGTGGAGAGGAAGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:4,0:4,2:0.25:0,0:38:1:34.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 59480331 . GA G 69 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAGAGAGAGAGAGAGAGA;RSEQ=AAGTGGAGAGGAAGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:0,0:0,4:0.6667:0,0:24.3:1:34.8:1:1:0:60:8:1:0:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 59481523 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGTTCCGACACTGTGGCACT;RSEQ=CTTTAGGCCTGTGTGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:32.5:1:34:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:27:1:1:0:60:4:1:0:1 +17 59760499 . A G 182 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGACTCTGTCTCAAAAAAA;RSEQ=AAACCCAAAAACTCAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:43,1:0,0:0,44:1:0,1:20.4:1:33.5:1:1:0:58.5:88:1:0:1 0/1:15:7:7,0:6,2:8,7:0.4667:2,0:14.3:1:29.7:1:0.46667:0:59.4:6:0.4286:0:1 +17 59760996 . A G 308 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00235;LSEQ=TCATCTGTATCTTCAGGATC;RSEQ=TAAAGTTCAGGTGTAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:972:971:506,465:1,0:1,971:0.999:0,2:24.4:1:31.1:1:1:0:59.9:193.2:0.999:0:1.1 1/0:842:587:291,296:126,127:253,587:0.6971:2,2:23.5:1:30.3:1:1:1.00916:59.9:96.833:0.6966:0:1.1 +17 59761706 . A G 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAATGTTTCCTAGCCCA;RSEQ=GTTATAATGCTGTCTGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:25.8:1:32:1:1:0:60:10:0.5556:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:32:0:1:0:60:2:1:0:1 +17 59763114 . A T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=0.50127;LSEQ=ACCACCATATTTAAGGAATT;RSEQ=ATCTATACCCAAATAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:339:170:124,46:116,52:168,170:0.5015:2,2:25.4:1:30.3:1:0.47263:1.21:60:55.667:0.4985:0:1.1 0/1:209:70:50,20:81,58:139,70:0.3349:2,2:22.9:1:29.4:1:0.07034:1.79:60:140:0.3382:0:1.1 +17 59763180 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02036;SOR=Inf;LSEQ=TTCTCTATCAAAGGTAAATG;RSEQ=GAAGAACTTTTCATACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:640:0:0,0:406,234:640,0:0:2,0:23.9:1:31.2:1:1:0:59.9:41.667:1:0:0.2 0/1:390:4:3,1:225,160:385,4:0.0103:2,2:13.8:1:27.5:1:0.6452:2.13:60:8:0.0104:0:1.3 +17 59763347 . A G 318 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01425;LSEQ=TGCTTCCAGTAAATAAGGTG;RSEQ=GGTACTGTACTTTAAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1251:1245:607,638:1,1:2,1245:0.9952:2,2:23.9:1:31:1:1:1.05105:60:55.591:0.9959:0:1.1 1/0:958:716:352,364:110,131:241,716:0.7474:2,2:25.9:1:30.1:1:0.37138:1.15:60:78.556:0.7489:0:1.1 +17 59763465 . T C 292 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGGAAAATTCAGCCAAGGA;RSEQ=TCCAGTGCACTTTCAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:482:482:177,305:0,0:0,482:1:0,2:24.3:1:32.8:1:1:0:60:119.5:1:0:1.1 1/0:429:338:137,201:38,53:91,338:0.7879:2,2:26.1:1:31.3:1:0.90443:1.05178:60:83.5:0.7859:0:1.1 +17 59763504 . C T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12709;SOR=0;LSEQ=GTTGAATGGTGCTGAATCTG;RSEQ=TGCCGTACCCATTTAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:4:2,2:116,258:374,4:0.0106:2,2:16:1:30.8:1:0.59189:2.22:60:8:0.0106:0:2 0/0:332:0:0,0:127,205:332,0:0:2,0:24.4:1:31.4:1:1:0:60:82:1:0:0.7 +17 59770936 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19478;SOR=Inf;LSEQ=AATAAATCCAGTTTTCCAGT;RSEQ=GGACAGACAGAAAATTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:28,222:250,0:0:2,0:22:1:31.7:1:1:0:59.8:82.333:1:0:0.1 0/1:198:2:1,1:28,167:195,2:0.0101:2,2:5.5:1:28.5:1:0.27339:5.88:60:4:0.0103:0:1 +17 59820068 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGGTACAGTATGAGAT;RSEQ=CCCCAAAACAATTACAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:21.7:1:28.3:1:1:0:60:6:0.4286:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:21:0:32:0:1:0:60:2:1:0:0 +17 59820170 . C A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.24992;SOR=2.70478;LSEQ=AAATATCGTGAGAATTAACC;RSEQ=AAATGTGAAACAGAAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:12:12,0:20,0:20,12:0.375:1,0:19.8:1:31.5:1:1:0:58:24:0.375:0:1 1/0:8:5:5,0:3,0:3,5:0.625:0,0:34.6:1:29.8:1:1:0:60:10:0.625:0:1 +17 59820230 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATGGTGCTGAAAGACTTG;RSEQ=ACAATGCAGGGTTACCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:77,1:78,2:0.025:1,2:35.5:1:30.5:1:0.04968:54.83374:60:4:0.025:0:1 0/0:27:0:0,0:27,0:27,0:0:1,0:27.9:1:31.8:1:1:0:60:54:1:0:0.1 +17 59821173 . T C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTCCCACCTCGGCCTCC;RSEQ=AAGTAGTTGGAACTATAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:2:0:31:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:31:1:1:0:57:4:1:0:1 +17 59856810 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAAAATGGCAAAACCCC;RSEQ=TCTCTACTAAAAATACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:28.5:1:1:0:60:4:1:0:1 +17 59857393 . TAGA T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.13846;SOR=Inf;LSEQ=TTACAAAACTAAAACTTACT;RSEQ=AGAAGAAGCTGAAATACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:16,0:0:1,0:20.6:1:28.9:1:1:0:58.1:32:1:0:0 0/1:10:2:1,1:6,2:8,2:0.2:2,2:19:1:28.5:1:1:2.64575:60:4:0.2:0:0 +17 59857599 . CA C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.26018;LSEQ=TAGAAACACTGAAGGCCTTC;RSEQ=AAAAAAAAAACAACAACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:76:56,20:257,77:334,76:0.1827:2,2:26.2:1:32:1:0.55168:1.19146:60:152:0.1849:0.0288:0.2 0/1:328:18:11,7:227,82:309,18:0.0549:2,2:20.8:1:31.3:1:0.27843:1.75822:60:36:0.055:0.0061:0.2 +17 59857809 . C G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00089;SOR=2.1858;LSEQ=AAAATTATCTTTAGAAGAGG;RSEQ=TGGGCAAAGTGGCTCACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:85:9,76:17,85:102,85:0.4545:2,2:21.9:1:32:1:0.29028:1.68426:57.3:84:0.4516:0:1.1 1/0:130:84:10,74:7,38:45,84:0.6462:2,2:23.4:1:31.3:1:0.59151:1.35973:59.5:41:0.6406:0:1 +17 59858089 . AAAC A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.7578;SOR=0.72001;LSEQ=AAGAGCAAGACCCTGCCTCA;RSEQ=AACAACAACAACAACAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:9:9,0:144,7:151,9:0.0563:1,0:20.6:1:30.9:1:1:0:59.8:18:0.0566:0.0125:0 0/1:73:3:2,1:69,0:69,3:0.0411:1,2:17.7:1:31.3:1:0.04167:0:60:6:0.0417:0:0 +17 59858343 . G A 65 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50886;SOR=1.67684;LSEQ=AGGAGTAAGTCTGTTGAATC;RSEQ=CAATTTTATAATCATCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:667:4:3,1:210,453:663,4:0.006:2,2:9:1:27.3:1:0.09841:6.45:60:8:0.0061:0:1 0/1:499:5:3,2:173,321:494,5:0.01:2,2:17.6:1:28:1:0.35085:2.78:60:10:0.0102:0:1.2 +17 59861820 . T G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17839;SOR=Inf;LSEQ=CATATTAAGTATAGAGGGGT;RSEQ=GGGAGGGAATTGGAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:36,229:265,0:0:2,0:22.6:1:30.4:1:1:0:60:52:0.9962:0:0.1 0/1:195:2:1,1:26,166:192,2:0.0103:2,2:38.5:1:30.5:1:0.2596:6.28:60:4:0.0104:0:1.5 +17 59870617 . A G 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTAAATTAAGATGAAC;RSEQ=AAATAGGAATTTCTCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:8.3:1:30.7:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 59876352 . C T 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAAGGAACAATTCATTTC;RSEQ=CAAGAAGCCTAGTTAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:98,0:98,0:0:1,0:24:1:31.4:1:1:0:60:97:1:0:0.1 0/1:60:16:16,0:44,0:44,16:0.2667:1,1:22.4:1:31.4:1:1:0:60:32:0.2712:0:1 +17 59876667 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09997;SOR=Inf;LSEQ=AGATTTAAATCCATCTATAA;RSEQ=ATAAAAGAATTTTCTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:84,252:336,0:0:2,0:25.1:1:32.1:1:1:0:60:41:1:0:0.1 0/1:292:3:1,2:94,195:289,3:0.0103:2,2:21.3:1:22.3:1:1:1.04:60:2:0.0069:0:1.3 +17 59876784 . CAG C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.52557;SOR=0.53408;LSEQ=AAATGCAATTACATAAGCAA;RSEQ=AGATTCTAGGTCTTAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:38:0,38:0,2:2,38:0.95:0,1:22.9:1:32.2:1:1:0:60:76:0.95:0.2:0 1/1:11:10:0,10:0,1:1,10:0.9091:0,0:15.1:1:31.9:1:1:0:60:20:0.9091:0.3636:0 +17 59878416 . G C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02273;SOR=Inf;LSEQ=TCACTATGTTCCTTAAAACT;RSEQ=CTTGTTATTTTGGAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:15,0:15,0:0:1,0:26.9:1:33.5:1:1:0:55:30:1:0:0 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:15.7:1:32:0:1:0:60:6:0.4286:0:1 +17 59878522 . C CA 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.88505;SOR=0.95504;LSEQ=TTTATTTACATAAATTAAAG;RSEQ=AAAAAAAATTAAAACATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:72:69,3:71,3:74,72:0.4898:1,1:19.6:1:30.7:1:1:1.02879:59.5:71:0.4863:0.1497:0.1 0/1:69:33:32,1:30,4:34,33:0.4783:2,1:22.5:1:30.3:1:0.35591:4.19:60:66:0.4783:0.1594:0.1 +17 59886113 . AG A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.01975;SOR=Inf;LSEQ=CAGCACCTAGAACAGTGGCC;RSEQ=GGGGCTGTAAGAAAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:135,293:428,0:0:2,0:24.8:1:31.7:1:1:0:59.9:52.5:1:0:0.1 0/1:361:5:3,2:128,228:356,5:0.0139:2,2:11:1:29.6:1:0.35759:2.66:60:10:0.014:0.0055:0.6 +17 59886992 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGGTTCTTAATAACTAC;RSEQ=TCCTTCTAAGTCTCAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15:1:29:1:1:0:60:4:1:0:1 +17 59924512 . C T 168 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02023;LSEQ=CAGTGGAGAGTTGAGTTTTA;RSEQ=AGTCTTTCCTGAATCAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1267:56:26,30:616,593:1209,56:0.0442:2,2:21.6:1:29.1:1:0.58495:1.19843:60:112:0.0446:0:1.1 0/0:1071:1:0,1:520,550:1070,1:9e-04:2,0:1:0:23:0:1:0:60:2:9e-04:0:1 +17 59924612 . G C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.45111;LSEQ=AGAACCAAAATGAAGTTTAA;RSEQ=GTGAACTAGAAGTTTAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:135:27,108:86,273:359,135:0.2733:2,2:22.3:1:30.7:1:0.40075:1.25949:60:134:0.274:0:1.1 0/1:414:60:14,46:114,239:353,60:0.1449:2,2:24.2:1:30:1:0.17762:1.56565:60:120:0.146:0:1.1 +17 59924643 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17714;SOR=Inf;LSEQ=AGTTTAACTGGCTAGTTGTT;RSEQ=TCAAAGGCCAAAACAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:30,239:269,0:0:2,0:23.1:1:33:1:1:0:59.9:66.25:1:0:0.3 0/1:196:2:1,1:29,165:194,2:0.0102:2,2:11.5:1:26.5:1:0.28336:5.61:60:4:0.0104:0:1.5 +17 59924684 . CA C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.54708;SOR=0;LSEQ=ATGTATTTTTTTCCTGCATC;RSEQ=AAAAAAGACTATTTCTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:1,116:117,2:0.0168:1,2:33:1:33:1:0.03347:82.30:60:4:0.0171:0:0 0/0:62:0:0,0:2,60:62,0:0:1,0:21.8:1:30.4:1:1:0:60:61:1:0:0.2 +17 59924862 . T C 84 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84516;LSEQ=AAAATGAACTTCTCATAAAA;RSEQ=AGTCCCATCATATGGACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:0,6:0,5:5,6:0.5455:0,0:23.7:1:32.8:1:1:0:56.5:12:0.5455:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:40:0:34:0:1:0:60:2:0.5:0:1 +17 59926633 . T TA 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.48512;SOR=0.4917;LSEQ=GGAGTCTTATATAAGTAATT;RSEQ=AAAAAAAACAGCATAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:6:2,4:113,277:390,6:0.0151:2,2:20.8:1:29:1:1:1.22:56.7:12:0.0154:0:1.2 0/0:268:2:0,2:79,187:266,2:0.0075:2,0:35.5:1:32.5:1:1:0:60:4:0.0076:0:0 +17 59926645 . C T 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTAATTTAAAAAAAACAG;RSEQ=ATAAATAACTTACAGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:138:32,106:47,146:193,138:0.4157:2,2:20.4:1:28.8:1:0.89607:1.06617:59.9:276:0.4169:0:1.1 0/0:210:0:0,0:54,156:210,0:0:2,0:23:1:31.2:1:1:0:60:104:1:0:0.1 +17 59926837 . A AT 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAGGAAAAGTCCAATTTG;RSEQ=TTTTTTAAATCGCCTTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:0,6:0,8:8,6:0.4286:0,0:34.3:1:30.2:1:1:0:57:12:0.4286:0:0.2 0/0:1:0:0,0:0,1:1,0:0:0,0:42:0:30:0:1:0:60:2:1:0:0 +17 59934879 . G C 69 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCAATTGAAGTCAGGA;RSEQ=TTTGAGACCAGCCTGGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:34:1:34.5:1:1:0:56.5:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 59938736 . A C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06905;SOR=Inf;LSEQ=TGAGAATATGAATGCAGTCA;RSEQ=ATACTCAATGTACTTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:150,11:161,0:0:2,0:21.8:1:30.8:1:1:0:60:79.5:1:0:0 0/1:113:3:3,0:102,8:110,3:0.0265:2,0:31.7:1:32.7:1:1:0:60:6:0.0265:0:1 +17 59939001 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08168;SOR=Inf;LSEQ=ACCAGAGAACCAAAACTAAG;RSEQ=GAGAAATCTGGAAACAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:2,135:137,0:0:1,0:27.5:1:31.1:1:1:0:60:21.833:1:0:0.1 0/1:106:3:0,3:4,99:103,3:0.0283:1,0:17.3:1:27.7:1:1:0:60:2:0.0192:0:2.3 +17 59939018 . G A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.15639;SOR=Inf;LSEQ=AAGGGAGAAATCTGGAAACA;RSEQ=AAACTGGAATTAATAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:1,119:120,0:0:1,0:24.5:1:32.5:1:1:0:60:119:1:0:0.1 0/1:79:2:0,2:2,75:77,2:0.0253:1,0:6:1:29.5:1:1:0:60:4:0.0256:0:2 +17 60324448 . C T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09207;SOR=0.24561;LSEQ=CACAATGAAGGGATGCCTTA;RSEQ=TTCCTCCAGAATATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:8:3,5:10,15:25,8:0.2424:2,2:19.5:1:31.4:1:1:1.10757:26.4:16:0.2424:0:1.4 0/1:28:2:0,2:13,13:26,2:0.0714:2,0:28.5:1:31:0:0.48413:0:25.5:4:0.0714:0:1 +17 61307574 . AT A 40 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.25361;SOR=0;LSEQ=GCAGTCCATCCATTTTATTA;RSEQ=TTTTTTCAAAAAAACAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:2,1:24,15:39,3:0.0714:2,2:7.3:1:25.7:1:1:1.24:44:2:0.0476:0.0238:0.3 0/0:32:0:0,0:21,11:32,0:0:2,0:23.6:1:29.6:1:1:0:59.7:64:1:0:0.4 +17 61307604 . G A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14362;SOR=Inf;LSEQ=AAAAAACAGCTCCTGGATTT;RSEQ=TTGATTTTTTTTGAAGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:41,27:68,0:0:2,0:28.1:1:33:1:1:0:58.8:136:1:0:0.2 0/1:42:2:1,1:24,16:40,2:0.0476:2,2:12:0:29.5:1:1:1.48518:35:4:0.0476:0:2 +17 61307608 . A AT 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.11002;LSEQ=AACAGCTCCTGGATTTGTTG;RSEQ=TTTTTTTTGAAGGGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:3:2,1:39,26:65,3:0.0441:2,2:39:1:31.3:1:1:1.33:60:6:0.0441:0:0 0/1:41:2:1,1:22,17:39,2:0.0488:2,2:36:0:31:0:1:1.28591:59:4:0.05:0:0 +17 61307646 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTGTCTCTGTCTCCCTC;RSEQ=GTTCTGCTGTAATCTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:33,29:62,2:0.0313:2,2:24.5:1:29.5:1:1:1.13563:60:4:0.0317:0:1.5 0/0:31:0:0,0:12,19:31,0:0:2,0:26.3:1:29.4:1:1:0:56.8:30:1:0:0.2 +17 61307713 . C G 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24786;SOR=0;LSEQ=GTTTCTTTGCTCTTGGTTCT;RSEQ=TAGTTCTTTTAGTTGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:1,12:13,3:0.1875:1,0:20:1:34.3:1:1:0:57:6:0.1875:0:1 0/0:11:0:0,0:1,10:11,0:0:2,0:27.6:1:31.9:1:1:0:54.6:22:1:0:0.3 +17 61851435 . C T 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TATCTGAGGAGCCTGTGAGG;RSEQ=GTTCTGGAGCTTTAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:15.5:1:30.5:1:1:0:60:4:0.5:0:2.5 1/0:2:1:0,1:0,1:1,1:0.5:0,0:41:0:30:0:1:0:60:2:0.5:0:1 +17 61851485 . C A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGAGCCGTAGCCCCGGCC;RSEQ=CGCCCTTCTGCCCGCGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:26.7:1:29:1:1:0:60:6:0.4286:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:47:0:33:0:1:0:60:2:1:0:0 +17 61851588 . C T 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.73647;SOR=1.38827;LSEQ=GGCGGTGGTGGCGGTGGCGG;RSEQ=GGCGGTGGTGGTGGTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:8,6:5,9:14,14:0.5:2,2:30:1:27.7:1:0.44948:2.32:58.9:6:0.48:0:1.4 1/0:12:7:4,3:3,2:5,7:0.5833:2,2:22.4:1:28:1:1:1.11403:58.6:6:0.5455:0:1.1 +17 61851603 . TGGC T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.70392;SOR=0.72224;LSEQ=GGCGGCGGCGGTGGTGGTGG;RSEQ=GGCGGCGGCGGCGAAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:14:8,6:3,5:8,14:0.6364:2,2:30.9:1:32.4:1:0.65944:2.14:58.9:28:0.6364:0:1.5 1/0:9:5:2,3:3,1:4,5:0.5556:2,2:20.6:1:30.4:1:0.52381:3.76419:58:10:0.625:0.1111:1 +17 61851751 . T G 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAGGTTTGTGCGTGGGG;RSEQ=TTCTGGACGCAAGGCCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:40:1:32.5:1:1:0:60:4:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:29:1:31.5:1:1:0:60:4:1:0:1 +17 61878355 . C CCTTT 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTCTTTCTCCCTTTCTCTTT;RSEQ=CTTTTTTTCCTCTCTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19:1:32.7:1:1:0:60:4:1:0.5:0.5 0/0:1:0:0,0:1,0:1,0:0:0,0:48:0:29:0:1:0:60:2:1:0:0 +17 61878535 . G A 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00699;SOR=0;LSEQ=TCTGCCTGCCTCAGCCTCCT;RSEQ=GGTAACTGGGATTACAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:3,5:0,1:1,8:0.8889:0,2:38.1:1:29.6:1:1:0:60:7:0.875:0:1.4 0/0:4:0:0,0:1,3:4,0:0:2,0:25.5:1:29.8:1:1:0:60:8:1:0:0 +17 61878584 . T A 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATGCCTGGCTAATTTTTTT;RSEQ=AAATATTTTTGGTAGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:31.5:1:1:0:45:4:1:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:29:0:1:0:60:2:1:0:0 +17 62006432 . GG AC 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00226;SOR=Inf;LSEQ=GGCCCTTTGGCAAGAGCTGG;RSEQ=ACCAGGGGCTGGAGACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:59,0:59,0:0:1,0:24.5:1:30.6:1:1:0:59.5:18.667:1:0:0.1 0/1:18:4:4,0:13,1:14,4:0.2222:1,0:25.3:1:30.5:1:1:0:60:8:0.2222:0.0556:1.5 +17 62006497 . A G 162 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=374.76648;LSEQ=AGAGGCCAGCTGGGGGGTCC;RSEQ=GGAAAGGGGTTGGGCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:1,0:192,2:194,1:0.0051:1,0:34:0:32:0:1:0:60:2:0.0052:0:1 1/0:69:46:45,1:21,2:23,46:0.6667:2,1:23.2:1:29.4:1:0.25593:4.19:60:92:0.6765:0:1.1 +17 62006931 . G A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05594;SOR=Inf;LSEQ=GGCCAGGGAGAGGGGTGAGG;RSEQ=GTCAGGAGTGAGGTGCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:86,287:373,0:0:2,0:23.7:1:31.1:1:1:0:60:61.167:1:0:0.1 0/1:232:3:2,1:53,176:229,3:0.0129:2,2:12.3:1:21.7:1:0.14072:6.57:60:6:0.0132:0:1 +17 62006968 . TGAAG T 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=4.000;MSILEN=4;SSF=0.2466;SOR=4.20404;LSEQ=ATTCTGCAAGAACAGCTGAA;RSEQ=GAAGGAAGGAAGGAATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:0,1:82,165:247,1:0.004:2,0:22:0:28:0:1:0:60:2:0.0041:0:0 0/1:119:2:1,1:25,92:117,2:0.0168:2,2:28.5:1:32:1:0.39069:3.63:60:4:0.0171:0:1 +17 62006984 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.09644;SOR=Inf;LSEQ=TGAATGAAGGAAGGAAGGAA;RSEQ=GAATGATTGAATTGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:104,125:229,0:0:2,0:24.4:1:31.6:1:1:0:60:18.083:0.9954:0:0.1 0/1:105:2:0,2:39,63:102,2:0.019:2,0:13:1:24.5:1:0.5267:0:60:4:0.0194:0:2.5 +17 62006997 . T C 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGGAAGGAATGATTGAAT;RSEQ=GGTGAGCCAGTGGGGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:135,105:240,0:0:2,0:24.3:1:31.2:1:1:0:59.9:39:1:0:0.2 0/1:99:43:22,21:30,26:56,43:0.4343:2,2:24.1:1:30.8:1:0.84144:1.10032:60:86:0.4343:0:1.2 +17 62007081 . C T 57 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16675;SOR=5.64763;LSEQ=CTGCATATGCCTGGCCTATG;RSEQ=GGTGGCCTCCTCTGCGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:1:1,0:348,164:512,1:0.0019:2,0:11:0:31:0:1:0:60:2:0.002:0:1 0/1:366:4:1,3:244,118:362,4:0.0109:2,2:14.5:1:28.5:1:0.10748:6.17066:59:8:0.011:0:1.3 +17 62007498 . A G 294 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1086.20074;LSEQ=GTGTTGTTGCACTTCTGCTG;RSEQ=CAGAAGTAGATGCCATTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1491:3:2,1:793,691:1484,3:0.002:2,2:23.7:1:31.3:1:1:1.74:60:6:0.0021:0:4 1/0:1161:798:421,377:193,169:362,798:0.6873:2,2:24.8:1:30.5:1:0.899:1.02264:60:45.941:0.6869:0:1.2 +17 62007552 . G A 185 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=34.19433;LSEQ=CCTTGGATGGTGAGGGTGGC;RSEQ=AGAGATTCGTTCTGGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1744:3:3,0:858,883:1741,3:0.0017:2,0:1:0:26:1:0.12012:0:60:6:0.0017:0:1 0/1:1311:73:39,34:611,626:1237,73:0.0557:2,2:26:1:30:1:0.54783:1.18:60:146:0.0562:0:1.5 +17 62007775 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15771;SOR=Inf;LSEQ=CCAAGGCCAGGCTCAGCATT;RSEQ=CGCTTGGCATCTTCCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:42,147:189,0:0:2,0:24.3:1:31.4:1:1:0:60:46.25:1:0:0.1 0/1:125:2:1,1:38,85:123,2:0.016:2,2:16:1:26.5:1:0.52839:2.22:60:4:0.0161:0:1 +17 62007805 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.53071;SOR=0;LSEQ=TCTTCCTGAGTGCCAGCCCC;RSEQ=GCAGCAGGCCCCTGCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:13,87:100,2:0.0196:2,2:27.5:1:29.5:1:0.25684:6.49:60:4:0.0198:0:1 0/0:60:0:0,0:9,51:60,0:0:2,0:23.2:1:30.3:1:1:0:60:59:1:0:0.1 +17 62007829 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.13921;SOR=Inf;LSEQ=GCAGGCCCCTGCCCTGGCTG;RSEQ=CACAGACTCCCTGGGCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:1,62:63,0:0:1,0:25.7:1:32.9:1:1:0:60:126:1:0:0.1 0/1:38:2:1,1:0,36:36,2:0.0526:1,2:16.5:1:28:1:0.05263:0:60:4:0.0526:0:1 +17 62008437 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05983;SOR=Inf;LSEQ=CTGAGTCCTAGAGGAACCCC;RSEQ=AGGCTCCCTTGCTATGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:20,0:0:1,0:27.1:1:30:1:1:0:58.8:19:1:0:0.1 0/1:7:2:2,0:4,1:5,2:0.2857:2,0:33.5:1:30.5:1:1:0:60:4:0.2857:0:1 +17 62008535 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGTGGGCTGGGGGTGGG;RSEQ=CTCAGAGGAGATCCTAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:134,2:136,2:0.0145:1,2:11.5:1:31:1:0.04316:54.93918:60:4:0.0154:0:1.5 0/0:65:0:0,0:62,3:65,0:0:1,0:23.7:1:31.1:1:1:0:60:64:1:0:0.2 +17 62008606 . C T 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.75127;SOR=1.349;LSEQ=ATCAGGCAAGGGTGGGAAGG;RSEQ=GGACCGCCCCCAGGACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:5:2,3:333,111:444,5:0.0111:2,2:10.4:1:27.6:1:0.10648:4.4811:60:10:0.0114:0:1.2 0/1:334:5:2,3:235,94:329,5:0.015:2,2:11.4:1:26.6:1:0.14902:3.73293:60:10:0.0153:0:1 +17 62008611 . C T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16675;SOR=5.64763;LSEQ=GCAAGGGTGGGAAGGCGGAC;RSEQ=GCCCCCAGGACAGGGACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:1:0,1:366,146:512,1:0.0019:2,0:1:0:28:0:0.28655:0:60:2:0.002:0:1 0/1:366:4:1,3:250,112:362,4:0.0109:2,2:13:1:27.8:1:0.09366:6.65864:60:8:0.0111:0:1.3 +17 62008760 . G A 248 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCAGCTGCTGGGTGGGAG;RSEQ=AAGTGGGCGGGGCCAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:290:113,177:282,396:678,290:0.299:2,2:26.7:1:30.4:1:0.47553:1.11532:60:47.333:0.298:0:1.2 0/0:713:0:0,0:294,419:713,0:0:2,0:25.1:1:30.1:1:1:0:60:46.533:1:0:0.2 +17 62008857 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57276;SOR=0;LSEQ=ACTTCCTCCTTCCATGACAG;RSEQ=AGCTTCAAGACCCCTCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:0,3:2,188:190,3:0.0155:1,0:29:1:30:0:1:0:60:6:0.016:0:1 0/0:66:0:0,0:3,63:66,0:0:1,0:23.8:1:31.5:1:1:0:60:32:1:0:0.2 +17 62008885 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACCCCTCGGTCCTCCCTG;RSEQ=CCCCAGTACTTGGGAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:3,120:123,0:0:1,0:24.7:1:31.3:1:1:0:59.9:29.75:1:0:0.1 0/1:37:11:1,10:1,25:26,11:0.2973:1,2:23.5:1:29.2:1:0.51201:2.43:60:22:0.3056:0:1.2 +17 62008965 . T G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00342;SOR=Inf;LSEQ=CTTTCTGCCTTTGACCCTCA;RSEQ=GGTGGCTTTGAGCAGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:1,21:22,0:0:1,0:20.4:1:29.8:1:1:0:60:21:1:0:0 1/0:5:3:0,3:0,2:2,3:0.6:0,0:15.7:1:32:0:1:0:60:6:0.6:0:1.7 +17 62009443 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16171;SOR=Inf;LSEQ=CCATGAGAGGGAGACAGGCG;RSEQ=TAAAGAGTGAGAGACAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:224,28:252,0:0:2,0:20.3:1:31.4:1:1:0:60:41:1:0:0.1 0/1:170:2:1,1:140,28:168,2:0.0118:2,2:20.5:1:26:1:0.31291:4.93067:60:4:0.0118:0:1 +17 62009460 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06517;SOR=Inf;LSEQ=GCGGTAAAGAGTGAGAGACA;RSEQ=AGGAGGAGGGTGGAGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:291,55:346,0:0:2,0:23.3:1:33.3:1:1:0:59.9:68.2:1:0:0.1 0/1:234:3:1,2:174,57:231,3:0.0128:2,2:11.3:1:27.7:1:0.15745:6.04685:60:6:0.013:0:1 +17 62009719 . G A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14369;SOR=5.19517;LSEQ=CTGCAGCCTGTCCCCTCCCC;RSEQ=CCTCTTCCTCACCAGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:1:1,0:59,278:337,1:0.003:2,0:1:0:25:0:0.17751:0:60:2:0.0031:0:1 0/1:197:3:2,1:34,160:194,3:0.0152:2,2:25.3:1:26.3:1:0.08652:9.25:60:6:0.0156:0:1 +17 63313715 . A T 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCATTACATCAGCTCTG;RSEQ=GTGGCAGGTTCTTTGATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,0:1,5:0.7143:0,0:32.4:1:31.2:1:1:0:59.4:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 63314191 . G T 223 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTTATGCCAAACCACTC;RSEQ=TTCGTGCTTGGATACCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:0:0,0:347,357:704,0:0:2,0:24.3:1:31.1:1:1:0:60:87:0.9986:0:0.1 0/1:557:193:100,93:176,188:364,193:0.3465:2,2:25.6:1:29.4:1:0.47641:1.15:59.6:63.333:0.3473:0:1.1 +17 63314330 . A C 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TAGAAGTTATTATATATATC;RSEQ=CAAAGACTCCCATTGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:0,89:89,0:0:1,0:24:1:29.9:1:1:0:59.8:28.667:1:0:0 0/1:47:10:0,10:0,37:37,10:0.2128:1,0:20.9:1:29.8:1:1:0:60:9:0.1957:0:1 +17 63529650 . T A 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCAGTGTGCCTGTCCCTC;RSEQ=TTTTGCTCCCTGCTCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:30.5:1:30.5:1:1:0:58.8:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 63529821 . C T 143 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01283;SOR=0;LSEQ=GTCCCCCAGAGAACCCTCCA;RSEQ=GCAGCCTCCCTCTTGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:25,1:0,0:0,26:1:0,1:18.4:1:30.5:1:1:0:60:52:1:0:1 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:30.5:1:30:1:1:0:55.8:12:0.6667:0:1 +17 63529905 . C A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16688;SOR=5.79334;LSEQ=GAGAAGGGAGCCTCCCCCAG;RSEQ=GCCTGCTGAGCCCCCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:1,0:156,2:158,1:0.0063:1,0:49:0:15:0:1:0:60:0:0:0:6 0/1:56:2:2,0:54,0:54,2:0.0357:1,0:33:1:30.5:1:1:0:60:4:0.037:0:1 +17 63531884 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02051;SOR=Inf;LSEQ=ATTTAGAGGTACACTGTTGT;RSEQ=CCCAGAGCAATTGAAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:109,442:551,0:0:2,0:23.6:1:31.3:1:1:0:59.9:44.917:1:0:0.1 0/1:337:4:2,2:85,247:332,4:0.0119:2,2:27.5:1:29.3:1:0.2763:2.90:60:8:0.0121:0:1 +17 63531958 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGAACCCGACTTCCATCC;RSEQ=TACGGAGACCCAACCAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:5,122:127,2:0.0155:1,2:10.5:1:31.5:1:0.09121:22.37:60:4:0.0163:0:1 0/0:59:0:0,0:2,57:59,0:0:1,0:22.5:1:29.4:1:1:0:59.5:28.5:1:0:0.2 +17 63532175 . A G 146 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAGGAATGGGATTTGTA;RSEQ=GCAATTGCTGAAATTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:16,5:0,0:0,21:1:0,2:21.2:1:33.3:1:1:0:60:42:1:0:1.1 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:31:0:1:0:60:2:1:0:1 +17 63532365 . C T 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAGAAAGAGAGGCCCTCC;RSEQ=CATTAGCCACAGACCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:351,138:489,0:0:2,0:22.3:1:31:1:1:0:59.9:96.8:1:0:0.1 0/1:314:15:12,3:217,82:299,15:0.0478:2,2:21.3:1:30.7:1:0.7669:1.51:60:30:0.0482:0:1.2 +17 63532517 . G A 203 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCGTGTTGGGTGGGGTCA;RSEQ=GGGAGGCATCGCAGGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1022:0:0,0:489,533:1022,0:0:2,0:23.9:1:32.3:1:1:0:59.9:126.75:1:0:0.2 0/1:821:104:53,51:324,390:714,104:0.1267:2,2:22.6:1:30.4:1:0.29422:1.25:59.8:208:0.1287:0:1.3 +17 63532527 . C T 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGGGTCAGGGGAGGCAT;RSEQ=GCAGGGTCCTGGGTGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:990:0:0,0:473,515:988,0:0:2,0:24.1:1:30.9:1:1:0:59.9:48.4:0.9979:0:0.2 0/1:805:28:12,16:357,417:774,28:0.0348:2,2:19.9:1:29.8:1:0.84765:1.1413:60:56:0.0353:0:1.2 +17 63532746 . T C 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=ACTGGAAAATGTGACTTCAA;RSEQ=AGAAACTTGTCTATTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:28,88:116,0:0:2,0:25.9:1:28.2:1:1:0:59.7:13.5:1:0:0.8 0/1:55:7:0,7:2,46:48,7:0.1273:1,0:32:1:32.1:1:1:0:60:14:0.1321:0:1.9 +17 63532767 . C G 210 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAAACTTGTCTATTCTGCT;RSEQ=AGAGAGAGAGTTAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:102:102:36,66:0,0:0,102:1:0,2:26.2:1:31.5:1:1:0:59.6:19.4:1:0:1.1 1/0:41:27:3,24:1,13:14,27:0.6585:1,2:26:1:31:1:1:1.61:60:26:0.65:0:1.3 +17 63532779 . T TA 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.06011;SOR=0;LSEQ=ATTCTGCTCAGAGAGAGAGT;RSEQ=AAAAAAAAAACTACCATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:9:2,7:40,47:87,9:0.0938:2,2:34.1:1:28:1:0.29081:2.94815:60:8:0.087:0:1 0/0:38:0:0,0:7,31:38,0:0:2,0:25:1:27.7:1:1:0:60:18:1:0:0.9 +17 63532854 . G A 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=TGTGGTCTGCTCAGTCCAAC;RSEQ=TTTAATATTAAGATGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:120,19:139,0:0:2,0:24.6:1:30.4:1:1:0:59.3:45.333:1:0:0.7 0/1:60:7:4,3:50,3:53,7:0.1167:2,2:13.6:1:29.9:1:0.01736:11.513:60:14:0.1167:0:1 +17 63532914 . A G 251 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTCCGCGGACTGCAAAAAC;RSEQ=GCCATTCCCACAATACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:339:339:306,33:0,0:0,339:1:0,2:25.1:1:29.9:1:1:0:59.8:47.429:1:0:1.1 1/0:215:150:131,19:55,9:64,150:0.6977:2,2:23.7:1:29.3:1:0.82585:1.13:59.9:49:0.6967:0:1.1 +17 63532948 . A T 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCTCCGTACTGAGTGCCC;RSEQ=TGACCCTCGCGGCCGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:623:0:0,0:441,182:623,0:0:2,0:23:1:30.2:1:1:0:59.9:68.222:1:0:0.6 0/1:487:52:33,19:298,137:435,52:0.1068:2,2:20.1:1:29.6:1:0.5295:1.25175:60:104:0.1074:0:1.2 +17 63533264 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.12434;SOR=Inf;LSEQ=ATCAGACAATTCAGCAAGTC;RSEQ=GGGGGCTGGTGACACGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:62,228:290,0:0:2,0:25.3:1:31:1:1:0:59.7:95.667:0.9965:0:0.1 0/1:159:2:0,2:30,127:157,2:0.0126:2,0:12.5:1:31:0:1:0:60:4:0.0127:0:1 +17 63533423 . C A 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCCCCACACGGGACACTG;RSEQ=GGTCCGCCCGGCACTTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:0:0,0:453,306:759,0:0:2,0:24.8:1:30.9:1:1:0:60:62.25:0.996:0:0.1 0/1:539:76:48,28:271,191:462,76:0.141:2,2:25.4:1:29.1:1:0.52913:1.21:60:75:0.1412:0:1.2 +17 63533732 . ATGG A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.86263;SOR=1.08175;LSEQ=AGCAGGGAGTGGTACTGCGA;RSEQ=TGGTGGTGGTGGTGGTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:809:20:11,9:362,422:784,20:0.0247:2,2:26.1:1:31.2:1:0.49949:1.42:60:40:0.0254:0.0025:1.9 0/1:562:15:7,8:253,293:546,15:0.0267:2,2:30.1:1:30.6:1:1:1.01:60:30:0.0272:0.0036:0.9 +17 63533768 . G A 300 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.0026;LSEQ=TGGTCCGGGGAGCGGGAGCG;RSEQ=GGGCTATAGCGGCCTACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:853:852:417,435:0,0:0,852:0.9988:0,2:24.7:1:30.9:1:1:0:59.8:59.857:1:0:1.9 1/0:660:455:230,225:107,98:205,455:0.6894:2,2:24.2:1:29.3:1:0.73662:1.06797:59.6:150.667:0.6901:0:2 +17 63533789 . T C 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11263;LSEQ=GGGCTATAGCGGCCTACGCC;RSEQ=GGAGACTGGCAGCCAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:851:847:407,440:0,1:1,847:0.9953:0,2:25.7:1:30.5:1:1:0:59.4:76:0.9952:0:1.9 1/1:695:667:336,331:14,14:28,667:0.9597:2,2:25.1:1:29.3:1:1:1.02:59.5:46.643:0.9589:0:1.7 +17 63534036 . AC A 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=GTTGCAACATTCGGCTCCCT;RSEQ=GCAGGAGCACGCACACCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:26,46:72,0:0:2,0:26.4:1:31:1:1:0:59.4:144:1:0:0.1 0/1:34:7:3,4:5,22:27,7:0.2059:2,2:26.9:1:31.9:1:0.31525:3.16:60:14:0.2059:0.0588:0 +17 63534154 . C T 244 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0137;LSEQ=ACCCACACGCAACCCATGCA;RSEQ=ATGCGCACACAGCCCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:243:241:217,24:1,0:1,241:0.9918:0,2:24:1:30.9:1:1:0:59.8:47.2:0.9958:0:1.2 1/0:121:75:69,6:37,9:46,75:0.6198:2,2:25.8:1:30.5:1:0.08712:2.77:60:150:0.6303:0:1.3 +17 63534221 . C T 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCATGCGCATGCAACCCA;RSEQ=GCACATGCGCACACCCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:608:0:0,0:375,233:608,0:0:2,0:24.4:1:30.9:1:1:0:60:75:1:0:1.1 0/1:434:67:39,28:237,130:367,67:0.1544:2,2:23.9:1:29.7:1:0.33572:1.30801:60:66:0.1531:0:2 +17 63534250 . T C 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12427;LSEQ=GCACACCCTAACGCACCCCA;RSEQ=GCACATGCGCATACACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:777:772:432,340:1,1:2,772:0.9936:2,2:25.8:1:31.3:1:1:1.27:59.9:95.5:0.9948:0:1.2 1/1:625:594:343,251:15,14:29,594:0.9504:2,2:25.2:1:30.5:1:0.56672:1.27:59.9:147.5:0.9547:0:1.3 +17 63534478 . G A 167 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=63.64327;LSEQ=TTCTCTACAGGACGTGGAAA;RSEQ=GAAAGGGAGGAGGCACGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:1:1,0:114,298:412,1:0.0024:2,0:1:0:26:0:0.27845:0:60:2:0.0025:0:1 0/1:350:47:18,29:98,205:303,47:0.1343:2,2:25.3:1:30.2:1:0.41099:1.30:60:94:0.1358:0:1.2 +17 63534504 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32914;SOR=3.74016;LSEQ=GGAGGAGGCACGTTCAGCAG;RSEQ=CTAGGTGGGCGGTGGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:1,0:56,204:260,1:0.0038:2,0:40:0:28:0:0.21839:0:60:2:0.0038:0:1 0/1:211:3:2,1:47,161:208,3:0.0142:2,2:25.7:1:27.3:1:0.13537:6.77:60:6:0.0145:0:2.3 +17 63534514 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18036;SOR=Inf;LSEQ=CGTTCAGCAGGCTAGGTGGG;RSEQ=GGTGGCTTGGCCGGAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:31,181:212,0:0:2,0:21.8:1:29.9:1:1:0:59.8:41.4:1:0:0.5 0/1:157:2:0,2:30,125:155,2:0.0127:2,0:27:1:31:0:1:0:60:4:0.0131:0:1.5 +17 63534538 . C A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10391;LSEQ=GGCTTGGCCGGAGCTTCCCG;RSEQ=ACCAGGCGCTGTGCACCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:117:99:4,95:1,17:18,99:0.8462:1,1:25.5:1:30.5:1:0.57312:1.39263:59.6:32:0.8421:0:1.2 0/1:86:31:1,30:4,51:55,31:0.3605:2,1:23.1:1:30:1:0.64971:2.33271:60:30:0.3571:0:1.1 +17 63534715 . T C 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGAGGCCCTGCTTGTTCT;RSEQ=TCTGTAGTACAACCAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:19:1:33.7:1:1:0:60:14:1:0:1.1 1/1:2:2:0,2:0,0:0,2:1:0,0:11:1:32.5:1:1:0:60:4:1:0:3 +17 63537142 . A G 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCTGGGACTACAGGCGC;RSEQ=CGTCACCACGCTAGGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:15:1:30.3:1:1:0:53.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 63537751 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15478;SOR=Inf;LSEQ=CACATGGGCTACTGTCATAT;RSEQ=CCATCTTGAGATCCCGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:26,223:249,0:0:2,0:22.3:1:32.4:1:1:0:60:40.5:1:0:0.1 0/1:162:2:1,1:21,139:160,2:0.0123:2,2:22:1:25.5:1:0.25389:6.49:60:4:0.0124:0:1 +17 63537898 . T C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=TCTATGGAAACTTGGCTTCC;RSEQ=TGGATGCAGAAGCATCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:0,20:1:0,1:20.3:1:34.3:1:1:0:58.8:40:1:0:1 1/1:6:5:1,4:0,1:1,5:0.8333:0,2:30:1:31.4:1:1:0:60:10:0.8333:0:1.4 +17 63545622 . T C 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGCAAGCCCACGGAAGGG;RSEQ=GGCCAGGATACTCACACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:800:0:0,0:507,289:796,0:0:2,0:24.6:1:29.9:1:1:0:60:55.857:1:0:0.2 0/1:623:48:30,18:372,203:575,48:0.077:2,2:23.9:1:31.2:1:0.75564:1.09934:60:96:0.0784:0:1.1 +17 63554307 . A G 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTTCAGCTGCTTGGAGAC;RSEQ=ATGCTGTTGTTCTCAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1308:0:0,0:641,666:1307,0:0:2,0:26.7:1:30.8:1:1:0:60:92.357:0.9992:0:0.1 0/1:993:62:32,30:462,466:928,62:0.0624:2,2:26:1:30:1:0.79459:1.08:60:124:0.0635:0:1.2 +17 63554591 . G A 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27153;LSEQ=CCTGGTGTTGGAAGAGACAG;RSEQ=CATGGGTTTGGTGACCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:684:490:223,267:92,102:194,490:0.7164:2,2:24.4:1:29.9:1:0.67104:1.0798:60:53.444:0.7147:0:1.1 0/1:460:187:90,97:118,154:272,187:0.4065:2,2:22.8:1:28.5:1:0.3405:1.21:59.9:92.5:0.4129:0:1.1 +17 63554802 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14792;SOR=Inf;LSEQ=CCAGTTCCTCTCAGCAATCG;RSEQ=CGTGGTCTCTCTGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:9,83:92,0:0:2,0:24.4:1:32.4:1:1:0:60:91:1:0:0 0/1:58:2:1,1:6,50:56,2:0.0345:2,2:32.5:1:28:1:0.22868:7.79:60:4:0.0345:0:1 +17 64938182 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCCAGGCTGGAAGCAG;RSEQ=CGGCCCGCATCCAGGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:58,3:61,2:0.0317:1,2:15.5:1:30.5:1:0.12391:16.88608:60:4:0.0328:0:1 0/0:26:0:0,0:26,0:26,0:0:1,0:26.2:1:32:1:1:0:60:52:1:0:0.1 +17 64938281 . C G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29753;SOR=0.71422;LSEQ=TCCCTGTCAACCTCAGGAAG;RSEQ=CAAGAAGCAGTCTTCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:33:20,13:141,104:245,33:0.1183:2,2:27:1:31.9:1:0.85161:1.13:60:66:0.1204:0:1.5 0/1:206:18:12,6:108,80:188,18:0.0874:2,2:29.2:1:30.8:1:0.61798:1.48:60:36:0.0887:0:1.6 +17 64938342 . A C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04869;SOR=1.63652;LSEQ=CGGCTTCTCTGATCCAGCAC;RSEQ=GGCCTGCTGCCCTCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:36:14,22:125,153:278,36:0.1146:2,2:28.6:1:30.5:1:0.59345:1.28284:60:72:0.1161:0:1.5 0/1:240:42:22,20:88,110:198,42:0.175:2,2:24.5:1:29.5:1:0.39563:1.37:60:84:0.1772:0:1.2 +17 64938402 . GG TT 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0033;SOR=0;LSEQ=CTCCTGTGACCATTATTTCA;RSEQ=AAACAAACTCCTTTAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:11:1,10:58,124:182,11:0.057:2,2:18.7:1:30.1:1:0.17751:4.65062:60:22:0.0576:0.0052:0.9 0/0:137:0:0,0:43,94:137,0:0:2,0:24.2:1:30.5:1:1:0:60:44.667:1:0:0.3 +17 66511448 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24359;SOR=Inf;LSEQ=AAAAAAATCCCTGTGAATCA;RSEQ=TTGTCTAATGAATTTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:56,3:59,0:0:2,0:23.2:1:33.2:1:1:0:60:58:1:0:0.2 0/1:58:2:1,1:53,3:56,2:0.0345:2,2:22:1:30:1:0.1343:15.44073:60:4:0.0351:0:1 +17 66511500 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.499;SOR=0;LSEQ=GATTGACATTTTGCTTTATA;RSEQ=TTTATACAAGCATGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:118,36:154,2:0.0128:2,2:14:1:30:1:0.41927:3.24683:60:4:0.013:0:1 0/0:145:0:0,0:104,41:145,0:0:2,0:26.9:1:31.4:1:1:0:60:290:1:0:0.1 +17 66511803 . G GA 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16712;SOR=Inf;LSEQ=TTACTAATTTGTATTTTTTG;RSEQ=AAGAAAAGGAATCTGACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:4,137:141,0:0:1,0:24.8:1:32.2:1:1:0:60:140:1:0:0.1 0/1:98:2:1,1:4,92:96,2:0.0204:1,2:23:1:26.5:1:0.09994:20.68:60:4:0.0204:0.0102:0.5 +17 66518663 . A G 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAATGGCTTGTACTAATG;RSEQ=CTTTTGCCCATTAATAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:13,0:13,4:0.2353:1,0:28.3:1:32.5:1:1:0:60:8:0.25:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 +17 66518780 . TA T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.80298;SOR=1.19485;LSEQ=TTGGTGTTTTCCTCTTAACT;RSEQ=CATTGTTAATGGAAGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:13:13,0:70,0:70,13:0.1566:1,1:23.3:1:33.3:1:1:0:60:26:0.1566:0.012:0 0/1:44:8:8,0:36,0:36,8:0.1818:1,0:20.1:1:31.6:1:1:0:60:16:0.1818:0.0227:0 +17 66518875 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0464;SOR=Inf;LSEQ=ATGCCGAAGGATCTCATTTT;RSEQ=CAAACTCGTAATTTCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:290,131:421,0:0:2,0:25.1:1:32.2:1:1:0:60:59.143:0.9976:0:0.1 0/1:367:4:2,2:241,121:362,4:0.0109:2,2:33.8:1:27.5:1:0.60498:1.98775:60:8:0.0109:0:1 +17 66519787 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18581;SOR=Inf;LSEQ=ATACCATAATGTGGCTTGAC;RSEQ=TTTAATTGAAGCGCAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:214,48:262,0:0:2,0:22.4:1:30.5:1:1:0:60:64.5:1:0:0.1 0/1:199:2:1,1:155,42:197,2:0.0101:2,2:24:1:29:1:0.38633:3.65941:60:4:0.0102:0:1 +17 66519857 . C CT 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.23292;SOR=1.20098;LSEQ=TTGTCATTTGACCTTCAGTT;RSEQ=TTTTCTAGGTTATACCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:116:62,54:354,226:580,116:0.1664:2,2:29.3:1:31.3:1:0.14645:1.36361:59.9:232:0.1679:0.023:0.1 0/1:548:106:54,52:239,203:442,106:0.1934:2,2:27.2:1:30:1:0.58874:1.13347:60:212:0.1959:0.0237:0.1 +17 66520274 . A AT 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.18917;SOR=Inf;LSEQ=AGAGGAGGCGAGACTAGAGG;RSEQ=TTTTTTTGGTTTTGTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:32,209:241,0:0:2,0:24.7:1:31.1:1:1:0:60:119.5:1:0:0.1 0/1:186:2:1,1:31,153:184,2:0.0108:2,2:35:1:29.5:1:0.31526:4.87:60:4:0.0109:0:0 +17 66520325 . C CT 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.28752;SOR=2.34829;LSEQ=TTTCCTCTTTGATCCTACCA;RSEQ=TTTTTTTTTTCTGTTATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:5:0,5:6,103:109,5:0.0431:2,0:37.4:1:31.8:1:1:0:60:10:0.0435:0:0 0/1:52:5:0,5:1,45:46,5:0.0962:1,0:16.8:1:30.3:1:1:0:60:10:0.1:0.0192:0 +17 66520427 . C T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38596;SOR=4.1833;LSEQ=GGGAACTAATATTTTTGATA;RSEQ=AGTTTTGTTTATAATTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:1,13:14,3:0.1765:1,0:22.3:1:28.3:1:1:0:60:6:0.1875:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:2:0:29:0:1:0:60:2:0.5:0:1 +17 66520970 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=CTCTCACAGTACCACTGTAA;RSEQ=ATAAGTTTATTGTTTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:107,15:122,2:0.0161:2,2:17:1:27.5:1:0.24233:6.93899:60:4:0.0165:0:1 0/0:116:0:0,0:95,21:116,0:0:2,0:20.3:1:29.7:1:1:0:60:232:1:0:0.1 +17 66520989 . A G 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.6201;SOR=2.04974;LSEQ=AAATAAGTTTATTGTTTTGT;RSEQ=ATAATTTTGATAATTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:1,0:152,40:192,1:0.0052:2,0:5:0:32:0:1:0:60:2:0.0053:0:1 0/1:189:2:1,1:135,51:186,2:0.0106:2,2:16:0:32.5:1:0.47776:2.63118:60:4:0.0106:0:1.5 +17 66521160 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08501;SOR=Inf;LSEQ=CCAATGTATTGATCGCTTCC;RSEQ=AGCAATAAGAATAGTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:21,137:158,0:0:2,0:22.5:1:31.7:1:1:0:60:78:1:0:0.1 0/1:125:3:2,1:22,100:122,3:0.024:2,2:10.3:1:27:1:0.0941:8.86:60:6:0.0242:0:1 +17 66522047 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06743;SOR=Inf;LSEQ=CGAGACAGCTATAGAAGAAT;RSEQ=CTCATGGTAAGAGACCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:113,292:405,0:0:2,0:24.5:1:31.4:1:1:0:60:56.857:1:0:0.1 0/1:279:3:2,1:74,202:276,3:0.0108:2,2:20:1:26.7:1:0.1812:5.42:60:6:0.0109:0:1 +17 66522186 . T TTC 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.03492;LSEQ=TTCTTTTAATAAGCGAATAT;RSEQ=TTTCTTTTAATGAGCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:0,29:29,8:0.2162:1,0:28.4:1:32.2:1:1:0:60:16:0.2162:0.0541:0.3 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:18:1:31:1:1:0:60:4:0.2222:0.1111:0 +17 66522195 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCGAATATTTTTCTTTT;RSEQ=ATGAGCAAATACTTTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:0,2:0,28:28,2:0.0667:1,0:11.5:1:34:0:1:0:60:4:0.0667:0:1 0/0:7:0:0,0:0,7:7,0:0:0,0:22.4:1:31:1:1:0:60:14:1:0:0 +17 66523772 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12121;SOR=Inf;LSEQ=GAATTGGGCATAATATTGGC;RSEQ=GAAAATAAAAATCACAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:14,0:0:1,0:25.4:1:30.7:1:1:0:60:28:1:0:0.1 0/1:8:2:1,1:5,1:6,2:0.25:2,2:15:1:31.5:1:0.46429:3.87298:60:4:0.25:0:1 +17 66523900 . CTT C 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00654;SOR=Inf;LSEQ=GTTTTAAAATTTATTTGAAA;RSEQ=AATATTTATTATTCCATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:121,3:124,0:0:1,0:23.8:1:32.4:1:1:0:60:61:1:0:0.1 0/1:97:6:6,0:91,0:91,6:0.0619:1,0:25.5:1:31.5:1:1:0:60:12:0.0625:0:0 +17 66524121 . C A 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26774;SOR=0;LSEQ=ATGGACTTGGGAAAAGCCTT;RSEQ=TGAAAGTATAATTGCTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:2,1:34,208:242,3:0.0122:2,2:10.3:1:24.7:1:0.05733:12.02:60:6:0.0124:0:1 0/0:177:0:0,0:35,142:177,0:0:2,0:19.6:1:31.1:1:1:0:60:87.5:1:0:0.1 +17 66524987 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=16.45038;LSEQ=GCACCAAATAATACAGAGCA;RSEQ=TTATTTTGATTCTTGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:50:38,12:184,92:276,50:0.1534:2,2:28.6:1:29.9:1:0.24829:1.58:60:15.667:0.146:0:1.1 1/0:228:171:121,50:40,16:56,171:0.75:2,2:25.1:1:29.7:1:1:1.03291:60:41.75:0.7455:0:1.1 +17 66525001 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03114;SOR=Inf;LSEQ=AGAGCAGTTATTTTGATTCT;RSEQ=GTCTTTCAGAGTCTCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:252,138:390,0:0:2,0:26.4:1:30.9:1:1:0:59.9:129:1:0:0.2 0/1:284:4:2,2:185,95:280,4:0.0141:2,2:23.8:1:31.5:1:0.60799:1.94253:60:8:0.0141:0:1.5 +17 66525115 . T A 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16783;SOR=5.5538;LSEQ=AGGGAGAACCAGGGGATGAG;RSEQ=TCTTCATTATTTTAGAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:1:1,0:179,287:466,1:0.0021:2,0:1:0:25:0:0.38544:0:60:2:0.0022:0:1 0/1:339:4:3,1:128,207:335,4:0.0118:2,2:9.3:1:26.3:1:0.30269:4.83:47:8:0.0119:0:1.3 +17 66525176 . A G 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27129;SOR=0;LSEQ=TTGAATTTTAGAGGTAAAGA;RSEQ=CTCAGAATTTAATACTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:3:1,2:23,146:169,3:0.0174:2,2:18:1:24.3:1:0.36473:3.14:55:2:0.0118:0:3.7 0/0:120:0:0,0:20,100:120,0:0:2,0:20.2:1:29:1:1:0:60:119:1:0:0.1 +17 66525943 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGTGACTAACTTTAAA;RSEQ=TCATTTTTTATCATATGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:133,5:138,2:0.0143:1,2:25.5:1:28:1:0.08417:24.37392:60:4:0.0145:0:2 0/0:59:0:0,0:57,2:59,0:0:1,0:25.3:1:31.7:1:1:0:60:58:1:0:0.3 +17 66525970 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55571;SOR=0;LSEQ=TTTATCATATGCACACATTT;RSEQ=CAAGGTAGTTAAAATTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:2,1:192,24:216,3:0.0137:2,2:16.3:1:30.3:1:0.3061:3.95927:60:6:0.0139:0:1 0/0:123:0:0,0:112,11:123,0:0:2,0:21.3:1:31.5:1:1:0:60:60.5:1:0:0.6 +17 66526027 . G T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=11.2099;LSEQ=CACCCTGGGTTTGAGAGTGT;RSEQ=TGTTTGTTTAGCTTTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:88:60,28:336,157:493,88:0.1515:2,2:26.6:1:30.7:1:1:1.00:60:176:0.1525:0:1.1 1/0:418:279:193,86:90,49:139,279:0.6675:2,2:23.8:1:29.5:1:0.37594:1.22:60:54.8:0.6683:0:1.1 +17 66526233 . T C 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00047;SOR=Inf;LSEQ=TCCATAATTTTGTCTTCTCC;RSEQ=GAATTTTATTTTCTAACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:40,135:175,0:0:2,0:24.5:1:31.4:1:1:0:59.9:350:1:0:0 0/1:91:7:2,5:13,71:84,7:0.0769:2,2:18.6:1:29.3:1:0.32475:2.16:60:14:0.0769:0:1 +17 66526316 . A T 141 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04327;LSEQ=TTTACTCATTTAATGAAATT;RSEQ=CTGATTGTCTCATATCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:23:14,9:100,32:132,23:0.1484:2,2:26.1:1:31.2:1:0.19804:1.99892:60:46:0.1494:0:1.3 0/1:91:14:13,1:62,15:77,14:0.1538:2,1:16.3:1:30.2:1:0.44974:3.12:60:28:0.1556:0:1.1 +17 66526675 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15468;SOR=Inf;LSEQ=TTATTTTCCCTACTTGCAGC;RSEQ=CCAAGTGGCCACTGGCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:10,162:172,0:0:2,0:25.5:1:32.3:1:1:0:60:85:1:0:0 0/1:112:2:1,1:13,96:109,2:0.0179:2,2:15:1:28:1:0.23735:7.15:60:4:0.0179:0:1 +17 66545635 . CA C 32 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAATGCAAAACTCCATCT;RSEQ=AAAAAAAAAAAAAAGTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:25.5:1:32:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 66547249 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.60238;LSEQ=CCTCATCATCTCAAGGAGGA;RSEQ=CATTCCCCTGGGCTAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2066:298:152,146:919,846:1765,298:0.1442:2,2:26.1:1:30.3:1:0.75419:1.04341:60:148:0.1457:0:1.2 0/1:1467:312:162,150:604,550:1154,312:0.2127:2,2:24:1:29.5:1:0.89854:1.01683:60:155:0.2136:0:1.2 +17 66547409 . G C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15048;SOR=0.66622;LSEQ=TGTTTCACAAAATTTTCAAG;RSEQ=CATGTAGTTGCTGTTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:57:0,57:4,273:277,57:0.1707:1,1:26.1:1:31.2:1:1:0:60:18:0.1651:0:1.1 0/1:166:20:0,20:4,142:146,20:0.1205:1,1:24.5:1:31.2:1:1:0:60:40:0.1212:0:1 +17 68920798 . T C 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11798;LSEQ=GAATTCCTATTTTTAAGCAA;RSEQ=ATCTTCGAGGAAGCAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:9,4:0.3077:0,0:27.8:1:29.3:1:1:0:60:3:0.25:0:1.3 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:29.5:1:33:0:0.33333:0:60:4:0.3333:0:1 +17 68920884 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96025;LSEQ=GCCTAGTGTGTATGCAGTAA;RSEQ=GGTGAATTCTTCTGTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:19:19,0:29,2:31,19:0.38:2,1:21.9:1:32.5:1:0.51918:0:59.9:38:0.38:0:1.1 0/1:27:10:10,0:17,0:17,10:0.3704:1,0:17.8:1:32.8:1:1:0:60:20:0.3704:0:1.1 +17 68920943 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0299;SOR=Inf;LSEQ=TAATTATTCTACCAGTCTTT;RSEQ=GCAATAATTTTCTCGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:117,34:151,0:0:2,0:21.8:1:32:1:1:0:60:302:1:0:0.2 0/1:109:4:4,0:80,25:105,4:0.0367:2,0:35.8:1:30.3:1:0.57182:0:60:8:0.0367:0:1 +17 68920957 . C T 127 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=34.98228;LSEQ=GTCTTTCGCAATAATTTTCT;RSEQ=GTATCTACTGTAATTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:1:1,0:146,48:194,1:0.0051:2,0:3:0:28:0:1:0:60:2:0.0052:0:1 0/1:130:20:15,5:85,25:110,20:0.1538:2,2:19.6:1:29.6:1:0.77962:1.1322:60:40:0.155:0:1.5 +17 68921040 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.31455;LSEQ=CAGCCATGTCTTCTGTACCC;RSEQ=TTCATTTTCTGTCTGTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:444:341:165,176:50,53:103,341:0.768:2,2:27.4:1:30.9:1:1:1.00628:59.9:67.2:0.7742:0:1.1 1/0:410:209:103,106:99,101:200,209:0.5098:2,2:27.6:1:29.6:1:1:1.00873:59.9:208:0.5136:0:1.2 +17 68921097 . C T 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.86781;SOR=0.91314;LSEQ=TGCAAAGTGTACCACAGTGA;RSEQ=TTCCATGCCTCCTGGCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:21:8,13:66,161:227,21:0.084:2,2:23.2:1:29.7:1:0.45519:1.50:60:20:0.082:0:1.2 0/1:233:18:7,11:75,140:215,18:0.0773:2,2:26:1:29.4:1:0.79893:1.19:60:36:0.0779:0:1.1 +17 68921135 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00069;SOR=0.34536;LSEQ=ACGGTATGCAAGAGTCACCA;RSEQ=CCTAGCATGCCCATCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:48:4,44:15,62:77,48:0.384:2,2:26:1:32.2:1:0.12491:2.64241:60:23:0.374:0:1.2 0/1:102:18:4,14:17,67:84,18:0.1765:2,2:25.1:1:31.1:1:1:1.12:60:36:0.1765:0:1.3 +17 69889050 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8628;SOR=0.91024;LSEQ=ATGGGTGTTCTCTTGTCCCC;RSEQ=TCCAATATAAACCTAGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:33:28,5:78,5:83,33:0.2845:2,2:22.1:1:30.7:1:0.14468:2.75742:60:32:0.2832:0:1 0/1:64:17:16,1:45,2:47,17:0.2656:1,1:22.2:1:29.6:1:1:1.39825:60:34:0.2656:0:1.1 +17 69889186 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.68539;LSEQ=AATAAACAGTGAAACAAAGT;RSEQ=GTTTCATCACAGGGTATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:128:61,67:154,201:355,128:0.265:2,2:29.6:1:30.3:1:0.40881:1.19:59.8:127:0.2696:0:1.1 0/1:323:159:73,86:72,91:163,159:0.4923:2,2:25.4:1:28.8:1:0.82282:1.07:60:158:0.4938:0:1.2 +17 69889220 . G A 47 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67967;LSEQ=GTATCAGAGTAACCCACGGA;RSEQ=CACATCACTGTATTAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:4:4,0:139,168:307,4:0.0129:2,0:10.5:1:23.5:1:0.04369:0:60:3:0.0099:0:2.5 0/0:228:2:1,1:101,125:226,2:0.0088:2,2:20:1:18.5:1:1:1.24:60:1:0.0045:0:2.5 +17 69889230 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57976;SOR=2.66045;LSEQ=AACCCACGGAGCACATCACT;RSEQ=TATTAAAATTCCATTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:1:0,1:107,128:235,1:0.0042:2,0:44:0:16:0:1:0:60:0:0:0:3 0/1:179:2:1,1:79,97:176,2:0.0112:2,2:35:1:29:1:1:1.23:60:4:0.0112:0:1.5 +17 69889259 . T G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.03607;SOR=0.42064;LSEQ=TTCCATTGGCTGGTGGGGGG;RSEQ=GGGGGGTGGGGGGTGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:24:1,23:38,23:61,24:0.2759:2,1:8.1:1:20.9:1:0:36.60243:42.5:1.667:0.2174:0:3 0/1:80:11:0,11:41,28:69,11:0.1375:2,0:7.5:1:27.1:1:0.00016:0:41.3:10:0.1316:0:3.1 +17 69889266 . T G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.31463;SOR=0.60912;LSEQ=GGCTGGTGGGGGGTGGGGGG;RSEQ=GGGGGGTGGGGTGCAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:26:1,25:31,10:41,26:0.3611:2,1:12.4:1:25.1:1:0:71.41326:43.7:5.5:0.386:0:2.7 0/1:47:12:1,11:27,7:34,12:0.2553:2,2:13.5:1:24.8:1:2e-05:38.09497:44.7:5:0.2381:0:2.9 +17 69889290 . C T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02285;SOR=Inf;LSEQ=GGGTGGGGTGCAGTGGCTCA;RSEQ=GCCTGCAATCCTAGCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:8,50:58,0:0:2,0:22.2:1:28.6:1:1:0:48.1:57:1:0:1.5 0/1:24:3:1,2:7,14:21,3:0.125:2,2:25.3:1:23.7:1:1:1:46:2:0.0909:0:2.3 +17 70114569 . G T 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGCAGAAATGCAGGACC;RSEQ=ATCCACTCGCGAGCTGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:653:0:0,0:180,471:651,0:0:2,0:22.8:1:31.5:1:1:0:60:107.5:0.9969:0:0.1 0/1:254:13:3,10:65,175:240,13:0.0512:2,2:27.9:1:29:1:1:1.23708:60:26:0.0512:0:1.3 +17 70114592 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1949;SOR=5.09337;LSEQ=CCACTCGCGAGCTGACAATG;RSEQ=CACGCGCTAGACTTGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:0,1:42,348:390,1:0.0026:2,0:43:0:29:0:1:0:60:2:0.0026:0:1 0/1:155:2:1,1:26,127:153,2:0.0129:2,2:10:1:30.5:1:0.31898:4.81:60:4:0.013:0:2 +17 70117442 . G T 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGCTCCGCATCCGGGCA;RSEQ=CCGAGGGGAGAGGAGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:157,8:165,2:0.012:1,0:5.5:1:32.5:1:1:0:60:4:0.0124:0:1.5 0/0:74:0:0,0:66,8:74,0:0:2,0:1:0:16:0:1:0:60:0:0:0:1 +17 70117487 . G T 57 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13362;SOR=3.17804;LSEQ=CGAGTCCCCGAGCCGCCGCG;RSEQ=CTTCTCGCCTTTCCCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:3:0,3:384,142:526,3:0.0056:2,0:1:0:26:1:0.02028:0:60:6:0.0058:0:1 0/1:282:5:1,4:184,93:277,5:0.0177:2,2:11.6:1:24.8:1:0.04919:7.85558:60:10:0.0181:0:1.2 +17 70117975 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.10261;SOR=Inf;LSEQ=GCTCTGGAGGTAGGACCCGG;RSEQ=GGGGGCGGCGCGGCAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:102,264:366,0:0:2,0:24.2:1:30.2:1:1:0:59.7:44.75:1:0:0.2 0/1:173:2:1,1:57,114:171,2:0.0116:2,2:23:1:26:1:1:1.99:60:4:0.0119:0:1 +17 70118061 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGCCTCCCATCGCCCGG;RSEQ=AGTTGCCGTTCCGGGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:0,2:0,51:51,2:0.0377:1,0:29.5:1:26.5:1:1:0:60:4:0.0377:0:1 0/0:24:0:0,0:1,23:24,0:0:1,0:19.7:1:31.5:1:1:0:60:48:1:0:0.3 +17 70118699 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20416;SOR=0.57458;LSEQ=TTTATTTATTTTTAAGAAAA;RSEQ=TTATGAGCTGTGGTTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:100:62:60,2:38,0:38,62:0.62:1,1:21.3:1:29.8:1:0.52404:0:59.8:14.5:0.6105:0:1.3 0/1:29:14:13,1:15,0:15,14:0.4828:1,1:15.2:1:29.4:1:0.48276:0:60:28:0.4828:0:1.1 +17 70118935 . C T 212 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=101.77068;LSEQ=GTGCAGCACAAGAAGGACCA;RSEQ=CCGGATTACAAGTACCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1606:3:1,2:818,781:1599,3:0.0019:2,2:25:1:24.3:1:0.61652:2.0938:60:2:0.0013:0:1.3 0/1:1067:171:82,89:434,461:895,171:0.1603:2,2:24.4:1:28.7:1:0.93353:1.02178:59.8:23.429:0.1568:0:1.1 +17 70119107 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0454;SOR=Inf;LSEQ=AGGTGCACTCCCCCGGCGAG;RSEQ=ACTCGGGTGAGTCGCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:81,267:348,0:0:2,0:25.2:1:32.1:1:1:0:60:57:1:0:0.2 0/1:194:3:1,2:51,140:191,3:0.0155:2,2:28:1:27.7:1:1:1.37:60:6:0.0155:0:1 +17 70119245 . C G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.44886;SOR=0.40015;LSEQ=ACACTGCCCTTTGCGCCCGT;RSEQ=CCGCTCCCCTCTCTACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:16:2,14:2,19:21,16:0.4211:2,2:17.5:1:32.3:1:1:1.35:60:32:0.4324:0:1.1 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:22:1:30.5:1:1:0:60:4:0.2222:0:1 +17 70119631 . C T 63 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06063;SOR=3.21922;LSEQ=GAGGGTGCCTAAGACTAGGG;RSEQ=GTCTGCACAGCCCTTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1000:4:0,4:689,307:996,4:0.004:2,0:1:0:26.8:1:0.00923:0:60:8:0.0041:0:1.5 0/1:548:7:2,5:371,170:541,7:0.0128:2,2:14.1:1:22.6:1:0.03674:5.43717:60:2.5:0.0093:0:1 +17 70119964 . C T 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.11358;SOR=5.95145;LSEQ=ACGGGCAGCTACGGCATCAG;RSEQ=AGCACCGCGGCCACCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:1:0,1:107,414:521,1:0.0019:2,0:40:0:29:0:1:0:60:2:0.0019:0:1 0/1:265:3:1,2:71,191:262,3:0.0113:2,2:15.7:1:22.3:1:1:1.34:60:2:0.0077:0:1 +17 70119998 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14099;SOR=Inf;LSEQ=CCCCGGCGAGCGCGGGCCAC;RSEQ=TGTGGATGTCCAAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:42,200:242,0:0:2,0:25.7:1:32.7:1:1:0:60:241:1:0:0.1 0/1:146:2:1,1:34,110:144,2:0.0137:2,2:17.5:1:30:1:0.42324:3.20:41:4:0.0138:0:1.5 +17 70120067 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=CACAGGCCCCGCCGGCCCCG;RSEQ=AGGCGCCCCCGCAGCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:23:0:31:1:1:2.23609:60:4:0.2222:0:1.5 0/0:7:0:0,0:4,3:7,0:0:2,0:6.7:1:28.7:1:1:0:60:14:1:0:0.3 +17 70120084 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09323;SOR=Inf;LSEQ=CCGCAGGCGCCCCCGCAGCC;RSEQ=CAGGCGGCGCCCCCACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:55,3:58,0:0:2,0:9.3:1:31.2:1:1:0:60:116:1:0:0.4 0/1:26:2:1,1:22,2:24,2:0.0769:2,2:13:0:31:0:0.22154:9.18332:51:4:0.0769:0:1.5 +17 70120097 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCAGCCGCAGGCGGCGCCC;RSEQ=CACAGCAGCCGGCGGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:103,3:106,2:0.0185:1,2:29.5:1:33:1:0.07304:29.87118:60:4:0.0185:0:1.5 0/0:47:0:0,0:43,4:47,0:0:2,0:15.6:1:31.1:1:1:0:59.6:46:1:0:0.1 +17 70120111 . G A 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00271;SOR=0;LSEQ=GCGCCCCCACAGCAGCCGGC;RSEQ=GCACCCCCGCAGCAGCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:20:18,2:173,13:186,20:0.0971:2,2:22.1:1:31.3:1:0.64418:1.47542:60:40:0.0995:0:1.1 0/0:74:0:0,0:66,8:74,0:0:2,0:20.4:1:30.3:1:1:0:59.8:148:1:0:0.1 +17 70120178 . C T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10404;SOR=4.63144;LSEQ=GCGAGCCGGGCCAGTCCCAG;RSEQ=GAACGCACATCAAGACGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:833:2:0,2:681,150:831,2:0.0024:2,0:1:0:28:1:0.03312:0:60:4:0.0024:0:1 0/1:453:5:2,3:351,97:448,5:0.011:2,2:13.2:1:26.4:1:0.074:5.40095:60:10:0.0111:0:1 +17 70120551 . A C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34642;LSEQ=AGGCCTCCCACGAAGGGCGA;RSEQ=GATGGCCGAGATGATCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:529:347:53,294:34,148:182,347:0.656:2,2:22.3:1:30:1:0.32516:1.27372:60:56.833:0.6558:0:1.1 0/1:312:124:32,92:37,151:188,124:0.3974:2,2:24.9:1:29.8:1:0.21222:1.42:59.9:248:0.4:0:1.2 +17 70120652 . TTTC T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.56239;SOR=0;LSEQ=TTTTTTATTTTGTTTTGTTT;RSEQ=TTCTTCTTCTTCTTCCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:3:0,3:1,70:71,3:0.0405:1,0:36:1:28.3:1:1:0:60:6:0.0411:0:0 0/0:27:0:0,0:1,26:27,0:0:1,0:24.1:1:29.6:1:1:0:60:12.5:1:0:0.1 +17 70122108 . G A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGTCATCCATATTTCTCT;RSEQ=CATCTTCTCTTGGAGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:11,0:4,0:4,11:0.7333:0,0:24.9:1:29.1:1:1:0:58.5:22:0.7333:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:5.5:1:29.5:1:1:0:60:4:1:0:1 +17 70122227 . C CT 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05081;SOR=3.20051;LSEQ=TTTTTAAAAAAGACAGCAAA;RSEQ=TTTTTTTTTTATTTAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:7:7,0:112,1:113,7:0.0583:1,0:14.1:1:32.9:1:1:0:60:14:0.0583:0.025:0.6 0/1:42:7:7,0:35,0:35,7:0.1667:1,0:21.7:1:31.1:1:1:0:60:14:0.1707:0.0476:0 +17 70122505 . CT C 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0;SOR=0.50995;LSEQ=ACCTTTCCCTTTTTCTTTCT;RSEQ=TTTTTTTTTTTGTATATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1163:454:100,354:241,397:638,454:0.3904:2,2:28.9:1:32.3:1:0:2.1475:59.7:44.4:0.3964:9e-04:0.4 0/1:833:205:45,160:207,379:586,205:0.2461:2,2:28.2:1:31:1:0.00035:1.94041:59.5:50.25:0.2497:0:0.5 +17 70122660 . G GT 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00217;SOR=0.17225;LSEQ=CTGATTGCTGTGATGTTTTT;RSEQ=TTTTTTATCAGCACCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:67:40:0,40:0,27:27,40:0.597:1,1:26.4:1:31:1:1:0:59.6:80:0.597:0.0597:0.1 0/1:20:4:0,4:0,16:16,4:0.2:1,0:24.8:1:31.3:1:1:0:60:8:0.2105:0:0 +17 72768970 . G A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87769;LSEQ=TGCCCACCCTTTGCAGCCTC;RSEQ=GCAGGCTCAGTCAGCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:22:10,12:6,5:11,22:0.6667:2,2:30.4:1:31:1:0.72068:1.42407:60:44:0.6667:0:1.1 1/0:11:7:4,3:3,1:4,7:0.6364:2,2:18.1:1:30.7:1:1:2.09375:60:14:0.6364:0:1 +17 72839130 . A AGCTCCGGGG 64 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGCAGCGGCAGGTCCTCC;RSEQ=GCTCCGGGAAGAGCGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:27.5:1:32.4:1:1:0:60:8:1:0:0.3 +17 72840514 . C T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52638;SOR=0;LSEQ=CAGGCGAAGACCAGCAGGGC;RSEQ=AGCCCCATGGCCACCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:137,60:197,2:0.0101:2,2:7.5:1:28.5:1:0.52018:2.27282:60:4:0.0104:0:1 0/0:123:0:0,0:82,41:123,0:0:2,0:23.6:1:30.5:1:1:0:59.7:60.5:1:0:0.2 +17 72840630 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17832;SOR=Inf;LSEQ=CCCTGAGAGCCACACTGTCT;RSEQ=CAGTTTCTGTGTCTCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:61,147:208,0:0:2,0:24:1:31.1:1:1:0:59.9:51:0.9903:0:0.1 0/1:154:2:1,1:51,99:150,2:0.013:2,2:42:1:29:1:1:1.93:60:4:0.0132:0:1 +17 72842873 . C A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGACACACGGATGAAGA;RSEQ=AGCGGGTGCAGGGCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 72843378 . C T 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CCAGACTCGACTGTCCAGGG;RSEQ=CTGCCCACTCACGGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:6,0:6,5:0.4167:0,0:17.6:1:32:0:1:0:60:10:0.4545:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:38.5:1:31:1:1:0:60:4:1:0:1 +17 72843411 . GC G 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28327;SOR=0;LSEQ=GGCCTGTCCCCACCCTCAGT;RSEQ=CCCCCCCCACCCCCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:13,0:13,7:0.35:1,0:36.4:1:34:1:1:0:60:14:0.3684:0:1.4 0/0:4:0:0,0:3,1:4,0:0:2,0:19:1:32.8:1:1:0:60:8:1:0:0.8 +17 72843527 . C T 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53584;SOR=0;LSEQ=CAGGTTGGCCGTGTAGCTGG;RSEQ=GAGGAAGATGACAGCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:94,76:170,2:0.0116:2,2:30:1:24:1:1:1.2353:60:4:0.0118:0:1 0/0:98:0:0,0:58,40:98,0:0:2,0:24.8:1:30.2:1:1:0:60:196:1:0:0.1 +17 72843551 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53417;SOR=0;LSEQ=GAAGATGACAGCAAAGAAGG;RSEQ=CCAGACCAGAACCATGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:84,94:178,2:0.0111:2,2:20.5:1:29.5:1:1:1.12:60:4:0.0113:0:1 0/0:104:0:0,0:57,47:104,0:0:2,0:28.8:1:30.6:1:1:0:60:51:1:0:0.1 +17 72843567 . G T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53377;SOR=0;LSEQ=AAGGCCCAGACCAGAACCAT;RSEQ=ATCTTGCTGGTGGTGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:62,95:157,2:0.0126:2,2:47:0:30.5:1:1:1.53:60:4:0.0131:0:2 0/0:92:0:0,0:44,48:92,0:0:2,0:29.4:1:31.2:1:1:0:60:184:1:0:0.1 +17 72843588 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15648;SOR=Inf;LSEQ=ATCTTGCTGGTGGTGCCCCG;RSEQ=GGGTTCTCGATGGGCACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:33,90:123,0:0:2,0:23.5:1:30.3:1:1:0:60:29.75:1:0:0.2 0/1:81:2:1,1:31,47:78,2:0.0247:2,2:26.5:1:28:1:1:1.51:60:4:0.0247:0:1.5 +17 72843609 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51642;SOR=0;LSEQ=GGGTTCTCGATGGGCACTGA;RSEQ=TTGTTGAAGACCAGCGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:14,65:79,2:0.0247:2,2:7.5:1:29:1:0.33796:4.52:60:4:0.025:0:2 0/0:54:0:0,0:20,34:54,0:0:2,0:22.8:1:31:1:1:0:60:108:1:0:0.1 +17 72846043 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10938;SOR=Inf;LSEQ=TCATTGATGGTGAGGGAGCC;RSEQ=ATGGCCATGTCTGCCCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:34,52:86,0:0:2,0:25.1:1:31:1:1:0:60:172:1:0:0.1 0/1:43:2:1,1:14,27:41,2:0.0465:2,2:31:1:29.5:1:1:1.90:60:4:0.0476:0:1 +17 72846086 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53729;SOR=0;LSEQ=AGTACACCTGGGGGCCGGAC;RSEQ=CCACGGAGGTTTGAAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:7,30:37,2:0.0513:2,2:22.5:1:29:1:0.37247:4.08:60:4:0.0513:0:1 0/0:21:0:0,0:5,16:21,0:0:2,0:24.3:1:31.8:1:1:0:60:42:1:0:0.1 +17 72904115 . G A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27778;SOR=0;LSEQ=AGCCTTTTCCTGTAAACGCC;RSEQ=GGTGGCATCTCTTACTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:1,4:5,4:9,5:0.3571:2,2:39.2:1:33:1:0.3007:4.45211:43.4:10:0.3571:0:1 0/0:4:0:0,0:1,3:4,0:0:2,0:33.8:1:26:1:1:0:46:3:1:0:0 +17 72939446 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=4.08106;LSEQ=ACCAACTTCACTAGGTAAGA;RSEQ=TTCTCTCCCTCCCAAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:85:43,42:300,323:623,85:0.1201:2,2:25.9:1:30.3:1:0.72893:1.10:60:41.5:0.1179:0:1.1 0/1:542:194:95,99:163,185:348,194:0.3579:2,2:23.8:1:29.9:1:0.65444:1.09:60:193:0.3594:0:1.2 +17 72939663 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00051;SOR=Inf;LSEQ=GGTTTGGCACCTGGGGAGCC;RSEQ=GCCAGGGTGTGTGAGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:33,0:0:1,0:21:1:32.1:1:1:0:60:66:1:0:0 1/0:4:3:0,3:0,1:1,3:0.75:0,0:29:1:30.3:1:1:0:60:6:0.75:0:1 +17 73401705 . AGCC A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.48889;SOR=Inf;LSEQ=ACAGGCACAGACTCTGCCAC;RSEQ=GCCGCCGCCGCTGCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,7:22,0:0:2,0:24:1:33.5:1:1:0:60:44:1:0:0.1 0/1:23:2:1,1:13,8:21,2:0.087:2,2:33.5:1:32:1:1:1.58984:60:4:0.087:0:0.5 +17 73584696 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49804;SOR=0;LSEQ=CTGCGGCCCACGCCGGAGCC;RSEQ=ACGGACATGGGCTCGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:33,28:61,2:0.0317:2,2:10.5:1:32:1:1:1.17549:60:4:0.0328:0:1 0/0:55:0:0,0:29,26:55,0:0:2,0:23.6:1:27.8:1:1:0:60:26.5:1:0:0.2 +17 73584728 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2467;SOR=0;LSEQ=CTCGGAAGGGACAAAAACCG;RSEQ=GCCGGAGTCAGCGCTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:3:1,2:47,45:92,3:0.0316:2,2:14.3:1:32:1:0.61698:2.07327:57.7:6:0.033:0:1.3 0/0:89:0:0,0:43,46:89,0:0:2,0:24.7:1:30.1:1:1:0:60:43.5:1:0:0.2 +17 73584793 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20126;SOR=Inf;LSEQ=ACTGGCCCCACGCAGATACC;RSEQ=GGGGCCGGGAAGGGTCGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:51,0:0:2,0:22.1:1:29.6:1:1:0:60:24.5:1:0:0.1 0/1:42:2:1,1:18,22:40,2:0.0476:2,2:27:1:28.5:1:1:1.22:60:4:0.0476:0:1 +17 73584858 . CGA TTT 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCATTCCGGCGGGGACTC;RSEQ=CTCGAGTCCGCTGGGGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:1,11:12,2:0.1429:2,0:29.5:1:30.7:0:1:0:60:4:0.1429:0:1 0/0:5:0:0,0:0,5:5,0:0:0,0:31:1:25.8:1:1:0:60:4:1:0:0 +17 73586184 . C G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGGGAGCTGTGGGAACC;RSEQ=GAGGATGAGGACGAGGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:31.5:1:1:0:60:4:1:0:2 +17 73586235 . G T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTGGAGCTGAGCCTCCG;RSEQ=CCGGGCCTGGAGGCGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:28:1:1:0:60:4:1:0:2 +17 73774692 . C A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03316;LSEQ=TCACTTAAGCTCTCTCTCCC;RSEQ=GTATCCGGCGAGCCAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:2,0:34,59:93,2:0.0211:2,0:1:0:25:0:0.1411:0:60:4:0.0215:0:1 0/1:92:2:1,1:24,66:90,2:0.0217:2,2:9.5:1:30.5:1:0.47181:2.71:60:4:0.022:0:1 +17 73774722 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=GAGCCAACTGGATGTCTTTG;RSEQ=GCATGATGGTGACTCTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:55,109:164,0:0:2,0:5.5:1:29.2:1:1:0:41.4:26.333:1:0:0.1 0/1:170:2:1,1:63,105:168,2:0.0118:2,2:7.5:1:27.5:1:1:1.66:60:4:0.0119:0:1 +17 73774841 . G A 173 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=62.66076;LSEQ=CCGCACTATTAATCCCACTC;RSEQ=GGGAGCGGAAACCGCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1217:1:1,0:612,603:1215,1:8e-04:2,0:1:0:31:0:1:0:60:2:8e-04:0:1 0/1:1223:60:33,27:576,584:1160,60:0.0491:2,2:23.2:1:29.3:1:0.43046:1.24:60:59:0.049:0:1.1 +17 73774877 . G A 238 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGCCCTCCCCCGGCTCCA;RSEQ=GCCTTTGTCTTACCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1320:0:0,0:690,628:1318,0:0:2,0:24.7:1:32:1:1:0:59.3:46.071:1:0:0.1 0/1:1392:274:147,127:595,519:1114,274:0.1968:2,2:23.4:1:29.5:1:0.94624:1.01:58.9:67.5:0.1959:0:1.1 +17 73775270 . G C 208 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCATTTTCTTTCACCTAA;RSEQ=AAAGACGCCCCGAAGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1026:0:0,0:369,656:1025,0:0:2,0:25.2:1:32.2:1:1:0:58:47.81:1:0:0.2 0/1:1243:102:41,61:457,683:1140,102:0.0821:2,2:26.3:1:31.3:1:1:1.00:51:33:0.0811:0:1.2 +17 73775397 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15517;SOR=Inf;LSEQ=GCCCCACCTCGCGGCAGCAG;RSEQ=TGGCCGAGGGCCGCCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:0,70:70,0:0:1,0:21.5:1:31.8:1:1:0:60:140:1:0:0.1 0/1:46:2:0,2:5,39:44,2:0.0435:2,0:13.5:1:33:0:1:0:60:4:0.0465:0:1.5 +17 73775739 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=Inf;LSEQ=TAAACCTACGAACGCCTACC;RSEQ=AACGCCGAAGTTTTAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:31.3:1:30.5:1:1:0:60:12:1:0:0.2 0/1:8:2:1,1:3,3:6,2:0.25:2,2:8.5:1:28.5:1:1:1:29:4:0.2857:0:2.5 +17 73775763 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=GCCGAAGTTTTAGGCCACTT;RSEQ=TCCGACCGCCGCGCCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:30.3:1:31.1:1:1:0:60:14:1:0:0.1 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:32:0:30:1:1:1.41:29:4:0.2857:0:2.5 +17 74017823 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51373;SOR=0;LSEQ=GTCGTCCTCCAGCTGGTTCA;RSEQ=GCTCTGCTCCTGGCTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:17,12:29,2:0.0645:2,2:31.5:1:29.5:1:1:1.40053:25.5:4:0.0645:0:1 0/0:20:0:0,0:11,9:20,0:0:2,0:32.9:1:30.9:1:1:0:37.3:40:1:0:0.3 +17 74681305 . C A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08866;SOR=Inf;LSEQ=TAGAGGCTGGCCCCACAAAC;RSEQ=CCGGCCCCCTTTCCCTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:195,56:251,0:0:2,0:22.2:1:31:1:1:0:60:82.667:1:0:0.1 0/1:203:3:2,1:157,43:200,3:0.0148:2,2:22:1:22.3:1:0.52147:1.81929:60:2:0.01:0:1.7 +17 74681435 . A G 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06829;LSEQ=CCCTTAAATCCTACAACGAG;RSEQ=CAGCCAGAGAGAAAGCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:516:511:195,316:2,0:2,511:0.9903:0,2:24.6:1:31.8:1:0.14701:0:59.9:72:0.9921:0:1.1 1/1:438:383:158,225:19,36:55,383:0.8744:2,2:25.3:1:30.4:1:0.38029:1.33:60:33.818:0.8753:0:1.1 +17 74681539 . A G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00051;SOR=3.08529;LSEQ=TTGCCCTGGCCCTGCCCAGC;RSEQ=GGTCCTCTCGGCTACTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:34:3,31:5,62:67,34:0.3366:2,2:24.4:1:31.6:1:1:1.20:60:68:0.3366:0:1.3 1/0:67:41:3,38:3,23:26,41:0.6119:2,2:19.7:1:31.2:1:0.6702:1.63932:60:82:0.6212:0:1.1 +17 74681613 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.26667;SOR=0;LSEQ=CTCATCTTGGGACACACACC;RSEQ=CGCCTGCCTGGGCTTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:0,22:0,0:0,22:1:0,1:18.5:1:30.8:1:1:0:60:10:1:0:1.1 1/1:8:7:0,7:0,1:1,7:0.875:0,0:21.6:1:31.6:1:1:0:60:14:0.875:0:1.4 +17 74717369 . A T 21 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22727;SOR=Inf;LSEQ=AGAGCTGGTCCCTCCAGGTC;RSEQ=GGGTTGGGACACAGTGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:17,0:0:1,0:28.5:1:30.8:1:1:0:60:34:1:0:0.2 0/1:16:2:1,1:14,0:14,2:0.125:1,2:14:1:21.5:1:0.125:0:60:4:0.125:0:1 +17 74717604 . C T 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.29868;LSEQ=GCTAGCTTTGAAAAACAAAA;RSEQ=ACAAAACAAAACGAGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:14:1:30:0:1:0:60:4:0.3333:0:1 0/1:5:2:0,2:0,3:3,2:0.4:0,0:29.5:1:29.5:1:1:0:60:4:0.4:0:1 +17 74732507 . A G 320 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9207;LSEQ=CGGCTGCGAGACCTGGAACG;RSEQ=CTCCGACTCCGGGATCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1166:1160:456,704:4,1:5,1160:0.9949:2,2:24.6:1:31.5:1:0.08269:6.16645:60:49.435:0.9956:0:1.1 1/1:1432:1424:583,841:6,2:8,1424:0.9944:2,2:25:1:30.6:1:0.0709:4.32335:60:60.913:0.9943:0:1.2 +17 74732811 . C T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.99181;LSEQ=ACCACGTGCTTCGCCGCGGA;RSEQ=CTTTGTGAGGTCGCCCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:0,1:61,19:80,1:0.0123:2,0:1:0:25:0:0.24691:0:60:2:0.0127:0:1 0/1:82:2:1,1:57,23:80,2:0.0244:2,2:17:1:25.5:1:0.50226:2.44728:60:4:0.0244:0:1 +17 74732824 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5003;SOR=Inf;LSEQ=CCGCGGACCTTTGTGAGGTC;RSEQ=CCCGGGCCTCCCGCGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:87,42:129,0:0:2,0:22:1:30.6:1:1:0:60:42:0.9921:0:0.2 0/1:148:2:1,1:90,54:144,2:0.0135:2,2:23.5:1:31.5:1:1:1.66052:60:4:0.0138:0:1 +17 74732830 . G T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62643;SOR=2.63257;LSEQ=ACCTTTGTGAGGTCGCCCGG;RSEQ=CCTCCCGCGCGCCCCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:0,1:102,59:161,1:0.0062:2,0:1:0:25:0:0.37037:0:60:2:0.0064:0:1 0/1:186:3:1,2:114,69:183,3:0.0161:2,2:12.7:1:28.3:1:0.55896:3.28252:60:6:0.0164:0:1.3 +17 74732842 . C T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10117;SOR=0;LSEQ=TCGCCCGGGCCTCCCGCGCG;RSEQ=CCCGCCCCGCCTCCCGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:3:0,3:132,85:217,3:0.0136:2,0:15.7:1:22:1:0.06269:0:60:2:0.0093:0:2.3 0/0:251:0:0,0:154,97:251,0:0:2,0:23.3:1:30.9:1:1:0:60:40.833:1:0:0.3 +17 74732844 . C T 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.6264;SOR=2.66306;LSEQ=GCCCGGGCCTCCCGCGCGCC;RSEQ=CGCCCCGCCTCCCGCGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:1:0,1:139,94:233,1:0.0043:2,0:1:0:29:0:0.40598:0:60:2:0.0043:0:1 0/1:265:3:0,3:161,101:262,3:0.0113:2,0:12:1:21.7:1:0.05938:0:60:2:0.0077:0:1.3 +17 74733099 . G A 312 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0105;LSEQ=CGGGACTCCTTGGTGTAGCG;RSEQ=TCCCGCGGGATGTACACGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1258:1256:661,595:1,1:2,1256:0.9984:2,2:24.6:1:30.4:1:1:1.11:59.7:51.333:0.9992:0:1.1 1/1:1419:1232:675,557:94,92:186,1232:0.8682:2,2:23.4:1:28.9:1:0.3048:1.19:59.8:50.333:0.8678:0:1.2 +17 74733365 . C T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01436;SOR=Inf;LSEQ=CACTGGGAAAGGCCTTGCCG;RSEQ=AGAACAGCACGGACGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:3,140:143,0:0:1,0:24.1:1:32.3:1:1:0:59.9:27.6:1:0:0.3 0/1:109:5:0,5:1,102:103,5:0.0459:1,0:14.6:1:24.6:1:1:0:60:10:0.0481:0:1.2 +17 74733403 . G A 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71081;SOR=0.83553;LSEQ=CTCCGCAGGCTAGCGCACCT;RSEQ=AGTAACAACTGGGCGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:48:3,45:0,29:29,48:0.6234:1,2:24.6:1:31:1:0.2864:0:60:47:0.6184:0:1.2 1/0:50:29:0,29:0,21:21,29:0.58:1,1:19:1:30.6:1:1:0:60:58:0.58:0:1 +17 76356096 . T G 28 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGGGCCGGGCGGGCGGC;RSEQ=GGCGGCTGGCTGCGTGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:28:1:1:0:60:4:1:0:1 +17 77278686 . T A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGTCACTGCACGGGGATG;RSEQ=GGCTGCAGGGCCGGCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 77280257 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08834;SOR=Inf;LSEQ=AGTACTTATAAATGGAGATG;RSEQ=CTTCTACAGGACAGTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:140,58:198,0:0:2,0:25.3:1:32.4:1:1:0:54.3:197:1:0:0.2 0/1:160:3:1,2:109,48:157,3:0.0188:2,2:22:1:26:1:0.2304:4.4938:55.3:6:0.0191:0:1.7 +17 77280267 . G A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00045;SOR=Inf;LSEQ=AATGGAGATGCCTTCTACAG;RSEQ=ACAGTTGATTCTCATCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:158,72:230,0:0:2,0:25.7:1:31.4:1:1:0:55.1:45:1:0:0.2 0/1:203:10:6,4:122,70:192,10:0.0493:2,2:22.2:1:27.2:1:1:1.16102:56.7:20:0.0503:0:1.7 +17 77280338 . G C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16859;SOR=0.80168;LSEQ=ACAGTCCGTTTCCAATGCAG;RSEQ=GTTGCTGAAGAGAATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:171:72,99:78,105:183,171:0.4817:2,2:26.8:1:30.9:1:1:1.02137:59.6:170:0.4843:0:1.1 0/1:335:143:65,78:80,110:190,143:0.4269:2,2:25.4:1:30:1:0.57741:1.15:60:142:0.429:0:1.2 +17 77280442 . A G 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATTTAATAACTTTCTTCA;RSEQ=TGTTTTGTTATTCCAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:6,84:90,0:0:2,0:20.6:1:31.5:1:1:0:59.4:89:1:0:0.4 0/1:34:10:1,9:3,21:24,10:0.2941:2,2:24.2:1:33:1:1:1.27668:60:20:0.2941:0:1.1 +17 77280452 . A G 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTTTCTTCAATGTTTTGTT;RSEQ=TTCCAAATCCACAACCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:37:1,36:1,24:25,37:0.5968:1,1:28.1:1:33.1:1:1:1.48993:59.4:74:0.5968:0:1 0/0:27:0:0,0:1,26:27,0:0:1,0:24:1:31.1:1:1:0:60:54:1:0:0.4 +17 77386075 . A G 105 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TCCGGGTCTCCGCAGCCTCC;RSEQ=GGTCTCCGCAGCCTCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:13,1:14,0:0:1,0:30:1:26.6:1:1:0:47.2:6:1:0:1.3 1/0:20:13:6,7:7,0:7,13:0.65:0,2:7:1:28.6:1:0.04445:0:24.7:26:0.6842:0:1.4 +17 77386092 . A G 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14084;SOR=0.38921;LSEQ=TCCAGGTCTCCGCAGCCTCC;RSEQ=GGTCTCCGCAGCCTCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:6,4:12,1:13,10:0.4167:1,2:4.9:1:27.9:1:0.12687:7.26989:31.6:9:0.4091:0:1.5 0/1:28:6:5,1:14,8:22,6:0.2143:2,2:11.5:1:30.2:1:0.62962:2.76:31.3:12:0.2222:0:1.8 +17 77386101 . C T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05311;SOR=Inf;LSEQ=CCGCAGCCTCCAGGTCTCCG;RSEQ=AGCCTCCAGGTCTCCGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:20,13:33,0:0:2,0:9.5:1:30:1:1:0:38.4:15.5:1:0:1.5 0/1:32:4:4,0:18,10:28,4:0.125:2,0:16:1:24.8:1:0.28268:0:25:8:0.1379:0:1.8 +17 77386106 . T G 76 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00782;SOR=0;LSEQ=GCCTCCAGGTCTCCGCAGCC;RSEQ=CCAGGTCTCCGTAGCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:8:7,1:16,18:34,8:0.1905:2,2:7.4:1:25.4:1:0.05408:7.54:37.1:7:0.1795:0:2 0/0:33:0:0,0:23,10:33,0:0:2,0:23.7:1:28.1:1:1:0:38.3:7.25:1:0:1 +17 77386109 . A G 62 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03005;SOR=0;LSEQ=TCCAGGTCTCCGCAGCCTCC;RSEQ=GGTCTCCGTAGCCTCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:6:6,0:17,20:37,6:0.1395:2,0:6.2:1:24:1:0.02292:0:33:5:0.125:0:2.3 0/0:35:0:0,0:24,11:35,0:0:2,0:24.5:1:29.3:1:1:0:39.5:34:1:0:0.9 +17 77386118 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06595;LSEQ=CCGCAGCCTCCAGGTCTCCG;RSEQ=AGCCTCCAGGTCTCCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:34:15,19:10,6:16,34:0.68:2,2:17.1:1:31.9:1:0.3635:2.0794:45.2:33:0.6875:0:1.4 0/1:42:5:4,1:23,14:37,5:0.119:2,2:5.4:1:31:1:0.63896:2.39:34.6:10:0.1282:0:1.6 +17 77452609 . G T 30 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCTCTCACCCAGGCTTTGC;RSEQ=CTGGGTTCCCAAAGGGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 77453148 . A G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18618;LSEQ=ACAGATGACACACACGTGGC;RSEQ=CAGGTGTAGACAGGCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:14:14,0:24,1:25,14:0.359:1,1:27.9:1:30.8:1:1:0:60:28:0.359:0:2.5 0/1:10:4:4,0:6,0:6,4:0.4:0,0:32.5:1:29.3:1:1:0:60:8:0.4:0:1.8 +17 77453159 . C G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4938;SOR=0.50628;LSEQ=ACACGTGGCACAGGTGTAGA;RSEQ=AGGCAGGGTGAGGTCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:18,0:23,1:24,18:0.4286:1,1:26.1:1:33.6:1:1:0:60:36:0.439:0:2.2 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:42.3:1:30.7:1:1:0:60:6:0.2727:0:2 +17 77453256 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51265;SOR=0;LSEQ=CCCCTGAGCAGAAGGCCTGG;RSEQ=CCCATGTCCAGCATGGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:144,45:189,2:0.0105:2,2:34.5:1:30:1:0.42463:3.17599:60:4:0.0108:0:1 0/0:136:0:0,0:102,34:136,0:0:2,0:23.4:1:30.1:1:1:0:60:33:1:0:0.3 +17 77453332 . A C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=0.58463;LSEQ=ACGGATGAGGGCCTCATGGC;RSEQ=TGGCCTCGGGTAGCAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:193:107,86:167,144:311,193:0.3807:2,2:26.9:1:31.8:1:0.71384:1.07:60:47.25:0.378:0:2.2 0/1:439:116:59,57:176,146:322,116:0.2642:2,2:27.3:1:30.2:1:0.51545:1.16421:60:28:0.2623:0:2.5 +17 77453340 . G A 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=95.59479;LSEQ=GGGCCTCATGGCATGGCCTC;RSEQ=GGTAGCAGTGGAAAAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:1:1,0:277,239:516,1:0.0019:2,0:1:0:31:0:1:0:58:2:0.002:0:1 0/1:441:69:36,33:189,183:372,69:0.1565:2,2:28.4:1:29.3:1:0.89594:1.06:60:68:0.156:0:3 +17 77453363 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=0.59093;LSEQ=TAGCAGTGGAAAAGGAGCTG;RSEQ=TGTGGAGACACAGGACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:510:203:105,98:144,161:305,203:0.398:2,2:24.6:1:32.4:1:0.36496:1.20:59.8:49.75:0.3948:0:2.4 0/1:381:107:47,60:131,143:274,107:0.2808:2,2:26.1:1:31:1:0.56797:1.16899:60:106:0.2797:0:2.8 +17 77453406 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.49694;LSEQ=TGGAATCAATAGCTCTCACC;RSEQ=TGTGGTGTGTGCCATCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:158:55,103:75,137:212,158:0.427:2,2:27.2:1:31.3:1:1:1.02515:59.8:78:0.4321:0:2.1 0/1:237:64:19,45:66,107:173,64:0.27:2,2:27.7:1:30.7:1:0.28571:1.45861:60:128:0.2712:0:2.2 +17 77453639 . A G 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCAGCAGCCCCGTGTAG;RSEQ=TGCCCCGGGACCTCCGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:33:1:27.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 77454426 . C T 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCCTTCACTCAGCTCCC;RSEQ=GCAATGTTGACGTCTCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:32:1:1:0:60:4:1:0:1 +17 78114602 . AT A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATAAAATGGGTACAATTT;RSEQ=TTTTTTTTTGAGACAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:30:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78431533 . A G 34 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACCTGCCACTGCCCTTCTT;RSEQ=TCCACACTCTTCCTGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:50:0:27:0:1:0:60:2:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:26:1:34:0:1:0:60:4:1:0:2.5 +17 78519169 . G A 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGCAGCCAGTGGCTTG;RSEQ=GACCTGGGGTGGTGTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:39:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:41:0:30:0:1:0:60:2:1:0:0 +17 78519325 . C A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50499;SOR=0;LSEQ=ATCCATTTGGTTTTCGATTT;RSEQ=CCGTTTTTGTTTCTTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:79,2:81,2:0.0241:1,2:8.5:1:25:0:0.07141:32.44332:60:4:0.0244:0:1 0/0:64:0:0,0:62,2:64,0:0:1,0:24.9:1:30.4:1:1:0:60:63:1:0:0.1 +17 78519382 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49903;SOR=0;LSEQ=GCTAGTTTTTAAGGCTGGAG;RSEQ=TTCTCGAGCGCTTGCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:151,44:195,2:0.0102:2,2:28.5:1:28.5:1:0.40557:3.40461:60:4:0.0102:0:3 0/0:187:0:0,0:134,53:187,0:0:2,0:40:0:15:0:1:0:60:0:0:0:3 +17 78519392 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11607;SOR=0;LSEQ=AAGGCTGGAGGTTCTCGAGC;RSEQ=CTTGCTGCCAAGGACTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:164,54:218,3:0.0136:2,2:21.7:1:29.7:1:1:1.51537:60:6:0.0137:0:2.3 0/0:231:0:0,0:150,81:231,0:0:2,0:23.3:1:29.3:1:1:0:60:45.2:1:0:0.3 +17 78519404 . G T 45 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36183;SOR=0.31563;LSEQ=TCTCGAGCGCTTGCTGCCAA;RSEQ=GACTCCCCCACCCCCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:183,75:258,3:0.0115:2,2:6:1:28.7:1:0.20877:4.84612:60:6:0.0118:0:1.3 0/0:274:1:1,0:169,104:273,1:0.0036:2,0:25:0:32:0:1:0:60:2:0.0037:0:1 +17 78519519 . T C 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGAACCTACCTTTGGCTTT;RSEQ=ATGAAAAAGAGGCACTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:0:0,0:274,275:549,0:0:2,0:25.5:1:29.5:1:1:0:60:77.429:1:0:0.1 0/1:530:87:42,45:219,224:443,87:0.1642:2,2:27.9:1:30.9:1:0.90677:1.04744:60:174:0.1657:0:1.1 +17 78599313 . G A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25909;SOR=0.32813;LSEQ=TGTGAAACCCTGCCTTCAAA;RSEQ=AAGGGCGTTACTCCTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:11,0:14,0:14,11:0.44:1,0:22:1:31:1:1:0:60:22:0.44:0:1.1 0/1:10:2:2,0:7,1:8,2:0.2:2,0:31:1:32:0:1:0:60:4:0.2:0:1 +17 78599401 . A G 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02768;SOR=Inf;LSEQ=GTGGGTAGGGAAGGGGCTCA;RSEQ=TGTTCTGGGGGACATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:80,2:82,0:0:1,0:23:1:30.9:1:1:0:59.9:164:1:0:0.1 0/1:58:4:4,0:54,0:54,4:0.069:1,0:22.5:1:33.3:1:1:0:60:8:0.0714:0:1 +17 78599562 . C G 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCCCGATGTGGTGAAGAC;RSEQ=ACGCCCTGTGCACGCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:842:0:0,0:383,458:841,0:0:2,0:24.9:1:31.5:1:1:0:60:63.692:0.9988:0:0.1 0/1:893:30:14,16:394,469:863,30:0.0336:2,2:25.6:1:29.5:1:1:1.04:60:60:0.0341:0:1.4 +17 78599655 . G T 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=159.4796;LSEQ=GCCGGCTCTGGCCTGGGCGG;RSEQ=GCTCGCCAAGCCTGTGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:0,1:18,179:197,1:0.0051:2,0:13:0:32:0:1:0:60:2:0.0051:0:1 0/1:162:73:9,64:12,77:89,73:0.4506:2,2:23.2:1:29.3:1:1:1.10751:59.8:146:0.4506:0:1.1 +17 78617338 . C T 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30502;SOR=0.38121;LSEQ=TAAAACACTGGCCTTCACGG;RSEQ=GTGTCAGCTTGTTTGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:12:10,2:26,0:26,12:0.3077:1,2:28.3:1:29.4:1:0.09388:0:60:24:0.3158:0:1.4 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:20:1:28:1:1:0:60:4:0.1538:0:1.5 +17 78617403 . G A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00095;SOR=0.27953;LSEQ=AACACTGATCAACCTTAGGC;RSEQ=TTGTGTTACTTTTAGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:42:41,1:53,1:54,42:0.4375:1,1:19.4:1:31.6:1:1:1.28918:60:41:0.4316:0:2.1 0/1:62:11:11,0:51,0:51,11:0.1774:1,0:22.6:1:30.1:1:1:0:60:22:0.1774:0:2.1 +17 78617439 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.01789;SOR=2.26504;LSEQ=TCAAAGGTGACTTTGAAGTG;RSEQ=GTTATATAAGGAGAAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:131:108,23:30,5:35,131:0.7892:2,2:26.8:1:31.6:1:0.80152:1.27594:60:42.667:0.7901:0:1.4 1/1:133:119:99,20:12,2:14,119:0.8947:2,2:25.9:1:31:1:1:1.21045:60:38.667:0.8923:0:1.2 +17 78617651 . G A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2631;SOR=0;LSEQ=CTTCCCTTTCCTTCTTACAG;RSEQ=GAAACTCCAGTTCCTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:69,197:266,3:0.0112:2,2:18.7:1:30.7:1:0.17119:5.67:60:6:0.0113:0:1 0/0:203:0:0,0:58,145:203,0:0:2,0:23.9:1:30.1:1:1:0:60:66.667:1:0:0.1 +17 78617681 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51525;SOR=0;LSEQ=GTTCCTTGGTTTCCAACACT;RSEQ=TTTGGATCCAAGTGAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:16,128:144,2:0.0136:2,2:9.5:1:30.5:1:0.22003:7.79:60:4:0.0138:0:1 0/0:101:0:0,0:13,87:100,0:0:2,0:20.1:1:31.3:1:1:0:60:200:0.9901:0:0.1 +17 78681520 . A G 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17256;SOR=1.53027;LSEQ=TTTTATAGATGGAGAAACTC;RSEQ=GAGCCATGTGTCCAGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:53:53,0:71,1:72,53:0.424:1,1:22.6:1:30.3:1:1:0:60:52:0.4194:0:1.6 1/0:66:35:34,1:30,1:31,35:0.5303:1,1:19.2:1:29.8:1:1:1.13:60:34:0.5231:0:1.7 +17 78681543 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.54219;SOR=0;LSEQ=GCCATGTGTCCAGGACCACA;RSEQ=AGCTATTAACTGCAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:182,11:193,2:0.0103:2,2:15.5:1:29.5:1:0.11959:15.87718:60:4:0.0104:0:1 0/0:106:0:0,0:97,9:106,0:0:2,0:24.1:1:31.5:1:1:0:60:34.333:1:0:1.2 +17 78681579 . G C 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCCAGAGGAAAGGGTAGGG;RSEQ=ATGAGTTCCAAGCATTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:283,96:379,0:0:2,0:23.8:1:30.9:1:1:0:60:62.167:1:0:0.9 0/1:278:18:13,5:187,73:260,18:0.0647:2,2:24.1:1:31.6:1:1:1.01:60:36:0.0657:0:1.9 +17 78681590 . A G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.2959;LSEQ=AGGGTAGGGGATGAGTTCCA;RSEQ=GCATTCCCTGGAGTCCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:457:345:247,98:75,36:111,345:0.7549:2,2:24:1:32.2:1:0.4724:1.21:60:85.25:0.7528:0:1.2 1/1:335:305:203,102:17,12:29,305:0.9104:2,2:24:1:30.8:1:0.41571:1.40:60:610:0.9132:0:1.3 +17 78681833 . G A 58 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34754;SOR=1.94089;LSEQ=CCAGCTTCCTTCCCGTTTCT;RSEQ=CCAAAAGCCATGCCAATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:4:3,1:190,425:615,4:0.0065:2,2:13.5:1:25.5:1:0.0922:6.69:60:8:0.0066:0:1 0/1:481:6:4,2:168,307:475,6:0.0125:2,2:11.5:1:22.8:1:0.19347:3.64:60:5:0.0105:0:1.2 +17 78681860 . C A 43 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14431;SOR=0;LSEQ=GCCATGCCAATTGCGGTGGT;RSEQ=GGAGCAGGTCCTGCCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:4:3,1:73,311:384,4:0.0103:2,2:10.8:1:21.8:1:0.02497:12.67:60:3:0.0079:0:1.3 0/0:279:0:0,0:75,204:279,0:0:2,0:23.4:1:29:1:1:0:60:54.8:1:0:0.1 +17 78681943 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09311;SOR=Inf;LSEQ=ACCCAAATGCCATAACTGAA;RSEQ=GGACCAGGTAGTCAGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:3,71:74,0:0:1,0:23.4:1:29.4:1:1:0:60:23.667:1:0:0.1 0/1:33:2:0,2:0,31:31,2:0.0606:1,0:24:1:31.5:1:1:0:60:4:0.0606:0:1.5 +17 78703899 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGAGGAGATGTGGAGAA;RSEQ=TTCAGTTTGATGGTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21:1:34:1:1:0:53.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78704240 . A C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61306;SOR=0.79275;LSEQ=ATAGTTTTGTATAAAGGCTA;RSEQ=CTCAGCGTCTCTCCAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:36:36,0:68,1:69,36:0.3429:1,1:27.8:1:32:1:1:0:60:35:0.3365:0:1 0/1:65:19:19,0:46,0:46,19:0.2923:1,1:20.5:1:31.5:1:1:0:60:18:0.2857:0:1.1 +17 78704264 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20303;SOR=Inf;LSEQ=AGCGTCTCTCCAGCCACCAG;RSEQ=CTCAATGTGTGTGCCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:146,18:164,0:0:2,0:23.7:1:31.5:1:1:0:60:40:1:0:0.3 0/1:135:2:1,1:116,17:133,2:0.0148:2,2:17.5:1:31:1:0.24975:6.66013:44:4:0.0153:0:1.5 +17 78704278 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23337;SOR=Inf;LSEQ=CACCAGGCTCAATGTGTGTG;RSEQ=CTTTTGTAACGGTGCAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:158,33:191,0:0:2,0:26.7:1:32.1:1:1:0:60:94.5:1:0:0.2 0/1:179:2:2,0:144,33:177,2:0.0112:2,0:27.5:1:31:0:1:0:60:4:0.0112:0:1 +17 78704479 . C A 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28859;SOR=2.85361;LSEQ=GTCAAGTCCTTCAAGCAGTT;RSEQ=GCACTACAGCGGGAGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:2:1,1:169,288:457,2:0.0044:2,2:2:1:25.5:1:1:1.70:60:4:0.0045:0:1 0/1:486:6:4,2:205,275:480,6:0.0123:2,2:21:1:27.3:1:0.40977:2.68:60:12:0.0125:0:1.2 +17 78704513 . G A 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00182;SOR=Inf;LSEQ=AGCAGGAGCTGGAGGTGAGC;RSEQ=CTCTGGTGCTTGGAGAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:89,216:305,0:0:2,0:24:1:31.4:1:1:0:60:42.571:1:0:0.1 0/1:311:10:3,7:100,201:301,10:0.0322:2,2:20.8:1:28.3:1:1:1.16031:56.6:9:0.0293:0:1.1 +17 78704550 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49914;SOR=Inf;LSEQ=GCGGTGCTGGGTTTGGTTTT;RSEQ=TTTTCCCTGGGGGTGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:28,132:160,0:0:2,0:24.5:1:32.3:1:1:0:60:39:1:0:0.1 0/1:172:2:1,1:35,135:170,2:0.0116:2,2:26.5:1:30:1:0.37576:3.82:60:4:0.0118:0:1 +17 78704563 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.49805;SOR=Inf;LSEQ=TGGTTTTGTTTTCCCTGGGG;RSEQ=TGGGGTTTGGGTGGGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:17,112:129,0:0:2,0:23.8:1:32.4:1:1:0:60:258:1:0:0.1 0/1:129:2:1,1:20,107:127,2:0.0155:2,2:20:0:30.5:1:0.30015:5.25:60:4:0.0156:0:1.5 +17 78704618 . G T 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65947;SOR=1.89513;LSEQ=CATCCTCTGAATGGAGCAGG;RSEQ=CTCAGAATGCCAAGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:3:0,3:0,44:44,3:0.0638:1,0:20.3:1:31:1:1:0:60:6:0.0638:0:1 0/1:26:3:0,3:0,23:23,3:0.1154:1,0:28.3:1:29:1:1:0:60:6:0.12:0:1 +17 78705418 . C A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGTTTCGATTAAGAGGC;RSEQ=TCCATCTTGTGGCCTGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78727548 . C T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GGTCCTGCAAAGAGGAAAAC;RSEQ=GGGAAGAAAACAGAGTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:21.5:1:28:1:1:0:60:3:0.3333:0:1.5 0/0:3:0:0,0:2,1:3,0:0:2,0:28.3:1:30:1:1:0:60:6:1:0:0.3 +17 78727734 . T C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01985;SOR=0.63237;LSEQ=TTTATTCTTTCCTTCTGTGT;RSEQ=ACAGCTGCAGCTTACTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:112:95,17:204,26:230,112:0.3275:2,2:22.9:1:32.3:1:0.3039:1.40264:60:111:0.3265:0:1.1 0/1:238:56:45,11:165,17:182,56:0.2353:2,2:23.6:1:31:1:0.05502:2.36249:60:55:0.2331:0:1.1 +17 78727756 . G T 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCTGCAGCTTACTATTTG;RSEQ=TTGTGACCAGCAGCTAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:391,127:518,0:0:2,0:23.2:1:31.2:1:1:0:60:63.75:1:0:0.3 0/1:439:20:13,7:303,115:418,20:0.0456:2,2:23.5:1:29.2:1:0.45234:1.41752:60:40:0.0463:0:1.1 +17 78728057 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14443;SOR=Inf;LSEQ=AGGGACCCCAACCCATGTGG;RSEQ=CCCCAGGCATTCACCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:11,135:146,0:0:2,0:27.3:1:32.6:1:1:0:60:145:1:0:0 0/1:90:2:1,1:6,82:88,2:0.0222:2,2:30.5:1:27.5:1:0.15031:12.73:60:4:0.0222:0:1 +17 78728314 . G A 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTGGACTTTCTTTCAGG;RSEQ=GAAGAAAAGGCTGTTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:38.5:1:33:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78765080 . A C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=0.0996;LSEQ=GCCTTGACAGAATGGCAATG;RSEQ=GATTTTCTTTACAAATCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:19:19,0:22,0:22,19:0.4634:1,1:21.6:1:32.8:1:1:0:60:38:0.4872:0:1.1 0/1:26:2:2,0:22,2:24,2:0.0769:2,0:9.5:1:32:1:1:0:60:4:0.0769:0:1 +17 78765219 . A G 270 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTGGGTGACTGTTCCATTC;RSEQ=TGCCGTTCACATTCTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:440:440:283,157:0,0:0,440:1:0,2:25.7:1:30.8:1:1:0:60:87:1:0:1.1 1/0:451:300:195,105:99,51:150,300:0.6652:2,2:24.3:1:29.8:1:0.91636:1.04516:60:74:0.6637:0:1.1 +17 78765477 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15417;SOR=Inf;LSEQ=TGTGTTTGTGATTGTCACAC;RSEQ=GGGGCTTAGTGCAGGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:0,58:58,0:0:1,0:25.1:1:31.3:1:1:0:60:116:1:0:0.1 0/1:38:2:1,1:4,32:36,2:0.0526:2,2:21.5:1:30:0:0.24893:7.27:60:4:0.0541:0:1 +17 78795868 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04298;SOR=2.07684;LSEQ=GATTCTCCCTGCCGTGCGCC;RSEQ=AGCTTCTGCTCAGAGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:40:39,1:60,0:60,40:0.4:1,1:21.1:1:30.2:1:0.4:0:59.2:80:0.4082:0:1.3 1/0:55:32:30,2:23,0:23,32:0.5818:1,2:20.6:1:30.3:1:0.50438:0:60:64:0.5818:0:1 +17 78795895 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14151;SOR=Inf;LSEQ=TGCTCAGAGCCTTCCTCCCT;RSEQ=GCTCAGAGCCTTTCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:162,3:165,0:0:1,0:23.3:1:32:1:1:0:59.9:54:1:0:0.4 0/1:100:2:2,0:94,4:98,2:0.02:1,0:31.5:1:32:0:1:0:60:4:0.0202:0:1 +17 78796361 . T A 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCGGTGCACAGCCCTTAC;RSEQ=GCGCACCGGCGGCTTATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:30:1:31.2:1:1:0:59.6:10:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78796595 . C CGTGT 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTACACCTGTATGTGTGTG;RSEQ=GTGTATTTGTGTATGCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:7,2:0.2222:2,0:24:1:29:1:1:0:49:4:0.2222:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78796666 . T C 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.35307;SOR=2.70428;LSEQ=CCTGTGCACACACATGTATG;RSEQ=ATGCATGTGTGCATGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:7,1:15,0:15,8:0.3478:1,2:21.4:1:32.3:1:0.34783:0:60:16:0.3478:0:1.3 1/0:5:3:3,0:1,1:2,3:0.6:2,0:22:1:33.3:1:0.4:0:60:6:0.6:0:1.3 +17 78796738 . CGT C 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1.50725;LSEQ=TGTGTACGTGTGTGTTTAAG;RSEQ=GTGTGTGTGTTGCTGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:2,0:50,3:53,2:0.0364:2,0:30:1:34:0:1:0:60:4:0.0364:0:0 0/1:37:2:1,1:30,5:35,2:0.0541:2,2:24.5:1:29:1:0.3018:5.56782:60:4:0.0541:0.027:0 +17 78796907 . C G 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAAAGCTCTTCAGACAGGA;RSEQ=TTGCTGGTGGCTAGTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:37:22,15:385,304:689,37:0.0508:2,2:25.6:1:32.6:1:0.73556:1.16:60:74:0.0514:0:1.1 0/0:620:0:0,0:336,283:619,0:0:2,0:25.3:1:31.1:1:1:0:60:87.429:1:0:0.2 +17 78797066 . T A 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGCCGTGCTCCCCCGCCC;RSEQ=CCGTGGCACTGTGATGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:13,172:185,0:0:2,0:23.6:1:29.5:1:1:0:60:22.125:1:0:0.1 0/1:133:15:4,11:17,101:118,15:0.1128:2,2:25.9:1:29.1:1:0.25635:2.15:60:30:0.1181:0:1.1 +17 78797072 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15969;SOR=Inf;LSEQ=GTGCTCCCCCGCCCTCCGTG;RSEQ=CACTGTGATGTCATGGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:6,148:154,0:0:1,0:26.2:1:32.2:1:1:0:60:50.333:1:0:0.1 0/1:103:2:1,1:15,85:100,2:0.0194:2,2:20.5:1:24.5:1:0.29043:5.52:60:4:0.0196:0:1 +17 78797412 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAATTAAACTGTTGGGCT;RSEQ=ATGATCAATTAGTTTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:25:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78809957 . G A 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTCAGGCCCTCATCCTCCGG;RSEQ=CGAGGCAGCGAGGCAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:32:0:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 +17 78811244 . T C 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCCTTTCCCTGACTGCA;RSEQ=GCCGACCCCTCCTGATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:22.3:1:34.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78811497 . G A 98 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25744;SOR=0.24744;LSEQ=ATGGTGAGGATGCTGGCAGC;RSEQ=CCAGCGTTCCCGGCCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:9:9,0:35,0:35,9:0.2045:1,0:21.7:1:31.1:1:1:0:60:18:0.2045:0:1.1 0/1:17:1:1,0:16,0:16,1:0.0588:1,0:26:0:32:0:1:0:60:2:0.0588:0:1 +17 78811530 . T C 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10319;SOR=Inf;LSEQ=GCCTGCACTCTCTCCTGGCC;RSEQ=CCCCTCGGACGTCTTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:75,0:75,0:0:1,0:25.3:1:32:1:1:0:60:74:1:0:0.2 0/1:36:2:1,1:34,0:34,2:0.0556:1,2:6:1:27.5:1:0.05556:0:60:4:0.0556:0:1 +17 78820023 . T C 105 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCCCCAGCTCGGTGCCC;RSEQ=GGCCAAAAGCCTTGGAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:0,10:1:0,0:23.6:1:31.9:1:1:0:60:20:1:0:1.1 1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:32:0:1:0:60:2:1:0:1 +17 78820167 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07214;SOR=0.36218;LSEQ=ATCCTCGCGGCCCTGCAGGG;RSEQ=GGGCCCTTCGTGAAGGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:22:22,0:120,3:123,22:0.1517:1,1:23.6:1:29.6:1:1:0:60:21:0.1489:0:2 0/1:66:4:4,0:60,2:62,4:0.0606:1,0:27.8:1:29.5:1:1:0:60:8:0.0625:0:2 +17 78820212 . G A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.38377;LSEQ=CCCGGCAGGTGGCAGGGGTG;RSEQ=GCAAGACCAGGCCATCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:232:180,52:90,23:113,232:0.6725:2,2:22.8:1:30.3:1:0.78104:1.13:60:28:0.6667:0:1.2 0/1:184:81:68,13:82,20:102,81:0.4402:2,2:26:1:28.7:1:0.56717:1.27:60:80:0.442:0:1.2 +17 78820329 . C T 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.47101;LSEQ=CAGGTGTGGCTCACCATGGG;RSEQ=GTGGAGAACCGAAACCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1118:729:369,360:188,198:386,729:0.6521:2,2:26.8:1:29.9:1:0.57115:1.08:60:59.75:0.6524:0:1.2 0/1:896:420:216,204:238,238:476,420:0.4688:2,2:24.9:1:28.7:1:0.68818:1.06:60:83:0.4721:0:1.1 +17 78820374 . G A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23037;LSEQ=CAGCTGCCCATCGTCCTGCA;RSEQ=GTGAGTTTCTTCAGACCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:951:342:140,202:258,351:609,342:0.3596:2,2:24.8:1:31.3:1:0.68159:1.06053:60:67.4:0.36:0:1.2 0/1:795:91:41,50:305,398:703,91:0.1145:2,2:27.4:1:29.7:1:0.8224:1.07:60:90:0.1144:0:1.2 +17 78821382 . G A 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGCCGTGGGGAGGGGCT;RSEQ=CCCAGCAGCAGGCAGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:23:0:31:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78828266 . T G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTGAGTGGGTTCAGCC;RSEQ=CAGGGTCATTTGGTAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78829114 . G C 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15805;SOR=0;LSEQ=CTAAAAGCATGAACTTGTAA;RSEQ=GAAAGGAGCACCAGCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:5:5,0:85,1:86,5:0.0549:1,0:29:1:33.2:1:1:0:55.8:10:0.0562:0:1 0/0:53:0:0,0:52,1:53,0:0:1,0:24.5:1:31.7:1:1:0:60:52:1:0:0.1 +17 78829361 . G A 59 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47776;SOR=2.10992;LSEQ=GAGCCTGGTGCGTGCCTTCC;RSEQ=CATTAACCTGGGGGCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:606:3:3,0:194,409:603,3:0.005:2,0:1:0:28:1:0.034:0:60:6:0.005:0:1 0/1:481:5:4,1:178,298:476,5:0.0104:2,2:10.4:1:25.8:1:0.07042:6.67:60:10:0.0105:0:1 +17 78829375 . G A 190 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=184.80704;LSEQ=CCTTCCGCATTAACCTGGGG;RSEQ=CTGAGGGAGGTGGGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:1:1,0:133,366:499,1:0.002:2,0:1:0:16:0:0.268:0:60:0:0:0:1 0/1:380:103:40,63:88,189:277,103:0.2711:2,2:22.9:1:28.5:1:0.22228:1.36:60:50.5:0.2708:0:1.2 +17 78829484 . T G 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCGAGTGTGTCCACCGTG;RSEQ=TGGTGTCCTGTCACTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:1,64:65,0:0:1,0:25.4:1:31:1:1:0:59.6:130:1:0:0.2 0/1:26:9:0,9:2,15:17,9:0.3462:2,0:22:1:30.7:1:0.52923:0:60:8:0.32:0:1.8 +17 78829531 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14879;SOR=6.79742;LSEQ=CAAGGAGCCCACTCTGTACC;RSEQ=GTGCAGCCTGCAGTGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:0,1:0,29:29,1:0.0333:1,0:8:0:32:0:1:0:60:2:0.0333:0:1 0/1:10:2:0,2:0,8:8,2:0.2:0,0:8.5:1:27:1:1:0:60:4:0.25:0:1.5 +17 78831135 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTGTTGAGCAAGCTGGC;RSEQ=GTGCCGTCACGGAGAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78831782 . G T 46 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2778;SOR=0;LSEQ=GAGCCCTGCGTTTCCAGCCT;RSEQ=CCCTTTCTCCAGCCTCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:1,2:29,261:290,3:0.0102:2,2:7.3:1:29.3:1:0.27764:4.46:60:6:0.0103:0:1 0/0:197:0:0,0:33,164:197,0:0:2,0:22.2:1:31.1:1:1:0:60:196:1:0:0.1 +17 78831881 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07071;SOR=Inf;LSEQ=CTCGGCAGCCACCTCTGGGT;RSEQ=GTGGGGGCTGTCACCTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:2,38:40,0:0:2,0:18.6:1:30:1:1:0:60:39:1:0:0.3 0/1:15:2:0,2:0,13:13,2:0.1333:1,0:30:1:31.5:1:1:0:60:4:0.1333:0:1 +17 78853252 . G A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCTCCCACTCCCACATCCC;RSEQ=GGCCTGGACCTGCCATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:45:0:28:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:10.5:1:29.5:1:1:0:60:4:0.6667:0:1.5 +17 78854056 . A G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.19813;LSEQ=AGGAAAGCATGTCTGCAGGC;RSEQ=CCGGCTGCAGCTGTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:12:12,0:62,2:64,12:0.1579:1,0:27.8:1:30.1:1:1:0:60:24:0.1622:0:1 1/0:47:30:30,0:16,1:17,30:0.6383:1,1:23.8:1:30.2:1:0.3617:0:60:60:0.6383:0:1.1 +17 78854223 . A G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1585;SOR=1.16618;LSEQ=CTTTCTGTCCAGTCGTGCCA;RSEQ=GCGGACCTCGTGAAGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1170:215:115,100:497,455:952,215:0.1838:2,2:26.2:1:32:1:0.76259:1.05:60:42:0.184:0:1.2 0/1:1005:209:104,105:393,402:795,209:0.208:2,2:24.2:1:30.4:1:0.93821:1.01:60:68.667:0.2077:0:1.2 +17 78854316 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25889;SOR=1.17683;LSEQ=ACGGGGCAGCACGCTCTCCA;RSEQ=GGGCTTGGGACTCAGCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:680:129:45,84:202,348:550,129:0.1897:2,2:26.4:1:30.6:1:0.76054:1.08342:60:128:0.1913:0:1.2 0/1:574:124:54,70:179,269:448,124:0.216:2,2:26:1:29.2:1:0.47192:1.16:60:123:0.2158:0:1.2 +17 78854370 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17466;SOR=Inf;LSEQ=CGCTGCACTGCGGTGGGGCC;RSEQ=TTTGACGGGGGCTACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:23,226:249,0:0:2,0:24.2:1:30.2:1:1:0:60:48.8:0.9959:0:0.2 0/1:180:2:1,1:33,145:178,2:0.0111:2,2:26:1:29.5:1:0.34295:4.34:60:4:0.0112:0:1 +17 78854487 . A G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06505;SOR=4.92265;LSEQ=CTACCATGAGCGCAGCTGTT;RSEQ=TTTCGTGTCTGTCTCTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:0,4:0,26:26,4:0.1333:1,0:28.5:1:32.3:1:1:0:56.8:8:0.1333:0:2.3 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:10.3:1:32.5:1:1:0:60:8:0.4444:0:1 +17 78854496 . C T 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GCGCAGCTGTTATTTCGTGT;RSEQ=TGTCTCTAAACAAGAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:0,4:0,25:25,4:0.1379:1,0:24:1:27.8:1:1:0:56.8:3:0.1071:0:2.3 0/0:5:0:0,0:0,5:5,0:0:0,0:5.4:1:31.4:1:1:0:60:10:1:0:0.4 +17 78857523 . A T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05948;SOR=Inf;LSEQ=GTTGTCCCGTGCAGGTACCC;RSEQ=CCACGTGCCTGCCATTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:285,82:367,0:0:2,0:24:1:30:1:1:0:59.9:39.778:1:0:0.1 0/1:236:3:1,2:168,65:233,3:0.0127:2,2:11:1:26:1:0.1949:5.12732:60:6:0.013:0:1 +17 78857631 . C T 162 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03123;LSEQ=ATCTGCCTGGAGCAGCTCAA;RSEQ=GACCCGCACCCCTTGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:861:40:17,23:397,424:821,40:0.0465:2,2:27.5:1:30.5:1:0.5191:1.26644:60:39:0.0461:0:1.1 0/0:659:1:0,1:342,316:658,1:0.0015:2,0:1:0:23:0:0.48103:0:60:2:0.0015:0:1 +17 78857700 . G A 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCTGGCAGAACTTCGACTC;RSEQ=GCGAGGTGGTGCGGCGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:861:0:0,0:408,453:861,0:0:2,0:25.2:1:30.5:1:1:0:60:65.231:1:0:0.2 0/1:689:76:36,40:296,317:613,76:0.1103:2,2:22:1:29.5:1:0.90366:1.03746:59.4:75:0.1106:0:1.2 +17 78857809 . G A 57 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0705;SOR=6.6535;LSEQ=CTCAGAGTCCAGTCCTCCTG;RSEQ=CTGCCGACTGCGGGGGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:1:1,0:115,287:402,1:0.0025:2,0:1:0:26:0:0.28784:0:60:2:0.0026:0:1 0/1:245:4:2,2:78,163:241,4:0.0163:2,2:21:1:28.5:1:0.5985:2.08:60:8:0.0168:0:1.3 +17 78857812 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04832;SOR=Inf;LSEQ=AGAGTCCAGTCCTCCTGGCT;RSEQ=CCGACTGCGGGGGTAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:108,276:384,0:0:2,0:23.8:1:31.6:1:1:0:59.9:41.667:1:0:0.2 0/1:221:3:2,1:68,150:218,3:0.0136:2,2:12.3:1:24.3:1:0.23633:4.38:60:6:0.014:0:1 +17 78857840 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5536;SOR=0;LSEQ=CGGGGGTAAGGCAGAGGTCT;RSEQ=CTCGCGTGCGGGTGTGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:3:0,3:34,192:226,3:0.0131:2,0:32.7:1:31.7:1:1:0:60:6:0.0137:0:1 0/0:114:0:0,0:18,96:114,0:0:2,0:22.6:1:31.2:1:1:0:60:37:1:0:0.2 +17 78857885 . G A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33077;SOR=1.6008;LSEQ=CGTGTCCAGGAACTTCAGGG;RSEQ=CTGCACGCTAATAAGAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:17:1,16:3,85:88,17:0.1619:1,1:28.6:1:30.6:1:0.51218:1.76:60:34:0.165:0:1.1 0/1:38:9:0,9:0,29:29,9:0.2368:1,0:26.3:1:28.2:1:1:0:60:18:0.2432:0:1.1 +17 78858122 . T A 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCCACTTTACGGGCAAGGAG;RSEQ=CAGGCCAGTGGCTCGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:4:0:29:0:1:0:60:2:0.3333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:8:1:29:1:1:0:60:4:1:0:2.5 +17 78858180 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGCGGGGCACTGCCCACAGA;RSEQ=TGGCCGCGGGCTGGAACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:35:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:27:1:1:0:60:4:1:0:3.5 +17 78858662 . A G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00498;SOR=3.42876;LSEQ=CCTTCCCCGTTGCCACTCTG;RSEQ=TAGTGCGAGGAGAGCCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:19:19,0:59,0:59,19:0.2436:1,1:28.9:1:31.9:1:1:0:60:38:0.2468:0:1.3 1/0:36:19:17,2:15,2:17,19:0.5278:2,2:21.4:1:30.3:1:1:1.13:60:38:0.5429:0:1.1 +17 78858769 . C T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=AGGCAGGCTGCAGCATGGCC;RSEQ=GGTGTGGGACATGCCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:0:0,0:322,143:465,0:0:2,0:25.3:1:30.7:1:1:0:60:92:0.9978:0:0.2 0/1:348:10:7,3:233,105:338,10:0.0287:2,2:23.5:1:30.8:1:1:1.05:60:20:0.0297:0:1 +17 78859004 . C T 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02552;SOR=1.64309;LSEQ=CCAGGCTGGACCCCGTGACA;RSEQ=CTGGGGCCAAGCCCGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:51:12,39:41,198:239,51:0.1759:2,2:22.5:1:29.6:1:0.31839:1.48:60:24.5:0.1725:0:1.1 0/1:204:53:15,38:36,114:150,53:0.2598:2,2:21.7:1:28:1:0.58176:1.25:60:25.5:0.255:0:1.1 +17 78859110 . G A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50783;SOR=1.65491;LSEQ=TTTCATTCTCTTCAAGTTGC;RSEQ=TTTCTTTACCAGACACCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:9:0,9:0,48:48,9:0.1579:1,0:18.9:1:31.8:1:1:0:60:18:0.1698:0:1 0/1:21:5:0,5:0,16:16,5:0.2381:1,0:28:1:30.6:1:1:0:60:10:0.2381:0:1 +17 78859284 . TC T 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAAGGTTTGTGTGCTGGG;RSEQ=CCCCCCAACACCCCATGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:21.5:1:33:0:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78860487 . G T 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGAGGCACTGAGACGAA;RSEQ=CTCCCCCTCCACCGGGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78863393 . C G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGAGAGAGAGGGGAGCT;RSEQ=CCACACCCCTGGCTGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45:0:32.5:1:1:0:60:4:1:0:1.5 +17 78865491 . C G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37623;LSEQ=TCATTTTCCAGCCCCAGTGA;RSEQ=TGTTATTGTCCCTTCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:148:111,37:268,89:357,148:0.2931:2,2:26.3:1:32.6:1:1:1.00374:59.9:48.333:0.2935:0:1.7 0/1:319:43:32,11:204,70:274,43:0.1348:2,2:26.5:1:30.7:1:1:1.00178:60:86:0.1374:0:1.5 +17 78865546 . T C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.97589;LSEQ=GTGGTGGCTCTGAGTCATCT;RSEQ=GTGGTTCAGTATGAAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:928:298:150,148:329,301:630,298:0.3211:2,2:25.7:1:31.1:1:0.62258:1.07836:60:98.333:0.3231:0:1.6 1/0:725:424:221,203:160,140:300,424:0.5848:2,2:25.8:1:29.9:1:0.76291:1.04973:60:211:0.5869:0:1.3 +17 78865630 . A G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21084;SOR=0.85167;LSEQ=TACGCCTTGCCTTCTCCAGC;RSEQ=ACCACAGGTATGGCGTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:668:225:85,140:157,285:442,225:0.3368:2,2:24.3:1:31.1:1:0.60946:1.10:60:111.5:0.3384:0:1.3 0/1:520:157:57,100:140,223:363,157:0.3019:2,2:23.4:1:29.7:1:0.69381:1.10119:60:30.4:0.2963:0:1.4 +17 78865662 . C A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14357;SOR=0;LSEQ=GGCGTCTTCTCCTGTGAACC;RSEQ=GCAGAGCACCTCGCCTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:4:2,2:104,279:383,4:0.0103:2,2:30.3:1:30.3:1:0.30222:2.67:60:8:0.0104:0:1 0/0:280:0:0,0:80,200:280,0:0:2,0:24.7:1:28.9:1:1:0:59.9:55:1:0:0.4 +17 78865824 . A G 100 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.3791;SOR=0.27776;LSEQ=AAAGGGCAGGAAAGAGGGCC;RSEQ=CACTGACCCTCTTACATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:0,8:1,14:15,8:0.3478:1,0:23.9:1:33.5:1:1:0:54.1:16:0.3478:0:1 0/1:8:1:0,1:0,7:7,1:0.125:0,0:33:0:32:0:1:0:60:2:0.125:0:1 +17 78866410 . A G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05162;SOR=1.9569;LSEQ=TGTGCAGCCCCTGCTCTGAC;RSEQ=TTTGTTGCAGCACAGGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:38:35,3:69,1:70,38:0.3519:1,2:24.6:1:29.7:1:0.12396:5.81345:60:76:0.3619:0:1 1/0:62:32:31,1:30,0:30,32:0.5161:1,1:25.1:1:28.7:1:1:0:60:31:0.5082:0:1 +17 78866732 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52661;SOR=0;LSEQ=GGTTGTTTTTTCTGAAACAC;RSEQ=GTATCTGAGTAAGCACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:22,153:175,2:0.0113:2,2:14:1:29:1:0.24364:6.82:60:4:0.0116:0:1 0/0:109:0:0,0:12,97:109,0:0:2,0:22.7:1:29.8:1:1:0:60:108:1:0:0.1 +17 78867041 . C T 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGTGTGTGCGCCGGGG;RSEQ=GTGTGTGCCAGGGTGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:24:1:26.5:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78867061 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGTGTGCCAGGGTGTGTG;RSEQ=GCCAGGGTGCGTGTGTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:33.5:1:29:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78867123 . C T 57 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTGTGCGCCAGGTGTGTG;RSEQ=GCGCGCCAGGTGTGTGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:2,0:2,4:0.6667:0,2:29.3:1:28.5:1:1:0:56.3:8:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78867242 . A G 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GTGTGTGCCAGGGTGTGTGT;RSEQ=CTGGGTGTGTATACGCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:3,1:7,0:7,4:0.3636:0,2:34.3:1:32.5:1:0.36364:0:60:8:0.4:0:2.8 0/0:3:0:0,0:2,1:3,0:0:2,0:25.3:1:21.7:1:1:0:60:2:1:0:1.3 +17 78867271 . CTGTACGCGCCAGGG C 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.34005;SOR=2.68912;LSEQ=GTATACGCGCCAGGTTGTGT;RSEQ=TGTGTGCGCCAGGGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:4,0:13,2:15,4:0.2105:2,0:27.8:1:32.8:1:1:0:60:8:0.2105:0:0.8 0/1:7:3:3,0:3,1:4,3:0.4286:2,0:10.3:1:30.4:1:1:0:60:6:0.4286:0.2857:0.3 +17 78867363 . GGT G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.13195;SOR=Inf;LSEQ=CCAGGGTGTGTGCGCACCAG;RSEQ=GTGTGTGTACCAGGGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:75,2:77,0:0:1,0:22.4:1:31:1:1:0:59.8:24.667:1:0:0.4 0/1:45:2:1,1:41,2:43,2:0.0444:1,2:33:1:31:1:0.1303:16.94013:60:4:0.0455:0:0.5 +17 78867377 . A G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=3.000;MSILEN=1;SSF=0.715;SOR=1.14897;LSEQ=CACCAGGGTGTGTGTGTACC;RSEQ=GGGTGTGTTTGTGCCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:29:28,1:62,1:63,29:0.3152:1,1:21.4:1:31.3:1:0.53344:2.19329:60:58:0.3258:0:1 0/1:52:18:18,0:31,3:34,18:0.3462:2,1:22.2:1:28.6:1:0.54308:0:60:17:0.3469:0:1.2 +17 78867453 . G T 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06828;SOR=Inf;LSEQ=AGTCATGCCATTAACTGTAA;RSEQ=ACCAAAAGGAGGGTCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:303,76:379,0:0:2,0:24.3:1:32.5:1:1:0:60:33.455:1:0:0.2 0/1:263:3:1,2:182,77:259,3:0.0114:2,2:5.7:1:25.3:1:0.21696:4.69556:60:6:0.0115:0:1 +17 78867691 . T A 60 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03877;SOR=4.96279;LSEQ=TCCGCCTGCCCCTTTCTGCT;RSEQ=CCGAGGGGCCCCGAGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:882:2:2,0:308,572:880,2:0.0023:2,0:1:0:23.5:1:0.12328:0:60:4:0.0023:0:1 0/1:627:7:6,1:233,387:620,7:0.0112:2,2:5.7:1:21.4:1:0.01401:9.93:60:6:0.0097:0:1.1 +17 78867733 . A G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.57854;LSEQ=CTCCCCACACAGAGCAGCAC;RSEQ=GACCTGTGTCTGCATCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:115:20,95:27,247:274,115:0.2956:2,2:22.6:1:30.9:1:0.04194:1.92:60:114:0.3024:0:1.1 1/0:248:149:28,121:16,83:99,149:0.6008:2,2:21:1:29.6:1:0.61595:1.20:60:28.8:0.5926:0:1.2 +17 78867822 . C T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11408;SOR=2.08238;LSEQ=GGACTGCGAGGCAGGGAGAA;RSEQ=GTTTTGCTGGGGCAAGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:20:0,20:0,42:42,20:0.3226:1,1:21.4:1:31.3:1:1:0:60:40:0.3226:0:1.5 1/0:30:15:0,15:0,15:15,15:0.5:1,1:19.8:1:29.6:1:1:0:60:30:0.5:0:1.7 +17 78867885 . T C 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17228;SOR=3.79788;LSEQ=TGGGGTAGTATTTTACAGGC;RSEQ=GCTCCGGAGCCATCGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:0,6:0,18:18,6:0.25:1,0:34.7:1:30.8:1:1:0:60:12:0.2609:0:2.2 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:16:1:31:0:1:0:60:8:0.5714:0:2.5 +17 78867906 . G A 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56459;SOR=2.4775;LSEQ=GCTCCGGAGCCATCGGAGCT;RSEQ=GCCAGTTTGGCTGGGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:0,5:0,13:13,5:0.2778:1,0:25.6:1:33.2:1:1:0:60:10:0.2778:0:2.2 1/0:4:2:0,2:0,2:2,2:0.5:0,0:26.5:1:32:0:1:0:60:4:0.5:0:3 +17 78868185 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGTCGGGCTGGGGGCTGTC;RSEQ=TCCCCGCCCTGCTCACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78869374 . G A 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGCTCAATACACATAAAC;RSEQ=GGCACGTGTGTGGTGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:32:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:16.5:1:29:1:1:0:60:4:1:0:0 +17 78869413 . G A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTTCTTCAGCGTGGATACAC;RSEQ=TGAGTGCCTCTCGCCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29.5:1:1:0:60:4:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:37:1:30.5:1:1:0:60:4:1:0:0 +17 78881443 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAGCCCGTGCCTGCCCCC;RSEQ=CTTCTGGTTTCCAAGTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:31:1:1:0:60:4:1:0:1.5 +17 78882329 . G A 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=GTGGTCATGCCCTCCGATCC;RSEQ=CTGAGGCATTTCAAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:31.4:1:30.4:1:1:0:59.3:14:1:0:1.1 0/0:1:0:0,0:1,0:1,0:0:0,0:49:0:32:0:1:0:60:2:1:0:0 +17 78882806 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.30108;LSEQ=GCATGCCAGGAACTCCAGGT;RSEQ=TGCCCGGGTCCACACCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:215:127:3,124:6,82:88,127:0.5907:2,1:24.8:1:31.7:1:0.16464:3.00863:60:254:0.5935:0:2.2 0/1:139:42:2,40:5,92:97,42:0.3022:2,1:22.3:1:30:1:1:1.08631:60:84:0.3022:0:2 +17 78882824 . CA TG 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12465;SOR=Inf;LSEQ=GTGTGCCCGGGTCCACACCA;RSEQ=GTTTAGAAAGTAACAAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:3,160:163,0:0:1,0:23.9:1:29.8:1:1:0:59.9:31.6:1:0:2.3 0/1:90:2:0,2:0,88:88,2:0.0222:1,0:29.5:1:31.8:1:1:0:60:4:0.0227:0:1 +17 78882825 . A G 227 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01128;LSEQ=TGTGCCCGGGTCCACACCAC;RSEQ=GTTTAGAAAGTAACAAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:156:155:3,152:0,1:1,155:0.9936:0,1:24.8:1:31.3:1:1:0:59.9:30:0.9934:0:2.4 1/0:87:55:0,55:0,30:30,55:0.6322:1,1:26.9:1:30:1:1:0:60:17.333:0.642:0:1.8 +17 78882840 . A G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.02819;LSEQ=ACCACAGTTTAGAAAGTAAC;RSEQ=AAACGAGCTTCAGCAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:116:109:2,107:0,7:7,109:0.9397:0,1:23.7:1:32.3:1:1:0:59.9:53.5:0.9469:0:2.6 0/1:67:20:0,20:0,47:47,20:0.2985:1,1:25.2:1:30.2:1:1:0:60:40:0.2985:0:2.9 +17 78882953 . G A 105 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.46629;LSEQ=GATTTACTGATGCCTGTCAA;RSEQ=GCAATTAGGGGAGGACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:0,10:0,9:9,10:0.5263:0,0:24.6:1:31.7:1:1:0:56.3:20:0.5263:0:1.8 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:30:0:32:0:1:0:60:2:0.3333:0:2 +17 78882972 . A C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51703;SOR=Inf;LSEQ=AGGCAATTAGGGGAGGACTG;RSEQ=CATTATCTTTCAGGATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:0,10:0,6:6,10:0.625:0,0:25:1:30.5:1:1:0:56.3:20:0.625:0:1.9 1/1:3:3:0,3:0,0:0,3:1:0,0:19:1:31.7:1:1:0:60:6:1:0:1.3 +17 78883030 . A AT 58 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTGCTGGCCCTTCTTCC;RSEQ=TTTTTTTTTTCTTTCTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:21.5:1:29.3:1:1:0:60:8:0.6667:0.1667:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78895788 . C T 29 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAAGGGCGGTCTTGAGTT;RSEQ=CAGGCCCCGTCACAGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78896428 . A T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0558;SOR=Inf;LSEQ=GGCCAAAGGCCTTTTCTGTG;RSEQ=TTCTGAAGCGGCTCCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:385,37:422,0:0:2,0:23:1:30:1:1:0:59.9:51.75:1:0:0.7 0/1:262:3:1,2:226,32:258,3:0.0115:2,2:13:1:27:1:0.04552:13.86123:60:6:0.0119:0:1 +17 78896488 . C T 324 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00097;LSEQ=GGCCTCCGCGGAGCACGTCC;RSEQ=GTCTGACCTTCACACCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1397:1393:808,585:3,1:4,1393:0.9971:2,2:25.8:1:31.1:1:0.64372:2.17093:59.9:91.867:0.9971:0:1.1 0/1:954:239:144,95:414,301:715,239:0.2505:2,2:23.9:1:29.9:1:0.5447:1.10:60:118.5:0.2511:0:1.2 +17 78896529 . C T 192 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=22.39879;LSEQ=TTCCTTTGCCCCTAGGCCAC;RSEQ=GTGAACGCCCGGCCGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1825:6:0,6:912,907:1819,6:0.0033:2,0:7.3:1:27.2:1:0.03099:0:60:12:0.0033:0:1.3 0/1:1409:97:48,49:667,645:1312,97:0.0688:2,2:22.5:1:29.2:1:0.83369:1.05564:60:23.25:0.0671:0:1.2 +17 78896762 . C T 199 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCTCCTCCCCCCTCTCCAG;RSEQ=GGGCGTTCTTTCCCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:90:90:0,90:0,0:0,90:1:0,1:22.3:1:30.8:1:1:0:59.7:44:1:0:2 0/1:32:9:0,9:1,22:23,9:0.2813:1,0:20.9:1:30.6:1:1:0:60:18:0.2813:0:2 +17 78896768 . T C 209 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=TCCCCCCTCTCCAGCGGGCG;RSEQ=TCTTTCCCTCTCCCTCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:76:0,76:0,0:0,76:1:0,1:23.3:1:33.6:1:1:0:59.6:152:1:0:2.2 1/0:32:24:1,23:0,8:8,24:0.75:0,1:24.6:1:32.7:1:1:0:60:48:0.75:0:1.4 +17 78897056 . C G 142 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=CCGCGCCACCTCCCAGGGTG;RSEQ=TGGAGTTCAATGAGGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:19,3:0,0:0,22:1:0,2:16.8:1:31.9:1:1:0:60:44:1:0:1 1/0:4:3:3,0:1,0:1,3:0.75:0,0:25:1:32.3:1:1:0:60:6:0.75:0:1 +17 78897146 . T C 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CAGCTGGGGTTCGGGAGCCA;RSEQ=GATGGCATGCTGGGTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:89,4:93,0:0:1,0:24.3:1:31.6:1:1:0:60:92:1:0:0.2 0/1:31:10:10,0:21,0:21,10:0.3226:1,0:21.2:1:32.4:1:1:0:60:20:0.3448:0:1 +17 78897209 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04407;SOR=Inf;LSEQ=CACCTGGGAGGGTGCAGGTG;RSEQ=CCCAGGAAGTTGTTCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:231,29:260,0:0:2,0:23.8:1:31.6:1:1:0:60:42.333:1:0:0.1 0/1:143:3:2,1:116,23:139,3:0.021:2,2:14.7:1:28:1:0.42867:2.50048:60:6:0.0221:0:1 +17 78897547 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGGGGCTCATGGCCTCAG;RSEQ=CTCAGGCTGCTCACATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:21,232:253,0:0:2,0:26.5:1:31:1:1:0:60:18.462:1:0:1.3 0/1:167:20:5,15:13,134:147,20:0.1198:2,2:22.2:1:28.9:1:0.04512:3.40:60:40:0.1227:0:2 +17 78897561 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02119;LSEQ=CCTCAGCCTCAGGCTGCTCA;RSEQ=ATCACCATGGGATGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:206:205:7,198:0,1:1,205:0.9951:0,1:26.2:1:28.5:1:1:0:60:67.333:0.9951:0:1.7 1/1:122:99:6,93:0,23:23,99:0.8115:1,2:21.7:1:27.9:1:0.59303:0:60:48.5:0.8083:0:1.7 +17 78897587 . A G 233 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02169;LSEQ=CATGGGATGGGGCAGGACCC;RSEQ=CCCTGCCGTCCTGGGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:138:0,138:0,1:1,138:0.9928:0,1:22.9:1:32.9:1:1:0:60:68:0.9927:0:2 1/0:63:47:0,47:0,16:16,47:0.746:1,1:22.7:1:31.9:1:1:0:60:22.5:0.7377:0:2.3 +17 78897674 . C T 151 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00106;SOR=0;LSEQ=GCACCCCTCTGCCTGCACTC;RSEQ=TTAGGAGCACTGCTGGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:1,28:0,0:0,29:1:0,1:22.7:1:31.1:1:1:0:60:58:1:0:1.7 1/0:8:4:1,3:1,3:4,4:0.5:2,2:11.3:1:31:1:1:1:48.5:8:0.5:0:1.5 +17 78897732 . CT TA 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00735;SOR=0;LSEQ=TGCACTCTTTAGGAGCACTG;RSEQ=GGGTGTGTCCCGGTTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:0,15:1:0,1:26:1:29.9:1:1:0:60:30:1:0:1.4 0/0:2:0:0,0:1,1:2,0:0:2,0:9:0:33.5:1:1:0:60:4:1:0:0.5 +17 78898600 . C G 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGTGCCCAGCCTCACT;RSEQ=CACAAGCACACACAGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42:1:32:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:36:0:34:0:1:0:60:2:1:0:1 +17 78898778 . T C 34 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGGAGTCCCCGCTCTCAG;RSEQ=CTGGTGTCACGGGGCCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24:1:34.5:1:1:0:60:4:1:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:23:0:32:0:1:0:60:2:1:0:2 +17 78898788 . C T 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCTCTCAGTCTGGTGTCA;RSEQ=GGGGCCATCACAGGAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:18.7:1:30.3:1:1:0:60:6:1:0:1.7 1/1:1:1:0,1:0,0:0,1:1:0,0:13:0:31:0:1:0:60:2:1:0:2 +17 78898912 . G A 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=AGAATTGACTTGGGAGCTGT;RSEQ=CTGGGTCGGCCCTGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:10,0:10,0:0:0,0:23.7:1:33.4:1:1:0:60:20:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:30.5:1:1:0:60:4:1:0:1.5 +17 78899307 . T A 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17707;SOR=5.04769;LSEQ=CCGGGGTGTGGGGTTCAGAG;RSEQ=AGAGTCCTAGCGAACATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:1:1,0:149,248:397,1:0.0025:2,0:1:0:28:0:0.37688:0:60:2:0.0026:0:1 0/1:318:4:3,1:119,194:313,4:0.0126:2,2:11.5:1:25.3:1:0.16073:4.87:60:8:0.0127:0:1 +17 78899365 . G C 34 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5111;SOR=0;LSEQ=AGCATAAACGCTCAAGGCTT;RSEQ=TGGCTGTGGGAGCGTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:10,124:134,2:0.0147:2,2:7:0:34.5:1:0.15577:11.87:60:4:0.0149:0:1.5 0/0:98:0:0,0:16,82:98,0:0:2,0:25.1:1:31.1:1:1:0:60:48:1:0:0.1 +17 78914245 . G T 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATACCCCATTGATACCAAGA;RSEQ=ACAACCCTGTTTCATCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:345:345:260,85:0,0:0,345:1:0,2:24.7:1:30.6:1:1:0:59.9:85.25:1:0:1.1 0/1:266:85:67,18:133,48:181,85:0.3195:2,2:19.8:1:29.8:1:0.36606:1.34:60:84:0.3243:0:1.1 +17 78914414 . G A 89 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54007;SOR=0.54684;LSEQ=TCAGAAGGGTAAGGGCACCC;RSEQ=CACAGCCAGCCAGGGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:8:5,3:238,395:633,8:0.0125:2,2:15.4:1:29.9:1:0.16305:2.76:60:16:0.0128:0:1.1 0/0:438:3:2,1:158,277:435,3:0.0068:2,2:11.7:1:28.3:1:0.3024:3.50:60:6:0.007:0:1 +17 78914465 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13372;SOR=Inf;LSEQ=GGGGCCTGGGGCGAGGGTCC;RSEQ=CTGTGAGCAGGCCCCCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:31,237:268,0:0:2,0:23:1:31.2:1:1:0:59.9:43.667:1:0:0.1 0/1:155:2:1,1:24,128:152,2:0.0129:2,2:16:1:31:0:0.29921:5.25:60:4:0.0132:0:1 +17 78914493 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00393;SOR=Inf;LSEQ=CAGGCCCCCCGCGGCCCACG;RSEQ=ACAACCTTCTCCAGCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:4,146:150,0:0:1,0:25.5:1:32.4:1:1:0:59.9:49:1:0:0.1 0/1:76:5:1,4:0,71:71,5:0.0658:1,2:19.8:1:26.6:1:0.06579:0:60:4:0.0548:0:1.4 +17 78914545 . A G 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGACCCGCCCCGCACCCC;RSEQ=CCTCCCTTGCAGATAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:3,65:68,0:0:1,0:22.6:1:30.1:1:1:0:60:67:1:0:0.2 0/1:27:12:0,12:0,15:15,12:0.4444:1,0:23.6:1:31.8:1:1:0:60:24:0.4444:0:1.4 +17 78914553 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0731;SOR=Inf;LSEQ=GCCCCGCACCCCACCTCCCT;RSEQ=GCAGATAAGCACATCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:2,56:58,0:0:1,0:22.7:1:30.9:1:1:0:60:116:1:0:0.1 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:29.5:1:27.5:1:1:0:60:4:0.0909:0:2 +17 78914748 . G A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCAGGTGGAACTCATGGA;RSEQ=GCGGAACTTTGCATGTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:37:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78919162 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCACTTTGGGAGGCCGAG;RSEQ=CGGGCAGATCACAAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:26.5:1:32:0:1:0:33:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78919327 . GCTTGCAGTGAGC G 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGTGAACCTGGGAGGCGGA;RSEQ=CAAGATTGCACCACTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:4:0:33:0:1:0:25:2:1:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:9:1:27.6:1:1:0:20:4:0.6667:0.6667:1 +17 78919349 . A G 166 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00076;SOR=0.05366;LSEQ=TTGCAGTGAGCCAAGATTGC;RSEQ=CCACTGCACTCCAGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:41:41,0:1,0:1,41:0.9762:0,1:9.1:1:31.1:1:1:0:28.9:40:0.9756:0:2 1/0:28:19:19,0:9,0:9,19:0.6786:0,1:9.1:1:30.6:1:1:0:27.8:38:0.6786:0:1.7 +17 78919387 . G A 241 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00517;LSEQ=GGGCGACAGAGCGAGACTCC;RSEQ=TCTCAAAAAAAATAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:229:227:197,30:1,0:1,227:0.9913:0,2:19.5:1:30.8:1:1:0:53.1:55.75:0.9911:0:1.3 0/1:153:56:50,6:83,13:96,56:0.366:2,2:23.5:1:29.4:1:0.80013:1.30:50.2:55:0.3667:0:1.3 +17 78919396 . AAAAT A 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=1.10304;LSEQ=AGCGAGACTCCGTCTCAAAA;RSEQ=AAATAAATAAATAAGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:5:4,1:279,63:342,5:0.0144:2,2:27.6:1:31.1:1:1:1.10683:48.4:10:0.0145:0.0029:1.2 0/1:252:4:4,0:204,44:248,4:0.0159:2,0:24.3:1:30.8:1:1:0:59.5:8:0.016:0.004:0.8 +17 78919466 . G T 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTGTGTGTTTCTTTTGACA;RSEQ=GCATTACGAGATTGGACGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1178:37:21,16:631,510:1141,37:0.0314:2,2:29.2:1:30.4:1:1:1.06:60:74:0.0321:0:1.4 0/0:966:0:0,0:521,444:965,0:0:2,0:26.6:1:30.5:1:1:0:60:40.957:1:0:0.2 +17 78919546 . G A 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09046;SOR=4.06533;LSEQ=GTGAAATTCCACCCCTTCAC;RSEQ=CCGTGCATCGCCGTAGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:2:2,0:250,458:708,2:0.0028:2,0:1:0:26:0:0.12565:0:60:4:0.0029:0:1 0/1:616:7:5,2:237,370:607,7:0.0114:2,2:11.4:1:26:1:0.11875:3.89:60:14:0.0116:0:1.7 +17 78919558 . C T 286 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00222;LSEQ=CCCTTCACGCCGTGCATCGC;RSEQ=GTAGCCGACAAGGACAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:626:623:210,413:0,2:2,623:0.9952:0,2:24.9:1:30.9:1:0.55308:0:60:68.222:0.9968:0:1.1 0/1:523:164:59,105:129,230:359,164:0.3136:2,2:26:1:29.6:1:1:1.00:60:163:0.3135:0:1.1 +17 78919590 . C T 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGACAGCATCTGGTATGCAC;RSEQ=GCGCTGGTCAGGCCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:0:0,0:83,278:361,0:0:2,0:23.3:1:30.2:1:1:0:59.9:71.2:1:0:0.9 0/1:326:24:8,16:88,214:302,24:0.0736:2,2:28.5:1:29.8:1:0.64755:1.22:60:48:0.0738:0:1.2 +17 78919837 . G C 62 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCCTGCAGGTCAGAGG;RSEQ=GAGTGGCAGGGACTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:27:1:31.3:1:1:0:60:8:1:0:2.3 1/1:1:1:0,1:0,0:0,1:1:0,0:1:0:31:0:1:0:60:2:1:0:1 +17 78919859 . G C 81 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGCAGGGACTCCCCAGT;RSEQ=ACACTTGTAATAGAGGCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:17.5:1:31.7:1:1:0:60:12:1:0:2.2 1/1:1:1:1,0:0,0:0,1:1:0,0:1:0:30:0:1:0:60:2:1:0:3 +17 78919892 . A G 45 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCGTACACAGGGGGGCC;RSEQ=GCTTGCTGCCCTGCCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:43:1:29:1:1:0:60:6:1:0:2.3 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:27.5:1:1:0:60:4:1:0:2.5 +17 78919920 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.1;SOR=Inf;LSEQ=GCCCTGCCCGCAGAAGCAAG;RSEQ=ATGTGATAGACAAGCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:15:1:33.7:1:1:0:60:6:1:0:2.3 1/1:2:2:1,1:0,0:0,2:1:0,2:38.5:1:27.5:1:1:0:60:4:1:0:2.5 +17 78920172 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTTAACCGTTCTGAGTGC;RSEQ=CAGCCAGTGGCATTCAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78920945 . G A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00424;SOR=Inf;LSEQ=TGGTTTTTTGATAGCAGCCC;RSEQ=GTGGGTTTCAGGAGGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:251,32:283,0:0:2,0:24.3:1:30.4:1:1:0:60:282:1:0:0.1 0/1:193:6:5,1:160,27:187,6:0.0311:2,2:21.7:1:29.3:1:1:1.18406:60:12:0.0313:0:1 +17 78920947 . T C 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00155;SOR=Inf;LSEQ=GTTTTTTGATAGCAGCCCGG;RSEQ=GGGTTTCAGGAGGTATCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:256,42:298,0:0:2,0:24:1:29.9:1:1:0:60:148:1:0:0.1 0/1:199:7:6,1:163,29:192,7:0.0352:2,2:29.1:1:29.6:1:1:1.07:60:14:0.0357:0:1.1 +17 78921108 . G A 170 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=63.58828;LSEQ=ACGAGGGTCACTGCCATGGA;RSEQ=TATCTGAACGGCCAGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:866:1:1,0:398,467:865,1:0.0012:2,0:1:0:30:0:0.46074:0:60:2:0.0012:0:1 0/1:758:52:23,29:318,388:706,52:0.0686:2,2:23.7:1:29.9:1:1:1.03335:60:51:0.0684:0:1.2 +17 78921117 . C T 203 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=74.76126;LSEQ=ACTGCCATGGAGTATCTGAA;RSEQ=GGCCAGGACTGCTCGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:796:2:1,1:354,440:794,2:0.0025:2,2:12.5:1:19:1:1:1.24:60:1:0.0013:0:1 0/1:699:111:43,68:260,327:587,111:0.1588:2,2:24:1:29.9:1:0.29764:1.25697:60:110:0.1599:0:1.1 +17 78921211 . G A 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGGAGGAGTGGCGGGGAGG;RSEQ=TGTGTGATCCTGAGATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:40,239:279,0:0:2,0:25:1:32.1:1:1:0:60:92:0.9964:0:0.2 0/1:186:24:2,22:34,128:162,24:0.129:2,2:20.5:1:29.1:1:0.17511:2.90888:60:11:0.1215:0:1 +17 78921916 . CG AT 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCTGGGCGGGAGGCAGG;RSEQ=GGGGAGGCCAGCACGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29.5:1:1:0:60:4:1:0:1 +17 78921988 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCTGTCCCTGTCGGCC;RSEQ=CAGCCCCTGGACACCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78922683 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCCCTGAAGAGCAGGGC;RSEQ=GTGCGTCCCTGCCCACGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78922952 . C G 99 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGAAGGGCAGCCCCGG;RSEQ=TCCCAGGGCAGCCAAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:0,10:1:0,0:20.4:1:30.1:1:1:0:56.8:9:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78923126 . T G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.11713;LSEQ=CCACGGGTAGTGAGTCAGGC;RSEQ=GGCCGCCCAGGGTCACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:54:53,1:92,0:92,54:0.3699:1,1:22.1:1:29.9:1:0.36986:0:60:26:0.3611:0:1.1 0/1:47:3:3,0:43,1:44,3:0.0638:1,0:21:1:31:0:1:0:60:6:0.0652:0:1 +17 78923151 . G A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00214;SOR=Inf;LSEQ=GCCCAGGGTCACTGCAGCAC;RSEQ=TCTGCCAGGAAGGGCTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:209,15:224,0:0:2,0:23.5:1:30.1:1:1:0:60:36.333:1:0:0.8 0/1:95:5:5,0:84,6:90,5:0.0526:2,0:25.2:1:30.2:1:1:0:60:10:0.0543:0:1 +17 78923178 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01057;SOR=0.62452;LSEQ=AGGAAGGGCTCTTACCACCA;RSEQ=GCACAGAGCACAGGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:342:200:171,29:114,28:142,200:0.5848:2,2:23.2:1:31.3:1:0.23901:1.45:60:65.667:0.5811:0:1.1 0/1:186:87:69,18:80,19:99,87:0.4677:2,2:20.6:1:29.1:1:0.85497:1.09784:59.9:20.75:0.4611:0:1.1 +17 78923193 . C T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06983;SOR=6.68061;LSEQ=CACCACGCACAGAGCACAGG;RSEQ=CAGGCCATCGAGGGGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:1:1,0:317,100:417,1:0.0024:2,0:36:0:32:0:1:0:60:2:0.0024:0:2 0/1:253:4:2,2:183,66:249,4:0.0158:2,2:26:1:29.3:1:0.29309:2.7596:60:8:0.0162:0:1.5 +17 78923203 . G T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0381;SOR=7.74813;LSEQ=AGAGCACAGGCCAGGCCATC;RSEQ=AGGGGCCTGGTTCACATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:1:0,1:354,139:493,1:0.002:2,0:1:0:24:0:0.2834:0:60:2:0.002:0:1 0/1:323:5:1,4:223,95:318,5:0.0155:2,2:16:1:25.4:1:0.03221:9.31999:60:10:0.0157:0:1.4 +17 78923325 . G A 75 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19992;SOR=0.31128;LSEQ=ACCGCGTGGCAGGGGCTCTC;RSEQ=GACATGCTGCCAACGACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:8:7,1:280,469:749,8:0.0106:2,2:8.6:1:25.3:1:0.00579:11.69:60:3:0.0081:0:1 0/0:604:2:2,0:256,346:602,2:0.0033:2,0:1:0:24:0:0.18205:0:60:4:0.0034:0:1 +17 78923355 . C T 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAACGACGCGAGGTGGGTC;RSEQ=GCCCGGCTCCTCCCCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:458:0:0,0:118,340:458,0:0:2,0:24.5:1:29.9:1:1:0:59.9:49.889:1:0:0.1 0/1:350:22:6,16:106,222:328,22:0.0629:2,2:17.5:1:27.8:1:0.81399:1.27247:60:10:0.0585:0:1.3 +17 78923388 . C T 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12787;SOR=Inf;LSEQ=CCCAGAGCAGAATGTGTTCC;RSEQ=GGGGCTGCGGACGCACTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:29,227:256,0:0:2,0:21.2:1:30.1:1:1:0:59.9:84.333:1:0:0.1 0/1:143:2:1,1:19,122:141,2:0.014:2,2:6.5:1:31.5:1:0.26101:6.28:60:4:0.0141:0:1 +17 78931260 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08734;SOR=Inf;LSEQ=GGACGTGGGGCACACCAGGG;RSEQ=CCCTAGCGGGAGCTCATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:55,1:56,0:0:1,0:22.5:1:29.8:1:1:0:60:112:1:0:0 0/1:24:2:2,0:19,3:22,2:0.0833:2,0:30.5:1:32.5:1:1:0:60:4:0.087:0:1 +17 78931354 . G T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29964;SOR=3.52402;LSEQ=GCTGGCCAAATTGCTGCCCA;RSEQ=AGCAGGCCCCAAAGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:1:0,1:249,69:318,1:0.0031:2,0:1:0:25:0:0.21944:0:60:2:0.0032:0:1 0/1:182:2:1,1:136,44:180,2:0.011:2,2:25:1:25:1:0.4344:3.06745:60:4:0.0112:0:1.5 +17 78931414 . A G 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGATGCCATGTCCCACTGT;RSEQ=TCTCTCCAGGAGCTGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:0:0,0:448,307:755,0:0:2,0:25.3:1:29.2:1:1:0:59.9:38.737:1:0:0.2 0/1:540:36:22,14:304,198:502,36:0.0667:2,2:23.5:1:31.6:1:1:1.02:58.7:72:0.0673:0:1.3 +17 78932003 . C CA 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCCTCCCACCTCACCCCC;RSEQ=CCCCCCACCACCAAGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:23.5:1:28:1:1:0:56.5:4:1:0.5:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78932006 . C G 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCCACCTCACCCCCCCC;RSEQ=CCCACCACCAAGTAGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:18.3:1:30:1:1:0:57.7:6:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 78933289 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAGTGCACAACCCAGCACC;RSEQ=CCCATCGTGCGTGGAAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:43.5:1:29.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:31.5:1:1:0:60:4:1:0:1.5 +17 78933424 . A G 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGACCCCTCCTGGACTC;RSEQ=TCCCATAGCTCATTAGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:24.4:1:28.2:1:1:0:60:4:1:0:1.4 1/1:1:1:0,1:0,0:0,1:1:0,0:37:0:32:0:1:0:60:2:1:0:1 +17 78933756 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATAGAGAGAAAGGCCCCT;RSEQ=CAGCCAGGGAGGGTGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:140,4:144,2:0.0136:1,2:33:1:31.5:1:0.06755:31.41546:60:4:0.014:0:1 0/0:65:0:0,0:61,4:65,0:0:2,0:22.2:1:31.7:1:1:0:59.6:64:1:0:0.1 +17 78934034 . G C 142 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.30463;LSEQ=ACCCTGTCCTCTCCCTCCCC;RSEQ=AGTGCTGGCAGGGTACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:1:1,0:124,336:460,1:0.0022:2,0:1:0:11:0:0.27115:0:60:0:0:0:2 0/1:356:24:8,16:102,229:331,24:0.0674:2,2:25.4:1:31.1:1:0.82078:1.12:60:48:0.0684:0:1.3 +17 78934088 . G A 200 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGTGTCACTGCCATTTGGTT;RSEQ=GGTCCAGGTTTCTCAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:68:2,66:6,88:94,68:0.4198:2,1:24.3:1:32.9:1:0.46971:2.23975:60:136:0.4198:0:1.1 0/0:89:0:0,0:5,84:89,0:0:2,0:23.9:1:30.6:1:1:0:60:178:1:0:0.1 +17 78935071 . G A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14338;LSEQ=ACTAGCCCCTCGTGGGGAGC;RSEQ=GACGGGCGAGGGCCTGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:110:65:64,1:45,0:45,65:0.5909:1,1:23.7:1:30.9:1:1:0:60:64:0.6095:0:1.1 0/1:53:9:9,0:44,0:44,9:0.1698:1,0:20.9:1:31.2:1:1:0:60:18:0.1765:0:1 +17 78935166 . C G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACGTCCTTCAGGGAAGCCC;RSEQ=ACGCTGAGCGTGCCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:397,204:601,0:0:2,0:23.6:1:31.3:1:1:0:60:59.1:0.9983:0:0.7 0/1:415:30:19,11:241,144:385,30:0.0723:2,2:26.6:1:30.1:1:1:1.03:60:60:0.0735:0:1 +17 78935197 . C T 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21305;LSEQ=TGCCCCCTCCCCTACAGCCG;RSEQ=GTCATGACGTACCGGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:847:542:321,221:182,123:305,542:0.6399:2,2:26.3:1:30.1:1:0.94193:1.0187:60:76.429:0.6415:0:1.1 0/1:645:177:98,79:267,201:468,177:0.2744:2,2:26.9:1:29.1:1:0.72225:1.07071:59.9:176:0.2772:0:1.1 +17 78936118 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0129;SOR=Inf;LSEQ=GGGCAGCCCTCACTGGGGAC;RSEQ=CTGAGCATCCAGGCAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:123,1:124,0:0:1,0:24.9:1:29.6:1:1:0:60:30:1:0:0.1 0/1:39:3:3,0:35,1:36,3:0.0769:1,0:12:1:31.3:1:1:0:60:6:0.0769:0:1 +17 78936409 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.38197;SOR=2.37294;LSEQ=CCACCTCCCTGGCCTGCACC;RSEQ=CTCACCCGCCTCGGGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:2:1,1:91,341:432,2:0.0046:2,2:7.5:1:30:1:0.37941:3.73:60:4:0.0047:0:1 0/1:277:3:1,2:74,200:274,3:0.0108:2,2:36.3:1:27.7:1:1:1.35:60:6:0.0109:0:1 +17 78936652 . C T 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00103;SOR=15.2599;LSEQ=GTCTAGCCGGCCTGTCCCCG;RSEQ=GGTCTCGGCATCTGCGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:1,0:215,17:232,1:0.0043:2,0:18:0:32:0:1:0:60:2:0.0043:0:1 0/1:145:9:8,1:124,12:136,9:0.0621:2,2:18.1:1:27.9:1:0.58142:1.28917:60:18:0.0625:0:1 +17 78937925 . C T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09516;SOR=0.59738;LSEQ=TGGGACCGGCCCGGCATTTC;RSEQ=GGGCCTGAGGTGGGCGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:158:99:95,4:59,0:59,99:0.6266:1,1:24.1:1:32.1:1:0.29761:0:60:32:0.6358:0:1.4 1/0:62:31:31,0:31,0:31,31:0.5:1,1:19.1:1:30.9:1:1:0:60:62:0.5082:0:1.6 +17 78938011 . C A 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCGCCCCCCCGCCCCCCG;RSEQ=AGTGTCTGCCCGCACCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:772:0:0,0:484,286:770,0:0:2,0:23:1:29.8:1:1:0:59.7:20.389:0.9986:0:1.3 0/1:545:59:33,26:284,201:485,59:0.1083:2,2:19.4:1:25:1:0.78001:1.113:59.7:2.278:0.0809:0:2 +17 78938191 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.28735;SOR=0;LSEQ=ACATAGTGAAGCTGTCACTC;RSEQ=CCGGGGCACGGGGCGTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:43,247:290,3:0.0102:2,2:17.7:1:27.3:1:0.06259:11.33:60:6:0.0103:0:1.3 0/0:185:0:0,0:38,145:183,0:0:2,0:19.7:1:30.4:1:1:0:60:182:1:0:0.2 +17 78938204 . G C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.36536;LSEQ=GTCACTCGCCGGGGCACGGG;RSEQ=CGTCGGCTGCTGCGGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:89:6,83:7,123:130,89:0.4045:2,2:23.4:1:30.9:1:0.77355:1.27:59.8:43.5:0.4028:0:1.1 0/1:126:25:5,20:13,86:99,25:0.1984:2,2:17.8:1:29.4:1:0.35918:1.65:60:24:0.1951:0:1.2 +17 78939414 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGGCGGTGAGAGGCCCA;RSEQ=GACCACGGGAGTGAGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 79088915 . G GT 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACTTCTTGTCTTGAGTC;RSEQ=TATTTGTGCATCAGCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:28:1:1:0:60:4:1:0:0 +17 79090448 . C A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.67603;SOR=1.84301;LSEQ=CTCCTGGGTGGACCTCCCCC;RSEQ=CCCACCTCCGCTGACTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:7,9:2,3:5,16:0.7619:2,2:24.8:1:30.6:1:1:1.16:60:32:0.7619:0:1.1 1/1:14:12:5,7:1,1:2,12:0.8571:2,2:24.1:1:27.6:1:1:1.36624:57.2:11:0.8462:0:1.6 +17 79915629 . A G 64 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCCCACACCCCTTCCATGC;RSEQ=CCCTGCACACCGTCCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:11:0:32:0:1:0:60:2:1:0:0 1/1:5:4:2,2:0,1:1,4:0.8:0,2:31.3:1:32:1:1:0:60:8:0.8:0:2 +17 79915647 . A G 62 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCACCCTGCACACCGTCCTC;RSEQ=CCCCTCACCTCCAGCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:32:0:1:0:60:2:1:0:0 1/1:5:4:2,2:0,1:1,4:0.8:0,2:31:1:31.3:1:1:0:60:8:0.8:0:2 +17 79988254 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGGTGCGCGTGGAGCT;RSEQ=CAGGAGCAGAACGGCCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:28.5:1:29.5:1:1:1.7321:60:4:0.4:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:31:1:32:1:1:0:60:4:1:0:0 +17 79988999 . G T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCGCGCGGCGGGGTTTG;RSEQ=AAATACAGCGCGTTTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:26.5:1:1:0:60:4:1:0:1 +17 79989619 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.15152;SOR=Inf;LSEQ=CGGCTCGCGGCCGCGCCCGC;RSEQ=GCCGCCCGGCCCGCGCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:6.9:1:28.9:1:1:0:60:6:1:0:0.1 0/1:5:2:1,1:2,1:3,2:0.4:2,2:29:0:31.5:1:1:1.7321:60:4:0.4:0:1.5 +17 79989710 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.11084;SOR=Inf;LSEQ=AGGCCGCTTGGCTGGGCTGG;RSEQ=CGGGAGGGGGGCTCGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:19,0:0:2,0:14.8:1:30.3:1:1:0:60:38:1:0:0.5 0/1:10:2:1,1:4,4:8,2:0.2:2,2:28:1:27:1:1:1:60:4:0.2:0:1 +17 79991603 . C T 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43628;SOR=2.02833;LSEQ=AAATACCTGGAGTGCTCAGC;RSEQ=CTGACCCAGCGGGGCCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:2,1:26,17:43,3:0.0652:2,2:30.3:1:32:1:1:1.30:60:6:0.0667:0:1 0/1:32:4:3,1:18,10:28,4:0.125:2,2:21.3:1:29:1:1:1.64:60:8:0.125:0:1 +17 79992613 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGTCGGGGTGTGGTGTGG;RSEQ=GAGTGAAGAGAGCAGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:40:1:30.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 79995436 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCTATACCTGCCGGGAGCG;RSEQ=GCTCAGTGAAGGCGTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:33:0:1:0:60:2:1:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:18.5:1:28.5:1:1:1.7321:60:4:0.4:0:1.5 +17 79996915 . T C 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTTCTTGTCCACTTCCA;RSEQ=GTTCCTCCCGTACTCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1:0,2:44:1:32.6:1:1:0:50.6:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 80759327 . C T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12768;SOR=0.72985;LSEQ=GGCGTGTGCGTCGTGTGGCT;RSEQ=GGAGTCAGCGTGGCAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:65:42,23:105,77:182,65:0.2632:2,2:25.1:1:29.6:1:0.37822:1.34:56.8:15.25:0.2563:0:1.3 0/1:300:62:41,21:141,97:238,62:0.2067:2,2:24.2:1:29.1:1:0.38179:1.34:55:30:0.2055:0:1.5 +17 80759400 . G A 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.41079;SOR=0.38166;LSEQ=GTGGCAGGATGGCGGCATGT;RSEQ=TGTCGTCGTGTGGCTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:4:3,1:79,116:195,4:0.0201:2,2:14.3:1:27.3:1:0.308:4.37:56.5:8:0.0219:0:1.5 0/0:258:2:2,0:100,155:255,2:0.0078:2,0:1:0:22.5:1:0.15658:0:52:4:0.0083:0:1.5 +17 80759416 . C A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25505;SOR=Inf;LSEQ=ATGTGTGTCGTCGTGTGGCT;RSEQ=AGGGTCAGCGTGGCAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:64,98:162,0:0:2,0:27.4:1:30.5:1:1:0:57.9:10.571:1:0:0.6 0/1:197:3:2,1:68,125:193,3:0.0152:2,2:22.3:1:22.3:1:0.29053:3.65:51.3:2:0.0113:0:2.7 +17 80759466 . C T 36 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12215;SOR=0;LSEQ=GCGTCGTGTGGCTCGGTCAG;RSEQ=GTGGCAGGAGGGTGGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:3:1,2:64,63:127,3:0.0229:2,2:5:1:23:1:1:2.02108:47:2:0.0174:0:1.3 0/0:132:0:0,0:57,75:132,0:0:2,0:21.6:1:28:1:1:0:55.2:7.8:1:0:1 +17 80759521 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49851;SOR=0;LSEQ=AGAGTCAGCGTGGCAGGAGG;RSEQ=CGGCGTGTGCGTTGTGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:88,61:149,2:0.0132:2,2:29:1:31.5:1:1:1.43902:57:4:0.0141:0:1 0/0:145:0:0,0:83,62:145,0:0:2,0:23.3:1:29.4:1:1:0:52.1:15.111:1:0:1 +17 80759523 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12248;SOR=Inf;LSEQ=AGTCAGCGTGGCAGGAGGGC;RSEQ=GCGTGTGCGTTGTGTGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:90,59:149,0:0:2,0:25.7:1:28.8:1:1:0:49.5:15.556:1:0:1.4 0/1:148:3:1,2:81,64:145,3:0.0203:2,2:19.3:1:27.3:1:0.58597:2.51567:43:6:0.0208:0:1.7 +17 80759541 . G C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19861;SOR=0.64462;LSEQ=GCGGCGTGTGCGTTGTGTGG;RSEQ=TCGGAGTCAGCGTGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:26:15,11:84,60:144,26:0.1512:2,2:18.4:1:28.5:1:1:1.02652:30.1:4.2:0.1522:0:2.7 0/1:175:18:10,8:86,68:154,18:0.1029:2,2:20.6:1:26.1:1:1:1.0117:25.4:2.6:0.0878:0:1.8 +17 80759544 . G A 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27663;SOR=0.38043;LSEQ=GCGTGTGCGTTGTGTGGGTC;RSEQ=GAGTCAGCGTGGCAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:5:2,3:97,68:165,5:0.0292:2,2:6.4:1:32:1:0.65044:2.12999:25.2:10:0.0336:0:2.8 0/1:177:2:0,2:100,75:175,2:0.0113:2,0:7:1:29.5:1:0.18785:0:22.5:4:0.0119:0:3 +17 80759562 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2489;SOR=Inf;LSEQ=TCGGAGTCAGCGTGGCAGGA;RSEQ=GGCGGCGTGTGCGTTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:104,80:184,0:0:2,0:22.6:1:30.3:1:1:0:47.4:11.267:1:0:1.3 0/1:197:3:1,2:97,97:194,3:0.0152:2,2:19:1:23:1:1:1.99322:57:2:0.0107:0:1.3 +17 80759565 . C T 100 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02833;SOR=0.2477;LSEQ=GAGTCAGCGTGGCAGGAGGG;RSEQ=GGCGTGTGCGTTGTGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:11:4,7:98,71:169,11:0.0601:2,2:11.6:1:29.1:1:0.21245:2.40359:24.6:22:0.0688:0:2.8 0/1:193:3:1,2:92,94:186,3:0.0155:2,2:4.7:1:30:1:1:1.95076:28.7:6:0.0175:0:1.7 +17 80759568 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCAGCGTGGCAGGAGGGCGG;RSEQ=GTGTGCGTTGTGTGGCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:107,74:181,0:0:2,0:23.6:1:29.3:1:1:0:47.8:10.313:1:0:1.3 0/1:200:26:13,13:91,83:174,26:0.13:2,2:28.3:1:26.5:1:0.83679:1.09588:48:7.667:0.123:0:2.3 +17 80759574 . C T 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3755;SOR=3.63657;LSEQ=TGGCAGGAGGGCGGCGTGTG;RSEQ=GTTGTGTGGCTCGGAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:0,1:117,78:195,1:0.0051:2,0:29:0:14:0:0.40306:0:54:0:0:0:2 0/1:219:4:1,3:113,101:214,4:0.0183:2,2:11.5:1:23.3:1:0.34992:3.33924:46.5:3:0.0148:0:1.5 +17 80759610 . A G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.30364;SOR=0.81998;LSEQ=GTCAGCGTGGCAGGAGGGTG;RSEQ=CGTGTGCGTGATCGTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:105:72,33:85,65:150,105:0.407:2,2:27.2:1:29.7:1:0.067:1.67:46:7.75:0.4429:0:2 0/1:225:81:50,31:72,67:139,81:0.36:2,2:25.9:1:28.6:1:0.1624:1.50:46.3:6.364:0.3723:0:2.1 +17 80759633 . A G 33 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52414;SOR=0.5382;LSEQ=TGTGCGTGATCGTGTGGCTC;RSEQ=GGGTCAGCGTGGCAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:7:5,2:190,93:283,7:0.0239:2,2:35.3:1:12.1:1:1:1.22:44.7:0.167:0.0044:0:3.6 0/1:231:3:2,1:145,81:226,3:0.013:2,2:19:1:20.7:1:1:1.12:54:2:0.0099:0:4 +17 80759687 . C T 129 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.84906;LSEQ=GTCGTGTGGCTCGGAGTCAG;RSEQ=GTGGCAGGAGGGCGGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:4:2,2:329,239:568,4:0.007:2,2:17.3:1:20:1:1:1.37577:43.3:1:0.0042:0:3 0/1:495:32:20,12:278,183:461,32:0.0646:2,2:21.7:1:25.8:1:0.85388:1.10:45.7:5.4:0.0609:0:1.4 +17 80759701 . G A 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.91612;LSEQ=AGTCAGCGTGGCAGGAGGGC;RSEQ=GCGTGTGCGTCGTGTGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:1:1,0:349,279:628,1:0.0016:2,0:44:0:16:0:1:0:27:0:0:0:3 0/1:569:20:15,5:311,238:549,20:0.0351:2,2:27.8:1:25.6:1:0.11327:2.29:46:2.333:0.0262:0:2.2 +17 80759703 . C T 62 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.36848;SOR=1.93063;LSEQ=TCAGCGTGGCAGGAGGGCGG;RSEQ=GTGTGCGTCGTGTGGTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:4:2,2:350,277:627,4:0.0062:2,2:25.3:1:20.8:1:1:1.26306:32.8:1:0.0037:0:1.3 0/1:585:7:1,6:329,246:575,7:0.012:2,2:11.7:1:22.1:1:0.04659:7.99957:41.3:2.5:0.0099:0:2 +17 80759723 . G C 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTGTGCGTCGTGTGGTTCG;RSEQ=AGTCAGCGTGGCAGGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:0:0,0:406,324:730,0:0:2,0:27:1:30.4:1:1:0:52.8:14.87:1:0:0.8 0/1:693:25:17,8:354,310:664,25:0.0361:2,2:24.7:1:27.5:1:0.15902:1.86:48:4:0.0316:0:2 +17 80759801 . C T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.50943;LSEQ=GAGGGCGGCGTGTGTGTCGT;RSEQ=GTGTGGCTCGGAGTCAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:258:94,164:154,218:372,258:0.4076:2,2:25.8:1:28.6:1:0.21481:1.23207:47:7.897:0.3935:0:1.9 0/1:663:172:70,102:211,280:491,172:0.2594:2,2:25.8:1:27.8:1:0.65414:1.09789:47.6:9.75:0.2476:0:1.8 +17 80759836 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02124;SOR=0.71885;LSEQ=CAGCGTGGCAGCAGGGTGGC;RSEQ=TGTGTGTCGTGTGGCTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:188:48,140:79,180:259,188:0.4206:2,2:23.8:1:31.8:1:0.28822:1.27939:50.6:93:0.4266:0:2.1 0/1:423:145:50,95:95,183:278,145:0.3428:2,2:24.6:1:30.1:1:1:1.01:53.5:71.5:0.3454:0:1.8 +17 80759875 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.21157;SOR=Inf;LSEQ=GGGTCAGCTCAGCCTCCCTG;RSEQ=CGTGGCAGCGTGTGTGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:33,164:197,0:0:2,0:22.7:1:32.1:1:1:0:59.7:48.25:0.9948:0:0.9 0/1:170:2:1,1:38,129:167,2:0.0118:2,2:23.5:1:27.5:1:0.40934:3.36:60:4:0.0121:0:1 +17 80759915 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36968;SOR=0.71332;LSEQ=CGTGTTGCTCAGAGGCGGTG;RSEQ=GGCCTCCCTGGTGTGGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:29:0,29:1,46:47,29:0.3816:1,1:22.9:1:30.4:1:1:0:60:58:0.3867:0:2.2 0/1:59:18:0,18:1,40:41,18:0.3051:1,1:31.1:1:28.7:1:1:0:60:17:0.2931:0:2.1 +17 80759933 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.98292;LSEQ=TGCGGCCTCCCTGGTGTGGA;RSEQ=GCGCTGTGGGGGAAAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:20:0,20:1,37:38,20:0.3448:1,1:30.1:1:30.4:1:1:0:59.8:40:0.3509:0:2.4 0/1:44:15:0,15:1,28:29,15:0.3409:1,1:32.7:1:30.4:1:1:0:60:30:0.3488:0:2.1 +17 80782917 . G C 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00385;SOR=Inf;LSEQ=ATGGGTGAGCTATTGCAGAT;RSEQ=ACCTTTGGAGGAATTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:81,33:114,0:0:2,0:25.4:1:31.9:1:1:0:60:37:1:0:0.1 0/1:97:7:4,3:64,26:90,7:0.0722:2,2:26.9:1:30.7:1:0.42346:1.83352:60:14:0.0745:0:1.1 +17 80782949 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22667;SOR=Inf;LSEQ=AATTGTGTCGGAGTGTAGAA;RSEQ=TTTCACAGTGTAGCTCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:87,61:148,0:0:2,0:25.4:1:31.1:1:1:0:60:296:1:0:0.3 0/1:135:2:1,1:82,51:133,2:0.0148:2,2:18.5:1:30.5:1:1:1.60193:60:4:0.015:0:1 +17 80782978 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23999;SOR=Inf;LSEQ=TGTAGCTCGCCATGCATCAG;RSEQ=CACATGTAGCCTGTGCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:85,79:164,0:0:2,0:24.8:1:31.6:1:1:0:60:328:1:0:0.4 0/1:158:2:1,1:86,70:156,2:0.0127:2,2:27:1:29.5:1:1:1.22696:60:4:0.0129:0:1 +17 80782994 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24318;SOR=Inf;LSEQ=TCAGGCACATGTAGCCTGTG;RSEQ=CACAACCATTGTGCTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:73,93:166,0:0:2,0:25.8:1:31.3:1:1:0:60:54.333:1:0:0.5 0/1:162:2:1,1:82,78:160,2:0.0123:2,2:42:1:28:1:1:1.05098:60:4:0.0126:0:2 +17 80783009 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00685;SOR=0.52221;LSEQ=CTGTGCCACAACCATTGTGC;RSEQ=TGGGCGGGGTTCTCCATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:68:27,41:41,60:101,68:0.4024:2,2:27.6:1:32.8:1:1:1.03744:60:136:0.4048:0:1.1 0/1:154:40:21,19:54,60:114,40:0.2597:2,2:23.6:1:30.2:1:0.5873:1.23:60:39:0.2566:0:1.2 +17 80783030 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49844;SOR=0;LSEQ=TGGGCGGGGTTCTCCATGCT;RSEQ=CCCTGTTGCAGGAGGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:59,97:156,2:0.0127:2,2:8:1:28.5:1:1:1.64:60:4:0.0128:0:2 0/0:155:0:0,0:70,85:155,0:0:2,0:24.6:1:31.2:1:1:0:60:76.5:1:0:0.4 +17 80783045 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22174;SOR=Inf;LSEQ=ATGCTGCCCTGTTGCAGGAG;RSEQ=ATGCTCTGCCCCTGCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:52,98:150,0:0:2,0:25.3:1:31.7:1:1:0:60:74:1:0:0.4 0/1:134:2:1,1:52,80:132,2:0.0149:2,2:39.5:1:29:1:1:1.53:60:4:0.0149:0:2 +17 80783049 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49989;SOR=0;LSEQ=TGCCCTGTTGCAGGAGGATG;RSEQ=TCTGCCCCTGCTTCTCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:51,91:142,2:0.0139:2,2:22.5:1:26.5:1:1:1.78:60:4:0.014:0:1.5 0/0:128:0:0,0:50,78:128,0:0:2,0:24.2:1:31.2:1:1:0:60:127:1:0:0.4 +17 80783051 . C A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.5697;LSEQ=CCCTGTTGCAGGAGGATGCT;RSEQ=TGCCCCTGCTTCTCCCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:50,91:141,2:0.014:2,2:26.5:1:31:1:1:1.81:60:4:0.0144:0:2 0/0:125:1:1,0:49,75:124,1:0.008:2,0:1:0:22:0:0.4:0:60:2:0.008:0:1 +17 80807777 . T C 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00363;SOR=Inf;LSEQ=TGCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:19,0:0:2,0:27.8:1:26.9:1:1:0:44.4:5.333:1:0:1 0/1:21:8:4,4:6,7:13,8:0.381:2,2:18.4:1:31.6:1:1:1.16:48:16:0.381:0:1.5 +17 80807852 . C T 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1968;SOR=0.22976;LSEQ=TGCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:2,5:3,3:6,7:0.5385:2,2:20.7:1:30.7:1:0.59207:2.32357:30.7:14:0.5385:0:1.1 0/1:10:2:1,1:3,5:8,2:0.2:2,2:28:1:28.5:1:1:1.58:32:4:0.2:0:1 +17 80807927 . T C 92 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGTTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:31.5:1:1:0:24:4:1:0:3 1/1:7:7:4,3:0,0:0,7:1:0,2:8:1:33.1:1:1:0:27.6:14:1:0:1.7 +17 80808007 . T C 60 d5;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGCTGCTGTTGGCTGTGTTG;RSEQ=TGTTGGCTGTGCTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:14:1:30:1:1:0:33.5:8:1:0:2 1/0:4:3:2,1:1,0:1,3:0.75:0,2:11:1:24:1:1:0:34.3:2:0.6667:0:3 +17 80808127 . T C 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=TGCTGCTGTTGGCTGTGCTG;RSEQ=TGTTGGCTGTGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:17.5:1:32.5:1:1:1.7321:25:4:0.4:0:2 0/0:11:0:0,0:5,6:11,0:0:2,0:24.7:1:27.8:1:1:0:38.4:10:1:0:0.4 +17 80808142 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.51515;SOR=Inf;LSEQ=TGCTGTTGTTGGCTGTGTTG;RSEQ=TGTTGGCTGTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:23.8:1:30.4:1:1:0:37.6:16:1:0:0.6 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:15.5:1:30:1:1:1.37:21:4:0.1429:0:1.5 +17 80808156 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50198;SOR=Inf;LSEQ=GTGTTGTTGTTGGCTGTGCT;RSEQ=CTGTTGGCTGTGCTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:9,0:0:2,0:24.3:1:32.8:1:1:0:37:18:1:0:1 0/1:14:2:1,1:4,8:12,2:0.1429:2,2:30.5:1:26.5:1:1:1.90:36.5:4:0.1429:0:1 +17 80808263 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GCTGTCCTGTTGTTGGCTGT;RSEQ=CTGTTGTTGGCTGTGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:2,3:5,2:0.2857:2,0:8:1:32:1:1:0:60:4:0.4:0:1 0/0:8:0:0,0:5,3:8,0:0:2,0:34:1:31.6:1:1:0:51.9:16:1:0:0.8 +17 80808318 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=5;SSF=0.53333;SOR=Inf;LSEQ=TGGCTGTGCTGTTGTTGGCT;RSEQ=TGCTGTTTTGCTGTTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:15.3:1:28.7:1:1:0:35.3:6:1:0:1 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:20:1:28:1:1:1:31:4:0.1667:0:1 +17 80808501 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15584;SOR=0;LSEQ=CTGTTGTTGGCTGTGCTGTT;RSEQ=TGCTGTTGGCTGTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:27.5:1:33:1:1:1.29:51:4:0.2222:0:1 0/0:13:0:0,0:7,6:13,0:0:2,0:30.7:1:29.6:1:1:0:38.1:26:1:0:0.2 +17 80808544 . T A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.21429;SOR=0;LSEQ=GGCTGTGCTGTTGTTGGTTG;RSEQ=GTGTGCTGACCCCGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:8,2:0.2:2,2:36.5:1:32:0:1:1.58:46.5:4:0.2:0:1 0/0:11:0:0,0:5,6:11,0:0:2,0:23.5:1:28.3:1:1:0:40.9:22:1:0:0.1 +17 81073882 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACTGACAAGCCCTGCGT;RSEQ=GACATGAGGTGCTGTCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:47.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +17 81075004 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCCAAAAGGTAGAGCCC;RSEQ=GTTCCTCTCCCCTGAACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:28.5:1:1:0:60:4:1:0:1 +18 110370 . C G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCTTGTCTAGGCTCTGT;RSEQ=TATGGGGGCATTGTGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:33.5:1:1:0:21:4:1:0:1.5 +18 111914 . A G 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GCGCAGGCGCAGAGGAGGCG;RSEQ=GCCGCCGGAGGGTGTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:13.3:1:25.3:1:1:0:47.3:2:1:0:2.3 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:30:1:1:0:24:4:1:0:2 +18 111921 . G A 29 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CGCAGAGGAGGCGAGCCGCC;RSEQ=GAGGGTGTCAGGCCTGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:20.3:1:30.3:1:1:0:47.3:6:1:0:2.3 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:29.5:1:1:0:24:4:1:0:2 +18 111923 . A AT 28 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CAGAGGAGGCGAGCCGCCGG;RSEQ=GGGTGTCAGGCCTGGACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:22.3:1:29.3:1:1:0:47.3:6:1:0:2.3 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:28.5:1:1:0:24:4:1:0:2 +18 724180 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01818;SOR=Inf;LSEQ=TACCATGCTGTCACCCACAC;RSEQ=GTCATCAGTATCTTAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:9,0:0:0,0:21.7:1:29.3:1:1:0:58.1:8:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:30.5:1:1:0:55.5:4:1:0:1 +18 724330 . G A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02523;SOR=Inf;LSEQ=TACCATTAAAAACATGCAGA;RSEQ=TAAAGAAGATTTTCTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:105,7:112,0:0:2,0:25.7:1:33.3:1:1:0:58.9:224:1:0:0 0/1:105:5:4,1:91,9:100,5:0.0476:2,2:20.6:1:29.2:1:0.39996:2.49694:60:10:0.0476:0:1.8 +18 724360 . T C 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TTTTCTTCTTTTGATTCCTG;RSEQ=AGAAAATCTACACAAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:177,38:215,0:0:2,0:22.1:1:29.7:1:1:0:59.7:214:1:0:0.1 0/1:211:15:9,6:153,43:196,15:0.0711:2,2:19.7:1:30.3:1:0.12017:2.36059:60:14:0.0667:0:1.3 +18 724555 . G T 42 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62355;SOR=0.33667;LSEQ=CAGATTCATCAATTCATGGA;RSEQ=GGATTCTGGACAGCCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:0,3:90,160:250,3:0.0119:2,0:11:1:27:1:0.55448:0:50:6:0.0119:0:2 0/0:249:1:0,1:99,149:248,1:0.004:2,0:1:0:25:0:1:0:60:2:0.0041:0:2 +18 724569 . C T 44 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12425;SOR=0;LSEQ=CATGGAGGGATTCTGGACAG;RSEQ=CCTGAGGGCACGGCATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:4:0,4:121,212:333,4:0.0118:2,0:9:1:22.3:1:0.30101:0:53:3:0.009:0:3 0/0:323:0:0,0:127,196:323,0:0:2,0:26.3:1:30.5:1:1:0:41.7:106.667:1:0:1.1 +18 724612 . A G 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCTCGCTCCACTTGTTCTA;RSEQ=TACTTCACGGTTCACCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:508:507:184,323:1,0:1,507:0.998:0,2:27:1:32.9:1:0.36417:0:48.4:125.75:0.998:0:1.1 1/1:482:482:189,293:0,0:0,482:1:0,2:26.7:1:31.6:1:1:0:47.8:159.667:1:0:1.1 +18 732812 . G C 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCACTCATGAGATAACCAA;RSEQ=AGCTATAAAATGCAAGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:737:0:0,0:487,250:737,0:0:2,0:26.3:1:32.5:1:1:0:60:66:1:0:0.1 0/1:700:21:11,10:409,269:678,21:0.03:2,2:31:1:31.5:1:0.5019:1.38154:60:42:0.0304:0:1.2 +18 736907 . G A 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TACAAGAATATTAGCAGCCC;RSEQ=AAGATCTCGGTGAATATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:264,445:709,0:0:2,0:25.1:1:31.1:1:1:0:59.2:77.778:0.9986:0:0.1 0/1:780:18:5,13:314,448:762,18:0.0231:2,2:29:1:30.8:1:0.33424:1.82101:30.3:36:0.0235:0:1.3 +18 739918 . AT A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.75765;SOR=0.89802;LSEQ=ACAAAACTTCTTAGCTTTTC;RSEQ=TTTTTTTAAATTTTGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:47:0,47:1,46:47,47:0.5:1,1:24.9:1:32.1:1:1:0:60:94:0.5054:0.0532:0.1 0/1:74:35:3,32:0,39:39,35:0.473:1,2:24.1:1:30.4:1:0.10097:0:60:70:0.4795:0.0541:0 +18 742845 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.219;SOR=Inf;LSEQ=TAAATTAGAAAACAGTATAA;RSEQ=TCTATATGCATACAAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:151,11:162,0:0:2,0:22.4:1:33.7:1:1:0:60:324:1:0:0.6 0/1:143:2:1,1:128,13:141,2:0.014:2,2:14:1:27.5:1:0.18684:9.52499:60:4:0.0142:0:2 +18 742858 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02975;SOR=0.64585;LSEQ=AGTATAAGTCTATATGCATA;RSEQ=AAATCAAGACTCTTAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:122:103,19:74,7:81,122:0.601:2,2:23.5:1:30.8:1:0.1984:1.94405:60:244:0.601:0:1 0/1:209:103:83,20:90,16:106,103:0.4928:2,2:20.4:1:29.7:1:0.46571:1.35344:60:206:0.4952:0:1.1 +18 743226 . A G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=0.68014;LSEQ=GCACTTTAATCCACAGCTAA;RSEQ=CAATGACAGAAAACAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:624:366:223,143:151,106:257,366:0.5865:2,2:24.8:1:32.6:1:0.61842:1.09:59.9:60:0.5844:0:1.1 0/1:776:381:228,153:235,159:394,381:0.491:2,2:24.4:1:31.3:1:1:1.01:60:94.25:0.4902:0:1.1 +18 743436 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01856;SOR=0.64949;LSEQ=CTAGATAAATGAATAAACTA;RSEQ=ACTGTAATATCAATTACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:255:151:24,127:19,85:104,151:0.5922:2,2:24.4:1:32.6:1:0.61476:1.18205:59.9:302:0.5992:0:1 0/1:235:114:17,97:28,92:120,114:0.4851:2,2:23.6:1:31.4:1:0.13491:1.73248:60:56:0.4848:0:1.1 +18 745884 . A C 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAAAAATAAATACTTTCACT;RSEQ=TATCTTTCTCAAAATACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:0:0,0:198,235:433,0:0:2,0:23.2:1:30:1:1:0:59.8:107.25:1:0:0.1 0/1:381:24:10,14:189,168:357,24:0.063:2,2:17.9:1:31.2:1:0.29983:1.57311:60:48:0.0632:0:1.1 +18 745924 . A T 52 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03024;SOR=Inf;LSEQ=CCCCAAGAAATTTTATACTT;RSEQ=TACTAATATAACAATATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:205,179:384,0:0:2,0:25.9:1:29.6:1:1:0:59.8:53.857:1:0:0.1 0/1:381:5:0,5:212,164:376,5:0.0131:2,0:10.6:1:22.4:1:0.01661:0:60:4:0.0106:0:2.4 +18 746126 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49859;SOR=Inf;LSEQ=ACAGAAGTGTCAGTAAGAAT;RSEQ=GACTGGGATAGGTTTGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:7,104:111,0:0:2,0:25.7:1:31.2:1:1:0:60:36:0.9908:0:0 0/1:121:2:0,2:10,108:118,2:0.0165:2,0:10.5:1:26:1:1:0:60:4:0.0169:0:1.5 +18 747825 . A G 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0061;SOR=Inf;LSEQ=AGCTGTATTAAGACTGGTAT;RSEQ=TAATTCTGTGTGTGTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:104,1:105,0:0:1,0:26.4:1:28.2:1:1:0:60:34:1:0:0.2 0/1:101:7:7,0:91,3:94,7:0.0693:1,0:19.1:1:31.6:1:1:0:60:14:0.0693:0:1 +18 748360 . C CT 44 d5;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTACTCAGTATTCTTTT;RSEQ=TTTTTTTTTTTTTTAAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:21:1:28:1:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 751596 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50107;SOR=0;LSEQ=ATCGTTAAACACAGTGGGCA;RSEQ=CCCATGCCCTACCTCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:2,0:97,1:98,2:0.02:1,0:26.5:1:32:1:1:0:60:4:0.0202:0:1 0/0:84:0:0,0:82,2:84,0:0:1,0:23.6:1:31.5:1:1:0:60:41:1:0:0 +18 751858 . GA G 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGCTAACTTAACAAAACA;RSEQ=AAAAAAGAACTATTGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:36,154:190,0:0:2,0:23.2:1:30.5:1:1:0:59.8:37:1:0:0.3 0/1:213:19:3,16:48,146:194,19:0.0892:2,2:24.9:1:31.3:1:0.57397:1.74937:60:38:0.0909:0:0 +18 751880 . C CA 157 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.00743;SOR=0.40331;LSEQ=AAAAAAGAACTATTGCCAGC;RSEQ=AAAAAAAAAAAAGCTTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:38:2,36:11,63:74,38:0.314:2,2:28.4:1:30.1:1:0.21263:3.11618:59.3:18:0.3103:0:0.3 0/1:103:16:1,15:11,70:81,16:0.1553:2,1:35.6:1:30.6:1:0.6838:2.34084:60:32:0.1616:0:0.7 +18 756282 . T TG 66 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTTCCCGGTGCCTACAG;RSEQ=GGGGGGGGGCTCAATAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:27.3:1:33.3:1:1:0:60:8:1:0:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 756505 . AC A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.2423;SOR=Inf;LSEQ=ACAAGCCTTAAGTATATATT;RSEQ=CCAAGGTGATGTTCTCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:166,14:180,0:0:2,0:21.5:1:32.1:1:1:0:59.7:89:1:0:0 0/1:175:2:1,1:152,21:173,2:0.0114:2,2:21.5:1:29.5:1:0.23626:7.09472:60:4:0.0117:0:0 +18 1784672 . A G 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGATGAATGGGTTTCCCCCC;RSEQ=GAAAAACACACAAAGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:20.5:1:31:1:1:0:60:4:1:0:0 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:14.5:1:27.5:1:1:1.41418:60:4:0.2857:0:1 +18 1785171 . C T 102 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00366;SOR=0;LSEQ=ATGATCACAATGTCTCTCCA;RSEQ=TGGGGCAGAGAACTGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:2,8:0,0:0,10:1:0,2:25.5:1:30.8:1:1:0:51.9:20:1:0:1 0/1:5:1:0,1:1,3:4,1:0.2:2,0:44:0:29:0:1:0:60:2:0.2:0:1 +18 2224625 . G A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=ATGGTAAAATTTACTCATTA;RSEQ=GAATACGTTGAGGTCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:107,11:118,0:0:2,0:24.1:1:33.1:1:1:0:60:117:1:0:0.2 0/1:65:8:7,1:51,5:56,8:0.1231:2,2:13.1:1:30.1:1:0.56694:1.44757:60:16:0.1231:0:2 +18 2224631 . C T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=4.06945;LSEQ=AAATTTACTCATTAGGAATA;RSEQ=GTTGAGGTCTTTTGGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:27:22,5:91,11:102,27:0.2093:2,2:22.6:1:30.6:1:0.32491:1.8698:60:26:0.2047:0:1 1/0:73:38:34,4:33,2:35,38:0.5205:2,2:20.5:1:30:1:0.67565:1.92416:60:76:0.5205:0:1.3 +18 2224638 . G T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53468;SOR=0;LSEQ=CTCATTAGGAATACGTTGAG;RSEQ=TCTTTTGGGAAACAAAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:134,19:153,2:0.0129:2,2:7.5:1:30.5:1:0.24214:6.8995:60:4:0.0129:0:1.5 0/0:89:0:0,0:76,13:89,0:0:2,0:20.8:1:30.8:1:1:0:60:88:1:0:0.6 +18 2224644 . TG T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.53025;SOR=0;LSEQ=AGGAATACGTTGAGGTCTTT;RSEQ=GGAAACAAAGCTAGTAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:143,31:174,2:0.0114:2,2:8.5:1:30:1:0.33143:4.55612:60:4:0.0115:0.0057:1 0/0:105:0:0,0:84,20:104,0:0:2,0:21.4:1:31.4:1:1:0:60:208:0.9905:0:0.6 +18 2224646 . G T 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00245;SOR=Inf;LSEQ=GAATACGTTGAGGTCTTTTG;RSEQ=GAAACAAAGCTAGTAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:147,33:180,0:0:2,0:22.8:1:31.2:1:1:0:59.9:59:1:0:0.2 0/1:107:6:6,0:80,21:101,6:0.0561:2,0:12.5:1:29.3:1:0.59532:0:60:12:0.0566:0:1.8 +18 2224742 . T C 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTAGAAATCCATCCTTGA;RSEQ=GTAAACTACACTGGTCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:0:0,0:241,262:503,0:0:2,0:28.5:1:30.5:1:1:0:59.9:34.929:1:0:0.1 0/1:403:95:49,46:154,154:308,95:0.2357:2,2:26.3:1:29.3:1:0.81515:1.07:60:30.667:0.2341:0:1.1 +18 2224790 . CT C 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.97512;LSEQ=GGTGTAATTTTAAATGGGTT;RSEQ=TTTTTTTTTTAATTCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:41:15,26:86,177:263,41:0.134:2,2:28.8:1:33:1:0.72172:1.19:59:82:0.1367:0.0065:0.2 0/1:267:35:13,22:86,134:220,35:0.1311:2,2:26.1:1:30.5:1:0.85454:1.08578:59.9:34:0.1303:0.0075:0.2 +18 2315063 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.46154;SOR=0;LSEQ=AATCAGATCCACAGTGTATT;RSEQ=TCTGTTCCGGTGGCCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:24.5:1:28:1:1:0:60:4:0.2857:0:1 0/0:7:0:0,0:6,1:7,0:0:2,0:17.7:1:31.1:1:1:0:60:14:1:0:0 +18 2547799 . A T 70 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCAGTAATTTTACTATT;RSEQ=ACAATATTTTTTTCTCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:20.5:1:32.5:1:1:0:60:4:1:0:1 1/1:5:5:5,0:0,0:0,5:1:0,0:18.4:1:30.4:1:1:0:60:10:1:0:1.4 +18 2547832 . A G 64 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3007;SOR=0.22461;LSEQ=TCTCCAATTCAAAATTAAGC;RSEQ=AATATTGTTGTTTAGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:16.8:1:32:0:1:0:60:8:0.5:0:1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:43:0:29:0:1:0:60:2:0.1667:0:2 +18 2548101 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06086;SOR=1.24925;LSEQ=CCCACTGCATTTGCAACCCC;RSEQ=AATCTATCATCTTGCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:204:96,108:194,209:403,204:0.3355:2,2:24.5:1:32:1:0.86345:1.0442:59.8:408:0.3377:0:1.8 0/1:654:253:117,136:199,201:400,253:0.3869:2,2:26.8:1:30.4:1:0.42163:1.15058:60:62.25:0.3866:0:1.9 +18 2548128 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01961;SOR=1.3345;LSEQ=TCATCTTGCTTTTTGCCTTC;RSEQ=CAGTCAATTCCACTGGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:547:174:74,100:168,204:372,174:0.3181:2,2:27.1:1:31.2:1:0.58022:1.11266:59.8:173:0.3198:0:1.9 0/1:615:236:100,136:173,206:379,236:0.3837:2,2:25.7:1:30:1:0.45306:1.14189:60:46.2:0.385:0:2 +18 2548199 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49973;SOR=0;LSEQ=ACAAAATCTATAATCTTGTA;RSEQ=CTCCTGGCCATAGAGTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:37,149:186,2:0.0106:2,2:16.5:1:28.5:1:0.36426:3.99:60:4:0.011:0:1.5 0/0:171:0:0,0:31,140:171,0:0:2,0:20.7:1:30.2:1:1:0:60:41.75:1:0:0.3 +18 2548202 . C A 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.13954;LSEQ=AAATCTATAATCTTGTACCT;RSEQ=CTGGCCATAGAGTATAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:2,0:29,142:171,2:0.0116:2,0:1:0:23:0:0.03125:0:60:4:0.0118:0:1.5 0/1:152:2:1,1:23,126:149,2:0.0132:2,2:9.5:1:25.5:1:0.29351:5.38:60:4:0.0137:0:1 +18 2548370 . C CA 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.19643;SOR=0;LSEQ=CTATAACTCATCCACCTTTG;RSEQ=AAAAAAAAACCCTGTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:31:1:31.7:1:1:0:60:6:0.6:0:1 0/0:3:0:0,0:1,2:3,0:0:2,0:29:1:32:1:1:0:60:6:1:0:0 +18 3406566 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49776;SOR=Inf;LSEQ=TACGCACATTAATTCTTTTG;RSEQ=CAAGAATCTTGCCCTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:84,24:108,0:0:2,0:20.2:1:31.6:1:1:0:46.4:107:0.9907:0:0.2 0/1:111:2:1,1:90,19:109,2:0.018:2,2:19:1:30.5:1:0.32924:4.64251:51:4:0.0182:0:1 +18 3406591 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01298;SOR=0.2695;LSEQ=AATCTTGCCCTTGTTTGTTT;RSEQ=TGCAATGCCAACAGCATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:17:12,5:85,40:125,17:0.1197:2,2:30.9:1:32.5:1:1:1.13:41.4:34:0.1206:0:1.1 0/1:142:5:3,2:95,42:137,5:0.0352:2,2:29.2:1:30.4:1:0.64528:1.5033:50.4:10:0.0352:0:1 +18 3406787 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19843;SOR=Inf;LSEQ=CCAGAGAACATATATCGGGT;RSEQ=CCTCTCCTCTTTCCTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:8,20:28,0:0:2,0:34.8:1:30.9:1:1:0:51.3:13:1:0:0.3 0/1:23:2:1,1:6,15:21,2:0.087:2,2:39:1:30:0:0.52569:2.39:54.5:4:0.087:0:1 +18 3406885 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16374;SOR=Inf;LSEQ=TTCTTTCTGCCATCTTCACT;RSEQ=ATCCAAAGGCAGGCTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:11,0:0:2,0:31.3:1:32.2:1:1:0:60:22:1:0:0.1 0/1:8:2:1,1:1,5:6,2:0.25:2,2:5.5:1:28:1:0.46429:3.87:60:4:0.25:0:1 +18 4131501 . C G 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CTTTTCTAGAACAAAAGCAG;RSEQ=CACAGACAATACATAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:20.8:1:31.4:1:1:0:60:10:0.7143:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:24:1:30:1:1:0:60:4:1:0:0 +18 4459041 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CTCTAGTTACATCAAAATGG;RSEQ=GGCACTCCTAGACCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:21.8:1:31.8:1:1:0:60:8:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:28.5:1:1:0:60:4:1:0:1 +18 4459279 . G A 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.20178;SOR=0;LSEQ=TGTGAAGGCCCTGGTGCCAT;RSEQ=TATGTCAAATTGATATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:96,86:182,2:0.0109:2,2:49:0:30.5:1:1:1.11561:42.5:4:0.0109:0:1 0/0:225:0:0,0:119,106:225,0:0:2,0:30.8:1:31.6:1:1:0:46:111.5:1:0:0.1 +18 7023484 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11551;SOR=Inf;LSEQ=TCAGACGGACTCTGTTCCCT;RSEQ=AGATTTACTGTGAAAGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:57,10:67,0:0:2,0:25.4:1:32.2:1:1:0:60:66:1:0:0.2 0/1:35:2:1,1:26,7:33,2:0.0571:2,2:32:0:31:1:0.41008:3.5403:60:4:0.0571:0:1.5 +18 7023508 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16823;SOR=Inf;LSEQ=TTTACTGTGAAAGGGATATG;RSEQ=CTCCCCACTCGGGCATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:63,24:87,0:0:2,0:25.2:1:29.5:1:1:0:60:86:1:0:0.2 0/1:61:2:1,1:42,17:59,2:0.0328:2,2:23.5:1:30:1:0.50656:2.42941:60:4:0.0328:0:1 +18 7023556 . G C 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCACCTGTCGCGGTGAAG;RSEQ=GGGAGAGCATCCAAAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:109,84:193,0:0:2,0:21.8:1:31.3:1:1:0:60:95.5:0.9948:0:0.2 0/1:132:28:16,12:58,46:104,28:0.2121:2,2:30.4:1:30.3:1:1:1.06:60:56:0.2154:0:2.9 +18 7023565 . A G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=22.667;LSEQ=TCGCGGTGAAGGGGGAGAGC;RSEQ=TCCAAAATGAGGCATAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:10:6,4:114,88:202,10:0.0472:2,2:24.4:1:31.4:1:1:1.16:60:20:0.0472:0:1.6 1/0:143:76:43,33:37,30:67,76:0.5315:2,2:27.8:1:30.2:1:1:1.06:60:152:0.5352:0:2.4 +18 7023594 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=32.72263;LSEQ=GAGGCATAAATCCAGGGGAC;RSEQ=TGCACCTGTTTCCAGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:9:4,5:128,121:249,9:0.0349:2,2:27.6:1:31.1:1:0.74457:1.32088:60:18:0.035:0:1.7 1/0:182:99:55,44:45,37:82,99:0.544:2,2:25.7:1:30.5:1:1:1.03:60:198:0.55:0:2 +18 7023637 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26571;SOR=0;LSEQ=TCTGACCCACCCCTGACCAC;RSEQ=CCGGATGCCGCACAGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:3:1,2:93,126:219,3:0.0135:2,2:12.7:1:26:1:1:1.4737:60:2:0.0097:0:2 0/0:163:0:0,0:79,84:163,0:0:2,0:25.8:1:28.6:1:1:0:60:31.6:1:0:0.7 +18 7023644 . GC G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50431;SOR=0;LSEQ=CACCCCTGACCACTCCGGAT;RSEQ=CGCACAGCCTCCTGCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:75,114:189,2:0.0105:2,2:13.5:1:32:1:1:1.52:60:4:0.0106:0:0.5 0/0:154:0:0,0:69,85:154,0:0:2,0:25:1:30.5:1:1:0:60:153:1:0:0.6 +18 7023652 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21799;SOR=Inf;LSEQ=ACCACTCCGGATGCCGCACA;RSEQ=CCTCCTGCAGGCTCAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:59,98:157,0:0:2,0:24.6:1:31.8:1:1:0:60:38.25:1:0:0.3 0/1:138:2:1,1:59,77:136,2:0.0145:2,2:31.5:1:29:1:1:1.30:60:4:0.0147:0:1.5 +18 7023705 . C T 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47659;SOR=1.87746;LSEQ=AGACGCACACATAGGAAAGA;RSEQ=AGCACTGGCCTTCAGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:0,3:3,48:51,3:0.0556:2,0:15.3:1:29.7:1:1:0:60:6:0.0556:0:1.3 0/1:50:5:0,5:9,35:44,5:0.1:2,0:22.6:1:27.2:1:0.56866:0:60:10:0.102:0:2 +18 7023733 . G C 122 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=49.73235;LSEQ=GCCTTCAGGAGCCAGAAGAC;RSEQ=GCTACTAAAGCAAACCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:0,31:31,1:0.0313:1,0:5:0:30:0:1:0:60:2:0.0357:0:2 1/0:30:19:1,18:0,11:11,19:0.6333:0,1:24:1:28.9:1:1:0:60:18:0.6207:0:2 +18 7023748 . C A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGACGGCTACTAAAGCAAA;RSEQ=CACCTGTCATCTCCAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:23,0:0:1,0:24.7:1:31:1:1:0:60:22:1:0:0.1 1/0:21:14:1,13:0,7:7,14:0.6667:0,1:27.4:1:28.5:1:1:0:60:13:0.65:0:2.3 +18 8412485 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20536;SOR=Inf;LSEQ=CCCCTCCCCTCTCCAACAGG;RSEQ=TCATCAACTCATATAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:59,14:73,0:0:2,0:21.4:1:32.5:1:1:0:60:72:1:0:0 0/1:61:2:1,1:47,12:59,2:0.0328:2,2:23.5:1:27:1:0.38361:3.80283:60:4:0.0351:0:1 +18 8412561 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21311;SOR=Inf;LSEQ=TATGATTGAAGAGGCATACA;RSEQ=GACAAAATAAGGCCACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:130,84:214,0:0:2,0:28:1:31:1:1:0:59.8:52.5:1:0:0.1 0/1:184:2:1,1:110,72:182,2:0.0109:2,2:41.5:1:30:1:1:1.52412:60:4:0.011:0:2 +18 8412650 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17667;SOR=Inf;LSEQ=CCAAGTATAACTATGTTGTG;RSEQ=ACAATACTAACCATCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:189,82:271,0:0:2,0:25.3:1:31.7:1:1:0:60:134.5:1:0:0 0/1:197:2:1,1:114,81:195,2:0.0102:2,2:15.5:1:26.5:1:1:1.4049:60:4:0.0104:0:1.5 +18 8412855 . CAGA C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0;SOR=2.2636;LSEQ=TCATGTTGGAGTTACTAGTT;RSEQ=AGAAGAAACAACTGGAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:68:30,38:206,272:478,68:0.1245:2,2:27.9:1:31.8:1:0.89642:1.04:57.5:67:0.1243:0.0092:0.1 0/1:439:107:43,64:143,189:332,107:0.2437:2,2:25.8:1:31:1:0.65321:1.12582:58:214:0.2454:0.0205:0.1 +18 8413015 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07847;SOR=Inf;LSEQ=TAAAAGAGTGGAAGAAATGA;RSEQ=TGGCTTACACTCTCCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:172,194:366,0:0:2,0:24.5:1:32.6:1:1:0:59.5:72.2:1:0:0.1 0/1:275:3:1,2:133,139:272,3:0.0109:2,2:25.3:1:29:1:1:1.90933:60:6:0.011:0:1 +18 8413075 . C A 33 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28002;SOR=0;LSEQ=TCAACTTGAAGCTCCTCCTG;RSEQ=ATCACACAGTAGTATTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:107,172:279,3:0.0106:2,2:6:1:21.3:1:0.56146:3.20:60:2:0.0072:0:1.7 0/0:186:0:0,0:72,114:186,0:0:2,0:24.2:1:31:1:1:0:59.4:45.5:1:0:0.2 +18 8413087 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.16731;SOR=Inf;LSEQ=TCCTCCTGCATCACACAGTA;RSEQ=TATTATGGATTCCACAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:80,149:229,0:0:2,0:22.7:1:32.4:1:1:0:60:228:1:0:0.1 0/1:159:2:1,1:61,96:157,2:0.0126:2,2:22:1:27.5:1:1:1.57:60:4:0.0127:0:1.5 +18 8413097 . T A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69543;LSEQ=TCACACAGTAGTATTATGGA;RSEQ=TCCACAGAATATAGCCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:60,122:182,2:0.0109:2,2:17:1:28.5:1:1:2.02:60:4:0.0112:0:1 0/0:132:1:1,0:46,85:131,1:0.0076:2,0:1:0:25:0:0.35606:0:60:2:0.0078:0:1 +18 8413099 . C T 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACACAGTAGTATTATGGATT;RSEQ=CACAGAATATAGCCAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:60,119:179,0:0:2,0:23.9:1:31:1:1:0:59.8:28.833:1:0:0.2 0/1:129:19:7,12:38,72:110,19:0.1473:2,2:27.1:1:28.1:1:1:1.10:60:38:0.1484:0:1.1 +18 8413193 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53226;SOR=0;LSEQ=TTAACATCAAAATTAAAATG;RSEQ=CCCACTGCTCATTTTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:78,67:145,2:0.0136:2,2:33.5:1:29:1:1:1.16297:60:4:0.0139:0:1 0/0:86:0:0,0:51,35:86,0:0:2,0:25.8:1:31:1:1:0:60:172:1:0:0.1 +18 8413202 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13263;SOR=Inf;LSEQ=AAATTAAAATGGCCCACTGC;RSEQ=CATTTTGAAGACCTGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:85,73:158,0:0:2,0:26.2:1:31.4:1:1:0:60:316:1:0:0.1 0/1:91:2:1,1:55,34:89,2:0.022:2,2:8.5:1:28.5:1:1:1.60874:60:4:0.0222:0:1.5 +18 8413255 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51668;SOR=0;LSEQ=TACAAGGTTGTCTCGTATCT;RSEQ=AGATGACAGTTGAACTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:87,82:169,2:0.0117:2,2:23:1:27.5:1:1:1.06064:60:4:0.0119:0:1 0/0:116:0:0,0:64,52:116,0:0:2,0:25.7:1:30.9:1:1:0:60:232:1:0:0.1 +18 8413300 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19604;SOR=Inf;LSEQ=ATTGGATGAACTTCAGAAAT;RSEQ=CTTGTCCAAGGTTACTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:63,65:128,0:0:2,0:25.7:1:32.7:1:1:0:60:256:1:0:0.1 0/1:103:2:2,0:46,54:100,2:0.0194:2,0:10:1:25:1:0.21899:0:60:4:0.0198:0:1.5 +18 8413344 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19735;SOR=Inf;LSEQ=AATCAATATGAACTTTAGCC;RSEQ=CATTATCATGCCCTAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:99,53:152,0:0:2,0:21.8:1:30.4:1:1:0:60:75:1:0:0.1 0/1:122:2:1,1:74,46:120,2:0.0164:2,2:13:1:27.5:1:1:1.60215:60:4:0.0164:0:1 +18 8413517 . G T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=7.46156;LSEQ=CATTACCGTGTGAATGAAAT;RSEQ=ACCTCAATTCCAAAATCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:90:53,37:287,204:491,90:0.1546:2,2:23.2:1:29.7:1:1:1.02:54.2:89:0.1556:0:1.1 1/0:431:249:158,91:119,63:182,249:0.5777:2,2:22.9:1:29:1:0.68555:1.08768:51.9:82:0.5748:0:1.1 +18 8413657 . G A 160 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GTCTAACAGGAGCGTGAGAA;RSEQ=AGGTGTTGAAGTGTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:39:21,18:266,341:607,39:0.0604:2,2:20.4:1:30.4:1:0.24658:1.49:59.3:38:0.0599:0:1.1 0/0:485:0:0,0:215,270:485,0:0:2,0:23.1:1:30.8:1:1:0:59.6:120.25:1:0:0.1 +18 8413804 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.14521;LSEQ=GTGCTGTGTTAAATTCAGCC;RSEQ=CTCTTCCAGATGCCATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:81:40,41:222,236:458,81:0.1503:2,2:25.8:1:30.1:1:0.90446:1.04:49.2:80:0.1527:0:1.1 0/1:534:191:87,104:154,189:343,191:0.3577:2,2:24.3:1:28.9:1:0.92778:1.03:50.2:190:0.3598:0:1.1 +18 8413833 . T C 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=Inf;LSEQ=GATGCCATTTGGCTTTTGGC;RSEQ=GTGCGGATCATTGTGTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:245,276:521,0:0:2,0:22.5:1:30.8:1:1:0:58.4:56.889:1:0:0.2 0/1:433:11:4,7:187,234:421,11:0.0254:2,2:26.7:1:30.2:1:0.76167:1.39744:60:22:0.0255:0:1.1 +18 8413903 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.6273;LSEQ=AATCATGGTATTCAAAGGAC;RSEQ=CCAAAAAGCAGTCTCTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:673:116:66,50:280,277:557,116:0.1724:2,2:26.1:1:30.2:1:0.22058:1.31:44.6:37.667:0.1699:0:1.2 0/1:520:184:91,93:174,162:336,184:0.3538:2,2:26.9:1:29.1:1:0.64684:1.09748:43.3:183:0.3567:0:1.2 +18 8413996 . A G 283 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01432;LSEQ=AACACTGTGGAATGTAGGGA;RSEQ=ACTGTACTGCCTACATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:415:413:170,243:1,0:1,413:0.9952:0,2:23.6:1:32.6:1:0.41304:0:59.3:81.6:0.9976:0:1.1 1/0:308:230:101,129:36,42:78,230:0.7468:2,2:23.3:1:30.8:1:0.79235:1.09444:59.7:75.667:0.7467:0:1.2 +18 8414149 . T C 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTTTGCTAACTTTTAAGT;RSEQ=TGATACAGTCAAAAGTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:238,251:489,0:0:2,0:26.1:1:30.6:1:1:0:47.6:68.857:0.9979:0:0.1 0/1:444:17:9,8:229,198:427,17:0.0383:2,2:30.2:1:30.2:1:1:1.028:44.9:16:0.0367:0:1.3 +18 8414275 . A AG 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=GCTGATTGCTGCTAACAGTG;RSEQ=GGGTACAATTAAGGTGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:130,159:289,0:0:2,0:24.1:1:31.2:1:1:0:59.4:95.333:0.9965:0:0.3 0/1:241:12:5,7:99,130:229,12:0.0498:2,2:22:1:30.3:1:1:1.06589:60:24:0.0504:0.0124:0.1 +18 8414345 . T A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.06267;LSEQ=AATGTACTTGATCCTGCTGA;RSEQ=ATACCTCTGCAGCTGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:223:201:90,111:8,14:22,201:0.9013:2,2:26.3:1:30.7:1:0.5041:1.42:47.4:402:0.9013:0:1.1 0/1:185:67:26,41:43,75:118,67:0.3622:2,2:30.6:1:29.7:1:0.75438:1.11:50.2:66:0.3626:0:1.1 +18 8414713 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAAATTATGTAGGTTA;RSEQ=AACATGCAGAAGTACAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:22.5:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 8785010 . G GT 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTCTTGGTTGGGCTCC;RSEQ=TTTTTTTTGTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:26.5:1:29:1:0.33333:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 8785069 . C T 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTGTTTCTTTTTCCTTT;RSEQ=TCCTGTCTTATTTTTAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:19:1:30.5:1:1:0:60:8:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 8786031 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=CGCGCGGGAGCTGCACCGCC;RSEQ=CGCAGACGGGGACACCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:22.1:1:27:1:1:0:60:6:1:0:0.1 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:18.5:1:28.5:1:0.33333:0:60:4:0.6667:0:1.5 +18 8786053 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02064;SOR=Inf;LSEQ=GCAGACGGGGACACCGGGAG;RSEQ=CACGGGCTGGGAGGCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,5:12,0:0:2,0:25.5:1:31:1:1:0:59.6:24:1:0:0.1 1/0:6:3:1,2:2,1:3,3:0.5:2,2:15.3:1:27.3:1:1:3.10575:60:6:0.5:0:1.3 +18 8786117 . C CCCA 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAAGCAATCCCCCCCC;RSEQ=CCGCCCTCCCCCTCCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:5,3:8,3:0.2143:2,0:36:1:31:1:0.18182:0:60:6:0.2308:0:0 0/0:4:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 9708049 . CGGGGCCGGGA C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCGGGCCCTGCGGCCAGG;RSEQ=GGGGCGGATGCCGGAGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 9708081 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGGATGCCGGAGGGCGC;RSEQ=GGGGGAGGCCGACCCGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 9708582 . C T 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.1009;SOR=Inf;LSEQ=CCCCGTCCCCCTCGTCCGCG;RSEQ=GCCCCCTGGTTCCCCGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:4,1:5,5:0.5:2,2:23.4:1:30.4:1:1:1:60:10:0.5:0:1 1/1:5:5:4,1:0,0:0,5:1:0,2:18.8:1:28:1:1:0:60:10:1:0:1 +18 9709183 . A G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAAGCAGCCAGAAACAAA;RSEQ=AAGCAGTCAATCCGTGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:32:1:1:0:60:4:1:0:1 +18 9924309 . G T 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGTTTCTATTTTAATCAA;RSEQ=ATGTTAAATTATTAGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:12.3:1:32:1:1:0:60:6:0.5:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:36:0:27:0:1:0:60:2:1:0:1 +18 9924504 . T C 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06671;SOR=Inf;LSEQ=GTTAAGACTATTGTTTATTT;RSEQ=CTCTGCCTTGTTTTCAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:147,45:192,0:0:2,0:21.6:1:30.2:1:1:0:59.9:23:1:0:0.1 0/1:132:3:2,1:96,33:129,3:0.0227:2,2:15.7:1:29:1:1:1.45008:60:6:0.0229:0:1 +18 9924617 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00237;SOR=1.52712;LSEQ=CGTTTAAGGTAGTTTTTTAA;RSEQ=ATGAAATGTCAATAAAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:160:78,82:109,146:255,160:0.3846:2,2:26.1:1:30.9:1:0.26497:1.27:60:320:0.3865:0:1.1 0/1:434:212:97,115:103,119:222,212:0.4885:2,2:24.5:1:29.8:1:0.92341:1.02611:59.8:69.667:0.4883:0:1.1 +18 10004711 . T TTA 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=0.00078;SOR=Inf;LSEQ=TAGCAATAACCTTTCATCCT;RSEQ=TATATATATATATATATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:9,31:40,0:0:2,0:23.6:1:29.6:1:1:0:60:19:0.9744:0:0 0/1:32:8:1,7:4,18:22,8:0.25:2,2:29.8:1:26.7:1:1:1.53446:60:16:0.2581:0.0313:0 +18 10004836 . A C 58 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTGTCTGGACCAGAAAA;RSEQ=ATATATTATAGTAATGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:18.3:1:29.3:1:1:0:35.8:3:1:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:11:0:33:0:1:0:26:2:1:0:1 +18 10054446 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50136;SOR=0;LSEQ=GAACTGCCATTTCACAAGGA;RSEQ=TTGATATGGAAGGTGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:18,26:44,2:0.0435:2,2:31.5:1:31.5:1:1:1.43:60:4:0.0444:0:1 0/0:36:0:0,0:17,19:36,0:0:2,0:30.6:1:29.4:1:1:0:60:35:1:0:0.2 +18 10054466 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16517;SOR=Inf;LSEQ=ATTGATATGGAAGGTGAGAG;RSEQ=AGGAGTCAGCGTTTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:19,27:46,0:0:2,0:32.5:1:31.6:1:1:0:60:45:1:0:0.2 0/1:32:2:1,1:12,18:30,2:0.0625:2,2:34:1:27:1:1:1.48:60:4:0.0714:0:1 +18 10054484 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51213;SOR=0;LSEQ=AGGAGGAGTCAGCGTTTCCC;RSEQ=GGTTTTCCTGCCTTTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:15,26:41,2:0.0465:2,2:19.5:1:31:1:1:1.71:60:4:0.0465:0:1 0/0:29:0:0,0:10,19:29,0:0:2,0:22.2:1:29.2:1:1:0:60:28:1:0:0.3 +18 10056249 . G A 24 d5;v3;q25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGAGTGACAGTGAAAT;RSEQ=TAAGTAGAAAAAAAAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:24.5:1:1:0:60:4:1:0:1 +18 10151780 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51643;SOR=0;LSEQ=GCCTTTAGTGTATGGGCCTG;RSEQ=CCAGACCAGCACATGGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:126,31:157,2:0.0126:2,2:10:1:26.5:1:0.36303:4.01635:60:4:0.0127:0:1 0/0:108:0:0,0:77,31:108,0:0:2,0:23:1:30.8:1:1:0:60:53:1:0:0.1 +18 10151807 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19888;SOR=Inf;LSEQ=CAGCACATGGGCATCTGTTT;RSEQ=CCAGGAAAAACCCAGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:148,73:221,0:0:2,0:25.7:1:31.7:1:1:0:60:109.5:0.991:0:0.1 0/1:180:2:1,1:113,65:178,2:0.0111:2,2:40:0:30.5:1:1:1.73277:60:4:0.0112:0:1 +18 10151838 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09856;SOR=Inf;LSEQ=CCCAGCAGTGGCTGTGGTGG;RSEQ=TGGATGTGGGATTGGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:184,134:318,0:0:2,0:25:1:32.6:1:1:0:60:105:1:0:0.2 0/1:274:3:1,2:156,115:271,3:0.0109:2,2:12:1:27:1:0.57748:2.70324:60:6:0.0111:0:2 +18 10151860 . A T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09314;SOR=Inf;LSEQ=GGATGTGGGATTGGATGGGC;RSEQ=CACAGAAAAACATAAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:189,168:357,0:0:2,0:24.4:1:30.2:1:1:0:59.9:118:1:0:0.3 0/1:297:3:1,2:165,129:294,3:0.0101:2,2:20:1:22.7:1:0.58494:2.55019:60:2:0.0068:0:1.3 +18 10151888 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.88115;LSEQ=AAACATAAAAACCATGGCAA;RSEQ=AGTAATCATAATAGTAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:87:42,45:151,165:316,87:0.2153:2,2:21.2:1:29.2:1:1:1.02:60:42.5:0.2141:0:1.2 0/1:353:156:77,79:102,95:197,156:0.4419:2,2:25.3:1:28:1:0.66929:1.10127:60:51:0.4461:0:1.2 +18 10151994 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52723;SOR=0;LSEQ=TTTTTCTTAATGTCCTAGAT;RSEQ=GAACAGGATGATTGGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:32,115:147,2:0.0134:2,2:26.5:1:28.5:1:0.39507:3.55:60:4:0.0135:0:1 0/0:91:0:0,0:21,70:91,0:0:2,0:3:0:15:0:1:0:60:0:0:0:4 +18 10152122 . C CT 59 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0.7602;LSEQ=GCAACATTAGACTTTCTGGA;RSEQ=TTTTTTTTTTTTCTGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:0,9:9,4:0.3077:0,0:28.8:1:29.8:1:1:0:60:8:0.3333:0.0769:0 0/1:8:2:0,2:0,6:6,2:0.25:0,0:25.5:1:29:1:1:0:60:4:0.25:0:1 +18 10451547 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04413;SOR=Inf;LSEQ=AATAGAGCGTTCTACTACTC;RSEQ=GTACTCACTAAAAATCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:67,8:75,0:0:2,0:22.1:1:31.9:1:1:0:60:74:1:0:0 0/1:42:3:2,1:32,7:39,3:0.0714:2,2:32:1:30.7:1:0.47875:2.23132:60:6:0.0714:0:1 +18 10451595 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58036;SOR=2.63961;LSEQ=CTAAGAAAATCAAGCTAAGG;RSEQ=GATCACCCAAGCTCTACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:1,0:115,36:151,1:0.0066:2,0:31:0:32:0:1:0:60:2:0.0066:0:1 0/1:116:2:1,1:83,31:114,2:0.0172:2,2:13.5:1:29.5:1:0.47736:2.65108:60:4:0.0174:0:1 +18 10451695 . A G 241 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAAGACAGGCGATTATAGA;RSEQ=GCTCATAGGGCAACTGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:0:0,0:223,189:412,0:0:2,0:25.7:1:31.1:1:1:0:60:81.4:1:0:0.1 1/0:404:236:118,118:88,79:167,236:0.5842:2,2:26.8:1:30.7:1:0.61408:1.11362:60:46.2:0.5863:0:1.2 +18 10451751 . G A 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21435;SOR=4.08154;LSEQ=GCTTGGTAGACACGTGACAG;RSEQ=CCTCGTGAGTTGGTAACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:1,0:129,190:319,1:0.0031:2,0:1:0:26:0:0.40625:0:60:2:0.0032:0:1 0/1:316:4:3,1:131,181:312,4:0.0127:2,2:12.8:1:26.3:1:0.31506:4.13:60:8:0.0129:0:1 +18 10451769 . T A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10413;SOR=Inf;LSEQ=AGGCCTCGTGAGTTGGTAAC;RSEQ=GAACAAATCACAGGCGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:94,166:260,0:0:2,0:24.8:1:30.5:1:1:0:60:64:1:0:0.1 0/1:232:3:2,1:86,143:229,3:0.0129:2,2:14.3:1:27.3:1:0.55896:3.31:60:6:0.0133:0:3 +18 10451796 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17021;SOR=Inf;LSEQ=ATCACAGGCGTTCCAAGAGG;RSEQ=GATGTGTTGTGTGGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:33,140:173,0:0:2,0:24.8:1:30:1:1:0:60:42.25:1:0:0.1 0/1:122:2:1,1:33,87:120,2:0.0164:2,2:22.5:1:29:1:0.48137:2.61:60:4:0.0165:0:1 +18 10451813 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14365;SOR=Inf;LSEQ=AGGCGATGTGTTGTGTGGCT;RSEQ=GGAACTTAGCTCCTTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:18,126:144,0:0:2,0:23.6:1:31.4:1:1:0:60:143:0.9931:0:0.1 0/1:89:2:0,2:14,73:87,2:0.0225:2,0:12.5:1:29:1:1:0:60:4:0.0227:0:1 +18 11751952 . T A 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACCCCGGTGGCGCGCTC;RSEQ=GTCCTCCGCGCCACGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 11752482 . A T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78892;LSEQ=GACGGAAGACCAGGGCGTCG;RSEQ=TGAAAAAGAACGACGCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:0,2:57,46:103,2:0.019:2,0:1:0:25:1:0.20659:0:60:4:0.0194:0:1.5 0/1:199:3:1,2:101,95:196,3:0.0151:2,2:13:1:21.3:1:0.61378:2.11852:60:2:0.0104:0:3.3 +18 11752554 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49812;SOR=Inf;LSEQ=AGAGCGCCTGGCTTACAAGG;RSEQ=TACCCACCGCCTGCTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:39,77:116,0:0:2,0:29.1:1:33:1:1:0:60:232:1:0:0.1 0/1:122:2:1,1:40,80:120,2:0.0164:2,2:28:0:31.5:1:1:1.99:60:4:0.0168:0:1.5 +18 11879931 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGCCGCTGCACCGTCCA;RSEQ=TACAGAACCACTGGGCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:22:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 11881026 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50267;SOR=Inf;LSEQ=GGTGACGGCAAACATTACTG;RSEQ=TACCCGCACTTCACCTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:57,31:88,0:0:2,0:25.8:1:32.4:1:1:0:60:176:1:0:0.1 0/1:108:2:1,1:61,45:106,2:0.0185:2,2:44:1:28:1:1:1.35167:60:4:0.0187:0:1 +18 11881069 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50187;SOR=Inf;LSEQ=TGGACACAGAGAACATCCGC;RSEQ=GGGTGTTCAACGACTGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:49,58:107,0:0:2,0:25.1:1:31.3:1:1:0:60:214:1:0:0.1 0/1:128:2:1,1:58,68:126,2:0.0156:2,2:21.5:1:28.5:1:1:1.17:60:4:0.0163:0:1.5 +18 11881080 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50073;SOR=Inf;LSEQ=AACATCCGCAGGGTGTTCAA;RSEQ=GACTGCCGCGACATCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:44,57:101,0:0:2,0:24.3:1:30.2:1:1:0:60:32.667:1:0:0.2 0/1:118:2:1,1:53,63:116,2:0.0169:2,2:18.5:1:28:1:1:1.19:60:4:0.0172:0:1 +18 11881085 . G A 26 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60297;SOR=0.4431;LSEQ=CCGCAGGGTGTTCAACGACT;RSEQ=CCGCGACATCATCCAGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:41,57:98,2:0.02:2,2:19:1:26.5:1:1:1.39:60:4:0.02:0:1 0/0:112:1:1,0:48,63:111,1:0.0089:2,0:1:0:22:0:0.4375:0:60:2:0.009:0:1 +18 11881113 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25513;SOR=Inf;LSEQ=ATCATCCAGCGGATGCACCT;RSEQ=AAGCAGTATGAGCTCTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:20,39:59,0:0:2,0:29:1:31.7:1:1:0:60:28.5:1:0:0.2 0/1:75:3:2,1:26,46:72,3:0.04:2,2:14.3:1:27.3:1:0.55175:3.48:60:6:0.0405:0:1 +18 11881143 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49333;SOR=0;LSEQ=GAGCTCTTGTGAGGATGCTG;RSEQ=CGCCACCCTGCGACGGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:5,31:36,2:0.0526:2,2:11:0:32:0:0.29445:5.75:60:4:0.0526:0:1.5 0/0:37:0:0,0:9,28:37,0:0:2,0:22.4:1:30.1:1:1:0:60:36:1:0:0.2 +18 12101808 . G A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTCACAATTTCTTAGTC;RSEQ=TAATTCCTCTCAAACCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:8,1:0,0:0,9:1:0,2:17.8:1:30.8:1:1:0:47:18:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:31.5:1:1:0:60:4:1:0:1 +18 12102156 . G C 317 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00289;LSEQ=TAACAACTTGTCCAAGGCCC;RSEQ=AGTAACTATGAAGAGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1110:1108:534,574:0,0:0,1108:0.9982:0,2:26.7:1:31.4:1:1:0:46.6:60.556:0.9982:0:1.2 1/0:870:535:261,274:164,168:332,535:0.6149:2,2:26.3:1:30.6:1:0.88893:1.02479:44.9:132.75:0.6174:0:1.5 +18 12102188 . G T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=5.68261;LSEQ=AGAGTGAGGGTTGCAGCAAG;RSEQ=AGTAGAGTCCGTCACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:86:38,48:357,474:831,86:0.0938:2,2:18.2:1:29:1:0.82029:1.05:50.9:172:0.0952:0:1.7 0/1:734:272:126,146:224,237:461,272:0.3706:2,2:22.9:1:27.9:1:0.59225:1.09503:53.2:271:0.3717:0:1.8 +18 12102407 . G A 238 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGTGTGACCACTGGGGTTC;RSEQ=CAGCAACAGAGCTCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:247:247:137,110:0,0:0,247:1:0,2:23.7:1:30:1:1:0:59.9:48.4:1:0:1.1 1/0:194:118:66,52:42,34:76,118:0.6082:2,2:22.7:1:29.1:1:1:1.03:60:236:0.6114:0:1.1 +18 12325864 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.6;SOR=2.25968;LSEQ=CGTGTGCGACATCCCGCCCC;RSEQ=CGGCCTGAAGATGGCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:1,0:12,11:23,1:0.0417:2,0:1:0:26:0:1:0:60:2:0.0455:0:1 0/1:22:2:1,1:9,11:20,2:0.0909:2,2:40.5:1:30:1:1:1.21:52:4:0.0909:0:1 +18 12911159 . C G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCGGGCCGCACTGCTG;RSEQ=CGCGTCTAGCCGCCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:0:33:0:1:0:60:4:1:0:2 +18 12911214 . G T 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCTCGCCCCCGGGACTT;RSEQ=CCAGCAGCGAGTGGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:28:1:1:0:60:4:1:0:2 +18 12912750 . C T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01884;SOR=0;LSEQ=TGTTGGATCAGGAACTGTGT;RSEQ=TGCTCTTAAGTGCTTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:7:7,0:95,2:97,7:0.0673:1,0:25.6:1:31.4:1:1:0:51.3:14:0.0686:0:1.4 0/0:81:0:0,0:80,1:81,0:0:1,0:24:1:31:1:1:0:60:80:1:0:0 +18 12912821 . G C 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTCTTTTCAGTTGGGTGTT;RSEQ=AGTGGTTTTCCAGATCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:22:18,4:306,90:396,22:0.0526:2,2:22.7:1:32:1:0.79519:1.32:60:44:0.0534:0:1.3 0/0:399:0:0,0:293,105:398,0:0:2,0:22.4:1:30.8:1:1:0:60:78.6:0.9975:0:0.1 +18 12912932 . T C 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCAACTGGGATGAGATTG;RSEQ=TGATAACTTTGATGATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:800:0:0,0:381,419:800,0:0:2,0:25.1:1:30.1:1:1:0:59.9:159:1:0:0.1 0/1:804:28:12,16:352,423:775,28:0.0348:2,2:20:1:31.8:1:0.84856:1.10936:60:56:0.0353:0:1.3 +18 12913743 . T C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTATGATCCACCTACCAA;RSEQ=TGTGAAAACAACATTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:204,209:413,0:0:2,0:22:1:30.6:1:1:0:59.9:102.25:1:0:0.1 0/1:405:20:15,5:208,177:385,20:0.0494:2,2:19:1:31.1:1:0.10442:2.55:60:40:0.0501:0:1 +18 13910706 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52896;SOR=0;LSEQ=GGTCCCTGGTCTAGTCCTGG;RSEQ=TGGGCTGAGGCTGCTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:99,78:177,2:0.0112:2,2:20:1:29:1:1:1.26752:60:4:0.0112:0:2 0/0:108:0:0,0:64,44:108,0:0:2,0:24.4:1:31.4:1:1:0:60:35:1:0:0.5 +18 13910713 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52914;SOR=0;LSEQ=GGTCTAGTCCTGGCTGGGCT;RSEQ=AGGCTGCTCCAGTTACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:103,89:192,2:0.0103:2,2:27.5:1:28.5:1:1:1.15643:60:4:0.0104:0:1.5 0/0:117:0:0,0:65,52:117,0:0:2,0:23.4:1:31.1:1:1:0:60:234:1:0:0.5 +18 13910730 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.19022;LSEQ=GCTGAGGCTGCTCCAGTTAC;RSEQ=CTCAGCACTAGGGCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:201:171:85,86:13,17:30,171:0.8507:2,2:28.8:1:30.8:1:0.55751:1.29:60:84.5:0.8492:0:1.1 1/0:133:69:36,33:35,28:63,69:0.5188:2,2:23.9:1:29.7:1:0.72925:1.14465:59.9:33.5:0.5115:0:1.1 +18 13912411 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGTTATTCCAAAGAGCC;RSEQ=GAGAGGCTGAGTGTTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:28:1:1:0:60:4:1:0:1.5 +18 14156643 . A T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60994;SOR=2.17039;LSEQ=TGAGGGCTTACACGAAGGCA;RSEQ=GAAACAAGGCAGTCAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:0,1:145,67:212,1:0.0047:2,0:22:0:14:0:0.31925:0:21:0:0:0:7 0/1:197:2:1,1:124,71:195,2:0.0102:2,2:45:1:31:1:1:1.7412:22:4:0.0102:0:1 +18 14156807 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16944;SOR=Inf;LSEQ=ATATGTAATAACATCAACAC;RSEQ=TTATCCATATAGATGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:2,23:25,0:0:2,0:12.4:1:28.4:1:1:0:21.3:24:1:0:0.4 0/1:18:2:0,2:0,16:16,2:0.1111:1,0:14.5:1:29:1:1:0:21:4:0.1111:0:1 +18 14157129 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49866;SOR=0;LSEQ=GCTAGAAAATTAATTTAATT;RSEQ=TCTTAAACTTTGTAGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:112,18:130,2:0.0152:2,2:41:1:30:1:0.2681:6.08326:22:4:0.0152:0:1 0/0:123:0:0,0:91,32:123,0:0:2,0:33.3:1:30.6:1:1:0:22:122:1:0:0.1 +18 14157291 . A T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15638;SOR=1.42093;LSEQ=GAACTTTTTGTCAGCTGCCT;RSEQ=CTTCCTCCGTGGCCAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:70:17,53:21,60:81,70:0.4636:2,2:34.4:1:30.4:1:0.85271:1.09054:25:140:0.4667:0:1.2 1/0:136:75:16,59:21,40:61,75:0.5515:2,2:33.7:1:28.6:1:0.12077:1.92637:25.6:150:0.5515:0:1.1 +18 14157373 . T A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATAGCGATAAGATAAT;RSEQ=TATGAAGTTTCTTCTATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:7,15:0,0:0,22:1:0,2:15.7:1:30.4:1:1:0:23.4:44:1:0:1.5 1/1:20:20:8,12:0,0:0,20:1:0,2:10.6:1:28.2:1:1:0:26:19:1:0:1.3 +18 18511711 . T C 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAGGTTTCAGACACTCT;RSEQ=TCTGTAGTATCTGGAAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:32.5:1:1:0:20.5:4:1:0:4 +18 18511744 . T C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGTGGACATTTCGAGTG;RSEQ=TTTCAGGCCTATGGTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:0:33:1:1:0:20.5:4:1:0:4 +18 18511779 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACAAGGAAATATCTTCC;RSEQ=ATAAAAACCAGACACAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:12.5:1:28.5:1:1:0:20.5:4:0.6667:0:4 +18 18511786 . A G 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAATATCTTCCCATAAAA;RSEQ=CCAGACACAAGCATTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:5.5:1:28.5:1:1:0:20.5:4:0.6667:0:4 +18 18512186 . A G 34 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCCTCAGCTAACAGAGTT;RSEQ=AACCTTTCTATTTACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:34:0:1:0:25:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 18512208 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTTCTATTTACAGAGCA;RSEQ=TTTTCAAAGACTCTTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:32.5:1:1:0:25:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 18512260 . A T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=GTGGATATCTGGAGATCTTT;RSEQ=AGGATTTCATTGGAAACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:13.5:1:28.5:1:1:2.44949:25:4:0.4:0:3.5 1/0:4:2:1,1:1,1:2,2:0.5:2,2:6:0:31.5:1:1:1:29.5:4:0.5:0:1.5 +18 18512269 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TGGAGATCTTTAAGGATTTC;RSEQ=TTGGAAACCGGAATATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:10.8:1:29.9:1:1:0:26.1:16:1:0:3.9 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:8.5:1:29:1:1:1.41418:47:4:0.2857:0:2.5 +18 18512270 . T C 34 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.52315;LSEQ=GGAGATCTTTAAGGATTTCA;RSEQ=TGGAAACCGGAATATCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:6,2:0.25:2,2:21:0:34.5:1:1:1:20:4:0.25:0:4.5 0/1:7:1:1,0:3,3:6,1:0.1429:2,0:6:0:33:0:1:0:20:2:0.1429:0:6 +18 18512279 . G C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.175;SOR=0;LSEQ=TAAGGATTTCATTGGAAACC;RSEQ=GAATATCTTCAGGTAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:30:0:33:1:1:1.41:20:4:0.2857:0:4.5 0/0:9:0:0,0:4,4:8,0:0:2,0:17.1:1:29.6:1:1:0:31.6:16:0.8889:0:3.6 +18 18512311 . A T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=GGTAAAATCTAGACAGAGGC;RSEQ=TTCTCAGAAACTTCTTCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:34.4:1:30.6:1:1:0:28.6:18:1:0:4 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:15:0:32:1:1:1.22474:47:4:0.1818:0:2.5 +18 18512328 . C T 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=3.3097;LSEQ=GGCATTCTCAGAAACTTCTT;RSEQ=GTGATGTGCGTCCTCAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:3,3:6,1:0.1429:2,0:38:0:32:0:1:0:20:2:0.1429:0:5 0/1:8:3:2,1:2,3:5,3:0.375:2,2:28.7:1:31.7:1:1:2.60:26:6:0.375:0:4.3 +18 18512331 . G A 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCTCAGAAACTTCTTCGT;RSEQ=ATGTGCGTCCTCAACTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:35.4:1:30.1:1:1:0:31:14:1:0:3.9 1/1:7:7:4,3:0,0:0,7:1:0,2:37:1:29:1:1:0:26.1:14:1:0:5 +18 18512337 . C T 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAACTTCTTCGTGATGTG;RSEQ=GTCCTCAACTAACAGAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:29.4:1:30.4:1:1:0:31:14:1:0:3.9 1/1:7:7:4,3:0,0:0,7:1:0,2:31:1:29.4:1:1:0:26.1:14:1:0:5 +18 18512353 . A T 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGCGTCCTCAACTAACAG;RSEQ=GTACAACCTGTCTTTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:13.4:1:29.1:1:1:0:31:14:1:0:3.9 1/1:6:6:4,2:0,0:0,6:1:0,2:18:1:29:1:1:0:27:12:1:0:5.2 +18 18512363 . G A 64 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTAACAGAGTACAACCT;RSEQ=TCTTTTGATACATCAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:9.5:1:29.5:1:1:0:29.5:8:1:0:4.3 1/1:5:5:3,2:0,0:0,5:1:0,2:11.4:1:27.8:1:1:0:26:10:1:0:5 +18 18514672 . A T 26 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATATAAAATCTAGACAG;RSEQ=GGCACTCTCAGAAACTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:29:0:26.5:1:1:0:25:4:1:0:4.5 +18 18515016 . A G 44 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTAGACAGCAGCATTCTC;RSEQ=GAACCTTCTTTGTGATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:22.3:1:28:1:1:0:33:6:1:0:6.7 +18 18515018 . A G 41 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGACAGCAGCATTCTCAG;RSEQ=ACCTTCTTTGTGATGTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:24.3:1:26:1:1:0:33:2:1:0:6.7 +18 18515020 . CC GA 46 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGCAGCATTCTCAGAA;RSEQ=TTCTTTGTGATGTTTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:27.3:1:29.2:1:1:0:33:6:1:0:5.7 +18 18515043 . A C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTGTGATGTTTGCTTTT;RSEQ=AGTCACAGAGTTGAATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:45:0:32:1:1:0:35:4:0.6667:0:6.5 +18 18515068 . AC CA 45 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGTTGAATATTCCCTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:14.3:1:28.5:1:1:0:33:6:1:0.3333:5.3 +18 18515774 . T A 27 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGAGCAGGTTTGAAACCC;RSEQ=CTTTCCGTAGTATCTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:27.5:1:1:0:25:4:1:0:6.5 +18 18515780 . C T 43 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTTTGAAACCCTCTTTC;RSEQ=GTAGTATCTGGATGTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:8.7:1:27.3:1:1:0:23.3:6:1:0:5.3 +18 18515813 . T G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGACACTTGGAGCGCTT;RSEQ=GACGCTTACGGTGCAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:44.5:1:32:1:1:0:25:4:0.6667:0:6.5 +18 18515822 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAGCGCTTTGACGCTTA;RSEQ=GGTGCAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:47:1:29.5:1:1:1:25:4:0.5:0:6.5 +18 18515827 . C A 46 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTTTGACGCTTACGGTG;RSEQ=AAAAGGAAATATCTTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:1,0:1,3:0.75:0,2:35.3:1:29.3:1:1:0:21.3:6:1:0:4.7 +18 18515858 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTCCCATAAAAACTAGA;RSEQ=AGAAGCATTCTCACAAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:30.5:1:28.5:1:1:1:20:4:0.5:0:4 +18 18515914 . A C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAACTAACAGAGTTGAA;RSEQ=CTTTCTATTTACAGAGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:18.7:1:32:1:1:0:24:6:1:0:6.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 18515933 . C G 30 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AACTTTCTATTTACAGAGCA;RSEQ=TTTTGAAAGACTCTTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:37.3:1:33.7:1:1:0:24:6:1:0:6.3 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:30.5:1:1:0:25:4:1:0:3.5 +18 18515947 . TTT AA 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AGAGCACTTTTGAAAGACTC;RSEQ=TTGGAGAATCTGCAAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:36.3:1:31.8:1:1:0:24:6:1:0:4.3 0/0:2:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 18515956 . A T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TTGAAAGACTCTTTTTGGAG;RSEQ=ATCTGCAAGTGGATATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:33.7:1:30.7:1:1:0:24:6:1:0:6.3 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:29.5:1:1:0:25:4:1:0:3.5 +18 18515963 . A T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ACTCTTTTTGGAGAATCTGC;RSEQ=AGTGGATATTTGGAGAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:30.3:1:30.7:1:1:0:24:6:1:0:6.3 1/1:2:2:1,1:0,0:0,2:1:0,2:36:0:30.5:1:1:0:25:4:1:0:3.5 +18 18515978 . G A 29 d5;v3;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=AGCTTTAAGGATTTCATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:29:1:1:0:22:4:1:0:7.5 0/0:2:0:0,0:1,1:2,0:0:2,0:21:0:31:1:1:0:25:4:1:0:3.5 +18 18515989 . A T 30 d5;v3;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATATTTGGAGAGCTTTAAGG;RSEQ=TTTCATTGGAAACGGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12:1:30.5:1:1:0:22:4:1:0:7.5 0/0:2:0:0,0:1,1:2,0:0:2,0:10:0:31:1:1:0:25:4:1:0:3.5 +18 18516117 . C G 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGCAGTTTGGAAACACT;RSEQ=TTTTTGTAGAATCTGCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:11:0:34:0:1:0:23:2:1:0:7 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:8:0:29.5:1:1:0:21:4:0.6667:0:6.5 +18 18516123 . G A 27 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTTTGGAAACACTCTTTTT;RSEQ=TAGAATCTGCAAGTGGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:17:0:34:0:1:0:23:2:1:0:7 1/0:4:2:1,1:1,1:2,2:0.5:2,2:6.5:1:27.5:1:1:1:27:4:0.5:0:6.5 +18 18516129 . T A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACACTCTTTTTGTAGAA;RSEQ=CTGCAAGTGGATATTTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:23:0:32:0:1:0:23:2:1:0:7 1/0:4:2:1,1:1,1:2,2:0.5:2,2:20:0:27.5:1:1:1:21:4:0.5:0:6.5 +18 18516133 . C T 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCTTTTTGTAGAATCTG;RSEQ=AAGTGGATATTTGGATAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:27:0:30:0:1:0:23:2:1:0:7 1/0:4:2:1,1:1,1:2,2:0.5:2,2:24:0:27:1:1:1:21:4:0.5:0:6.5 +18 18516143 . T G 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GTAGAATCTGCAAGTGGATA;RSEQ=TTGGATAGCTCTAACGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:14:1:30.3:1:1:0:21.3:6:1:0:5 1/0:4:2:1,1:1,1:2,2:0.5:2,2:26.5:1:31.5:1:1:1:27:4:0.5:0:6.5 +18 18516155 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=AGTGGATATTTGGATAGCTC;RSEQ=AACGATTTCGTTGGAAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:17.8:1:30.2:1:1:0:23.5:12:1:0:4.7 0/1:5:2:1,1:2,1:3,2:0.4:2,2:38.5:1:32.5:1:1:1.7321:27:4:0.4:0:6.5 +18 18516157 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=TGGATATTTGGATAGCTCTA;RSEQ=CGATTTCGTTGGAAACGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:11:0:34.5:1:1:2.45:28:4:0.3333:0:5.5 0/0:5:0:0,0:3,2:5,0:0:2,0:35:1:29.2:1:1:0:23.2:10:1:0:6.8 +18 18516158 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GGATATTTGGATAGCTCTAA;RSEQ=GATTTCGTTGGAAACGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:17.5:1:32.5:1:1:2.45:20.5:4:0.3333:0:4 0/0:5:0:0,0:3,2:5,0:0:2,0:34.6:1:30.8:1:1:0:23.2:10:1:0:6.8 +18 18516181 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=TTTCGTTGGAAACGGGAATA;RSEQ=CTTCATAAAAAATCTAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:24.3:1:32.3:1:1:0:23.5:12:1:0:4.7 0/1:5:2:1,1:2,1:3,2:0.4:2,2:13:0:32.5:1:1:1.7321:27:4:0.4:0:6.5 +18 18516183 . T A 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54545;SOR=0.33624;LSEQ=TCGTTGGAAACGGGAATATC;RSEQ=TCATAAAAAATCTAGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:0,1:1,5:0.8333:0,2:20.4:1:32.4:1:1:0:24:10:0.8333:0:5.2 1/0:5:3:2,1:1,1:2,3:0.6:2,2:25.3:1:29:1:1:1.73:20.7:6:0.6:0:7 +18 18516186 . A C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=TTGGAAACGGGAATATCTTC;RSEQ=TAAAAAATCTAGACAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:19.3:1:32.7:1:1:0:23.5:12:1:0:4.7 0/1:5:2:1,1:2,1:3,2:0.4:2,2:8:0:33:0:1:1.7321:27:4:0.4:0:6.5 +18 18516188 . AA CT 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.54545;SOR=0.33624;LSEQ=GGAAACGGGAATATCTTCAT;RSEQ=AAAATCTAGACAGAAGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:0,1:1,5:0.8333:0,2:14.4:1:33.2:1:1:0:24:10:0.8333:0:4.2 1/0:5:3:2,1:1,1:2,3:0.6:2,2:23.3:1:29.5:1:1:1.73:20.7:6:0.6:0:6 +18 18516189 . A T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.54545;SOR=2.97405;LSEQ=GAAACGGGAATATCTTCATA;RSEQ=AAAATCTAGACAGAAGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,0:0,1:0.1667:0,0:26:0:30:0:1:0:21:2:1:0:2 0/1:5:2:1,1:0,0:0,2:0.4:0,2:5:0:31:1:1:0:27:4:1:0:6.5 +18 18516195 . C G 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.55247;LSEQ=GGAATATCTTCATAAAAAAT;RSEQ=TAGACAGAAGCACTCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:16:1:33:1:1:0:28:4:0.5:0:4.5 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:43:0:34:0:1:0:20:2:0.3333:0:7 +18 18516916 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAACATGTTTGTGATGT;RSEQ=TGTACTCAGCTAAGAGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:16.5:1:28:1:1:0:25:4:1:0:6 +18 18516930 . G C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATGTATGTACTCAGCTAA;RSEQ=AGAGTGGAACCTTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:30.5:1:30:1:1:0:25:4:1:0:6 +18 18516966 . T A 129 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTACAGAGCAGCTTTGA;RSEQ=ACACTATTTTTGTAGAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:30:1:1:0:25.5:4:1:0:7 1/1:19:19:8,11:0,0:0,19:1:0,2:18.6:1:30.4:1:1:0:28.8:38:1:0:7.1 +18 18516969 . A T 125 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTACAGAGCAGCTTTGATAC;RSEQ=CTATTTTTGTAGAATCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:30.5:1:1:0:25.5:4:1:0:7 1/1:19:19:8,11:0,0:0,19:1:0,2:20.9:1:29.5:1:1:0:28.8:18:1:0:7.1 +18 18516980 . A G 137 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGATACACTATTTTTGT;RSEQ=GAATCTGCAATTTGATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:48:0:31.5:1:1:0:25.5:4:1:0:7 1/1:20:20:9,11:0,0:0,20:1:0,2:29:1:31.7:1:1:0:29.2:40:1:0:7.1 +18 18516983 . A T 131 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATACACTATTTTTGTAGA;RSEQ=TCTGCAATTTGATATTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:45:0:30.5:1:1:0:25.5:4:1:0:7 1/1:20:20:9,11:0,0:0,20:1:0,2:30.1:1:30.4:1:1:0:29.2:40:1:0:7.1 +18 18516991 . T A 128 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTGTAGAATCTGCAA;RSEQ=TTGATATTTTGATTGCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:30.5:1:1:0:25.5:4:1:0:7 1/1:19:19:9,10:0,0:0,19:1:0,2:29.8:1:30.3:1:1:0:29.6:38:1:0:7.1 +18 18516993 . T G 82 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTTGTAGAATCTGCAATT;RSEQ=GATATTTTGATTGCTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:35:0:30:1:1:0:25.5:4:1:0:7 0/1:19:6:2,4:7,6:13,6:0.3158:2,2:32.2:1:31.8:1:0.62848:2.23102:28.3:12:0.3158:0:8 +18 18517001 . T A 122 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTGCAATTTGATATTT;RSEQ=GATTGCTTTAAAGATATCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:29.5:1:1:0:25.5:4:1:0:7 1/1:18:18:9,9:0,0:0,18:1:0,2:22.3:1:29.4:1:1:0:29.3:36:1:0:7.2 +18 18517013 . A C 108 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATATTTTGATTGCTTTAA;RSEQ=GATATCGTTGGAAACAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:30:1:1:0:25.5:4:1:0:7 1/1:15:13:6,7:0,0:0,13:0.8667:0,2:12.9:1:29.2:1:1:0:28.7:12:0.8571:0:7.3 +18 18517130 . G C 79 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22222;SOR=7.2181;LSEQ=ACGTTCCCTTTCTTAGAGCA;RSEQ=GTTTGAAACACTCTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:11.5:1:29:1:0.4:0:25.5:4:0.4:0:6 1/1:7:6:3,3:0,1:1,6:0.8571:0,2:11.8:1:30.7:1:1:0:24.2:12:0.8571:0:6 +18 18517134 . T G 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24242;SOR=7.95544;LSEQ=TCCCTTTCTTAGAGCAGGTT;RSEQ=GAAACACTCTTTTTGTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:4,0:4,1:0.2:0,0:20:0:15:0:0.2:0:22:0:0:0:8 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:17.8:1:31:1:1:1.41418:20.6:10:0.7143:0:6.2 +18 18517151 . A C 51 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01225;SOR=0;LSEQ=GTTTGAAACACTCTTTTTGT;RSEQ=GTATCTGGAAGTGGACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:2,3:0.6:2,0:26:0:32.3:1:0.4:0:23:6:0.6:0:2.7 0/0:13:0:0,0:6,7:13,0:0:2,0:23.6:1:29.1:1:1:0:23.5:26:1:0:5.3 +18 18517154 . A G 100 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32598;SOR=3.13525;LSEQ=TGAAACACTCTTTTTGTAGT;RSEQ=TCTGGAAGTGGACATTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:35.5:1:32.5:1:0.4:0:25.5:4:0.4:0:6 1/0:13:9:4,5:2,2:4,9:0.6923:2,2:29.6:1:31.6:1:1:1.22862:23.9:18:0.6923:0:5.6 +18 18517160 . A T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52206;SOR=Inf;LSEQ=ACTCTTTTTGTAGTATCTGG;RSEQ=AGTGGACATTTGGAGCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:37.6:1:30.2:1:1:0:24:10:1:0:4 0/1:13:3:2,1:4,6:10,3:0.2308:2,2:15.7:1:30.3:1:0.55944:2.75:23.3:6:0.2308:0:4.7 +18 18517177 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00877;SOR=0;LSEQ=TGGAAGTGGACATTTGGAGC;RSEQ=CTTTGACGCCTTTGGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:2,3:0.6:2,0:26.7:1:28.3:1:0.4:0:23:6:0.6:0:2.7 0/0:15:0:0,0:7,8:15,0:0:2,0:33.9:1:31.3:1:1:0:23.7:30:1:0:5.3 +18 18517184 . C T 94 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.66859;LSEQ=GGACATTTGGAGCGCTTTGA;RSEQ=GCCTTTGGTGAAAAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:35.5:1:31.5:1:0.4:0:25.5:4:0.4:0:6 1/0:15:8:4,4:3,3:6,8:0.5333:2,2:32.1:1:31.4:1:1:1:23.1:16:0.5333:0:5.6 +18 18517187 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTTGGAGCGCTTTGACGC;RSEQ=TTTGGTGAAAAAGGAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:23:1:30.2:1:1:0:24:10:1:0:4 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:29:0:32.5:1:1:1.15:20:4:0.1333:0:4.5 +18 18517202 . A G 99 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.4677;LSEQ=GACGCCTTTGGTGAAAAAGG;RSEQ=AATGTCTTCCCATAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:17.5:1:31:1:1:0:25.5:4:0.5:0:6 1/0:15:9:4,5:2,3:5,9:0.6:2,2:15.4:1:31.3:1:1:1.18:23.9:18:0.6:0:5.4 +18 18517205 . T C 51 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCTTTGGTGAAAAAGGAAA;RSEQ=GTCTTCCCATAAAAACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:10:1:30.3:1:1:0:25.7:6:1:0:5 0/1:14:3:2,1:5,6:11,3:0.2143:2,2:13.3:1:32.3:1:1:2.26:28:6:0.2143:0:6 +18 18517206 . GTCTTC ATCTT 58 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTTGGTGAAAAAGGAAAT;RSEQ=CCATAAAAACTAGACAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:34:0:1:0:25.5:4:1:0:6 0/1:14:4:2,2:4,4:8,4:0.2857:2,2:38.5:1:29.3:1:1:1:23.5:8:0.2857:0:4.8 +18 18517237 . T C 62 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACTAGACAGAAGCATTC;RSEQ=AAGAAACTTCTTTGGGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:2,0:2,4:0.6667:0,2:13.8:1:31.3:1:0.46667:0:23.5:8:0.6667:0:4.8 +18 18517243 . A T 47 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGAAGCATTCTAAGAA;RSEQ=CTTCTTTGGGATATATGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:2,0:2,3:0.6:0,2:11.3:1:29.7:1:0.4:0:23:6:0.6:0:4.7 +18 18517248 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCATTCTAAGAAACTTC;RSEQ=TTGGGATATATGTACTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:0,2:2,0:2,2:0.5:0,0:9.5:1:31.5:1:0.33333:0:23:4:0.5:0:5 +18 18517252 . G C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCTAAGAAACTTCTTTG;RSEQ=GATATATGTACTCAACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:14:1:32:1:1:0:23:4:0.6667:0:6 +18 18517298 . TC GA 62 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACCTTTCTATTTATAGA;RSEQ=AGTTTTGAAACGCTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:2,4:0.6667:2,2:5.3:1:31.1:1:1:1:20:8:0.6667:0.5:0.8 +18 18517608 . A C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51087;SOR=Inf;LSEQ=TGTGATGTGTGTCCTCAACT;RSEQ=ACAGAGCTGTACCTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:41.3:1:29.6:1:1:0:34.9:18:1:0:3.2 0/1:15:2:0,2:5,8:13,2:0.1333:2,0:46:1:31:1:0.52381:0:29:4:0.1333:0:5 +18 18517615 . C A 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51087;SOR=0;LSEQ=TGTGTCCTCAACTAACAGAG;RSEQ=TGTACCTTTCTTTTGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:4,5:0,0:0,9:1:0,2:39.3:1:30.7:1:1:0:34.9:18:1:0:3.2 1/1:15:13:5,8:0,0:0,13:0.8667:0,2:40.6:1:29.7:1:1:0:35.5:26:0.8667:0:3.5 +18 18517617 . GT CA 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51087;SOR=Inf;LSEQ=TGTCCTCAACTAACAGAGCT;RSEQ=ACCTTTCTTTTGATACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:37.3:1:32:1:1:0:34.9:18:1:0:3.2 0/1:15:2:0,2:5,8:13,2:0.1333:2,0:45:1:33.3:1:0.52381:0:29:4:0.1333:0:4 +18 18517618 . T A 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51087;SOR=0;LSEQ=GTCCTCAACTAACAGAGCTG;RSEQ=ACCTTTCTTTTGATACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:4,5:0,0:0,9:1:0,2:36.3:1:30.9:1:1:0:34.9:18:1:0:3.2 1/1:15:13:5,8:0,0:0,13:0.8667:0,2:38.1:1:29.8:1:1:0:35.5:26:1:0:3.5 +18 18517625 . C G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAACAGAGCTGTACCTTT;RSEQ=TTTTGATACAGCAGTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:4,5:0,0:0,9:1:0,2:29.3:1:32.6:1:1:0:34.9:18:1:0:3.2 1/1:15:15:5,10:0,0:0,15:1:0,2:32:1:31.6:1:1:0:34.6:30:1:0:3.5 +18 18518092 . T A 49 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGATTCTACAAAAATAG;RSEQ=GTATCAAAGCTGCTCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:17.7:1:31:1:1:0:23.3:6:1:0:4.3 +18 18518095 . A T 40 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTCTACAAAAATAGTGT;RSEQ=TCAAAGCTGCTCTGTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:20.7:1:25.7:1:1:0:23.3:2:1:0:4.3 +18 18518116 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAAGCTGCTCTGTAAAAA;RSEQ=AAAGGTTCCACTCTGTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:6.7:1:34:1:1:0:36.4:22:1:0:4.6 0/1:28:2:1,1:13,13:26,2:0.0714:2,2:12.5:1:30:1:1:1:42:4:0.0714:0:6.5 +18 18518118 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.11683;LSEQ=AAAGCTGCTCTGTAAAAAGA;RSEQ=AGGTTCCACTCTGTTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:3,3:6,5:0.4545:2,2:7:0:34.4:1:1:1.44544:36:10:0.4545:0:5.4 0/1:29:14:8,6:7,8:15,14:0.4828:2,2:5.9:1:32.3:1:0.71525:1.50:30.6:28:0.4828:0:2.4 +18 18518120 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5328;SOR=Inf;LSEQ=AGCTGCTCTGTAAAAAGAAA;RSEQ=GTTCCACTCTGTTAGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:17,0:0:2,0:7.5:1:31.7:1:1:0:33.3:16:1:0:3.7 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:16.5:1:29:1:1:1.07:42:4:0.0645:0:6.5 +18 18518134 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14541;SOR=0;LSEQ=AAGAAAGGTTCCACTCTGTT;RSEQ=GCTGAGTACACACATCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:29:0:33.5:1:1:1.40:21:4:0.1053:0:2.5 0/0:30:0:0,0:15,15:30,0:0:2,0:23.1:1:29.8:1:1:0:31.9:60:1:0:2.9 +18 18518157 . A T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTACACACATCACAAAC;RSEQ=TGTTTCTGAGAATCCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:8,11:0,0:0,19:1:0,2:26.5:1:32.1:1:1:0:32.6:38:1:0:3.9 1/1:24:24:12,12:0,0:0,24:1:0,2:19.7:1:30.2:1:1:0:33.5:48:1:0:3.6 +18 18518161 . T C 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.40451;LSEQ=TACACACATCACAAACATGT;RSEQ=TCTGAGAATCCTTCTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:24:0:34.5:1:1:1.40:27:4:0.1053:0:5.5 0/1:21:3:1,2:9,9:18,3:0.1429:2,2:19.7:1:31.7:1:1:1.93674:34:6:0.1429:0:5 +18 18518165 . G C 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.09701;LSEQ=CACATCACAAACATGTTTCT;RSEQ=AGAATCCTTCTGTGTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:4,6:3,4:7,10:0.5882:2,2:18.2:1:33.5:1:1:1.11721:29.7:20:0.5882:0:4.1 1/0:18:11:6,5:3,4:7,11:0.6111:2,2:21.6:1:31:1:1:1.56:35.5:22:0.6111:0:5.1 +18 18518170 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=CACAAACATGTTTCTGAGAA;RSEQ=CCTTCTGTGTAGTTTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:15,2:0.1176:2,2:18.5:1:30:1:1:1.46:38:4:0.125:0:4 0/0:17:0:0,0:9,8:17,0:0:2,0:13.1:1:28.3:1:1:0:37.4:16:1:0:4 +18 18518177 . G C 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49231;SOR=0;LSEQ=ATGTTTCTGAGAATCCTTCT;RSEQ=TGTAGTTTTTATAGGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:19:0:34.5:1:1:1.55:51:4:0.1333:0:5.5 0/0:11:0:0,0:6,5:11,0:0:2,0:10.3:1:31.1:1:1:0:36:22:1:0:5 +18 18518179 . G C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.65136;LSEQ=GTTTCTGAGAATCCTTCTGT;RSEQ=TAGTTTTTATAGGAAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:5,6:0,1:1,11:0.9167:0,2:9.5:1:33:1:1:0:35.2:22:0.9167:0:4.9 1/1:8:7:4,3:0,1:1,7:0.875:0,2:12.6:1:29.7:1:1:0:36.3:14:0.875:0:6 +18 18518181 . A C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42105;SOR=0;LSEQ=TTCTGAGAATCCTTCTGTGT;RSEQ=GTTTTTATAGGAAGATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:5,6:0,0:0,11:1:0,2:9.8:1:31.3:1:1:0:37.5:22:1:0:5.2 1/1:8:7:4,3:0,1:1,7:0.875:0,2:10.6:1:29:1:1:0:36.3:14:0.875:0:6 +18 18518190 . A G 53 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTCTGTGTAGTTTTTAT;RSEQ=GGAAGATATTTCCTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:9:1:33.7:1:1:0:49:6:1:0:5.7 1/1:1:1:1,0:0,0:0,1:1:0,0:22:0:27:0:1:0:29:2:1:0:8 +18 18518393 . TA CC 47 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTTTCCAACGAAATCCTC;RSEQ=AGCTATCCAAATATCCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:23.3:1:29.7:1:1:0:20:6:1:0:2.3 +18 18518400 . T G 49 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACGAAATCCTCTAAGCTA;RSEQ=CCAAATATCCACTTGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:29.3:1:31.3:1:1:0:20:6:1:0:2.3 +18 18518848 . T G 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACATCACAGACAAGTTTC;RSEQ=GAGAATGCTTCTGTCTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:8.7:1:32.3:1:1:0:31:6:1:0:4.3 0/1:15:2:1,1:7,6:13,2:0.1333:2,2:9.5:1:28:1:1:1.1547:24:4:0.1333:0:6.5 +18 18518886 . C A 44 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTTTATGGGAAGATATTT;RSEQ=CTTTTTCACCATAGGCGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:6,0:0:2,0:34.2:1:32.8:1:1:0:28.2:12:1:0:4.5 0/1:21:3:1,2:8,10:18,3:0.1429:2,2:7.7:1:28.3:1:1:1.56568:27.7:6:0.1429:0:7 +18 18518897 . A G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72771;LSEQ=AAGATATTTCCTTTTTCACC;RSEQ=TAGGCGTCAAAGCGCTCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:40.2:1:30:1:1:0:27.4:10:0.8333:0:4.4 1/0:23:18:9,9:2,3:5,18:0.7826:2,2:36.6:1:30.7:1:1:1.47:28.7:36:0.7826:0:4.3 +18 18518903 . GTCAAAGCGC TCAAGGCGA 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTCCTTTTTCACCATAGGC;RSEQ=TCGAAATGTCCACTTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,1:6,0:0:2,0:36.8:1:29.5:1:1:0:28.2:12:0.8571:0:4.5 0/1:25:3:1,2:9,11:20,3:0.12:2,2:24.7:1:30.3:1:1:1.60281:27.7:6:0.12:0:5 +18 18518908 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35827;SOR=2.42293;LSEQ=TTTTTCACCATAGGCGTCAA;RSEQ=GCGCTCGAAATGTCCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:1,2:3,6:0.6667:2,2:35.2:1:31.5:1:0.22619:7.11:28.2:12:0.6667:0:4.5 1/1:24:20:9,11:1,3:4,20:0.8333:2,2:29.2:1:31.8:1:0.61462:2.37:30.5:40:0.8333:0:4.2 +18 18518912 . C A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18676;SOR=2.53066;LSEQ=TCACCATAGGCGTCAAAGCG;RSEQ=TCGAAATGTCCACTTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:5,1:3,4:7,6:0.4615:2,2:33.8:1:26.8:1:0.26573:5.70:28.2:5:0.4167:0:4.5 1/0:29:20:9,11:5,4:9,20:0.6897:2,2:26:1:30:1:0.69985:1.50543:30.5:40:0.6897:0:4.2 +18 18518914 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCATAGGCGTCAAAGCGCT;RSEQ=GAAATGTCCACTTCCACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:13,0:0:2,0:19.1:1:31:1:1:0:30.6:26:1:0:4.8 0/1:33:2:1,1:14,17:31,2:0.0606:2,2:21:0:31.5:1:1:1.21:24:4:0.0606:0:6.5 +18 18518915 . G C 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19594;SOR=0.31971;LSEQ=CCATAGGCGTCAAAGCGCTC;RSEQ=AAATGTCCACTTCCACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:1,3:7,2:9,4:0.3077:2,2:10.3:1:30.5:1:0.21678:8.36696:37.5:8:0.3333:0:3.8 0/1:33:4:1,3:14,15:29,4:0.1212:2,2:10.8:1:29:1:0.6074:2.72016:23.5:8:0.1212:0:3.5 +18 18518925 . C T 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67209;SOR=0.62438;LSEQ=CAAAGCGCTCGAAATGTCCA;RSEQ=TTCCACATACTACAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:6,4:10,3:0.2308:2,2:15:0:32.7:1:1:1.30:26.3:6:0.2308:0:7 0/1:32:5:4,1:10,17:27,5:0.1563:2,2:15:0:31.6:1:0.14196:6.41:28:10:0.1563:0:7.4 +18 18518933 . T A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17809;SOR=2.65507;LSEQ=TCGAAATGTCCACTTCCACA;RSEQ=ACTACAAAAAGAGTGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:5,1:3,4:7,6:0.4615:2,2:19.3:1:27.2:1:0.26573:5.70:28.2:5:0.4167:0:4.5 1/0:30:21:7,14:5,4:9,21:0.7:2,2:13.1:1:29.2:1:0.41811:2.42062:31.1:42:0.7:0:4.8 +18 18518937 . A C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0.87789;LSEQ=AATGTCCACTTCCACATACT;RSEQ=CAAAAAGAGTGTTTCAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:6,4:10,4:0.2857:2,2:21:1:32.3:1:1:1.45647:26:8:0.2857:0:6.8 0/1:27:7:5,2:6,14:20,7:0.2593:2,2:20.3:1:30.7:1:0.08401:5.42:27.1:14:0.2593:0:7 +18 18518940 . A C 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.87603;LSEQ=GTCCACTTCCACATACTACA;RSEQ=AAAGAGTGTTTCAAACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:4,4:8,3:0.2143:2,2:30:0:34.3:1:1:1.88:26.3:6:0.2143:0:7 0/1:26:5:4,1:4,11:15,5:0.1923:2,2:30:0:32.2:1:0.10888:9.56:28:10:0.1923:0:7.4 +18 18518945 . A T 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.91118;LSEQ=CTTCCACATACTACAAAAAG;RSEQ=GTGTTTCAAACCTTCTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:6,6:12,3:0.2:2,2:35:0:31.7:1:1:1.91:26.3:6:0.2143:0:7 0/1:27:5:4,1:7,12:19,5:0.1852:2,2:35:0:29.2:1:0.14208:6.32:28:10:0.1852:0:7.4 +18 18518948 . G A 67 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43883;SOR=2.32319;LSEQ=CCACATACTACAAAAAGAGT;RSEQ=TTTCAAACCTTCTCTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:7.5:1:31:1:1:1.13389:26.5:4:0.125:0:7.5 0/1:25:6:3,3:8,11:19,6:0.24:2,2:8.7:1:26.3:1:1:1.36:30:12:0.24:0:7.7 +18 18518957 . C G 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.28801;LSEQ=ACAAAAAGAGTGTTTCAAAC;RSEQ=TTCTCTATGAAAGGGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:7,7:14,3:0.1765:2,2:45.3:1:32.3:1:1:1.92:26.3:6:0.1875:0:7 0/1:23:5:4,1:6,9:15,5:0.2174:2,2:45.2:1:29.8:1:0.30341:5.49:28:10:0.2174:0:7.4 +18 18518959 . T G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAAAGAGTGTTTCAAACCT;RSEQ=CTCTATGAAAGGGAATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:9,8:0,0:0,17:1:0,2:27.8:1:33.1:1:1:0:29.1:34:1:0:5.6 1/1:25:24:12,12:0,1:1,24:0.96:0,2:27.4:1:31.1:1:1:0:26.4:48:0.96:0:6.7 +18 18518961 . T C 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49211;SOR=1.87988;LSEQ=AAAGAGTGTTTCAAACCTTC;RSEQ=CTATGAAAGGGAATGTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:2,1:7,8:15,3:0.1667:2,2:16:1:33:0:1:2.18:24.3:6:0.1765:0:7.7 0/1:29:8:3,5:11,10:21,8:0.2759:2,2:18.1:1:28:1:0.68166:1.79538:29:16:0.2759:0:7.5 +18 18518962 . C G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.35684;SOR=0.55362;LSEQ=AAGAGTGTTTCAAACCTTCT;RSEQ=TATGAAAGGGAATGTTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:3,4:6,5:11,7:0.3889:2,2:41.7:1:33.3:1:1:1.55841:32.7:14:0.4118:0:5.1 0/1:31:8:4,4:11,12:23,8:0.2581:2,2:41.4:1:31.6:1:1:1.09:25.9:16:0.2581:0:6 +18 18518966 . G T 40 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33637;SOR=0.3409;LSEQ=GTGTTTCAAACCTTCTCTAT;RSEQ=AAAGGGAATGTTCAACTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:2,1:8,8:16,3:0.1579:2,2:15.7:1:25.3:1:1:1.93:30:2:0.1111:0:5 0/1:34:2:1,1:15,17:32,2:0.0588:2,2:7.5:1:26.5:1:1:1.13:28:4:0.0588:0:6 +18 18518972 . GA CC 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54499;SOR=Inf;LSEQ=CAAACCTTCTCTATGAAAGG;RSEQ=ATGTTCAACTCTATGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:19,0:0:2,0:25.8:1:32.2:1:1:0:28.1:38:1:0:6.1 0/1:34:3:1,2:16,15:31,3:0.0882:2,2:15:1:32:1:1:2.08761:41.3:6:0.0882:0:4 +18 18518976 . G C 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73621;SOR=0.73046;LSEQ=CCTTCTCTATGAAAGGGAAT;RSEQ=TTCAACTCTATGAGTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:7,7:14,5:0.2632:2,2:31:1:32.2:1:1:1.46843:24.2:10:0.2632:0:6 0/1:34:7:4,3:13,14:27,7:0.2059:2,2:33.9:1:32:1:1:1.42:22.6:14:0.2059:0:6 +18 18518977 . T C 50 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54499;SOR=Inf;LSEQ=CTTCTCTATGAAAGGGAATG;RSEQ=TCAACTCTATGAGTTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:19,0:0:2,0:27.1:1:31.2:1:1:0:28.1:38:1:0:6.1 0/1:34:3:2,1:15,16:31,3:0.0882:2,2:34.7:1:31.7:1:1:2.09:23.3:6:0.0882:0:8 +18 18518981 . A T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54499;SOR=Inf;LSEQ=TCTATGAAAGGGAATGTTCA;RSEQ=CTCTATGAGTTGAATGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:19,0:0:2,0:28.2:1:31.1:1:1:0:28.1:38:1:0:6.1 0/1:34:3:1,2:16,15:31,3:0.0882:2,2:17.7:1:29:1:1:2.08761:41.3:6:0.0882:0:4 +18 18518996 . T C 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12409;SOR=0;LSEQ=GTTCAACTCTATGAGTTGAA;RSEQ=GCAAACATCAGAACGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:6:1:30.5:1:1:1.12:47.5:4:0.1053:0:4.5 0/0:34:0:0,0:17,17:34,0:0:2,0:27.5:1:30.2:1:1:0:27.7:68:1:0:6.5 +18 18519000 . A G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54737;SOR=1.45795;LSEQ=AACTCTATGAGTTGAATGCA;RSEQ=ACATCAGAACGAAATTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:5,5:2,5:7,10:0.5882:2,2:37.7:1:33.8:1:0.62207:2.37:24.6:20:0.5882:0:6.9 1/0:31:21:11,10:4,6:10,21:0.6774:2,2:37.6:1:32:1:0.70425:1.62:26.4:42:0.6774:0:7 +18 18519002 . C G 74 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1415;SOR=Inf;LSEQ=CTCTATGAGTTGAATGCAAA;RSEQ=ATCAGAACGAAATTTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:17,0:0:2,0:27.6:1:33.1:1:1:0:28:34:1:0:6.1 0/1:29:5:2,3:12,12:24,5:0.1724:2,2:36.6:1:32.2:1:1:1.47932:32.4:10:0.1724:0:7.4 +18 18519010 . C A 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGAATGCAAACATCAGAA;RSEQ=GAAATTTCTGAGAATGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:6,6:0,0:0,12:1:0,2:34.3:1:31.8:1:1:0:25.3:24:1:0:6.6 1/1:23:23:12,11:0,0:0,23:1:0,2:35.8:1:30.9:1:1:0:26.5:46:1:0:7 +18 18519013 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11092;SOR=0;LSEQ=GAATGCAAACATCAGAACGA;RSEQ=ATTTCTGAGAATGCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:26.5:1:29:1:1:1:29:4:0.1667:0:5 0/0:23:0:0,0:12,11:23,0:0:2,0:33.8:1:30.9:1:1:0:26.5:46:1:0:7 +18 18519035 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTGAGAATGCTGCTGTC;RSEQ=ACTTTTTATATGAATGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:4,5:0,0:0,9:1:0,2:17.1:1:29.1:1:1:0:24.4:18:1:0:7.1 1/1:22:22:12,10:0,0:0,22:1:0,2:15.9:1:29.4:1:1:0:27:44:1:0:7 +18 18519038 . T C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGAATGCTGCTGTCCAC;RSEQ=TTTTATATGAATGCGCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:0,7:1:0,2:18.3:1:31.6:1:1:0:24.1:14:1:0:7.3 1/1:19:17:8,9:1,1:2,17:0.8947:2,2:17.2:1:31.5:1:1:1.11803:26.3:34:0.8947:0:7.1 +18 18519045 . A T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCTGCTGTCCACTTTTTAT;RSEQ=TGAATGCGCGCTTTCAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:16:1:28.8:1:1:0:22.4:10:1:0:7.6 1/1:18:17:8,9:1,0:1,17:0.9444:0,2:12.1:1:30.1:1:1:0:26.1:34:0.9444:0:6.9 +18 18519051 . G T 111 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTCCACTTTTTATATGAAT;RSEQ=CGCGCTTTCAACGAAATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:16.7:1:28.3:1:1:0:24:6:1:0:8 1/1:13:13:7,6:0,0:0,13:1:0,2:13:1:30.2:1:1:0:26:26:1:0:7.1 +18 18519053 . G C 103 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCACTTTTTATATGAATGC;RSEQ=CGCTTTCAACGAAATCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:14.7:1:28.7:1:1:0:24:6:1:0:8 1/1:11:11:6,5:0,0:0,11:1:0,2:14.5:1:30:1:1:0:25.6:22:1:0:7.3 +18 18519059 . T C 106 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATATGAATGCGCGCTT;RSEQ=CAACGAAATCCTCAAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:7.5:1:29.3:1:1:0:23.3:8:1:0:7.3 1/1:11:11:6,5:0,0:0,11:1:0,2:14.2:1:30.7:1:1:0:24.1:22:1:0:6.6 +18 18519073 . A C 51 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54118;SOR=Inf;LSEQ=GCGCTTTCAACGAAATCCTC;RSEQ=AAGCAATCCAAATATCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:12.3:1:30.5:1:1:0:24.5:8:1:0:4.5 0/1:13:3:2,1:4,6:10,3:0.2308:2,2:10.3:1:32.7:1:0.55944:2.75:26.7:6:0.2308:0:6.7 +18 18519078 . A T 50 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54118;SOR=Inf;LSEQ=TTCAACGAAATCCTCAAAGC;RSEQ=ATCCAAATATCCACTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:17.3:1:30.8:1:1:0:24.5:8:1:0:4.5 0/1:13:3:2,1:4,6:10,3:0.2308:2,2:5.3:1:32:1:0.55944:2.75:26.7:6:0.2308:0:6.7 +18 18519100 . T A 98 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAATATCCACTTGCAGA;RSEQ=TCCACAAAAAGAGTGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:39.3:1:31.5:1:1:0:24.5:8:1:0:4.5 1/1:10:10:4,6:0,0:0,10:1:0,2:37.2:1:29.8:1:1:0:22.8:20:1:0:5 +18 18519126 . C G 101 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAGAGTGTTTCAAAACT;RSEQ=CTCTATCAATAGAAAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:35.8:1:33:1:1:0:24.5:8:1:0:4.5 1/1:9:9:3,6:0,0:0,9:1:0,2:35.8:1:31.9:1:1:0:23:18:1:0:4.8 +18 18519143 . T G 97 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCTCTATCAATAGAAAG;RSEQ=TTCAACTCTGTTAGTTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:18.8:1:32.5:1:1:0:24.5:8:1:0:4.5 1/1:9:9:3,6:0,0:0,9:1:0,2:18.8:1:30.9:1:1:0:23:18:1:0:4.8 +18 18519153 . G T 82 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATAGAAAGTTTCAACTCT;RSEQ=TTAGTTGAGGACACACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:8.8:1:30:1:1:0:24.5:8:1:0:4.5 1/1:8:8:3,5:0,0:0,8:1:0,2:10.1:1:27.5:1:1:0:23.4:7:1:0:4.9 +18 18519636 . AC CG 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAAAAGAGTGTTTCCAA;RSEQ=TGCTGTATCAAAAGAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:32.3:1:1:0:23:4:1:0:6.5 +18 18519653 . A T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACTGCTGTATCAAAAGA;RSEQ=AGGTTGAACTTTGTTAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35:0:30:0:1:0:23:4:1:0:6.5 +18 18519660 . A T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTATCAAAAGAAAGGTTG;RSEQ=ACTTTGTTAGTTGAGGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:29.5:1:1:0:23:4:1:0:6.5 +18 18519663 . TT AC 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCAAAAGAAAGGTTGAAC;RSEQ=TGTTAGTTGAGGACACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:31.3:1:1:0:23:4:1:0:5.5 +18 18519688 . A G 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TAGTTGAGGACACACATTAC;RSEQ=AAGAAGTTTCTGAGAATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:9:1:30.5:1:1:0:21:4:1:0:2.5 1/0:4:2:1,1:2,0:2,2:0.5:0,2:9.5:1:28.5:1:1:0:23:4:0.5:0:5.5 +18 18519731 . A G 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTAGATTTTATATGAAG;RSEQ=TTTTCCCGTTTCCAATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:22:0:31:1:1:0:21:4:1:0:2.5 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:27:1:1:0:21.5:4:1:0:2 +18 18519959 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATGTCCACATTCAGATACT;RSEQ=CAAAAAGAGTGTTTCAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:33:0:1:0:27.5:4:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 18519962 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCACATTCAGATACTACA;RSEQ=AAAGAGTGTTTCAAACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:33.5:1:1:0:27.5:4:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 18519985 . G T 29 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGTTTCAAACCTGCTC;RSEQ=ATGAAAGGGAATGTTCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:29.5:1:1:0:27.5:4:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 18520076 . CT TA 31 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTAGATTTTATATGAAGATA;RSEQ=CCCGTTTCCAATGAAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:31.3:1:1:0:25:4:1:0:5.5 0/0:1:0:0,0:1,0:1,0:0:0,0:46:0:29:0:1:0:26:2:1:0:6 +18 18520079 . C G 33 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GATTTTATATGAAGATACTC;RSEQ=CGTTTCCAATGAAATCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:33:1:1:0:25:4:1:0:5.5 0/0:1:0:0,0:1,0:1,0:0:0,0:43:0:28:0:1:0:26:2:1:0:6 +18 18520103 . CT GC 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTCCAATGAAATCCACAAAG;RSEQ=ATCCAAATATCCACTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29.5:1:33.3:1:1:0:25:4:0.6667:0:4.5 0/0:3:0:0,0:2,1:3,0:0:2,0:10.7:1:28:1:1:0:23.3:6:1:0:5 +18 18520104 . T C 43 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCCAATGAAATCCACAAAGC;RSEQ=ATCCAAATATCCACTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,0:0,1:0.3333:0,0:6:0:33:0:1:0:30:2:1:0:5 1/1:3:3:2,1:0,0:0,3:1:0,2:11:1:27.3:1:1:0:23.3:6:1:0:5 +18 18520122 . C T 29 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=GCTATCCAAATATCCACTTG;RSEQ=AGATTCTACAGAAAGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:11.5:1:29:1:1:0:25:4:0.6667:0:4.5 0/1:4:1:1,0:1,2:3,1:0.25:2,0:1:0:31:0:1:0:24:2:0.25:0:7 +18 18520133 . G A 58 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCACTTGCAGATTCTACA;RSEQ=AAAGCGTGTTTCCAAACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:30:1:1:0:27:4:1:0:5 1/1:4:4:2,2:0,0:0,4:1:0,2:25.3:1:29.3:1:1:0:22:8:1:0:5 +18 18520137 . G T 71 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGCAGATTCTACAGAAA;RSEQ=CGTGTTTCCAAACTGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:39:0:32:0:1:0:30:2:1:0:5 1/1:6:6:3,3:0,0:0,6:1:0,2:20.3:1:27.7:1:1:0:23.7:12:1:0:4.8 +18 18520163 . C T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCAAACTGCTCTGTCAAA;RSEQ=GAAATGTTCAACTCCGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:31:1:32:0:1:0:34.5:4:1:0:4 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:35:1:31:1:1:1.18321:28:4:0.1538:0:6 +18 18520178 . C T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAACGAAATGTTCAACTC;RSEQ=GTTAGTTGAGGACACACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:31:1:32:0:1:0:34.5:4:1:0:4 0/1:13:2:2,0:5,6:11,2:0.1538:2,0:40:1:31.5:1:0.46154:0:21:4:0.1538:0:5.5 +18 18520181 . T G 118 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGAAATGTTCAACTCCGT;RSEQ=AGTTGAGGACACACATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31:1:34:0:1:0:34.5:4:1:0:4 1/1:13:13:7,6:0,0:0,13:1:0,2:29.5:1:32.1:1:1:0:26.5:26:1:0:4.5 +18 18520200 . G C 109 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGTTGAGGACACACATCA;RSEQ=AAACAAGTTTCTGCGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:28:0:34:0:1:0:39:2:1:0:3 1/1:11:11:6,5:0,0:0,11:1:0,2:28.5:1:31.6:1:1:0:27.3:22:1:0:4.5 +18 18520203 . A T 76 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTGAGGACACACATCAGAA;RSEQ=CAAGTTTCTGCGAATGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:25:0:32:0:1:0:39:2:1:0:3 1/0:11:6:3,3:3,2:5,6:0.5455:2,2:27.8:1:29.5:1:1:1.44544:29:12:0.5455:0:4.8 +18 18520227 . G C 79 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTCTGCGAATGCTTCTGT;RSEQ=TAGTTTTTATGGGAAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:1:0:31:0:1:0:39:2:1:0:3 1/1:6:6:3,3:0,0:0,6:1:0,2:7.5:1:30.8:1:1:0:27.5:12:1:0:4.8 +18 18520241 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=TTCTGTGTAGTTTTTATGGG;RSEQ=AGATATTTCCTTTTCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:6,0:0:2,0:2:0:32.5:1:1:0:25.5:12:1:0:5 1/0:4:2:0,2:2,0:2,2:0.5:0,0:14:1:28.5:1:0.33333:0:26.5:4:0.5:0:4 +18 18520245 . T C 34 v3;p8;pSTD;NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69379;LSEQ=GTGTAGTTTTTATGGGAAGA;RSEQ=ATTTCCTTTTCCACCATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:6:0:34:0:1:2.44949:24.5:4:0.3333:0:8 0/1:4:1:0,1:1,2:3,1:0.25:2,0:1:0:33:0:1:0:30:2:0.25:0:8 +18 18520246 . A G 68 p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07619;SOR=0;LSEQ=TGTAGTTTTTATGGGAAGAT;RSEQ=TTTCCTTTTCCACCATAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:1,1:2,4:0.6667:2,2:7:0:34.3:1:1:2.45:26:8:0.6667:0:3.5 0/0:4:0:0,0:1,3:4,0:0:2,0:11.8:1:29.3:1:1:0:32.8:8:1:0:5.3 +18 18520255 . TC CT 33 v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69379;LSEQ=TATGGGAAGATATTTCCTTT;RSEQ=CACCATAGGCCTGAAAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:17:0:33.8:1:1:2.44949:24.5:4:0.3333:0:7 0/1:4:1:0,1:1,2:3,1:0.25:2,0:12:0:31.5:0:1:0:30:2:0.25:0:7 +18 18520256 . C T 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53707;LSEQ=ATGGGAAGATATTTCCTTTT;RSEQ=CACCATAGGCCTGAAAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:0,0:0,4:0.6667:0,2:17:0:32.8:1:1:0:26:8:1:0:3.5 1/0:4:2:0,2:1,0:1,2:0.5:0,0:29:1:27:1:0.33333:0:26.5:4:0.6667:0:4 +18 18520259 . CC AA 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=Inf;LSEQ=GGAAGATATTTCCTTTTCCA;RSEQ=ATAGGCCTGAAAGCGCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,2:6,0:0:2,0:20:0:33.8:1:1:0:25.5:12:0.8571:0:4.7 0/1:5:2:1,1:0,3:3,2:0.4:0,2:15:1:28.2:1:0.4:0:49:4:0.4:0.2:3 +18 18520261 . A T 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58462;SOR=0.3561;LSEQ=AAGATATTTCCTTTTCCACC;RSEQ=TAGGCCTGAAAGCGCTCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:3,3:6,3:0.3333:2,2:15:1:31.3:1:1:1.8525:23.3:6:0.3333:0:5 0/1:7:1:0,1:2,4:6,1:0.1429:2,0:17:0:32:0:1:0:30:2:0.1429:0:7 +18 18520263 . A G 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.93674;LSEQ=GATATTTCCTTTTCCACCAT;RSEQ=GGCCTGAAAGCGCTCGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:5,4:9,1:0.1:2,0:6:0:32:0:1:0:36:2:0.1:0:5 0/1:11:2:0,2:4,5:9,2:0.1818:2,0:36:1:29.5:1:0.49091:0:26.5:4:0.1818:0:4 +18 18520274 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48;SOR=0;LSEQ=TTCCACCATAGGCCTGAAAG;RSEQ=GCTCGAAATGTCCACTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:9.5:1:31:1:1:1.18:20:4:0.1538:0:2.5 0/0:13:0:0,0:5,8:13,0:0:2,0:20.8:1:30.5:1:1:0:27.8:26:1:0:3.5 +18 18520278 . C T 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01784;SOR=Inf;LSEQ=ACCATAGGCCTGAAAGCGCT;RSEQ=GAAATGTCCACTTCCAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:26.2:1:31.9:1:1:0:24.2:26:1:0:3.4 0/1:15:6:3,3:3,6:9,6:0.4:2,2:17.5:1:30.7:1:0.62238:1.91:20.7:12:0.4:0:3.8 +18 18520284 . GT AC 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58333;SOR=0.40606;LSEQ=GGCCTGAAAGCGCTCGAAAT;RSEQ=CCACTTCCAGATACTACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:42.5:1:32.5:1:1:1.18:24.5:4:0.1538:0:6 0/1:15:1:0,1:6,8:14,1:0.0667:2,0:41:0:32.5:0:1:0:30:2:0.0667:0:6 +18 18520298 . A C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.48413;SOR=Inf;LSEQ=CGAAATGTCCACTTCCAGAT;RSEQ=CTACAGAAAGAGTGTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:31.9:1:30.9:1:1:0:24.2:26:1:0:3.2 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:36.5:1:31:1:1:1.55:20:4:0.1333:0:6 +18 18520299 . C G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05571;SOR=0.17415;LSEQ=GAAATGTCCACTTCCAGATA;RSEQ=TACAGAAAGAGTGTTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:4,5:2,2:4,9:0.6923:2,2:32.6:1:33.2:1:1:1.22862:24.9:18:0.6923:0:3.2 0/1:15:4:2,2:4,7:11,4:0.2667:2,2:25:1:29.5:1:1:1.68:38.5:8:0.2667:0:2 +18 18520301 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.48413;SOR=Inf;LSEQ=AATGTCCACTTCCAGATACT;RSEQ=CAGAAAGAGTGTTTCAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:29.6:1:29.9:1:1:0:24.2:26:1:0:3.2 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:27:0:33.5:1:1:1.55:24:4:0.1333:0:3.5 +18 18520307 . A T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10159;SOR=Inf;LSEQ=CACTTCCAGATACTACAGAA;RSEQ=GAGTGTTTCAAACCTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:24.5:1:31.9:1:1:0:24.2:26:1:0:3.2 0/1:15:4:2,2:4,7:11,4:0.2667:2,2:36.3:1:31.3:1:1:1.68:21:8:0.2667:0:5.3 +18 18520308 . G C 34 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58333;SOR=0.40606;LSEQ=ACTTCCAGATACTACAGAAA;RSEQ=AGTGTTTCAAACCTGCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:19.5:1:34:0:1:1.18:24.5:4:0.1538:0:6 0/1:15:1:0,1:6,8:14,1:0.0667:2,0:27:0:33:0:1:0:30:2:0.0667:0:6 +18 18520311 . T G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=TCCAGATACTACAGAAAGAG;RSEQ=GTTTCAAACCTGCTCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:20.6:1:30.3:1:1:0:24.2:26:1:0:3.2 0/1:13:2:1,1:4,7:11,2:0.1538:2,2:28.5:1:31.5:1:1:1.67:24:4:0.1538:0:3.5 +18 18520313 . T A 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.47196;LSEQ=CAGATACTACAGAAAGAGTG;RSEQ=TTCAAACCTGCTCTATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:14.5:1:32.5:1:1:1.18:24.5:4:0.1538:0:6 0/1:13:1:0,1:5,7:12,1:0.0769:2,0:22:0:32:0:1:0:30:2:0.0769:0:6 +18 18520315 . T G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22;SOR=0;LSEQ=GATACTACAGAAAGAGTGTT;RSEQ=CAAACCTGCTCTATGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:6,4:10,3:0.2308:2,0:24.3:1:33.3:1:0.19231:0:26.7:6:0.2308:0:3.3 0/0:13:0:0,0:5,8:13,0:0:2,0:21.4:1:30.2:1:1:0:27.2:26:1:0:3.8 +18 18520316 . C G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=ATACTACAGAAAGAGTGTTT;RSEQ=AAACCTGCTCTATGAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:15.6:1:33:1:1:0:24.2:26:1:0:3.2 0/1:13:2:1,1:4,7:11,2:0.1538:2,2:23.5:1:31.5:1:1:1.67:24:4:0.1538:0:3.5 +18 18520319 . A C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=CTACAGAAAGAGTGTTTCAA;RSEQ=CCTGCTCTATGAAAGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:12.6:1:30.6:1:1:0:24.2:26:1:0:3.2 0/1:13:2:1,1:4,7:11,2:0.1538:2,2:24:0:33:1:1:1.67:20:4:0.1538:0:6 +18 18520330 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=GTGTTTCAAACCTGCTCTAT;RSEQ=AAAGGGAATGTTTTATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:6.9:1:31.3:1:1:0:26.3:14:1:0:3.4 0/1:9:2:1,1:2,3:5,2:0.2222:2,2:13:0:30.5:1:1:1.41:20:4:0.2222:0:6 +18 18520333 . A C 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09091;SOR=0.09107;LSEQ=TTTCAAACCTGCTCTATGAA;RSEQ=GGGAATGTTTTATATTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:1,4:0.8:0,2:6.3:1:30.5:1:1:0:29:8:0.8:0:4 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:8.5:1:32:1:1:1.29:49:4:0.2222:0:3 +18 18520335 . G T 58 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20808;SOR=Inf;LSEQ=TCAAACCTGCTCTATGAAAG;RSEQ=GAATGTTTTATATTTGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:4.3:1:31.5:1:1:0:29:8:1:0:4 1/0:8:4:2,2:2,2:4,4:0.5:2,2:8.3:1:29:1:1:1:21:8:0.5:0:5.3 +18 18699289 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52923;SOR=0;LSEQ=GGCTTCTTTCTTTTTCTGAT;RSEQ=ATTTTCTTTCACGCGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:11,3:14,2:0.1176:2,2:29:1:31:1:0.45:3.31654:34.5:4:0.125:0:1 0/0:9:0:0,0:9,0:9,0:0:0,0:26.3:1:31:1:1:0:41.7:18:1:0:0 +18 18699370 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15239;SOR=0;LSEQ=ACGCACATTAATTCTCTTGG;RSEQ=AAGAATCTTGCCCTTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:13,6:19,2:0.0952:2,2:27:1:30:1:1:2.08171:23:4:0.1:0:1 0/0:32:0:0,0:23,8:31,0:0:2,0:24:1:30.4:1:1:0:25.2:62:0.9688:0:0 +18 18699435 . C A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51627;SOR=Inf;LSEQ=GCTGGGGAACATTGTAGACT;RSEQ=TTCCAGTTTTGCCAAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:17,26:43,0:0:2,0:38.9:1:32.9:1:1:0:25:42:1:0:0.2 0/1:65:2:1,1:31,32:63,2:0.0308:2,2:41:0:29:1:1:1.03:33:4:0.0313:0:1 +18 18699447 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5141;SOR=Inf;LSEQ=TGTAGACTCTTCCAGTTTTG;RSEQ=CAAGGTAACACTTGTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:17,27:44,0:0:2,0:26.5:1:31.3:1:1:0:25.8:43:1:0:0.2 0/1:65:2:1,1:31,32:63,2:0.0308:2,2:22:1:27:1:1:1.03:25:4:0.0317:0:1 +18 18699606 . C T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.19631;LSEQ=ATCGGGTGCCTCTCCTCTTT;RSEQ=CCTTTGTGTTCGTCATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:0,1:51,34:85,1:0.0116:2,0:1:0:24:0:0.40698:0:60:2:0.0118:0:1 0/1:144:2:1,1:86,56:142,2:0.0139:2,2:5.5:1:27:1:1:1.53096:36.5:4:0.0139:0:1 +18 18699671 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.50545;SOR=Inf;LSEQ=CCGGCCAAAAGGAAGGGAGT;RSEQ=TTTTGTTTGTTTGTTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:51,78:129,0:0:2,0:22.1:1:30:1:1:0:56.7:128:1:0:0.1 0/1:164:2:1,1:70,92:162,2:0.0122:2,2:12.5:1:27.5:1:1:1.31:48:4:0.0123:0:1 +18 18699672 . TTTTG T 91 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.19435;SOR=3.21948;LSEQ=CGGCCAAAAGGAAGGGAGTT;RSEQ=TTTGTTTGTTTGTTTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:48,78:126,2:0.0156:2,2:14:1:23.8:1:1:1.62:59.5:4:0.0157:0.0078:0 0/1:164:8:3,5:66,89:155,8:0.0488:2,2:39.4:1:30.6:1:1:1.23438:60:16:0.0491:0:0 +18 19020856 . T C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.29479;SOR=0.54601;LSEQ=CAATTGTAAATATACTGGTT;RSEQ=TAAGACATAAATGAGTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:9:8,1:46,6:52,9:0.1475:2,2:20.7:1:32.4:1:1:1.04:60:18:0.15:0:1 0/1:93:8:7,1:73,12:85,8:0.086:2,2:24.6:1:31.5:1:1:1.15:60:16:0.0879:0:1 +18 19020950 . G A 196 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAATAATTATGCCAGTCT;RSEQ=TCACTATGGTTGCTTGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:174,126:300,0:0:2,0:28.1:1:32.4:1:1:0:60:299:1:0:0.1 0/1:388:116:54,62:145,127:272,116:0.299:2,2:26.1:1:28.6:1:0.26726:1.30995:59.9:115:0.2987:0:1.1 +18 19021022 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49948;SOR=Inf;LSEQ=TCACACTTTTCTATACCTTT;RSEQ=AAAATGTATGTAATGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:52,120:172,0:0:2,0:23.5:1:31.8:1:1:0:60:85:1:0:0.1 0/1:187:2:1,1:65,120:185,2:0.0107:2,2:21:1:32.5:1:1:1.84:60:4:0.0107:0:2 +18 19756974 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.25257;SOR=Inf;LSEQ=AACTGCGGCTCCATCCAGAC;RSEQ=CCGCTGTGGCGGCGGGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:68,35:103,0:0:2,0:26.6:1:30.2:1:1:0:60:50.5:1:0:0.1 0/1:123:3:1,2:72,48:120,3:0.0244:2,2:23.3:1:27.3:1:0.56579:2.97302:60:6:0.025:0:1 +18 19757048 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24691;SOR=Inf;LSEQ=CTACAGCAAGATGAACGGCC;RSEQ=CAGCCGGCCCCTCATCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:43,79:122,0:0:2,0:24.8:1:30.5:1:1:0:59.9:60:1:0:0.1 0/1:121:2:1,1:47,72:119,2:0.0165:2,2:19:1:29.5:1:1:1.53:60:4:0.0165:0:1 +18 21337438 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26281;SOR=Inf;LSEQ=CCTCCCCAGTCCCCTCCCCA;RSEQ=CCCCCACCCTCACTGCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:126,52:178,0:0:2,0:21:1:28.4:1:1:0:59.9:3.944:1:0:0.8 0/1:237:3:2,1:156,76:232,3:0.0127:2,2:14.7:1:25.3:1:1:1.02622:60:2:0.0108:0:1.7 +18 21337563 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23897;SOR=Inf;LSEQ=CTTCTGTGGAGTGGTGGCGC;RSEQ=ATCTTAGGTGAGAGAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:36,112:148,0:0:2,0:21.1:1:31:1:1:0:60:73:1:0:0.1 0/1:143:2:1,1:30,111:141,2:0.014:2,2:17.5:1:28.5:1:0.38777:3.66:60:4:0.014:0:1 +18 22265718 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=AGTGGGGCAGGGCAAGGAGT;RSEQ=GGGGGCGTGGACATTCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:29.4:1:32.3:1:1:0:58.6:14:1:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:38:1:29:0:1:0:60:4:0.5:0:1 +18 22265894 . C T 23 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21288;SOR=Inf;LSEQ=CTCTTTAGCTGTAGCTCAAC;RSEQ=CTGTGGATAGGTGATGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:111,32:143,0:0:2,0:23.4:1:31.3:1:1:0:60:46.667:1:0:0.2 0/1:123:2:1,1:86,35:121,2:0.0163:2,2:6.5:1:23:0:0.5014:2.43684:60:4:0.0163:0:1.5 +18 22265897 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=90.53229;LSEQ=TTTAGCTGTAGCTCAACCCT;RSEQ=TGGATAGGTGATGGGAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:9:8,1:108,32:140,9:0.0604:2,2:30.4:1:27:1:0.68425:2.36:60:8:0.0544:0:1.1 1/1:140:120:87,33:11,7:18,120:0.8571:2,2:19.9:1:27.6:1:0.40344:1.67:60:39:0.8603:0:1.1 +18 22266007 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=TGATGGGCATGTTGGAACAT;RSEQ=GTGGTGAATATCAGGATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:55,114:169,2:0.0117:2,2:31.5:1:30:1:0.54902:2.06:60:4:0.0118:0:1 0/0:153:0:0,0:49,103:152,0:0:2,0:21.8:1:30.8:1:1:0:60:151:0.9934:0:0.1 +18 22266010 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23046;SOR=Inf;LSEQ=TGGGCATGTTGGAACATGGT;RSEQ=GTGAATATCAGGATACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:51,112:163,0:0:2,0:24.2:1:31.8:1:1:0:60:326:1:0:0.1 0/1:151:2:1,1:46,103:149,2:0.0132:2,2:11.5:1:28.5:1:0.52706:2.23:60:4:0.0132:0:1 +18 22266046 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49796;SOR=Inf;LSEQ=CCACTTTGCACAGGTATTTT;RSEQ=AAATGATGCAGGACTCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:38,85:123,0:0:2,0:26.8:1:32.5:1:1:0:60:122:1:0:0.1 0/1:123:2:1,1:48,73:121,2:0.0163:2,2:31.5:1:28:1:1:1.52:60:4:0.0163:0:1 +18 22266143 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49209;SOR=Inf;LSEQ=TCATATTCTGTCATCCAGTT;RSEQ=TATCCCTTGAGCCCAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:2,27:29,0:0:2,0:27.7:1:32.4:1:1:0:59.7:58:1:0:0 0/1:31:2:0,2:4,25:29,2:0.0645:2,0:14.5:1:31:1:1:0:60:4:0.0667:0:1 +18 23784839 . A G 111 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00205;SOR=0.04814;LSEQ=CACGCCTCCACCCCATGGGA;RSEQ=ATTCGATGGACATGGACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:8,2:5,1:6,10:0.625:2,2:22.4:1:33.7:1:1:1.23302:54.8:20:0.625:0:1 0/1:15:1:1,0:9,5:14,1:0.0667:2,0:15:0:34:0:1:0:56:2:0.0667:0:1 +18 23785015 . C A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14223;SOR=0.46378;LSEQ=TTGAATTGCACATTGTTGAA;RSEQ=CTGAGGCAATGAATTTCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:12:3,9:22,27:49,12:0.1967:2,2:26.6:1:29.7:1:0.32766:2.41091:58:24:0.2:0:1.1 0/1:69:7:3,4:24,38:62,7:0.1014:2,2:18.1:1:29.3:1:1:1.18:60:14:0.1014:0:1.3 +18 23785060 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49327;SOR=Inf;LSEQ=ATCCCATTAAAGTAACACCG;RSEQ=CAACTTGAAGTGTATATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:31,0:0:2,0:27.3:1:31.1:1:1:0:59.2:14.5:1:0:0.5 0/1:34:2:1,1:7,25:32,2:0.0588:2,2:8.5:1:26.5:1:0.42068:3.41:60:4:0.0606:0:1 +18 23785095 . C T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16651;SOR=0.43082;LSEQ=TATACAGCCAACGGCTTCCC;RSEQ=TGGGAGCTTTGAAATAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:12:6,6:10,6:16,12:0.4286:2,2:26.4:1:29.8:1:0.70217:1.63612:60:11:0.4074:0:1.4 0/1:29:7:3,4:9,13:22,7:0.2414:2,2:10.7:1:28.7:1:1:1.08:60:14:0.2414:0:1.1 +18 23785115 . C G 54 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.64567;SOR=0.50652;LSEQ=CTGGGAGCTTTGAAATAACA;RSEQ=CCCTCCATGGTCTTACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:9,12:21,3:0.125:2,0:34.7:1:34.7:1:0.21739:0:60:6:0.125:0:2 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:22.5:1:33.5:1:1:1.14834:60:4:0.0667:0:1.5 +18 23785313 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5357;SOR=Inf;LSEQ=AAGATGAAGAAGAGGAGGAT;RSEQ=TGAAACTCTTAAGTATATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:25,39:64,0:0:2,0:20.3:1:32.5:1:1:0:48.4:128:1:0:0 0/1:113:2:1,1:41,70:111,2:0.0177:2,2:25:1:27:1:1:1.70:42:4:0.018:0:1 +18 23785648 . A G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10865;SOR=0.18681;LSEQ=AAAGACTCAAAACCATCAAC;RSEQ=CCAAGATAAAAAAGACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:3,4:4,4:8,7:0.4667:2,2:7:1:31.4:1:1:1.30792:31.4:14:0.4667:0:1.3 0/1:15:2:1,1:9,4:13,2:0.1333:2,2:25.5:1:31.5:1:1:2.12136:28:4:0.1333:0:1.5 +18 23785705 . CA C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5298;SOR=Inf;LSEQ=GAAAAAAACTCCTAAAACAC;RSEQ=AAAGACCTAGTTCTGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:18,0:0:2,0:27.2:1:30.7:1:1:0:47.7:36:1:0:0.5 0/1:32:2:1,1:20,10:30,2:0.0625:2,2:24:1:29.8:1:1:1.95408:42:4:0.0645:0.0313:0 +18 23785855 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49024;SOR=Inf;LSEQ=CTATTCAAGATCTCTGGCAG;RSEQ=GGAGGAAGCCTCTTGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:24.2:1:31.3:1:1:0:59.2:38:1:0:0.5 0/1:22:2:1,1:5,15:20,2:0.0909:2,2:29:1:27.5:1:0.48052:2.83:30.5:4:0.0909:0:1 +18 23812510 . A T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1706;SOR=0.38234;LSEQ=AGATGGCTGTCACAGGACCT;RSEQ=GAAAGGGGAGAAGCCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:4,2:7,5:12,6:0.3333:2,2:22.3:1:30.8:1:1:1.40:30.7:12:0.3333:0:1.2 0/1:38:6:4,2:19,13:32,6:0.1579:2,2:21.3:1:30.5:1:1:1.36:43:12:0.1579:0:1.2 +18 24173846 . TAAG T 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAAGGAGGAAGAGGAAGA;RSEQ=GAGGAGGAGGAGGAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,7:20,0:0:2,0:24.5:1:29.3:1:1:0:60:40:0.9524:0:0.2 1/0:36:23:13,10:7,4:11,23:0.6389:2,2:21.3:1:31.2:1:1:1.33452:59:46:0.6571:0.1944:0.3 +18 24173847 . AAGG A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.1908;SOR=0;LSEQ=ACAAGGAGGAAGAGGAAGAT;RSEQ=AGGAGGAGGAGGAAGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:13,8:21,2:0.087:2,0:6.5:1:30.7:1:0.52569:0:60:4:0.087:0.0435:0 0/0:29:0:0,0:7,4:11,0:0:2,0:22.3:1:29.9:1:1:0:59:22:1:0:0.1 +18 26620725 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49799;SOR=Inf;LSEQ=TTAATACATTTATGTAAGAA;RSEQ=AGCTTCATAAACACCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:96,23:119,0:0:2,0:21.5:1:32.6:1:1:0:60:28.75:1:0:0.6 0/1:122:2:1,1:95,25:120,2:0.0164:2,2:29:0:31:1:0.3822:3.74587:60:4:0.0165:0:1.5 +18 26620796 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2058;LSEQ=TCTCAGCTCCTATGCATTCT;RSEQ=TGATAATGGACATTAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:281:213:130,83:36,32:68,213:0.758:2,2:24.5:1:31.7:1:0.25878:1.39:60:70:0.7581:0:1.9 0/1:368:144:85,59:116,108:224,144:0.3913:2,2:26.7:1:31:1:0.19818:1.34:59.9:47:0.3895:0:2 +18 26620819 . A G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0.25211;LSEQ=ATAATGGACATTAAAGGAGC;RSEQ=TTTTTTTAGGAGCCAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:309:225:124,101:40,41:81,225:0.7282:2,2:25.8:1:30.7:1:0.43589:1.26:60:44:0.7237:0:1.9 0/1:457:184:99,85:136,136:272,184:0.4026:2,2:25:1:29.9:1:0.44581:1.16:60:91:0.4018:0:1.9 +18 26620907 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24765;LSEQ=TTTTTAGGTAAGAAGACTTC;RSEQ=ACTTCTGACCTAGGTGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:119:20,99:7,22:29,119:0.8041:2,2:24.4:1:29.2:1:0.42126:1.56974:60:238:0.8041:0:1.4 1/0:173:87:24,63:23,63:86,87:0.5029:2,2:20.4:1:27.7:1:1:1.04:60:174:0.5029:0:1.4 +18 26620985 . A C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00209;SOR=0.13202;LSEQ=TTTAAACTAGAAAAACAGAC;RSEQ=AAATATAAGAAATGATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:0,29:0,4:4,29:0.8788:0,1:15.8:1:33:1:1:0:60:58:0.8788:0:1.6 0/1:23:11:0,11:0,12:12,11:0.4783:0,0:24.6:1:32.4:1:1:0:60:22:0.4783:0:1.5 +18 28787355 . T A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00307;SOR=0.11065;LSEQ=TCATTTTATAAATTCTTTCC;RSEQ=AATTACCTCAAATCACAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:14:14,0:21,0:21,14:0.4:1,1:28:1:29.9:1:1:0:60:13:0.3939:0:1.1 0/1:30:2:2,0:26,2:28,2:0.0667:2,0:28.5:1:28:1:1:0:60:4:0.0667:0:1 +18 28787426 . G T 29 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.61827;SOR=2.06752;LSEQ=AGTCTGTCCTCATAGACAGA;RSEQ=CACTCTGATGACAATCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:1:0,1:86,26:112,1:0.0088:2,0:1:0:25:0:0.23894:0:60:2:0.0089:0:1 0/1:110:2:1,1:78,30:108,2:0.0182:2,2:40:0:29.5:1:0.48607:2.57407:60:4:0.0182:0:1 +18 28787475 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21207;SOR=0;LSEQ=ACAGCTAGACACTCGGTTAG;RSEQ=TCAGCTCCTTAGGTCTTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:107,81:188,2:0.0105:2,2:22:1:30:1:1:1.31902:60:4:0.0109:0:1.5 0/0:222:0:0,0:129,93:222,0:0:2,0:26.1:1:30.4:1:1:0:60:73:1:0:0.4 +18 28787479 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20701;SOR=0;LSEQ=CTAGACACTCGGTTAGGTCA;RSEQ=CTCCTTAGGTCTTGCGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:108,80:188,2:0.0105:2,2:27.5:1:29.5:1:1:1.34782:60:4:0.0107:0:2 0/0:227:0:0,0:127,99:226,0:0:2,0:26.6:1:31.2:1:1:0:60:112:0.9956:0:0.4 +18 28787520 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16048;SOR=0;LSEQ=TGCCTCATGTAAATGCTGCA;RSEQ=GATATCCATTCGAGTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:85,114:199,2:0.01:2,2:25:1:30:1:1:1.34:60:4:0.0101:0:2 0/0:300:0:0,0:140,158:298,0:0:2,0:23.9:1:29.9:1:1:0:60:98.333:0.9933:0:0.6 +18 28787524 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=0.4525;LSEQ=TCATGTAAATGCTGCACGAT;RSEQ=TCCATTCGAGTGCAGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:200:126:51,75:33,41:74,126:0.63:2,2:22:1:31.9:1:0.65645:1.18264:60:62:0.6263:0:1.2 0/1:299:130:57,73:82,87:169,130:0.4348:2,2:23.9:1:31.2:1:0.483:1.20633:60:129:0.4329:0:1.1 +18 28787593 . G T 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.54275;LSEQ=GCACTCATTTCTTTATGGTA;RSEQ=TCATAATAATCGCAATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:0,1:39,90:129,1:0.0077:2,0:34:0:16:0:1:0:60:0:0:0:3 0/1:169:2:1,1:61,105:166,2:0.0118:2,2:13:0:30.5:1:1:1.72:60:4:0.012:0:1.5 +18 28787634 . G T 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=0;LSEQ=ATAATAACTTCCATTTATTG;RSEQ=TCTAGAAATCACTGTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:11:2,9:9,37:46,11:0.193:2,2:24.7:1:30:1:1:1.09289:60:22:0.193:0:1.1 0/0:63:0:0,0:14,49:63,0:0:2,0:13:0:14:0:1:0:60:0:0:0:2 +18 28787710 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21773;SOR=0.26369;LSEQ=AAGAACCCTTTGAAGGTAGG;RSEQ=ATTTTTAGAGTAAACAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:8,8:0.5:0,0:25.1:1:29.4:1:1:0:60:16:0.5:0:1.1 0/1:10:2:0,2:1,6:7,2:0.2:2,0:29:1:29.5:1:1:0:60:4:0.2222:0:1 +18 29691526 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5311;SOR=Inf;LSEQ=TAATTGTTCAAATATTCCCA;RSEQ=CTAGTCCAGTTATCAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:40,12:52,0:0:2,0:22.8:1:30.6:1:1:0:60:25:1:0:0.3 0/1:89:2:1,1:59,28:87,2:0.0225:2,2:15:1:28.5:1:0.54801:2.08802:60:4:0.0225:0:1.5 +18 29691607 . C T 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.30542;LSEQ=ATTTATGTACATATGAGTAG;RSEQ=CTAACTTATTTAATATGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:57:25,32:13,14:27,57:0.6786:2,2:23.7:1:29.2:1:0.81552:1.18612:60:114:0.6786:0:1.1 0/1:151:59:27,32:42,50:92,59:0.3907:2,2:23.8:1:28.3:1:1:1.00:60:58:0.3919:0:1.2 +18 29691678 . AT A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50129;SOR=Inf;LSEQ=TTATAGAGATGAAGAGAGTA;RSEQ=TTTTTTTGTAATTAATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:10,33:43,0:0:2,0:24.9:1:30.7:1:1:0:60:86:1:0:0.3 0/1:54:2:1,1:11,41:52,2:0.037:2,2:33:1:29:1:0.39832:3.61:60:4:0.037:0:0 +18 30089439 . T G 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAATCTTCCCTTCTTCCCT;RSEQ=GGATGTCATCATTTCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:199,201:400,0:0:2,0:26.8:1:30.6:1:1:0:60:199:1:0:0.6 0/1:512:24:9,15:254,234:488,24:0.0469:2,2:29:1:29.6:1:0.20982:1.80703:60:11:0.0435:0:1.3 +18 30089478 . T C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.16852;LSEQ=TGAGTTTTAATCCTTACTTC;RSEQ=TTCCCCTGTAGAAAACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:331:270:107,163:27,33:60,270:0.8157:2,2:24.8:1:32.2:1:0.46951:1.24553:60:53:0.8204:0:1.1 0/1:443:189:81,108:118,134:252,189:0.4266:2,2:26.7:1:30.8:1:0.43969:1.1737:60:188:0.4273:0:1.1 +18 30089518 . CT C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16242;SOR=0;LSEQ=CCTCACGAGAGGAGGCAAAT;RSEQ=TTTTTTGAATTTCTGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:49,123:172,2:0.0115:2,2:22.5:1:30:1:0.49332:2.50:60:4:0.0116:0:0 0/0:257:0:0,0:87,167:254,0:0:2,0:22.7:1:29.5:1:1:0:60:62.5:0.9881:0:0.5 +18 30089578 . C T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2385;SOR=0;LSEQ=CCATAGTAACTTAATTATTC;RSEQ=TCCAATTCCAGCTAAACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:12,60:72,2:0.027:2,2:11:0:33:1:0.32247:4.84:60:4:0.0274:0:1.5 0/0:77:0:0,0:12,65:77,0:0:2,0:22:1:31.2:1:1:0:60:154:1:0:0.2 +18 31418065 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24952;SOR=Inf;LSEQ=ATAATAAATAAGTAAATTGA;RSEQ=GAAGAGAGAGAAAGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:203,67:270,0:0:2,0:22.7:1:32.7:1:1:0:60:44:1:0:0.1 0/1:289:3:1,2:195,91:286,3:0.0104:2,2:11.7:1:28:1:0.2432:4.26196:60:6:0.0106:0:1 +18 31418131 . T C 233 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGAATTGACATGTAGCTC;RSEQ=GAGCCTTCTGTCAACAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:242,214:456,0:0:2,0:24.9:1:30.8:1:1:0:60:56:1:0:0.1 0/1:502:237:126,111:141,121:262,237:0.4721:2,2:25.6:1:29.6:1:0.92845:1.02652:60:58.25:0.4707:0:1.2 +18 31418248 . A C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19198;SOR=Inf;LSEQ=TTAACATATGAACTTCTTTT;RSEQ=CTTTCACAATTGCCCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:21,113:134,0:0:2,0:22.6:1:29.8:1:1:0:60:66:1:0:0.1 0/1:105:2:1,1:13,90:103,2:0.019:2,2:5:1:29.5:1:0.25:6.71:60:4:0.019:0:1 +18 31418249 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50371;SOR=0;LSEQ=TAACATATGAACTTCTTTTA;RSEQ=TTTCACAATTGCCCTATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:19,106:125,2:0.0156:2,2:18:1:30:1:0.29121:5.46:60:4:0.0157:0:1 0/0:103:0:0,0:13,90:103,0:0:2,0:20.3:1:31.1:1:1:0:60:33.333:1:0:0.1 +18 31705614 . A G 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34409;SOR=1.21316;LSEQ=ATAGTATAAATATTTTCTTT;RSEQ=TTAATGTTCGGAGTAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:217:116:53,63:45,55:100,116:0.5346:2,2:22.8:1:31.4:1:1:1.03:60:37.667:0.5305:0:1.2 1/0:237:138:63,75:39,59:98,138:0.5823:2,2:25.7:1:31.5:1:0.42418:1.27:60:276:0.5823:0:1.1 +18 31705717 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.23142;SOR=Inf;LSEQ=TCATATTAAAAGCATTTTTT;RSEQ=AAAAAAAGAGACAATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:4,44:48,0:0:2,0:22.7:1:29.3:1:1:0:60:96:1:0:0.1 0/1:45:2:0,2:4,39:43,2:0.0444:2,0:36:1:30.5:1:1:0:60:4:0.0455:0:1 +18 34882741 . T C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5467;SOR=0.36007;LSEQ=CCCAGACCAGCAGGGTGAGC;RSEQ=TTCAGGAGGCAGAGGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:9,0:2,0:2,9:0.8182:0,0:28.3:1:30.9:1:1:0:60:18:0.8182:0:1 1/0:5:3:3,0:2,0:2,3:0.6:0,0:26.3:1:31.3:1:1:0:60:6:0.6:0:1 +18 34882891 . T C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23262;SOR=Inf;LSEQ=TGAGGGACAGGGTGCACAGC;RSEQ=AGGCCAGGCACAGAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:80,59:139,0:0:2,0:25.2:1:29.9:1:1:0:60:68.5:1:0:0.7 0/1:130:2:1,1:70,58:128,2:0.0154:2,2:7:0:33:1:1:1.20514:60:4:0.0157:0:1.5 +18 34882899 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05402;SOR=Inf;LSEQ=AGGGTGCACAGCTAGGCCAG;RSEQ=CACAGAGGAGGGGTGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:87,65:152,0:0:2,0:24.3:1:31:1:1:0:60:24.333:1:0:0.7 0/1:143:4:2,2:73,66:139,4:0.028:2,2:33:1:29.3:1:1:1.10528:60:8:0.0286:0:1.3 +18 34882932 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00035;SOR=0.40235;LSEQ=GTGGGAGAGGAGAGTGGGAA;RSEQ=GGGGCTCCATCTCCTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:151:115:59,56:16,19:35,115:0.7616:2,2:27:1:31.3:1:0.6998:1.25:60:230:0.7616:0:1.2 1/0:146:82:36,46:30,34:64,82:0.5616:2,2:27.1:1:29.4:1:0.74022:1.12652:60:26.333:0.5524:0:1.2 +18 34883082 . T G 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10526;SOR=0;LSEQ=GTACCATTGTTCTCAGCACT;RSEQ=CCTTTGGCTCATTTGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:0,17:0,1:1,17:0.9444:0,1:21.6:1:32.5:1:1:0:60:34:0.9444:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:19:0:30:0:1:0:60:2:1:0:0 +18 35069156 . C T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01767;SOR=0;LSEQ=ATCCGATGCAGCGGCTGACA;RSEQ=GCCAGCATGGCAGATTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:8,2:10,6:0.375:2,0:20.3:1:32.2:1:0.5:0:60:12:0.375:0:1 0/0:16:0:0,0:12,4:16,0:0:2,0:28.1:1:30.6:1:1:0:60:32:1:0:0.2 +18 35070733 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGGCCCTCCCAGCTGTG;RSEQ=GACTCTGACGGGACATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:31:0:1:0:60:4:1:0:1 +18 35071242 . C T 30 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTCACCTGAGAGGGACG;RSEQ=CGTGCCCACCTCCTCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:30:0:1:0:60:4:1:0:1 +18 36969660 . C T 45 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CACACAGGGCAGGGGAGCCC;RSEQ=CACCCCCCAAGCCAAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:26.5:1:33:1:1:0:60:4:1:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:10:1:29:1:1:0:45:6:1:0:1.3 +18 36970447 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GGTGAGACCCTCCAAAAGGG;RSEQ=TTGTCAGACACCCTATACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:22.4:1:31.1:1:1:0:52.3:16:1:0:0.1 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:25.5:1:31:1:1:1.29:60:4:0.25:0:1.5 +18 36970621 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16471;SOR=0;LSEQ=AATAGGGCCTGAAGTGAACC;RSEQ=CCAGCAAACTGCAGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:7,12:19,2:0.0952:2,2:30:1:30:1:1:1.67:53.5:4:0.0952:0:1 0/0:30:0:0,0:14,16:30,0:0:2,0:29.7:1:29.3:1:1:0:46.2:29:1:0:0.1 +18 38529854 . C CT 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATTTGTCCTTTGTGTTCA;RSEQ=TGCCATAGGAGGGGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:159,34:193,0:0:2,0:25.1:1:32.7:1:1:0:59.8:386:1:0:0.1 0/1:129:17:15,2:93,19:112,17:0.1318:2,2:23.5:1:30.6:1:0.73761:1.53:60:34:0.1339:0.0233:0.2 +18 38529883 . G T 40 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24893;SOR=0;LSEQ=GAGGGGAATAAAATGAAAGA;RSEQ=AGGGAGAGTCAGGCCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:198,96:294,3:0.0101:2,2:6.3:1:25.3:1:0.25402:4.10357:60:6:0.0102:0:1 0/0:287:0:0,0:195,92:287,0:0:2,0:23:1:31:1:1:0:60:46.833:1:0:0.3 +18 38529971 . A C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5013;SOR=1.09857;LSEQ=TTGAAAGTGACAAGAAGGTC;RSEQ=AATGAAGTTAACAGGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:191:84,107:97,112:209,191:0.4775:2,2:25.6:1:31.6:1:0.68761:1.10294:60:94.5:0.4749:0:1.1 1/0:493:247:111,136:109,137:246,247:0.501:2,2:25.2:1:30.5:1:0.92788:1.03:60:122.5:0.499:0:1.2 +18 38530035 . G C 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAATGGAATCCAGTTCAT;RSEQ=GGTGTGGGCATATCACGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:48,145:193,0:0:2,0:24.6:1:31.7:1:1:0:59.9:95.5:1:0:0.4 0/1:193:40:12,28:41,112:153,40:0.2073:2,2:24.6:1:28.8:1:0.69384:1.17:60:19:0.2:0:1.6 +18 38530039 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23707;SOR=Inf;LSEQ=ATGGAATCCAGTTCATGGGT;RSEQ=TGGGCATATCACGGTGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:43,143:186,0:0:2,0:23.5:1:32.4:1:1:0:59.9:185:1:0:0.3 0/1:177:2:1,1:44,131:175,2:0.0113:2,2:14:1:26:1:0.44492:2.96:60:4:0.0113:0:2.5 +18 38530053 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22767;SOR=Inf;LSEQ=ATGGGTGTGGGCATATCACG;RSEQ=TGTTCAATGAACATACGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:26,117:143,0:0:2,0:22.7:1:32.2:1:1:0:59.9:70.5:1:0:0.2 0/1:131:2:1,1:26,103:129,2:0.0153:2,2:21:0:31:0:0.37099:3.91:60:4:0.0155:0:2.5 +18 38530160 . A G 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCCTTCTTTCCTTCCTC;RSEQ=TTTCTCTTTCTTTCCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:1,29:0,0:0,30:1:0,1:21.8:1:33:1:1:0:57.9:60:1:0:1.1 1/1:16:16:0,16:0,0:0,16:1:0,1:21.4:1:31.3:1:1:0:56.8:15:1:0:1.3 +18 38530881 . A T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTTTTCCAAGTGCTTAGA;RSEQ=TAAAATTCAAACTACTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:28:1:1:0:60:4:1:0:1 +18 38531882 . C T 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACAGGCGTGAGCCACTG;RSEQ=GCCCAGCTCCTTAGTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:48:0:29.5:1:1:0:59:4:1:0:1 +18 39535169 . T TC 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGGGGGCGGAACCGGAAGT;RSEQ=CCGTGTTGTGGGGCTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:125,34:159,0:0:2,0:23.7:1:30.5:1:1:0:59.8:78.5:1:0:0.2 0/1:181:29:24,5:118,34:152,29:0.1602:2,2:18.7:1:29.9:1:0.62962:1.38:60:58:0.1629:0.0552:0.1 +18 39535420 . C G 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01425;SOR=Inf;LSEQ=GAGGCAGAAAGTACGTGACT;RSEQ=GTCTCAAGGCCCAGATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:3,76:79,0:0:1,0:21.6:1:29.2:1:1:0:60:25.333:1:0:0.1 0/1:86:7:0,7:6,73:79,7:0.0814:2,0:31.1:1:31.9:1:1:0:60:14:0.0814:0:1 +18 39537688 . G C 249 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAGCCTTTGGCCTTGCCAGT;RSEQ=AGAACATCCTACAAAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:220:90,130:117,163:280,220:0.44:2,2:24.5:1:32:1:0.85534:1.03675:60:109:0.4404:0:1.1 0/0:622:0:0,0:268,354:622,0:0:2,0:25.4:1:30.6:1:1:0:60:61.2:1:0:0.1 +18 39537777 . TG T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5016;SOR=0;LSEQ=ACTGTTCTTACCTTTCTTTA;RSEQ=GATGCTGCAAGTATAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:25,142:167,2:0.0118:2,2:15.5:1:30:1:0.2848:5.59:60:4:0.0119:0.0059:1 0/0:144:0:0,0:26,118:144,0:0:2,0:21.1:1:30.3:1:1:0:60:47:1:0:0.1 +18 39542407 . GAT G 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0;SOR=42.66667;LSEQ=GTTTGTTAATTTAAAAGAAA;RSEQ=ATATATATATGTATTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:3,0:152,21:173,3:0.0169:2,0:24.7:1:33:1:1:0:60:6:0.0172:0.0056:0 0/1:202:86:72,14:98,18:116,86:0.4257:2,2:24.5:1:31.2:1:1:1.05832:59.7:172:0.4279:0.099:0.1 +18 39542645 . C A 55 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12787;SOR=Inf;LSEQ=GGAGTGTAGCAGCTTTCTGA;RSEQ=CCTTTTCTTTTTCGGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:85,249:334,0:0:2,0:22.3:1:31.1:1:1:0:60:26.833:1:0:0.1 0/1:386:4:3,1:102,279:381,4:0.0104:2,2:5.5:1:27.8:1:0.06354:8.15:60:8:0.0106:0:1.3 +18 39550227 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49946;SOR=Inf;LSEQ=TTCTCTTTATTTTTAGGAAT;RSEQ=TAAAATTTCCTGTAATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:155,31:186,0:0:2,0:24:1:32.3:1:1:0:59.9:185:1:0:0.1 0/1:201:2:1,1:158,40:198,2:0.01:2,2:15:1:25.5:1:0.36879:3.91386:60:4:0.0101:0:3.5 +18 39550271 . A T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0676;SOR=Inf;LSEQ=ATTAATTTACTTCTACCCTG;RSEQ=ACATTCTCTTTTTCCCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:286,123:409,0:0:2,0:25.1:1:30.4:1:1:0:60:101.25:1:0:0.1 0/1:496:5:1,4:307,184:491,5:0.0101:2,2:10:1:24.6:1:0.07089:6.64948:60:10:0.0102:0:1 +18 39570304 . T C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16481;LSEQ=AATAAAATAAAAATGTGTTA;RSEQ=GTTTTGACTTGTATTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:6,0:41,1:42,6:0.125:1,0:23.8:1:32.3:1:1:0:60:12:0.1277:0:1 0/1:49:7:7,0:42,0:42,7:0.1429:1,0:22.6:1:31.6:1:1:0:60:14:0.1429:0:1 +18 39570409 . A AT 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.27317;SOR=0.68871;LSEQ=AATCATTTTTCATGAAAATC;RSEQ=TTTTTTTTTTCAGAGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:24:16,8:266,113:379,24:0.0594:2,2:22.5:1:30.4:1:0.81862:1.17648:60:48:0.0597:0.0149:0.3 0/1:456:19:12,7:298,139:437,19:0.0417:2,2:20.5:1:29.6:1:0.62374:1.24993:59.7:38:0.042:0.0132:0.2 +18 39570536 . GT G 73 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=1.26755;LSEQ=AAGGTATTTCCCTTGGAACT;RSEQ=TTTTGGTCTCTAAAGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:3:1,2:117,255:372,3:0.008:2,2:37:1:31:1:1:1.09:60:6:0.0081:0:0 0/1:494:5:2,3:161,327:488,5:0.0101:2,2:12.8:1:31.6:1:0.66742:1.35:60:10:0.0102:0:0 +18 39570683 . A G 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01348;SOR=Inf;LSEQ=AATCAAATCATATAACTACA;RSEQ=CAAGATTACAAAAGCCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:26,0:0:1,0:22.4:1:31.2:1:1:0:59.9:52:1:0:0 0/1:15:4:0,4:0,11:11,4:0.2667:0,0:22.8:1:32.3:1:1:0:60:8:0.2667:0:1 +18 39571373 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTTTGAAACCACATAAA;RSEQ=TATCTTCTATTATTGTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:31:1:28.5:1:1:0:60:4:0.6667:0:1.5 +18 39575790 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4978;SOR=0;LSEQ=TAAGTACCTTTTCTATTTAT;RSEQ=AATAGCTTTTGAAATTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:2,0:107,5:112,2:0.0175:1,0:28.5:1:33:0:1:0:60:4:0.0175:0:1 0/0:113:0:0,0:110,3:113,0:0:1,0:20.3:1:31.8:1:1:0:60:226:1:0:0 +18 39576759 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19732;SOR=Inf;LSEQ=TTTGTTATTAATGATCAAGA;RSEQ=GAGGAAAATGCCATGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:8,124:132,0:0:2,0:22.9:1:30.8:1:1:0:60:264:1:0:0.1 0/1:106:2:1,1:6,98:104,2:0.0189:2,2:32:1:31:1:0.1283:15.20:60:4:0.019:0:1 +18 39584264 . C T 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00537;SOR=Inf;LSEQ=GTGGAACTCTGCCTAGTCAA;RSEQ=TTCTCTATCCCAGGAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:74,7:81,0:0:2,0:22.7:1:32.2:1:1:0:60:80:1:0:0.2 0/1:76:7:6,1:62,7:69,7:0.0921:2,2:21.6:1:30.7:1:0.55656:1.46764:60:14:0.0921:0:1 +18 39584319 . G T 40 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33761;SOR=0.28071;LSEQ=TTAAATATTTTCTGATTTTA;RSEQ=GCCTTGACAAAATTCTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:2,1:231,59:290,3:0.0102:2,2:14.7:1:25.7:1:0.49845:1.95241:60:2:0.007:0:1.7 0/0:346:1:0,1:252,92:344,1:0.0029:2,0:1:0:25:0:0.26957:0:60:2:0.0029:0:1 +18 39584412 . T C 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=GGAAAATGGAAGCCGATGGA;RSEQ=GTAGAGGACTCCTTGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:0:0,0:357,338:695,0:0:2,0:24.1:1:30.6:1:1:0:60:56.917:1:0:0.1 0/1:882:79:42,37:419,384:803,79:0.0896:2,2:20.9:1:29.9:1:0.90637:1.04:60:78:0.0897:0:1.2 +18 39593363 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=ATTATGTCTGTAATAATTTT;RSEQ=CATTCTTTTCCTAATATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:125,18:143,0:0:2,0:23.6:1:32.2:1:1:0:60:70.5:1:0:0 0/1:143:2:1,1:127,14:141,2:0.014:2,2:46:1:29.5:1:0.19945:8.79957:60:4:0.0141:0:1 +18 39593388 . CT C 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00858;SOR=0;LSEQ=CTTTTCCTAATATTACTTTA;RSEQ=TTTTTTTGTTTTCCAGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:6:5,1:171,42:213,6:0.0274:2,2:30.8:1:33.5:1:1:1.23:60:12:0.0274:0:0 0/0:262:0:0,0:202,60:262,0:0:2,0:24.1:1:30.2:1:1:0:60:261:1:0:0.1 +18 39595382 . C T 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=44.13184;LSEQ=CTGTTCCATAAAAAATTGTG;RSEQ=GTTCTCTTATGGACAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:2:0,2:274,102:376,2:0.0053:2,0:1:0:28:1:0.07517:0:60:4:0.0053:0:1 0/1:378:72:56,16:225,81:306,72:0.1905:2,2:19.2:1:29:1:0.54909:1.26:60:71:0.1898:0:1.1 +18 39600527 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20776;SOR=0;LSEQ=TACAGATGAAAACTGATAGG;RSEQ=AAATGTAAACTTACTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:113,17:130,2:0.0152:2,2:17:1:30.5:1:0.25503:6.4883:60:4:0.0153:0:1 0/0:157:0:0,0:137,20:157,0:0:2,0:22.1:1:31.8:1:1:0:60:314:1:0:0.1 +18 39600755 . A G 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAACACAAAGATGATTTAAA;RSEQ=TAAGATATGAGCAATCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:1,89:90,0:0:1,0:25.5:1:32.2:1:1:0:59.6:180:1:0:0 0/1:54:11:0,11:1,42:43,11:0.2037:1,0:15.7:1:30.7:1:1:0:60:10:0.1923:0:1.2 +18 39617591 . A T 23 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.22355;SOR=Inf;LSEQ=ATATATCAACATTTTCTTGT;RSEQ=TGTATAGTACAATTTTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:142,18:160,0:0:2,0:23.6:1:28.5:1:1:0:60:79:1:0:0.1 0/1:144:2:1,1:126,16:142,2:0.0139:2,2:7:1:23.5:1:0.2229:7.67002:60:4:0.0141:0:1 +18 39617865 . C CAG 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.00067;SOR=Inf;LSEQ=TTCATTTGCTGTTTATGGAA;RSEQ=AGAAGTATTTGTAACATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:12,171:183,0:0:2,0:23.6:1:32.6:1:1:0:59.8:90.5:1:0:0.1 0/1:150:9:0,9:14,127:141,9:0.06:2,0:26.6:1:31.1:1:1:0:60:18:0.0608:0.0067:0 +18 39620446 . TA T 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.47868;LSEQ=CAGACTAAATCAGCTTAATT;RSEQ=AAAAAAAAAAGTTTTCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:15,2:0.1176:1,0:29.5:1:31.5:1:1:0:45:4:0.1176:0:0 0/1:12:2:2,0:9,1:10,2:0.1667:2,0:29.5:1:29:1:1:0:60:4:0.1667:0:0 +18 39620557 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22808;SOR=Inf;LSEQ=ATGGAATGCATTTATTCAGA;RSEQ=ATGAGGATTATTCTTAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:117,17:134,0:0:2,0:22.7:1:33.4:1:1:0:60:268:1:0:0.1 0/1:123:2:1,1:106,15:121,2:0.0163:2,2:11:1:27:1:0.24417:6.87422:60:4:0.0163:0:1 +18 39623621 . C T 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10305;SOR=0;LSEQ=TATGCTAGACACTTGCTGGT;RSEQ=ACTATTTATAGTTTCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:3:1,2:140,16:156,3:0.0189:2,2:8:1:27:1:0.03406:16.85848:60:6:0.0195:0:1 0/0:179:0:0,0:157,22:179,0:0:2,0:21.7:1:30.5:1:1:0:60:43.75:1:0:0 +18 39623865 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18808;SOR=Inf;LSEQ=GCCATAATCATATACATTTA;RSEQ=AACATGTTAATATTTAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:8,182:190,0:0:1,0:22.3:1:32.2:1:1:0:60:46.5:1:0:0.2 0/1:146:2:1,1:17,127:144,2:0.0137:2,2:30.5:1:27.5:1:0.23212:7.29:60:4:0.0139:0:1 +18 39623942 . A G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGTCATTGATGCTTTGAC;RSEQ=TAATAGTATTAACAAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:55:1,54:0,0:0,55:1:0,1:25.4:1:32.6:1:1:0:59.3:110:1:0:1 1/1:26:26:0,26:0,0:0,26:1:0,1:26.8:1:31.7:1:1:0:60:52:1:0:1 +18 39629423 . C T 105 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00111;SOR=13.71388;LSEQ=TATTAAAGTTGCACAAACTG;RSEQ=TTTTATATTCAGTAGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:154,15:169,1:0.0059:2,0:1:0:25:0:0.09412:0:60:2:0.006:0:1 0/1:159:12:12,0:130,17:147,12:0.0755:2,0:28:1:29.3:1:0.36591:0:60:24:0.0764:0:1.2 +18 39629472 . AT A 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06749;SOR=0.28957;LSEQ=GTTTGCATTTGTTTTCACAT;RSEQ=TTTTTTTAACTGTTACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:8:5,3:266,108:374,8:0.0209:2,2:22.4:1:30.8:1:0.6959:1.47616:60:16:0.0211:0.0052:0.1 0/0:488:3:2,1:314,171:485,3:0.0061:2,2:24.3:1:30.4:1:1:1.09:60:6:0.0062:0.002:0 +18 39637814 . C A 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07583;SOR=Inf;LSEQ=CCCAGTTCTTTAAGATAATT;RSEQ=TGGAAACAAATGAGTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:218,76:294,0:0:2,0:25.7:1:32.1:1:1:0:60:48:1:0:0.1 0/1:398:5:3,2:270,123:393,5:0.0126:2,2:16.2:1:24.8:1:0.65128:1.46195:60:4:0.0102:0:2.4 +18 39638072 . CA C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49863;SOR=Inf;LSEQ=ATTTATTTTATTTTATAGAA;RSEQ=AGAGAATTTGTTTAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:18,142:160,0:0:2,0:24.5:1:30.8:1:1:0:59.9:159:1:0:0 0/1:166:2:1,1:21,143:164,2:0.012:2,2:30:1:30.5:1:0.24819:6.68:60:4:0.0123:0:0 +18 39638115 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.02711;SOR=Inf;LSEQ=GCATTCTTTAGCATTGATCA;RSEQ=TTTTTCAAAATGACAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:0,71:71,0:0:1,0:24:1:34:1:1:0:59.8:142:1:0:0 0/1:50:4:0,4:2,44:46,4:0.08:1,0:36.3:1:30.5:1:1:0:60:8:0.08:0:1 +18 39644675 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62365;SOR=2.88316;LSEQ=TGCAGAATTCTTAATCGTTG;RSEQ=TATTTTTTTCTTTTCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:1:0,1:176,33:209,1:0.0048:2,0:1:0:26:0:0.1619:0:60:2:0.0048:0:1 0/1:220:3:1,2:184,33:217,3:0.0136:2,2:20.3:1:26:1:0.06662:10.95198:60:6:0.0139:0:1 +18 39647276 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12112;SOR=0;LSEQ=CATGTTACCTTATAATGTCT;RSEQ=CATCAGTTTGATTCTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:1,2:193,41:234,3:0.0126:2,2:8.7:1:28.3:1:0.0856:9.28078:60:6:0.0128:0:1 0/0:242:0:0,0:196,44:240,0:0:2,0:23.3:1:31:1:1:0:60:29:0.9915:0:0.2 +18 39660959 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49573;SOR=Inf;LSEQ=TAATTGCAATCCTCTTGGTA;RSEQ=CATTTAGCAAACTAATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:55,3:58,0:0:2,0:25.7:1:32.8:1:1:0:60:28:1:0:0.2 0/1:59:2:1,1:49,8:57,2:0.0339:2,2:20:1:27.5:1:0.28404:5.83337:60:4:0.0339:0:1 +18 39661005 . T A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.2182;SOR=0;LSEQ=TTTTATTTTATTAGTAGTCT;RSEQ=TTTTAAAACTATAGACTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:118,19:137,2:0.0144:2,2:18.5:1:32:1:0.26796:6.07889:60:4:0.0144:0:1 0/0:158:0:0,0:120,38:158,0:0:2,0:25.1:1:30.4:1:1:0:60:157:1:0:0.1 +18 42288477 . A T 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGAAATTTTGTTTCCTG;RSEQ=TAGATTTCTCTCTGATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:89,104:193,0:0:2,0:26.9:1:30.4:1:1:0:60:31.167:1:0:0.1 0/1:306:39:16,23:130,137:267,39:0.1275:2,2:24.8:1:29.2:1:0.39565:1.36267:60:78:0.1296:0:1.1 +18 42288703 . AAAAAGAAAAG A 62 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAGCTTCTACATGTTCAAA;RSEQ=AAAAGAAAAGAAAAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:44:1:31:1:1:0:60:8:0.6667:0:0 1/1:1:1:0,1:0,0:0,1:1:0,0:38:0:31:0:1:0:60:2:1:0:0 +18 43015532 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00155;SOR=0.55622;LSEQ=AGACAATTTTGGCAAGACTG;RSEQ=TGTTCTTATTTTTACACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:242:132:63,69:51,58:109,132:0.5455:2,2:24:1:30:1:0.89758:1.04:60:264:0.5477:0:1.1 0/1:250:100:47,53:69,81:150,100:0.4:2,2:24.5:1:28.8:1:0.89758:1.04:60:99:0.4024:0:1.1 +18 43015609 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50691;SOR=0;LSEQ=GCTGAAGAGTTTGCCTTTGG;RSEQ=TGGGACATAAACTCCAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:33,91:124,2:0.0159:2,2:21.5:1:29:1:0.46844:2.73:60:4:0.0159:0:1.5 0/0:96:0:0,0:30,66:96,0:0:2,0:20.1:1:31.8:1:1:0:60:192:1:0:0.3 +18 44240423 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2073;SOR=Inf;LSEQ=GAGGATCCTGCACATAGCTG;RSEQ=CTGTGAACGGGTGCTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:111,20:131,0:0:2,0:22.8:1:31.5:1:1:0:60:42.667:1:0:0.1 0/1:110:2:1,1:79,29:108,2:0.0182:2,2:19.5:1:27:1:0.47289:2.69525:60:4:0.0185:0:1 +18 44240426 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50155;SOR=0;LSEQ=GATCCTGCACATAGCTGGCT;RSEQ=TGAACGGGTGCTCAGGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:114,19:133,2:0.0148:2,2:22:1:29.5:1:0.27529:5.8737:60:4:0.0152:0:1 0/0:114:0:0,0:83,31:114,0:0:2,0:21.7:1:31.4:1:1:0:60:228:1:0:0.1 +18 44240453 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49903;SOR=Inf;LSEQ=GGTGCTCAGGGCATGCTTTG;RSEQ=AGACCCACTTCTCATCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:143,43:186,0:0:2,0:26.8:1:32.4:1:1:0:60:185:1:0:0.4 0/1:196:2:1,1:136,58:194,2:0.0102:2,2:22:0:30.5:1:0.51251:2.33343:60:4:0.0103:0:1.5 +18 44240526 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33577;LSEQ=AGGCCTCAGTAGGCATAGCA;RSEQ=AAGGCCCTGAACTGTGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:434:298:153,145:73,63:136,298:0.6866:2,2:27.1:1:29.5:1:0.67944:1.09791:60:58.6:0.6846:0:1.1 0/1:484:205:110,95:149,130:279,205:0.4236:2,2:24.5:1:28.7:1:1:1.01:60:204:0.4232:0:1.2 +18 45368374 . G T 47 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.2486;SOR=Inf;LSEQ=AATTCAAGTCCACAGGCAGG;RSEQ=AAAATGGCTATGTTTAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:39,229:268,0:0:2,0:23.7:1:32.2:1:1:0:59.9:133:1:0:0.1 0/1:268:3:1,2:48,217:265,3:0.0112:2,2:12:0:30:1:0.45571:2.25:60:6:0.0112:0:1.3 +18 45371509 . C T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16976;SOR=2.34715;LSEQ=CGTTAAAATGCACGCCTGTG;RSEQ=ATGTTTTAATATCTTCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:18:18,0:25,0:25,18:0.4186:1,1:31.2:1:30.6:1:1:0:60:36:0.4186:0:1 1/0:19:12:12,0:6,1:7,12:0.6316:2,0:23.8:1:29.8:1:0.36842:0:60:24:0.6316:0:1 +18 45371686 . T C 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=ATAATTACACTGTGGAAATT;RSEQ=AAGAACCAAATATGTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:592:0:0,0:349,243:592,0:0:2,0:24.8:1:29.8:1:1:0:60:295:1:0:0.1 0/1:708:15:6,9:394,298:692,15:0.0212:2,2:23.3:1:32:1:0.20064:1.98131:60:30:0.0213:0:1.1 +18 45374776 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.52035;LSEQ=GCACACAAGCTCTTGATGTG;RSEQ=CACACCATGCAATGCCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:0,1:106,12:118,1:0.0084:2,0:47:0:32:0:0.10924:0:60:2:0.0085:0:1 0/1:157:2:2,0:130,24:154,2:0.0127:2,0:14:1:29.5:1:1:0:60:4:0.0129:0:1 +18 45374802 . A T 35 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08791;SOR=0;LSEQ=CATGCAATGCCTACATTATG;RSEQ=GTATACAGCATTTATTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:1,2:182,53:235,3:0.0126:2,2:7.7:1:22.3:1:0.13431:6.79581:60:2:0.0085:0:1.7 0/0:296:0:0,0:210,86:296,0:0:2,0:23.2:1:28.9:1:1:0:60:295:1:0:0.1 +18 45377602 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26075;SOR=Inf;LSEQ=ATTTTTATTATTAAGTAGGT;RSEQ=ATACAGTATAAAAATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:134,59:193,0:0:2,0:24.5:1:32.4:1:1:0:60:192:1:0:0.1 0/1:250:3:1,2:160,87:247,3:0.012:2,2:24.7:1:27.3:1:0.28917:3.65795:60:6:0.012:0:1 +18 45377744 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18087;SOR=0;LSEQ=ATGAAGTATTTCCAGAACTT;RSEQ=TGATCAAGTAATCATAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:25,103:128,2:0.0154:2,2:31:1:30.5:1:0.36124:4.06:60:4:0.0155:0:1 0/0:175:0:0,0:53,122:175,0:0:2,0:23.2:1:31.1:1:1:0:60:174:1:0:0.1 +18 45391419 . AT A 103 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.11506;SOR=0.39667;LSEQ=ACTGAGGAATTTTCAAAGAC;RSEQ=TTTTTTTACCTGTGTCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:10:5,5:298,203:501,10:0.0196:2,2:30.6:1:31.2:1:0.53749:1.46682:60:20:0.0197:0:0 0/0:637:5:3,2:374,258:632,5:0.0078:2,2:19.6:1:29.6:1:1:1.03:60:10:0.0079:0.0016:0.2 +18 45394601 . A T 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.49806;SOR=Inf;LSEQ=AAAAACTCAAAAGCATTTTT;RSEQ=AAAAAGTGAAACCACAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:67,1:68,0:0:1,0:23.4:1:28.8:1:1:0:60:67:1:0:0 0/1:76:2:2,0:70,4:74,2:0.0263:2,0:5:1:31:1:1:0:60:4:0.027:0:1 +18 45394634 . A T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25248;SOR=Inf;LSEQ=CACAATTTACTAAAACTTGA;RSEQ=TGCTTATGAACAAAATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:123,27:150,0:0:2,0:22.6:1:30.7:1:1:0:60:74:1:0:0.1 0/1:176:3:1,2:139,34:173,3:0.017:2,2:10:1:22.3:1:0.10674:8.0406:60:2:0.0116:0:2.3 +18 45394919 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20448;SOR=Inf;LSEQ=TTCAACAAGAAGAGAAGTTG;RSEQ=AGCTTAATTTTTAAAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,43:43,0:0:1,0:23.4:1:28.3:1:1:0:60:20.5:1:0:0.1 0/1:36:2:0,2:0,34:34,2:0.0556:1,0:15.5:1:29:1:1:0:60:4:0.0571:0:1 +18 45397062 . A T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23065;SOR=Inf;LSEQ=AGAAAATATACAATTGCTTC;RSEQ=CTTTTTCACAGGCATGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:33,0:0:1,0:21.3:1:29.3:1:1:0:60:15.5:1:0:0.2 0/1:31:2:1,1:0,29:29,2:0.0645:1,2:31:0:31:1:0.06452:0:60:4:0.0667:0:1.5 +18 45423757 . CAT C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGAGAGAAATTTTTTAACA;RSEQ=GTTTTTTTCATTTTCATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:30.5:1:1:0:60:4:1:0:0.5 +18 46385146 . C G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=10.74891;LSEQ=CAGTTTGTATTTCTCTCCCC;RSEQ=ACTTCCTGTCACAAGCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:5,0:39,2:41,5:0.1087:1,0:27.4:1:30.6:1:1:0:60:10:0.1111:0:1.2 1/0:47:27:21,6:20,0:20,27:0.5745:1,2:19.3:1:29:1:0.03118:0:60:26:0.5652:0:1 +18 46385291 . A T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.5017;LSEQ=ATGTAATAATGACTAAGCTC;RSEQ=TTGCCAGAGAGACGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:19:8,11:110,132:242,19:0.0728:2,2:29.8:1:31.3:1:0.81566:1.14524:60:18:0.0706:0:1.3 0/1:248:118:53,65:66,64:130,118:0.4758:2,2:27.4:1:30.4:1:0.37532:1.26353:60:236:0.4777:0:1.2 +18 46385334 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.2364;SOR=Inf;LSEQ=AGTGAAAATGACCACAGGGC;RSEQ=CCCTGATCACCAAGGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:61,116:177,0:0:2,0:26.4:1:30.5:1:1:0:60:28.5:1:0:0.2 0/1:168:2:1,1:63,101:164,2:0.0119:2,2:42.5:1:29:1:1:1.60:60:4:0.012:0:1.5 +18 46996347 . C T 132 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00042;SOR=16.58424;LSEQ=GCTTTCCCCCCAGGTGGACG;RSEQ=CCTCATCCTGTGCCACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:2,9:11,2:0.1538:2,0:25.5:1:29:1:1:0:60:4:0.1538:0:1 1/0:30:23:7,16:3,4:7,23:0.7667:2,2:27.5:1:29.2:1:0.65729:1.68229:58.1:46:0.7667:0:1.3 +18 46996404 . A G 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00281;SOR=0;LSEQ=GGGTCCCTACCTTCCTCCAT;RSEQ=CCCACCACCTGCCCCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:4,6:0.6:0,2:21.7:1:33.3:1:1:0:60:12:0.6:0:1.3 0/0:12:0:0,0:3,9:12,0:0:2,0:21.8:1:28.2:1:1:0:60:24:1:0:0.8 +18 48190440 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGTTTGGTGCTGTCGGCC;RSEQ=TGGACAGCCGGGCCTGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 48190685 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.78215;LSEQ=GCACGCCTGCTGGAGCAGGG;RSEQ=ACGCTGGCAGAAGAGCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:124,42:166,1:0.006:2,0:1:0:27:0:0.25749:0:60:2:0.006:0:1 0/1:188:2:1,1:134,52:186,2:0.0106:2,2:9.5:1:27:1:0.48544:2.56201:60:4:0.0108:0:1 +18 48190817 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10694;LSEQ=ATCAGCACAGAGGACCTCGT;RSEQ=CTCAAGATTGGGGATTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:80:22,58:26,59:85,80:0.4848:2,2:18.6:1:28.9:1:0.73266:1.16073:60:25.667:0.4753:0:1.2 0/1:209:19:8,11:56,134:190,19:0.0909:2,2:17.5:1:28.4:1:0.29807:1.74:60:38:0.0927:0:1.2 +18 48573268 . CT C 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.65455;SOR=1.81878;LSEQ=AAATGTGTTCTGATGTGTGT;RSEQ=TTTTTTTTTTTCTTTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:3,0:24,0:24,3:0.1111:1,0:21:1:31.4:1:1:0:60:6:0.1111:0.0741:1 0/1:16:3:3,0:13,0:13,3:0.1875:1,0:30:1:31.3:1:1:0:60:6:0.1875:0:1 +18 48573728 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49925;SOR=0;LSEQ=ATTTAAAAACTTGCTACGTT;RSEQ=CCTTTCAAGCTACTACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:6,58:64,2:0.0303:2,2:22.5:1:30.5:1:0.20233:9.03:60:4:0.0308:0:1 0/0:56:0:0,0:6,50:56,0:0:2,0:18.5:1:29:1:1:0:60:27:1:0:0.2 +18 48575389 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00336;SOR=0.09892;LSEQ=TATACGTATTTAAATTTGAA;RSEQ=TTAGGAACAAACTTATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:28:6,22:2,1:3,28:0.9032:2,2:18.9:1:33.7:1:0.15573:6.74669:60:56:0.9032:0:1.3 0/1:13:6:0,6:2,5:7,6:0.4615:2,0:28.8:1:32.3:1:0.46154:0:60:12:0.4615:0:1 +18 48575746 . G GT 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02709;SOR=0;LSEQ=TGTTTTGTCCTATCCTCTCT;RSEQ=TTTTTTTGTTGACCTAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:4:2,2:107,240:347,4:0.0114:2,2:25.3:1:28.4:1:0.59097:2.24:60:8:0.0116:0.0028:0 0/0:512:0:0,0:191,321:512,0:0:2,0:25.2:1:31.1:1:1:0:60:84.333:1:0:0.1 +18 48575929 . TA T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.05728;SOR=0.10257;LSEQ=ATTTATGAACTAAAGTACTG;RSEQ=AAAAAATATGATAGAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:1,8:0,1:1,9:0.9:0,2:34.2:1:32:1:1:0:60:18:0.9:0:0.8 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:18.5:1:32:0:1:0:60:8:0.4444:0:0 +18 48581415 . C A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.77379;LSEQ=TTGAGTTTTCCTAATCATTG;RSEQ=TTATTTATGTGTAGTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:1,0:18,116:134,1:0.0074:2,0:1:0:25:0:0.14074:0:60:2:0.0075:0:1 0/1:231:3:2,1:37,191:228,3:0.013:2,2:29.7:1:28:1:0.07467:10.16:60:6:0.0132:0:1.3 +18 48581601 . C A 73 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22619;SOR=0.14055;LSEQ=TACTTTACTATTACATGTAG;RSEQ=AGTAAGTAGCCTCTTAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:21.6:1:31.8:1:1:0:60:10:0.8333:0:1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:22:0:32:0:1:0:60:2:0.3333:0:1 +18 48584855 . A TTT 97 q25;Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1e-05;SOR=0.09986;LSEQ=CTTGTTTTTGTTGTAAGGGC;RSEQ=TTTTTTTTTTTTTTTTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:20:0,20:138,218:356,20:0.0498:2,1:27.5:1:22.6:1:0.00014:0:48:4:0.0494:0:3 0/0:578:3:0,3:201,360:561,3:0.0052:2,0:36.7:1:23:1:0.55597:0:47.7:2:0.0043:0:3 +18 48586141 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49923;SOR=Inf;LSEQ=TGTTTTAAACAATTCCTAAC;RSEQ=TATAATAGTTATATTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:86,15:101,0:0:2,0:24.3:1:31.5:1:1:0:59.6:24.25:1:0:0.1 0/1:113:2:1,1:97,14:111,2:0.0177:2,2:5.5:1:27.5:1:0.24889:6.72937:60:4:0.018:0:1.5 +18 48593133 . G A 67 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTAGAATAATAGTACTT;RSEQ=TTGAGTTGTAAGGGTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:15:1:29:1:1:0:60:10:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:2:0:29:0:1:0:60:2:1:0:1 +18 48593582 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=GTTACAATTTTATTTGAATA;RSEQ=TTTAGACTTAAAGCTCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:35,135:170,0:0:2,0:24.6:1:30.4:1:1:0:60:55.667:1:0:0.1 0/1:186:2:1,1:50,134:184,2:0.0108:2,2:12:1:27:1:0.47428:2.66:60:4:0.0109:0:1 +18 48593600 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50155;SOR=Inf;LSEQ=TATTTTAGACTTAAAGCTCT;RSEQ=TTTGTTGTCAAAAGAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:17,97:114,0:0:2,0:26.6:1:31.2:1:1:0:60:228:1:0:0.1 0/1:135:2:1,1:33,100:133,2:0.0148:2,2:21:1:33.5:1:0.44168:3.00:60:4:0.0148:0:1 +18 48603212 . T A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50376;SOR=Inf;LSEQ=TTTTATCTTGATTTACTCAG;RSEQ=TGATTAGTTTCTTTGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:6,76:82,0:0:2,0:24.8:1:30.7:1:1:0:60:81:1:0:0.1 0/1:103:2:1,1:5,96:101,2:0.0194:1,2:16.5:1:24.5:1:0.11365:17.61:60:4:0.0194:0:1 +18 48603247 . G GT 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.16449;LSEQ=GAGCAGTAATAGAAATTAAA;RSEQ=TTTTTTTTTACTGGGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:0,3:1,34:35,3:0.0789:1,0:12.7:1:31.3:1:1:0:60:6:0.0789:0.0263:0.3 0/1:44:4:0,4:1,38:39,4:0.0909:1,0:17.8:1:31:1:1:0:57.5:8:0.0909:0.0227:0.5 +18 48603403 . T C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=ATTATTATATTATACTGTTC;RSEQ=ATCTCCTCCTTTTTTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:16:1:34:0:1:0:60:6:1:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:27.5:1:27:1:1:0:60:4:1:0:0 +18 48604582 . A G 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.5023;SOR=Inf;LSEQ=AATGTAGGGAGGATGGGAAG;RSEQ=GATCACCCTGTCCCTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:121,31:152,0:0:2,0:24:1:30.5:1:1:0:59.8:75:1:0:0 0/1:181:2:1,1:149,29:178,2:0.011:2,2:5.5:1:30:1:0.30633:5.06864:60:4:0.0112:0:1 +18 48604586 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50284;SOR=Inf;LSEQ=TAGGGAGGATGGGAAGAGAT;RSEQ=ACCCTGTCCCTCTGATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:130,33:163,0:0:2,0:24.3:1:32.3:1:1:0:59.8:80.5:1:0:0 0/1:196:2:1,1:159,35:194,2:0.0102:2,2:17:1:26.5:1:0.33438:4.4934:60:4:0.0103:0:1 +18 48604591 . T C 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13157;SOR=Inf;LSEQ=AGGATGGGAAGAGATCACCC;RSEQ=GTCCCTCTGATGTCTTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:137,35:172,0:0:2,0:25.4:1:32:1:1:0:59.8:344:1:0:0 0/1:213:4:2,2:167,42:209,4:0.0188:2,2:24.5:1:23:1:0.18956:3.94193:60:3:0.0142:0:1 +18 49294155 . A T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03492;SOR=Inf;LSEQ=TCATACCTTATTCCCAGCAA;RSEQ=GGGTTTCCTGCTTTGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:14,1:15,0:0:1,0:20.7:1:30.1:1:1:0:60:14:1:0:0.1 0/1:13:4:4,0:9,0:9,4:0.3077:0,0:33.5:1:30.8:1:1:0:60:8:0.3077:0:1 +18 49294236 . A G 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01018;SOR=Inf;LSEQ=TCTAGAAACCAGTTGCCAGC;RSEQ=CCTGCTGCTGCTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:40,17:57,0:0:2,0:20.3:1:30.3:1:1:0:58.4:114:1:0:0.2 0/1:76:9:6,3:44,22:66,9:0.1184:2,2:27.8:1:29.6:1:1:1:56.6:18:0.1184:0:1.1 +18 49294237 . CCTG C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.07483;SOR=0;LSEQ=CTAGAAACCAGTTGCCAGCA;RSEQ=CTGCTGCTGCTGCTGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:2,1:38,19:57,3:0.05:2,2:28.7:1:33.7:1:1:1:60:6:0.0517:0:0.7 0/0:81:0:0,0:52,28:80,0:0:2,0:21.8:1:30:1:1:0:56.3:79:1:0:0.5 +18 49294253 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=1.5427;LSEQ=AGCACCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:0,1:46,29:75,1:0.0132:2,0:1:0:27:0:0.39474:0:53:2:0.0139:0:1 0/1:99:2:2,0:56,41:97,2:0.0202:2,0:30:1:29:1:0.50979:0:47.5:4:0.0204:0:3 +18 49294256 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.14813;SOR=Inf;LSEQ=ACCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGCTGCTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:48,29:77,0:0:2,0:24.1:1:31.6:1:1:0:58.6:24.667:1:0:0.2 0/1:113:4:2,2:62,45:107,4:0.0354:2,2:30.3:1:29.3:1:1:1.37372:46:8:0.036:0:3.3 +18 49294268 . T TTGC 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=9.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TGCTGCTGCTGTTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:53,36:89,0:0:2,0:25.6:1:29.3:1:1:0:58.8:28.667:1:0:0.2 0/1:121:27:13,14:50,42:92,27:0.2231:2,2:28.1:1:30.4:1:0.66264:1.27936:54.7:54:0.2231:0.0083:0.8 +18 51274616 . G A 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.69183;LSEQ=CAAAAAAAATTCCACAACAG;RSEQ=TGTTGTGAATCTTTTAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:43.3:1:31:1:1:0:60:6:0.5:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:49:1:26.5:1:1:0:60:4:0.4:0:1 +18 51274758 . C A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89626;SOR=0.93443;LSEQ=TTCTTAGTTCAGAAGTGAAA;RSEQ=AGCTATTTTTTTTACACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:61:45,16:26,18:44,61:0.581:2,2:24.2:1:30.5:1:0.14044:1.93:59.9:122:0.5865:0:1.1 1/0:140:79:49,30:40,21:61,79:0.5643:2,2:26.6:1:29.5:1:0.72484:1.1649:60:158:0.5683:0:1.3 +18 51274763 . AT A 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.38373;SOR=3.30245;LSEQ=AGTTCAGAAGTGAAACAGCT;RSEQ=TTTTTTTACACTTTCCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:1:1,0:76,45:121,1:0.0082:2,0:17:0:33:0:1:0:60:2:0.0082:0:1 0/1:150:4:2,2:87,59:146,4:0.0267:2,2:21.3:1:25.2:1:1:1.47064:60:3:0.0203:0.0133:0.8 +18 51274836 . T C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41065;SOR=1.24869;LSEQ=GATTTGAGAATTTCTCTCAT;RSEQ=CAGTGCTTAATAAACTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:42:18,24:52,65:117,42:0.2642:2,2:28:1:32.1:1:1:1.06627:60:84:0.2642:0:1.2 0/1:197:61:24,37:66,68:134,61:0.3096:2,2:27.6:1:30.4:1:0.21781:1.49322:60:122:0.3112:0:1.3 +18 51274843 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50403;SOR=Inf;LSEQ=GAATTTCTCTCATTCAGTGC;RSEQ=TAATAAACTGAGGGGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:67,92:159,0:0:2,0:24.2:1:30.9:1:1:0:60:158:1:0:0.5 0/1:196:2:1,1:87,107:194,2:0.0102:2,2:29.5:1:31:1:1:1.23:60:4:0.0104:0:2.5 +18 51274997 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TTCTAATGAAAATGTAAGCG;RSEQ=GTTGGCCTCATATTGACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:29.5:1:30.5:1:1:0:60:7:1:0:0.8 0/1:7:2:1,1:0,5:5,2:0.2857:0,2:29.5:1:28:1:0.28571:0:60:4:0.3333:0:1 +18 51275014 . C T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08081;SOR=0;LSEQ=GCGGGTTGGCCTCATATTGA;RSEQ=TAGCAGTTACTGCCACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:28.8:1:30.5:1:1:0:60:8:0.5714:0:1.5 0/0:5:0:0,0:0,5:5,0:0:0,0:27.6:1:31.2:1:1:0:60:10:1:0:0.6 +18 52896000 . A G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TCTACTGTCTGCCACTGCTC;RSEQ=AGACTGGCGTGCCCATCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:43,1:44,0:0:1,0:26.2:1:31.1:1:1:0:59.7:88:1:0:0.1 0/1:29:10:9,1:19,0:19,10:0.3448:1,2:30.3:1:25.6:1:0.34483:0:56.6:4:0.2963:0:2.1 +18 52896003 . A G 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ACTGTCTGCCACTGCTCAAG;RSEQ=CTGGCGTGCCCATCTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:45,1:46,0:0:1,0:26.5:1:30.6:1:1:0:59.7:45:1:0:0.1 0/1:32:11:10,1:21,0:21,11:0.3438:1,2:28.8:1:30.8:1:0.34375:0:56.9:22:0.3438:0:2 +18 52896063 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23554;SOR=Inf;LSEQ=TCACGAGCTCTGCAAGGAGG;RSEQ=TGGCCTGCACTGACCTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:110,4:114,0:0:1,0:21.7:1:31.9:1:1:0:60:27.5:1:0:0.1 0/1:108:2:1,1:97,9:106,2:0.0185:2,2:14:1:31:0:0.1774:10.27733:60:4:0.0189:0:1.5 +18 52896509 . G A 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAAGATATTTGGTTTTCTC;RSEQ=CAGACATTAAACCCAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:25.2:1:28.8:1:1:0:60:10:0.8333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:28:1:1:0:60:4:1:0:1 +18 53303101 . C G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGGAGAGGCACCTGTG;RSEQ=TATTTTCTCCAGCCTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:0,9:1:0,0:27.2:1:32.7:1:1:0:60:18:1:0:1 1/1:21:21:17,4:0,0:0,21:1:0,2:29.1:1:30.9:1:1:0:60:42:1:0:1.1 +18 53303583 . T TA 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AATAAAGACCTTGGGATGGT;RSEQ=AAAAAAAAAAAGAAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31.5:1:33:0:1:0:60:4:1:0:0 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 53630757 . A G 48 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGCTAGATTAGGCCAC;RSEQ=GGATAAGGCTTGGAAGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:32.3:1:24.3:1:1:0:60:3:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:11:1:30.5:1:1:0:60:4:1:0:2 +18 53631042 . C G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19669;LSEQ=GGCAGATTCATATTTTTGAG;RSEQ=TAAAAGCATAACTGTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:413:365:159,206:24,24:48,365:0.8838:2,2:26.9:1:31.6:1:0.44113:1.29477:60:72:0.8824:0:1.5 1/0:551:330:145,185:90,131:221,330:0.5989:2,2:25.6:1:31:1:0.48254:1.14:60:329:0.6004:0:1.4 +18 53631064 . AT A 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.25032;SOR=0.31086;LSEQ=AAAAGCATAACTGTGGCAGC;RSEQ=TTTTTCTTTCTTTGAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:5:2,3:79,118:197,5:0.0138:2,2:32.4:1:31:1:1:1.00422:60:10:0.014:0:0.6 0/0:462:2:1,1:136,241:377,2:0.0043:2,2:15.5:1:28.5:1:1:1.77:60:4:0.0044:0:0 +18 53631065 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0;SOR=0.28322;LSEQ=AAAGCATAACTGTGGCAGCA;RSEQ=TTTTTCTTTCTTTGAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:158:60,98:79,118:197,158:0.4365:2,2:25.2:1:32.9:1:0.74295:1.09323:60:157:0.4385:0:2 0/1:462:83:33,50:136,241:377,83:0.1797:2,2:28.4:1:30.9:1:0.53192:1.17:60:82:0.1802:0:2 +18 54917169 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50089;SOR=Inf;LSEQ=CATCCAAAGAAGTTGGCTGA;RSEQ=AAACAATATTGTTAAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:99,66:165,0:0:2,0:23.7:1:32.4:1:1:0:60:54:1:0:0.5 0/1:189:2:1,1:97,90:187,2:0.0106:2,2:29:1:28.5:1:1:1.07733:60:4:0.0109:0:1.5 +18 54917232 . G C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.57084;SOR=1.14447;LSEQ=GTAAAATGTGTGCTCAGAGA;RSEQ=AGCGGGGCCATCCATCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:207:154:79,75:26,27:53,154:0.744:2,2:25.9:1:32.2:1:0.87365:1.09:59.7:76:0.7415:0:1.2 1/0:212:163:69,94:22,27:49,163:0.7689:2,2:25.9:1:31.3:1:0.74554:1.10949:59.8:53.333:0.7656:0:1.2 +18 54917264 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49852;SOR=Inf;LSEQ=CCATCATGAGTGAGAAGCCT;RSEQ=ATTTACAGAGACAACTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:68,98:166,0:0:2,0:24.2:1:31.7:1:1:0:60:54.333:1:0:0.7 0/1:168:2:1,1:69,97:166,2:0.0119:2,2:16.5:1:30.5:1:1:1.40:60:4:0.0121:0:2 +18 55178817 . TA T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAACTTAAAGTATAATAA;RSEQ=AAAAAAAAGAATTCATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:34:1:33.5:1:1:0:58.5:4:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 55178937 . T C 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00915;SOR=10.66038;LSEQ=TGAAAGGGCAAGAGTTTCTA;RSEQ=GGAAAAGGCCCCCAAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:6,0:14,0:14,6:0.3:1,0:25.5:1:33:1:1:0:60:12:0.3:0:2 1/1:12:10:9,1:2,0:2,10:0.8333:0,2:26.3:1:31.9:1:1:0:60:20:0.8333:0:2.7 +18 55178959 . A G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=17.44582;LSEQ=GAAAAGGCCCCCAAATTAGA;RSEQ=GGAGCATGAGGTTTAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:4,0:20,0:20,4:0.1667:1,0:35.8:1:34.5:1:1:0:60:8:0.1667:0:2.5 1/0:24:19:18,1:5,0:5,19:0.7917:0,1:23.8:1:32.2:1:1:0:60:38:0.7917:0:2.4 +18 55179004 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.97219;LSEQ=GGAAACATGAGAATGGGAAG;RSEQ=GTCAATCCCAGGGAGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:8:6,2:46,5:51,8:0.1356:2,2:15.6:1:29.5:1:0.23831:2.98981:60:16:0.1379:0:1.5 1/0:73:48:42,6:21,4:25,48:0.6575:2,2:22:1:28.1:1:0.72744:1.33:60:23:0.6765:0:1.5 +18 55179042 . C T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51535;SOR=Inf;LSEQ=GGGATCCAGGGACCATCCCA;RSEQ=AAAGAGCAACGAGGTCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:85,25:110,0:0:2,0:27.4:1:32.3:1:1:0:59.9:109:1:0:0.1 0/1:160:2:1,1:117,41:158,2:0.0125:2,2:39:0:27.5:1:0.45731:2.83151:60:4:0.0128:0:1.5 +18 55179134 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08916;SOR=0;LSEQ=GGGACCTGAGCCTCTGTTTT;RSEQ=AGTCTTGTAGACCTAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:123,135:258,3:0.0115:2,2:11:1:29:1:1:1.8182:60:6:0.0116:0:1.3 0/0:322:0:0,0:141,180:321,0:0:2,0:23:0:15:0:1:0:60:0:0:0:3 +18 55179142 . T G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.73949;LSEQ=AGCCTCTGTTTTGAGTCTTG;RSEQ=AGACCTAGCTTTCTGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:26:10,16:112,127:239,26:0.0981:2,2:24.5:1:32:1:0.5351:1.40921:60:52:0.0992:0:1.3 1/0:311:219:97,122:38,54:92,219:0.7042:2,2:26.3:1:29.9:1:0.7071:1.13:59.8:30.286:0.6974:0:1.2 +18 55179209 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.23654;SOR=0;LSEQ=TGATGATGAGTGAGGTGGAG;RSEQ=AGCAAGGATGCCCCTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:45,105:150,2:0.0132:2,2:41:1:30:1:0.51507:2.32:60:4:0.0133:0:2.5 0/0:160:0:0,0:45,115:160,0:0:2,0:21.8:1:30:1:1:0:60:39:1:0:0.9 +18 55179225 . T C 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=13.66121;LSEQ=GGAGGAGCAAGGATGCCCCT;RSEQ=CTCATGGGAAAGCTCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:12:4,8:24,84:108,12:0.0992:2,2:22.4:1:31.7:1:0.47152:1.74:60:24:0.1008:0:1.7 1/0:96:58:10,48:10,28:38,58:0.6042:2,2:22.8:1:30.5:1:0.31283:1.7043:60:116:0.6105:0:1.4 +18 55179231 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50988;SOR=0;LSEQ=GCAAGGATGCCCCTTCTCAT;RSEQ=GGAAAGCTCTGAGACATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:20,84:104,2:0.0189:2,2:43:1:30:1:0.35849:4.12:60:4:0.019:0:1 0/0:77:0:0,0:15,62:77,0:0:2,0:23.8:1:30.4:1:1:0:60:154:1:0:0.8 +18 55179269 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCAGACACCGTGTCCCCT;RSEQ=AGTGCTCATGCTGCTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:5,48:53,2:0.0364:2,2:10:1:29:1:0.20808:8.86:60:4:0.037:0:1 0/0:27:0:0,0:2,25:27,0:0:2,0:23.1:1:30.3:1:1:0:60:26:1:0:0.7 +18 55466451 . C G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.13994;LSEQ=ATGAGGCCTGCGTTCCAACC;RSEQ=AGGTCAAAAGACTCCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:25:23,2:21,0:21,25:0.5435:1,2:17.9:1:29.8:1:0.49275:0:60:24:0.5333:0:1.9 0/1:50:7:6,1:42,1:43,7:0.14:1,2:21.1:1:30.1:1:0.26286:6.55744:60:14:0.14:0:1.9 +18 55466490 . T A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.10472;LSEQ=GCTGGCAACCTCTGTTTCAC;RSEQ=GCTGCCTCTGGACTGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:58:46,12:30,6:36,58:0.617:2,2:26.6:1:31.2:1:0.78899:1.30074:60:116:0.617:0:1.5 0/1:133:19:16,3:85,29:114,19:0.1429:2,2:21.6:1:30.3:1:0.56251:1.81:60:38:0.1462:0:1.3 +18 55466495 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50891;SOR=Inf;LSEQ=CAACCTCTGTTTCACTGCTG;RSEQ=CTCTGGACTGCTTGCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:84,23:107,0:0:2,0:26.3:1:32.2:1:1:0:59.9:214:1:0:0.8 0/1:144:2:1,1:106,34:140,2:0.0139:2,2:10.5:1:30:1:0.43352:3.08701:60:4:0.0143:0:1 +18 55466510 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25658;SOR=Inf;LSEQ=TGCTGCCTCTGGACTGCTTG;RSEQ=AGGGACCAGTTATGAAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:106,42:148,0:0:2,0:24.2:1:32.1:1:1:0:59.9:73:1:0:0.8 0/1:184:3:1,2:128,53:181,3:0.0163:2,2:15:1:25.7:1:0.21324:4.78318:60:6:0.0165:0:1.3 +18 55466516 . C T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32146;SOR=0.25423;LSEQ=CTCTGGACTGCTTGCAGGGA;RSEQ=CAGTTATGAAACATATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:1,2:116,51:167,3:0.0175:2,2:18.7:1:30:1:0.22954:4.50381:60:6:0.0178:0:1.7 0/0:222:1:0,1:147,73:220,1:0.0045:2,0:1:0:23:0:0.33484:0:60:2:0.0045:0:2 +18 55466518 . A G 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18635;SOR=0;LSEQ=CTGGACTGCTTGCAGGGACC;RSEQ=GTTATGAAACATATTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:121,55:176,2:0.0112:2,2:46:0:31.5:1:0.53145:2.1893:60:4:0.0115:0:2 0/0:235:0:0,0:157,77:234,0:0:2,0:23.8:1:29.6:1:1:0:60:57.5:0.9957:0:0.4 +18 55466550 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0576;SOR=0;LSEQ=TATTTCTCATTGTGGAAGGG;RSEQ=TGGGCAACAATTTATTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:2,1:147,113:260,3:0.0114:2,2:29.7:1:26:1:1:1.54:60:2:0.0077:0:2 0/0:418:0:0,0:242,175:417,0:0:2,0:23.5:1:28.8:1:1:0:60:68.5:1:0:0.5 +18 55466596 . A G 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.08572;LSEQ=AGTGCATTTATAAGTATCAA;RSEQ=GAAAGTACCAATATGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:291:258:116,142:14,19:33,258:0.8866:2,2:27.7:1:32.1:1:0.85366:1.11:60:63.5:0.8881:0:1.2 0/1:477:191:85,106:139,146:285,191:0.4004:2,2:26.5:1:31:1:0.39935:1.18684:60:190:0.4034:0:1.2 +18 55466664 . C A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1658;SOR=Inf;LSEQ=GTTTTTTAAGAAAATGAGGC;RSEQ=GGGTGCGGTGGCTCACGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:22,68:90,0:0:2,0:22.7:1:30.6:1:1:0:59.5:180:1:0:0.6 0/1:167:5:3,2:48,112:160,5:0.0299:2,2:25.8:1:25:1:0.17208:3.47:43:4:0.0247:0:3.4 +18 55466668 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53143;SOR=Inf;LSEQ=TTTAAGAAAATGAGGCCGGG;RSEQ=GCGGTGGCTCACGCCTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:19,64:83,0:0:2,0:22.4:1:30.3:1:1:0:59.4:82:1:0:0.5 0/1:141:2:1,1:41,98:139,2:0.0142:2,2:37.5:1:30.5:1:0.50851:2.37:33.5:4:0.0147:0:6 +18 55466670 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53263;SOR=Inf;LSEQ=TAAGAAAATGAGGCCGGGTG;RSEQ=GGTGGCTCACGCCTATAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:19,62:81,0:0:2,0:22:1:30.1:1:1:0:59.4:39.5:1:0:0.5 0/1:139:2:1,1:40,97:137,2:0.0144:2,2:35.5:1:30.5:1:0.50443:2.41:33.5:4:0.0147:0:6 +18 55466680 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28902;SOR=Inf;LSEQ=AGGCCGGGTGCGGTGGCTCA;RSEQ=GCCTATAATCCCAGCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:12,58:70,0:0:2,0:20.6:1:30.3:1:1:0:59.3:69:1:0:0.4 0/1:114:3:2,1:28,83:111,3:0.0263:2,2:26.7:1:31.7:1:0.16884:5.82:34.7:6:0.0268:0:6 +18 55466682 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52597;SOR=Inf;LSEQ=GCCGGGTGCGGTGGCTCACG;RSEQ=CTATAATCCCAGCACTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:11,54:65,0:0:2,0:21.4:1:30.9:1:1:0:59.1:64:1:0:0.3 0/1:106:2:1,1:27,77:104,2:0.0189:2,2:23.5:1:30.5:1:0.46038:2.82:33.5:4:0.0198:0:6 +18 55466685 . A G 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27862;SOR=Inf;LSEQ=GGGTGCGGTGGCTCACGCCT;RSEQ=TAATCCCAGCACTTTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:11,55:66,0:0:2,0:19.9:1:30.3:1:1:0:59.1:132:1:0:0.3 0/1:101:3:2,1:23,74:97,3:0.0297:2,2:21.7:1:33.3:1:0.15337:6.29:39.7:6:0.0306:0:4.7 +18 55466751 . G GTA 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0054;SOR=0;LSEQ=CAGGAGTTTGAGACTAGCCT;RSEQ=GCCAACATGGTGAAACCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:0,9:0,14:14,9:0.375:1,0:25.8:1:30.5:1:1:0:54.2:18:0.375:0.0417:0.4 0/0:18:0:0,0:0,18:18,0:0:1,0:26.2:1:31.1:1:1:0:53.2:36:1:0:0.2 +18 56338678 . A C 78 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=GCGCGGCTGGCGCGGCCAGC;RSEQ=GGCCAGGCTCCCCTCGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:13:0:32:0:1:0:60:2:1:0:0 1/1:6:6:4,2:0,0:0,6:1:0,2:13.7:1:30.3:1:1:0:60:12:1:0:1.2 +18 56338743 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGCTTCCTCCTCTGAGGG;RSEQ=CGTGCCGCGCTGCCAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:19.6:1:29.6:1:1:0:60:4:1:0:0.2 0/1:12:2:1,1:7,3:10,2:0.1667:2,2:38.5:1:29:1:1:2.16028:60:4:0.1818:0:1 +18 56338878 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59925;SOR=0.48092;LSEQ=GGGTCGCCGGCGAGGGCCAT;RSEQ=TCGCTGTTGGGGGACCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:66,66:132,2:0.0149:2,2:32.5:1:29.5:1:1:1:60:4:0.0152:0:1 0/0:277:2:1,1:136,139:275,2:0.0072:2,2:34.5:1:28:1:1:1.02:60:4:0.0072:0:1 +18 56338909 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11389;SOR=0;LSEQ=GGGACCCGCTACAGGCCCTG;RSEQ=CGCCCTCGGCCGCCCCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:64,70:134,2:0.0147:2,2:31:1:30.5:1:1:1.09:60:4:0.015:0:2 0/0:266:0:0,0:131,134:265,0:0:2,0:24:1:31:1:1:0:59.9:52:0.9962:0:0.4 +18 56338918 . G A 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14272;SOR=0.19116;LSEQ=TACAGGCCCTGCCGCCCTCG;RSEQ=CCGCCCCCACGGGGCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:2,1:66,63:129,3:0.0227:2,2:11.7:1:28.7:1:1:1.90:60:6:0.0236:0:1 0/0:227:1:1,0:113,112:225,1:0.0044:2,0:1:0:26:0:1:0:60:2:0.0046:0:1 +18 56338920 . C G 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13065;SOR=0;LSEQ=CAGGCCCTGCCGCCCTCGGC;RSEQ=GCCCCCACGGGGCCGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:65,62:127,2:0.0155:2,2:7:0:32.5:1:1:1.04802:60:4:0.0157:0:1.5 0/0:227:0:0,0:114,113:227,0:0:2,0:23.6:1:29.4:1:1:0:60:55.75:1:0:0.4 +18 56338924 . C A 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.36607;SOR=0.39236;LSEQ=CCCTGCCGCCCTCGGCCGCC;RSEQ=CCACGGGGCCGCTGCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:3:2,1:65,60:125,3:0.0234:2,2:11.3:1:30.3:1:1:1.84:60:6:0.024:0:1 0/0:215:2:1,1:109,104:213,2:0.0093:2,2:11.5:1:27:1:1:1.04787:60:4:0.0096:0:1.5 +18 56338946 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11614;SOR=0;LSEQ=CACGGGGCCGCTGCTCGCCC;RSEQ=TCCGGCCGGCGCGACCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:61,43:104,2:0.0187:2,2:24.5:1:30:1:1:1.41382:60:4:0.0189:0:2 0/0:206:0:0,0:113,90:203,0:0:2,0:17.1:1:30.8:1:1:0:59.9:202:0.9902:0:0.3 +18 56338983 . G A 56 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71685;SOR=0.63712;LSEQ=CTCAACCGCCTGCGGGAGCC;RSEQ=CTGCTGCGGAGGCTCAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:4:3,1:94,58:152,4:0.0253:2,2:23:1:17.8:1:1:1.84:55:0.333:0.0066:0:0.8 0/1:246:4:3,1:138,103:241,4:0.0163:2,2:20.3:1:28.3:1:0.6391:2.23:60:8:0.0164:0:1 +18 56338990 . C T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.93926;LSEQ=GCCTGCGGGAGCCGCTGCTG;RSEQ=GGAGGCTCAGCGAGCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:0,1:106,72:178,1:0.0056:2,0:1:0:26:0:0.40782:0:60:2:0.0056:0:1 0/1:278:3:1,2:155,120:275,3:0.0108:2,2:13:1:27.3:1:0.58361:2.57465:60:6:0.0109:0:1 +18 56339018 . C T 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65363;SOR=2.54139;LSEQ=CAGCGAGCTCCTGGATCAGG;RSEQ=GCCCGAGGGCCGGGGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:0,1:128,118:246,1:0.004:2,0:1:0:15:0:0.48178:0:60:0:0:0:1 0/1:397:4:1,3:206,187:393,4:0.0101:2,2:11.3:1:26.8:1:0.35295:3.29566:56.8:8:0.0103:0:1 +18 56339066 . G A 52 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41662;SOR=3.06813;LSEQ=GGCGGAGCTGGCGGGGAGTC;RSEQ=CGGGCGCCTCCGCCTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:97,131:228,1:0.0044:2,0:1:0:27:0:0.42795:0:60:2:0.0045:0:1 0/1:376:5:5,0:167,204:371,5:0.0133:2,0:10:1:22.8:1:0.0194:0:60:4:0.0109:0:1.2 +18 56339103 . C T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52062;SOR=Inf;LSEQ=AGGTGAGCTCAGGGCCGCGG;RSEQ=AGGCCGGGCGCGCGGGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:43,71:114,0:0:2,0:19.2:1:32.1:1:1:0:59.9:27.5:1:0:0.3 0/1:175:2:1,1:69,103:172,2:0.0114:2,2:29:0:29.5:1:1:1.49:60:4:0.0121:0:2 +18 56339139 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.53939;SOR=Inf;LSEQ=GTCGAGCGGGGTGGGCTGCG;RSEQ=TGGGGAGGTGGGGGCGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:13.6:1:31.6:1:1:0:59.5:38:1:0:0.2 0/1:36:2:1,1:10,24:34,2:0.0556:2,2:9:0:29.5:1:0.52381:2.34:60:4:0.0571:0:1 +18 56348181 . A T 28 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=26.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=CAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAAATAATCATGGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:13.1:1:31.9:1:1:0:52.6:24:1:0:2.3 1/0:4:2:2,0:1,1:2,2:0.5:2,0:24.5:1:28.5:1:1:0:48:4:0.5:0:1.5 +18 56348724 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11986;SOR=0.46205;LSEQ=GGTTGAAGCAAATGCAATGC;RSEQ=TGAATATTGGTTGGATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:16:0,16:0,49:49,16:0.2462:1,1:19.5:1:32.6:1:1:0:60:32:0.25:0:1 0/1:69:9:0,9:0,60:60,9:0.1304:1,0:24.6:1:30.8:1:1:0:60:18:0.1304:0:1.1 +18 56363494 . A T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=GATTTATGACAAAGATAAAT;RSEQ=TGCAAGTTATTTCTAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:52,0:52,0:0:1,0:19.5:1:28.9:1:1:0:60:51:1:0:0 0/1:39:11:11,0:28,0:28,11:0.2821:1,0:17.3:1:30.5:1:1:0:60:22:0.2821:0:1 +18 56363765 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25173;SOR=Inf;LSEQ=TTCTTCCAAGGAGAGAGAAT;RSEQ=ATAGAGAATTAATTAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:43,202:245,0:0:2,0:23.5:1:31.4:1:1:0:60:19.417:1:0:0.1 0/1:279:3:2,1:59,215:274,3:0.0108:2,2:12:1:27:1:0.12308:7.22:60:6:0.0109:0:1 +18 56363908 . A C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02821;SOR=Inf;LSEQ=CAGAATTGTCTCATGAAAAC;RSEQ=TTGTAAACAATAATGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:0,15:15,0:0:1,0:18.3:1:31.6:1:1:0:60:30:1:0:0.4 0/1:12:4:0,4:0,8:8,4:0.3333:0,0:18.8:1:33:1:1:0:60:8:0.3333:0:1.3 +18 56367946 . TCATC T 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.18765;SOR=Inf;LSEQ=CAAAATTTCACATAGGTACT;RSEQ=CATTATAATGTCAACCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:0,70:70,0:0:1,0:26.2:1:32:1:1:0:59.6:22.333:1:0:0 0/1:54:2:0,2:2,50:52,2:0.037:1,0:34:1:33.5:1:1:0:60:4:0.037:0:0 +18 56368000 . CT C 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.87198;LSEQ=GATCCATGTGTTTTGTCTTT;RSEQ=TTTTTTTTTAATTTAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:0,4:0,29:29,4:0.1212:1,0:37:1:34:1:1:0:60:8:0.125:0:0 0/1:28:3:2,1:2,23:25,3:0.1071:2,2:22.3:1:32.7:1:0.04518:18.20:60:6:0.1071:0:0.3 +18 56377000 . A G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.70476;SOR=0.59575;LSEQ=GGCTTATATGTAAAATGTCA;RSEQ=ATAGTATTGCATGAAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:7:3,4:19,12:31,7:0.1842:2,2:20.1:1:32.7:1:0.42501:2.06868:60:14:0.1892:0:1 0/1:17:2:0,2:9,6:15,2:0.1176:2,0:23:1:31:0:0.20588:0:60:4:0.1176:0:1 +18 56378058 . AT A 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00061;SOR=0.42468;LSEQ=GCATGTGTTGGTTTGCCAAC;RSEQ=TATCTCTATGATATTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:52:43,9:148,21:169,52:0.2353:2,2:27.3:1:31.9:1:0.36216:1.4723:60:104:0.2385:0.0271:0 0/1:260:30:25,5:201,29:230,30:0.1154:2,2:24.9:1:30.5:1:0.5639:1.3843:60:60:0.1167:0.0308:0.1 +18 56378529 . C T 66 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAGAAAGATAGGTGGCTA;RSEQ=GTGATCATGGATATTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:16.2:1:28.6:1:1:0:53.4:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 56383323 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.22866;SOR=1.39488;LSEQ=CATTGGGACCAAATGTTTTA;RSEQ=TTTTTTGTATCTGTAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:31:0,31:1,95:96,31:0.2441:1,1:23.6:1:33:1:1:0:60:30:0.2419:0:1.1 0/1:148:46:1,45:1,101:102,46:0.3108:1,1:24:1:32.2:1:0.52648:2.23:60:45:0.3061:0:1.2 +18 56390265 . C CT 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.88614;SOR=1.08132;LSEQ=CTTCTTTAAACACCCCCTTT;RSEQ=TTTTTTTTTCAAAGCGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:611:22:16,6:414,174:588,22:0.036:2,2:23.6:1:31.2:1:1:1.12:60:44:0.0365:0.0115:0.3 0/1:747:29:22,7:473,245:718,29:0.0388:2,2:24.4:1:29.7:1:0.31992:1.63:60:58:0.0394:0.0054:0.2 +18 56390553 . A G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATACAAGTTAGGTTAAGA;RSEQ=TTGAAAATCAGATAAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:204:204:14,190:0,0:0,204:1:0,2:27.2:1:32.2:1:1:0:59.8:67:1:0:1.1 1/1:209:209:19,190:0,0:0,209:1:0,2:24.4:1:31.5:1:1:0:60:103.5:1:0:1 +18 56400351 . C T 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGTTTCACCACGTTGGC;RSEQ=AGGCTGGTTTCGAACCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:29.5:1:32.8:1:1:0:39:8:0.3636:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 56400378 . A T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=GTTTCGAACCCCTGACCTCA;RSEQ=GTGATCTGCCTGCCTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:16,0:0:1,0:26:1:31.3:1:1:0:40.8:32:1:0:0.3 0/1:5:2:1,1:2,1:3,2:0.4:2,2:8:0:31:1:1:1.7321:52.5:4:0.4:0:1.5 +18 56400396 . G A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05435;SOR=Inf;LSEQ=CAAGTGATCTGCCTGCCTCG;RSEQ=CCTCCCAAAGTGCTGGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:18,0:18,0:0:1,0:23.1:1:31.7:1:1:0:43.3:36:1:0:0.2 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:7.5:1:30:0:1:2.44949:50:4:0.3333:0:2 +18 56400547 . T G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04521;SOR=0.56686;LSEQ=AAAATTAAAGTCAAGGTTTT;RSEQ=CTACAAAAAGTTATGCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:41:39,2:146,7:153,41:0.2113:1,1:23.7:1:31.8:1:1:1.06923:60:19.5:0.2063:0:1.1 0/1:205:27:25,2:170,8:178,27:0.1317:1,2:28.3:1:31.5:1:0.62401:1.69478:60:54:0.133:0:1.1 +18 56400826 . T C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24303;SOR=1.15737;LSEQ=GGTAAGTTTTCTAATCTTTA;RSEQ=TAAAGAATTGTTGGAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:568:152:40,112:132,284:416,152:0.2676:2,2:25.6:1:33:1:0.25647:1.30082:59.8:304:0.27:0:1.1 0/1:757:225:72,153:188,342:530,225:0.2972:2,2:23.1:1:31.4:1:0.40248:1.16789:60:224:0.2979:0:1.1 +18 56400852 . G A 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=AATTGTTGGAGTTAAATATC;RSEQ=ACCATGACAAACTAGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:64,283:347,0:0:2,0:25.6:1:31.7:1:1:0:60:85.75:0.9971:0:0.3 0/1:432:18:5,13:88,326:414,18:0.0417:2,2:16.1:1:29.5:1:0.55736:1.42:60:36:0.0421:0:1.1 +18 56401758 . C T 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06917;SOR=Inf;LSEQ=TCACTGCTCCTGGGCTCAAG;RSEQ=GATCCTCCTGCCTCAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:0,83:83,0:0:1,0:21.3:1:30.2:1:1:0:60:82:1:0:0 0/1:107:5:0,5:2,100:102,5:0.0467:1,0:15.2:1:29.8:1:1:0:59.4:10:0.0472:0:1 +18 56402297 . ACC A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=9.000;MSILEN=1;SSF=1;SOR=1.48109;LSEQ=ACAGTCCCCACGCTGTCCCC;RSEQ=CCCCCCCAGCCTCTGGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:43:43,0:2,0:2,43:0.9556:0,1:25.9:1:32.7:1:1:0:60:86:0.9556:0.1333:0 1/1:33:32:32,0:0,0:0,32:0.9697:0,1:24.6:1:32.2:1:1:0:60:64:1:0.1515:0 +18 56406968 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTGCAGGTTTCAGACT;RSEQ=GCACCGCCACAATTCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 56409002 . A C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.85006;SOR=0.90748;LSEQ=GTGAATAAATGATACTGAGA;RSEQ=TATAACCTGATAATGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:27:26,1:80,1:81,27:0.25:1,1:26.1:1:31.8:1:0.43925:3.03816:59.9:54:0.25:0:1.2 0/1:56:13:12,1:43,0:43,13:0.2321:1,1:23.2:1:31.6:1:0.23214:0:60:26:0.2321:0:1 +18 56409291 . G A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00889;SOR=Inf;LSEQ=AGATCTACAATATACTTAAC;RSEQ=TTAAATCATAAAGTTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:103,312:415,0:0:2,0:22.5:1:31.5:1:1:0:60:50.875:1:0:0.1 0/1:485:8:3,5:125,352:477,8:0.0165:2,2:19:1:28.5:1:0.4404:1.69:60:16:0.0165:0:1 +18 56411493 . A T 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAAGCAAAAGAAATGCTA;RSEQ=CTATATTCTCCTCCATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:217,20:237,0:0:2,0:23:1:30.6:1:1:0:60:236:1:0:0 0/1:289:59:53,6:195,35:230,59:0.2042:2,2:23.4:1:31:1:0.40546:1.58:60:118:0.2049:0:1.1 +18 56411823 . A AAT 25 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.49835;SOR=0;LSEQ=TTGATGGTAAATATAAAGGA;RSEQ=ATATATATATTTATATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:0,2:0,139:139,2:0.0142:1,0:38:0:25.3:1:1:0:53.5:4:0.0143:0:3 0/0:136:0:0,0:0,136:136,0:0:1,0:22.4:1:30.9:1:1:0:60:135:1:0:0 +18 56412690 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0.37796;LSEQ=AGAGCTCACTTTACTTTTTA;RSEQ=ATGGCTTAGTACAGAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:14,0:1,0:1,14:0.9333:0,1:19.6:1:31:1:1:0:59.5:28:0.9333:0:1.2 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:26.8:1:30.4:1:1:0:60:10:0.8333:0:1 +18 56412784 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04442;SOR=0.39206;LSEQ=TTTGGGATTACCAAAATTCA;RSEQ=GAGAGGCCAGAATTCACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:30:30,0:47,1:48,30:0.3846:1,1:24.3:1:31.8:1:1:0:59.8:60:0.3896:0:1.2 0/1:46:9:8,1:36,1:37,9:0.1957:1,2:31.6:1:30.3:1:0.35652:4.30117:60:18:0.1957:0:1 +18 56412882 . A AT 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.09942;SOR=1.44271;LSEQ=TTCATTATTAACAGTCCCTA;RSEQ=TTTTTTTTTTTACAGGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:38:31,7:276,87:363,38:0.0931:2,2:27.8:1:31.8:1:0.5482:1.39:60:76:0.096:0:0.3 0/1:550:71:55,16:352,122:474,71:0.1291:2,2:23.9:1:29.1:1:0.66118:1.19:59.6:34.5:0.1287:0.0218:0.2 +18 56412894 . A T 47 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01399;SOR=0;LSEQ=AGTCCCTAATTTTTTTTTTT;RSEQ=CAGGATCTAGATATTGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:3,2:341,151:492,5:0.01:2,2:10.6:1:20.6:1:0.64578:1.5042:60:1.5:0.0062:0:1.8 0/0:669:0:0,0:458,211:669,0:0:2,0:23.4:1:27.2:1:1:0:59.9:38.353:1:0:0.1 +18 56413121 . G C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04882;SOR=0.50462;LSEQ=TATGCTGCCTTATTATTAAA;RSEQ=TAGAGATAACCAGTCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:28:0,28:3,108:111,28:0.2014:1,1:26:1:34.1:1:1:0:60:56:0.2014:0:1 0/1:142:16:1,15:1,125:126,16:0.1127:1,1:25.6:1:31.7:1:0.21337:8.10:60:32:0.1127:0:1.3 +18 56413217 . G T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73966;SOR=0.69636;LSEQ=TTATGTGTGCTTACCCTCCA;RSEQ=AATGCTAAAAAATTAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:11:0,11:1,32:33,11:0.25:1,0:27.4:1:29.2:1:1:0:60:22:0.2558:0:1 0/1:16:3:0,3:0,13:13,3:0.1875:1,0:14.7:1:29:0:1:0:60:6:0.1875:0:1.3 +18 56413237 . CATT C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.26412;LSEQ=GAATGCTAAAAAATTAGTAA;RSEQ=AGAGTATATTCTTTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:22:0,22:0,4:4,22:0.8462:0,1:22.6:1:32:1:1:0:60:21:0.84:0.1538:0.4 1/1:8:7:0,7:0,1:1,7:0.875:0,0:18.7:1:32.5:1:1:0:60:14:0.875:0.25:0.1 +18 57560606 . T G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01213;SOR=0.72243;LSEQ=ACTTTCTTGGCTGACAGAGG;RSEQ=TCTAAGCCTATTCCCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:145:62,83:219,313:532,145:0.2142:2,2:25:1:31.9:1:0.77564:1.07:60:71.5:0.2138:0:1.1 0/1:991:163:74,89:374,454:828,163:0.1645:2,2:24.2:1:31:1:1:1.01:59.9:80.5:0.165:0:1.2 +18 57567451 . C T 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AAGAACGCTCAACCGAGCCC;RSEQ=GCGCGGGCTCCAGCAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:0:0,0:207,353:560,0:0:2,0:26:1:30.1:1:1:0:60:45.667:0.9982:0:0.1 0/1:829:58:25,33:316,453:769,58:0.07:2,2:22.5:1:29.4:1:0.78323:1.09:60:116:0.0713:0:1.1 +18 57567510 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17201;SOR=0;LSEQ=GAAGACCCAGGCCGGGCGGG;RSEQ=TCGGGGCCGGGGTCGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:29,158:187,2:0.0106:2,2:35.5:1:27.5:1:0.29298:5.37:60:4:0.0107:0:1 0/0:266:0:0,0:54,212:266,0:0:2,0:20.6:1:31.1:1:1:0:60:65.5:1:0:0.3 +18 57568601 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68653;SOR=1.05449;LSEQ=TCAGGGCTTCCAGTGTCGGA;RSEQ=GCTGAATGGTATTTGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:233:95,138:106,151:257,233:0.4745:2,2:23.7:1:30.8:1:0.92697:1.01969:60:232:0.4754:0:1.1 0/1:779:380:150,230:168,230:398,380:0.4878:2,2:24.3:1:29.6:1:0.46589:1.11984:60:94:0.4896:0:1.1 +18 57568693 . A G 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08835;SOR=1.78616;LSEQ=ATGTAAATACTTCCCAACAT;RSEQ=TTTGATCTTGTAGCCCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:22:1,21:1,60:61,22:0.2651:1,1:28:1:32.7:1:0.46224:2.81:60:44:0.275:0:1.2 0/1:107:42:1,41:2,62:64,42:0.3925:1,1:21.2:1:31.4:1:1:1.31921:60:84:0.4:0:1.1 +18 57570044 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51678;SOR=Inf;LSEQ=AGTTTTCTCAGGAGGTGCAC;RSEQ=TTTCATCAATTTGAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:15,85:100,0:0:2,0:22.3:1:31.7:1:1:0:60:99:1:0:0.1 0/1:148:2:1,1:23,123:146,2:0.0135:2,2:31:1:28.5:1:0.29895:5.26:60:4:0.0135:0:1 +18 57571885 . A T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62504;SOR=1.20625;LSEQ=ACCTCTGCCTCCTGGGTCTA;RSEQ=GTGATTCTCGTGCTAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:30:0,30:0,38:38,30:0.4412:1,1:26.2:1:27.7:1:1:0:53.7:6.5:0.4063:0:1.1 0/1:84:41:2,39:1,42:43,41:0.4881:1,1:26.8:1:29:1:0.61145:2.13:54.6:12.667:0.475:0:1.1 +18 57571922 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19814;SOR=Inf;LSEQ=AGCCTCCCCCACACGCCACC;RSEQ=CACTGGGTAATTTTTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,43:43,0:0:1,0:21.4:1:29.6:1:1:0:58.8:42:1:0:0.6 0/1:35:2:0,2:2,31:33,2:0.0571:2,0:14.5:1:29:1:1:0:55.5:4:0.0588:0:2 +18 57572213 . A G 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGATTGCTTCATCTGAGGTT;RSEQ=GTCATGTGCAAAAGTAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:31.5:1:1:0:60:4:1:0:1 +18 59254083 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50013;SOR=0;LSEQ=GGGAAAAGTCAAGTTATTAT;RSEQ=AATACATTTCCTGATTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:118,56:174,2:0.0114:2,2:26.5:1:31:1:0.54409:2.09746:60:4:0.0114:0:1 0/0:157:0:0,0:99,58:157,0:0:2,0:27.1:1:28.2:1:1:0:60:51.333:1:0:0.4 +18 59254138 . C G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10558;SOR=1.35598;LSEQ=TCTGAAGCTAAATTACAGAG;RSEQ=TTATATTTTGGATAAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:85:45,40:82,75:157,85:0.3512:2,2:26.9:1:31.4:1:1:1.03:60:170:0.3527:0:1.4 0/1:281:119:67,52:83,79:162,119:0.4235:2,2:23:1:30.7:1:0.46789:1.23:60:238:0.4281:0:1.7 +18 59254190 . A T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.18117;LSEQ=TATAAACAATGATTTGGCAC;RSEQ=TTTGTTTAATTCCCCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:93:32,61:34,69:103,93:0.4745:2,2:25.5:1:30.9:1:0.8803:1.06:60:92:0.4718:0:2.4 0/1:257:36:13,23:96,125:221,36:0.1401:2,2:30.1:1:30.2:1:0.4696:1.35718:60:72:0.1412:0:2.6 +18 59254198 . A C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=33.8671;LSEQ=ATGATTTGGCACATTTGTTT;RSEQ=ATTCCCCTTTGTGTCTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:172:151:44,107:4,17:21,151:0.8779:2,2:25.1:1:32.7:1:0.44033:1.74:60:302:0.8779:0:2.4 1/1:246:245:99,146:0,0:0,245:0.9959:0,2:24.4:1:30.8:1:1:0:60:121.5:0.9959:0:2 +18 59254211 . G A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57824;SOR=0.37161;LSEQ=TTTGTTTAATTCCCCTTTGT;RSEQ=TCTAAGTAAGGGCAACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:33,113:146,2:0.0135:2,2:27.5:1:31:1:0.40789:3.39:60:4:0.0137:0:3.5 0/0:198:1:1,0:72,125:197,1:0.0051:2,0:1:0:22:0:0.36869:0:60:2:0.0051:0:3 +18 59254213 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17933;SOR=0;LSEQ=TGTTTAATTCCCCTTTGTGT;RSEQ=TAAGTAAGGGCAACAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:32,109:141,2:0.014:2,2:15.5:1:30:1:0.40953:3.37:60:4:0.0141:0:1.5 0/0:194:0:0,0:69,125:194,0:0:2,0:21.9:1:30.7:1:1:0:60:63.667:1:0:2.1 +18 59254227 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00035;SOR=17.40004;LSEQ=TTGTGTCTAAGTAAGGGCAA;RSEQ=AGAAAAAAGATCTTCAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:113:100:18,82:2,11:13,100:0.885:2,2:23.2:1:28.9:1:1:1.21:60:99:0.8839:0:2.5 1/1:136:135:41,94:0,0:0,135:0.9926:0,2:22.6:1:27.6:1:1:0:60:32.75:0.9924:0:2.4 +18 59254309 . G A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3532;SOR=3.90045;LSEQ=TGGGGGCATTTGGCTTTTCC;RSEQ=TGCATTCTACCCTGATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:22:3,19:0,4:4,22:0.8462:0,2:21.4:1:31.6:1:1:0:60:44:0.8462:0:1.5 1/1:23:22:0,22:0,0:0,22:0.9565:0,1:16.5:1:30.3:1:1:0:60:44:1:0:1.6 +18 59254399 . T G 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15385;SOR=8.0749;LSEQ=TACAAATATTCACAAAATGC;RSEQ=TTTCCTGCACCAGGCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:0,10:10,1:0.0909:0,0:34:0:32:0:1:0:60:2:0.0909:0:1 1/0:4:2:0,2:0,2:2,2:0.5:0,0:24:1:30.5:1:1:0:60:4:0.5:0:1.5 +18 59899349 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49666;SOR=Inf;LSEQ=AATGGTATTTTAAATCTGTT;RSEQ=CTAGCCCAAAGAAATATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:32,11:43,0:0:2,0:23.9:1:31:1:1:0:60:86:1:0:0.2 0/1:49:2:1,1:33,14:47,2:0.0408:2,2:33.5:1:30.5:1:0.52296:2.31149:60:4:0.0408:0:1 +18 59899398 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.23394;SOR=Inf;LSEQ=GGAGCACTGTTGCTGTTGTT;RSEQ=CTGCTGCTGCTGCTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:49,38:87,0:0:2,0:26.2:1:31.8:1:1:0:58.3:28:1:0:0.2 0/1:82:2:1,1:41,39:80,2:0.0244:2,2:15.5:1:31:1:1:1.05066:60:4:0.0247:0:1 +18 60646484 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=TTTGCTGCCCCGGCTCAGCC;RSEQ=GATCCTGATGATCAGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:15.5:1:27.5:1:0.4:0:60:4:0.4:0:1 0/0:6:0:0,0:5,1:6,0:0:2,0:15.7:1:29.5:1:1:0:60:12:1:0:0.2 +18 60795696 . TTG T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.57432;SOR=2.72629;LSEQ=TGCCTGAAGACTGTTAATTG;RSEQ=TGTGTGTGTGTGTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:50,1:51,1:0.0192:1,0:15:0:33:0:1:0:60:2:0.0204:0:0 0/1:39:2:1,1:35,2:37,2:0.0513:2,2:25.5:1:29:1:0.1498:14.49018:60:4:0.0526:0.0256:0 +18 60796065 . GA G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49735;SOR=0;LSEQ=AGAGAATGCCACCCCACAGA;RSEQ=AAGAGGCATCCTGCCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:7,85:92,2:0.0211:2,2:33:1:31.5:1:0.16381:11.43:60:4:0.0217:0:0 0/0:95:0:0,0:12,83:95,0:0:2,0:22.1:1:29.4:1:1:0:59.9:22.75:1:0:0.1 +18 60847763 . T C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCCCACCCCAGACCGCCCA;RSEQ=CCCACCCCAGGCTTAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:23:0:27:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:29.5:1:1:0:60:4:1:0:1 +18 60849930 . G A 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AGGCTTCATTGGCCCATTCT;RSEQ=CAAATCAACTCTGCAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:212,47:259,0:0:2,0:23:1:32.3:1:1:0:60:63.75:1:0:0.1 0/1:297:18:13,5:224,55:279,18:0.0606:2,2:22.7:1:27.9:1:0.3762:1.56379:60:36:0.061:0:1.1 +18 60850071 . TG T 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAAACCTCATGTCCCTACC;RSEQ=GGGTATTTGCCTGAAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:759:0:0,0:366,391:757,0:0:2,0:24.4:1:31.4:1:1:0:59.8:49.467:0.9973:0:0.1 0/1:962:44:21,23:430,485:915,44:0.0457:2,2:30.2:1:31.1:1:1:1.03:59.8:88:0.0468:0.0021:0.1 +18 60850310 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.82767;LSEQ=AGATGCATGTCACACTGATG;RSEQ=TGGGGCTCAGACCCACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:0,15:0,4:4,15:0.7895:0,1:25.7:1:32.6:1:1:0:60:30:0.7895:0:1.1 1/1:8:7:0,7:0,1:1,7:0.875:0,0:21.6:1:30.4:1:1:0:60:14:0.875:0:1 +18 60850631 . A G 39 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AGCAGGCTTCATGGAAGTTG;RSEQ=GCTATTATGGCGAAGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:29:0:32:0:1:0:60:2:1:0:3 1/1:3:3:1,2:0,0:0,3:1:0,2:27.3:1:25:1:1:0:60:2:1:0:3 +18 60850642 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGAAGTTGAGCTATTATGG;RSEQ=GAAGAGGGTGAGGTGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:18:0:29:0:1:0:60:2:1:0:3 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:27.5:1:27.5:1:1:0:60:4:0.6667:0:2 +18 60851849 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16222;SOR=0;LSEQ=CTGAAGATAAGTGCAACTCA;RSEQ=TGCAAAAGGATTCCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:93,95:188,2:0.0105:2,2:20:1:34:1:1:1.02:60:4:0.0109:0:1 0/0:281:0:0,0:132,149:281,0:0:2,0:29:1:29.6:1:1:0:57.1:92.667:1:0:0.4 +18 60851880 . G A 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02145;SOR=1.79706;LSEQ=TTCCTGCTGTAATACAGACT;RSEQ=TAGCCCATCAGGGGAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:29:15,14:57,90:147,29:0.1648:2,2:25.4:1:28.2:1:0.2188:1.69:50.1:28:0.1618:0:1.2 0/1:229:60:24,36:70,99:169,60:0.262:2,2:27.4:1:29:1:0.87964:1.06036:48.6:120:0.2643:0:1.2 +18 60852085 . T C 92 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGGCCACTTCTTGAATTTC;RSEQ=ACCCTTCTTCTTGAATGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:1,6:0,2:2,7:0.7778:0,2:24.6:1:33:1:1:0:49.3:14:0.7778:0:1.7 1/1:1:1:0,1:0,0:0,1:1:0,0:40:0:32:0:1:0:60:2:1:0:1 +18 60909860 . T C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.44444;SOR=0;LSEQ=ACAATCCCTTATTACCAGTC;RSEQ=CTCCTCATTAAAACATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:20,0:0,0:0,20:1:0,1:31.7:1:31.7:1:1:0:60:40:1:0:1.1 1/1:16:15:15,0:1,0:1,15:0.9375:0,1:16.6:1:29.5:1:1:0:60:14:0.9333:0:1.2 +18 60910012 . G T 54 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13516;SOR=Inf;LSEQ=ATTAGATAAAATTTCAAATT;RSEQ=CTGAAAATGCATGTGGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:195,95:290,0:0:2,0:26.1:1:32.4:1:1:0:60:144:1:0:0.1 0/1:371:4:1,3:232,134:366,4:0.0108:2,2:6.8:1:27.3:1:0.14541:5.17081:59:8:0.011:0:1 +18 60910135 . C T 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GAGAAGACAATGAAAGGGAA;RSEQ=GGAGAGGCGCTGGAATATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:85,197:282,0:0:2,0:23.5:1:30.4:1:1:0:60:69.5:0.9964:0:0.1 0/1:332:18:7,11:101,211:312,18:0.0542:2,2:29.7:1:29.4:1:0.60874:1.33:60:36:0.0545:0:1.1 +18 60910163 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24852;SOR=Inf;LSEQ=CGCTGGAATATTGTGAAATG;RSEQ=CCCAAAAAGTTGTTTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:32,117:149,0:0:2,0:23:1:31.7:1:1:0:60:148:1:0:0.1 0/1:160:3:2,1:34,123:157,3:0.0188:2,2:18:1:27.7:1:0.12727:7.12:60:6:0.0194:0:1.3 +18 60910366 . G A 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTGATAGACTGGATAAA;RSEQ=AAAATTTGGTACATATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:22.8:1:31.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 60950140 . A T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0936;SOR=0;LSEQ=GATTCCATTCCATTTTGTAA;RSEQ=TTACTGATCTGTACCAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:3:1,2:193,52:245,3:0.0121:2,2:14.3:1:22:1:0.12041:7.34263:60:2:0.0083:0:1 0/0:297:0:0,0:240,57:297,0:0:2,0:22.6:1:29.7:1:1:0:60:296:1:0:0 +18 60950363 . T A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17139;SOR=0;LSEQ=TTCCCCTCTTTTGAAAAATT;RSEQ=CTAGTTATTTTTTTCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:28,145:173,2:0.0114:2,2:22:1:25:1:0.30476:5.11:60:4:0.0115:0:1 0/0:247:0:0,0:57,190:247,0:0:2,0:22.8:1:28.9:1:1:0:60:81.333:1:0:0.1 +18 60985601 . G A 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.39242;LSEQ=GGCGGGAGAAGTCGTCGCCG;RSEQ=CCTGGCGGAGGGTCAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:2:1,1:41,233:274,2:0.0072:2,2:24:1:27:1:0.28166:5.63:60:4:0.0075:0:1 0/1:298:3:1,2:71,224:295,3:0.0101:2,2:28:1:29:1:0.56522:1.57:60:6:0.0102:0:1.7 +18 60985622 . AC A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24868;SOR=Inf;LSEQ=CCTGGCGGAGGGTCAGGTGG;RSEQ=CACAGGTGGCACCGGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:27,163:190,0:0:2,0:26.2:1:31.5:1:1:0:59.8:22.75:1:0:0.1 0/1:202:3:2,1:49,150:199,3:0.0149:2,2:9.3:1:26.3:1:0.15764:6.05:60:6:0.0155:0.0099:0.7 +18 60985637 . G A 45 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05798;SOR=Inf;LSEQ=GGTGGACCACAGGTGGCACC;RSEQ=GGCTGAGCGCAGGCCCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:21,130:151,0:0:2,0:23.5:1:31.6:1:1:0:60:150:1:0:0.2 0/1:147:4:3,1:38,105:143,4:0.0272:2,2:5.8:1:22.5:1:0.06594:8.15:60:3:0.0221:0:1 +18 60985671 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.80056;LSEQ=CCCCGCGGCGGCGCCGGGGG;RSEQ=AGCCGGGGTCTGCAGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:52,59:111,1:0.0089:2,0:1:0:23:0:1:0:60:2:0.0092:0:1 0/1:125:2:1,1:59,63:122,2:0.016:2,2:9.5:1:26.5:1:1:1.07:60:4:0.0168:0:1 +18 60985689 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51095;SOR=Inf;LSEQ=GGCAGCCGGGGTCTGCAGCG;RSEQ=CGAGGTCCTGGCGACCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:81,55:136,0:0:2,0:20.6:1:31.7:1:1:0:60:33:1:0:0.2 0/1:187:2:1,1:106,79:185,2:0.0107:2,2:6.5:1:28:1:1:1.33962:60:4:0.0109:0:1.5 +18 60985691 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17351;SOR=0;LSEQ=CAGCCGGGGTCTGCAGCGGC;RSEQ=AGGTCCTGGCGACCGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:86,56:142,2:0.0139:2,2:38.5:1:29.5:1:1:1.53096:60:4:0.0141:0:1 0/0:201:0:0,0:117,84:201,0:0:2,0:20.2:1:29.8:1:1:0:60:32.5:1:0:0.3 +18 60985879 . T C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.55285;LSEQ=ATCTCCCGGTTATCGTACCC;RSEQ=GTTCTCCCAGCGTGCGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1001:630:310,320:179,191:370,630:0.6294:2,2:25.8:1:30.5:1:0.84421:1.03:59.9:104:0.6303:0:1.1 0/1:1357:657:317,340:349,348:697,657:0.4842:2,2:25.5:1:29.6:1:0.51431:1.07558:60:108.5:0.4837:0:1.1 +18 61199883 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25298;SOR=Inf;LSEQ=TCTTCAAGAGCAGGTTGTTT;RSEQ=AGATTAAAGAGGTTGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:159,89:248,0:0:2,0:24.9:1:32:1:1:0:60:123:1:0:0.5 0/1:289:3:1,2:175,109:284,3:0.0104:2,2:26.3:1:22.7:1:0.56157:3.19766:60:2:0.0071:0:3.7 +18 61199950 . G C 258 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.0231;LSEQ=TTCAGTAGGAGTTTGCTGAG;RSEQ=GGTTGCTAACCTCTCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:334:332:155,177:1,0:1,332:0.994:0,2:26.8:1:30.9:1:0.46847:0:60:82:0.997:0:1.1 1/0:391:310:145,165:39,38:77,310:0.7928:2,2:26.2:1:30.1:1:0.6104:1.1674:60:61:0.7963:0:1.1 +18 66080132 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.12539;SOR=0;LSEQ=GAGATTTTGGAATAGATATT;RSEQ=TTATGTACAATGGTTAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:42,18:60,2:0.0317:2,2:17.5:1:31:1:0.52247:2.298:60:4:0.0323:0:1 0/0:114:0:0,0:70,44:114,0:0:2,0:27:1:29.4:1:1:0:60:56:1:0:0.3 +18 66080181 . C A 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=TTTTACTCAAAAACACAAAT;RSEQ=TTTTAATATAAATATGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:38,35:73,0:0:2,0:28.1:1:32.7:1:1:0:60:72:1:0:0.8 0/1:145:21:10,11:62,62:124,21:0.1448:2,2:21.2:1:28.4:1:1:1.09928:60:42:0.1458:0:1.2 +18 66080203 . T C 206 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTAATATAAATATGAAATG;RSEQ=TTATTTTCACATATACTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:85:40,45:0,0:0,85:1:0,2:21.5:1:32.2:1:1:0:60:27.333:1:0:1 1/0:137:76:36,40:25,36:61,76:0.5547:2,2:23.7:1:31.1:1:0.49231:1.29:60:75:0.5515:0:1.2 +18 66533736 . G C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19355;SOR=0;LSEQ=ATGTCAACATGTAGACTTTT;RSEQ=TCCAGGCCGGACACAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:26,0:26,2:0.0714:1,2:8:1:29.5:1:0.07143:0:60:4:0.0741:0:1 0/0:35:0:0,0:28,7:35,0:0:2,0:20.1:1:30.7:1:1:0:60:70:1:0:0.1 +18 66533842 . TG T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1316;SOR=Inf;LSEQ=TATCAGAAAAGCTGCTCCTT;RSEQ=GGAACCTTAGTCAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:64,36:100,0:0:2,0:23.8:1:31.8:1:1:0:60:99:0.99:0:0.1 0/1:58:2:1,1:26,30:56,2:0.0345:2,2:16:1:28.5:1:1:1.15:60:4:0.0364:0:0 +18 66533990 . G T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10617;SOR=0;LSEQ=TGGGTCTGGTATTGCTTTGA;RSEQ=TGCACGGGTCTGTCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:205,88:293,3:0.0101:2,2:25.3:1:22.7:1:1:1.16414:60:2:0.0068:0:1.7 0/0:328:0:0,0:228,100:328,0:0:2,0:23.2:1:31.1:1:1:0:60:81:1:0:0.1 +18 66534313 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50096;SOR=0;LSEQ=CCACACACTATTAAGGTCAC;RSEQ=TATCCTCCCATTTGTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:8,38:46,2:0.0417:2,2:16:1:28.5:1:0.34309:4.54:60:4:0.0426:0:1 0/0:38:0:0,0:8,30:38,0:0:2,0:19.4:1:32.2:1:1:0:59.4:76:1:0:0.1 +18 66534349 . A G 83 NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4057;SOR=0.31717;LSEQ=CACTCTTGTCTCCAGTCTGG;RSEQ=CAAAGTTCTCCTGATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:3,3:4,23:27,6:0.1765:2,2:8.7:1:32.3:1:0.09293:5.35:23.8:12:0.1818:0:7.8 0/1:16:1:1,0:3,12:15,1:0.0625:2,0:12:0:33:0:0.25:0:26:2:0.0625:0:8 +18 66534362 . G C 85 NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40689;SOR=0.32734;LSEQ=AGTCTGGACAAAGTTCTCCT;RSEQ=ATTTATTTAGATCCTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:3,3:4,21:25,6:0.1935:2,2:21.7:1:33:1:0.11003:4.89:23.8:12:0.2:0:7.8 0/1:14:1:1,0:3,10:13,1:0.0714:2,0:25:0:21:0:0.28571:0:26:2:0.0714:0:8 +18 66534366 . TA AG 82 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.41183;SOR=0.34054;LSEQ=TGGACAAAGTTCTCCTGATT;RSEQ=TTTAGATCCTTTTGGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:3,3:4,20:24,6:0.2:2,2:26.7:1:32.1:1:0.12013:4.67:23.8:12:0.2069:0:6.8 0/1:13:1:1,0:3,9:12,1:0.0769:2,0:30:0:29.5:0:0.30769:0:26:2:0.0769:0:7 +18 66534382 . G T 80 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64856;SOR=0.37475;LSEQ=GATTTATTTAGATCCTTTTG;RSEQ=GCTTTCAGATCCCCTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:3,3:4,18:22,6:0.2143:2,2:36:0:31:1:0.14426:4.21:23.8:12:0.2143:0:6.8 0/1:11:1:1,0:3,7:10,1:0.0909:2,0:36:0:28:0:0.36364:0:26:2:0.0909:0:7 +18 66534389 . A T 83 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39682;SOR=0.32439;LSEQ=TTAGATCCTTTTGGGCTTTC;RSEQ=GATCCCCTGGAGCTCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:3,3:1,16:17,6:0.2609:1,2:29:0:32.2:1:0.04009:13.39:23.8:12:0.2609:0:6.8 0/1:10:1:1,0:3,6:9,1:0.1:2,0:29:0:28:0:0.4:0:26:2:0.1:0:7 +18 66534393 . CCCC ACCCT 82 NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.14475;SOR=0;LSEQ=ATCCTTTTGGGCTTTCAGAT;RSEQ=TGGAGCTCAGTAGCAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:3,3:1,15:16,6:0.2727:1,2:25:0:31.9:1:0.0458:12.57:23.8:12:0.2727:0:7.8 0/0:9:0:0,0:3,5:8,0:0:2,0:18.5:1:28.9:1:1:0:60:16:1:0:0.3 +18 66534417 . T GTAACTGGAAGAC 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0.67824;LSEQ=TGGAGCTCAGTAGCAGTAGA;RSEQ=CATAGTAGTGGAAAAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:0,10:10,6:0.375:0,2:22.3:1:31.1:1:0.03571:0:23.8:12:0.375:0.375:7.8 0/1:7:2:2,0:3,2:5,2:0.2857:2,0:13.5:1:23.9:1:1:0:26:4:0.2857:0.2857:8 +18 66534418 . C A 64 NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61313;LSEQ=GGAGCTCAGTAGCAGTAGAT;RSEQ=ATAGTAGTGGAAAAGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:2,2:0,10:10,4:0.25:0,2:9.3:1:32.3:1:0.06593:0:24.3:8:0.2857:0.25:7.8 0/1:6:1:1,0:3,2:5,1:0.1667:2,0:6:1:23:1:1:0:26:2:0.1667:0.1667:8 +18 66534419 . A T 76 p8;NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.61582;SOR=0.34872;LSEQ=GAGCTCAGTAGCAGTAGATC;RSEQ=TAGTAGTGGAAAAGGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:0,10:10,6:0.375:0,2:7.3:1:29.7:1:0.03571:0:23.8:12:0.375:0.375:7.8 0/1:6:1:1,0:3,2:5,1:0.1667:2,0:5:1:26:1:1:0:26:2:0.1667:0.1667:8 +18 66534420 . T A 83 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35116;SOR=0.27199;LSEQ=AGCTCAGTAGCAGTAGATCA;RSEQ=AGTAGTGGAAAAGGGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:0,9:9,7:0.4375:0,2:7.6:1:29.7:1:0.0625:0:29:14:0.4375:0.375:7 0/1:6:1:1,0:3,2:5,1:0.1667:2,0:4:1:21:1:1:0:26:2:0.1667:0.1667:8 +18 66534421 . A G 72 p8;NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.62268;SOR=0.41621;LSEQ=GCTCAGTAGCAGTAGATCAT;RSEQ=GTAGTGGAAAAGGGCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:2,3:0,10:10,5:0.3333:0,2:6.4:1:31.4:1:0.09524:0:23.4:10:0.3333:0.3333:7.8 0/1:6:1:1,0:3,2:5,1:0.1667:2,0:3:1:28:1:1:0:26:2:0.2:0.1667:8 +18 66534422 . G T 66 p8;NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.46785;LSEQ=CTCAGTAGCAGTAGATCATA;RSEQ=TAGTGGAAAAGGGCCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:2,3:0,9:9,5:0.3571:0,2:5.4:1:28.6:1:0.10989:0:23.4:10:0.3571:0.3571:7.8 0/1:5:1:1,0:2,2:4,1:0.2:2,0:2:1:24:1:1:0:26:2:0.2:0.2:8 +18 66534423 . T A 59 p8;NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57964;LSEQ=TCAGTAGCAGTAGATCATAG;RSEQ=AGTGGAAAAGGGCCCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:0,9:9,4:0.3077:0,2:5.5:1:29.8:1:0.07692:0:23.5:8:0.3077:0.3077:7.8 0/1:5:1:1,0:2,2:4,1:0.2:2,0:1:1:13:1:1:0:26:0:0:0.2:8 +18 66534425 . G T 30 v3;p8;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGTAGCAGTAGATCATAGTA;RSEQ=TGGAAAAGGGCCCAGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:0,9:9,2:0.1667:0,2:6.5:1:30:1:0.18182:0:23:4:0.1667:0.1667:7.5 0/0:4:0:0,0:2,2:4,0:0:2,0:24:1:32.3:1:1:0:60:8:1:0:0.8 +18 66534426 . T G 30 v3;p8;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCAGTAGATCATAGTAG;RSEQ=GGAAAAGGGCCCAGATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:0,8:8,2:0.2:0,2:5.5:1:30:1:0.2:0:23:4:0.2:0.2:7.5 0/0:4:0:0,0:2,2:4,0:0:2,0:24:1:28.5:1:1:0:60:8:1:0:0.8 +18 67870203 . CTT C 53 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TAACAGGTTAAGCATCAAAA;RSEQ=TTTTTTTTTTTTTTTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:21.7:1:33.5:1:1:0:60:6:1:0.3333:0 0/0:3:0:0,0:3,0:3,0:0:0,0:24.3:1:31.7:1:1:0:60:6:1:0:1 +18 67870440 . C CT 28 v3;MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CGATTCTATGAGAAAGTGTT;RSEQ=TTTTTTTTTTTTCGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:31.5:1:28.5:1:1:0:52.5:4:0.3333:0:0.5 0/0:3:0:0,0:0,3:3,0:0:0,0:29.7:1:23.3:1:1:0:58.7:2:1:0:1.7 +18 67870507 . C A 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAATGGAGTGATCTCAG;RSEQ=TCACCGTTGCAACCTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:8:0:34:0:1:0:45:2:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:25.5:1:31.5:1:1:0:53.5:4:1:0:1.5 +18 68060541 . T C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCCTGACCTCAGGTAAT;RSEQ=CGCCCACCTTGGCCTCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:23,1:0,0:0,24:1:0,1:17.5:1:33.2:1:1:0:43.6:48:1:0:1.1 1/1:14:14:14,0:0,0:0,14:1:0,1:26.1:1:30.9:1:1:0:35.6:28:1:0:1.1 +18 68060723 . C G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=0.15931;LSEQ=ACACACAATGCGGATGTAAT;RSEQ=GATCGTATCCCCCTGCGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:545:309:170,139:124,112:236,309:0.567:2,2:25.8:1:31.6:1:0.60307:1.10:60:60.8:0.5682:0:2.1 0/1:934:161:84,77:381,388:769,161:0.1724:2,2:26.8:1:30.6:1:0.60315:1.11:60:79.5:0.1719:0:2 +18 68060733 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.16558;LSEQ=CGGATGTAATCGATCGTATC;RSEQ=CCCTGCGTAGTTGCTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:545:303:158,145:121,121:242,303:0.556:2,2:26.9:1:30.9:1:0.66644:1.09:60:42.286:0.5574:0:2.1 0/1:962:165:88,77:377,420:797,165:0.1715:2,2:26.3:1:29.1:1:0.17119:1.27:60:54:0.1709:0:2 +18 69372730 . A G 84 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGCATTTAAAAAAATTATT;RSEQ=TCTATGCCTAGTTTCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:25.7:1:32.8:1:1:0:60:12:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 69372908 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21886;SOR=0;LSEQ=ATGTCAATACTCAAGCCAAT;RSEQ=TTCTTACTAACACCAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:7,17:24,2:0.0769:2,2:25.5:1:31:1:0.52923:2.34:60:4:0.0769:0:2 0/0:29:0:0,0:7,22:29,0:0:2,0:24.9:1:29.7:1:1:0:60:58:1:0:0.2 +18 69372974 . T C 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTTTGATTTTGAAGGA;RSEQ=ATGTTTTGTGTAATAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:32:1:34:0:1:0:60:10:1:0:2.2 1/1:1:1:0,1:0,0:0,1:1:0,0:11:0:33:0:1:0:60:2:1:0:2 +18 69372976 . T A 77 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTTGATTTTGAAGGATA;RSEQ=GTTTTGTGTAATAGTAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:31.2:1:33.4:1:1:0:60:10:1:0:2.2 1/1:1:1:0,1:0,0:0,1:1:0,0:9:0:32:0:1:0:60:2:1:0:2 +18 69373446 . T G 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACATGTTAAACTGCTTT;RSEQ=CTAAACAAAAATGCTCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:34:0:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 69373493 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGAATTGAGCTCCCCAGC;RSEQ=TCCAGTCACCATTATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:31:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 70571137 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.197;SOR=0;LSEQ=AAGTGTACAATGTGCTCTTG;RSEQ=GCATACTAATCACAATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:90,33:123,2:0.016:2,2:24:1:29.5:1:0.47161:2.70175:60:4:0.0164:0:1 0/0:156:0:0,0:110,46:156,0:0:2,0:21.4:1:29.9:1:1:0:60:30.2:1:0:0.2 +18 70571152 . A G 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTTGGGCATACTAATCACA;RSEQ=TTCAATTGACTCAGTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:110,49:159,0:0:2,0:23.5:1:30.6:1:1:0:59.8:78.5:1:0:0.3 0/1:209:20:12,8:127,62:189,20:0.0957:2,2:29.3:1:31.3:1:0.6191:1.36353:60:40:0.0976:0:1 +18 70571238 . T G 247 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00466;LSEQ=TTTTACTACAAACCAAATAC;RSEQ=ATGCTAATAAAATTGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:261:260:123,137:0,1:1,260:0.9962:0,2:24.6:1:30.8:1:1:0:60:64:0.9961:0:1.1 1/0:313:171:78,93:70,71:141,171:0.5463:2,2:23:1:29.8:1:0.49604:1.1749:60:84.5:0.5469:0:1.1 +18 71915176 . T G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAGACCACCAGCCCTCG;RSEQ=CTACTCTTTCGGCCCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:28:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:32:1:1:0:60:4:1:0:1 +18 71915587 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.18657;LSEQ=TACAACAGATGTCTTCCGGA;RSEQ=AGAGAAGGTGTTTTTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:28:13,15:74,45:119,28:0.1905:2,2:30.7:1:32.5:1:0.13975:1.88894:60:56:0.1931:0:1.1 0/1:215:9:5,4:132,74:206,9:0.0419:2,2:23.6:1:31.2:1:0.72612:1.42452:59.2:18:0.0421:0:1 +18 71915673 . C G 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00049;SOR=2.81049;LSEQ=ACAATACTTTCAGATTTAGT;RSEQ=ATTCCAACTTACAGTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:250:214:102,112:17,18:35,214:0.856:2,2:25.1:1:31.8:1:1:1.0369:60:52.5:0.8571:0:1.1 1/1:337:318:148,170:7,9:16,318:0.9436:2,2:23.9:1:30.8:1:1:1.12:59.9:105:0.9488:0:1.1 +18 71915785 . T A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29668;SOR=Inf;LSEQ=TTTCAACTCAAAACCTTGAA;RSEQ=GTTTCTGTGAGCCAGGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:5,40:45,0:0:2,0:22.2:1:30.3:1:1:0:60:44:1:0:0 0/1:72:4:0,4:10,58:68,4:0.0556:2,0:26.8:1:31.3:1:1:0:60:8:0.0556:0:1 +18 72515764 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16731;SOR=0;LSEQ=CTGTGTGTCAGCTGTGAATG;RSEQ=CAGAGATAATGTGGTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:111,55:166,2:0.0119:2,2:24.5:1:33.5:1:1:2.00913:60:4:0.012:0:1 0/0:242:0:0,0:165,77:242,0:0:2,0:24.4:1:28:1:1:0:60:47.4:1:0:0.1 +18 72515839 . G A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.35662;LSEQ=AAGGTCAGGAATGACGGAGC;RSEQ=AAAAATGTTCACGAGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:70:37,33:128,130:258,70:0.2134:2,2:30.8:1:30.8:1:0.68668:1.14:60:140:0.2147:0:1.1 0/1:488:43:20,23:218,227:445,43:0.0881:2,2:26.7:1:30.3:1:0.8733:1.10418:60:86:0.0885:0:1.1 +18 72515919 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17903;SOR=0;LSEQ=CTTGATTGTCCTTGGCTTCA;RSEQ=AGTAAAGGTTGCATATCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:44,121:165,2:0.012:2,2:16:0:31.5:1:0.4675:2.73:60:4:0.012:0:1.5 0/0:227:0:0,0:69,158:227,0:0:2,0:23.2:1:30.5:1:1:0:60:74.667:1:0:0.2 +18 72516095 . C CT 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=2.16028;LSEQ=AGTTAGACATATTTCATTGT;RSEQ=TTTTTTTTTTTCCTTTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:7,3:0.3:0,0:21.3:1:31.7:1:1:0:60:6:0.3333:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:35:0:31:0:1:0:60:2:0.5:0:0 +18 73601806 . T C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=AGCTAGGAGAGGAAGCCACA;RSEQ=GTCCGTCCCAGAAGAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19.5:1:33:1:1:0:60:4:0.5:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:48:0:32:1:1:0:60:4:0.4:0:1.5 +18 73601954 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00077;SOR=0.43912;LSEQ=GAGCCTCCCCTCCTTGGCAT;RSEQ=AAAGGCTTTGGAAGTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:121:69:43,26:31,21:52,69:0.5702:2,2:24.6:1:28.7:1:0.85105:1.12:60:33.5:0.5678:0:1.6 0/1:166:61:36,25:60,45:105,61:0.3675:2,2:25.4:1:27.8:1:0.87121:1.08:60:29.5:0.362:0:1.6 +18 73602003 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51361;SOR=Inf;LSEQ=GGCAGGTGAATTTGTCAGCT;RSEQ=TTGTTGGTTGCTCAGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:70,63:133,0:0:2,0:27.3:1:30.7:1:1:0:60:43.333:1:0:1.2 0/1:189:2:1,1:87,100:187,2:0.0106:2,2:16:1:30:1:1:1.15:60:4:0.0107:0:1 +18 73602007 . T C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11022;SOR=0.68834;LSEQ=GGTGAATTTGTCAGCTTTTG;RSEQ=TGGTTGCTCAGCCCAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:80:43,37:26,28:54,80:0.5926:2,2:27.6:1:32.4:1:0.59812:1.25:60:39:0.5909:0:2.1 1/0:178:89:40,49:41,46:87,89:0.5:2,2:28.3:1:31.6:1:0.87985:1.0913:60:88:0.5:0:1.9 +18 73602031 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19151;SOR=0;LSEQ=TTGCTCAGCCCAGGCCAGCT;RSEQ=GTGTGGTGCGCTGTGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:54,61:115,2:0.0169:2,2:28:1:29.5:1:1:1.13:60:4:0.0171:0:2.5 0/0:151:0:0,0:65,86:151,0:0:2,0:24.3:1:30.6:1:1:0:60:150:1:0:1.1 +18 73602051 . A G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.88497;SOR=1.05023;LSEQ=GGTGTGGTGCGCTGTGCTGC;RSEQ=GAGCATCCTGTCCTTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:56:21,35:14,22:36,56:0.6087:2,2:28.1:1:30.4:1:1:1.05992:60:55:0.6111:0:1.9 1/0:108:67:25,42:15,26:41,67:0.6204:2,2:23.9:1:29:1:1:1.03:60:21.333:0.6154:0:1.7 +18 73984673 . CA C 81 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.12447;SOR=0.27443;LSEQ=ACGACAGAGGAAGACTGTTT;RSEQ=AAAAAAAAAAAAAAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:5,1:2,1:3,6:0.5:2,2:38.7:1:31.7:1:1:2.24:60:12:0.5:0:0.5 0/1:24:5:4,1:8,2:10,5:0.2083:2,2:24.2:1:31.8:1:1:1:56.2:10:0.2083:0:1.8 +18 74386967 . T C 43 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCTTCAGGTCTCAGCT;RSEQ=CAACGTTCTCCCTCATGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:14.7:1:27.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +18 74387215 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29757;SOR=Inf;LSEQ=TGGCCTCAGACAGGAGCCGG;RSEQ=AGAACAGCCCACACAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:33,18:51,0:0:2,0:24:1:31.7:1:1:0:60:50:1:0:0.4 0/1:94:4:1,3:58,32:90,4:0.0426:2,2:20.8:1:26:1:0.1438:5.33842:60:8:0.044:0:1.5 +18 74387275 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51567;SOR=Inf;LSEQ=CAGCTGCCATGTCACACTCA;RSEQ=CTCCCAGCCTGTGCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:64,54:118,0:0:2,0:26.6:1:32.6:1:1:0:60:38.333:1:0:0.9 0/1:172:2:1,1:93,77:170,2:0.0116:2,2:17:0:31:1:1:1.20646:60:4:0.012:0:1.5 +18 74387296 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5019;SOR=Inf;LSEQ=CTCCCAGCCTGTGCTGCCTC;RSEQ=GGTCTGCTCTCCCGGGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:67,67:134,0:0:2,0:24.4:1:30.6:1:1:0:60:66:0.9925:0:1 0/1:160:2:1,1:82,76:158,2:0.0125:2,2:24.5:1:28.5:1:1:1.07841:60:4:0.0128:0:2 +18 74387299 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01721;SOR=0.5601;LSEQ=CCAGCCTGTGCTGCCTCGGG;RSEQ=CTGCTCTCCCGGGATACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:87:42,45:22,22:44,87:0.6641:2,2:26:1:31.5:1:0.85571:1.07085:60:28:0.6563:0:1.5 1/0:160:84:46,38:37,39:76,84:0.525:2,2:28.8:1:30.6:1:0.52654:1.27:60:83:0.5287:0:1.4 +18 74387326 . T G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00931;SOR=0.41655;LSEQ=TCCCGGGATACAGTGTCCCA;RSEQ=TGCCAGCCCCCGCCCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:29:12,17:36,47:83,29:0.2589:2,2:27.7:1:32.7:1:1:1.08429:60:58:0.2589:0:2 0/1:150:19:9,10:59,72:131,19:0.1267:2,2:21.1:1:30.7:1:1:1.10:60:38:0.1293:0:1.8 +18 74387332 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50975;SOR=Inf;LSEQ=GATACAGTGTCCCATTGCCA;RSEQ=CCCCCGCCCCACACTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:42,60:102,0:0:2,0:29.2:1:32.5:1:1:0:60:50:1:0:0.9 0/1:139:2:1,1:57,79:136,2:0.0144:2,2:31:0:30.5:1:1:1.38:60:4:0.0147:0:2.5 +18 74387341 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13027;SOR=Inf;LSEQ=TCCCATTGCCAGCCCCCGCC;RSEQ=CACACTGCTGCCCCTACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:37,63:100,0:0:2,0:27.2:1:30.9:1:1:0:60:99:1:0:0.9 0/1:124:4:2,2:46,74:120,4:0.0323:2,2:25.5:1:27.8:1:0.6403:1.60:60:8:0.0333:0:2 +18 74387348 . G A 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18426;SOR=0;LSEQ=GCCAGCCCCCGCCCCACACT;RSEQ=CTGCCCCTACGCCCATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:33,55:88,2:0.0222:2,2:37:0:28.5:1:1:1.66:60:4:0.023:0:1 0/0:119:0:0,0:42,77:119,0:0:2,0:22.8:1:30.6:1:1:0:60:18.833:1:0:0.7 +18 74463123 . G T 47 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGAAGACTTCCAGCAGTTT;RSEQ=TTTTTCTTTTTTTTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,0:0,3:0.75:0,0:10:1:31.3:1:1:0:60:6:1:0:1.3 1/1:3:3:3,0:0,0:0,3:1:0,0:27.7:1:29.7:1:1:0:60:6:1:0:1 +18 74463129 . C CT 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=ACTTCCAGCAGTTTGTTTTT;RSEQ=TTTTTTTTTTTCTTTTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:15.5:1:32.3:1:1:0:60:8:1:0:1.3 1/0:4:2:2,0:2,0:2,2:0.5:0,0:15.5:1:31.1:1:1:0:60:4:0.6667:0.25:0.5 +18 74463340 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50525;SOR=Inf;LSEQ=TGCCTGGATCGCTACCTGTC;RSEQ=AGCATCTCCACCCAATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:59,55:114,0:0:2,0:25.3:1:31.3:1:1:0:60:113:1:0:0.1 0/1:145:2:1,1:67,76:143,2:0.0138:2,2:15:1:27.5:1:1:1.13:60:4:0.0141:0:1 +18 74463373 . C G 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01481;SOR=Inf;LSEQ=CAATGGCACAGTTGCAGCTC;RSEQ=TGGGTGCAGTCCACATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:42,44:86,0:0:2,0:24:1:31.8:1:1:0:59.9:42:1:0:0.1 0/1:96:7:4,3:42,47:89,7:0.0729:2,2:25.7:1:31.3:1:0.7067:1.49:60:14:0.0737:0:1 +18 74463394 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17717;SOR=0;LSEQ=TGGGTGCAGTCCACATCCTG;RSEQ=TGGCCTCCAAGCTGGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:42,43:85,2:0.023:2,2:14.5:1:28.5:1:1:1.02:60:4:0.0235:0:1 0/0:119:0:0,0:62,57:119,0:0:2,0:20.8:1:31.4:1:1:0:60:238:1:0:0.2 +18 74463468 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17444;SOR=0;LSEQ=TGCACCAACCACGCTGTCTC;RSEQ=CCTCGCCAGTTGTGGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:35,51:86,2:0.0227:2,2:31.5:1:30.5:1:1:1.45:60:4:0.0233:0:1 0/0:122:0:0,0:54,68:122,0:0:2,0:24:1:29.1:1:1:0:60:244:1:0:0.1 +18 75379986 . T C 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATATTGAATATAATTTCA;RSEQ=ATTTGTCATTTATCTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:24:0:28:0:1:0:60:2:1:0:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:22:1:33:1:1:0:60:4:0.6667:0:2 +18 75380032 . G A 60 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=3.1622;LSEQ=TTTAGTGCAGATATTTTCAC;RSEQ=TTTCTGTCAATGTATTACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:1,1:0.5:0,0:19:0:32:0:1:0:60:2:0.5:0:1 1/1:5:4:4,0:1,0:1,4:0.8:0,0:36:1:30:1:1:0:60:8:0.8:0:1.5 +18 75380175 . A C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.9304;LSEQ=CCTTCTCCCTGGGTCTCAGC;RSEQ=GGGAGCACTGGCTGGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:6,6:3,3:6,12:0.6667:2,2:29.1:1:29:1:1:1:60:11:0.6471:0:1.1 1/0:20:13:5,8:3,4:7,13:0.65:2,2:30.7:1:29.4:1:1:1.18903:60:26:0.65:0:1.2 +18 75381671 . T G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCCTTATAAAAGGGAAC;RSEQ=TTGGACACAGAGACACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 806673 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGTCTGCGCCTCTGCCC;RSEQ=GGCAGCCCCTCTGCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:37.5:1:30:1:1:0:60:4:0.6667:0:1.5 +19 872802 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGGGCAGCAGCAGCAG;RSEQ=AGCAAGGCGAACCGGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 872969 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGGGCTCCGAGGTGGGG;RSEQ=AGGGCTCCGAGGTGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:32.5:1:1:0:32.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 872987 . G C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGGCTCCGAGGTGGGG;RSEQ=AGGGCTCCGAGGTGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:1:34.5:1:1:0:32.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 874449 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGCCTGCCAGGCACAGTG;RSEQ=CTCACGCCTGTAATCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:18.5:1:30.9:1:1:0:60:16:1:0:0.1 0/1:24:2:1,1:11,11:22,2:0.0833:2,2:10:1:26.5:1:1:1:60:4:0.0833:0:1 +19 874457 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGGCACAGTGGCTCACGC;RSEQ=TGTAATCCCAGCGCTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:18.5:1:30.4:1:1:0:60:16:1:0:0.1 0/1:24:2:1,1:10,12:22,2:0.0833:2,2:36:1:30.5:1:1:1.19:60:4:0.0833:0:1 +19 875389 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGGTAGTCGCACACGCG;RSEQ=GTCACCGTGCAGGGCGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:29:1:1:0:60:4:1:0:1 +19 1206796 . C CT 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.75933;LSEQ=CCTTTTGGGGTTTTTGTTGC;RSEQ=TTTTTTTTTTCTTTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:7,0:52,0:52,7:0.1167:1,0:19.4:1:31.1:1:1:0:60:14:0.1167:0.05:0 0/1:33:3:3,0:29,1:30,3:0.0909:1,0:17.3:1:31.8:1:1:0:60:6:0.0909:0.0303:0 +19 1206863 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17069;SOR=Inf;LSEQ=GAACACAAGGAAGGACCGCT;RSEQ=ACCCGCGGACTCAGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:141,33:174,0:0:2,0:26:1:31.5:1:1:0:60:57:1:0:0.1 0/1:123:2:1,1:93,27:120,2:0.0163:2,2:44.5:1:29:1:0.4078:3.40043:60:4:0.0167:0:1 +19 1206890 . G T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04381;SOR=Inf;LSEQ=GGACTCAGGGCTGGCGGCGG;RSEQ=ACTCCAGGACCCTGGGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:159,74:233,0:0:2,0:25.2:1:30.9:1:1:0:60:76.667:1:0:0.1 0/1:198:4:1,3:123,71:194,4:0.0202:2,2:22:1:24.8:1:0.14793:5.15381:60:8:0.0206:0:1 +19 1206942 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02856;SOR=Inf;LSEQ=GTGGACCCGCAGCAGCTGGG;RSEQ=ATGTTCACGGAGGGCGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:183,159:342,0:0:2,0:25.9:1:32.5:1:1:0:60:84.5:1:0:0.1 0/1:332:5:1,4:186,141:327,5:0.0151:2,2:14.8:1:25.6:1:0.17194:5.25315:60:10:0.0153:0:1 +19 1207217 . C A 32 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32115;SOR=3.95445;LSEQ=GAAGAAGTAAGTATGGCTTG;RSEQ=TGGGGTCGGGGCCGGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:1:0,1:113,270:383,1:0.0026:2,0:11:0:15:0:1:0:60:0:0:0:3 0/1:293:3:2,1:82,208:290,3:0.0102:2,2:16.3:1:20.3:1:0.19855:5.04:60:2:0.0069:0:1 +19 1207238 . G T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.37076;LSEQ=TGGGGTCGGGGCCGGGCCGG;RSEQ=CCAGTCACGGTGCTGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:257:143:34,109:26,87:113,143:0.5564:2,2:25:1:29.8:1:1:1.04:60:34.75:0.5605:0:1.4 0/1:183:58:14,44:26,99:125,58:0.3169:2,2:25.2:1:28.4:1:0.70105:1.21:60:116:0.3169:0:1.4 +19 1207280 . C T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02631;SOR=0.4658;LSEQ=CTGTCTTCCTTCCTTCTCTC;RSEQ=TCCCTCCCTCCCTTACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:119:61:1,60:3,55:58,61:0.5126:2,1:21.7:1:30.3:1:0.35618:3.24273:60:29.5:0.5086:0:1.7 0/1:61:20:1,19:3,38:41,20:0.3279:2,1:22.4:1:29.8:1:1:1.49072:60:40:0.3333:0:2 +19 1218219 . C T 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.12995;LSEQ=GACTAGAGGGCGCTGTGCTC;RSEQ=CACCCCCTACCGCCCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:15,0:16,1:17,15:0.4688:1,1:27.1:1:33.5:1:1:0:60:30:0.5:0:1 1/0:10:5:4,1:5,0:5,5:0.5:0,2:19.8:1:30.2:1:1:0:60:10:0.5556:0:1.2 +19 1218384 . C T 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATCATCCTGACGTTGGGT;RSEQ=GGCTGATACACCCCTGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:285,163:448,0:0:2,0:25.5:1:31:1:1:0:60:63:1:0:0.1 0/1:465:35:20,15:274,156:430,35:0.0753:2,2:24.1:1:29.3:1:0.46841:1.31647:60:34:0.0747:0:1.2 +19 1218523 . G T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28535;LSEQ=TCCTTTCCGGTGTTGGGACC;RSEQ=CGGGGCCTCCGTGGGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:329:174:57,117:49,106:155,174:0.5289:2,2:24.1:1:30.5:1:0.90598:1.05:60:86:0.5342:0:1.1 0/1:322:78:24,54:86,158:244,78:0.2422:2,2:28.3:1:28.6:1:0.49592:1.22392:60:77:0.2414:0:1.1 +19 1219274 . G A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02552;SOR=0.71225;LSEQ=TCTGGCCCCCGTGCTCCCTG;RSEQ=GCCTGTGAGTGGGGCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:426:228:166,62:142,54:196,228:0.5352:2,2:23:1:30.5:1:1:1.02:59.9:75:0.5383:0:1.1 0/1:313:141:98,43:119,53:172,141:0.4505:2,2:22.4:1:28.1:1:1:1.02:59.8:27.2:0.4474:0:1.2 +19 1219411 . G A 70 v3;p8;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18231;SOR=3.21375;LSEQ=TCCCAGTGTGCCAGGCCCAC;RSEQ=GGTGCGTGCGCGGGGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:2:2,0:249,374:623,2:0.0032:2,0:1:0:27.5:1:0.1609:0:60:4:0.0032:0:1 0/1:686:7:7,0:305,374:679,7:0.0102:2,0:6.9:1:25.1:1:0.00388:0:60:14:0.0103:0:1.1 +19 1219443 . G GCGGGGGC 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11025;SOR=0.71622;LSEQ=GGGGCAGGGGCCAGGGTGGG;RSEQ=CGGGGGCCGGGGGCCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:69:14,55:73,194:267,69:0.2012:2,2:26.6:1:30.5:1:0.28126:1.47665:59.4:138:0.2029:0.0292:0.3 0/1:347:53:14,39:90,203:293,53:0.1527:2,2:33.1:1:30.5:1:0.62616:1.23428:59.5:106:0.1563:0:0.2 +19 1219553 . G T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=3e-04;SOR=0.17572;LSEQ=TTGTTTTTTTGTTTTTTTGT;RSEQ=TTTTTTTTCGAGATGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:39:0,39:1,4:5,39:0.78:2,1:17.5:1:31.4:1:0.11364:0:56.9:78:0.8864:0:1.1 0/1:37:14:0,14:1,17:18,14:0.3784:1,1:24.1:1:29.9:1:1:0:59.1:28:0.4118:0:1.1 +19 1220321 . T C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.28408;LSEQ=GCAGCTGCAAAGGGGACCCC;RSEQ=GTGAGGGGCAGGGAGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:344:202:155,47:103,39:142,202:0.5872:2,2:25.5:1:30.4:1:0.37943:1.25:60:39.4:0.5863:0:1.1 0/1:261:75:48,27:125,61:186,75:0.2874:2,2:23.1:1:29.4:1:0.66508:1.15202:60:74:0.2891:0:1.1 +19 1220600 . G A 124 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=25.28723;LSEQ=GCACTGCACCCGTTCGCGGC;RSEQ=GACGACACCTGCCGGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:1:1,0:419,361:780,1:0.0013:2,0:47:0:32:0:1:0:60:2:0.0013:0:1 0/1:636:20:11,9:328,287:615,20:0.0314:2,2:21.6:1:28.7:1:1:1.07:60:19:0.0304:0:1.2 +19 1220654 . T A 147 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=45.37962;LSEQ=GCTTTCCAGCCGCCCGAGAT;RSEQ=GCCAACGGCCTGGACACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:950:1:1,0:463,486:949,1:0.0011:2,0:1:0:24:0:0.48842:0:60:2:0.0011:0:1 0/1:831:38:20,18:395,397:792,38:0.0457:2,2:23.1:1:28.1:1:0.86837:1.12:60:37:0.0451:0:1.2 +19 1221125 . G T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33802;SOR=3.55379;LSEQ=TGGTCCAGCAGCCACGGGAC;RSEQ=CCTCTGTCCCTGGGGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:1:0,1:263,48:311,1:0.0032:2,0:1:0:26:0:0.15705:0:60:2:0.0033:0:1 0/1:265:3:1,2:220,42:262,3:0.0113:2,2:15.3:1:25.7:1:0.07249:10.32853:60:6:0.0115:0:1 +19 1221161 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09565;LSEQ=TAGAGCTGGGGCTCCTAGGG;RSEQ=GTCAACCACCTTGACTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:605:207:133,74:257,141:398,207:0.3421:2,2:24.4:1:29.9:1:1:1.01411:60:68:0.3406:0:1.1 0/1:613:29:18,11:346,238:584,29:0.0473:2,2:23.2:1:28.4:1:0.84781:1.13:60:28:0.0462:0:1.1 +19 1221403 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16211;SOR=Inf;LSEQ=CTTTTGTGCAGAAATGTAGG;RSEQ=TTGGGGGTGTCAGGTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:26,178:204,0:0:2,0:24.1:1:32.1:1:1:0:59.8:203:1:0:0.2 0/1:138:2:1,1:17,119:136,2:0.0145:2,2:12.5:1:27:1:0.24468:6.83:60:4:0.0149:0:1.5 +19 1221484 . C T 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26539;SOR=0.46394;LSEQ=AGTGGAGAGGCCGACCTCCC;RSEQ=GCAGGGCCTGGTTTGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:0,24:0,22:22,24:0.5217:1,1:23.5:1:31.5:1:1:0:60:48:0.5333:0:1.1 0/1:18:6:1,5:0,12:12,6:0.3333:0,2:21.2:1:31.3:1:0.33333:0:60:12:0.3333:0:1.2 +19 1221545 . C T 96 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.46249;LSEQ=TCTGGGCCCTGTTCACCCTC;RSEQ=GAACTCCCACCCCAGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:3,6:1,7:8,9:0.5294:2,2:29.7:1:30.3:1:0.57647:3.26:54.4:18:0.5294:0:1.3 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:50:0:28:0:1:0:60:2:0.3333:0:1 +19 1221991 . G A 105 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02268;SOR=0.1909;LSEQ=AAGAGGTTCTCCATCCGGCA;RSEQ=ATCCGGCAGCACAGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:908:11:6,5:365,531:896,11:0.0121:2,2:17.9:1:30.6:1:0.37158:1.74:60:22:0.0123:0:1.3 0/0:857:2:1,1:366,489:855,2:0.0023:2,2:9:1:19:1:1:1.34:60:1:0.0012:0:3.5 +19 1222012 . G C 191 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=113.57824;LSEQ=ATCCGGCAGCACAGGTGAGC;RSEQ=GCCCCTGGGGGCAGTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:685:1:1,0:260,421:681,1:0.0015:2,0:3:0:14:0:0.3827:0:60:0:0:0:1 0/1:666:95:39,56:218,350:568,95:0.1426:2,2:25.5:1:29.2:1:0.64976:1.12:60:46.5:0.1413:0:1.2 +19 1222268 . A G 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTAGGCATGGAGATGCGCC;RSEQ=GGAAGGGCACAGCTGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:32.7:1:32.3:1:1:0:59.2:12:0.8571:0:1 1/1:3:3:0,3:0,0:0,3:1:0,0:37.3:1:31:1:1:0:60:6:1:0:1.3 +19 1222951 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10495;SOR=Inf;LSEQ=TGGACCGCCCTGGTGCCAGC;RSEQ=TGACAGGCGCCACTGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:167,29:196,0:0:2,0:23.6:1:31.6:1:1:0:60:97:1:0:0.1 0/1:176:3:1,2:133,40:173,3:0.017:2,2:18:1:23:1:0.14202:6.55867:60:2:0.0116:0:1 +19 1226675 . G A 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15973;SOR=Inf;LSEQ=GCCTGCAGGTGGGGCGCGGC;RSEQ=GGGCCCGGGTGGGGCATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:25,152:177,0:0:2,0:24.4:1:31:1:1:0:60:87.5:0.9943:0:0.2 0/1:119:2:1,1:18,99:117,2:0.0168:2,2:10:1:23:1:0.29497:5.38:60:4:0.0168:0:1 +19 1226772 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.41032;SOR=2.60072;LSEQ=TGGTGACCGTCACGTGGCTG;RSEQ=GCGTGGTTGCCATGTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:1,14:1,15:16,15:0.4839:1,1:28.9:1:30.1:1:1:1.07:60:30:0.5:0:1 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:18.6:1:31.2:1:1:0:60:10:0.7143:0:1 +19 1226901 . G T 28 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGGCGGGGCTCTGGGGG;RSEQ=GCGTGCCGTCCTCACAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:27.5:1:28.5:1:1:0:49:4:0.6667:0:2.5 0/0:1:0:0,0:0,1:1,0:0:0,0:40:0:33:0:1:0:60:2:1:0:0 +19 1271910 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49091;SOR=Inf;LSEQ=GGCTGGCATGGGGGCTGGCG;RSEQ=CTCAGCCTGTTGTGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:26,2:28,0:0:2,0:29.8:1:31.1:1:1:0:60:56:1:0:0 0/1:28:2:1,1:25,1:26,2:0.0714:1,2:12:1:25.5:1:0.14021:18.02309:60:4:0.0714:0:1 +19 1272040 . T C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.71205;LSEQ=GGGTCCTACAGAGACAGTTA;RSEQ=GACAGTTACGGTAAGTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:16:3,13:10,20:30,16:0.3404:2,2:28.3:1:30.3:1:0.49291:2.13232:60:32:0.3404:0:1.1 1/0:68:53:21,32:4,11:15,53:0.7794:2,2:23.4:1:30.1:1:0.54527:1.79:60:106:0.7794:0:1.1 +19 1272143 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=CAAGCACTTTAGGCTGGACA;RSEQ=TCAGACCTTGTCACTGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:4,0:0:0,0:28.8:1:35:0:1:0:60:8:1:0:0 0/1:7:2:1,1:0,5:5,2:0.2857:0,2:18.5:1:28:1:0.28571:0:60:4:0.2857:0:1 +19 1611547 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCAGTGTCACCTTGGCC;RSEQ=CCCCCATCACTCCGAACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:83,2:85,2:0.023:1,2:11.5:1:29.5:1:0.06816:34.10659:60:4:0.0235:0:1 0/0:41:0:0,0:34,7:41,0:0:2,0:22.4:1:29.6:1:1:0:59.3:40:1:0:0.2 +19 1611647 . G A 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=46.43769;LSEQ=GCCCGGGGTCTCGAGTGGCC;RSEQ=TTCTGGGGCCAGAGCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:1:1,0:416,131:547,1:0.0018:2,0:1:0:27:0:1:0:60:2:0.0018:0:1 0/1:485:38:28,10:332,115:447,38:0.0784:2,2:22.2:1:28.6:1:1:1.03099:60:11.667:0.0732:0:1.3 +19 1611856 . G A 169 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01687;LSEQ=TTCAGGTTCCGCTCTGGAGG;RSEQ=AGGGGGGAGAGCTCTGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:49:17,32:386,560:946,49:0.0492:2,2:24.9:1:30.2:1:0.45682:1.29715:58.2:23.5:0.0484:0:1.2 0/0:1147:1:1,0:490,656:1146,1:9e-04:2,0:1:0:22:0:0.42807:0:60:2:9e-04:0:3 +19 1611917 . G T 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01797;SOR=Inf;LSEQ=AAGATGTGAGGTGGGAGTGG;RSEQ=GGGTAGGATGTCGGGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:29,101:130,0:0:2,0:11:1:31.3:1:1:0:59.5:31.5:1:0:0.3 0/1:160:7:1,6:34,118:152,7:0.0438:2,2:10.7:1:29.7:1:1:1.72363:60:14:0.0449:0:1 +19 1611929 . C CG 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.11325;SOR=Inf;LSEQ=GGGAGTGGGGGGTAGGATGT;RSEQ=GGGGGGGGGGGTGGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:12,35:47,0:0:2,0:6.7:1:28.6:1:1:0:59.7:14.667:0.9778:0:0.6 0/1:46:3:2,1:10,33:43,3:0.0652:2,2:18.7:1:25.3:1:0.16232:6.27:60:6:0.0667:0.0217:1 +19 1612144 . C T 43 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03637;SOR=Inf;LSEQ=CAAGCACAGGAGGACCCCAG;RSEQ=ATCTGCACCTGGGTGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:226,21:247,0:0:2,0:23.2:1:32.6:1:1:0:59.9:60.75:1:0:0.1 0/1:193:4:1,3:163,26:189,4:0.0207:2,2:9.3:1:21.8:1:0.01112:18.31979:60:3:0.0156:0:1.8 +19 1612178 . C T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43115;SOR=2.21993;LSEQ=TGTGGGGAAGGGAGAGGGTG;RSEQ=TGGGGCAGCCCTGGCCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:2:1,1:321,69:390,2:0.0051:2,2:21:1:29.5:1:0.32563:4.62604:60:4:0.0052:0:1.5 0/1:355:4:2,2:253,97:350,4:0.0113:2,2:19.5:1:27.3:1:0.31223:2.60009:60:8:0.0115:0:1.3 +19 1615203 . C T 45 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69844;SOR=1.39336;LSEQ=GAGGGCTGGCTCCAGGAAGG;RSEQ=GGGCGGGGAAGGAGAACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:3:2,1:300,36:336,3:0.0088:2,2:14.3:1:25.3:1:0.29377:4.13842:60:2:0.006:0:1 0/1:244:3:2,1:201,40:241,3:0.0123:2,2:11.3:1:28.7:1:0.42558:2.50016:60:6:0.0127:0:1 +19 1615796 . G A 171 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=21.44506;LSEQ=GCTTGATCTCGCTGGCGGCC;RSEQ=CCGTGGCACCTGCTCGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1326:3:3,0:594,727:1321,3:0.0023:2,0:1:0:26:1:0.09142:0:60:6:0.0023:0:1 0/1:1444:67:32,35:634,741:1375,67:0.0464:2,2:26.9:1:28.3:1:0.80307:1.07:60:21.333:0.0452:0:1.3 +19 1615852 . C T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05496;SOR=1.57052;LSEQ=CTAGGGTCAGGGGCCTGCGT;RSEQ=GGCCTCCAGGGCCAACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:35:10,25:135,427:562,35:0.0586:2,2:26:1:29.9:1:0.54461:1.26:60:70:0.0599:0:1 0/1:561:50:18,32:131,380:511,50:0.0891:2,2:18.9:1:28.8:1:0.13075:1.63:60:100:0.0901:0:1.2 +19 1618982 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00239;SOR=Inf;LSEQ=CCTGAAGTTGCTGACTGGGG;RSEQ=GCCCATGTCACCAGGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:80,2:82,0:0:1,0:26.8:1:32:1:1:0:59.2:40:1:0:0.2 0/1:37:5:5,0:32,0:32,5:0.1351:1,0:28.2:1:29:1:1:0:60:10:0.1351:0:1 +19 1619333 . G A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.27002;SOR=0.73592;LSEQ=ACCAGGCCTGCGTGCCGCCC;RSEQ=CCCAGTGACATGGGGCCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:916:43:24,19:449,424:873,43:0.0469:2,2:20.9:1:30.3:1:0.6404:1.19:60:86:0.0474:0:2 0/1:772:27:17,10:391,354:745,27:0.035:2,2:21.9:1:28.2:1:0.3297:1.54:60:12.5:0.033:0:3.2 +19 1619339 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.04825;LSEQ=CCTGCGTGCCGCCCGCCCAG;RSEQ=GACATGGGGCCGGTGAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:946:42:25,17:467,436:903,42:0.0444:2,2:21:1:31.4:1:0.34674:1.37:60:84:0.0455:0:2 0/1:802:198:105,93:319,284:603,198:0.2469:2,2:24.7:1:30.4:1:1:1.01:60:98:0.2472:0:1.5 +19 1619348 . G A 120 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.16802;LSEQ=CGCCCGCCCAGTGACATGGG;RSEQ=CCGGTGAAACCTGAGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:956:1:0,1:492,463:955,1:0.001:2,0:40:0:32:0:0.48536:0:60:2:0.0011:0:2 0/1:850:21:15,6:430,398:828,21:0.0247:2,2:26.2:1:27.4:1:0.11952:2.31:60:20:0.0238:0:3.6 +19 1619350 . C T 129 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=22.13052;LSEQ=CCCGCCCAGTGACATGGGGC;RSEQ=GGTGAAACCTGAGGCCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:964:1:0,1:495,466:961,1:0.001:2,0:1:0:27:0:0.48545:0:60:2:0.0011:0:1 0/1:845:19:13,6:432,394:826,19:0.0225:2,2:29.4:1:30.4:1:0.24473:1.97:60:38:0.0228:0:3.8 +19 1619749 . A AGGGTG 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=4.000;MSILEN=1;SSF=0;SOR=2.47573;LSEQ=CCTGCAAATTCTGTCGGGGA;RSEQ=GGGTGGGGTGGGGCGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1177:37:31,6:685,422:1107,37:0.0314:2,2:32.6:1:31.5:1:0.00559:3.18:59.3:74:0.0418:0:0.3 0/1:1129:84:64,20:610,391:1001,84:0.0744:2,2:31.8:1:29.9:1:0.00675:2.05:57.9:83:0.0966:0.0097:0.4 +19 1619757 . G C 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTGTCGGGGAAGGGTGGG;RSEQ=TGGGGCGGGGCAGGCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1290:0:0,0:751,533:1284,0:0:2,0:27.6:1:29.3:1:1:0:59.7:10.069:0.9983:0:0.5 0/1:1281:113:67,46:664,500:1164,113:0.0882:2,2:28.7:1:29.3:1:0.69087:1.10:59.7:6.063:0.0841:0:1.3 +19 1619792 . C T 170 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=31.23427;LSEQ=CACTCACCAGGCCGTGGAGA;RSEQ=CCCCGTCGTAGCTGGGCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1634:2:0,2:807,824:1631,2:0.0012:2,0:1:0:28.5:1:0.49976:0:59:4:0.0013:0:1 0/1:1708:63:31,32:813,829:1642,63:0.0369:2,2:24.2:1:28.5:1:1:1.01233:59.5:30.5:0.0364:0:1.4 +19 1619992 . C T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14769;SOR=Inf;LSEQ=GGCCATTCCGGGGCACCCCA;RSEQ=ACTGATGCAAAGCTGCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:5,148:153,0:0:1,0:24:1:32.6:1:1:0:59.8:50:1:0:0.1 0/1:96:2:1,1:3,91:94,2:0.0208:1,2:32:0:27.5:1:0.08202:26.41:60:4:0.0215:0:1.5 +19 1621800 . C T 49 q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.13199;SOR=0;LSEQ=CCCTGCCTGGAGCCCAGTGT;RSEQ=CCCTCGGAGAGGCCGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:4:0,4:277,108:385,4:0.0103:2,0:8.3:1:24.5:1:0.00661:0:60:3:0.0078:0:1.8 0/0:316:0:0,0:223,92:315,0:0:2,0:23.3:1:30:1:1:0:59.9:44:0.9968:0:0.2 +19 1622012 . C T 78 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09902;SOR=2.70499;LSEQ=GGTGGGTTAGATGGGCACTG;RSEQ=CACCCTCCGCCCACCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1024:4:2,2:494,525:1019,4:0.0039:2,2:13:1:28.3:1:1:1.06:60:8:0.004:0:1 0/1:857:9:3,6:419,429:848,9:0.0105:2,2:14.4:1:24.7:1:0.50596:1.9519:60:8:0.0095:0:1.7 +19 1622115 . C T 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCCACTGCTGCCCACCGGGC;RSEQ=GCTACCGGGCGGGAGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1121:33:14,19:523,565:1088,33:0.0294:2,2:23.5:1:31.4:1:0.59738:1.256:60:32:0.0291:0:1.1 0/0:950:0:0,0:466,482:948,0:0:2,0:24.9:1:29.9:1:1:0:59.9:93.8:0.9989:0:0.5 +19 1622116 . G A 239 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACTGCTGCCCACCGGGCC;RSEQ=CTACCGGGCGGGAGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1111:0:0,0:536,575:1111,0:0:2,0:23.6:1:31:1:1:0:60:73.067:1:0:0.2 0/1:945:299:146,153:322,324:646,299:0.3164:2,2:26.5:1:29.1:1:0.78004:1.04145:59.9:48.833:0.314:0:1.2 +19 1623850 . G C 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01644;SOR=Inf;LSEQ=ACAGGGGGCCTGTCCACTCA;RSEQ=GGCCCACCCCGCCATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:291,67:358,0:0:2,0:22.8:1:32.6:1:1:0:60:118.333:1:0:0.1 0/1:283:5:4,1:225,51:276,5:0.0177:2,2:18.6:1:32:1:1:1.10257:60:10:0.0182:0:1 +19 1624007 . A G 206 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGGCTGCGTGTCTGTTAG;RSEQ=AGCAAAAGGGGTGAGAACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1385:0:0,0:672,713:1385,0:0:2,0:25:1:30.3:1:1:0:60:34.513:1:0:0.2 0/1:1561:114:65,49:713,729:1442,114:0.073:2,2:26.1:1:30.2:1:0.14418:1.36:59.9:56:0.0731:0:1.1 +19 1624263 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0117;SOR=Inf;LSEQ=AAAGTAGCCGGGCGTGGTGG;RSEQ=GGGTGCCTATAATTCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:13,0:0:1,0:25.5:1:29.8:1:1:0:47.1:26:1:0:0 1/0:8:4:0,4:0,4:4,4:0.5:0,0:8.5:1:30.5:1:1:0:32.5:8:0.5:0:1 +19 1625558 . G A 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGAAGCCCCCGATGCCCC;RSEQ=GCCAGACCCCGCTCACCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:933:0:0,0:573,359:932,0:0:2,0:25.1:1:30.1:1:1:0:60:50.778:1:0:0.2 0/1:871:46:30,16:473,351:824,46:0.0528:2,2:25.3:1:29.7:1:0.35795:1.39:59.4:45:0.0526:0:1.2 +19 1625791 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2845;SOR=0;LSEQ=AAGAAAAAACTGCAAAGGCC;RSEQ=AAGCCACTCAGACCCGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:22,253:275,3:0.0108:2,2:14.7:1:27.7:1:0.02036:22.38:60:6:0.0109:0:1 0/0:178:0:0,0:23,155:178,0:0:2,0:24:1:30.7:1:1:0:60:356:1:0:0.1 +19 1625811 . T C 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=Inf;LSEQ=GAAGCCACTCAGACCCGCCC;RSEQ=GCAGTGGGTGATGCCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:6,172:178,0:0:1,0:24:1:30.7:1:1:0:60:43.5:1:0:0.1 0/1:110:8:0,8:7,95:102,8:0.0727:2,0:22.5:1:30.5:1:1:0:60:16:0.0727:0:1 +19 1627422 . T C 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGCGCCCCGCTCACCGCTC;RSEQ=TGCCTGCAAGGGGAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1045:0:0,0:510,534:1044,0:0:2,0:25:1:30.7:1:1:0:60:36.286:0.999:0:0.2 0/1:936:30:14,16:404,501:905,30:0.0321:2,2:30:1:30.1:1:0.85363:1.08:60:29:0.0315:0:1.2 +19 1627619 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCAGTATGCCCATCTCCC;RSEQ=CAGAGCCCTGCCCTCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:1,2:1,47:48,3:0.0588:1,2:21:1:31.7:1:0.11529:19.40:60:6:0.06:0:1 0/0:16:0:0,0:1,15:16,0:0:1,0:28.6:1:31.6:1:1:0:60:32:1:0:0.1 +19 1631811 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12243;SOR=Inf;LSEQ=GAACGGCCTCCCTGCCTCTA;RSEQ=GCTCAGGCGGGGAAGCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:163,7:170,0:0:1,0:25.7:1:32.7:1:1:0:60:169:1:0:0.1 0/1:92:2:1,1:85,5:90,2:0.0217:2,2:31:1:31:0:0.12685:15.60585:60:4:0.0217:0:1 +19 1632160 . G GC 173 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=34.012;LSEQ=GAGGTGCTGGGGCTTCACAG;RSEQ=CCCCCCCTCCACCCCGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:915:2:1,1:351,561:912,2:0.0022:2,2:33.5:1:32:1:1:1.60:60:4:0.0022:0:0.5 0/1:749:52:13,39:282,411:693,52:0.0694:2,2:29.7:1:30.4:1:0.02738:2.05655:59.9:51:0.0701:0.0027:0.1 +19 1646161 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04416;SOR=Inf;LSEQ=GGGCTCAGGGGCTCGGGCTC;RSEQ=CAAGGCAGGTCACACGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:63,1:64,0:0:1,0:24.8:1:31.6:1:1:0:60:128:1:0:0 0/1:36:3:3,0:32,1:33,3:0.0833:1,0:29:1:31.3:1:1:0:60:6:0.0833:0:1.7 +19 1646221 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.39576;LSEQ=GTCTTCAGGCTCGCTGCCCC;RSEQ=GACCCGGCCTGTGTGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:8:8,0:172,4:176,8:0.0435:1,0:24.9:1:32.1:1:1:0:60:16:0.0437:0:1.1 0/1:143:43:40,3:98,2:100,43:0.3007:1,2:19.2:1:30.4:1:0.16022:3.63713:60:86:0.3028:0:1.2 +19 1646229 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19642;SOR=Inf;LSEQ=GCTCGCTGCCCCCGACCCGG;RSEQ=CTGTGTGGCCCTTTCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:219,4:223,0:0:1,0:23:1:32.4:1:1:0:60:43.6:1:0:0.1 0/1:178:2:2,0:169,7:176,2:0.0112:1,0:32:1:27.5:1:1:0:60:4:0.0115:0:1.5 +19 1646471 . C A 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04918;SOR=Inf;LSEQ=GAGCGGGGCGGGTGGCAAAC;RSEQ=AAACCCTACAGTCCCGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:105,317:422,0:0:2,0:23.5:1:31.5:1:1:0:60:34.167:0.9976:0:0.2 0/1:378:4:3,1:105,269:374,4:0.0106:2,2:13.3:1:22.3:1:0.07224:7.64:60:3:0.0081:0:2.3 +19 1646644 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACCCTGGACACCCACGC;RSEQ=CAGAGTGAGAAAACTCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:1,17:18,2:0.1:1,0:17:1:32:0:1:0:60:4:0.1:0:1 0/0:6:0:0,0:1,5:6,0:0:2,0:24.3:1:32.5:1:1:0:60:12:1:0:0.3 +19 1650134 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.89243;LSEQ=AACCTTCCCGTGAACTGTGG;RSEQ=GGCAAAGGGGTGTCGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:783:38:26,12:481,263:744,38:0.0485:2,2:24.7:1:30.4:1:0.72902:1.18:59.3:18:0.0477:0:1.1 0/1:706:237:170,67:290,177:467,237:0.3357:2,2:23.3:1:29.9:1:0.01194:1.55:60:38.5:0.3358:0:1.1 +19 2164109 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23411;SOR=Inf;LSEQ=GCCCCTCCCTCCCGCCCGCC;RSEQ=TCCTCCGCCCACCGGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:52,4:56,0:0:2,0:10.4:1:32.3:1:1:0:59.8:112:1:0:0.8 0/1:53:2:2,0:42,9:51,2:0.0377:2,0:6:1:27:1:1:0:60:4:0.0377:0:2 +19 2164138 . C A 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.49918;SOR=0;LSEQ=CCACCGGCGGCCCCGCCCCT;RSEQ=CCCCAACCGCCCGCCTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:168,26:194,2:0.0102:2,2:30:1:24:0:0.25714:6.3596:60:4:0.0104:0:4 0/0:184:0:0,0:144,40:184,0:0:2,0:19.9:1:30.5:1:1:0:60:45:1:0:0.3 +19 2164139 . C T 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.1166;SOR=Inf;LSEQ=CACCGGCGGCCCCGCCCCTC;RSEQ=CCCAACCGCCCGCCTAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:173,28:201,0:0:2,0:20:1:31.7:1:1:0:60:66:1:0:0.3 0/1:193:3:1,2:148,42:190,3:0.0155:2,2:7:1:25.7:1:0.13072:6.95437:60:6:0.0158:0:2 +19 2164167 . C T 45 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19538;SOR=0.22341;LSEQ=GCCCGCCTAGCATGGTGCGG;RSEQ=GGCCGCGCGCGCGGACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:4:1,3:305,92:397,4:0.01:2,2:8.3:1:22.5:1:0.04291:9.872:60:3:0.0076:0:1.3 0/0:446:1:0,1:294,151:445,1:0.0022:2,0:1:0:25:0:0.34081:0:60:2:0.0023:0:1 +19 2164351 . T A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.77027;LSEQ=CAAACCCCCCCAAGCCGCGC;RSEQ=CACCGGTCCCCCCTGCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:38:4,34:36,230:266,38:0.1246:2,2:24.8:1:29.3:1:0.79884:1.32927:60:18:0.1263:0:1.3 0/1:226:64:9,55:24,136:160,64:0.2832:2,2:19.9:1:28.7:1:1:1.07808:60:15:0.2871:0:1.2 +19 2164363 . C A 29 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.5655;SOR=3.05467;LSEQ=AGCCGCGCTCACCGGTCCCC;RSEQ=CTGCGGAACGGAGACCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:1:1,0:13,229:242,1:0.0041:2,0:1:0:27:0:0.05761:0:60:2:0.0042:0:1 0/1:160:2:1,1:12,146:158,2:0.0125:2,2:5:0:29.5:1:0.15637:11.73:37:4:0.0128:0:0 +19 2164394 . C G 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15469;SOR=Inf;LSEQ=GAGACCCTGGACTCCACTGT;RSEQ=GCTGCTCCACCCCCGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:0,118:118,0:0:1,0:22.3:1:30.2:1:1:0:60:117:1:0:0.3 0/1:77:2:1,1:2,73:75,2:0.026:1,2:7.5:1:29:1:0.0769:30.00:60:4:0.0263:0:1.5 +19 2186237 . G A 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGACGGCCAGAAGTCCGC;RSEQ=TTCCTGCCTGAGGCTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:33.8:1:32:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 2189588 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGGAAAGCGAGGCTTCT;RSEQ=CCAGAAGGGTCTTGGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:2,0:118,1:119,2:0.0165:1,0:20:1:27.5:1:1:0:60:4:0.0168:0:1 0/0:50:0:0,0:47,3:50,0:0:2,0:22.5:1:31.5:1:1:0:60:49:1:0:0 +19 2189631 . G T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55384;SOR=0;LSEQ=GCTGGTGGCTGTCCAGGCAG;RSEQ=GACCACACCTTGGAGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:3:3,0:231,13:244,3:0.0121:2,0:27.7:1:21.7:1:1:0:60:2:0.0083:0:1.7 0/0:120:0:0,0:111,9:120,0:0:2,0:22.7:1:30.5:1:1:0:60:59:1:0:0.1 +19 2190774 . T A 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69379;LSEQ=GAGAGGCCCGTGGCAGGAGG;RSEQ=GGAGCCTCCTAGGACCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:39:1:29.5:1:1:0:60:4:0.3333:0:1 0/1:4:1:1,0:2,1:3,1:0.25:2,0:20:0:30:0:1:0:60:2:0.25:0:1 +19 2190919 . C G 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00867;SOR=Inf;LSEQ=GAGGCCATGCAGCCGACTCC;RSEQ=TGCTTCCGCTGGGAAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:111,9:120,0:0:2,0:25:1:31.6:1:1:0:59.8:240:1:0:0.2 0/1:102:6:5,1:84,12:96,6:0.0588:2,2:9.2:1:29.3:1:0.56845:1.39485:60:12:0.0588:0:1.3 +19 2190947 . TTGG T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.00058;SOR=2.67841;LSEQ=GCTGGGAAAGGTCCCGGGTC;RSEQ=TGGTGGAGGGGCTGGGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:23:17,6:145,35:180,23:0.1127:2,2:18.8:1:30.9:1:0.42088:1.45921:59.6:46:0.115:0.0441:0.1 0/1:169:43:32,11:90,36:126,43:0.2544:2,2:23.1:1:30:1:0.84419:1.16:59.9:86:0.2575:0.0828:0.1 +19 2190994 . C T 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6863;SOR=2.00857;LSEQ=GTTTATGTGACATGGCCGGG;RSEQ=CACCCTCCGTCCGCAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:2:1,1:283,106:389,2:0.0051:2,2:20.5:1:29:1:0.47294:2.662:60:4:0.0052:0:1 0/1:392:4:1,3:245,142:387,4:0.0102:2,2:11.8:1:24.8:1:0.14608:5.15422:60:3:0.0079:0:1.3 +19 2191338 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53041;SOR=0;LSEQ=AAGAGTTTATCAGGGACTTG;RSEQ=GACGTTGGCGTGGACAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:5,156:161,2:0.0123:1,2:14:1:30.5:1:0.07248:28.59:60:4:0.0126:0:1 0/0:97:0:0,0:6,91:97,0:0:2,0:18.7:1:29.3:1:1:0:60:47.5:1:0:0.2 +19 2193925 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGACGTCTTGGTTGCCTG;RSEQ=AGCGTGTGCCTGTGAATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:4,66:70,2:0.0278:2,2:23.5:1:28:1:0.13498:14.87:60:4:0.0278:0:1 0/0:25:0:0,0:0,24:24,0:0:1,0:20.9:1:31.4:1:1:0:60:48:1:0:0.2 +19 2194437 . C T 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25407;SOR=3.0568;LSEQ=TCCTCAGCCTCCCAAAGTGC;RSEQ=GGGATTACAGGCGTGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:2:1,1:358,117:475,2:0.0042:2,2:4.5:1:30:1:0.43395:3.05102:60:4:0.0043:0:1.5 0/1:393:5:3,2:280,106:386,5:0.0127:2,2:13.6:1:28.6:1:0.61932:1.75814:50:10:0.0128:0:2 +19 2194657 . C T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=2.69016;LSEQ=TGTCAGCCCCTCCTTTCTTG;RSEQ=CGATGTTGGCACATGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:33:5,28:36,247:283,33:0.1044:2,2:23:1:29.6:1:0.78325:1.22:59.1:15.5:0.1016:0:1.2 0/1:230:55:10,45:33,142:175,55:0.2391:2,2:23.4:1:28.2:1:1:1.04557:60:26.5:0.2377:0:1.1 +19 2194660 . A ATGTTGGCACATGGC 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=1.929;MSILEN=1;SSF=0.03963;SOR=1.9492;LSEQ=CAGCCCCTCCTTTCTTGCCG;RSEQ=TGTTGGCACATGGCTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:19:1,18:29,242:271,19:0.0655:2,1:26.8:1:30.1:1:0.70415:2.15265:58.2:38:0.0669:0.0138:1.2 0/1:216:26:0,26:35,154:189,26:0.1204:2,1:32.7:1:30.7:1:0.01015:0:60:52:0.1244:0.0231:0.9 +19 2194769 . A G 73 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02627;SOR=9.87065;LSEQ=CAGCAGGCGCCTCTGTTGGT;RSEQ=CCGTCCCTCTCGTCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:0,1:0,31:31,1:0.0313:1,0:45:0:35:0:1:0:60:2:0.0323:0:1 0/1:20:5:0,5:1,14:15,5:0.25:1,0:26.6:1:31.6:1:1:0:60:10:0.25:0:1 +19 2194896 . T C 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GGACAGGCTGGGTTCTGGGC;RSEQ=GGCTGCGGCATCCTTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:20.5:1:29.8:1:1:0:60:12:1:0:1.3 0/0:2:0:0,0:1,1:2,0:0:2,0:1:0:31:0:1:0:57.5:4:1:0:0.5 +19 2196170 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCCCTCCGCACTGTCCCACA;RSEQ=CACAAGTGAAGGCCGGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:31.3:1:33.7:1:1:0:60:6:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:35:1:28.5:1:1:1:60:4:0.5:0:1.5 +19 2199748 . TG T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.53018;SOR=0;LSEQ=GCTCCCAGGGCTGCAGCCGG;RSEQ=GGGCCTGGGCCTCCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:125,1:126,2:0.0156:1,2:9.5:1:30.5:1:0.03113:88.97262:60:4:0.0167:0.0078:0.5 0/0:76:0:0,0:74,2:76,0:0:1,0:23.6:1:31.5:1:1:0:60:37:1:0:0.2 +19 2199950 . G A 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.31495;LSEQ=CAACACGAGGTATGGCCAGC;RSEQ=TGGGGCATGCAGGGCATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:724:1:1,0:314,409:723,1:0.0014:2,0:1:0:26:0:0.43508:0:60:2:0.0014:0:1 0/1:699:37:16,21:280,381:661,37:0.0529:2,2:27.9:1:29.5:1:1:1.04:60:36:0.0525:0:1.2 +19 2199993 . G A 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1781;SOR=5.00823;LSEQ=GTGTGCGCTCACAGGCGGGC;RSEQ=GTGGCCATGGCACCGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:465:1:1,0:137,327:464,1:0.0022:2,0:1:0:26:0:0.29677:0:60:2:0.0022:0:1 0/1:374:4:3,1:119,251:370,4:0.0107:2,2:13:1:26.5:1:0.10369:6.29:60:3:0.0084:0:2.3 +19 2200022 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17474;SOR=Inf;LSEQ=GGCACCGGGGACCGGGAGCG;RSEQ=CCCCTCGCTCCTGTGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:54,214:268,0:0:2,0:24.6:1:32.2:1:1:0:60:267:1:0:0.1 0/1:193:2:1,1:44,147:191,2:0.0104:2,2:13:1:30:1:0.41289:3.31:60:4:0.0105:0:1.5 +19 2200037 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51929;SOR=0;LSEQ=GAGCGGCCCCTCGCTCCTGT;RSEQ=CTGGCTGTGGCAGGAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:0,2:26,173:199,2:0.01:2,0:38.5:1:32:0:1:0:60:4:0.0103:0:1 0/0:133:0:0,0:20,111:131,0:0:2,0:24.8:1:31.4:1:1:0:60:64.5:0.9847:0:0.2 +19 2202887 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12718;SOR=Inf;LSEQ=CAGCTCAGACTTGGGGTCTT;RSEQ=AGTCCCCTTGGAGCCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:9,212:221,0:0:1,0:27.6:1:32.7:1:1:0:60:442:1:0:0 0/1:123:2:1,1:6,115:121,2:0.0163:1,2:11.5:1:27:1:0.11102:17.82:60:4:0.0167:0:1 +19 2202921 . C CT 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.55376;SOR=0;LSEQ=CCAGGTGGTCTTCCTTTATG;RSEQ=TTTTTTTTCTTTTTTTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:3:0,3:2,119:121,3:0.0242:1,0:22.7:1:31.3:1:1:0:60:6:0.0242:0.0081:0 0/0:55:0:0,0:1,54:55,0:0:1,0:20.1:1:32.4:1:1:0:60:110:1:0:0.1 +19 2206520 . CA C 64 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=23.000;MSILEN=1;SSF=0.39704;SOR=2.35688;LSEQ=TGAGCCGGGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:15,0:15,4:0.1905:1,0:14.5:1:32.8:1:1:0:50.8:8:0.1905:0.0476:1 0/1:11:4:4,0:5,0:5,4:0.3636:0,0:15.3:1:32.3:1:1:0:47:8:0.3636:0.0909:3.3 +19 2206575 . G T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37645;SOR=0.47634;LSEQ=AATAGGCTTCAACTTGGAAG;RSEQ=TGTTTCCTAGTGTTGCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:10:10,0:106,0:106,10:0.0862:1,0:25.4:1:31.1:1:1:0:60:20:0.0877:0:1.1 0/1:70:3:3,0:67,0:67,3:0.0429:1,0:13.3:1:26.3:1:1:0:60:2:0.0323:0:1 +19 2206610 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51125;SOR=0;LSEQ=GCTTGTAGGCAGGTGGACAG;RSEQ=ACCCGGAGCCCAGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:178,5:183,2:0.0108:1,2:19.5:1:27.5:1:0.06398:32.57716:60:4:0.011:0:1 0/0:134:0:0,0:128,5:133,0:0:1,0:26.9:1:30.3:1:1:0:59.7:18:1:0:0.3 +19 2206622 . AGT A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1.0885;LSEQ=GTGGACAGGACCCGGAGCCC;RSEQ=GTGTGTGTGTTCCGTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:6:6,0:228,15:243,6:0.0241:2,0:25.7:1:32.3:1:1:0:60:12:0.0242:0.004:0 0/1:191:5:4,1:170,16:186,5:0.0262:2,2:20.8:1:30.6:1:0.3758:2.63665:60:10:0.0266:0:0 +19 2207041 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07368;SOR=Inf;LSEQ=GCACTGTGTGCCATGGGGGT;RSEQ=GAATCACTCCTCGGGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:11,0:0:2,0:21.8:1:32.8:1:1:0:60:22:1:0:0.2 0/1:9:3:1,2:1,5:6,3:0.3333:2,2:17.7:1:31.3:1:1:2.24:60:6:0.3333:0:1 +19 2207269 . A G 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGTGCCTGTGTTGCTGG;RSEQ=TGCTGGCCGTTCTTGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:5,0:5,2:0.2857:0,2:15.5:1:32:1:0.28571:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 2207386 . G C 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16227;SOR=0;LSEQ=GGTTGGAGGGGCCCAGGCCA;RSEQ=GTGGTGTTGAATGGTGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:11,0:23,0:23,11:0.3235:1,0:26.2:1:31.8:1:1:0:60:22:0.3235:0:1.5 0/0:6:0:0,0:6,0:6,0:0:0,0:18.5:1:33.3:1:1:0:60:12:1:0:0.2 +19 2207517 . T C 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15319;SOR=Inf;LSEQ=GCCCTGGGGTGGGTGAGGTC;RSEQ=GCATGGAGGGGCTGTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:253,51:304,0:0:2,0:25.5:1:31.9:1:1:0:59.9:100.333:1:0:0.1 0/1:196:2:1,1:159,35:194,2:0.0102:2,2:30:1:24.5:1:0.33438:4.4934:60:4:0.0105:0:2 +19 2207536 . C T 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17769;SOR=5.02228;LSEQ=CTGCATGGAGGGGCTGTGGG;RSEQ=AGGCGCAGGCCCCGGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:1:0,1:300,94:394,1:0.0025:2,0:1:0:24:0:0.24051:0:60:2:0.0026:0:1 0/1:318:4:1,3:227,87:314,4:0.0126:2,2:9.5:1:24.3:1:0.07018:7.76926:60:8:0.0127:0:1 +19 2207549 . C T 86 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05144;SOR=4.66511;LSEQ=CTGTGGGCAGGCGCAGGCCC;RSEQ=GGCCTCACCTGTGGCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:482:2:0,2:344,135:479,2:0.0041:2,0:1:0:25.5:1:0.0807:0:60:4:0.0042:0:1 0/1:419:8:5,3:280,131:411,8:0.0191:2,2:22:1:28.9:1:0.71446:1.28161:60:16:0.0193:0:1 +19 2207797 . GC G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCTCAGAGCCCTCAAC;RSEQ=CCCCCGGCCCCTGAGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:0,2:2,118:120,2:0.0164:1,0:15:1:32.5:1:1:0:60:4:0.0169:0.0082:0.5 0/0:58:0:0,0:3,55:58,0:0:2,0:23.6:1:30.4:1:1:0:60:28:1:0:0.1 +19 2208410 . T G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGGAGCGCTGGTGCCG;RSEQ=CTGGGGACCGACAGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 2208859 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.04815;LSEQ=CACTGTCCAGGTTGCTGTTG;RSEQ=TACCTGGGTGTCCAGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:33:22,11:261,134:395,33:0.0771:2,2:23.2:1:31.6:1:1:1.03:60:32:0.0757:0:1 0/1:378:163:109,54:138,77:215,163:0.4312:2,2:23.4:1:31.5:1:0.66258:1.13:59.8:162:0.4309:0:1.2 +19 2209142 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17746;SOR=Inf;LSEQ=CTCCTTCCTGCTCCTCCCCA;RSEQ=TGTCACTCCTGGTCCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:1,67:68,0:0:1,0:26.5:1:33.4:1:1:0:59.6:136:1:0:0.1 0/1:50:2:1,1:0,48:48,2:0.04:1,2:20:1:28:1:0.04:0:60:4:0.04:0:1 +19 2210357 . C T 36 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.63759;SOR=0.43779;LSEQ=CGGTGCAGGAGGGCCGTGGG;RSEQ=AGCGCTGGGGCTTCCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:2,1:197,60:257,3:0.0115:2,2:31.7:1:23:1:0.55322:1.63815:60:2:0.0079:0:2.3 0/0:197:1:0,1:138,58:196,1:0.0051:2,0:1:0:22:0:0.29949:0:60:2:0.0051:0:1 +19 2210736 . C T 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=28.65991;LSEQ=AAGATGGCTGGCCGCAAGCG;RSEQ=GGGCGCCCCAAGAAGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:902:2:1,1:437,462:899,2:0.0022:2,2:17:1:30:1:1:1.06:60:4:0.0023:0:1 0/1:901:54:26,28:401,446:847,54:0.0599:2,2:24.2:1:28.1:1:1:1.03:60:108:0.0605:0:1.1 +19 2210778 . G A 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGCGAACCCCGAGCGGAA;RSEQ=CCCAAGAAGAACCAAACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:0:0,0:296,390:686,0:0:2,0:25:1:32.3:1:1:0:59.9:44.733:1:0:0.2 0/1:674:31:16,15:274,368:642,31:0.046:2,2:25:1:28.4:1:0.35655:1.43:59.2:30:0.0451:0:1.3 +19 2211050 . C T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43555;LSEQ=ATGCTGACGCCTCTGCCCAC;RSEQ=GCTCTCCCGACCCGCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:600:271:170,101:225,104:329,271:0.4517:2,2:23.7:1:30.9:1:0.1664:1.2848:60:53.2:0.4501:0:1.1 0/1:504:133:89,44:244,127:371,133:0.2639:2,2:23.5:1:29.5:1:0.83179:1.05:60:43.333:0.261:0:1.1 +19 2211220 . G T 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGAAGCTTCTAGGTGAGCCC;RSEQ=TGTGAGGCGTCCGGCGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:24:7,17:182,344:526,24:0.0434:2,2:21.7:1:30.7:1:0.6653:1.28434:60:48:0.0442:0:1.1 0/0:535:0:0,0:195,340:535,0:0:2,0:22.5:1:30.4:1:1:0:60:88.167:1:0:0.2 +19 2211221 . T C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=GAAGCTTCTAGGTGAGCCCG;RSEQ=GTGAGGCGTCCGGCGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:0:0,0:188,359:547,0:0:2,0:24.2:1:29.7:1:1:0:60:41.077:1:0:0.2 0/1:526:15:5,10:181,327:508,15:0.0285:2,2:22.7:1:29.7:1:1:1.10684:60:30:0.0294:0:1 +19 2211638 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50154;SOR=0;LSEQ=TCTGCTGAGCTCCTGCCTCA;RSEQ=GAGTGCCTGACACCTGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:177,9:186,2:0.0106:1,0:34.5:1:34:0:1:0:60:4:0.0108:0:1 0/0:162:0:0,0:153,9:162,0:0:2,0:24.4:1:30.1:1:1:0:60:80:1:0:0.1 +19 2211951 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52197;SOR=0;LSEQ=TGGAGCGCAGGCCTGAGTGG;RSEQ=CTCCCTCCTCTGCTCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:0,2:1,110:111,2:0.0177:1,0:19:1:32:0:1:0:60:4:0.0182:0:1 0/0:72:0:0,0:2,69:71,0:0:1,0:21.4:1:31.3:1:1:0:59.8:22.667:0.9855:0:0.2 +19 2212683 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAAGCGGGGGCAGGGGAGG;RSEQ=TGACAAGCAGGCATCAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:29.5:1:1:0:60:4:1:0:1.5 +19 2213298 . G T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGGCTGAGTCCAGGTG;RSEQ=GGTGGCAGGTGCAGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:4,0:18,1:19,4:0.1739:1,0:20.5:1:32:0:1:0:60:8:0.1739:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:4:1:29.5:1:1:0:60:4:1:0:0 +19 2213563 . C T 87 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03064;SOR=5.04677;LSEQ=GAACGCCCAGCTCCTGGGTG;RSEQ=GGCTCAGCAGCTCCTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:863:2:1,1:500,361:861,2:0.0023:2,2:14:1:29:1:1:1.38449:60:4:0.0024:0:1 0/1:776:9:3,6:417,350:767,9:0.0116:2,2:21.7:1:27.7:1:0.31435:2.38026:60:18:0.0117:0:1.1 +19 2213721 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14955;SOR=Inf;LSEQ=GTCCGTCGGTATGGCTTCCT;RSEQ=TGGCTTCCTGTCTATGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:74,217:291,0:0:2,0:23.9:1:32.3:1:1:0:60:71.75:1:0:0.1 0/1:184:2:1,1:36,146:182,2:0.0109:2,2:33:1:28:1:0.36262:4.01:60:4:0.0109:0:1 +19 2213885 . A G 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01273;SOR=Inf;LSEQ=GACCTACAACGACCTGATTC;RSEQ=AGCGCAGAAGGAGATCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:577:0:0,0:303,274:577,0:0:2,0:26.2:1:30.5:1:1:0:59.9:81.429:1:0:0.1 0/1:542:6:4,2:290,246:536,6:0.0111:2,2:34.2:1:27.2:1:0.69255:1.69:60:5:0.0094:0:1.5 +19 2214057 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0909;SOR=0.58024;LSEQ=GGGCGGGTGTGTCCTCTGTG;RSEQ=GGGTGGGAGGCTCTGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:98:59:10,49:7,32:39,59:0.602:2,2:25.6:1:28.9:1:1:1.07111:60:10.8:0.587:0:1.2 0/1:75:35:5,30:8,32:40,35:0.4667:2,2:24.1:1:28.6:1:0.55709:1.49199:60:34:0.4658:0:1.2 +19 2214242 . G A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGAGGTGTGGGGTCATGC;RSEQ=AGCATCCCACCATCGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:5,1:6,5:11,6:0.3529:2,2:20.8:1:27.8:1:0.33339:3.85:60:5:0.3333:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:23:0:1:0:60:2:1:0:0 +19 2214423 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15663;SOR=Inf;LSEQ=CTGAGAGTGTGGGGTGTGCT;RSEQ=GGCAGGCAGCCAGCCAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:225,75:300,0:0:2,0:25:1:32:1:1:0:59.9:74:1:0:0.1 0/1:197:2:1,1:141,54:195,2:0.0102:2,2:29:1:29:1:0.48146:2.59643:60:4:0.0103:0:1 +19 2214634 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09602;SOR=Inf;LSEQ=TGCACTCCGTGGTGTCCGAG;RSEQ=CTCTCCCATCAGCCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:55,222:277,0:0:2,0:25.1:1:31.5:1:1:0:60:54.4:1:0:0.1 0/1:235:3:2,1:55,177:232,3:0.0128:2,2:23:1:26.7:1:0.14674:6.37:60:6:0.0129:0:1 +19 2216175 . C A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03791;SOR=Inf;LSEQ=GTTTTTCCATCCCACACAAG;RSEQ=AGCGGGGGTCCTGGCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:77,6:83,0:0:2,0:24.5:1:31.7:1:1:0:60:26.667:1:0:0.1 0/1:43:3:3,0:36,4:40,3:0.0698:2,0:15.3:1:29.3:1:1:0:60:6:0.0698:0:1 +19 2216738 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24879;SOR=Inf;LSEQ=GACCACACGGTGCCCGGCAG;RSEQ=CCGGCTGCCAGTGAGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:107,189:296,0:0:2,0:25.4:1:31.9:1:1:0:59.9:97.667:1:0:0.1 0/1:301:3:2,1:114,184:298,3:0.01:2,2:11.3:1:27:1:0.56126:3.22:60:6:0.0101:0:1 +19 2216750 . T A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24859;SOR=Inf;LSEQ=CCCGGCAGGCCGGCTGCCAG;RSEQ=GAGCTGCATTCGAGGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:98,162:260,0:0:2,0:24.7:1:30.1:1:1:0:59.9:51:1:0:0.1 0/1:263:3:2,1:97,163:260,3:0.0114:2,2:28.7:1:26.7:1:0.55854:3.34:60:6:0.0116:0:1 +19 2216784 . TG T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.09564;SOR=Inf;LSEQ=GGTGAGTGCCCTGGTGGGGC;RSEQ=GGGGTCTGCAGCTGGTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:74,104:178,0:0:2,0:22.8:1:31.7:1:1:0:59.9:43.5:1:0:0.1 0/1:151:3:1,2:47,101:148,3:0.0199:2,2:11.3:1:30.3:1:1:1.07:60:6:0.0201:0:0.3 +19 2216789 . G C 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.204;SOR=Inf;LSEQ=GTGCCCTGGTGGGGCTGGGG;RSEQ=TCTGCAGCTGGTACCTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:71,102:173,0:0:2,0:22.7:1:32:1:1:0:60:85.5:1:0:0.1 0/1:143:2:1,1:41,100:141,2:0.014:2,2:5:0:32.5:1:0.50261:2.42:60:4:0.0142:0:0.5 +19 2216794 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50638;SOR=0;LSEQ=CTGGTGGGGCTGGGGGTCTG;RSEQ=AGCTGGTACCTGCCGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:2,0:73,94:167,2:0.0118:2,0:24.5:1:28.5:1:0.19548:0:60:4:0.012:0:2.5 0/0:131:0:0,0:41,90:131,0:0:2,0:23.2:1:31.4:1:1:0:60:31.75:1:0:0.2 +19 2216810 . A T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5106;SOR=0;LSEQ=TCTGCAGCTGGTACCTGCCG;RSEQ=CTCTGCCTGGTGTGCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:90,70:160,2:0.0123:2,2:18:0:32:0:1:1.28369:60:4:0.0127:0:1.5 0/0:118:0:0,0:50,68:118,0:0:2,0:23.4:1:29.2:1:1:0:60:117:1:0:0.2 +19 2216827 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15219;SOR=Inf;LSEQ=CCGACTCTGCCTGGTGTGCT;RSEQ=AGGCTGTCGGGTTCTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:113,66:179,0:0:2,0:24.5:1:31.9:1:1:0:60:43.75:1:0:0.2 0/1:115:2:1,1:65,48:113,2:0.0174:2,2:35:0:31:1:1:1.35053:60:4:0.0174:0:1 +19 2216894 . G T 124 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=8.74555;LSEQ=GTGGGGAGGTGCTGGGCCAG;RSEQ=CCGCTGCCTCTGAGTGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:3:0,3:304,138:442,3:0.0067:2,0:12.7:1:23:1:0.03135:0:60:2:0.0046:0:2 0/1:374:21:13,8:231,121:352,21:0.0561:2,2:19.3:1:28.3:1:0.81407:1.1743:60:42:0.0572:0:1.1 +19 2216896 . C T 57 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18412;SOR=4.79273;LSEQ=GGGGAGGTGCTGGGCCAGGC;RSEQ=GCTGCCTCTGAGTGCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:1:0,1:309,147:456,1:0.0022:2,0:11:0:15:0:0.32385:0:60:0:0:0:4 0/1:384:4:1,3:247,133:380,4:0.0104:2,2:5.5:1:28.5:1:0.1293:5.54591:60:8:0.0106:0:1 +19 2217123 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18023;SOR=Inf;LSEQ=CCCCTGCCCCGGGCTCAGGG;RSEQ=GGTGCTCAGCAGAGGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:66,199:265,0:0:2,0:24.1:1:31.3:1:1:0:59.9:52:1:0:0.1 0/1:196:2:1,1:64,130:194,2:0.0102:2,2:21.5:1:28.5:1:1:2.02:60:4:0.0104:0:1 +19 2217203 . G A 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04334;SOR=0;LSEQ=TTGGGGCACGGTGAGGTACT;RSEQ=GGGCTGACCTGGAGTAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:7:1,6:1,51:52,7:0.1186:1,2:24.9:1:31.1:1:0.22501:7.95:60:14:0.1207:0:1 0/0:35:0:0,0:2,33:35,0:0:2,0:18.3:1:31.1:1:1:0:60:70:1:0:0.2 +19 2217659 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15225;SOR=Inf;LSEQ=AAGGTTGCAGGGCCTTGGCA;RSEQ=CGTGGGGGCCGCCTTGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:137,6:143,0:0:1,0:26.6:1:33.2:1:1:0:59.8:70.5:1:0:0.2 0/1:92:2:1,1:85,5:90,2:0.0217:2,2:21.5:1:28:1:0.12685:15.60585:60:4:0.0217:0:1 +19 2217754 . C T 117 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00058;SOR=6.57188;LSEQ=GTTGACCCACGACTGGGGGT;RSEQ=GGGCCTTCGTCTGCAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:638:3:1,2:410,225:635,3:0.0047:2,2:7.7:1:29.7:1:0.28938:3.63666:60:6:0.0048:0:1 0/1:597:18:10,8:346,233:579,18:0.0302:2,2:22.1:1:28.2:1:0.80869:1.18763:60:17:0.029:0:1.3 +19 2217970 . C T 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=CCACGTTGAGGCAAAACAGT;RSEQ=TGGGGTGCTCGAGACCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:59,270:329,0:0:2,0:23.9:1:32.9:1:1:0:60:64.8:0.9969:0:0.1 0/1:257:12:2,10:55,190:245,12:0.0467:2,2:18.4:1:29.9:1:1:1.44545:60:24:0.0476:0:1 +19 2219783 . G A 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGCTTGGAGAACACAGCC;RSEQ=CTTCCCGGTGAGGGCGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:30:1:32:0:1:0:60:4:0.4:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:6:0:32:0:1:0:60:2:1:0:1 +19 2220254 . TCTG T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.07388;SOR=2.42307;LSEQ=CTGTGCCCTACCCTCAGGAC;RSEQ=CTGCTGCTGCTGCTCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:7:2,5:110,345:455,7:0.0151:2,2:32.1:1:32.1:1:0.67837:1.25:60:14:0.0154:0:0.1 0/1:390:14:2,12:123,253:376,14:0.0359:2,2:32.9:1:32.9:1:0.24183:2.91064:60:28:0.0366:0:0.2 +19 2220642 . C A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTTCCTTGAGAAGGTGCCGC;RSEQ=TGAGCAGTCTCTGCTGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:18:1:33:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:28.5:1:1:0:60:4:1:0:1.5 +19 2221792 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01081;SOR=Inf;LSEQ=CACAGGGTCAGCCCTGAGCC;RSEQ=TGAGCTTGCCCACAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:26,2:28,0:0:2,0:26.9:1:30.6:1:1:0:59.1:13:1:0:0.2 0/1:9:3:3,0:3,3:6,3:0.3333:2,0:17.7:1:30.7:1:0.46429:0:60:6:0.3333:0:1.3 +19 2221892 . C A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=CTCTCCTGGAGCCCACAGAG;RSEQ=TCCTAGGGGGTGGTGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:142,21:163,0:0:2,0:21.8:1:33:1:1:0:60:326:1:0:0.2 0/1:68:8:7,1:52,8:60,8:0.1176:2,2:19:1:28.6:1:1:1.08:60:16:0.1194:0:1 +19 2221918 . A T 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28928;SOR=0;LSEQ=GGGGGTGGTGCTCCCACAGC;RSEQ=AGGCTTTCTCTTTGGCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:202,59:261,3:0.0114:2,2:17.3:1:21:1:0.1344:6.78275:60:2:0.0077:0:1.7 0/0:164:0:0,0:119,45:164,0:0:2,0:19.9:1:29.5:1:1:0:60:81:1:0:0.1 +19 2222393 . T A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.082;SOR=Inf;LSEQ=GCCAGCGCCCGTGGGGACTG;RSEQ=GTGCCGAGCCACGGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:135,236:371,0:0:2,0:23.5:1:30:1:1:0:60:52:1:0:0.1 0/1:286:3:2,1:112,171:283,3:0.0105:2,2:10.3:1:27:1:0.56547:3.04:60:6:0.0106:0:1 +19 2222429 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07447;SOR=Inf;LSEQ=CAGGACAGTCGCAGGCGCGG;RSEQ=CGGCGGAAGCGAGCATCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:104,181:285,0:0:2,0:24.3:1:31.2:1:1:0:60:34.625:1:0:0.1 0/1:208:3:1,2:101,104:205,3:0.0144:2,2:29.3:1:30.3:1:1:1.93635:60:6:0.0144:0:1.3 +19 2222530 . C A 44 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.37384;SOR=3.86879;LSEQ=TGGCCTTTTCACACAGCCTT;RSEQ=GGGGTCTCCCCTCAACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:1:1,0:174,198:372,1:0.0027:2,0:1:0:24:0:0.46917:0:60:2:0.0027:0:1 0/1:388:4:3,1:178,205:383,4:0.0103:2,2:7.3:1:22.3:1:0.34378:3.44:57:3:0.0079:0:2 +19 2222567 . G A 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.435;SOR=2.16837;LSEQ=CTCAACTCCATGGTAAGGAT;RSEQ=GGGACCGGCAGGGCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:2:2,0:92,161:253,2:0.0078:2,0:1:0:24:1:0.13497:0:60:4:0.0079:0:1 0/1:237:4:3,1:93,140:233,4:0.0169:2,2:23.5:1:25.8:1:0.30623:4.49:60:8:0.0169:0:1 +19 2222588 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22045;SOR=Inf;LSEQ=GGGACCGGCAGGGCTGGGGA;RSEQ=CGCGGCCTGTGAAAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:45,116:161,0:0:2,0:20.5:1:31.9:1:1:0:59.7:52.667:1:0:0.1 0/1:143:2:1,1:45,96:141,2:0.014:2,2:35.5:1:28.5:1:0.54142:2.12:60:4:0.0143:0:1 +19 2222590 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22715;SOR=Inf;LSEQ=GACCGGCAGGGCTGGGGAGC;RSEQ=CGGCCTGTGAAAGAAAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:43,108:151,0:0:2,0:20.6:1:30.8:1:1:0:59.6:36.75:1:0:0.1 0/1:138:2:1,1:44,92:136,2:0.0145:2,2:14.5:1:31:1:0.54745:2.08:60:4:0.0147:0:1 +19 2222654 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14132;SOR=Inf;LSEQ=TCACGCCTGTAATCCCAGCA;RSEQ=TTTGGGAGGCCGAGGCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:39,0:0:1,0:22.4:1:30.6:1:1:0:50.8:78:1:0:0.1 0/1:24:2:0,2:0,22:22,2:0.0833:1,0:8:1:33:0:1:0:60:4:0.0833:0:1.5 +19 2223327 . G A 200 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=39.51785;LSEQ=ATTACAGCCATCTCGTCCCC;RSEQ=GAGACCTCCCTGAAGAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1344:3:3,0:683,657:1340,3:0.0022:2,0:12.3:1:22.3:1:0.24979:0:60:2:0.0015:0:3.7 0/1:1315:107:56,51:613,594:1207,107:0.0814:2,2:23.7:1:29.8:1:0.76339:1.06:60:106:0.0817:0:1.3 +19 2223511 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.56259;SOR=3.15738;LSEQ=TCCAGGGGCCCGGAGGGGGG;RSEQ=GGGGCCTGGCAGCAGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:22,162:184,1:0.0053:2,0:2:0:30:0:1:0:60:2:0.0055:0:1 0/1:120:2:0,2:16,102:118,2:0.0167:2,0:23.5:1:30:1:1:0:60:4:0.0169:0:1 +19 2223514 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15211;SOR=Inf;LSEQ=AGGGGCCCGGAGGGGGGCGG;RSEQ=GCCTGGCAGCAGGGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:17,148:165,0:0:2,0:23.4:1:31.8:1:1:0:59.8:81.5:1:0:0.3 0/1:106:2:1,1:13,91:104,2:0.0189:2,2:28.5:1:30:0:0.2478:6.78:60:4:0.019:0:1.5 +19 2223548 . T C 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0.05212;SOR=Inf;LSEQ=GGCAGGAGGTGCCTGCTCAC;RSEQ=GTGTGTGTGTGGGTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:0,54:54,0:0:1,0:18:1:29.4:1:1:0:58.5:5.75:0.9787:0:0.9 0/1:35:3:0,3:1,31:32,3:0.0857:1,0:10.7:1:25.7:1:1:0:60:2:0.0667:0:1.7 +19 2223560 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.54762;SOR=0;LSEQ=CTGCTCACTGTGTGTGTGTG;RSEQ=GTGGGTGGGTGGGGAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:0,3:0,47:47,3:0.0588:1,0:30.7:1:31.7:1:1:0:58.3:6:0.0625:0:2.3 0/0:23:0:0,0:1,20:21,0:0:1,0:11.6:1:28.9:1:1:0:57.4:20:0.9524:0:1.9 +19 2225371 . CT C 97 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.59963;SOR=0.72154;LSEQ=GGGTTTCAAGCATTAATGAC;RSEQ=TTTTTTCTTAACAGAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:663:8:4,4:368,287:655,8:0.0121:2,2:28:1:32.4:1:0.73535:1.28174:60:16:0.0122:0:0.1 0/0:687:6:3,3:378,303:681,6:0.0087:2,2:15.2:1:27.7:1:1:1.24711:60:5:0.0074:0.0044:1 +19 2225535 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50474;SOR=0;LSEQ=GCTGCTGACCCACCTGCTGG;RSEQ=CCGCTGCATCGTGTCCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:0,2:30,168:198,2:0.01:2,0:35.5:1:28:1:1:0:60:4:0.0103:0:1 0/0:161:0:0,0:30,131:161,0:0:2,0:22.5:1:30.3:1:1:0:60:52.667:1:0:0.1 +19 2225871 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGACCTCAGCATTTTCCC;RSEQ=AGAGCTCATCCCGCATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:21:1:33:1:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 +19 2226041 . C A 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCCTGTCCTCTCCCATC;RSEQ=TGTCCCGCTTGGCATCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:2,0:88,5:93,2:0.0211:2,0:7:1:32.5:1:1:0:60:4:0.0213:0:1.5 0/0:41:0:0,0:39,2:41,0:0:1,0:23.7:1:30.1:1:1:0:60:40:1:0:0.3 +19 2226092 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51573;SOR=0;LSEQ=CCAGCCCTGCCTGCAGAGTT;RSEQ=CCCGGGCCGTGGCAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:169,14:183,2:0.0108:2,2:14:1:30.5:1:0.15599:11.69678:60:4:0.011:0:1 0/0:127:0:0,0:109,18:127,0:0:2,0:23.6:1:31.6:1:1:0:60:62.5:1:0:0.2 +19 2226104 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15423;SOR=Inf;LSEQ=GCAGAGTTGCCCGGGCCGTG;RSEQ=CAGCAGCCCCGGTTAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:206,36:242,0:0:2,0:23.1:1:31.2:1:1:0:59.9:39.333:1:0:0.2 0/1:157:2:1,1:125,30:155,2:0.0127:2,2:14.5:1:26.5:1:0.35693:4.11528:60:4:0.0132:0:1 +19 2226128 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08878;SOR=Inf;LSEQ=CAGCCCCGGTTAGCCTCATG;RSEQ=GTAGCCCGGGCAGGTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:0:0,0:268,101:369,0:0:2,0:24.3:1:31.2:1:1:0:59.9:122:1:0:0.1 0/1:299:3:1,2:212,84:296,3:0.01:2,2:15:1:26.3:1:0.19972:5.016:60:6:0.0103:0:1 +19 2226676 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.53071;LSEQ=TGAAGGGCGAGGGCAGCCGC;RSEQ=GCAAGGAGGCAGGGGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:62:32,30:283,259:542,62:0.1023:2,2:24.5:1:30.9:1:1:1.02434:60:30:0.1008:0:1.1 0/1:484:139:73,66:178,165:343,139:0.2872:2,2:25:1:29.4:1:0.92012:1.03:60:68.5:0.2866:0:1.2 +19 2226705 . G A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00387;SOR=Inf;LSEQ=GCAGGGGAGGGCGGCCTACC;RSEQ=CTGTGCGGGCCCACGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:655:0:0,0:332,322:654,0:0:2,0:24.2:1:30.7:1:1:0:60:58.455:0.9984:0:0.2 0/1:544:7:4,3:287,250:537,7:0.0129:2,2:27.3:1:26.3:1:1:1.16:60:6:0.0113:0:1.3 +19 2226772 . G C 214 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAGGCCCGGGACCGCGAG;RSEQ=TCGACCTCAAGAATGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:792:0:0,0:316,475:791,0:0:2,0:25:1:31.7:1:1:0:60:97.875:0.9987:0:0.2 0/1:730:119:55,64:270,340:610,119:0.163:2,2:25.2:1:31.1:1:0.76243:1.08:59.8:118:0.1646:0:1.2 +19 2226826 . G A 61 v3;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01504;SOR=Inf;LSEQ=CTGCGGCGGCCGTGCCTCCC;RSEQ=GAAGCCTCCTCAGCGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:178,337:515,0:0:2,0:25.8:1:30.8:1:1:0:60:38.615:1:0:0.2 0/1:511:6:6,0:197,306:503,6:0.0117:2,0:9.2:1:23.7:1:0.00385:0:60:5:0.0099:0:1.3 +19 2226847 . G T 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGCCTCCTCAGCGGCCCC;RSEQ=GCCTGGCCCCGGCGGCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:138,247:385,0:0:2,0:22.1:1:30.5:1:1:0:60:41.778:1:0:0.2 0/1:350:23:10,13:129,196:325,23:0.0657:2,2:29.9:1:28.7:1:0.8263:1.17:60:10.5:0.0618:0:1.4 +19 2226879 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.62757;SOR=2.60621;LSEQ=GCGGCGTCCTCCGCAGGCGG;RSEQ=GCGGCGTCCTCCGCCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:1:0,1:118,130:248,1:0.004:2,0:1:0:28:0:1:0:60:2:0.0041:0:1 0/1:288:3:1,2:138,147:285,3:0.0104:2,2:8.7:1:26.3:1:1:1.8736:60:6:0.0105:0:1 +19 2226945 . G A 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22007;SOR=4.59988;LSEQ=CCGCCGGGACCGCAGTTCGC;RSEQ=CTCGGCCCCATGTCCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:1:0,1:263,167:430,1:0.0023:2,0:13:0:12:0:0.38979:0:60:0:0:0:1 0/1:475:5:3,2:269,201:470,5:0.0105:2,2:29.4:1:29:1:1:1.12:60:10:0.0107:0:1.6 +19 2226997 . G A 47 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06046;SOR=0;LSEQ=GCTCCGTGGCCGGCTCCTCC;RSEQ=TGCTGCAGTCGCTGTTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:3,1:203,184:387,4:0.0102:2,2:11:1:23.5:1:0.62525:2.71:60:3:0.0078:0:1.3 0/0:396:0:0,0:194,201:395,0:0:2,0:25.4:1:29.9:1:1:0:60:64.833:0.9974:0:0.2 +19 2227064 . C T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24857;SOR=0;LSEQ=GCACGTGTCGTCCGCTGCCA;RSEQ=CAGACTGACCAACTCGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:0,3:101,142:243,3:0.0122:2,0:12:1:22.7:1:0.27103:0:60:2:0.0083:0:1 0/0:240:0:0,0:93,147:240,0:0:2,0:23.7:1:30.8:1:1:0:60:119:1:0:0.2 +19 2227080 . G T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35329;SOR=3.29131;LSEQ=GCCACCAGACTGACCAACTC;RSEQ=CACGCCATGGGCAGCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:0,1:103,150:253,1:0.0039:2,0:1:0:28:0:1:0:60:2:0.004:0:1 0/1:234:3:1,2:93,138:231,3:0.0128:2,2:19.7:1:25.7:1:1:1.34617:60:6:0.0129:0:1 +19 2227115 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09598;SOR=Inf;LSEQ=CTTTTCCGGGGTGGCAGGCG;RSEQ=CACAGTTGGAGGTAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:95,143:238,0:0:2,0:29.3:1:31.5:1:1:0:60:25.444:1:0:0.2 0/1:202:3:2,1:82,117:199,3:0.0149:2,2:14:1:28:1:0.57156:2.84:60:6:0.0149:0:1.3 +19 2227146 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.32427;SOR=3.85094;LSEQ=GGTAGGCAGGGCGGCCGTCC;RSEQ=TCCGCCCCCCGCCCCGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:1,0:64,110:174,1:0.0057:2,0:1:0:26:0:0.37143:0:60:2:0.0058:0:1 0/1:138:3:2,1:51,82:133,3:0.0217:2,2:17.3:1:26.7:1:0.56014:3.19:60:6:0.0222:0:1 +19 2227150 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.26474;SOR=0;LSEQ=GGCAGGGCGGCCGTCCGTCC;RSEQ=CCCCCCGCCCCGGCCCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:2,1:60,108:168,3:0.0175:2,2:21.7:1:27.3:1:0.29792:3.57:60:6:0.0182:0:1 0/0:126:0:0,0:47,77:124,0:0:2,0:25.5:1:30.6:1:1:0:60:123:0.984:0:0.3 +19 2227161 . C G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50755;SOR=0;LSEQ=CGTCCGTCCGCCCCCCGCCC;RSEQ=GGCCCCCGCCGGAGGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:43,95:138,2:0.0143:2,2:10:0:32.5:1:0.53135:2.20:60:4:0.0145:0:1.5 0/0:106:0:0,0:37,69:106,0:0:2,0:22.6:1:29.2:1:1:0:60:105:1:0:0.2 +19 2227621 . C A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00058;SOR=Inf;LSEQ=CGCTGCTTGTGCTTGGTGCC;RSEQ=GCACACGCCTGGCGGCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:89,1:90,0:0:1,0:26.5:1:31.7:1:1:0:60:89:1:0:0 0/1:62:8:8,0:54,0:54,8:0.129:1,0:29.5:1:30.1:1:1:0:60:16:0.1311:0:1.1 +19 2227669 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78398;LSEQ=TCCCTTTTTGTGAGCCTGCG;RSEQ=CTGCTGCTCTGCGCTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:1,2:186,62:248,3:0.012:2,2:9.3:1:29:1:0.16077:5.94732:60:6:0.0122:0:1 0/0:213:2:0,2:152,59:211,2:0.0094:2,0:1:0:22.5:1:0.08105:0:60:4:0.0094:0:1 +19 2227849 . G A 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.34424;SOR=3.43805;LSEQ=CGAGCCCGCTGCAGGCGGCG;RSEQ=CCAGCGCCTCGGCCTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:0,1:73,174:247,1:0.004:2,0:20:0:29:0:1:0:60:2:0.0041:0:1 0/1:218:3:2,1:67,147:214,3:0.0138:2,2:18.3:1:23:1:0.23792:4.36:60:2:0.0093:0:1 +19 2227861 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60174;SOR=2.27996;LSEQ=AGGCGGCGGCCAGCGCCTCG;RSEQ=CCTCTTCCTTTCAGGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:1:0,1:70,155:225,1:0.0044:2,0:44:0:12:0:1:0:60:0:0:0:2 0/1:199:2:1,1:65,131:196,2:0.0101:2,2:23:1:27:1:1:2.01:60:4:0.0102:0:1 +19 2227873 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24852;SOR=0;LSEQ=GCGCCTCGGCCTCTTCCTTT;RSEQ=AGGCCCCGGCCTCGGTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:60,144:204,3:0.0144:2,2:22.7:1:26:1:1:1.20:60:6:0.0148:0:1 0/0:199:0:0,0:70,129:199,0:0:2,0:21.9:1:31.6:1:1:0:59.7:198:1:0:0.3 +19 2227899 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24194;SOR=0;LSEQ=CCGGCCTCGGTTGAGACCCG;RSEQ=CCGCCCCCTCCGCCTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:57,107:164,2:0.012:2,2:40.5:1:31.5:1:1:1.87:60:4:0.012:0:1 0/0:172:0:0,0:76,96:172,0:0:2,0:25.3:1:31.4:1:1:0:59.6:56.333:1:0:0.5 +19 2227902 . G C 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.90001;LSEQ=GCCTCGGTTGAGACCCGGCC;RSEQ=CCCCCTCCGCCTCCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:1,0:61,96:157,1:0.0063:2,0:30:0:8:0:0.39241:0:60:0:0:0:3 0/1:168:2:1,1:76,90:166,2:0.0119:2,2:42.5:1:30.5:1:1:1.18:60:4:0.0121:0:1.5 +19 2227905 . CCCTCCG C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12294;SOR=Inf;LSEQ=TCGGTTGAGACCCGGCCGCC;RSEQ=CCTCCGCCTCCGCCTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:75,97:172,0:0:2,0:21.9:1:31.4:1:1:0:59.6:56.333:1:0:0.7 0/1:176:4:2,2:85,87:172,4:0.0227:2,2:33:1:31.5:1:1:1.02:60:8:0.0229:0:0.3 +19 2227919 . C T 34 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.24986;SOR=Inf;LSEQ=GCCGCCCCCTCCGCCTCCGC;RSEQ=TCCGCCTCCCCCGCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:108,77:185,0:0:2,0:19.8:1:32.2:1:1:0:59.5:36:1:0:1.1 0/1:204:3:1,2:118,83:201,3:0.0147:2,2:5:1:22:1:0.57195:2.82882:60:2:0.0101:0:1.7 +19 2227923 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.22402;SOR=0;LSEQ=CCCCCTCCGCCTCCGCCTCC;RSEQ=CCTCCCCCGCTGCCCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:124,74:198,2:0.01:2,2:26:0:32:1:1:1.67109:60:4:0.0104:0:1.5 0/0:222:0:0,0:131,88:219,0:0:2,0:18:1:29.4:1:1:0:59.6:18.909:0.9952:0:0.7 +19 2227928 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.6254;SOR=2.72065;LSEQ=TCCGCCTCCGCCTCCGCCTC;RSEQ=CCCGCTGCCCCCGCCTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:1:0,1:139,80:219,1:0.0045:2,0:1:0:25:0:0.36818:0:60:2:0.0046:0:1 0/1:244:3:1,2:148,92:240,3:0.0123:2,2:9.7:1:26.3:1:0.56121:3.20156:60:6:0.0123:0:1 +19 2227935 . G A 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.12145;SOR=0;LSEQ=CCGCCTCCGCCTCCCCCGCT;RSEQ=CCCCCGCCTGCGCACCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:2,1:173,81:254,3:0.0115:2,2:17.7:1:23.7:1:1:1.06762:60:6:0.0127:0:1.3 0/0:264:0:0,0:166,95:261,0:0:2,0:17.4:1:30.1:1:1:0:59.5:9.44:0.9874:0:0.8 +19 2227944 . T A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06145;SOR=Inf;LSEQ=CCTCCCCCGCTGCCCCCGCC;RSEQ=GCGCACCTGGGCCGGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:212,81:293,0:0:2,0:18.6:1:30.3:1:1:0:59.7:8.452:1:0:1.2 0/1:295:4:3,1:193,96:289,4:0.0136:2,2:10:1:26.5:1:1:1.49:60:8:0.0143:0:1 +19 2228273 . C T 67 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15764;SOR=3.40646;LSEQ=ACAGGCCAGCGCCACGGGGC;RSEQ=GTCCGCGGTGTGGGTGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:2:0,2:315,284:599,2:0.0033:2,0:1:0:27.5:1:0.22604:0:60:4:0.0034:0:1 0/1:533:6:1,5:271,254:525,6:0.0113:2,2:7.2:1:26:1:0.11461:5.32025:57.5:5:0.0096:0:2.3 +19 2229679 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10515;SOR=Inf;LSEQ=ATGGTGCTGGCCCCAGGTGG;RSEQ=GTGTGTGCTCGTGGGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:292,38:330,0:0:2,0:25.6:1:32.2:1:1:0:60:164:1:0:0.1 0/1:296:3:2,1:251,42:293,3:0.0101:2,2:23.3:1:25:1:0.37665:2.97263:60:6:0.0104:0:1 +19 2229864 . C T 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCGCGGCATGGTGCCCGC;RSEQ=GGCCTGCCGGGCTCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:0:0,0:166,377:543,0:0:2,0:22.6:1:29.6:1:1:0:59.9:44.25:0.9962:0:0.1 0/1:500:38:10,28:157,305:462,38:0.076:2,2:24.3:1:29.7:1:0.37599:1.44032:60:76:0.0771:0:1.1 +19 2229892 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04387;SOR=Inf;LSEQ=CGGGCTCCCACCCCTGGACG;RSEQ=CAGAGGCAAGGACGGACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:46,271:317,0:0:2,0:23.2:1:31.9:1:1:0:59.9:62.4:1:0:0.1 0/1:269:4:2,2:58,207:265,4:0.0149:2,2:15.3:1:28.8:1:0.21615:3.55:60:8:0.0151:0:1.3 +19 2230029 . CTT C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02956;SOR=Inf;LSEQ=AAAAGTATAAACAATTCTGA;RSEQ=ATTTTATTCCATCTAAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:0,20:20,0:0:1,0:25.4:1:31.2:1:1:0:59.5:40:1:0:0.1 0/1:10:3:0,3:0,7:7,3:0.3:0,0:9.3:1:30.6:1:1:0:60:6:0.3333:0.2:0.3 +19 2250803 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.04329;SOR=Inf;LSEQ=GGGAGCCGGGTCGACTGCCC;RSEQ=CGGGCCCCCAGCCCCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:17,0:0:2,0:20.2:1:31.4:1:1:0:60:34:1:0:0.1 0/1:5:2:1,1:2,1:3,2:0.4:2,2:30.5:1:29.5:1:1:1.7321:60:4:0.4:0:1.5 +19 3094613 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.2111;SOR=0;LSEQ=GGCCGGGGGCCGGGGGGCGG;RSEQ=GGCGGGCAGGCGGCCGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:61,14:75,2:0.026:2,2:8.5:1:27.5:1:0.35373:4.24377:48.5:4:0.026:0:1 0/0:90:0:0,0:64,26:90,0:0:2,0:9.6:1:29.5:1:1:0:56.8:21.5:1:0:0.4 +19 3094624 . C T 34 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.24891;SOR=Inf;LSEQ=GGGGGGCGGCGGCGGGCAGG;RSEQ=GGCCGCGTCGGCCGGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:109,34:143,0:0:2,0:14.7:1:31.9:1:1:0:56.4:70.5:1:0:0.1 0/1:156:3:0,3:101,52:153,3:0.0192:2,0:5:1:22:1:0.04227:0:32.7:2:0.0132:0:1.7 +19 3094793 . C T 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3515;SOR=0.30126;LSEQ=CTGCTGCTGCTCGGTGAGTG;RSEQ=GGCCCCCGGGCCTGCCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:3:1,2:63,203:266,3:0.0111:2,2:23.7:1:32:0:0.55896:1.61:60:6:0.0113:0:1.3 0/0:297:1:0,1:95,200:295,1:0.0034:2,0:44:0:27:0:1:0:60:2:0.0035:0:1 +19 3094811 . G A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98813;LSEQ=TGCGGCCCCCGGGCCTGCCG;RSEQ=CTGCGGGCCCTGCCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:42,124:166,2:0.0119:2,2:32.5:1:31:1:0.44753:2.93:60:4:0.0121:0:1.5 0/1:170:2:1,1:47,121:168,2:0.0118:2,2:18.5:1:28.5:1:0.48618:2.56:55:4:0.0123:0:1 +19 3094847 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23217;SOR=0;LSEQ=TGCCTGTGCCTGCCCTGCCT;RSEQ=TCCGGGTCGGGCCGGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:15,30:45,2:0.0426:2,2:33:1:30:1:1:1.97:60:4:0.0435:0:1 0/0:50:0:0,0:18,32:50,0:0:2,0:15:1:31.1:1:1:0:60:49:1:0:0.4 +19 3095927 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTGTAAAGTGTTGTCAC;RSEQ=CCAAATAAGGGCCCCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:32:0:1:0:60:4:1:0:1 +19 3109758 . T C 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTGTGCTGTCCCTCTGG;RSEQ=GAGCATTGGTCATGAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 3110098 . G A 192 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.24304;LSEQ=GTAAGAGGGGGCAGCAGCAC;RSEQ=AGAGTCAGGCCCCGGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:142:80:70,10:60,2:62,80:0.5634:1,2:23.3:1:30.5:1:0.06749:4.24851:60:79:0.5603:0:1.1 0/1:101:24:23,1:72,4:76,24:0.2376:2,1:24:1:28.9:1:1:1.27:60:11:0.2245:0:1.3 +19 3110126 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20235;SOR=Inf;LSEQ=GGCCCCGGCTGCCGCCCGCC;RSEQ=TCACGTGCCCCGTCCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:196,48:244,0:0:2,0:22:1:31.7:1:1:0:60:243:1:0:0.3 0/1:200:2:1,1:151,47:198,2:0.01:2,2:28.5:1:32:0:0.42332:3.18963:60:4:0.0103:0:1 +19 3110349 . T G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10183;SOR=1.30209;LSEQ=AAGGTGAGCCCGCGGGCGCC;RSEQ=GGGGAGGGGAGCGCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:106:28,78:72,184:256,106:0.2912:2,2:23.1:1:31:1:0.79689:1.08983:60:212:0.3003:0:1.9 0/1:393:137:39,98:82,174:256,137:0.3486:2,2:26:1:29.6:1:0.49311:1.1837:59.8:136:0.3532:0:1.2 +19 3110361 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07767;LSEQ=CGGGCGCCTGGGGAGGGGAG;RSEQ=GCCTGGGCAGCTGTGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:86:19,67:43,164:207,86:0.2935:2,2:25.6:1:30:1:0.87532:1.08:60:85:0.2951:0:2.1 0/1:321:10:2,8:82,228:310,10:0.0312:2,2:21.9:1:28.7:1:1:1.43705:60:20:0.0321:0:2 +19 3110487 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72224;SOR=0.72114;LSEQ=TTCCTGTCATGGACATGGAA;RSEQ=CAGCAACCGCTGACTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:19:0,19:0,17:17,19:0.5278:1,1:25.7:1:33.7:1:1:0:60:38:0.5278:0:1 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:15.3:1:32:1:1:0:60:8:0.4444:0:1 +19 3110515 . A G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CGCTGACTTCCTGGGGGCCA;RSEQ=CTGGAGAGTTGTGATGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:0,11:0,11:11,11:0.5:0,0:17.8:1:31.9:1:1:0:60:10:0.4762:0:1.5 1/0:6:3:0,3:0,3:3,3:0.5:0,0:19.7:1:32.7:1:1:0:60:6:0.5:0:1 +19 3110585 . A G 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CCAAGTAGCTGTGGGCGCCC;RSEQ=CATCCTGTGGGTGGGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:39.7:1:33:1:1:0:56:12:1:0:1.2 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:31:0:1:0:60:2:1:0:0 +19 3112793 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGATAAGCATTTTTCGGA;RSEQ=GAAAGAGAGAAGCCGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:11:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 3113176 . C T 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00334;SOR=0;LSEQ=GGCCTCGCGTTTTTCTGACA;RSEQ=GTGTTCACACGGAACTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:71:70,1:0,0:0,71:1:0,1:23:1:31.6:1:1:0:59.8:70:1:0:1.1 1/1:24:20:19,1:4,0:4,20:0.8333:0,1:24:1:29.6:1:1:0:60:9:0.8182:0:1.3 +19 3113305 . G C 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCCCAGCGAGCTCTCGAC;RSEQ=TCTCCCCTGCCCGCCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:554:554:362,192:0,0:0,554:1:0,2:25.3:1:31.8:1:1:0:60:137.5:1:0:1.1 1/1:519:442:291,151:42,33:75,442:0.8516:2,2:24:1:30.7:1:0.11737:1.51:60:109.5:0.8555:0:1.2 +19 3113516 . CGGCAGCTGCGGGCCG C 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCGCTGGCGGCCTGGGGA;RSEQ=GTGCCTGGGACCCTTCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:60,271:331,0:0:2,0:24.8:1:31.3:1:1:0:60:330:0.997:0:0.1 0/1:288:25:8,17:57,206:263,25:0.0868:2,2:25.6:1:31.6:1:0.31436:1.70:59.6:50:0.088:0.0174:0.2 +19 3113574 . GC G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52746;SOR=0;LSEQ=GCCTCCGCGGCGTCTGTGGT;RSEQ=CCCCTGCCTGCTCGCCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:0,2:1,85:86,2:0.0227:1,0:38.5:1:34.5:1:1:0:60:4:0.0233:0:0 0/0:53:0:0,0:3,50:53,0:0:2,0:20.9:1:30.8:1:1:0:60:25.5:1:0:0.1 +19 3114545 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGACTCTCCTAATGATGCGC;RSEQ=TGTTTGTGAAGCCTCATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:41:1:32:1:1:0:51:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 3114864 . C T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14971;LSEQ=CTGGTGGCTTTCCGTCCTCC;RSEQ=GCTGGTTTGGGTGCTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:47:40,7:117,19:136,47:0.2568:2,2:23.2:1:32:1:1:1.07718:60:94:0.2626:0:1.1 0/1:143:7:5,2:117,19:136,7:0.049:2,2:19.7:1:30.4:1:0.27337:2.44297:60:14:0.0493:0:1 +19 3115124 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1974;LSEQ=CACTGAGAGGCTCATTTGCC;RSEQ=GGTGTGCCGGCTCATGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:271:168:50,118:33,68:101,168:0.6199:2,2:23:1:30.9:1:0.68291:1.14471:60:336:0.6222:0:1.1 0/1:284:69:18,51:67,146:213,69:0.243:2,2:20.3:1:28.9:1:0.45216:1.29905:60:68:0.2429:0:1.2 +19 3115141 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23005;SOR=Inf;LSEQ=GCCCGGTGTGCCGGCTCATG;RSEQ=CTGCGCACCCAGTGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:34,164:198,0:0:2,0:21.4:1:31.1:1:1:0:60:48.5:1:0:0.6 0/1:183:2:1,1:33,147:180,2:0.0109:2,2:22.5:1:27:1:0.33957:4.40:60:4:0.0113:0:1 +19 3115402 . C T 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGGGAGACCCTGTTT;RSEQ=GTCTTATTAAACAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:15.3:1:31.8:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 3118851 . G T 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=GGCAGGAGGGGCTTGGGTGG;RSEQ=AGCCGTCCTGGGATTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:20:18,2:208,19:227,20:0.081:2,2:27.9:1:29.3:1:0.68184:1.21534:60:40:0.0823:0:1.3 0/0:143:0:0,0:125,18:143,0:0:2,0:20.9:1:30.5:1:1:0:60:142:1:0:0.2 +19 3119184 . T G 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02344;LSEQ=GGAGGGCCCCTCTGATTCCC;RSEQ=CTGCCTTCGCTCCCGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:658:655:388,267:0,1:1,655:0.9954:0,2:24.7:1:30.4:1:0.40854:0:58.3:49.385:0.9969:0:1.3 1/1:605:506:291,215:52,46:98,506:0.8364:2,2:25:1:29.6:1:0.43672:1.20:57.9:35.143:0.8367:0:1.4 +19 3119239 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01867;SOR=1.26434;LSEQ=AGCAAAGCCCTGTTCCGGAC;RSEQ=ATCATCACCTACCCCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1002:278:141,137:382,340:722,278:0.2774:2,2:25.1:1:30.3:1:0.57197:1.09156:51.9:91.667:0.2795:0:1.6 0/1:976:319:173,146:354,303:657,319:0.3268:2,2:23.3:1:28.9:1:0.94546:1.01:50.9:105.333:0.3271:0:1.6 +19 3119365 . G C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCGAGTTCGATGGTGCGCC;RSEQ=GGCTGCGGCATGGGGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:556:0:0,0:192,363:555,0:0:2,0:24.6:1:30.3:1:1:0:59.9:41.692:0.9982:0:0.6 0/1:564:52:21,31:180,331:511,52:0.0922:2,2:24.8:1:29.7:1:0.4522:1.25:58.5:104:0.0937:0:1.5 +19 3119405 . T G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.33859;LSEQ=GCTCGCGGGCAGGGCCTTAC;RSEQ=GGGGGGAGGGGGCTGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:249:178:27,151:0,0:0,178:0.7149:0,2:24.4:1:31.2:1:1:0:59.8:88:0.7243:0:1.2 0/1:229:105:14,91:5,41:46,105:0.4585:2,2:25.4:1:30:1:0.7938:1.26:60:51.5:0.4578:0:1.3 +19 3119441 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50741;SOR=0;LSEQ=ATATGGGAGAGGGGCTCATA;RSEQ=AGGCCGGGAGCTCTAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:0,2:5,134:139,2:0.0142:1,0:29.5:1:28:1:1:0:60:4:0.0144:0:2 0/0:107:0:0,0:4,103:107,0:0:1,0:21.5:1:31.9:1:1:0:60:214:1:0:0.8 +19 3120511 . C T 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCCGGTGGGAAGCAGCG;RSEQ=CCCTGCTGGAGCCCCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:16:0:16:0:1:0:60:0:0:0:1 1/1:3:3:1,2:0,0:0,3:1:0,2:19:1:29.7:1:1:0:60:6:1:0:1.3 +19 3120739 . T G 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=CTGAGCAGAGGGAGCAGCGG;RSEQ=GGGTGCAGAGCCCCAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:24.4:1:30.4:1:1:0:54:10:0.5:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:30.5:1:1:0:60:4:1:0:1 +19 3121246 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52661;SOR=0;LSEQ=TTCCACGGAGCCTGCGGCTG;RSEQ=CGGGCGGGTGGCGCTGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:0,2:13,138:151,2:0.0131:2,0:22:1:32:0:1:0:60:4:0.0135:0:1 0/0:94:0:0,0:10,84:94,0:0:2,0:27.3:1:29.3:1:1:0:60:14.667:1:0:0.2 +19 3121260 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52841;SOR=0;LSEQ=CGGCTGCCGGGCGGGTGGCG;RSEQ=TGCCGAGTCCGGGCCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:8,121:129,2:0.0153:2,2:22:1:29.5:1:0.13318:14.31:60:4:0.0156:0:1 0/0:79:0:0,0:5,73:78,0:0:2,0:27.8:1:30.9:1:1:0:60:18.5:1:0:0.1 +19 3121299 . AT A 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01651;LSEQ=GCCTCTGCCCGCGGGAGGAG;RSEQ=TTTTTTTTTTCATATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:5:0,5:1,60:61,5:0.0758:1,0:25.8:1:33:1:1:0:60:10:0.0758:0:0.4 0/1:39:3:0,3:1,35:36,3:0.0769:1,0:24.7:1:28.9:1:1:0:60:6:0.0811:0.0256:0 +19 3121609 . T C 69 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCCCCACACCGCAGCCCCC;RSEQ=GTGGCTGTCCTTCCAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:30.2:1:29.8:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 3148552 . C G 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGTCGGGGGTGGGAGTCC;RSEQ=GTGGAGGGCTGAGCGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:68,5:73,0:0:2,0:25.2:1:31.4:1:1:0:60:72:1:0:0.1 0/1:62:21:20,1:39,2:41,21:0.3387:1,1:20.8:1:30:1:1:1.03:60:42:0.3443:0:1 +19 3148577 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24485;SOR=Inf;LSEQ=AGGGCTGAGCGGTTCTGCTG;RSEQ=TCCATCCCCAGGCCCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:86,36:122,0:0:2,0:23.1:1:32.2:1:1:0:60:39.667:1:0:0 0/1:120:2:1,1:87,31:118,2:0.0167:2,2:27:1:28.5:1:0.46387:2.77808:60:4:0.0168:0:1 +19 3148593 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22922;SOR=0;LSEQ=GCTGCTCCATCCCCAGGCCC;RSEQ=GGCGAGAGCGGGAAGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:103,59:162,2:0.0122:2,2:27:1:33:1:1:1.73945:60:4:0.0125:0:1 0/0:178:0:0,0:114,64:178,0:0:2,0:23:1:29.2:1:1:0:59.3:43.5:1:0:0.3 +19 3148631 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12758;SOR=Inf;LSEQ=CACCTTCATCAAGCAGATGC;RSEQ=GATCATCCACGGCGCCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:146,118:264,0:0:2,0:25.2:1:30.1:1:1:0:59.7:51.8:1:0:0.2 0/1:305:4:1,3:163,138:301,4:0.0131:2,2:27:1:29:1:0.33896:3.52983:60:8:0.0132:0:1 +19 3148656 . G T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1002;SOR=0;LSEQ=ATCCACGGCGCCGGCTACTC;RSEQ=GAGGAGGAGCGCAAGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:130,149:279,3:0.0106:2,2:23:1:25:1:1:1.74166:60:2:0.0072:0:1 0/0:324:0:0,0:153,170:323,0:0:2,0:26.5:1:29.6:1:1:0:58.6:106.667:0.9969:0:0.2 +19 3148708 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23663;SOR=Inf;LSEQ=TCTACCAGAACATCTTCGTG;RSEQ=CCATGCGGGCCATGATCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:60,119:179,0:0:2,0:23.9:1:29.5:1:1:0:60:34.8:1:0:0.2 0/1:171:2:1,1:59,110:169,2:0.0117:2,2:17:1:31.5:1:1:1.86:60:4:0.012:0:1 +19 3148740 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22583;SOR=Inf;LSEQ=ATGATCGAGGCCATGGAGCG;RSEQ=CTGCAGATTCCATTCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:19,71:90,0:0:2,0:22.6:1:31.9:1:1:0:60:44:1:0:0.1 0/1:82:2:1,1:13,67:80,2:0.0244:2,2:14:0:27:1:0.31406:5.00:60:4:0.0247:0:1 +19 3148746 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49664;SOR=Inf;LSEQ=GAGGCCATGGAGCGGCTGCA;RSEQ=ATTCCATTCAGCAGGCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:11,64:75,0:0:2,0:23.8:1:32.5:1:1:0:60:74:1:0:0.2 0/1:75:2:1,1:12,60:72,2:0.0267:2,2:29.5:1:30.5:1:0.32247:4.84:60:4:0.0267:0:1 +19 3148819 . G T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0017;SOR=22.00852;LSEQ=CCAGGGCAGGCAGGGGCCCA;RSEQ=GGCAGGGTTCCCCAGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:14,5:0.2632:1,0:43.8:1:31.2:1:1:0:60:10:0.2632:0:1 1/1:10:9:1,8:0,1:1,9:0.9:0,2:17.3:1:29.2:1:1:0:60:18:0.9:0:1.1 +19 3150418 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCTCCAGGATGAGGTC;RSEQ=TTCCAGGGGGACCCTAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:25.5:1:30:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 3779127 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50041;SOR=0;LSEQ=GACCAGGATGTTGCGGGCGG;RSEQ=CAGGTCGCGGTGCACAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:28,31:59,2:0.0328:2,2:26:1:29:1:1:1.11:60:4:0.0339:0:1 0/0:50:0:0,0:24,26:50,0:0:2,0:29.2:1:30.9:1:1:0:60:49:1:0:0.1 +19 3780533 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCCAGGTCACGCCATTC;RSEQ=CCTGCCTCAGCCTCCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:28.5:1:1:0:23:4:1:0:2.5 +19 4025041 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAATGCTGGGATTACAGG;RSEQ=GTGAGCCACTGCGCCTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:31:1:1:0:57:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 4025484 . C T 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCATGGCAGGGCTGGGC;RSEQ=GGGCGCCCCCATTTAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14:1:32.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:26:0:26:0:1:0:60:2:1:0:1 +19 4025616 . G A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21041;SOR=0;LSEQ=GTAAGGGTTCAGATCCAGCC;RSEQ=AGCCAGGCTTGGCCATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:15,8:0,0:0,23:1:0,2:23.4:1:29.4:1:1:0:60:46:1:0:1.2 1/1:20:18:12,6:1,1:2,18:0.9:2,2:24.9:1:30:1:1:1.93:58.6:36:0.9:0:1.1 +19 4025686 . C CGTCTTTCTCAGCCTT 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GACCTCGTCTTTCTCAGCCT;RSEQ=GTCTTCCTTGTCTATGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:8,16:0,0:0,24:1:0,2:27:1:31.3:1:1:0:59.8:48:1:0.3333:0.4 1/1:21:20:7,13:1,0:1,20:0.9524:0,2:23.8:1:29.6:1:0.38095:0:58.5:40:0.9524:0.4762:0.7 +19 4090113 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTCTCCTTCCTTTTGG;RSEQ=GAGAGCCGCCATCGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 4090422 . G T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.70494;LSEQ=AGAGGCACCCCGGCCAGGAC;RSEQ=GGCAGGAGAGGAGACCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:8:8,0:26,2:28,8:0.2222:2,0:18.5:1:32.5:1:1:0:41.6:16:0.2222:0:1.3 0/1:12:2:1,1:8,2:10,2:0.1667:2,2:45.5:1:32.5:1:0.45455:3.4638:58.5:4:0.1667:0:1 +19 4090530 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49794;SOR=0;LSEQ=CGCCAGCCTGTCCTCAGCTG;RSEQ=AAGGGCGGGGCATGGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:78,42:120,2:0.0164:2,2:20:1:28.5:1:1:1.84722:25:4:0.0169:0:1.5 0/0:122:0:0,0:85,37:122,0:0:2,0:18:1:30.4:1:1:0:50.8:39.667:1:0:0.3 +19 4090537 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=CTGTCCTCAGCTGGAAGGGC;RSEQ=GGGCATGGACAGGGACGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:100,56:156,2:0.0127:2,2:21.5:1:29:1:1:1.77872:41.5:4:0.0127:0:2 0/0:154:0:0,0:110,44:154,0:0:2,0:20.5:1:29.4:1:1:0:51.9:50.333:1:0:0.3 +19 4090563 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=TGGACAGGGACGGTGGGCAG;RSEQ=TCACCAGCGGGACGCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:185,87:272,0:0:2,0:26.9:1:31.9:1:1:0:53.8:67:1:0:0.2 0/1:279:3:1,2:193,83:276,3:0.0108:2,2:15:1:26:1:0.221:4.62176:38.7:6:0.0109:0:1.7 +19 4090572 . G A 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=ACGGTGGGCAGGTCACCAGC;RSEQ=GGACGCAGGGAGCCCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:212,99:311,0:0:2,0:26.6:1:30.6:1:1:0:54.2:50.833:1:0:0.2 0/1:337:13:11,2:224,98:322,13:0.0386:2,2:26.2:1:29.9:1:0.35836:2.40:37.2:26:0.0396:0:1 +19 4090622 . C T 72 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.35235;SOR=2.05664;LSEQ=GGCGGTGCGCGTGGGTGTGC;RSEQ=GGGCTGGTTCAGCCGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:593:3:0,3:346,243:589,3:0.0051:2,0:1:0:23:1:0.07124:0:60:2:0.0035:0:1 0/1:676:7:1,6:386,283:669,7:0.0104:2,2:11.6:1:26:1:0.04615:8.16156:58.4:14:0.0105:0:1 +19 4094110 . G T 46 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAGGGAAAGGAGCCTG;RSEQ=GGGGCTGAGAGCTGCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:29.3:1:29.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 4094375 . C T 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.78869;LSEQ=GCTCCCCGGGCAGGGCCAGG;RSEQ=CCAGCAGCCTTATTTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:1,2:208,90:298,3:0.01:2,2:8.3:1:27.7:1:0.22233:4.5958:60:6:0.0102:0:1 0/0:254:2:0,2:171,81:252,2:0.0079:2,0:1:0:23.5:1:0.10591:0:60:4:0.008:0:1 +19 4094555 . G A 64 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01695;SOR=Inf;LSEQ=GAGACAAGACAGGGCAGTCA;RSEQ=CTGGTGGCCCCGGGGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:159,240:399,0:0:2,0:25.8:1:32.3:1:1:0:59.9:56:1:0:0.2 0/1:461:7:6,1:178,276:454,7:0.0152:2,2:6.3:1:23:1:0.0179:9.26:60:6:0.0133:0:1.1 +19 4094587 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12341;SOR=Inf;LSEQ=GGGGCACCCGCGTGTGGGCC;RSEQ=TGGTCGGAGGGGGCCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:57,178:235,0:0:2,0:23.9:1:31.5:1:1:0:60:77.333:0.9957:0:0.1 0/1:235:3:2,1:56,176:232,3:0.0128:2,2:14.7:1:27.7:1:0.15146:6.22:60:6:0.013:0:1 +19 4094775 . G A 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GGTGGGTCAGAAGCCTGGAC;RSEQ=CAACCCCAGCTAACTGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:3,5:0.625:0,2:22:1:31.8:1:1:0:60:10:0.625:0:1.2 0/0:1:0:0,0:0,1:1,0:0:0,0:47:0:34:0:1:0:60:2:1:0:0 +19 4095290 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50886;SOR=0;LSEQ=TAACGCTGCACTGGGATTCT;RSEQ=GATGGGCAGGCTGGGCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:151,21:172,2:0.0115:2,2:23:1:30.5:1:0.23753:7.04831:60:4:0.0117:0:1 0/0:130:0:0,0:114,16:130,0:0:2,0:25:1:31.4:1:1:0:60:64:1:0:0.2 +19 4095506 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.22825;SOR=Inf;LSEQ=TCGTCAGGGACCCTCGGCTG;RSEQ=AGCCCTCTCTACCCCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:32,150:182,0:0:2,0:23.2:1:32.1:1:1:0:59.9:44.5:1:0:0.1 0/1:167:2:1,1:33,132:165,2:0.012:2,2:36:0:28:1:0.36671:3.96:60:4:0.0121:0:1 +19 4097231 . G A 39 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.20979;LSEQ=AAAAAAAAAAAAAAAAGAAA;RSEQ=AAGAAAGAAAAGGAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:4:4,0:97,65:162,4:0.024:2,0:21.5:1:25.5:1:0.15602:0:41.8:3:0.0201:0:4.8 0/1:208:6:6,0:105,95:200,6:0.0288:2,0:23.2:1:15.3:1:0.03177:0:44.2:0.2:0.0053:0:4.2 +19 4097234 . G A 56 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06605;SOR=0.28599;LSEQ=AAAAAAAAAAAAAGAAAGAA;RSEQ=AAAGAAAAGGAAAAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:8:8,0:110,71:181,8:0.0423:2,0:16.5:1:18.8:1:0.02587:0:41.8:0.6:0.0178:0:5 0/1:241:3:3,0:131,106:237,3:0.0124:2,0:15:1:21.3:1:0.25711:0:45.7:2:0.0091:0:4.3 +19 4099187 . T C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=23.88427;LSEQ=TCCAGACCGGAAGTTGCAGA;RSEQ=TCAGGCCGTACCGCTGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:176:116,60:179,98:277,176:0.3885:2,2:23.9:1:32.2:1:0.83983:1.06:59.8:43:0.3909:0:1.2 1/1:406:381:231,150:18,6:24,381:0.9384:2,2:25.1:1:30.8:1:0.19707:1.94511:59.9:26.214:0.9386:0:1.2 +19 4100970 . A G 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12237;SOR=Inf;LSEQ=GGGTGGGGAGAGCTTGGGGG;RSEQ=GAGCAGCAGGGAGGAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:215,69:284,0:0:2,0:24.2:1:29.9:1:1:0:59.9:34.5:0.9964:0:0.3 0/1:282:3:2,1:207,72:279,3:0.0106:2,2:29:1:24:1:1:1.4355:60:2:0.0074:0:1.3 +19 4101059 . G A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62371;SOR=2.98456;LSEQ=ACGAAGGAGTTGGCCATGGA;RSEQ=TCGATGAGCTGGCCGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:1,0:177,109:286,1:0.0035:2,0:1:0:29:0:1:0:60:2:0.0036:0:1 0/1:290:3:2,1:155,132:287,3:0.0103:2,2:17.3:1:28:1:1:1.70:43.3:6:0.0106:0:1.7 +19 4101062 . G T 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.05262;LSEQ=AAGGAGTTGGCCATGGAGTC;RSEQ=ATGAGCTGGCCGCTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:125:75,50:100,57:157,125:0.4433:2,2:19.1:1:29.9:1:0.5391:1.16893:41.3:61.5:0.4473:0:1.1 1/0:288:220:121,99:31,36:67,220:0.7639:2,2:18.9:1:28.3:1:0.26337:1.42:42.1:72.333:0.7668:0:1.2 +19 4101079 . C T 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.35769;SOR=3.2264;LSEQ=GTCGATGAGCTGGCCGCTCA;RSEQ=CCCGAAGTCACACAGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:1:0,1:142,150:292,1:0.0034:2,0:1:0:25:0:1:0:43:2:0.0035:0:1 0/1:274:3:1,2:138,132:270,3:0.0109:2,2:8.3:1:22:1:0.61681:2.08545:31:6:0.0112:0:1.3 +19 4101212 . C T 89 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.387;SOR=1.92123;LSEQ=CCCCGGGGCTCTGGGGAGGG;RSEQ=GGGCTGGGCCTTACCTCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:4:2,2:321,321:642,4:0.0062:2,2:9:1:29:1:1:1:55:8:0.0064:0:1 0/1:676:8:3,5:338,330:668,8:0.0118:2,2:24:1:29.9:1:0.50172:1.70573:57.5:16:0.0122:0:1.3 +19 4102132 . A C 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06061;SOR=0;LSEQ=GGGACCAGTGTGGCAAACAG;RSEQ=GGATACTAAGAGTGAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:24.2:1:29:1:1:0:59.5:5:0.7143:0:2.2 0/0:4:0:0,0:4,0:4,0:0:0,0:25.5:1:28:1:1:0:60:8:1:0:0 +19 4102294 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18967;SOR=Inf;LSEQ=ACCCCCACCACACTGTGAGT;RSEQ=GCTCCCGGAACCCTGGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:138,13:151,0:0:2,0:24.2:1:31.8:1:1:0:60:24.167:1:0:0.2 0/1:117:2:1,1:100,14:114,2:0.0171:2,2:9.5:1:28.5:1:0.24288:6.93504:60:4:0.0179:0:1.5 +19 4102310 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49937;SOR=0;LSEQ=GAGTGGCTCCCGGAACCCTG;RSEQ=CCGTGTGGAAGAGGTCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:153,28:181,2:0.0109:2,2:27:1:30.5:1:0.29256:5.38686:60:4:0.0114:0:1 0/0:169:0:0,0:140,29:169,0:0:2,0:23.4:1:30.5:1:1:0:60:32.8:1:0:0.2 +19 4102313 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11109;SOR=Inf;LSEQ=TGGCTCCCGGAACCCTGGCC;RSEQ=TGTGGAAGAGGTCCGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:167,35:202,0:0:2,0:23.8:1:29.8:1:1:0:60:39.4:1:0:0.2 0/1:188:3:1,2:149,36:185,3:0.016:2,2:17:1:28.3:1:0.1045:8.14739:60:6:0.0161:0:1 +19 4102330 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24868;SOR=0;LSEQ=GCCGTGTGGAAGAGGTCCGT;RSEQ=CAGAGTGCGGTGGGGGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:213,68:281,3:0.0106:2,2:17:1:28.3:1:0.1513:6.21404:60:6:0.0106:0:1 0/0:282:0:0,0:211,71:282,0:0:2,0:23.2:1:31.5:1:1:0:60:55.4:1:0:0.2 +19 4102338 . C T 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49404;SOR=0.5631;LSEQ=GAAGAGGTCCGTGCAGAGTG;RSEQ=GGTGGGGGCGCGATGTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:5:2,3:225,91:316,5:0.0156:2,2:17:1:28.4:1:0.15205:3.69164:60:10:0.0158:0:1.2 0/0:340:3:1,2:240,97:337,3:0.0088:2,2:15.3:1:25.7:1:0.20421:4.9217:60:6:0.0089:0:1 +19 4102449 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04035;LSEQ=ACCTGGTCCAGGGAGCCGCC;RSEQ=TCCTAGAGGGCACACAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:626:384:164,220:109,132:241,384:0.6134:2,2:26.8:1:30.5:1:0.56237:1.10754:51.5:53.857:0.619:0:1.1 0/1:700:42:17,25:288,370:658,42:0.06:2,2:29.7:1:29:1:0.74941:1.14444:52.2:20:0.0581:0:1.2 +19 4102486 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06065;SOR=Inf;LSEQ=AGGAGTGAGTGCAGGCTCTG;RSEQ=GCAGGTGGCCGGGAAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:100,271:371,0:0:2,0:23.9:1:30.5:1:1:0:59.9:122.667:1:0:0.6 0/1:367:4:2,2:112,250:362,4:0.0109:2,2:25:1:29:1:0.5915:2.23:60:8:0.011:0:1.3 +19 4102623 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07338;SOR=Inf;LSEQ=TCTTCTGACAGTTCTGCCTT;RSEQ=GGGTCTGAACACCCACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:2,37:39,0:0:2,0:23.8:1:29.5:1:1:0:59:18.5:1:0:0.3 0/1:15:2:0,2:2,11:13,2:0.1333:2,0:18.5:1:31:0:1:0:60:4:0.1333:0:1 +19 4110318 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=GCCTCTCAAAAAAACAAAAA;RSEQ=AAAACAAAACAAAACCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:15,1:16,2:0.1111:1,0:22.5:1:31.5:1:1:0:60:4:0.1111:0:1 0/0:11:0:0,0:11,0:11,0:0:0,0:19.3:1:33.2:1:1:0:60:22:1:0:0 +19 4110408 . T C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01744;SOR=4.60546;LSEQ=CCCTGGAAGCCAGCGCACTG;RSEQ=TGCCTCTGAGGAAAGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:4:4,0:81,1:82,4:0.0465:1,0:22.8:1:32.5:1:1:0:60:8:0.0465:0:1 0/1:54:10:10,0:43,1:44,10:0.1852:1,0:25.6:1:30.3:1:1:0:60:9:0.1698:0:1.2 +19 4112080 . T G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGGAGCAGCCTGAGGCT;RSEQ=TGGGACGGCACCCTGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:30:1:1:0:60:4:1:0:1 +19 4116162 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGTGATTAACCTTTAAAT;RSEQ=GGCAGACTCTGAGCAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 4117290 . T C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00115;SOR=0;LSEQ=TCAGGACCTAGAGTCCCTGG;RSEQ=GGGGATGAGGGACAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:83:83:83,0:0,0:0,83:1:0,1:24.4:1:32.3:1:1:0:60:40.5:1:0:1.1 1/1:54:47:46,1:7,0:7,47:0.8704:0,1:22.7:1:32.4:1:1:0:60:94:0.8704:0:1.2 +19 4117528 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27676;LSEQ=TCATCGTCTTTGAGTTCGCC;RSEQ=ACCTTGGCTTTCTGGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:74:47,27:109,124:233,74:0.241:2,2:35.4:1:30.6:1:0.01599:1.98:30.1:23.667:0.2336:0:1.1 0/1:310:25:14,11:141,144:285,25:0.0806:2,2:22.2:1:29.5:1:0.67732:1.30:38.2:50:0.0812:0:1.1 +19 4117681 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19717;SOR=Inf;LSEQ=CTAGGGAGACTCCATCTGGC;RSEQ=GTTTGCTATGTGGCCGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:18,213:231,0:0:2,0:24.2:1:30.3:1:1:0:60:45.2:1:0:0.7 0/1:185:2:0,2:31,152:183,2:0.0108:2,0:30.5:1:26:1:1:0:60:4:0.011:0:2 +19 4117690 . T A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.035;SOR=Inf;LSEQ=CTCCATCTGGCCGTTTGCTA;RSEQ=GTGGCCGTGGTGCATCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:13,191:204,0:0:2,0:23.5:1:30.6:1:1:0:60:50:1:0:0.8 0/1:157:4:2,2:20,133:153,4:0.0255:2,2:13.5:1:24:1:0.09461:6.52:60:3:0.0196:0:2.5 +19 4117695 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50946;SOR=0;LSEQ=TCTGGCCGTTTGCTATGTGG;RSEQ=CGTGGTGCATCGGCCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:8,174:182,2:0.0108:1,2:18:1:27:0:0.09569:20.56:60:4:0.011:0:2 0/0:138:0:0,0:15,123:138,0:0:2,0:21.4:1:30:1:1:0:60:18.714:1:0:0.9 +19 4117705 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03024;LSEQ=TGCTATGTGGCCGTGGTGCA;RSEQ=CGGCCCCCAGGAGGACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:147:1,146:0,0:0,147:0.9932:0,1:24.2:1:31.3:1:1:0:60:23.5:1:0:1.1 1/1:108:88:2,86:1,19:20,88:0.8148:1,1:21.3:1:29.5:1:0.46249:2.24198:60:13.667:0.8039:0:1.3 +19 4122876 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCATTATTGAGGGACCCT;RSEQ=ACCCCGTCTTTTCCTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:29.5:1:1:0:60:4:1:0:1 +19 4123543 . TCCGAGGGCCCCCTGCCCCGTCCTCCC T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCACCCTTCGCCCCGTCC;RSEQ=CCGAGGGCCCCCTGCCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:3,0:15,0:15,3:0.1667:1,0:8.3:1:32:1:1:0:34.3:6:0.1765:0.1667:1.7 0/0:5:0:0,0:4,1:5,0:0:2,0:21.8:1:30.6:1:1:0:50.2:10:1:0:1.6 +19 4123656 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07444;SOR=Inf;LSEQ=GCCCCGTGCACCACTCACCC;RSEQ=GTCCTCCCCCGTGACCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:83,1:84,0:0:1,0:21:1:31.6:1:1:0:59.5:83:1:0:1.4 0/1:62:3:3,0:58,1:59,3:0.0484:1,0:26.7:1:32.7:1:1:0:60:6:0.0484:0:1 +19 4123680 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20967;SOR=Inf;LSEQ=CTCCCCCGTGACCCCCCTGC;RSEQ=TCGTGCACTCCTCGCGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:121,11:132,0:0:2,0:23.5:1:31.6:1:1:0:60:65:1:0:0.7 0/1:112:2:1,1:100,10:110,2:0.0179:2,2:12.5:1:28.5:1:0.18758:9.58219:60:4:0.018:0:1 +19 4123693 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.5044;SOR=0;LSEQ=CCCCTGCCTCGTGCACTCCT;RSEQ=GCGAACCCCCGTCCCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:149,27:176,2:0.0112:2,2:24:1:27:1:0.29061:5.43732:59:4:0.0116:0:3 0/0:143:0:0,0:122,21:143,0:0:2,0:23.2:1:29.1:1:1:0:60:13.3:1:0:0.5 +19 5159183 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21427;SOR=0;LSEQ=GGCAAGTAATAGCAAGATGG;RSEQ=TGTCACGGGACCTAGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:112,83:195,2:0.0102:2,2:26.5:1:28.5:1:1:1.3473:29.5:4:0.0103:0:1 0/0:228:0:0,0:126,101:227,0:0:2,0:25.3:1:30.9:1:1:0:44.4:74.667:0.9956:0:0.2 +19 5159187 . C T 33 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31022;LSEQ=AGTAATAGCAAGATGGCTGT;RSEQ=ACGGGACCTAGAAAGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:2:0,2:120,95:215,2:0.0092:2,0:1:0:24.5:1:0.19867:0:36:4:0.0093:0:1.5 0/1:249:3:1,2:135,111:246,3:0.012:2,2:7.7:1:21:1:0.59194:2.42395:42.3:2:0.0081:0:1.3 +19 5159191 . G T 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.10223;LSEQ=ATAGCAAGATGGCTGTCACG;RSEQ=GACCTAGAAAGGGGAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:131,103:234,3:0.0127:2,2:15.3:1:28:1:0.58559:2.53385:26.3:6:0.0128:0:1 0/1:287:4:0,4:152,130:282,4:0.0139:2,0:1:0:25.5:1:0.04704:0:36.5:8:0.0144:0:1 +19 5159196 . T C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08449;SOR=0;LSEQ=AAGATGGCTGTCACGGGACC;RSEQ=AGAAAGGGGAAAAGCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:3:1,2:137,112:249,3:0.0119:2,2:22.3:1:32:1:0.59111:2.43794:40.7:6:0.012:0:1.3 0/0:321:0:0,0:171,150:321,0:0:2,0:23.8:1:28.5:1:1:0:41.9:63.2:1:0:0.2 +19 5159288 . G A 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93176;LSEQ=AGAAGCCTTTTCCTGTAAAC;RSEQ=CCAGGCGGCGTCTCCTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:43,93:136,2:0.0145:2,2:26.5:1:29:1:0.53761:2.15:52:4:0.0145:0:1 0/1:148:2:1,1:55,91:146,2:0.0135:2,2:26.5:1:29:1:1:1.65:41.5:4:0.0136:0:1 +19 5174025 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15239;SOR=Inf;LSEQ=TGAGGCAGGAGAATGGCGTG;RSEQ=ATCCAGGAGGCGGAGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:32,0:32,0:0:1,0:17.7:1:31.1:1:1:0:32.6:64:1:0:0.6 0/1:21:2:2,0:19,0:19,2:0.0952:1,0:8:1:31.5:1:1:0:47:4:0.0952:0:2 +19 5174030 . A G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.80439;SOR=0.79614;LSEQ=CAGGAGAATGGCGTGAATCC;RSEQ=GGAGGCGGAGCTTGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:20:20,0:17,0:17,20:0.5405:1,1:16.2:1:31.2:1:1:0:34.9:40:0.5405:0:1.1 0/1:29:14:14,0:15,0:15,14:0.4828:1,1:12.6:1:30.4:1:1:0:42.4:28:0.4828:0:1.1 +19 5174086 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.59276;LSEQ=CTGCACTCCAGCCTGGGCGA;RSEQ=ACTCCGTCTAAAAAACAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:120,54:174,2:0.0114:2,2:37.5:1:29.5:1:0.52857:2.21112:44.5:4:0.0114:0:1.5 0/0:148:1:0,1:102,45:147,1:0.0068:2,0:1:0:22:0:0.31081:0:60:2:0.0068:0:1 +19 5174098 . AAAAC A 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.19376;SOR=4.51575;LSEQ=CTGGGCGAGACTCCGTCTAA;RSEQ=AAACAAACAAACAAAACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:0,1:161,96:257,1:0.0039:2,0:45:0:33:0:0.37597:0:60:2:0.0039:0:0 0/1:231:4:3,1:148,79:227,4:0.0173:2,2:16.8:1:31.2:1:1:1.60:60:8:0.0175:0.0087:0.3 +19 5174101 . A T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.25095;SOR=0;LSEQ=GGCGAGACTCCGTCTAAAAA;RSEQ=CAAACAAACAAACAAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:3:0,3:164,102:266,3:0.0111:2,0:8:1:22.3:1:0.05843:0:60:2:0.0075:0:1.3 0/0:241:0:0,0:156,83:239,0:0:2,0:20.4:1:29.1:1:1:0:58.5:238:1:0:0.5 +19 5174132 . CT C 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.12002;SOR=5.14898;LSEQ=AACAAAACACGTATAAGCAC;RSEQ=TTTTCCAGGAATGCCAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:1,0:217,174:391,1:0.0026:2,0:47:0:34:0:1:0:60:2:0.0026:0:0 0/1:384:5:2,3:204,174:378,5:0.013:2,2:15.8:1:31.2:1:0.66571:1.75602:60:10:0.0133:0.0026:1 +19 5174155 . C T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00758;SOR=Inf;LSEQ=TTTCCAGGAATGCCAACATC;RSEQ=TTCCAAGGGAAAAGAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:213,219:432,0:0:2,0:26.4:1:32.4:1:1:0:59.9:60.714:1:0:0.6 0/1:440:8:3,5:216,216:432,8:0.0182:2,2:27:1:29:1:0.72407:1.66476:59.4:16:0.0185:0:2 +19 5174180 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=0.5865;LSEQ=AAGGGAAAAGAGCAAAGTCT;RSEQ=GTCACCACGGTCCAGCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:365:235:98,137:58,71:129,235:0.6438:2,2:26.1:1:30.4:1:0.58062:1.14157:60:77.333:0.6427:0:1.1 1/0:381:196:84,112:81,102:183,196:0.5144:2,2:24.2:1:29.2:1:0.83589:1.05864:60:195:0.5145:0:1.2 +19 5174221 . T A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.52588;LSEQ=CCTACAGCTGATGAGGGTGA;RSEQ=GGAGCTGCTGTAATGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:50,139:189,2:0.0105:2,2:8.5:1:30.5:1:0.46376:2.76:60:4:0.0106:0:2 0/0:181:1:1,0:49,131:180,1:0.0055:2,0:1:0:25:0:0.27624:0:60:2:0.0056:0:1 +19 5174304 . G A 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0069;SOR=0;LSEQ=TTTGCTGAATAAAGCAGTGT;RSEQ=GGATTTGTGGTTCCCGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:9:0,9:0,22:22,9:0.2903:1,0:28.3:1:29.2:1:1:0:60:8:0.2667:0:1.7 0/0:22:0:0,0:2,20:22,0:0:2,0:19.5:1:29:1:1:0:60:10:1:0:0.1 +19 5206724 . C A 203 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTCCAGGCCTCAGGAGGTC;RSEQ=GCCCGGGAGGGGCAGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:101:77,24:180,36:216,101:0.3186:2,2:24:1:30.6:1:0.1656:1.55619:59.9:202:0.3248:0:1.7 0/0:303:0:0,0:233,70:303,0:0:2,0:24:1:29.6:1:1:0:60:49.5:1:0:0.7 +19 5206775 . A G 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09156;LSEQ=GTGGTGTCGGGCCTGGGGGG;RSEQ=ACCATGGCTTTAGGTTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:735:724:424,300:0,0:0,724:0.985:0,2:26.7:1:31.1:1:1:0:59.9:33.476:0.9874:0:1.2 1/1:744:638:361,277:55,50:105,638:0.8575:2,2:26.1:1:30.2:1:0.45818:1.18:59.9:44.571:0.8583:0:1.2 +19 5207183 . T C 100 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGGCTCCCTGCAACCTCTG;RSEQ=CTCCTGGGTTCAAGTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:26.8:1:31.8:1:1:0:34.2:18:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 5207878 . T A 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAGGAGGAAACTGGAGCT;RSEQ=AGGGGCAGTCGGGGCGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:294,108:402,0:0:2,0:21.7:1:30.1:1:1:0:59.9:66:1:0:0.1 0/1:365:23:16,7:259,82:341,23:0.063:2,2:23.6:1:28.1:1:0.46154:1.38055:60:46:0.0635:0:1.1 +19 5208110 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09234;SOR=Inf;LSEQ=CAGCCATTCAGGGGCAGGTG;RSEQ=TGGGGAGCCCTGATCTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:112,219:331,0:0:2,0:24.5:1:32.2:1:1:0:60:24.462:1:0:0.1 0/1:274:3:1,2:90,181:271,3:0.0109:2,2:16:1:31:0:1:1.01:60:6:0.0112:0:1 +19 5208115 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08305;SOR=Inf;LSEQ=ATTCAGGGGCAGGTGCTGGG;RSEQ=AGCCCTGATCTGACCACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:113,210:323,0:0:2,0:24.2:1:31.3:1:1:0:60:23.846:1:0:0.1 0/1:251:3:2,1:82,166:248,3:0.012:2,2:8.7:1:25.7:1:0.26014:4.02:60:6:0.0122:0:1 +19 5208202 . A G 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04804;SOR=Inf;LSEQ=GGCTGTCCCCACCAGGCCTC;RSEQ=GTTTCCCCAGCAGGGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:258,164:422,0:0:2,0:23.2:1:30.8:1:1:0:59.8:51.75:1:0:1.1 0/1:373:4:2,2:251,118:369,4:0.0107:2,2:34.3:1:29.3:1:0.59672:2.12245:60:8:0.0108:0:1 +19 5208216 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07001;LSEQ=GGCCTCAGTTTCCCCAGCAG;RSEQ=GCCAAAAGCTGGGACACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:486:249:151,98:139,94:233,249:0.5123:2,2:24.8:1:30.4:1:0.85257:1.04:59.8:40.5:0.5137:0:2 0/1:483:33:21,12:284,164:448,33:0.0683:2,2:23.2:1:27.7:1:1:1.01:60:66:0.0689:0:1.8 +19 5208236 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18739;LSEQ=GGCCAAAAGCTGGGACACTC;RSEQ=AGGGAGCTCACCTGCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:635:330:191,139:174,130:304,330:0.5197:2,2:23.9:1:30.1:1:0.87261:1.03:59.8:54:0.5184:0:1.8 0/1:683:115:69,46:330,237:567,115:0.1684:2,2:19.7:1:29.6:1:0.75621:1.08:59.8:230:0.1704:0:1.3 +19 5208257 . A T 170 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01616;LSEQ=AGGGAGCTCACCTGCAGTGG;RSEQ=CAGAGATGGGGCCGTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:796:54:33,21:395,347:742,54:0.0678:2,2:25.8:1:29.7:1:0.32252:1.38:60:108:0.0693:0:1.1 0/0:853:1:0,1:458,394:852,1:0.0012:2,0:1:0:25:0:0.46307:0:60:2:0.0012:0:1 +19 5208471 . C T 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00732;SOR=Inf;LSEQ=GGGGTTTTTCTCCATCCTCC;RSEQ=TATCTTCACCCCCATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:33,187:220,0:0:2,0:22.4:1:32.6:1:1:0:60:54:0.9954:0:0.1 0/1:221:8:2,6:42,170:212,8:0.0362:2,2:15.8:1:30.9:1:0.66178:1.35:59.3:16:0.0364:0:1.3 +19 5208488 . TTTTG T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.21822;SOR=Inf;LSEQ=TCCCTATCTTCACCCCCATT;RSEQ=TTTGTTTGTTTGTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:17,133:150,0:0:2,0:23.4:1:30.3:1:1:0:59.3:149:1:0:0.1 0/1:132:2:0,2:12,118:130,2:0.0152:2,0:10.5:1:31:1:1:0:53.5:4:0.0153:0.0076:0.5 +19 5208514 . TG T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1036;LSEQ=TTGTTTGTTTGTTTTTGAGA;RSEQ=GAGTTTCACTCTTGTCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:44:0,44:1,53:54,44:0.449:1,1:26.8:1:32.3:1:1:0:55.2:88:0.4536:0.0816:0.2 0/1:65:5:1,4:0,60:60,5:0.0769:1,2:28.4:1:31.6:1:0.07692:0:60:10:0.0769:0.0154:0.2 +19 5208588 . G A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0167;SOR=Inf;LSEQ=CTGCAACCTCCACCTCCAGT;RSEQ=ATTCAAGTAATTCTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:29,0:0:1,0:24.6:1:31.9:1:1:0:48.1:28:1:0:0.2 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:15.3:1:32.3:1:1:0:49.3:6:0.2727:0:1 +19 5210622 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23206;LSEQ=TCTCCTGTGGAGGAGATGGC;RSEQ=GCCGTGGTCAGCGCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:209:127,82:115,98:213,209:0.4953:2,2:22.6:1:31.1:1:0.16914:1.32:60:68.667:0.4964:0:1.1 0/1:405:75:37,38:172,157:329,75:0.1852:2,2:21.9:1:30:1:0.70143:1.12482:60:74:0.1845:0:1.1 +19 5210782 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22772;LSEQ=GTCTTCCGTGGTCTCCGCCA;RSEQ=CGGCCCCTGTGTCGCGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:775:401:171,230:161,212:373,401:0.5174:2,2:25.8:1:29.2:1:0.88474:1.02144:60:27.643:0.5119:0:1.2 0/1:918:180:79,101:322,416:738,180:0.1961:2,2:25.5:1:28.8:1:1:1.01:60:59:0.1947:0:1.2 +19 5211335 . T A 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.23609;LSEQ=GTACTCATGAAAATAAGAAA;RSEQ=ATCCTCAGGGTGTCAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:28.5:1:29:1:1:1.41418:60:4:0.2857:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:16:0:31:0:1:0:60:2:0.5:0:1 +19 5211551 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22953;SOR=Inf;LSEQ=ACTGGAGGCCTCTTGAGAGT;RSEQ=GAGATGGGCTCCTTCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:176,42:218,0:0:2,0:24.3:1:28.8:1:1:0:59.9:108:1:0:0.4 0/1:201:2:1,1:148,51:199,2:0.01:2,2:43:0:31:0:0.45144:2.88361:60:4:0.01:0:1.5 +19 5211552 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22497;SOR=Inf;LSEQ=CTGGAGGCCTCTTGAGAGTA;RSEQ=AGATGGGCTCCTTCTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:177,43:220,0:0:2,0:24.4:1:32.8:1:1:0:59.9:72.333:1:0:0.4 0/1:199:2:1,1:146,51:197,2:0.0101:2,2:28.5:1:28.5:1:0.45531:2.84478:60:4:0.0104:0:1 +19 5211568 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.30728;SOR=1.19892;LSEQ=AGTAGAGATGGGCTCCTTCT;RSEQ=GGGCCCTGAGGTGGGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:126:90,36:122,50:172,126:0.4228:2,2:21.5:1:28.4:1:1:1.02:59.9:30.5:0.4192:0:1.1 0/1:263:123:81,42:92,45:137,123:0.4677:2,2:22.7:1:28.2:1:0.89541:1.05982:60:60.5:0.4727:0:1.2 +19 5211870 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52028;SOR=0;LSEQ=GGTGGATAGGTAGGTAGGGG;RSEQ=ACCCTGCCACCACCTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:75,120:195,2:0.0102:2,2:25:1:28.5:1:1:1.60:60:4:0.0102:0:1 0/0:129:0:0,0:54,75:129,0:0:2,0:22.3:1:31.8:1:1:0:60:42:1:0:0.1 +19 5211884 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16911;SOR=Inf;LSEQ=TAGGGGCACCCTGCCACCAC;RSEQ=TCTAGTCCCCATTGCTCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:98,96:194,0:0:2,0:24.3:1:31.7:1:1:0:60:193:1:0:0.1 0/1:136:2:1,1:74,60:134,2:0.0147:2,2:12:1:29:1:1:1.23141:60:4:0.0148:0:0 +19 5211967 . C T 144 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.30912;LSEQ=GCCCACAGCAGCCTCCACCC;RSEQ=GCTGGCACCTTGAACTCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:1:0,1:239,155:394,1:0.0025:2,0:45:0:13:0:0.39494:0:60:0:0:0:1 0/1:392:28:17,11:220,144:364,28:0.0714:2,2:28.9:1:30:1:1:1.01:60:56:0.072:0:1.1 +19 5212209 . G A 75 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07253;SOR=6.33838;LSEQ=TGTCTTCTCTGGCTTGATCC;RSEQ=CTCAAGCATGGCGTCGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:1,0:216,318:534,1:0.0019:2,0:21:0:26:0:0.40561:0:60:2:0.0019:0:1 0/1:596:7:5,2:265,323:588,7:0.0117:2,2:13.3:1:26.9:1:0.25399:3.04:60:14:0.0119:0:1 +19 5212230 . C T 62 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03085;SOR=Inf;LSEQ=CTCAAGCATGGCGTCGATGA;RSEQ=GATAAAGCAGCCTGTGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:200,257:457,0:0:2,0:23.6:1:30.8:1:1:0:60:64.286:1:0:0.1 0/1:471:6:2,4:207,258:465,6:0.0127:2,2:31:1:24:1:0.69739:1.6031:55.7:2:0.0086:0:2.2 +19 5212311 . G A 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGCTGGGCTGCGGGGACC;RSEQ=GGGGGAAGCGGATGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:225,179:404,0:0:2,0:21.9:1:30.2:1:1:0:59.9:79.8:1:0:0.3 0/1:364:38:21,17:165,158:323,38:0.1044:2,2:20.4:1:29.1:1:0.73202:1.18:60:37:0.1036:0:1.5 +19 5212380 . C T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.30681;LSEQ=ACGATGGGGCCGGCATCTGG;RSEQ=GGGTTGCAGGTCTTGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:720:393:214,179:162,164:326,393:0.5458:2,2:26:1:29.9:1:0.23016:1.21:59.9:48.125:0.5461:0:1.2 0/1:780:210:112,98:308,262:570,210:0.2692:2,2:25:1:28.5:1:0.87167:1.0286:59.9:41:0.2701:0:1.3 +19 5212482 . G A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03134;LSEQ=AACTGGAACTGGCGGACCTC;RSEQ=CGTTTCTCACTGGAGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:720:419:194,225:145,156:301,419:0.5819:2,2:25.9:1:30.1:1:0.64995:1.0779:60:68.833:0.5817:0:1.2 0/1:767:32:16,16:343,392:735,32:0.0417:2,2:25.3:1:28.9:1:0.72149:1.14:60:64:0.0422:0:1.2 +19 5212571 . G A 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00173;SOR=Inf;LSEQ=CATGTGCTGAAGATGCCCAA;RSEQ=TGGCCGGGTGTGGTGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:39,190:229,0:0:2,0:22.1:1:32.1:1:1:0:57.3:31.714:1:0:0.6 0/1:192:8:3,5:37,146:183,8:0.0417:2,2:18.6:1:27.3:1:0.36749:2.35:51.9:7:0.0372:0:1 +19 5212584 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19396;SOR=Inf;LSEQ=TGCCCAAGTGGCCGGGTGTG;RSEQ=TGGCTCATGCCTGTTATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:13,149:162,0:0:2,0:23.1:1:32.4:1:1:0:54.5:53:1:0:0.6 0/1:128:2:1,1:12,114:126,2:0.0156:2,2:25:1:29:1:0.19353:9.17:59.5:4:0.0157:0:2 +19 5212586 . G T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05347;LSEQ=CCCAAGTGGCCGGGTGTGGT;RSEQ=GCTCATGCCTGTTATCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:153:78:4,74:5,70:75,78:0.5098:2,2:23.5:1:31.2:1:0.74241:1.31902:55.7:156:0.5132:0:1.1 0/1:115:6:1,5:8,101:109,6:0.0522:2,2:21:1:30.5:1:0.39372:2.50:59.8:12:0.0536:0:1.3 +19 5212680 . C T 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=GCCTGACCAACATGGAGAAA;RSEQ=CTCGTCTCAACTAAAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:9,5:0.3571:0,0:24.4:1:29.2:1:1:0:24.6:10:0.3571:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:26.7:1:31.3:1:1:0:26:6:1:0:0 +19 5212853 . C CA 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAAACTCCATCT;RSEQ=AAAAAAAAAAACACCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:26.5:1:1:0:48:4:1:0:2 +19 5212923 . T C 44 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGACTTGGGCTCTAGC;RSEQ=GGCCCTGGACGGTTTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:33.7:1:28:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:8:0:29:0:1:0:60:2:1:0:2 +19 5214116 . A G 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.11111;SOR=0;LSEQ=GGGCATGAGTAAAGGCAAGA;RSEQ=GAAATCAGGCTCATTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:23.9:1:34:1:1:0:60:16:1:0:1.8 0/0:1:0:0,0:0,1:1,0:0:0,0:10:0:32:0:1:0:60:2:1:0:0 +19 5214158 . T C 135 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04135;SOR=0.04344;LSEQ=TTGGGCTCTGCCGGCTTTGT;RSEQ=CTCCTGCCGTGGGTGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:17,0:1,0:1,17:0.9444:0,1:28.1:1:33.2:1:1:0:60:34:0.9444:0:1.4 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:30:0:32:0:1:0:60:2:0.3333:0:1 +19 5214258 . C T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00067;SOR=Inf;LSEQ=GTAGTCAGCCTGGGTAGACA;RSEQ=GCTCCGCTTTCTCTCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:99,2:101,0:0:1,0:23.4:1:32.2:1:1:0:60:49.5:1:0:0.1 0/1:58:7:7,0:47,4:51,7:0.1207:2,0:27:1:31:1:1:0:60:14:0.1228:0:2.1 +19 5214264 . G A 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=AGCCTGGGTAGACACGCTCC;RSEQ=CTTTCTCTCTGTCCCATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:119,3:122,0:0:1,0:22.8:1:30.2:1:1:0:60:121:1:0:0.1 0/1:70:8:8,0:58,4:62,8:0.1143:2,0:26:1:29.6:1:1:0:60:16:0.1143:0:2 +19 5214533 . A G 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14434;LSEQ=GTGTCAGCAGGGACAGGCTG;RSEQ=CTGGCAGGGGCTTGAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:678:644:340,304:16,17:33,644:0.9499:2,2:24.8:1:31.3:1:0.72158:1.19:60:28.273:0.9482:0:1.1 1/0:720:527:271,256:98,94:192,527:0.7319:2,2:23.4:1:30.4:1:0.93301:1.02:60:39.538:0.7301:0:1.2 +19 5214689 . G A 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGCGTGGCAATGTACGC;RSEQ=TTCTGACACCGGTAGCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:753:0:0,0:336,416:752,0:0:2,0:23.4:1:31:1:1:0:60:74.2:0.9987:0:1 0/1:776:43:20,23:326,407:733,43:0.0554:2,2:22.2:1:29.5:1:0.87489:1.09:60:42:0.055:0:2 +19 5214697 . A G 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11753;SOR=5.21931;LSEQ=GGCAATGTACGCGTTCTGAC;RSEQ=CCGGTAGCCGTCCACGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:695:690:296,394:4,0:4,690:0.9928:0,2:24.3:1:31:1:0.03452:0:60:56.5:0.9927:0:1.1 1/1:722:721:309,412:1,0:1,721:0.9986:0,2:24.7:1:30.3:1:0.42936:0:60:54.462:0.9986:0:1.2 +19 5214873 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08807;SOR=Inf;LSEQ=TCCCCAAGGTGACCATGGGA;RSEQ=GTGTACTTCACAGTTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:2,75:77,0:0:1,0:23.8:1:29.8:1:1:0:60:37.5:1:0:0.4 0/1:33:2:0,2:0,31:31,2:0.0606:1,0:21:1:27.5:1:1:0:60:4:0.0645:0:1 +19 5214904 . C T 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=0;LSEQ=CAGTTTCTCCCCCTCAGCGC;RSEQ=ATCACCATTTGGGGCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:19:1,18:1,19:20,19:0.4872:1,1:19.1:1:28.9:1:1:1.05:60:38:0.5:0:1.1 0/0:15:0:0,0:0,15:15,0:0:1,0:27.3:1:31.9:1:1:0:60:30:1:0:0.2 +19 5214986 . G A 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03251;SOR=0;LSEQ=GAGCAGCATCCCTGGCCTCC;RSEQ=CCCACTCCACGCCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:5,4:1,4:5,9:0.6429:2,2:30.2:1:30.2:1:0.3007:4.45:60:18:0.75:0:1.1 0/0:5:0:0,0:1,4:5,0:0:2,0:26:1:32.2:1:1:0:60:10:1:0:0.4 +19 5215040 . T G 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AGTTGTGACAACCAAAGATG;RSEQ=CCCTGGACATTGCCAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:4,1:5,3:8,5:0.3846:2,2:31.6:1:32.6:1:1:2.25:60:10:0.3846:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:33:0:33:0:1:0:60:2:1:0:1 +19 5215472 . C T 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=87.1684;LSEQ=CAGGGTAGGTGCCTGTGAGG;RSEQ=CGAGGTGATGAGGGTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:548:1:0,1:272,274:546,1:0.0018:2,0:30:0:32:0:1:0:60:2:0.0019:0:1 0/1:610:84:44,40:285,240:525,84:0.1377:2,2:26.2:1:28.4:1:0.81377:1.07941:60:41:0.1383:0:1.1 +19 5215474 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07902;LSEQ=GGGTAGGTGCCTGTGAGGCC;RSEQ=AGGTGATGAGGGTGGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:554:284:142,142:138,132:270,284:0.5126:2,2:24.3:1:30.3:1:0.79935:1.0454:59.9:34.5:0.5102:0:1.1 0/1:627:48:28,20:313,265:578,48:0.0766:2,2:25.9:1:30.3:1:0.65182:1.18:58.7:47:0.0768:0:1.1 +19 5215662 . C A 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12169;SOR=0;LSEQ=CTTGGGGGGCCAGCCGGGGA;RSEQ=TCGGGGGAGGGGGGTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:3:2,1:30,135:165,3:0.0179:2,2:12:1:21.7:1:0.09329:8.83:60:2:0.0127:0:2.7 0/0:170:0:0,0:30,136:166,0:0:2,0:37:0:18:0:1:0:60:0:0:0:6 +19 5215826 . T G 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGCAGCAGGTTTGAGGCCC;RSEQ=CTGCTCCGTGCAGAGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:1,9:0,1:1,10:0.9091:0,2:24.3:1:33.5:1:1:0:60:20:0.9091:0:1.2 1/1:2:2:0,2:0,0:0,2:1:0,0:37:1:32:1:1:0:60:4:1:0:1 +19 5216248 . T C 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTATCCTTTCAAGCCCCC;RSEQ=AGGATGGCTGCCGAAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:34.7:1:30.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 5216514 . ACACATACACAC A 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=CTCACCCACATCCCTGACAC;RSEQ=CACACACACAGCAGTCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:49,4:53,0:0:2,0:24.3:1:32.8:1:1:0:60:106:1:0:0 0/1:26:9:9,0:16,1:17,9:0.3462:1,0:29.6:1:31.8:1:1:0:60:18:0.36:0:0.2 +19 5216574 . C A 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00188;SOR=Inf;LSEQ=CTGAGGGCCCAATGGACCAA;RSEQ=CCCCTGCCCTCTTCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:111,5:116,0:0:1,0:24.2:1:32:1:1:0:59.8:115:1:0:0.2 0/1:83:7:5,2:73,2:75,7:0.0843:1,2:26.4:1:30.9:1:0.03484:13.51722:60:14:0.0854:0:1.1 +19 5216632 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12383;SOR=Inf;LSEQ=GGCAAAGGCCGGTGATGGGT;RSEQ=GGCGTGTGGACAGAGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:256,58:314,0:0:2,0:22.1:1:32:1:1:0:60:38.25:1:0:0.2 0/1:317:4:2,2:253,60:313,4:0.0126:2,2:22:1:27.8:1:0.17305:4.19049:60:8:0.0127:0:1 +19 5216635 . C T 56 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37317;SOR=0.24899;LSEQ=AAAGGCCGGTGATGGGTGGG;RSEQ=GTGTGGACAGAGACAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:4:1,3:266,72:338,4:0.0117:2,2:5.5:1:28:1:0.03436:10.97733:60:8:0.0121:0:1 0/0:341:1:0,1:264,75:339,1:0.0029:2,0:1:0:25:0:0.22353:0:60:2:0.003:0:1 +19 5216821 . TA T 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGAAAACATGCAGGGGG;RSEQ=GGGGGGGGTCCCACCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:38,174:212,0:0:2,0:23.4:1:30.8:1:1:0:60:22.556:1:0:0.3 0/1:245:36:10,26:49,154:203,36:0.1469:2,2:23.5:1:29.9:1:0.6762:1.21:60:35:0.1458:0.0327:0.3 +19 5216822 . AG A 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.76185;SOR=0.7261;LSEQ=AATGAAAACATGCAGGGGGT;RSEQ=GGGGGGGTCCCACCTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:6:1,5:34,168:202,6:0.0288:2,2:27.7:1:31.9:1:1:1.01185:60:12:0.0291:0.0048:0.2 0/1:237:5:2,3:54,176:230,5:0.0211:2,2:33:1:29.4:1:0.59526:2.16:59:10:0.0216:0:0.2 +19 5216896 . C CG 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.09552;SOR=2.15406;LSEQ=GGGCAGAGCAACGCGGACAA;RSEQ=GGGGGGTATGTACAGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:20:0,20:1,32:33,20:0.3704:1,1:29.6:1:31.9:1:1:0:60:40:0.3846:0.037:0.1 1/0:41:23:0,23:0,18:18,23:0.561:1,1:23.1:1:31.3:1:1:0:59.8:46:0.561:0.0488:0.3 +19 5217759 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGAACCCATAAGGAGAA;RSEQ=AGCAGCCATCAGTAAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:30:1:1:0:60:4:1:0:1 +19 5218213 . T TA 67 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGGTTAAATGTTAACTT;RSEQ=AAAAAAAAAAAAGCCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:5,0:10,0:10,5:0.2941:0,0:19.6:1:29.2:1:1:0:60:10:0.2941:0.1176:0.8 0/0:2:0:0,0:2,0:2,0:0:0,0:17.5:1:32:0:1:0:60:4:1:0:0.5 +19 5218214 . A T 48 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGGTTAAATGTTAACTTT;RSEQ=AAAAAAAAAAAGCCTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:3,0:14,0:14,3:0.1667:1,0:7.3:1:30.3:1:1:0:60:6:0.1667:0:1.3 0/0:3:0:0,0:3,0:3,0:0:0,0:12:1:23.7:1:1:0:60:2:1:0:0.3 +19 5218659 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12737;SOR=Inf;LSEQ=CCATGGACCCGTATGACTAG;RSEQ=GTTTCCAGGACCAAGTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:139,134:273,0:0:2,0:23.7:1:31.7:1:1:0:59.9:67.25:1:0:0.3 0/1:152:2:1,1:88,62:150,2:0.0132:2,2:7.5:1:27:1:1:1.416:60:4:0.0132:0:1 +19 5218684 . G A 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CCAGGACCAAGTACAGCTAC;RSEQ=TGTACAAGCTGTGGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:88:60,28:132,67:199,88:0.3056:2,2:28.3:1:30.9:1:0.78714:1.09:60:176:0.3088:0:1 0/0:194:0:0,0:137,57:194,0:0:2,0:22.5:1:29.5:1:1:0:60:193:1:0:0.1 +19 5218836 . G A 163 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=51.02659;LSEQ=CCGAAAGCAGACACAGGTGA;RSEQ=AAGGGGGAAAAAAAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:1:1,0:281,398:679,1:0.0015:2,0:1:0:30:0:0.41471:0:60:2:0.0015:0:1 0/1:743:52:22,30:298,393:691,52:0.07:2,2:23.3:1:28.7:1:1:1.03396:60:51:0.0699:0:1.1 +19 5219493 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.05612;SOR=0;LSEQ=AAAGGTCTGCAGGGAAAGGA;RSEQ=GGGGGTCTCCATCAGTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:4:2,2:97,273:370,4:0.0106:2,2:22.5:1:25.3:1:0.28628:2.81:60:3:0.0082:0:1.3 0/0:396:0:0,0:117,279:396,0:0:2,0:24.2:1:30.5:1:1:0:59.9:131:1:0:0.1 +19 5219803 . T C 110 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=32.86214;LSEQ=AAGAAACCTTCGTTTCAGGA;RSEQ=CCCTCCGCTCCCAAGTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:2,0:39,3:42,2:0.0455:2,0:34:0:34:0:1:0:60:4:0.0513:0:2 1/0:19:12:12,0:7,0:7,12:0.6316:0,0:22.8:1:30.8:1:1:0:60:24:0.6316:0:1.8 +19 5219829 . T G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.32148;LSEQ=CGCTCCCAAGTCTTCCCCTC;RSEQ=GCCCAGCTCTGACCACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:5:5,0:63,2:65,5:0.0714:1,0:20.4:1:26.6:1:1:0:60:4:0.058:0:1.4 1/0:35:18:18,0:15,2:17,18:0.5143:2,1:26.2:1:28.8:1:0.22857:0:60:17:0.5152:0:1.6 +19 5219852 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52174;SOR=0;LSEQ=CCAGCTCTGACCACAGGGAG;RSEQ=TGCCTGTGACTGACCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:89,8:97,2:0.0202:2,2:24.5:1:27.5:1:0.1744:10.54764:60:4:0.0204:0:1 0/0:63:0:0,0:54,9:63,0:0:2,0:20.8:1:31:1:1:0:60:62:1:0:0.4 +19 5219891 . TG T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49862;SOR=0;LSEQ=GAGGTCAGGGCCCTGGGGAA;RSEQ=GGGTCTGCCTCATTCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:129,47:176,2:0.0112:2,2:41:1:31:1:0.46772:2.72645:60:4:0.0115:0:1 0/0:175:0:0,0:124,47:171,0:0:2,0:22.2:1:31.3:1:1:0:60:342:0.9771:0:0.1 +19 5219897 . C T 26 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.5089;LSEQ=AGGGCCCTGGGGAATGGGGT;RSEQ=TGCCTCATTCAGAGGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:0,2:135,55:190,2:0.0104:2,0:17.5:1:26:0:0.08704:0:60:4:0.0106:0:1 0/0:188:1:0,1:134,53:187,1:0.0053:2,0:1:0:26:0:0.28723:0:60:2:0.0053:0:1 +19 5220003 . G A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03441;SOR=Inf;LSEQ=GAGGACATAGCGGTGGCCGG;RSEQ=CTCCAGGCCCCGGTTATCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:245,195:440,0:0:2,0:24.8:1:31.2:1:1:0:59.9:32.846:1:0:0.1 0/1:525:6:4,2:275,244:519,6:0.0114:2,2:11.5:1:26.7:1:0.68944:1.77:60:12:0.0117:0:1 +19 5220134 . C T 57 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01908;SOR=0;LSEQ=GACGCGAGTGCCGCAGGCTG;RSEQ=GCCTCTGTAGCCGTGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:5:2,3:146,174:320,5:0.0154:2,2:19.6:1:24.6:1:1:1.25774:60:4:0.0125:0:1 0/0:390:0:0,0:177,213:390,0:0:2,0:24.8:1:30:1:1:0:60:64:1:0:0.1 +19 5220406 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50025;SOR=0;LSEQ=TCAGAGGGGCTGTCGATAGG;RSEQ=ATGACCAAGGGATGCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:0,2:33,162:195,2:0.0102:2,0:12.5:1:27.5:1:1:0:60:4:0.0102:0:1 0/0:176:0:0,0:24,151:175,0:0:2,0:23.7:1:30.4:1:1:0:60:42.75:0.9942:0:0.2 +19 5220436 . C T 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATGCTTCATGGGGGCAAA;RSEQ=GGGGGAAGCCGTTTCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:5,121:126,0:0:1,0:24.2:1:29.4:1:1:0:60:17:1:0:0.2 0/1:78:13:0,13:0,64:64,13:0.1667:1,1:19.2:1:30.6:1:1:0:60:26:0.1688:0:1.2 +19 5220441 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52907;SOR=0;LSEQ=CTTCATGGGGGCAAACGGGG;RSEQ=AAGCCGTTTCTCTGAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:2,112:114,2:0.0171:1,2:24:1:28:1:0.05127:45.93:60:4:0.0177:0:1 0/0:70:0:0,0:0,70:70,0:0:1,0:20:1:30.4:1:1:0:60:16.5:1:0:0.3 +19 5220900 . T C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=6.18694;LSEQ=GAACTAGGGCTGATAGGGTC;RSEQ=GTGTTTCATAGGCAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:41:38,3:35,1:36,41:0.5325:1,2:24.9:1:30.5:1:0.61826:2.73025:60:82:0.5395:0:1.1 1/1:57:50:49,1:5,1:6,50:0.8772:2,1:25.6:1:30.8:1:0.20455:9.04:60:49:0.8909:0:1.1 +19 5221408 . CTGATCCCAGG C 94 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01072;SOR=8.35085;LSEQ=AATCTAACACTGACTGATCC;RSEQ=CTGAGTCCCCAACTCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:0,2:0,20:20,2:0.0909:1,0:31.5:1:35.5:1:1:0:60:4:0.0952:0:0 0/1:17:8:3,5:1,8:9,8:0.4706:2,2:25.4:1:31.5:1:0.29412:4.37:59.4:16:0.4706:0.1176:0.1 +19 5222047 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5026;SOR=0;LSEQ=AGCCCTGATCCCTCACTTCA;RSEQ=ACCAACTCCAAACTGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:118,3:121,2:0.0163:1,2:20:0:31.5:1:0.06424:34.224:60:4:0.0164:0:1.5 0/0:101:0:0,0:96,5:101,0:0:1,0:26.1:1:31.5:1:1:0:60:49.5:1:0:0.9 +19 5222071 . G C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.83718;LSEQ=AACTCCAAACTGAGCCTTAA;RSEQ=CCCTGCTGAACTACAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:180:101:95,6:73,6:79,101:0.5611:2,2:23:1:32.3:1:0.76653:1.30:60:202:0.5642:0:1.9 1/1:160:133:119,14:26,1:27,133:0.8313:1,2:24.3:1:31.2:1:0.46981:3.04352:60:266:0.8313:0:1.1 +19 5222073 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=CTCCAAACTGAGCCTTAAGC;RSEQ=CTGCTGAACTACAACCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:170,13:183,0:0:2,0:25.1:1:31.5:1:1:0:60:90.5:1:0:1.1 0/1:160:2:1,1:144,14:158,2:0.0125:2,2:21:1:27:1:0.17925:9.97142:60:4:0.0126:0:2 +19 5222088 . C G 231 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAGCCCTGCTGAACTACAA;RSEQ=CCCTGACCCTGCCTGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:246:128:108,20:98,19:117,128:0.5203:2,2:21.9:1:33.1:1:1:1.05:60:127:0.5205:0:1.7 0/0:216:0:0,0:182,34:216,0:0:2,0:22.7:1:31.1:1:1:0:60:107:1:0:0.7 +19 5222095 . CCCTG C 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=5.000;MSILEN=4;SSF=0.34567;SOR=0.46891;LSEQ=TGCTGAACTACAACCCCTGA;RSEQ=CCTGCCTGCCTGCCTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:7:5,2:225,56:281,7:0.0241:2,2:25.4:1:31.9:1:0.63145:1.60414:60:14:0.0244:0.0034:1.3 0/1:262:3:2,1:197,62:259,3:0.0115:2,2:34.3:1:32.7:1:0.56341:1.58559:60:6:0.0115:0:0.3 +19 5222655 . G A 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21052;SOR=4.15602;LSEQ=GGGCTGGGGTGGGGGTGGGC;RSEQ=CAAGGCCCGGTCCGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:1,0:99,70:169,1:0.0058:2,0:8:0:32:0:1:0:60:2:0.0059:0:1 0/1:167:4:3,1:100,63:163,4:0.024:2,2:16.3:1:25.8:1:1:1.88:60:8:0.0248:0:1.5 +19 5222836 . C T 45 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.15501;LSEQ=GTGAGCGCGTTCTCCGCGCC;RSEQ=GGCTCAGCCGCTGCCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:3:1,2:172,133:305,3:0.0097:2,2:13.3:1:28.7:1:0.5835:2.57861:60:6:0.01:0:1 0/1:267:3:1,2:153,111:264,3:0.0112:2,2:21:1:28.7:1:0.5756:2.74635:60:6:0.0114:0:1 +19 5223018 . G A 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAATCTGCGGGTGGCCAC;RSEQ=GGGCGTGTCCTCCGGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:0:0,0:296,236:532,0:0:2,0:25.3:1:30.6:1:1:0:60:87.667:1:0:0.1 0/1:439:66:36,30:209,163:372,66:0.1503:2,2:22.3:1:29.7:1:0.8931:1.06834:60:65:0.1515:0:1.3 +19 5223279 . G A 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.30512;SOR=4.64151;LSEQ=CAGGCTGCCCTCGGGGGTCT;RSEQ=CTGCACCGACAGGGTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:1,0:52,198:250,1:0.004:2,0:1:0:23:0:0.21116:0:60:2:0.0041:0:1 0/1:164:3:2,1:41,120:161,3:0.0183:2,2:18:1:22.7:1:0.16848:5.78:60:6:0.0185:0:1.3 +19 5225558 . G C 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00119;SOR=0;LSEQ=AAAGGAGGAGGCAGGGGCGG;RSEQ=GGGGGCCAAGCTGGGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:20:20,0:25,1:26,20:0.4348:1,1:26.8:1:33:1:1:0:60:40:0.4348:0:1 0/0:16:0:0,0:15,1:16,0:0:1,0:19.4:1:30.3:1:1:0:60:15:1:0:0.3 +19 5225611 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51395;SOR=0;LSEQ=AGCAGCCCTCACACCTTTGT;RSEQ=TCACTGTTCCAGCTGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:96,2:98,2:0.02:1,2:8.5:1:31.5:1:0.05939:39.3701:60:4:0.0204:0:1.5 0/0:69:0:0,0:64,5:69,0:0:2,0:21.9:1:30.9:1:1:0:60:68:1:0:0.2 +19 5225676 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10533;SOR=Inf;LSEQ=GCTCAAGGACTCTGGAGTCA;RSEQ=GCTCTGGTGCCAGTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:254,79:333,0:0:2,0:23.7:1:31.3:1:1:0:59.9:32.3:1:0:0.1 0/1:299:3:1,2:207,89:296,3:0.01:2,2:27:1:29.7:1:0.22066:4.62475:60:6:0.0102:0:1.3 +19 5225686 . C T 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44182;SOR=2.09938;LSEQ=TCTGGAGTCACGCTCTGGTG;RSEQ=CAGTGGGGGCAAAGGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:2:0,2:285,108:393,2:0.0051:2,0:19.5:1:17.5:1:0.07704:0:60:1:0.0026:0:1 0/1:379:4:2,2:250,125:375,4:0.0106:2,2:22.5:1:24:1:0.60444:1.99611:60:3:0.0081:0:1 +19 5225802 . G A 186 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=80.38476;LSEQ=TCGCCCTTCATGGTGTAGGC;RSEQ=GCTACCGTGATGGAGTACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:864:1:1,0:394,469:863,1:0.0012:2,0:1:0:26:0:0.45718:0:60:2:0.0012:0:1 0/1:879:75:36,39:371,433:804,75:0.0853:2,2:26.8:1:30:1:0.80905:1.08:60:150:0.086:0:1.2 +19 5225931 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17866;SOR=Inf;LSEQ=ACCCCCACTCCCCGTGCTGA;RSEQ=AACAAGCAAGGAGGATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:6,134:140,0:0:1,0:24.4:1:32.4:1:1:0:60:69:1:0:0.1 0/1:103:2:0,2:7,94:101,2:0.0194:2,0:14:1:29:0:1:0:60:4:0.0198:0:1 +19 5225981 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09987;SOR=Inf;LSEQ=CAGGGGTGGAGACGTGCACA;RSEQ=GAGCTCATGCAGAGACCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:3,63:66,0:0:1,0:23.7:1:30.2:1:1:0:60:32:1:0:0 0/1:31:2:0,2:1,28:29,2:0.0645:1,0:14:1:31:0:1:0:60:4:0.0667:0:1 +19 5228988 . A G 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGACATACTCACAGGAG;RSEQ=AATGACTACGGGCAGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:11.5:1:30.5:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 5229490 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.24779;SOR=0;LSEQ=CGTCCCCGGCCCCGCCCCGG;RSEQ=CCCCCGCCCACCTGGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:3:0,3:66,84:150,3:0.0196:2,0:11:1:28.3:1:0.25929:0:60:6:0.0196:0:1.7 0/0:147:0:0,0:62,85:147,0:0:2,0:23.3:1:30.4:1:1:0:59.9:23.5:1:0:0.3 +19 5229495 . C T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24613;SOR=0;LSEQ=CCGGCCCCGCCCCGGCCCCC;RSEQ=GCCCACCTGGGCATCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:76,82:158,2:0.0125:2,2:8:0:33:1:1:1.08:60:4:0.0127:0:1.5 0/0:162:0:0,0:75,87:162,0:0:2,0:22.7:1:29.8:1:1:0:59.9:53:1:0:0.3 +19 5229510 . C T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67922;SOR=0.63486;LSEQ=CCCCCCGCCCACCTGGGCAT;RSEQ=GGCCAGCATGACGTCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:3:1,2:100,95:195,3:0.0152:2,2:13.3:1:28.3:1:0.61556:2.09762:60:6:0.0155:0:1 0/0:207:2:0,2:97,108:205,2:0.0097:2,0:5.5:1:19.5:1:0.49955:0:60:1:0.005:0:1.5 +19 5229511 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23383;SOR=0;LSEQ=CCCCCGCCCACCTGGGCATC;RSEQ=GCCAGCATGACGTCCTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:101,96:197,2:0.0101:2,2:9:1:30:1:1:1.05184:60:4:0.0104:0:1 0/0:212:0:0,0:100,112:212,0:0:2,0:22.1:1:29.7:1:1:0:59.9:41.4:1:0:0.3 +19 5229601 . G T 48 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25643;SOR=0;LSEQ=TGGTAGCCGCGGATCTGGCC;RSEQ=TGCTGCCGGCCGGGCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:104,143:247,3:0.012:2,2:7.3:1:30.7:1:1:1.45245:54:6:0.0124:0:1.3 0/0:203:0:0,0:90,113:203,0:0:2,0:26.5:1:30.2:1:1:0:60:49.75:1:0:0.3 +19 5229604 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.24935;LSEQ=TAGCCGCGGATCTGGCCGTG;RSEQ=TGCCGGCCGGGCGCGGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:2:0,2:101,139:240,2:0.0083:2,0:6:1:19:1:0.51164:0:60:1:0.0042:0:1.5 0/1:194:2:1,1:86,106:192,2:0.0103:2,2:43.5:1:29.5:1:1:1.23:60:4:0.0105:0:1.5 +19 5229617 . G T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49926;SOR=0;LSEQ=GGCCGTGCTGCCGGCCGGGC;RSEQ=CGGGCGAGCGCCACAGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:75,99:174,2:0.0113:2,2:22:0:33:1:1:1.32:60:4:0.0116:0:1.5 0/0:164:0:0,0:74,90:164,0:0:2,0:28.4:1:30:1:1:0:60:40:1:0:0.3 +19 5229622 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.49839;SOR=0;LSEQ=TGCTGCCGGCCGGGCGCGGG;RSEQ=GAGCGCCACAGCACGCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:69,85:154,2:0.0128:2,2:25.5:1:28:1:1:1.23:60:4:0.0131:0:1.5 0/0:155:0:0,0:69,85:154,0:0:2,0:27.9:1:29.7:1:1:0:60:37.5:0.9934:0:0.3 +19 5229623 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24751;SOR=0;LSEQ=GCTGCCGGCCGGGCGCGGGC;RSEQ=AGCGCCACAGCACGCGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:68,80:148,2:0.0133:2,2:17:0:32.5:1:1:1.18:60:4:0.0134:0:1.5 0/0:151:0:0,0:70,81:151,0:0:2,0:27.9:1:29.7:1:1:0:60:302:1:0:0.3 +19 5229633 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49886;SOR=Inf;LSEQ=GGGCGCGGGCGAGCGCCACA;RSEQ=CACGCGGATGGCCGTGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:64,74:138,0:0:2,0:20.7:1:32.9:1:1:0:60:276:1:0:0.4 0/1:148:2:1,1:69,77:146,2:0.0135:2,2:19:1:24.5:1:1:1.12:60:4:0.0135:0:2 +19 5229644 . G A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5858;SOR=0.39504;LSEQ=AGCGCCACAGCACGCGGATG;RSEQ=CCGTGGCGTTGAGCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:49,62:111,2:0.0177:2,2:46:1:30.5:1:1:1.26:60:4:0.018:0:1 0/0:142:1:1,0:67,74:141,1:0.007:2,0:1:0:22:0:0.47887:0:60:2:0.0072:0:1 +19 5229647 . G A 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75971;LSEQ=GCCACAGCACGCGGATGGCC;RSEQ=TGGCGTTGAGCGCCTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:49,58:107,2:0.0183:2,0:1:0:25.5:1:0.21662:0:60:4:0.0185:0:1.5 0/1:143:2:1,1:68,73:141,2:0.014:2,2:27:0:32:0:1:1.07:60:4:0.0142:0:1.5 +19 5229662 . T A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.482;LSEQ=TGGCCGTGGCGTTGAGCGCC;RSEQ=CCGCCTCCACCTTCCGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:33,42:75,1:0.0132:2,0:1:0:31:0:0.44737:0:58:2:0.0137:0:1 0/1:103:2:1,1:44,57:101,2:0.0194:2,2:11:1:29:1:1:1.29:60:4:0.0202:0:1 +19 5229719 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49126;SOR=Inf;LSEQ=GCGGGCGGGAGGGGAGGGGA;RSEQ=GGGCGGGCGGAGCCGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:26,0:0:2,0:18.6:1:31.6:1:1:0:60:25:1:0:0.5 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:20.5:1:31.5:1:1:1.34838:60:4:0.0714:0:1 +19 5229728 . G A 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00199;SOR=0;LSEQ=AGGGGAGGGGAGGGGCGGGC;RSEQ=GAGCCGTTACCAGGGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:5,2:8,7:15,7:0.3182:2,2:22.7:1:29.7:1:0.64783:2.11:60:14:0.3684:0:1.1 0/0:27:0:0,0:15,12:27,0:0:2,0:14.2:1:28.7:1:1:0:60:26:1:0:0.4 +19 5229739 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=Inf;LSEQ=GGGGCGGGCGGAGCCGTTAC;RSEQ=AGGGCGCCCGGCCCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:14,0:0:2,0:15.5:1:29.9:1:1:0:60:13:1:0:0.6 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:14.5:1:28:1:1:1.18321:60:4:0.1538:0:1 +19 5231135 . T C 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37652;SOR=2.52553;LSEQ=TGCAGAGCTAAGCCTGCCCA;RSEQ=GTCTAGAATCGCCAATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:7,1:8,3:0.2727:2,0:18.3:1:33:1:1:0:60:6:0.2727:0:1 1/0:8:4:4,0:4,0:4,4:0.5:0,0:19.3:1:33:1:1:0:60:8:0.5:0:1.3 +19 5231264 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17795;SOR=Inf;LSEQ=GTTTCCAGATGGAAGGCTTC;RSEQ=AGGCGGGGGCCGGGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:154,18:172,0:0:2,0:22.8:1:29.8:1:1:0:60:33.4:1:0:0.2 0/1:126:2:1,1:109,15:124,2:0.0159:2,2:12.5:1:27.5:1:0.23873:7.06799:60:4:0.016:0:1 +19 5231289 . C T 38 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.64649;SOR=0.47402;LSEQ=GGGGGCCGGGCTGGGGCCTG;RSEQ=GGGGGGTCCCGGGCCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:3,0:209,47:256,3:0.0115:2,0:22:1:24:1:1:0:60:2:0.0079:0:1 0/0:182:1:0,1:132,49:181,1:0.0055:2,0:1:0:24:0:0.27473:0:60:2:0.0056:0:1 +19 5231316 . C T 56 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04925;SOR=Inf;LSEQ=TCCCGGGCCTGGGGCAGGTA;RSEQ=TTACCATCCTCGTCGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:274,124:398,0:0:2,0:24.9:1:32.1:1:1:0:60:32.167:1:0:0.2 0/1:356:4:2,2:234,118:352,4:0.0112:2,2:7.3:1:28:1:0.60556:1.979:60:8:0.0115:0:1.3 +19 5231584 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05534;SOR=0;LSEQ=TTACCAAAATGGCCGTGGAG;RSEQ=GCACGCTGACACATTTAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:4:2,2:74,223:297,4:0.0133:2,2:31.5:1:25.3:1:0.26524:3.00:60:3:0.0104:0:2.5 0/0:318:0:0,0:86,230:316,0:0:2,0:24.7:1:29.6:1:1:0:60:25.333:0.9935:0:0.3 +19 5231610 . A AG 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.62294;SOR=2.89435;LSEQ=CTGACACATTTAACGTCTTG;RSEQ=GGGGGGGCTGACGGTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:0,1:29,118:147,1:0.0066:2,0:18:0:33:0:1:0:60:2:0.0072:0:0 0/1:158:3:1,2:48,103:151,3:0.019:2,2:24.3:1:32.3:1:1:1.07:60:6:0.0203:0:0.3 +19 5238771 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03162;SOR=Inf;LSEQ=GGGATACTGAGGCACAGCGC;RSEQ=GGTAGATGGATCCGAGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:14,1:15,0:0:1,0:22.9:1:29.5:1:1:0:60:14:1:0:0.4 0/1:8:3:3,0:4,1:5,3:0.375:2,0:25.3:1:30.7:1:1:0:60:6:0.4286:0:1 +19 5238944 . C T 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06435;SOR=0;LSEQ=ACCTACTGGACTGCAGCGTG;RSEQ=GCTGCCGCACCACGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:5:3,2:356,94:450,5:0.011:2,2:31:1:29.6:1:0.28501:2.51844:60:10:0.0112:0:1.2 0/0:400:0:0,0:277,122:399,0:0:2,0:24:1:30.5:1:1:0:59.9:38.9:1:0:0.1 +19 5239140 . GGA G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.20008;SOR=1.71121;LSEQ=GAGAGAGACAGAAACAAAGG;RSEQ=GAGAGAGAGAGACAGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:12:4,8:116,346:462,12:0.0252:2,2:26.7:1:32.2:1:0.50948:1.49:56.4:24:0.0261:0:0.9 0/1:449:19:5,14:117,312:429,19:0.0423:2,2:29.2:1:31.1:1:1:1.04988:59.2:38:0.0435:0.0022:0.8 +19 5239175 . G GGA 180 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=13.000;MSILEN=2;SSF=3e-05;SOR=0.35921;LSEQ=CAGAAACAGAGGGGGGAGGG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:71:1,70:9,99:108,71:0.3568:2,1:33.2:1:29.4:1:0.09132:6.31621:56.7:22.667:0.3716:0.0151:1.1 0/1:187:31:3,28:3,67:70,31:0.1658:1,2:33.8:1:29.2:1:0.36753:2.37:57.9:30:0.1786:0.0053:0.9 +19 5239200 . C G 37 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82632;LSEQ=GAGAGAGAGAGAGAGAGAGA;RSEQ=AGAGAAATAGAGACAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:3:0,3:4,129:133,3:0.0217:1,0:15.3:1:23.7:1:1:0:56.7:2:0.016:0:1.7 0/1:111:2:1,1:5,104:109,2:0.018:1,2:15:1:23.5:1:0.10565:19.09:40.5:1:0.0098:0:4 +19 5239214 . CA C 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=GAGAGACAGAGAAATAGAGA;RSEQ=GGGGTGCGGCAGAGAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:5,101:106,0:0:1,0:22.8:1:31.1:1:1:0:58.4:20.2:1:0:0.9 0/1:80:10:2,8:3,58:61,10:0.125:1,2:23.6:1:29.1:1:0.14226:4.67:56.2:9:0.1216:0.0125:0.5 +19 5240115 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14852;SOR=Inf;LSEQ=GAGCAGAATCCGCAGCACAC;RSEQ=TAGGGACAAAGAGGGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:118,4:122,0:0:1,0:27.2:1:30.8:1:1:0:60:121:1:0:0.1 0/1:77:2:1,1:68,7:75,2:0.026:2,2:24:1:29.5:1:0.19822:9.15346:60:4:0.0263:0:1 +19 5240392 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.06494;LSEQ=GTCGGGGAGCGTCCACCCCA;RSEQ=AAAGGGGGCCCCACCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:115:32,83:37,132:169,115:0.4049:2,2:25.3:1:28.7:1:0.26262:1.37:60:56.5:0.4036:0:1.1 0/1:261:11:3,8:70,180:250,11:0.0421:2,2:21.3:1:26.6:1:1:1.03686:60:22:0.0423:0:1.2 +19 5240416 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23253;SOR=Inf;LSEQ=GGGGGCCCCACCTGCTGAGT;RSEQ=TCCCCACTAAAAGATGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:24,158:182,0:0:2,0:24.6:1:32.5:1:1:0:59.9:59.667:1:0:0.5 0/1:170:2:1,1:28,140:168,2:0.0118:2,2:32:1:28.5:1:0.31291:4.93:60:4:0.012:0:1 +19 5240432 . G T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=GAGTGTCCCCACTAAAAGAT;RSEQ=CCAGCTCTGGGTGCTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:8,133:141,0:0:2,0:23.2:1:32.2:1:1:0:59.9:34.25:1:0:0.4 0/1:118:2:1,1:7,109:116,2:0.0169:2,2:11:0:27:1:0.13154:14.63:60:4:0.0171:0:1 +19 5240463 . T A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02795;SOR=Inf;LSEQ=GTGCTTCTAGAATGTTCTTT;RSEQ=ATTTTCCTGGGGACCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:4,82:86,0:0:1,0:24.1:1:28.7:1:1:0:59.8:172:1:0:0.3 0/1:61:4:0,4:3,54:57,4:0.0656:2,0:19.5:1:30:1:1:0:60:8:0.0667:0:2 +19 5243702 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=CATGTTGGCCATGCTGGTCT;RSEQ=GAACTCCTGACCTCCGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:12,0:12,1:0.0769:0,0:13:0:33:0:1:0:42:2:0.0769:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:27:1:30.5:1:1:0:44.5:4:1:0:1 +19 5243846 . C T 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14766;SOR=0;LSEQ=ACAAACCGCTCTGCGGCTTC;RSEQ=AGGGAGCATGCAAAGAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:4:1,3:156,35:191,4:0.0205:2,2:11:1:26.5:1:0.02394:13.11975:60:8:0.0208:0:1.3 0/0:135:0:0,0:93,42:135,0:0:2,0:23.8:1:30.4:1:1:0:60:66.5:1:0:0.1 +19 5243864 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1895;SOR=Inf;LSEQ=TCCAGGGAGCATGCAAAGAA;RSEQ=CAAGCCGCACGGCCGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:186,65:251,0:0:2,0:26.1:1:31.9:1:1:0:59.7:124.5:1:0:0.1 0/1:194:2:1,1:125,67:192,2:0.0103:2,2:28.5:1:28:1:1:1.85937:60:4:0.0105:0:1 +19 5244506 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49989;SOR=0;LSEQ=GGGGAGAGCTGTGGGCAGGA;RSEQ=GCAGCTGTGTCACGCATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:23,101:124,2:0.0159:2,2:26.5:1:33:1:0.3459:4.32:60:4:0.0163:0:1 0/0:111:0:0,0:22,89:111,0:0:2,0:22.5:1:30.9:1:1:0:60:222:1:0:0.1 +19 5244554 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52532;SOR=0;LSEQ=GGTTGAGGACCCTGAAGGCT;RSEQ=TGTGACTTTTCACCATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:0,48:48,2:0.04:1,0:8:0:32:0:1:0:60:4:0.0408:0:1 0/0:30:0:0,0:1,28:29,0:0:1,0:19:1:31.9:1:1:0:60:58:0.9667:0:0 +19 5245630 . A G 129 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00036;SOR=11.46047;LSEQ=ATTTATAACCAATAAATAAT;RSEQ=CCTGTTCAAAGAACAACCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:32,0:32,2:0.0588:1,0:25.5:1:34:0:1:0:60:4:0.0588:0:1 0/1:40:17:16,1:22,1:23,17:0.425:1,1:22.8:1:31.8:1:1:1.36391:59.6:34:0.425:0:1.1 +19 5245665 . T G 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01585;SOR=Inf;LSEQ=AACCGTCCCCTTCCTAGCCA;RSEQ=GAATGACTGAAGCCAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:78,2:80,0:0:1,0:23.6:1:31.4:1:1:0:59.7:39:1:0:0.1 0/1:64:5:5,0:55,4:59,5:0.0781:2,0:31.4:1:31.6:1:1:0:60:10:0.0794:0:1 +19 5245699 . G A 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19658;SOR=Inf;LSEQ=CAAGAGGGTAACTCGGAGGT;RSEQ=CTCCCACGCTGCCTCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:134,11:145,0:0:2,0:24.4:1:32.4:1:1:0:59.8:35.25:1:0:0.1 0/1:116:2:1,1:103,11:114,2:0.0172:2,2:19:0:26.5:1:0.197:9.00842:60:4:0.0174:0:1.5 +19 5245732 . C T 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.32573;SOR=3.82144;LSEQ=CTCCCACCTGTGCCTGAAGT;RSEQ=GGGGATCGACTCCAGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:0,1:203,41:244,1:0.0041:2,0:1:0:25:0:0.17143:0:60:2:0.0042:0:1 0/1:194:3:0,3:146,45:191,3:0.0155:2,0:7.7:1:26.3:1:0.01444:0:60:6:0.0157:0:1 +19 5245971 . G A 175 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGGCATGGGCGAGCCCAC;RSEQ=GCCACGCAGGTGATGTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:874:0:0,0:378,494:872,0:0:2,0:24.9:1:30.4:1:1:0:59.9:71.667:0.9977:0:0.1 0/1:741:61:29,32:310,368:678,61:0.0823:2,2:24.4:1:29.6:1:0.7902:1.08:60:29.5:0.0812:0:1.2 +19 5245977 . G A 187 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=111.71649;LSEQ=ATGGGCGAGCCCACGGCCAC;RSEQ=CAGGTGATGTTCACGTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:845:1:0,1:367,475:842,1:0.0012:2,0:15:0:21:0:1:0:60:2:0.0012:0:1 0/1:726:85:34,51:292,347:639,85:0.1171:2,2:25.1:1:29.2:1:0.35416:1.26184:60:170:0.1184:0:1.2 +19 5246041 . G A 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19891;SOR=4.39241;LSEQ=TGGGCAGGATGGAGAAGCGC;RSEQ=GGGCCACGCGGCGGACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:1:1,0:117,301:418,1:0.0024:2,0:1:0:28:0:0.28162:0:60:2:0.0025:0:1 0/1:384:4:2,2:135,245:380,4:0.0104:2,2:25.5:1:28:1:0.61888:1.81:60:8:0.0105:0:1 +19 5246058 . T A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11362;SOR=Inf;LSEQ=CGCGGGGCCACGCGGCGGAC;RSEQ=GGGGAGGGGGCGGCAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:65,215:280,0:0:2,0:24.5:1:30.5:1:1:0:60:45.667:1:0:0.1 0/1:264:3:3,0:78,183:261,3:0.0114:2,0:11.3:1:20.3:1:0.02814:0:60:2:0.0079:0:1.7 +19 5246097 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.16201;SOR=Inf;LSEQ=GCGGCGGGAGGGAGATGCGA;RSEQ=GGGTGAGGTGGGGTGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:25,142:167,0:0:2,0:22.8:1:31.2:1:1:0:59.9:54.667:1:0:0.1 0/1:113:2:1,1:17,94:111,2:0.0177:2,2:20.5:1:27.5:1:0.29441:5.40:60:4:0.0177:0:1 +19 5246125 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGTGAGGTTGGGAGGG;RSEQ=AAGACAGGATGCGGAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:7,109:116,2:0.0169:2,2:40:1:30.5:1:0.13154:14.63:60:4:0.0174:0:1 0/0:58:0:0,0:7,51:58,0:0:2,0:25:1:30.9:1:1:0:60:57:1:0:0.1 +19 5246158 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGAGAAAAAGAAAAGCA;RSEQ=GAAGGAAGAAAGAAAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:0,2:3,70:73,2:0.0267:1,0:25.5:1:31.5:1:1:0:60:4:0.0267:0:1 0/0:36:0:0,0:4,32:36,0:0:2,0:23.5:1:30:1:1:0:60:35:1:0:0.2 +19 5246194 . G GA 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.10606;SOR=Inf;LSEQ=GAAGGAAAGAAAGAAAAAAA;RSEQ=AAAAAAAAAGGAAAACCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:30,0:0:1,0:19.9:1:32.7:1:1:0:59.5:60:1:0:0.1 0/1:15:2:0,2:0,13:13,2:0.1333:1,0:26:1:32:0:1:0:60:4:0.1429:0:0 +19 5255992 . A AT 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00285;SOR=0.24673;LSEQ=AAATTGTTGTTCATTTTTCT;RSEQ=TTTTTTTTCCGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:18:18,0:16,0:16,18:0.5294:1,1:25.7:1:32.3:1:1:0:60:36:0.5294:0.0588:0.1 0/1:56:12:12,0:38,4:42,12:0.2143:2,0:29.8:1:31.4:1:0.5644:0:60:24:0.2143:0:0 +19 5256056 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.51133;SOR=Inf;LSEQ=ACATGTGTTTTGTGTGTGTG;RSEQ=GTGTCATTTTCAGAATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:114,11:125,0:0:2,0:26.6:1:32.2:1:1:0:60:124:1:0:0.1 0/1:173:2:1,1:143,28:171,2:0.0116:2,2:16:0:31:0:0.30797:5.03598:60:4:0.012:0:1 +19 5256073 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18122;SOR=0;LSEQ=GTGCGTGTCATTTTCAGAAT;RSEQ=TAAAAATGTGGGTAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:151,38:189,2:0.0105:2,2:9.5:1:29.5:1:0.36754:3.93538:60:4:0.0106:0:1 0/0:257:0:0,0:183,74:257,0:0:2,0:21.9:1:31:1:1:0:60:50.4:1:0:0.1 +19 5256251 . G GT 144 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00023;SOR=0.31794;LSEQ=AAAAGCTGCAATAGTTTGTT;RSEQ=TTTTTTTTTTCTTTAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:46:1,45:3,67:70,46:0.377:1,1:27.3:1:26.2:1:1:2.00391:59.6:3.6:0.3636:0:1.2 0/1:112:18:1,17:8,82:90,18:0.1607:2,1:24.9:1:29.2:1:1:1.65181:58.3:17:0.1789:0.0089:1.6 +19 5256270 . CA C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.2272;SOR=0.3877;LSEQ=TGTTTTTTTTTTCTTTAAAC;RSEQ=AAAAAAAAAATTAAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:9:0,9:0,74:74,9:0.1084:1,0:25.8:1:31.4:1:1:0:58.9:18:0.1098:0:1.3 0/1:67:3:0,3:2,60:62,3:0.0448:1,0:37:1:31.3:1:1:0:60:6:0.0455:0:2.3 +19 5257811 . C A 40 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2451;SOR=6.606;LSEQ=ACGGGGCATCTCTCGCAAGG;RSEQ=ACGAGGAAGGGAATTTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:9,1:10,1:0.0909:2,0:7:0:31:0:1:0:60:2:0.0909:0:1 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:16.7:1:25.7:1:1:0:60:6:0.4286:0:2.3 +19 5257926 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52329;SOR=0;LSEQ=GGGAGGGGCCTTCCTGCTTG;RSEQ=GTGTGCAGGGGACGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:81,5:86,2:0.0227:2,2:8.5:1:29.5:1:0.13245:14.8795:60:4:0.0235:0:1 0/0:55:0:0,0:55,0:55,0:0:1,0:23.2:1:31.1:1:1:0:60:54:1:0:0.2 +19 5257982 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11097;SOR=0;LSEQ=CCCGAGGAGGGAGGGGGATG;RSEQ=GACGGGGCGGGTCCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:3:1,2:178,67:245,3:0.0121:2,2:23:1:30.3:1:0.18807:5.27134:60:6:0.0124:0:1.3 0/0:267:0:0,0:193,74:267,0:0:2,0:23.5:1:29.9:1:1:0:60:52.4:1:0:0.2 +19 5258309 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13143;SOR=0;LSEQ=CTTGGCCAGGCCTTGTATAA;RSEQ=CTCCACCCCCACATCTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:0,4:0,18:18,4:0.1818:1,0:26.3:1:29:1:1:0:60:8:0.1905:0:1 0/0:15:0:0,0:1,14:15,0:0:1,0:16.1:1:31.3:1:1:0:60:30:1:0:0.1 +19 5258490 . G A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGCTCTCCTGGCCAGAA;RSEQ=GAAAGAGTGGGTTGGCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31:1:33.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 5260674 . G A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01696;SOR=Inf;LSEQ=CAGACACAGACGCAGAGACC;RSEQ=GACTAACACTGGGTGGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:38,1:39,0:0:1,0:19.4:1:30.5:1:1:0:60:78:1:0:0.2 0/1:33:5:3,2:25,3:28,5:0.1515:2,2:24.2:1:26:1:0.15455:5.14903:60:4:0.125:0:1.2 +19 5260718 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=1.92487;LSEQ=GTGGTGGCAGGGTGGACACG;RSEQ=ATGGAAGGGGGCCTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:0,1:72,13:85,1:0.0116:2,0:1:0:24:0:0.16279:0:60:2:0.0119:0:1 0/1:90:2:1,1:72,15:87,2:0.0222:2,2:21:1:30:1:0.32891:4.67978:60:4:0.0225:0:1 +19 5260731 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49798;SOR=0;LSEQ=GGACACGCATGGAAGGGGGC;RSEQ=TGGGGGCAGGCCCTGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:99,23:122,2:0.0161:2,2:29.5:1:31:1:0.3509:4.23495:60:4:0.0164:0:1 0/0:123:0:0,0:96,27:123,0:0:2,0:2:0:15:0:1:0:60:0:0:0:2 +19 5260761 . C T 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25095;SOR=Inf;LSEQ=GCCCTGTGGAGCCTGAGGGG;RSEQ=TGAGTGGGCAGCAAGAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:137,68:205,0:0:2,0:24.2:1:32.4:1:1:0:60:204:1:0:0.1 0/1:231:3:1,2:148,80:228,3:0.013:2,2:10.7:1:20:1:0.2877:3.67787:60:2:0.0087:0:1.7 +19 5260878 . TGT CG 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25518;SOR=1.23844;LSEQ=GGTGAATGTCACAAGGCGGT;RSEQ=TGGGGGGCCGGGGGGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:310:191:78,113:53,65:118,191:0.6161:2,2:24.3:1:30.4:1:0.55371:1.18062:59.9:30.833:0.6167:0.1323:1.4 1/0:260:173:65,108:33,49:82,173:0.6654:2,2:23.1:1:29.6:1:0.682:1.1185:59.8:42.25:0.6733:0.1615:1.3 +19 5260879 . GT G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50944;SOR=1.24886;LSEQ=GTGAATGTCACAAGGCGGTT;RSEQ=TGGGGGGCCGGGGGGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:24:16,8:51,69:120,24:0.1667:2,2:5.8:1:29.3:1:0.0427:2.69:59.4:48:0.1714:0.1528:1.3 0/1:105:21:12,9:33,49:82,21:0.2:2,2:5.9:1:28.9:1:0.21844:1.97:58.8:42:0.2039:0.1714:1.3 +19 5260895 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07891;SOR=Inf;LSEQ=GGTTGTTGGGGGGCCGGGGG;RSEQ=CCCCAGGGAAGCTGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:82,147:229,0:0:2,0:23.9:1:31.5:1:1:0:60:31.714:1:0:1 0/1:173:3:2,1:53,116:169,3:0.0173:2,2:14.7:1:27:1:0.23997:4.34:60:6:0.0175:0:2.3 +19 5260900 . AG A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.169;SOR=Inf;LSEQ=TTGGGGGGCCGGGGGGCCCC;RSEQ=GGAAGCTGGGCTGGGCCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:66,138:204,0:0:2,0:23.3:1:31.8:1:1:0:60:408:0.9855:0:1 0/1:145:2:1,1:38,105:143,2:0.0138:2,2:7.5:1:28.7:1:0.46695:2.74:57.5:4:0.0139:0.0069:1.5 +19 5260912 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16257;SOR=Inf;LSEQ=GGGGCCCCAGGGAAGCTGGG;RSEQ=TGGGCCGTAAGCCAGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:46,121:167,0:0:2,0:21.9:1:32.8:1:1:0:60:166:0.994:0:1 0/1:114:2:1,1:24,88:112,2:0.0175:2,2:20.5:1:27.5:1:0.39202:3.61:60:4:0.0175:0:2.5 +19 5260933 . A T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3152;SOR=0.69657;LSEQ=TGGGCCGTAAGCCAGGCCTC;RSEQ=GCACTCTGCCCCAGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:100:59:3,56:3,38:41,59:0.59:2,2:23.7:1:30.6:1:0.68692:1.46782:60:58:0.5859:0:1.8 1/0:56:28:2,26:6,22:28,28:0.5:2,2:22.1:1:29.8:1:0.25156:3.46949:59.8:56:0.5091:0:1.9 +19 5260935 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53855;SOR=0;LSEQ=GGCCGTAAGCCAGGCCTCAG;RSEQ=ACTCTGCCCCAGGGAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:4,90:94,2:0.0208:1,2:16:1:31:1:0.10197:20.23:60:4:0.0211:0:1 0/0:53:0:0,0:7,46:53,0:0:2,0:20.6:1:31.8:1:1:0:59.9:106:1:0:1.1 +19 5261506 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGAAAAGGCGGCTCGG;RSEQ=GCTGGAACGTTACTCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:29.5:1:1:0:60:4:1:0:1.5 +19 5262853 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21681;SOR=Inf;LSEQ=GAGGGCGTTAGTAAACATAC;RSEQ=AGGCAGAGTGGGTCACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:182,23:205,0:0:2,0:23.3:1:30.9:1:1:0:60:24.625:0.9949:0:0.1 0/1:180:2:2,0:147,30:177,2:0.0111:2,0:23:1:31:1:1:0:60:4:0.0114:0:1 +19 5262856 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2124;SOR=Inf;LSEQ=GGCGTTAGTAAACATACCAG;RSEQ=CAGAGTGGGTCACAGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:188,29:217,0:0:2,0:23.5:1:31.5:1:1:0:60:35.167:1:0:0.1 0/1:186:2:2,0:150,34:184,2:0.0108:2,0:14:1:31:0:1:0:60:4:0.011:0:1 +19 5262979 . G C 190 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGAAATCAGACTTACCAAA;RSEQ=GTTTCTGAACGTTTACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:786:0:0,0:376,408:784,0:0:2,0:27.4:1:32.2:1:1:0:59.9:195:0.9987:0:0.2 0/1:947:81:37,44:413,453:866,81:0.0855:2,2:26.7:1:30.1:1:0.81617:1.08406:60:162:0.0872:0:1.3 +19 5263061 . G T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36578;SOR=1.20484;LSEQ=CAAAGAATCCTATGTCCTCA;RSEQ=CGAGGAGGGGAGGGCGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:167:30,137:19,59:78,167:0.6761:2,2:22.7:1:27.4:1:0.30342:1.46825:59.9:6.591:0.6744:0:1.5 1/0:218:156:28,128:8,48:56,156:0.7156:2,2:19.9:1:26.9:1:0.67886:1.31:60:7.667:0.7263:0:1.5 +19 5263077 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.075;SOR=Inf;LSEQ=CTCAGCGAGGAGGGGAGGGC;RSEQ=GGGGAGGGGAGGGGGACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:23,158:181,0:0:2,0:22:1:31:1:1:0:59.9:89.5:1:0:1.5 0/1:133:3:1,2:12,118:130,3:0.0226:2,2:17.3:1:27.7:1:0.26732:4.81:60:6:0.0227:0:3 +19 5264967 . A G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.00087;SOR=1.98624;LSEQ=GGGCCCTGGAGATGCTCCCC;RSEQ=CCCCCTGCTGCCCTCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:314:212:160,52:80,21:101,212:0.6752:2,2:22.7:1:30.4:1:0.5676:1.23727:60:211:0.6828:0:1.1 1/1:231:186:128,58:36,9:45,186:0.8052:2,2:23.4:1:29.6:1:0.14839:1.8082:60:45.5:0.8018:0:1.1 +19 5265222 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36929;LSEQ=GGTCCTCTGAGGGCAGAGAC;RSEQ=TGAGAGAAATGGGCATGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:335:206:60,146:41,87:128,206:0.6149:2,2:23.4:1:30.8:1:0.62447:1.14627:60:205:0.6193:0:1.1 0/1:340:126:37,89:68,146:214,126:0.3706:2,2:23.8:1:30:1:0.71568:1.11995:60:125:0.3709:0:1.2 +19 5265318 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCAGCTCCTCCCTGGCTG;RSEQ=GTGACCTCAGCCATGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:0,2:1,68:69,2:0.0282:1,0:45.5:1:31:1:1:0:60:4:0.029:0:1 0/0:27:0:0,0:0,27:27,0:0:1,0:25.4:1:29.7:1:1:0:60:26:1:0:0.1 +19 5265414 . T A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAGGCTGGAGTACAGTGGC;RSEQ=CGATCATAGCTCACCGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:29.3:1:31:1:1:0:48:12:0.75:0:1.7 1/1:3:3:0,3:0,0:0,3:1:0,0:22.3:1:31.3:1:1:0:46.3:6:1:0:1.7 +19 5265429 . C T 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGCTCGATCATAGCTCAC;RSEQ=GCAGTCTCAACAACCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:34.3:1:25:1:1:0:43.5:3:0.75:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:27.5:1:31:1:1:0:40.5:4:1:0:2 +19 5273331 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13781;SOR=Inf;LSEQ=ACTGGTTGGATAAGGGAGAT;RSEQ=AAGGTCCTCCCAAAAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:92,2:94,0:0:1,0:26.6:1:32.4:1:1:0:60:93:1:0:0.1 0/1:56:2:2,0:52,2:54,2:0.0357:1,0:15.5:1:29:0:1:0:60:4:0.0364:0:1 +19 5273571 . T G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=0.59915;LSEQ=TGGATCCTCAGCACTGCCCC;RSEQ=GCACTCTCATCAAACTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:146:53,93:119,272:391,146:0.2714:2,2:25.6:1:30.5:1:0.21266:1.30:59.8:72:0.2748:0:1.1 0/1:658:120:50,70:211,324:535,120:0.1824:2,2:24.7:1:29.8:1:0.68041:1.10:60:119:0.1836:0:1.2 +19 5273650 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2187;SOR=Inf;LSEQ=CTGGGGTCCCAGGAAGGTTC;RSEQ=TGTCTAGGCTGGGCTAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:19,125:144,0:0:2,0:23:1:33.1:1:1:0:60:143:1:0:0.2 0/1:127:2:1,1:12,112:124,2:0.0157:2,2:15:1:28.5:1:0.19644:9.01:60:4:0.016:0:1 +19 5273746 . G C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.55243;SOR=1.49317;LSEQ=GCTGCAGGCTGAATGTGCAC;RSEQ=TGTGTCGGTGTCCAGTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:1,8:2,27:29,9:0.2368:2,2:27:1:33.7:1:1:1.66:60:18:0.2432:0:1 0/1:22:7:0,7:0,15:15,7:0.3182:1,0:15:1:30.9:1:1:0:60:14:0.3182:0:1 +19 5274089 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10085;SOR=Inf;LSEQ=AGGCTGCGCAGCCATGCTTG;RSEQ=TTGGCCACAGATGATGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:126,4:130,0:0:1,0:24.5:1:32.7:1:1:0:60:64:1:0:0.1 0/1:61:2:2,0:58,1:59,2:0.0328:1,0:14.5:1:30.5:1:1:0:60:4:0.0333:0:1 +19 5274384 . C T 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=37.77457;LSEQ=ACAGTGGAAAGAAGGGGGGG;RSEQ=GCTGATGGGTCCAGGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:0,3:88,205:293,3:0.0101:2,0:23:1:14.7:1:0.55723:0:60:0:0:0:3.7 0/1:268:75:27,48:56,136:192,75:0.2799:2,2:23.5:1:27.9:1:0.30445:1.36:59.9:11.5:0.284:0:1.3 +19 5285985 . CCA C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.73703;SOR=0.74056;LSEQ=GGAGGAGGTGGGGAGTGTGC;RSEQ=CACACACACAGCCATAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:5:4,1:235,66:301,5:0.0163:2,2:31:1:33.4:1:1:1.12:60:10:0.0166:0:0.2 0/1:247:3:2,1:184,59:243,3:0.0121:2,2:28.7:1:30.3:1:0.56946:1.55621:60:6:0.0123:0:0 +19 5286192 . GC G 33 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.57184;SOR=2.85667;LSEQ=CTCCGCCCTGGAGGGGGATG;RSEQ=CCCCCGGTCCCTCACAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:1:0,1:46,226:272,1:0.0037:2,0:18:0:34:0:1:0:60:2:0.0037:0:0 0/1:192:2:0,2:33,157:190,2:0.0104:2,0:21:1:33:0:1:0:60:4:0.0106:0:0 +19 5286222 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5217;SOR=0;LSEQ=CCCTCACAGAGAGGCCTCGA;RSEQ=CCGAGCGTCAGATGGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:7,148:155,2:0.0127:1,2:12:1:29:1:0.09962:19.85:60:4:0.0127:0:1 0/0:101:0:0,0:6,95:101,0:0:2,0:23:1:31.8:1:1:0:60:100:1:0:0.1 +19 5286348 . G A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.27018;SOR=0.22752;LSEQ=GGAGCAGGGGAGGGTCCTGC;RSEQ=GGGGCTGGTCATGGGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:0,12:0,1:1,12:0.9231:0,0:16.7:1:29.8:1:1:0:60:5:0.9091:0:1.4 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:26:1:31.4:1:1:0:60:10:0.7143:0:1 +19 5299547 . C A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTACTGTCACCTGAAATT;RSEQ=TCTGTCTTTACTCACTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 5301061 . C A 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAAGCAAAAGCCACATTG;RSEQ=TGGGCTTTGAACCTGGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:10:1:30:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:36:0:28:0:1:0:60:2:1:0:0 +19 5301160 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15172;SOR=Inf;LSEQ=ACTTGGAAAAGGCTTCCAGG;RSEQ=CACAGCCGGAGTCAGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:18,0:0:2,0:28.4:1:32.4:1:1:0:60:36:1:0:0.1 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:25:1:27.5:1:1:1:60:4:0.1667:0:1 +19 5301281 . G GCCCA 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCTGGGCCCCTGCCAG;RSEQ=CCGTCTCCCACCTTGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:29.5:1:33:0:1:0:60:4:0.6667:0:0 0/0:1:0:0,0:0,1:1,0:0:0,0:48:0:31:0:1:0:60:2:1:0:0 +19 6494915 . C G 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGTGCGGTTTCCAGAGT;RSEQ=AGAAGGGGTGAAGCGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:27:1:1:0:59:4:1:0:1 +19 6495736 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGCAGGCGAGGAAAGGG;RSEQ=ACCATGTTGACGGCCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:9:1:29.5:1:1:0:24.5:4:0.6667:0:1 +19 6554328 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5003;SOR=Inf;LSEQ=TGACACTTGATGGTGAGTGA;RSEQ=AGTGCGGTTGTGGCAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:55,38:93,0:0:2,0:29:1:31.9:1:1:0:60:45.5:1:0:0.1 0/1:108:2:1,1:54,51:105,2:0.0185:2,2:22.5:1:25.5:1:1:1.05828:60:4:0.0189:0:1.5 +19 6554418 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=TCTATGAGACCTGGGCCAGG;RSEQ=GACGGCTTCATAGTAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:15,33:48,0:0:2,0:21:1:29.8:1:1:0:60:47:1:0:0.1 0/1:46:9:4,5:12,25:37,9:0.1957:2,2:21.4:1:28.4:1:0.69819:1.65:60:8:0.1778:0:1.1 +19 7116778 . TG T 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=TTCCATCTGCTGGGGGCGGG;RSEQ=GGGGGAACGAAAAAACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:30.6:1:32.7:1:1:0:60:14:1:0:0.1 0/0:1:0:0,0:1,0:1,0:0:0,0:38:0:34:0:1:0:60:2:1:0:0 +19 7116843 . G A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24451;SOR=0;LSEQ=GCCCCAAAGGAGCAGCAACT;RSEQ=TGGAAACCCCTTGCCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:17.8:1:28.6:1:1:0:60:10:0.4167:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:14.2:1:32.8:1:1:0:60:10:1:0:0 +19 7116963 . T C 224 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGAACGATCTCTGAACTCCA;RSEQ=TGGACATGGTAGAGTCGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:119:119:116,3:0,0:0,119:1:0,1:23.5:1:32.5:1:1:0:59.6:58.5:1:0:1.1 1/0:108:85:80,5:22,1:23,85:0.787:1,2:23.5:1:32.1:1:1:1.37126:60:84:0.7925:0:1.1 +19 7117487 . C T 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00101;SOR=Inf;LSEQ=CACGCATCCTCCCAAACCCC;RSEQ=ACTCTTGTCCCTGCAGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:7,107:114,0:0:2,0:23.1:1:32.2:1:1:0:60:37:1:0:0.1 0/1:103:9:1,8:10,83:93,9:0.0874:2,2:17.6:1:27.3:1:1:1.04:60:18:0.0882:0:1.7 +19 7117506 . G A 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00224;SOR=Inf;LSEQ=CCACTCTTGTCCCTGCAGCC;RSEQ=ACACCCACGGACCACATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:4,78:82,0:0:1,0:25.8:1:31.3:1:1:0:59.5:19.5:1:0:0.1 0/1:62:7:1,6:4,51:55,7:0.1129:2,2:30:1:28.9:1:0.46241:2.09:60:14:0.1129:0:1.9 +19 7119636 . GAC G 108 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.02354;SOR=5.05952;LSEQ=AGTAACAAAGAAGCCATTTA;RSEQ=ACACACACACACGCGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:2:0,2:62,209:271,2:0.0073:2,0:36.5:1:32.5:1:1:0:60:4:0.0074:0:0 0/1:306:11:1,10:90,204:294,11:0.0359:2,2:26.6:1:31.3:1:0.1834:4.39731:59.1:22:0.0364:0:0.2 +19 7119649 . A G 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.67587;SOR=0.61889;LSEQ=CCATTTAGACACACACACAC;RSEQ=CGCGCGCGCGCAAACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:1,2:40,188:228,3:0.0129:2,2:15.7:1:32.3:1:0.44512:2.34:60:6:0.0134:0:1 0/0:250:2:0,2:63,184:247,2:0.008:2,0:21.5:1:33:0:1:0:57.5:4:0.0082:0:1 +19 7119651 . G A 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATTTAGACACACACACACAC;RSEQ=CGCGCGCGCAAACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:18:3,15:33,169:202,18:0.0818:2,2:20.9:1:29.9:1:1:1.02:56.6:36:0.0841:0:2.2 0/0:247:0:0,0:40,156:196,0:0:2,0:23.1:1:30.3:1:1:0:60:27:1:0:0.1 +19 7119653 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.1105;SOR=1.76381;LSEQ=TTAGACACACACACACACGC;RSEQ=CGCGCGCAAACACACACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:15:3,12:26,164:190,15:0.0732:2,2:20.2:1:29.1:1:0.45093:1.57:57.2:30:0.0743:0:2.4 0/1:237:29:13,16:43,164:207,29:0.1224:2,2:21:1:28:1:0.00878:3.08:60:58:0.1239:0:2.1 +19 7119659 . GCA G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=0.50563;SOR=Inf;LSEQ=ACACACACACACGCGCGCGC;RSEQ=AACACACACACGCAAACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:14,138:152,0:0:2,0:25.3:1:32.4:1:1:0:59.7:49.667:1:0:0.3 0/1:193:2:1,1:38,152:190,2:0.0104:2,2:17:0:32:0:0.36584:3.96:60:4:0.0106:0:0 +19 7119775 . A AAACACG 59 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.36341;SOR=0.2895;LSEQ=GCACACACATGCAAATACAC;RSEQ=CAAACACGCATGCGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:0,4:0,18:18,4:0.1818:1,0:26.8:1:29.7:1:1:0:60:8:0.1905:0.0455:0.8 0/1:17:1:0,1:0,16:16,1:0.0588:1,0:31:0:29.3:0:1:0:60:2:0.0588:0:2 +19 7119783 . G A 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85311;LSEQ=ATGCAAATACACACAAACAC;RSEQ=CATGCGCACACATGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:0,14:14,3:0.1765:1,0:21:1:29.7:1:1:0:60:6:0.1765:0:1 0/1:13:2:0,2:0,11:11,2:0.1538:0,0:24.5:1:26:0:1:0:60:4:0.1538:0:2 +19 7119834 . CACACAA C 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.28571;SOR=0;LSEQ=AACACACAAACACATATACA;RSEQ=ACACACACACCCAAACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:23.8:1:33.8:1:1:0:60:10:1:0.2:0 1/0:2:1:0,1:0,1:1,1:0.5:0,0:21:0:34:0:1:0:60:2:0.5:0:0 +19 7119865 . GCA G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACACCCAAACACACACAC;RSEQ=CACACATGCAAACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:11:1:33.2:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7121011 . C CT 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAAGAAGCTACATTTTT;RSEQ=TTTTTTTTTTTCTTTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:1,8:9,2:0.1667:2,0:9:1:28.5:1:1:0:56:4:0.1818:0.0833:0 0/0:2:0:0,0:0,2:2,0:0:0,0:12.5:1:33:0:1:0:60:4:1:0:0 +19 7121115 . T A 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCTCCCTGATTCAAGCAAT;RSEQ=CTCTTGCCTCAGCCTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:30:1:25:1:1:0:52.3:3:0.6:0:2.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7121192 . T C 43 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATGTTTTGTATTTTGAG;RSEQ=AGAGACAGGGTTTCACCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:11:1:27.7:1:1:0:46.3:6:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7122322 . C T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTAGCCAGGCATGGTGG;RSEQ=GCACACCTGTAGTCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:31.3:1:30.7:1:1:0:26.7:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7122389 . G T 87 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=ACTTGAACCTGGGAGGTGGA;RSEQ=GTTGCAGTGAGCTGAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:18.3:1:31.1:1:1:0:37.9:14:1:0:1.6 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:21:0:32:0:1:0:48:2:0.3333:0:1 +19 7122430 . GGCA ATG 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18347;SOR=Inf;LSEQ=CACCACTGCACTCCAGCCTG;RSEQ=ACAGACAGAGTAAGACTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:18,0:18,0:0:1,0:22.2:1:31.7:1:1:0:53.8:36:1:0:0.2 0/1:14:2:1,1:12,0:12,2:0.1429:0,2:30:1:26.6:1:0.14286:0:43:4:0.1429:0:1.5 +19 7122481 . CA C 32 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.91322;LSEQ=AACAAAAAGACAAAACAAAA;RSEQ=AAAAAAACCCCACAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:51,0:51,1:0.0192:1,0:24:0:34:0:1:0:60:2:0.02:0:0 0/1:55:2:2,0:51,2:53,2:0.0364:1,0:7:1:32.3:1:1:0:60:4:0.0377:0.0182:0 +19 7122495 . C CA 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.36783;SOR=0.4948;LSEQ=ACAAAACAAAAAAAACCCCA;RSEQ=AAAAAAAAAAGAAGTATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:8:8,0:65,0:65,8:0.1096:1,0:19.6:1:31.5:1:1:0:59.4:16:0.1127:0.0274:0.1 0/1:70:4:4,0:61,2:63,4:0.0571:1,0:25.3:1:30.6:1:1:0:60:8:0.0615:0.0143:0 +19 7122511 . AT A 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06578;LSEQ=CCCACAAAAAAAAAAGAAGT;RSEQ=CTTGCCCCTTTATATTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:90:86:83,3:4,0:4,86:0.9556:0,1:25.6:1:31.5:1:1:0:59.4:42:0.9655:0.1222:0.3 1/0:91:53:52,1:36,2:38,53:0.5824:2,1:26.8:1:31:1:0.56897:2.86:59.8:52:0.5843:0.0989:0.3 +19 7123031 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.06548;LSEQ=AGCAACCAGGGTTCTTGGAG;RSEQ=AGGGTCCGTGATTCGACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:179:52,127:119,211:330,179:0.3503:2,2:25.5:1:30.5:1:0.11669:1.37655:60:43.75:0.3507:0:1.1 0/1:529:18:5,13:196,315:511,18:0.034:2,2:21.8:1:29.7:1:0.46269:1.6164:60:36:0.0342:0:1.3 +19 7123073 . G A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11722;SOR=Inf;LSEQ=CAGGGTTCTCCTCCCTCCCT;RSEQ=GTGTCTATGTCACACACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:43,198:241,0:0:2,0:20.7:1:31:1:1:0:60:25.778:1:0:0.5 0/1:232:3:2,1:44,185:229,3:0.0129:2,2:14.7:1:20.7:1:0.1011:8.30:60:2:0.0088:0:1 +19 7123192 . T A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00812;SOR=0.19373;LSEQ=CCTTTGTATTTTTTTTTTTT;RSEQ=AATTTTCGAGACGGAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:25:0,25:0,6:6,25:0.7813:0,1:16.8:1:31.3:1:1:0:57.8:50:0.7813:0:1.4 0/1:20:8:1,7:0,10:10,8:0.4:0,2:19.3:1:29.4:1:0.44444:0:58:16:0.4:0:1.9 +19 7124986 . C T 85 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3;SOR=0;LSEQ=TGGAAAATGATGGAAGATTC;RSEQ=GGAAAGTGGTGGAAGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:35.1:1:30.4:1:1:0:58.3:6:1:0:1.3 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:12.5:1:27.5:1:1:0:60:4:0.6667:0:1 +19 7125225 . C T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62332;SOR=2.99341;LSEQ=GTGTCCTCTGTCGCTCTGTG;RSEQ=AGGAGGAGGAGGCAGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:1:1,0:166,54:220,1:0.0045:2,0:29:0:32:0:1:0:60:2:0.0046:0:1 0/1:223:3:2,1:158,62:220,3:0.0135:2,2:23:1:25.3:1:1:1.27277:60:6:0.0138:0:1 +19 7125267 . C T 73 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12448;SOR=5.73639;LSEQ=GGAAGGGTCAGGAAAGCCAG;RSEQ=CCATGTCCCACCCCCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:1:0,1:278,151:429,1:0.0023:2,0:1:0:26:0:0.35349:0:60:2:0.0024:0:1 0/1:454:6:3,3:273,175:448,6:0.0132:2,2:26.2:1:28.5:1:0.68325:1.55837:60:12:0.0135:0:1 +19 7125297 . G A 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCCCCACTGGACTCACCAC;RSEQ=TGATGGCAGGTGAAGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:0:0,0:348,232:580,0:0:2,0:25.5:1:30.8:1:1:0:60:81.857:0.9983:0:0.1 0/1:639:25:14,11:362,251:613,25:0.0391:2,2:27.2:1:29.4:1:0.83662:1.13295:60:24:0.038:0:1.2 +19 7125518 . C T 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00197;SOR=7.03283;LSEQ=CACCTCCCACTCGTCCGGCA;RSEQ=GTACACAGAGCATGGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:648:2:0,2:232,414:646,2:0.0031:2,0:18.5:1:30:1:0.5396:0:60:4:0.0031:0:1 0/1:797:17:6,11:325,455:780,17:0.0213:2,2:25:1:29.7:1:0.80439:1.30909:60:34:0.0215:0:1.1 +19 7125519 . G A 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCCCACTCGTCCGGCAC;RSEQ=TACACAGAGCATGGAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:0:0,0:229,403:632,0:0:2,0:25.8:1:31.5:1:1:0:59.9:78:1:0:0.1 0/1:785:85:31,54:296,404:700,85:0.1083:2,2:24.4:1:29.9:1:0.35162:1.27588:60:84:0.1085:0:1.1 +19 7125900 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGGGATGGAAGACAGG;RSEQ=TGTAATAGGTTGGGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:34:1:1:0:46.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7126218 . A G 42 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTGGGACCACCCAGCCT;RSEQ=CTGACCACCAGACATGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:39.3:1:27:1:1:0:60:2:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7126324 . T C 62 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCAAGACCAGAAGAAC;RSEQ=GCCCAGCTGAGCCCAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:28.3:1:31:1:1:0:60:8:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:31:0:33:0:1:0:60:2:1:0:1 +19 7126505 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11208;SOR=Inf;LSEQ=CTTTTCTTGGCCTCCCTGGG;RSEQ=AACCCATCCTTCACTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:171,31:202,0:0:2,0:22.2:1:31.2:1:1:0:60:32.667:1:0:0.1 0/1:190:3:1,2:142,45:187,3:0.0158:2,2:12.7:1:25.3:1:0.1518:6.23456:60:6:0.0161:0:1 +19 7126889 . G GT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCATCCCTCCCTGGGTG;RSEQ=TTTTTTTTTTGTTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:0,11:11,2:0.1538:0,0:37.5:1:29:1:1:0:60:4:0.1667:0:0.5 0/0:3:0:0,0:0,3:3,0:0:0,0:20.3:1:33:1:1:0:60:6:1:0:0 +19 7128815 . C T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2487;SOR=Inf;LSEQ=ATATCAAGGCATGTTTTCCC;RSEQ=CAGAGAACCAACTGTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:208,74:282,0:0:2,0:24.9:1:31.1:1:1:0:60:55.4:1:0:0.1 0/1:285:3:2,1:194,87:281,3:0.0105:2,2:15:1:20.7:1:1:1.1145:60:2:0.0071:0:1.7 +19 7128928 . G C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAAGACAAAGATGAGGGG;RSEQ=CCGATGATAATTTTTGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:0:0,0:202,318:520,0:0:2,0:28.2:1:31.7:1:1:0:60:56.778:1:0:0.1 0/1:604:21:11,10:252,328:580,21:0.0348:2,2:31.3:1:30.6:1:0.5035:1.43:60:20:0.0334:0:1.1 +19 7128950 . T A 51 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06307;SOR=Inf;LSEQ=CGATGATAATTTTTGCAATA;RSEQ=TTGACGGGACGTCTACTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:157,295:452,0:0:2,0:26.1:1:30.7:1:1:0:60:149.667:1:0:0.1 0/1:494:5:5,0:197,291:488,5:0.0101:2,0:6.2:1:22.2:1:0.01121:0:60:4:0.0082:0:1.2 +19 7128977 . T A 33 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95324;LSEQ=GGACGTCTACTGAAATAGAA;RSEQ=AAGAAAATATATGTTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:80,205:285,3:0.0104:2,2:9.7:1:21.7:1:0.19612:5.09:60:2:0.0071:0:1.7 0/0:302:3:3,0:107,192:299,3:0.0099:2,0:1:0:21:1:0.04748:0:60:2:0.0067:0:1.7 +19 7128994 . C G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=Inf;LSEQ=GAATAAGAAAATATATGTTT;RSEQ=ATATCAATGTGTTTCCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:44,154:198,0:0:2,0:22.1:1:32.2:1:1:0:60:65:1:0:0.1 0/1:197:2:1,1:50,145:195,2:0.0102:2,2:31:1:31.5:1:0.45172:2.88:60:4:0.0102:0:1 +19 7129086 . A G 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49291;SOR=0;LSEQ=TCCTTCCCTCCCTTGTCCAT;RSEQ=AACCTCTCTGCTGCTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:1,21:0,0:0,22:1:0,1:23.6:1:32.3:1:1:0:57.4:44:1:0:1 1/1:26:24:0,24:0,2:2,24:0.9231:0,1:20.3:1:30.4:1:1:0:59.5:23:0.92:0:1.2 +19 7132081 . C T 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00374;SOR=Inf;LSEQ=AAGGCCAGGGCCAGCACCTG;RSEQ=GGCCTCTCCAAGTCATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:144,5:149,0:0:1,0:25.8:1:32.3:1:1:0:59.8:48.667:1:0:0.1 0/1:125:7:6,1:111,7:118,7:0.056:2,2:15:1:28.3:1:0.37805:2.61323:60:14:0.0569:0:1.1 +19 7132173 . G C 185 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=51.90433;LSEQ=TGCCATGGAGACTTACAATA;RSEQ=TCTGTCACGTAGAAATAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:700:1:1,0:389,309:698,1:0.0014:2,0:7:0:14:0:1:0:60:0:0:0:3 0/1:896:62:30,32:467,367:834,62:0.0692:2,2:25.6:1:31.2:1:0.28942:1.35683:60:124:0.0703:0:1.2 +19 7132343 . G A 198 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCTCCTGGGAGGAAGAGA;RSEQ=GAGGAGAAGGAGGGTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:82:21,61:31,125:156,82:0.3445:2,2:24.4:1:31.2:1:0.32524:1.39:60:40:0.3448:0:1.1 0/0:241:0:0,0:56,185:241,0:0:2,0:24.2:1:30.8:1:1:0:60:59.25:1:0:0.2 +19 7132570 . T C 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTTCCTAAGCCAGAAGC;RSEQ=GAGCATTAAACCCTGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:23.5:1:27.5:1:1:0:54.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7132655 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGTTGCCCAGGCTGGAG;RSEQ=GCAATGGCTTAATCTCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:23:1:32.5:1:1:0:41:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7141858 . G A 55 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23939;SOR=3.90604;LSEQ=AGGAAGTGAGAGGCAGGGAT;RSEQ=TAACTCTTGGATGAGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:1:1,0:104,266:370,1:0.0027:2,0:1:0:23:0:0.28302:0:60:2:0.0027:0:1 0/1:478:5:4,1:164,309:473,5:0.0105:2,2:6:1:24:1:0.0539:7.51:60:10:0.0106:0:1.2 +19 7141976 . C A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23557;SOR=Inf;LSEQ=CGGACATCTAAAACTCATCC;RSEQ=ACAAGATTGTTAGGAAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:44,0:0:1,0:28.3:1:32.5:1:1:0:59.4:43:1:0:0.4 0/1:42:2:0,2:2,38:40,2:0.0476:2,0:25.5:1:32.5:1:1:0:60:4:0.0476:0:1 +19 7142064 . C T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08492;SOR=0;LSEQ=GTCTTGCTCTGTCACCCAGG;RSEQ=GGGAGTGCAGTGGTGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:31.5:1:28:1:1:0:56.3:3:0.4286:0:1 0/0:6:0:0,0:1,4:5,0:0:2,0:26.6:1:27.4:1:1:0:50.4:4:1:0:0 +19 7142773 . G T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21661;SOR=0;LSEQ=AGGGTGGAGAATCTGTCCTT;RSEQ=GTCAGCCTTGATGTCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:156,41:197,2:0.0101:2,2:44:0:30.5:1:0.37841:3.77137:60:4:0.0103:0:1.5 0/0:228:0:0,0:159,69:228,0:0:2,0:25.1:1:30.6:1:1:0:60:37:1:0:0.1 +19 7143098 . T A 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03405;SOR=0;LSEQ=AGGGACCTGCGTTTCCGAGA;RSEQ=GGCCTGGAACGACAGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:4:2,2:77,169:246,4:0.016:2,2:18:1:26.8:1:0.59287:2.19:60:8:0.0162:0:1 0/0:330:0:0,0:114,216:330,0:0:2,0:25.4:1:29.4:1:1:0:60:46.143:1:0:0.1 +19 7150418 . C G 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CCGCCGCATGCAAAAAGCCA;RSEQ=AGAAACCCCTGGGTTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:164:164:150,14:0,0:0,164:1:0,2:23.8:1:33.3:1:1:0:60:163:1:0:1.1 1/0:178:136:119,17:37,5:42,136:0.764:2,2:22:1:31.4:1:1:1.05682:60:67:0.7614:0:1.1 +19 7151049 . T C 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTCTTTCCTTCCTTCTT;RSEQ=TTTTCATTTTCTTTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:34.5:1:33.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:32:0:1:0:60:2:1:0:2 +19 7152389 . CAAA C 32 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGATAGAGTGAGACTCTGT;RSEQ=AAAAAAAAAAAAAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:12:1:32.7:1:1:0:60:4:0.6667:0.3333:2.5 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7152404 . A G 55 d5;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCAAAAAAAAAAAAAA;RSEQ=AGAGAGAGAGAGAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:27.7:1:35:1:1:0:60:6:1:0:2.3 1/1:2:2:2,0:0,0:0,2:1:0,0:16.5:1:33.5:1:1:0:60:4:1:0:2 +19 7152418 . A G 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAAAAGAGAGAGAGAGA;RSEQ=AAAAAAAAATGTTAATCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:25.8:1:36:0:1:0:60:8:0.8:0:2 1/1:2:2:2,0:0,0:0,2:1:0,0:30.5:1:33:1:1:0:60:4:1:0:2 +19 7153006 . A C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=0.00048;SOR=0.20935;LSEQ=ACACATACACACACACACAC;RSEQ=CCCCACACACACACACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:88:11,77:1,3:4,88:0.9263:2,2:21:1:31.9:1:0.43397:2.30527:58:176:0.9362:0:2 1/0:83:60:6,54:2,21:23,60:0.7229:2,2:19.2:1:30.2:1:1:1.16:58.3:29:0.716:0:2.2 +19 7153011 . A C 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TACACACACACACACACCCC;RSEQ=CACACACACACACCACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:1,3:4,0:0:2,0:15:1:30.3:1:1:0:53.8:8:1:0:2.3 1/1:67:62:6,56:0,5:5,62:0.9254:0,2:19.1:1:30.5:1:1:0:57.1:61:0.9242:0:2.1 +19 7153013 . A C 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.38074;SOR=0.30144;LSEQ=CACACACACACACACCCCAC;RSEQ=CACACACACACCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:4:1,3:7,66:73,4:0.0519:2,2:21.8:1:26:1:0.36118:3.07:44:3:0.0411:0:2.5 0/1:62:1:0,1:6,55:61,1:0.0161:2,0:28:0:33:0:1:0:60:2:0.0169:0:2 +19 7153020 . CACACCACA C 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.16216;SOR=Inf;LSEQ=ACACACACCCCACACACACA;RSEQ=CACACACACCACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:2,64:66,0:0:1,0:19.5:1:28.3:1:1:0:55.7:12.2:1:0:2.2 0/1:45:2:0,2:1,41:42,2:0.0444:1,0:15.5:1:25.5:1:1:0:36.5:4:0.0465:0.0222:1 +19 7153022 . CACCACA C 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.06865;SOR=Inf;LSEQ=ACACACCCCACACACACACA;RSEQ=CACACACACCACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:1,60:61,0:0:1,0:19.5:1:27.8:1:1:0:55.8:9.167:1:0:2.2 0/1:44:3:0,3:0,37:37,3:0.0682:1,0:8.7:1:28.1:1:1:0:48.3:6:0.0732:0.0455:2.3 +19 7153026 . A C 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.3056;SOR=4.35638;LSEQ=ACCCCACACACACACACACC;RSEQ=CACACACACACCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:1:0,1:1,54:55,1:0.0175:1,0:14:0:11:0:1:0:40:0:0:0:3 0/1:41:3:1,2:0,36:36,3:0.0732:1,2:12.3:1:23.7:1:0.07692:0:53.7:2:0.0571:0:3.3 +19 7153028 . A ACACACAC 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.50078;SOR=0;LSEQ=CCCACACACACACACACCAC;RSEQ=CACACACACCACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:0,2:1,44:45,2:0.0408:1,0:22.5:1:31.6:1:1:0:41:4:0.0444:0.0204:2.5 0/0:39:0:0,0:1,35:36,0:0:1,0:13.8:1:29.3:1:1:0:55.5:72:1:0:2 +19 7153044 . C CACCACACAT 148 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=7.000;MSILEN=2;SSF=0.01052;SOR=0.08207;LSEQ=CCACACACACACACCACACA;RSEQ=ACACACACCACACACCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:34:0,34:0,0:0,34:0.9714:0,1:18.5:1:29.2:1:1:0:50.2:33:0.9706:0.4571:2.3 1/0:22:16:0,16:0,2:2,16:0.7273:0,1:13.1:1:30.5:1:1:0:50.5:32:0.8:0.5909:2 +19 7153064 . CCA C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=7.000;MSILEN=1;SSF=1;SOR=0.72704;LSEQ=CACACACACCACACACCCCC;RSEQ=CACACACACACCACACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:13:0,13:0,7:7,13:0.65:0,1:30.5:1:31.4:1:1:0:46.4:26:0.65:0.1:1.9 1/0:7:4:0,4:0,2:2,4:0.5714:0,0:18.3:1:24.8:1:1:0:31:3:0.5:0.4286:1.8 +19 7153065 . CACA C 44 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.53435;SOR=0;LSEQ=ACACACACCACACACCCCCC;RSEQ=CACACACACCACACACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:0,3:0,3:3,3:0.1667:0,0:6.3:1:28.3:1:1:0:42.3:6:0.4286:0.1111:1.7 0/0:7:0:0,0:0,1:1,0:0:0,0:11:0:31:0:1:0:23:2:0.25:0:3 +19 7162789 . T C 82 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGATGAGCCAAGGTCGCG;RSEQ=CATTGCACTCCAGCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:11.7:1:31.8:1:1:0:42.7:12:0.8571:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7162912 . G T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03964;SOR=Inf;LSEQ=GTTTTCATATGAGATAGAAT;RSEQ=GAGTGTGTGTGTGTGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:85,0:85,0:0:1,0:24.9:1:32.2:1:1:0:60:41.5:1:0:0.1 0/1:70:4:4,0:66,0:66,4:0.0571:1,0:13.8:1:26.8:1:1:0:60:8:0.0597:0:1 +19 7162914 . AGT A 137 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0;SOR=15.99157;LSEQ=TTTCATATGAGATAGAATGG;RSEQ=GTGTGTGTGTGTGCCTTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:2,0:85,0:85,2:0.023:1,0:48.5:1:33.5:1:1:0:60:4:0.0235:0:0 0/1:76:21:21,0:55,0:55,21:0.2763:1,1:23.2:1:31.3:1:1:0:60:42:0.2763:0.0526:0 +19 7162968 . C T 77 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10488;SOR=0.17588;LSEQ=CAGGAAGAGATAGCTGCTTC;RSEQ=CTAGAGGTGAAGCAAAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:5:5,0:144,18:162,5:0.0299:2,0:31.2:1:33.4:1:1:0:60:10:0.0299:0:1 0/0:186:1:0,1:153,32:185,1:0.0054:2,0:1:0:24:0:0.17742:0:60:2:0.0056:0:1 +19 7163065 . G A 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGAGGCAATAATCCAGCTC;RSEQ=AACAGCTCACTGTCTTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:0:0,0:365,289:654,0:0:2,0:24.3:1:30.7:1:1:0:60:92.429:1:0:0.2 0/1:914:63:40,23:471,380:851,63:0.0689:2,2:21.7:1:28.8:1:0.23742:1.40:59.8:30.5:0.0677:0:1.3 +19 7163140 . T G 225 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGCCATTGGGGTCGGAGGG;RSEQ=GGTTTCCACTTCAGAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:886:0:0,0:435,451:886,0:0:2,0:24.8:1:30:1:1:0:60:58.067:1:0:0.2 0/1:1182:178:81,97:479,519:998,178:0.1506:2,2:25.4:1:30.2:1:0.56897:1.10514:59.9:43.5:0.1488:0:2.2 +19 7163154 . G A 220 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=154.06151;LSEQ=GGAGGGTGGTTTCCACTTCA;RSEQ=AATAATCTGGGATGATGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:811:1:1,0:395,415:810,1:0.0012:2,0:1:0:26:0:0.48829:0:60:2:0.0013:0:1 0/1:1038:166:73,93:409,463:872,166:0.1599:2,2:27.6:1:29.9:1:0.49829:1.12526:59.9:165:0.1603:0:2.5 +19 7163214 . T C 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGGCACAGAGGGGTCTG;RSEQ=CAGGGAGAAAGGAAATGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:0:0,0:139,307:446,0:0:2,0:24:1:29.6:1:1:0:60:48.556:1:0:0.1 0/1:483:80:23,57:134,268:402,80:0.1656:2,2:23.6:1:29.5:1:0.51381:1.23858:60:15:0.1572:0:3 +19 7163230 . T C 219 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGTCAGGGAGAAAGGAAA;RSEQ=GGGTCCATCATGAGAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:87,254:341,0:0:2,0:23.4:1:30.3:1:1:0:60:67.2:0.9941:0:0.1 0/1:370:178:51,127:56,134:190,178:0.4811:2,2:23.7:1:29.4:1:0.90875:1.04058:60:88:0.4796:0:1.6 +19 7163326 . T C 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02735;SOR=Inf;LSEQ=TGAGGGCACCCATCCCAGCA;RSEQ=TTTGGGCGGCCAAGGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,43:43,0:0:1,0:26.3:1:30.7:1:1:0:56:42:1:0:0 0/1:31:4:0,4:0,27:27,4:0.129:1,0:32.3:1:34:0:1:0:56.3:8:0.1333:0:1 +19 7166006 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01912;SOR=Inf;LSEQ=GCCATGATCACCCCACTGCA;RSEQ=TGCACTCTAGCCTGGGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:20,0:20,0:0:1,0:21.8:1:31:1:1:0:50.4:40:1:0:0.6 0/1:14:4:4,0:10,0:10,4:0.2857:0,0:25.3:1:31.5:1:1:0:39.8:8:0.2857:0:3 +19 7166014 . T C 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00826;SOR=Inf;LSEQ=CACCCCACTGCATTGCACTC;RSEQ=AGCCTGGGTGACAAAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:24,0:0:1,0:21.8:1:32:1:1:0:46.8:48:1:0:1.1 0/1:17:5:5,0:12,0:12,5:0.2941:0,0:21:1:30:1:1:0:36.6:10:0.2941:0:3 +19 7166036 . C A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00491;SOR=Inf;LSEQ=GCCTGGGTGACAAAGTAAGA;RSEQ=CCTGTCTAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:33,0:0:1,0:18.8:1:32.5:1:1:0:50.2:66:1:0:1.9 0/1:34:8:8,0:26,0:26,8:0.2353:1,0:25.3:1:30.4:1:1:0:47.8:16:0.2353:0:3.6 +19 7166109 . A G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88274;SOR=1.08203;LSEQ=CAACCTCACTGCATCAGCCT;RSEQ=TTAAAAGCAAGAGGTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:171:145:129,16:24,1:25,145:0.848:1,2:26.4:1:31.9:1:0.47281:2.96309:59.6:19.714:0.8625:0:1.8 1/1:197:169:132,37:19,4:23,169:0.8579:2,2:23.6:1:30.5:1:0.78892:1.32955:60:14.364:0.8778:0:1.4 +19 7166138 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14802;LSEQ=AAGAGGTCTGATTCACATAC;RSEQ=AATTCACATTCCCAAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:154:123,31:116,42:158,154:0.4936:2,2:23.9:1:30.3:1:0.18431:1.43:59.7:153:0.4968:0:1.6 0/1:342:43:31,12:195,102:297,43:0.1257:2,2:24.3:1:29.2:1:0.49043:1.35:60:42:0.1257:0:1.7 +19 7166376 . C T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11943;LSEQ=GTCCAACTGTTGGAACCACA;RSEQ=GCATCCTGCCCGTCGAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:644:337:146,191:129,175:304,337:0.5233:2,2:25.5:1:31.1:1:0.87305:1.04:60:336:0.5266:0:1.1 0/1:864:100:45,55:354,410:764,100:0.1157:2,2:24.3:1:29.4:1:0.83165:1.05524:60:32.333:0.114:0:1.1 +19 7166388 . G A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02745;SOR=1.27818;LSEQ=GAACCACACGCATCCTGCCC;RSEQ=TCGAACTCCGTCACATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:595:217:89,128:166,212:378,217:0.3647:2,2:25.2:1:30.5:1:0.54698:1.12591:59.9:71.333:0.3633:0:1.1 0/1:808:342:148,194:210,256:466,342:0.4233:2,2:24.9:1:29.8:1:0.61675:1.07517:60:84.5:0.422:0:1.2 +19 7166541 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=0.19744;LSEQ=TCACCCAACAATCTAATGCC;RSEQ=CAAGAAAAAATAACTCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:45:0,45:0,8:8,45:0.8491:0,1:28.2:1:32.7:1:1:0:59.8:90:0.8491:0:1.1 1/0:46:24:0,24:0,22:22,24:0.5217:1,1:28:1:31.9:1:1:0:60:48:0.5217:0:1 +19 7167601 . AT A 27 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTCAAAAAAAAAAAAAAA;RSEQ=TGGGGATAAAAAAGAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:14:1:27.5:1:1:0:38.5:4:1:0.3333:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7167715 . A G 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACACAGGCAAGGCAAAAT;RSEQ=GAATATTGCCCCAGGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:18.7:1:32.7:1:1:0:59.3:6:0.4286:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7167817 . C A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01557;SOR=0.19227;LSEQ=GACACTATTGACTTTGCATG;RSEQ=CATCGACTGGTGAGATTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:17:14,3:11,0:11,17:0.6071:0,2:26.9:1:30.6:1:0.25794:0:60:34:0.6296:0:1.1 0/1:18:4:4,0:14,0:14,4:0.2222:1,0:22.3:1:28.8:1:1:0:60:8:0.2222:0:1 +19 7167951 . T G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.14133;LSEQ=GCCAGCCAGCCCTCGCCTCC;RSEQ=CAGCGTCTCTCTAACTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:282:142:98,44:98,42:140,142:0.5035:2,2:25.2:1:30.4:1:0.89745:1.04747:60:70:0.5147:0:1.2 0/1:352:44:28,16:212,96:308,44:0.125:2,2:22.8:1:29.3:1:0.49276:1.26101:60:21:0.121:0:1.2 +19 7168159 . C G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50226;SOR=Inf;LSEQ=TATTTCAGTGTAGTTTCAGA;RSEQ=CAAAGCCTGGGACCCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:17,116:133,0:0:2,0:25.7:1:31.4:1:1:0:59.9:65.5:1:0:0.2 0/1:159:2:1,1:27,130:157,2:0.0126:2,2:19:1:33:0:0.32211:4.75:60:4:0.0127:0:1 +19 7168213 . C G 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=0.1266;LSEQ=CCGTGAGAAGGCAGAGGTGA;RSEQ=GCTGCTATTCCCTTAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:29:0,29:0,26:26,29:0.5273:1,1:23.8:1:31.1:1:1:0:60:13.5:0.5094:0:1 0/1:33:4:1,3:0,23:23,4:0.1212:1,2:26.8:1:31.8:1:0.14815:0:60:8:0.129:0:1.3 +19 7168240 . C G 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03778;SOR=0;LSEQ=ATTCCCTTAAGGGTCTCCTC;RSEQ=CCATGTGCCTGGCTGAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:0,9:0,18:18,9:0.3333:1,0:27.4:1:33.8:1:1:0:60:18:0.3462:0:1 0/0:11:0:0,0:0,11:11,0:0:0,0:26.5:1:31.4:1:1:0:60:22:1:0:0.3 +19 7170241 . C T 61 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACTGTGTACATGAGGTA;RSEQ=CTAGACTGCACACTCCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:27.5:1:30.8:1:1:0:51:8:1:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:5:0:28:0:1:0:32:2:1:0:1 +19 7170450 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19935;SOR=Inf;LSEQ=TAAATGTAATGCACTTGAAT;RSEQ=ATGCTGAAACCATCCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:74,1:75,0:0:1,0:23.6:1:32.4:1:1:0:59.7:74:1:0:0.7 0/1:61:2:2,0:58,1:59,2:0.0328:1,0:14.5:1:32:0:1:0:60:4:0.0328:0:1.5 +19 7170505 . C A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.91516;SOR=0.96218;LSEQ=GGAAAAACCATCTTCCACTA;RSEQ=ACCGGTCCCTCATGCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:72:66,6:103,19:122,72:0.3711:2,2:22.1:1:30.6:1:0.18512:2.02:60:144:0.3711:0:2 0/1:185:67:56,11:101,17:118,67:0.3622:2,2:22.3:1:28.9:1:0.83134:1.16602:60:66:0.3587:0:2 +19 7170517 . A G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.186;LSEQ=TTCCACTACACCGGTCCCTC;RSEQ=TGCCAAAAAGGTTGGGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:252:219:180,39:28,4:32,219:0.869:2,2:22.4:1:30.2:1:0.61727:1.51435:59.9:72:0.8675:0:1.4 1/0:252:139:106,33:83,29:112,139:0.5516:2,2:21.6:1:29.2:1:0.76879:1.12:60:45.333:0.5462:0:1.5 +19 7172209 . C T 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CTGGGATTACAGGCATCAGC;RSEQ=ACCACACCTGGCCAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:122,20:142,0:0:2,0:23.1:1:31.2:1:1:0:59.7:141:1:0:0.1 0/1:159:42:33,9:97,20:117,42:0.2642:2,2:24.2:1:29.5:1:0.64155:1.32033:60:41:0.2611:0:1.1 +19 7172469 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25753;SOR=Inf;LSEQ=AGGAAAGGAGAGAATATCCA;RSEQ=TGGGTTTCTATAGACATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:45,165:210,0:0:2,0:24.1:1:32.9:1:1:0:60:420:1:0:0.2 0/1:262:3:2,1:75,184:259,3:0.0115:2,2:27.3:1:27.7:1:0.20736:4.87:60:6:0.0116:0:1 +19 7172526 . C A 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCCATGGTGAGAAGATAA;RSEQ=CCTCAGGCTGCAAATGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:26:0,26:0,40:40,26:0.3939:1,1:27:1:31.2:1:1:0:60:52:0.4:0:1.1 0/0:68:0:0,0:3,65:68,0:0:1,0:23.5:1:31.1:1:1:0:60:67:1:0:0.1 +19 7174490 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18077;SOR=Inf;LSEQ=ACGACCATCCTAAAAGTGCT;RSEQ=TAGGAGCACGCAGCAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:115,5:120,0:0:1,0:22.6:1:32.7:1:1:0:59.9:240:1:0:0 0/1:90:2:2,0:85,3:88,2:0.0222:1,0:25.5:1:31.5:1:1:0:60:4:0.0225:0:1.5 +19 7174755 . CAG C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.63155;SOR=0.747;LSEQ=ACAGCAAGCTAAGGACGGAG;RSEQ=AGAGAGAGAGAAAGAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:9:1,8:75,204:279,9:0.0311:2,2:27.8:1:33:1:0.4533:2.93262:60:18:0.0318:0:0.1 0/1:384:9:3,6:102,273:375,9:0.0234:2,2:27.2:1:32.4:1:0.7097:1.34:60:18:0.0239:0:0.1 +19 7184154 . A G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00573;SOR=0.20459;LSEQ=GAAAAAGGTAGTCAACTCCC;RSEQ=CTCCCAAGCCCAGGACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:25:24,1:21,0:21,25:0.5435:1,1:27.2:1:30.6:1:1:0:60:50:0.5435:0:1.6 0/1:26:5:4,1:21,0:21,5:0.1923:1,2:17.4:1:30.8:1:0.19231:0:60:10:0.2:0:1.4 +19 7184238 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06736;LSEQ=AGCCAATTAACCCTGGGTTT;RSEQ=CACACAGTTTTAACAAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:163:84:74,10:67,12:79,84:0.5153:2,2:23.4:1:28.7:1:0.64806:1.32:60:168:0.5217:0:2.2 0/1:181:12:9,3:144,23:167,12:0.0663:2,2:19.5:1:27.4:1:0.38627:2.07638:60:24:0.0678:0:2 +19 7184243 . C G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.04819;LSEQ=ATTAACCCTGGGTTTGCACA;RSEQ=AGTTTTAACAAGCGGCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:89:76,13:76,18:94,89:0.4863:2,2:24.3:1:33.4:1:0.43729:1.38:60:178:0.4863:0:2.1 0/1:208:9:6,3:164,35:199,9:0.0433:2,2:20.4:1:30.8:1:0.2138:2.33092:60:18:0.0433:0:2.3 +19 7184275 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.95156;LSEQ=GCGGCATCGTCACAACCAAC;RSEQ=CCACGTTCCTTCTCCTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:9:8,1:225,92:317,9:0.0276:2,2:28.4:1:32.8:1:0.45456:3.26:60:18:0.0282:0:1.1 0/1:405:50:35,15:242,112:354,50:0.1235:2,2:24.1:1:29.9:1:0.87203:1.08:60:49:0.1222:0:1.1 +19 7184490 . G A 229 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.00534;LSEQ=GTCCTGGAAGTGGTAGTACG;RSEQ=GGGCGGGCAGGTCTCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:174:65,109:122,190:312,174:0.3573:2,2:25:1:30.9:1:0.7706:1.07657:60:57:0.357:0:1.1 0/0:679:2:2,0:290,387:677,2:0.0029:2,0:1:0:24.5:1:0.18458:0:60:4:0.003:0:1 +19 7184518 . G A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=2.36434;LSEQ=CAGGTCTCCACACACCTGCC;RSEQ=TCCAGGTAGAAGTTGCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:24:10,14:116,224:340,24:0.0659:2,2:26.8:1:31.2:1:0.50726:1.38:60:48:0.067:0:1 0/1:496:71:30,41:165,260:425,71:0.1431:2,2:23.1:1:29.3:1:0.60128:1.15:60:70:0.1431:0:1.2 +19 7184545 . G A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1395;SOR=Inf;LSEQ=TAGAAGTTGCGGCAGGCCAC;RSEQ=CACTTGGTGGGGTCGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:88,194:282,0:0:2,0:25.4:1:31.7:1:1:0:60:69.5:1:0:0.4 0/1:377:4:1,3:147,226:373,4:0.0106:2,2:33.5:1:30:1:1:1.94819:60:8:0.0107:0:1.3 +19 7184560 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13454;SOR=Inf;LSEQ=GCCACGCACTTGGTGGGGTC;RSEQ=TCGGGCTGAGAACAGTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:72,169:241,0:0:2,0:24.1:1:31.4:1:1:0:60:47.2:1:0:0.3 0/1:307:4:3,1:111,192:303,4:0.013:2,2:18.8:1:27.5:1:0.14626:5.16:60:8:0.0131:0:1 +19 7184618 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50434;SOR=Inf;LSEQ=AACAGAGGCCTTCGGCGGTG;RSEQ=AGCCGTGTGACTTACAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:27,91:118,0:0:2,0:28.4:1:32.1:1:1:0:59.9:38.333:1:0:0.2 0/1:150:2:1,1:42,106:148,2:0.0133:2,2:26.5:1:30:1:0.49253:2.51:60:4:0.0139:0:1.5 +19 7184651 . GGA G 144 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=10.000;MSILEN=2;SSF=0.00037;SOR=0.15829;LSEQ=TACAGATGGTCGGGCAAACT;RSEQ=GAGAGAGAGAGAGAGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:21:5,16:9,52:61,21:0.2442:2,2:27.3:1:33:1:0.33523:1.79:58.5:42:0.2471:0.0116:0.5 0/1:83:4:0,4:19,60:79,4:0.0482:2,0:16.5:1:26.5:1:0.56922:0:60:8:0.0494:0.0241:0.3 +19 7184721 . C T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.44565;SOR=0.38356;LSEQ=ATAAATAAATAAATAAATGG;RSEQ=TTTGTCCAATTCCTGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:0,8:0,18:18,8:0.3077:1,0:25.5:1:31:1:1:0:54.4:16:0.32:0:2 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:26.5:1:30.5:1:1:0:42.5:4:0.1429:0:2 +19 7184762 . A G 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.40825;LSEQ=ATATGCAGCAATTCTGGATC;RSEQ=GACAGTGAAAGCCAACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:3,8:0.7273:0,0:25.1:1:30.6:1:1:0:57.6:16:0.7273:0:2.1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:1:0:31:0:1:0:60:2:0.5:0:1 +19 7184801 . C T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACTAACAGTAAAAGCGG;RSEQ=ACGTCTACATCATTACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:31.5:1:29:1:1:0:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 7267253 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18882;SOR=Inf;LSEQ=CCACCACCCACTATTCCCCG;RSEQ=CCCCTACCTAATGACCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:52,2:54,0:0:1,0:21.4:1:31.2:1:1:0:59.8:108:1:0:0.1 0/1:42:2:1,1:39,1:40,2:0.0476:1,2:15:1:27:1:0.09408:27.93708:60:4:0.0476:0:1 +19 7267267 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49645;SOR=Inf;LSEQ=TCCCCGGCCCCTACCTAATG;RSEQ=CCATTTAACATTTTTAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:60,10:70,0:0:2,0:20.6:1:29.3:1:1:0:59.9:16.5:1:0:0.1 0/1:71:2:2,0:61,8:69,2:0.0282:2,0:23.5:1:31:0:1:0:60:4:0.0282:0:1 +19 7267277 . AT A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.02652;SOR=0.4782;LSEQ=CTACCTAATGACCATTTAAC;RSEQ=TTTTAAGCCATAAAACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:36:29,7:45,5:50,36:0.4186:2,2:22.4:1:31.2:1:0.22747:2.1523:60:72:0.4286:0.0698:0 0/1:94:24:20,4:60,10:70,24:0.2553:2,2:24.7:1:30.5:1:0.7487:1.19757:60:48:0.2581:0.0213:0 +19 7267332 . T G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00254;SOR=Inf;LSEQ=ACAAGGCACGAGACACTGCT;RSEQ=AGAACCCTGTATCCCCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:174,71:245,0:0:2,0:25.5:1:30.4:1:1:0:60:121.5:0.9959:0:0.1 0/1:296:10:6,4:200,86:286,10:0.0338:2,2:21.7:1:29.7:1:0.49864:1.54793:60:9:0.0308:0:1.2 +19 7267523 . C T 80 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21876;SOR=0.41154;LSEQ=CCTCCACGGAATCCAGGATA;RSEQ=GGGACCAGTCGATAGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:7:1,6:314,304:618,7:0.0112:2,2:16.4:1:28.6:1:0.06688:6.18265:60:14:0.0113:0:1 0/0:864:4:1,3:435,424:859,4:0.0046:2,2:18.5:1:30.5:1:0.36898:3.07431:59.5:8:0.0047:0:1 +19 7267746 . A G 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGACCCGGAAGAGCAGCA;RSEQ=GTAATCAGTGATCATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:184,196:380,0:0:2,0:24.6:1:30.9:1:1:0:59.9:41.222:0.9973:0:0.1 0/1:491:32:16,16:200,259:459,32:0.0652:2,2:24.7:1:30.4:1:0.58122:1.29:60:64:0.0657:0:1.1 +19 7267980 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49613;SOR=Inf;LSEQ=TGCATCAGAAGGATCAGGGG;RSEQ=AGAGCCGGCTTCATGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:6,40:46,0:0:2,0:24.6:1:32.6:1:1:0:60:92:1:0:0 0/1:51:2:1,1:5,44:49,2:0.0392:2,2:19:1:26.5:1:0.22353:8.12:60:4:0.0417:0:1 +19 7293734 . AT A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.19779;SOR=0;LSEQ=AGTCCACAAGCGGGGGCTCG;RSEQ=TTTGGCTTGGGTGGGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:60,21:81,2:0.0241:2,2:18:1:31.1:1:0.46224:2.81462:60:4:0.0244:0.012:0 0/0:103:0:0,0:72,31:103,0:0:2,0:22.3:1:29.4:1:1:0:60:33.333:1:0:0.2 +19 7293748 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50104;SOR=Inf;LSEQ=GGCTCGATTTTGGCTTGGGT;RSEQ=GGGTCCTCTCCCCATCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:73,47:120,0:0:2,0:21.2:1:31.5:1:1:0:60:119:1:0:0.1 0/1:140:2:1,1:79,59:138,2:0.0143:2,2:32.5:1:30:1:1:1.33614:60:4:0.0143:0:1 +19 7293765 . G T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59618;SOR=0.42371;LSEQ=GGTGGGGTCCTCTCCCCATC;RSEQ=CGGCGCTCCCCGCCCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:76,77:153,2:0.0129:2,2:11.5:1:30.5:1:1:1.01:60:4:0.0134:0:1.5 0/0:182:1:0,1:89,92:181,1:0.0055:2,0:1:0:22:0:1:0:60:2:0.0056:0:1 +19 7293788 . C T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.20414;SOR=0;LSEQ=GCGCTCCCCGCCCACGCCCG;RSEQ=GCCCCCAGACTCACCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:70,109:179,2:0.011:2,2:5:0:32:0:1:1.55:60:4:0.0113:0:0.5 0/0:219:0:0,0:95,124:219,0:0:2,0:28:1:29.6:1:1:0:60:108.5:1:0:0.2 +19 7293818 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22271;SOR=0;LSEQ=CTCACCCTCTCCGGGGTACA;RSEQ=GTGGCCCGCGGCGCCCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:50,104:154,2:0.0128:2,2:8.5:1:30:1:0.54839:2.07:60:4:0.0129:0:1.5 0/0:174:0:0,0:64,110:174,0:0:2,0:25.6:1:31.2:1:1:0:59.7:173:1:0:0.3 +19 7293823 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50008;SOR=Inf;LSEQ=CCTCTCCGGGGTACAGGTGG;RSEQ=CCGCGGCGCCCAGTAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:47,98:145,0:0:2,0:25:1:30.9:1:1:0:59.9:15.111:1:0:0.2 0/1:163:2:1,1:56,105:161,2:0.0123:2,2:12.5:1:28.5:1:1:1.87:60:4:0.0125:0:1 +19 7293838 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21285;SOR=0;LSEQ=GGTGGCCCGCGGCGCCCAGT;RSEQ=GCAGCGCGGCCACCGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:24,73:97,2:0.0202:2,2:9.5:1:31:1:0.44321:3.00:60:4:0.0213:0:1 0/0:115:0:0,0:34,81:115,0:0:2,0:17.4:1:30.1:1:1:0:59.3:230:1:0:0.3 +19 7293898 . G C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCCGCCGGCCCCCGGTG;RSEQ=CCATGGCTGCGGGAGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:25.5:1:33.1:1:1:0:60:16:1:0:1.4 1/1:10:10:6,4:0,0:0,10:1:0,2:15.2:1:30.4:1:1:0:59.8:9:1:0:1.3 +19 7805128 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10832;SOR=6.25391;LSEQ=TAACTCAGTCCCTGTTCCTC;RSEQ=GTCTGAGCACTTAGGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:15,0:14,0:14,15:0.5172:1,1:29.9:1:29.6:1:1:0:60:14:0.5:0:1.3 1/1:8:7:7,0:1,0:1,7:0.875:0,0:25.9:1:31:0:1:0:60:14:0.875:0:1 +19 7805278 . C T 131 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=11.45129;LSEQ=ACCAGATTGGGCTGAATCTG;RSEQ=GGTTACAATGTTTACCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:2:0,2:272,96:368,2:0.0054:2,0:8:1:19:1:0.06963:0:60:1:0.0028:0:2.5 0/1:426:25:20,5:288,113:401,25:0.0587:2,2:24:1:28.3:1:0.4919:1.57:60:50:0.059:0:1.1 +19 7805296 . G T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.94695;LSEQ=TGCGGTTACAATGTTTACCA;RSEQ=TTTATTATAAAGGATACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:109:73,36:292,121:413,109:0.2088:2,2:24:1:30.8:1:0.4816:1.18966:59.7:35.333:0.2062:0:1.2 1/0:627:406:274,132:145,76:221,406:0.6475:2,2:24:1:29.8:1:0.65756:1.09:59.6:405:0.648:0:1.1 +19 7805664 . G A 69 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02001;SOR=Inf;LSEQ=AGTTAAAGGAACAATGGGAA;RSEQ=AACAGCAGAGGAAAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:218,238:456,0:0:2,0:24.6:1:32.6:1:1:0:59.4:75:1:0:0.1 0/1:579:7:5,2:260,312:572,7:0.0121:2,2:16.1:1:24.6:1:0.2556:2.99:59.6:6:0.0105:0:1 +19 7805951 . A T 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0047;LSEQ=CATGTTTACAGTGTTTGGAA;RSEQ=GGAGCAGTGCAGGAGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:993:933:489,444:36,24:60,933:0.9396:2,2:25.4:1:30.8:1:0.28675:1.36154:38.6:76.75:0.9398:0:1.1 0/1:1230:83:46,37:582,565:1147,83:0.0675:2,2:23.7:1:30.3:1:0.42804:1.21:38.2:82:0.0673:0:1.1 +19 7806219 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAAGAATTAGCTGGGCGC;RSEQ=GTGGTGCACGCCCAGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:61:11,50:0,0:0,61:1:0,2:24.4:1:31.5:1:1:0:56.4:60:1:0:1.4 1/1:39:39:3,36:0,0:0,39:1:0,2:25.5:1:31.3:1:1:0:53.2:78:1:0:1.4 +19 7806229 . GC G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=43.94141;LSEQ=AGCTGGGCGCAGTGGTGCAC;RSEQ=CCAGCTAATTTTTGTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:10:2,8:12,35:47,10:0.1754:2,2:23.2:1:32:1:1:1.36425:54.8:20:0.1818:0.0702:1.7 1/1:33:30:4,26:0,3:3,30:0.9091:0,2:23.1:1:32.1:1:1:0:50.6:60:0.9091:0.1515:1.5 +19 7806255 . G A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATTTTTGTACTTTTAGT;RSEQ=GAGTCCCAGCTACTCGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:18,22:0,0:0,40:1:0,2:25.5:1:30.9:1:1:0:49.2:80:1:0:1.7 1/1:18:18:7,11:0,0:0,18:1:0,2:18.9:1:29.8:1:1:0:48.7:17:1:0:1.9 +19 7806377 . T TA 57 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.19733;LSEQ=ACAGAGCAAGACCCCATCTT;RSEQ=AAAAAAAAATAGTAATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:4:4,0:120,10:130,4:0.0292:2,0:32.5:1:30:0:1:0:60:8:0.0294:0:0.3 0/1:115:4:4,0:99,5:104,4:0.0348:1,0:25.8:1:28.5:1:1:0:60:8:0.0351:0.0087:0.3 +19 7806723 . G A 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.83916;LSEQ=GCTCCAAGGGGAGAGAGAGG;RSEQ=TGGGCCACCACGATGAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:744:741:382,359:1,0:1,741:0.996:0,2:25.1:1:30.5:1:1:0:57.5:56:0.9986:0:1.1 1/1:833:829:450,379:0,0:0,829:0.9952:0,2:24.4:1:29:1:1:0:57.3:62.769:0.9951:0:1.1 +19 7806868 . T A 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.69226;SOR=0.58246;LSEQ=CAGGAGAGGCACAATTCACC;RSEQ=AGCAGAGGAAGAAATAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:513:511:208,303:0,0:0,511:0.9961:0,2:26.9:1:30.8:1:1:0:59.6:62.875:0.998:0:1.1 1/1:599:595:270,325:0,0:0,595:0.9933:0,2:26:1:29.9:1:1:0:59.3:118:0.9966:0:1.2 +19 7807027 . A G 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04727;LSEQ=GTTCAGAGTCCCAAATCCCA;RSEQ=TAAACCTGTTTTATTCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:315:311:99,212:3,0:3,311:0.9873:0,2:26:1:32.6:1:0.0336:0:59.6:61.2:0.9903:0:1.1 1/0:448:352:131,221:37,57:94,352:0.7857:2,2:24.3:1:31.5:1:0.7203:1.09486:59.6:116.333:0.7896:0:1.2 +19 7807066 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51112;SOR=Inf;LSEQ=ACAAAAAATAATAGGCCAGG;RSEQ=GCGGTGGCTCACACCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:35,97:132,0:0:2,0:20.9:1:29.8:1:1:0:58.2:25.4:1:0:0.9 0/1:182:2:1,1:52,127:179,2:0.011:2,2:29.5:1:27:1:0.50104:2.43:60:4:0.0112:0:2 +19 7807115 . G A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07732;SOR=Inf;LSEQ=ATTTTGGGAGGCCGAGGCGG;RSEQ=CAGATCATCTGAGGTCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:0,32:32,0:0:1,0:26.1:1:33.4:1:1:0:47:64:1:0:0.3 0/1:51:6:0,6:0,45:45,6:0.1176:1,0:21:1:30.3:1:1:0:46:12:0.1176:0:1.8 +19 7807171 . A G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95448;LSEQ=GACCAACACGGAGAAACCCC;RSEQ=TCTGTACTAAAAATACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:0,7:0,1:1,7:0.7778:0,0:36.7:1:32.3:1:1:0:23:14:0.875:0:1.9 1/0:13:10:0,10:0,3:3,10:0.7692:0,0:39:1:32:1:1:0:26.4:20:0.7692:0:2.3 +19 7807203 . T C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49474;SOR=0;LSEQ=AATACAAAAAATTAGCCGGG;RSEQ=CTGGTGGCGCCTGCCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:27.3:1:32:1:1:0:26.8:16:1:0:2.1 1/1:12:10:0,10:0,2:2,10:0.8333:0,0:16:1:31:1:1:0:23.1:20:0.8333:0:2.3 +19 7808679 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTAGGGATCTGTGT;RSEQ=TATGAGAAGCTATTCACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:30.5:1:1:0:60:4:1:0:4 +19 7808692 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTGTATATGAGAAGCTA;RSEQ=TCACAATGGCAGGTGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:31:1:1:0:60:4:1:0:4 +19 7808709 . C A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTCACAATGGCAGGTGT;RSEQ=TCCTGAGCTGGTGGCCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38.5:1:29.5:1:1:0:60:4:1:0:4 +19 7815543 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50579;SOR=Inf;LSEQ=AGAGGTGCCTTTTGGCCGTA;RSEQ=CTGCCATCTTCCAGTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:33,27:60,0:0:2,0:27.6:1:30.1:1:1:0:56.2:120:1:0:0.8 0/1:79:2:1,1:41,36:77,2:0.0253:2,2:25:1:31:1:1:1.13701:60:4:0.0253:0:1 +19 7815572 . G C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50862;SOR=Inf;LSEQ=TTCCAGTAATTTGCCAAAAT;RSEQ=ATGAACGCAAAGGGGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:27,36:63,0:0:2,0:28.5:1:32.2:1:1:0:53.9:62:1:0:0.9 0/1:86:2:1,1:39,45:84,2:0.0233:2,2:22:0:33:0:1:1.15:29:4:0.0233:0:1.5 +19 7815587 . G C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07604;LSEQ=AAAATGATGAACGCAAAGGG;RSEQ=AAGAGGAGAGGCACCCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:36:12,24:11,15:26,36:0.5806:2,2:22:1:32.8:1:0.59556:1.45748:49.6:72:0.5902:0:1.3 0/1:75:7:3,4:31,37:68,7:0.0933:2,2:26.3:1:32.1:1:1:1.11546:42.7:14:0.0933:0:1.1 +19 7815594 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50358;SOR=Inf;LSEQ=TGAACGCAAAGGGGAAGAGG;RSEQ=GAGGCACCCAATATATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:21,32:53,0:0:2,0:23.8:1:30.5:1:1:0:52.2:25.5:1:0:0.8 0/1:68:2:1,1:29,37:66,2:0.0294:2,2:23:1:28.5:1:1:1.27:58.5:4:0.0294:0:1 +19 7815690 . G T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=GTAAGAAAGGTGATATTGTA;RSEQ=ACATCAAGGGAATGGGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:15:11,4:30,14:44,15:0.2542:2,2:28.5:1:31.7:1:1:1.28:47.9:30:0.2632:0:1 0/0:54:0:0,0:37,17:54,0:0:2,0:22.5:1:31.3:1:1:0:42.6:53:1:0:0.1 +19 7815732 . A G 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01005;SOR=Inf;LSEQ=TTCAAAAAGGAATGGACCAC;RSEQ=AGGGTTACCGTGGCAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:50,29:79,0:0:2,0:25.6:1:30.7:1:1:0:38.1:78:1:0:0.3 0/1:102:8:6,2:58,36:94,8:0.0784:2,2:13.1:1:30.4:1:0.70669:1.85:32.1:16:0.0784:0:1 +19 7815800 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51213;SOR=Inf;LSEQ=GCTGTTGGCATTGTTGTAAA;RSEQ=AAACAAGGGCAAGATTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:22,39:61,0:0:2,0:25.1:1:31.8:1:1:0:39.5:60:1:0:0.1 0/1:87:2:1,1:33,52:85,2:0.023:2,2:35:1:27.5:1:1:1.57:56:4:0.0233:0:1.5 +19 7815817 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20737;SOR=0;LSEQ=AAACAAACAAGGGCAAGATT;RSEQ=ATGCCGAGAGAATTAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:12,35:47,2:0.0408:2,2:22:1:28:1:0.46429:2.84:55.5:4:0.0417:0:1 0/0:58:0:0,0:19,39:58,0:0:2,0:22.9:1:30.9:1:1:0:42:116:1:0:0.2 +19 8463260 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TTGCATCTTGGCAAGCTGCT;RSEQ=TGCTGTGCACCCCCCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:10:1:31.5:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:29.5:1:1:0:60:4:1:0:1 +19 8464809 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49061;SOR=0;LSEQ=TGTCGCGCTTCACCCGCAAC;RSEQ=AGTTCAACCTGGAGAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:23,1:24,2:0.0769:1,2:18.5:1:28.5:1:0.15077:16.61257:60:4:0.0769:0:1 0/0:24:0:0,0:23,1:24,0:0:1,0:24.8:1:28.8:1:1:0:60:23:1:0:0.1 +19 8464838 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22435;SOR=0;LSEQ=CTGGAGAGCAAGAGCACCAT;RSEQ=GGCGTGGAGTTCGCCACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:37,2:39,2:0.0488:2,2:30.5:1:29.5:1:0.14268:15.3059:60:4:0.0488:0:1 0/0:45:0:0,0:43,2:45,0:0:1,0:22.5:1:30.6:1:1:0:60:44:1:0:0 +19 8465005 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20216;SOR=0;LSEQ=CGTGGGCTTGCAGCGCGTGG;RSEQ=CTTGGAAGGATGTGTAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:1,31:32,2:0.0588:1,2:28:1:31.5:1:0.11586:22.27:60:4:0.0588:0:1.5 0/0:41:0:0,0:3,38:41,0:0:2,0:22.8:1:32:1:1:0:60:82:1:0:0.1 +19 8465083 . G A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAGTGAGGCTGGAAGAAC;RSEQ=CTTTAGCCATGCGCCGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:3,12:0,0:0,15:1:0,2:20:1:30.7:1:1:0:60:30:1:0:1.4 1/1:8:8:2,6:0,0:0,8:1:0,2:26.3:1:27:1:1:0:60:7:1:0:1.8 +19 8465102 . G A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTTAGCCATGCGCCGTG;RSEQ=GACCCTCAGGCTGACCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:2,9:11,2:0.1538:2,2:22:0:33:1:0.42308:3.87:60:4:0.1538:0:2 0/0:6:0:0,0:1,5:6,0:0:2,0:39:1:30.8:1:1:0:60:12:1:0:2 +19 8988233 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTAGCTGGGACCACAGGC;RSEQ=TGCACCACCACACCTGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29.5:1:1:0:30.5:4:1:0:1 +19 8989995 . A G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAGGCTGGCAGTGACCCAC;RSEQ=GAGAGAAGGAAGAGCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:7,7:0,0:0,14:1:0,2:19.6:1:28.9:1:1:0:48.9:13:1:0:1.1 1/1:8:8:4,4:0,0:0,8:1:0,2:30:1:29.5:1:1:0:41.9:16:1:0:1.1 +19 8990077 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16256;SOR=Inf;LSEQ=CCCCTCCTTCCAGCCAAGGG;RSEQ=GGTGGTGAGTGAGCGGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:17,0:0:2,0:21.1:1:30.7:1:1:0:56:34:1:0:0.3 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:34:1:31:1:1:1.4491:60:4:0.1667:0:1 +19 8990129 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=GAAACTGTGCTTTTTCCACG;RSEQ=AACTGTGCAACTCACAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:26:1:28:1:1:1.13389:60:4:0.1176:0:1 0/0:17:0:0,0:10,7:17,0:0:2,0:29.6:1:31:1:1:0:60:34:1:0:0.2 +19 8990409 . A G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAATAGCTCCAGGCTGT;RSEQ=CTTTTCCCCTGCTAGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:5,7:0,0:0,12:1:0,2:22.2:1:31.6:1:1:0:54.4:24:1:0:1 1/1:10:10:4,6:0,0:0,10:1:0,2:23.4:1:32.2:1:1:0:48.4:20:1:0:1.3 +19 8990627 . A G 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCCCTGGGCTTGGGCCCCT;RSEQ=GTGGGAGGGATGGCTGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:25.5:1:32.5:1:1:0:60:4:0.6667:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:16:0:32:0:1:0:60:2:1:0:2 +19 8990629 . T C 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCTGGGCTTGGGCCCCTAG;RSEQ=GGGAGGGATGGCTGTAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:25.5:1:32.5:1:1:0:60:4:0.6667:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:18:0:31:0:1:0:60:2:1:0:2 +19 8990761 . C A 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CTCCACCAGGGGACAAAGTG;RSEQ=TTCATTAAATGGGTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:41.5:1:33:0:1:0:60:4:0.6667:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:28:1:32.8:1:1:0:60:8:1:0:0 +19 8991073 . T A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.42857;SOR=Inf;LSEQ=TGACAATAACATCATCATCA;RSEQ=CAACAACAACAACCAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:27.3:1:28.3:1:1:0:52.3:6:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:25.5:1:27:1:1:1:60:4:0.5:0:1 +19 8991200 . G A 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.04727;LSEQ=GCTGAAAACCCAAAAGGCCA;RSEQ=AGTGCCTCTTTTCCTCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:3,0:3,5:0.625:0,2:16.4:1:30.4:1:0.46429:0:52.4:10:0.625:0:1 1/0:11:7:4,3:2,2:4,7:0.6364:2,2:18.9:1:29.4:1:1:1.30:55.6:14:0.6364:0:1 +19 9291308 . G A 47 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGCATCTGTTGTCAACAT;RSEQ=AGATTAATTTGCAGATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:27.3:1:29.7:1:1:0:60:6:1:0:1 +19 9291693 . CA TG 28 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCTGTAGTCATAGCTACT;RSEQ=GGAGGCTGAGGTGGGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:28.8:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 9293025 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16451;SOR=0;LSEQ=CTGAAATGAGTTAACAGTTT;RSEQ=TTATAATTTATTGTATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:125,40:165,2:0.012:2,2:14.5:1:29.5:1:0.43186:3.09927:60:4:0.0124:0:1 0/0:244:0:0,0:176,68:244,0:0:2,0:24.6:1:28:1:1:0:58.4:80.333:1:0:0.1 +19 9293144 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16653;SOR=0;LSEQ=CTGTTAGCGTAGCGAACCTT;RSEQ=TACATAAAATACATGCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:0,2:38,116:154,2:0.0127:2,0:11:1:29:1:1:0:60:4:0.0128:0:1 0/0:227:0:0,0:63,164:227,0:0:2,0:21:1:31:1:1:0:59.6:55.75:1:0:0.1 +19 9293159 . G A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27956;SOR=Inf;LSEQ=ACCTTGTACATAAAATACAT;RSEQ=CATACTTTATTTATTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:17,80:97,0:0:2,0:24:1:32.2:1:1:0:57.9:31.333:1:0:0.2 0/1:148:3:2,1:18,127:145,3:0.0203:2,2:7:1:25.7:1:0.04809:13.66:60:6:0.0205:0:1 +19 9293193 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21336;SOR=0;LSEQ=TTTATTTATTTATTTATTAT;RSEQ=ATTATTATTATTATTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:5,39:44,2:0.0435:2,2:12.5:1:30.5:1:0.24638:7.21:60:4:0.0444:0:1 0/0:53:0:0,0:4,49:53,0:0:2,0:23.1:1:31.5:1:1:0:58:106:1:0:0.1 +19 9293518 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49317;SOR=Inf;LSEQ=CATGCATATACTTTTGATAG;RSEQ=ACATGTGAAGGGATCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:22,12:34,0:0:2,0:23:1:31.8:1:1:0:55.5:33:1:0:0.1 0/1:36:2:1,1:23,11:34,2:0.0556:2,2:28:0:31:1:1:2.045:60:4:0.0556:0:1 +19 9293524 . T TG 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0611;SOR=0.2618;LSEQ=TATACTTTTGATAGCACATG;RSEQ=GAAGGGATCTCTCTAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:5,4:19,8:27,9:0.25:2,2:23.9:1:32.7:1:0.44283:1.8645:53.9:18:0.25:0.0278:0.1 0/1:38:3:2,1:24,11:35,3:0.0789:2,2:28:1:33:0:1:1.08838:54:6:0.0789:0:0 +19 9293701 . G A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58462;SOR=0.39042;LSEQ=TCAGGGCCTTCACAGCCACC;RSEQ=TAGGTTTTCTTCTCACCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:86,101:187,2:0.0106:2,2:35:1:31.5:1:1:1.17:26.5:4:0.0108:0:1 0/0:241:1:0,1:108,132:240,1:0.0041:2,0:40:0:28:0:1:0:27:2:0.0042:0:1 +19 9293747 . T A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24619;SOR=Inf;LSEQ=TGTTCTTACGAAATTCTACT;RSEQ=TGCTTCCCCAGGAACTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:28,68:96,0:0:2,0:22:1:30.7:1:1:0:58.1:192:1:0:0.3 0/1:98:3:2,1:29,66:95,3:0.0306:2,2:5.7:1:27.7:1:0.23439:4.47:60:6:0.0313:0:1 +19 9293782 . G C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65824;SOR=0.80224;LSEQ=CTTTAGTAGTTTCTCGTCAG;RSEQ=CCCACAGCCAGCGCAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:20:1,19:0,22:22,20:0.4762:1,1:21.9:1:32.3:1:0.47619:0:57.2:40:0.4762:0:1.1 0/1:38:16:2,14:1,21:22,16:0.4211:1,2:21.6:1:30.8:1:0.56188:2.91:57.9:32:0.4324:0:1.2 +19 9425404 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=CATTTGTAAGACCCTCTGTA;RSEQ=CTTGATGGCCTCGATCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:23.2:1:33.8:1:1:0:55:10:1:0:0.2 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:32:1:27:1:1:2.44949:44.5:4:0.3333:0:1 +19 9425482 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20029;SOR=0;LSEQ=CCCAAAGGCAAGTAATAGCA;RSEQ=GATGGCTGTCCTGAGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:14,8:22,2:0.0833:2,2:22:1:31:1:1:1.70775:50.5:4:0.0833:0:1 0/0:29:0:0,0:17,12:29,0:0:2,0:21.9:1:29.4:1:1:0:49:58:1:0:0.1 +19 10244476 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21533;SOR=Inf;LSEQ=GGACCATCAGGAAACATTAA;RSEQ=GTACTGATGTTAACAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:20,170:190,0:0:2,0:24:1:30.4:1:1:0:59.8:94:1:0:0.1 0/1:165:2:1,1:21,142:163,2:0.0121:2,2:28.5:1:29:1:0.24959:6.63:60:4:0.0123:0:1 +19 10244554 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03998;SOR=0.20204;LSEQ=AGACTGAACACTCCTCAAAC;RSEQ=GTCCCCAGAGGGTTCTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:19:2,17:5,27:32,19:0.3725:2,2:27.7:1:31.5:1:0.69903:1.56079:58.2:18:0.3673:0:1.3 0/1:19:2:1,1:1,16:17,2:0.1053:1,2:14.5:1:31.5:1:0.20468:11.66:60:4:0.1053:0:1 +19 10244805 . A G 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09573;SOR=Inf;LSEQ=GTGACCCGCCTGAGTCCCAG;RSEQ=GCCCAAAACGGTGGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:291,46:337,0:0:2,0:23:1:30.3:1:1:0:60:41.125:1:0:0.1 0/1:286:3:1,2:237,45:282,3:0.0105:2,2:8.7:1:24.3:1:0.07164:10.39431:60:2:0.0071:0:1.3 +19 10246029 . G A 44 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATGAAAATACACTTAACT;RSEQ=AGACTAACTCATAGACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:24:1:28.3:1:1:0:60:6:0.3333:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 10246947 . G A 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25131;SOR=Inf;LSEQ=TTGAACTGCCTGGCTGCGGG;RSEQ=TCGCAGGCTTTGCCGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:83,167:250,0:0:2,0:23.6:1:31.8:1:1:0:60:249:1:0:0.1 0/1:282:3:2,1:106,173:279,3:0.0106:2,2:7:1:27:1:0.56043:3.25:60:6:0.0109:0:1 +19 10246979 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49909;SOR=Inf;LSEQ=GCCGGCTGGAAGACAGGACA;RSEQ=TGATGAGGCTGCAGTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:52,129:181,0:0:2,0:26.7:1:32.6:1:1:0:59.9:362:1:0:0.1 0/1:192:2:1,1:57,133:190,2:0.0104:2,2:34.5:1:28.5:1:0.51402:2.32:60:4:0.0105:0:1 +19 10246990 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21778;SOR=0;LSEQ=GACAGGACAGTGATGAGGCT;RSEQ=CAGTTGTGGGATGGGGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:40,109:149,2:0.0132:2,2:18:1:29.5:1:0.47064:2.70:60:4:0.0134:0:1 0/0:172:0:0,0:49,123:172,0:0:2,0:24.5:1:31.3:1:1:0:59:56.333:1:0:0.1 +19 10247043 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23352;SOR=Inf;LSEQ=TGGCTCTTAGAGCTTTGGGA;RSEQ=GCAGAGATGGCACCTCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:8,45:53,0:0:2,0:21.4:1:31.8:1:1:0:49.1:106:1:0:0.1 0/1:51:2:1,1:7,42:49,2:0.0392:2,2:26.5:1:28:1:0.29176:5.68:52:4:0.0392:0:1 +19 10247946 . G A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24895;SOR=Inf;LSEQ=GCATGCGGGCAGCCACCAAT;RSEQ=CACTCATGTCCTGAAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:72,203:275,0:0:2,0:22.3:1:31.4:1:1:0:60:24:1:0:0.1 0/1:286:3:1,2:87,196:283,3:0.0105:2,2:14.7:1:22:1:1:1.13:60:2:0.0072:0:1 +19 10247971 . G A 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.10095;SOR=Inf;LSEQ=CATGTCCTGAAAGAGTGTGG;RSEQ=GGGCCCAGCTGTCACCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:20,151:171,0:0:2,0:25.2:1:30.4:1:1:0:60:27.5:1:0:0.1 0/1:150:3:2,1:27,120:147,3:0.02:2,2:7.3:1:26.7:1:0.09574:8.70:60:6:0.02:0:1.7 +19 10247979 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19309;SOR=Inf;LSEQ=GAAAGAGTGTGGGGGGCCCA;RSEQ=CTGTCACCTCATGTGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:16,139:155,0:0:2,0:25.9:1:31.7:1:1:0:60:30:1:0:0.1 0/1:122:2:1,1:16,104:120,2:0.0164:2,2:21:1:25:1:0.26026:6.34:60:4:0.0165:0:1 +19 10249340 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18785;SOR=Inf;LSEQ=GACACTCCCAACTGGACTGG;RSEQ=CAGACCCAGGCCCAGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:7,93:100,0:0:2,0:26.2:1:31.3:1:1:0:59.7:32.333:1:0:0.2 0/1:77:2:1,1:9,66:75,2:0.026:2,2:29:0:30.5:1:0.24436:7.01:60:4:0.0263:0:1.5 +19 10250311 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60058;SOR=2.29389;LSEQ=GGCTGCTGGCCGGGTCACGT;RSEQ=CTGGCCACATCTGTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:0,1:140,21:161,1:0.0062:2,0:1:0:26:0:0.1358:0:60:2:0.0064:0:1 0/1:142:2:1,1:118,22:140,2:0.0141:2,2:24:1:27:1:0.29867:5.26803:60:4:0.0143:0:1 +19 10250332 . G A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10735;SOR=Inf;LSEQ=CTGGCCACATCTGTCTGCCC;RSEQ=CCCCAGCCCCAGGGCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:196,48:244,0:0:2,0:23.1:1:29.8:1:1:0:60:29.5:1:0:0.1 0/1:222:3:2,1:166,53:219,3:0.0135:2,2:7:1:26:1:0.56851:1.56254:60:6:0.0137:0:1 +19 10250515 . G A 62 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03568;SOR=Inf;LSEQ=TGTAGGGGGCAGGAGAGACT;RSEQ=CAGGAGTCACCTCCACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:159,309:468,0:0:2,0:25.1:1:32.1:1:1:0:60:65.857:1:0:0.1 0/1:574:6:5,1:204,363:567,6:0.0105:2,2:12.2:1:24.2:1:0.02632:8.87:60:12:0.0106:0:1 +19 10250567 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20086;SOR=Inf;LSEQ=ACGACCCACTGTGCCGGAAG;RSEQ=CCCTCACGAATGTTATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:47,142:189,0:0:2,0:23:1:31:1:1:0:60:22.625:1:0:0.2 0/1:154:2:1,1:34,118:152,2:0.013:2,2:34:1:27:1:0.40404:3.44:60:4:0.0137:0:1 +19 10250613 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1891;SOR=Inf;LSEQ=TCCCTGGTGAGAGCTGAGCT;RSEQ=TGAGCTTCCGGGGGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:89,64:153,0:0:2,0:25.9:1:32.8:1:1:0:60:75.5:1:0:0.2 0/1:119:2:1,1:74,43:117,2:0.0168:2,2:33:1:31.5:1:1:1.71264:60:4:0.0169:0:1 +19 10250687 . C T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20145;SOR=4.33568;LSEQ=CATGCGGCACAGCCCCGGGC;RSEQ=GTCTGGCAACACTGGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:1:0,1:275,117:392,1:0.0025:2,0:1:0:26:0:0.30025:0:60:2:0.0026:0:1 0/1:365:4:1,3:235,126:361,4:0.011:2,2:8.8:1:27:1:0.12852:5.56818:60:8:0.0111:0:1 +19 10251396 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0948;SOR=0;LSEQ=CGGGGTTGGAAGTCGTTTCA;RSEQ=GTAGCACCTGCCCGGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:235,52:287,3:0.0103:2,2:14:1:31.7:1:0.45545:2.25168:60:6:0.0105:0:1.3 0/0:346:0:0,0:264,82:346,0:0:2,0:21.6:1:30.9:1:1:0:60:172:1:0:0.1 +19 10251709 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24893;SOR=Inf;LSEQ=TAACACCAGAGGTGGTTTTA;RSEQ=ACTGAGGGATTCACAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:176,90:266,0:0:2,0:24.9:1:32:1:1:0:60:32.25:0.9961:0:0.5 0/1:278:3:1,2:187,88:275,3:0.0108:2,2:8:1:25:1:0.24572:4.22571:60:6:0.0109:0:2 +19 10251717 . G T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12379;SOR=Inf;LSEQ=GAGGTGGTTTTACACTGAGG;RSEQ=ATTCACAGGCAGCCTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:202,108:310,0:0:2,0:23.8:1:31.6:1:1:0:60:50.667:1:0:0.5 0/1:310:4:2,2:204,101:305,4:0.0129:2,2:14:1:23.8:1:0.60301:2.01489:60:3:0.0099:0:2 +19 10251747 . A G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00351;SOR=1.45377;LSEQ=CAGCCTCCAAGTTACAGAAG;RSEQ=ATAACTTGAAAAGAAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:215:143,72:148,88:236,215:0.4746:2,2:22.6:1:31.4:1:0.43109:1.18:59.9:70.667:0.4743:0:1.1 1/0:553:314:201,113:141,95:236,314:0.5678:2,2:23.7:1:30.2:1:0.32896:1.20:60:43.857:0.5633:0:1.1 +19 10252620 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51875;SOR=Inf;LSEQ=AGCTGAAACCCTGCAGCCAA;RSEQ=CCGCCTTGTGTATAACCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:91,11:102,0:0:2,0:23.3:1:32.5:1:1:0:60:33:1:0:0.1 0/1:154:2:1,1:125,26:151,2:0.013:2,2:17.5:1:27.5:1:0.32276:4.7367:60:4:0.0133:0:1 +19 10252760 . G A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03107;SOR=Inf;LSEQ=GTACACCTGGACGCACTCGG;RSEQ=CAGGTCCTCCCCATACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:0:0,0:266,228:494,0:0:2,0:26.7:1:31.7:1:1:0:59.9:69.571:1:0:0.1 0/1:519:6:5,1:268,245:513,6:0.0116:2,2:12.7:1:27.2:1:0.21985:4.56:59.3:12:0.0118:0:1.2 +19 10252936 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2267;SOR=0;LSEQ=CGTTAGGAGCTCTCCTTTGT;RSEQ=GTGAGCTTATGCTGAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:43,140:183,2:0.0108:2,2:21.5:1:30.5:1:0.42009:3.23:60:4:0.011:0:1 0/0:203:0:0,0:59,144:203,0:0:2,0:25:1:30.6:1:1:0:60:100.5:1:0:0.1 +19 10253099 . T G 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=1;SOR=1.39581;LSEQ=TGGGGAACTGCAAGGTAGAC;RSEQ=CCCCCCCATTTAGGGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:5,7:0.5833:0,0:24:1:30.1:1:1:0:60:6:0.5455:0:1.7 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:37:1:33.5:1:1:0:60:4:0.6667:0:1.5 +19 10254733 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22791;SOR=0;LSEQ=GTCAGTCAGGCATGACTGAC;RSEQ=AGTGAAAATAACCATTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:9,111:120,2:0.0164:2,2:12:0:32:1:0.15784:11.75:60:4:0.0165:0:1 0/0:133:0:0,0:16,116:132,0:0:2,0:23:1:31.1:1:1:0:60:32:1:0:0.1 +19 10256889 . CCA C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10476;SOR=Inf;LSEQ=CGATTTATGTTGTCTGTTTG;RSEQ=CCTATGCCAACGTGACGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:45,2:47,0:0:1,0:25.4:1:31.7:1:1:0:59.6:94:1:0:0.2 0/1:23:2:1,1:21,0:21,2:0.087:1,2:43.5:1:30.5:1:0.08696:0:60:4:0.0909:0:0 +19 10256971 . C T 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=AGGAGGGGGACACCACAAAG;RSEQ=CAGCCTGGCTCAGCCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:146,26:172,2:0.0115:2,2:7:1:26.5:1:0.28702:5.52933:60:4:0.0116:0:1 0/0:168:0:0,0:143,25:168,0:0:2,0:23:1:31.5:1:1:0:60:167:1:0:0.1 +19 10257245 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=0.40264;LSEQ=CATAAGGCCCTGAGGTGGCC;RSEQ=GCAGTGGCCGCAGCAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:146:81:15,66:13,52:65,81:0.5548:2,2:23.7:1:31.7:1:0.83552:1.09928:60:162:0.5664:0:1.1 0/1:123:41:9,32:22,60:82,41:0.3333:2,2:23.1:1:30:1:0.66177:1.30096:60:40:0.3279:0:1 +19 10257412 . T C 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58403;SOR=2.13794;LSEQ=GAGAGAACATAGCAAGAAAA;RSEQ=CAGGCAACTTTTGAGTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:30.5:1:33:0:1:0:60:4:0.1818:0:1.5 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:25.5:1:27:1:1:0:60:4:0.3333:0:1 +19 10259732 . G A 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62772;SOR=0.38786;LSEQ=GTGTCAGGCCAGGCGCAGTG;RSEQ=CTCATGCCTGTATTCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:3:2,1:28,174:202,3:0.0146:2,2:17:1:27.7:1:0.05667:12.17:59.7:6:0.0152:0:1 0/0:175:1:1,0:35,139:174,1:0.0057:2,0:1:0:22:0:0.20571:0:60:2:0.0057:0:1 +19 10259739 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21313;SOR=Inf;LSEQ=GCCAGGCGCAGTGGCTCATG;RSEQ=CTGTATTCCCAGCACTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:20,152:172,0:0:2,0:25.6:1:31.4:1:1:0:56.7:42:1:0:0.1 0/1:148:2:1,1:27,119:146,2:0.0135:2,2:30:1:28:1:0.34363:4.35:56:4:0.0137:0:1 +19 10260006 . C CA 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.97372;LSEQ=AGCGAAACTCAGTCTCAAAA;RSEQ=AAAAAAAAAAACAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:9:9,0:67,2:69,9:0.1154:1,0:14.6:1:31.3:1:1:0:41:18:0.1154:0.0513:2.9 0/1:71:8:8,0:61,1:62,8:0.1127:1,0:26.6:1:29.4:1:1:0:56.1:16:0.1143:0:1.4 +19 10260018 . C CA 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01794;LSEQ=TCTCAAAACAAAAAAAAAAA;RSEQ=AAAAAAAAAACCAAATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:4:4,0:101,2:103,4:0.0342:1,0:23.8:1:31.5:1:1:0:57:8:0.0412:0:2.3 0/1:115:4:4,0:98,3:101,4:0.0348:1,0:18:1:29.7:1:1:0:48.3:8:0.0435:0.0087:2.8 +19 10260030 . C A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01815;SOR=3.12315;LSEQ=AAAAAAAACAAAAAAAAAAC;RSEQ=AAATTAAAAAAAAATACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:6:5,1:135,4:139,6:0.0411:1,2:27.3:1:26.2:1:0.19293:6.55483:48.2:2:0.0339:0:2.5 0/1:152:18:16,2:126,8:134,18:0.1184:2,2:23.2:1:29.3:1:0.33638:1.95792:55:36:0.1333:0:2.1 +19 10260035 . T TA 65 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.72445;SOR=1.57418;LSEQ=AAACAAAAAAAAAACCAAAT;RSEQ=AAAAAAAAATACAAATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:3:3,0:143,7:150,3:0.0188:1,0:22.7:1:29:1:1:0:60:6:0.0256:0:2.7 0/1:171:5:5,0:148,16:164,5:0.0292:2,0:31.8:1:28.2:1:1:0:56.2:10:0.0365:0:1.6 +19 10260362 . A G 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11491;SOR=Inf;LSEQ=AGAAGACGGGCATGGGGAGA;RSEQ=AGTTCTGACTTGGCCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:66,157:223,0:0:2,0:25.7:1:30.9:1:1:0:60:110.5:1:0:0.1 0/1:212:3:2,1:79,130:209,3:0.0142:2,2:40:1:26:1:0.55946:3.27:60:2:0.0096:0:1 +19 10260400 . T C 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01473;SOR=0;LSEQ=CAGATATGTGACCAAGTCTA;RSEQ=GCAGGAGCACTCGTCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:7:2,5:43,105:148,7:0.0452:2,2:25:1:30.7:1:1:1.02367:60:14:0.0467:0:1 0/0:148:0:0,0:60,88:148,0:0:2,0:23.8:1:29.7:1:1:0:60:73:1:0:0.1 +19 10260543 . C T 92 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03871;SOR=4.76761;LSEQ=GCAAACCTTGCTAGATACAG;RSEQ=GGTTTTGAGGAATCATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:693:2:1,1:424,267:691,2:0.0029:2,2:7:1:28.5:1:1:1.58686:60:4:0.0029:0:1 0/1:734:10:2,8:401,323:724,10:0.0136:2,2:17.6:1:27.9:1:0.0492:4.95681:60:20:0.0138:0:1 +19 10262651 . C T 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=Inf;LSEQ=TTGCAGACCAGCCTGGCCAA;RSEQ=GTGGTGAAACCCCATCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:0,55:55,0:0:1,0:23.9:1:30.2:1:1:0:55.1:26.5:1:0:0.1 0/1:36:8:0,8:0,28:28,8:0.2222:1,0:21:1:29.5:1:1:0:56.5:16:0.2222:0:1.1 +19 10264885 . CAG C 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.77391;SOR=1.20345;LSEQ=GCAGCCAGAGTCTCAAGCCA;RSEQ=AGAGAAAGATGGAGCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:6:6,0:101,5:106,6:0.0536:1,0:39.8:1:32.5:1:1:0:60:12:0.0536:0:0 0/1:94:6:5,1:84,4:88,6:0.0638:1,2:19.5:1:31.1:1:0.2863:4.09141:60:12:0.0652:0.0106:0.2 +19 10265248 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.51026;LSEQ=CCAGTCTTCACTCTGGTCCC;RSEQ=GCCGCATCCTTACCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:498:275:155,120:129,92:221,275:0.5522:2,2:25.7:1:30.9:1:0.715:1.08537:59.9:274:0.5547:0:1.5 0/1:632:244:123,121:200,188:388,244:0.3861:2,2:23.3:1:29.6:1:0.80657:1.04648:60:121:0.3878:0:1.6 +19 10265312 . T C 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03239;SOR=0;LSEQ=ATCAGGTCCCGCATGCAGGG;RSEQ=GTCAGGAAGATGGGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:637:637:322,315:0,0:0,637:1:0,2:26.1:1:30.7:1:1:0:59.9:56.909:1:0:1.3 1/1:713:707:346,361:2,2:4,707:0.9916:2,2:24.4:1:30.1:1:1:1.04331:59.9:116.833:0.9929:0:1.3 +19 10265593 . G T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38002;LSEQ=TCTCTTACCTCGATCTTGTT;RSEQ=ATCAGGTCCTCATAGGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:639:271:155,116:215,151:366,271:0.4241:2,2:25.6:1:29.9:1:0.74536:1.06548:60:270:0.4265:0:1.1 0/1:723:158:85,73:313,251:564,158:0.2185:2,2:23.7:1:28.8:1:0.71809:1.07086:60:316:0.2207:0:1.1 +19 10266418 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16646;SOR=Inf;LSEQ=TAAGGTTCCCAGTCACATGG;RSEQ=CTTCTGCAAGCCTGCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:107,4:111,0:0:1,0:23.4:1:32:1:1:0:60:36:1:0:0.1 0/1:77:2:2,0:71,4:75,2:0.026:2,0:16.5:1:30:1:1:0:60:4:0.0263:0:1 +19 10266681 . G A 41 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.90215;LSEQ=ACATCCCAAACCCAGGAGGC;RSEQ=CTCTAAGCGCCCACTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:1,2:51,179:230,3:0.0129:2,2:23:1:28.3:1:0.53297:1.75:60:6:0.0133:0:1 0/1:258:3:2,1:57,198:255,3:0.0116:2,2:9:1:26:1:0.13185:6.88:60:6:0.0118:0:1 +19 10267011 . C A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.82477;SOR=1.18945;LSEQ=AGGATTACAGATGTGAGCCA;RSEQ=CCTGCCTGGCTGTTTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:9:7,2:162,95:257,9:0.0338:2,2:33.7:1:29.8:1:0.49379:2.05:60:18:0.035:0:1.4 0/1:300:12:11,1:196,92:288,12:0.04:2,2:22.3:1:29.7:1:0.1129:5.14:60:24:0.0412:0:1.5 +19 10267077 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.42391;LSEQ=TATTCCTTACCTTCAAGAGA;RSEQ=GGGTCATCATCATAGATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:524:302:153,149:118,104:222,302:0.5763:2,2:26.6:1:31.3:1:0.59621:1.10474:59.9:150:0.5758:0:1.2 0/1:744:272:149,123:251,220:471,272:0.3656:2,2:27.9:1:30.4:1:0.70322:1.06:60:89.667:0.368:0:1.2 +19 10267223 . C T 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=CACATGCTTACCAGCTAAGC;RSEQ=GTGAAGGCGGGTCTTCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:78,169:247,0:0:2,0:24.3:1:29.7:1:1:0:60:48.4:1:0:0.1 0/1:314:16:5,11:95,203:298,16:0.051:2,2:23.2:1:28.6:1:1:1.02946:60:32:0.0519:0:1.2 +19 10267252 . G T 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19751;SOR=1.84635;LSEQ=GGGTCTTCGTGCAGACTTCA;RSEQ=ATCAGGCACGAGGCAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:8:0,8:19,128:147,8:0.0516:2,0:19.1:1:28.6:1:0.59677:0:60:16:0.0523:0:1.9 0/1:164:15:3,12:17,132:149,15:0.0915:2,2:21.3:1:27.9:1:0.39876:1.93:60:30:0.0926:0:1.7 +19 10267266 . C A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4534;SOR=1.59002;LSEQ=ACTTCAGATCAGGCACGAGG;RSEQ=AATGAGAGAATGTACAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:7:0,7:11,115:126,7:0.0526:2,0:31:1:32.1:1:1:0:60:14:0.0538:0:2 0/1:123:10:2,8:6,107:113,10:0.0813:2,2:22.6:1:30.1:1:0.12812:4.37:60:20:0.0826:0:2.1 +19 10267318 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11108;SOR=Inf;LSEQ=TTTTGTTTGTTTTTGAGACA;RSEQ=AGTCTTGCTCTATCCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:2,51:53,0:0:1,0:26.4:1:32.5:1:1:0:59.7:52:1:0:0.2 0/1:27:2:0,2:0,25:25,2:0.0741:1,0:16.5:1:28:1:1:0:60:4:0.0741:0:2 +19 10270593 . G A 162 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0;SOR=56.56194;LSEQ=CACTGAATGCACTTGGGAGG;RSEQ=TGGGTCTGTGGGAGCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:1:1,0:297,252:549,1:0.0018:2,0:1:0:27:0:1:0:60:2:0.0018:0:1 0/1:620:58:30,28:297,263:560,58:0.0935:2,2:19.2:1:27.7:1:0.89057:1.05393:60:8.667:0.0852:0:1.2 +19 10270746 . GA G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05138;SOR=0.75811;LSEQ=TTTTTTTCTCCGTTCTGGGG;RSEQ=AAAAAAAAAATCACAAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:406:279:102,177:47,49:96,279:0.6872:2,2:30.3:1:31.9:1:0.03964:1.66207:59.9:278:0.6898:0.0172:0.2 1/0:517:323:111,212:67,84:151,323:0.6248:2,2:29.1:1:30.4:1:0.04176:1.52194:59.8:160.5:0.6344:0.0309:0.2 +19 10270801 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50033;SOR=Inf;LSEQ=TTTCAGAAAATATCAAAATC;RSEQ=CCCCTGTGAGGTTTCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:22,106:128,0:0:2,0:23.9:1:31.6:1:1:0:59.8:31:1:0:0.3 0/1:146:2:0,2:18,126:144,2:0.0137:2,0:22.5:1:26:1:1:0:57.5:4:0.0142:0:1 +19 10270942 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49796;SOR=Inf;LSEQ=TGGTCCTATGTTCACCAACC;RSEQ=GATCCAAAATGAGCCTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:101,19:120,0:0:2,0:24:1:31.5:1:1:0:60:240:1:0:0.1 0/1:122:2:2,0:101,19:120,2:0.0164:2,0:46.5:1:29:1:1:0:60:4:0.0164:0:1 +19 10271034 . C G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.59562;LSEQ=TTAACATTACCATCTGCTTT;RSEQ=GATAATGTCAAGAATAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:25:14,11:266,210:476,25:0.0498:2,2:24.3:1:31:1:1:1.00:60:50:0.0506:0:1.1 0/1:701:84:47,37:358,255:613,84:0.1198:2,2:24.2:1:31.1:1:0.72385:1.10505:60:168:0.1214:0:1.1 +19 10271141 . A C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12895;SOR=1.78003;LSEQ=AAAGGCTAAGAGAGTGTTTT;RSEQ=CACCCAGATAGTGCTTCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:11:2,9:100,199:299,11:0.0355:2,2:29:1:32.2:1:0.35044:2.25625:60:22:0.0358:0:1 0/1:439:27:8,19:129,283:412,27:0.0615:2,2:24.5:1:29.9:1:1:1.08241:60:26:0.0599:0:1.2 +19 10271159 . G A 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31034;SOR=0.22998;LSEQ=TTACACCCAGATAGTGCTTC;RSEQ=GTGTTAAGAACTTTGTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:2,1:53,161:214,3:0.0138:2,2:13.7:1:30.7:1:0.15885:6.01:60:6:0.0142:0:1 0/0:312:1:1,0:78,233:311,1:0.0032:2,0:1:0:23:0:0.25321:0:60:2:0.0032:0:1 +19 10273372 . T C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8263;SOR=1.07118;LSEQ=CTCGTCTTTTTCATCAGAAA;RSEQ=CTGTGGATTTACTTTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:832:36:20,16:423,372:795,36:0.0433:2,2:30.1:1:30.7:1:0.86506:1.10:58.4:35:0.0438:0:1.5 0/1:1147:53:26,27:569,524:1093,53:0.0462:2,2:29.4:1:30.5:1:0.67582:1.12752:59.2:52:0.0467:0:1.5 +19 10277204 . C T 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11633;SOR=3.50748;LSEQ=GAACCCAGAGCCCCACCCTG;RSEQ=GCACTCCCGCCCAAGCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:2:1,1:298,162:460,2:0.0043:2,2:22:1:30:1:1:1.837:60:4:0.0044:0:1 0/1:532:8:3,5:351,173:524,8:0.015:2,2:12.1:1:26.3:1:0.12503:3.37305:60:7:0.0134:0:1.1 +19 10277266 . G A 169 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=41.84939;LSEQ=AGTTCAGAAACAAATAACCC;RSEQ=CCTTTACTTTCTCGTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:981:1:1,0:504,475:979,1:0.001:2,0:25:0:14:0:1:0:60:0:0:0:1 0/1:1342:55:28,27:674,612:1286,55:0.041:2,2:24:1:29.3:1:0.89066:1.06189:60:110:0.0415:0:1.3 +19 10277400 . C CG 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.21419;SOR=2.46261;LSEQ=CACACACAGGCTGGTCAGCT;RSEQ=GGGGGGGGCCCTGCACCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:74,221:295,3:0.01:2,2:22.3:1:31.7:1:1:1.49:48:6:0.0102:0.0033:0.3 0/1:288:7:3,4:78,202:280,7:0.0243:2,2:34.7:1:31:1:0.40712:1.94:49.6:14:0.0249:0:0.6 +19 10277417 . CG C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.22694;SOR=Inf;LSEQ=GCTCGGGGGGGGCCCTGCAC;RSEQ=GGGCCAACAGCTCCTAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:43,149:192,0:0:2,0:26.4:1:31.2:1:1:0:52.4:63:0.9895:0:0.1 0/1:177:2:1,1:50,125:175,2:0.0113:2,2:40.5:1:31.5:1:0.49441:2.49:51:4:0.0114:0:0 +19 10277421 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10876;SOR=Inf;LSEQ=GGGGGGGGCCCTGCACCGGG;RSEQ=CCAACAGCTCCTAAGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:37,136:173,0:0:2,0:26.7:1:32.3:1:1:0:51.5:27.833:1:0:0.1 0/1:159:3:1,2:44,112:156,3:0.0189:2,2:26.3:1:29.3:1:1:1.27:48.7:6:0.0191:0:1.7 +19 10278859 . G T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53487;SOR=0.57875;LSEQ=TCAGCCTTCACTTCAGGGTG;RSEQ=TCTCACCTTTCACAAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:8:8,0:114,3:117,8:0.064:1,0:24.6:1:30.9:1:1:0:60:16:0.0645:0:1.1 0/1:79:3:3,0:75,1:76,3:0.038:1,0:15.7:1:31.3:1:1:0:60:6:0.039:0:1 +19 10278953 . T G 214 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTATTTTACCAAGATACTTA;RSEQ=GTTAGCAATTCAGTTTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:93:64,29:228,150:378,93:0.1975:2,2:26.5:1:32.8:1:0.15254:1.45:60:186:0.2009:0:1.1 0/0:585:0:0,0:357,227:584,0:0:2,0:22.6:1:29.3:1:1:0:60:63.889:1:0:0.1 +19 10279189 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2113;SOR=0.51799;LSEQ=CCAGTGGGCACAGTAGCTCA;RSEQ=GCCTGTAATCTCAGAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:27:0,27:0,18:18,27:0.6:1,1:23.5:1:30:1:1:0:60:54:0.6:0:1.1 0/1:23:10:0,10:0,13:13,10:0.4348:1,0:33.3:1:27.6:1:1:0:60:9:0.4091:0:1.2 +19 10279454 . G A 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAGGAATGAAATAGGATG;RSEQ=CCCAATCTGAAAAGTAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:29.5:1:31:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 10283932 . C T 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.92117;LSEQ=TTTTCATAAAGCTCCTCTTT;RSEQ=CCCCAAAAGCAATCTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:8:1,7:22,144:166,8:0.0457:2,2:22.9:1:29.8:1:1:1.06906:60:16:0.0471:0:1.3 0/1:142:6:1,5:16,120:136,6:0.0423:2,2:23.8:1:27.2:1:0.54153:1.50:60:5:0.036:0:1 +19 10284415 . A G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.3805;SOR=1.74234;LSEQ=TGACCTCAAGTGATTCGCCC;RSEQ=TCTTGGCCTCCCAAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:5:4,1:63,2:65,5:0.0714:1,2:16.6:1:30.6:1:0.20205:7.39874:53.4:10:0.0714:0:1 0/1:59:7:7,0:52,0:52,7:0.1186:1,0:24.7:1:30.3:1:1:0:48.4:14:0.1186:0:1 +19 10284422 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49655;SOR=0;LSEQ=AAGTGATTCGCCCATCTTGG;RSEQ=CTCCCAAAGTGCTGAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:2,0:68,3:71,2:0.0274:1,0:33.5:1:27.5:1:1:0:51.5:4:0.0278:0:2 0/0:73:0:0,0:70,3:73,0:0:1,0:22.8:1:31.9:1:1:0:54.8:146:1:0:0.2 +19 10284461 . C T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=0.39576;LSEQ=TACAGGCATGAGTCACCGTG;RSEQ=CCGGCCTTAAACTTTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:72:51,21:81,29:110,72:0.3956:2,2:18.9:1:30.2:1:0.73518:1.14921:58.7:71:0.3989:0:1 0/1:224:46:35,11:141,36:177,46:0.2054:2,2:17.7:1:29.2:1:0.68497:1.2298:58.5:92:0.2063:0:1.1 +19 10284622 . G T 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22455;SOR=4.34306;LSEQ=ACAAAAAAGATTAGAATACT;RSEQ=GTTTCAAGGGAAGGTCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:1:0,1:95,220:315,1:0.0032:2,0:14:0:15:0:1:0:60:0:0:0:7 0/1:367:5:1,4:124,238:362,5:0.0136:2,2:25.6:1:24.6:1:0.66509:2.08043:57:1.5:0.0082:0:2 +19 10284778 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27785;SOR=0.38119;LSEQ=CCCACCAACCCCAAAACAAA;RSEQ=GCAGGTCCGAGAAGTAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:15:0,15:0,13:13,15:0.5357:1,1:21.3:1:32:1:1:0:60:30:0.5556:0:1 0/1:10:3:0,3:0,7:7,3:0.3:0,0:30:1:32:0:1:0:60:6:0.3:0:1 +19 10286416 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23573;SOR=Inf;LSEQ=AGTTTAATGTTTCTCTGAAT;RSEQ=ACGGGTTTAGAATGTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:1,79:80,0:0:1,0:25.7:1:31.9:1:1:0:59.9:25.667:1:0:0.1 0/1:76:2:0,2:1,73:74,2:0.0263:1,0:13.5:1:29:1:1:0:60:4:0.0263:0:1 +19 10286465 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17187;SOR=Inf;LSEQ=TGTAAGTCCTAAGAAATCAC;RSEQ=GGTCTAAACACCGATCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:2,34:36,0:0:2,0:20.9:1:31.7:1:1:0:59.7:72:1:0:0.1 0/1:26:2:0,2:1,23:24,2:0.0769:1,0:11.5:1:28.5:1:1:0:60:4:0.08:0:1 +19 10287635 . A T 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.44444;SOR=0;LSEQ=CTAGAAATATACTAAACTAT;RSEQ=TATGGACAAAGTAATCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:18.2:1:30.4:1:1:0:58.2:10:0.625:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:8.5:1:30:1:1:0:60:4:1:0:0 +19 10288072 . G GA 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.49317;SOR=1.3298;LSEQ=AGAAGAAAAAGCATTAAAAA;RSEQ=AAAAAAAAAAGCCACTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:14:4,10:97,203:300,14:0.0433:2,2:23.9:1:31.9:1:1:1.1939:58.6:28:0.0491:0:0.4 0/1:387:22:6,16:129,231:360,22:0.0568:2,2:25.6:1:29.5:1:0.49619:1.48771:59.5:44:0.0603:0:0.4 +19 10291064 . C T 76 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1923;SOR=2.96981;LSEQ=ACTTGCTCCTCCTGGGCGTG;RSEQ=GAGGTTTGGAAAGGGGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:2:1,1:374,178:552,2:0.0036:2,2:44:0:26.5:1:0.54221:2.0981:60:4:0.0037:0:1 0/1:657:7:2,5:408,241:649,7:0.0107:2,2:18.1:1:27.3:1:0.10949:4.22285:60:14:0.0108:0:1 +19 10291298 . G A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24885;SOR=Inf;LSEQ=GAATGTAAACAAGTGTCAGA;RSEQ=AACAAGGAAACACATGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:90,124:214,0:0:2,0:24.6:1:32.8:1:1:0:59.9:70.333:1:0:0.1 0/1:226:3:1,2:77,146:223,3:0.0133:2,2:18:1:22:1:1:1.05455:60:2:0.0092:0:2.7 +19 10292523 . C CA 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=TCAAAAAACAAAAACAACAA;RSEQ=AAAAAAAAACACCACCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:19,1:20,0:0:1,0:26.4:1:33.3:1:1:0:58.3:40:1:0:0.3 0/1:20:2:2,0:18,0:18,2:0.1:1,0:15:1:31.3:1:1:0:60:4:0.1:0.05:0 +19 10292608 . C A 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00478;SOR=0;LSEQ=TCCAAATTATCTTTGAAACT;RSEQ=CATGGGAAAAAATGCAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:7:7,0:68,4:72,7:0.0886:2,0:25.9:1:27.9:1:1:0:60:14:0.0886:0:1 0/0:87:0:0,0:79,8:87,0:0:2,0:23.1:1:30.1:1:1:0:60:86:1:0:0.1 +19 10292826 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23413;SOR=0;LSEQ=TTGCCTGTAAGAATATCACA;RSEQ=TTCTAAAGAAGTTTTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:33,138:171,2:0.0116:2,2:23.5:1:31:0:0.35536:4.13:60:4:0.0117:0:1 0/0:184:0:0,0:42,142:184,0:0:2,0:22.6:1:31.3:1:1:0:60:368:1:0:0 +19 10292901 . C T 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06512;SOR=0.15027;LSEQ=TAAGCTGGCTTTTGTCTCCC;RSEQ=GCAAGAGTCTAGAGTGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:7:0,7:1,33:34,7:0.1707:1,0:23.4:1:31.6:1:1:0:60:14:0.175:0:1 0/1:34:1:0,1:1,32:33,1:0.0294:1,0:50:0:29:0:1:0:60:2:0.0294:0:1 +19 10305282 . G A 60 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.8165;LSEQ=CTAGCCACCAGGGAGCTACG;RSEQ=GGGAATCCACGGTCCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:1,1:0.5:0,0:40:0:28:0:1:0:60:2:0.5:0:1 0/1:9:4:2,2:3,2:5,4:0.4444:2,2:25.8:1:30:1:1:1.43328:60:8:0.4444:0:1.3 +19 10305389 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23619;SOR=Inf;LSEQ=GCCGCACCACCCCACGCATG;RSEQ=GCGCCCGTCTGTCAGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:144,12:156,0:0:2,0:27:1:32.7:1:1:0:60:51:1:0:0.2 0/1:148:2:1,1:129,17:146,2:0.0135:2,2:16.5:1:27.5:1:0.22918:7.4034:60:4:0.0143:0:1.5 +19 10305434 . C T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00435;SOR=0;LSEQ=CCGGCCACCCCGAGGGGAAG;RSEQ=GACCCCCCACCCAGCGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:7:1,6:325,151:476,7:0.0144:2,2:8:1:27.3:1:0.00563:12.84973:60:14:0.0147:0:1.1 0/0:566:0:0,0:371,195:566,0:0:2,0:23.1:1:29.9:1:1:0:60:25.952:1:0:0.4 +19 10305615 . G A 46 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12365;SOR=Inf;LSEQ=GCGGCGGCGGCAGCGCAGGC;RSEQ=CCCCGGCTTTTCGCGCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:82,186:268,0:0:2,0:23.4:1:31.4:1:1:0:59.9:133:1:0:0.2 0/1:272:4:4,0:83,184:267,4:0.0147:2,0:7.8:1:23.3:1:0.01013:0:60:3:0.0114:0:2.3 +19 10305639 . G A 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23193;SOR=Inf;LSEQ=CGGCTTTTCGCGCGGAAACC;RSEQ=ATGGGGAGGGGCGATGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:32,144:176,0:0:2,0:23.5:1:31.7:1:1:0:60:57.667:1:0:0.2 0/1:164:2:1,1:36,126:162,2:0.0122:2,2:5:0:30.5:1:0.40139:3.47:60:4:0.0124:0:1.5 +19 10305664 . C T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62758;SOR=0.39457;LSEQ=GGAGGGGCGATGAGCGGAGG;RSEQ=GGCGTCTACCACCCCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:3:1,2:10,102:112,3:0.0261:2,2:30.3:1:30:1:0.26245:4.97:60:6:0.027:0:1.3 0/1:96:1:0,1:10,85:95,1:0.0104:2,0:1:0:24:0:1:0:60:2:0.0108:0:1 +19 10472221 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22727;SOR=0;LSEQ=ACACAGACGCCATGCACGAA;RSEQ=GCCAGGTGCGTGTGGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:14,2:0.125:2,2:32.5:1:27.5:1:1:1.30929:60:4:0.125:0:1 0/0:17:0:0,0:9,8:17,0:0:2,0:22.5:1:29.9:1:1:0:60:16:1:0:0.1 +19 10597746 . T A 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAAATGGCCAGGC;RSEQ=TGGTAGCTCACGCCTATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:23:1:32.7:1:1:0:54.3:6:1:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 10599685 . G A 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.11974;SOR=2.88153;LSEQ=GGAGGCTGAGGCAGGAGGAT;RSEQ=GCTGGAGCCCAGGCTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:6,0:16,0:16,6:0.2727:1,0:26.5:1:26.5:1:1:0:58.2:5:0.3846:0:1.8 1/0:19:10:10,0:9,0:9,10:0.5263:0,0:22.3:1:27.9:1:1:0:59.9:20:0.7143:0:1.8 +19 10599836 . G C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19699;LSEQ=AGTCCACAAAAGATGGGCTA;RSEQ=TCAGGACTCTTCCCCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:162:100,62:199,125:324,162:0.3326:2,2:27.8:1:32:1:1:1.01:59.9:31.4:0.3305:0:1.3 0/1:616:55:32,23:311,248:559,55:0.0893:2,2:24.2:1:31.5:1:0.77684:1.11:59.6:54:0.0896:0:1.3 +19 10600052 . G A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12857;SOR=Inf;LSEQ=AGGACGCAGACGCCTAAAGG;RSEQ=CACCATGCAGAGAAGGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:117,212:329,0:0:2,0:25.4:1:31.7:1:1:0:59.8:40.125:1:0:0.1 0/1:385:4:3,1:122,259:381,4:0.0104:2,2:18:1:25.5:1:0.10242:6.34:60:8:0.0106:0:1 +19 10600094 . AC A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.08104;SOR=Inf;LSEQ=CTGGGGGTCTGGCTTTGGGA;RSEQ=CCCAGCCATCACCTCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:50,144:194,0:0:2,0:22.7:1:31.4:1:1:0:59.8:193:1:0:0.1 0/1:149:3:2,1:36,110:146,3:0.0201:2,2:12.3:1:26.3:1:0.16005:6.02:60:6:0.0207:0.0067:0.3 +19 10600442 . G C 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.36469;LSEQ=AAGCCCCCCACGGCATAAAG;RSEQ=AGACGATTGAGGACAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:738:477:225,252:122,137:259,477:0.6463:2,2:26.2:1:32.1:1:1:1.00:59.9:58.625:0.6478:0:1.1 0/1:918:367:171,196:255,293:548,367:0.3998:2,2:24.5:1:31.3:1:1:1.00:60:90.75:0.3993:0:1.2 +19 10600615 . C CT 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.03983;SOR=0;LSEQ=GCCAGATACTCTTTTTTTTC;RSEQ=TTTTTTTTTTCCCCCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:0,6:1,60:61,6:0.0896:1,0:18:1:30.3:1:1:0:60:12:0.0909:0.0299:0.7 0/0:48:0:0,0:1,47:48,0:0:1,0:17:0:12:0:1:0:60:0:0:0:1 +19 10600654 . G A 89 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02631;SOR=0.10715;LSEQ=AAGAGACAGGTTCATCCGGC;RSEQ=CGATGGCTCATGCCTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:0,8:0,13:13,8:0.381:1,0:19.1:1:29.9:1:1:0:42.3:16:0.381:0:1.1 0/1:17:1:0,1:0,16:16,1:0.0588:1,0:44:0:27:0:1:0:58:2:0.0667:0:1 +19 10602180 . A C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=0;LSEQ=GAAACAGCCTCAGGAAGAAT;RSEQ=CCCGGATCTCAGTGTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:139:139:121,18:0,0:0,139:1:0,2:24.9:1:31.9:1:1:0:60:26.8:1:0:1.2 1/1:116:104:86,18:7,5:12,104:0.8966:2,2:24.8:1:30.4:1:0.05961:3.37:60:208:0.8966:0:1.1 +19 10602767 . C T 80 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.76293;SOR=0.70475;LSEQ=CGTCAACGAGTGGCAGCGCA;RSEQ=GGCCCGCAGCAGCGCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:6:3,3:280,267:547,6:0.0108:2,2:26.3:1:31.2:1:1:1.04862:60:12:0.011:0:1.2 0/0:652:5:2,3:319,326:645,5:0.0077:2,2:22:1:26.8:1:1:1.46693:60:10:0.0077:0:1.2 +19 10602989 . T C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13118;SOR=Inf;LSEQ=TCTCCAGTCACCCCCACACC;RSEQ=CACCAAGCAGGACCGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:46,171:217,0:0:2,0:22.6:1:29.9:1:1:0:60:26.125:1:0:0.1 0/1:266:4:2,2:78,182:260,4:0.015:2,2:18.8:1:30.3:1:0.58696:2.32:60:8:0.0156:0:1 +19 10603024 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50197;SOR=0;LSEQ=GGGACAAGTAACTTATCACT;RSEQ=CCGCTGACAGTCTCAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:8,124:132,2:0.0149:2,2:17:1:27.5:1:0.13029:14.67:60:4:0.0152:0:2 0/0:112:0:0,0:11,101:112,0:0:2,0:28:0:15:0:1:0:60:0:0:0:2 +19 10603059 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14577;SOR=Inf;LSEQ=AGCTTCCTTATCTGCTAAAT;RSEQ=GGGATTCAAATAATAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:1,84:85,0:0:1,0:27.4:1:31.6:1:1:0:60:84:1:0:0.1 0/1:53:2:0,2:5,46:51,2:0.0377:2,0:26:1:28.5:1:1:0:60:4:0.0385:0:1 +19 10603115 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10476;SOR=Inf;LSEQ=GACTAAATGAGTTAATCCTG;RSEQ=CGGGCGCGGTGGCTCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,24:24,0:0:1,0:22.9:1:31.4:1:1:0:59.9:23:1:0:0 0/1:12:2:1,1:1,9:10,2:0.1667:2,2:31:1:28.5:1:0.31818:6.71:57.5:4:0.1667:0:1 +19 10610011 . G T 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62561;SOR=2.71968;LSEQ=TCAAGGGGAGACAGTGATGA;RSEQ=CACTCGTCCATCCCTGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:0,1:186,71:257,1:0.0039:2,0:1:0:15:0:0.27907:0:60:0:0:0:1 0/1:286:3:1,2:203,80:283,3:0.0105:2,2:12.7:1:23.7:1:0.19855:5.0416:60:2:0.007:0:1.3 +19 10610017 . G C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07214;LSEQ=GGAGACAGTGATGAGCACTC;RSEQ=TCCATCCCTGGTCCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:119:80,39:118,46:164,119:0.4205:2,2:21.9:1:31:1:0.43149:1.24953:59.9:28.75:0.4152:0:1.1 0/1:323:16:10,6:211,96:307,16:0.0495:2,2:20.6:1:30.4:1:0.59035:1.31762:60:32:0.0497:0:1.2 +19 10610236 . A G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16761;LSEQ=TCGATCTGGTACATGACAGC;RSEQ=CCGTTCATGACGTGGAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:247:125,122:201,194:395,247:0.3847:2,2:24.9:1:30.6:1:1:1.0112:60:34.286:0.381:0:1.2 0/1:897:85:42,43:418,391:809,85:0.0948:2,2:26.9:1:30.5:1:0.73281:1.0944:60:84:0.0944:0:1.2 +19 10610644 . C T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12855;SOR=Inf;LSEQ=TCCCCTGCCCCCTCAGGGCA;RSEQ=TGTGACTGCAGGGGCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:94,162:256,0:0:2,0:24.7:1:32.7:1:1:0:59.9:63:1:0:0.1 0/1:301:4:2,2:122,174:296,4:0.0133:2,2:14.5:1:28:1:1:1.42:60:8:0.0134:0:1 +19 10610648 . G T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04535;SOR=0;LSEQ=CTGCCCCCTCAGGGCACTGT;RSEQ=ACTGCAGGGGCAGGAATCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:4:2,2:80,159:239,4:0.0164:2,2:29.8:1:28.8:1:0.60503:1.98:60:8:0.0167:0:1 0/0:283:0:0,0:114,168:282,0:0:2,0:23.9:1:30.6:1:1:0:59.8:69.5:0.9964:0:0.2 +19 10610657 . G A 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.62661;SOR=2.64476;LSEQ=CAGGGCACTGTGACTGCAGG;RSEQ=GCAGGAATCGGCAGCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:1,0:69,143:212,1:0.0047:2,0:1:0:26:0:0.32864:0:60:2:0.0048:0:1 0/1:243:3:3,0:89,151:240,3:0.0123:2,0:8:1:25.7:1:0.05317:0:60:6:0.0126:0:1 +19 10610681 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49953;SOR=Inf;LSEQ=GGAATCGGCAGCAGGCCCCA;RSEQ=CCCCGCTAGGCCTGGGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:47,107:154,0:0:2,0:24:1:32.4:1:1:0:59.9:37.5:0.9934:0:0.1 0/1:170:2:1,1:54,114:168,2:0.0118:2,2:6:1:28.5:1:0.54368:2.10:60:4:0.0122:0:1 +19 10610682 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49903;SOR=Inf;LSEQ=GAATCGGCAGCAGGCCCCAG;RSEQ=CCCGCTAGGCCTGGGATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:45,110:155,0:0:2,0:23.5:1:31.3:1:1:0:59.9:30:1:0:0.1 0/1:166:2:1,1:51,113:164,2:0.012:2,2:16.5:1:27.5:1:0.52968:2.20:60:4:0.0128:0:1.5 +19 10610759 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52119;SOR=0;LSEQ=CCTCTGGCACTCAGGGACCT;RSEQ=GAGGGGAGAGAGCACAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:7,53:60,2:0.0323:2,2:15.5:1:28.5:1:0.24326:7.15:60:4:0.0328:0:1 0/0:39:0:0,0:5,34:39,0:0:2,0:22.7:1:30.1:1:1:0:60:78:1:0:0.1 +19 11095896 . T C 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGCAGCGCATAGCTGCGC;RSEQ=GCCACCTCACGTTCCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:225,46:271,0:0:2,0:23.4:1:31.7:1:1:0:60:66.75:1:0:0.1 0/1:228:32:26,6:151,44:195,32:0.1404:2,2:24.7:1:29.4:1:0.81842:1.26:60:15:0.1333:0:1.1 +19 11096829 . C T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06259;SOR=0;LSEQ=GTAAAAATCACAGACATATG;RSEQ=TGCCGAGTGACCAGTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:5:1,4:341,151:492,5:0.0101:2,2:15.6:1:27.6:1:0.03476:8.99098:60:10:0.0102:0:1.2 0/0:464:0:0,0:301,163:464,0:0:2,0:24.7:1:31.3:1:1:0:60:76.333:1:0:0.2 +19 11096851 . A G 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGAGTGACCAGTGGGCTG;RSEQ=CCTTTCTCTGCAGGTTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:0:0,0:411,256:667,0:0:2,0:25.2:1:30.1:1:1:0:59.9:110.167:1:0:0.1 0/1:623:47:27,20:346,228:574,47:0.0754:2,2:24.7:1:30.8:1:0.7574:1.12389:60:46:0.0749:0:1.2 +19 11096912 . C G 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCATGCCTCTAGTCCAGTT;RSEQ=CAGCCAGTGGCCCGTCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:926:0:0,0:475,451:926,0:0:2,0:24.5:1:31.6:1:1:0:59.9:60.733:1:0:0.2 0/1:1009:62:30,32:483,464:947,62:0.0614:2,2:25.1:1:31.6:1:0.69656:1.11023:60:124:0.0624:0:1.2 +19 11097098 . C T 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCCAGGGGGCAGCCCCTC;RSEQ=CCGACCACCTGCAGATGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:697:0:0,0:317,379:696,0:0:2,0:24.4:1:31:1:1:0:59.9:115:1:0:0.1 0/1:678:21:7,14:294,362:656,21:0.031:2,2:18:1:27.5:1:0.3746:1.62319:59.5:9.5:0.0283:0:1.2 +19 11097205 . T C 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.13552;SOR=0;LSEQ=TCCGCAACAGGACCCGGCCC;RSEQ=GGCCCTGGCCCTGGCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:4:2,2:151,220:371,4:0.0107:2,2:12.5:1:28.8:1:1:1.46:60:8:0.0108:0:1 0/0:292:0:0,0:119,172:291,0:0:2,0:23.1:1:29.3:1:1:0:59.9:35.375:0.9965:0:0.2 +19 11097207 . G T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.08379;SOR=Inf;LSEQ=CGCAACAGGACCCGGCCCTG;RSEQ=CCCTGGCCCTGGCCCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:148,216:364,0:0:2,0:24.9:1:31.5:1:1:0:59.9:35.4:0.9972:0:0.1 0/1:285:3:1,2:116,165:281,3:0.0105:2,2:14.3:1:20.7:1:1:1.40444:60:2:0.0074:0:1 +19 11097450 . C T 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00628;SOR=Inf;LSEQ=AATGCTGCTTCCCCAGCTCC;RSEQ=CGCTTCCCCTGGGGCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:144,16:160,0:0:2,0:23:1:32:1:1:0:60:79:1:0:0.1 0/1:123:6:6,0:114,3:117,6:0.0488:1,0:15.8:1:32:1:1:0:60:12:0.0488:0:1.2 +19 11097509 . C T 50 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11361;SOR=5.34829;LSEQ=TGTGTCCCCTGGAGCCAGGG;RSEQ=TGCCCACGGGGCTGGGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:1:0,1:352,144:496,1:0.002:2,0:1:0:25:0:0.29175:0:60:2:0.002:0:1 0/1:468:5:2,3:315,147:462,5:0.0107:2,2:18:1:21.8:1:0.33378:3.20537:60:1.5:0.0065:0:1.2 +19 11097744 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19529;SOR=Inf;LSEQ=CATCTCAAGCTTGGGTCCTT;RSEQ=AGATGAGCTTTGTCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:18,191:209,0:0:2,0:24.1:1:32.3:1:1:0:60:103.5:1:0:0.1 0/1:166:2:1,1:29,135:164,2:0.012:2,2:32:1:27.5:1:0.32968:4.59:60:4:0.0123:0:1 +19 11098455 . G A 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00661;SOR=0;LSEQ=TCCCACCCGCCGCCTCGCCC;RSEQ=TGATGCCACCGCAGACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:7:4,3:305,331:636,7:0.0109:2,2:17.6:1:26:1:0.7158:1.45:60:2.5:0.0079:0:1.7 0/0:671:0:0,0:315,353:668,0:0:2,0:1:0:15:0:1:0:60:0:0:0:1 +19 11098651 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.24845;SOR=Inf;LSEQ=TGCCCTGTGTCCCCCATGTC;RSEQ=CCCTGGGGAAGCCACTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:60,177:237,0:0:2,0:24.4:1:30.9:1:1:0:60:25.333:1:0:0.1 0/1:240:3:1,2:59,178:237,3:0.0125:2,2:9.7:1:26:1:1:1.51:60:6:0.0127:0:1.3 +19 11098666 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50018;SOR=0;LSEQ=ATGTCCCCCTGGGGAAGCCA;RSEQ=TCAACTTTCTCCCCCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:31,154:185,2:0.0107:2,2:33:1:30:0:0.31373:4.91:60:4:0.0109:0:1 0/0:167:0:0,0:28,139:167,0:0:2,0:23.2:1:31.7:1:1:0:60:82.5:1:0:0.1 +19 11098724 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54362;SOR=0;LSEQ=GCCCACCACTGCCACTTGGC;RSEQ=TACACCTCCTTCCTCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:3,67:70,2:0.0278:1,2:20.5:1:28.5:1:0.10876:19.49:60:4:0.0286:0:1 0/0:38:0:0,0:3,35:38,0:0:2,0:21.4:1:32.1:1:1:0:60:37:1:0:0.2 +19 11100147 . C A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3563;SOR=3.24679;LSEQ=CTGGCATGGCCGCAGCTTTC;RSEQ=GAAAAGGGCCTTTGTCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:1,0:68,241:309,1:0.0032:2,0:14:0:14:0:0.22258:0:38:0:0:0:7 0/1:288:3:2,1:80,203:283,3:0.0104:2,2:9.7:1:26.3:1:0.19855:5.04:60:6:0.0106:0:1.7 +19 11100224 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50815;SOR=0;LSEQ=CTAGTATTACACCTGCCTGG;RSEQ=CTGTGAAAAGCAGCCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:0,2:0,64:64,2:0.0303:1,0:36:1:32:0:1:0:60:4:0.0303:0:1 0/0:48:0:0,0:1,47:48,0:0:1,0:27.5:1:32:1:1:0:59.3:96:1:0:0.1 +19 11101993 . G A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCGCAAGCGCCGGCAGAA;RSEQ=CACCAGGTACGCTCCGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:117,193:310,0:0:2,0:24:1:32.5:1:1:0:60:61:1:0:0.1 0/1:348:25:8,17:128,195:323,25:0.0718:2,2:23.7:1:29.1:1:0.52752:1.39358:60:50:0.0731:0:1.4 +19 11102076 . G A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51591;SOR=0;LSEQ=CCAGCGGTTGCCACGGGGCT;RSEQ=TGTTTGCTTTGTTCCTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:9,94:103,2:0.019:2,2:16.5:1:25.5:1:0.18223:9.96:60:4:0.0194:0:1 0/0:71:0:0,0:7,64:71,0:0:2,0:22.7:1:31.2:1:1:0:59.5:142:1:0:0.1 +19 11105449 . G T 21 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.342;LSEQ=TTAAACAAGCCTTGCGGGGA;RSEQ=ATGTGTCCACCATGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:145,35:180,2:0.011:2,2:16:1:28:1:0.35736:4.09898:60:4:0.0111:0:1.5 0/1:136:2:0,2:102,32:134,2:0.0147:2,0:1:0:21.5:1:0.06111:0:60:4:0.0149:0:1 +19 11105468 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20235;SOR=Inf;LSEQ=AGATGTGTCCACCATGCTGC;RSEQ=GAAGGGTCAGCCTTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:182,62:244,0:0:2,0:25.1:1:31.7:1:1:0:60:121:1:0:0.1 0/1:200:2:1,1:139,59:198,2:0.01:2,2:34:1:29:1:0.51106:2.34463:60:4:0.0101:0:1 +19 11105593 . A G 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCAGAAGCTGACCAAGGC;RSEQ=GTGGCCACGTACCATGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:0:0,0:216,265:481,0:0:2,0:26.3:1:31.2:1:1:0:60:159.333:1:0:0.1 0/1:560:41:18,23:249,270:519,41:0.0732:2,2:23.2:1:28.9:1:0.63055:1.17805:60:12.667:0.0688:0:1.9 +19 11105608 . T C 230 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCAGTGGCCACGTACCA;RSEQ=GCCAACACGGAGCGGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:204,281:485,0:0:2,0:24.4:1:30.7:1:1:0:60:120.25:1:0:0.1 0/1:532:188:84,104:161,183:344,188:0.3534:2,2:25.7:1:30.5:1:0.65024:1.08908:59.9:187:0.3542:0:1.3 +19 11105714 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50084;SOR=Inf;LSEQ=TTGACGTGCGCTCTTCTACA;RSEQ=GTGTAGCTGGTACTGCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:46,122:168,0:0:2,0:21.1:1:30.9:1:1:0:59.7:336:1:0:0.1 0/1:192:2:1,1:66,123:189,2:0.0104:2,2:30:1:28:1:1:1.86:60:4:0.0106:0:1 +19 11106790 . T C 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCACGGCACCCGCGTGAGC;RSEQ=ACGCGTGCCCTCAGTGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:115,3:118,0:0:1,0:24.1:1:32.4:1:1:0:59.9:117:1:0:0.2 1/0:69:38:38,0:31,0:31,38:0.5507:1,1:25:1:30.6:1:1:0:60:76:0.5507:0:1.1 +19 11106814 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18084;SOR=Inf;LSEQ=CGTGCCCTCAGTGCGCTTCT;RSEQ=GATTGACTGGCCATGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:184,14:198,0:0:2,0:23.1:1:32.4:1:1:0:59.9:48.5:1:0:0.1 0/1:147:2:1,1:129,16:145,2:0.0136:2,2:25.5:1:28.5:1:0.21862:7.85179:60:4:0.0137:0:1 +19 11107081 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09978;SOR=Inf;LSEQ=GCTGGGCCTGGCATGGTGCC;RSEQ=GCCGCGGGTGGGATGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:170,119:289,0:0:2,0:24.7:1:30.7:1:1:0:60:47.167:1:0:0.1 0/1:251:3:1,2:141,106:247,3:0.012:2,2:8.7:1:27.7:1:0.57979:2.65008:60:6:0.0123:0:1.7 +19 11107085 . G A 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GGCCTGGCATGGTGCCCGCC;RSEQ=CGGGTGGGATGGGAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:184,105:289,0:0:2,0:25.4:1:30.5:1:1:0:60:40.286:0.9965:0:0.1 0/1:258:34:17,17:134,89:223,34:0.1318:2,2:25.3:1:29.4:1:0.26937:1.50313:60:68:0.1344:0:1.6 +19 11107133 . T C 228 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=350.57526;LSEQ=CGTGTGTGGCCTCAGCCTTG;RSEQ=GGGTCAGGGCCTGACCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:1:0,1:248,180:428,1:0.0023:2,0:36:0:28:0:0.42191:0:60:2:0.0024:0:1 0/1:432:195:105,90:137,98:235,195:0.4514:2,2:25.4:1:30.1:1:0.38012:1.19774:59.8:194:0.4543:0:1.3 +19 11107295 . G A 111 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00154;SOR=13.39726;LSEQ=TGTTTCAGACTTTAAAACCT;RSEQ=TGTTCTTTTAAAATTACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:1:1,0:30,146:176,1:0.0056:2,0:1:0:27:0:0.17514:0:60:2:0.0057:0:2 0/1:183:13:3,10:43,127:170,13:0.071:2,2:15.1:1:30.2:1:1:1.12788:60:26:0.071:0:1.1 +19 11107297 . G A 42 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12071;SOR=0;LSEQ=TTTCAGACTTTAAAACCTGT;RSEQ=TTCTTTTAAAATTACGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:3:2,1:26,143:169,3:0.0174:2,2:5:1:27:1:0.06925:10.75:60:6:0.0176:0:1 0/0:175:0:0,0:41,134:175,0:0:2,0:20.4:1:31.3:1:1:0:59.9:350:1:0:0.2 +19 11111535 . CAAAAA C 32 d5;v3;pSTD;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAGTCATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:18:0:32:0:0.33333:0:60:4:0.6667:0:0.5 +19 11113651 . T C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCACCTTGGCCTCTGTAAG;RSEQ=GTTTGGTCTGGAGGCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:223,77:300,0:0:2,0:22.1:1:30.1:1:1:0:60:99:1:0:0.1 0/1:319:45:31,14:190,84:274,45:0.1411:2,2:25:1:30.8:1:1:1.02145:60:90:0.142:0:1 +19 11113902 . G A 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGGCCTTGTTCCAGGGA;RSEQ=GTGGCAGCCAGGAGCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:123,137:260,0:0:2,0:22.9:1:31.8:1:1:0:59.9:42.333:1:0:0.1 0/1:200:40:20,20:69,91:160,40:0.2:2,2:21.7:1:29.1:1:0.47918:1.32:60:19:0.1949:0:1.1 +19 11113997 . G T 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=18.43804;LSEQ=CTGAGCAGATTTGTATGAAA;RSEQ=CCCTTACATTTTTTCTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:2:1,1:296,242:538,2:0.0037:2,2:17:1:29.5:1:1:1.22268:60:4:0.0038:0:1 0/1:576:37:24,13:312,226:538,37:0.0642:2,2:27.2:1:29.5:1:0.49163:1.34:60:74:0.0648:0:1 +19 11114206 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=CAGCAGGGCCCAGGCCTGCC;RSEQ=GAAGTCGGTGCTTTAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:1,74:75,0:0:1,0:24.5:1:30.4:1:1:0:60:74:1:0:0 0/1:41:8:1,7:0,33:33,8:0.1951:1,2:29.4:1:30.3:1:0.19512:0:60:16:0.1951:0:1 +19 11118575 . TAGG T 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.73085;SOR=0.69253;LSEQ=GACATGGGCTTGTCTCTTGG;RSEQ=AGGAGGAGGAAGAGCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:5:4,1:256,96:352,5:0.014:2,2:29.4:1:31:1:1:1.50:60:10:0.0141:0:0.2 0/0:309:3:2,1:217,88:305,3:0.0097:2,2:9:1:27:1:1:1.23204:60:6:0.0099:0.0032:0.7 +19 11118711 . C T 162 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=19.58651;LSEQ=CATCATTGAGTAAGGGGTCC;RSEQ=GACACAGGTTGTTCTGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:2:1,1:281,379:660,2:0.003:2,2:21.5:1:16:1:1:1.35:60:0:0:0:2 0/1:732:41:17,24:308,381:689,41:0.056:2,2:24.2:1:30.4:1:0.74784:1.14106:60:82:0.0566:0:1.2 +19 11120937 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01823;SOR=Inf;LSEQ=CTGCACCTCTATGTGTCTTA;RSEQ=AGTGCTGGCCACAGGTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:108,3:111,0:0:1,0:27.4:1:32.9:1:1:0:59.7:222:1:0:0.1 0/1:66:4:3,1:62,0:62,4:0.0606:1,2:25.3:1:29.5:1:0.06061:0:60:8:0.0606:0:1 +19 11121234 . G A 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05303;SOR=7.08852;LSEQ=TAGGGGGTGGGGAGGCCACC;RSEQ=CCACGTAGCTGCCTCGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:1:1,0:155,322:477,1:0.0021:2,0:1:0:30:0:0.32636:0:60:2:0.0021:0:1 0/1:409:6:4,2:144,259:403,6:0.0147:2,2:8.7:1:25.5:1:0.19516:3.59:60:12:0.0147:0:1 +19 11123738 . C T 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCGCGCTCATCACGTACCT;RSEQ=ATGGAGCACAAACGCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:689:0:0,0:318,371:689,0:0:2,0:24.9:1:32.2:1:1:0:59.9:97.429:1:0:0.1 0/1:757:55:30,25:337,363:700,55:0.0727:2,2:22.7:1:28.5:1:0.40174:1.29:60:110:0.074:0:1.2 +19 11123859 . G A 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24489;SOR=Inf;LSEQ=GTTTGTTTCCTAAGTTTGCC;RSEQ=CAGTAGAATACCACAAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:20,152:172,0:0:2,0:24.6:1:32.3:1:1:0:60:85:1:0:0.1 0/1:169:2:1,1:27,140:167,2:0.0118:2,2:5:1:24.5:1:0.30473:5.11:60:4:0.0122:0:1 +19 11123888 . A G 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=TACCACAAACGAGGTGGCTT;RSEQ=ATTACAGAAATTTGTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:0,2:0,93:93,2:0.0211:1,0:15:1:26:1:1:0:60:4:0.0211:0:1 0/0:86:0:0,0:3,83:86,0:0:1,0:22.3:1:29.9:1:1:0:60:42:1:0:0.1 +19 11129429 . C G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54742;SOR=0.63095;LSEQ=TTTTCCCAGTGGCCTCCCTT;RSEQ=TGTCCTCTGAGGCAGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:22:22,0:11,0:11,22:0.6667:0,1:25.7:1:32.6:1:1:0:60:44:0.6667:0:1 1/0:18:10:9,1:6,2:8,10:0.5556:2,2:18.9:1:32.7:1:0.55882:2.82:60:20:0.5556:0:1.1 +19 11129600 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.69827;SOR=0.95015;LSEQ=GTGAGCCATTGATGAGAGAC;RSEQ=GGCACTTGACTCTCATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:153:92,61:286,207:493,153:0.2361:2,2:24.4:1:31.4:1:0.70727:1.09:60:75.5:0.2359:0:1.1 0/1:696:158:99,59:310,228:538,158:0.227:2,2:25.7:1:29.8:1:0.27116:1.23:59.6:157:0.2285:0:1.1 +19 11130114 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09684;SOR=Inf;LSEQ=GTGGTGAGGTCTGGGGACGC;RSEQ=CCAGCGGCCCTGCCAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:48,4:52,0:0:2,0:23:1:29:1:1:0:58.3:16.333:1:0:0.2 0/1:24:2:1,1:20,1:21,2:0.0833:1,2:34.5:1:28.5:1:0.16996:14.49116:60:4:0.087:0:1 +19 11130190 . AG A 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.2001;SOR=Inf;LSEQ=CCGTGTCACTGGGCAGTTGC;RSEQ=GGGGTGCCTGTGCCCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:167,14:181,0:0:2,0:22.6:1:32.8:1:1:0:60:29.167:1:0:0.1 0/1:147:2:1,1:129,16:145,2:0.0136:2,2:19:1:33.5:1:0.21862:7.85179:60:4:0.0138:0:0.5 +19 11130195 . G A 81 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01323;SOR=9.87111;LSEQ=TCACTGGGCAGTTGCAGGGG;RSEQ=TGCCTGTGCCCCTCTTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:1:1,0:171,20:191,1:0.0052:2,0:44:0:14:0:1:0:60:0:0:0:1 0/1:162:8:7,1:135,19:154,8:0.0494:2,2:25.5:1:27.1:1:1:1.01494:60:7:0.044:0:1.1 +19 11130431 . G A 211 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00555;LSEQ=GGCCGAGTGCTCACACGTGG;RSEQ=TCACGCTGCCCGTCTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:114:29,85:82,213:295,114:0.2787:2,2:24.2:1:31:1:0.7102:1.12801:60:113:0.279:0:1.1 0/0:469:1:1,0:142,326:468,1:0.0021:2,0:1:0:23:0:0.3049:0:60:2:0.0022:0:1 +19 11130477 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=CCCTACAAGTTTCTTCCCGG;RSEQ=GTCCCACCTGCATGTGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:4,140:144,0:0:1,0:25.6:1:31.8:1:1:0:59.4:27.8:1:0:0.4 0/1:153:2:0,2:5,146:151,2:0.0131:1,0:32.5:1:32.5:1:1:0:60:4:0.0133:0:1 +19 11132080 . G A 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTCTTCTGCCAGAACGT;RSEQ=CTCGGCATTTTTCTGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:114,4:118,0:0:1,0:23.5:1:32.3:1:1:0:60:117:1:0:0.1 0/1:92:27:26,1:65,0:65,27:0.2935:1,1:23.6:1:28.1:1:0.29348:0:60:54:0.2967:0:1 +19 11132244 . G A 160 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.92648;LSEQ=GTGTGGCTCCAACTCGGTGA;RSEQ=TCAGCCCCGGGGCAGGACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:744:2:2,0:382,359:741,2:0.0027:2,0:25.5:1:20.5:1:0.49989:0:60:1:0.0014:0:2.5 0/1:716:40:19,21:330,346:676,40:0.0559:2,2:24.4:1:30.2:1:1:1.05409:59.8:80:0.0566:0:1.2 +19 11132315 . G A 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCCACCTGGAGCCTTCCTG;RSEQ=CTGCTGGGCGCAGAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:707:0:0,0:358,348:706,0:0:2,0:23.9:1:31.6:1:1:0:60:77.444:0.9986:0:0.1 0/1:654:58:32,26:324,270:594,58:0.0887:2,2:26.1:1:27.7:1:1:1.03:60:28:0.0871:0:1.2 +19 11132687 . G A 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71174;SOR=0.65999;LSEQ=TGCTGACGGTTCCAGGTGCG;RSEQ=CTGGCTTTGCTGGTTGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:4:3,1:129,258:387,4:0.0102:2,2:15.3:1:28:1:0.11379:5.97:60:8:0.0104:0:1 0/0:443:3:2,1:162,278:440,3:0.0068:2,2:17:1:27.3:1:0.55807:3.42:60:6:0.0069:0:1 +19 11134090 . A G 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAAGGGCAAGATCACCCC;RSEQ=GGGGACCCCGTCCACCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:141,1:142,0:0:1,0:27.9:1:30.6:1:1:0:60:46.333:1:0:0.1 0/1:96:20:19,1:73,3:76,20:0.2083:1,1:23.7:1:27.4:1:1:1.27719:60:19:0.2021:0:1.3 +19 11134270 . G A 72 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19041;SOR=3.00568;LSEQ=GCGGCCCTTCTTGCTCCGAC;RSEQ=ACTCAAGAAGGAAGTCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:2:2,0:243,338:581,2:0.0034:2,0:1:0:27.5:1:0.17618:0:60:4:0.0035:0:1 0/1:683:7:6,1:293,382:675,7:0.0102:2,2:7.6:1:26:1:0.04756:7.80:60:14:0.0104:0:1 +19 11134301 . C T 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTCGAGGCCCAGTTGCC;RSEQ=GAAAAGGTGATGGAGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:160,250:410,0:0:2,0:24.7:1:30.2:1:1:0:60:67.333:0.9975:0:0.1 0/1:476:37:12,25:162,275:437,37:0.0777:2,2:24.1:1:28.6:1:0.72278:1.22673:60:11.333:0.0734:0:1.4 +19 11135163 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07602;SOR=Inf;LSEQ=CCCCACTGGGTGTCCAAGGC;RSEQ=GGCAGCGTGGCAGGCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:41,159:200,0:0:2,0:24.1:1:30.2:1:1:0:60:99:1:0:0.1 0/1:148:3:2,1:37,108:145,3:0.0203:2,2:20.3:1:29.7:1:0.16983:5.75:60:6:0.0204:0:1.3 +19 11135164 . G A 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68735;LSEQ=CCCACTGGGTGTCCAAGGCC;RSEQ=GCAGCGTGGCAGGCAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:40,155:195,2:0.0102:2,2:12.5:1:25.5:1:0.37377:3.84:60:4:0.0103:0:1 0/0:143:1:1,0:37,105:142,1:0.007:2,0:1:0:25:0:0.26573:0:60:2:0.0071:0:1 +19 11136006 . A C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00742;SOR=0.4593;LSEQ=TTCCCCACTAGAGCGTCCCC;RSEQ=TGGCCCTTCTCCCAACACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:48:43,5:191,20:211,48:0.1846:2,2:22.4:1:31:1:0.79031:1.11002:60:47:0.1843:0:1.2 0/1:202:19:17,2:153,29:182,19:0.0941:2,2:26.4:1:30.2:1:0.74373:1.61:60:38:0.0955:0:1.3 +19 11136215 . C G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74373;SOR=1.06655;LSEQ=CGCGGCTGGGACGGCTCAGG;RSEQ=CCTGCTGTCTGCTGAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:105:28,77:56,185:241,105:0.3035:2,2:24.3:1:31.3:1:0.49805:1.20:60:34:0.3036:0:1.1 0/1:353:112:33,79:79,160:239,112:0.3173:2,2:22.7:1:29.7:1:0.54045:1.18145:60:15:0.3088:0:1.1 +19 11136315 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.64409;SOR=0.72094;LSEQ=GGTAATGCCTGTACATCTGT;RSEQ=TCTCATTTGGTCTTCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:16:0,16:1,45:46,16:0.2581:1,1:25.2:1:30.4:1:1:0:60:32:0.2581:0:1 0/1:45:9:0,9:1,35:36,9:0.2:1,0:15.3:1:28.7:1:1:0:60:8:0.1818:0:1 +19 11136857 . C T 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00044;SOR=Inf;LSEQ=TCTCAGAGCCGCCGTGGGCC;RSEQ=GTGCCGAGCACACAGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:115,6:121,0:0:1,0:21.6:1:31.3:1:1:0:60:120:1:0:0.1 0/1:78:8:8,0:66,4:70,8:0.1026:2,0:26.8:1:30.4:1:1:0:60:16:0.1053:0:1.1 +19 11137135 . T C 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAATTTCAAAGGCAGAAAAT;RSEQ=AGAAAATACAGAAGAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:7,170:177,0:0:1,0:27.2:1:28.3:1:1:0:58.5:58:1:0:0.5 0/1:158:26:3,23:8,124:132,26:0.1646:2,2:22.5:1:30.3:1:0.39141:2.01:59.2:7.667:0.1503:0:1.5 +19 11138292 . A G 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00107;SOR=0;LSEQ=GCTTATTTCAGTTGGGGGAA;RSEQ=TGGCTTTGCTGAAGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:19:19,0:24,0:24,19:0.4419:1,1:22.1:1:34.3:1:1:0:60:38:0.4524:0:1.1 0/0:15:0:0,0:13,2:15,0:0:2,0:19.5:1:29.1:1:1:0:60:14:1:0:0.4 +19 11141724 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.5054;SOR=0;LSEQ=CCCATATCTCCATAGGTCAT;RSEQ=AGGGAGAAAAGAGGCGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:1,83:84,2:0.0233:1,2:25:1:28.5:1:0.04624:59.00:60:4:0.0241:0:1 0/0:66:0:0,0:6,60:66,0:0:2,0:20.9:1:30:1:1:0:60:15.5:1:0:0.1 +19 11143811 . C G 113 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15518;SOR=0.17968;LSEQ=CATGGCGGCCCAGGCTCCAC;RSEQ=AGCTCTGTTTTCATGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:14:14,0:30,1:31,14:0.3043:1,1:31.5:1:29.9:1:1:0:60:28:0.3043:0:1.1 0/1:14:1:1,0:12,1:13,1:0.0714:1,0:43:0:30:0:1:0:60:2:0.0714:0:1 +19 11143895 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16134;SOR=Inf;LSEQ=ACAGCACACCTCTCCAGCTA;RSEQ=TGTCAGAGGCCACCTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:145,33:178,0:0:2,0:24:1:32.7:1:1:0:60:177:1:0:0.1 0/1:120:2:1,1:88,30:118,2:0.0167:2,2:21.5:1:29:1:0.45154:2.90217:60:4:0.0172:0:1.5 +19 11143914 . CT C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.19514;SOR=Inf;LSEQ=AGTGTCAGAGGCCACCTTCC;RSEQ=TTTATGACCTCCTGGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:175,67:242,0:0:2,0:25.9:1:31.3:1:1:0:60:120:1:0:0.1 0/1:192:2:2,0:137,53:190,2:0.0104:2,0:25:1:27:1:1:0:60:4:0.0107:0.0052:0.5 +19 11144243 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19695;SOR=Inf;LSEQ=CCAGCGTGAATGGTGGACGC;RSEQ=TGAGCGGCTTTCATTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:42,193:235,0:0:2,0:23.9:1:32:1:1:0:60:46:1:0:0.1 0/1:188:2:1,1:32,154:186,2:0.0106:2,2:15:1:29.5:1:0.32103:4.75:60:4:0.0107:0:1 +19 11144287 . AT A 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.07859;SOR=0;LSEQ=TTTACCTTTTTTGCACTCTT;RSEQ=TTTTTTTGCATCCCTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:5:4,1:64,74:138,5:0.035:2,2:31:1:31.8:1:0.19117:4.58:60:10:0.0355:0:0 0/0:101:0:0,0:47,54:101,0:0:2,0:20.9:1:30:1:1:0:60:100:1:0:0.2 +19 11144367 . G GT 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08185;SOR=0.43562;LSEQ=CTTGCTTTTTCTTTGAAGTG;RSEQ=TTTTTTTTTCTAAACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:15:9,6:181,66:247,15:0.0573:2,2:17.8:1:29.5:1:0.36993:1.82353:59.7:30:0.0579:0.0229:0.1 0/1:272:7:4,3:180,83:263,7:0.0257:2,2:21:1:22.7:1:0.68309:1.62338:60:2.5:0.0188:0.0037:0.7 +19 11144610 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12419;SOR=Inf;LSEQ=GGCTGAGACGGCCAGCAAGG;RSEQ=CCCTGGTCCCACGGAGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:116,229:345,0:0:2,0:22.7:1:31.8:1:1:0:60:42.125:1:0:0.1 0/1:358:4:3,1:132,221:353,4:0.0112:2,2:12.5:1:25.3:1:0.15365:5.00:60:8:0.0116:0:1.3 +19 11144616 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1238;SOR=Inf;LSEQ=GACGGCCAGCAAGGGCCCTG;RSEQ=TCCCACGGAGCGTGCGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:99,210:309,0:0:2,0:21.8:1:32:1:1:0:60:153.5:1:0:0.1 0/1:311:4:2,2:105,202:307,4:0.0129:2,2:15.8:1:29:1:0.6098:1.92:60:8:0.0132:0:1.3 +19 11144928 . C A 42 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62339;SOR=0.34044;LSEQ=GGCATCCCACTCTGCTGCCA;RSEQ=CAGGAGCAAAGCAGACGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:1,2:47,166:213,3:0.0138:2,2:30.3:1:27:1:0.53137:1.76:60:6:0.0143:0:2.7 0/0:211:1:1,0:44,166:210,1:0.0047:2,0:1:0:27:0:0.21327:0:60:2:0.0048:0:1 +19 11144945 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24105;SOR=Inf;LSEQ=CCACCAGGAGCAAAGCAGAC;RSEQ=TCCTAGTGCCCATGGTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:20,135:155,0:0:2,0:25.3:1:32:1:1:0:60:50.667:1:0:0.2 0/1:150:2:1,1:21,126:147,2:0.0133:2,2:20:1:31.5:1:0.27435:5.89:60:4:0.0133:0:1 +19 11145547 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18144;SOR=Inf;LSEQ=GGCTCTAGCGTGCCCCTGGT;RSEQ=CCTGCATGCTGATGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:154,34:188,0:0:2,0:24.2:1:32:1:1:0:60:61.667:1:0:0.1 0/1:140:2:1,1:109,29:138,2:0.0143:2,2:21:0:27.5:1:0.38386:3.71257:60:4:0.0145:0:1.5 +19 11145691 . C T 166 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=16.17183;LSEQ=TCGTGGATCATCAAGGACGA;RSEQ=GCGGAGGTGGAGCGGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:691:3:0,3:374,313:687,3:0.0043:2,0:1:0:27.3:1:0.09556:0:60:6:0.0044:0:1 0/1:819:54:29,25:414,351:765,54:0.0659:2,2:21.7:1:29:1:1:1.01678:60:108:0.0666:0:1.2 +19 11145715 . TGAG T 135 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.02743;SOR=2.80213;LSEQ=GAGGTGGAGCGGCTGACCTG;RSEQ=GAGGAGGAGGAGAAGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:742:6:4,2:379,355:734,6:0.0081:2,2:24.8:1:31:1:0.68739:1.87:60:12:0.0082:0.0027:0.2 0/1:895:20:10,10:441,429:870,20:0.0223:2,2:26:1:31.3:1:1:1.02795:60:40:0.0227:0.0034:0.1 +19 11145842 . G A 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20507;SOR=4.25933;LSEQ=AGGCCCAGCAGCTGCCGCAG;RSEQ=CCAGCGCCAGGCAGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:1:1,0:77,241:318,1:0.0031:2,0:1:0:25:0:0.24451:0:60:2:0.0032:0:1 0/1:302:4:2,2:82,216:298,4:0.0132:2,2:20.3:1:29:1:0.30951:2.62:60:8:0.0133:0:1.3 +19 11145848 . G A 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34718;SOR=3.38886;LSEQ=AGCAGCTGCCGCAGGCCAGC;RSEQ=CCAGGCAGGGCTGGGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:1:0,1:55,228:283,1:0.0035:2,0:36:0:32:0:1:0:60:2:0.0035:0:1 0/1:253:3:2,1:61,189:250,3:0.0119:2,2:28.3:1:21:1:0.15402:6.14:60:2:0.0081:0:1 +19 11145853 . G A 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCCGCAGGCCAGCGCCAG;RSEQ=CAGGGCTGGGGAGACAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:49,221:270,0:0:2,0:23.2:1:32:1:1:0:59.9:53:1:0:0.1 0/1:233:16:4,12:52,165:217,16:0.0687:2,2:28.1:1:29.3:1:1:1.06:60:32:0.069:0:1.1 +19 11150013 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14589;SOR=Inf;LSEQ=GCACTCCAGCCTGGGCGACA;RSEQ=AATGAGACCCTGTCTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:71,1:72,0:0:1,0:22.4:1:33.6:1:1:0:59.6:71:1:0:0.1 0/1:45:2:2,0:42,1:43,2:0.0444:1,0:21:1:33:0:1:0:60:4:0.0455:0:1 +19 11150067 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25038;SOR=Inf;LSEQ=ACCTAAATGCCCAAGAACAA;RSEQ=GGGAGGCTAAATTAGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:155,50:205,0:0:2,0:24.9:1:32.3:1:1:0:60:67.333:1:0:0.1 0/1:228:3:1,2:164,61:225,3:0.0132:2,2:20.7:1:26.7:1:0.18567:5.33021:60:6:0.0135:0:1 +19 11150265 . C T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09391;SOR=0;LSEQ=GTGGTGGGTGGCGCTGAGGG;RSEQ=TGCACAACACTGGGGACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:74,184:258,3:0.0115:2,2:19:1:23.7:1:1:1.24:60:2:0.0078:0:2 0/0:312:0:0,0:92,220:312,0:0:2,0:23.6:1:31.3:1:1:0:59.9:311:1:0:0.1 +19 11151997 . C A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04308;SOR=0;LSEQ=CTGAAGGCCATCGAGGAGGG;RSEQ=ACGCTGGAGGAGATCGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:4:2,2:188,130:318,4:0.0124:2,2:11.3:1:31:1:1:1.44443:60:8:0.0125:0:1 0/0:383:0:0,0:228,154:382,0:0:2,0:24.9:1:31.3:1:1:0:60:62.667:1:0:0.1 +19 11152282 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49914;SOR=0;LSEQ=GGGCTGTAGGGGTCCCCGTG;RSEQ=GAGCAGGCCTGGCATCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:23,139:162,2:0.0122:2,2:12.5:1:30.5:1:0.27203:5.94:60:4:0.0124:0:1 0/0:152:0:0,0:33,119:152,0:0:2,0:23.4:1:29.8:1:1:0:60:24.333:1:0:0.1 +19 11167071 . A G 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAAGGGTATGTGCTCCC;RSEQ=TGCTGGACCGGCTGGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:32.5:1:1:0:60:4:1:0:1.5 +19 11168798 . G A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0025;SOR=Inf;LSEQ=GTCTCAAAAAAAAAAAAAGC;RSEQ=CATGTGCAAGAAATAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:46,1:47,0:0:1,0:21.4:1:26.9:1:1:0:57.3:6.833:1:0:0.5 0/1:30:6:6,0:23,0:23,6:0.2:1,0:17:1:26.5:1:1:0:57.3:5:0.1923:0:1 +19 11168896 . A G 211 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGGCTCCCGGGTGGGCGG;RSEQ=CTCGGGGGTGATAGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:201,88:289,0:0:2,0:24.1:1:29.5:1:1:0:60:56.8:1:0:0.1 0/1:332:140:95,45:133,59:192,140:0.4217:2,2:25.5:1:29.6:1:0.81127:1.06758:60:19:0.4118:0:1.2 +19 11169305 . T C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.08133;LSEQ=GCTGGGCCTCAGTCATGCAG;RSEQ=TCCCATGCCTAGTGAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:30:26,4:37,11:48,30:0.3846:2,2:26.9:1:32.8:1:0.38274:1.92:60:60:0.3846:0:1.4 0/1:42:2:2,0:36,3:39,2:0.0476:2,0:21.5:1:26.5:1:1:0:60:4:0.0488:0:1 +19 11169401 . C T 57 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06386;SOR=Inf;LSEQ=GTGGGGTCTCCAGCACACAG;RSEQ=CAGGCCTGCGGGCAGGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:239,90:329,0:0:2,0:24.2:1:31.8:1:1:0:60:64.8:1:0:0.1 0/1:371:5:1,4:256,110:366,5:0.0135:2,2:5:1:24.6:1:0.03266:9.24951:60:10:0.0136:0:1 +19 11169514 . C T 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAACGACCTAGAGAAGGA;RSEQ=GTCATGCTCCTGTGCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:0:0,0:440,442:882,0:0:2,0:24.9:1:31:1:1:0:60:62:1:0:0.1 0/1:973:29:14,15:452,491:943,29:0.0298:2,2:25.6:1:29.7:1:1:1.01:59.9:28:0.0289:0:1.4 +19 11169785 . TA T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATAACAAGACCCTGTCTT;RSEQ=AAAAAAAAAAAGAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:0,3:1,17:18,3:0.1364:1,0:26.7:1:32:1:1:0:60:6:0.1364:0.0455:1 0/0:2:0:0,0:0,2:2,0:0:0,0:26:1:32:0:1:0:60:4:1:0:0 +19 11170589 . G A 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05126;SOR=Inf;LSEQ=CCGGGGGGGTTCAGGACGCC;RSEQ=GGGTTCACGCTGGCCCGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:133,111:244,0:0:2,0:26:1:30.1:1:1:0:59.9:39.667:1:0:0.2 0/1:223:4:2,2:114,104:218,4:0.0179:2,2:13:1:31.8:1:1:1.0957:60:8:0.0186:0:1.5 +19 11170839 . T C 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCCGGTCGTGAGTGACGA;RSEQ=GACAGTGAGGAGGAACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:81,190:271,0:0:2,0:26.4:1:30.1:1:1:0:60:29.111:1:0:0.2 0/1:283:71:24,47:71,140:211,71:0.2509:2,2:25:1:29.4:1:1:1.01:60:34.5:0.2509:0:1.1 +19 11170909 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20201;SOR=Inf;LSEQ=GAGCTGGCATGTGGCAGGAG;RSEQ=CATCCCGGGGCCCTGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:17,111:128,0:0:2,0:24.7:1:32.4:1:1:0:59.8:63:1:0:0.1 0/1:105:2:1,1:19,84:103,2:0.019:2,2:28:1:29.5:1:0.34615:4.33:60:4:0.0196:0:1 +19 11170916 . G C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08482;SOR=Inf;LSEQ=CATGTGGCAGGAGGCATCCC;RSEQ=GGGCCCTGATGGGACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:13,98:111,0:0:2,0:24.4:1:30.6:1:1:0:59.8:21.2:1:0:0.1 0/1:88:3:1,2:12,73:85,3:0.0341:2,2:28.7:1:31.7:1:0.38466:2.99:60:6:0.0345:0:1 +19 11172299 . G A 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00213;SOR=Inf;LSEQ=CCTGACCTCGTGATCCGCCC;RSEQ=CCTTGGCCTTCCAAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:34,0:34,0:0:1,0:18.8:1:31.1:1:1:0:51.1:68:1:0:0 0/1:34:9:9,0:24,1:25,9:0.2647:1,0:22.3:1:31.3:1:1:0:47.3:18:0.2647:0:1 +19 11172439 . C T 79 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.02795;SOR=0.12147;LSEQ=GGGTGGCCAACGCACACTCT;RSEQ=TCCTCCTGTCCCCTCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:7:3,4:373,241:614,7:0.0113:2,2:21.6:1:28.4:1:0.4427:2.06117:60:14:0.0114:0:1.1 0/0:724:1:0,1:423,300:723,1:0.0014:2,0:1:0:25:0:0.41575:0:60:2:0.0014:0:1 +19 11446366 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5109;SOR=0;LSEQ=CTGCACAGCGGCAAAGGATT;RSEQ=CTGATTGGCGATGTCATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:90,13:103,2:0.0189:2,2:20.5:1:31:1:0.25:6.70931:60:4:0.0192:0:1 0/0:76:0:0,0:61,15:76,0:0:2,0:18.1:1:29.9:1:1:0:60:75:1:0:0.1 +19 11446520 . T G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11611;SOR=1.67958;LSEQ=TTCCCAGTCCACCCCTGTCT;RSEQ=AGAGGGGCACTGCCCTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:21:3,18:4,61:65,21:0.2442:2,2:22.6:1:32.9:1:0.35436:2.51:60:42:0.2471:0:1.1 0/1:105:37:6,31:14,53:67,37:0.3524:2,2:22.8:1:30.2:1:0.61422:1.36082:60:17.5:0.3431:0:1.2 +19 12984252 . C T 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55751;SOR=2.97834;LSEQ=TCCAGCGATAGTCTCCCGGG;RSEQ=TCGCCTACGCACGGGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:13,4:17,1:0.0556:2,0:1:0:25:0:0.27778:0:60:2:0.0588:0:1 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:25:1:27:1:1:2.4495:60:4:0.1667:0:1 +19 12984358 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19886;SOR=0;LSEQ=GCACCTGCGCGGGGACCGAG;RSEQ=AGCGCGGGGTGGCCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:3,10:13,2:0.1333:2,2:29:1:30.5:1:0.47619:3.03:60:4:0.1429:0:1 0/0:18:0:0,0:5,13:18,0:0:2,0:25.4:1:30.8:1:1:0:60:17:1:0:0.5 +19 13049423 . G T 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.3161;SOR=4.1159;LSEQ=CAAGGCGGGCGGCGGCGTCC;RSEQ=TCCGTACTGCAGAGCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:1:1,0:304,48:352,1:0.0028:2,0:31:0:29:0:1:0:60:2:0.0029:0:1 0/1:259:3:0,3:200,55:255,3:0.0116:2,0:12.3:1:24.3:1:0.01091:0:60:6:0.0118:0:1 +19 13049895 . T TG 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10847;SOR=0.25907;LSEQ=CTCTCGGCAGATGTTTGGTG;RSEQ=GGGGGGGGATTAGCACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:8:6,2:371,101:472,8:0.0166:2,2:15.3:1:31.9:1:0.68266:1.22388:60:16:0.0168:0.0083:0.1 0/0:460:2:1,1:353,105:458,2:0.0043:2,2:14.5:1:25:1:0.40816:3.3507:60:4:0.0044:0:0 +19 13050526 . AT A 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19029;SOR=4.60721;LSEQ=CATTGACTTTCTTAATAATG;RSEQ=TTTTTTTGGAAGGGGAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:1:0,1:56,288:344,1:0.0029:2,0:47:0:30:0:1:0:60:2:0.0029:0:1 0/1:302:4:0,4:61,237:298,4:0.0132:2,0:36.8:1:31.3:1:0.58633:0:60:8:0.0134:0:0 +19 13050675 . AT A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.50874;SOR=1.66653;LSEQ=TTTTGAGTTCTAGAGCACTG;RSEQ=TTTTTTTTTTTCTCCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:7:5,2:42,19:61,7:0.1029:2,2:21:1:31:1:1:1.13:60:14:0.1045:0.0294:0.9 0/1:31:5:5,0:18,6:24,5:0.1613:2,0:29.4:1:29.5:1:0.55261:0:60:10:0.1613:0.0323:0 +19 13051554 . G T 265 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00312;LSEQ=TCGGTTTCCTTCTCCCTTCT;RSEQ=CAGGGTGAGTGGAAGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:418:204,214:447,467:914,418:0.3138:2,2:23.5:1:30.5:1:1:1.00409:60:51.25:0.3125:0:1.1 0/0:1401:2:0,2:733,660:1393,2:0.0014:2,0:1:0:26.5:1:0.22502:0:60:4:0.0014:0:1 +19 13052115 . AT A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTATCTCTACAAAAAAA;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:13.5:1:32:1:1:0:60:4:0.5:0.25:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 13054649 . TGAGGATGAG T 211 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGATGATGAGGACAAAGA;RSEQ=GAGGATGAGGAGGACAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1737:0:0,0:863,869:1732,0:0:2,0:25.4:1:32.4:1:1:0:59.8:77.727:0.9971:0:0.2 0/1:2022:105:51,54:952,961:1913,105:0.0519:2,2:31.4:1:31.5:1:0.84153:1.0489:59.3:210:0.0524:0.001:0.3 +19 13054781 . G T 264 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00363;LSEQ=AGCGCTCCTGCCGCAGAGCT;RSEQ=GCCGCGCCAAATAATGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:390:388:34,354:0,1:1,388:0.9949:0,2:24.1:1:30.8:1:1:0:59.8:193:0.9948:0:1.1 0/1:360:148:18,130:37,175:212,148:0.4111:2,2:21.9:1:29.4:1:0.18319:1.52524:60:147:0.4118:0:1.1 +19 13056829 . G T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGATCCGCATGGAGCCTGAC;RSEQ=AGACGGTGCGGGCCGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:30.5:1:1:0:60:4:1:0:2 +19 13519148 . C A 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51287;SOR=0;LSEQ=GAGCCACGATCTTGCCACTG;RSEQ=ACTCTAGCCTGGGCAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:58,0:58,2:0.0333:1,2:5:0:32.5:1:0.03333:0:50:4:0.0333:0:2 0/0:41:0:0,0:39,2:41,0:0:1,0:23.2:1:32.3:1:1:0:60:82:1:0:0.2 +19 13519150 . C T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50842;SOR=0;LSEQ=GCCACGATCTTGCCACTGCA;RSEQ=TCTAGCCTGGGCAACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:59,0:59,2:0.0328:1,2:7:0:32:1:0.03279:0:50:4:0.0333:0:2 0/0:44:0:0,0:42,2:44,0:0:1,0:22.9:1:32.2:1:1:0:60:88:1:0:0.2 +19 13519178 . C T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.24144;LSEQ=TGGGCAACAGAGTGAGACCC;RSEQ=GTTTCAAAAATATATATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:39:29,10:61,6:67,39:0.3645:2,2:19.7:1:30.9:1:0.02648:3.46057:58.9:78:0.3645:0:1.1 0/1:91:11:9,2:61,19:80,11:0.1209:2,2:20.2:1:30:1:1:1.40:60:22:0.1209:0:1.1 +19 13519199 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4986;SOR=Inf;LSEQ=GTTTCAAAAATATATATGTG;RSEQ=TGAAACAAAAGAACTAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:125,44:169,0:0:2,0:21.6:1:31.6:1:1:0:60:168:1:0:0.3 0/1:173:2:1,1:124,47:171,2:0.0116:2,2:20:1:27:1:0.4791:2.62118:60:4:0.0116:0:1 +19 13519205 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23549;SOR=0;LSEQ=AAAATATATATGTGGTGAAA;RSEQ=AAAAGAACTAATGAATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:136,51:187,2:0.0105:2,2:23.5:1:32.5:1:0.47563:2.6506:60:4:0.0107:0:1.5 0/0:201:0:0,0:143,58:201,0:0:2,0:20.9:1:31:1:1:0:60:200:1:0:0.2 +19 13519258 . A G 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATACTTTGAGCAGGGTAT;RSEQ=AGGAACCTGGGTAAGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:0:0,0:252,178:430,0:0:2,0:26:1:29.4:1:1:0:59.9:214:1:0:0.4 0/1:470:33:19,14:240,197:437,33:0.0702:2,2:27.8:1:31.2:1:0.85678:1.11:60:66:0.0707:0:1.2 +19 13519303 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00099;SOR=0.60861;LSEQ=TTCCAAGATCTTCAAAGGTA;RSEQ=CTTTCTAGGCACTAAGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:142:71,71:143,150:293,142:0.3257:2,2:25.1:1:30.7:1:0.83841:1.05:60:284:0.3272:0:1.1 0/1:458:104:50,54:160,193:353,104:0.2271:2,2:26.7:1:29.2:1:0.65504:1.12:60:103:0.2289:0:1.1 +19 14581049 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22938;SOR=Inf;LSEQ=CCCCTGAGGTGCTGACGGAC;RSEQ=CGTCGTACACGCGAGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:31,0:0:2,0:26.3:1:29.7:1:1:0:60:30:1:0:0.1 0/1:29:2:1,1:11,15:26,2:0.069:2,2:39.5:1:28:1:1:1.35:60:4:0.0714:0:1 +19 14627050 . G A 313 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01045;LSEQ=TCAGCTCTTGCCCAGAGGCC;RSEQ=TCTGCCATAGATAAGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1145:1141:580,561:0,0:0,1141:0.9965:0,2:24.7:1:30.9:1:1:0:60:125.778:0.9982:0:1.2 1/0:1296:970:514,456:169,156:325,970:0.7485:2,2:24.8:1:29.7:1:0.7974:1.04:60:106.778:0.7484:0:1.2 +19 14627093 . T C 239 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=270.19005;LSEQ=AGGCCTCTGCAGCTAAGACC;RSEQ=GGCCCCCAAATCTACACGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1360:1:0,1:746,612:1358,1:7e-04:2,0:1:0:32:0:0.45107:0:60:2:7e-04:0:2 0/1:1649:275:161,114:736,637:1373,275:0.1668:2,2:24:1:29.6:1:0.14454:1.22:59.9:33.375:0.1646:0:1.6 +19 14627140 . C T 265 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00126;LSEQ=ACGAAAGCTCCACAACAGCG;RSEQ=CCTGGTCAGTCCTGTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1566:464:243,221:587,513:1100,464:0.2963:2,2:23:1:30:1:0.73943:1.04065:60:153.667:0.2988:0:1.2 0/0:1895:1:1,0:978,915:1893,1:5e-04:2,0:2:0:28:0:1:0:60:2:5e-04:0:1 +19 14627215 . T C 225 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=125.11275;LSEQ=CAACACATTGGTTCAGCAAA;RSEQ=ACTAAACTGCTTCAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1631:1:0,1:781,848:1629,1:6e-04:2,0:27:0:35:0:1:0:60:2:6e-04:0:1 0/1:1977:141:70,71:898,934:1832,141:0.0713:2,2:23.3:1:31.6:1:0.93041:1.03:60:46:0.0707:0:1.2 +19 14628083 . G A 182 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=37.06267;LSEQ=AGTGGAAAAGGACTCATGCG;RSEQ=TTAGGTGTTCACCTCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1415:2:1,1:747,666:1413,2:0.0014:2,2:38.5:1:30:1:1:1.12153:60:4:0.0014:0:1 0/1:1584:79:43,36:788,717:1505,79:0.0499:2,2:20.5:1:28.9:1:0.73054:1.09:60:38.5:0.0493:0:1.3 +19 14628242 . G A 317 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0588;LSEQ=GGGCTAATGGTGCGTAGGAA;RSEQ=AGAAGAAAAAAAAAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1447:1298:647,651:72,74:146,1298:0.897:2,2:23.5:1:30.7:1:0.93057:1.02:59.8:128.8:0.9039:0:1.3 0/1:1775:601:304,297:578,591:1169,601:0.3386:2,2:23.5:1:29.5:1:0.65185:1.05:59.7:84.857:0.3488:0:1.3 +19 14628247 . G GA 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30696;SOR=0.88388;LSEQ=AATGGTGCGTAGGAAGAGAA;RSEQ=AAAAAAAAAAACAAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1404:147:67,80:650,580:1230,147:0.1047:2,2:27.8:1:30.4:1:0.09781:1.33784:59.1:72.5:0.11:0:1.4 0/1:1740:163:72,91:797,744:1541,163:0.0937:2,2:28.7:1:29.4:1:0.07019:1.35367:59.5:162:0.0988:0:0.8 +19 14628259 . C A 195 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=7.67839;LSEQ=GAAGAGAAGAAAAAAAAAAA;RSEQ=AAAAATAAATAGGGAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1513:15:15,0:791,706:1497,15:0.0099:2,1:16.5:1:17.5:1:9e-05:0:58.4:0.667:0.0043:0:3.7 0/1:1764:126:75,51:822,795:1617,126:0.0714:2,2:22.5:1:28:1:0.06438:1.42:59.6:8:0.0678:0:2.1 +19 14628261 . A T 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGAAGAAAAAAAAAAACA;RSEQ=AAATAAATAGGGAGTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1505:0:0,0:811,693:1504,0:0:2,0:21.4:1:30.7:1:1:0:59.7:124.333:0.9993:0:1 0/1:1756:83:45,38:851,799:1650,83:0.0473:2,2:24.2:1:28:1:0.65428:1.11:60:19.75:0.0455:0:2.1 +19 14628524 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03689;SOR=1.43003;LSEQ=CCCAAGCCCACGAACGGGGT;RSEQ=GGCTCCTGCATTCACAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:837:63:23,40:259,515:774,63:0.0753:2,2:23.1:1:29.3:1:0.67782:1.14:59.6:20:0.0731:0:1.2 0/1:911:95:34,61:308,504:812,95:0.1043:2,2:26.4:1:29.2:1:0.73777:1.09632:59.8:94:0.105:0:1.1 +19 14628541 . A G 204 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTCGGCTCCTGCATTCACA;RSEQ=CCCCTCGCCCCGCAGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:0:0,0:211,466:677,0:0:2,0:25.2:1:29.2:1:1:0:60:28.435:1:0:0.3 0/1:705:98:35,63:217,389:606,98:0.139:2,2:25.4:1:30.9:1:1:1.00411:60:31.667:0.1381:0:1.1 +19 14628557 . C A 64 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11068;SOR=5.45112;LSEQ=CACAACCCCTCGCCCCGCAG;RSEQ=TGAGCCGGAGGCGCCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:1:1,0:136,363:499,1:0.002:2,0:1:0:25:0:0.274:0:60:2:0.002:0:1 0/1:462:5:3,2:146,311:457,5:0.0108:2,2:9.8:1:27.6:1:0.33425:3.19:60:10:0.011:0:1.6 +19 14628629 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52835;SOR=Inf;LSEQ=CGGGTCCGCAGCGGGCTCCG;RSEQ=CGCGCCGTCCCCGTCGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:20,16:36,0:0:2,0:21.7:1:32.1:1:1:0:59.9:35:1:0:0.3 0/1:61:2:1,1:30,29:59,2:0.0328:2,2:33.5:1:29:1:1:1.03392:60:4:0.0333:0:1.5 +19 14628633 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13729;SOR=0;LSEQ=TCCGCAGCGGGCTCCGCCGC;RSEQ=CCGTCCCCGTCGTCACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:21,14:35,2:0.0541:2,2:16.5:1:29:1:1:1.4832:60:4:0.0556:0:1.5 0/0:62:0:0,0:33,29:62,0:0:2,0:24.5:1:30.9:1:1:0:59.8:61:1:0:0.3 +19 14628649 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53976;SOR=Inf;LSEQ=CCGCGCCGTCCCCGTCGTCA;RSEQ=CCCCGGCTCCCCCACCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:29,14:43,0:0:2,0:26.9:1:32.7:1:1:0:60:86:1:0:0.3 0/1:79:2:1,1:42,35:77,2:0.0253:2,2:24:0:31:1:1:1.19722:60:4:0.0253:0:1.5 +19 14628720 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51197;SOR=Inf;LSEQ=CGGGAGGAGGCGCCCGGGGA;RSEQ=GGGCAGCCCCAGACATGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:45,30:75,0:0:2,0:24.4:1:32:1:1:0:60:150:1:0:0.1 0/1:106:2:1,1:58,46:104,2:0.0189:2,2:31.5:1:28.5:1:1:1.25808:60:4:0.0192:0:1 +19 14628765 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49769;SOR=Inf;LSEQ=CTTCTGGCCGAGCGGCTGGG;RSEQ=CAAGGCTCCTCCTCCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:39,53:92,0:0:2,0:25:1:31.2:1:1:0:59.8:29.667:1:0:0.2 0/1:97:2:1,1:43,52:95,2:0.0206:2,2:27:1:30:0:1:1.21:60:4:0.0211:0:1 +19 14628803 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21178;SOR=Inf;LSEQ=CCGCGCGGCCGCCAATCCGA;RSEQ=GGCGGAGGCCCGCGAGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:42,36:78,0:0:2,0:21.9:1:32.2:1:1:0:60:77:1:0:0.2 0/1:67:2:1,1:36,29:65,2:0.0299:2,2:20.5:1:28:1:1:1.23734:60:4:0.0303:0:1 +19 14628828 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GAGGCCCGCGAGGCCGGAGG;RSEQ=CGGGGCAGCTCGGCCCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:114,37:151,2:0.0131:2,2:18:1:31.5:1:0.43627:3.05348:60:4:0.0137:0:1 0/0:120:0:0,0:98,22:120,0:0:2,0:16.7:1:30.8:1:1:0:60:29:1:0:0.2 +19 14628840 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49882;SOR=Inf;LSEQ=GCCGGAGGGCGGGGCAGCTC;RSEQ=GCCCCACGGCCCGGGGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:155,41:196,0:0:2,0:19.8:1:30.8:1:1:0:60:97:1:0:0.1 0/1:201:2:1,1:159,40:199,2:0.01:2,2:24.5:1:27.5:1:0.36716:3.93855:60:4:0.0102:0:1 +19 14628890 . C T 80 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00406;SOR=Inf;LSEQ=GGGCCGCCGAGAGGGGCCAG;RSEQ=GTGCCTCAGTTTCCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:0:0,0:482,226:708,0:0:2,0:23.5:1:31.3:1:1:0:60:53.462:1:0:0.2 0/1:771:9:1,8:503,259:762,9:0.0117:2,2:7.4:1:25.4:1:0.00121:15.48798:60:18:0.0118:0:1 +19 14629138 . C T 180 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.83182;LSEQ=GCGCCGCGGGCCAGGCCCAA;RSEQ=GTCTGGTAGTAGTCTTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1180:2:0,2:546,631:1177,2:0.0017:2,0:1:0:26.5:1:0.5023:0:60:4:0.0017:0:1 0/1:1468:64:30,34:635,769:1404,64:0.0436:2,2:24.6:1:30:1:0.79888:1.07:49.8:128:0.044:0:1.1 +19 14629150 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=2.63978;LSEQ=AGGCCCAACGTCTGGTAGTA;RSEQ=TCTTTACCCATGACCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1152:106:42,64:465,580:1045,106:0.092:2,2:23.4:1:30.4:1:0.35672:1.22146:52.7:52:0.0915:0:1.2 0/1:1440:304:132,172:497,638:1135,304:0.2111:2,2:23.4:1:29.7:1:0.94812:1.01505:49.1:75:0.2108:0:1.2 +19 14629171 . C T 209 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCTTTACCCATGACCCCCTC;RSEQ=TGCGGCCCGCCGACCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:936:0:0,0:388,547:935,0:0:2,0:27.1:1:32.3:1:1:0:59.2:132.571:0.9989:0:0.3 0/1:1125:137:55,82:409,577:986,137:0.1218:2,2:28.2:1:29.5:1:0.78205:1.05678:59.6:44.667:0.121:0:1.1 +19 14629296 . CG C 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.63299;SOR=1.66669;LSEQ=CCAGAACCTTCCGCCCCGCC;RSEQ=CCCCCGCGGCGCCGGCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:0,2:0,0:0,2:0.0183:0,0:36.5:1:33:0:1:0:60:4:0.02:0:0 0/1:66:2:0,2:0,11:11,2:0.0303:0,0:26.5:1:29.5:1:1:0:60:4:0.0357:0:0.5 +19 14629297 . G C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1e-05;SOR=0.12649;LSEQ=CAGAACCTTCCGCCCCGCCC;RSEQ=CCCCCGCGGCGCCGGCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:109:103:0,103:0,0:0,103:0.945:0,1:24.3:1:31.3:1:1:0:59.8:19.6:0.98:0:1.4 1/0:66:45:0,45:0,11:11,45:0.6818:0,1:23.8:1:30.4:1:1:0:59.8:21.5:0.7679:0:1.7 +19 14629336 . G A 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00404;SOR=0;LSEQ=ATCGCCGCCGCCCTTTCAGC;RSEQ=ACACGCGACATCCGGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:0,11:0,23:23,11:0.3235:1,0:11.5:1:32.2:1:1:0:60:22:0.3333:0:2 0/0:20:0:0,0:0,20:20,0:0:1,0:14.2:1:31.5:1:1:0:60:40:1:0:1.5 +19 15271135 . T G 79 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAAAAAAAAAAGAAAAA;RSEQ=AAAAATAATAATAATTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:23.5:1:30.7:1:1:0:53.2:5:0.8333:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15271355 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52845;SOR=0;LSEQ=CTGCAAGGCAAGGATGCAGG;RSEQ=GGGTTGGTGGAAAGAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:2,0:197,1:198,2:0.01:1,0:23.5:1:32:0:1:0:60:4:0.0106:0:1 0/0:122:0:0,0:118,4:122,0:0:1,0:23:1:28.5:1:1:0:60:39.667:1:0:0.1 +19 15271771 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.67511;LSEQ=GGCTGCTGTGTGCCCCAGCC;RSEQ=CCGGGTACTCCTCGCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:259:97,162:161,250:411,259:0.3866:2,2:25.5:1:30.3:1:0.68395:1.07541:60:258:0.3903:0:1.1 1/0:567:356:137,219:84,127:211,356:0.6279:2,2:23.8:1:29.1:1:0.78949:1.05719:60:70.2:0.6268:0:1.2 +19 15271934 . G A 43 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02699;LSEQ=CAGCCGGGCCCAATCGAGGG;RSEQ=CACAGCCACAGGGTTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:3:2,1:140,164:304,3:0.0098:2,2:10.3:1:29.3:1:0.59767:2.34:60:6:0.0099:0:1.3 0/1:299:3:1,2:143,153:296,3:0.01:2,2:19:1:27.7:1:1:1.86552:60:6:0.0101:0:1 +19 15272001 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.04495;SOR=Inf;LSEQ=GGGGGCTGGCGCCCTAGACC;RSEQ=GCCCGGCCTGGGCCACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:120,128:248,0:0:2,0:22.2:1:30.3:1:1:0:60:61:1:0:0.1 0/1:214:4:2,2:110,100:210,4:0.0187:2,2:14.8:1:27.5:1:1:1.09951:60:8:0.0189:0:1 +19 15272045 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.25019;SOR=0;LSEQ=TGCCAGAGACACTGCAGTGG;RSEQ=AGTGGCAGCTGCATAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:1,2:130,133:263,3:0.0112:2,2:43:1:28:1:1:1.95015:60:6:0.0116:0:1 0/0:243:0:0,0:114,129:243,0:0:2,0:26.3:1:31.1:1:1:0:60:80:1:0:0.1 +19 15272116 . G T 44 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.2555;SOR=0;LSEQ=GGGGCCCACCGAAAGGCCGC;RSEQ=GGGAGTCCAGCGAGTCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:1,2:118,120:238,3:0.0124:2,2:7.7:1:28.3:1:1:1.96135:60:6:0.0127:0:1 0/0:198:0:0,0:83,115:198,0:0:2,0:23.1:1:29.7:1:1:0:60:65:1:0:0.2 +19 15272125 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17;SOR=Inf;LSEQ=CGAAAGGCCGCGGGGAGTCC;RSEQ=GCGAGTCCACGGGCGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:125,128:253,0:0:2,0:21.3:1:31:1:1:0:59.9:83.333:1:0:0.1 0/1:178:2:1,1:76,100:176,2:0.0112:2,2:33:1:30.5:1:1:1.31:60:4:0.0114:0:1 +19 15272127 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16863;SOR=Inf;LSEQ=AAAGGCCGCGGGGAGTCCAG;RSEQ=GAGTCCACGGGCGACAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:123,126:249,0:0:2,0:21.7:1:30.6:1:1:0:59.9:30.125:1:0:0.1 0/1:174:2:1,1:75,97:172,2:0.0115:2,2:23.5:1:28:1:1:1.29:60:4:0.0116:0:1 +19 15272146 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5665;SOR=3.01751;LSEQ=GCGAGTCCACGGGCGACAGC;RSEQ=TGACCGAGCTGTCAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:1,0:112,118:230,1:0.0043:2,0:10:0:14:0:0.48918:0:60:0:0:0:2 0/1:154:2:1,1:80,72:152,2:0.013:2,2:27.5:1:30.5:1:1:1.11035:60:4:0.0132:0:1.5 +19 15272225 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25523;SOR=0;LSEQ=CCGGGGCCCCTGCGGCCCCA;RSEQ=CCCCGCCTTCCCGGGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:1,2:142,133:275,3:0.0108:2,2:21.3:1:29.7:1:0.61306:2.1297:60:6:0.011:0:1 0/0:230:0:0,0:121,109:230,0:0:2,0:24.9:1:31.2:1:1:0:60:31.857:1:0:0.1 +19 15272336 . C CG 86 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02064;SOR=8.14965;LSEQ=AGGCCCCAGGCCGTGGGGAC;RSEQ=GGGGGGGCTGCGGGGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:1:1,0:304,197:501,1:0.002:2,0:29:0:29:0:1:0:60:2:0.002:0:0 0/1:500:8:5,3:281,209:490,8:0.016:2,2:25.5:1:28.8:1:1:1.24:60:16:0.0164:0.002:0.5 +19 15272943 . C T 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGACTACAGGTGTGCA;RSEQ=CACTACGCCCAGCTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:0,1:1,3:0.75:0,0:37:1:29.7:1:0.25:0:38:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15273047 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAGTAATCCACCCATCTCGA;RSEQ=CTCCCAAAGTGCTGGGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:26.1:1:32.3:1:1:0:55.9:16:0.6667:0:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:16.5:1:31:1:1:0:60:4:0.6667:0:1 +19 15273221 . T C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01756;SOR=1.47399;LSEQ=ACTCTGTTGCCCAGGCTGGA;RSEQ=TGCAATGGCACTGTGCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:466:335:270,65:105,26:131,335:0.7189:2,2:25.5:1:32.4:1:0.89732:1.03:59.7:166.5:0.7192:0:2.9 1/0:396:313:241,72:61,22:83,313:0.7904:2,2:23.3:1:31.2:1:0.56174:1.21:60:77.25:0.7883:0:3 +19 15273231 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=1.63465;LSEQ=CCAGGCTGGATTGCAATGGC;RSEQ=CTGTGCCACTGCTGACACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:542:385:293,92:115,37:152,385:0.7103:2,2:25.5:1:30.1:1:0.91112:1.02:59.7:63.167:0.7111:0:2.8 1/1:476:381:272,109:66,28:94,381:0.8004:2,2:23.6:1:29.4:1:0.80089:1.06:60:53.429:0.8009:0:2.8 +19 15273248 . A C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00511;SOR=1.43248;LSEQ=GGCACTGTGCCACTGCTGAC;RSEQ=CCCAGTGGACCAAGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:700:511:337,174:126,63:189,511:0.73:2,2:24:1:30.6:1:0.92835:1.0326:59.8:41.583:0.7274:0:2.4 1/0:658:523:323,200:78,53:131,523:0.7948:2,2:24.7:1:29.7:1:0.68843:1.10:59.9:57.111:0.7932:0:2.3 +19 15273381 . A G 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=1.53774;LSEQ=AAGGCTGATTTCCCTGGAGG;RSEQ=TGAAGGGGAGAGAGGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:753:530:194,336:86,136:222,530:0.7039:2,2:26.3:1:31.8:1:0.61992:1.09507:60:105:0.7047:0:1.1 1/0:717:563:237,326:63,89:152,563:0.7852:2,2:24.5:1:30.7:1:0.92633:1.03:60:36.533:0.7817:0:1.2 +19 15273401 . G A 54 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10119;SOR=5.85547;LSEQ=ATGAAGGGGAGAGAGGTCAG;RSEQ=ACCAGGCACCTGTCCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:1:1,0:176,393:569,1:0.0018:2,0:3:0:14:0:0.31053:0:60:0:0:0:4 0/1:491:5:4,1:172,314:486,5:0.0102:2,2:15:1:23.4:1:0.05793:7.27:60:4:0.0083:0:2 +19 15273525 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13315;SOR=Inf;LSEQ=GTGTCTGGATCCATGTGTGT;RSEQ=CAAATCTGCAAAATGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:1,66:67,0:0:1,0:24.7:1:32.6:1:1:0:59.4:66:1:0:0.2 0/1:39:2:1,1:0,37:37,2:0.0513:1,2:34.5:1:29.5:1:0.05128:0:60:4:0.0526:0:1.5 +19 15273576 . GTGTGTGTT G 119 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=13.000;MSILEN=2;SSF=0.05882;SOR=0;LSEQ=GAAGCACTTTGTGTCTGTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:0,13:0,11:11,13:0.5:0,1:23.2:1:32.3:1:1:0:53.9:26:0.5417:0.0769:1.3 0/0:6:0:0,0:0,6:6,0:0:0,0:12.8:1:27:1:1:0:59.8:5:1:0:1.5 +19 15273605 . C T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GTGCATGTGCATGACTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:0,9:0,3:3,9:0.6923:0,0:34:1:30.7:1:1:0:48.3:18:0.75:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:21:1:28:1:1:0:59.5:4:1:0:2.5 +19 15273624 . T C 113 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGTGCATGTGCATGACTGT;RSEQ=TATACACAGGGGGTGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:21:1:32.9:1:1:0:50.5:22:1:0:1.8 1/1:1:1:0,1:0,0:0,1:1:0,0:49:0:30:0:1:0:59:2:1:0:4 +19 15273749 . C T 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGAGGTAGTGTCTTGTT;RSEQ=TGTCACCCAGGCTGGAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:24:1:28.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15276007 . C A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56302;SOR=1.52508;LSEQ=TTTTCTAAATCCCTGAGGCA;RSEQ=CCTAAGGACTAGTGGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:13,0:18,0:18,13:0.4194:1,1:15.1:1:31.2:1:1:0:60:26:0.4333:0:1.9 1/0:19:10:10,0:9,0:9,10:0.5263:0,0:32.4:1:29.5:1:1:0:60:20:0.5263:0:1.9 +19 15276055 . C G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66941;SOR=0.81698;LSEQ=ACCCTGCAGGCTTCATGAAG;RSEQ=CTGGTTATGTGTGCGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:58:58,0:15,0:15,58:0.7945:1,1:29:1:31.8:1:1:0:60:57:0.7917:0:1.5 1/0:54:41:41,0:13,0:13,41:0.7593:1,1:20.8:1:30.8:1:1:0:60:82:0.7736:0:1.6 +19 15276143 . C T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.87616;SOR=0.97324;LSEQ=CCTCAGGGCCCAGGTGACAC;RSEQ=AACCCAGCTTAGACTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:445:336:225,111:71,38:109,336:0.7551:2,2:26.5:1:30.7:1:0.7274:1.08:59.9:83:0.7545:0:1.2 1/0:436:327:221,106:65,44:109,327:0.75:2,2:24.3:1:29.5:1:0.1323:1.41:60:108:0.7517:0:1.2 +19 15276386 . AC A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18704;SOR=Inf;LSEQ=GGAACAGAGGAATCAGGAGC;RSEQ=CCCTAAGTCCCATGAAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:37,108:145,0:0:2,0:22.8:1:30.8:1:1:0:60:28:1:0:0.2 0/1:111:2:1,1:16,93:109,2:0.018:2,2:17:1:27.5:1:0.28403:5.67:60:4:0.0185:0.009:0.5 +19 15276523 . C T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12366;SOR=Inf;LSEQ=GAAAAAATGAGTCTGAAAGG;RSEQ=AGAACTGGGGCTCAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:184,55:239,0:0:2,0:24.4:1:32.1:1:1:0:60:46.8:1:0:0.1 0/1:247:4:1,3:186,57:243,4:0.0162:2,2:11:1:24.8:1:0.0455:9.67487:60:8:0.0165:0:1 +19 15276919 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00173;SOR=1.93401;LSEQ=CCATCTGCAGGGACAGGAGT;RSEQ=TGTCAGCAGGAAGGTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:335:252:68,184:27,55:82,252:0.7522:2,2:24.1:1:30.3:1:0.325:1.32722:60:251:0.756:0:2.1 1/1:282:241:80,161:14,26:40,241:0.8546:2,2:23.6:1:29.1:1:0.85721:1.08334:59.9:240:0.8541:0:2.1 +19 15276923 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00608;SOR=1.82188;LSEQ=CTGCAGGGACAGGAGTGTGT;RSEQ=AGCAGGAAGGTAAACACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:237:63,174:22,51:73,237:0.7596:2,2:23.4:1:28.5:1:0.55151:1.1907:60:32.857:0.7591:0:2.2 1/1:257:219:69,150:12,25:37,219:0.8521:2,2:23.5:1:28:1:1:1.04329:59.9:35.5:0.8486:0:2.2 +19 15277006 . T C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00647;SOR=Inf;LSEQ=TAATGGGACACATGGAAAAA;RSEQ=GACAATTAGCAGATCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:33:1,32:0,19:19,33:0.6346:1,1:25.5:1:29.8:1:1:0:59.3:32:0.6275:0:4.1 1/1:14:14:0,14:0,0:0,14:1:0,1:24.6:1:29.1:1:1:0:60:28:1:0:3.9 +19 15277009 . CA TG 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00561;SOR=Inf;LSEQ=TGGGACACATGGAAAAATGA;RSEQ=ATTAGCAGATCCTCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:29:1,28:0,18:18,29:0.5918:1,1:26.3:1:30.9:1:1:0:59.2:28:0.6087:0.0204:3.1 1/1:13:13:0,13:0,0:0,13:1:0,1:24.3:1:29.1:1:1:0:60:26:1:0.1538:2.8 +19 15277010 . A G 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACACATGGAAAAATGAC;RSEQ=ATTAGCAGATCCTCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:0,2:0,18:18,2:0.0417:1,0:22.5:1:29.5:1:1:0:60:4:0.1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15277027 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18294;SOR=3.2352;LSEQ=GACAATTAGCAGATCCTCCT;RSEQ=TCTGCACACCCACACCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:25:1,24:0,13:13,25:0.625:1,1:23.9:1:30.4:1:1:0:59:24:0.6316:0:2.8 1/1:13:11:0,11:1,1:2,11:0.8462:2,0:19.8:1:30:1:0.15385:0:60:22:0.8462:0:2.5 +19 15277317 . AG A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCATTTGAGTGTTTTAAA;RSEQ=GGGGGGGGAAAAAAAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24:1:33:1:1:0:60:4:1:0.5:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15277336 . GC AA 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGGGGGGGAAAAAAAGA;RSEQ=TGCCCCCAGGGACATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:21:1:28.8:1:1:0:60:6:1:0.3333:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15277429 . T A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTACAGGCCATTTGGAGCA;RSEQ=AAGCAAAATGAAGCTAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:22.5:1:29.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15277601 . T C 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAAGCCCTGGGTAGAGAC;RSEQ=GACCTCCCCGCTCCACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:32.3:1:29.3:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15277610 . C T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTAGAGACTGACCTCCC;RSEQ=GCTCCACCAGCAGACCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:29.3:1:30.3:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15277620 . G C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACCTCCCCGCTCCACCA;RSEQ=CAGACCCGACCCCCACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:26:1:31:1:1:0:60:6:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15277765 . T TG 90 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATGCATCCTGAGACTTT;RSEQ=CTGGAGCATTAAGAAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:18.9:1:32.3:1:1:0:60:14:1:0.2857:0 1/1:1:1:1,0:0,0:0,1:1:0,0:18:0:27:0:1:0:60:2:1:0:0 +19 15277938 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.27211;SOR=1.37219;LSEQ=ACCAAGAGTGTTGCTGAATA;RSEQ=ACACACCCTTCACAGAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:156:107:107,0:48,1:49,107:0.6859:1,1:21.6:1:31.4:1:0.3141:0:60:52.5:0.6863:0:1.2 1/0:108:81:79,2:27,0:27,81:0.75:1,1:22.7:1:30.4:1:1:0:60:162:0.75:0:1.1 +19 15278057 . A G 307 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=1.53041;LSEQ=TTGGGAGGGGCACTGTCACT;RSEQ=ACCTGGGCCACGCACATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1016:729:410,319:153,133:286,729:0.7175:2,2:26.1:1:32.3:1:0.44059:1.12:60:144.8:0.7175:0:1.1 1/0:875:696:378,318:93,84:177,696:0.7954:2,2:26.2:1:30.9:1:0.67396:1.07:59.9:76.333:0.797:0:1.2 +19 15278373 . A ATTTG 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0.58737;SOR=0.67086;LSEQ=TACCATCTGTTTGGTGTTTT;RSEQ=TTTGTTTTTGAGACAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:0,24:0,22:22,24:0.5217:1,1:24.8:1:31.6:1:1:0:54.3:48:0.5217:0.1087:0 0/1:19:8:0,8:0,11:11,8:0.4211:0,0:23.4:1:29.7:1:1:0:50.1:16:0.4211:0.0526:0 +19 15280765 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10453;SOR=1.99349;LSEQ=AGGGTTGCAAAGCTGGGACT;RSEQ=TTCTCTGGAGCTAGGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:133:98:96,2:35,0:35,98:0.7368:1,1:21.3:1:32.8:1:1:0:60:97:0.7348:0:1.1 1/1:66:56:54,2:10,0:10,56:0.8485:0,1:24.8:1:32.3:1:1:0:60:112:0.8485:0:1.1 +19 15280794 . C T 26 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25726;SOR=4.0548;LSEQ=AGCTAGGGAGGTGGGGACAG;RSEQ=GGTGCCATCCCCTGATCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:1:1,0:212,10:222,1:0.0045:1,0:17:0:32:0:1:0:60:2:0.0045:0:1 0/1:111:2:1,1:104,5:109,2:0.018:1,2:5.5:1:26.5:1:0.10565:19.08943:60:4:0.0182:0:1.5 +19 15280830 . G A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06017;SOR=Inf;LSEQ=TCACGCCCATCATCCACTGG;RSEQ=GACCCCACCCAGTACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:330,58:388,0:0:2,0:25.2:1:30.8:1:1:0:60:31.333:1:0:0.3 0/1:251:3:1,2:203,45:248,3:0.012:2,2:25:1:25:1:0.09091:8.90884:60:2:0.0084:0:3.3 +19 15281359 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08779;SOR=Inf;LSEQ=GGGTTCTGGAGGCTCCAGCG;RSEQ=CTCCCCTAAGAGCAGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:137,178:315,0:0:2,0:24.4:1:31.9:1:1:0:60:44:1:0:0.4 0/1:253:3:1,2:105,145:250,3:0.0119:2,2:25.3:1:24:1:1:1.44624:60:2:0.0082:0:2.7 +19 15281386 . C A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=3.36866;LSEQ=TAAGAGCAGGAAGCAGAGGG;RSEQ=GGGGCTTCAGCCGAGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:103:55,48:94,96:190,103:0.3515:2,2:24.1:1:31.2:1:0.54247:1.17:60:102:0.3554:0:1.1 1/0:201:130:70,60:36,34:70,130:0.6468:2,2:22.7:1:29.3:1:0.76808:1.10:60:31.5:0.6495:0:1.2 +19 15281459 . C G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.35106;SOR=1.35652;LSEQ=CCAGCTCCGCCCCCGCCACC;RSEQ=CCTCCCCAAGGCAGGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:20:14,6:318,200:518,20:0.0372:2,2:23.1:1:29:1:0.49139:1.47:60:9:0.0342:0:1.2 0/1:462:23:12,11:259,179:438,23:0.0498:2,2:28.6:1:28.8:1:0.52169:1.3255:60:10.5:0.0465:0:1.2 +19 15282138 . T C 29 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCGTGAGCCGCCACTGTGCC;RSEQ=GGCCTGTTTTTTTTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:49:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:29:1:1:0:43:4:1:0:1.5 +19 15284546 . AAAAAAAGAAAAGAAGAAGGAGAAGGAGAAGGAGAAGG A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCGTCTCAAAAAAAAAA;RSEQ=AGAAGGAGAAGGAGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16.5:1:31.8:1:1:0:44:4:1:1:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15284589 . G A 32 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=6;SSF=1;SOR=0;LSEQ=AGGAGAAGGAGAAGGAGAAG;RSEQ=AGAAGGAGAAGAAGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:6:0:32:0:1:0:44:4:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15284595 . G A 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=6;SSF=1;SOR=0;LSEQ=AGGAGAAGGAGAAGGAGAAG;RSEQ=AGAAGAAGAAGAAGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:10:1:32.3:1:1:0:49.3:6:0.75:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15284611 . A C 76 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GAAGGAGAAGAAGAAGAAGA;RSEQ=GAAGAAAAAAACCCTACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:18.7:1:29.7:1:1:0:54.7:5:0.7143:0:2.3 1/1:1:1:1,0:0,0:0,1:1:0,0:9:0:34:0:1:0:60:2:1:0:1 +19 15284855 . G T 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20671;SOR=4.22544;LSEQ=TCCTCTCCCCAGCCACCACG;RSEQ=CTTTTCCAGGTGGGGTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:1:0,1:281,137:418,1:0.0024:2,0:1:0:27:0:0.32936:0:60:2:0.0025:0:1 0/1:400:4:2,2:247,148:395,4:0.01:2,2:21.5:1:23.3:1:0.63343:1.66661:60:3:0.0077:0:1.3 +19 15285052 . T C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=1.89809;LSEQ=CTGGAACGCAGTAGCTCCTC;RSEQ=GGCGGCAGCAGCACTGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:475:326:160,166:80,69:149,326:0.6863:2,2:26.9:1:30.7:1:0.37423:1.20243:59.8:64.2:0.6859:0:1.2 1/1:397:320:158,162:36,41:77,320:0.806:2,2:25.7:1:29.7:1:0.70476:1.11:59.8:105.667:0.8066:0:1.1 +19 15285272 . T C 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08389;SOR=1.55912;LSEQ=GTCAGAGGAGACAATCCCCT;RSEQ=CCATGCATTCACACCGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:208:154:27,127:6,47:53,154:0.7404:2,2:20.8:1:31.2:1:0.38511:1.66:60:37.5:0.75:0:1.1 1/1:169:138:33,105:6,25:31,138:0.8166:2,2:18.2:1:29.9:1:0.81365:1.31:60:68:0.8193:0:1.1 +19 15285382 . ATTTT A 88 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=18.000;MSILEN=1;SSF=0.69599;SOR=1.50394;LSEQ=ATCTTGCCATTCACTGGATA;RSEQ=TTTTTTTTTTTTTTGAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:0,7:0,13:13,7:0.3043:1,0:28.7:1:31.6:1:1:0:58.1:14:0.3043:0:0.3 0/1:10:4:0,4:0,6:6,4:0.4:0,0:33.8:1:29.8:1:1:0:56.8:8:0.4:0:0 +19 15288062 . G GGA 100 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCAAGACTCCATCTCGG;RSEQ=AAAAAAAAAAAAAAGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:9,0:8,0:8,9:0.5:0,0:22.2:1:31.6:1:1:0:58.8:18:0.5:0.1667:1.2 0/0:1:0:0,0:1,0:1,0:0:0,0:7:0:32:0:1:0:60:2:1:0:5 +19 15288072 . A T 101 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=0.13364;SOR=0;LSEQ=TCCATCTCGGGAAAAAAAAA;RSEQ=AAAAGTAATTATTGGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:10,0:12,0:12,10:0.4167:0,0:23.9:1:30.7:1:1:0:58.9:9:0.3913:0:1.2 0/0:5:0:0,0:5,0:5,0:0:0,0:7.8:1:29.8:1:1:0:60:10:1:0:1 +19 15288518 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08458;SOR=Inf;LSEQ=CCGTCCCAGCCGCAGCCTGG;RSEQ=CTGTTGCACTCGCGGTCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:64,175:239,0:0:2,0:23.3:1:32.5:1:1:0:59.9:78.667:1:0:0.3 0/1:188:3:2,1:56,129:185,3:0.016:2,2:19:1:26:1:0.22549:4.57:60:6:0.0161:0:1 +19 15288572 . G A 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.24476;SOR=0;LSEQ=CGCTTGGCCTGGCAGGCGGC;RSEQ=CGCGGGCACCGCGGCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:14,19:33,3:0.0833:2,0:11:1:23.7:1:0.09524:0:59.3:2:0.0571:0:1.3 0/0:30:0:0,0:14,16:30,0:0:2,0:26.2:1:31:1:1:0:60:60:1:0:0.5 +19 15288655 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20653;SOR=Inf;LSEQ=GGTCCAGCCCTGCGCGCAAG;RSEQ=GCAGCGGAAGAAGGGCGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:27,0:0:2,0:19:1:30.9:1:1:0:60:26:1:0:0.3 0/1:23:2:1,1:10,10:20,2:0.087:2,2:15:0:31:0:1:1:60:4:0.087:0:1.5 +19 15288677 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10213;SOR=Inf;LSEQ=CAGCGGAAGAAGGGCGCGAG;RSEQ=GGCGCGGGGCGGCAGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:24,17:41,0:0:2,0:23.7:1:31.4:1:1:0:59.3:19.5:1:0:0.4 0/1:37:3:2,1:20,14:34,3:0.0811:2,2:12:1:29.3:1:1:1.39:60:6:0.0811:0:1.3 +19 15288689 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49669;SOR=0;LSEQ=GGCGCGAGCGGCGCGGGGCG;RSEQ=CAGGAGCCCCCGTGGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:38,23:61,2:0.0317:2,2:30.5:1:32:0:1:1.63846:60:4:0.0323:0:1.5 0/0:58:0:0,0:37,20:57,0:0:2,0:15.9:1:31.2:1:1:0:60:114:0.9828:0:0.4 +19 15288720 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24567;SOR=0;LSEQ=CGTGGAGACAGGGGGCGGCC;RSEQ=CGCAGCTGGCGTTGCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:74,66:140,2:0.014:2,2:22.5:1:29:1:1:1.12031:60:4:0.0143:0:1 0/0:145:0:0,0:74,70:144,0:0:2,0:21.7:1:30.2:1:1:0:59.5:143:0.9931:0:0.4 +19 15288722 . G T 50 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37198;SOR=3.82932;LSEQ=TGGAGACAGGGGGCGGCCGC;RSEQ=CAGCTGGCGTTGCTGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:0,1:79,69:148,1:0.0067:2,0:1:0:29:0:0.4698:0:60:2:0.0068:0:1 0/1:158:4:1,3:80,74:154,4:0.0253:2,2:7.3:1:25.3:1:0.3578:3.22105:60:8:0.0258:0:1.3 +19 15288735 . C T 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62433;SOR=2.78528;LSEQ=CGGCCGCGCAGCTGGCGTTG;RSEQ=TGGCCCCCGGCGGCGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:103,85:188,1:0.0053:2,0:1:0:26:0:0.45503:0:60:2:0.0054:0:1 0/1:205:3:1,2:110,91:201,3:0.0146:2,2:17.7:1:23:1:0.59277:2.40737:60:2:0.0099:0:1.7 +19 15288758 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24994;SOR=Inf;LSEQ=GCCCCCGGCGGCGACCCCGG;RSEQ=AAGCTGCGGCAGGAGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:149,116:265,0:0:2,0:23.6:1:31.6:1:1:0:60:65.25:0.9962:0:0.3 0/1:289:3:1,2:160,126:286,3:0.0104:2,2:25.7:1:26.3:1:0.5859:2.53164:60:6:0.0106:0:1.3 +19 15288787 . C A 35 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.35188;SOR=0.30178;LSEQ=GCAGGAGGGTCCCGACAACC;RSEQ=TGGGGGGCAGGCGCAGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:3,0:154,137:291,3:0.0102:2,0:13.3:1:22.7:1:0.25092:0:60:2:0.007:0:1.7 0/0:323:1:1,0:170,152:322,1:0.0031:2,0:1:0:26:0:1:0:60:2:0.0031:0:1 +19 15288788 . TG T 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.26379;SOR=0.35446;LSEQ=CAGGAGGGTCCCGACAACCC;RSEQ=GGGGGCAGGCGCAGCGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:5:3,2:150,133:283,5:0.0173:2,2:37.6:1:30.9:1:1:1.33:58:10:0.0177:0.0035:0 0/0:323:2:1,1:167,153:320,2:0.0062:2,2:43.5:1:30:1:1:1.0912:60:4:0.0063:0:0 +19 15288928 . G A 103 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.00297;SOR=12.56922;LSEQ=GTCGGGTTTGGGGAGGGAGG;RSEQ=ATAAAAATGAGGGTGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:1,0:75,126:201,1:0.005:2,0:1:0:25:0:0.37624:0:60:2:0.005:0:1 0/1:203:12:6,6:79,112:191,12:0.0591:2,2:23.6:1:29:1:0.56257:1.42:60:24:0.06:0:1.2 +19 15289366 . T G 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51648;SOR=0;LSEQ=CCACTACGCCCGGCTAATTT;RSEQ=TATATTTTTAGTAGAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:18.8:1:31:1:1:0:40.3:8:0.3333:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:23:1:30.7:1:1:0:35:6:1:0:0 +19 15289613 . A T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.38671;LSEQ=ACGCCCCTACTCCTCCTCCA;RSEQ=AGGCCGCCACCCACACCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:983:392:214,178:325,263:588,392:0.3988:2,2:26.9:1:29.5:1:0.84436:1.02784:60:55:0.4048:0:1.2 1/0:863:529:292,237:185,146:331,529:0.613:2,2:25.9:1:28.3:1:0.88789:1.02843:60:30.118:0.6103:0:1.2 +19 15290125 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.97087;LSEQ=AACGAGGGGTGGTCAAGAGG;RSEQ=AATGAAGACAGCCTCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:244:128,116:184,140:324,244:0.4288:2,2:22.8:1:30.7:1:0.30824:1.1907:60:47.8:0.4275:0:1.1 1/0:449:268:143,125:94,87:181,268:0.5969:2,2:21.2:1:29.2:1:0.77342:1.06:60:267:0.6:0:1.1 +19 15290236 . G T 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTCAATGCATGAACCCCC;RSEQ=TGCTGGCAGGGCTGGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1194:0:0,0:612,581:1193,0:0:2,0:26.2:1:31.1:1:1:0:60:73.563:0.9992:0:0.2 0/1:1113:44:22,22:549,517:1066,44:0.0395:2,2:25.8:1:30.1:1:0.8786:1.06187:59.9:88:0.04:0:1.2 +19 15290380 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12227;SOR=Inf;LSEQ=CTGGACATACCCATGAAGAC;RSEQ=CAAAGAACCCCAGCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:16,236:252,0:0:2,0:23.3:1:32.1:1:1:0:59.9:41:1:0:0.4 0/1:136:2:1,1:11,123:134,2:0.0147:2,2:11.5:1:29:1:0.16928:10.75:60:4:0.0148:0:1.5 +19 15290412 . G A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44164;SOR=0.772;LSEQ=AGCACAAAAGGACACACACA;RSEQ=ATGTTCAGCGCACTACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:93:1,92:3,40:43,93:0.6788:2,1:23.9:1:31.2:1:0.09323:6.79325:58.2:30:0.687:0:1.2 1/0:71:44:1,43:2,25:27,44:0.6197:2,1:21.7:1:30.7:1:0.55311:3.37829:57.9:43:0.6143:0:1.1 +19 15290491 . G A 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02019;SOR=0;LSEQ=TCACCTGAGATCAGGAGTTC;RSEQ=AGACCAGCCTGGCCAACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:2,8:2,6:8,10:0.5556:2,2:19.9:1:29.8:1:1:1.31198:30.1:9:0.5294:0:2.1 0/0:7:0:0,0:0,7:7,0:0:0,0:18.4:1:30.1:1:1:0:35.7:14:1:0:1.1 +19 15290558 . T G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAAAAATTAGCTGGGCGTGG;RSEQ=GGTGGGTGCCTGTACTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:8.5:1:33:0:1:1.4491:52.5:4:0.1667:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:16:0:31:0:1:0:26:2:1:0:0 +19 15290648 . C T 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.28083;SOR=0;LSEQ=AGGTTGCAGTGAGCTGAGAT;RSEQ=GCGCCACTGCACTCGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:7,1:14,1:15,8:0.3478:1,2:30.1:1:32.3:1:1:1.93655:58.1:16:0.3478:0:1 0/0:5:0:0,0:4,1:5,0:0:2,0:11.6:1:29.2:1:1:0:60:10:1:0:0 +19 15291428 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16722;SOR=Inf;LSEQ=CCCCATTCGGCTCACACTAG;RSEQ=AGGAGGTACGTGCATGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:183,62:245,0:0:2,0:23.2:1:32.3:1:1:0:60:80.667:1:0:0.1 0/1:170:2:1,1:126,42:168,2:0.0118:2,2:8:0:30:0:0.44302:2.97664:60:4:0.012:0:1.5 +19 15291576 . C G 258 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGGGGACAAAGGCAATAGG;RSEQ=CCCAGTCTGGACGCAGCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:284:139,145:286,282:568,284:0.3326:2,2:25.7:1:31.7:1:0.71668:1.05786:60:46.333:0.3337:0:1.1 0/0:808:0:0,0:416,388:804,0:0:2,0:23.8:1:30.7:1:1:0:59.9:66:0.9975:0:0.2 +19 15291675 . TG T 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.03664;SOR=0;LSEQ=TCAGAGTCAGTACTGTGGGG;RSEQ=GGGGGTAGTCTGGGAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:6:2,4:159,253:412,6:0.0143:2,2:36.8:1:32.5:1:1:1.25623:55.8:12:0.0146:0:1.3 0/0:334:0:0,0:116,215:331,0:0:2,0:22.4:1:30.3:1:1:0:60:40.375:0.9908:0:0.2 +19 15291699 . T C 210 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GGGTAGTCTGGGAGAAACTG;RSEQ=GCCCCGACTTGGCTTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:108:55,53:108,152:260,108:0.2935:2,2:18.7:1:31.1:1:0.10749:1.46:60:107:0.2972:0:1.1 0/0:250:0:0,0:106,143:249,0:0:2,0:22.3:1:29.5:1:1:0:60:248:1:0:0.1 +19 15292055 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54897;SOR=0;LSEQ=TCCTGAGTCCCGCTGTTAGC;RSEQ=CTGGGGACGTCCCACTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:0,2:4,105:109,2:0.018:1,0:16.5:1:30:1:1:0:60:4:0.0187:0:1 0/0:57:0:0,0:4,52:56,0:0:2,0:23.3:1:31.7:1:1:0:59.9:55:0.9821:0:0.4 +19 15292088 . G C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39839;SOR=1.83873;LSEQ=CACTCCCTGACCCTTATCTC;RSEQ=GCAAGAAGCTGCAGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:39:2,37:1,16:17,39:0.6964:1,2:27.9:1:30.6:1:1:1.15317:60:38:0.7037:0:1.2 1/1:21:17:0,17:0,4:4,17:0.8095:0,1:30.7:1:30.5:1:1:0:59.6:34:0.8095:0:1.6 +19 15292271 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00121;SOR=4.12611;LSEQ=CCCCATCAGTCATCAGAGTC;RSEQ=GCAGTGGGTACCAAGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:32:31,1:40,3:43,32:0.4267:2,1:27:1:31.8:1:0.6315:2.30:60:15:0.4167:0:1.4 1/0:37:28:27,1:8,0:8,28:0.7568:0,1:27.7:1:31.2:1:1:0:60:56:0.7568:0:1.1 +19 15292366 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.63041;LSEQ=CAAGCCAGAGTCCCTGCTCT;RSEQ=CAAGCAGAGGCCCCGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:148:106,42:154,60:214,148:0.4088:2,2:27.1:1:30.5:1:1:1.01694:60:36:0.4045:0:1.5 1/1:277:233:149,84:30,14:44,233:0.8412:2,2:25.4:1:29.3:1:0.73128:1.20724:60:76.667:0.8425:0:1.6 +19 15292437 . T C 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=5.96079;LSEQ=CAGTGGAAGCCTCCGTAGCC;RSEQ=GGCGGGCAGGTGCAGGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:719:306:168,138:220,191:411,306:0.4256:2,2:23.6:1:30:1:0.7619:1.06:60:29.6:0.4235:0:1.3 1/1:564:460:259,201:57,45:102,460:0.8156:2,2:23.9:1:29.7:1:1:1.02:60:64.714:0.8177:0:1.4 +19 15292440 . C T 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36452;SOR=0.47339;LSEQ=TGGAAGCCTCCGTAGCCTGG;RSEQ=GGGCAGGTGCAGGTGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:8:1,7:385,342:727,8:0.0109:2,2:13.5:1:26.3:1:0.03042:7.86246:60:7:0.0099:0:1.4 0/0:580:3:0,3:320,256:576,3:0.0052:2,0:4.3:1:28.7:1:0.08893:0:60:6:0.0052:0:2.3 +19 15292632 . G A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04933;SOR=Inf;LSEQ=TCTGCGGACAGGAGGAAGGC;RSEQ=GTCTGGTCACCTACCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:73,217:290,0:0:2,0:23.6:1:30.6:1:1:0:60:57:1:0:0.2 0/1:260:4:2,2:72,184:256,4:0.0154:2,2:12.5:1:26.3:1:0.32078:2.54:60:3:0.0118:0:1.5 +19 15292853 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAAAGGTCCCTTTAAGCT;RSEQ=CCAAGCAAACGCTGCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:0,7:7,2:0.2222:0,2:15:0:31:1:0.22222:0:60:4:0.2222:0:1.5 0/0:3:0:0,0:1,2:3,0:0:2,0:13.7:1:32.7:1:1:0:60:6:1:0:0 +19 15294991 . C T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15749;SOR=1.92607;LSEQ=CAGTTTCCATATAAATAAAA;RSEQ=GGGAAAAGTAAGATAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:79:78,1:24,1:25,79:0.7524:1,1:20.8:1:31.3:1:0.42476:3.20:60:25.333:0.7525:0:1.1 1/1:55:47:47,0:8,0:8,47:0.8545:0,1:19:1:30.7:1:1:0:60:46:0.8679:0:1.1 +19 15295027 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=ACTGTGAAGATGAAATGACA;RSEQ=CACAGTGCCAGGCACACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:207,26:233,0:0:2,0:25.7:1:33.1:1:1:0:60:37.833:1:0:0.4 0/1:189:2:1,1:156,31:187,2:0.0106:2,2:21:1:28:1:0.31071:4.96899:60:4:0.0106:0:2 +19 15295082 . C A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20623;SOR=0.68644;LSEQ=TGTGTTCCCCAGAGCAGCAC;RSEQ=CCCAAGAGCTCCCCTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:33:24,9:376,171:547,33:0.0568:2,2:24.4:1:30.1:1:0.70234:1.21:60:66:0.0575:0:1.9 0/1:504:20:10,10:308,176:484,20:0.0397:2,2:29.1:1:29.4:1:0.24101:1.74787:60:40:0.0404:0:1.8 +19 15295134 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.51896;LSEQ=CAGTCATTGATGTCCTGATC;RSEQ=CAGGAAGGGCCAGTGTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:897:344:186,158:288,265:553,344:0.3835:2,2:25.6:1:30.2:1:0.58248:1.08:60:113.667:0.3836:0:1.3 1/0:814:497:264,233:160,155:315,497:0.6106:2,2:24.8:1:29.2:1:0.56417:1.10:59.9:123.25:0.6132:0:1.2 +19 15295902 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13896;SOR=Inf;LSEQ=ATCCCATCTCCCCCCACCTC;RSEQ=CCCAACCCCAGGGTCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:146,187:333,0:0:2,0:23.4:1:30.8:1:1:0:59.8:40.625:0.9969:0:0.1 0/1:199:2:1,1:89,108:197,2:0.0101:2,2:15:1:27.5:1:1:1.21:60:4:0.0103:0:1 +19 15296513 . C T 206 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=0;LSEQ=GGGGAGTACACAAGCAATCT;RSEQ=ATCTCAGAACAAAGTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:153:48,105:101,245:346,153:0.306:2,2:24.8:1:28.5:1:0.67151:1.11:60:37.25:0.3028:0:1.1 0/0:434:0:0,0:135,298:433,0:0:2,0:23.3:1:30.7:1:1:0:60:85.6:1:0:0.1 +19 15296917 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTGCGTGTTTATCTAC;RSEQ=TATTGACTAATCTGGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:36:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15297576 . C T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06125;SOR=0.52462;LSEQ=CACAGACTCAGGGCAAAGCA;RSEQ=GGACAACCTCGTTGGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:44:44,0:88,0:88,44:0.3333:1,1:28.4:1:32.2:1:1:0:60:43:0.3282:0:1 0/1:82:17:16,1:64,1:65,17:0.2073:1,1:24.7:1:30.8:1:0.37368:3.91077:60:34:0.2073:0:1.1 +19 15298031 . C T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TGGCTCTCGCAGCGTGTGCC;RSEQ=GTGTAGCCAGGAGCACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:684:0:0,0:329,355:684,0:0:2,0:25.1:1:30.2:1:1:0:59.8:56:1:0:0.1 0/1:588:15:8,7:280,293:573,15:0.0255:2,2:16.3:1:29.6:1:0.79769:1.20:60:30:0.0259:0:1.2 +19 15298159 . C A 54 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05272;SOR=Inf;LSEQ=GCCCTCAAAGCCTGTGGGGC;RSEQ=AAGAGGGTCAGGCTCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:150,269:419,0:0:2,0:25.3:1:31.8:1:1:0:60:68.833:1:0:0.1 0/1:387:4:3,1:151,232:383,4:0.0103:2,2:5.3:1:27:1:0.30567:4.59:60:8:0.0105:0:1 +19 15298171 . G A 60 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22626;SOR=0.23399;LSEQ=TGTGGGGCCAAGAGGGTCAG;RSEQ=CTCCGCCCACTTGCCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:353:5:3,2:111,237:348,5:0.0142:2,2:21.4:1:26.2:1:0.33362:3.19:60:4:0.0114:0:1.4 0/0:299:1:1,0:101,197:298,1:0.0033:2,0:1:0:22:0:0.34114:0:60:2:0.0034:0:1 +19 15298270 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00264;SOR=4.06977;LSEQ=CATCAAGCTGTCAGGAGGCG;RSEQ=GCTCAATACAGGCCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:22:1,21:1,34:35,22:0.386:1,1:22.3:1:31.8:1:1:1.60:60:44:0.386:0:1.1 1/0:36:26:1,25:0,10:10,26:0.7222:0,1:25.5:1:31:1:1:0:59.6:52:0.7222:0:1.6 +19 15298604 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.56126;SOR=3.23409;LSEQ=TGCCTTGCTACAACCCCGCC;RSEQ=CCAAGCTCTCCCCAAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:218,35:253,1:0.0039:2,0:24:0:17:0:1:0:60:0:0:0:5 0/1:158:2:1,1:130,26:156,2:0.0127:2,2:11.5:1:27.5:1:0.31347:4.92548:60:4:0.0128:0:1.5 +19 15298632 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32898;SOR=3.74809;LSEQ=CTCCCCAAGTCTGTTATTGG;RSEQ=CCTGTCGCCCACAAGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:0,1:268,94:362,1:0.0027:2,0:1:0:28:0:0.26171:0:60:2:0.0028:0:1 0/1:293:3:1,2:203,87:290,3:0.0102:2,2:14:1:28.3:1:0.21989:4.63901:60:6:0.0106:0:1 +19 15298952 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1433;SOR=Inf;LSEQ=ACATATGGTTTCTATTGTAA;RSEQ=TTATCCGCTAACGTGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:187,65:252,0:0:2,0:24.3:1:33:1:1:0:59.8:62:1:0:0.2 0/1:154:2:1,1:129,23:152,2:0.013:2,2:18:0:31.5:1:0.28826:5.51192:60:4:0.0135:0:1 +19 15299048 . G A 241 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCTCCTGAGGTCCTCACCC;RSEQ=AGGGGCAGGTGCAGCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:254:151,103:320,205:525,254:0.3261:2,2:23.9:1:30.2:1:0.69652:1.06468:59.9:62.5:0.3255:0:1.1 0/0:718:0:0,0:403,315:718,0:0:2,0:24.4:1:29.5:1:1:0:60:78.778:1:0:0.2 +19 15299051 . G A 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTGAGGTCCTCACCCGAG;RSEQ=GGCAGGTGCAGCTGAAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:804:0:0,0:486,317:803,0:0:2,0:24.1:1:31.1:1:1:0:59.9:65.917:0.9987:0:0.4 0/1:739:19:12,7:398,320:718,19:0.0257:2,2:22.1:1:28.2:1:0.64155:1.38:60:38:0.0259:0:1.2 +19 15299217 . G A 41 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0436;SOR=Inf;LSEQ=CCCTATGGTGTGAACGGGGT;RSEQ=CAAGGAAGGAGGTACTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:73,277:350,0:0:2,0:24.6:1:32.4:1:1:0:60:115.667:1:0:0.1 0/1:296:4:3,1:64,228:292,4:0.0135:2,2:8.5:1:20.5:1:0.03745:10.57:60:3:0.0105:0:2.3 +19 15299648 . T C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5756;SOR=0.72566;LSEQ=AGAATCACACAGTATTCCCT;RSEQ=CTGGTCCTGACCCCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:36:35,1:13,1:14,36:0.72:1,1:25.8:1:32.3:1:0.48571:2.63:60:72:0.7347:0:1.1 1/0:20:13:13,0:7,0:7,13:0.65:0,1:24.5:1:31.4:1:1:0:60:26:0.65:0:1 +19 15300069 . T C 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.05854;LSEQ=CCCAGCCCATTCACAGACGA;RSEQ=GGAGCTCCCCTCACCGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:599:412:235,177:105,82:187,412:0.6878:2,2:23.9:1:30.7:1:0.85901:1.04:59.9:57.857:0.6888:0:1.1 1/1:432:354:201,153:45,33:78,354:0.8194:2,2:23.9:1:30.3:1:0.90023:1.03791:60:117:0.8201:0:1.2 +19 15300136 . A G 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCCACCCGTGAAGCCGGG;RSEQ=GGACAGGTGCAAATGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:863:0:0,0:450,412:862,0:0:2,0:25.7:1:30.7:1:1:0:60:42.1:1:0:0.3 0/1:814:44:23,21:431,338:769,44:0.0541:2,2:23.8:1:29.8:1:0.64238:1.16404:60:43:0.0544:0:1.4 +19 15301796 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCTTGGCCTCCCAAAG;RSEQ=GCTGGGATTACAGGCATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:42.5:1:31.5:1:1:0:50.5:4:1:0:1.5 +19 15301857 . A T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCTTTTTTTTATTTTTT;RSEQ=AATTTGAGAAGGAGTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:23.5:1:31.5:1:1:0:38.5:4:0.5:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 15302146 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20844;SOR=Inf;LSEQ=GAGCCACTGTGCCCAGCCTA;RSEQ=CATAATCTTTCTAACACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:154,18:172,0:0:2,0:21.6:1:33:1:1:0:59.9:56.333:1:0:0.1 0/1:145:2:1,1:123,20:143,2:0.0138:2,2:19.5:1:28:1:0.26954:6.02616:60:4:0.014:0:1 +19 15302370 . C T 91 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03053;SOR=3.90693;LSEQ=TGTCCAGCCATTGACACACA;RSEQ=GCAGCTGTGGCCACCCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:935:3:0,3:462,470:932,3:0.0032:2,0:1:0:25.3:1:0.2493:0:60:6:0.0032:0:1 0/1:885:11:2,9:433,441:874,11:0.0124:2,2:11.8:1:26.5:1:0.06421:4.41184:60:10:0.0114:0:1.1 +19 15302733 . G A 63 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48357;SOR=1.9215;LSEQ=GGCTGGCCTGCTGTCCCCAC;RSEQ=CCCACCCCTCTGACTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:3:3,0:188,330:518,3:0.0058:2,0:1:0:27:1:0.04878:0:60:6:0.0059:0:1 0/1:454:5:4,1:150,299:449,5:0.011:2,2:5:1:27.2:1:0.0473:7.94:60:10:0.0111:0:1.2 +19 15302844 . T C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=1.76078;LSEQ=CCGTTACGGCATGGTGAGGG;RSEQ=GCACAGGGCACCGCGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:473:324:170,154:73,76:149,324:0.685:2,2:25.6:1:31.3:1:0.48999:1.15:59.9:648:0.6864:0:1.1 1/0:401:318:166,152:41,39:80,318:0.793:2,2:26.8:1:30:1:0.90089:1.04:60:38.75:0.7969:0:1.2 +19 15303225 . G A 218 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=104.12926;LSEQ=CACCGGCATGAGAATCGGGC;RSEQ=GTGCCAGCCACCACTGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:769:2:2,0:412,355:767,2:0.0026:2,0:1:0:26.5:1:0.5023:0:60:4:0.0026:0:1 0/1:748:160:87,73:300,288:588,160:0.2139:2,2:26.4:1:29.8:1:0.47603:1.14:60:320:0.2177:0:1.2 +19 15303359 . G A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04047;SOR=Inf;LSEQ=AGAGATGGCTTGGTTGGGCA;RSEQ=CACAGGGCAGGATGGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:113,286:399,0:0:2,0:25.8:1:32.2:1:1:0:60:65.5:1:0:0.2 0/1:326:4:2,2:113,209:322,4:0.0123:2,2:23.3:1:24:1:0.6158:1.85:60:3:0.0093:0:2.5 +19 15308068 . T C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28677;SOR=Inf;LSEQ=TGCAGACCATGACACTGAGA;RSEQ=GTAAAGAGTTTAATTCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:17:17,0:5,0:5,17:0.7727:0,1:25.6:1:32.7:1:1:0:58.2:34:0.7727:0:1.2 1/1:8:8:7,1:0,0:0,8:1:0,2:26.5:1:32:1:1:0:60:16:1:0:1.3 +19 15308096 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02631;SOR=Inf;LSEQ=GTTTAATTCCTAGCCGGTCA;RSEQ=CAACATGATGTGGGACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:33,0:0:1,0:28:1:33.5:1:1:0:60:66:1:0:0.5 0/1:15:3:2,1:11,1:12,3:0.2:2,2:25:1:29.7:1:0.37143:4.69047:60:6:0.2:0:1.3 +19 15308179 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51802;SOR=0;LSEQ=TGGGGAAACACGAGAGGTTG;RSEQ=CCAAGCCACACACATGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:119,1:120,2:0.0164:1,0:23:1:29.5:1:1:0:60:4:0.0171:0:1 0/0:81:0:0,0:79,2:81,0:0:1,0:24.1:1:32.3:1:1:0:60:80:1:0:0.1 +19 15308287 . G C 232 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCACACACAGGGCCCACT;RSEQ=GTGGCTCTGAGCCAGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:753:230:134,96:297,222:519,230:0.3054:2,2:26.1:1:29.6:1:0.8104:1.04:59.8:16.692:0.3113:0:1.5 0/0:694:0:0,0:391,303:694,0:0:2,0:24.4:1:29.2:1:1:0:59.8:10.966:1:0:0.5 +19 15308541 . CCA C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCCCCCATCCACAGTTC;RSEQ=CGCCCCCCCCCCCCCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:0,2:1,65:66,2:0.0294:1,0:46:1:30:1:1:0:50:4:0.0323:0:6.5 0/0:28:0:0,0:0,27:27,0:0:1,0:20.4:1:31:1:1:0:59.5:54:1:0:0.8 +19 15308545 . G A 119 q25;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=1e-04;SOR=0.0489;LSEQ=CCCCCATCCACAGTTCCCAC;RSEQ=CCCCCCCCCCCCCCGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:28:0,28:1,21:22,28:0.4667:1,1:19.3:1:24.9:1:0.44:0:59.2:2.5:0.5405:0:1.9 0/1:25:1:0,1:0,23:23,1:0.04:1,0:42:0:26:0:1:0:60:2:0.0455:0:1 +19 15308555 . C CCA 118 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=0.25385;SOR=2.09598;LSEQ=CAGTTCCCACGCCCCCCCCC;RSEQ=CCCCGCCCCAGCCCCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:14:0,14:1,25:26,14:0.2979:1,1:27.8:1:31.2:1:1:0:58.4:13:0.2826:0.0426:2.2 0/1:19:9:0,9:0,3:3,9:0.4737:0,0:16.8:1:30.9:1:1:0:58.9:18:0.4737:0.2105:0.8 +19 15310866 . C CG 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAGGAGAGGAGGAGGGG;RSEQ=GGGGGCCCCTGGCCGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:32:1:1:0:60:4:1:0:0.5 +19 15311535 . C T 28 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02554;LSEQ=GAACCCCCGCCAGCCCCGGC;RSEQ=TTGGGGGTTCTTGCACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:0,2:73,47:120,2:0.0164:2,0:1.5:1:27.5:1:0.15933:0:60:4:0.0168:0:1 0/1:119:2:1,1:76,40:116,2:0.0168:2,2:14:0:28:1:1:1.88906:60:4:0.0171:0:1 +19 15311552 . TC T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50055;SOR=0;LSEQ=GGCCTTGGGGGTTCTTGCAC;RSEQ=CCCCTCTGCCGCCCTCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:88,83:171,2:0.0116:2,2:20:1:30:1:1:1.05991:60:4:0.0116:0:0 0/0:152:0:0,0:82,70:152,0:0:2,0:23.5:1:29.9:1:1:0:60:151:1:0:0.2 +19 15311566 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25426;SOR=0;LSEQ=TTGCACTCCCCCTCTGCCGC;RSEQ=CTCGTCCCATCCGCCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:1,2:99,107:206,3:0.0143:2,2:25:1:29:1:1:1.84524:60:6:0.0143:0:1 0/0:175:0:0,0:82,93:175,0:0:2,0:25.7:1:29.6:1:1:0:60:86.5:1:0:0.2 +19 15311594 . C G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19058;SOR=Inf;LSEQ=CATCCGCCAGGTCCCGGCCC;RSEQ=TCACCTGCAGCCCCCGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:95,147:242,0:0:2,0:26.2:1:32.1:1:1:0:59.9:47.4:1:0:0.3 0/1:188:2:1,1:70,114:184,2:0.0106:2,2:46:0:31:1:1:1.62:60:4:0.0108:0:1 +19 15311604 . GC G 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.06948;SOR=0;LSEQ=GTCCCGGCCCCTCACCTGCA;RSEQ=CCCCGGCCCCGCTAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:5:2,3:86,139:225,5:0.0217:2,2:30:1:33.2:1:1:1.08:60:10:0.0221:0:0 0/0:182:0:0,0:66,116:182,0:0:2,0:26.8:1:30.6:1:1:0:60:90:1:0:0.2 +19 15311616 . G A 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33568;SOR=3.59549;LSEQ=CACCTGCAGCCCCCGGCCCC;RSEQ=CTAGCAGCAGCAGCAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:1,0:69,126:195,1:0.0051:2,0:1:0:26:0:0.35714:0:60:2:0.0052:0:1 0/1:166:3:1,2:56,107:163,3:0.0181:2,2:31.3:1:29:1:1:1.04645:60:6:0.0183:0:1 +19 15311618 . TAGC T 90 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.08658;SOR=4.21132;LSEQ=CCTGCAGCCCCCGGCCCCGC;RSEQ=AGCAGCAGCAGGGGCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:0,2:65,121:186,2:0.0106:2,0:16.5:1:28:1:0.54517:0:60:4:0.0109:0.0053:0.5 0/1:161:7:3,4:51,103:154,7:0.0435:2,2:36:1:32.1:1:0.68791:1.51:60:14:0.0435:0:0.1 +19 15311669 . C T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11775;SOR=0;LSEQ=GGTGGCGGTGGCGGTGGCGG;RSEQ=GACATCGGGCGACGGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:4:2,2:13,34:47,4:0.0769:2,2:16:1:32:1:0.57143:2.56:60:8:0.08:0:1.3 0/0:51:0:0,0:18,33:51,0:0:2,0:15.5:1:30.5:1:1:0:58.6:50:1:0:0.3 +19 15349342 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.30026;SOR=0;LSEQ=TACCCGCTACCAGCAGTCAG;RSEQ=CCCGTAGCCCTCCCCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:4:0,4:33,138:171,4:0.0229:2,0:13:1:30.3:1:1:0:60:8:0.0233:0:1 0/0:103:0:0,0:16,87:103,0:0:2,0:23:1:30.7:1:1:0:60:102:1:0:0.1 +19 15349501 . TC T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08005;SOR=Inf;LSEQ=TCCAGTCCCCCTTTCCCAGC;RSEQ=CCTCAGGAGCTAATCCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:223,82:305,0:0:2,0:25.4:1:32:1:1:0:60:304:1:0:0.1 0/1:232:3:2,1:155,74:229,3:0.0129:2,2:22.3:1:29.7:1:1:1.04709:60:6:0.0132:0.0043:0.3 +19 15349507 . A T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32239;SOR=3.91629;LSEQ=CCCCCTTTCCCAGCTCCCTC;RSEQ=GGAGCTAATCCTTAGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:1:0,1:234,97:331,1:0.003:2,0:3:0:27:0:0.29518:0:60:2:0.003:0:1 0/1:256:3:1,2:168,84:252,3:0.0117:2,2:17.3:1:21.3:1:0.26364:3.97647:60:2:0.0081:0:1.7 +19 15349680 . TTGC T 61 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.70528;SOR=1.69215;LSEQ=GCCACCGCAGCTGCTTGCTG;RSEQ=TGCTGCTGCTGTTGCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:3:0,3:129,200:329,3:0.009:2,0:27:1:30.7:1:0.28511:0:60:6:0.0091:0.003:0.3 0/1:263:4:2,2:110,149:259,4:0.0152:2,2:28.3:1:30.5:1:1:1.35:60:8:0.0153:0:0 +19 15349705 . CGCT C 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=1;SOR=0.74826;LSEQ=GCTGCTGCTGTTGCTCCTGG;RSEQ=GCTGCTGCTGCTGCTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:0,3:104,153:257,3:0.0115:2,0:38.3:1:32.7:1:0.27722:0:60:6:0.0116:0:0 0/0:232:2:1,1:92,138:230,2:0.0086:2,2:38.5:1:30.5:1:1:1.50:60:4:0.0087:0:0 +19 15349752 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25739;SOR=0;LSEQ=CGACGTGCCTCCTCATGGGC;RSEQ=CGCCGGGCCTGCTCCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:1,2:139,144:283,3:0.0105:2,2:11.7:1:28.3:1:1:1.92628:60:6:0.0109:0:1 0/0:230:0:0,0:102,127:229,0:0:2,0:23.5:1:29.8:1:1:0:59.9:44.8:0.9956:0:0.2 +19 15349754 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08577;SOR=Inf;LSEQ=ACGTGCCTCCTCATGGGCCC;RSEQ=CCGGGCCTGCTCCAGCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:145,144:289,0:0:2,0:24.4:1:31:1:1:0:60:95.333:1:0:0.2 0/1:229:3:1,2:101,125:226,3:0.0131:2,2:12.7:1:28.7:1:1:1.61275:60:6:0.0133:0:1 +19 15349811 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16051;SOR=Inf;LSEQ=CCTGGGCAGAGGGTCCCAGT;RSEQ=AGCCTGGGGACTGGTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:147,135:282,0:0:2,0:26:1:32.2:1:1:0:60:93:1:0:0.1 0/1:189:2:1,1:88,99:187,2:0.0106:2,2:21:0:30.5:1:1:1.12:60:4:0.0107:0:1.5 +19 15349813 . G A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06299;SOR=Inf;LSEQ=TGGGCAGAGGGTCCCAGTCA;RSEQ=CCTGGGGACTGGTGTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:147,139:286,0:0:2,0:25.4:1:32.4:1:1:0:60:27.6:1:0:0.1 0/1:190:3:2,1:90,97:187,3:0.0158:2,2:5:1:25.3:1:0.61137:2.15:60:6:0.016:0:1 +19 15349848 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15099;SOR=Inf;LSEQ=TGGCCCCAAGAGTCCCCATG;RSEQ=CCCACCCAGACACCCGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:143,130:273,0:0:2,0:23.6:1:31.6:1:1:0:60:53.6:1:0:0.1 0/1:174:2:1,1:94,78:172,2:0.0115:2,2:43.5:1:29:1:1:1.20383:60:4:0.0119:0:1 +19 15350428 . C CG 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.10082;SOR=Inf;LSEQ=CTTATGTCCAACACGGGCCT;RSEQ=GGGGGGCCTGAGCCCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:135,182:317,0:0:2,0:22.7:1:30.3:1:1:0:59.6:51.833:1:0:0.1 0/1:277:3:1,2:117,157:274,3:0.0108:2,2:26:1:29.7:1:1:1.48838:60:6:0.011:0:0 +19 15350433 . G A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.10983;SOR=Inf;LSEQ=GTCCAACACGGGCCTCGGGG;RSEQ=GCCTGAGCCCTGGCTGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:145,175:320,0:0:2,0:23.5:1:30.8:1:1:0:59.8:39:0.9968:0:0.1 0/1:296:3:2,1:130,163:293,3:0.0101:2,2:18.3:1:25:1:0.58765:2.50:60:2:0.0069:0:1.7 +19 15350575 . TCTC T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GATGATGGGTGAGTGGATCT;RSEQ=CTCCTTCACCACCACGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:560:0:0,0:326,229:555,0:0:2,0:24.5:1:32.7:1:1:0:59.9:91.5:0.991:0:0.2 0/1:541:15:8,7:291,236:527,15:0.0277:2,2:20.3:1:29.6:1:1:1.07876:59.7:30:0.0279:0.0037:0.8 +19 15350594 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.40244;LSEQ=TTCTCCTCCTTCACCACCAC;RSEQ=AGGGGCTGGGGCTGGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:590:29:17,12:336,225:561,29:0.0492:2,2:25.3:1:29.8:1:1:1.05401:58.7:28:0.0482:0:1.1 0/1:521:78:44,34:247,196:443,78:0.1497:2,2:26.8:1:29.5:1:1:1.03:60:38:0.1487:0:1.3 +19 15353850 . C T 84 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22339;SOR=1.98136;LSEQ=TGGCCCTGGGGTGGCGGGGG;RSEQ=TGTTGGATGTGGGTGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:778:6:0,6:310,457:767,6:0.0077:2,0:5.8:1:16.3:1:0.08641:0:60:0.2:0.0014:0:3.3 0/1:725:11:1,10:294,420:714,11:0.0152:2,2:8:1:24.4:1:0.03287:6.98592:60:4.5:0.0134:0:1.5 +19 15353935 . G A 56 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48008;SOR=1.99094;LSEQ=GCTGCTGGGGTGGAGGCTGG;RSEQ=GCTGGGGTGGTGGGGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:3:3,0:216,218:434,3:0.0069:2,0:1:0:26.3:1:0.24828:0:60:6:0.007:0:1 0/1:368:5:4,1:173,188:361,5:0.0136:2,2:10.4:1:24.4:1:0.20175:4.33:57:4:0.0111:0:1.4 +19 15353963 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.57569;SOR=2.75062;LSEQ=TGGTGGGGGTGGTGGCGGCT;RSEQ=CTGCTGCAGCTGCTGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:1,0:99,101:200,1:0.005:2,0:1:0:25:0:0.49751:0:60:2:0.0051:0:1 0/1:147:2:1,1:63,82:145,2:0.0136:2,2:8.5:1:28:1:1:1.30:60:4:0.0136:0:1.5 +19 15353976 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.5112;SOR=0;LSEQ=GGCGGCTGCTGCTGCAGCTG;RSEQ=TGCTGCACAGAGGGGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:2,0:78,67:145,2:0.0136:2,0:10:1:27:0:0.50051:0:60:4:0.0145:0:3.5 0/0:106:0:0,0:52,54:106,0:0:2,0:13.8:1:31.9:1:1:0:59.6:105:1:0:1.3 +19 15354023 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50896;SOR=0;LSEQ=CGGCAGGGGGGGTGGGGGCT;RSEQ=GGACTGCACCTTCACGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:84,80:164,2:0.0118:2,2:36.5:1:30.5:1:1:1.04971:53.5:4:0.0125:0:4 0/0:126:0:0,0:75,51:126,0:0:2,0:19.5:1:30.1:1:1:0:59.3:41:1:0:0.5 +19 15354026 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51069;SOR=0;LSEQ=CAGGGGGGGTGGGGGCTGGG;RSEQ=CTGCACCTTCACGGAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:91,88:179,2:0.011:2,2:18.5:1:29:1:1:1.03391:60:4:0.0117:0:1 0/0:132:0:0,0:79,53:132,0:0:2,0:20.6:1:28:1:1:0:59.3:25.4:1:0:0.5 +19 15354033 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18742;SOR=Inf;LSEQ=GGTGGGGGCTGGGACTGCAC;RSEQ=TCACGGAAGGGAGTAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:104,101:205,0:0:2,0:21.2:1:30.1:1:1:0:59:17.636:1:0:0.6 0/1:157:2:1,1:92,63:155,2:0.0127:2,2:17.5:1:29.5:1:1:1.45669:60:4:0.013:0:0.5 +19 15354041 . A T 31 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.32928;SOR=3.73459;LSEQ=CTGGGACTGCACCTTCACGG;RSEQ=AGGGAGTAGCGGCGTAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:0,1:115,110:225,1:0.0044:2,0:1:0:24:0:0.49115:0:60:2:0.0046:0:1 0/1:184:3:1,2:103,78:181,3:0.0163:2,2:13.3:1:20:1:0.58049:2.62726:60:2:0.0116:0:1.7 +19 15354093 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09729;SOR=Inf;LSEQ=TGCAGCTGCTGCAGGTACAG;RSEQ=TGCATCTGCATGGAGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:185,124:309,0:0:2,0:27.2:1:32.1:1:1:0:60:21.071:1:0:0.4 0/1:265:3:2,1:142,120:262,3:0.0113:2,2:41:1:30:1:1:1.69:60:6:0.0119:0:1 +19 15354334 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25162;SOR=0;LSEQ=ACCGAGGCGGTGAGGCCTGA;RSEQ=CACCTGTGGCCCCAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:1,2:91,202:293,3:0.0101:2,2:18.3:1:27.7:1:1:1.11:60:6:0.0102:0:1.7 0/0:261:0:0,0:84,177:261,0:0:2,0:25.2:1:31:1:1:0:60:51.2:1:0:0.1 +19 15354369 . C A 22 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58941;SOR=2.46848;LSEQ=GCCTGGCCTTTCTGCTCCAT;RSEQ=CTGACCTCATCTGGACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:1,0:17,139:156,1:0.0064:2,0:1:0:23:0:0.11465:0:60:2:0.0065:0:1 0/1:128:2:1,1:21,105:126,2:0.0156:2,2:7:1:22.5:1:0.31533:4.91:60:4:0.0159:0:1 +19 15354998 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.58776;SOR=2.50267;LSEQ=CACCACATGGGTAAACCGAG;RSEQ=CAGGAAGGGGTCTCAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:1:1,0:192,43:235,1:0.0042:2,0:48:0:14:0:1:0:60:0:0:0:5 0/1:191:2:1,1:145,43:188,2:0.0105:2,2:28:1:27.5:1:0.41047:3.34498:60:4:0.0108:0:1 +19 15354999 . C T 43 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04032;SOR=Inf;LSEQ=ACCACATGGGTAAACCGAGG;RSEQ=AGGAAGGGGTCTCAACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:196,46:242,0:0:2,0:22.4:1:32.2:1:1:0:60:120:1:0:0.1 0/1:198:4:1,3:149,45:194,4:0.0202:2,2:8.5:1:21.5:1:0.0449:9.78708:60:3:0.0155:0:2.5 +19 15355214 . G T 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.05593;SOR=6.83701;LSEQ=GGCTCCAGGACGGGCACCTG;RSEQ=GTGGCAATGAAGGGTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:1:0,1:229,402:631,1:0.0016:2,0:1:0:29:0:1:0:60:2:0.0016:0:1 0/1:559:6:2,4:220,333:553,6:0.0107:2,2:17.7:1:30.5:1:1:1.32068:58.8:12:0.011:0:1.2 +19 15355248 . G A 63 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48772;SOR=1.85458;LSEQ=GTGGGGGCGAGGACTTCATC;RSEQ=CCGGGGCTGCCTGCTGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:3:3,0:183,278:461,3:0.0065:2,0:1:0:27.3:1:0.06379:0:60:6:0.0069:0:1 0/1:419:5:3,2:174,237:411,5:0.0119:2,2:9.6:1:27.2:1:0.65468:2.04:60:10:0.0128:0:1.2 +19 15355257 . G A 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0417;SOR=Inf;LSEQ=AGGACTTCATCGCCGGGGCT;RSEQ=CCTGCTGCGGCATGGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:181,231:412,0:0:2,0:22.7:1:31.1:1:1:0:59.9:11.875:1:0:0.6 0/1:342:4:2,2:143,189:332,4:0.0117:2,2:19:1:22.8:1:1:1.32:60:3:0.0098:0:2.5 +19 15355286 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.06558;SOR=Inf;LSEQ=GGCATGGAGGGTGGGGGAGG;RSEQ=GGGGGTGGCGGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:168,119:287,0:0:2,0:25.2:1:29.5:1:1:0:59.6:9.63:0.9962:0:0.7 0/1:199:3:1,2:105,86:191,3:0.0151:2,2:13.3:1:27:1:0.59127:2.43088:57.3:6:0.0169:0:1 +19 15355423 . GAGAC G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.80085;SOR=1.12861;LSEQ=ATGATGGTGCTGCAGACAGA;RSEQ=AGACAGACAGACAGGCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:702:8:5,3:468,226:694,8:0.0114:2,2:28:1:32.6:1:0.72013:1.24205:60:16:0.0116:0.0014:0.1 0/1:545:7:1,6:338,197:535,7:0.0128:2,2:20.4:1:28.6:1:0.01263:10.25274:56.4:14:0.0131:0.0037:0.7 +19 15356795 . A G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGCAGCATGCCACCAAA;RSEQ=GGGATGGGGAAGGACCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:27.5:1:33:0:1:1:60:4:0.5:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:28:0:1:0:60:2:1:0:0 +19 15359971 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49902;SOR=Inf;LSEQ=GGACAGGCCCAGGGCTCTGA;RSEQ=GAATTCCATAACTTGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:136,17:153,0:0:2,0:23.8:1:32.8:1:1:0:59.9:75.5:1:0:0.1 0/1:164:2:1,1:137,25:162,2:0.0122:2,2:19:1:27.5:1:0.29276:5.39325:60:4:0.0123:0:1 +19 15360009 . G T 55 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45715;SOR=2.21968;LSEQ=GGAGTCCTGTCCCTTTCACG;RSEQ=AAGAAAATGGACTTAAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:2:1,1:228,84:312,2:0.0064:2,2:35.5:1:28:1:0.46875:2.70418:60:4:0.0065:0:1 0/1:356:5:2,3:242,109:351,5:0.014:2,2:5:1:24:1:0.18147:3.31784:60:10:0.0142:0:1.2 +19 15360216 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16756;SOR=Inf;LSEQ=TCCTGCGCCCTGGTGGCTGA;RSEQ=GGGCACAAGAACGGCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:10,148:158,0:0:2,0:24.6:1:30.4:1:1:0:60:30.6:1:0:0.1 0/1:110:2:1,1:5,103:108,2:0.0182:1,2:13:1:29:1:0.10659:18.89:60:4:0.0182:0:1 +19 15364464 . C T 70 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31353;SOR=2.45359;LSEQ=CCAGCAGCAGACTGGCGATG;RSEQ=GGCTGGCCAGCTGCAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:650:3:0,3:347,300:647,3:0.0046:2,0:1:0:26:1:0.10076:0:60:6:0.0047:0:1 0/1:533:6:1,5:301,226:527,6:0.0113:2,2:17.3:1:27.3:1:0.08995:6.63781:60:12:0.0114:0:1 +19 15364655 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16885;SOR=Inf;LSEQ=CCCCACGCCCACAGTCCTCA;RSEQ=GGCCCAGCTTCCCCGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:50,235:285,0:0:2,0:23.4:1:30.1:1:1:0:59.7:22.75:0.9964:0:0.1 0/1:200:2:1,1:46,151:197,2:0.01:2,2:34.5:1:29.5:1:0.41749:3.26:60:4:0.0103:0:1 +19 15364669 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18021;SOR=Inf;LSEQ=TCCTCATGGCCCAGCTTCCC;RSEQ=GCCCACCATCCAGGGCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:27,196:223,0:0:2,0:23.9:1:30.2:1:1:0:59.8:73.333:1:0:0.1 0/1:165:2:1,1:27,136:163,2:0.0121:2,2:21.5:1:28:0:0.31146:4.96:60:4:0.0121:0:1 +19 15364683 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17099;SOR=Inf;LSEQ=CTTCCCCGCCCACCATCCAG;RSEQ=GCTCCGCAGTGTCAACGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:12,166:178,0:0:2,0:23.6:1:31.4:1:1:0:59.7:43.5:1:0:0.1 0/1:126:2:1,1:14,110:124,2:0.0159:2,2:29:1:27.5:1:0.22476:7.62:60:4:0.0161:0:1 +19 15364894 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50059;SOR=0;LSEQ=GGCTCTAGCATCCTGGACAC;RSEQ=GGACCGAGCTAGTGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:152,41:193,2:0.0102:2,2:24:1:30:1:0.38525:3.67526:60:4:0.0104:0:1 0/0:173:0:0,0:129,44:173,0:0:2,0:24.2:1:29.2:1:1:0:60:42.25:1:0:0.1 +19 15366000 . GA G 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.42562;SOR=0.3558;LSEQ=GAACACAGATATTATAATTG;RSEQ=AAAAAAAAAGGGGGGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:5:5,0:121,3:124,5:0.0388:1,0:16:1:32.3:1:1:0:60:10:0.0407:0.0155:0 0/1:71:1:1,0:64,6:70,1:0.0141:2,0:17:0:32:0:1:0:60:2:0.0147:0:0 +19 15366010 . A AG 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.10989;LSEQ=ATTATAATTGGAAAAAAAAA;RSEQ=GGGGGGGGGCGCAGAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:75:73,2:61,0:61,75:0.4967:1,1:24.3:1:32.8:1:0.50163:0:59.6:24:0.518:0.1457:0.7 0/1:103:10:9,1:65,9:74,10:0.0971:2,2:27.4:1:31.9:1:1:1.24:60:20:0.1053:0:0.8 +19 15366029 . A T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26964;SOR=0;LSEQ=AAGGGGGGGGGCGCAGAAAG;RSEQ=GTGGACTGAGCAAGGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:208,22:230,3:0.0128:2,2:18.3:1:22.3:1:0.26891:4.67294:60:2:0.01:0:1 0/0:167:0:0,0:142,24:166,0:0:2,0:21.5:1:26.8:1:1:0:60:5.385:1:0:0.4 +19 15366449 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20785;SOR=Inf;LSEQ=TCAAGAACGGGCCCCCTGAG;RSEQ=AAGCCAGGCACTCATTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:37,145:182,0:0:2,0:21.4:1:31.6:1:1:0:59.8:90:1:0:0.1 0/1:153:2:1,1:37,114:151,2:0.0131:2,2:20:1:27:1:0.43627:3.05:60:4:0.0131:0:1 +19 15366663 . G A 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01247;SOR=0;LSEQ=ATCCTCCCCAACCAAACATG;RSEQ=TGAGCTCCGAAGGCTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:17:15,2:27,4:31,17:0.3542:2,2:26.9:1:29.9:1:1:1.11:58.2:16:0.3404:0:1.2 0/0:13:0:0,0:11,2:13,0:0:2,0:25.6:1:30.7:1:1:0:60:26:1:0:0 +19 15367141 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14376;SOR=Inf;LSEQ=TCCTGTCACCCAAGACCCAG;RSEQ=CGTCTGCTCCAAAAAACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:9,131:140,0:0:2,0:22:1:32.2:1:1:0:59.7:45.667:1:0:0.1 0/1:86:2:1,1:6,78:84,2:0.0233:2,2:31:1:27.5:1:0.15705:12.11:60:4:0.0238:0:1 +19 15367720 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58937;SOR=2.47408;LSEQ=TCTTAGAAACTTCTGGGGAG;RSEQ=CCACCCTGGTCCACGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:1:1,0:183,55:238,1:0.0042:2,0:4:0:31:0:1:0:60:2:0.0043:0:1 0/1:194:2:2,0:131,59:190,2:0.0103:2,0:18.5:1:30:0:1:0:60:4:0.0105:0:1 +19 15367734 . C T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25187;SOR=0;LSEQ=GGGGAGGCCACCCTGGTCCA;RSEQ=GGACTCTGGGGATTAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:212,77:289,3:0.0103:2,2:28.7:1:24.7:1:1:1.37501:60:2:0.0069:0:1 0/0:256:0:0,0:168,88:256,0:0:2,0:22.9:1:30.3:1:1:0:60:255:1:0:0.2 +19 15374138 . G GA 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58232;SOR=0.60445;LSEQ=TTATCCCAAGGAAAGTGACA;RSEQ=AAAAAAAAACTCTGCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:11:11,0:143,3:146,11:0.0701:1,0:20.5:1:30.6:1:1:0:60:22:0.071:0.0191:0.1 0/1:92:4:4,0:84,0:84,4:0.0435:1,0:25.3:1:29:1:1:0:60:8:0.0444:0:0 +19 15374435 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28559;SOR=0;LSEQ=GTGGCTGGCAGCAGACGAAA;RSEQ=GGATGCCTAGAAGAGCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:1,2:14,237:251,3:0.0118:2,2:15.3:1:32.3:1:0.16753:8.30:60:6:0.0119:0:1 0/0:162:0:0,0:15,146:161,0:0:2,0:22.7:1:30.5:1:1:0:60:79.5:0.9938:0:0 +19 15374491 . T TG 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.85479;LSEQ=CAGTTTGGTCAAGACTCTAG;RSEQ=GGGGGGACAGGCCATCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:2,68:70,2:0.0278:1,0:25.5:1:33:0:1:0:43:4:0.0282:0:0 0/1:42:1:0,1:1,40:41,1:0.0238:1,0:25:0:32:0:1:0:60:2:0.0238:0:1 +19 15376011 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54783;SOR=0;LSEQ=GACCTTTGAGTCAGTGGGGC;RSEQ=GCTGTTTCTGGGCTGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:3:3,0:55,1:56,3:0.0508:1,0:33:1:29:1:1:0:60:6:0.0536:0:1 0/0:29:0:0,0:28,1:29,0:0:1,0:24.1:1:29.9:1:1:0:60:58:1:0:0 +19 15376087 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17685;SOR=Inf;LSEQ=GTGCCCGGGACCCAGGACAG;RSEQ=CTCTGTGTAAAGCACGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:162,44:206,0:0:2,0:21.7:1:31.2:1:1:0:60:102:1:0:0.1 0/1:150:2:1,1:116,30:146,2:0.0133:2,2:30.5:1:28.5:1:0.37617:3.82015:60:4:0.0135:0:1 +19 15376099 . G T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31133;SOR=4.29121;LSEQ=CAGGACAGGCTCTGTGTAAA;RSEQ=CACGGGCAAGGACAGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:0,1:186,68:254,1:0.0039:2,0:7:0:32:0:0.27059:0:60:2:0.004:0:1 0/1:180:3:2,1:131,46:177,3:0.0167:2,2:24.7:1:25.7:1:1:1.4209:60:6:0.0167:0:1 +19 15376184 . G A 68 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.169;SOR=3.16321;LSEQ=CCTTCACAGGCTGTGGGGTG;RSEQ=CCGCGATGATGGGTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:2:1,1:353,277:630,2:0.0032:2,2:29:0:32:0:1:1.27387:60:4:0.0033:0:1.5 0/1:603:6:4,2:322,274:596,6:0.01:2,2:19.5:1:26.5:1:0.69243:1.70:60:12:0.0102:0:1 +19 15378434 . GCCAC G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=7e-05;SOR=5.9886;LSEQ=CTGTAGACAGGGCACCCCAT;RSEQ=CCACCCCCTGCCCCCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:7:0,7:4,123:127,7:0.0522:1,0:21.4:1:33.1:1:1:0:60:14:0.0526:0:0 0/1:72:18:1,17:6,48:54,18:0.25:2,1:30.1:1:32.6:1:0.67154:2.10633:60:36:0.25:0:0.1 +19 15379563 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16093;SOR=Inf;LSEQ=AGTCACAGGAACAACCACAG;RSEQ=TCTCATTACCTCTACCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:49,1:50,0:0:1,0:24.2:1:31.6:1:1:0:60:24:1:0:0.1 0/1:34:2:1,1:29,3:32,2:0.0588:2,2:21.5:1:26:0:0.2246:8.51255:60:4:0.0588:0:1 +19 15379632 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20689;SOR=Inf;LSEQ=CAGCCACACCCAACACCCCT;RSEQ=CCCACGGGCTCCTGACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:150,9:159,0:0:2,0:24.5:1:32.3:1:1:0:60:30.8:1:0:0.1 0/1:134:2:1,1:120,12:132,2:0.0149:2,2:14.5:1:27.5:1:0.18528:9.64765:60:4:0.0153:0:1 +19 15379640 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50464;SOR=0;LSEQ=CCCAACACCCCTGCCCACGG;RSEQ=CTCCTGACATGCCCACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:177,18:195,2:0.0102:2,2:25:1:29.5:1:0.18404:9.59807:60:4:0.0106:0:1 0/0:158:0:0,0:140,18:158,0:0:2,0:22.9:1:30.4:1:1:0:59.8:78:1:0:0.2 +19 15379660 . C T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66169;SOR=1.83725;LSEQ=GCTCCTGACATGCCCACTGC;RSEQ=GTCGCCTCCCCTCCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:2:0,2:217,43:260,2:0.0076:2,0:1:0:28.5:1:0.02895:0:60:4:0.0078:0:1 0/1:215:3:1,2:174,38:212,3:0.014:2,2:15.3:1:27:1:0.08962:9.01732:60:6:0.0142:0:1 +19 15379908 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20054;SOR=Inf;LSEQ=AGGCAGCCAGGCAGCACAAA;RSEQ=GCTGGGCTGGCCAGGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:21,188:209,0:0:2,0:24.2:1:30.5:1:1:0:59.9:103.5:1:0:0.1 0/1:170:2:1,1:25,143:168,2:0.0118:2,2:32:1:32.5:1:0.28326:5.63:60:4:0.0119:0:1 +19 15383516 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03562;SOR=4.34564;LSEQ=AAGGGCCCTGCAGCTCTCAC;RSEQ=ATGATTCCAAATGCATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:4:4,0:90,3:93,4:0.0412:1,0:38:1:33.5:1:1:0:60:8:0.0421:0:1.3 0/1:44:7:7,0:34,3:37,7:0.1591:2,0:31:1:31.3:1:1:0:60:14:0.1628:0:1.9 +19 15383542 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.17248;SOR=Inf;LSEQ=TCCAAATGCATCTCCTACCC;RSEQ=CCCCCCAGGAACTGCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:119,7:126,0:0:2,0:27.1:1:31.7:1:1:0:59.9:24.2:1:0:0.1 0/1:90:2:2,0:75,13:88,2:0.0222:2,0:22.5:1:32:0:1:0:60:4:0.023:0:2 +19 15383582 . C A 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=13.47339;LSEQ=ACCAGGAGACATGCAGGAGA;RSEQ=GACCTCCAGGACGGCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:4:4,0:185,64:249,4:0.0158:2,0:20.3:1:32:0:0.57483:0:60:8:0.0161:0:1.3 0/1:224:40:33,7:123,58:181,40:0.1786:2,2:25.6:1:29.8:1:0.08428:2.22:60:80:0.1802:0:1.2 +19 15383958 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21985;SOR=Inf;LSEQ=AGGCACTCTACAAAGGAAGA;RSEQ=AAGAGCCCCCGTGAGATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:24,168:192,0:0:2,0:22.8:1:31.8:1:1:0:60:47:1:0:0.1 0/1:170:2:1,1:31,137:168,2:0.0118:2,2:32.5:1:28:1:0.34194:4.37:60:4:0.0118:0:1 +19 15383972 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22494;SOR=Inf;LSEQ=GGAAGAGAAGAGCCCCCGTG;RSEQ=GATATCAGTCAGCAGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:13,125:138,0:0:2,0:26.4:1:31.3:1:1:0:60:26.6:1:0:0.1 0/1:125:2:1,1:19,104:123,2:0.016:2,2:38:1:29.5:1:0.29548:5.36:60:4:0.0163:0:1 +19 15449749 . T TA 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.6233;LSEQ=AGACAGAGCAAGACTCCGTT;RSEQ=AAAAAAAAAAACAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:7,3:10,2:0.1667:2,0:24.5:1:27:1:1:0:60:4:0.1667:0.0833:0.5 0/1:8:2:2,0:4,2:6,2:0.25:2,0:24:1:29.7:1:1:0:58.5:4:0.25:0.125:0 +19 15449967 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=GCTGTTGGGATTCTTCTAAA;RSEQ=GGACAAGTTAAGGGCAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:6,11:17,0:0:2,0:22.1:1:30.1:1:1:0:60:34:1:0:0.1 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:26:1:28.5:1:1:1.18321:60:4:0.1538:0:1 +19 15888953 . T A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.33333;SOR=Inf;LSEQ=ACTACAGAGGAATGAGTGAG;RSEQ=GAGGAGAGGAGTGAGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:43:0:31:0:1:0:46:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:30:0:1:0:60:4:1:0:1 +19 15889924 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAGTGAGTGAGTGAGGAG;RSEQ=GGAGTGCGTGAGTGAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:27.5:1:1:0:20.5:4:1:0:2 +19 15889945 . G GGAGT 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=4.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GGAGTGCGTGAGTGAGGAGA;RSEQ=GAGTGAGTGAGTGCATGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:29.9:1:1:0:20.5:4:1:0:2 +19 15890134 . AGAG A 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGAGTGAGTGCATGGGT;RSEQ=GAGTGAGTGAGTGCATGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:36.5:1:32.5:1:1:0:22.5:4:0.6667:0:0.5 +19 15890316 . G A 156 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=4.000;MSILEN=1;SSF=9e-05;SOR=0;LSEQ=GGGAGTGAGTGAGTGAGGAG;RSEQ=GGAGTGAGTGCATGGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:37,1:0,0:0,38:1:0,1:21.3:1:29.9:1:1:0:38.2:18:1:0:1.8 1/0:34:23:22,1:9,2:11,23:0.6765:2,1:23.3:1:28:1:0.23897:4.64:37:10.5:0.6563:0:1.9 +19 15890386 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23293;SOR=0;LSEQ=GCATGGGTAGAGGAGTGAGT;RSEQ=AATGAGCCGCCTCCCTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:146,40:186,2:0.0106:2,2:34.5:1:30:0:0.38952:3.61717:60:4:0.0108:0:2 0/0:201:0:0,0:158,43:201,0:0:2,0:21.5:1:31:1:1:0:57.8:32.5:1:0:1.1 +19 15890388 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00045;SOR=0.06626;LSEQ=ATGGGTAGAGGAGTGAGTGA;RSEQ=TGAGCCGCCTCCCTCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:197:196:152,44:0,0:0,196:0.9949:0,2:22.7:1:32.6:1:1:0:57.8:38.2:0.9948:0:1.2 1/1:209:194:150,44:10,5:15,194:0.9282:2,2:21.6:1:31.4:1:0.35089:1.70:57.8:47.5:0.9268:0:1.2 +19 15890517 . A C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.47562;LSEQ=CAGAGTCATCCTGCTGCCAC;RSEQ=CTCACGAGGTCCTGGTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:114:48,66:108,171:279,114:0.2886:2,2:24.9:1:30.6:1:0.5706:1.15:60:21.8:0.2861:0:1.2 1/0:384:265:104,161:49,70:119,265:0.6901:2,2:22.2:1:30:1:0.73629:1.08343:60:65.25:0.6941:0:1.1 +19 15890568 . G T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11358;SOR=Inf;LSEQ=TTTCTGTTTTGGGGGTTGTG;RSEQ=AAAGTACTGAAGGCGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:95,184:279,0:0:2,0:25.5:1:31.5:1:1:0:60:26.9:1:0:0.7 0/1:263:3:1,2:99,161:260,3:0.0114:2,2:24.7:1:21.7:1:1:1.22884:60:2:0.0078:0:1.7 +19 15890625 . CG GA 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01285;LSEQ=ATAGGTCCAGGCCAGGAAGC;RSEQ=GCCAGGAGCCGGGAGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:80:24,56:0,1:1,80:0.6107:0,2:21.8:1:31.4:1:1:0:59.4:79:0.627:0.0763:1 0/1:103:2:1,1:10,19:29,2:0.0194:2,2:17:1:26.8:1:1:1.86:60:4:0.0198:0.0097:0.5 +19 15890626 . G A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25444;SOR=0;LSEQ=TAGGTCCAGGCCAGGAAGCC;RSEQ=GCCAGGAGCCGGGAGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:0,3:10,34:44,3:0.0254:2,0:24:1:31.3:1:1:0:60:6:0.0625:0:3 0/0:96:0:0,0:28,67:95,0:0:2,0:23.4:1:29.9:1:1:0:59.2:30.667:1:0:0.9 +19 15890725 . G T 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00255;SOR=0;LSEQ=AGGCTCAGCTGCGGCATCCT;RSEQ=CAGGGCAGACAGGATGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:0,10:0,6:6,10:0.625:0,0:17.3:1:30.2:1:1:0:50.7:20:0.625:0:1 0/0:10:0:0,0:0,10:10,0:0:0,0:26.3:1:30.8:1:1:0:44.6:20:1:0:0.6 +19 15890771 . T G 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.45385;LSEQ=ATCCTGAGGCCCAGGGAAAG;RSEQ=CTCAGGGAGCTCCAGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:20.8:1:33.5:1:1:0:44.8:8:0.5:0:2.3 1/0:5:3:0,3:0,2:2,3:0.6:0,0:18.7:1:33:1:1:0:38:6:0.6:0:2 +19 15890777 . G T 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=AGGCCCAGGGAAAGTCTCAG;RSEQ=GAGCTCCAGGGACAGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:25:1:31.3:1:1:0:49.7:6:0.4286:0:2.7 1/0:4:2:0,2:0,2:2,2:0.5:0,0:19:1:31:1:1:0:42:4:0.5:0:2.5 +19 15890800 . A G 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=GCTCCAGGGACAGTGGAGAG;RSEQ=AGCAGGGAAGGGGTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:25.3:1:31.7:1:1:0:60:6:0.4286:0:2.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:9:0:32:0:1:0:60:2:0.5:0:3 +19 16044851 . C T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TGGGCAGAGGAATGAGTGAG;RSEQ=GGGGAGAGGAATGAGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,1:3,3:0.5:2,0:13.7:1:24.7:1:1:0:59.3:2:0.4:0:1.7 0/0:2:0:0,0:1,1:2,0:0:2,0:24:1:22:1:1:0:47.5:1:1:0:1.5 +19 16044871 . T C 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76645;LSEQ=CGGGGAGAGGAATGAGTGAG;RSEQ=GGGCAGAGGAATGAGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:5,1:6,2:0.25:2,2:15.5:1:33:1:0.46429:3.87298:42.5:4:0.2857:0:2.5 0/1:5:1:0,1:3,1:4,1:0.2:2,0:1:0:30:0:0.4:0:35:2:0.2:0:3 +19 16045035 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15455;SOR=Inf;LSEQ=ACTCACCAGGCCCTGGTGTC;RSEQ=CCAAAACCAGTTCTGTTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:27,0:0:2,0:27.2:1:31.1:1:1:0:60:54:1:0:0 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:36.5:1:27.5:1:1:1.26772:60:4:0.1111:0:1 +19 16045141 . T C 91 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15152;SOR=0;LSEQ=CGGGCCAGGAGCCAGGAGCC;RSEQ=CCAACCAGCAGCAGAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:26.7:1:32.6:1:1:0:60:14:1:0:1 1/0:5:3:0,3:1,1:2,3:0.6:2,0:13:1:32:0:0.4:0:60:6:0.6:0:1 +19 16045817 . G C 29 d5;v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGCTGGGTGCAGAGGAGCCA;RSEQ=CTCAGGGTGACACAGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:29:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:37:0:33:1:1:0:60:4:1:0:0.5 +19 16126203 . T G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGTTGGGGCCTGGTCAG;RSEQ=GAGGATCAGATCAGTGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 16133219 . C T 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTGGAGTTTCCTTTTCC;RSEQ=GCCCTGGAGCAGGCAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:32:0:1:0:57:4:1:0:1.5 +19 16133428 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49758;SOR=0;LSEQ=AGCCCCAAGGACCTCTGCTG;RSEQ=TCCCATTAGGACAAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:17,7:24,2:0.0769:2,2:24.5:1:31:1:0.52923:2.3376:60:4:0.08:0:1 0/0:20:0:0,0:11,9:20,0:0:2,0:17:1:30.5:1:1:0:60:40:1:0:0.3 +19 16133492 . C A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49392;SOR=Inf;LSEQ=TTACGCTGACTCCTCCAGTG;RSEQ=CTCATCAATGAAGTAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,15:29,0:0:2,0:26.6:1:31.1:1:1:0:58.7:28:1:0:0.2 0/1:33:2:1,1:13,18:31,2:0.0606:2,2:26:0:27.5:1:1:1.37:60:4:0.0606:0:1.5 +19 16133647 . T C 53 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGACCCTCCTGCCCCA;RSEQ=ACTCCCCAGATCCCCCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:18:1:34:0:1:0:60:6:1:0:1.7 1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:33:0:1:0:60:2:1:0:1 +19 16435563 . T A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCCATCCGGGACGCGTT;RSEQ=CCGCCGCCGCCGCTTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 16435911 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGACGCGAAGGCGGGGACTG;RSEQ=AGACTCAGGAGAGGAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:12:0:27:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:28:1:1:0:60:4:1:0:1 +19 16436765 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCCGCAAACGCACCGCCACT;RSEQ=ACACCTGCAGCTACGCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:45,25:70,0:0:2,0:23.3:1:31.9:1:1:0:60:34:1:0:0.1 0/1:141:2:1,1:86,52:138,2:0.0142:2,2:38.5:1:30:1:1:1.6476:60:4:0.0143:0:1 +19 16436817 . T C 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5524;SOR=Inf;LSEQ=CTACACCAAGAGTTCGCATC;RSEQ=GAAGGCGCATCTGCGCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:30,40:70,0:0:2,0:26:1:31:1:1:0:60:69:1:0:0.1 0/1:142:3:1,2:62,75:137,3:0.0211:2,2:20:1:22.3:1:1:1.64765:60:2:0.0146:0:1 +19 16436824 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGAGTTCGCATCTGAAGGC;RSEQ=CATCTGCGCACGCACACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:24,37:61,0:0:2,0:26.1:1:31.4:1:1:0:60:60:1:0:0.1 0/1:125:2:1,1:52,71:123,2:0.016:2,2:12:1:25:1:1:1.36:60:4:0.0163:0:1 +19 16437671 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCCCTCCCTGCAGGTGA;RSEQ=AAGCCCTACCACTGCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:28:1:1:0:60:4:1:0:1 +19 17193435 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.4983;SOR=Inf;LSEQ=TTTCCTGGTGAATGTGCCAT;RSEQ=GGGGGCAAGGGGTAGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:121,16:137,0:0:2,0:26.3:1:32.4:1:1:0:60:274:1:0:0.3 0/1:141:2:1,1:124,15:139,2:0.0142:2,2:17.5:1:28:1:0.21479:8.03591:60:4:0.0144:0:1.5 +19 17193518 . A G 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19747;LSEQ=GGAGATGCTGTTTATTGGGT;RSEQ=GGCACAAGAACAAGAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:468:426:231,195:22,20:42,426:0.9103:2,2:26.9:1:31.5:1:0.87176:1.08:59.9:37.727:0.9081:0:1.9 1/0:588:392:207,185:104,91:195,392:0.6667:2,2:26.7:1:30.7:1:0.93017:1.02136:60:129.667:0.6684:0:1.9 +19 17193551 . A G 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29173;LSEQ=AGAGAGGCGGAGAAAGTGTG;RSEQ=TCGTACTTATTTGGCCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:531:487:229,258:21,23:44,487:0.9171:2,2:25.1:1:31.7:1:1:1.02862:59.9:120.75:0.9165:0:1.8 1/0:655:500:237,263:75,80:155,500:0.7634:2,2:25.5:1:30.9:1:0.85425:1.0403:60:99:0.7627:0:1.8 +19 17193654 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49864;SOR=0;LSEQ=GCAGGGAAGGGAGAAGGTAA;RSEQ=GGTTGGGGTGTCCTGGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:21,125:146,2:0.0135:2,2:11:1:30.5:1:0.27606:5.84:60:4:0.014:0:1 0/0:140:0:0,0:19,121:140,0:0:2,0:21.1:1:30.6:1:1:0:60:280:1:0:0.1 +19 17700442 . A T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGGAAGAGGTTCCAGCAGCT;RSEQ=AGGCTCCTTCCCACTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:3,0:0:0,0:14.3:1:29.7:1:1:0:57.3:6:1:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:40:1:28.5:1:1:0:53:4:0.5:0:1 +19 17700634 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11659;SOR=Inf;LSEQ=CACATCAATTCTCTTGGCAA;RSEQ=GATCTTGCCCTCGTTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:50,17:67,0:0:2,0:21.4:1:32.4:1:1:0:59.9:134:1:0:0.1 0/1:65:3:1,2:47,15:62,3:0.0462:2,2:21.7:1:29.3:1:0.16502:6.05045:57:6:0.0462:0:1.3 +19 17700647 . G A 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTGGCAAGGATCTTGCCCTC;RSEQ=TTTGTTTACAACAATGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:59,35:94,0:0:2,0:20:1:30.3:1:1:0:59.1:46:1:0:0.1 0/1:83:15:11,4:47,21:68,15:0.1807:2,2:19.1:1:29.5:1:1:1.23:57:30:0.1829:0:1 +19 17700751 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51554;SOR=Inf;LSEQ=CTTTTTGAACAGTACCTTCT;RSEQ=TTGATGTCTACAATATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:23,35:58,0:0:2,0:22.8:1:32.2:1:1:0:59.2:57:1:0:0.1 0/1:86:2:1,1:31,53:84,2:0.0233:2,2:19.5:1:28.5:1:1:1.70:60:4:0.0235:0:1.5 +19 17700770 . C T 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00111;SOR=Inf;LSEQ=TCTTGATGTCTACAATATCA;RSEQ=CTTTCTTATAGATTCACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:17,34:51,0:0:2,0:23.9:1:31.4:1:1:0:56:50:1:0:0.1 0/1:64:11:3,8:17,35:52,11:0.1719:2,2:22.8:1:27.7:1:1:1.2901:56:10:0.1587:0:1 +19 17700822 . TA T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.01859;SOR=2.63829;LSEQ=AGGAACAACTTCATGTTTTC;RSEQ=AAAAAGCCTAGAGAACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:27:15,12:13,12:25,27:0.5192:2,2:24.3:1:31.2:1:1:1.15:46.1:26:0.5098:0.1346:0.3 1/0:62:46:27,19:12,4:16,46:0.7419:2,2:26.4:1:30.8:1:0.36883:2.08697:43.7:92:0.7419:0.1129:0.2 +19 17700893 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24765;SOR=0;LSEQ=TTTGTCATCTTGGCAAATTA;RSEQ=TGGAAGATGGCGGTTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:2,0:87,70:157,2:0.0126:2,0:35.5:1:30:1:0.50402:0:60:4:0.0127:0:1 0/0:160:0:0,0:88,72:160,0:0:2,0:29.7:1:31.1:1:1:0:56.9:159:1:0:0.2 +19 17700902 . G A 22 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=TTGGCAAATTACTGGAAGAT;RSEQ=GCGGTTCTGGCCGAAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:86,76:162,0:0:2,0:29.3:1:31.6:1:1:0:58:80:1:0:0.2 0/1:164:2:2,0:81,81:162,2:0.0122:2,0:6.5:1:22:0:0.49701:0:41.5:4:0.0123:0:1 +19 17700904 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=GGCAAATTACTGGAAGATGG;RSEQ=GGTTCTGGCCGAAAAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:84,76:160,2:0.0123:2,2:38:0:31.5:1:1:1.10458:60:4:0.0125:0:1.5 0/0:161:0:0,0:80,81:161,0:0:2,0:29.3:1:29.9:1:1:0:57.7:160:1:0:0.2 +19 17700920 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24749;SOR=Inf;LSEQ=ATGGCGGTTCTGGCCGAAAA;RSEQ=CCCCACTGGTATCCTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:74,76:150,0:0:2,0:23.5:1:32.6:1:1:0:58.6:300:1:0:0.3 0/1:149:2:1,1:69,78:147,2:0.0134:2,2:31.5:1:28.5:1:1:1.13:55.5:4:0.0134:0:1.5 +19 17700980 . T C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11503;SOR=2.57282;LSEQ=ACTCCAAGTCACTCCAATCC;RSEQ=TTCAATGCTATGTATTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:35:0,35:0,13:13,35:0.7292:1,1:21.3:1:32.4:1:1:0:60:34:0.7234:0:1.5 1/1:40:35:0,35:0,5:5,35:0.875:0,1:24.5:1:32.5:1:1:0:60:70:0.875:0:1.4 +19 17701011 . T C 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01121;SOR=Inf;LSEQ=TGTATTCACCTAACCTCTTG;RSEQ=CTCCCTCTTCTAAGGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:29,0:0:1,0:27.6:1:30.3:1:1:0:60:58:1:0:1.3 0/1:22:5:0,5:0,17:17,5:0.2273:1,0:23.2:1:32.2:1:1:0:60:10:0.2273:0:2.6 +19 17701030 . T C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91903;LSEQ=GTCTCCCTCTTCTAAGGACA;RSEQ=TTGTGATTACATTTAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:16:0,16:0,4:4,16:0.8:0,1:31.3:1:34.1:1:1:0:60:32:0.8:0:1.9 1/0:14:11:0,11:0,3:3,11:0.7857:0,0:23.5:1:32.5:1:1:0:60:22:0.7857:0:1.9 +19 17937429 . A G 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=3.65424;LSEQ=GCCCCCCCAAATGCAATGTC;RSEQ=TGGGGGTGTTCCTGAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:20:20,0:134,5:139,20:0.1258:1,1:25.7:1:30.5:1:1:0:60:40:0.1266:0:1.2 0/1:107:37:35,2:70,0:70,37:0.3458:1,2:23.3:1:29.6:1:0.11744:0:60:74:0.3458:0:1.1 +19 17937434 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51041;SOR=0;LSEQ=CCCAAATGCAATGTCATGGG;RSEQ=GTGTTCCTGAAGTAGAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:169,4:173,2:0.0114:1,2:29:1:29.5:1:0.05649:37.88902:60:4:0.0117:0:1 0/0:128:0:0,0:125,3:128,0:0:1,0:20.2:1:30.3:1:1:0:60:41.667:1:0:0.4 +19 17937479 . A G 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATAAGGCCTCTGAGGCCCAG;RSEQ=GAGGGGCAGCTCCGGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:433:0:0,0:314,119:433,0:0:2,0:22.4:1:30.2:1:1:0:60:53.125:1:0:0.2 0/1:383:17:12,5:258,107:365,17:0.0444:2,2:21.4:1:28.6:1:1:1.00466:60:16:0.0428:0:1 +19 17937749 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50686;SOR=0;LSEQ=GGGGGACAGATAATGGGGTC;RSEQ=TGCCTGAGCAGTCCAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:32,154:186,2:0.0106:2,2:42:1:31:1:0.32103:4.75:60:4:0.0108:0:1 0/0:145:0:0,0:41,104:145,0:0:2,0:26.1:1:30.5:1:1:0:60:71.5:1:0:0.5 +19 17937758 . C T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.93721;LSEQ=ATAATGGGGTCGTGCCTGAG;RSEQ=AGTCCAAAGGACACAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:11:2,9:22,131:153,11:0.0671:2,2:19.8:1:28.6:1:0.66457:1.32:60:22:0.0683:0:1 0/1:126:46:14,32:20,60:80,46:0.3651:2,2:23.5:1:27.4:1:0.53663:1.31:60:45:0.3659:0:1.7 +19 17937786 . C T 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=55.41565;LSEQ=AGGACACAACTCCCATTCAG;RSEQ=GTATTTGTTTTTGTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:1:0,1:4,100:104,1:0.0095:1,0:14:0:32:0:1:0:45:2:0.0097:0:1 0/1:71:25:5,20:10,36:46,25:0.3521:2,2:20.6:1:29.7:1:1:1.10951:59.2:50:0.3676:0:2.2 +19 17938018 . T C 34 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGTTGGTCTCAAATTCCTGA;RSEQ=CTCAGGTGATCCACCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,2:2,2:0.5:0,0:6:0:34.5:1:0.33333:0:50:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 17940705 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01781;SOR=Inf;LSEQ=CCTCACCCTATAAGGCATTA;RSEQ=TATTCTCATTTTGGAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:45,2:47,0:0:1,0:21.3:1:32.3:1:1:0:60:94:1:0:0 0/1:40:5:4,1:31,4:35,5:0.125:2,2:16.8:1:29.6:1:0.50664:1.89953:60:10:0.1316:0:1.2 +19 17940758 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22666;SOR=Inf;LSEQ=TCTGAAAGTGCTCTGACTTG;RSEQ=CACACAGTGAGAGAGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:120,6:126,0:0:1,0:24.7:1:31.8:1:1:0:60:17:1:0:0.4 0/1:115:2:1,1:95,17:112,2:0.0174:2,2:24:1:30.5:1:0.29204:5.45938:60:4:0.0183:0:2 +19 17940765 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49987;SOR=0;LSEQ=GTGCTCTGACTTGCCACACA;RSEQ=TGAGAGAGTAGCCAAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:132,12:144,2:0.0137:2,2:17:1:29.5:1:0.17071:10.60856:60:4:0.0139:0:1 0/0:130:0:0,0:107,23:130,0:0:2,0:25.8:1:31.3:1:1:0:60:42.333:1:0:0.5 +19 17940785 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22438;SOR=Inf;LSEQ=GTGAGAGAGTAGCCAAGTGG;RSEQ=GGCCAGGATCCTCATCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:176,39:215,0:0:2,0:24.1:1:31.1:1:1:0:59.9:42:1:0:0.5 0/1:194:2:1,1:139,53:192,2:0.0103:2,2:22:1:28.5:1:0.48026:2.60758:60:4:0.0105:0:2.5 +19 17940816 . G C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04417;SOR=1.39032;LSEQ=CTCATCGGCCTCACACTCTA;RSEQ=CCTTTCTTCTCAGTACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:95:63,32:164,92:256,95:0.2699:2,2:25.5:1:31.6:1:0.80164:1.10:59.8:190:0.2794:0:1.9 0/1:374:127:81,46:144,102:246,127:0.3396:2,2:21.2:1:31:1:0.3719:1.25:60:254:0.3442:0:2 +19 17940842 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01013;SOR=1.45048;LSEQ=CTTCTCAGTACAGAGACTCA;RSEQ=GCGCCAGCTGGCTTGCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:114:65,49:180,141:321,114:0.2621:2,2:27.3:1:30.6:1:0.91263:1.04:59.8:113:0.2659:0:1.9 0/1:494:168:93,75:174,152:326,168:0.3401:2,2:27.4:1:29.7:1:0.70366:1.08:60:83:0.3437:0:1.9 +19 17941060 . A G 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27129;SOR=2.70534;LSEQ=AGGAGCGCATGTGGTGGGGG;RSEQ=GGAGCCTCCGTGGGTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:2:0,2:141,222:363,2:0.0055:2,0:10:1:21.5:1:0.52455:0:60:1:0.0029:0:1.5 0/1:340:5:2,3:139,196:335,5:0.0147:2,2:31.2:1:27.2:1:1:1.06359:60:4:0.0123:0:1.4 +19 17941079 . G T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01856;SOR=Inf;LSEQ=GAGGAGCCTCCGTGGGTGGA;RSEQ=GGGGAGGGGCCACCCGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:82,179:261,0:0:2,0:23.6:1:31.4:1:1:0:60:51.2:1:0:0.2 0/1:216:5:2,3:71,140:211,5:0.0231:2,2:14.2:1:29.2:1:1:1.31:60:10:0.0235:0:1.2 +19 17941084 . A G 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25754;SOR=0;LSEQ=GCCTCCGTGGGTGGAGGGGG;RSEQ=GGGGCCACCCGTGGTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:0,3:66,169:235,3:0.0125:2,0:36:1:24.3:1:0.56253:0:60:2:0.0092:0:2.3 0/0:192:0:0,0:60,131:191,0:0:2,0:21.9:1:28.3:1:1:0:60:11.733:1:0:0.3 +19 17941102 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.1786;SOR=Inf;LSEQ=GGAGGGGCCACCCGTGGTGG;RSEQ=GGTAGGGGCCATCTGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:32,134:166,0:0:2,0:22:1:31.1:1:1:0:60:54.333:1:0:0.3 0/1:122:2:1,1:19,101:120,2:0.0164:2,2:11:1:27.5:1:0.30213:5.21:60:4:0.0165:0:1 +19 17941143 . A C 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCGGGGAGGGGCTGCCTG;RSEQ=ACCGTGAAGGGGTCAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:21,67:88,0:0:2,0:26:1:30.8:1:1:0:60:43:1:0:0.3 0/1:48:11:2,9:4,33:37,11:0.2292:2,2:19.6:1:30.6:1:0.60927:1.81:60:10:0.2128:0:2.1 +19 17941173 . C G 92 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-04;SOR=18.28882;LSEQ=GGGTCAGAAAGGTGAGGAAG;RSEQ=GTCCTCCCCACTGGGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:28,47:75,1:0.0132:2,0:17:0:11:0:0.38158:0:60:0:0:0:2 0/1:40:8:4,4:13,19:32,8:0.2:2,2:27.9:1:30.8:1:0.70247:1.45:60:16:0.2:0:2.1 +19 17941181 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11295;SOR=Inf;LSEQ=AAGGTGAGGAAGCGTCCTCC;RSEQ=CACTGGGGCCTATGATGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:38,42:80,0:0:2,0:22.1:1:31.3:1:1:0:60:25.667:1:0:0.3 0/1:41:2:1,1:18,21:39,2:0.0488:2,2:23.5:1:31:1:1:1.16:60:4:0.05:0:2.5 +19 17941254 . T C 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00913;SOR=Inf;LSEQ=AGGCGCAGACAGGTTGGAGA;RSEQ=TGGCCACGAGGGGCGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:104,25:129,0:0:2,0:23.7:1:30.9:1:1:0:59.9:63.5:1:0:0.1 0/1:112:6:4,2:86,20:106,6:0.0536:2,2:23.3:1:30.8:1:0.33561:2.13236:60:12:0.055:0:1.3 +19 17941294 . T C 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGAAGAAGGCTGGGGGC;RSEQ=CTGGGAAGCCGACTCACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:181,91:272,0:0:2,0:23.5:1:31:1:1:0:60:44.333:1:0:0.1 0/1:250:73:50,23:120,56:176,73:0.292:2,2:24.2:1:29.4:1:1:1.01:60:17.25:0.2851:0:1.1 +19 17941477 . GAAGAG AAAGA 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27422;SOR=Inf;LSEQ=CGAGGGTGTAGAAAGGACAG;RSEQ=GGGGGCAGCCTTGGAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:27,114:141,0:0:2,0:22.4:1:31.4:1:1:0:60:34.25:1:0:0.1 0/1:206:3:2,1:43,159:202,3:0.0146:2,2:17.3:1:26.5:1:0.12198:7.30:60:6:0.0148:0.0049:1 +19 17941927 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02138;SOR=Inf;LSEQ=CCAAAGCTGCAGCGGAGGAA;RSEQ=GGCGGGGCTAAGGCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:86,2:88,0:0:1,0:21.7:1:32.9:1:1:0:59.9:43:1:0:0.3 0/1:56:4:4,0:52,0:52,4:0.0714:1,0:21:1:29.8:1:1:0:60:8:0.0741:0:1 +19 17941937 . A G 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AGCGGAGGAAGGGCGGGGCT;RSEQ=AGGCTGGGGAGCAAAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:108,2:110,0:0:1,0:22:1:28.6:1:1:0:60:54:1:0:0.2 0/1:72:11:11,0:60,1:61,11:0.1528:1,0:24.2:1:32.3:1:1:0:60:22:0.1594:0:1.6 +19 17941998 . G T 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.04705;SOR=Inf;LSEQ=CTGGGGGCGGAGCCAGAGCC;RSEQ=TGGGGAATAGGGGCGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:266,120:386,0:0:2,0:24.5:1:30.4:1:1:0:60:772:1:0:0.3 0/1:338:4:1,3:221,113:334,4:0.0118:2,2:11.8:1:23.3:1:0.11873:5.83534:60:3:0.0091:0:1.5 +19 17942005 . A G 213 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGAGCCAGAGCCGTGGGGA;RSEQ=TAGGGGCGGAGCCTAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:0:0,0:289,147:436,0:0:2,0:24.3:1:29.8:1:1:0:60:28.067:0.9976:0:0.3 0/1:376:121:79,42:159,95:254,121:0.3218:2,2:25.6:1:30.8:1:0.64747:1.12:60:59.5:0.3278:0:1.3 +19 17942180 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01915;SOR=Inf;LSEQ=GCGGCCAGGTCGCGGTGCAC;RSEQ=CAGCGGCGGGAGCCCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:0:0,0:172,326:498,0:0:2,0:25.2:1:31:1:1:0:60:32.2:1:0:0.2 0/1:415:5:3,2:144,266:410,5:0.012:2,2:14.6:1:26.4:1:0.35147:2.76:60:10:0.0124:0:1.2 +19 17942298 . C G 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57005;SOR=2.86512;LSEQ=CTGGCACCCCAACCCAGACC;RSEQ=CAACTATAACCCTACCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:1,0:26,62:88,1:0.0112:2,0:40:0:9:0:0.30337:0:60:0:0:0:3 0/1:63:2:1,1:21,40:61,2:0.0317:2,2:18:1:29:1:1:1.88:60:4:0.0317:0:1 +19 17942370 . T C 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTAAGCCAACCCCACCAC;RSEQ=CCCGAGACCTGGACCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:82,22:104,0:0:2,0:25.5:1:31.8:1:1:0:60:208:1:0:0 0/1:104:26:22,4:66,12:78,26:0.25:2,2:24.9:1:29.2:1:1:1:60:25:0.2475:0:1 +19 17942411 . C T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25268;SOR=Inf;LSEQ=CCACTCCTCAGCCTTCACCG;RSEQ=GACCTCCAAGCAGACCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:145,61:206,0:0:2,0:23:1:31.1:1:1:0:60:40.2:1:0:0.1 0/1:240:3:0,3:165,72:237,3:0.0125:2,0:11.3:1:24.7:1:0.02968:0:60:6:0.0128:0:1 +19 17942412 . G A 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CACTCCTCAGCCTTCACCGC;RSEQ=ACCTCCAAGCAGACCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:151,65:216,0:0:2,0:22.4:1:30:1:1:0:60:53:1:0:0.1 0/1:246:17:11,6:158,71:229,17:0.0691:2,2:24.9:1:29.9:1:0.78754:1.21282:60:34:0.0702:0:1.1 +19 17942451 . A G 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04033;SOR=7.30846;LSEQ=GCCCAGGCCGTGCCAGCTGA;RSEQ=TCCCCACAAGTCCCGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:1:1,0:216,162:378,1:0.0026:2,0:5:0:35:0:1:0:60:2:0.0026:0:0 0/1:421:8:5,3:222,191:413,8:0.019:2,2:18.4:1:32.8:1:0.73075:1.43:60:16:0.0193:0:1.5 +19 17942604 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01221;SOR=Inf;LSEQ=TGACCAGCCGCAGGCTCTGG;RSEQ=GGCCTGGAGAAGGCAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:120,183:303,0:0:2,0:25.7:1:30.4:1:1:0:60:49.5:1:0:0.1 0/1:283:6:1,5:104,173:277,6:0.0212:2,2:21:1:29.5:1:0.41751:2.99625:60:12:0.0217:0:1.2 +19 17942609 . T C 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24952;SOR=0;LSEQ=AGCCGCAGGCTCTGGCGGCC;RSEQ=GGAGAAGGCAGGATCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:1,2:113,175:288,3:0.0103:2,2:28:1:24.3:1:1:1.29032:60:2:0.007:0:1.3 0/0:272:0:0,0:101,171:272,0:0:2,0:25.6:1:29.5:1:1:0:60:67:1:0:0.2 +19 17942637 . GC G 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49956;SOR=0;LSEQ=GCAGGATCTGTCACAGCAGG;RSEQ=CCAGCCCTGCTCGTCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:60,138:198,2:0.01:2,2:7.5:1:31.5:1:0.51804:2.29:60:4:0.0101:0.005:0 0/0:185:0:0,0:52,133:185,0:0:2,0:24:1:30.3:1:1:0:60:36:1:0:0.2 +19 17943383 . G A 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.49703;LSEQ=AAATCACTGTGCAGTGCTTT;RSEQ=AGGATCTGAATCTCCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:981:1:1,0:506,473:979,1:0.001:2,0:1:0:25:0:1:0:60:2:0.001:0:1 0/1:960:29:14,15:476,452:928,29:0.0302:2,2:21.5:1:28.3:1:0.85099:1.12818:60:28:0.0295:0:1.3 +19 17943771 . G A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0908;SOR=Inf;LSEQ=CATGGGCAGTGGTAAGCAGC;RSEQ=CCTCTCATCCTGGGCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:59,196:255,0:0:2,0:24.2:1:31.3:1:1:0:60:62.75:0.996:0:0.1 0/1:210:3:2,1:54,153:207,3:0.0143:2,2:6:1:26.3:1:0.17409:5.61:60:6:0.0145:0:1.7 +19 17943897 . G A 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGTGGAGACTGGAAAAA;RSEQ=GTGTCTCCCACTCTGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:0,26:26,2:0.0714:1,0:18:1:34:0:1:0:47.5:4:0.08:0:1 0/0:10:0:0,0:0,10:10,0:0:0,0:15.3:1:29.2:1:1:0:57.4:9:1:0:0.5 +19 17945471 . G A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGCACTGTTGAATCAGCAG;RSEQ=GCCAGCTCTGTCCACTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:649:0:0,0:291,356:647,0:0:2,0:25:1:30.8:1:1:0:60:34.944:0.9984:0:0.2 0/1:684:27:13,14:292,365:657,27:0.0395:2,2:20.2:1:27.4:1:0.69885:1.16:60:26:0.0392:0:1.1 +19 17945546 . G A 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19355;SOR=4.52163;LSEQ=AGTTTCTGAGGGTGAGAGGA;RSEQ=CAGTCGGTAATCCCCAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:1:1,0:171,222:393,1:0.0025:2,0:1:0:29:0:0.43655:0:60:2:0.0026:0:1 0/1:351:4:3,1:163,184:347,4:0.0114:2,2:13.3:1:27.8:1:0.34784:3.38:60:8:0.0116:0:1.3 +19 17945636 . C T 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12401;SOR=5.93216;LSEQ=TCAAAGTGGGGGTTCGGAGA;RSEQ=CGATGCCGGGTGAGGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:1:0,1:321,267:588,1:0.0017:2,0:1:0:26:0:0.45501:0:60:2:0.0017:0:1 0/1:600:6:2,4:343,251:594,6:0.01:2,2:17.8:1:27.3:1:0.40952:2.72852:60:12:0.0101:0:1 +19 17946054 . G A 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGACACAGGAAAATGCCC;RSEQ=GGAGGGTTTGATGAATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:53,234:287,0:0:2,0:23.4:1:30.7:1:1:0:59.9:46.833:1:0:0.1 0/1:242:39:9,30:55,148:203,39:0.1612:2,2:25.4:1:29.6:1:0.69452:1.23772:60:38:0.159:0:1.2 +19 17946206 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTACACTGACCTGGCTAT;RSEQ=TCCCTCCCCTTCTCAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:2,19:21,2:0.087:2,2:20:1:29:1:0.24901:7.96:60:4:0.087:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:25.7:1:29.5:1:1:0:60:5:1:0:0.5 +19 17946662 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.62301;SOR=2.01777;LSEQ=TGCATACTACAGAGCCCACT;RSEQ=CCAATTCCTCTTCCACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:156,33:189,1:0.0053:2,0:1:0:25:0:0.17895:0:60:2:0.0054:0:1 0/1:189:2:1,1:149,38:187,2:0.0106:2,2:10.5:1:28.5:1:0.37099:3.88342:60:4:0.0108:0:1 +19 17946900 . C A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28009;SOR=2.59226;LSEQ=GGCGGGGTTGGGAGACTGAA;RSEQ=TGCACTTGTGTTGAGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:2:2,0:82,215:297,2:0.0067:2,0:4.5:1:20:1:0.07825:0:60:1:0.0036:0:1.5 0/1:291:5:4,1:75,211:286,5:0.0172:2,2:11.8:1:21.2:1:0.0203:11.15:60:1.5:0.0109:0:2.6 +19 17947194 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGCCTCCCGGGTTCAAG;RSEQ=GATTCTCCTGTCTCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:33:1:31.5:1:1:0:43.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 17947911 . T G 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.77185;SOR=1.36225;LSEQ=AGACTTGGGTGAGGCAGGGG;RSEQ=GGGGTGGGTGGGTGGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:5:0,5:215,3:218,5:0.022:1,0:6.6:1:24.4:1:0:0:58.2:4:0.019:0:3.8 0/1:235:7:2,5:222,4:226,7:0.0298:1,2:8:1:22.9:1:0:121.76155:60:2.5:0.0233:0:3.1 +19 17947916 . T G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18532;SOR=1.91526;LSEQ=TGGGTGAGGCAGGGGTGGGG;RSEQ=GGGTGGGTGGGGGGCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:7:2,5:224,7:231,7:0.0292:1,2:16.9:1:24.4:1:0:73.53464:60:2.5:0.0224:0:3.3 0/1:257:14:1,13:235,6:241,14:0.0545:1,1:9.1:1:25.4:1:0:447.72693:60:6:0.049:0:3.3 +19 17947920 . T G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08582;SOR=1.88554;LSEQ=TGAGGCAGGGGTGGGGTGGG;RSEQ=GGGTGGGGGGCTCTCACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:12:1,11:238,14:252,12:0.0455:2,2:11.5:1:23.3:1:0:176.16842:59.3:3:0.0364:0:2.8 0/1:291:24:2,22:253,13:266,24:0.0825:1,2:8.6:1:25.9:1:0:201.63477:60:11:0.08:0:2.8 +19 17947924 . T G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.03857;SOR=1.91123;LSEQ=GCAGGGGTGGGGTGGGTGGG;RSEQ=GGGGGGCTCTCACTGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:17:0,17:253,20:273,17:0.0584:2,1:7.2:1:23.5:1:0:0:60:3.25:0.0474:0:2 0/1:311:33:2,31:260,16:276,33:0.1061:2,2:9.3:1:20.6:1:0:239.3067:59.4:1.75:0.0732:0:2.4 +19 17948131 . CT C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.28123;SOR=0;LSEQ=AACACCTGGCCACAGGTCAC;RSEQ=TTGGCCCTGGAGTCTGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:1,2:3,130:133,3:0.0221:1,2:15.7:1:32.3:1:0.08628:19.85:60:6:0.0224:0.0074:0 0/0:88:0:0,0:1,87:88,0:0:1,0:24.8:1:30.1:1:1:0:60:176:1:0:0.1 +19 17948732 . T C 218 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCAAAAGTCTGGTCCACAT;RSEQ=GCTCTCACCTCCATGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:456,264:720,0:0:2,0:25.8:1:30.6:1:1:0:60:59:1:0:0.1 0/1:729:160:90,70:347,222:569,160:0.2195:2,2:25.4:1:29.8:1:0.31519:1.21538:60:159:0.2214:0:1.1 +19 17950172 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14626;SOR=Inf;LSEQ=ACAAATCACCTTTTCTTCCC;RSEQ=AACCCACCTTGACCTGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:172,134:306,0:0:2,0:24.4:1:30.5:1:1:0:59.9:42.714:1:0:0.1 0/1:190:2:2,0:102,86:188,2:0.0105:2,0:9:1:31.5:1:0.50187:0:60:4:0.0108:0:1 +19 17950457 . C A 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05257;SOR=Inf;LSEQ=GATGAGGCAGCCCTTATAAT;RSEQ=AGGACCAAGGGGGTTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:106,245:351,0:0:2,0:24.5:1:31.9:1:1:0:59.9:69.2:1:0:0.1 0/1:324:4:3,1:108,212:320,4:0.0123:2,2:21.3:1:22.3:1:0.11811:5.86:60:3:0.0094:0:1.8 +19 17950500 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22325;SOR=Inf;LSEQ=GAAGAGTGGCCCCTGAGTGG;RSEQ=ACTGAGCGACAGACACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:29,158:187,0:0:2,0:28.9:1:32.2:1:1:0:59.3:186:1:0:0.3 0/1:168:2:1,1:33,133:166,2:0.0119:2,2:17:0:30:1:0.36477:3.99:60:4:0.012:0:1.5 +19 17950514 . C A 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.34175;SOR=3.47779;LSEQ=GAGTGGGACTGAGCGACAGA;RSEQ=ACTCTCCTTCTCAGTCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:1:0,1:20,129:149,1:0.0067:2,0:21:0:14:0:1:0:60:0:0:0:1 0/1:131:3:1,2:23,105:128,3:0.0229:2,2:25.7:1:24.3:1:0.45791:2.26:50.7:2:0.0171:0:3 +19 17950520 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50286;SOR=0;LSEQ=GACTGAGCGACAGACACTCT;RSEQ=CTTCTCAGTCCTTCTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:0,2:18,120:138,2:0.0143:2,0:30:1:31.5:1:1:0:60:4:0.0154:0:1 0/0:115:0:0,0:18,97:115,0:0:2,0:24.3:1:29.7:1:1:0:59.3:11.778:1:0:0.7 +19 17950528 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49899;SOR=0;LSEQ=GACAGACACTCTCCTTCTCA;RSEQ=TCCTTCTTCCTTTTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:11,96:107,2:0.0182:2,2:21:1:32.5:1:0.20897:8.40:60:4:0.019:0:1 0/0:99:0:0,0:16,83:99,0:0:2,0:20.7:1:30.8:1:1:0:59.2:18.8:1:0:0.7 +19 17951178 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1904;SOR=0.8322;LSEQ=GGAAGGTGAGAGGGAATGGG;RSEQ=AGGAGTCAGAGATAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:158:52,106:115,180:295,158:0.348:2,2:23.9:1:30.5:1:0.2208:1.30159:60:78:0.349:0:1.1 0/1:504:155:55,100:128,221:349,155:0.3075:2,2:25.1:1:29.1:1:0.8412:1.05297:60:76.5:0.3066:0:1.1 +19 17951229 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49882;SOR=Inf;LSEQ=CCTGGGCTCAAATTCAGGTA;RSEQ=CTCTGTAGCCCTGGGATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:13,139:152,0:0:2,0:26:1:31.7:1:1:0:60:151:1:0:0.3 0/1:162:2:1,1:16,144:160,2:0.0123:2,2:35:1:27:1:0.19945:8.76:60:4:0.0123:0:1 +19 17951234 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24015;SOR=Inf;LSEQ=GCTCAAATTCAGGTACCTCT;RSEQ=TAGCCCTGGGATCCTTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:10,131:141,0:0:2,0:26.2:1:32.3:1:1:0:60:46:1:0:0.3 0/1:136:2:1,1:11,123:134,2:0.0147:2,2:11:1:26.5:1:0.16928:10.75:60:4:0.0147:0:1 +19 17952156 . C T 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.32492;SOR=3.83879;LSEQ=CATAGAGAAGGGGAGGGGCC;RSEQ=TGAGTGGCCACAGAGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:1,0:143,65:208,1:0.0048:2,0:47:0:17:0:1:0:54:0:0:0:7 0/1:165:3:1,2:118,44:162,3:0.0182:2,2:10.3:1:24:1:0.18819:5.2994:60:6:0.0186:0:2.3 +19 17952185 . G T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45272;SOR=0.86438;LSEQ=CACAGAGGCCGGGAATGGGG;RSEQ=ACAGGTCCTTACGTGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:83:57,26:140,91:231,83:0.2643:2,2:24.3:1:29.2:1:0.23364:1.42:60:40.5:0.2656:0:1.2 0/1:287:68:45,23:135,84:219,68:0.2369:2,2:25.6:1:28.6:1:0.56671:1.22:60:136:0.2411:0:1.2 +19 17952209 . G A 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01552;SOR=Inf;LSEQ=GGTCCTTACGTGATGGGGCC;RSEQ=TGGCACTGCTCGGCCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:216,150:366,0:0:2,0:25.8:1:30.7:1:1:0:60:44.75:0.9972:0:0.4 0/1:391:7:3,4:220,164:384,7:0.0179:2,2:29.9:1:28.9:1:0.46896:1.78588:60:14:0.0182:0:1.6 +19 17952607 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12427;SOR=Inf;LSEQ=AGTACCGAAGTGGGGGCCCA;RSEQ=CTGGACCCCGCCAAACCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:74,165:239,0:0:2,0:25.3:1:32.2:1:1:0:60:58.75:1:0:0.5 0/1:255:4:1,3:85,166:251,4:0.0157:2,2:13:1:28.5:1:1:1.53376:60:8:0.0162:0:1 +19 17952609 . T G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01215;LSEQ=TACCGAAGTGGGGGCCCAGC;RSEQ=GGACCCCGCCAAACCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:78:25,53:46,106:152,78:0.3362:2,2:25.3:1:30.8:1:0.88025:1.09:60:156:0.3436:0:1.1 0/1:239:81:26,55:52,106:158,81:0.3389:2,2:26.4:1:29.5:1:1:1.03758:60:39.5:0.3362:0:1.1 +19 17952639 . AC A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50263;SOR=0;LSEQ=CAAACCACGCCCATGAACCC;RSEQ=CCCCAAGCCACACCATCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:22,120:142,2:0.0139:2,2:15.5:1:30.4:1:0.29487:5.36:60:4:0.0141:0.0069:0 0/0:119:0:0,0:17,102:119,0:0:2,0:21.8:1:30.5:1:1:0:60:118:1:0:0.5 +19 17952647 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18422;SOR=Inf;LSEQ=GCCCATGAACCCACCCCCAA;RSEQ=CCACACCATCCACTCCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:14,113:127,0:0:2,0:22.4:1:32.1:1:1:0:60:41.333:1:0:0.4 0/1:96:2:1,1:10,84:94,2:0.0208:2,2:22:1:25.5:1:0.21711:8.06:60:4:0.0217:0:1 +19 17953044 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50546;SOR=0;LSEQ=TCTTTCGTTTTGGCTCCGCC;RSEQ=CACATCCCCTACCACTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:112,8:120,2:0.0164:2,0:20:1:33:1:1:0:60:4:0.0165:0:1 0/0:95:0:0,0:84,11:95,0:0:2,0:23.7:1:30.2:1:1:0:60:94:1:0:0.3 +19 17953067 . C A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19909;SOR=Inf;LSEQ=CATCCCCTACCACTCTCCGG;RSEQ=CCCTCCCCGAGCCCCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:163,30:193,0:0:2,0:23.5:1:31.8:1:1:0:59.9:37.6:1:0:0.2 0/1:156:2:1,1:112,41:153,2:0.0128:2,2:23:0:27:1:0.46979:2.71101:60:4:0.0132:0:2 +19 17953088 . C T 119 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.75491;LSEQ=CCCTCCCCGAGCCCCGCCCC;RSEQ=ACGTTGGCCCCGCCCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:1:0,1:198,68:266,1:0.0037:2,0:24:0:9:0:0.25843:0:60:0:0:0:2 0/1:234:20:10,10:138,76:214,20:0.0855:2,2:22.6:1:27.6:1:0.22873:1.81099:60:9:0.0779:0:1.8 +19 17953254 . C T 88 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58169;SOR=1.50612;LSEQ=GCGGCCCCGGCTGGATCCAG;RSEQ=CGCTCCAGGTCCATGATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:618:5:2,3:304,308:612,5:0.0081:2,2:24.4:1:27.4:1:1:1.47958:60:4:0.0066:0:1.6 0/1:659:8:4,4:337,313:650,8:0.0121:2,2:27.4:1:29.6:1:1:1.07653:60:16:0.0123:0:1.4 +19 17953355 . T G 87 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03878;SOR=7.73353;LSEQ=CACCGTCCTCCGAATACGCC;RSEQ=CCGCGTCACGAAGCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:1:1,0:277,325:602,1:0.0017:2,0:3:0:10:0:0.46103:0:33:0:0:0:3 0/1:631:8:2,6:310,313:623,8:0.0127:2,2:22.1:1:29.3:1:0.28617:2.96674:60:7:0.0113:0:1.3 +19 17953472 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.65881;LSEQ=CAGCGTCGGGAGGGGTCCCC;RSEQ=CGGGGACACACACAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:1:1,0:17,133:150,1:0.0065:2,0:1:0:25:0:0.11921:0:60:2:0.0068:0:1 0/1:185:2:1,1:38,145:183,2:0.0108:2,2:34.5:1:27.5:1:0.37808:3.78:60:4:0.0109:0:1 +19 17953864 . G A 85 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39595;SOR=1.78255;LSEQ=CTTCAGCAGCTCTCCCGGCC;RSEQ=CTGGGCCTGCTCTCGCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:4:3,1:350,299:649,4:0.0061:2,2:13:1:28.5:1:0.6288:2.56:60:8:0.0062:0:1 0/1:737:8:5,3:390,336:726,8:0.0109:2,2:23.5:1:28.5:1:0.73146:1.44:60:7:0.0097:0:1 +19 17953950 . G C 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTTGAGACTGAGGCCCACG;RSEQ=GGAGGCGCCCACTCACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:35:11,24:203,317:520,35:0.0631:2,2:24:1:30.1:1:0.47356:1.39638:60:34:0.0622:0:1.1 0/0:585:0:0,0:251,333:584,0:0:2,0:29:0:12:0:1:0:60:0:0:0:5 +19 17954008 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3615;SOR=3.17264;LSEQ=GGCCGCCACAGGGAGCATCA;RSEQ=CTGAGGCCACCCAACTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:1:1,0:73,175:248,1:0.004:2,0:1:0:29:0:0.29719:0:60:2:0.0041:0:1 0/1:237:3:2,1:73,160:233,3:0.0127:2,2:11:1:27:1:0.23778:4.35:60:6:0.013:0:1 +19 17954107 . G T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.34567;SOR=3.41306;LSEQ=CCACAGGGAGGGTCAGACGA;RSEQ=GCCCCACCTGATTGCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:0,1:171,56:227,1:0.0044:2,0:1:0:25:0:0.25:0:60:2:0.0045:0:1 0/1:202:3:2,1:146,52:198,3:0.0149:2,2:33.7:1:28:1:1:1.4013:60:6:0.0155:0:1.3 +19 17954485 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21582;SOR=Inf;LSEQ=TGTTTCCTCATCTGAGAAAT;RSEQ=GGTAGTGACCATACCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:76,26:102,0:0:2,0:24.8:1:32.6:1:1:0:59.9:204:1:0:0.1 0/1:89:2:2,0:74,13:87,2:0.0225:2,0:19:1:26:0:1:0:60:4:0.0225:0:1 +19 17954947 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16663;SOR=1.47886;LSEQ=TCCCCCAAAGCCCCAGCTCC;RSEQ=ATGCTGACTTCTGCAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:45:35,10:84,5:89,45:0.3333:2,2:24.2:1:30.8:1:0.00728:4.73662:59:90:0.3409:0:2.7 0/1:94:40:36,4:46,8:54,40:0.4255:2,2:20.8:1:30.2:1:0.54838:1.56:60:80:0.4348:0:3 +19 17955001 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.5467;LSEQ=CAATCTTGGCCCCACACAGC;RSEQ=CCATCCTTCCCTCTGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:71:54,17:157,58:215,71:0.2483:2,2:25.2:1:31.1:1:0.64465:1.17:59.6:22.667:0.242:0:3.4 0/1:269:123:83,40:99,46:145,123:0.4572:2,2:24:1:29.3:1:0.89633:1.03707:59.9:23.6:0.4521:0:3.3 +19 17955003 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.6192;LSEQ=ATCTTGGCCCCACACAGCCC;RSEQ=ATCCTTCCCTCTGGCCCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:73:55,18:161,61:222,73:0.2475:2,2:24.9:1:31:1:0.76077:1.16:59.6:35.5:0.2465:0:3.3 0/1:285:132:88,44:102,51:153,132:0.4632:2,2:23.2:1:29:1:1:1:59.9:65:0.4659:0:3.2 +19 17955021 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.31683;LSEQ=CCCATCCTTCCCTCTGGCCC;RSEQ=ATCCACTAGGGATGCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:108:71,37:181,98:279,108:0.2791:2,2:21.4:1:30.4:1:0.90581:1.04:59.7:107:0.2801:0:2.5 0/1:427:202:126,76:133,92:225,202:0.4731:2,2:23.3:1:29.3:1:0.55175:1.15:59.8:66.333:0.4738:0:2.4 +19 18266621 . C A 25 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50106;SOR=0;LSEQ=GGACCCTCCCAGCCCTGCTT;RSEQ=AACCAATGGGGCCAGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:147,52:199,2:0.01:2,2:6.5:1:25.5:1:0.45881:2.80964:60:4:0.0101:0:1 0/0:175:0:0,0:126,49:175,0:0:2,0:22.4:1:30.5:1:1:0:60:350:1:0:0.1 +19 18266640 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10877;SOR=Inf;LSEQ=TCAACCAATGGGGCCAGTGG;RSEQ=GCTCCAAGCAGCCACCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:176,101:277,0:0:2,0:24.4:1:30.7:1:1:0:60:33.625:1:0:0.2 0/1:254:3:1,2:160,91:251,3:0.0118:2,2:32:1:27.7:1:0.55619:3.49832:60:6:0.012:0:1 +19 18266694 . C T 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22164;SOR=4.50006;LSEQ=CCCCACTCACGCGGCCATGG;RSEQ=GGGCCCTGAGGGCTTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:1:0,1:231,207:438,1:0.0023:2,0:1:0:27:0:0.4738:0:60:2:0.0023:0:1 0/1:491:5:2,3:257,229:486,5:0.0102:2,2:22.2:1:27:1:0.67083:1.68162:60:4:0.0082:0:1.6 +19 18266861 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06176;SOR=Inf;LSEQ=CACAGAGCGTGGGCTGGATG;RSEQ=CCGGCCTCAACGAGCGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:192,225:417,0:0:2,0:25.6:1:31.6:1:1:0:60:51.125:1:0:0.1 0/1:420:5:1,4:191,224:415,5:0.0119:2,2:11.6:1:26.2:1:0.38124:3.40205:60:10:0.0122:0:1.2 +19 18266882 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0294;SOR=0;LSEQ=CCGGCCTCAACGAGCGCACA;RSEQ=GGCAGCGAGGTGACTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:5:1,4:186,257:443,5:0.0111:2,2:9.6:1:25.4:1:0.40613:2.88904:60:4:0.009:0:1 0/0:458:0:0,0:204,254:458,0:0:2,0:25.4:1:30:1:1:0:59.9:90.6:1:0:0.3 +19 18266964 . GC G 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.12278;SOR=0;LSEQ=GCCCGGCCCTCGCCCACGGG;RSEQ=CCCCGCCCACTGCCCGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:4:2,2:43,105:148,4:0.0263:2,2:18:1:34:1:0.58212:2.43:60:8:0.0272:0:0.5 0/0:146:0:0,0:59,87:146,0:0:2,0:20.2:1:29.8:1:1:0:60:28.2:1:0:0.3 +19 18266977 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49765;SOR=0;LSEQ=CCACGGGGCCCCCGCCCACT;RSEQ=CCCGCCAGGCCCCGTGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:33,72:105,2:0.0187:2,2:9:1:30:1:0.53659:2.16:60:4:0.0192:0:1.5 0/0:107:0:0,0:38,67:105,0:0:2,0:20.2:1:30.8:1:1:0:60:34:0.9808:0:0.3 +19 18266983 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50258;SOR=Inf;LSEQ=GGCCCCCGCCCACTGCCCGC;RSEQ=AGGCCCCGTGATGGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:22,55:77,0:0:2,0:20.5:1:31.9:1:1:0:60:37.5:1:0:0.2 0/1:95:2:1,1:36,57:93,2:0.0211:2,2:15.5:1:30.5:1:1:1.58:60:4:0.0215:0:1 +19 18271576 . C T 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=TGACCAGGCCACTGCATGTG;RSEQ=TGTGCCCTCTCCCAGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:17:12,5:37,13:50,17:0.2537:2,2:32.5:1:31.3:1:0.76166:1.1828:60:34:0.2615:0:1 0/0:45:0:0,0:37,8:45,0:0:2,0:21.3:1:31.7:1:1:0:60:90:1:0:0.2 +19 18271645 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49863;SOR=Inf;LSEQ=CTGGGCAGCAAAGGGAGACT;RSEQ=CAGGGGGGTTGAGCGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:147,35:182,0:0:2,0:24.5:1:32.4:1:1:0:60:35.4:0.9944:0:0.1 0/1:183:2:1,1:132,49:181,2:0.0109:2,2:16.5:1:26.5:1:0.47289:2.67689:60:4:0.011:0:1 +19 18271987 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20708;SOR=Inf;LSEQ=CTCGGCCGAGGCGCGCCGGG;RSEQ=CCTGCGGGGTGAGCCTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:48,141:189,0:0:2,0:22.8:1:31.5:1:1:0:59.8:30.5:0.9892:0:0.1 0/1:160:2:1,1:38,120:158,2:0.0125:2,2:16:0:31:1:0.42925:3.13:60:4:0.0129:0:1.5 +19 18271988 . C A 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21023;SOR=Inf;LSEQ=TCGGCCGAGGCGCGCCGGGC;RSEQ=CTGCGGGGTGAGCCTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:45,141:186,0:0:2,0:22.6:1:31.7:1:1:0:59.8:185:1:0:0.1 0/1:158:2:1,1:37,119:156,2:0.0127:2,2:5:0:30.5:1:0.42433:3.19:60:4:0.0132:0:1.5 +19 18272037 . C T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.21639;SOR=Inf;LSEQ=GGGGAAGGAGGGGGCTGTAG;RSEQ=GGGTGGGAGGGCCCAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:39,57:96,0:0:2,0:22:1:30.5:1:1:0:60:31:1:0:0.1 0/1:84:2:1,1:31,51:82,2:0.0238:2,2:6:0:31:0:1:1.63:60:4:0.0244:0:1.5 +19 18272107 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49802;SOR=Inf;LSEQ=AGAGGCCGCGGGGCCCGTGG;RSEQ=GCCGGCGCTGGAGCCACCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:39,51:90,0:0:2,0:27.1:1:30.9:1:1:0:60:44:1:0:0.2 0/1:97:2:1,1:44,51:95,2:0.0206:2,2:27:1:28:1:1:1.16:60:4:0.0217:0:1 +19 18272147 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17673;SOR=0;LSEQ=ACGCTGCCGCTGCACCGCGC;RSEQ=CTCACGCTGCGCTTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:20,30:50,2:0.0385:2,2:39.5:1:28:1:1:1.49:60:4:0.0392:0:1.5 0/0:71:0:0,0:31,40:71,0:0:2,0:21.4:1:31:1:1:0:60:70:1:0:0.7 +19 18272190 . A C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00118;SOR=Inf;LSEQ=AGCACCTGGGCCGCGTGGCC;RSEQ=GCCGCGCCCCGGCCCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:6,7:3,3:6,13:0.6842:2,2:26.2:1:31:1:1:1.15722:59.8:26:0.6842:0:1.4 1/1:34:34:17,17:0,0:0,34:1:0,2:20.5:1:30.1:1:1:0:59.8:68:1:0:1.4 +19 18272252 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.51304;SOR=Inf;LSEQ=GCCACCTTTGGGCCGCTGCT;RSEQ=CTGCGCGCGCCGCCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:18,0:0:2,0:26.3:1:33.5:1:1:0:60:36:1:0:0.4 0/1:28:2:1,1:13,13:26,2:0.0714:2,2:35.5:1:30:1:1:1:60:4:0.0769:0:1 +19 18272683 . A AC 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.50347;SOR=0;LSEQ=GCACATACTGTCTCGTATAT;RSEQ=CCCCCAGGCGTGCAAGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:2,0:158,22:180,2:0.011:2,0:21:1:31.5:1:1:0:60:4:0.0112:0:0 0/0:149:0:0,0:133,16:149,0:0:2,0:22.1:1:27.7:1:1:0:60:148:1:0:0.1 +19 18272695 . G T 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20288;SOR=Inf;LSEQ=TCGTATATACCCCCAGGCGT;RSEQ=CAAGCGCACGCACAATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:197,31:228,0:0:2,0:23.3:1:31.7:1:1:0:59.9:24.333:0.991:0:0.1 0/1:189:2:2,0:159,28:187,2:0.0106:2,0:5.5:1:31.5:1:1:0:60:4:0.0109:0:1 +19 18273013 . G A 214 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=87.90917;LSEQ=TTGTTTTCCTGTCCCCCAGC;RSEQ=CTGCCGCCTAAACCCCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:876:2:2,0:443,429:872,2:0.0023:2,0:11.5:1:28.5:1:0.4996:0:60:4:0.0023:0:3.5 0/1:978:164:81,83:407,406:813,164:0.1677:2,2:23.8:1:29.1:1:0.93181:1.02719:60:40:0.1668:0:1.8 +19 18273047 . T C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.14516;LSEQ=CCCCCAAGGCAAAGCCGGCC;RSEQ=CCACAGTCCTGGCCAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:820:816:412,404:0,2:2,816:0.9951:0,2:25.7:1:31:1:0.24604:0:59.9:50:0.9975:0:1.2 1/1:887:858:425,433:15,13:28,858:0.9673:2,2:25.8:1:30.1:1:0.70493:1.17535:59.9:46.667:0.9677:0:1.3 +19 18273410 . A G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0059;SOR=0;LSEQ=ATGTGCGGTTTCAAGAATGG;RSEQ=GGGCCAGGCACGGTGGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:98:5,93:0,0:0,98:1:0,2:21.2:1:31.7:1:1:0:59.2:97:1:0:1.1 1/1:75:69:2,67:0,6:6,69:0.92:0,1:20.8:1:30.7:1:1:0:59.1:138:0.9324:0:1 +19 18273537 . AT A 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.72822;LSEQ=AACCCCGTCTCTACTAAAAA;RSEQ=TAAAAAAAAAAATTAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:3,0:7,6:13,3:0.1579:2,0:16.7:1:32.7:1:0.25:0:44.3:6:0.1667:0.0526:0.3 0/1:4:1:0,1:2,1:3,1:0.25:2,0:34:0:31:0:1:0:42:2:0.25:0:0 +19 18273539 . T A 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=1.14655;LSEQ=CCCCGTCTCTACTAAAAAAT;RSEQ=AAAAAAAAAAATTAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:7,6:3,0:3,13:0.7222:0,2:27:1:29.8:1:0.25:0:42.6:26:0.8125:0:1.3 1/0:4:3:2,1:0,1:1,3:0.75:0,2:15:1:27.3:1:1:0:37.3:6:0.75:0:1 +19 18273668 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.21127;SOR=Inf;LSEQ=CGAAATCGCACCACTGCACT;RSEQ=CAGCCTGGACAACAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:73,4:77,0:0:2,0:20.4:1:33.1:1:1:0:57.1:154:1:0:0.2 0/1:66:2:1,1:63,1:64,2:0.0303:1,2:18:1:25.5:1:0.06014:44.90018:55:4:0.0313:0:1.5 +19 18273702 . C CA 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.96199;LSEQ=AGAGCAGCAAGACTCTGTCT;RSEQ=AAAAAAAAAGGGGACAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:8:8,0:144,11:155,8:0.0491:2,0:26.5:1:32:1:1:0:55.5:16:0.0491:0:0 0/1:148:7:7,0:121,20:141,7:0.0473:2,0:21.4:1:29.3:1:0.59406:0:60:14:0.0486:0.0135:0.3 +19 18274631 . C CTAAAAACAAA 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGGGCACGACCTTGTCT;RSEQ=TAAAAACAGAAATAAGCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:26:1:30.9:1:1:0:52.5:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 18275984 . T G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTAAGGAGTTCAAGACCAG;RSEQ=CTGGCCAACATGGTGAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:31:1:1:0:47.5:4:1:0:1 +19 18276856 . T C 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGTTAGAAGAATGACACTC;RSEQ=GATAGAGGGACCAGCTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:51,2:0,0:0,53:1:0,1:23.7:1:31.2:1:1:0:60:52:1:0:1 1/1:39:39:39,0:0,0:0,39:1:0,1:24.2:1:31.3:1:1:0:60:78:1:0:1.1 +19 18277175 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22916;SOR=Inf;LSEQ=GGTGCAGTACAAGCCAGGGA;RSEQ=GGAAGGAAGCAGAAGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:33,120:153,0:0:2,0:21.1:1:31.7:1:1:0:60:152:1:0:0.4 0/1:141:2:0,2:25,114:139,2:0.0142:2,0:27:1:28:1:1:0:60:4:0.0144:0:1.5 +19 18277206 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.18458;LSEQ=AGAAGGAGGCCAGCCACTTG;RSEQ=AGGCAAAGAGTAGTCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:80:68:0,68:1,11:12,68:0.85:2,1:23.6:1:31.6:1:0.15:0:60:136:0.85:0:1 1/0:63:32:2,30:1,30:31,32:0.5079:1,2:20.8:1:31.1:1:1:1.98:60:64:0.5161:0:1.1 +19 18277820 . C G 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0028;SOR=0;LSEQ=GCCAGACATGGTGGTGCACA;RSEQ=CTGTGGTCCCAGCTACTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:11:10,1:90,0:90,11:0.1089:1,2:23.3:1:34.3:1:0.10891:0:59.3:22:0.11:0:1.1 0/0:73:0:0,0:72,1:73,0:0:1,0:26.6:1:31.8:1:1:0:60:72:1:0:0.1 +19 18279467 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24874;SOR=0;LSEQ=GGGAGGAAAAGTTGTCCAGG;RSEQ=AGCTGGGGAGCCTCGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:1,2:198,95:293,3:0.0101:2,2:8.3:1:28.7:1:0.25101:4.14647:60:6:0.0104:0:1 0/0:294:0:0,0:189,105:294,0:0:2,0:24.2:1:31.5:1:1:0:60:97:1:0:0.1 +19 18279638 . T C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03973;LSEQ=CAGGCAGAGGAGATGCTGAG;RSEQ=GGCAAGCGGGATGGCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:562:560:231,329:1,0:1,560:0.9964:0,2:25.1:1:30.8:1:0.41355:0:59.9:92.333:0.9964:0:1.1 1/1:666:611:251,360:20,35:55,611:0.9174:2,2:23.5:1:30:1:0.56741:1.22:59.9:54.545:0.9174:0:1.1 +19 18279736 . G A 51 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02369;SOR=Inf;LSEQ=CCGCAGCGGTGGGGATTCCC;RSEQ=CGTCCCTCCCAGAGCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:52,134:186,0:0:2,0:23.8:1:32.2:1:1:0:60:185:1:0:0.3 0/1:169:5:4,1:56,108:164,5:0.0296:2,2:11.4:1:22:1:0.05416:7.62:60:1.5:0.0184:0:1 +19 18279737 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21231;SOR=Inf;LSEQ=CGCAGCGGTGGGGATTCCCG;RSEQ=GTCCCTCCCAGAGCTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:52,137:189,0:0:2,0:23.1:1:31:1:1:0:60:93.5:1:0:0.3 0/1:162:2:1,1:55,105:160,2:0.0123:2,2:13:1:30:1:1:1.90:60:4:0.0126:0:1.5 +19 18279816 . A G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.06133;LSEQ=CTGGTGGGGTCATCCGGGAC;RSEQ=GGGGAGCACGCGGCCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:184:172:127,45:6,5:11,172:0.9348:2,2:22.8:1:30.2:1:0.17505:2.34:60:56.333:0.9337:0:1.1 0/1:144:67:45,22:57,19:76,67:0.4653:2,2:23.2:1:29.6:1:0.35565:1.46268:60:134:0.4653:0:1.1 +19 18279852 . C T 48 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.70808;SOR=1.58298;LSEQ=CTGGAACGGGGAAAGCTTGG;RSEQ=GGGGAGGCCAGCCTTCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:0,3:201,83:284,3:0.0105:2,0:14.7:1:22.7:1:0.02625:0:60:2:0.0071:0:1.3 0/1:243:4:0,4:160,79:239,4:0.0165:2,0:1:0:24.3:1:0.01297:0:60:8:0.0167:0:1 +19 18279861 . C T 98 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00691;SOR=0.09972;LSEQ=GGAAAGCTTGGCGGGGAGGC;RSEQ=AGCCTTCCGACTCCCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:11:6,5:221,104:325,11:0.0326:2,2:19.3:1:28.6:1:0.34471:1.7675:60:22:0.0328:0:1.2 0/0:299:1:0,1:192,106:298,1:0.0033:2,0:1:0:23:0:0.35786:0:60:2:0.0034:0:1 +19 18280044 . C T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67278;SOR=1.24412;LSEQ=CAGCACAACGACGCGCTCAC;RSEQ=GTCACCCTGGCGCACCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:10:2,8:51,174:225,10:0.0426:2,2:27.1:1:31.3:1:1:1.17165:60:20:0.0431:0:1.2 0/1:248:13:3,10:61,172:233,13:0.0524:2,2:23.5:1:29.8:1:1:1.18139:60:26:0.0535:0:1 +19 18280080 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49943;SOR=Inf;LSEQ=CCAGTGCGCGCCCCGGGCCC;RSEQ=GGCCCGCCGCCTGCCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:22,86:108,0:0:2,0:21:1:30.7:1:1:0:60:53:1:0:0.5 0/1:121:2:1,1:37,82:119,2:0.0165:2,2:38:0:31.5:1:0.53127:2.20:60:4:0.0168:0:1 +19 18280082 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24925;SOR=Inf;LSEQ=AGTGCGCGCCCCGGGCCCCG;RSEQ=CCCGCCGCCTGCCGCCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:22,79:101,0:0:2,0:20.7:1:32.9:1:1:0:60:100:1:0:0.5 0/1:114:3:2,1:36,75:111,3:0.0263:2,2:10.3:1:26.3:1:0.25727:4.11:60:6:0.0265:0:1 +19 18280089 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.65567;LSEQ=GCCCCGGGCCCCGGCCCGCC;RSEQ=CCTGCCGCCCGCTGAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:1:0,1:21,62:83,1:0.0119:2,0:25:0:32:0:1:0:60:2:0.012:0:2 0/1:102:2:1,1:32,68:100,2:0.0196:2,2:11.5:1:28:1:0.54455:2.11:60:4:0.02:0:1 +19 18280096 . G A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.05158;LSEQ=GCCCCGGCCCGCCGCCTGCC;RSEQ=CCCGCTGAGCACCGAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:23:7,16:14,35:49,23:0.3194:2,2:19.3:1:29.9:1:1:1.09:60:22:0.3099:0:1.5 0/1:86:2:0,2:30,54:84,2:0.0233:2,0:11:1:30.5:1:0.54036:0:60:4:0.0238:0:1 +19 18280110 . G A 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03968;SOR=Inf;LSEQ=CCTGCCGCCCGCTGAGCACC;RSEQ=AGGACCCGCCCCAAGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:13,27:40,0:0:2,0:14.5:1:31.6:1:1:0:60:39:1:0:0.9 0/1:60:7:3,4:23,30:53,7:0.1167:2,2:23.3:1:32:1:1:1.02185:60:14:0.1273:0:1.3 +19 18280114 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.15714;SOR=0;LSEQ=CCGCCCGCTGAGCACCGAGG;RSEQ=CCCGCCCCAAGCAGAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:10,22:32,2:0.0588:2,2:11.5:1:30.5:1:1:2.14:60:4:0.0606:0:2.5 0/0:51:0:0,0:24,27:51,0:0:2,0:18.7:1:28.4:1:1:0:60:16:1:0:0.4 +19 18280187 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GCGGGAGCCACGGACCAGAC;RSEQ=AGCCACATCCAGGGGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:13:1:28.5:1:1:0:60:8:1:0:0.8 0/1:10:2:1,1:4,4:8,2:0.2:2,2:19.5:1:27.5:1:1:1:60:4:0.2:0:1 +19 18391999 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49231;SOR=Inf;LSEQ=GGCGCTCGAGCTCGGGGGAG;RSEQ=CCAGCTTCAGCAGCCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:4,14:18,0:0:2,0:18.4:1:29.9:1:1:0:60:8:1:0:0.3 0/1:22:2:1,1:6,14:20,2:0.0909:2,2:44.5:1:28.5:1:1:2.24:60:4:0.0909:0:1 +19 18758169 . C A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21654;LSEQ=GAATGTCATCCCACCTCCCC;RSEQ=ACGGCGATTACTTTTTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:468:247:153,94:132,89:221,247:0.5278:2,2:26.2:1:29.8:1:0.63632:1.10:60:40.167:0.5274:0:1.1 0/1:442:86:52,34:218,138:356,86:0.1946:2,2:23.7:1:29.1:1:0.90246:1.03283:60:85:0.1959:0:1.1 +19 18758255 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.70659;SOR=1.05579;LSEQ=CTCCAGCCCTTTGGTTTTTT;RSEQ=CTTTTTCTGATATTTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:195:70,125:122,181:303,195:0.3916:2,2:25:1:30.4:1:0.34661:1.20318:59.9:390:0.398:0:1.1 0/1:566:229:90,139:132,202:334,229:0.4046:2,2:25.9:1:28.7:1:1:1.00923:59.9:75.333:0.405:0:1.1 +19 18758348 . AGAG A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.50312;SOR=0;LSEQ=AGAGGCCCTGGAGGAGGAAG;RSEQ=GAGGAGGAGGAAGAGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:0,75:75,2:0.026:1,0:25.5:1:28:1:1:0:60:4:0.026:0.013:0 0/0:61:0:0,0:1,60:61,0:0:1,0:22.7:1:30.5:1:1:0:60:29.5:1:0:0.1 +19 19256537 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61531;SOR=2.09831;LSEQ=TCTCTGAAGAGGCCTGGAGG;RSEQ=AGGTGGGGTCCCCACGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:1:1,0:62,16:78,1:0.0127:2,0:41:0:31:0:1:0:60:2:0.0135:0:1 0/1:76:2:1,1:54,20:74,2:0.0263:2,2:12.5:1:26.5:1:0.47895:2.65922:60:4:0.0263:0:1.5 +19 19256584 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07631;SOR=Inf;LSEQ=GTACCTGGCGAGCGCTCTGG;RSEQ=CTGGTGCCACCGGGTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:146,59:205,0:0:2,0:25:1:31.3:1:1:0:60:33.167:1:0:0.2 0/1:152:3:1,2:102,47:149,3:0.0197:2,2:28.3:1:27.7:1:0.24321:4.2943:60:6:0.0197:0:1.3 +19 19256596 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58684;SOR=2.51909;LSEQ=CGCTCTGGGCTGGTGCCACC;RSEQ=GGTGATCTCCTACCGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:1,0:158,72:230,1:0.0043:2,0:28:0:15:0:1:0:60:0:0:0:6 0/1:185:2:1,1:121,62:183,2:0.0108:2,2:18.5:1:30:1:1:1.94411:60:4:0.0109:0:1 +19 19256633 . C T 54 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05031;SOR=Inf;LSEQ=GGCCAGCCGTCGGCCAAGGG;RSEQ=AGCCGGCGCAGGGCGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:228,125:353,0:0:2,0:22.7:1:31.9:1:1:0:60:34.3:1:0:0.2 0/1:320:4:1,3:193,122:315,4:0.0125:2,2:6:1:27.3:1:0.3036:4.72317:60:8:0.0127:0:1.3 +19 19256637 . C T 60 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1108;SOR=5.44848;LSEQ=AGCCGTCGGCCAAGGGCAGC;RSEQ=GGCGCAGGGCGGGCCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:1:0,1:226,129:355,1:0.0028:2,0:1:0:26:0:0.36517:0:60:2:0.0029:0:1 0/1:331:5:1,4:199,127:326,5:0.0151:2,2:5.2:1:26.2:1:0.08222:6.235:60:10:0.0153:0:1 +19 19256768 . TG T 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06176;SOR=0;LSEQ=CGCTCAGACTTGATGCTGAC;RSEQ=GGGGGGTCGGCGGGGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:5:2,3:156,247:403,5:0.0122:2,2:30.6:1:31.6:1:1:1.06:60:10:0.0123:0:0 0/0:404:0:0,0:180,224:404,0:0:2,0:23.6:1:30.8:1:1:0:60:201:1:0:0.3 +19 19256855 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49858;SOR=0;LSEQ=CAGGGGGAAAGAGAGAGGGA;RSEQ=GCCGTGAGCTCAGCGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:2,0:38,99:137,2:0.0144:2,0:17:1:32.5:1:0.08133:0:60:4:0.0149:0:1.5 0/0:131:0:0,0:43,88:131,0:0:2,0:26:1:30.7:1:1:0:60:130:1:0:0.4 +19 19256870 . G A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.06809;SOR=0.58972;LSEQ=AGGGAGGCCGTGAGCTCAGC;RSEQ=AGGAAGGGAAGGAAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:43:17,26:27,44:71,43:0.3772:2,2:21.9:1:30.1:1:1:1.06:58.9:42:0.375:0:1.2 0/1:118:31:14,17:25,62:87,31:0.2627:2,2:19.3:1:29.2:1:0.12035:2.03:60:62:0.2627:0:1.2 +19 19257036 . C T 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25745;SOR=2.95981;LSEQ=CACCAGGGGTCAGCAGCGGC;RSEQ=GGGGCTTTGGAGGACTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:2:0,2:259,195:454,2:0.0044:2,0:1:0:26:1:0.1861:0:60:4:0.0045:0:1 0/1:388:5:2,3:212,171:383,5:0.0129:2,2:23.8:1:27.4:1:0.66053:1.85665:60:4:0.0106:0:1.6 +19 19257037 . G T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02004;SOR=Inf;LSEQ=ACCAGGGGTCAGCAGCGGCC;RSEQ=GGGCTTTGGAGGACTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:466:0:0,0:263,203:466,0:0:2,0:25.5:1:30.2:1:1:0:60:92.2:1:0:0.2 0/1:395:5:2,3:215,173:388,5:0.0127:2,2:24.2:1:29.4:1:0.66035:1.86118:60:10:0.0128:0:1.2 +19 19257152 . G T 43 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03239;SOR=Inf;LSEQ=GGGGGCCAGGGTGGGGGGCT;RSEQ=CAACAAGCCAGGGGGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:216,218:434,0:0:2,0:21.5:1:29.9:1:1:0:60:7.189:1:0:0.6 0/1:322:4:0,4:158,158:316,4:0.0124:2,0:12.3:1:21.8:1:0.12277:0:60:3:0.0105:0:2.3 +19 19257160 . C T 53 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0171;SOR=Inf;LSEQ=GGGTGGGGGGCTGCAACAAG;RSEQ=CAGGGGGCGGTGGAGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:221,229:450,0:0:2,0:22.9:1:30.1:1:1:0:60:10.25:1:0:0.6 0/1:361:5:1,4:178,177:355,5:0.0139:2,2:11:1:23.2:1:0.37154:4.00877:60:4:0.0122:0:1.8 +19 19257315 . A T 47 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18608;SOR=4.72943;LSEQ=GTGTGGAACCCCCAGAGGGC;RSEQ=GGAGTGCGGACGCTTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:1:0,1:299,130:429,1:0.0023:2,0:36:0:14:0:0.30465:0:60:0:0:0:1 0/1:367:4:1,3:238,125:363,4:0.0109:2,2:9.8:1:23.8:1:0.12407:5.68403:60:3:0.0084:0:2 +19 19257383 . G A 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGGGGGCCTCCGGGGAG;RSEQ=AAGGGGAAGCTCCCCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:856:0:0,0:495,361:856,0:0:2,0:23.6:1:31.2:1:1:0:60:37.909:1:0:0.2 0/1:899:74:38,36:449,371:820,74:0.0823:2,2:25:1:28.8:1:0.62641:1.14637:60:73:0.0831:0:1.3 +19 19257803 . G T 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02796;SOR=8.23028;LSEQ=AGCCAAGATGCACCCAAACA;RSEQ=CCCCTCAGGACCTCACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:638:1:0,1:372,265:637,1:0.0016:2,0:1:0:26:0:0.41693:0:60:2:0.0016:0:1 0/1:548:7:3,4:305,235:540,7:0.0128:2,2:31.6:1:25.4:1:0.70465:1.72871:60:2.5:0.0093:0:1.6 +19 19258018 . GAGGACCCCAGGCCAGATGGGGGTGCCAAGTCCAAGGGAGAAAATCCTGATGAGTTCAGGGGCCCAGCTCTACCTTCAGGAAGCCTTTGCTCCACCTCCCACCAGGCTCCCTACCTGCTCCTCCCCCTGCCCTAACCCTACAGGCTGGGGGAGCTTCTGTCTGGCTCTGCCTGTCCTTGACAGGTAGGTCCAGAGCCAAGACCTCTCACTTAGTGTAGAGTTGGCACTGAGGGGGCTGCACAGAGTGTTTGATGAATCAAAGATGAAATGAAGGA G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.02206;SOR=0.67792;LSEQ=GGTAGAGAAGGGATGGGTCA;RSEQ=AGGAACTGTTTGCCTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:132:35,97:58,205:263,132:0.3333:2,2:26.8:1:32.9:1:0.37888:1.27:57:264:0.3385:0.0152:0.1 0/1:328:83:22,61:73,171:244,83:0.253:2,2:26.7:1:30.8:1:0.57915:1.18306:56.9:82:0.2547:0.0152:0.2 +19 19258656 . G A 206 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=73.96215;LSEQ=CAGCGTCTATGGGGACAGGA;RSEQ=ACAACAGGGTAGACCCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:2:2,0:168,379:547,2:0.0036:2,0:1:0:25:0:0.0955:0:60:4:0.0037:0:1 0/1:553:118:37,81:134,301:435,118:0.2134:2,2:25.1:1:30:1:0.91095:1.03:60:236:0.2161:0:1.1 +19 19258697 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.58764;SOR=2.50512;LSEQ=CCCTACCCCACCCAGGGAAC;RSEQ=CAGTTCTATGGGAGAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:1:0,1:39,207:246,1:0.004:2,0:28:0:26:0:1:0:60:2:0.0041:0:1 0/1:198:2:1,1:45,151:196,2:0.0101:2,2:9.5:1:27:1:0.41158:3.33:60:4:0.0103:0:1.5 +19 19259489 . CTTAT C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=42;MSI=11.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CCCAGTGAAGACTCCTCTGT;RSEQ=TTATTTATTTATTTATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:30:1:1:0:23.5:4:1:0:0.5 +19 19259945 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20736;SOR=Inf;LSEQ=CACAAAGCCAGATGAAGACA;RSEQ=TCATCTTTTGTGCAAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:156,23:179,0:0:2,0:23.7:1:32.5:1:1:0:59.8:58.667:1:0:0.1 0/1:151:2:1,1:115,34:149,2:0.0132:2,2:29.5:1:27.5:1:0.41104:3.34809:60:4:0.0133:0:1 +19 19259952 . T C 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49996;SOR=0;LSEQ=CCAGATGAAGACACTCATCT;RSEQ=TTGTGCAAACCAAGAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:166,28:194,2:0.0102:2,2:36:0:34.5:1:0.27467:5.84302:60:4:0.0107:0:1.5 0/0:177:0:0,0:135,42:177,0:0:2,0:21.7:1:29.6:1:1:0:60:176:1:0:0.1 +19 19259975 . G T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.099;SOR=Inf;LSEQ=GTGCAAACCAAGAGTCCCTG;RSEQ=GCTCTGAGAAAGCAGCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:222,87:309,0:0:2,0:24.2:1:30.5:1:1:0:60:22.769:1:0:0.1 0/1:267:3:1,2:183,81:264,3:0.0112:2,2:17.3:1:20.7:1:0.22891:4.49004:60:2:0.0077:0:1 +19 19260105 . T C 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTACTTCAGCAGCACACGG;RSEQ=CCATGTCCGTGCTGGCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:24:9,15:333,321:654,24:0.0353:2,2:27.2:1:32:1:0.21768:1.72759:60:48:0.036:0:1.1 0/0:641:0:0,0:332,309:641,0:0:2,0:23.2:1:28.4:1:1:0:60:52.417:1:0:0.2 +19 19260386 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0238;SOR=Inf;LSEQ=ATTCTCATGTCACAACCTGG;RSEQ=AAACTCCTACTGGAGCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:1,51:52,0:0:1,0:25.2:1:33:1:1:0:60:51:1:0:0.1 0/1:10:2:1,1:0,8:8,2:0.2:0,2:12:0:30.5:1:0.2:0:60:4:0.2222:0:1.5 +19 19260760 . G C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTAGCCTAGCCAGGCGTGGT;RSEQ=GTGGGCGCCTGTAATCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:28.5:1:1:0:60:4:1:0:1.5 +19 19261065 . G A 46 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAACACTGACAGACCAGGC;RSEQ=CGGTGGCTCACGCCTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:3:0:30:1:1:0:55:4:1:0:1.5 1/1:3:3:1,2:0,0:0,3:1:0,2:13.3:1:29.3:1:1:0:60:6:1:0:1 +19 19261367 . G A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13509;SOR=Inf;LSEQ=AAAAAAGAAAGGCTGACATG;RSEQ=CATCAGGACTCCTCATGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:149,4:153,0:0:1,0:16.9:1:30.2:1:1:0:57.8:7.5:1:0:0.4 0/1:90:2:2,0:85,3:88,2:0.0222:1,0:7.5:1:29.5:1:1:0:60:4:0.0238:0:1 +19 19261634 . G A 34 p8;q25;Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62379;SOR=0.35141;LSEQ=GAGTGGGGAGGGGTACCCCA;RSEQ=CCTCACACCTCTCCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:3:3,0:29,174:203,3:0.0146:2,0:7.3:1:21.7:1:0.00345:0:60:2:0.01:0:1 0/0:194:1:1,0:32,161:193,1:0.0052:2,0:1:0:24:0:0.1701:0:60:2:0.0052:0:1 +19 19261833 . A G 26 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACTTTGGGAGGCCAAGGC;RSEQ=GGAGGATCACTTGAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:27.5:1:26.5:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:18:0:32:0:1:0:60:2:1:0:1 +19 19850027 . A G 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCACACAGATGTTCACCCAC;RSEQ=CGGGATGCTCACATGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:52,23:75,0:0:2,0:23.5:1:29.8:1:1:0:60:36.5:1:0:0.2 0/1:80:28:19,9:42,10:52,28:0.35:2,2:25.3:1:29.3:1:0.27083:1.97147:60:56:0.35:0:1.1 +19 19850032 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23431;SOR=0;LSEQ=CAGATGTTCACCCACACGGG;RSEQ=TGCTCACATGCACAGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:54,27:81,2:0.0238:2,2:26.5:1:31:1:1:1.98212:60:4:0.0253:0:1.5 0/0:89:0:0,0:66,23:89,0:0:2,0:23.2:1:27.5:1:1:0:60:11.714:1:0:0.4 +19 20100284 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAGGGGTTGTCGGACACC;RSEQ=TATACAGGAGCAATCATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:11:1:32.5:1:1:1.7321:60:4:0.4:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:23.5:1:33:1:1:0:60:4:1:0:0 +19 20101636 . A G 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66685;SOR=0.54001;LSEQ=TTGGTGTTAAGCCCAAGCAC;RSEQ=TCTAATATATGCTGGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:3,8:0.7273:0,0:31.3:1:30.9:1:1:0:59.8:16:0.7273:0:1 1/0:12:7:7,0:5,0:5,7:0.5833:0,0:17.4:1:30.4:1:1:0:59.4:14:0.5833:0:1 +19 20101780 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10206;SOR=Inf;LSEQ=ATAAAAGGAATAGCAAAGTA;RSEQ=CTTGTTCAAAAGGATCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:49,57:106,0:0:2,0:26.3:1:31.7:1:1:0:59.1:212:1:0:0.1 0/1:94:3:1,2:38,53:91,3:0.0319:2,2:33.3:1:27.7:1:1:1.42867:60:6:0.0323:0:1 +19 20101792 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50072;SOR=0;LSEQ=GCAAAGTACCTTGTTCAAAA;RSEQ=GATCAGATATAGTTACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:43,52:95,2:0.0206:2,2:33:1:30:1:1:1.21:57.5:4:0.0206:0:1 0/0:82:0:0,0:31,51:82,0:0:2,0:26.6:1:30.7:1:1:0:57.8:81:1:0:0.1 +19 27732000 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTCTGTTTGTAAAGTCT;RSEQ=CAAGTGGATATTCAGACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:0,7:1:0,2:2.9:1:32.1:1:1:0:24:14:1:0:3.6 1/1:24:23:9,14:1,0:1,23:0.9583:0,2:12.6:1:30.3:1:0.41667:0:30.4:46:0.9583:0:4.6 +19 27732011 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAAAGTCTACAAGTGGATA;RSEQ=TCAGACCTCTTTGAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:17,8:25,0:0:2,0:7.7:1:30.6:1:1:0:30.4:50:1:0:3 0/1:61:2:1,1:31,28:59,2:0.0328:2,2:16.5:1:28:1:1:1.10529:33:4:0.0333:0:4.5 +19 27732018 . C T 72 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.02434;LSEQ=CTACAAGTGGATATTCAGAC;RSEQ=TCTTTGAGGCCTTCGTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:16,9:25,2:0.0741:2,0:14.5:1:34:0:0.53846:0:21.5:4:0.0769:0:5 0/1:66:5:3,2:31,27:58,5:0.0758:2,2:16.4:1:31.2:1:1:1.30:31.8:10:0.0758:0:4.4 +19 27732021 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38077;SOR=2.0229;LSEQ=CAAGTGGATATTCAGACCTC;RSEQ=TTGAGGCCTTCGTTGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:17,7:24,3:0.1111:2,2:12:1:34.3:1:0.25026:4.54608:20:6:0.1111:0:2.3 0/1:69:14:6,8:30,25:55,14:0.2029:2,2:25.8:1:30.1:1:0.55255:1.58905:28.4:28:0.2029:0:3.9 +19 27732029 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31829;SOR=Inf;LSEQ=TATTCAGACCTCTTTGAGGC;RSEQ=TTCGTTGGAAACGGGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:27,0:0:2,0:25:1:32.5:1:1:0:30:54:1:0:3 0/1:71:5:2,3:34,31:65,5:0.0704:2,2:36.4:1:29.2:1:0.66905:1.63357:30.6:10:0.0714:0:5 +19 27732030 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCAGACCTCTTTGAGGCC;RSEQ=TCGTTGGAAACGGGATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:27,0:0:2,0:26:1:31.7:1:1:0:30:26:1:0:3 0/1:71:2:1,1:36,33:69,2:0.0282:2,2:34:1:30.5:1:1:1.08956:21:4:0.0282:0:3 +19 27732033 . G T 56 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38675;SOR=0.47466;LSEQ=CAGACCTCTTTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:1,2:17,7:24,3:0.1111:2,2:28.7:1:29:1:0.25026:4.54608:34.7:6:0.1154:0:3.7 0/1:72:4:2,2:35,33:68,4:0.0556:2,2:33.3:1:28.3:1:1:1.05977:23:8:0.0563:0:4 +19 27732040 . A G 63 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65393;SOR=0.70682;LSEQ=CTTTGAGGCCTTCGTTGGAA;RSEQ=CGGGATTTCTTTATATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:16,9:25,2:0.0741:2,0:36.5:1:34.5:1:0.53846:0:21.5:4:0.0769:0:5 0/1:75:4:2,2:37,34:71,4:0.0533:2,2:25.8:1:31.8:1:1:1.087:34.8:8:0.0533:0:4.3 +19 27732041 . C A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.71487;LSEQ=TTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTTATATTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:17,9:26,1:0.037:2,0:50:0:32:0:1:0:32:2:0.037:0:4 0/1:75:2:2,0:37,36:73,2:0.0267:2,0:35.5:1:31.5:1:0.49405:0:20:4:0.0267:0:5 +19 27732044 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGGCCTTCGTTGGAAACGG;RSEQ=ATTTCTTTATATTATGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:27,0:0:2,0:39.8:1:31.6:1:1:0:30:26:1:0:3 0/1:75:2:0,2:39,33:72,2:0.0267:2,0:10:0:29:0:0.22029:0:45:4:0.0274:0:4 +19 27732051 . TT AC 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32144;SOR=Inf;LSEQ=TCGTTGGAAACGGGATTTCT;RSEQ=ATATTATGCTAGACAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:17,9:26,0:0:2,0:45.1:1:31.2:1:1:0:28.8:52:0.963:0:3 0/1:75:5:3,2:34,33:67,5:0.0667:2,2:31.2:1:28.4:1:1:1.45:30:10:0.0685:0:2.4 +19 27732052 . T C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.54865;SOR=0.54758;LSEQ=CGTTGGAAACGGGATTTCTT;RSEQ=ATATTATGCTAGACAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:24:15,9:0,0:0,24:0.8889:0,2:45.3:1:32.6:1:1:0:29.4:48:0.9231:0:2.9 1/1:75:61:30,31:1,1:2,61:0.8133:2,2:39:1:30.8:1:1:1.0328:29.5:60:0.9091:0:3.2 +19 27732056 . T C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26801;SOR=0.51832;LSEQ=GGAAACGGGATTTCTTTATA;RSEQ=TATGCTAGACAGAAGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:5,3:13,6:19,8:0.2963:2,2:46.5:1:33.5:1:1:1.28715:41.3:16:0.3077:0:2.6 0/1:73:13:6,7:33,27:60,13:0.1781:2,2:42.8:1:32:1:0.76022:1.41895:38.4:26:0.1831:0:3.5 +19 27732058 . A C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.92337;LSEQ=AAACGGGATTTCTTTATATT;RSEQ=TGCTAGACAGAAGAATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:12:9,3:9,6:15,12:0.4444:2,2:44.9:1:32.2:1:0.68284:1.95:24.3:24:0.4615:0:3.3 0/1:73:31:15,16:21,14:35,31:0.4247:2,2:41:1:30.7:1:0.45825:1.58848:28.2:30:0.4167:0:3.6 +19 27732061 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGATTTCTTTATATTATG;RSEQ=TAGACAGAAGAATTCTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:17,9:26,0:0:2,0:43.9:1:32.3:1:1:0:30.3:25:0.9615:0:2.9 0/1:72:2:1,1:37,32:69,2:0.0278:2,2:44:1:29:1:1:1.15388:24:4:0.0278:0:3 +19 27732065 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTCTTTATATTATGCTAG;RSEQ=CAGAAGAATTCTCAGTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:27,0:0:2,0:40:1:30.4:1:1:0:30:54:1:0:2.9 0/1:72:2:1,1:38,32:70,2:0.0278:2,2:34.5:1:31:1:1:1.18465:40.5:4:0.0282:0:4 +19 27732070 . A T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.79605;LSEQ=TTTATATTATGCTAGACAGA;RSEQ=GAATTCTCAGTAACTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:18,8:26,1:0.0357:2,0:41:0:28:0:0.33333:0:22:2:0.0357:0:2 0/1:70:2:1,1:37,31:68,2:0.0286:2,2:31.5:1:28:1:1:1.19052:26.5:4:0.0286:0:3.5 +19 27732071 . G T 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17438;SOR=Inf;LSEQ=TTATATTATGCTAGACAGAA;RSEQ=AATTCTCAGTAACTTCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:20,10:30,0:0:2,0:30.8:1:32.9:1:1:0:29.1:60:1:0:3.2 0/1:70:6:3,3:35,29:64,6:0.0857:2,2:35.7:1:29.3:1:1:1.20364:23.8:12:0.087:0:2.5 +19 27732077 . T C 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24144;SOR=0.40704;LSEQ=TATGCTAGACAGAAGAATTC;RSEQ=CAGTAACTTCCTTGTGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:2,2:18,9:27,4:0.129:2,2:7:1:31.8:1:0.60146:1.95297:21.5:8:0.129:0:5.5 0/1:71:4:2,2:36,31:67,4:0.0563:2,2:10.8:1:30:1:1:1.15884:21:8:0.0571:0:5.8 +19 27732081 . T A 58 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84204;LSEQ=CTAGACAGAAGAATTCTCAG;RSEQ=AACTTCCTTGTGTTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:18,11:29,2:0.0645:2,0:16.5:1:29:1:0.52688:0:27.5:4:0.0667:0:5 0/1:73:4:2,2:35,33:68,4:0.0548:2,2:17.8:1:29.3:1:1:1.05977:21:8:0.0548:0:5.3 +19 27732098 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.11825;SOR=0;LSEQ=CAGTAACTTCCTTGTGTTGT;RSEQ=TGTATTCAACTCACAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:19,12:31,2:0.0606:2,2:12:0:31.5:1:1:1.56069:20:4:0.0606:0:4.5 0/0:62:0:0,0:32,30:62,0:0:2,0:12:1:30.4:1:1:0:28.6:124:1:0:2.9 +19 27732099 . T A 22 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGTAACTTCCTTGTGTTGTG;RSEQ=GTATTCAACTCACAGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,13:27,0:0:2,0:12.1:1:30.1:1:1:0:29.4:54:0.9643:0:3.4 0/1:57:2:2,0:29,26:55,2:0.0351:2,0:5.5:1:22:0:0.49499:0:41.5:4:0.0351:0:3 +19 27732101 . T C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56285;SOR=0.63859;LSEQ=TAACTTCCTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:3,4:11,8:19,7:0.2593:2,2:24.7:1:32.4:1:0.66522:1.79045:21:14:0.2593:0:5.1 0/1:55:10:4,6:26,19:45,10:0.1818:2,2:21.4:1:30:1:0.48433:2.02558:21.3:20:0.1818:0:4.7 +19 27732111 . A C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGTTGTGTGTATTCAACTC;RSEQ=CAGAGTTGAACGGTTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:27.7:1:29.7:1:1:0:21.8:18:1:0:4.7 0/1:23:2:1,1:9,11:20,2:0.087:2,2:11:0:32:0:1:1.21:20.5:4:0.087:0:2 +19 27732122 . C T 97 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=ATTCAACTCACAGAGTTGAA;RSEQ=GGTTCTTTACACAGAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:43.6:1:30.9:1:1:0:21:14:1:0:5.1 1/0:13:10:4,6:0,3:3,10:0.7692:0,2:36.3:1:29.3:1:0.4965:0:21.5:20:0.7692:0:4.2 +19 27732124 . G A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACTCACAGAGTTGAACG;RSEQ=TTCTTTACACAGAGCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:42.6:1:30.9:1:1:0:21:14:1:0:5.1 1/1:12:12:4,8:0,0:0,12:1:0,2:38.8:1:28:1:1:0:22.3:11:1:0:4.3 +19 27732159 . T G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGATTTGAGACACTCTTTT;RSEQ=GTGGAATTTGTAAGTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:3,6:0,0:0,9:1:0,2:13.3:1:30.3:1:1:0:23.7:18:1:0:5.3 1/1:13:12:5,7:0,1:1,12:0.9231:0,2:14.5:1:30.8:1:1:0:24.9:24:0.9231:0:4.1 +19 27732180 . T A 62 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=GTGGAATTTGTAAGTGGAGA;RSEQ=TTCAGCCGCTTTGAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:29:1:30.5:1:1:0:26.8:8:1:0:5.3 1/0:7:4:2,2:1,1:2,4:0.5714:2,2:13.3:1:31:1:1:1:29.5:8:0.5714:0:3.3 +19 27732187 . C T 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=TTGTAAGTGGAGATTTCAGC;RSEQ=GCTTTGAGGTCAGTGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:38.5:1:31.5:1:1:0:23:4:0.6667:0:5.5 0/0:7:0:0,0:4,2:6,0:0:2,0:8.7:1:31.3:1:1:0:33.5:12:0.8571:0:3 +19 27732196 . G T 28 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGATTTCAGCCGCTTTGAG;RSEQ=TCAGTGGTAGAAAAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:37.7:1:33.7:1:1:0:28.7:6:1:0:5.3 0/1:9:2:1,1:3,3:6,2:0.2222:2,2:8.5:1:28.5:1:1:1:28.5:4:0.2222:0:7.5 +19 27732200 . GT AC 82 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=TTTCAGCCGCTTTGAGGTCA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:0,6:1:0,2:18.5:1:32:1:1:0:25:12:1:0.5:3.3 0/1:7:3:2,1:1,0:1,3:0.4286:0,2:6.3:1:31.1:1:1:0:20.7:6:0.4286:0.1429:2 +19 27732209 . A T 47 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20879;SOR=Inf;LSEQ=CTTTGAGGTCAGTGGTAGAA;RSEQ=AGGAAATATCTTCGTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:16.3:1:32.5:1:1:0:25:12:1:0:3.3 0/1:8:3:2,1:3,2:5,3:0.375:2,2:15.3:1:30:1:1:1.29:27:6:0.375:0:7.3 +19 27732223 . G C 51 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=TATAAAAACTAGACAGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:16.3:1:33:1:1:0:25:12:1:0:3.3 0/1:10:3:2,1:4,3:7,3:0.3:2,2:29.3:1:32.3:1:1:1.44:27:6:0.3:0:7.3 +19 27732228 . A G 50 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AAAGGAAATATCTTCGTATA;RSEQ=AAACTAGACAGAATGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:16.3:1:31.7:1:1:0:25:12:1:0:3.3 0/1:10:3:2,1:4,3:7,3:0.3:2,2:34.3:1:32:1:1:1.44:27:6:0.3:0:7.3 +19 27732232 . C G 51 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50893;SOR=Inf;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATGATTCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:19.8:1:33.6:1:1:0:22:10:1:0:3.2 0/1:11:3:2,1:5,3:8,3:0.2727:2,2:38.3:1:32.3:1:1:1.18:27:6:0.2727:0:7.3 +19 27732235 . G C 51 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATCTTCGTATAAAAACTA;RSEQ=ACAGAATGATTCTCAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:34:0:34.3:1:1:0:21.3:6:1:0:2.3 0/1:11:3:2,1:5,3:8,3:0.2727:2,2:40.3:1:32.3:1:1:1.18:27:6:0.2727:0:7.3 +19 27732251 . GA TT 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03297;SOR=0;LSEQ=ACTAGACAGAATGATTCTCA;RSEQ=AACTGCTTTGTGATGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:34.5:1:30.5:1:1:0:22:4:0.6667:0:2 0/0:11:0:0,0:7,4:11,0:0:2,0:32.7:1:30.9:1:1:0:24.5:22:1:0:3.7 +19 27732257 . G T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAATGATTCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:33:1:33:1:1:0:21.3:6:1:0:1.7 0/1:11:2:2,0:5,4:9,2:0.1818:2,0:24.5:1:28.5:1:0.49091:0:22.5:4:0.1818:0:2 +19 27732258 . C T 63 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20879;SOR=0;LSEQ=AGAATGATTCTCAGAAACTG;RSEQ=TTTGTGATGTGTGCGTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:32:1:30.7:1:1:0:21.3:6:1:0:1.7 0/1:11:5:3,2:4,2:6,5:0.4545:2,2:33.6:1:27.4:1:1:1.29868:24.8:10:0.4545:0:2.4 +19 27732271 . G C 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAACTGCTTTGTGATGTGT;RSEQ=CGTTCAACTCACAGAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:19:1:32.3:1:1:0:21.3:6:1:0:1.7 0/1:11:2:1,1:6,3:9,2:0.1818:2,2:46:0:31.5:1:1:1.87089:31:4:0.1818:0:3 +19 27732290 . T C 45 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCGTTCAACTCACAGAGTT;RSEQ=AACCTTCCTTTTCATAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:7:0:32:0:1:0:20:2:1:0:1 0/1:7:3:1,2:3,1:4,3:0.4286:2,2:15.7:1:29:1:0.48571:4.4496:22.7:6:0.5:0:6 +19 27732297 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCACAGAGTTTAACCTT;RSEQ=CTTTTCATAGAGCAGTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:15:1:27:1:1:1.7321:22:4:0.4:0:5 +19 27732305 . T A 27 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTTAACCTTCCTTTTCA;RSEQ=AGAGCAGTTAGGAAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,1:2,2:0.4:2,2:12:0:27.5:1:1:1:31:4:0.4:0:3 +19 27732670 . A C 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCTGTTTGTAATGTCTGC;RSEQ=AGTGGATATTCGGACCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:1,4:0.8:0,2:4.8:1:29:1:1:0:23.3:8:0.8:0:3.8 1/1:2:2:1,1:0,0:0,2:1:0,2:6:1:28.5:1:1:0:24:4:1:0:5 +19 27732679 . T A 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTAATGTCTGCAAGTGGATA;RSEQ=TCGGACCTCTTTGAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:3,2:5,1:0.1667:2,0:3:0:28:0:1:0:33:2:0.1667:0:4 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:6:1:29:1:1:1.45:23.5:4:0.1667:0:4 +19 27732732 . GAA TTC 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6534;SOR=0.53831;LSEQ=GATTTCTTCATATTATGCTA;RSEQ=AGAAGAATTCTCAGTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:2,1:17,11:28,3:0.0968:2,2:28:1:33.1:1:1:1.28:52.3:6:0.0968:0:2 0/1:37:2:2,0:17,18:35,2:0.0541:2,0:35:1:28.5:1:0.48649:0:26.5:4:0.0541:0:3.5 +19 27732734 . A C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.2108;LSEQ=TTTCTTCATATTATGCTAGA;RSEQ=AGAAGAATTCTCAGTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:28:17,11:0,0:0,28:0.9032:0,2:33.2:1:32.7:1:1:0:39.6:56:1:0:2.6 1/1:37:34:17,17:0,1:1,34:0.9189:0,2:33.1:1:31.4:1:1:0:36:68:0.9714:0:2.5 +19 27732741 . A T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49649;SOR=0;LSEQ=ATATTATGCTAGAAAGAAGA;RSEQ=TTCTCAGTAACTTCTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:19,12:0,0:0,31:1:0,2:35.3:1:31.3:1:1:0:40.8:62:1:0:2.6 1/1:37:35:18,17:1,1:2,35:0.9459:2,2:35.2:1:29.7:1:1:1.06:35.7:70:0.9459:0:2.5 +19 27732760 . T G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12402;SOR=Inf;LSEQ=AATTCTCAGTAACTTCTTTG;RSEQ=GTTGTGTGTATGCAACTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:19,12:31,0:0:2,0:32.8:1:29.9:1:1:0:40.8:30:1:0:2.6 0/1:39:4:3,1:17,17:34,4:0.1026:2,2:27:1:31.3:1:0.60618:2.92:27.8:8:0.1026:0:3.5 +19 27732772 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19831;SOR=0;LSEQ=CTTCTTTGTGTTGTGTGTAT;RSEQ=CAACTCACAGAGTTCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:16,9:25,2:0.0741:2,2:22:1:30.5:1:1:1.73837:42:4:0.0741:0:3 0/0:33:0:0,0:16,16:32,0:0:2,0:25.1:1:31.9:1:1:0:38.6:64:0.9697:0:2.3 +19 27732809 . C G 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCTTCCTTTAGACAGAGCA;RSEQ=ATCGGAAACACTCTTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:2:0:31:0:1:0:45.5:4:1:0:3.5 1/1:3:3:1,2:0,0:0,3:1:0,2:5:1:30.7:1:1:0:37.3:6:1:0:3.7 +19 27733190 . A C 51 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTTTGCAAGTGGAGATTT;RSEQ=AAGCGCTTTGAGGCCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:13.3:1:32.7:1:1:0:47.3:6:1:0:3.7 +19 27733216 . A G 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CTTTGAGGCCAAAGGCAGAA;RSEQ=AGGAAATATCTTCGTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:31.5:1:1:0:28:4:1:0:3 0/0:3:0:0,0:2,1:3,0:0:2,0:39.3:1:31:1:1:0:47.3:6:1:0:3.7 +19 27733232 . A T 49 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=AGAAAAGGAAATATCTTCGT;RSEQ=TAAAAACTAGACAGAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:24.8:1:30:1:1:0:24.5:8:1:0:2.3 1/1:3:3:2,1:0,0:0,3:1:0,2:38.3:1:31:1:1:0:47.3:6:1:0:3.7 +19 27733234 . A T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=AAAAGGAAATATCTTCGTAT;RSEQ=AAAACTAGACAGAATCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:24.8:1:30:1:1:0:24.5:8:1:0:2.3 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:38:1:29:1:1:0:59.5:4:0.6667:0:4 +19 27733240 . T A 31 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AAATATCTTCGTATAAAAAC;RSEQ=AGACAGAATCATTCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:27:0:31:1:1:1:28:4:0.5:0:3 0/0:3:0:0,0:2,1:3,0:0:2,0:30.3:1:30.3:1:1:0:47.3:6:1:0:3.7 +19 27733243 . A T 30 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TATCTTCGTATAAAAACTAG;RSEQ=CAGAATCATTCTCAGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:24:0:30.5:1:1:1:28:4:0.5:0:3 0/0:3:0:0,0:2,1:3,0:0:2,0:27.3:1:28.3:1:1:0:47.3:6:1:0:3.7 +19 27733268 . T C 33 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=ATCATTCTCAGAAACTGCTG;RSEQ=GTGATGTGTGCTTTCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:33:1:1:0:21:4:1:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:31:0:1:0:59:2:1:0:5 +19 27733335 . T C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGTTTGGAAACACTCTG;RSEQ=TTGTAAAGTCTGCAAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:34:0:25:0:1:0:23:2:1:0:5 0/1:12:2:1,1:4,5:9,2:0.1667:2,2:28.5:1:31:1:1:1.22:21.5:4:0.2:0:5.5 +19 27733359 . A C 94 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAAAGTCTGCAAGTGGATAT;RSEQ=TTGACCTCTTAGGGTCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:43:0:33:0:1:0:23:2:1:0:5 1/0:12:8:4,4:2,2:4,8:0.6667:2,2:42.4:1:31.4:1:1:1:22.3:16:0.6667:0:5.3 +19 27733363 . A G 104 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGCAAGTGGATATATTG;RSEQ=CCTCTTAGGGTCCTTCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:39:0:33:0:1:0:23:2:1:0:5 1/1:12:10:5,5:1,1:2,10:0.8333:2,2:36.9:1:31.4:1:1:1:22:20:0.8333:0:4.9 +19 27733370 . A T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGGATATATTGACCTCTT;RSEQ=GGGTCCTTCGTTGGAAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:32:0:1:0:23:2:1:0:5 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:23:1:28:1:1:1:21.5:4:0.1667:0:5.5 +19 27733372 . G A 103 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATATATTGACCTCTTAG;RSEQ=GTCCTTCGTTGGAAACGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:30:0:31:0:1:0:23:2:1:0:5 1/1:11:11:5,6:0,0:0,11:1:0,2:29.3:1:29.8:1:1:0:21.9:22:1:0:5.1 +19 27733374 . T G 102 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATATTGACCTCTTAGGG;RSEQ=CCTTCGTTGGAAACGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:28:0:31:0:1:0:23:2:1:0:5 1/1:11:10:5,5:0,1:1,10:0.9091:0,2:25.9:1:30.9:1:1:0:22:20:0.9091:0:4.9 +19 27733386 . A T 43 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTAGGGTCCTTCGTTGGA;RSEQ=ACGGGTTTTTTTTCATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:16:0:33:0:1:0:23:2:1:0:5 0/1:11:3:1,2:4,4:8,3:0.2727:2,2:22.3:1:27.7:1:1:1.87936:22.3:6:0.3:0:6 +19 27733387 . ACGGGTT GCGGG 73 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTAGGGTCCTTCGTTGGAA;RSEQ=TTTTTTCATGTAAGGCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:15:0:31:0:1:0:23:2:1:0:5 0/1:11:5:3,2:2,4:6,5:0.4545:2,2:11.2:1:31.6:1:0.5671:2.70:22.4:10:0.4545:0.2727:5.2 +19 27733391 . GTT G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTCCTTCGTTGGAAACGG;RSEQ=TTTTTTCATGTAAGGCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:9:2:1,1:2,1:3,2:0.2222:2,2:10.5:1:30.5:1:1:1.7321:22:4:0.3333:0.1111:6 +19 27733511 . C G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGAAACAATCTTTTTGTG;RSEQ=AATTTGCAGGTGGAGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:1:30:1:1:0:34.5:4:1:0:2.5 +19 27733521 . G C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTTGTGCAATTTGCAG;RSEQ=TGGAGATTTCAAGCGCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:32:1:1:0:34.5:4:1:0:2.5 +19 27734269 . A C 74 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTATAAAAACAAGACAAA;RSEQ=TCATTCCCAGAAACTGCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:34.2:1:32.2:1:1:0:22.8:10:1:0:4.4 +19 27734272 . A G 72 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAAAAACAAGACAAAATC;RSEQ=TTCCCAGAAACTGCGTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:37.2:1:31.4:1:1:0:22.8:10:1:0:4.4 +19 27734281 . A C 75 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGACAAAATCATTCCCAGA;RSEQ=ACTGCGTAGTGAGGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:38:1:32.4:1:1:0:22.8:10:1:0:4.4 +19 27734294 . G T 70 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAGAAACTGCGTAGTGA;RSEQ=GTGTGTGTTTAACTCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:25:1:30.4:1:1:0:22.8:10:1:0:4.4 +19 27735216 . T G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACTCTTTTTGTGCAATT;RSEQ=GCAAGTGGAGATTTCAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:32.5:1:1:0:24:4:1:0:2.5 +19 27735289 . A C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGCATAAAAACTAGACAAA;RSEQ=TCATTCCCAGAAACTGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:29.5:1:1:0:24.5:4:1:0:7 +19 27735292 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAAACTAGACAAAATC;RSEQ=TTCCCAGAAACTGCATAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:28.5:1:1:0:24.5:4:1:0:7 +19 27735301 . A C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACAAAATCATTCCCAGA;RSEQ=ACTGCATAGTGATGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29.5:1:1:0:24.5:4:1:0:7 +19 27735307 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCATTCCCAGAAACTGC;RSEQ=TAGTGATGTGTGTGTTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:29.5:1:1:0:24.5:4:1:0:7 +19 27735362 . T C 66 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTTTTCATACAGCATT;RSEQ=TGGAAACACTCTGTTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:1,0:1,4:0.8:0,2:11.8:1:33:1:1:0:23.3:8:0.8:0:4 +19 27735370 . A C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCATACAGCATTTTGGAAAC;RSEQ=CTCTGTTTGTAAATTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:9.5:1:32:0:1:0:24.5:4:0.6667:0:7 +19 27736286 . T C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATGGCAGAAAAGGAAATA;RSEQ=CTTCGTATAAAAACTAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:31:1:1:0:22:4:1:0:7 +19 27736297 . A T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAAATATCTTCGTATAA;RSEQ=AACTAGACAGAATCATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:27.5:1:1:0:22:4:1:0:7 +19 27736300 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATATCTTCGTATAAAAA;RSEQ=TAGACAGAATCATTTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:29:1:1:0:22:4:1:0:7 +19 27736306 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCGTATAAAAACTAGAC;RSEQ=GAATCATTTTCAGAAACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:28.5:1:1:0:22:4:1:0:7 +19 27736315 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACTAGACAGAATCATT;RSEQ=TCAGAAACTGCTCTGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:30:1:1:0:22:4:1:0:7 +19 27736531 . G T 30 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCAACTCACGGAGTTGAAC;RSEQ=TTCCTTTAGAGAGAGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:37.5:1:32.5:1:1:0:60:4:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:7:1:30.5:1:1:0:20:4:1:0:6 +19 27736542 . G A 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GAGTTGAACGTTCCTTTAGA;RSEQ=AGAGCAGACTTGAAACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29:0:34.5:1:1:0:60:4:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:18:1:31:0:1:0:20:4:1:0:6 +19 27736544 . G C 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GTTGAACGTTCCTTTAGAGA;RSEQ=AGCAGACTTGAAACTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:27:0:34.5:1:1:0:60:4:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:20:1:33.5:1:1:0:20:4:1:0:6 +19 27736551 . C G 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTTCCTTTAGAGAGAGCAGA;RSEQ=TTGAAACTCTCTTTTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:20:0:34.5:1:1:0:60:4:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:27:1:33.5:1:1:0:20:4:1:0:6 +19 27736602 . TT AG 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGATTTCAAGAGCTTTG;RSEQ=GCCAATGGTAGAAAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:32:0:1:0:20:4:1:0:5 +19 27736690 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATGTGTGTGTTTATCTC;RSEQ=CAGAGTTTAACCTTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:1:28.5:1:1:0:31:4:1:0:2 +19 27736716 . C A 58 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAACCTTTCTTTTCATAC;RSEQ=GCATTCTGGAAACACTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:25.3:1:29:1:1:0:29.5:8:1:0:2.5 +19 27736730 . A C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCATACCGCATTCTGGAAAC;RSEQ=CTCTGTTTGTAAAGTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:26.5:1:31:1:1:1:28:4:0.5:0:3 +19 27736733 . C G 33 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACCGCATTCTGGAAACACT;RSEQ=TGTTTGTAAAGTCTGCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:29.5:1:33:1:1:1:28:4:0.5:0:3 +19 27737428 . T C 33 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCTGTTTATAAAGTCTG;RSEQ=AAGTGGATATTTTGACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:33:0:1:0:24.5:4:1:0:6 +19 27737436 . T C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATAAAGTCTGTAAGTGGA;RSEQ=ATTTTGACCTCTTTGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:33.5:1:1:0:24.5:4:1:0:6 +19 27737440 . TT CA 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTCTGTAAGTGGATATT;RSEQ=GACCTCTTTGAGGCCTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:32.8:1:1:0:24.5:4:1:0:5 +19 27737446 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAGTGGATATTTTGACC;RSEQ=CTTTGAGGCCTTCGTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:32.5:1:1:0:24.5:4:1:0:5 +19 27737959 . G T 59 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=GTGGAGATTTCAAGCGCTTT;RSEQ=AGGCCAATTGTAGAAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:29:0:1:0:20:2:1:0:5 1/1:4:4:2,2:0,0:0,4:1:0,2:20.3:1:29.8:1:1:0:24:8:1:0:2 +19 27737967 . T A 63 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TTCAAGCGCTTTGAGGCCAA;RSEQ=TGTAGAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:19:1:31.8:1:1:0:24:8:1:0:2 +19 27738359 . T A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACAGAATCATTCCCACA;RSEQ=AGTGCGTTGTTATGTGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:30.5:1:1:0:57:4:1:0:1.5 +19 27738461 . G C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=AGTCTGCAAGTGGATATTTT;RSEQ=ACCTCTTTGAGGCCTTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:2,0:2,1:0.3333:0,0:42:0:15:0:0.33333:0:52:0:0:0:4 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:46:1:31.5:1:1:0:24.5:4:0.6667:0:3 +19 27738491 . T TA 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=AGGCCTTCGTTGGAAACGGG;RSEQ=TTTTTTCATGTAAGGCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:3,1:0.25:2,0:28:0:32:0:1:0:52:2:0.25:0:4 0/1:5:2:1,1:1,1:2,2:0.4:2,2:15:1:27:1:1:1:24.5:4:0.4:0:3 +19 27738501 . G A 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=TGGAAACGGGTTTTTTTCAT;RSEQ=TAAGGCTAGACAGAAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:28:1:26.5:1:1:1:36.5:4:0.5:0:3.5 1/0:5:3:1,2:1,1:2,3:0.6:2,2:13.7:1:30.7:1:1:1.7321:37:6:0.6:0:4.7 +19 27738505 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AACGGGTTTTTTTCATGTAA;RSEQ=GCTAGACAGAAGAATTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:18.5:1:29.8:1:1:0:37.8:8:1:0:4 1/0:4:2:1,1:1,1:2,2:0.5:2,2:24:0:31.5:1:1:1:42.5:4:0.5:0:5.5 +19 27738523 . TT CC 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAGGCTAGACAGAAGAATTC;RSEQ=AGTAACTTCCTTGTGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:29.6:1:1:0:36.5:4:1:0.5:3.5 0/0:2:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 27738925 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGTTCCTTTAGACAGAG;RSEQ=AGATTTGAAACACGCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:34:1:29:0:1:0:41:4:1:0:6 +19 27738931 . T G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTTAGACAGAGCAGATT;RSEQ=GAAACACGCTTTTTGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:28:1:32:0:1:0:41:4:1:0:6 +19 27738939 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGCAGATTTGAAACAC;RSEQ=CTTTTTGTGGAATTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:20:1:29.5:1:1:0:41:4:1:0:6 +19 27739321 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAATTCAGCCGCTTTGA;RSEQ=GACAATGTTAGAAAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:31:1:1:0:23.5:4:1:0:4.5 +19 27739323 . A T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATTCAGCCGCTTTGAAG;RSEQ=CAATGTTAGAAAAGGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:29.5:1:1:0:23.5:4:1:0:4.5 +19 27739328 . GT AG 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGCCGCTTTGAAGACAAT;RSEQ=TAGAAAAGGAAATATCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:30.8:1:1:0:23.5:4:1:0:3.5 +19 28778454 . T C 120 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11688;SOR=0.10983;LSEQ=GCATTTGCGACGATCATCAT;RSEQ=GTCATCATCATCATCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:16:9,7:1,0:1,16:0.8421:0,2:32.1:1:30.1:1:1:0:54.6:15:0.9375:0:3.6 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:44:0:32:0:1:0:54:2:0.3333:0:4 +19 28778470 . ATCATCATCG GTCA 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=7.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCATTGTCATCATCATCATC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:29:1:25.8:1:1:1.40151:48:4:0.1053:0:3 0/0:3:0:0,0:1,2:3,0:0:2,0:32.3:1:30.3:1:1:0:58:6:1:0:1.3 +19 28778476 . A G 112 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.27018;SOR=0.22752;LSEQ=TCATCATCATCATCATCATC;RSEQ=TCGTCATCATCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:6,6:2,1:3,12:0.7059:2,2:31.6:1:31.5:1:1:1.91151:54.8:24:0.8571:0:4.1 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:22:0:33:0:1:0:54:2:0.3333:0:4 +19 28778494 . A G 118 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.16883;SOR=0.15007;LSEQ=TCATCGTCATCATCATCATC;RSEQ=TCATCGTCAACATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:7,8:2,2:4,15:0.7895:2,2:23:1:30.3:1:1:1.13484:54.3:30:0.8333:0:3.7 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:4:0:30:0:1:0:54:2:0.3333:0:4 +19 28780326 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGAGAGAGTTTTTCCAC;RSEQ=CTGGGTACTGGCAAAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:28,1:29,2:0.0645:1,0:8.5:1:31.5:1:1:0:60:4:0.0645:0:1 0/0:12:0:0,0:11,1:12,0:0:2,0:21.6:1:29.4:1:1:0:60:11:1:0:0 +19 28780398 . G T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0.78894;LSEQ=TGGGGAGGGGCAGTGCAGGG;RSEQ=GCTCCAGCCCTCAGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:84,20:104,2:0.0189:2,2:33:1:31:1:0.35849:4.12311:60:4:0.0194:0:1 0/1:67:1:0,1:54,12:66,1:0.0149:2,0:1:0:27:0:0.19403:0:60:2:0.0152:0:1 +19 28780443 . G A 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5013;SOR=0;LSEQ=GGCGGACAGGGCAGGACACA;RSEQ=CTGCCTGATTCCAGCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:97,81:178,2:0.0111:2,2:27:0:29.5:1:1:1.19632:60:4:0.0112:0:2 0/0:155:0:0,0:92,63:155,0:0:2,0:23.3:1:30.7:1:1:0:60:50.667:1:0:0.5 +19 28780457 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22331;SOR=Inf;LSEQ=GACACAGCTGCCTGATTCCA;RSEQ=CCCAGCATCAAAGCACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:102,95:197,0:0:2,0:25.9:1:32.5:1:1:0:60:64.667:1:0:1 0/1:177:2:1,1:98,77:175,2:0.0113:2,2:14.5:1:28.5:1:1:1.27097:60:4:0.0114:0:1 +19 28780462 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=0.0443;LSEQ=AGCTGCCTGATTCCAGCCCA;RSEQ=CATCAAAGCACCCACATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:202:189:95,94:8,5:13,189:0.9356:2,2:26.8:1:30.3:1:0.56913:1.5796:60:378:0.9356:0:1.1 0/1:190:74:43,31:61,54:115,74:0.3895:2,2:25.1:1:28.9:1:0.55016:1.23:60:73:0.3925:0:1.1 +19 28780531 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09914;SOR=Inf;LSEQ=TGACAGAAAGTTGCTTTTAT;RSEQ=TGAATGCACCCAAGCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:54,105:159,0:0:2,0:25.6:1:31.6:1:1:0:60:18.875:1:0:0.5 0/1:138:3:2,1:49,86:135,3:0.0217:2,2:22:1:26:1:0.55478:3.48:60:6:0.0222:0:1 +19 28780545 . G A 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57689;SOR=2.71137;LSEQ=TTTTATGTGAATGCACCCAA;RSEQ=CCATGTTGGATCACTGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:1:0,1:43,85:128,1:0.0078:2,0:8:0:12:0:1:0:60:0:0:0:1 0/1:96:2:1,1:27,67:94,2:0.0208:2,2:6.5:1:27:1:0.50044:2.45:60:4:0.0215:0:1 +19 28780552 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51175;SOR=0;LSEQ=TGAATGCACCCAAGCCATGT;RSEQ=GGATCACTGTTTAGAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:34,82:116,2:0.0169:2,2:34:1:30:1:0.50703:2.39:60:4:0.0175:0:1 0/0:84:0:0,0:22,62:84,0:0:2,0:22.2:1:29.4:1:1:0:60:83:1:0:0.3 +19 28780554 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18237;SOR=Inf;LSEQ=AATGCACCCAAGCCATGTTG;RSEQ=ATCACTGTTTAGAATGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:30,78:108,0:0:2,0:25.4:1:30.9:1:1:0:60:12.5:1:0:0.3 0/1:81:2:1,1:20,59:79,2:0.0247:2,2:22.5:1:25:1:0.4537:2.90:60:4:0.0253:0:1.5 +19 28780590 . GT G 79 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.67249;SOR=0.47616;LSEQ=GATTTGGTATTTCTTTTATT;RSEQ=TTTTTTTTTTTATTTAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:6:0,6:5,46:51,6:0.1053:2,0:30.2:1:30.8:1:1:0:60:12:0.1071:0:1 0/1:19:1:0,1:1,17:18,1:0.0526:1,0:33:0:33:0:1:0:60:2:0.0588:0:0 +19 28788849 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26436;SOR=0;LSEQ=CTGCACATAATCCGTGCAGT;RSEQ=AGGGGTGAGCCACTCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:1,2:119,18:137,3:0.0214:2,2:25.7:1:29.7:1:0.05349:12.79711:60:6:0.0214:0:2.3 0/0:103:0:0,0:90,13:103,0:0:2,0:24.8:1:31.5:1:1:0:60:102:1:0:0.9 +19 28788858 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20524;LSEQ=ATCCGTGCAGTGAGGGGTGA;RSEQ=CCACTCGGCTGGTCTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:161:131:109,22:23,7:30,131:0.8137:2,2:25.3:1:30.3:1:0.43195:1.50:60:130:0.8125:0:1.7 0/1:121:57:48,9:52,12:64,57:0.4711:2,2:22.7:1:29.1:1:0.81084:1.23:60:56:0.4706:0:1.9 +19 28788918 . A C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17419;LSEQ=CCCATTGCCCTGGCAGGCAG;RSEQ=CTGGATGGCAGAGGAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:394:301:164,137:49,39:88,301:0.764:2,2:25.4:1:31.4:1:0.90329:1.04945:60:59.2:0.7789:0:1.4 0/1:314:113:59,54:102,97:199,113:0.3599:2,2:26.6:1:29.5:1:0.90648:1.04:60:21.6:0.3649:0:1.4 +19 28789135 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08276;SOR=Inf;LSEQ=CCAGACTGGAGTGCAGCAGC;RSEQ=TGATCATAGCTCACTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:0,21:21,0:0:1,0:18.8:1:31.6:1:1:0:59.7:42:1:0:0.4 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:20.5:1:31:0:1:0:60:4:0.2222:0:1 +19 28789169 . G A 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.09491;SOR=0.10512;LSEQ=CTGCAGCCTCAACTTCGGGG;RSEQ=CTCAAGTGATCCTCCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:0,1:1,8:0.8889:0,0:31:1:30.9:1:1:0:59.1:16:0.8889:0:1 0/1:5:2:0,2:0,3:3,2:0.4:0,0:26:1:29:0:1:0:60:4:0.4:0:1 +19 29401768 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGAATGTCAGCAAAACA;RSEQ=ACCTGCCTGCAAGTGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:31:1:1:0:60:4:1:0:2.5 +19 29403570 . C A 76 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23575;SOR=3.18952;LSEQ=TTGGTGAGGGCTGCTTCTGA;RSEQ=GTGTGCAAGAATGGCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:8,2:10,2:0.1667:2,0:16:1:32.5:1:1:0:60:4:0.1667:0:1 0/1:15:6:3,3:5,4:9,6:0.4:2,2:28.5:1:29.5:1:1:1.23147:60:12:0.4:0:1 +19 29403630 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16121;SOR=Inf;LSEQ=GGAGTTGCAGATGTTGACTG;RSEQ=CGGCGACTCTGACTTCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:17,21:38,0:0:2,0:29.9:1:30.3:1:1:0:60:76:1:0:0.2 0/1:26:2:1,1:10,14:24,2:0.0769:2,2:23:1:27.5:1:1:1.38:60:4:0.0769:0:1 +19 29403700 . T G 44 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09874;SOR=8.45755;LSEQ=CTCATTAGGGCTCCACCTCC;RSEQ=TCATTGCCATCTCATGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:2,8:10,1:0.0909:2,0:34:0:34:0:1:0:60:2:0.1:0:1 1/0:6:3:1,2:1,2:3,3:0.5:2,2:15.7:1:28.3:1:1:1:60:6:0.5:0:1.3 +19 29917563 . T CTGCTGCTGC 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0.80845;LSEQ=AAGGAGATACTACATTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:3,1:7,8:15,4:0.2105:2,2:13.5:1:31.6:1:0.58204:3.22:60:8:0.2105:0.1053:4 0/1:17:3:2,1:5,5:10,3:0.1765:2,2:6:1:30.7:1:1:1.90:45:8:0.1729:0.1837:1.3 +19 29917584 . T C 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13587;SOR=0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGTTTGTTGTTGTTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:3,1:6,10:16,4:0.2:2,2:34.5:1:33.8:1:0.28483:4.60:60:8:0.2:0:4 0/0:13:0:0,0:6,7:13,0:0:2,0:25.3:1:29.5:1:1:0:52.6:26:1:0:0.5 +19 29917589 . TG GT 66 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=16.000;MSILEN=3;SSF=0.12767;SOR=0;LSEQ=CTGCTGCTGCTGCTGTTGTT;RSEQ=TTGTTGTTGTTGTTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:3,1:4,6:10,4:0.2105:2,2:34.5:1:33:1:0.55944:4.03:60:8:0.2857:0:3 0/0:13:0:0,0:5,6:11,0:0:2,0:23.9:1:30.3:1:1:0:52.5:22:1:0:0.4 +19 29918435 . T C 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGGCATTTGAGCTTTA;RSEQ=CTTGAAGGATGGTTAGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:37:1:30.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 29918979 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTATCCTCCCCACCACCAA;RSEQ=GTCTCCCCTCTCCTCACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 30303379 . GA G 57 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.41206;SOR=2.30717;LSEQ=GCCGCCCGCGCGCAAAGGGG;RSEQ=AGGGGTACTGGGCCCGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:2,0:11,8:19,2:0.0909:2,0:33:1:31.5:1:0.50476:0:60:4:0.0909:0:0.5 0/1:21:4:2,2:8,5:13,4:0.1905:2,2:10:1:28.8:1:1:1.55528:60:8:0.1905:0.1429:0.3 +19 30303399 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.87389;LSEQ=GAAGGGGTACTGGGCCCGCG;RSEQ=CCTGACCCCGCCGCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:1:0,1:35,29:64,1:0.0154:2,0:1:0:24:0:0.46154:0:60:2:0.0159:0:1 0/1:70:2:1,1:36,32:68,2:0.0286:2,2:19:1:27:1:1:1.1231:60:4:0.0303:0:1 +19 30303409 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.4973;SOR=Inf;LSEQ=TGGGCCCGCGGCCTGACCCC;RSEQ=CCGCCGCCTCACCCCGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:54,39:93,0:0:2,0:17.6:1:29.8:1:1:0:60:17.6:1:0:0.3 0/1:93:2:1,1:52,39:91,2:0.0215:2,2:9:1:32:0:1:1.32915:60:4:0.0222:0:1 +19 30303421 . C T 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01553;SOR=Inf;LSEQ=CTGACCCCGCCGCCGCCTCA;RSEQ=CCCGCGCCGCCCCGCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:77,53:130,0:0:2,0:20:1:31.7:1:1:0:60:129:1:0:0.3 0/1:146:7:2,5:82,57:139,7:0.0479:2,2:14.6:1:26.1:1:0.13505:3.56545:60:6:0.0417:0:1.6 +19 30303425 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.73609;LSEQ=CCCCGCCGCCGCCTCACCCC;RSEQ=CGCCGCCCCGCAGGCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:82,58:140,1:0.0071:2,0:28:0:15:0:0.41844:0:60:0:0:0:1 0/1:163:2:1,1:91,70:161,2:0.0123:2,2:11.5:1:28.5:1:1:1.29788:60:4:0.0127:0:1 +19 30303435 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09641;SOR=0;LSEQ=GCCTCACCCCGCGCCGCCCC;RSEQ=CAGGCCTCAGGCCGGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:108,76:184,3:0.0159:2,2:22.3:1:25.7:1:0.57191:2.82625:60:2:0.011:0:1.3 0/0:222:0:0,0:127,95:222,0:0:2,0:22.8:1:30.2:1:1:0:60:73:1:0:0.4 +19 30303484 . C T 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30431;SOR=2.50064;LSEQ=TGCCGAGGGAGCGCAGGGAG;RSEQ=GGTGAGTGCCCGCGCCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:2:1,1:229,213:442,2:0.0045:2,2:27:1:28.5:1:1:1.07492:60:4:0.0046:0:1 0/1:537:6:2,4:271,260:531,6:0.0112:2,2:25:1:28:1:0.44332:2.08185:60:12:0.0116:0:1.2 +19 30303508 . CGGACG C 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=5.000;MSILEN=5;SSF=1;SOR=0.96284;LSEQ=GAGTGCCCGCGCCGCGGGGC;RSEQ=GGACGGGACGGGACGGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:5:4,1:281,207:488,5:0.0101:2,2:17.2:1:33.2:1:0.40282:2.94:60:10:0.0102:0:0.2 0/0:516:5:2,3:280,228:508,5:0.0097:2,2:28.8:1:29.4:1:0.66166:1.83989:60:10:0.0098:0.0019:0.2 +19 30303714 . T TC 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=2.78597;LSEQ=AAGAGACAGGTTGGGGAGCA;RSEQ=CCCCCCCATCTCACCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:194:64,130:145,211:356,194:0.3514:2,2:26.7:1:31:1:0.08095:1.39503:60:37.8:0.352:0.029:0.1 1/0:447:269:90,179:70,106:176,269:0.6018:2,2:25.8:1:30:1:0.18966:1.31258:59.9:52.8:0.6014:0.0358:0.1 +19 30303950 . T A 53 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12148;SOR=5.10866;LSEQ=CAGTGTGGGAGCCAGGTAGG;RSEQ=CCGCCCGGGGTTGGGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:1:1,0:116,228:344,1:0.0029:2,0:1:0:26:0:0.33913:0:60:2:0.0029:0:1 0/1:341:5:4,1:125,211:336,5:0.0147:2,2:5.6:1:23.2:1:0.06994:6.72:60:4:0.0119:0:1 +19 30303995 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20475;SOR=Inf;LSEQ=AGGTCCTTCTCCCCCTGGGT;RSEQ=ACATGGGGTTTCATGCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:36,134:170,0:0:2,0:23.4:1:32.3:1:1:0:60:84:1:0:0.1 0/1:141:2:1,1:30,109:139,2:0.0142:2,2:6:0:31.5:1:0.3926:3.59:60:4:0.0143:0:1.5 +19 30304011 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50993;SOR=0;LSEQ=GGGTCACATGGGGTTTCATG;RSEQ=TGTCTTGTCTCTTGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:22,109:131,2:0.0149:2,2:24.5:1:31.5:1:0.31704:4.87:60:4:0.015:0:1 0/0:98:0:0,0:17,81:98,0:0:2,0:21.9:1:31.6:1:1:0:60:196:1:0:0.1 +19 30304013 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50761;SOR=0;LSEQ=GTCACATGGGGTTTCATGCT;RSEQ=TCTTGTCTCTTGCTGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:20,104:124,2:0.0159:2,2:14.5:1:29.5:1:0.30667:5.10:60:4:0.0161:0:1 0/0:95:0:0,0:15,80:95,0:0:2,0:21.3:1:31.3:1:1:0:60:190:1:0:0.1 +19 30304018 . G T 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00155;SOR=Inf;LSEQ=ATGGGGTTTCATGCTGTCTT;RSEQ=TCTCTTGCTGGAGACACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:16,101:117,0:0:2,0:21.7:1:31.6:1:1:0:59.6:57.5:1:0:0.1 0/1:80:7:3,4:10,63:73,7:0.0875:2,2:20.1:1:29.6:1:0.08072:4.59:60:14:0.0875:0:1.1 +19 30304028 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52317;SOR=0;LSEQ=ATGCTGTCTTGTCTCTTGCT;RSEQ=GAGACACTCTGGTGAGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:4,85:89,2:0.022:1,2:9:1:29.5:1:0.10745:19.13:60:4:0.0225:0:1 0/0:57:0:0,0:5,52:57,0:0:2,0:22.1:1:30.7:1:1:0:60:114:1:0:0.1 +19 30306546 . TTG T 30 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTTTTTTTTTTTTTTTT;RSEQ=GGGGGGGGACAGAGTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:30:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 30308385 . T C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTTAAGGGATCAGCACTT;RSEQ=CTTGAGCAACACCCTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:826:0:0,0:386,437:823,0:0:2,0:24.7:1:30.6:1:1:0:59.9:136.167:0.9976:0:0.1 0/1:811:47:24,23:360,402:762,47:0.058:2,2:22.6:1:30.5:1:0.65328:1.16:60:94:0.0583:0:1.1 +19 30311454 . C CA 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.80333;LSEQ=GGTGACAGAATAAGGCACCT;RSEQ=AAAAAAAAAACAAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:5:5,0:33,3:36,5:0.122:2,0:26.8:1:32.4:1:1:0:60:10:0.125:0:0.6 0/1:10:1:1,0:9,0:9,1:0.1:0,0:33:0:31:0:1:0:60:2:0.1:0:0 +19 30311542 . G GT 176 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.31162;SOR=1.30014;LSEQ=CTTCACCAAAGTCATTACAA;RSEQ=TTTTTTTTTTTTCCCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:58:51,7:103,7:110,58:0.3187:2,2:27.8:1:30.1:1:0.24385:2.01061:59.7:57:0.3202:0:0.3 0/1:111:42:39,3:51,9:60,42:0.3784:2,2:26:1:29:1:0.35044:2.28:59.8:84:0.3818:0.0811:0.3 +19 30311555 . CCCCT TC 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.00041;SOR=0;LSEQ=ATTACAAGTTTTTTTTTTTT;RSEQ=CCCTCAAGTAAAACTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:17:15,2:187,30:217,17:0.0717:2,2:18.5:1:28.7:1:1:1.20:59.1:16:0.0727:0.0338:1.2 0/0:148:0:0,0:124,23:147,0:0:2,0:21.9:1:29.4:1:1:0:59.7:13.7:1:0:0.3 +19 30312454 . CTTT C 49 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=24.000;MSILEN=1;SSF=0.3287;SOR=2.87764;LSEQ=TGGTGGGTGGGAGTTGTGTT;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:9,0:9,3:0.1429:0,0:35.7:1:32:1:1:0:55:6:0.1429:0:2.7 0/1:9:3:3,0:2,2:4,3:0.3333:2,0:21:1:31:1:0.42857:0:60:6:0.3333:0:1.3 +19 30312542 . G T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25287;SOR=0;LSEQ=CTCTCTCTTTCCATGCCAGG;RSEQ=TACTGAGAAGTCATTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:3:2,1:142,23:165,3:0.0179:2,2:40:1:31.3:1:0.37215:3.05779:60:6:0.0183:0:1 0/0:142:0:0,0:115,27:142,0:0:2,0:23.7:1:30.3:1:1:0:59.9:46.333:1:0:0.2 +19 30312874 . C T 251 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00499;LSEQ=GAACTTCTTTTCTCAATCAT;RSEQ=GGTCTCTTTTCTCTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:788:296:187,109:299,193:492,296:0.3756:2,2:24.5:1:30.6:1:0.54512:1.11:60:58.2:0.3755:0:1.1 0/0:670:2:0,2:406,262:668,2:0.003:2,0:1:0:24.5:1:0.1549:0:60:4:0.003:0:1 +19 30313523 . CCTT C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=1.92005;LSEQ=ATTTGCTGGTCAGTGCTGCT;RSEQ=CTTTCAGTCCTTCTTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:89:22,67:153,325:478,89:0.1561:2,2:24.2:1:32.7:1:0.21117:1.43284:59.8:43.5:0.1559:0.0211:0.4 0/1:469:123:43,80:117,228:345,123:0.2623:2,2:25:1:30.9:1:0.8258:1.05:59.7:122:0.2641:0.0341:0.4 +19 30313576 . C T 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=3.27605;LSEQ=AACTGCCTAAATAGGCCAGC;RSEQ=GCGGTGGTTCAGGCCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:21:2,19:16,142:158,21:0.1167:2,2:24:1:30.7:1:1:1.07005:58.7:20:0.1124:0:1.6 0/1:142:43:6,37:15,84:99,43:0.3028:2,2:17.5:1:29.3:1:1:1.10047:56.4:86:0.305:0:1.6 +19 30313603 . C G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00505;SOR=2.91285;LSEQ=GTTCAGGCCTGTAAACCCAG;RSEQ=ACTTTGGGAGGCCGAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:13:1,12:4,97:101,13:0.114:1,1:19.5:1:31.9:1:0.46044:2.01:54.4:26:0.115:0:2 0/1:84:23:0,23:2,59:61,23:0.2738:1,1:27:1:31.1:1:1:0:50.5:46:0.2738:0:1.9 +19 30313622 . G T 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01107;SOR=0;LSEQ=GCACTTTGGGAGGCCGAGGT;RSEQ=GGCCGATCACTTGAGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:0,9:1,78:79,9:0.1023:1,0:26.7:1:30.4:1:1:0:48.6:18:0.1059:0:1.2 0/0:60:0:0,0:0,60:60,0:0:1,0:27.7:1:30.9:1:1:0:49.5:120:1:0:0.6 +19 30313721 . G T 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=ATTAGCCGGCTATGGTGGTG;RSEQ=GCACCTGTAGTCCCAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:12,0:0:0,0:25.2:1:31.6:1:1:0:49.8:24:1:0:0 1/0:4:2:2,0:0,2:2,2:0.5:0,0:5:0:30:0:0.33333:0:50:4:0.5:0:2 +19 30313737 . G C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03297;SOR=Inf;LSEQ=GGTGGGCACCTGTAGTCCCA;RSEQ=CTACTCGAGAGGCTAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:11,0:0:0,0:21.5:1:32.4:1:1:0:53.5:22:1:0:0 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:9:0:33:0:0.33333:0:50:4:0.6667:0:2 +19 30313850 . CA C 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGCGAAACTATGTCT;RSEQ=AAAAAAAAAAAACTGCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:23:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 30314457 . A AG 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.35424;LSEQ=GAAAGCAAGTCTCCATCTTG;RSEQ=GAAAAAAAAAAAATTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:2,0:174,8:182,2:0.0108:1,0:27:1:33.8:1:1:0:60:4:0.0109:0.0054:0 0/1:137:2:2,0:133,2:135,2:0.0146:1,0:26.5:1:33.5:1:1:0:60:4:0.0149:0:0 +19 30314459 . A G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0;SOR=3.84011;LSEQ=AAGCAAGTCTCCATCTTGAG;RSEQ=AAAAAAAAAAATTTAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:23:23,0:174,10:184,23:0.1036:2,1:23.9:1:32.3:1:0.60648:0:58.9:46:0.105:0:1.4 0/1:159:49:49,0:97,3:100,49:0.3082:1,1:22.4:1:31:1:0.55106:0:60:48:0.3057:0:1.1 +19 30314471 . T A 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2254;SOR=3.00833;LSEQ=ATCTTGAGAAAAAAAAAAAA;RSEQ=TTAAAAATTAAAAAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:2:2,0:284,19:303,2:0.0066:2,0:27.5:1:11.5:1:1:0:60:0:0:0:2 0/1:205:4:3,1:194,7:201,4:0.0195:1,2:29.3:1:30:1:0.14822:8.97556:60:8:0.0198:0:2.5 +19 30314666 . C T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.32316;LSEQ=AGCGGTAAGAAGCAGAGCAG;RSEQ=GGGCCGGAAATGGCGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:772:91:27,64:248,433:681,91:0.1179:2,2:25.1:1:30.4:1:0.2439:1.35711:60:182:0.1194:0:1.1 0/1:663:204:79,125:173,285:458,204:0.3077:2,2:25.3:1:29.1:1:0.86242:1.04:60:50:0.3058:0:1.2 +19 30315112 . C A 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGCTGGGCAGGGGGCTG;RSEQ=CCTCTCCACATTATCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:3,2:0.4:2,0:37.5:1:30.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 31301619 . T TCA 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTAGACTTCAGCTCTTTGT;RSEQ=CAGTTATCTCCATTACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:9.8:1:31.2:1:1:0:60:10:1:0.6:0 1/1:3:3:3,0:0,0:0,3:1:0,0:41:1:30.2:1:1:0:60:6:1:0:0 +19 31301718 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00348;SOR=0;LSEQ=TGATCCTTTTATCACCTCAA;RSEQ=ACCCTGCACTACAATGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:63:62,1:0,0:0,63:1:0,1:26.7:1:32.9:1:1:0:60:126:1:0:1.1 1/1:32:27:26,1:5,0:5,27:0.8438:0,1:17.5:1:31.7:1:1:0:60:54:0.8438:0:1.1 +19 31301886 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17312;LSEQ=AGGTTTCCAGCCCGCTGAGT;RSEQ=CTGCCTTTCTTTCTGTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:482:406:192,214:38,38:76,406:0.8423:2,2:25.2:1:30:1:0.70814:1.11433:59.9:39.6:0.8498:0:1.1 0/1:373:179:86,93:93,101:194,179:0.4799:2,2:25.1:1:28.7:1:1:1.00:60:58.667:0.4783:0:1.1 +19 31301979 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51312;SOR=0;LSEQ=ATTTAATAATCTTTTTTGTG;RSEQ=TTTGTCTTTAATGCCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:38,116:154,2:0.0128:2,2:19:1:29:1:0.43871:3.03:60:4:0.0131:0:1.5 0/0:110:0:0,0:25,85:110,0:0:2,0:22.4:1:31.1:1:1:0:60:220:1:0:0.2 +19 31704226 . G A 47 d5;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCCAATATCACACCACT;RSEQ=CACTCCAGCCTGAGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:23:0:29.7:1:1:0:40:6:1:0:2.3 1/1:1:1:0,1:0,0:0,1:1:0,0:37:0:30:0:1:0:41:2:1:0:1 +19 31706411 . A G 282 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03404;LSEQ=TTAAAAAACTAAAACTCTGA;RSEQ=GATAGCTGGTCCCAATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:492:472:180,292:8,12:20,472:0.9593:2,2:26.3:1:31.8:1:1:1.08131:60:66.429:0.9607:0:1.1 0/1:470:209:88,121:108,152:260,209:0.4447:2,2:25.3:1:30.7:1:0.92513:1.02:60:103.5:0.4471:0:1.1 +19 31706513 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1771;SOR=Inf;LSEQ=TCTAAGCTGGGTGTGGTGGC;RSEQ=CACGCCTATAATCCCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:5,69:74,0:0:2,0:22.5:1:29.7:1:1:0:58.8:17.5:0.9859:0:0.1 0/1:55:2:1,1:3,50:53,2:0.0364:2,2:10:0:31:0:0.14141:14.58:55:4:0.0377:0:1 +19 32988213 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18525;SOR=Inf;LSEQ=GGAGGGTGAGTCGTCCAAGT;RSEQ=ATTGATAAGGTCAAGCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:70,63:133,0:0:2,0:29.4:1:32.1:1:1:0:57.7:43.333:1:0:0.1 0/1:101:2:1,1:50,49:99,2:0.0198:2,2:28.5:1:30:1:1:1.02021:43:4:0.0208:0:1 +19 33185013 . A G 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.46001;LSEQ=CCTTGATTCTAGAGGAAACA;RSEQ=ATTTGACAAGGAGGTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,2:3,2:0.4:2,0:7:0:30.5:1:0.4:0:21:4:0.4:0:1 1/0:10:5:3,2:4,1:5,5:0.5:2,2:39.4:1:30.8:1:1:2.41422:38.8:10:0.5:0:1 +19 33185051 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AAAATACAGGGCCCGAAGGC;RSEQ=AGTAATAGTAAAACGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:17,4:21,0:0:2,0:15.2:1:29.9:1:1:0:45:20:1:0:0.3 0/1:28:2:1,1:19,7:26,2:0.0714:2,2:8.5:1:28.5:1:0.49735:2.60494:38:4:0.0714:0:1.5 +19 33782249 . C T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTGACCCCTCCAGCCCTG;RSEQ=ATCGGCCTTGAGATCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:11:0:30:1:1:1:60:4:0.5:0:1.5 +19 33782794 . G A 48 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=3.51553;LSEQ=CACGCTGACCTCCTGGGCCC;RSEQ=AGCTGGGTTGGGCAAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:1,0:1,3:4,1:0.2:2,0:47:0:30:0:0.4:0:60:2:0.2:0:1 1/0:6:3:1,2:1,2:3,3:0.5:2,2:35:1:30.3:1:1:1:60:6:0.5:0:1.3 +19 33784339 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0855;SOR=Inf;LSEQ=AAACACACATTTCCTAACAG;RSEQ=GAGTAGACACCGTGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:97,1:98,0:0:1,0:25:1:32.6:1:1:0:59.3:97:1:0:0.1 0/1:41:2:2,0:38,1:39,2:0.0488:1,0:39:1:28.5:1:1:0:60:4:0.0488:0:1 +19 33784657 . T C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCGGGAGGGCATGGCATTC;RSEQ=TGGGGGGTGCTGGGGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:837:0:0,0:276,560:836,0:0:2,0:24:1:30.3:1:1:0:60:37:0.9988:0:0.1 0/1:581:22:9,13:198,360:558,22:0.0379:2,2:23.3:1:30.1:1:0.65231:1.26:60:44:0.0389:0:1.1 +19 33784680 . T A 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00731;SOR=Inf;LSEQ=GGGGGTGCTGGGGAGGGTGC;RSEQ=CTGGTTGGCTGGAGGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:0:0,0:122,448:570,0:0:2,0:24.1:1:30.3:1:1:0:60:50.818:1:0:0.1 0/1:343:5:4,1:80,256:336,5:0.0146:2,2:8.6:1:24.2:1:0.01412:12.68:60:4:0.012:0:1.2 +19 33789010 . G A 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=21.68768;LSEQ=CCCAGTGCCCCATCTTTGGC;RSEQ=CAGGCCCTGGCATACAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:1:1,0:366,32:398,1:0.0025:2,0:29:0:32:0:1:0:60:2:0.0026:0:1 0/1:212:11:10,1:182,18:200,11:0.0519:2,2:32.2:1:28.6:1:1:1.01106:60:10:0.0476:0:1.5 +19 33789248 . G GC 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.26344;SOR=0.69966;LSEQ=CCTTCCTCCCCTCTACTTTG;RSEQ=CCCCCCCCGGGGGCCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1284:36:12,24:458,782:1240,36:0.028:2,2:30.2:1:31.1:1:0.72838:1.17125:60:35:0.0277:0.0039:0.3 0/1:910:18:6,12:362,525:887,18:0.0198:2,2:29.2:1:29.6:1:0.63174:1.37857:59.7:17:0.0191:0.0011:0.5 +19 33789251 . CC T 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCCCCTCTACTTTGGCC;RSEQ=CCCCGGGGGCCTCGCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1271:0:0,0:464,801:1265,0:0:2,0:24.8:1:31.4:1:1:0:59.9:59.238:0.9952:0:0.2 0/1:897:46:15,31:339,492:831,46:0.0513:2,2:25.4:1:30.2:1:0.28505:1.42343:59.6:45:0.0511:0.01:0.4 +19 33789397 . A G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.28286;SOR=1.67861;LSEQ=TTCCGGGAGCCATCAGCTTT;RSEQ=AAAGAGGAAGCCCCTAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:44:1,43:0,48:48,44:0.4783:1,1:20.4:1:31.3:1:0.47826:0:60:21:0.4719:0:1.2 1/0:28:17:1,16:0,11:11,17:0.6071:0,1:28.5:1:31.1:1:1:0:60:34:0.6071:0:1 +19 33792302 . C T 109 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00116;SOR=6.41028;LSEQ=CTGGCAGCTGGCGGAAGATG;RSEQ=CCCGCAGCGTGTCCAGTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1681:3:1,2:883,792:1675,3:0.0018:2,2:13.7:1:25:1:0.60576:2.22878:60:2:0.0012:0:1 0/1:1323:15:6,9:668,639:1307,15:0.0113:2,2:28.4:1:28.1:1:0.4442:1.56754:59.3:30:0.0115:0:1.2 +19 33792520 . G A 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04964;SOR=0.14019;LSEQ=GCCTTGCCCGCGCCGCTGCC;RSEQ=CCACTCGCGCGGAGGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:793:9:6,3:240,544:784,9:0.0113:2,2:17.1:1:30.1:1:0.02911:4.52:60:18:0.0116:0:1.3 0/0:623:1:1,0:215,407:622,1:0.0016:2,0:1:0:24:0:0.34671:0:60:2:0.0016:0:1 +19 33792620 . C T 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40487;SOR=0.34419;LSEQ=GCGCGGGCGCGGGGTGCGGG;RSEQ=TGGGCACGGGCGTGGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:4:1,3:129,88:217,4:0.0181:2,2:8.3:1:28.8:1:0.30837:4.36931:60:8:0.0183:0:1.3 0/0:159:1:0,1:94,64:158,1:0.0063:2,0:1:0:28:0:0.40881:0:60:2:0.0063:0:1 +19 33792623 . G T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19174;SOR=Inf;LSEQ=CGGGCGCGGGGTGCGGGCTG;RSEQ=GCACGGGCGTGGGCGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:136,97:233,0:0:2,0:15.8:1:31.3:1:1:0:59.5:57.25:1:0:0.3 0/1:182:2:1,1:104,76:180,2:0.011:2,2:6:0:31.5:1:1:1.36601:60:4:0.0112:0:1 +19 33792625 . C T 41 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.27154;LSEQ=GGCGCGGGGTGCGGGCTGGG;RSEQ=ACGGGCGTGGGCGGCGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:1,2:137,105:242,3:0.0122:2,2:11.3:1:24:1:0.58222:2.59945:60:2:0.0082:0:1.3 0/1:194:3:1,2:108,83:191,3:0.0155:2,2:8:1:26:1:0.58243:2.58977:60:6:0.0155:0:1 +19 33792631 . C A 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTGCGGGCTGGGCACGGG;RSEQ=GTGGGCGGCGGCGTGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:163,130:293,0:0:2,0:19.2:1:31.6:1:1:0:59.7:292:0.9932:0:0.3 0/1:246:19:11,8:122,102:224,19:0.0772:2,2:14.6:1:29.2:1:0.81496:1.15:60:38:0.0802:0:1.3 +19 33792637 . C T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.66236;SOR=1.82836;LSEQ=GGGCTGGGCACGGGCGTGGG;RSEQ=GGCGGCGTGGGGTGACCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:2:0,2:174,153:327,2:0.0061:2,0:1:0:27:1:0.2212:0:60:4:0.0062:0:1 0/1:271:3:1,2:145,123:268,3:0.0111:2,2:21:1:28.7:1:0.59666:2.35046:60:6:0.0113:0:1.3 +19 33792740 . G A 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32929;SOR=3.73689;LSEQ=GGTGCGCGGGCGGCGGGTGC;RSEQ=GGTGCGGGTGCGAGGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:1:1,0:143,122:265,1:0.0037:2,0:1:0:26:0:1:0:60:2:0.0038:0:1 0/1:216:3:2,1:110,103:213,3:0.0139:2,2:17.7:1:31.3:1:1:1.87:60:6:0.0142:0:1.3 +19 33792751 . C T 65 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.07836;SOR=0;LSEQ=GGCGGGTGCGGGTGCGGGTG;RSEQ=GAGGGCGGCGGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:5:2,3:145,115:260,5:0.0187:2,2:6:1:28:1:0.65853:1.88672:60:10:0.019:0:1.2 0/0:192:0:0,0:104,86:190,0:0:2,0:13.5:1:30:1:1:0:59.8:30.667:0.9892:0:0.3 +19 33792754 . GGGC G 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.81672;SOR=1.13967;LSEQ=GGGTGCGGGTGCGGGTGCGA;RSEQ=GGCGGCGGCGGCGGCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:10:6,4:138,107:245,10:0.0389:2,2:23.3:1:33.7:1:1:1.16:60:20:0.0397:0:0.1 0/1:204:9:5,4:109,83:192,9:0.0441:2,2:22.6:1:30.9:1:1:1.05031:60:18:0.0462:0.0049:0.4 +19 33792759 . G T 51 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.03496;SOR=Inf;LSEQ=CGGGTGCGGGTGCGAGGGCG;RSEQ=CGGCGGCGGCGGCGGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:147,107:254,0:0:2,0:15.6:1:31.9:1:1:0:60:126:1:0:0.3 0/1:195:4:1,3:111,79:190,4:0.0205:2,2:5.3:1:25.5:1:0.3125:4.1853:60:8:0.0208:0:1.3 +19 33792772 . C T 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=1;SOR=0.71049;LSEQ=GAGGGCGGCGGCGGCGGCGG;RSEQ=GGCTGGTAAGGGAAGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:4:1,3:209,129:338,4:0.0117:2,2:11.3:1:28.5:1:0.16205:4.83829:60:8:0.0118:0:1 0/0:240:2:0,2:143,95:238,2:0.0083:2,0:1:0:28:1:0.16234:0:60:4:0.0084:0:1 +19 33792865 . C T 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0309;SOR=Inf;LSEQ=ACCAGCGGCCGCAGCGCCGG;RSEQ=GCCCCGACGCGCTCGTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:0:0,0:234,305:539,0:0:2,0:25.5:1:30.7:1:1:0:60:76:1:0:0.2 0/1:554:6:2,4:252,294:546,6:0.0108:2,2:11.8:1:27:1:0.69178:1.71268:56.3:12:0.011:0:1.2 +19 33792894 . G A 56 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44026;SOR=0.47315;LSEQ=GCGCTCGTACAGGGGCTCCA;RSEQ=CCTGCCGTCCAGGTAGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:4:3,1:98,195:293,4:0.0135:2,2:7.5:1:28.3:1:0.11567:5.93:59.5:8:0.0137:0:1 0/0:312:2:2,0:118,192:310,2:0.0064:2,0:1:0:24.5:1:0.14717:0:60:4:0.0065:0:1 +19 33792938 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50387;SOR=Inf;LSEQ=CCGCGCAGCCGTAGCCGGGC;RSEQ=GGGGCCCGTGCGCTCCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:15,27:42,0:0:2,0:18.9:1:30.7:1:1:0:60:41:1:0:0.4 0/1:55:2:1,1:18,34:52,2:0.0364:2,2:16.5:1:26:1:1:1.87:60:4:0.0364:0:1.5 +19 33793007 . TCGC T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=1;SOR=1.26184;LSEQ=GCGCGCCCGGGTAGTCAAAG;RSEQ=CGCCGCCGCCGCCGCCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:2:2,0:183,43:226,2:0.0088:2,0:33:0:34:0:1:0:60:4:0.0089:0:0 0/1:181:2:1,1:135,44:179,2:0.011:2,2:19:1:28:1:0.43646:3.04505:60:4:0.0111:0:0 +19 33793011 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=3;SSF=0.13563;SOR=0;LSEQ=GCCCGGGTAGTCAAAGTCGC;RSEQ=GCCGCCGCCGCCGCCCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:4:1,3:212,54:266,4:0.0148:2,2:15.8:1:29:1:0.0306:11.6279:60:8:0.0149:0:1.3 0/0:209:0:0,0:152,56:208,0:0:2,0:14.7:1:30.4:1:1:0:60:40.6:0.9951:0:0.3 +19 33793016 . C T 46 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=1;SOR=1.2909;LSEQ=GGTAGTCAAAGTCGCCGCCG;RSEQ=CGCCGCCGCCCGTGGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:3:1,2:251,68:319,3:0.0093:2,2:13.3:1:30:1:0.12033:7.3209:60:6:0.0093:0:1 0/1:250:3:1,2:179,68:247,3:0.012:2,2:12:1:29.3:1:0.19022:5.22369:60:6:0.0122:0:1 +19 33793372 . C T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16435;SOR=Inf;LSEQ=CCTCGGCGGCCTCCAGCCTG;RSEQ=GCGGGGCGTCGCCGCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:49,160:209,0:0:2,0:21:1:30.9:1:1:0:60:103.5:1:0:0.1 0/1:143:2:1,1:35,105:140,2:0.014:2,2:19:0:27.5:1:0.44411:2.97:60:4:0.0142:0:1 +19 33795172 . C A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16767;SOR=5.57091;LSEQ=TGCTGAGCCAAATGCAGGAC;RSEQ=CATTCATATAGCATTCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:1:0,1:106,406:512,1:0.0019:2,0:3:0:27:0:1:0:60:2:0.002:0:1 0/1:371:4:3,1:96,269:365,4:0.0108:2,2:10.5:1:24.5:1:0.06068:8.35:60:8:0.011:0:1 +19 33795241 . G A 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00044;SOR=Inf;LSEQ=AAGCACCAAGAGCGATTTGC;RSEQ=TTTTTTTCTGCGGTGCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:1,126:127,0:0:1,0:23.1:1:32.6:1:1:0:59.7:62.5:1:0:0.1 0/1:66:7:0,7:0,58:58,7:0.1061:1,0:16:1:29.3:1:1:0:60:14:0.1077:0:1.1 +19 33796867 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54848;SOR=0;LSEQ=GAAGCCTAAAAGTGTACCTC;RSEQ=GGATGAGGAGGAAATGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:2,0:180,1:181,2:0.0109:1,0:17:1:30:1:1:0:60:4:0.0112:0:1 0/0:95:0:0,0:90,5:95,0:0:2,0:23.5:1:30:1:1:0:60:190:1:0:0.1 +19 33796881 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11052;SOR=Inf;LSEQ=TACCTCGGGATGAGGAGGAA;RSEQ=TGGTTTTGAGGGCAAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:250,2:252,0:0:1,0:23.8:1:30.4:1:1:0:60:41:1:0:0.1 0/1:126:2:1,1:120,4:124,2:0.0159:1,2:12.5:1:27:1:0.0781:26.94449:60:4:0.016:0:1 +19 33797172 . A G 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGAAGTGGCTCTGGCTC;RSEQ=TGTGCAACTGAGACAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:857:0:0,0:226,630:856,0:0:2,0:23.2:1:31.1:1:1:0:59.9:213:1:0:0.1 0/1:660:43:17,26:196,421:617,43:0.0652:2,2:25.4:1:29.5:1:0.31305:1.40:60:42:0.0645:0:1.1 +19 33797283 . TG T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGTACACAGGCCCAGTG;RSEQ=GGGGGTTGAGCGTGAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:0,2:2,85:87,2:0.0225:1,0:13.5:1:27:1:1:0:60:4:0.023:0.0112:0.5 0/0:43:0:0,0:0,43:43,0:0:1,0:20.9:1:29.1:1:1:0:60:9.75:1:0:0.1 +19 33798450 . CCCTT C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=5.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTTTCTTTTTCTTTTCTTTT;RSEQ=CCTTCCTTCCTTCCTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:31.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 33798509 . C T 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTCTTTCTCTCTCTCTCT;RSEQ=TCTTTCTTTCTTTCTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:15:0:32.5:1:1:0:29.5:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 33905969 . G A 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00832;SOR=0;LSEQ=CCACATGGCAAGCCCTGTGC;RSEQ=CCAGGCCAGACAGGCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:8,1:24,2:26,9:0.2571:2,2:27.4:1:31.1:1:1:1.48133:60:18:0.2571:0:1.1 0/0:23:0:0,0:19,4:23,0:0:2,0:25:1:28.3:1:1:0:60:22:1:0:0.6 +19 33905985 . A G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00101;SOR=6.5112;LSEQ=GTGCGCCAGGCCAGACAGGC;RSEQ=GCCTCAGAAGCCACTTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:5:4,1:40,3:43,5:0.1042:2,2:21.2:1:32.2:1:0.36576:3.21397:60:10:0.1042:0:1 0/1:32:14:10,4:14,4:18,14:0.4375:2,2:25.4:1:27.4:1:0.70349:1.38516:60:13:0.4194:0:1.1 +19 33906015 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59713;SOR=2.33509;LSEQ=GCCACTTCACACCTCTGTGG;RSEQ=GCCCTCCCAGAAAGCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:1:0,1:69,12:81,1:0.0122:2,0:1:0:25:0:0.15854:0:60:2:0.0125:0:1 0/1:71:2:1,1:46,23:69,2:0.0282:2,2:17.5:1:27.5:1:1:1.97912:60:4:0.0286:0:1.5 +19 33906052 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21818;SOR=Inf;LSEQ=CGAGAAGAGGCCTGACCCAC;RSEQ=CCGTGGAACAGGGGTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:104,61:165,0:0:2,0:24.9:1:30.2:1:1:0:60:40.25:1:0:0.6 0/1:146:2:1,1:87,57:144,2:0.0137:2,2:38:1:29:1:1:1.52173:60:4:0.0137:0:1 +19 33906063 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.20705;SOR=Inf;LSEQ=CTGACCCACGCCGTGGAACA;RSEQ=GGGTGCTCCCTTGGCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:126,77:203,0:0:2,0:24.9:1:32:1:1:0:60:66.667:1:0:0.7 0/1:170:2:1,1:100,68:168,2:0.0118:2,2:30:1:27.5:1:1:1.46714:60:4:0.012:0:1 +19 33906068 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2049;SOR=Inf;LSEQ=CCACGCCGTGGAACAGGGGT;RSEQ=CTCCCTTGGCTTTGTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:126,85:211,0:0:2,0:25.8:1:31.5:1:1:0:60:22.444:1:0:0.7 0/1:175:2:1,1:103,70:173,2:0.0114:2,2:32:0:28.5:1:1:1.46807:60:4:0.0118:0:1 +19 33906102 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.72246;LSEQ=GTGAGATGTGGTCCTGCACC;RSEQ=ACAGAAGCGAACCTCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:36:20,16:124,104:228,36:0.1358:2,2:27.1:1:30.7:1:1:1.05:59.9:35:0.1357:0:3 0/1:185:79:42,37:57,49:106,79:0.427:2,2:24.4:1:29.6:1:1:1.02465:59.3:158:0.4341:0:2.8 +19 33906110 . C T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.99556;LSEQ=TGGTCCTGCACCAACAGAAG;RSEQ=GAACCTCAGAGGTCACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:37:20,17:121,114:235,37:0.1355:2,2:27.2:1:29.8:1:0.86008:1.11:59.9:17.5:0.1296:0:3 0/1:184:81:41,40:53,50:103,81:0.4402:2,2:23.1:1:29.1:1:1:1.03397:59.3:80:0.4469:0:2.9 +19 33906123 . T C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0268;SOR=1.55208;LSEQ=ACAGAAGCGAACCTCAGAGG;RSEQ=CACATGGTCATTCTCGACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:130:63,67:63,77:140,130:0.4797:2,2:26:1:31:1:0.62572:1.15:60:31.5:0.4719:0:1.6 1/0:180:106:50,56:35,39:74,106:0.5889:2,2:22.4:1:30.3:1:1:1.0051:59.5:105:0.5899:0:2.3 +19 33906150 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56272;SOR=3.16252;LSEQ=GTCATTCTCGACGTGATGGC;RSEQ=ACAGCGGACCTCTGTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:0,1:102,128:230,1:0.0043:2,0:45:0:12:0:1:0:60:0:0:0:1 0/1:147:2:2,0:61,84:145,2:0.0136:2,0:8:1:30.5:1:0.182:0:55.5:4:0.0138:0:1 +19 33906191 . C T 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00106;SOR=Inf;LSEQ=AAGTGACCTGCAGACAACCA;RSEQ=GGGCTGCGCTGGGACTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:45,111:156,0:0:2,0:23.2:1:30:1:1:0:60:38:1:0:0.4 0/1:97:7:3,4:26,63:89,7:0.0722:2,2:18.1:1:30.6:1:0.42823:1.80:60:14:0.0722:0:2.7 +19 33906196 . TG T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71329;SOR=0.55689;LSEQ=ACCTGCAGACAACCACGGGC;RSEQ=CGCTGGGACTGGCCGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:6:1,5:38,97:135,6:0.0426:2,2:21.7:1:29.9:1:1:1.9508:60:12:0.0429:0.0142:0.2 0/1:83:2:1,1:26,55:81,2:0.0241:2,2:32.5:1:28.5:1:0.54746:2.09:60:4:0.0241:0:0.5 +19 34080051 . TAC T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTTACTGAATATATATATA;RSEQ=ACATATATATATTTTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23.5:1:31.5:1:1:0:45:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 34080228 . C G 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTTCAGTTGAACCCAGGTAC;RSEQ=TTTCTCTTTGGCTTCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:4,1:5,5:0.5:2,0:20.6:1:31.2:1:1:0:43.4:10:0.5:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:2:0:29:0:1:0:60:2:0.5:0:1 +19 34080254 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGCTTCTTTCTTTTTC;RSEQ=GATCATTTTCCTTCATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:14,3:17,2:0.1053:2,2:20:0:32.5:1:0.38596:4.1833:50:4:0.1053:0:1.5 0/0:4:0:0,0:4,0:4,0:0:0,0:21.5:1:32:0:1:0:53.8:8:1:0:0.3 +19 34080443 . CC TT 163 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGACACTTGTGAGGCATT;RSEQ=TTTTTGAACAGTGCCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:38:14,24:24,38:62,38:0.3725:2,2:27.9:1:31.1:1:1:1.08183:38.2:76:0.3838:0:1.3 0/0:70:0:0,0:32,38:70,0:0:2,0:22.7:1:30.3:1:1:0:42.6:140:1:0:0.2 +19 34080511 . G C 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.06947;LSEQ=TTATAGATTCGCATATACGT;RSEQ=GCCAAAGGAACAACTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:4,3:6,4:10,7:0.4118:2,2:13.1:1:32.6:1:1:1.11721:34:14:0.4375:0:1 0/1:21:9:4,5:6,6:12,9:0.4286:2,2:10.3:1:29.7:1:1:1.23677:39.1:18:0.4286:0:1 +19 34080579 . C G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50043;SOR=0.76995;LSEQ=TCGGGTGCCTCTCCTCTTTC;RSEQ=CTTTGTCTTCGTCATTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:30:15,15:28,20:48,30:0.3797:2,2:29.1:1:31.3:1:0.4927:1.3939:47.1:60:0.3896:0:1.1 0/1:75:24:13,11:27,24:51,24:0.32:2,2:24.4:1:31.1:1:1:1.05:50:48:0.3288:0:1.2 +19 34080659 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20274;SOR=Inf;LSEQ=TTTACTGAATATTTTAAACC;RSEQ=ACTGTTGAGACCTACTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:15,32:47,0:0:2,0:22.4:1:30.6:1:1:0:52.2:10.75:1:0:0.4 0/1:39:2:1,1:14,23:37,2:0.0513:2,2:29:1:28:1:1:1.62:56:4:0.0526:0:1 +19 34113746 . C A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAACTCTCCAGGGCACCGGC;RSEQ=TGTGAGTGCTGGAGGCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:48:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:30:1:1:0:60:4:1:0:1 +19 34115267 . G A 71 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CTTGGTAGAACATCCCCCTC;RSEQ=GACTGTAACCGACGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:4,1:10,0:10,5:0.3333:0,2:17.6:1:31:1:0.33333:0:60:10:0.3333:0:1.2 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:11:0:31:0:1:0:60:2:0.3333:0:2 +19 34115326 . A T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03527;SOR=4.9005;LSEQ=CTGCTGTTAGAGATGCCTTT;RSEQ=TAATCTTGTAGCCAGAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:4,0:22,1:23,4:0.1481:1,0:39.8:1:32:1:1:0:60:8:0.1481:0:1.3 0/1:17:8:8,0:9,0:9,8:0.4706:0,0:26.8:1:30.6:1:1:0:60:16:0.4706:0:1.1 +19 34115396 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53153;SOR=0;LSEQ=TGTTTCCATAATGAACATTT;RSEQ=CTGATTACAGGGTATCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:94,5:99,2:0.0198:2,2:17:1:31:1:0.11584:17.25167:60:4:0.0198:0:1 0/0:59:0:0,0:59,0:59,0:0:1,0:24.2:1:27.9:1:1:0:60:118:1:0:0.1 +19 34115548 . T C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.19224;LSEQ=TGGGCTACTCTCAGAATTTG;RSEQ=CTTCAGTTCTCTTAAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:114:48,66:166,210:376,114:0.2327:2,2:24.4:1:31.7:1:0.74686:1.0867:60:113:0.234:0:1.1 0/1:398:159:72,87:89,150:239,159:0.3995:2,2:27:1:30.6:1:0.11849:1.39:60:52:0.398:0:1.1 +19 34115930 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCCACACTGGAGAAAC;RSEQ=TGGGGCAGCGGGGAACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:42:1:30.5:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 34115967 . A T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGTGAGCAGGAAAGAGGAC;RSEQ=CAGGATTATGGCAGCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:18.5:1:32:0:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 34116248 . G A 28 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCCACCTTGGCCTCCCA;RSEQ=AGTGTTGGGATTACAGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:28:1:1:0:35:4:1:0:1 +19 34356388 . GG AA 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00185;SOR=Inf;LSEQ=TAACGTATCCTCTCTGCTGC;RSEQ=TGCTGGACGGACTTAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:35,48:83,0:0:2,0:24.6:1:30.2:1:1:0:59.9:40.5:1:0:0.7 0/1:73:8:3,5:27,38:65,8:0.1096:2,2:26.4:1:30.3:1:1:1.18151:60:16:0.1111:0.0137:0.9 +19 34356389 . G A 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.41494;SOR=1.32556;LSEQ=AACGTATCCTCTCTGCTGCG;RSEQ=TGCTGGACGGACTTAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:43:18,25:16,23:39,43:0.5244:2,2:24.6:1:30:1:1:1.03:60:42:0.525:0:1.1 1/0:69:41:17,24:8,13:21,41:0.5942:2,2:27.2:1:29.1:1:1:1.15:60:40:0.6557:0:1.1 +19 34357872 . G A 50 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGTGAGAACCCAGGGTC;RSEQ=GCGAGCAGGCAGGCAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:40:1:32:1:1:0:60:6:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:29:1:1:0:60:4:1:0:1 +19 36227688 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CATCTGCGCTTCGAGATCAG;RSEQ=AGTGAGGATGGGTTCAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:31.5:1:1:0:60:4:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:34.5:1:27.5:1:1:1:60:4:0.5:0:1 +19 36228954 . G T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGTTCCCTGTTCATCCT;RSEQ=CCCTGCAGATCAGCCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:27.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 36229192 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.48908;SOR=0;LSEQ=CATCCCTGCAGGGCATCGGG;RSEQ=GCTATATGTTCCGCATGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:15,2:17,2:0.1053:2,2:25.5:1:30.5:1:0.29825:6.32456:60:4:0.1053:0:1.5 0/0:16:0:0,0:12,4:16,0:0:2,0:28.6:1:28.3:1:1:0:60:32:1:0:0.1 +19 36229256 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.12848;SOR=Inf;LSEQ=GATGCATGGCAATGCCGCCC;RSEQ=CTTCATCAACCACTCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:33,18:51,0:0:2,0:24.9:1:31:1:1:0:60:102:1:0:0.2 0/1:29:2:1,1:14,13:27,2:0.069:2,2:28:1:28:1:1:1.07415:60:4:0.069:0:1 +19 36229296 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GAGCCCAACTGCTTCTCTCG;RSEQ=GTCATCCACGTGGAGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:45,21:66,2:0.0294:2,2:26:1:31:1:0.54565:2.11677:60:4:0.0313:0:1 0/0:43:0:0,0:30,13:43,0:0:2,0:25.5:1:31.1:1:1:0:60:42:1:0:0.1 +19 36229351 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=0;LSEQ=TCTTCGCCCTGCGCCGCATC;RSEQ=TGCGTGGTGAGGAGCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:86,48:134,2:0.0147:2,2:12.5:1:29.5:1:1:1.78348:60:4:0.015:0:1.5 0/0:124:0:0,0:78,46:124,0:0:2,0:20.1:1:30.3:1:1:0:60:123:1:0:0.1 +19 36229471 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50141;SOR=0;LSEQ=TTAACTGAGGCCGTGGCTGC;RSEQ=CACCACGACCCCTCACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:28,73:101,2:0.0194:2,2:15.5:1:29.5:1:0.48582:2.58:60:4:0.0202:0:2 0/0:86:0:0,0:28,58:86,0:0:2,0:23.5:1:28.3:1:1:0:60:13.333:1:0:0.1 +19 36229477 . C T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18035;SOR=4.89002;LSEQ=GAGGCCGTGGCTGCCCACCA;RSEQ=GACCCCTCACACCTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:1,0:23,67:90,1:0.011:2,0:18:0:15:0:0.26374:0:60:0:0:0:1 0/1:77:4:1,3:22,51:73,4:0.0519:2,2:31.8:1:29.8:1:1:1.28996:60:8:0.0519:0:1 +19 36229524 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1124;SOR=Inf;LSEQ=GCTGCCATCTTGCCCCTAGC;RSEQ=TGGGGGCTCCCTAGCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:30,0:0:1,0:22.1:1:33.7:1:1:0:60:29:1:0:0 0/1:30:4:0,4:0,26:26,4:0.1333:1,0:28.5:1:30.3:1:1:0:60:8:0.1379:0:1 +19 36234762 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16131;SOR=Inf;LSEQ=CTGGAGGTTCTGGGAAATGG;RSEQ=CCGCAGATGCATGAAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:15,20:35,0:0:2,0:28.7:1:30.7:1:1:0:60:16.5:1:0:0.1 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:14:0:30:0:1:1.19087:60:4:0.087:0:1.5 +19 36833695 . C CAG 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.15459;LSEQ=TATTATTAATTTTCTTAAAA;RSEQ=GGGTGAAAGGGCTCCTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:162:130:95,35:27,5:32,130:0.8025:2,2:21.2:1:31.1:1:0.25314:1.98195:60:260:0.8075:0.2407:0.1 0/1:138:53:34,19:60,24:84,53:0.3841:2,2:21.2:1:29:1:0.45017:1.39356:59.8:25.5:0.3806:0.1014:0.1 +19 36833798 . A G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.20836;LSEQ=AGCTAGCTCCACTGGACTAG;RSEQ=AAAATTACTCATAAGCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:251:108,143:56,54:110,251:0.6953:2,2:26:1:31.4:1:0.17051:1.37188:60:34.857:0.6912:0:2 0/1:373:120:62,58:131,122:253,120:0.3217:2,2:25.4:1:30.2:1:1:1.00448:60:59:0.3198:0:2 +19 36833811 . A G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19291;LSEQ=GGACTAGAAAAATTACTCAT;RSEQ=AGCCAATCATCTACATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:339:233:95,138:51,55:106,233:0.6873:2,2:27:1:31.9:1:0.23698:1.34577:60:45.6:0.6888:0:2 0/1:360:107:51,56:122,131:253,107:0.2972:2,2:27.5:1:30.7:1:1:1.02254:60:214:0.2997:0:2.1 +19 36833881 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24384;SOR=Inf;LSEQ=GTGTACCATGGGACAGATTG;RSEQ=ACTCTCATCATTTTGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:34,109:143,0:0:2,0:23:1:32.4:1:1:0:60:142:1:0:0.7 0/1:140:2:1,1:41,97:138,2:0.0143:2,2:7.5:1:27.5:1:0.51151:2.35:60:4:0.0145:0:1 +19 36834637 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGGGACTGCATCTGGTGAG;RSEQ=GCCTTCTTGCTGGTGACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 38205212 . A AAACAACAAC 76 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=31;MSI=13.000;MSILEN=3;SSF=0.13193;SOR=7.61356;LSEQ=CAGAGCAAGACTCCGTCTCA;RSEQ=AACAACAACAACAACAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:6,0:6,2:0.25:0,2:25:0:32.6:1:0.25:0:21:4:0.25:0:0 1/0:8:6:3,3:0,0:0,6:0.75:0,2:12.5:1:29.6:1:1:0:29.8:12:0.75:0.625:0 +19 39103257 . G C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=CCACGCCTGCCTACCTGAGA;RSEQ=GGTGCACATCAAAGAGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:15.5:1:29.5:1:1:2.4495:60:4:0.1667:0:1 0/0:14:0:0,0:9,5:14,0:0:2,0:16.5:1:32.1:1:1:0:60:28:1:0:0.1 +19 39350370 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49671;SOR=0;LSEQ=GGGGGCAGGGTAAGGAGGGT;RSEQ=AATCCTCTAAGTGATTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:28,20:48,2:0.0392:2,2:23.5:1:28:1:1:1.39042:50.5:4:0.04:0:1 0/0:45:0:0,0:27,18:45,0:0:2,0:28.7:1:29.8:1:1:0:52.5:10.25:1:0:0.4 +19 39350421 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49657;SOR=Inf;LSEQ=AGTCACGTGATCATAGGACG;RSEQ=GGGTGGGGGGCCCTTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:27,28:55,0:0:2,0:23.9:1:30.5:1:1:0:50.5:26.5:1:0:0.5 0/1:60:2:1,1:29,29:58,2:0.0333:2,2:48:0:30:1:1:1:42:4:0.0339:0:2 +19 39350452 . A G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00949;SOR=4.6998;LSEQ=CCCTTCCCTTTTAGGTAGCC;RSEQ=AAGCAGAGAGAGAAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:3,1:10,16:26,4:0.1333:2,2:25.3:1:31:1:0.29035:4.55:27.3:8:0.1379:0:1.3 0/1:40:17:8,9:11,12:23,17:0.425:2,2:27.5:1:29.6:1:1:1.03047:29.8:34:0.425:0:1 +19 39350462 . G T 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.50273;SOR=Inf;LSEQ=TTAGGTAGCCAAAGCAGAGA;RSEQ=AGAAGGCAGCATACGTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:11,15:26,0:0:2,0:20.7:1:32.2:1:1:0:44.9:25:1:0:0.5 0/1:35:2:1,1:13,20:33,2:0.0571:2,2:7:0:26:1:1:1.52:42:4:0.0571:0:2 +19 39538324 . C T 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCCTGACCTCAAGTGAGC;RSEQ=GCCCGTCTTGGCCTTCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:12.3:1:33.7:1:1:0:60:6:0.4286:0:2.3 1/1:1:1:1,0:0,0:0,1:1:0,0:9:0:33:0:1:0:60:2:1:0:2 +19 39538403 . G A 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68562;SOR=1.40133;LSEQ=GTGTCAGAACTGAACTGAAT;RSEQ=AGAAAACACCCAAGTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:17,0:17,4:0.1905:1,0:23.8:1:25:1:1:0:60:3:0.15:0:3 0/1:12:3:3,0:9,0:9,3:0.25:0,0:21.7:1:28.7:1:1:0:60:6:0.25:0:2 +19 39538417 . G C 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18608;LSEQ=CTGAATGAGAAAACACCCAA;RSEQ=TGGTGTCTGCTGTCAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:7,0:25,0:25,7:0.2188:1,0:16.1:1:29.6:1:1:0:60:6:0.1935:0:2.1 0/1:16:4:4,0:12,0:12,4:0.25:0,0:18.8:1:32.8:1:1:0:60:8:0.25:0:1.5 +19 39538478 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51961;SOR=0;LSEQ=CCCCCTATACACCCAGAGTC;RSEQ=CTGAAGTATTCTGTGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:80,24:104,2:0.0189:2,2:12.5:1:26.5:1:0.41779:3.28631:60:4:0.0198:0:2 0/0:69:0:0,0:56,13:69,0:0:2,0:21.1:1:30:1:1:0:60:33.5:1:0:0.8 +19 39538536 . G T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66244;SOR=0.89953;LSEQ=ACTGGATTTGTTTTTCTTGT;RSEQ=TGGGGGGACAGGAGGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:58:32,26:118,80:198,58:0.2266:2,2:28.3:1:30.1:1:0.54869:1.19758:60:57:0.2253:0:2.1 0/1:235:49:30,19:115,69:184,49:0.2085:2,2:28.4:1:29.9:1:0.86979:1.0553:60:98:0.2103:0:2.2 +19 39538538 . G T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.8265;SOR=0.93336;LSEQ=TGGATTTGTTTTTCTTGTGT;RSEQ=GGGGGACAGGAGGAAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:57:30,27:119,84:203,57:0.2192:2,2:28.8:1:30.3:1:0.45072:1.27378:60:56:0.2179:0:2.2 0/1:236:49:30,19:117,70:187,49:0.2076:2,2:29:1:29.9:1:0.8698:1.05831:60:98:0.2094:0:2.2 +19 39538545 . C T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.48991;LSEQ=GTTTTTCTTGTGTGGGGGGA;RSEQ=AGGAGGAAGTAAGGAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:66:41,25:117,97:214,66:0.2357:2,2:26.2:1:30.1:1:0.32167:1.36:59.2:32:0.237:0:1.8 1/0:258:150:91,59:63,45:108,150:0.5814:2,2:24.9:1:28.5:1:0.79705:1.10:60:36.5:0.5771:0:1.8 +19 39538592 . G T 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.61663;LSEQ=AGGATGCTGCTCAGAGACAG;RSEQ=TGAGACAGGAGGGTGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:90:47,43:116,112:228,90:0.283:2,2:24:1:29.8:1:0.90101:1.06:60:89:0.2825:0:1.6 1/0:316:186:92,94:63,67:130,186:0.5886:2,2:27.2:1:29.2:1:0.90913:1.04:60:372:0.5886:0:1.7 +19 39538623 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01535;SOR=0.61889;LSEQ=GGGTGGACCAGCCCAGGACC;RSEQ=GGGCATAGGAGCCAGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:87:44,43:74,112:186,87:0.3187:2,2:29.2:1:31.1:1:0.11553:1.55:60:42.5:0.3148:0:1.4 0/1:263:59:22,37:88,115:203,59:0.2243:2,2:24.2:1:30:1:0.45532:1.28573:60:58:0.2214:0:1.3 +19 39538678 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19261;SOR=Inf;LSEQ=ATAGATTTGAGGGTGCCCAC;RSEQ=GGATTTGCTGAAGAATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:28,112:140,0:0:2,0:23.6:1:31.6:1:1:0:60:69:1:0:0.8 0/1:110:2:1,1:27,81:108,2:0.0182:2,2:32:1:28.5:1:0.44604:2.96:60:4:0.0183:0:2 +19 39538680 . G A 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGATTTGAGGGTGCCCACAG;RSEQ=ATTTGCTGAAGAATTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:21:6,15:18,93:111,21:0.1591:2,2:22.3:1:30.8:1:0.21631:2.05:60:42:0.1603:0:2.1 0/0:108:0:0,0:28,80:108,0:0:2,0:23.2:1:30.6:1:1:0:60:216:1:0:0.7 +19 39538706 . T A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=3.86425;LSEQ=CTGAAGAATTGGGCATGGGA;RSEQ=GCTGGGCCACACAGAACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:20:2,18:4,59:63,20:0.241:2,2:20.5:1:32.5:1:0.62756:1.63:60:40:0.2439:0:1 1/0:56:31:5,26:6,19:25,31:0.5536:2,2:24.2:1:29.8:1:0.51389:1.62737:60:30:0.5455:0:1.3 +19 39538726 . G A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02052;SOR=0.285;LSEQ=TGCTGGGCCACACAGAACAC;RSEQ=TTCAGGATATCAGGCGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:22:0,22:1,32:33,22:0.4:1,1:24.5:1:30.3:1:1:0:60:21:0.3889:0:1.4 0/1:38:6:1,5:2,30:32,6:0.1579:2,2:22.8:1:31.2:1:0.41204:2.89:60:12:0.1579:0:1 +19 39538836 . A G 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTAATCCCAGCACTTTGGG;RSEQ=GGATGAGGTGGGAGGATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:20:1:30.5:1:1:0:60:4:1:0:0 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:11.5:1:32:0:0.33333:0:52.5:4:0.3333:0:1.5 +19 40739513 . A G 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00303;SOR=0;LSEQ=TTGTGTGGATTAAAACCTGA;RSEQ=TCTCCAACCGCCCAACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:29.7:1:31.9:1:1:0:60:14:1:0:1 0/0:4:0:0,0:3,1:4,0:0:2,0:27.5:1:31.3:1:1:0:60:8:1:0:0 +19 40739701 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16615;SOR=Inf;LSEQ=TGGGGACACAAACCAAAAAG;RSEQ=CTAAGTAAAAAGTTAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:174,36:210,0:0:2,0:22.5:1:31.7:1:1:0:60:209:1:0:1 0/1:145:2:2,0:121,22:143,2:0.0138:2,0:12.5:1:26.5:1:1:0:60:4:0.0144:0:1.5 +19 40739715 . T C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26456;SOR=0;LSEQ=AAAAAGGCTAAGTAAAAAGT;RSEQ=AGGGGGAAAAAACCACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:218,57:275,3:0.0108:2,2:8.3:1:32.7:1:0.50581:1.90694:60:6:0.0111:0:2.3 0/0:207:0:0,0:165,42:207,0:0:2,0:23.2:1:29.2:1:1:0:60:24.875:1:0:0.6 +19 40739721 . G T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=0.08537;LSEQ=GCTAAGTAAAAAGTTAGGGG;RSEQ=AAAAAACCACCCAGCGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:308:280:220,60:18,10:28,280:0.9091:2,2:23.6:1:29.5:1:0.09866:2.03:60:139:0.9205:0:1.1 0/1:233:107:84,23:98,28:126,107:0.4592:2,2:25.1:1:27.8:1:1:1.04:60:20.4:0.4513:0:1.1 +19 40739765 . C T 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCGAGCGTGCGTCCTCTG;RSEQ=GTGGGCAGACTGCTCACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:638:0:0,0:422,216:638,0:0:2,0:25.3:1:31.3:1:1:0:60:44.571:1:0:0.5 0/1:524:27:15,12:305,192:497,27:0.0515:2,2:25.5:1:29.6:1:0.54958:1.27022:60:54:0.0521:0:1.3 +19 40739942 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12847;SOR=Inf;LSEQ=CTCCCTGGGGAAACGGCCCC;RSEQ=GCTGGCGGGGGCTGCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:10,186:196,0:0:2,0:25.5:1:32.4:1:1:0:59.9:195:1:0:0.1 0/1:110:2:1,1:12,96:108,2:0.0182:2,2:22:1:28:1:0.22335:7.73:60:4:0.0183:0:1 +19 40741297 . G A 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.31707;SOR=0.39156;LSEQ=AGCACCTGCCTCCCGGAGCA;RSEQ=CTGGGTTCGGGCAGACGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:578:7:5,2:161,410:571,7:0.0121:2,2:9.6:1:28.1:1:0.02309:6.34:60:14:0.0124:0:1.1 0/0:419:2:0,2:123,294:417,2:0.0048:2,0:37:1:32:0:1:0:60:4:0.0049:0:1 +19 40741338 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17521;SOR=Inf;LSEQ=TTTCGGAGCAGGCAGGCCCT;RSEQ=TATGGCCCTTAATGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:24,242:266,0:0:2,0:22.8:1:32.3:1:1:0:60:43.333:1:0:0.1 0/1:192:2:1,1:16,174:190,2:0.0104:2,2:12.5:1:29:1:0.16967:10.58:60:4:0.0105:0:1 +19 40741684 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14563;SOR=Inf;LSEQ=TTTCAGGGGCTGTGTGGGGA;RSEQ=GACACACTGCGACCCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:61,3:64,0:0:1,0:26.1:1:32:1:1:0:60:31:1:0:0.2 0/1:40:2:2,0:35,3:38,2:0.05:2,0:17.5:1:30.5:1:1:0:60:4:0.05:0:3 +19 40741694 . C T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01315;SOR=Inf;LSEQ=TGTGTGGGGACGACACACTG;RSEQ=GACCCTACAAGCGAGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:78,3:81,0:0:1,0:24:1:32.1:1:1:0:60:39.5:1:0:0.2 0/1:43:4:4,0:36,3:39,4:0.093:2,0:21:1:31.3:1:1:0:60:8:0.0952:0:2.5 +19 40741707 . G T 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.056;SOR=7.55029;LSEQ=CACACTGCGACCCTACAAGC;RSEQ=AGCACCCTTGTGGACGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:1,0:87,3:90,1:0.011:1,0:33:0:16:0:1:0:58:0:0:0:8 0/1:51:4:4,0:41,6:47,4:0.0784:2,0:22.5:1:31.3:1:1:0:60:8:0.0784:0:2.8 +19 40741988 . G A 82 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10657;SOR=2.49896;LSEQ=CCCCACCAGTCCACGGCCCG;RSEQ=CCATAGTCATTGTCCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1137:5:3,2:509,621:1130,5:0.0044:2,2:19.6:1:29.8:1:0.66278:1.83:52.6:10:0.0045:0:1.2 0/1:824:9:8,1:346,467:813,9:0.0109:2,2:11.7:1:26:1:0.00633:10.77:58.8:18:0.0111:0:1 +19 40742105 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.64274;LSEQ=CTGGGCTGGAAACACACAGG;RSEQ=CTGGGGGATCCCCCTACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:650:48:31,17:333,269:602,48:0.0738:2,2:27.2:1:31.7:1:0.22998:1.47:60:23:0.0721:0:1.1 0/1:395:89:53,36:173,129:302,89:0.2253:2,2:21.7:1:30.5:1:0.71615:1.10:60:43.5:0.226:0:1.1 +19 40742320 . T C 287 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01449;LSEQ=AAAAGTCAACGGATCTCAGG;RSEQ=GCATGCTCCCAAGGCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:699:695:223,472:1,1:2,695:0.9943:2,2:24.5:1:30.4:1:0.53978:2.11415:60:62.182:0.9942:0:1.1 1/0:534:382:136,246:55,96:151,382:0.7154:2,2:25.5:1:29.9:1:0.92019:1.03626:60:126.333:0.7178:0:1.1 +19 40742428 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51128;SOR=0;LSEQ=GCTGGGCCCAGCACACACAG;RSEQ=CTCACCCTCTGAGGCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:0,2:1,94:95,2:0.0206:1,0:45:1:31:1:1:0:60:4:0.0211:0:1 0/0:69:0:0,0:2,67:69,0:0:1,0:25.3:1:30.3:1:1:0:60:22:1:0:0.2 +19 40743523 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCACACCACTGCACTCAA;RSEQ=AGAGTAAGACTCCTCAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 40744160 . T TA 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.57011;LSEQ=AGGCAGAGCGCAGAAGCTCA;RSEQ=AAGTGACACAGAGCTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:0,4:3,40:43,4:0.0851:2,0:22.3:1:32.1:1:1:0:60:8:0.0889:0.0426:0.3 0/1:20:1:0,1:1,18:19,1:0.05:1,0:41:0:31:0:1:0:60:2:0.05:0:1 +19 40744677 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53899;SOR=0;LSEQ=AAATGGAGACGAAGCCGCCT;RSEQ=CCTCAAGGGAGAGGGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:157,3:160,2:0.0123:1,2:33:0:31:0:0.04892:45.46662:60:4:0.0127:0:1.5 0/0:90:0:0,0:87,3:90,0:0:1,0:22.7:1:31.5:1:1:0:60:29:1:0:0.3 +19 40744697 . T C 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTCAAGGGAGAGGGGCAC;RSEQ=AGATGACACTGAAATTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:238,12:250,0:0:1,0:22.1:1:32.2:1:1:0:59.9:124:1:0:0.2 0/1:135:24:22,2:101,10:111,24:0.1778:2,2:26:1:30.9:1:1:1.09:60:48:0.1791:0:1 +19 40744970 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11329;SOR=Inf;LSEQ=GCCCTGGCCCTGCTTATTCT;RSEQ=CACACACACACCCTGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:9,195:204,0:0:1,0:25.8:1:32.3:1:1:0:60:33:1:0:0.1 0/1:104:2:1,1:5,96:101,2:0.0192:1,2:21.5:1:30:1:0.11365:17.61:60:4:0.0194:0:1 +19 40745621 . CA C 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.64991;SOR=0.48883;LSEQ=AGCATATCTGAAAACAAAAA;RSEQ=AAAAAAATAATGTTTCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:3:2,1:156,2:158,3:0.0186:1,2:23.3:1:32.3:1:0.0552:34.46865:60:6:0.0188:0:0 0/0:109:1:1,0:107,1:108,1:0.0092:1,0:16:0:31:0:1:0:60:2:0.0092:0:0 +19 40746088 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52292;SOR=0;LSEQ=ACTCCGCCCCGACGAAGGGG;RSEQ=GCAAGGCCTTGTGAAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:9,171:180,2:0.011:2,2:31.5:1:33:1:0.10716:18.07:60:4:0.0114:0:1 0/0:116:0:0,0:13,103:116,0:0:2,0:21.1:1:29.8:1:1:0:60:28:1:0:0.1 +19 40747717 . T G 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03772;SOR=Inf;LSEQ=CAGGCTCCCCCTTTTCTGAC;RSEQ=AGGGGGAATTTGTGGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:101,6:107,0:0:2,0:24.9:1:31.6:1:1:0:59.7:52.5:1:0:0.1 0/1:55:3:3,0:50,2:52,3:0.0545:1,0:19:1:29.3:1:1:0:60:6:0.0556:0:1 +19 40748022 . G A 55 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02153;SOR=Inf;LSEQ=CAGTCAGCGCCTGGCTCATG;RSEQ=CCCGTGGGAGGAAATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:0:0,0:148,402:550,0:0:2,0:24:1:31.8:1:1:0:60:60.111:1:0:0.1 0/1:343:4:3,1:93,246:339,4:0.0117:2,2:5:1:27.8:1:0.06814:7.88:60:8:0.0118:0:1 +19 40748026 . G A 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02629;SOR=8.84436;LSEQ=CAGCGCCTGGCTCATGGCCC;RSEQ=TGGGAGGAAATTTTAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:1:1,0:134,389:523,1:0.0019:2,0:10:0:15:0:0.25763:0:60:0:0:0:1 0/1:300:5:3,2:73,221:294,5:0.0167:2,2:9.2:1:28.2:1:0.10618:4.51:60:10:0.0167:0:1 +19 40748648 . C T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=GGAGTCCTGGGCCTCAGAGT;RSEQ=GAACAGCTGAGTGCCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:21,256:277,0:0:2,0:23.3:1:30.2:1:1:0:60:38.571:1:0:0.1 0/1:186:9:1,8:23,153:176,9:0.0484:2,2:19.1:1:27.7:1:1:1.20149:60:8:0.0444:0:1.1 +19 40760939 . C T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.003;SOR=Inf;LSEQ=GCCCCAGCTGGAGAGACCCC;RSEQ=CAACCAGAAGCGCAGATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:78,1:79,0:0:1,0:26.3:1:31.5:1:1:0:60:158:1:0:0.1 0/1:38:5:5,0:33,0:33,5:0.1316:1,0:20.6:1:30.8:1:1:0:60:10:0.1316:0:1.6 +19 40761026 . C A 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTCCTCACACCAGGCTTG;RSEQ=TCCCTCTCAAGGGCAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:318,101:419,0:0:2,0:25.5:1:32.6:1:1:0:60:103.75:1:0:0.1 0/1:320:18:14,4:220,78:298,18:0.0563:2,2:19.2:1:27.7:1:1:1.24:60:17:0.0538:0:1.2 +19 40761212 . G A 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACAGACAGCAGGGGGCTGAG;RSEQ=GGATAGCCCTGCTAGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:93,322:415,0:0:2,0:22.7:1:31.1:1:1:0:59.9:58.286:1:0:0.1 0/1:347:14:7,7:90,243:333,14:0.0403:2,2:18.9:1:29.9:1:0.07189:2.69:60:28:0.0413:0:1.1 +19 40761345 . AGT A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCACAGGGCTCAGGGTCT;RSEQ=GTGTGTGTGTGTGGAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:0,3:1,31:32,3:0.0857:1,0:10.3:1:31.8:1:1:0:60:6:0.0857:0.0571:0 0/0:11:0:0,0:0,11:11,0:0:0,0:15:1:32.5:1:1:0:60:22:1:0:0.1 +19 40762720 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03474;SOR=Inf;LSEQ=GGGTGAAAACAGATCCAAGG;RSEQ=CAAGCAGGCCCAGGACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:125,3:128,0:0:1,0:26:1:31.5:1:1:0:60:24.6:1:0:0.1 0/1:63:3:3,0:58,2:60,3:0.0476:1,0:18:1:29:1:1:0:60:6:0.0484:0:1 +19 40770737 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGCCCCACCCCCACTGGAAT;RSEQ=TAAGCTCCATCAGGGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:24:1:34:0:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:23.5:1:28:1:1:0:60:4:0.6667:0:1.5 +19 40770860 . G A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15485;SOR=0.17482;LSEQ=CACTGTGTTAGTTCAGTGAC;RSEQ=TGACTTCCCCTCTCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:18,1:2,0:2,19:0.9048:0,1:20.5:1:31.6:1:1:0:60:38:0.9048:0:1.1 1/0:5:3:3,0:2,0:2,3:0.6:0,0:33.7:1:29.3:1:1:0:60:6:0.75:0:1 +19 40770982 . T C 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACTGAAGGAGTCCACGAAA;RSEQ=GGGGGCATAAGCAGCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:158:158:156,2:0,0:0,158:1:0,1:23:1:32.1:1:1:0:60:51.667:1:0:1.1 1/0:76:56:52,4:19,1:20,56:0.7368:1,2:26.1:1:32:1:1:1.4549:60:112:0.7368:0:1.1 +19 40771024 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14248;SOR=Inf;LSEQ=CCTGGGGCTGCGGAATGCTG;RSEQ=CTCCTCAGGCTGGTAAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:229,37:266,0:0:2,0:25:1:31.1:1:1:0:60:43.333:0.9962:0:0.5 0/1:163:2:1,1:130,30:160,2:0.0123:2,2:24.5:1:25.5:1:0.34706:4.27924:60:4:0.0124:0:1.5 +19 40771042 . A T 43 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02887;SOR=Inf;LSEQ=TGGCTCCTCAGGCTGGTAAG;RSEQ=CCCTCCGCCTCTGCCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:276,114:390,0:0:2,0:22.2:1:29.5:1:1:0:60:64:1:0:0.3 0/1:275:4:0,4:182,88:270,4:0.0145:2,0:9.8:1:21.8:1:0.01216:0:60:3:0.0111:0:2 +19 41073996 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.51567;SOR=Inf;LSEQ=GCCTGAGCGGCAAGAGTCAG;RSEQ=CGATCAATCCGAGGAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:10,0:0:2,0:28.8:1:30.1:1:1:0:60:20:1:0:0 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:32.5:1:27.5:1:1:1.13389:60:4:0.1176:0:1 +19 41073998 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51567;SOR=Inf;LSEQ=CTGAGCGGCAAGAGTCAGTC;RSEQ=ATCAATCCGAGGAGGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:10,0:0:2,0:29.2:1:29.2:1:1:0:60:20:1:0:0 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:26:1:28.5:1:1:1.13389:60:4:0.1176:0:1 +19 41173874 . TTGC T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.29851;SOR=0;LSEQ=ACTGAGGCTGCTTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:4:2,2:52,45:97,4:0.0396:2,2:29.3:1:32.8:1:1:1.1539:60:8:0.0404:0:0 0/0:62:0:0,0:29,33:62,0:0:2,0:25.9:1:29.2:1:1:0:55.9:61:1:0:0.9 +19 41173880 . C T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0;SOR=11.38787;LSEQ=GCTGCTTGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:11:6,5:50,44:94,11:0.1048:2,2:17.6:1:30.2:1:1:1.06:59.3:22:0.1058:0:1 1/0:66:38:18,20:13,15:28,38:0.5758:2,2:22.7:1:28:1:1:1.04:53.6:18:0.5625:0:1.4 +19 41173889 . CTGCTGCTGT C 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.00662;SOR=Inf;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:59,55:114,0:0:2,0:24.1:1:30.9:1:1:0:59:27.5:1:0:0.2 0/1:68:5:2,3:30,33:63,5:0.0735:2,2:36:1:30.8:1:1:1.35751:58.6:10:0.0758:0:1 +19 41173892 . CTGCTGT C 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0;SOR=10.1327;LSEQ=TGTTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:6:2,4:57,55:112,6:0.0513:2,2:23.7:1:32.7:1:0.67928:2.06035:58.7:12:0.0541:0.0085:0.8 0/1:70:25:13,12:18,22:40,25:0.3571:2,2:25.1:1:31.6:1:0.61819:1.32:48.6:50:0.3906:0.0857:1.5 +19 41173904 . TTGC T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.16149;SOR=0;LSEQ=TGCTGCTGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:5:1,4:50,53:103,5:0.0463:2,2:34.2:1:31.4:1:0.36715:3.733:60:10:0.0476:0:0 0/0:60:0:0,0:26,34:60,0:0:2,0:26:1:29.4:1:1:0:53.4:29:1:0:0.8 +19 41723887 . G T 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGAGCAGAGGGATAGAC;RSEQ=CCCAGCCTCCTCCTCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:43:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:28.5:1:1:0:60:4:1:0:1 +19 41724687 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=4;SSF=0.33333;SOR=Inf;LSEQ=TGTGCGTGCGTGCGTGCGTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:28.5:1:1:0:60:4:1:0:2 +19 41724694 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=11.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GCGTGCGTGCGTGCGTGTGT;RSEQ=TGTGTGTGTGTGTGTCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:38:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:27:1:1:0:60:4:1:0:2 +19 41725271 . A G 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.3279;SOR=1.12766;LSEQ=CCTCCCCCGCTGGGAGCCCA;RSEQ=CAACTTCTGAGGAAAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:817:212:128,84:368,236:604,212:0.2595:2,2:23.5:1:32.5:1:0.93486:1.02329:60:69.667:0.2596:0:1.1 0/1:579:164:99,65:250,162:412,164:0.2832:2,2:24.6:1:30.4:1:1:1.0132:59.9:22.429:0.2769:0:1.2 +19 41726492 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17058;SOR=Inf;LSEQ=ACAGGGTGGAACTGAGGGCC;RSEQ=GAAGGAGCTGGGGGGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:226,49:275,0:0:2,0:22.4:1:30.3:1:1:0:60:274:1:0:0.1 0/1:194:2:1,1:143,49:192,2:0.0103:2,2:35.5:1:29:1:0.45003:2.89925:60:4:0.0106:0:1 +19 41726531 . T C 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02777;SOR=8.26302;LSEQ=CTAAGCTAACTCTTCCCATC;RSEQ=CCCCTCCAGGCACGCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:1:0,1:385,166:551,1:0.0018:2,0:20:0:12:0:0.30254:0:60:0:0:0:3 0/1:473:7:3,4:301,165:466,7:0.0148:2,2:25.3:1:25.7:1:0.25467:2.42746:60:2.5:0.0109:0:1.4 +19 41726903 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12351;SOR=Inf;LSEQ=GAACCTCTAGGTTTCGTTTT;RSEQ=CTCTTCTGCAAAATGAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:139,52:191,0:0:2,0:24.2:1:32.3:1:1:0:59.9:190:1:0:0.1 0/1:104:2:2,0:77,25:102,2:0.0192:2,0:21:1:28.5:1:1:0:60:4:0.0194:0:1 +19 41727143 . G C 223 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCCCAGCCTGGCTATGTTG;RSEQ=GCTGGAGGGTGAGCTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:845:154:63,91:276,415:691,154:0.1822:2,2:26.8:1:30.8:1:0.8559:1.04:59.9:153:0.1841:0:1.1 0/0:748:0:0,0:312,432:744,0:0:2,0:25.1:1:30:1:1:0:59.9:42.765:0.9945:0:0.2 +19 41727197 . C T 195 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGGGTCAGAGGACATGTGG;RSEQ=GCTCATAGGTTGTGGGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:87:16,71:46,240:286,87:0.2332:2,2:22.7:1:30.3:1:0.62336:1.18:59.8:86:0.2356:0:1.1 0/0:274:0:0,0:65,209:274,0:0:2,0:23.3:1:29.2:1:1:0:60:29.444:1:0:0.1 +19 41727231 . GGGTCAA G 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGAAGTCAGGAATCCTGAG;RSEQ=GGTCAAAGGGTGCTGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:39:3,36:6,142:148,39:0.2074:1,2:27.5:1:31.7:1:0.39773:1.96:59.9:38:0.2077:0.0213:1 0/0:119:0:0,0:8,111:119,0:0:2,0:21.1:1:30.2:1:1:0:60:58.5:1:0:0.1 +19 41727279 . T C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGATGAACCTAGCGTCA;RSEQ=ACAGCCTAAGAATGTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:0,2:3,81:84,2:0.0233:1,0:17.5:1:27:1:1:0:60:4:0.0241:0:1.5 0/0:42:0:0,0:1,41:42,0:0:1,0:24.9:1:27.8:1:1:0:60:84:1:0:0 +19 41727951 . G A 71 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57707;SOR=1.50804;LSEQ=CACGGCCCCCAGCGCAGCCT;RSEQ=CATGTTCCAGGTGAGTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:871:6:5,1:340,524:864,6:0.0069:2,2:9.3:1:25.3:1:0.03887:7.69:60:12:0.007:0:1 0/1:676:7:3,4:285,384:669,7:0.0104:2,2:23.9:1:25.4:1:1:1.01:60:6:0.009:0:1 +19 41728211 . G GTC 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.55128;SOR=0;LSEQ=TTCTGTCTCTCTTTGTATGT;RSEQ=TCTCTCTCTCTGTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:0,3:1,17:18,3:0.1429:1,0:26:1:31.1:1:1:0:60:6:0.1429:0.0476:0 0/0:7:0:0,0:3,4:7,0:0:2,0:26.3:1:31.4:1:1:0:60:14:1:0:0.1 +19 41736788 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15022;SOR=Inf;LSEQ=ACTGCCCCTGGTCAGGCAGG;RSEQ=CATGGTAGGAGTGGCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:234,67:301,0:0:2,0:24.2:1:32:1:1:0:60:149.5:1:0:0.1 0/1:191:2:1,1:143,46:189,2:0.0105:2,2:17.5:1:27:1:0.43257:3.08596:60:4:0.0106:0:1 +19 41737344 . C T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0075;SOR=0.24069;LSEQ=GGGGGGTTAAGCCAGATGTC;RSEQ=TGGGTTCGAATCCTAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:25:0,25:0,44:44,25:0.3623:1,1:22.5:1:30.6:1:1:0:58.4:50:0.3623:0:1.3 0/1:42:5:0,5:2,35:37,5:0.119:2,0:20.8:1:31:0:1:0:60:10:0.122:0:1.2 +19 41737410 . C T 88 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.60825;LSEQ=GGTAGGTGGCTTAATCTGTC;RSEQ=GGGGCTCAGCTCTCTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:0,7:0,21:21,7:0.25:1,0:31.1:1:31.7:1:1:0:60:14:0.2593:0:1.9 0/1:6:1:0,1:1,4:5,1:0.1667:2,0:23:0:31:0:1:0:60:2:0.1667:0:2 +19 41743454 . C A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCGTGCCCAGTCTATTTG;RSEQ=GTTATTATTGTCATCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:34.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 41743861 . A G 329 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.88884;LSEQ=CTCCTCAGGCTGTGCTGTCA;RSEQ=ACGATGGGATGGGCATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1164:1160:669,491:1,0:1,1160:0.9966:0,2:26.1:1:32.4:1:1:0:60:60.053:0.9983:0:1.2 1/1:1035:1031:574,457:1,0:1,1031:0.9961:0,2:25.1:1:30.8:1:1:0:60:56.278:0.9961:0:1.2 +19 41744134 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.2833;SOR=3.71377;LSEQ=ATCAGTGCCACCCCCATTGT;RSEQ=CCCTTTCACTCCTTTACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:1,0:49,236:285,1:0.0035:2,0:44:0:13:0:0.17483:0:60:0:0:0:2 0/1:155:2:1,1:21,132:153,2:0.0129:2,2:19:1:29:1:0.26452:6.16:60:4:0.0131:0:1 +19 41744285 . C T 34 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28137;SOR=0;LSEQ=ACGAGTTGCCCACGTGTGTG;RSEQ=CCTTGGCACCCTGCACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:1,2:243,33:276,3:0.0107:2,2:7.3:1:22:1:0.04237:14.45945:60:2:0.0072:0:1 0/0:183:0:0,0:156,27:183,0:0:2,0:24:1:31.2:1:1:0:60:182:1:0:0.1 +19 41744831 . C T 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28397;SOR=0.33285;LSEQ=TGATTTTCACAAAGGCACTC;RSEQ=TATCAGGGCTAGCAATACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:15:10,5:20,2:22,15:0.4054:2,2:24.3:1:30.8:1:0.09526:4.77126:59.8:14:0.3889:0:1.2 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:20:1:32.5:1:1:0:60:4:0.1818:0:1 +19 41744906 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10612;SOR=Inf;LSEQ=AAGGGGATGGAGGGATACAG;RSEQ=TTAAAGGATGAGGATGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:114,5:119,0:0:1,0:22.2:1:31.4:1:1:0:59.8:28.75:1:0:0.2 0/1:58:2:1,1:53,2:55,2:0.0345:1,2:34.5:1:28:1:0.10338:21.8405:60:4:0.0357:0:1.5 +19 41745414 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.85176;SOR=0.873;LSEQ=CACGGCCTCACTCCTTTACC;RSEQ=GTGCCACACCCTCACTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:25:14,11:52,29:81,25:0.2358:2,2:26.9:1:31.7:1:0.48628:1.40417:58.2:50:0.2404:0:1.2 0/1:66:14:9,5:36,16:52,14:0.2121:2,2:21:1:29.2:1:0.75336:1.24565:59.6:13:0.2031:0:1.1 +19 41745493 . C A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10133;SOR=Inf;LSEQ=CCTTCACTCCCTTACTCGTG;RSEQ=CACACCCTCACTCCCTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:252,64:316,0:0:2,0:22.5:1:31.7:1:1:0:59.3:38.5:1:0:0.2 0/1:277:3:1,2:207,66:273,3:0.0108:2,2:33.3:1:23:1:0.15116:6.22047:58:2:0.0075:0:1.7 +19 41745680 . G A 67 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00289;SOR=Inf;LSEQ=ACCCTCAACACCTAGTGGGG;RSEQ=CACTGTCACCATGCATACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:800:0:0,0:258,538:796,0:0:2,0:24.4:1:31.6:1:1:0:59.9:38.8:0.9961:0:0.1 0/1:616:7:4,3:211,398:609,7:0.0114:2,2:10.7:1:23.9:1:0.24566:2.51:60:6:0.0098:0:1.7 +19 41746281 . G GTGGA 64 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=7.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ATATATGGATGGGTAGATGG;RSEQ=TGGATGGATGGATGGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:30.8:1:32.3:1:1:0:60:8:0.8:0.2:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 41748753 . T C 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29928;LSEQ=CAGAGAGCTGGATCCAAGGC;RSEQ=TCATCCATGACCTGTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:897:579:362,217:188,125:313,579:0.6455:2,2:25.4:1:31.7:1:0.47171:1.11:60:63.333:0.6433:0:1.1 0/1:712:251:144,107:254,207:461,251:0.3525:2,2:23.6:1:30:1:0.58082:1.10:59.9:30.375:0.3501:0:1.2 +19 41748982 . G A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07553;SOR=0;LSEQ=GAGAGGCTGGAGGCAGGGAG;RSEQ=CCAGTGAGGAGGCTGGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:5:3,2:73,304:377,5:0.0131:2,2:16:1:28.8:1:0.05591:6.20:60:10:0.0134:0:1 0/0:283:0:0,0:58,225:283,0:0:2,0:22.4:1:31.2:1:1:0:60:93.333:1:0:0.1 +19 41749325 . CA C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGTGAGATCCTGTTTT;RSEQ=AAAAAAAGAATGAGGGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:2,0:59,8:67,2:0.029:2,0:23:1:32:1:1:0:60:4:0.029:0.0145:3.5 0/0:26:0:0,0:23,3:26,0:0:2,0:19.8:1:30.1:1:1:0:60:52:1:0:0 +19 41749397 . C T 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=0;LSEQ=GTAGCTGCCCAAGGCATGCT;RSEQ=AGCAAATGTTAGCACAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:17:17,0:219,5:224,17:0.0705:1,1:25.9:1:31.9:1:1:0:59.6:34:0.0723:0:1.1 0/0:146:0:0,0:141,5:146,0:0:1,0:26.8:1:31.2:1:1:0:60:72:1:0:0.1 +19 41749511 . TC T 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00022;SOR=0;LSEQ=CTGCCCTCACCTACTCCCCC;RSEQ=CCCCCCAGAGAAGTGTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1346:14:9,5:706,625:1331,14:0.0104:2,2:20.6:1:30.8:1:0.43468:1.59:60:28:0.0106:0.0015:0.1 0/0:1118:0:0,0:594,523:1117,0:0:2,0:24.6:1:30.2:1:1:0:60:43.68:1:0:0.2 +19 41754190 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCAGGGTGCCCACTGGAG;RSEQ=AAGAGCGTGGCCAGGCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:4,0:19,1:20,4:0.1667:1,0:14:1:30.3:1:1:0:60:8:0.1667:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:23:1:32.7:1:1:0:60:6:1:0:0.7 +19 41754217 . G T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45767;SOR=0.4627;LSEQ=GTGGCCAGGCTTTACCCCTT;RSEQ=AGTTCCCTTTGAGGGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:10,1:19,1:20,11:0.3548:1,2:21.8:1:31.5:1:1:1.85871:60:22:0.3667:0:1.4 0/1:10:2:2,0:8,0:8,2:0.2:0,0:16.5:1:32:1:1:0:60:4:0.2:0:1 +19 41754537 . C T 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAGTCCCCCGGCAGCATACA;RSEQ=ACATCCTTCTGAACTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1175:0:0,0:530,644:1174,0:0:2,0:24.7:1:32.2:1:1:0:60:57.7:0.9991:0:0.2 0/1:973:60:23,37:405,506:911,60:0.0617:2,2:26.3:1:28.9:1:0.42094:1.28726:60:120:0.0622:0:1.2 +19 41755660 . GA G 28 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGCAAGACTCCGTCT;RSEQ=AAAAAAAAAAAAATTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:28.5:1:1:0:45.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 41758016 . TA T 58 MSI12;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACAGAGTGAGACTCCATC;RSEQ=AAAAAAAAAAAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:9,4:0.3077:0,0:20:1:29.3:1:1:0:58.5:8:0.3077:0.1538:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 41758044 . ATT A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAAGAAAATATAT;RSEQ=TTATATATATATATATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:4,0:19,1:20,4:0.1739:1,0:12.8:1:30.3:1:1:0:59.5:8:0.1818:0.1304:1 0/0:3:0:0,0:3,0:3,0:0:0,0:5.7:1:30:1:1:0:60:6:1:0:0 +19 41758880 . G C 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGACCAGCCAGTGGTAAGGG;RSEQ=CGTTTAATCATTCAGTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:876:0:0,0:317,556:873,0:0:2,0:24.8:1:31.6:1:1:0:60:40.571:0.9965:0:0.1 0/1:769:37:13,24:285,445:730,37:0.0481:2,2:22.4:1:29.5:1:0.73069:1.18209:60:11.333:0.045:0:1.2 +19 41758945 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18229;SOR=Inf;LSEQ=GTACCCAGTGCTGCTCAGAC;RSEQ=CTGGGAAGACCACGGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:23,229:252,0:0:2,0:22.6:1:30.9:1:1:0:60:24.2:0.9959:0:0.1 0/1:189:2:1,1:33,154:187,2:0.0106:2,2:25:1:25.5:1:0.32821:4.61:60:4:0.0108:0:1 +19 41759474 . C T 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGCATCAAGGACTCTGTTGA;RSEQ=CTCTCCTCCCACCTGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:55:38,17:406,181:587,55:0.0857:2,2:21.6:1:30.5:1:1:1.00348:60:26.5:0.0841:0:1.1 0/0:515:0:0,0:327,188:515,0:0:2,0:23.2:1:30.9:1:1:0:60:127.75:1:0:0.2 +19 41759631 . AC A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.94403;SOR=0.9879;LSEQ=CATGTGAGTGCCTTTCAGGG;RSEQ=CCCCCCCCCCCAACTGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:830:137:57,80:176,241:417,137:0.1651:2,2:31:1:31:1:0.92086:1.02493:59.2:26.4:0.1798:0:0.9 0/1:661:108:48,60:192,189:381,108:0.1634:2,2:32.3:1:29.2:1:0.27835:1.26922:59.9:11:0.1713:0:1.1 +19 41759634 . CCCC T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=12.000;MSILEN=1;SSF=0.00096;SOR=0.6393;LSEQ=ATGTGAGTGCCTTTCAGGGA;RSEQ=CCCCCCAACTGCTCCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:830:186:75,111:176,241:417,186:0.2241:2,2:27.3:1:31.6:1:0.72064:1.08067:59.9:185:0.252:0.0241:0.2 0/1:661:103:42,61:192,189:381,103:0.1558:2,2:26.5:1:30.4:1:0.0956:1.47424:60:206:0.1782:0.0363:0.4 +19 41759637 . C T 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.66899;SOR=0.78706;LSEQ=AGTGCCTTTCAGGGACCCCC;RSEQ=CCCCCCAACTGCTCCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:13:2,11:225,374:599,13:0.0212:2,2:17.9:1:24.1:1:0.14656:3.30365:58.8:1.6:0.0136:0:1.3 0/1:536:9:2,7:224,302:526,9:0.0168:2,2:21.9:1:22.2:1:0.31429:2.59193:60:2:0.0117:0:1.1 +19 41762263 . G C 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=ACCCGCAGCCAGGACAGTGA;RSEQ=GGGAGGAGGTGCAGATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:238,14:252,0:0:2,0:26:1:33.1:1:1:0:60:62:0.996:0:0.1 0/1:174:9:9,0:155,9:164,9:0.0517:2,0:26.4:1:32.6:1:1:0:60:18:0.052:0:1 +19 41762525 . A G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03609;SOR=1.49627;LSEQ=AAGAGCGATGTGGTAGGTGC;RSEQ=CTCCCGCCAAGAGTGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:63:20,43:84,270:354,63:0.1507:2,2:22.6:1:31.3:1:0.20563:1.49:60:62:0.1512:0:1 0/1:343:72:22,50:78,193:271,72:0.2099:2,2:21.1:1:30:1:0.77191:1.09:59.8:23:0.2041:0:1.1 +19 41762601 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGGTGGCTGTGGATGC;RSEQ=AGGGTCACAGGGACATGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:0,2:7,111:118,2:0.0165:2,0:20.5:1:32.5:1:1:0:60:4:0.0175:0:1 0/0:55:0:0,0:5,50:55,0:0:2,0:23.4:1:30.3:1:1:0:59.6:54:1:0:0.4 +19 41762670 . T C 114 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08084;SOR=0.15232;LSEQ=GGGCTGGGCATGTCTTGGGG;RSEQ=ATGGTGGGCATCTCTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:13:1,12:0,27:27,13:0.325:1,1:17.8:1:31:1:0.325:0:60:12:0.3243:0:1.5 0/1:15:1:0,1:2,12:14,1:0.0667:2,0:7:0:33:0:1:0:60:2:0.0667:0:1 +19 41762699 . TA T 72 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.53369;LSEQ=CATCTCTGAATAGTGGTGTG;RSEQ=CATGCCCAGGATAAATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:1,20:21,5:0.1923:1,0:27:1:31.4:1:1:0:60:10:0.1923:0:0.8 0/1:9:1:0,1:1,7:8,1:0.1111:2,0:17:0:27:0:1:0:60:2:0.1111:0:0 +19 41763269 . A T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15993;SOR=0;LSEQ=AAAGTATTATGTTTCTATGA;RSEQ=TACTTGTGATGCTCCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:5:5,0:152,1:153,5:0.0316:1,0:26.2:1:31.2:1:1:0:60:10:0.0318:0:1 0/0:101:0:0,0:99,2:101,0:0:1,0:19:1:30.1:1:1:0:60:100:1:0:0.2 +19 41765229 . T C 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31732;SOR=3.23194;LSEQ=CATCAGAATACTACTCCATA;RSEQ=ACAGACAGGTTTCCCGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:18,0:18,2:0.1:1,0:14:1:32.5:1:1:0:60:4:0.1:0:1 0/1:11:3:2,1:8,0:8,3:0.2727:0,2:24.3:1:31.3:1:0.27273:0:60:6:0.3:0:1.3 +19 41765368 . C T 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57804;SOR=2.69986;LSEQ=CCTCTAAAATGCCCCCAGTC;RSEQ=CCTGAGTGTCCTAAAATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:220,33:253,1:0.0039:2,0:32:0:16:0:1:0:60:0:0:0:1 0/1:189:2:1,1:162,25:187,2:0.0106:2,2:5.5:1:28.5:1:0.25684:6.37375:60:4:0.0107:0:1 +19 41765407 . A C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00845;SOR=1.59014;LSEQ=TCCCCAGGCTTCCAGAATGC;RSEQ=CCCCTTCTGAGTCCCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:73:48,25:302,153:455,73:0.1383:2,2:20:1:30.6:1:0.89488:1.02802:60:35.5:0.1363:0:1.1 0/1:418:85:54,31:216,116:332,85:0.2033:2,2:24.4:1:29.7:1:0.80016:1.06879:60:41.5:0.2029:0:1.1 +19 41765806 . C A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06987;SOR=Inf;LSEQ=CCAGGGCAGGAGGATGGTGC;RSEQ=TGAGACAACCCTCCACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:92,245:337,0:0:2,0:25.3:1:32.3:1:1:0:60:47.143:1:0:0.1 0/1:237:3:2,1:61,173:234,3:0.0127:2,2:22.3:1:30.3:1:0.17325:5.62:60:6:0.0128:0:1 +19 41765858 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.56002;SOR=3.26068;LSEQ=AGGATCCAAGCTAAGCACTG;RSEQ=CACTGGGGAAAACTCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:0,1:19,135:154,1:0.0065:2,0:20:0:13:0:1:0:60:0:0:0:6 0/1:96:2:1,1:13,81:94,2:0.0208:2,2:37:1:28.5:1:0.27171:6.04:60:4:0.0215:0:1 +19 42382729 . C G 83 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCAGAGTACAAAGTG;RSEQ=GTATGCGGGAGGGGGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:15:1:32.3:1:1:0:60:12:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 42382745 . A G 66 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCGTATGCGGGAGGGGG;RSEQ=CAAGAGATGGCGCTGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:26.2:1:28.6:1:1:0:60:4:0.5714:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 42383511 . TG T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.1277;SOR=Inf;LSEQ=CCTCTGCAGAGTGGGGTCTC;RSEQ=GGGGGTCTGGGGCCTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:223,98:321,0:0:2,0:25:1:32.3:1:1:0:59.9:79.25:1:0:0.1 0/1:179:2:2,0:129,48:177,2:0.0112:2,0:20.5:1:30.5:1:1:0:60:4:0.0114:0.0056:0.5 +19 42383810 . G GT 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0021;SOR=Inf;LSEQ=GTAGCCCTCTAGAGCCTGAG;RSEQ=TTCCCCATCCAAAACTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:12,313:325,0:0:1,0:25.6:1:32.3:1:1:0:60:64:1:0:0 0/1:233:7:0,7:16,210:226,7:0.03:2,0:30.1:1:31.3:1:1:0:60:14:0.0303:0.0043:0 +19 42383918 . G T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01464;SOR=0.20898;LSEQ=ACTGGCGCTGAGCCCAGGGG;RSEQ=TGTCTTCAATTTAGTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:30:0,30:0,23:23,30:0.566:1,1:24.3:1:31:1:1:0:60:60:0.566:0:1.1 0/1:19:4:0,4:1,14:15,4:0.2105:1,0:19.8:1:24.8:1:1:0:60:3:0.1667:0:2 +19 42384461 . AAGAG A 62 MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=15.000;MSILEN=2;SSF=0.52105;SOR=2.46307;LSEQ=AAGAAAGAGAGAGAGAGAGA;RSEQ=AGAGAGAGAGAGAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:8,0:8,5:0.2778:0,0:26.2:1:27:1:1:0:55.8:4:0.25:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:28:0:31:0:1:0:60:2:1:0:1 +19 42384518 . GAAGGGAAG AAGGAA 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.01244;SOR=Inf;LSEQ=AGGGAGGGAGGGAAGGAAGG;RSEQ=GGAAGGAAGGAAGGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:43,0:43,0:0:1,0:26.6:1:31.7:1:1:0:49.4:20.5:1:0:0.6 0/1:14:3:3,0:11,0:11,3:0.2143:0,0:9.3:1:30.6:1:1:0:40.7:6:0.25:0.1429:0 +19 42384526 . G GGAA 120 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=0.27253;SOR=0.25929;LSEQ=AGGGAAGGAAGGGAAGGGAA;RSEQ=GGAAGGAAGGAAGGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:16:16,0:35,1:36,16:0.2623:1,1:14.1:1:30:1:1:0:49.8:32:0.2759:0.1803:0.1 0/1:12:1:1,0:7,0:7,1:0.0833:0,0:25:0:31:0:1:0:32:2:0.0833:0:0 +19 42578291 . CA C 33 d5;v3;pSTD;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAATTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:33.5:1:1:0:38.5:4:1:0:1 +19 42579984 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15796;SOR=Inf;LSEQ=TGGCGCCCGCGGCCGCGCTC;RSEQ=GCCGCCTAACGTCATCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:25,0:0:2,0:24:1:29.3:1:1:0:60:24:1:0:0.2 0/1:17:2:1,1:6,9:15,2:0.1176:2,2:35:1:28.5:1:1:1.46:60:4:0.1176:0:1 +19 42579985 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55575;SOR=3.11044;LSEQ=GGCGCCCGCGGCCGCGCTCC;RSEQ=CCGCCTAACGTCATCGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:1:0,1:12,12:24,1:0.04:2,0:27:0:32:0:1:0:60:2:0.0417:0:1 0/1:17:2:1,1:6,9:15,2:0.1176:2,2:27.5:1:28:1:1:1.46:60:4:0.1176:0:1 +19 42787490 . A G 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATGAGGATGCGGGTTGGCGA;RSEQ=GCATGTGTGACAGGGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:32.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:33:0:33:0:1:0:60:2:1:0:0 +19 42788752 . TC T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49194;SOR=0;LSEQ=ATGCGGCGACGGCCTCCCGC;RSEQ=CCCCCGGGCCCAAGCGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:12,4:16,2:0.1111:2,2:12.5:1:31:1:0.4902:2.79285:60:4:0.1111:0:0.5 0/0:14:0:0,0:11,3:14,0:0:2,0:11.3:1:31.1:1:1:0:59.8:28:1:0:0.3 +19 42788786 . G T 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3254;SOR=3.82093;LSEQ=AGCGGCGACGGCCGAGGAGC;RSEQ=GGCTGCGGGCGGAGCGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:1:0,1:118,47:165,1:0.006:2,0:1:0:25:0:0.28916:0:60:2:0.0062:0:1 0/1:132:3:2,1:92,37:129,3:0.0227:2,2:24.7:1:29.7:1:1:1.24115:60:6:0.0229:0:1 +19 42788791 . G T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17556;SOR=5.09163;LSEQ=CGACGGCCGAGGAGCGGGCT;RSEQ=CGGGCGGAGCGGCGTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:0,1:140,53:193,1:0.0052:2,0:1:0:25:0:0.27835:0:60:2:0.0053:0:1 0/1:155:4:2,2:106,45:151,4:0.0258:2,2:22:1:27.5:1:0.58516:2.34102:60:8:0.0258:0:1 +19 42790821 . G C 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00123;SOR=0;LSEQ=GGTGTTGGGGGTGGGGGGTA;RSEQ=ACAAAAGGGGTGGGGCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:13:13,0:309,10:319,13:0.0389:1,1:17.5:1:31.8:1:1:0:60:26:0.0406:0:1 0/0:226:0:0,0:213,12:225,0:0:2,0:17:0:14:0:1:0:60:0:0:0:8 +19 42791015 . C A 174 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05001;LSEQ=GCCAGCCTGACCCCTCCGTG;RSEQ=AGCCGAGCGAGGCCCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1159:54:23,31:472,633:1105,54:0.0466:2,2:23.2:1:30.4:1:1:1.00501:60:53:0.0462:0:1.1 0/0:821:2:2,0:345,472:817,2:0.0024:2,0:1:0:24.5:1:0.17921:0:60:4:0.0024:0:1 +19 42792901 . G GT 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.21434;SOR=0.34344;LSEQ=TGGACTGGTGGTGGGTGGTG;RSEQ=TTTTTTTTTTTCACCAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:12:11,1:48,1:49,12:0.1905:1,2:22.1:1:30.4:1:0.35738:4.22116:60:24:0.1935:0.0476:0.4 0/1:27:2:2,0:22,0:22,2:0.0741:1,0:18.5:1:28:1:1:0:60:4:0.0741:0:0 +19 42792980 . C G 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.57443;SOR=2.7877;LSEQ=AATATCTATGGGTTGTTGGG;RSEQ=CAGTCTAGGTGCTGGTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:1:1,0:231,40:271,1:0.0037:2,0:2:0:15:0:1:0:60:0:0:0:3 0/1:196:2:1,1:155,37:192,2:0.0102:2,2:12:1:29:1:0.3542:4.14702:60:4:0.0103:0:1 +19 42793590 . G A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28685;SOR=1.13179;LSEQ=AGGGCCCAGAATCTTGCCCA;RSEQ=GACCCAGCAGGCCAAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:326:111,215:125,243:368,326:0.4691:2,2:26.4:1:31.4:1:1:1.00:60:325:0.4731:0:1.1 1/0:588:294:108,186:112,181:293,294:0.5:2,2:24.8:1:29.6:1:0.73346:1.06555:60:146:0.5009:0:1.1 +19 42793920 . G T 39 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.38222;SOR=2.37045;LSEQ=TGCCGGTTTGGAGCAGAGCT;RSEQ=AGATCCAGGCTCCAGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:2:1,1:322,90:412,2:0.0048:2,2:34.5:1:28.5:1:0.39171:3.56332:60:4:0.0049:0:1 0/1:264:3:1,2:197,64:261,3:0.0114:2,2:7.3:1:24.7:1:0.15518:6.10359:60:6:0.0116:0:1.7 +19 42794080 . G A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01054;SOR=Inf;LSEQ=GCGAGAGTGGGGACAGCTCT;RSEQ=GGGAGGACCCAGAGGGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:674:0:0,0:243,431:674,0:0:2,0:24.3:1:31.6:1:1:0:59.9:111.333:1:0:0.1 0/1:596:6:5,1:232,358:590,6:0.0101:2,2:12.8:1:26.5:1:0.03913:7.69:58.2:12:0.0101:0:1.2 +19 42794913 . T C 42 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.67491;SOR=1.7195;LSEQ=GGGCCCCAGCAGCTCCCCTG;RSEQ=CCCGTCCTGCCGCCACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:3:1,2:229,258:487,3:0.0061:2,2:19.7:1:18:1:1:1.7732:60:0.5:0.0021:0:2.3 0/1:286:3:2,1:143,140:283,3:0.0105:2,2:12.3:1:26.7:1:1:1.95:60:2:0.0071:0:1 +19 42794925 . G A 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42748;SOR=0.35379;LSEQ=CTCCCCTGTCCCGTCCTGCC;RSEQ=CCACCATGGTCACCAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:2,3:251,242:493,5:0.01:2,2:29.4:1:26.8:1:0.68132:1.55441:60:4:0.0082:0:1.8 0/0:280:1:1,0:148,131:279,1:0.0036:2,0:1:0:23:0:1:0:60:2:0.0036:0:1 +19 42795554 . T C 228 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCAACGGCAAAGTCCTGGC;RSEQ=GCCACTGCACCCACTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1331:198:109,89:583,549:1132,198:0.1488:2,2:25.9:1:29.9:1:0.39646:1.15:60:32:0.1469:0:1.1 0/0:1079:0:0,0:549,528:1077,0:0:2,0:23:0:9:0:1:0:60:0:0:0:7 +19 42795961 . C CT 47 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.68698;SOR=1.51517;LSEQ=GTACCCCATCATTTCTTTGT;RSEQ=TTTTTTTTCAGTCTTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:3:0,3:54,368:422,3:0.007:2,0:19:1:31.7:1:1:0:60:6:0.0071:0.0023:0.3 0/1:282:3:0,3:55,224:279,3:0.0106:2,0:27.3:1:29.9:1:1:0:60:6:0.0108:0.0035:0 +19 42796287 . C T 187 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.43774;LSEQ=CACACCCAGCGGCCTGGTGC;RSEQ=GCCCCTGAGCCCAGCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1381:4:1,3:721,654:1375,4:0.0029:2,2:6:1:28.3:1:0.35256:3.30474:60:8:0.0029:0:1 0/1:1137:84:38,46:526,526:1052,84:0.0739:2,2:27.5:1:29.3:1:0.42858:1.21032:59.6:41:0.0734:0:1.1 +19 42797603 . C T 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0229;SOR=0;LSEQ=CTCCTCTCCCATCTGAGGCC;RSEQ=CTGTCTTGGCCTTCCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:15:7,8:56,33:89,15:0.1442:2,2:28.2:1:31.8:1:0.26298:1.92661:60:30:0.1456:0:1.2 0/0:30:0:0,0:23,7:30,0:0:2,0:23.9:1:30.7:1:1:0:60:60:1:0:0 +19 42798740 . C T 56 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09359;SOR=6.33182;LSEQ=GCTGCAGCCTTGCCATGCTG;RSEQ=CTGTGCCCTGCACAGGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:606:1:1,0:388,217:605,1:0.0017:2,0:1:0:31:0:1:0:60:2:0.0017:0:1 0/1:482:5:1,4:281,195:476,5:0.0104:2,2:5.6:1:24.4:1:0.16509:5.74502:60:10:0.0105:0:1 +19 42799049 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=1.81043;LSEQ=GTTTGTCTGCAGTTGAAGAT;RSEQ=CGTGAGGTGCGCCAGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:96:40,56:290,404:694,96:0.1215:2,2:25.9:1:30.2:1:1:1.00494:60:95:0.1226:0:1.1 0/1:579:116:58,58:207,255:462,116:0.2003:2,2:23.8:1:29.3:1:0.34861:1.23:59.9:57:0.2:0:1.2 +19 42799230 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.08453;SOR=Inf;LSEQ=ACTCTGGCACGGCCCAGGCT;RSEQ=CCCCGCCACTGCCTCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:147,234:381,0:0:2,0:23.4:1:30.7:1:1:0:59.9:13.654:1:0:0.5 0/1:299:3:2,1:123,172:295,3:0.01:2,2:11:1:25.7:1:0.57407:2.79:60:6:0.0106:0:1 +19 42799296 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08194;SOR=Inf;LSEQ=GCTGGGAGGGGGCTCCCCAG;RSEQ=CCTCCCCCCCACCCCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:56,164:220,0:0:2,0:27:1:29.2:1:1:0:59.6:6.857:0.9897:0:0.7 0/1:173:3:2,1:64,103:167,3:0.0173:2,2:33.7:1:28.7:1:0.56057:3.20:60:6:0.0201:0:1 +19 42799299 . TC T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=1.29253;LSEQ=GGGAGGGGGCTCCCCAGCCC;RSEQ=CCCCCCACCCCCAGGTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:2:0,2:57,159:216,2:0.0092:2,0:35:1:27:0:1:0:60:4:0.0102:0:0 0/1:169:2:2,0:60,104:164,2:0.0118:2,0:19:1:30:1:0.13808:0:59:4:0.0132:0.0059:0.5 +19 42799314 . G C 20 p8;pSTD;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99133;LSEQ=AGCCCTCCCCCCCACCCCCA;RSEQ=GTCCCTCCACAGCTGCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:3,0:28,142:170,3:0.0172:2,0:16:1:13:1:0.0053:0:60:0:0:0:4 0/1:117:2:2,0:26,86:112,2:0.0171:2,0:6:0:23.5:1:0.05869:0:50:4:0.0213:0:5 +19 42799347 . A G 39 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.37752;SOR=2.41543;LSEQ=CTGCCACAGGCAGGTGAGGG;RSEQ=CCCCTGAGAAGATGCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:10,91:101,2:0.0192:2,0:42:0:13:1:1:0:60:0:0:0:1.5 0/1:66:3:1,2:7,56:63,3:0.0455:2,2:25.7:1:25:1:0.3257:3.87:60:2:0.0317:0:1.3 +19 43941594 . C T 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16506;SOR=0.2341;LSEQ=TGCAGAGAAGAAAACGCTGA;RSEQ=GTACGTTGCCTTCCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:6,2:8,4:0.3333:2,0:22:1:32.5:1:0.51515:0:58:8:0.3333:0:2 0/1:20:2:1,1:13,5:18,2:0.1:2,2:16:1:28.5:1:0.52105:2.46307:42:4:0.1:0:2.5 +19 43941596 . T C 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1587;SOR=0.22199;LSEQ=CAGAGAAGAAAACGCTGACG;RSEQ=ACGTTGCCTTCCCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:6,2:8,4:0.3333:2,0:23:1:34.3:1:0.51515:0:58:8:0.3333:0:2 0/1:21:2:1,1:14,5:19,2:0.0952:2,2:16:1:30:1:0.5:2.64575:42:4:0.0952:0:2.5 +19 43941641 . GC G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.29054;SOR=Inf;LSEQ=AGGCTACCCAAGAGGGAAGG;RSEQ=CCCCGTCCTATGATCACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:17,10:27,0:0:2,0:27.1:1:31.1:1:1:0:45.4:26:1:0:0.3 0/1:49:4:2,2:22,23:45,4:0.0816:2,2:31.8:1:30.8:1:1:1.04:39.8:8:0.0816:0:0.3 +19 43948553 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49671;SOR=Inf;LSEQ=TAACTGGGATTACAGGCATG;RSEQ=GCCACCATGCCCGGCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:25,20:45,0:0:2,0:28.4:1:30.1:1:1:0:59.3:90:1:0:0.1 0/1:51:2:1,1:27,22:49,2:0.0392:2,2:15:0:31.5:1:1:1.22232:36:4:0.0392:0:3.5 +19 43948561 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50318;SOR=Inf;LSEQ=ATTACAGGCATGTGCCACCA;RSEQ=GCCCGGCTAATTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:27,23:50,0:0:2,0:29.6:1:31.1:1:1:0:58.5:100:1:0:0.1 0/1:64:2:1,1:33,28:61,2:0.0313:2,2:23:0:32.5:1:1:1.17549:36:4:0.0323:0:3.5 +19 43948565 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50746;SOR=Inf;LSEQ=CAGGCATGTGCCACCATGCC;RSEQ=GGCTAATTTGTTGTTGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:26,24:50,0:0:2,0:30.5:1:31.2:1:1:0:58.5:100:1:0:0.1 0/1:68:2:1,1:36,30:66,2:0.0294:2,2:27:0:31.5:1:1:1.19677:36:4:0.0299:0:3.5 +19 43948586 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.16531;SOR=0;LSEQ=GGCTAATTTGTTGTTGTTGT;RSEQ=GCTGTTGCTGCTGCTGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:28,26:54,2:0.0357:2,2:40.5:1:30:1:1:1.07547:60:4:0.0357:0:1 0/0:81:0:0,0:43,38:81,0:0:2,0:27:1:30:1:1:0:55.3:80:1:0:0.4 +19 43948630 . C A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51053;SOR=Inf;LSEQ=TGTTGAGACGGAGTCTCACT;RSEQ=TGTCATCCAGGCTGGAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:31,0:0:2,0:23.5:1:32.8:1:1:0:57.5:62:1:0:0.1 0/1:45:2:1,1:20,23:43,2:0.0444:2,2:6.5:1:29.5:1:1:1.15:60:4:0.0476:0:1 +19 45854503 . CCCTCA C 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGTGGATGTAACACTTGC;RSEQ=CCTCCCCTCCAACCATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:22.5:1:31:1:1:0:60:4:0.5:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:16:0:32:0:1:0:59:2:1:0:0 +19 45854919 . T G 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1711;LSEQ=AGCAATCTGCTCTATCCTCT;RSEQ=CAGCGTCTCCTCTGATTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1029:556:229,327:196,276:472,556:0.5403:2,2:25.6:1:32.2:1:0.94934:1.01404:60:60.778:0.5389:0:1.1 0/1:1028:172:68,104:362,490:852,172:0.1673:2,2:26.3:1:31.4:1:0.49879:1.12975:60:171:0.1685:0:1.1 +19 45855055 . A AC 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.35387;SOR=1.58044;LSEQ=GCTGCTGCACTTCCCCAACC;RSEQ=CCCCCCCGAATGGCCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:13:1,12:14,126:140,13:0.085:2,1:23.9:1:31.8:1:1:1.33106:59.2:26:0.0872:0.0131:0.2 0/1:78:10:2,8:9,58:67,10:0.1282:2,2:22.1:1:28.6:1:0.62884:1.60:59.5:9:0.1216:0.0128:0.1 +19 45855060 . C G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0.11592;LSEQ=TGCACTTCCCCAACCACCCC;RSEQ=CCGAATGGCCAGTAGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:71:6,65:3,61:64,71:0.5259:1,2:22.5:1:31.9:1:0.49829:1.87:60:22.667:0.5231:0:1.1 0/1:62:7:0,7:5,50:55,7:0.1129:2,0:21.1:1:32.3:1:1:0:60:14:0.1167:0:1.1 +19 45855262 . G T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74878;SOR=1.30946;LSEQ=CCAACTTCTCTCACCCTGCC;RSEQ=TGCCTGGGCCACCTGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:15,2:10,3:13,17:0.5484:2,2:29.4:1:30.8:1:0.62781:2.19:59.6:16:0.5517:0:1.6 1/0:13:8:6,2:4,1:5,8:0.6154:2,2:22.4:1:29.1:1:1:1.30472:60:16:0.6154:0:1.4 +19 45855318 . A G 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05042;SOR=4.38875;LSEQ=AATCTCCCCCTTCCCCCCAG;RSEQ=GCCTGGCACGTAGATGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:3,0:62,5:67,3:0.0429:2,0:19:1:31.3:1:1:0:60:6:0.0435:0:1.7 0/1:30:5:5,0:23,2:25,5:0.1667:2,0:30.2:1:31.2:1:1:0:60:10:0.1667:0:1.2 +19 45855524 . G A 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16369;LSEQ=TTGGCCACCTGGACACCCTC;RSEQ=TCCACGGTCAGGTTGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1162:652:340,312:257,250:507,652:0.5611:2,2:25:1:30.5:1:0.63586:1.06:60:53.333:0.5599:0:1.1 0/1:1012:175:89,86:405,431:836,175:0.1729:2,2:25.1:1:29.5:1:0.61793:1.10:59.9:86.5:0.1737:0:1.1 +19 45856014 . C T 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12486;SOR=5.72177;LSEQ=AGCTACTCACCTTGAGAATG;RSEQ=GGCTCTGTGTGTAGACGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:1:0,1:284,286:570,1:0.0018:2,0:1:0:24:0:1:0:60:2:0.0018:0:1 0/1:603:6:3,3:304,293:597,6:0.01:2,2:29.8:1:27.7:1:1:1.03749:60:12:0.0101:0:1 +19 45856141 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00028;SOR=Inf;LSEQ=GTGGGACAGGGACAGCCTCA;RSEQ=GCGACCCAGGATGCTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:92,173:265,0:0:2,0:23.3:1:30.2:1:1:0:60:36.857:0.9961:0:0.6 0/1:184:9:2,7:45,130:175,9:0.0489:2,2:17.7:1:31.2:1:1:1.21032:60:18:0.0506:0:1.1 +19 45856144 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20482;LSEQ=GGACAGGGACAGCCTCACGC;RSEQ=ACCCAGGATGCTGTGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:144:59,85:33,71:104,144:0.5806:2,2:23.2:1:30.3:1:0.14523:1.49:59.9:35:0.5761:0:1.1 0/1:168:37:13,24:31,100:131,37:0.2202:2,2:22.1:1:29:1:0.20349:1.74:60:36:0.2182:0:1.1 +19 45856221 . GC G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.12777;SOR=Inf;LSEQ=GGGACAGAGGGGAGGGGAGG;RSEQ=CCCTCTGTGCACCTAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:181,41:222,0:0:2,0:24.6:1:32:1:1:0:60:36:1:0:0.3 0/1:124:2:1,1:96,26:122,2:0.0161:2,2:16.5:1:29:1:0.38946:3.64248:60:4:0.0169:0:0 +19 45856260 . G A 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGGGTGGGTGGTTCCCC;RSEQ=CGGGAGCAGACAGCAGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:27:19,8:249,94:343,27:0.073:2,2:22.3:1:30.3:1:0.82419:1.115:60:54:0.074:0:1.3 0/0:276:0:0,0:196,80:276,0:0:2,0:23.6:1:29.5:1:1:0:59.9:68:1:0:0.2 +19 45856267 . C T 47 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41497;SOR=2.5117;LSEQ=TGGGTGGTTCCCCGCGGGAG;RSEQ=AGACAGCAGAGCGGGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:2:0,2:297,132:429,2:0.0046:2,0:1:0:24:1:0.09616:0:60:4:0.0048:0:1 0/1:346:4:1,3:235,107:342,4:0.0116:2,2:11.3:1:23.8:1:0.09663:6.55003:60:8:0.0118:0:1 +19 45856468 . G C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49136;LSEQ=CTCCTCAGAGCCACCTCCCC;RSEQ=ACCCCTCTCCACGCTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:730:631:338,293:53,44:97,631:0.8644:2,2:23.9:1:31.6:1:0.913:1.04413:59.9:69.111:0.8675:0:1.1 1/0:603:457:242,215:82,62:144,457:0.7579:2,2:23.8:1:30.6:1:0.44341:1.1747:60:90.4:0.7571:0:1.2 +19 45856630 . G A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41592;SOR=2.48978;LSEQ=GAGGTCAGGGTGGGTTCAGG;RSEQ=CACAGCCATCCTGGTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:2:2,0:138,347:485,2:0.0041:2,0:1:0:20.5:1:0.08222:0:60:1:0.0021:0:1 0/1:394:4:2,2:117,273:390,4:0.0102:2,2:19.3:1:24.8:1:0.58743:2.33:60:8:0.0103:0:1.3 +19 45856926 . C G 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGACTTCCCATATGACA;RSEQ=TACAATAGAGACAGTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:14.5:1:32.5:1:1:0:59:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:8:0:32:0:1:0:60:2:1:0:1 +19 45857049 . T C 29 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTGGAGCAAGTGGATTT;RSEQ=CAAATGGAACCAAAAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:35:1:29:0:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:6:0:33:0:1:0:60:2:1:0:1 +19 45857820 . G A 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00116;SOR=8.63197;LSEQ=AGCCTGATGTACTGGGGGCG;RSEQ=GGCATGGGGGTGTGTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:7,0:29,0:29,7:0.1944:1,0:22.1:1:32:0:1:0:60:14:0.2059:0:2 1/0:16:11:9,2:5,0:5,11:0.6875:0,2:29.5:1:28.4:1:1:0:60:22:0.7333:0:1.8 +19 45857867 . A G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.31481;SOR=0;LSEQ=CCCATTCCTACATGCTGCAC;RSEQ=CACTCTCCTGTCACACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:74:73,1:0,0:0,74:1:0,1:26.7:1:29.9:1:1:0:59.5:36:1:0:1.2 1/1:34:33:31,2:0,0:0,33:0.9706:0,2:23.3:1:29.5:1:1:0:60:32:0.9697:0:1.3 +19 45857920 . A T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27617;SOR=0;LSEQ=TCAGAGTGTGAGAGGAATGA;RSEQ=GCTGACATAGCGGTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:3:1,2:160,24:184,3:0.016:2,2:13.3:1:23:1:0.05121:13.00669:60:2:0.011:0:1.7 0/0:126:0:0,0:101,25:126,0:0:2,0:23.2:1:29.4:1:1:0:60:62:1:0:0.3 +19 45858228 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14134;SOR=Inf;LSEQ=GTCAGGCTTTTCACACATAT;RSEQ=CCCCTCCTCCTCCTCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:1,120:121,0:0:1,0:23.2:1:31.5:1:1:0:59.6:29.25:0.9915:0:0.3 0/1:74:2:0,2:4,68:72,2:0.027:2,0:24.5:1:25.5:1:1:0:60:4:0.027:0:2.5 +19 45858245 . C T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34618;SOR=1.42687;LSEQ=TATCCCCCTCCTCCTCCTCC;RSEQ=GGGCGTGTCTGAGGACCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:26:0,26:1,61:62,26:0.2955:1,1:24:1:30.3:1:1:0:58.5:25:0.2874:0:1.1 0/1:48:18:1,17:2,27:29,18:0.375:2,1:27.1:1:29.4:1:1:1.25325:60:36:0.383:0:1.3 +19 45858605 . ACT A 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCTAGGCAACAGAGCAAG;RSEQ=CTGTCTCAAAAAAAGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:7,1:8,3:0.2727:2,2:17.3:1:33.6:1:0.49091:3.05504:55:6:0.2727:0.0909:0 0/0:1:0:0,0:0,1:1,0:0:0,0:50:0:30:0:1:0:59:2:1:0:0 +19 45858784 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13459;SOR=Inf;LSEQ=CCTACCAGCTCACAGTGGAC;RSEQ=TGTACCACGGGCAAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:149,2:151,0:0:1,0:22.5:1:30.4:1:1:0:60:74.5:1:0:0.1 0/1:88:2:1,1:82,4:86,2:0.0227:1,2:22:0:31.5:1:0.11102:18.441:60:4:0.023:0:1 +19 45859092 . A T 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64922;SOR=0.36382;LSEQ=CTTTTTTTTTTTTTTTTTTT;RSEQ=AAGAGAGACAGGGTGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:4:0,4:4,92:96,4:0.0396:1,0:10.8:1:29.5:1:1:0:54.3:8:0.0404:0:5.3 0/1:68:1:0,1:7,60:67,1:0.0147:2,0:20:0:30:0:1:0:32:2:0.0154:0:1 +19 45860158 . G A 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGTTACAGAGACGGAGAC;RSEQ=GAGAGGAAGGCTCACTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:32.5:1:30.5:1:1:0:60:4:0.3333:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 45861345 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAGCCTCGCGCTGTCGC;RSEQ=CAGGCTAGAGTGCAGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:22.5:1:28.5:1:1:0:52.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 45862016 . A AT 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.73398;SOR=0.71993;LSEQ=ATATTCCAACACAACAATGT;RSEQ=TTTTTTTTCATGATAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:5:5,0:259,23:282,5:0.0174:2,0:23.4:1:31.7:1:1:0:60:10:0.0177:0.0069:0 0/1:239:3:2,1:211,25:236,3:0.0126:2,2:33:1:30:1:0.29324:4.17882:60:6:0.0127:0:0 +19 45862022 . T C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAACACAACAATGTATTTTT;RSEQ=TTCATGATAACTGTCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:290,36:326,0:0:2,0:23.1:1:31.1:1:1:0:60:107.667:1:0:0.1 0/1:277:20:18,2:212,45:257,20:0.0722:2,2:19.1:1:31.2:1:0.54349:1.91:60:40:0.0725:0:1.1 +19 45862194 . A G 200 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TTTGTTGAAGAAATAAATGA;RSEQ=TGAATGAATTTACATATTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:0:0,0:192,436:628,0:0:2,0:22.9:1:30.7:1:1:0:60:56.091:1:0:0.1 0/1:588:84:28,56:169,335:504,84:0.1429:2,2:24.2:1:31.4:1:1:1.00894:60:83:0.1446:0:1.1 +19 45862449 . A G 81 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATCTCTACTAAGCTGAGA;RSEQ=CCTAAGGATGAGGGGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:23.8:1:31.7:1:1:0:56:12:0.8571:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:23:0:33:0:1:0:26:2:1:0:1 +19 45864751 . G T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01497;SOR=Inf;LSEQ=CTGATTCCAGCTGCTAGGAG;RSEQ=CCCAGCAGGGACAGAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:605:0:0,0:400,204:604,0:0:2,0:24.2:1:31.6:1:1:0:59.9:85.286:0.9983:0:0.1 0/1:599:6:2,4:385,208:593,6:0.01:2,2:14.3:1:26:1:0.19232:3.69336:60:12:0.0102:0:1 +19 45865002 . C A 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42316;LSEQ=TCACGTGCCTGTCTCCCCAG;RSEQ=CAATGAGCACTCAGTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:606:479:224,255:62,63:125,479:0.7904:2,2:25.7:1:29.9:1:0.61537:1.12011:59.9:118.75:0.7917:0:1.1 1/0:493:303:139,164:91,99:190,303:0.6146:2,2:24:1:28.5:1:0.71078:1.08433:60:74.75:0.6152:0:1.2 +19 45865094 . G A 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41878;SOR=2.41713;LSEQ=TGTCACAAATAGCCATTGCC;RSEQ=CATAATGGCACAGACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:2:1,1:136,250:386,2:0.0052:2,2:22.5:1:28:1:1:1.84:60:4:0.0052:0:1 0/1:323:4:2,2:126,193:319,4:0.0124:2,2:19.3:1:28:1:0.65009:1.53:60:8:0.0126:0:1 +19 45865100 . T A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09452;SOR=Inf;LSEQ=AAATAGCCATTGCCGCATAA;RSEQ=GGCACAGACAGAGCAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:118,237:355,0:0:2,0:23.5:1:30.2:1:1:0:60:70:1:0:0.1 0/1:298:3:2,1:115,180:295,3:0.0101:2,2:10:1:21.7:1:0.56349:3.12:60:2:0.0068:0:3.3 +19 45865191 . CTTTT C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.48463;SOR=0.6828;LSEQ=CCTAAGTGGGTTCTTTTTTT;RSEQ=TCTTTTTTTTCTTTGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:18:0,18:1,55:56,18:0.2432:1,1:18.9:1:34.3:1:1:0:60:36:0.2571:0.0405:0.5 0/1:39:7:0,7:0,32:32,7:0.1795:1,0:20.6:1:28.6:1:1:0:60:6:0.1667:0.0256:0.6 +19 45865217 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12981;SOR=0.36435;LSEQ=CTTTTTTTTCTTTGTTCAGA;RSEQ=GGAGTCTTGCCCTGTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:28:0,28:0,9:9,28:0.7568:0,1:20.4:1:29.6:1:1:0:58.9:27:0.75:0:1.2 1/0:19:10:0,10:0,9:9,10:0.5263:0,0:25.3:1:27.9:1:1:0:60:9:0.5:0:1.1 +19 45867026 . C T 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.34937;SOR=0.29819;LSEQ=GGGCTTGCGCTGGATGCACA;RSEQ=GCGCTGGGCCAGGCCGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:165,127:292,3:0.0102:2,2:40:1:30.7:1:1:1.54:60:6:0.0103:0:2 0/0:328:1:0,1:177,150:327,1:0.003:2,0:1:0:28:0:0.46037:0:60:2:0.0031:0:2 +19 45867190 . C T 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16742;SOR=5.54258;LSEQ=CTGCGAGGAGACGCTATCAG;RSEQ=GGCGACGGGGAGGCGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:0,1:123,136:259,1:0.0038:2,0:12:0:19:0:1:0:60:0:0:0:2 0/1:191:4:2,2:91,96:187,4:0.0209:2,2:20:1:24.3:1:1:1.05:60:3:0.0167:0:1.8 +19 45867216 . T TG 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.02178;SOR=1.72489;LSEQ=CGGGGAGGCGGGAAAGGGAC;RSEQ=GGGGGGCAGCGGGGGGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:40:21,19:87,98:185,40:0.1762:2,2:24:1:31.6:1:0.60178:1.24:60:80:0.1778:0.0132:0.1 0/1:215:58:33,25:78,79:157,58:0.2698:2,2:28.8:1:30:1:0.36094:1.34:60:28:0.2679:0.0186:0.2 +19 45867259 . C T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1534;LSEQ=CTCACCCTGCAGCACTTCGT;RSEQ=GGGCAGCACGGGGTTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:263:176:103,73:44,43:87,176:0.6692:2,2:23.7:1:30.8:1:0.23695:1.38:59.8:57.667:0.6758:0:1.2 0/1:233:55:27,28:97,81:178,55:0.2361:2,2:25.5:1:29.4:1:0.53746:1.24072:60:110:0.2402:0:1.3 +19 45867301 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08078;SOR=Inf;LSEQ=GTGGGCGTCCGTCTCCCGGG;RSEQ=GGCGCTGGCCTCCCGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:166,140:306,0:0:2,0:25.8:1:30.5:1:1:0:59.9:37.25:1:0:0.5 0/1:234:3:1,2:110,121:231,3:0.0128:2,2:23.3:1:29:1:1:1.81373:58.7:6:0.0132:0:1.3 +19 45868006 . A T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00274;SOR=0.46704;LSEQ=CAGACAGGCAGACTCACAGC;RSEQ=AGCAACAGACAGACATGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:185:142:124,18:35,8:43,142:0.7676:2,2:23.5:1:31.3:1:0.325:1.57:59.8:46.333:0.7637:0:1.6 1/0:132:80:67,13:45,7:52,80:0.6061:2,2:22.7:1:30.5:1:0.80524:1.24528:59.8:160:0.6061:0:1.5 +19 45868038 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.47018;LSEQ=GACATGGGCAGACAGGAGAC;RSEQ=GGCGGGCAGCCCACACCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:319:166:123,43:115,37:152,166:0.5204:2,2:22.8:1:30.1:1:0.79646:1.08628:59.8:54.333:0.5175:0:1.6 0/1:240:81:52,29:117,42:159,81:0.3375:2,2:22.2:1:29:1:0.13781:1.55069:59.8:80:0.339:0:1.6 +19 45868309 . T G 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38486;LSEQ=CCTCCAGTAACCTCATAGAA;RSEQ=CGGCAGTGGGGCAGGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:797:628:337,291:93,75:168,628:0.788:2,2:25.3:1:32.5:1:0.72779:1.07062:60:40.867:0.7899:0:1.1 1/0:634:373:210,163:142,119:261,373:0.5883:2,2:23.9:1:31.5:1:0.68482:1.08:60:123.333:0.5949:0:1.1 +19 45868478 . T A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33088;LSEQ=CCCAACCACTCTTCAAACCC;RSEQ=GGTCTCCACACCTCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:276:229:36,193:3,43:46,229:0.8297:2,2:23.3:1:31.4:1:0.16157:2.67:60:37.167:0.8352:0:1.1 1/0:193:119:21,98:13,61:74,119:0.6166:2,2:23:1:30.3:1:1:1.01:60:238:0.6198:0:1.1 +19 45868487 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16712;SOR=Inf;LSEQ=TCTTCAAACCCTGGTCTCCA;RSEQ=ACCTCCCAGCTGGCTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:23,211:234,0:0:2,0:24.5:1:32.2:1:1:0:59.9:45.8:1:0:0.9 0/1:163:2:1,1:25,135:160,2:0.0123:2,2:27:1:28.5:1:0.29607:5.31:60:4:0.0124:0:1 +19 45868647 . G A 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00481;SOR=0;LSEQ=CACTTTGTGAGGCTGAGGTG;RSEQ=GCAGATCACGAGGTCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:0,2:2,9:0.8182:0,0:26.8:1:32.4:1:1:0:41.1:18:0.8182:0:2 0/0:5:0:0,0:0,5:5,0:0:0,0:19.6:1:31.8:1:1:0:48.6:10:1:0:0.4 +19 45868649 . C G 102 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01786;SOR=0;LSEQ=CTTTGTGAGGCTGAGGTGGG;RSEQ=AGATCACGAGGTCAGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:24.5:1:29.6:1:1:0:42.1:4.5:1:0:2.2 0/1:5:2:0,2:0,3:3,2:0.4:0,0:14.5:1:31.5:1:1:0:46:4:0.4:0:1 +19 45871606 . T C 98 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15385;SOR=0.12384;LSEQ=AAATGCCTCTCCATAAATAC;RSEQ=GGGCTAGTAAGTTTCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:2,10:0.8333:0,0:25.1:1:29.8:1:1:0:56.9:9:0.8182:0:1.6 0/1:3:1:1,0:1,0:1,1:0.3333:0,0:1:0:30:0:1:0:60:2:0.3333:0:1 +19 45872036 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02011;SOR=0.64349;LSEQ=GGGGGCAGGGGGAGCTTGTG;RSEQ=TCATTGGAGGCACAAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:234:79,155:30,62:92,234:0.7178:2,2:22.4:1:30.3:1:0.89662:1.05:59.7:233:0.7169:0:1.1 1/0:224:139:46,93:18,67:85,139:0.6205:2,2:22.5:1:29.4:1:0.06745:1.84:60:138:0.6244:0:1.1 +19 45872446 . G A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09839;SOR=Inf;LSEQ=GGGCAACACACAGGGTCTCA;RSEQ=AACCTTGGGCACACAAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:87,257:344,0:0:2,0:25.8:1:32.2:1:1:0:60:85:1:0:0.1 0/1:296:3:2,1:84,209:293,3:0.0101:2,2:9.3:1:21.3:1:0.20331:4.95:60:2:0.0069:0:2.7 +19 45873366 . C T 67 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72636;SOR=0.63399;LSEQ=AGCCCCACCGGTCGAGTGGG;RSEQ=GGGTCGGGCCCACCGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:5:1,4:298,191:489,5:0.0101:2,2:16:1:29:1:0.08199:6.21909:60:10:0.0103:0:1.8 0/0:466:3:1,2:273,189:462,3:0.0064:2,2:9:1:24.7:1:0.57094:2.88228:60:6:0.0065:0:1 +19 45873531 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16107;SOR=Inf;LSEQ=GTCAGTTCCCGTCCCCTCAG;RSEQ=CCCTCTCCCGCCTCCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:53,170:223,0:0:2,0:24.1:1:31.6:1:1:0:60:54.75:1:0:0.1 0/1:150:2:1,1:34,114:148,2:0.0133:2,2:22.5:1:30.5:1:0.41342:3.32:60:4:0.0133:0:1 +19 45873591 . GC G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGGTGACGGGCCCGGC;RSEQ=CCCCGGTAACCCTCAGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:67,69:136,2:0.0145:2,2:28:1:33:1:1:1.03:60:4:0.0147:0:0 0/0:52:0:0,0:19,33:52,0:0:2,0:24.8:1:30.7:1:1:0:60:51:1:0:0.4 +19 45873942 . G C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00125;SOR=0.20428;LSEQ=CCCGTCAATCCGCTAGGGCA;RSEQ=AGCCAATCGGGATACTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:88:81:1,80:1,6:7,81:0.9205:2,1:20.2:1:32.4:1:0.15361:12.42128:60:80:0.9195:0:1 1/0:50:35:0,35:0,14:14,35:0.7:1,1:22.8:1:32.3:1:1:0:60:70:0.7:0:1.3 +19 45873959 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14605;SOR=Inf;LSEQ=GCAGAGCCAATCGGGATACT;RSEQ=CGCGTGCGCACGGAAAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:1,58:59,0:0:1,0:26.2:1:32.3:1:1:0:60:58:1:0:0.9 0/1:37:2:0,2:0,35:35,2:0.0541:1,0:13:1:28.5:1:1:0:60:4:0.0571:0:1.5 +19 46375666 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19228;SOR=Inf;LSEQ=TGGCCATCCAGCAGGCGCCG;RSEQ=GCAAGATGCTGACCTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:145,49:194,0:0:2,0:22.5:1:31.1:1:1:0:60:47.5:1:0:0.1 0/1:152:2:1,1:110,40:150,2:0.0132:2,2:30.5:1:29:1:0.46802:2.72858:60:4:0.0135:0:1 +19 46375779 . C T 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCCACTCGCTGTCTTTCAA;RSEQ=GACTGCTTCGTCAAGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:150,199:349,0:0:2,0:24.6:1:30.7:1:1:0:59.9:57.167:0.9971:0:0.1 0/1:350:99:43,56:113,138:251,99:0.2829:2,2:24.4:1:29.2:1:0.81219:1.06624:50.5:32:0.2807:0:1.2 +19 46375844 . A T 28 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19459;SOR=Inf;LSEQ=GGGCTCCTACTGGGCCCTAC;RSEQ=CCCCAGCTCAGGGAACATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:30,128:158,0:0:2,0:23.3:1:30.2:1:1:0:60:157:1:0:0.1 0/1:126:2:1,1:30,94:124,2:0.0159:2,2:5:0:28:1:0.43302:3.10:60:4:0.0163:0:0 +19 46375850 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1954;SOR=Inf;LSEQ=CTACTGGGCCCTACACCCCA;RSEQ=CTCAGGGAACATGTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:26,116:142,0:0:2,0:23.3:1:32.6:1:1:0:60:141:1:0:0.1 0/1:113:2:1,1:25,86:111,2:0.0177:2,2:9.5:1:30:1:0.40882:3.39:60:4:0.0177:0:1 +19 46375973 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAACGGGACAGGGTCTG;RSEQ=TGCCTCGACCACCACCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:3,24:27,2:0.069:2,2:20:1:26:1:0.26108:7.07:60:4:0.069:0:1 0/0:8:0:0,0:1,7:8,0:0:2,0:14.9:1:31.5:1:1:0:60:16:1:0:0.1 +19 46376217 . C A 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06619;SOR=0;LSEQ=GAACAGACACCAGCACCTCC;RSEQ=AAACTGGACGTGGGGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:2,3:10,19:29,5:0.1471:2,2:24.8:1:30.2:1:1:1.26:60:10:0.1471:0:1 0/0:25:0:0,0:11,14:25,0:0:2,0:25.7:1:28.9:1:1:0:60:24:1:0:0.1 +19 47724690 . CCT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCGAGAGGAGAGCCCCCC;RSEQ=CCCAGTGTCACCCCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:11,1:12,2:0.1538:2,2:25:1:31:1:0.27473:8.12278:60:4:0.1818:0.0769:0.5 0/0:1:0:0,0:1,0:1,0:0:0,0:20:0:32:0:1:0:60:2:1:0:0 +19 47725036 . G A 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.86236;LSEQ=CTGCCCCCCGAGTCCCTGAC;RSEQ=TCCACCGGGCGGGTGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:881:1:1,0:415,464:879,1:0.0011:2,0:1:0:25:0:0.47273:0:60:2:0.0012:0:1 0/1:909:25:12,13:444,440:884,25:0.0275:2,2:25.3:1:29:1:0.84242:1.09306:59.8:24:0.0268:0:1.2 +19 47726823 . C CA 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AACAGAGCAAGACTCCGTGT;RSEQ=AAAAAAAAAATTTTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:25,1:26,2:0.0714:1,0:20.5:1:32:0:1:0:60:4:0.0714:0:0 0/1:14:1:1,0:13,0:13,1:0.0714:1,0:43:0:32:0:1:0:60:2:0.0714:0:0 +19 47729764 . C T 52 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12383;SOR=Inf;LSEQ=CATCTGGCGGGGGCCGCCTG;RSEQ=CGCCCCCTCCTCCGGCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:263,54:317,0:0:2,0:23.2:1:31.6:1:1:0:60:34.222:1:0:0.2 0/1:319:4:1,3:246,69:315,4:0.0125:2,2:7.3:1:26.3:1:0.03722:10.58981:58.3:8:0.0127:0:1.5 +19 47731304 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50311;SOR=0;LSEQ=GCCACACCCTCCCAGTGGCC;RSEQ=GGCTGGGCCCGCCACCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:50,0:50,2:0.0385:1,2:19.5:1:27.5:1:0.03846:0:60:4:0.0392:0:1 0/0:40:0:0,0:39,1:40,0:0:1,0:25.2:1:30.1:1:1:0:60:39:1:0:0.3 +19 47731354 . C T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22929;SOR=0;LSEQ=TCCCACTTCTCCAGTTCCTC;RSEQ=GAGTCTCCAGCCCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:87,53:140,2:0.0141:2,2:6:1:30.5:1:1:1.63549:60:4:0.0143:0:1 0/0:154:0:0,0:91,63:154,0:0:2,0:22:1:29.2:1:1:0:60:76:1:0:0.3 +19 47731359 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22782;SOR=0;LSEQ=CTTCTCCAGTTCCTCCGAGT;RSEQ=TCCAGCCCTCTCTCTTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:88,63:151,2:0.0131:2,2:20:1:28.5:1:1:1.3937:60:4:0.0135:0:1 0/0:167:0:0,0:98,69:167,0:0:2,0:23.5:1:30.1:1:1:0:60:26.833:1:0:0.3 +19 47731444 . C T 45 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15914;SOR=0.20495;LSEQ=GCGGGCCTCGGGGCCGGCTG;RSEQ=GGGGACCCCCAGGCCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:0,3:66,132:198,3:0.0149:2,0:6.7:1:29:1:0.55226:0:60:6:0.0153:0:1.3 0/0:324:1:0,1:142,181:323,1:0.0031:2,0:1:0:26:0:1:0:60:2:0.0032:0:1 +19 47731480 . G T 30 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25873;SOR=0.24822;LSEQ=AGCGGGAACCCCCCAGGGCG;RSEQ=CGGTGACGGCGGGTGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:63,76:139,2:0.0142:2,2:17:0:30.5:1:1:1.20:60:4:0.0147:0:1.5 0/0:282:1:0,1:135,143:278,1:0.0035:2,0:1:0:25:0:1:0:60:2:0.0037:0:1 +19 47731544 . C T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.55297;SOR=Inf;LSEQ=GGGCAGCAGGGTGGGGGCGG;RSEQ=GGGGGCGGCAGCCAGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:37,35:72,0:0:2,0:22.1:1:27.7:1:1:0:59.4:5.545:1:0:0.5 0/1:142:3:1,2:67,70:137,3:0.0211:2,2:6.3:1:26:1:1:1.90576:60:6:0.0222:0:1.7 +19 47731549 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.54457;SOR=Inf;LSEQ=GCAGGGTGGGGGCGGCGGGG;RSEQ=CGGCAGCCAGGCCGGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:37,38:75,0:0:2,0:23.7:1:31.3:1:1:0:59.3:24:1:0:0.6 0/1:141:2:1,1:70,69:139,2:0.0142:2,2:45.5:1:29.5:1:1:1.01439:60:4:0.0145:0:1.5 +19 47731560 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52225;SOR=Inf;LSEQ=GCGGCGGGGGCGGCAGCCAG;RSEQ=CCGGGCTCGCAGAGGCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:47,44:91,0:0:2,0:21.5:1:31.2:1:1:0:59.7:29.333:0.9888:0:0.5 0/1:144:2:1,1:74,68:142,2:0.0139:2,2:42:1:28.5:1:1:1.08758:60:4:0.0141:0:3 +19 47731594 . G T 53 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15949;SOR=Inf;LSEQ=GGCCGCAGGACACTGCCGAG;RSEQ=GCACCAGGCGGCCGAGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:93,71:164,0:0:2,0:21.6:1:31.4:1:1:0:60:53.667:1:0:0.3 0/1:256:4:1,3:135,115:250,4:0.0156:2,2:6.5:1:26.8:1:0.34015:3.50554:60:8:0.0162:0:1 +19 47731606 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63168;SOR=2.4414;LSEQ=CTGCCGAGGGCACCAGGCGG;RSEQ=CGAGCGGGAAGGGGCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:0,1:118,85:203,1:0.0049:2,0:1:0:27:0:0.42157:0:60:2:0.005:0:1 0/1:252:3:2,1:134,113:247,3:0.0119:2,2:13.3:1:28:1:1:1.68:60:6:0.0124:0:1 +19 47731632 . G T 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62527;SOR=2.74877;LSEQ=GGGAAGGGGCGCGGGCCGTC;RSEQ=CGGGCCAGGCCCTCTACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:1:0,1:174,94:268,1:0.0037:2,0:1:0:27:0:0.35316:0:60:2:0.0038:0:1 0/1:295:3:0,3:176,116:292,3:0.0102:2,0:9:1:22.3:1:0.06465:0:60:2:0.0069:0:2.3 +19 47731653 . C T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37852;SOR=3.52887;LSEQ=CGGGCCAGGCCCTCTACGGG;RSEQ=TCCGGGGAGCTGCCCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:1:1,0:192,112:304,1:0.0033:2,0:30:0:13:0:1:0:60:0:0:0:2 0/1:348:4:1,3:206,138:344,4:0.0115:2,2:14.3:1:26.3:1:0.30759:4.45958:60:3:0.0088:0:2.3 +19 47731692 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09039;SOR=0;LSEQ=TGGCGTGCGCGGGCCATGGC;RSEQ=CTCCCTGGGGCCTGCGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:2,1:171,125:296,3:0.01:2,2:31:1:29:1:1:1.46:60:6:0.0103:0:1.7 0/0:366:0:0,0:200,164:364,0:0:2,0:26.6:1:29.8:1:1:0:60:59.667:0.9944:0:0.2 +19 47731744 . C A 27 v3;p8;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.77302;LSEQ=AGCAGGTCAGCAGGGAAGTA;RSEQ=CAGGGCCCACTGTACCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:61,118:179,2:0.011:2,2:7:0:32:0:1:1.93:60:4:0.0112:0:1 0/0:235:2:2,0:97,136:233,2:0.0085:2,0:1:0:27:1:0.17643:0:60:4:0.0088:0:1 +19 47731758 . A C 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50297;SOR=Inf;LSEQ=GAAGTACCAGGGCCCACTGT;RSEQ=CCTCCAGCCTACCCGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:38,110:148,0:0:2,0:24.4:1:29.4:1:1:0:60:147:1:0:0.1 0/1:179:2:1,1:65,112:177,2:0.0112:2,2:5:0:29:1:1:1.72:60:4:0.0114:0:0 +19 47731829 . C T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10656;SOR=0.44893;LSEQ=TGTGCATGCGGAGGGGGTGA;RSEQ=GGCCCCACAGAGACACGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:1,17:2,22:24,18:0.4286:2,1:24.1:1:31.1:1:1:1.5301:60:36:0.4286:0:1 0/1:40:10:1,9:3,27:30,10:0.25:2,2:23.9:1:28.3:1:1:1:60:20:0.2632:0:1 +19 47735745 . G A 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCCCACTGCACACACGTC;RSEQ=GAGCATGCACACCTGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:0:0,0:360,211:571,0:0:2,0:25.2:1:30.1:1:1:0:60:56.1:1:0:0.1 0/1:697:28:18,10:403,264:667,28:0.0402:2,2:28.4:1:29.9:1:0.84394:1.18:60:56:0.0406:0:1.1 +19 47735875 . T C 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCATCCTGTCTCATAGCTT;RSEQ=CCATTCCGTTTCTTTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:278,449:727,0:0:2,0:27.1:1:30.4:1:1:0:59.9:37.263:0.9986:0:0.1 0/1:992:81:35,46:383,528:911,81:0.0817:2,2:29.4:1:30.7:1:0.90662:1.05:59.8:80:0.0818:0:1.2 +19 48922772 . CT C 30 d5;v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTGGGAATTGTAGTTCTTT;RSEQ=TTTTTTTTTTTTCCCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:7:0:34:0:1:0:60:2:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:14:1:30.6:1:1:0:60:4:1:0.5:0 +19 48923101 . C A 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12874;SOR=5.91384;LSEQ=GGCCCAGGGCTGGGCTGGAG;RSEQ=TGGGGCTGGGGCTGGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:1,9:10,2:0.1667:2,0:39:1:33:0:1:0:60:4:0.1667:0:1 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:17.3:1:30.3:1:1:0:60:8:0.5714:0:1 +19 48945339 . T TC 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14773;SOR=Inf;LSEQ=AAGGGGCTAAGGGCCTACAT;RSEQ=CCCACATCACAGACAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:18,2:20,0:0:2,0:25:1:31.2:1:1:0:60:40:1:0:0.1 0/1:13:2:2,0:11,0:11,2:0.1538:0,0:11:1:27.5:1:1:0:60:4:0.1538:0.0769:0 +19 48945528 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50146;SOR=0;LSEQ=GTCTTCTACATGCTCCTGGT;RSEQ=GCCATGGGCCTGTCCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:70,110:180,2:0.0109:2,2:32.5:1:29.5:1:1:1.57:33:4:0.0111:0:1.5 0/0:157:0:0,0:53,104:157,0:0:2,0:25.4:1:29.9:1:1:0:59.1:30.4:1:0:0.2 +19 49004919 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20085;SOR=0;LSEQ=ACCCCTCCCATGACCCTGCC;RSEQ=CGCCACACTGACTCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,6:17,2:0.1:2,2:47:0:31:1:1:1.77272:60:4:0.1:0:1.5 0/0:24:0:0,0:12,12:24,0:0:2,0:24.1:1:29.7:1:1:0:60:48:1:0:0.4 +19 49256974 . AG A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50435;SOR=Inf;LSEQ=TATTTATTGTATACAAGACA;RSEQ=GGGGGGCAGGATAAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:19,0:0:2,0:19.8:1:32.1:1:1:0:50.6:38:1:0:0 0/1:27:2:2,0:19,6:25,2:0.0741:2,0:27.5:1:30.5:1:1:0:37:4:0.0769:0.037:0 +19 49610389 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGTGAGCGTGGGGACAC;RSEQ=GGGAAAGGCCTGGGACACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:28.5:1:1:0:60:4:1:0:1.5 +19 49611319 . C T 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00036;SOR=Inf;LSEQ=CGCAAGGAGGAGCTGCGTGG;RSEQ=GGCGGTGGCGACATGGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:27,0:0:2,0:28.7:1:31:1:1:0:60:54:1:0:0.1 0/1:16:7:2,5:4,5:9,7:0.4375:2,2:32.1:1:30.3:1:0.63287:1.91506:60:14:0.4375:0:1.4 +19 49611329 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13289;SOR=Inf;LSEQ=AGCTGCGTGGCGGCGGTGGC;RSEQ=ACATGGCGGAGCCCTCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:13,14:27,0:0:2,0:25.9:1:30.4:1:1:0:60:26:1:0:0.1 0/1:16:2:1,1:5,9:14,2:0.125:2,2:30.5:1:28:1:1:1.73:60:4:0.125:0:1.5 +19 50143171 . G C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.49854;SOR=0;LSEQ=AGGGCTCAGTTCTGGGTCCC;RSEQ=GGGGACACCCTCCCGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:20,11:31,2:0.0606:2,2:21:1:29.5:1:1:1.78367:60:4:0.0606:0:1 0/0:26:0:0,0:18,8:26,0:0:2,0:21.3:1:27.3:1:1:0:60:25:1:0:0.2 +19 50143214 . G C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50279;SOR=Inf;LSEQ=GCCCACTACCTGGATGAACT;RSEQ=GATGGTCAGCGCGCTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:36,0:0:2,0:31.9:1:31.5:1:1:0:60:35:1:0:0.3 0/1:47:2:1,1:19,26:45,2:0.0426:2,2:48:1:27.5:1:1:1.36:60:4:0.0426:0:1 +19 50143225 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.1897;SOR=0;LSEQ=GGATGAACTGGATGGTCAGC;RSEQ=CGCTCTTGCCCACGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:12,22:34,2:0.0556:2,2:46.5:1:30.5:1:1:1.80:60:4:0.0556:0:1 0/0:46:0:0,0:17,29:46,0:0:2,0:31.2:1:29.8:1:1:0:60:22:1:0:0.2 +19 50902014 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15519;SOR=Inf;LSEQ=CCAGTCCAGAGTAGGAAAAG;RSEQ=CTCGTGGTCATGGTGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:202,8:210,0:0:1,0:23.9:1:31.4:1:1:0:59.9:69:1:0:0.1 0/1:137:2:2,0:126,9:135,2:0.0146:2,0:23:1:29.5:1:1:0:60:4:0.0148:0:1 +19 50902265 . CAGG C 139 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.30164;SOR=0.66951;LSEQ=CAGAACACAGGCTGCAGGAG;RSEQ=AGGAGGAGGAGCTGCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1750:20:11,9:826,901:1727,20:0.0114:2,2:27.5:1:32.2:1:0.65384:1.33:60:40:0.0116:0.0034:0.4 0/0:1823:14:5,9:878,927:1805,14:0.0077:2,2:21.6:1:31.1:1:0.42495:1.70436:58.6:28:0.0077:0.0022:0.1 +19 50902843 . G A 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGCTCCTGGGGCAGAGGCC;RSEQ=GGCCAGGTCAGCCCCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:4,224:228,0:0:1,0:25.4:1:31.6:1:1:0:60:227:1:0:0.1 0/1:185:16:0,16:8,161:169,16:0.0865:1,1:21.7:1:31.3:1:1:0:60:32:0.0865:0:1.1 +19 50905412 . A G 185 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=77.78165;LSEQ=CCCCAGGATCAGCGGGTTGG;RSEQ=GGGTCCCCTCGGGAGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1486:1:1,0:723,762:1485,1:7e-04:2,0:47:0:30:0:0.48721:0:60:2:7e-04:0:1 0/1:1385:69:33,36:640,674:1314,69:0.0498:2,2:20.5:1:30.3:1:0.90234:1.03586:60:68:0.0501:0:1.2 +19 50905655 . G A 192 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=113.48622;LSEQ=GGCCTCTGCCTCACTTCTCC;RSEQ=GCCTCTATCCCCACCCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1349:1:1,0:659,689:1348,1:7e-04:2,0:1:0:27:0:0.48925:0:60:2:8e-04:0:1 0/1:1248:97:47,50:559,590:1149,97:0.0777:2,2:24.1:1:29.1:1:1:1.00793:60:96:0.0781:0:1.2 +19 50905762 . T C 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTGGCTGGAGCTCCCAGC;RSEQ=GGGAAATACGCCCTGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1395:0:0,0:709,685:1394,0:0:2,0:24.7:1:31.1:1:1:0:60:65.381:0.9993:0:0.2 0/1:1429:83:44,39:664,678:1342,83:0.0581:2,2:23.5:1:29.7:1:0.57248:1.15:60:166:0.059:0:1.2 +19 50906159 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13538;SOR=Inf;LSEQ=GCACAGAGGGTGTGGAGATG;RSEQ=CCTGGAGGTGAGAGCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:67,73:140,0:0:2,0:26.8:1:31.6:1:1:0:59.8:22.333:1:0:0.1 0/1:82:2:2,0:38,42:80,2:0.0244:2,0:23:1:31:0:0.23487:0:60:4:0.0256:0:1 +19 50906179 . CAGGAGCCAGGGTGA GCCGTACCGGATCTCAAAGTCGACGTTG 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.55465;SOR=0;LSEQ=GCCTGGAGGTGAGAGCAGAG;RSEQ=GCCACGTAGGGCCGGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:3:2,1:91,70:161,3:0.0183:2,2:21:1:30.5:1:1:1.53:60:6:0.0188:0.0183:0 0/0:91:0:0,0:55,36:91,0:0:2,0:22.4:1:31.3:1:1:0:59.8:21.75:1:0:0.3 +19 50906239 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13828;SOR=Inf;LSEQ=GGACAGCCCCGGGGAGATGG;RSEQ=AGGTGCAGCCTCCCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:277,60:337,0:0:2,0:22.9:1:32.3:1:1:0:59.9:55.167:1:0:0.1 0/1:200:2:1,1:165,33:198,2:0.01:2,2:23.5:1:25.5:1:0.31181:4.94095:60:4:0.0101:0:1 +19 50906507 . C T 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCACGCCCCACACCATTT;RSEQ=CCGGGGTCCCCGCCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:716:63:20,43:273,380:653,63:0.088:2,2:24.1:1:30.1:1:0.14026:1.5437:59.7:62:0.0883:0:1.1 0/0:692:0:0,0:272,419:691,0:0:2,0:21:0:16:0:1:0:60:0:0:0:7 +19 50906519 . G A 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03453;SOR=7.40025;LSEQ=CACCATTTCCCGGGGTCCCC;RSEQ=CCAGCCTCCGCGTCCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:597:1:1,0:231,365:596,1:0.0017:2,0:1:0:26:0:0.38861:0:60:2:0.0017:0:1 0/1:570:7:5,2:213,350:563,7:0.0123:2,2:24.1:1:28.1:1:0.11244:4.10:60:14:0.0125:0:1 +19 50906529 . G A 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=35.48886;LSEQ=CGGGGTCCCCGCCAGCCTCC;RSEQ=CGTCCTGAGCCATCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:1:1,0:205,333:538,1:0.0019:2,0:1:0:26:0:0.38219:0:60:2:0.0019:0:1 0/1:485:30:12,18:165,287:452,30:0.0619:2,2:16.3:1:28.1:1:0.6997:1.16:60:29:0.0614:0:1.1 +19 50909389 . T G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07302;SOR=1.321;LSEQ=CAATCTCCGTTCTTCAGGCT;RSEQ=ATGTGACGGGGACCCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:614:485:357,128:92,35:127,485:0.7899:2,2:24.8:1:32:1:0.8218:1.06:60:68.286:0.7888:0:1.1 1/1:555:462:318,144:68,24:92,462:0.8324:2,2:23.2:1:30.8:1:0.38518:1.28244:60:76:0.8367:0:1.2 +19 50909405 . G A 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTTATGTGACGGGGACCC;RSEQ=CAGCCTGCTGCACACCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:816:0:0,0:527,285:812,0:0:2,0:24.1:1:30.2:1:1:0:60:46.765:0.995:0:0.7 0/1:751:47:30,17:437,266:703,47:0.0626:2,2:25.1:1:29.6:1:0.87746:1.07:60:94:0.0639:0:1.9 +19 50909765 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01314;SOR=1.36669;LSEQ=GTGCAGCACAGCATCATCAC;RSEQ=GACCTGCAGGTGCCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1292:130:58,72:585,577:1162,130:0.1006:2,2:24.2:1:31.4:1:0.22988:1.25836:60:129:0.1009:0:1.2 0/1:1244:165:83,82:545,530:1075,165:0.1326:2,2:25.9:1:29.8:1:0.93356:1.0159:60:330:0.1336:0:1.2 +19 50910079 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11546;SOR=Inf;LSEQ=CTCCCTGGCCCCCAACCCTA;RSEQ=CTCCATCCCCACCCAGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:89,13:102,0:0:2,0:26.3:1:32.1:1:1:0:59.9:33:1:0:0.3 0/1:53:2:1,1:47,4:51,2:0.0377:2,2:36.5:1:27:1:0.18142:10.62088:60:4:0.0385:0:1 +19 50910196 . A G 178 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.02125;LSEQ=CTTCTCCTGCTCCACCTCCC;RSEQ=CCCCCAACCCCTGGTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:791:81:60,21:469,239:708,81:0.1024:2,2:26.8:1:28.1:1:0.17109:1.46:60:12.5:0.1019:0:1.1 0/0:829:2:1,1:513,307:820,2:0.0024:2,2:25.5:1:11.5:1:1:1.66985:49.5:0:0:0:4 +19 50911847 . C A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01051;SOR=Inf;LSEQ=ATAGGGTTTTGCCATGTTGC;RSEQ=CAGGCTGATCTGAAACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:113,0:113,0:0:1,0:26.1:1:31.7:1:1:0:60:55.5:1:0:0.1 0/1:78:5:5,0:73,0:73,5:0.0641:1,0:26:1:28.6:1:1:0:60:10:0.0649:0:1 +19 50911947 . AT A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.57879;SOR=0.8964;LSEQ=CTGCTCCCAGCCAATGAATG;RSEQ=TTTTTTTTTTTAAAGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:62:47,15:370,172:542,62:0.1013:2,2:28.7:1:31.6:1:0.24854:1.46:60:124:0.1035:0.0016:0.4 0/1:741:68:42,26:432,230:662,68:0.0918:2,2:20.3:1:29.6:1:0.59441:1.16248:59.8:136:0.0933:0.0283:0.3 +19 50911960 . A T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.75932;SOR=0.90672;LSEQ=ATGAATGATTTTTTTTTTTT;RSEQ=AAGGGTGAGGCCACAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:780:21:14,7:490,263:753,21:0.0269:2,2:25.3:1:29.3:1:1:1.07:58.6:20:0.0266:0:1.7 0/1:899:22:9,13:529,343:872,22:0.0245:2,2:17.7:1:28:1:0.07719:2.22569:60:44:0.0251:0:1 +19 50912211 . T C 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCCATCTGGGCCTTCCCT;RSEQ=GGGGGGCTCAGTCTGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:838:0:0,0:361,477:838,0:0:2,0:25.3:1:29.9:1:1:0:60:26.032:1:0:0.2 0/1:677:45:22,23:252,378:630,45:0.0665:2,2:26.2:1:29.3:1:0.27228:1.43:60:44:0.0664:0:1.1 +19 50912821 . G C 221 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGACCCCCTCCGGCGCCA;RSEQ=GTCCTGGATGGACGGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1184:136:68,68:545,502:1047,136:0.1149:2,2:25:1:31.3:1:0.71535:1.08558:60:135:0.1152:0:1.1 0/0:1115:0:0,0:544,566:1110,0:0:2,0:23.5:1:30.8:1:1:0:60:68.375:0.9955:0:0.2 +19 50916571 . A G 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00241;SOR=Inf;LSEQ=GGAGGGGCAGAGTGGCTTGT;RSEQ=CATAAGCCTATGCCACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:127,0:127,0:0:1,0:25.1:1:28.4:1:1:0:60:30.75:1:0:0.2 0/1:96:7:7,0:88,1:89,7:0.0729:1,0:25.9:1:31.7:1:1:0:60:14:0.0753:0:1.3 +19 50916597 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24181;SOR=Inf;LSEQ=GCCTATGCCACTGGGAAATG;RSEQ=CAGAGGCGGGACCCCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:185,15:200,0:0:2,0:25:1:31.5:1:1:0:59.8:65.667:1:0:0.2 0/1:194:2:1,1:185,7:192,2:0.0103:1,2:12:1:26.5:1:0.08098:24.78877:60:4:0.0105:0:1 +19 50916772 . T C 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGAATGGCTACAGCACCAG;RSEQ=GCCAAGGTCGGGGGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1046:0:0,0:464,580:1044,0:0:2,0:24.6:1:29.9:1:1:0:60:64.25:0.999:0:0.2 0/1:1128:78:36,42:466,581:1047,78:0.0691:2,2:25.4:1:30.1:1:0.81385:1.07:60:77:0.0691:0:1.2 +19 50916902 . TG T 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CCACTCTCCTGTTGCATCCT;RSEQ=GGTCCCGTTGGCATTAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:153,135:288,0:0:2,0:24.6:1:32:1:1:0:60:56.6:1:0:0.1 0/1:197:12:9,3:105,80:185,12:0.0609:2,2:15.4:1:30.6:1:0.24584:2.28:60:24:0.0622:0.0203:0 +19 50916904 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16846;SOR=Inf;LSEQ=ACTCTCCTGTTGCATCCTTG;RSEQ=GTCCCGTTGGCATTAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:155,133:288,0:0:2,0:24.5:1:31.6:1:1:0:60:71:1:0:0.1 0/1:201:2:1,1:116,83:199,2:0.01:2,2:13.5:1:27:1:1:1.3952:60:4:0.0103:0:1 +19 50918969 . A G 163 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=23.11042;LSEQ=CCTCACCCACCCGCCACCCC;RSEQ=TCTCCACGCAGGATGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:970:3:1,2:429,503:932,3:0.0031:2,2:45.3:1:25.3:1:1:1.70483:60:2:0.0026:0:2 0/1:881:59:29,30:404,396:800,59:0.067:2,2:26.4:1:27.8:1:0.89307:1.05534:59.9:7.429:0.0689:0:1.5 +19 50919530 . G GC 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.2705;LSEQ=CGACCCCATCCCAGACCCAG;RSEQ=CCCCCCCCATGTCACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:3,0:139,6:145,3:0.0203:1,0:32.3:1:33:1:1:0:60:6:0.0214:0:0 0/1:78:2:2,0:69,6:75,2:0.0256:2,0:4.1:1:29.3:1:1:0:60:6:0.0257:0.0221:0 +19 50919797 . C T 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.57621;LSEQ=TGCTACTGCGTACGGGGGCA;RSEQ=CAGGGGACTGGGGGCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:729:566:283,283:74,82:156,566:0.7764:2,2:24.2:1:30.2:1:0.58832:1.11:60:24.727:0.7749:0:1.2 1/0:693:462:232,230:115,114:229,462:0.6667:2,2:22.8:1:28.8:1:1:1.00006:59.9:41:0.6652:0:1.2 +19 50919828 . A G 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCACCCTGGGGGGGCAG;RSEQ=GGAGATCACCGGCCCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:365,353:718,0:0:2,0:22.7:1:30.6:1:1:0:60:24.643:0.9986:0:0.7 0/1:707:45:28,17:339,323:662,45:0.0636:2,2:22.8:1:30.7:1:0.16735:1.57:60:90:0.0648:0:1.1 +19 50919865 . AG A 107 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.11275;SOR=0.38711;LSEQ=CCACCTGCCTCCTCTCCTGC;RSEQ=GGGGGGACCACACGCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:928:10:5,5:477,439:916,10:0.0108:2,2:26.4:1:32.3:1:1:1.08645:60:20:0.0109:0.0011:0.5 0/0:953:4:3,1:505,441:946,4:0.0042:2,2:30.5:1:32.3:1:0.62783:2.62:60:8:0.0042:0:0.3 +19 50919929 . G A 90 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02206;SOR=5.49031;LSEQ=TGGGCGGCCTCCTGGCCTTC;RSEQ=CCAAACGCCGCAACTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:977:2:1,1:453,522:975,2:0.002:2,2:19:1:29:1:1:1.15:60:4:0.0021:0:1 0/1:987:11:8,3:463,511:974,11:0.0111:2,2:6.1:1:26.1:1:0.13019:2.94:60:22:0.0112:0:1 +19 50920100 . T C 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGGCCCAGGGCCCCTGGG;RSEQ=GGGTGGCCCCTGTCTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:35,82:117,0:0:2,0:26.8:1:30.4:1:1:0:60:234:1:0:0.1 0/1:59:14:5,9:9,35:44,14:0.2373:2,2:25.5:1:29.6:1:0.29068:2.13:60:13:0.2321:0:1 +19 50920410 . C T 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGCGGGGGCGCCCTGCT;RSEQ=AGCCGCTGCCGTCCCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1006:0:0,0:444,562:1006,0:0:2,0:23.7:1:32.1:1:1:0:60:54.889:1:0:0.2 0/1:1008:66:24,42:424,517:941,66:0.0655:2,2:20.7:1:28.4:1:0.20018:1.4347:59.5:132:0.0665:0:1.1 +19 50920536 . A G 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCTGCACCAGGTGTGTGCC;RSEQ=TGTCCCGACCCTGGGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:302,408:710,0:0:2,0:25.2:1:30.7:1:1:0:59.9:100.429:1:0:0.2 0/1:670:36:14,22:295,339:634,36:0.0537:2,2:27.1:1:29.8:1:0.39544:1.36684:59.5:17:0.0515:0:1.9 +19 50920558 . C T 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCCGACCCTGGGCTGCCC;RSEQ=GCCCCTTCCCAGCTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:579:0:0,0:234,343:577,0:0:2,0:25.6:1:30.1:1:1:0:59.9:71.125:0.9982:0:0.2 0/1:512:26:11,15:213,270:483,26:0.0508:2,2:25.8:1:29.7:1:1:1.07563:59.3:25:0.0498:0:2.1 +19 50920581 . T C 53 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06382;SOR=0;LSEQ=CCCTTCCCAGCTCCCAGGCC;RSEQ=GTGGGTTGTGGACCCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:5:3,2:126,286:412,5:0.0119:2,2:13.6:1:23.2:1:0.17441:3.39:60:1.5:0.0074:0:1.6 0/0:373:0:0,0:142,227:369,0:0:2,0:24.4:1:29.3:1:1:0:60:40:0.989:0:0.2 +19 50920902 . C T 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAGCCATGGCCCTGCAC;RSEQ=TCGCCAGGCACCCGCTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:31,2:33,3:0.0833:2,0:21.7:1:34:0:1:0:54:6:0.0857:0:1.7 0/0:10:0:0,0:9,1:10,0:0:2,0:16.8:1:30:1:1:0:53.4:20:1:0:0.7 +19 50920928 . TC T 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.6024;LSEQ=AGGCACCCGCTGTTATCGGC;RSEQ=CCCCCCCCCACCCCCCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:5,1:25,0:25,6:0.1935:1,2:20.7:1:29.1:1:0.19355:0:55.8:5:0.1613:0.0323:2.3 0/1:8:1:0,1:7,0:7,1:0.125:0,0:50:0:33:0:0.125:0:60:2:0.125:0:0 +19 50920939 . A C 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.4962;SOR=0.57802;LSEQ=GTTATCGGCTCCCCCCCCCC;RSEQ=CCCCCCCCGTGCCTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:21:21,0:13,1:14,21:0.5385:1,1:9.9:1:27.4:1:0.4:0:53.3:6:0.6:0:1.2 0/1:10:4:4,0:4,1:5,4:0.4:2,0:9:0:30.8:1:1:0:43.5:8:0.4444:0:1 +19 50921074 . A ACCCTGC 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGGCCTTGGCTGGTCCTG;RSEQ=CCCTGCCCCTGCCCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:784:0:0,0:494,288:782,0:0:2,0:25.5:1:29.4:1:1:0:60:27.963:0.9974:0:0.2 0/1:686:29:19,10:415,238:653,29:0.0423:2,2:29.4:1:30.9:1:1:1.09:60:58:0.0433:0.0058:0 +19 50921272 . T C 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AAAGTTCTGGACTTTTGCTA;RSEQ=ATGGTGCTTTGTGGTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:58,279:337,0:0:2,0:20.7:1:28.7:1:1:0:60:66.4:0.997:0:0.2 0/1:300:40:7,33:52,207:259,40:0.1333:2,2:19.6:1:31:1:0.83249:1.18361:60:39:0.1345:0:1.3 +19 50921317 . C A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07763;SOR=Inf;LSEQ=ACACTGTCTGGTTTCATAAG;RSEQ=CCTGGCCTTGGCTGGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:0,125:125,0:0:1,0:22.2:1:31.6:1:1:0:60:124:1:0:0.1 0/1:94:3:0,3:1,90:91,3:0.0319:1,0:19.3:1:31:0:1:0:60:6:0.0337:0:1.3 +19 51108018 . T C 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04614;SOR=Inf;LSEQ=GGAGTGAGGGGTGTTGGACG;RSEQ=GGCACGGGAACCCGGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:17,6:23,0:0:2,0:34.4:1:29.8:1:1:0:43.3:46:1:0:0 0/1:47:8:5,3:22,17:39,8:0.1702:2,2:36.9:1:30.9:1:1:1.28:32:16:0.1739:0:1 +19 51108208 . G C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=AGATCAAAGGGAAGAAAGGA;RSEQ=AGCCCCGACAGCCGGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:9:0:27:0:1:0:60:2:1:0:1 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:8.5:1:32.5:1:1:0:24.5:4:0.3333:0:2 +19 51231068 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCCAGCATCGCCTGGCA;RSEQ=ATGGGAGCCCTTTGAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:33:1:33:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 51231314 . CAG C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.21189;SOR=Inf;LSEQ=CAGGGCCAGCTGTGGGCATG;RSEQ=AGAGAGAGGTCTGAAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:83,36:119,0:0:2,0:24.5:1:30.8:1:1:0:60:58.5:1:0:0.3 0/1:102:2:1,1:62,38:100,2:0.0196:2,2:25:1:29.6:1:1:1.6234:60:4:0.02:0.0098:0 +19 51231337 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09637;SOR=Inf;LSEQ=AGAGAGAGGTCTGAAGTGGG;RSEQ=AGTGGCGTGCCTGCAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:96,67:163,0:0:2,0:25.3:1:30.9:1:1:0:60:39.75:1:0:0.5 0/1:139:3:1,2:74,62:136,3:0.0216:2,2:18.7:1:25.7:1:0.59451:2.37254:60:6:0.0222:0:1.7 +19 51231339 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50027;SOR=0;LSEQ=AGAGAGGTCTGAAGTGGGGA;RSEQ=TGGCGTGCCTGCAAGGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:96,66:162,2:0.0122:2,2:25:0:32.5:1:1:1.45112:60:4:0.0123:0:1.5 0/0:145:0:0,0:80,65:145,0:0:2,0:25.5:1:30.9:1:1:0:60:71.5:1:0:0.6 +19 51231363 . A T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24826;SOR=Inf;LSEQ=CGTGCCTGCAAGGACGGTTT;RSEQ=TGCATCAGAACAGCACGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:92,81:173,0:0:2,0:27.7:1:29.6:1:1:0:60:85.5:1:0:0.6 0/1:181:3:1,2:90,88:178,3:0.0166:2,2:38.7:1:23.7:1:0.62082:2.03766:60:2:0.0112:0:2.7 +19 51231391 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10931;SOR=Inf;LSEQ=GAACAGCACGCCTATATGTG;RSEQ=CATTCGGCGCTGATTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:84,107:191,0:0:2,0:24.4:1:32:1:1:0:60:190:1:0:0.7 0/1:176:3:2,1:84,89:173,3:0.017:2,2:13.3:1:25.7:1:0.61439:2.11:60:6:0.0171:0:2 +19 51231399 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.81414;LSEQ=CGCCTATATGTGGCATTCGG;RSEQ=GCTGATTCCTGACTCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:189:113:48,65:30,45:75,113:0.5979:2,2:22.9:1:29.7:1:0.76422:1.11:60:36.667:0.5914:0:1.1 1/1:174:148:69,79:15,11:26,148:0.8506:2,2:26.2:1:29:1:0.39517:1.55724:59.8:48.333:0.8529:0:1.2 +19 51231451 . G GC 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50293;SOR=0;LSEQ=CCTACTCTCTCCTCCAGGAA;RSEQ=CCCCCCCAGACTTCCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:46,84:130,2:0.0152:2,2:33.5:1:31:1:1:1.82:60:4:0.0154:0:1.5 0/0:108:0:0,0:43,65:108,0:0:2,0:23.1:1:31.1:1:1:0:59.9:107:1:0:0.8 +19 51231465 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51155;SOR=0;LSEQ=CAGGAAGCCCCCCCAGACTT;RSEQ=CTGCGGGCCAGAGTTTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:34,79:113,2:0.0174:2,2:27.5:1:31.5:1:0.51793:2.30:60:4:0.0179:0:1.5 0/0:82:0:0,0:30,52:82,0:0:2,0:24.1:1:30.1:1:1:0:60:81:1:0:0.6 +19 51322211 . T C 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTGTTCTGGCGTCCCTGACT;RSEQ=GCCCTTTGGGATCTGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:25:0:27:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:28.5:1:1:0:60:4:1:0:1 +19 51805209 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50239;SOR=Inf;LSEQ=TTTAGCTATCTTCAGTTTGA;RSEQ=ACTTGCATAAATGAAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:103,27:130,0:0:2,0:24.1:1:32.9:1:1:0:60:260:1:0:0.1 0/1:156:2:1,1:103,51:154,2:0.0128:2,2:27.5:1:26:1:1:2.00984:60:4:0.013:0:1 +19 51805318 . G A 258 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00169;LSEQ=GAAATTGCTGGATCATAGGA;RSEQ=TGCTCAGCTTTAGTAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:351:350:165,185:0,0:0,350:0.9972:0,2:24.6:1:30.6:1:1:0:60:174:1:0:1.1 0/1:370:137:67,70:115,118:233,137:0.3703:2,2:24.2:1:30.2:1:1:1.01817:60:274:0.3733:0:1.1 +19 51805440 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1675;SOR=Inf;LSEQ=AGTCCTTTTCATTTTAGTCA;RSEQ=TCTGGCAGCAGAGTAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:4,66:70,0:0:2,0:25.2:1:30.5:1:1:0:60:69:1:0:0.2 0/1:49:2:0,2:2,45:47,2:0.0408:1,0:32:1:33.5:1:1:0:60:4:0.0417:0:1 +19 52693277 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.19547;SOR=Inf;LSEQ=CCACGCCCGCCCTTCCTTCT;RSEQ=CTCCCAGCATTGCCCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:112,35:147,0:0:2,0:22.4:1:29.8:1:1:0:59.9:23.5:1:0:0.2 0/1:117:2:2,0:93,22:115,2:0.0171:2,0:14:0:32:0:1:0:60:4:0.0177:0:2 +19 52693289 . G GC 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=7.28666;LSEQ=TTCCTTCTTCTCCCAGCATT;RSEQ=CCCCCCCCACGTTTCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:7:4,3:124,44:168,7:0.0395:2,2:17.3:1:30.5:1:0.38757:2.1034:60:14:0.0407:0.0169:0.1 0/1:138:32:27,5:77,24:101,32:0.2319:2,2:27.6:1:30.9:1:0.46216:1.68:59.1:31:0.2385:0:0.5 +19 52693295 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.20637;SOR=Inf;LSEQ=CTTCTCCCAGCATTGCCCCC;RSEQ=CCACGTTTCAGCACAGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:133,52:185,0:0:2,0:24.4:1:30.9:1:1:0:59.8:36:0.9945:0:0.2 0/1:157:2:1,1:121,34:155,2:0.0127:2,2:35:1:27.5:1:0.39727:3.52187:60:4:0.0128:0:1 +19 52693297 . C CT 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCCCAGCATTGCCCCCCC;RSEQ=ACGTTTCAGCACAGCGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:55:39,16:98,41:139,55:0.2821:2,2:24.4:1:30.7:1:1:1.02:60:110:0.288:0.0564:0.3 0/0:164:0:0,0:126,38:164,0:0:2,0:23.1:1:30:1:1:0:59.8:40:1:0:0.3 +19 52693298 . A G 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0936;SOR=Inf;LSEQ=CTCCCAGCATTGCCCCCCCC;RSEQ=CGTTTCAGCACAGCGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:139,56:195,0:0:2,0:24.8:1:29.1:1:1:0:59.8:31.5:1:0:0.2 0/1:164:3:2,1:122,37:159,3:0.0183:2,2:27:1:26.7:1:0.55411:1.64294:56.7:6:0.0194:0:2 +19 52693540 . C T 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCGGAAGGGGGCGACGGC;RSEQ=AATCAGCGTGCGTCTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:134,221:355,0:0:2,0:25.3:1:31.7:1:1:0:60:38.444:1:0:0.2 0/1:503:32:10,22:205,265:470,32:0.0636:2,2:23.1:1:28.2:1:0.19872:1.70016:59.4:64:0.0643:0:1.2 +19 52693613 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=CTCCCGATTGGGTGTCGGCC;RSEQ=AGTGGAGGGCGGGGGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:18,97:115,2:0.0171:2,2:16.5:1:29:1:0.29959:5.27:60:4:0.0172:0:1.5 0/0:104:0:0,0:20,83:103,0:0:2,0:20.4:1:30.7:1:1:0:60:24.75:1:0:0.2 +19 52695551 . C CT 30 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAACAGATATGTAATGGC;RSEQ=TTTTTTTTTTTTTCTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:30.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 52704961 . T C 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.68385;LSEQ=CAACTGAGTAGGTGTCACCT;RSEQ=CATAAGACCCAAGGGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:34:1:32.3:1:1:0:60:8:0.3636:0:1 1/0:4:2:2,0:1,1:2,2:0.5:2,0:30:1:31:1:1:0:60:4:0.5:0:1 +19 52705523 . GCAGCTCCAA G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.1049;SOR=Inf;LSEQ=GGTAGAACGAGGTTTGAGTT;RSEQ=CAGTTGGAAGCTGGTGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:29.8:1:32.4:1:1:0:60:10:1:0:0 1/0:8:4:0,4:0,4:4,4:0.5:0,0:27:1:31.3:1:1:0:60:8:0.5:0.125:0 +19 52705688 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATATGCTTACTGTATGCCA;RSEQ=GTGGTGTTCTACACCGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:3,2:0.4:0,2:36.5:1:31:1:0.4:0:60:4:0.4:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:39:0:27:0:1:0:60:2:1:0:0 +19 52709064 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05652;SOR=Inf;LSEQ=CCTGTACCTTAATATCTGTG;RSEQ=CAGCCCAGGTGGAGAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:60,1:61,0:0:1,0:25.4:1:31.4:1:1:0:60:29.5:1:0:0.2 0/1:39:3:3,0:35,1:36,3:0.0769:1,0:38.7:1:29.7:1:1:0:60:6:0.0789:0:1 +19 52709171 . C T 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.94914;LSEQ=TTCTGAGCTTGGGCTGGGGT;RSEQ=AGAGTTGAGATGGGATAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:1:1,0:196,95:291,1:0.0034:2,0:43:0:10:0:1:0:60:0:0:0:7 0/1:379:30:20,10:224,125:349,30:0.0792:2,2:32.6:1:28.5:1:0.84506:1.12:60:60:0.0806:0:1.1 +19 52714298 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACCTTTGTGGAAGGCAC;RSEQ=CTGACAGAGACCTTCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:44.5:1:32.5:1:1:0:60:4:0.1818:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:20.4:1:30.8:1:1:0:60:10:1:0:0 +19 52714719 . C T 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTGCTACCCCCGAGTGTC;RSEQ=AGTGCTGTGAAGGCGGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:232,334:566,0:0:2,0:25.5:1:31.5:1:1:0:59.9:39.429:1:0:0.2 0/1:645:40:14,26:254,351:605,40:0.062:2,2:21.3:1:28.5:1:0.41264:1.34331:60:80:0.0632:0:1.2 +19 52714742 . G A 68 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28748;SOR=2.92846;LSEQ=TGCTGTGAAGGCGGAACTTC;RSEQ=ACAGTGAGTCTCTGCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:2:2,0:171,298:469,2:0.0042:2,0:1:0:28.5:1:0.13442:0:60:4:0.0043:0:1 0/1:486:6:5,1:177,303:480,6:0.0123:2,2:13:1:26.5:1:0.02959:8.53:60:12:0.0125:0:1.3 +19 52714917 . G A 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.06636;SOR=0;LSEQ=GAGAGTTGGTCTCTGGACAC;RSEQ=GCCACGTGTCAGTTTACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:10,6:0.375:0,0:15.3:1:32.3:1:1:0:59.8:12:0.375:0:2.3 0/0:8:0:0,0:0,8:8,0:0:0,0:23.5:1:29.3:1:1:0:52.9:16:1:0:0 +19 52716301 . C T 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01596;SOR=Inf;LSEQ=CCCTGGTGATGCCCACTCTG;RSEQ=GCCAGGCCGCTGAAGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:280,328:608,0:0:2,0:25.3:1:30.8:1:1:0:60:42.429:0.9983:0:0.1 0/1:663:7:2,5:313,342:655,7:0.0106:2,2:15.9:1:26.9:1:0.4545:2.28524:60:14:0.0107:0:1.1 +19 52718799 . C T 103 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.21106;LSEQ=ATTTTTAATGCTGACAACAC;RSEQ=GTGAGGTAGGTGCCCTCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:9,0:11,0:11,9:0.45:0,0:24.2:1:32.6:1:1:0:60:18:0.45:0:1.1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:45:0:33:0:1:0:60:2:0.5:0:2 +19 52718884 . T A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00234;SOR=0.18562;LSEQ=GAGCCTTGCCCCGGGGCCAG;RSEQ=CTTGGCACTCGAATTAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:27:26,1:32,0:32,27:0.4576:1,1:26.2:1:30.3:1:0.45763:0:60:26:0.4561:0:1.1 0/1:30:4:4,0:25,1:26,4:0.1333:1,0:32.8:1:29.5:1:1:0:60:8:0.1379:0:1 +19 52719190 . A G 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAAGTGGGGTGGGTATCC;RSEQ=AGGGGCTGGAGGTGGAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:536:0:0,0:302,234:536,0:0:2,0:23.5:1:30.4:1:1:0:60:75.571:1:0:0.1 0/1:595:33:16,17:296,264:560,33:0.0555:2,2:22.4:1:29.5:1:0.72055:1.19093:60:32:0.0546:0:1.2 +19 52719416 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51411;SOR=0;LSEQ=GCTTTGGGGATAGTCAGCTG;RSEQ=AAACTAGGTTCCCAGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:13,146:159,2:0.0123:2,2:9.5:1:28:1:0.16685:10.86:60:4:0.0126:0:1 0/0:113:0:0,0:15,98:113,0:0:2,0:21.9:1:31.6:1:1:0:60:226:1:0:0.1 +19 52719436 . C T 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00137;SOR=Inf;LSEQ=CAAACTAGGTTCCCAGCCCT;RSEQ=TGGGACCAGGCAGCTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:8,109:117,0:0:2,0:21.5:1:32.8:1:1:0:59.4:28.25:1:0:0.1 0/1:61:6:0,6:1,54:55,6:0.0984:1,0:23.2:1:30.5:1:1:0:60:12:0.0984:0:1.2 +19 52719690 . A G 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27663;SOR=0;LSEQ=TGAATGAGAGGGGCAGAAGC;RSEQ=GGTTATTGTCTCTTAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:2,1:210,19:229,3:0.0129:2,2:15.3:1:21.7:1:0.2379:5.4501:60:2:0.0088:0:2.7 0/0:157:0:0,0:151,6:157,0:0:1,0:24.4:1:29.8:1:1:0:60:51.333:1:0:0.1 +19 52723571 . C T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34687;SOR=3.39227;LSEQ=GCAGGATGGATTGGCTGGGG;RSEQ=TGTGGCGGGCAGTGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:0,1:42,161:203,1:0.0049:2,0:24:0:26:0:1:0:60:2:0.005:0:1 0/1:182:3:1,2:38,141:179,3:0.0165:2,2:21.3:1:27:1:0.51714:1.85:60:6:0.017:0:1 +19 52723584 . T C 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00201;SOR=Inf;LSEQ=GCTGGGGCTGTGGCGGGCAG;RSEQ=GGAGGAGGCTAGAGTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:17,142:159,0:0:2,0:24.7:1:30.4:1:1:0:60:38.75:1:0:0.1 0/1:139:8:0,8:17,113:130,8:0.0576:2,0:31.3:1:31.1:1:0.59542:0:60:16:0.0584:0:1.1 +19 52723865 . G A 31 v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTGCCTTGGGGCCATTAT;RSEQ=AGAATGGCTCATTGTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:41:0:31:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 52723930 . C T 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATATTTATCTCTGTGAAG;RSEQ=CCTGTTTGAAGTAATAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:33.7:1:30.3:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 52724095 . T C 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.54143;SOR=1.50119;LSEQ=ATATAGCACATAGTAAGTCC;RSEQ=TTTTTCTCTCTTTGGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:5,0:54,0:54,5:0.0847:1,0:25.2:1:32:1:1:0:60:10:0.0847:0:1 0/1:49:6:6,0:43,0:43,6:0.1224:1,0:22.3:1:29.2:1:1:0:60:12:0.1224:0:1 +19 52724448 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61751;SOR=2.07782;LSEQ=GGAGCGCGTGGGAGAGGAGG;RSEQ=ATGCTAGAGGGTTCCCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:0,1:14,137:151,1:0.0066:2,0:35:0:33:0:1:0:60:2:0.0068:0:1 0/1:147:2:1,1:19,126:145,2:0.0136:2,2:13:1:27:1:0.2544:6.49:60:4:0.0137:0:1 +19 52724461 . TC T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.22892;SOR=Inf;LSEQ=GAGGAGGGATGCTAGAGGGT;RSEQ=CCCAAGGGAGACACCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:5,110:115,0:0:1,0:22.8:1:31.7:1:1:0:60:56.5:1:0:0.1 0/1:106:2:1,1:11,93:104,2:0.0189:2,2:25.5:1:29.1:1:0.21456:8.14:60:4:0.0192:0.0094:0.5 +19 52724465 . C CT 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22955;SOR=Inf;LSEQ=AGGGATGCTAGAGGGTTCCC;RSEQ=AAGGGAGACACCTGGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:3,103:106,0:0:1,0:23.2:1:32.8:1:1:0:60:105:1:0:0 0/1:98:2:1,1:8,88:96,2:0.0204:2,2:21:1:25.2:1:0.1761:10.43:60:4:0.0206:0.0102:0 +19 52725271 . A G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0361;SOR=Inf;LSEQ=TGGGGCCTGATGATCACCAG;RSEQ=GTGGCCTGGTCAGAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:124,19:143,0:0:2,0:25.7:1:30.2:1:1:0:59.9:19.429:1:0:0.1 0/1:112:4:4,0:93,15:108,4:0.0357:2,0:19:1:30.8:1:1:0:60:8:0.0377:0:1.5 +19 52725338 . T C 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCATACTCACCCCTGCCAC;RSEQ=CACTGGCCCCCAGGTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:0:0,0:281,147:428,0:0:2,0:25.6:1:31.1:1:1:0:59.9:70.333:1:0:0.1 0/1:419:22:16,6:259,138:397,22:0.0525:2,2:27.7:1:30.7:1:0.64539:1.42:60:44:0.053:0:1.2 +19 52728890 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05222;SOR=Inf;LSEQ=GTGTCTGTGTACACTCTCTT;RSEQ=CCCAAGAGCCCTGTGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:172,36:208,0:0:2,0:22.6:1:32.7:1:1:0:59.9:207:1:0:0.1 0/1:192:4:2,2:151,37:188,4:0.0208:2,2:22.3:1:29.8:1:0.18401:4.041:60:8:0.0212:0:1 +19 52729082 . A C 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAAGACCTAGAAAGCACGG;RSEQ=GCCCTAGCAGGAGGGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:246,274:520,0:0:2,0:23.7:1:30.9:1:1:0:60:56.778:1:0:0.1 0/1:586:34:16,18:256,296:552,34:0.058:2,2:27.4:1:30.2:1:1:1.03:60:68:0.0591:0:1.2 +19 53081658 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53902;SOR=Inf;LSEQ=ATCAATCACTTAGAAGATTC;RSEQ=CCCTCCTTACCCTGCCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,5:14,0:0:2,0:23.4:1:31.1:1:1:0:32.1:28:1:0:0.2 0/1:27:2:1,1:9,16:25,2:0.0741:2,2:9.5:1:28.5:1:1:1.74:27.5:4:0.0769:0:1 +19 53081735 . C T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01409;SOR=0;LSEQ=TTTGGGGCCACTACCTGTCT;RSEQ=CGCGTCTTGATGGTAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:1,5:1,4:5,6:0.5455:2,2:27.8:1:29.7:1:1:1.22474:46:12:0.5455:0:1 0/0:9:0:0,0:3,6:9,0:0:2,0:24.1:1:30.8:1:1:0:46.7:18:1:0:0.1 +19 53082892 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCAGTAATTTGGGAGGC;RSEQ=GAGGTGGGCAGATCACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:28.5:1:1:0:60:4:1:0:1 +19 53792794 . G C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCACCACGCCTGGCTT;RSEQ=CATTTTTTTTTTCTACTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19.5:1:34:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 53792953 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23547;SOR=Inf;LSEQ=CTTTGCTTGAAATCAATAAC;RSEQ=GCGCTGCACATGGGACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:66,30:96,0:0:2,0:26.4:1:30.8:1:1:0:60:47:1:0:0.2 0/1:91:2:1,1:52,36:88,2:0.022:2,2:28:1:31.5:1:1:1.4384:60:4:0.0222:0:1 +19 53792954 . GC AT 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00596;SOR=Inf;LSEQ=TTTGCTTGAAATCAATAACC;RSEQ=GCTGCACATGGGACATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:66,30:96,0:0:2,0:26.8:1:30.2:1:1:0:60:23:1:0:0.2 0/1:92:7:5,2:48,37:85,7:0.0761:2,2:21.9:1:29.4:1:0.69453:1.91:60:14:0.0761:0.0109:0.9 +19 53793007 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24397;SOR=Inf;LSEQ=GCACATTGTTTACAAGTGAC;RSEQ=AGATGTCCACAAGGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:86,60:146,0:0:2,0:24.4:1:31.6:1:1:0:59.5:47.667:1:0:0.5 0/1:143:2:1,1:67,74:141,2:0.014:2,2:26:1:31:1:1:1.10:60:4:0.0142:0:1 +19 53793014 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.215;SOR=Inf;LSEQ=GTTTACAAGTGACCAGATGT;RSEQ=CACAAGGAATAAAAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:82,62:144,0:0:2,0:25.6:1:31.8:1:1:0:59.5:143:1:0:0.5 0/1:125:2:1,1:57,66:123,2:0.016:2,2:17:1:31:1:1:1.16:60:4:0.0161:0:2 +19 53793032 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17586;SOR=Inf;LSEQ=GTCCACAAGGAATAAAAACA;RSEQ=CAGCGATATGTCTGTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:84,69:153,0:0:2,0:24.9:1:29.7:1:1:0:60:37.25:1:0:0.6 0/1:111:2:1,1:54,54:108,2:0.018:2,2:34:0:33.5:1:1:1:60:4:0.0183:0:1.5 +19 53793039 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20018;SOR=Inf;LSEQ=AGGAATAAAAACAACAGCGA;RSEQ=ATGTCTGTCCATGCAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:84,71:155,0:0:2,0:24.8:1:29.6:1:1:0:60:76.5:1:0:0.6 0/1:126:2:1,1:63,61:124,2:0.0159:2,2:46:1:27:1:1:1.03253:60:4:0.016:0:2 +19 53793042 . G A 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00253;SOR=2.12269;LSEQ=AATAAAAACAACAGCGATAT;RSEQ=TCTGTCCATGCAGATTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:76:42,34:43,36:79,76:0.4903:2,2:23.9:1:29.8:1:1:1.03:60:152:0.4903:0:1.1 1/0:128:86:46,40:20,21:41,86:0.6719:2,2:22.7:1:27.9:1:0.70501:1.21:60:27.667:0.6694:0:1.1 +19 53793048 . C A 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50219;SOR=0;LSEQ=AACAACAGCGATATGTCTGT;RSEQ=CATGCAGATTTTACAAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:78,73:151,2:0.0131:2,2:22:1:24.5:1:1:1.068:60:4:0.0134:0:2 0/0:128:0:0,0:66,62:128,0:0:2,0:23.3:1:30.4:1:1:0:60:127:1:0:0.9 +19 53793055 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58664;SOR=2.51692;LSEQ=GCGATATGTCTGTCCATGCA;RSEQ=ATTTTACAAAGCTTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:1:1,0:76,73:149,1:0.0067:2,0:1:0:26:0:1:0:60:2:0.0067:0:1 0/1:120:2:1,1:61,57:118,2:0.0167:2,2:23:1:29.5:1:1:1.06954:60:4:0.0167:0:2 +19 53793084 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17345;SOR=Inf;LSEQ=AAGCTTCTCCTCTTGCAGAC;RSEQ=CCTTAGCGGCTCTTCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:62,69:131,0:0:2,0:27.2:1:30.5:1:1:0:60:20.833:1:0:0.4 0/1:94:2:1,1:42,50:92,2:0.0213:2,2:27.5:1:31:0:1:1.19:60:4:0.0217:0:1 +19 53793162 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05015;SOR=Inf;LSEQ=TTCTGTAGTGTCTTTCTGAG;RSEQ=GCTCACTAGATCTGCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:74,49:123,0:0:2,0:25.5:1:31.8:1:1:0:60:246:1:0:0 0/1:112:4:2,2:66,42:108,4:0.0357:2,2:12.8:1:28.5:1:0.64496:1.56484:60:8:0.0364:0:1.3 +19 53793528 . C A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.56299;LSEQ=AAAGCACTGTACTTTATCCT;RSEQ=TTGACCTATAGCATAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:69,121:190,2:0.0104:2,2:28:1:28.5:1:1:1.75:60:4:0.0105:0:1 0/0:170:1:1,0:67,102:169,1:0.0059:2,0:1:0:21:0:0.4:0:60:2:0.0061:0:1 +19 53793533 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22072;SOR=Inf;LSEQ=ACTGTACTTTATCCTCTTGA;RSEQ=CTATAGCATAAAATCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:65,115:180,0:0:2,0:22.7:1:31.2:1:1:0:60:59:1:0:0.3 0/1:160:2:0,2:61,97:158,2:0.0125:2,0:22.5:1:27:1:0.52524:0:60:4:0.0126:0:2.5 +19 53793555 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22217;SOR=Inf;LSEQ=TATAGCATAAAATCCAGCTC;RSEQ=TGCAAGCTGCTCTTTGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:54,89:143,0:0:2,0:25.1:1:30.7:1:1:0:60:34.75:1:0:0.4 0/1:128:2:1,1:48,78:126,2:0.0156:2,2:33:1:29:1:1:1.62:60:4:0.0159:0:2 +19 53793574 . A G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.63492;LSEQ=CTTGCAAGCTGCTCTTTGTT;RSEQ=ACGGAGTACATCCATGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:46:18,28:35,48:83,46:0.3566:2,2:26.7:1:32.9:1:0.85211:1.13315:59.4:92:0.3622:0:1.1 1/0:112:85:31,54:10,17:27,85:0.7589:2,2:27:1:31.1:1:1:1.02446:59.5:170:0.7658:0:1 +19 53793583 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50148;SOR=0;LSEQ=TGCTCTTTGTTAACGGAGTA;RSEQ=ATCCATGTCCCAAAAGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:52,74:126,2:0.0156:2,0:24:1:28:1:0.17606:0:60:4:0.0159:0:2 0/0:108:0:0,0:43,65:108,0:0:2,0:26.8:1:31.8:1:1:0:59.6:216:1:0:0.7 +19 53793798 . C T 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCCCAGTTTTTCAGTTTTC;RSEQ=GCCACAACAGAAGCACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:252,264:516,0:0:2,0:27.4:1:30.2:1:1:0:59.9:45.909:1:0:0.2 0/1:497:39:18,21:220,237:457,39:0.0785:2,2:26.4:1:29.1:1:0.86831:1.08278:57.3:38:0.0772:0:1.2 +19 53793874 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5052;SOR=0;LSEQ=CTGGCCAGCTCTCTCGGGGT;RSEQ=AAGTGGGCAGAGGCTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:21,160:181,2:0.0109:2,2:30.5:1:29.5:1:0.22657:7.47:60:4:0.0109:0:1 0/0:145:0:0,0:19,126:145,0:0:2,0:31:0:15:0:1:0:60:0:0:0:1 +19 53793888 . C A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01369;SOR=Inf;LSEQ=CGGGGTCAAGTGGGCAGAGG;RSEQ=TGGCCAGTTGTGAAACGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:21,138:159,0:0:2,0:24.1:1:33.4:1:1:0:60:158:1:0:0.3 0/1:119:5:0,5:12,102:114,5:0.042:2,0:22.8:1:30.4:1:1:0:60:10:0.0424:0:1.8 +19 53793911 . T A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.22769;LSEQ=GCCAGTTGTGAAACGACTGT;RSEQ=ATCTAGCTTCTTCACTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:35:8,27:14,68:82,35:0.2991:2,2:23.1:1:30.2:1:0.45198:1.43:60:16.5:0.2895:0:1.1 1/0:93:60:9,51:6,27:33,60:0.6452:2,2:23.4:1:29.7:1:0.77093:1.25605:60:59:0.6413:0:1.2 +19 53793969 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18846;SOR=Inf;LSEQ=GTGTATGGAGTCTGATCTAT;RSEQ=CACCACCTGTCCAGCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:14,44:58,0:0:2,0:25.4:1:30.9:1:1:0:59.2:28:1:0:0.6 0/1:45:2:1,1:10,32:42,2:0.0444:2,2:46:1:29.5:1:0.44186:3.10:60:4:0.0476:0:1 +19 53793995 . C T 81 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12964;SOR=0.18206;LSEQ=CCTGTCCAGCTCTCAAAAGC;RSEQ=GGTCTGCACGAGTCTCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:7:2,5:3,32:35,7:0.1667:2,2:29:1:29.1:1:0.18752:4.07:56.3:6:0.1579:0:2 0/1:29:1:0,1:7,21:28,1:0.0345:2,0:44:0:32:0:1:0:60:2:0.037:0:2 +19 53794353 . G A 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19962;SOR=Inf;LSEQ=TGATGTCTGCAGACACATAC;RSEQ=TTTTAGATCCTTCGAAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:34,31:65,0:0:2,0:25.4:1:30.5:1:1:0:59.6:130:1:0:0.1 0/1:53:2:1,1:28,23:51,2:0.0377:2,2:6:1:24.5:1:1:1.21285:60:4:0.0385:0:1 +19 53794385 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21406;SOR=Inf;LSEQ=TCGAAACTGTTCAAAGTTAT;RSEQ=TTCTCTTGAATATAGGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:24,30:54,0:0:2,0:26.1:1:32:1:1:0:59.5:108:1:0:0.1 0/1:47:2:1,1:20,25:45,2:0.0426:2,2:39:1:29:0:1:1.24:60:4:0.0426:0:1 +19 53794388 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49907;SOR=0;LSEQ=AAACTGTTCAAAGTTATCTT;RSEQ=TCTTGAATATAGGACTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:22,30:52,2:0.037:2,2:17.5:1:28.5:1:1:1.36:60:4:0.0385:0:1 0/0:45:0:0,0:19,26:45,0:0:2,0:27.7:1:30.4:1:1:0:60:44:1:0:0.2 +19 53812461 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49773;SOR=Inf;LSEQ=AGTGTGCTTTCAGCGATATC;RSEQ=GCATTTCTAGAACAGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:55,39:94,0:0:2,0:25.3:1:30.4:1:1:0:60:93:1:0:0.2 0/1:99:2:1,1:56,41:97,2:0.0202:2,2:24:1:28.5:1:1:1.36147:60:4:0.0204:0:1 +19 53812496 . A G 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0024;SOR=Inf;LSEQ=GCATTTATTTTTGCATATGC;RSEQ=TGTAGGACACAGATACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:70,60:130,0:0:2,0:25.4:1:30.9:1:1:0:60:260:1:0:0.2 0/1:157:10:6,4:74,73:147,10:0.0637:2,2:26.3:1:31.1:1:0.74619:1.48:60:20:0.0641:0:1.1 +19 53812507 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50304;SOR=Inf;LSEQ=TGCATATGCATGTAGGACAC;RSEQ=GATACACAGGGCGGGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:72,63:135,0:0:2,0:25.7:1:30.9:1:1:0:60:44:1:0:0.2 0/1:164:2:1,1:85,77:162,2:0.0122:2,2:17:0:32:0:1:1.10323:60:4:0.0126:0:1.5 +19 53812523 . T C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00024;SOR=4.02764;LSEQ=ACACAGATACACAGGGCGGG;RSEQ=TTGGGGCGGGACCTCGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:8:4,4:70,64:134,8:0.0563:2,2:27.3:1:33.6:1:1:1.09306:60:16:0.0576:0:1.1 0/1:180:35:18,17:75,70:145,35:0.1944:2,2:25.1:1:31.2:1:1:1.01184:60:34:0.1954:0:1.4 +19 53812535 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50666;SOR=Inf;LSEQ=AGGGCGGGTTTGGGGCGGGA;RSEQ=CTCGTGCGGTGCAGGCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:70,62:132,0:0:2,0:26.3:1:32:1:1:0:60:65:1:0:0.2 0/1:171:2:1,1:86,83:169,2:0.0117:2,2:13:1:28.5:1:1:1.03594:60:4:0.0121:0:2 +19 53812552 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19336;SOR=0;LSEQ=GGACCTCGTGCGGTGCAGGC;RSEQ=CTGTGGGAAGCGTTGCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:62,66:128,2:0.0154:2,2:32:1:31:1:1:1.06:60:4:0.0157:0:1 0/0:165:0:0,0:81,84:165,0:0:2,0:25.3:1:29.8:1:1:0:60:32:1:0:0.4 +19 53812559 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50296;SOR=Inf;LSEQ=GTGCGGTGCAGGCGCTGTGG;RSEQ=AAGCGTTGCCCTAACGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:59,66:125,0:0:2,0:25.3:1:31.1:1:1:0:60:30.25:1:0:0.2 0/1:152:2:1,1:73,77:150,2:0.0132:2,2:26.5:1:28.5:1:1:1.05:60:4:0.0132:0:1.5 +19 53812582 . C G 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=GCGTTGCCCTAACGGCTGGT;RSEQ=TCCAGGGCTGCAGGTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:39,57:96,0:0:2,0:25.8:1:31.8:1:1:0:60:23:0.9892:0:0.2 0/1:126:14:4,10:51,60:111,14:0.1111:2,2:24.9:1:31.1:1:0.26299:2.1129:60:28:0.1129:0:1.6 +19 53812688 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06363;SOR=Inf;LSEQ=TAGCTGTCCCTCTCATCCCC;RSEQ=CCCCTGCAACCTGAGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:1,17:18,0:0:1,0:28.4:1:31.1:1:1:0:60:17:1:0:0.2 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:43.7:1:30:1:1:0:60:6:0.2308:0:1 +19 54380850 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19861;SOR=0;LSEQ=AGGGTGCCCTTCCCTCTTAG;RSEQ=TAGCCGAAGCAGAGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:14.5:1:30:1:1:1.40:56:4:0.1111:0:1 0/0:23:0:0,0:9,14:23,0:0:2,0:23.7:1:30.3:1:1:0:56.5:46:1:0:0.1 +19 56007371 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGTCTTGGCCTCCCTAA;RSEQ=TGCTGGGATTATAGGCGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:15:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 56172495 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=CCGGTGCCCGTGGTCGGGAG;RSEQ=CAGATGACCAGACAAGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:9,0:0:2,0:36.3:1:32:1:1:0:60:18:1:0:0 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:19.5:1:28:1:1:1:60:4:0.1429:0:1.5 +19 56709003 . CGAGAAAATAAATGCAT C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49965;SOR=Inf;LSEQ=CGCTGCCTTCACAAAGTCTC;RSEQ=GAGAAAATAAACCCAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:38,37:75,0:0:2,0:27.1:1:30.5:1:1:0:50.7:74:1:0:0.1 0/1:87:2:0,2:45,40:85,2:0.023:2,0:14.5:1:30.5:1:0.23015:0:45.5:4:0.0235:0.023:0 +19 56709008 . A G 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.86162;LSEQ=CCTTCACAAAGTCTCCGAGA;RSEQ=AATAAATGCATGAGAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:32,36:68,2:0.0286:2,2:25:0:17.5:1:1:1.12:60:1:0.0149:0:1.5 0/1:81:2:1,1:37,40:77,2:0.0247:2,2:21:1:28.5:1:1:1.08:51:4:0.0256:0:1 +19 56709105 . C T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.17564;LSEQ=TCGCCGCTGGACACTCACCT;RSEQ=CTTCCCGGCTTCTGCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:1,10:0,4:4,11:0.7333:0,2:22.3:1:30.4:1:1:0:49.6:22:0.7857:0:1 1/0:17:13:1,12:0,4:4,13:0.7647:0,1:22.6:1:28.7:1:1:0:46.1:26:0.8125:0:1.1 +19 56739528 . GA G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51443;SOR=Inf;LSEQ=TGCCTTCACAAAGTCTCCGA;RSEQ=AAACGCACGAAAAAATAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:22,36:58,0:0:2,0:25.3:1:30.3:1:1:0:50:57:1:0:0.2 0/1:85:2:1,1:28,55:83,2:0.0235:2,2:15.5:1:29:1:1:1.95:36.5:4:0.0238:0:3.5 +19 56739565 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50834;SOR=Inf;LSEQ=TAAACCCAAACTTTCTGAAA;RSEQ=CAACCCCCGACATGCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:5,23:28,0:0:2,0:27.1:1:31:1:1:0:54.1:27:1:0:0.1 0/1:40:2:1,1:7,31:38,2:0.05:2,2:17:1:27.5:1:0.3641:4.21:45.5:4:0.0513:0:1 +19 56751782 . T C 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAACCAATCATGGGGCAG;RSEQ=GCAGGAACTGGAAATGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:23.8:1:32.5:1:1:0:51.5:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 56751951 . G T 217 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01363;LSEQ=TGGGGTTTAGGAGCTGGCAT;RSEQ=CAGGGGGGTTAGTTTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:130:104,26:1,0:1,130:0.9924:0,2:25.7:1:31:1:1:0:59.8:260:1:0:1.3 1/0:135:86:59,27:36,13:49,86:0.637:2,2:23.7:1:29.6:1:0.6954:1.26508:59.5:172:0.637:0:1.2 +19 56752018 . AG A 258 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00985;LSEQ=TTGCTTGGAGACCTTGTGAA;RSEQ=CATCGGGTCTCCTTTGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:279:277:147,130:1,1:2,277:0.9928:2,2:25.4:1:31.9:1:1:1.13:59.7:554:0.9928:0.1541:1.2 1/0:358:206:108,98:80,72:152,206:0.5754:2,2:25.3:1:30.6:1:1:1.00821:59.7:412:0.5787:0.1089:1.2 +19 56752041 . C T 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00505;LSEQ=ATCGGGTCTCCTTTGCACCC;RSEQ=GTGATTAACTCTGGCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:311:310:142,168:0,1:1,310:0.9968:0,2:26.2:1:31.1:1:1:0:59.8:154:0.9968:0:1.2 1/0:381:232:107,125:72,77:149,232:0.6089:2,2:26.4:1:29.5:1:0.67571:1.09211:59.7:231:0.6095:0:1.2 +19 56752069 . C A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12923;SOR=Inf;LSEQ=ACTCTGGCTTGTTATGAAAC;RSEQ=CTTATGTAAACTAGGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:109,176:285,0:0:2,0:27.6:1:31.5:1:1:0:59.9:284:1:0:0.9 0/1:338:4:3,1:135,199:334,4:0.0118:2,2:21.3:1:26.8:1:0.30859:4.40:60:8:0.012:0:1.5 +19 56752143 . A C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20472;SOR=Inf;LSEQ=TAGAGACGGGGGTCTCACTC;RSEQ=TTGCCCAGGCTGGCTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:11,61:72,0:0:2,0:23.6:1:31.1:1:1:0:60:144:1:0:0 0/1:60:2:1,1:9,49:58,2:0.0333:2,2:13.5:1:30:1:0.30791:5.22:60:4:0.0339:0:1.5 +19 56752381 . T A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCACCTTGCCGGCCGCAC;RSEQ=CCACTTGTTAAAAAGCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:32:0:1:0:36.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 56754157 . T TA 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTTCTTTCTTTCTCTCTT;RSEQ=TTTTTTTGAGACGGAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:27:1:1:0:29.5:4:1:0:0 +19 57396817 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=Inf;LSEQ=GGTCACTGGAGCTGTGACCT;RSEQ=CAAATTAGGATACTTGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:8,0:0:2,0:21.6:1:30:1:1:0:60:16:1:0:0.3 0/1:10:2:1,1:4,4:8,2:0.2:2,2:34.5:1:29.5:1:1:1:60:4:0.2:0:1 +19 57396818 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18301;SOR=0;LSEQ=GTCACTGGAGCTGTGACCTT;RSEQ=AAATTAGGATACTTGTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:6,2:0.25:2,2:22.5:1:27.5:1:1:1.83:60:4:0.25:0:1 0/0:10:0:0,0:5,5:10,0:0:2,0:23.8:1:31.2:1:1:0:60:20:1:0:0.3 +19 57742472 . G C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCGAAGCCTGTGTAGCA;RSEQ=TGAGACATCAGTGAGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:36:1:34:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 57742489 . CTGCAGGACGAGCAGGATTGGAAGCG TTGCAGGAAGCGC 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGAGACATCAGTGAGG;RSEQ=CCCCGGCCAGAAAGTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:28.3:1:30.8:1:1:0:60:8:1:0.5:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +19 57743039 . T C 46 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCTCTACTGTTCTCCTC;RSEQ=CCTCTCTTTCTCTCCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:30.3:1:29.3:1:1:0:60:6:1:0:1.3 +19 57744965 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.47895;SOR=0;LSEQ=TTTGGCTGGTCTGTGCACAC;RSEQ=CCCTCCCTGAGGTAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:27:0:32:0:1:1.87:60:4:0.1818:0:1 0/0:9:0:0,0:4,5:9,0:0:2,0:31.8:1:30.1:1:1:0:60:18:1:0:0 +19 57746302 . A T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27007;SOR=Inf;LSEQ=CTTGCCGCCAGAAATGATTG;RSEQ=GGGGAGAACATATGATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:76,43:119,0:0:2,0:26.5:1:30.3:1:1:0:60:58.5:1:0:0 0/1:169:3:1,2:103,63:166,3:0.0178:2,2:7.7:1:27:1:0.55945:3.24634:60:6:0.0181:0:1 +19 58288034 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50505;SOR=Inf;LSEQ=CCTTGACACTTATATCCTCC;RSEQ=TGGGTAAGGTACTCATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:57,11:68,0:0:2,0:21.1:1:31.1:1:1:0:52.8:136:1:0:0 0/1:88:2:1,1:73,13:86,2:0.0227:2,2:22:1:28.5:1:0.29441:5.44814:52.5:4:0.023:0:1 +19 58288169 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38278;LSEQ=GGAGAGGTTCTGTTGTTGGT;RSEQ=GGACTGAGGTGTACGTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:340:184:85,99:84,72:156,184:0.5412:2,2:24.9:1:30.6:1:0.19148:1.35757:59.9:91:0.5433:0:1.2 0/1:473:147:65,82:152,173:325,147:0.3108:2,2:23.9:1:29.4:1:0.61944:1.10816:60:146:0.3126:0:1.1 +19 58288210 . G T 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02896;SOR=0;LSEQ=CCCTGTCCTTTCCTTGAGCA;RSEQ=CCCCAACCTGCTTTGTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:4:1,3:87,138:225,4:0.0175:2,2:36:1:26.5:1:1:1.88653:60:3:0.0133:0:1 0/0:324:0:0,0:122,202:324,0:0:2,0:26.4:1:31:1:1:0:59.9:39.5:1:0:0.4 +19 58288231 . G T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18539;SOR=0;LSEQ=CCCCAACCTGCTTTGTTGCA;RSEQ=GCTTCCAGGGAAGGAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:61,122:183,2:0.0108:2,2:24:0:30.5:1:1:1.99:60:4:0.011:0:2 0/0:244:0:0,0:79,165:244,0:0:2,0:22.1:1:30.2:1:1:0:59.9:33.857:1:0:0.4 +19 58288238 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20146;SOR=0;LSEQ=CTGCTTTGTTGCAGGCTTCC;RSEQ=GGGAAGGAGTCAGGGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:51,112:163,2:0.0121:2,2:8.5:1:30:1:0.5323:2.18:60:4:0.0123:0:1 0/0:202:0:0,0:63,139:202,0:0:2,0:21.7:1:29.5:1:1:0:59.9:32.667:1:0:0.3 +19 58288257 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24493;SOR=Inf;LSEQ=CAGGGAAGGAGTCAGGGTCA;RSEQ=GAGTCTTAAAGTCACCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:28,96:124,0:0:2,0:22.8:1:31.6:1:1:0:59.9:61:1:0:0.2 0/1:122:2:1,1:24,96:120,2:0.0164:2,2:45.5:1:30:1:0.36919:3.94:52.5:4:0.0168:0:1 +2 740482 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGGCGCGGCCCAGCCAGGA;RSEQ=AGCTGGAGAGGCAGCGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:33.5:1:30.5:1:1:1.7321:41:4:0.4:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:48:0:34:0:1:0:41:2:1:0:2 +2 740483 . A G 33 v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GGGCGCGGCCCAGCCAGGAG;RSEQ=GCTGGAGAGGCAGCGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:34:0:33:0:1:1.7321:36.5:4:0.4:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:49:0:33:0:1:0:41:2:1:0:2 +2 741921 . G T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01494;SOR=0.10522;LSEQ=TTACTGCTGTACCTGCTGTG;RSEQ=AATCTAGTGAGATTCTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:7,5:2,1:3,12:0.8:2,2:20.4:1:28.4:1:1:1.39581:60:24:0.8:0:1.8 0/1:11:3:2,1:5,3:8,3:0.2727:2,2:26.3:1:27.7:1:1:1.18:60:6:0.2727:0:1.7 +2 741946 . C G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00893;SOR=0.14146;LSEQ=TAGTGAGATTCTAAGTAGTC;RSEQ=TATTTAATTGTGAGTCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:15:8,7:2,1:3,15:0.8333:2,2:28.3:1:30.5:1:1:1.69794:60:30:0.8333:0:1.7 0/1:20:8:4,4:8,4:12,8:0.4:2,2:14.6:1:31.5:1:0.64792:1.92981:60:16:0.4211:0:1.5 +2 742090 . T G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAGGGAACGTGAGAATTAGG;RSEQ=CAACCAGAGTGTTTTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24:1:33.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:48:0:30:0:1:0:60:2:1:0:1 +2 1107063 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19119;SOR=Inf;LSEQ=GCTGGAAGCAGGAAGGGGAG;RSEQ=CAGCGTACGGCCGGGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:34,40:74,0:0:2,0:28.3:1:29.6:1:1:0:60:73:1:0:0.3 0/1:58:2:1,1:24,32:56,2:0.0345:2,2:37.5:1:27.5:1:1:1.33:60:4:0.0345:0:2.5 +2 1107122 . G A 111 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06107;SOR=0.20319;LSEQ=CTGCTGTTGAGATTAGGACC;RSEQ=CAGGTGTGCAGCAGAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:14:3,11:7,18:25,14:0.359:2,2:28:1:29.3:1:0.72115:1.41332:60:13:0.3611:0:1.1 0/1:20:2:1,1:5,13:18,2:0.1:2,2:4.5:1:28.5:1:0.52105:2.46:60:4:0.1:0:2.5 +2 1826996 . A G 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=CAGGCAGACCCAGCAGGGGC;RSEQ=CCCAGCTGGTGGTGCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:4,0:9,2:11,4:0.2667:2,0:21.8:1:30.8:1:1:0:60:8:0.3077:0:2 0/0:4:0:0,0:4,0:4,0:0:0,0:24:1:30.3:1:1:0:60:8:1:0:0 +2 1827040 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08005;SOR=0.27603;LSEQ=ATAGTCGTGGTGGTTGTGGT;RSEQ=GTGAGGGCTGTTGCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:18:11,7:15,11:26,18:0.4091:2,2:25.6:1:31.4:1:1:1.15:60:36:0.4091:0:1.4 0/1:19:3:2,1:10,6:16,3:0.1579:2,2:18.3:1:32:1:1:1.19:60:6:0.1579:0:2.3 +2 2526697 . A C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0061;SOR=Inf;LSEQ=AGCCGGAGTTCAGCGCCAGG;RSEQ=AGCCCGGTGGCCCCCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:23:1:30.6:1:1:0:60:60:1:0:0.2 0/1:19:5:2,3:7,7:14,5:0.2632:2,2:24.2:1:28.8:1:1:1.46843:60:4:0.2222:0:1 +2 4561867 . T C 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24482;SOR=0.33497;LSEQ=TCCAGAAGCCATTATTCACG;RSEQ=AATTGATGAACTTGGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:3,2:15,3:18,5:0.2174:2,2:29.8:1:30.8:1:0.29068:3.1287:53.6:10:0.2174:0:1 0/1:24:2:2,0:17,5:22,2:0.0833:2,0:35.5:1:32.5:1:1:0:48.5:4:0.0833:0:1 +2 4562125 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.50416;SOR=0;LSEQ=CACCTTTTCTTCAGTTTCCT;RSEQ=ATCATCAAAATTATCATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:46,40:86,2:0.0227:2,2:22.5:1:28:1:1:1.14817:60:4:0.0227:0:1 0/0:69:0:0,0:36,33:69,0:0:2,0:22.6:1:30.9:1:1:0:59.8:68:1:0:0.1 +2 4562144 . GTCA G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.25225;SOR=0;LSEQ=TCATCATCAAAATTATCATT;RSEQ=TCATCATCATCATCTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:2,1:49,41:90,3:0.0323:2,2:39.7:1:33.3:1:1:1.66:60:6:0.0326:0:0 0/0:77:0:0,0:40,37:77,0:0:2,0:25:1:29.1:1:1:0:59.1:154:1:0:0.1 +2 4562168 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51039;SOR=0;LSEQ=TCATCATCATCATCTTCATC;RSEQ=GCAGCAAGTTTTACTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:55,47:102,2:0.0192:2,2:27.5:1:30.5:1:1:1.16844:58.5:4:0.0194:0:1 0/0:75:0:0,0:37,38:75,0:0:2,0:27.4:1:30.3:1:1:0:59.1:150:1:0:0.1 +2 4562203 . TACC T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.45298;SOR=0.59047;LSEQ=TTGTTTCCATGGAAACTTGC;RSEQ=ACCCCCTGGGGCAGATTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:13:8,5:38,27:65,13:0.1667:2,2:24.1:1:31.8:1:1:1.13:59.8:26:0.1688:0.0256:0.1 0/1:57:6:3,3:25,26:51,6:0.1053:2,2:35.2:1:30:1:1:1.04:60:12:0.1053:0:0 +2 4562211 . C A 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=ATGGAAACTTGCTACCACCC;RSEQ=CTGGGGCAGATTGCTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:2,0:44,31:75,2:0.026:2,0:6.5:1:26.5:1:0.51265:0:47.5:4:0.026:0:1.5 0/0:56:0:0,0:28,28:56,0:0:2,0:21.9:1:29.8:1:1:0:59.7:55:1:0:0.1 +2 4562266 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13513;SOR=Inf;LSEQ=TTTCACATCCTCCTCCTCTT;RSEQ=ATCTCCTGACTCTGCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:98,25:123,0:0:2,0:25.3:1:32.3:1:1:0:58.8:60.5:1:0:0.1 0/1:72:2:1,1:52,18:70,2:0.0278:2,2:47:1:29.5:1:0.46088:2.83875:31.5:4:0.0278:0:1 +2 4562410 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07586;SOR=Inf;LSEQ=CATTGCTGTACAGACATTTT;RSEQ=AAAGTTACCAGTGTTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:102,165:267,0:0:2,0:23.6:1:31.9:1:1:0:51.9:43.5:1:0:0.1 0/1:197:3:2,1:75,119:194,3:0.0152:2,2:14.7:1:25.7:1:0.56189:3.15:43.7:6:0.0153:0:1 +2 4562427 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51239;SOR=0;LSEQ=TTTCAAAGTTACCAGTGTTA;RSEQ=TTTAATTGGACTGCCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:62,136:198,2:0.01:2,2:15:1:29.5:1:0.53186:2.18:47:4:0.0101:0:1 0/0:143:0:0,0:52,91:143,0:0:2,0:22.2:1:31.1:1:1:0:50.8:142:1:0:0.1 +2 4562511 . T C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17513;SOR=Inf;LSEQ=ACCAACCACTAAACTGACTG;RSEQ=TTTTAAAGATAACTTGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:13,53:66,0:0:2,0:25.1:1:30.1:1:1:0:57.5:65:1:0:0.1 0/1:48:2:1,1:10,36:46,2:0.0417:2,2:5:0:33.5:1:0.40957:3.48:47:4:0.0426:0:0 +2 4562591 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09729;SOR=Inf;LSEQ=TGGCCTTTAGTTCACAACTG;RSEQ=AAAGGTAATTCTGGGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:43,0:0:2,0:21.7:1:30.9:1:1:0:57.3:86:1:0:0.1 0/1:20:2:1,1:10,8:18,2:0.1:2,2:43:1:30.5:1:1:1.23603:41.5:4:0.1:0:1 +2 4562621 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15892;SOR=Inf;LSEQ=TCTGGGGCCTCAGGGTGCTC;RSEQ=TGTCCATGTCCATCGAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:23,23:46,0:0:2,0:23.3:1:31.2:1:1:0:59:92:1:0:0.1 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:16.5:1:26.5:1:1:1.07:43.5:4:0.0645:0:1 +2 4562657 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49425;SOR=0;LSEQ=AATCTTCCATGAGGTGGTGG;RSEQ=ATGTACTTAGGTGGGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:21,21:42,2:0.0455:2,2:47.5:1:31:1:1:1:60:4:0.0476:0:1 0/0:43:0:0,0:20,23:43,0:0:2,0:25.3:1:31.3:1:1:0:58.8:42:1:0:0.3 +2 4562775 . G A 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.41422;LSEQ=TAAAGAGCAGGTAAGCTCCC;RSEQ=CAGTGTCGCACAGCCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:25.7:1:32:0:1:0:60:6:0.4286:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:23:1:31:0:1:0:60:4:1:0:1 +2 4716777 . T G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTAAAACTCATCTTTGCT;RSEQ=TACCTTTTGAGAACAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:42.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 4717009 . A G 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20546;SOR=Inf;LSEQ=TAGTATATATGTTAATAATT;RSEQ=TTTGATAATTATTATTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:141,54:195,0:0:2,0:22.3:1:28.7:1:1:0:59.9:64:0.9948:0:0.4 0/1:163:2:1,1:116,45:161,2:0.0123:2,2:19:0:27.5:1:0.48603:2.56058:60:4:0.0125:0:1 +2 4717038 . C T 154 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.20204;LSEQ=TTATTATTTGATTAGCCAAA;RSEQ=GCCATGAGAAAGTCTCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:2:0,2:218,118:336,2:0.0059:2,0:1:0:26.5:1:0.12537:0:60:4:0.006:0:2 0/1:285:36:23,13:144,105:249,36:0.1263:2,2:24.8:1:29.8:1:0.58813:1.29:60:35:0.1246:0:1 +2 4717057 . TA T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.41484;SOR=2.51258;LSEQ=ACGCCATGAGAAAGTCTCAG;RSEQ=AAGAACATTTTGGAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:2:1,1:240,160:400,2:0.005:2,2:26:1:32:1:1:1.49841:60:4:0.0051:0:1 0/1:322:4:1,3:171,147:318,4:0.0124:2,2:20.8:1:27.3:1:0.34186:3.47724:60:8:0.0125:0.0062:1 +2 4717089 . C A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33617;LSEQ=TGGAAAAAGCAGTTTCATAT;RSEQ=TATACGCATCACACATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:452:345:182,163:64,42:106,345:0.7633:2,2:25.8:1:29.6:1:0.18184:1.36379:59.9:68:0.764:0:1.1 1/0:379:197:97,100:87,95:182,197:0.5198:2,2:25.2:1:28.8:1:0.83712:1.06:60:196:0.5213:0:1.1 +2 4717156 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17339;SOR=Inf;LSEQ=ATTGCACTCATCAAAACTCA;RSEQ=AGAACCTTATGATTTTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:78,195:273,0:0:2,0:25.8:1:29:1:1:0:60:90:0.9963:0:0.4 0/1:196:2:1,1:64,130:194,2:0.0102:2,2:23:1:28:1:1:2.02:60:4:0.0103:0:1 +2 4717162 . C A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.57189;SOR=2.85332;LSEQ=CTCATCAAAACTCATAGAAC;RSEQ=TTATGATTTTAAGACATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:1:1,0:64,182:246,1:0.004:2,0:1:0:26:0:0.26316:0:60:2:0.0041:0:1 0/1:174:2:1,1:51,121:172,2:0.0115:2,2:25:1:26:1:0.5096:2.36:60:4:0.0116:0:1 +2 4717192 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.529;SOR=0;LSEQ=TAAGACATTTTGAGCTCTCT;RSEQ=ATAACACTTGTAGATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:18,127:145,2:0.0135:2,2:22.5:1:27:1:0.24257:6.89:60:4:0.0138:0:1 0/0:89:0:0,0:12,77:89,0:0:2,0:23.6:1:31.7:1:1:0:60:178:1:0:0.1 +2 4717291 . T C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64446;SOR=0.67517;LSEQ=TTGACTGTAAAATTATTGAG;RSEQ=AAATGGATTAACAGGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:21:0,21:0,7:7,21:0.75:0,1:26.6:1:33:1:1:0:60:42:0.75:0:1 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:23:1:31.8:1:1:0:52.3:8:0.6667:0:1 +2 4900640 . T G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATACACCATCTAAGGCC;RSEQ=GCCCTAGGAGGATAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:35.5:1:31:1:1:0:51:4:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 4900652 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAGGCCTGCCCTAGGAGG;RSEQ=TAAGAGAATGATTTGTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:40:1:31:1:1:0:51:4:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 4900678 . A C 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGATTTGTAATGTGAAA;RSEQ=TGGCAAAGAAGCCACCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:26.5:1:31.5:1:1:0:55.5:8:0.8:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 4901103 . A C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.6067;LSEQ=AGAGTTGCGCTCAAATGGTG;RSEQ=CTACATGTTGTAATGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:649:395:196,199:116,137:253,395:0.6086:2,2:25.1:1:31.3:1:0.37565:1.16:59.2:31.917:0.6051:0:1.1 0/1:478:232:117,115:110,133:243,232:0.4854:2,2:26.2:1:30.9:1:0.27131:1.23:58.6:57:0.4872:0:1.1 +2 4901179 . AAAT A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00083;SOR=0.54131;LSEQ=GCTATTATGTGAGATACAGA;RSEQ=AATAACCTGGAAAAGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:305:182:32,150:35,88:123,182:0.5967:2,2:25.9:1:31.2:1:0.03395:1.86045:60:181:0.5954:0.059:0.4 0/1:207:92:17,75:34,80:114,92:0.4444:2,2:27.9:1:29.9:1:0.07424:1.86935:60:91:0.4527:0.029:0.4 +2 4901307 . G A 128 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19652;SOR=0.2076;LSEQ=AATATATAAATTGTACTATA;RSEQ=TGGTACCTATAGTAGCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:0,16:0,16:16,16:0.5:1,1:23.6:1:32.1:1:1:0:60:32:0.5:0:1 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:49:0:33:0:1:0:60:2:0.1667:0:1 +2 4901589 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCAAAGAATTAGAAAA;RSEQ=TGGAAATATGTAAGACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:14.5:1:31.5:1:1:0:53.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 5429063 . T C 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTCTATTTAAAAAATAC;RSEQ=CCTAATGAAACAATGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:18,0:0,0:0,18:1:0,1:24.4:1:31.6:1:1:0:59.2:36:1:0:1 1/1:9:9:8,1:0,0:0,9:1:0,2:31:1:30:1:1:0:60:18:1:0:1 +2 5429187 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15252;SOR=Inf;LSEQ=CTGGGTCCACTCTGAGGGAC;RSEQ=CTCCCATCATGTGGATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:112,62:174,0:0:2,0:25.1:1:30.9:1:1:0:59.7:173:1:0:0.4 0/1:112:2:1,1:68,42:110,2:0.0179:2,2:13:0:31:0:1:1.61177:60:4:0.018:0:3 +2 5429197 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=10.83728;LSEQ=TCTGAGGGACGCTCCCATCA;RSEQ=GTGGATGCTTCTTCATAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:40:21,19:96,61:157,40:0.203:2,2:26.1:1:30:1:0.36862:1.42125:58.8:12.333:0.1947:0:2 1/0:125:92:54,38:20,13:33,92:0.736:2,2:27.4:1:30.3:1:1:1.0819:60:184:0.736:0:1.7 +2 5429215 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15039;SOR=Inf;LSEQ=CATGTGGATGCTTCTTCATA;RSEQ=GCAAGGGCAGAGCTCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:124,112:236,0:0:2,0:24.6:1:32.1:1:1:0:60:58:1:0:0.5 0/1:150:2:1,1:83,65:148,2:0.0133:2,2:37:0:31.5:1:1:1.27482:60:4:0.0134:0:1.5 +2 5429237 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55574;SOR=0;LSEQ=CAAGGGCAGAGCTCCAAGGA;RSEQ=CACCTCCTCCTCACCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:138,138:276,3:0.0108:2,2:14.3:1:25.7:1:1:1.99521:60:2:0.0073:0:1.3 0/0:155:0:0,0:81,74:155,0:0:2,0:25.3:1:31.3:1:1:0:60:76.5:1:0:1.7 +2 5429260 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.65429;LSEQ=CCTCCTCCTCACCTTCTGCA;RSEQ=GTAGTGGGGGAGATCGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:51:24,27:102,126:228,51:0.1821:2,2:25.6:1:29.7:1:0.87646:1.10:59.1:11.75:0.1728:0:2.6 1/1:161:130:66,64:15,16:31,130:0.8075:2,2:24.4:1:28.9:1:0.84383:1.10:60:17.571:0.7987:0:2.7 +2 5429279 . G A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=28.99916;LSEQ=ACGTAGTGGGGGAGATCGCC;RSEQ=GTACCAACATCCTTGGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:39:20,19:94,124:218,39:0.1518:2,2:28.2:1:30.6:1:0.38391:1.39:60:18.5:0.1468:0:2.8 1/1:144:121:59,62:10,13:23,121:0.8403:2,2:26.8:1:29.4:1:0.65758:1.24:59.6:120:0.8392:0:2.8 +2 5429284 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13672;SOR=Inf;LSEQ=GTGGGGGAGATCGCCGGTAC;RSEQ=AACATCCTTGGAGTGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:107,141:248,0:0:2,0:26.4:1:31.9:1:1:0:60:247:1:0:0.5 0/1:146:2:1,1:67,77:144,2:0.0137:2,2:20:0:31:1:1:1.15:60:4:0.014:0:4 +2 5429303 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14339;SOR=Inf;LSEQ=CCAACATCCTTGGAGTGGAG;RSEQ=TGAAGACTTTTTGAAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:81,120:201,0:0:2,0:24.4:1:32.4:1:1:0:60:99.5:1:0:0.4 0/1:123:2:1,1:47,74:121,2:0.0163:2,2:13:0:30:1:1:1.57:38:4:0.0167:0:3.5 +2 5429313 . T C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=28.17397;LSEQ=TGGAGTGGAGCTGAAGACTT;RSEQ=TTGAAGCTGTTCATGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:25:10,15:53,98:151,25:0.142:2,2:14:1:31:1:0.65693:1.23:60:50:0.1429:0:2.7 1/1:115:95:34,61:7,13:20,95:0.8261:2,2:25.1:1:30.9:1:1:1.03:59.5:94:0.8246:0:2.6 +2 5429341 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15311;SOR=Inf;LSEQ=TGTTCATGCCAGCTCATGGA;RSEQ=CTCTTCATGCCACACTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:23,82:105,0:0:2,0:22.9:1:32.3:1:1:0:60:210:1:0:0.1 0/1:68:2:1,1:17,48:65,2:0.0294:2,2:34:1:30:1:0.46811:2.77:60:4:0.0303:0:1 +2 5429475 . T G 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAAGATGTCAGCTTGCAT;RSEQ=GCTCCTCCATGCCCACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:9,3:0.25:0,0:31.7:1:29.7:1:1:0:54:6:0.25:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 5429486 . G A 45 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTGCATTGCTCCTCCAT;RSEQ=CCCACACACATAGCTAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:9,3:0.25:0,0:20.7:1:28.7:1:1:0:54:6:0.25:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 5429997 . G C 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCTTCTCTTGCCCTTG;RSEQ=GCTTCAGTGTTCCTGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 5490556 . G A 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CAGCAAAATGAATCTACATA;RSEQ=CCTGTATAAATGTGACATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:24.5:1:31:1:1:0:60:4:0.5:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:35.3:1:33.7:1:1:0:60:6:1:0:0 +2 6635870 . TA T 105 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=1.08625;LSEQ=TCATACAGAAATAACTAGTG;RSEQ=AAAAAAAAAAAAGGTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:13:13,0:28,1:29,13:0.2826:1,1:35:1:28.6:1:1:0:60:12:0.2667:0.0435:1.1 0/1:10:3:3,0:7,0:7,3:0.3:0,0:18.3:1:30.7:1:1:0:60:6:0.3:0.1:0 +2 6635991 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19159;SOR=Inf;LSEQ=GCGGCTGCCTCCTCTCGGGC;RSEQ=GGGGCAGGGAGGAGCCGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:207,47:254,0:0:2,0:21.4:1:30.6:1:1:0:59.9:30.75:0.996:0:0.2 0/1:199:2:1,1:144,52:196,2:0.0101:2,2:23.5:1:28.5:1:0.4647:2.75249:60:4:0.0102:0:1 +2 6636076 . G GGCTTCGTTAAACTTCACTCGGAAGTGCTTCGGTTAAACTTCACTCGGAAGT 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01242;SOR=0.67654;LSEQ=GGTTTCCAGCTCTCGCGGAG;RSEQ=GCTTCGTTAAACTTCACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:831:136:68,68:384,311:695,136:0.1637:2,2:9.6:1:29.3:1:0.30046:1.2344:36.6:44.333:0.1636:0.1637:1.1 0/1:616:72:39,33:295,249:544,72:0.1169:2,2:8.9:1:28.4:1:1:1.00247:36.3:144:0.1194:0.1169:0.8 +2 6636082 . G T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22022;SOR=0.54923;LSEQ=CAGCTCTCGCGGAGGGCTTC;RSEQ=TTAAACTTCACTCGGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:18:9,9:468,395:863,18:0.0204:2,2:6.1:1:29.4:1:0.81288:1.18458:24.9:8:0.0184:0:1.3 0/1:619:7:3,4:323,281:604,7:0.0113:2,2:8.4:1:29.7:1:0.71056:1.53154:33.6:14:0.0116:0:1.3 +2 6636107 . G T 74 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56834;SOR=1.41488;LSEQ=ACTTCACTCGGAAGTGCTTC;RSEQ=TTAAACTTCACTCGGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:841:6:2,4:430,404:834,6:0.0071:2,2:30:1:31.3:1:0.43922:2.12685:23:12:0.0072:0:1.2 0/1:596:6:3,3:301,289:590,6:0.0101:2,2:27.8:1:28.8:1:1:1.04146:31.3:12:0.0102:0:1 +2 6636119 . T A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06798;LSEQ=AGTGCTTCGTTAAACTTCAC;RSEQ=CGGAAGTGCTTCGTTAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:815:106:46,60:363,345:708,106:0.1301:2,2:21.8:1:30.4:1:0.14505:1.37186:51.3:105:0.1316:0:1.8 0/1:597:6:3,3:301,290:591,6:0.0101:2,2:21.2:1:27.5:1:1:1.03788:53.3:12:0.0103:0:1.5 +2 6636132 . G T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25706;SOR=0.83186;LSEQ=ACTTCACTCGGAAGTGCTTC;RSEQ=TTAAACTTCACTCGGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:133:59,74:346,315:661,133:0.1675:2,2:17:1:31:1:0.10602:1.3771:47:25.6:0.1635:0:1.6 0/1:565:81:37,44:250,234:484,81:0.1434:2,2:15.5:1:30:1:0.33854:1.26996:46.8:80:0.1429:0:1.2 +2 6636414 . G A 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATGGGACACGCTGACGGTT;RSEQ=ATTCCAAACGTGGTCTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:54:22,32:443,477:920,54:0.0554:2,2:25.3:1:30:1:0.32759:1.35045:44.5:108:0.0562:0:2 0/0:695:0:0,0:344,350:694,0:0:2,0:24.9:1:30.8:1:1:0:50.5:85.75:0.9985:0:0.5 +2 6636424 . G T 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8015;SOR=1.02819;LSEQ=GCTGACGGTTGATTCCAAAC;RSEQ=TGGTCTTGAAATTCCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:935:444:206,238:221,269:490,444:0.4749:2,2:26.3:1:30.8:1:0.69376:1.05:40:54.5:0.4734:0:1.2 0/1:687:331:166,165:167,188:355,331:0.4818:2,2:24.9:1:29.8:1:0.44482:1.13:40.5:330:0.4839:0:1.1 +2 6636578 . C T 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0823;SOR=6.1913;LSEQ=AGAGGGTGAACTCTTCGTTG;RSEQ=CTCCATCCATGTTGCGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:1:0,1:199,253:452,1:0.0022:2,0:1:0:27:0:1:0:60:2:0.0022:0:1 0/1:296:4:1,3:133,159:292,4:0.0135:2,2:17.3:1:25:1:0.62922:2.50232:55.3:3:0.0103:0:1.5 +2 6636622 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07264;SOR=Inf;LSEQ=AGTTGGATGTTGGCGATGGT;RSEQ=TCTGGGTGGAGTAGCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:231,188:419,0:0:2,0:25.3:1:32.4:1:1:0:59.8:58.857:1:0:0.1 0/1:301:3:2,1:172,126:298,3:0.01:2,2:9:1:26:1:1:1.46:54:6:0.0101:0:1 +2 6636735 . G A 132 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=CCACAGGACGTCCATGAGCC;RSEQ=GATCGTCTGCATGGTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:20:10,10:305,322:627,20:0.0309:2,2:31.2:1:30.6:1:1:1.06:57.9:19:0.0299:0:2.1 0/0:443:0:0,0:217,226:443,0:0:2,0:26.5:1:29.7:1:1:0:59.5:62.286:1:0:1 +2 6636747 . T C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06552;SOR=0;LSEQ=CATGAGCCGGATCGTCTGCA;RSEQ=GGTCAGCATGTCCTGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:607:607:291,316:0,0:0,607:1:0,2:25.1:1:30.7:1:1:0:59.8:85.714:1:0:1.1 1/1:411:408:203,205:1,1:2,408:0.9927:2,2:24.8:1:30.4:1:1:1.00983:59.9:203:0.9927:0:1.1 +2 6636940 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08505;SOR=0.6659;LSEQ=GACTGCAGGTGTAAGTGGCT;RSEQ=TGGGTGAGTGAGTGAGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:91:10,81:23,101:124,91:0.4233:2,2:25.9:1:30.5:1:0.17955:1.83951:60:182:0.4252:0:1.6 0/1:125:41:5,36:18,66:84,41:0.328:2,2:25.6:1:29.8:1:0.32514:1.95387:59.9:40:0.3226:0:1.6 +2 6636974 . T C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19379;SOR=0.63265;LSEQ=GAGGGTATTACTTAAAATAC;RSEQ=CTTTCTATGTTTAGAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:61:6,55:13,64:77,61:0.442:2,2:23.3:1:30.7:1:0.32087:1.8539:60:19.333:0.4296:0:1.9 0/1:54:18:1,17:3,33:36,18:0.3333:2,1:19.8:1:31.1:1:1:1.5339:60:17:0.3208:0:2.1 +2 6636996 . C CA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTATGTTTAGAAAGAGT;RSEQ=AAAAAAAATTTTAAGTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:0,2:1,71:72,2:0.0267:1,0:27:1:30:1:1:0:60:4:0.0278:0:0 0/0:25:0:0,0:1,24:25,0:0:1,0:17.8:1:31.3:1:1:0:60:50:1:0:0.6 +2 6637065 . G GA 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.51088;LSEQ=TTAATTTATAATTGACAAAA;RSEQ=AAAAAAATTCATAAATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:0,3:0,20:20,3:0.1154:1,0:29.7:1:32.7:1:1:0:60:6:0.1154:0:0 0/1:6:1:0,1:0,4:4,1:0.1667:0,0:21:0:32:0:1:0:60:2:0.1667:0:0 +2 6851114 . GC G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28848;SOR=0.46551;LSEQ=AAGACATGAGGCTGGATAAG;RSEQ=AAGTAAATTGGGTAAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:18:18,0:51,1:52,18:0.2571:1,1:32.2:1:32.7:1:1:0:60:36:0.2571:0:0.1 0/1:29:4:4,0:24,1:25,4:0.1379:1,0:23.8:1:32.8:1:1:0:60:8:0.1429:0:0 +2 6851238 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.831;LSEQ=AAATTTAAATAGTATACTAC;RSEQ=GTAAATCCAGAAATATCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:94:52,42:246,192:438,94:0.1767:2,2:24.9:1:31.2:1:0.90912:1.03481:60:188:0.179:0:1.8 0/1:349:132:83,49:127,90:217,132:0.3782:2,2:23.7:1:29.7:1:0.4324:1.20:59.8:131:0.3786:0:1.9 +2 6851269 . T C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.41643;LSEQ=AAATATCACTGGGTGGGTAG;RSEQ=GTGGAAAAAATGTTTTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:108:56,52:238,257:495,108:0.1782:2,2:25.6:1:31:1:0.52419:1.16:60:107:0.1786:0:1.8 0/1:404:139:72,67:126,137:263,139:0.3441:2,2:26.9:1:29.6:1:0.46501:1.17:60:68.5:0.3434:0:1.8 +2 7541706 . TA T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=0.13436;LSEQ=TTATAAAATTCACAGATTCA;RSEQ=AAAAAAAAAGCAAAATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:47:40,7:93,18:111,47:0.2938:2,2:27:1:31.6:1:1:1.11:59.8:94:0.2994:0.0563:2.4 0/1:152:8:7,1:115,29:144,8:0.0526:2,2:22.6:1:31.2:1:1:1.76:60:16:0.0533:0.0132:1.4 +2 7541718 . C G 182 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGATTCATAAAAAAAAAAG;RSEQ=AAAATGTTCTCTCTTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:59:49,10:104,29:133,59:0.3026:2,2:24.4:1:31.1:1:0.56038:1.36:59.9:28.5:0.3167:0:3 0/0:192:0:0,0:146,45:191,0:0:2,0:23.4:1:30.9:1:1:0:60:22.875:1:0:1.3 +2 7541750 . A C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03885;SOR=1.44083;LSEQ=TCTTTTCTATCCAAGAGAGG;RSEQ=AAATCTATATATAGCACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:286:184,102:67,44:111,286:0.7204:2,2:24.2:1:31.7:1:0.48754:1.18:60:30.778:0.7195:0:2.3 1/0:330:260:154,106:42,28:70,260:0.7879:2,2:25.4:1:30.7:1:1:1.03237:60:36.143:0.7857:0:2 +2 7541769 . A G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.75659;SOR=1.05206;LSEQ=GAAAATCTATATATAGCACT;RSEQ=AAATCCTAAGGAGGACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:498:370:209,161:70,57:127,370:0.743:2,2:26.2:1:31.8:1:0.83598:1.06:60:40.111:0.7398:0:2 1/0:392:295:158,137:53,42:95,295:0.7526:2,2:27.8:1:30.4:1:0.72393:1.09392:60:58:0.7532:0:2 +2 7541865 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4084;SOR=0.8217;LSEQ=GTTTTAAAGTCCTGTTTTAC;RSEQ=CAATATTCTTCTACTATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:239:187:44,143:12,38:50,187:0.7824:2,2:22.3:1:30.3:1:1:1.02623:60:186:0.7815:0:1.2 1/0:170:127:36,91:12,31:43,127:0.7471:2,2:21.7:1:29.1:1:1:1.02:60:126:0.7456:0:1.1 +2 8822912 . A C 29 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=25.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAACCCTTTCTACTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:30.5:1:29.5:1:1:0:57.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 9036068 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.52266;SOR=0;LSEQ=GCCCAACTCCAGAGGTTGGT;RSEQ=TAAGAGTTGTGAAAGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:24,26:50,2:0.0385:2,2:36.5:1:33:1:1:1.08:42:4:0.04:0:1 0/0:32:0:0,0:18,14:32,0:0:2,0:30.7:1:28.6:1:1:0:38.2:64:1:0:0.3 +2 9036089 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13169;SOR=Inf;LSEQ=TAAGAGTTGTGAAAGGGAGC;RSEQ=GGGCACGGTGGCTCATGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:19,24:43,0:0:2,0:23.5:1:29.8:1:1:0:42.8:86:1:0:0.3 0/1:25:2:1,1:12,11:23,2:0.08:2,2:20.5:1:28.5:1:1:1.0871:35:4:0.08:0:1.5 +2 11805745 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGTTCTACATACCTATG;RSEQ=AACTCCCAGTGGTCATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:46:1:32:1:1:0:60:4:1:0:1 +2 11805999 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.20376;SOR=Inf;LSEQ=CTTGGCTTTGTAGACACGAC;RSEQ=CCAAGTGCCTCAGCCTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:27,21:48,0:0:2,0:28.6:1:30.9:1:1:0:60:47:1:0:0.1 0/1:40:2:1,1:20,18:38,2:0.05:2,2:47:0:30.5:1:1:1.10818:60:4:0.0513:0:1.5 +2 11806057 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05343;SOR=Inf;LSEQ=AACAGGTCCTCAAGCGGCTC;RSEQ=CACTTGCTGGACAGCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:18,25:43,0:0:2,0:23.8:1:30.5:1:1:0:60:42:1:0:0.1 0/1:27:3:2,1:8,16:24,3:0.1111:2,2:11:1:29.3:1:0.53504:3.79:60:6:0.12:0:1.3 +2 12737845 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52869;SOR=0;LSEQ=ATGCTTGGTTCAATTGCAAA;RSEQ=GAAAAGGACAGCCAAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:33,18:51,2:0.0377:2,2:18.5:1:29.5:1:1:1.81117:60:4:0.0385:0:1 0/0:31:0:0,0:21,10:31,0:0:2,0:21.1:1:31:1:1:0:60:62:1:0:0.4 +2 12737918 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5326;SOR=0;LSEQ=AGAGCTGACTCCGGCCAATG;RSEQ=CCAAGTTGTAAACTAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:35,48:83,2:0.0235:2,2:29:0:32:0:1:1.37:60:4:0.0238:0:1.5 0/0:49:0:0,0:20,29:49,0:0:2,0:23.8:1:29.5:1:1:0:60:15.333:1:0:0.1 +2 14528016 . C T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.94818;SOR=0.98355;LSEQ=CTTTTCTATTTAAAAAATAG;RSEQ=GGTCCAGGAGAAAACCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:610:425:227,198:86,98:184,425:0.6967:2,2:23.7:1:30.1:1:0.13441:1.31:59.9:850:0.699:0:1.1 1/0:515:357:180,177:78,80:158,357:0.6932:2,2:25.1:1:29.1:1:0.84881:1.04:60:118:0.6928:0:1.1 +2 14528089 . C T 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TCATCCTCCTTTCTCTTTCC;RSEQ=TCTCTTTCTCTCATCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:42:13,29:119,250:369,42:0.1019:2,2:24.9:1:30:1:1:1.0617:60:20:0.1003:0:1.2 0/0:308:0:0,0:106,201:307,0:0:2,0:23.8:1:31:1:1:0:58.3:152.5:0.9967:0:0.7 +2 14528108 . C TTCTTTCCTCTCTCTCTCTCTT 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.0822;SOR=0.74756;LSEQ=CTTTCCCTCTCTTTCTCTCA;RSEQ=TCTCCTCCTTCCCTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:146:23,123:73,102:175,146:0.422:2,2:25:1:30.4:1:0:3.81136:55.6:35.5:0.4201:0.1647:1.2 0/1:272:96:16,80:61,97:158,96:0.3529:2,2:30.9:1:29.7:1:0.00023:3.13078:54.8:31:0.347:0.0956:1.1 +2 16079871 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCTCCTCCGCAGTGGT;RSEQ=AGGACGCGTGGACAGTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 16080157 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTGCACCTTCGGACTA;RSEQ=CCTTCTTTCGTAATTACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 16080895 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCTTGCAAACCGCCCGG;RSEQ=GCCCAGGGAAGCGACGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:155,4:159,2:0.0124:1,0:24.5:1:32:0:1:0:60:4:0.0126:0:1 0/0:76:0:0,0:73,3:76,0:0:1,0:25.2:1:31.5:1:1:0:60:75:1:0:0 +2 16080911 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12792;SOR=Inf;LSEQ=CCGGCGCCCAGGGAAGCGAC;RSEQ=AGCGCCGGGGCAAGGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:204,16:220,0:0:2,0:24.3:1:29.9:1:1:0:60:43:1:0:0.1 0/1:123:2:1,1:102,19:121,2:0.0163:2,2:8:1:31:0:0.29988:5.25819:60:4:0.0164:0:1 +2 16080936 . G T 39 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15813;SOR=4.89585;LSEQ=CCGGGGCAAGGCAAGCCCTG;RSEQ=ACGGGATTGCGACGTGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:1:0,1:280,80:360,1:0.0028:2,0:1:0:23:0:0.22438:0:60:2:0.0028:0:1 0/1:223:3:1,2:164,56:220,3:0.0135:2,2:5.7:1:24.7:1:0.1665:5.80061:60:6:0.0136:0:1 +2 16081186 . AC A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.25795;SOR=0;LSEQ=CGGAGAGCCGGTGCGTCCCC;RSEQ=CCCAGGCTGGGGTTCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:2,1:36,212:248,3:0.012:2,2:8.3:1:31:1:0.06074:11.58:60:6:0.0123:0.004:0.3 0/0:200:0:0,0:35,164:199,0:0:2,0:19.6:1:30.2:1:1:0:60:65.333:0.9949:0:0.1 +2 16081233 . AG A 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGCCCCTGGAGGAAGAAG;RSEQ=GGGGGGATTAGGCAGGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:2,113:115,2:0.0171:1,0:18.5:1:34:0:1:0:60:4:0.0172:0:0 0/0:48:0:0,0:0,48:48,0:0:1,0:22.5:1:31.3:1:1:0:60:96:1:0:0 +2 16082313 . AC A 98 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.07738;SOR=3.48241;LSEQ=ACTTCGGCGGCCCCGACTCG;RSEQ=CCCCCCGGGGGAGGACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1017:3:2,1:475,538:1013,3:0.0029:2,2:16:1:29.7:1:0.60316:2.26:60:6:0.003:0:0 0/1:882:9:5,4:419,453:872,9:0.0102:2,2:17.4:1:31:1:0.74488:1.35:60:18:0.0105:0.0011:0.6 +2 16082393 . G A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAGCCGTGGCTTCGCGGA;RSEQ=CACAGCTCCGAGCCCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:0:0,0:317,369:686,0:0:2,0:24.5:1:32.5:1:1:0:60:67.6:1:0:0.1 0/1:548:34:18,16:240,273:513,34:0.062:2,2:19.7:1:28.8:1:0.59524:1.28:60:68:0.0628:0:1.1 +2 16082706 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49652;SOR=0;LSEQ=GAGCCGGCCGCGCCGGGGCC;RSEQ=CCCTGCCCGCCGAGCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:28,13:41,2:0.0465:2,2:18:0:32:0:1:2.11228:60:4:0.0465:0:1 0/0:37:0:0,0:21,16:37,0:0:2,0:9:1:28.8:1:1:0:60:11.333:1:0:0.3 +2 16082734 . C T 42 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62286;SOR=0.35644;LSEQ=CGCCGAGCTCGCCCACCCGG;RSEQ=CGCCGAGTGCGTGGATCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:1,2:64,51:115,3:0.0254:2,2:19:1:27:1:0.58699:2.49063:60:6:0.0256:0:1 0/0:109:1:0,1:58,50:108,1:0.0092:2,0:1:0:26:0:0.46789:0:60:2:0.0097:0:1 +2 16082775 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26021;SOR=0;LSEQ=CCGTGGTCTTCCCCTTTCCC;RSEQ=TGAACAAGCGCGAGCCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:2,1:89,87:176,3:0.0168:2,2:29.3:1:30:1:1:1.95:60:6:0.0169:0:1 0/0:138:0:0,0:69,69:138,0:0:2,0:28.6:1:30.4:1:1:0:60:68:1:0:0.4 +2 16082778 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50664;SOR=0;LSEQ=TGGTCTTCCCCTTTCCCGTG;RSEQ=ACAAGCGCGAGCCAGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:88,86:174,2:0.0114:2,2:26:1:30:1:1:1.02313:60:4:0.0116:0:1 0/0:136:0:0,0:68,68:136,0:0:2,0:28.5:1:28.8:1:1:0:60:26.2:1:0:0.4 +2 16082784 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50638;SOR=0;LSEQ=TCCCCTTTCCCGTGAACAAG;RSEQ=GCGAGCCAGCGCCCGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:83,84:167,2:0.0118:2,2:24:1:31.5:1:1:1.01:60:4:0.0121:0:1 0/0:131:0:0,0:64,66:130,0:0:2,0:2:0:13:0:1:0:60:0:0:0:1 +2 16082881 . CG C 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1032;SOR=Inf;LSEQ=TGCCGCCCCAGCCGGGGCCC;RSEQ=GGGGTCGCCCCTCCGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:42,1:43,0:0:1,0:18:1:30.6:1:1:0:60:42:1:0:0.1 0/1:39:3:1,2:31,5:36,3:0.0769:2,2:10:1:27:1:0.07736:11.162:60:6:0.0769:0.0256:0.7 +2 16083525 . C CT 33 v3;MSI12;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTATTCTTTTTCTTTTT;RSEQ=TTTTTTTTTTTTTTTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:0,2:2,2:0.3333:0,0:36.5:1:33.5:1:0.33333:0:60:4:0.3333:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 16083861 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTTGAAGGTGAGGGCAG;RSEQ=CACTCAGCAGCCTCTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:138,2:140,2:0.0141:1,0:22.5:1:30:1:1:0:60:4:0.0146:0:1 0/0:58:0:0,0:58,0:58,0:0:1,0:25.3:1:30.7:1:1:0:59.4:28:1:0:0.1 +2 16084202 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15501;SOR=Inf;LSEQ=TCTGTCCCTTTAATGTCTGT;RSEQ=CCTTGACAGCTTTTGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:21,220:241,0:0:2,0:24.2:1:32.7:1:1:0:59.9:240:1:0:0.1 0/1:157:2:0,2:16,139:155,2:0.0127:2,0:24:1:31.5:1:1:0:60:4:0.013:0:1 +2 16084594 . T C 58 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGTTAAATGAAAAACTG;RSEQ=TTATTGTATAAAACTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:22.5:1:29:1:1:0:60:3:0.75:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 16085519 . C T 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10683;SOR=0;LSEQ=AGCAGTCTGCCAGGGTCTGC;RSEQ=GGAAGAGACAGATAAGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:8:8,0:83,1:84,8:0.087:1,0:19:1:33.1:1:1:0:60:16:0.0879:0:1.1 0/0:34:0:0,0:34,0:34,0:0:1,0:22.4:1:30.4:1:1:0:60:16:1:0:0.2 +2 16085563 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08974;SOR=Inf;LSEQ=ATTAACATGGATATATATGT;RSEQ=AATTTCATTCAAATGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:147,22:169,0:0:2,0:25.2:1:32.5:1:1:0:60:168:1:0:0.1 0/1:138:3:1,2:117,17:134,3:0.0217:2,2:17.3:1:22.3:1:0.05044:13.29618:60:2:0.015:0:1 +2 16086264 . AT A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.32779;SOR=0.47057;LSEQ=CTGCCACTTTGCACATTTTG;RSEQ=TTTTTTTTTAAACAAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:6:0,6:25,129:154,6:0.0375:2,0:28.5:1:32.3:1:0.59103:0:60:12:0.039:0.0063:0 0/1:167:3:1,2:29,135:164,3:0.018:2,2:24.3:1:27.7:1:0.4501:2.31:60:6:0.018:0:0 +2 16086469 . C T 73 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGCGCTAAACGTTGGTGA;RSEQ=GGTTGGGAGCCTCTGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:30.8:1:31.8:1:1:0:58:10:0.8333:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 16087661 . G T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1664;SOR=5.64956;LSEQ=AGAATAAACAGATGGAAATG;RSEQ=GTTCCTCCCTTCAATGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:1:0,1:69,284:353,1:0.0028:2,0:19:0:14:0:1:0:60:0:0:0:8 0/1:254:4:2,2:56,193:249,4:0.0157:2,2:22.8:1:27:1:0.22621:3.43:60:8:0.0161:0:1 +2 16087781 . T G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10448;SOR=Inf;LSEQ=GGGTCACAATGGAGACCCCA;RSEQ=ATGGGTGGCATGGCTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:0,45:45,0:0:1,0:25.2:1:28.4:1:1:0:59.7:44:1:0:0.2 0/1:22:2:0,2:0,19:19,2:0.0909:1,0:25.5:1:31.5:1:1:0:60:4:0.0952:0:1 +2 16797699 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52074;SOR=0;LSEQ=CCAGCCTTCCCTGGCTCCCC;RSEQ=GGGCTCCTGCTTCCACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:19,18:37,2:0.0513:2,2:38:0:32.5:1:1:1.05412:60:4:0.0526:0:1.5 0/0:24:0:0,0:13,11:24,0:0:2,0:28.2:1:30:1:1:0:60:48:1:0:0.2 +2 17626751 . G C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGGCGAGGCCAAGATGGC;RSEQ=GACTAGAAGCAGTGGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:0,7:1:0,2:35.4:1:30.6:1:1:0:60:14:1:0:1.6 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:32:0:1:0:60:4:1:0:1 +2 17626983 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49057;SOR=Inf;LSEQ=AGGTGAGTGAGTATGCTACC;RSEQ=AGCCTGGGAAACCATGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:26,0:0:2,0:26.1:1:31.9:1:1:0:59.6:52:1:0:0.3 0/1:27:2:1,1:15,10:25,2:0.0741:2,2:29:1:28:1:1:1.47706:60:4:0.0769:0:1.5 +2 17627057 . C T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60041;SOR=0.68179;LSEQ=ATCCCACTCAGAAGCCCATG;RSEQ=AACCAGGGCCTTGGGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:6,6:8,9:17,12:0.4138:2,2:21.2:1:28.8:1:1:1.12:54.3:24:0.4138:0:1.2 0/1:34:11:4,7:11,12:23,11:0.3235:2,2:16.2:1:25.9:1:0.71521:1.58211:54.4:22:0.3333:0:1.3 +2 17627857 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAATCAATGAAAAAATG;RSEQ=TGAAAACTCAAAAGGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:18:1:31:1:1:1.7321:58:4:0.4:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:15:1:29:1:1:0:48.5:4:1:0:0 +2 17675655 . TTTTCA T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03507;SOR=0;LSEQ=GGCCAGTGATGATGACCATT;RSEQ=TGCCTGACACCCTATTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:6:4,2:90,44:134,6:0.0426:2,2:32.5:1:32.3:1:1:1.02258:60:12:0.0426:0:0 0/0:113:0:0,0:66,47:113,0:0:2,0:23.1:1:29.7:1:1:0:57.7:112:1:0:0.5 +2 17675662 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57389;SOR=2.7897;LSEQ=GATGATGACCATTTTTTCAT;RSEQ=CCTGACACCCTATTCTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:1,0:107,54:161,1:0.0062:2,0:9:0:32:0:1:0:60:2:0.0063:0:2 0/1:117:2:1,1:67,48:115,2:0.0171:2,2:19.5:1:27.5:1:1:1.39177:42.5:4:0.0174:0:1.5 +2 17675684 . T A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14771;SOR=0.73323;LSEQ=CTGACACCCTATTCTTGATA;RSEQ=TTATGGGGTCTTCAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:110:63,47:68,48:116,110:0.4867:2,2:24.9:1:30.3:1:0.89303:1.05659:58.2:35.667:0.4842:0:1.1 0/1:161:66:34,32:51,44:95,66:0.4099:2,2:26.7:1:30.1:1:0.87271:1.09032:59.6:132:0.4125:0:1.1 +2 17675722 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1663;SOR=Inf;LSEQ=AGAAGAAAGTGTGAATATGG;RSEQ=ATATGAGATGGAGCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:135,146:281,0:0:2,0:25.3:1:31.9:1:1:0:60:562:1:0:0.6 0/1:194:2:1,1:89,103:192,2:0.0103:2,2:38.5:1:29.5:1:1:1.16:60:4:0.0104:0:2.5 +2 17675735 . G T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=2.46039;LSEQ=AATATGGGATATGAGATGGA;RSEQ=CAAAGAATTCTTGAACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:34:15,19:106,120:226,34:0.1308:2,2:25.2:1:30:1:0.85437:1.11841:60:33:0.1294:0:1.5 0/1:170:46:20,26:60,64:124,46:0.2706:2,2:26.4:1:29.4:1:0.60704:1.21733:60:92:0.2722:0:1.5 +2 17675745 . C A 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28381;SOR=0;LSEQ=ATGAGATGGAGCAAAGAATT;RSEQ=TTGAACATGGAGAGTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:3,0:107,135:242,3:0.0122:2,0:8:1:20.3:1:0.08914:0:60:2:0.0083:0:3.3 0/0:158:0:0,0:67,91:158,0:0:2,0:25.3:1:31.2:1:1:0:60:157:1:0:0.7 +2 17675754 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13638;SOR=Inf;LSEQ=AGCAAAGAATTCTTGAACAT;RSEQ=GAGAGTCTCACTCCTGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:94,134:228,0:0:2,0:26.2:1:31.7:1:1:0:60:227:1:0:0.5 0/1:134:2:1,1:55,77:132,2:0.0149:2,2:20:1:30.5:1:1:1.40:60:4:0.0152:0:1 +2 17675774 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53255;SOR=0;LSEQ=GGAGAGTCTCACTCCTGTGA;RSEQ=GTGCAGATGCACTGCCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:64,110:174,2:0.0114:2,2:42:1:32:1:1:1.71:60:4:0.0115:0:1 0/0:103:0:0,0:40,63:103,0:0:2,0:26:1:30.6:1:1:0:60:33.333:1:0:0.5 +2 17675779 . A T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12894;SOR=1.70089;LSEQ=GTCTCACTCCTGTGAGGTGC;RSEQ=GATGCACTGCCCCAAAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:23:7,16:49,90:139,23:0.142:2,2:27.3:1:29.9:1:0.81382:1.2428:60:10.5:0.1338:0:1.8 0/1:100:22:8,14:32,46:78,22:0.22:2,2:22.2:1:29.9:1:0.80731:1.21502:60:44:0.22:0:1.9 +2 17675959 . G A 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTAGGTGACTTCAAGTAC;RSEQ=GGACAAAGTGGGAACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:28.3:1:33.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 17986417 . A G 52 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=TAAATACCCAGCCTGTGAAA;RSEQ=TCATCTGTTCACACATTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:25.5:1:28.5:1:1:0:60:8:1:0:0 1/1:3:3:3,0:0,0:0,3:1:0,0:29.7:1:33.3:1:1:0:60:6:1:0:1 +2 17986612 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06856;SOR=Inf;LSEQ=ACACAGGCTTTGCTGAAACT;RSEQ=TCACAGGCTTGACAGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:191,89:280,0:0:2,0:24.6:1:31.9:1:1:0:60:92.333:1:0:0.2 0/1:195:3:1,2:128,64:192,3:0.0154:2,2:17:1:28.3:1:0.265:3.96923:60:6:0.0155:0:1.3 +2 17986683 . G T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.49264;LSEQ=CACCACTTTCAGTTCTCTTT;RSEQ=CTAACTCAAGGACACAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:60:28,32:162,209:371,60:0.1392:2,2:23.7:1:29.7:1:0.67646:1.13:60:59:0.1382:0:1.1 0/1:357:129:59,70:105,123:228,129:0.3613:2,2:28.6:1:29.6:1:1:1.01278:60:258:0.3665:0:1.1 +2 17986739 . T TAC 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.16423;SOR=1.38171;LSEQ=TTAGTTGTTTTCTTCACACA;RSEQ=ACACACACACCTATATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:48:14,34:72,135:207,48:0.1868:2,2:27.1:1:31.2:1:0.50199:1.29396:60:96:0.1882:0.0078:0 0/1:195:47:17,30:51,97:148,47:0.241:2,2:29.5:1:29.4:1:0.86151:1.08:59.9:94:0.2448:0.0103:0.2 +2 17987407 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGCAGGGATGGGCGAGA;RSEQ=TACTGCAGCTGGCTCTCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 20614873 . G C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCAGCAGGGCAGTGACGT;RSEQ=GACTCTGTGTAGGTCGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:48:1:30.5:1:1:0:60:4:1:0:1 +2 20616307 . G T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1638;SOR=5.84919;LSEQ=CTAAAGGAAAGAGGCTTATT;RSEQ=GTGGACTGTCAGAAAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:199,33:232,1:0.0043:2,0:1:0:25:0:0.14592:0:60:2:0.0043:0:2 0/1:162:4:3,1:134,24:158,4:0.0247:2,2:29.3:1:30.5:1:0.49203:1.85243:60:8:0.0247:0:2 +2 20616374 . G C 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.3808;LSEQ=CTAGTCATTTGCAATAAAGG;RSEQ=AGATACTTTGGGACCTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:669:615:380,235:35,18:53,615:0.9193:2,2:25.8:1:32.3:1:0.65827:1.20214:60:101.5:0.9199:0:1.4 1/1:528:429:250,179:54,45:99,429:0.8125:2,2:26.2:1:31:1:0.50095:1.16:60:38:0.8101:0:1.5 +2 20616425 . C T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10996;SOR=1.19075;LSEQ=TCTTGGTTGAAAAAACTTCA;RSEQ=AGGTTGCAGCTTTTTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:818:422:211,211:201,194:395,422:0.5159:2,2:25.6:1:29.5:1:0.83372:1.03606:60:83.4:0.5155:0:1.6 1/0:624:349:167,182:135,139:274,349:0.5593:2,2:25.3:1:28.3:1:0.74704:1.05834:60:68.8:0.5621:0:1.6 +2 20616665 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTTGCCATATGTTGAGC;RSEQ=CAGAATGTTTCTGAAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:0,4:0,25:25,4:0.1379:1,0:27:1:30:1:1:0:60:8:0.1429:0:1.8 0/0:3:0:0,0:0,3:3,0:0:0,0:21.7:1:31.3:1:1:0:60:6:1:0:0.7 +2 20616708 . G C 103 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTAAGTGAGTTCTATAAT;RSEQ=TGAAACTGGTTCATCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:3,8:0.7273:0,0:24.5:1:34.6:1:1:0:60:16:0.7273:0:1.5 1/1:1:1:0,1:0,0:0,1:1:0,0:20:0:33:0:1:0:60:2:1:0:1 +2 20647241 . C T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28327;SOR=0;LSEQ=CCGCTCATGGCGGCCATCCG;RSEQ=AAGAAGCTGGTGGTGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:13,0:13,4:0.2353:1,0:31.5:1:29.5:1:1:0:60:8:0.2353:0:1 0/0:7:0:0,0:7,0:7,0:0:0,0:14.6:1:32.6:1:1:0:60:14:1:0:0 +2 20764031 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCTCACCACCTCTCAGG;RSEQ=GGTCTACTGCAGGGTGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:28.5:1:1:0:60:4:1:0:1.5 +2 21058065 . C G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08809;SOR=0.30485;LSEQ=AAATAAGTTAATCAGTGTTG;RSEQ=TGGAGATCAAGGTTCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:15:15,0:28,1:29,15:0.3333:1,1:25.9:1:33.2:1:1:0:60:30:0.3488:0:2 0/1:23:3:3,0:20,0:20,3:0.1304:1,0:20.7:1:32:0:1:0:60:6:0.1304:0:2 +2 21058088 . A G 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03505;SOR=0.36507;LSEQ=GAGATCAAGGTTCTGGAGTG;RSEQ=GGAAAGGCACAGAAGGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:44:44,0:17,0:17,44:0.7213:1,1:29:1:31.7:1:1:0:60:88:0.7213:0:1.5 0/1:29:14:14,0:15,0:15,14:0.4828:1,1:25.9:1:29.1:1:1:0:60:13:0.4643:0:1.2 +2 21058264 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00066;SOR=0.5966;LSEQ=TCCAATGGTAAAAGTGAGAG;RSEQ=TTTTGAAAACTTTAATCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:402:277:130,147:58,66:124,277:0.6891:2,2:27.2:1:30.5:1:1:1.01:60:68.25:0.6929:0:1.1 1/0:383:218:108,110:73,92:165,218:0.5692:2,2:24.7:1:28.9:1:0.35235:1.24:60:217:0.5711:0:1.2 +2 21059930 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=GGGCTGGATTTGAAGACTGA;RSEQ=ATGTGTAAATGCATTGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:29.5:1:28.7:1:1:0:60:5:1:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:23:1:27.5:1:1:1.73:60:4:0.4:0:1 +2 21324980 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20635;SOR=0;LSEQ=CACGGGACCTAGAAAGGGGA;RSEQ=AAGCCATGTTGCCCAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:9,2:11,2:0.1538:2,2:20.5:1:28.5:1:0.42308:3.87298:45:4:0.1538:0:1 0/0:15:0:0,0:10,5:15,0:0:2,0:15.9:1:30.5:1:1:0:43.9:30:1:0:0.3 +2 21325188 . A T 40 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTCTAGGGGAGGGAGGTA;RSEQ=CCACTGGGCGGAGGCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:24.7:1:29.7:1:1:0:60:6:0.75:0:1.3 1/1:3:3:1,2:0,0:0,3:1:0,2:18.3:1:25.7:1:1:0:58.3:6:1:0:1 +2 22412449 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26056;SOR=0;LSEQ=TGACAGAGATGCATCAAATC;RSEQ=GGATCTTAATACTGGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:2,1:25,14:39,3:0.0714:2,2:13.3:1:32.3:1:1:1.12:60:6:0.0714:0:1 0/0:30:0:0,0:17,13:30,0:0:2,0:23.5:1:28.3:1:1:0:60:14:1:0:0.1 +2 22412483 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51698;SOR=0;LSEQ=GGTTTAAGTGAGCATTCAGG;RSEQ=GACTGGTGGGATCAGGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:30,32:62,2:0.0313:2,2:19:1:29.5:1:1:1.07:60:4:0.0313:0:1 0/0:42:0:0,0:22,20:42,0:0:2,0:27.3:1:29.1:1:1:0:58.5:84:1:0:0.1 +2 22412715 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18301;SOR=0;LSEQ=TTTATTAAATGAAATTAATC;RSEQ=TCCTCTTCTAGGCCATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:6,2:0.25:2,2:8:1:27:1:1:1.8258:60:4:0.25:0:1 0/0:10:0:0,0:5,5:10,0:0:2,0:25.2:1:29.4:1:1:0:60:20:1:0:0 +2 24166747 . TG T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19791;SOR=0;LSEQ=CTTGCTGAGACATGTTGGAG;RSEQ=GTCATTGCCTCCGAGCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:112,58:170,2:0.0116:2,2:22:1:30:1:1:1.92319:51.5:4:0.0119:0:0.5 0/0:214:0:0,0:132,81:213,0:0:2,0:24.9:1:30.7:1:1:0:59.8:105.5:0.9953:0:0.1 +2 24166826 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09952;SOR=0;LSEQ=TGGGAATCATGGCCAAAGAA;RSEQ=AGATGGAATGGTTCTGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:1,2:102,105:207,3:0.0143:2,2:33.3:1:28.7:1:1:1.93695:60:6:0.0144:0:1 0/0:242:0:0,0:110,132:242,0:0:2,0:27:1:30.8:1:1:0:60:120:1:0:0.1 +2 24166853 . A G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2508;SOR=Inf;LSEQ=AATGGTTCTGGAATAAGAAC;RSEQ=CAGGTTCAAACCGTCCCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:104,98:202,0:0:2,0:25.7:1:30.5:1:1:0:59.9:201:1:0:0.1 0/1:227:3:2,1:96,128:224,3:0.0132:2,2:34:1:29:1:0.57944:2.66:60:6:0.0133:0:1.7 +2 24166854 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22204;SOR=0;LSEQ=ATGGTTCTGGAATAAGAACA;RSEQ=AGGTTCAAACCGTCCCGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:101,98:199,2:0.01:2,2:35.5:1:29:1:1:1.03046:60:4:0.0101:0:1 0/0:225:0:0,0:97,128:225,0:0:2,0:26.1:1:31.6:1:1:0:60:111.5:1:0:0.1 +2 24166869 . C T 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00741;SOR=Inf;LSEQ=GAACACAGGTTCAAACCGTC;RSEQ=CGTATCTCCCCACGTCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:106,89:195,0:0:2,0:23.3:1:31.3:1:1:0:59.8:96.5:1:0:0.1 0/1:205:8:3,5:91,106:197,8:0.039:2,2:29.9:1:28.5:1:0.7289:1.42837:60:16:0.0398:0:1.3 +2 24167267 . A G 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTACACATTATTGTATTC;RSEQ=CCCATCTTTCAGTTTGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:669:0:0,0:254,413:667,0:0:2,0:26.2:1:30.4:1:1:0:58.9:46.643:0.9969:0:0.8 0/1:745:23:11,12:300,421:721,23:0.0309:2,2:22.4:1:30.6:1:0.66847:1.29:58.9:46:0.0316:0:1.1 +2 24167268 . C T 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.428;LSEQ=CCTACACATTATTGTATTCA;RSEQ=CCATCTTTCAGTTTGTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:670:467:171,296:83,118:201,467:0.697:2,2:25.7:1:30.5:1:0.25978:1.21719:58.5:65.714:0.698:0:1.1 0/1:744:369:146,223:165,210:375,369:0.496:2,2:24.9:1:28.9:1:0.23463:1.1998:58.2:183.5:0.5:0:1.1 +2 24167385 . G A 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=AGTACCTTGTAGACCGTAAT;RSEQ=GTGGAAAAGGGTCTAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:6,142:148,0:0:1,0:23.9:1:31.6:1:1:0:58.1:48.333:1:0:0.1 0/1:130:12:2,10:8,110:118,12:0.0923:2,2:25.8:1:29.9:1:0.23144:2.72:44.8:24:0.0952:0:1.5 +2 24167445 . C T 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=9e-04;SOR=Inf;LSEQ=GGGTGGCTGCAAAAACTCCC;RSEQ=TTTTTTTGCCCACAGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:2,60:62,0:0:1,0:23.3:1:33.3:1:1:0:53.1:61:0.9839:0:0.1 0/1:31:6:1,5:0,25:25,6:0.1935:1,2:19:1:28.2:1:0.19355:0:39.7:12:0.2069:0:1.8 +2 24167751 . C A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCCCAGCTAGAGAGAG;RSEQ=TAAAGAGGACTAGTTAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:32.4:1:30.2:1:1:0:47.4:10:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:28:1:1:0:52:4:1:0:1 +2 25100674 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10112;SOR=Inf;LSEQ=ACCAGACAGAGAGGGAAGAG;RSEQ=CTCCTTGGCCTGGGGCGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:62,32:94,0:0:2,0:27.7:1:31.5:1:1:0:60:46:1:0:0.2 0/1:83:3:1,2:52,28:80,3:0.0361:2,2:30.3:1:28.3:1:0.29511:3.65262:60:6:0.0361:0:1.7 +2 25100707 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4978;SOR=Inf;LSEQ=GGGCGAGACAGCTGGCGCTC;RSEQ=AAGCCTTACTTCTGGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:64,49:113,0:0:2,0:23.7:1:30.2:1:1:0:60:55.5:1:0:0.4 0/1:114:2:1,1:62,50:112,2:0.0175:2,2:6.5:1:28.5:1:1:1.23764:60:4:0.0175:0:1.5 +2 25100723 . G T 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22665;SOR=0;LSEQ=GCTCGAAGCCTTACTTCTGG;RSEQ=CCCAAGGGCAACAGCTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:48,55:103,2:0.019:2,2:7:1:26:1:1:1.14:60:4:0.0192:0:1 0/0:115:0:0,0:55,60:115,0:0:2,0:43:0:14:0:1:0:60:0:0:0:2 +2 25100738 . C A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68729;SOR=1.14242;LSEQ=TCTGGGCCCAAGGGCAACAG;RSEQ=TGTACCTGGGAGCTGACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:50:22,28:22,29:51,50:0.495:2,2:28:1:30.4:1:1:1.04:60:100:0.5051:0:1.1 1/0:123:65:29,36:28,30:58,65:0.5285:2,2:27:1:29.6:1:0.71985:1.15723:59.3:130:0.5285:0:1.2 +2 25100902 . C G 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33591;SOR=0.2973;LSEQ=GGCTCTGTGGTGACAGAGGT;RSEQ=CACAGCCCCTGGGGTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:0,9:0,5:5,9:0.6429:0,0:27:1:32:1:1:0:60:18:0.6429:0:1.7 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:6.5:1:31:1:1:0:60:4:0.3333:0:1 +2 25458067 . T C 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCTCTTTTTTTTTTTTT;RSEQ=CCCTTTGAGATGGAATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:0,0:0,4:0.6667:0,0:27.5:1:31:1:1:0:58:8:0.8:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 25458100 . C A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTCTCTGTTGCACAGG;RSEQ=TGGAGCACAGTGGCGCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:33.5:1:28.5:1:1:0:56:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 25458379 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30492;SOR=1.78589;LSEQ=ACTCCTCTTACTTGGGACCA;RSEQ=CCTTAAAATACCCAGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:25:25,0:27,1:28,25:0.4545:1,1:22.7:1:30.7:1:1:0:58.6:50:0.4808:0:1.1 1/0:20:12:12,0:8,0:8,12:0.6:0,0:22:1:30.3:1:1:0:59.8:24:0.6:0:1.3 +2 25458424 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14229;SOR=Inf;LSEQ=GTGTCAGGAGTCCACCCCAG;RSEQ=AGTCTGCCATGTTGGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:120,3:123,0:0:1,0:26.2:1:31.2:1:1:0:60:23.6:1:0:0.3 0/1:75:2:2,0:71,1:72,2:0.0267:1,0:5:1:28.5:1:1:0:60:4:0.0282:0:1 +2 25458546 . C T 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.60016;LSEQ=AGCAATCAGAACAGCCACAC;RSEQ=GCAGCCAGATGCCAGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1049:590:362,228:267,188:455,590:0.5624:2,2:26:1:31.2:1:0.40746:1.12:60:117:0.5647:0:1.1 0/1:937:408:230,178:293,236:529,408:0.4354:2,2:26.8:1:29.7:1:0.79086:1.04:59.9:101:0.4349:0:1.1 +2 25458853 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAGCAGAGTTCGCAGGGC;RSEQ=GGAGCCTCCACAGACCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:0,38:38,2:0.05:1,0:8:1:32:1:1:0:60:4:0.05:0:1 0/0:12:0:0,0:0,12:12,0:0:0,0:25.1:1:30.5:1:1:0:60:24:1:0:0 +2 25459718 . C T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56804;SOR=2.97051;LSEQ=ACACTAGCTGGAGAAGCAGG;RSEQ=GGGACAAGGCCCTGGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:1:0,1:200,68:268,1:0.0037:2,0:1:0:26:0:0.25651:0:60:2:0.0038:0:1 0/1:182:2:1,1:137,43:180,2:0.011:2,2:20.5:1:25.5:1:0.42608:3.1611:60:4:0.0112:0:1 +2 25462138 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08334;SOR=Inf;LSEQ=AGGAGGAGCATGAAACAGCG;RSEQ=CGGCATGCTGCTGGGGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:49,254:303,0:0:2,0:25.6:1:31.4:1:1:0:59.8:59.6:1:0:0.1 0/1:236:3:2,1:49,184:233,3:0.0127:2,2:16.3:1:27.3:1:0.11868:7.42:60:6:0.0128:0:1.3 +2 25463077 . TC T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.27443;SOR=0;LSEQ=TGCAAAGCAGAAGTCACCAG;RSEQ=CCCAGCTCCACAATGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:1,2:211,24:235,3:0.0126:2,2:23:1:29.3:1:0.03223:17.1438:60:6:0.0128:0.0042:0.3 0/0:163:0:0,0:146,17:163,0:0:2,0:23.2:1:30.6:1:1:0:60:326:1:0:0.1 +2 25463090 . A G 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26686;SOR=0;LSEQ=TCACCAGTCCCCAGCTCCAC;RSEQ=ATGCAGATGAGACAGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:248,49:297,3:0.01:2,2:16.3:1:22.7:1:0.42246:2.52033:60:2:0.0067:0:1 0/0:219:0:0,0:180,39:219,0:0:2,0:21.9:1:29.2:1:1:0:60:72:1:0:0.1 +2 25463116 . C T 54 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.45856;SOR=1.87852;LSEQ=GATGAGACAGGATGAAGCAG;RSEQ=AGTCCAAGGTAGAAGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:3:2,1:341,137:478,3:0.0062:2,2:21.3:1:28:1:1:1.24398:60:6:0.0064:0:1 0/1:343:4:2,2:230,109:339,4:0.0117:2,2:27:1:27:1:0.5976:2.10512:60:8:0.0119:0:1 +2 25463399 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12535;SOR=Inf;LSEQ=CTCGGGCACGGGGAGGGCAC;RSEQ=GGAAGACAGGGTCATCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:172,119:291,0:0:2,0:23.4:1:30.3:1:1:0:59.9:40.571:1:0:0.2 0/1:160:2:1,1:102,56:158,2:0.0125:2,2:28:1:31.5:1:1:1.81411:60:4:0.0127:0:1 +2 25463483 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00144;SOR=1.41222;LSEQ=GCGGAAGCACCAGCTGAGAA;RSEQ=GTGGAGGGGACAGGATGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:839:295:188,107:349,195:544,295:0.3516:2,2:25.1:1:30.6:1:0.93998:1.01862:60:72.75:0.3519:0:1.1 0/1:634:275:167,108:223,136:359,275:0.4338:2,2:25.6:1:29.5:1:0.74224:1.0603:60:54:0.4348:0:1.2 +2 25463748 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12396;SOR=Inf;LSEQ=GCAGGCTCACGACCCTAGCT;RSEQ=CAACCATGGACAAGTCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:0,69:69,0:0:1,0:26.6:1:31.8:1:1:0:59.7:12.8:1:0:0.2 0/1:38:2:1,1:0,36:36,2:0.0526:1,2:42:1:29:1:0.05263:0:60:4:0.0541:0:1 +2 25463871 . C T 41 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGGAAGGTGACCCAAGTGGA;RSEQ=GGCTGAGTCTGAAGGTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:14:1:26.3:1:1:0:53.7:2:0.2857:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:24:0:31:0:1:0:60:2:1:0:1 +2 25464631 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08349;SOR=Inf;LSEQ=GCCATCTCCCTGGCACCCTG;RSEQ=TCTCGGCAGGTGAGCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:0:0,0:56,265:321,0:0:2,0:23.7:1:31.5:1:1:0:60:28.182:1:0:0.2 0/1:251:3:2,1:60,188:248,3:0.012:2,2:15.3:1:26:1:0.15177:6.21:60:6:0.0121:0:1 +2 25464653 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18601;SOR=Inf;LSEQ=CTCGGCAGGTGAGCCTGCTG;RSEQ=CCAACAGGACCCATGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:17,191:208,0:0:2,0:25.8:1:32.1:1:1:0:60:28.714:0.995:0:0.2 0/1:159:2:1,1:20,136:156,2:0.0126:2,2:21.5:1:27.5:1:0.24889:6.66:60:4:0.0128:0:1 +2 25466810 . C T 162 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02818;LSEQ=GACAGCACCCGGATGGGCTT;RSEQ=CTCTTCTCAGCTGGGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1076:40:18,22:479,556:1035,40:0.0372:2,2:26.1:1:30.5:1:1:1.05292:60:80:0.0384:0:1.2 0/0:921:1:0,1:425,492:917,1:0.0011:2,0:1:0:27:0:1:0:60:2:0.0011:0:1 +2 25466888 . G T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12426;SOR=0.78594;LSEQ=ACAGGTCAGATGCAGGCCCA;RSEQ=CGGTGTCCCAAGCTCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:463:305:119,186:52,105:157,305:0.6587:2,2:23.2:1:30.5:1:0.22377:1.29:60:75.25:0.6659:0:1.1 1/0:302:182:64,118:44,76:120,182:0.6026:2,2:21.4:1:28.8:1:0.80711:1.0672:60:59.667:0.6007:0:1.1 +2 25467285 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12825;SOR=Inf;LSEQ=GTGTGCTACCTGGAATGGAA;RSEQ=GACCGGGTCTGGAGCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:154,200:354,0:0:2,0:22.2:1:31.5:1:1:0:59.9:43.25:1:0:0.2 0/1:198:2:1,1:81,115:196,2:0.0101:2,2:23:1:30:1:1:1.42:60:4:0.0101:0:1.5 +2 25467290 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13008;SOR=Inf;LSEQ=CTACCTGGAATGGAAAGACC;RSEQ=GGTCTGGAGCATGGCTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:165,178:343,0:0:2,0:22.6:1:30.9:1:1:0:59.9:56.167:1:0:0.2 0/1:194:2:1,1:89,103:192,2:0.0103:2,2:19:1:27.5:1:1:1.16:60:4:0.0104:0:1 +2 25467308 . G A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11417;SOR=0.3897;LSEQ=CCGGGTCTGGAGCATGGCTA;RSEQ=GGGGTGGAGGGTCTGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:19:10,9:207,122:329,19:0.0546:2,2:30.6:1:31.7:1:0.46578:1.52506:60:38:0.0551:0:1.4 0/1:182:4:2,2:107,71:178,4:0.022:2,2:16:1:29.8:1:1:1.50352:60:8:0.0222:0:1 +2 25467591 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15824;SOR=Inf;LSEQ=GGCCAGGACGAAGGGAGGCT;RSEQ=CACACCTGGCCTCACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:32,214:246,0:0:2,0:24.2:1:31.1:1:1:0:60:26.333:1:0:0.1 0/1:163:2:1,1:24,137:161,2:0.0123:2,2:22.5:1:25.5:1:0.28403:5.61:60:4:0.0123:0:1.5 +2 25467986 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCATCAGGACTCTGCTTC;RSEQ=AGAGGAAGCTCTGAAGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:2,0:149,5:154,2:0.0127:1,0:30.5:1:32:0:1:0:60:4:0.0129:0:1 0/0:63:0:0,0:61,2:63,0:0:1,0:22:1:31:1:1:0:60:126:1:0:0.1 +2 25468012 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.09645;SOR=Inf;LSEQ=AAGCTCTGAAGTCTACATCA;RSEQ=ACGCACACCGGGTGTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:200,11:211,0:0:2,0:24.9:1:32.6:1:1:0:59.8:104.5:1:0:0.1 0/1:96:2:2,0:90,4:94,2:0.0208:1,0:12.5:1:32:0:1:0:60:4:0.0213:0:1 +2 25468034 . G A 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCACACCGGGTGTCACCCT;RSEQ=TACATGCCCAGAAGCGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:269,31:300,0:0:2,0:23.5:1:32.6:1:1:0:59.9:299:1:0:0.1 0/1:174:13:11,2:147,14:161,13:0.0747:2,2:20.3:1:27.2:1:0.34039:1.90033:60:12:0.0698:0:1.2 +2 25468251 . C A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.35805;SOR=2.66357;LSEQ=GTACCACCGAAGGGCCTCTC;RSEQ=CTCCCCGGGCCGGAGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:2:2,0:125,346:471,2:0.0042:2,0:1:0:28:0:0.07168:0:60:4:0.0043:0:1 0/1:269:3:2,1:69,197:266,3:0.0112:2,2:24.7:1:27.3:1:0.17119:5.67:60:6:0.0113:0:1 +2 25468763 . G T 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGACAGTGCACGAAGCAC;RSEQ=GTGAAGGTGGTGTGACACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:179,2:181,2:0.0109:1,2:7.5:1:31:1:0.03261:73.29687:60:4:0.0111:0:1 0/0:84:0:0,0:80,4:84,0:0:1,0:26.7:1:29.7:1:1:0:60:168:1:0:0.1 +2 25468793 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14805;SOR=Inf;LSEQ=GTGTGACACGCAGGACGTGG;RSEQ=CCCTGGTCCCATGTCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:266,37:303,0:0:2,0:22.7:1:31.9:1:1:0:60:36.875:1:0:0.1 0/1:190:2:1,1:151,37:188,2:0.0105:2,2:27.5:1:28:1:0.36085:4.04034:60:4:0.0108:0:1 +2 25468820 . C T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02906;SOR=Inf;LSEQ=TCCCATGTCATTCAAACCTT;RSEQ=CTAAGTGCCTCTGCTACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:487:0:0,0:331,155:486,0:0:2,0:23.7:1:31.5:1:1:0:60:68.429:1:0:0.1 0/1:344:4:1,3:222,118:340,4:0.0116:2,2:11.3:1:26.8:1:0.12682:5.6149:60:8:0.0117:0:1 +2 25468969 . G A 52 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01352;SOR=Inf;LSEQ=AGCTGGCGTCAGAGGAGGCC;RSEQ=CGCCTGCTCCTCGGATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:681:0:0,0:351,330:681,0:0:2,0:23.5:1:30.8:1:1:0:60:74.667:1:0:0.1 0/1:501:5:5,0:260,235:495,5:0.01:2,0:10.6:1:22.8:1:0.0635:0:60:4:0.0082:0:1.2 +2 25469405 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09157;SOR=Inf;LSEQ=CTCTGTGGAGGCCTTGGCAG;RSEQ=CCTCCCTAAGCATGGCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:234,46:280,0:0:2,0:23.2:1:31.9:1:1:0:60:45.667:1:0:0.1 0/1:122:2:1,1:97,23:120,2:0.0164:2,2:8:1:27:1:0.35605:4.14982:60:4:0.0167:0:1 +2 25469502 . C T 204 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=216.16418;LSEQ=CATTTACCTTCTGGTGGCTC;RSEQ=AGGCCCTTAGGGCCAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:987:1:0,1:576,410:986,1:0.001:2,0:1:0:25:0:0.41641:0:60:2:0.001:0:1 0/1:733:132:73,59:357,244:601,132:0.1801:2,2:22.2:1:29:1:0.43499:1.18224:60:131:0.1814:0:1.2 +2 25469628 . C T 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CACACCGGGAACAGCTTCCC;RSEQ=GCGCGGCTGCTGGCCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:954:0:0,0:388,566:954,0:0:2,0:23.2:1:30.3:1:1:0:60:94.4:1:0:0.1 0/1:722:78:36,42:283,358:641,78:0.108:2,2:26.6:1:29.8:1:0.80943:1.08:59.9:38:0.1063:0:1.3 +2 25469714 . C A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29574;SOR=0;LSEQ=CAGATGGGTCAGGCTCAAGG;RSEQ=CAGACTCTGAGTAGTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:53,228:281,3:0.0106:2,2:17.3:1:23.3:1:0.09697:8.51:60:2:0.0072:0:1 0/0:170:0:0,0:24,143:167,0:0:2,0:25.2:1:30.2:1:1:0:60:26.833:0.9817:0:0.2 +2 25469715 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13744;SOR=Inf;LSEQ=AGATGGGTCAGGCTCAAGGC;RSEQ=AGACTCTGAGTAGTGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:54,232:286,0:0:2,0:23.7:1:32.1:1:1:0:60:94.333:1:0:0.1 0/1:169:2:1,1:22,145:167,2:0.0118:2,2:17:1:30.5:1:0.25437:6.47:60:4:0.0122:0:1 +2 25469913 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=1.64912;LSEQ=CTCCGAGCTCCCAGCAGGGA;RSEQ=ACTCACCTGCAGGACCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:626:373:240,133:150,103:253,373:0.5958:2,2:24.2:1:29.9:1:0.20833:1.24:60:40.444:0.5938:0:1.2 1/0:508:360:222,138:89,59:148,360:0.7087:2,2:23.6:1:28.8:1:0.76434:1.07:60:71:0.7086:0:1.2 +2 25469945 . C T 90 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02584;SOR=0.13132;LSEQ=GGACCTCGTAGATGGCTTTG;RSEQ=GGTACATGGGCTGCTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:871:9:2,7:465,396:861,9:0.0103:2,2:11:1:28.4:1:0.08951:4.10401:59.4:18:0.0105:0:1.2 0/0:731:1:1,0:391,336:727,1:0.0014:2,0:47:0:29:0:1:0:60:2:0.0014:0:2 +2 25470667 . G A 42 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68427;SOR=1.54967;LSEQ=CACAGTGGTCACGAGGCCCT;RSEQ=CCACCCTGATCCCCCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:3:3,0:97,300:397,3:0.0075:2,0:7.3:1:25.3:1:0.01527:0:60:6:0.0077:0:1.3 0/1:259:3:2,1:69,187:256,3:0.0116:2,2:15:1:27:1:0.18319:5.38:60:6:0.0118:0:1 +2 25470803 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.26867;SOR=3.89515;LSEQ=CCGGGGTCAGGTGGAGAGAG;RSEQ=GAGCGGCCCGTGGGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:1:0,1:244,53:297,1:0.0034:2,0:40:0:32:0:0.18121:0:60:2:0.0034:0:1 0/1:154:2:2,0:129,22:151,2:0.013:2,0:11.5:1:30:1:1:0:60:4:0.0131:0:1 +2 25471158 . T A 45 v3;p8;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03313;SOR=Inf;LSEQ=CAAAAAGTCACCTTGACCTC;RSEQ=CCAGGAATTAGCAAGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:95,367:462,0:0:2,0:22.2:1:30.1:1:1:0:59.9:37.5:1:0:0.1 0/1:346:4:4,0:83,259:342,4:0.0116:2,0:6.8:1:22.8:1:0.00379:0:60:8:0.0118:0:1 +2 25471169 . GC G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1406;LSEQ=CTTGACCTCTCCAGGAATTA;RSEQ=AAGGCCACCTGACACTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:118:18,100:33,208:241,118:0.3278:2,2:20.1:1:32.2:1:0.74801:1.13:60:117:0.3296:0.0694:0.2 0/1:250:16:4,12:40,194:234,16:0.064:2,2:18.4:1:30.6:1:0.4938:1.61:60:32:0.0643:0.012:0.4 +2 25471246 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11538;SOR=Inf;LSEQ=AAGGTCAAGGGCTGGAGAGA;RSEQ=CCAACCAGCTGCCTTGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:1,103:104,0:0:1,0:24:1:32.8:1:1:0:59.7:103:1:0:0.1 0/1:54:2:0,2:1,51:52,2:0.037:1,0:33.5:1:29:1:1:0:60:4:0.0377:0:1 +2 25472666 . G A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2957;SOR=0;LSEQ=TTACTGAATCTAGGAAACAC;RSEQ=GCCCTCTGACTTCAAGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:29,242:271,3:0.0109:2,2:17:1:23:1:0.03465:16.34:60:2:0.0074:0:1 0/0:164:0:0,0:24,140:164,0:0:2,0:22.4:1:30.4:1:1:0:60:81:1:0:0.1 +2 25472784 . C T 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.24211;LSEQ=TGGGCCTAGAGCTGCGAATG;RSEQ=AAACCCATCCTCAAGGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:1,13:0,10:10,14:0.5833:0,1:25.9:1:27.6:1:1:0:56.4:28:0.6087:0:1.4 1/0:11:7:0,7:1,3:4,7:0.6364:2,0:23.6:1:28:1:0.36364:0:60:14:0.6364:0:1.4 +2 25474918 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.53374;SOR=0;LSEQ=TAAGTCAGCATCTCCAGAAC;RSEQ=CGGGCCAGGCCGGGACGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:110,1:111,2:0.0177:1,2:20:1:29.5:1:0.03524:78.10229:60:4:0.018:0:1 0/0:65:0:0,0:63,1:64,0:0:1,0:21.9:1:30.7:1:1:0:60:63:1:0:0.1 +2 25475126 . T A 55 v3;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00492;SOR=Inf;LSEQ=GAGCCGCGGCCCTGAAGCTC;RSEQ=GGAAGTAGCTGCCCGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:807:0:0,0:297,501:798,0:0:2,0:25.1:1:29.8:1:1:0:59.9:13.509:1:0:0.3 0/1:569:6:6,0:223,337:560,6:0.0105:2,0:8:1:21.5:1:0.00422:0:60:2:0.0075:0:1.2 +2 25475140 . C A 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08164;SOR=6.20616;LSEQ=AAGCTCTGGAAGTAGCTGCC;RSEQ=GTCTTGGGGGAGGGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:618:1:1,0:219,393:612,1:0.0016:2,0:1:0:26:0:0.35889:0:60:2:0.0018:0:1 0/1:401:4:3,1:147,250:397,4:0.01:2,2:19:1:25:1:0.14947:5.08:60:8:0.0106:0:1.5 +2 25475155 . G A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07214;SOR=6.58041;LSEQ=CTGCCCGTCTTGGGGGAGGG;RSEQ=AAGGGGGCGATGGGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:1:0,1:119,321:440,1:0.0023:2,0:48:0:13:0:1:0:60:0:0:0:2 0/1:272:4:2,2:87,180:267,4:0.0147:2,2:19:1:24.8:1:0.59982:2.06:56:3:0.0118:0:2 +2 25475210 . C G 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.07871;SOR=3.09745;LSEQ=CTGGGAGGGGAGGGGGGCGG;RSEQ=GGGGGGGAGGGAGGGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:9:0,9:2,77:79,9:0.1011:1,0:9.6:1:20.4:1:1:0:56.6:1.25:0.0694:0:2.9 0/1:23:6:0,6:0,17:17,6:0.2609:1,0:6.2:1:20.7:1:1:0:58.2:2:0.2353:0:2.5 +2 25497684 . A AC 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.15842;LSEQ=GAGCAGATGAACCAGTCATC;RSEQ=TGACTAGAGATTAAGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:138:110:108,2:27,1:28,110:0.7971:1,1:24.1:1:32:1:0.49638:1.99:60:109:0.8074:0.1884:0.1 0/1:97:37:36,1:58,2:60,37:0.3814:1,1:28.3:1:32.2:1:1:1.24:60:74:0.3814:0.0515:0 +2 25498504 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.50562;SOR=0;LSEQ=CCTTGTGCCTGGGGTCCCTG;RSEQ=CACAGGGGATGGGGGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:18,142:160,2:0.0123:2,2:8.5:1:27.5:1:0.22146:7.71:60:4:0.0128:0:1 0/0:127:0:0,0:19,108:127,0:0:2,0:23.1:1:30.3:1:1:0:60:20.167:1:0:0.1 +2 25505793 . T C 90 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63948;SOR=0.34368;LSEQ=CCCTTGAAATCACGAGTCTG;RSEQ=GGACTCCAGCTTCAGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:0,8:0,16:16,8:0.3333:1,0:17.8:1:30.1:1:1:0:58.8:16:0.3478:0:1.1 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:30:0:31:0:1:0:60:2:0.1429:0:1 +2 25521806 . AC A 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACCTCCAGGAACTCACC;RSEQ=CCCCCCCGCCTCTACTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:32.5:1:1:0:60:4:1:0:0.5 +2 25522795 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00641;SOR=0.1282;LSEQ=GGGCAACAGAGTGAGACTCC;RSEQ=TCTCAGTAAAAAAGTAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:26:26,0:21,0:21,26:0.5532:1,1:24.1:1:30.6:1:1:0:50.3:52:0.5652:0:1 0/1:15:2:2,0:13,0:13,2:0.1333:1,0:13:1:28.5:1:1:0:60:4:0.1333:0:1 +2 25522925 . G T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.015;SOR=Inf;LSEQ=AATGTCTCCAGGTCCCTGCA;RSEQ=GACATACATCACTGCCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:587:0:0,0:442,143:585,0:0:2,0:21.7:1:32.2:1:1:0:60:52.182:1:0:0.1 0/1:448:5:1,4:333,109:442,5:0.0112:2,2:14.8:1:21.4:1:0.01575:12.13864:60:1.5:0.0069:0:1 +2 25523196 . T C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00879;SOR=0.50242;LSEQ=TGTCTGGGGCTGGCCCTGGC;RSEQ=TCCCTTCCAGCCCCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:91:3,88:7,93:100,91:0.4691:2,1:24.7:1:32.7:1:0.33623:2.19923:60:44.5:0.4709:0:1.1 0/1:101:31:2,29:5,65:70,31:0.3069:2,2:21.3:1:31.8:1:1:1.1142:60:62:0.31:0:1.1 +2 25535032 . G T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATCCGACAGAGAAAGCAA;RSEQ=CCAGGCCCAAGAAGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 25536827 . G A 175 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=51.46989;LSEQ=GCAGAGCTGCTGGTGTCCCC;RSEQ=GGGCCGCTGGAGGGCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1002:2:2,0:440,559:999,2:0.002:2,0:1:0:27.5:1:0.19473:0:60:4:0.002:0:1 0/1:748:70:34,36:308,369:677,70:0.0936:2,2:24.3:1:28.6:1:0.70567:1.13:60:13:0.0889:0:1.2 +2 25536863 . G A 80 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01049;SOR=9.99982;LSEQ=ATGGCGGGCATCTGGGCGCC;RSEQ=GGAGGCAGGCTGGGGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:715:1:1,0:236,477:713,1:0.0014:2,0:47:0:14:0:0.33193:0:60:0:0:0:1 0/1:506:7:5,2:188,311:499,7:0.0138:2,2:12.6:1:28.6:1:0.1117:4.12:60:14:0.014:0:1.1 +2 25966872 . TG T 105 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.2136;SOR=0.4879;LSEQ=ACGGCAGGTGTTGGAGGCAC;RSEQ=GGGGGGTTTGCTGTAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1069:11:6,5:585,473:1058,11:0.0103:2,2:23.8:1:30.5:1:1:1.03064:60:10:0.0095:0.0028:0.4 0/0:991:5:3,2:527,457:984,5:0.005:2,2:31.2:1:30.4:1:1:1.30:60:10:0.0051:0.001:0 +2 25967169 . T TGCGGCG 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=4.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ACTGAGGCGGCTGCAGCAGC;RSEQ=GCGGCGGCAGCGGCAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:526:0:0,0:275,251:526,0:0:2,0:22.3:1:31:1:1:0:60:39.462:1:0:0.1 0/1:498:21:13,8:245,231:476,21:0.0422:2,2:30.4:1:28.9:1:0.38059:1.53:59.8:20:0.0412:0.006:0.2 +2 25972936 . C T 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTCTCAGATTCCTGTTCAG;RSEQ=AGAGGTGACTGGCTTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:72:33,39:466,447:913,72:0.0729:2,2:22:1:28.7:1:0.46285:1.23179:60:71:0.0727:0:1.1 0/0:784:0:0,0:374,408:782,0:0:2,0:24.1:1:31.3:1:1:0:60:77.2:0.9974:0:0.1 +2 25973309 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37286;SOR=1.27922;LSEQ=AGGGGAAAAAAGAAATATTC;RSEQ=AGTTGAAAAATAGCCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:54:7,47:24,126:150,54:0.2634:2,2:22.9:1:29.3:1:0.6647:1.27747:60:53:0.2598:0:1.1 0/1:121:38:8,30:18,65:83,38:0.314:2,2:16.7:1:27.4:1:1:1.03814:60:37:0.3109:0:1.1 +2 25973405 . G A 97 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42031;SOR=0.33566;LSEQ=CTGACACAGCAGGTATTCAT;RSEQ=TATTATCTTCACTATTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:0,29:29,8:0.2162:1,0:21.4:1:32.4:1:1:0:60:16:0.2286:0:1.1 0/1:12:1:0,1:0,11:11,1:0.0833:0,0:3:0:28:0:1:0:60:2:0.0833:0:2 +2 25976268 . C CA 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.67457;SOR=1.23782;LSEQ=CTAAAGAAGAATCAGTGAGA;RSEQ=AAAAAAAAAAACAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:19:19,0:118,1:119,19:0.1348:1,1:21.4:1:31.4:1:1:0:59.5:38:0.1357:0.0355:0.4 0/1:68:11:11,0:56,1:57,11:0.1618:1,0:27.1:1:30.3:1:1:0:60:22:0.1618:0:0.7 +2 25978827 . G T 39 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64732;SOR=0.47686;LSEQ=ACTGCGTAATTACCTGATGA;RSEQ=GAAGAGAGGTGCTCTGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:1,2:228,52:280,3:0.0106:2,2:22:1:24.7:1:0.09431:8.67272:60:2:0.0072:0:1 0/0:197:1:0,1:150,45:195,1:0.0051:2,0:1:0:24:0:0.23469:0:60:2:0.0051:0:1 +2 25990640 . T C 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=7e-05;SOR=0.26212;LSEQ=GACTGGTAGCACTGAGATTA;RSEQ=AGACAGAATCAATTAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:46:7,39:36,159:195,46:0.1901:2,2:23.1:1:31.9:1:0.67488:1.26027:60:92:0.1917:0:1 0/1:173:10:1,9:33,130:163,10:0.0578:2,2:26.7:1:32:1:0.68893:2.27593:59.4:20:0.0585:0:1 +2 25991534 . A T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=Inf;LSEQ=ATTTAAAAATAAATGATGTC;RSEQ=TAAACAAATCAGGAAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:150,25:175,0:0:2,0:22.8:1:31.1:1:1:0:60:174:1:0:0.1 0/1:179:2:1,1:145,32:177,2:0.0112:2,2:7.5:1:27:1:0.33557:4.47744:60:4:0.0112:0:1 +2 25991793 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5047;SOR=0;LSEQ=AATCAGTTTTTTAGTAATAA;RSEQ=ATAAATTACTTCTTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:12,154:166,2:0.0119:2,2:17.5:1:31.5:1:0.1492:12.37:60:4:0.0123:0:1 0/0:134:0:0,0:18,116:134,0:0:2,0:19.9:1:28.1:1:1:0:59.8:133:1:0:0.1 +2 25991820 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.14094;SOR=Inf;LSEQ=TACTTCTTTTTTAAATGGCA;RSEQ=GAAGCATGCTGATCGTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:1,88:89,0:0:1,0:25.6:1:31.9:1:1:0:60:43.5:1:0:0.2 0/1:54:2:1,1:2,50:52,2:0.037:1,2:24:1:29:1:0.10901:20.61:60:4:0.037:0:1 +2 25994220 . A C 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCAAGGGCCCAATGTAAAA;RSEQ=ATTTTCAAAAAATATCCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:181,11:192,0:0:2,0:22.1:1:30.6:1:1:0:59.8:191:1:0:0.1 0/1:151:15:13,2:123,13:136,15:0.0993:2,2:19.1:1:31.4:1:0.6464:1.45155:60:14:0.094:0:1.1 +2 25994298 . G T 76 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00489;SOR=Inf;LSEQ=TACTTGATAAATACAGACTA;RSEQ=CAATGCTTACCTGCTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:772:0:0,0:530,241:771,0:0:2,0:24.9:1:32.7:1:1:0:60:54.071:1:0:0.1 0/1:681:7:1,6:419,255:674,7:0.0103:2,2:6.4:1:27.1:1:0.01447:9.82795:56.7:14:0.0104:0:1.1 +2 25994412 . A AG 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0.44712;LSEQ=GCGGGGAGGACGACGATACT;RSEQ=GGGAAAAAAAAGTGACAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:828:127:44,83:249,452:701,127:0.1534:2,2:25.7:1:32.1:1:0.91975:1.03913:59.8:126:0.1546:0.0229:0.2 0/1:761:57:26,31:275,429:704,57:0.0749:2,2:27.6:1:30.9:1:0.32866:1.31:59.2:56:0.0746:0.0105:0.3 +2 26022303 . ACTG A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=0.96935;LSEQ=TCCTTGTTGCTGCCACCATC;RSEQ=CTGCTGCTGCTGTTCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1148:29:13,16:562,557:1119,29:0.0253:2,2:33.5:1:33.4:1:0.5793:1.24158:60:58:0.0256:0:0 0/1:1265:31:17,14:607,623:1230,31:0.0245:2,2:31.3:1:31.2:1:0.5888:1.25:60:62:0.0248:8e-04:0 +2 26022461 . TA T 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50701;SOR=0;LSEQ=CCATTTAAGCAAACAGAAAT;RSEQ=AAACTTCTGATATGCAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:8,181:189,2:0.0105:1,2:6:1:27.8:1:0.09226:21.39:60:4:0.0106:0.0052:0 0/0:147:0:0,0:15,132:147,0:0:2,0:24.8:1:30:1:1:0:60:72.5:1:0:0 +2 26029255 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=0;LSEQ=GAACACAACAATTAATTTCT;RSEQ=TCTCTGAATATCCTATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:25,170:195,2:0.0102:2,2:9.5:1:26:1:0.24713:6.69:60:4:0.0103:0:1 0/0:198:0:0,0:31,167:198,0:0:2,0:24.9:1:31.6:1:1:0:60:48.5:1:0:0.1 +2 26029407 . A C 85 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.67843;LSEQ=AATCATTTCCATGTATCTAC;RSEQ=AAATAGTAATTCCTTAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:12,6:0.3333:0,0:42.3:1:33:1:1:0:60:12:0.3333:0:1 0/1:4:1:0,1:0,3:3,1:0.25:0,0:38:0:32:0:1:0:60:2:0.25:0:1 +2 26068509 . C T 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.44211;SOR=0.77778;LSEQ=ATATATATTTCTTATAATTA;RSEQ=GTCTTAAAAGCTAAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:40:0,40:0,101:101,40:0.2837:1,1:25.2:1:31.2:1:1:0:60:80:0.2837:0:1 0/1:85:20:0,20:1,64:65,20:0.2353:1,1:29.2:1:30.5:1:1:0:60:40:0.2353:0:1 +2 26101168 . CT C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.04714;SOR=Inf;LSEQ=GCCTGCTCTGCCCTGCGCTG;RSEQ=TTTCCCGCGGTGCCGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:62,342:404,0:0:2,0:23.3:1:30.3:1:1:0:60:30.077:1:0:0.2 0/1:354:4:1,3:67,283:350,4:0.0113:2,2:21.8:1:30.8:1:0.57569:1.41:60:8:0.0115:0.0028:0 +2 26836683 . T C 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAGAGGAGAAGGAATGTCC;RSEQ=CAACAGGTCTCTCTGTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:1,1:0.5:0,0:35:0:32:0:1:0:60:2:0.5:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:27.5:1:1:0:60:4:1:0:1 +2 26836738 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=CCTGTCCTGCCTCTCTGCAC;RSEQ=TGGGTGAATGTGTCCCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:6,0:0:2,0:19.8:1:29.2:1:1:0:60:5:1:0:0.2 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:23.5:1:27.5:1:1:1.29098:60:4:0.25:0:1 +2 26837395 . A G 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACCTCAGACACATGAAC;RSEQ=GTTTTCCCAGGAGGCAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:0:31:1:1:0:60:4:1:0:1.5 +2 26838050 . A G 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACAGTAACAGTCTGAATGCT;RSEQ=CTTCCCAGTAAGATGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:31:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:25.5:1:27.5:1:1:0:60:4:1:0:0 +2 26838128 . A T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGAAAGCAGAATGCCTCTCC;RSEQ=TCCCCTGCCCCCAGACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:30:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:28.5:1:1:0:60:4:1:0:0 +2 27009046 . G A 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66013;SOR=1.87432;LSEQ=AGCCGTGGGACCGGGCGCCA;RSEQ=CACCCTCTGCGGCGTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:2:1,1:127,152:279,2:0.0071:2,2:29:1:28.5:1:1:1.20:60:4:0.0072:0:1 0/1:226:3:1,2:103,118:221,3:0.0133:2,2:40.7:1:31:1:1:1.7416:60:6:0.0137:0:1 +2 27009059 . C T 58 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.7106;SOR=1.53083;LSEQ=GGCGCCAGCACCCTCTGCGG;RSEQ=GTGTCATGGGCCCGCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:3:0,3:145,179:324,3:0.0092:2,0:15.7:1:28.7:1:0.25733:0:60:6:0.0093:0:1.3 0/1:286:4:2,2:130,151:281,4:0.014:2,2:20.3:1:29:1:1:1.16:60:8:0.0145:0:1.3 +2 27009070 . C T 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26314;SOR=2.83501;LSEQ=CCTCTGCGGCGTGTCATGGG;RSEQ=CCGCGCCGCCGGAGCCGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:2:1,1:168,192:360,2:0.0055:2,2:23:1:23:1:1:1.14:60:4:0.0057:0:1.5 0/1:322:5:2,3:149,168:317,5:0.0155:2,2:28.8:1:28.4:1:1:1.32919:60:10:0.016:0:1.2 +2 27009338 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCGAGGGGCTGGAGCAGG;RSEQ=GGTTCCGAAAGCGGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:0,37:37,2:0.0513:1,0:18.5:1:26.5:1:1:0:60:4:0.0513:0:1 0/0:19:0:0,0:0,19:19,0:0:1,0:23.4:1:28.1:1:1:0:60:18:1:0:0.1 +2 27009478 . C T 44 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGTGCGTTATCTCAGCTT;RSEQ=ATATTGTGCCCATTTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:3,3:0.5:2,0:15.3:1:28:1:1:0:60:6:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 27014522 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAGTCTCTCAGATTCTTT;RSEQ=CAGCTGTAAAAAACAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:35:1:30:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 27014808 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05553;SOR=Inf;LSEQ=AAAATTACTATATATCAGGT;RSEQ=GGTGCAAAAGTATTGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:45,2:47,0:0:1,0:20.8:1:31.3:1:1:0:59.2:94:1:0:0.1 0/1:15:2:1,1:13,0:13,2:0.1333:1,2:30.5:1:28.5:1:0.13333:0:60:4:0.1429:0:1 +2 27014885 . G A 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01526;SOR=0;LSEQ=TAAAACAGACAAAAATCCCT;RSEQ=CTCTGTGGAGGGTAGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:10:10,0:162,3:165,10:0.0571:1,0:30.8:1:28:1:1:0:60:20:0.0578:0:1.6 0/0:108:0:0,0:107,1:108,0:0:1,0:20.5:1:31.2:1:1:0:60:35:1:0:0.2 +2 27014901 . G A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06426;SOR=Inf;LSEQ=CCCTGCTCTGTGGAGGGTAG;RSEQ=CACATAGATATAGTCTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:216,1:217,0:0:1,0:24.4:1:31.5:1:1:0:60:35.167:1:0:0.3 0/1:146:3:3,0:142,1:143,3:0.0205:1,0:35:1:23.7:1:1:0:60:2:0.0139:0:2.3 +2 27014980 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00193;SOR=0.73198;LSEQ=CCACCTATTTTCCACTGAAC;RSEQ=TACCTTTCTTTTGCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:865:340:215,125:342,183:525,340:0.3931:2,2:25.6:1:31.9:1:0.61092:1.08644:59.9:112.333:0.3937:0:1.1 0/1:877:282:185,97:363,232:595,282:0.3216:2,2:22.5:1:30.2:1:0.20456:1.22:60:93:0.3218:0:1.1 +2 27015118 . G A 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00051;SOR=0.73074;LSEQ=TCAGCCGCCTGGTAAGCTCC;RSEQ=GGAGCTTCCCACCAACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1082:466:179,287:240,375:615,466:0.4307:2,2:27.7:1:31.2:1:0.85022:1.02613:59.9:57.25:0.4292:0:1.2 0/1:1031:367:143,224:283,379:662,367:0.356:2,2:26.1:1:29.9:1:0.26141:1.16948:59.9:90.75:0.3562:0:1.2 +2 27015141 . G GC 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.56634;LSEQ=AGCTTCCCACCAACCCCTAT;RSEQ=CCACCCTCCTTTTTTTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:857:338:108,230:164,352:516,338:0.3944:2,2:24.3:1:31.5:1:1:1.01:59.9:168:0.3967:0.0513:1.1 0/1:761:205:63,142:195,356:551,205:0.2694:2,2:27.5:1:30.5:1:0.26204:1.23428:60:40:0.2685:0.0079:1.1 +2 27015610 . CCA C 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.49715;LSEQ=ACTCCTACTCCTCCCCTTCC;RSEQ=CTCCTTCACAGGCAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1448:421:246,175:565,463:1028,421:0.2907:2,2:28:1:32.1:1:0.24383:1.15:60:420:0.2952:0.0304:0.1 0/1:1477:250:132,118:667,559:1226,250:0.1693:2,2:26.5:1:30.6:1:0.67621:1.06659:59.9:124:0.1699:0.0217:0.2 +2 27015827 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAAGAACAATGAGGTAA;RSEQ=CTCTGAGGGTTTGGAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:73,222:295,0:0:2,0:24.1:1:31.8:1:1:0:59.9:58:1:0:0.1 0/1:152:19:2,17:24,109:133,19:0.125:2,2:25.2:1:29.2:1:0.5317:1.86511:60:38:0.1258:0:1.1 +2 27015903 . T C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55136;SOR=1.14562;LSEQ=GTTCAGTCTCATTCTGTGAA;RSEQ=AGTTTCCTACAATCCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:124:98,26:155,38:193,124:0.3912:2,2:24:1:32.3:1:0.77648:1.0819:60:30:0.3871:0:1.5 0/1:158:67:60,7:82,9:91,67:0.4241:2,2:22.3:1:31.6:1:1:1.06254:59.4:134:0.4295:0:1.6 +2 27015953 . C CA 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.52724;SOR=0.55181;LSEQ=GATTAAGTTTAGCAGGTTTC;RSEQ=AAAAAAAAGCAGCCCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:626:7:6,1:471,146:617,7:0.0112:2,2:35.9:1:31.5:1:1:1.86:60:14:0.0113:0.0016:0.9 0/0:484:3:3,0:372,107:479,3:0.0062:2,0:28:1:28.3:1:1:0:60:6:0.0063:0:0 +2 27015963 . C T 69 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20122;SOR=2.76045;LSEQ=AGCAGGTTTCCAAAAAAAAG;RSEQ=AGCCCGTGGCCCTTCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:724:3:1,2:526,194:720,3:0.0041:2,2:13.7:1:28.7:1:0.18025:5.4076:47:6:0.0043:0:1.7 0/1:616:7:2,5:438,171:609,7:0.0114:2,2:15:1:24.6:1:0.02261:6.38046:60:14:0.0116:0:1.3 +2 27015969 . G A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.87456;SOR=0.9802;LSEQ=TTTCCAAAAAAAAGCAGCCC;RSEQ=TGGCCCTTCATCTGTGTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:843:302:212,90:378,161:539,302:0.3582:2,2:23.5:1:30.3:1:1:1.00:59.9:74.5:0.3595:0:1.3 0/1:738:261:179,82:330,145:475,261:0.3537:2,2:22.6:1:29.4:1:0.80296:1.04249:59.9:129.5:0.3533:0:1.3 +2 27016259 . A G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.48581;SOR=0.79095;LSEQ=GTAATTTCCTTTCTCCATCC;RSEQ=TAGTCCCTTGTCACCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:54:3,51:1,79:80,54:0.403:1,2:26:1:32.2:1:0.30233:4.60:60:53:0.4109:0:1.1 0/1:92:32:0,32:2,58:60,32:0.3478:1,1:21.6:1:32.3:1:0.54133:0:60:64:0.3556:0:1.2 +2 27016302 . G GT 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.62251;SOR=1.36043;LSEQ=CCCTTTGTTCTCTAGTAAAG;RSEQ=TTGATCTAGTTTTGACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:29:1,28:0,33:33,29:0.4677:1,1:26.5:1:30.3:1:0.46774:0:60:28:0.459:0.0645:1.1 1/0:22:12:0,12:0,10:10,12:0.5455:0,0:31:1:30.5:1:1:0:60:24:0.5714:0.0455:1.3 +2 27016351 . G A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00372;SOR=Inf;LSEQ=TGTGGTTTGTGCCCTTTTGT;RSEQ=CAATGTTAGATAAAAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:0,9:0,19:19,9:0.3214:1,0:16.9:1:30.3:1:1:0:56.8:18:0.3214:0:1.1 1/1:6:6:1,5:0,0:0,6:1:0,2:16:1:29.7:1:1:0:60:12:1:0:1.5 +2 27016988 . C T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01025;LSEQ=CTGTGGTATGGGAGAAAAGG;RSEQ=TATGTACTTATTATTTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:684:683:406,277:0,0:0,683:0.9985:0,2:25.3:1:29.7:1:1:0:60:55.917:0.9985:0:1.1 1/1:559:489:288,201:40,30:70,489:0.8748:2,2:25.1:1:28.7:1:0.79627:1.07:60:53.333:0.8743:0:1.1 +2 27017552 . CT TC 32 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGCCACAATTTTTTTTT;RSEQ=TTTTTTTTTTTTTGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:11.5:1:32.3:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 27247832 . T C 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81204;LSEQ=GCCTGCCCCACTCGCCCGCC;RSEQ=GCTTGCTTTGCACTAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:2,2:4,5:0.5556:2,2:13.2:1:29:1:0.52381:3.39:60:10:0.5556:0:1 1/0:6:3:3,0:3,0:3,3:0.5:0,0:15:1:32:0:1:0:60:6:0.5:0:2 +2 27249245 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCCCTGGCTGACTGCAC;RSEQ=GCTTCCCCGTGCCTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:29.5:1:1:0:60:4:1:0:1 +2 28539745 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15376;SOR=Inf;LSEQ=CACTTTAGAAATGAAACAAG;RSEQ=GAGAATTCTGCCCAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:150,12:162,0:0:2,0:25:1:31.2:1:1:0:60:31.4:1:0:0.1 0/1:105:2:1,1:90,12:102,2:0.019:2,2:8.5:1:29.5:1:0.23544:7.2445:60:4:0.0198:0:1 +2 28539774 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16123;SOR=Inf;LSEQ=TGCCCAAGGTCACAGATTTT;RSEQ=AGTCTGAATTCAGGTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:220,52:272,0:0:2,0:24.1:1:32.2:1:1:0:60:89.667:1:0:0.1 0/1:183:2:1,1:146,35:181,2:0.0109:2,2:23.5:1:27:1:0.35561:4.12715:60:4:0.0109:0:1 +2 28539877 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.29936;LSEQ=CTTGTTGGTTGGTTTCTGGG;RSEQ=ATTTTCACTGGATTACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:763:141:77,64:300,321:621,141:0.1848:2,2:25.6:1:29.1:1:0.19191:1.29:59.9:282:0.186:0:1.1 0/1:605:259:121,138:168,176:344,259:0.4281:2,2:25.3:1:28.2:1:0.62198:1.0885:60:258:0.4293:0:1.2 +2 28539937 . G A 44 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0327;SOR=Inf;LSEQ=CACTTGGCTGCATGTCCTTC;RSEQ=GCACTGCCGTGCTCAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:0:0,0:163,308:471,0:0:2,0:24.6:1:30.4:1:1:0:60:41.818:1:0:0.2 0/1:350:4:4,0:123,223:346,4:0.0114:2,0:5.5:1:22.3:1:0.01682:0:60:3:0.0087:0:1.3 +2 28539946 . G A 106 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=17.27984;LSEQ=GCATGTCCTTCGGCACTGCC;RSEQ=TGCTCAGCTTTATGCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:1:1,0:120,283:403,1:0.0025:2,0:1:0:29:0:0.2995:0:60:2:0.0025:0:1 0/1:291:12:6,6:85,194:279,12:0.0412:2,2:29.2:1:29.8:1:0.20191:2.28:60:24:0.0418:0:1.4 +2 28736687 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATCCTCTTTTGAGCCC;RSEQ=ATTAAAACCTTTGAATTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:11,9:0,0:0,20:1:0,2:27.8:1:32:1:1:0:60:40:1:0:1.1 1/1:15:15:10,5:0,0:0,15:1:0,2:23.3:1:30.7:1:1:0:60:30:1:0:1.1 +2 29414782 . A G 35 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTATGTGTGTAAAATTAA;RSEQ=CAGATTCCCAATGCGTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:35:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29415792 . G A 93 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAGAGCACACACAATTT;RSEQ=AAAGAAGCATAAGGAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:26:1:26.9:1:1:0:60:10:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29416025 . C CATTG 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=3e-05;SOR=0.34313;LSEQ=TCTCTGGTTTGTGAAGGAGC;RSEQ=ATTGCCTCTCTCTCCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:93:77,16:69,22:91,93:0.5054:2,2:24.9:1:31.4:1:0.27711:1.53:60:186:0.5082:0.125:0.1 0/1:112:29:23,6:64,19:83,29:0.2589:2,2:21.5:1:30:1:1:1.14:60:58:0.2613:0.0804:0.1 +2 29416366 . G C 319 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27345;LSEQ=TCCAGCCCCAGGTTACCCCT;RSEQ=TCGTGTGGCTCCTTCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1523:900:412,488:292,327:619,900:0.5909:2,2:26.5:1:32.6:1:0.60088:1.05763:59.9:68.231:0.5913:0:1.1 0/1:1187:336:151,185:399,448:847,336:0.2831:2,2:26.1:1:31:1:0.51841:1.09108:60:83:0.2823:0:1.2 +2 29416481 . T C 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22117;LSEQ=TGTTTCTGGATCCGTGGACC;RSEQ=TGTGCAACTCCGAAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1391:809:384,425:276,303:579,809:0.5816:2,2:25.6:1:32.1:1:0.95656:1.00814:59.9:66.417:0.5801:0:1.2 0/1:1268:298:148,150:466,504:970,298:0.235:2,2:26.7:1:30.7:1:0.64305:1.07:60:58.6:0.2331:0:1.2 +2 29416572 . T C 315 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04869;LSEQ=TCTAGGGACTCGAACAGAGA;RSEQ=CTCTGCAGCTGTGGGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1017:1014:487,527:0,3:3,1014:0.9971:0,2:24.9:1:31.6:1:0.2506:0:60:47.286:0.998:0:1.2 1/1:837:789:353,436:23,25:48,789:0.9427:2,2:25.6:1:30.4:1:0.76536:1.13614:60:40.526:0.9448:0:1.2 +2 29416791 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16049;SOR=Inf;LSEQ=GTTGATTACATCCGGGTCCT;RSEQ=CCGTAGGGGAAATTATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:73,217:290,0:0:2,0:21.4:1:32.1:1:1:0:59.9:57:0.9965:0:0.1 0/1:195:2:1,1:65,127:192,2:0.0103:2,2:25.5:1:26.5:1:1:1.95:60:4:0.0104:0:2 +2 29416794 . G A 124 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=31.60383;LSEQ=GATTACATCCGGGTCCTGCC;RSEQ=TAGGGGAAATTATTAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:1,0:65,196:261,1:0.0038:2,0:1:0:27:0:0.25191:0:60:2:0.0038:0:1 0/1:175:19:10,9:49,107:156,19:0.1086:2,2:12.5:1:29.3:1:0.07552:2.41:60:38:0.1092:0:1.2 +2 29416946 . T C 106 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.22188;SOR=0.18655;LSEQ=AGGCACTGGGGCATACAAAA;RSEQ=GAATGGGAAGTCATCCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:0,12:0,4:4,12:0.75:0,0:24.3:1:29.7:1:1:0:60:24:0.8:0:1.1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:47:0:32:0:1:0:60:2:0.3333:0:1 +2 29419252 . C T 38 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTATATGCAATTAATTA;RSEQ=TTCACATGTTGTTATTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:26.3:1:24:1:1:0:60:2:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29419413 . T C 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTCCCCAGTTTTTACTGTG;RSEQ=GTCTGGCACTGTGCTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1:0,1:19.3:1:32.5:1:1:0:60:26:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:12:1:29:1:1:0:60:4:1:0:1 +2 29419591 . G T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=1.96496;LSEQ=TATTTGCCATCTTTAAGACT;RSEQ=TTTCATATAGAGTAAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:156:111,45:153,72:225,156:0.4084:2,2:27:1:30.8:1:0.57257:1.16:59.8:77:0.4096:0:1.1 1/0:323:186:134,52:84,52:136,186:0.5759:2,2:25.3:1:29.7:1:0.0546:1.59:60:61:0.5737:0:1.1 +2 29420315 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.26298;LSEQ=AGGGAGGGCAGCCATCTGCC;RSEQ=CTTCATCTTAAAGAAGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:204:123:116,7:77,4:81,123:0.6029:1,2:25.4:1:32.5:1:1:1.16077:60:246:0.6119:0:1.1 0/1:116:33:31,2:80,3:83,33:0.2845:1,2:22.9:1:30.1:1:0.62191:1.71159:60:32:0.2807:0:1.2 +2 29420595 . TCA T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.77791;SOR=0.7401;LSEQ=ATAGACACACCCACCCACAT;RSEQ=CACACACACACAGGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:10:2,8:25,195:220,10:0.0435:2,2:28.7:1:31.2:1:0.33204:1.94:60:20:0.0444:0.0043:0.2 0/1:123:4:0,4:16,103:119,4:0.0325:2,0:28:1:31:1:1:0:60:8:0.0325:0:0 +2 29429642 . GGTGT G 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=12.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTAAAAGACTCCCTTTATT;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:32.7:1:31.3:1:1:0:60:6:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29429741 . C CTT 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCTGTTAATGTGTGGTC;RSEQ=CAGCCAGCAATGGCAGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:28.8:1:31.4:1:1:0:60:10:0.8333:0.1667:0.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29429888 . G A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40114;SOR=1.38885;LSEQ=GAATTCTGATAGATGCTCAC;RSEQ=TTTGAGAACCACTGTTGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:141:97:95,2:43,1:44,97:0.6879:1,1:25.1:1:30.9:1:1:1.10:60:96:0.6857:0:1 1/0:61:46:45,1:14,0:14,46:0.7541:1,1:23.9:1:29.3:1:1:0:60:92:0.7667:0:1.1 +2 29429948 . C T 178 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02378;LSEQ=TTTCCCTCCCTACTAACACA;RSEQ=GGGCTCCCGGCTTAGAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:57:48,9:267,37:304,57:0.1579:2,2:24.1:1:30.6:1:0.51498:1.35182:59.1:56:0.1569:0:1.1 0/0:226:1:1,0:180,45:225,1:0.0044:2,0:2:0:28:0:1:0:60:2:0.0045:0:1 +2 29430195 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13943;SOR=Inf;LSEQ=GAGATGGCATTAAGCATCTG;RSEQ=CCTGCTGGGAAAGTTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:23,248:271,0:0:2,0:23.1:1:31.2:1:1:0:60:29.111:1:0:0.1 0/1:162:2:1,1:17,143:160,2:0.0123:2,2:22.5:1:30.5:1:0.21049:8.20:60:4:0.0126:0:1 +2 29430519 . G T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAATGCAAGATCCAAAAT;RSEQ=GGAGAACTGAGAGCAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:25:1:30.7:1:1:0:59.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29432408 . CAAAAA C 49 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=21.000;MSILEN=1;SSF=0.25531;SOR=5.95357;LSEQ=ACAAGAGCGAAACTCCGTCT;RSEQ=AAAAAAAAAAAAAAAAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:7,0:7,1:0.0833:0,0:20:0:34:0:1:0:60:2:0.0833:0:0 0/1:8:3:2,1:4,0:4,3:0.375:0,2:15:1:31.4:1:0.42857:0:60:6:0.375:0.125:0.3 +2 29432776 . T C 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=GGAAATGCATTTCCTAATTT;RSEQ=ATCCCTAGGAAGATGAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:0:0,0:166,462:628,0:0:2,0:23.6:1:28.8:1:1:0:60:68.778:0.9968:0:0.1 0/1:460:10:3,7:146,303:449,10:0.0217:2,2:21.5:1:30.4:1:1:1.12403:60:20:0.022:0:1.3 +2 29432803 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0254;SOR=Inf;LSEQ=AGGAAGATGAGTGTACAACG;RSEQ=CCATCACTAGGATTTTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:66,320:386,0:0:2,0:23.7:1:32:1:1:0:60:54.143:1:0:0.1 0/1:258:4:3,1:56,198:254,4:0.0155:2,2:8.3:1:26.8:1:0.03839:10.48:60:8:0.0157:0:1 +2 29432814 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15538;SOR=Inf;LSEQ=TGTACAACGGCCATCACTAG;RSEQ=ATTTTATCTCCAAGCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:32,269:301,0:0:2,0:24.7:1:32:1:1:0:60:49.167:1:0:0.1 0/1:197:2:1,1:33,162:195,2:0.0102:2,2:8.5:1:25.5:1:0.31612:4.85:60:4:0.0103:0:1.5 +2 29432982 . C T 101 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61794;LSEQ=AAAAATGTTTAATGGGGCAA;RSEQ=CATAATGAAATGCATCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:1,9:0,6:6,10:0.625:0,2:29.8:1:30.5:1:1:0:60:20:0.625:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:17:0:30:0:1:0:60:2:0.5:0:1 +2 29433205 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGGTACAAACCACGGG;RSEQ=TGGTTTCTGCCAGTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29436633 . G T 150 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02779;SOR=0.07132;LSEQ=GCCAAGGTGGGAGGATTACT;RSEQ=GAGCCCAGAAATTCGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:31:31,0:0,0:0,31:0.9688:0,1:24.1:1:30.3:1:1:0:58.2:30:1:0:1.3 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:16.8:1:27.5:1:1:0:59.8:5:0.625:0:1.2 +2 29437182 . T C 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05495;SOR=0;LSEQ=GTATTTGTACATTTGAAGTC;RSEQ=TCCCAGGTAATATGATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:1,7:0,3:3,8:0.7273:0,2:22.3:1:32.6:1:1:0:58.8:16:0.7273:0:1.4 0/0:3:0:0,0:0,3:3,0:0:0,0:14:1:31:0:1:0:60:6:1:0:0 +2 29443373 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=1.10921;LSEQ=AGCCTTGCACAAGCTCCTTG;RSEQ=GGCTGGGGCTCAGCCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:30:30,0:25,0:25,30:0.5455:1,1:30.9:1:29.5:1:1:0:60:14:0.5714:0:1.2 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:24.3:1:30:1:1:0:60:8:0.5714:0:1.3 +2 29443758 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16731;SOR=Inf;LSEQ=AGCTGAGTCTGGGCAAATCT;RSEQ=AAACTGGGAGGAACAGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:22,246:268,0:0:2,0:23.9:1:28.6:1:1:0:60:66:1:0:0.1 0/1:186:2:1,1:23,160:183,2:0.0108:2,2:28.5:1:29:1:0.24324:6.83:60:4:0.0109:0:1 +2 29444076 . G T 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGCCTCAGGCAGAAGGT;RSEQ=AAGCAAAACAACTGCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:43.3:1:29:1:1:0:54.7:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29444095 . C T 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGCAAAACAACTGCTTC;RSEQ=AAGAGAGACTGGGTGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:26.7:1:30:0:1:0:54.7:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29445113 . C T 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=9e-05;SOR=20.54953;LSEQ=AGGGGACATGCTAGGGACAA;RSEQ=ACGATTTCCCTTGGAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:1:1,0:346,61:407,1:0.0025:2,0:46:0:33:0:1:0:60:2:0.0025:0:1 0/1:228:11:9,2:178,39:217,11:0.0482:2,2:18.6:1:28.6:1:1:1.01418:60:22:0.0487:0:1.1 +2 29445458 . G T 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.24351;LSEQ=TCATACACCTCCCCAAAGGC;RSEQ=CCATGGCCCAGACCCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1347:790:352,438:235,317:552,790:0.5865:2,2:25.2:1:30.4:1:0.50227:1.08:59.9:27.214:0.5848:0:1.2 0/1:1025:263:106,157:352,408:760,263:0.2566:2,2:25.7:1:29.2:1:0.09814:1.27753:59.9:36.571:0.2545:0:1.1 +2 29445798 . T C 108 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTTTCCCCGGGGGAGG;RSEQ=TCATGCTCCTTGGGGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:6,6:0,0:0,12:1:0,2:25.1:1:30.3:1:1:0:58.9:11:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29446112 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11032;SOR=Inf;LSEQ=TGCCCATAGGGAGGGCTCTG;RSEQ=CGGCCTTTTGTGGCTAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:176,12:188,0:0:2,0:25.5:1:32.5:1:1:0:59.9:61.667:1:0:0.4 0/1:94:2:1,1:90,2:92,2:0.0213:1,2:16:1:27.5:1:0.06314:36.93876:60:4:0.0215:0:1 +2 29446138 . G T 24 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29909;SOR=3.53057;LSEQ=TTTTGTGGCTAGAGGAGTCT;RSEQ=CGGTGCTGTGATAACATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:1,0:255,53:308,1:0.0032:2,0:49:0:13:0:1:0:60:0:0:0:3 0/1:176:2:1,1:138,36:174,2:0.0114:2,2:6:1:24.5:1:0.37721:3.79485:60:4:0.0117:0:1 +2 29446141 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0473;SOR=Inf;LSEQ=TGTGGCTAGAGGAGTCTGCG;RSEQ=TGCTGTGATAACATTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:265,57:322,0:0:2,0:23.5:1:31.4:1:1:0:59.8:63.4:1:0:0.6 0/1:184:3:2,1:140,40:180,3:0.0163:2,2:28:1:26.7:1:0.53502:1.74389:60:2:0.0112:0:3 +2 29446184 . C G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.26618;LSEQ=TACACTGCACCCCTCTCCTC;RSEQ=CAGGACGGCAGCAGGGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:657:392:287,105:177,86:263,392:0.5967:2,2:25.9:1:30.4:1:0.11453:1.33:59.9:42.556:0.5947:0:1.1 0/1:496:140:92,48:230,126:356,140:0.2823:2,2:25:1:29.7:1:0.83519:1.05:60:139:0.2837:0:1.1 +2 29446202 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.22019;LSEQ=TCCCAGGACGGCAGCAGGGC;RSEQ=CTCACCGAATGAGGGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:837:54:36,18:520,262:782,54:0.0645:2,2:21.9:1:30.7:1:1:1.01:60:108:0.0655:0:1.1 0/1:619:186:122,64:262,170:432,186:0.3005:2,2:24.8:1:29.6:1:0.27804:1.24:59.7:92:0.2992:0:1.2 +2 29446701 . T C 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06829;SOR=0.88617;LSEQ=AGATGGGATTAGACCCAATA;RSEQ=GGTCTGCAGATTTTATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2658:907:463,444:888,858:1746,907:0.3412:2,2:23.9:1:31.1:1:0.93478:1.01:60:180.4:0.3418:0:1.9 0/1:1780:560:267,293:625,594:1219,560:0.3146:2,2:24.4:1:30.2:1:0.16817:1.15455:59.9:111:0.315:0:1.8 +2 29446721 . A G 360 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0128;LSEQ=TGGTCTGCAGATTTTATTAG;RSEQ=AGAAATGCCCATGAGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2649:2643:1333,1310:1,0:1,2643:0.9977:0,2:23.1:1:31.7:1:1:0:59.9:100.654:0.9985:0:1.4 1/1:1789:1519:753,766:133,129:262,1519:0.8491:2,2:24.3:1:30.4:1:0.73832:1.0488:59.9:167.778:0.8502:0:1.4 +2 29447064 . C A 176 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=101.59746;LSEQ=TCCTATAGTTGGAGAACTGC;RSEQ=AAGCCACAGAGTTGGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2736:1:1,0:1309,1422:2731,1:4e-04:2,0:1:0:26:0:0.4795:0:60:2:4e-04:0:1 0/1:1869:67:31,36:884,912:1796,67:0.0358:2,2:23.2:1:29.1:1:0.70927:1.12556:60:134:0.0363:0:1.9 +2 29447108 . G A 318 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00114;SOR=1.23649;LSEQ=CACATCATGAAAAGATCTCT;RSEQ=AATTGGTGTCTGGGGATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2643:1684:821,863:473,481:954,1684:0.6372:2,2:23.3:1:29.7:1:0.68548:1.03368:60:87.632:0.6372:0:1.1 1/0:1795:1229:589,640:271,291:562,1229:0.6847:2,2:23.5:1:28.8:1:0.91888:1.0119:59.9:75.813:0.6865:0:1.2 +2 29447253 . A G 351 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06546;LSEQ=CCTGCCCTGTTTCCCTAACC;RSEQ=CTGCCACTCCCCACCCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2671:2453:1160,1293:101,109:210,2453:0.9184:2,2:25.5:1:31.2:1:0.82934:1.03284:60:67.139:0.918:0:1.1 0/1:1823:773:390,383:536,509:1045,773:0.424:2,2:24:1:30.1:1:0.73988:1.03414:60:84.889:0.4235:0:1.2 +2 29447615 . T C 219 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=105.86467;LSEQ=ATGCAACAAGTGTTAGCTCC;RSEQ=ATTATCCTGTCCCTTTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2628:2:1,1:1347,1279:2626,2:8e-04:2,2:14.5:1:31:0:1:1.05317:60:4:8e-04:0:1.5 0/1:1754:131:71,60:792,828:1620,131:0.0747:2,2:25.5:1:31.2:1:0.27564:1.24:60:130:0.0749:0:1.2 +2 29448760 . C T 38 q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGGAAGAGATGTGGGGGC;RSEQ=GCAGGTGACCAAACAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:1,4:5,3:0.375:2,0:26.3:1:24:1:1:0:60:2:0.2857:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29449344 . CAAAAAAAAAA C 33 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=24.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAACAGTGAAACTCCGCCT;RSEQ=AAAAAAAAAAAAAAGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,0:0,2:0.5:0,0:20.5:1:33.4:1:1:0:60:4:0.5:0.25:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29449423 . G A 81 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACATGCACAGCTGCTGCT;RSEQ=TAAGGAAACCTAGGAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:9,0:5,0:5,9:0.6429:0,0:21.3:1:25.6:1:1:0:54.2:8:0.6154:0:1.9 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29449526 . C T 47 MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAAGATCCCTGTCACTGGG;RSEQ=ATGTTTAAGTGGAGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:5.3:1:30:1:1:0:60:6:0.5:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:31:0:1:0:21:2:1:0:1 +2 29449819 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.05812;LSEQ=ACGCCATCCTCAGCCAGCAC;RSEQ=GTCCCGTGGTCACAGAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1237:81:42,39:639,517:1156,81:0.0655:2,2:24.6:1:31:1:0.56513:1.14756:59.7:80:0.0657:0:1.1 0/1:909:238:134,104:365,306:671,238:0.2618:2,2:24.4:1:29.5:1:0.64938:1.08:60:476:0.2647:0:1.2 +2 29450072 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCCCATAGCCACTGGAA;RSEQ=CACAACTGTGTAGAAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:10,164:174,2:0.0114:2,2:22.5:1:32:0:0.12143:15.68:60:4:0.0116:0:1 0/0:72:0:0,0:4,68:72,0:0:2,0:22.1:1:32.2:1:1:0:60:71:1:0:0 +2 29450286 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06653;SOR=Inf;LSEQ=AGCACACATCCTGACTTCTG;RSEQ=AAAATGTGGTGACCTGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:101,4:105,0:0:1,0:26.7:1:31.6:1:1:0:59.7:34:1:0:0.1 0/1:37:2:2,0:34,1:35,2:0.0541:1,0:12.5:1:31:0:1:0:60:4:0.0556:0:1 +2 29450383 . G A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGAGACTCTGAGGTTTTA;RSEQ=CTTGGTGGGAGGACTGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:423,95:518,0:0:2,0:23.2:1:32.9:1:1:0:59.9:85.333:0.9981:0:0.1 0/1:296:24:18,6:211,59:270,24:0.0811:2,2:18.5:1:29.5:1:0.79735:1.19138:60:48:0.0816:0:1.1 +2 29450592 . AAC A 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=0.88144;LSEQ=GGGGTGGGTGCCAAAATCTT;RSEQ=ACACACACACGTCAGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:4:2,2:55,329:384,4:0.0103:2,2:20:1:29:1:0.10459:5.94:60:8:0.0104:0.0026:0.3 0/0:221:2:0,2:49,169:218,2:0.009:2,0:23:1:32:0:1:0:60:4:0.0093:0:0 +2 29450684 . G A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72837;SOR=0.6442;LSEQ=GGATGCGGGGAGGGAAGGGA;RSEQ=GCTCAGGGCACAGAGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:9:0,9:0,78:78,9:0.1034:1,0:19.3:1:32.8:1:1:0:60:18:0.1098:0:1 0/1:29:2:0,2:0,27:27,2:0.069:1,0:26.5:1:31.5:1:1:0:60:4:0.0714:0:1 +2 29451354 . A G 90 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGGAAGCTGGTGGGCTG;RSEQ=GGTAGGGAGCAGGAGTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:0,7:1:0,2:16.4:1:32.4:1:1:0:54.6:14:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29451511 . C G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07269;SOR=4.20037;LSEQ=TTATCATCGACTTTGGGGGA;RSEQ=ATCAAGAATCACATGGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:14:14,0:25,1:26,14:0.35:1,1:19:1:33.1:1:1:0:60:28:0.359:0:1.1 1/0:10:7:7,0:3,0:3,7:0.7:0,0:17.1:1:32.1:1:1:0:60:14:0.7:0:1 +2 29451557 . GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.33914;SOR=0;LSEQ=GCTGTCGCTGAGGAAGCCTG;RSEQ=AGGCAGGTCGAGAGGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:6:6,0:64,0:64,6:0.0857:1,0:28.8:1:30.4:1:1:0:56.8:12:0.0896:0.0857:0.5 0/0:18:0:0,0:18,0:18,0:0:1,0:26.3:1:28.9:1:1:0:60:17:1:0:0.4 +2 29451675 . A AGGGCG 160 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCCAGGGGAGGGCAGGGG;RSEQ=GGGCAGGGCAGGGAGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:598:35:29,6:428,128:556,35:0.0585:2,2:20.9:1:31.2:1:0.53437:1.44:59.9:70:0.0609:0.0217:0.1 0/0:300:0:0,0:218,81:299,0:0:2,0:22.3:1:28.2:1:1:0:59.9:32.222:1:0:0.1 +2 29451679 . C T 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.18959;SOR=3.82989;LSEQ=CAGGGGAGGGCAGGGGAGGG;RSEQ=AGGGCAGGGAGGTGAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:2:0,2:471,158:629,2:0.0032:2,0:1:0:24:0:0.064:0:60:4:0.0032:0:1 0/1:333:4:1,3:232,97:329,4:0.012:2,2:15.3:1:24.5:1:0.08267:7.12799:60:8:0.0123:0:1 +2 29451986 . C T 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=0;LSEQ=GCTGGCAAGGTTCAATTAGC;RSEQ=ATGCTGGCCAGAGAAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:19:2,17:45,299:344,19:0.0523:2,2:24.5:1:28.6:1:1:1.27846:60:38:0.0532:0:1.1 0/0:189:0:0,0:29,160:189,0:0:2,0:21:1:31.3:1:1:0:60:62:1:0:0.2 +2 29454701 . A G 48 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCCATTAATGAGGGAGGAG;RSEQ=GCTCAGCCGTGGAGAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:28.3:1:30.3:1:1:0:60:6:1:0:1 +2 29454901 . G GCAAGTTGGTAAAACC 103 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGGAGGCTCTAACAATT;RSEQ=CAGGGAGGGCCAGCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:11,0:6,1:7,11:0.6111:2,0:18.3:1:30:1:0.38889:0:56.5:22:0.6471:0.5:0.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29454985 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCCAAGCTCCAGGTCAG;RSEQ=AAGATGGCCTGCAGGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:66,1:67,2:0.029:1,2:19.5:1:30:1:0.05754:47.02217:60:4:0.029:0:1.5 0/0:14:0:0,0:14,0:14,0:0:1,0:16.5:1:32.9:1:1:0:60:28:1:0:0.6 +2 29455016 . C T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=4.59948;LSEQ=GCAGGGCTCCCAGGGTGCTG;RSEQ=CTGCCCTCCCTCCCTGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:27:26,1:88,0:88,27:0.2348:1,1:26.6:1:30.7:1:0.23478:0:60:54:0.2368:0:1.1 1/0:34:20:20,0:14,0:14,20:0.5882:1,1:25.2:1:30.4:1:1:0:60:40:0.6061:0:1.1 +2 29455107 . C T 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04744;SOR=7.88355;LSEQ=TGCCCTCAGGCATGCGATGG;RSEQ=ATCGGGGCCCAGCTGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:637:1:0,1:481,155:636,1:0.0016:2,0:1:0:24:0:0.2449:0:60:2:0.0016:0:1 0/1:326:4:1,3:241,81:322,4:0.0123:2,2:9.5:1:24:1:0.05409:8.85273:60:8:0.0125:0:1 +2 29455267 . A G 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.60601;LSEQ=TTGGCCCCGTAGGCCCTGCC;RSEQ=CCACCTCCGGCTGCAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1189:501:218,283:287,401:688,501:0.4214:2,2:24.8:1:31:1:0.55269:1.08:59.9:82.5:0.4209:0:1.1 1/0:805:434:191,243:164,205:369,434:0.5391:2,2:26.4:1:30:1:0.94318:1.01778:60:71.333:0.5384:0:1.1 +2 29455738 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACCCCCAAAGATTCAAG;RSEQ=TTAAGCCCTCAGCATCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:36:1:31:1:0.33333:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29455767 . G C 40 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TCAGCATCACAGTCCTGTGG;RSEQ=AGGACCTAGCAGGTGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:1,0:1,3:0.75:0,0:12.7:1:25.7:1:0.25:0:60:2:0.6667:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29456180 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05121;SOR=Inf;LSEQ=CACCAAAACTGGCTAATTTT;RSEQ=AAATTTTTTTTGGTAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:28,1:29,0:0:1,0:14.4:1:31.7:1:1:0:58.8:58:1:0:0 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:30:1:29:0:1:0:60:4:0.2222:0:1 +2 29456336 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03888;SOR=Inf;LSEQ=TCATCTTTACACGGGGATAA;RSEQ=AGCATCTGAGGTGTTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:527:0:0,0:471,55:526,0:0:2,0:23.8:1:33:1:1:0:60:74.143:1:0:0.2 0/1:271:3:2,1:224,44:268,3:0.0111:2,2:22:1:22.7:1:0.4213:2.53385:60:2:0.0075:0:2 +2 29456384 . T C 267 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGTCATGAGGCTCTGACAT;RSEQ=GCAGATGCACAGGAACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1304:370:240,130:602,332:934,370:0.2837:2,2:24.8:1:31.3:1:0.89801:1.02:60:369:0.2856:0:1.1 0/0:813:0:0,0:437,297:734,0:0:2,0:37:0:18:0:1:0:60:0:0:0:2 +2 29456865 . T TG 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAGGATAGGGAGTTTTT;RSEQ=TTTGTTTGTTTTTGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:6,5:0.4545:0,0:29.2:1:31.4:1:1:0:59:10:0.4545:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29456882 . T C 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTGTTTGTTTTTGTT;RSEQ=TTTTCACAGAGAGTGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:32.6:1:32.4:1:1:0:59:10:0.5556:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29462271 . G A 60 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGCTTCAGGTGAGGGAG;RSEQ=GGGGGAGCCTGGCCCAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:13.3:1:30:1:1:0:55.8:8:0.3636:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29462298 . T A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGCCCAACCAGGAGAT;RSEQ=CACCTGGCAGGGTGCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:9,3:0.25:0,0:39.7:1:29.7:1:1:0:60:6:0.25:0:2 0/0:2:0:0,0:2,0:2,0:0:0,0:9.5:1:32:0:1:0:60:4:1:0:0 +2 29462405 . A G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03588;SOR=0.44016;LSEQ=GGGGTGCTGGGAGTTTGCAA;RSEQ=GCTGCTGTTTAATTACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:42:41,1:67,2:69,42:0.3784:1,1:24.9:1:32.6:1:1:1.22:60:20:0.3774:0:1.1 0/1:57:12:12,0:42,3:45,12:0.2105:2,0:20.3:1:32.2:1:1:0:60:24:0.2143:0:1.5 +2 29462520 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21304;LSEQ=GGGCCTGACAGAGTGCAGAC;RSEQ=AGAAACCCCTGCTCTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:825:227:151,76:399,199:598,227:0.2752:2,2:25.4:1:30.4:1:1:1.00914:59.9:112.5:0.2778:0:1.1 0/1:602:45:24,21:341,216:557,45:0.0748:2,2:26.7:1:29.4:1:0.3418:1.38057:60:44:0.0747:0:1.2 +2 29472936 . T G 56 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCCAGGAGGCCCAGGATGT;RSEQ=GTGGATCCCGGAGGCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:7.3:1:28.3:1:1:0:60:8:1:0:1.5 +2 29473851 . G T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00381;SOR=0.33733;LSEQ=TATACCCCCTATGGGCCTGA;RSEQ=TCTGTTGCCTTTGAACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:56:55,1:106,5:111,56:0.3353:1,1:23.4:1:32.1:1:0.66476:2.58:60:112:0.3394:0:1 0/1:69:10:9,1:58,1:59,10:0.1449:1,2:17.2:1:30.5:1:0.27067:6.16623:60:20:0.1493:0:1.1 +2 29473898 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06561;SOR=Inf;LSEQ=CTGGGCACCCCAGGAACATG;RSEQ=ACCCATAGGCAAGACTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:251,36:287,0:0:2,0:24:1:32.4:1:1:0:60:94.667:1:0:0.2 0/1:195:3:2,1:153,38:191,3:0.0154:2,2:13.3:1:27:1:0.49198:2.00456:60:6:0.0158:0:1 +2 29474176 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.13296;SOR=Inf;LSEQ=GTCACTCATGTGGCCAGGCC;RSEQ=TCCCTCCTCCAGGGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:37,281:318,0:0:2,0:25.5:1:32.5:1:1:0:59.9:23.462:1:0:0.1 0/1:183:2:1,1:31,150:181,2:0.0109:2,2:35.5:1:31:1:0.31994:4.78:60:4:0.0112:0:1 +2 29497967 . G A 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGAGCTGAACCCTTACCT;RSEQ=TAGGGTCAAAGATGGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1178:0:0,0:734,441:1175,0:0:2,0:25.8:1:32.1:1:1:0:60:60.842:0.9983:0:0.1 0/1:921:49:29,20:525,345:870,49:0.0532:2,2:23.1:1:28.1:1:0.88161:1.0494:60:48:0.0526:0:1.1 +2 29498181 . ACAGT A 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=CACTGAGGGAGGTGGGAGAG;RSEQ=CAGGCTTAGGCTGAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:243,199:442,0:0:2,0:23.9:1:32.4:1:1:0:60:72.667:1:0:0.8 0/1:278:12:6,6:162,104:266,12:0.0432:2,2:28.5:1:32.2:1:0.54947:1.55508:60:24:0.0438:0.0036:0.9 +2 29498210 . A G 298 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.1112;LSEQ=CTTAGGCTGAGGAGGGGACA;RSEQ=TGAGGCCATGGGCCATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:547:544:338,206:0,1:1,544:0.9945:0,2:22.6:1:32.8:1:0.37982:0:60:180.333:0.9963:0:1.1 1/1:359:342:216,126:8,9:17,342:0.9526:2,2:23.7:1:31:1:0.20462:1.92:60:113:0.9549:0:1.1 +2 29498217 . C T 41 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02336;SOR=Inf;LSEQ=TGAGGAGGGGACAATGAGGC;RSEQ=ATGGGCCATGGGGGTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:364,234:598,0:0:2,0:22.5:1:31.2:1:1:0:60:27.476:1:0:1 0/1:386:4:1,3:235,147:382,4:0.0104:2,2:9.3:1:20.8:1:0.30346:4.77675:60:3:0.0079:0:1.5 +2 29499956 . A G 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGTGTCAAGAGCAGAAAACC;RSEQ=GAGCAGGGTGGCACTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:31.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:29.5:1:1:0:60:4:1:0:1.5 +2 29519622 . C T 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGTGTGCACGTGCGTGCACG;RSEQ=GCACATATCGGTGTGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:89:89:89,0:0,0:0,89:1:0,1:21.8:1:30.1:1:1:0:60:43.5:1:0:1.2 1/0:48:33:32,1:15,0:15,33:0.6875:1,1:24.8:1:29.7:1:1:0:60:66:0.7174:0:1 +2 29519631 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=0.13335;SOR=Inf;LSEQ=GTGCGTGCACGCGCACATAT;RSEQ=GGTGTGTGGGCACATCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:93,0:93,0:0:1,0:24.8:1:32.5:1:1:0:60:92:1:0:1.1 0/1:54:2:2,0:51,1:52,2:0.037:1,0:26:1:29.5:1:1:0:60:4:0.0392:0:1 +2 29519715 . T C 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTTTTCATTTTAGCTGA;RSEQ=AGAGGAGAAGGGTATTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:0:0,0:374,140:514,0:0:2,0:22.8:1:29.9:1:1:0:60:33.267:1:0:0.2 0/1:381:16:10,6:250,115:365,16:0.042:2,2:24.1:1:31.4:1:0.59353:1.30345:60:32:0.0423:0:1.3 +2 29519851 . C A 175 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02257;LSEQ=CATCCTGCCTTGCTCCTTCC;RSEQ=GGTTTTGTTCTCCACTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1147:51:22,29:523,573:1096,51:0.0445:2,2:25.6:1:30.9:1:0.56788:1.20296:59.6:50:0.0439:0:1.1 0/0:954:1:1,0:439,512:951,1:0.001:2,0:1:0:25:0:0.46218:0:60:2:0.0011:0:1 +2 29519934 . G A 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08101;SOR=4.01737;LSEQ=ACATTCGGAGCTGTGAGGGC;RSEQ=AGAAGAGTCAGAGGACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:2:2,0:171,427:598,2:0.0033:2,0:1:0:27:1:0.08279:0:60:4:0.0034:0:1 0/1:452:6:3,3:151,295:446,6:0.0133:2,2:21.7:1:26.2:1:0.41431:1.95:60:5:0.0113:0:1.2 +2 29519951 . A G 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03157;SOR=Inf;LSEQ=GGCGAGAAGAGTCAGAGGAC;RSEQ=AGGTATGATTGCTGAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:92,329:421,0:0:2,0:23.4:1:31:1:1:0:59.9:104.25:1:0:0.1 0/1:309:4:2,2:83,222:305,4:0.0129:2,2:31.5:1:29.5:1:0.30418:2.66:60:8:0.0131:0:2 +2 29520085 . G A 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCTCACCAAGAGGCTTTCA;RSEQ=TGAAGTTCAAGTATCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:35:0,35:0,0:0,35:0.9722:0,1:26.9:1:32.6:1:1:0:60:70:0.9722:0:1.1 1/1:14:14:0,14:0,0:0,14:1:0,1:20.6:1:31.3:1:1:0:60:28:1:0:1 +2 29540686 . C CCA 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGGGCGCCAGTCCCTCCAC;RSEQ=CACACCAATGAGATAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:30:1:32:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29541104 . C T 251 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.007;LSEQ=AGCTAGGCTACTTTCTTAAT;RSEQ=TGGGTTCCGGAAGTGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:293:292:241,51:0,0:0,292:0.9966:0,2:22.1:1:30.7:1:1:0:60:96.333:1:0:1 1/0:218:146:114,32:51,21:72,146:0.6697:2,2:19.4:1:29.2:1:0.24516:1.46:60:35.5:0.6698:0:1.1 +2 29543663 . T C 337 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02454;LSEQ=TTTAGGGTCCTGACCTGCCA;RSEQ=TGAGGAGTGTGGGGTGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1371:1364:696,668:0,3:3,1364:0.9949:0,2:26.3:1:32.4:1:0.118:0:59.9:47.714:0.9948:0:1.1 1/1:1086:898:466,432:98,88:186,898:0.8269:2,2:25.8:1:31.2:1:0.87207:1.03236:59.9:88.8:0.8299:0:1.2 +2 29543699 . G A 151 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.15893;LSEQ=GACAGTGTGCCTTGGGTCCA;RSEQ=CCACAGAAGCCATCTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1263:4:3,1:555,704:1259,4:0.0032:2,2:16:1:29:1:0.32702:3.80:60:8:0.0032:0:1.8 0/1:971:39:20,19:451,481:932,39:0.0402:2,2:18.9:1:28.6:1:0.74621:1.12:60:78:0.0408:0:1.9 +2 29543829 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14184;SOR=Inf;LSEQ=TGCCAAGTCGAATTAGCCAG;RSEQ=CATGACCAAATTATCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:11,205:216,0:0:2,0:22.1:1:32.7:1:1:0:59.8:107:1:0:0.1 0/1:131:2:1,1:5,124:129,2:0.0153:1,2:33:0:28.5:1:0.08984:22.73:60:4:0.0156:0:1 +2 29544336 . C T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCCTTTCTCTCCCAACC;RSEQ=GCTTGCAGTTAAGTGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:31.3:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29544512 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGGGTGACACTATATTGA;RSEQ=GGAGGAGCCTCTGCCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29550841 . G C 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGCCGGAGCTGGGGTGCATG;RSEQ=AGGAGGGAGAGGATGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:26:1:32:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:12:0:33:0:1:0:60:2:1:0:0 +2 29551161 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0.4348;LSEQ=CCTGGGATAATGGGGACAAC;RSEQ=GGGTTATGAGCATGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:146:113,33:253,81:334,146:0.3035:2,2:25.5:1:30.8:1:0.72791:1.10:60:72:0.3019:0:1.1 0/1:289:46:32,14:171,72:243,46:0.1592:2,2:27.8:1:28.9:1:1:1.03891:60:14.333:0.1503:0:1.2 +2 29551401 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.1275;SOR=Inf;LSEQ=TTTGCATGGCCCCAGGCAGC;RSEQ=GCTGGCCTGATGGGTTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:55,279:334,0:0:2,0:23:1:32:1:1:0:60:65.8:1:0:0.1 0/1:186:2:1,1:37,147:184,2:0.0108:2,2:18.5:1:29:1:0.36774:3.93:60:4:0.0109:0:1 +2 29551493 . G C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78453;SOR=1.13472;LSEQ=AAGGCCTGATTGAGACATCT;RSEQ=CATCTCCATCTGGCCAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:12:0,12:0,50:50,12:0.1935:1,0:21.8:1:31.7:1:1:0:60:24:0.1935:0:1 0/1:28:6:0,6:0,22:22,6:0.2143:1,0:34.5:1:30.2:1:1:0:60:12:0.2143:0:1 +2 29606520 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29194;SOR=0;LSEQ=CATAAGTGTGCACATTCCCA;RSEQ=CCAAACATGGTTGCAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:2,1:155,13:168,3:0.0175:2,2:17.3:1:29.3:1:0.22728:5.8417:60:6:0.0176:0:1 0/0:104:0:0,0:93,11:104,0:0:2,0:23.5:1:31.1:1:1:0:60:19.8:1:0:0.2 +2 29606533 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1589;SOR=Inf;LSEQ=ATTCCCAGCCAAACATGGTT;RSEQ=CAGGTTATTGACACATCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:190,28:218,0:0:2,0:24:1:32.1:1:1:0:60:35.333:1:0:0.1 0/1:145:2:1,1:119,24:143,2:0.0138:2,2:8.5:1:27:1:0.31609:4.87862:60:4:0.0141:0:1 +2 29606824 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02469;SOR=Inf;LSEQ=TGTCCTTGCAGGGACTTCAG;RSEQ=ACTCACATTCTTCATGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:1,128:129,0:0:1,0:26.2:1:32.7:1:1:0:60:128:1:0:0.1 0/1:54:3:0,3:0,51:51,3:0.0556:1,0:22.7:1:28.7:1:1:0:60:6:0.0556:0:1 +2 29754721 . T C 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGTCACAGACTCTGGAAATG;RSEQ=GTAACCAAAAGCCAAATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:334,84:418,0:0:2,0:23.2:1:30:1:1:0:60:417:1:0:0.1 0/1:276:39:26,13:170,66:236,39:0.1413:2,2:20.2:1:30.2:1:0.56682:1.28669:60:38:0.1387:0:1.1 +2 29755018 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26458;SOR=0;LSEQ=GAAAACGAATCTGCAGATGT;RSEQ=TTCAGGTAAGACCAGCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:45,189:234,3:0.0127:2,2:18.3:1:30.7:1:0.47818:2.09:60:6:0.013:0:1 0/0:176:0:0,0:46,130:176,0:0:2,0:21.8:1:31.2:1:1:0:60:175:1:0:0.1 +2 29917150 . C A 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACCACAGGAAGCATCACA;RSEQ=CAAGCAAATGTGTCGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:29.8:1:27.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 29917621 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30072;SOR=3.52009;LSEQ=AGGTTTCAAAGTAAACAGAG;RSEQ=AGAACAGGAGTGAAGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:1:1,0:196,9:205,1:0.0049:1,0:24:0:32:0:1:0:60:2:0.005:0:1 0/1:118:2:2,0:111,5:116,2:0.0169:1,0:10.5:1:29.5:1:1:0:60:4:0.0171:0:1 +2 29917940 . C G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00039;SOR=2.36614;LSEQ=CCAAACGTGACTTTTCAGCC;RSEQ=CCTCCACTCCACACTAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:366:281:53,228:19,65:84,281:0.7678:2,2:23.3:1:31.9:1:0.43872:1.25669:60:92.667:0.768:0:1.1 1/1:212:188:45,143:6,18:24,188:0.8868:2,2:22.6:1:30.3:1:1:1.05897:60:46:0.8846:0:1.1 +2 29918087 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03252;SOR=Inf;LSEQ=TCTTTCTGTAACTCATATTA;RSEQ=GGGAGATGTTCTCAGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:0,34:34,0:0:1,0:20.8:1:30.4:1:1:0:58.9:68:1:0:0.2 0/1:8:2:0,2:0,6:6,2:0.25:0,0:26.5:1:31.5:1:1:0:60:4:0.25:0:1 +2 29940332 . A G 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00845;SOR=0;LSEQ=GAAAGACTTCTTTTGCATAT;RSEQ=GGGAGCTGAGGGAATGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:12:12,0:82,1:83,12:0.1263:1,0:27.6:1:31.7:1:1:0:60:11:0.1222:0:1.2 0/0:52:0:0,0:51,1:52,0:0:1,0:18.7:1:28.7:1:1:0:60:104:1:0:0.1 +2 29940400 . G T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09243;SOR=Inf;LSEQ=TCACAGAGTCCTTATTATGA;RSEQ=ATAGTGACAGTGTATCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:273,59:332,0:0:2,0:23.2:1:32.6:1:1:0:60:26.667:1:0:0.1 0/1:275:3:1,2:209,63:272,3:0.0109:2,2:8:1:25:1:0.14015:6.57646:60:6:0.011:0:1 +2 29940529 . A T 297 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30881;SOR=1.12962;LSEQ=AAATAATCAGGAGAAGGAGA;RSEQ=GGCATGTTTGTTGGTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1153:912:414,498:120,120:240,912:0.791:2,2:27.4:1:30.3:1:0.21646:1.2027:60:56:0.7894:0:1.1 1/1:844:684:313,371:72,87:159,684:0.8104:2,2:25.7:1:29.5:1:0.92979:1.02:60:96.714:0.8118:0:1.2 +2 29940820 . C T 108 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGATCTCTGGGAGATGAA;RSEQ=TAGAAGCCAGGGCACTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:0,12:0,1:1,12:0.9231:0,0:26.9:1:30.4:1:1:0:57.6:24:0.9231:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 30142798 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16428;SOR=Inf;LSEQ=GAAGTGAAGATTATTTAATG;RSEQ=TTGCATATCAATGTGACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:173,17:190,0:0:2,0:23.1:1:31.5:1:1:0:59.9:46.5:1:0:0.1 0/1:130:2:1,1:110,18:128,2:0.0154:2,2:20.5:1:31:0:0.27191:5.97512:60:4:0.0157:0:1 +2 30142801 . G T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51786;SOR=0;LSEQ=GTGAAGATTATTTAATGGTT;RSEQ=CATATCAATGTGACTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:180,19:199,2:0.01:2,2:5.5:1:30.5:1:0.18955:9.25942:60:4:0.01:0:1 0/0:135:0:0,0:114,20:134,0:0:2,0:22.5:1:31:1:1:0:60:43.667:0.9924:0:0.2 +2 30142817 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.13866;SOR=Inf;LSEQ=GGTTGCATATCAATGTGACT;RSEQ=AAAACACTAAATCCCGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:241,43:284,0:0:2,0:23.2:1:29:1:1:0:60:283:1:0:0.1 0/1:169:2:1,1:132,35:167,2:0.0118:2,2:32.5:1:30:1:0.38166:3.73289:60:4:0.0121:0:1.5 +2 30142837 . C T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.38362;SOR=2.35651;LSEQ=AAAAACACTAAATCCCGGCA;RSEQ=ACTCAGGCGGGAGCTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:2:0,2:314,84:398,2:0.005:2,0:1:0:23.5:1:0.0458:0:60:4:0.0051:0:1 0/1:256:3:1,2:177,76:253,3:0.0117:2,2:16.3:1:25.3:1:0.22095:4.62637:60:6:0.012:0:1 +2 30143420 . G A 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14332;SOR=5.19936;LSEQ=CTCCCGGGGCTGCAGCGGCG;RSEQ=CCCCGCAGCTGGGGAGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:1,0:123,268:391,1:0.0026:2,0:1:0:26:0:0.31633:0:60:2:0.0026:0:1 0/1:228:3:3,0:74,151:225,3:0.0132:2,0:29:1:25.3:1:0.03752:0:60:6:0.0133:0:1.3 +2 30143450 . C T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13332;SOR=5.44027;LSEQ=TGGGGAGCCCGCGCGCTGGC;RSEQ=GGTCCCCATCCCGGAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:1:0,1:88,196:284,1:0.0035:2,0:1:0:25:0:1:0:60:2:0.0036:0:2 0/1:159:3:1,2:46,110:156,3:0.0189:2,2:24.3:1:29:1:1:1.19:60:6:0.0194:0:1.7 +2 30143499 . G C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGGAAAGCAGCAGCGGCAG;RSEQ=AGCCACAGGAGCCCGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:218:79,139:0,0:0,218:1:0,2:25.9:1:32.5:1:1:0:60:217:1:0:1.1 1/1:136:122:48,74:6,8:14,122:0.8971:2,2:26.5:1:31.3:1:0.78195:1.155:60:244:0.8971:0:1.1 +2 30143519 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16117;SOR=Inf;LSEQ=GAGCCACAGGAGCCCGATGG;RSEQ=TCCCATCCCGCCGGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:76,129:205,0:0:2,0:25:1:32.8:1:1:0:60:101.5:1:0:0.9 0/1:138:2:1,1:54,82:136,2:0.0145:2,2:18.5:1:27.5:1:1:1.51:60:4:0.0149:0:1.5 +2 30143539 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51461;SOR=0;LSEQ=CTCCCATCCCGCCGGAGGAG;RSEQ=CCGTTTACACTGCTCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:61,107:168,2:0.0118:2,2:37:1:29.5:1:1:1.75:60:4:0.0118:0:2 0/0:118:0:0,0:48,70:118,0:0:2,0:27.8:1:30.5:1:1:0:60:38.333:1:0:0.8 +2 30433204 . T G 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12131;SOR=0;LSEQ=TTATGATGGGGAACATTTCA;RSEQ=TCTCAAAAAAAAAAAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:7,4:11,5:0.3125:2,2:40.8:1:33:1:1:1.15538:60:10:0.3333:0:1.6 0/0:10:0:0,0:6,4:10,0:0:2,0:24.1:1:29.4:1:1:0:60:20:1:0:0.1 +2 30433208 . C CA 94 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0.83876;LSEQ=GATGGGGAACATTTCATTCT;RSEQ=AAAAAAAAAAAAAATCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:4,4:7,3:10,8:0.4444:2,2:25.3:1:31.4:1:0.63047:2.22221:59.8:16:0.4706:0.1111:1 0/1:10:4:3,1:2,2:4,4:0.4:2,2:39.5:1:28.5:1:1:2.60:60:8:0.4:0:0 +2 31513661 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=Inf;LSEQ=TTGGCTGGAACTGCCATCTT;RSEQ=CAGTAATTTGCCAAAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:11,0:0:2,0:33.3:1:31.8:1:1:0:60:22:1:0:0.1 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:23:1:27.5:1:1:1.18321:60:4:0.1818:0:1 +2 31513677 . A C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.48;SOR=Inf;LSEQ=TCTTCCAGTAATTTGCCAAA;RSEQ=TAATGAACACAAAGGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:13,0:0:2,0:34.5:1:30.3:1:1:0:60:26:1:0:0.2 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:30:1:27:1:1:1.18:60:4:0.1667:0:1 +2 31514140 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22414;SOR=0;LSEQ=AATGGGTACTGTTCAGAAAG;RSEQ=AAGGCCCTACAAGTGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:14:0:31:1:1:1.36624:60:4:0.1429:0:1.5 0/0:15:0:0,0:9,6:15,0:0:2,0:22.3:1:30.3:1:1:0:60:30:1:0:0.2 +2 34654129 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16554;LSEQ=TACTTATTAAAGGCAGCAAT;RSEQ=CTAGCAGTGTACTTAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:360:209:107,102:76,75:151,209:0.5806:2,2:28.7:1:31.5:1:0.91507:1.04:60:33.833:0.5734:0:1.1 0/1:328:61:31,30:135,132:267,61:0.186:2,2:26.5:1:30.2:1:1:1.01:60:122:0.1865:0:1.1 +2 34654198 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20711;SOR=Inf;LSEQ=GATTAAATTTTCATTTTTGG;RSEQ=CAGGTGCAGTGGCTCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:57,121:178,0:0:2,0:23.5:1:31.3:1:1:0:60:88:0.9944:0:0.4 0/1:150:2:1,1:51,97:148,2:0.0133:2,2:25.5:1:28.5:1:1:1.89:60:4:0.0135:0:1 +2 36353114 . A G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.627;LSEQ=ACACTTACCCTAAACAGAGC;RSEQ=CAGTCTTTTCATCCACCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:149:77,72:142,176:318,149:0.3184:2,2:27.5:1:30.8:1:0.16477:1.32:60:73.5:0.3161:0:1.1 1/0:439:332:160,172:54,53:107,332:0.7563:2,2:25.9:1:30.4:1:0.73893:1.09506:59.9:82:0.754:0:1.2 +2 36526768 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19811;SOR=Inf;LSEQ=TCTTGGCAAGAATCTTGCCC;RSEQ=TACCTTGTTTATTTACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:156,79:235,0:0:2,0:21:1:31.6:1:1:0:59.8:470:1:0:0.1 0/1:189:2:1,1:125,61:186,2:0.0106:2,2:14.5:1:28.5:1:0.552:2.04076:60:4:0.0106:0:1 +2 36526875 . C A 43 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23701;LSEQ=CTTCCTTTTTGGACAGTACC;RSEQ=ATTCCCTTGATGTCTACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:115,182:297,3:0.01:2,2:9.7:1:28.3:1:0.56266:3.15:30.3:6:0.0105:0:1.3 0/1:243:3:2,1:92,148:240,3:0.0123:2,2:11.7:1:27.7:1:0.56121:3.20:30:6:0.0126:0:1.7 +2 38467056 . C T 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00175;SOR=Inf;LSEQ=GGGTTTTTCTAGACCTCCCC;RSEQ=ATCCCCAAGGGTCTGACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:27,0:27,0:0:1,0:24.4:1:30.9:1:1:0:60:26:1:0:0.1 0/1:17:6:6,0:11,0:11,6:0.3529:0,0:25.3:1:30.8:1:1:0:60:12:0.3529:0:2.2 +2 38467073 . C G 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=CCCCATCCCCAAGGGTCTGA;RSEQ=GCAGGGCCCTGGTTTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:38,0:0:1,0:24.3:1:32.7:1:1:0:60:76:1:0:0.1 0/1:22:8:8,0:14,0:14,8:0.3636:1,0:27.9:1:31.9:1:1:0:60:16:0.3636:0:1.9 +2 38467176 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17306;SOR=Inf;LSEQ=GAGGGATGCTGGGTCCCAAG;RSEQ=GTCCAAAGGTGCCCTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:174,85:259,0:0:2,0:26:1:31.2:1:1:0:60:36:1:0:0.1 0/1:185:2:1,1:124,59:183,2:0.0108:2,2:17:1:25:1:0.54465:2.09254:60:4:0.0109:0:1.5 +2 38467256 . G A 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATCTCAACTCTTTCTTGAGC;RSEQ=CGTTGAGATGAATTTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:172,209:381,0:0:2,0:25.8:1:31:1:1:0:60:380:0.9974:0:0.1 0/1:367:54:23,31:147,166:313,54:0.1471:2,2:25.9:1:29:1:0.65787:1.19298:60:108:0.1484:0:1.1 +2 38467258 . G A 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTCAACTCTTTCTTGAGCGC;RSEQ=TTGAGATGAATTTTGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:170,207:377,0:0:2,0:25.8:1:31:1:1:0:60:124.667:1:0:0.1 0/1:366:16:6,10:162,188:350,16:0.0437:2,2:29.3:1:30.4:1:0.61098:1.43478:60:32:0.0442:0:1.3 +2 38978149 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGCTTTAGGCTGGATTGGG;RSEQ=CACAAAAATGCCCAAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:10,0:0:2,0:17.7:1:29.5:1:1:0:60:9:1:0:0 0/1:22:2:1,1:18,2:20,2:0.0909:2,2:24.5:1:25:1:0.25974:7.54971:60:4:0.0909:0:1 +2 39095413 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.4929;SOR=Inf;LSEQ=TTTCTGTTGCCGCCACCTCC;RSEQ=CCACCACCACCACCGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:15,14:29,0:0:2,0:22.7:1:29.8:1:1:0:59.4:58:1:0:0.2 0/1:32:2:1,1:15,14:29,2:0.0625:2,2:34:1:28:1:1:1.06901:60:4:0.0645:0:1 +2 39841994 . G C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31943;SOR=1.3499;LSEQ=ATTTCAGCGTGTACACATAC;RSEQ=CAGATCTGGTTAATTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:43:41,2:85,7:92,43:0.3162:2,1:25.7:1:31.8:1:0.71845:1.68:60:86:0.3209:0:1 0/1:91:35:34,1:55,1:56,35:0.3846:1,1:23.8:1:30.7:1:1:1.60874:60:34:0.382:0:1.1 +2 39842140 . G C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-04;SOR=1.49616;LSEQ=AGGGTTGGGCTGTCCGTGAC;RSEQ=ATTTTTCCTGTGATGTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:710:214:97,117:227,266:493,214:0.3014:2,2:28.9:1:31.5:1:0.86987:1.0293:60:213:0.3034:0:1.1 0/1:655:257:118,139:187,201:388,257:0.3924:2,2:25.1:1:30.7:1:0.57406:1.09576:60:127.5:0.3929:0:1.2 +2 39842175 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01963;SOR=Inf;LSEQ=GTGAACAGGGTCCATCTATG;RSEQ=CAAGAGAGAATGAGGTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:0:0,0:195,368:563,0:0:2,0:24.7:1:32:1:1:0:60:280.5:0.9982:0:0.3 0/1:474:5:4,1:187,282:469,5:0.0105:2,2:13.8:1:25.8:1:0.16296:6.01:60:10:0.0108:0:1 +2 39842241 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.51059;SOR=0;LSEQ=ACAGAAAGAAGTAGATCTGA;RSEQ=AGAGGCAGAGAAAAAGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:13,151:164,2:0.012:2,2:31:1:28.5:1:0.16203:11.23:60:4:0.0123:0:1 0/0:121:0:0,0:16,104:120,0:0:2,0:23.9:1:30.4:1:1:0:60:19:0.9913:0:0.1 +2 39842288 . CAGATAGAG C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=2;SSF=0.42016;SOR=0.58756;LSEQ=AGATAGAGATGATAGATAGA;RSEQ=AGATAGACAGATAGACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:13:0,13:1,40:41,13:0.2407:1,1:22.2:1:31.1:1:1:0:57.5:12:0.2264:0.0926:1.2 0/1:32:5:0,5:0,27:27,5:0.1563:1,0:26.4:1:30.6:1:1:0:60:10:0.1613:0.0625:1.4 +2 39842361 . T G 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.41248;SOR=2.51158;LSEQ=AGAAAGTGAGAATGAGCCCT;RSEQ=GTGAATAGTTTGAGATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:14,9:0.3913:1,0:31.2:1:31:1:1:0:60:18:0.3913:0:1.1 1/0:8:5:1,4:0,3:3,5:0.625:0,2:22.6:1:31.8:1:1:0:60:10:0.625:0:1.8 +2 40904636 . A T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.11319;SOR=0;LSEQ=GAGTTGGGCGACATGGCTTC;RSEQ=CCCCTTTCTAGGTCCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:15,17:0,0:0,32:1:0,2:22.9:1:30.3:1:1:0:27.6:64:1:0:1.2 1/1:32:28:16,12:0,4:4,28:0.875:0,2:21.9:1:28.3:1:0.10122:0:27.9:27:0.871:0:1.1 +2 40904919 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAAGTAGCTAAAGCGGTCAT;RSEQ=GCCCAATTCCCGACAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:5:0:29:0:1:0:52:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:27:1:1:0:56:4:1:0:1 +2 41449888 . A G 49 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03497;SOR=0;LSEQ=GCTGGAATCTGCTTAAGCCT;RSEQ=CCAAACTCCCAGTGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:34:1:31.3:1:1:0:60:6:1:0:1 0/1:10:2:1,1:5,3:8,2:0.2:2,2:22:1:31:1:1:1.58108:60:4:0.2:0:1 +2 41450141 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51087;SOR=0;LSEQ=GCCCAAAATACACCAGCTGT;RSEQ=GCAGTCTGTGGTGAGAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:38:0:32:1:1:1.15:60:4:0.1333:0:1.5 0/0:9:0:0,0:5,4:9,0:0:2,0:35.7:1:31.8:1:1:0:60:18:1:0:0.2 +2 41450292 . A G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31373;SOR=0.2328;LSEQ=GAGCCACTAGCGGGAGGAGC;RSEQ=GCTGCAGTCTCTGCAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:1,0:1,7:0.875:0,0:24:1:31.7:1:1:0:52.6:14:0.875:0:1 1/0:10:6:4,2:3,1:4,6:0.6:2,2:18.8:1:26:1:1:1.44135:54.8:5:0.5556:0:1 +2 41450618 . A T 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTAGGCACAGGAGCAAG;RSEQ=CAGATGAACAGGGGCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:6,4:0,0:0,10:1:0,2:20.8:1:29.9:1:1:0:60:20:1:0:1 1/1:4:4:2,2:0,0:0,4:1:0,2:31:1:28.3:1:1:0:60:8:1:0:1.5 +2 41450696 . A AAAAC 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.17037;SOR=Inf;LSEQ=GAAGGACCTGACTATTGAAA;RSEQ=AAACAAACAAACAAGCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:27,5:32,0:0:2,0:20.8:1:29.9:1:1:0:60:15:1:0:0.3 0/1:23:2:2,0:20,1:21,2:0.087:1,0:17.5:1:31.6:1:1:0:60:4:0.087:0:1 +2 41450721 . T A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04579;SOR=Inf;LSEQ=AAACAAACAAGCTGAAAGTG;RSEQ=CAACAACAGCATCACCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:37,17:54,0:0:2,0:23.5:1:29.4:1:1:0:60:26:1:0:0.1 0/1:48:4:3,1:33,11:44,4:0.0833:2,2:31.5:1:27.3:1:1:1:60:8:0.0833:0:1 +2 41450758 . G A 67 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28678;SOR=2.72525;LSEQ=ACCACCAACAACAAAAGGCC;RSEQ=CACAAAAACGCCATTCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:47,37:84,2:0.0233:2,2:16:0:29:1:1:1.2667:54:4:0.0235:0:1 0/1:98:6:3,3:49,43:92,6:0.0612:2,2:16.7:1:26.2:1:1:1.13801:52.5:12:0.0645:0:1.2 +2 41450783 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.5004;SOR=Inf;LSEQ=AAAACGCCATTCAAGGGTCA;RSEQ=CAGCCTCAAAGACCAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:44,46:90,0:0:2,0:28:1:32.5:1:1:0:59.1:89:1:0:0.2 0/1:105:2:1,1:51,52:103,2:0.019:2,2:38:1:27:1:1:1.02:60:4:0.0194:0:1 +2 41764773 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14486;SOR=Inf;LSEQ=TTATTTGACATTCTCCTGCT;RSEQ=TAGCTCCATCTTATGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:192,22:214,0:0:2,0:23.2:1:32.2:1:1:0:59.9:29.571:1:0:0 0/1:132:2:1,1:104,26:130,2:0.0152:2,2:13.5:1:26.5:1:0.36849:3.94405:60:4:0.0154:0:1 +2 41764905 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.27546;LSEQ=TGACTCTCCGAATCAAAACC;RSEQ=TCATCCAAATAACCATACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:478:217:84,133:97,163:260,217:0.454:2,2:26:1:29.4:1:0.77671:1.06:59.8:11.765:0.4566:0:1.4 0/1:462:86:38,48:170,206:376,86:0.1861:2,2:24.9:1:29.7:1:0.90471:1.04233:60:20.5:0.1843:0:1.3 +2 42758255 . C A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGGGATTACATGTGTGAG;RSEQ=TACCATGCCCGGCCCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:31:1:1:0:60:4:1:0:1 +2 42760158 . G T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24873;SOR=0;LSEQ=CCTTGTTTGTTTACAGCAAT;RSEQ=CCAACAGCATGCTGGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:1,2:103,72:175,3:0.0168:2,2:11.7:1:26.3:1:0.57114:2.84422:54.7:2:0.0122:0:4.7 0/0:167:0:0,0:102,64:166,0:0:2,0:24.8:1:30.5:1:1:0:57.7:19.75:1:0:0.6 +2 42760199 . C T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24799;SOR=0;LSEQ=ATTGCAGACTTCCACTTTTG;RSEQ=CATGGTAACACTTGTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:3:1,2:95,78:173,3:0.017:2,2:27.3:1:25:1:0.59158:2.42386:52:2:0.0127:0:4.3 0/0:171:0:0,0:101,70:171,0:0:2,0:28.5:1:30.3:1:1:0:55.6:27.5:1:0:0.8 +2 42760201 . A G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97567;LSEQ=TGCAGACTTCCACTTTTGCC;RSEQ=TGGTAACACTTGTGGGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:41:24,17:68,61:129,41:0.2384:2,2:35.4:1:28:1:0.59079:1.26:59.2:5.833:0.2273:0:1.7 0/1:171:40:23,17:78,52:130,40:0.2339:2,2:30.8:1:28.1:1:0.85445:1.10802:59.5:12.333:0.2284:0:1.6 +2 42760390 . G A 25 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=3.10575;LSEQ=CTGCGCCCGCCACCATGCCC;RSEQ=GCTAATTTTTCTATTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:45:0:34:0:1:0:52:2:0.3333:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:21.5:1:25.5:1:1:0:47:4:0.6667:0:2 +2 43081218 . CGT C 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.15097;SOR=0;LSEQ=TGTGTGTTTACATGTGTCTG;RSEQ=GTGTGTGTGTTGTGCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:3,2:20,15:35,5:0.125:2,2:37:1:30.8:1:1:1.12:60:10:0.125:0:0.2 0/0:22:0:0,0:13,9:22,0:0:2,0:32.1:1:30:1:1:0:59.9:44:1:0:0.1 +2 43082062 . G A 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGACCCGGGTCCAGAGGA;RSEQ=GGGAAAAGAGGCGGCTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:43:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:32:1:1:0:60:4:1:0:1.5 +2 43083070 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGTGGATTATTCTAGCC;RSEQ=GTGAATGTGGGGCCGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 43451509 . G A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGGCAGGCGGCGGCCAGG;RSEQ=TCGAGGCTGGGAGACTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:31:1:1:0:60:4:1:0:1 +2 43452183 . A G 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCTGAGGCTGTGGTGCA;RSEQ=CTTGGGCCGCGGCTCCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:18:0:35:0:1:0:60:2:1:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:23.5:1:30.5:1:1:0:60:4:0.6667:0:1 +2 43951871 . A G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.86565;SOR=1.03574;LSEQ=ACAATATTTTTCTTTTCAAT;RSEQ=AGCAGTTTTGAGACTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:137:96,41:115,62:177,137:0.4349:2,2:23.6:1:32.1:1:0.3964:1.26:60:136:0.4359:0:1.8 0/1:257:114:78,36:94,47:141,114:0.4436:2,2:26.4:1:31.3:1:0.78944:1.08:60:228:0.4471:0:1.7 +2 43951922 . T A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7328;SOR=1.05247;LSEQ=CTTTTGATCCAATAACTTAA;RSEQ=CAAATTGCTGATCAATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:217:112,105:134,131:265,217:0.4502:2,2:27.4:1:30.3:1:0.85486:1.04:60:216:0.45:0:1.5 0/1:391:181:93,88:108,102:210,181:0.4629:2,2:25.9:1:28.9:1:1:1.00189:60:89.5:0.4674:0:1.5 +2 43952068 . G A 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0017;SOR=0;LSEQ=TTCTTGTTCTCAAGGACAAG;RSEQ=AGATCTGGGTCATGGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:10:1,9:1,51:52,10:0.1613:1,2:18.2:1:30.5:1:0.29878:5.43:60:20:0.1639:0:1 0/0:53:0:0,0:2,51:53,0:0:1,0:20.4:1:30.7:1:1:0:60:52:1:0:0.1 +2 44311676 . C A 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26749;SOR=0;LSEQ=ATTCTCTGCTTGGCCAAACT;RSEQ=TAGTCAGCCTTCTGAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:8,2:10,6:0.375:2,2:22.5:1:28.8:1:0.6044:1.91107:60:12:0.375:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:19.8:1:31.5:1:1:0:60:8:1:0:0.3 +2 44312262 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAGCTGGGACTACAGGC;RSEQ=TGCACCACCATGCCCAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:32.5:1:1:0:57.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 44561412 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21325;SOR=Inf;LSEQ=TTAGATACCTGAGAGAAACA;RSEQ=GTTCAGTTTTAGCACTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:74,7:81,0:0:2,0:27:1:33.3:1:1:0:60:162:1:0:0.1 0/1:70:2:2,0:64,4:68,2:0.0286:2,0:11:1:31:1:1:0:60:4:0.029:0:1 +2 44561532 . G A 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23228;LSEQ=TCTAAATAAAACTGATGTTA;RSEQ=CATACAGCAAAAAACGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:385:347:177,170:18,20:38,347:0.9013:2,2:26.7:1:30.1:1:0.73386:1.16:60:172.5:0.9055:0:1.1 1/0:399:271:133,138:61,65:126,271:0.6792:2,2:25.2:1:29.1:1:0.91451:1.03:60:66.75:0.6811:0:1.2 +2 44561591 . C CA 69 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.11433;SOR=0.18755;LSEQ=ATCATAACTTCTTTTTGTGA;RSEQ=AAAAAAAAATACTTCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:5:1,4:68,147:215,5:0.0227:2,2:24:1:29.8:1:1:1.8458:60:10:0.0236:0.0045:1 0/0:231:1:1,0:82,146:228,1:0.0043:2,0:49:0:32:0:0.36245:0:60:2:0.0044:0:0 +2 44561607 . C A 29 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTGACAAAAAAAAATACTTC;RSEQ=AGAAAATACTGATGGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:2,0:41,142:183,2:0.0108:2,0:9:1:20:1:0.05306:0:60:1:0.0055:0:3 0/1:185:2:1,1:53,130:183,2:0.0108:2,2:5.5:1:29.5:1:0.49971:2.44:60:4:0.0109:0:2 +2 44561616 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24128;SOR=Inf;LSEQ=AAAAATACTTCCAGAAAATA;RSEQ=TGATGGCATGGTGACCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:34,125:159,0:0:2,0:23.3:1:32.7:1:1:0:60:158:1:0:1.1 0/1:154:2:1,1:34,117:151,2:0.013:2,2:17.5:1:27.5:1:0.40635:3.41:60:4:0.0132:0:2 +2 44561627 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.22498;LSEQ=CAGAAAATACTGATGGCATG;RSEQ=TGACCAAGGATACGAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:114:16,98:3,7:10,114:0.9194:2,2:25.5:1:30.9:1:0.18112:2.59854:60:56:0.918:0:1.2 1/0:110:79:11,68:7,24:31,79:0.7182:2,2:23.3:1:29.9:1:0.26828:1.79265:60:38.5:0.713:0:1.1 +2 45237593 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22067;SOR=Inf;LSEQ=GGCAGCTGCGACGCAGAACC;RSEQ=CGGACGGCGCAGACCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:22,0:0:2,0:26.4:1:31:1:1:0:60:44:1:0:0.1 0/1:20:2:1,1:8,10:18,2:0.1:2,2:27.5:1:28.5:1:1:1.24:60:4:0.1:0:1.5 +2 46128389 . C G 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00215;SOR=Inf;LSEQ=AAAACCGTCTGTGTTGAGTA;RSEQ=TCCTAATCGGTTGCTTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:290,158:448,0:0:2,0:24.2:1:32.3:1:1:0:60:63:1:0:0.3 0/1:322:7:6,1:196,118:314,7:0.0217:2,2:34.6:1:31.6:1:0.2657:3.60:60:14:0.022:0:1.6 +2 46128458 . G T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=1.68728;LSEQ=TGTTTCAGAATGTTAAAATG;RSEQ=TTCTTACCCAAGGCCAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:720:195:92,103:256,269:525,195:0.2708:2,2:24.1:1:29.5:1:0.73743:1.06534:60:26.857:0.2674:0:1.1 0/1:519:200:87,113:157,162:319,200:0.3854:2,2:27.1:1:29.1:1:0.20751:1.2582:60:99:0.3852:0:1.2 +2 46128526 . C A 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GTAAGGTATTAGCCTGTTCA;RSEQ=ATATTTCTCATGTAATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:40:10,30:115,256:371,40:0.0973:2,2:24.2:1:31.5:1:0.47553:1.34673:60:80:0.0978:0:1 0/0:240:0:0,0:79,160:239,0:0:2,0:24.8:1:31.5:1:1:0:60:78.667:1:0:0.3 +2 46128576 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10429;SOR=Inf;LSEQ=AGATCCAATAAAGTTTGCCC;RSEQ=GGGCCTTCTTGGAAAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:18,134:152,0:0:2,0:23.7:1:30.8:1:1:0:60:75:1:0:0.2 0/1:73:2:1,1:8,62:70,2:0.0274:2,2:25:1:29:1:0.23592:7.37:60:4:0.0278:0:1 +2 46128729 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=CTGTGAGTGTAAAGTTTGAA;RSEQ=GATTTTTTTATAATTCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:12,0:0:0,0:24.3:1:29.3:1:1:0:56.9:11:1:0:0.1 1/0:4:2:1,1:0,2:2,2:0.5:0,2:43:0:30:0:1:0:60:4:0.5:0:1 +2 47257865 . C T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.48111;LSEQ=CCCGCCTGTTCCCCCTCCAT;RSEQ=CTGGCCTAGGCAGGTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:208:86,122:126,187:313,208:0.3985:2,2:25.3:1:30.1:1:0.85557:1.05:60:25:0.3922:0:1.1 0/1:265:64:26,38:88,113:201,64:0.2415:2,2:29.2:1:28.9:1:0.77206:1.13764:60:128:0.2462:0:1.2 +2 47257887 . T C 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03756;SOR=Inf;LSEQ=TGGCCTAGGCAGGTCCCCAC;RSEQ=GCTCACAGCCAGGTGTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:157,268:425,0:0:2,0:24.2:1:30.5:1:1:0:60:41.5:1:0:0.5 0/1:215:3:1,2:86,126:212,3:0.014:2,2:26.7:1:25.7:1:1:1.36317:60:6:0.0144:0:1.3 +2 47257977 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76113;SOR=0.88418;LSEQ=CCCTGATTCTGAGCCTTGCC;RSEQ=CAGCAGCATTCAAGAGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:46:3,43:9,49:58,46:0.4381:2,2:24.5:1:31.7:1:0.21941:2.61017:58.3:92:0.4466:0:1.1 0/1:76:31:9,22:12,33:45,31:0.4079:2,2:21.7:1:30.5:1:1:1.12:58.9:62:0.4247:0:1.3 +2 47257989 . A C 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00068;SOR=Inf;LSEQ=GCCTTGCCTCAGCAGCATTC;RSEQ=AGAGACTACTAAAGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:6,78:84,0:0:2,0:20.5:1:30.7:1:1:0:56.5:27:1:0:0.5 0/1:60:8:2,6:11,41:52,8:0.1333:2,2:27.8:1:31.6:1:1:1.24:58.1:16:0.1356:0:2 +2 47413836 . C G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=8.2064;LSEQ=TGCTGCTTTGTGCCGCCTTT;RSEQ=TGGGAGGCAGAGAAGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:19:7,12:12,16:28,19:0.4043:2,2:24.8:1:31.7:1:0.76724:1.27887:59.6:18:0.3913:0:1.2 1/1:47:40:15,25:3,4:7,40:0.8511:2,2:27.9:1:31.7:1:1:1.24396:60:80:0.8511:0:1.1 +2 47596597 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17608;SOR=Inf;LSEQ=CTCCCGGCGCACGCCCTCCC;RSEQ=CGAGTCCCGGGCCCCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:107,32:139,0:0:2,0:16:1:30.5:1:1:0:60:68.5:1:0:0.2 0/1:101:2:1,1:70,29:99,2:0.0198:2,2:20.5:1:29:1:0.50792:2.39013:60:4:0.02:0:1 +2 47596649 . C T 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TCGGCGCGCGCGCAGCATGG;RSEQ=GCCCCCGCAGGTCCTCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:271,131:402,0:0:2,0:27.5:1:31.4:1:1:0:60:35.545:1:0:0.2 0/1:359:13:9,4:219,127:346,13:0.0362:2,2:18.2:1:28.9:1:0.77551:1.30:60:26:0.0369:0:1.1 +2 47596653 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.04503;SOR=Inf;LSEQ=CGCGCGCGCAGCATGGCGCC;RSEQ=CCGCAGGTCCTCGCGTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:294,148:442,0:0:2,0:26.4:1:31.2:1:1:0:60:54.25:1:0:0.2 0/1:379:4:1,3:238,137:375,4:0.0106:2,2:9.8:1:26.3:1:0.14454:5.18887:60:8:0.0107:0:1.3 +2 47596694 . C T 82 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23011;SOR=0.40872;LSEQ=GCTTCTGCTTGCCGCGGCGA;RSEQ=GGCGACTTTTGCCGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:8:3,5:413,271:684,8:0.0116:2,2:13.8:1:27.6:1:0.27675:2.53648:60:7:0.0103:0:1 0/0:631:3:1,2:344,284:628,3:0.0048:2,2:22:1:27.3:1:0.59277:2.41922:60:6:0.0048:0:1.3 +2 47596775 . GC G 64 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.7055;SOR=1.71218;LSEQ=GGCTGGGCTGGGGGGCAGCG;RSEQ=CCCCGGCCCTCGGCCCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:3:1,2:203,283:486,3:0.0061:2,2:18.7:1:30.4:1:1:1.43361:60:6:0.0063:0.002:0 0/1:383:4:1,3:150,228:378,4:0.0104:2,2:28:1:32.3:1:1:1.9705:60:8:0.0106:0:0 +2 47596853 . C CG 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07254;SOR=Inf;LSEQ=TTTCCAGCGTGGAGACCGGA;RSEQ=GGTGCGGCCGTGCTCCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:1,117:118,0:0:1,0:25.8:1:30.1:1:1:0:60:58:1:0:0.1 0/1:44:2:0,2:1,41:42,2:0.0455:1,0:15.5:1:32:0:1:0:60:4:0.0476:0:0.5 +2 47596866 . C G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07037;SOR=Inf;LSEQ=GACCGGACGGTGCGGCCGTG;RSEQ=TCCGGCTCAGGCCCTCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:0,90:90,0:0:1,0:28.5:1:33.3:1:1:0:60:29:1:0:0.1 0/1:33:2:0,2:0,31:31,2:0.0606:1,0:21.5:1:33:1:1:0:60:4:0.0625:0:1 +2 47600555 . G T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26046;SOR=0;LSEQ=AACTTAGCTGGGACATGAGA;RSEQ=TTAATAGATCCACATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:3:2,1:195,17:212,3:0.014:2,2:16.3:1:24.7:1:0.23171:5.6474:60:2:0.0095:0:1.3 0/0:166:0:0,0:147,19:166,0:0:2,0:22.2:1:32.1:1:1:0:60:332:1:0:0.1 +2 47600581 . AT A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.85363;SOR=0.91874;LSEQ=AGATCCACATTTTAAAGTAG;RSEQ=TTTTTTTTTAATTTTCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:17:14,3:288,76:364,17:0.0446:2,2:21.8:1:31.5:1:1:1.23:60:34:0.0452:0.0105:0.2 0/1:316:13:11,2:238,65:303,13:0.0411:2,2:31.4:1:31.1:1:1:1.50:60:26:0.0415:0:0.6 +2 47600782 . T C 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06908;SOR=Inf;LSEQ=TTAATTGATGTGCCTTGAGT;RSEQ=GGAAAGAGTTTTATTGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:56,230:286,0:0:2,0:23.3:1:30.5:1:1:0:59.9:285:1:0:0.1 0/1:200:3:1,2:39,158:197,3:0.015:2,2:27.3:1:29:1:0.48993:2.02:60:6:0.0152:0:1 +2 47600881 . A AT 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.99513;LSEQ=ACCCTGGAACTTTAGAGTTA;RSEQ=TTTTTTTTTTCCCGTAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:14:9,5:163,74:237,14:0.0556:2,2:25:1:31.6:1:0.76991:1.22268:60:28:0.0569:0.004:0.1 0/1:217:12:8,4:132,72:204,12:0.0553:2,2:26.8:1:28.8:1:1:1.09:60:24:0.0561:0:0.7 +2 47601106 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07664;SOR=0.79441;LSEQ=GCAGTGCAACGGCACCTCCA;RSEQ=GTGCTGGTGTGTGAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:507:277:123,154:107,123:230,277:0.5464:2,2:24.6:1:30.8:1:0.65481:1.08898:60:137.5:0.5478:0:1.1 0/1:495:242:113,129:113,140:253,242:0.4889:2,2:24:1:29.8:1:0.65309:1.09:60:47.4:0.4867:0:1.1 +2 47601257 . T C 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00109;SOR=Inf;LSEQ=TAATTAAATTTATTTTTGAT;RSEQ=ATGTAATATGATTTCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:12,95:107,0:0:2,0:23.1:1:28.7:1:1:0:60:106:1:0:0.1 0/1:83:8:2,6:8,67:75,8:0.0964:2,2:20.6:1:31.5:1:0.24612:2.75:60:16:0.0964:0:1.1 +2 47602178 . A T 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00252;SOR=0.10309;LSEQ=TGTCCAGAGAACAGAGGGTC;RSEQ=ATATTAGAAAAGGTGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:19:19,0:15,0:15,19:0.5588:1,1:25.5:1:32.9:1:1:0:58.9:38:0.5588:0:1 0/1:18:2:2,0:16,0:16,2:0.1111:1,0:10.5:1:32:0:1:0:60:4:0.1111:0:1 +2 47602241 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16796;SOR=Inf;LSEQ=GGATGTGTAAGGGAAGAAAT;RSEQ=ATAGGAATAGCTACTGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:90,0:90,0:0:1,0:23.1:1:31.4:1:1:0:60:44:1:0:0.2 0/1:63:2:2,0:59,2:61,2:0.0317:1,0:15:1:28.5:1:1:0:60:4:0.0333:0:1 +2 47604118 . A AT 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00088;SOR=3.04679;LSEQ=TACTGTTGTGTGGTACAAAC;RSEQ=TTTTTTTTTAATACAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:594:12:8,4:397,182:579,12:0.0202:2,2:24.4:1:31.8:1:1:1.09049:59.6:24:0.0205:0.0051:0.1 0/1:524:31:15,16:307,184:491,31:0.0592:2,2:29.8:1:29.6:1:0.12956:1.77759:60:62:0.0598:0.0019:0.6 +2 47604148 . T C 158 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=37.55252;LSEQ=AATACAGATTTTAAATTCTT;RSEQ=ACAGTGCACTTCAGAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:801:1:0,1:479,321:800,1:0.0012:2,0:40:0:15:0:0.402:0:60:0:0:0:4 0/1:802:36:19,17:434,332:766,36:0.0449:2,2:23.1:1:30.7:1:0.73151:1.16939:60:35:0.0439:0:1.1 +2 47604368 . G GT 57 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.18346;SOR=3.91203;LSEQ=AATGTGAATTTCCTGTTACT;RSEQ=TTTTTTTTTGTTTGTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:0,2:1,86:87,2:0.0225:1,0:35:1:32:0:1:0:60:4:0.0235:0:0 0/1:48:4:0,4:1,42:43,4:0.0833:1,0:20.3:1:28.5:1:1:0:60:8:0.0851:0:0 +2 47605839 . C T 118 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTCAATATAAGAAAAT;RSEQ=CTCTTAGGAAAAATTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1:0,1:16.3:1:32:1:1:0:58.8:26:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:2:0:29:0:1:0:60:2:1:0:1 +2 47606239 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10012;SOR=Inf;LSEQ=TGTTCAGGAATGTAGTCTAT;RSEQ=ATGCCTCAATGAATTAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:65,228:293,0:0:2,0:22.2:1:32.3:1:1:0:59.9:96.667:1:0:0.1 0/1:255:3:2,1:56,196:252,3:0.0118:2,2:9:1:25.3:1:0.13053:6.93:60:6:0.0119:0:1 +2 47606774 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.83825;SOR=0.8651;LSEQ=AGTTTTTTAAAGTTCCAATA;RSEQ=ATTAGATTGTTATCACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:50:49,1:27,0:27,50:0.6494:1,1:25.2:1:33.5:1:1:0:60:49:0.6447:0:1 1/0:39:24:24,0:15,0:15,24:0.6154:1,1:25.6:1:31.8:1:1:0:60:48:0.6154:0:1 +2 47606829 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20002;SOR=Inf;LSEQ=TGGCAGCGGTTCTTTTGGCA;RSEQ=ACAATTTGTATGTAATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:143,22:165,0:0:2,0:22.2:1:31.2:1:1:0:59.9:330:1:0:0.2 0/1:134:2:1,1:114,18:132,2:0.0149:2,2:26.5:1:30:1:0.26439:6.1914:60:4:0.0156:0:1 +2 47606851 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11953;SOR=Inf;LSEQ=CAATTTGTATGTAATTATAT;RSEQ=TGGCCATGGTTGGTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:187,53:240,0:0:2,0:23.9:1:31.9:1:1:0:60:29:1:0:0.2 0/1:234:3:2,1:172,59:231,3:0.0128:2,2:28.3:1:29.3:1:1:1.45508:60:6:0.013:0:1.3 +2 47607186 . T C 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TAGTGGCTGGGCGCGGTGGC;RSEQ=CACCACACCTGTTATCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:7,117:124,0:0:2,0:24.2:1:30.1:1:1:0:60:40.333:1:0:0.1 0/1:90:11:1,10:2,77:79,11:0.1222:1,2:19.4:1:31.2:1:0.32687:3.76:60:22:0.1222:0:1.1 +2 47612198 . G GT 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.19831;SOR=Inf;LSEQ=ATGGATAGATGTTAAAATTA;RSEQ=TTTTTTTTCAGATCAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:230,16:246,0:0:2,0:24.7:1:33.7:1:1:0:60:245:1:0:0.4 0/1:198:2:2,0:174,22:196,2:0.0101:2,0:24:1:27:1:1:0:60:4:0.0102:0:0 +2 47612224 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.51084;LSEQ=TTTCAGATCAAAATTATGTC;RSEQ=ATTAAAAGCATATATGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:158:131,27:195,57:252,158:0.3854:2,2:24.5:1:31.5:1:0.20887:1.42:60:316:0.3901:0:1.1 0/1:330:80:64,16:187,62:249,80:0.2424:2,2:23.7:1:30.2:1:0.45035:1.33:60:160:0.2469:0:1 +2 47613635 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50403;SOR=0;LSEQ=TTCCTTTAATTTCATTTTTA;RSEQ=TTAATACTATTTTCAGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:2,0:159,35:194,2:0.0102:2,0:15:1:34:0:1:0:60:4:0.0103:0:1 0/0:159:0:0,0:126,33:159,0:0:2,0:22.9:1:29.6:1:1:0:60:78.5:1:0:0 +2 47613870 . T C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05601;LSEQ=TTTGTTAGTTTAACATCATA;RSEQ=ATTTGTAATAGTGAAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:33:3,30:1,37:38,33:0.4648:1,2:22.5:1:32.8:1:0.33147:3.64:59.5:66:0.4714:0:1.2 0/1:44:2:0,2:1,41:42,2:0.0455:1,0:27:1:33.5:1:1:0:60:4:0.0455:0:1 +2 47630213 . T C 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06602;LSEQ=AACGCAGCCCTGGAAGCTGA;RSEQ=TGGGTGTGGTCGCCGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:53:51,2:70,4:74,53:0.4141:2,1:24.2:1:32.2:1:1:1.45:60:52:0.4228:0:1.1 0/1:68:3:2,1:61,3:64,3:0.0441:1,2:25:1:30.3:1:0.17105:9.36402:60:6:0.0448:0:1 +2 47630314 . G T 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGCATTTTCTTCAACCAGGA;RSEQ=GTGAGGAGGTTTCGACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:38:19,19:302,266:568,38:0.0627:2,2:25.8:1:31.3:1:0.73921:1.1351:60:76:0.0638:0:1.1 0/0:492:0:0,0:274,218:492,0:0:2,0:26.4:1:30.8:1:1:0:60:43.727:1:0:0.2 +2 47630371 . C T 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03863;SOR=0;LSEQ=GACGCTGCAGTTGGAGAGCG;RSEQ=GGCCGAGGTCGGCTTCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:6:2,4:262,307:569,6:0.0104:2,2:26.3:1:28.7:1:0.69216:1.70532:60:12:0.0106:0:1 0/0:444:0:0,0:210,233:443,0:0:2,0:24.7:1:29.8:1:1:0:60:109.75:0.9977:0:0.2 +2 47630550 . C G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01845;SOR=1.39737;LSEQ=TGGGGCCGGCAGGTGAGGGC;RSEQ=GGGACGGCGCGTGCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:452:175:56,119:104,172:276,175:0.3872:2,2:23.8:1:30.5:1:0.22728:1.28417:60:57.333:0.3883:0:1.2 0/1:403:189:80,109:84,130:214,189:0.469:2,2:24.9:1:29.8:1:0.5436:1.14:60:188:0.4724:0:1.3 +2 47630592 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19647;SOR=Inf;LSEQ=GGACCCGGGGCCTTGTGGCG;RSEQ=GGCTCCTTTCCCGCCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:45,188:233,0:0:2,0:24.9:1:29.8:1:1:0:60:37.833:1:0:0.5 0/1:186:2:0,2:52,132:184,2:0.0108:2,0:25:1:25.5:1:1:0:60:4:0.011:0:3 +2 47630620 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12898;SOR=Inf;LSEQ=TTCCCGCCTCAGAGAGTGGG;RSEQ=GGTGAGCAGCCTCTCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:12,137:149,0:0:2,0:22.3:1:30:1:1:0:60:36.25:1:0:0.6 0/1:84:2:1,1:7,75:82,2:0.0238:2,2:24:1:27.5:1:0.18244:10.09:60:4:0.0238:0:1 +2 47630639 . T C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.72921;SOR=1.19423;LSEQ=GCGGTGAGCAGCCTCTCCAG;RSEQ=GCGGAGGCACGGGGGCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:46:0,46:1,54:55,46:0.4554:1,1:24:1:30.6:1:1:0:60:92:0.4554:0:1.3 1/0:50:25:0,25:2,23:25,25:0.5:2,1:19.4:1:30.1:1:0.4898:0:60:50:0.5:0:1.4 +2 47635566 . C T 51 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49568;SOR=0.56745;LSEQ=AGAATCTGCAGAGTGTTGTG;RSEQ=TTAGTAAAATGAATTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:5:3,2:272,124:396,5:0.0125:2,2:27.6:1:22.2:1:0.65142:1.46091:60:1.5:0.0086:0:2.4 0/0:422:3:3,0:258,161:419,3:0.0071:2,0:20.3:1:14.3:1:0.29043:0:60:0:0:0:4.3 +2 47637065 . C T 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTGCAGTGAGTTGAGAT;RSEQ=GCACCATTGCACTCTAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:13,0:13,6:0.3158:1,0:30.7:1:31.8:1:1:0:48.5:12:0.3158:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:12:1:31:1:1:0:60:4:1:0:0.5 +2 47638795 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTCCTGACCTTGTGATCC;RSEQ=CCCGCCTTGGCCTCCCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:42.5:1:32:1:1:0:43.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 47639329 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=AAAGAGTTGTTACCGTTGGG;RSEQ=CTATTTTTTGAAAGCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:25.5:1:33:0:1:0:45:4:0.2222:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:22.2:1:28.2:1:1:0:60:12:1:0:0 +2 47639493 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1951;SOR=Inf;LSEQ=AGTTATCAATGTTATAATTT;RSEQ=CATTTTTGCTTTTCTTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:138,32:170,0:0:2,0:22.5:1:30.9:1:1:0:59.8:55.667:1:0:0.1 0/1:135:2:1,1:111,22:133,2:0.0148:2,2:30.5:1:27:1:0.31277:4.95686:60:4:0.0152:0:1 +2 47641295 . C T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21645;SOR=Inf;LSEQ=TTTGGATTGGGAAGGAACAC;RSEQ=AAGGAAAATGAGGGACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:148,2:150,0:0:1,0:26.4:1:31.1:1:1:0:60:29:1:0:0.1 0/1:131:2:1,1:128,1:129,2:0.0153:1,2:5.5:1:28.5:1:0.03042:91.02182:60:4:0.0156:0:1 +2 47641586 . A G 67 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50857;SOR=1.86708;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=GGGTTAAAAATGTTGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:499:3:3,0:171,323:494,3:0.006:2,0:13.7:1:14:1:0.04243:0:37.7:0:0:0:5 0/1:537:6:3,3:183,348:531,6:0.0112:2,2:21:1:26.2:1:0.42192:1.90:58.3:2:0.0083:0:1.8 +2 47641587 . G A 68 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10044;SOR=0.26995;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=GGTTAAAAATGTTGAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:7:5,2:143,324:467,7:0.0147:2,2:5.7:1:24.3:1:0.03317:5.64:57.1:6:0.0133:0:1.9 0/0:500:2:2,0:145,351:496,2:0.004:2,0:12:1:10:1:0.08671:0:40:0:0:0:4 +2 47641746 . CT C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.92622;SOR=0.97225;LSEQ=TCCTCCACTCCACTTTTTAA;RSEQ=TTTTTTTTTTTAAGTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:64:23,41:193,305:498,64:0.1119:2,2:26.6:1:32.3:1:0.68503:1.12774:60:128:0.1141:0.014:0.5 0/1:614:67:23,44:195,345:540,67:0.1091:2,2:28.3:1:30.8:1:0.89271:1.08116:60:32.5:0.1085:0.0065:0.3 +2 47641758 . T A 91 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=CTTTTTAACTTTTTTTTTTT;RSEQ=AAGTCAGAGTCTCACTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:167,302:469,0:0:2,0:21.2:1:28.7:1:1:0:59.9:38.083:0.9956:0:0.4 0/1:491:11:5,6:158,322:480,11:0.0224:2,2:7.1:1:26.5:1:0.51794:1.70:60:22:0.0227:0:1.1 +2 47641781 . C A 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69902;LSEQ=GTCAGAGTCTCACTTGTTCC;RSEQ=TAGGCCAGAGTGCAGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:2,1:56,207:263,3:0.0113:2,2:16:1:27.3:1:0.1208:7.32:60:6:0.0116:0:1.7 0/0:253:2:2,0:45,205:250,2:0.0079:2,0:1:0:23.5:1:0.03418:0:60:4:0.0082:0:1 +2 47643274 . C T 62 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64481;SOR=0.45017;LSEQ=GAAATGTACAGTTGAACATA;RSEQ=GGATTAAGAGGTTGAAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:4,0:23,0:23,4:0.1481:1,0:22.5:1:31:1:1:0:60:8:0.1481:0:1.5 0/1:14:1:1,0:13,0:13,1:0.0714:1,0:19:0:32:0:1:0:60:2:0.0714:0:1 +2 47643457 . G A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTGTTGAAGATACCACTG;RSEQ=CTCTCAGTCTCTGGCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:0:0,0:416,185:601,0:0:2,0:25.9:1:31.5:1:1:0:60:65.778:1:0:0.1 0/1:561:34:24,10:332,195:527,34:0.0606:2,2:20.6:1:28.7:1:0.46352:1.41:60:68:0.0612:0:1.1 +2 47643746 . GT G 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.67563;SOR=1.58463;LSEQ=GAACTCATTTTTTTAAATAA;RSEQ=TTTTTTTTTTTCACTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:5:0,5:0,32:32,5:0.1351:1,0:38.6:1:32.4:1:1:0:60:10:0.1351:0:0 0/1:15:3:0,3:0,12:12,3:0.2:0,0:44.3:1:33:1:1:0:60:6:0.2:0:0 +2 47656801 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04858;SOR=0.46949;LSEQ=TGGAATTTTGAGCTGATTTA;RSEQ=TTGAGACTTACGTGCTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:48:47,1:28,0:28,48:0.6316:1,1:23:1:30.4:1:1:0:59.9:96:0.6316:0:1.1 0/1:54:24:22,2:27,3:30,24:0.4444:2,2:24.9:1:30:1:1:1.22:60:48:0.4528:0:1.2 +2 47656871 . T C 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTACATTAATTCAAGTTAA;RSEQ=TTATTTCAGATTGAATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:257,78:335,0:0:2,0:24.2:1:30.9:1:1:0:59.8:29.455:1:0:0.2 0/1:304:35:25,10:190,79:269,35:0.1151:2,2:23.5:1:31:1:1:1.04:60:70:0.1163:0:1.1 +2 47657117 . T A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62559;SOR=0.37122;LSEQ=TTTTTTTGTTTTCCTTCAAC;RSEQ=CATACAATATATACTTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:3:1,2:29,181:210,3:0.0141:2,2:11:1:29.7:1:0.36729:3.10:60:6:0.0146:0:1 0/0:190:1:1,0:41,148:189,1:0.0053:2,0:1:0:24:0:0.22105:0:60:2:0.0054:0:1 +2 47657134 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17993;SOR=Inf;LSEQ=AACTCATACAATATATACTT;RSEQ=GCAATGTGCTGTCCTCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:7,142:149,0:0:1,0:27:1:30.7:1:1:0:59.9:20.286:1:0:0.2 0/1:111:2:1,1:10,99:109,2:0.018:2,2:16.5:1:29:1:0.18919:9.49:60:4:0.0187:0:1 +2 47672475 . T A 102 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62208;SOR=0.43602;LSEQ=GTGTATTATTAGTGGGAAGC;RSEQ=TTGAGTGCTACATCATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:11,0:13,1:14,11:0.44:1,0:19:1:29.6:1:1:0:60:10:0.4167:0:1.3 0/1:4:1:1,0:3,0:3,1:0.25:0,0:25:0:31:0:1:0:60:2:0.25:0:1 +2 47672569 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00185;SOR=0.29785;LSEQ=AATAGTAACTTTGGAGACCT;RSEQ=CTGTACTATTTGTACCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:69:68,1:26,0:26,69:0.7263:1,1:24.5:1:28.7:1:1:0:59.6:68:0.7234:0:1.1 0/1:41:18:17,1:23,0:23,18:0.439:1,1:20.2:1:28.6:1:0.43902:0:60:36:0.439:0:1.1 +2 47673515 . T C 27 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTTTTCCATGTAGAGTTCTT;RSEQ=GCAGGAGGAGGTTAGAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:27.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:20.5:1:26.5:1:1:0:60:4:1:0:0 +2 47690404 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0271;SOR=0.35502;LSEQ=CTGTCCCCAAGATGATGACT;RSEQ=CACATCTCTGTCAAACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:49:0,49:1,30:31,49:0.6125:1,1:27.2:1:31.6:1:0.3875:0:60:48:0.6076:0:2.9 0/1:28:10:0,10:1,17:18,10:0.3571:1,0:17.2:1:29.9:1:1:0:60:20:0.3571:0:2.4 +2 47690408 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02977;SOR=0.32531;LSEQ=CCCCAAGATGATGACTTCAC;RSEQ=TCTCTGTCAAACAGAAATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:45:0,45:1,30:31,45:0.5921:1,1:27.7:1:32.6:1:0.40789:0:60:44:0.5867:0:3.1 0/1:22:7:0,7:1,14:15,7:0.3182:1,0:22:1:31:1:1:0:60:14:0.3182:0:3 +2 47690411 . T C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04629;SOR=0.34128;LSEQ=CAAGATGATGACTTCACATC;RSEQ=CTGTCAAACAGAAATCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:43:0,43:1,28:29,43:0.5972:1,1:27.7:1:32:1:0.40278:0:60:86:0.5972:0:3.1 0/1:21:7:0,7:1,13:14,7:0.3333:1,0:21.1:1:29.6:1:1:0:60:14:0.3333:0:2.9 +2 47693706 . G T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.85934;SOR=1.1131;LSEQ=TTGTCATATAATAACAGTAT;RSEQ=TTTTTCACTATTTAAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:39:39,0:50,0:50,39:0.4333:1,1:24.9:1:31.2:1:1:0:60:38:0.427:0:1.3 0/1:50:23:22,1:27,0:27,23:0.46:1,1:23.9:1:31.1:1:0.46:0:60:46:0.46:0:1.1 +2 47693788 . A T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10365;LSEQ=TACTTTTTCTTTTCTTCTTG;RSEQ=TTATCAAGGCTTGGACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:210:150,60:248,97:345,210:0.3784:2,2:21:1:29.5:1:0.9228:1.02265:60:51.5:0.378:0:1.2 0/1:422:25:19,6:276,121:397,25:0.0592:2,2:19:1:29.5:1:0.65389:1.39:60:50:0.0601:0:1.1 +2 47693959 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.51012;LSEQ=TACCAACAGGTTTGCAAGTC;RSEQ=TTATTATATTTTTAACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:686:326:112,214:133,227:360,326:0.4752:2,2:24.6:1:30.9:1:0.52339:1.11931:60:652:0.4766:0:1.1 0/1:649:205:77,128:170,273:443,205:0.3159:2,2:25.1:1:29.6:1:0.86229:1.03511:60:204:0.3168:0:1.1 +2 47694037 . T C 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTATGATAAGTTTTACTAA;RSEQ=GTAGTCATCAGGTAAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:2,151:153,0:0:1,0:25.2:1:30.7:1:1:0:60:152:1:0:0.2 0/1:118:39:2,37:1,78:79,39:0.3305:1,2:23.9:1:30.3:1:0.25356:4.16:60:78:0.3333:0:1.1 +2 47694252 . C G 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTATTAGAGCTAGTTCCC;RSEQ=CTCATATCTCTGCTTTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:26.7:1:34:1:1:0:60:6:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 47698254 . A T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08494;SOR=Inf;LSEQ=GTCACCTGGCTTTTGGTAAC;RSEQ=GAAGAAAAATCATGATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:29,189:218,0:0:2,0:23.3:1:31.8:1:1:0:60:217:1:0:0.3 0/1:172:3:0,3:24,145:169,3:0.0174:2,0:18.7:1:30.7:1:1:0:60:6:0.0176:0:1 +2 47698308 . A G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1544;SOR=0.58901;LSEQ=TTATTTTCGCAAGCCATTAC;RSEQ=TTCTGACTATTTAATATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:50:0,50:0,36:36,50:0.5814:1,1:23.7:1:32.9:1:1:0:60:100:0.5814:0:1.2 0/1:49:22:0,22:0,27:27,22:0.449:1,1:22.5:1:32.4:1:1:0:60:44:0.449:0:1 +2 47698384 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.66533;SOR=0.64874;LSEQ=AGTAGGACACATAACTGGAA;RSEQ=TTACTCTTGCACATAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:7,11:0.6111:0,0:18.4:1:32.8:1:1:0:60:22:0.6111:0:1.7 1/0:6:3:0,3:0,3:3,3:0.5:0,0:34.3:1:31:1:1:0:60:6:0.5:0:1 +2 47701705 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCTGGGTTCATGCAATT;RSEQ=TGGTGCCTCAGCCTCCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:10.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 47702102 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16498;SOR=Inf;LSEQ=GGGATTAAATGTATTTTTAC;RSEQ=GCTTATATCTGTTTATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:138,6:144,0:0:1,0:26.3:1:30.3:1:1:0:60:288:1:0:0.1 0/1:99:2:2,0:89,8:97,2:0.0202:2,0:37.5:1:28:1:1:0:60:4:0.0202:0:1 +2 47702493 . T TA 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.19501;SOR=Inf;LSEQ=TCTTGGAGTAGAAATATATT;RSEQ=AAAATTGATGGAGAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:0,55:55,0:0:1,0:24.6:1:28.4:1:1:0:58.1:54:1:0:1 0/1:44:2:0,2:4,38:42,2:0.0455:2,0:37.5:1:32:0:1:0:60:4:0.0488:0:0 +2 47703241 . A G 112 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTCTAGGCCACAGTCA;RSEQ=ATTACAGGTATATTTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:12,0:4,0:4,12:0.75:0,0:29.2:1:31.4:1:1:0:54.9:11:0.7333:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 47703290 . G A 89 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATGAAAGGCCCAGTATC;RSEQ=GTTTGTCTGAAGATATATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:7,0:9,0:9,7:0.4375:0,0:21.7:1:32:1:1:0:60:14:0.4375:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 47703379 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCAGGCTGTGGTTCTGC;RSEQ=TTTATATGCTATGTCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:108:108:107,1:0,0:0,108:1:0,1:24.1:1:32.3:1:1:0:60:35:1:0:1.1 1/1:51:51:51,0:0,0:0,51:1:0,1:24:1:31.3:1:1:0:60:102:1:0:1 +2 47703500 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.28195;SOR=1.18859;LSEQ=GCTTTCTGATATAATTTGTT;RSEQ=TGTAGGCCCCAATATGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:793:103:63,40:426,264:690,103:0.1299:2,2:24.5:1:32.1:1:0.91386:1.02451:59.8:102:0.1293:0:1.1 0/1:637:96:72,24:315,226:541,96:0.1507:2,2:23.9:1:31.1:1:0.00208:2.15:59.9:192:0.1531:0:1.1 +2 47703766 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15356;SOR=Inf;LSEQ=GTATGTCTCTGTCCTGTGAG;RSEQ=AGGAAAAGTATATTTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:34,198:232,0:0:2,0:24:1:30.9:1:1:0:60:57:1:0:0 0/1:150:2:1,1:25,123:148,2:0.0133:2,2:31.5:1:29:1:0.31758:4.84:60:4:0.0134:0:1 +2 47703885 . G A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23465;SOR=0.34815;LSEQ=TCTTAAAAGAGTGATTGATG;RSEQ=TAGCTACGGAAAACTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:19:0,19:1,7:8,19:0.7037:2,1:28.7:1:31.9:1:0.2963:0:58.7:38:0.7037:0:1.1 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:8.8:1:31.8:1:1:0:60:8:0.4444:0:1 +2 47703984 . T G 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATCTCCACTACCATGTT;RSEQ=TTGCTTGGACTGTTCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:16.5:1:31.8:1:1:0:60:8:0.5:0:2.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 47704027 . G C 87 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGAATGGTCCTTCTTGCC;RSEQ=TTTATCCAACTTCTTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:17.4:1:31:1:1:0:60:14:1:0:2.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 47708066 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18766;SOR=Inf;LSEQ=CTCTATTATTACATAAACAG;RSEQ=ACACTAAGATGAAGGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:34,175:209,0:0:2,0:22.2:1:32.1:1:1:0:60:103.5:0.9952:0:0.2 0/1:161:2:1,1:33,126:159,2:0.0124:2,2:14.5:1:25.5:1:0.3788:3.78:60:4:0.0124:0:1.5 +2 47709704 . T C 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54404;SOR=1.83231;LSEQ=GCACACATAAATAATAAATA;RSEQ=GTTCTTCAAATATTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:17,0:17,3:0.15:1,0:27.7:1:32.7:1:1:0:60:6:0.15:0:1 0/1:4:1:1,0:3,0:3,1:0.25:0,0:16:0:33:0:1:0:60:2:0.25:0:1 +2 47709796 . T TA 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.69626;LSEQ=GTCTCTAAAAATATGAAAAA;RSEQ=AAAAAAAAAATTTTTTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:7:7,0:107,0:107,7:0.0614:1,0:27.7:1:29.1:1:1:0:60:14:0.0619:0:0.3 0/1:46:2:2,0:44,0:44,2:0.0435:1,0:20.5:1:25.5:1:1:0:60:4:0.0435:0:0 +2 47709807 . T A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.01542;SOR=0.19343;LSEQ=TATGAAAAATAAAAAAAAAA;RSEQ=TTTTTAAATGTGTGATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:21:21,0:109,0:109,21:0.1591:1,1:20.5:1:30:1:1:0:60:20:0.1563:0:1 0/1:57:2:1,1:54,0:54,2:0.0351:1,2:18.5:1:31.5:1:0.03571:0:60:4:0.0357:0:1 +2 47710121 . AT A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14249;SOR=Inf;LSEQ=ATGGAATGAAGGTAATATTG;RSEQ=AAGCTATTGTCTGTAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:91,237:328,0:0:2,0:23.4:1:29.1:1:1:0:60:108.333:0.9969:0:0.1 0/1:200:2:1,1:52,146:198,2:0.01:2,2:5:1:30:1:0.46075:2.79:60:4:0.0102:0.005:0.5 +2 47739551 . A G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.38543;LSEQ=TCGGCCAGAGAGACAGAACC;RSEQ=GGGCAGTGGTGAGCTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:455:301:84,217:43,110:153,301:0.6615:2,2:27.4:1:30.8:1:1:1.00983:59.9:74.25:0.6659:0:1.1 0/1:361:155:55,100:68,136:204,155:0.4294:2,2:24.7:1:29.6:1:0.73641:1.10:59.7:37.75:0.4302:0:1.3 +2 47739567 . C T 128 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=31.38285;LSEQ=AACCAGGGCAGTGGTGAGCT;RSEQ=TCATGACCTGGTGTCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:1:0,1:84,284:368,1:0.0027:2,0:21:0:13:0:1:0:60:0:0:0:3 0/1:267:21:6,15:67,177:244,21:0.0787:2,2:26.2:1:29.2:1:1:1.06:60:42:0.0811:0:2.1 +2 47740566 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTCTTGGTTTTCTCCCA;RSEQ=ATCTCTGACCCTCTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:45:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 47887915 . TC T 60 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18528;SOR=0.20944;LSEQ=TTTGACATCTTTGATAGGTT;RSEQ=CCCAGCATCAAAATACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:3,1:16,1:17,4:0.1905:1,2:17:1:30.1:1:0.35238:4.76102:60:8:0.1905:0.0952:0.3 0/1:22:1:1,0:18,3:21,1:0.0455:2,0:13:0:33:0:1:0:60:2:0.0476:0:0 +2 47888014 . A G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03158;LSEQ=CTTCAAAGAATGTATCTCTC;RSEQ=TCCTGTAGAGATATTAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:100:55,45:14,9:23,100:0.8065:2,2:26.7:1:30.7:1:0.64867:1.27026:60:99:0.8049:0:1.1 0/1:114:13:6,7:53,48:101,13:0.114:2,2:26.2:1:31.4:1:0.77178:1.28533:60:26:0.1161:0:1.1 +2 47888018 . T C 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49847;SOR=0;LSEQ=AAAGAATGTATCTCTCATCC;RSEQ=GTAGAGATATTAAATGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:67,56:123,2:0.016:2,2:25:1:25.5:1:1:1.1947:60:4:0.0163:0:2 0/0:117:0:0,0:58,58:116,0:0:2,0:22.9:1:29.5:1:1:0:59.4:57:1:0:0.4 +2 47888022 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21674;SOR=Inf;LSEQ=AATGTATCTCTCATCCTGTA;RSEQ=AGATATTAAATGATTAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:67,61:128,0:0:2,0:25.9:1:31.5:1:1:0:60:20.333:1:0:0.9 0/1:112:2:1,1:54,55:109,2:0.0179:2,2:13.5:1:27:1:1:1.02:60:4:0.0182:0:1 +2 47888040 . A C 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00206;SOR=Inf;LSEQ=TAGAGATATTAAATGATTAG;RSEQ=CTTATTTGGTAAATTGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:60,63:123,0:0:2,0:27.3:1:28.9:1:1:0:60:23.6:1:0:0.8 0/1:109:8:4,4:49,52:101,8:0.0734:2,2:33:1:30.6:1:1:1.06:60:16:0.0762:0:1 +2 47888091 . CT C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.82288;SOR=1.13255;LSEQ=TATTTTTTCTTTTTCTTTTT;RSEQ=TTTTTTTTTTTGAGACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:11:9,2:45,39:84,11:0.1146:2,2:28.6:1:29.6:1:0.10723:3.85:55.9:10:0.1064:0.0208:0.5 0/1:86:11:5,6:42,30:72,11:0.1279:2,2:22.4:1:32.3:1:0.51972:1.66929:59.1:22:0.1279:0.0116:0.3 +2 47888189 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22218;SOR=Inf;LSEQ=TCTGCCTCCTGGACTCAAGC;RSEQ=ATCCTCCTACCTCAACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:161,19:180,0:0:2,0:21.1:1:30.5:1:1:0:57.9:360:1:0:0.1 0/1:161:2:1,1:137,22:159,2:0.0124:2,2:19.5:1:27:1:0.26607:6.1126:42:4:0.0124:0:3 +2 47888212 . A T 33 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62379;SOR=2.96506;LSEQ=CCTCCTACCTCAACCTCCCA;RSEQ=GTAGCTGGGACCACAGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:0,1:205,90:295,1:0.0034:2,0:1:0:26:0:0.30743:0:60:2:0.0034:0:1 0/1:301:3:1,2:200,98:298,3:0.01:2,2:5:1:21:1:0.25704:4.06092:58.7:2:0.0068:0:2.7 +2 47888224 . C T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37449;SOR=3.79265;LSEQ=ACCTCCCAAGTAGCTGGGAC;RSEQ=ACAGACTCATGCCACCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:1:0,1:235,142:377,1:0.0026:2,0:1:0:27:0:0.37831:0:52:2:0.0027:0:1 0/1:401:4:2,2:242,154:396,4:0.01:2,2:8.5:1:27:1:0.64495:1.56954:59.8:8:0.0102:0:1.3 +2 47888366 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50441;SOR=0;LSEQ=AATGTTATAAAAATCTAAAA;RSEQ=GTTATCAGTCATAATTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:15,184:199,2:0.01:2,2:15.5:1:33:1:0.15323:11.91:60:4:0.0101:0:1 0/0:162:0:0,0:20,142:162,0:0:2,0:18.9:1:29.6:1:1:0:60:161:1:0:0 +2 47905390 . C A 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTGCTTCATTTCCTAGGC;RSEQ=TGAAATTCATTGCTTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:832:0:0,0:414,417:831,0:0:2,0:26.2:1:32:1:1:0:60:82.1:1:0:0.3 0/1:806:38:21,17:393,375:768,38:0.0471:2,2:25.6:1:29.2:1:0.73999:1.18:60:76:0.0476:0:1.3 +2 47905398 . C A 219 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00473;LSEQ=CATTTCCTAGGCCTGAAATT;RSEQ=ATTGCTTGTGTACCCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:170:79,91:308,330:638,170:0.2104:2,2:26.3:1:29.6:1:0.72978:1.07498:60:41.5:0.2083:0:1.1 0/0:795:1:1,0:394,400:794,1:0.0013:2,0:1:0:25:0:0.49686:0:60:2:0.0013:0:2 +2 48010214 . C T 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54404;SOR=0;LSEQ=GGGGCCTGGCGCGCACCGCC;RSEQ=GCGCACGGCGAGGCGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:14,5:0.2632:1,0:21.8:1:34:0:1:0:60:10:0.2632:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:18:1:32.2:1:1:0:60:10:1:0:0.2 +2 48010481 . G A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.06106;SOR=Inf;LSEQ=AAGGCGGCCGTGCCGCCGCT;RSEQ=CCCCCGGGGCCTCTCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:391:0:0,0:166,225:391,0:0:2,0:23.9:1:32.3:1:1:0:60:38.1:1:0:0.2 0/1:388:4:3,1:152,232:384,4:0.0103:2,2:9.8:1:26:1:0.30612:4.56:60:8:0.0106:0:1.3 +2 48010488 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=2.69339;LSEQ=CCGTGCCGCCGCTGCCCCCG;RSEQ=GGCCTCTCCTTCCCCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:32:17,15:145,199:344,32:0.0851:2,2:20.9:1:31:1:0.26467:1.55:60:64:0.0867:0:1.1 0/1:354:71:31,40:111,172:283,71:0.2006:2,2:24.8:1:29.6:1:0.50143:1.20:60:70:0.2023:0:1.2 +2 48010501 . C A 43 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18345;SOR=4.81239;LSEQ=GCCCCCGGGGCCTCTCCTTC;RSEQ=CCAGGCGGGGATGCGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:1:1,0:166,180:346,1:0.0029:2,0:1:0:26:0:0.48127:0:60:2:0.0029:0:1 0/1:291:4:3,1:130,157:287,4:0.0137:2,2:6.8:1:21.5:1:0.33489:3.61:60:3:0.0105:0:2.3 +2 48010548 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04726;SOR=Inf;LSEQ=GGCTGGGCCTGGGCCCAGGC;RSEQ=CTTGGCGCGCTCCGCGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:272,159:431,0:0:2,0:24.6:1:30.8:1:1:0:60:38.182:1:0:0.2 0/1:378:4:2,2:215,158:373,4:0.0106:2,2:20.8:1:29.5:1:1:1.35961:60:8:0.011:0:1.8 +2 48010555 . G T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.04257;SOR=Inf;LSEQ=CCTGGGCCCAGGCCCTTGGC;RSEQ=CGCTCCGCGTCACCGCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:284,184:468,0:0:2,0:24.8:1:30.4:1:1:0:60:57.5:1:0:0.2 0/1:391:4:2,2:221,166:387,4:0.0102:2,2:33:1:28.5:1:1:1.33032:60:8:0.0106:0:2.3 +2 48010558 . C A 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCCAGGCCCTTGGCGCG;RSEQ=TCCGCGTCACCGCCCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:300,190:490,0:0:2,0:24.6:1:32:1:1:0:60:36.692:1:0:0.2 0/1:395:96:54,42:172,125:297,96:0.243:2,2:24.9:1:28.4:1:0.8127:1.07004:60:47:0.2442:0:1.3 +2 48010654 . C G 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGCGGGGTGGGGGTGGGGT;RSEQ=GAAGGCGGGGGCATAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:159,243:402,0:0:2,0:23.2:1:30.2:1:1:0:60:49.25:1:0:0.2 0/1:282:57:17,40:92,132:224,57:0.2021:2,2:20.6:1:30.7:1:0.13029:1.63714:60:114:0.2096:0:1.4 +2 48010676 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.26907;SOR=0;LSEQ=AAGGCGGGGGCATAGCGGCG;RSEQ=GGCGCTTGGAACCCGGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:2,1:70,183:253,3:0.0117:2,2:16.3:1:24.3:1:0.19176:5.19:60:2:0.0079:0:2.7 0/0:183:0:0,0:52,131:183,0:0:2,0:22.7:1:29.6:1:1:0:60:60:1:0:0.4 +2 48010872 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46429;SOR=0;LSEQ=GAAGAGGGCTGCAGGGGAGA;RSEQ=GCGGAGAGTTCGGGCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:3,3:0.5:0,2:17:1:30:1:1:0:60:6:0.5:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:25.5:1:27.5:1:1:0:60:4:1:0:0 +2 48018081 . A G 219 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=91.53997;LSEQ=AACAGTTGTGACTTCTCACC;RSEQ=GGAGATTTGGTTTGGGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:793:3:2,1:470,320:790,3:0.0038:2,2:21.3:1:26.7:1:1:1.36:60:6:0.0038:0:1 0/1:704:182:98,84:302,218:520,182:0.2585:2,2:27:1:29.2:1:0.33924:1.18712:60:35.4:0.2547:0:1.2 +2 48018281 . ATG A 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.68686;SOR=0.52811;LSEQ=AGGTAAGAGTCACTACTGCC;RSEQ=TGTGTGTGTTTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:4:1,3:81,243:324,4:0.0122:2,2:34.8:1:32.8:1:1:1:60:8:0.0128:0:0.5 0/0:310:2:1,1:112,196:308,2:0.0065:2,2:31:1:32.5:1:1:1.75:60:4:0.0067:0:0.5 +2 48018288 . T A 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=0.36193;SOR=3.16693;LSEQ=AGTCACTACTGCCATGTGTG;RSEQ=GTGTTTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:1:1,0:61,231:292,1:0.0034:2,0:1:0:30:0:0.2116:0:60:2:0.0034:0:1 0/1:281:3:2,1:100,178:278,3:0.0107:2,2:27:1:23.7:1:0.29895:3.54:60:2:0.0073:0:1.7 +2 48018314 . T A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=2;SSF=0.37312;SOR=0.80299;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GAGAGAAACAGACAGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:69:10,59:18,121:139,69:0.3317:2,2:22.7:1:32.1:1:0.82988:1.14:59.7:138:0.3366:0:1.2 0/1:172:49:13,36:36,85:121,49:0.2849:2,2:25.1:1:29.3:1:0.71284:1.17176:58.9:48:0.2874:0:1.4 +2 48018322 . A C 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19451;SOR=Inf;LSEQ=TGTGTGTGTGTGTGAGAGAA;RSEQ=CAGACAGACAGGCAGACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:14,159:173,0:0:2,0:22.6:1:30.5:1:1:0:59.7:85.5:1:0:0.5 0/1:137:2:1,1:26,109:135,2:0.0146:2,2:12:0:29:1:0.35648:4.13:60:4:0.0149:0:2 +2 48022875 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52577;SOR=0;LSEQ=CCACCTAAGCCTCCCAAAAT;RSEQ=CTGGGATTACAGGCGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:2,0:45,0:45,2:0.0426:1,0:28.5:1:30.5:1:1:0:58.5:4:0.0426:0:1 0/0:28:0:0,0:28,0:28,0:0:1,0:22.5:1:31.6:1:1:0:59.2:56:1:0:0.7 +2 48022900 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00031;SOR=4.89444;LSEQ=GATTACAGGCGTGAGCCACC;RSEQ=CACCTGGCATATATATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:34:34,0:45,0:45,34:0.4304:1,1:25.2:1:30.8:1:1:0:59.9:68:0.4359:0:1.2 1/0:38:30:30,0:8,0:8,30:0.7895:0,1:26.4:1:30:1:1:0:59.8:60:0.7895:0:1.1 +2 48022981 . G T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00927;SOR=1.68425;LSEQ=TTGAACTGCTGGGATTACAG;RSEQ=CGTGAGCCTCTGCACCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:55:42,13:275,64:339,55:0.1396:2,2:25.1:1:29.9:1:0.46289:1.32896:60:110:0.1429:0:1.2 0/1:312:67:47,20:178,67:245,67:0.2147:2,2:23.7:1:28.1:1:0.75866:1.13006:60:32.5:0.2117:0:1.1 +2 48023000 . G T 49 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09864;SOR=5.99266;LSEQ=GGCGTGAGCCTCTGCACCCG;RSEQ=CCCTTATTGTTTATAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:1:0,1:398,153:551,1:0.0018:2,0:1:0:26:0:0.27899:0:60:2:0.0019:0:1 0/1:464:5:1,4:303,156:459,5:0.0108:2,2:6.2:1:21.4:1:0.05025:7.73488:60:4:0.0088:0:1.4 +2 48023115 . T C 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00225;SOR=0.77132;LSEQ=AGAGCAATGCAACGTGCAGA;RSEQ=GAAGCCTTAAATAAAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1529:472:252,220:575,479:1054,472:0.3087:2,2:23.1:1:31.1:1:0.69732:1.04798:60:117:0.3099:0:1.1 0/1:1296:332:174,158:514,450:964,332:0.2562:2,2:22.8:1:30.4:1:0.79882:1.03718:60:82:0.2553:0:1.2 +2 48025694 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=0.23839;LSEQ=TCATAAGTTGAACTGTCTTA;RSEQ=ATTATGGTTTTCCAAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:41:39,2:96,10:106,41:0.2789:2,1:24.3:1:31.8:1:0.51094:2.02:60:82:0.2808:0:1.6 0/1:119:10:9,1:94,15:109,10:0.084:2,2:20.9:1:30.4:1:1:1.43:60:20:0.0855:0:1.1 +2 48025729 . T C 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24858;SOR=Inf;LSEQ=AATTTTGATTTGTTTTTAAA;RSEQ=ACTCTTTCCTTGCCTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:216,42:258,0:0:2,0:24.1:1:31:1:1:0:59.9:257:1:0:0.5 0/1:261:3:2,1:196,61:257,3:0.0115:2,2:25.3:1:29:1:0.55996:1.60329:60:6:0.0116:0:2.3 +2 48025764 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13647;LSEQ=TGGCAGGTAGGCACAACTTA;RSEQ=GTAACAGATAAGAGTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:122:86,36:231,102:333,122:0.2681:2,2:23.6:1:30.8:1:0.90841:1.05:60:121:0.2695:0:1.3 0/1:526:25:17,8:321,180:501,25:0.0475:2,2:21.5:1:28.9:1:0.83162:1.19:60:24:0.046:0:1.4 +2 48026289 . C T 141 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=33.78723;LSEQ=AGGAGGAGGCCTGATCACCC;RSEQ=GATTTTGATGCATCTACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:653:1:0,1:315,337:652,1:0.0015:2,0:1:0:25:0:1:0:60:2:0.0016:0:1 0/1:588:29:13,16:270,289:559,29:0.0493:2,2:25:1:29.2:1:0.84928:1.14958:60:58:0.0495:0:1.1 +2 48027216 . G A 63 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05262;SOR=7.13008;LSEQ=AAAAAATGCCTTATTGATCA;RSEQ=GAGCTTTTATCAATGGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:665:1:1,0:305,359:664,1:0.0015:2,0:1:0:26:0:0.46015:0:60:2:0.0015:0:1 0/1:564:6:5,1:288,270:558,6:0.0106:2,2:6.5:1:24.5:1:0.2184:4.68:60:5:0.009:0:1.3 +2 48028337 . T C 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=TCTCAGGCTTTGATAAGTAG;RSEQ=GCTGTTTGCCAGCTGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:80,238:318,0:0:2,0:24.7:1:30.2:1:1:0:59.9:52:1:0:0.2 0/1:308:12:4,8:75,221:296,12:0.039:2,2:23.9:1:31.4:1:0.51191:1.47:60:24:0.039:0:1.1 +2 48028465 . C T 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14877;SOR=0;LSEQ=AATTTAAGTTACTTGAAACT;RSEQ=GCTTTTATCTTAGTAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:0,21:21,5:0.1923:1,0:23.4:1:31.8:1:1:0:60:10:0.1923:0:1 0/0:13:0:0,0:0,13:13,0:0:1,0:28.6:1:29.1:1:1:0:60:12:1:0:0 +2 48030458 . G C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.69462;LSEQ=GGACTGTAATTGAAAGTTAT;RSEQ=TCTTATAATGAAATGTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:107:98,9:99,9:108,107:0.4954:2,2:21.6:1:32.3:1:1:1.01016:60:214:0.5:0:1 1/0:168:122:112,10:41,5:46,122:0.7262:2,2:22.2:1:31:1:0.55751:1.36:60:60:0.7229:0:1.1 +2 48030629 . G T 183 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTCGCCCAGTAATTCTGTT;RSEQ=CCGGAAGATACCCCCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:73:30,43:599,691:1290,73:0.0536:2,2:24.7:1:29.6:1:0.4:1.2423:60:23.333:0.0524:0:1.1 0/0:1438:0:0,0:678,759:1437,0:0:2,0:25.4:1:31.1:1:1:0:60:48.552:1:0:0.2 +2 48030639 . AC A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.67396;SOR=1.1014;LSEQ=TAATTCTGTTGCCGGAAGAT;RSEQ=CCCCCCCTTCTTAGAGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1336:43:17,26:583,710:1293,43:0.0322:2,2:31.2:1:30.6:1:0.53459:1.25563:60:42:0.032:0.0022:0.4 0/1:1415:50:22,28:630,731:1361,50:0.0353:2,2:31:1:30.1:1:0.77471:1.09678:60:49:0.0355:0.0021:0.1 +2 48030838 . A T 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGACAGGTAACTGATTCTT;RSEQ=AAGTTTTGTTATCAGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:54,151:205,0:0:2,0:25.1:1:30.1:1:1:0:59.8:101.5:1:0:0.1 0/1:214:85:25,60:38,91:129,85:0.3972:2,2:24.4:1:27.8:1:1:1.00219:60:41.5:0.3934:0:1.1 +2 48031975 . G A 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=3e-04;SOR=Inf;LSEQ=TGCCTAGCTCTTACGTAAGG;RSEQ=TTCATAAGAAAGACAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:197,40:237,0:0:2,0:21.9:1:31.5:1:1:0:59.9:78:1:0:0.1 0/1:194:10:8,2:145,39:184,10:0.0515:2,2:16.6:1:26:1:1:1.08:60:9:0.0474:0:1.4 +2 48032312 . G A 124 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=50.68711;LSEQ=CACTTTTTAAGAACTGCATA;RSEQ=TCTCTCTCTCTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:0,1:1,43:44,1:0.0217:1,0:31:0:29:0:1:0:60:2:0.0263:0:2 1/0:35:19:0,19:1,15:16,19:0.5429:1,1:16.7:1:29.4:1:0.45714:0:59.3:18:0.6429:0:1.3 +2 48032572 . C T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02696;SOR=0;LSEQ=GGTGATCTGCTTGCCTCGGC;RSEQ=TCCCAAAGTGCTGGGATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:5,1:11,3:14,6:0.3:2,2:22:1:29.3:1:1:1.34:40.2:5:0.2632:0:2 0/0:15:0:0,0:14,1:15,0:0:1,0:22.7:1:31:1:1:0:41.9:30:1:0:0.8 +2 48032613 . G A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=12.53454;LSEQ=AGGCGTGAGCCACCGTGCCC;RSEQ=GCCAATAATTGCATAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:7,2:19,1:20,9:0.3103:1,2:19.6:1:31.7:1:0.22003:5.07055:50.2:18:0.3103:0:1.7 1/1:21:18:17,1:3,0:3,18:0.8571:0,1:30.1:1:29:1:1:0:48.5:36:0.8571:0:1.1 +2 48032874 . ACTAT A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0;SOR=4.31539;LSEQ=ATTAAACTTCTCATTTGAAG;RSEQ=CTATCTTAAAAACATTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:501:134:35,99:119,248:367,134:0.2675:2,2:26.4:1:32.7:1:0.19043:1.35645:60:133:0.2676:0.022:0.4 1/0:495:303:94,209:76,113:189,303:0.6121:2,2:25.9:1:31.7:1:0.0409:1.49409:59.9:606:0.6159:0.0202:0.3 +2 48032937 . T C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.93354;LSEQ=GAAGATTATCTGAAGTACAT;RSEQ=TAAACAATATGAATGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:56:3,53:4,99:103,56:0.3522:1,2:21.8:1:33.1:1:0.69763:1.40:60:55:0.3548:0:1 1/0:126:86:1,85:3,36:39,86:0.6825:2,1:23.4:1:32.2:1:0.08959:6.9615:59.9:85:0.68:0:1.1 +2 48032955 . T G 33 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.17891;SOR=Inf;LSEQ=ATTTAAACAATATGAATGTT;RSEQ=TTAGAGCACGCACTCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:4,114:118,0:0:1,0:23.4:1:30.9:1:1:0:60:117:1:0:0.3 0/1:87:2:0,2:1,84:85,2:0.023:1,0:7.5:1:33.5:1:1:0:60:4:0.023:0:2 +2 48033195 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06993;SOR=Inf;LSEQ=ATGGGCTGCTAAGCAGACTC;RSEQ=TGTAGCTAAACAAGGCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:55,2:57,0:0:1,0:23.8:1:30.5:1:1:0:60:56:1:0:0.1 0/1:21:2:2,0:19,0:19,2:0.0952:1,0:37:1:29:1:1:0:60:4:0.0952:0:1 +2 48033271 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21637;SOR=Inf;LSEQ=ATGTTGCTTTTCTGTCCTAG;RSEQ=ATTTTTGTTTTAATTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:150,15:165,0:0:2,0:24.2:1:32.5:1:1:0:60:164:1:0:0 0/1:144:2:1,1:123,19:142,2:0.0139:2,2:18:1:25.5:1:0.25932:6.33537:60:4:0.0141:0:1 +2 48033272 . ATTTTTGTTTTAATTCCT A 170 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=6.000;MSILEN=1;SSF=0;SOR=0.01883;LSEQ=TGTTGCTTTTCTGTCCTAGC;RSEQ=TTTTTGTTTTAATTCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:45:39,6:119,14:133,45:0.2514:2,2:24.5:1:31.1:1:0.59258:1.30563:60:44:0.2472:0.0559:0.1 0/0:160:1:1,0:135,24:159,1:0.0063:2,0:48:0:33:0:1:0:60:2:0.0063:0:0 +2 48033502 . G A 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCCTAGGACATATGGTAT;RSEQ=TGCAAATTGTTTTTTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:134,266:400,0:0:2,0:23.7:1:32.2:1:1:0:59.9:99:1:0:0.2 0/1:339:17:7,10:106,216:322,17:0.0501:2,2:15.9:1:27.8:1:0.59819:1.42:60:34:0.0511:0:1.3 +2 48033546 . C CT 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01589;SOR=0;LSEQ=TTCGGTTTTTTGAGAGGGCA;RSEQ=TTCTCTTGCTAGCACATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:10:5,5:78,128:206,10:0.0338:2,2:13.3:1:29.7:1:0.51269:1.64:60:20:0.0345:0.027:1.1 0/0:175:0:0,0:73,98:171,0:0:2,0:26.1:1:31.3:1:1:0:60:27.5:0.9763:0:0.8 +2 48033549 . CTC TCTG 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.06448;LSEQ=TCGGTTTTTTGAGAGGGCAC;RSEQ=TTGCTAGCACATGTATCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:79:35,44:78,128:206,79:0.2669:2,2:24.4:1:31.6:1:0.34521:1.30:59.8:78:0.269:0.0608:1.1 0/1:175:4:1,3:73,98:171,4:0.0229:2,2:17:1:31.5:1:0.6387:2.22541:60:8:0.0237:0.0057:1 +2 48033551 . C G 220 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTTGAGAGGGCACTTCT;RSEQ=TTGCTAGCACATGTATCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:82,124:206,0:0:2,0:21.3:1:32.9:1:1:0:59.7:205:1:0:0.1 1/0:176:118:50,68:25,29:54,118:0.6705:2,2:25.6:1:32.1:1:0.7406:1.17132:60:117:0.6842:0:1.1 +2 48033791 . GTAAC G 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=3.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=CAGTCACTACGATTATTTCG;RSEQ=TAACTAACTATAATGGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:0:0,0:207,317:524,0:0:2,0:23.2:1:28.9:1:1:0:59.9:523:1:0:0.1 0/1:474:17:7,10:173,284:457,17:0.0359:2,2:30.1:1:31.6:1:0.80272:1.15:59.9:34:0.0362:0:0.3 +2 48033829 . C G 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TGGAATTATAACTAACTGAC;RSEQ=TTAAGTTTCAAAGAAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:116,228:344,0:0:2,0:27.5:1:32.1:1:1:0:59.8:42:1:0:0.2 0/1:273:12:2,10:99,162:261,12:0.044:2,2:32.8:1:31:1:0.22049:3.04526:60:24:0.0441:0:1 +2 48033846 . CAGTAAA C 217 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACCTTAAGTTTCAAAGAAA;RSEQ=AGGGGAAGGGATGATGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:107:42,65:67,128:195,107:0.3531:2,2:24.7:1:32.2:1:0.45254:1.23:59.5:52.5:0.3559:0.0462:0.3 0/0:206:0:0,0:84,122:206,0:0:2,0:25.1:1:30.1:1:1:0:59.9:40.2:1:0:0.3 +2 48033909 . A T 62 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.79901;SOR=1.18144;LSEQ=ACTTTTTTTTTTTTTTTTTT;RSEQ=ATTTTAAGGGAAGTTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:7:4,3:225,137:362,7:0.0188:2,2:12.6:1:20.1:1:1:1.23103:53.7:1.333:0.012:0:1.4 0/1:361:8:4,4:212,139:351,8:0.0222:2,2:7.6:1:20.8:1:0.7179:1.52329:52.8:3:0.02:0:1.6 +2 49394705 . T G 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.68644;LSEQ=TAGCTGACAAGAAAGACAGG;RSEQ=AGAGGATATACAGAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:510:72:37,35:227,210:437,72:0.1412:2,2:25.6:1:31.1:1:1:1.02248:60:71:0.1406:0:1.1 0/1:368:178:96,82:90,99:189,178:0.4837:2,2:25.9:1:30.7:1:0.25099:1.29:59.9:356:0.4917:0:1.1 +2 49394735 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00046;SOR=2.48031;LSEQ=ACAGAGAAAAATAGTCTACT;RSEQ=AAGTCTTTGTACGGACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:26:12,14:221,277:498,26:0.0496:2,2:28.7:1:32.5:1:1:1.07:60:52:0.0501:0:1.2 0/1:366:42:17,25:141,181:322,42:0.1148:2,2:29.4:1:30.9:1:0.74235:1.14517:60:84:0.1157:0:1.1 +2 50178087 . C T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26364;SOR=0;LSEQ=GACCATAAATCAGCTGTCTG;RSEQ=TTGGGAAAAAGGCAGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:1,2:167,103:270,3:0.011:2,2:21.7:1:29.3:1:0.56083:3.2284:60:6:0.0113:0:1 0/0:205:0:0,0:124,81:205,0:0:2,0:25:1:31:1:1:0:60:50.25:1:0:0.4 +2 50178130 . AT A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.13708;SOR=0;LSEQ=AGCCATTCAATTTTCTTCGA;RSEQ=TTTTTTCAGCTGTTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:4:2,2:190,182:372,4:0.0106:2,2:27.8:1:31:1:1:1.04385:60:8:0.0107:0:0 0/0:288:0:0,0:143,145:288,0:0:2,0:26.1:1:29.6:1:1:0:59.7:71:1:0:0.7 +2 50178151 . A T 220 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTTTCAGCTGTTTAAAA;RSEQ=GTATGCAATGGTTCCAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:185,195:380,0:0:2,0:25.4:1:31.2:1:1:0:60:189:1:0:0.1 1/0:291:181:86,95:55,55:110,181:0.622:2,2:25.2:1:29.4:1:0.71749:1.10427:59.5:59.333:0.6202:0:1.2 +2 50178197 . ACT A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00372;SOR=Inf;LSEQ=AAGTGGGTTTGAGTAGAAGA;RSEQ=CTGCCGTGGTAAAGAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:99,164:263,0:0:2,0:24.2:1:32.9:1:1:0:60:130.5:1:0:0.1 0/1:218:7:1,6:87,124:211,7:0.0321:2,2:26:1:32.3:1:0.24588:4.18791:60:14:0.0327:0.0092:0.9 +2 51288299 . T C 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TTTGATTAAATCAACAACTT;RSEQ=TTAAATAAAAGTACCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:164,1:165,0:0:1,0:23.7:1:30.9:1:1:0:60:26.5:1:0:0.1 0/1:93:10:10,0:81,2:83,10:0.1075:1,0:22.9:1:31.4:1:1:0:60:20:0.1075:0:1 +2 51288348 . C CA 45 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.70222;SOR=1.36143;LSEQ=ATTAAAGACAACTTTCTCAA;RSEQ=AAAAAAAAGGACATTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:3:3,0:327,68:395,3:0.0075:2,0:33.7:1:30:1:1:0:60:6:0.0076:0:0 0/1:293:3:2,1:223,66:289,3:0.0102:2,2:17:1:28.7:1:0.5439:1.68596:60:6:0.0104:0:0.7 +2 51288460 . C G 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2221;LSEQ=CAGGATGCCTGCCTTTAACA;RSEQ=TGCTATTCAACATTGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:391:188,203:317,297:614,391:0.3887:2,2:24:1:32.3:1:0.30056:1.15233:60:34.545:0.3835:0:1.3 0/1:736:91:41,50:332,313:645,91:0.1236:2,2:26.4:1:30.2:1:0.26439:1.29308:59.7:10.375:0.1153:0:1.4 +2 51288569 . A G 232 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=CACACATATTTTATAGATAG;RSEQ=TAGATGGTATCCAAGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1268:0:0,0:759,506:1265,0:0:2,0:24.5:1:30.3:1:1:0:58.5:51.708:0.9976:0:0.4 0/1:1096:224:135,89:491,379:870,224:0.2044:2,2:24.5:1:29.8:1:0.32518:1.17:58.3:10.2:0.1932:0:1.3 +2 51288710 . A C 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10562;LSEQ=GCAAAGTTGCGGGGTACAAG;RSEQ=TTGATACTCAAAAATCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1204:487:153,334:222,494:716,487:0.4045:2,2:25.6:1:32.4:1:0.89916:1.02:60:47.7:0.4032:0:1.1 0/1:957:64:22,42:315,578:893,64:0.0669:2,2:24.2:1:31:1:1:1.04038:60:63:0.0669:0:1.2 +2 52993022 . G T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=AGCAGCTGTGGAAGTCTGCA;RSEQ=CCAGAGTGCCTCTTCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:36:0:29.5:1:1:1.22474:60:4:0.1818:0:1 0/0:8:0:0,0:4,4:8,0:0:2,0:30.5:1:32.8:1:1:0:56.6:16:1:0:0.1 +2 52993507 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=Inf;LSEQ=GAATCAGATGAATAGGGCCT;RSEQ=AAGTGAATCCCCAGCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:31:1:32.8:1:1:0:42.2:10:1:0:0.2 0/1:10:2:1,1:4,4:8,2:0.2:2,2:18.5:1:32.5:1:1:1:42.5:4:0.2:0:1 +2 52993657 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17143;SOR=Inf;LSEQ=CCAAAACTAGACAAACTCAC;RSEQ=ATAATGAGAAAGAGTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,15:29,0:0:2,0:26.2:1:29.8:1:1:0:58.6:28:1:0:0.6 0/1:21:2:2,0:8,9:17,2:0.0952:2,0:21:1:25:1:0.47368:0:60:4:0.1111:0:1.5 +2 52993660 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.76661;SOR=1.41489;LSEQ=AAACTAGACAAACTCACGAT;RSEQ=ATGAGAAAGAGTCAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:5,7:7,7:14,12:0.4615:2,2:34.4:1:30:1:0.71269:1.38191:56.7:11:0.44:0:1.2 1/0:20:11:5,6:4,5:9,11:0.55:2,2:26.5:1:28:1:1:1.04:57.2:4.5:0.5:0:1.6 +2 52993673 . C CA 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.60386;SOR=0.32306;LSEQ=TCACGATAATGAGAAAGAGT;RSEQ=AAAAAAAAAAATGCTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:6,10:16,3:0.1579:2,2:39.3:1:32:1:1:1.18873:60:6:0.1765:0:0.7 0/1:18:1:0,1:9,8:17,1:0.0556:2,0:19:0:32:0:1:0:60:2:0.0625:0:0 +2 52994119 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=ACGAAGCCTTCAAGAAATAT;RSEQ=GGACTTTATAAAAAGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:6,0:0:2,0:30:1:32.2:1:1:0:54.7:12:1:0:0.2 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:28.5:1:1:0:56.5:4:1:0:1 +2 54256901 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23142;SOR=Inf;LSEQ=GCCAACAGCATGCTGGGGAA;RSEQ=ATTGTAGGCTCTTCCAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:26,22:48,0:0:2,0:32.1:1:31.8:1:1:0:46.5:47:1:0:0.3 0/1:45:2:1,1:21,22:43,2:0.0444:2,2:35:1:29:1:1:1.05:52:4:0.0444:0:1 +2 54257795 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.175;SOR=Inf;LSEQ=GAATATCTACCCAGCGCCTC;RSEQ=CCTCTCTCCCTTTGTGTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:22.6:1:30.3:1:1:0:60:18:1:0:0.3 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:47.5:1:30:1:1:1.41418:60:4:0.2857:0:1 +2 54257826 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=TTTGTGTTCGTTATTTTGGC;RSEQ=AATTACTGGAAGACGGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:43.5:1:31:1:1:1.41:60:4:0.2857:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:17.8:1:28:1:1:0:60:10:1:0:0.4 +2 54652827 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.21142;SOR=Inf;LSEQ=CAACAGCAGCACCAGCAGCA;RSEQ=CAAGATGAGAAGGCTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:37,0:0:2,0:27.4:1:31.9:1:1:0:60:36:1:0:0.2 0/1:32:2:1,1:12,18:30,2:0.0625:2,2:41.5:1:26:0:1:1.48:60:4:0.0645:0:1 +2 54652923 . C T 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=CTCAGAAATAACTGATGGGA;RSEQ=AGTGACAGTAGCTGATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:15.5:1:27:1:1:0:60:4:0.2222:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:3:0:28:0:1:0:60:2:1:0:1 +2 54659980 . C G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTGAACAGCCCATTCCCT;RSEQ=TTTGTTTCAACTTTGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:1,3:0.75:0,2:10.3:1:31:1:1:0:60:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 54660456 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24443;LSEQ=CCTAAATGTTTCCTTCCAAT;RSEQ=CTTTCATGTATGATGTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:95:74,21:116,29:145,95:0.3942:2,2:23.6:1:28.3:1:0.74609:1.13453:60:94:0.3983:0:1.3 0/1:190:26:18,8:116,46:162,26:0.1368:2,2:21.2:1:27.7:1:0.81752:1.12007:60:52:0.1376:0:1.4 +2 54660484 . G A 150 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.03495;LSEQ=GTATGATGTTAGGGATCTGC;RSEQ=TGTTCATAGGCTTCACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:31:22,9:241,95:336,31:0.0845:2,2:26.1:1:30.3:1:1:1.03769:60:30:0.0845:0:1.3 0/0:312:1:1,0:194,117:311,1:0.0032:2,0:36:0:29:0:1:0:60:2:0.0033:0:1 +2 54660542 . C T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04579;SOR=0.77769;LSEQ=CAGCCATTCCCTGGGGCCCA;RSEQ=GACCAGTGACTACTAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:608:410:222,188:106,92:198,410:0.6743:2,2:26.2:1:30.6:1:0.93087:1.02:60:57.571:0.6717:0:1.2 1/0:522:322:176,146:97,102:199,322:0.6169:2,2:26:1:29.6:1:0.2066:1.27:60:79.5:0.6139:0:1.2 +2 55685927 . C A 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGTCAGGAGATCGAGAC;RSEQ=AGCCTATCCAACATGGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:30.5:1:1:0:53:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:38:0:26:0:1:0:44:2:1:0:1 +2 55687290 . G C 49 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TTTCTGTATCGTGATTCCTC;RSEQ=GTCTCGAGAAATGGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:19:1:31.3:1:1:0:60:6:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:10:0:31:0:1:0:23:2:1:0:0 +2 55687526 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49903;SOR=0;LSEQ=TCTACTGACAAAATAAATGT;RSEQ=AAAGGTAACTGTCTGCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:123,41:164,2:0.012:2,2:11.5:1:32:1:0.44315:2.97608:60:4:0.0123:0:2 0/0:155:0:0,0:109,46:155,0:0:2,0:23.4:1:27.9:1:1:0:60:310:1:0:0.5 +2 55687597 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0;LSEQ=GCCAGAGTTAAAGCAAGATT;RSEQ=AGCCTAGGAGACACAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:304:304:152,152:0,0:0,304:1:0,2:26.1:1:29.5:1:1:0:59.9:151:1:0:1.8 1/1:303:290:138,152:7,5:12,290:0.9571:2,2:25.7:1:28.5:1:0.56131:1.53981:59.9:95.667:0.9599:0:1.6 +2 55687618 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18838;LSEQ=AGCCTAGGAGACACAGAGAC;RSEQ=TGGTAGTTTCTGGATAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:307:262:120,142:18,27:45,262:0.8534:2,2:25.9:1:32.3:1:0.51882:1.27:60:130:0.8553:0:1.9 1/0:291:152:70,82:65,74:139,152:0.5223:2,2:26.5:1:30.6:1:0.90696:1.02887:60:75:0.5282:0:2 +2 55687681 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25082;SOR=0;LSEQ=TAGATACATTTTTGGAAACA;RSEQ=TTTTATTCTAGTTCTACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:1,2:56,127:183,3:0.0161:2,2:13:1:24.3:1:1:1.13:60:2:0.0108:0:2.7 0/0:164:0:0,0:50,114:164,0:0:2,0:24.8:1:31.3:1:1:0:59.8:163:1:0:0.6 +2 55844445 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGCTGTCTCCACCGCTC;RSEQ=AGCCGCCGCCTCCTCGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 55844521 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.54282;SOR=Inf;LSEQ=AGGCAGTAGTGGCGGTGGCG;RSEQ=CGGCGGCGGCTTCGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:18,0:0:2,0:31.7:1:32.1:1:1:0:60:36:1:0:0.2 0/1:35:2:1,1:18,15:33,2:0.0571:2,2:23:0:31:0:1:1.19373:60:4:0.0606:0:1.5 +2 55844616 . A AG 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGAGGCCTCTCCGCCCGG;RSEQ=GCCCCGTTACCTCTCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:25:1:30.6:1:1:0:60:12:0.8571:0.1429:0 1/1:6:6:0,6:0,0:0,6:1:0,0:18:1:29.5:1:1:0:60:12:1:0.5:0.3 +2 57016125 . T G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.13484;LSEQ=AATGAGAAATGAATCAATGA;RSEQ=TTTGTCAATTAAAATATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:8,7:0.4667:0,0:15.6:1:34.1:1:1:0:60:14:0.4667:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:8.5:1:32:1:1:0:60:4:0.5:0:1 +2 57016218 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07649;SOR=Inf;LSEQ=ATGGAATGCAGAGAATTATA;RSEQ=TTGGTAGGAATGAATGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:84,1:85,0:0:1,0:24.1:1:32.9:1:1:0:60:170:1:0:0.1 0/1:33:2:2,0:31,0:31,2:0.0606:1,0:32.5:1:32.5:1:1:0:60:4:0.0625:0:1 +2 57016287 . G T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14028;SOR=Inf;LSEQ=AGACAGCTGTGTGTTTGTGA;RSEQ=CCACTTACACTTGGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:198,55:253,0:0:2,0:23.6:1:33.1:1:1:0:60:125.5:1:0:0.2 0/1:152:2:1,1:117,33:150,2:0.0132:2,2:10:1:23.5:1:0.39848:3.50763:60:4:0.0132:0:1.5 +2 57016366 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03076;SOR=0.76432;LSEQ=GGAAAGAAAGTACTGTTGAA;RSEQ=TCTGTTCAGTAATTAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:652:305:147,158:168,179:347,305:0.4678:2,2:26.8:1:30.6:1:1:1.00877:60:100.667:0.4675:0:1.9 0/1:448:180:92,88:129,139:268,180:0.4018:2,2:25.7:1:29.4:1:0.56377:1.13:59.8:89:0.4:0:1.8 +2 57016392 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11499;SOR=0.80987;LSEQ=TCAGTAATTAACAGGTGTTT;RSEQ=TATACACATCATTTTATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:609:275:116,159:147,187:334,275:0.4516:2,2:27:1:32.3:1:0.68138:1.07736:60:90.667:0.4511:0:1.9 0/1:385:154:68,86:105,126:231,154:0.4:2,2:25.9:1:31.5:1:0.83472:1.05381:59.8:153:0.3984:0:1.9 +2 57016409 . T C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTATATACACATCATTTTA;RSEQ=TCCATCTATGTCTTTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:0:0,0:204,320:524,0:0:2,0:25.3:1:30.8:1:1:0:60:261:1:0:0.9 0/1:322:13:5,8:123,185:308,13:0.0404:2,2:26.1:1:31.4:1:1:1.06359:60:26:0.0411:0:1.4 +2 57016461 . G A 57 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16218;SOR=6.01566;LSEQ=TCAAGATTTACAAAGGTTGG;RSEQ=ATGAACAGAAGTCTCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:1,0:34,161:195,1:0.0051:2,0:1:0:25:0:0.17857:0:60:2:0.0051:0:1 0/1:133:4:1,3:29,100:129,4:0.0301:2,2:12.8:1:28.5:1:1:1.15:60:8:0.0305:0:2 +2 58496276 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.80505;LSEQ=CAAAACCTTTCTCAAAACTC;RSEQ=TCTCCAAAATCATCCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:651:193:73,120:181,272:453,193:0.2965:2,2:26.7:1:30.4:1:0.66015:1.0937:59.9:18.3:0.2985:0:1.3 0/1:560:242:103,139:121,189:310,242:0.4321:2,2:26.3:1:29.4:1:0.43211:1.16:60:19.167:0.4299:0:1.3 +2 58496321 . A T 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCTAATTTTAATCCATCCTT;RSEQ=ATCTAGCACTGTATGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:573:0:0,0:222,348:570,0:0:2,0:26.6:1:29.6:1:1:0:60:80.429:0.9965:0:0.4 0/1:478:14:4,10:195,269:464,14:0.0293:2,2:29.6:1:27.4:1:0.41378:1.81016:60:13:0.0277:0:2 +2 58496397 . T A 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACTATGTTTTTACTTGTT;RSEQ=CATTGTTCTGTTTCATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:3,121:124,0:0:1,0:23.4:1:30.4:1:1:0:60:123:1:0:0.1 0/1:93:19:2,17:6,68:74,19:0.2043:2,2:25.1:1:29:1:0.66426:1.33:60:38:0.2043:0:1 +2 59093379 . A G 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0799;SOR=Inf;LSEQ=AGTCCCATTGAAAAGGCGAG;RSEQ=GCTGCCTGCTGAGCTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:161,106:267,0:0:2,0:22.3:1:30.2:1:1:0:60:28.667:1:0:0.1 0/1:203:3:1,2:123,77:200,3:0.0148:2,2:28:1:25.7:1:0.56144:3.17614:60:2:0.01:0:1.3 +2 59093487 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50192;SOR=0;LSEQ=TGTGGGTTCTGACTCGCTCT;RSEQ=GATGATATTGGAGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:53,121:174,2:0.0114:2,2:26:1:30:1:0.52071:2.27:60:4:0.0115:0:1 0/0:149:0:0,0:49,98:147,0:0:2,0:20.3:1:29.1:1:1:0:60:48:0.9863:0:0.1 +2 59093502 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.50663;SOR=0;LSEQ=GCTCTTGATGATATTGGAGT;RSEQ=TGTGTTTGTGGCACTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:27,99:126,2:0.0156:2,2:23:1:30.5:1:0.39099:3.62:60:4:0.0156:0:1 0/0:98:0:0,0:28,70:98,0:0:2,0:28:0:14:0:1:0:60:0:0:0:5 +2 59093686 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTTAGGAAGGGAGATTT;RSEQ=GGGCTTTTTTTCCCCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:19:1:32:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 59400645 . T C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70339;SOR=1.64348;LSEQ=AAAGGGAAGGGCCCCCCGTC;RSEQ=TGTGATCACGTGACTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:7,5:3,2:5,12:0.7059:2,2:30.2:1:31.3:1:1:1.06713:38.3:24:0.7059:0:1.2 1/1:20:16:8,8:2,2:4,16:0.8:2,2:28.8:1:31.4:1:1:1:35.7:32:0.8:0:1.3 +2 60170649 . CTG C 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=9.000;MSILEN=2;SSF=0.6494;SOR=0.46079;LSEQ=TAGTAAATATATGTGTGTGT;RSEQ=TGTGTGTGTGTGTGTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:27.3:1:32.8:1:1:0:60:12:0.4286:0.0714:0 0/1:8:2:2,0:5,1:6,2:0.25:2,0:32.5:1:29.5:1:1:0:60:4:0.2857:0:1 +2 60170678 . G A 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.12644;SOR=Inf;LSEQ=TGTGTGTGTGGTGTGTGTGT;RSEQ=TGTTTCTGTAGATATTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:19,0:19,0:0:1,0:21.8:1:32.1:1:1:0:60:38:1:0:0 0/1:11:2:2,0:8,1:9,2:0.1818:2,0:29:1:23.5:1:1:0:60:4:0.1818:0:1 +2 60170875 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36306;LSEQ=TGGTCTTATCTCTAAAATAA;RSEQ=ATGATCAACTCTCTGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:179:82,97:92,74:166,179:0.5188:2,2:24.6:1:29.3:1:0.0849:1.46898:60:178:0.5205:0:1.1 0/1:242:68:35,33:88,85:173,68:0.281:2,2:24.5:1:28.7:1:1:1.02:60:136:0.281:0:1 +2 60170956 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16076;SOR=Inf;LSEQ=GTTGAAGAAAAACTTTCTTA;RSEQ=ACAACAGCAAGAAAGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:48,141:189,0:0:2,0:24.1:1:29.3:1:1:0:60:378:1:0:0.6 0/1:127:2:1,1:36,89:125,2:0.0157:2,2:22:0:31.5:1:0.49944:2.45:60:4:0.016:0:2.5 +2 60170973 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=0.33185;LSEQ=TTATACAACAGCAAGAAAGT;RSEQ=TTTGTAGCATGAATTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:145:75:17,58:10,60:70,75:0.5172:2,2:20.7:1:32.3:1:0.20879:1.75:60:150:0.5172:0:1.1 0/1:88:23:6,17:13,52:65,23:0.2614:2,2:25.5:1:31.3:1:0.56359:1.41:60:46:0.2614:0:1.2 +2 60171126 . T C 34 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0.76645;LSEQ=TGCAGTTGTCAAAGTGAATG;RSEQ=ATGTACTGGGGACAAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:27:1:34:0:1:0:60:4:0.2857:0:1 0/1:5:1:0,1:0,4:4,1:0.2:0,0:8:0:32:0:1:0:60:2:0.2:0:1 +2 60902384 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=CCTGATTCTGATCCAGTAGG;RSEQ=CCAAGTTGAGGCCTGATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:11,4:15,2:0.1176:2,2:10.5:1:31.5:1:0.51471:2.56905:60:4:0.1176:0:1 0/0:17:0:0,0:10,7:17,0:0:2,0:18.7:1:27.8:1:1:0:60:34:1:0:0.4 +2 60902408 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13564;SOR=Inf;LSEQ=AGTTGAGGCCTGATAGCCCA;RSEQ=ACCTGTAACAGGCTTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:18,12:30,0:0:2,0:23.8:1:32.1:1:1:0:60:60:1:0:0.2 0/1:18:2:1,1:8,8:16,2:0.1111:2,2:45:1:30.5:1:1:1:60:4:0.1111:0:1 +2 60902430 . G A 85 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.00113;SOR=18.94817;LSEQ=CCTGTAACAGGCTTCCAGCT;RSEQ=CTGCTGCTGCTGGTGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:1,0:22,13:35,1:0.0278:2,0:8:0:23:0:1:0:60:2:0.0278:0:1 0/1:22:8:5,3:7,7:14,8:0.3636:2,2:26.9:1:28.5:1:0.67492:1.63:60:16:0.3636:0:1 +2 60902510 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGTTATTCGGGGTCCACA;RSEQ=CCTCAGCTGTAGCCTTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:5,14:19,2:0.0952:2,2:18.5:1:29:1:0.5:2.65:60:4:0.1:0:1.5 0/0:7:0:0,0:2,5:7,0:0:2,0:21.7:1:29.4:1:1:0:60:14:1:0:0.1 +2 61079090 . A G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTGCATGTGTGTGTGT;RSEQ=TTAAAAAATAATTTATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:32:1:1:0:60:4:1:0:1 +2 61079440 . C A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11196;SOR=Inf;LSEQ=CGCAACCCGTGTTCTCTAGG;RSEQ=CTTTTAGAAAACATGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:29,0:0:2,0:27.8:1:32.2:1:1:0:51.9:58:1:0:0.2 0/1:28:3:2,1:14,11:25,3:0.1071:2,2:24:1:22.7:1:1:1.55:57.3:2:0.08:0:1 +2 61079589 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=CTGGAAGAGTCTACAGTGTT;RSEQ=CACAGCATGCTGTTGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:8:1:31.6:1:1:0:60:16:1:0:0.4 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:7.5:1:26:1:1:1.41:60:4:0.2857:0:1.5 +2 61079674 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TAATGTGGGTATTTATTGAG;RSEQ=ACAGCCACCATAGCATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:23.5:1:32.5:1:1:1.13389:60:4:0.1176:0:1 0/0:5:0:0,0:3,2:5,0:0:2,0:20.2:1:31:1:1:0:60:10:1:0:0.6 +2 61079678 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGTATTTATTGAGCACA;RSEQ=CCACCATAGCATTATTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:22:1:29:1:1:1.13389:60:4:0.1176:0:1 0/0:5:0:0,0:3,2:5,0:0:2,0:19.4:1:30:1:1:0:60:10:1:0:0.6 +2 61108829 . G A 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09018;SOR=0.51587;LSEQ=GAGCCGCAAACCCAGCGGAG;RSEQ=GCGGGAAGAAGGAGGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:32:31,1:25,0:25,32:0.5614:1,1:23.5:1:29.8:1:1:0:60:64:0.5714:0:1 0/1:53:21:19,2:28,4:32,21:0.3962:2,2:26.4:1:28.3:1:1:1.35:60:20:0.3922:0:1.1 +2 61108891 . C A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49897;SOR=Inf;LSEQ=GGGGCCCCGCCGGCAGAGGT;RSEQ=CCTCGGCCTCCTGACTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:147,22:169,0:0:2,0:24.2:1:32.4:1:1:0:59.9:168:1:0:0.5 0/1:179:2:1,1:138,39:177,2:0.0112:2,2:34.5:1:24:1:0.39797:3.5064:60:4:0.0114:0:2 +2 61108894 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49888;SOR=Inf;LSEQ=GCCCCGCCGGCAGAGGTCCC;RSEQ=CGGCCTCCTGACTGACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:154,28:182,0:0:2,0:23.5:1:32:1:1:0:59.9:90:1:0:0.5 0/1:190:2:1,1:143,45:188,2:0.0105:2,2:27.5:1:30:1:0.42657:3.15401:60:4:0.0109:0:2 +2 61108896 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24833;SOR=Inf;LSEQ=CCCGCCGGCAGAGGTCCCTC;RSEQ=GCCTCCTGACTGACTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:159,35:194,0:0:2,0:22.8:1:30.1:1:1:0:59.9:63.667:1:0:0.5 0/1:201:3:2,1:148,50:198,3:0.0149:2,2:19:1:29.7:1:1:1.47686:60:6:0.0152:0:1.7 +2 61108926 . C G 218 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGACTGACTGCGGCCGCCT;RSEQ=CGGCCAGGACGCTGGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:122:71,51:133,68:201,122:0.3754:2,2:24.7:1:31.5:1:0.15547:1.40339:60:60:0.3727:0:1.1 0/0:381:0:0,0:231,150:381,0:0:2,0:23.4:1:30:1:1:0:60:33.636:1:0:0.3 +2 61108996 . A T 188 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=70.90866;LSEQ=ATGGCCTCCGGTGAGTGTTC;RSEQ=TGGGGCGCGGGCCTGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:1:1,0:216,251:467,1:0.0021:2,0:38:0:16:0:0.46368:0:60:0:0:0:7 0/1:583:77:36,41:241,264:505,77:0.1321:2,2:24.9:1:30:1:0.90299:1.03961:59.8:24.667:0.1298:0:1.4 +2 61109147 . A G 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.66468;LSEQ=TTAAAAAAGTTACCTGCTTC;RSEQ=GGGTTTGCGTGCAGAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:0,4:0,41:41,4:0.0889:1,0:11.8:1:31.5:1:1:0:60:8:0.0909:0:1.3 0/1:33:2:0,2:1,30:31,2:0.0606:1,0:33:1:31:1:1:0:60:4:0.0606:0:1.5 +2 61109544 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGGCCGGGCGCGGTGGC;RSEQ=CATGCCTGTATTCCCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 61118738 . TA T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.24694;SOR=0;LSEQ=TTTGTTTTAGTCTGCTGTTA;RSEQ=AAAAAAACAGAATGTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:108,12:120,2:0.0164:2,0:39:1:32:1:1:0:60:4:0.0167:0:0 0/0:123:0:0,0:75,7:82,0:0:2,0:22.5:1:27.7:1:1:0:59.5:81:0.6639:0:0 +2 61119075 . C T 28 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACAGGTTTATCTTTTT;RSEQ=TTTTTTCCTTTTTTTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:0,2:2,111:113,2:0.0174:1,0:6:0:28:1:1:0:58.5:4:0.0196:0:1.5 0/0:46:0:0,0:0,46:46,0:0:1,0:23.7:1:30.2:1:1:0:60:8.2:1:0:0.1 +2 61119083 . C CT 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.82394;LSEQ=GTTTATCTTTTTCTTTTTTC;RSEQ=TTTTTTTTTTTAAACGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:10:0,10:2,94:96,10:0.0943:1,0:27.2:1:30.2:1:1:0:60:20:0.098:0.0094:0.8 0/1:38:3:0,3:0,35:35,3:0.0789:1,0:15.3:1:28.3:1:1:0:60:6:0.0789:0:0 +2 61121472 . G C 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62188;SOR=0.49265;LSEQ=GTAAATTGAATTCTCATTTA;RSEQ=TAGATCAGTTTATAATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:0,2:148,30:178,2:0.0111:2,0:13:1:30:1:0.03079:0:60:4:0.0111:0:2 0/0:182:1:1,0:140,41:181,1:0.0055:2,0:3:0:31:0:1:0:60:2:0.0056:0:2 +2 61121492 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.07376;LSEQ=GTAGATCAGTTTATAATGCA;RSEQ=TCTATTTGGATCATGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:258:257:189,68:0,0:0,257:0.9961:0,2:24:1:30.6:1:1:0:60:84.667:1:0:1.1 1/1:277:276:193,83:0,0:0,276:0.9964:0,2:24.9:1:29.6:1:1:0:60:68:0.9963:0:1.1 +2 61128034 . C T 41 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.11319;SOR=0;LSEQ=GCTTTGGTATGTACAACTGA;RSEQ=AGCATGATAACTTCAGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:3:1,2:102,15:117,3:0.025:2,2:5.7:1:26.3:1:0.0523:13.08025:60:6:0.0254:0:1 0/0:127:0:0,0:110,17:127,0:0:2,0:20.4:1:31.7:1:1:0:60:62.5:1:0:0.1 +2 61128268 . G A 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATTTGGGTGTTGATTTCT;RSEQ=TTTCTTTTTTCTTTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:16,72:88,0:0:2,0:16.8:1:31.6:1:1:0:59.3:13.667:1:0:0.6 0/1:100:39:14,25:12,49:61,39:0.39:2,2:18.2:1:28.9:1:0.10129:2.27:60:78:0.4021:0:1.7 +2 61128284 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00583;SOR=3.95895;LSEQ=TTCTGTTTCTTTTTTCTTTC;RSEQ=CTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:26:5,21:2,15:17,26:0.5778:2,2:8.8:1:31.4:1:0.68452:1.76:59.3:52:0.6341:0:1.3 1/1:52:44:14,30:0,8:8,44:0.8462:0,2:8.4:1:29.5:1:0.09041:0:60:88:0.88:0:1.7 +2 61143965 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20475;SOR=Inf;LSEQ=GGAGGACCTAGCAAGTCTTT;RSEQ=GGTCTATGTGACTATTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:159,11:170,0:0:2,0:26:1:28.4:1:1:0:60:41.5:1:0:0.1 0/1:141:2:1,1:128,11:139,2:0.0142:2,2:15:1:28:1:0.16353:11.1847:60:4:0.0143:0:1 +2 61143993 . A AT 114 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.6727;SOR=1.27452;LSEQ=GTGACTATTACATTTAAAAA;RSEQ=TTTTTTTTTTCTATTCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:10:6,4:242,60:302,10:0.0316:2,2:27.5:1:30.4:1:0.12662:2.67812:60:20:0.0321:0:0.1 0/1:325:13:13,0:242,69:311,13:0.04:2,1:18.9:1:30.9:1:0.07834:0:60:26:0.0404:0.0123:0.3 +2 61145241 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14792;SOR=Inf;LSEQ=AAAACTTTTATTCTGTGAAT;RSEQ=CTTTTCCTCAAATTCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:119,5:124,0:0:1,0:22.6:1:32.8:1:1:0:60:248:1:0:0.1 0/1:78:2:1,1:71,5:76,2:0.0256:2,2:19.5:1:26:1:0.14885:13.05378:60:4:0.0263:0:1 +2 61147110 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49987;SOR=Inf;LSEQ=TATATGTGAATAAAATATTT;RSEQ=TTTATTAAAGGAGAGGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:141,29:170,0:0:2,0:22.9:1:32.7:1:1:0:60:169:1:0:0 0/1:188:2:1,1:148,38:186,2:0.0106:2,2:32:1:26:1:0.37274:3.85745:60:4:0.0108:0:1 +2 61147323 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.5062;SOR=0;LSEQ=AGTTTTTCAAATTTTATTAT;RSEQ=TTTGTTTTGTTTTGTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:10,149:159,2:0.0124:2,2:11:1:34.5:1:0.13238:14.25:60:4:0.0124:0:1 0/0:125:0:0,0:15,110:125,0:0:2,0:22:1:29.6:1:1:0:60:124:1:0:0.1 +2 61147590 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.2354;SOR=Inf;LSEQ=AGGTGATCCACCCACCTTGG;RSEQ=CTCCCAAAGTGCTGGGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:135,30:165,0:0:2,0:26:1:31.6:1:1:0:50.6:32:1:0:0.1 0/1:156:2:1,1:127,27:154,2:0.0128:2,2:27.5:1:27:1:0.32771:4.63712:51:4:0.0131:0:1 +2 61147604 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.23235;SOR=0;LSEQ=CCTTGGCCTCCCAAAGTGCT;RSEQ=GGATTACAGGTGGGAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:0,2:146,47:193,2:0.0103:2,0:21:1:31.5:1:0.06217:0:43:4:0.0104:0:3 0/0:209:0:0,0:153,56:209,0:0:2,0:23:1:30.7:1:1:0:54.9:51.25:1:0:0.1 +2 61705919 . G T 40 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6264;SOR=0.37435;LSEQ=TGCTGTTTTCCTCTGCTAAC;RSEQ=AGTTGCAGAGAAAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:247,49:296,3:0.01:2,2:5.7:1:25.7:1:0.07641:9.961:60:6:0.0102:0:1 0/0:265:1:0,1:202,62:264,1:0.0038:2,0:1:0:22:0:0.23774:0:60:2:0.0038:0:1 +2 61706131 . G A 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37328;SOR=0.25432;LSEQ=CAGATAGTTGAAATGTCAAC;RSEQ=CAATAAACTTCAACTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:4:2,2:77,252:329,4:0.012:2,2:13.8:1:29.5:1:0.23965:3.26:60:8:0.0121:0:1 0/0:326:1:1,0:91,234:325,1:0.0031:2,0:1:0:30:0:0.28221:0:55:2:0.0031:0:1 +2 61708575 . GT G 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.7113;LSEQ=TGCCTCAGCGTCCCAATAAT;RSEQ=TTTTTTTTTTTAATCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:0,24:24,2:0.0769:1,0:37.5:1:33.5:1:1:0:60:4:0.0769:0:0 0/1:18:1:0,1:0,17:17,1:0.0556:1,0:35:0:32:0:1:0:60:2:0.0588:0:0 +2 61709349 . C A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.09871;SOR=2.66411;LSEQ=ATGCATACCACTTCTGACTA;RSEQ=TTTTTTTTTTGTAGAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:13:13,0:29,0:29,13:0.2889:1,1:19.9:1:31.5:1:1:0:60:26:0.2889:0:1.1 1/0:21:11:11,0:9,0:9,11:0.5238:0,0:26.7:1:28.7:1:1:0:60:22:0.5238:0:1.2 +2 61709447 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.2397;SOR=Inf;LSEQ=CCTTAGGCTTCCCAAAGTGC;RSEQ=GGATTACAGGTGTGAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:154,30:184,0:0:2,0:22.9:1:31.6:1:1:0:60:19.444:1:0:0.1 0/1:177:2:1,1:146,29:175,2:0.0113:2,2:9:1:29.4:1:0.31106:4.96692:60:4:0.0117:0.0056:0 +2 61709715 . T A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11403;SOR=Inf;LSEQ=ATTAACTCCAAAATGTAATA;RSEQ=AACTATAGATCTTAGCGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:31,172:203,0:0:2,0:24.6:1:27.2:1:1:0:59.6:10.941:0.9947:0:0.3 0/1:194:3:2,1:43,148:191,3:0.0155:2,2:12:1:21.3:1:0.13496:6.79:51.3:2:0.0114:0:2.7 +2 61709732 . G GT 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.59716;SOR=2.3426;LSEQ=ATATAACTATAGATCTTAGC;RSEQ=TTTTTTTTTGTTTTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:0,1:14,127:141,1:0.007:2,0:13:0:32:0:1:0:60:2:0.0074:0:0 0/1:122:2:0,2:14,102:116,2:0.0164:2,0:32.5:1:30.5:1:1:0:60:4:0.0183:0:0 +2 61709736 . T G 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00782;SOR=3.00186;LSEQ=AACTATAGATCTTAGCGTTT;RSEQ=TTTTTGTTTTGTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:10:1,9:9,109:118,10:0.0781:2,2:21.1:1:28.4:1:0.57039:1.34:60:4:0.064:0:1.8 0/1:113:23:2,21:9,81:90,23:0.2035:2,2:20:1:25.4:1:1:1.16513:59.6:1.875:0.1515:0:2.3 +2 61709742 . G T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00116;SOR=3.48293;LSEQ=AGATCTTAGCGTTTTTTTTT;RSEQ=TTTTGTTTTTTTTTTTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:11:1,10:4,90:94,11:0.1038:1,2:19.8:1:27.5:1:0.43154:2.23:55.5:4.5:0.1023:0:2.8 0/1:97:28:0,28:5,63:68,28:0.2887:2,1:20.1:1:30.3:1:0.31702:0:56.1:56:0.3415:0:2.9 +2 61709747 . GT G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.03798;SOR=2.12897;LSEQ=TTAGCGTTTTTTTTTGTTTT;RSEQ=TTTTTTTTTTTAGACGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:17:0,17:1,70:71,17:0.1868:1,1:28.9:1:33:1:1:0:60:34:0.1932:0.022:0.6 0/1:85:28:0,28:3,49:52,28:0.3294:2,1:24.8:1:31.2:1:0.5481:0:58:56:0.3544:0.0353:1.7 +2 61710077 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=TGGCACTTAACATTTAAATC;RSEQ=TATTAAATTCTTACCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:141,53:194,0:0:2,0:24.4:1:30.4:1:1:0:59.8:37.8:1:0:0.1 0/1:194:2:1,1:134,58:192,2:0.0103:2,2:19:1:28.5:1:0.51685:2.29924:60:4:0.0103:0:1 +2 61710320 . T A 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0396;SOR=0;LSEQ=AAGTATTCTGAATCTAACCC;RSEQ=GTTCTCCCTTTTTTTTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:6:0,6:1,86:87,6:0.0645:1,0:26.7:1:33.7:1:1:0:60:12:0.0659:0:1 0/0:68:0:0,0:0,68:68,0:0:1,0:24:1:29.6:1:1:0:60:136:1:0:0.1 +2 61710328 . CT C 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.35404;LSEQ=TGAATCTAACCCTGTTCTCC;RSEQ=TTTTTTTGGGATGATGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:0,2:0,76:76,2:0.0256:1,0:31:1:35:0:1:0:60:4:0.0256:0:0.5 0/1:58:2:0,2:0,56:56,2:0.0345:1,0:28:1:30.5:1:1:0:60:4:0.0351:0:0 +2 61711293 . G C 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06117;SOR=Inf;LSEQ=TCAGTGTCTTTGTTGTGCTA;RSEQ=ACAGGAGGGGAAAAGCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:21,137:158,0:0:2,0:21.2:1:32.4:1:1:0:60:316:1:0:0.1 0/1:168:5:1,4:25,138:163,5:0.0298:2,2:16.6:1:30.6:1:0.57335:1.38:60:10:0.0299:0:1.2 +2 61711440 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03226;SOR=Inf;LSEQ=AACTGTCCCGTTACGCACAT;RSEQ=AGTTATCAAATTGAAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:0,25:25,0:0:1,0:30.6:1:31:1:1:0:58:11.5:1:0:0.1 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:24.5:1:31.5:1:1:0:60:4:0.3333:0:1 +2 61711815 . G T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTCTGTCACCCAGGCTGGA;RSEQ=TGCGTGGCGCGATCTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:34:0:34:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:23.5:1:31.5:1:1:0:25:4:0.6667:0:2 +2 61713110 . GA G 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.06469;SOR=0;LSEQ=TCAGCGACCTGTTGGGGAGG;RSEQ=AAAAAAAGTTATGTTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:5:1,4:66,293:359,5:0.0137:2,2:25.6:1:31.3:1:1:1.11:60:10:0.0139:0.0027:0.6 0/0:316:0:0,0:89,227:316,0:0:2,0:22.2:1:29.5:1:1:0:60:157:1:0:0.1 +2 61713210 . GAAAATCTTGT TAGG 119 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.28622;LSEQ=TGATCATCTACTGAAAACAG;RSEQ=GTTTGTATTAGGGTTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:0,2:0,48:48,2:0.04:1,0:39.5:1:31.4:1:1:0:60:4:0.0408:0:0 0/1:32:15:0,15:0,15:15,15:0.4688:1,1:19.5:1:30.7:1:1:0:60:30:0.4688:0.0938:0.1 +2 61713218 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05141;SOR=Inf;LSEQ=TACTGAAAACAGGAAAATCT;RSEQ=GTGTTTGTATTAGGGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:0,46:46,0:0:1,0:22.6:1:30.8:1:1:0:59.9:92:1:0:0.2 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:25.5:1:28.5:1:1:0:60:4:0.1429:0:2 +2 61713220 . T G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04559;SOR=Inf;LSEQ=CTGAAAACAGGAAAATCTTG;RSEQ=GTTTGTATTAGGGTTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:0,46:46,0:0:1,0:21.6:1:30.8:1:1:0:59.9:92:1:0:0.2 0/1:13:2:0,2:0,11:11,2:0.1538:0,0:27:1:28:1:1:0:60:4:0.1538:0:2 +2 61713320 . CT C 35 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=GGACACACTGTCATTCAAGA;RSEQ=TTTTTTTTTTGAGACAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:15.5:1:35:0:1:0:60:4:0.4:0:0 1/0:2:1:0,1:0,1:1,1:0.5:0,0:27:0:31:0:1:0:60:2:1:0:1 +2 61713526 . C G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCAGTGGGTGTCTCCAA;RSEQ=TTAGGTGGCAGAATCAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 61715159 . GACT G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04763;SOR=2.4177;LSEQ=TATTAGTATATTAACGTAAG;RSEQ=ACAATAAATAAAATGCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:12:12,0:72,2:74,12:0.1395:1,0:20.8:1:31.6:1:1:0:60:24:0.1463:0.0581:0.1 0/1:53:15:15,0:38,0:38,15:0.283:1,1:18.1:1:31:1:1:0:60:30:0.283:0.1321:0.1 +2 61715436 . T A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02749;SOR=Inf;LSEQ=AGAATCAAATGGAATCTAAT;RSEQ=TTACCACTAAACTTATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:111,294:405,0:0:2,0:23.8:1:30.1:1:1:0:59.9:49.625:1:0:0.1 0/1:387:5:3,2:97,285:382,5:0.0129:2,2:9.2:1:26.4:1:0.11118:4.39:60:10:0.0131:0:1 +2 61715955 . G A 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-04;SOR=Inf;LSEQ=ATCATATAAGAATTATCCAC;RSEQ=GCTGGGAACAGTGGCTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:12,137:149,0:0:2,0:22.7:1:31.2:1:1:0:59.4:148:1:0:0 0/1:125:9:3,6:10,106:116,9:0.072:2,2:19.2:1:30.4:1:0.05157:5.18:60:18:0.072:0:1.1 +2 61717338 . A ATT 29 d5;v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CCGGCCCAGATTTTTCATTT;RSEQ=TTTTTTTTTTTTTGAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:3,0:3,1:0.25:0,0:15:0:33:0:1:0:60:2:0.3333:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:29.3:1:1:0:60:4:1:0:1.5 +2 61719969 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15287;SOR=Inf;LSEQ=ATTTAGAAAATATTTAGAAA;RSEQ=TACAAGTACATTTCCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:149,101:250,0:0:2,0:22.8:1:32.8:1:1:0:59.8:61.5:1:0:0.1 0/1:161:2:1,1:99,60:159,2:0.0124:2,2:5.5:1:27:1:1:1.6446:60:4:0.0125:0:1.5 +2 61719985 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.1469;SOR=Inf;LSEQ=GAAACTACAAGTACATTTCC;RSEQ=AAAATGTATTTCCACCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:188,96:284,0:0:2,0:23:1:31.1:1:1:0:59.8:141:1:0:0.1 0/1:177:2:1,1:126,49:175,2:0.0113:2,2:29.5:1:31:1:0.48633:2.55567:60:4:0.0114:0:1.5 +2 61722519 . G GA 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=5.98146;LSEQ=CAAAAGGTACATACATTTTA;RSEQ=AAAAAGGCACTTTTAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:46:37,9:118,23:141,46:0.246:2,2:24.1:1:30.7:1:0.65363:1.24645:60:92:0.246:0.0374:0 1/0:160:106:87,19:44,10:54,106:0.6625:2,2:25:1:28.7:1:1:1.04:60:105:0.6604:0.1375:0.2 +2 61722778 . G A 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34671;SOR=0.29435;LSEQ=TTAAAAGGGACGATCAGTTC;RSEQ=CATTTTATAAAACAACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:2,1:47,243:290,3:0.0102:2,2:17.3:1:27.7:1:0.07359:10.21:60:6:0.0103:0:1 0/0:330:1:1,0:87,242:329,1:0.003:2,0:1:0:26:0:0.26667:0:60:2:0.0031:0:1 +2 61722904 . C T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=30.52108;LSEQ=GCAGCCTCCACCTCCTAGGC;RSEQ=CAATCAGTCCTCCTCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:0,3:0,24:24,3:0.1111:1,0:11.7:1:29.3:1:1:0:60:6:0.12:0:1.3 1/1:11:9:0,9:0,2:2,9:0.8182:0,0:24.8:1:29.3:1:1:0:60:18:0.8182:0:1 +2 61725501 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATTATCAGTTAAAAGAT;RSEQ=AACTTTTCATTTTTCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:14.5:1:28:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 61726050 . TA T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.81598;SOR=0.92406;LSEQ=TGAGAATTCATTGCACATGC;RSEQ=AAAAAAAAAACACACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:44:17,27:151,232:383,44:0.103:2,2:30.6:1:31.4:1:1:1.03365:59.6:88:0.104:0:0.1 0/1:396:38:16,22:145,213:358,38:0.096:2,2:32.6:1:30.3:1:0.86347:1.07:59.6:76:0.0967:0:0.3 +2 61726086 . G A 111 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00526;SOR=5.24699;LSEQ=CAAAAATATCAGATTTAGAA;RSEQ=ACACAGAAATAAGTATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:3,0:46,192:238,3:0.0124:2,0:22.3:1:13.7:1:0.008:0:60:0:0:0:4 0/1:225:14:6,8:48,162:210,14:0.0622:2,2:24.4:1:29.2:1:0.10803:2.52:60:28:0.0707:0:2.1 +2 61727056 . G A 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36282;SOR=0.317;LSEQ=CAAGACATGAAATGTTAATC;RSEQ=CACTTCATTTCTCAAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:2,1:38,204:242,3:0.0122:2,2:18.7:1:28.7:1:0.07013:10.57:60:6:0.0124:0:1 0/0:256:1:1,0:53,200:253,1:0.0039:2,0:1:0:26:0:0.2126:0:60:2:0.004:0:2 +2 61727215 . G A 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=GGTAGAAAACAAAACACAAA;RSEQ=TCTTTTATCTTAATCACCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:19.7:1:33:0:1:0:60:6:0.2308:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:12.5:1:31.5:1:1:0:60:4:1:0:1 +2 61728900 . C CAT 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51354;SOR=1.53734;LSEQ=AAAGATAAATAAGAATCCAA;RSEQ=AGAGTCCAGTCCACACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:10:10,0:28,1:29,10:0.2439:1,0:15:1:31:1:1:0:57.9:20:0.2778:0.0976:0.1 0/1:15:5:5,0:9,1:10,5:0.3333:2,0:22.8:1:30.8:1:1:0:60:10:0.3846:0.0667:0 +2 61729258 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.62931;LSEQ=CAATCCTAACAAATGATTAC;RSEQ=GCTCTACTGTAAATGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:93:41,52:79,152:231,93:0.287:2,2:24.2:1:31:1:0.10007:1.51:60:186:0.2906:0:1.9 1/0:244:145:56,89:40,49:89,145:0.5943:2,2:22.4:1:30.1:1:0.34247:1.2959:60:144:0.595:0:1.9 +2 61729268 . T C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.38803;LSEQ=AAATGATTACAGCTCTACTG;RSEQ=AAATGACTGACTGTGCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:94:44,50:90,142:232,94:0.2883:2,2:24:1:32.3:1:0.21413:1.39:59.8:188:0.2892:0:1.9 1/0:231:148:66,82:39,44:83,148:0.6407:2,2:22.3:1:31.6:1:0.78347:1.10078:60:147:0.6476:0:1.9 +2 61729446 . C A 63 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06304;SOR=0;LSEQ=AACAACGTATTTTTTTATTC;RSEQ=TATTAAAAAAATTGCACGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:501:5:4,1:184,312:496,5:0.01:2,2:6.2:1:27.2:1:0.06839:6.76:60:10:0.0101:0:1 0/0:459:0:0,0:187,272:459,0:0:2,0:24.6:1:30.9:1:1:0:60:90.8:1:0:0.1 +2 61729641 . TC AA 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59993;LSEQ=ACGCTTGTAATCCCAGCAAT;RSEQ=TTTGGGAGGCTGAGGTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:0,6:0,7:7,6:0.4615:0,0:28.2:1:31.8:1:1:0:56.5:12:0.4615:0.0769:1.2 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:27:1:32.3:1:1:0:60:4:0.3333:0:1 +2 61749472 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTGTTAGGATTACAGGC;RSEQ=TGGGCCACTGTGCCATAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:23:1:29:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 61749690 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.09573;LSEQ=CCCCCTCAAACAGTCAACTA;RSEQ=AATAAAAATGCCAGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:89:60,29:188,80:268,89:0.2493:2,2:27.3:1:30.6:1:0.69047:1.13542:60:178:0.2507:0:2 1/0:329:207:137,70:83,39:122,207:0.6292:2,2:22.8:1:28.8:1:0.80856:1.0871:59.8:40.4:0.6254:0:2.1 +2 61749716 . C T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.47021;LSEQ=AAATGCCAGGAAAAACAAAA;RSEQ=TCTGAATTTATAATTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:116:73,43:217,137:354,116:0.2468:2,2:27.3:1:31:1:0.82595:1.07:60:232:0.2495:0:1.7 1/0:475:323:183,140:89,63:152,323:0.68:2,2:25.6:1:29.5:1:0.76559:1.08056:59.8:106.667:0.678:0:1.7 +2 61753513 . G T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12413;SOR=Inf;LSEQ=TTCCTCAAAGTTTATGACTG;RSEQ=AAGAAAAGAAATAACAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:276,108:384,0:0:2,0:25.2:1:31.5:1:1:0:60:191:1:0:0.1 0/1:393:4:1,3:274,115:389,4:0.0102:2,2:16:1:25.5:1:0.08283:7.10801:60:8:0.0104:0:1 +2 61753669 . T TA 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.72584;SOR=1.57104;LSEQ=ATTCTTTGCTAAAATATTAT;RSEQ=AAAAAAAACAAAACTTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:0,3:63,219:282,3:0.0105:2,0:33.3:1:32.3:1:1:0:60:6:0.0106:0:0 0/1:305:5:2,3:76,224:300,5:0.0164:2,2:30.4:1:26.4:1:0.60514:1.96:60:10:0.0167:0.0033:0.4 +2 61753696 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23377;SOR=Inf;LSEQ=AACAAAACTTAAGCTAATGT;RSEQ=TTCTTTTGAATCATTCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:25,155:180,0:0:2,0:23.8:1:31.1:1:1:0:60:179:1:0:0.1 0/1:169:2:1,1:22,145:167,2:0.0118:2,2:15:1:28.5:1:0.25437:6.47:60:4:0.012:0:1.5 +2 61753786 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00257;SOR=6.08301;LSEQ=ATTATTGATGTTCAGAAATA;RSEQ=TCAAAAATTAGACCTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:0,11:0,26:26,11:0.2973:1,0:19.9:1:30.5:1:1:0:60:22:0.2973:0:1 1/0:22:16:0,16:0,6:6,16:0.7273:0,1:22:1:29.8:1:1:0:60:32:0.7273:0:1.1 +2 61760756 . A C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0046;SOR=6.04692;LSEQ=AACATGCAATTTCTTTCTCC;RSEQ=AACCAATTTTCATTATGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:4,0:69,0:69,4:0.0548:1,0:24.5:1:32.5:1:1:0:60:8:0.0548:0:1 0/1:38:10:9,1:28,0:28,10:0.2632:1,2:22.6:1:30:1:0.26316:0:60:20:0.2632:0:1 +2 61760814 . C T 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAATGCAAACTATGGAATAT;RSEQ=TTTTTTAAAGGTGATAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:27:23,4:172,8:180,27:0.1304:1,2:22.3:1:31:1:0.05474:3.70438:60:54:0.1311:0:1 0/0:150:0:0,0:138,12:150,0:0:2,0:22.7:1:31.1:1:1:0:60:149:1:0:0.1 +2 61761050 . G GA 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.25592;SOR=0;LSEQ=CATAGATTACTGAAAATAAA;RSEQ=AAAAAAAATTGAAGCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:3:1,2:33,192:225,3:0.0132:2,2:10.3:1:31:1:0.3854:2.89:60:6:0.0136:0.0044:0.3 0/0:186:0:0,0:29,157:186,0:0:2,0:22.5:1:30.6:1:1:0:60:185:1:0:0.1 +2 61761169 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAGAGACTTTAATTACA;RSEQ=AAAACTGAGATAGTAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:0,30:0,0:0,30:1:0,1:30.4:1:31:1:1:0:60:29:1:0:1 1/1:9:9:0,9:0,0:0,9:1:0,0:22.4:1:29:1:1:0:60:8:1:0:1 +2 62759659 . CT C 31 d5;v3;MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGTTTTTGCTACTTCATT;RSEQ=TTTTTTTTTTTTTTACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31:1:31.5:1:1:0:43:4:1:0:0 1/1:1:1:1,0:0,0:0,1:1:0,0:29:0:32:0:1:0:60:2:1:0:3 +2 62759961 . G C 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08774;SOR=Inf;LSEQ=AAGAATCTTGCCCTTAATTT;RSEQ=TTTGTTTACAACAATGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:42,3:45,0:0:2,0:30.4:1:32.2:1:1:0:34.3:90:1:0:0 0/1:37:3:3,0:32,2:34,3:0.0811:2,0:24:1:25.3:1:1:0:36:2:0.0571:0:1 +2 62760131 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49398;SOR=0;LSEQ=TGGCCAAAGAACAACTCCAT;RSEQ=TTTTCTAAAAGGCCTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:30,10:40,2:0.0476:2,2:9.5:1:30.5:1:0.45993:2.90751:22:4:0.0476:0:1 0/0:41:0:0,0:29,12:41,0:0:2,0:23.6:1:31.7:1:1:0:22:82:1:0:0 +2 62760259 . T A 33 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09646;SOR=Inf;LSEQ=TCATTCTTTTACAGTCCTTT;RSEQ=CTCCAAGTCATAAACTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:73,169:242,0:0:2,0:21.1:1:29.9:1:1:0:60:47.4:1:0:0.1 0/1:206:3:2,1:75,128:203,3:0.0146:2,2:7.7:1:21.3:1:0.55725:3.39:59.7:2:0.0099:0:1 +2 66015029 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48413;SOR=0;LSEQ=GGTAATGTCTGATCACCCTG;RSEQ=CATCTATCTTCAGCAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:11,2:13,2:0.1333:2,2:24.5:1:29:1:0.37143:4.69047:60:4:0.1333:0:1 0/0:13:0:0,0:8,5:13,0:0:2,0:21.1:1:29.6:1:1:0:60:26:1:0:0.2 +2 66015141 . T C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74903;LSEQ=TGCTCCTCGGCTATAAATTC;RSEQ=GAGTTGCCCACACTGTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:5,9:3,10:13,14:0.5185:2,2:19.4:1:31.1:1:0.67762:1.81:60:28:0.5185:0:1.1 0/1:9:4:1,3:1,4:5,4:0.4444:2,2:22:1:28.5:1:1:1.29:60:8:0.4444:0:1 +2 66352599 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.04341;LSEQ=CAAAGCTGGAATTTGTTTGT;RSEQ=TGGTTCCTCCACAGCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:55:55,0:19,0:19,55:0.7432:1,1:26.2:1:29.1:1:1:0:60:110:0.7432:0:1 0/1:37:4:4,0:33,0:33,4:0.1081:1,0:19.5:1:28.5:1:1:0:60:8:0.1081:0:1 +2 66352795 . C G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1268;LSEQ=AAATGATAACCCAGATTGAG;RSEQ=TGGGTTTGGTTTCATTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:550:513:184,329:15,21:36,513:0.9327:2,2:26.3:1:31.7:1:0.47901:1.27656:60:41.75:0.933:0:1.1 1/0:562:358:145,213:74,129:203,358:0.637:2,2:25.3:1:30.8:1:0.36846:1.19:59.9:88.5:0.6378:0:1.2 +2 67047320 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16513;SOR=Inf;LSEQ=TGTGTCACTACCTCAGTTTG;RSEQ=CCCCATGTCCCTTACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:146,106:252,0:0:2,0:26.9:1:30.7:1:1:0:59.3:17:1:0:0.5 0/1:173:2:1,1:102,69:171,2:0.0116:2,2:18:1:26:1:1:1.47481:60:4:0.0122:0:2 +2 67047340 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15613;SOR=Inf;LSEQ=CCCCCATGTCCCTTACACAC;RSEQ=AGCAAAATACCCCTTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:137,124:261,0:0:2,0:29.1:1:28.4:1:1:0:59.2:7.7:1:0:0.4 0/1:171:2:1,1:93,75:168,2:0.0117:2,2:30:0:32:0:1:1.23841:58.5:4:0.0126:0:1.5 +2 67047383 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14935;SOR=Inf;LSEQ=GGGAAGAATTGGCAAGTGAC;RSEQ=GCTATGCTCCATGACTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:106,98:204,0:0:2,0:20.6:1:30.9:1:1:0:59.9:101:1:0:0.1 0/1:129:2:1,1:57,70:127,2:0.0155:2,2:26:1:27.5:1:1:1.23:60:4:0.0155:0:1 +2 67047384 . G T 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14957;SOR=Inf;LSEQ=GGAAGAATTGGCAAGTGACT;RSEQ=CTATGCTCCATGACTCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:103,96:199,0:0:2,0:20.7:1:31.6:1:1:0:59.9:98.5:1:0:0.1 0/1:126:2:1,1:55,69:124,2:0.0159:2,2:7:0:26.5:1:1:1.25:60:4:0.016:0:1 +2 67047403 . G A 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51714;SOR=0;LSEQ=TGCTATGCTCCATGACTCAC;RSEQ=CAACAGTCTCTGCCTTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:57,75:132,2:0.0149:2,2:5.5:1:26.5:1:1:1.31:60:4:0.0155:0:1 0/0:90:0:0,0:28,62:90,0:0:2,0:25.1:1:30.3:1:1:0:60:29:1:0:0.1 +2 67047640 . A G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00218;SOR=0.48797;LSEQ=TGCAGCTCCAGCTTACATTC;RSEQ=TAGTGAATGCCAATGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:83:23,60:37,80:117,83:0.415:2,2:24.3:1:31.9:1:0.63902:1.20539:60:166:0.4256:0:1.1 0/1:148:38:9,29:38,72:110,38:0.2568:2,2:21.3:1:31.3:1:0.23341:1.69481:60:76:0.2603:0:1.1 +2 67047656 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18637;SOR=Inf;LSEQ=ATTCATAGTGAATGCCAATG;RSEQ=CCTGCTCTTACTGGGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:47,133:180,0:0:2,0:21.5:1:32.1:1:1:0:60:89:0.9944:0:0.5 0/1:138:2:1,1:42,94:136,2:0.0145:2,2:8:0:29:1:0.52766:2.22:60:4:0.0148:0:2.5 +2 67047717 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=3.78048;LSEQ=TGGTGTGCAGCTGACACTTC;RSEQ=TTGGCATTAATCATCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:43:17,26:28,57:85,43:0.3359:2,2:28.2:1:31.1:1:0.55705:1.33:60:42:0.3387:0:1.1 1/0:79:52:21,31:9,18:27,52:0.6582:2,2:26.1:1:29.6:1:0.62874:1.35:60:25:0.6494:0:1.1 +2 67047766 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12416;SOR=Inf;LSEQ=AAAAAAATTGTGAGATGTCT;RSEQ=TCTTTTGACTAGTGCCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:40,62:102,0:0:2,0:21.8:1:32.5:1:1:0:59.4:50:1:0:0.4 0/1:56:2:1,1:26,28:54,2:0.0357:2,2:34.5:1:30.5:1:1:1.08:60:4:0.0364:0:1 +2 67047812 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.46001;SOR=0.73845;LSEQ=CACACTCTCAAGGAGCCACA;RSEQ=GAAGGGTGATCATCTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:30:12,18:20,36:56,30:0.3488:2,2:28.4:1:32.1:1:0.81555:1.20:59.2:60:0.3488:0:1.3 0/1:53:15:8,7:20,18:38,15:0.283:2,2:26.1:1:31.1:1:1:1.03:60:30:0.283:0:1 +2 67047831 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52544;SOR=0;LSEQ=AAGAAGGGTGATCATCTCCC;RSEQ=CCTTGGGCTGTGCATGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:28,47:75,2:0.026:2,2:26.5:1:32:1:1:1.67:60:4:0.0267:0:2.5 0/0:47:0:0,0:25,22:47,0:0:2,0:25:1:29.6:1:1:0:60:94:1:0:0.3 +2 67048002 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12185;SOR=Inf;LSEQ=GTATCCCTGATGTGCATGAT;RSEQ=CTCCCCTGGTGCCACAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:69,55:124,0:0:2,0:25.1:1:31.4:1:1:0:60:61:1:0:0.1 0/1:67:2:1,1:41,24:65,2:0.0299:2,2:12:0:30:1:1:1.69403:60:4:0.0303:0:1.5 +2 67048161 . G A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61397;SOR=0.73467;LSEQ=TGGGCGGCTTCCTTTTCTCA;RSEQ=CTGGGACAGGCGAGTAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:10:2,8:71,77:148,10:0.0633:2,2:25.9:1:30.2:1:0.10838:3.66132:60:20:0.0637:0:1 0/1:127:6:4,2:52,69:121,6:0.0472:2,2:23:1:28.7:1:0.40406:2.63:60:12:0.0484:0:1 +2 67048329 . G GCAA 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01814;LSEQ=CTTCCTTAATGGTCACCTGG;RSEQ=CAACCTCTGGCCCAACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:46:27,19:85,50:135,46:0.2541:2,2:22:1:30.5:1:0.60348:1.19509:60:45:0.2557:0.0552:0.2 0/1:132:34:19,15:61,37:98,34:0.2576:2,2:25.9:1:29.9:1:0.54557:1.29891:60:68:0.2656:0.0455:0.1 +2 67048418 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11956;SOR=Inf;LSEQ=ATGAGCACCTCGTGCCCACA;RSEQ=CAGCAGATGGTGCAGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:121,177:298,0:0:2,0:28.9:1:32.4:1:1:0:60:48.667:1:0:0.1 0/1:158:2:1,1:62,94:156,2:0.0127:2,2:8:1:28.5:1:1:1.51:60:4:0.0127:0:1 +2 67048433 . G A 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64557;LSEQ=CCACAGCAGCAGATGGTGCA;RSEQ=CAGAACTGATAGCCTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:3:2,1:97,170:267,3:0.0111:2,2:18:1:28.3:1:0.55644:3.49:60:6:0.0113:0:1 0/0:139:1:1,0:47,91:138,1:0.0072:2,0:1:0:28:0:0.34532:0:60:2:0.0072:0:1 +2 67048521 . G A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.34059;SOR=0.44379;LSEQ=ATATTCCTAGCATGAAGAGG;RSEQ=GCTGTTCCAGAGTGACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:15:0,15:1,17:18,15:0.4545:1,1:24.3:1:32.1:1:1:0:60:30:0.4545:0:1.1 0/1:15:4:0,4:0,11:11,4:0.2667:0,0:25.8:1:32.3:1:1:0:60:8:0.2667:0:1.3 +2 67048595 . T C 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56923;SOR=3.83897;LSEQ=TTCTGGCACTTCTTCCTCAC;RSEQ=TTGTACACTAACTACTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:1,6:7,5:0.4167:2,0:20:1:31.6:1:1:0:60:10:0.4167:0:1.8 1/0:4:3:0,3:0,1:1,3:0.75:0,0:41.7:1:32:1:1:0:60:6:0.75:0:1 +2 67048932 . T A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53623;SOR=0;LSEQ=CAAGGTGCTGGGATTACAGG;RSEQ=GTGAGCTACTGTGCCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:24,4:28,2:0.0667:2,2:17.5:1:33:1:0.31034:5.47729:55:4:0.069:0:3 0/0:16:0:0,0:12,4:16,0:0:2,0:20.3:1:28.3:1:1:0:58:32:1:0:0 +2 67048934 . T A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5461;SOR=0;LSEQ=AGGTGCTGGGATTACAGGTG;RSEQ=GAGCTACTGTGCCTGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:26,4:30,2:0.0625:2,2:19.5:1:33:1:0.29234:5.92455:55:4:0.0645:0:3 0/0:16:0:0,0:12,4:16,0:0:2,0:21.1:1:27.9:1:1:0:58:32:1:0:0 +2 67049133 . T C 29 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03552;LSEQ=GAACCCCCCAAAGGTCCATC;RSEQ=GAATATCTGCTTGCTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:109,36:145,2:0.0136:2,2:7:1:29:1:0.44134:3.00025:60:4:0.0136:0:1 0/1:71:1:1,0:54,16:70,1:0.0141:2,0:38:0:32:0:1:0:60:2:0.0143:0:1 +2 67049224 . C T 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=30.71315;LSEQ=AACAGCTCCCCTGTACACTG;RSEQ=TGGCCACCGGCAGGACTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:1:0,1:180,127:307,1:0.0032:2,0:1:0:26:0:0.41558:0:60:2:0.0033:0:1 0/1:219:20:9,11:115,84:199,20:0.0913:2,2:22.2:1:28.2:1:0.345:1.66924:60:40:0.0922:0:1.1 +2 67049232 . C T 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCCTGTACACTGCTGGCCAC;RSEQ=GGCAGGACTTCGTAGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:191,142:333,0:0:2,0:22.9:1:30.2:1:1:0:60:36:1:0:0.2 0/1:257:14:8,6:132,110:242,14:0.0545:2,2:23.6:1:30.8:1:1:1.11:60:28:0.0556:0:1.3 +2 67049237 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08329;SOR=Inf;LSEQ=TACACTGCTGGCCACCGGCA;RSEQ=GACTTCGTAGATGGCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:203,153:356,0:0:2,0:22.8:1:31.7:1:1:0:59.9:28.667:1:0:0.2 0/1:277:3:1,2:149,125:274,3:0.0108:2,2:19.7:1:26.7:1:0.59498:2.37672:60:6:0.011:0:1 +2 67049381 . T C 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCAAGCCACATGACACAG;RSEQ=GGGTGCCTTCAGCTGCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:71:46,25:198,165:363,71:0.1636:2,2:27:1:31.2:1:0.11836:1.53:58.9:70:0.1624:0:1.1 0/0:277:0:0,0:155,122:277,0:0:2,0:23.8:1:28.8:1:1:0:59.8:45.167:1:0:0.1 +2 67049554 . C T 45 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04375;SOR=Inf;LSEQ=CTTGTTCCCAGCCTCAGTCC;RSEQ=CACAGGCTCAGGTGTGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:122,139:261,0:0:2,0:22.5:1:30.8:1:1:0:60:28:1:0:0.1 0/1:143:3:1,2:70,70:140,3:0.021:2,2:6.7:1:28.7:1:1:1.99067:60:6:0.0214:0:1 +2 67049598 . C T 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3028;SOR=0;LSEQ=CAGTGGGGGATGTGGGGTTG;RSEQ=TGGGCTGCCGCACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:4:1,3:168,189:357,4:0.0111:2,2:10.5:1:27.8:1:0.62598:2.65998:60:8:0.0113:0:1 0/0:220:0:0,0:122,98:220,0:0:2,0:27.5:1:31.2:1:1:0:60:72.333:1:0:0.1 +2 67049643 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06261;SOR=Inf;LSEQ=TGGCCTCCTCCACCTTTGCA;RSEQ=ACTCCTCTGAGCCCTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:160,212:372,0:0:2,0:27.2:1:32.6:1:1:0:59.9:73.4:1:0:0.1 0/1:246:3:2,1:117,126:243,3:0.0122:2,2:16.7:1:24.3:1:0.61154:2.15:60:6:0.0122:0:1.3 +2 67049699 . CT C 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15958;SOR=0;LSEQ=ATTACTGCAGTGACCTCGGC;RSEQ=TTCTTCTCAGCCCATGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:4:1,3:61,134:195,4:0.0201:2,2:14.5:1:31.5:1:1:1.3637:60:8:0.0205:0.0101:0 0/0:127:0:0,0:35,92:127,0:0:2,0:24.3:1:29.3:1:1:0:60:62.5:1:0:0.2 +2 67049832 . CT C 103 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.64822;SOR=0.46002;LSEQ=ACCCCTATGAGATGCGATGC;RSEQ=TTTTTTTTTCTTTCTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:0,8:2,16:18,8:0.3077:2,0:26.4:1:34.4:1:1:0:59.3:16:0.32:0:0 0/1:6:1:0,1:1,4:5,1:0.1667:2,0:23:0:34:0:1:0:60:2:0.1667:0:0 +2 67673780 . G A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80563;SOR=0.87125;LSEQ=CCTCTATAATTAATTTCCTT;RSEQ=AGTCACTGAATACCTTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:22,1:23,3:26,23:0.4694:2,1:22.7:1:28.1:1:0.61192:2.81:60:46:0.4694:0:1.9 0/1:23:10:10,0:13,0:13,10:0.4348:1,0:16.2:1:28.5:1:1:0:60:20:0.4348:0:2 +2 67673823 . A T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.65678;SOR=1.18164;LSEQ=CCTTCTGCCATAAACGTCTC;RSEQ=TTTTCTCTAATATCCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:41:33,8:53,13:66,41:0.3832:2,2:27.3:1:32:1:1:1.01:60:82:0.3868:0:1.5 0/1:85:36:28,8:34,15:49,36:0.4235:2,2:24.5:1:30.2:1:0.46356:1.54:60:72:0.4235:0:1.3 +2 67673875 . T C 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00711;SOR=Inf;LSEQ=AACCAGAATTGAGCACAACA;RSEQ=GGCTTTTCCTTTCAATGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:126,64:190,0:0:2,0:24.3:1:30.4:1:1:0:60:26.143:1:0:0.5 0/1:188:7:3,4:114,67:181,7:0.0372:2,2:20.6:1:28.1:1:0.42887:2.25831:60:6:0.0328:0:1.4 +2 67673881 . T A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62126;SOR=2.0371;LSEQ=AATTGAGCACAACATGGCTT;RSEQ=TCCTTTCAATGGCGCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:1,0:130,71:201,1:0.005:2,0:1:0:23:0:1:0:60:2:0.005:0:1 0/1:199:2:1,1:119,78:197,2:0.0101:2,2:18:1:27:1:1:1.52227:60:4:0.0101:0:2 +2 67673930 . C G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00151;SOR=1.75053;LSEQ=TCTGACTCATGCTCTGCACA;RSEQ=TGAGCAGTGACAGGACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:132:72,60:85,78:163,132:0.4475:2,2:24.5:1:32.6:1:0.72537:1.10:60:131:0.4471:0:1.1 1/0:254:149:79,70:58,47:105,149:0.5866:2,2:23.2:1:30.8:1:0.79844:1.09307:59.8:48.667:0.5863:0:1.2 +2 67673938 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10251;SOR=Inf;LSEQ=ATGCTCTGCACACTGAGCAG;RSEQ=GACAGGACAGTCTGTGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:143,148:291,0:0:2,0:27.3:1:30.3:1:1:0:60:582:1:0:0.5 0/1:257:3:1,2:128,126:254,3:0.0117:2,2:12.3:1:30:1:0.62206:2.02634:60:6:0.0118:0:2.7 +2 67674042 . G A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78505;SOR=0.92593;LSEQ=TCTGCTCTCTGTTAAGCCTT;RSEQ=TTATCATTTGAGGCTATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:57:15,42:17,60:77,57:0.4254:2,2:23.5:1:29.9:1:0.68248:1.26:60:27.5:0.4198:0:1.1 0/1:91:37:7,30:13,41:54,37:0.4066:2,2:23.3:1:29.6:1:0.61508:1.35438:60:36:0.4:0:1 +2 67977367 . G GT 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00028;SOR=0.0802;LSEQ=ATCAAGGAGTCAATAGGGTT;RSEQ=TTTTTTTTTTTCCTAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:16:13,3:15,4:19,16:0.4103:2,2:22.6:1:29.6:1:1:1.15:60:32:0.4324:0.1538:0.6 0/1:39:2:2,0:27,10:37,2:0.0513:2,0:12:1:31:0:1:0:60:4:0.0526:0:0 +2 67977405 . A T 76 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15631;SOR=3.38204;LSEQ=GCTGAGACAGGATCTGTTTC;RSEQ=TGTCTCCCTTCTAGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:2,0:52,32:84,2:0.0233:2,0:23:1:16:0:0.52722:0:60:0:0:0:5 0/1:80:6:4,2:39,35:74,6:0.075:2,2:20.5:1:29.5:1:0.6809:1.78:58.5:12:0.0759:0:1 +2 67977433 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=0;LSEQ=CTTCTAGCTTCTGGGGGTTT;RSEQ=CCGGCAAGCTTTGGCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:55,49:104,2:0.0189:2,2:22.5:1:29.5:1:1:1.12122:60:4:0.02:0:1.5 0/0:93:0:0,0:45,48:93,0:0:2,0:30.6:1:31:1:1:0:59.7:92:1:0:0.2 +2 67977529 . G T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06073;SOR=0.21;LSEQ=ACATGCTTGTCTGTCTCTGC;RSEQ=TCCAGATTTCTTCCTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:0,20:0,4:4,20:0.8333:0,1:33.1:1:31:1:1:0:60:40:0.8333:0:1.1 1/0:14:7:0,7:0,7:7,7:0.5:0,0:21.1:1:30.3:1:1:0:60:14:0.5:0:1 +2 68104810 . A T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25542;SOR=Inf;LSEQ=AATTAGCTAAACAGTTCCTC;RSEQ=TTTAGAGCTTTCCTGGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:9,0:3,1:4,9:0.6923:2,0:23.3:1:32.8:1:0.30769:0:60:18:0.6923:0:1.3 1/1:6:6:5,1:0,0:0,6:1:0,2:18:1:28.3:1:1:0:60:12:1:0:1.3 +2 68104870 . C A 26 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52439;SOR=0;LSEQ=TCCAGGCAGCATCTTCAGGA;RSEQ=CAAAGGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:13,11:24,2:0.0769:2,2:20:0:26:0:1:1.17422:60:4:0.0769:0:1.5 0/0:15:0:0,0:9,6:15,0:0:2,0:31.6:1:31.9:1:1:0:60:30:1:0:0.3 +2 68104885 . ACAG A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.26395;SOR=4.14219;LSEQ=CAGGACCAAAGGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:1,0:14,16:30,1:0.0323:2,0:29:0:35:0:0.48387:0:60:2:0.0323:0:0 0/1:16:2:1,1:8,6:14,2:0.125:2,2:41:1:31:1:1:1.30929:60:4:0.125:0:0 +2 68104888 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.11594;SOR=Inf;LSEQ=GACCAAAGGCAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:13,16:29,0:0:2,0:24.8:1:32:1:1:0:60:28:1:0:0.3 0/1:16:2:1,1:7,5:12,2:0.125:2,2:30.5:1:28:1:1:1.36624:60:4:0.1429:0:1.5 +2 69741609 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18301;SOR=Inf;LSEQ=TGGTTGATTCTTACCGCTGG;RSEQ=TCCTGGGCAGGGGCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:10,0:0:2,0:34.8:1:33.2:1:1:0:60:20:1:0:0.1 0/1:8:2:1,1:5,1:6,2:0.25:2,2:25.5:1:29:1:0.46429:3.87298:60:4:0.25:0:1 +2 69741731 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49666;SOR=0;LSEQ=CAGCTGTTGTTGATGCAGGG;RSEQ=TGTGGCCAGCTGTTGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:35,35:70,2:0.0278:2,2:39:1:31:1:1:1:60:4:0.0286:0:1 0/0:69:0:0,0:35,33:68,0:0:2,0:27.5:1:30.9:1:1:0:58.6:33:0.9851:0:0.3 +2 69741753 . CTGT C 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTGGCCAGCTGTTGCTGTTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:45,43:88,0:0:2,0:26.8:1:31:1:1:0:57.9:176:1:0:0.4 0/1:81:29:16,13:24,28:52,29:0.358:2,2:29:1:31.8:1:0.49193:1.43:59.5:58:0.358:0.0741:0.3 +2 69741765 . C T 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.68393;SOR=0.54255;LSEQ=TGCTGTTGCTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:4:2,2:38,42:80,4:0.0476:2,2:29.8:1:29.3:1:1:1.10:60:8:0.0482:0:1 0/1:76:2:1,1:35,39:74,2:0.0263:2,2:23.5:1:27.5:1:1:1.11:52.5:4:0.0267:0:1.5 +2 69741801 . C T 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00119;SOR=0.22147;LSEQ=TGGTAGAAATTCTGCATTAG;RSEQ=TGCTGTTGAGAGCCTCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:26:9,17:10,12:22,26:0.5417:2,2:21.1:1:30.7:1:0.55702:1.55905:59.2:52:0.5417:0:1.3 0/1:44:9:4,5:13,22:35,9:0.2045:2,2:26.2:1:28.6:1:0.71607:1.34:60:18:0.2045:0:1.1 +2 69741805 . T C 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4953;SOR=0;LSEQ=AGAAATTCTGCATTAGCTGC;RSEQ=GTTGAGAGCCTCCTTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:18,26:44,2:0.0435:2,2:30:1:24.5:1:1:1.43:60:4:0.0444:0:2 0/0:42:0:0,0:15,27:42,0:0:2,0:23:1:29.3:1:1:0:59.6:41:1:0:0.6 +2 69741854 . T G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACTGAGCAATTGCTGGTT;RSEQ=CTGGGTTGCTGGATGTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:3,18:0,0:0,21:1:0,2:27:1:32.6:1:1:0:60:42:1:0:1.3 1/1:11:11:0,11:0,0:0,11:1:0,0:25.9:1:32.3:1:1:0:60:22:1:0:1.2 +2 69746137 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.49677;SOR=Inf;LSEQ=AACGTGCCTGCCGGCTGCTG;RSEQ=TGTGCTGGCGGTGGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:35,25:60,0:0:2,0:25.1:1:32:1:1:0:60:59:1:0:0.1 0/1:65:2:1,1:41,22:63,2:0.0308:2,2:29.5:1:30.5:1:1:1.84484:60:4:0.0308:0:1 +2 69746188 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24914;SOR=Inf;LSEQ=TGCTGCTTGAGGAAGAGTTG;RSEQ=TGCTGGTGCTGGGGTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:31,36:67,0:0:2,0:29.5:1:32.5:1:1:0:60:66:1:0:0.1 0/1:78:3:2,1:33,42:75,3:0.0385:2,2:15.3:1:28:1:0.58456:2.52:58.3:6:0.04:0:1 +2 69746199 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49646;SOR=Inf;LSEQ=GAAGAGTTGCTGCTGGTGCT;RSEQ=GGGTGTGGCCTGGGCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:26,34:60,0:0:2,0:27.6:1:31.7:1:1:0:60:59:1:0:0.1 0/1:64:2:1,1:26,36:62,2:0.0313:2,2:17:1:27.5:1:1:1.38:60:4:0.0313:0:1 +2 69746224 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58116;SOR=2.58244;LSEQ=GTGGCCTGGGCCTGAGCGGG;RSEQ=AGACCCTGGGCCTGAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:1:0,1:17,30:47,1:0.0208:2,0:1:0:31:0:1:0:60:2:0.0208:0:1 0/1:38:2:1,1:10,26:36,2:0.0526:2,2:21.5:1:27.5:1:0.50071:2.53:60:4:0.0526:0:1 +2 69746296 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52632;SOR=0;LSEQ=GGCTGCTTGGCCTGAGTTTG;RSEQ=GGCAGAGGCTGGCTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:0,12:12,3:0.2:0,0:21:1:32:0:1:0:60:6:0.2:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:14.7:1:28.7:1:1:0:60:12:1:0:0 +2 69747759 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACCCGCCTTAGCCTCCC;RSEQ=AAGTGTTGGGATTACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 69751151 . T A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00622;SOR=0.14642;LSEQ=GGGCATTTCCCCAAATAACA;RSEQ=CTTCGTTTAATCCTCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:4,8:7,10:17,12:0.4138:2,2:25.8:1:29.9:1:0.71669:1.3839:60:24:0.4444:0:1.4 0/1:33:3:1,2:11,19:30,3:0.0909:2,2:26.3:1:30.3:1:1:1.15289:60:6:0.0909:0:1.3 +2 69751203 . C T 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81119;LSEQ=TTGGAAGAACCTAGGTTGAA;RSEQ=AGACTGTGATTAGCTAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:21.7:1:28:1:1:0:60:6:0.3333:0:1.7 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:21:1:28.5:1:1:0:60:4:0.2857:0:1 +2 70165296 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17134;SOR=Inf;LSEQ=CTGGACTGGAGCAGCAGCAG;RSEQ=GTGAGCGACTCTGACGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:31,32:63,0:0:2,0:26.3:1:30.5:1:1:0:60:126:1:0:0.2 0/1:45:2:1,1:21,22:43,2:0.0444:2,2:27:1:28:1:1:1.05:60:4:0.0444:0:1 +2 70166936 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCGACCTAAGGGCTCAA;RSEQ=GGCTGACTCGGCAGCGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:38.5:1:30.5:1:1:1:60:4:0.5:0:1.5 +2 70585033 . G C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.78786;SOR=0.84636;LSEQ=AAAGAAGTGGGATGTGAGCT;RSEQ=TCAAATGTCACAGAAGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:10,2:5,4:9,12:0.5714:2,2:20.5:1:31.3:1:0.33105:3.72:60:11:0.55:0:1.2 1/0:34:18:11,7:9,7:16,18:0.5294:2,2:23.7:1:30.7:1:1:1.22:60:36:0.5294:0:1.1 +2 71182900 . T C 80 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52273;SOR=0.28305;LSEQ=GCTAGGCAAAAAAACAAATC;RSEQ=GCTTTGCAGTGAACTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:3,0:3,6:0.6667:0,2:13.8:1:31.2:1:1:0:60:12:0.6667:0:1 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:11:0:32:0:1:0:60:2:0.3333:0:1 +2 71183017 . A AT 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.64823;SOR=0.39808;LSEQ=AGAGTTAACAGTTTATTATA;RSEQ=TTTTTTTTTTCACAATCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:4:4,0:52,16:68,4:0.0556:2,0:21:1:32.8:1:0.56889:0:60:8:0.0556:0:0 0/1:44:1:1,0:34,9:43,1:0.0227:2,0:31:0:32:0:1:0:60:2:0.0233:0:0 +2 71183397 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18801;SOR=Inf;LSEQ=AAATCCTCCTTTGCTTCCCA;RSEQ=GGAACTTGAGAAGTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:54,187:241,0:0:2,0:22.6:1:31.6:1:1:0:59.1:47.2:1:0:0.1 0/1:185:2:1,1:55,127:182,2:0.0108:2,2:9.5:1:29:1:0.51722:2.30:43.5:4:0.011:0:1 +2 71183445 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03374;SOR=Inf;LSEQ=CACAGCCACCATAGCCGGGT;RSEQ=CCCATGTACTGCCATAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:1,110:111,0:0:1,0:25.1:1:31.4:1:1:0:60:36:1:0:0.1 0/1:54:3:0,3:1,50:51,3:0.0556:1,0:19:1:28.7:1:1:0:58.7:6:0.0566:0:3 +2 71210606 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=AGCAGGTGTAATTACATAGG;RSEQ=TGCAAAACCCAGAAAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:8,2:0.2:2,2:17:1:31.5:1:1:1:60:4:0.2:0:1 0/0:11:0:0,0:7,4:11,0:0:2,0:22:1:29.1:1:1:0:60:22:1:0:0.1 +2 71735047 . A G 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCGCCTCAGCCTCCTGA;RSEQ=TAGCTGGGACTACAAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:24.8:1:32.3:1:1:0:59.8:12:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:18.5:1:33.5:1:1:0:60:4:1:0:1 +2 71735178 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50404;SOR=0;LSEQ=CCTCATGCTAATCTTGGAGG;RSEQ=CCGGAGTCAGCATGGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:29,29:58,2:0.0333:2,2:19:1:29.5:1:1:1:60:4:0.0339:0:1 0/0:46:0:0,0:26,20:46,0:0:2,0:20.9:1:31.1:1:1:0:59.5:92:1:0:0.2 +2 72126420 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.85515;SOR=0.95879;LSEQ=CTGGGGGAAAAAGTGCCAAC;RSEQ=GCGGTGTTTCAGACACCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:100:47,53:125,139:264,100:0.2747:2,2:22.4:1:30.2:1:1:1.01405:60:24:0.2689:0:1.1 0/1:259:69:35,34:98,92:190,69:0.2664:2,2:27:1:29.5:1:1:1.03466:60:138:0.2727:0:1.1 +2 72126508 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.53647;SOR=0;LSEQ=ACAGAGAAGGAAAGGACGGA;RSEQ=AAGAAGAAAGAGCGCTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:34,109:143,2:0.0138:2,2:11:0:32.5:1:0.42577:3.17:60:4:0.0138:0:1.5 0/0:82:0:0,0:19,63:82,0:0:2,0:21.7:1:30.7:1:1:0:60:81:1:0:0.2 +2 74317094 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50548;SOR=0;LSEQ=TCTCCTTTGGTTGTTCCTGG;RSEQ=GCATGTACTTCAACGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:26,27:53,2:0.0364:2,2:27:1:33:0:1:1.04:60:4:0.037:0:1 0/0:41:0:0,0:16,25:41,0:0:2,0:24.4:1:29:1:1:0:60:19.5:1:0:0.2 +2 74317132 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18937;SOR=Inf;LSEQ=TGCAAGTATGCTCGGAGCAA;RSEQ=ACACCTCGCAAGTTCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:24,0:0:2,0:20.7:1:31.5:1:1:0:60:48:1:0:0.2 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:6.5:1:27:1:1:1.40:60:4:0.1053:0:1.5 +2 75399893 . T A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.52746;SOR=0.65816;LSEQ=AAATAGAAATTTATTTATAG;RSEQ=TTTGGAGGCTAGAAGTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:23:12,11:5,4:9,23:0.7188:2,2:21.3:1:29.3:1:1:1.14098:60:22:0.7097:0:1.1 1/0:16:10:6,4:3,3:6,10:0.625:2,2:22:1:27.7:1:1:1.46:60:20:0.625:0:1 +2 75660748 . G A 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.28205;SOR=0.21386;LSEQ=CTGCTAGTTCTGAGTAATCC;RSEQ=GGCAACTCAGACGAGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:4,3:0.4286:2,0:25:1:32.3:1:1:0:58:6:0.4286:0:2 0/1:8:1:1,0:5,2:7,1:0.125:2,0:31:0:32:0:1:0:60:2:0.125:0:1 +2 75660828 . G T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05355;SOR=0.24775;LSEQ=CCAAAGTGCTTTGTTAAATG;RSEQ=GTCCTGCTCCCCGTGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:6,6:4,4:8,12:0.6:2,2:26:1:29.6:1:1:1:58.4:24:0.6:0:1.3 0/1:19:5:3,2:7,7:14,5:0.2632:2,2:22.6:1:29.8:1:1:1.47:59.8:10:0.2632:0:1.2 +2 75660834 . G T 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00866;SOR=0;LSEQ=TGCTTTGTTAAATGGGTCCT;RSEQ=CTCCCCGTGCCACCCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:4,3:5,8:13,7:0.35:2,2:21.3:1:31.3:1:0.64241:2.05:58.3:14:0.35:0:1 0/0:18:0:0,0:9,9:18,0:0:2,0:24.7:1:31.1:1:1:0:59.9:36:1:0:0.6 +2 75660847 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15766;SOR=Inf;LSEQ=GGGTCCTGCTCCCCGTGCCA;RSEQ=CCAACTGGGTGAGACCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:22,0:0:2,0:32.6:1:31.6:1:1:0:58.2:44:1:0:0.9 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:28:0:28.5:1:1:1.15:59.5:4:0.1333:0:1 +2 76787924 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.34836;LSEQ=CTTTTTTATTGTTACTATAA;RSEQ=GGAGGTTTTAAAATAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:242:136,106:164,122:286,242:0.4583:2,2:24.8:1:31.1:1:0.7922:1.04761:60:241:0.4582:0:1.1 0/1:466:106:62,44:198,162:360,106:0.2275:2,2:21.7:1:29.8:1:0.57842:1.15:60:212:0.2299:0:1.1 +2 79227376 . A G 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GGTGCCAACACCTGTGCTCT;RSEQ=TGCAGTTGAAGGGCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:13.5:1:32.3:1:1:0:60:8:0.4:0:3 1/1:2:2:2,0:0,0:0,2:1:0,0:8:1:33.5:1:1:0:60:4:1:0:3 +2 79227379 . C T 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53846;SOR=3.18702;LSEQ=GCCAACACCTGTGCTCTATG;RSEQ=AGTTGAAGGGCCAGGAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:16.5:1:31.3:1:1:0:60:8:0.3636:0:3 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:11:1:31:0:1:0:60:4:0.6667:0:3 +2 79227405 . A G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.91372;LSEQ=AAGGGCCAGGAGTGTGGATC;RSEQ=GGGATCCCACACCAGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:11:11,0:5,0:5,11:0.6875:0,0:24.2:1:28.7:1:1:0:60:10:0.6667:0:1.8 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:37:1:31.5:1:1:0:60:4:0.6667:0:3 +2 79227455 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12896;SOR=Inf;LSEQ=TGCAACCATGTGAACTTCAT;RSEQ=CCAAGGTCCTCTTTCGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:33,0:0:1,0:23.3:1:30.9:1:1:0:60:15.5:1:0:0.6 0/1:19:2:2,0:16,1:17,2:0.1053:1,0:36.5:1:32.5:1:1:0:60:4:0.1111:0:1 +2 79227583 . A G 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGAAGCTTTCCCTGCTGC;RSEQ=GCCTTCAAAATGTCCCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:285,125:410,0:0:2,0:24.7:1:30.9:1:1:0:60:135.667:1:0:0.4 0/1:275:69:48,21:132,73:205,69:0.2509:2,2:25.6:1:29.1:1:0.46665:1.26:59.5:68:0.2509:0:1.1 +2 79227650 . G C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3592;LSEQ=TCTTCCCTCTGGTTTTCCCT;RSEQ=ATCTTCTCATCTCCTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:703:457:252,205:140,105:245,457:0.6501:2,2:23.5:1:32:1:0.63289:1.08452:60:113.25:0.649:0:1.1 0/1:520:208:109,99:168,144:312,208:0.4:2,2:23.4:1:30.8:1:0.788:1.0595:60:207:0.4019:0:1.1 +2 79227759 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32704;LSEQ=CATTGTTTTCTACTTATTCA;RSEQ=CTTTCCCATAGTCTGAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:356:239:55,184:22,95:117,239:0.6713:2,2:23.4:1:31.4:1:0.41227:1.29:59.8:478:0.6751:0:1.1 0/1:220:88:26,62:34,98:132,88:0.4:2,2:23.7:1:30.5:1:0.54084:1.21:60:176:0.4037:0:1.2 +2 79227772 . C CTG 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00284;SOR=0.54358;LSEQ=TTATTCATCTTTCCCATAGT;RSEQ=TGAGCATTTTTCAGTCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:139:15,124:26,105:131,139:0.511:2,2:31.1:1:31.3:1:0.04268:2.0416:59.8:68.5:0.5131:0.0184:1.1 0/1:163:59:11,48:21,83:104,59:0.362:2,2:26:1:30.6:1:1:1.10342:60:118:0.3642:0.0245:1.1 +2 79227782 . T C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00548;SOR=Inf;LSEQ=TTCCCATAGTCTGAGCATTT;RSEQ=TCAGTCATAGACCACTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:26,205:231,0:0:2,0:25.1:1:30.6:1:1:0:59.9:76:1:0:0.6 0/1:128:5:1,4:16,107:123,5:0.0391:2,2:16.4:1:31.8:1:0.51557:1.66:60:10:0.0391:0:1.8 +2 79227813 . G GT 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.17744;SOR=0.60842;LSEQ=ACCACTCCTTCATTTTATTT;RSEQ=TTTTTTTATAGAAAGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:55:2,53:0,71:71,55:0.4297:1,1:28.5:1:30.8:1:0.18857:0:59.8:110:0.4331:0:0.7 0/1:51:16:1,15:0,35:35,16:0.3137:1,1:27.6:1:30.8:1:0.31373:0:60:32:0.3137:0.0196:0.8 +2 79228733 . T G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAATAACATGGTGAAAAA;RSEQ=AAAAGCATAGGCAATAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:22:1:33:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 79228861 . A ATATTTATT 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=4;SSF=0.04762;SOR=0;LSEQ=AGGGACACAGATGCACATTT;RSEQ=TATTTATTTATTGGATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:31.5:1:1:0:60:4:1:0.5:3.5 0/0:5:0:0,0:5,0:5,0:0:0,0:31:1:28.4:1:1:0:60:10:1:0:0 +2 79228890 . G A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00699;SOR=0;LSEQ=TATTGGATGCCATCCACATG;RSEQ=CAAATGAGTAGGCTAAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,1:2,5:0.7143:2,2:22.4:1:27.4:1:1:3.16:60:4:0.6667:0:3.2 0/0:8:0:0,0:5,3:8,0:0:2,0:22.6:1:30.5:1:1:0:60:16:1:0:0 +2 79228904 . T C 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01923;SOR=0;LSEQ=CACATGGCAAATGAGTAGGC;RSEQ=AAACGGAAGGTAGCACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:1,1:2,4:0.5714:2,2:27.8:1:32.3:1:1:2.45:60:8:0.6667:0:3 0/0:9:0:0,0:5,4:9,0:0:2,0:23.3:1:28.6:1:1:0:60:18:1:0:0 +2 79228925 . T A 90 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00191;SOR=0.03262;LSEQ=AAACGGAAGGTAGCACAGAA;RSEQ=TGTCTCTGTCCTCAACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:6,3:1,1:2,9:0.8182:2,2:23.8:1:28.7:1:1:1.87:60:8:0.8:0:2.6 0/1:10:1:1,0:4,5:9,1:0.1:2,0:18:0:31:0:1:0:60:2:0.1:0:2 +2 79229006 . A G 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28613;SOR=0.18597;LSEQ=TTCCAGAAAACAAAGCCCCT;RSEQ=CCTTCCTCTGGTTATTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:1,1:2,5:0.7143:2,0:25:1:33.4:1:0.28571:0:60:10:0.7143:0:1.6 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:26:1:31:1:1:1.41:60:4:0.2857:0:1.5 +2 79422965 . C G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4672;SOR=0.88794;LSEQ=CTGAATCAATACATATCACT;RSEQ=AATGAAAGTTCTAGACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:148:73,75:71,88:159,148:0.4821:2,2:24.6:1:32:1:0.42527:1.21:60:73:0.4834:0:1.1 0/1:305:138:65,73:78,89:167,138:0.4525:2,2:26.5:1:30.4:1:1:1.02:60:33.5:0.4467:0:1.2 +2 79423056 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51678;SOR=0;LSEQ=TGGAAAGTAGGGGGATGAAC;RSEQ=CAGTTTTTTGTTTGTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:25,92:117,2:0.0168:2,2:9.5:1:29.5:1:0.39069:3.63:60:4:0.0171:0:1.5 0/0:80:0:0,0:19,61:80,0:0:2,0:24.2:1:28.8:1:1:0:60:79:1:0:0.2 +2 79423062 . TTTTG T 107 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.03318;SOR=0.1254;LSEQ=GTAGGGGGATGAACTCAGTT;RSEQ=TTTGTTTGTTTTATGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:12:4,8:17,79:96,12:0.1101:2,2:25.3:1:29.9:1:0.2432:2.30:59:24:0.1121:0.0092:0 0/1:66:1:0,1:14,51:65,1:0.0152:2,0:48:0:28:0:1:0:60:2:0.0152:0:0 +2 79524985 . C T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13075;SOR=0;LSEQ=CTTGAAGTCAAATTCTGAGG;RSEQ=AGATTATCCACACTCATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:4:1,3:217,125:342,4:0.0115:2,2:20.3:1:27:1:0.14499:5.18305:60:8:0.0119:0:2 0/0:287:0:0,0:162,125:287,0:0:2,0:26:1:31.5:1:1:0:60:142.5:1:0:0.5 +2 79524994 . C T 233 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAATTCTGAGGCAGATTATC;RSEQ=ACACTCATTGGAAACAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:209:125,84:104,65:169,209:0.5529:2,2:27.7:1:30.3:1:0.75173:1.07498:60:103.5:0.5535:0:1.1 0/0:315:0:0,0:172,143:315,0:0:2,0:25.9:1:31:1:1:0:60:314:1:0:0.5 +2 79524996 . C T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03483;SOR=0;LSEQ=ATTCTGAGGCAGATTATCCA;RSEQ=ACTCATTGGAAACAAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:6:3,3:226,154:380,6:0.0155:2,2:38.2:1:26.8:1:0.69065:1.46601:60:5:0.0131:0:2 0/0:319:0:0,0:174,145:319,0:0:2,0:26:1:31.7:1:1:0:60:158.5:1:0:0.5 +2 79525033 . T A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.38565;LSEQ=TAACTGCAAATAGTTACTCA;RSEQ=CTATCTCTCATTTGATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:147:74,73:142,149:291,147:0.3349:2,2:27.5:1:29.7:1:0.76263:1.06:60:72.5:0.3356:0:1.1 1/0:381:208:107,101:90,82:172,208:0.5459:2,2:25.3:1:29:1:0.91793:1.03594:60:51:0.544:0:1.1 +2 79525176 . C T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.01303;SOR=0.34399;LSEQ=TATGGTACCACATGTCTTGG;RSEQ=CCATTTTGCATTGCTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:47:1,46:0,28:28,47:0.6267:1,1:25.6:1:30.8:1:1:0:60:46:0.6301:0:1 0/1:33:12:1,11:0,21:21,12:0.3636:1,2:19.2:1:29.6:1:0.36364:0:60:24:0.3636:0:1 +2 79600541 . CG GT 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATACAGAATACTATTAAA;RSEQ=TAGTGATTCATACCTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:33.3:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 79601273 . A T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=3;SSF=1;SOR=1.16426;LSEQ=GTCCCTGATTATTCATCATC;RSEQ=TCACCAGCAACAACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:36:19,17:4,2:6,36:0.8571:2,2:28.8:1:30.5:1:0.67286:1.76554:59.5:35:0.8537:0:1.9 1/1:32:28:14,14:3,1:4,28:0.875:2,2:24.6:1:29.4:1:0.60289:2.90535:60:56:0.875:0:2.1 +2 79601323 . T G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.09812;LSEQ=AGCAGAAATAGAGAATTACT;RSEQ=GTTCAAGTAGTAAAACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:25:8,17:2,3:5,25:0.8333:2,2:27.2:1:30.6:1:1:1.39974:60:11.5:0.8214:0:2.6 1/1:26:22:7,15:2,2:4,22:0.8462:2,2:29.5:1:31.2:1:0.59064:2.07641:60:44:0.8462:0:2.8 +2 79601338 . A G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.71606;LSEQ=TTACTTGTTCAAGTAGTAAA;RSEQ=CCTTCTGTGGAAGTCTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:5,14:1,2:3,19:0.8636:2,2:27.9:1:32.6:1:1:1.37755:60:38:0.8636:0:2.8 1/1:22:18:6,12:2,2:4,18:0.8182:2,2:23.6:1:31.2:1:0.60191:1.93443:60:36:0.8182:0:2.9 +2 79601392 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14286;SOR=0;LSEQ=ACCTTCCCCTGTCTCTAACC;RSEQ=TCTTGTTTTCTAAAATTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:23:1:31:1:1:0:60:6:0.75:0:3 0/0:4:0:0,0:0,4:4,0:0:0,0:16.5:1:32:1:1:0:60:8:1:0:1.3 +2 80688324 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49754;SOR=Inf;LSEQ=AATCCTGTTAAGTCAGTTTA;RSEQ=TAAGAACCACCCACCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:12,0:0:2,0:21.5:1:32.8:1:1:0:60:24:1:0:0.1 0/1:17:2:1,1:5,10:15,2:0.1176:2,2:11.5:1:30:1:1:1.91:60:4:0.1176:0:1.5 +2 81267146 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTCCTCTAGGATCAAG;RSEQ=CCATCAAGCTACAGATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:12:1:30.5:1:1:1:36:4:0.5:0:1 +2 81267220 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=AACTTCTACTGAGGACCCCT;RSEQ=GACTCACCCGCTGGCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:23.5:1:31:1:1:0:51.3:8:1:0:0 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:23:1:27.5:1:1:1.41:29.5:4:0.2857:0:1 +2 81420681 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAGTTATTTACAACTGTGCA;RSEQ=TAATGTGTTGCAAACTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:17:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:42:0:31:1:1:0:24.5:4:1:0:1.5 +2 81421230 . C G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07143;SOR=Inf;LSEQ=GCCCCCGGCATGGTCTTCTC;RSEQ=TCCCGCCGGGGCCGGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:8:7,1:26,0:26,8:0.2353:1,2:31.8:1:31.1:1:0.23529:0:57.4:16:0.2353:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:30.5:1:30:0:1:0:49.5:4:1:0:1 +2 81421702 . C T 236 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=311.30522;LSEQ=ATGAACTGGCTGGTGTTGAG;RSEQ=CGGTCGCGCACTGACTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1049:2:0,2:521,526:1047,2:0.0019:2,0:12.5:1:26:1:0.49955:0:60:4:0.0019:0:1 0/1:865:323:180,143:284,257:541,323:0.3734:2,2:27.3:1:28.4:1:0.3604:1.14:59.5:28.364:0.3701:0:1.1 +2 81421951 . A G 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.09371;LSEQ=ACAGCTAGTTCAGGGACTCC;RSEQ=CCAGCGAGGGAGGGGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:975:163:80,83:427,385:812,163:0.1672:2,2:25:1:30.8:1:0.4399:1.15051:59.3:39.75:0.1672:0:1.2 1/0:738:523:271,252:107,107:214,523:0.7087:2,2:23.5:1:29.9:1:0.68511:1.08:59.2:64.375:0.7123:0:1.2 +2 81422135 . G T 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=11.21754;LSEQ=GTGCAGGAATTCGAAGTAGG;RSEQ=GTTGGCCCTGTCGCTGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1811:316:161,155:773,721:1494,316:0.1745:2,2:24.5:1:30.2:1:0.80459:1.03216:51.4:157:0.1761:0:1.1 1/0:1427:1004:506,498:218,205:423,1004:0.7036:2,2:24.9:1:28.9:1:0.72801:1.04659:51.5:51.842:0.7026:0:1.2 +2 81422297 . G A 144 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=21.62786;LSEQ=GCGCGGATGCTGGGCTGGGC;RSEQ=TAGTCCTCCTCCGAGCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1027:2:1,1:442,583:1025,2:0.0019:2,2:1:0:29:1:1:1.32:57.5:4:0.002:0:1.5 0/1:740:30:10,20:308,402:710,30:0.0405:2,2:21.9:1:29.4:1:0.34746:1.53149:59.6:60:0.0408:0:1 +2 81422395 . C T 62 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01695;SOR=9.33039;LSEQ=TCTGCCGGTTCCTGGTGATG;RSEQ=AGTGAGGGATCTACCCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:898:1:0,1:474,423:897,1:0.0011:2,0:1:0:23:0:0.47216:0:60:2:0.0011:0:1 0/1:582:6:1,5:321,255:576,6:0.0103:2,2:12.2:1:24:1:0.09409:6.27634:60:12:0.0105:0:1 +2 81422495 . C T 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGCCGCAGGGAGGGCCTT;RSEQ=GGCTGGGGCGGCAGCACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:0:0,0:224,435:659,0:0:2,0:24.5:1:30.3:1:1:0:59.8:53.917:0.9985:0:0.1 0/1:464:29:10,19:154,278:432,29:0.0625:2,2:20.4:1:29.3:1:1:1.05241:60:58:0.0637:0:1.2 +2 81422590 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08753;SOR=1.90095;LSEQ=CAGTGTCCATGGGGGGCAAG;RSEQ=GGTGTCGGGGGCACAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:23:9,14:36,93:129,23:0.1513:2,2:20.8:1:31.3:1:0.3232:1.65:57.6:46:0.1513:0:1.9 0/1:67:17:6,11:10,40:50,17:0.2537:2,2:20.2:1:29.2:1:0.20899:2.15:60:34:0.2615:0:1.8 +2 81422631 . T G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.35887;LSEQ=ATGCGGCAGGGGGTAGGAGG;RSEQ=GTTCAGCCTCGGCCCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:28:14,14:61,56:117,28:0.1931:2,2:26.5:1:32.4:1:1:1.08864:58:56:0.1958:0:2.1 1/0:68:52:32,20:11,5:16,52:0.7647:2,2:23.6:1:29.9:1:0.76894:1.36872:60:25:0.7576:0:2 +2 81422682 . C G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.17901;LSEQ=CCAGTTGGCACTGTTCAGGG;RSEQ=GAACGGGTGTGGGCTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:42:28,14:122,44:166,42:0.2019:2,2:25:1:31:1:0.44138:1.38412:58.7:84:0.2059:0:1.7 1/0:108:78:53,25:24,6:30,78:0.7222:2,2:23.8:1:30.5:1:0.24465:1.87639:60:77:0.7196:0:1.7 +2 81422771 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.52355;LSEQ=TCCGTAGCTTCTAGAGCCAC;RSEQ=TCCAGCTTTGGCTCCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:63:45,18:285,149:434,63:0.1268:2,2:21.8:1:31:1:0.39523:1.31:60:62:0.127:0:1.1 1/0:318:216:128,88:62,38:100,216:0.6792:2,2:24.2:1:29.6:1:0.71131:1.1213:59.4:107:0.6772:0:1.2 +2 81423100 . GTCC T 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTAGACAGGCTGTGGCTGTT;RSEQ=AGGAGGCTATTTTCCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:0:0,0:314,286:600,0:0:2,0:25.3:1:32:1:1:0:59.9:41.857:0.9983:0:0.2 0/1:320:11:5,6:141,166:307,11:0.0344:2,2:23.5:1:30:1:1:1.01922:60:22:0.0347:0:0 +2 81423277 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.24718;LSEQ=GGTAGAGATGGTGGCGGGGA;RSEQ=GGCTTCCACCCTGTCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:504:104:39,65:139,260:399,104:0.2063:2,2:21.7:1:30.9:1:0.6457:1.12:59.7:33.667:0.2061:0:1.3 1/0:354:279:116,163:31,44:75,279:0.7881:2,2:23.1:1:29.4:1:1:1.01:60:45.5:0.7867:0:1.2 +2 81423349 . C T 57 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30224;SOR=0;LSEQ=AGTGTTCTGGGAGAGAGAGG;RSEQ=GGAAAGGGGGGGGCGGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:4:2,2:245,152:397,4:0.01:2,2:6.5:1:28.8:1:0.63999:1.60979:60:8:0.0104:0:2.3 0/0:230:0:0,0:134,95:229,0:0:2,0:22:1:29.5:1:1:0:60:24.444:1:0:0.7 +2 81423354 . A AG 123 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00019;SOR=6.87813;LSEQ=TCTGGGAGAGAGAGGCGGAA;RSEQ=GGGGGGGGCGGGTATGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:4:3,1:270,148:418,4:0.0095:2,2:18:1:34:1:1:1.64:60:8:0.01:0.0024:0 0/1:259:16:9,7:150,93:243,16:0.0618:2,2:22.2:1:30.8:1:0.79191:1.25334:60:32:0.0632:0.0039:0.9 +2 81423356 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.01707;SOR=1.57012;LSEQ=TGGGAGAGAGAGGCGGAAAG;RSEQ=GGGGGGCGGGTATGGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:79:51,28:229,119:348,79:0.1846:2,2:19.8:1:30.4:1:0.89575:1.05638:59.9:18.75:0.1816:0:1.8 0/1:263:69:36,33:128,66:194,69:0.2624:2,2:19.5:1:29:1:0.04446:1.77379:60:33.5:0.2597:0:1.7 +2 81423424 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08716;SOR=1.26983;LSEQ=CAGAGTGGAGGGAGTCCGCG;RSEQ=AGCAGAAGTATTCTGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:982:148:87,61:511,321:832,148:0.1507:2,2:24.9:1:30:1:0.58335:1.11603:59.9:73:0.1518:0:1.4 0/1:647:119:72,47:295,231:526,119:0.1839:2,2:23.8:1:28.7:1:0.4129:1.20:60:118:0.1844:0:1.3 +2 81423752 . T C 283 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=509.33585;LSEQ=GGGAAGGTTTTGCTTGTAAA;RSEQ=TTGAGAAGACGCCCTCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2123:2:1,1:1115,1005:2120,2:9e-04:2,2:16.5:1:31.5:1:1:1.1094:40:4:0.001:0:1 0/1:1631:535:287,248:550,543:1093,535:0.328:2,2:24.1:1:31.3:1:0.22472:1.14:39.5:52.5:0.3285:0:1.2 +2 81424068 . G A 185 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=53.58029;LSEQ=TTGGCAGGAGCCTGGCTGGC;RSEQ=TTTTCCAAAAGCCCACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1387:2:1,1:723,662:1385,2:0.0014:2,2:15:1:20:1:1:1.09207:60:1:7e-04:0:2.5 0/1:1098:79:45,34:538,480:1018,79:0.0719:2,2:24.7:1:29.4:1:0.5587:1.18:59.3:78:0.0717:0:1.2 +2 81424158 . G T 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=13.73624;LSEQ=CAGTGGGCACGGGCGTGGAG;RSEQ=GCGGGGAGTGGGCGCAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1129:200:104,96:453,476:929,200:0.1771:2,2:26.9:1:29.9:1:0.43585:1.14:57:39:0.1768:0:1.1 1/0:832:622:294,328:107,102:209,622:0.7476:2,2:23.3:1:29:1:0.3378:1.17011:56.4:68.111:0.7467:0:1.2 +2 81424517 . C T 264 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=131.78591;LSEQ=CGTCGTCTGCTGGCTTCGCC;RSEQ=TCTCCTTGAGGTTGGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2587:7:3,4:1361,1217:2578,7:0.0027:2,2:20.4:1:30.6:1:0.71371:1.49086:38.9:14:0.0027:0:2 0/1:1725:455:231,224:645,621:1266,455:0.2638:2,2:25.3:1:29.9:1:0.95645:1.00717:38.5:112.75:0.2641:0:1.2 +2 81424736 . T C 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGATACTTTATCATCCCCT;RSEQ=TGCTCATCTTCACAGAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1845:0:0,0:925,917:1842,0:0:2,0:24.9:1:30.5:1:1:0:60:64.786:0.9994:0:0.2 0/1:1375:82:49,33:658,634:1292,82:0.0596:2,2:22.5:1:30.4:1:0.13856:1.43:60:81:0.0598:0:1.2 +2 81424759 . C T 237 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01716;LSEQ=CTCATCTTCACAGAGTCGTC;RSEQ=TTTTCTTTTTCTGCACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1860:203:106,97:825,832:1657,203:0.1091:2,2:26.9:1:31:1:0.55205:1.10:60:39.6:0.1081:0:1.2 0/0:1431:3:0,3:724,704:1428,3:0.0021:2,0:1:0:26:1:0.12034:0:47.3:6:0.0021:0:1 +2 81425140 . T C 180 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=77.66957;LSEQ=ATCTTCTATGACAGCTTTCA;RSEQ=GTTGTAAGAAACTCCATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1898:1:1,0:1012,884:1896,1:5e-04:2,0:8:0:34:0:1:0:60:2:5e-04:0:1 0/1:1473:58:25,33:695,719:1414,58:0.0394:2,2:24.4:1:30.8:1:0.42193:1.27573:60:116:0.0395:0:1.1 +2 81425437 . C A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=18.50766;LSEQ=GCTCCTGCCCTCAGTCTGTG;RSEQ=AGCTGTCAGAGGAGACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1204:177:102,75:599,426:1025,177:0.147:2,2:22.8:1:30.3:1:0.86899:1.03389:53.5:87.5:0.1471:0:1.1 1/0:722:550:325,225:107,62:169,550:0.7618:2,2:24.5:1:28.9:1:0.36927:1.19449:53.3:60.111:0.7598:0:1.2 +2 81425558 . C T 138 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=0.11197;LSEQ=ACTTCTCAAGGACTTCCTCT;RSEQ=CTTGGAATATTCTTTATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2039:24:16,8:1008,1005:2013,24:0.0118:2,2:21.5:1:30.3:1:0.14932:1.99:59.6:48:0.012:0:1.1 0/0:1502:2:0,2:763,735:1498,2:0.0013:2,0:1:0:23:0:0.24124:0:60:4:0.0013:0:1 +2 81425585 . C T 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11141;LSEQ=ATATTCTTTATCTGACTTCT;RSEQ=TTTGTGTTTGCTGTTAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1954:595:302,293:676,675:1351,595:0.3045:2,2:24.5:1:30.6:1:0.80568:1.03:59.9:73.375:0.3051:0:1.1 0/1:1463:68:39,29:713,681:1394,68:0.0465:2,2:22.6:1:29.3:1:0.32378:1.28:60:67:0.0463:0:1.1 +2 81425899 . G A 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCATAGGCCTCCCGCCCTTC;RSEQ=TCCTTCTCCTAGAGGTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:824:0:0,0:359,465:824,0:0:2,0:25.3:1:31.3:1:1:0:59.9:102:1:0:0.1 0/1:552:26:11,15:240,286:526,26:0.0471:2,2:22.7:1:29.6:1:0.84118:1.14403:60:52:0.0474:0:1.2 +2 81426046 . A AT 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.75997;SOR=1.04677;LSEQ=TTCTCCTTGCCTTTCTTGTC;RSEQ=TTTTTTTTTTCAGAGAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1788:104:57,47:899,765:1664,104:0.0582:2,2:30.9:1:30.7:1:0.9194:1.03:57.3:33.667:0.0582:0:0.2 0/1:1334:81:40,41:652,594:1246,81:0.0607:2,2:31.4:1:29.5:1:0.64692:1.12498:57.8:39.5:0.0611:0:0.3 +2 81426131 . C CT 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.42158;SOR=0.73551;LSEQ=CTTGGTCAAGAGACACTTTC;RSEQ=TTTTTTTTGTCTTTGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1792:26:13,13:904,860:1764,26:0.0145:2,2:25.8:1:31:1:1:1.05115:58.9:52:0.0147:0.0017:0.2 0/1:1307:14:9,5:676,611:1287,14:0.0107:2,2:28.4:1:30.4:1:0.43072:1.63:57.5:28:0.0109:0:0.2 +2 81426483 . C A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.76283;LSEQ=GGCCCTGCAGTCCCTGTGCT;RSEQ=CTTGGAGCTCTGGAGGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:96:57,39:236,180:416,96:0.1868:2,2:25.2:1:28.9:1:0.64927:1.11:60:47:0.1858:0:1.1 1/0:329:211:127,84:72,46:118,211:0.6413:2,2:22.4:1:27.9:1:0.90686:1.03516:60:69.333:0.644:0:1.1 +2 81426529 . G A 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTCCTGGCTGGCCTCTAC;RSEQ=GACTCTCTCTCCTCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:702:0:0,0:471,229:700,0:0:2,0:22.5:1:30.3:1:1:0:60:62.636:0.9971:0:0.2 0/1:450:29:19,10:283,138:421,29:0.0644:2,2:26.3:1:29.9:1:0.84029:1.07914:60:58:0.0649:0:1.5 +2 81426638 . G A 174 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=93.09793;LSEQ=CAAATAGTCCTTGTCCTTTT;RSEQ=GAAGAAGGGCTCTCTGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2016:1:1,0:1108,904:2012,1:5e-04:2,0:1:0:26:0:1:0:60:2:5e-04:0:1 0/1:1493:66:36,30:767,655:1422,66:0.0442:2,2:25.6:1:28.9:1:1:1.02:57:132:0.0447:0:1.2 +2 81426909 . C T 273 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CTGATTTTTATTAAAATATT;RSEQ=ATCAAAAGCAGAATCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2197:558:301,257:822,815:1637,558:0.254:2,2:26.4:1:30:1:0.12889:1.16:37.7:185:0.2549:0:1.1 0/0:1644:0:0,0:832,809:1641,0:0:2,0:26.1:1:31:1:1:0:41.4:163.1:0.9988:0:0.1 +2 81427036 . C T 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.39394;LSEQ=TTCTTTTTCTCTAATTTTGA;RSEQ=GGCCCGTCTTTTCACTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2207:388:191,197:878,939:1817,388:0.1758:2,2:23.8:1:30.8:1:0.77971:1.04:56.7:387:0.177:0:1.1 1/0:1610:1141:538,603:214,252:466,1141:0.7087:2,2:24.5:1:29.8:1:0.65983:1.05:56.1:284.25:0.7093:0:1.1 +2 81427187 . C T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=12.15796;LSEQ=TGCTGATATCTTTGTTCATG;RSEQ=CTTTGATTCTCTTCAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1297:240:117,123:528,529:1057,240:0.185:2,2:24.5:1:30.2:1:0.77496:1.04928:57.9:480:0.1879:0:1.1 1/0:956:702:358,344:131,122:253,702:0.7343:2,2:25.4:1:28.8:1:0.88339:1.03176:57.5:233:0.735:0:1.1 +2 81427308 . G A 265 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTTTTTTAAAGTGGTCTC;RSEQ=ATCAAGCTATAACACTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1281:379:181,198:460,441:901,379:0.2959:2,2:24:1:31:1:0.29811:1.14093:58.8:188.5:0.2964:0:1.1 0/0:961:0:0,0:471,489:960,0:0:2,0:25:1:29.9:1:1:0:59.3:67.571:0.9989:0:0.1 +2 81427526 . C T 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=11.49143;LSEQ=CTCCTTGTTCAGCTTGGGGA;RSEQ=GGTGCCCTCTGCGCTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1268:204:82,122:471,593:1064,204:0.1609:2,2:22.8:1:30.7:1:0.31644:1.18156:52.4:203:0.1628:0:1.1 1/0:821:565:232,333:105,150:255,565:0.6882:2,2:23.6:1:29.6:1:1:1.00474:51.3:55.5:0.6843:0:1.1 +2 81428037 . A AT 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.98834;LSEQ=TTTTCCTTCACTTCTTTTTC;RSEQ=TTTTTTTTTCCTTCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1123:34:22,12:721,365:1086,34:0.0303:2,2:24.7:1:30.3:1:0.85479:1.07739:59:16:0.0296:0.0036:0.4 0/1:902:27:18,9:545,323:868,27:0.0299:2,2:27.9:1:30.7:1:0.84019:1.19:54.6:54:0.0306:0:1 +2 81428075 . C T 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=13.8083;LSEQ=TGCTTGGCATTAGAAGCCTC;RSEQ=CATTTCTTACTACCAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1699:255:153,102:874,569:1443,255:0.1501:2,2:26.9:1:31.1:1:0.88955:1.02402:51.7:50:0.1491:0:1.1 1/0:1294:918:501,417:211,163:374,918:0.7094:2,2:25.6:1:29.2:1:0.57897:1.07736:51.5:90.8:0.7116:0:1.1 +2 81428378 . C A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00142;SOR=2.31561;LSEQ=AAAATAAAAAATAATGCCTT;RSEQ=GATGGCTTCCTCTACTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:41:1,40:3,192:195,41:0.1737:1,1:27.5:1:32.6:1:0.5364:1.60:60:40:0.1709:0:1.1 0/1:125:41:3,38:3,80:83,41:0.328:1,2:20.5:1:30.6:1:0.39598:2.09:60:82:0.328:0:1 +2 82017107 . T C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.64818;SOR=1.27263;LSEQ=TAGACATTTTCATGGCTTTT;RSEQ=AAAAACATTTTTATAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:17:17,0:30,1:31,17:0.3542:1,1:26.4:1:32.5:1:1:0:60:16:0.3404:0:1.1 0/1:34:14:14,0:19,1:20,14:0.4118:1,1:25.6:1:30.7:1:1:0:60:28:0.4242:0:1 +2 82017114 . A G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.05877;SOR=Inf;LSEQ=TTTCATGGCTTTTTAAAAAC;RSEQ=TTTTTATAAAATCTGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:54,1:55,0:0:1,0:21.5:1:31.1:1:1:0:60:54:1:0:0.4 0/1:36:3:3,0:32,1:33,3:0.0833:1,0:36.3:1:29.7:1:1:0:60:6:0.0857:0:1 +2 82017237 . C G 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCATATTAGTTGGGTTTGAG;RSEQ=TCTTTGTGAACTTCAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:275,212:487,0:0:2,0:26.6:1:32.4:1:1:0:60:59.875:0.9958:0:0.3 0/1:404:25:14,11:215,163:378,25:0.0619:2,2:31.1:1:30.3:1:1:1.0363:60:24:0.0605:0:1.2 +2 82017300 . T A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00391;SOR=1.54651;LSEQ=AGGAAAAATAAATGTATTGG;RSEQ=TCAGATATTTTAGTTACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:145:58,87:90,158:248,145:0.369:2,2:27.2:1:30.8:1:0.51759:1.17:60:144:0.3721:0:1.2 0/1:360:171:71,100:76,113:189,171:0.475:2,2:24.9:1:29.6:1:0.83042:1.06:60:84.5:0.4761:0:1.2 +2 82017339 . AATC A 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.69286;SOR=0.59615;LSEQ=TGTAAAATAATAATAATAGT;RSEQ=ATCATCATCATCACTCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:4:3,1:44,162:206,4:0.019:2,2:7.8:1:24:1:0.03583:10.88:60:8:0.0195:0.0143:1 0/1:175:2:1,1:43,129:172,2:0.0114:2,2:25.5:1:28.8:1:0.44289:2.98:60:4:0.0118:0.0057:1.5 +2 82017373 . C A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06692;SOR=1.78046;LSEQ=TCACTCCAAATGGCTTAAGC;RSEQ=ACAAAGTAAGTTTCAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:39:1,38:4,62:66,39:0.3714:2,1:23.3:1:31.2:1:0.64884:2.43359:60:78:0.3939:0:1.5 1/0:74:38:4,34:3,33:36,38:0.5135:2,2:22.2:1:30.7:1:1:1.29:60:76:0.5205:0:1.6 +2 83593573 . G T 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=1.00832;LSEQ=TGGATGGGCAAGTGCTTTGA;RSEQ=ATATCCCCTGCATTCGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:106:51,55:182,206:388,106:0.2146:2,2:27.4:1:29.6:1:0.82725:1.05:60:105:0.2147:0:1.2 0/1:338:73:37,36:131,133:264,73:0.216:2,2:26:1:28.9:1:0.89543:1.04:59.7:146:0.2186:0:1.2 +2 83738306 . C A 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.31815;SOR=3.42481;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGATGATGAAGGAGGGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:2,0:19,23:42,2:0.0455:2,0:33:1:31:1:0.22199:0:60:4:0.0465:0:1 0/1:21:3:1,2:9,9:18,3:0.1429:2,2:30.3:1:31.7:1:1:1.93674:60:6:0.1429:0:1 +2 85408298 . G A 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GAAAGAGGTGCGGAGAGCAG;RSEQ=GAGCACCTGAGAGAGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:11,1:12,2:0.1429:2,0:28:1:29:1:1:0:60:4:0.1429:0:1 0/1:7:1:1,0:6,0:6,1:0.1429:0,0:8:0:29:0:1:0:60:2:0.1667:0:2 +2 85408364 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01311;SOR=Inf;LSEQ=GCCCAATGAGAGTAGCCAGC;RSEQ=TGTGCATGTGAGGGGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:37,3:40,0:0:2,0:24:1:30.9:1:1:0:60:39:1:0:0.1 0/1:22:4:4,0:18,0:18,4:0.1818:1,0:23.5:1:27.8:1:1:0:60:8:0.1818:0:1.3 +2 85408551 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.42886;LSEQ=GGTGTGCCTCCCTGCTGGGC;RSEQ=TGGGCCCGCCTGCTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:115:42,73:77,102:179,115:0.3912:2,2:27.4:1:31:1:0.27627:1.31087:60:56.5:0.391:0:1.1 1/0:223:136:60,76:40,47:87,136:0.6099:2,2:25.8:1:30.6:1:0.89027:1.07765:60:272:0.6154:0:1.1 +2 85408559 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03607;SOR=Inf;LSEQ=TCCCTGCTGGGCATGGGCCC;RSEQ=CCTGCTGGGGGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:106,173:279,0:0:2,0:26.7:1:31.1:1:1:0:59.9:138.5:1:0:0.5 0/1:217:4:3,1:90,123:213,4:0.0184:2,2:21.8:1:27:1:0.31597:4.07:60:8:0.0185:0:1.5 +2 85408601 . G GA 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05719;SOR=Inf;LSEQ=AGGAAGCAAGTAGCCCGGAG;RSEQ=AAAAAAAGAACTATGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:63,134:197,0:0:2,0:22.7:1:32:1:1:0:59.8:196:1:0:0.3 0/1:191:4:2,2:71,114:185,4:0.0209:2,2:32.5:1:31:1:0.64069:1.60:60:8:0.0212:0:0 +2 85408621 . T C 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.24756;SOR=0;LSEQ=GAAAAAAAGAACTATGTGTG;RSEQ=GACTGTGTGGTGGCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:1,2:46,104:150,3:0.0195:2,2:18.3:1:25.3:1:1:1.13:60:2:0.0132:0:1.3 0/0:154:0:0,0:55,99:154,0:0:2,0:23.9:1:29.4:1:1:0:60:153:1:0:0.4 +2 85408669 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07991;SOR=Inf;LSEQ=GAGGGTTCAGCACACACAGG;RSEQ=AACCCCAGGCAGCTCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:14,60:74,0:0:2,0:24.6:1:31.5:1:1:0:60:36:1:0:0.1 0/1:57:3:0,3:13,41:54,3:0.0526:2,0:28:1:32:0:1:0:60:6:0.0526:0:1 +2 85531579 . C A 23 d5;v3;q25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCTCACCCTCCCCCCA;RSEQ=CTCTCTTTGATCAAGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:23.5:1:1:0:60:4:1:0:1 +2 85533450 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=TGGTGGCTGAGTGCACCCTG;RSEQ=AGGAAAGTGCAGCCATTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:20,35:55,0:0:2,0:25.1:1:30.9:1:1:0:60:110:1:0:0.1 0/1:22:2:1,1:3,17:20,2:0.0909:2,2:15.5:1:28.5:1:0.33766:5.05:60:4:0.0909:0:1 +2 85533634 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2469;SOR=0;LSEQ=GAGCTGGCCCGGAAGGAGCG;RSEQ=CAGCTTCACTCGCAGCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:3:1,2:44,44:88,3:0.033:2,2:32.3:1:29:1:1:1.98535:60:6:0.033:0:1 0/0:84:0:0,0:43,41:84,0:0:2,0:28.9:1:31.1:1:1:0:60:168:1:0:0.1 +2 85533668 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50022;SOR=0;LSEQ=AGCTCTACCCAACCTGGTCA;RSEQ=CCCGGGACAACTATGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:24,48:72,2:0.027:2,2:30:1:28.5:1:1:1.98:60:4:0.0274:0:1 0/0:62:0:0,0:27,35:62,0:0:2,0:24.7:1:30.8:1:1:0:60:124:1:0:0.1 +2 85533678 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50197;SOR=0;LSEQ=AACCTGGTCAGCCCGGGACA;RSEQ=CTATGTAAGTGCACACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:1,1:19,51:70,2:0.0278:2,2:10.5:1:29:0:0.48122:2.64:60:4:0.0286:0:1.5 0/0:58:0:0,0:24,34:58,0:0:2,0:21.1:1:28.3:1:1:0:60:116:1:0:0.1 +2 85960749 . C T 67 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=TGGGGCCTTGGCCATCTCTC;RSEQ=CCTCCCCGCTGGGCCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:39.8:1:33.5:1:1:0:60:8:0.6667:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:28:0:26:0:1:0:60:2:0.3333:0:1 +2 86184026 . CA TG 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGAAATGACACTCCCCA;RSEQ=GGAAGTCCTTGGTTAACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:42:1:33:1:1:0:47:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 86184199 . C T 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.39581;LSEQ=CAGGTGGCATTTATGAAATG;RSEQ=AATCCTTTGGGAAAAATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:7,0:5,0:5,7:0.5833:0,0:27.6:1:30.3:1:1:0:60:14:0.5833:0:1.1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:17:1:31:0:1:0:60:4:0.6667:0:1 +2 86184354 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18636;SOR=Inf;LSEQ=CTGATATCATAGCTGGTGCG;RSEQ=TATGAAGCAATGTTATAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:134,22:156,0:0:2,0:22.1:1:31.1:1:1:0:59.8:51:1:0:0.3 0/1:119:2:1,1:97,20:117,2:0.0168:2,2:13:1:27.5:1:0.32303:4.7575:60:4:0.0169:0:1 +2 86184441 . A G 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00057;SOR=1.5767;LSEQ=TTTGGATACCAATGGTCCAA;RSEQ=AGGAAGGTCCTGATTCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:637:422:238,184:117,97:214,422:0.6625:2,2:26.8:1:32.8:1:0.73543:1.07:59.7:421:0.664:0:1.7 1/0:512:387:214,173:69,56:125,387:0.7559:2,2:25.8:1:30.8:1:1:1.00:60:76.4:0.7535:0:1.7 +2 86184486 . T G 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00354;SOR=1.46447;LSEQ=TTGGGGAGGAATGTCACAAC;RSEQ=TGCTACAAGCTCACCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:678:441:213,228:114,123:237,441:0.6504:2,2:24.7:1:31.3:1:1:1.01:59.9:219.5:0.6513:0:1.7 1/0:503:368:173,195:65,69:134,368:0.7316:2,2:24:1:30.1:1:0.83992:1.06167:60:91:0.7309:0:1.7 +2 86184565 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15359;SOR=Inf;LSEQ=GTTGTGGGAATTGCTCTCAG;RSEQ=CTTCCCCAGGGTAGTAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:80,228:308,0:0:2,0:23.8:1:31.9:1:1:0:60:101.667:1:0:0.3 0/1:199:2:1,1:51,146:197,2:0.0101:2,2:32:1:27.5:1:0.45531:2.84:60:4:0.0101:0:1 +2 86184608 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.1428;SOR=Inf;LSEQ=CCAAGCTATTTCAAACCAAT;RSEQ=TTTTTTTCTTCTTTTTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:7,114:121,0:0:2,0:24.9:1:32.5:1:1:0:60:59.5:1:0:0.1 0/1:74:2:1,1:5,67:72,2:0.027:2,2:17:0:29:1:0.15661:12.32:60:4:0.0274:0:1 +2 86650358 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50958;SOR=Inf;LSEQ=GTTCCCGAAGAGGGTGATGA;RSEQ=GCACAGCAGAAAAACATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:42,26:68,0:0:2,0:25.5:1:31.2:1:1:0:60:67:0.9853:0:0.2 0/1:95:2:1,1:56,37:93,2:0.0211:2,2:25.5:1:29.5:1:1:1.5067:60:4:0.0213:0:1.5 +2 86650379 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51253;SOR=Inf;LSEQ=GCACAGCAGAAAAACATGGA;RSEQ=AAGTTAGCAACAGCAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:57,40:97,0:0:2,0:27.3:1:32.5:1:1:0:59.6:47.5:1:0:0.3 0/1:137:2:1,1:75,60:135,2:0.0146:2,2:13:0:27.5:1:1:1.24794:60:4:0.015:0:1 +2 86650444 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17865;SOR=0;LSEQ=TGAAGTATGTTGCCAGCACC;RSEQ=GAATGCTGCAGTCATTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:26,34:60,2:0.0323:2,2:18.5:1:32.5:1:1:1.30:60:4:0.0328:0:2 0/0:84:0:0,0:35,49:84,0:0:2,0:24.1:1:29.2:1:1:0:60:41:1:0:0.4 +2 86650474 . T G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16927;SOR=2.32679;LSEQ=AGTCATTCCTTTGAATAGTT;RSEQ=GACAGGCTAATTCAGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:20:4,16:4,7:11,20:0.6452:2,2:25.1:1:31.6:1:0.40549:2.22149:60:40:0.6667:0:1.1 1/1:37:30:5,25:1,6:7,30:0.8108:2,2:17.7:1:29.4:1:1:1.19:60:14:0.8:0:1 +2 89853196 . C G 52 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTATTCCATTCCATTGTTTT;RSEQ=CATTCCATTCCATTTGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:34:0:1:0:47:2:1:0:4 1/0:4:3:2,1:0,1:1,3:0.75:0,2:7.3:1:33:1:1:0:29.7:6:0.75:0:5.3 +2 89853211 . T G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27451;SOR=0.20422;LSEQ=GTTTTCCATTCCATTCCATT;RSEQ=GATTACATTCCATTCGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:5,4:1,0:1,9:0.9:0,2:11.6:1:32.7:1:1:0:31.4:18:0.9:0:3.9 1/0:8:5:2,3:0,0:0,5:0.625:0,2:16.6:1:31.4:1:1:0:28.4:10:0.625:0:4.2 +2 89853214 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18301;SOR=Inf;LSEQ=TTCCATTCCATTCCATTTGA;RSEQ=TACATTCCATTCGATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:17.6:1:31.7:1:1:0:33:20:1:0:3.9 0/1:8:2:2,0:1,5:6,2:0.25:2,0:26.5:1:32.5:1:0.10714:0:24.5:4:0.25:0:6 +2 89853216 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55882;SOR=0.35469;LSEQ=CCATTCCATTCCATTTGATT;RSEQ=CATTCCATTCGATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:5,4:1,0:1,9:0.9:0,2:16.6:1:33.4:1:1:0:31.4:18:0.9:0:3.9 1/0:8:6:3,3:0,2:2,6:0.75:0,2:21.2:1:33.2:1:0.46429:0:27.5:12:0.75:0:4.3 +2 89853225 . T G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.18301;SOR=Inf;LSEQ=TCCATTTGATTACATTCCAT;RSEQ=CGATTCCATTCCATTCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:27.1:1:32.2:1:1:0:33:20:1:0:3.9 0/1:8:2:0,2:3,3:6,2:0.25:2,0:31:1:27.5:1:0.46429:0:20:4:0.25:0:4 +2 89853237 . CAT GAAA 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.18301;SOR=Inf;LSEQ=CATTCCATTCGATTCCATTC;RSEQ=TCGAATCAATTACATTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:31.7:1:33.2:1:1:0:33:20:1:0:3.9 0/1:8:2:0,2:3,3:6,2:0.25:2,0:32:0:28.5:1:0.46429:0:20:4:0.25:0:4 +2 89853255 . T A 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55;SOR=0.33678;LSEQ=TCCATTCGAATCAATTACAT;RSEQ=GCAATCCATTACATTCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:1,0:1,8:0.8889:0,2:19.5:1:31:1:1:0:32.6:16:0.8889:0:4.1 1/0:7:5:3,2:0,2:2,5:0.7143:0,2:12.2:1:28.8:1:0.42857:0:28.8:10:0.7143:0:4.8 +2 89853272 . AC CA 27 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGCAATCCATTACATTC;RSEQ=GTCCGTTCTATTCCACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:14:0:27.8:1:1:0:37.5:4:0.6667:0:5 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:33:0:1:0:32:2:1:0:3 +2 89853277 . C T 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATCCATTACATTCACGTC;RSEQ=GTTCTATTCCACTCCATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:31:1:1:0:37.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 89853780 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCCATTAGGTTCCATT;RSEQ=CGTTCCATTCCATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:32:1:1:0:22:4:1:0:4.5 +2 89853782 . G A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTAGGTTCCATTTC;RSEQ=TTCCATTCCATTCCATTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:30:1:1:0:22:4:1:0:4.5 +2 89853801 . GT CA 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTCCATTCCATTCCATTC;RSEQ=TTCCATTCCAATCGAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:31.3:1:1:0:22:4:1:0:3.5 +2 89872092 . C A 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0.54771;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CTGTTGATTCCATTCCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:25:0:27:0:1:0:32:2:0.5:0:3 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:18:1:28:1:1:2.44949:23.5:4:0.4:0:3 +2 89872094 . T G 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=GTTGATTCCATTCCATTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:25:0:33:0:1:0:24:2:0.5:0:2 1/0:6:3:2,1:1,1:2,3:0.5:2,2:23.3:1:30.3:1:1:1.73:22.7:6:0.6:0:2.7 +2 89872096 . T A 66 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCTG;RSEQ=TGATTCCATTCCATTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28:1:30.5:1:1:0:28:4:1:0:2.5 1/1:6:5:3,2:1,0:1,5:0.8333:0,2:24:1:28.8:1:1:0:23:10:0.8333:0:2.8 +2 89872128 . C G 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTGCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:6:0:33.5:1:1:0:28:4:1:0:2.5 0/1:6:2:2,0:2,2:4,2:0.3333:2,0:28:1:28:1:0.46667:0:20:4:0.4:0:5.5 +2 89872512 . C T 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=1.7321;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCAGATTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:14:0:25:0:1:0:22:2:0.5:0:4 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:14.5:1:30.5:1:1:0:22:4:0.6667:0:3.5 +2 89872517 . C A 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=1.7321;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCAGATTGATTCTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:19:0:26:0:1:0:22:2:0.5:0:4 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:19.5:1:30:1:1:0:22:4:0.6667:0:3.5 +2 89872538 . C A 32 d5;v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCAGATTGATTCTATTC;RSEQ=ATTCCCTTCAATTCCACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:9:0:30.5:1:1:0:21.5:4:1:0:4 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:9:0:32:1:1:0:22:4:0.6667:0:3.5 +2 91884897 . T A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CCTTGGATTATAGGCAGAAA;RSEQ=GTTACATGTTTTTAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1:0,2:16:1:31.7:1:1:0:26.2:12:1:0:2.2 0/0:1:0:0,0:0,1:1,0:0:0,0:18:0:27:0:1:0:21:2:1:0:0 +2 91884911 . A T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.11111;SOR=0;LSEQ=CAGAAATGTTACATGTTTTT;RSEQ=AAAAATGGTCTTCCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:2,6:0,0:0,8:1:0,2:23.8:1:29.4:1:1:0:34.6:16:1:0:1.9 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:32:0:1:0:21:2:1:0:0 +2 91885008 . C T 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGATCACGAGGTCAGGAGAT;RSEQ=GAGACCATCCTGGCAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:24:1:31.7:1:1:0:43.3:6:0.5:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:21:0:31:0:1:0:52:2:1:0:1 +2 91885859 . C A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TACGGAATTTGGATAGAACA;RSEQ=CCATATGATTGAAGCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:6,0:0:2,0:38.5:1:33:1:1:0:60:12:1:0:0 0/1:10:2:1,1:4,4:8,2:0.2:2,2:7.5:1:30.5:1:1:1:39:4:0.2:0:1.5 +2 91885974 . G T 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACTAGCTCTTTTACTTTT;RSEQ=TGACAATTTGTGCTACAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:22.5:1:32.5:1:1:0:23.5:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:19:0:34:0:1:0:20:2:1:0:2 +2 91887802 . A G 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.71637;LSEQ=ACTTTAGTCTGGAGTTGAGA;RSEQ=TTCAAAACAGGAAATCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:16,1:17,3:0.15:1,0:16.7:1:31:1:1:0:30.7:6:0.15:0:1.3 0/1:9:1:1,0:7,1:8,1:0.1111:2,0:22:0:26:0:1:0:36:2:0.1111:0:1 +2 91894184 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.54503;SOR=Inf;LSEQ=TGCTAGAAAACAACACAACC;RSEQ=TATCGAGCACAGAGTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:13,30:43,0:0:2,0:20.2:1:31.7:1:1:0:24:86:1:0:0.4 0/1:82:2:1,1:24,56:80,2:0.0244:2,2:37:1:29.5:1:0.51942:2.31:29:4:0.025:0:1 +2 91894194 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0012;SOR=3.86308;LSEQ=CAACACAACCATATCGAGCA;RSEQ=AGAGTTTTCTTCATCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:2,9:11,21:32,11:0.2558:2,2:17.2:1:29.9:1:0.45592:2.31451:21.2:22:0.2558:0:1 1/0:82:47:14,33:11,24:35,47:0.5732:2,2:17.1:1:28.8:1:1:1.07934:21.4:22.5:0.5625:0:1.1 +2 92150253 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28349;SOR=0;LSEQ=TCCTCCCTCTTTCCACAGGG;RSEQ=CATGCCACCCCTGTCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:3:3,0:137,21:158,3:0.0186:2,0:15.3:1:29.3:1:1:0:30.3:6:0.0196:0:1 0/0:103:0:0,0:79,24:103,0:0:2,0:23:1:29.8:1:1:0:34.7:19.6:1:0:0.1 +2 92150264 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15976;SOR=Inf;LSEQ=TCCACAGGGGCATGCCACCC;RSEQ=TGTCATTCTAGGATTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:169,36:205,0:0:2,0:25.1:1:31.5:1:1:0:31.7:50.25:1:0:0.1 0/1:137:2:1,1:102,33:135,2:0.0146:2,2:22:1:28.5:1:0.43613:3.05988:27.5:4:0.0148:0:1 +2 92151432 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09059;SOR=Inf;LSEQ=TATGACAACCAGTAATTTTT;RSEQ=GTACTAGAATTTCACATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:27,2:29,0:0:2,0:32.1:1:31.7:1:1:0:37:28:1:0:0.1 0/1:13:2:1,1:10,1:11,2:0.1538:2,2:28:0:32:0:0.29487:7.41607:25:4:0.1538:0:1.5 +2 92281281 . T C 30 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAGTCACAGAGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:30.5:1:1:0:22:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 92281291 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:31.5:1:1:0:22:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 92281327 . G T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCTTTTTGTAGTGTCTG;RSEQ=AAGTGGACATTTGGATTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:27.6:1:30.6:1:1:0:24.6:10:1:0:5 1/1:8:8:4,4:0,0:0,8:1:0,2:22.4:1:29.3:1:1:0:23.6:16:1:0:3.9 +2 92281333 . G A 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTAGTGTCTGGAAGTG;RSEQ=ACATTTGGATTGCTTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:28.8:1:32:1:1:0:24.6:10:1:0:5 1/1:8:8:4,4:0,0:0,8:1:0,2:26:1:30.4:1:1:0:23.6:16:1:0:3.9 +2 92281355 . T C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38462;SOR=Inf;LSEQ=CATTTGGATTGCTTTCAGGC;RSEQ=TAAGGTGAAAAAGGAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:1,4:0.8:0,2:15:1:33:1:1:0:25:8:0.8:0:4.5 1/1:8:8:4,4:0,0:0,8:1:0,2:21.1:1:32.4:1:1:0:23.6:16:1:0:3.9 +2 92284320 . G T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCCTCAGAAACATCTTTG;RSEQ=GATGTTTGCATTCAAGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:14:0:31.4:1:1:0:24:10:1:0:7.2 1/1:17:17:9,8:0,0:0,17:1:0,2:14:0:30.3:1:1:0:25.8:34:1:0:6.1 +2 92284329 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATCTTTGGGATGTTTG;RSEQ=ATTCAAGTCACAGAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:23:0:30.6:1:1:0:24:10:1:0:7.2 1/1:17:17:9,8:0,0:0,17:1:0,2:23:0:29.2:1:1:0:25.8:34:1:0:6.1 +2 92284335 . A G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGGATGTTTGCATTCA;RSEQ=GTCACAGAGTTGAACATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:29:0:33.6:1:1:0:24:10:1:0:7.2 1/1:17:17:9,8:0,0:0,17:1:0,2:29:0:31.5:1:1:0:25.8:34:1:0:6.1 +2 92284337 . T A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGGATGTTTGCATTCAAG;RSEQ=CACAGAGTTGAACATTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:31:0:31.2:1:1:0:24:10:1:0:7.2 1/1:17:17:9,8:0,0:0,17:1:0,2:31:0:29.5:1:1:0:25.8:34:1:0:6.1 +2 92284363 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTGAACATTCCCTATCAT;RSEQ=GAGCAGGTTTGAAACACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:26.2:1:28.4:1:1:0:24:10:1:0:7.2 1/1:17:17:9,8:0,0:0,17:1:0,2:17:1:28.4:1:1:0:25.8:34:1:0:6.1 +2 92284377 . A T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATCATGGAGCAGGTTTGAA;RSEQ=CACTCTTTTTGTGGAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:12.2:1:28.4:1:1:0:24:10:1:0:7.2 1/1:8:8:4,4:0,0:0,8:1:0,2:8.9:1:29.3:1:1:0:26:16:1:0:6.9 +2 92284383 . T C 81 d5 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCAGGTTTGAAACACTC;RSEQ=TTTTGTGGAATCTGGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:8:1:29.8:1:1:0:23.3:8:1:0:7.5 1/1:7:7:4,3:0,0:0,7:1:0,2:4:1:29.1:1:1:0:25.9:14:1:0:7 +2 92290548 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATCTGGAAGTGTCCATT;RSEQ=GGAGTGCATTCAGGCTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:32.5:1:1:0:26:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 92290553 . T A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGAAGTGTCCATTTGGAG;RSEQ=GCATTCAGGCTTGTGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:32.5:1:1:0:26:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 92290929 . C A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAAGGAAATATCTTCCC;RSEQ=TGAAAACTAGACAGAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:0,7:1:0,2:7:1:31.3:1:1:0:21.1:14:1:0:2.9 1/1:7:7:3,4:0,0:0,7:1:0,2:17.3:1:31.4:1:1:0:22.6:14:1:0:2.4 +2 92290985 . A G 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.57842;LSEQ=TGTGATGTGTGCCCTCAACT;RSEQ=ACAATGTTGAACCTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:5,3:1,0:1,8:0.8889:0,2:27:1:33.9:1:1:0:21.1:16:0.8889:0:3.9 1/1:11:9:4,5:1,1:2,9:0.8182:2,2:29.4:1:32:1:1:1.22474:27.9:18:0.8182:0:4 +2 92290989 . A G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGTGCCCTCAACTAACA;RSEQ=TGTTGAACCTTTCTTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:0,8:1:0,2:24.4:1:34.8:1:1:0:21.1:16:1:0:3.9 1/1:10:9:4,5:1,0:1,9:0.9:0,2:27.2:1:32.6:1:1:0:27.9:18:0.9:0:4 +2 92291002 . C G 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAACAATGTTGAACCTTT;RSEQ=TTTTGATAGAGCAGTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:20:1:34.4:1:1:0:21.8:10:1:0:4.4 1/1:9:9:4,5:0,0:0,9:1:0,2:15.2:1:31.2:1:1:0:27.9:18:1:0:4 +2 92291008 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=AATGTTGAACCTTTCTTTTG;RSEQ=TAGAGCAGTTTTGAAACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:14:1:32.8:1:1:0:21.8:10:1:0:4.4 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:15.5:1:31:1:1:1.29:23:4:0.25:0:5 +2 92291089 . T A 58 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTTCGTTGGAAACGGGA;RSEQ=TGTCTTCATATAAACTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:3,1:0,0:0,4:1:0,2:11.8:1:29.3:1:1:0:24.5:8:1:0:6.3 +2 92291099 . A G 71 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAAACGGGATTGTCTTCAT;RSEQ=TAAACTCTAGACAGAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:19.4:1:30.8:1:1:1.41:25.6:10:0.7143:0:6 +2 92291100 . T G 30 d5;v3;p8;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACGGGATTGTCTTCATA;RSEQ=AAACTCTAGACAGAAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:7:1:30:1:1:1.41418:21:4:0.2857:0:7.5 +2 92291104 . C A 27 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGGGATTGTCTTCATATAAA;RSEQ=TCTAGACAGAAGCATTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:11:1:27.5:1:1:1.41418:21:4:0.2857:0:7.5 +2 92291109 . G C 87 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTTCATATAAACTCTA;RSEQ=ACAGAAGCATTCTCAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:7:4,3:1,1:2,7:0.7778:2,2:21.3:1:31:1:1:1.29:24.3:14:0.7778:0:5.4 +2 92291129 . T C 101 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAAGCATTCTCAGAAA;RSEQ=TTCTTTGGGATGTTTCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:9:9:5,4:0,0:0,9:1:0,2:33.4:1:32.1:1:1:0:23.6:18:1:0:5.9 +2 92291131 . T G 90 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAGCATTCTCAGAAATT;RSEQ=CTTTGGGATGTTTCAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:7:4,3:1,1:2,7:0.7778:2,2:32.6:1:32.4:1:1:1.29:24.3:14:0.7778:0:5.4 +2 92291156 . A C 85 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATGTTTCAATTGAAGTC;RSEQ=CAGTGTTGAACATTCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:7:4,3:0,0:0,7:0.7778:0,2:13.4:1:30.4:1:1:0:24.3:14:0.7778:0:5.4 +2 92291164 . G A 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATTGAAGTCACAGTGTT;RSEQ=AACATTCCCTTTGTTAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:30:1:30.5:1:1:1.41418:21:4:0.2857:0:7.5 +2 92291177 . GT CA 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGTTGAACATTCCCTTT;RSEQ=TAGAGCAGGTTTGAAACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:32:1:1:0:21:4:1:0:6.5 +2 92296844 . A G 31 d5;v3;MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGGGGAATATGCAAGTGG;RSEQ=TATTAGGCCAGCTTGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:31:1:1:0:20:4:1:0:3.5 1/1:1:1:0,1:0,0:0,1:1:0,0:9:0:33:0:1:0:29:2:1:0:6 +2 92296884 . C A 31 d5;v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCGTTGGAAACGGGAAT;RSEQ=CATATAAAAAGCAGACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32:0:31:1:1:0:20:4:1:0:3.5 1/1:1:1:0,1:0,0:0,1:1:0,0:49:0:31:0:1:0:29:2:1:0:6 +2 92296886 . A G 33 d5;v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCGTTGGAAACGGGAATCC;RSEQ=TATAAAAAGCAGACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:33:1:1:0:20:4:1:0:3.5 1/1:1:1:0,1:0,0:0,1:1:0,0:50:0:34:0:1:0:29:2:1:0:6 +2 92305618 . T A 42 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTAGACAGAAGCATTCTC;RSEQ=GAACCTAGTTTCTGAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:29.5:1:1:0:21:4:1:0:6 1/1:3:3:1,2:0,0:0,3:1:0,2:14.3:1:27:1:1:0:22:6:1:0:6.7 +2 92305622 . C A 89 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30769;SOR=Inf;LSEQ=AGACAGAAGCATTCTCTGAA;RSEQ=CTAGTTTCTGAGATGTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0,3:0.75:0,2:7.7:1:28:1:1:0:22:6:0.75:0:6.3 1/1:9:9:4,5:0,0:0,9:1:0,2:7.3:1:28.1:1:1:0:25.1:18:1:0:6.7 +2 92305634 . GA TG 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28142;SOR=4.01342;LSEQ=TCTCTGAACCTAGTTTCTGA;RSEQ=TGTGTCCTCAACTAACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:3,6:0,0:0,9:0.8182:0,2:11.9:1:29.5:1:1:0:21.4:18:0.8182:0.2727:3.9 1/1:20:19:10,9:0,0:0,19:0.95:0,2:12.9:1:29.6:1:1:0:24.1:38:0.95:0.15:4.8 +2 92305649 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGAGATGTGTCCTCAACT;RSEQ=ACAGAGTTGAACATTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:11,0:0:2,0:23.6:1:28.5:1:1:0:21.8:10:1:0:4.4 0/1:37:2:1,1:19,16:35,2:0.0541:2,2:25:1:29.5:1:1:1.18197:26.5:4:0.0541:0:6 +2 92305653 . G C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02937;SOR=13.19036;LSEQ=AGATGTGTCCTCAACTAACA;RSEQ=AGTTGAACATTTCTTTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:2,6:2,1:3,8:0.7273:2,2:27.9:1:31.4:1:0.49091:4.9538:21.6:16:0.7273:0:3.8 1/1:39:38:21,17:1,0:1,38:0.9744:0,2:22:1:30.9:1:1:0:23.7:76:0.9744:0:4.5 +2 92305659 . A T 99 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24989;SOR=4.19115;LSEQ=GTCCTCAACTAACAGAGTTG;RSEQ=ACATTTCTTTTGACAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:4,6:10,1:0.0909:2,0:35:0:25:0:1:0:22:2:0.1:0:5 0/1:40:12:6,6:16,12:28,12:0.3:2,2:28.3:1:27.7:1:0.73845:1.32369:24.5:24:0.3:0:4.5 +2 92305662 . A T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCAACTAACAGAGTTGAAC;RSEQ=TTTCTTTTGACAGAACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:11,0:0:2,0:36.5:1:29.8:1:1:0:21.8:10:1:0:4.4 0/1:40:3:1,2:21,16:37,3:0.075:2,2:36:1:30.7:1:0.57915:2.56289:27.3:6:0.075:0:6 +2 92305670 . T A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01534;SOR=10.12008;LSEQ=ACAGAGTTGAACATTTCTTT;RSEQ=GACAGAACAGTTTTGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:2,5:1,0:1,7:0.6364:0,2:39.9:1:29.3:1:0.375:0:21.6:6:0.6:0:3.6 1/1:40:38:21,17:0,0:0,38:0.95:0,2:36.3:1:28.8:1:1:0:23.7:76:0.95:0:4.4 +2 92305673 . C G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04314;SOR=0;LSEQ=GAGTTGAACATTTCTTTTGA;RSEQ=AGAACAGTTTTGAAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:43:0:34:0:1:1.87:23.5:4:0.1818:0:6.5 0/0:40:0:0,0:22,18:40,0:0:2,0:37.7:1:31.6:1:1:0:23.6:80:1:0:4.4 +2 92305676 . A T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02773;SOR=0.07388;LSEQ=TTGAACATTTCTTTTGACAG;RSEQ=ACAGTTTTGAAACACTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:2,6:8,3:0.2727:2,2:43.3:1:29.7:1:0.49091:4.95:22.3:6:0.3:0:6 0/1:40:1:1,0:21,18:39,1:0.025:2,0:41:0:32:0:1:0:20:2:0.025:0:6 +2 92305678 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04314;SOR=0;LSEQ=GAACATTTCTTTTGACAGAA;RSEQ=AGTTTTGAAACACTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:41.5:1:30.5:1:1:1.87:23.5:4:0.1818:0:6.5 0/0:40:0:0,0:22,18:40,0:0:2,0:37.3:1:31.8:1:1:0:23.6:80:1:0:4.4 +2 92305704 . A G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00842;SOR=0;LSEQ=TGAAACACTCTTTTTGTGGA;RSEQ=TCTGCAAGTGGATACTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:2,6:8,3:0.2727:2,2:15.3:1:31:1:0.49091:4.95:22.3:6:0.2727:0:6 0/0:39:0:0,0:20,18:38,0:0:2,0:16.6:1:29.9:1:1:0:23.7:76:0.9744:0:4.3 +2 92305713 . T A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTTGTGGAATCTGCAAG;RSEQ=GGATACTTTGCTGGCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:9,0:0:2,0:5.1:1:29.8:1:1:0:22:18:1:0:4.1 0/1:35:2:1,1:19,14:33,2:0.0571:2,2:6.5:1:27.5:1:1:1.34517:23:4:0.0571:0:4.5 +2 92305716 . A C 78 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.57335;LSEQ=TTTGTGGAATCTGCAAGTGG;RSEQ=TACTTTGCTGGCTTTGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:4,1:0.2:2,0:6:0:35:0:1:0:24:2:0.2:0:6 0/1:21:6:5,1:7,7:14,6:0.2857:2,2:14:1:30.2:1:0.32456:4.63:23.8:12:0.2857:0:6.3 +2 92305719 . C T 101 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51471;SOR=2.56905;LSEQ=GTGGAATCTGCAAGTGGATA;RSEQ=TTTGCTGGCTTTGAGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:3:0:29:0:1:0:24:2:0.5:0:6 1/0:15:11:8,3:2,1:3,11:0.7333:2,2:12.7:1:29.2:1:1:1.31:26.3:22:0.7333:0:6.8 +2 92305722 . T G 93 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATCTGCAAGTGGATACTT;RSEQ=GCTGGCTTTGAGGATTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:8:8:7,1:0,0:0,8:1:0,2:15.1:1:31.3:1:1:0:24.3:16:1:0:6.9 +2 92305726 . G A 80 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAAGTGGATACTTTGCT;RSEQ=GCTTTGAGGATTTCGTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:3:0:28.5:1:1:0:24:4:1:0:8 1/1:8:8:7,1:0,0:0,8:1:0,2:12.1:1:26.8:1:1:0:24.3:16:1:0:6.9 +2 92305728 . C A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11415;SOR=Inf;LSEQ=GCAAGTGGATACTTTGCTGG;RSEQ=TTTGAGGATTTCGTTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:3.2:1:28.2:1:1:0:24.8:4:1:0:7.4 0/1:13:6:5,1:3,4:7,6:0.4615:2,2:11.8:1:27.7:1:0.26573:5.70:22.7:12:0.4615:0:7 +2 92305733 . A G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63336;SOR=0.40108;LSEQ=TGGATACTTTGCTGGCTTTG;RSEQ=GGATTTCGTTGGAAACGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:1,6:0.8571:0,2:7:1:30.8:1:1:0:25.5:12:0.8571:0:7.3 1/0:20:14:8,6:5,1:6,14:0.7:2,2:5.6:1:29.7:1:0.35436:3.52899:31:28:0.7:0:6.9 +2 92305742 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=2.16029;LSEQ=TGCTGGCTTTGAGGATTTCG;RSEQ=TGGAAACGGGAATACATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:7,2:1,0:1,9:0.9:0,2:13.3:1:33.9:1:1:0:24.9:18:0.9:0:7 1/1:21:20:10,10:0,1:1,20:0.9524:0,2:12.3:1:31.4:1:1:0:29.4:40:0.9524:0:6.7 +2 92305748 . A G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTTTGAGGATTTCGTTGGAA;RSEQ=CGGGAATACATATAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:7,2:1,0:1,9:0.9:0,2:19.3:1:29.8:1:1:0:24.9:3.5:0.875:0:7 1/1:20:20:10,10:0,0:0,20:1:0,2:18.3:1:31.5:1:1:0:29.4:40:1:0:6.7 +2 92305770 . G C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60152;SOR=1.95703;LSEQ=GGGAATACATATAAAAAGCA;RSEQ=ACAGCAGCGTTGTGAGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:7,3:1,0:1,10:0.8333:0,2:37.3:1:32.4:1:1:0:26:20:0.9091:0:6.7 1/1:22:20:10,10:1,1:2,20:0.9091:2,2:36.1:1:32.1:1:1:1:29.4:40:0.9091:0:6.7 +2 92305782 . G C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAGCAGACAGCAGCGTT;RSEQ=TGAGAAACTTCTTTGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:9,3:0,0:0,12:1:0,2:35.3:1:32.4:1:1:0:25.4:24:1:0:6.4 1/1:22:22:11,11:0,0:0,22:1:0,2:31.3:1:30.9:1:1:0:30:21:1:0:6.5 +2 92305789 . A G 35 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11765;SOR=0;LSEQ=AGACAGCAGCGTTGTGAGAA;RSEQ=CTTCTTTGTGATGTTTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:8,2:10,2:0.1667:2,2:24:0:35:0:0.45455:3.4638:30:4:0.1667:0:5.5 0/0:22:0:0,0:11,11:22,0:0:2,0:25.5:1:29.9:1:1:0:30:44:1:0:6.5 +2 92305792 . T G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65256;SOR=1.74387;LSEQ=CAGCAGCGTTGTGAGAAACT;RSEQ=CTTTGTGATGTTTGCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:7,2:2,1:3,9:0.75:2,2:24.7:1:32:1:1:1.66:24.9:18:0.75:0:6.9 1/1:19:16:8,8:0,1:1,16:0.8421:0,2:26:1:32.1:1:1:0:27.4:32:0.8421:0:6.8 +2 92305796 . T G 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.28368;LSEQ=AGCGTTGTGAGAAACTTCTT;RSEQ=GTGATGTTTGCATTCAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:8,3:11,1:0.0833:2,0:35:0:30:0:1:0:21:2:0.0909:0:4 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:29.5:1:32.5:1:1:1.12:36.5:4:0.1053:0:4 +2 92305797 . G C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77901;LSEQ=GCGTTGTGAGAAACTTCTTT;RSEQ=TGATGTTTGCATTCAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:8,3:1,0:1,11:0.9167:0,2:19:1:30.8:1:1:0:25.8:10:0.9091:0:6.6 1/1:19:17:8,9:1,1:2,17:0.8947:2,2:21:1:31.8:1:1:1.11803:28:34:0.8947:0:6.8 +2 92305805 . T C 33 v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.54349;SOR=0.2901;LSEQ=AGAAACTTCTTTGTGATGTT;RSEQ=GCATTCAAGTCACAGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:8,2:10,2:0.1667:2,2:8:0:33:1:0.45455:3.4638:30:4:0.1818:0:5.5 0/1:19:1:0,1:9,9:18,1:0.0526:2,0:13:0:32:0:1:0:38:2:0.0526:0:7 +2 92305818 . CAG AA 29 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATGTTTGCATTCAAGTCA;RSEQ=AGTTGAACGTTCCGTATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:13:0:27:0:1:0:21:2:1:0:4 1/0:4:2:1,1:1,1:2,2:0.5:2,2:6:1:29:1:1:1:28:4:0.5:0.25:7 +2 92306098 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGTTGGAAACGGGATTACAT;RSEQ=TAAAAAGCAGACAGCAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:29.5:1:1:0:23:4:1:0:3 +2 92306101 . A C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAACGGGATTACATATA;RSEQ=AAAGCAGACAGCAGCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:33.5:1:1:0:23:4:1:0:3 +2 92306788 . A T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTACATATAAAAAGCAG;RSEQ=CAGCAGCATTCCCAGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:19:0:31:0:1:0:24:2:1:0:5 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:18:0:31:0:1:0:23:4:0.6667:0:5 +2 92306800 . C T 50 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=CAGAAACTTCTTTGTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:31:0:34:0:1:0:24:2:1:0:5 1/1:3:3:3,0:0,0:0,3:1:0,0:27.3:1:32:0:1:0:22:6:1:0:4.7 +2 92306807 . C G 52 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGCAGCATTCCCAGAAA;RSEQ=TTCTTTGTGATGTTTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:38:0:36:0:1:0:24:2:1:0:5 1/1:3:3:3,0:0,0:0,3:1:0,0:34.3:1:33:1:1:0:22:6:1:0:4.7 +2 92306820 . T A 44 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGAAACTTCTTTGTGATG;RSEQ=TTGCATTCAAGTCACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:50:0:32:0:1:0:24:2:1:0:5 1/1:3:3:3,0:0,0:0,3:1:0,0:47.3:1:28.3:1:1:0:22:6:1:0:4.7 +2 92306839 . G A 44 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCATTCAAGTCACAGA;RSEQ=TTGAACATTCCCTTTCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:31:0:32:0:1:0:24:2:1:0:5 1/1:3:3:3,0:0,0:0,3:1:0,0:34.7:1:28:1:1:0:22:6:1:0:4.7 +2 92307734 . C G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTTTAAACACTCTTTTT;RSEQ=TAAAATCTGCAAGAGGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:30.5:1:1:0:20.5:4:1:0:7 +2 92307737 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTAAACACTCTTTTTCTA;RSEQ=AATCTGCAAGAGGATATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:42:1:31.5:1:1:0:20.5:4:1:0:7 +2 92307741 . C G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACTCTTTTTCTAAAAT;RSEQ=TGCAAGAGGATATTTGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:31:1:1:0:20.5:4:1:0:7 +2 92307747 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTTCTAAAATCTGCAA;RSEQ=AGGATATTTGGATAGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:49:1:29.5:1:1:0:20.5:4:1:0:7 +2 92307758 . G C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCTGCAAGAGGATATTTG;RSEQ=ATAGCTTTGAGGATTTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:32:0:1:0:20.5:4:1:0:7 +2 92307778 . T G 33 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAGCTTTGAGGATTTCGT;RSEQ=GGAAACGGGATTGTCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:33:1:1:0:20.5:4:1:0:7 +2 92316016 . A G 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTCAAGTCACACAGTTGAAC;RSEQ=TTCCCTTTCATAGAGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:19:0:32.5:1:1:0:37:4:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:32:1:1:0:20:4:1:0:6.5 +2 92316021 . C A 32 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTCACACAGTTGAACATTCC;RSEQ=TTTCATAGAGCAGGTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:32.5:1:1:0:37:4:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:27:0:33:1:1:0:20:4:1:0:6.5 +2 92316025 . C A 31 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CACAGTTGAACATTCCCTTT;RSEQ=ATAGAGCAGGTTTGAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:31.5:1:1:0:37:4:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:31:0:33:1:1:0:20:4:1:0:6.5 +2 92316039 . G C 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCTTTCATAGAGCAGGTTT;RSEQ=AAACACTCTTTTTGTAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:5:0:33.5:1:1:0:37:4:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:32:1:1:0:20:4:1:0:6.5 +2 92316044 . A C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCATAGAGCAGGTTTGAAAC;RSEQ=CTCTTTTTGTAGTATCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:30.5:1:1:0:20:4:1:0:6.5 +2 92316051 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGTTTGAAACACTCTTT;RSEQ=TGTAGTATCTGGAAGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:30.5:1:1:0:20:4:1:0:6.5 +2 92316054 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGTTTGAAACACTCTTTTTG;RSEQ=AGTATCTGGAAGTGGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:31:1:1:0:20:4:1:0:6.5 +2 92317326 . CC TG 80 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGCAGACAGCAGCATTC;RSEQ=AGAAACTTCTTTCTGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:5,1:0,0:0,6:1:0,2:9.3:1:31:1:1:0:29.3:12:1:0.8333:7 +2 92317335 . T G 92 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAGCATTCCCAGAAACT;RSEQ=CTTTCTGATGTTTGCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:8:0:27.5:1:1:0:27:4:1:0:7 1/1:7:7:5,2:0,0:0,7:1:0,2:12.1:1:33:1:1:0:28.4:14:1:0:7 +2 92317361 . CAG AA 85 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGTTTGCATTCAAGTCA;RSEQ=AGTTGAACATTCCCTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:34:0:29.5:1:1:0:27:4:1:0:6 1/1:7:7:5,2:0,0:0,7:1:0,2:33.1:1:30.6:1:1:0:28.4:14:1:0:6.1 +2 92317373 . T C 89 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAGTCACAGAGTTGAACA;RSEQ=TCCCTTTCATAGAGCAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:45:0:33:0:1:0:27:4:1:0:7 1/1:7:7:5,2:0,0:0,7:1:0,2:41:1:31.9:1:1:0:28.4:14:1:0:7.1 +2 92317391 . GT TC 71 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=2.23609;LSEQ=CATTCCCTTTCATAGAGCAG;RSEQ=TTGAAACACTCTTTTTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:29:0:33.5:0:1:0:27:2:0.5:0:6 1/0:7:5:3,2:0,0:0,5:0.7143:0,2:28.8:1:31:1:1:0:28.8:10:0.7143:0:6 +2 92317402 . T C 71 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=3.87298;LSEQ=ATAGAGCAGGTTTGAAACAC;RSEQ=CTTTTTGTAGTATCTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:19:0:33:0:1:0:27:2:0.5:0:6 1/1:6:5:3,2:1,0:1,5:0.8333:0,2:18.8:1:30.8:1:1:0:28.8:10:0.8333:0:6 +2 92317404 . T C 77 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AGAGCAGGTTTGAAACACTC;RSEQ=TTTTGTAGTATCTGGATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:17:0:34:0:1:0:27:2:0.5:0:5 1/1:6:6:4,2:0,0:0,6:1:0,2:16.5:1:30:1:1:0:29:12:1:0:5.8 +2 92317751 . G T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTTGAAACACTCTTTTT;RSEQ=TAGTATATGGAAGTGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:31.5:1:1:0:27.5:4:1:0:1 +2 92320445 . T C 88 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTGAACATTCCCTTTCA;RSEQ=AGAGCAGGTTTGAAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:31:0:33.3:1:1:0:22.5:8:1:0:1.8 1/1:8:7:5,2:0,1:1,7:0.875:0,2:31:0:31.6:1:0.375:0:23.6:14:0.875:0:1.6 +2 92322002 . GTG CCT 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTTTGAAACACTCTTTTT;RSEQ=GAATCTGCAAGTGGATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:29.7:1:1:0:42:4:1:0.5:2.5 +2 92322014 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTTTTGTGGAATCTGCA;RSEQ=GTGGATATTTGTCTAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:31.5:1:1:0:42:4:1:0:2.5 +2 92322030 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAGTGGATATTTGTCTA;RSEQ=GTTTGAGGATTTCGTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:33.5:1:1:0:42:4:1:0:2.5 +2 92324216 . C G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACTCTTTTTGTAGTTT;RSEQ=TGGAAGTGGACATTTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:33:0:1:0:28:4:1:0:1 +2 95490959 . T TTGC 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.12137;SOR=Inf;LSEQ=GGTTGTTGCTGCTGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:28,33:61,0:0:2,0:29:1:30.6:1:1:0:48.4:122:1:0:0.3 0/1:68:4:2,2:34,30:64,4:0.0588:2,2:26.5:1:31.5:1:1:1.13124:48.3:8:0.0588:0:0.3 +2 95490970 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.03071;SOR=0.32772;LSEQ=CTGCTGTTGTTGCTGCTGCT;RSEQ=CTGCTGTTGTTGTTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:14:7,7:20,27:47,14:0.2295:2,2:31.8:1:29.8:1:0.76127:1.34:53:28:0.2295:0:1.1 0/1:68:6:3,3:33,29:62,6:0.0882:2,2:14.3:1:28.8:1:1:1.13576:37:12:0.0882:0:1.3 +2 95490974 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.49804;SOR=Inf;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGTTGTTGTTGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:26,31:57,0:0:2,0:27.6:1:33.2:1:1:0:49.6:114:1:0:0.3 0/1:65:2:1,1:33,30:63,2:0.0308:2,2:18:1:28.5:1:1:1.09839:36:4:0.0308:0:1 +2 95849653 . T C 79 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGATTACAGACGTAAG;RSEQ=CACCGTGCCCGGCCTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:30:1:30.7:1:1:0:45.8:12:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 96028398 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=GCTCCTATGAGAATTTAATG;RSEQ=CGCTGCTCATCTGACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:9,0:0:2,0:25.4:1:33.6:1:1:0:60:18:1:0:0 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:24.5:1:26.5:1:1:1.4491:60:4:0.1667:0:1 +2 96918481 . C A 30 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGTTCCTAAACTGAGGC;RSEQ=AGGTTCCATCTCAGTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:7.5:1:30.5:1:1:0:60:4:0.6667:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:29:0:1:0:60:2:1:0:0 +2 96919642 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.15457;LSEQ=ATCTCTGAGAGCAGCTCCAG;RSEQ=GCCTGCTCCTCTTCCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1023:76:39,37:456,489:945,76:0.0743:2,2:24.2:1:30.3:1:0.63458:1.13:60:75:0.0746:0:1.1 0/1:778:284:131,153:240,253:493,284:0.365:2,2:23.5:1:29:1:0.50293:1.10778:60:46.333:0.3629:0:1.1 +2 96919780 . ATGC A 109 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.11484;SOR=2.16382;LSEQ=TGGGATCCATGGTACTTCTT;RSEQ=TGCTGCTGCTGGGCCAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:816:7:3,4:350,458:808,7:0.0086:2,2:26.6:1:32.3:1:1:1.0189:60:14:0.0088:0.0012:0.3 0/1:707:13:5,8:317,377:694,13:0.0184:2,2:31.5:1:29.7:1:0.78049:1.3448:60:26:0.0185:0:0.2 +2 96920501 . C T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5841;SOR=2.56823;LSEQ=AGAGAAACCAGAGCCCCCAC;RSEQ=GGCAACTCAGACAGGATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:154,34:188,1:0.0053:2,0:1:0:22:0:0.18519:0:60:2:0.0053:0:2 0/1:148:2:1,1:112,34:146,2:0.0135:2,2:7:1:27.5:1:0.41828:3.26116:60:4:0.0135:0:1 +2 96920728 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01707;SOR=Inf;LSEQ=AGCACTGTCTGGGGATTCAT;RSEQ=CAGAAATCTGTAGAGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:0:0,0:238,373:611,0:0:2,0:26.1:1:32.3:1:1:0:60:100.833:1:0:0.1 0/1:488:5:3,2:183,300:483,5:0.0102:2,2:18:1:25.6:1:0.37421:2.45:60:10:0.0103:0:1 +2 96920793 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15153;SOR=Inf;LSEQ=ACACTTGGTGCAGGAAGTCC;RSEQ=CACCTAGAAGGAGTTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:33,189:222,0:0:2,0:22.3:1:31.3:1:1:0:60:54.5:1:0:0.1 0/1:142:2:1,1:23,116:139,2:0.0141:2,2:39.5:1:30.5:1:0.31246:4.96:60:4:0.0145:0:1.5 +2 96920893 . T G 61 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07555;SOR=5.04481;LSEQ=CTCCTGGGTGGTCTGCAGGG;RSEQ=AGCTGGAGCAAATTCCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:1,33:34,2:0.0556:1,0:20:1:34:0:1:0:60:4:0.0571:0:1 0/1:17:4:0,4:1,12:13,4:0.2353:1,0:19.3:1:30.5:1:1:0:60:8:0.2353:0:1 +2 96924666 . A C 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=CCAGGCAGTTGGAGTAAGAA;RSEQ=AGTAATATGTGCAGGCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:33,235:268,0:0:2,0:24.1:1:30.9:1:1:0:60:43.667:1:0:0.1 0/1:175:9:0,9:26,140:166,9:0.0514:2,0:29.7:1:30.9:1:0.35924:0:60:8:0.0465:0:1.1 +2 96927965 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02795;SOR=3.41691;LSEQ=TGAGATGGCGCCGCTGCACT;RSEQ=CAGCCTGGGTGACAGAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:8,0:38,0:38,8:0.1739:1,0:19.1:1:31.9:1:1:0:54.9:16:0.1739:0:2.1 0/1:26:11:11,0:15,0:15,11:0.4231:1,0:22.4:1:30.1:1:1:0:45.4:22:0.4231:0:1.8 +2 96928042 . C T 43 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0082;LSEQ=CTATATGCACCACATCTGTG;RSEQ=TTGACAGCTCTGCTCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:7:7,0:281,36:317,7:0.0215:2,0:42.6:1:15.4:1:1:0:53.3:0.4:0.0077:0:5.1 0/1:231:5:3,2:195,31:226,5:0.0216:2,2:21:1:20.2:1:0.15008:4.1546:53.8:1.5:0.0155:0:3 +2 96931025 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05955;SOR=Inf;LSEQ=GGGCGCCAGGCAGGGCCGAG;RSEQ=CCAGGCTACGCTCCGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:84,312:396,0:0:2,0:25.7:1:32.3:1:1:0:60:65:0.9949:0:0.1 0/1:256:3:1,2:65,188:253,3:0.0117:2,2:13.3:1:27.7:1:1:1.44:58.7:6:0.0118:0:1.3 +2 96931044 . G A 46 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26782;SOR=2.32004;LSEQ=GGCCAGGCTACGCTCCGGCT;RSEQ=CTTGGGCAGAGCGCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:2,1:50,222:272,3:0.0109:2,2:15.3:1:27.3:1:0.0927:8.78:60:6:0.011:0:1.3 0/1:160:4:3,1:36,120:156,4:0.025:2,2:8.3:1:23:1:0.04518:9.82:59.5:3:0.0189:0:1.5 +2 96931061 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55677;SOR=3.48069;LSEQ=GCTGCTTGGGCAGAGCGCTG;RSEQ=CTCCCGGGCTCCTCCGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:1:0,1:29,165:194,1:0.0051:2,0:1:0:26:0:1:0:60:2:0.0052:0:1 0/1:113:2:1,1:25,86:111,2:0.0177:2,2:44.5:1:28:1:0.40882:3.39:60:4:0.0179:0:2 +2 96931077 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13724;SOR=Inf;LSEQ=GCTGCCTCCCGGGCTCCTCC;RSEQ=CCGGCGCCCGCCGGGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:16,97:113,0:0:2,0:18.3:1:32.7:1:1:0:60:112:1:0:0.2 0/1:67:2:1,1:17,48:65,2:0.0299:2,2:9:0:31.5:1:0.46811:2.77:60:4:0.0299:0:1.5 +2 96931591 . G T 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAGACCCTCCCCACGCC;RSEQ=CCCACTGTTCCTCACCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:3,2:0.4:0,2:10.5:1:30.5:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 97569926 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5013;SOR=Inf;LSEQ=AGAGGCACTAGAAGGTTTGC;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:24,0:0:2,0:29.5:1:29.8:1:1:0:60:23:1:0:0 0/1:32:2:1,1:17,12:29,2:0.0625:2,2:38.5:1:29.5:1:1:1.40053:60:4:0.0645:0:1 +2 98354139 . G T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=1.56622;LSEQ=CTACTACACTGTAAGCCTCT;RSEQ=CCCCTGTGATGCCCGACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:14,2:16,2:0.1111:2,0:28:1:30:1:1:0:60:4:0.1176:0:1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:6:0:30:0:1:0:60:2:0.1667:0:1 +2 98354171 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGACTGGATGGGCTGGGT;RSEQ=GGTAGAGGGTCCCTGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:27,2:29,2:0.0645:2,0:17:1:29.5:1:1:0:60:4:0.0667:0:1.5 0/0:14:0:0,0:14,0:14,0:0:1,0:23.4:1:30.7:1:1:0:60:13:1:0:0.1 +2 98354224 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22505;SOR=Inf;LSEQ=ATCTCCCCCTCCCCAGGCCC;RSEQ=CTCAGCAGGGAAGTGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:53,24:77,0:0:2,0:23.5:1:30.7:1:1:0:60:154:1:0:0.1 0/1:70:2:1,1:44,24:68,2:0.0286:2,2:20.5:1:28.5:1:1:1.81649:60:4:0.029:0:1 +2 98354290 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09959;SOR=Inf;LSEQ=CAACTTCCGCAAGTTCTCCA;RSEQ=CCGCAGCGATGTCTGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:43,60:103,0:0:2,0:26.1:1:31.6:1:1:0:60:24.75:1:0:0.1 0/1:90:3:1,2:36,50:86,3:0.0333:2,2:15.3:1:25.7:1:1:1.43433:60:2:0.0235:0:3 +2 99117251 . T G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19476;SOR=Inf;LSEQ=TGAGGAGGGGAGGTTTTTGC;RSEQ=AAACTGGCTCAGCAGGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:34,16:50,0:0:2,0:26.2:1:30.8:1:1:0:59.7:100:1:0:0.1 0/1:40:2:1,1:24,14:38,2:0.05:2,2:23:1:29:1:1:1.69023:60:4:0.05:0:1 +2 99117310 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22125;SOR=0;LSEQ=TACAAAGAAGTGCACAGATG;RSEQ=GCCTAGAAGGTTCAGGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:30,36:66,2:0.0294:2,2:41:1:30:1:1:1.20:60:4:0.0294:0:1 0/0:76:0:0,0:36,40:76,0:0:2,0:26.7:1:29.8:1:1:0:55.9:37:1:0:0.1 +2 99117369 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1908;SOR=Inf;LSEQ=GCAGAAAATCTTTGTTACTG;RSEQ=CACTGGTGGAATGGCTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:6,23:29,0:0:2,0:22.1:1:31.7:1:1:0:60:58:1:0:0 0/1:23:2:1,1:3,18:21,2:0.087:2,2:15.5:1:27:1:0.32411:5.34:60:4:0.087:0:1 +2 99117526 . T C 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCCTATAATCCCAGCAC;RSEQ=GGGATATTTTTGGGAGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31:1:27.5:1:1:0:49.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 99136704 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15893;SOR=Inf;LSEQ=GCAGTGCTGGCAGGTACCCA;RSEQ=TGATTCCCCATGACTACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:8,127:135,0:0:2,0:23.1:1:31.1:1:1:0:59.7:44:1:0:0.1 0/1:90:2:1,1:2,86:88,2:0.0222:1,2:22.5:1:31.5:1:0.06592:35.31:60:4:0.0225:0:1 +2 99137272 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24153;SOR=Inf;LSEQ=AAAAACACTACCACCAGTGC;RSEQ=TGGGCTTGTCTCAGAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:7,127:134,0:0:2,0:24.1:1:31.5:1:1:0:59.7:66:1:0:0 0/1:130:2:0,2:7,121:128,2:0.0154:2,0:37.5:1:33:1:1:0:60:4:0.0155:0:1 +2 99149946 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.65774;LSEQ=TGGACGAAGCATGCACAGAC;RSEQ=GAGATCATTGAGGTGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:645:55:27,28:260,330:590,55:0.0853:2,2:23.5:1:30.8:1:0.48176:1.22:60:54:0.0846:0:1.2 0/1:750:149:65,84:252,346:598,149:0.1987:2,2:26.1:1:30.1:1:0.7813:1.06:60:298:0.1995:0:1.2 +2 99150118 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54764;SOR=0;LSEQ=TACATTGATATTTTTCATCA;RSEQ=ATTTACTCATCTGGGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:0,3:2,41:43,3:0.0652:1,0:19.7:1:28.7:1:1:0:60:6:0.0667:0:1 0/0:20:0:0,0:1,19:20,0:0:1,0:20.7:1:31.4:1:1:0:60:40:1:0:0.1 +2 99152383 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14501;SOR=Inf;LSEQ=AATCGTTTGAATGAGAGATG;RSEQ=ACACAGATTGACTTCACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:57,243:300,0:0:2,0:23.3:1:31.2:1:1:0:59.8:74:1:0:0.1 0/1:185:2:1,1:32,151:183,2:0.0108:2,2:25.5:1:26.5:1:0.32573:4.66:60:4:0.0109:0:1 +2 99152770 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06532;SOR=Inf;LSEQ=TATACTGAGAGAGCACCCTT;RSEQ=CCTTCCCAGAAGCCAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:12,206:218,0:0:2,0:24.6:1:31.6:1:1:0:59.9:71.667:1:0:0.1 0/1:148:3:1,2:6,139:145,3:0.0203:1,2:30.3:1:24.3:1:0.13617:11.07:60:2:0.0138:0:1.7 +2 99154229 . C T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11581;SOR=1.88245;LSEQ=CAGCTCGGCCCTGCTGCCCC;RSEQ=AGGACCCTGATGACCCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:15:12,3:94,6:100,15:0.1304:2,2:23.3:1:32.3:1:0.09354:3.84923:60:30:0.1304:0:1.1 0/1:77:17:16,1:58,2:60,17:0.2208:1,1:23.6:1:31.2:1:0.53219:1.79646:60:34:0.2208:0:1 +2 99154610 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACCTTGAAGCAGGAAAA;RSEQ=GGGCTCCTGCCTGTAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:0,2:0,47:47,2:0.0408:1,0:29:1:33:0:1:0:60:4:0.0408:0:1.5 0/0:19:0:0,0:0,19:19,0:0:1,0:29.5:1:31.1:1:1:0:60:38:1:0:0.4 +2 99155520 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16021;SOR=Inf;LSEQ=CCGCAGTCCCCTTTGCTCCC;RSEQ=ACCTGCTGCGATTGTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:25,199:224,0:0:2,0:21.5:1:32.3:1:1:0:59.9:55:1:0:0.1 0/1:150:2:1,1:19,129:148,2:0.0133:2,2:32.5:1:27:1:0.24966:6.64:60:4:0.0134:0:1 +2 99155881 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14203;SOR=Inf;LSEQ=TAATTCCCATGAGATGAACA;RSEQ=TGAGAGGACTTGAGGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:221,8:229,0:0:1,0:23.4:1:33.5:1:1:0:60:75.333:1:0:0.1 0/1:139:2:2,0:133,4:137,2:0.0144:1,0:14:1:30.5:1:1:0:60:4:0.0147:0:1 +2 99155895 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16222;SOR=Inf;LSEQ=TGAACAGTGAGAGGACTTGA;RSEQ=GTGTCACCATCCCTGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:260,21:281,0:0:2,0:25.4:1:33.2:1:1:0:60:92.667:1:0:0.1 0/1:190:2:1,1:168,20:188,2:0.0105:2,2:13:1:29:1:0.20936:8.2211:60:4:0.0109:0:1 +2 99156212 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15021;SOR=Inf;LSEQ=TCCTTTCTGAGATATAGCGG;RSEQ=CAGAGCACTGGCATCAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:16,127:143,0:0:2,0:21.9:1:32.1:1:1:0:60:34.75:1:0:0.1 0/1:91:2:1,1:12,77:89,2:0.022:2,2:27:1:26.5:1:0.26667:6.21:60:4:0.0222:0:1 +2 99160361 . G C 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGTGTGAGCTGGAGGAGCT;RSEQ=GGAGAGCTGTCCCCTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:55:34,21:485,361:846,55:0.061:2,2:25.7:1:30.9:1:0.57452:1.20:60:54:0.0609:0:1.2 0/0:785:0:0,0:440,339:779,0:0:2,0:24.8:1:30.7:1:1:0:60:40:0.9922:0:0.2 +2 99160528 . T A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17512;SOR=5.12438;LSEQ=GCACACACACACACACACAC;RSEQ=CTCACTCTCACTCAGTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:1:0,1:47,249:296,1:0.0033:2,0:14:0:32:0:1:0:60:2:0.0035:0:2 0/1:236:4:1,3:38,194:232,4:0.0169:2,2:10.5:1:24.8:1:0.51693:1.70:60:3:0.0133:0:1.5 +2 99162384 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07833;SOR=Inf;LSEQ=TCTACTTGCAACTCGTGAAT;RSEQ=CAGCATGTATGCTGATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:269,84:353,0:0:2,0:23.6:1:32.2:1:1:0:60:69.6:1:0:0.1 0/1:265:3:2,1:189,71:260,3:0.0113:2,2:30:1:22.3:1:1:1.32945:60:2:0.0076:0:1.7 +2 99162585 . C A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08299;SOR=Inf;LSEQ=AATCACATTTCGCTGCTTTT;RSEQ=TCTGTGGGTACTTGGTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:95,254:349,0:0:2,0:23:1:32.6:1:1:0:60:48.857:1:0:0.1 0/1:271:3:2,1:80,187:267,3:0.0111:2,2:5.3:1:26:1:0.21975:4.64:60:6:0.0112:0:1 +2 99163213 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07959;SOR=Inf;LSEQ=GCTTTCTGATGCTTCTTTTC;RSEQ=CAGTTTAAAATAAAATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:33,224:257,0:0:2,0:20.9:1:30.1:1:1:0:60:41.833:1:0:0.1 0/1:195:3:1,2:35,157:192,3:0.0154:2,2:17.7:1:29.7:1:0.45979:2.23:60:6:0.0157:0:1 +2 99163261 . T A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.08711;SOR=3.19955;LSEQ=CGCAAAAACACCCAGCCATC;RSEQ=GATCTGCTTTTGCGTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:4:0,4:1,83:84,4:0.0455:1,0:27.5:1:32:1:1:0:60:8:0.0455:0:1 0/1:45:6:0,6:1,38:39,6:0.1333:1,0:19.7:1:31:1:1:0:60:12:0.1333:0:1 +2 99165588 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54356;SOR=0;LSEQ=ACAGTCCTCCCTTCCAACTG;RSEQ=AATGTTCTTTAATAATGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:0,81:81,2:0.0241:1,2:21.5:1:29.5:1:0.0241:0:60:4:0.0241:0:1 0/0:44:0:0,0:1,43:44,0:0:1,0:22.7:1:31.5:1:1:0:60:21:1:0:0.1 +2 99168953 . T C 115 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACGATCATTTGGGTGATTA;RSEQ=GGGATATGATTGTTCAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:22.6:1:33.4:1:1:0:60:22:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 99170727 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03802;SOR=1.67558;LSEQ=GCAGCCTTGGTTTGTGTGCA;RSEQ=CTGCAGACACGGCAGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:34:25,9:281,114:395,34:0.0793:2,2:25.1:1:30.8:1:0.84564:1.13:60:68:0.081:0:1.1 0/1:333:42:29,13:201,90:291,42:0.1261:2,2:25.8:1:30:1:1:1.00115:60:84:0.1292:0:1.1 +2 99171929 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54835;SOR=0;LSEQ=AGTGTGGAAGCCTAGGGCAG;RSEQ=GGATCAGTGGAGGGCGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:141,17:158,2:0.0125:2,2:34.5:1:30:1:0.21297:8.08842:60:4:0.0131:0:1 0/0:83:0:0,0:71,12:83,0:0:2,0:25.7:1:30.2:1:1:0:60:26.667:1:0:0.2 +2 99171949 . T C 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56184;SOR=3.20099;LSEQ=GGGATCAGTGGAGGGCGATT;RSEQ=GGTTTGTGTTATGTTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:187,41:228,1:0.0044:2,0:32:0:15:0:1:0:60:0:0:0:5 0/1:144:2:1,1:105,37:142,2:0.0139:2,2:23.5:1:25:1:0.4595:2.81355:60:4:0.0144:0:1 +2 99171957 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16363;SOR=Inf;LSEQ=TGGAGGGCGATTTGGTTTGT;RSEQ=TTATGTTTGTGTTTCTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:202,49:251,0:0:2,0:25.8:1:32.3:1:1:0:60:61.75:1:0:0.2 0/1:171:2:1,1:125,44:169,2:0.0117:2,2:24.5:1:27.5:1:0.4582:2.82038:60:4:0.0118:0:1 +2 99171963 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17295;SOR=Inf;LSEQ=GCGATTTGGTTTGTGTTATG;RSEQ=TTGTGTTTCTGTTCGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:210,66:276,0:0:2,0:25.8:1:30:1:1:0:60:552:1:0:0.1 0/1:197:2:1,1:142,53:195,2:0.0102:2,2:24.5:1:29.5:1:0.4741:2.66365:60:4:0.0105:0:1 +2 99172243 . C T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.45529;LSEQ=TGCCCCTCCACCATGCCCTC;RSEQ=ACTGCATGCCATCCTCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1318:183:71,112:481,654:1135,183:0.1388:2,2:24.5:1:29.7:1:0.37554:1.16005:59.9:366:0.141:0:1.2 0/1:1214:83:34,49:511,618:1129,83:0.0684:2,2:23.4:1:28.1:1:0.49352:1.19148:60:82:0.0684:0:1.1 +2 99172244 . A G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.25484;LSEQ=GCCCCTCCACCATGCCCTCC;RSEQ=CTGCATGCCATCCTCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1304:88:31,57:515,699:1214,88:0.0675:2,2:28.9:1:30.6:1:0.21848:1.35439:60:16.6:0.0656:0:1.1 0/1:1206:230:105,125:437,535:972,230:0.1907:2,2:26.8:1:29.8:1:0.88291:1.03:59.7:31.857:0.1904:0:1.1 +2 99172299 . G A 62 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.80452;LSEQ=TGCATCCATGCTTCCCATAT;RSEQ=CTGCCTCCATTTCACCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:596:6:4,2:136,454:590,6:0.0101:2,2:16:1:24.2:1:0.02949:6.65:60:5:0.0086:0:1.5 0/0:493:4:4,0:124,365:489,4:0.0081:2,0:13.3:1:23:1:0.00439:0:60:8:0.0083:0:1.8 +2 99172368 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATGCCCTCCTCCCCCAT;RSEQ=CAGACTGCAGGGAGGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:0,2:2,145:147,2:0.0134:1,0:12:1:26:0:1:0:60:4:0.0139:0:1 0/0:70:0:0,0:2,68:70,0:0:1,0:24.2:1:32.2:1:1:0:60:140:1:0:0.1 +2 99175795 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18884;SOR=Inf;LSEQ=GGAAGAGGCAGCCAGGCACC;RSEQ=AGACCTCTTTTCTGTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:156,6:162,0:0:1,0:22.3:1:31.6:1:1:0:60:161:1:0:0.1 0/1:125:2:1,1:117,6:123,2:0.016:1,2:48.5:1:30.5:1:0.10929:18.12619:60:4:0.016:0:1.5 +2 99179756 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=8;SSF=0.29248;SOR=3.6645;LSEQ=GCTGGAAAGAGCTGGGGCTA;RSEQ=AGGGCTAGAGGGCTAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:1:1,0:62,3:65,1:0.0152:1,0:13:0:33:0:1:0:60:2:0.0154:0:1 0/1:37:2:1,1:33,2:35,2:0.0541:2,2:24:1:27.5:1:0.15766:13.6748:60:4:0.0541:0:1 +2 99179971 . C G 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGCTGCTGACCACTCTCAC;RSEQ=GACTGCGTGGCCATGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1145:0:0,0:593,550:1143,0:0:2,0:25.4:1:30.5:1:1:0:59.9:80.643:0.9982:0:0.1 0/1:1040:45:21,24:494,499:993,45:0.0433:2,2:21.2:1:29.5:1:0.7612:1.13127:60:44:0.0428:0:1.1 +2 99180947 . GC G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCCATGGCCAGGGCAT;RSEQ=CCCACCTGGGCTTCTCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:61,4:65,2:0.0299:2,2:21:1:31:1:0.14473:13.75137:60:4:0.0308:0:0 0/0:26:0:0,0:26,0:26,0:0:1,0:23.5:1:32:1:1:0:60:52:1:0:0.2 +2 99181315 . AT A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04192;SOR=2.74442;LSEQ=CTTTTCTCACTATACCAGTA;RSEQ=GCGTGCTTATTGAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:8:0,8:2,101:103,8:0.0721:1,0:15.5:1:30.7:1:1:0:60:16:0.0748:0.027:0.3 0/1:85:15:0,15:2,68:70,15:0.1765:1,1:10.7:1:30.6:1:1:0:60:30:0.1807:0.0941:0.2 +2 99182040 . G T 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51847;SOR=0;LSEQ=CCTGGGCTTGGCTGCCTTCT;RSEQ=CTGAGACTGGGGAGAGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:167,20:187,2:0.0106:2,0:7.5:1:32:1:1:0:60:4:0.0107:0:1 0/0:126:0:0,0:102,24:126,0:0:2,0:23.6:1:31:1:1:0:60:62:1:0:0.1 +2 99182079 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03081;SOR=Inf;LSEQ=GCAGGGCCCTCTGCCTGACA;RSEQ=CCCTGCCCCTCTCTCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:310,102:412,0:0:2,0:24.1:1:32.9:1:1:0:60:57.857:0.9951:0:0.1 0/1:300:4:2,2:200,95:295,4:0.0133:2,2:20.3:1:29.5:1:0.59777:2.09959:60:8:0.0137:0:1.5 +2 99182085 . C T 53 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01449;SOR=Inf;LSEQ=CCCTCTGCCTGACAGCCCTG;RSEQ=CCCTCTCTCATGTCCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:324,125:449,0:0:2,0:25:1:31.9:1:1:0:60:48.889:1:0:0.1 0/1:339:5:2,3:218,116:334,5:0.0147:2,2:12.6:1:23:1:0.34866:2.80973:60:1.5:0.0091:0:1.8 +2 99182258 . C A 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22971;SOR=0.24012;LSEQ=TTGGTTTAAAATTCTCTGAG;RSEQ=CAGAGAGCGGTTTTCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:493:5:3,2:149,338:487,5:0.0101:2,2:16.2:1:27:1:0.17404:3.39:60:4:0.0082:0:2 0/0:408:1:1,0:132,275:407,1:0.0025:2,0:1:0:22:0:0.32598:0:60:2:0.0025:0:1 +2 99182393 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17954;SOR=Inf;LSEQ=TTAAAGGTCTGTGGTTGGCA;RSEQ=TTTGGCCATCACTAAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:185,35:220,0:0:2,0:25.1:1:33.2:1:1:0:60:109:0.9954:0:0.1 0/1:163:2:1,1:142,17:159,2:0.0123:2,2:22:1:29:1:0.21172:8.14547:60:4:0.0124:0:1 +2 99184905 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGCTCGGAAGAGGGAGA;RSEQ=TGGCTTAGAATTTAGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:2,0:107,1:108,2:0.0182:1,0:16:1:31.5:1:1:0:60:4:0.0183:0:1 0/0:48:0:0,0:48,0:48,0:0:1,0:18.7:1:32.3:1:1:0:60:96:1:0:0 +2 99185227 . G A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.27798;SOR=0;LSEQ=CCCTGCCTCTGTGAGTGCAT;RSEQ=CCTGTGCATGTGTGTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:2,1:3,173:176,3:0.0168:1,2:12.3:1:25:1:0.00186:96.71:60:6:0.0168:0:1 0/0:119:0:0,0:4,115:119,0:0:1,0:22.8:1:31.9:1:1:0:60:118:1:0:0.1 +2 99185276 . CAG C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.69992;SOR=1.37568;LSEQ=TCTCCCTAAACACACACACG;RSEQ=AGAGAGAGAGAGAAGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:5:0,5:0,68:68,5:0.0676:1,0:36.4:1:33.4:1:1:0:60:10:0.0685:0:0 0/1:33:3:0,3:0,30:30,3:0.0909:1,0:17.7:1:30.5:1:1:0:60:6:0.0909:0.0606:0 +2 99185423 . C G 83 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCATGCATTGTGCACCT;RSEQ=CTGGTAGGACTTGGGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:24:1:32.2:1:1:0:60:12:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 99189424 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03163;SOR=Inf;LSEQ=AGAGGAAAAGGAGGCTATTG;RSEQ=GGTGCCCACAGCTGAACGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:112,273:385,0:0:2,0:24.6:1:30.4:1:1:0:60:95.25:0.9974:0:0.1 0/1:283:4:1,3:94,185:279,4:0.0141:2,2:37:1:30.8:1:1:1.52223:60:8:0.0144:0:1.3 +2 99193007 . A G 84 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTACCTTCCAGGGAGACCT;RSEQ=GAGACCTGGCCCAGGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1:0,2:26.8:1:32.7:1:1:0:54.2:12:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 99193496 . C T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.38395;LSEQ=CGGTTCACCAGCTGCAAGAG;RSEQ=GCTAAGGACCGTACAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1323:99:48,51:586,636:1222,99:0.0748:2,2:25.9:1:29.8:1:0.91721:1.02:60:48.5:0.0751:0:1.2 0/1:1149:247:120,127:432,467:899,247:0.215:2,2:23.5:1:29.1:1:0.88595:1.02:59.8:122.5:0.2174:0:1.1 +2 99193650 . G A 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65186;SOR=0.37687;LSEQ=CGCCCCGCCTGCCCCGGCCC;RSEQ=TGTAAACTGCAGATGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:4:2,2:29,171:200,4:0.0196:2,2:19:1:25.3:1:0.1103:5.82:60:3:0.0149:0:1.5 0/0:134:1:0,1:13,120:133,1:0.0075:2,0:8:0:31:0:1:0:60:2:0.0075:0:1 +2 99197896 . AT A 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.49417;LSEQ=TTCTATTGTGACTTCATTTC;RSEQ=TTTTTTTTAACCTTATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:3:3,0:51,2:53,3:0.0536:1,0:20:1:32.7:1:1:0:60:6:0.0545:0:0 0/1:37:1:1,0:34,2:36,1:0.027:2,0:47:0:31:0:1:0:60:2:0.027:0:0 +2 99197971 . T C 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=7.000;MSILEN=1;SSF=0.08259;SOR=Inf;LSEQ=AATCCATCGCATGTGTCTTC;RSEQ=TTTTTTCTTTATTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:229,16:245,0:0:2,0:24.4:1:32.5:1:1:0:59.9:490:1:0:0.1 0/1:190:3:3,0:171,16:187,3:0.0158:2,0:10:1:27.3:1:1:0:60:6:0.0158:0:1 +2 99203871 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21527;SOR=0;LSEQ=AAAATGATCAGTTCATTTCA;RSEQ=CTTAGTTTAAGTCTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:160,22:182,2:0.0109:2,2:29.5:1:31.5:1:0.23497:7.13472:60:4:0.0111:0:1 0/0:212:0:0,0:179,33:212,0:0:2,0:23:1:30:1:1:0:60:105:1:0:0.1 +2 99204138 . T C 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27192;SOR=0;LSEQ=CCTCTAGTGTCATATATGAA;RSEQ=TCTTCAAGAAGACCTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:1,2:14,153:167,3:0.0176:2,2:24.7:1:27:1:0.24334:5.36:60:2:0.0123:0:2 0/0:118:0:0,0:12,105:117,0:0:2,0:23.2:1:29.3:1:1:0:60:18.5:0.9911:0:0.1 +2 99373720 . T C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42518;LSEQ=GATTTCTGTTGACTTACCCC;RSEQ=CACTTCCCCCTATCTTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:768:576:308,268:104,87:191,576:0.75:2,2:26.4:1:31.2:1:0.86707:1.04012:60:114.2:0.7523:0:1.1 1/0:869:487:237,250:195,185:380,487:0.5604:2,2:26.7:1:30:1:0.45202:1.11173:59.9:47.7:0.5585:0:1.1 +2 100441349 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00425;SOR=0.11081;LSEQ=CCAATGAAATAATGGCTCAT;RSEQ=TTCAAAAAACAGTTAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:3,16:0,2:2,19:0.9048:0,2:21.9:1:31.4:1:1:0:60:38:0.9048:0:1 1/0:24:12:3,9:3,9:12,12:0.5:2,2:21.3:1:28.4:1:1:1:60:24:0.5:0:1 +2 100515319 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50879;SOR=Inf;LSEQ=TGCCTGGGGCTCTCTCGCTT;RSEQ=GGCCAACGCTGACTCCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:46,52:98,0:0:2,0:27.5:1:29.9:1:1:0:60:48:1:0:0.1 0/1:132:2:1,1:68,62:130,2:0.0152:2,2:34:1:29:1:1:1.096:60:4:0.0152:0:1 +2 100515321 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1842;SOR=0;LSEQ=CCTGGGGCTCTCTCGCTTTG;RSEQ=CCAACGCTGACTCCCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:44,53:97,2:0.0202:2,2:35:0:31:1:1:1.20:60:4:0.0211:0:1.5 0/0:131:0:0,0:68,63:131,0:0:2,0:26.6:1:30.4:1:1:0:60:42.667:1:0:0.3 +2 100515343 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50145;SOR=Inf;LSEQ=CAACGCTGACTCCCACTTTG;RSEQ=CCTGCCCTCACAGGGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:35,57:92,0:0:2,0:26.3:1:30.8:1:1:0:60:45:1:0:0.1 0/1:111:2:2,0:47,62:109,2:0.018:2,0:17.5:1:27.5:1:0.19263:0:60:4:0.0183:0:1 +2 100515353 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TCCCACTTTGCCCTGCCCTC;RSEQ=CAGGGCCTGTCCTGCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:26,52:78,0:0:2,0:27.8:1:29.5:1:1:0:60:77:1:0:0.1 0/1:101:2:1,1:38,61:99,2:0.0198:2,2:44:0:31.5:1:1:1.60:60:4:0.02:0:1.5 +2 100801091 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18704;SOR=Inf;LSEQ=TTCGTGAATCAAGAGAAATT;RSEQ=TGTCACAGGTCCAAATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:114,31:145,0:0:2,0:26.4:1:32.1:1:1:0:60:35.25:1:0:0.1 0/1:111:2:1,1:78,31:109,2:0.018:2,2:19.5:1:31.5:1:0.49533:2.49234:60:4:0.0185:0:1 +2 100801198 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32651;LSEQ=CTTTCATGGACTCTTCTCAA;RSEQ=TCTGCTTTGAACTGGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:289:195:91,104:47,46:93,195:0.6747:2,2:25.7:1:32.6:1:0.61406:1.16707:60:96.5:0.6772:0:1.1 0/1:300:121:62,59:87,91:178,121:0.4033:2,2:25.8:1:30.9:1:0.72446:1.10:60:29.25:0.3993:0:1.2 +2 101852256 . T C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=0;LSEQ=CTAACCAGTAAGGGATAGTA;RSEQ=GAGATGCTGCCCAGAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:0,9:1:0,2:27.8:1:32.3:1:1:0:38.3:18:1:0:1 1/1:13:11:8,3:1,1:2,11:0.8462:2,2:21.3:1:30.7:1:1:2.45:34.5:22:0.8462:0:1 +2 101992072 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14936;SOR=0;LSEQ=GAGGTGGCTGAGTGCCCTCT;RSEQ=TGGCACCCCAGGAGGCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:13,2:0.1333:2,2:25:1:29.5:1:1:1.54914:60:4:0.1333:0:1.5 0/0:23:0:0,0:15,8:23,0:0:2,0:22.3:1:30.8:1:1:0:60:46:1:0:0.9 +2 101992105 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCGAGCTCTGCTTCTCC;RSEQ=AACTCCAGTGGTCAGACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:13,11:0,0:0,24:1:0,2:27.5:1:31.5:1:1:0:59.8:48:1:0:1.5 1/1:39:39:21,18:0,0:0,39:1:0,2:26.8:1:29.6:1:1:0:59.7:78:1:0:1.3 +2 101992167 . C T 81 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.44236;SOR=2.52567;LSEQ=GGGACCACCCTACCCCAGGA;RSEQ=GGGGTGGGGTGCGGCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:7,7:14,2:0.125:2,0:12.5:1:30:1:0.475:0:60:4:0.125:0:2 0/1:26:7:2,5:9,10:19,7:0.2692:2,2:22.4:1:29:1:0.65761:2.18265:60:14:0.2692:0:1.7 +2 101992173 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50166;SOR=Inf;LSEQ=ACCCTACCCCAGGACGGGGT;RSEQ=GGGTGCGGCACATTCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:18,0:0:2,0:21.1:1:30.3:1:1:0:60:17:1:0:0.9 0/1:25:2:1,1:9,14:23,2:0.08:2,2:25.5:1:28:1:1:1.53:60:4:0.08:0:2 +2 101992225 . T C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.66075;LSEQ=CCATTCTGGCTCCAAGGCTG;RSEQ=GTCTCTCCCCTGAACTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:5,6:11,1:0.0833:2,0:41:0:32:0:1:0:60:2:0.0833:0:2 0/1:15:2:2,0:5,8:13,2:0.1333:2,0:40.5:1:32:1:0.2:0:60:4:0.1333:0:1 +2 101992329 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14675;SOR=Inf;LSEQ=CAAGGGCCTATGCTGCGGCT;RSEQ=CACCCCTTCCTCTCCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:21,12:33,0:0:2,0:25.8:1:32.1:1:1:0:60:66:1:0:0 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:16.5:1:26:1:1:1.11:60:4:0.1:0:1 +2 101992383 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24352;SOR=Inf;LSEQ=GACAAGTCGTTACTGACTGT;RSEQ=TTCAAGGGGGTGGATCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:16,22:38,0:0:2,0:26.3:1:32.2:1:1:0:60:76:1:0:0.2 0/1:43:3:2,1:20,20:40,3:0.0698:2,2:35.7:1:30:1:1:1.97:60:6:0.0698:0:1.3 +2 101992421 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49675;SOR=Inf;LSEQ=CAGAAGGCTGTCAAGGCAGG;RSEQ=CTGTCGGCAGTTTCAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:6,19:25,0:0:2,0:20.7:1:31.6:1:1:0:60:50:1:0:0.5 0/1:31:2:1,1:12,17:29,2:0.0645:2,2:28:1:28:1:1:1.40:60:4:0.0645:0:1 +2 101992445 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=TCGGCAGTTTCAGCTTTCAG;RSEQ=TTTGCTGGGCTGTGCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:2,12:14,2:0.125:2,2:21:1:29.5:1:0.35:5.10:60:4:0.125:0:1 0/0:15:0:0,0:4,11:15,0:0:2,0:22.6:1:29.9:1:1:0:60:14:1:0:0.7 +2 101992474 . A G 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47432;LSEQ=GCTGTGCTGTTTCAACTGTC;RSEQ=CGACATGGGCATCTGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:0,2:2,8:0.8:0,0:25.3:1:32.8:1:1:0:60:16:0.8:0:1 1/1:14:12:3,9:1,1:2,12:0.8571:2,2:26.4:1:30.4:1:0.50549:2.73861:60:11:0.8462:0:1.1 +2 102578173 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24194;SOR=Inf;LSEQ=GTGCCATTTGCTGGTGCTGG;RSEQ=CCTTGGTCAAATCCACTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:21,26:47,0:0:2,0:26.3:1:31.7:1:1:0:60:46:1:0:0.2 0/1:47:3:1,2:19,25:44,3:0.0638:2,2:13:1:25.3:1:1:1.50701:60:6:0.0638:0:1.3 +2 106021437 . C T 168 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCGTCGGATACAGTTTCCA;RSEQ=TGTGGCTTTGATACCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:47:33,14:185,111:296,47:0.137:2,2:26.8:1:30.4:1:0.3325:1.41:60:22.5:0.1335:0:1.1 0/0:310:0:0,0:186,124:310,0:0:2,0:24.6:1:31.4:1:1:0:60:61:1:0:0.4 +2 106021465 . ACT A 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TTGATACCTCTTTAAGAAAG;RSEQ=CTGTTTGGTACATTAATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:22:12,10:230,176:406,22:0.0514:2,2:21.7:1:32.3:1:1:1.0888:60:44:0.0518:0.0093:1 0/0:410:0:0,0:231,176:407,0:0:2,0:25.4:1:31.4:1:1:0:60:100.75:0.9975:0:0.6 +2 106021488 . C G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00796;SOR=0.69469;LSEQ=CTGTTTGGTACATTAATGAC;RSEQ=AATAGAATGAAACTATTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:437:275:131,144:90,69:159,275:0.6293:2,2:26.3:1:31.1:1:0.07395:1.43257:60:274:0.6299:0:1.1 1/0:451:244:129,115:108,95:203,244:0.541:2,2:26.5:1:29.7:1:1:1.01344:60:243:0.5424:0:1.1 +2 106021547 . G A 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CCAGTAAATGTTGCTGGATG;RSEQ=TTTCAGATGAAAAGTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:120,219:339,0:0:2,0:25.6:1:31.9:1:1:0:60:168.5:1:0:0.4 0/1:333:13:5,8:127,193:320,13:0.039:2,2:21.8:1:30.1:1:1:1.05269:60:26:0.0395:0:1.2 +2 106021801 . G C 34 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGCTTCCCTAAAATACCT;RSEQ=AAATGGGAGATTCTTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:12.5:1:34:0:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:47:0:16:0:1:0:60:0:0:0:2 +2 106678447 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09693;SOR=Inf;LSEQ=AAAATGAAGCCCTCTCGGCT;RSEQ=TCGAATCTCTCTTACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:37,3:40,0:0:2,0:21.1:1:31.2:1:1:0:59.3:19:1:0:1.3 0/1:35:3:3,0:31,1:32,3:0.0857:1,0:19:1:29:0:1:0:60:6:0.0882:0:2 +2 106678449 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10097;SOR=Inf;LSEQ=AATGAAGCCCTCTCGGCTGT;RSEQ=GAATCTCTCTTACTGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:36,3:39,0:0:2,0:22.2:1:31.2:1:1:0:59.3:38:1:0:1.4 0/1:35:3:3,0:30,2:32,3:0.0857:2,0:21:1:31.7:1:1:0:60:6:0.0857:0:2 +2 106678450 . G A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.64822;SOR=1.24953;LSEQ=ATGAAGCCCTCTCGGCTGTC;RSEQ=AATCTCTCTTACTGCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:24:21,3:16,0:16,24:0.5854:1,2:21.7:1:29.5:1:0.26154:0:60:11:0.5789:0:1.9 1/0:36:23:22,1:11,2:13,23:0.6389:2,1:21.4:1:28.9:1:0.53936:3.84:60:10.5:0.6176:0:1.9 +2 106678497 . T C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26055;SOR=0.68367;LSEQ=AGGCAGAGTCAAGATGGACC;RSEQ=GGCCTTGCTGTGGTTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:47:32,15:22,7:29,47:0.6184:2,2:26.3:1:28.9:1:0.60433:1.46585:60:10.75:0.5972:0:1.5 1/0:80:42:31,11:27,11:38,42:0.525:2,2:26.2:1:29.1:1:0.80702:1.15:60:41:0.519:0:1.5 +2 106678555 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24453;SOR=0;LSEQ=ATCAAAGGCAGCTCCGTCTT;RSEQ=GACCCTGCCCCCTTTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:90,66:156,2:0.0127:2,2:20.5:1:31:1:1:1.3609:60:4:0.013:0:2 0/0:161:0:0,0:85,76:161,0:0:2,0:26:1:28.5:1:1:0:60:79.5:1:0:0.6 +2 106678562 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24777;SOR=0;LSEQ=GCAGCTCCGTCTTAGACCCT;RSEQ=CCCCCTTTCCCCTGTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:94,72:166,2:0.0119:2,2:29:1:31:1:1:1.30345:60:4:0.0123:0:1 0/0:169:0:0,0:83,86:169,0:0:2,0:25.6:1:30.9:1:1:0:59.8:23.143:1:0:0.6 +2 106678595 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50122;SOR=0;LSEQ=TGTGTGCATTCAGCTCACGG;RSEQ=ACGCTCGCAGAGTGATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:93,88:181,2:0.0109:2,2:32.5:1:31:1:1:1.05652:60:4:0.011:0:2 0/0:158:0:0,0:72,86:158,0:0:2,0:27.3:1:31.5:1:1:0:60:316:1:0:0.7 +2 106678604 . A T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25408;SOR=0;LSEQ=TCAGCTCACGGCACGCTCGC;RSEQ=GAGTGATGGCACTTCCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:2,1:96,93:189,3:0.0156:2,2:16.7:1:29.3:1:1:1.93:60:6:0.0161:0:2 0/0:160:0:0,0:69,91:160,0:0:2,0:26.3:1:29.5:1:1:0:60:52.333:1:0:0.8 +2 106678606 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.91195;SOR=0.9622;LSEQ=AGCTCACGGCACGCTCGCAG;RSEQ=GTGATGGCACTTCCTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:191:119:62,57:35,37:72,119:0.623:2,2:24.3:1:30.2:1:0.657:1.15:60:18.833:0.6209:0:1.1 1/0:158:97:43,54:26,35:61,97:0.6139:2,2:25.4:1:29.7:1:0.87022:1.07:60:31.333:0.6184:0:1.2 +2 106678644 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20633;SOR=Inf;LSEQ=AGTCCTCTATCTGCTATTGC;RSEQ=AGGTATCTGTGAATTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:68,96:164,0:0:2,0:27.2:1:31.4:1:1:0:60:40:1:0:0.7 0/1:137:2:1,1:54,81:135,2:0.0146:2,2:27:1:27.5:1:1:1.50:60:4:0.015:0:1.5 +2 106678692 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51072;SOR=0;LSEQ=GGGAGGACCACTGAGGCCCC;RSEQ=GAGTCACGTGGAGGAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:27,66:93,2:0.0211:2,2:18:1:30:1:0.50482:2.42:60:4:0.0211:0:1 0/0:68:0:0,0:19,47:66,0:0:2,0:26.1:1:29.3:1:1:0:60:65:0.9701:0:0.5 +2 106678715 . A G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53778;SOR=0.72216;LSEQ=GTCACGTGGAGGAAGGGAAC;RSEQ=CCATGTCTGGACTGTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:37:12,25:3,19:22,37:0.6271:2,2:18.2:1:31.3:1:0.13309:2.99:60:74:0.6379:0:1.2 1/0:42:23:5,18:7,12:19,23:0.5476:2,2:23.2:1:31.1:1:0.32267:2.06232:60:22:0.5366:0:1.1 +2 106678755 . G A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.13937;SOR=0.27827;LSEQ=GAGAAGGTCAGTCTGACAAT;RSEQ=TGTGACAATGGTATGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:2,14:1,9:10,16:0.6154:2,2:29.9:1:30.9:1:1:1.27:60:15:0.625:0:1.9 0/1:10:3:0,3:0,7:7,3:0.3:0,0:26.7:1:32:0:1:0:60:6:0.3:0:1.7 +2 108622946 . G A 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGTCTCCCAAAGTGCTGG;RSEQ=ATTATAGGTGTGAGCTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1:0,2:17.2:1:30.3:1:1:0:44:12:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 108623227 . G T 44 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08394;SOR=Inf;LSEQ=TGTTCTTTTAAAACCCCTAG;RSEQ=TGAGTTGAGAGCCAGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:217,77:294,0:0:2,0:25.4:1:31.5:1:1:0:60:146:1:0:0.1 0/1:230:3:1,2:159,68:227,3:0.013:2,2:5.7:1:28:1:0.22041:4.64113:60:6:0.0131:0:1.3 +2 108623322 . T G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00536;SOR=1.46371;LSEQ=CACTTTGAACTTGAGATTTC;RSEQ=GCTTTACACCTTTAGTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:478:198:81,117:118,161:279,198:0.4142:2,2:24.6:1:30.8:1:0.77811:1.0585:59.8:396:0.4168:0:1.1 1/0:401:204:91,113:90,107:197,204:0.5087:2,2:27.3:1:30:1:0.8415:1.04438:60:203:0.5088:0:1.1 +2 108623340 . G T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02128;SOR=Inf;LSEQ=TCTGCTTTACACCTTTAGTA;RSEQ=TTTTTAATTAGGGGTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:162,252:414,0:0:2,0:23.9:1:32.6:1:1:0:59.9:137:1:0:0.5 0/1:359:5:2,3:150,203:353,5:0.0139:2,2:14:1:30.4:1:1:1.10809:60:10:0.014:0:1.8 +2 108623538 . T C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54118;SOR=0;LSEQ=AATTTAATTAAATGTATTAA;RSEQ=TACTCCTGACCTTTATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:27:1:33:1:1:0:60:6:0.2308:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:12.8:1:29:1:1:0:60:8:1:0:0 +2 108623666 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTAAAGTTCACCTTTTG;RSEQ=CCTGTGGTATTCTGTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:21:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 108623876 . GA G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTATGTAGTGTTTGTCTCT;RSEQ=AAAAAAAAAAGATAGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:33:0:1:0:60:4:1:0:0.5 +2 109004001 . C T 45 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=CCAGTTATCAGAATAGTTTA;RSEQ=TGTGTTTGCTCTTATTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:25.3:1:33.5:1:1:0:60:8:1:0:0 0/1:10:3:2,1:5,2:7,3:0.3:2,2:11.7:1:29:1:1:1.22183:60:6:0.3333:0:1 +2 109004506 . T C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACCCCATGATCCACCCGC;RSEQ=TCGGCCTCCCAAAGTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:18:0:29:0:1:0:45:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:32.5:1:1:0:30:4:1:0:1.5 +2 109201157 . A G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=CAGGTTTTCTGAGTTGTTTG;RSEQ=GGATGTGAGCATTAGCGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:27,11:38,2:0.05:2,2:8.5:1:28:1:0.51538:2.39319:60:4:0.0513:0:1.5 0/0:28:0:0,0:20,8:28,0:0:2,0:18.5:1:28.8:1:1:0:60:56:1:0:0.1 +2 109201345 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GGGCCTGGAGCAGTAGCTCA;RSEQ=GCTTGTAATCCCAGCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:30.5:1:30.5:1:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:11.5:1:29.5:1:1:0:60:4:1:0:0 +2 110053094 . T A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49834;SOR=Inf;LSEQ=TGTGGTATAAAAGATTTCGT;RSEQ=CAGCTCATTCCTCTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:118,33:151,0:0:2,0:22.6:1:30.8:1:1:0:60:74.5:1:0:0.1 0/1:151:2:2,0:114,35:149,2:0.0132:2,0:19:1:25:1:1:0:60:4:0.0133:0:1 +2 110053209 . T G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05894;SOR=0.7375;LSEQ=CTTCTGCCCAGTGACGGGCA;RSEQ=TGTTTTAGGACCTCGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:144:63,81:84,109:193,144:0.4273:2,2:26.5:1:32.7:1:1:1.01:60:143:0.4269:0:1.1 0/1:341:121:58,63:96,124:220,121:0.3548:2,2:24.2:1:30.8:1:0.49534:1.19:60:39.333:0.3522:0:1.3 +2 110053248 . C T 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCAGATCAGTTGGCCTTCAT;RSEQ=TCTTAAAGCCAGCAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:84,166:250,0:0:2,0:26.3:1:32.8:1:1:0:60:61.5:1:0:0.4 0/1:216:16:6,10:61,139:200,16:0.0741:2,2:22.9:1:29.9:1:0.58042:1.37:60:32:0.0755:0:2 +2 111726228 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51019;SOR=Inf;LSEQ=GTCCCAAAATGTCCATTGCC;RSEQ=AGAAGAAAGATCAGATAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:27,25:52,0:0:2,0:27.2:1:31.3:1:1:0:36.5:51:1:0:0.2 0/1:73:2:1,1:37,34:71,2:0.0274:2,2:18:1:27.5:1:1:1.08696:28:4:0.0294:0:1 +2 111727161 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTGGGAGGCCGAGGTGG;RSEQ=CAGCTTACCTGAGGTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:29:1:1:0:43.5:4:1:0:1 +2 111881124 . CA C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTGGGGGTACCCTCTAC;RSEQ=AAAAAAAATTACACCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:2,0:22,0:22,2:0.0833:1,0:26.5:1:31.6:1:1:0:60:4:0.087:0.0417:1.5 0/0:5:0:0,0:5,0:5,0:0:0,0:24.4:1:30.2:1:1:0:60:10:1:0:0 +2 111881156 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCTTTATTATTTTAGGT;RSEQ=CAATTTTTTTATTTGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:40,0:40,2:0.0476:1,0:23.5:1:30:0:1:0:60:4:0.0488:0:1 0/0:13:0:0,0:13,0:13,0:0:1,0:19.7:1:31.2:1:1:0:60:12:1:0:0.3 +2 111881263 . AT A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.99781;LSEQ=GCTAATTTGTTTATTCATCG;RSEQ=TTTTTTTTTTGCTTAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:27:20,7:173,20:193,27:0.1216:2,2:23.9:1:31.6:1:0.03025:3.00718:60:54:0.1227:0.027:0.1 0/1:173:21:16,5:129,21:150,21:0.1214:2,2:25.6:1:29.9:1:0.32531:1.91109:59.7:42:0.1221:0.0173:0.4 +2 111881275 . G T 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25217;SOR=0;LSEQ=ATTCATCGATTTTTTTTTTT;RSEQ=CTTAAAATAATCTTAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:2,1:218,47:265,3:0.0112:2,2:16:1:21.3:1:0.44818:2.30997:60:2:0.008:0:2.3 0/0:233:0:0,0:174,57:231,0:0:2,0:20.8:1:30.4:1:1:0:59.9:22.1:1:0:0.2 +2 111881810 . C T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00231;SOR=0.19305;LSEQ=AAAATCCCCTTTTAAAACCC;RSEQ=GTAACTGATTTATTCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:18:0,18:1,54:55,18:0.2466:1,1:27.8:1:30.8:1:1:0:60:36:0.2571:0:1.1 0/1:68:4:1,3:2,61:63,4:0.0588:1,2:23.8:1:30.3:1:0.17105:9.36:60:8:0.0625:0:1.3 +2 111883066 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12327;SOR=0;LSEQ=AGGAAACCCAGTACAGAGTC;RSEQ=ATTATAATTTAGATTGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:136,77:213,3:0.0139:2,2:28:1:26.3:1:1:1.13:60:2:0.0094:0:1 0/0:217:0:0,0:130,87:217,0:0:2,0:24.3:1:29:1:1:0:60:107.5:1:0:0.1 +2 111883077 . A T 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24843;SOR=0;LSEQ=TACAGAGTCTATTATAATTT;RSEQ=GATTGTACCTCATGATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:142,94:236,3:0.0126:2,2:7:1:27.3:1:0.5662:3.00716:60:6:0.0129:0:1 0/0:237:0:0,0:141,96:237,0:0:2,0:26.3:1:28.5:1:1:0:60:58.25:1:0:0.1 +2 111883196 . G A 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.62359;SOR=0.33144;LSEQ=GCTTCAGTGAGGTAAATCAG;RSEQ=CAGGCCTTTGCCCATGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:2,1:116,149:265,3:0.0112:2,2:18:1:28.3:1:0.58433:2.56:60:6:0.0115:0:1 0/0:268:1:1,0:110,156:266,1:0.0037:2,0:1:0:22:0:0.41573:0:60:2:0.0039:0:1 +2 111883400 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49916;SOR=0;LSEQ=GGGCTGGAAGTTTTATTATT;RSEQ=CTGTTACTACTGCTCGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:94,85:179,2:0.011:2,2:22.5:1:26:1:1:1.10527:60:4:0.0114:0:1 0/0:169:0:0,0:88,81:169,0:0:2,0:24.6:1:30.8:1:1:0:59.9:27.167:1:0:0.2 +2 111883401 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23529;SOR=Inf;LSEQ=GGCTGGAAGTTTTATTATTG;RSEQ=TGTTACTACTGCTCGTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:94,87:181,0:0:2,0:26.4:1:32.3:1:1:0:60:29.167:1:0:0.2 0/1:171:2:1,1:88,81:169,2:0.0117:2,2:27.5:1:26:1:1:1.08588:60:4:0.012:0:1.5 +2 111883407 . C A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49987;SOR=0;LSEQ=AAGTTTTATTATTGCTGTTA;RSEQ=TACTGCTCGTGAACTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:98,88:186,2:0.0106:2,2:7.5:1:28:1:1:1.113:60:4:0.0106:0:1 0/0:170:0:0,0:88,82:170,0:0:2,0:24:1:31.2:1:1:0:59.9:169:1:0:0.2 +2 111883412 . G A 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61092;SOR=2.15742;LSEQ=TTATTATTGCTGTTACTACT;RSEQ=CTCGTGAACTCATTTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:1,0:99,88:187,1:0.0053:2,0:10:0:11:0:1:0:60:0:0:0:5 0/1:175:2:1,1:91,82:173,2:0.0114:2,2:29.5:1:24:1:1:1.10909:60:4:0.0116:0:1 +2 111883494 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21502;SOR=Inf;LSEQ=ATGCTCCCCCATATATATGA;RSEQ=CATTCTCGCTTACTATAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:94,87:181,0:0:2,0:24:1:30.9:1:1:0:59.9:180:1:0:0.1 0/1:157:2:1,1:89,66:155,2:0.0127:2,2:27.5:1:27.5:1:1:1.34587:60:4:0.0129:0:1.5 +2 111883499 . C G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49949;SOR=0;LSEQ=CCCCCATATATATGATCATT;RSEQ=TCGCTTACTATAACATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:95,83:178,2:0.0111:2,2:26:1:32:1:1:1.14372:60:4:0.0113:0:2 0/0:165:0:0,0:94,71:165,0:0:2,0:22.3:1:30.7:1:1:0:60:81.5:1:0:0.1 +2 111883682 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21933;SOR=Inf;LSEQ=GTTCCCTTTCAAGCAAAATG;RSEQ=ATACATTGGTCTCTGTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:108,106:214,0:0:2,0:25.3:1:32.1:1:1:0:60:52.5:1:0:0.1 0/1:189:2:1,1:89,98:187,2:0.0106:2,2:12:1:28.5:1:1:1.10:60:4:0.0108:0:1 +2 111883779 . T A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24906;SOR=Inf;LSEQ=AGATAGTGTATTTTTTAATG;RSEQ=AAAGACAGGCACAAATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:109,116:225,0:0:2,0:26.4:1:29.5:1:1:0:60:450:1:0:0.1 0/1:239:3:2,1:111,125:236,3:0.0126:2,2:6.3:1:26.3:1:0.60394:2.24:60:6:0.0126:0:1 +2 111883806 . T A 86 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03708;SOR=7.21465;LSEQ=AGGCACAAATGCTTTTTTTG;RSEQ=TGATAAATACTATTTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:1:1,0:92,118:210,1:0.0047:2,0:1:0:28:0:0.44076:0:60:2:0.0047:0:1 0/1:210:7:4,3:93,110:203,7:0.0333:2,2:29.3:1:30.9:1:0.7061:1.57:60:14:0.0338:0:1.3 +2 111883823 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24683;SOR=Inf;LSEQ=TTGTTGATAAATACTATTTT;RSEQ=CAAGCTAATTATAAGTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:90,108:198,0:0:2,0:23:1:29.4:1:1:0:59.8:197:1:0:0.1 0/1:196:2:1,1:80,114:194,2:0.0102:2,2:18:1:30:1:1:1.42:60:4:0.0105:0:1 +2 111883855 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19706;SOR=Inf;LSEQ=TAAGTTAAGCACTGTTACTT;RSEQ=AGATGAAATATACAGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:87,89:176,0:0:2,0:23.4:1:32.4:1:1:0:59.6:175:1:0:0.1 0/1:141:2:1,1:56,82:138,2:0.0142:2,2:25:1:27.5:1:1:1.46:60:4:0.0144:0:1 +2 111884280 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15312;SOR=Inf;LSEQ=GGTTCTCTTGACTTTGTTTA;RSEQ=TATTCTTTACTCAACCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:86,89:175,0:0:2,0:24.9:1:32.7:1:1:0:59.8:86.5:1:0:0 0/1:113:2:1,1:52,58:110,2:0.0177:2,2:21.5:1:27:0:1:1.11:60:4:0.0177:0:1 +2 111884464 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50133;SOR=0;LSEQ=CAAAGCAGTTTTTTGCTCAG;RSEQ=AACTTGGGGTAGAGATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:67,72:139,2:0.0142:2,2:29.5:1:30:1:1:1.07:60:4:0.0145:0:1 0/0:120:0:0,0:58,61:119,0:0:2,0:25.6:1:31.5:1:1:0:60:238:0.9917:0:0 +2 111884472 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50062;SOR=0;LSEQ=TTTTTTGCTCAGCAACTTGG;RSEQ=GTAGAGATCAGTGTGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:67,76:143,2:0.0138:2,2:8.5:1:27.5:1:1:1.13:60:4:0.0139:0:1 0/0:126:0:0,0:57,69:126,0:0:2,0:24.4:1:30.3:1:1:0:60:252:1:0:0.1 +2 111884592 . CT C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00965;SOR=1.91222;LSEQ=AACACTGTTTTCATATTTTC;RSEQ=TTTATGTCTCTGATTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:56:24,32:56,58:114,56:0.3275:2,2:24.3:1:32.9:1:0.51393:1.28544:60:112:0.3275:0.0292:0.1 0/1:116:56:28,28:32,28:60,56:0.4828:2,2:22.7:1:30.6:1:0.85263:1.14154:60:112:0.487:0.069:0.4 +2 111884658 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50335;SOR=0;LSEQ=TCTCTGTGGGGCAACAGATA;RSEQ=AGTTTTTTCACTTTTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:61,76:137,2:0.0144:2,2:13:0:31.5:1:1:1.24:60:4:0.0145:0:1 0/0:113:0:0,0:61,52:113,0:0:2,0:22.5:1:31.3:1:1:0:60:36.667:1:0:0.2 +2 111884689 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22047;SOR=Inf;LSEQ=CTTTTCCTCAATTTTAGTCT;RSEQ=CTTACACTCTGGGAGGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:71,64:135,0:0:2,0:25.9:1:32.1:1:1:0:60:66.5:1:0:0.1 0/1:120:2:1,1:68,50:118,2:0.0167:2,2:33:1:31:1:1:1.35645:60:4:0.0169:0:1 +2 111884802 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49907;SOR=Inf;LSEQ=GTGCCTTTTTGGATGAGTGT;RSEQ=TTATGCCATATGTGTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:80,94:174,0:0:2,0:25.8:1:30.2:1:1:0:60:33.8:1:0:0.1 0/1:185:2:1,1:87,96:183,2:0.0108:2,2:21.5:1:29:1:1:1.10:60:4:0.0109:0:1 +2 111884909 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23483;SOR=Inf;LSEQ=AAGTCAGGATATGGAGGAAT;RSEQ=CTCCCTAGTGTCATGTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:37,55:92,0:0:2,0:21.8:1:32.4:1:1:0:60:91:1:0:0.1 0/1:87:2:1,1:31,54:85,2:0.023:2,2:12:0:30:1:1:1.73:60:4:0.0233:0:1 +2 111884937 . T G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5005;SOR=Inf;LSEQ=GTGTCATGTTAGTAAATGTC;RSEQ=TAAATTTTATACTTGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:35,42:77,0:0:2,0:27.7:1:31:1:1:0:59.9:76:1:0:0.2 0/1:91:2:1,1:39,50:89,2:0.022:2,2:28.5:1:30.5:1:1:1.28:60:4:0.022:0:1 +2 111885058 . C A 31 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62629;LSEQ=CTCTTATAGCTGGTACTTGT;RSEQ=TGACCCCTCCTTTAGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:71,46:117,2:0.0164:2,2:22:0:31.5:1:1:1.53764:60:4:0.0187:0:1 0/1:97:1:0,1:48,46:94,1:0.0103:2,0:2:0:29:0:0.49474:0:55:2:0.0112:0:1 +2 111885088 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19387;SOR=Inf;LSEQ=CTTTAGTTTGTGAGCTCCCT;RSEQ=GGCGGGGAATAATGGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:89,54:143,0:0:2,0:26.6:1:31:1:1:0:60:16.875:1:0:0.3 0/1:113:2:1,1:57,54:111,2:0.0177:2,2:29:0:28.5:1:1:1.05507:60:4:0.0185:0:1.5 +2 111885134 . A G 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22045;SOR=Inf;LSEQ=CTAGCGAGTGCCTGACAAAG;RSEQ=GGAGAAGCCCAGGAGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:85,76:161,0:0:2,0:24.7:1:29.9:1:1:0:59.9:15.1:1:0:0.2 0/1:143:2:1,1:71,70:141,2:0.014:2,2:8:0:27.5:1:1:1.01419:60:4:0.0148:0:1 +2 111885189 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50238;SOR=0;LSEQ=CTCTGCCTGTTAGCCTTTCA;RSEQ=ACAAATAAAGTTGAAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:80,112:192,2:0.0103:2,2:28:1:30:1:1:1.40:60:4:0.0105:0:1 0/0:163:0:0,0:78,85:163,0:0:2,0:24.4:1:30.5:1:1:0:60:39.75:1:0:0.2 +2 111885199 . G T 29 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58341;SOR=2.58187;LSEQ=TAGCCTTTCAGACAAATAAA;RSEQ=TTGAAGAAGGCAGGTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:76,113:189,1:0.0053:2,0:12:0:13:0:1:0:60:0:0:0:6 0/1:148:2:1,1:67,79:146,2:0.0135:2,2:5:1:29.5:1:1:1.18:60:4:0.0135:0:1 +2 111885210 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51168;SOR=0;LSEQ=ACAAATAAAGTTGAAGAAGG;RSEQ=AGGTAGCAAGAAAAAGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:78,106:184,2:0.0108:2,2:8:0:31:1:1:1.36:60:4:0.011:0:1.5 0/0:134:0:0,0:60,74:134,0:0:2,0:26:1:31.2:1:1:0:60:66:1:0:0.2 +2 111885244 . G T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02808;SOR=Inf;LSEQ=AAGATCCTGACCTCTGCTCT;RSEQ=CCAAAGTGTTTTTAATTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:61,84:145,0:0:2,0:25.3:1:32:1:1:0:60:23.167:1:0:0.2 0/1:102:4:1,3:46,52:98,4:0.0392:2,2:25.3:1:28.3:1:0.62225:2.6307:60:8:0.0396:0:1 +2 111885270 . C A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28352;SOR=0;LSEQ=GTGTTTTTAATTACCTGGAT;RSEQ=TAGCTGTAAGGTTTGCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:3:1,2:63,52:115,3:0.0254:2,2:27.7:1:25.7:1:0.59214:2.40535:60:2:0.0172:0:1.3 0/0:75:0:0,0:40,35:75,0:0:2,0:26.8:1:31.1:1:1:0:60:74:1:0:0.1 +2 111885392 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16764;SOR=Inf;LSEQ=CTGAACTGAGTTGTGCTGTC;RSEQ=TTATTGATACACACTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:95,99:194,0:0:2,0:26.4:1:31:1:1:0:59.9:193:1:0:0.1 0/1:135:2:1,1:66,67:133,2:0.0148:2,2:38:1:31.5:1:1:1.02:60:4:0.0148:0:1 +2 111885507 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18411;SOR=Inf;LSEQ=TATATAGGTTAAATAAAATA;RSEQ=AAACTTGTATTGCAGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:97,62:159,0:0:2,0:25.1:1:30.4:1:1:0:60:318:1:0:0.2 0/1:120:2:1,1:70,48:118,2:0.0167:2,2:24.5:1:29:1:1:1.45362:60:4:0.0167:0:1 +2 111885515 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18073;SOR=Inf;LSEQ=TTAAATAAAATATAAACTTG;RSEQ=ATTGCAGTTAAACACAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:102,65:167,0:0:2,0:24.9:1:29.5:1:1:0:59.9:334:1:0:0.2 0/1:124:2:1,1:75,47:122,2:0.0161:2,2:12:1:26.5:1:1:1.58947:60:4:0.0161:0:1 +2 111885554 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22366;SOR=Inf;LSEQ=GCGTAAAATTTACCATCTGA;RSEQ=CCATTTATTTCTAAGTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:130,89:219,0:0:2,0:24.7:1:29.4:1:1:0:60:26.375:1:0:0.3 0/1:197:2:1,1:120,75:195,2:0.0102:2,2:23:1:31:1:1:1.59599:60:4:0.0104:0:1 +2 111885565 . C T 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCATCTGAACCATTTATTT;RSEQ=TAAGTGTACTGTTCAGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:47:27,20:108,82:190,47:0.1983:2,2:26.4:1:30.9:1:1:1.02:59.8:94:0.2009:0:1.1 0/0:218:0:0,0:133,85:218,0:0:2,0:24.9:1:30.3:1:1:0:60:26.25:1:0:0.1 +2 111885578 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11863;SOR=0;LSEQ=TTTATTTCTAAGTGTACTGT;RSEQ=CAGTAGTGTTAAGTGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:1,2:138,116:254,3:0.0117:2,2:32:1:26:1:0.59525:2.37149:60:2:0.008:0:1.7 0/0:265:0:0,0:155,110:265,0:0:2,0:23.9:1:29:1:1:0:59.9:52:1:0:0.1 +2 111885684 . TC T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.12352;SOR=0;LSEQ=AACAACTCCCCATTTCCCCC;RSEQ=CCCCCAGCTTCTGACAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:4:2,2:98,118:216,4:0.0181:2,2:26.8:1:31:1:1:1.20:60:8:0.0184:0.0045:0.3 0/0:213:0:0,0:88,125:213,0:0:2,0:23.3:1:30:1:1:0:59.7:41.6:1:0:0.1 +2 111885697 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24547;SOR=0;LSEQ=TTCCCCCTCCCCCCAGCTTC;RSEQ=GACAACCACCATTCTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:83,106:189,2:0.0105:2,2:13.5:1:29.5:1:1:1.28:60:4:0.0106:0:1 0/0:194:0:0,0:77,117:194,0:0:2,0:23.8:1:29.5:1:1:0:59.7:47.5:1:0:0.2 +2 111885720 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24889;SOR=0;LSEQ=CAACCACCATTCTATTTTCT;RSEQ=TCTATTAATTTGACAACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:1,2:68,104:172,3:0.0171:2,2:22.7:1:32.3:1:1:1.30575:50:6:0.0171:0:2 0/0:162:0:0,0:56,106:162,0:0:2,0:24.8:1:31.2:1:1:0:59.8:53:1:0:0.1 +2 111885727 . A T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5969;SOR=2.34828;LSEQ=CATTCTATTTTCTGTCTATT;RSEQ=ATTTGACAACTTCAGATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:66,100:166,1:0.006:2,0:10:0:11:0:1:0:60:0:0:0:5 0/1:143:2:1,1:48,93:141,2:0.014:2,2:20:1:25.5:1:1:1.93:60:4:0.0147:0:1.5 +2 111885947 . T C 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24893;SOR=0;LSEQ=ATACTTGGGTTGCTTCCACT;RSEQ=TTTGGCTATTGTGAGTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:2,1:75,29:104,3:0.028:2,2:29.3:1:27:1:1:1.28987:60:2:0.0194:0:1.3 0/0:95:0:0,0:63,32:95,0:0:2,0:21.1:1:28.5:1:1:0:60:30.667:1:0:0.1 +2 111885951 . G C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50057;SOR=0;LSEQ=TTGGGTTGCTTCCACTTTTT;RSEQ=GCTATTGTGAGTAGTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:84,37:121,2:0.0163:2,2:15:1:28:1:0.52419:2.25353:60:4:0.0164:0:1 0/0:106:0:0,0:67,39:106,0:0:2,0:21.1:1:30.1:1:1:0:59.8:52:1:0:0.1 +2 111886041 . G A 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68659;SOR=1.8804;LSEQ=TTTTGGATATATACTTGGAA;RSEQ=TGGAATTGCTGGATCATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:2:2,0:108,117:225,2:0.0088:2,0:1:0:20:1:0.23371:0:60:1:0.0045:0:1 0/1:243:4:3,1:114,125:239,4:0.0165:2,2:14:1:26.3:1:0.35421:3.27:60:8:0.0167:0:1 +2 111886066 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=ATTGCTGGATCATATGGTAA;RSEQ=TCTATTTTTAATTTTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:70,79:149,0:0:2,0:20.9:1:30.5:1:1:0:59.5:36.25:1:0:0.1 0/1:154:2:1,1:75,77:152,2:0.013:2,2:10:0:33:0:1:1.03:48.5:4:0.013:0:1.5 +2 111886332 . C T 247 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAGGATTTCTCATGATAC;RSEQ=TTTTTATAGCCACAGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:993:0:0,0:410,583:993,0:0:2,0:25.6:1:32.2:1:1:0:60:75.385:1:0:0.1 0/1:935:326:152,174:254,353:607,326:0.3487:2,2:26.5:1:29.7:1:0.16651:1.21:58.5:162:0.3514:0:1.2 +2 111886444 . T C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.08367;SOR=Inf;LSEQ=TTTCTCTGTTTCTTTCTACC;RSEQ=TTTTAAACATGGCTACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:94,207:301,0:0:2,0:24.5:1:31.1:1:1:0:59.8:59.2:1:0:0.1 0/1:235:3:0,3:75,156:231,3:0.0128:2,0:10.3:1:33:1:0.55313:0:60:6:0.0129:0:1 +2 111886914 . C T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGGAAACTTTTTAGGTC;RSEQ=TAAGTGGGGAGAGAAAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:1,3:0.75:0,2:31.3:1:31.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 111887368 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22206;SOR=Inf;LSEQ=CTTTCTGTCTCTTCCTTACC;RSEQ=ATGATAACCACTCATCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:62,153:215,0:0:2,0:20.9:1:31.7:1:1:0:59.9:70.667:1:0:0.1 0/1:193:2:1,1:62,129:191,2:0.0104:2,2:28.5:1:28:1:0.54744:2.07:60:4:0.0105:0:1 +2 111887384 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11975;SOR=Inf;LSEQ=TACCCATGATAACCACTCAT;RSEQ=TGATCTACATATCTGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:24,119:143,0:0:2,0:21.9:1:33.3:1:1:0:59.8:142:1:0:0.1 0/1:140:3:2,1:36,101:137,3:0.0214:2,2:13:1:24.3:1:0.17906:5.53:60:6:0.0214:0:1 +2 111887564 . C T 39 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36228;SOR=3.16193;LSEQ=ATAGTATTCCATAGATGATG;RSEQ=ACCACAGTTTGCTTAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:1,0:163,81:244,1:0.0041:2,0:12:0:30:0:1:0:60:2:0.0042:0:1 0/1:234:3:1,2:165,65:230,3:0.0128:2,2:7:1:24.7:1:0.19938:5.03594:60:6:0.013:0:2 +2 111887621 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0641;SOR=Inf;LSEQ=ACTGTGTTTGCATGTTCTGG;RSEQ=AAGGCCCTGGCACAGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:0:0,0:206,226:432,0:0:2,0:28:1:31.8:1:1:0:59.8:23:0.9976:0:0.3 0/1:492:5:2,3:239,246:485,5:0.0102:2,2:30.4:1:27.8:1:1:1.45621:60:10:0.0105:0:1 +2 111887672 . G A 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.42867;LSEQ=GATTAAAAGAAGTATTTATT;RSEQ=TACTTTTACTTCTCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:2:2,0:101,182:283,2:0.007:2,0:1:0:24.5:1:0.1298:0:60:4:0.008:0:1 0/1:301:3:2,1:113,182:295,3:0.01:2,2:26.3:1:25.7:1:0.56139:3.21:60:6:0.0115:0:1.7 +2 111887703 . T A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-04;SOR=2.55188;LSEQ=TCTCTTTTTTTTTTTTTTTG;RSEQ=GACAGTCTCACTCTGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:34:5,29:24,69:93,34:0.2656:2,2:18:1:30.6:1:0.23652:2.00727:53.6:7.5:0.2479:0:1.7 0/1:131:63:14,49:16,52:68,63:0.4809:2,2:19:1:29.3:1:1:1.07629:51.4:11.6:0.4677:0:1.7 +2 111887885 . T G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGATGGGTTTCACCATGT;RSEQ=GGCCAGGCTGGTCTCGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:10:0:33.5:1:0.33333:0:52.5:4:0.3333:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:30:0:1:0:35:2:1:0:0 +2 111899787 . A T 25 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52305;SOR=0;LSEQ=CTTAACTTGCACTTGTGCTA;RSEQ=TGAAGACTCTACCTCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:150,7:157,2:0.0126:1,2:5:1:25.5:1:0.0984:20.11132:60:4:0.0127:0:1 0/0:101:0:0,0:95,6:101,0:0:2,0:23.8:1:29.6:1:1:0:60:100:1:0:0.1 +2 111899881 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21075;LSEQ=TATTTATACAACATTTTTAT;RSEQ=GCTTGCAGATGACTCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:195:114,81:267,180:447,195:0.3033:2,2:24.1:1:29.6:1:0.79348:1.05384:60:194:0.306:0:1.1 0/1:560:47:29,18:296,216:512,47:0.0839:2,2:21.8:1:29.6:1:0.64579:1.18:60:94:0.0848:0:1.2 +2 111901935 . GGT G 90 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.14474;SOR=0.18843;LSEQ=GAGAAATAGACCTGGAGGGA;RSEQ=GTGTGTGTGTGTTGTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:7:5,2:166,14:180,7:0.0374:2,2:25.4:1:32.2:1:0.11203:4.67441:60:14:0.0378:0.0053:0.1 0/0:138:1:1,0:121,14:135,1:0.0072:2,0:20:0:33:0:1:0:60:2:0.0075:0:0 +2 111907691 . T C 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=2.02366;LSEQ=GCCCAAGAGTTGCGGCGTAT;RSEQ=GGAGACGAGTTTAACGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1325:706:340,366:299,320:619,706:0.5328:2,2:26.5:1:30.9:1:1:1.00582:60:63.182:0.5309:0:1.1 1/0:1254:875:423,452:183,190:373,875:0.6978:2,2:26.8:1:29.8:1:0.8528:1.02918:60:124:0.6983:0:1.2 +2 111907770 . T A 52 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05148;SOR=7.25051;LSEQ=TTCTGCTCACACCCTCCCCT;RSEQ=CCACACTATATTTTTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:1:1,0:165,422:587,1:0.0017:2,0:1:0:23:0:0.28231:0:60:2:0.0017:0:1 0/1:491:6:5,1:142,342:484,6:0.0122:2,2:7.5:1:20.3:1:0.0105:11.98:60:5:0.0106:0:2 +2 111909247 . A G 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACACTATCAGTTCTTCAGT;RSEQ=TGGAATTTCTGTAAGAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:148,0:148,0:0:1,0:26.7:1:28.8:1:1:0:59.7:73:1:0:0.1 0/1:96:39:38,1:56,1:57,39:0.4063:1,1:22.2:1:31.9:1:1:1.46757:59.7:78:0.4105:0:1 +2 111909271 . A T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07108;SOR=Inf;LSEQ=AATTTCTGTAAGAGTCAAGA;RSEQ=AACACACATCGGATCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:214,8:222,0:0:1,0:23.4:1:30.5:1:1:0:59.9:444:1:0:0.1 0/1:158:3:1,2:141,14:155,3:0.019:2,2:15.3:1:25.7:1:0.02729:19.29977:60:6:0.0194:0:1 +2 111909542 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18065;SOR=Inf;LSEQ=ATTCCCTCCAGTTCCTCTGC;RSEQ=TGGTTTACCTAAAGGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:26,229:255,0:0:2,0:21.9:1:30.5:1:1:0:60:62.75:1:0:0.1 0/1:189:2:1,1:20,167:187,2:0.0106:2,2:21.5:1:29.5:1:0.2104:8.17:60:4:0.0106:0:0 +2 111909610 . A G 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.25788;SOR=0.2206;LSEQ=GGCTGTCTCTATTGACTAGG;RSEQ=AGAACTGGTGAGAAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:7:0,7:1,74:75,7:0.0854:1,0:22.1:1:33.9:1:1:0:60:14:0.0854:0:1.1 0/1:50:1:0,1:1,48:49,1:0.02:1,0:7:0:31:0:1:0:60:2:0.0204:0:1 +2 111911182 . ATCC A 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00038;SOR=0;LSEQ=GCTGTCTTCACAAGGGAATT;RSEQ=TCTCTTGGCAAGCGAGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:22:22,0:32,2:34,22:0.3929:2,1:27.1:1:32.3:1:0.51429:0:60:44:0.4:0.0179:0 0/0:20:0:0,0:19,1:20,0:0:1,0:26.3:1:30.6:1:1:0:59.9:40:1:0:0.4 +2 111911251 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=0;LSEQ=TATTAACCTTTTAAATGTTG;RSEQ=GTGTCTTTATTTGCTTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:125,19:144,2:0.0137:2,2:22.5:1:29:1:0.25602:6.43797:60:4:0.014:0:1 0/0:133:0:0,0:110,23:133,0:0:2,0:19.5:1:28.7:1:1:0:60:43.333:1:0:0.1 +2 111911418 . G T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.05544;SOR=Inf;LSEQ=CAGTCCACTTAAGGGCAGTG;RSEQ=GGAAGCGTTTGAGACGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:144,231:375,0:0:2,0:24.5:1:31.2:1:1:0:60:92.75:1:0:0.1 0/1:355:4:2,2:140,210:350,4:0.0113:2,2:8.5:1:31.3:1:1:1.50:60:8:0.0115:0:1.5 +2 111918842 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17707;SOR=Inf;LSEQ=CAGCCCATAAAGAGGAAGAT;RSEQ=CCCAGAAGTTTCAGGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:64,0:64,0:0:1,0:21.6:1:28.7:1:1:0:60:63:1:0:0.1 0/1:47:2:1,1:44,1:45,2:0.0426:1,2:40:1:32:1:0.08418:31.46141:60:4:0.0435:0:1 +2 111921438 . CTTTT C 34 v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=22.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAACATTTTTTTGAGTG;RSEQ=TTTTTTTTTTTTTTTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,1:4,2:0.2857:2,0:29.5:1:34.5:1:1:0:52:4:0.2857:0:3.5 0/0:2:0:0,0:1,0:1,0:0:0,0:4:0:31:0:1:0:60:2:0.5:0:4 +2 113103646 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1784;SOR=Inf;LSEQ=GGGTGCCCACCCAGCACTCC;RSEQ=TCGCCCTCCCTGTCCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:61,19:80,0:0:2,0:21.9:1:31:1:1:0:60:25.667:1:0:0.1 0/1:59:2:1,1:45,12:57,2:0.0339:2,2:33:0:32:0:0.39509:3.64304:60:4:0.0339:0:1.5 +2 113103670 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50145;SOR=0;LSEQ=CCCTCCCTGTCCCCTGGCAG;RSEQ=CACGAGGAAGACAGGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:66,43:109,2:0.018:2,2:19:1:27.5:1:1:1.52875:60:4:0.018:0:1 0/0:93:0:0,0:59,34:93,0:0:2,0:24.8:1:30.5:1:1:0:59.9:186:1:0:0.1 +2 113103716 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23759;SOR=Inf;LSEQ=TGGATGACCACCTGTCCAGG;RSEQ=TCCTCAAGACCCCTGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:73,80:153,0:0:2,0:26.4:1:31.5:1:1:0:59.6:50:1:0:0.2 0/1:146:2:1,1:75,69:144,2:0.0137:2,2:13.5:1:29:1:1:1.08632:60:4:0.0138:0:1.5 +2 113103726 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49853;SOR=0;LSEQ=CCTGTCCAGGGTCCTCAAGA;RSEQ=CCCTGGCTGCCAGTCACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:66,85:151,2:0.0131:2,2:25:0:32:0:1:1.29:60:4:0.0132:0:1.5 0/0:147:0:0,0:70,77:147,0:0:2,0:26.5:1:30.5:1:1:0:58.9:28.4:1:0:0.1 +2 113103819 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49336;SOR=Inf;LSEQ=ACCACCACCACCATCACCAC;RSEQ=AACATCACCATCACCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:1,24:25,0:0:1,0:23.3:1:32.8:1:1:0:59.4:50:1:0:0.8 0/1:29:2:1,1:0,27:27,2:0.069:1,2:34.5:1:30.5:1:0.06897:0:60:4:0.069:0:1 +2 113608823 . A G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATAGCCTGGGGTTCCTTA;RSEQ=AGAAAATGGAGAAGGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:32.5:1:1:0:60:4:1:0:1 +2 113609886 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTACCTTATCAGTTAAT;RSEQ=GGACTCTTTGATATGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:24.5:1:28.5:1:1:1:25:4:0.5:0:1 +2 113610950 . TCATC T 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=37;MSI=10.000;MSILEN=4;SSF=0;SOR=39.42071;LSEQ=CAAGAAATCAATCCATCCAT;RSEQ=CATCCATCCATCCATCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:1,0:102,15:117,1:0.0084:2,0:29:0:34:0:1:0:60:2:0.0089:0:0 0/1:63:16:15,1:39,9:48,16:0.254:2,1:24:1:30.3:1:0.42885:3.41:59.5:32:0.254:0.0635:0.3 +2 113611639 . T A 41 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0379;SOR=Inf;LSEQ=AAACAATGTGCTGAAGTGGT;RSEQ=GACAAATGTCTCAAGTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:157,316:473,0:0:2,0:25.4:1:30.4:1:1:0:59.9:117.25:1:0:0.1 0/1:375:4:3,1:133,238:371,4:0.0107:2,2:5.8:1:20.8:1:0.13767:5.34:60:3:0.008:0:1.3 +2 113687740 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGCTCATGCCTGTAATCCC;RSEQ=CACTTTGGGAGGCTGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:31:1:1:0:42:4:1:0:1.5 +2 113688731 . A G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGATGCCTGGAGTTCTGGC;RSEQ=TGTCTTCTAGCACAATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:14.5:1:29.6:1:1:0:60:16:0.6667:0:1.3 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:36:1:29:1:1:0:60:4:0.6667:0:1 +2 113688869 . G A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=3.56432;LSEQ=ACAGATTAAAGATGGCTGCA;RSEQ=ATCCTTTGGTCCAGGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:127:68:67,1:53,6:59,68:0.5354:2,1:25:1:30.7:1:0.04896:7.48:60:33:0.528:0:2.9 1/1:77:62:57,5:13,2:15,62:0.8052:2,2:20.5:1:29.7:1:0.61655:1.74:60:61:0.8026:0:2.8 +2 113688885 . G T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.10826;LSEQ=TGCAGATCCTTTGGTCCAGG;RSEQ=TTGGGATACAGGCAGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:169:97:90,7:63,9:72,97:0.574:2,2:23.5:1:29.2:1:0.29283:1.83:60:23.25:0.5706:0:2.7 1/1:105:89:75,14:13,3:16,89:0.8476:2,2:21.4:1:28.7:1:0.72061:1.23:60:43.5:0.8529:0:2.6 +2 113688894 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=3.26865;LSEQ=TTTGGTCCAGGGTTGGGATA;RSEQ=AGGCAGCATTTGTATTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:207:125:107,18:71,11:82,125:0.6039:2,2:22.5:1:30.8:1:1:1.08541:59.6:61.5:0.6:0:2.3 1/1:120:100:83,17:16,4:20,100:0.8333:2,2:24.1:1:30:1:0.75083:1.22:60:99:0.8319:0:2.5 +2 113688949 . C T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04516;SOR=0;LSEQ=GGCCATGAAAAGTCCACCTG;RSEQ=AGTAGTGGTAGGAGGAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:6:2,4:308,183:491,6:0.0121:2,2:22:1:27.5:1:0.20443:3.35761:54.3:12:0.0122:0:1.7 0/0:350:0:0,0:218,132:350,0:0:2,0:24.4:1:31:1:1:0:59.7:69:1:0:0.6 +2 113689223 . C A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05198;SOR=Inf;LSEQ=GAGAAATTCTAAGCTGCCCC;RSEQ=TTAAGAGGCCCACATGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:1,7:8,8:0.5:2,0:25.4:1:31.8:1:1:0:60:16:0.5:0:1.1 1/1:7:7:0,7:0,0:0,7:1:0,0:16:1:30.6:1:1:0:60:14:1:0:1 +2 113689329 . T G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCGAGTGAACCACTTAG;RSEQ=ACTGTATACTCCAGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25:1:32:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 113690077 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00307;SOR=Inf;LSEQ=AAACTTCTAGGGCTGGTCCC;RSEQ=TGGAAGCCTCACACATGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:17:17,0:9,0:9,17:0.6296:0,1:16.1:1:30.1:1:1:0:58.6:16:0.6154:0:1.1 1/1:18:18:18,0:0,0:0,18:1:0,1:18.8:1:30.1:1:1:0:60:17:1:0:1.1 +2 113690132 . T G 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.2106;SOR=Inf;LSEQ=TGAAAAGAAACGTAAGTGTG;RSEQ=TTTTTGGTTTAATAAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:55,1:56,0:0:1,0:23:1:30:1:1:0:59.6:112:1:0:0.4 0/1:48:2:2,0:46,0:46,2:0.0417:1,0:5.5:1:31.5:1:1:0:60:4:0.0417:0:1 +2 113690289 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25843;SOR=0;LSEQ=GGCATTATACCAAAGCTATT;RSEQ=ATAGTTGGGCTTATAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:157,137:294,3:0.0101:2,2:21.7:1:28.3:1:0.60114:2.28576:60:6:0.0102:0:1.3 0/0:236:0:0,0:123,113:236,0:0:2,0:22.1:1:30.7:1:1:0:59.9:77.667:1:0:0.3 +2 113690316 . T C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15516;LSEQ=GGGCTTATAGGGTGTATGTT;RSEQ=GAAGAACTACTAATGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:105:57,48:110,80:190,105:0.3559:2,2:24.2:1:31.6:1:0.62375:1.15731:60:104:0.3574:0:1 0/1:254:20:10,10:118,115:233,20:0.0787:2,2:19.2:1:30.7:1:1:1.02599:60:40:0.0803:0:1.2 +2 113690350 . G A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.36135;LSEQ=TGTCAAAACCAATATTTCAC;RSEQ=GTCGACAAGAGGACATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:60:36,24:170,128:298,60:0.1671:2,2:27.5:1:31.3:1:0.77491:1.13:60:120:0.1709:0:1.2 0/1:305:123:69,54:101,79:180,123:0.4033:2,2:26.6:1:29.8:1:1:1.00055:60:23.6:0.396:0:1.2 +2 113690442 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.31282;LSEQ=GGATTTCCTGCAAATAAAGA;RSEQ=GGGGAAGATATAAAAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:70:36,34:204,168:372,70:0.1584:2,2:25.3:1:29.7:1:0.60381:1.14647:52.9:22.333:0.1544:0:2.1 0/1:388:174:90,84:114,99:213,174:0.4485:2,2:24.7:1:28.8:1:0.75926:1.07455:51.2:16.4:0.435:0:2.1 +2 113690452 . A G 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.92789;LSEQ=CAAATAAAGACGGGGAAGAT;RSEQ=TAAAAAAGATGCCTGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:458:457:251,206:0,0:0,457:0.9978:0,2:25.1:1:32:1:1:0:56.8:49.778:1:0:1.2 1/1:425:424:223,201:0,0:0,424:0.9976:0,2:25.9:1:31.2:1:1:0:54.1:59.571:0.9976:0:1.5 +2 113690661 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGAAGACCCACTTCCTAC;RSEQ=TCAGACGTTTTCACCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:207:207:128,79:0,0:0,207:1:0,2:23.5:1:30.8:1:1:0:59.9:68:1:0:1.5 1/1:145:145:79,66:0,0:0,145:1:0,2:21.6:1:30.2:1:1:0:60:290:1:0:1.4 +2 113690670 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18524;SOR=Inf;LSEQ=CCACTTCCTACGTCAGACGT;RSEQ=TTCACCAGTTGTCAAATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:146,77:223,0:0:2,0:24.3:1:30.5:1:1:0:60:36.167:1:0:1.4 0/1:169:2:1,1:104,63:167,2:0.0118:2,2:24:1:27.5:1:1:1.64563:60:4:0.0119:0:3 +2 113690675 . C A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0057;SOR=0.56131;LSEQ=TCCTACGTCAGACGTTTTCA;RSEQ=CAGTTGTCAAATCCCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:107:67,40:80,40:120,107:0.4693:2,2:24.3:1:30.1:1:0.5785:1.19309:59.9:34.667:0.4685:0:1.8 0/1:172:57:38,19:76,38:114,57:0.3314:2,2:23.6:1:29.7:1:1:1:60:114:0.3373:0:1.8 +2 113690935 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.66544;LSEQ=ACATGCTGCCTATATCCCAA;RSEQ=CCTGGACCAAGCACATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:944:72:31,41:375,497:872,72:0.0763:2,2:26:1:29.5:1:1:1.00:59.8:23:0.0742:0:1.2 0/1:770:179:79,100:264,327:591,179:0.2325:2,2:26.6:1:27.9:1:0.93171:1.02192:59.6:12.769:0.2216:0:1.1 +2 113691060 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06435;SOR=0.63408;LSEQ=GGAATCTTGTCCGTGCACTG;RSEQ=TGTGAATGCTGCAGGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:95:14,81:16,92:108,95:0.468:2,2:24:1:32.7:1:1:1.00618:52.2:46.5:0.4697:0:1.1 0/1:123:44:9,35:19,59:78,44:0.3577:2,2:23.2:1:31.3:1:0.66143:1.25008:52.9:43:0.3583:0:1.1 +2 113691072 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52875;SOR=0;LSEQ=GTGCACTGTTGTGAATGCTG;RSEQ=AGGGCTGACTGTGCAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:18,144:162,2:0.0122:2,2:23:1:27.5:1:0.21891:7.81:45:4:0.0125:0:2 0/0:99:0:0,0:19,80:99,0:0:2,0:21.5:1:31.6:1:1:0:56.3:48.5:1:0:0.5 +2 113691404 . A G 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCCAGTGTAACAACATT;RSEQ=TCTGACCAATAGTACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:15.3:1:29:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 113977703 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60717;SOR=2.20554;LSEQ=TTGGGGAAGCGCCAGGCCTC;RSEQ=CTGTAGGAGGAGTAGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:0,1:143,56:199,1:0.005:2,0:1:0:17:0:0.285:0:60:0:0:0:1 0/1:183:2:1,1:122,58:180,2:0.0109:2,2:9.5:1:28.5:1:0.54447:2.09413:60:4:0.0111:0:1 +2 113977862 . T G 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0.92209;LSEQ=TGGGCAAGCTCAGGAATGGT;RSEQ=GGGGAGACAGTTGGAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:578:577:319,258:0,0:0,577:0.9983:0,2:25.4:1:31.6:1:1:0:60:71.125:0.9982:0:1.3 1/1:533:532:281,251:0,0:0,532:0.9981:0,2:24.6:1:30.8:1:1:0:59.9:75:1:0:1.3 +2 113977936 . C T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50295;LSEQ=TCATCCCTTTTGGAACCCAT;RSEQ=GATCTGGAAAATTTGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:743:419:197,222:147,177:324,419:0.5639:2,2:26.2:1:30.5:1:0.65715:1.07:59.9:68.833:0.5642:0:1.3 0/1:731:288:154,134:219,223:442,288:0.394:2,2:25.2:1:29.6:1:0.32491:1.17:60:56.6:0.3909:0:1.4 +2 113978183 . A G 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=24.2027;LSEQ=CTGCTGCCTGGACCTTCTGG;RSEQ=GAAGGGCTCTTCTGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:482:2:1,1:218,262:480,2:0.0041:2,2:33:1:29.5:1:1:1.20:60:4:0.0043:0:1 0/1:403:37:16,21:176,190:366,37:0.0918:2,2:23.5:1:28.9:1:0.60813:1.2152:60:11.333:0.0876:0:1.2 +2 113978293 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09049;SOR=Inf;LSEQ=AGGTATGAGTGTGTGTGTTT;RSEQ=TGTGCATGGGGGGCTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:208,156:364,0:0:2,0:24.4:1:32.3:1:1:0:59.9:71.8:0.9917:0:0.1 0/1:300:3:1,2:168,129:297,3:0.01:2,2:16.7:1:27:1:0.58257:2.59646:60:6:0.01:0:1 +2 113978650 . C T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.54813;LSEQ=ATACATTATGATCTTTTATT;RSEQ=TCAAGACTACCCCATGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:92:44,48:156,125:281,92:0.246:2,2:23.7:1:30.8:1:0.2287:1.3603:59.6:45:0.2432:0:1.2 0/1:339:154:81,73:98,86:184,154:0.4543:2,2:22.7:1:29.6:1:0.9133:1.02692:59.8:153:0.454:0:1.1 +2 113978894 . G A 232 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00427;LSEQ=AATGTCCACCCAGCCTTTCA;RSEQ=AAACTCACCTACGATTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:190:102,88:187,188:375,190:0.3351:2,2:24.5:1:30.7:1:0.42305:1.16:59.9:189:0.3357:0:1.1 0/0:467:1:1,0:230,236:466,1:0.0021:2,0:1:0:25:0:0.49465:0:60:2:0.0022:0:1 +2 113978906 . C T 164 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=67.83103;LSEQ=GCCTTTCAGAAACTCACCTA;RSEQ=GATTGGGAGCTATGTGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:548:1:1,0:271,276:547,1:0.0018:2,0:35:0:33:0:0.49635:0:60:2:0.0019:0:1 0/1:461:51:22,29:205,204:409,51:0.1106:2,2:21.8:1:29:1:0.3754:1.32383:59.7:50:0.1092:0:1.8 +2 113978940 . C G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.10238;LSEQ=GTGGTTCTGAGTCTCCTTCC;RSEQ=CAGACTCTTTGGAGGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:124:53,71:213,232:445,124:0.2175:2,2:23.5:1:31:1:0.3598:1.22946:60:40.333:0.2157:0:1.2 0/1:451:209:101,108:113,128:241,209:0.4634:2,2:25.6:1:30.6:1:0.77712:1.06:59.9:418:0.4655:0:1.3 +2 113979073 . C A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29003;SOR=0;LSEQ=CTCTCTGAGTGAGTGACTTA;RSEQ=AGGTGAACCTTGGTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:2,1:118,173:291,3:0.0102:2,2:14.7:1:23:1:0.56918:2.92:58:2:0.0069:0:3.3 0/0:182:0:0,0:78,104:182,0:0:2,0:24.4:1:31.1:1:1:0:60:364:1:0:0.1 +2 113979081 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14359;SOR=Inf;LSEQ=GTGAGTGACTTACAGGTGAA;RSEQ=CTTGGTTTCCTTATCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:117,169:286,0:0:2,0:23.3:1:31.6:1:1:0:59.7:56.2:1:0:0.1 0/1:175:2:1,1:73,99:172,2:0.0114:2,2:15:1:27.5:1:1:1.35:60:4:0.0116:0:1 +2 113979098 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15662;SOR=Inf;LSEQ=GAACCTTGGTTTCCTTATCT;RSEQ=TAAAATGGGCCAAATAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:105,137:242,0:0:2,0:24.4:1:32.5:1:1:0:59.7:484:1:0:0.2 0/1:159:2:1,1:71,86:157,2:0.0126:2,2:37.5:1:28.5:1:1:1.21:60:4:0.0127:0:1 +2 113979129 . A T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06981;SOR=Inf;LSEQ=CAAATAATTATCCCTATCTC;RSEQ=TTTGGTTTAATGAGAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:130,130:260,0:0:2,0:22.9:1:31:1:1:0:59.9:129:1:0:0.2 0/1:183:3:1,2:91,89:180,3:0.0164:2,2:18.3:1:24:1:0.62087:2.03724:60:2:0.0111:0:1.7 +2 113979133 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17353;SOR=Inf;LSEQ=TAATTATCCCTATCTCATTT;RSEQ=GTTTAATGAGAATTAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:135,129:264,0:0:2,0:22.8:1:31.9:1:1:0:59.9:263:1:0:0.2 0/1:189:2:1,1:96,91:187,2:0.0106:2,2:7.5:1:27.5:1:1:1.05467:60:4:0.0108:0:1.5 +2 113979160 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=7e-05;SOR=0.32552;LSEQ=TGAGAATTAAATGACAAAAT;RSEQ=TGTATTAAATGCTTAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:59:26,33:126,116:242,59:0.196:2,2:24.4:1:31.7:1:0.31028:1.37716:60:28.5:0.1906:0:1.1 0/1:218:16:7,9:106,96:202,16:0.0734:2,2:24:1:31.7:1:0.60629:1.41735:60:32:0.0741:0:1.1 +2 113979230 . T C 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.65417;SOR=2.09741;LSEQ=AAATCTAAGCTTTTATTATT;RSEQ=TCCCATTAAACAGGTGCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:2:0,2:187,161:348,2:0.0057:2,0:16.5:1:22:1:0.21618:0:60:1:0.0029:0:2 0/1:253:3:1,2:129,120:249,3:0.0119:2,2:21.7:1:29:1:0.61185:2.14368:60:6:0.012:0:1 +2 113979352 . A T 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAGACAAGTAGGCATTTAT;RSEQ=CAGGAAGAAGAGAGATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:0:0,0:254,226:480,0:0:2,0:25.1:1:29.1:1:1:0:59.8:79:1:0:0.2 0/1:416:16:8,8:220,180:400,16:0.0385:2,2:18.3:1:29.8:1:0.79965:1.22162:60:15:0.0364:0:1.3 +2 113979364 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.12278;LSEQ=GCATTTATACAGGAAGAAGA;RSEQ=AGATGAAGAGGAGCAGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:70:34,36:209,198:407,70:0.1468:2,2:24.6:1:31:1:0.69911:1.11739:60:140:0.1471:0:1.1 0/1:436:9:5,4:233,194:427,9:0.0206:2,2:15:1:28.3:1:1:1.04:60:18:0.0207:0:1.1 +2 113979446 . C T 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCAATGACGGACTGAGAACA;RSEQ=AGTAAGAAAGTTCCTTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:0:0,0:290,283:573,0:0:2,0:24.1:1:32:1:1:0:59.9:113.6:0.9982:0:0.1 0/1:509:50:22,28:239,219:458,50:0.0982:2,2:24.9:1:28.5:1:0.29889:1.38805:60:100:0.0996:0:1.2 +2 113979545 . G GA 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.87921;SOR=0.93814;LSEQ=TAAAGAAGTAAAAAAGCAAA;RSEQ=AAAAAAAAACCTAAGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:24:10,14:199,241:440,24:0.0511:2,2:30.5:1:31:1:0.83444:1.15566:60:48:0.0527:0.0021:0.2 0/1:437:21:10,11:184,227:411,21:0.0481:2,2:27.9:1:28.9:1:0.8252:1.12:60:42:0.0495:0:0.1 +2 113979580 . T A 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAATAATCTAATCGAAACA;RSEQ=CTATTTAACAGATGAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:186,194:380,0:0:2,0:27.2:1:30.5:1:1:0:59.9:33.545:1:0:0.1 0/1:381:29:16,13:162,190:352,29:0.0761:2,2:25.8:1:28.3:1:0.43919:1.44:60:58:0.0773:0:1 +2 113979653 . T C 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=CAGATAACACAGCTGTGACA;RSEQ=AGGGAAGTAAAGACATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:191,190:381,0:0:2,0:24.9:1:29.7:1:1:0:59.8:126:1:0:0.1 0/1:378:11:7,4:187,179:366,11:0.0291:2,2:20.1:1:32.4:1:0.54472:1.67:60:22:0.0294:0:1.1 +2 113980189 . G A 178 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.0555;LSEQ=ACCTTTCCAAGGATTTGGCC;RSEQ=CTCCAATGATCCCGTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:763:3:3,0:403,357:760,3:0.0039:2,0:6.3:1:22.3:1:0.25211:0:60:2:0.0027:0:2.3 0/1:728:75:38,37:342,311:653,75:0.103:2,2:22.7:1:28.7:1:0.80796:1.07062:60:150:0.1045:0:1.2 +2 113980203 . G A 149 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=37.85297;LSEQ=TTGGCCGCTCCAATGATCCC;RSEQ=TTTTCTGTTTCATCAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:790:1:1,0:421,366:787,1:0.0013:2,0:1:0:29:0:1:0:60:2:0.0013:0:1 0/1:741:34:17,17:359,348:707,34:0.0459:2,2:23.7:1:29.3:1:1:1.03157:60:68:0.0464:0:1.2 +2 113980645 . C G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00484;SOR=0.61637;LSEQ=CAATGGCTGAAATTTATACT;RSEQ=TAGTCAGGATTCTTTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:125:63,62:162,156:318,125:0.2815:2,2:22:1:32.7:1:1:1.02193:60:124:0.2838:0:1.1 0/1:360:70:34,36:144,146:290,70:0.1944:2,2:22.7:1:31:1:0.89471:1.04421:60:22.333:0.1882:0:1.1 +2 113980736 . C T 184 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=25.61651;LSEQ=TAGGCATCTCAATCATAACA;RSEQ=GGCCCAAAAAACTCTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:789:4:3,1:420,365:785,4:0.0051:2,2:35:1:26.8:1:0.62797:2.60:60:3:0.0038:0:1.3 0/1:666:77:39,38:324,265:589,77:0.1156:2,2:24.9:1:29.5:1:0.54315:1.19097:60:154:0.1165:0:1.1 +2 113981022 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.2815;LSEQ=GTCCCCTAACTGGTCTTTGT;RSEQ=CTTTCTCTCTTGACTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:110:50,60:152,200:352,110:0.2381:2,2:23.6:1:28.9:1:0.74129:1.10:60:54:0.2358:0:1.1 1/0:375:190:87,103:87,98:185,190:0.5067:2,2:23.5:1:28.3:1:0.83635:1.05085:60:94:0.5054:0:1.1 +2 113981137 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=2.65171;LSEQ=AAACTAGTTCCTGCCTTAGG;RSEQ=CCTTTGCCCTTGCTGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:161:88,73:317,240:557,161:0.2242:2,2:24.7:1:31.8:1:0.65211:1.09555:60:52.667:0.2225:0:1.2 0/1:569:247:129,118:170,148:318,247:0.4341:2,2:24.7:1:30.4:1:0.79908:1.05058:60:40.167:0.4342:0:1.1 +2 113981691 . T A 150 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06931;LSEQ=ATGGATGATGAAAGGATAGA;RSEQ=GGAAAGACAGATTAAAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:686:27:14,13:328,331:659,27:0.0394:2,2:30.6:1:31.7:1:0.8472:1.09:60:54:0.0398:0:1 0/0:707:2:1,1:380,325:705,2:0.0028:2,2:24.5:1:15.5:1:1:1.16897:60:0:0:0:1 +2 113981810 . A G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=1.8462;LSEQ=AGATGGATGATAGATAACTG;RSEQ=AAAGACAGATGAATTAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:661:267:103,164:165,229:394,267:0.4039:2,2:25.2:1:31.7:1:0.41996:1.147:59.8:65.75:0.4052:0:1.1 1/0:671:373:154,219:119,178:297,373:0.5559:2,2:25.6:1:30.4:1:0.75235:1.05:59.7:92.25:0.5566:0:1.1 +2 113982039 . AC GA 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04694;SOR=0.15231;LSEQ=GAGGCTGAGGCAGGAGAATC;RSEQ=TTGAACCCGGGAGGCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:7,9:0,0:0,16:0.6667:0,2:25.3:1:31.4:1:1:0:44.7:32:0.6957:0:1 0/1:9:2:2,0:0,0:0,2:0.2222:0,0:13.5:1:31:0:1:0:27:4:0.25:0:1 +2 113982143 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00199;SOR=2.1237;LSEQ=CCAAAAAAAAAAAAAAAAAA;RSEQ=GAAAGATGGATGGAAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:36:20,16:87,43:130,36:0.2105:2,2:12.1:1:29:1:0.23963:1.6138:54.9:11:0.2089:0:1.4 0/1:174:63:32,31:60,31:91,63:0.3621:2,2:11.1:1:29.3:1:0.06763:1.86719:59:126:0.4091:0:1.5 +2 113982413 . AAATAT A 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00305;SOR=Inf;LSEQ=TAAAAAAATAAAATAAAATA;RSEQ=AAAATAAAATAAAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:91,47:138,0:0:2,0:28.1:1:30.7:1:1:0:47.4:68:0.9927:0:0.1 0/1:88:6:4,2:48,34:82,6:0.0682:2,2:18:1:29:1:1:1.41:48:12:0.0706:0.0568:1 +2 113982414 . AATAT A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.02289;SOR=Inf;LSEQ=AAAAAAATAAAATAAAATAA;RSEQ=AAAATAAAATAAAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:92,47:139,0:0:2,0:28.1:1:30.5:1:1:0:47.5:45.333:1:0:0.1 0/1:90:4:3,1:50,35:85,4:0.0444:2,2:9.3:1:28.5:1:0.64444:2.08:42:8:0.0455:0.0333:0 +2 113982416 . TATAAAATAAAATAAA T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=9.000;MSILEN=5;SSF=0.00135;SOR=0.42922;LSEQ=AAAAATAAAATAAAATAAAA;RSEQ=ATAAAATAAAATAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:162:95:70,25:26,30:56,95:0.5864:2,2:25.5:1:31:1:0.00094:3.20:35.5:190:0.5901:0.2037:0.2 0/1:98:37:22,15:30,18:48,37:0.3776:2,2:23.9:1:29.9:1:0.82476:1.13465:37.4:74:0.3895:0.1429:0.3 +2 113982428 . TAAA T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13689;SOR=0;LSEQ=AAATAAAATATAAAATAAAA;RSEQ=ATAAAATAAAATAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:4:2,2:35,23:58,4:0.0323:2,2:11:1:33:0:1:1.51115:20.5:8:0.0645:0:0.5 0/0:93:0:0,0:45,18:63,0:0:2,0:17:1:27.9:1:1:0:50:126:1:0:0.3 +2 113982433 . TAAA T 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AAATATAAAATAAAATAAAA;RSEQ=ATAAAATAAAATAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:106,51:157,0:0:2,0:22.4:1:28.9:1:1:0:42.5:156:0.9936:0:0.2 0/1:115:12:9,3:64,33:97,12:0.1043:2,2:9.8:1:29.2:1:0.74732:1.54:57.3:24:0.1132:0.0522:0.4 +2 113982584 . T C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=3.27578;LSEQ=TATGGTGTAGAGGAAAGAGC;RSEQ=TTAGACTTGAAATTGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:558:130:54,76:185,242:427,130:0.233:2,2:24.4:1:32.3:1:0.76184:1.0758:60:42.333:0.2301:0:1.8 0/1:517:258:120,138:129,130:259,258:0.499:2,2:24.5:1:30.7:1:0.48177:1.14086:60:63.5:0.499:0:1.4 +2 113982608 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15909;SOR=0.79952;LSEQ=GACTTGAAATTGAAAAATCC;RSEQ=TGTTTGCATAACTCAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:113:50,63:191,210:401,113:0.2194:2,2:26:1:31:1:0.59378:1.1457:60:55.5:0.2198:0:1.9 0/1:496:91:48,43:192,212:404,91:0.1835:2,2:26.6:1:30:1:0.4167:1.23:60:90:0.1829:0:1.9 +2 113982769 . C G 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07591;SOR=Inf;LSEQ=TACATATTTGAATGGCTAGA;RSEQ=ATGCAAAAGTACATAATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:188,196:384,0:0:2,0:24:1:32.3:1:1:0:60:95:1:0:0.1 0/1:283:3:2,1:140,140:280,3:0.0106:2,2:7.7:1:32:1:1:2.00:60:6:0.0106:0:1.3 +2 113983156 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04843;SOR=Inf;LSEQ=GCAGTCAGTGTCCTAGTTGT;RSEQ=CTATTTTTTTTCTTTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:167,163:330,0:0:2,0:22.9:1:32.2:1:1:0:60:81.5:1:0:0.1 0/1:294:4:2,2:130,159:289,4:0.0136:2,2:23.3:1:26.5:1:1:1.22:60:8:0.0139:0:1 +2 113983157 . C A 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.34345;SOR=3.45354;LSEQ=CAGTCAGTGTCCTAGTTGTG;RSEQ=TATTTTTTTTCTTTTTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:1:1,0:166,165:331,1:0.003:2,0:1:0:25:0:1:0:60:2:0.003:0:1 0/1:290:3:2,1:128,158:286,3:0.0103:2,2:6:1:26.3:1:0.58985:2.46:60:6:0.0105:0:1 +2 113983159 . A AT 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02317;SOR=Inf;LSEQ=GTCAGTGTCCTAGTTGTGCT;RSEQ=TTTTTTTTCTTTTTCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:165,163:328,0:0:2,0:22.9:1:29.6:1:1:0:60:64.6:1:0:0.1 0/1:294:5:2,3:132,157:289,5:0.017:2,2:37.6:1:25.8:1:1:1.26016:60:4:0.0138:0:0 +2 113983367 . G A 125 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.12282;LSEQ=TCCTCCTCCTCTAAGCAGGC;RSEQ=GCAGGGGAAGGTGGAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:1:1,0:289,219:508,1:0.002:2,0:1:0:28:0:1:0:60:2:0.002:0:1 0/1:419:19:12,7:210,190:400,19:0.0453:2,2:24.2:1:29.6:1:0.48179:1.55:60:38:0.0455:0:1.2 +2 113983522 . AAGGG A 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.55585;SOR=1.47021;LSEQ=ATTTCACGCTCCAGAAGAGG;RSEQ=AGGGAGGGAGGGAGTCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:423:5:2,3:222,195:417,5:0.0118:2,2:33.4:1:31.4:1:0.66902:1.70552:60:10:0.0121:0:0 0/1:347:6:2,4:194,146:340,6:0.0173:2,2:35.3:1:29.2:1:0.4093:2.65011:60:12:0.0177:0:0 +2 113983689 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17694;SOR=Inf;LSEQ=CCCTCCCTCTTTCTCTCCCT;RSEQ=CCTTCCCTCTGCCCAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:107,154:261,0:0:2,0:23.6:1:31.5:1:1:0:60:64.25:1:0:0.1 0/1:190:2:1,1:71,117:188,2:0.0105:2,2:6.5:1:28:1:1:1.64:53.5:4:0.0108:0:1 +2 113983708 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.17887;SOR=Inf;LSEQ=TCCCTTCCCTCTGCCCAGGA;RSEQ=ATCCCAGCCCACCTGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:96,138:234,0:0:2,0:24:1:32.5:1:1:0:60:116:1:0:0.1 0/1:172:2:1,1:79,91:170,2:0.0116:2,2:29:1:29:0:1:1.15:60:4:0.012:0:1 +2 113983815 . T A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08618;SOR=Inf;LSEQ=CTAGGTAAATACGCCAAGTC;RSEQ=CTGGGGTCACAGCCAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:208,132:340,0:0:2,0:24.8:1:31.2:1:1:0:60:36.778:1:0:0.1 0/1:270:3:2,1:145,122:267,3:0.0111:2,2:14:1:21.3:1:1:1.68:60:2:0.0077:0:1.3 +2 113983840 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03456;SOR=Inf;LSEQ=GGTCACAGCCAGAGAGGCTG;RSEQ=CCTAGGGCTGGCATGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:207,138:345,0:0:2,0:25.3:1:31.5:1:1:0:60:48.286:1:0:0.1 0/1:263:4:3,1:153,106:259,4:0.0152:2,2:28:1:28.3:1:0.64809:2.07:60:8:0.0156:0:1.3 +2 113983869 . C A 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0344;SOR=Inf;LSEQ=TGGCATGGGGGTCACAGATG;RSEQ=CTTGTGTTCAGAGCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:255,170:425,0:0:2,0:23.5:1:31.6:1:1:0:60:46.222:1:0:0.1 0/1:323:4:3,1:187,132:319,4:0.0124:2,2:21:1:22.8:1:0.64594:2.11:60:3:0.0096:0:1 +2 113983937 . T C 222 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACCAGTGACAATGGCTCAA;RSEQ=TATGTCTCATCCATCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:635:0:0,0:313,322:635,0:0:2,0:25.5:1:30.5:1:1:0:60:104.833:1:0:0.1 0/1:555:147:74,73:211,197:408,147:0.2649:2,2:25.5:1:30.9:1:0.84743:1.05646:59.7:28.4:0.261:0:1.2 +2 113984033 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33793;LSEQ=TCTTCATTTGTCCAGACCTT;RSEQ=TCATCTTGAATCATCATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:309:199:77,122:44,66:110,199:0.644:2,2:23.1:1:29.9:1:0.90318:1.05608:60:48.75:0.6436:0:1.1 0/1:285:108:37,71:72,104:176,108:0.3789:2,2:23.3:1:29.3:1:0.31477:1.32715:60:107:0.3794:0:1.1 +2 113984227 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.10521;SOR=Inf;LSEQ=GAGATGTGAAGCATATATTT;RSEQ=ATCATCATCATCGTCATCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:174,157:331,0:0:2,0:24.3:1:32.3:1:1:0:59.9:164.5:1:0:0.2 0/1:297:3:2,1:148,146:294,3:0.0101:2,2:13.7:1:25.7:1:1:1.97:60:6:0.0102:0:1.3 +2 113984239 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.09015;SOR=Inf;LSEQ=ATATATTTCATCATCATCAT;RSEQ=GTCATCGTCATCATCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:171,139:310,0:0:2,0:24.2:1:31.2:1:1:0:59.9:76.5:1:0:0.2 0/1:253:3:2,1:136,113:249,3:0.0119:2,2:19.3:1:27:1:1:1.66:34.7:6:0.012:0:1 +2 113984246 . G GTCA 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=24;MSI=9.000;MSILEN=3;SSF=0.03634;SOR=1.56096;LSEQ=TCATCATCATCATCGTCATC;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:58:32,26:142,100:242,58:0.1902:2,2:30.9:1:31.2:1:0.65843:1.15319:59.8:57:0.1932:0.0098:0.6 0/1:231:62:33,29:95,64:159,62:0.2684:2,2:30.7:1:30.6:1:0.44855:1.30285:60:124:0.2719:0.026:0.6 +2 113984303 . T C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=2.16014;LSEQ=TTCAGATTTTACAGAACGGG;RSEQ=AAACTGGGATTCATCAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:413:117:73,44:182,112:294,117:0.2833:2,2:24:1:31.8:1:1:1.02:60:38:0.2822:0:1.1 0/1:332:153:86,67:103,76:179,153:0.4608:2,2:26.3:1:30.5:1:0.82475:1.05565:59.9:37.25:0.4571:0:1.2 +2 113984503 . C T 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATCATGGAGGGTAATGTAG;RSEQ=AGGCCTGGGAAGAAGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:215,168:383,0:0:2,0:25.3:1:32:1:1:0:60:41.556:1:0:0.1 0/1:326:42:25,17:160,124:284,42:0.1288:2,2:23.8:1:27.8:1:0.74097:1.14:60:41:0.1269:0:1.2 +2 113984515 . G T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04364;SOR=Inf;LSEQ=TAATGTAGCAGGCCTGGGAA;RSEQ=AAGGAGGCCGAGCTGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:232,182:414,0:0:2,0:24.9:1:32.5:1:1:0:60:58.143:1:0:0.1 0/1:350:4:2,2:191,154:345,4:0.0114:2,2:33:1:24.5:1:1:1.23948:60:3:0.0088:0:2.3 +2 113984562 . TG T 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGGGAGTCAGGACTGCAC;RSEQ=GGACATCGTCTCCAGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:275,253:528,0:0:2,0:25:1:31.8:1:1:0:60:263:1:0:0.2 0/1:440:29:15,14:201,209:410,29:0.0659:2,2:28.1:1:31.2:1:0.84873:1.11:59.8:58:0.0668:0.0068:0.4 +2 113984594 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.42155;LSEQ=TCCAGGCATTTACAAGGAGA;RSEQ=GCCCTCTTTGGTCCATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:86:43,43:245,238:483,86:0.1511:2,2:24.4:1:31.1:1:0.90744:1.02937:60:85:0.1507:0:1.2 0/1:473:33:14,19:208,232:440,33:0.0698:2,2:28.3:1:30.8:1:0.71817:1.21625:60:66:0.0705:0:1.2 +2 113985170 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.52718;LSEQ=GAGGTTATGTCTTCTGTTTT;RSEQ=TGTTACCCCCAACAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:96:54,42:172,192:364,96:0.2087:2,2:25.1:1:31.1:1:0.13577:1.43:59.5:47:0.2084:0:1.9 0/1:396:191:87,104:91,114:205,191:0.4823:2,2:25.3:1:29.4:1:0.84022:1.05:60:94.5:0.4859:0:1.3 +2 113985186 . C G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00749;SOR=0.5977;LSEQ=TTTTCTGTTACCCCCAACAG;RSEQ=AGCCAGCAGAGCAGTGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:94:53,41:156,193:349,94:0.2122:2,2:24.9:1:31.9:1:0.04824:1.60:59.5:46:0.2125:0:1.9 0/1:368:51:25,26:148,168:316,51:0.1386:2,2:27.5:1:29.9:1:0.88:1.09:60:50:0.1385:0:1.9 +2 113985902 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08311;SOR=Inf;LSEQ=AGGTGATGACCAGTATCCCA;RSEQ=CATATTTGTTAATAATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:125,224:349,0:0:2,0:24:1:32.4:1:1:0:59.9:48.857:0.9971:0:0.1 0/1:272:3:1,2:105,163:268,3:0.011:2,2:32.3:1:27.7:1:1:1.28717:60:6:0.0112:0:1 +2 113985910 . G T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32262;SOR=3.91017;LSEQ=ACCAGTATCCCAGCATATTT;RSEQ=TTAATAATGCCCATTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:1:0,1:126,211:337,1:0.003:2,0:20:0:26:0:1:0:60:2:0.003:0:1 0/1:261:3:1,2:103,155:258,3:0.0115:2,2:27.3:1:29:1:1:1.32763:60:6:0.0116:0:1 +2 113986019 . G A 39 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63692;SOR=0.43552;LSEQ=TCTCAGTCTCAGCAACATTG;RSEQ=CATGTTAGGCTGCACAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:2,1:104,119:223,3:0.0133:2,2:21.7:1:25:1:0.60133:2.28:60:2:0.0091:0:3 0/0:172:1:1,0:73,98:171,1:0.0058:2,0:1:0:24:0:0.43023:0:60:2:0.0059:0:1 +2 113986031 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16114;SOR=Inf;LSEQ=CAACATTGGCATGTTAGGCT;RSEQ=CACAATTCTTTGCTGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:102,109:211,0:0:2,0:24.4:1:32.3:1:1:0:59.8:69.333:1:0:0.1 0/1:142:2:2,0:56,84:140,2:0.0141:2,0:24.5:1:24:1:0.16512:0:60:4:0.0144:0:1 +2 113986071 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52365;SOR=0;LSEQ=AGGCTGTCCTGTGCATTGTA;RSEQ=GATGTTTAGCAGCATTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:83,78:161,2:0.0123:2,2:8.5:1:30:1:1:1.06373:60:4:0.0123:0:1 0/0:103:0:0,0:62,41:103,0:0:2,0:19.8:1:31:1:1:0:60:102:1:0:0.1 +2 113986086 . T C 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52566;SOR=0;LSEQ=TTGTAGGATGTTTAGCAGCA;RSEQ=TTCTGGCCTCCATCCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:93,71:164,2:0.012:2,2:17:1:35:1:1:1.30769:60:4:0.0123:0:1 0/0:103:0:0,0:71,32:103,0:0:2,0:20.7:1:30.1:1:1:0:60:102:1:0:0.1 +2 113986629 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02215;SOR=0.67617;LSEQ=GGATGCTAAATTAGCAAGGC;RSEQ=GGGCACTAAATCAAGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:127:73,54:242,195:437,127:0.2252:2,2:24.9:1:31.3:1:0.68613:1.09:60:41.333:0.225:0:1.1 0/1:402:66:36,30:169,166:335,66:0.1642:2,2:26.8:1:29.7:1:0.59107:1.18:60:32:0.1628:0:1.1 +2 113986858 . G GA 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.70945;SOR=1.19917;LSEQ=GTTTCTTCATATGCAAAATG;RSEQ=AAAAAAAAACATAGCTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:17:9,8:211,191:402,17:0.0406:2,2:28.6:1:30:1:1:1.02:59.4:16:0.0391:0.0048:0.2 0/1:290:14:7,7:139,133:272,14:0.0483:2,2:30.9:1:29.6:1:1:1.04497:60:28:0.0495:0:0.1 +2 113986881 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25514;LSEQ=AAAAAAACATAGCTGTAGGC;RSEQ=CCTTATTACAATTTCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:72:42,30:199,157:356,72:0.1678:2,2:22.8:1:31.5:1:0.79466:1.10:59.9:144:0.1718:0:1.1 0/1:307:15:11,4:152,139:291,15:0.0489:2,2:25.1:1:29.7:1:0.12127:2.51:60:30:0.0492:0:1.1 +2 113987465 . C T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1306;SOR=0;LSEQ=GTGATGGAAGAAGGTGGTGG;RSEQ=GGATTCAGGCCTGCTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:4:3,1:188,184:372,4:0.0106:2,2:19.5:1:31:1:0.62318:2.93:59.3:8:0.0107:0:1.5 0/0:312:0:0,0:151,161:312,0:0:2,0:25.3:1:30.4:1:1:0:60:61.4:1:0:0.2 +2 113987699 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08361;SOR=Inf;LSEQ=CTCCTGGCACCCAGTGTTGA;RSEQ=AAGGATTCTGAGGCAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:120,203:323,0:0:2,0:25.4:1:32.4:1:1:0:60:106.667:1:0:0.1 0/1:252:3:3,0:107,142:249,3:0.0119:2,0:14:1:26.7:1:0.08189:0:60:6:0.012:0:1 +2 113987725 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1758;SOR=Inf;LSEQ=TTCTGAGGCAGCCTGTGTCT;RSEQ=CCATGATCGGGGTGGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:96,172:268,0:0:2,0:24:1:32.2:1:1:0:60:52.6:1:0:0.1 0/1:194:2:1,1:75,117:192,2:0.0103:2,2:19.5:1:29.5:1:1:1.56:60:4:0.0104:0:1 +2 113987800 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50059;SOR=0;LSEQ=TTGCTGGTGCTGGCCTTGTG;RSEQ=CCTGCAGGGCTGCTTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:96,85:181,2:0.0109:2,2:17.5:1:29:1:1:1.12866:60:4:0.0114:0:1 0/0:161:0:0,0:76,84:160,0:0:2,0:23.8:1:30.5:1:1:0:60:52.333:1:0:0.1 +2 113987825 . C T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62643;SOR=0.37986;LSEQ=CAGGGCTGCTTCTGGCCTGG;RSEQ=AGCCTGTGGCCCCGCACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:2,1:108,75:183,3:0.0161:2,2:25:1:29.7:1:1:1.39:60:6:0.0167:0:1 0/0:162:1:0,1:86,75:161,1:0.0062:2,0:1:0:21:0:0.46914:0:60:2:0.0062:0:1 +2 113987835 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.21588;SOR=Inf;LSEQ=TCTGGCCTGGCAGCCTGTGG;RSEQ=CCCGCACTCCCCTTCCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:116,77:193,0:0:2,0:24.4:1:31.2:1:1:0:59.8:23.125:1:0:0.1 0/1:168:2:1,1:86,80:166,2:0.0119:2,2:28:1:27:1:1:1.07451:60:4:0.0124:0:1.5 +2 113987856 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21258;SOR=Inf;LSEQ=CCCGCACTCCCCTTCCCCCT;RSEQ=CCTTCATCCTGTTCCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:138,80:218,0:0:2,0:24.7:1:32.2:1:1:0:60:30.143:1:0:0.1 0/1:187:2:1,1:98,87:185,2:0.0107:2,2:16:1:27:1:1:1.12572:60:4:0.0109:0:1 +2 113987892 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08602;SOR=Inf;LSEQ=TTCTCGTTCTATTACCTGAA;RSEQ=CTGCTGCCTCTCGAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:152,96:248,0:0:2,0:26.5:1:32.1:1:1:0:60:247:1:0:0.1 0/1:197:3:2,1:107,87:194,3:0.0152:2,2:14.7:1:27.3:1:1:1.62:60:6:0.0154:0:1.3 +2 113988252 . A G 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACAATAAACTCTCCCAAC;RSEQ=GCCCTACAAAACTCTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:702:0:0,0:329,371:700,0:0:2,0:26.9:1:31.2:1:1:0:60:99:1:0:0.1 0/1:561:19:11,8:281,261:542,19:0.0339:2,2:26.4:1:30.7:1:0.64736:1.28:60:38:0.0344:0:1.1 +2 113988492 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.47205;LSEQ=TCCAACGTGGTCCTATTTTA;RSEQ=GAAGTTGACAGAAAGCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:112:49,63:178,164:342,112:0.2467:2,2:24.3:1:30.6:1:0.1568:1.39443:60:36.333:0.2466:0:1.1 1/0:323:172:77,95:67,84:151,172:0.5325:2,2:24.4:1:29.6:1:1:1.02:60:171:0.5377:0:1.1 +2 113988729 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00681;SOR=0.5901;LSEQ=AATTCCTTATCTCGTTCTGA;RSEQ=AGCAAGGAGAATTTATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:88:38,50:246,299:545,88:0.139:2,2:25.7:1:32.5:1:0.81746:1.08239:60:176:0.1413:0:1.1 0/1:506:44:23,21:207,255:462,44:0.087:2,2:22.6:1:30.3:1:0.34729:1.35:60:88:0.0885:0:1 +2 113989082 . C A 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07435;SOR=Inf;LSEQ=AATCACACTATCAGAGCCAC;RSEQ=AGGCGGAAATAAGTGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:200,190:390,0:0:2,0:23.1:1:32.1:1:1:0:60:96.5:1:0:0.1 0/1:284:3:3,0:146,135:281,3:0.0106:2,0:5.3:1:27:1:0.24918:0:60:6:0.0108:0:1 +2 113989122 . A AG 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.29194;LSEQ=AGAGAAAAACGCTATGAAGT;RSEQ=GTGAAGGAGTTGCAGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:93:60,33:199,127:326,93:0.222:2,2:26.1:1:32.2:1:0.62859:1.16:59.9:92:0.2228:0.0406:0.1 0/1:364:144:88,56:131,87:218,144:0.3956:2,2:23.3:1:30.7:1:0.91261:1.04:60:288:0.4045:0.0879:0.1 +2 113989236 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.85928;SOR=0.97771;LSEQ=GAATGAAAACTCACTGTGTC;RSEQ=TCTCTCCTCTCTCCTGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:981:195:91,104:367,418:785,195:0.1988:2,2:28.1:1:30.5:1:1:1.00341:59.9:38:0.1983:0:2 0/1:835:163:75,88:322,347:669,163:0.1952:2,2:25.7:1:29.4:1:0.66232:1.08868:59.9:80.5:0.1983:0:1.8 +2 113989267 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.27301;LSEQ=CTCCTGGTCTGCAGCATTAC;RSEQ=TAGGAATAATGTGGCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:847:184:70,114:254,409:663,184:0.2172:2,2:27.1:1:32.5:1:1:1.01137:59.6:183:0.2179:0:2.2 0/1:693:330:138,192:155,207:362,330:0.4762:2,2:27:1:30.8:1:0.81746:1.04176:59.5:109:0.4788:0:1.6 +2 113989327 . T C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.58888;LSEQ=TATTTTTTTCTTTTTTGAGA;RSEQ=GGAGTTTCGCTCTTGTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:57:15,42:37,173:210,57:0.2127:2,2:23.3:1:31.1:1:0.1855:1.67:52.4:114:0.2151:0:2.1 0/1:182:75:12,63:23,81:104,75:0.4121:2,2:20.7:1:29.8:1:0.34447:1.48748:54.2:74:0.4134:0:2 +2 113989558 . G A 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGTGATCCACCCACCTTG;RSEQ=CCTCCCAAAGTGCTGGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:143,83:226,0:0:2,0:20.5:1:31.7:1:1:0:51.7:112:1:0:0.1 0/1:206:62:37,25:97,47:144,62:0.301:2,2:19:1:28.9:1:0.3396:1.39213:52.1:124:0.3024:0:1.3 +2 113989968 . A G 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07886;SOR=Inf;LSEQ=GCCTCTGTGCTGAATTGTCA;RSEQ=CCCTTGGGCTAGGGGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:170,151:321,0:0:2,0:26.2:1:30.1:1:1:0:59.8:63.2:1:0:0.1 0/1:242:3:1,2:110,128:238,3:0.0124:2,2:25.7:1:22.3:1:1:1.71505:60:2:0.0086:0:1.7 +2 113990078 . C T 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04685;SOR=Inf;LSEQ=CACCAGCCTGAAAGATATGC;RSEQ=GGTGCTGCATATTTGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:181,192:373,0:0:2,0:24.5:1:30.4:1:1:0:59.9:73.6:1:0:0.2 0/1:326:4:1,3:169,153:322,4:0.0123:2,2:22.3:1:24.3:1:0.35245:3.30252:60:3:0.0094:0:1 +2 113990101 . G A 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.12401;SOR=0;LSEQ=TGCTGCATATTTGGCTGCCT;RSEQ=CTTCCTACATGACTACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:4:2,2:166,177:343,4:0.0115:2,2:21.5:1:29.5:1:1:1.07:60:8:0.0117:0:1 0/0:339:0:0,0:178,160:338,0:0:2,0:26.4:1:31.3:1:1:0:60:55.333:1:0:0.2 +2 113990242 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.46217;SOR=0.88108;LSEQ=GTTGGAGGCGTCACCTCTGA;RSEQ=TGACTGCATGTTGACAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:120:74,46:233,137:370,120:0.2449:2,2:22.4:1:32.6:1:0.82839:1.05709:59.8:119:0.2459:0:1.9 0/1:360:80:44,36:157,123:280,80:0.2222:2,2:22.7:1:31.1:1:0.89879:1.04425:60:79:0.2219:0:1.9 +2 113990261 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.18027;LSEQ=ATTGACTGCATGTTGACAGG;RSEQ=GATGCTAACAGGATGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:578:120:72,48:267,190:457,120:0.2076:2,2:25.1:1:30.4:1:0.83502:1.07:59.8:119:0.2073:0:1.9 1/0:411:215:119,96:109,87:196,215:0.5231:2,2:24.2:1:28.9:1:1:1.0107:60:34.833:0.5186:0:1.4 +2 113990393 . C A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.47557;LSEQ=ATACATCTATCCACTTCCAG;RSEQ=TGCCCTACATCCTTCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:133:64,69:186,232:418,133:0.2409:2,2:26.4:1:30.5:1:0.485:1.16:60:132:0.244:0:1.1 0/1:477:210:100,110:130,136:266,210:0.4403:2,2:27:1:28.9:1:0.85347:1.05133:60:69:0.4376:0:1.2 +2 113990440 . C T 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGGTCTTGCCAAGCTTCT;RSEQ=CGCGGCTTCCACAGCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:204,260:464,0:0:2,0:25:1:31.6:1:1:0:59.8:65.286:1:0:0.3 0/1:425:45:21,24:159,221:380,45:0.1059:2,2:26.3:1:28.9:1:0.63261:1.22:60:44:0.1055:0:1.6 +2 113990504 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07396;SOR=Inf;LSEQ=CACACCCTCACCCCTTGCCT;RSEQ=CCCCATGACCGCCGCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:98,184:282,0:0:2,0:25.5:1:31.7:1:1:0:60:39.286:1:0:0.1 0/1:205:3:0,3:71,130:201,3:0.0146:2,0:23:1:26.3:1:0.55298:0:60:2:0.0101:0:1 +2 113990509 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17875;SOR=Inf;LSEQ=CCTCACCCCTTGCCTGCCCC;RSEQ=TGACCGCCGCCAGCTCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:93,178:271,0:0:2,0:25.3:1:30.7:1:1:0:60:89.333:1:0:0.1 0/1:199:2:1,1:69,128:197,2:0.0101:2,2:28:1:32:1:1:1.85:60:4:0.0102:0:1 +2 113990552 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.52974;SOR=0;LSEQ=GCCATTCTCAGAAGACATGC;RSEQ=GGCTTGCGTAACTCCCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:72,121:193,2:0.0103:2,2:26:1:32:0:1:1.68:60:4:0.0104:0:1 0/0:117:0:0,0:41,76:117,0:0:2,0:25:1:30:1:1:0:59.9:234:1:0:0.5 +2 113990597 . CCCCCT C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=5.000;MSILEN=5;SSF=0.25252;SOR=4.13415;LSEQ=ACATGAACCTCTTCTCCTCA;RSEQ=CCCCTCCCCTCCCCTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:1:1,0:74,79:153,1:0.0065:2,0:27:0:35:0:0.48701:0:43:2:0.0069:0:8 0/1:76:2:1,1:31,43:74,2:0.0263:2,2:25:1:29:1:1:1.38:60:4:0.0274:0.0132:1.5 +2 113990602 . T TC 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.66631;SOR=0.39054;LSEQ=AACCTCTTCTCCTCACCCCC;RSEQ=CCCCTCCCCTCCCCTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:5:5,0:64,74:138,5:0.0336:2,0:49.4:1:25.1:1:0.0242:0:47.8:4:0.0367:0.0201:3.4 0/1:75:1:1,0:27,44:71,1:0.0133:2,0:35:0:32:0:0.38889:0:40:2:0.0179:0:4 +2 113990621 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=0.27522;SOR=0;LSEQ=CTCCCCTCCCCTCCCCTCCC;RSEQ=TCCCTTCCCTTCCCCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:3:1,2:84,77:161,3:0.0183:2,2:24.7:1:26:1:0.60925:2.1718:60:6:0.0189:0:2.3 0/0:111:0:0,0:63,47:110,0:0:2,0:15.4:1:30:1:1:0:58.5:26.5:1:0:0.7 +2 113990872 . G A 62 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23852;SOR=2.13932;LSEQ=GGATGTCCCTCTCTTCTAAG;RSEQ=AAACTTCTCACATTAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:4:2,2:264,487:751,4:0.0053:2,2:10.5:1:17.5:1:0.61641:1.84:47.8:0.333:0.0014:0:4 0/1:621:7:4,3:248,366:614,7:0.0113:2,2:7:1:22.3:1:0.44991:1.97:58.3:2.5:0.0085:0:2.3 +2 113990907 . G GA 206 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.01842;SOR=0.66596;LSEQ=AGGTGCTGGGATGTACGGAG;RSEQ=AAAAAAAAAAAAAAACCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:123:27,96:71,116:187,123:0.3075:2,2:25.8:1:29.7:1:0.00396:2.17091:58.5:29.75:0.3199:0.0575:1.4 0/1:320:73:12,61:86,119:205,73:0.2281:2,2:31.6:1:28.8:1:6e-05:3.65808:57.6:23.333:0.2365:0:1.8 +2 113990922 . A C 97 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0374;SOR=3.96823;LSEQ=CGGAGGAAAAAAAAAAAAAA;RSEQ=CCCGGGTGCCAGCCAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:3:1,2:84,257:341,3:0.0087:2,2:8.3:1:18.3:1:0.57443:1.53:53:0.5:0.003:0:5 0/1:267:9:4,5:73,173:246,9:0.0337:2,2:8:1:30.9:1:0.45972:1.89:56.7:18:0.0347:0:1.2 +2 113990923 . C A 92 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGAAAAAAAAAAAAAAA;RSEQ=CCGGGTGCCAGCCAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:61,247:308,0:0:2,0:21.5:1:29.8:1:1:0:57.9:8.625:1:0:1.1 0/1:239:14:9,5:47,178:225,14:0.0586:2,2:8.6:1:24.4:1:0.00091:6.74:57.2:3.667:0.05:0:3 +2 113990941 . A G 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCCGGGTGCCAGCCAGAA;RSEQ=GAAAATGTAGAGCCAGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:43,185:228,0:0:2,0:25.6:1:31.6:1:1:0:58.2:27.5:1:0:1 0/1:187:18:2,16:36,133:169,18:0.0963:2,2:25:1:30.2:1:0.53649:2.15816:57.6:17:0.0955:0:1.9 +2 113990977 . G T 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5023;SOR=0;LSEQ=GTTATAAAAAAGGGTCCATG;RSEQ=GCTGGGTGCAGTGGCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:31,110:141,2:0.014:2,2:14:0:28:1:0.3987:3.51:60:4:0.0147:0:1.5 0/0:119:0:0,0:29,90:119,0:0:2,0:27:1:30.3:1:1:0:58.9:58.5:1:0:0.6 +2 113991254 . C CA 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.94143;LSEQ=AACAGAGTGAGATTCCATCT;RSEQ=AAAAAACAAAAAAACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:11:10,1:83,19:102,11:0.0909:2,2:16.9:1:31.8:1:0.68566:2.28:47.7:22:0.1068:0:2 0/1:93:8:7,1:64,11:75,8:0.086:2,2:22.1:1:30.3:1:1:1.20:41.4:16:0.1026:0:3.3 +2 113991259 . AAC A 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0.90351;LSEQ=AGTGAGATTCCATCTCAAAA;RSEQ=AAAAAAACAAAAAAAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:3,0:119,48:167,3:0.0175:2,0:22.3:1:32:0:0.55958:0:48.3:6:0.0178:0:0 0/1:126:2:1,1:90,34:124,2:0.0159:2,2:15.5:1:28:1:0.48:2.62343:47.5:4:0.0159:0:1.5 +2 113991261 . C A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.23415;SOR=1.59266;LSEQ=TGAGATTCCATCTCAAAAAA;RSEQ=AAAAAAACAAAAAAAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:186:158:113,45:0,0:0,158:0.8495:0,2:13.9:1:30.8:1:1:0:53.8:157:0.8674:0:2 1/1:130:117:85,32:0,0:0,117:0.9:0,2:15.8:1:29.4:1:1:0:54.1:116:0.9134:0:2.1 +2 113991269 . C CA 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.41783;SOR=1.56027;LSEQ=CATCTCAAAAAACAAAAAAA;RSEQ=AAAAAAAAAAGGGTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:7:4,3:150,70:220,7:0.0285:2,2:15.6:1:30.1:1:0.68349:1.60358:59.6:14:0.0343:0.0122:1 0/1:160:7:5,2:105,41:146,7:0.0438:2,2:15.7:1:30.2:1:1:1.02423:54.9:14:0.0511:0.0125:1.7 +2 113991518 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03165;SOR=Inf;LSEQ=GATGGACTGTCTGACTCTGG;RSEQ=CTGCCTCTGTGACAGGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:137,216:353,0:0:2,0:24.2:1:31.5:1:1:0:59.9:69.6:1:0:0.1 0/1:259:4:2,2:93,160:253,4:0.0154:2,2:26.8:1:28.5:1:0.62787:1.72:60:8:0.0157:0:1 +2 113991554 . G A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1308;SOR=Inf;LSEQ=GTCTCACACACCCCACCCAC;RSEQ=CACTGGTCTCTGCTCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:133,202:335,0:0:2,0:25.4:1:31.4:1:1:0:59.9:82.75:0.991:0:0.1 0/1:192:2:1,1:84,106:190,2:0.0104:2,2:6:0:31.5:1:1:1.26:57.5:4:0.0107:0:1 +2 113991561 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1353;SOR=Inf;LSEQ=ACACCCCACCCACGCACTGG;RSEQ=CTCTGCTCCAGCATTTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:132,204:336,0:0:2,0:25.7:1:30.1:1:1:0:59.9:66.2:1:0:0.1 0/1:196:2:1,1:85,109:194,2:0.0102:2,2:8:1:31:1:1:1.28:60:4:0.0104:0:1 +2 113991567 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05024;SOR=Inf;LSEQ=CACCCACGCACTGGTCTCTG;RSEQ=TCCAGCATTTCAAGGTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:138,203:341,0:0:2,0:25.4:1:33.1:1:1:0:59.9:112.667:0.9971:0:0.1 0/1:201:3:1,2:88,110:198,3:0.0149:2,2:8:1:27.3:1:1:1.59641:60:6:0.0151:0:1.3 +2 113991570 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29904;SOR=3.52925;LSEQ=CCACGCACTGGTCTCTGCTC;RSEQ=AGCATTTCAAGGTCGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:1:0,1:144,208:352,1:0.0028:2,0:1:0:23:0:1:0:60:2:0.0029:0:1 0/1:201:2:1,1:87,112:199,2:0.01:2,2:26.5:1:27.5:1:1:1.29:60:4:0.0102:0:1 +2 113991793 . T A 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CTTGAGGTATCTGAAGACCA;RSEQ=ATGGGTCTCTGCTTCCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:138,168:306,0:0:2,0:24.8:1:29.7:1:1:0:59.9:75.5:1:0:0.1 0/1:221:12:5,7:108,101:209,12:0.0543:2,2:20.8:1:29.9:1:0.56291:1.4943:60:24:0.0545:0:1 +2 113991841 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2631;SOR=0;LSEQ=CATCTCAGGCCCTCTCCAAC;RSEQ=CAAGCCAAGCGCTTGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:140,156:296,3:0.01:2,2:28.3:1:29.7:1:1:1.7915:60:6:0.0102:0:1.7 0/0:226:0:0,0:109,117:226,0:0:2,0:25.3:1:30.1:1:1:0:60:112:1:0:0.2 +2 113991871 . C T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17082;SOR=Inf;LSEQ=CGCTTGACTCTCAGCCATTC;RSEQ=TCAGGCCCTGGCTGGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:134,135:269,0:0:2,0:24.7:1:31.9:1:1:0:60:52.8:1:0:0.2 0/1:190:2:1,1:85,103:188,2:0.0105:2,2:6.5:1:30.5:1:1:1.21:56.5:4:0.0106:0:1.5 +2 113991948 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19197;SOR=Inf;LSEQ=GAGGTCTGACTCATGCAGTG;RSEQ=AGGCCCAGGCCTCAACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:163,80:243,0:0:2,0:27.2:1:32.4:1:1:0:60:59.75:1:0:0.3 0/1:190:2:1,1:127,61:188,2:0.0105:2,2:15:1:28.5:1:0.54731:2.07328:60:4:0.0106:0:3 +2 113991970 . A G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.28478;LSEQ=GGCCCAGGCCTCAACCAGCT;RSEQ=CAGATGGTGCTCCTGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:69:46,23:146,76:222,69:0.2371:2,2:23.9:1:32.2:1:1:1.04:60:68:0.2353:0:1.1 0/1:243:101:65,36:91,50:141,101:0.4156:2,2:25.2:1:31:1:1:1.00797:60:100:0.4132:0:1.2 +2 113992201 . G A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78118;SOR=0.7663;LSEQ=TATGCCTCCTGGGTTCAAGC;RSEQ=ATTCTCCTGCCTCGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:16:2,14:16,28:44,16:0.2667:2,2:21.6:1:31.7:1:0.11206:3.92072:38.6:32:0.2712:0:1 0/1:23:5:4,1:3,15:18,5:0.2174:2,2:21.8:1:29:1:0.01727:16.56:45:10:0.2174:0:1 +2 113992344 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00058;SOR=Inf;LSEQ=TGACCTTGTGATCCACCTGC;RSEQ=TCGGCCTCCCAAACTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:155,34:189,0:0:2,0:22:1:31.3:1:1:0:48.2:36.8:1:0:0.4 0/1:175:10:8,2:127,38:165,10:0.0571:2,2:26.7:1:30.7:1:1:1.20:42.1:20:0.0575:0:2 +2 113992360 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1136;SOR=Inf;LSEQ=CTGCCTCGGCCTCCCAAACT;RSEQ=CTGGAATTACAGGGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:188,75:263,0:0:2,0:21.5:1:32.2:1:1:0:52.8:130.5:1:0:0.5 0/1:248:3:1,2:169,74:243,3:0.0121:2,2:14.3:1:25.7:1:0.22636:4.53601:60:6:0.0123:0:1.7 +2 113992365 . A G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12101;SOR=Inf;LSEQ=TCGGCCTCCCAAACTGCTGG;RSEQ=ATTACAGGGGTGAGCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:194,87:281,0:0:2,0:22.3:1:30.1:1:1:0:53.8:92.667:0.9964:0:0.5 0/1:277:3:1,2:185,89:274,3:0.0108:2,2:10.3:1:29.7:1:0.25204:4.13397:43:6:0.011:0:6.7 +2 113992374 . G C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00156;SOR=1.63885;LSEQ=CAAACTGCTGGAATTACAGG;RSEQ=GTGAGCCACCTCGCCCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:136:84,52:141,67:208,136:0.3931:2,2:23.4:1:30.4:1:0.29682:1.30174:54.2:26.2:0.391:0:1.1 1/0:332:171:111,60:100,52:152,171:0.5151:2,2:24.4:1:30.1:1:0.90704:1.03939:55.1:56:0.5169:0:1.3 +2 113992515 . G T 131 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.12956;LSEQ=AGATGTCTGACTGTCCTCCC;RSEQ=GTGATGCTGTTAAGCTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:572:2:1,1:311,258:569,2:0.0035:2,2:23.5:1:31.5:1:1:1.20503:60:4:0.0036:0:1 0/1:476:21:11,10:239,215:454,21:0.0441:2,2:22.9:1:30:1:1:1.01055:60:42:0.0451:0:1.2 +2 113992624 . T C 228 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=260.96486;LSEQ=AAATGGGCTCCAAAAGCCAA;RSEQ=TCCTTTTTCCCTCCAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:809:1:0,1:359,448:807,1:0.0012:2,0:1:0:32:0:1:0:60:2:0.0013:0:1 0/1:683:167:80,87:247,267:514,167:0.2445:2,2:26.6:1:30.9:1:1:1.00603:60:32.4:0.2411:0:1.1 +2 113992792 . G T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31615;SOR=4.10911;LSEQ=ACAGCATCCGCCCCTTCCGA;RSEQ=CATGTCTTCCCCGTCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:1:0,1:108,189:297,1:0.0033:2,0:1:0:26:0:1:0:60:2:0.0034:0:1 0/1:220:3:1,2:85,132:217,3:0.0136:2,2:19:1:28.7:1:1:1.28644:60:6:0.014:0:1.3 +2 113992800 . TCC T 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=2e-04;SOR=2.05077;LSEQ=CGCCCCTTCCGAGCATGTCT;RSEQ=CCGTCACAGAGAACTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:75:27,48:77,135:212,75:0.2613:2,2:23.7:1:31.3:1:1:1.01394:60:74:0.2671:0.0453:0.1 0/1:221:93:37,56:52,76:128,93:0.4208:2,2:24.4:1:30.5:1:1:1.03541:60:186:0.4247:0.0407:0.2 +2 113992872 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50474;SOR=0;LSEQ=TAGGGAACAGGGTGGGGGTG;RSEQ=ATGAGACTGAGGCCAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:64,106:170,2:0.0116:2,2:34.5:1:28.5:1:1:1.65:60:4:0.012:0:1 0/0:138:0:0,0:54,84:138,0:0:2,0:23.7:1:29.9:1:1:0:60:26.6:1:0:0.2 +2 113993073 . A G 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTTGCTGCAGATCCAAAA;RSEQ=GGCGGAGCTAGATAAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:0:0,0:280,189:469,0:0:2,0:25:1:30.9:1:1:0:59.9:92.8:1:0:0.2 0/1:364:25:14,11:193,145:338,25:0.0687:2,2:33:1:31.3:1:1:1.04571:60:50:0.0691:0:1.2 +2 113993235 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16334;SOR=Inf;LSEQ=ACACGCACAAGCCAAGCCGT;RSEQ=GGATGTGGAGGGTGCGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:94,150:244,0:0:2,0:23.2:1:31.6:1:1:0:60:80.333:1:0:0.2 0/1:166:2:1,1:68,96:164,2:0.012:2,2:31.5:1:28:1:1:1.41:60:4:0.0121:0:2 +2 113993252 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16697;SOR=Inf;LSEQ=CGTGGGATGTGGAGGGTGCG;RSEQ=GCGGGGCGCGGGGCAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:77,122:199,0:0:2,0:24.5:1:31:1:1:0:60:48.75:1:0:0.2 0/1:138:2:1,1:59,77:136,2:0.0145:2,2:31.5:1:27.5:1:1:1.30:60:4:0.0146:0:2 +2 113993253 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51336;SOR=0;LSEQ=GTGGGATGTGGAGGGTGCGG;RSEQ=CGGGGCGCGGGGCAGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:74,118:192,2:0.0103:2,2:19:1:27:1:1:1.59:60:4:0.0105:0:1 0/0:137:0:0,0:60,77:137,0:0:2,0:24.1:1:31:1:1:0:60:67.5:1:0:0.2 +2 113993331 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.50584;SOR=0;LSEQ=CACGAGGCGTGGCAAGGCGG;RSEQ=GAGAGAGAAGCTAGACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:42,70:112,2:0.0175:2,2:30:1:29:1:1:1.66:60:4:0.0179:0:1 0/0:88:0:0,0:37,51:88,0:0:2,0:24.1:1:30.7:1:1:0:60:176:1:0:0.6 +2 113993344 . A C 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=3.61364;LSEQ=AAGGCGGGGAGAGAGAAGCT;RSEQ=GACCTCCCTGCTGCGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:20:6,14:34,57:91,20:0.1802:2,2:21.4:1:27.9:1:0.61418:1.3878:60:5.667:0.1574:0:1.7 0/1:81:36:16,20:19,26:45,36:0.4444:2,2:23.2:1:30.1:1:1:1.09:60:72:0.4444:0:1.5 +2 113993385 . C G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02712;SOR=2.30182;LSEQ=GCAGCGAAAATGGAGAGACC;RSEQ=GGAAGGCGTGTGTGCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:19:6,13:29,37:66,19:0.2235:2,2:26:1:30.2:1:0.43098:1.68791:60:18:0.2169:0:1.7 0/1:60:24:13,11:15,21:36,24:0.4:2,2:27.9:1:29.5:1:0.43096:1.64:60:23:0.4035:0:1.8 +2 113993527 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52893;SOR=0;LSEQ=CCCCTGGGCCCACCTTGAGG;RSEQ=CCGGCCTAGGACTGGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:13,25:38,2:0.05:2,2:32:1:31.5:1:1:1.89:22:4:0.0513:0:1 0/0:23:0:0,0:10,13:23,0:0:2,0:28.9:1:30.3:1:1:0:22.5:22:1:0:0.1 +2 113993583 . A G 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63791;SOR=1.61995;LSEQ=CCTTGCGGGAGCCGCCTAGG;RSEQ=CCGGAGGCGCGACCCCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:22,35:57,2:0.0339:2,2:17.5:1:33.5:1:1:1.58:25.5:4:0.0339:0:1 0/1:37:2:1,1:17,18:35,2:0.0541:2,2:16.5:1:32.5:1:1:1.06:26.5:4:0.0541:0:1 +2 113993592 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50802;SOR=0;LSEQ=AGCCGCCTAGGACCGGAGGC;RSEQ=CGACCCCTCGGCCCAGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:23,37:60,2:0.0323:2,2:14:1:28.5:1:1:1.60:22.5:4:0.0333:0:1 0/0:45:0:0,0:22,23:45,0:0:2,0:9.7:1:28.8:1:1:0:23.6:14:1:0:0.2 +2 113993631 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25151;SOR=0;LSEQ=TGAGGCCCGGCCTAGGACCG;RSEQ=AGGCGCGACCCCTCGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:3:1,2:15,22:37,3:0.075:2,2:43.3:1:29.3:1:1:1.35343:22:6:0.075:0:1.3 0/0:31:0:0,0:17,14:31,0:0:2,0:42.8:1:30.3:1:1:0:24.3:30:1:0:0.2 +2 113993895 . T C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09192;SOR=Inf;LSEQ=CTTGAGGCCCGGCCTAGGAC;RSEQ=GGAGGCGCGACCCCTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,14:30,0:0:2,0:11.4:1:28.8:1:1:0:37.7:9:0.9643:0:0.1 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:6.5:1:28:1:1:1.36624:29:4:0.1429:0:1.5 +2 113993983 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=CTTGAGGCCCGGCCTAGGAC;RSEQ=GGAGGCGCGACCCCTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:10,2:12,2:0.1429:2,2:29.5:1:32.5:1:0.3956:4.28175:20.5:4:0.1429:0:1 0/0:7:0:0,0:3,4:7,0:0:2,0:6.3:1:28.9:1:1:0:30.9:14:1:0:0.1 +2 113994069 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52736;SOR=0;LSEQ=ACCTGGCGGCCCGGCCGGCA;RSEQ=AGCCCGCCTCTCCTCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:116,65:181,2:0.0109:2,2:23:1:29:1:1:1.77857:59.5:4:0.0112:0:1 0/0:112:0:0,0:68,44:112,0:0:2,0:23.2:1:30.8:1:1:0:56.4:27:1:0:0.4 +2 113994074 . C T 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84094;LSEQ=GCGGCCCGGCCGGCACAGCC;RSEQ=GCCTCTCCTCTCCAGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:120,75:195,2:0.0102:2,2:19:1:33:1:1:1.59599:60:4:0.0103:0:1 0/0:117:1:0,1:69,47:116,1:0.0085:2,0:2:0:26:0:0.41026:0:60:2:0.0088:0:2 +2 113994079 . C T 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCGGCCGGCACAGCCCGCCT;RSEQ=TCCTCTCCAGGCCAGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:124,79:203,0:0:2,0:23.3:1:32:1:1:0:58:66.667:1:0:0.2 0/1:120:26:16,10:56,38:94,26:0.2167:2,2:23.3:1:28.8:1:1:1.09:57.7:12:0.2069:0:1.2 +2 113994082 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14277;SOR=Inf;LSEQ=GCCGGCACAGCCCGCCTCTC;RSEQ=TCTCCAGGCCAGGGCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:125,80:205,0:0:2,0:23.6:1:31.5:1:1:0:58.5:40:1:0:0.2 0/1:125:2:1,1:73,50:123,2:0.016:2,2:24.5:1:30.5:1:1:1.45545:60:4:0.0164:0:1.5 +2 113994118 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5866;SOR=2.52294;LSEQ=CCCACACCTTCCGCCTGACA;RSEQ=CCAGCCAAGCTCTTCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:1:0,1:103,117:220,1:0.0045:2,0:50:0:29:0:1:0:60:2:0.0047:0:1 0/1:176:2:1,1:93,81:174,2:0.0114:2,2:32.5:1:27:1:1:1.14724:60:4:0.0116:0:1 +2 113994119 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20119;SOR=Inf;LSEQ=CCACACCTTCCGCCTGACAG;RSEQ=CAGCCAAGCTCTTCAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:100,117:217,0:0:2,0:27.6:1:31.4:1:1:0:60:42.4:1:0:0.2 0/1:177:2:1,1:94,81:175,2:0.0113:2,2:35:1:27.5:1:1:1.15951:60:4:0.0115:0:2 +2 113994145 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19794;SOR=Inf;LSEQ=AAGCTCTTCAGTCCCCCGCC;RSEQ=TCCACCTGCCAGGGAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:79,120:199,0:0:2,0:26.1:1:32:1:1:0:60:65.333:1:0:0.2 0/1:160:2:1,1:75,83:158,2:0.0125:2,2:13:1:27.5:1:1:1.11:60:4:0.0125:0:1 +2 114000920 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCTGACATCTTCAACTT;RSEQ=AGCCTACCTTGTGCTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:44:1:28.5:1:1:0:60:4:1:0:1 +2 114002052 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13894;SOR=Inf;LSEQ=TGTCATTGTCACAGACGCCC;RSEQ=CAGCCAGGAGCCGGTCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:33,20:53,0:0:2,0:31.2:1:31.5:1:1:0:60:106:1:0:0.2 0/1:32:2:1,1:18,12:30,2:0.0625:2,2:37:1:31:1:1:1.48061:60:4:0.0645:0:1 +2 115200297 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=AAGTCCAATAGAGGAGACTT;RSEQ=ATCTCTAGTTCATTCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:1,10:11,0:0:2,0:28.2:1:31.9:1:1:0:60:22:1:0:0 0/1:17:2:1,1:5,10:15,2:0.1176:2,2:9.5:1:26.5:1:1:1.91:60:4:0.1176:0:1 +2 117045275 . C A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATAGACTCTTTGACAG;RSEQ=AGTGACTTTCCAAAACCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:11:0:32.5:1:1:0:30.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 117045438 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22229;SOR=0;LSEQ=GCTTCTGAACTCAGGCAATG;RSEQ=CTTTCAAACTCTTATACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:25,19:44,2:0.0435:2,2:14.5:1:27.5:1:1:1.30786:43.5:4:0.0435:0:1 0/0:51:0:0,0:30,21:51,0:0:2,0:25.4:1:30.8:1:1:0:41.9:102:1:0:0.3 +2 117045503 . C T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26095;SOR=0.57853;LSEQ=TCTCTCCTTTCTAGGTCCCA;RSEQ=GACAGCCATCTTGCTACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:18:6,12:8,17:25,18:0.4186:2,2:20.3:1:31:1:1:1.06:37.3:36:0.4286:0:1.1 0/1:41:12:5,7:11,18:29,12:0.2927:2,2:18.1:1:30.3:1:1:1.16:40.6:24:0.2927:0:1 +2 119592580 . GA G 61 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGGGCTCACCTGGTGCAG;RSEQ=AAAGTTCAGTTGGCAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:0,0:0,4:0.8:0,2:33.3:1:30.5:1:1:0:60:8:1:0:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 119592934 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50913;SOR=0;LSEQ=TACCAGGGGAAGGGCGCTCC;RSEQ=CTTTTCCCTGGTAATACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:82,67:149,2:0.0132:2,2:39:1:30:1:1:1.22223:60:4:0.0137:0:2 0/0:112:0:0,0:59,53:112,0:0:2,0:24.3:1:29.9:1:1:0:60:55:1:0:0.6 +2 119592943 . T G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50845;SOR=0;LSEQ=AAGGGCGCTCCCCTTTTCCC;RSEQ=GGTAATACTCCGGGAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:86,72:158,2:0.0125:2,2:38:1:30:1:1:1.19311:60:4:0.0128:0:2 0/0:120:0:0,0:65,55:120,0:0:2,0:24.7:1:29.8:1:1:0:60:240:1:0:0.7 +2 119592977 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14343;LSEQ=GAGCCCCTACTCGGAAGCCC;RSEQ=AGAGTCAAAGGGATACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:175:162:82,80:5,8:13,162:0.9257:2,2:26.6:1:30.9:1:0.56604:1.64:60:161:0.9253:0:1.2 1/0:136:87:42,45:22,27:49,87:0.6397:2,2:25.9:1:30.1:1:0.72408:1.14:60:86:0.637:0:1.2 +2 119594426 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAATTGCCTGCACTCTGC;RSEQ=AAATGGACAAGTCCTGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 119594504 . C G 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGCTGTGGTCGTTACTGGGA;RSEQ=TCGCTTTTGTTTTCTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:11:0:28:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:30.5:1:1:0:60:4:1:0:1 +2 119641913 . A G 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GCCAGCGGGTCGGTCCAAGG;RSEQ=TCCTCACTAGAAATTGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:1:0:30:0:1:0:43:2:0.3333:0:4 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:30:1:1:0:26:4:1:0:3.5 +2 119641921 . T C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTCGGTCCAAGGATCCTCAC;RSEQ=AGAAATTGTTAGTTGAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:7.5:1:33.5:1:1:0:41.5:4:0.5:0:3.5 1/0:4:2:1,1:2,0:2,2:0.5:0,2:32:1:30.5:1:1:0:26:4:0.5:0:3.5 +2 119641926 . A G 53 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6977;LSEQ=TCCAAGGATCCTCACTAGAA;RSEQ=TTGTTAGTTGAGCTCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:10:1:34:1:1:0:39.7:6:0.6:0:3 1/0:4:2:1,1:2,0:2,2:0.5:0,2:37:1:31:1:1:0:26:4:0.5:0:3.5 +2 119641993 . G A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71525;SOR=1.47899;LSEQ=GTTTGATGGCCTCAATCCTA;RSEQ=AGGAAACAAATTTTACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:8,1:9,6:0.4:2,0:22.7:1:31:1:1:0:49.8:12:0.4:0:2 1/0:14:7:5,2:7,0:7,7:0.5:0,2:30.4:1:29.6:1:0.46154:0:53.3:14:0.5:0:1.4 +2 119642167 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15556;SOR=Inf;LSEQ=CCTTTTCCTGTAAACGCCGG;RSEQ=CAGCATCTCTTACTATCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:13,20:33,0:0:2,0:25:1:31.3:1:1:0:41.5:66:1:0:0 0/1:22:2:1,1:6,14:20,2:0.0909:2,2:22:1:30:1:1:2.24:26:4:0.0952:0:1 +2 120048537 . G A 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1321;LSEQ=AGCTATCAGACGCCAAGGCT;RSEQ=ACTTACAGGGGGACAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:12.9:1:26.6:1:1:0:60:6:0.6:0:1.7 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:40.5:1:26:1:1:0:60:4:0.6667:0:2 +2 120048550 . A T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68017;SOR=1.94206;LSEQ=CAAGGCTGACTTACAGGGGG;RSEQ=CAAACCTATTGAACACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:18.3:1:29.8:1:1:0:60:12:0.4286:0:2 1/0:10:6:6,0:4,0:4,6:0.6:0,0:14.7:1:30.2:1:1:0:60:12:0.6:0:2.2 +2 120048632 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0144;SOR=2.43896;LSEQ=AGGCCCAGACAGACTCTGCT;RSEQ=CCACCTGGTGGCTGAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:73:44:33,11:27,2:29,44:0.6027:2,2:23.4:1:28.1:1:0.06302:4.42108:60:88:0.6197:0:1.2 1/0:85:67:44,23:12,6:18,67:0.7882:2,2:24.2:1:27.5:1:1:1.04492:60:66:0.7857:0:1.3 +2 120048649 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4999;SOR=Inf;LSEQ=GCTGCCACCTGGTGGCTGAA;RSEQ=GGTAGGCAAAGGCGGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:74,21:95,0:0:2,0:21.2:1:32:1:1:0:60:22.75:1:0:0.8 0/1:109:2:1,1:68,39:107,2:0.0183:2,2:30.5:1:28.5:1:1:1.73419:60:4:0.0183:0:1 +2 120048677 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49899;SOR=Inf;LSEQ=AAAGGCGGACAAGTGCAGAG;RSEQ=CACTCCACCTGACCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:90,46:136,0:0:2,0:25.3:1:31.4:1:1:0:60:18.429:1:0:0.8 0/1:147:2:1,1:87,58:145,2:0.0136:2,2:30.5:1:29.5:1:1:1.49572:60:4:0.014:0:2.5 +2 120048729 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=3.82227;LSEQ=CGCGTAACGAGGCTCTGCTA;RSEQ=TATGGCAGGAAAGGTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:114:55,59:62,58:120,114:0.4851:2,2:25:1:32.4:1:0.69488:1.14603:60:113:0.485:0:1.2 1/0:226:177:98,79:25,24:49,177:0.7832:2,2:25.5:1:31.5:1:0.62884:1.19:60:354:0.7832:0:1.2 +2 120048774 . A T 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AGGAGAAGCTGCTCGGCAAG;RSEQ=TGTAAAGATGAACGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:99,141:240,0:0:2,0:25.8:1:30.8:1:1:0:60:119:1:0:0.5 0/1:221:16:7,9:97,108:205,16:0.0724:2,2:21.9:1:28.1:1:0.80207:1.15401:60:32:0.0748:0:1.8 +2 120048803 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5019;SOR=0;LSEQ=TGAACGGCTGGGCATTAATC;RSEQ=GCTGGTGCCTGGCAGGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:74,117:191,2:0.0104:2,2:6.5:1:29.5:1:1:1.58:60:4:0.0105:0:3 0/0:164:0:0,0:66,98:164,0:0:2,0:24:1:29.5:1:1:0:60:40:1:0:0.4 +2 120048808 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21333;SOR=Inf;LSEQ=GGCTGGGCATTAATCGGCTG;RSEQ=TGCCTGGCAGGTATCTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:70,110:180,0:0:2,0:26.9:1:31.8:1:1:0:59.9:89:1:0:0.3 0/1:155:2:1,1:59,94:153,2:0.0129:2,2:20.5:1:27:1:1:1.59:60:4:0.0132:0:1.5 +2 121107321 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15408;SOR=Inf;LSEQ=CGCATGCGGGGTCTGAACCC;RSEQ=GGCACGGTGAACTCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:25,16:41,0:0:2,0:25.1:1:30.8:1:1:0:60:82:1:0:0.1 0/1:27:2:1,1:16,9:25,2:0.0741:2,2:33:1:29.5:1:1:1.73837:60:4:0.0741:0:1 +2 121107864 . A G 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCGCCTTCCGAGCACACAT;RSEQ=AAAGCACAAAGACAGAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:27:0:28:0:1:0:60:2:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:35.5:1:30:1:1:1:60:4:0.5:0:1 +2 121726310 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50184;SOR=0;LSEQ=TGTCCCGTTTCTCCAGCCCG;RSEQ=GGGTGACGCCCCGCCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:2,0:121,22:143,2:0.0138:2,0:20.5:1:26.5:1:1:0:60:4:0.0138:0:1.5 0/0:122:0:0,0:99,23:122,0:0:2,0:23.2:1:31.1:1:1:0:60:60:1:0:0.1 +2 121726338 . G T 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33389;SOR=3.6361;LSEQ=GCCCCGCCTGAGCCGCAAGC;RSEQ=GGCGCTGTCCATCTCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:1:0,1:186,90:276,1:0.0036:2,0:1:0:26:0:0.32852:0:60:2:0.0036:0:1 0/1:231:3:1,2:138,89:227,3:0.013:2,2:10.7:1:22.3:1:0.56393:3.08563:60:2:0.0089:0:1 +2 121726353 . C T 34 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08882;SOR=Inf;LSEQ=CAAGCGGGCGCTGTCCATCT;RSEQ=CCCACTCTCAGACGCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:208,146:354,0:0:2,0:25.4:1:31.5:1:1:0:60:58:1:0:0.2 0/1:287:3:1,2:159,125:284,3:0.0105:2,2:7.7:1:22:1:0.58567:2.53587:60:2:0.007:0:2.3 +2 121726439 . A G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16042;SOR=0;LSEQ=CCTACATCAACAACTCCCGA;RSEQ=GCAGCTCGGCGGCCAGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:4:2,2:54,156:210,4:0.0187:2,2:18.8:1:26.3:1:0.2807:2.87:60:3:0.0144:0:1.5 0/0:136:0:0,0:40,96:136,0:0:2,0:47:0:16:0:1:0:60:0:0:0:2 +2 121726447 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00321;SOR=0;LSEQ=AACAACTCCCGAAGCAGCTC;RSEQ=GCGGCCAGCGGTTCCTACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:166:166:31,135:0,0:0,166:1:0,2:20.8:1:31.4:1:1:0:60:40.5:1:0:1.1 1/1:106:100:24,76:1,5:6,100:0.9434:2,2:17.7:1:28.9:1:1:1.57:60:13.286:0.949:0:1.2 +2 121726469 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54113;SOR=0;LSEQ=CGGCCAGCGGTTCCTACGGG;RSEQ=ATCTGTCAGCGGGTGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:0,2:2,83:85,2:0.023:1,0:25.5:1:29.5:1:1:0:60:4:0.0238:0:2 0/0:47:0:0,0:0,47:47,0:0:1,0:21.7:1:31.6:1:1:0:60:46:1:0:1 +2 121726496 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13426;SOR=Inf;LSEQ=CAGCGGGTGCCCTCAGGTGA;RSEQ=CCCCGCCTGCAAGCAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:2,48:50,0:0:1,0:24.9:1:32.1:1:1:0:60:24:1:0:0.6 0/1:30:2:0,2:0,28:28,2:0.0667:1,0:40:1:30:1:1:0:60:4:0.0667:0:2 +2 121726571 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCGCTGGCTTTTCAGTG;RSEQ=GCGCTTTTGACCCGAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:1,19:20,2:0.0909:1,2:28:1:30:1:0.17749:13.79:60:4:0.0952:0:1 0/0:9:0:0,0:1,8:9,0:0:2,0:27:1:31:1:1:0:60:18:1:0:0 +2 121735497 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCATGTGTTATTTTTCTA;RSEQ=TGAAACAAAATATGTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 121735983 . C T 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGCCTCTGGCCCTGCTTAC;RSEQ=CTCTTCTGGGCATGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:19:13,6:187,96:283,19:0.0629:2,2:23.5:1:30:1:1:1.11:60:18:0.061:0:1.2 0/0:268:0:0,0:177,91:268,0:0:2,0:22.2:1:30.1:1:1:0:59.8:133:1:0:0.2 +2 121736077 . G T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01562;SOR=Inf;LSEQ=CCGCTGGCAGGCCTGCACGC;RSEQ=GGAGCAGAAGCCCTTCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:628:0:0,0:326,302:628,0:0:2,0:23.6:1:30.4:1:1:0:60:77.5:1:0:0.1 0/1:486:5:2,3:251,230:481,5:0.0103:2,2:18:1:27.4:1:0.6743:1.6353:60:4:0.0084:0:1.2 +2 121736194 . CA C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10477;SOR=Inf;LSEQ=CCCCACCCCCGCCGCAGCAT;RSEQ=AGACTGGCCTGTCAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:34,151:185,0:0:2,0:23.6:1:30.6:1:1:0:60:25.429:1:0:0.2 0/1:166:3:0,3:33,130:163,3:0.0181:2,0:19:1:32:1:1:0:60:6:0.0183:0.006:0 +2 121740190 . C T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATGCTTCTGAGTGCGCTGA;RSEQ=GGGTTGGAGCAGAGCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:33:33,0:0,0:0,33:0.9706:0,1:25.8:1:32.3:1:1:0:60:66:1:0:2 1/1:12:12:11,1:0,0:0,12:1:0,2:26.1:1:30.4:1:1:0:60:24:1:0:2.1 +2 121740194 . T G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTGAGTGCGCTGACGGG;RSEQ=TGGAGCAGAGCAGAGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:35,0:0,0:0,35:1:0,1:26.9:1:32.3:1:1:0:60:70:1:0:2.1 1/1:13:13:11,2:0,0:0,13:1:0,2:28:1:31.1:1:1:0:60:26:1:0:2 +2 121740348 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.09823;SOR=Inf;LSEQ=AACCTGAAGACACACCTGCG;RSEQ=TCCCACACCGGGGAGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:212,116:328,0:0:2,0:27:1:31.4:1:1:0:60:53.667:1:0:0.1 0/1:282:3:1,2:175,104:279,3:0.0106:2,2:17.7:1:27.3:1:0.55857:3.35042:60:6:0.0109:0:1.3 +2 121740454 . G A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05129;SOR=Inf;LSEQ=AGAATCGCACCCACTCCAAC;RSEQ=AGGTACCTCTGCGGGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:44,168:212,0:0:2,0:21.7:1:31.4:1:1:0:60:52:1:0:0.4 0/1:194:4:2,2:53,137:190,4:0.0206:2,2:12.3:1:26:1:0.31865:2.57:60:8:0.0208:0:1 +2 121740505 . C T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=GCACACTGGGGCCCCACTGA;RSEQ=GCCCCATGGCTTCCAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:4,78:0,0:0,82:1:0,1:25.2:1:29.3:1:1:0:60:10.714:1:0:1.1 1/1:44:36:2,34:1,7:8,36:0.8182:2,2:23.5:1:27.7:1:0.46089:2.36808:60:6.2:0.7949:0:1.1 +2 121740609 . CTT C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55882;SOR=0.35469;LSEQ=CTCAGATACAGACCAGGACT;RSEQ=TGAGACCTAGACAGACCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,1:1,9:0.9:0,0:25.9:1:32.6:1:1:0:57.2:18:0.9:0.1:1.1 1/0:8:6:0,6:0,2:2,6:0.75:0,0:16.3:1:31.4:1:1:0:60:12:0.75:0.375:0.5 +2 121740743 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAATAAATATAATAGTG;RSEQ=CCTCCCCAAAGGCCATCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 122466293 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24814;SOR=Inf;LSEQ=CGTATGGATTTCTTCACCGG;RSEQ=GCTTTTTCTTCAGCTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:76,82:158,0:0:2,0:28.5:1:31:1:1:0:46.2:157:1:0:0.1 0/1:166:3:1,2:79,83:162,3:0.0181:2,2:14.3:1:31:0:1:1.89648:55.3:6:0.0183:0:1 +2 122466505 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49635;SOR=Inf;LSEQ=TAAGTGCTGTCCACTAATAT;RSEQ=CACTGGCCCTGAACCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:27,39:66,0:0:2,0:24.1:1:31.7:1:1:0:34.4:21:1:0:0.1 0/1:68:2:1,1:25,41:66,2:0.0294:2,2:26.5:1:29:0:1:1.63:26:4:0.0299:0:1.5 +2 122466563 . T C 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00076;SOR=Inf;LSEQ=GGTGGTGTGATTTCAAAGCC;RSEQ=CCAAGGGAATCCTTTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:43,79:122,0:0:2,0:22.2:1:30.5:1:1:0:39.4:23.4:1:0:0.1 0/1:104:9:5,4:32,63:95,9:0.0865:2,2:30.2:1:30:1:0.27481:2.44:28.4:18:0.0909:0:1.2 +2 122466739 . G GT 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.27296;SOR=0;LSEQ=ACACCAGGTTTTTTTTTGTT;RSEQ=TTTTTTTTTTGAGATAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:1,2:6,21:27,3:0.1:2,2:34:1:31.3:1:1:1.71:60:6:0.1034:0:1 0/0:19:0:0,0:4,10:14,0:0:2,0:24.1:1:31.5:1:1:0:60:28:0.7778:0:0.6 +2 123421479 . TTGC T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=11.000;MSILEN=3;SSF=0.05022;SOR=Inf;LSEQ=GTCACCACATCAAAAAAGCT;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:18,0:0:2,0:25.2:1:30.4:1:1:0:51.7:36:1:0:0.4 0/1:21:5:3,2:11,5:16,5:0.2381:2,2:27.2:1:29:1:1:1.43927:47.8:10:0.25:0.0476:0.8 +2 123421570 . A G 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07737;SOR=0.32407;LSEQ=GCTGCTGCTGAGCCCAACTT;RSEQ=TCCTTGGTGCTGCTCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:4,7:4,7:11,11:0.5:2,2:32.7:1:33.6:1:1:1:54.4:22:0.5238:0:1.5 0/1:25:6:4,2:6,13:19,6:0.24:2,2:38.7:1:30.8:1:0.1753:4.06:60:12:0.25:0:1.2 +2 123421606 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.05766;SOR=0;LSEQ=TGGCCTGAGTCCGGGTTCCC;RSEQ=GGGCCCTGCCATGCATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:4,6:10,3:0.2308:2,2:21.3:1:30:1:1:1.30472:60:6:0.2308:0:1 0/0:19:0:0,0:6,13:19,0:0:2,0:22.6:1:28.9:1:1:0:60:38:1:0:0.4 +2 125301057 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACAGGCTGAGTAGTGAA;RSEQ=GCTTGTAAAGTTGGCGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:9:1:30.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 125301394 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01921;LSEQ=AATGCCATCTAAAGCCTCTT;RSEQ=ATTTAATAAAAAGGAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:40:31,9:41,5:46,40:0.4651:2,2:20.7:1:29.9:1:0.24097:2.35658:60:80:0.4651:0:1.5 0/1:83:39:31,8:34,10:44,39:0.4699:2,2:27.4:1:29.3:1:1:1.14:60:78:0.4699:0:1.4 +2 125301476 . C A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.87869;SOR=1.02481;LSEQ=GTTTCTACAGTGGATTCTAA;RSEQ=TAGAATCACCTAGGTTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:170:99,71:113,83:196,170:0.4645:2,2:25.6:1:30.6:1:0.91591:1.02:60:169:0.4656:0:2 0/1:323:152:82,70:92,79:171,152:0.4706:2,2:28.7:1:29.3:1:1:1.01:59.8:37:0.4684:0:2 +2 125301502 . G T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82414;SOR=1.04002;LSEQ=TCACCTAGGTTTACTAAAAT;RSEQ=CAACAATTGGACCAGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:171:84,87:101,99:200,171:0.4597:2,2:27.1:1:30.2:1:0.83521:1.05646:60:84.5:0.4617:0:1.9 0/1:360:169:88,81:94,96:190,169:0.4694:2,2:26.2:1:28.4:1:0.67258:1.11:59.9:32.8:0.4686:0:1.9 +2 125301528 . G GT 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.23758;SOR=0.81337;LSEQ=ATTGGACCAGATGCTAGCTA;RSEQ=TTTTTTTTTCCTGCTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:117:41,76:81,104:185,117:0.3703:2,2:29:1:30:1:0.14917:1.44195:60:116:0.373:0.0285:1.4 0/1:303:98:41,57:87,95:182,98:0.3234:2,2:29.1:1:29:1:0.37941:1.27207:60:48:0.3265:0.0033:1.3 +2 125301538 . C T 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02851;SOR=Inf;LSEQ=ATGCTAGCTAGTTTTTTTTT;RSEQ=CTGCTAATTTTCTTGTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:93,182:275,0:0:2,0:25.9:1:31.3:1:1:0:60:90.667:1:0:0.7 0/1:272:5:3,2:108,159:267,5:0.0184:2,2:10.8:1:24.4:1:0.40112:2.20:50.4:4:0.0154:0:4.2 +2 125301638 . T C 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.81019;SOR=0.7947;LSEQ=GACACTGAGGTTCACAGGTA;RSEQ=GAAATTACTTTCCCAAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:19:0,19:0,26:26,19:0.4222:1,1:31.7:1:29.3:1:1:0:60:18:0.4091:0:1.2 0/1:30:11:0,11:1,18:19,11:0.3667:1,0:28:1:28.7:1:1:0:60:22:0.3667:0:1.1 +2 125301742 . C T 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36364;SOR=0;LSEQ=AAGTTAAACTAACCATCTAA;RSEQ=AGGTCTTAAGGGATCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:1,6:0,3:3,7:0.7:0,2:17.7:1:27.6:1:1:0:60:6:0.6667:0:1.6 0/0:1:0:0,0:0,1:1,0:0:0,0:33:0:34:0:1:0:60:2:1:0:0 +2 125301795 . T A 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTATCCATGCAAGGCTAG;RSEQ=TAGTGCTTGGACTAAGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:18.3:1:32:1:1:0:53.3:8:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 125424512 . T TG 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00465;SOR=0.39996;LSEQ=AAGATGTTCAGGATGGTGCA;RSEQ=AACTACAGCAAAGAACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:90:75,15:15,6:21,90:0.8036:2,2:23.6:1:32.1:1:0.22426:1.99:60:89:0.8091:0.1696:0.9 1/0:92:57:46,11:29,6:35,57:0.6196:2,2:20.6:1:30.9:1:1:1.15399:60:114:0.6196:0.1522:0.9 +2 125424553 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0028;SOR=0.51217;LSEQ=GGGAGACTATTACTCTGGAC;RSEQ=TTAAATACACATTTTATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:253:204:141,63:30,19:49,204:0.8063:2,2:22.3:1:30.7:1:0.31028:1.42:60:408:0.8063:0:1.8 1/0:194:132:93,39:41,21:62,132:0.6804:2,2:26:1:30.2:1:0.61776:1.22:60:131:0.6788:0:1.8 +2 125424600 . TG T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.06705;SOR=0.74592;LSEQ=ATGTGCTTTAAGAAGAACGA;RSEQ=GGGGAAACATGAGCAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:409:300:159,141:58,50:108,300:0.7335:2,2:28.2:1:31.8:1:0.91098:1.02862:60:600:0.7389:0.0709:1.5 1/0:351:236:124,112:65,50:115,236:0.6724:2,2:27.1:1:30.4:1:0.49594:1.17365:59.8:472:0.6743:0.0684:1.5 +2 125424612 . G T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01162;SOR=0.66534;LSEQ=AAGAACGATGGGGGAAACAT;RSEQ=AGCAATGATTGGGCAGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:420:318:168,150:50,52:102,318:0.7571:2,2:26.7:1:29.6:1:0.56926:1.16:60:52:0.7554:0:1.5 1/0:378:255:129,126:64,59:123,255:0.6746:2,2:26:1:28.5:1:0.82662:1.05933:59.9:254:0.6737:0:1.5 +2 125424686 . G A 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20021;SOR=4.36447;LSEQ=CTTTAAACATCTTGGTAGCT;RSEQ=GGAAAGATTAACCAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:1:1,0:60,136:196,1:0.0051:2,0:1:0:24:0:0.30964:0:60:2:0.0051:0:1 0/1:183:4:2,2:59,120:179,4:0.0219:2,2:25.8:1:24.3:1:0.60167:2.03:60:3:0.0165:0:1.3 +2 125424690 . A C 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02427;SOR=Inf;LSEQ=AAACATCTTGGTAGCTGGGA;RSEQ=AGATTAACCAAGGAATGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:52,129:181,0:0:2,0:24.1:1:30.7:1:1:0:60:59.333:1:0:0.3 0/1:166:5:1,4:51,110:161,5:0.0301:2,2:27:1:33:1:1:1.84849:60:10:0.0301:0:1.4 +2 127721295 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21187;SOR=Inf;LSEQ=GCATGGTTCTGGGGTTGGGG;RSEQ=TCTAGGCCCCCGTGGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:28,23:51,0:0:2,0:27.2:1:32.6:1:1:0:60:102:1:0:0.1 0/1:44:2:1,1:24,18:42,2:0.0455:2,2:26:1:31:1:1:1.32452:60:4:0.0476:0:1 +2 127773880 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52367;SOR=Inf;LSEQ=GGAATTGGCTGCCAGCCTCA;RSEQ=CCCTGAGGACGTGCCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:17,0:0:2,0:24.5:1:33.3:1:1:0:58.2:34:1:0:0 0/1:29:2:1,1:18,9:27,2:0.069:2,2:30.5:1:30:0:1:1.94942:60:4:0.0714:0:2 +2 127773898 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.54839;SOR=Inf;LSEQ=CAGCCCTGAGGACGTGCCCG;RSEQ=GCAGGGTTTATCTGCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,8:20,0:0:2,0:31.1:1:30.3:1:1:0:60:19:0.95:0:0 0/1:42:2:1,1:23,17:40,2:0.0476:2,2:38:1:29:1:1:1.34309:60:4:0.0476:0:2 +2 127773985 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23729;SOR=0;LSEQ=TCTACCCCCAGAGGGAGCTA;RSEQ=GGGTGTGTGGCCCCAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:10,17:27,2:0.069:2,2:13.5:1:33.5:1:1:1.67:60:4:0.069:0:2 0/0:30:0:0,0:10,19:29,0:0:2,0:26.6:1:29.4:1:1:0:60:28:0.9655:0:0.3 +2 127774020 . T C 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01686;SOR=Inf;LSEQ=AGGCCCACCCTCCCCAACAG;RSEQ=AGGCTCCTTCTGGGCCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:4,11:15,0:0:2,0:25.2:1:26.9:1:1:0:60:14:1:0:0.2 0/1:14:5:1,4:2,7:9,5:0.3571:2,2:17.8:1:32:1:1:1.1321:60:10:0.3846:0:1.2 +2 127965811 . A C 34 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CTGGCATAACCCACGGAGAG;RSEQ=AGGAAGAACAGTGTAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:23:1:34.5:1:1:0:60:4:0.5:0:1.5 0/0:4:0:0,0:2,2:4,0:0:2,0:32.3:1:28.5:1:1:0:60:8:1:0:0.5 +2 127965845 . A G 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.51811;LSEQ=TAGTGCAGTGGCCCACCTGG;RSEQ=AGCCACACGGGGAAGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:8,2:0.2:2,2:22.5:1:33.5:1:1:2.64575:60:4:0.2:0:1 0/1:9:1:1,0:5,3:8,1:0.1111:2,0:29:0:26:0:1:0:60:2:0.1111:0:1 +2 127965922 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49675;SOR=Inf;LSEQ=GGCTACCCAGCTGGGGAAAC;RSEQ=GTGCTTTTTCCACAGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:25,0:0:2,0:18.8:1:30.9:1:1:0:60:50:1:0:0.1 0/1:31:2:1,1:21,8:29,2:0.0645:2,2:29:1:31:0:0.50323:2.53312:59:4:0.0645:0:1 +2 127966823 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=AAGTGAACCCCCAGCAAACT;RSEQ=CAGCAGCCCTACAGAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:40.5:1:29:1:1:1.18:58.5:4:0.1538:0:1 0/0:7:0:0,0:4,3:7,0:0:2,0:19:1:30.4:1:1:0:47.9:14:1:0:0.1 +2 128014913 . C T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38462;SOR=0;LSEQ=TCAGAACGGTAACATAAATA;RSEQ=ACCTTAAATATTAACATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:27.5:1:27.9:1:1:0:56.1:7:0.6364:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:40:0:32:0:1:0:60:2:1:0:0 +2 128015066 . A G 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00175;SOR=Inf;LSEQ=TCCTCAGCACAATTTGGCCA;RSEQ=CGCTGGAGGGAAGGTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:93,2:95,0:0:1,0:23.7:1:30:1:1:0:60:46.5:1:0:0.2 0/1:82:8:8,0:69,5:74,8:0.0976:2,0:19:1:29.6:1:1:0:60:7:0.0864:0:1.1 +2 128015350 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24205;SOR=Inf;LSEQ=GTTAGTCTCCAGAAGAAAAG;RSEQ=TACTCCTTTTATAATACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:26,180:206,0:0:2,0:24.6:1:30.9:1:1:0:59.7:40.2:1:0:0.6 0/1:200:2:1,1:33,165:198,2:0.01:2,2:20.5:1:29.5:1:0.31181:4.94:60:4:0.0101:0:1.5 +2 128015356 . CT C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.21292;SOR=Inf;LSEQ=CTCCAGAAGAAAAGATACTC;RSEQ=TTTATAATACTTATAATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:22,170:192,0:0:2,0:22.9:1:30.4:1:1:0:59.7:63:1:0:0.7 0/1:165:2:0,2:26,137:163,2:0.0121:2,0:29.5:1:32.5:1:1:0:60:4:0.0121:0:0 +2 128015367 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.028;SOR=0.50635;LSEQ=AAGATACTCCTTTTATAATA;RSEQ=TTATAATCACAGCAAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:146:121:7,114:0,25:25,121:0.8288:1,2:23.9:1:30.5:1:0.6037:0:59.5:120:0.8333:0:1.1 1/0:124:88:7,81:4,32:36,88:0.7097:2,2:23.7:1:29.4:1:0.72862:1.44187:60:176:0.7097:0:1.1 +2 128015370 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50404;SOR=0;LSEQ=ATACTCCTTTTATAATACTT;RSEQ=TAATCACAGCAAATTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:4,135:139,2:0.0141:1,2:24:1:31:1:0.06991:30.29:60:4:0.0143:0:2 0/0:114:0:0,0:8,106:114,0:0:2,0:22.7:1:29.9:1:1:0:60:113:1:0:0.8 +2 128016761 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.13314;SOR=Inf;LSEQ=TCCGTGTTTTCCAACATTTC;RSEQ=AAAAAAATCCCATGGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:160,1:161,0:0:1,0:24.1:1:31.7:1:1:0:60:39.25:1:0:0.1 0/1:93:2:1,1:90,1:91,2:0.0215:1,2:31:1:28.5:1:0.04278:63.9884:60:4:0.022:0:1 +2 128018710 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1982;SOR=Inf;LSEQ=TAATCTCCTAATGCTTGGTG;RSEQ=CTGCCTGCTGACAGTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:190,15:205,0:0:2,0:24.6:1:32.5:1:1:0:60:101.5:1:0:0 0/1:165:2:1,1:140,23:163,2:0.0121:2,2:12.5:1:30.5:1:0.27051:5.98006:60:4:0.0123:0:1 +2 128018973 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22488;SOR=Inf;LSEQ=GAAGACAACATTAGCCATTA;RSEQ=AATGCCAAGAGCTAAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:30,178:208,0:0:2,0:22.4:1:32.4:1:1:0:59.7:68.333:1:0:0.1 0/1:189:2:1,1:20,167:187,2:0.0106:2,2:41:1:28.5:1:0.2104:8.17:60:4:0.0108:0:1 +2 128019178 . G C 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATAAGGGATTTGTATCTA;RSEQ=GTTATACAAAGAACTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:37.5:1:28:0:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 128028792 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.96541;LSEQ=AGGTCTTTGCTTTGGGATTC;RSEQ=CTCCCTCCAGAGTCTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:145:121:118,3:24,0:24,121:0.8345:1,1:26.1:1:31.9:1:1:0:60:242:0.8403:0:1.1 1/1:88:73:72,1:15,0:15,73:0.8295:1,1:23.1:1:30.5:1:1:0:60:23.333:0.8235:0:1.1 +2 128029065 . GA G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.0061;SOR=0.56487;LSEQ=GGAAGGTTTTTATATATGAG;RSEQ=AAAAAAAAAAGTCAACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:84:15,69:42,128:170,84:0.3218:2,2:29.1:1:31.8:1:0.26393:1.50702:59.9:168:0.3294:0.0153:0.1 0/1:232:49:11,38:53,127:180,49:0.2112:2,2:26.2:1:30.3:1:0.37404:1.43947:60:48:0.2115:0.0086:0.2 +2 128029082 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22081;SOR=Inf;LSEQ=GAGGAAAAAAAAAAAGTCAA;RSEQ=TGATCCAGAATTTAAATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:34,172:206,0:0:2,0:24.5:1:32.8:1:1:0:59.9:40.2:1:0:0.3 0/1:184:2:1,1:41,141:182,2:0.0109:2,2:41:1:30:1:0.40538:3.41:60:4:0.0113:0:1 +2 128030377 . T C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3115;LSEQ=AATTCACTGTCCAGGAATCA;RSEQ=AGTGTACCCCCCAGGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:76:55,21:338,107:445,76:0.1459:2,2:22.8:1:32.6:1:0.5641:1.20563:60:152:0.1467:0:1.1 0/1:436:22:13,9:293,121:414,22:0.0505:2,2:28.4:1:30.7:1:0.24098:1.67426:60:44:0.0507:0:1.2 +2 128036654 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20106;SOR=Inf;LSEQ=GGAGCCCAAGAAGTTCCTGA;RSEQ=AGAAAAACAAAAAAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:143,4:147,0:0:1,0:21.8:1:32.5:1:1:0:60:23.5:1:0:0.2 0/1:120:2:1,1:101,17:118,2:0.0167:2,2:35.5:1:27.5:1:0.27857:5.80234:60:4:0.0167:0:1 +2 128036662 . C CA 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20017;SOR=Inf;LSEQ=AGAAGTTCCTGAGAGAAAAA;RSEQ=AAAAAAACAAAACAACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:166,10:176,0:0:2,0:20.5:1:31.7:1:1:0:60:24.143:1:0:0.1 0/1:143:2:2,0:122,19:141,2:0.014:2,0:15:1:30.4:1:1:0:60:4:0.014:0.007:0 +2 128036701 . G T 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06563;SOR=0;LSEQ=CCACCTTCTGCACTCTCAAT;RSEQ=GGGAAGAGAAACTGGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:5:3,2:294,93:387,5:0.0128:2,2:9.6:1:29.4:1:0.59858:2.1029:60:10:0.0128:0:1 0/0:334:0:0,0:232,102:334,0:0:2,0:23.2:1:30.8:1:1:0:60:54.667:1:0:0.1 +2 128037201 . G A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52857;SOR=0;LSEQ=TACAAAAATTAGCTGGGTGT;RSEQ=GTAGTGCATGTCTGTAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:0,9:9,4:0.3077:0,0:33.5:1:33:1:1:0:51.5:8:0.3077:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:5:1:31:1:1:0:36.3:6:1:0:0 +2 128037478 . C T 27 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGATTTTTAAATGCAATCA;RSEQ=ATCCAGGGAGTTATTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:7:1:27.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 128037942 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50939;SOR=0;LSEQ=TAAGTCCTGACCTGTGTCTG;RSEQ=CCATGAGGAATCGATCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:149,19:168,2:0.0118:2,2:17:1:27.5:1:0.22207:7.66904:60:4:0.012:0:1.5 0/0:126:0:0,0:111,15:126,0:0:2,0:23.5:1:31.1:1:1:0:60:41:1:0:0.1 +2 128037999 . C T 146 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=31.38241;LSEQ=GGAGGAGGCCCTTTCCCAGA;RSEQ=GCCCCCAGCCCAGGCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:1:0,1:318,138:456,1:0.0022:2,0:1:0:30:0:0.30416:0:60:2:0.0022:0:1 0/1:465:30:20,10:285,148:433,30:0.0645:2,2:25.6:1:29.9:1:1:1.04:60:60:0.0654:0:1.1 +2 128038005 . C A 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCCTTTCCCAGACGCCCC;RSEQ=AGCCCAGGCCCAGCTACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:25:19,6:325,168:493,25:0.0483:2,2:21.2:1:29.7:1:0.38715:1.64:58.2:11.5:0.0451:0:1.3 0/0:511:0:0,0:326,184:510,0:0:2,0:25.5:1:30.2:1:1:0:60:38.231:0.998:0:0.3 +2 128038065 . C T 165 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=49.31975;LSEQ=ATGTAGCCATTATTCTGCAG;RSEQ=TCCATCCAGTTGGCTTCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:780:1:0,1:390,387:777,1:0.0013:2,0:1:0:27:0:0.49871:0:60:2:0.0013:0:1 0/1:822:49:28,21:391,382:773,49:0.0596:2,2:23.6:1:29.5:1:0.38164:1.30:59.9:98:0.0603:0:1.2 +2 128044048 . G T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGAACTGCTTGAACCTG;RSEQ=GAGGTGGAAGTTGTGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:30:1:29:1:1:0:53.5:8:0.5:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:32:0:1:0:55:2:1:0:0 +2 128044121 . C CA 59 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.19537;SOR=3.14555;LSEQ=GACAGAGTGAGACTCCCTCT;RSEQ=AAAAAAAAAAAAAAGAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:4,0:24,1:25,4:0.1333:1,0:24:1:32.3:1:1:0:48.5:8:0.1333:0:0 0/1:12:4:4,0:7,1:8,4:0.3333:2,0:17:1:29.9:1:1:0:50:8:0.3333:0.1667:1 +2 128044217 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58054;SOR=2.64024;LSEQ=ACAGCAGTCCCTTTCCCAAC;RSEQ=TAACAACTGGAAATTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:1,0:170,17:187,1:0.0053:2,0:9:0:14:0:1:0:60:0:0:0:1 0/1:144:2:1,1:119,23:142,2:0.0139:2,2:20.5:1:27.5:1:0.30653:5.08635:60:4:0.014:0:1 +2 128044653 . G A 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.82974;LSEQ=TGAAATGAAGGACAGGGACA;RSEQ=GCAGAATGACTCACAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:2,1:57,208:265,3:0.0112:2,2:15:1:22:1:0.12297:7.23:60:2:0.0076:0:2.7 0/0:215:2:2,0:55,158:213,2:0.0093:2,0:1:0:23:0:0.06938:0:60:4:0.0094:0:1 +2 128044930 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACCTGGCTGAGCCACC;RSEQ=TGCCACGGTGGCTCATACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:30:1:1:0:36:4:1:0:1.5 +2 128046548 . C A 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06402;SOR=2.0517;LSEQ=GTGGCATTCTATCTAAACTT;RSEQ=TACAAGATTTTAGATCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:35:2,33:3,46:49,35:0.4118:2,2:21.7:1:31.7:1:1:1.07517:60:70:0.4268:0:1 1/0:44:26:0,26:0,18:18,26:0.5909:1,1:26.3:1:31.2:1:1:0:60:52:0.5909:0:1 +2 128046943 . CTCT C 112 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.12165;SOR=2.07106;LSEQ=TCAAAAGACACTGTCTGTGT;RSEQ=TCTTCTTCTTCTTCATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:846:7:4,3:481,358:839,7:0.0083:2,2:28:1:32:1:1:1.00767:60:14:0.0084:0:0 0/1:765:13:7,6:393,355:748,13:0.017:2,2:16.4:1:30.5:1:1:1.05:58.8:26:0.0173:0.0052:0.1 +2 128047685 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51487;SOR=0;LSEQ=TCTTGTTTCTCTTCTCTTAT;RSEQ=TGTGCTTCACAGAAAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:149,28:177,2:0.0112:2,2:16.5:1:29:1:0.29854:5.24651:60:4:0.0113:0:1 0/0:124:0:0,0:102,22:124,0:0:2,0:20.6:1:30.9:1:1:0:60:123:1:0:0.1 +2 128047998 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02014;SOR=Inf;LSEQ=TCCTAAAGTGGTCAGATGTG;RSEQ=CTAAACTGAGCTTTTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:2,108:110,0:0:1,0:24.5:1:31.9:1:1:0:60:54:1:0:0.1 0/1:68:4:0,4:0,64:64,4:0.0588:1,0:23.5:1:30.3:1:1:0:60:8:0.0597:0:1 +2 128050000 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.65665;SOR=0.54199;LSEQ=TGTAGCGGCTCATGAGAAGC;RSEQ=TGGCCTCACCCAGAACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:24,1:4,0:4,25:0.8621:0,1:21.9:1:29.6:1:1:0:51.3:24:0.8571:0:1.3 1/0:13:10:10,0:3,0:3,10:0.7692:0,0:19.5:1:30:1:1:0:55.1:20:0.7692:0:1.1 +2 128050068 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=GTAATCAGTCGTTATGCTCC;RSEQ=CACAGGAAATCTGAATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:91,0:91,0:0:1,0:22.9:1:31.5:1:1:0:59.4:44.5:1:0:0.7 0/1:48:8:7,1:40,0:40,8:0.1667:1,2:17.5:1:30:1:0.16667:0:60:16:0.1702:0:1 +2 128050125 . A T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07532;SOR=Inf;LSEQ=ACAGGCTGACAACATGGAGC;RSEQ=CCTATGCCTATTGTTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:208,56:264,0:0:2,0:22.8:1:29.9:1:1:0:60:51.8:1:0:0.9 0/1:194:3:1,2:140,51:191,3:0.0155:2,2:23.7:1:27.3:1:0.18172:5.43295:60:6:0.0155:0:2 +2 128050134 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34105;LSEQ=CAACATGGAGCACCTATGCC;RSEQ=ATTGTTACATTAGCAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:257:198,59:31,8:39,257:0.8653:2,2:23.1:1:31:1:0.83915:1.15412:60:35.714:0.8711:0:1.1 1/0:239:164:121,43:47,28:75,164:0.6862:2,2:25.5:1:30.4:1:0.09397:1.67:60:53.667:0.6851:0:1.2 +2 128050273 . G A 79 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11378;SOR=3.59666;LSEQ=TCACTGGTTTGCAGCCCAAC;RSEQ=CTGACAGCTGCATACAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:703:2:1,1:358,340:698,2:0.0028:2,2:15.5:1:22:1:1:1.05289:48.5:1:0.0015:0:1 0/1:787:8:5,3:394,382:776,8:0.0102:2,2:25.5:1:26.4:1:0.72551:1.61:60:7:0.009:0:1 +2 128050416 . C T 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01034;SOR=Inf;LSEQ=TTCCAAGAAGATATGGCCAT;RSEQ=GGGAGCCTGAGAGATACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:493:0:0,0:172,321:493,0:0:2,0:25.5:1:30.6:1:1:0:60:97.6:1:0:0.1 0/1:434:6:3,3:161,267:428,6:0.0138:2,2:27.7:1:30.3:1:0.67714:1.66:60:12:0.014:0:1.2 +2 128050483 . T C 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00049;SOR=0.21066;LSEQ=AGTTGCAGAGACTACTGGGC;RSEQ=CTTGCCCATATCATTATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:31:5,26:16,143:159,31:0.1623:2,2:28.4:1:31.3:1:0.348:1.71:60:62:0.1649:0:1.1 0/1:128:5:1,4:20,103:123,5:0.0391:2,2:18.6:1:29.4:1:1:1.28:60:10:0.0394:0:1 +2 128051381 . G A 83 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.02855;SOR=5.99566;LSEQ=AGCATTTCACCTGCGCCGCC;RSEQ=CAAACTCCTAGCTAAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:12,85:97,2:0.0202:2,0:9:1:32:0:1:0:60:4:0.0211:0:1 0/1:63:7:1,6:6,50:56,7:0.1111:2,2:25.7:1:29.7:1:0.58082:1.38:60:14:0.1129:0:1.3 +2 128051487 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTCCAGCATCTCTCCC;RSEQ=CCCAAAGGCCTGTCCCAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:64,16:80,2:0.0244:2,2:28:1:28.5:1:0.37368:3.91077:60:4:0.0256:0:1 0/0:36:0:0,0:28,8:36,0:0:2,0:24.1:1:29.1:1:1:0:60:11:1:0:0.1 +2 128051525 . C T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6363;SOR=0.43412;LSEQ=ACGGGGTGCGCGCGGGAGGG;RSEQ=CAGCAGGGTCGGCCGGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:3:1,2:138,40:178,3:0.0166:2,2:20:1:29:1:0.13494:6.80462:60:6:0.0171:0:1 0/0:138:1:0,1:110,27:137,1:0.0072:2,0:1:0:25:0:0.2029:0:60:2:0.0074:0:1 +2 128051542 . C T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13098;SOR=0;LSEQ=GGGCCAGCAGGGTCGGCCGG;RSEQ=GCAGAGGCCCGGAGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:4:1,3:224,78:302,4:0.0131:2,2:17.3:1:28.8:1:0.05824:8.54263:60:8:0.0133:0:1 0/0:251:0:0,0:187,64:251,0:0:2,0:20.6:1:30.4:1:1:0:59.9:30.375:1:0:0.1 +2 128051726 . G A 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCGGCATCCGCTCTGGGGG;RSEQ=ACTTCCGGCTCAATCCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:748:0:0,0:280,468:748,0:0:2,0:25.6:1:31.4:1:1:0:59.9:52.429:1:0:0.1 0/1:619:35:12,23:239,345:584,35:0.0565:2,2:23.7:1:28.9:1:0.48269:1.32719:60:70:0.0571:0:1.2 +2 128051821 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14914;SOR=Inf;LSEQ=CTGGAAGAGCGGAGAGCCAG;RSEQ=GACCGCCGATCTGTTAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:3,117:120,0:0:1,0:25:1:30.4:1:1:0:60:119:1:0:0.3 0/1:76:2:0,2:6,68:74,2:0.0263:2,0:22:1:31:0:1:0:60:4:0.0263:0:1 +2 128975123 . A G 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87218;LSEQ=AAAAAAATAAAGTAACTATA;RSEQ=CTTTTTCGGCTGGCACCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:11,2:13,3:0.1875:2,0:9.7:1:33.7:1:1:0:47:6:0.1875:0:1.3 0/1:6:1:1,0:3,2:5,1:0.1667:2,0:22:0:33:0:1:0:60:2:0.1667:0:1 +2 128975230 . C A 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.73843;SOR=1.34045;LSEQ=AGGCCTTTTGGAAAACATGC;RSEQ=GTTTTTCCTTTGGTCACGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:3,2:23,12:35,5:0.125:2,2:19.2:1:31:1:1:1.26973:31.8:10:0.125:0:1.8 0/1:31:5:3,2:24,2:26,5:0.1613:2,2:14.2:1:28.4:1:0.11171:7.19006:27.8:10:0.1613:0:2.2 +2 128975303 . C G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22381;SOR=0.57029;LSEQ=ACATCAAGGGAATGGGTACT;RSEQ=TTCAAAAAGGAGTGCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:17:9,8:78,41:119,17:0.125:2,2:19.3:1:33.4:1:0.41828:1.68429:27.2:34:0.125:0:1.3 0/1:133:10:5,5:72,50:122,10:0.0752:2,2:12:1:30.9:1:0.74088:1.43592:28.1:20:0.0775:0:1.9 +2 128975331 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49948;SOR=Inf;LSEQ=AGGAGTGCCCACAAGTGTTA;RSEQ=CATGGCAAAACTGGAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:100,73:173,0:0:2,0:28.4:1:31.8:1:1:0:54.7:42.25:1:0:0.2 0/1:188:2:1,1:96,90:186,2:0.0106:2,2:25.5:1:29:1:1:1.06633:55:4:0.0109:0:1 +2 128975346 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50002;SOR=Inf;LSEQ=TGTTACCATGGCAAAACTGG;RSEQ=AGAGTTTACAATGTTACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:89,80:169,0:0:2,0:29.9:1:30.8:1:1:0:55.2:168:1:0:0.2 0/1:188:2:1,1:87,99:186,2:0.0106:2,2:45:0:31.5:1:1:1.14:26.5:4:0.0108:0:2 +2 128975378 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49822;SOR=0;LSEQ=TGTTACTCAGCATGCTGTTG;RSEQ=CATTGTTGTAAACAAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:60,76:136,2:0.0145:2,2:9.5:1:28.5:1:1:1.26:60:4:0.0146:0:1.5 0/0:135:0:0,0:55,80:135,0:0:2,0:25.4:1:30.9:1:1:0:58.4:66.5:1:0:0.2 +2 128975405 . G A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50089;SOR=Inf;LSEQ=TGTAAACAAACAAGTTCAGG;RSEQ=CAAGATTCTTGCCAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:15,55:70,0:0:2,0:23.8:1:32.1:1:1:0:59.1:140:1:0:0.1 0/1:84:2:1,1:27,55:82,2:0.0238:2,2:6:1:30.5:1:1:2.02:60:4:0.025:0:1 +2 129053496 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13664;SOR=Inf;LSEQ=TGTGTTCCACCAAAACTCAT;RSEQ=TTGAAGTCCTAATCTCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:23,0:0:2,0:24:1:31.5:1:1:0:60:46:1:0:0.2 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:33.5:1:30.5:1:1:1:60:4:0.1429:0:1 +2 129521630 . C A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCTGCGTTTTTTTGCTTT;RSEQ=CATTTGTTTGGTAAATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:30:1:1:0:38:4:1:0:1 +2 129523137 . A G 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.9301;LSEQ=GGTGTCTGGCAACCCCTGTC;RSEQ=GAGGGTCTCATCCAGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:3,5:8,1:0.1111:2,0:8:0:33:0:1:0:60:2:0.1111:0:1 0/1:10:2:1,1:3,5:8,2:0.2:2,2:28:1:32:1:1:1.58:26.5:4:0.2:0:1 +2 129523348 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=GGCTCAGGCCCAGGGAGATC;RSEQ=GAATTCTGTCCCTGAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:17:0:32.5:1:1:3.1622:22:4:0.3333:0:1.5 0/0:5:0:0,0:5,0:5,0:0:0,0:29.8:1:27.8:1:1:0:30.8:4:1:0:0.8 +2 129523431 . T G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06658;SOR=0.29023;LSEQ=TGAGGAAGGATGGATCAGGG;RSEQ=TAGGCCTGAAGAGGCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:6,6:4,2:6,12:0.6667:2,2:24.3:1:29.5:1:0.63801:1.9247:45.3:11:0.6875:0:1.6 0/1:25:9:4,5:9,6:15,9:0.36:2,2:25:1:32.2:1:0.67517:1.82559:43.2:18:0.36:0:1.8 +2 129523483 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49053;SOR=0.4955;LSEQ=GCCACAGCTGGTGTGTTGGG;RSEQ=TGTGGGGACAAGTCTTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:5,6:2,4:6,11:0.6471:2,2:24.5:1:30.3:1:1:1.62:52.6:22:0.6471:0:1.6 0/1:17:8:3,5:3,6:9,8:0.4706:2,2:17.9:1:29.3:1:1:1.19:44.5:16:0.5:0:1.9 +2 129523508 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=0;LSEQ=GGGACAAGTCTTGGGACCAA;RSEQ=CCGTTCAGCCTCCCTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:27.5:1:29.5:1:1:1.18:43:4:0.1538:0:2 0/0:11:0:0,0:4,7:11,0:0:2,0:26.3:1:30.3:1:1:0:47.2:10:1:0:0.5 +2 129523511 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=0;LSEQ=ACAAGTCTTGGGACCAAGCC;RSEQ=TTCAGCCTCCCTGGCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:24.5:1:29.5:1:1:1:43:4:0.1667:0:2 0/0:10:0:0,0:4,6:10,0:0:2,0:27.5:1:30:1:1:0:45.9:20:1:0:0.5 +2 129737822 . A G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGAATAAGGGGGATTCT;RSEQ=GCTAAACCAACCTAACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:10,13:0,0:0,23:1:0,2:24:1:31:1:1:0:58.5:22:1:0:1.1 1/1:14:14:7,7:0,0:0,14:1:0,2:28.4:1:30.4:1:1:0:60:28:1:0:1.1 +2 129739742 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGATTTTGGAAGCACATA;RSEQ=CTTGTTTGGCTTCAAAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:27.5:1:1:0:60:4:1:0:1 +2 129739875 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGCTCCAGAGCTCATGCC;RSEQ=GTGCGAGTTTAGACCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:30:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 131495401 . C CG 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53964;SOR=0;LSEQ=GTCGCTGCAACACCATCCCC;RSEQ=GGGCAGCAGAGCCCCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:2,0:34,9:43,2:0.0444:2,0:23.5:1:32:0:1:0:60:4:0.0444:0:0 0/0:24:0:0,0:19,5:24,0:0:2,0:18.9:1:29.9:1:1:0:60:48:1:0:0.1 +2 131495488 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=CACCAAGGGTGGCACCGTGG;RSEQ=GACTCTGAGACCTACCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:65,66:131,2:0.015:2,2:26.5:1:29:1:1:1.02:60:4:0.015:0:1 0/0:122:0:0,0:65,57:122,0:0:2,0:25.7:1:30.2:1:1:0:60:60:1:0:0.2 +2 131495494 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49851;SOR=0;LSEQ=GGGTGGCACCGTGGCGACTC;RSEQ=GAGACCTACCCAGGATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:60,67:127,2:0.0155:2,2:12:0:32.5:1:1:1.12:60:4:0.0157:0:1.5 0/0:121:0:0,0:64,57:121,0:0:2,0:24.7:1:29.7:1:1:0:60:59.5:1:0:0.2 +2 131946147 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1567;SOR=0;LSEQ=TGCCTAAAAGAAAAAGAACA;RSEQ=AGTACCTCTGAGGCTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:23.5:1:29:1:1:1.87:47:4:0.1818:0:1.5 0/0:16:0:0,0:8,8:16,0:0:2,0:9.9:1:30:1:1:0:56:32:1:0:0.3 +2 131947472 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=CCCATAACCCAGTCTGTCAG;RSEQ=TATTCCACCATCTTATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:67,56:123,0:0:2,0:13.9:1:31:1:1:0:32.6:60.5:1:0:0.1 0/1:132:2:1,1:76,54:130,2:0.0152:2,2:19:0:31:0:1:1.40368:32:4:0.0153:0:1 +2 131947526 . AT A 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.01804;SOR=0;LSEQ=GAAAAGAGAAACAGCAAACA;RSEQ=TTTTTTGAAGTCACACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:5:1,4:87,134:221,5:0.0221:2,2:31.8:1:29.6:1:0.6509:2.58763:38.4:10:0.0227:0:0.2 0/0:276:0:0,0:112,164:276,0:0:2,0:33:1:29.5:1:1:0:42.2:137:1:0:0.2 +2 131947551 . C A 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.34747;SOR=0.29555;LSEQ=TTTGAAGTCACACCTCACCC;RSEQ=CACACACACACCTTTAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:2,1:79,151:230,3:0.0129:2,2:27:1:31:1:0.27763:3.80:47.3:6:0.0131:0:1 0/0:261:1:1,0:94,165:259,1:0.0038:2,0:44:0:29:0:0.36538:0:29:2:0.0039:0:6 +2 131947586 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TAGTCATGTAAGATTACTTA;RSEQ=AGTGCAAATAATTTGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:22,94:116,0:0:2,0:26.1:1:32.4:1:1:0:46.6:115:1:0:0.1 0/1:95:13:4,9:9,72:81,13:0.1368:2,2:21.5:1:27.5:1:0.07785:3.49:35.5:26:0.1398:0:1.5 +2 131947925 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16319;SOR=Inf;LSEQ=ACTTCATTGAACAAACTAAG;RSEQ=TTTACAAGACCCTACATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:126,8:134,0:0:2,0:24:1:30.5:1:1:0:43.8:133:1:0:0.1 0/1:92:2:1,1:83,7:90,2:0.0217:2,2:8:1:31:1:0.16722:11.15825:47.5:4:0.0227:0:1 +2 131948173 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14086;SOR=Inf;LSEQ=AAGATAAGGCATTCAAAATA;RSEQ=TTTAATCATCAAATAAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:17,107:124,0:0:2,0:29.2:1:34:1:1:0:35.4:248:1:0:0.1 0/1:75:2:0,2:3,70:73,2:0.0267:1,0:16:1:26.5:1:1:0:48:4:0.0267:0:1.5 +2 131948232 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00874;SOR=Inf;LSEQ=AAACAGTAAGATATTTATTT;RSEQ=TAGGAGAGCATACACAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:25,51:76,0:0:2,0:24.9:1:32.6:1:1:0:49.2:152:1:0:0 0/1:35:4:3,1:9,22:31,4:0.1143:2,2:11:1:29.3:1:0.10609:6.88:47.5:8:0.1176:0:1.8 +2 131948248 . A T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08202;SOR=Inf;LSEQ=ATTTGTAGGAGAGCATACAC;RSEQ=ATTTCTGGTTACCTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:29,41:70,0:0:2,0:25.4:1:31.2:1:1:0:46.3:140:1:0:0 0/1:29:2:2,0:11,16:27,2:0.069:2,0:33:1:32:1:0.19212:0:35:4:0.069:0:2 +2 131948539 . CTA C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.21064;SOR=0;LSEQ=TTGGTATCAGTCAATAAAAC;RSEQ=TAGAGAGAACAAATATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:92,105:197,2:0.0101:2,2:22.5:1:34.5:1:1:1.14:32:4:0.0102:0:0 0/0:234:0:0,0:125,109:234,0:0:2,0:23.3:1:28.9:1:1:0:23.4:468:1:0:0.1 +2 131949169 . G A 164 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTTCACTGACCGGACCCAC;RSEQ=GGTGGGCTATAGGTTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:18,22:0,0:0,40:1:0,2:30.4:1:30.9:1:1:0:37.6:39:1:0:1.2 1/0:40:20:9,11:10,10:20,20:0.5:2,2:27.7:1:29.4:1:1:1.21609:34.5:40:0.5128:0:1.1 +2 131950765 . C CAA 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=ATAGACAAAAGGCAACTTTA;RSEQ=AAACTTACCTGGCCATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:202,58:260,0:0:2,0:28.1:1:32.2:1:1:0:37.3:259:1:0:0.2 0/1:269:15:12,3:178,76:254,15:0.0558:2,2:32.1:1:30.1:1:0.56422:1.70:30.8:30:0.0562:0:0.1 +2 131950767 . A G 184 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGACAAAAGGCAACTTTACA;RSEQ=ACTTACCTGGCCATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:49:46,3:155,54:209,49:0.1899:2,2:33.2:1:32.9:1:0.0019:5.32:32.1:98:0.1922:0:1 0/0:267:0:0,0:189,78:267,0:0:2,0:28.9:1:29.5:1:1:0:37.7:132.5:1:0:0.1 +2 131951015 . T C 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00032;SOR=Inf;LSEQ=ACTTCAAAAGCTATTCCTCA;RSEQ=CACACATATGTAACAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:134,67:201,0:0:2,0:21.4:1:30.8:1:1:0:33:99.5:1:0:0.1 0/1:191:11:10,1:134,46:180,11:0.0576:2,2:24.3:1:33.2:1:0.29894:3.42:28.5:22:0.0585:0:1 +2 131951211 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21654;SOR=0;LSEQ=TCACTGCACTTAGAGCCCTG;RSEQ=CTGCCAATGGAGAACCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:37,79:116,2:0.0169:2,2:13:1:29:1:0.54223:2.12:21.5:4:0.0174:0:1 0/0:135:0:0,0:41,94:135,0:0:2,0:25.3:1:30.7:1:1:0:27.7:66.5:1:0:0.2 +2 131951231 . T A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00139;SOR=Inf;LSEQ=CCTGCCAATGGAGAACCTGA;RSEQ=AAGCCCCACCCAAAAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:16,39:55,0:0:2,0:19.3:1:29.5:1:1:0:21.9:54:1:0:0.2 0/1:78:12:4,8:20,46:66,12:0.1538:2,2:20.6:1:31.8:1:1:1.15:21.5:24:0.1622:0:1.2 +2 131951299 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12276;SOR=Inf;LSEQ=AGTGATAAAGCCAAAAACTT;RSEQ=GTTCACTAACCTCACAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:4,22:26,0:0:2,0:27:1:30.2:1:1:0:38.6:52:1:0:0.1 0/1:33:4:1,3:4,25:29,4:0.1212:2,2:22.3:1:28.5:1:0.49963:2.03:25.5:8:0.1212:0:1 +2 131951587 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22066;SOR=Inf;LSEQ=AATTTCCCCTGTAAACTTAC;RSEQ=GAATAGTAACCTTAAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:55,2:57,0:0:1,0:26.9:1:31.1:1:1:0:49.1:114:1:0:0 0/1:51:2:1,1:44,5:49,2:0.0392:2,2:26:1:28:1:0.22353:8.12333:48:4:0.0392:0:1 +2 131951717 . G A 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAACTCCATGAATGTGTTA;RSEQ=AGTTGGGCAAGAGGTTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:220,177:397,0:0:2,0:27.8:1:32.9:1:1:0:36.5:131.333:0.9975:0:0.1 0/1:386:20:10,10:208,158:366,20:0.0518:2,2:29.7:1:29.5:1:0.64501:1.31549:31.4:40:0.0526:0:1.1 +2 131951961 . G A 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTATATTTGCAACTTGGGTA;RSEQ=TTTCATGTAAAAAACCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:86,243:329,0:0:2,0:23.1:1:32.1:1:1:0:58.4:35.556:1:0:0.2 0/1:321:68:23,45:71,181:252,68:0.2118:2,2:24.8:1:28.6:1:0.37118:1.30:42.5:16:0.2071:0:1.2 +2 131951969 . TA T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.24919;SOR=0;LSEQ=GCAACTTGGGTAGTTTCATG;RSEQ=AAAAACCCAATGACGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:60,216:276,3:0.0108:2,2:24:1:29:1:0.5244:1.80:53.7:6:0.0109:0:0 0/0:264:0:0,0:72,192:264,0:0:2,0:23.5:1:29:1:1:0:55.4:87:1:0:0.4 +2 131952108 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16522;SOR=Inf;LSEQ=CAAACCCCAAAATATCTTGT;RSEQ=CAAATGAGAAATGAGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:5,22:27,0:0:2,0:25.8:1:32.7:1:1:0:34.1:54:1:0:0 0/1:19:2:1,1:2,15:17,2:0.1053:2,2:12.5:1:27:1:0.29825:6.32:44.5:4:0.1053:0:1 +2 131953240 . G A 49 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.24306;SOR=Inf;LSEQ=GAGCACACGAGATGATACAG;RSEQ=AAAATTACAAAAGAAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:24,9:33,0:0:2,0:8.4:1:31.4:1:1:0:24.4:66:1:0:0.1 0/1:38:3:2,1:15,20:35,3:0.0789:2,2:7:1:31:1:0.57681:2.60:25.3:6:0.0789:0:1 +2 131953329 . C T 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGTGACACTTCAAGACCCA;RSEQ=GGACATTTGACTGGTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:158,171:329,0:0:2,0:26.9:1:31.1:1:1:0:40.4:328:1:0:0.1 0/1:319:48:31,17:125,146:271,48:0.1505:2,2:31.4:1:29.9:1:0.01946:2.12:22.3:96:0.1524:0:1.1 +2 131953403 . T C 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGGAGAAAGTGACAGGAA;RSEQ=TTCTATCTGCCTGCTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:81,180:261,0:0:2,0:24.7:1:30.3:1:1:0:37.7:51.2:1:0:0.1 0/1:209:31:10,21:63,115:178,31:0.1483:2,2:24.6:1:30.8:1:0.83952:1.14964:25.4:62:0.1498:0:1.2 +2 131953444 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.80979;LSEQ=AAAGAAAGAAATAAGCTTTA;RSEQ=TGATGCACTGACAACCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:1:1,0:23,94:117,1:0.0085:2,0:1:0:25:0:0.20339:0:29:2:0.0087:0:1 0/1:131:2:1,1:36,93:129,2:0.0153:2,2:12.5:1:28.5:1:0.48667:2.56:53:4:0.0153:0:1.5 +2 131954747 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCAACAGTGTGGTTTTA;RSEQ=GGCCAAAGTTTCAGAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:33:1:33.5:1:0.33333:0:31:4:0.3333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:4:0:29:0:1:0:60:2:1:0:0 +2 131954927 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23714;SOR=0;LSEQ=TATTCTCCCATTTTTTAAAG;RSEQ=TGTCATTTTGCTTACCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:96,24:120,2:0.0164:2,2:10.5:1:30.5:1:0.36919:3.93954:52:4:0.0165:0:1 0/0:128:0:0,0:95,32:127,0:0:2,0:24.5:1:28.5:1:1:0:52.5:62.5:1:0:0.1 +2 131955247 . G C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08235;SOR=Inf;LSEQ=AAATGTTAAGAAATGGTAAG;RSEQ=GCAATTAAGAATCTGATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:9,0:0:2,0:21.4:1:30.8:1:1:0:29.7:8:1:0:0 0/1:8:3:0,3:1,4:5,3:0.375:2,0:36.3:1:30:0:1:0:22:6:0.375:0:1 +2 131955431 . T TA 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.25967;SOR=0;LSEQ=GGTAATTTTGAGACATTTCA;RSEQ=AAAAAAACACTTACACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:2,1:126,49:175,3:0.0169:2,2:17.7:1:29:1:1:1.28383:23:6:0.017:0:0 0/0:138:0:0,0:90,48:138,0:0:2,0:23.5:1:28.2:1:1:0:36.5:68:1:0:0 +2 132181346 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.19499;SOR=Inf;LSEQ=GCCCACCATGGAAGGGCAGG;RSEQ=CGGGTGTCTAGGAGGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:170,56:226,0:0:2,0:25.3:1:31.7:1:1:0:52.1:74.333:0.9955:0:0.1 0/1:180:2:1,1:130,47:177,2:0.0111:2,2:20:1:30.5:1:0.46551:2.7475:21.5:4:0.0114:0:1 +2 132181483 . G T 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.72821;SOR=0.90963;LSEQ=GAAGTGGGAGTAGATAATTT;RSEQ=GTCACTGGGTTCAGGTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:543:41:19,22:255,245:500,41:0.0755:2,2:18.6:1:31:1:0.62741:1.20474:28.2:82:0.0769:0:1 0/1:564:39:17,22:244,278:522,39:0.0691:2,2:24.2:1:29.9:1:0.74172:1.13559:26.4:78:0.0701:0:1 +2 132181860 . C G 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAATGACACTTTGTAAGT;RSEQ=AAAGGGGTATTCGACGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:803:0:0,0:407,394:801,0:0:2,0:24.1:1:31.9:1:1:0:54.4:49.063:0.9975:0:0.2 0/1:661:46:23,23:298,316:614,46:0.0696:2,2:23.3:1:30.4:1:0.87937:1.06:46.2:92:0.0701:0:1 +2 132181872 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51867;SOR=1.11444;LSEQ=TTGTAAGTCAAAGGGGTATT;RSEQ=GACGATCCCTGTGGTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:92:55,37:354,341:695,92:0.1166:2,2:25.2:1:30.9:1:0.12062:1.43:45.4:184:0.1179:0:1.1 0/1:655:84:38,46:278,291:569,84:0.1282:2,2:22:1:29.5:1:0.56033:1.15619:47.3:41:0.1275:0:1.1 +2 132182028 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19737;SOR=Inf;LSEQ=CCTGGATTCCAGGATCATTC;RSEQ=ATAAACTCTTTATTGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:81,91:172,0:0:2,0:7.5:1:30.8:1:1:0:33.2:56.333:1:0:0.1 0/1:138:2:1,1:59,76:135,2:0.0145:2,2:7.5:1:26.5:1:1:1.29:42:4:0.0149:0:1 +2 132182138 . G T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01191;LSEQ=ACTTGTATGTGCTCATACTT;RSEQ=TATGGGATCTTGAGTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:595:56:35,21:280,258:538,56:0.0941:2,2:31.2:1:30.7:1:0.15971:1.53:52.4:112:0.0951:0:2 0/1:452:43:21,22:203,206:409,43:0.0951:2,2:34.5:1:30:1:1:1.0323:52.7:42:0.0938:0:1.9 +2 132182159 . T C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90567;SOR=1.03668;LSEQ=TATGGGATCTTGAGTGAGTC;RSEQ=ATGGCTCTGATCATGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:43:28,15:260,238:498,43:0.0795:2,2:25.9:1:31.6:1:0.11315:1.71:49.5:86:0.0799:0:2.3 0/1:426:35:18,17:205,186:391,35:0.0822:2,2:26.6:1:30.6:1:1:1.04084:52:70:0.0825:0:2.1 +2 132182199 . C T 87 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5246;SOR=0.52067;LSEQ=GCATGGCCGTGAAGATGTTC;RSEQ=GATACACCAGCTTGGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:7:6,1:193,193:386,7:0.0178:2,2:5.4:1:31:1:0.12186:5.98:25.6:14:0.0181:0:3 0/0:321:3:1,2:162,156:318,3:0.0093:2,2:5:1:29:1:0.61802:2.07235:26.3:6:0.0095:0:3 +2 132182489 . T G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99303;LSEQ=GCCGGCACCCCCTGCTCACA;RSEQ=CGCGCACACACGCCTTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:9:0,9:16,197:213,9:0.0405:2,0:28.1:1:31.4:1:1:0:27.9:18:0.0419:0:2.2 0/1:149:6:0,6:15,128:143,6:0.0403:2,0:16.5:1:29.3:1:1:0:30.2:12:0.0405:0:2.2 +2 132182552 . G A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55862;SOR=1.44848;LSEQ=GTGGCTGCCGAGCCCCCGCC;RSEQ=CCTGGGCGCGCGTCCGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:11:0,11:0,56:56,11:0.1642:1,0:20.6:1:28:1:1:0:33.3:4.5:0.1385:0:2.5 0/1:27:6:0,6:0,21:21,6:0.2222:1,0:21.5:1:30.7:1:1:0:30.2:12:0.2308:0:2.2 +2 132182587 . G A 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.58108;LSEQ=CGGGACGAGCTCCGGGAACC;RSEQ=CCGCGGGGGCGGCGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:10:1:27.3:1:1:0:45.7:2:0.2857:0:3.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:1:0:31:0:1:0:34:2:0.5:0:3 +2 132182592 . G C 44 p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGCTCCGGGAACCGCCGC;RSEQ=GGGGCGGCGGCCAGGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:5:1:28.3:1:1:0:45.7:6:0.6:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 132184299 . G GAA 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGAGAAGGAAGAGGAGGA;RSEQ=AAAGAAGAGGAAGAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:28.3:1:1:0:60:4:1:0:0 +2 133317889 . C G 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3066;LSEQ=CTTTCCCACCTCTTTTTCCT;RSEQ=AACCATAAACCTGTTTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:738:359:170,189:194,184:378,359:0.4864:2,2:26.7:1:32.1:1:0.30235:1.17193:60:50.286:0.4869:0:1.1 0/1:747:168:77,91:300,277:577,168:0.2249:2,2:25.2:1:30.9:1:0.16207:1.27951:60:167:0.2248:0:1.2 +2 133317891 . A T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCCCACCTCTTTTTCCTCA;RSEQ=CCATAAACCTGTTTGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:737:0:0,0:358,379:737,0:0:2,0:26.7:1:29.8:1:1:0:60:60.417:1:0:0.6 0/1:740:32:13,19:360,347:707,32:0.0432:2,2:28:1:29.2:1:0.28175:1.51544:60:64:0.0439:0:1.1 +2 133317983 . C T 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=8e-05;SOR=Inf;LSEQ=CTTCCACTGCTCTCCAGTCT;RSEQ=TCCCCATCCTCACACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:34,210:244,0:0:2,0:24.7:1:32.5:1:1:0:60:33.857:1:0:0.2 0/1:233:13:2,11:43,177:220,13:0.0558:2,2:18.5:1:29.8:1:1:1.33462:60:26:0.0565:0:1 +2 133919324 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50016;SOR=0;LSEQ=AAACTCTCAACTGAGATTCA;RSEQ=GTTTCAAAGTAATGGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:88,23:111,2:0.0177:2,2:38.5:1:29.5:1:0.38116:3.76677:60:4:0.0182:0:1 0/0:98:0:0,0:67,31:98,0:0:2,0:25.9:1:30.7:1:1:0:60:97:1:0:0.1 +2 133919333 . G C 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20861;SOR=Inf;LSEQ=ACTGAGATTCACGTTTCAAA;RSEQ=TAATGGCATCCTGAAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:104,31:135,0:0:2,0:24.4:1:33:1:1:0:60:44:1:0:0.2 0/1:114:2:1,1:74,38:112,2:0.0175:2,2:5.5:1:30:1:1:1.93525:60:4:0.0177:0:1 +2 133919370 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21162;SOR=Inf;LSEQ=GCTCAGGCCTGTCCAAGGAA;RSEQ=GTTTATTTTATTCTTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:159,74:233,0:0:2,0:24.4:1:32.2:1:1:0:60:57.25:1:0:0.5 0/1:199:2:0,2:124,73:197,2:0.0101:2,0:7.5:1:27:1:0.14086:0:60:4:0.0102:0:1 +2 133919427 . C A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.36599;LSEQ=TATATAGGGCCCAGAACTGT;RSEQ=CACAAAGACATCTTCTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:332:180:87,93:77,75:152,180:0.5422:2,2:25.2:1:29.2:1:0.74113:1.09716:59.9:360:0.5505:0:1.1 0/1:298:90:44,46:106,102:208,90:0.302:2,2:26.3:1:28.1:1:0.8011:1.08615:60:180:0.3051:0:1.1 +2 133919631 . G A 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01806;SOR=0;LSEQ=ATTTGCACTTACTCATTCTT;RSEQ=GCCTTTTCTGTGCCCTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:5,8:0.6154:0,0:27:1:31.3:1:1:0:60:7:0.5833:0:1.5 0/0:6:0:0,0:1,5:6,0:0:2,0:30.5:1:28.7:1:1:0:60:12:1:0:0.5 +2 133919662 . A G 54 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.79151;LSEQ=TGCCCTCTTGTATAGTTCAT;RSEQ=TATAGAACCTATAATTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:7,3:0.3:0,0:19:1:34.3:1:1:0:60:6:0.3:0:1 0/1:4:1:0,1:0,3:3,1:0.25:0,0:42:0:31:0:1:0:60:2:0.25:0:1 +2 134775183 . A T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10948;SOR=0.46159;LSEQ=TTAACCACTTTTTGAAGTTG;RSEQ=AAAGGGATTGTATACAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:22:21,1:17,0:17,22:0.5641:1,1:23.1:1:30.2:1:1:0:59.8:44:0.5641:0:1.1 0/1:35:13:13,0:21,1:22,13:0.3714:1,1:26.5:1:29.6:1:1:0:60:26:0.4063:0:1.1 +2 134775262 . CA C 188 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.31427;SOR=1.26753;LSEQ=CTACAAATGACTTTTTAAAC;RSEQ=AAAAAAAAAAAACAGCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:74:56,18:53,12:65,74:0.4596:2,2:27.6:1:30.7:1:0.41816:1.41608:59.9:23.667:0.4581:0.0683:0.5 1/0:158:82:58,24:34,19:53,82:0.519:2,2:26.3:1:29.6:1:0.45344:1.35:60:81:0.5226:0.1013:0.7 +2 134775344 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00053;SOR=2.04876;LSEQ=CTGTGGCTTGTGTTCTCTTA;RSEQ=TAACAGATCAAAATCTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:41:20,21:152,172:324,41:0.1123:2,2:31.8:1:33:1:0.86897:1.08:60:82:0.1136:0:1 0/1:398:82:42,40:154,162:316,82:0.206:2,2:29.6:1:31.1:1:0.71137:1.10:59.9:40:0.2041:0:1.2 +2 134775446 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49775;SOR=0;LSEQ=TTAGTTTTATGTAAAAAAAG;RSEQ=CCTCACATTTTTCACGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:9,81:90,2:0.0217:2,2:22.5:1:29.5:1:0.20664:8.59:60:4:0.022:0:1 0/0:86:0:0,0:8,78:86,0:0:2,0:21.1:1:28.1:1:1:0:60:42:1:0:0.1 +2 134775529 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36341;SOR=3.4542;LSEQ=ACTTTATAGCTTTATCAATG;RSEQ=AAGCTTCATATTCAAAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:18:1,17:0,4:4,18:0.8182:0,1:22.5:1:32:1:1:0:60:36:0.8182:0:1 1/1:17:16:0,16:0,1:1,16:0.9412:0,1:20.8:1:30.5:1:1:0:60:15:0.9375:0:1 +2 134776262 . T C 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCAAGAGAATTGCTTGAACC;RSEQ=AGGAGAGGGAGGTTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:13:0:28:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:33:0:1:0:51:4:1:0:1 +2 135069340 . T A 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11851;SOR=0;LSEQ=AAAACTTTGTTTGTAGTAAG;RSEQ=GAATGTTTTATGATGCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:2,1:49,5:54,3:0.0526:2,2:6:1:27.7:1:0.28828:4.67695:60:6:0.0536:0:2.7 0/0:58:0:0,0:50,7:57,0:0:2,0:24:1:29.3:1:1:0:60:114:1:0:0 +2 135069472 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01436;SOR=1.55294;LSEQ=TAGCCTTGTGTGACACCCAA;RSEQ=GCACCTAGCATCTGATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:276:168:86,82:53,55:108,168:0.6087:2,2:28:1:31.3:1:0.80529:1.09:60:167:0.6095:0:1.1 1/0:311:220:108,112:44,47:91,220:0.7074:2,2:26:1:29.8:1:1:1.03:59.9:219:0.7087:0:1.1 +2 135069544 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24479;SOR=Inf;LSEQ=TTAAGATTTTCTCCAGGCCG;RSEQ=GTACAGTGGCTTATGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:51,118:169,0:0:2,0:22.2:1:31.3:1:1:0:60:168:1:0:0.3 0/1:166:2:1,1:51,113:164,2:0.012:2,2:15:1:25.5:1:0.52968:2.20:60:4:0.0123:0:1 +2 135343919 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53131;SOR=Inf;LSEQ=TTCCTTCTACAGGCTGCAGA;RSEQ=GAAACTGGCCCCAGCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:16,0:0:2,0:24.3:1:32.3:1:1:0:60:32:1:0:0.3 0/1:29:2:1,1:15,12:27,2:0.069:2,2:22.5:1:29:1:1:1.24034:60:4:0.0714:0:1.5 +2 135343920 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54296;SOR=Inf;LSEQ=TCCTTCTACAGGCTGCAGAG;RSEQ=AAACTGGCCCCAGCCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:11,6:17,0:0:2,0:23.1:1:30.5:1:1:0:60:16:1:0:0.3 0/1:31:3:1,2:16,12:28,3:0.0968:2,2:11:1:27.7:1:0.57642:2.58395:60:6:0.1:0:2.3 +2 135343934 . C G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00076;SOR=9.44872;LSEQ=GCAGAGGAAACTGGCCCCAG;RSEQ=CCTCTCTCTAGCTGCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:9,9:18,3:0.1429:2,0:21.7:1:32.7:1:0.22857:0:60:6:0.15:0:1 1/0:37:23:13,10:8,6:14,23:0.6216:2,2:26.9:1:28.3:1:1:1.02495:58.9:4.75:0.5758:0:1.3 +2 135894862 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51475;SOR=Inf;LSEQ=CGTATTCCACACATCTGTAC;RSEQ=ATTCTTGAGTATGATCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:15,9:24,0:0:2,0:28.9:1:30.2:1:1:0:58.7:48:1:0:0.1 0/1:37:2:1,1:23,12:35,2:0.0541:2,2:34.5:1:30.5:1:1:1.88115:60:4:0.0556:0:1.5 +2 135894904 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12564;SOR=0;LSEQ=GGGTGTCAAATTGAGAACCA;RSEQ=GCAGATCCACCACCTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:14,18:32,2:0.0588:2,2:20.5:1:29:1:1:1.28:50:4:0.0588:0:1 0/0:61:0:0,0:30,31:61,0:0:2,0:29.3:1:30.8:1:1:0:43.3:29.5:1:0:0.4 +2 136869825 . G A 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.3083;SOR=0;LSEQ=TGGGAAGCCTGCAGTAGGGG;RSEQ=AGATAAATTTTCAAGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:4:4,0:49,0:49,4:0.0755:1,0:28:1:32:0:1:0:51.3:8:0.0784:0:1 0/0:23:0:0,0:23,0:23,0:0:1,0:22.4:1:30.7:1:1:0:60:46:1:0:0.1 +2 136869873 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.73356;SOR=0.86826;LSEQ=AAAACAAAGGCTTTGCAAGA;RSEQ=AAAACATCCACTTTCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:25:25,0:94,0:94,25:0.2101:1,1:22.1:1:30.2:1:1:0:60:24:0.2051:0:1.2 0/1:96:18:18,0:78,0:78,18:0.1875:1,1:21:1:30.2:1:1:0:60:36:0.1895:0:1.1 +2 136872392 . TA T 81 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.22801;SOR=2.48993;LSEQ=TATCTGAAAAATGTGTAACT;RSEQ=AAAAAAAGTTATTTATCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:3:2,1:416,126:542,3:0.0055:2,2:19.7:1:29.3:1:0.54959:1.64908:60:6:0.0056:0.0018:0.3 0/1:588:8:4,4:419,161:580,8:0.0136:2,2:15.6:1:27.2:1:0.22935:2.5976:60:16:0.0136:0.0085:0.5 +2 136873084 . G A 200 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.62489;LSEQ=TGACTGTTGGTGGCGTGGAC;RSEQ=ATGGCCAGGTAGCGGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1922:3:1,2:934,983:1917,3:0.0016:2,2:10.7:1:30.3:1:1:1.89969:60:6:0.0016:0:1.3 0/1:2178:118:62,56:1000,1054:2054,118:0.0542:2,2:23.5:1:29.1:1:0.44916:1.17:59.9:38.333:0.0533:0:1.2 +2 136873549 . A T 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.38167;LSEQ=CATTAACCCAGTTAAAAAAA;RSEQ=TTTTTAAAGCAATTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:757:433:113,320:92,232:324,433:0.572:2,2:23.4:1:30.5:1:0.50879:1.1228:59.9:71.167:0.5701:0:1.1 0/1:853:288:90,198:186,378:564,288:0.3376:2,2:22.5:1:29.4:1:0.64275:1.08247:60:287:0.3376:0:1.1 +2 136874692 . T G 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01643;SOR=8.88445;LSEQ=AGCCAAACGGTTTCCCCACT;RSEQ=GCACCTGCCAGTCTTCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:1:0,1:64,360:424,1:0.0024:2,0:21:0:14:0:1:0:60:0:0:0:2 0/1:389:8:2,6:61,319:380,8:0.0206:2,2:16:1:29.5:1:0.62134:1.74:60:16:0.0207:0:1 +2 136874906 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGCGGCCGTGGGGAAGAGGC;RSEQ=CGCTTCGGACGGCGGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:0,11:11,2:0.1538:0,2:30.5:1:30:1:0.15385:0:47.5:4:0.1538:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:18:1:31:1:1:0:60:6:1:0:0 +2 136874926 . GT G 102 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCTTCGGACGGCGGGAAG;RSEQ=TTTCCCCCTCAAACCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:2,7:0,0:0,9:1:0,2:29.8:1:32.2:1:1:0:57.2:18:1:0:0.3 1/1:1:1:0,1:0,0:0,1:1:0,0:19:0:33:0:1:0:60:2:1:0:0 +2 136875448 . A C 54 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46877;SOR=0.44641;LSEQ=TCCAATCCTGCTCCCCCCCC;RSEQ=CCCACCCGCACTATATAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:6,0:19,3:22,6:0.2143:2,0:5:1:21.2:1:1:0:51.7:2:0.1905:0:1.3 0/1:28:3:3,0:24,1:25,3:0.1071:1,0:5:1:25:0:1:0:60:6:0.1154:0:1.3 +2 136875497 . CT C 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.0151;SOR=Inf;LSEQ=GAAAACTCCTTTCGGTGACC;RSEQ=TTTTTGGAGTACGGGTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:252,32:284,0:0:2,0:23.6:1:32.4:1:1:0:59.8:70:0.9929:0:0.1 0/1:292:7:6,1:250,35:285,7:0.024:2,2:17.4:1:32:1:1:1.18971:60:14:0.0241:0.0068:0.3 +2 138749676 . T C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTGGAAGATCCCACTCG;RSEQ=GAACCCACACCACCAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:31:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:31:1:1:0:60:4:1:0:1 +2 138750570 . A C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=CAGAAAGCAACAACAACAGC;RSEQ=TCAACAACAAGAACAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:29.1:1:31.1:1:1:0:56.9:16:1:0:0 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:5:0:33:1:1:1:37:4:0.1538:0:0 +2 138750684 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51772;SOR=0;LSEQ=AAAGAATCAATGAAACAATG;RSEQ=TGAAAACCCAAAAGGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:17,19:36,2:0.0526:2,2:19:1:32:0:1:1.11:58:4:0.0526:0:1 0/0:24:0:0,0:11,13:24,0:0:2,0:24.3:1:31.7:1:1:0:56.7:48:1:0:0.3 +2 138750696 . A T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15239;SOR=Inf;LSEQ=AAACAATGCTGAAAACCCAA;RSEQ=AGGTCAGAGTGCCTTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:15,17:32,0:0:2,0:22.4:1:30.4:1:1:0:59.9:64:1:0:0.1 0/1:21:2:1,1:7,12:19,2:0.0952:2,2:9:0:29.5:1:1:1.67:60:4:0.0952:0:1.5 +2 139259201 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49621;SOR=Inf;LSEQ=CCGGCTGCGGAACCTGCCCC;RSEQ=CCGGGAGCCTAGTGCCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:14,0:0:2,0:33.9:1:30.1:1:1:0:60:13:1:0:1 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:12.5:1:27:1:1:1.12:60:4:0.1111:0:1.5 +2 139259220 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4949;SOR=Inf;LSEQ=CGCCGGGAGCCTAGTGCCAT;RSEQ=CAGCAGCGGCGGCGGTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:23,0:0:2,0:25.1:1:32.1:1:1:0:60:22:1:0:1 0/1:28:2:1,1:12,14:26,2:0.0714:2,2:27:0:31:1:1:1.16:60:4:0.0714:0:2.5 +2 139259222 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.3908;LSEQ=CCGGGAGCCTAGTGCCATGC;RSEQ=GCAGCGGCGGCGGTGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:20:7,13:1,1:2,20:0.9091:2,2:25.9:1:31.1:1:1:1.80284:60:40:0.9091:0:1.2 1/1:30:28:13,15:1,1:2,28:0.9333:2,2:21.1:1:30:1:1:1.14834:60:56:0.9333:0:1.5 +2 139308127 . G A 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0094;SOR=0;LSEQ=CGAGAGGAAATGGGTGAAGT;RSEQ=TTAAAAAGTTCAACATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:5,4:4,4:8,9:0.5294:2,2:22.9:1:29.7:1:1:1.23:60:18:0.5294:0:1 0/0:9:0:0,0:5,4:9,0:0:2,0:29.6:1:32.1:1:1:0:60:18:1:0:0 +2 139316829 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49491;SOR=Inf;LSEQ=AATGCATTTATGCATAAAAT;RSEQ=ATGATACATAATCTTGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:21,0:0:2,0:17.2:1:30:1:1:0:60:42:1:0:0.2 0/1:26:2:1,1:17,7:24,2:0.0769:2,2:13.5:1:28.5:1:0.52923:2.3376:60:4:0.0833:0:1 +2 139316917 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17421;SOR=0;LSEQ=AAAGCAAAAAGGTAAACATG;RSEQ=CTTAAAGGCTAATATTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:20,2:0.0909:2,2:36.5:1:31:1:1:1.21:60:4:0.0909:0:1 0/0:30:0:0,0:9,21:30,0:0:2,0:23.7:1:30.9:1:1:0:60:60:1:0:0.2 +2 139316934 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13892;SOR=Inf;LSEQ=ATGGCTTAAAGGCTAATATT;RSEQ=AATTTATATAAACGTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:12,0:0:2,0:20.3:1:32.4:1:1:0:60:24:1:0:0.6 0/1:19:4:1,3:3,12:15,4:0.2105:2,2:38:1:29:1:1:1.31:60:8:0.2105:0:1 +2 139318426 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11429;SOR=Inf;LSEQ=AAGTTTTTAAAGAAATGATG;RSEQ=GATTCATTTACACAGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:29,17:46,0:0:2,0:29.2:1:30.6:1:1:0:60:92:1:0:0.2 0/1:24:2:1,1:13,9:22,2:0.0833:2,2:40.5:1:30.5:1:1:1.42202:60:4:0.0833:0:1 +2 139690082 . C CA 85 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.29226;SOR=2.91172;LSEQ=CAGAGACACGAAAAAGCCTC;RSEQ=AAAAAAAAAAATTAATGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:20,22:42,2:0.0455:2,2:39:1:31.5:1:1:1.10:60:4:0.0455:0:2 0/1:57:7:4,3:23,26:49,7:0.1228:2,2:37.7:1:30.3:1:0.70045:1.50:60:14:0.125:0:0.1 +2 141599025 . C G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19928;SOR=0;LSEQ=ATAGCACATCTTTCTAGTTA;RSEQ=GAGAAAGTACTTGTGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1:0,1:25.3:1:33.5:1:1:0:60:12:1:0:1.1 1/1:11:9:9,0:2,0:2,9:0.8182:0,0:18.9:1:31:1:1:0:60:18:0.8182:0:1 +2 141599218 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=0.51336;LSEQ=TATTTTAACATCCCTTCAAC;RSEQ=TGGATTCTGCAGAAAATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:153:69,84:45,42:87,153:0.6375:2,2:27.8:1:30.3:1:0.34846:1.30288:60:50:0.6383:0:1.1 0/1:329:156:78,78:83,90:173,156:0.4742:2,2:24.9:1:28.9:1:0.74117:1.08:60:38:0.4691:0:1.1 +2 141599395 . G GA 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.4873;SOR=Inf;LSEQ=TAAAAACTGCACCTTTTCAA;RSEQ=AAAAAAAATGAGGTGTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:17,0:0:1,0:27.6:1:32.3:1:1:0:60:34:1:0:0 0/1:19:2:1,1:0,17:17,2:0.1053:1,2:45:1:29.5:1:0.10526:0:60:4:0.1111:0:0 +2 141599495 . T TTACTC 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCAATTTATAGCATTTGA;RSEQ=TACCTTGATTTTGGTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,1:1,5:0.7143:0,0:30:1:32.4:1:1:0:60:10:0.8333:0.1429:0 1/1:1:1:0,1:0,0:0,1:1:0,0:16:0:31.2:0:1:0:60:2:1:0:0 +2 141641717 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04792;SOR=Inf;LSEQ=ATTTCAACTTTGAGAGATTG;RSEQ=AAAAGTGCTACCTAGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:28,0:28,0:0:1,0:27.2:1:33.1:1:1:0:60:56:1:0:0.1 0/1:17:3:3,0:14,0:14,3:0.1765:1,0:36.3:1:30:1:1:0:60:6:0.1765:0:1 +2 141641859 . C A 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTCTGAGGCTAATAACAA;RSEQ=GTTGAGGTTGCAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:136,91:227,0:0:2,0:26.4:1:31.2:1:1:0:60:74.667:0.9956:0:0.3 0/1:243:34:17,17:116,93:209,34:0.1399:2,2:28.1:1:29.7:1:0.58119:1.24616:60:33:0.1375:0:1.1 +2 141641870 . CA C 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.80065;SOR=0.77814;LSEQ=TAATAACAACGTTGAGGTTG;RSEQ=AAAAAAAAGTTATTTCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:9:4,5:154,106:260,9:0.0335:2,2:25.6:1:33.2:1:0.49506:1.81186:60:18:0.0335:0.0074:0.4 0/1:267:7:4,3:135,124:259,7:0.0262:2,2:25.3:1:31.8:1:1:1.22:60:14:0.0264:0.0037:0.7 +2 141641896 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05335;SOR=0;LSEQ=AAAAGTTATTTCTTGTTCCT;RSEQ=ACTTTTTTATACAGAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:4:2,2:165,136:301,4:0.0131:2,2:20:1:25.3:1:1:1.21246:60:3:0.01:0:1.8 0/0:328:0:0,0:166,160:326,0:0:2,0:23.1:1:30.7:1:1:0:59.9:53.333:0.9938:0:0.5 +2 141641929 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.4498;LSEQ=AGAGCAAAGGATTTTGGAAA;RSEQ=AATAATGATATTCTGGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:295:177:90,87:52,66:118,177:0.6:2,2:26.5:1:29.7:1:0.285:1.31:60:87.5:0.5993:0:1.1 0/1:313:126:61,65:85,102:187,126:0.4026:2,2:29.5:1:28.5:1:0.64475:1.13:59.9:125:0.4019:0:1.2 +2 141641945 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24881;SOR=Inf;LSEQ=GAAACAATAATGATATTCTG;RSEQ=TTAAAATCAGTGCAACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:130,164:294,0:0:2,0:24.9:1:31.6:1:1:0:60:97:1:0:0.6 0/1:300:3:1,2:139,158:297,3:0.01:2,2:12.3:1:29.3:1:1:1.75632:60:6:0.0102:0:1.3 +2 141641999 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.24457;SOR=Inf;LSEQ=CTTCAAGAGTAGAATAAAAT;RSEQ=AAAAGAAAAAGCCCACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:42,119:161,0:0:2,0:26.3:1:32.3:1:1:0:59.8:160:0.9938:0:0.3 0/1:159:2:1,1:50,106:156,2:0.0126:2,2:8:0:30.5:1:0.54277:2.11:60:4:0.0128:0:1.5 +2 141642010 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23808;SOR=Inf;LSEQ=GAATAAAATCAAAAGAAAAA;RSEQ=CCCACCAGAGCTAAGATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:28,110:138,0:0:2,0:25:1:32.5:1:1:0:59.8:68:1:0:0.2 0/1:132:2:1,1:34,96:130,2:0.0152:2,2:8.5:1:28:1:0.46149:2.80:60:4:0.0155:0:2 +2 142098069 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=0.3284;LSEQ=TCTTCTATACAATTCTTATA;RSEQ=AAGCAAAAATGCCTTTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:82:66,16:30,7:37,82:0.6833:2,2:22.6:1:33.3:1:1:1.03863:60:164:0.6891:0:1.2 0/1:104:43:36,7:45,16:61,43:0.4135:2,2:26.3:1:31.7:1:0.3374:1.82:60:86:0.4135:0:1.3 +2 142098098 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24357;SOR=Inf;LSEQ=ATGCCTTTAATAAATGCAGT;RSEQ=ACCCTGATAAAAATAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:122,54:176,0:0:2,0:25.8:1:32.4:1:1:0:60:87:1:0:0.7 0/1:172:2:1,1:111,59:170,2:0.0116:2,2:23:0:30.5:1:1:1.87407:60:4:0.0118:0:2 +2 142098153 . G A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10232;SOR=Inf;LSEQ=CCATTACAAATGTTCTAAAA;RSEQ=GTTTCATGTAGTACTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:183,154:337,0:0:2,0:25.9:1:32.1:1:1:0:59.9:66.4:1:0:0.7 0/1:298:3:2,1:157,138:295,3:0.0101:2,2:5:1:27.3:1:1:1.75:60:6:0.0102:0:1.3 +2 142098162 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03409;SOR=0.71044;LSEQ=ATGTTCTAAAAGGTTTCATG;RSEQ=AGTACTTCACTAATTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:358:215:110,105:67,74:141,215:0.6006:2,2:25.7:1:32.3:1:0.51717:1.16:60:214:0.6045:0:1.2 1/0:306:158:79,79:74,74:148,158:0.5163:2,2:24.3:1:31.6:1:1:1:60:316:0.518:0:1.2 +2 142098235 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20752;SOR=Inf;LSEQ=ATTATCATAATTTTATTGCT;RSEQ=ACCCACCAAAGAAAAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:58,141:199,0:0:2,0:24:1:32.2:1:1:0:59.9:98.5:1:0:0.4 0/1:167:2:1,1:53,112:165,2:0.012:2,2:5.5:1:26.5:1:0.54347:2.10:60:4:0.0122:0:2 +2 142098325 . T C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16248;SOR=0.42352;LSEQ=TTTAAACAGTCAATACCCCT;RSEQ=GAAAAGTAGTCTTCTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:21:0,21:0,7:7,21:0.75:0,1:25:1:30.6:1:1:0:60:42:0.75:0:1 1/0:27:15:1,14:0,12:12,15:0.5556:0,1:26.7:1:30.1:1:1:0:60:30:0.5556:0:1.1 +2 142100281 . A T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACAAAGCCTTCAAGAAAT;RSEQ=TGGGACTATGTGAAAAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:44:0:31:1:1:0:28:4:1:0:2.5 +2 142100310 . A C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAAAAGACCAAACCTAC;RSEQ=TTGGAATGGTGTACCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:32.5:1:1:0:28:4:1:0:2.5 +2 147565133 . T TAAA 28 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTATGTTATTACAAAGT;RSEQ=AAAAAAAAAAAAAATTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:28.3:1:1:0:60:4:1:0:1 +2 147565661 . G T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTGAGCTCCCTGAGCGGGG;RSEQ=GAAGGGCGGCACCCATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:45.5:1:32:1:1:0:60:4:1:0:0.5 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:13.5:1:29.5:1:1:1.41418:50.5:4:0.2857:0:1 +2 147566461 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=GTGTCAGCAGCCTTGAAGAC;RSEQ=AAAACTAGAGAAACTCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:26.8:1:32.2:1:1:0:59.6:10:1:0:0.2 0/1:8:2:0,2:3,3:6,2:0.25:2,0:25:1:32.5:1:0.46429:0:55:4:0.25:0:2 +2 147566997 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50263;SOR=0;LSEQ=CTGGAGTACCAGAAGGAGAT;RSEQ=GGGAGAATGGAAACAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:23,29:52,2:0.037:2,2:33:1:31.5:1:1:1.26:49:4:0.0377:0:1 0/0:42:0:0,0:18,24:42,0:0:2,0:29.3:1:31.4:1:1:0:41.1:84:1:0:0.1 +2 147568623 . C CA 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATACACAAAAAACCCTC;RSEQ=AAAAAAAAAAATCAATGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:32.5:1:1:0:32:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 148075953 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11515;SOR=Inf;LSEQ=GGCAACATGGCTTCTCCCCT;RSEQ=TCTAGGTCCTGTGGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:36,0:0:2,0:36.5:1:29:1:1:0:30.9:11:1:0:0.1 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:42.5:1:32:1:1:1.11803:47.5:4:0.1053:0:1 +2 148076060 . A T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1455;SOR=Inf;LSEQ=TCAAGGCCATCAAGCTACAG;RSEQ=TGATCTTACAAATGGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:4,13:17,0:0:2,0:26.2:1:31.8:1:1:0:54.6:34:1:0:0 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:8:0:31:0:1:1.87:40:4:0.1818:0:1.5 +2 148468930 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21394;SOR=0;LSEQ=TGCTGCTACTGCTGTTGCTG;RSEQ=TGCAGAGAACTCACTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:24,27:51,2:0.0377:2,2:25.5:1:29.5:1:1:1.12:60:4:0.0385:0:1 0/0:61:0:0,0:23,38:61,0:0:2,0:25.6:1:31.5:1:1:0:60:60:1:0:0.2 +2 148468933 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49648;SOR=Inf;LSEQ=TGCTACTGCTGTTGCTGCTG;RSEQ=AGAGAACTCACTTGATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:25,28:53,0:0:2,0:28.2:1:32.7:1:1:0:60:106:1:0:0.2 0/1:58:2:1,1:20,36:56,2:0.0345:2,2:32.5:1:29:1:1:1.78:60:4:0.0345:0:1 +2 148779023 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22588;SOR=0;LSEQ=TTAGCAACACAGACCCTTTG;RSEQ=TGCTGCTGTTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:29,32:61,2:0.0317:2,2:30.5:1:30.5:1:1:1.10:60:4:0.0317:0:1 0/0:69:0:0,0:33,35:68,0:0:2,0:29.3:1:31.2:1:1:0:57.7:136:1:0:0.2 +2 148779032 . TTGC T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.2451;SOR=Inf;LSEQ=CAGACCCTTTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:32,34:66,0:0:2,0:31.3:1:30.5:1:1:0:58.7:132:1:0:0.1 0/1:70:3:1,2:31,36:67,3:0.0429:2,2:40.7:1:30.7:1:1:1.70942:60:6:0.0429:0:0.3 +2 148779065 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.2439;SOR=Inf;LSEQ=TGCTGTTGCTGCTGCTGCTG;RSEQ=TACTGCTGCTGCTGCTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:26,36:62,0:0:2,0:20.6:1:31.4:1:1:0:58.6:30:1:0:0.1 0/1:61:2:1,1:24,35:59,2:0.0328:2,2:29.5:1:29:1:1:1.45:60:4:0.0328:0:1 +2 151649843 . G A 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGTGGGTTTCCCTCGAG;RSEQ=GAAGCACACCCCCTCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:2:0:30:0:1:0:60:2:1:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26.5:1:30:1:1:0:60:4:0.6667:0:1 +2 151649991 . A G 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CATCAGGTTGGTGACCCTCA;RSEQ=GGTCAGAGGTTCCAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:31.8:1:31.8:1:1:0:60:8:1:0:0.3 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:40:0:32.5:1:1:0:39:4:0.6667:0:1 +2 152156132 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18886;SOR=0;LSEQ=TTTTGCCATATTCTTTAATG;RSEQ=ACTGTACACGTAAGAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:44,6:50,2:0.0385:2,2:25:1:27.5:1:0.25339:6.86595:60:4:0.04:0:1 0/0:67:0:0,0:53,14:67,0:0:2,0:20.7:1:28.7:1:1:0:59.2:134:1:0:0.1 +2 152156169 . GT G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=AGATGGGTAATATTGAGTGG;RSEQ=TTTTTGTGATGTAGTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:86,33:119,0:0:2,0:25.7:1:30.1:1:1:0:59.7:118:1:0:0.2 0/1:130:2:1,1:86,42:128,2:0.0154:2,2:39.5:1:29.5:1:1:2.03546:60:4:0.0154:0:0 +2 152156204 . C T 21 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.90663;LSEQ=GTCTCTGAAGATATACCAAG;RSEQ=AGCAATTGTTTTCTCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:0,2:115,69:184,2:0.0108:2,0:23:1:25.5:1:0.14443:0:60:4:0.0109:0:1 0/0:205:2:0,2:122,81:203,2:0.0098:2,0:1:0:21.5:1:0.16275:0:60:4:0.0099:0:1.5 +2 152156237 . CTT C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00094;SOR=0.49946;LSEQ=CTCTGCTGCTCATACAGCCC;RSEQ=TTATGTGGCCACAAACCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:76:47,29:85,84:169,76:0.3102:2,2:25.6:1:32.5:1:0.09868:1.60:59.5:152:0.3154:0.0408:1.1 0/1:262:48:26,22:115,99:214,48:0.1832:2,2:27.1:1:30.8:1:1:1.02:59.9:96:0.186:0.042:1.1 +2 152156258 . A C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00414;SOR=0.55868;LSEQ=TTTTATGTGGCCACAAACCT;RSEQ=ATCTGGCCTCCTGCAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:82:43,39:66,82:148,82:0.3565:2,2:27.7:1:31.9:1:0.27236:1.37:59.6:40:0.3571:0:1.2 0/1:271:64:34,30:103,102:205,64:0.2362:2,2:26.1:1:30.8:1:0.7748:1.12:59.9:63:0.2368:0:1.3 +2 152156338 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50527;SOR=Inf;LSEQ=TCAAAAATTCTGCCCAGTTT;RSEQ=ATTTCTCATGCCACAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:16,72:88,0:0:2,0:23.8:1:32.1:1:1:0:60:43:1:0:0.3 0/1:113:2:1,1:28,83:111,2:0.0177:2,2:14.5:1:26.5:1:0.44912:2.93:60:4:0.018:0:2 +2 152771082 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11712;SOR=0;LSEQ=CACTCTTGCCTTTTGGGTTT;RSEQ=CAGCATTTTTCATTGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:9,2:11,2:0.1538:2,2:20:1:30.5:1:0.42308:3.87298:53:4:0.1538:0:1 0/0:24:0:0,0:15,9:24,0:0:2,0:28.4:1:30:1:1:0:55.3:48:1:0:0.1 +2 152771292 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48617;SOR=0;LSEQ=CGGGGGTTCACTTCAGGCCC;RSEQ=ATTCATCTGATTCACTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:2,9:11,2:0.1538:2,2:35.5:1:32.5:1:0.42308:3.87:44:4:0.1538:0:1.5 0/0:10:0:0,0:3,7:10,0:0:2,0:27.3:1:28.9:1:1:0:60:20:1:0:0 +2 152772103 . T C 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTGGCTCATGCATATAG;RSEQ=CCCAGCACTTTGGGAGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 154688399 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTATAGTTCTTGTTCTATA;RSEQ=TCGTGTGACATATTTCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31:1:32.5:1:1:0:53:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 154688728 . G A 254 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAAAAATGAAGAAGGCATA;RSEQ=TGGAGACTAACAAAGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:309:309:120,189:0,0:0,309:1:0,2:27.2:1:30.8:1:1:0:60:76.25:1:0:1.1 1/0:360:259:115,144:41,60:101,259:0.7194:2,2:26.9:1:29.5:1:0.55482:1.17:60:85.333:0.7273:0:1.1 +2 158593900 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03558;SOR=Inf;LSEQ=TGTCTCCCCAACACATGGCT;RSEQ=GGTACGACGTCTGCCTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:101,1:102,0:0:1,0:26.7:1:32.9:1:1:0:60:101:1:0:0.3 0/1:51:3:3,0:48,0:48,3:0.0588:1,0:8.3:1:28.3:1:1:0:60:6:0.06:0:2 +2 158593905 . C T 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.72798;SOR=1.15056;LSEQ=CCCCAACACATGGCTGGGTA;RSEQ=GACGTCTGCCTTGTCAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:33:32,1:80,0:80,33:0.292:1,1:28.5:1:31.5:1:0.29204:0:60:66:0.292:0:1 0/1:59:19:19,0:40,0:40,19:0.322:1,1:21.6:1:31.8:1:1:0:60:38:0.3333:0:1.2 +2 158617379 . A G 252 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTAAGACAATATTATATTAG;RSEQ=TTAGATACCTACCATTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1395:265:162,103:683,445:1128,265:0.19:2,2:25.2:1:31.4:1:0.88899:1.02:60:52:0.1898:0:1.1 0/0:1333:0:0,0:791,540:1331,0:0:2,0:24.2:1:29:1:1:0:60:109.917:0.9985:0:0.1 +2 158617791 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACTAAATGTCAGAAACA;RSEQ=TCTAAGGCTATCAGGTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:0,24:24,2:0.0769:1,0:13:1:33.5:1:1:0:60:4:0.08:0:1 0/0:8:0:0,0:0,8:8,0:0:0,0:24.4:1:31:1:1:0:60:16:1:0:0.1 +2 158622572 . C A 223 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00711;LSEQ=AGACCACTAGCTATGGACAG;RSEQ=ACTATTCGAAGGCAGCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1923:157:72,85:848,917:1765,157:0.0816:2,2:26:1:30.7:1:0.61774:1.09165:60:77.5:0.0818:0:1.2 0/0:1581:1:1,0:756,819:1575,1:6e-04:2,0:1:0:23:0:0.48033:0:60:2:6e-04:0:1 +2 158626980 . C T 329 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04151;LSEQ=AAGATCTTCACGGCAACATT;RSEQ=TCCCCTTGCCAGCTGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1811:1801:831,970:0,0:0,1801:0.9945:0,2:24.9:1:30.5:1:1:0:59.9:61.103:0.9944:0:1.1 1/1:1830:1614:767,847:99,108:207,1614:0.882:2,2:25.3:1:29.7:1:0.94121:1.01227:59.9:99.875:0.8829:0:1.2 +2 158627188 . A AT 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCACAACCTTTATTTTTT;RSEQ=TTTTTTTTGGCCTATAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:0,2:1,80:81,2:0.0238:1,0:21:1:28.5:1:1:0:60:4:0.025:0:0.5 0/0:32:0:0,0:1,31:32,0:0:1,0:19.9:1:30:1:1:0:60:31:1:0:0.3 +2 158630481 . A G 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00133;SOR=Inf;LSEQ=CAGAATAGAGACCACATCTC;RSEQ=TAAGTTTAATAAGGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:137,1:138,0:0:1,0:24.1:1:30.9:1:1:0:59.8:137:1:0:0.1 0/1:71:6:6,0:65,0:65,6:0.0845:1,0:19.7:1:28.3:1:1:0:60:12:0.0845:0:1.2 +2 158634289 . G A 92 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAAAGGTGCCTTTTTAAA;RSEQ=GAGCACTTTTATGGCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:26.5:1:30.8:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 158635051 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCAATTAGACACAACT;RSEQ=GAATTTGAAAAAATTCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:0,40:0,0:0,40:1:0,1:30.9:1:31.2:1:1:0:59.4:80:1:0:1 1/1:13:13:0,13:0,0:0,13:1:0,1:23.5:1:31.8:1:1:0:60:26:1:0:1 +2 158636320 . C T 67 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAACTACAGGGTTTGTG;RSEQ=GAAATCTCATCCTGCTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:25.8:1:29:1:1:0:60:10:1:0:2.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 158636341 . A G 73 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATCTCATCCTGCTTCAA;RSEQ=TTTCAGTGATAGGGTCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:21.6:1:31.8:1:1:0:60:10:1:0:2.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 158636510 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTACTAGCAGAATTGTT;RSEQ=CAGAAATTATGAATGACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1:0,1:20.4:1:31.5:1:1:0:60:26:1:0:1.3 1/1:2:2:2,0:0,0:0,2:1:0,0:8.5:1:31.5:1:1:0:60:4:1:0:2 +2 158636910 . G A 340 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30296;LSEQ=TCCCCTTGGCAGCACTCCAC;RSEQ=GCTTGGCCAGGGGACGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2073:1913:929,984:78,78:156,1913:0.9228:2,2:24.6:1:31.2:1:0.7397:1.0592:60:105.278:0.9257:0:1.1 1/0:1964:1539:789,750:203,217:420,1539:0.7836:2,2:24.2:1:29.8:1:0.29582:1.12:59.9:84.5:0.7832:0:1.2 +2 158637132 . A AG 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00111;SOR=0.64391;LSEQ=TCTGCAAAGGAGAGAAAGGA;RSEQ=GGGGAAAAAAAAAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1324:147:51,96:453,717:1170,147:0.111:2,2:30.5:1:29.2:1:0.36877:1.1891:59.9:10.308:0.1058:0.0038:0.7 0/1:1384:103:38,65:533,742:1275,103:0.0744:2,2:32.8:1:28.1:1:0.35085:1.22854:59.4:9.3:0.0696:0:1.1 +2 158637137 . A G 293 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAGGAGAGAAAGGAAGGGG;RSEQ=AAAAAAAAAAAAAGAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1173:760:292,468:76,138:214,760:0.6479:2,2:21:1:30.7:1:0.47287:1.13:59.8:22.03:0.6462:0:1.4 0/0:1213:0:0,0:117,167:284,0:0:2,0:26.3:1:28.2:1:1:0:59.2:16.75:0.5403:0:0.8 +2 158637445 . A C 115 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCAGCGTGATTGGCTCT;RSEQ=AGATCCCAATTACTGCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:29.2:1:33.3:1:1:0:58.9:22:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 158655838 . G C 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=CCAAATATTTATTATAAAAA;RSEQ=AGTGTTTTAAGTTTGATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:20:20,0:230,11:241,20:0.0766:1,1:26.2:1:33.1:1:1:0:58.8:40:0.0797:0:1.4 0/0:182:0:0,0:174,8:182,0:0:1,0:22.7:1:31.6:1:1:0:59.3:44.5:1:0:0.4 +2 158655883 . C CAA 252 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=0.00672;SOR=0.705;LSEQ=AGAAGTAGTTTATAGTAAGC;RSEQ=AAAAAAAAAAATCACAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:537:309:246,63:53,12:65,309:0.5754:2,2:28.5:1:30.5:1:0.86489:1.13073:59.4:153.5:0.5782:0:0.6 0/1:479:234:180,54:73,23:96,234:0.4885:2,2:29.2:1:29.7:1:0.88651:1.05:59.6:468:0.4937:0:0.5 +2 158739387 . A G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93661;LSEQ=GAAATTTTTTCAAAGAACTC;RSEQ=TAGAGCTTTGACTTGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:11:11,0:18,0:18,11:0.3793:1,0:29.1:1:28.3:1:1:0:60:10:0.3571:0:1.2 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:24.8:1:28.3:1:1:0:60:8:0.4444:0:1 +2 158739584 . C T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01567;SOR=0.68329;LSEQ=TTTAAAAGCTAGTCCCATGG;RSEQ=GGGAAGATCAAATTAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:334:196:94,102:65,73:138,196:0.5868:2,2:26.9:1:30.1:1:0.91165:1.03:60:195:0.5873:0:1.1 0/1:327:161:81,80:84,82:166,161:0.4924:2,2:25.1:1:29.1:1:1:1.01171:60:322:0.4939:0:1.2 +2 158739600 . A G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.86545;SOR=0.93534;LSEQ=ATGGCGGGAAGATCAAATTA;RSEQ=TTTCTTCCTCAAATTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:19:9,10:140,160:300,19:0.0596:2,2:26.9:1:33:1:1:1.03:60:38:0.0601:0:1.2 0/1:304:17:8,9:140,147:287,17:0.0559:2,2:30.5:1:31.6:1:1:1.07122:60:34:0.0567:0:1.2 +2 158739646 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2249;SOR=0;LSEQ=ATTTCAAATATAACTGTGTG;RSEQ=CTCTTGGTAGAACCCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:58,120:178,2:0.0111:2,2:5.5:1:28.5:1:0.54935:2.06:60:4:0.0111:0:1.5 0/0:199:0:0,0:73,125:198,0:0:2,0:26.6:1:31.2:1:1:0:60:396:0.995:0:0.4 +2 159559834 . T C 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58799;SOR=2.17536;LSEQ=CCAAACTTAGACGACATCTA;RSEQ=ATTTCCTTGTGTTCATCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:31,0:31,2:0.0606:1,0:17:0:31:1:1:0:40.5:4:0.0606:0:1.5 0/1:16:2:2,0:14,0:14,2:0.125:1,0:12:1:31:1:1:0:41:4:0.125:0:1.5 +2 159560007 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.00006;LSEQ=TACACATGGGTAATTTGCTT;RSEQ=AATTATTTTTTCCCTCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:681:409:233,176:154,117:271,409:0.6006:2,2:26:1:30:1:1:1.01:48.6:408:0.6027:0:1.2 1/1:546:447:248,199:49,50:99,447:0.8187:2,2:25.6:1:28.8:1:0.31578:1.27:49.2:88.4:0.8185:0:1.4 +2 159560048 . C A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.38687;LSEQ=TACTGTTTTTGAAATGTTTG;RSEQ=CCTTCCTGGTTATCTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:36:16,20:307,352:659,36:0.0516:2,2:22.4:1:29.6:1:0.86475:1.09003:52.6:17:0.0498:0:2.1 0/1:507:131:60,71:177,198:375,131:0.2584:2,2:27.4:1:28.5:1:0.83897:1.05774:50.7:130:0.26:0:2.2 +2 159560098 . C T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.81628;SOR=0.95958;LSEQ=TAAGTTTGCTAAATTGGGGT;RSEQ=AAAAGGCTGATTTTAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:231:75,156:50,120:170,231:0.5718:2,2:24.7:1:29.1:1:0.58558:1.15:60:462:0.5761:0:1.2 1/0:292:164:56,108:45,82:127,164:0.5616:2,2:25.9:1:28.1:1:0.90125:1.05814:60:163:0.566:0:1.5 +2 159560213 . GA G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.80233;LSEQ=ATAAAGTATTGCTTATCATG;RSEQ=AAAAAAAAAGAACCTTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:11:0,11:0,44:44,11:0.2:1,0:22.3:1:32.7:1:1:0:60:22:0.2075:0.0182:0.1 0/1:18:3:0,3:0,15:15,3:0.1667:1,0:26.3:1:31.7:1:1:0:60:6:0.1667:0:0 +2 163928821 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16774;SOR=0;LSEQ=CAGGGATAGTACGAGATGCC;RSEQ=CCCAGCATTTACAAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:19:1:31.5:1:1:2.4495:39:4:0.1538:0:1 0/0:18:0:0,0:14,4:18,0:0:2,0:18.3:1:29.2:1:1:0:34.8:36:1:0:0.7 +2 163928850 . A T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22761;SOR=0;LSEQ=TTACAAGAAAAGGCTTCTGA;RSEQ=ATCAGACAATACCTTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:23,12:35,2:0.0541:2,2:7.5:1:28.5:1:1:1.88115:27:4:0.0541:0:3.5 0/0:40:0:0,0:24,16:40,0:0:2,0:21.4:1:29.6:1:1:0:34.6:80:1:0:1 +2 163928879 . C A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50049;SOR=Inf;LSEQ=ATACCTTTCAAACTCTTATA;RSEQ=CAACCTCTGGACTTCGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:33,25:58,0:0:2,0:27.7:1:32.2:1:1:0:42.6:116:1:0:1.2 0/1:70:2:1,1:36,32:68,2:0.0286:2,2:20:0:28:1:1:1.1231:23:4:0.0286:0:3.5 +2 163928884 . C T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00019;SOR=0.23596;LSEQ=TTTCAAACTCTTATACCAAC;RSEQ=TCTGGACTTCGGCAACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:31:18,13:14,12:26,31:0.5439:2,2:32.3:1:31.2:1:0.79366:1.18:37.2:62:0.5439:0:2.2 0/1:69:15:7,8:28,24:52,15:0.2174:2,2:35.5:1:30.3:1:0.7709:1.32759:33.1:30:0.2174:0:1.9 +2 163928905 . A C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.9808;LSEQ=TCTGGACTTCGGCAACATGG;RSEQ=TTTTCCCCTTTCTAGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:31:17,14:13,11:24,31:0.5636:2,2:32.5:1:32.4:1:1:1.03:36.2:30:0.5556:0:2.2 1/0:68:38:18,20:15,15:30,38:0.5588:2,2:31.2:1:31.2:1:1:1.10939:33.4:37:0.5522:0:1.6 +2 163928925 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49634;SOR=Inf;LSEQ=ATTTTCCCCTTTCTAGGTCC;RSEQ=ATGACAGCCATCTTGCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:25,25:50,0:0:2,0:22.2:1:31.6:1:1:0:42.5:49:1:0:1.3 0/1:55:2:1,1:24,29:53,2:0.0364:2,2:33.5:1:28:1:1:1.20:28.5:4:0.0364:0:2 +2 164133568 . A T 190 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTTTAAATAAAGTTCCTTA;RSEQ=GATGTTCATTTTTAAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:208,192:400,0:0:2,0:24.4:1:31:1:1:0:59.9:99:1:0:0.1 0/1:413:86:51,35:157,169:326,86:0.2082:2,2:25.7:1:29.6:1:0.07003:1.57:60:85:0.2078:0:1.1 +2 169205164 . T G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7595;SOR=1.12712;LSEQ=TGGGTATTGGGTGGCTCTAT;RSEQ=ATGCCATCATGGCGACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:27:25,2:91,15:106,27:0.203:2,2:25.3:1:33.5:1:0.52246:2.05:60:54:0.2061:0:1 0/1:121:27:22,5:76,18:94,27:0.2231:2,2:23:1:30.9:1:1:1.04:60:54:0.2231:0:1.1 +2 169205178 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49994;SOR=0;LSEQ=CTCTATTATGCCATCATGGC;RSEQ=ACTGTCACATTAAATAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:141,35:176,2:0.0112:2,2:8.5:1:28.5:1:0.3645:3.98629:60:4:0.0112:0:1 0/0:160:0:0,0:120,40:160,0:0:2,0:23.4:1:29.6:1:1:0:60:79:1:0:0.3 +2 169205230 . C T 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04927;SOR=Inf;LSEQ=GAATTTAAGGGAATGTTTGA;RSEQ=CTGCCCCACAGTATATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:227,190:417,0:0:2,0:26.4:1:31.3:1:1:0:59.9:51.125:1:0:0.3 0/1:373:4:1,3:195,174:369,4:0.0107:2,2:5.5:1:25.3:1:0.34933:3.35199:60:8:0.0109:0:1.5 +2 169205282 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.20462;LSEQ=TAGGCCATAGGGAAAGTCAG;RSEQ=AAATGTTCAGGAGAGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:79:31,48:156,200:356,79:0.1812:2,2:24.1:1:28.5:1:0.53023:1.20722:60:38.5:0.1812:0:1.1 1/0:395:243:102,141:71,80:151,243:0.6152:2,2:24.6:1:28:1:0.34833:1.22619:59.8:80:0.6138:0:1.2 +2 169205353 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50883;SOR=0;LSEQ=AAGGACCTCCTGTAAGGAAG;RSEQ=CTGGGCTCAGGGAACTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:32,119:151,2:0.0131:2,2:32.5:1:29:1:0.38596:3.68:60:4:0.0135:0:1.5 0/0:114:0:0,0:30,83:113,0:0:2,0:22.9:1:30.3:1:1:0:60:36.667:0.991:0:0.3 +2 169205451 . G A 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.83996;LSEQ=GAGTTGTCATTAGGATCAAC;RSEQ=GAATATATTGGTTGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:0,5:0,23:23,5:0.1786:1,0:25.8:1:32.8:1:1:0:60:10:0.1786:0:1 0/1:13:2:0,2:0,11:11,2:0.1538:0,0:35.5:1:31.5:1:1:0:58.5:4:0.1538:0:1 +2 170170329 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52389;SOR=0;LSEQ=CTGTTCCTATTCGGCCATCT;RSEQ=GGAACCTCCCTCCTCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:107,45:152,2:0.013:2,2:31:1:32:1:0.50955:2.36278:46:4:0.0133:0:1 0/0:97:0:0,0:63,34:97,0:0:2,0:21.9:1:29.2:1:1:0:54.9:194:1:0:0.1 +2 170170404 . G A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57174;SOR=2.85471;LSEQ=ATTCATGTTTTTGTCCATTA;RSEQ=TGGTCCGTGGGTATCTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:1:1,0:97,120:217,1:0.0045:2,0:1:0:27:0:0.44954:0:60:2:0.0047:0:1 0/1:155:2:1,1:69,84:153,2:0.0129:2,2:27.5:1:31.5:1:1:1.22:43.5:4:0.013:0:1 +2 170845304 . TA T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.24751;SOR=0;LSEQ=ATAGAGTAAGACCCTATCTT;RSEQ=AAAAAATTAAAAAAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:129,19:148,2:0.0133:2,2:9.5:1:30:1:0.24966:6.6432:60:4:0.0135:0.0067:0.5 0/0:151:0:0,0:127,24:151,0:0:2,0:19.2:1:27.9:1:1:0:60:74.5:1:0:0.3 +2 170845313 . T C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00546;SOR=2.53494;LSEQ=GACCCTATCTTTAAAAAAAT;RSEQ=AAAAAAGAAAAAAAGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:15:12,3:153,23:176,15:0.0785:2,2:18.2:1:32.5:1:0.4354:1.6579:60:30:0.0798:0:1 0/1:191:34:27,7:130,27:157,34:0.178:2,2:23.4:1:30.2:1:0.6259:1.24677:60:68:0.1789:0:1 +2 170845320 . G T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.12252;SOR=Inf;LSEQ=TCTTTAAAAAAATTAAAAAA;RSEQ=AAAAAAAGAAACTGACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:195,32:227,0:0:2,0:22.6:1:33.2:1:1:0:59.9:44.4:1:0:0.2 0/1:225:3:2,1:176,46:222,3:0.0133:2,2:17:1:31:1:0.50663:1.90646:60:6:0.0135:0:1.3 +2 170845413 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.51844;LSEQ=TGTTTCCTTCTTTACCATCT;RSEQ=AGCCTTATCCACCCATTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:53:29,24:375,358:733,53:0.0672:2,2:25.6:1:31.8:1:0.67062:1.15:60:106:0.0679:0:1.1 0/1:823:355:181,174:237,231:468,355:0.4313:2,2:25.6:1:30.9:1:0.94394:1.01:59.8:117.333:0.4335:0:1.2 +2 170845438 . TC A 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATCCACCCATTGATACTT;RSEQ=CCCCTTTTACCCCTTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:783:0:0,0:342,441:783,0:0:2,0:26.8:1:30.9:1:1:0:60:96.875:1:0:0.2 0/1:843:31:13,18:381,429:810,31:0.0368:2,2:28.5:1:29.8:1:0.71442:1.22939:60:62:0.0372:0.0047:1.2 +2 170845609 . T C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01631;SOR=Inf;LSEQ=CTGGCTAATTTTATTTCATT;RSEQ=GTTCCCTCCTTATTAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:2,42:44,0:0:1,0:21:1:30.5:1:1:0:60:88:1:0:0.1 0/1:26:4:1,3:0,22:22,4:0.1538:1,2:33.5:1:30:1:0.15385:0:60:8:0.1538:0:1 +2 172443775 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18706;SOR=0;LSEQ=TGCCCCACAAATGTTAACCA;RSEQ=GGCAAAACTGGGAGAGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:42,35:77,2:0.0253:2,2:28.5:1:32.5:1:1:1.19722:55:4:0.0256:0:1.5 0/0:103:0:0,0:52,51:103,0:0:2,0:31.1:1:29.1:1:1:0:59.9:33.333:1:0:0.1 +2 173022484 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52;SOR=0;LSEQ=GCATCACTCTAATCTCTGCT;RSEQ=CCATTGTCACATGGCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:3,11:14,2:0.125:2,2:18:1:28.5:1:0.45:3.32:60:4:0.125:0:1 0/0:9:0:0,0:3,6:9,0:0:2,0:27.7:1:31.8:1:1:0:60:18:1:0:0.2 +2 173022501 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=GCTGCCATTGTCACATGGCT;RSEQ=TCTTCTTCCTGTGTGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:2,7:9,2:0.1818:2,2:33:1:29.5:1:0.49091:3.06:60:4:0.1818:0:1 0/0:8:0:0,0:1,6:7,0:0:2,0:20.4:1:33:1:1:0:60:14:0.875:0:0 +2 173353511 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51446;SOR=Inf;LSEQ=GCCTCAAATGGCAAGCATGG;RSEQ=CCCACCTGACTCCGGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:18,23:41,0:0:2,0:27.4:1:32:1:1:0:60:40:1:0:0.1 0/1:61:2:1,1:29,30:59,2:0.0328:2,2:28.5:1:28:1:1:1.03:60:4:0.0333:0:1 +2 173914558 . G T 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GTTTTCATCTATTAATTTAC;RSEQ=TTGTGTTTAAAGATGTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:29,0:0:1,0:23.5:1:30.3:1:1:0:60:58:1:0:0 1/0:14:7:7,0:7,0:7,7:0.5:0,0:33:1:30.1:1:1:0:60:14:0.5:0:1 +2 173914775 . T C 228 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAAATAATATGCTTTGTT;RSEQ=TATGAGCTTCTTTGGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:147,211:358,0:0:2,0:26:1:30:1:1:0:60:58.667:1:0:0.1 0/1:355:164:67,97:80,110:190,164:0.462:2,2:24.4:1:31.1:1:0.82944:1.0528:60:163:0.4631:0:1.1 +2 173915007 . G A 30 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=GTAATTACAGTATATTGTAC;RSEQ=TGTAGAGTACACTGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:42:1:32:1:1:0:60:4:1:0:1 1/0:4:2:0,2:0,2:2,2:0.5:0,0:13:1:30:1:1:0:60:4:0.5:0:1 +2 175584493 . AT A 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.10537;LSEQ=AGCCATTTGGGTTGCTTCTG;RSEQ=TTTTTTTTTTACTAGTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:6:6,0:49,3:52,6:0.1034:2,0:28.3:1:32.2:1:1:0:59.3:12:0.1053:0:0 0/1:53:6:6,0:43,4:47,6:0.1132:2,0:33:1:31.8:1:1:0:59.7:12:0.1132:0:0 +2 175585567 . T TAAA 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTAAAATACATTAAACTA;RSEQ=AAAAAAAAAAAAAAGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:18:1:31.5:1:1:0:60:4:1:0.5:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 175585616 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATATATGCATACACATTT;RSEQ=TGTGTGGGCATGTGTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28.5:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 175586803 . CAT C 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGTTTACATAATTCTTGA;RSEQ=GTGGTAACTGCTGCTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:33.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 175898771 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20094;SOR=Inf;LSEQ=CATAATAACACTTGTGGGGC;RSEQ=TTCCTTTTTGAACAGTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:40,48:88,0:0:2,0:24.2:1:30.7:1:1:0:59.5:176:1:0:0.1 0/1:72:2:1,1:30,40:70,2:0.0278:2,2:32:1:30.5:1:1:1.33:59:4:0.0278:0:1 +2 175898881 . T G 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.10694;LSEQ=TGTTTTCTAAAAGACCAACA;RSEQ=ATATTGGGTGCCTCTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:1,7:8,3:0.2727:2,2:12:1:32:1:0.49091:3.06:60:6:0.2727:0:1 0/1:17:5:0,5:2,10:12,5:0.2941:2,0:21.2:1:31.6:1:1:0:60:10:0.2941:0:1 +2 177739275 . TTGC T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.51429;SOR=Inf;LSEQ=TTTATTAGATGCTGTTGCTG;RSEQ=TGCTGCTGCTGCAAAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:34,0:0:2,0:24.8:1:31.1:1:1:0:60:68:1:0:0.1 0/1:51:2:1,1:24,25:49,2:0.0392:2,2:30:0:32:0:1:1.04:60:4:0.0392:0:0 +2 178095460 . TTAGTA T 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=TCACATCACAGTAGGAGCTT;RSEQ=TAATAGTACAAAAAAACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:248,59:307,0:0:2,0:24:1:30.4:1:1:0:60:60.4:1:0:0.1 0/1:294:11:7,4:206,77:283,11:0.0374:2,2:29.8:1:28.9:1:0.50222:1.52637:60:22:0.0377:0:0 +2 178095536 . TCTTA T 175 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTTTCTTAACATCTGGCT;RSEQ=CTTTTGGGAACAAGGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:891:0:0,0:535,356:891,0:0:2,0:25.9:1:32.5:1:1:0:60:73.25:1:0:0.1 0/1:878:53:28,25:466,356:822,53:0.0604:2,2:24.5:1:30.7:1:0.66845:1.16853:58.8:106:0.0612:0.0103:0.2 +2 178097082 . T TA 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.62278;SOR=3.00915;LSEQ=ATGACTAAAGGCACTGAATA;RSEQ=AAAAAAAATCTCCAGTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:1:1,0:137,31:168,1:0.0059:2,0:16:0:24:0:1:0:60:2:0.0062:0:0 0/1:170:3:3,0:139,28:167,3:0.0176:2,0:9:1:29.3:1:1:0:60:6:0.0178:0.0118:0 +2 178097666 . C T 96 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=0;LSEQ=TGCCCAGCTGGCTCTTTACT;RSEQ=ACCAAACCTCTTAGATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:0,9:1:0,0:25.2:1:30.4:1:1:0:56:18:1:0:1.1 1/0:5:3:3,0:2,0:2,3:0.6:0,0:15.3:1:32.3:1:1:0:60:6:0.6:0:1 +2 178097778 . G GT 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.10289;SOR=2.62316;LSEQ=GGTTTTGTATTGTGTGAAGG;RSEQ=TTTTTTTTTTTCTTAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:7:6,1:60,2:62,7:0.1:1,2:26.7:1:30:1:0.27816:4.80468:60:14:0.1:0.0143:0 0/1:44:10:9,1:33,1:34,10:0.2273:1,2:21.6:1:29.8:1:0.40698:3.53056:60:20:0.2381:0.0455:0 +2 178098087 . CA C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5074;SOR=1.28712;LSEQ=CCTGATAAAAGGGAATGACA;RSEQ=AAGGAAAACAAAAATGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:20:1,19:27,156:183,20:0.098:2,1:23.8:1:33.2:1:0.32088:3.27518:58.7:40:0.1:0.0196:0.1 0/1:171:21:6,15:30,120:150,21:0.1228:2,2:26.6:1:30.8:1:0.39396:1.60:60:42:0.1235:0.0234:0.1 +2 178098917 . C T 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=36.36819;LSEQ=TTTCCAGCTCATACTCTTTC;RSEQ=GTCGCTGACTGAAGTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:843:1:1,0:334,507:841,1:0.0012:2,0:14:0:16:0:0.39786:0:60:0:0:0:2 0/1:941:39:16,23:391,509:900,39:0.0414:2,2:23.9:1:29.7:1:0.86933:1.10417:60:78:0.0416:0:1.1 +2 178099012 . CA C 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.36013;SOR=0.31332;LSEQ=TCCATGTCCTATGTTTAAGA;RSEQ=AAAAAAGGAAGGAGAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:2,1:50,192:242,3:0.0122:2,2:21:1:31.3:1:0.11483:7.59:60:6:0.0124:0.0041:0.3 0/0:259:1:0,1:63,195:258,1:0.0039:2,0:24:0:33:0:1:0:60:2:0.0039:0:0 +2 178099031 . G A 30 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61092;SOR=2.15742;LSEQ=ACAAAAAAAGGAAGGAGAGA;RSEQ=CTCATGTTTTTTAAATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:1,0:29,157:186,1:0.0053:2,0:1:0:26:0:0.16043:0:60:2:0.0054:0:1 0/1:175:2:1,1:36,137:173,2:0.0114:2,2:6:0:30:1:0.37911:3.77:60:4:0.0116:0:1.5 +2 178099051 . A G 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59292;SOR=2.40664;LSEQ=GCTCATGTTTTTTAAATGAC;RSEQ=GATACCACATAAATTAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:0,1:10,112:122,1:0.0081:2,0:34:0:14:0:1:0:60:0:0:0:1 0/1:103:2:1,1:9,92:101,2:0.0194:2,2:17.5:1:28.5:1:0.18561:9.75:60:4:0.0198:0:1 +2 178129188 . C T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24968;SOR=0;LSEQ=CCGGTTGCGGCTGTCCCTCC;RSEQ=GGGCCGCGGTTCCCTAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:3:3,0:165,9:174,3:0.0169:2,0:34.3:1:25.7:1:1:0:60:2:0.0115:0:2 0/0:160:0:0,0:144,16:160,0:0:2,0:22.5:1:30.3:1:1:0:60:39:1:0:0.4 +2 178129390 . TGGC T 136 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=3e-04;SOR=9.11747;LSEQ=CGCGGACAGGGCGGCTCTGG;RSEQ=GGCGGCGGCGGCGGTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:13,78:91,2:0.0215:2,2:24:0:33.5:1:0.2798:5.82:60:4:0.0215:0:0.5 0/1:131:22:3,19:27,81:108,22:0.1679:2,2:9.3:1:30.5:1:0.40434:2.10065:59.7:44:0.1692:0.0916:0.7 +2 178129399 . C T 93 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=3;SSF=0.02619;SOR=Inf;LSEQ=GGCGGCTCTGGTGGCGGCGG;RSEQ=GGCGGCGGTGGCGGCTGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:7,43:50,0:0:2,0:7.4:1:30.2:1:1:0:60:49:1:0:0.3 0/1:84:9:1,8:16,58:74,9:0.1071:2,2:5.2:1:29.6:1:0.67777:2.18976:58.9:18:0.1111:0:1.6 +2 178129402 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.53455;SOR=Inf;LSEQ=GGCTCTGGTGGCGGCGGCGG;RSEQ=GGCGGTGGCGGCTGCGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:3,33:36,0:0:2,0:7.2:1:30.5:1:1:0:60:72:1:0:0.3 0/1:64:2:1,1:12,50:62,2:0.0313:2,2:32:1:31.5:1:0.36756:4.04:60:4:0.0313:0:1.5 +2 178130037 . T G 43 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGGGGAGATGTGGACAGC;RSEQ=CCGGCAGCTCGTGTTCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:10:1:27.3:1:1:0:60:6:1:0:1.7 +2 178130073 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCAGTCACCCTGAACGCCC;RSEQ=CCTCTGAACTCCCACGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:29.5:1:1:0:60:4:1:0:2 +2 178209345 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34375;SOR=0;LSEQ=GAAGTCCATAAGCTTCTGAT;RSEQ=TGCAAACTTCCCTTCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:16,5:0,0:0,21:1:0,2:23:1:30:1:1:0:60:20:1:0:1.2 1/1:11:10:9,1:1,0:1,10:0.9091:0,2:22.3:1:30.8:1:1:0:60:20:0.9091:0:1.1 +2 178209494 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23296;SOR=0;LSEQ=GATAACAACCTATGTGTCCT;RSEQ=TATGCCAAATGTGTAACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:50,39:89,2:0.022:2,2:34.5:1:31:1:1:1.27851:60:4:0.022:0:1.5 0/0:97:0:0,0:59,38:97,0:0:2,0:24.4:1:30.2:1:1:0:60:96:1:0:0.1 +2 178209507 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.50209;SOR=Inf;LSEQ=GTGTCCTCTATGCCAAATGT;RSEQ=TAACAATTATGGCAAAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:54,49:103,0:0:2,0:27.5:1:32.4:1:1:0:60:102:1:0:0.2 0/1:124:2:1,1:72,49:121,2:0.0161:2,2:24:1:27:1:1:1.46465:60:4:0.0163:0:1 +2 178209534 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20558;SOR=0;LSEQ=TTATGGCAAAAGACATCCAG;RSEQ=TAGCACACCACATATGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:45,63:108,2:0.0182:2,2:39.5:1:32:1:1:1.40:60:4:0.0183:0:1 0/0:132:0:0,0:61,71:132,0:0:2,0:28.3:1:30.8:1:1:0:60:65:1:0:0.2 +2 178209544 . A T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50002;SOR=Inf;LSEQ=AGACATCCAGCTAGCACACC;RSEQ=CATATGTGAAGAACATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:39,65:104,0:0:2,0:26.8:1:30:1:1:0:60:208:1:0:0.1 0/1:119:2:1,1:49,68:117,2:0.0168:2,2:33:0:31:1:1:1.38:60:4:0.0169:0:1.5 +2 178209572 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50857;SOR=Inf;LSEQ=GAAGAACATGCTTAAGAATT;RSEQ=ACTGTGCTGGAAAACATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:20,53:73,0:0:2,0:23.9:1:31.8:1:1:0:60:72:1:0:0.2 0/1:99:2:1,1:38,59:97,2:0.0202:2,2:31.5:1:27.5:1:1:1.55:60:4:0.0202:0:1 +2 178209597 . TTC T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.51513;SOR=Inf;LSEQ=TGCTGGAAAACATTTCATTC;RSEQ=TCTCTCTCTCTTCTTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:3,30:33,0:0:2,0:25.5:1:30.5:1:1:0:60:32:1:0:0 0/1:50:2:0,2:9,39:48,2:0.04:2,0:32:1:32:0:1:0:60:4:0.0417:0:0 +2 178848343 . AAAAC A 80 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.39563;SOR=0.28412;LSEQ=GTGATAAATTAATTACTTAA;RSEQ=AAACAAACAAACAAACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:5,1:25,0:25,6:0.1935:1,2:17.2:1:31.3:1:0.19355:0:60:12:0.1935:0:0.3 0/1:16:1:1,0:15,0:15,1:0.0625:1,0:39:0:32:0:1:0:60:2:0.0625:0:1 +2 178848402 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20115;SOR=Inf;LSEQ=TGCTATTTGGTGGACTAAAG;RSEQ=AAACTTTTTTGTATGTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:68,15:83,0:0:2,0:23.3:1:30.9:1:1:0:60:26.667:1:0:0.2 0/1:68:2:1,1:61,5:66,2:0.0294:2,2:28.5:1:30:1:0.16989:11.22821:60:4:0.0313:0:1 +2 178848433 . TA T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00041;SOR=Inf;LSEQ=GTATGTTCTGGGTTTCTTAA;RSEQ=TTTTTTATTTTGAAATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:112,43:155,0:0:2,0:24.1:1:28.9:1:1:0:60:76.5:1:0:0.5 0/1:136:10:7,3:90,36:126,10:0.0735:2,2:20.4:1:29.2:1:1:1.07088:60:20:0.0746:0.0294:1 +2 178848447 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24398;SOR=Inf;LSEQ=TCTTAATATTTTTTATTTTG;RSEQ=AATACATGGCACTGATGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:138,50:188,0:0:2,0:25.3:1:30.2:1:1:0:60:61.667:1:0:0.5 0/1:184:2:1,1:121,61:182,2:0.0109:2,2:25.5:1:28.5:1:1:1.97572:60:4:0.011:0:1 +2 178848451 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23716;SOR=0;LSEQ=AATATTTTTTATTTTGAAAT;RSEQ=CATGGCACTGATGAATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:139,55:194,2:0.0102:2,2:40:1:32:1:0.49084:2.51361:60:4:0.0102:0:1 0/0:207:0:0,0:135,72:207,0:0:2,0:22.8:1:27.9:1:1:0:60:68:1:0:0.4 +2 178848487 . T C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31884;LSEQ=TTTATCATTGAACTGCAAGA;RSEQ=AGCCAGAAAACTAAGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:139:78,61:96,68:164,139:0.4587:2,2:26.1:1:32.2:1:0.72681:1.10371:60:138:0.46:0:1.1 0/1:306:65:36,29:130,111:241,65:0.2124:2,2:28.1:1:31.5:1:0.88889:1.06:60:130:0.2138:0:1.2 +2 178882890 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19862;SOR=Inf;LSEQ=TGCCACCCAGCCGCCATTCT;RSEQ=TTTCCAAGGCTGCGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:99,26:125,0:0:2,0:22.4:1:32.5:1:1:0:60:124:1:0:0.1 0/1:101:2:2,0:82,17:99,2:0.0198:2,0:32:1:31.5:1:1:0:60:4:0.0202:0:1 +2 178882923 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22125;SOR=Inf;LSEQ=CGTCTGTCCACTGGACTGGT;RSEQ=ACGGGGTTGTCAGTGTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:141,78:219,0:0:2,0:25.8:1:32:1:1:0:60:108.5:1:0:0.1 0/1:195:2:1,1:129,64:193,2:0.0103:2,2:23:1:25.5:1:1:2.00786:60:4:0.0105:0:1 +2 178883022 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49859;SOR=0;LSEQ=CAGCCCTCACTCTCCTTAGT;RSEQ=ACTAAGACTTTGAACAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:56,120:176,2:0.0112:2,2:31.5:1:28:1:0.53914:2.13:60:4:0.0114:0:1 0/0:178:0:0,0:55,122:177,0:0:2,0:24.6:1:30.9:1:1:0:60:87.5:0.9943:0:0.1 +2 178883096 . T TTTGGCACACTTGACTTTAAC 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=12.23819;LSEQ=AAAGCTGCCAAGGCAGGCCT;RSEQ=TTGGCACACTTGACTTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:9:1,8:4,40:44,9:0.1698:2,2:24:1:30.7:1:1:1.24:57.7:18:0.1731:0.0566:0.3 1/0:36:26:4,22:0,10:10,26:0.7222:0,2:23.2:1:30.3:1:0.55861:0:58.2:52:0.7222:0.3333:0.4 +2 178883104 . A ACTTGACTTTAACTTGGCACG 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CAAGGCAGGCCTTTTGGCAC;RSEQ=CTTGACTTTAACCTTTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:33:3,30:1,18:19,33:0.6346:1,2:25.4:1:30.1:1:1:1.78:56.5:32:0.6275:0.2308:0.2 0/0:31:0:0,0:2,22:24,0:0:2,0:13.1:1:30.7:1:1:0:59.5:48:0.7742:0:0.2 +2 178883193 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=Inf;LSEQ=CCATGCTGTGGAAGCTCTGA;RSEQ=CTTTTAGACTTAACACCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:9,0:0:2,0:24.8:1:32.2:1:1:0:60:18:1:0:0.4 0/1:12:2:1,1:3,7:10,2:0.1667:2,2:45.5:1:29:1:1:2.16:60:4:0.1667:0:1 +2 178883209 . C A 46 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26154;SOR=0.18798;LSEQ=CTGACCTTTTAGACTTAACA;RSEQ=CTTAAAAAGTAATTCTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:0,4:4,3:0.4286:0,2:22.3:1:29.3:1:0.42857:0:60:6:0.4286:0:1 0/1:9:1:0,1:2,6:8,1:0.1111:2,0:28:0:31:0:1:0:60:2:0.1111:0:1 +2 178883450 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCAGCTATTCTTTTTTA;RSEQ=TTTTTGTAGACACAGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 179632710 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=5.24424;LSEQ=ATTCAGAGGAAACTGGGAAT;RSEQ=ACTGGAATGTAGCAAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:584:194:97,97:204,186:390,194:0.3322:2,2:24.9:1:31.7:1:0.66036:1.0966:59.9:63.667:0.3316:0:1.1 1/0:495:358:194,164:74,62:136,358:0.7232:2,2:25.7:1:30.4:1:1:1.00896:59.8:43.75:0.7202:0:1.1 +2 180262226 . TAC T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATATATACACACATACGCA;RSEQ=ACACACATATACGTATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:28.4:1:1:0:60:4:1:0.5:0 +2 180264359 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22304;SOR=Inf;LSEQ=GATAAATCCTTAGCAATAAA;RSEQ=GTAATTCTTCACGAGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:118,20:138,0:0:2,0:19.6:1:32.6:1:1:0:60:68:1:0:0.1 0/1:124:2:1,1:103,19:122,2:0.0161:2,2:14:1:29.5:1:0.29767:5.30948:60:4:0.0164:0:1.5 +2 180264698 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11234;SOR=Inf;LSEQ=GCTTGACCACACCATCCCCT;RSEQ=CATCTGGAGTCACATCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:71,151:222,0:0:2,0:24.3:1:32.1:1:1:0:59.9:73:1:0:0.1 0/1:208:3:1,2:78,127:205,3:0.0144:2,2:10.7:1:25.7:1:1:1.22713:60:2:0.0097:0:1 +2 180264701 . T C 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACCACACCATCCCCTGCA;RSEQ=CTGGAGTCACATCCCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:63,146:209,0:0:2,0:24.9:1:30.3:1:1:0:60:103.5:1:0:0.1 0/1:205:20:9,11:68,117:185,20:0.0976:2,2:25.9:1:29.5:1:0.47584:1.41:58.6:19:0.0945:0:1 +2 180264797 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22418;SOR=Inf;LSEQ=GGACTTGCTGTTTCTCCATC;RSEQ=GCTCCCAGAACTGCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:78,55:133,0:0:2,0:24.8:1:31.7:1:1:0:59.6:132:0.9925:0:0.1 0/1:121:2:1,1:55,64:119,2:0.0165:2,2:36:1:29:1:1:1.16:60:4:0.0167:0:1 +2 180264857 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.18783;SOR=Inf;LSEQ=TCTGCTGGTTCGTGGCCTCT;RSEQ=TCACCAATAGTGGATGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:108,43:151,0:0:2,0:23.4:1:32.2:1:1:0:59.6:74.5:1:0:0.1 0/1:116:2:1,1:62,52:114,2:0.0172:2,2:9:0:31.5:1:1:1.19049:60:4:0.0174:0:1.5 +2 180265078 . AG A 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGAGGCAGCTGGCGTGGA;RSEQ=CTTGTTTAGTGACCTCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:219,178:397,0:0:2,0:25.6:1:32.8:1:1:0:60:78.4:0.9975:0:0.3 0/1:389:27:15,12:190,172:362,27:0.0694:2,2:27.9:1:32.6:1:0.84284:1.13:60:54:0.0705:0.0077:0.2 +2 180265135 . C T 199 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00986;LSEQ=TACAATTTCCAAGTGCGTTC;RSEQ=GAAAACTCCTGGGGGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:84:47,37:287,198:485,84:0.1476:2,2:24.6:1:31.2:1:0.63155:1.14082:56.3:168:0.1495:0:1.9 0/0:588:1:0,1:349,238:587,1:0.0017:2,0:1:0:24:0:0.40646:0:47:2:0.0017:0:2 +2 180265158 . T C 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04213;LSEQ=AAACTCCTGGGGGCTTGCTT;RSEQ=AGCCCGTCTGTCACCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:661:660:365,295:0,1:1,660:0.9985:0,2:26:1:32.2:1:0.44781:0:53.2:219:0.9985:0:1.4 1/1:748:722:392,330:13,13:26,722:0.9652:2,2:25.9:1:30.6:1:0.69289:1.19:52:50.571:0.9646:0:1.1 +2 180265174 . G A 212 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01165;LSEQ=GCTTTAGCCCGTCTGTCACC;RSEQ=CCTCCTTCCTTGCCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:129:64,65:348,291:639,129:0.168:2,2:23.8:1:30.3:1:0.33386:1.21425:55.4:128:0.1684:0:1.8 0/0:854:2:1,1:440,411:851,2:0.0023:2,2:35.5:1:30:1:1:1.07044:34:4:0.0024:0:2.5 +2 180265634 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1833;SOR=Inf;LSEQ=TTGACCTCTCTGGCACTGCA;RSEQ=AGTGCATGCAGGTAGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:28,161:189,0:0:2,0:24.4:1:32.6:1:1:0:59.9:36.8:1:0:0.1 0/1:142:2:1,1:31,109:140,2:0.0141:2,2:27.5:1:27:1:0.40116:3.48:60:4:0.0141:0:1.5 +2 180265684 . G T 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=TTTTGTTTATCCACTCACTT;RSEQ=TTAATGGTCATTTAAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:1,54:55,0:0:1,0:24.3:1:32.6:1:1:0:59.5:26.5:1:0:0.1 0/1:51:9:0,9:2,39:41,9:0.1765:1,0:26.2:1:30.2:1:1:0:60:18:0.1837:0:1 +2 180265720 . G C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07219;SOR=Inf;LSEQ=GTTGTTTCCACCTTTTGGCT;RSEQ=TTGTGCACAGCGCTCCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:28,0:0:1,0:23.5:1:32.3:1:1:0:59.1:56:1:0:0.1 0/1:21:3:0,3:0,18:18,3:0.1429:1,0:23:1:32.3:1:1:0:60:6:0.1429:0:3 +2 181049373 . A T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATCTTCACATGGTGTTC;RSEQ=TCCTCTGCACATCTGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:4,8:0,0:0,12:1:0,2:21.5:1:30.9:1:1:0:60:24:1:0:1 1/1:3:3:1,2:0,0:0,3:1:0,2:17.7:1:28.7:1:1:0:60:6:1:0:1 +2 182275634 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=TCCTTCACCGGCAACAAAGG;RSEQ=ATCCAGGTTCCCTCATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:34.6:1:28.8:1:1:0:60:16:1:0:0.1 0/1:5:2:1,1:2,1:3,2:0.4:2,2:25:0:31.5:1:1:1.7321:26:4:0.4:0:1.5 +2 182276161 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46154;SOR=Inf;LSEQ=GGGGTCCCAAGACTTTTCCC;RSEQ=ACAGCCCAACACACCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:7,0:0:2,0:33.1:1:31.1:1:1:0:60:14:1:0:0 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:37.5:1:28:1:1:1.41418:60:4:0.2857:0:1 +2 182276675 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51588;SOR=0;LSEQ=AAATCAGATGAATAAGGCCT;RSEQ=AAATGAACTTCCAGCAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:24,33:57,2:0.0339:2,2:11:1:31.5:1:1:1.37:32.5:4:0.0345:0:1 0/0:39:0:0,0:19,20:39,0:0:2,0:23.9:1:30.9:1:1:0:58.6:78:1:0:0.1 +2 182276873 . T TCAA 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.18347;SOR=0;LSEQ=CTCACGAAGATGAGAAAGAA;RSEQ=CAACAACAACAACAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:42:0:32.3:1:1:1.37:43:4:0.1429:0:0.5 0/0:18:0:0,0:6,11:17,0:0:2,0:24.8:1:29.1:1:1:0:58.5:34:1:0:0.1 +2 183484910 . C CTTTA 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ACTTTAAAATGTATTTATTT;RSEQ=TTTATTTAATAAATAACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:32:1:31.6:1:1:0:60:6:0.4286:0.1429:0.3 0/0:1:0:0,0:1,0:1,0:0:0,0:19:0:32:0:1:0:60:2:1:0:0 +2 183484981 . T C 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.0634;SOR=0;LSEQ=CAACTATTAACACATTTCTA;RSEQ=ATTAATATGAATTTCAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:6,0:17,0:17,6:0.2609:1,0:27.5:1:33.7:1:1:0:60:12:0.2727:0:1 0/0:15:0:0,0:15,0:15,0:0:1,0:17.1:1:31.1:1:1:0:60:30:1:0:0 +2 183485158 . A C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13561;LSEQ=ATATGTGTGGAATTATCCTG;RSEQ=CAAAAATATAAGTTGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:403:304:164,140:54,44:98,304:0.7543:2,2:25.8:1:31.6:1:0.90731:1.04757:60:42.429:0.75:0:1.1 0/1:375:110:64,46:143,121:264,110:0.2933:2,2:25.3:1:30.6:1:0.49535:1.18:60:35.667:0.2908:0:1.1 +2 183485213 . TC T 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.66089;SOR=1.8631;LSEQ=AAATTTATCTTCTATTGTTA;RSEQ=CCCCATCCAAACTGGGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:2:1,1:155,213:368,2:0.0054:2,2:33.5:1:30.5:1:1:1.37:60:4:0.0054:0:0 0/1:299:3:1,2:116,178:294,3:0.01:2,2:32.7:1:30.7:1:1:1.30224:60:6:0.01:0:0 +2 184373044 . C T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01095;SOR=0;LSEQ=CAGAAGCCTTTTCCTGTAAA;RSEQ=GCCAGGTGGCAGTCGTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:2,8:10,4:0.2857:2,2:29.3:1:31:1:1:1.31:28.5:8:0.2857:0:1 0/0:26:0:0,0:7,19:26,0:0:2,0:33:1:29.8:1:1:0:35.8:52:1:0:0.2 +2 184756508 . C T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCAGGAATAACAAAAT;RSEQ=TATCCTTGCTTTACAATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:38:0:30:1:1:0:33:4:0.5:0:1 +2 184756657 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14541;SOR=Inf;LSEQ=ACACTAAACAGTCAGGGATA;RSEQ=TATGAGATGCTGCCCAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:25,5:30,0:0:2,0:26.3:1:33:1:1:0:58.8:60:1:0:0.1 0/1:19:2:1,1:14,3:17,2:0.1053:2,2:32.5:1:31:0:0.38596:4.1833:30:4:0.1111:0:2.5 +2 184756669 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16594;SOR=Inf;LSEQ=CAGGGATAGTATGAGATGCT;RSEQ=CCCAGTATTTACAGGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:29,11:40,0:0:2,0:22.8:1:31.8:1:1:0:59:39:1:0:0.1 0/1:28:2:1,1:18,8:26,2:0.0714:2,2:27:0:30.5:1:1:2.17949:30:4:0.0714:0:2.5 +2 184756721 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4969;SOR=0;LSEQ=CAGACAATGTCTTTCAAACT;RSEQ=TTTTACCAACCTCTGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:44,34:78,2:0.025:2,2:48:1:30.5:1:1:1.2899:22:4:0.0253:0:1 0/0:78:0:0,0:45,33:78,0:0:2,0:29.1:1:30.6:1:1:0:55.9:38:1:0:0.2 +2 184756785 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49606;SOR=0;LSEQ=CTAGGTCCCGTGGCAGCCAT;RSEQ=TTGCTGTTATTCCTCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:24,38:62,2:0.0313:2,2:34.5:1:30:1:1:1.57:51:4:0.0313:0:1 0/0:64:0:0,0:29,35:64,0:0:2,0:24.8:1:30.9:1:1:0:58.3:63:1:0:0.2 +2 184756811 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.54455;LSEQ=GTTATTCCTCTTTGGACCCT;RSEQ=TATTTTTAATCTCCTTGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:9,31:40,2:0.0476:2,2:28:1:28.5:1:0.42393:3.32:56.5:4:0.0476:0:1 0/1:38:1:1,0:12,25:37,1:0.0263:2,0:1:0:23:0:0.34211:0:60:2:0.0263:0:1 +2 185198135 . C A 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.57733;LSEQ=GCAGACAGAGAAGCAAGAAT;RSEQ=AATACTGTTGACTCCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:25.5:1:30:0:1:0:60:4:0.6667:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:37:0:28:0:1:0:60:2:0.5:0:1 +2 185198375 . A G 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTAAGTAACAATGACCTA;RSEQ=GTGGAAAAATTAGAATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:221,160:381,0:0:2,0:25.8:1:30.8:1:1:0:60:53.429:1:0:0.7 0/1:298:16:10,6:155,125:280,16:0.0537:2,2:25.3:1:30:1:0.61617:1.34:60:15:0.0517:0:1.2 +2 185198425 . T A 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00058;SOR=0.56302;LSEQ=AGCCAGTAGCATATTCAGAC;RSEQ=TTCATTTAGCCTGGACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:425:343:158,185:38,44:82,343:0.8071:2,2:25.8:1:30.4:1:1:1.01119:60:41.875:0.8053:0:1.8 1/0:389:273:133,140:56,60:116,273:0.7018:2,2:25.6:1:29.8:1:1:1.02:59.9:44.5:0.7008:0:1.8 +2 185198456 . A C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43447;SOR=1.1733;LSEQ=CTGGACACCTCTTGACTCCA;RSEQ=AGGGAAGCCACAAGTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:360:286:104,182:33,41:74,286:0.7944:2,2:24.5:1:32.3:1:0.22677:1.40712:60:142:0.7955:0:1.9 1/1:310:254:114,140:26,29:55,254:0.8194:2,2:25.6:1:31.2:1:0.76686:1.10068:60:62.5:0.8197:0:1.8 +2 185198788 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCAAATAAAATTATTC;RSEQ=CAGACTAGAGTTAGCAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25.5:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 186821397 . C G 40 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=GTATACTTCTTTGGGTAGAG;RSEQ=AGGCTGGCACTTCAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:18.5:1:33.8:1:1:0:60:8:1:0:0.3 1/1:3:3:2,1:0,0:0,3:1:0,2:26.3:1:25.7:1:1:0:60:2:1:0:1 +2 186821594 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49847;SOR=Inf;LSEQ=TGCCAACAGCATGCTGGGTA;RSEQ=ATTGTAGAATATTCCAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:49,39:88,0:0:2,0:34.9:1:31.8:1:1:0:60:21:1:0:0.1 0/1:97:2:1,1:54,41:95,2:0.0206:2,2:26:0:28.5:1:1:1.31328:60:4:0.0208:0:1 +2 186821699 . C T 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01153;SOR=Inf;LSEQ=TCACCATTCTTACAGGTTCA;RSEQ=ATGTATATGGCCAAAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:3,22:25,0:0:2,0:23.7:1:32.4:1:1:0:60:24:1:0:0.1 0/1:29:7:1,6:5,17:22,7:0.2414:2,2:20.6:1:28.9:1:1:1.73356:60:14:0.2414:0:1 +2 186821709 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48986;SOR=Inf;LSEQ=TACAGGTTCACATGTATATG;RSEQ=CCAAAGGAGCACCTCCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:3,19:22,0:0:2,0:24:1:32.3:1:1:0:60:44:1:0:0.1 0/1:24:2:1,1:5,17:22,2:0.0833:2,2:21.5:1:27:1:0.44565:3.19:60:4:0.0833:0:1 +2 187558960 . G A 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20455;SOR=0;LSEQ=CTCGGCCTGGCCGTGGTGCT;RSEQ=CTGAAAGCGCGGCTGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:3,1:4,5:0.5556:2,0:34.6:1:29:1:0.44444:0:60:10:0.5556:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:43:1:31.3:1:1:0:60:6:1:0:0 +2 187559029 . A ACAG 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.71617;SOR=1.56464;LSEQ=TCCGACCTCAGCCTCATCCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:3,3:8,11:19,6:0.24:2,2:13.7:1:32.8:1:1:1.36:60:12:0.24:0.16:0.8 0/1:15:5:2,3:4,3:7,5:0.3333:2,2:38:1:29.3:1:1:1.88578:60:10:0.3333:0:0 +2 187559047 . G GCAA 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.55606;SOR=0.65568;LSEQ=CAACAGCAGCAGCAGCAGCA;RSEQ=CAACAACAACAACAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:6,8:3,4:7,14:0.5833:2,2:32.9:1:30.6:1:1:1:51.5:28:0.5833:0:0.1 0/1:21:10:5,5:4,7:11,10:0.4762:2,2:24.7:1:30.2:1:0.66992:1.70:59.4:20:0.4762:0.1429:0.4 +2 189541688 . A T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=16.68219;LSEQ=TTGCAAGGATTCCATTTACT;RSEQ=AATAAAAAATAGAGCAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:342:188:88,100:68,86:154,188:0.5497:2,2:26.5:1:29.7:1:0.6631:1.11:60:376:0.5529:0:1 1/1:343:327:146,181:6,10:16,327:0.9534:2,2:26.9:1:28.4:1:0.61716:1.34:60:108:0.9529:0:1.1 +2 189541807 . C G 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=0;LSEQ=CATAAAACATTCAAAATTAT;RSEQ=TTGATTATTTGCTTTATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:13:0,13:2,34:36,13:0.2653:2,1:24.8:1:33.1:1:1:0:60:26:0.2708:0:1.2 0/0:39:0:0,0:0,39:39,0:0:1,0:22.1:1:31.8:1:1:0:60:38:1:0:0 +2 190656296 . T G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GAGGTTGCAGTGAGTCGAGA;RSEQ=CACGCCACTGCACTCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:25.6:1:30.4:1:1:0:55:10:1:0:0 0/1:5:2:1,1:3,0:3,2:0.4:0,2:11.5:1:33.5:1:0.4:0:52.5:4:0.4:0:1.5 +2 190656341 . CA C 50 v3;MSI12;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.07792;SOR=Inf;LSEQ=TGACAGCGAGATTTCATCTC;RSEQ=AAAAAAAAAAAAGAAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:10,1:11,0:0:2,0:16.9:1:30.5:1:1:0:57.5:22:0.9167:0:0.5 0/1:10:3:3,0:6,0:6,3:0.3:0,0:20:1:31.7:1:1:0:60:6:0.3:0:0 +2 190656484 . C T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25027;SOR=Inf;LSEQ=TGTTGGTCAGGAATGCTTAA;RSEQ=AATTCTTACAAGTTGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:192,58:250,0:0:2,0:23:1:32.5:1:1:0:60:500:1:0:0.1 0/1:275:3:1,2:207,65:272,3:0.0109:2,2:7.3:1:26.7:1:0.14811:6.31521:60:6:0.011:0:1.3 +2 190656496 . G T 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37601;SOR=3.65401;LSEQ=ATGCTTAACAATTCTTACAA;RSEQ=TTGCATTTTTATCTTCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:1:0,1:215,87:302,1:0.0033:2,0:1:0:27:0:0.29043:0:60:2:0.0034:0:1 0/1:334:4:2,2:240,90:330,4:0.012:2,2:16.5:1:28:1:0.30485:2.65756:60:8:0.0122:0:1.3 +2 190670363 . GT G 89 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.20693;SOR=0.38545;LSEQ=AAGTGTTAGTTTTATTAGAT;RSEQ=TTTTTTCCCCCAGGTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:691:7:4,3:429,255:684,7:0.0101:2,2:22.3:1:31.8:1:0.71618:1.26131:60:14:0.0102:0.0014:0.3 0/0:764:3:1,2:442,319:761,3:0.0039:2,2:22.3:1:30.7:1:0.5755:2.76748:60:6:0.004:0.0013:0.7 +2 190670539 . T TA 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.42557;SOR=0.76325;LSEQ=TTCTGTCTTAATTGTTGGTT;RSEQ=AAAAAAAAAAAGTTACTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:27:1,26:12,136:148,27:0.1517:2,1:29:1:30.4:1:0.69464:2.28576:60:12.5:0.1462:0.0112:0 0/1:150:18:2,16:18,112:130,18:0.12:2,2:22.3:1:30.6:1:1:1.28368:59.7:36:0.1241:0.0067:0.3 +2 190670808 . CAT C 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGATTAAAATTTTATTGAAA;RSEQ=ATAAAACATAATTGATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:39.8:1:31.5:1:1:0:54.3:8:0.6667:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 190682613 . CT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.54167;SOR=0;LSEQ=AGTAGTTTGCAAAGTTGAGC;RSEQ=TTGGGTTTCTAGAATTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:40,0:40,2:0.0476:1,2:28:1:31:1:0.04762:0:60:4:0.05:0:0 0/0:22:0:0,0:22,0:22,0:0:1,0:18:1:30:1:1:0:60:44:1:0:0.1 +2 190682632 . G C 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.3588;SOR=0.49813;LSEQ=CCTTTGGGTTTCTAGAATTG;RSEQ=AGGAGGAGACCTTCAGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:9:9,0:42,1:43,9:0.1731:1,0:31.6:1:30:1:1:0:60:8:0.1569:0:1.1 0/1:32:3:3,0:29,0:29,3:0.0938:1,0:16:1:32.7:1:1:0:60:6:0.0938:0:1 +2 190682693 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50392;SOR=0;LSEQ=TGTATACGGATTTGAAGATC;RSEQ=GTGACGTTCCTTCCAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:127,50:177,2:0.0111:2,2:33:1:30.5:1:0.4898:2.52487:60:4:0.0112:0:1 0/0:146:0:0,0:103,43:146,0:0:2,0:25.9:1:30.1:1:1:0:60:145:1:0:0.1 +2 190682952 . T TAAAC 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.00087;SOR=Inf;LSEQ=TTTCTGGGTATATGATATAA;RSEQ=AAACAATGTATACTTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:21,117:138,0:0:2,0:23.7:1:29.2:1:1:0:60:276:1:0:0 0/1:149:11:4,7:27,110:137,11:0.0738:2,2:24.8:1:29.2:1:0.24302:2.31:60:22:0.0738:0.0134:0.1 +2 190708712 . G A 225 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTTATTTGGCAGAAAAGCA;RSEQ=AGTATCAGATCACAAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:171:99,72:475,353:828,171:0.171:2,2:27.5:1:30.4:1:0.93241:1.02:60:56:0.169:0:1.1 0/0:837:0:0,0:453,383:836,0:0:2,0:26.1:1:30.9:1:1:0:60:118.429:0.9988:0:0.1 +2 190710798 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGTAACTTCCACAGAAAG;RSEQ=GGGGACATGAGAGGTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:30:1:1:0:60:4:1:0:1.5 +2 190717314 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTTTTTATACCTTTCAAA;RSEQ=TGTTATATATAGCCAGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:0,2:148,22:170,2:0.0116:2,0:24.5:1:28.5:1:0.01877:0:60:4:0.0118:0:1 0/0:83:0:0,0:73,10:83,0:0:2,0:21.4:1:31.8:1:1:0:60:82:1:0:0 +2 190717517 . G GA 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.0237;LSEQ=CTTAAAGGTAGTATGCTTTA;RSEQ=AAAAAAAAAATTATTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:21:10,11:89,202:291,21:0.0654:2,2:26.7:1:30.8:1:0.14317:2.06:59:42:0.0693:0.0031:0.1 0/1:329:22:5,17:103,199:302,22:0.0669:2,2:27.5:1:29.9:1:0.3522:1.75701:60:44:0.0692:0.0091:0.4 +2 190717528 . T A 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71439;SOR=0.683;LSEQ=TATGCTTTAGAAAAAAAAAA;RSEQ=TATTTGAATTGGAAATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:4:1,3:73,190:263,4:0.015:2,2:6.5:1:30.3:1:1:1.15203:60:8:0.0154:0:1 0/1:292:3:0,3:79,210:289,3:0.0103:2,0:5.6:1:29.8:1:0.5657:0:60:8:0.0093:0:1 +2 190717570 . T A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=Inf;LSEQ=ACATTGTAACAAGGACTGCT;RSEQ=CCAAGAATTTGCTCTAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:7,106:113,0:0:2,0:23.4:1:30.6:1:1:0:59.8:226:1:0:0.1 0/1:127:2:1,1:8,117:125,2:0.0157:2,2:17:1:24:1:0.13723:13.85:60:4:0.016:0:3.5 +2 190717628 . T C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01685;SOR=Inf;LSEQ=ATGTCATTTATTAAACATTA;RSEQ=GCATGATAGAAAGACATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:47,0:0:1,0:21.6:1:30.8:1:1:0:59.5:94:1:0:0.1 0/1:28:4:0,4:2,22:24,4:0.1429:2,0:14.3:1:30.3:1:1:0:60:8:0.1429:0:1 +2 190718940 . A C 197 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTATTTTCATAATTTCCCCT;RSEQ=ACATTTGTTAATTTGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:70:48,22:109,55:164,70:0.2991:2,2:24.4:1:32.3:1:0.87934:1.10:60:140:0.3004:0:1 0/0:228:0:0,0:160,68:228,0:0:2,0:23.3:1:28.1:1:1:0:60:113:1:0:0.1 +2 190719922 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23647;SOR=Inf;LSEQ=TTCTATATGACTCACTGTTT;RSEQ=AAAAGAATTTTTTTCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:7,96:103,0:0:2,0:24.2:1:31.8:1:1:0:60:206:1:0:0.1 0/1:98:2:1,1:10,86:96,2:0.0204:2,2:22.5:1:30:1:0.21292:8.25:60:4:0.0208:0:1 +2 190720748 . A AT 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.26847;SOR=0;LSEQ=ACTACCTAGATACTTGACCA;RSEQ=TTTTTTTTTTCATTCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:0,3:1,14:15,3:0.1667:1,0:26:1:23:1:1:0:60:2:0.125:0:0 0/0:11:0:0,0:1,10:11,0:0:2,0:24.3:1:29.8:1:1:0:60:22:1:0:0.2 +2 190720880 . CT C 29 d5;v3;MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=TCTTCAGCCTTTTTTGTCAT;RSEQ=TTTTTTTTTTTTAAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:3,1:0.25:0,0:25:0:31:0:1:0:60:2:0.25:0:0 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:27.5:1:29.5:1:1:2.45:60:4:0.4:0:0 +2 190728895 . T C 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GCCCTGCTATTTAAAAGACT;RSEQ=CTTGAGAATCATAAACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:126,158:284,0:0:2,0:25.7:1:30.2:1:1:0:59.9:55.8:1:0:0.1 0/1:322:19:5,14:138,165:303,19:0.059:2,2:25.7:1:30.5:1:0.1519:2.33602:60:18:0.0571:0:1.3 +2 190738206 . A AT 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24945;SOR=0;LSEQ=GAACTTAACTATGTGTTTTT;RSEQ=TTTTTTTTCTTTCAGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:3:2,1:158,54:212,3:0.014:2,2:22.7:1:28.8:1:1:1.46015:58.3:6:0.0141:0.0047:0.3 0/0:198:0:0,0:154,44:198,0:0:2,0:22.8:1:27.7:1:1:0:59.9:65:1:0:0.1 +2 190738435 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4973;SOR=0;LSEQ=ACAGGGGTCCCAACTCCCGG;RSEQ=CCAAGCCGGTTAGGAACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:10,81:91,2:0.0215:2,2:9.5:1:28.5:1:0.2237:7.77:60:4:0.0215:0:1 0/0:92:0:0,0:15,77:92,0:0:2,0:24.7:1:31.5:1:1:0:60:91:1:0:0.1 +2 191848154 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGGAATCACTGACTGCCC;RSEQ=AGCTTACCCACATGGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:29.5:1:1:0:60:4:1:0:1 +2 191848312 . T C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTTCAGAGATGCAGCAG;RSEQ=GAGAGCGTGGGGTCTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28:1:34:0:1:0:60:4:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:22.5:1:30.5:1:1:0:60:4:1:0:1 +2 191848392 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.18586;SOR=0;LSEQ=GGTTCCGCCACCAGCATGTT;RSEQ=TACCAAAGGATGGAGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:14,8:22,2:0.0833:2,2:25.5:1:32:0:1:1.70775:60:4:0.0833:0:1 0/0:31:0:0,0:20,11:31,0:0:2,0:26.2:1:29.8:1:1:0:60:14.5:1:0:0.2 +2 191848434 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49875;SOR=Inf;LSEQ=CCGCTCGGGAGCTGGCTGAC;RSEQ=TTGGAGATCACCACAACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:25,0:0:2,0:30.6:1:31.1:1:1:0:60:50:1:0:0.1 0/1:32:2:1,1:14,16:30,2:0.0625:2,2:31:1:31.5:1:1:1.14:60:4:0.0625:0:1 +2 191851586 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51607;SOR=0;LSEQ=ACTGATGTCCCTACCAGGTG;RSEQ=CGAAATTCAGCCGCCAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:23,11:34,2:0.0556:2,2:31:1:29.5:1:1:2.045:60:4:0.0588:0:1 0/0:23:0:0,0:15,8:23,0:0:2,0:23.8:1:31.7:1:1:0:60:46:1:0:0 +2 191869163 . G A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08309;SOR=1.33965;LSEQ=GGAAGGGGGTCCTTTCCAAT;RSEQ=GAGTGAGCAGTTGTCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:82:46,36:171,167:338,82:0.1948:2,2:24.2:1:29.6:1:0.39068:1.25:59.9:81:0.1938:0:1.1 0/1:433:106:53,53:164,163:327,106:0.2448:2,2:28.9:1:29.1:1:1:1.00612:60:212:0.2465:0:1.1 +2 192745796 . C T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55261;SOR=0;LSEQ=GTACAAAAGCCCTCCCTGGG;RSEQ=CCTCCCACCCTCTCATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:2,1:142,6:148,3:0.0199:1,2:9.7:1:22.3:1:0.13357:11.30149:48.3:2:0.0136:0:2.3 0/0:76:0:0,0:69,7:76,0:0:2,0:17.8:1:31.1:1:1:0:44.7:37:1:0:0.1 +2 192746182 . G A 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04722;LSEQ=CAGAACCATCTCTCTTAAAG;RSEQ=TATTGTGTGGCTTGTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:811:806:451,355:0,0:0,806:0.9938:0,2:19.4:1:30:1:1:0:41.1:39.3:0.9975:0:1.1 1/1:757:669:403,266:44,41:85,669:0.8838:2,2:19.9:1:28.6:1:0.15936:1.41:40.4:110.5:0.8876:0:1.1 +2 192746735 . T C 320 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09123;LSEQ=TTAGGGCTTCCTCCCGGTAG;RSEQ=GGTCGAAGATCTCGCGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1299:1291:704,587:1,4:5,1291:0.9938:2,2:24.6:1:31:1:0.1842:4.79:49.3:63.55:0.9961:0:1.1 1/1:1084:1015:578,437:37,31:68,1015:0.9363:2,2:23.8:1:30.4:1:0.70567:1.11:48.3:111.778:0.9376:0:1.1 +2 193538630 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08802;SOR=0.3259;LSEQ=ACTTGCTCTGATGGAGGCAG;RSEQ=CATTCTTGTGCAACATTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:34:34,0:24,0:24,34:0.5862:1,1:28.3:1:31.9:1:1:0:60:33:0.5789:0:1 0/1:16:5:5,0:11,0:11,5:0.3125:0,0:20.8:1:31.4:1:1:0:60:10:0.3125:0:1 +2 193538820 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0.65828;LSEQ=TCCTCCTAGAGTAACTGATA;RSEQ=CACACTATCTGCTTTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:772:359:182,177:197,216:413,359:0.465:2,2:26.7:1:30.4:1:0.42758:1.13:60:58.833:0.4626:0:1.1 0/1:742:270:134,136:237,232:469,270:0.3639:2,2:25.7:1:29.1:1:0.81918:1.03677:60:53:0.3615:0:1.2 +2 193538925 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18828;SOR=Inf;LSEQ=AGTTTTGTGGATGCTTTCTT;RSEQ=AGTAGGCATTCCAAACGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:25,187:212,0:0:2,0:24.5:1:28.3:1:1:0:59.6:52:1:0:0.2 0/1:163:2:1,1:21,140:161,2:0.0123:2,2:10:1:31:1:0.25244:6.54:60:4:0.0124:0:1 +2 193538931 . G A 46 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0.91942;LSEQ=GTGGATGCTTTCTTTAGTAG;RSEQ=CATTCCAAACGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:3:1,2:19,163:182,3:0.0162:2,2:19.7:1:29.3:1:0.29193:4.23:60:6:0.017:0:1 0/1:134:2:1,1:13,119:132,2:0.0149:2,2:22:1:27:1:0.19874:8.86:60:4:0.0153:0:1 +2 193538936 . C A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51703;SOR=0;LSEQ=TGCTTTCTTTAGTAGGCATT;RSEQ=CAAACGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:15,159:174,2:0.0114:2,2:13.5:1:25:0:0.17403:10.30:60:4:0.012:0:3.5 0/0:119:0:0,0:9,110:119,0:0:2,0:25.1:1:30:1:1:0:60:18.833:1:0:0.2 +2 193538963 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51197;SOR=0;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=CCGGTGCATCTGTTTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:0,2:3,101:104,2:0.0189:1,0:24:1:30:0:1:0:60:4:0.0196:0:1 0/0:75:0:0,0:1,74:75,0:0:1,0:21.9:1:30.2:1:1:0:60:74:1:0:0.1 +2 193562102 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.5085;SOR=0;LSEQ=GGGTGAGGGAACAACATTTT;RSEQ=ATCAGGCTCAAAGAATTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:72,21:93,2:0.0211:2,2:17.5:1:27.5:1:0.41142:3.37286:60:4:0.0213:0:1 0/0:70:0:0,0:52,18:70,0:0:2,0:21.6:1:30.6:1:1:0:60:140:1:0:0 +2 193562104 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50931;SOR=0;LSEQ=GTGAGGGAACAACATTTTCA;RSEQ=CAGGCTCAAAGAATTATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:73,21:94,2:0.0208:2,2:27.5:1:32:1:0.40768:3.41935:60:4:0.0211:0:1 0/0:70:0:0,0:52,18:70,0:0:2,0:22.7:1:29.6:1:1:0:60:69:1:0:0 +2 193562208 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30555;LSEQ=ATACGTATTTATAATCTAAA;RSEQ=GACTGTTAAAAACAATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:95:43,52:31,42:73,95:0.5655:2,2:25.2:1:30.8:1:0.75546:1.12:60:190:0.5655:0:1.1 0/1:141:40:17,23:41,60:101,40:0.2837:2,2:26.8:1:29.3:1:0.85144:1.08:60:39:0.2806:0:1.2 +2 196859045 . C T 112 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=5e-05;SOR=19.17967;LSEQ=AAAGATATCACTGATGCCTT;RSEQ=CTCCTCCCCAAGGCTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:465:1:1,0:305,159:464,1:0.0022:2,0:13:0:13:0:1:0:60:0:0:0:4 0/1:377:15:11,4:224,138:362,15:0.0398:2,2:21.8:1:28.7:1:0.42818:1.69:59:14:0.0375:0:1 +2 196859205 . G A 164 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.90475;LSEQ=GCCATAGAAATTGACCAATC;RSEQ=CCATGTCCTGTGTTGGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:1:1,0:234,265:499,1:0.002:2,0:6:0:33:0:0.47:0:60:2:0.002:0:1 0/1:450:49:26,23:193,207:400,49:0.1089:2,2:25.2:1:29.3:1:0.54793:1.21:60:98:0.1104:0:1 +2 196860048 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21867;SOR=Inf;LSEQ=AGTTTTTCTGCCTTGTTCAA;RSEQ=TCCAAGACCCCATGGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:111,74:185,0:0:2,0:26:1:30.1:1:1:0:59.9:45.25:1:0:0.3 0/1:163:2:1,1:100,61:161,2:0.0123:2,2:43.5:1:31.5:1:1:1.63412:60:4:0.0124:0:1 +2 196860056 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21778;SOR=Inf;LSEQ=TGCCTTGTTCAAATCCAAGA;RSEQ=CCCATGGAGAGACTGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:114,74:188,0:0:2,0:26:1:31.6:1:1:0:59.9:93:1:0:0.3 0/1:165:2:1,1:104,59:163,2:0.0121:2,2:15.5:1:25:1:1:1.75626:60:4:0.0121:0:1 +2 196860059 . C A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57615;LSEQ=CTTGTTCAAATCCAAGACCC;RSEQ=ATGGAGAGACTGGCTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:115,76:191,2:0.0104:2,2:37.5:1:29.5:1:1:1.50978:60:4:0.0106:0:1 0/0:167:1:1,0:104,62:166,1:0.006:2,0:1:0:24:0:1:0:60:2:0.0061:0:1 +2 196860081 . C A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32868;SOR=0.77384;LSEQ=TGGAGAGACTGGCTCAGGAG;RSEQ=TGAATGAACTTCTTGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:53:31,22:82,65:147,53:0.2637:2,2:26.4:1:30.2:1:0.7496:1.12:60:52:0.2653:0:1.2 0/1:166:36:24,12:64,66:130,36:0.2169:2,2:24.1:1:27.8:1:0.08878:2.05:60:17:0.2099:0:1.1 +2 196860155 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20462;SOR=Inf;LSEQ=GAGGGAGATTTTTGGAGTTT;RSEQ=AGGACTATCTGGACTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:134,93:227,0:0:2,0:25.7:1:29.8:1:1:0:60:55.75:1:0:0.2 0/1:188:2:1,1:107,79:186,2:0.0106:2,2:31.5:1:30:1:1:1.3522:60:4:0.0108:0:1.5 +2 196860191 . T A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25331;SOR=0;LSEQ=TCATAGAGCAGCTCTTCTTT;RSEQ=GCCCTCAGGGGTTTTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:3:2,1:161,106:267,3:0.0111:2,2:32.3:1:22.7:1:1:1.32:60:2:0.0075:0:1.7 0/0:230:0:0,0:141,89:230,0:0:2,0:22:0:11:0:1:0:60:0:0:0:6 +2 196860313 . G A 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=48.44129;LSEQ=CTGGCTCAGCAGGGGAAGAT;RSEQ=GGAGGCCAGCTAGAGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:1:1,0:123,206:329,1:0.003:2,0:1:0:24:0:0.37576:0:60:2:0.0031:0:1 0/1:326:42:16,26:112,172:284,42:0.1288:2,2:24.4:1:28.5:1:1:1.05797:60:20:0.1246:0:1 +2 196860410 . G T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.09;LSEQ=ACTAGGGAGAGAAGATAAAG;RSEQ=GTGGTGGTGCTGGGCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:34:2,32:1,35:36,34:0.4857:1,2:25.4:1:30.8:1:0.6087:2.16:60:33:0.4783:0:1.1 0/1:39:3:0,3:1,35:36,3:0.0769:1,0:26.3:1:27.3:1:1:0:60:6:0.0769:0:1.3 +2 197719100 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22531;SOR=Inf;LSEQ=GTGATACTAGATCTTCTTTC;RSEQ=GTTATATTCATGTTATTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:26,0:0:2,0:23.1:1:30.8:1:1:0:60:25:1:0:0.1 0/1:24:2:1,1:9,13:22,2:0.0833:2,2:15.5:1:28.5:1:1:1.42:60:4:0.0833:0:1 +2 198244785 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4987;SOR=Inf;LSEQ=ATCAAAGTCATCATCATCAT;RSEQ=TTCATCATCGTGATCTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:71,112:183,0:0:2,0:26.2:1:33.1:1:1:0:58.2:182:1:0:0.1 0/1:187:2:1,1:81,104:185,2:0.0107:2,2:24.5:1:27.5:1:1:1.28:57:4:0.0108:0:1 +2 198244800 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49949;SOR=Inf;LSEQ=ATCATCTTCATCATCGTGAT;RSEQ=TTCGTCATCATCTTCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:68,100:168,0:0:2,0:26.4:1:32.6:1:1:0:59.5:41:1:0:0.1 0/1:183:2:1,1:79,101:180,2:0.0109:2,2:32:1:27.5:1:1:1.28:60:4:0.0112:0:1 +2 198244885 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=CAGACCACTTTCCTGATATA;RSEQ=GTAAGAGTTTCACATCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:63,51:114,0:0:2,0:25.5:1:30.9:1:1:0:55.2:27.5:1:0:0.1 0/1:123:2:1,1:69,52:121,2:0.0163:2,2:15:1:28.5:1:1:1.32382:43:4:0.0164:0:1 +2 198244927 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21918;SOR=0;LSEQ=CCTCTCATCTTCTGACTTTG;RSEQ=ATCTTCCTCCACAGCTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:119,67:186,2:0.0106:2,2:39:1:30:0:1:1.77031:32:4:0.0107:0:1 0/0:213:0:0,0:132,81:213,0:0:2,0:24.9:1:31.2:1:1:0:43.4:70:1:0:0.1 +2 198245297 . G A 104 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04985;SOR=0.09255;LSEQ=ATGTTAGCCAGGATGGTCTC;RSEQ=ATCTCCTGACCTTGTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:10,0:4,0:4,10:0.7143:0,0:30.9:1:31.6:1:1:0:26.4:20:0.7143:0:1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:21:0:31:0:1:0:32:2:0.1667:0:1 +2 198245341 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.49494;SOR=Inf;LSEQ=TGCCTCGGCTCGGCCTCCCA;RSEQ=AGTGCTGGGATTACAGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:33,4:37,0:0:2,0:22.1:1:33.2:1:1:0:48.5:74:1:0:0.4 0/1:42:2:1,1:34,6:40,2:0.0476:2,2:10:0:32.5:1:0.30894:5.323:32.5:4:0.0488:0:1 +2 198245413 . C A 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12318;SOR=Inf;LSEQ=TGTTACTTTAATTGGACTGC;RSEQ=TTCATCATTCATGGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:78,37:115,0:0:2,0:19:1:31.7:1:1:0:41.3:230:0.9914:0:0.1 0/1:126:4:3,1:78,44:122,4:0.0317:2,2:28.3:1:24.8:1:1:1.69:27.8:3:0.0248:0:1.3 +2 198245464 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12324;SOR=Inf;LSEQ=GTGCAGTTCATCCCTTGCAC;RSEQ=AGCCCCTAAACTGACCGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:121,92:213,0:0:2,0:30.6:1:31.5:1:1:0:45.3:29.429:1:0:0.1 0/1:212:3:2,1:104,105:209,3:0.0142:2,2:29:1:30:1:1:2.01:28:6:0.0144:0:1 +2 198245541 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49853;SOR=Inf;LSEQ=CTTAAAGTGATCATCTTTGT;RSEQ=GGCCTTTAGTTCACAACCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:62,38:100,0:0:2,0:13.4:1:31:1:1:0:33.6:99:1:0:0 0/1:109:2:2,0:59,47:106,2:0.0183:2,0:38.5:1:31:1:0.50381:0:23.5:4:0.0187:0:1 +2 198245718 . C A 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10768;SOR=0;LSEQ=GGAATCACACCAGGGATGTT;RSEQ=TGTATGCATTCTATCCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:2,1:60,193:253,3:0.0117:2,2:19.3:1:26.7:1:0.14643:6.37:60:6:0.0119:0:2.3 0/0:281:0:0,0:78,202:280,0:0:2,0:22.6:1:30.6:1:1:0:59.9:39:1:0:0.1 +2 198245733 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.499;SOR=Inf;LSEQ=ATGTTCTGTATGCATTCTAT;RSEQ=CACATCCACAAGAGTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:17,161:178,0:0:2,0:24.3:1:32:1:1:0:60:88:1:0:0.1 0/1:188:2:1,1:33,153:186,2:0.0106:2,2:11:1:26.5:1:0.32979:4.58:60:4:0.0108:0:1 +2 198245734 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2397;SOR=0;LSEQ=TGTTCTGTATGCATTCTATC;RSEQ=ACATCCACAAGAGTTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:16,159:175,2:0.0113:2,2:32.5:1:30.5:1:0.18336:9.67:60:4:0.0114:0:1.5 0/0:184:0:0,0:31,153:184,0:0:2,0:21.8:1:31.4:1:1:0:60:60.333:1:0:0.1 +2 198245740 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49839;SOR=0;LSEQ=GTATGCATTCTATCCACATC;RSEQ=ACAAGAGTTCAAATATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:10,144:154,2:0.0128:2,2:25:1:29:1:0.13648:13.78:60:4:0.0128:0:1 0/0:156:0:0,0:18,138:156,0:0:2,0:21.6:1:31.4:1:1:0:60:155:1:0:0.1 +2 198245965 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGAGGTGGGAGGATCACC;RSEQ=GACCAAGCCCAGGAGGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:20.5:1:32.5:1:1:0:54:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 198257008 . C G 222 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGAAGTAGCTGTGCATTAAA;RSEQ=ACAAAATAAACAATAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:110:80,30:118,54:172,110:0.3901:2,2:25.2:1:32.8:1:0.50577:1.22:60:220:0.3901:0:1.2 0/0:247:0:0,0:164,83:247,0:0:2,0:24.4:1:31.5:1:1:0:60:494:1:0:0.1 +2 198257075 . G A 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATAGGTGTTCTTATCATC;RSEQ=TTGTAGATTCTTGGGTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:0:0,0:354,267:621,0:0:2,0:26.3:1:30.9:1:1:0:60:102.5:1:0:0.2 0/1:571:29:17,12:303,237:540,29:0.0508:2,2:30.8:1:30.6:1:0.84947:1.11:60:58:0.0511:0:1.1 +2 198257278 . A T 32 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.73419;LSEQ=TAAAGATATGATTCAAAATT;RSEQ=TTTCCCTTGGGGAGTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:3:0,3:5,40:45,3:0.0625:2,0:15.3:1:20.7:1:1:0:56.7:2:0.0513:0:4.7 0/1:43:2:0,2:1,40:41,2:0.0465:1,0:19:1:14:0:1:0:49:0:0:0:5.5 +2 198257294 . T TG 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.0083;SOR=5.34101;LSEQ=AATTATTTCCCTTGGGGAGT;RSEQ=GGGGGGGGGGGAACCTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:4:0,4:3,20:23,4:0.1111:2,0:33.8:1:20.5:1:1:0:54.3:1:0.0645:0:0.8 0/1:27:11:0,11:1,14:15,11:0.4074:1,0:33.5:1:26.3:1:1:0:56.4:10:0.4348:0.037:3.3 +2 198257299 . G GGC 46 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.08662;SOR=Inf;LSEQ=TTTCCCTTGGGGAGTTGGGG;RSEQ=GGGGGGAACCTACTAATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:4,30:34,0:0:2,0:22.5:1:30.9:1:1:0:58.2:68:1:0:1.6 0/1:28:3:0,3:1,24:25,3:0.1071:1,0:7:1:29.3:1:1:0:60:6:0.12:0.0714:0.7 +2 198257652 . T TA 198 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.00114;SOR=0.51903;LSEQ=CCAGAACTTAAAGTATTATT;RSEQ=AAAAAAAAAAAATCACCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:211:120:106,14:61,7:68,120:0.5687:2,2:24.9:1:28.7:1:1:1.15006:57.9:39:0.5821:0.0664:0.5 0/1:202:82:70,12:82,18:100,82:0.4059:2,2:23:1:27.8:1:0.68854:1.28:58.6:81:0.4154:0.0693:0.5 +2 198257673 . TA T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.19857;SOR=1.69178;LSEQ=AAAAAAAAAAAATCACCGAT;RSEQ=AAAAAAAAATCTTTAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:12:9,3:277,77:354,12:0.0327:2,2:17.7:1:30.9:1:0.72948:1.19853:60:24:0.0334:0.0136:0.3 0/1:351:19:12,7:235,97:332,19:0.0541:2,2:27:1:28.7:1:0.45156:1.41176:59.5:38:0.0548:0.0057:0.9 +2 198257795 . T C 313 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35268;LSEQ=ACATGAGGAGATGTCTCAAA;RSEQ=ACATTGGGCCATACATAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:962:811:422,389:77,74:151,811:0.843:2,2:23.6:1:32.4:1:0.85932:1.04:60:114.857:0.8428:0:1.1 1/0:975:638:350,288:178,157:335,638:0.6544:2,2:24.7:1:31.3:1:0.63563:1.07:60:158.5:0.6563:0:1.1 +2 198258179 . C CT 49 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCATATTTTCTAATTAA;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:34.7:1:31.3:1:1:0:58.7:6:0.4286:0:0.3 0/0:1:0:0,0:0,1:1,0:0:0,0:6:0:34:0:1:0:60:2:1:0:1 +2 198260098 . A T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTATTAATGAATAACTT;RSEQ=AATCTGTACACAAAAGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:28:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 198261055 . G GA 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.12906;SOR=0;LSEQ=GCCAATACATCATGAGGGCT;RSEQ=AAAAAAACAAATGGGTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:4:3,1:90,256:346,4:0.0114:2,2:15.8:1:27.8:1:0.05901:8.47:60:8:0.0116:0.0057:0.5 0/0:297:0:0,0:74,223:297,0:0:2,0:23.7:1:30.7:1:1:0:60:296:1:0:0.1 +2 198262599 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50533;SOR=0;LSEQ=ATGAAGAGCTTTCTCAACTG;RSEQ=ATTATTCAGACCATGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:2,0:74,0:74,2:0.0263:1,0:39:1:30.5:1:1:0:60:4:0.0274:0:1 0/0:58:0:0,0:58,0:58,0:0:1,0:30.2:1:31.4:1:1:0:59.9:28:1:0:0.2 +2 198262606 . C G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25562;SOR=0;LSEQ=GCTTTCTCAACTGCATTATT;RSEQ=AGACCATGCCTCAAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:3:3,0:82,0:82,3:0.0353:1,0:21:1:33.3:1:1:0:60:6:0.0357:0:3.3 0/0:67:0:0,0:66,0:66,0:0:1,0:28.4:1:30.5:1:1:0:60:32:1:0:0.1 +2 198262677 . A AT 113 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.01083;SOR=0.21846;LSEQ=AATGCATTTATTATAAAGTA;RSEQ=TTTTTTTTTAATGGAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:13:9,4:242,83:325,13:0.0385:2,2:18.9:1:30.6:1:0.74693:1.2948:59.6:26:0.0387:0.0089:0.5 0/0:347:3:2,1:229,111:340,3:0.0086:2,2:33.7:1:28.3:1:1:1.03147:60:6:0.0087:0:0.7 +2 198263146 . T C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71411;SOR=1.06065;LSEQ=AAAGTGGCCAAATTTGAAAA;RSEQ=TGATACTGCTTATAAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:115:73,42:221,114:335,115:0.2556:2,2:25.2:1:32.6:1:0.65053:1.11508:60:114:0.2539:0:1.1 0/1:517:138:83,55:237,142:379,138:0.2669:2,2:24.1:1:31.2:1:0.6823:1.10575:60:276:0.2685:0:1.1 +2 198264715 . G GA 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00804;SOR=2.49801;LSEQ=CTAAATAAGATTTTACTTAC;RSEQ=AAAAAAAAAAGAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:13:13,0:218,22:240,13:0.0512:2,1:28.5:1:31.6:1:0.61176:0:55.8:26:0.0522:0.0079:0.5 0/1:227:27:21,6:180,19:199,27:0.1189:2,2:22.4:1:28.7:1:0.09239:2.6911:60:54:0.1205:0.0044:0.1 +2 198264903 . AAAT A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40712;SOR=1.1252;LSEQ=AATTTTTCCTATAATAAAAC;RSEQ=AATGTTAAAATGTTACTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:125:39,86:165,279:444,125:0.2197:2,2:27.2:1:31:1:0.24597:1.30351:59.7:124:0.2206:0.0281:0.1 0/1:611:147:69,78:188,276:464,147:0.2406:2,2:26:1:29.6:1:0.18023:1.30:59.9:146:0.2413:0.0262:0.1 +2 198265167 . T A 33 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1009;SOR=0;LSEQ=CATTACTGAGTCCTAAAAAA;RSEQ=AAATTTAAAAAAAAGACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:81,194:275,3:0.0108:2,2:5.7:1:21.3:1:0.21327:4.76:59.7:2:0.0073:0:2.7 0/0:318:0:0,0:98,220:318,0:0:2,0:22.7:1:28.2:1:1:0:60:52:1:0:0.7 +2 198265170 . AT A 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.72833;SOR=1.49016;LSEQ=TACTGAGTCCTAAAAAATAA;RSEQ=TTAAAAAAAAGACATATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:0,3:71,184:255,3:0.0116:2,0:28.3:1:33:0:0.56354:0:60:6:0.0119:0:0 0/1:290:5:2,3:83,202:285,5:0.0172:2,2:30.6:1:29.2:1:0.63214:1.62:60:10:0.0175:0.0034:0.2 +2 198265173 . T A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=6e-05;SOR=0.42582;LSEQ=TGAGTCCTAAAAAATAAATT;RSEQ=AAAAAAAAGACATATTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:247:207:58,149:5,27:32,207:0.8381:2,2:21.5:1:30.2:1:0.19501:2.10:59.8:33.5:0.8627:0:1.2 1/0:272:187:57,130:22,61:83,187:0.6875:2,2:22.1:1:29.5:1:0.56352:1.21:59.9:186:0.6966:0:1.1 +2 198265247 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55251;SOR=0;LSEQ=AGTCAACCTTTTCTAACCAC;RSEQ=CAAACATCTGTTGCTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:0,2:28,68:96,2:0.0204:2,0:14.5:1:31.5:1:1:0:60:4:0.0213:0:1.5 0/0:49:0:0,0:13,36:49,0:0:2,0:21.7:1:30.2:1:1:0:59.7:23.5:1:0:0.4 +2 198265350 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.61823;LSEQ=AAAAATTACTTCAAATTCAA;RSEQ=TGCATTCTAGAAAAATTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:15:14,1:133,20:153,15:0.0893:2,1:25.8:1:30.9:1:0.69643:2.10:60:14:0.0848:0:1.2 0/1:129:46:42,4:73,10:83,46:0.3566:2,2:17.1:1:31.8:1:0.76903:1.43:60:92:0.3566:0:1 +2 198265526 . A G 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41573;LSEQ=ATATCTGCTGCTCCCAAATT;RSEQ=CCCATAATTTTCTCAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:865:748:372,376:60,56:116,748:0.8647:2,2:25.4:1:32.4:1:0.76478:1.08283:60:123.667:0.8678:0:1.1 1/0:969:704:367,337:138,126:264,704:0.7265:2,2:26.9:1:31.2:1:1:1.0057:60:63:0.7241:0:1.1 +2 198265952 . CA C 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14086;SOR=0;LSEQ=TAAGTATTAATCCTCGAATC;RSEQ=AAATCAAAATGGAAGTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:5,0:17,7:24,5:0.1724:2,0:34.2:1:32.4:1:0.29649:0:60:10:0.1724:0:0 0/0:18:0:0,0:17,1:18,0:0:1,0:22.2:1:30.8:1:1:0:60:36:1:0:0.2 +2 198266043 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2193;SOR=Inf;LSEQ=GAGATAATCAAGGCAAAAAA;RSEQ=AATATACAACATGCATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:111,19:130,0:0:2,0:22.5:1:30.8:1:1:0:60:42.333:1:0:0.1 0/1:115:2:1,1:89,24:113,2:0.0174:2,2:26.5:1:31:1:0.38902:3.65411:60:4:0.018:0:1.5 +2 198266602 . G A 159 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=ACCCAATAGCCTTCAAGAAA;RSEQ=CAGCCAAACCCTATTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:38:18,20:201,279:480,38:0.0731:2,2:22.4:1:30.4:1:0.60933:1.25:60:76:0.0738:0:1.1 0/0:506:0:0,0:230,275:505,0:0:2,0:24.1:1:31.4:1:1:0:59.8:100:1:0:0.1 +2 198266943 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45926;SOR=0;LSEQ=CTCTCAATATATCAACTATT;RSEQ=AGCCAAACTGCAGAATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:146:146:6,140:0,0:0,146:1:0,1:25.6:1:28.9:1:1:0:60:145:1:0:1.1 1/1:124:123:5,118:0,0:0,123:0.9919:0,1:23.3:1:28:1:1:0:60:122:0.9919:0:1.1 +2 198267770 . G GAA 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.00026;SOR=0.53473;LSEQ=CCACGAGGATCTGAAAAAGA;RSEQ=AAAAGAGAAGAAGCTACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:310:242:89,153:29,39:68,242:0.7806:2,2:26.6:1:30.6:1:0.39856:1.27725:59.9:484:0.7857:0.1161:0.2 1/0:412:270:111,159:62,80:142,270:0.6553:2,2:27:1:29.3:1:0.67458:1.10985:59.9:89:0.6544:0.0898:0.1 +2 198267791 . T A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26202;SOR=Inf;LSEQ=AAAAGAGAAGAAGCTACACT;RSEQ=TCACATCAATTACTGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:70,160:230,0:0:2,0:23.2:1:30:1:1:0:59.9:37.333:1:0:0.1 0/1:301:3:2,1:104,194:298,3:0.01:2,2:6:1:25.3:1:0.28402:3.71:60:6:0.0101:0:1 +2 198269717 . A T 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10728;SOR=0;LSEQ=AGCCTGGGCAACATGGCAAA;RSEQ=CCCTGTCTCTACAAAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:252,33:285,3:0.0104:2,2:8.3:1:21.3:1:0.03987:14.99424:60:2:0.007:0:1.7 0/0:317:0:0,0:250,67:317,0:0:2,0:19.6:1:29.1:1:1:0:60:157.5:1:0:0.1 +2 198272802 . G A 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00196;SOR=12.14641;LSEQ=ATCAATTTCTCTTTCCCACC;RSEQ=CCAAGCCTGAAGCTGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:736:1:1,0:292,443:735,1:0.0014:2,0:1:0:25:0:0.3981:0:60:2:0.0014:0:1 0/1:799:13:9,4:333,452:785,13:0.0163:2,2:14.3:1:26.7:1:0.08621:3.05:60:26:0.0166:0:1.1 +2 198273027 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19159;SOR=Inf;LSEQ=CATTAATAGTACACAGAATA;RSEQ=CACAAAGGAAAAAATTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:196,50:246,0:0:2,0:23:1:31.9:1:1:0:60:81:1:0:0.1 0/1:192:2:1,1:156,33:189,2:0.0104:2,2:9.5:1:28.5:1:0.3251:4.67217:60:4:0.0106:0:1 +2 198273347 . T C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19963;SOR=1.32741;LSEQ=AAAACCACAATTTTAATCAC;RSEQ=GTTAAAATAATATTCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:59:5,54:27,157:184,59:0.2418:2,2:20.8:1:30.3:1:0.27278:1.85316:60:118:0.2448:0:1.1 0/1:205:61:14,47:26,117:143,61:0.2976:2,2:21.6:1:29.3:1:0.44545:1.34:60:60:0.2941:0:1.2 +2 198273591 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGGGAGGCAGAGGTTGCAGT;RSEQ=AGCCGAGAGCGCACCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:20.7:1:29.7:1:1:0:60:6:0.6:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:37.5:1:34:0:1:0:60:4:1:0:0 +2 198274299 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.21142;SOR=Inf;LSEQ=TACTAACTTTACTTTTACCT;RSEQ=AGGTTCTTCCTTAAATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:37,0:37,0:0:1,0:22.5:1:27.9:1:1:0:59.8:36:1:0:0.1 0/1:32:2:1,1:27,3:30,2:0.0625:2,2:44.5:1:32:1:0.2379:7.93681:60:4:0.0667:0:1.5 +2 198274742 . C CA 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04252;SOR=Inf;LSEQ=GCCCAGGGGTCTTAAAAAAG;RSEQ=AAAAAAATTTTATTTCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:76,254:330,0:0:2,0:24.8:1:32.2:1:1:0:60:65:1:0:0.1 0/1:276:4:2,2:83,189:272,4:0.0145:2,2:10.5:1:29.4:1:0.58925:2.27:60:8:0.015:0.0072:0.3 +2 198274758 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.18286;SOR=Inf;LSEQ=AAAGCAAAAAAATTTTATTT;RSEQ=ACACACCCACACAGAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:39,220:259,0:0:2,0:23.5:1:32.4:1:1:0:59.9:85.333:1:0:0.1 0/1:194:2:1,1:41,151:192,2:0.0103:2,2:39:1:29:0:0.387:3.65:60:4:0.0106:0:1 +2 198274929 . G A 67 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.8165;LSEQ=ATGATTAAAAACAATGTAAA;RSEQ=TTTCAATCCGAAGCACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:16:1:29:1:1:0:60:4:0.5:0:2.4 1/0:2:1:0,1:0,1:1,1:0.5:0,0:17:0:32:0:1:0:60:2:0.5:0:1 +2 198281743 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07148;SOR=0.39651;LSEQ=TTTATACTTTGCTCATTCTC;RSEQ=TTTCTATGTACTGGTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:51:42:0,42:0,9:9,42:0.8235:0,1:21.8:1:32.6:1:1:0:60:20:0.8163:0:1.5 1/0:51:33:0,33:0,18:18,33:0.6471:1,1:25.5:1:32.7:1:1:0:60:66:0.6471:0:1.5 +2 198281776 . C A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5293;SOR=0.59869;LSEQ=GGTGATCTCCTTTCTACGCT;RSEQ=GCTGGTTCCATAGTCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:19:0,19:0,6:6,19:0.76:0,1:24.6:1:32.6:1:1:0:60:18:0.7826:0:1.9 1/0:23:15:0,15:0,8:8,15:0.6522:0,1:18.5:1:31.9:1:1:0:60:30:0.6522:0:2 +2 198283305 . T C 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.32267;LSEQ=TTCATTTTAGGATCAGGGGT;RSEQ=TTCCCTCCTGCAGAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:767:669:270,399:43,55:98,669:0.8722:2,2:25.4:1:32.6:1:0.51116:1.15513:60:65.9:0.8728:0:1.1 1/0:669:460:202,258:89,120:209,460:0.6876:2,2:24.7:1:30.8:1:0.80081:1.06:60:64.714:0.6895:0:1.1 +2 198283516 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1888;SOR=Inf;LSEQ=TTTGAACACAAACATCTACA;RSEQ=CAGTTTAAAACAAATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:112,24:136,0:0:2,0:24.4:1:33.5:1:1:0:60:272:1:0:0.1 0/1:105:2:1,1:95,8:103,2:0.019:2,2:22.5:1:25:1:0.16484:11.25491:60:4:0.0194:0:1 +2 198285074 . C CA 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.76215;SOR=0.70412;LSEQ=AAGCAAATTCAGAAGCATGC;RSEQ=AAAAAAAATCAAAGGGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:6:4,2:219,95:314,6:0.0187:2,2:29.5:1:31:1:1:1.15209:60:12:0.0191:0.0031:0.2 0/1:378:5:2,3:251,122:373,5:0.0132:2,2:22.4:1:29.1:1:0.3372:3.07597:60:10:0.0135:0.0026:0 +2 198285554 . C G 130 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GAGGTTGAGACAGGAGGAAT;RSEQ=CTTGAGCCCAGGAGTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:7,8:0,0:0,15:1:0,2:23.9:1:33.3:1:1:0:60:30:1:0:1.3 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:27:1:33.5:1:1:0:60:4:0.6667:0:1 +2 198285583 . G C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24026;SOR=0;LSEQ=CAGGAGTTTGGGATCAGCCT;RSEQ=AGCAAGACAGCAAAACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:6,4:10,3:0.2308:2,0:39.7:1:32.7:1:0.4965:0:60:6:0.2308:0:2.3 0/0:9:0:0,0:8,1:9,0:0:2,0:16.6:1:31.8:1:1:0:60:18:1:0:0.2 +2 198285697 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18712;SOR=Inf;LSEQ=TTATGGATTTCTATGGGAAC;RSEQ=CAGACATTCACTTTTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:139,23:162,0:0:2,0:24.3:1:31.5:1:1:0:59.7:26:1:0:0.1 0/1:124:2:1,1:99,23:122,2:0.0161:2,2:33:1:29.5:1:0.3509:4.23495:60:4:0.0161:0:1 +2 198285744 . A C 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAACTATGCTTTTAAAATG;RSEQ=AAGATCACCTGTTCTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:221,80:301,0:0:2,0:24.6:1:30.3:1:1:0:59.9:99.333:0.9967:0:0.1 0/1:302:37:27,10:178,86:264,37:0.1225:2,2:21.8:1:31.9:1:0.57509:1.30:59.9:74:0.1237:0:1.1 +2 198286004 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18733;SOR=Inf;LSEQ=TAAAACTTAGAAACACAATT;RSEQ=GTCTTCTTTCACTTCAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:0,57:57,0:0:1,0:22.2:1:31.6:1:1:0:60:114:1:0:0.1 0/1:44:2:1,1:1,41:42,2:0.0455:1,2:33:1:28.5:1:0.08985:29.33:60:4:0.0465:0:1 +2 198288213 . T C 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACAGATGGCTATTTACAA;RSEQ=TAAGTCACTTCTCACACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:9.5:1:26.3:1:1:0:60:3:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 198288753 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21646;SOR=Inf;LSEQ=CTTTCCAAAAGAACTCCCAA;RSEQ=ACAATGCATTTCTTTACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:17,210:227,0:0:2,0:23.8:1:32.7:1:1:0:60:454:1:0:0.1 0/1:198:2:1,1:23,173:196,2:0.0101:2,2:8:1:28:1:0.22827:7.39:60:4:0.0103:0:1 +2 198299579 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49808;SOR=Inf;LSEQ=GAGGAGACGACCCTTGGCCC;RSEQ=GAAACGCGGGCTCAGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:69,3:72,0:0:1,0:24.8:1:32:1:1:0:60:144:1:0:0 0/1:80:2:1,1:69,9:78,2:0.025:2,2:15.5:1:28:1:0.23576:7.32689:60:4:0.025:0:1 +2 198299594 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19103;SOR=0;LSEQ=GGCCCCGAAACGCGGGCTCA;RSEQ=CTCCTACGAAAGAAACCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:78,16:94,2:0.0208:2,2:14:1:29:1:0.32434:4.75972:60:4:0.0215:0:1 0/0:123:0:0,0:97,26:123,0:0:2,0:20.3:1:31.2:1:1:0:60:122:1:0:0.1 +2 198299672 . C T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08707;SOR=Inf;LSEQ=GGCTAGCAACGAAGAAAACA;RSEQ=GTAAGCAGGGAAAGACCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:214,151:365,0:0:2,0:26.3:1:31.3:1:1:0:60:90.25:1:0:0.1 0/1:571:6:2,4:316,249:565,6:0.0105:2,2:17:1:27.5:1:0.41372:2.53409:60:12:0.0106:0:1 +2 198299785 . G A 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.67057;SOR=0.59442;LSEQ=AACTTCCGCTCGTCGCCGCC;RSEQ=CCACGGAGAAAAATAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:3:2,1:41,145:186,3:0.0158:2,2:15.3:1:29:1:0.13019:6.98:60:6:0.016:0:1.3 0/0:212:2:2,0:64,146:210,2:0.0094:2,0:1:0:25.5:1:0.0959:0:60:4:0.0097:0:1 +2 198299792 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24052;SOR=0;LSEQ=GCTCGTCGCCGCCGCCACGG;RSEQ=GAAAAATAGCTGGGGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:29,136:165,2:0.012:2,2:18.5:1:29.5:1:0.3279:4.63:60:4:0.0121:0:1 0/0:173:0:0,0:45,128:173,0:0:2,0:24.6:1:29.5:1:1:0:60:56.667:1:0:0.1 +2 198299819 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49987;SOR=Inf;LSEQ=TAGCTGGGGGCTGCACTCTG;RSEQ=GCGTGCGCCAAACGGGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:10,72:82,0:0:2,0:25:1:30.6:1:1:0:60:81:1:0:0.1 0/1:95:2:1,1:13,80:93,2:0.0211:2,2:14:1:30.5:1:0.27436:5.97:60:4:0.0215:0:1 +2 199565710 . AT A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCCAAGGAATGTCAAGG;RSEQ=TTGCCAGAGCCACCAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:32.8:1:32.3:1:1:0:60:10:1:0.2:0.2 1/1:5:5:0,5:0,0:0,5:1:0,0:21.8:1:30.2:1:1:0:60:10:1:0:0 +2 200019363 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGGCCAAGATGGCCGA;RSEQ=TAGAAGAAGGGGCGTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:26.5:1:31.5:1:1:1.41:60:4:0.2857:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:24:0:34:0:1:0:60:2:1:0:0 +2 200020274 . T C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51049;SOR=0.24443;LSEQ=CTATACAGGAGCAATCCTAC;RSEQ=GGCATCAGGTTGGTGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:3,4:1,0:1,7:0.875:0,2:20.7:1:30.9:1:1:0:57:14:0.875:0:1 1/0:5:3:3,0:1,1:2,3:0.6:2,0:15.7:1:31.7:1:0.4:0:60:6:0.6:0:1 +2 200020501 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52425;SOR=Inf;LSEQ=ACAACACCAACAACAAAAAT;RSEQ=GGGCCCCCACAAAAACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:22,0:0:2,0:25.9:1:29.4:1:1:0:60:10:1:0:0.3 0/1:37:2:1,1:15,20:35,2:0.0541:2,2:8:0:31.5:1:1:1.32:60:4:0.0541:0:1.5 +2 202082459 . T A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96767;LSEQ=TGCCCCTGGATGCACTTTCA;RSEQ=TATAGCAGAGAGTTTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:5,6:3,6:9,11:0.55:2,2:17.2:1:31.8:1:0.66992:1.62:60:22:0.55:0:1.1 1/0:24:13:5,8:4,7:11,13:0.5417:2,2:23.3:1:28.8:1:1:1.09:60:12:0.5217:0:1.2 +2 202122901 . G GT 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.17025;SOR=0.34027;LSEQ=CTCCTCCTTTTATCTTTTGT;RSEQ=TTTTTTTTCAAGCCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:6:4,2:233,66:299,6:0.0197:2,2:19.7:1:30.4:1:0.61836:1.76139:60:12:0.02:0.0098:0.3 0/0:443:3:2,1:341,95:436,3:0.0068:2,2:18.7:1:29.8:1:0.52395:1.79197:60:6:0.0068:0.0023:0 +2 202122995 . A G 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.20991;LSEQ=CAGGGTGGTTATTGAAAGTA;RSEQ=AAGAAACTTCTTCCTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:800:640:313,327:79,79:158,640:0.8:2,2:26.2:1:32.6:1:0.85903:1.04469:60:90.429:0.8013:0:1.2 0/1:1245:568:269,299:329,348:677,568:0.4562:2,2:25.7:1:30.8:1:0.69026:1.05076:60:80.143:0.4554:0:1.2 +2 202129706 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAACATGATCGCAGTGGG;RSEQ=TGGGAGTAGGGGATGAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:29.5:1:1:0:60:4:1:0:2.5 +2 202130133 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGAAAACTAAATACCGTA;RSEQ=GTTCTCACTTAAAAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:31.5:1:1:0:60:4:1:0:1 +2 202131130 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18871;SOR=0;LSEQ=AGTAGCCTTTGATGAACAAG;RSEQ=CAGCAAATGGTACTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:110,16:126,2:0.0156:2,2:13:1:31:1:0.24889:6.7009:60:4:0.0159:0:1 0/0:166:0:0,0:132,33:165,0:0:2,0:24.6:1:31:1:1:0:60:40.25:1:0:0.1 +2 202131541 . T A 36 q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11245;SOR=0;LSEQ=GGAAACTCCCATTGTGGGAC;RSEQ=GGGAGGTGTGGGTTGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:3:3,0:36,157:193,3:0.0153:2,0:9.7:1:23:1:0.0074:0:60:2:0.0103:0:2 0/0:209:0:0,0:51,158:209,0:0:2,0:25.6:1:29.3:1:1:0:60:51.25:1:0:0.2 +2 202131587 . T G 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=CTCTGAGCTGATTGGGGCTT;RSEQ=TTTTTGTGGTACCCTGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:5,87:92,0:0:2,0:25.6:1:30.7:1:1:0:59.6:91:1:0:0.1 0/1:87:11:0,11:5,71:76,11:0.1264:2,0:25.5:1:31.2:1:1:0:60:22:0.1279:0:1 +2 202134144 . G T 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TAAGGCACTTATTCATTAAG;RSEQ=CGCCAGTTAGTCCTAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:154,43:197,0:0:2,0:21.6:1:31.4:1:1:0:60:48.25:1:0:0.1 0/1:216:30:21,9:140,46:186,30:0.1389:2,2:22.4:1:28:1:0.50799:1.30269:60:29:0.1368:0:1.1 +2 202136014 . G T 87 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.76929;LSEQ=TGAAATAAACTGAAAGAAAA;RSEQ=TTGATAGAACTTTAAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:6,1:16,0:16,7:0.3043:1,2:28.6:1:31:1:0.30435:0:60:14:0.3043:0:1.1 0/1:4:1:1,0:3,0:3,1:0.25:0,0:45:0:31:0:1:0:60:2:0.25:0:1 +2 202136272 . C T 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=11.46168;LSEQ=CAGATTTCAGAAGAAGTGAG;RSEQ=AGATCAGAATTGAGGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:687:2:1,1:352,333:685,2:0.0029:2,2:13.5:1:28.5:1:1:1.057:60:4:0.0029:0:1 0/1:864:28:14,14:449,385:834,28:0.0324:2,2:23.9:1:28:1:0.70446:1.16602:60:56:0.0327:0:1.1 +2 202136398 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=GAGACTTGGTTAGCCAGGGG;RSEQ=CATTTCTGAGACCAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:27,158:185,0:0:2,0:23.4:1:32.3:1:1:0:60:60.667:1:0:0 0/1:188:2:1,1:28,158:186,2:0.0106:2,2:23.5:1:27:0:0.28541:5.56:60:4:0.0109:0:1 +2 202136547 . CAG C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.125;SOR=Inf;LSEQ=GTTAATTATTGGGAGCAAGG;RSEQ=AGTCAGAGGCCGGGAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:10,0:0:0,0:21.8:1:33.5:1:1:0:60:20:1:0:0 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:41:1:29.5:1:1:0:60:4:0.3333:0:0 +2 202137288 . TA T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.51186;SOR=1.39129;LSEQ=TGGTTGGAGAAATTGGAAAT;RSEQ=AAAAAAAAAATCTAATCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:9:8,1:72,14:86,9:0.0947:2,2:18:1:31.1:1:1:1.55:60:18:0.0957:0.0211:0.1 0/1:110:14:12,2:74,20:94,14:0.1273:2,2:17.8:1:29.4:1:0.73039:1.62:60:28:0.1296:0.0455:0.1 +2 202137321 . G T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26656;SOR=Inf;LSEQ=CTAATCTAAAAACCAGTAGG;RSEQ=CTCAATCCAGATTCCCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:123,40:163,0:0:2,0:25.7:1:31.3:1:1:0:60:22.286:1:0:0.2 0/1:225:3:1,2:157,65:222,3:0.0133:2,2:8.7:1:20.3:1:0.21207:4.79227:60:2:0.0091:0:1.3 +2 202139528 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49899;SOR=Inf;LSEQ=CATCTTAAAAAAGACCTTAT;RSEQ=TTGTCCTATGTGCTACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:167,24:191,0:0:2,0:24.4:1:32.5:1:1:0:60:94.5:1:0:0.1 0/1:201:2:1,1:166,33:199,2:0.01:2,2:9.5:1:31.5:1:0.3104:4.97082:60:4:0.01:0:2 +2 202139698 . CT C 87 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.7821;SOR=0.83013;LSEQ=TAGACGGAAACCTCCAAATC;RSEQ=TTTTTTTACATTACAGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:6:4,2:186,348:534,6:0.0111:2,2:29.3:1:31.3:1:0.1912:3.73:60:12:0.0115:0.0018:0.2 0/0:759:7:3,4:299,453:752,7:0.0092:2,2:26.4:1:31:1:1:1.14:59.1:14:0.0095:0:1.1 +2 202141737 . AT A 88 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10388;SOR=3.94954;LSEQ=GTAAAATATTTCTTATGCCT;RSEQ=TTTTTTTTAAATCAAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:0,2:16,109:125,2:0.0157:2,0:36:1:32:1:1:0:60:4:0.0164:0:0 0/1:134:8:1,7:25,100:125,8:0.0597:2,2:20.6:1:29.4:1:1:1.74368:60:16:0.062:0.0075:0.1 +2 202146409 . TTG T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=0.22755;SOR=Inf;LSEQ=TCTTTTATTCAAAAATTGTT;RSEQ=TTTTTTTCTGATTATGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:73,1:74,0:0:1,0:23.9:1:31:1:1:0:60:23.667:1:0:0.1 0/1:68:2:2,0:66,0:66,2:0.0294:1,0:42:1:28.5:1:1:0:60:4:0.0299:0:0 +2 202146653 . ATTC A 57 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37407;SOR=3.72922;LSEQ=CTCTTGAATTTCTGGTTCAA;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:0,1:73,124:197,1:0.005:2,0:33:0:31:0:1:0:60:2:0.0052:0:2 0/1:219:4:0,4:79,134:213,4:0.0183:2,0:42.3:1:28.8:1:0.29912:0:47.8:8:0.0196:0:2 +2 202146679 . A T 63 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00552;SOR=Inf;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=TTGATCATTCTTGGGTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:1,31:32,0:0:1,0:8.7:1:30.9:1:1:0:53:31:1:0:2.7 0/1:36:8:6,2:1,25:26,8:0.2222:1,2:8:1:21:1:0.00014:56.43:60:1.667:0.1667:0:2.4 +2 202149391 . CGGGGAGAGG C 90 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14888;SOR=3.6176;LSEQ=GCATGAGAGGGAGAGGGAGA;RSEQ=GAGAGGGAGAGGGAGACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:4,0:4,2:0.1111:0,0:16:1:34:0:1:0:44.5:4:0.1176:0:0 0/1:22:7:7,0:7,0:7,7:0.3182:0,0:14:1:32.1:1:1:0:44:14:0.3333:0.0909:0 +2 202149392 . G GAGA 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05344;SOR=0.24817;LSEQ=CATGAGAGGGAGAGGGAGAC;RSEQ=GGGAGAGGGAGAGGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:11,0:4,0:4,11:0.6111:0,0:15.3:1:29:1:1:0:31:22:0.6471:0.0556:1.2 0/1:22:6:6,0:7,0:7,6:0.2727:0,0:10.8:1:26.8:1:1:0:42.7:5:0.2381:0.1364:0.2 +2 202149406 . G GGAGAC 54 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.93433;LSEQ=GGAGACGGGGAGAGGGAGAG;RSEQ=GAGAGGGAGACGGGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:4,0:28,0:28,4:0.125:1,0:30:1:32.7:1:1:0:29.8:8:0.129:0:1.3 0/1:34:4:4,0:30,0:30,4:0.1176:1,0:26.8:1:27.2:1:1:0:41.5:3:0.0938:0:1.3 +2 202149416 . ACG A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=6;SSF=1;SOR=0.87324;LSEQ=AGAGGGAGAGGGAGAGGGAG;RSEQ=GGGAGAGGGAGAGGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:39:39,0:0,0:0,39:0.8864:0,1:22:1:32:1:1:0:50.6:18.5:0.9024:0.2273:0.5 1/1:39:34:34,0:1,0:1,34:0.8718:0,1:21.3:1:31.4:1:1:0:51.5:33:0.8919:0.1538:0.3 +2 202149417 . C G 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.83516;LSEQ=GAGGGAGAGGGAGAGGGAGA;RSEQ=GGGGAGAGGGAGAGGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:4:4,0:0,0:0,4:0.0909:0,0:45:1:33.5:1:1:0:29.8:8:0.0976:0:1.3 0/1:39:3:3,0:1,0:1,3:0.0769:0,0:41.3:1:33.7:1:1:0:40.3:6:0.0811:0:1 +2 202149418 . G GGAGA 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.71058;SOR=0.70925;LSEQ=AGGGAGAGGGAGAGGGAGAC;RSEQ=GGGAGAGGGAGAGGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:4:4,0:0,0:0,4:0.1111:0,0:46:1:30.5:1:1:0:29.8:8:1:0:1.3 0/1:37:3:3,0:2,0:2,3:0.0811:0,0:43.3:1:29.7:1:1:0:40.3:6:0.75:0:1 +2 202149589 . G C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15569;LSEQ=ATTTTGAGATCAAGCCCCAC;RSEQ=ATGACTGCACAGTAGAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:90:38,52:263,264:527,90:0.1454:2,2:25.7:1:32:1:0.20943:1.36255:60:180:0.1461:0:1.1 0/1:776:20:11,9:389,365:754,20:0.0258:2,2:21.2:1:30.8:1:0.82353:1.15:60:40:0.026:0:1.1 +2 202149737 . A G 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGACAGGAGGCCCCCATCT;RSEQ=TGAGCTGACATCTCAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:0:0,0:350,376:726,0:0:2,0:25.8:1:29.6:1:1:0:60:79.667:1:0:0.1 0/1:847:32:13,19:403,409:812,32:0.0378:2,2:26.8:1:31.8:1:0.3694:1.43948:60:64:0.0382:0:1.2 +2 202151140 . T G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.22852;LSEQ=GGAGACAGTTCATCAGTTGC;RSEQ=TTCCCCCACAGACAGTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:40:34,6:125,34:159,40:0.201:2,2:26.1:1:30.6:1:0.50816:1.54:60:80:0.201:0:1.9 0/1:203:11:10,1:159,33:192,11:0.0542:2,2:21.5:1:29.7:1:0.69484:2.07:60:22:0.0542:0:1.9 +2 202151163 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.1028;LSEQ=CCCCCACAGACAGTCACAAT;RSEQ=TTATGTGATGTATTTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:109:84,25:127,40:167,109:0.3949:2,2:24.4:1:32.8:1:0.88543:1.06:60:218:0.3978:0:1.4 1/0:349:202:154,48:109,38:147,202:0.5788:2,2:21.5:1:31.4:1:0.70634:1.12:60:201:0.5809:0:1.1 +2 202151400 . G A 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20532;SOR=0.6333;LSEQ=CCAGGCTGGAGTGCAGTGGC;RSEQ=TGATCTCGGCTCACCGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:19:0,19:0,48:48,19:0.2836:1,1:24.1:1:31.4:1:1:0:32.5:18:0.2727:0:1.1 0/1:110:22:0,22:1,86:87,22:0.2:1,1:20:1:30.8:1:1:0:35.2:44:0.2:0:1 +2 202151416 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25256;SOR=Inf;LSEQ=TGGCGTGATCTCGGCTCACC;RSEQ=CAAGCTCCGCCTCCCGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:47,0:0:1,0:15.8:1:33.6:1:1:0:33.1:94:1:0:0.3 0/1:59:3:0,3:0,56:56,3:0.0508:1,0:11.3:1:31:0:1:0:39.3:6:0.0508:0:1 +2 202151492 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06316;SOR=Inf;LSEQ=GGGACTACAGGGGCCCGCCA;RSEQ=CACACCTGGCTAATTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:12,0:0:0,0:24.7:1:31.7:1:1:0:40.2:24:1:0:0.1 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:37:1:26.7:1:1:0:44.7:6:0.3333:0:1 +2 202151746 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGAGCTAAAGTTAAATAGG;RSEQ=TATTAACAACAATAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:14,3:17,0:0:2,0:20.9:1:29.9:1:1:0:60:34:1:0:0 0/1:48:2:2,0:31,15:46,2:0.0417:2,0:30:1:32:0:1:0:60:4:0.0444:0:1 +2 202151826 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11921;SOR=0;LSEQ=AGCTGGTGGCAATAAATACC;RSEQ=GACACGTACAAAATCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:15,22:37,2:0.0513:2,2:36:1:31:1:1:1.45:60:4:0.0513:0:1 0/0:73:0:0,0:29,44:73,0:0:2,0:25.8:1:29.6:1:1:0:59.6:146:1:0:0.1 +2 202948109 . G C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCCTCCCACCCTGCCCC;RSEQ=ACCTCTACTCCAGTTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:11.5:1:21.5:1:1:0:60:1:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:32.5:1:1:0:60:4:1:0:1.5 +2 202948195 . C T 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CAACGACAATGATCAGTCAC;RSEQ=GTGTTCTAAGATTTGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:21,10:31,0:0:2,0:17.7:1:30.2:1:1:0:60:30:1:0:0.3 0/1:30:13:8,5:11,6:17,13:0.4333:2,2:28:1:30.4:1:1:1.14063:60:26:0.4333:0:1.1 +2 203369783 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=GGCATGATTGTTACACGTTT;RSEQ=GCATGGATAACATACAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:18,2:0.1:2,2:31.5:1:31.5:1:1:1:60:4:0.1:0:1 0/0:14:0:0,0:8,6:14,0:0:2,0:22.1:1:31.1:1:1:0:60:13:1:0:0 +2 203723989 . A T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00159;SOR=2.24281;LSEQ=ATTATAATTGAATTCAGATT;RSEQ=TAAATATAAATCTTTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:36:18,18:45,50:95,36:0.2748:2,2:22.8:1:30.3:1:0.846:1.11:60:72:0.2748:0:1.1 0/1:163:75:38,37:46,42:88,75:0.4601:2,2:22.7:1:29.5:1:0.87587:1.06599:60:150:0.463:0:1.1 +2 203724058 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=ATGATTTGGTTACTGAGATA;RSEQ=TGATCTAGTCCAGGACTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:31,64:95,0:0:2,0:27.4:1:33.6:1:1:0:60:190:1:0:0.2 0/1:107:2:1,1:39,66:105,2:0.0187:2,2:27:1:29.5:1:1:1.68:60:4:0.0187:0:1 +2 203724085 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49624;SOR=Inf;LSEQ=AGTCCAGGACTACAGTAGTT;RSEQ=AAATTTACACACAGAGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:22,45:67,0:0:2,0:21.4:1:31.8:1:1:0:60:66:1:0:0.1 0/1:67:2:1,1:17,48:65,2:0.0299:2,2:12:1:24.5:1:0.46811:2.77:60:4:0.0299:0:1 +2 204637162 . G T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCCATACCAAGCAAAG;RSEQ=GTGGAGTTCCATCTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:14:1:26.5:1:1:0:38:4:0.6667:0:1 +2 204637529 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19726;SOR=0;LSEQ=CAGAACTAGGTCCTTTTGGT;RSEQ=TTTTGGGAGTTTTTTCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:43,37:80,2:0.0244:2,2:29.5:1:28:1:1:1.16002:21.5:4:0.0247:0:1 0/0:102:0:0,0:61,41:102,0:0:2,0:22.6:1:31.4:1:1:0:38.5:101:1:0:0.1 +2 204637705 . TTCATCATCATCA T 162 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=11.000;MSILEN=3;SSF=0;SOR=0.07412;LSEQ=TCATCAAAATCATTATCATT;RSEQ=TCATCATCATCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:38:21,17:8,11:19,38:0.5:2,2:28.5:1:30.9:1:0.40767:1.68:33.5:76:0.5:0.1316:0.2 0/1:59:4:4,0:5,7:12,4:0.0678:2,0:30.8:1:31.5:1:0.08846:0:28.8:8:0.0678:0.0169:0.5 +2 204637740 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50115;SOR=Inf;LSEQ=ATCATCATCATCATCATCAT;RSEQ=TTCATCAGCAGCAAGTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:57,51:108,0:0:2,0:24.4:1:32.9:1:1:0:46.4:216:1:0:0.2 0/1:127:2:1,1:77,48:125,2:0.0157:2,2:12.5:1:28:1:1:1.59793:60:4:0.0159:0:1.5 +2 204637754 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50176;SOR=Inf;LSEQ=CATCATCTTCATCAGCAGCA;RSEQ=GTTTTCCTTTTTTCTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:73,65:138,0:0:2,0:23:1:30.8:1:1:0:49:33.5:0.9926:0:0.2 0/1:164:2:1,1:93,69:162,2:0.0122:2,2:44:1:31:1:1:1.34532:22:4:0.0125:0:1 +2 204637901 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51831;SOR=Inf;LSEQ=AGCACTGTCTACTAATATGC;RSEQ=CTGGCCCTGAACCACACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:46,49:95,0:0:2,0:24.9:1:30.3:1:1:0:46.5:94:1:0:0.1 0/1:143:2:1,1:67,74:141,2:0.014:2,2:38:1:31.5:1:1:1.10:37:4:0.014:0:1 +2 204638147 . TG T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13194;SOR=Inf;LSEQ=CACCTTAAAGTGATCATCTT;RSEQ=TCGGCCTTTAGTTCACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:32,43:75,0:0:2,0:14.4:1:31.3:1:1:0:31.5:74:1:0:0.1 0/1:96:4:1,3:31,60:91,4:0.0417:2,2:21.3:1:29.5:1:1:1.54339:28.8:8:0.0421:0:0 +2 204638317 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51052;SOR=Inf;LSEQ=CACGCAGGATGGAATCACAC;RSEQ=AGTTTGCTAAGCATTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:1,16:17,0:0:1,0:30.1:1:32.6:1:1:0:60:34:1:0:0 0/1:26:2:0,2:5,19:24,2:0.0769:2,0:11:1:29:0:1:0:60:4:0.0769:0:1 +2 204729153 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89671;SOR=0.97746;LSEQ=AATTAAGGAATCTGGTAAGA;RSEQ=GTCTTTGAAAGTTCTAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:460:252:173,79:145,63:208,252:0.5478:2,2:23.7:1:30.8:1:0.83966:1.05092:60:83:0.5485:0:1.1 1/0:498:270:183,87:154,74:228,270:0.5422:2,2:25.4:1:29.8:1:1:1.01:60:134:0.5436:0:1.1 +2 204729356 . G A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12252;SOR=Inf;LSEQ=GGCAACTATTTTCCATGGAT;RSEQ=CCATAAACTCAACATACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:58,245:303,0:0:2,0:24.6:1:32.5:1:1:0:60:302:1:0:0.1 0/1:300:3:2,1:79,216:295,3:0.01:2,2:5:1:25.7:1:0.18056:5.43:60:6:0.0101:0:1 +2 204729357 . C T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12372;SOR=0;LSEQ=GCAACTATTTTCCATGGATG;RSEQ=CATAAACTCAACATACTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:4:2,2:53,236:289,4:0.0136:2,2:22.8:1:29.5:1:0.16111:4.42:60:8:0.0137:0:1.3 0/0:293:0:0,0:78,214:292,0:0:2,0:25.1:1:30.6:1:1:0:60:96.333:0.9966:0:0.1 +2 204732223 . T A 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCCTAGTAGTTTTGGAG;RSEQ=TGTCAATGAAATGAATTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:35.7:1:28.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 204732714 . A G 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.5541;LSEQ=AGGCTCAGCTGAACCTGGCT;RSEQ=CCAGGACCTGGCCCTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:793:466:247,219:163,162:325,466:0.5876:2,2:25.6:1:32.1:1:0.4696:1.12:60:57.25:0.5842:0:1.1 0/1:943:416:210,206:271,252:523,416:0.4411:2,2:25.3:1:31.3:1:0.6938:1.05483:59.9:103:0.4392:0:1.2 +2 204732850 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTGTTTCAGCAGTCAA;RSEQ=GGCAGTGATTTATAGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:194:194:20,174:0,0:0,194:1:0,2:24.7:1:31.6:1:1:0:59.7:37.8:1:0:1.1 1/1:155:155:15,140:0,0:0,155:1:0,2:23.5:1:30.9:1:1:0:60:154:1:0:1 +2 204735238 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11829;SOR=0;LSEQ=GGGGATGAAGCTAGAAGGCA;RSEQ=AAGGGCTTGCCTGGGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:3:1,2:70,8:78,3:0.0366:2,2:33.3:1:30.7:1:0.03885:16.29545:60:6:0.0375:0:1 0/0:84:0:0,0:63,21:84,0:0:2,0:21.9:1:30.7:1:1:0:60:83:1:0:0.2 +2 204735616 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07528;SOR=Inf;LSEQ=CTCATGTACCCACCGCCATA;RSEQ=TACCTGGGCATAGGCAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:90,187:277,0:0:2,0:24.9:1:32.7:1:1:0:60:54.4:1:0:0.1 0/1:373:5:1,4:138,228:366,5:0.0134:2,2:21.6:1:27.8:1:0.65437:2.41611:60:10:0.0134:0:1 +2 204735710 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49704;SOR=Inf;LSEQ=TTGCATTGCAGTCTTCTATG;RSEQ=ACAAAAACAGTTTTGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:12,73:85,0:0:2,0:24.6:1:32.7:1:1:0:60:170:1:0:0.1 0/1:85:2:1,1:18,65:83,2:0.0235:2,2:7.5:1:27.5:1:0.39916:3.54:60:4:0.0235:0:1 +2 204736887 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAGGCCAGCTTTGCCATT;RSEQ=CAAACTCTCCCTTCTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 204737586 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49936;SOR=0;LSEQ=TCAATTTCCAAGAGCTGAGG;RSEQ=AATTCTAACTTTTTTGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:20,170:190,2:0.0104:2,2:14:1:32.5:1:0.2073:8.32:60:4:0.0105:0:1 0/0:178:0:0,0:24,154:178,0:0:2,0:22.6:1:31.5:1:1:0:59.8:88:1:0:0.1 +2 204836074 . A T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AAAACAGTACAAATTTATTT;RSEQ=CTTACAGTTCCGAAGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 204836514 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77058;SOR=0.93367;LSEQ=CCACCTTCCTCACACGTTCA;RSEQ=GCTTCCAATGTGCACGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:83:51,32:70,37:107,83:0.4368:2,2:24.3:1:30.4:1:0.64864:1.18599:60:166:0.4392:0:1.3 0/1:250:105:65,40:89,56:145,105:0.42:2,2:27.1:1:30.1:1:1:1.02:60:210:0.4217:0:1.4 +2 204836598 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20113;SOR=1.248;LSEQ=ATTTGATTTCTAGCAAATAA;RSEQ=ATTATCTACTACATTACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:106:47,59:60,82:142,106:0.4257:2,2:27.3:1:32.1:1:0.79592:1.09:60:34.333:0.4221:0:1.3 0/1:310:149:67,82:68,93:161,149:0.4806:2,2:25.4:1:30.8:1:0.64792:1.12:60:73.5:0.4804:0:1.3 +2 204836610 . C T 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=GCAAATAATATTATCTACTA;RSEQ=ATTACACCTTGAGTTTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:110,137:247,0:0:2,0:23.1:1:32.4:1:1:0:60:494:1:0:0.5 0/1:289:14:5,9:118,157:275,14:0.0484:2,2:26.6:1:26.5:1:0.7832:1.35149:60:13:0.0458:0:1 +2 204836648 . TG T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49947;SOR=Inf;LSEQ=ACGAGAAAGTCACATTGAAA;RSEQ=GAGGCTTTGGGTGGGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:63,115:178,0:0:2,0:26.4:1:31.5:1:1:0:60:58.333:1:0:0.4 0/1:193:2:1,1:63,128:191,2:0.0104:2,2:26.5:1:31.5:1:1:2.02:60:4:0.0105:0:0 +2 204836654 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50006;SOR=Inf;LSEQ=AAGTCACATTGAAATGGAGG;RSEQ=TTTGGGTGGGGTGTGGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:54,110:164,0:0:2,0:28.3:1:32.6:1:1:0:60:81:1:0:0.4 0/1:183:2:1,1:56,125:181,2:0.0109:2,2:36:1:31:0:0.52711:2.22:60:4:0.011:0:1 +2 204836692 . CT C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51428;SOR=0;LSEQ=TGGAGAATCCCCTATGCACC;RSEQ=TCCTTCCACTCCCAACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:24,80:104,2:0.0189:2,2:23.5:1:30:1:0.41779:3.29:60:4:0.0192:0:0 0/0:73:0:0,0:17,56:73,0:0:2,0:23.6:1:29.4:1:1:0:60:35.5:1:0:0.2 +2 206545779 . G C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCACTCTAAAATCCCGC;RSEQ=CCACCCCCCAACACAGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 208229946 . T TA 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=2.10911;LSEQ=TGAGAAATACCCTAGAGCTC;RSEQ=AAATTCTTTCTTCCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:13,0:13,1:0.0714:1,0:50:0:30:0:1:0:60:2:0.0714:0:0 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:27:1:28.5:1:1:0:60:4:0.1429:0:0 +2 208230026 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50494;SOR=Inf;LSEQ=GATAAATTATACTCTGACCC;RSEQ=ATTTTCTAAATTTCATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:63,10:73,0:0:2,0:22.2:1:31.7:1:1:0:60:72:1:0:0.2 0/1:94:2:1,1:73,19:92,2:0.0213:2,2:18:1:27.5:1:0.38206:3.77038:60:4:0.0213:0:1 +2 208230050 . A AT 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.11478;SOR=0.40549;LSEQ=TTCTAAATTTCATTAAAAAC;RSEQ=TTTTTTTTTCTGTATCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:10:6,4:93,37:130,10:0.0709:2,2:30.2:1:30.8:1:0.47864:1.66899:60:20:0.0714:0:0.2 0/1:167:5:4,1:115,47:162,5:0.0299:2,2:20.6:1:31.2:1:1:1.63:60:10:0.0303:0.012:0.2 +2 208230091 . A C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=3.31569;LSEQ=AATGCCTCTCTCAACTCTTA;RSEQ=AAAGACACTCCTGGGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:23:14,9:156,95:251,23:0.0836:2,2:23.7:1:32.7:1:1:1.05542:60:46:0.0846:0:1.5 0/1:374:87:53,34:176,111:287,87:0.2326:2,2:24.4:1:30.9:1:1:1.01713:60:86:0.2324:0:1.8 +2 208230143 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=17.78715;LSEQ=ATAAGTAACGTGCTACTGTG;RSEQ=GCACTGACTGTAATCAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:17:7,10:147,143:290,17:0.0554:2,2:25.4:1:31.4:1:0.46719:1.4667:60:34:0.0565:0:1.6 1/0:397:203:99,104:96,97:193,203:0.5113:2,2:25.2:1:30.2:1:0.91993:1.0396:60:100.5:0.5154:0:1.4 +2 209101905 . GA G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.0689;SOR=0.73142;LSEQ=CGTTGCACACTAACGGGAAG;RSEQ=AAAAAAAAAGAAAATTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:257:47,210:31,47:78,257:0.7604:2,2:26.6:1:32.1:1:2e-04:2.93611:59.8:256:0.7596:0.0325:0.1 1/0:405:283:53,230:40,77:117,283:0.6988:2,2:27.6:1:30.5:1:0.00115:2.24934:59.9:93.333:0.7:0.037:0.1 +2 209102117 . A ACT 106 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTAGGCAACCGGCAGTAGAG;RSEQ=CAGCCATACATACTCAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1:0,2:24.1:1:32.1:1:1:0:60:20:1:0.2:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 209103013 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTGATCCACCCACCTCGG;RSEQ=CTCCCAAAGTGCTAGGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:28:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 209103095 . C T 29 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAATTTAAATTAAGAAA;RSEQ=ATGCAGTGACCAAGTATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:29:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 209103748 . G A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00053;SOR=Inf;LSEQ=CGATGCTCTGAGCCCAGTGA;RSEQ=GATAAGTGTTAATTTGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:293,108:401,0:0:2,0:24.6:1:32.4:1:1:0:59.9:56.286:0.9975:0:0.1 0/1:444:12:7,5:287,145:432,12:0.027:2,2:16.8:1:29.8:1:0.54954:1.41269:60:11:0.0252:0:1.2 +2 209103969 . G GA 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00398;SOR=0;LSEQ=AAATGGAAGCTAAAAGAGGG;RSEQ=AAAAAAAACACAACACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:9:3,6:99,238:337,9:0.0259:2,2:28.4:1:31.6:1:0.7264:1.20:60:18:0.0264:0:0.2 0/0:317:0:0,0:107,210:317,0:0:2,0:23.8:1:30.3:1:1:0:60:104.667:1:0:0.1 +2 209104230 . A G 54 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.40825;LSEQ=ATCTCTTCTATCTCTTGTCT;RSEQ=TATTGGTCTCCTTTTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:1,3:0.75:0,2:33:1:34.3:1:1:0:60:6:0.75:0:1 1/0:2:1:0,1:1,0:1,1:0.5:0,0:24:0:33:0:1:0:60:2:0.5:0:4 +2 209104740 . G C 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCATACCCTGTAAGTAGTG;RSEQ=AGCATGAAGCGTTGGGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:74,254:328,0:0:2,0:24:1:32:1:1:0:60:163:1:0:0.1 0/1:351:24:5,19:84,242:326,24:0.0684:2,2:19.5:1:31:1:0.80838:1.31799:58.4:48:0.069:0:1 +2 209104798 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2282;SOR=Inf;LSEQ=GAGTCTCTCAGAGATGAGAG;RSEQ=ATAAATGACTCAATCTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:9,114:123,0:0:2,0:25.3:1:32.7:1:1:0:59.7:60.5:1:0:0.1 0/1:113:2:1,1:15,96:111,2:0.0177:2,2:7:1:27.5:1:0.26422:6.23:60:4:0.018:0:1 +2 209106589 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13948;SOR=Inf;LSEQ=TTAATTTCCTTAGCTGTCAG;RSEQ=TAAGACGGTGGACCTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:78,0:78,0:0:1,0:22.3:1:31.8:1:1:0:59.8:77:1:0:0.1 0/1:47:2:2,0:44,1:45,2:0.0426:1,0:22:1:28:1:1:0:60:4:0.0426:0:1 +2 209106897 . A G 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=7e-05;SOR=Inf;LSEQ=ACAAAAGGTAAAAGAGAATA;RSEQ=TAATAAAGAAAATTGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:59,178:237,0:0:2,0:23.2:1:30.9:1:1:0:59.9:78:1:0:0.1 0/1:314:17:6,11:88,209:297,17:0.0541:2,2:28.8:1:30.8:1:0.59582:1.29:60:34:0.0552:0:1.1 +2 209108118 . A T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0826;SOR=0;LSEQ=AAATGTCAGCTTACTTGAGA;RSEQ=TAAAGAAAAAGTTAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:207,78:285,3:0.0104:2,2:9.3:1:22.3:1:0.18768:5.27149:60:2:0.007:0:1 0/0:372:0:0,0:248,124:372,0:0:2,0:23.2:1:29.3:1:1:0:60:61:1:0:0.1 +2 209108317 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00424;SOR=0.6291;LSEQ=ATTATACATCCCCATGGCAA;RSEQ=ACCACCACCTTCTGTAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:106:35,71:170,293:463,106:0.1856:2,2:27.8:1:29.2:1:0.50271:1.17665:58.8:105:0.1875:0:1.2 0/1:662:83:35,48:223,356:579,83:0.1254:2,2:23.6:1:28.7:1:0.54843:1.16:57.7:166:0.1261:0:1.2 +2 209108497 . A G 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50749;LSEQ=CCAACAAATTTCTGAGGCAC;RSEQ=TAATGAGAGAAAAGCCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:0,5:0,25:25,5:0.1667:1,0:25:1:34:0:1:0:60:10:0.1667:0:1 0/1:11:1:0,1:0,10:10,1:0.0909:0,0:26:0:34:0:1:0:60:2:0.1:0:1 +2 209110006 . T TA 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.15298;SOR=0.70371;LSEQ=TATTATCTAAATCATTTGTT;RSEQ=AAAAAAAAAAGAAGCTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:46:38,8:203,68:271,46:0.1433:2,2:24.1:1:27.7:1:0.35006:1.59:60:22:0.141:0.028:0.3 0/1:323:34:28,6:210,77:287,34:0.1053:2,2:26.4:1:27.8:1:0.30384:1.71:60:33:0.1044:0:0.3 +2 209110175 . GA G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.10523;SOR=0.45367;LSEQ=AGAGGGGAAAAAGGTATAAA;RSEQ=AAAAAAAAATACCCTAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:12:2,10:61,199:260,12:0.044:2,2:29.6:1:31.3:1:0.73877:1.53046:60:24:0.0443:0:0 0/1:392:8:1,7:107,276:383,8:0.0204:2,2:25.1:1:30.5:1:0.45355:2.70826:60:16:0.0207:0:0.4 +2 209110196 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2567;SOR=Inf;LSEQ=AAAAAAAAAATACCCTAGCA;RSEQ=GAATTGTAAGGAGAATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:33,165:198,0:0:2,0:25:1:31.5:1:1:0:60:197:0.9949:0:0.2 0/1:246:3:0,3:38,205:243,3:0.0122:2,0:27.3:1:24:1:1:0:49:2:0.0083:0:2.7 +2 209110216 . C A 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24029;SOR=0;LSEQ=GGAATTGTAAGGAGAATATT;RSEQ=ATATAATATAGACCTAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:9,126:135,2:0.0145:2,2:7.5:1:26.5:1:0.14116:13.33:60:4:0.0155:0:4 0/0:143:0:0,0:11,132:143,0:0:2,0:24.7:1:31.5:1:1:0:59.8:27.6:1:0:0.3 +2 209110386 . T C 67 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTTTTCTGAGCACTGAT;RSEQ=TGAAGAGGACAGAGAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:27.2:1:29:1:1:0:60:4:1:0:1.8 1/1:1:1:0,1:0,0:0,1:1:0,0:6:0:34:0:1:0:60:2:1:0:1 +2 209113048 . G GA 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.60355;SOR=0.78348;LSEQ=GTTGGAAATTTCTGGGCCAT;RSEQ=AAAAAAAAAACATGCAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:21:19,2:190,44:234,21:0.0808:2,2:28.7:1:31.2:1:0.38497:2.19:58.8:42:0.0824:0.0115:0.7 0/1:233:15:8,7:154,63:217,15:0.0644:2,2:31.5:1:30.2:1:0.15695:2.13115:60:30:0.0661:0.0086:0.7 +2 209113192 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9991;LSEQ=ATGGCTTCTCTGAAGACCGT;RSEQ=CCACCCAGAATATTTCGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:847:164:92,72:366,313:679,164:0.1936:2,2:25.4:1:29.3:1:0.66251:1.09:50.5:163:0.1945:0:1.1 0/1:1013:196:101,95:426,388:814,196:0.1935:2,2:25.8:1:28:1:0.87356:1.03269:49.1:64.333:0.1942:0:1.2 +2 209115941 . CT C 77 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.6561;SOR=0.45267;LSEQ=AAAATAATTCAGATTATATT;RSEQ=TTTTTTTTTTCCTGTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:5,0:29,0:29,5:0.1471:1,0:22.8:1:33.5:1:1:0:59:10:0.1471:0.0294:1 0/1:14:1:1,0:13,0:13,1:0.0714:1,0:45:0:33:0:1:0:60:2:0.0714:0:0 +2 209115978 . C CT 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.56793;SOR=1.50518;LSEQ=TTCTCCTTCCCTTTTTTTTC;RSEQ=TTTTTTTTTTAAAGTGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:8:8,0:53,0:53,8:0.1231:1,0:28.1:1:29.6:1:1:0:56.1:7:0.1207:0.0462:1.8 0/1:40:7:7,0:32,0:32,7:0.175:1,0:28.3:1:31.3:1:1:0:54.3:14:0.1842:0.025:1.3 +2 209116049 . C T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.88604;SOR=1.04533;LSEQ=AATTCCTGGTCTTGAGGGAT;RSEQ=CTCCTGCCTCTGCCTCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:29:28,1:133,5:138,29:0.1737:1,1:28.2:1:31:1:1:1.05:60:58:0.1801:0:1.2 0/1:161:29:28,1:126,5:131,29:0.1801:1,1:24.9:1:30:1:1:1.11:59.3:58:0.1835:0:1.3 +2 209116097 . C T 54 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.07006;SOR=Inf;LSEQ=GGACTTCACGTGTGCACCAC;RSEQ=ATGCCCAGCCAGATTATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:246,110:356,0:0:2,0:22.7:1:31.5:1:1:0:60:177:0.9972:0:0.1 0/1:450:5:1,4:295,150:445,5:0.0111:2,2:6.8:1:23.6:1:0.04885:7.83045:60:10:0.0113:0:1.2 +2 209116134 . C T 155 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.52436;LSEQ=TCCTTTCTGAGTTTGCTACA;RSEQ=GGAGGGGTAACTCATTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:644:4:0,4:362,278:640,4:0.0062:2,0:1:0:26.3:1:0.03633:0:60:8:0.0063:0:1 0/1:823:37:22,15:440,345:785,37:0.045:2,2:22.2:1:29.8:1:0.73678:1.15:60:74:0.0454:0:1.2 +2 209116299 . G GA 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.89354;SOR=0.95321;LSEQ=GACTTCAATAAACCTAAAAA;RSEQ=AAAAAAAAAATACATGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:27:6,21:86,233:319,27:0.0763:2,2:23.2:1:30.9:1:0.82062:1.2909:57.2:26:0.0767:0.0056:0.2 0/1:466:34:8,26:109,319:428,34:0.073:2,2:28.7:1:28.9:1:1:1.11025:56.8:33:0.0743:0:0.3 +2 209330917 . A AT 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.24041;SOR=0;LSEQ=AAAAGGAAGAAGAGCTTTTC;RSEQ=TTTTTTTTTCTTTGAGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:2,1:25,8:33,3:0.0833:2,2:23:1:30.9:1:1:1.54148:60:6:0.0882:0.0278:0 0/0:33:0:0,0:25,8:33,0:0:2,0:18.7:1:29.5:1:1:0:60:66:1:0:0.3 +2 209330966 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.20787;SOR=0;LSEQ=CCCATCATAGTGGATTGTCA;RSEQ=GCAAGTTCTCCATGAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:32,24:56,2:0.0333:2,2:13.5:1:29:1:1:1.32664:60:4:0.0357:0:1 0/0:71:0:0,0:41,30:71,0:0:2,0:28.8:1:29.6:1:1:0:60:142:1:0:0.2 +2 209330985 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49664;SOR=0;LSEQ=AAGCAAGTTCTCCATGAATG;RSEQ=AGCATGGATGTCTTTTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:37,36:73,2:0.0267:2,2:27:1:32.5:1:1:1.02741:60:4:0.0274:0:1 0/0:74:0:0,0:38,36:74,0:0:2,0:29:1:30.8:1:1:0:60:36:1:0:0.2 +2 209331070 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49061;SOR=Inf;LSEQ=CCAGAGAGGCCAACCTGATA;RSEQ=ACGTCACTTTTCTCCTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:7,17:24,0:0:2,0:19.7:1:31.5:1:1:0:60:23:1:0:0.2 0/1:26:2:1,1:5,19:24,2:0.0769:2,2:9.5:1:25.5:1:0.41538:3.56:60:4:0.0769:0:1.5 +2 212248286 . G T 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.21073;SOR=4.14782;LSEQ=ACCACCAGAGAAAGAGAGGG;RSEQ=GGTGGGGAAATTGGAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:1:0,1:251,96:347,1:0.0029:2,0:1:0:26:0:0.27874:0:60:2:0.0029:0:1 0/1:338:4:1,3:230,104:334,4:0.0118:2,2:11:1:25.8:1:0.09549:6.59443:60:8:0.0119:0:1 +2 212251070 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTAATTTTTGAAAAACGTC;RSEQ=TATAAGAACATAATATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:39:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212251864 . T C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20695;SOR=1.25186;LSEQ=GCAAAACCTCCATCTCGGTA;RSEQ=ACAAACTGGTTCTGTTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:76:21,55:117,211:328,76:0.1881:2,2:28:1:32.1:1:0.22689:1.45098:60:152:0.1891:0:1.1 0/1:458:103:42,61:137,218:355,103:0.2249:2,2:27.1:1:31:1:0.73118:1.10:60:33.333:0.2227:0:1.1 +2 212251910 . G A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15394;LSEQ=AACATATGTGGAGAGAAGGC;RSEQ=TTGTTAGAAATAGTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:55:13,42:29,132:161,55:0.2546:2,2:21.7:1:31.2:1:0.42992:1.41:60:110:0.2558:0:1.1 0/1:221:11:2,9:53,157:210,11:0.0498:2,2:19:1:30.9:1:0.73544:1.51644:60:22:0.0505:0:1.1 +2 212252384 . TA T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTAGTACATGACCAA;RSEQ=ATCAGGGAAGTAAAGATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:16.5:1:31:1:1:0:60:4:0.5:0.25:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212252440 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATAATTTATGTGCCCAGG;RSEQ=AAATCCTTCAGATAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:15,2:0.1176:1,0:44:1:32:1:1:0:60:4:0.1176:0:1 0/0:8:0:0,0:7,1:8,0:0:2,0:24.3:1:29.1:1:1:0:60:16:1:0:0 +2 212252570 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=AAATTCTTAACTCACTGTTG;RSEQ=CAAAGGCAAAATGAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:123,19:142,0:0:2,0:26.6:1:31.3:1:1:0:60:34.5:1:0:0.1 0/1:143:2:1,1:119,21:140,2:0.014:2,2:33:1:28:1:0.28678:5.55967:60:4:0.0141:0:1 +2 212252809 . G A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19528;LSEQ=CGAAAAAGAAAAGCCACATG;RSEQ=GTCGTATGAACCAAAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:61:5,56:1,26:27,61:0.6932:1,2:19.9:1:31.4:1:0.662:2.30:60:60:0.6977:0:1.2 0/1:79:24:2,22:8,47:55,24:0.3038:2,2:26.3:1:30.1:1:0.71491:1.85899:60:23:0.2949:0:1.2 +2 212284621 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTTCAAAACTTAAATCT;RSEQ=CTTCTTAAAAACAAAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:26:1:33.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212285103 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58908;SOR=0.84535;LSEQ=TTTTGAAATGTTAGTGCTTA;RSEQ=GAACTATTACATGATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:69:65,4:65,3:68,69:0.5036:1,2:24.9:1:32.4:1:1:1.33055:60:68:0.5113:0:1 0/1:91:42:35,7:46,3:49,42:0.4615:2,2:23.2:1:31.1:1:0.17769:3.02958:60:84:0.4615:0:1.1 +2 212285339 . AAAAG A 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCATACGATCATCACCCT;RSEQ=AAAGATTGCCCATCAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:0:0,0:165,327:492,0:0:2,0:25.2:1:30.6:1:1:0:60:48.2:1:0:0.1 0/1:513:34:11,23:176,303:479,34:0.0663:2,2:28.1:1:30.1:1:0.71358:1.21404:60:68:0.0672:0.0097:0.1 +2 212285785 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTCTATAGCATACTGACT;RSEQ=CATTATCAAAGTAGGGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:19:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212286462 . G GTGTC 62 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=1;SOR=1.22474;LSEQ=AAATCAAGGTGCTAAAATAA;RSEQ=TGTCTGAGGATTAAGACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:28.8:1:31.4:1:1:0:60:8:0.4444:0.1111:0 1/0:2:1:1,0:1,0:1,1:0.5:0,0:13:0:31.8:0:1:0:60:2:0.5:0:0 +2 212286805 . C A 82 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02478;SOR=7.77392;LSEQ=CCAGTTCCTTAAATTTAGGT;RSEQ=TACTGTCAGCATCAATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:1:1,0:271,347:618,1:0.0016:2,0:1:0:25:0:0.43942:0:60:2:0.0016:0:1 0/1:726:9:7,2:321,395:716,9:0.0124:2,2:17.6:1:25.9:1:0.08673:4.30:60:18:0.0125:0:1.1 +2 212286934 . A T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19852;SOR=0.59888;LSEQ=GTTTGAAAAATGTTGTTTTA;RSEQ=TCGTAATGATCTGAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:31:0,31:0,36:36,31:0.4627:1,1:20.5:1:31:1:1:0:60:62:0.4627:0:1.2 0/1:56:19:2,17:1,36:37,19:0.3393:1,2:25.5:1:29.7:1:0.2632:4.12:60:38:0.3393:0:1 +2 212287069 . T C 77 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATAAATTTTTTCTCTGATG;RSEQ=GTATAGACGTGACTGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:23.7:1:29.8:1:1:0:55.3:12:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:30:0:31:0:1:0:60:2:1:0:1 +2 212288782 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50276;SOR=0;LSEQ=ATAATTGTTTTTGAACTGTC;RSEQ=TATTTTTCAATACAGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:95,3:98,2:0.02:1,2:17.5:1:27.5:1:0.07879:27.56815:60:4:0.0202:0:1 0/0:81:0:0,0:77,4:81,0:0:1,0:25.7:1:29.3:1:1:0:59.7:80:1:0:0.1 +2 212289142 . TA T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.81858;SOR=1.19848;LSEQ=CAATCCAAACACCAATCAAT;RSEQ=AAAAAAAAAAAGCTCCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:14:0,14:0,52:52,14:0.2029:1,1:28.9:1:31.9:1:1:0:60:28:0.209:0:0.3 0/1:47:11:1,10:2,34:36,11:0.234:2,2:32.1:1:31:1:0.55967:1.68:60:22:0.234:0:0.3 +2 212292929 . G C 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GCAGGTTCTGCATGTGTATC;RSEQ=CAGAACTTAAAATAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:23.3:1:29.7:1:1:0:43.3:6:0.3:0.1:0.7 0/0:4:0:0,0:4,0:4,0:0:0,0:31.3:1:30.5:1:1:0:60:8:1:0:0 +2 212292936 . T TTAAAATAAAA 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=8.000;MSILEN=5;SSF=0.26749;SOR=0;LSEQ=CTGCATGTGTATCGCAGAAC;RSEQ=TAAAATAAAATAAAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:10,0:10,6:0.375:0,0:8:1:30.5:1:1:0:54.2:12:0.375:0.375:0.2 0/0:4:0:0,0:4,0:4,0:0:0,0:34:1:31.3:1:1:0:60:8:1:0:0 +2 212292968 . AT A 112 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03504;SOR=0.11962;LSEQ=AAAATAAAATAAAATAAAAT;RSEQ=TTTTTTTTCATTGAGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:11:11,0:19,0:19,11:0.3667:1,0:23.2:1:32.4:1:1:0:58:22:0.3667:0.0333:0 0/1:16:1:1,0:15,0:15,1:0.0625:1,0:13:0:32:0:1:0:60:2:0.0667:0:1 +2 212295468 . GTA G 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.00585;SOR=0;LSEQ=ACGGAAGCTGGTAATATATG;RSEQ=TATATATATGTGTGTGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:13,0:13,0:13,13:0.5:1,1:26.8:1:32.2:1:1:0:43.5:26:0.5:0.0769:0 0/0:10:0:0,0:10,0:10,0:0:0,0:23:1:29.9:1:1:0:60:20:1:0:0.3 +2 212295492 . GATATAT ATATATC 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=2e-05;SOR=0;LSEQ=ATATATATGTGTGTGTATAT;RSEQ=ATATACACACACATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:24:24,0:19,0:19,24:0.5581:1,1:23.5:1:30.7:1:1:0:50.3:48:0.5714:0.186:0.1 0/0:17:0:0,0:17,0:17,0:0:1,0:23.6:1:32.3:1:1:0:60:34:1:0:0.2 +2 212295590 . G GT 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.11159;SOR=1.51061;LSEQ=CCTAAGCTTCAGGCTTATTG;RSEQ=TTTCTTGTATAAAATATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:51:44,7:94,21:115,51:0.3072:2,2:22.3:1:29.8:1:0.65358:1.40:60:50:0.3106:0.0843:0.1 0/1:132:53:44,9:66,13:79,53:0.4015:2,2:16.7:1:29.2:1:1:1.03819:60:106:0.4015:0.1591:0 +2 212295600 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50091;SOR=0;LSEQ=AGGCTTATTGGTTTCTTGTA;RSEQ=AAAATATAAGGAGATAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:154,43:197,2:0.0101:2,2:24.5:1:32:1:0.39419:3.55169:60:4:0.0101:0:1 0/0:174:0:0,0:132,42:174,0:0:2,0:18.3:1:29.2:1:1:0:60:348:1:0:0 +2 212295875 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08076;SOR=0.67594;LSEQ=TCAGTTAATGCCCAGGTTTT;RSEQ=CCATTTTTCTAAAACAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:234:191:31,160:6,37:43,191:0.8162:2,2:22.2:1:30.4:1:0.8202:1.19:60:94.5:0.8147:0:1.1 1/0:256:192:42,150:13,48:61,192:0.75:2,2:23.5:1:28.3:1:1:1.03:60:47:0.752:0:1.1 +2 212296094 . G C 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTATTTTTCCAAGTGACTT;RSEQ=ATATCCTTTTGCAAACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:19.7:1:32.7:1:1:0:60:6:0.5:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:44:0:34:0:1:0:60:2:1:0:1 +2 212426466 . A C 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00631;SOR=Inf;LSEQ=ATATCACGCATTTAATCTGT;RSEQ=GTTTACCTAAAAGTACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:49,2:51,0:0:1,0:23.2:1:29:1:1:0:59.5:102:1:0:0 0/1:41:6:5,1:34,1:35,6:0.1463:1,2:17:1:29.5:1:0.27439:6.29815:60:12:0.1463:0:1 +2 212426554 . A T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35835;SOR=3.21696;LSEQ=TGGGAAGACAACATATTTTC;RSEQ=ATATGAAAACTGTTCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:0,1:223,66:289,1:0.0034:2,0:1:0:26:0:0.23103:0:60:2:0.0035:0:1 0/1:272:3:1,2:193,76:269,3:0.011:2,2:10:1:27.7:1:0.19857:5.04379:60:6:0.0112:0:1 +2 212426588 . C T 164 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01849;LSEQ=TCCAGGTTAGGAAATATTAA;RSEQ=CTAAAAATGTAATTTCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:41:31,10:271,146:417,41:0.0895:2,2:25.6:1:30.7:1:0.22631:1.67:60:40:0.0879:0:1 0/0:553:1:0,1:351,200:551,1:0.0018:2,0:1:0:24:0:0.36413:0:60:2:0.0018:0:1 +2 212483804 . T C 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00129;SOR=Inf;LSEQ=TAATATTTCCATAAGAGAAA;RSEQ=TTGTAAGTTGTGGAGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:200,12:212,0:0:2,0:22.8:1:31.2:1:1:0:60:52:1:0:0 0/1:167:8:7,1:147,12:159,8:0.0479:2,2:13.8:1:32.4:1:0.48467:1.74276:60:16:0.05:0:1.1 +2 212485648 . T C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGACCAGCATAGGCAACA;RSEQ=AGAGACATTCCAACTCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:33.5:1:1:0:20:4:1:0:1 +2 212488815 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49985;SOR=Inf;LSEQ=TACTTTCAGTCCGATAGTCA;RSEQ=TCCTCTCTCTCTGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:26,146:172,0:0:2,0:25.1:1:31.8:1:1:0:59.9:27.667:1:0:0.2 0/1:190:2:1,1:39,148:187,2:0.0105:2,2:24:1:31.5:1:0.37938:3.76:60:4:0.0106:0:1 +2 212488817 . CCT C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.21832;SOR=0;LSEQ=CTTTCAGTCCGATAGTCAGT;RSEQ=CTCTCTCTGTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:19,140:159,2:0.0124:2,2:38:1:32.5:1:0.2337:7.21:60:4:0.0126:0:0 0/0:183:0:0,0:33,150:183,0:0:2,0:21.8:1:30.5:1:1:0:59.7:19.333:1:0:0.3 +2 212488870 . G GC 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25561;SOR=0.61911;LSEQ=TTGGTTCTCTTTCTTACAAA;RSEQ=AAAAACACACCAACTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:63:45:0,45:0,18:18,45:0.7143:1,1:27.2:1:32.3:1:1:0:60:90:0.7377:0.0794:0.1 1/0:61:37:0,37:1,23:24,37:0.6066:1,1:24.9:1:31.8:1:0.39344:0:59.7:74:0.6167:0.1475:0.3 +2 212495336 . GA G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.57865;SOR=0.76764;LSEQ=AGTTCTGACAACCAGAATGA;RSEQ=AAAAAAAAAATAAAAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:19:5,14:68,225:293,19:0.0607:2,2:22.3:1:31.1:1:0.78096:1.18:60:38:0.0609:0.0064:0.2 0/1:254:12:1,11:73,168:241,12:0.0472:2,2:24:1:30.7:1:0.18936:4.76006:58.9:24:0.0478:0.0039:0.5 +2 212495342 . A AT 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=11.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACAACCAGAATGAGAAAAA;RSEQ=AAAAATAAAAAGTATGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:55,207:262,0:0:2,0:22.6:1:31.1:1:1:0:60:524:1:0:0.2 0/1:214:50:11,39:51,113:164,50:0.2336:2,2:20.6:1:27.8:1:0.28521:1.59683:60:100:0.2336:0.0561:0.2 +2 212522384 . A G 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.57327;SOR=0.35666;LSEQ=TTGATATATTATGAGTTACA;RSEQ=TATATTATAAATTTAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:96,12:108,2:0.0182:2,2:21.5:1:31.5:1:0.22335:7.72593:60:4:0.0185:0:1 0/0:153:1:1,0:134,17:151,1:0.0065:2,0:14:0:33:0:1:0:60:2:0.0067:0:1 +2 212522450 . C T 212 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00299;LSEQ=TAACTAGGAAAGGATTTGAG;RSEQ=GACAAAATGGAAACATGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:143:94,49:154,81:235,143:0.3773:2,2:24.3:1:29.7:1:1:1.01:60:46.667:0.3794:0:1.1 0/0:556:1:0,1:324,230:554,1:0.0018:2,0:1:0:24:0:0.41622:0:60:2:0.0018:0:1 +2 212522651 . A G 234 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGAGCCTTGGAGGAAGAAC;RSEQ=TGGGAAGCAAGCACACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:187:99,88:225,242:467,187:0.2859:2,2:26.4:1:31.1:1:0.29917:1.21:60:92.5:0.2864:0:1.1 0/0:808:0:0,0:391,415:806,0:0:2,0:26.4:1:29.8:1:1:0:60:200.5:0.9975:0:0.1 +2 212522738 . TA T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.12488;SOR=Inf;LSEQ=ACCTGCAGAAAATGCAAATT;RSEQ=AAAAAATACAAGGGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:99,273:372,0:0:2,0:25.6:1:30.3:1:1:0:60:371:1:0:0.1 0/1:398:4:2,2:126,268:394,4:0.0101:2,2:29.3:1:28:1:0.59677:2.12:60:8:0.0101:0:0 +2 212529910 . C A 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01021;SOR=Inf;LSEQ=AAATCATTCTCTCAGTATTT;RSEQ=TCTTAAAATCAGCATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:53,1:54,0:0:1,0:23.4:1:32.6:1:1:0:60:108:1:0:0.2 0/1:38:5:5,0:32,1:33,5:0.1316:1,0:29.2:1:28.2:1:1:0:60:10:0.1316:0:1 +2 212529962 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5103;SOR=0;LSEQ=AGTAGAGTTCTATGAGAATG;RSEQ=TATACATTTCAGAGATGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:134,4:138,2:0.0143:1,2:8.5:1:29.5:1:0.0704:30.0704:60:4:0.0149:0:1 0/0:102:0:0,0:97,5:102,0:0:1,0:23.9:1:30.1:1:1:0:60:19.4:1:0:0.1 +2 212530218 . G GA 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.14062;SOR=0.50988;LSEQ=GGACCCTGAAATGTGAAAAC;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:15:3,12:65,250:315,15:0.0449:2,2:28.9:1:29.3:1:1:1.0399:60:14:0.0435:0:0.3 0/1:342:8:2,6:80,254:334,8:0.0234:2,2:21.3:1:28.6:1:1:1.06:60:16:0.0238:0.0058:0.1 +2 212530340 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51919;SOR=0;LSEQ=ATTGGAGAACATTTTCAGCA;RSEQ=TGCAAATGTGGATGTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:0,26:26,2:0.0714:1,0:24.5:1:32:0:1:0:60:4:0.0714:0:1.5 0/0:17:0:0,0:0,17:17,0:0:1,0:23.4:1:29.8:1:1:0:60:16:1:0:0.1 +2 212530466 . C T 25 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTGAAATATTTTCCTTTT;RSEQ=GACATAAGCAGTTCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:23:1:25.5:1:1:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212543722 . A G 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20719;SOR=0;LSEQ=AAAAAAAAAAAAAAATCAGA;RSEQ=CTAATCAGTCCTTCAAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:133,59:192,2:0.0102:2,2:5:0:33.5:1:0.52401:2.24379:60:4:0.0108:0:1.5 0/0:234:0:0,0:134,100:234,0:0:2,0:17:1:27.8:1:1:0:58.5:22.4:1:0:0.8 +2 212543924 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=5.58265;LSEQ=CAGCAGCTGTGAAACACCAA;RSEQ=ATCAAGGGGAAATAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:86:23,63:94,194:288,86:0.2299:2,2:24:1:32.7:1:0.35401:1.32623:60:172:0.2318:0:1 1/0:390:244:80,164:45,101:146,244:0.6256:2,2:26.1:1:30.5:1:0.73711:1.09:59.9:80.333:0.6276:0:1.1 +2 212544024 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=8.57881;LSEQ=AAAAGAGATATATGGCAAAT;RSEQ=ACTTTGGTGGCCTATCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:8:0,8:1,44:45,8:0.1509:1,0:25:1:31.6:1:1:0:60:16:0.1538:0:1.3 1/0:36:22:1,21:0,13:13,22:0.6111:1,1:26.1:1:30.7:1:1:0:60:44:0.6111:0:1 +2 212544026 . CT C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51163;SOR=0;LSEQ=AAGAGATATATGGCAAATGA;RSEQ=TTGGTGGCCTATCCCATCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:0,2:1,48:49,2:0.0392:1,0:34.5:1:34.5:1:1:0:60:4:0.04:0:0.5 0/0:35:0:0,0:2,33:35,0:0:2,0:21.9:1:30.1:1:1:0:60:34:1:0:0.6 +2 212544080 . T C 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00814;SOR=0;LSEQ=TACCCACAACTTCTTCTATA;RSEQ=TGCAGAGTCCTAGTAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:1,7:8,7:0.4667:2,0:26.6:1:34.7:1:1:0:60:14:0.4667:0:1 0/0:12:0:0,0:1,11:12,0:0:2,0:31.3:1:30.1:1:1:0:60:24:1:0:0.3 +2 212566481 . CAAAAAAAA C 32 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=28.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AACAGAGCGAGACTCCGTCT;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:12.5:1:32.7:1:1:0:52.5:4:1:0.5:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:30:0:1:0:60:2:1:0:2 +2 212566935 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20257;SOR=Inf;LSEQ=CGGAACCATGAAACGCATTC;RSEQ=GGAGTAAAATAAGGCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:21,158:179,0:0:2,0:24.5:1:29.8:1:1:0:60:58.667:1:0:0.1 0/1:147:2:1,1:22,123:145,2:0.0136:2,2:21.5:1:31.5:1:0.28935:5.49:60:4:0.014:0:1 +2 212568257 . T C 34 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCATAAATAAGAACATCA;RSEQ=ACAGATGACATCAGAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:11:1:34:0:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:12:0:32:0:1:0:60:2:1:0:0 +2 212569005 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51101;SOR=0;LSEQ=TTGAAATATGGTGAAAATGT;RSEQ=TTGAAAGTTGGGAAGTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:3,116:119,2:0.0165:1,2:29:1:29.5:1:0.06529:33.66:60:4:0.0167:0:1 0/0:87:0:0,0:3,84:87,0:0:1,0:24.4:1:31.8:1:1:0:60:174:1:0:0.1 +2 212569879 . T C 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAGTAGAGACAGGGTTTC;RSEQ=CCATGTTGGCCAGGATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:39,0:39,0:0:1,0:24.8:1:32.9:1:1:0:50.5:78:1:0:0.1 0/1:31:15:15,0:16,0:16,15:0.4839:1,1:28.1:1:30.3:1:1:0:44.5:14:0.4667:0:1.5 +2 212569924 . G A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=CCTGACCTCATGATCCACCC;RSEQ=CCTCAACCTCCCTAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:91,1:92,0:0:1,0:24.3:1:29.8:1:1:0:58.6:45:1:0:0.2 0/1:84:12:12,0:72,0:72,12:0.1429:1,0:21.4:1:29.7:1:1:0:46.1:24:0.15:0:2.1 +2 212569969 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49887;SOR=Inf;LSEQ=TTACTGGTGTGAGCCACGAT;RSEQ=CCCAGTCAATCTTGTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:156,34:190,0:0:2,0:22:1:32.2:1:1:0:59.9:189:1:0:0.2 0/1:197:2:1,1:159,36:195,2:0.0102:2,2:17.5:1:26.5:1:0.34114:4.37026:57.5:4:0.0103:0:2.5 +2 212569983 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=8.57212;LSEQ=CACGATGCCCAGTCAATCTT;RSEQ=TGTAATTTTTAAAAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:22:15,7:173,50:223,22:0.0898:2,2:25.4:1:29.2:1:0.30258:1.61119:58.8:44:0.0909:0:1.1 0/1:294:135:96,39:108,51:159,135:0.4592:2,2:23.8:1:27.9:1:0.61208:1.16:60:270:0.4639:0:1.1 +2 212576951 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4999;SOR=0;LSEQ=TTGAGAAACTTATTTTTGGC;RSEQ=AATAAATCATTGCATCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:26,155:181,2:0.0109:2,2:27:1:29:1:0.274:5.87:60:4:0.0112:0:1 0/0:165:0:0,0:34,131:165,0:0:2,0:25.4:1:31.1:1:1:0:60:330:1:0:0.1 +2 212576980 . T C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47801;SOR=1.42611;LSEQ=ATTGCATCTTCATTATAAAA;RSEQ=AGCAGAGTATTTTTAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:9:0,9:7,101:108,9:0.0769:2,0:33.2:1:32.2:1:1:0:60:18:0.0769:0:1 0/1:94:10:1,9:8,76:84,10:0.1064:2,2:17.9:1:32.1:1:1:1.05:60:20:0.1099:0:1 +2 212577264 . T G 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTTTGAAAATATCATT;RSEQ=TTAATGATTTTGAAATGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:27:1:33.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212578379 . TA T 202 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.05729;SOR=0.69707;LSEQ=CTACCACAAAGTTATCTGAT;RSEQ=AAAAAAAAAAAAAGGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:96:18,78:47,147:194,96:0.2866:2,2:28:1:30.7:1:0.36936:1.38398:59.8:31:0.2853:0.0179:0.6 0/1:311:68:15,53:75,142:217,68:0.2186:2,2:31:1:29.4:1:0.07213:1.86236:59.9:33:0.2171:0.0096:1.1 +2 212578523 . C T 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03386;SOR=0;LSEQ=ACAACTCTTTGTTTAAATAT;RSEQ=TCAACCTGAAATTGTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:0,6:0,22:22,6:0.2143:1,0:21.5:1:31:1:1:0:60:12:0.2222:0:1 0/0:20:0:0,0:1,19:20,0:0:1,0:20.9:1:32.4:1:1:0:60:40:1:0:0.1 +2 212579599 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAGCAAATGGTTAAGAG;RSEQ=CCCCCATGCCATCCACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212587321 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25517;LSEQ=ATAATACTTGTTAATGAAAC;RSEQ=CTGCCAAAACAGGAGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:163:115:9,106:7,40:47,115:0.7055:2,2:22.5:1:30.6:1:0.24351:2.05096:59.5:114:0.7125:0:1.1 0/1:119:45:6,39:9,64:73,45:0.3782:2,2:22.1:1:28.5:1:1:1.09:60:21.5:0.3739:0:1.2 +2 212589742 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49996;SOR=Inf;LSEQ=GACAAAGATTCAGTATGCCT;RSEQ=AATCAAATAGGGAAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:138,20:158,0:0:2,0:23.2:1:32.8:1:1:0:60:78:1:0:0.1 0/1:176:2:1,1:144,30:174,2:0.0114:2,2:15:1:27:1:0.32208:4.73836:60:4:0.0116:0:1 +2 212589774 . A G 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGGAAAGGAGAGCAGGAT;RSEQ=ATAAAAGAGAGAAATCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:21:17,4:194,76:270,21:0.0722:2,2:30.2:1:33:1:0.45452:1.66:60:42:0.0724:0:1.1 0/0:346:0:0,0:243,103:346,0:0:2,0:24:1:28:1:1:0:60:85.5:1:0:0.1 +2 212589986 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25445;SOR=0.7598;LSEQ=GAAACTCATAAGCTGAGTTC;RSEQ=GGAGTGACAATTTCTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:152:96:6,90:7,48:55,96:0.6316:2,2:23.5:1:30.3:1:0.22858:2.17549:60:95:0.6376:0:1 1/0:168:95:15,80:7,66:73,95:0.5655:2,2:21.6:1:28.9:1:0.25926:1.76:60:30.667:0.5576:0:1.1 +2 212590067 . T G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24;SOR=Inf;LSEQ=TTACAACTAGATCAAAATTT;RSEQ=TATACAAAAATCTCCAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:1,37:38,0:0:1,0:27.6:1:30.4:1:1:0:60:76:1:0:0.1 0/1:37:2:0,2:1,34:35,2:0.0541:1,0:26:1:33:0:1:0:60:4:0.0541:0:1 +2 212590228 . T TG 55 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCGTAATCCCAACTACT;RSEQ=GGAGACTGAGACAGGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:29:1:27.9:1:1:0:60:8:0.8:0.2:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212615284 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=0;LSEQ=GCTCATTTCATGTTTTAGAT;RSEQ=ACCAGAGGCATGAAATGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:156,28:184,2:0.0108:2,2:29.5:1:29:1:0.28823:5.49213:60:4:0.0108:0:1 0/0:170:0:0,0:140,30:170,0:0:2,0:21.9:1:31.1:1:1:0:60:169:1:0:0.1 +2 212615516 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0128;SOR=1.80238;LSEQ=CTCCTCAAAGGAAATACTCC;RSEQ=GCTCCTTTATGAGGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:177:99:16,83:8,70:78,99:0.5593:2,2:18.5:1:30.3:1:0.27807:1.68:60:48.5:0.5575:0:1 1/0:158:110:27,83:6,41:47,110:0.6962:2,2:19.8:1:29.3:1:0.13385:2.21:60:109:0.6987:0:1.1 +2 212652939 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23783;SOR=Inf;LSEQ=AAACTGCTTGTTGATGAAAA;RSEQ=GTAATCAACAAAAGTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:8,148:156,0:0:2,0:23.4:1:31.6:1:1:0:60:77:1:0:0.1 0/1:149:2:1,1:17,130:147,2:0.0134:2,2:13.5:1:29:1:0.22773:7.46:60:4:0.0137:0:1 +2 212698718 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77423;SOR=1.04939;LSEQ=CAGAGCATTTACTATGAAAA;RSEQ=GAGTGTAGTCGATCTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:180:88,92:92,89:181,180:0.4986:2,2:25:1:30.4:1:0.75254:1.08046:60:44:0.4958:0:1.2 1/0:421:215:97,118:99,104:203,215:0.5107:2,2:26.2:1:29.8:1:0.49281:1.1576:60:70.667:0.5072:0:1.2 +2 212698775 . T A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0616;LSEQ=TAATTTTATGTCTATGAAAC;RSEQ=GACAATATGTCATCCTTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:129:46,83:45,74:119,129:0.5202:2,2:25.8:1:31:1:0.79226:1.09683:60:42:0.5207:0:1.7 0/1:241:15:7,8:82,144:226,15:0.0622:2,2:20.6:1:29.1:1:0.42147:1.53:60:30:0.0622:0:1.3 +2 212698795 . G A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08374;SOR=Inf;LSEQ=TGACAATATGTCATCCTTCC;RSEQ=CAATTTGCTACCATGTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:54,135:189,0:0:2,0:24.2:1:30.9:1:1:0:59.8:30.5:1:0:1.6 0/1:148:3:3,0:43,102:145,3:0.0203:2,0:7:1:25.7:1:0.02867:0:60:6:0.0204:0:1.7 +2 212698806 . C G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATCCTTCCGCAATTTGCTA;RSEQ=CATGTCAGTTTGCTTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:166:166:39,127:0,0:0,166:1:0,2:23.1:1:32:1:1:0:59.8:32.2:1:0:1.6 1/1:122:104:26,78:4,14:18,104:0.8525:2,2:21.7:1:31.6:1:1:1.17:60:103:0.8512:0:1.3 +2 212811801 . G T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGCTTGGATATTACTAAGC;RSEQ=CTAATGATAGTTATCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:32:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212811923 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=CAGAGCATTTCCAGAGTTTA;RSEQ=TCCTGTTCAGCTGAGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:8,0:0:0,0:34.1:1:32.8:1:1:0:60:16:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:33.5:1:30.5:1:1:2.44949:60:4:0.3333:0:1.5 +2 212812057 . G A 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00015;SOR=0;LSEQ=TGATATTTAAATGCCTTAGA;RSEQ=TGTTCCTCAATGTAACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:17:17,0:117,1:118,17:0.1259:1,1:22.2:1:29.9:1:1:0:60:16:0.1203:0:1 0/0:88:0:0,0:84,4:88,0:0:1,0:25.2:1:32:1:1:0:60:176:1:0:0.4 +2 212812060 . T C 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTTAAATGCCTTAGAGTG;RSEQ=TCCTCAATGTAACAAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:141,1:142,0:0:1,0:24.9:1:30.7:1:1:0:60:284:1:0:0.1 0/1:93:17:15,2:73,2:75,17:0.1828:1,2:28.2:1:31.5:1:0.15417:4.74882:60:34:0.1848:0:1.9 +2 212812097 . T C 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TATGACAGTAACCCTACATA;RSEQ=ACAATTGCCTTATATTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:214,35:249,0:0:2,0:24.2:1:30.8:1:1:0:60:123.5:1:0:0.1 0/1:221:34:26,8:150,37:187,34:0.1538:2,2:24:1:31.4:1:0.64492:1.24611:60:68:0.156:0:1.5 +2 212989308 . T C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77978;SOR=0.83965;LSEQ=AGTCATTATGGCTTTGTTAC;RSEQ=CTTGTTCTTTTCCTGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:23,0:11,0:11,23:0.6765:0,1:21.5:1:30.3:1:1:0:60:22:0.6667:0:1 1/0:22:14:14,0:7,1:8,14:0.6364:2,1:21.8:1:30.6:1:0.36364:0:60:28:0.6667:0:1.1 +2 212989396 . G T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52418;LSEQ=CAGAAGAGCACCCCTTCCAG;RSEQ=TATCAGCACACAGGTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:165,15:180,2:0.011:2,2:31.5:1:28.5:1:0.16854:10.6831:60:4:0.0114:0:1 0/0:173:1:0,1:161,11:172,1:0.0058:2,0:1:0:24:0:0.06936:0:60:2:0.006:0:1 +2 212989410 . G C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=TTCCAGGTATCAGCACACAG;RSEQ=TCTGCCTGTATGCATCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:193,33:226,0:0:2,0:24.3:1:31.6:1:1:0:59.8:44.2:0.9955:0:0 0/1:251:14:12,2:197,39:236,14:0.0558:2,2:33.1:1:30.7:1:1:1.19:60:28:0.0569:0:1 +2 212989698 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23439;SOR=Inf;LSEQ=TGCGCAATGATAATATCTTT;RSEQ=TCAAAACTCTCTATTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:6,116:122,0:0:1,0:23:1:33.1:1:1:0:60:60:1:0:0.1 0/1:115:2:1,1:17,96:113,2:0.0174:2,2:28:1:29:0:0.2897:5.52:60:4:0.0175:0:1 +2 212989940 . AT A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTTACTTTTATTTAAAC;RSEQ=TTTTTTTTTTAGGACATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:30.5:1:29:1:1:0:55:4:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 212990868 . C T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTATTCCTATGTGAGCACA;RSEQ=AAGTTTACACAAGTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:26.5:1:1:0:60:4:1:0:2 +2 212990921 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTGGCTGGGCATGGTG;RSEQ=CTCACACCTGTTATCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:30:0:1:0:60:4:1:0:2 +2 213402641 . G C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGCGAGTTGCGTCTGAC;RSEQ=CCACAAGGCTCGGGCGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:33:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 213402705 . A G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACACAGGTGCAAAGCCCG;RSEQ=TTTTCTGAGCGCCGCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:31:1:1:0:60:4:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:32.5:1:1:0:57:4:1:0:1.5 +2 213402964 . A AC 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01457;SOR=0;LSEQ=AGGAGAGAAAAGAGGGACTC;RSEQ=GAGTGATTTTTCACGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:9,0:15,0:15,9:0.375:1,0:18.8:1:33.5:1:1:0:60:18:0.375:0.0833:0 0/0:13:0:0,0:11,2:13,0:0:2,0:24.8:1:30.5:1:1:0:60:26:1:0:0.1 +2 213403040 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51227;SOR=0;LSEQ=TGGAAAGAGGGGTGACCGAA;RSEQ=GCCCAGGGAAGAGGCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:101,2:103,2:0.019:1,2:25:1:28.5:1:0.05659:41.48291:60:4:0.0196:0:1 0/0:74:0:0,0:68,6:74,0:0:2,0:25.4:1:30.1:1:1:0:60:148:1:0:0.4 +2 213403091 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46393;SOR=0.8505;LSEQ=CCTCCACGCCTCCCGGGATG;RSEQ=GTGAAGAGGGCAGGGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:82:71,11:149,22:171,82:0.3241:2,2:24.2:1:30:1:1:1.04909:60:40:0.3252:0:1.2 0/1:183:53:47,6:109,20:129,53:0.2896:2,2:22.2:1:28.5:1:0.64146:1.43:60:106:0.2961:0:1 +2 213404504 . GC G 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCACCGCCCCGCCTCCC;RSEQ=CCCCAGTTATGCCATCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34:0:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 214575258 . G T 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63386;SOR=0.46614;LSEQ=ATTAGGATGGGAATCACATT;RSEQ=TATGGCTGTGTTGTAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:7,6:13,3:0.1875:2,0:21:1:31.3:1:0.25:0:60:6:0.1875:0:1 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:45:1:30:1:1:1.10554:60:4:0.0952:0:1 +2 215145376 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49643;SOR=Inf;LSEQ=GGTTTAGCTCTCAGTAGCCT;RSEQ=CCCCTGAGCTGTGAGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:34,18:52,0:0:2,0:22.4:1:32.5:1:1:0:58:104:1:0:0.2 0/1:57:2:1,1:37,18:55,2:0.0351:2,2:31:1:28:1:1:2.02764:60:4:0.0357:0:1 +2 215145663 . G T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=GCTGATAATGTGCTTCCAGT;RSEQ=TACTTCTGCATTAAATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:17:1:34:0:1:0:60:8:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:30.5:1:1:0:59.5:4:1:0:1 +2 215593233 . T C 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17553;SOR=2.98875;LSEQ=CAGCTTCTAAATGGTAAACA;RSEQ=AACATGAATTCCTAATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:13,0:10,0:10,13:0.5652:0,1:25.5:1:33.2:1:1:0:55.2:26:0.5652:0:1.6 1/1:15:12:11,1:3,0:3,12:0.8:0,2:22.1:1:30:1:1:0:60:5:0.7692:0:2 +2 215593261 . C CTT 88 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=17.000;MSILEN=1;SSF=0.53687;SOR=1.51809;LSEQ=ATTCCTAATCTGGCATTAGA;RSEQ=TTTTTTTTTTTTTTTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:6,0:8,0:8,6:0.2222:0,0:35.2:1:31.7:1:1:0:56.8:12:0.2308:0:1.3 0/1:23:7:7,0:9,1:10,7:0.3043:2,0:32.7:1:31.4:1:1:0:60:14:0.3043:0:2.1 +2 215593349 . G T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58654;SOR=0.39597;LSEQ=AAAAACAGTACAATGACTGG;RSEQ=CTCTCACAAACCGTGCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:166,30:196,2:0.0101:2,2:30.5:1:28.5:1:0.28929:5.45981:60:4:0.0105:0:1 0/0:249:1:1,0:178,70:248,1:0.004:2,0:5:0:28:0:1:0:60:2:0.0041:0:1 +2 215593851 . G C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31333;SOR=2.32624;LSEQ=CCTTACCTGAAACATTTGGA;RSEQ=GAGAAGCATTTCAGATTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:17:0,17:0,11:11,17:0.6071:0,1:28.2:1:31.1:1:1:0:60:34:0.6071:0:1.7 1/0:14:11:0,11:1,2:3,11:0.7857:2,0:21.5:1:29.8:1:0.21429:0:60:22:0.7857:0:1.6 +2 215593871 . T G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.63781;SOR=2.55248;LSEQ=GGAGAAGCATTTCAGATTCA;RSEQ=AAATTTTTTGGGTTTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:16:0,16:0,7:7,16:0.6957:0,1:19.6:1:32.6:1:1:0:60:32:0.6957:0:1.8 1/1:7:6:0,6:1,0:1,6:0.8571:0,0:14.3:1:31.8:1:0.14286:0:60:12:0.8571:0:2 +2 215595069 . T G 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTTGAAAGGGCAGAAGTTCT;RSEQ=CCTGATGGTGATAATAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:146,16:162,0:0:2,0:24.8:1:31.3:1:1:0:60:161:1:0:0.1 0/1:188:18:16,2:150,20:170,18:0.0957:2,2:27.9:1:32.7:1:1:1.07:60:36:0.0973:0:1 +2 215595203 . A G 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATACTTTTCTTCCTGTTCAC;RSEQ=TACTTTTCTTCGTAGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:793:0:0,0:364,429:793,0:0:2,0:25.3:1:30.6:1:1:0:60:71.091:1:0:0.1 0/1:851:20:9,11:369,462:831,20:0.0235:2,2:24.9:1:30.7:1:1:1.02:60:40:0.0238:0:1.3 +2 215595440 . T A 66 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61637;LSEQ=AAGAAAATATTTTAAAAAAC;RSEQ=CTTTCTTTGGAGGATTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:9,5:0.3571:0,0:32.8:1:28.6:1:1:0:60:10:0.3846:0:1 0/1:4:1:0,1:0,3:3,1:0.25:0,0:1:0:31:0:1:0:60:2:0.25:0:1 +2 215595445 . C A 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22794;SOR=Inf;LSEQ=AATATTTTAAAAAACTCTTT;RSEQ=TTTGGAGGATTAAGCCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:0,7:0,6:6,7:0.5:0,0:19.4:1:30:1:1:0:60:6:0.5455:0:1.3 1/1:3:3:0,3:0,0:0,3:1:0,0:21:1:30:1:1:0:60:6:1:0:1 +2 215595512 . C T 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATCTCCTTTCTGAAAAA;RSEQ=CTAAGCCAGGATACTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:21:1:31:1:1:0:60:6:0.375:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 215595645 . C T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTTACCATCTATACTGCT;RSEQ=ATTTTGACAGTTATATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:31:0:30:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:29:1:1:0:60:4:1:0:1 +2 215609570 . T C 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29187;SOR=3.2706;LSEQ=CTTCACCGTGTTAGCCAGGA;RSEQ=GATCTCGATCTCCTGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:14,0:14,2:0.125:1,0:45.5:1:32.5:1:1:0:43:4:0.1333:0:1 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:40:1:30.5:1:1:0:42:4:0.3333:0:1.5 +2 215609645 . A G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.83492;SOR=0.8417;LSEQ=GATTACAGGCTTGAGCCACC;RSEQ=CGCCCAGCCAGAAGCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:28:28,0:26,0:26,28:0.5185:1,1:18.6:1:28.3:1:1:0:53.4:6:0.48:0:1.2 0/1:40:19:19,0:21,0:21,19:0.475:1,1:22.2:1:30.1:1:1:0:56.2:38:0.475:0:1.1 +2 215609913 . G T 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09014;SOR=0;LSEQ=AAAAAAAGCAGTAAGAGAAA;RSEQ=AAAGATACAAGCCAAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:49,240:289,3:0.0103:2,2:19.3:1:21:1:0.43197:2.44:60:2:0.007:0:1.3 0/0:358:0:0,0:75,283:358,0:0:2,0:24.1:1:30.6:1:1:0:60:58.667:1:0:0.2 +2 215609960 . T C 112 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00098;SOR=14.25543;LSEQ=GGCCTGCTTCTTATAACTCA;RSEQ=CTATATTTTGTAAGCTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:1:0,1:5,116:121,1:0.0082:1,0:23:0:27:0:1:0:60:2:0.0083:0:1 0/1:113:12:0,12:2,99:101,12:0.1062:1,0:14.2:1:31.3:1:1:0:60:24:0.1081:0:1.9 +2 215610313 . G T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56607;SOR=0.79116;LSEQ=TACTGAAAAAAAATTTAGAT;RSEQ=TATTACAAGATGCAAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:38:38,0:30,0:30,38:0.5588:1,1:26.1:1:31.6:1:1:0:60:76:0.5588:0:1.1 1/0:44:22:21,1:22,0:22,22:0.5:1,1:21.6:1:30.6:1:1:0:60:44:0.5:0:1 +2 215610740 . A T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCCAGAACCTTTTAAATAA;RSEQ=TTTTTTCTCTTTATTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:34:0,34:0,0:0,34:0.9714:0,1:21.9:1:30.9:1:1:0:60:68:1:0:1.3 1/1:16:16:0,16:0,0:0,16:1:0,1:25.7:1:28.7:1:1:0:59.9:15:1:0:1.3 +2 215610777 . T C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.23779;LSEQ=TTCCCTCAAGAAAATGTCAA;RSEQ=TGTGATAGCTCTCTATACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:10,6:0.375:0,0:21:1:33.7:1:1:0:60:12:0.375:0:2.2 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:24.3:1:26.7:1:1:0:60:2:0.3333:0:1.7 +2 215617082 . T G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04229;SOR=Inf;LSEQ=TGTTTGGTGAATGTAAGCAA;RSEQ=TGGTCAAATGGAAATTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:91,6:97,0:0:2,0:24.9:1:31.2:1:1:0:60:47.5:1:0:0.2 0/1:82:4:3,1:77,1:78,4:0.0488:1,2:13:1:31.3:1:0.09575:22.37217:60:8:0.0488:0:1 +2 215617500 . T C 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.31595;LSEQ=TGTTTTTACTGAATATAGTA;RSEQ=TATGAATTTTTCACAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:23.8:1:34.8:1:1:0:60:8:0.4444:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:27.5:1:31:1:1:0:60:4:0.6667:0:1 +2 215631932 . T C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATATATGTAACACATTTT;RSEQ=TTTATCCGATCTGTCATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:21.7:1:32:1:1:0:50.7:6:0.5:0:1.7 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:32:0:1:0:60:2:1:0:0 +2 215631987 . A G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.28006;SOR=0.24597;LSEQ=TTTTGATCTGCAGTTGGCTG;RSEQ=ATCCTCAAGTGTAGAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:9,0:3,0:3,9:0.75:0,0:23.2:1:29.8:1:1:0:56.9:8:0.7273:0:2 0/1:5:2:2,0:3,0:3,2:0.4:0,0:18:1:31.5:1:1:0:60:4:0.4:0:2.5 +2 215632035 . A AAGAG 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.72102;SOR=1.53569;LSEQ=GAAGGACCAACTGTATCATA;RSEQ=AAAGGGCATGAAGGCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:9,0:14,0:14,9:0.3913:1,0:25.4:1:29.2:1:1:0:60:18:0.3913:0.1304:1.7 1/0:12:6:6,0:6,0:6,6:0.5:0,0:24.8:1:30.8:1:1:0:60:12:0.5:0.0833:1.5 +2 215632048 . G T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34703;SOR=1.969;LSEQ=TATCATAAAAAGGGCATGAA;RSEQ=GCTGATTATGAGTGCAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:10:10,0:20,0:20,10:0.3333:1,0:17:1:31.5:1:1:0:60:20:0.3333:0:1.5 1/0:16:8:8,0:8,0:8,8:0.5:0,0:22.4:1:30.4:1:1:0:60:16:0.5:0:1.4 +2 215632124 . ATT A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.31311;SOR=0.73358;LSEQ=AGAAAGCCATCAACTTGACT;RSEQ=TTAAAGTCTGCTTTATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:61:61,0:71,0:71,61:0.4656:1,1:28.4:1:32:1:1:0:60:122:0.4656:0.0687:1.6 0/1:77:30:28,2:41,2:43,30:0.3896:1,2:24.1:1:29.7:1:1:1.45645:60:60:0.3896:0.0519:1.6 +2 215632155 . T C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00179;SOR=0.51015;LSEQ=TGCTTTATCACACACCTTGA;RSEQ=TCAAGAATATAGGTCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:108:94,14:99,13:112,108:0.4909:2,2:23.8:1:32.3:1:0.83838:1.13356:60:107:0.4954:0:1.8 0/1:167:55:49,6:91,21:112,55:0.3293:2,2:22.3:1:31:1:0.26431:1.88:60:110:0.3354:0:1.9 +2 215632192 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.55521;LSEQ=ATTTTAAAAATAATTTTTAC;RSEQ=TTGAACTACTTACACAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:207:146,61:183,52:235,207:0.4673:2,2:23.8:1:30.6:1:0.08146:1.46904:60:206:0.4682:0:2.5 0/1:446:146:106,40:211,88:299,146:0.3274:2,2:21.2:1:29.5:1:0.73807:1.10:60:72:0.3265:0:2.5 +2 215632255 . CA TG 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0024;SOR=0.74864;LSEQ=TAACAGCTTGACTATATCCA;RSEQ=TGCCCATTCTTGGCTGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:856:366:210,156:269,213:482,366:0.4276:2,2:26.1:1:31.6:1:0.67503:1.07:60:732:0.4331:0.0129:1.4 0/1:1029:369:194,175:368,282:650,369:0.3586:2,2:25.7:1:30.4:1:0.21399:1.17696:59.9:738:0.3621:0.036:1.3 +2 215632256 . A G 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.6249;LSEQ=AACAGCTTGACTATATCCAC;RSEQ=TGCCCATTCTTGGCTGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:855:497:276,221:0,0:0,497:0.5813:0,2:26:1:30.6:1:1:0:60:54.222:0.998:0:1.1 0/1:999:464:261,203:113,88:201,464:0.4645:2,2:24.4:1:29.8:1:1:1.00:60:57:0.6962:0:1.2 +2 215632629 . G T 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTTGGGTCAAGCACTTTTCT;RSEQ=TTTTTTAGAAGAAAATGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:19.5:1:31:1:1:0:60:4:0.25:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:37:0:30:0:1:0:60:2:1:0:2 +2 215632659 . A T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AGAAAATGTAGTTTTAAACC;RSEQ=ACGGTAGCTCCTTAAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:36:1:28:1:1:0:60:6:0.5:0:1.7 1/0:2:1:0,1:0,1:1,1:0.5:0,0:7:0:29:0:1:0:60:2:0.5:0:2 +2 215632703 . G GA 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CAATAAATGTAACACATTAA;RSEQ=AAAAAAGTCTACATATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:28:1:31.3:1:1:0:49.8:8:0.6667:0:0.8 0/0:1:0:0,0:0,1:1,0:0:0,0:40:0:33:0:1:0:60:2:1:0:0 +2 215634055 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0401;SOR=0.75065;LSEQ=CCCTAGAAAAATGAACAAAA;RSEQ=GGAAATTAAAAAGCATTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:413:166:43,123:85,162:247,166:0.4019:2,2:22.7:1:30.6:1:0.08232:1.49939:60:82:0.399:0:1 0/1:522:175:58,117:132,211:343,175:0.3352:2,2:24.7:1:29.4:1:0.24838:1.26141:59.8:86.5:0.3353:0:1.2 +2 215634232 . A G 64 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAACACTTTGAGAGGCC;RSEQ=AGGTGGGTGGATCACCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:14.5:1:32:1:1:0:48:8:1:0:1.8 1/1:2:2:0,2:0,0:0,2:1:0,0:17:0:32.5:1:1:0:44:4:1:0:2 +2 215634236 . T C 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACTTTGAGAGGCCAAGG;RSEQ=GGGTGGATCACCTGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21.5:1:32:0:1:0:38:4:1:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:13:0:28:1:1:0:44:4:1:0:2 +2 215645046 . C T 68 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTTGGCAAAATAAAAGC;RSEQ=GAAATATTCAAATATTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:25.5:1:34:0:1:0:60:8:0.4444:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 215645135 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72808;SOR=1.48429;LSEQ=GAAGTAGAGATGCTCTCCCT;RSEQ=TGAATCTGGCTTCTCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:15,0:10,0:10,15:0.6:0,1:27.1:1:31.9:1:1:0:59:14:0.6087:0:1.1 1/0:13:9:9,0:4,0:4,9:0.6923:0,0:29.6:1:32.9:1:1:0:60:18:0.6923:0:1 +2 215645464 . C G 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.48809;LSEQ=TCGGACATGTTACTGTTTTT;RSEQ=CTCCCTGATGTACCACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1114:611:287,324:248,253:501,611:0.5485:2,2:25.8:1:32.2:1:0.43301:1.10651:59.9:100.833:0.5505:0:1.1 1/0:1199:772:373,399:219,203:422,772:0.6439:2,2:24.8:1:31.5:1:0.2502:1.15388:59.9:192:0.6454:0:1.1 +2 215645545 . C G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30852;LSEQ=GGTATATTTTCTGAGGGCAC;RSEQ=GTTTGCTTAACAAAATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:284:122,162:161,198:359,284:0.441:2,2:24.3:1:30.4:1:0.68923:1.0796:60:55.8:0.4408:0:1.1 0/1:772:151:61,90:289,328:617,151:0.1956:2,2:25.9:1:29.7:1:0.17168:1.29953:60:150:0.1966:0:1.1 +2 215646015 . C T 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04036;SOR=7.33659;LSEQ=TCTTGCAGAAGCCTTTTTAG;RSEQ=CCTCTCAGAAACATCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:662:1:0,1:301,360:661,1:0.0015:2,0:1:0:24:0:1:0:60:2:0.0015:0:1 0/1:728:8:4,4:320,400:720,8:0.011:2,2:30.1:1:28.3:1:1:1.25:60:16:0.0111:0:1.3 +2 215656874 . T TA 75 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=0.28071;SOR=2.4842;LSEQ=AGAGAGACTCAATGGCTATT;RSEQ=AAAAAAAAAAAAAAAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:4,0:20,0:20,4:0.1538:1,0:11.5:1:29.1:1:1:0:51.3:8:0.16:0.0769:0.3 0/1:19:6:5,1:9,0:9,6:0.3158:0,2:21.7:1:29.2:1:0.4:0:55.8:12:0.3158:0.1579:2.5 +2 215656919 . G T 39 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14753;SOR=5.19052;LSEQ=GATTTTAAAATCTGAAATAC;RSEQ=TATTCCAGAACTCCAGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:1,0:89,0:89,1:0.0109:1,0:1:0:31:0:1:0:60:2:0.013:0:2 0/1:55:3:3,0:49,3:52,3:0.0545:2,0:34.7:1:24.7:1:1:0:46:2:0.0426:0:5 +2 215656968 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20682;SOR=Inf;LSEQ=TATACTTTATGAATATGAAT;RSEQ=CATCAGTTTTTAACTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:190,30:220,0:0:2,0:24.2:1:30.4:1:1:0:60:30.429:1:0:0.1 0/1:184:2:1,1:152,30:182,2:0.0109:2,2:26.5:1:27:1:0.30934:5.00079:60:4:0.0112:0:1 +2 215657182 . TA T 186 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.1188;SOR=0.7359;LSEQ=CACAATTACTTTAAAATAAT;RSEQ=AAAAAAAAAAAAAAAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:73:13,60:55,81:136,73:0.3216:2,2:27:1:29.8:1:0.00105:3.11763:58.6:72:0.3258:0.022:0.9 0/1:294:76:11,65:83,108:191,76:0.2585:2,2:29.4:1:29.8:1:0:4.51796:59:75:0.2595:0.017:0.9 +2 215657560 . C T 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACACTGGGAAAGACCTT;RSEQ=TGTTTTGTTTTGGGACTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:40:0:31:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 215661918 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23719;SOR=Inf;LSEQ=CACCCAATATTTCATCCAAG;RSEQ=CCCAACACTACCATATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:15,153:168,0:0:2,0:22.6:1:32.5:1:1:0:60:55:1:0:0.1 0/1:160:2:0,2:18,140:158,2:0.0125:2,0:27.5:1:27:1:1:0:60:4:0.0129:0:1.5 +2 215673937 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11422;SOR=0.25166;LSEQ=GATTCAGGGCAAGGGGAGGC;RSEQ=GGTAAGTCGCCCAAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:14,0:5,0:5,14:0.7368:0,1:18.5:1:32.2:1:1:0:60:28:0.7368:0:1.1 0/1:10:4:4,0:5,1:6,4:0.4:2,0:28.8:1:31.3:1:1:0:60:8:0.4:0:1 +2 215674052 . C A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49889;SOR=0;LSEQ=GCGGGAACGGAAGGAGGAAA;RSEQ=GGAAGATTTGAAAAGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:138,17:155,2:0.0127:2,2:7.5:1:30:1:0.21681:7.91716:60:4:0.0128:0:2.5 0/0:147:0:0,0:125,22:147,0:0:2,0:23.1:1:30.5:1:1:0:60:23.5:1:0:0.7 +2 215674090 . T G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00045;SOR=1.81294;LSEQ=TCTGCCGCCCCCAGAAACTG;RSEQ=GCGACCCGTGCCCTCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:289:157:122,35:100,32:132,157:0.5433:2,2:26.6:1:31.4:1:0.77981:1.12:59.9:51.333:0.548:0:1.1 1/0:319:218:149,69:74,26:100,218:0.6834:2,2:22.8:1:29.8:1:0.35624:1.31689:59.9:23.222:0.6808:0:1.2 +2 215674224 . G A 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00047;SOR=0.689;LSEQ=ACCATCCGGTTCCATGGCGG;RSEQ=CGCGGAACGAGGCTCGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:712:335:145,190:166,210:376,335:0.4705:2,2:27:1:30.2:1:0.82075:1.03576:60:110.667:0.477:0:1.1 0/1:748:284:114,170:216,247:463,284:0.3797:2,2:24.3:1:28.5:1:0.09493:1.3036:59.8:39.571:0.3815:0:1.2 +2 215674275 . G A 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21902;SOR=4.68813;LSEQ=CCTCGGCTGCCGGTTCCTCG;RSEQ=CTGCCGATTATCCGGCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:1:1,0:152,294:446,1:0.0022:2,0:31:0:32:0:0.34228:0:60:2:0.0023:0:3 0/1:480:5:4,1:186,289:475,5:0.0104:2,2:9.4:1:25.4:1:0.08277:6.19:60:10:0.0106:0:2 +2 215674323 . C G 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00799;SOR=1.70523;LSEQ=TTCGGATGAAAGGCTCCTCG;RSEQ=AGAGCGGGAAGCAAGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:127:25,102:14,82:96,127:0.567:2,2:24.8:1:32.1:1:0.37537:1.43:60:126:0.5701:0:2.1 1/0:220:152:52,100:15,52:67,152:0.6909:2,2:24.4:1:30.4:1:0.11098:1.80:60:151:0.6927:0:2.1 +2 215674341 . A G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05135;SOR=1.60512;LSEQ=CGCAGAGCGGGAAGCAAGGA;RSEQ=GCCTCGGGAAACCACAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:161:90:12,78:9,61:70,90:0.559:2,2:25.1:1:31.9:1:1:1.04:60:89:0.5669:0:2.6 1/0:161:108:31,77:6,47:53,108:0.6708:2,2:23.1:1:30.2:1:0.01627:3.13:60:107:0.6815:0:2.6 +2 215674353 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49813;SOR=Inf;LSEQ=AGCAAGGAAGCCTCGGGAAA;RSEQ=CACAGGGAAGCTGCAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:15,113:128,0:0:2,0:24.2:1:31.7:1:1:0:60:63:1:0:1.6 0/1:131:2:1,1:25,104:129,2:0.0153:2,2:8:0:31.5:1:0.35878:4.10:60:4:0.0153:0:3.5 +2 215674371 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.64026;SOR=1.17136;LSEQ=AACCACAGGGAAGCTGCAGG;RSEQ=CAGCGACTCGAAACCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:91:57:3,54:2,32:34,57:0.6264:2,2:21.7:1:30.9:1:1:1.12352:60:114:0.6264:0:2.9 1/0:86:57:6,51:4,25:29,57:0.6628:2,2:23.8:1:28.7:1:0.72717:1.35491:60:114:0.6706:0:3 +2 215674436 . C T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGCCGCCAGAGGGGCGGGG;RSEQ=GCGCGGGGAGGGGCGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:0,31:0,0:0,31:1:0,1:25.8:1:30.7:1:1:0:60:62:1:0:1.5 1/1:21:21:1,20:0,0:0,21:1:0,1:19:1:29.7:1:1:0:60:42:1:0:1.8 +2 215674466 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGCGGGGCACGGCGGCCG;RSEQ=AATGCTCCCAAAATAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:0,19:19,2:0.0952:1,2:13.5:1:29.5:1:0.09524:0:60:4:0.1:0:1 0/0:7:0:0,0:0,7:7,0:0:0,0:26.7:1:33.1:1:1:0:60:14:1:0:1 +2 216768578 . A G 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02777;SOR=Inf;LSEQ=AGAGTCTGAAAACTTCCAAC;RSEQ=TCCCACTGGCCCAGAGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:16.7:1:30:1:1:0:60:6:0.3333:0:1 1/1:6:6:6,0:0,0:0,6:1:0,0:24:1:29.5:1:1:0:60:12:1:0:1 +2 216768702 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50132;SOR=0;LSEQ=TCACTCTGTGATTTTAGGTT;RSEQ=CTGTGTTTATTAGCGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:116,14:130,2:0.0152:2,2:31:1:30.5:1:0.21513:8.03872:60:4:0.0153:0:1 0/0:112:0:0,0:91,20:111,0:0:2,0:23.1:1:31.7:1:1:0:60:222:0.9911:0:0.1 +2 216768707 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.50066;SOR=0;LSEQ=CTGTGATTTTAGGTTGCTGT;RSEQ=TTTATTAGCGACTTGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:121,20:141,2:0.014:2,2:5:1:29.5:1:0.27302:5.92857:60:4:0.0141:0:1 0/0:124:0:0,0:100,24:124,0:0:2,0:23.1:1:31:1:1:0:60:30:1:0:0.1 +2 216768797 . G T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06218;SOR=Inf;LSEQ=GCAGCTAATTAGGGAGCAGG;RSEQ=TGTCAAACTCAAGTAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:243,171:414,0:0:2,0:25.4:1:31.6:1:1:0:59.9:40.4:1:0:0.4 0/1:436:5:1,4:240,189:429,5:0.0115:2,2:14.2:1:26.2:1:0.17642:5.06287:60:10:0.0115:0:1 +2 216768824 . G T 52 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06212;SOR=Inf;LSEQ=ACTCAAGTAAACAAGACAGG;RSEQ=ATGCTTTTATCCTTGTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:245,217:462,0:0:2,0:23.7:1:31.4:1:1:0:59.9:65:1:0:0.5 0/1:482:5:1,4:247,229:476,5:0.0104:2,2:21.6:1:22.8:1:0.20304:4.30249:60:4:0.0085:0:1.8 +2 216768839 . G T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00041;SOR=0.62718;LSEQ=ACAGGGATGCTTTTATCCTT;RSEQ=TATGATCCTTGGCCAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:226:110,116:128,127:255,226:0.4689:2,2:24.9:1:30.3:1:0.78416:1.0627:60:55.5:0.4693:0:1.1 0/1:480:171:91,80:153,156:309,171:0.3563:2,2:25.4:1:29.2:1:0.44726:1.16:60:84.5:0.3558:0:1.1 +2 216768907 . A G 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=4e-04;SOR=Inf;LSEQ=TATGGTAAATCTGTGCCTAA;RSEQ=GGGGAATCACTACAAATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:107,229:336,0:0:2,0:24.2:1:31.1:1:1:0:60:32.6:1:0:0.3 0/1:329:11:4,7:118,200:318,11:0.0334:2,2:23.1:1:31.5:1:1:1.0324:60:22:0.0338:0:1 +2 216826471 . G C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=0.06091;LSEQ=CTCCTCCTTTTTGACCCAGA;RSEQ=CTATCTACTTGCCCTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:80:77,3:1,0:1,80:0.9877:0,1:25.6:1:32.8:1:1:0:59.6:79:0.9875:0:1.1 1/1:99:82:70,12:14,3:17,82:0.8283:2,2:22.3:1:30.8:1:0.71825:1.25:60:26.333:0.8229:0:1.1 +2 216826486 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17684;SOR=0;LSEQ=CCAGAGCTATCTACTTGCCC;RSEQ=TTCACTGAATCCCAGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:94,9:103,2:0.019:2,2:10.5:1:31.5:1:0.18223:9.96106:60:4:0.0194:0:2 0/0:144:0:0,0:102,42:144,0:0:2,0:23.4:1:29.9:1:1:0:60:143:1:0:0.8 +2 216826579 . T G 256 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00749;LSEQ=TCCCATCACCAGGCCCTAAG;RSEQ=TCCCACCCCAGATGCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:300:299:146,153:0,1:1,299:0.9967:0,2:26.9:1:31.2:1:1:0:60:22:0.9965:0:1.5 1/0:407:281:129,152:64,62:126,281:0.6904:2,2:26.5:1:30.7:1:0.3911:1.21571:60:69.25:0.6908:0:1.5 +2 216826606 . A G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.68451;SOR=0.92753;LSEQ=CCCAGATGCTCTGATACTTA;RSEQ=AAGATTAATAAAGTGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:124:52,72:75,89:164,124:0.4291:2,2:25.5:1:31.9:1:0.55034:1.16618:60:19.667:0.4275:0:2 0/1:336:138:65,73:83,115:198,138:0.4107:2,2:23.3:1:30.6:1:0.37255:1.23:60:68:0.4096:0:1.9 +2 216826660 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35724;SOR=3.23186;LSEQ=TCTCTATATACCATGCGGAG;RSEQ=CTCAAACCCCAAATCACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:66,122:188,1:0.0053:2,0:24:0:12:0:1:0:60:0:0:0:1 0/1:177:3:1,2:60,114:174,3:0.0169:2,2:22:1:28.3:1:1:1.05233:55.7:6:0.0172:0:1.3 +2 216826690 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5054;SOR=0;LSEQ=CAAATCACACCTTGGAGTTA;RSEQ=TGCTTAGAGCACCTTAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:33,98:131,2:0.015:2,2:19.5:1:29.5:1:0.44737:2.94:60:4:0.015:0:1 0/0:104:0:0,0:33,71:104,0:0:2,0:21.7:1:31.4:1:1:0:59.8:51:1:0:0.4 +2 216826707 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51959;SOR=0;LSEQ=TTACTGCTTAGAGCACCTTA;RSEQ=ACAGGCACATCCATAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:22,76:98,2:0.02:2,2:12.5:1:27.5:1:0.40889:3.40:60:4:0.0204:0:1 0/0:65:0:0,0:13,52:65,0:0:2,0:21.5:1:31:1:1:0:60:130:1:0:0.1 +2 216827773 . G C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTAGGAGGATTGCTTGAG;RSEQ=CTGGGAGGTCAAGGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:29:1:1:0:43:4:1:0:1 +2 217736023 . A G 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGTAAAGAGAGATCACAC;RSEQ=AACCCTGGACCTACCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:144,25:169,0:0:2,0:22.1:1:30.8:1:1:0:59.8:168:1:0:0.1 0/1:142:32:29,3:95,15:110,32:0.2254:2,2:24.4:1:29.1:1:0.76365:1.52:60:31:0.2214:0:1.1 +2 217736131 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26742;SOR=1.17215;LSEQ=GGTCCCTATATGAAAAACAC;RSEQ=TGGGTTCTTGGAGTGTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:124:63,61:215,229:444,124:0.2179:2,2:26.5:1:30.4:1:0.68478:1.10:60:61:0.2186:0:1.1 0/1:597:147:68,79:217,232:449,147:0.2462:2,2:25.2:1:29.7:1:0.70392:1.08649:60:294:0.2475:0:1.1 +2 219219875 . G A 57 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGAAGTTTGTAGTAGAT;RSEQ=GCGGTAGAAGAAATAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:21.3:1:28.8:1:1:0:30.5:8:1:0:1.5 1/1:4:4:3,1:0,0:0,4:1:0,2:26.3:1:28.5:1:1:0:31.3:8:1:0:1 +2 220431802 . G A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.0076;SOR=Inf;LSEQ=AAGACGGCATCTTCCCCGTC;RSEQ=TATACCTGCACATCCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:56,0:56,0:0:1,0:21:1:29.6:1:1:0:60:27:1:0:0.1 0/1:25:4:4,0:21,0:21,4:0.16:1,0:18.3:1:31:1:1:0:60:8:0.16:0:1.3 +2 220431919 . A G 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50676;SOR=Inf;LSEQ=GCAGAGGCTGGCGGATGGCA;RSEQ=GCCTGTGAGAGGACCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:491:489:416,73:0,0:0,489:0.9959:0,2:23.5:1:32.8:1:1:0:60:60.125:1:0:1.2 1/1:385:385:309,76:0,0:0,385:1:0,2:22.4:1:31.1:1:1:0:60:76:1:0:1.2 +2 220431921 . C T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09538;SOR=6.19517;LSEQ=AGAGGCTGGCGGATGGCAAG;RSEQ=CTGTGAGAGGACCAGCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:1:1,0:417,82:499,1:0.002:2,0:31:0:27:0:1:0:60:2:0.002:0:2 0/1:407:5:2,3:311,91:402,5:0.0123:2,2:11:1:26.6:1:0.0832:5.09971:60:10:0.0127:0:1.8 +2 220432014 . G A 301 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32206;LSEQ=CCAAGGTGAGCAGAACCGTG;RSEQ=AACACCACGTGGGGACTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1546:927:466,461:296,321:617,927:0.5996:2,2:25.6:1:30.6:1:0.3777:1.10:60:76.25:0.6036:0:1.2 0/1:1617:526:268,258:551,538:1089,526:0.3253:2,2:26:1:29.4:1:0.91545:1.01:59.9:130.5:0.3263:0:1.2 +2 220432709 . A T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGAGATGCGGACAGGA;RSEQ=TCCATCAACCTGGAATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:25.5:1:32:0:0.33333:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 220435034 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGATCCTTGGCCTGGCAGTA;RSEQ=AGCACCTTGAGCACGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:28.5:1:1:0:60:4:1:0:1 +2 220436108 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15158;SOR=Inf;LSEQ=GCCTCCCGCTCCCGGCTCGC;RSEQ=TCCTTACCCTCGGCCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:184,5:189,0:0:1,0:22.2:1:31.8:1:1:0:60:46.25:1:0:0.1 0/1:121:2:1,1:111,8:119,2:0.0165:2,2:31.5:1:29:1:0.1438:13.14031:60:4:0.0167:0:1 +2 220436138 . TGCG T 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.81544;SOR=1.18807;LSEQ=TCGGCCCCGAGCTGCAGCTC;RSEQ=GCGGCGGCGGCGGCGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:10:10,0:314,59:373,10:0.026:2,0:30.5:1:33.1:1:0.3719:0:60:20:0.0265:0:0.1 0/1:293:9:6,3:214,69:283,9:0.0307:2,2:22.6:1:30:1:0.69408:1.54816:60:18:0.0313:0.0034:0.3 +2 220436696 . T TGAGA 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTCTGTGTGTGTGTGTG;RSEQ=GAGAGAGTGTGTGTGTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,1:1,2:0.3333:0,2:22:1:29.1:1:1:0:60:4:0.3333:0.1667:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 220436754 . TGTGA T 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=11.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGTGTGTGTGAGTGTGTG;RSEQ=GTGTGTGTGTGTGTAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0,3:0.75:0,2:30:1:34.7:1:1:0:54.7:6:1:0:0.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 220436973 . A G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01575;SOR=0.58594;LSEQ=AAAGGACTGGGGAAGACTGG;RSEQ=TGAGAAGGGTAGAAGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:149:146,3:95,2:97,149:0.6008:1,1:22.9:1:31.9:1:1:1.02:60:298:0.6107:0:1.1 0/1:126:59:58,1:63,4:67,59:0.4683:2,1:19.4:1:31.3:1:0.37007:3.65:60:118:0.4876:0:1.1 +2 220437081 . C T 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTGTGAGTTCCCCACTAG;RSEQ=AGGGCCAGGTGAGCTATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1233:0:0,0:685,548:1233,0:0:2,0:26.7:1:32.1:1:1:0:60:52.609:1:0:0.1 0/1:1171:115:62,53:596,459:1055,115:0.0982:2,2:23.5:1:27.5:1:0.62136:1.10989:60:37.333:0.097:0:1.2 +2 220437864 . T C 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTGTTCCACTGACTGAA;RSEQ=GGATAAGCCCTCCTGTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:19.3:1:29.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 220439102 . G T 66 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTGAAGTCTAATACAAA;RSEQ=TCTTAGTGCTGGTGAAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:29.5:1:33:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 220439206 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGCAATGTCTTCTATTTT;RSEQ=TTAAGTCCCTTCATGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:14,0:14,2:0.125:1,2:29:0:32.5:1:0.125:0:60:4:0.125:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:32:0:1:0:32:2:1:0:0 +2 220439330 . G A 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=CCATCATTGGCTCATGACTG;RSEQ=TGGCCACATCCCTCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:100,6:106,0:0:2,0:24.6:1:31.2:1:1:0:60:34.333:1:0:0.1 0/1:52:6:5,1:44,2:46,6:0.1154:1,2:15.5:1:29.7:1:0.31312:4.20593:60:12:0.1154:0:1 +2 220439350 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51449;SOR=0;LSEQ=GTGGCCACATCCCTCCTGCT;RSEQ=AAGAGGAGGGGTGCCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:127,20:147,2:0.0133:2,2:43.5:1:30:1:0.26283:6.22133:60:4:0.0136:0:1 0/0:104:0:0,0:90,14:104,0:0:2,0:19.4:1:31.3:1:1:0:60:51:1:0:0.1 +2 220439364 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18436;SOR=Inf;LSEQ=CCTGCTGAAGAGGAGGGGTG;RSEQ=CAGGTCCTGCCAGTCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:170,34:204,0:0:2,0:22.2:1:32:1:1:0:60:67:1:0:0.1 0/1:154:2:1,1:128,24:152,2:0.013:2,2:10.5:1:27:1:0.29921:5.24607:60:4:0.0132:0:1 +2 220439678 . C T 241 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=79.01553;LSEQ=CATGCTCCCCCTCACTGGGC;RSEQ=GTGCTGCACCTGGCCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1555:4:0,4:806,745:1551,4:0.0026:2,0:1:0:27.8:1:0.0536:0:57.5:8:0.0026:0:1.3 0/1:1546:262:140,122:663,619:1282,262:0.1695:2,2:23.3:1:30:1:0.63509:1.07:59.6:261:0.1709:0:1.2 +2 220439679 . G A 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=66.11669;LSEQ=ATGCTCCCCCTCACTGGGCC;RSEQ=TGCTGCACCTGGCCACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1562:1:1,0:815,743:1558,1:6e-04:2,0:1:0:25:0:1:0:60:2:7e-04:0:1 0/1:1549:63:32,31:778,707:1485,63:0.0407:2,2:23.5:1:29.9:1:0.89766:1.06596:59.9:126:0.041:0:1.1 +2 220439916 . G A 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGGCCTCCGGAGGAACCG;RSEQ=CTGCCCATGCCAACTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1441:0:0,0:735,705:1440,0:0:2,0:25:1:31.5:1:1:0:60:39:0.9993:0:0.1 0/1:1515:34:18,16:742,736:1478,34:0.0224:2,2:19:1:28.4:1:0.86268:1.12:60:68:0.0229:0:1.1 +2 220440431 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACACAGTGCATATGACT;RSEQ=GACATATGTTCTCCAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:2,72:74,2:0.0263:1,2:29.5:1:31.5:1:0.07789:29.59:60:4:0.0278:0:1 0/0:19:0:0,0:0,19:19,0:0:1,0:16.4:1:30.5:1:1:0:60:38:1:0:0.3 +2 220441405 . A C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04136;SOR=Inf;LSEQ=TCCACCCCAGGGTCCCTGCT;RSEQ=TCAGCCACTGGTTCCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:33,1:34,0:0:1,0:23.8:1:28.7:1:1:0:56.8:68:1:0:0.4 0/1:19:3:3,0:15,1:16,3:0.1579:1,0:29:1:31.3:1:1:0:57.3:6:0.1765:0:1.3 +2 220441436 . C CGTGT 123 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=17.000;MSILEN=2;SSF=0.04259;SOR=0.21205;LSEQ=GTTCCATCCAGTCTCCAACA;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:16:16,0:18,0:18,16:0.3137:1,1:31.8:1:30.8:1:1:0:57.9:32:0.3137:0.0196:0.3 0/1:23:2:2,0:7,0:7,2:0.087:0,0:46:1:29.5:1:1:0:56:4:0.087:0:0.5 +2 220441467 . TTG T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.83925;LSEQ=GTGTGTGTGTGTGTGTGTGT;RSEQ=TGTGTGTGTGTTTAGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:2,0:107,2:109,2:0.018:1,0:40:1:29:0:1:0:60:4:0.0189:0:0 0/1:66:1:1,0:64,1:65,1:0.0152:1,0:21:0:32:0:1:0:60:2:0.0154:0:0 +2 220441802 . G A 39 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06933;SOR=Inf;LSEQ=TACACGCCCCAGTCTCTGTT;RSEQ=ACACTGAGTCCCCCAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:35,368:403,0:0:2,0:24.6:1:32:1:1:0:60:49.375:1:0:0.1 0/1:282:3:2,1:19,260:279,3:0.0106:2,2:6:1:24.7:1:0.01518:26.50:60:2:0.0072:0:1 +2 222085393 . C T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.64168;LSEQ=CAGGCGTGAGCCACCGCGCC;RSEQ=GGCCCACTTTTTTCTATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:22.2:1:30.3:1:1:0:54.3:5:0.7143:0:1 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:24.4:1:30.4:1:1:0:50.6:10:0.5556:0:1.2 +2 222085613 . G T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.27504;LSEQ=GGAAAGCATGTCAGCTATGG;RSEQ=CTCTTCTCCTTAAGCCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:62:30,32:122,139:261,62:0.192:2,2:25.3:1:29.4:1:0.88767:1.07:60:61:0.1918:0:1 0/1:363:159:82,77:89,113:202,159:0.438:2,2:24.6:1:28.3:1:0.1684:1.35:59.8:158:0.4401:0:1.1 +2 222085727 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51753;SOR=Inf;LSEQ=GTCTGGTGAGCTGCACAGTG;RSEQ=CTAAGTTTCAGGACCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:9,56:65,0:0:2,0:21.3:1:32.3:1:1:0:60:130:1:0:0.2 0/1:98:2:1,1:18,78:96,2:0.0204:2,2:5.5:1:27:1:0.35178:4.24:60:4:0.0204:0:1.5 +2 222085787 . C T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75983;SOR=1.38865;LSEQ=AATCATGAGCTGTGCATCAA;RSEQ=CTGCTTTGATCTCAGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:0,6:0,22:22,6:0.2143:1,0:20.3:1:31.5:1:1:0:60:12:0.2143:0:1 0/1:29:8:1,7:0,21:21,8:0.2759:1,2:25.8:1:30.1:1:0.27586:0:60:16:0.2759:0:1.1 +2 222202431 . AAGAAAGAAAG A 29 d5;v3;pSTD;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=17.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AAAGAAAGAAAGAAAGAAAG;RSEQ=AGAAAGAAAGAAAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:50:0:29.5:1:1:0:24:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 222202862 . C T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00148;SOR=1.51855;LSEQ=TTTGAAAAACATCTGTGTGT;RSEQ=CCTGGTAAAAATTAGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:185:87,98:141,157:298,185:0.3822:2,2:25.4:1:30.3:1:1:1.01162:60:36:0.3789:0:1.1 0/1:485:235:105,130:120,130:250,235:0.4845:2,2:22.7:1:29.1:1:0.46788:1.14254:59.8:470:0.4906:0:1.1 +2 222202971 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11974;SOR=Inf;LSEQ=ACATAACTATGTTTTCGGTT;RSEQ=CAAGCACAACCACCCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:17,103:120,0:0:2,0:22.5:1:32.1:1:1:0:60:29:1:0:0.1 0/1:64:2:1,1:7,55:62,2:0.0313:2,2:9:1:26.5:1:0.23611:7.42:60:4:0.0323:0:1 +2 222298873 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16435;SOR=Inf;LSEQ=GAGACTTACATCTTGATTGG;RSEQ=CATATCCCAATAGGGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:88,33:121,0:0:2,0:21.3:1:29.5:1:1:0:60:29.25:1:0:0.2 0/1:83:2:1,1:63,18:81,2:0.0241:2,2:12.5:1:26:1:0.40758:3.43346:60:4:0.0247:0:1 +2 222298879 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18313;SOR=Inf;LSEQ=TACATCTTGATTGGACATAT;RSEQ=CCAATAGGGCCTCTCCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:89,40:129,0:0:2,0:23:1:31.6:1:1:0:60:63.5:1:0:0.2 0/1:97:2:1,1:68,27:95,2:0.0206:2,2:17.5:1:25:1:0.49613:2.49126:60:4:0.0208:0:1 +2 222298962 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49856;SOR=0;LSEQ=CACTTGCTGATGTGAATTTA;RSEQ=GATAGGCAATTGCTTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:58,97:155,2:0.0127:2,2:25:1:30:1:1:1.67:60:4:0.0129:0:1 0/0:151:0:0,0:58,91:149,0:0:2,0:25.8:1:30.2:1:1:0:59.5:148:0.9867:0:0.2 +2 222298986 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23895;SOR=0;LSEQ=AGGCAATTGCTTCTGGCGCA;RSEQ=TCCACCGGATAGGAATCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:25,72:97,2:0.0202:2,2:13:1:32.5:1:0.45826:2.84:60:4:0.0206:0:1 0/0:103:0:0,0:30,73:103,0:0:2,0:23.4:1:30.7:1:1:0:60:33.333:1:0:0.1 +2 222301212 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48148;SOR=Inf;LSEQ=AAGTTGCTGTTCACCAGGAT;RSEQ=TTCCGTGCGGCCAGATCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:13,0:0:2,0:16.1:1:30.7:1:1:0:60:26:1:0:0.1 0/1:14:2:1,1:3,9:12,2:0.1429:2,2:23:1:27.5:1:0.50549:2.74:60:4:0.1429:0:1 +2 222301357 . T C 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAAGGAGTGAGGAACAATC;RSEQ=CATTAGCATTAGGCCAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24:1:33:0:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:8:0:32:0:1:0:60:2:1:0:1 +2 222307534 . G T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.45612;SOR=1.5117;LSEQ=CTAGCTTGGCTTTGTAAAGG;RSEQ=GGTGACCCACGTACATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:9:8,1:35,6:41,9:0.18:2,2:26.8:1:30.7:1:1:1.36:56.2:18:0.1837:0:1.1 0/1:44:11:11,0:24,9:33,11:0.25:2,0:27.7:1:29.4:1:0.08488:0:60:22:0.2558:0:1.1 +2 222307572 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=TAGTGACCACGCCTTCCAAG;RSEQ=GAATGATGTTCGGATGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:71,38:109,0:0:2,0:23.7:1:29.8:1:1:0:59.7:218:1:0:0.2 0/1:116:2:1,1:61,53:114,2:0.0172:2,2:38.5:1:31:0:1:1.14954:60:4:0.0174:0:1.5 +2 222307614 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24493;SOR=0;LSEQ=ACTGTCCCATGATGCTGGCC;RSEQ=CACTCAGGAAGTCTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:56,64:120,2:0.0164:2,2:33:1:29:1:1:1.14:60:4:0.0165:0:1 0/0:124:0:0,0:56,68:124,0:0:2,0:29.1:1:29.2:1:1:0:60:123:1:0:0.2 +2 222428870 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49256;SOR=0;LSEQ=ACTGGTTCTCTCTGATGAAA;RSEQ=GCTCTTTGTCGTTGTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:11,20:31,2:0.0606:2,2:21:1:30.5:1:1:1.78:60:4:0.0625:0:1 0/0:31:0:0,0:10,21:31,0:0:2,0:23:1:29.8:1:1:0:60:62:1:0:0 +2 223360792 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTGTCACATAGTGCCCC;RSEQ=ACTCCCTTCGTGCAAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:14:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 223360949 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22236;SOR=0.2985;LSEQ=GTCTGTTAACACACGACAAC;RSEQ=TGAAACACAGATGTAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:18,0:2,0:2,18:0.9:0,1:25.1:1:29.9:1:1:0:60:36:0.9:0:1.8 1/0:18:13:13,0:5,0:5,13:0.7222:0,1:23.4:1:29.2:1:1:0:60:26:0.7222:0:1.8 +2 223361000 . T A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ATGAGGTCTTCACTTCTCAG;RSEQ=TTGAGACGCTTTCCAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:64,1:0,0:0,65:1:0,1:27.3:1:30.4:1:1:0:60:31.5:1:0:1.3 1/1:40:38:35,3:2,0:2,38:0.95:0,2:26.1:1:28.1:1:1:0:60:37:0.9487:0:1.4 +2 223361050 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49839;SOR=Inf;LSEQ=GTCTTATTCTCCAGGGAGCC;RSEQ=GGGTTGTTGCATTTATTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:115,30:145,0:0:2,0:24.2:1:30:1:1:0:60:23.167:1:0:0.4 0/1:149:2:1,1:102,44:146,2:0.0134:2,2:22:1:29:1:0.5171:2.30352:60:4:0.0136:0:1.5 +2 223361058 . TG T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24904;SOR=Inf;LSEQ=CTCCAGGGAGCCAGGGTTGT;RSEQ=CATTTATTCATTTAATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:132,46:178,0:0:2,0:22.5:1:31.9:1:1:0:60:34.6:1:0:0.4 0/1:192:3:1,2:123,66:189,3:0.0156:2,2:6.3:1:25.9:1:0.2864:3.70034:60:6:0.0159:0.0104:1 +2 223361065 . A T 34 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24961;SOR=Inf;LSEQ=GAGCCAGGGTTGTTGCATTT;RSEQ=TTCATTTAATAAAGACTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:136,60:196,0:0:2,0:22.2:1:29.1:1:1:0:60:97:1:0:0.4 0/1:215:3:1,2:132,80:212,3:0.014:2,2:7:1:21.7:1:0.55931:3.28116:60:2:0.0096:0:1.3 +2 223361153 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06901;SOR=1.31001;LSEQ=TTCCCTCCATTCAGGCCTGC;RSEQ=TCATCTTTATTTTGCACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:165:78,87:113,123:236,165:0.4115:2,2:26.4:1:30.6:1:0.91938:1.02465:60:54:0.4112:0:1.4 0/1:366:175:82,93:93,97:190,175:0.4781:2,2:25.4:1:29.2:1:0.75318:1.08713:60:57.333:0.4738:0:1.4 +2 223361209 . G T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0015;SOR=0.41393;LSEQ=CATCAGTCTCCCTCGAGCTA;RSEQ=TCTTATACCTTCAAATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:216:192:53,139:10,12:22,192:0.8889:2,2:24.1:1:30.4:1:0.08935:2.17667:60:191:0.8884:0:1.4 1/0:198:152:48,104:18,28:46,152:0.7677:2,2:25:1:29.9:1:0.37429:1.39052:60:151:0.7704:0:1.5 +2 224504471 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14634;SOR=Inf;LSEQ=TGAAAGCATCAACTTATTTC;RSEQ=TAAGTCACAATAAGAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,8:24,0:0:2,0:23.2:1:32.5:1:1:0:59.8:48:0.96:0:0.1 0/1:16:2:1,1:11,3:14,2:0.125:2,2:30.5:1:28.5:1:0.45:3.31654:60:4:0.1333:0:1 +2 224504527 . CA C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.12707;LSEQ=ACAAAAAAAATCAACCCCCC;RSEQ=AAAAAAACTCAACTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:31:19,12:1,1:2,31:0.9394:2,2:32.5:1:32.2:1:1:1.56:59.8:62:0.9394:0:0.2 1/1:37:35:17,18:2,0:2,35:0.9459:0,2:28:1:30.7:1:0.48649:0:60:34:0.9444:0.0811:0.4 +2 225069340 . C A 125 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCAAAGGATTTTTCAGTT;RSEQ=CATTTTTCTTATAGGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:19:8,11:97,102:199,19:0.0872:2,2:23.3:1:29.5:1:0.63691:1.306:58.2:38:0.0884:0:1.1 0/0:224:0:0,0:116,108:224,0:0:2,0:26.7:1:30.4:1:1:0:60:55:1:0:0.4 +2 225069368 . T C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1451;SOR=0.74219;LSEQ=CTTATAGGAAAAGTTTTATA;RSEQ=CTAAGGTAATACAATCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:97:45,52:49,63:112,97:0.4641:2,2:24.2:1:31.5:1:0.7806:1.11:60:194:0.4732:0:1.1 0/1:225:88:41,47:64,73:137,88:0.3911:2,2:23.1:1:30:1:1:1.00499:60:28.333:0.3864:0:1.1 +2 225338880 . C T 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49856;SOR=Inf;LSEQ=TTAATAGAAGAGATGGTCGT;RSEQ=TTAATATTTAATGATTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:153,15:168,0:0:2,0:22.2:1:32.2:1:1:0:59.9:55:1:0:0.1 0/1:171:2:1,1:145,24:169,2:0.0117:2,2:8.5:1:22:1:0.27176:5.94001:60:4:0.0117:0:3 +2 225339145 . C A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6201;SOR=2.04974;LSEQ=AAACACATAAAAATTCGTAT;RSEQ=TTTGAACAGAACTGATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:24,168:192,1:0.0052:2,0:10:0:32:0:1:0:60:2:0.0052:0:3 0/1:189:2:0,2:23,164:187,2:0.0106:2,0:30:1:29.5:1:1:0:60:4:0.0106:0:1.5 +2 225339154 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49835;SOR=0;LSEQ=AAAATTCGTATCTTTGAACA;RSEQ=AACTGATATGTCATTTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:0,2:6,144:150,2:0.0132:1,0:26:1:27.5:1:1:0:60:4:0.0133:0:1 0/0:152:0:0,0:9,143:152,0:0:2,0:23.1:1:30.5:1:1:0:60:37:1:0:0.1 +2 225342597 . A T 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATGAAAGCATTTAATGA;RSEQ=TGGTAACCATTATTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:10.5:1:31.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 225343208 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09107;SOR=Inf;LSEQ=TTAATTCAAGTACGCATTCA;RSEQ=AAACTGTCTTAATGTTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:1,43:44,0:0:1,0:21.4:1:32.4:1:1:0:60:88:1:0:0 0/1:37:3:0,3:0,34:34,3:0.0811:1,0:8.7:1:30.7:1:1:0:60:6:0.0811:0:1 +2 225346548 . A AT 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0654;SOR=Inf;LSEQ=AAAGAAATCCAATAGATGAG;RSEQ=TTTTTTTTCTAAAGAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:146,24:170,0:0:2,0:23.4:1:29.9:1:1:0:59.9:23.286:1:0:0.1 0/1:203:5:4,1:170,27:197,5:0.0246:2,2:15.2:1:29.4:1:0.52959:1.56996:60:10:0.0253:0.0049:0.2 +2 225346646 . T C 196 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGTAGTTTGGATGTGAA;RSEQ=TGATCATTAACTGTAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:746:0:0,0:425,320:745,0:0:2,0:27.4:1:31:1:1:0:60:92.125:0.9986:0:0.1 0/1:863:76:38,38:418,369:787,76:0.0881:2,2:28.7:1:31.4:1:0.63159:1.13263:60:75:0.0875:0:1.1 +2 225362392 . C T 23 v3;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.58702;LSEQ=ACAGAAGTAAGTAATTTACC;RSEQ=AGGTCAACATAAATCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:97,26:123,2:0.016:2,2:9:1:23:1:0.38671:3.68014:60:4:0.0163:0:1 0/0:106:1:0,1:84,21:105,1:0.0094:2,0:1:0:21:0:0.20755:0:60:2:0.0094:0:1 +2 225362478 . C T 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.38455;LSEQ=ATCAATATTTACCTTTTTAA;RSEQ=TGGTCCATAAAATGTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:1:1,0:249,167:416,1:0.0024:2,0:23:0:33:0:1:0:60:2:0.0024:0:1 0/1:485:43:28,15:258,183:441,43:0.0887:2,2:24.3:1:29.7:1:0.42212:1.32:60:42:0.0884:0:1.1 +2 225362644 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49751;SOR=Inf;LSEQ=CAAACTACAGGATAACATCC;RSEQ=TTAAACATTTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:4,86:90,0:0:1,0:23.1:1:33:1:1:0:60:89:1:0:0.1 0/1:94:2:1,1:5,87:92,2:0.0213:2,2:25.5:1:31.5:1:0.12423:15.98:60:4:0.0225:0:1 +2 225365056 . A G 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACACTTACTTGTACACAGTG;RSEQ=TACAAAGTCTGATTTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:281,111:392,0:0:2,0:25.2:1:30.2:1:1:0:59.9:48:1:0:0.1 0/1:488:31:23,8:322,134:456,31:0.0635:2,2:25.5:1:30.9:1:0.83859:1.20:60:62:0.064:0:1 +2 225367669 . C T 173 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.10051;LSEQ=AATATCTAAGTAGAAATTAA;RSEQ=GCAGAATCTTACACCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:614:2:0,2:380,232:612,2:0.0033:2,0:1:0:26:1:0.14486:0:60:4:0.0033:0:1 0/1:712:58:34,24:380,274:654,58:0.0815:2,2:24:1:29.6:1:1:1.02:60:116:0.0822:0:1.1 +2 225368321 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.14469;LSEQ=CGTTGTCAGTACACAATCAT;RSEQ=ATAAACCTCAGTTAGGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:74:50,24:154,54:208,74:0.2624:2,2:22:1:32.4:1:0.29286:1.36735:59.8:148:0.2624:0:1.1 0/1:381:165:108,57:141,75:216,165:0.4331:2,2:24.5:1:31:1:1:1.01:60:164:0.4362:0:1.1 +2 225368622 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23048;SOR=Inf;LSEQ=TCATTTACAGCTTAAAAACA;RSEQ=TATTGTTTGAAAACATAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:5,119:124,0:0:1,0:24.5:1:33.7:1:1:0:60:248:1:0:0 0/1:115:2:1,1:7,105:112,2:0.0174:2,2:29:1:28:1:0.136:14.10:60:4:0.0175:0:1 +2 225370554 . C A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.92538;LSEQ=TTTTTAATAGACCATGGCAC;RSEQ=CATTTAAGCACAGCAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:16:16,0:33,0:33,16:0.3265:1,1:21.1:1:31.1:1:1:0:60:32:0.3265:0:1.1 0/1:42:13:13,0:29,0:29,13:0.3095:1,1:28.3:1:30.2:1:1:0:60:26:0.3095:0:1 +2 225371505 . AAAGTGGCCTTTTT A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.22178;SOR=Inf;LSEQ=ACACAATACACAGCATGGTA;RSEQ=AGCACTTGTCAAAATGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:195,28:223,0:0:2,0:26.5:1:30.1:1:1:0:60:43.6:1:0:0.1 0/1:199:2:2,0:153,44:197,2:0.0101:2,0:9.5:1:30:1:1:0:60:4:0.0103:0.0101:0 +2 225371801 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50591;SOR=0;LSEQ=TGTTCACGCTATAATACTGA;RSEQ=AGAAGCTTATTTCTCCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:0,2:7,155:162,2:0.0122:1,0:29:1:30:0:1:0:60:4:0.0123:0:1.5 0/0:128:0:0,0:6,122:128,0:0:1,0:22.5:1:30.9:1:1:0:60:127:1:0:0.1 +2 225376032 . G C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36795;LSEQ=TTAAAAATATCGATAAGGCA;RSEQ=AGTAAGGATTTAATTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:167:122,45:135,54:189,167:0.4691:2,2:23.4:1:32.1:1:0.81274:1.08:60:40.75:0.4644:0:1.1 0/1:408:100:71,29:197,110:307,100:0.2451:2,2:23.8:1:31.4:1:0.22662:1.37:60:99:0.2463:0:1.1 +2 225376034 . G A 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAATATCGATAAGGCAGA;RSEQ=TAAGGATTTAATTATTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:267,105:372,0:0:2,0:23.2:1:33:1:1:0:60:744:1:0:0.5 0/1:430:34:24,10:258,137:395,34:0.0791:2,2:23.4:1:29.2:1:0.57832:1.27:60:68:0.0798:0:1 +2 225378177 . TA T 24 v3;p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49865;SOR=0;LSEQ=GGTCAAAATAGTTAAATTAG;RSEQ=ACTATATTAAATAACATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:160,18:178,2:0.0111:2,2:5:1:24.5:1:0.2005:8.68078:60:4:0.0112:0.0056:0.5 0/0:176:0:0,0:157,18:175,0:0:2,0:21.8:1:27.7:1:1:0:60:42.75:0.9942:0:0.1 +2 225378382 . ATAAT A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32655;LSEQ=AAAAAAGTTATTATCACTTG;RSEQ=TAAATTACATTTAAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:163:41,122:35,138:173,163:0.4851:2,2:27.3:1:31.1:1:0.29879:1.32:60:162:0.485:0.0446:0.1 0/1:417:98:31,67:91,228:319,98:0.235:2,2:28.6:1:30:1:0.61179:1.16:60:196:0.2356:0.0288:0.1 +2 225379531 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24882;SOR=Inf;LSEQ=TATGAGTACAGTTCTTGTGA;RSEQ=CATAATAATTATTGTGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:42,159:201,0:0:2,0:23:1:32.3:1:1:0:60:66:0.995:0:0 0/1:214:3:1,2:48,163:211,3:0.014:2,2:27:1:23:1:0.54356:1.69:60:2:0.0095:0:2.3 +2 225400176 . C T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21758;SOR=0;LSEQ=GGATTACAGGCGTGAGCCAC;RSEQ=GTGCCCAGCCTTCAACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:2,0:129,19:148,2:0.0133:2,0:33.5:1:34:0:1:0:52.5:4:0.0134:0:1 0/0:171:0:0,0:125,46:171,0:0:2,0:21.6:1:29.8:1:1:0:58.4:170:1:0:0.1 +2 225400185 . CCTTCAA C 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0.00094;SOR=Inf;LSEQ=GCGTGAGCCACCGTGCCCAG;RSEQ=CTTCAAATGCTTAACTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:161,30:191,0:0:2,0:20.4:1:31.7:1:1:0:58.2:94.5:1:0:0.1 0/1:209:11:7,4:143,55:198,11:0.0526:2,2:25:1:31.7:1:0.50897:1.4827:58.7:22:0.0529:0:0 +2 225422080 . GA G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGATTAAATCATTTTAAG;RSEQ=AAAAAATTCCTTGTAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:47:1:29:1:1:0:60:4:0.3333:0:0.5 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:30:0:1:0:60:2:1:0:1 +2 225422239 . AT A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03068;SOR=2.63168;LSEQ=TAAATTTTTCATGAGTGCTT;RSEQ=TAACAGTCACGAATTAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:15:15,0:42,0:42,15:0.2632:1,1:31.5:1:30.5:1:1:0:60:14:0.2593:0:0.5 0/1:39:19:19,0:20,0:20,19:0.4872:1,1:18.7:1:30.6:1:1:0:60:38:0.4872:0.1795:0.3 +2 225422300 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=CCTTTAAAAAGAACACTTCC;RSEQ=GTCAAAGTGCAATATGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:169,19:188,2:0.0105:2,2:36:1:30.5:1:0.19994:8.69703:60:4:0.0106:0:1 0/0:176:0:0,0:156,20:176,0:0:2,0:22.8:1:29.1:1:1:0:60:43:1:0:0.1 +2 225422594 . AAG A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=1.86195;LSEQ=CTGTAATATCCAAGAGAGAG;RSEQ=AGACAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:32,132:164,1:0.006:2,0:29:0:25:0:1:0:55:2:0.0063:0:5 0/1:180:2:0,2:61,117:178,2:0.0111:2,0:36.5:1:27:0:0.54941:0:60:4:0.0115:0:2 +2 225422598 . GAC G 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24957;SOR=Inf;LSEQ=AATATCCAAGAGAGAGAAGA;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:26,95:121,0:0:2,0:12.3:1:28.6:1:1:0:58.6:12.444:1:0:1 0/1:140:3:0,3:52,80:132,3:0.0214:2,0:39.7:1:24.7:1:0.28425:0:60:2:0.0159:0:0.3 +2 225423683 . G C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGGAGGCTGTGGCAGGA;RSEQ=AATGGTGTGAGCCCGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:30:1:1:0:22.5:4:1:0:1 +2 225434256 . C G 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72582;SOR=1.48338;LSEQ=CAGGATTACAATTTTCCCAT;RSEQ=AGAAAAGTATCAATAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:6,0:15,0:15,6:0.2857:1,0:17:1:33.5:1:1:0:60:12:0.2857:0:1 0/1:16:6:6,0:10,0:10,6:0.375:0,0:20.2:1:32.2:1:1:0:60:12:0.375:0:1 +2 225434445 . A G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-04;SOR=1.81519;LSEQ=ATTACTGAGAGAACTACATC;RSEQ=TGAGACAAATTAAAACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:91:41,50:135,144:279,91:0.2459:2,2:27:1:30.7:1:0.62943:1.14288:60:44.5:0.2438:0:1.1 0/1:465:173:91,82:136,155:291,173:0.372:2,2:28.1:1:30.3:1:0.24931:1.26:60:346:0.3745:0:1.1 +2 225434527 . G T 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=CAAGAAGTCTTTAGTCCTCT;RSEQ=TGAATAATTTTCTACAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:36,114:150,0:0:2,0:22.6:1:32.1:1:1:0:60:49:1:0:0.2 0/1:176:14:4,10:38,123:161,14:0.0795:2,2:23:1:29.6:1:0.74509:1.29:60:28:0.0795:0:1 +2 226701156 . C G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACATCCTTCAATCCAAT;RSEQ=AAGTTGGCACTCAATATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:28:1:33:1:1:0:52.5:4:0.4:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:32:0:1:0:60:2:1:0:0 +2 226701301 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2236;SOR=0;LSEQ=TTTCATTTCCAATAAGAAGA;RSEQ=ATTACACCTCCAAGAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:75,15:90,2:0.0217:2,2:37:1:31.5:1:0.31916:4.87349:60:4:0.0217:0:1 0/0:102:0:0,0:79,23:102,0:0:2,0:23.1:1:29.6:1:1:0:60:101:1:0:0.1 +2 226701342 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22782;SOR=0;LSEQ=CATGGTCTGTTCAATCAGTG;RSEQ=TCTGTAATTATATAAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:106,66:172,2:0.0115:2,2:23.5:1:31:1:1:1.60147:60:4:0.0116:0:1.5 0/0:190:0:0,0:128,62:190,0:0:2,0:26:1:28.8:1:1:0:60:37:1:0:0.2 +2 226701408 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02561;SOR=0.61518;LSEQ=TGGTTCTTTTTAATAGAAAC;RSEQ=TATATTCAGCAATGTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:63:28,35:82,90:172,63:0.2681:2,2:21.4:1:30.6:1:0.76806:1.13826:60:126:0.2681:0:1.1 0/1:283:52:23,29:116,115:231,52:0.1837:2,2:29.4:1:29.4:1:0.44754:1.27075:60:51:0.1815:0:1.2 +2 226701471 . T A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50518;SOR=Inf;LSEQ=TATCTCTTCTAAAATGACAC;RSEQ=TCTGTGTAAAAACTTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:42,99:141,0:0:2,0:25:1:30.6:1:1:0:60:69.5:1:0:0.2 0/1:178:2:1,1:61,115:176,2:0.0112:2,2:5:1:27.5:1:1:1.88:60:4:0.0115:0:1 +2 226701521 . C CA 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.40468;SOR=3.19705;LSEQ=TAAAACAAAAAGTCATTTCA;RSEQ=AAAAAAAAACTGTAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:0,1:1,39:40,1:0.0244:1,0:36:0:33:0:1:0:60:2:0.025:0:0 0/1:67:5:1,4:7,53:60,5:0.0746:2,2:23.8:1:28.8:1:0.49308:1.87:60:10:0.0781:0.0149:0.2 +2 226701540 . A C 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.00756;SOR=0;LSEQ=ACAAAAAAAAACTGTAAAAC;RSEQ=AAAAGGTCATTATGTCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:6:0,6:0,26:26,6:0.1875:1,0:30:1:34:0:1:0:60:12:0.1875:0:1 0/0:37:0:0,0:0,37:37,0:0:1,0:25.2:1:31.2:1:1:0:60:74:1:0:0.1 +2 227597887 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49816;SOR=0;LSEQ=CAGGGCTTCAGTATTGTAAA;RSEQ=TACTGTTTCTTACCATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:128,0:128,2:0.0154:1,2:10.5:1:31.5:1:0.01538:0:60:4:0.0156:0:1 0/0:126:0:0,0:124,2:126,0:0:1,0:23.6:1:29.4:1:1:0:60:41:1:0:0 +2 227598134 . G T 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03074;SOR=Inf;LSEQ=CATTATTGACTCAGGTGGTT;RSEQ=ATCATTAATGGATTCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:140,314:454,0:0:2,0:24.3:1:32:1:1:0:59.9:74.667:0.9956:0:0.1 0/1:455:5:2,3:163,286:449,5:0.011:2,2:39.6:1:28.6:1:1:1.17:60:10:0.0111:0:1.2 +2 227651909 . C CT 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.5159;SOR=0;LSEQ=AAGATCCAAAGCAAAGATAT;RSEQ=TTTTTTCCTGCTTTTTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:128,7:135,2:0.0145:2,2:28.5:1:28:1:0.11378:17.17024:60:4:0.0148:0:0 0/0:94:0:0,0:90,4:94,0:0:1,0:23.3:1:31.2:1:1:0:60:188:1:0:0.1 +2 227651920 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51567;SOR=0;LSEQ=CAAAGATATCTTTTTTCCTG;RSEQ=TTTTTGTCAATATTATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:2,0:160,10:170,2:0.0116:2,0:41.5:1:32:0:1:0:60:4:0.0119:0:1 0/0:118:0:0,0:109,9:118,0:0:2,0:23.2:1:31.4:1:1:0:60:58:1:0:0.1 +2 227660306 . G A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0469;SOR=Inf;LSEQ=AGTGGGCAGCCAGCTCTGCT;RSEQ=CCCCTTGAGGCCCAGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:145,237:382,0:0:2,0:23.6:1:32:1:1:0:59.9:62.667:1:0:0.2 0/1:334:4:3,1:128,202:330,4:0.012:2,2:18.3:1:24:1:0.30383:4.71:60:8:0.0122:0:1 +2 227660544 . C T 148 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=42.03453;LSEQ=CCTGCAAATGCTAGCAGCCC;RSEQ=GGGAGGTGCAGGGCCCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:0,1:215,146:361,1:0.0028:2,0:1:0:27:0:0.40608:0:60:2:0.0028:0:1 0/1:335:35:19,16:162,138:300,35:0.1045:2,2:22.2:1:29:1:1:1.01:60:16.5:0.1:0:1.1 +2 227660807 . GGCT G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.54476;SOR=0.72355;LSEQ=GCTCTGGAGGGTGCAGCAAG;RSEQ=GCTGCTGCTGCTGCTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:602:15:7,8:306,281:587,15:0.0249:2,2:33:1:32.5:1:0.79552:1.24408:60:30:0.0255:0.0017:0.1 0/1:551:10:3,7:268,272:540,10:0.0181:2,2:32.4:1:31.4:1:0.33976:2.29587:60:20:0.0186:0:0.1 +2 227661395 . TTGC T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.25269;SOR=1.37573;LSEQ=TGGTCCCGGAAGGGACGGCG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:845:30:19,11:372,441:813,30:0.0355:2,2:27.5:1:31.1:1:0.06386:2.05:60:60:0.0361:0.0047:0.1 0/1:726:35:15,20:299,388:687,35:0.0482:2,2:27.7:1:29.9:1:1:1.02746:59.1:70:0.0487:0.0069:0.4 +2 227661663 . G GC 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.05026;SOR=0.36871;LSEQ=GGAGCTGTCTGGGCGGTGGT;RSEQ=CCCCCCCCGACGCTCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:16:8,8:278,279:557,16:0.0278:2,2:15.4:1:31.3:1:1:1.00:60:32:0.0284:0.0069:0.1 0/1:576:6:3,3:265,303:568,6:0.0104:2,2:27:1:29.6:1:1:1.14:60:12:0.0106:0.0017:0 +2 227662753 . C T 175 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCACCTGCATCCAGAACTC;RSEQ=CCGGGCCCCGTCACGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:851:0:0,0:374,477:851,0:0:2,0:25.8:1:30.8:1:1:0:60:29.393:1:0:0.2 0/1:927:63:27,36:388,473:861,63:0.068:2,2:24.9:1:29.3:1:0.79366:1.09359:60:62:0.0683:0:1.1 +2 227663428 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4995;SOR=0;LSEQ=ACCTTGCGCACGTCCGAGAA;RSEQ=CCATCGCTCTCCGGAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:61,113:174,2:0.0113:2,2:42:1:30:1:1:1.85:60:4:0.0116:0:1 0/0:162:0:0,0:68,94:162,0:0:2,0:24.2:1:31.3:1:1:0:59.8:80:1:0:0.2 +2 227663433 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22068;SOR=Inf;LSEQ=GCGCACGTCCGAGAAGCCAT;RSEQ=GCTCTCCGGAGGGCTCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:57,114:171,0:0:2,0:22.7:1:30.2:1:1:0:60:56:1:0:0.2 0/1:152:2:1,1:61,89:150,2:0.0132:2,2:27:1:27.5:1:1:1.46:60:4:0.0133:0:1 +2 227663446 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49821;SOR=0;LSEQ=AAGCCATCGCTCTCCGGAGG;RSEQ=CTCGCCATGCTGCCACCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:46,91:137,2:0.0144:2,2:35:1:30:1:1:1.97:60:4:0.0146:0:1 0/0:137:0:0,0:56,81:137,0:0:2,0:25.7:1:30.9:1:1:0:59.7:44.667:1:0:0.2 +2 227664109 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23469;SOR=Inf;LSEQ=GCTGCTGCTGCTGCTGCTGC;RSEQ=GCCGCCCGCGGGCGCGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:25,0:0:2,0:27.2:1:27.2:1:1:0:60:5.25:1:0:0.2 0/1:24:2:1,1:7,15:22,2:0.0833:2,2:29.5:1:31:1:1:2.07:54:4:0.0833:0:1.5 +2 227665416 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18794;SOR=Inf;LSEQ=CTGTTAGGGACCTTCAGAGG;RSEQ=TTCATAAGGCCAAAACCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:214,31:245,0:0:2,0:22.5:1:31.7:1:1:0:59.9:121.5:1:0:0.1 0/1:188:2:1,1:161,25:186,2:0.0106:2,2:20.5:1:27.5:1:0.25811:6.33453:60:4:0.0108:0:1 +2 227665694 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21603;SOR=Inf;LSEQ=CCCAGAGTTTTTTTATTTTT;RSEQ=AAGCCGACCTATAAACAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:11,160:171,0:0:2,0:20.4:1:28.6:1:1:0:60:56:1:0:0.1 0/1:149:2:1,1:10,137:147,2:0.0134:2,2:10.5:1:27:1:0.14266:13.11:60:4:0.0134:0:1 +2 227665698 . C A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50476;SOR=0;LSEQ=GAGTTTTTTTATTTTTTAAG;RSEQ=CGACCTATAAACAAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:7,147:154,2:0.0128:1,2:9:1:26:1:0.10025:19.71:60:4:0.0131:0:1 0/0:124:0:0,0:5,119:124,0:0:1,0:23.8:1:31:1:1:0:60:248:1:0:0.1 +2 230579184 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50026;SOR=Inf;LSEQ=CGGAGCCAGGACGCAGTGAC;RSEQ=GCGGCGGCGGTGGCAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:27,0:0:2,0:26:1:30:1:1:0:60:26:1:0:0.3 0/1:35:2:1,1:19,14:33,2:0.0571:2,2:40.5:1:28.5:1:1:1.34517:60:4:0.0588:0:1 +2 232422661 . T C 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0.20187;LSEQ=GGCAGGCCCAAGAACACGCA;RSEQ=GCCTAGGAAGTCTCCAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:20.8:1:30.3:1:1:0:60:5:0.7143:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:37:0:28:0:1:0:60:2:0.3333:0:1 +2 232422782 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=TGGGTTCCTGTCCCAAGTCT;RSEQ=CCCCCTGATGGTAAGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:9,19:28,0:0:2,0:21:1:32.1:1:1:0:60:56:1:0:0.1 0/1:28:3:2,1:12,13:25,3:0.1071:2,2:25:1:27:1:1:2.11:60:6:0.1111:0:1.3 +2 232422824 . A AATCAGTGGAGAGGTAATAC 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.78393;LSEQ=CTTCTTCAGCCAAATTTCAT;RSEQ=ATTTACCTCCTGGGGTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:2,7:2,6:8,9:0.5294:2,2:24.1:1:31.9:1:1:1.15611:60:18:0.5294:0.2353:0.2 0/1:15:7:2,5:3,5:8,7:0.4667:2,2:13.7:1:28.8:1:1:1.46001:60:14:0.4667:0.4667:0.4 +2 232424786 . T C 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25314;SOR=Inf;LSEQ=ATGCCCCACAAGTGTCACCA;RSEQ=GGCAAAACTGGAAGAGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:111,103:214,0:0:2,0:28.6:1:30.7:1:1:0:47.4:52.5:1:0:0.1 0/1:251:3:2,1:134,114:248,3:0.012:2,2:36.7:1:23:1:1:1.70:53.7:2:0.0081:0:1.3 +2 232424847 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=TTGGCATTGTAAACAAACAA;RSEQ=TTCAGGGCAACATTCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:44,89:133,0:0:2,0:19.7:1:32.1:1:1:0:52.3:132:0.9925:0:0.1 0/1:147:2:1,1:53,91:144,2:0.0136:2,2:19:1:27.5:1:1:1.71:49.5:4:0.0138:0:1 +2 233708806 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.00102;SOR=0.18989;LSEQ=GCTCTTCAGCAGCAGCAGCA;RSEQ=CAGCAACAGCAGAAACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:24:14,10:7,8:15,24:0.6154:2,2:26.3:1:31.5:1:0.52538:1.58:59.1:11:0.5946:0:1.2 0/1:35:8:4,4:15,12:27,8:0.2286:2,2:27.6:1:30.9:1:1:1.242:60:16:0.2353:0:1.1 +2 233708909 . AAGC A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.51475;SOR=Inf;LSEQ=AAGAGGCCAGGCAAATGCAA;RSEQ=AGCAGCAGCAGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:24,0:0:2,0:29.9:1:31.8:1:1:0:60:48:1:0:0.1 0/1:37:2:1,1:14,21:35,2:0.0541:2,2:22.5:1:29.5:1:1:1.48:60:4:0.0541:0:0.5 +2 233790649 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24242;SOR=Inf;LSEQ=AACAAAATTCCGGAGTCAGC;RSEQ=CGGCTTAACAGCATGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:20,0:0:2,0:29.8:1:31.8:1:1:0:60:40:1:0:0.1 0/1:25:3:2,1:11,11:22,3:0.12:2,2:11.7:1:29.3:1:1:1.95:60:6:0.12:0:1.3 +2 233791390 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGGCTTCCAGGTCTTCC;RSEQ=TGATGGGGGATAGTGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 237242082 . T C 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01283;SOR=0.10489;LSEQ=CCACATCTTCACTTGAGATC;RSEQ=GGTGTGTCTTCCGTCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:6,1:2,1:3,7:0.6364:2,2:15.9:1:29.1:1:1:2.65:60:14:0.6364:0:2.1 0/1:21:3:2,1:9,4:13,3:0.1429:2,2:39.3:1:30.7:1:1:1.11662:60:6:0.15:0:2 +2 237242097 . C T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04074;SOR=0.19619;LSEQ=AGATCTGGTGTGTCTTCCGT;RSEQ=CAAATTTATAACATCTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:7,3:2,1:3,10:0.7692:2,2:22:1:30.8:1:1:1.15:60:20:0.7692:0:1.8 0/1:26:10:7,3:10,6:16,10:0.3846:2,2:28:1:29.5:1:1:1.38:60:20:0.3846:0:1.9 +2 237242244 . T C 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GGGTTTCATGCTTGCGGACT;RSEQ=GGTTCTGGGCACGCATGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:21.7:1:29.5:1:1:0:60:12:1:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:38:1:31:0:1:0:60:4:1:0:0 +2 237971395 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49485;SOR=0;LSEQ=TTGAAGGAATCTCAGGATTT;RSEQ=CAACCTGCTGGAAGGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:39,8:47,2:0.0408:2,2:21.5:1:28:1:0.33673:4.65478:60:4:0.0408:0:1 0/0:48:0:0,0:37,11:48,0:0:2,0:23.4:1:31.2:1:1:0:60:47:1:0:0.1 +2 237971465 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50951;SOR=Inf;LSEQ=CCACGCAATGACAGCATGGC;RSEQ=CACGCTGACCCCGGCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:59,63:122,0:0:2,0:26:1:30.1:1:1:0:60:39.667:1:0:0.2 0/1:165:2:1,1:84,79:163,2:0.0121:2,2:27:1:32:1:1:1.06293:60:4:0.0123:0:1 +2 238791396 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCAAGTAACTAGTGGAGG;RSEQ=GAAGAGGGCCCTGGAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:29:1:1:0:60:4:1:0:1.5 +2 238792003 . A G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32518;LSEQ=AGGCGGCCGGCCAGCCTTTT;RSEQ=TGGGATACACACACAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:86:48,38:43,49:92,86:0.4831:2,2:25.8:1:32.2:1:0.23451:1.44:60:172:0.4831:0:1.1 0/1:215:50:25,25:80,84:164,50:0.2326:2,2:27.5:1:31.6:1:1:1.05:60:49:0.229:0:1.3 +2 238792133 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05771;SOR=0.38042;LSEQ=CCGTGATCCCTGCTTTACTC;RSEQ=GGACGTTGAATAGAAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:20:3,17:2,13:15,20:0.5714:2,2:20.7:1:31.7:1:1:1.14:60:40:0.5882:0:1 0/1:36:12:2,10:6,18:24,12:0.3333:2,2:19.1:1:31:1:0.69099:1.64434:60:24:0.3333:0:1.3 +2 239542321 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52797;SOR=0;LSEQ=CCTTGTCAGTCAGTTCAGCG;RSEQ=GTCGCCTTCCTTGTCAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:7,3:0.3:2,0:16.3:1:32:0:1:0:60:6:0.3333:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:10.7:1:31:0:1:0:60:6:1:0:0 +2 239999464 . T C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49053;SOR=1.83912;LSEQ=AAACAGCAGACATCAGGCGC;RSEQ=GCGACTCCTAAAACACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:3,3:5,4:9,6:0.4:2,2:24.8:1:30.7:1:1:1.23147:60:12:0.4:0:1 1/0:18:10:5,5:4,3:7,10:0.5556:2,2:29:1:29.4:1:1:1.31092:60:20:0.5882:0:1 +2 240678139 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.49913;SOR=Inf;LSEQ=CTGAGCATGGCTCTGTTAGC;RSEQ=TCCTTCGCAGGAGACACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:97,47:144,0:0:2,0:24.8:1:32.1:1:1:0:59.8:288:1:0:1 0/1:156:2:1,1:95,59:154,2:0.0128:2,2:36:0:31.5:1:1:1.60502:60:4:0.0132:0:1.5 +2 240678158 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.98644;LSEQ=CCTCCTTCGCAGGAGACACA;RSEQ=GGCCGTGGGAAGGAAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:119,76:195,1:0.0051:2,0:3:0:14:0:0.39286:0:60:0:0:0:3 0/1:198:2:1,1:116,80:196,2:0.0101:2,2:13.5:1:28.5:1:1:1.44719:60:4:0.0103:0:1.5 +2 240678163 . G T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61014;SOR=1.12561;LSEQ=TTCGCAGGAGACACACGGCC;RSEQ=TGGGAAGGAAGCTGCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:211:135:78,57:50,25:75,135:0.6398:2,2:25.7:1:31.4:1:0.23865:1.45891:60:134:0.6381:0:1.9 1/0:213:142:82,60:43,28:71,142:0.6667:2,2:26.9:1:29.4:1:0.76835:1.12308:60:27.4:0.6618:0:1.8 +2 240678202 . T G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4284;SOR=1.15098;LSEQ=GTGTTCACTCGCATCAATGT;RSEQ=CATTGTTCTTCACGGCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:279:181:93,88:49,48:97,181:0.6487:2,2:25.3:1:32.3:1:0.90052:1.04:60:180:0.6569:0:1.7 1/0:297:202:106,96:51,42:93,202:0.6801:2,2:24.5:1:31.3:1:0.80179:1.09938:60:100:0.6826:0:1.6 +2 240712124 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12581;SOR=0;LSEQ=GCACCGAGCACTCTTCCTCC;RSEQ=GGGCATGGAGCCCTCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:25:1:30:1:1:1.13389:60:4:0.1176:0:1 0/0:30:0:0,0:16,14:30,0:0:2,0:27.8:1:30.3:1:1:0:60:60:1:0:0.3 +2 240712125 . G A 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33632;SOR=0.34187;LSEQ=CACCGAGCACTCTTCCTCCC;RSEQ=GGCATGGAGCCCTCCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:7,7:14,3:0.1765:2,2:42:1:32:0:1:1.92:60:6:0.1765:0:1.3 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:6:0:32:0:1:1.14834:60:4:0.0714:0:1.5 +2 241362873 . G T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.21257;LSEQ=CAAGGCTCGCTCAGGGTTCA;RSEQ=TTAGAAAAACAATGCCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:100,25:125,2:0.0157:2,0:26.5:1:25:1:1:0:60:1:0.008:0:1 0/1:105:2:1,1:82,21:103,2:0.019:2,2:6.5:1:27.5:1:0.37674:3.83818:60:4:0.019:0:1.5 +2 241362975 . T A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10675;SOR=0;LSEQ=GCGCCCACAGTGGCTCACCC;RSEQ=GATCACTCTGGGTGAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:113,172:285,3:0.0104:2,2:19.7:1:29.7:1:0.56574:3.03:60:6:0.0105:0:1 0/0:318:0:0,0:140,178:318,0:0:2,0:26.5:1:29.5:1:1:0:60:78.5:1:0:0.5 +2 241362987 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24935;SOR=Inf;LSEQ=GCTCACCCTGATCACTCTGG;RSEQ=TGAGGGTGTGAATGGGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:96,170:266,0:0:2,0:25.1:1:32:1:1:0:60:265:1:0:0.2 0/1:283:3:2,1:112,167:279,3:0.0106:2,2:27:1:23:1:0.56755:2.97:60:2:0.0072:0:1 +2 241363000 . T C 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCTGGGTGAGGGTGTGAA;RSEQ=GGGAACCCTCTTTTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:76,151:227,0:0:2,0:23.4:1:30.6:1:1:0:60:112.5:1:0:0.2 0/1:235:93:31,62:53,88:141,93:0.3957:2,2:23.3:1:29.9:1:0.578:1.20359:60:30:0.3879:0:1.2 +2 241363006 . C A 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.62391;SOR=2.8313;LSEQ=GGTGAGGGTGTGAATGGGAA;RSEQ=CCTCTTTTTTCTTTTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:1,0:60,133:193,1:0.0052:2,0:1:0:27:0:0.31443:0:60:2:0.0052:0:1 0/1:207:3:2,1:71,133:204,3:0.0145:2,2:16.3:1:29:1:0.2844:3.72:60:6:0.0148:0:1.3 +2 242440221 . G A 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.6044;SOR=0.52327;LSEQ=AGCTTGGTGCTCTGGGACCG;RSEQ=AGACAAACCCATCAGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:9:0:32.5:1:1:2.44949:60:4:0.3333:0:1.5 0/1:10:2:1,1:5,3:8,2:0.2:2,2:16.5:1:27:1:1:1.58108:60:4:0.2:0:1 +2 242440325 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20168;SOR=0;LSEQ=GCCCCACCGGTCCCATCCCT;RSEQ=CCAAGAACCCTGAACAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:14,2:0.125:2,2:45.5:1:30:0:1:1.30929:60:4:0.125:0:1.5 0/0:19:0:0,0:8,11:19,0:0:2,0:25.4:1:30.3:1:1:0:60:18:1:0:0.3 +2 242440327 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50202;SOR=Inf;LSEQ=CCCACCGGTCCCATCCCTGC;RSEQ=AAGAACCCTGAACAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:13,0:0:2,0:29:1:31.8:1:1:0:60:26:1:0:0.4 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:35.5:1:29:1:1:1.40:60:4:0.1053:0:1 +2 242793115 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16464;SOR=Inf;LSEQ=CTCAGCCCCTGGACGGCCTG;RSEQ=AATGGCCTGCACCCTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:118,16:134,0:0:2,0:21.8:1:32.6:1:1:0:60:268:1:0:0.1 0/1:92:2:1,1:82,8:90,2:0.0217:2,2:24.5:1:32:0:0.18705:9.72255:60:4:0.0222:0:1 +2 242793122 . C T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3173;SOR=4.04307;LSEQ=CCTGGACGGCCTGCAATGGC;RSEQ=TGCACCCTGCCTGCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:1:1,0:128,21:149,1:0.0067:2,0:16:0:31:0:1:0:60:2:0.0068:0:1 0/1:113:3:1,2:93,17:110,3:0.0265:2,2:10.7:1:27:1:0.07279:10.57542:60:6:0.0268:0:1 +2 242793273 . A G 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.44755;LSEQ=TGGGCACTCCGAGGGCCGTC;RSEQ=GCTGAGCCCCTGCGGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:645:524:272,252:68,53:121,524:0.8124:2,2:24.9:1:30.3:1:0.41995:1.18836:60:64.5:0.8152:0:1.1 1/0:605:399:217,182:106,98:204,399:0.6595:2,2:23.7:1:29.4:1:0.60494:1.10:60:48.875:0.6582:0:1.2 +2 242793503 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19352;SOR=Inf;LSEQ=CGGCCCACCGCAGGAAGGAG;RSEQ=CCCGCGGCTCCACAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:46,207:253,0:0:2,0:24.4:1:31.8:1:1:0:60:30.625:1:0:0.2 0/1:200:2:1,1:42,155:197,2:0.01:2,2:17:1:26.5:1:0.38633:3.66:60:4:0.0103:0:1 +2 242793519 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18837;SOR=Inf;LSEQ=GGAGGCCCGCGGCTCCACAG;RSEQ=CTGGCTGCAGTACCGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:20,158:178,0:0:2,0:24:1:31.9:1:1:0:60:58.333:1:0:0.3 0/1:137:2:1,1:19,116:135,2:0.0146:2,2:28.5:1:29:1:0.27158:5.98:60:4:0.0149:0:1.5 +2 242793559 . T C 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05845;SOR=0.43741;LSEQ=CGAACCTGGGCCCCCCACTA;RSEQ=GAGCTGCTTACCCTGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:65:6,59:1,15:16,65:0.8025:1,2:23.9:1:30.6:1:1:1.52:60:130:0.8125:0:1.1 1/0:47:30:2,28:2,15:17,30:0.6383:2,2:24.1:1:29.9:1:0.61304:1.8407:60:60:0.6383:0:1 +2 242793977 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20491;SOR=Inf;LSEQ=TGCTGCCTGGGGGCTGGGGA;RSEQ=GTGGGGTCCTGGCTATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:150,9:159,0:0:2,0:23.8:1:33:1:1:0:60:38.75:1:0:0.1 0/1:132:2:1,1:119,11:130,2:0.0152:2,2:25:1:28.5:1:0.17418:10.40114:60:4:0.0155:0:1 +2 242793992 . A T 35 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24983;SOR=0;LSEQ=GGGGAGGTGGGGTCCTGGCT;RSEQ=TAATAGAATGTGAGTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:181,24:205,3:0.0144:2,2:7.3:1:22.7:1:0.04177:14.71021:60:2:0.0099:0:1 0/0:189:0:0,0:157,32:189,0:0:2,0:21.1:1:27.9:1:1:0:60:46.25:1:0:0.1 +2 242794190 . T TG 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTGAGCCGTGCTCCTAGG;RSEQ=GGGGGGTCTTAGTCCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:170,237:407,0:0:2,0:24.4:1:29.1:1:1:0:60:15.28:1:0:0.2 0/1:381:22:8,14:128,227:355,22:0.0577:2,2:28.7:1:31.2:1:1:1.01:60:44:0.0603:0:0.1 +2 242794234 . CG C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16023;SOR=Inf;LSEQ=TCATCAGGGACTTAGCCTGG;RSEQ=GGGAGATGGGGGGAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:113,92:205,0:0:2,0:20.6:1:30.7:1:1:0:59.5:101.5:0.9951:0:0.7 0/1:138:2:1,1:64,71:135,2:0.0145:2,2:21:1:28.5:1:1:1.11:60:4:0.0147:0.0072:0.5 +2 242794289 . G T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18604;SOR=4.72993;LSEQ=AGGGTGGAGGAAGGGGAGGC;RSEQ=GGAGTGAGGGCCGCCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:1:0,1:240,125:365,1:0.0027:2,0:37:0:17:0:0.34426:0:50:0:0:0:8 0/1:312:4:1,3:205,103:308,4:0.0128:2,2:11.3:1:27.3:1:0.11544:5.93515:60:8:0.0129:0:1.5 +2 242794530 . T G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09568;SOR=Inf;LSEQ=AAGGGCACAAAGGTCAGGGG;RSEQ=TAGGACGGGGTCAGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:81,250:331,0:0:2,0:25.3:1:29.8:1:1:0:59.9:35.778:1:0:0.2 0/1:280:3:1,2:74,203:277,3:0.0107:2,2:13.3:1:30.3:1:1:1.37:60:6:0.0108:0:1.3 +2 242796574 . G A 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCTGCATAGGCGTGTGC;RSEQ=GCGTGGGCCCGGGGAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:12:1:29.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 242796660 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGACTCTCAGGGCCAGC;RSEQ=GGCAGCCAGGCCAGGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:13:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +2 242800561 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10294;SOR=Inf;LSEQ=CCCGTCATTCTACAGAAACA;RSEQ=GCAGCCCCAAGGACCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:24:1:32.1:1:1:0:60:14:1:0:0 0/1:10:4:2,2:3,3:6,4:0.4:2,2:16.5:1:28.5:1:1:1:60:8:0.4:0:1.5 +2 242800740 . AC A 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAGGCTGGGCCTGCCACAGC;RSEQ=CCCCCGACCTGCCAGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:87,7:94,2:0.0208:2,2:16.5:1:32:1:0.16053:11.6927:60:4:0.0208:0:0 0/1:48:1:1,0:44,3:47,1:0.0208:2,0:19:0:33:0:1:0:60:2:0.0213:0:0 +2 242800832 . AC A 75 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.25012;SOR=3.23337;LSEQ=AGGGCCAGGCCCGCCTCAGC;RSEQ=CCCCCGACCTGCCAGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:476:2:2,0:360,113:473,2:0.0042:2,0:24:1:34:0:1:0:60:4:0.0043:0:0 0/1:371:5:4,1:261,105:366,5:0.0135:2,2:26:1:32.6:1:1:1.61:60:10:0.0136:0:0.2 +2 242802389 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACACCCACCCTTGTGCC;RSEQ=CAGGGGCTGGGGCTCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:0:32.5:1:1:0:60:4:1:0:1.5 +2 242982298 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50489;SOR=Inf;LSEQ=GATGTAGCAAAACTTGAAAC;RSEQ=CCACTGTTGAGTTTTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:68,41:109,0:0:2,0:27:1:30.7:1:1:0:60:108:1:0:0.1 0/1:138:2:1,1:70,66:136,2:0.0145:2,2:28.5:1:30:0:1:1.06018:60:4:0.0145:0:1.5 +2 242982321 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22825;SOR=0;LSEQ=ACTGTTGAGTTTTCTTCCCG;RSEQ=GGAGGATGGACCCAAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:66,56:122,2:0.0161:2,2:17.5:1:28.5:1:1:1.177:60:4:0.0163:0:1 0/0:135:0:0,0:63,72:135,0:0:2,0:29.3:1:30.3:1:1:0:59.4:66.5:1:0:0.2 +20 61053 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATCAACAGACCACTTGCAG;RSEQ=TATACTTCACAGCCCACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:20.5:1:29:1:1:1.11803:60:4:0.1111:0:1.5 0/0:9:0:0,0:5,3:8,0:0:2,0:26:1:29.6:1:1:0:60:16:0.8889:0:0.4 +20 61098 . C T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06342;SOR=0;LSEQ=CTGCCAAGCACAGACAACCA;RSEQ=TGGGCCCCAGGGGAGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:2,4:5,6:11,6:0.3529:2,2:20.7:1:32.3:1:1:1.6177:60:12:0.3529:0:1.3 0/0:9:0:0,0:5,4:9,0:0:2,0:25.3:1:31.2:1:1:0:60:18:1:0:0.2 +20 61138 . C CT 31 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.18333;SOR=8.44314;LSEQ=AGGTCTCCTGGTCACCTAAT;RSEQ=TTTTTTTTTTTTATACTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:2,4:6,1:0.1429:2,0:48:0:31:0:0.42857:0:60:2:0.1667:0:2 1/0:3:2:0,2:0,0:0,2:0.6667:0,0:23.5:1:31:0:1:0:58.5:4:0.6667:0:0 +20 306766 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=GACCAGTGGCCCGACATGCA;RSEQ=AACGCCGAGATCTCCAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:10,0:0:2,0:20:1:32.8:1:1:0:60:20:1:0:0.1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:20:0:32.5:1:1:1:60:4:0.5:0:1.5 +20 308878 . C T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCCTGTCCCTGTTGCTGTGG;RSEQ=CCCTCTCACGCCGCCATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:18.3:1:33.3:1:1:0:60:6:1:0:1.7 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:30.5:1:1:0:60:4:1:0:2.5 +20 308884 . T C 34 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=CCCTGTTGCTGTGGCCCCTC;RSEQ=CACGCCGCCATCTCTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:15:0:34:0:1:0:60:4:0.6667:0:2.5 0/0:2:0:0,0:1,1:2,0:0:2,0:28:0:31.5:1:1:0:60:4:1:0:2.5 +20 345775 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=0;LSEQ=TCAGCAAGCCTTGCAGGTCT;RSEQ=TTCTGGTTTCAGAACCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:99,82:181,2:0.0109:2,2:17:1:29:1:1:1.20606:60:4:0.0112:0:1 0/0:167:0:0,0:100,66:166,0:0:2,0:23.5:1:30.9:1:1:0:60:54.333:1:0:0.2 +20 345816 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10405;SOR=Inf;LSEQ=CATTTTGTCCTTCACTCCAG;RSEQ=CTGCCTCAGAGACATGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:115,135:250,0:0:2,0:26.8:1:31.6:1:1:0:59.8:40.667:1:0:0.4 0/1:223:3:2,1:112,108:220,3:0.0135:2,2:16.7:1:26.3:1:1:1.92:60:6:0.014:0:1.7 +20 345864 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.041;SOR=1.63135;LSEQ=TACACAACAATGTGTGCACG;RSEQ=TGGCACACATGCACATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:67:21,46:35,62:97,67:0.4085:2,2:24.9:1:29.9:1:0.61597:1.23496:59.4:134:0.4085:0:1.1 1/0:149:79:28,51:26,43:69,79:0.5302:2,2:23.9:1:29.1:1:0.86443:1.10061:60:158:0.5374:0:1.1 +20 345885 . GCA G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.49945;SOR=0;LSEQ=TGGCACACATGCACATGCAT;RSEQ=CACACACACTCTGCATGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:32,84:116,2:0.0169:2,0:21.5:1:34:0:1:0:60:4:0.0171:0:0.5 0/0:105:0:0,0:32,73:105,0:0:2,0:22.6:1:30.5:1:1:0:60:51.5:1:0:0.6 +20 1420200 . CT C 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGGTATAAGATGGAAC;RSEQ=TAAGTTCAAAGCCTGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:47:0:33.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 1421627 . GC G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAACACAGGAGCCCAAC;RSEQ=CCATTTAAAGAAGGAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:20.5:1:32.5:1:1:0:60:4:0.6667:0.3333:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 1421836 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16256;SOR=Inf;LSEQ=ATGGGTATGAAAAGGGCCGC;RSEQ=GCCCCTCTGGAAGACACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:94,37:131,0:0:2,0:21.7:1:31:1:1:0:60:42.667:1:0:0.2 0/1:89:2:1,1:64,23:87,2:0.0225:2,2:35:1:30:1:0.46885:2.74522:60:4:0.0227:0:1.5 +20 1421932 . C T 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09198;SOR=1.35171;LSEQ=CCTTCTACTGAGGAAGCAGC;RSEQ=GGATCTGTGCAAGACTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:138:69,69:80,86:166,138:0.4525:2,2:22.6:1:31:1:0.81789:1.07:60:276:0.4554:0:1.3 1/0:216:114:53,61:49,53:102,114:0.5278:2,2:27.9:1:29.6:1:0.89158:1.06376:60:37:0.5236:0:1.2 +20 1421958 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17961;SOR=Inf;LSEQ=TGTGCAAGACTCTACCTACA;RSEQ=GGTTGCTGGGCATGATTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:110,149:259,0:0:2,0:26.3:1:31.6:1:1:0:59.9:85.333:1:0:0.6 0/1:191:2:1,1:81,108:189,2:0.0105:2,2:19:0:32:1:1:1.33:60:4:0.0111:0:1 +20 1421974 . T C 171 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACAGGGTTGCTGGGCATGA;RSEQ=TGTTAACAAGATCAAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:36:14,22:63,124:187,36:0.1614:2,2:26.2:1:33.1:1:0.5693:1.25:60:72:0.1644:0:1.9 0/0:152:0:0,0:57,95:152,0:0:2,0:23.6:1:28.8:1:1:0:60:29.4:1:0:0.7 +20 1422057 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5443;SOR=0;LSEQ=AAGGGCATCATGACAATTAC;RSEQ=TTGCCTATTTTTCATTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:0,50:50,2:0.0385:1,2:18.5:1:30:1:0.03846:0:60:4:0.04:0:1 0/0:27:0:0,0:2,25:27,0:0:2,0:22.3:1:29.2:1:1:0:60:26:1:0:0.1 +20 1624766 . G A 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15967;SOR=0.19579;LSEQ=GGAGTGAGTGTGCTTCAGTG;RSEQ=GGAAAAACCCACTTATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:1,3:4,5:0.5556:2,2:25.8:1:31.2:1:1:1.85:60:10:0.5556:0:1 0/1:11:2:1,1:2,7:9,2:0.1818:2,2:10.5:1:27.5:1:0.49091:3.06:60:4:0.1818:0:1 +20 1626068 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGTAAACATTTTTGTCA;RSEQ=AGTTTCCCAGGTGATTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 2135803 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17976;SOR=Inf;LSEQ=TTCCTGAGCCTCTGCTATGT;RSEQ=CAAAACTCCATGCACCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:183,50:233,0:0:2,0:23.9:1:32.3:1:1:0:59.8:76.667:1:0:0.1 0/1:172:2:1,1:123,47:170,2:0.0116:2,2:8.5:1:26.5:1:0.48144:2.60013:60:4:0.0119:0:1 +20 2135905 . A G 190 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=120.10928;LSEQ=ACCTTGAGAACTTTTGTTCC;RSEQ=GGCAAGAGGGATCTAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:1:1,0:348,330:678,1:0.0015:2,0:23:0:29:0:1:0:60:2:0.0015:0:1 0/1:591:89:49,40:256,245:501,89:0.1506:2,2:25.1:1:29.4:1:0.56515:1.17:60:178:0.1527:0:1.2 +20 4040556 . TG T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50094;SOR=Inf;LSEQ=GAACAATGCCAACGGCATGC;RSEQ=GGGAACATTGCAGACTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:38,23:61,0:0:2,0:25.8:1:31.7:1:1:0:55:60:1:0:0.1 0/1:74:2:1,1:38,34:72,2:0.027:2,2:30:1:31.5:1:1:1.11596:60:4:0.027:0:1 +20 4040763 . T C 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02533;SOR=0.15028;LSEQ=TTCCTCTGTGTTCATCATCT;RSEQ=GGCGAATTACTGGAAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:3,9:2,3:5,12:0.7059:2,2:28.5:1:30.6:1:0.60003:1.91473:38.3:24:0.7059:0:1.1 0/1:12:3:0,3:2,7:9,3:0.25:2,0:28.3:1:25.3:1:1:0:48:6:0.25:0:1 +20 4040828 . T C 34 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=GTGTTTATTATTTGATCAAA;RSEQ=ATATCAAATCAAATAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:7.5:1:34:0:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:13.5:1:29.5:1:1:0:60:4:1:0:0 +20 4040961 . C G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTGCCTGCCAGCAGAAC;RSEQ=TGAGACAAAGGCTTGTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:20.5:1:34.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 4610341 . A C 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61637;LSEQ=TACACAGGTTACCAGTGTCG;RSEQ=ACCTGATGAAGTCAGTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:9,0:9,3:0.25:0,2:23.3:1:33.7:1:0.25:0:41.7:6:0.2727:0:1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:1:0:30:0:1:0:49:2:0.1667:0:1 +20 4610408 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08951;SOR=Inf;LSEQ=GGTGTCATTCACCTTGATGA;RSEQ=GGGATCAGGGTAGCAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:30,18:48,0:0:2,0:25.6:1:32.4:1:1:0:50.8:96:1:0:0.1 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:17.5:1:31.5:1:1:1.11:60:4:0.0952:0:2 +20 4610410 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCATTCACCTTGATGAGG;RSEQ=GATCAGGGTAGCAGATGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:27,17:44,2:0.0435:2,2:11.5:1:28.5:1:1:1.57176:49.5:4:0.0435:0:1 0/0:21:0:0,0:10,11:21,0:0:2,0:25.6:1:30.3:1:1:0:46.1:20:1:0:0.4 +20 5529295 . T C 26 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAATAAAACAAAGATTC;RSEQ=TTTCAATAAAATCCGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:9,1:10,2:0.1667:2,0:17:0:26.5:1:1:0:60:4:0.1667:0:2 0/0:4:0:0,0:4,0:4,0:0:0,0:28.3:1:31.3:1:1:0:60:8:1:0:0.3 +20 5529310 . G A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36146;SOR=0.2838;LSEQ=GATTCTTTTCAATAAAATCC;RSEQ=TAAGTAAGAGAAAAACCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:8,1:6,0:6,9:0.6:0,2:29.3:1:31.6:1:1:0:60:18:0.6:0:1.3 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:20.5:1:31:0:1:0:60:4:0.2857:0:1 +20 5529992 . A T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08671;SOR=Inf;LSEQ=ACTACTGAATGTGAAAACAG;RSEQ=GAAGCTGTTACACATATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:57,113:170,0:0:2,0:25.4:1:30.8:1:1:0:59.3:33:1:0:0.1 0/1:136:3:1,2:37,96:133,3:0.0221:2,2:16.7:1:26.7:1:1:1.29:60:6:0.0226:0:1 +20 5530075 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13543;SOR=Inf;LSEQ=GATTGGTTATCAGTCCCATG;RSEQ=AGACACAGCTACTAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:13,72:85,0:0:2,0:26.3:1:32.5:1:1:0:56.1:170:1:0:0.1 0/1:50:2:1,1:19,29:48,2:0.04:2,2:25.5:1:28:1:1:1.51:45.5:4:0.04:0:1.5 +20 5530428 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAATCCTTAATGA;RSEQ=TTCAGGGAAATAGCATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:18.5:1:27.5:1:1:0:53.5:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 6201402 . G T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTGCTCAAGTAGCATGTG;RSEQ=CAAACTTGTGGGGTTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:15.8:1:31:1:1:0:60:8:1:0:0 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:37:1:29.5:1:1:2.24:60:4:0.2222:0:1 +20 6952343 . A C 112 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00879;SOR=0;LSEQ=CCATGAAAAGGCAGACTGAT;RSEQ=AAATTTAAGACGATATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:31:1:32.6:1:1:0:60:22:1:0:1 0/1:4:1:1,0:3,0:3,1:0.25:0,0:36:0:27:0:1:0:60:2:0.25:0:1 +20 6952495 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19575;SOR=Inf;LSEQ=AATTTAGACTTAATTGAAAG;RSEQ=CATTTTAAGTCTAATTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:140,61:201,0:0:2,0:25.3:1:31.9:1:1:0:60:200:1:0:0.2 0/1:160:2:1,1:101,57:158,2:0.0125:2,2:8.5:1:26.5:1:1:1.76517:60:4:0.0127:0:2 +20 6952571 . C A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.63302;LSEQ=AGCAATTACCACCATAATAG;RSEQ=CAGAAATAAATTGATTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:106:49,57:100,130:230,106:0.3155:2,2:25.9:1:29.4:1:0.63881:1.12:60:105:0.3144:0:1.1 1/0:226:124:55,69:42,60:102,124:0.5487:2,2:25.6:1:28.6:1:0.68607:1.14:60:40.333:0.5426:0:1.2 +20 6952618 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.16606;SOR=Inf;LSEQ=ATGTTTTGAACCAAATGCAT;RSEQ=CATAATTTTTGCCTAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:71,158:229,0:0:2,0:24.1:1:32.2:1:1:0:60:37.167:1:0:0.3 0/1:158:2:1,1:57,99:156,2:0.0127:2,2:10:0:31:1:1:1.73:60:4:0.0127:0:2.5 +20 6952790 . C T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTCCATATTTCCTCTCTCA;RSEQ=TCTAGGAGCTTAAGGATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:24.1:1:31.3:1:1:0:60:20:1:0:1.4 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:28.5:1:1:0:60:4:1:0:1.5 +20 6952829 . T G 79 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATATTGAGTATGGGCCAG;RSEQ=TAGCTTGCCGCCAAAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:17.4:1:34.4:1:1:0:60:10:1:0:1.8 1/1:1:1:0,1:0,0:0,1:1:0,0:26:0:34:0:1:0:60:2:1:0:2 +20 7600865 . AT A 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.25701;SOR=0.22815;LSEQ=TTGCTCTGCTGTCTTTGAGC;RSEQ=TTTTTTTTTCCTGGTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:7:7,0:73,3:76,7:0.0843:1,0:20.3:1:32.6:1:1:0:60:14:0.0843:0.0241:0 0/1:49:1:1,0:46,2:48,1:0.0204:1,0:37:0:31:0:1:0:60:2:0.0208:0:0 +20 7601013 . A T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.63201;LSEQ=TGTAAATGAATCTGAATGTT;RSEQ=TCAACAGACAGAACAGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:154:63,91:107,144:251,154:0.3793:2,2:24.8:1:30.4:1:0.75649:1.07309:60:153:0.3806:0:1.1 1/0:342:211:95,116:59,71:130,211:0.617:2,2:26.1:1:29.6:1:1:1.01464:60:104.5:0.6183:0:1.1 +20 7601180 . A AATG 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00432;SOR=6.98701;LSEQ=CCTCCCAAAGAAATACTGAA;RSEQ=ATATTATAAATGATGTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:0,9:1,23:24,9:0.2727:1,0:33.2:1:31.1:1:1:0:60:18:0.2813:0.0303:0 1/0:15:11:0,11:1,3:4,11:0.7333:2,0:24:1:29.5:1:0.26667:0:60:22:0.7857:0.2667:0 +20 7602473 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGTCTGTTTCAACAAGGT;RSEQ=CTGATTGGTGCGTTTACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:29:1:1:0:60:4:1:0:1.5 +20 8678446 . G A 48 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TCAAGGTAGAGTATATGAAT;RSEQ=TTACTAAGAGAGGCAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:24:1:30.7:1:1:0:60:6:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:31:0:1:0:60:2:1:0:0 +20 8679696 . A T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31712;SOR=4.0635;LSEQ=CTGGGGTCCTAGGTACTTGG;RSEQ=GAGTGACTGGAGAAAGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:1:0,1:137,70:207,1:0.0048:2,0:1:0:27:0:0.34135:0:60:2:0.005:0:1 0/1:156:3:1,2:100,53:153,3:0.0192:2,2:20.7:1:26.3:1:0.28394:3.73987:60:6:0.0194:0:1 +20 8679723 . C T 47 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13748;SOR=0;LSEQ=CTGGAGAAAGAAGTTGTGGG;RSEQ=TTCAGGGAACATGTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:4:1,3:191,151:342,4:0.0115:2,2:12.3:1:23.8:1:0.32718:3.78098:60:3:0.0087:0:1.8 0/0:266:0:0,0:153,113:266,0:0:2,0:25.3:1:31.3:1:1:0:60:43.333:1:0:0.2 +20 8679854 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01872;SOR=Inf;LSEQ=CCTGTTGCCTGGGATACCTG;RSEQ=GTCTCAGGGAAGTGTCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:2,84:86,0:0:1,0:26.9:1:31.5:1:1:0:60:85:1:0:0 0/1:52:4:0,4:1,47:48,4:0.0769:1,0:39.5:1:29.8:1:1:0:60:8:0.0769:0:1 +20 9520133 . G A 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGATGCCTGTATTGTCTCAT;RSEQ=AGGGGGACGATGCAAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1082:0:0,0:613,466:1079,0:0:2,0:24.7:1:32:1:1:0:59.9:82:0.9972:0:0.4 0/1:654:33:16,17:346,273:619,33:0.0505:2,2:24.3:1:29.3:1:0.47313:1.34598:60:66:0.051:0:1.1 +20 9520142 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42889;LSEQ=TATTGTCTCATGAGGGGGAC;RSEQ=ATGCAAGACGGTGGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1128:271:158,113:462,394:856,271:0.2402:2,2:25.3:1:30.5:1:0.23369:1.19:60:66.75:0.2399:0:1.1 0/1:712:85:47,38:340,286:626,85:0.1194:2,2:26:1:29.5:1:0.9079:1.04:60:170:0.1206:0:1.2 +20 9523379 . A G 211 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGTCCACCTGTTAGGCAC;RSEQ=CCCTACTGGTTATCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:910:0:0,0:337,572:909,0:0:2,0:24:1:30.1:1:1:0:60:89.9:0.9989:0:0.1 0/1:623:136:57,79:174,313:487,136:0.2183:2,2:25.6:1:29.9:1:0.19307:1.30:59.7:67:0.2179:0:1.1 +20 9523663 . C T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGTAGTTAACTGTCTAT;RSEQ=AGGGCAGATGAGAAAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:17:1:29.5:1:1:0:40:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 9525091 . C T 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=61.78625;LSEQ=CCAACCAATGATTTCCTCTT;RSEQ=GGCACCTCTTTGGAAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1392:1:0,1:669,722:1391,1:7e-04:2,0:1:0:25:0:1:0:60:2:7e-04:0:1 0/1:1127:48:21,27:536,541:1077,48:0.0426:2,2:27.8:1:29.8:1:0.46219:1.27356:60:96:0.043:0:1.1 +20 9543622 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=1.54648;LSEQ=CATCGCCGACAAGGTAGCTG;RSEQ=TGTACATGTCAACCACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1142:282:127,155:377,481:858,282:0.2469:2,2:25.6:1:30.3:1:0.7823:1.05:59.9:140:0.2489:0:1.1 0/1:939:316:138,178:304,318:622,316:0.3365:2,2:23.9:1:29.2:1:0.14617:1.23279:59.8:104.333:0.338:0:1.5 +20 9543681 . C T 200 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=201.17597;LSEQ=ATGATCACGACCTGGGGAAA;RSEQ=GGGAAATATACTTTTGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:1:1,0:224,468:692,1:0.0014:2,0:43:0:30:0:0.32468:0:60:2:0.0015:0:6 0/1:475:107:35,72:118,229:347,107:0.2253:2,2:23.7:1:29.7:1:0.90693:1.05989:59.9:214:0.2286:0:2.6 +20 9543688 . T G 204 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=186.52167;LSEQ=CGACCTGGGGAAACGGGAAA;RSEQ=ATACTTTTGACTTGTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:623:1:1,0:199,423:622,1:0.0016:2,0:50:0:32:0:0.32103:0:60:2:0.0016:0:6 0/1:415:96:33,63:100,218:318,96:0.2313:2,2:22.7:1:31:1:0.61874:1.14:59.9:192:0.2336:0:2.7 +20 9543833 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02023;SOR=Inf;LSEQ=AAAAGCATCAAGGGTAGCTA;RSEQ=TAGAAATAAAAGGAATCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:48,0:0:1,0:22.9:1:31.7:1:1:0:60:47:1:0:0.1 0/1:19:3:0,3:1,15:16,3:0.1579:1,0:22.3:1:32:0:1:0:60:6:0.1579:0:1 +20 9546554 . G A 131 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=36.75635;LSEQ=CTTTACCTCATTGAAAAGCA;RSEQ=TTCTCGTCTCTGTTGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:978:1:1,0:613,364:977,1:0.001:2,0:1:0:26:0:1:0:60:2:0.001:0:1 0/1:744:27:19,8:440,274:714,27:0.0363:2,2:27.4:1:27.6:1:0.42321:1.48:58.7:12.5:0.0343:0:1.4 +20 9547018 . C G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07588;SOR=0.67137;LSEQ=GGCTGAGGACCATCTGTGCT;RSEQ=GATCGTAATCCACCTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:80:15,65:57,205:262,80:0.2332:2,2:24.6:1:31.4:1:0.63989:1.20428:59.5:79:0.2365:0:1.1 0/1:236:40:9,31:53,143:196,40:0.1695:2,2:24.2:1:30.6:1:0.69399:1.2753:60:80:0.1709:0:1.1 +20 9547028 . C A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15334;SOR=Inf;LSEQ=CATCTGTGCTCGATCGTAAT;RSEQ=CACCTGGGAAGACAGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:55,227:282,0:0:2,0:24.2:1:31.5:1:1:0:59.8:34.25:1:0:0.4 0/1:182:2:1,1:41,139:180,2:0.011:2,2:16:1:24.5:1:0.40926:3.36:60:4:0.011:0:1 +20 9547288 . T G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCTATTTTCTTGTTCAG;RSEQ=AATGAAAAACCCCATCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:40:1:31:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 9560633 . C T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74146;SOR=0.67656;LSEQ=GCCTTATCCTAAACCTCTGC;RSEQ=CTGGGGCCTCACAAGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:15:15,0:37,0:37,15:0.2885:1,1:21.7:1:33.1:1:1:0:60:30:0.3:0:1.4 0/1:14:3:3,0:11,0:11,3:0.2143:0,0:17.7:1:29:1:1:0:60:6:0.2143:0:2 +20 9560712 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36172;SOR=0.76967;LSEQ=AAACAAGTACTTTACAATCC;RSEQ=ATCGTATAAAAAGGTCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:58:53,5:94,7:101,58:0.3648:2,2:25.2:1:30.2:1:0.75926:1.26489:60:116:0.3694:0:1.2 0/1:111:34:33,1:67,10:77,34:0.3063:2,1:23.1:1:29.3:1:0.16762:4.87:60:33:0.3:0:1.1 +20 9561601 . G A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16124;SOR=4.84552;LSEQ=GGAATAATAGAGGGAATATT;RSEQ=TTTAAAGAAAATATTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:1,0:50,210:260,1:0.0038:2,0:1:0:24:0:0.1954:0:60:2:0.0039:0:1 0/1:164:3:2,1:42,119:161,3:0.0183:2,2:25:1:28:1:0.17563:5.59:60:6:0.0186:0:1 +20 9624587 . C T 157 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.00202;SOR=0;LSEQ=ACATCTAAAGCCAAAGTTCC;RSEQ=TTTCATGGGCTGCAATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:30,0:0,0:0,30:1:0,1:26:1:32:1:1:0:59.8:29:1:0:1.2 0/0:2:0:0,0:2,0:2,0:0:0,0:18:1:30.5:1:1:0:60:4:1:0:0 +20 9625003 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01874;SOR=0;LSEQ=AAAACCTGGGAAATATAAAT;RSEQ=GAAAAGAGGCAGCCATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:299:299:39,260:0,0:0,299:1:0,2:22:1:31.6:1:1:0:59.9:36.375:1:0:1.1 1/1:248:243:36,207:1,4:5,243:0.9798:2,2:23.5:1:30:1:0.55737:1.43513:60:33.714:0.9793:0:1.2 +20 9625011 . G A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10191;SOR=Inf;LSEQ=GGAAATATAAATGGAAAAGA;RSEQ=GCAGCCATTTATATCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:24,227:251,0:0:2,0:21.4:1:31.4:1:1:0:59.9:49.2:1:0:1 0/1:221:3:1,2:26,191:217,3:0.0136:2,2:14:1:25:1:0.32614:3.64:60:2:0.0093:0:4 +20 9625015 . G T 51 p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25155;SOR=0;LSEQ=ATATAAATGGAAAAGAGGCA;RSEQ=CCATTTATATCTTGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:3:1,2:19,202:221,3:0.0134:2,2:7:0:32.3:1:0.24565:5.24:60:6:0.0135:0:2.3 0/0:196:0:0,0:20,176:196,0:0:2,0:20.8:1:31.5:1:1:0:60:38.2:1:0:1.1 +20 10488852 . G A 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11778;SOR=0.32357;LSEQ=AGCCAGTGTGTGTGCCCACA;RSEQ=CCCTGCCCTTGGAGCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:4,5:10,10:20,9:0.3103:2,2:31.9:1:28.2:1:1:1.24042:60:8:0.2857:0:1.1 0/1:32:4:2,2:14,14:28,4:0.125:2,2:30:1:25.3:1:1:1:60:3:0.0968:0:1.3 +20 10869335 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11661;SOR=Inf;LSEQ=ACTTTAATGACTAAAGTCCC;RSEQ=GTAGCAGCACTGGGTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:195,182:377,0:0:2,0:25.1:1:30.7:1:1:0:59.9:187.5:1:0:0.1 0/1:196:2:1,1:90,104:194,2:0.0102:2,2:32:1:27:0:1:1.15:60:4:0.0104:0:1.5 +20 10869731 . A G 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12412;SOR=Inf;LSEQ=TTTTCTGCAATTACAGTCAC;RSEQ=TGAACCTCTTTTTTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:64,266:330,0:0:2,0:21.5:1:31:1:1:0:59.8:32:1:0:0.2 0/1:180:2:1,1:47,131:178,2:0.0111:2,2:7:0:32:1:0.46331:2.77:60:4:0.0114:0:1.5 +20 10869747 . AT A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.78834;SOR=1.19349;LSEQ=TCACATGAACCTCTTTTTTT;RSEQ=TTTTTTTTTTGACGGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:10:1,9:28,174:202,10:0.0465:2,2:31.9:1:31.1:1:1:1.44604:57:20:0.0476:0.0047:1.5 0/1:109:6:0,6:21,82:103,6:0.055:2,0:31.5:1:31.7:1:0.59374:0:60:12:0.055:0:0.3 +20 10869778 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28864;SOR=0.58353;LSEQ=TGACGGAGTTTTGCTCTGTC;RSEQ=CCCAGGCTGGAGTGTCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:36:2,34:2,44:46,36:0.439:1,2:23.6:1:30.1:1:1:1.29:54.3:35:0.4375:0:1.3 0/1:32:10:1,9:1,21:22,10:0.3125:1,2:27.6:1:31.1:1:0.53427:2.27:59.7:20:0.3333:0:1 +20 11361032 . G A 56 q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCAAATCAGATTAATAG;RSEQ=GCCTGAACTGAACCCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:1,5:0.8333:0,2:24.6:1:24.4:1:1:0:57.8:1.5:0.75:0:2.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 11361090 . TG T 69 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.06014;SOR=0.09974;LSEQ=CAGAAGAGGGAACTGACCAC;RSEQ=GGGGGAAAAAAAAAAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:3,0:3,6:0.6667:0,2:34.3:1:27:1:1:0:60:2:0.8:0:1.5 0/1:7:1:1,0:6,0:6,1:0.1429:0,0:37:0:32:0:1:0:60:2:0.1667:0:2 +20 11361096 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=AGGGAACTGACCACTGGGGG;RSEQ=AAAAAAAAAAACAGAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,1:8,2:0.2:2,0:30:1:28.5:1:1:0:54.5:4:0.25:0:4 0/0:8:0:0,0:5,0:5,0:0:0,0:29.2:1:17.4:1:1:0:60:0.25:0.3333:0:2 +20 12158670 . G C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.26953;LSEQ=ATTTTAAAGTTTAATATCTT;RSEQ=TTGTTAGGTTTGTATTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:6,1:8,1:9,7:0.4375:2,2:19.9:1:32.4:1:1:1.30929:60:14:0.4375:0:1.1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19:1:29:1:1:0:60:4:0.5:0:1.5 +20 12158734 . C T 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01218;LSEQ=GCACTGAAAAACACAGCTGC;RSEQ=GGAGTCAGATGGGTGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:2,1:22,19:41,3:0.0682:2,2:30:1:28.7:1:1:1.71:60:6:0.0682:0:1.3 0/1:29:2:1,1:15,12:27,2:0.069:2,2:37:1:29.5:1:1:1.24034:60:4:0.069:0:1.5 +20 12335467 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17622;SOR=Inf;LSEQ=AAAAACATTAGAGCACTTTG;RSEQ=AGTCTAAGGAAGTTTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:25,13:38,0:0:2,0:21.4:1:31.4:1:1:0:60:37:1:0:0.2 0/1:28:2:1,1:14,12:26,2:0.0714:2,2:32:1:27:1:1:1.16024:60:4:0.0714:0:1 +20 12335510 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51787;SOR=0;LSEQ=GCCATTCAGTGTTCTTGAGC;RSEQ=AAAGTCTGTCATCAGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:20,19:39,2:0.0488:2,2:36.5:1:33:1:1:1.05134:60:4:0.0488:0:1 0/0:26:0:0,0:10,16:26,0:0:2,0:34.4:1:29.3:1:1:0:60:52:1:0:0.1 +20 15770383 . A G 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.4179;LSEQ=ACACTACATAAAGAAGGAAG;RSEQ=AAACACAAGTGCATAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:136:57,79:78,85:163,136:0.4548:2,2:28.2:1:31.6:1:0.35071:1.27079:60:135:0.453:0:1.2 0/1:333:86:44,42:118,129:247,86:0.2583:2,2:25.8:1:30.4:1:0.61773:1.14:60:85:0.256:0:1.5 +20 15770394 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05266;SOR=0;LSEQ=AGAAGGAAGAAAACACAAGT;RSEQ=CATAAAATTTAAAATGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:4:2,2:123,166:289,4:0.0137:2,2:16.5:1:30:1:1:1.35:60:8:0.0138:0:1 0/0:317:0:0,0:144,173:317,0:0:2,0:25.7:1:31.1:1:1:0:60:104.667:1:0:0.4 +20 15770428 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03696;LSEQ=ATGGCATAAAGGAAATGAGA;RSEQ=TTATATTAGAAATTAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:27:7,20:54,127:181,27:0.1292:2,2:27.8:1:30.8:1:0.82194:1.21378:60:54:0.1337:0:1.8 0/1:210:28:13,15:60,121:181,28:0.1333:2,2:28.3:1:29.6:1:0.20234:1.74:60:56:0.1346:0:2 +20 16141991 . G T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAACCTGAATCACCCAAA;RSEQ=TTCTCCCTGGGACCTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:28.7:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 16142184 . C T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4196;SOR=0.71374;LSEQ=GGTACATAGGTTGCACCACC;RSEQ=TTATTAAGAAGAATCACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:41:41,0:25,0:25,41:0.6212:1,1:22.8:1:32:1:1:0:60:19.5:0.6094:0:1 1/0:39:21:21,0:18,0:18,21:0.5385:1,1:24.9:1:31.5:1:1:0:60:42:0.5385:0:1 +20 16142254 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17416;SOR=Inf;LSEQ=ACAAATCTATGGATTGTCTG;RSEQ=ATGCCTAGAAGGCATTCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:177,81:258,0:0:2,0:24.4:1:31.5:1:1:0:60:128:1:0:0.4 0/1:186:2:1,1:126,58:184,2:0.0108:2,2:12:1:25.5:1:0.53496:2.1625:60:4:0.0108:0:1 +20 16142258 . C T 23 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57004;SOR=2.90912;LSEQ=ATCTATGGATTGTCTGGATG;RSEQ=CTAGAAGGCATTCGATAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:1:0,1:187,89:276,1:0.0036:2,0:1:0:27:0:0.32491:0:60:2:0.0037:0:1 0/1:192:2:0,2:128,62:190,2:0.0104:2,0:6.5:1:23:0:0.10995:0:60:4:0.0105:0:1 +20 16142333 . A C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0839;LSEQ=ATTTTCCTACAGACGACAAC;RSEQ=TCTGAGCAACAGAATAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:464:279:139,140:93,92:185,279:0.6013:2,2:25.7:1:31.9:1:1:1.01811:59.9:54.8:0.6009:0:1.1 0/1:366:41:17,24:160,165:325,41:0.112:2,2:22.4:1:30.1:1:0.40816:1.36781:59.6:82:0.1142:0:1.2 +20 16142702 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTTAGCCAACCTCCCTG;RSEQ=CCCAAACAATAAATTACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:27:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 16911203 . T C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCTGACAGCCACACAGGG;RSEQ=CGTGGAGCCCACATCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:36.7:1:31.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 16911205 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGACAGCCACACAGGGTC;RSEQ=TGGAGCCCACATCCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:34.7:1:30.3:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 16912013 . T G 68 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCAGGAGCGATCCTACTG;RSEQ=CATCGGGTTGGTGCCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:22.8:1:34:1:1:0:52.5:8:1:0:1.3 1/1:3:3:1,2:0,0:0,3:1:0,2:28:1:29.7:1:1:0:56.3:6:1:0:1 +20 16912245 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GCATCAACAACAAAAAAAGT;RSEQ=CCCACAAAACCCCATCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:19.5:1:29.5:1:1:2.44949:48.5:4:0.3333:0:1 0/0:4:0:0,0:3,1:4,0:0:2,0:34.8:1:31.8:1:1:0:56:8:1:0:0.3 +20 16912401 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=ATGTCTCTCCAGGAAGGATG;RSEQ=AGACCTGGATAGAGGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:6,2:0.25:2,2:41.5:1:30:1:1:1.83:60:4:0.25:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:28.6:1:32.6:1:1:0:60:10:1:0:0 +20 16985836 . C T 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.77001;LSEQ=TGCTTCCCTCCAGACTCTAT;RSEQ=TTTATGGAATAGAAACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:15.5:1:29.8:1:1:0:60:8:0.5714:0:1.3 1/0:4:2:0,2:0,2:2,2:0.5:0,0:36.5:1:28.5:1:1:0:60:4:0.5:0:1 +20 16985920 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAACCAATTTATTAATAA;RSEQ=TTATATGTCTTTAACTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:19:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 18465583 . G T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGCGGCTTTTTAGAATT;RSEQ=CAGCTTCATATTTTCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:33.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 18465644 . T A 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTATCCAAGCCAAAAACA;RSEQ=GGGACCCATGGAAAGGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:24.6:1:29.4:1:1:0:60:10:0.7143:0:1.4 1/1:2:2:2,0:0,0:0,2:1:0,0:25:1:28.5:1:1:0:60:4:1:0:1 +20 18465840 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06542;SOR=Inf;LSEQ=CAAAAATTATTTCAAGTATT;RSEQ=AATATACATACATATATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:177,66:243,0:0:2,0:22:1:32:1:1:0:60:59.75:1:0:0.1 0/1:165:3:1,2:115,47:162,3:0.0182:2,2:14:1:26.3:1:0.21063:4.83989:60:6:0.0186:0:1 +20 18465846 . A T 51 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.01363;SOR=Inf;LSEQ=TTATTTCAAGTATTGAATAT;RSEQ=CATACATATATAAGATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:188,91:279,0:0:2,0:22.2:1:28.8:1:1:0:60:558:1:0:0.1 0/1:207:5:1,4:134,68:202,5:0.0242:2,2:10.2:1:22.2:1:0.05068:7.80339:60:4:0.0195:0:1 +20 18465943 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05812;SOR=Inf;LSEQ=CGGAAAGAGGAGAGGCACCC;RSEQ=ATATATGTTCTCTAGGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:122,173:295,0:0:2,0:22.7:1:30.7:1:1:0:56.9:58:0.9932:0:0.2 0/1:288:4:3,1:112,172:284,4:0.0139:2,2:14.3:1:27.3:1:0.30518:4.58:56.5:8:0.0141:0:1 +20 18466063 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49758;SOR=Inf;LSEQ=GGGTACTGTTCAAAAAGGAA;RSEQ=GCCCCACAAGTGTTACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:20,0:0:2,0:4.2:1:29.5:1:1:0:24.5:40:1:0:0.1 0/1:26:2:1,1:15,9:24,2:0.0769:2,2:47:0:31.5:1:1:1.63293:42.5:4:0.0769:0:3.5 +20 18466107 . G A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.50018;SOR=Inf;LSEQ=AAACTGGAAGAGTCTACAGT;RSEQ=TTACCCAGCATGCTGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:39,58:97,0:0:2,0:31.9:1:32:1:1:0:36.9:194:1:0:0.1 0/1:112:2:1,1:42,68:110,2:0.0179:2,2:6.5:1:26.5:1:1:1.61:42.5:4:0.0182:0:3.5 +20 18466346 . G A 60 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=GGCTCAGGCGGGCAGATCAC;RSEQ=AGGTGAAGAGATCGAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:27.8:1:30.3:1:1:0:44.5:8:0.5714:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:39:0:32:0:1:0:26:2:0.5:0:1 +20 19414754 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08425;SOR=Inf;LSEQ=AGGAAATGAAAGACGTGATT;RSEQ=ATACACATCACTGAGCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:55,0:55,0:0:1,0:22.6:1:28.9:1:1:0:60:54:1:0:0.1 0/1:23:2:1,1:21,0:21,2:0.087:1,2:21.5:1:28:1:0.08696:0:60:4:0.087:0:1 +20 19414947 . G A 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCCCCTTTTGATCACTCC;RSEQ=CAGCGAGGGCTTGGGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:144,240:384,0:0:2,0:26:1:31:1:1:0:59.8:47:1:0:0.2 0/1:267:109:45,64:74,84:158,109:0.4082:2,2:24:1:28.7:1:0.38337:1.25185:60:108:0.4091:0:1.1 +20 19414986 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.18071;SOR=Inf;LSEQ=GCTCTCTAGAGAGAAGCAGG;RSEQ=AGCTGAACAAGGTGCGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:56,157:213,0:0:2,0:23.1:1:32.2:1:1:0:59.9:41.6:1:0:0.1 0/1:158:2:1,1:48,108:156,2:0.0127:2,2:10.5:1:25:1:0.52544:2.24:60:4:0.0131:0:1 +20 19506525 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACAGGCGCGGCTGTGC;RSEQ=GTGAGGATTCACATGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:2,0:27,1:28,2:0.0667:1,0:16.5:1:29.5:1:1:0:60:4:0.0667:0:1 0/0:8:0:0,0:8,0:8,0:0:0,0:25.3:1:31.4:1:1:0:60:16:1:0:0.1 +20 19506547 . G A 97 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14993;SOR=0.20446;LSEQ=TGAGGATTCACATGCCTCAC;RSEQ=AGGGTCCTCTGGGAGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:10,0:29,1:30,10:0.25:1,0:25.2:1:29.5:1:1:0:60:9:0.2308:0:1.4 0/1:16:1:1,0:15,0:15,1:0.0625:1,0:33:0:31:0:1:0:60:2:0.0625:0:1 +20 19506609 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54482;SOR=0;LSEQ=ATTCTCCTGGAGTTTCTCCA;RSEQ=TTCTGAACGAACTCGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:81,23:104,2:0.0189:2,2:22:1:32.5:1:0.40323:3.46866:60:4:0.019:0:1 0/0:56:0:0,0:48,8:56,0:0:2,0:22.4:1:31.2:1:1:0:60:112:1:0:0.1 +20 19506623 . C T 24 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27605;SOR=3.81968;LSEQ=TCTCCAGTTCTGAACGAACT;RSEQ=GGAGGTAGGGGAGTGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:1,0:110,38:148,1:0.0067:2,0:6:0:33:0:1:0:60:2:0.0068:0:1 0/1:79:2:1,1:58,19:77,2:0.0253:2,2:7:1:24:1:0.44466:3.00087:60:4:0.0253:0:1 +20 19506644 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14159;SOR=Inf;LSEQ=GGAGGTAGGGGAGTGGGAGA;RSEQ=GATGCCCTGCCTCTCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:149,64:213,0:0:2,0:25.2:1:32.2:1:1:0:60:29.429:1:0:0.3 0/1:129:2:1,1:88,39:127,2:0.0155:2,2:28:0:31.5:1:0.52568:2.24068:60:4:0.0155:0:1.5 +20 19506665 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1626;SOR=Inf;LSEQ=GATGCCCTGCCTCTCATCCA;RSEQ=CTACCCAGCTTTGACACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:174,101:275,0:0:2,0:26.4:1:32.7:1:1:0:60:136.5:1:0:0.4 0/1:187:2:1,1:120,65:185,2:0.0107:2,2:16.5:1:26:1:1:1.8398:60:4:0.0108:0:1 +20 19506666 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16086;SOR=Inf;LSEQ=ATGCCCTGCCTCTCATCCAG;RSEQ=TACCCAGCTTTGACACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:177,103:280,0:0:2,0:26.3:1:32.4:1:1:0:60:55:1:0:0.4 0/1:188:2:1,1:121,65:186,2:0.0106:2,2:31:0:31.5:1:1:1.85507:60:4:0.0107:0:1.5 +20 19506707 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.36204;SOR=1.28075;LSEQ=CCTGGAATGGTCACACCCTC;RSEQ=GCGGGTGTGCTGTGTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:33:14,19:172,156:328,33:0.0914:2,2:22:1:30.7:1:0.28043:1.49466:60:66:0.0922:0:1.8 0/1:289:33:18,15:138,118:256,33:0.1142:2,2:22.3:1:29.2:1:1:1.03:60:32:0.1115:0:1.8 +20 19506729 . A G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63764;SOR=1.07784;LSEQ=CGGGTGTGCTGTGTCACCCC;RSEQ=CTGCCAGTCTCCCCGATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:155:71,84:99,114:213,155:0.4212:2,2:25:1:30.8:1:0.916:1.02736:60:76.5:0.4227:0:1.3 0/1:298:131:69,62:78,88:166,131:0.4396:2,2:27.3:1:29.9:1:0.35132:1.25:60:42.667:0.4414:0:1.3 +20 19506958 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05714;SOR=Inf;LSEQ=TGCAAGCCCTGGCTATGCCA;RSEQ=GTACTGCCTATGTGACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:0,11:11,0:0:0,0:27.2:1:28.7:1:1:0:60:10:1:0:0.2 1/0:4:2:0,2:0,2:2,2:0.5:0,0:39.5:1:32:0:1:0:60:4:0.5:0:1 +20 19601874 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10644;SOR=Inf;LSEQ=CTCTTTGTGCAGCAGTCATG;RSEQ=AGGATGCTTGAGTGGATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:125,2:127,0:0:1,0:25.8:1:32.2:1:1:0:60:62.5:1:0:0 0/1:62:2:2,0:60,0:60,2:0.0323:1,0:32.5:1:31.5:1:1:0:60:4:0.0328:0:1 +20 19602042 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.47947;LSEQ=TCAGAAGTAGATTTGTAGAA;RSEQ=GGTTGTTGGTTGGTTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1229:145:68,77:546,535:1081,145:0.118:2,2:23.8:1:31.2:1:0.42718:1.1555:60:144:0.118:0:1.1 0/1:875:218:114,104:327,330:657,218:0.2491:2,2:24.4:1:29.5:1:0.53252:1.11:60:35.333:0.2448:0:1.3 +20 19602477 . T C 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCTCCACCATTTCTCCT;RSEQ=AGAAATGCTCCTCTTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:17.5:1:28.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 20566463 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTAAAAAGACACAGCTG;RSEQ=CAGTGGGCCTTGAACCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:23,3:26,2:0.0714:2,0:27:1:31:1:1:0:60:4:0.0714:0:1 0/0:11:0:0,0:10,1:11,0:0:2,0:22.1:1:31.4:1:1:0:60:22:1:0:0.1 +20 20566526 . A T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08084;SOR=Inf;LSEQ=AGAGTTAAAAGAAAAAAAAG;RSEQ=ATGCCCCACAAATGTTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:34,29:63,0:0:2,0:26.3:1:30.4:1:1:0:60:126:1:0:0.1 0/1:49:3:2,1:23,21:44,3:0.0612:2,2:31.7:1:26.3:1:1:1.80:60:6:0.0612:0:1 +20 21115991 . G A 43 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATGTTAGGTTCTACCTCT;RSEQ=TTACAGTTACTTGCGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:35.7:1:27.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 21116216 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.509;SOR=0;LSEQ=TTGCAAATCTTTGTTTTGAG;RSEQ=GTGAATATTTTTGTCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:2,0:103,9:112,2:0.0175:2,0:42.5:1:29.5:1:1:0:60:4:0.0175:0:1 0/0:84:0:0,0:68,16:84,0:0:2,0:22.9:1:30.4:1:1:0:60:168:1:0:0.3 +20 21116302 . A G 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.42371;SOR=0.85814;LSEQ=GCCAACAATTGAAATGCTGT;RSEQ=TAACAGGGAAGAAGAGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:449:374:205,169:32,42:74,374:0.833:2,2:28.3:1:32.3:1:0.07507:1.59:60:92.5:0.8315:0:1.1 1/1:417:338:191,147:46,33:79,338:0.8106:2,2:26.7:1:31.2:1:0.80213:1.07267:59.9:66.6:0.8182:0:1.1 +20 21117899 . CT C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTCTCTGGTTCTGGCAC;RSEQ=TTTTCCCCTTGAAGTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:32.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 21177898 . G A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.40061;LSEQ=AGACTCTTATCACTTACTCA;RSEQ=TAGACTGGATATAGATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:61:27,34:157,220:377,61:0.1393:2,2:22.7:1:30.3:1:0.78001:1.11:60:122:0.1422:0:1 0/1:325:91:38,53:112,122:234,91:0.28:2,2:25.5:1:29.7:1:0.38581:1.27944:60:182:0.2844:0:1.1 +20 21377044 . C T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56425;SOR=3.0829;LSEQ=GAGAAGAGCACGCGGCGCTT;RSEQ=CTTCGCGGAGCGGCTGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:0,1:10,151:161,1:0.0062:2,0:39:0:28:0:1:0:60:2:0.0064:0:1 0/1:106:2:1,1:8,95:103,2:0.0189:2,2:14:0:31:1:0.16484:11.25:60:4:0.019:0:2 +20 21377119 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GCGTCCGCGATGCCGGTCAG;RSEQ=GACCCCATGCCGGCCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:22.4:1:31.8:1:1:0:60:10:1:0:0.4 1/0:4:2:0,2:1,1:2,2:0.5:2,0:18.5:1:29:1:1:0:60:4:0.5:0:1 +20 21377205 . G A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGGGGAAGGCGAGTGA;RSEQ=CTCCAGGCCCGCCGGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:14:0:31:0:1:1:60:4:0.5:0:1 +20 21377636 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52569;SOR=0;LSEQ=GGGTTGGCGCCGTACCAGCC;RSEQ=GTGGCCGCGCCGCCCCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:34.5:1:31:1:1:1.55:60:4:0.1429:0:1.5 0/0:8:0:0,0:4,4:8,0:0:2,0:19.3:1:25.8:1:1:0:60:7:1:0:0.3 +20 21492794 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13254;SOR=Inf;LSEQ=CACCCGGCGCGGCGAGGGCA;RSEQ=GGGCGTCACCTCCATACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:251,91:342,0:0:2,0:21.8:1:32:1:1:0:59.9:37:0.9911:0:0.2 0/1:198:2:1,1:137,59:196,2:0.0101:2,2:24.5:1:29:1:0.51531:2.31102:60:4:0.0103:0:1.5 +20 21493012 . TC T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.52758;SOR=1.80625;LSEQ=GCTTTCGCTTCTTGCCGGCG;RSEQ=CCCCCCGCCGCCCGGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:2,78:80,2:0.0244:1,0:45.5:1:30.5:1:1:0:60:4:0.0253:0:0.5 0/1:23:1:0,1:0,22:22,1:0.0435:1,0:35:0:32:0:1:0:60:2:0.0476:0:1 +20 22562674 . T C 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=2.00063;LSEQ=TTGAGGTCCATTTTGTGGGG;RSEQ=TGGTGGTGGTGGTGGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:769:603:371,232:89,69:158,603:0.7841:2,2:23.9:1:31.9:1:0.23638:1.24:59.9:36.688:0.7922:0:1.1 1/1:488:429:255,174:26,20:46,429:0.8791:2,2:24.9:1:30.4:1:0.75312:1.13:60:27.6:0.9099:0:1.2 +20 22562823 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGGGCCCAGCAGGTGGG;RSEQ=CGCGGCCTGCTGCTGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:3,171:174,2:0.0114:1,2:5.5:1:29:1:0.04506:49.50:60:4:0.0119:0:1.5 0/0:85:0:0,0:4,81:85,0:0:1,0:22.2:1:30.9:1:1:0:60:27.333:1:0:0.1 +20 22563356 . G T 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02918;SOR=0;LSEQ=GGCTCTGCTGGATGGCCATG;RSEQ=TGATGAGCGAGATGTACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:8:3,5:245,465:710,8:0.0111:2,2:12.8:1:27.6:1:1:1.14:50:7:0.0099:0:1.8 0/0:424:0:0,0:187,237:424,0:0:2,0:26.6:1:31:1:1:0:55.8:211:1:0:0.2 +20 22563439 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53411;SOR=0;LSEQ=GGGTCGCGGGCGCGGCTCAG;RSEQ=CCCGCCTGCCCGTACATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:38,157:195,2:0.0102:2,2:5:1:29.5:1:0.35756:4.09:60:4:0.0103:0:1 0/0:114:0:0,0:28,86:114,0:0:2,0:20.7:1:30.5:1:1:0:59.9:37:1:0:0.1 +20 22964590 . C T 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10109;SOR=3.07349;LSEQ=ATCAGCTTCAAAGCTACTTT;RSEQ=CCTTTTCCACATTCTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:12:12,0:27,0:27,12:0.3077:1,0:19.3:1:30.6:1:1:0:60:24:0.3158:0:1.2 1/0:12:7:7,0:5,0:5,7:0.5833:0,0:36.9:1:31.4:1:1:0:55:14:0.5833:0:1 +20 22964619 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCTGCTCTGTGGAAGT;RSEQ=CATAAGAGCCGCCCCCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:57,0:57,2:0.0339:1,0:22:1:26:1:1:0:60:4:0.0339:0:1.5 0/0:19:0:0,0:19,0:19,0:0:1,0:22.9:1:31.6:1:1:0:58.2:38:1:0:0.4 +20 22964757 . C G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.41684;LSEQ=AGATGCGTAGATACTTCTCT;RSEQ=TATGTTTGTGAAAACACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:258:154,104:175,104:279,258:0.4787:2,2:25.4:1:31.5:1:0.4795:1.13609:60:22.455:0.4687:0:1.8 0/1:376:104:62,42:154,118:272,104:0.2766:2,2:24.6:1:30.9:1:0.64176:1.13:60:33.667:0.2737:0:1.8 +20 22964799 . T G 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.55089;LSEQ=TCAATTAAAGACAAAAGCCA;RSEQ=CTTGTCCTCTGCTCCCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:717:357:178,179:183,177:360,357:0.4979:2,2:26:1:32.5:1:0.82284:1.03967:60:58.5:0.5007:0:1.6 0/1:487:172:88,84:151,163:314,172:0.3532:2,2:23.9:1:31.2:1:0.5693:1.13:60:33.4:0.3523:0:1.7 +20 22964817 . C A 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=30.61535;LSEQ=CATCTTGTCCTCTGCTCCCC;RSEQ=CTACATCCTTCCTCCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:689:1:1,0:324,363:687,1:0.0015:2,0:1:0:25:0:0.47238:0:60:2:0.0015:0:3 0/1:492:21:10,11:223,248:471,21:0.0427:2,2:23.4:1:27.7:1:1:1.01:60:20:0.0411:0:2 +20 22964937 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.08452;SOR=Inf;LSEQ=ATGTTAGGCAGTCTCTTGGG;RSEQ=GGTCGAAAGGGCCAAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:4,107:111,0:0:1,0:24.6:1:31.6:1:1:0:60:110:1:0:0.4 0/1:46:2:1,1:3,41:44,2:0.0435:2,2:15.5:1:27.5:1:0.16812:11.98:60:4:0.0435:0:1 +20 22964954 . T C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54847;SOR=1.30661;LSEQ=GGGGGGTCGAAAGGGCCAAA;RSEQ=GTGTACTTAGATGTGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:32:0,32:1,54:55,32:0.3678:1,1:23.2:1:30.9:1:1:0:60:64:0.3678:0:1.5 0/1:37:16:2,14:0,21:21,16:0.4324:1,2:21.3:1:27.9:1:0.18018:0:60:15:0.4167:0:1.6 +20 22964982 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41919;SOR=1.62497;LSEQ=TAGATGTGGATTTCACAGAG;RSEQ=GATTAGGTATGTGGATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:19:0,19:0,28:28,19:0.4043:1,1:26.2:1:30.5:1:1:0:60:38:0.4043:0:1.8 1/0:19:10:0,10:0,9:9,10:0.5263:0,0:28.4:1:27.1:1:1:0:60:4:0.4706:0:2.2 +20 23946690 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49826;SOR=0;LSEQ=GGACCCACAAAGGACACTCA;RSEQ=TTGCACGCACATGTGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:22,2:0.0833:2,2:8.5:1:29.5:1:1:1:60:4:0.0909:0:2.5 0/0:18:0:0,0:12,6:18,0:0:2,0:25.9:1:31.6:1:1:0:60:36:1:0:1.1 +20 23946710 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCACGCACATGTGCACA;RSEQ=GCACACACGCAATTAGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:9,12:0,0:0,21:1:0,2:32.6:1:31:1:1:0:60:42:1:0:1.2 1/1:19:19:11,8:0,0:0,19:1:0,2:32.1:1:30.3:1:1:0:60:38:1:0:1.2 +20 25079639 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04743;SOR=Inf;LSEQ=CTGCACTCCAGCCTGGGAGA;RSEQ=AGAGTGAGACTCTGTCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:14,0:0:1,0:16.9:1:33.2:1:1:0:36.4:28:1:0:2.3 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:13.3:1:25:1:1:0:23:2:0.25:0:5.7 +20 25079657 . CA C 125 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.28041;SOR=0.50478;LSEQ=GACAGAGTGAGACTCTGTCT;RSEQ=AAAAAAAAAAAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:15:15,0:20,0:20,15:0.3333:1,1:17.4:1:32.1:1:1:0:50.3:30:0.3333:0.1333:1 0/1:25:5:5,0:8,0:8,5:0.2:0,0:9.8:1:30.6:1:1:0:56:10:0.2:0.12:1.2 +20 25080206 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.0515;SOR=Inf;LSEQ=TAGACTATAATGCCAACTCA;RSEQ=AGACCTTGCGATGTGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:174,280:454,0:0:2,0:23:1:32.3:1:1:0:59.9:40.273:1:0:0.1 0/1:270:3:2,1:100,167:267,3:0.0111:2,2:33.3:1:24:1:0.55894:3.32:60:2:0.0075:0:1 +20 25080375 . A T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02263;SOR=Inf;LSEQ=GCTCTACAATGTTACGATCA;RSEQ=CAACACATACTCCTGTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:0:0,0:299,240:539,0:0:2,0:15.9:1:29.8:1:1:0:36.2:133.75:1:0:0.1 0/1:343:4:1,3:189,150:339,4:0.0117:2,2:14.3:1:25.5:1:0.32779:3.76626:34:8:0.0117:0:1 +20 25519823 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.48846;SOR=0;LSEQ=TGGGACAGCAAAGATAAGGA;RSEQ=TCAGCGAACAGCCATGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:37.5:1:30:1:1:1.11:60:4:0.0952:0:1.5 0/0:19:0:0,0:10,9:19,0:0:2,0:21.9:1:31.3:1:1:0:60:38:1:0:0.2 +20 25560101 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12919;SOR=Inf;LSEQ=AGCCACAACCAGTGCACAAG;RSEQ=CATGCACGGGGACTGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:27,22:49,0:0:2,0:28.3:1:29.4:1:1:0:60:98:1:0:0.2 0/1:28:2:1,1:14,12:26,2:0.0714:2,2:8:0:33.5:1:1:1.16024:60:4:0.0714:0:1.5 +20 25560148 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16553;SOR=Inf;LSEQ=CACGCTACCTTATGGTGAGG;RSEQ=TCACACAGCCCCCACGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:16,26:42,0:0:2,0:27.6:1:32.8:1:1:0:59.7:41:1:0:0.3 0/1:30:2:1,1:14,14:28,2:0.0667:2,2:17:0:31:1:1:1:60:4:0.069:0:1 +20 25733062 . T G 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31484;SOR=0;LSEQ=CTTTAACCATACCCAAAGTC;RSEQ=ATTTTTATTTCTTGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:6:6,0:31,1:32,6:0.1579:1,0:13.8:1:26.2:1:1:0:54.8:5:0.1351:0:1 0/0:11:0:0,0:10,1:11,0:0:2,0:30.2:1:30.9:1:1:0:59.5:22:1:0:0 +20 25733278 . C T 62 d5;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TGGAGATGATCAAAATGCTT;RSEQ=ACCTTCAAAACTTTCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:11:0:31.3:1:1:0:35.5:8:1:0:5 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:11:0:30.5:1:1:0:37:4:0.6667:0:5 +20 25733297 . G C 65 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=TCACCTTCAAAACTTTCAAA;RSEQ=GAAGAGTTAATACAGAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:30:0:32.8:1:1:0:35.5:8:1:0:5 0/0:3:0:0,0:1,0:1,0:0:0,0:45:0:33:0:1:0:20:2:0.3333:0:1 +20 25733312 . G A 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=TCAAAGGAAGAGTTAATACA;RSEQ=AGTATGGATCGTGTAGATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:19,9:0,0:0,28:1:0,2:10.3:1:31.1:1:1:0:27.9:56:1:0:3.3 1/1:27:25:17,8:1,1:2,25:0.9259:2,2:8.9:1:29.5:1:1:2.06:28.2:50:0.9259:0:3.2 +20 25733328 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2226;SOR=Inf;LSEQ=TACAGAGTATGGATCGTGTA;RSEQ=ATCGAGAAATTGCAAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:46,43:89,0:0:2,0:11:1:32.2:1:1:0:26.2:178:1:0:2 0/1:80:2:1,1:43,35:78,2:0.025:2,2:11:0:30.5:1:1:1.22539:30:4:0.0253:0:1 +20 25733331 . C T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23332;SOR=1.47921;LSEQ=AGAGTATGGATCGTGTAGAT;RSEQ=GAGAAATTGCAAAAGTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:62:33,29:17,24:41,62:0.6019:2,2:16.3:1:30.9:1:0.3144:1.60:28.4:124:0.6019:0:2.9 1/0:94:65:37,28:13,16:29,65:0.6915:2,2:15.5:1:29.3:1:0.37115:1.62:28.7:130:0.6915:0:2.9 +20 25733334 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01079;SOR=1.94783;LSEQ=GTATGGATCGTGTAGATCGA;RSEQ=AAATTGCAAAAGTAGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:63:33,30:22,44:66,63:0.4809:2,2:18.7:1:31:1:0.03362:2.19:28.3:126:0.4809:0:2.9 1/0:118:76:42,34:17,25:42,76:0.6441:2,2:16:1:29.7:1:0.17802:1.81:28.1:75:0.6522:0:2.8 +20 25733412 . A G 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.05143;SOR=3.52;LSEQ=TTGCCTAATATATTCTAAGA;RSEQ=TGTATTTTTTTCTCCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:1,2:62,192:254,3:0.0117:2,2:8.7:1:32:1:0.5715:1.55:28.7:6:0.0118:0:3.7 0/1:250:10:4,6:86,153:239,10:0.04:2,2:9:1:32.9:1:0.75087:1.19:28.6:20:0.0403:0:2.7 +20 25733418 . T G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1e-05;SOR=2.98606;LSEQ=AATATATTCTAAGAATGTAT;RSEQ=TTTTTCTCCCTACCGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:26:9,17:44,171:215,26:0.1079:2,2:8.3:1:32.3:1:0.13002:2.05:26.1:52:0.1083:0:2.6 0/1:222:59:20,39:53,110:163,59:0.2658:2,2:7.2:1:31:1:0.87232:1.06:26.3:28.5:0.2591:0:2.3 +20 26084101 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17021;SOR=Inf;LSEQ=AGAAAAACATACATTCTTAG;RSEQ=ATATATTAGACGAAGACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:124,49:173,0:0:2,0:30.7:1:30.6:1:1:0:29:85.5:1:0:0.1 0/1:122:2:1,1:84,36:120,2:0.0164:2,2:13.5:1:26.5:1:0.51633:2.31527:21:4:0.0164:0:1 +20 26084127 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51362;SOR=0;LSEQ=TTAGACGAAGACTTTTACTT;RSEQ=TTTCTTTTTCAGTTTAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:136,58:194,2:0.0102:2,2:46:0:31.5:1:0.51251:2.33343:22:4:0.0103:0:1 0/0:138:0:0,0:93,45:138,0:0:2,0:32.6:1:31.4:1:1:0:27.1:137:1:0:0.1 +20 26084377 . A C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15409;SOR=2.14546;LSEQ=CCAGATTGCCTTAAATGAAA;RSEQ=AGTCAGTTTTAAACCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:33:1,32:1,24:25,33:0.569:1,1:23.5:1:31.2:1:1:1.32664:23.6:32:0.5614:0:2.8 1/0:27:20:2,18:1,6:7,20:0.7407:2,2:19.5:1:28.9:1:1:1.47595:24.4:40:0.7407:0:3 +20 26084383 . GT G 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.09106;SOR=0;LSEQ=TGCCTTAAATGAAAAAGTCA;RSEQ=TTTAAACCACAGCAGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:6:0,6:1,58:59,6:0.0923:1,0:39.5:1:32.3:1:1:0:28.5:12:0.0938:0:0 0/0:34:0:0,0:2,32:34,0:0:2,0:20.7:1:27.4:1:1:0:26.4:68:1:0:2.2 +20 26084411 . C A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1668;SOR=1.81861;LSEQ=CCACAGCAGAGCCATGTGTA;RSEQ=TATGTGTCTAATGAAACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:89:56:1,55:0,33:33,56:0.6292:1,1:30.1:1:30.7:1:1:0:25.1:27:0.6207:0:2.7 1/0:41:31:2,29:0,10:10,31:0.7561:0,2:35.3:1:29.4:1:1:0:25.2:62:0.7561:0:2.8 +20 26084435 . T C 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16624;SOR=1.81127;LSEQ=GTGTCTAATGAAACCTTTAG;RSEQ=AGTAACTTTCATATTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:79:48:1,47:0,31:31,48:0.6076:1,1:33.6:1:33.1:1:1:0:25.8:96:0.6076:0:2.8 1/0:42:31:2,29:0,11:11,31:0.7381:0,2:31.9:1:31.6:1:1:0:24.8:30:0.7317:0:2.8 +20 26084497 . C A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6169;SOR=2.88746;LSEQ=TTTTATAGTTTAGATATACC;RSEQ=TGTACTATTTTGAAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:0,12:0,9:9,12:0.5714:0,0:6.4:1:32.1:1:1:0:25.8:24:0.5714:0:3.1 1/1:5:4:0,4:0,1:1,4:0.8:0,0:14.5:1:31.8:1:1:0:22:8:0.8:0:3 +20 26084507 . T C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51648;SOR=3.98567;LSEQ=TAGATATACCCTGTACTATT;RSEQ=TGAAGAGCCTAAAAGCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:4.5:1:33:1:1:0:21:4:0.1818:0:3.5 1/0:4:2:0,2:0,2:2,2:0.5:0,0:6:1:32.5:1:1:0:21.5:4:0.5:0:3.5 +20 26094476 . CAAAAAACAT AAAAAAC 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=1.84197;LSEQ=AGGAAAAGTAAAGAAAAACA;RSEQ=GTGCAATTTGCATAGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:452:134:114,20:229,87:316,134:0.2965:2,2:26.5:1:31.8:1:0.00368:2.16:22.2:268:0.2991:0:0.2 0/1:382:167:136,31:143,72:215,167:0.4372:2,2:27.1:1:30.8:1:0.00113:2.20:22.2:334:0.4395:0:0.4 +20 26094501 . T C 176 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.95375;LSEQ=AACATGTGCAATTTGCATAG;RSEQ=ATTTGTTCCTTACCTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:4:3,1:351,118:469,4:0.0085:2,2:45.8:1:33:1:1:1.01:21:8:0.0085:0:1 0/1:397:45:36,9:245,107:352,45:0.1134:2,2:45.1:1:32.1:1:0.16689:1.74:22.4:90:0.1139:0:1 +20 26094564 . T G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08547;SOR=1.43096;LSEQ=ACTTTACAGAGTGAGGAGGA;RSEQ=AATGACTTTGTTCTGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:93:47,46:93,55:148,93:0.3859:2,2:32.8:1:32.8:1:0.0623:1.65146:27.6:92:0.3915:0:3.6 0/1:171:81:47,34:52,38:90,81:0.4737:2,2:30:1:31.8:1:1:1.01:25.7:162:0.4737:0:3.6 +20 26094567 . T C 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13398;SOR=1.38479;LSEQ=TTACAGAGTGAGGAGGATAA;RSEQ=GACTTTGTTCTGTGCTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:84:38,46:79,47:126,84:0.4:2,2:38.6:1:31.5:1:0.01588:2.02767:28.4:83:0.3971:0:3.9 0/1:152:73:39,34:44,34:78,73:0.4803:2,2:35.4:1:31.3:1:0.74539:1.1273:26.3:146:0.4803:0:3.8 +20 26094605 . G A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00982;SOR=2.36069;LSEQ=AATGCTCCTTGGTTGGGAGG;RSEQ=TAACCTGAACTTGACATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:125:75:34,41:18,32:50,75:0.6:2,2:14.2:1:31.1:1:0.35599:1.47:26.9:74:0.6066:0:4.1 1/0:82:64:35,29:4,14:18,64:0.7805:2,2:12.4:1:28.9:1:0.01752:4.15:25.9:63:0.7778:0:4.1 +20 26094609 . C A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00654;SOR=2.38718;LSEQ=CTCCTTGGTTGGGAGGGTAA;RSEQ=CTGAACTTGACATTATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:123:73:33,40:18,32:50,73:0.5935:2,2:10.5:1:30.1:1:0.35426:1.46:26.1:35.5:0.5917:0:4.1 1/0:81:63:35,28:4,14:18,63:0.7778:2,2:8.6:1:28.4:1:0.01619:4.30:25.8:62:0.7848:0:4.1 +20 30253628 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53894;SOR=0;LSEQ=GGACCAGATCTGGGCCCAAC;RSEQ=CTGTGATGGGCAGGTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:123,5:128,2:0.0154:1,2:23:1:28:1:0.09052:22.54813:60:4:0.0157:0:1 0/0:72:0:0,0:69,3:72,0:0:1,0:22.4:1:30.9:1:1:0:60:71:1:0:0.1 +20 30253937 . T G 27 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16514;SOR=Inf;LSEQ=TTTTAGTCCTCAGAGAGTGA;RSEQ=GTAGGTGGGTGGGGAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:45,169:214,0:0:2,0:23.1:1:30.2:1:1:0:60:34.667:1:0:0.2 0/1:147:2:1,1:25,120:145,2:0.0136:2,2:5:0:27.5:1:0.32346:4.73:60:4:0.0137:0:0.5 +20 30254264 . A G 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATGATGGTGCAGGGGTG;RSEQ=GCAAGAGCCAGACCATACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:35:1:31.5:1:1:1.73:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 30254773 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGACGCTTAGAACATAAC;RSEQ=TTTATGAGTAAGCGTAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:29.5:1:1:0:60:4:1:0:1.5 +20 30263317 . G T 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04165;SOR=0.49797;LSEQ=CGGAGACTCGGAAGAAGTGA;RSEQ=GTTTGTGGTTGGAATCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:60:59,1:64,0:64,60:0.4839:1,1:23.4:1:32.1:1:0.48387:0:60:120:0.4878:0:1.1 0/1:63:20:20,0:43,0:43,20:0.3175:1,1:21.2:1:31.7:1:1:0:60:40:0.3175:0:1.1 +20 30263418 . T C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33483;LSEQ=TCCTCTCCCCCACGGAAACA;RSEQ=AGGCCTGGAGGTGGGCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:313:232,81:268,86:354,313:0.4679:2,2:22:1:31.9:1:0.65507:1.08787:60:312:0.472:0:1.1 0/1:550:125:87,38:305,117:422,125:0.2273:2,2:23.2:1:31.5:1:0.57314:1.13834:60:124:0.2279:0:1.1 +20 30263528 . G A 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=24.80359;LSEQ=GTCCAGCCGGCCCAGGTATG;RSEQ=GTGGGTGCCACAGCAAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1573:2:1,1:725,844:1569,2:0.0013:2,2:6.5:1:21.5:1:1:1.16:60:1:6e-04:0:2.5 0/1:1404:43:21,22:645,712:1357,43:0.0306:2,2:26.6:1:29.1:1:0.87806:1.05:60:86:0.031:0:1.2 +20 30281755 . T TA 63 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.87218;LSEQ=GTATTTATGATAAATTTCTT;RSEQ=AAAAAAAAAAAGTGTACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:12,1:13,5:0.2778:1,0:20.4:1:27.2:1:1:0:60:10:0.2778:0.0556:0.2 0/1:4:1:1,0:3,0:3,1:0.25:0,0:15:0:27:0:1:0:60:2:0.25:0:1 +20 30281959 . A AG 73 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0891;SOR=6.79417;LSEQ=GCCCAGGAACTGGCACCTGT;RSEQ=GGGGGGGCTTCTGGACAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:1:1,0:382,167:549,1:0.0018:2,0:42:0:33:0:1:0:60:2:0.0018:0:1 0/1:409:5:3,2:261,141:402,5:0.0122:2,2:20.8:1:31.5:1:1:1.23337:60:10:0.0123:0.0073:0.2 +20 30282223 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00402;SOR=0.39501;LSEQ=TGAGAATGAGATTAGGTTTC;RSEQ=TGGGAAGGGCTCATCTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:65:0,65:3,68:71,65:0.4779:1,1:24.1:1:33:1:0.24592:0:60:31.5:0.4701:0:1.1 0/1:68:18:1,17:1,49:50,18:0.2647:1,1:19.7:1:30.4:1:0.46225:2.83:60:36:0.2687:0:1.3 +20 30282238 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTTTCTTGGGAAGGGCTCAT;RSEQ=TATCTAATGCTCCCCGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:1,101:102,2:0.0192:1,2:28.5:1:30.5:1:0.03827:71.89:60:4:0.0196:0:1 0/0:43:0:0,0:0,43:43,0:0:1,0:20.8:1:31.2:1:1:0:60:42:1:0:0.3 +20 30282922 . A T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCAGTTGGTCCAACCTTC;RSEQ=AATTGTATTGAAGCTCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:27:1:1:0:60:4:1:0:1 +20 30296095 . A C 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGCACACACAAGGGAAG;RSEQ=AGCAGCAGCCTTACTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:42.5:1:31.5:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 30296396 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15091;SOR=Inf;LSEQ=CCCACCCTCCCTGAAATCTG;RSEQ=ACCTGCTCCCAAACTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:198,9:207,0:0:1,0:24.1:1:32.6:1:1:0:59.8:68:1:0:0.7 0/1:132:2:2,0:118,12:130,2:0.0152:2,0:23.5:1:29:1:1:0:60:4:0.0153:0:1.5 +20 30296422 . C T 216 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCCAAACTGACCCCTCCC;RSEQ=CCAGCTGAGCCCAGCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:118:97,21:188,32:220,118:0.3471:2,2:23.9:1:31.5:1:0.43676:1.27095:60:117:0.3514:0:1.1 0/0:248:0:0,0:200,48:248,0:0:2,0:22.7:1:30.4:1:1:0:60:247:1:0:0.1 +20 30296428 . T C 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACTGACCCCTCCCCCCAGC;RSEQ=GAGCCCAGCTGTCAACGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:78:63,15:251,57:308,78:0.2021:2,2:22.8:1:30.5:1:0.87164:1.04833:60:25:0.1979:0:1.2 0/0:267:0:0,0:210,57:267,0:0:2,0:23.5:1:29.9:1:1:0:60:52.4:1:0:0.1 +20 30296664 . G C 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05439;SOR=0;LSEQ=CTGGCATTGTCACTGCAGGT;RSEQ=GCAGGAGACAGGTGATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:8:1,7:16,199:215,8:0.0359:2,2:22.6:1:29.5:1:0.47532:1.77:60:16:0.0369:0:1 0/0:121:0:0,0:9,112:121,0:0:2,0:22.2:1:30.9:1:1:0:60:242:1:0:0.1 +20 30309261 . TG T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22121;SOR=0.5062;LSEQ=TGACCAGGGTGAAAGATGCC;RSEQ=ATCTCTGAAGCACAGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:35:35,0:41,3:44,35:0.443:2,1:23.8:1:31.8:1:0.25024:0:60:34:0.4416:0.0506:0.2 0/1:21:6:6,0:14,1:15,6:0.2857:1,0:24.2:1:30.9:1:1:0:60:12:0.3158:0.0952:0 +20 30309960 . C G 160 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAAACTGACTCCAGCTGTAT;RSEQ=CTTTCTGGGAAAGCTTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:29:7,22:232,409:641,29:0.0433:2,2:26.9:1:33:1:0.23537:1.78134:60:58:0.0438:0:1.1 0/0:574:0:0,0:238,336:574,0:0:2,0:24.9:1:30.2:1:1:0:60:70.75:1:0:0.1 +20 30310051 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15017;SOR=Inf;LSEQ=AGGGATGGGCTCAACCAGTC;RSEQ=ATTGTCCAAAACACCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:24,137:161,0:0:2,0:24.1:1:31.9:1:1:0:60:31.2:1:0:0.1 0/1:103:2:1,1:23,78:101,2:0.0194:2,2:36:1:28.5:1:0.41348:3.34:60:4:0.0196:0:1.5 +20 30310158 . G GA 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAGAGAAAGAGCTTCAG;RSEQ=AAAAAAAAATAATTAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:1,37:38,2:0.05:1,0:40:1:31.5:1:1:0:60:4:0.05:0:0 0/0:14:0:0,0:0,14:14,0:0:1,0:18.9:1:30.9:1:1:0:60:28:1:0:0.1 +20 30433033 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0348;SOR=Inf;LSEQ=GCGGCGGCGTAGGAAGCTGC;RSEQ=GTGCTCAAACATGTCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:82,17:99,0:0:2,0:21.5:1:31:1:1:0:60:98:1:0:0.1 0/1:49:3:3,0:40,6:46,3:0.0612:2,0:14.7:1:30.3:1:1:0:60:6:0.0612:0:1 +20 30433139 . G A 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCACTCGTTGAGTGACAG;RSEQ=TTGTGGCGGATGCTGTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:114,134:248,0:0:2,0:28.3:1:31.7:1:1:0:59.8:81.667:1:0:0.2 0/1:168:14:5,9:69,84:153,14:0.0833:2,2:26.4:1:29:1:0.58222:1.4752:60:28:0.0843:0:1 +20 30433175 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18407;SOR=Inf;LSEQ=TTCTGCCAGCCGGGCCGGTT;RSEQ=TGGCGGTAGAAGGCGAATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:58,117:175,0:0:2,0:24.1:1:31.9:1:1:0:60:57.333:1:0:0.2 0/1:132:2:1,1:44,86:130,2:0.0152:2,2:36:1:28.5:1:1:1.94:60:4:0.0152:0:1.5 +20 30433352 . C T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GGCTGCTGCTGCATGCTGGC;RSEQ=GGGCTGCCAGGCTGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:0,2:2,4:0.6667:0,2:29.8:1:30.8:1:1:0:60:8:0.6667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:10:0:1:0:60:0:0:0:0 +20 30434084 . GAC G 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACACACACAGAAACACAGA;RSEQ=ACAGACACAGACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:29:1:1:0:60:4:1:0:0 +20 30672279 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18542;SOR=Inf;LSEQ=TGGGAGAAAGATGCCTGGGA;RSEQ=ATCCCTCGGGAATCCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:27,12:39,0:0:2,0:20.2:1:32.9:1:1:0:60:78:1:0:0.2 0/1:30:2:1,1:20,8:28,2:0.0667:2,2:5:1:28.5:1:0.51724:2.41524:60:4:0.0667:0:1 +20 30672319 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15745;SOR=Inf;LSEQ=AGCTGGAGAAGAAACTTGGA;RSEQ=CTGGGCAGTTTGGGGAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:28,29:57,0:0:2,0:32.5:1:32.3:1:1:0:60:56:1:0:0.2 0/1:38:2:1,1:20,16:36,2:0.0526:2,2:20:1:26.5:1:1:1.24262:60:4:0.0541:0:1 +20 30946526 . C T 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.06257;SOR=Inf;LSEQ=GCCCCGCGCCACCGCCCCAG;RSEQ=CCGCCCAGCCCGGAGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:121,43:164,0:0:2,0:14.8:1:32:1:1:0:60:26.333:1:0:0.2 0/1:183:5:1,4:126,52:178,5:0.0273:2,2:9.2:1:24.4:1:0.03118:9.5626:60:10:0.0276:0:1.2 +20 30946542 . G T 51 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12461;SOR=Inf;LSEQ=CCAGCCCGCCCAGCCCGGAG;RSEQ=TCCCGCGTGGAGCTGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:224,107:331,0:0:2,0:19:1:31.8:1:1:0:59.9:65.2:1:0:0.2 0/1:352:4:1,3:226,122:348,4:0.0114:2,2:5.8:1:25.5:1:0.13012:5.52968:60:8:0.0115:0:1 +20 30946563 . G A 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.03228;SOR=Inf;LSEQ=TCCCGCGTGGAGCTGCCGCC;RSEQ=CCGCCGGGGAGAAGGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:506:0:0,0:300,204:504,0:0:2,0:26.3:1:30.9:1:1:0:59.9:62:1:0:0.2 0/1:566:6:3,3:334,224:558,6:0.0106:2,2:30:1:28:1:0.6889:1.48995:60:12:0.0108:0:1 +20 30946591 . CAGA C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.3715;SOR=1.48028;LSEQ=GGAGAAGGATGAAGGACAAA;RSEQ=AGAAGAAGAAGGAGCGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:784:12:7,5:409,361:770,12:0.0153:2,2:31.9:1:32.2:1:0.77825:1.24:60:24:0.0157:0:0.2 0/1:889:20:10,10:456,412:868,20:0.0225:2,2:17.7:1:30.8:1:0.82555:1.10667:59.3:40:0.023:0.009:0.5 +20 30946676 . TG T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49937;SOR=0;LSEQ=GGGCTCCGTGGGGCCCGGGG;RSEQ=GGGGGGGCTCGCCGCGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:49,131:180,2:0.0109:2,2:25:0:33.5:1:0.47508:2.66:60:4:0.0109:0:0.5 0/0:170:0:0,0:44,126:170,0:0:2,0:16.1:1:30.6:1:1:0:60:84:1:0:0.4 +20 30946683 . G A 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.42489;SOR=2.28355;LSEQ=GTGGGGCCCGGGGTGGGGGG;RSEQ=GCTCGCCGCGCACCCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:2,0:35,106:141,2:0.0139:2,0:1:0:25:1:0.0656:0:60:4:0.0142:0:1 0/1:128:4:3,1:26,98:124,4:0.0313:2,2:21.5:1:26.8:1:0.03614:11.03:58.8:8:0.0323:0:1 +20 30946705 . T TG 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.632;LSEQ=CTCGCCGCGCACCCCCCCAC;RSEQ=GGGGGGGGAGGGGCAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:0,2:8,36:44,2:0.0435:2,0:8:1:31.7:1:1:0:60:4:0.0465:0.0217:0.5 0/1:36:1:0,1:8,27:35,1:0.0278:2,0:18:0:27:0:1:0:60:2:0.0278:0:5 +20 30946712 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.18995;SOR=Inf;LSEQ=CGCACCCCCCCACTGGGGGG;RSEQ=GAGGGGCAAGGCCCTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:5,28:33,0:0:2,0:18.5:1:31.9:1:1:0:60:66:1:0:0.8 0/1:26:2:1,1:3,21:24,2:0.0769:2,2:21:1:29:1:0.28923:6.21:60:4:0.0769:0:1.5 +20 30946846 . G GC 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTCCGCTCGCCCTCGC;RSEQ=CCCCCCCCGCCCCGCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43:0:33:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 30954295 . A G 237 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTGTTCTTGTTGCTTAAC;RSEQ=TGAGGGTTTCATAGGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:674:0:0,0:238,436:674,0:0:2,0:25.3:1:30.9:1:1:0:60:133.8:1:0:0.1 0/1:600:204:74,130:145,251:396,204:0.34:2,2:26.2:1:30.9:1:1:1.01484:59.9:408:0.3429:0:1.1 +20 30955332 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTTTAGGGTCAAAAGGC;RSEQ=TTCACTTTCCAGTTGTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:39,1:40,2:0.0476:1,0:20.5:1:32.5:1:1:0:60:4:0.0476:0:1 0/0:12:0:0,0:12,0:12,0:0:0,0:29.4:1:31.2:1:1:0:60:24:1:0:0 +20 30956937 . T C 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACGCTCAAGGTAAGTGATA;RSEQ=GAACTCTCTTTTGGTGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:906:0:0,0:365,541:906,0:0:2,0:25.8:1:30.6:1:1:0:59.9:44.3:1:0:0.1 0/1:801:31:13,18:317,450:767,31:0.0387:2,2:22.7:1:30.8:1:1:1.03:60:62:0.0389:0:1.2 +20 30956978 . G A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03031;SOR=Inf;LSEQ=GATTCTTGGACTTTTAATGT;RSEQ=CATAAAAATCACCTGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:130,407:537,0:0:2,0:22.9:1:31.7:1:1:0:59.9:47.818:1:0:0.1 0/1:386:4:2,2:91,291:382,4:0.0104:2,2:17.5:1:25.5:1:0.24591:3.19:60:8:0.0105:0:1.8 +20 30959704 . A G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07656;SOR=9.1772;LSEQ=GCAACCATACCTGGCCCTCT;RSEQ=TTATCTCATATATAGCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:14,4:0.2222:1,0:13.3:1:32.5:1:1:0:60:8:0.2222:0:1 1/0:4:3:3,0:1,0:1,3:0.75:0,0:25.3:1:33.3:1:1:0:60:6:0.75:0:1 +20 30959782 . A G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00351;SOR=Inf;LSEQ=TTAATACATATATGTTTATT;RSEQ=CAAATATGCCTGTTAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:108,1:109,0:0:1,0:24:1:28.6:1:1:0:59.9:26.25:1:0:0.1 0/1:54:5:5,0:49,0:49,5:0.0926:1,0:14:1:32.8:1:1:0:60:10:0.0926:0:1 +20 31015838 . C T 31 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55422;SOR=3.52677;LSEQ=CTTGTCAGTATTCTAAATCC;RSEQ=TCTTTTTCAAAAGCATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:0,1:85,4:89,1:0.0111:1,0:2:0:28:0:0.05556:0:60:2:0.0112:0:1 0/1:52:2:2,0:47,3:50,2:0.0385:2,0:6.5:1:31:1:1:0:60:4:0.0392:0:1 +20 31016119 . C T 235 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=0.01054;LSEQ=GGACTAACCTTTATTTTCCT;RSEQ=TCTTCCAGTATCTCTTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1680:206:109,97:720,754:1474,206:0.1226:2,2:24.4:1:30.7:1:0.29777:1.18:60:205:0.123:0:1.1 0/0:1361:2:1,1:708,651:1359,2:0.0015:2,2:3.5:1:27.5:1:1:1.08748:60:4:0.0015:0:1 +20 31016287 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51823;SOR=0;LSEQ=ACAGGTATAAGGCAAGATCC;RSEQ=TCCTTCTCCTGTAGTGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:7,181:188,2:0.0105:1,2:37.5:1:32:1:0.08265:24.25:60:4:0.0106:0:2 0/0:127:0:0,0:9,118:127,0:0:2,0:23:1:31.4:1:1:0:60:62.5:1:0:0.3 +20 31016291 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52063;SOR=0;LSEQ=GTATAAGGCAAGATCCCTCC;RSEQ=TCTCCTGTAGTGAGCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:6,164:170,2:0.0116:1,2:33.5:1:33:0:0.07997:25.38:60:4:0.0118:0:2 0/0:112:0:0,0:8,104:112,0:0:2,0:23.8:1:28.7:1:1:0:60:15:1:0:0.3 +20 31016314 . A G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTGTAGTGAGCTGTGAAC;RSEQ=TGTTCAGAGAGTGAAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:0,108:108,0:0:1,0:22:1:31.6:1:1:0:59.8:107:1:0:0.1 0/1:62:25:0,25:1,36:37,25:0.4032:1,1:24.2:1:31.8:1:1:0:60:50:0.4032:0:1.1 +20 31017119 . T C 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGTTGACTTGGGCTCTCT;RSEQ=TTGTTCTCTCTTGGAACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:691:0:0,0:451,240:691,0:0:2,0:24.6:1:30.6:1:1:0:60:85.375:1:0:0.1 0/1:571:19:13,6:335,217:552,19:0.0333:2,2:32.8:1:31.1:1:0.63458:1.40:60:38:0.0336:0:1.1 +20 31017650 . A T 43 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16577;SOR=5.72837;LSEQ=GAGAAATGAGCTTGTCTGAG;RSEQ=GCCATGGGCGCGGCTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:1:0,1:285,157:442,1:0.0023:2,0:1:0:27:0:0.35666:0:60:2:0.0023:0:2 0/1:312:4:0,4:191,117:308,4:0.0128:2,0:6.8:1:21.5:1:0.02194:0:60:3:0.0097:0:1 +20 31017651 . G T 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24123;SOR=2.8164;LSEQ=AGAAATGAGCTTGTCTGAGA;RSEQ=CCATGGGCGCGGCTTGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:2:1,1:288,159:447,2:0.0045:2,2:18.5:1:28:1:1:1.80868:60:4:0.0046:0:1 0/1:321:4:1,3:196,121:317,4:0.0125:2,2:11.8:1:25.3:1:0.3025:4.83589:60:8:0.0126:0:1 +20 31019024 . C T 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGATTGTGTGCAGATAACT;RSEQ=CTGGGTAGCTTGGGTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:54:53,1:135,3:138,54:0.2813:1,1:26.1:1:31.2:1:1:1.18:59.3:53:0.2789:0:1.1 1/1:86:86:86,0:0,0:0,86:1:0,1:24.4:1:30.3:1:1:0:60:85:1:0:1.2 +20 31019299 . C T 185 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03248;LSEQ=GACAGACAGGTGCACATGGG;RSEQ=AGCCTCCCCTTTGCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:900:82:29,53:332,486:818,82:0.0911:2,2:27.8:1:29.1:1:0.40859:1.24817:60:164:0.0927:0:1.1 0/0:617:2:1,1:252,362:614,2:0.0032:2,2:37:1:27.5:1:1:1.44:60:4:0.0033:0:1 +20 31019509 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08448;SOR=Inf;LSEQ=AGACTTGGTCATCTCGGACG;RSEQ=CTTGCGACGCACCTGTCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:62,235:297,0:0:2,0:22.8:1:32:1:1:0:59.8:41.429:0.9966:0:0.1 0/1:234:3:2,1:63,168:231,3:0.0128:2,2:28:1:26:1:0.18746:5.29:60:6:0.0132:0:1 +20 31020649 . A T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07704;SOR=Inf;LSEQ=GACAGACATTAATATCCCGA;RSEQ=TGCACTTACTAGAAGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:281,93:374,0:0:2,0:23.9:1:30.4:1:1:0:59.9:186:1:0:0.1 0/1:278:3:1,2:190,85:275,3:0.0108:2,2:12.7:1:21.3:1:0.23164:4.4438:60:2:0.0074:0:1 +20 31021743 . G A 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01073;LSEQ=AGGAGACTGTTTGATTCCTG;RSEQ=CTGCCCTGGAGCCAGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:2,1:62,173:235,3:0.0126:2,2:16.7:1:28:1:0.17689:5.53:60:6:0.0132:0:1 0/1:157:2:2,0:45,110:155,2:0.0127:2,0:1:0:22.5:1:0.08827:0:60:4:0.0128:0:1 +20 31021769 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14005;SOR=Inf;LSEQ=CTGGAGCCAGGTTTTCTTTG;RSEQ=GGGTCATGAGATTATAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:29,124:153,0:0:2,0:24.5:1:31:1:1:0:60:18.125:1:0:0.1 0/1:92:2:1,1:14,76:90,2:0.0217:2,2:29:1:29.5:1:0.301:5.28:60:4:0.022:0:1 +20 31022186 . G T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01808;SOR=Inf;LSEQ=TTTTGCTTTACAGTCCCTAG;RSEQ=TCAGATCACCCAGTCAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:0:0,0:423,152:575,0:0:2,0:25.9:1:31.5:1:1:0:60:62.889:1:0:0.1 0/1:469:5:1,4:332,132:464,5:0.0107:2,2:8:1:26.4:1:0.02647:10.00621:60:10:0.0109:0:1.2 +20 31022441 . AG A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05413;SOR=2.29662;LSEQ=GCGGCCACCACTGCCATCGG;RSEQ=GGGGGGGTGGCCCGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:10:5,5:234,216:450,10:0.0217:2,2:29.9:1:33.4:1:1:1.08313:60:20:0.0222:0.0022:0 0/1:288:14:7,7:131,141:272,14:0.0486:2,2:29.9:1:31.5:1:1:1.08:60:28:0.0493:0.0035:0.3 +20 31022495 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04955;SOR=Inf;LSEQ=GCCACCGATGAGGGAGGTGG;RSEQ=AGAGGCAGCAGCAGTGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:0:0,0:338,165:503,0:0:2,0:23.9:1:32.1:1:1:0:59.9:44.727:1:0:0.1 0/1:293:3:2,1:196,94:290,3:0.0102:2,2:8:1:25.3:1:1:1.0424:60:6:0.0103:0:1 +20 31022766 . G A 136 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=39.10582;LSEQ=GAGATGCCTCCCAACTCCCC;RSEQ=TTGCTCCCACTGGGGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:703:1:1,0:341,358:699,1:0.0014:2,0:1:0:26:0:0.48857:0:60:2:0.0014:0:1 0/1:416:22:12,10:197,196:393,22:0.0529:2,2:26.1:1:30.6:1:0.82728:1.19:60:44:0.0541:0:1.2 +20 31022959 . T C 307 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00374;SOR=0.08267;LSEQ=TGCAGACAATGGTCCCATTC;RSEQ=GTCTCTAGTGGGAGATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1094:1093:605,488:0,1:1,1093:0.9991:0,2:24.6:1:30.5:1:0.44698:0:60:67.313:1:0:1.1 1/1:730:722:384,338:1,3:4,722:0.989:2,2:23.4:1:29.7:1:0.34641:3.40:60:119.333:0.9931:0:1.1 +20 31024274 . T C 247 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=533.52683;LSEQ=CGTGCTATGTCACAGGACAG;RSEQ=AATTCAAATGCTGCTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:926:1:1,0:499,422:921,1:0.0011:2,0:10:0:34:0:1:0:60:2:0.0011:0:1 0/1:660:240:120,120:221,198:419,240:0.3636:2,2:23.2:1:31.3:1:0.51754:1.11597:59.9:47:0.361:0:1.1 +20 31024488 . C T 164 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=75.26927;LSEQ=GGCCTGCGGACCCGATGCCT;RSEQ=TTCCTGCTGAGATCCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1060:1:0,1:531,527:1058,1:9e-04:2,0:1:0:26:0:0.49858:0:60:2:0.001:0:1 0/1:752:50:25,25:338,363:701,50:0.0665:2,2:21:1:29.1:1:0.88384:1.07:60:49:0.0661:0:1.2 +20 31025163 . A G 201 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=92.16935;LSEQ=AAATTATGGCCATGGGAAAC;RSEQ=TTGTATATTTAGTGTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:2:1,1:117,274:391,2:0.0051:2,2:24.5:1:28.5:1:0.51089:2.34:60:4:0.0051:0:1.5 0/1:295:95:26,69:66,134:200,95:0.322:2,2:24:1:30.6:1:0.34955:1.30595:60:46.5:0.3185:0:1.2 +20 31025208 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12016;SOR=Inf;LSEQ=GATAATGATTGATCTTAAAT;RSEQ=TGTATACAGAATATCATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:12,168:180,0:0:2,0:22.9:1:33.1:1:1:0:60:59:1:0:0.1 0/1:96:2:1,1:9,85:94,2:0.0208:2,2:17.5:1:30.5:1:0.19846:9.01:60:4:0.0208:0:2.5 +20 31025231 . T C 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATACAGAATATCATTGATA;RSEQ=AATACTCTTTAGGCAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:1,118:119,0:0:1,0:24.4:1:28.7:1:1:0:60:118:1:0:0.1 0/1:55:13:0,13:0,42:42,13:0.2364:1,1:26.2:1:31.8:1:1:0:60:26:0.2364:0:1.8 +20 31367948 . C T 151 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=52.02171;LSEQ=CCAAGTCCTGAGCCTCCAAG;RSEQ=TTGGTGAGGGGGAGGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:768:1:1,0:330,434:764,1:0.0013:2,0:47:0:25:0:0.43268:0:60:2:0.0013:0:1 0/1:644:41:17,24:266,337:603,41:0.0637:2,2:27.2:1:28.2:1:0.87107:1.11412:60:40:0.0629:0:1.1 +20 31368060 . G T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03166;SOR=Inf;LSEQ=AACACAGAGCCCATGGCGGG;RSEQ=GAACACTGTCCCTCTCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:0:0,0:320,181:501,0:0:2,0:23.7:1:30.9:1:1:0:60:26.833:1:0:0.1 0/1:367:4:0,4:233,130:363,4:0.0109:2,0:11.5:1:23.8:1:0.01727:0:60:3:0.0084:0:1.3 +20 31368254 . G A 75 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08152;SOR=4.00374;LSEQ=CCCAATCCTGGAGGCTATCC;RSEQ=CACCCCGGAGATCAGAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:2:2,0:235,393:628,2:0.0032:2,0:1:0:27.5:1:0.14115:0:60:4:0.0032:0:1 0/1:476:6:4,2:180,290:470,6:0.0126:2,2:16.8:1:29.2:1:0.2119:3.21:60:12:0.0129:0:1.2 +20 31368350 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11008;SOR=Inf;LSEQ=CAGACAACTGGAGGCTTTGG;RSEQ=GAGAGTCTCTGACAACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:11,133:144,0:0:2,0:23.2:1:31.5:1:1:0:60:71:1:0:0.2 0/1:72:2:1,1:3,67:70,2:0.0278:1,2:28:1:30.5:1:0.10876:19.49:60:4:0.0278:0:1 +20 31368423 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07684;SOR=Inf;LSEQ=GCAAGGAGGGATGCAGGGTC;RSEQ=AGCCCTTCACACCTGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,43:43,0:0:1,0:23.2:1:31.8:1:1:0:60:20.5:1:0:0 0/1:17:2:1,1:1,14:15,2:0.1176:1,2:39:1:30.5:1:0.22794:10.25:60:4:0.1176:0:1 +20 31368957 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03168;SOR=Inf;LSEQ=TTTGGGTCCTGTCACGTGCC;RSEQ=GGCCCAGGGCTCTGTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:41,0:41,0:0:1,0:21.2:1:32.6:1:1:0:60:82:1:0:0.4 0/1:20:3:3,0:17,0:17,3:0.15:1,0:12:1:31.3:1:1:0:60:6:0.15:0:1 +20 31368960 . C A 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16263;SOR=2.31538;LSEQ=GGGTCCTGTCACGTGCCTGG;RSEQ=CCAGGGCTCTGTTGTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:11:11,0:31,0:31,11:0.2619:1,0:19.2:1:27.3:1:1:0:60:4.5:0.2368:0:1.1 0/1:22:10:10,0:12,0:12,10:0.4545:0,0:20.4:1:29.5:1:1:0:60:20:0.4545:0:1 +20 31369067 . C T 42 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41293;SOR=2.55299;LSEQ=AGTGTAGGGGAGATCCCAGG;RSEQ=CACGCCACGGAGAAAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:2:0,2:232,57:289,2:0.0069:2,0:1:0:25:0:0.04055:0:60:4:0.007:0:1 0/1:230:4:1,3:171,55:226,4:0.0174:2,2:5.8:1:21:1:0.05046:9.21517:60:3:0.0133:0:1 +20 31369126 . C G 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCCAGACTGGTGCCTGCCCC;RSEQ=ACAAAACAGACTCCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:436,290:726,0:0:2,0:25.8:1:31.6:1:1:0:60:89.75:0.9972:0:0.2 0/1:689:31:17,14:397,260:657,31:0.045:2,2:28.4:1:30.7:1:0.57567:1.25703:58.4:62:0.0454:0:1.2 +20 31369136 . AC A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.10458;LSEQ=TGCCTGCCCCCACAAAACAG;RSEQ=TCCTGGCTGTTTCCTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:799:202:118,84:332,265:597,202:0.2528:2,2:25.3:1:31.1:1:0.51208:1.12:59.9:404:0.2554:0.0451:0.2 1/0:759:389:228,161:212,158:370,389:0.5125:2,2:26:1:30.1:1:0.7686:1.06:59.8:388:0.5146:0.0711:0.3 +20 31369479 . G A 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55731;SOR=2.66173;LSEQ=CTTGCAGTCAACTGCCGTCT;RSEQ=AAAGTATTAAATGGAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:14,5:0.2632:1,0:33:1:32.8:1:1:0:60:10:0.2778:0:1 1/0:4:2:0,2:0,2:2,2:0.5:0,0:19.5:1:32:0:1:0:60:4:0.5:0:1 +20 31372736 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17623;SOR=Inf;LSEQ=GCATACATAGCATGCTACAT;RSEQ=CATAGCATAGCTCCTTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:20,188:208,0:0:2,0:20.6:1:29.9:1:1:0:59.9:68.333:1:0:0.1 0/1:151:2:1,1:15,134:149,2:0.0132:2,2:12.5:1:27.5:1:0.20132:8.68:60:4:0.0132:0:1 +20 31372748 . T A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56872;SOR=2.93134;LSEQ=TGCTACATACATAGCATAGC;RSEQ=CCTTAGGGGAGCTTTTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:0,1:6,149:155,1:0.0064:1,0:37:0:31:0:1:0:60:2:0.0066:0:1 0/1:108:2:1,1:7,99:106,2:0.0185:2,2:24.5:1:29.5:1:0.1433:13.30:60:4:0.0189:0:1 +20 31372847 . C CT 38 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.31935;SOR=3.13885;LSEQ=GTTGGAGGGTTTTCTTTTTT;RSEQ=TTTTTTTTTTTCTGAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:0,3:1,23:24,3:0.1034:1,0:21.7:1:30:1:1:0:60:6:0.1034:0:0 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:19.7:1:24:1:1:0:60:2:0.2:0.0909:0.3 +20 31374259 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.4638;LSEQ=CTTCTGGCCCCGCCAGACCC;RSEQ=AGGCCTCCAGTCACCTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:154:105,49:340,155:495,154:0.2373:2,2:24.7:1:30.8:1:0.92101:1.02364:60:153:0.2394:0:1.1 1/0:474:246:157,89:144,84:228,246:0.519:2,2:25.4:1:28.7:1:0.92401:1.03:60:40:0.5161:0:1.1 +20 31374520 . A G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.91035;LSEQ=CACTACTGGTTGTGGCTGGT;RSEQ=GATAATCTGTGTCCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:87:9,78:18,207:225,87:0.2788:2,2:24.2:1:31.1:1:0.50613:1.33:60:42.5:0.2778:0:1 1/0:234:141:15,126:10,83:93,141:0.6026:2,2:24:1:30.5:1:1:1.012:60:140:0.6087:0:1 +20 31374848 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06707;SOR=Inf;LSEQ=TCATCTTTCTGTCTCTGGGA;RSEQ=AGTTACAATGACTTTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:27,3:30,0:0:2,0:20.8:1:31.5:1:1:0:59.6:14:1:0:0.5 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:25.5:1:30:1:1:0:60:4:0.1818:0:1 +20 31374959 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18887;SOR=Inf;LSEQ=TCTTTCTTTTTGCCTAGGAG;RSEQ=CATATGGGGGTGCCGTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:180,20:200,0:0:2,0:23.2:1:32:1:1:0:59.4:32.333:0.9949:0:0.3 0/1:155:2:2,0:135,18:153,2:0.0129:2,0:20.5:1:27:1:1:0:60:4:0.0136:0:1.5 +20 31374991 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.72219;LSEQ=GCCGTTGGTCTCTGGTCACC;RSEQ=ACATCCTTTGCTCTGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:114:88,26:202,57:259,114:0.3056:2,2:25:1:30.2:1:0.89284:1.04692:59.2:56:0.3019:0:1 1/0:319:174:126,48:112,33:145,174:0.5455:2,2:23.4:1:29.4:1:0.36657:1.29189:59.9:173:0.5475:0:1.1 +20 31375287 . T C 131 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=32.08866;LSEQ=AGAGGGGCTCCTGCCCAGGG;RSEQ=GACTGAGGACCCTGAACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:1:0,1:117,319:436,1:0.0023:2,0:16:0:8:0:1:0:60:0:0:0:4 0/1:320:22:8,14:77,219:296,22:0.0688:2,2:20.3:1:29.5:1:0.31964:1.62:60:21:0.0675:0:1 +20 31375311 . A G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00257;SOR=1.80822;LSEQ=TGAGGACCCTGAACACGGGG;RSEQ=AAAACCAGTTACCTGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:95:16,79:35,158:193,95:0.3287:2,2:24.5:1:32:1:0.87028:1.09343:59.3:94:0.3298:0:1.1 0/1:183:86:12,74:14,83:97,86:0.4699:2,2:22.2:1:30.6:1:1:1.03995:60:172:0.4778:0:1 +20 31375386 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13483;SOR=Inf;LSEQ=TCGTAATTGTAATAATTGAC;RSEQ=TGTTTGAATTCTAAGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:0,56:56,0:0:1,0:23.2:1:31:1:1:0:58.9:17.667:1:0:0.4 0/1:33:2:1,1:0,31:31,2:0.0606:1,2:27.5:1:32:0:0.06061:0:60:4:0.0606:0:1 +20 31376490 . T C 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07591;SOR=3.20605;LSEQ=CTGGCCTCAAGCGATCCCCC;RSEQ=GCCTCGGTCTCCCAAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:11,0:23,0:23,11:0.3235:1,0:21.1:1:30.7:1:1:0:60:22:0.3235:0:1.2 1/0:18:11:10,1:6,1:7,11:0.6111:2,2:24:1:30.6:1:1:1.62:60:22:0.6471:0:1 +20 31379184 . C A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93553;LSEQ=TCCACAGTGGAAGTGTCGTA;RSEQ=CTAACAAGGTTCTGGATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:10,0:14,0:14,10:0.4167:1,0:24.3:1:30.2:1:1:0:60:20:0.4167:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:9.5:1:31:0:1:0:60:4:0.4:0:2 +20 31379310 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13481;SOR=Inf;LSEQ=AATGGTCTCTTGGTTAAAGT;RSEQ=TGTGAAAATCTTCTGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:171,16:187,0:0:2,0:24.5:1:32.2:1:1:0:60:61.333:1:0:0.1 0/1:109:2:1,1:100,7:107,2:0.0183:2,2:5:1:28.5:1:0.14203:13.42973:60:4:0.0185:0:1.5 +20 31379323 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.56087;SOR=3.24831;LSEQ=TTAAAGTGTGTGAAAATCTT;RSEQ=TGCATCTGATGGACAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:1:1,0:203,30:233,1:0.0043:2,0:25:0:11:0:1:0:60:0:0:0:5 0/1:145:2:1,1:125,18:143,2:0.0138:2,2:13.5:1:28:1:0.24569:6.7853:60:4:0.014:0:1.5 +20 31379665 . C T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24005;SOR=2.1769;LSEQ=CAACATAACATGATGGCCAC;RSEQ=GGATTGGGCCTCCCAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:11:0,11:1,26:27,11:0.2895:1,0:21.5:1:31.9:1:1:0:60:22:0.2973:0:1 0/1:19:9:0,9:0,10:10,9:0.4737:0,0:29.1:1:29:1:1:0:60:18:0.5:0:1 +20 31380201 . A T 60 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27778;SOR=Inf;LSEQ=ACATTCCCTAGGGGGAAGAG;RSEQ=TCCTATTTGGTGCCTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:12,1:13,4:0.2353:1,0:21.8:1:30:1:1:0:60:8:0.2667:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:8:0:31:0:1:0:60:2:1:0:1 +20 31380309 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=4.1263;LSEQ=TACCACAGCCCAGGACAGCT;RSEQ=TCTGGCTATGAAAGGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:34:34,0:72,1:73,34:0.3178:1,1:23:1:28.1:1:1:0:60:68:0.3238:0:1.2 1/0:50:33:32,1:17,0:17,33:0.66:1,1:21.3:1:27.7:1:1:0:60:66:0.66:0:1.1 +20 31380332 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.54353;SOR=0;LSEQ=TGGCTATGAAAGGGCCCAGT;RSEQ=TGAAGGGGAATGTAGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:2,0:151,9:160,2:0.0123:2,0:8.5:1:30:1:1:0:60:4:0.0123:0:1.5 0/0:87:0:0,0:82,5:87,0:0:2,0:23.4:1:31.3:1:1:0:60:42.5:1:0:0.7 +20 31380340 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13343;SOR=Inf;LSEQ=AAAGGGCCCAGTGTGAAGGG;RSEQ=AATGTAGGCCCTGGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:166,26:192,0:0:2,0:21.8:1:31.3:1:1:0:60:37.4:1:0:0.3 0/1:111:2:1,1:100,9:109,2:0.018:2,2:23.5:1:29:1:0.17281:10.59364:60:4:0.0187:0:1.5 +20 31380350 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14127;SOR=Inf;LSEQ=GTGTGAAGGGGAATGTAGGC;RSEQ=CTGGCTGGGGGAATCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:179,44:223,0:0:2,0:23.3:1:31.1:1:1:0:60:54.75:0.9955:0:0.3 0/1:136:2:1,1:114,19:133,2:0.0147:2,2:16:1:27:1:0.27529:5.8737:60:4:0.0149:0:1 +20 31380364 . TC T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15563;SOR=Inf;LSEQ=GTAGGCCCTGGCTGGGGGAA;RSEQ=CCTGGGTGTGGCCTGGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:229,68:297,0:0:2,0:24.5:1:31.8:1:1:0:59.9:41.429:1:0:0.2 0/1:194:2:1,1:154,38:192,2:0.0103:2,2:13:1:27.5:1:0.36248:4.01331:60:4:0.0105:0.0052:0.5 +20 31380398 . AC A 90 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.0042;SOR=11.83707;LSEQ=CTGGCGAGCACCTCCTCCCC;RSEQ=CCCCCCATTCATCACAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:1:1,0:389,171:560,1:0.0018:2,0:22:0:34:0:1:0:60:2:0.0018:0:0 0/1:387:8:5,3:263,116:379,8:0.0207:2,2:14.4:1:30.1:1:0.70565:1.35924:58.8:16:0.0211:0.0129:0.4 +20 31380639 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1806;SOR=Inf;LSEQ=TGGGACCACTTCTTGGGAGA;RSEQ=TCAGCCACCCCTGCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:20,208:228,0:0:2,0:23.6:1:32.5:1:1:0:60:113:1:0:0.1 0/1:169:2:1,1:22,145:167,2:0.0118:2,2:24:1:31:0:0.25437:6.47:60:4:0.012:0:1 +20 31380643 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18434;SOR=Inf;LSEQ=ACCACTTCTTGGGAGAGTCA;RSEQ=CCACCCCTGCTGCCCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:18,190:208,0:0:2,0:23.9:1:32.6:1:1:0:60:103:1:0:0.2 0/1:157:2:1,1:17,138:155,2:0.0127:2,2:15:1:24.5:1:0.21681:7.92:60:4:0.013:0:1 +20 31381229 . G A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13894;SOR=2.69082;LSEQ=GGTTGCAGTGCGCCGAGATC;RSEQ=CACCACTGCATTCAAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:8,0:19,1:20,8:0.2857:1,0:21.9:1:31.3:1:1:0:59.9:16:0.2857:0:1 1/0:21:11:11,0:10,0:10,11:0.5238:0,0:24.5:1:29.8:1:1:0:58.5:22:0.5238:0:1.5 +20 31381507 . T G 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00761;SOR=Inf;LSEQ=GAATCAAATTTCTTGAAAAG;RSEQ=CAATCTGAACTCCCTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:8,111:119,0:0:2,0:23.8:1:30.3:1:1:0:60:58.5:1:0:0 0/1:74:5:0,5:7,62:69,5:0.0676:2,0:23.8:1:31.6:1:1:0:60:10:0.0676:0:1 +20 31381690 . A T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.7321;LSEQ=TTGTCACTAAAGGGTCCTTA;RSEQ=GATTTTTAATGGCTGTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:49:0:30:0:1:0:60:2:0.5:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:27.5:1:31.5:1:1:0:60:4:0.6667:0:1 +20 31383353 . T G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.80456;LSEQ=GAGCCGAGGTGATTGTTGGG;RSEQ=ACCTGGGATCATGGGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:877:227:92,135:267,381:648,227:0.2588:2,2:24.6:1:31.7:1:0.87568:1.0283:60:55.75:0.2593:0:1.1 0/1:697:345:137,208:136,214:350,345:0.495:2,2:25.2:1:30.3:1:0.87657:1.04:60:48.286:0.4927:0:1.2 +20 31383530 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.01349;LSEQ=TCTCCCTCCCAGTCATCCCC;RSEQ=TCACACCCTGGCTAGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:958:251:113,138:315,389:704,251:0.262:2,2:26.5:1:30.8:1:0.94123:1.01:59.9:61.75:0.2614:0:1.1 1/0:880:455:198,257:190,232:422,455:0.517:2,2:26:1:29.4:1:0.68325:1.06291:59.7:64:0.5155:0:1.2 +20 31383726 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05556;SOR=Inf;LSEQ=AAGGGTATGGTGAGGAACAA;RSEQ=GGAAGCTGGGCCATTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:0,34:34,0:0:1,0:22.9:1:32.1:1:1:0:58.6:68:1:0:0.4 0/1:11:2:1,1:1,8:9,2:0.1818:2,2:26:1:29.5:1:0.34545:6.00:60:4:0.1818:0:1 +20 31384136 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCAGGGATGCAACTCC;RSEQ=TGCTGACCTGGTGATATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:12.5:1:33:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 31384488 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1367;SOR=Inf;LSEQ=TGAGGTGCAAAGAGTCCTTG;RSEQ=CAAGCTGCTGGCCTGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:185,17:202,0:0:2,0:25:1:31.3:1:1:0:59.8:27.857:1:0:0.1 0/1:119:2:1,1:108,9:117,2:0.0168:2,2:49:1:28:1:0.16166:11.43704:60:4:0.0168:0:1.5 +20 31384764 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15119;SOR=Inf;LSEQ=CAGCACCTGTGTGGAGACTC;RSEQ=GTGAAGCCCACTCATCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:36,276:312,0:0:2,0:22.7:1:31.8:1:1:0:59.9:77:1:0:0.1 0/1:199:2:1,1:26,171:197,2:0.0101:2,2:16.5:1:30.5:1:0.25354:6.47:60:4:0.0103:0:1 +20 31385234 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.1111;SOR=Inf;LSEQ=GGAGCTAATTTGCCCTGGAA;RSEQ=CAGCACACAGGGTTTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:4,119:123,0:0:1,0:22.7:1:32.4:1:1:0:60:29.75:1:0:0.2 0/1:62:2:1,1:2,58:60,2:0.0323:1,2:18:0:31:1:0.09519:23.88:60:4:0.0328:0:2 +20 31385269 . G T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01271;SOR=3.19437;LSEQ=TATATTTTGTGGTGGCTGTG;RSEQ=TTGTAGCATAATTGGAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:21:1,20:0,44:44,21:0.3231:1,1:30.8:1:30.7:1:0.32308:0:60:42:0.3281:0:1 1/0:28:17:2,15:0,11:11,17:0.6071:0,2:24.2:1:29.6:1:0.50529:0:60:34:0.6071:0:1.1 +20 31386332 . G A 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=33.78727;LSEQ=GCGGCCGAGGCCAAGCTTCA;RSEQ=GAGCCCTGGAGCTGTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:887:2:2,0:433,452:885,2:0.0023:2,0:1:0:26:1:0.24023:0:60:4:0.0023:0:1 0/1:718:51:25,26:332,334:666,51:0.071:2,2:23.2:1:29.4:1:1:1.03373:60:50:0.0701:0:1.9 +20 31386347 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.565;LSEQ=CTTCAGGAGCCCTGGAGCTG;RSEQ=TACATGTGTCTCCCGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:249:122,127:308,345:653,249:0.2757:2,2:24:1:32.6:1:0.65479:1.08:59.9:82:0.2742:0:1.2 1/0:684:394:190,204:150,138:288,394:0.576:2,2:22.8:1:31.1:1:0.35225:1.16678:59.9:48.25:0.5719:0:1.3 +20 31386449 . T C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.83353;LSEQ=AGTGACACGGGGCTTGAATA;RSEQ=GTAAGCCACAGGCTCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:796:205:88,117:247,342:589,205:0.2575:2,2:27.2:1:31:1:0.80603:1.04:60:101.5:0.2609:0:1.1 1/0:704:402:165,237:131,167:298,402:0.571:2,2:25.7:1:29.5:1:0.48627:1.12653:60:32.5:0.5702:0:1.2 +20 31387737 . CTAGT C 63 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05929;SOR=6.77641;LSEQ=TAAGTATAATTGGAGATAAA;RSEQ=TAACAACTACTGCTACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:15,2:0.1176:1,0:35:1:34:0:1:0:60:4:0.1176:0:0 1/0:8:4:4,0:4,0:4,4:0.5:0,0:38.3:1:31.5:1:1:0:60:8:0.5:0:0 +20 31387951 . C G 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTTCTGTGTCTCTCTGGC;RSEQ=CCCACAGGCTACCTAGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:457,270:727,0:0:2,0:24.3:1:30.9:1:1:0:60:50.929:0.9986:0:0.4 0/1:609:36:22,14:337,211:548,36:0.0591:2,2:26.9:1:29.7:1:1:1.01635:60:72:0.0604:0:1.2 +20 31387954 . C G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.10486;LSEQ=TTCTGTGTCTCTCTGGCCCC;RSEQ=ACAGGCTACCTAGTCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:198:120,78:350,222:572,198:0.2571:2,2:24:1:30.4:1:0.93265:1.02475:60:48.5:0.2563:0:1.1 0/1:638:269:175,94:209,160:369,269:0.4216:2,2:26.4:1:29.4:1:0.03351:1.42:59.9:66.25:0.4233:0:1.2 +20 31388080 . C T 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AATATCAAATACGTGAACGA;RSEQ=GTGAGGAACATCACAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:749:0:0,0:287,461:748,0:0:2,0:25.2:1:30.7:1:1:0:59.9:67:0.9986:0:0.1 0/1:669:36:13,23:262,369:631,36:0.0538:2,2:23.9:1:29.6:1:0.6032:1.25578:60:35:0.0532:0:1.1 +20 31388461 . C T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03113;SOR=3.75851;LSEQ=TTCTAGTAGAGTTGGGGTTT;RSEQ=TCCATGTTGGCCAAGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:12:11,1:39,2:41,12:0.2264:1,2:20.5:1:29.9:1:0.54495:1.75109:55.9:11:0.2157:0:1.2 1/0:17:9:9,0:8,0:8,9:0.5294:0,0:19.6:1:28.7:1:1:0:59.6:8:0.5:0:1 +20 31388496 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01895;SOR=Inf;LSEQ=GCTGGTCTCGAACTCCTGAC;RSEQ=TCAGGTAATCCACCCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:97,2:99,0:0:1,0:27:1:30.8:1:1:0:59:18.8:1:0:0.2 0/1:37:3:3,0:34,0:34,3:0.0811:1,0:21.7:1:29.3:1:1:0:60:6:0.0833:0:1 +20 31388636 . T C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=3.43421;LSEQ=TCCTGACTCTGTCTCTCTCT;RSEQ=TCAGATTGAAGAATGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:897:237:128,109:377,281:658,237:0.2642:2,2:28:1:32.2:1:0.40111:1.14231:60:117.5:0.2667:0:1.2 1/0:811:448:253,195:196,164:360,448:0.5524:2,2:24.8:1:30.7:1:0.56962:1.09:60:111:0.555:0:1.1 +20 31388737 . C T 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAGGCCTGTATGGTGAG;RSEQ=ATCCTTCTCTCTGGCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:0:0,0:235,406:641,0:0:2,0:24.4:1:32.2:1:1:0:60:70.222:1:0:0.1 0/1:533:21:9,12:192,318:510,21:0.0394:2,2:25:1:27.4:1:0.65088:1.24:60:42:0.0396:0:1 +20 31388805 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52352;SOR=0;LSEQ=GGCCCAGGTGCAGCAGCCTG;RSEQ=GAAGGAGCCACTTGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:0,2:17,177:194,2:0.0102:2,0:17:1:30.5:1:1:0:60:4:0.0105:0:1 0/0:125:0:0,0:17,108:125,0:0:2,0:24.5:1:29.9:1:1:0:60:40.667:1:0:0.2 +20 31389009 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.42097;LSEQ=AGGAGGCCATTGGGAACCTG;RSEQ=TGGTCTCAGGGAATAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:60:50,10:144,28:172,60:0.2586:2,2:21:1:30.1:1:1:1.02842:60:29:0.2566:0:1.1 1/0:174:114:93,21:45,15:60,114:0.6552:2,2:21.8:1:29.3:1:0.32937:1.47:60:228:0.659:0:1.1 +20 31389036 . G T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41142;SOR=2.62821;LSEQ=CAGGGAATAAGGTGGGTTGG;RSEQ=CTGGAGGTTTCAAATGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:2:1,1:261,118:379,2:0.0052:2,2:2.5:1:27.5:1:0.52768:2.20681:60:4:0.0054:0:1 0/1:292:4:2,2:198,90:288,4:0.0137:2,2:27.8:1:27:1:0.59278:2.19349:60:8:0.0139:0:1.3 +20 31389279 . A G 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19649;SOR=Inf;LSEQ=CACAGACAGCCAGGGCAGGG;RSEQ=AAGCGCTGCTGGCAGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:32,206:238,0:0:2,0:22.7:1:31.1:1:1:0:60:118:1:0:0.1 0/1:190:2:1,1:32,156:188,2:0.0105:2,2:22.5:1:26:0:0.31796:4.82:60:4:0.0106:0:1 +20 31389284 . G A 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.82371;LSEQ=ACAGCCAGGGCAGGGAAAGC;RSEQ=CTGCTGGCAGTGATGATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:25,179:204,3:0.0144:2,2:11.7:1:31.7:1:0.33287:3.55:60:6:0.0146:0:1 0/1:168:2:2,0:23,143:166,2:0.0119:2,0:1:0:23.5:1:0.02139:0:60:4:0.012:0:1 +20 31389349 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04774;SOR=Inf;LSEQ=ACTTTCCCGTTCTTGGTCTG;RSEQ=CTAGATCCAATAGTGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:1,71:72,0:0:1,0:29:1:32.5:1:1:0:60:71:1:0:0.1 0/1:42:3:0,3:0,39:39,3:0.0714:1,0:30.7:1:29:1:1:0:60:6:0.0714:0:1 +20 31389518 . A G 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTACCTCAGCCTCCCAA;RSEQ=TGGCTGGGACTACAGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:26.3:1:33.7:1:1:0:60:6:0.3333:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 31390128 . G T 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.3032;LSEQ=ATAGCCCTGTCACCTGCAAA;RSEQ=GTCTGGTTGACACTGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:2:1,1:177,46:223,2:0.0089:2,2:2.5:1:28.5:1:0.37488:3.81741:60:4:0.009:0:1 0/1:173:2:1,1:131,40:171,2:0.0116:2,2:5:1:28:1:0.41887:3.24712:60:4:0.0116:0:1 +20 31390138 . A G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00113;SOR=Inf;LSEQ=CACCTGCAAAGGTCTGGTTG;RSEQ=CACTGAAACTCTAATAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:209,68:277,0:0:2,0:23.6:1:29.7:1:1:0:60:45.167:1:0:0.1 0/1:211:8:7,1:147,56:203,8:0.0379:2,2:27.6:1:31.4:1:0.68552:2.66:60:16:0.0381:0:1 +20 31390533 . T C 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AAGTCCCACGTGGCTGGGTG;RSEQ=GGTGGCTCACGCCTGTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:9:1:31.7:1:1:0:60:6:0.3333:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:44:0:27:0:1:0:51:2:1:0:1 +20 31393065 . T G 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00119;SOR=Inf;LSEQ=CAGGGCACATCTCTGCAACA;RSEQ=AGACCCTCACTCCCACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:256,63:319,0:0:2,0:23.5:1:30.7:1:1:0:60:62.8:1:0:0.1 0/1:245:8:6,2:181,56:237,8:0.0327:2,2:19.1:1:31.8:1:1:1.07706:60:16:0.0332:0:1.3 +20 31393256 . C A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04029;SOR=Inf;LSEQ=GGAAAAATGCACTTGGTGAC;RSEQ=TCCAAGTGGGGACTTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:149,305:454,0:0:2,0:24.8:1:32.4:1:1:0:60:74.667:1:0:0.1 0/1:370:4:3,1:121,245:366,4:0.0108:2,2:21.5:1:29:1:0.11151:6.04:60:8:0.0108:0:1 +20 31393352 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=4.0676;LSEQ=TGGGCTTCCCTCTCCCACAT;RSEQ=ATTGTTCTGTCCCATCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:18:0,18:0,71:71,18:0.2022:1,1:26.9:1:30.1:1:1:0:60:17:0.1932:0:1.1 1/0:47:24:0,24:2,21:23,24:0.5106:2,1:23.6:1:31.2:1:0.23404:0:60:48:0.5106:0:1 +20 31393803 . T C 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17391;SOR=Inf;LSEQ=AAGCACAAAATGTTCTTGTC;RSEQ=CTCCAACTCTGCTTTTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:3,0:18,1:19,3:0.1364:1,0:26.7:1:31:1:1:0:57:6:0.1364:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:12:0:32:0:1:0:60:2:1:0:1 +20 31393918 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52929;SOR=0;LSEQ=TGCCACTCTTCTGCCGCACC;RSEQ=GCGCTCTCCCCTCCATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:2,0:141,7:148,2:0.0133:1,0:38.5:1:31.5:1:1:0:60:4:0.0134:0:1 0/0:90:0:0,0:82,8:90,0:0:2,0:23.4:1:30.2:1:1:0:60:89:1:0:0.1 +20 31394185 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50652;SOR=0;LSEQ=GTGTAGATCAAAACACAAAT;RSEQ=GGCAGACATGGGCAGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:31,154:185,2:0.0107:2,2:21.5:1:29.5:1:0.31373:4.91:60:4:0.0109:0:1 0/0:145:0:0,0:21,124:145,0:0:2,0:23:1:30.2:1:1:0:60:47.333:1:0:0.1 +20 31395475 . G T 23 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.96025;LSEQ=ACTGATGGGACTGAGGGATG;RSEQ=CGAGGGCAGAAAGAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:0,1:142,22:164,1:0.0061:2,0:1:0:28:0:0.13939:0:60:2:0.0063:0:1 0/1:169:2:1,1:144,23:167,2:0.0118:2,2:7.5:1:23:1:0.26458:6.15031:60:4:0.0122:0:1 +20 31999353 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15441;SOR=Inf;LSEQ=GACTGCAGCACCTCCCCACT;RSEQ=CCATCCTGCACTCTCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:10,0:0:2,0:23.6:1:30.3:1:1:0:60:20:1:0:0.3 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:27:1:29:1:1:1.41:60:4:0.2857:0:1 +20 32452555 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0991;SOR=Inf;LSEQ=CGGAGGCCATGCAGTCACTG;RSEQ=CTCTGCAGAACCTGGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:9,16:25,0:0:2,0:29.7:1:32.3:1:1:0:60:50:1:0:0 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:6.5:1:27.5:1:1:1:60:4:0.1667:0:1 +20 33345691 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49772;SOR=Inf;LSEQ=GTTGCTGTGGGGGTCTTGCC;RSEQ=GCAACTGTTGTTGCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:49,60:109,0:0:2,0:28.9:1:30.5:1:1:0:59.6:35.333:1:0:0.1 0/1:110:2:1,1:61,47:108,2:0.0182:2,2:22.5:1:29.5:1:1:1.29476:57.5:4:0.0183:0:1.5 +20 33345787 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.53782;SOR=Inf;LSEQ=GCTGCAGCTGGGGAAAATTA;RSEQ=CTGGGTTCATTTGTCTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:9,21:30,0:0:2,0:15.6:1:31.9:1:1:0:59.9:29:1:0:0.1 0/1:55:2:1,1:15,38:53,2:0.0364:2,2:25.5:1:28:1:0.50101:2.48:60:4:0.037:0:2 +20 33578899 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97877;LSEQ=GCCAAGGGTTCCCCAACAGG;RSEQ=TGCTCTACACCGACTTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:31:20,11:10,3:13,31:0.7045:2,2:26.3:1:32.8:1:0.49843:1.80934:60:30:0.6977:0:1.2 1/0:30:21:14,7:6,3:9,21:0.7:2,2:15.4:1:30.3:1:1:1:60:20:0.6897:0:1.3 +20 33579073 . T C 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=CCAGGTATCCCAGCAAGACA;RSEQ=GGGGGTGGCTCAGACCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:28.3:1:28.7:1:1:0:60:6:0.375:0:1 1/1:4:4:0,4:0,0:0,4:1:0,0:25.8:1:31.5:1:1:0:60:8:1:0:1 +20 34962410 . A G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50226;SOR=0;LSEQ=GGGTGACCAGGTATCTGGGG;RSEQ=GTGGCGACTCTGTGGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,14:28,2:0.0667:2,2:17:1:28:1:1:1:60:4:0.0667:0:1 0/0:22:0:0,0:12,10:22,0:0:2,0:27.1:1:29.9:1:1:0:60:44:1:0:0.3 +20 35477852 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTTTTACTTATTTTATT;RSEQ=TTTAAGACAGGGTCCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:43:1:33:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 35478058 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50467;SOR=0;LSEQ=TTAGTGATTTACCAGCCTGG;RSEQ=CTGGTAAATCACACTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:85,30:115,2:0.0169:2,2:34:1:30:1:0.46139:2.80361:60:4:0.0183:0:1 0/0:93:0:0,0:72,20:92,0:0:2,0:22.1:1:30.6:1:1:0:60:184:0.9892:0:0.2 +20 35478072 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22542;SOR=Inf;LSEQ=GCCTGGGCTGGTAAATCACA;RSEQ=TTTAAGTGTTCTAAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:105,46:151,0:0:2,0:27.8:1:31.5:1:1:0:59.8:24.167:1:0:0.3 0/1:137:2:1,1:103,32:135,2:0.0146:2,2:23.5:1:27.5:1:0.42508:3.18495:60:4:0.0147:0:1.5 +20 35478142 . C A 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=0.48873;LSEQ=TAAAATGATTTACGTTTGTA;RSEQ=ACTGAGGACAGCGGGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:110:58,52:99,94:193,110:0.363:2,2:26.3:1:30.6:1:0.90488:1.06:60:109:0.3633:0:1.2 0/1:317:69:38,31:133,114:247,69:0.2177:2,2:25.9:1:28.8:1:0.89193:1.05:59.8:138:0.2219:0:1.1 +20 35478151 . C T 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37509;SOR=3.71617;LSEQ=TTACGTTTGTACACTGAGGA;RSEQ=AGCGGGGGGAAGTTTAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:0,1:158,151:309,1:0.0032:2,0:1:0:24:0:0.49032:0:60:2:0.0033:0:1 0/1:336:4:1,3:176,156:332,4:0.0119:2,2:9.3:1:24.8:1:0.34797:3.37328:60:8:0.0122:0:1 +20 35478182 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11448;SOR=Inf;LSEQ=AGTTTAGATTTGGGGCCCAC;RSEQ=GGAACCTTTGCACGTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:131,172:303,0:0:2,0:24.9:1:30.9:1:1:0:60:100:1:0:0.4 0/1:287:3:1,2:117,166:283,3:0.0105:2,2:36:1:31:1:1:1.40801:60:6:0.0106:0:1.7 +20 35478214 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49911;SOR=0;LSEQ=ACGTGGCTCCAGATGCATGG;RSEQ=TATGACGGAATTGGCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:2,0:67,129:196,2:0.0101:2,0:13:1:27.5:1:0.12029:0:60:4:0.0102:0:2 0/0:187:0:0,0:65,122:187,0:0:2,0:25.2:1:30.9:1:1:0:60:45.75:1:0:0.3 +20 35478228 . G A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50294;SOR=0;LSEQ=GCATGGCTATGACGGAATTG;RSEQ=CCTGCAGCAGCTGGTGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:2,0:49,114:163,2:0.012:2,0:5:1:29:1:0.09424:0:60:4:0.0122:0:1.5 0/0:137:0:0,0:42,94:136,0:0:2,0:26.2:1:31:1:1:0:60:135:0.9926:0:0.2 +20 35478352 . G A 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.23147;LSEQ=GCTCCCAGCTGGGAGGACAC;RSEQ=GAGAGAACCAAGGGGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:19.3:1:30.8:1:1:0:60:8:0.4444:0:1 1/0:6:3:0,3:0,3:3,3:0.5:0,0:22:1:30:1:1:0:60:6:0.5:0:1 +20 36012348 . C A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30042;SOR=0.36998;LSEQ=CGGGTTTCCGCGTGTTGGCC;RSEQ=GGCAGGTCTCAAACTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:11,0:26,0:26,11:0.2973:1,0:22.5:1:30.4:1:1:0:36.1:10:0.2778:0:1.3 0/1:15:2:2,0:13,0:13,2:0.1333:1,0:6.5:1:28.5:1:1:0:33.5:4:0.1333:0:1.5 +20 36012386 . G A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.07905;SOR=7.49111;LSEQ=TGATCTCAAGTGATCCGCCC;RSEQ=CTTCGGCCTCCCAAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:1:1,0:73,1:74,1:0.0133:1,0:1:0:32:0:1:0:60:2:0.0141:0:1 0/1:32:3:3,0:29,0:29,3:0.0938:1,0:33:1:28.3:1:1:0:35:6:0.0968:0:1 +20 36012434 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCGTGAGCCACCGCGCC;RSEQ=GGCCCTGCTGCCTCTCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:2,0:171,3:174,2:0.0113:1,0:9:1:33:1:1:0:40:4:0.0116:0:1.5 0/0:72:0:0,0:70,2:72,0:0:1,0:23.8:1:30.8:1:1:0:54.9:71:1:0:0.1 +20 36012494 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0195;SOR=Inf;LSEQ=GTGGAATGGGTGGGAGGGAG;RSEQ=CCGGCCAAGGGGCCCCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:517:0:0,0:371,144:515,0:0:2,0:21.8:1:31:1:1:0:60:41.917:0.996:0:0.1 0/1:310:4:2,2:220,85:305,4:0.0129:2,2:13.5:1:26.8:1:0.31549:2.57906:60:8:0.0132:0:1 +20 36012701 . G A 60 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37509;SOR=0.26793;LSEQ=CCTCGGCCGACGGCCACCGC;RSEQ=GCCCCAGCGCGGCCTTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:4:3,1:211,171:382,4:0.0104:2,2:14.8:1:30:1:0.63196:2.43:60:8:0.0108:0:1.3 0/0:358:1:1,0:192,163:355,1:0.0028:2,0:1:0:28:0:1:0:60:2:0.0029:0:1 +20 36012785 . C A 61 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30049;SOR=2.21954;LSEQ=CGGACACCGTCACCTCCCCG;RSEQ=AGAGGGCGGGCCCGCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:3:3,0:299,350:649,3:0.0046:2,0:1:0:27.7:1:0.09884:0:53.3:6:0.0047:0:1.3 0/1:492:5:4,1:224,263:487,5:0.0102:2,2:7.6:1:26.4:1:0.18756:4.68:60:10:0.0102:0:1.4 +20 36012799 . G A 77 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02411;SOR=9.41692;LSEQ=TCCCCGCAGAGGGCGGGCCC;RSEQ=CTGGCCGGTCAGTGCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:1:1,0:226,292:518,1:0.0019:2,0:1:0:29:0:0.43738:0:60:2:0.002:0:1 0/1:392:7:5,2:171,214:385,7:0.0179:2,2:11.4:1:27.6:1:0.25074:3.12:60:14:0.018:0:1.1 +20 36012837 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25565;SOR=0;LSEQ=GGGCGGCGCGGGGTCCTCGC;RSEQ=CACCTGGGGCCACGGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:3:2,1:43,112:155,3:0.019:2,2:10.7:1:30.3:1:0.19546:5.15:60:6:0.019:0:1 0/0:128:0:0,0:41,87:128,0:0:2,0:13.6:1:30.6:1:1:0:60:63:1:0:0.3 +20 36013017 . A G 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGCTTTGGGGTGGAGCA;RSEQ=GCGCAAAAGACACGGGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:10.3:1:30.3:1:1:0:60:8:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 36014324 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGGATGCAGTGGACACGT;RSEQ=CACAGGCCCATCTTCACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:2,0:108,0:108,2:0.0182:1,0:27:1:30:0:1:0:60:4:0.0189:0:1 0/0:42:0:0,0:42,0:42,0:0:1,0:22:1:31.8:1:1:0:60:41:1:0:0.1 +20 36014631 . C T 99 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00031;SOR=17.71241;LSEQ=TGGGTGGTGGGACTTCAAAG;RSEQ=GGGCAGGGGCTCATGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:1:0,1:97,342:439,1:0.0023:2,0:11:0:25:0:1:0:60:2:0.0023:0:1 0/1:257:10:1,9:59,188:247,10:0.0389:2,2:24.1:1:29.9:1:0.46082:2.81609:60:20:0.0395:0:1 +20 36014794 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02381;SOR=Inf;LSEQ=GAACTCCTCCCAATCCCTGG;RSEQ=TCTCGCTTGCTCCCTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:2,28:30,0:0:2,0:25.4:1:33.6:1:1:0:58.6:60:1:0:0.1 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:12:0:31:1:0.33333:0:60:4:0.3333:0:1.5 +20 36022097 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01333;SOR=Inf;LSEQ=ATCTGATCCAGCTTTGGCAA;RSEQ=AAGGCGTCTGCGCCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:65,0:65,0:0:1,0:21.1:1:31:1:1:0:60:130:1:0:0 0/1:9:2:1,1:7,0:7,2:0.2222:0,2:24.5:1:31:1:0.22222:0:60:4:0.2222:0:1.5 +20 36022169 . G A 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGTGGGGACTCACGCTG;RSEQ=CCCCACCACCTCCCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:2,0:191,1:192,2:0.0103:1,0:6.5:1:31.5:1:1:0:60:4:0.0109:0:1 0/0:61:0:0,0:59,2:61,0:0:1,0:20.4:1:30.7:1:1:0:60:29.5:1:0:0.1 +20 36022539 . T C 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ACTGTGAGTGGGCAGAAGCC;RSEQ=GGACAGTCAGCACCATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:661:0:0,0:381,280:661,0:0:2,0:23.4:1:31.4:1:1:0:59.9:81.625:1:0:0.1 0/1:395:11:5,6:230,154:384,11:0.0278:2,2:23.2:1:29.3:1:0.36402:1.78943:60:22:0.0281:0:1.2 +20 36022763 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13457;SOR=Inf;LSEQ=TGTGGAATGAGCAGGAGTTT;RSEQ=GTTTGTGGAGTAGGGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:22,293:315,0:0:2,0:23.4:1:31.4:1:1:0:59.9:34:1:0:0.1 0/1:183:2:1,1:17,164:181,2:0.0109:2,2:9.5:1:27.5:1:0.18753:9.40:60:4:0.011:0:1 +20 36024493 . G T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55513;SOR=0;LSEQ=TCCAATGTCAGGCAGGCACA;RSEQ=AACGGTGTCCAGAGCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:257,31:288,3:0.0103:2,2:24.3:1:22.7:1:0.29585:4.11265:60:2:0.0071:0:2.3 0/0:158:0:0,0:137,21:158,0:0:2,0:24:1:31.4:1:1:0:59.9:78:1:0:0.1 +20 36024741 . C T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01576;SOR=Inf;LSEQ=CAGCCTCGGAGGGCGGAGGG;RSEQ=GGGCGGGCAAAGCCTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:0:0,0:118,445:563,0:0:2,0:22.5:1:30:1:1:0:60:50.182:1:0:0.1 0/1:311:4:2,2:79,228:307,4:0.0129:2,2:16.5:1:23.5:1:0.27886:2.87:60:3:0.0097:0:2.5 +20 36024820 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.00627;SOR=Inf;LSEQ=GGGACTTCTGTTATCCTGCT;RSEQ=CTCTCCCCACTTCCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:1,156:157,0:0:1,0:24.1:1:30.1:1:1:0:60:30.4:1:0:0.2 0/1:63:4:0,4:3,56:59,4:0.0635:2,0:21.3:1:31.8:1:1:0:60:8:0.0656:0:1 +20 36025230 . A G 67 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACCCACCTGGGCATCCG;RSEQ=AGCTGACTGCAGTGTCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:29:1:33.5:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 36025965 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05851;SOR=Inf;LSEQ=GGCTGTGTGCACACAGATGT;RSEQ=GATGCCTGGCTTTGAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:151,1:152,0:0:1,0:24.5:1:28.4:1:1:0:59.9:75:1:0:0.1 0/1:49:2:2,0:47,0:47,2:0.0408:1,0:20.5:1:28.5:1:1:0:60:4:0.0408:0:1 +20 36026026 . G T 54 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01314;LSEQ=CTGTGTGCATCTGGCATGTA;RSEQ=GGCGACACACACTGAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:4:2,2:336,49:385,4:0.0103:2,2:14.3:1:27:1:0.08505:6.79821:60:3:0.0079:0:2 0/1:192:2:1,1:160,30:190,2:0.0104:2,2:19.5:1:27.5:1:0.29756:5.26309:60:4:0.0106:0:1 +20 36026071 . C T 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1088;SOR=4.27285;LSEQ=AGGCCCCAGGGCAGAAGACC;RSEQ=GCCTAACTGCTCCTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:837:2:0,2:543,292:835,2:0.0024:2,0:1:0:28.5:1:0.12311:0:60:4:0.0024:0:1 0/1:493:5:1,4:315,173:488,5:0.0101:2,2:11.2:1:27.2:1:0.05827:7.25447:59:10:0.0103:0:1 +20 36028831 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04806;SOR=Inf;LSEQ=GAGCCAAATTCTCTGTTGCC;RSEQ=GGGCCGGAGTGTGGTGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:0,77:77,0:0:1,0:21.7:1:30.6:1:1:0:60:76:1:0:0 0/1:45:3:0,3:4,38:42,3:0.0667:2,0:13.7:1:30.7:1:1:0:60:6:0.0667:0:1 +20 36029758 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTCCTGTTGTTGCTGAG;RSEQ=GGGACTCCGCTGTCTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:2,0:28,0:28,2:0.0667:1,0:18:1:32:0:1:0:60:4:0.0667:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:10.5:1:32:1:1:0:60:4:1:0:0 +20 36029901 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13792;SOR=Inf;LSEQ=TTTACGTAAAATCTGCTGTG;RSEQ=TGGTTAAAGCAAGGCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:287,27:314,0:0:2,0:23.3:1:32.4:1:1:0:59.9:43.857:1:0:0.1 0/1:186:2:1,1:157,27:184,2:0.0108:2,2:27:1:25.5:1:0.2791:5.72824:60:4:0.0109:0:1 +20 36030405 . CTT C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGGCAGTGGTCAACAAGC;RSEQ=TTTTTTTTTCATTTAATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:2,4:6,2:0.25:2,2:13:1:28.1:1:1:1.83:60:4:0.25:0.125:0 0/0:2:0:0,0:1,1:2,0:0:2,0:25:1:29.5:1:1:0:60:4:1:0:0 +20 36030658 . C T 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28003;SOR=0;LSEQ=GTGCCCTGTGCTCCCTACTC;RSEQ=CGCAGAGCACTGCTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:5,4:14,2:16,9:0.36:2,2:26.2:1:30.2:1:0.14245:5.16859:60:8:0.381:0:1.3 0/0:4:0:0,0:3,1:4,0:0:2,0:32:1:30:1:1:0:60:8:1:0:0 +20 36030939 . G C 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68682;SOR=0.65692;LSEQ=AACCTGGTGTGCAAAGTGGC;RSEQ=GACTTTGGGCTGGCTCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:941:938:462,476:0,1:1,938:0.9968:0,2:26.6:1:30.3:1:1:0:60:51.111:0.9989:0:1.2 1/1:619:616:299,317:0,0:0,616:0.9952:0,2:26:1:29.3:1:1:0:59.9:43:0.995:0:1.2 +20 36030995 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02557;SOR=Inf;LSEQ=GTACACGGCGCGGCAAGGTG;RSEQ=GCAGGGGCTGTGTGGTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:589:0:0,0:243,346:589,0:0:2,0:24.9:1:31.1:1:1:0:59.9:57.9:1:0:0.6 0/1:394:4:3,1:153,237:390,4:0.0102:2,2:9.8:1:27.8:1:0.30519:4.63:60:8:0.0102:0:1.8 +20 36031055 . C T 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=GTCACGTCCCGCTCTGAGCC;RSEQ=CAGTTTTTTCCTCAGCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:214,170:384,0:0:2,0:22.9:1:31.2:1:1:0:60:31:1:0:0.6 0/1:201:8:4,4:88,105:193,8:0.0398:2,2:24.4:1:28.8:1:1:1.19:58.8:7:0.0357:0:2.1 +20 36031097 . A G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCTCATGGTGCTTATCTA;RSEQ=CAGAGCGGTCATGACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:528:527:357,170:0,0:0,527:0.9981:0,2:24.6:1:32.8:1:1:0:59.9:57.556:0.9981:0:1.1 1/1:255:255:167,88:0,0:0,255:1:0,2:21.3:1:31.2:1:1:0:60:62.75:1:0:1.2 +20 36031843 . G A 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTGGGTGGCCCCTGTCTC;RSEQ=GGGCTTGCCCCACTCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:46,290:336,0:0:2,0:22.5:1:30.7:1:1:0:59.9:32.6:0.9969:0:0.1 0/1:176:18:3,15:25,132:157,18:0.1023:2,2:26.8:1:30.9:1:1:1.06:60:36:0.1065:0:1.2 +20 36031871 . G C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00347;SOR=Inf;LSEQ=CCCCACTCTGCCTGCCTGCT;RSEQ=TTGGTCCTCTCTCTGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:11,191:202,0:0:2,0:26:1:32.5:1:1:0:59.9:66.333:1:0:0.1 0/1:98:5:1,4:5,88:93,5:0.051:2,2:26.6:1:31.8:1:0.27586:4.28:60:10:0.0532:0:1.2 +20 36970823 . C A 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.22078;SOR=0;LSEQ=CAAGATCCCTGGGGGACTTG;RSEQ=CTGCACGTCTTTGTTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:15.6:1:32:0:1:0:55.6:10:0.5:0:1 0/0:4:0:0,0:3,1:4,0:0:2,0:26:1:31.8:1:1:0:60:8:1:0:0 +20 36970964 . AC A 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56514;SOR=1.28477;LSEQ=GGCCTTGACAAAAAACCTGT;RSEQ=AGACTTTGGAAAAGGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:23:21,2:73,1:74,23:0.2371:1,2:28.3:1:30.5:1:0.13899:6.77386:60:46:0.2371:0.0309:0.1 0/1:56:16:16,0:40,0:40,16:0.2857:1,1:26.3:1:30.2:1:1:0:60:32:0.2857:0.0179:0.1 +20 36971052 . G A 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0412;SOR=0;LSEQ=CAGAAGAAATGCTCAGTGTT;RSEQ=CTAATTGTGTCCAACAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:6:3,3:334,174:508,6:0.0117:2,2:25:1:28.5:1:0.41923:1.917:60:12:0.0119:0:1 0/0:382:0:0,0:228,153:381,0:0:2,0:25.1:1:31.2:1:1:0:60:75.2:0.9973:0:0.3 +20 36971119 . T A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.2231;SOR=1.19104;LSEQ=CATTGGTTCTTGGGATTTGA;RSEQ=TAAAGTGGCTATTTCTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:663:121:48,73:246,296:542,121:0.1825:2,2:27.1:1:30.8:1:0.26689:1.26349:59.7:120:0.1838:0:1.1 0/1:576:121:56,65:211,244:455,121:0.2101:2,2:24.5:1:29.5:1:1:1.00373:60:242:0.2115:0:1.1 +20 37606544 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51678;SOR=0;LSEQ=GCTTTCTTTACTGGGGCTTT;RSEQ=TCTTCAGTTTCCTCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:47,41:88,2:0.0222:2,2:21:1:28:1:1:1.1446:53:4:0.0222:0:1 0/0:60:0:0,0:29,31:60,0:0:2,0:21.6:1:29.6:1:1:0:56.8:120:1:0:0.2 +20 37606562 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52519;SOR=0;LSEQ=TTTTCTTCAGTTTCCTCATC;RSEQ=TCAAAATCATCATCATTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:41,37:78,2:0.025:2,2:27:1:29.5:1:1:1.10668:49:4:0.026:0:1 0/0:49:0:0,0:24,25:49,0:0:2,0:22.9:1:28.7:1:1:0:57.6:15.333:1:0:0.1 +20 37606668 . A T 21 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23914;SOR=Inf;LSEQ=CAGATATACTTAAGAATTTC;RSEQ=CATCTTCTTCCTCTTCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:84,44:128,0:0:2,0:24.1:1:30.6:1:1:0:59.7:127:1:0:0.1 0/1:123:2:1,1:80,41:121,2:0.0163:2,2:18:1:21.5:1:1:1.93993:41.5:4:0.0164:0:1 +20 37606675 . C A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1068;SOR=Inf;LSEQ=ACTTAAGAATTTCACATCTT;RSEQ=TTCCTCTTCATCTTCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:91,53:144,0:0:2,0:23.5:1:32.8:1:1:0:58.9:143:1:0:0.1 0/1:131:3:2,1:85,43:128,3:0.0229:2,2:37:1:23.3:1:1:1.01:60:2:0.0156:0:1 +20 37606749 . G A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.58419;LSEQ=CACTAATATGCACTGGCCCT;RSEQ=AGCCACACTTCAACTGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:93,96:189,2:0.0105:2,2:23.5:1:31.5:1:1:1.03:44.5:4:0.0105:0:1.5 0/0:163:1:1,0:72,90:162,1:0.0061:2,0:1:0:21:0:0.44785:0:52:2:0.0063:0:1 +20 37606914 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25669;SOR=0;LSEQ=GCAATTCATCCTTTGCACCA;RSEQ=CCCCTGAGCTGACCGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:3:1,2:70,64:134,3:0.0219:2,2:21.7:1:29.3:1:0.60877:2.17543:36.3:6:0.0224:0:1 0/0:109:0:0,0:53,56:109,0:0:2,0:30:1:31:1:1:0:31:108:1:0:0.1 +20 37607141 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=TGCTCCAGAGAACAGCTGTG;RSEQ=AGGGCGGAATCACACCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:49,107:156,0:0:2,0:21.9:1:31.9:1:1:0:59.8:30.2:1:0:0.6 0/1:159:2:1,1:59,98:157,2:0.0126:2,2:37:1:27.5:1:1:1.66:60:4:0.0127:0:1 +20 37607146 . C T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21491;LSEQ=CAGAGAACAGCTGTGCAGGG;RSEQ=GGAATCACACCCTTTTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:136:75:23,52:15,46:61,75:0.5515:2,2:22.3:1:29.9:1:0.44993:1.35:60:74:0.5481:0:1.1 0/1:149:31:9,22:44,73:117,31:0.2081:2,2:22:1:28.2:1:0.40837:1.46963:59.4:30:0.2083:0:1.1 +20 37607201 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24139;SOR=Inf;LSEQ=TTTTAGTTTTTTGCTATTGA;RSEQ=TTGTTTGAGCACCTTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:41,0:0:1,0:23.4:1:31.1:1:1:0:60:19.5:1:0:0.4 0/1:43:3:0,3:0,40:40,3:0.0698:1,0:32.3:1:31:1:1:0:60:6:0.0714:0:1.7 +20 38290465 . C A 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTAGAAGTAAGATCAATA;RSEQ=AGGAGACTAGAACCCGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:23.8:1:33:0:1:0:60:10:1:0:1.8 1/1:1:1:0,1:0,0:0,1:1:0,0:3:0:28:0:1:0:60:2:1:0:1 +20 38290480 . C T 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATACAGGAGACTAGAACC;RSEQ=GTTGGTCTCTCTTCTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:20.5:1:32:0:1:0:60:8:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 38820366 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50198;SOR=0;LSEQ=ATATTTCAAACTCCAAGTGC;RSEQ=GGGCTCTCTTCATTGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:9,3:12,2:0.1429:2,2:20:1:31:1:0.50549:2.73861:60:4:0.1429:0:1 0/0:9:0:0,0:7,2:9,0:0:2,0:13.6:1:30.4:1:1:0:60:18:1:0:0.2 +20 39657098 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGGACGCCGGATACCAGC;RSEQ=CTGCCCAAGATTGCTGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:29.5:1:1:0:60:4:1:0:1 +20 39657625 . C A 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCGAGCCTCCGGAGTCCC;RSEQ=GTCCGCCCGCACAGGCCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:0:0,0:390,208:598,0:0:2,0:23.7:1:30.4:1:1:0:60:65.444:0.9983:0:0.1 0/1:441:36:23,13:261,142:403,36:0.0816:2,2:21.4:1:28.6:1:1:1.03877:60:35:0.0799:0:1.1 +20 39657783 . G A 63 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02619;SOR=Inf;LSEQ=CGGCCCCGGACCCCGGCCTG;RSEQ=CCGTCCCGCGACCCCCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:93,250:343,0:0:2,0:18.2:1:32.4:1:1:0:60:84.75:1:0:0.3 0/1:322:5:4,1:111,206:317,5:0.0155:2,2:5:1:27.2:1:0.05667:7.38:60:10:0.0159:0:1 +20 39657894 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5361;SOR=0;LSEQ=GAGTAGATCGGCTCGCTAGG;RSEQ=CGCGAGCGAGGGCCGCGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:153,0:153,2:0.0129:1,2:21.5:1:29:1:0.0129:0:60:4:0.0131:0:1 0/0:88:0:0,0:87,1:88,0:0:1,0:25.2:1:32.1:1:1:0:60:176:1:0:0.1 +20 39658170 . G A 57 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48232;SOR=1.94833;LSEQ=CCGCGCCCTGCCGGTGCCGG;RSEQ=CAGAGGACAGACATGGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:3:3,0:133,439:572,3:0.0052:2,0:1:0:26.3:1:0.01301:0:60:6:0.0053:0:1 0/1:494:5:4,1:125,363:488,5:0.0101:2,2:5:1:24.8:1:0.01801:11.55:60:10:0.0102:0:1.2 +20 39658311 . G A 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50376;SOR=0;LSEQ=CCCTCCCAAGAGGGGACAAC;RSEQ=GAGACCCCGTGTCGTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:0,2:0,31:31,2:0.0606:1,0:18:1:34:0:1:0:60:4:0.0606:0:1 0/0:24:0:0,0:2,22:24,0:0:2,0:21.8:1:30.8:1:1:0:60:48:1:0:0 +20 39690342 . T C 83 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07197;SOR=15.99491;LSEQ=GATGTATAAAGCAAGTATGT;RSEQ=TAATTTTCTTTTAATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:4,1:0.2:0,0:49:0:35:0:1:0:60:2:0.2:0:1 1/1:7:6:1,5:0,1:1,6:0.8571:0,2:17.8:1:32.3:1:1:0:60:12:0.8571:0:1 +20 39704995 . G A 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTTTTGTTTACCTTTGAAA;RSEQ=CAGATATCTTAATTGCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:29:3,26:26,130:156,29:0.1568:2,2:22.3:1:30.1:1:0.57872:1.7289:60:28:0.1547:0:1 0/0:159:0:0,0:27,132:159,0:0:2,0:22.3:1:31.5:1:1:0:60:158:1:0:0.1 +20 39706300 . G A 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12384;SOR=6.02433;LSEQ=AAGACTTTGCTGCTGCGTGG;RSEQ=CTTCCCTTTCTCTGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:1:1,0:207,356:563,1:0.0018:2,0:1:0:26:0:0.36879:0:60:2:0.0018:0:1 0/1:566:6:4,2:218,342:560,6:0.0106:2,2:15.2:1:25.5:1:0.21693:3.13:60:12:0.0108:0:1 +20 39706331 . G A 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12523;SOR=0;LSEQ=TCTGGGTGGACAGCAGGCCA;RSEQ=CTGCCTGTGTTGTAGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:4:2,2:98,279:377,4:0.0105:2,2:11:1:28.8:1:0.28244:2.84:60:8:0.0107:0:1 0/0:351:0:0,0:111,239:350,0:0:2,0:23.8:1:31.1:1:1:0:60:49:1:0:0.1 +20 39708708 . AT A 96 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01903;SOR=4.41031;LSEQ=TTCTAGCACTCTGACCAGCA;RSEQ=TTTTTTTCTCTTTAGTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:3:3,0:365,243:608,3:0.0049:2,0:17:1:32.1:1:0.28021:0:60:6:0.0049:0.0016:0 0/1:422:9:5,4:261,152:413,9:0.0213:2,2:28.7:1:30.6:1:0.73123:1.37258:60:18:0.0214:0:0.1 +20 39708889 . G A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19547;SOR=Inf;LSEQ=TTAAAGAATAAATGTGATGT;RSEQ=TTTCTTTATAATACATATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:10,137:147,0:0:2,0:23.7:1:32.6:1:1:0:59.8:294:1:0:0 0/1:117:2:1,1:14,101:115,2:0.0171:2,2:6:1:26.5:1:0.24094:7.00:60:4:0.0171:0:1 +20 39713352 . A C 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=TAGAGTAACTTTCTGAAGTA;RSEQ=GTTTTCCAACTTCTAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:0,27:27,0:0:1,0:25.2:1:32:1:1:0:60:26:1:0:0 1/0:11:6:1,5:0,5:5,6:0.5455:0,2:20.7:1:30.5:1:1:0:60:12:0.5455:0:1 +20 39721040 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04075;SOR=Inf;LSEQ=GTTGAGCGGATAATTATTTG;RSEQ=CATTTAATCAGTGATGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:282,42:324,0:0:2,0:23.5:1:31.5:1:1:0:59.9:53:1:0:0 0/1:171:3:1,2:138,30:168,3:0.0175:2,2:14.7:1:25.3:1:0.09026:9.02315:60:6:0.018:0:1 +20 39721346 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTATTTCATTTTGTTTT;RSEQ=TTGCCATGCAATTTTGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:1,92:93,2:0.0211:1,2:37:1:31.5:1:0.04188:65.40:60:4:0.0213:0:1 0/0:46:0:0,0:0,46:46,0:0:1,0:22:1:30.7:1:1:0:60:92:1:0:0.1 +20 39721373 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57003;SOR=0.6488;LSEQ=TGCAATTTTGAGGAAGGGGC;RSEQ=TCAGGTGTTAACTCTTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:15:1,14:1,45:46,15:0.2459:1,1:28.8:1:33.4:1:0.43443:3.14:60:30:0.2542:0:1 0/1:23:4:0,4:0,19:19,4:0.1739:1,0:26:1:33.5:1:1:0:60:8:0.1739:0:1 +20 39725802 . A G 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAATTCGCTAGCCCTGGGT;RSEQ=TTTATGCTTAGAACATGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:273,81:354,0:0:2,0:21.7:1:29.1:1:1:0:60:708:1:0:0.1 0/1:215:16:13,3:145,53:198,16:0.0744:2,2:22:1:31.2:1:0.57033:1.58:60:32:0.0755:0:1.1 +20 39725993 . C A 53 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02988;SOR=Inf;LSEQ=TGGAGAAAGGTACTGTAGCC;RSEQ=ATGTGTTAATATCCTAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:145,318:463,0:0:2,0:24.7:1:31.6:1:1:0:60:37.583:1:0:0.1 0/1:331:4:2,2:104,223:327,4:0.0121:2,2:6.3:1:26.8:1:0.59571:2.14:60:8:0.0122:0:1 +20 39726776 . T C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.19299;LSEQ=CTGAAAAAATGGTGCTTGGG;RSEQ=GTATTTGCAAAGAAACCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:40:36,4:105,14:119,40:0.2516:2,2:20.8:1:31.1:1:1:1.20:60:39:0.2516:0:1 0/1:99:6:5,1:85,7:92,6:0.0606:2,2:22.3:1:31.2:1:0.40851:2.39852:60:12:0.0612:0:1.2 +20 39728677 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03756;SOR=Inf;LSEQ=ATCTGAATCTATTTTGAGTA;RSEQ=TTTCTTGCTGTCTTCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:276,129:405,0:0:2,0:23:1:32.5:1:1:0:60:100.25:1:0:0.1 0/1:320:4:1,3:212,104:316,4:0.0125:2,2:18:1:25:1:0.11064:6.07896:60:3:0.0096:0:1.5 +20 39729777 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15739;SOR=Inf;LSEQ=TTATGCTCAGCAGATAGGTC;RSEQ=ACTTGGGGTCATGAAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:232,43:275,0:0:2,0:23.4:1:31.3:1:1:0:59.9:44.833:1:0:0.1 0/1:182:2:1,1:144,36:180,2:0.011:2,2:27.5:1:28:1:0.36616:3.95925:60:4:0.0111:0:1.5 +20 39730165 . AT A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCTTCCTACAGTGCCTCC;RSEQ=TTTTTTGGTCACATTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:0,2:0,46:46,2:0.0417:1,0:23.5:1:32:1:1:0:60:4:0.0435:0:0 0/0:16:0:0,0:0,16:16,0:0:1,0:19.8:1:29.1:1:1:0:60:32:1:0:0.1 +20 39741340 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53482;SOR=0;LSEQ=AGCTGGGATTATAGGCTTGC;RSEQ=CCACCTTGCCTGGCTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:2,0:131,5:136,2:0.0145:1,0:17:1:30.5:1:1:0:60:4:0.0148:0:1 0/0:79:0:0,0:74,5:79,0:0:2,0:22.6:1:29.3:1:1:0:60:38.5:1:0:0.1 +20 39741348 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.534;SOR=0;LSEQ=TTATAGGCTTGCGCCACCTT;RSEQ=CCTGGCTATATTCAAAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:150,9:159,2:0.0124:2,0:14.5:1:31:1:1:0:60:4:0.0126:0:1 0/0:93:0:0,0:83,10:93,0:0:2,0:22.9:1:31.5:1:1:0:60:92:1:0:0.1 +20 39741622 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53599;SOR=0;LSEQ=AGCTTAACAAAGGGAGTTTC;RSEQ=GCTCTGCCCCAGGCCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:25,166:191,2:0.0104:2,2:8:1:29.5:1:0.25189:6.53:60:4:0.0105:0:1 0/0:110:0:0,0:12,98:110,0:0:2,0:24.9:1:29.6:1:1:0:59.7:109:1:0:0.1 +20 39742944 . T C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01792;SOR=3.39053;LSEQ=CATGCCTGTAGACCCAGCTA;RSEQ=TCAGAAGGCTGAGACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:36:0,36:0,54:54,36:0.4:1,1:26.3:1:33.3:1:1:0:60:35:0.3977:0:1.3 1/0:23:16:0,16:0,7:7,16:0.6957:0,1:20.6:1:31.3:1:1:0:60:15:0.6818:0:1 +20 39743905 . G A 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00012;SOR=0;LSEQ=TCTCGGTGACGGATGTATGC;RSEQ=TGTTCCTTGTGCCTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:24:22,2:153,8:161,24:0.1297:1,2:22.3:1:30.8:1:0.62107:1.73244:60:48:0.1311:0:1.2 0/0:82:0:0,0:78,4:82,0:0:1,0:25.1:1:29.6:1:1:0:59.9:81:1:0:0.4 +20 39743916 . G A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11848;SOR=Inf;LSEQ=GATGTATGCGTGTTCCTTGT;RSEQ=CCTTTTTCTTTGCAAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:184,17:201,0:0:2,0:25.8:1:32.7:1:1:0:60:200:1:0:0.3 0/1:106:2:1,1:94,9:103,2:0.0189:2,2:7.5:1:25:1:0.18223:9.96106:60:4:0.0196:0:1 +20 39743921 . T G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGCGTGTTCCTTGTGCCTT;RSEQ=TTCTTTGCAAGTTTCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:193,21:214,0:0:2,0:25.8:1:31.5:1:1:0:60:428:1:0:0.2 0/1:126:27:21,6:89,10:99,27:0.2143:2,2:20.7:1:31:1:0.10842:2.52036:60:54:0.2195:0:1.1 +20 39744650 . A G 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.4697;SOR=Inf;LSEQ=TGAGCCCGGGAGGTGGAGGC;RSEQ=GCAGTGAACCGAGATTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:16.6:1:31.4:1:1:0:60:10:0.5:0:1.4 1/1:2:2:2,0:0,0:0,2:1:0,0:44.5:1:30:1:1:0:60:4:1:0:1 +20 39744789 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTCTTTTCCTCTTTCC;RSEQ=TAACTTCCCACTTGTAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:2,0:119,0:119,2:0.0165:1,0:35.5:1:30:1:1:0:60:4:0.0165:0:2.5 0/0:57:0:0,0:57,0:57,0:0:1,0:24.3:1:30.9:1:1:0:60:114:1:0:1 +20 39744810 . C A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32593;SOR=0;LSEQ=TAACTTCCCACTTGTAGGGC;RSEQ=ATAAACTTGACAAGATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:182:182:179,3:0,0:0,182:1:0,1:22.9:1:30.7:1:1:0:59.7:181:1:0:1.1 1/1:88:87:85,2:0,0:0,87:0.9886:0,1:25.7:1:29.6:1:1:0:60:174:1:0:1.2 +20 39745104 . C G 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00512;SOR=Inf;LSEQ=TGACCTTGCTTATCTAAGGC;RSEQ=TAGAGTCAGTTCTACTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:24,295:319,0:0:2,0:23.7:1:33.1:1:1:0:60:78.75:0.9968:0:0.1 0/1:173:5:0,5:20,148:168,5:0.0289:2,0:30.4:1:32.4:1:1:0:60:10:0.0292:0:1.2 +20 39746588 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05172;SOR=Inf;LSEQ=GAGTTCCTCTTGTGATAGGA;RSEQ=TTTACCCAGGCCAAGCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:22,0:0:1,0:27.1:1:31:1:1:0:58.6:44:1:0:0 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:24:1:27.5:1:1:3.1622:60:4:0.2857:0:1 +20 39750210 . G GT 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.24273;SOR=4.31955;LSEQ=GCCTTCATGAAGCCACCCTT;RSEQ=TTTTTTTTTATCTGACAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:1:1,0:78,3:81,1:0.0122:1,0:41:0:28:0:1:0:60:2:0.0123:0:0 0/1:39:2:2,0:37,0:37,2:0.0513:1,0:13.5:1:29.8:1:1:0:60:4:0.0513:0.0256:0 +20 39750722 . C T 61 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24968;SOR=3.28149;LSEQ=TGGAAGTTCAAGCCACAGAC;RSEQ=GAGAGGAAAATAAACAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:2:0,2:243,283:526,2:0.0038:2,0:1:0:27:1:0.50222:0:60:4:0.0038:0:1 0/1:406:5:1,4:199,201:400,5:0.0123:2,2:6.2:1:26.6:1:0.37209:3.94824:49.2:10:0.0125:0:1.4 +20 39750978 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGTCTGTAAATGCATTG;RSEQ=AACATTCTGGTTGCTCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:0,39:39,2:0.0488:1,2:24:1:27.5:1:0.04878:0:60:4:0.0488:0:1 0/0:8:0:0,0:0,8:8,0:0:0,0:25.9:1:33.4:1:1:0:60:16:1:0:0 +20 39751809 . C T 175 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0.02774;LSEQ=TTGCTGAGTCACCCTAATCC;RSEQ=CCCCTTATTTCTCCTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:52:32,20:545,373:918,52:0.0536:2,2:25.6:1:30.8:1:0.88471:1.09:58.1:104:0.0541:0:1.1 0/0:638:1:0,1:386,251:637,1:0.0016:2,0:1:0:22:0:0.39498:0:51:2:0.0016:0:1 +20 39763263 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCAGCCCCCGTCTGCC;RSEQ=TCCTGGTCTCATCACTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:1,13:14,2:0.125:1,2:29:1:32:1:0.24167:9.54:60:4:0.125:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:28.8:1:29.8:1:1:0:60:12:1:0:0.2 +20 39792593 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16663;SOR=Inf;LSEQ=GGACCAGTTCTCCAGTGAGT;RSEQ=CTCCTTGGAAGCCTATGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:86,51:137,0:0:2,0:26.6:1:30.9:1:1:0:60:26.4:1:0:0.2 0/1:95:2:1,1:55,38:93,2:0.0211:2,2:5:1:27.5:1:1:1.44159:60:4:0.0215:0:1 +20 39792604 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17834;SOR=Inf;LSEQ=CCAGTGAGTCCTCCTTGGAA;RSEQ=CCTATGCTCGCTGCCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:96,62:158,0:0:2,0:27.8:1:32.6:1:1:0:60:51.667:1:0:0.1 0/1:116:2:1,1:66,48:114,2:0.0172:2,2:7.5:1:27:1:1:1.37115:60:4:0.0174:0:1.5 +20 39792622 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16834;SOR=Inf;LSEQ=AAGCCTATGCTCGCTGCCTG;RSEQ=GGATGGGCTGTCGCTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:110,79:189,0:0:2,0:27.2:1:31.6:1:1:0:60:378:1:0:0.2 0/1:132:2:1,1:72,58:130,2:0.0152:2,2:25.5:1:31:0:1:1.23933:60:4:0.0157:0:1 +20 39792643 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15343;SOR=Inf;LSEQ=GGATGGGCTGTCGCTGCATT;RSEQ=AGTGTGCGTGGGGTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:100,98:198,0:0:2,0:25.6:1:32:1:1:0:60:32:1:0:0.2 0/1:128:2:1,1:61,65:126,2:0.0156:2,2:42.5:1:29.5:1:1:1.07:60:4:0.0157:0:1 +20 39792671 . A G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29259;SOR=0;LSEQ=GTGGGGTCCAGGGCTGGGGG;RSEQ=GGGAAGATGGGAGGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:1,2:73,81:154,3:0.0191:2,2:27.3:1:31:1:1:1.79599:60:6:0.0199:0:1 0/0:95:0:0,0:42,53:95,0:0:2,0:22.7:1:28.6:1:1:0:60:22.75:1:0:0.1 +20 39794101 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTTCCAGGAATGGTATCC;RSEQ=CACTACTTTGTTCTGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:13:1:33:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 39924558 . C T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01915;SOR=Inf;LSEQ=AGTGTAAGAATTTGTACATT;RSEQ=GCAAGAAATGAAATAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:303,188:491,0:0:2,0:27.8:1:30.8:1:1:0:59.8:39.917:0.9979:0:0.2 0/1:410:5:1,4:237,168:405,5:0.0122:2,2:8.2:1:24.6:1:0.16625:5.62133:60:4:0.0099:0:1.4 +20 39924613 . T G 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTTTGATCTTCTCGTTCAGT;RSEQ=GGTTGTCCTTTATAATGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:618:0:0,0:274,344:618,0:0:2,0:25.3:1:30.5:1:1:0:60:50.5:1:0:0.1 0/1:558:15:6,9:258,285:543,15:0.0269:2,2:31.5:1:30.7:1:0.61037:1.35716:60:30:0.027:0:1.9 +20 39924630 . G T 216 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=275.29396;LSEQ=AGTTGGTTGTCCTTTATAAT;RSEQ=CTATTTAAGTTCATAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:531:1:1,0:234,296:530,1:0.0019:2,0:34:0:13:0:0.44256:0:60:0:0:0:4 0/1:505:173:76,97:151,180:331,173:0.3426:2,2:25.2:1:29.1:1:0.77738:1.07052:60:85.5:0.3413:0:1.2 +20 39925035 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATACTACCTGTCACCAC;RSEQ=GGGATCACCAGGACTGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40709305 . G A 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5743;SOR=0;LSEQ=TGGCTGGTTAGGTTGAAAAG;RSEQ=AAGCCTGGGCCTTTTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:5:5,0:38,0:38,5:0.1163:1,0:22.4:1:29.6:1:1:0:60:10:0.119:0:1 0/0:12:0:0,0:12,0:12,0:0:0,0:23.9:1:31.1:1:1:0:60:24:1:0:0.1 +20 40709990 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACGTTAATATGGCCTCA;RSEQ=TTTGACTAAGACCACTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:45:1:31:1:0.33333:0:58.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40710055 . G A 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCTCCTCGTGCATGGTGC;RSEQ=GTGGTCCACCATGGTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:21.3:1:32:1:1:1.73:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40710486 . C T 57 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1631;SOR=0;LSEQ=AGGTCAAGGGAACTAGTCAG;RSEQ=CCTGGCTGTTGGAGAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:5:2,3:335,146:481,5:0.0103:2,2:11.6:1:24.6:1:0.17081:3.43182:60:4:0.0084:0:1 0/0:293:0:0,0:192,101:293,0:0:2,0:25.2:1:30.6:1:1:0:60:57.6:1:0:0.1 +20 40710711 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1321;SOR=Inf;LSEQ=TAGGTCCCTTCCAGGCACCT;RSEQ=ATGATTCTAAAGCTACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:14,148:162,0:0:2,0:20.9:1:31.7:1:1:0:60:39.5:1:0:0.1 0/1:93:2:1,1:12,79:91,2:0.0215:2,2:26:1:27.5:1:0.26134:6.36:60:4:0.0215:0:1 +20 40713251 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33946;SOR=3.03613;LSEQ=CCTAGGACTGGGGTATGTGG;RSEQ=CAGCAGCATCTGCAAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:2:0,2:413,107:520,2:0.0038:2,0:4:1:28.5:1:0.04329:0:60:4:0.0039:0:1 0/1:260:3:1,2:189,68:257,3:0.0115:2,2:19.7:1:26.3:1:0.17737:5.51497:60:6:0.0116:0:1 +20 40713469 . C T 131 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.76348;LSEQ=ACTGGAGGTGCTGGACTATA;RSEQ=GATAACCATCCTGTGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:935:1:0,1:360,573:933,1:0.0011:2,0:24:0:32:0:1:0:60:2:0.0011:0:1 0/1:601:21:8,13:249,330:579,21:0.0349:2,2:30:1:30:1:0.8231:1.22573:60:20:0.0341:0:1.1 +20 40713532 . G A 127 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.55048;LSEQ=GTTCTGCTGGGGATGCTTGC;RSEQ=TACATGCACCTTGCAGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:2:2,0:107,329:436,2:0.0046:2,0:1:0:26.5:1:0.0615:0:60:4:0.0046:0:1 0/1:281:21:8,13:81,177:258,21:0.0747:2,2:19.3:1:29.1:1:0.62685:1.34:60:42:0.0769:0:1.2 +20 40713538 . G A 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30465;SOR=4.73638;LSEQ=CTGGGGATGCTTGCGTACAT;RSEQ=CACCTTGCAGATACCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:1:0,1:83,300:383,1:0.0026:2,0:47:0:12:0:1:0:48:0:0:0:8 0/1:245:3:1,2:76,166:242,3:0.0122:2,2:25.7:1:29.3:1:1:1.09:60:6:0.0123:0:1.3 +20 40714097 . G C 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAGACACAGTGGGGAA;RSEQ=AGCTAATGTCTAAGAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:3,1:6,0:6,4:0.4:0,2:27.8:1:31.5:1:0.4:0:60:8:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40714218 . G A 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18296;SOR=0;LSEQ=TCATTGCTGAGTCTGGAGCC;RSEQ=GAATCAGCACAGGCATCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:6:6,0:73,1:74,6:0.075:1,0:31.2:1:31:1:1:0:60:12:0.0779:0:1 0/0:31:0:0,0:30,1:31,0:0:1,0:19.8:1:29.5:1:1:0:60:30:1:0:0.1 +20 40714305 . T C 192 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGGCTCAGCGGGATCCTCTC;RSEQ=CGGCAGCCTCCATCTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:66:56,10:254,62:316,66:0.1728:2,2:25:1:31.9:1:0.48988:1.37:60:132:0.1769:0:2.1 0/0:205:0:0,0:149,56:205,0:0:2,0:23.6:1:29.6:1:1:0:60:40:1:0:0.1 +20 40714307 . G A 211 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCAGCGGGATCCTCTCTC;RSEQ=GCAGCCTCCATCTGTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:121:97,24:220,64:284,121:0.298:2,2:25.3:1:30.6:1:0.59987:1.18:60:59.5:0.3013:0:1.7 0/0:224:0:0,0:159,65:224,0:0:2,0:22.6:1:29.3:1:1:0:60:55:1:0:0.1 +20 40714479 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=1.55218;LSEQ=CCGGAGGTCTTCTCAGGCCA;RSEQ=TACTGCATACAGAACTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:781:229:86,143:223,329:552,229:0.2932:2,2:24.8:1:30.3:1:0.47057:1.12689:60:37.167:0.2889:0:1.8 0/1:439:172:65,107:109,158:267,172:0.3918:2,2:26.1:1:29.6:1:0.54976:1.13531:60:85:0.3908:0:1.6 +20 40714524 . C G 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1187;SOR=0.77322;LSEQ=GAAAGAGGTCACAGAAGGAG;RSEQ=TCAAAGGCAGGGGGCGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:442:267:44,223:31,142:173,267:0.6041:2,2:26.3:1:32:1:0.69891:1.10618:60:88:0.6097:0:2.1 1/0:231:125:29,96:29,76:105,125:0.5411:2,2:23.4:1:30.2:1:0.45063:1.26186:59.8:30.25:0.545:0:2.2 +20 40714539 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07937;SOR=1.43231;LSEQ=AGGAGCTCAAAGGCAGGGGG;RSEQ=GGGTATCAAAGTCTCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:94:8,86:27,229:256,94:0.2655:2,2:26.3:1:30.7:1:0.68954:1.26661:60:93:0.2711:0:2.7 0/1:167:57:9,48:17,93:110,57:0.3413:2,2:25.4:1:28.7:1:1:1.03:59.1:27.5:0.3416:0:2.8 +20 40714540 . G C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00032;SOR=0.43536;LSEQ=GGAGCTCAAAGGCAGGGGGC;RSEQ=GGTATCAAAGTCTCATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:116:10,106:26,207:233,116:0.3324:2,2:26.3:1:30.1:1:0.57608:1.33034:60:115:0.3343:0:2 0/1:163:29:4,25:20,114:134,29:0.1779:2,2:25.1:1:29.1:1:1:1.09588:60:28:0.1761:0:2 +20 40714592 . CT C 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.73479;SOR=1.36089;LSEQ=TCTTTTCTTTTTTTCTTTTT;RSEQ=TTTTTTTTTTTGAGATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:7:0,7:1,104:105,7:0.0625:1,0:24.4:1:34.1:1:1:0:60:14:0.0654:0:1 0/1:48:4:0,4:2,42:44,4:0.0833:1,0:32.3:1:33.3:1:1:0:60:8:0.0909:0:1.5 +20 40726827 . C T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06118;SOR=Inf;LSEQ=CAACAGAGTCTGGTCCCGGG;RSEQ=GGGGAGTTGGACAAAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:15,0:13,1:14,15:0.5172:1,1:18.7:1:27.8:1:0.48276:0:57.3:6.5:0.4815:0:1.5 1/1:6:6:6,0:0,0:0,6:1:0,0:34:1:27.3:1:1:0:60:5:1:0:1 +20 40727000 . C T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGGCTGTCAAGGGATCTC;RSEQ=CTCCAGGTTTAGAGCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:527:0:0,0:408,119:527,0:0:2,0:24.3:1:30.8:1:1:0:60:36.643:1:0:0.1 0/1:227:28:22,6:148,51:199,28:0.1233:2,2:21.9:1:30.4:1:0.81652:1.26:60:56:0.1239:0:1.1 +20 40727005 . A T 32 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03076;SOR=Inf;LSEQ=CTGTCAAGGGATCTCCCTCC;RSEQ=GGTTTAGAGCATGGCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:0:0,0:422,139:561,0:0:2,0:24.8:1:30.4:1:1:0:60:42.154:1:0:0.1 0/1:257:3:0,3:188,66:254,3:0.0117:2,0:5.7:1:20.3:1:0.01874:0:60:2:0.0079:0:1 +20 40727345 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATCTCTCCACGCCCTGGC;RSEQ=GCAAAGGGGACCTTCTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:0,2:0,51:51,2:0.0377:1,0:26:1:32.5:1:1:0:60:4:0.0377:0:1 0/0:12:0:0,0:1,11:12,0:0:2,0:21.3:1:31:1:1:0:60:24:1:0:0 +20 40730515 . C T 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGACTTGCCATGGTGACA;RSEQ=GGGAGCCACCTTACGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:5,6:0.5455:0,0:28.8:1:30:1:1:0:58.5:12:0.5455:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:2:0:31:0:1:0:60:2:1:0:1 +20 40730976 . T A 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=AATAGATAGGCCCTGCTCAT;RSEQ=TGGCTGCCCCTGAGCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:47,228:275,0:0:2,0:25.1:1:30.3:1:1:0:60:38.286:1:0:0.1 0/1:145:8:3,5:28,109:137,8:0.0552:2,2:12.6:1:28.1:1:0.3682:2.32:60:16:0.0567:0:1 +20 40731628 . T C 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCTCTACTTCAGATCAATAA;RSEQ=GGCTATTTGTTTTAGGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:37:0:14:0:1:0:60:0:0:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:28:1:1:0:60:4:1:0:1 +20 40733082 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2766;SOR=0.67432;LSEQ=GATTTACTGGAAGCTTGATG;RSEQ=TGGGCTTCTCAGCCTCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:118:77:75,2:41,0:41,77:0.6525:1,1:27:1:30.7:1:0.54266:0:59.6:154:0.6581:0:1.1 1/0:43:24:24,0:19,0:19,24:0.5581:1,1:28.1:1:29.8:1:1:0:60:23:0.575:0:1 +20 40733136 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10589;SOR=Inf;LSEQ=AGTGTCTGTCATTTAAACCA;RSEQ=CCAATCTATGGAAATTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:293,104:397,0:0:2,0:21.4:1:31.9:1:1:0:60:98.25:1:0:0.2 0/1:192:2:1,1:145,45:190,2:0.0104:2,2:40:1:30:0:0.42272:3.19797:60:4:0.0105:0:1 +20 40733340 . G A 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06864;SOR=6.72323;LSEQ=CGCTTCCAGGATGGCATCGT;RSEQ=CACAAACACATATTGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:540:1:0,1:207,331:538,1:0.0019:2,0:20:0:26:0:1:0:60:2:0.0019:0:1 0/1:324:4:2,2:129,190:319,4:0.0123:2,2:9:1:27.8:1:1:1.47:60:8:0.0125:0:1 +20 40733361 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04909;SOR=Inf;LSEQ=CACAAACACATATTGCTCCT;RSEQ=CAAAGTCAGAAGAGAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:147,310:457,0:0:2,0:26.1:1:32:1:1:0:60:44.7:1:0:0.1 0/1:265:3:2,1:104,158:262,3:0.0113:2,2:13.7:1:26.3:1:0.56581:3.03:60:6:0.0114:0:1 +20 40733362 . C A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14183;SOR=5.22892;LSEQ=ACAAACACATATTGCTCCTG;RSEQ=AAAGTCAGAAGAGAGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:1:1,0:142,307:449,1:0.0022:2,0:1:0:27:0:0.31778:0:60:2:0.0023:0:1 0/1:260:3:2,1:100,155:255,3:0.0115:2,2:11.3:1:26.3:1:0.5641:3.09:60:6:0.0117:0:1 +20 40733421 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13139;SOR=Inf;LSEQ=AGTGGCCTGGGAATTAGCTG;RSEQ=CCACATTTAGTGTTGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:23,152:175,0:0:2,0:23.8:1:29.9:1:1:0:59.9:34:1:0:0 0/1:100:2:1,1:20,78:98,2:0.02:2,2:24.5:1:27.5:1:0.37758:3.83:60:4:0.0208:0:1.5 +20 40733646 . G T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTTGGTGTCCAGCCCAT;RSEQ=TCCCCTCAGCTTTCACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:30.5:1:29:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40738925 . C T 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12732;SOR=5.57706;LSEQ=TGGTCTCGAACTCCTGACCT;RSEQ=GTGATCTGCCCGCCTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:1:1,0:329,96:425,1:0.0023:2,0:20:0:14:0:1:0:33:0:0:0:1 0/1:231:3:2,1:172,56:228,3:0.013:2,2:20.7:1:29.3:1:0.57445:1.53258:50:6:0.013:0:1.3 +20 40738926 . G A 173 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTCTCGAACTCCTGACCTC;RSEQ=TGATCTGCCCGCCTCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:54:42,12:297,90:387,54:0.1219:2,2:23:1:30.2:1:1:1.06:49.4:53:0.1221:0:1.1 0/0:241:0:0,0:179,61:240,0:0:2,0:23.6:1:29.7:1:1:0:53.3:119:0.9958:0:0.1 +20 40739158 . G A 41 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30522;SOR=4.68844;LSEQ=AACGGGCCTCTGTTCTTCCA;RSEQ=CTGCTGCCCTCGCATACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:1:1,0:108,293:401,1:0.0025:2,0:1:0:28:0:0.27114:0:60:2:0.0025:0:1 0/1:259:3:2,1:79,177:256,3:0.0116:2,2:5.7:1:26:1:0.2313:4.45:60:6:0.0119:0:1.3 +20 40739205 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAACACGTGGAGCCATAGCT;RSEQ=CTGCACTGAGGAACCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:18,164:182,2:0.0109:2,2:25.5:1:26.5:1:0.19636:8.90:60:4:0.0111:0:1 0/0:85:0:0,0:13,72:85,0:0:2,0:22.3:1:31.4:1:1:0:60:41.5:1:0:0.2 +20 40739243 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06708;SOR=Inf;LSEQ=CCGCAGGGACAGGGCCCTCA;RSEQ=AGTGTTTGTTAATAGGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:1,112:113,0:0:1,0:23.5:1:32.3:1:1:0:59.7:36.667:1:0:0.1 0/1:40:2:1,1:0,38:38,2:0.05:1,2:39.5:1:29.5:1:0.05:0:60:4:0.0513:0:1 +20 40743756 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11384;SOR=Inf;LSEQ=GGGGCTGGACGTAGAGCAGA;RSEQ=CCTCAGTTACCACATGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:197,20:217,0:0:2,0:22.6:1:32.1:1:1:0:60:42.4:1:0:0.3 0/1:111:2:2,0:104,5:109,2:0.018:1,0:23:1:31:0:1:0:60:4:0.0187:0:2 +20 40743829 . A G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00072;SOR=1.47949;LSEQ=CCGGCTGCCCACAGCCTCCA;RSEQ=GAAGCTTACCTTCTGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:735:394:256,138:206,135:341,394:0.5361:2,2:24.5:1:32.4:1:0.22082:1.22:59.9:130.333:0.5364:0:1.1 1/0:542:342:223,119:118,81:199,342:0.631:2,2:23.5:1:30.8:1:0.19599:1.29:60:56:0.6316:0:1.2 +20 40744209 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGCAAAGCTCCTTGTAA;RSEQ=TTTCCAATGCATTATCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:7.5:1:29:1:1:0:60:4:0.2222:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:19:1:33:0:1:0:60:4:1:0:1 +20 40746918 . C T 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00068;SOR=0;LSEQ=AATAGGAGTGATGACACCTC;RSEQ=CTTGTAGGTTGCCGTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:25:25,0:92,2:94,25:0.2083:1,1:27.1:1:31.4:1:1:0:60:11.5:0.2054:0:1.2 0/0:41:0:0,0:41,0:41,0:0:1,0:20.8:1:30.5:1:1:0:60:40:1:0:0 +20 40747209 . C T 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGCTGAGAAGGTTTGTCCC;RSEQ=CCGGTTGGTCAAGTCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:43,242:285,0:0:2,0:23.8:1:30.9:1:1:0:60:34.625:1:0:0.1 0/1:173:12:1,11:36,125:161,12:0.0694:2,2:23.8:1:29.2:1:0.4652:3.15284:60:24:0.0714:0:1 +20 40747211 . C T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GCTGAGAAGGTTTGTCCCCC;RSEQ=GGTTGGTCAAGTCTCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:41,230:271,0:0:2,0:24.1:1:29.9:1:1:0:60:66.75:1:0:0.1 0/1:168:11:3,8:32,125:157,11:0.0655:2,2:16.6:1:29.5:1:0.6999:1.46:60:22:0.0671:0:1 +20 40748532 . C A 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGCCCTTTCCCCTGGGACC;RSEQ=CTGAAGCCTCTCTGAGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:27:20,7:368,185:553,27:0.0465:2,2:19:1:29.9:1:0.53145:1.44:60:54:0.0469:0:1.1 0/0:369:0:0,0:240,129:369,0:0:2,0:23.6:1:30:1:1:0:60:91.25:1:0:0.1 +20 40748802 . C A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31714;SOR=0;LSEQ=GTGTAGTAAGTCACTAAATG;RSEQ=TAGCTATTTTTATAGTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:5:0,5:0,57:57,5:0.0806:1,0:25.6:1:32.8:1:1:0:60:10:0.0806:0:1 0/0:23:0:0,0:0,23:23,0:0:1,0:22:1:32:1:1:0:60:22:1:0:0.1 +20 40750184 . C T 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTCCGGAACTCAGCTGC;RSEQ=TGGGTTTGAACGCTGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:16:0:32:0:1:1:60:4:0.5:0:1.5 +20 40756792 . T C 50 d5;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTGCTATTCTCTCTAAC;RSEQ=AGAGGCCCCTCTCCCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:5:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40757307 . C T 135 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=39.10074;LSEQ=CCAGACTGCTCTGGAAGGGC;RSEQ=ACCTTCTGGAGGAGAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:907:1:0,1:612,293:905,1:0.0011:2,0:1:0:24:0:0.3245:0:60:2:0.0011:0:1 0/1:555:23:17,6:354,177:531,23:0.0414:2,2:22.6:1:30:1:0.65117:1.42:60:46:0.0422:0:1.2 +20 40770705 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09473;SOR=Inf;LSEQ=AGCTTTATGGAAGTGGAGAT;RSEQ=AACCAACAGGGCAAAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:55,252:307,0:0:2,0:23.9:1:32.1:1:1:0:59.9:60.4:1:0:0.1 0/1:137:2:1,1:26,109:135,2:0.0146:2,2:19.5:1:29:1:0.35648:4.13:60:4:0.0149:0:1 +20 40790143 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02826;SOR=Inf;LSEQ=GGTAGGGATGAGTCTGGATC;RSEQ=TGAGGGTGGGCTGGGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:175,374:549,0:0:2,0:26.2:1:31.4:1:1:0:59.9:182:1:0:0.1 0/1:383:4:1,3:137,241:378,4:0.0104:2,2:20.5:1:25.3:1:1:1.70322:60:3:0.008:0:1 +20 40790182 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14236;SOR=Inf;LSEQ=GCTCCCCGCGGCTGCCATCT;RSEQ=CTTCGAAAAGAAGGAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:61,260:321,0:0:2,0:23:1:32.5:1:1:0:60:106:1:0:0.1 0/1:195:2:1,1:47,146:193,2:0.0103:2,2:21:1:26.5:1:0.43267:3.08:60:4:0.0105:0:1 +20 40790219 . T C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54097;SOR=0;LSEQ=GCAGAACAGATCATCACCTA;RSEQ=AGAAGCTTTGCCCTTTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:23,134:157,2:0.0126:2,2:33:0:31.5:1:0.27991:5.72:60:4:0.0129:0:1 0/0:87:0:0,0:16,71:87,0:0:2,0:20.8:1:27.7:1:1:0:60:42.5:1:0:0.1 +20 40790248 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCCTTTGTCCTCCCTGTC;RSEQ=CCCCCAGCTTGGCCTGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:11,86:97,2:0.0202:2,2:19.5:1:30:0:0.22882:7.53:60:4:0.0208:0:1.5 0/0:36:0:0,0:3,33:36,0:0:2,0:22.9:1:28.5:1:1:0:60:35:1:0:0.1 +20 40827713 . A T 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00925;SOR=0.24584;LSEQ=TTCCTTTTCATCTTAGGATG;RSEQ=ACTGCCCCAAGTCTTTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:36:36,0:68,0:68,36:0.3462:1,1:20:1:31.1:1:1:0:60:72:0.3529:0:1.2 0/1:35:4:4,0:30,1:31,4:0.1143:1,0:24.8:1:30.5:1:1:0:60:8:0.1143:0:1 +20 40827934 . C T 176 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=90.19426;LSEQ=GCCTTCATCATTGCGGCTGG;RSEQ=GCTGAGCTTGGTGGTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1310:1:0,1:644,665:1309,1:8e-04:2,0:1:0:30:0:1:0:60:2:8e-04:0:1 0/1:1007:65:27,38:447,495:942,65:0.0645:2,2:24.7:1:29.3:1:0.37144:1.27063:60:130:0.0658:0:1.2 +20 40828272 . A G 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCCTAAAATGGGAAATC;RSEQ=ATGAGACTTGTACAATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:28.7:1:34:0:1:0:60:6:0.2308:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40843031 . C G 76 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08462;SOR=5.24148;LSEQ=ATGAGCATCCTGTCTGCTCA;RSEQ=TGCCTCTGTTGGGTACCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:2,0:22,0:22,2:0.0833:1,0:36:1:30.5:1:1:0:60:4:0.0833:0:1 0/1:15:5:5,0:10,0:10,5:0.3333:0,0:16.6:1:32.8:1:1:0:60:10:0.3333:0:1 +20 40843115 . TC T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.16991;SOR=Inf;LSEQ=CCTCATCTAGGGCTTGTGAA;RSEQ=CCCCAGCATGGCAAAGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:93,66:159,0:0:2,0:26.8:1:31.7:1:1:0:60:158:1:0:0.2 0/1:112:2:1,1:64,46:110,2:0.0179:2,2:30:0:30:1:1:1.38711:60:4:0.0183:0:0 +20 40843148 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.51198;SOR=0;LSEQ=CAAAGTTACAGAAGCAACAG;RSEQ=AGCAGCAACAGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:98,99:197,2:0.0101:2,2:37.5:1:30:1:1:1.01:60:4:0.0102:0:1 0/0:143:0:0,0:72,71:143,0:0:2,0:28.3:1:31.8:1:1:0:59.5:142:1:0:0.1 +20 40863924 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTATTATTATTTTGAGA;RSEQ=GGAGTTTTGCTCTTGTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:30.5:1:1:0:36.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40877252 . CA C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54478;SOR=0;LSEQ=CTGGACAATGATCAACAGAG;RSEQ=AAAACCTGGCCACACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:163,17:180,2:0.011:2,2:16.5:1:31:1:0.18851:9.34663:60:4:0.011:0:0 0/0:97:0:0,0:82,15:97,0:0:2,0:26.4:1:30.2:1:1:0:60:194:1:0:0.1 +20 40877288 . C T 113 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=30.86869;LSEQ=CAGCAGTGTTGAGGTCACCT;RSEQ=GGGTCAGCAGAGTCTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:0,1:255,72:327,1:0.003:2,0:1:0:26:0:0.22256:0:60:2:0.0031:0:1 0/1:173:15:11,4:119,39:158,15:0.0867:2,2:22.3:1:29.1:1:1:1.10887:60:30:0.0867:0:1.1 +20 40877300 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11338;SOR=Inf;LSEQ=GGTCACCTCGGGTCAGCAGA;RSEQ=TCTTGCAGGCAGCAGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:391:0:0,0:289,102:391,0:0:2,0:25.2:1:32.6:1:1:0:59.9:47.875:1:0:0.1 0/1:199:2:1,1:142,55:197,2:0.0101:2,2:23:0:31.5:1:0.48465:2.56766:60:4:0.0102:0:1.5 +20 40877528 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15612;SOR=Inf;LSEQ=ATGCGACTAGACAATCATCA;RSEQ=AATGACAACAGCTTCCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:31,155:186,0:0:2,0:22.8:1:28.7:1:1:0:59.9:185:1:0:0.1 0/1:122:2:1,1:22,97:119,2:0.0164:2,2:20:1:29.5:1:0.34532:4.33:60:4:0.0167:0:1 +20 40898921 . T G 114 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=1;SOR=1.01166;LSEQ=TGGGTGAATGGGTGGGGGGG;RSEQ=GGGTGGGTGGGTGGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:502:28:1,27:467,0:467,28:0.0558:1,1:9.1:1:23.8:1:0:0:58.9:4.6:0.0497:0:4.3 0/1:266:15:1,14:247,1:248,15:0.0564:1,1:10.1:1:19.1:1:0:2054.06112:59.3:1.5:0.0363:0:4.3 +20 40898925 . T G 107 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=4;SSF=0.88894;SOR=1.06592;LSEQ=TGAATGGGTGGGGGGGTGGG;RSEQ=GGGTGGGTGGGGTGGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:39:1,38:493,1:494,39:0.0728:1,1:9.9:1:20.3:1:0:11158.95014:59.2:2:0.0519:0:4 0/1:285:22:1,21:257,6:263,22:0.0772:1,1:10.2:1:18.3:1:0:788.38971:57.5:1.2:0.0453:0:4.3 +20 40898929 . T G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=4;SSF=1;SOR=1.0012;LSEQ=TGGGTGGGGGGGTGGGTGGG;RSEQ=GGGTGGGGTGGAAAGACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:47:4,43:504,6:510,47:0.0838:1,2:12.8:1:22.2:1:0:802.95216:59.8:2.133:0.0625:0:3.5 0/1:310:26:0,26:272,11:283,26:0.0839:1,1:11.4:1:22.5:1:0:0:59:2.714:0.0655:0:3.7 +20 40898932 . G T 45 v3;q25;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=4;SSF=0.05908;SOR=7.18067;LSEQ=GTGGGGGGGTGGGTGGGTGG;RSEQ=TGGGGTGGAAAGACTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:1:0,1:535,73:608,1:0.0016:2,0:3:0:15:0:0.12151:0:60:0:0:0:1 0/1:342:4:0,4:289,49:338,4:0.0117:2,0:8.8:1:22.5:1:0.00052:0:58.8:3:0.0095:0:2.8 +20 40898933 . T G 144 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.75265;SOR=1.08129;LSEQ=TGGGGGGGTGGGTGGGTGGG;RSEQ=GGGGTGGAAAGACTGCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:616:68:6,62:530,16:546,68:0.1104:1,2:12.8:1:23.8:1:0:330.1406:59.9:3.857:0.0942:0:2.9 0/1:355:42:2,40:289,21:310,42:0.1183:2,1:11.8:1:20.4:1:0:264.54922:59.4:2:0.0872:0:2.8 +20 40900992 . T C 47 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGAAAATATTTACTATC;RSEQ=GTCCTTTTACAGAGGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:31.3:1:29.7:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:47:0:32:0:1:0:60:2:1:0:1 +20 40910575 . C T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCCAGGCAATTCAATTA;RSEQ=AATTAGGAAAACAAAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:17:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40910951 . G A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAACTTTTACTCTATTTTAC;RSEQ=CACTGTGCTACTAATATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:127,1:128,0:0:1,0:21.4:1:30.6:1:1:0:60:256:0.9922:0:0.1 0/1:44:8:8,0:36,0:36,8:0.1818:1,0:11.5:1:30.1:1:1:0:60:16:0.1818:0:1 +20 40944032 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGAGAGGTCATGTAATTT;RSEQ=CTCAAGTAAAGCACCATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:37.5:1:32:1:1:0:60:4:0.25:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:22:0:28:0:1:0:21:2:1:0:2 +20 40944069 . A G 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=TCTCTTTACTTTAATACAGG;RSEQ=GTGTGCAAAGGTTTTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:34.2:1:33:0:1:0:60:12:0.6667:0:1.5 0/0:2:0:0,0:2,0:2,0:0:0,0:24:1:22.5:1:1:0:40.5:1:1:0:1 +20 40944812 . C T 80 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTTGTAGAACTTTACCTC;RSEQ=ACTTAGCTGTCTCAGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:10,7:0.4118:0,0:25.7:1:28.6:1:1:0:60:14:0.4118:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40979160 . T C 222 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.05792;LSEQ=CTTCCTCCGAGGAAGCTTTG;RSEQ=TCCTGGCCAGTCTTGCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:121:119:119,0:2,0:2,119:0.9835:0,1:23.6:1:32.2:1:1:0:59.8:28.75:0.9829:0:1.1 1/0:57:44:44,0:13,0:13,44:0.7719:1,1:25.1:1:32.7:1:1:0:60:88:0.7719:0:1 +20 40979188 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52625;SOR=0;LSEQ=CAGTCTTGCCCATGGGCATT;RSEQ=CCAGTCACATGATTCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:165,19:184,2:0.0108:2,2:20.5:1:28:1:0.20401:8.48825:60:4:0.011:0:1.5 0/0:115:0:0,0:106,9:115,0:0:2,0:22.8:1:32:1:1:0:60:230:1:0:0.5 +20 40979190 . C T 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30074;SOR=0;LSEQ=GTCTTGCCCATGGGCATTGC;RSEQ=AGTCACATGATTCAACTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:4:4,0:170,24:194,4:0.0202:2,0:24:1:34:0:1:0:60:8:0.0204:0:1 0/0:117:0:0,0:108,9:117,0:0:2,0:23.4:1:30.9:1:1:0:60:116:1:0:0.4 +20 40979203 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16669;SOR=Inf;LSEQ=GCATTGCCAGTCACATGATT;RSEQ=AACTGGAGGCCCATGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:207,43:250,0:0:2,0:23.3:1:32.1:1:1:0:60:82.333:1:0:0.4 0/1:173:2:1,1:138,33:171,2:0.0116:2,2:14.5:1:30:1:0.35536:4.13476:60:4:0.0116:0:1.5 +20 40979430 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00932;SOR=0.53047;LSEQ=ATTCCCAACTGGCTCCCCAC;RSEQ=GCCCCTTGCTGCCATCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:186:95:5,90:4,87:91,95:0.5108:1,2:22.9:1:30.9:1:1:1.21:60:94:0.5137:0:1 0/1:118:42:2,40:2,74:76,42:0.3559:1,1:25.9:1:30.2:1:0.61524:1.84:60:41:0.3534:0:1.1 +20 40979469 . A T 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=0;LSEQ=TAAAGACACAGCATGGATAG;RSEQ=GGGAGGACGTTTAGGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:0,20:2,81:83,20:0.1942:1,1:23.4:1:30.9:1:1:0:60:40:0.198:0:1.5 0/0:57:0:0,0:1,56:57,0:0:1,0:22.2:1:30.7:1:1:0:60:56:1:0:0.3 +20 40980486 . G C 91 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTGTACTATTTAATGCAA;RSEQ=CCTGTGGGAAAATTATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:38.3:1:32.7:1:1:0:58.4:14:0.6364:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40980495 . A C 103 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTAATGCAAGCCTGTGGG;RSEQ=AAATTATTTAGTGGCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:10,0:4,0:4,10:0.7143:0,0:25.4:1:31.1:1:1:0:58.9:9:0.6923:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 40980684 . G T 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15612;SOR=0.21661;LSEQ=GAAAATCAGGAAGTGGGGGT;RSEQ=AAACAACCTTTTTTCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:7:1,6:277,65:342,7:0.0201:2,2:8.9:1:25.3:1:0.00035:25.23858:60:14:0.0202:0:1 0/0:227:1:0,1:176,50:226,1:0.0044:2,0:1:0:21:0:0.22467:0:60:2:0.0044:0:1 +20 40980773 . T C 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=51.6456;LSEQ=ACAGGGGGCCCAAAGCCCTT;RSEQ=GCTGTGCTGGCCTTGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1064:1:1,0:601,462:1063,1:9e-04:2,0:28:0:15:0:1:0:60:0:0:0:1 0/1:840:39:24,15:423,378:801,39:0.0464:2,2:24.9:1:29.8:1:0.32616:1.43:60:38:0.0455:0:1.2 +20 40980987 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09613;LSEQ=CACTCAGGAAGCTGGATGGA;RSEQ=CTCCTTTAGAGGAACCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:180:98:3,95:7,74:81,98:0.5444:2,1:25.3:1:29.7:1:0.18885:2.9776:60:18.6:0.5376:0:1.1 0/1:88:9:0,9:7,72:79,9:0.1023:2,0:19.8:1:29.6:1:1:0:60:18:0.1023:0:1 +20 40981002 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03276;SOR=Inf;LSEQ=ATGGAGCTCCTTTAGAGGAA;RSEQ=CTTAGGGAGGCGGGGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:4,132:136,0:0:1,0:22.7:1:31.2:1:1:0:59.5:26.2:1:0:0.7 0/1:65:3:0,3:3,59:62,3:0.0462:1,0:18.7:1:29.7:1:1:0:60:6:0.0476:0:1 +20 40981098 . C A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.22813;LSEQ=TTTCCAGATGATCCCAGCCT;RSEQ=CAAATACCCCATTGCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:0,17:0,14:14,17:0.5484:1,1:23.9:1:30.9:1:1:0:59.5:34:0.5484:0:1.1 1/0:5:3:0,3:0,2:2,3:0.6:0,0:10.7:1:29:1:1:0:60:6:0.6:0:1 +20 41076539 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTCCCAGACGAACTTTCA;RSEQ=TACTGTTTGCCAGGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:36:1:30.5:1:1:0:60:4:0.1667:0:1 0/0:3:0:0,0:2,1:3,0:0:2,0:30:1:30.7:1:1:0:60:6:1:0:0.3 +20 41076751 . T A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=3.60102;LSEQ=CAGAAACCTTTTGGTATGTC;RSEQ=CATCTTACTCACCTTTATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:27:27,0:182,3:185,27:0.1274:1,1:27.2:1:29.8:1:1:0:60:26:0.125:0:1.2 0/1:81:28:26,2:52,1:53,28:0.3457:1,2:20.2:1:29.5:1:0.27321:3.92691:60:27:0.3418:0:1.2 +20 41077028 . G A 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00298;SOR=Inf;LSEQ=CACATCATTTCTCCAGCCCC;RSEQ=CTGACCTAGAACAGGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:44,302:346,0:0:2,0:23.4:1:31.8:1:1:0:59.9:56.667:1:0:0.1 0/1:214:6:1,5:26,181:207,6:0.028:2,2:18.3:1:28.2:1:0.56119:1.39:60:12:0.0284:0:1 +20 41077037 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14831;SOR=Inf;LSEQ=TCTCCAGCCCCGCTGACCTA;RSEQ=AACAGGGGTTGACAAAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:23,262:285,0:0:2,0:25.2:1:32:1:1:0:59.8:39.714:1:0:0 0/1:179:2:1,1:15,162:177,2:0.0112:2,2:15.5:1:30:1:0.17124:10.49:60:4:0.0114:0:1 +20 41100774 . G A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02843;SOR=2.91681;LSEQ=TACATAGTCCTTCATTGAAG;RSEQ=CCTAAGAAAAGAAAGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:12:12,0:68,0:68,12:0.15:1,0:25.8:1:30.3:1:1:0:60:24:0.1538:0:1.2 0/1:38:13:13,0:25,0:25,13:0.3421:1,1:20.9:1:29.4:1:1:0:60:26:0.3421:0:1 +20 41100875 . A T 56 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01533;SOR=9.621;LSEQ=TGAATAGATTCAATATCCCC;RSEQ=TTCCCATGTAAGCTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:772:1:0,1:507,264:771,1:0.0013:2,0:1:0:25:0:0.34326:0:60:2:0.0013:0:1 0/1:486:6:1,5:299,180:479,6:0.0123:2,2:7.2:1:21.8:1:0.0322:8.27411:60:2:0.0084:0:1 +20 41100922 . C T 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=24.22539;LSEQ=TCACCGTCTTCCTCAGTCTG;RSEQ=ACCACCAGCTCCTCGCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1035:2:0,2:544,489:1033,2:0.0019:2,0:16:1:27.5:1:0.22481:0:60:4:0.002:0:1 0/1:758:34:17,17:386,338:724,34:0.0449:2,2:26.7:1:27.4:1:0.72812:1.14181:60:68:0.0452:0:1.1 +20 41101051 . G A 136 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=40.6052;LSEQ=TGGATGACCTCCTCGGCCTC;RSEQ=TACTGCTGCTGGTTGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1068:1:1,0:507,560:1067,1:9e-04:2,0:1:0:26:0:0.47566:0:60:2:9e-04:0:1 0/1:681:25:14,11:321,335:656,25:0.0367:2,2:19.2:1:29.5:1:0.54458:1.33:60:24:0.0355:0:1.2 +20 41101067 . A T 186 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTCGTACTGCTGCTGGTTG;RSEQ=ACACATACTGGTACTGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1062:90:43,47:455,516:971,90:0.0847:2,2:24.3:1:28.8:1:0.91227:1.04:60:89:0.0849:0:1.1 0/0:685:0:0,0:327,358:685,0:0:2,0:25.9:1:29.3:1:1:0:60:61.273:1:0:0.2 +20 41101161 . T G 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGTCAGCTGCCGGGCTC;RSEQ=GATGTCTACGATTTCCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:189,378:567,0:0:2,0:24.9:1:30.8:1:1:0:60:69.875:1:0:0.2 0/1:333:18:6,12:111,204:315,18:0.0541:2,2:24.8:1:28.2:1:1:1.08797:60:17:0.0518:0:2.2 +20 41101180 . G A 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGATGTCTACGATTTCCAC;RSEQ=TTCTGTGGGCCATGTACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:126,325:451,0:0:2,0:25.6:1:31.4:1:1:0:60:44.1:1:0:0.2 0/1:248:13:3,10:69,165:234,13:0.0524:2,2:21.2:1:29.5:1:0.76132:1.39222:60:12:0.0494:0:2.7 +20 41101195 . T C 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCCACGTTCTGTGGGCCATG;RSEQ=ACCGGATCTGCAAAACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:91,294:385,0:0:2,0:24.7:1:28.5:1:1:0:59.9:41.778:1:0:0.2 0/1:192:10:1,9:50,132:182,10:0.0521:2,2:18.7:1:32.1:1:0.29511:3.3928:60:20:0.0524:0:3 +20 41101274 . C A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07638;SOR=3.19008;LSEQ=CTGGGGTACATGTTCTGCTA;RSEQ=AACAGGGAACACAGCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:9:0,9:9,83:92,9:0.0891:2,0:22.6:1:32:1:1:0:60:18:0.09:0:1 0/1:25:6:0,6:4,15:19,6:0.24:2,0:21.7:1:30:1:0.5404:0:60:12:0.24:0:1 +20 41306435 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54565;SOR=0;LSEQ=GAATTATCTGTCACAGGAAG;RSEQ=CAAGAGGAAAGCCAGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:2,0:178,4:182,2:0.0108:1,0:18:1:32:0:1:0:60:4:0.0112:0:1 0/0:98:0:0,0:93,5:98,0:0:2,0:23.1:1:30.5:1:1:0:60:97:1:0:0.3 +20 41306488 . G GAA 204 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=0;SOR=2.33304;LSEQ=CCTCTCATAATGGAGCCTGG;RSEQ=AAAAAAAAAAATCTTACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:124:94,30:155,37:192,124:0.3131:2,2:28:1:30.2:1:0.32504:1.3357:59.7:61:0.3177:0:0.4 1/0:254:131:88,43:31,8:39,131:0.5157:2,2:29.3:1:29.1:1:0.16646:1.88686:59.7:262:0.5261:0.0079:0.4 +20 41306600 . A G 215 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCGGATCTCATACTCAAC;RSEQ=TCGGGGTCCAGATGCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1163:0:0,0:590,573:1163,0:0:2,0:24.8:1:30.4:1:1:0:60:37.767:1:0:0.1 0/1:886:153:74,79:377,354:731,153:0.1727:2,2:24.9:1:29.7:1:0.47826:1.13676:60:152:0.1749:0:1.1 +20 41306899 . CA C 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.7057;LSEQ=CAGAATTCTTGATGTAGCCA;RSEQ=AAAAAAATAGTCAGAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:3:0,3:1,75:76,3:0.038:1,0:26.3:1:32.5:1:1:0:60:6:0.038:0.0127:0 0/1:37:1:0,1:1,35:36,1:0.027:1,0:29:0:33:0:1:0:60:2:0.027:0:0 +20 41384481 . G A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAACTCATTGGATGAGATA;RSEQ=CATACGATCACTAAGCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:31:0:1:0:54:4:1:0:2.5 +20 41384942 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06198;SOR=Inf;LSEQ=GATTTTACCATAGTTTCTCC;RSEQ=GTTTGGGGAGTTTGTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:90,2:92,0:0:1,0:25.6:1:31.6:1:1:0:59.8:45:1:0:0.2 0/1:31:2:2,0:25,4:29,2:0.0645:2,0:32:1:32.5:1:1:0:60:4:0.0645:0:1.5 +20 41385323 . G A 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15842;SOR=4.88427;LSEQ=GGAGGAATCATAGCATCATA;RSEQ=GCTTCTAGGTGACTCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:1:1,0:125,353:478,1:0.0021:2,0:1:0:30:0:0.26305:0:56:2:0.0021:0:1 0/1:296:3:2,1:75,218:293,3:0.0101:2,2:8.7:1:21:1:0.16686:5.77:60:2:0.0068:0:1.7 +20 41385368 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08906;SOR=Inf;LSEQ=ATATCCACCCATCCTCACAC;RSEQ=CCTGGGGCTCAAGACTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:9,192:201,0:0:1,0:22:1:31.5:1:1:0:59.9:66:1:0:0.1 0/1:86:2:1,1:4,80:84,2:0.0233:1,2:16:1:29.5:1:0.11354:18.00:60:4:0.0233:0:1 +20 41386028 . C G 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTGGTGCCCTGCTACCCCA;RSEQ=CCCACAGGCTCTGAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:21:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:32.5:1:1:0:60:4:1:0:1.5 +20 41399995 . C T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55545;SOR=0;LSEQ=TGTTCAATACACTTGTGTTG;RSEQ=CATAGAGCTGCTTCCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:2,1:249,13:262,3:0.0113:1,2:9:1:23.7:1:0.1508:9.37022:60:2:0.0078:0:1.3 0/0:119:0:0,0:97,22:119,0:0:2,0:22:1:31.2:1:1:0:60:118:1:0:0.1 +20 41400114 . A T 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGAGACCACTTCCCACC;RSEQ=GCAATGCACTGAAATGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1018:0:0,0:493,525:1018,0:0:2,0:25.5:1:30.7:1:1:0:60:32.933:1:0:0.1 0/1:692:27:16,11:337,328:665,27:0.039:2,2:20.9:1:28.9:1:0.43553:1.41:60:54:0.0398:0:1 +20 41400229 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80362;SOR=1.0561;LSEQ=AACACAAGAGAATGAGATTC;RSEQ=ACAGCCTGCACCACTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:172:51,121:51,155:206,172:0.455:2,2:21.8:1:30.7:1:0.2971:1.28:60:85:0.4533:0:1.1 0/1:239:112:36,76:37,90:127,112:0.4686:2,2:21.2:1:29.7:1:0.67355:1.15:60:111:0.4684:0:1.1 +20 41408489 . GT G 49 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGTTTTGGTGGTGGTGT;RSEQ=TTTTTTTTTTTTAAGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:5,0:5,3:0.375:0,2:40.3:1:31.3:1:0.375:0:60:6:0.375:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 41408784 . G T 49 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0595;SOR=7.16253;LSEQ=GTTTGTAAGCTGAATGAATG;RSEQ=AAGGGATTGCAGGCTCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:1:1,0:440,102:542,1:0.0018:2,0:49:0:32:0:1:0:60:2:0.0019:0:1 0/1:306:4:1,3:241,60:301,4:0.0131:2,2:5.3:1:24.5:1:0.02887:11.91935:60:8:0.0135:0:1 +20 41408808 . C T 65 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00401;SOR=Inf;LSEQ=GGATTGCAGGCTCTATGCTA;RSEQ=CCAGTCTGGCATGGATCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:0:0,0:551,230:781,0:0:2,0:25.6:1:31.8:1:1:0:59.9:85.778:1:0:0.1 0/1:520:6:1,5:342,172:514,6:0.0115:2,2:6.2:1:25.3:1:0.01905:9.90029:60:12:0.0116:0:1 +20 41408964 . A G 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACACACAGGGCGGGAGTCA;RSEQ=TTTCACAGAAACAGTTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:741:0:0,0:248,492:740,0:0:2,0:25.2:1:30.6:1:1:0:60:81.222:1:0:0.1 0/1:525:22:7,15:186,317:503,22:0.0419:2,2:20.3:1:31:1:0.82178:1.25676:60:44:0.0428:0:1.2 +20 41419718 . A G 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33167;SOR=0.64828;LSEQ=GCTTGGCTAGGAGGAGAAGC;RSEQ=CAGTAAACACGAGTGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:49:49,0:70,2:72,49:0.405:1,1:26.1:1:30.2:1:0.51405:0:60:48:0.4:0:1.1 0/1:36:11:10,1:25,0:25,11:0.3056:1,2:21.5:1:29.5:1:0.30556:0:60:22:0.3056:0:1.2 +20 41420095 . T C 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCCCAGAGCTGTTCACCA;RSEQ=CATGAAAGATCCTGGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:687:0:0,0:176,511:687,0:0:2,0:25.5:1:30:1:1:0:60:48.071:1:0:0.1 0/1:407:24:3,21:107,276:383,24:0.059:2,2:24.3:1:31:1:0.15239:2.70852:60:48:0.0603:0:1 +20 41446905 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=AAGTGAACCCCCAGCAAACT;RSEQ=CAGAAGCCCTAATGAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:19,2:0.0952:2,2:35:1:29:1:1:1.35399:55.5:4:0.1:0:1 0/0:20:0:0,0:11,9:20,0:0:2,0:23.1:1:30.2:1:1:0:60:19:1:0:0.2 +20 41446916 . A T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23171;SOR=Inf;LSEQ=CAGCAAACTGCAGAAGCCCT;RSEQ=ATGAAGAGGGACCTGACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:21,0:0:2,0:27.2:1:29.5:1:1:0:59.6:20:1:0:0.2 0/1:20:2:0,2:12,6:18,2:0.1:2,0:7:1:28:1:0.14737:0:57:4:0.1:0:1.5 +20 41447003 . C CA 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05417;SOR=Inf;LSEQ=ACAACAACAACAAAAAGACC;RSEQ=AAAAAAAAAACCCATTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:24,0:0:2,0:21.9:1:30.3:1:1:0:58.4:7:1:0:0.2 0/1:28:5:2,3:12,11:23,5:0.1786:2,2:33.6:1:30.4:1:1:1.60791:60:10:0.1786:0:0.2 +20 41447118 . T C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAAAGGCCAGAGTGCCT;RSEQ=TCCTCCTCCAAACGACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:0,8:1:0,2:24:1:33.4:1:1:0:58.3:16:1:0:1 1/1:3:3:0,3:0,0:0,3:1:0,0:19.7:1:33.3:1:1:0:60:6:1:0:1 +20 41514162 . G A 90 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTCCCTGACACGCCACT;RSEQ=TCATCAGGCTCCCAAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:0,10:1:0,0:15:1:27.3:1:1:0:60:9:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:21:0:29:0:1:0:60:2:1:0:2 +20 41514406 . A G 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGATTCACGGTAAAAACT;RSEQ=GCCATCCCCATTACAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:0:0,0:429,202:631,0:0:2,0:25.7:1:29.3:1:1:0:60:51.583:1:0:0.1 0/1:486:17:12,5:311,158:469,17:0.035:2,2:23.5:1:30.5:1:0.79962:1.22:60:16:0.0333:0:1.4 +20 41514541 . G A 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGCCACACTATAACCACA;RSEQ=TTGCTGTAGTGCTCATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1008:0:0,0:415,592:1007,0:0:2,0:25.5:1:32.6:1:1:0:60:90.545:1:0:0.1 0/1:712:38:14,24:278,396:674,38:0.0534:2,2:20.5:1:29.8:1:0.6164:1.20315:60:76:0.0543:0:1.2 +20 41514613 . T A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12938;SOR=Inf;LSEQ=GGTAAATACATTCCCGTGTC;RSEQ=GAGGCTTGGTTCGTTACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:55,277:332,0:0:2,0:23.6:1:30.6:1:1:0:60:65.4:1:0:0.1 0/1:187:2:1,1:37,148:185,2:0.0107:2,2:7.5:1:27:1:0.36599:3.96:60:4:0.0108:0:1 +20 41514622 . G C 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00064;SOR=Inf;LSEQ=ATTCCCGTGTCTGAGGCTTG;RSEQ=TTCGTTACCTCTGTCTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:35,238:273,0:0:2,0:23.7:1:32:1:1:0:60:67.25:1:0:0.1 0/1:150:7:3,4:22,121:143,7:0.0467:2,2:26.1:1:32.9:1:0.09093:4.07:60:14:0.0476:0:1.4 +20 41514690 . C CAT 113 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=11.000;MSILEN=2;SSF=0.77399;SOR=0.69292;LSEQ=AAACTCTGGAGAAGATTTTC;RSEQ=ATATATATATATATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:16:0,16:1,52:53,16:0.2162:1,1:31.4:1:28.4:1:1:0:60:32:0.2254:0.027:0.1 0/1:25:4:0,4:0,17:17,4:0.16:1,0:24:1:27.4:1:1:0:60:8:0.1667:0.04:0.3 +20 41759356 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGTTCGTCATGCTGAAAA;RSEQ=GAGGCCAAGGGCTCTGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:17,1:18,2:0.1:1,2:31:0:34:1:0.19474:12.36938:60:4:0.1:0:1.5 0/0:7:0:0,0:7,0:7,0:0:0,0:17.1:1:30.3:1:1:0:60:14:1:0:0.3 +20 41759470 . G A 55 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97336;LSEQ=TTTTCAAAAAAAAAAAAAAA;RSEQ=GAAAAAGTATGTATGGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:7:7,0:91,18:109,7:0.0603:2,0:6.3:1:19.7:1:0.59365:0:50.3:0.75:0.0316:0:1.3 0/1:68:4:4,0:54,10:64,4:0.0588:2,0:7:0:24.5:1:1:0:34.5:3:0.0526:0:1.3 +20 41759483 . A T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.26518;SOR=0;LSEQ=AAAAAAAGGAAAAAGTATGT;RSEQ=TGGTACTAAAAGCAATATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:1,2:131,39:170,3:0.0173:2,2:10.3:1:22.3:1:0.1402:6.62322:57:2:0.0128:0:3.3 0/0:127:0:0,0:91,36:127,0:0:2,0:27:0:15:0:1:0:59:0:0:0:7 +20 41759523 . C T 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTAAAAAATCAATGAAA;RSEQ=GGAATAAAGCTCAGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:416:0:0,0:256,159:415,0:0:2,0:27.2:1:30.8:1:1:0:59.8:24.938:1:0:0.4 0/1:325:21:11,10:177,125:302,21:0.0646:2,2:27.6:1:27.8:1:0.64961:1.28624:60:20:0.0647:0:1.1 +20 41759541 . C G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=1.92082;LSEQ=AACGGAATAAAGCTCAGAAA;RSEQ=AAGCCAAAGTATAACAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:69:37,32:240,180:420,69:0.1397:2,2:27:1:31.9:1:0.60204:1.15281:59.6:22:0.1389:0:1.5 0/1:391:93:51,42:164,132:296,93:0.2379:2,2:27.5:1:31:1:1:1.02312:60:45.5:0.2414:0:1.4 +20 41759593 . G A 63 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06842;SOR=0;LSEQ=CAACTGGTGCAGAGACAGCT;RSEQ=GCTAAGCATCTAAATACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:5:4,1:133,226:359,5:0.0137:2,2:5:1:27.4:1:0.06875:6.76:60:10:0.0138:0:1.2 0/0:295:0:0,0:114,181:295,0:0:2,0:24.1:1:30.3:1:1:0:59.9:97.333:1:0:0.8 +20 41759619 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=0;LSEQ=GCATCTAAATACAAATGAAG;RSEQ=CAGGATCTCCACCTGACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:241:241:58,183:0,0:0,241:1:0,2:23.2:1:30:1:1:0:60:119.5:1:0:1.2 1/1:191:181:50,131:4,6:10,181:0.9476:2,2:23:1:27.9:1:0.47251:1.74102:59.8:59.333:0.9468:0:1.2 +20 41818162 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=CAAGCTGAGACCCGGGTTCC;RSEQ=GCCATGGGGACCCGCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:10,0:10,0:0:0,0:26.6:1:31:1:1:0:60:20:1:0:0.1 0/1:10:2:2,0:8,0:8,2:0.2:0,0:22.5:1:28:1:1:0:60:4:0.2:0:1.5 +20 41818236 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.5363;SOR=0;LSEQ=CCGCGGCTGGGGGCCCGCGC;RSEQ=CATCCAGGAGGGAGCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:66,49:115,2:0.0171:2,2:25:1:30:1:1:1.34345:60:4:0.0171:0:1.5 0/0:66:0:0,0:34,32:66,0:0:2,0:22.5:1:29.7:1:1:0:60:65:1:0:0.5 +20 41818242 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53297;SOR=0;LSEQ=CTGGGGGCCCGCGCGCATCC;RSEQ=GGAGGGAGCGGGGAGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:74,60:134,2:0.0147:2,2:11:0:33:1:1:1.23141:60:4:0.015:0:2 0/0:79:0:0,0:42,37:79,0:0:2,0:21.2:1:29.3:1:1:0:60:38.5:1:0:0.5 +20 41818251 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.14938;SOR=Inf;LSEQ=CGCGCGCATCCAGGAGGGAG;RSEQ=GGGGAGCCCAGGGGAGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:81,68:149,0:0:2,0:25.7:1:30.8:1:1:0:60:28.8:1:0:1.1 0/1:95:2:1,1:48,45:93,2:0.0211:2,2:33.5:1:29.5:1:1:1.06598:60:4:0.0215:0:1 +20 41818258 . C T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28184;SOR=0;LSEQ=ATCCAGGAGGGAGCGGGGAG;RSEQ=CCAGGGGAGCCGGGCGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:1,2:88,82:170,3:0.0173:2,2:16:1:29.3:1:0.61212:2.13718:60:6:0.0175:0:2.3 0/0:112:0:0,0:56,56:112,0:0:2,0:22.5:1:30.9:1:1:0:60:55:1:0:0.6 +20 41818274 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15661;SOR=Inf;LSEQ=GGAGCCCAGGGGAGCCGGGC;RSEQ=GGCGCACTCACCTGCGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:106,107:213,0:0:2,0:26.5:1:30.6:1:1:0:60:70:1:0:1.2 0/1:140:2:1,1:65,73:138,2:0.0143:2,2:28:0:32:1:1:1.12:60:4:0.0145:0:1.5 +20 41818289 . C G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09432;LSEQ=CGGGCGGGCGCACTCACCTG;RSEQ=GGCGCTCTGAGCCCGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:229:206:99,107:11,11:22,206:0.8996:2,2:25.4:1:31.1:1:1:1.08043:59.8:50.5:0.8978:0:1.3 0/1:136:62:28,34:35,39:74,62:0.4559:2,2:26.5:1:30.2:1:0.86367:1.08905:59.9:61:0.4519:0:1.2 +20 41818371 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23251;SOR=Inf;LSEQ=GCGAGCGCGGCGAGGCTCGC;RSEQ=ATCCGGGCGGCGGCGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:36,44:80,0:0:2,0:20.9:1:32.4:1:1:0:60:160:1:0:0.6 0/1:75:2:1,1:34,39:73,2:0.0267:2,2:43.5:1:29:1:1:1.14:60:4:0.0282:0:1 +20 41818376 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49767;SOR=Inf;LSEQ=CGCGGCGAGGCTCGCCATCC;RSEQ=GGCGGCGGCGGGCAGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:29,38:67,0:0:2,0:20.5:1:31.7:1:1:0:60:134:1:0:0.6 0/1:74:2:1,1:34,38:72,2:0.027:2,2:14:0:30:1:1:1.12:60:4:0.0286:0:1.5 +20 41818391 . G A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05546;SOR=0;LSEQ=CATCCGGGCGGCGGCGGGCA;RSEQ=CTCAGCCCCTTCCCGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:2,1:15,18:33,3:0.0789:2,2:13:1:30.7:1:0.59286:2.34:60:6:0.0789:0:1.3 0/0:60:0:0,0:30,29:59,0:0:2,0:17.6:1:30.3:1:1:0:59.6:28.5:1:0:0.5 +20 41955344 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CAGCACACACGCATGTGCGC;RSEQ=CGCACATACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:29:1:1:0:60:4:1:0:1 +20 41956519 . A G 66 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACATCCTGACTTTTTA;RSEQ=TGATCACCATTCTAACTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:23.5:1:33.3:1:1:0:56:8:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 41956785 . G T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91866;LSEQ=TTTCTCCCATCCTATAGGTT;RSEQ=CCTGTTTACTCTGATGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:93,8:101,2:0.0194:2,2:8.5:1:28:1:0.1679:11.01924:60:4:0.0196:0:1 0/1:56:1:0,1:47,8:55,1:0.0179:2,0:1:0:24:0:0.16071:0:60:2:0.0185:0:1 +20 41956808 . A G 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27957;SOR=0;LSEQ=TGTTTACTCTGATGATAAAG;RSEQ=GCTTCTGCACAGCAAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:2,1:120,28:148,3:0.0199:2,2:23:1:24:1:0.47511:2.1297:50.7:2:0.0133:0:1.3 0/0:99:0:0,0:70,29:99,0:0:2,0:21.9:1:28.1:1:1:0:59.2:32:1:0:0.1 +20 41956839 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1519;SOR=Inf;LSEQ=AGCAAAAGAGTCACCTATTT;RSEQ=TTAGAGCAACACTGACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:172,84:256,0:0:2,0:24.1:1:30.3:1:1:0:60:41.667:1:0:0.5 0/1:164:2:1,1:106,56:162,2:0.0122:2,2:19.5:1:29.5:1:1:1.88508:60:4:0.0124:0:1.5 +20 41956920 . A G 269 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGATAGGACCAAGAGCTC;RSEQ=CCTGCCAGTGGGTGGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:396:396:169,227:0,0:0,396:1:0,2:26:1:31.2:1:1:0:60:78.2:1:0:1.3 1/0:260:167:75,92:42,51:93,167:0.6423:2,2:23.9:1:29.7:1:1:1.01016:59.9:54.667:0.6381:0:1.4 +20 41956960 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=0.45162;LSEQ=ATTCTCAAAATATAAAGTAT;RSEQ=TAATTCTTTATACTGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:117:40,77:39,88:127,117:0.4795:2,2:21.9:1:32.4:1:0.58599:1.17:60:234:0.4795:0:1.8 0/1:167:49:16,33:40,78:118,49:0.2934:2,2:23.7:1:31.2:1:1:1.05735:60:98:0.2952:0:1.8 +20 42630762 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15024;SOR=Inf;LSEQ=ATCACCCCAGAAAGTAGAGT;RSEQ=CCACTGCCAGCTTTCCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:108,65:173,0:0:2,0:25:1:31.7:1:1:0:60:56.667:1:0:0.2 0/1:110:2:1,1:58,50:108,2:0.0182:2,2:25:1:27:1:1:1.15843:60:4:0.0183:0:1 +20 42630772 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28491;SOR=0;LSEQ=AAAGTAGAGTCCCACTGCCA;RSEQ=CTTTCCAGTTCAGAGTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:1,2:114,78:192,3:0.0154:2,2:28.7:1:30:1:0.56906:2.90694:60:6:0.0159:0:1 0/0:124:0:0,0:68,56:124,0:0:2,0:27.7:1:31.7:1:1:0:60:123:1:0:0.3 +20 42630773 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.56429;SOR=3.09145;LSEQ=AAGTAGAGTCCCACTGCCAG;RSEQ=TTTCCAGTTCAGAGTCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:0,1:117,80:197,1:0.0051:2,0:1:0:29:0:0.40909:0:60:2:0.0051:0:1 0/1:129:2:1,1:70,57:127,2:0.0155:2,2:34:1:28:1:1:1.2261:60:4:0.0156:0:1 +20 42630821 . G A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.16134;SOR=Inf;LSEQ=GAAGCCTTCCCAACCCCTCT;RSEQ=CCCATTCTAAGGCAAGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:77,101:178,0:0:2,0:26.3:1:31.9:1:1:0:59.9:43.5:1:0:0.2 0/1:120:2:1,1:56,62:118,2:0.0167:2,2:9:0:29.5:1:1:1.11:60:4:0.0167:0:1.5 +20 45867566 . TTGC T 70 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.2274;SOR=3.47386;LSEQ=TGAGGCTGCTGCTGCTGGTT;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:16,18:34,2:0.0556:2,2:48.5:1:30.5:1:1:1.12:60:4:0.0588:0:0 0/1:29:5:3,2:10,12:22,5:0.1724:2,2:31.6:1:30.4:1:0.64831:1.76:60:10:0.1724:0:0.2 +20 46250585 . C T 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTATTTTTAGTAGAGA;RSEQ=GGGGTTTCACCATGTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:30:1:28:1:1:0:55.5:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 46251242 . G GT 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.0452;LSEQ=ATCTTTTTGATGTAATAGAA;RSEQ=TTTTTTTTTTATTGCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:12:0,12:1,112:113,12:0.0945:1,0:28.2:1:31.7:1:1:0:60:24:0.0976:0:0.1 0/1:61:6:0,6:1,54:55,6:0.0984:1,0:43.3:1:27.2:1:1:0:60:5:0.0862:0:0 +20 46252535 . A AG 79 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.42764;SOR=0.30099;LSEQ=AGAGCGAAAACTCTGTCTCG;RSEQ=GGAAAAAAAAAAAAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:6:6,0:179,0:179,6:0.0323:1,0:20:1:30.9:1:1:0:60:5:0.0281:0.0108:1 0/0:101:1:1,0:99,1:100,1:0.0099:1,0:17:0:33:0:1:0:60:2:0.0104:0:0 +20 46252605 . G GAT 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.00141;SOR=Inf;LSEQ=TCTGCTAACAGCTCTTTTGT;RSEQ=ATATATATATTATGTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:820:0:0,0:605,214:819,0:0:2,0:25.3:1:31.4:1:1:0:59.9:19.475:1:0:0.2 0/1:531:7:3,4:355,169:524,7:0.0132:2,2:24.7:1:26.6:1:0.22256:2.7948:60:14:0.0138:0.0019:0.4 +20 46252975 . T C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00539;SOR=2.97086;LSEQ=CACATTACGTTTGTGGTGCA;RSEQ=TTTATTTCTATTATGGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:32:0,32:0,91:91,32:0.2602:1,1:28.2:1:33.7:1:1:0:59.3:64:0.2623:0:1 1/0:39:20:0,20:0,19:19,20:0.5128:1,1:25.4:1:32.9:1:1:0:60:40:0.5128:0:1 +20 46255238 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CTCCCCCACCCCCAATTATT;RSEQ=TTCTTTTTTTTTCCCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:7,0:0:2,0:22.9:1:24.7:1:1:0:60:1.333:1:0:0.6 1/0:4:2:1,1:1,1:2,2:0.5:2,2:17.5:1:29.5:1:1:1:60:4:0.5:0:1 +20 46255251 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=AATTATTCTTCTTTTTTTTT;RSEQ=CCCCCAGTAAGGCCTGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:33.2:1:29.6:1:1:0:60:4:1:0:0.4 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26:1:27:1:1:0:60:4:0.6667:0:1 +20 46256424 . C T 268 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00226;LSEQ=TAAACGCCAGTCCTGAAATG;RSEQ=GCCAGAGATATGAAACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1969:475:212,263:659,832:1491,475:0.2412:2,2:24.3:1:30.2:1:0.87372:1.02:59.8:157.333:0.2425:0:1.1 0/0:1401:1:0,1:663,734:1397,1:7e-04:2,0:1:0:24:0:1:0:60:2:7e-04:0:1 +20 46256785 . GTC G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.08888;SOR=0.72705;LSEQ=CAGGTAAAAACTCTTTTTTT;RSEQ=TCTCTCTCTCTCTGTGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1344:87:27,60:435,814:1249,87:0.0647:2,2:27.6:1:32.2:1:0.56013:1.18744:60:174:0.0655:0.0119:0.4 0/1:1002:48:20,28:352,597:949,48:0.0479:2,2:36.3:1:31.8:1:0.5427:1.21:59.9:96:0.0484:0:0.2 +20 46262180 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13868;SOR=Inf;LSEQ=CAGTGCTAAGCCATGTGTAG;RSEQ=CAGCCAGTAAATACTTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:300,16:316,0:0:2,0:24.3:1:31.6:1:1:0:60:51.667:1:0:0 0/1:188:2:1,1:171,15:186,2:0.0106:2,2:25:1:28:1:0.16339:11.07055:60:4:0.0112:0:1 +20 46262701 . T G 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCTTGGATTTTTAGAAA;RSEQ=GTACTTGAAGTATATTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:728:0:0,0:593,135:728,0:0:2,0:22.5:1:30.9:1:1:0:59.9:71.8:1:0:0.1 0/1:358:66:58,8:229,62:291,66:0.1844:2,2:20.9:1:30.8:1:0.12101:1.96:60:32:0.1818:0:1.3 +20 46262994 . G A 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCAGCAGTGTTCTCAAAAT;RSEQ=CTTTATTATTAAAGTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:607:0:0,0:95,510:605,0:0:2,0:21.6:1:32.4:1:1:0:59.9:99.833:0.9967:0:0.1 0/1:345:56:12,44:60,229:289,56:0.1623:2,2:19.3:1:28.7:1:0.85958:1.04:60:112:0.1642:0:1.1 +20 46263720 . A T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGATCTGTCACCCAGGC;RSEQ=GGTGTGCAGTAGTGCCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:5,0:5,3:0.375:0,2:26:1:33:1:0.375:0:60:6:0.4286:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:8:0:31:0:1:0:60:2:1:0:0 +20 46264508 . C G 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCTTTTTAAGTAATTATT;RSEQ=TTTCCATACTACTATAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1082:0:0,0:375,706:1081,0:0:2,0:22:1:32.7:1:1:0:60:62.588:0.9991:0:0.1 0/1:789:37:15,22:243,505:748,37:0.0469:2,2:25.6:1:30.8:1:0.3698:1.42:60:36:0.0465:0:1.1 +20 46267576 . CG C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTGGCTGGCAGGGGGG;RSEQ=GGGGGTGGCGGTGGTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:2,0:132,4:136,2:0.0145:1,0:26:1:32.5:1:1:0:60:4:0.015:0:1 0/0:34:0:0,0:34,0:34,0:0:1,0:24.3:1:29.7:1:1:0:60:33:1:0:0.1 +20 46267950 . C T 324 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01652;LSEQ=TTATGGCTCAAGTATGGGTA;RSEQ=GTTATTTCTAATTAGTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1568:1566:573,993:0,0:0,1566:0.9987:0,2:25.2:1:30.6:1:1:0:60:81.421:0.9987:0:1.1 1/1:1085:1007:387,620:30,46:76,1007:0.9281:2,2:25.4:1:29.7:1:0.90287:1.04476:60:90.545:0.9274:0:1.2 +20 46268008 . A G 171 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=106.27142;LSEQ=AGCATATTTAAAATACTTAA;RSEQ=GCCATCTAAATAATTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:1:0,1:70,478:548,1:0.0018:2,0:22:0:27:0:1:0:60:2:0.0018:0:1 0/1:288:47:4,43:33,208:241,47:0.1632:2,2:22.3:1:30.9:1:0.47471:1.7027:60:46:0.1608:0:1.8 +20 46268493 . A G 236 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGGTGGCTCTATTCCCAC;RSEQ=TTGCCTCTTCGGTCTAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2121:0:0,0:1051,1068:2119,0:0:2,0:24:1:30.6:1:1:0:60:83.76:0.999:0:0.1 0/1:1454:227:110,117:612,614:1226,227:0.1561:2,2:23.7:1:30.2:1:0.71807:1.06016:59.9:74.667:0.1556:0:1.1 +20 46270624 . T C 110 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTACCTCCTTCACTGTTTT;RSEQ=GTGAGGAGTATCTTCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:0,10:1:0,0:27:1:33.3:1:1:0:59.7:20:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:5:0:32:0:1:0:60:2:1:0:1 +20 46270865 . G T 38 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13576;SOR=5.36796;LSEQ=TTTGTAGCATTTGAGTTACT;RSEQ=TTCATTAAAAATACTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:1:1,0:431,21:452,1:0.0022:1,0:1:0:32:0:1:0:60:2:0.0022:0:2 0/1:255:3:1,2:232,20:252,3:0.0118:2,2:6.7:1:24.3:1:0.02027:22.48466:59.3:2:0.008:0:3.3 +20 46270911 . GA G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.45248;SOR=0.885;LSEQ=GCTGTGATCTATTACTCTTA;RSEQ=AAAAAAAAAAGCACCATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1130:128:93,35:707,283:990,128:0.1133:2,2:25.2:1:32.7:1:0.83533:1.06:59.6:127:0.1137:0.0168:0.2 0/1:768:78:49,29:445,239:684,78:0.1016:2,2:21.9:1:30.1:1:0.70838:1.10181:59.7:77:0.1017:0.026:0.1 +20 46271008 . G A 243 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02359;LSEQ=GTTGGGCCACCTTCCAACCT;RSEQ=GAAGGCCAGAGTGACGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2364:286:145,141:1061,1014:2075,286:0.121:2,2:25.2:1:29.9:1:0.89974:1.01748:60:56.2:0.121:0:1.1 0/0:1546:5:4,1:790,749:1539,5:0.0032:2,2:11.8:1:24.4:1:0.37521:3.79:60:10:0.0033:0:1 +20 46275917 . A C 217 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGACAGACATACCCAGCAC;RSEQ=GGGGCCTCCAATGCAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2347:145:71,74:1091,1108:2199,145:0.0618:2,2:24.3:1:30.3:1:0.93172:1.02626:59.9:28:0.0603:0:1.2 0/0:1521:0:0,0:777,743:1520,0:0:2,0:24:1:29.9:1:1:0:60:107.571:0.9993:0:0.1 +20 46277834 . A T 212 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01105;LSEQ=GGTGATGAGGCCTATGATGC;RSEQ=GCCCCAGGTGAGCTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1669:114:50,64:743,810:1553,114:0.0683:2,2:27.4:1:31.1:1:0.43787:1.17401:60:113:0.0686:0:1.2 0/0:1236:1:0,1:576,658:1234,1:8e-04:2,0:1:0:27:0:1:0:60:2:8e-04:0:1 +20 46279531 . T C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.12797;SOR=3.68735;LSEQ=GCAGAAGACTCACTTGAACC;RSEQ=GGGAGACGAAGGTTGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:11:11,0:21,0:21,11:0.3438:1,0:18.1:1:29.3:1:1:0:52.2:10:0.3226:0:1.3 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:17.2:1:31:1:1:0:53.3:12:0.6667:0:1.3 +20 46279604 . T TA 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.04529;SOR=4.41222;LSEQ=GCGACAGAGTGAGACCCTGT;RSEQ=AAAAAAAAGAAGGCCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:3:3,0:120,3:123,3:0.0238:1,0:20:1:29.7:1:1:0:60:6:0.0242:0.0079:1 0/1:51:5:5,0:43,2:45,5:0.098:1,0:26.6:1:28:1:1:0:59:10:0.098:0:1.4 +20 46279612 . AG A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0.74715;LSEQ=GTGAGACCCTGTTAAAAAAA;RSEQ=AAGGCCCTGGGTGTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:9:9,0:118,4:122,9:0.0566:1,0:19.1:1:30.8:1:1:0:55.3:18:0.0577:0.0063:0.3 0/1:70:3:2,1:26,0:26,3:0.0429:1,2:27.3:1:30.3:1:0.10345:0:60:6:0.0429:0:0.7 +20 46279613 . G A 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.83879;LSEQ=TGAGACCCTGTTAAAAAAAA;RSEQ=AAGGCCCTGGGTGTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:27:26,1:118,4:122,27:0.1698:1,1:20.4:1:30:1:1:1.13365:60:26:0.1667:0:1.1 1/0:70:41:40,1:26,0:26,41:0.5857:1,1:21.8:1:29.9:1:1:0:59.6:82:0.5857:0:1.5 +20 46279814 . TGCAGCAGCA T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=3;SSF=0;SOR=0.26167;LSEQ=ACAGAGGGTGGCTATGATGA;RSEQ=GCAGCAGCAGCAACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1015:83:52,31:487,418:905,83:0.0818:2,2:24.7:1:32.6:1:0.1348:1.44:57.3:166:0.0832:0.0069:0.1 0/1:747:17:11,6:395,324:719,17:0.0228:2,2:20.5:1:31:1:0.46958:1.50:55.8:34:0.0231:0.008:0.4 +20 46279827 . G A 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ATGATGATGCAGCAGCAGCA;RSEQ=CAGCAGCAACAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:948:0:0,0:514,433:947,0:0:2,0:22.7:1:32.5:1:1:0:59:44.095:1:0:0.1 0/1:732:130:67,63:328,271:599,130:0.1776:2,2:20.3:1:28.8:1:0.5603:1.13787:47.3:31.5:0.1748:0:1.6 +20 46279836 . ACAG A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=9.000;MSILEN=3;SSF=0;SOR=1.66693;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:957:225:124,101:391,339:730,225:0.2351:2,2:25.8:1:31.9:1:0.70261:1.06:58.1:224:0.237:0.0449:0.2 0/1:723:245:136,109:245,218:463,245:0.3389:2,2:27.6:1:31.1:1:0.52686:1.11:58.6:490:0.3431:0.0429:0.1 +20 46279866 . A G 184 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=6;SSF=0;SOR=89.52072;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAACAGCAACAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1231:1:1,0:686,542:1228,1:8e-04:2,0:44:0:34:0:1:0:33:2:8e-04:0:2 0/1:883:60:31,29:428,372:800,60:0.068:2,2:31.3:1:31.3:1:0.79016:1.0762:38.9:59:0.0695:0:2.1 +20 46281061 . T TA 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.2669;SOR=0.67519;LSEQ=CCCTCCACCCCCACCTCCTT;RSEQ=AAAAAAAAAACAAAATTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:33:33,0:320,9:329,33:0.0899:1,1:22.7:1:29.5:1:1:0:59.1:66:0.0897:0.0245:0.4 0/1:208:13:11,2:182,7:189,13:0.0625:1,2:30.9:1:28.5:1:0.1066:4.66204:59.2:26:0.0631:0:0.7 +20 46281422 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09957;SOR=Inf;LSEQ=CCTTTTTGGATGGAGAGGTT;RSEQ=AAAGGACTGGGTTCATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:18,213:231,0:0:2,0:24.3:1:32.2:1:1:0:59.5:56.75:1:0:0.1 0/1:107:2:1,1:5,100:105,2:0.0187:1,2:22:0:30.5:1:0.1095:18.34:60:4:0.0187:0:1.5 +20 46281500 . A G 32 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07625;SOR=Inf;LSEQ=CAAGCACGCACATATCTATT;RSEQ=GGGTGTCTAGTACAGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:82,53:135,0:0:2,0:22.1:1:30.5:1:1:0:59.6:134:1:0:0 0/1:52:2:1,1:33,17:50,2:0.0385:2,2:7.5:1:32:0:1:1.91492:60:4:0.04:0:1 +20 46282222 . T C 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGACACTGCACTAGGATTA;RSEQ=TGGGAAGGAATCATTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:724:0:0,0:337,386:723,0:0:2,0:24.3:1:30.1:1:1:0:60:35.15:1:0:0.2 0/1:498:26:13,13:213,259:472,26:0.0522:2,2:26.5:1:31.6:1:0.68809:1.22:60:52:0.0532:0:1.2 +20 47416665 . T A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=TACACTCATTTAAACTTCAC;RSEQ=ACAACCCTTAAGGTAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:1,3:1,4:5,4:0.4:2,2:21:1:31:1:1:1.29:60:8:0.5:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:29:1:24.2:1:1:0:60:4:1:0:0.2 +20 47418179 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACACCCACGTCTCTCCCC;RSEQ=GGGCTGTTGCAGTCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:27.5:1:1:0:60:4:1:0:1 +20 48191784 . G A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=1;SOR=1.20595;LSEQ=TGGGAGGATTGCTTGAACCC;RSEQ=GGAGGTAGAGGTTGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:6,0:16,0:16,6:0.2727:1,0:21.5:1:32.2:1:1:0:32.3:12:0.2857:0:1 0/1:16:5:5,0:10,1:11,5:0.3125:2,0:19.2:1:27.2:1:1:0:42.4:10:0.3125:0:1 +20 48191854 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCGACGGAGTGAGACCCT;RSEQ=TCTTAGCAACAACAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:0,2:70,42:112,2:0.0174:2,0:22:1:29.5:1:0.14687:0:59.5:4:0.0174:0:1 0/0:56:0:0,0:31,25:56,0:0:2,0:24.2:1:31.4:1:1:0:57.3:112:1:0:0.1 +20 48191860 . GCAA G 34 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=1.02448;LSEQ=CGGAGTGAGACCCTGTCTTA;RSEQ=CAACAACAACACAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:77,47:124,2:0.0157:2,2:14:0:34.5:1:1:1.63157:60:4:0.0157:0:0.5 0/1:62:1:1,0:33,27:60,1:0.0161:2,0:39:0:34:0:1:0:60:2:0.0164:0:0 +20 48191877 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.54798;SOR=0;LSEQ=TTAGCAACAACAACAACACA;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:85,64:149,2:0.0132:2,2:28.5:1:28.5:1:1:1.32559:60:4:0.0135:0:1 0/0:79:0:0,0:41,38:79,0:0:2,0:24.1:1:31.6:1:1:0:58.6:78:1:0:0.2 +20 48191955 . C G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15349;SOR=Inf;LSEQ=ATTACCAAGTATTTATTTGC;RSEQ=AACACTGTGCAGGCCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:13,39:52,0:0:2,0:24.3:1:32.2:1:1:0:59.5:104:1:0:0.1 0/1:34:2:1,1:10,22:32,2:0.0588:2,2:13:1:27.5:1:1:2.14:60:4:0.0625:0:2 +20 48450753 . C T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATATATATATATATATATA;RSEQ=ACACACACACTATGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:0,12:3,0:3,12:0.8:0,0:8:1:27.2:1:0.0022:0:57.5:24:0.8:0:1.1 1/1:2:2:0,2:0,0:0,2:1:0,0:7:0:26:1:1:0:60:4:1:0:1 +20 48450851 . G GTA 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.13571;SOR=8.85639;LSEQ=ACACACTATATATACAGTGT;RSEQ=TATATATATATATACTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,3:10,2:0.1538:2,2:32:1:31.3:1:1:2.16028:40.5:4:0.1667:0:2 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:18.5:1:29.1:1:1:0:60:4:0.6667:0.3333:0 +20 48450866 . C CTG 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGTGTATATATATATATA;RSEQ=TGTGTATATATATATATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:3,3:6,4:0.4:2,0:35:1:33.6:1:0.2:0:52.5:8:0.4:0:0 0/0:1:0:0,0:0,1:1,0:0:0,0:17:0:33:0:1:0:60:2:1:0:0 +20 48450870 . GTA G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTATATATATATATACTGT;RSEQ=TATATATATATACTGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:8,2:0.2:2,2:45:1:33.5:1:1:2.64575:32.5:4:0.2:0:4.5 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:29:0:1:0:60:2:1:0:0 +20 48450887 . GTA G 24 v3;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTATATATATATATACT;RSEQ=TATATATATATACTGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,0:7,2:0.2:0,0:13.5:1:24.9:1:1:0:58.5:4:0.2:0.1:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 48450891 . ATATATATATACTGTG A 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATATATATATACTGTAT;RSEQ=TATATATATATATACTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:4,1:5,5:0.5:2,0:26.6:1:31.2:1:1:0:53:10:0.625:0:0.2 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:31:0:1:0:39:2:1:0:1 +20 48450900 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATACTGTATATATATATA;RSEQ=ACTGTGTATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,0:1,2:0.25:0,2:18:1:34:0:1:0:32.5:4:0.6667:0:4.5 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:32:0:1:0:39:2:1:0:1 +20 48450903 . T A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACTGTATATATATATATAC;RSEQ=GTGTATATATATATATACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,0:1,2:0.25:0,2:15:1:33:1:1:0:32.5:4:1:0:4.5 0/0:1:0:0,0:1,0:1,0:0:0,0:12:0:32:0:1:0:39:2:1:0:1 +20 48450906 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTATATATATATATACTGT;RSEQ=TATATATATATATACTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:1,0:1,2:0.25:0,2:12:1:30.5:1:1:0:32.5:4:1:0:4.5 0/0:1:0:0,0:1,0:1,0:0:0,0:15:0:33:0:1:0:39:2:1:0:1 +20 48450925 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=2;SSF=0.04762;SOR=Inf;LSEQ=TGTATATATATATATACTGT;RSEQ=TATATATATATACTGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:23:1:31.8:1:1:0:53:10:1:0:0.2 1/1:2:2:2,0:0,0:0,2:1:0,0:21:1:28.5:1:1:0:36.5:4:1:0:1 +20 48450944 . ATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG A 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=8.000;MSILEN=2;SSF=0.01515;SOR=0;LSEQ=TGTATATATATATACTGTGT;RSEQ=TATATATATATATACTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:1,6:0.8571:0,2:20:1:29.2:1:1:0:59.2:12:0.8571:0.4286:0.5 0/0:4:0:0,0:4,0:4,0:0:0,0:23.3:1:31.3:1:1:0:48.3:8:1:0:0.8 +20 48450987 . C CTG 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.04482;SOR=0;LSEQ=ACTGTATATATATATATATA;RSEQ=TGTATATATATATACTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:10:9,1:23,0:23,10:0.2778:1,2:9.1:1:31.7:1:0.30303:0:55.6:20:0.303:0.1944:0.2 0/0:13:0:0,0:13,0:13,0:0:1,0:25.5:1:31.2:1:1:0:51.6:12:1:0:0.5 +20 48451006 . G GTA 112 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.21058;SOR=0.3484;LSEQ=ACTGTATATATATATACTGT;RSEQ=TATATATATATATACTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:13:11,2:28,1:29,13:0.2549:1,2:21.1:1:30.4:1:0.22195:4.8686:57.7:26:0.2889:0.0196:0.2 0/1:19:2:2,0:16,1:17,2:0.1053:1,0:32:1:26.5:1:1:0:40.5:4:0.1176:0:1 +20 48451012 . A ACAGTGTGTGTATATACATAGTGTGTGTG 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=2;SSF=0.00063;SOR=Inf;LSEQ=TATATATATACTGTGTATAT;RSEQ=TATATATACTGTATATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:50,6:56,0:0:2,0:25.8:1:29.3:1:1:0:58.8:112:0.9492:0:0.3 0/1:27:6:6,0:18,2:20,6:0.2222:2,0:17.7:1:30.9:1:1:0:59.2:12:0.2308:0.2222:1 +20 48451022 . T A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0.1962;SOR=1.63719;LSEQ=CTGTGTATATATATATATAC;RSEQ=GTATATATACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:28:25,3:61,8:69,28:0.2887:2,2:8.4:1:30.9:1:1:1.09:55.6:56:0.2917:0:1.1 0/1:50:20:15,5:27,3:30,20:0.4:2,2:10.2:1:29.2:1:0.23996:2.93113:56.7:40:0.4167:0:1.2 +20 48451030 . TAC T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.30367;SOR=0;LSEQ=ATATATATATACTGTATATA;RSEQ=ACACACACACTATATATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:4:3,1:107,15:122,4:0.0315:2,2:34.5:1:28.5:1:0.42321:2.35597:57.3:8:0.032:0.0079:0 0/0:63:0:0,0:52,11:63,0:0:2,0:17.8:1:27.7:1:1:0:58.9:62:1:0:0.5 +20 48451032 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=0.10337;SOR=Inf;LSEQ=ATATATATACTGTATATATA;RSEQ=ACACACACACTATATATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:113,18:131,0:0:2,0:21.3:1:31.8:1:1:0:58.6:31.75:1:0:0.6 0/1:64:2:1,1:52,10:62,2:0.0313:2,2:14.5:1:27:1:0.31647:5.00559:60:4:0.0317:0:2 +20 48451129 . A T 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0629;LSEQ=TAGATTGATTTGACCTAACT;RSEQ=TGAGCCTCAATCTCAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:481:426:209,217:26,29:55,426:0.8857:2,2:27:1:30.5:1:0.88626:1.07:59.9:70:0.8879:0:1.1 0/1:346:113:58,55:126,107:233,113:0.3266:2,2:26.9:1:29.7:1:0.64736:1.1163:59.9:112:0.3246:0:1.1 +20 48451219 . T C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01927;SOR=0.52106;LSEQ=ATAATAACAATAATATCACA;RSEQ=TGTATTTTACAGCGCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:64:15,49:20,81:101,64:0.3879:2,2:26.7:1:32.4:1:0.6963:1.24:60:31:0.3875:0:1.3 0/1:113:28:6,22:15,70:85,28:0.2478:2,2:20.4:1:31.5:1:0.77975:1.27:60:56:0.2523:0:1.4 +20 48631241 . G A 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTCATCTGGGTAAGCTGGT;RSEQ=TGTCTTTGTGTGTTGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:29.7:1:30:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 48631321 . A G 79 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=ATCTAGGAAGGGTGTCAGGC;RSEQ=GTGTGAGTCAGCGTGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:20.8:1:30.8:1:1:0:60:10:1:0:1.4 1/0:8:6:3,3:1,1:2,6:0.75:2,2:19.3:1:30.8:1:1:1:60:12:0.75:0:1.8 +20 48631365 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15441;SOR=0;LSEQ=GGCTGTGTGTGTGAGCAGGG;RSEQ=TCCGTTCTGAGAGTGCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:18.5:1:30.5:1:1:1.41:60:4:0.2857:0:1.5 0/0:10:0:0,0:5,5:10,0:0:2,0:24.7:1:31.5:1:1:0:60:20:1:0:1.3 +20 48631385 . G C 78 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03571;SOR=Inf;LSEQ=GTCCGTTCTGAGAGTGCGTT;RSEQ=TGTACGTGTGTGTCAGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:3:0:32.5:1:1:0:60:4:1:0:1.5 1/1:6:6:3,3:0,0:0,6:1:0,2:12.8:1:30.2:1:1:0:60:12:1:0:1.8 +20 48631777 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.17505;SOR=Inf;LSEQ=AGCCCCCTGCCTGCCGGCCC;RSEQ=CCCATCGGGGTGGGAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:31,10:41,0:0:2,0:24.9:1:30.2:1:1:0:60:40:1:0:0 0/1:30:2:1,1:19,9:28,2:0.0667:2,2:13.5:1:27.5:1:1:2.05485:60:4:0.0667:0:1 +20 48631827 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59381;SOR=2.38856;LSEQ=AGTAACAAATGTCCTGTAGC;RSEQ=AGCGTGGAGTCAGCGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:1:0,1:47,49:96,1:0.0103:2,0:1:0:23:0:1:0:60:2:0.0105:0:1 0/1:82:2:1,1:38,42:80,2:0.0244:2,2:49:1:30:0:1:1.10:60:4:0.0247:0:2 +20 48631860 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21777;SOR=Inf;LSEQ=GCGTGGAGCCGGCATGGAGG;RSEQ=AGCCCCCGCCCCACAGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:38,54:92,0:0:2,0:28.6:1:32.6:1:1:0:60:184:1:0:0.1 0/1:81:2:1,1:35,44:79,2:0.0247:2,2:30:0:30.5:1:1:1.25:60:4:0.025:0:1.5 +20 48631873 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20769;SOR=Inf;LSEQ=ATGGAGGCAGCCCCCGCCCC;RSEQ=CAGCGGGGGGTAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:31,52:83,0:0:2,0:25.1:1:30:1:1:0:60:166:1:0:0.1 0/1:70:2:1,1:30,38:68,2:0.0286:2,2:30:0:33:1:1:1.26:60:4:0.029:0:1.5 +20 48631877 . CG C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.23106;SOR=Inf;LSEQ=AGGCAGCCCCCGCCCCACAG;RSEQ=GGGGGTAGAGAGAGAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:26,48:74,0:0:2,0:24.7:1:30.4:1:1:0:60:73:1:0:0.1 0/1:69:2:1,1:29,37:66,2:0.029:2,2:25:0:33:1:1:1.27:60:4:0.0294:0:0.5 +20 48631884 . TAG T 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.6717;SOR=1.63208;LSEQ=CCCCGCCCCACAGCGGGGGG;RSEQ=AGAGAGAGAGTATAAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:19,40:59,2:0.0328:2,2:17:1:30.7:1:1:2.08:60:4:0.0328:0.0164:0 0/1:57:3:1,2:24,30:54,3:0.0526:2,2:23:1:31:1:1:1.58736:60:6:0.0545:0:0.3 +20 48807628 . G T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCCTGCCGCCGCCGCCGCCT;RSEQ=CCTTTAAATCCATGGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:29.5:1:31.3:1:1:0:60:8:1:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:38.5:1:29:1:1:1:60:4:0.4:0:1 +20 48808321 . G A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.30246;SOR=0;LSEQ=CCCCGACCGCCTGCTACGCG;RSEQ=GGGCCGCGCCGGCGCCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:255,16:271,3:0.0109:2,2:25.7:1:25:1:0.17542:7.82897:60:2:0.0075:0:2.7 0/0:158:0:0,0:145,13:158,0:0:2,0:20.2:1:30.9:1:1:0:60:51.667:1:0:0.1 +20 51363052 . A C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGCAGCAGCATTAGATT;RSEQ=TCATAGGAGTGCGAACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:2,6:0,0:0,8:1:0,2:19.6:1:33.6:1:1:0:57.8:16:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:49:1:34:0:1:0:60:4:1:0:1 +20 51970878 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10914;SOR=Inf;LSEQ=GTGTTGATTTGAAAACTTCT;RSEQ=ATATTCTTTCTTTTAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:163,63:226,0:0:2,0:23.1:1:28.3:1:1:0:60:21.6:1:0:0.3 0/1:112:2:1,1:74,36:110,2:0.0179:2,2:21.5:1:29.5:1:1:2.0413:60:4:0.0182:0:2 +20 51970913 . G C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1134;SOR=Inf;LSEQ=AGGAGATCTTCTTGATAGTT;RSEQ=CAGAAATTCTGACTGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:227,161:388,0:0:2,0:25.1:1:31.9:1:1:0:60:63.667:0.9974:0:0.4 0/1:198:2:1,1:108,87:195,2:0.0101:2,2:9:0:32:0:1:1.24:60:4:0.0103:0:1 +20 51970961 . T A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.51885;LSEQ=GTCTTGCTATTTGGCTTGTA;RSEQ=AGTAGCAGCATAAAATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:184:91,93:126,147:273,184:0.4026:2,2:25.9:1:30.3:1:0.50489:1.14:60:45:0.3991:0:1.1 1/0:243:153:81,72:41,48:89,153:0.6296:2,2:25.6:1:29.6:1:0.35104:1.32:60:50:0.6303:0:1.1 +20 51971037 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54681;SOR=0;LSEQ=ACAAGAAGATGACTCAAACT;RSEQ=AGCCACTGCAAAGCAGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:33,144:177,2:0.0112:2,2:29.5:1:28.5:1:0.34467:4.31:60:4:0.0114:0:1 0/0:94:0:0,0:24,70:94,0:0:2,0:25:1:30.4:1:1:0:59.9:22.5:1:0:0.3 +20 51971152 . T C 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14383;SOR=Inf;LSEQ=AAACATGATTTAATTATATA;RSEQ=GTCTTGCCTGATTTTTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:0,6:6,11:0.6471:0,0:15.5:1:31.1:1:1:0:60:22:0.6471:0:1.1 1/1:6:6:0,6:0,0:0,6:1:0,0:25.8:1:29.3:1:1:0:60:12:1:0:1 +20 52240073 . CCCT C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.53629;SOR=0;LSEQ=TTAAAGTCCCCTTGGCTCTG;RSEQ=CCTCCTCCTCCTCGTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:1,2:13,7:20,3:0.1304:2,2:24.7:1:31:1:0.53755:3.49692:60:6:0.1364:0:0 0/0:10:0:0,0:7,3:10,0:0:2,0:26.9:1:30.3:1:1:0:60:20:1:0:0.1 +20 52776739 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24359;LSEQ=TAAGAAATTCAAACATTGAG;RSEQ=TGAGTACTCCAGCTACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:90:81,9:92,39:131,90:0.4072:2,2:25.1:1:30.2:1:0.00043:3.79:60:180:0.4128:0:1.9 0/1:91:13:9,4:53,25:78,13:0.1429:2,2:19.2:1:27.1:1:1:1.06:60:12:0.1348:0:2.1 +20 52776755 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0214;SOR=Inf;LSEQ=TGAGCTGAGTACTCCAGCTA;RSEQ=AGTTTCTGACAAAGGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:205,89:294,0:0:2,0:24.5:1:32:1:1:0:60:72.5:1:0:0.9 0/1:114:3:1,2:69,42:111,3:0.0263:2,2:14.3:1:26.3:1:0.5581:3.25059:60:6:0.0273:0:1 +20 52776769 . G T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05484;SOR=0.66966;LSEQ=CAGCTACAGTTTCTGACAAA;RSEQ=GCCCACACCCTTTTAAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:147:106,41:124,79:203,147:0.42:2,2:24.2:1:30.8:1:0.03983:1.64:60:294:0.4249:0:2 0/1:144:47:28,19:56,41:97,47:0.3264:2,2:25.6:1:29.1:1:0.85889:1.08:60:14.667:0.3165:0:1.7 +20 52776805 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08958;SOR=Inf;LSEQ=AGTGGCATCTTTTATTTCCT;RSEQ=TGCACAGGCAATGACTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:0:0,0:244,209:453,0:0:2,0:25.9:1:32.4:1:1:0:60:89.6:1:0:0.8 0/1:194:2:1,1:99,93:192,2:0.0103:2,2:34:1:30.5:1:1:1.06421:60:4:0.0104:0:1 +20 52776841 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=0.46214;LSEQ=TAGAGAAAAAATATTGGTGG;RSEQ=AACAGCCAATGTAGCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:203:90,113:114,123:237,203:0.4603:2,2:26.2:1:31.9:1:0.4443:1.16328:60:406:0.4645:0:1.5 0/1:177:50:20,30:61,66:127,50:0.2825:2,2:24.4:1:30.1:1:0.40276:1.38381:60:49:0.2784:0:1.6 +20 52776892 . T A 90 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=21.34236;LSEQ=ATTCACCACTAGTAGTCATA;RSEQ=GTATTTATTTTTTAGGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:1:0,1:96,212:308,1:0.0032:2,0:3:0:29:0:1:0:60:2:0.0033:0:1 0/1:123:8:2,6:40,75:115,8:0.065:2,2:14.4:1:30.3:1:0.7144:1.59434:60:16:0.0656:0:1.1 +20 52776917 . T C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98071;LSEQ=TTATTTTTTAGGCCGTACTT;RSEQ=GCTAATTTAAGCCAAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:93:25,68:31,83:114,93:0.4493:2,2:24.6:1:30:1:1:1.01583:60:30:0.4455:0:1.4 0/1:72:32:8,24:9,31:40,32:0.4444:2,2:29:1:30.6:1:1:1.15:60:64:0.4444:0:1.5 +20 52777119 . G A 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCAGAGGACTGGCAGCCTC;RSEQ=GCTGCAAATAAACTGTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:23:1:32.8:1:1:0:60:10:0.5556:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 52779052 . G A 63 d5;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=ATGGAGGCACCGTGGCGTCT;RSEQ=GTATGAGGCCGTGCGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:19:0:31.8:1:1:0:58:8:1:0:2.3 0/0:1:0:0,0:0,1:1,0:0:0,0:49:0:29:0:1:0:60:2:1:0:0 +20 52779082 . C T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGCGCTGAGGCACCGTGG;RSEQ=ATAGATGCTGTGCGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:39:1:29.5:1:1:0:60:4:0.6667:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:22:0:33:0:1:0:60:2:1:0:0 +20 52908407 . ACAG A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.21344;SOR=4.96199;LSEQ=CAGGCTCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:1:0,1:17,19:36,1:0.027:2,0:45:0:31:0:1:0:60:2:0.027:0:0 0/1:16:2:2,0:6,8:14,2:0.125:2,0:35.5:1:30.5:1:0.46667:0:42.5:4:0.125:0:3 +20 54944939 . C A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACCATGCCTAGCACAGG;RSEQ=TGACGGGGCGGCTGCAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:6,0:6,3:0.3333:0,2:27.3:1:29.3:1:0.33333:0:54.7:6:0.375:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:14.5:1:29.5:1:1:0:44:4:1:0:0 +20 54945145 . C T 210 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCAGTCAATGGTAAAATAAA;RSEQ=TTCAGTAGCATGTTCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:110:88,22:320,69:389,110:0.22:2,2:24.4:1:31:1:0.57824:1.15904:45.4:54:0.2204:0:1.1 0/0:257:0:0,0:204,53:257,0:0:2,0:21.4:1:31.6:1:1:0:58.3:127.5:1:0:0.1 +20 54945688 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04844;SOR=Inf;LSEQ=ATCATTTCAGGGGGCAGGTA;RSEQ=TCCAGGGTGCCACAGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:0:0,0:159,357:516,0:0:2,0:33.7:1:32.5:1:1:0:55.7:128:1:0:0.1 0/1:297:3:1,2:105,189:294,3:0.0101:2,2:29.3:1:26.7:1:1:1.11074:45.3:6:0.0102:0:1 +20 54945783 . A G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96605;LSEQ=CACAACAGCTGCTAACAATC;RSEQ=TTAAAGAGTCCACTAACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:57:1,56:3,141:144,57:0.2836:1,1:23.2:1:32.4:1:1:1.19048:60:56:0.2963:0:1.1 0/1:94:26:0,26:4,64:68,26:0.2766:2,1:24.4:1:30.8:1:0.57271:0:60:25:0.2717:0:1 +20 54956064 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAAACTATCCTAGCCAGG;RSEQ=ACAATGGTGTGCACCTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:36.5:1:32:1:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 54956422 . G T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11672;SOR=5.85839;LSEQ=CCCACTCTACTATGATGAAA;RSEQ=GTACATTGCTATGGAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:1:1,0:421,127:548,1:0.0018:2,0:7:0:33:0:1:0:60:2:0.0018:0:1 0/1:283:3:0,3:210,70:280,3:0.0106:2,0:12:1:21.3:1:0.01664:0:60:2:0.0072:0:1 +20 54956707 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76674;SOR=0.88278;LSEQ=AAATGTCAAACAAACTCTTC;RSEQ=TGTAAAACCAGTGGTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:51:2,49:6,129:135,51:0.2742:1,1:21.3:1:32.9:1:1:1.13875:60:102:0.2757:0:1.1 0/1:84:21:1,20:2,61:63,21:0.25:1,1:20.4:1:30.6:1:1:1.52:60:42:0.25:0:1 +20 54957969 . G T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34473;SOR=2.90314;LSEQ=AAGGGACCTGGGCAGTGGGA;RSEQ=GCTGACATTACAGGAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:2:1,1:338,135:473,2:0.0042:2,2:21.5:1:20:1:0.49109:2.49818:60:1:0.0022:0:3 0/1:247:3:1,2:173,70:243,3:0.0121:2,2:17.3:1:27:1:0.20579:4.90601:60:6:0.0123:0:1 +20 54959296 . G C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12774;SOR=0.80098;LSEQ=TAATATATTCTAGTAGAACA;RSEQ=TACAGAACTTTGTAAATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:744:192:113,79:337,215:552,192:0.2581:2,2:23.5:1:32.4:1:0.60777:1.09569:59.4:384:0.2588:0:1.1 0/1:459:100:62,38:220,135:355,100:0.2179:2,2:25.5:1:31.6:1:1:1.00:59.4:99:0.2166:0:1.1 +20 54959467 . C A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55489;SOR=0;LSEQ=AGGTGAATCAAAGAATTGGT;RSEQ=ACCAAAATATTAATGGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:3:1,2:7,203:210,3:0.014:1,2:17.3:1:21:1:0.10899:13.92:60:2:0.0102:0:3.7 0/0:97:0:0,0:7,90:97,0:0:2,0:27.3:1:30.7:1:1:0:60:9.778:1:0:0.1 +20 54959505 . GT G 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.5511;SOR=0;LSEQ=ATGTCAAGAATGATAAATCT;RSEQ=TTTTTTTTTTTAAAGTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:3:0,3:0,95:95,3:0.0306:1,0:31.7:1:32.7:1:1:0:60:6:0.0316:0:0 0/0:47:0:0,0:0,47:47,0:0:1,0:20.6:1:29.6:1:1:0:60:46:1:0:0.1 +20 54959518 . A T 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.7493;LSEQ=TAAATCTGTTTTTTTTTTTT;RSEQ=AAGTTTTCCTTATAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:0,3:0,74:74,3:0.039:1,0:10.7:1:27.7:1:1:0:60:6:0.039:0:1.3 0/1:34:1:0,1:0,33:33,1:0.0294:1,0:34:0:29:0:1:0:60:2:0.0294:0:1 +20 54961073 . A G 107 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCAAAAGGACACCAATTT;RSEQ=TGCTGTGTCCTCCCTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:0,12:1:0,0:29.1:1:29.9:1:1:0:60:5:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:8:0:33:0:1:0:60:2:1:0:1 +20 54961214 . A C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55011;SOR=0;LSEQ=CCCATCCTCAACAGATATAA;RSEQ=AGCTAAGGCTCCAAACAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:173,12:185,2:0.0107:2,2:15.5:1:34:1:0.13455:13.89107:60:4:0.0108:0:1 0/0:96:0:0,0:87,9:96,0:0:2,0:23.2:1:29.7:1:1:0:60:47:1:0:0.1 +20 54961236 . G T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28033;SOR=3.74828;LSEQ=GCTAAGGCTCCAAACAATAA;RSEQ=TGCAAGTATATACACTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:1:0,1:249,63:312,1:0.0032:2,0:1:0:27:0:0.20447:0:60:2:0.0032:0:1 0/1:168:2:1,1:135,31:166,2:0.0119:2,2:16:1:30:1:0.34559:4.3021:60:4:0.0121:0:1 +20 54961463 . T C 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06614;LSEQ=CTTTTGTGCTTGCAAAGGAA;RSEQ=GCGCTGGGAAGAATTTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:481:477:225,252:0,3:3,477:0.9917:0,2:29.3:1:30.8:1:0.25137:0:29.8:52:0.9957:0:1.2 1/1:328:291:137,154:20,17:37,291:0.8872:2,2:30.1:1:30.1:1:0.48613:1.32132:27.7:71.75:0.8858:0:1.2 +20 54961541 . A T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51188;SOR=1.08922;LSEQ=TAATGGATTCTGACAAGGAA;RSEQ=TTGCTGAGTCACGAGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:189:75,114:219,328:547,189:0.2568:2,2:25:1:30.2:1:1:1.01486:50.4:62:0.2566:0:1.3 0/1:501:137:54,83:154,210:364,137:0.2735:2,2:27.7:1:30:1:0.61135:1.12689:45.4:136:0.2753:0:1.4 +20 54961545 . C T 78 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00969;SOR=10.21281;LSEQ=GGATTCTGACAAGGAAATTG;RSEQ=TGAGTCACGAGAACACGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:1:0,1:288,430:718,1:0.0014:2,0:1:0:29:0:1:0:60:2:0.0014:0:1 0/1:499:7:2,5:203,289:492,7:0.014:2,2:7.1:1:27.9:1:0.7055:1.7542:54.6:14:0.0141:0:1.6 +20 54961651 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.11214;SOR=Inf;LSEQ=GCAAAAGATGAATATATTGA;RSEQ=AATTTCACAAAGTTTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:14,130:144,0:0:2,0:22.3:1:31.9:1:1:0:60:35:1:0:0.1 0/1:73:2:1,1:6,65:71,2:0.0274:2,2:11.5:1:28:1:0.18379:10.11:60:4:0.0278:0:1 +20 54963149 . C CGACAAGACCAACCTCCATGTGGGTTTATAAATGTGAATGAGATTACAGATTATTCAATTTA 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00102;SOR=0.72685;LSEQ=GTAAAGGCGGAAAGAATTCC;RSEQ=GACAAGACCAACCTCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1497:1143:650,493:270,79:349,1143:0.7635:2,2:29.2:1:30.5:1:0:2.59066:59.4:380:0.7651:0.6286:0.1 1/0:850:596:337,259:170,81:251,596:0.7012:2,2:29.9:1:29.4:1:0.00273:1.61209:59.5:595:0.7017:0.5729:0.1 +20 54963303 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATTTGAACAAAGCCACCTG;RSEQ=TTAAAGTGCTGTTGCTCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:0:0,0:189,473:662,0:0:2,0:25:1:33.1:1:1:0:60:219.667:0.9985:0:0.1 0/1:416:20:8,12:135,260:395,20:0.0481:2,2:27:1:28.8:1:0.63277:1.28:60:40:0.0488:0:1.1 +20 54963331 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12824;SOR=5.55421;LSEQ=GCTGTTGCTCGATAGGCAGC;RSEQ=TTACAGTTCCCCAATCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:1:1,0:85,329:414,1:0.0024:2,0:1:0:25:0:0.20723:0:60:2:0.0024:0:1 0/1:226:3:2,1:55,168:223,3:0.0133:2,2:19:1:27.7:1:0.15749:6.05:60:6:0.0136:0:1 +20 54963739 . T G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGCTGAGCGTGGTGGCAG;RSEQ=CACCTGTAATCCCAGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:17.7:1:31:1:1:0:27.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 55177781 . C T 48 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCAGGAGAATCACTTGAACT;RSEQ=GGGAAGTGGAGGTTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:35.7:1:30.7:1:1:0:54:6:0.75:0:1.3 0/0:2:0:0,0:2,0:2,0:0:0,0:13:1:31.5:1:1:0:60:4:1:0:0 +20 55177856 . CA C 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.27679;SOR=0;LSEQ=GACAGAGCGAGACTCTACCT;RSEQ=AAAAAAAAAAAGCTGCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:14,4:0.2222:1,0:17:1:31.9:1:1:0:59:8:0.2222:0.0556:0.5 0/0:8:0:0,0:7,0:7,0:0:0,0:18.6:1:28.9:1:1:0:60:14:0.875:0:0 +20 55178081 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18134;LSEQ=TGGACATTTATGTGTTCCAT;RSEQ=GCAATACACGTATACATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:437:233:113,120:92,111:203,233:0.5332:2,2:26.4:1:30.2:1:0.56395:1.14:60:115.5:0.5347:0:1.1 0/1:327:56:25,31:132,139:271,56:0.1713:2,2:23.3:1:28.3:1:0.65991:1.17697:60:55:0.1708:0:1.1 +20 55178144 . A AT 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.16749;SOR=Inf;LSEQ=ATGTACGTATGCCTTCCTGG;RSEQ=TTTTAAAAATACATTAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:70,166:236,0:0:2,0:23.3:1:30.7:1:1:0:59.8:77.667:1:0:0.4 0/1:164:2:1,1:51,111:162,2:0.0122:2,2:31:1:29:1:0.53494:2.17:60:4:0.0122:0:0 +20 55178239 . C G 150 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=4e-05;SOR=0.06653;LSEQ=ACCCACCACTCACCTGCCTT;RSEQ=CCCACTTCCAGGCAGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:26:0,26:0,20:20,26:0.5652:1,1:29.3:1:32:1:1:0:60:52:0.5778:0:1.2 0/1:26:2:0,2:0,24:24,2:0.0769:1,0:10.5:1:24:1:1:0:60:1:0.0417:0:3 +20 57414681 . C A 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGGCCCACTAGGGTCTGCGC;RSEQ=ACAGGCTCGGCGCCACCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:35:1:31.5:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 57415082 . G T 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2211;SOR=4.59687;LSEQ=CATAGGGTGTACCTTTCCCG;RSEQ=CTCCAGCAGCCAATGTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:0,1:389,41:430,1:0.0023:2,0:15:0:26:0:0.09745:0:60:2:0.0024:0:2 0/1:189:2:1,1:157,30:187,2:0.0106:2,2:14.5:1:24.5:1:0.30187:5.16473:60:4:0.0106:0:1.5 +20 57415110 . A G 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01451;SOR=1.41298;LSEQ=AGCCAATGTGCTTCGGAGCC;RSEQ=CTCTCTGCAGAGCCAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:675:426:330,96:183,66:249,426:0.6311:2,2:24.1:1:30.5:1:0.26275:1.24:59.9:105.5:0.6317:0:1.1 1/0:376:266:184,82:79,31:110,266:0.7074:2,2:23.1:1:29.5:1:0.71084:1.13529:60:87.667:0.707:0:1.1 +20 57415294 . C A 74 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01871;SOR=6.11039;LSEQ=CCATCGCGCTCCTCCGCGCC;RSEQ=TTGCCACCTCCAACGCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1205:2:1,1:602,601:1203,2:0.0017:2,2:25.5:1:22:1:1:1.00166:57:1:8e-04:0:1.5 0/1:596:6:3,3:295,295:590,6:0.0101:2,2:20.5:1:28.8:1:1:1:60:12:0.0102:0:1 +20 57415455 . C T 216 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=58.57108;LSEQ=GACCTTGAGCTGTCCCTCCC;RSEQ=GAGTGCCTAGAGTACGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1889:5:1,4:935,948:1883,5:0.0026:2,2:7.6:1:27:1:0.37443:3.9424:60:10:0.0027:0:1 0/1:1122:151:79,72:503,462:965,151:0.1346:2,2:23.5:1:29.9:1:1:1.01:60:302:0.1354:0:1.1 +20 57415876 . C A 185 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=153.67037;LSEQ=AGTCCCCTTCCAAAAAGGGA;RSEQ=CCATCCCCATCCGGCGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1716:1:1,0:768,946:1714,1:6e-04:2,0:1:0:25:0:0.4484:0:60:2:6e-04:0:1 0/1:1008:83:39,44:430,493:923,83:0.0823:2,2:24.3:1:29.1:1:1:1.02:60:40.5:0.0815:0:1.4 +20 57415962 . C T 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTAGTTGCCCACCGCTAAA;RSEQ=TGGGGAGCCTGAGGGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:701:0:0,0:197,503:700,0:0:2,0:26.4:1:32.9:1:1:0:60:86.5:0.9986:0:0.4 0/1:412:98:29,69:95,217:312,98:0.2379:2,2:23:1:29.4:1:0.90041:1.04154:60:48:0.2376:0:1.8 +20 57415967 . G A 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGCCCACCGCTAAACTGGG;RSEQ=AGCCTGAGGGCGGTGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:651:0:0,0:174,476:650,0:0:2,0:26:1:32:1:1:0:60:129:1:0:0.5 0/1:374:23:5,18:99,252:351,23:0.0615:2,2:20.7:1:29.6:1:0.63415:1.4131:60:46:0.062:0:2.4 +20 57415995 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06745;SOR=1.42445;LSEQ=GGGCGGTGTGGGAGCAGCGC;RSEQ=GGTGGAAAGGAGGTGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:391:262:43,219:22,107:129,262:0.6701:2,2:23.3:1:31.4:1:0.88574:1.04703:60:261:0.671:0:1.1 1/0:222:165:26,139:11,45:56,165:0.7432:2,2:21.5:1:30.1:1:0.53611:1.30521:60:81.5:0.7443:0:1.4 +20 57416009 . T A 35 p8;q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55505;SOR=0;LSEQ=CAGCGCAGGTGGAAAGGAGG;RSEQ=GAGAAGGAAAGGCAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:3:3,0:33,250:283,3:0.0105:2,0:5.3:1:22.3:1:0.00185:0:60:2:0.0071:0:2.3 0/0:155:0:0,0:17,138:155,0:0:2,0:22.8:1:29.3:1:1:0:60:154:1:0:0.9 +20 57428201 . G A 23 v3;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92499;LSEQ=AGGGTTGGAAAGTGAGGCCG;RSEQ=TGAACTTTCCAGCTGGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:2,0:133,2:135,2:0.0146:1,0:21.5:1:23.5:1:1:0:60:4:0.0148:0:1 0/1:74:1:1,0:73,0:73,1:0.0135:1,0:32:0:29:0:1:0:60:2:0.0135:0:1 +20 57428215 . T G 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00328;SOR=Inf;LSEQ=AGGCCGGTGAACTTTCCAGC;RSEQ=GGTACTTTGATTTTAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:197,2:199,0:0:1,0:20.7:1:32.3:1:1:0:59.9:65.333:1:0:0.1 0/1:95:5:5,0:90,0:90,5:0.0526:1,0:28.8:1:25.4:1:1:0:60:4:0.0426:0:1.2 +20 57428287 . C G 195 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGTGCTCCATCTTACGGAG;RSEQ=CCCAAACTTATTTTGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1035:76:56,20:701,258:959,76:0.0734:2,2:27.9:1:31.3:1:1:1.03:60:24.333:0.0719:0:1.1 0/0:572:0:0,0:358,212:570,0:0:2,0:25.5:1:30.7:1:1:0:60:80.429:0.9982:0:0.2 +20 57429447 . C T 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=80.07843;LSEQ=GGGAGGAAAAGTACCCTCTC;RSEQ=GGGGTACGGATCCCCTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:886:1:0,1:375,510:885,1:0.0011:2,0:1:0:26:0:1:0:60:2:0.0011:0:1 0/1:420:35:18,17:158,226:384,35:0.0833:2,2:22.4:1:30.7:1:0.28374:1.51:60:70:0.0847:0:1.1 +20 57429607 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00542;SOR=Inf;LSEQ=GGGGCATTCGCAGCCGATCC;RSEQ=GACTCCGGGGCAGCCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:0:0,0:262,466:728,0:0:2,0:25.5:1:29.8:1:1:0:55.2:33.667:0.9986:0:0.2 0/1:399:5:3,2:158,235:393,5:0.0125:2,2:24.4:1:29:1:0.39803:2.23:58.4:10:0.0127:0:1.2 +20 57429626 . G A 59 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12813;SOR=3.29785;LSEQ=CCGACTCCGGGGCAGCCCCT;RSEQ=CCGCCCCAGCCGATCCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:3:2,1:198,439:637,3:0.0047:2,2:25:1:27:1:0.23155:4.42:54:6:0.0048:0:1 0/1:327:5:3,2:121,201:322,5:0.0153:2,2:14.2:1:25.8:1:0.3714:2.48:60:10:0.0156:0:1.4 +20 57429627 . C A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGACTCCGGGGCAGCCCCTG;RSEQ=CGCCCCAGCCGATCCCGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:637:0:0,0:194,443:637,0:0:2,0:25.3:1:31.2:1:1:0:53.7:36.471:1:0:0.2 0/1:322:28:14,14:108,186:294,28:0.087:2,2:29.9:1:28.1:1:0.22056:1.72:42.1:27:0.0863:0:1.1 +20 57429687 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59507;SOR=2.15687;LSEQ=CCCAGCCGATCCCGACTCCG;RSEQ=GGCGGCCCCTGACGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:2:2,0:77,232:309,2:0.0064:2,0:1:0:27.5:1:0.06391:0:27.5:4:0.0065:0:1 0/1:145:2:2,0:44,98:142,2:0.0138:2,0:9:1:27:1:0.10052:0:46.5:4:0.0138:0:1 +20 57429696 . C G 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01185;SOR=Inf;LSEQ=TCCCGACTCCGGGGCGGCCC;RSEQ=TGACGCCCCAGCCGATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:73,191:264,0:0:2,0:24.8:1:32.8:1:1:0:49.9:51.8:1:0:0.1 0/1:132:4:2,2:43,85:128,4:0.0303:2,2:19:1:29.8:1:0.60524:1.97:49:8:0.0308:0:1.5 +20 57429716 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55349;SOR=0;LSEQ=CTGACGCCCCAGCCGATCCA;RSEQ=ATGCCGGGGCGGCCCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:73,140:213,3:0.0139:2,2:27:1:28:1:0.27699:3.81:59.7:6:0.0141:0:1 0/0:108:0:0,0:47,61:108,0:0:2,0:22:1:30.8:1:1:0:49.8:35:1:0:0.3 +20 57429741 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12829;SOR=Inf;LSEQ=CGGGGCGGCCCCTGAGGCTC;RSEQ=CGCCGCCCCTGCGGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:84,71:155,0:0:2,0:22:1:30.9:1:1:0:57.3:30:1:0:0.2 0/1:87:2:1,1:42,43:85,2:0.023:2,2:22:1:31:1:1:1.02:60:4:0.023:0:1 +20 57429743 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.946;LSEQ=GGGCGGCCCCTGAGGCTCCC;RSEQ=CCGCCCCTGCGGCTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:92,65:157,2:0.0126:2,2:25:1:28.5:1:1:1.41221:50:4:0.0127:0:1 0/1:84:1:1,0:44,39:83,1:0.0119:2,0:1:0:24:0:1:0:39:2:0.0119:0:1 +20 57429767 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22051;SOR=4.6261;LSEQ=CCCCTGCGGCTGCTGAGACC;RSEQ=GGGCAGCCCATGTCGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:1:0,1:155,59:214,1:0.0047:2,0:1:0:26:0:0.27907:0:60:2:0.0047:0:1 0/1:94:2:1,1:61,31:92,2:0.0213:2,2:21:1:28.5:1:1:1.95263:60:4:0.0215:0:1 +20 57429782 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09497;SOR=Inf;LSEQ=AGACCCGGGCAGCCCATGTC;RSEQ=CCCCAGCTGCGCCAGACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:214,60:274,0:0:2,0:23.2:1:30.8:1:1:0:60:53.8:0.9963:0:0.2 0/1:123:2:1,1:87,34:121,2:0.0163:2,2:26:1:27:1:0.4898:2.53646:60:4:0.0165:0:1 +20 57429940 . G A 80 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00986;SOR=6.73451;LSEQ=GAGATCCAGGCTGCCGATCC;RSEQ=CCTACTCCGCGGCCTACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1304:2:1,1:648,654:1302,2:0.0015:2,2:16:1:30:1:1:1.01:60:4:0.0016:0:1 0/1:683:7:4,3:326,350:676,7:0.0102:2,2:32.6:1:28.7:1:0.71699:1.43:60:14:0.0105:0:1 +20 57430051 . C T 81 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00259;SOR=8.52871;LSEQ=AGCAGCGACGATGACTCCAG;RSEQ=GGAGACGAGTCCGACGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:931:2:0,2:530,398:928,2:0.0021:2,0:1:0:26:1:0.18473:0:60:4:0.0022:0:1 0/1:443:8:5,3:250,184:434,8:0.0181:2,2:23.5:1:27.3:1:1:1.23:60:7:0.0162:0:1 +20 57430477 . C G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=3.2658;LSEQ=CCTGGTGGGGCTAGGGGCTC;RSEQ=GCAGTGGGAGGAGGGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:48:0,48:1,185:186,48:0.2043:1,1:26.5:1:31.6:1:1:0:60:96:0.2078:0:1.3 0/1:70:32:1,31:1,37:38,32:0.4571:1,1:29.7:1:29.9:1:1:1.19:60:31:0.4493:0:1.1 +20 57430493 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCGCAGTGGGAGGAGGG;RSEQ=GTCCAGCCAAAGGCGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:1,188:189,2:0.0105:1,0:35.5:1:26:1:1:0:60:4:0.0107:0:4.5 0/0:54:0:0,0:1,53:54,0:0:1,0:22.6:1:30:1:1:0:60:17:1:0:0.6 +20 57466761 . CCCG C 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.03548;SOR=5.21421;LSEQ=CCGCCGCAGCCCGGCCGCGC;RSEQ=CCGCCGCCGCCGCCGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:2:2,0:171,35:206,2:0.0095:2,0:9:1:31.5:1:1:0:60:4:0.0096:0.0048:0 0/1:146:7:5,2:100,38:138,7:0.0479:2,2:8.4:1:31.6:1:1:1.05226:59.3:14:0.0479:0.0205:0.1 +20 57466764 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.17017;SOR=Inf;LSEQ=CCGCAGCCCGGCCGCGCCCC;RSEQ=CCGCCGCCGCCGCCGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:189,40:229,0:0:2,0:11.4:1:30.3:1:1:0:60:44.8:1:0:0.2 0/1:162:2:1,1:111,44:155,2:0.0123:2,2:21:0:31:0:0.49241:2.50576:60:4:0.0127:0:1.5 +20 57466776 . G A 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.01281;SOR=Inf;LSEQ=CGCGCCCCGCCGCCGCCGCC;RSEQ=CCGCCATGGGCTGCCTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:303,102:405,0:0:2,0:15.9:1:30.5:1:1:0:60:49.625:0.9975:0:0.2 0/1:294:5:3,2:197,91:288,5:0.017:2,2:25.2:1:28.4:1:0.65404:1.44134:60:10:0.0174:0:1 +20 57466901 . G A 96 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09669;SOR=2.35948;LSEQ=AAGCAGGTCTACCGGGCCAC;RSEQ=CACCGCCTGCTGCTGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:929:6:4,2:333,590:923,6:0.0065:2,2:23.2:1:29.2:1:0.19738:3.54:60:12:0.0066:0:1.5 0/1:794:12:10,2:304,477:781,12:0.0151:2,2:9.6:1:26.9:1:0.0024:7.83:59.6:24:0.0153:0:1.2 +20 57466907 . CCTG C 87 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.36324;SOR=2.07778;LSEQ=GTCTACCGGGCCACGCACCG;RSEQ=CTGCTGCTGGGTAAGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:807:4:1,3:264,538:802,4:0.005:2,2:29.3:1:32.5:1:1:1.47146:60:8:0.005:0.0012:0.3 0/1:683:7:3,4:252,423:675,7:0.0102:2,2:24.1:1:31:1:0.71657:1.26:60:14:0.0104:0.0029:0.6 +20 57467859 . CT C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTCATTTTACAGTGTGAC;RSEQ=TTTTTTCCCCTTCCAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:32.5:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 57470517 . G A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.14564;LSEQ=GATTTCCTTTTCTCTGCGTC;RSEQ=AAATGTCAAGGAAAGTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:9:9,0:80,0:80,9:0.1011:1,0:28.4:1:30.1:1:1:0:60:18:0.1011:0:1.1 0/1:35:4:4,0:31,0:31,4:0.1143:1,0:19.3:1:29.8:1:1:0:60:8:0.1212:0:1 +20 57473892 . T A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20299;SOR=Inf;LSEQ=CTGGCGCGCGAATTGTTGCT;RSEQ=TTGCTCTTGGCTGATGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:110,15:125,0:0:2,0:23:1:31.2:1:1:0:60:30.25:1:0:0.1 0/1:103:2:1,1:83,18:101,2:0.0194:2,2:13:0:30.5:1:0.33638:4.5151:60:4:0.0194:0:1 +20 57473904 . T C 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0815;SOR=Inf;LSEQ=TTGTTGCTTTTGCTCTTGGC;RSEQ=GATGGTTGAGGAATGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:132,30:162,0:0:2,0:24:1:31.2:1:1:0:60:26:1:0:0.1 0/1:125:3:2,1:94,28:122,3:0.024:2,2:17:1:22:1:0.55034:1.67075:60:2:0.0164:0:1 +20 57473962 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08824;SOR=Inf;LSEQ=TGTGACACTGCGGTGCCTTG;RSEQ=AGATTAGGTGAGCTTTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:201,123:324,0:0:2,0:25.1:1:31.6:1:1:0:60:28.455:1:0:0.1 0/1:261:3:2,1:157,100:257,3:0.0115:2,2:16.7:1:26.7:1:1:1.27:60:6:0.0116:0:1 +20 57473997 . G T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14292;SOR=0;LSEQ=TTCAATCTCTCTTTAAAAGG;RSEQ=GCGGCGAAGAGGACCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:4:1,3:209,177:386,4:0.0103:2,2:37.5:1:30:1:0.339:3.53171:60:8:0.0106:0:1.3 0/0:283:0:0,0:151,129:280,0:0:2,0:24.4:1:29.8:1:1:0:60:69:0.9928:0:0.1 +20 57478448 . A T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00884;SOR=3.96066;LSEQ=ATGTTTATTCAGCTACCTCC;RSEQ=ATCTTTGCACAGATCCGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:6:6,0:83,5:88,6:0.0638:2,0:29.3:1:33.3:1:1:0:60:12:0.0645:0:1.2 0/1:56:12:10,2:39,5:44,12:0.2143:2,2:20.4:1:29.8:1:0.63475:1.54647:60:11:0.2:0:1.1 +20 57478807 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.36332;LSEQ=CAGTTCAGAGTGGACTACAT;RSEQ=CTGAGTGTGATGAACGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:961:111:48,63:400,447:847,111:0.1155:2,2:25.1:1:30:1:0.47913:1.1743:60:26.75:0.1133:0:1.1 0/1:757:312:147,165:211,232:443,312:0.4122:2,2:25:1:28.5:1:0.94101:1.02083:59.9:25:0.4076:0:1.2 +20 57478939 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05372;LSEQ=GACAGCCCTGCACATGGGCA;RSEQ=GAGCATCCAAACCACACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:195:183:4,179:0,12:12,183:0.9385:0,1:24.8:1:32.4:1:1:0:59.9:366:0.9385:0:1.1 0/1:94:42:4,38:2,50:52,42:0.4468:1,2:23:1:31:1:0.40212:2.60:60:84:0.4516:0:1.1 +20 57480545 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=Inf;LSEQ=TGTGCCCAGTAGTAAGTAAC;RSEQ=GCCACCCAACCCATCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:183,305:488,0:0:2,0:25.2:1:30.1:1:1:0:60:43.364:1:0:0.1 0/1:394:10:5,5:151,233:384,10:0.0254:2,2:14:1:27.1:1:0.52594:1.54:60:9:0.0233:0:1.2 +20 57483948 . G A 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.56923;SOR=3.83897;LSEQ=TGTTTGTGTGGCCCCACTGC;RSEQ=TCGAGGCCACAGGCTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:35.6:1:30.2:1:1:0:54.4:10:0.625:0:1.6 1/1:8:7:6,1:1,0:1,7:0.875:0,2:18:1:30.9:1:1:0:60:14:0.875:0:1 +20 57484085 . T C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03312;SOR=3.03928;LSEQ=AACCAACACACAAGCAAATG;RSEQ=GCCATTGACTTAGTGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:7:7,0:100,5:105,7:0.0625:1,0:28.7:1:32.9:1:1:0:60:14:0.0636:0:1 0/1:59:10:10,0:47,2:49,10:0.1695:1,0:20.2:1:31.3:1:1:0:60:9:0.1552:0:1.1 +20 57484241 . C T 136 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.53372;LSEQ=CTGGACAAGATCGACGTGAT;RSEQ=AAGCAGGCTGACTATGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:4:1,3:397,313:710,4:0.0056:2,2:14.8:1:22.3:1:0.32694:3.79843:60:3:0.0042:0:1.3 0/1:499:28:15,13:248,223:471,28:0.0561:2,2:24.3:1:28.3:1:1:1.04:60:56:0.0567:0:1.3 +20 57484661 . G A 129 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=26.32704;LSEQ=TGCTGTGGGCTTGGCTGTTC;RSEQ=TAAAGAACGCTTTGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:550:1:1,0:299,249:548,1:0.0018:2,0:1:0:26:0:1:0:60:2:0.0018:0:1 0/1:458:21:13,8:231,205:436,21:0.0459:2,2:26.5:1:29.4:1:0.50506:1.44:60:20:0.0442:0:1.1 +20 57484934 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06391;SOR=0.73045;LSEQ=CTGTTTATAGAGAAGAACCC;RSEQ=GTGCAAGCATTCCAGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:147:66,81:176,196:372,147:0.2832:2,2:21.7:1:30.7:1:0.62693:1.10183:60:28.4:0.2779:0:1.2 0/1:326:73:33,40:127,125:252,73:0.2239:2,2:21.7:1:30.1:1:0.50651:1.23072:60:35.5:0.2205:0:1.1 +20 57485201 . G A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55912;SOR=3.35274;LSEQ=CTTTTTCAAACGGTCAGGCT;RSEQ=AAAACCCCCATCCCCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:46,221:267,1:0.0037:2,0:1:0:30:0:1:0:60:2:0.0038:0:1 0/1:162:2:1,1:28,132:160,2:0.0123:2,2:8.5:1:26.5:1:0.32689:4.65:60:4:0.0129:0:1.5 +20 57485324 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14589;SOR=Inf;LSEQ=AAGACTTCAGGAGCTACAGA;RSEQ=ATGCTAGCACCCCAGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:172,78:250,0:0:2,0:25.9:1:32.9:1:1:0:60:82.333:1:0:0.1 0/1:155:2:1,1:111,42:153,2:0.0129:2,2:24:1:27:1:0.47918:2.62369:60:4:0.013:0:1 +20 57485489 . G A 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TGTCTTTAGTTTCCTCTCTT;RSEQ=TTCCTCCTCTTTTTCTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:0:0,0:248,377:625,0:0:2,0:25.1:1:32:1:1:0:60:68.444:1:0:0.1 0/1:522:15:5,10:198,309:507,15:0.0287:2,2:24.8:1:28.6:1:0.79118:1.28096:60:30:0.0291:0:1.1 +20 57485538 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16179;SOR=Inf;LSEQ=TTTACTTAATTCCAAATTCA;RSEQ=GGGTTCAGCTACCCAGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:73,221:294,0:0:2,0:22.1:1:31.7:1:1:0:60:146:0.9966:0:0.3 0/1:199:2:1,1:43,153:196,2:0.0101:2,2:24:1:28.5:1:0.39594:3.53:60:4:0.0103:0:1 +20 57485611 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.009;SOR=0.36639;LSEQ=TTGAGCTCTTTGCGCCCCTC;RSEQ=TTTTGCTTTTGTTTTCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:185:107,78:9,5:14,185:0.9296:2,2:24.3:1:32.3:1:0.78145:1.3104:60:60.667:0.9286:0:1.1 1/1:99:82:50,32:11,6:17,82:0.8283:2,2:23.3:1:30.8:1:1:1.17146:60:40:0.8333:0:1.2 +20 57485941 . G T 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAATTAATTAAAAGTGAAAC;RSEQ=TAATTGTACAAGCAGTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:37,244:281,0:0:2,0:23.2:1:31.8:1:1:0:60:39.143:1:0:0.1 0/1:202:14:2,12:30,157:187,14:0.0693:2,2:22:1:29.5:1:1:1.14575:60:28:0.0697:0:1.2 +20 58054448 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0.53881;LSEQ=TAGTCACAAACCTTAAGTGT;RSEQ=TTTTACGGGAATGCAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:508:294:146,148:106,106:212,294:0.5787:2,2:26.6:1:29.6:1:1:1.01367:60:146:0.5817:0:1.1 0/1:381:162:79,83:105,112:217,162:0.4252:2,2:25.4:1:28.4:1:1:1.02:60:161:0.4248:0:1.1 +20 58054459 . A G 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTTAAGTGTGTTTTACGGGA;RSEQ=TGCAAGCACTTCAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:237,251:488,0:0:2,0:27.8:1:30.7:1:1:0:59.9:487:1:0:0.6 0/1:381:14:6,8:172,195:367,14:0.0367:2,2:28.1:1:31.6:1:0.79313:1.17557:60:28:0.0371:0:1.1 +20 58054528 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16991;SOR=Inf;LSEQ=TCTTCTAGTGTTTTAAAGAG;RSEQ=TGGTTAGCACAGCCACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:58,178:236,0:0:2,0:21.8:1:32.7:1:1:0:59.9:77.667:1:0:0.3 0/1:166:2:1,1:41,123:164,2:0.012:2,2:27.5:1:30.5:1:0.44315:2.98:60:4:0.0122:0:1 +20 58054565 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12363;SOR=Inf;LSEQ=ACACCACATGGGGAAGTTCT;RSEQ=GCTGATGGCGGACCATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:9,121:130,0:0:2,0:25.9:1:31.7:1:1:0:60:129:1:0:0.1 0/1:71:2:1,1:3,66:69,2:0.0282:1,2:13.5:1:28:1:0.11026:19.20:60:4:0.0286:0:1.5 +20 58054767 . A G 32 d5;v3;MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTACCATGCAGCCCAGGTGT;RSEQ=TAGTAGGCTGTACCATCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:7.5:1:32.5:1:1:0:35:4:0.6667:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:41:0:34:0:1:0:60:2:1:0:1 +20 58055043 . A G 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTCCTAATTAGTTAACT;RSEQ=CATTTTACAGTGATCTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:41:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:33:0:1:0:60:4:1:0:2 +20 58196318 . AC A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.10074;SOR=Inf;LSEQ=TAGGTTATTTGTAGGTGAGC;RSEQ=CCCAGTGCACATAGACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:79,21:100,0:0:2,0:25.7:1:31.5:1:1:0:59.8:19:1:0:0.2 0/1:47:2:1,1:35,10:45,2:0.0426:2,2:36:1:30.5:1:0.41721:3.38437:60:4:0.0426:0:0.5 +20 58196400 . G T 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15429;SOR=Inf;LSEQ=TTGCCCAGACTCCTGCTCTT;RSEQ=CCCTGTGGAAGGACCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:114,97:211,0:0:2,0:25.4:1:32.1:1:1:0:60:51.75:1:0:0.3 0/1:137:2:1,1:73,62:135,2:0.0146:2,2:5.5:1:24.5:1:1:1.17601:60:4:0.0147:0:1.5 +20 58196423 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27739;SOR=0;LSEQ=CTGTGGAAGGACCTATGAGT;RSEQ=GGACCCCACACAGGGATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:1,2:109,108:217,3:0.0136:2,2:12:1:31:1:1:2.01231:60:6:0.0139:0:1 0/0:148:0:0,0:72,74:146,0:0:2,0:25:1:30.2:1:1:0:60:292:0.9865:0:0.6 +20 58196424 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.56484;LSEQ=TGTGGAAGGACCTATGAGTC;RSEQ=GACCCCACACAGGGATTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:40:21,19:89,91:180,40:0.1818:2,2:24.3:1:30.8:1:0.86143:1.13:60:80:0.1843:0:1.1 0/1:149:66:31,35:43,40:83,66:0.443:2,2:26.1:1:29.4:1:0.62185:1.21212:60:65:0.4483:0:1.2 +20 58196450 . C T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29849;SOR=0;LSEQ=CACACAGGGATTAGGTGGGG;RSEQ=CATGCTGGGCAGCCCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:1,2:96,112:208,3:0.0142:2,2:19.3:1:22:1:1:1.71009:60:2:0.0101:0:1 0/0:124:0:0,0:56,67:123,0:0:2,0:26.6:1:30.4:1:1:0:59.9:40:0.9917:0:0.5 +20 58196490 . A T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29275;SOR=0;LSEQ=CAGCCTGGCACATCTTGGGG;RSEQ=CTGTCCACAGTGTCAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:3:1,2:51,95:146,3:0.0201:2,2:29:1:29:1:1:1.07318:60:6:0.021:0:1 0/0:90:0:0,0:33,57:90,0:0:2,0:20.8:1:28.1:1:1:0:60:44:1:0:0.3 +20 58197161 . GTT G 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=ATGTGCATGTACAAGTATGT;RSEQ=TGTGTGTGCAGGTGTGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:26.5:1:28.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:33:0:1:0:60:4:1:0:0.5 +20 58198325 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATCAGGCTTGGTCCAGCCC;RSEQ=TGTTATGACCTTCCAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 59632034 . C T 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02876;SOR=0;LSEQ=TCAGGATTTGAAGTTTCACG;RSEQ=CCAGCAGCAGCCCAGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:7,3:8,4:12,10:0.4545:2,2:26.7:1:30.6:1:1:1.16:57.9:20:0.4545:0:1.1 0/0:8:0:0,0:5,3:8,0:0:2,0:24.6:1:32.8:1:1:0:58.3:16:1:0:0.3 +20 59926780 . CT C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTTTTATTTTTATTTAT;RSEQ=TTTTTTTTTTTGAGACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:30:1:1:0:47:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 59927881 . T A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.29022;SOR=0.58698;LSEQ=TTTTCTGCTCTTCGGAGTTC;RSEQ=TCATCCGGCAGTGCAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:22:19,3:63,11:74,22:0.2292:2,2:23.3:1:30.7:1:1:1.10:60:44:0.234:0:1.1 0/1:54:8:7,1:39,7:46,8:0.1481:2,2:14.8:1:28.9:1:1:1.25:60:16:0.1481:0:1 +20 59927925 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14251;SOR=Inf;LSEQ=CCCATCACCCCGTGCACCTG;RSEQ=GAGACGCTGCGGACAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:129,73:202,0:0:2,0:24.4:1:30.1:1:1:0:59.7:404:1:0:0.4 0/1:123:2:1,1:73,48:121,2:0.0163:2,2:27:1:28.5:1:1:1.51547:60:4:0.0163:0:1 +20 59927968 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.88361;LSEQ=TGTCAATGTCCCATCCTTGC;RSEQ=GCGCACAGGAGGTTCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:11:7,4:137,123:260,11:0.0406:2,2:23.5:1:31.2:1:0.54953:1.57:60:22:0.041:0:2.4 0/1:198:34:16,18:82,82:164,34:0.1717:2,2:28.6:1:29.9:1:0.8511:1.12433:60:33:0.1701:0:2.1 +20 59927999 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07307;SOR=Inf;LSEQ=GGTTCCAGGACCCAGGAAGC;RSEQ=TCAACATTCTCTCTGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:129,148:277,0:0:2,0:25.1:1:31.9:1:1:0:59.9:45.167:1:0:1.1 0/1:200:3:1,2:88,109:197,3:0.015:2,2:33.7:1:23.3:1:1:1.61097:60:2:0.0102:0:4.3 +20 59928005 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43949;SOR=0.85747;LSEQ=AGGACCCAGGAAGCCTCAAC;RSEQ=TTCTCTCTGCCTGTGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:274:171:72,99:48,55:103,171:0.6241:2,2:25:1:31.3:1:0.52991:1.19919:59.8:342:0.6264:0:1.9 1/0:189:111:48,63:34,44:78,111:0.5873:2,2:25.5:1:30.6:1:1:1.01413:60:222:0.5936:0:2.1 +20 59928030 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49529;SOR=0.85424;LSEQ=CTCTGCCTGTGTGGCATGCC;RSEQ=GACCAAGGGGCCCCTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:214:140:52,88:31,43:74,140:0.6542:2,2:23.8:1:31.3:1:0.5559:1.21888:60:139:0.6557:0:2.2 1/0:136:84:33,51:22,30:52,84:0.6176:2,2:25.2:1:29.7:1:0.85745:1.13228:60:168:0.6222:0:2.3 +20 59928076 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09393;SOR=Inf;LSEQ=TCAGGCTCTGGGGACCCCAC;RSEQ=GGCCCCATCTCCTCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:20,92:112,0:0:2,0:21.7:1:30.7:1:1:0:60:55:1:0:1.3 0/1:50:2:1,1:11,36:47,2:0.04:2,2:9:1:24.5:1:0.43367:3.18:60:4:0.0408:0:3 +20 59928077 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09631;SOR=Inf;LSEQ=CAGGCTCTGGGGACCCCACG;RSEQ=GCCCCATCTCCTCCCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:19,91:110,0:0:2,0:21.5:1:30.8:1:1:0:60:35.667:1:0:1.3 0/1:50:2:1,1:11,37:48,2:0.04:2,2:19.5:1:28:1:0.42612:3.26:60:4:0.0417:0:1 +20 59928091 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=1.09208;LSEQ=CCCACGGGCCCCATCTCCTC;RSEQ=CCTCCCCTCTCTTAGCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:79:48:3,45:4,26:30,48:0.6076:2,2:24.2:1:29:1:0.41904:2.28184:60:15:0.6:0:2.1 1/0:35:22:4,18:2,11:13,22:0.6286:2,2:15.3:1:26.2:1:1:1.22:60:4.5:0.5806:0:2.2 +20 59928237 . T C 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.41667;SOR=0;LSEQ=GTTTCCACCTGTGGAAAGCA;RSEQ=ATACATGATGAATGTGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:1,6:0,4:4,7:0.6364:0,2:16.6:1:33:1:1:0:60:14:0.6364:0:1.3 0/0:1:0:0,0:0,1:1,0:0:0,0:19:0:29:0:1:0:60:2:1:0:0 +20 59931355 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAACCTGCTCTGTGTCATC;RSEQ=CAGCACCACATCCTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 60424439 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCACTGTGTAACGAATCAG;RSEQ=ACAAACTTAGTGGCTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:27.5:1:1:0:60:4:1:0:1 +20 60425089 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCAGCCTGAGTACGCTGAC;RSEQ=ACTGTGACACGTGTCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:7:0:29.5:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:28.5:1:1:0:60:4:1:0:1 +20 60426113 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04556;SOR=0.62287;LSEQ=GCGTGTGGGAAACACATCCA;RSEQ=AGCAGGACGGAGCTGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:217:151:68,83:24,42:66,151:0.6959:2,2:27.9:1:32.3:1:0.29598:1.43:60:302:0.6959:0:1.2 1/0:126:74:35,39:24,28:52,74:0.5873:2,2:24.4:1:31.4:1:1:1.05:59.7:73:0.5887:0:1.3 +20 60426146 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04258;SOR=Inf;LSEQ=CTGCAGATGGGTCGGGGATG;RSEQ=GGGAGTCTGCCCGCGACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:52,112:164,0:0:2,0:23:1:31.5:1:1:0:60:328:1:0:0.8 0/1:89:3:1,2:35,51:86,3:0.0337:2,2:33.7:1:29:1:1:1.36784:60:6:0.0341:0:2 +20 60426150 . A G 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55339;SOR=0;LSEQ=AGATGGGTCGGGGATGGGGG;RSEQ=GTCTGCCCGCGACGGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:3:2,1:48,105:153,3:0.0192:2,2:10.3:1:26:1:0.24081:4.33:60:2:0.013:0:3 0/0:83:0:0,0:32,51:83,0:0:2,0:26.3:1:28.7:1:1:0:60:15.6:1:0:0.9 +20 60426157 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12176;SOR=Inf;LSEQ=TCGGGGATGGGGGAGTCTGC;RSEQ=CGCGACGGGGCGGGGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:39,100:139,0:0:2,0:22:1:30.9:1:1:0:60:26.8:1:0:0.7 0/1:75:2:1,1:26,45:71,2:0.0267:2,2:26.5:1:28:1:1:1.72:60:4:0.027:0:3 +20 60426165 . G C 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=GGGGGAGTCTGCCCGCGACG;RSEQ=GGCGGGGACAGCCGGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:25,84:109,0:0:2,0:24.4:1:31.3:1:1:0:60:108:1:0:0.6 0/1:67:9:4,5:20,38:58,9:0.1343:2,2:26.1:1:29.6:1:0.71142:1.51:60:18:0.1364:0:2.2 +20 60427195 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCACGGATCCCCCCAC;RSEQ=CCACCACCCATATTCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 60561917 . A C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTCCAATTAATAAATGT;RSEQ=AACAGAAAGACAGAAATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29.5:1:1:0:60:4:1:0:1.5 +20 60562181 . C A 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01329;SOR=0.1462;LSEQ=GACACCACCTGCCTCCCAAT;RSEQ=CAGTGCTCTGAGGACACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:11,18:2,2:4,29:0.8788:2,2:27.4:1:28.3:1:1:1.61126:60:28:0.875:0:1.2 1/0:12:6:3,3:3,3:6,6:0.5:2,2:29.2:1:28.2:1:1:1:60:12:0.5:0:1 +20 60562394 . G A 51 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGGAGCCGAGGAGCCGC;RSEQ=AGGGTCCCGGGGCAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:0,3:0,0:0,3:1:0,0:33:1:32.7:1:1:0:60:6:1:0:1 +20 60577258 . G A 48 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=CTTCTCACTGAAGTATCAGC;RSEQ=TCACGCTGGGCCCAGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:30.3:1:30.7:1:1:0:60:6:0.75:0:1.7 1/0:2:1:0,1:0,1:1,1:0.5:0,0:48:0:30:0:1:0:60:2:0.5:0:1 +20 61041333 . C T 136 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00042;SOR=0.02774;LSEQ=CCCGGGGGTGGTGCCGCAGT;RSEQ=GGCCGGCCGGGACATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:19,0:3,0:3,19:0.8636:0,1:25.1:1:32.2:1:1:0:60:38:0.8636:0:1.1 0/1:8:1:1,0:7,0:7,1:0.125:0,0:33:0:31:0:1:0:60:2:0.125:0:1 +20 61041423 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17678;SOR=5.58319;LSEQ=CTTGGTCTGAGAGTGCGGAC;RSEQ=GCGCTCGCTAGGAGGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:1,0:99,3:102,1:0.0097:1,0:36:0:14:0:1:0:60:0:0:0:1 0/1:38:2:2,0:33,3:36,2:0.0526:2,0:16:1:28.5:1:1:0:60:4:0.0541:0:1 +20 61041456 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10284;SOR=Inf;LSEQ=AGGCTGGACAGAGGCCTCCC;RSEQ=GCCCTGCCCCGGGGACCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:157,57:214,0:0:2,0:21.7:1:30.4:1:1:0:60:41.8:0.9952:0:0.1 0/1:102:2:1,1:71,29:100,2:0.0196:2,2:39:1:25:1:0.50379:2.42403:60:4:0.0198:0:1 +20 61041467 . G C 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.55394;SOR=0;LSEQ=AGGCCTCCCCGCCCTGCCCC;RSEQ=GGGACCACACTCACCCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:1,2:187,73:260,3:0.0113:2,2:20:1:29.3:1:0.19658:5.08631:60:6:0.0115:0:1 0/0:135:0:0,0:91,43:134,0:0:2,0:23.9:1:29.5:1:1:0:59.7:133:0.9925:0:0.2 +20 61041544 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11947;SOR=Inf;LSEQ=CTCCCCCTCCGAGTTCCGCC;RSEQ=CCACAGCGTGGTGTTGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:171,201:372,0:0:2,0:29.1:1:30.6:1:1:0:60:73.4:1:0:0.1 0/1:197:2:1,1:87,107:194,2:0.0102:2,2:31:1:29:1:1:1.23:60:4:0.0104:0:2 +20 61041653 . G C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56342;SOR=0.72158;LSEQ=GAGCCCCGGGCCGGGTGCGC;RSEQ=GCTGGAGCAGGGGGACGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:71:48:0,48:0,23:23,48:0.6761:1,1:23.4:1:30.1:1:1:0:60:23:0.6667:0:1.1 1/0:15:9:0,9:1,5:6,9:0.6:2,0:27.8:1:30.1:1:0.4:0:60:18:0.6:0:1.3 +20 61041687 . C T 48 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02417;SOR=11.00425;LSEQ=GACGGAAGCGAGACTCAGGT;RSEQ=GGCCTTGCGGCCACGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:0,2:1,39:40,2:0.0476:1,0:11:1:33:0:1:0:60:4:0.0476:0:2.5 0/1:8:3:0,3:0,5:5,3:0.375:0,0:12.7:1:30.3:1:1:0:60:6:0.375:0:2 +20 61048479 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03112;SOR=Inf;LSEQ=CAGGCGCTTCTGAGGCCGAA;RSEQ=GAGCGGCCGGTTGACGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:295,167:462,0:0:2,0:25.7:1:30.7:1:1:0:59.9:50.333:1:0:0.5 0/1:213:3:1,2:131,79:210,3:0.0141:2,2:12.7:1:26.7:1:0.55898:3.29724:60:6:0.0144:0:1 +20 61048549 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.45973;LSEQ=CACAGGTAGTGGCCGGTGCC;RSEQ=TCTCGGCGCCACAGCGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:569:450:175,275:46,73:119,450:0.7909:2,2:25.4:1:30.6:1:1:1.01:59.3:63.286:0.7911:0:1.1 1/0:312:198:82,116:52,62:114,198:0.6346:2,2:26.2:1:29.4:1:0.47868:1.18581:58.3:65:0.6331:0:1.2 +20 61048601 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55251;SOR=0;LSEQ=CGCAGTTGACACACTCACGA;RSEQ=CCTCACCCGGGAACTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:0,2:15,177:192,2:0.0103:2,0:19.5:1:28.5:1:1:0:60:4:0.0106:0:2 0/0:98:0:0,0:12,86:98,0:0:2,0:19.6:1:30.1:1:1:0:60:48:1:0:0.6 +20 61048931 . G A 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTCCCGGCTCCGGGACC;RSEQ=GGGGCCAGCACTGGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:10:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 61283771 . G A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09306;LSEQ=TGCTTTCTGTTTCGGCGGCC;RSEQ=GCGGCCGGTGGAGCCCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:6,1:19,4:23,7:0.2333:2,2:21.7:1:29.6:1:1:1.25:60:14:0.2414:0:1.1 0/1:16:4:3,1:10,2:12,4:0.25:2,2:15.3:1:28.5:1:1:1.60994:60:8:0.2667:0:1 +20 61283797 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53329;SOR=0;LSEQ=CGGTGGAGCCCTTGCGCCTC;RSEQ=TCGTCAGTCCCGCCCCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:38,20:58,2:0.0333:2,2:13.5:1:30.5:1:1:1.87852:60:4:0.0339:0:1.5 0/0:34:0:0,0:21,13:34,0:0:2,0:24.2:1:29.6:1:1:0:60:16:1:0:0.4 +20 61283840 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14454;SOR=Inf;LSEQ=CTTGCTCCTCCGGCTTTTCC;RSEQ=CTGACTCCTGGCATTCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:49,48:97,0:0:2,0:29.8:1:30.9:1:1:0:60:31.333:1:0:0.2 0/1:60:2:1,1:31,27:58,2:0.0333:2,2:22:0:30.5:1:1:1.1455:60:4:0.0357:0:1.5 +20 61283891 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15099;SOR=Inf;LSEQ=CACATGCTCCTGGGACGTCA;RSEQ=CCTTGTGACAGCTCGCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:20,39:59,0:0:2,0:19.5:1:29.3:1:1:0:60:18.667:1:0:0.1 0/1:38:2:1,1:12,24:36,2:0.0526:2,2:28.5:1:30.5:1:1:1.96:60:4:0.0526:0:1 +20 61284092 . C G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTGGCATTGTAAATAAAC;RSEQ=CCCGGGTGTGGCCGCGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:22:1:32.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 61285758 . G C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=GCACCGGTCCGCCCACCCCA;RSEQ=CCCCAGCGCAGGCCCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:25.3:1:32.5:1:1:0:60:20:1:0:0.1 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:50:0:31.5:1:1:1.15:60:4:0.1333:0:1 +20 62173029 . A G 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAACGGCCGGTGAGGCC;RSEQ=GCGTCCACCCACGTCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:1,1:2,5:0.7143:2,0:28.6:1:31.4:1:0.28571:0:60:10:0.7143:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 62173796 . A G 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGATCTCGGGGCCTCACCTG;RSEQ=CTTGATGACCTTGATCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:4.3:1:28.3:1:1:0:60:6:1:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:25.5:1:29.5:1:1:0:60:4:0.5:0:1 +20 62174970 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCCTGAGATGGTCAGAGCT;RSEQ=TGTGGAGGAGGGAGTGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:29:0:1:0:60:4:1:0:1.5 +20 62678476 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGACAGGTCACCCGGGTG;RSEQ=GGGGAGCGCTGTGGGTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +20 62680235 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1162;SOR=Inf;LSEQ=CTTGTAGTTGGGGTGGTCGC;RSEQ=CAAGTGCTGCACGCGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:179,141:320,0:0:2,0:26.1:1:30.6:1:1:0:59.8:34.556:1:0:0.2 0/1:166:2:1,1:99,65:164,2:0.012:2,2:16:0:31.5:1:1:1.51907:60:4:0.0122:0:1 +20 62680270 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13267;SOR=Inf;LSEQ=GCAGCCGTTCGGCTTCCTCC;RSEQ=CGAAGGGCCGCTTCTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:154,181:335,0:0:2,0:26.7:1:29.6:1:1:0:59.8:40.875:1:0:0.2 0/1:193:2:1,1:89,102:191,2:0.0104:2,2:18:1:27:1:1:1.15:60:4:0.0105:0:1 +20 62680296 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14248;SOR=Inf;LSEQ=GGCCGCTTCTCCGCCGCGTT;RSEQ=AGCTCCTTCCACGCTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:98,170:268,0:0:2,0:23.6:1:31.9:1:1:0:59.9:52.6:1:0:0.2 0/1:163:2:1,1:60,101:161,2:0.0123:2,2:24.5:1:28:1:1:1.68:60:4:0.0124:0:1 +20 62680311 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16126;SOR=Inf;LSEQ=GCGTTCAGCTCCTTCCACGC;RSEQ=TTGCCTGCGGGCCGTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:56,134:190,0:0:2,0:24.9:1:30.3:1:1:0:60:26.143:1:0:0.2 0/1:128:2:1,1:40,86:126,2:0.0156:2,2:17:1:31.5:1:0.53974:2.14:60:4:0.0161:0:1 +20 62680322 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.56016;SOR=3.25529;LSEQ=CTTCCACGCTTTGCCTGCGG;RSEQ=CCGTGGGCGCCAGTGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:1,0:41,116:157,1:0.0063:2,0:1:0:26:0:0.26582:0:60:2:0.0065:0:1 0/1:98:2:0,2:21,74:95,2:0.0204:2,0:10:1:30.5:1:1:0:60:4:0.0211:0:1 +20 62680331 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14592;SOR=Inf;LSEQ=TTTGCCTGCGGGCCGTGGGC;RSEQ=CCAGTGAGTGGAACGCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:30,97:127,0:0:2,0:25:1:31.5:1:1:0:60:41.333:1:0:0.2 0/1:79:2:1,1:15,62:77,2:0.0253:2,2:6.5:1:26.5:1:0.36611:4.03:60:4:0.026:0:1.5 +20 62680504 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCTCTGCCGCCCTCCCG;RSEQ=CGCTCACCCAGCATCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:73,26:99,2:0.0196:2,2:40:1:29.5:1:0.46515:2.77402:60:4:0.0196:0:1.5 0/0:50:0:0,0:32,18:50,0:0:2,0:20:1:30.8:1:1:0:60:100:1:0:0.4 +20 62680539 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13233;SOR=Inf;LSEQ=CTTGCTGAGCACCGCGTTGT;RSEQ=CAGGTCCGGGTTCTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:127,82:209,0:0:2,0:27.8:1:32.5:1:1:0:60:208:1:0:0.2 0/1:120:2:1,1:67,51:118,2:0.0167:2,2:15:1:27:1:1:1.31069:60:4:0.0171:0:1 +20 62680559 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13023;SOR=Inf;LSEQ=GCAGGTCCGGGTTCTGCTGA;RSEQ=CCAGCCGCTTGCGCTCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:141,122:263,0:0:2,0:26.2:1:32.5:1:1:0:60:130.5:1:0:0.2 0/1:149:2:1,1:77,70:147,2:0.0134:2,2:16.5:1:27:1:1:1.0993:60:4:0.0139:0:1 +20 62680560 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30161;SOR=0;LSEQ=CAGGTCCGGGTTCTGCTGAG;RSEQ=CAGCCGCTTGCGCTCGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:4:1,3:141,123:264,4:0.0149:2,2:23.5:1:30.3:1:0.3448:3.42437:60:8:0.0151:0:1 0/0:150:0:0,0:79,71:150,0:0:2,0:27.4:1:30.5:1:1:0:59.8:49:1:0:0.3 +20 62680610 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12843;SOR=Inf;LSEQ=CCATGAAGGCGTTCATGGGC;RSEQ=GCCGGATGCGCGACTCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:64,140:204,0:0:2,0:25.9:1:29.7:1:1:0:59.8:50:0.995:0:0.1 0/1:115:2:1,1:41,72:113,2:0.0174:2,2:34.5:1:30:1:1:1.75:60:4:0.0177:0:1 +20 62680817 . CGGCG C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGGCCCATGCACAGTCG;RSEQ=GGCGGGCGGGTCGTCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:32:1:1:0:60:4:1:0:0.5 +20 62953632 . C A 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.2079;LSEQ=TACTAAGCTGCCGGCCTCAC;RSEQ=TCTGAGAGTCTGCTGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:11,6:17,3:0.15:2,2:36.7:1:32:0:0.53684:3.42394:45.3:6:0.15:0:2 0/1:17:3:1,2:8,6:14,3:0.1765:2,2:40.3:1:29:1:0.57647:2.51691:45:6:0.1765:0:2 +20 62953650 . T C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47778;LSEQ=ACCTCTGAGAGTCTGCTGGG;RSEQ=GCAGTGAGAGTGTCCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:7,4:1,2:3,11:0.7857:2,2:22.1:1:30.9:1:0.53846:3.19:42.6:22:0.7857:0:1.4 1/1:13:11:5,6:1,0:1,11:0.8462:0,2:28:1:29.3:1:1:0:41.4:22:0.9167:0:1.3 +21 9825838 . T C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGGGGGACCGGCCGCGAC;RSEQ=GCGGCGGCGGTGGTGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:31.5:1:1:0:41:4:1:0:1.5 +21 9825966 . A C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCGGTCGGCCGCGCTCG;RSEQ=GGGGTCCCCGTGGCGTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 9826870 . TCCCGTCCG T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=2.000;MSILEN=8;SSF=0.14737;SOR=Inf;LSEQ=CCCCGCGCCCGCTCGCTCCC;RSEQ=CCCGTCCGCGGCCCGTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:12,0:0:2,0:26.3:1:29.8:1:1:0:22.8:5:1:0:0.7 0/1:8:2:1,1:4,2:6,2:0.25:2,2:36:0:32:0:1:1.8258:21:4:0.25:0:0.5 +21 9826890 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48667;SOR=0;LSEQ=TCCCGTCCGCCCGTCCGCGG;RSEQ=CCGTCCGTCCGTCCGTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:34.5:1:29.5:1:1:1:20:4:0.1667:0:1 0/0:11:0:0,0:5,4:9,0:0:2,0:24.7:1:31.6:1:1:0:23.2:18:0.8182:0:0.4 +21 9829008 . C G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTTAAGTTGTGGGTGACT;RSEQ=ATGGAAAGGAGGAGTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:33:0:1:0:60:4:1:0:2.5 +21 9829054 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTTTCCACTGCTAGGCTGC;RSEQ=CGCGATGCTATTTAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:28.5:1:1:0:60:4:1:0:2.5 +21 10994373 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGGGGTTTCACTATGTTG;RSEQ=CCAGGCTGGGCTCGAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:29.5:1:1:0:48:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 10995994 . A AG 280 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0;SOR=0.04283;LSEQ=CCAAGGGGTTACATAAAAAA;RSEQ=AAAAAATTTTAAGTCAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:345:344:310,34:0,0:0,344:0.9971:0,2:24.8:1:33.3:1:1:0:36.3:85:1:0.1507:0.9 1/1:361:338:285,53:15,3:18,338:0.9363:2,2:24.4:1:31.7:1:1:1.08:36.2:111.667:0.9331:0.1496:1 +21 10996025 . C T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AAGTCAGTACTATACCATCA;RSEQ=CTCTGCAAGGTAACTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:283:283:249,34:0,0:0,283:1:0,2:33.9:1:30.5:1:1:0:36:69.75:1:0:1 1/1:331:313:256,57:13,5:18,313:0.9456:2,2:35.3:1:29.7:1:0.3487:1.72:35.4:51.167:0.9475:0:1.1 +21 10996028 . C A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00475;SOR=Inf;LSEQ=TCAGTACTATACCATCACCT;RSEQ=TGCAAGGTAACTGCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:242,34:276,0:0:2,0:33.9:1:31.7:1:1:0:35.9:68:1:0:1 0/1:329:9:6,3:261,59:320,9:0.0274:2,2:32.7:1:27.1:1:0.37859:2.20531:35.3:18:0.0276:0:1 +21 10996100 . C T 26 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57459;SOR=0.3626;LSEQ=ATCTTTTGGTTTTCCCTTGC;RSEQ=CAGTTCGACTTCTTTGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:29,45:74,2:0.026:2,0:5:1:26:1:0.52175:0:21:4:0.0263:0:1 0/0:105:1:0,1:44,60:104,1:0.0095:2,0:1:0:26:0:1:0:21:2:0.0097:0:1 +21 10996341 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCAAAGCCACTGTTACC;RSEQ=CTTATCAAACAGAATACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:2,12:0,0:0,14:1:0,2:13.1:1:32.7:1:1:0:41.3:28:1:0:2.1 1/1:3:3:0,3:0,0:0,3:1:0,0:15.7:1:32.3:1:1:0:24:6:1:0:3 +21 11021095 . T C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5114;SOR=1.266;LSEQ=TCAATGAGGAAGACAGTAAA;RSEQ=TGTCAAGTTCAAACCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:16:9,7:126,147:273,16:0.0552:2,2:8.4:1:32.6:1:0.45225:1.50:34.3:32:0.0565:0:1 0/1:334:23:11,12:132,179:311,23:0.0689:2,2:13.2:1:30.3:1:0.66556:1.24:32.8:46:0.0689:0:1.1 +21 11021097 . G T 66 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74178;SOR=0.71296;LSEQ=AATGAGGAAGACAGTAAATT;RSEQ=TCAAGTTCAAACCTGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:5:2,3:146,171:317,5:0.0155:2,2:7:1:28.8:1:1:1.27973:26.2:10:0.0157:0:3 0/1:361:4:2,2:150,207:357,4:0.0111:2,2:2.5:1:26.5:1:1:1.38:29:8:0.0112:0:2 +21 11021107 . A T 149 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02658;LSEQ=ACAGTAAATTGTCAAGTTCA;RSEQ=ACCTGATTCAAAGTGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:32:13,19:178,245:423,32:0.0703:2,2:17:1:29.8:1:1:1.06173:36.1:64:0.0716:0:1.1 0/0:499:1:0,1:204,294:498,1:0.002:2,0:1:0:25:0:1:0:20:2:0.002:0:1 +21 11021125 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.54847;LSEQ=CAAACCTGATTCAAAGTGAA;RSEQ=TTGTCACTGCTAGAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:558:40:21,19:213,305:518,40:0.0717:2,2:32.6:1:31.2:1:0.1842:1.58:30.8:80:0.0727:0:1.8 0/1:626:103:49,54:209,314:523,103:0.1645:2,2:30.7:1:30.3:1:0.15614:1.36:29.9:102:0.165:0:1.3 +21 11021134 . G A 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31875;SOR=0.4372;LSEQ=TTCAAAGTGAACTTGTCACT;RSEQ=CTAGAAAACAACACAACCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:6:3,3:235,325:560,6:0.0106:2,2:31:1:30.5:1:0.69968:1.38:38:12:0.0108:0:3.2 0/0:645:3:2,1:266,376:642,3:0.0047:2,2:38:1:29.3:1:0.57329:2.82:30:6:0.0047:0:2.3 +21 11021163 . T TA 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.65834;SOR=1.0495;LSEQ=CAACACAACCGTAGTGTGCA;RSEQ=AGAGTTTTCTTCATCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:885:290:121,169:226,366:592,290:0.3277:2,2:26.2:1:29.8:1:0.34026:1.16:31.2:57:0.3253:0.0192:0.3 0/1:984:333:127,206:259,392:651,333:0.3384:2,2:27.2:1:29.3:1:0.6297:1.0716:32.5:110:0.3381:0.0112:0.2 +21 11021189 . G A 153 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=0.1119;LSEQ=TTTCTTCATCATCCTTATTT;RSEQ=ATGAAATATCTGCAGTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:34:11,23:177,352:529,34:0.0604:2,2:25.5:1:30.1:1:1:1.05131:31.7:33:0.0591:0:1.2 0/0:561:4:4,0:186,371:557,4:0.0071:2,0:1:0:19.5:1:0.01288:0:37:3:0.0054:0:1.3 +21 11021195 . A G 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00715;SOR=Inf;LSEQ=CATCATCCTTATTTGATGAA;RSEQ=TATCTGCAGTAGACACCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:157,329:486,0:0:2,0:31.2:1:31.1:1:1:0:27.6:120.5:1:0:0.2 0/1:477:7:3,4:153,317:470,7:0.0147:2,2:32.1:1:32:1:0.68798:1.55:29:14:0.0148:0:1 +21 11021215 . T TA 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=2.64357;LSEQ=ATATCTGCAGTAGACACCTA;RSEQ=AAAAAGCAAAATACACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:71:25,46:74,154:228,71:0.2375:2,2:26.6:1:30.5:1:0.66739:1.13:22.3:142:0.2423:0:0.1 0/1:312:141:49,92:56,115:171,141:0.4519:2,2:26.7:1:29.8:1:0.7196:1.09:22.2:282:0.4519:0:0.1 +21 11021238 . C A 33 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24866;SOR=Inf;LSEQ=AAAGCAAAATACACAAAATA;RSEQ=GAAGTTATATTTTTCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:74,152:226,0:0:2,0:4.4:1:29.6:1:1:0:21.6:74.333:0.9955:0:0.1 0/1:236:3:3,0:75,158:233,3:0.0127:2,0:5:1:21.3:1:0.03517:0:22.3:2:0.0085:0:1.7 +21 11021767 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTGTAATAGC;RSEQ=TGATCTCAGCTCATTGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:32:1:1:0:28.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 11021780 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATAGCGTGATCTCAGCTC;RSEQ=TTGCAACCTCTGCCTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:47:1:32.5:1:1:0:28.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 11025880 . G C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAGAAAAGGGAGTACAC;RSEQ=GTTAACAAATACAACAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:31.5:1:1:0:25.5:4:1:0:1 +21 11026351 . A G 32 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGATTTTAATAAAATAGC;RSEQ=AAGTTATTACATAAAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14:1:32.5:1:1:0:32.5:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:6:0:32:0:1:0:24:2:1:0:1 +21 11026430 . T TAGTA 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=AATAAAGCTTCATAACATGA;RSEQ=AGCAAATATCTATCAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:10,0:0:2,0:36.7:1:29.2:1:1:0:45.1:9:1:0:0.4 1/0:4:2:1,1:2,0:2,2:0.5:0,2:20:1:27.5:1:1:0:26.5:4:0.5:0:0.5 +21 11026554 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63285;SOR=1.30439;LSEQ=GAAGGTAAGAAAAGAGAAAG;RSEQ=ATGAGAAAGTAAATATACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:11:9,2:23,1:24,11:0.3143:1,2:9.1:1:31.8:1:0.22689:4.84406:50.5:22:0.3143:0:1.3 0/1:40:15:13,2:21,4:25,15:0.375:2,2:14.6:1:28.7:1:1:1.23:37.4:30:0.375:0:1.1 +21 11026594 . CA C 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.52887;LSEQ=AGAAAATGTAACCAGAGGCT;RSEQ=AAAAAAAGTAGGACAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:2,0:90,7:97,2:0.0202:2,0:49.5:1:33:1:1:0:29.5:4:0.0202:0:1 0/1:93:1:1,0:78,14:92,1:0.0108:2,0:39:0:32:0:1:0:26:2:0.0108:0:0 +21 11026644 . C CATAAG 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14317;SOR=2.16193;LSEQ=TTTGACCTATTTATATGACT;RSEQ=ATCAAAATAACTTGCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:7:7,0:67,4:71,7:0.0897:2,0:7.4:1:27.7:1:1:0:45:14:0.0909:0.0641:0.7 0/1:68:12:12,0:46,9:55,12:0.1765:2,0:8.2:1:25.9:1:0.19589:0:40.3:24:0.1846:0.1471:0.9 +21 11027129 . C T 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=2.32631;LSEQ=CACTCCTACATTCTCGGTGA;RSEQ=GACAACAACTGTAGCCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:1,9:10,2:0.1667:2,2:25.5:1:29.5:1:0.31818:6.71:22:4:0.1667:0:2 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:17:0:31:0:1:0:22:2:0.3333:0:2 +21 11027175 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTCGAAGTGCAACAAAT;RSEQ=GTATTCAATATAGAGTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:0,6:6,2:0.25:0,2:29.5:1:30.5:1:0.25:0:22:4:0.25:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:50:0:31:0:1:0:21:2:1:0:0 +21 11027188 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAAATTGTATTCAATATA;RSEQ=AGTAAGGATAAGGAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,5:6,2:0.25:2,0:25.5:1:34.5:1:1:0:21.5:4:0.25:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:38:0:34:0:1:0:21:2:1:0:0 +21 11028504 . GC G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTTCAAACAATTCTCCT;RSEQ=CTCAGCTTCCCTAGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35:0:33.5:1:1:0:26:4:1:0:0.5 +21 11029520 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.24515;SOR=Inf;LSEQ=AGCTCAATCTAGAAAAGAAA;RSEQ=ATTTAATTCTTAACATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:42,5:47,0:0:2,0:14.1:1:33.8:1:1:0:24.6:94:1:0:0.2 0/1:53:3:2,1:45,5:50,3:0.0566:2,2:10.7:1:30.3:1:0.30782:4.30013:34.3:6:0.0577:0:1 +21 11029526 . A G 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00226;SOR=0;LSEQ=ATCTAGAAAAGAAAGATTTA;RSEQ=TTCTTAACATCCAGTAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:8:6,2:49,7:56,8:0.125:2,2:13.6:1:33.1:1:0.31229:2.29528:42.5:16:0.125:0:1 0/0:69:0:0,0:56,12:68,0:0:2,0:16.8:1:29.9:1:1:0:28.7:33:0.9851:0:0.3 +21 11029529 . C G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00384;SOR=Inf;LSEQ=TAGAAAAGAAAGATTTAATT;RSEQ=TTAACATCCAGTAGGGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:58,10:68,0:0:2,0:17.6:1:32.9:1:1:0:28.8:136:1:0:0.2 0/1:80:9:6,3:58,12:70,9:0.1125:2,2:18.6:1:30.6:1:0.36048:2.38411:22:8:0.1026:0:1 +21 11029596 . AC A 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTAAATGTAATTTTATGT;RSEQ=CACTTTGATGCTCCAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:143,73:216,0:0:2,0:32:1:31.9:1:1:0:27.9:107:1:0:0.1 0/1:248:35:18,17:140,73:213,35:0.1411:2,2:33.2:1:31.3:1:0.1289:1.80676:22:70:0.1429:0.0121:0.3 +21 11029616 . G T 108 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00347;SOR=11.3224;LSEQ=ACCACTTTGATGCTCCAAAT;RSEQ=GCACTGCCAGGAAGCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:1:1,0:113,69:182,1:0.0055:2,0:47:0:32:0:1:0:29:2:0.0056:0:2 0/1:204:12:6,6:114,78:192,12:0.0588:2,2:28:1:30.4:1:0.5566:1.45873:35.4:24:0.0591:0:2.3 +21 11029624 . C T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00201;SOR=Inf;LSEQ=GATGCTCCAAATGGCACTGC;RSEQ=AGGAAGCTGCCTGGGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:98,65:163,0:0:2,0:19.6:1:30.7:1:1:0:27.2:26.167:1:0:0.1 0/1:184:10:5,5:101,73:174,10:0.0543:2,2:21.6:1:29.5:1:0.74539:1.38106:38.3:20:0.0543:0:2.4 +21 11029630 . GC G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00822;SOR=Inf;LSEQ=CCAAATGGCACTGCCAGGAA;RSEQ=TGCCTGGGTTTAAAAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:94,86:180,0:0:2,0:13.5:1:31.4:1:1:0:24.8:59:1:0:0.1 0/1:206:8:4,4:104,94:198,8:0.0388:2,2:18.3:1:32.3:1:1:1.10584:40.3:16:0.0388:0:2.4 +21 11029679 . C G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12384;SOR=2.48932;LSEQ=CCTGAAATGTCTGGGGACCA;RSEQ=GAGGGTGGGCTCACTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:4:2,2:116,213:329,4:0.012:2,2:11.3:1:32.5:1:0.61696:1.83:60:8:0.0122:0:1.5 0/1:374:11:6,5:147,216:363,11:0.0294:2,2:10:1:31:1:0.36791:1.76:53.5:22:0.0295:0:1.3 +21 11038164 . A G 34 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTATCTTTACTTACTGAAA;RSEQ=TCAATAGTACAATTCTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:34:1:34.5:1:1:0:30.5:4:0.6667:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:33:0:33:0:1:0:25:2:1:0:1 +21 11038722 . C A 72 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05371;SOR=0;LSEQ=TGTCAATATCATTAAAATCA;RSEQ=CCTACCTGTTTGGACCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:0,6:1:0,2:6.3:1:30:1:1:0:20.5:12:1:0:1.7 1/0:12:6:3,3:3,2:5,6:0.5:2,2:5.2:1:28.2:1:1:1.44544:20.5:12:0.5:0:2.3 +21 11038738 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56863;SOR=Inf;LSEQ=ATCACCCTACCTGTTTGGAC;RSEQ=GAGGTCTACCAGGAGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:15,0:0:2,0:13.1:1:28.7:1:1:0:21:6.5:1:0:1.3 0/1:46:3:1,2:21,22:43,3:0.0652:2,2:8.7:1:27.3:1:1:1.88337:22:6:0.0652:0:1.7 +21 11038741 . G T 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91184;LSEQ=ACCCTACCTGTTTGGACCGA;RSEQ=GTCTACCAGGAGAAAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:9,8:17,1:0.0556:2,0:1:0:26:0:1:0:21:2:0.0556:0:1 0/1:59:3:0,3:28,28:56,3:0.0508:2,0:5.3:1:21.3:1:0.23904:0:21.7:2:0.0345:0:3 +21 11038748 . C T 51 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.36349;LSEQ=CTGTTTGGACCGAGGTCTAC;RSEQ=AGGAGAAAATTTTCTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:14,13:27,1:0.0357:2,0:1:0:23:0:1:0:20:2:0.037:0:1 0/1:83:4:1,3:39,39:78,4:0.0482:2,2:5.3:1:25.8:1:0.61603:2.96338:24.8:8:0.05:0:1.3 +21 11038783 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2922;SOR=Inf;LSEQ=TCTTAGTAATAGCTGGTTTA;RSEQ=CCATGCCAGTTTTTTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:76,71:147,0:0:2,0:15:1:31.7:1:1:0:23.1:48:1:0:0.6 0/1:241:3:2,1:111,127:238,3:0.0124:2,2:39.3:1:31:1:0.60135:2.28:20.7:6:0.0126:0:2 +21 11038796 . T C 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.05749;SOR=0;LSEQ=TGGTTTACCCATGCCAGTTT;RSEQ=TTGGAGTGACTGAGATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:2,1:78,74:152,3:0.0194:2,2:20.3:1:34.3:1:1:1.89:20.7:6:0.0197:0:1.3 0/0:245:0:0,0:116,129:245,0:0:2,0:24.7:1:29.8:1:1:0:22.6:60.25:1:0:1 +21 11038802 . G A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.47436;LSEQ=ACCCATGCCAGTTTTTTGGA;RSEQ=TGACTGAGATGTAAGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:13:7,6:73,69:142,13:0.0839:2,2:34.8:1:30.3:1:1:1.10:20.2:12:0.0789:0:2.1 0/1:245:82:39,43:77,86:163,82:0.3347:2,2:31.7:1:29.8:1:1:1.01:21.1:81:0.3361:0:1.9 +21 11038816 . AGTT A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.18223;SOR=0;LSEQ=TTTGGAGTGACTGAGATGTA;RSEQ=GTTGGCATGATGTTTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:73,69:142,2:0.0138:2,2:47:1:33:1:1:1.05758:27:4:0.0141:0:0 0/0:194:0:0,0:90,103:193,0:0:2,0:32.8:1:31.3:1:1:0:22.6:37.6:1:0:1 +21 11038843 . G C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=2.89796;LSEQ=GGCATGATGTTTCCAGCAGA;RSEQ=GAACTAAGAGCTGAAGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:31:13,18:46,42:88,31:0.2583:2,2:23.7:1:31.1:1:0.40444:1.51116:21.9:62:0.265:0:1.5 1/0:149:75:36,39:32,42:74,75:0.5034:2,2:16.6:1:29.8:1:0.62285:1.21:20.9:36.5:0.4966:0:1.8 +21 11039063 . G T 36 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10879;SOR=Inf;LSEQ=CAGAGTCCATCAATCCAGTA;RSEQ=AAAGTTCAGAATCTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:142,169:311,0:0:2,0:7.1:1:31.6:1:1:0:21.5:102.667:0.9968:0:0.6 0/1:286:3:0,3:138,145:283,3:0.0105:2,0:7.7:1:23:1:0.24829:0:22.3:6:0.0106:0:2 +21 11039072 . G T 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=67.37524;LSEQ=TCAATCCAGTAGAAAGTTCA;RSEQ=AATCTTCTTTCTGTTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:1:0,1:250,264:514,1:0.0019:2,0:1:0:24:0:1:0:23:2:0.002:0:1 0/1:482:56:22,34:218,208:426,56:0.1162:2,2:12.2:1:27.1:1:0.1175:1.61813:21.5:112:0.1181:0:1.1 +21 11039079 . C A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.48696;LSEQ=AGTAGAAAGTTCAGAATCTT;RSEQ=TTTCTGTTCCTTTTCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:119:55,64:179,180:359,119:0.2302:2,2:19.6:1:29.9:1:0.52624:1.15682:21.5:118:0.2309:0:1 0/1:496:63:30,33:209,201:410,63:0.127:2,2:18.8:1:28.9:1:0.6853:1.14345:21.6:126:0.1278:0:1.1 +21 11039091 . T A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.03497;SOR=0.56093;LSEQ=AGAATCTTCTTTCTGTTCCT;RSEQ=TTCTCCTTGTAGCCTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:39:18,21:238,244:482,39:0.0749:2,2:32.3:1:30.1:1:0.74117:1.1377:22:78:0.0757:0:1.3 0/1:507:22:18,4:240,245:485,22:0.0434:2,2:27.7:1:28.5:1:0.0037:4.58:25.6:21:0.042:0:1.3 +21 11039142 . T A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.83932;LSEQ=TTCCTCAGGACATAATGAAG;RSEQ=GCTTTCCTCATGTGGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1538:90:44,46:687,761:1448,90:0.0585:2,2:22:1:30.1:1:0.82818:1.06:29.2:17:0.0559:0:2 0/1:1608:165:88,77:704,738:1442,165:0.1026:2,2:22.7:1:28.6:1:0.28592:1.20:30:40.25:0.1012:0:2.1 +21 11039152 . A C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.90603;LSEQ=CATAATGAAGTGCTTTCCTC;RSEQ=TGTGGGGACACTAAGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1693:103:51,52:766,823:1589,103:0.0608:2,2:24.5:1:31.9:1:0.83903:1.05:30.2:50.5:0.0608:0:1.9 0/1:1774:195:96,99:759,816:1575,195:0.1099:2,2:24.3:1:30.1:1:0.81987:1.04:31.4:47.75:0.1101:0:2 +21 11039298 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0408;SOR=0.65803;LSEQ=AGTGATCTGGTGTGTAACGA;RSEQ=TTCAATGTTTTCTGTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:72:28,44:199,244:443,72:0.1398:2,2:11.5:1:30.6:1:0.37181:1.281:34.5:71:0.1387:0:1.1 0/1:497:48:18,30:215,234:449,48:0.0966:2,2:12.6:1:29.7:1:0.22321:1.53004:47:96:0.0978:0:1.1 +21 11039302 . A G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00053;SOR=0.37552;LSEQ=ATCTGGTGTGTAACGACTTC;RSEQ=ATGTTTTCTGTCACTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:44:15,29:188,247:435,44:0.0919:2,2:8.7:1:31.3:1:0.26598:1.47037:35.6:88:0.0926:0:1.4 0/1:465:17:8,9:203,245:448,17:0.0366:2,2:9.4:1:29.6:1:1:1.07:42.1:34:0.0366:0:1.2 +21 11039344 . G A 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.47992;LSEQ=TTATCTTCAATTTGATCTTC;RSEQ=CCACAAATATGCTTCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:646:370:146,224:91,182:273,370:0.5728:2,2:25.3:1:29.8:1:0.11677:1.30:35.4:60.667:0.5778:0:1.3 0/1:718:281:101,180:183,252:435,281:0.3914:2,2:23.6:1:28.5:1:0.11763:1.29373:36.2:280:0.3933:0:1.2 +21 11039393 . G A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00028;SOR=Inf;LSEQ=TTTTCATTTCTTCACTATCA;RSEQ=CCTCATTAGAAATCTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1100:0:0,0:367,733:1100,0:0:2,0:26:1:32.5:1:1:0:39:72.333:1:0:0.9 0/1:1217:13:6,7:439,765:1204,13:0.0107:2,2:36.6:1:28.5:1:0.56481:1.49:24.8:26:0.0108:0:1.6 +21 11039394 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.9608;LSEQ=TTTCATTTCTTCACTATCAG;RSEQ=CTCATTAGAAATCTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1107:192:56,136:313,602:915,192:0.1734:2,2:27.6:1:30.2:1:0.20648:1.26244:35:95:0.1748:0:1.5 0/1:1221:356:139,217:308,557:865,356:0.2916:2,2:29.1:1:28.5:1:0.26688:1.16:37:88:0.2919:0:1.3 +21 11039406 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.44973;LSEQ=ACTATCAGCCTCATTAGAAA;RSEQ=CTGTTTTTCCAATTCGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1019:103:28,75:298,618:916,103:0.1011:2,2:23.7:1:31.3:1:0.31611:1.29126:34.7:102:0.1018:0:2 0/1:1143:55:14,41:393,695:1088,55:0.0481:2,2:25.6:1:31.1:1:0.11429:1.65534:34.8:110:0.0485:0:2 +21 11039441 . G C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22433;SOR=0.81368;LSEQ=CGGTATTCACTGTATGTTGG;RSEQ=ATGATATTACAAAATTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:602:94:22,72:132,376:508,94:0.1561:2,2:26:1:33:1:0.69964:1.14869:36.9:188:0.158:0:1.9 0/1:642:84:22,62:170,388:558,84:0.1308:2,2:24.4:1:31.6:1:0.44678:1.23433:38.2:83:0.1307:0:2 +21 11039450 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00776;SOR=0.70391;LSEQ=CTGTATGTTGGGATGATATT;RSEQ=CAAAATTCAGAACATTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:209:47,162:65,215:280,209:0.4274:2,2:27.1:1:32.3:1:0.91348:1.04198:37.7:33.833:0.4212:0:1.3 0/1:514:177:52,125:91,246:337,177:0.3444:2,2:27.5:1:31.6:1:0.60487:1.12:35.8:58:0.3412:0:1.2 +21 11039487 . A C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69374;SOR=0.79808;LSEQ=TGTTATGGTAATGTACAAAC;RSEQ=AATTTTAAATTTTCTAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:15:1,14:23,127:150,15:0.0909:2,1:11.4:1:33.3:1:0.69948:2.52476:44:30:0.092:0:1.1 0/1:176:13:3,10:41,122:163,13:0.0739:2,2:16:1:31.8:1:1:1.11951:39.5:26:0.0743:0:1.1 +21 11039627 . T C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67288;SOR=0.67791;LSEQ=TTATGGATTAGAATCAGCCA;RSEQ=ACACCAGAAAACCTAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:2,10:0,6:6,12:0.6667:0,2:35.2:1:31.5:1:0.52941:0:32.1:24:0.6667:0:1.4 1/0:7:4:0,4:1,2:3,4:0.5714:2,0:26.8:1:30.5:1:0.42857:0:34.3:8:0.5714:0:2 +21 11039703 . T C 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90475;LSEQ=TGAAAATTACACAGGAAAAG;RSEQ=TCTCATACTCATTTTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:9,5:0.3571:0,0:26.2:1:32.4:1:1:0:32.4:10:0.3571:0:1.4 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:28:1:33.5:1:1:2.45:40:4:0.3333:0:1.5 +21 11040446 . TA T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49351;SOR=0;LSEQ=TGAAAGACTACAGGTAAGGA;RSEQ=AAAGAAAACTACCAAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:10,1:11,2:0.1538:2,0:28.5:1:33:0:1:0:36.5:4:0.1538:0:0.5 0/0:9:0:0,0:8,1:9,0:0:2,0:18.7:1:28.8:1:1:0:29.3:18:1:0:1.6 +21 11040477 . A G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7505;SOR=1.36383;LSEQ=TACCAAATAACAGATCTGAT;RSEQ=GTACAAAATATTTTTAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:4,2:19,1:20,6:0.2308:1,2:28:1:32.5:1:0.12308:8.40058:26.7:12:0.2308:0:3.5 0/1:24:7:6,1:15,2:17,7:0.2917:2,2:26.3:1:32.6:1:1:1.23798:29.6:14:0.2917:0:3.3 +21 11040478 . G A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59549;SOR=2.32493;LSEQ=ACCAAATAACAGATCTGATA;RSEQ=TACAAAATATTTTTAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:22,4:26,1:0.037:2,0:18:0:32:0:1:0:40:2:0.037:0:2 0/1:24:2:2,0:19,3:22,2:0.0833:2,0:23:1:31:0:1:0:43.5:4:0.0833:0:2 +21 11040501 . CATCCCCCCTCC TATGCCCCTCCAAAA 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.94196;LSEQ=CAAAATATTTTTAATCATGA;RSEQ=AAAAAAAAAGCCTTTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:2,0:27,3:30,2:0.0588:2,0:29:1:30:1:1:0:29.5:4:0.0606:0:4.5 0/1:36:2:2,0:23,3:26,2:0.0556:2,0:1:1:30.4:1:1:0:20:4:0.057:0.0571:4 +21 11040502 . A C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.80862;SOR=0.80856;LSEQ=AAAATATTTTTAATCATGAC;RSEQ=TCCCCCCTCCAAAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:22:20,2:9,2:11,22:0.6111:2,2:28.5:1:32.6:1:0.58602:2.16:32.5:44:0.6667:0:1.5 1/0:34:19:17,2:7,1:8,19:0.5588:2,2:29.9:1:31.4:1:1:1.21:29.2:38:0.7037:0:1.7 +21 11040512 . C CAA 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=11.000;MSILEN=1;SSF=0.43605;SOR=1.62979;LSEQ=TAATCATGACATCCCCCCTC;RSEQ=AAAAAAAAAGCCTTTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:10:8,2:13,1:14,10:0.2778:1,2:30.2:1:31.8:1:0.5504:3.08979:28.9:20:0.2857:0:2.3 0/1:31:12:10,2:7,2:9,12:0.3871:2,2:30.9:1:30.7:1:1:1.40:28.5:24:0.4286:0:1.5 +21 11040523 . C G 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07491;SOR=3.18098;LSEQ=TCCCCCCTCCAAAAAAAAAG;RSEQ=CTTTCAAGAGAAACTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:3,1:39,2:41,4:0.0851:1,2:18.8:1:22.8:1:0.24877:6.01934:30.3:1:0.0444:0:5.5 0/1:39:9:8,1:27,3:30,9:0.2308:2,2:22.8:1:28.2:1:1:1.12151:27.3:8:0.2286:0:3.7 +21 11040535 . A C 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42373;SOR=1.65902;LSEQ=AAAAAAAGCCTTTCAAGAGA;RSEQ=ACTAACCTACTTTAGATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:6:5,1:43,4:47,6:0.1132:2,2:26.2:1:32.7:1:0.46547:2.11116:31.2:12:0.1154:0:2.3 0/1:57:10:9,1:44,3:47,10:0.1754:2,2:18.3:1:28.9:1:0.54845:1.61377:25.3:9:0.1607:0:2.7 +21 11040542 . C A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04962;SOR=2.93725;LSEQ=GCCTTTCAAGAGAAACTAAC;RSEQ=TACTTTAGATCCATTGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:3,2:52,3:55,5:0.0833:2,2:12.8:1:28.4:1:0.05081:10.60035:27.8:4:0.0727:0:4.4 0/1:66:14:12,2:48,4:52,14:0.2121:2,2:19.6:1:28.4:1:0.59954:1.97578:25.1:13:0.2167:0:3.1 +21 11040581 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02919;SOR=3.22785;LSEQ=AATTCTTTTCCAGAATCTCT;RSEQ=AACTAAAAGATTTAGTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:5:5,0:86,1:87,5:0.0543:1,0:29.4:1:31:1:1:0:21:10:0.0556:0:3.4 0/1:89:14:14,0:72,3:75,14:0.1573:1,1:35.9:1:30.5:1:1:0:22.9:28:0.1609:0:3.1 +21 11040593 . T G 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00763;SOR=3.41977;LSEQ=GAATCTCTTAACTAAAAGAT;RSEQ=TAGTTACTGTAATGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:7:6,1:101,1:102,7:0.0642:1,2:29:1:34:1:0.12487:15.65714:32.4:14:0.0648:0:1.9 0/1:110:21:19,2:88,1:89,21:0.1909:1,2:26.2:1:32:1:0.09276:8.98909:34:42:0.1909:0:2.3 +21 11040610 . T G 110 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.02159;SOR=3.84842;LSEQ=GATTTAGTTACTGTAATGTA;RSEQ=ATACATACAGCAATTGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:4:4,0:125,13:138,4:0.0282:2,0:27.5:1:31.5:1:1:0:21:8:0.0284:0:3.5 0/1:129:13:13,0:106,10:116,13:0.1008:2,1:26.6:1:29.9:1:0.59698:0:22.7:26:0.1008:0:3.2 +21 11040635 . T C 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32545;SOR=2.16092;LSEQ=ATACAGCAATTGCAAAAATG;RSEQ=CTTTGGGATAAAGACATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:3,0:176,60:236,3:0.0125:2,0:14:1:31:1:0.57458:0:21.3:6:0.0126:0:3.7 0/1:225:6:6,0:163,56:219,6:0.0267:2,0:17.8:1:28.7:1:0.34055:0:22.7:12:0.0269:0:3.7 +21 11040641 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.45403;SOR=0.87452;LSEQ=CAATTGCAAAAATGTCTTTG;RSEQ=GATAAAGACATTATCTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:308:183:126,57:93,32:125,183:0.5942:2,2:23.9:1:30.4:1:0.30843:1.31357:32.2:90.5:0.5934:0:2.2 1/0:285:160:112,48:84,41:125,160:0.5614:2,2:21.1:1:28.5:1:0.69934:1.14:30.9:52.333:0.5627:0:2.4 +21 11040652 . T C 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31984;SOR=1.46114;LSEQ=ATGTCTTTGGGATAAAGACA;RSEQ=TATCTTATAACTCAGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:16:12,4:297,141:438,16:0.0352:2,2:9:1:32.8:1:0.7855:1.42:30.9:32:0.0356:0:3.2 0/1:434:22:15,7:266,146:412,22:0.0507:2,2:8:1:29.6:1:0.82185:1.18:33.2:44:0.051:0:3.1 +21 11040653 . T A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00077;SOR=Inf;LSEQ=TGTCTTTGGGATAAAGACAT;RSEQ=ATCTTATAACTCAGTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:0:0,0:318,149:467,0:0:2,0:20.1:1:29.9:1:1:0:41.7:92.4:1:0:1.6 0/1:450:10:7,3:281,159:440,10:0.0222:2,2:9.8:1:27.8:1:1:1.32:40.3:20:0.0223:0:2.7 +21 11040667 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00079;SOR=1.51163;LSEQ=AGACATTATCTTATAACTCA;RSEQ=TCAAATCAGACAATATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:162:98,64:277,174:451,162:0.2638:2,2:15.3:1:30.5:1:0.85127:1.03961:38.3:80:0.2627:0:2.5 0/1:643:226:119,107:256,158:414,226:0.3515:2,2:13.7:1:29.1:1:0.02895:1.45596:38:44.2:0.3497:0:2.6 +21 11040674 . C T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01894;SOR=1.36487;LSEQ=ATCTTATAACTCAGTCAAAT;RSEQ=AGACAATATGAACATACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:676:511:293,218:101,63:164,511:0.7559:2,2:23.1:1:29.8:1:0.3632:1.19249:41.5:126.75:0.759:0:2.1 1/1:711:575:322,253:81,55:136,575:0.8087:2,2:22.6:1:28.6:1:0.50083:1.15691:41:114:0.8097:0:2.3 +21 11040693 . G A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00404;SOR=Inf;LSEQ=TCAGACAATATGAACATACT;RSEQ=CTTACCAGCAATGAGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:784:0:0,0:382,402:784,0:0:2,0:29.8:1:32.2:1:1:0:47.1:77.4:1:0:1.4 0/1:849:9:5,4:404,436:840,9:0.0106:2,2:30.3:1:27:1:0.745:1.35:38.8:8:0.0095:0:2.8 +21 11040713 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=1.67606;LSEQ=GCTTACCAGCAATGAGAAGA;RSEQ=TATCTGTGTCCTCTATACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:801:134:59,75:287,378:665,134:0.1673:2,2:29.2:1:30.3:1:0.84914:1.04:44:43.667:0.1656:0:2.2 0/1:893:225:109,116:277,389:666,225:0.252:2,2:28.6:1:29.7:1:0.07417:1.32:43.9:450:0.2537:0:2.2 +21 11040737 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31026;SOR=0.73327;LSEQ=CTGTGTCCTCTATACCCTCA;RSEQ=TGTAGGGAAAGGCTTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:664:27:10,17:256,381:637,27:0.0407:2,2:24.9:1:30.2:1:0.84242:1.14199:48.9:26:0.0396:0:2 0/1:730:22:10,12:280,428:708,22:0.0301:2,2:20:1:28.6:1:0.65965:1.27:44.9:21:0.0292:0:2.1 +21 11040748 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00069;SOR=1.61441;LSEQ=ATACCCTCAGTGTAGGGAAA;RSEQ=GCTTTCTGAATATGACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:114:39,75:121,264:385,114:0.2285:2,2:23.1:1:31.7:1:0.57016:1.13:44.2:113:0.2292:0:2 0/1:544:176:54,122:137,231:368,176:0.3235:2,2:23.4:1:30.2:1:0.15008:1.33919:44.9:352:0.3265:0:2.1 +21 11040773 . CC AT 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29843;SOR=0.75386;LSEQ=TCTGAATATGACTCAAAAAT;RSEQ=AGAAGCAAAAGAAGATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:38:1,37:27,182:209,38:0.1538:2,1:17.9:1:30.1:1:0.09157:5.46611:39.8:76:0.1577:0.0283:0.9 0/1:249:30:4,26:33,186:219,30:0.1205:2,2:18.7:1:29.6:1:1:1.15259:42.2:60:0.121:0.008:1.1 +21 11040785 . G A 132 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58566;SOR=1.30362;LSEQ=TCAAAAATCCAGAAGCAAAA;RSEQ=AAGATTAATAAATCTAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:15:0,15:5,132:137,15:0.0987:1,1:18.4:1:32.7:1:1:0:29.1:30:0.0987:0:1 0/1:152:19:1,18:7,126:133,19:0.125:2,1:18:1:31.3:1:1:1:30.7:38:0.125:0:1.1 +21 11040829 . C CA 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.29312;SOR=5.03794;LSEQ=AAAAAGAAACTTTTGCATGG;RSEQ=AAAAAAATAATAATAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:0,1:2,46:48,1:0.0204:1,0:36:0:29:0:1:0:27:2:0.0204:0:1 0/1:31:3:0,3:1,27:28,3:0.0968:1,0:36:1:28.7:1:1:0:25:6:0.0968:0:1 +21 11040835 . AAT A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.35131;SOR=0.48032;LSEQ=AAACTTTTGCATGGCAAAAA;RSEQ=AATAATAAAAACAAAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:9:0,9:2,38:40,9:0.1837:2,0:26.1:1:33:0:1:0:22.3:18:0.1837:0:1.7 0/1:31:3:0,3:1,27:28,3:0.0968:1,0:27.3:1:30.3:1:1:0:22.7:6:0.0968:0:1.7 +21 11040836 . AT A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=9.000;MSILEN=1;SSF=0.5988;SOR=1.40696;LSEQ=AACTTTTGCATGGCAAAAAA;RSEQ=AATAATAAAAACAAAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:11:2,9:0,28:28,11:0.2245:1,2:38.4:1:31.3:1:0.07422:0:28.7:22:0.2895:0:0.7 0/1:31:9:1,8:0,15:15,9:0.2903:1,2:40.6:1:31.4:1:0.375:0:26.9:18:0.3214:0:0.8 +21 11040889 . G A 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.19191;LSEQ=TACAGCCTGGATAACATGGT;RSEQ=AGACCCTGTCTCTACAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:1,7:8,5:0.3846:2,0:6.8:1:32:1:1:0:31.8:10:0.3846:0:1.2 0/1:14:6:1,5:0,8:8,6:0.4286:0,2:10.2:1:29.5:1:0.42857:0:29:12:0.4286:0:1.3 +21 11046605 . A G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTACAGAATCTCTCTGC;RSEQ=TCTGCTCCCACCTCCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0,3:0.75:0,2:27:1:31.3:1:1:0:28.3:6:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 11046622 . G C 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATCTGCTCCCACCTCCT;RSEQ=CCCACACCAGGGACCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:1,4:0.8:0,2:35:1:32.8:1:1:0:28:8:0.8:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 11046628 . A G 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCCCACCTCCTGCCCAC;RSEQ=CCAGGGACCTGGGGTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:1,4:0.8:0,2:32:1:31.5:1:1:0:28:8:0.8:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 11047145 . G T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=4.17095;LSEQ=CATTTCAAAATAATTACACT;RSEQ=AGTTAAAGAAGCCAGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:16.5:1:30:1:1:0:41.5:4:0.2857:0:1.5 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:41:1:30.5:1:1:0:41.5:4:0.6667:0:2 +21 11047169 . C T 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=4.9538;LSEQ=TAAAGAAGCCAGACCAAAAA;RSEQ=GAGTATATACTATATGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:6,0:6,1:0.1429:0,0:46:0:30:0:1:0:23:2:0.1429:0:2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:35.5:1:27:1:1:0:41.5:4:0.5:0:2 +21 11047253 . A T 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.1722;LSEQ=AAAGCAGACTAGGAAGACAG;RSEQ=GGGTTTGGGTTTGAACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:2,0:46,1:47,2:0.0408:1,0:21.5:1:32:0:1:0:32:4:0.0417:0:1 0/1:21:1:1,0:16,4:20,1:0.0476:2,0:40:0:25:0:1:0:26:2:0.0476:0:1 +21 11047289 . A T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04784;SOR=Inf;LSEQ=CAGCCACAAAGCAAGCCAAG;RSEQ=GGCACCAGGAAACTTTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:92,8:100,0:0:2,0:25.7:1:30.5:1:1:0:35.4:49:1:0:0.6 0/1:58:3:2,1:44,11:55,3:0.0517:2,2:33.3:1:30.3:1:0.50804:1.97205:24.3:6:0.0517:0:2 +21 11047308 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31171;SOR=1.37327;LSEQ=GAGGCACCAGGAAACTTTGA;RSEQ=GGTGATGACTATGTTCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:41:37,4:79,8:87,41:0.3203:2,2:24.1:1:31.9:1:1:1.06702:27.3:82:0.328:0:1.3 0/1:89:35:27,8:45,9:54,35:0.3933:2,2:23.6:1:30.1:1:0.58268:1.47474:28.1:70:0.3977:0:1.2 +21 11047322 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16742;SOR=Inf;LSEQ=CTTTGACGGTGATGACTATG;RSEQ=TCATTATCTTGAAGAGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:158,16:174,0:0:2,0:22.1:1:30.3:1:1:0:39.9:57:1:0:0.5 0/1:121:2:1,1:101,18:119,2:0.0165:2,2:14.5:1:27:1:0.2905:5.4885:34.5:4:0.0167:0:1 +21 11047334 . A G 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05965;SOR=0.34826;LSEQ=TGACTATGTTCATTATCTTG;RSEQ=AGAGTGTACAGTTTACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:15:14,1:180,16:196,15:0.0704:2,1:17.9:1:31.1:1:1:1.24:39.7:30:0.0718:0:1.2 0/1:156:4:2,2:128,23:151,4:0.0256:2,2:33.8:1:29:1:0.12223:5.47167:30.3:8:0.0263:0:1 +21 11047339 . T C 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0332;SOR=Inf;LSEQ=ATGTTCATTATCTTGAAGAG;RSEQ=GTACAGTTTACTGTATGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:222,19:241,0:0:2,0:21.7:1:30.3:1:1:0:46.4:47.2:1:0:0.5 0/1:181:4:4,0:147,30:177,4:0.0221:2,0:31.8:1:31.3:1:1:0:32:8:0.0226:0:1 +21 11047371 . A G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.39638;LSEQ=TGTATGTCAGTTATATGTCA;RSEQ=TAAAGCTGTTTTTAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:81:77,4:349,24:373,81:0.1784:2,1:24.1:1:34:1:0.80028:1.32:46.7:162:0.1792:0:1.7 0/1:341:27:24,3:279,35:314,27:0.0792:2,2:25.5:1:31.6:1:1:1.00:50.3:26:0.0767:0:1.8 +21 11047421 . T C 122 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=19.25499;LSEQ=TGTATAGATTTGAATAGATA;RSEQ=CCGATTTGTCTGTTCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1127:1:0,1:1007,119:1126,1:9e-04:2,0:17:0:12:0:0.10648:0:60:0:0:0:4 0/1:951:16:12,4:795,140:935,16:0.0168:2,2:23.4:1:30.6:1:0.28438:1.89122:52.2:32:0.017:0:2.4 +21 11047441 . T C 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00275;SOR=0.7954;LSEQ=TCCGATTTGTCTGTTCTCCA;RSEQ=ATAAAACATACAGAGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1506:655:529,126:704,147:851,655:0.4349:2,2:25:1:32.3:1:0.34512:1.14059:53.5:162.75:0.4355:0:1.7 0/1:1380:524:419,105:662,194:856,524:0.3797:2,2:24.1:1:31.3:1:0.2814:1.17:52.8:173.667:0.3803:0:1.8 +21 11047496 . G A 324 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=0.70365;LSEQ=CTTACTTTGCATTTCCAGCC;RSEQ=TTGGTTGGTACAGATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2109:1855:1196,659:149,102:251,1855:0.8796:2,2:32:1:30.5:1:0.1235:1.24:42:62.966:0.8792:0:1.3 1/1:2394:2004:1223,781:219,162:381,2004:0.8371:2,2:32:1:29.6:1:0.20859:1.16:41.8:76.077:0.8381:0:1.4 +21 11047515 . A G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.70749;LSEQ=CGTTGGTTGGTACAGATTTC;RSEQ=TAATTCGTTGAAGACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2347:71:34,37:1250,1023:2273,71:0.0303:2,2:23.6:1:31.1:1:0.27585:1.32954:36.2:70:0.0301:0:1.9 0/1:2619:204:119,85:1293,1120:2413,204:0.0779:2,2:25.4:1:30:1:0.21365:1.21:35.7:408:0.0789:0:1.8 +21 11047582 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03553;SOR=0.75641;LSEQ=ACACACTAGCATCTTGCTAT;RSEQ=TTCTCCCGATTGTCTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1097:148:37,111:258,689:947,148:0.1349:2,2:20.2:1:30.2:1:0.61898:1.12326:24.9:147:0.1349:0:1.1 0/1:1090:115:36,79:319,655:974,115:0.1055:2,2:19.5:1:29:1:0.83352:1.06869:25.5:56.5:0.1044:0:1.1 +21 11047599 . A T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.20146;LSEQ=TATCTTCTCCCGATTGTCTA;RSEQ=AAAGTAAGATAGCATTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1094:76:15,61:195,823:1018,76:0.0695:2,2:21.2:1:28.3:1:0.88045:1.04:26.9:152:0.07:0:1 0/1:1013:15:3,12:247,751:998,15:0.0148:2,2:18.7:1:26.3:1:1:1.31523:25.8:30:0.015:0:1.1 +21 11047650 . C T 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00218;SOR=0;LSEQ=TTTAAACTTATGTTTTGCAA;RSEQ=ATAAGTAATCATGAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:921:10:1,9:81,830:911,10:0.0109:2,2:28.8:1:28.6:1:0.60832:1.14:39.1:20:0.0109:0:1 0/0:823:0:0,0:100,722:822,0:0:2,0:23.8:1:31.6:1:1:0:35.9:116.429:0.9988:0:0.2 +21 11047685 . C T 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03822;SOR=0.37907;LSEQ=AAATCATCAGTCCTGGGAAC;RSEQ=GCACAGTTCATAAATACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:18:0,18:13,380:393,18:0.0438:1,1:6:1:31.3:1:1:0:28.7:36:0.0441:0:1 0/1:352:6:0,6:14,332:346,6:0.017:1,0:8.2:1:30:1:1:0:21.7:12:0.0173:0:1 +21 11047909 . A G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTTTGAGAGGAAGGCGCT;RSEQ=TAACTGCTATGTGCTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:2,11:0,1:1,13:0.9286:0,2:31.7:1:32:1:1:0:45.9:26:0.9286:0:1.3 1/1:4:4:1,3:0,0:0,4:1:0,2:24:1:31.8:1:1:0:41:8:1:0:1.5 +21 11047958 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAAATCTTGGCACAGCAA;RSEQ=TTGAAAAGACTGTCATATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:5,2:0.2857:2,0:46.5:1:32.5:1:1:0:52.5:4:0.2857:0:3 0/0:2:0:0,0:1,1:2,0:0:2,0:15:1:31.5:1:1:0:38:4:1:0:2 +21 11047979 . CA TG 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=TTGAAAAGACTGTCATATAA;RSEQ=TAAAGAGGATCAAATTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:24.8:1:32.1:1:1:0:49.2:10:0.7143:0.1429:1.8 0/0:1:0:0,0:1,0:1,0:0:0,0:42:0:34:0:1:0:22:2:1:0:3 +21 11047980 . A G 34 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGAAAAGACTGTCATATAAC;RSEQ=TAAAGAGGATCAAATTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,0:0,2:0.3333:0,0:14.5:1:34:0:1:0:57:4:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:43:0:32:0:1:0:22:2:1:0:3 +21 11048020 . T C 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCAGATCTCTATTTGTAT;RSEQ=CAGGCTGCTGTTTTCTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17.5:1:33.5:1:1:0:20.5:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:18:0:33:0:1:0:22:2:1:0:3 +21 11049143 . C T 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.375;SOR=Inf;LSEQ=CCGGTGCCCCTGAAGACAAG;RSEQ=TACTTTATTCTTCTCATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:27:1:30.5:1:1:0:47:4:0.3333:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:19:0:30:0:1:0:60:2:1:0:2 +21 11049227 . AA GT 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.9145;LSEQ=AATTTAAATTAGCTCTTTAG;RSEQ=GATCAGAGCAATTTAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:11,0:11,3:0.2:0,0:19:1:32.5:0:1:0:33.7:6:0.2143:0:2 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:17:0:31.5:0:1:0:32:2:0.3333:0:2 +21 11049228 . A C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57647;SOR=2.51691;LSEQ=ATTTAAATTAGCTCTTTAGA;RSEQ=GATCAGAGCAATTTAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:4,0:4,6:0.4286:0,0:21.8:1:33:1:1:0:29.2:12:0.6667:0:2.2 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:6.5:1:30.5:1:1:0:39.5:4:1:0:3.5 +21 11049231 . T C 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22794;SOR=Inf;LSEQ=TAAATTAGCTCTTTAGAAGA;RSEQ=CAGAGCAATTTAAATGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:7,0:7,0:7,7:0.5:0,0:20.1:1:33.3:1:1:0:28.3:14:0.5833:0:2.3 1/1:3:3:3,0:0,0:0,3:1:0,0:13:1:33:1:1:0:37:6:1:0:3 +21 11049236 . G A 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.58265;LSEQ=TAGCTCTTTAGAAGATCAGA;RSEQ=CAATTTAAATGATTAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:13,0:13,2:0.1333:1,0:13.5:1:31.5:1:1:0:42:4:0.1333:0:2 0/1:5:1:1,0:4,0:4,1:0.2:0,0:11:0:31:0:1:0:51:2:0.2:0:3 +21 11049251 . A G 41 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.55509;LSEQ=TCAGAGCAATTTAAATGATT;RSEQ=AAATCAGTTTTGTTTAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:3,0:23,0:23,3:0.1154:1,0:36.7:1:26.3:1:1:0:35.7:2:0.0833:0:2 0/1:15:1:1,0:13,1:14,1:0.0667:1,0:15:0:33:0:1:0:60:2:0.0667:0:2 +21 11049300 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20363;SOR=Inf;LSEQ=AATAATATAAACGTTAATAT;RSEQ=CAGTAATTTTTTTAAGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:75,1:76,0:0:1,0:24.2:1:31.6:1:1:0:50.3:18:1:0:0.7 0/1:63:2:2,0:53,8:61,2:0.0317:2,0:23:1:32:0:1:0:50:4:0.0317:0:2 +21 11049306 . A AT 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.09892;SOR=Inf;LSEQ=ATAAACGTTAATATCCAGTA;RSEQ=TTTTTTTAAGTATGATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:85,1:86,0:0:1,0:24.2:1:30.3:1:1:0:49.4:42:1:0:0.8 0/1:75:3:2,1:64,8:72,3:0.04:2,2:9.7:1:29.7:1:0.32233:3.88636:46.3:6:0.04:0.0267:0.3 +21 11049343 . C T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04602;SOR=3.76004;LSEQ=GAAGTCACTCTGAATGAATA;RSEQ=AGCCAAAATATGAACAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:3,0:185,4:189,3:0.0156:1,0:13.3:1:30.3:1:1:0:37:6:0.0159:0:2.3 0/1:177:10:10,0:149,18:167,10:0.0565:2,0:26.9:1:30.6:1:0.6015:0:38.8:20:0.0565:0:1.8 +21 11049346 . C T 98 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02159;SOR=0.11923;LSEQ=GTCACTCTGAATGAATACAG;RSEQ=CAAAATATGAACAACCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:9:9,0:182,5:187,9:0.0459:1,0:33.8:1:31.1:1:1:0:45:18:0.0466:0:1.9 0/0:176:1:1,0:156,19:175,1:0.0057:2,0:45:0:31:0:1:0:44:2:0.0057:0:2 +21 11049360 . A T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.61039;SOR=1.43071;LSEQ=ATACAGCCAAAATATGAACA;RSEQ=CCTCTATTATATTACACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:7:7,0:171,5:176,7:0.0383:1,0:42.9:1:31.7:1:1:0:32.1:14:0.0387:0:3.9 0/1:167:9:9,0:140,18:158,9:0.0539:2,0:41.1:1:31.7:1:0.59933:0:32.9:18:0.0542:0:3.6 +21 11049364 . C T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15251;SOR=0.68257;LSEQ=AGCCAAAATATGAACAACCT;RSEQ=TATTATATTACACAAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:44:43,1:134,4:138,44:0.2418:1,1:34:1:31.4:1:1:1.28:41.3:88:0.2472:0:1.8 0/1:168:30:26,4:123,15:138,30:0.1786:2,2:31.1:1:31:1:0.75066:1.25969:41.9:60:0.1786:0:1.8 +21 11049384 . T C 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25876;SOR=0.45448;LSEQ=CTATTATATTACACAAACTT;RSEQ=TAGCGCCTAGTAATAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:9:9,0:147,5:152,9:0.0559:1,0:28.9:1:30.4:1:1:0:43.6:18:0.0573:0:1.9 0/1:153:4:4,0:133,16:149,4:0.0261:2,0:25.8:1:26.8:1:1:0:39.3:3:0.0199:0:1.5 +21 11049389 . G A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.79224;SOR=1.27627;LSEQ=ATATTACACAAACTTTTAGC;RSEQ=CCTAGTAATAGGGTCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:7:7,0:147,5:152,7:0.044:1,0:15.4:1:28.4:1:1:0:32.1:14:0.0449:0:3.9 0/1:144:8:8,0:122,14:136,8:0.0556:2,0:25.5:1:28.4:1:1:0:31.3:16:0.0556:0:3.9 +21 11049395 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42489;SOR=1.32857;LSEQ=CACAAACTTTTAGCGCCTAG;RSEQ=AATAGGGTCCCTCTTAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:151:123:118,5:27,0:27,123:0.8146:1,1:25.7:1:31:1:0.58566:0:37.3:122:0.8188:0:2.1 1/1:130:111:103,8:18,1:19,111:0.8538:1,2:27.3:1:30.3:1:1:1.39481:36.2:222:0.8538:0:2.1 +21 11049404 . C G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13897;SOR=1.52261;LSEQ=TTAGCGCCTAGTAATAGGGT;RSEQ=CCTCTTAAACCCAATACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:127:75:72,3:51,1:52,75:0.5906:1,1:22:1:30.9:1:0.64395:2.1136:35.4:74:0.5968:0:2.2 1/0:112:77:70,7:33,2:35,77:0.6875:2,2:21.8:1:30:1:0.71758:1.64327:34.4:154:0.6875:0:2.3 +21 11050676 . T TTTG 25 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTCCTTTTTTTTTTT;RSEQ=AGACAGTTTCACTCTGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:25.3:1:1:0:45:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 11056023 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTGAGGCAGGAGAAATC;RSEQ=CCTGAACCCGGAAAGCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:30:1:1:0:59.5:4:1:0:2.5 +21 11056032 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGAAATCACCTGAACC;RSEQ=GGAAAGCGGAGTTTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:28.5:1:1:0:59.5:4:1:0:2.5 +21 11057674 . AT A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAAAAGGTGCTAGCAGAG;RSEQ=TTCTATCACACCTATCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:48:1:32:1:1:0:50:4:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 11057701 . C A 70 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACACCTATCAGGGATACA;RSEQ=AATTTCCAAGAATTTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:2,1:3,5:0.5556:2,2:9.4:1:30.4:1:1:1.83:32.8:10:0.5556:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 11057855 . A T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06089;SOR=Inf;LSEQ=TTTAATAATTTTATAGTATA;RSEQ=GTCAGAAATACTGCACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:4,2:6,8:0.5714:2,0:26.8:1:32.4:1:0.16484:0:37:16:0.5714:0:3 1/1:7:7:7,0:0,0:0,7:1:0,0:19.7:1:31.9:1:1:0:36.1:14:1:0:2.6 +21 11057866 . C T 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61687;SOR=2.15079;LSEQ=TATAGTATAAGTCAGAAATA;RSEQ=TGCACAGTCCCTATTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:7,2:9,3:0.25:2,0:30:1:31:1:1:0:34:6:0.25:0:4 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:29:1:31.3:1:1:0:46:6:0.4286:0:3 +21 11057888 . T A 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13122;SOR=8.69127;LSEQ=GCACAGTCCCTATTTACATC;RSEQ=TTCTACAGTGGTTTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:6,2:8,4:0.3333:2,0:31.3:1:29.3:1:0.51515:0:40.5:8:0.3333:0:3.5 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:42.2:1:28:1:1:0:34:10:0.8333:0:2.6 +21 11057905 . A T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5331;SOR=3.75923;LSEQ=ATCTTTCTACAGTGGTTTTT;RSEQ=AAATGTTTTAAGAATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:1:1,0:13,1:14,1:0.0667:1,0:39:0:29:0:1:0:23:2:0.0667:0:3 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:21.5:1:31.5:1:1:0:23:4:0.2222:0:3 +21 11057929 . T C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20458;SOR=0.35481;LSEQ=TGTTTTAAGAATAAAAAACA;RSEQ=GCAAACTTTATTTGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:11,0:19,1:20,11:0.3235:1,0:11.4:1:30.2:1:1:0:26.5:10:0.3125:0:3.1 0/1:21:3:3,0:17,1:18,3:0.1429:1,0:14.7:1:32.3:1:1:0:24.7:6:0.1429:0:3 +21 11057931 . C A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.74394;SOR=1.28865;LSEQ=TTTTAAGAATAAAAAACATG;RSEQ=AAACTTTATTTGATTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:7,0:28,1:29,7:0.1944:1,0:16.3:1:31.7:1:1:0:25.1:14:0.1944:0:2.6 0/1:21:5:5,0:15,1:16,5:0.2381:1,0:17.4:1:28:1:1:0:26.2:10:0.25:0:2.4 +21 11057949 . T C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40222;SOR=0.56765;LSEQ=TGCAAACTTTATTTGATTTT;RSEQ=CTGAGGAAATAACTTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:12:12,0:41,3:44,12:0.2143:2,0:20.2:1:31.5:1:1:0:25.4:11:0.2075:0:3.8 0/1:30:4:3,1:22,4:26,4:0.1333:2,2:16.3:1:29.3:1:0.53841:1.79094:24.5:8:0.1379:0:4 +21 11057983 . G A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04259;SOR=0;LSEQ=TTTTTGGATTTAATTTCAAT;RSEQ=AAACCGTTGATAACATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:7:7,0:94,9:103,7:0.0636:2,0:34:1:29.1:1:1:0:23.6:14:0.0642:0:3.3 0/0:76:0:0,0:60,16:76,0:0:2,0:22.3:1:31.1:1:1:0:26:37:1:0:2.5 +21 11057984 . A C 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68962;SOR=1.46264;LSEQ=TTTTGGATTTAATTTCAATG;RSEQ=AACCGTTGATAACATTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:3:2,1:99,8:107,3:0.0273:2,2:30.7:1:31.7:1:0.22783:5.99093:23.3:6:0.0286:0:4 0/1:76:3:2,1:58,15:73,3:0.0395:2,2:41.7:1:33:1:0.51323:1.91365:25:6:0.04:0:4.3 +21 11057988 . C T 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70137;SOR=0.55227;LSEQ=GGATTTAATTTCAATGAAAC;RSEQ=GTTGATAACATTTCCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:5:5,0:97,9:106,5:0.045:2,0:28:1:32:1:1:0:23:10:0.045:0:3.4 0/1:79:2:2,0:61,16:77,2:0.0253:2,0:27:1:31.5:1:1:0:22.5:4:0.0256:0:4 +21 11058008 . G C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTTGATAACATTTCCCTCC;RSEQ=CAACAATCTCTGGCAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:112:102,10:0,0:0,112:1:0,2:29.9:1:31.2:1:1:0:23.5:55:1:0:2.7 1/1:78:78:62,16:0,0:0,78:1:0,2:30.1:1:30.3:1:1:0:26.2:38:1:0:2.6 +21 11058025 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02637;SOR=0.42204;LSEQ=TCCGCAACAATCTCTGGCAA;RSEQ=GATCCCTCAGATTTTAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:81:72,9:16,1:17,81:0.8265:1,2:30.8:1:31.4:1:1:1.98826:22.2:80:0.8247:0:3.1 1/0:69:46:36,10:18,4:22,46:0.6667:2,2:31.6:1:31.1:1:1:1.246:22.7:92:0.6667:0:3.2 +21 11058042 . AA GT 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46822;SOR=0.50245;LSEQ=CAATGATCCCTCAGATTTTA;RSEQ=GATTATGTATTATTACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:5:5,0:62,8:70,5:0.0667:2,0:16.4:1:30.1:1:1:0:22.8:10:0.0685:0.0133:3.6 0/1:58:2:2,0:44,12:56,2:0.0345:2,0:34.5:1:30:1:1:0:23:4:0.0357:0:4 +21 11058043 . A T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06068;LSEQ=AATGATCCCTCAGATTTTAA;RSEQ=GATTATGTATTATTACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:51:45,6:17,2:19,51:0.6892:2,2:23.7:1:29.7:1:1:1.13135:22.3:102:0.7391:0:3.2 1/0:57:40:32,8:12,3:15,40:0.7018:2,2:24.9:1:29.5:1:1:1:24.6:80:0.7273:0:3.2 +21 11058058 . A C 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05081;LSEQ=TTTAAAGATTATGTATTATT;RSEQ=CCTTTTAATACAAGTAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:5:4,1:41,5:46,5:0.098:2,2:9.2:1:29.6:1:0.47989:2.01457:20.6:10:0.098:0:4.2 0/1:39:4:4,0:29,6:35,4:0.1026:2,0:15.8:1:27:1:1:0:20.3:8:0.1053:0:4.3 +21 11058066 . A T 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.47487;LSEQ=TTATGTATTATTACCTTTTA;RSEQ=TACAAGTAGAATAACACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:2,0:39,4:43,2:0.0444:2,0:9.5:1:26.5:1:1:0:24:4:0.0444:0:4 0/1:31:2:2,0:26,3:29,2:0.0645:2,0:11.5:1:28.5:1:1:0:23:4:0.0714:0:4 +21 11058340 . A C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ATCGCTGAAAGGGGTAAAGG;RSEQ=GAGAAATCTCTTTATAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:32:0:1:0:28:2:1:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:9:0:32:1:1:0:60:4:0.6667:0:1.5 +21 11058349 . T G 40 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGGGTAAAGGAGAGAAATC;RSEQ=CTTTATAAAACCTTGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:18:0:29:0:1:0:28:2:1:0:1 1/1:3:3:0,3:0,0:0,3:1:0,0:10.7:1:25.7:1:1:0:34.7:6:1:0:1 +21 11059849 . G T 25 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAAATTAGCCGGACGTG;RSEQ=TGGCAGGCACCTGTAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:9:0:25.5:1:1:0:34:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 15373305 . C T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21243;SOR=Inf;LSEQ=GCCACGGAGGAAGTAGGCAG;RSEQ=TGACACAAAGTTCTGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:125,37:162,0:0:2,0:26.1:1:31.7:1:1:0:32.4:80:1:0:0.1 0/1:139:2:1,1:84,52:136,2:0.0144:2,2:42:0:29.5:1:1:1.60951:22:4:0.0144:0:1 +21 15373321 . C A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20586;SOR=Inf;LSEQ=GCAGCTGACACAAAGTTCTG;RSEQ=AATTGCCTGTGCCAAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:93,28:121,0:0:2,0:16.5:1:31.1:1:1:0:29.9:59.5:1:0:0.1 0/1:101:2:1,1:60,39:99,2:0.0198:2,2:19:0:29.5:1:1:1.53167:21:4:0.0198:0:1.5 +21 15373954 . G C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08777;SOR=Inf;LSEQ=CTGCCTTGTTTCTTGCCTTC;RSEQ=TGTAAGCCCTCACAACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:16,64:80,0:0:2,0:18.5:1:30.8:1:1:0:31.4:79:1:0:0.2 0/1:65:3:0,3:15,47:62,3:0.0462:2,0:17:1:32.7:1:1:0:23.7:6:0.0476:0:1 +21 15373965 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22351;SOR=Inf;LSEQ=CTTGCCTTCGTGTAAGCCCT;RSEQ=ACAACAACCAAGTTTAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:18,74:92,0:0:2,0:26:1:31.7:1:1:0:31.7:45:1:0:0.1 0/1:83:2:1,1:15,66:81,2:0.0241:2,2:38.5:1:29.5:1:0.35028:4.29:21:4:0.0244:0:1.5 +21 15373982 . A T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49993;SOR=0;LSEQ=CCTCACAACAACCAAGTTTA;RSEQ=GGTGAGGGCACTGGTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:18,88:106,2:0.0185:2,2:25:0:30.5:1:0.32226:4.79:20:4:0.0185:0:1.5 0/0:94:0:0,0:16,78:94,0:0:2,0:34.1:1:29.8:1:1:0:34.5:93:1:0:0.1 +21 15374017 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50112;SOR=0;LSEQ=TTTTTATCTAACTATGTTTA;RSEQ=TGATGCCGTTATCCTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:14,82:96,2:0.0202:2,2:19.5:1:30:1:0.28403:5.69:22:4:0.0204:0:1 0/0:83:0:0,0:10,73:83,0:0:2,0:27.8:1:32:1:1:0:36.2:82:1:0:0.1 +21 17798796 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05271;SOR=Inf;LSEQ=ATGACACTATGAAAGTTATT;RSEQ=AGCTATAGGTGAAAGAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:78,2:80,0:0:1,0:28:1:32.2:1:1:0:60:39:1:0:0.1 0/1:49:3:3,0:45,1:46,3:0.0612:1,0:36.7:1:31.7:1:1:0:60:6:0.0625:0:1 +21 17798845 . TG T 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.69301;LSEQ=TGTTCATAAAATGGTATGTG;RSEQ=GGGGGGAGGTGTGGGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:4:3,1:157,41:198,4:0.0198:2,2:32.3:1:33:1:1:1.27478:60:8:0.0201:0:0 0/1:145:2:1,1:116,27:143,2:0.0138:2,2:32.5:1:29.5:1:0.35:4.23703:60:4:0.0139:0:0 +21 17798860 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59085;SOR=2.44866;LSEQ=ATGTGTGGGGGGGAGGTGTG;RSEQ=GTGTGTATGTGTGAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:1:0,1:173,65:238,1:0.0042:2,0:18:0:16:0:0.27615:0:60:0:0:0:2 0/1:196:2:1,1:140,54:194,2:0.0102:2,2:12:1:28:1:0.48352:2.57808:60:4:0.0103:0:1 +21 17798960 . A G 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.34763;LSEQ=TGTTTGAAATATGCAAGTCT;RSEQ=TTAAATTGTTTTTACATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:391:313:126,187:26,51:77,313:0.8005:2,2:25.2:1:32.1:1:0.36132:1.32:60:103.333:0.801:0:1.1 1/0:335:195:82,113:53,86:139,195:0.5821:2,2:25.4:1:31.4:1:0.49866:1.18:59.8:390:0.5838:0:1.1 +21 18677386 . T A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATCCTATTACCACGCACTC;RSEQ=CAAAGGATTTCTCTGACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:21.5:1:29:1:1:1:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 18677639 . T C 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.16031;LSEQ=CAGACAACACCTTTCAAACT;RSEQ=TTATACCAACCTCTGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:3,4:7,3:0.3:2,0:19:1:28.7:1:0.2:0:32.3:6:0.3:0:1 0/1:18:6:5,1:7,5:12,6:0.3333:2,2:14.8:1:26.7:1:0.60003:3.34:32.2:12:0.3333:0:1 +21 18677740 . TTTTTA T 30 d5;v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=TCAGGCCCTGTATTTTTATT;RSEQ=TTTTTTTTTTTTAATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:3,1:0.25:2,0:34:0:32:0:1:0:32:2:0.25:0:5 0/1:5:2:0,2:0,3:3,2:0.4:0,0:7.5:1:30.5:1:1:0:38:4:0.4:0.2:2.5 +21 19048959 . T A 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGACACAAGACAAAACGAT;RSEQ=AAGAGAAAAGAGCTGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:25.1:1:28.1:1:1:0:60:14:1:0:1.3 1/1:3:3:3,0:0,0:0,3:1:0,0:23:1:29.3:1:1:0:60:6:1:0:1 +21 19048976 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTAAGAGAAAAGAGCTGG;RSEQ=CCCGGGGACCACTACCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:37.5:1:32.5:1:1:0:60:4:0.2857:0:2 0/0:2:0:0,0:2,0:2,0:0:0,0:26:1:30.5:1:1:0:60:4:1:0:1 +21 19049137 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.83198;LSEQ=ACATGATCACAGGACAGGTG;RSEQ=CCCTTCCTTCTTAGGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:8,17:25,1:0.0385:2,0:46:0:32:0:1:0:55:2:0.04:0:1 0/1:29:2:0,2:15,12:27,2:0.069:2,0:23.5:1:28.5:1:0.22414:0:41:4:0.069:0:1 +21 20195100 . T A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02411;SOR=Inf;LSEQ=ACAGATAGAGAAATGTAGAA;RSEQ=AACATGTACATAAATATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:108,45:153,0:0:2,0:22.5:1:30.3:1:1:0:60:306:1:0:0.3 0/1:101:4:3,1:74,23:97,4:0.0396:2,2:22.3:1:29.5:1:1:1.07172:60:8:0.0396:0:2 +21 20195110 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51677;SOR=0;LSEQ=AAATGTAGAATAACATGTAC;RSEQ=TAAATATACATATATCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:126,62:188,2:0.0105:2,2:31:1:33:1:1:2.02411:60:4:0.0106:0:1 0/0:129:0:0,0:88,39:127,0:0:2,0:24.7:1:29.6:1:1:0:60:126:0.9921:0:0.5 +21 20195182 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=0.52403;LSEQ=GGAATAGTAACAAATAGTTA;RSEQ=TTGAATATGCAAACAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:318:212:105,107:56,49:105,212:0.6667:2,2:27.1:1:30.8:1:0.55202:1.16406:60:105:0.6646:0:1.9 1/0:262:134:70,64:67,61:128,134:0.5115:2,2:26.9:1:29.5:1:1:1.0042:60:66:0.5116:0:1.9 +21 20195191 . G A 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1853;SOR=4.75263;LSEQ=ACAAATAGTTACTTGAATAT;RSEQ=CAAACAGTTAACACTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:1:1,0:151,161:312,1:0.0032:2,0:1:0:23:0:0.48562:0:60:2:0.0032:0:1 0/1:266:4:3,1:130,132:262,4:0.015:2,2:20:1:24:1:0.62215:3.03:60:3:0.0116:0:1.5 +21 20195198 . G A 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33721;SOR=3.56954;LSEQ=GTTACTTGAATATGCAAACA;RSEQ=TTAACACTAAATTTATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:1:1,0:145,165:310,1:0.0032:2,0:1:0:25:0:0.46945:0:60:2:0.0033:0:2 0/1:263:3:2,1:126,134:260,3:0.0114:2,2:23.7:1:30:1:0.61375:2.12:60:6:0.0116:0:3 +21 20195202 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00021;SOR=0.52186;LSEQ=CTTGAATATGCAAACAGTTA;RSEQ=CACTAAATTTATGTTTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:304:205:93,112:44,55:99,205:0.6743:2,2:24.8:1:32.5:1:0.90263:1.04:60:67.333:0.6733:0:2 1/0:262:136:66,70:57,69:126,136:0.5191:2,2:24.6:1:31.1:1:0.62161:1.14:60:135:0.5172:0:1.9 +21 20195250 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50239;SOR=0;LSEQ=TTGTATTTATTTTTCATATA;RSEQ=AGGGATCATAAAAATTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:59,125:184,2:0.0108:2,2:25:1:28.5:1:0.54228:2.11:60:4:0.011:0:2 0/0:156:0:0,0:50,106:156,0:0:2,0:26.6:1:31:1:1:0:60:77:1:0:0.7 +21 20195258 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21716;SOR=Inf;LSEQ=ATTTTTCATATACAGGGATC;RSEQ=TAAAAATTGTTACTCAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:50,111:161,0:0:2,0:26.1:1:30.6:1:1:0:60:31.2:1:0:0.7 0/1:141:2:1,1:41,98:139,2:0.0142:2,2:34:1:28.5:1:0.50851:2.37:60:4:0.0142:0:1.5 +21 20195300 . C T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03116;SOR=Inf;LSEQ=ATTTTGGTTTATTTCTTAAA;RSEQ=GTTAAATATTTCTTAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:15,74:89,0:0:2,0:24:1:30.5:1:1:0:60:178:1:0:0.1 0/1:66:4:0,4:10,52:62,4:0.0606:2,0:19.3:1:26.8:1:1:0:60:3:0.0462:0:1.8 +21 20195328 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.28063;SOR=0;LSEQ=ATTTCTTAAATGTATGTGAT;RSEQ=CAACAAAACATTAAGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:0,3:5,43:48,3:0.0588:2,0:34.3:1:29.3:1:1:0:60:6:0.0588:0:1 0/0:32:0:0,0:2,30:32,0:0:2,0:20.8:1:31.4:1:1:0:60:31:1:0:0.2 +21 20195560 . G A 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATTTTTTTACTGTCATGGT;RSEQ=TAACAAAAAAGATGATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:20:1:31:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 21055586 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTTGACATGAGACAAGA;RSEQ=CCCTGGTGGTCCTCCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 21055851 . G GT 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12969;SOR=0;LSEQ=TTTCTCATCTTCATGAGTTT;RSEQ=CTGGTTTTGATCGCTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:11,14:0,0:0,25:1:0,2:26.6:1:29.4:1:1:0:56.4:24:1:0.16:0.1 1/1:34:30:15,15:2,2:4,30:0.8824:2,2:30.4:1:28.3:1:1:1:57.2:29:0.8788:0.0588:0.3 +21 21056158 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01752;SOR=0.20322;LSEQ=CTTCTGTATATGGTGTCTGG;RSEQ=GACCTCTGTTGGGGTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:10,5:2,2:4,15:0.7895:2,2:18.8:1:31.4:1:0.60268:1.92:60:30:0.7895:0:1.4 0/1:26:11:7,4:9,6:15,11:0.4231:2,2:21.3:1:27.6:1:1:1.16:60:22:0.4231:0:1 +21 21056234 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01658;SOR=0.11888;LSEQ=AACGAAGCACTTTGGCTGTC;RSEQ=TTTGGTGGCGGGGCTGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:3,6:9,7:0.4375:2,2:23.9:1:31.4:1:1:1.46:60:14:0.4375:0:1.6 0/1:25:2:1,1:9,14:23,2:0.08:2,2:5.5:1:29.5:1:1:1.53:47:4:0.08:0:1.5 +21 21057031 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTATCAGATGGGCTGAGG;RSEQ=ACCACCCTGCTCTTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:22:1:29.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 27340014 . C T 67 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71643;LSEQ=TTCTGTCTATGAAGGATAAG;RSEQ=AGAACGCTGAGAGTTACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:33.4:1:29:1:1:0:60:10:0.4167:0:1.4 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:31:0:31:0:1:0:60:2:0.3333:0:2 +21 27340020 . G C 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.10574;LSEQ=CTATGAAGGATAAGCAGAAC;RSEQ=CTGAGAGTTACAAGGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:31:1:29:1:1:0:60:4:0.1818:0:2 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:37:0:33:0:1:0:60:2:0.3333:0:2 +21 27340191 . C T 67 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11905;SOR=0.19265;LSEQ=GTATTTAATCTGGTAGCTTG;RSEQ=AGGCCTCCAAAGGTGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:5:3,2:132,32:164,5:0.0294:2,2:19.2:1:29.2:1:0.26392:2.72924:60:10:0.0299:0:1 0/0:173:1:1,0:136,36:172,1:0.0058:2,0:15:0:31:0:1:0:60:2:0.0058:0:1 +21 27340215 . TA T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25043;SOR=Inf;LSEQ=CCTCCAAAGGTGGTAGAAGT;RSEQ=ACCTCCTGTGCTGCAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:178,69:247,0:0:2,0:24.3:1:28.9:1:1:0:60:122.5:1:0:0.1 0/1:273:3:1,2:194,76:270,3:0.011:2,2:25.3:1:26.7:1:0.19728:5.06987:60:6:0.0112:0.0037:2 +21 27340301 . A T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=5.38345;LSEQ=TGATTTTCCAAAGAAAGTCT;RSEQ=AGGAAAGTAAAAAGGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:69:37,32:304,269:573,69:0.1075:2,2:23.1:1:28.8:1:1:1.02:60:22:0.1039:0:1.1 0/1:719:283:145,138:212,224:436,283:0.3936:2,2:25.6:1:28.4:1:0.54143:1.11:60:93.333:0.3938:0:1.1 +21 27340400 . C CT 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10415;SOR=5.71573;LSEQ=AAAGACACAGCTCTGCTCAA;RSEQ=TTTTTTTTCCCATGGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:1:0,1:39,195:234,1:0.0043:2,0:32:0:32:0:1:0:60:2:0.0044:0:0 0/1:209:5:1,4:44,159:203,5:0.0239:2,2:31.8:1:29.2:1:1:1.10639:60:10:0.024:0:0 +21 28398955 . T A 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41631;LSEQ=CAGTTGAATTGGTAGACTAA;RSEQ=TAGAGTAGATGGCCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:13,0:13,3:0.1875:1,0:24.3:1:32:0:1:0:60:6:0.1875:0:1 0/1:4:1:1,0:3,0:3,1:0.25:0,0:1:0:30:0:1:0:60:2:0.25:0:1 +21 28399182 . T C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=1.84034;LSEQ=GACTCAGTCTAGATCCACAA;RSEQ=ATTTGCTCTCTTAGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:127:65,62:82,108:190,127:0.4006:2,2:26.8:1:32.3:1:0.16947:1.38:60:126:0.4:0:1.1 1/0:328:181:92,89:74,73:147,181:0.5518:2,2:25.8:1:30.8:1:1:1.02:59.9:59.333:0.5477:0:1.1 +21 28399257 . T A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4985;SOR=0;LSEQ=TTCATAAGATTATAAGCCAA;RSEQ=TCCTTCTGGTGACTATCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:37,122:159,2:0.0124:2,2:22.5:1:32.5:1:0.41747:3.27:60:4:0.0125:0:1 0/0:157:0:0,0:44,113:157,0:0:2,0:23.1:1:29:1:1:0:60:51.333:1:0:0.4 +21 28423608 . T A 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TCTGACAGTTCATCCATCTG;RSEQ=TCTTCCATTCAGGCACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:2,3:0.6:0,2:20.3:1:30.3:1:1:0:59.7:6:0.6:0:1.7 1/1:5:5:3,2:0,0:0,5:1:0,2:27.2:1:25:1:1:0:59.8:4:1:0:2.4 +21 28423657 . T G 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25824;SOR=Inf;LSEQ=GATGTTGTGATCATTTGGAG;RSEQ=AGAAGAGGTCCTCTGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:3,3:3,2:5,6:0.5455:2,2:21.7:1:31.7:1:1:1.44544:41.7:12:0.5455:0:1.5 1/1:3:3:1,2:0,0:0,3:1:0,2:22:1:32.3:1:1:0:59.7:6:1:0:3 +21 28424677 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACATATACACACATATATAC;RSEQ=TATACATATATACACACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:30:1:1:0:60:4:1:0:2 +21 28424718 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCATATACATATATACACA;RSEQ=ATATACATATACATATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:19.5:1:30.5:1:1:0:60:4:0.6667:0:2 +21 28424933 . T TATATATATATA 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAACATATATATATATAA;RSEQ=ATATATATATATAATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:17:1:30:1:1:0:53:6:0.6:0.4:0 0/0:1:0:0,0:0,1:1,0:0:0,0:13:0:30:0:1:0:20:2:1:0:0 +21 28425056 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12896;SOR=0;LSEQ=CAGCAGCCTCAAAGACCAAA;RSEQ=CTGGACAAACTCACAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:5,12:17,2:0.1053:2,2:10.5:1:31:1:1:2.28:50:4:0.1111:0:2.5 0/0:33:0:0,0:17,16:33,0:0:2,0:19:1:27.9:1:1:0:49:66:1:0:0.4 +21 28425059 . G A 22 v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63592;SOR=0.61361;LSEQ=CAGCCTCAAAGACCAAAACT;RSEQ=GACAAACTCACAAAGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:5,12:17,2:0.1053:2,2:7.5:1:28.5:1:1:2.28:50:4:0.1111:0:2.5 0/1:30:2:2,0:14,14:28,2:0.0667:2,0:1:0:22.5:1:0.48506:0:35:4:0.0714:0:1 +21 28425164 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18803;SOR=Inf;LSEQ=CGCAACATCTCTCCATCAAG;RSEQ=GTGCAGAACTGAATGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:31:1:31.7:1:1:0:60:30:1:0:0.1 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:14:1:25:1:1:1.4491:60:4:0.1667:0:1 +21 28978057 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATATGTCACTCGAGGAG;RSEQ=CTGGAGAACAGCAAAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:23:1:29.5:1:1:1.41:49.5:4:0.2857:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:19:1:22.5:1:1:0:52:1:1:0:0 +21 28978108 . A C 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63287;SOR=1.91506;LSEQ=CTTCCTCTGGGATCTCTAAA;RSEQ=TCAAGGCGTATCAACCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:3,2:2,2:4,5:0.5556:2,2:16.6:1:32.6:1:1:1.43:56:10:0.5556:0:1.2 1/0:7:5:4,1:1,1:2,5:0.7143:2,2:24:1:31.6:1:1:3.16:60:10:0.7143:0:1 +21 28978250 . G A 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03036;SOR=0;LSEQ=GAGCTGTCCCTTTTTGGAGG;RSEQ=GGTGTGCTACGTTGGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:6,8:14,8:0.3636:2,2:27.3:1:32.3:1:1:1.23744:60:16:0.3636:0:1 0/0:12:0:0,0:4,8:12,0:0:2,0:25:1:30.4:1:1:0:60:24:1:0:0 +21 28978809 . T C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGAGAATCTGTGCATCTC;RSEQ=GTGGTTGGGACCCTAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:32.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:29:1:1:0:60:4:1:0:1 +21 28978981 . G T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCAGTGTGGCTCTCAGGTG;RSEQ=GCGGCCTCAACACACTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:4:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:31:0:1:0:60:4:1:0:2 +21 28979005 . T C 49 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCAACACACTGCTCTTC;RSEQ=TTCCTCTCTGTGGGTCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:33:1:31.3:1:1:0:60:6:1:0:1.7 +21 31252048 . T A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.083;SOR=Inf;LSEQ=TTTAGGAAAAACGGTAGCTC;RSEQ=TTAAGGAGCTAGTTTATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:16,0:0:1,0:23.6:1:32.7:1:1:0:60:32:1:0:0 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:7.5:1:30:1:1:0:60:4:0.2857:0:1 +21 31252105 . C G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00672;SOR=Inf;LSEQ=AAGGCCAAGCAATTTTGCAA;RSEQ=TGTCTTCTGCTTATTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:61,0:61,0:0:1,0:24.1:1:33.2:1:1:0:60:122:1:0:0 0/1:26:4:4,0:22,0:22,4:0.1538:1,0:23.3:1:31.3:1:1:0:60:8:0.1538:0:1 +21 31252172 . A AT 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.4012;SOR=0.33882;LSEQ=CACACAGCCCCAGTTCTTTG;RSEQ=TTTTTTTTTTAACAAATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:4:4,0:121,14:135,4:0.0288:2,0:20.3:1:31.4:1:1:0:60:8:0.0299:0.0072:0 0/0:101:1:1,0:90,10:100,1:0.0099:2,0:50:0:28:0:1:0:60:2:0.01:0:0 +21 31252298 . T C 119 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=19.41063;LSEQ=AAAGAGTTTACATATGCAAT;RSEQ=GTTACAGTAATAGTTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:1:1,0:205,261:466,1:0.0021:2,0:30:0:15:0:0.44111:0:60:0:0:0:1 0/1:375:15:7,8:154,205:359,15:0.04:2,2:28:1:30.7:1:0.7954:1.16:60:30:0.04:0:1 +21 31252311 . G A 183 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=115.94698;LSEQ=ATGCAATTGTTACAGTAATA;RSEQ=TTCCCTGAAGCCCCTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:1:1,0:172,255:427,1:0.0023:2,0:1:0:26:0:0.40421:0:60:2:0.0024:0:1 0/1:336:72:28,44:113,150:263,72:0.2143:2,2:23.3:1:29.8:1:0.59095:1.18322:60:144:0.2162:0:1.1 +21 31252384 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15391;SOR=Inf;LSEQ=GAATACGATTTGTATAATAA;RSEQ=CCTAATCAGAAAAATAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:41,141:182,0:0:2,0:22.9:1:31.8:1:1:0:60:181:1:0:0.1 0/1:118:2:1,1:33,83:116,2:0.0169:2,2:32.5:1:29.5:1:0.495:2.49:60:4:0.0171:0:1 +21 31384240 . C T 136 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00166;SOR=0.16797;LSEQ=GCCTTTTGACCCAAAAAGAC;RSEQ=GCATAGCCTCCAATTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:19:8,11:187,141:328,19:0.0548:2,2:32.2:1:32.1:1:0.23816:1.82035:60:38:0.0556:0:1.5 0/0:312:3:1,2:170,139:309,3:0.0096:2,2:29:1:29:1:0.5912:2.43919:60:6:0.0098:0:1.3 +21 31384297 . A G 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25222;LSEQ=ATTTCATCTGCATTCTACCT;RSEQ=TTTCAGTACATAATCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:433:400:165,235:15,17:32,400:0.9238:2,2:26.4:1:31.7:1:0.57862:1.256:60:43.444:0.9243:0:1.1 1/0:389:293:134,159:43,53:96,293:0.7532:2,2:26.5:1:31.1:1:0.90636:1.04:60:145.5:0.7519:0:1.1 +21 31384366 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=TGTTAATAAGGTCTTATGTA;RSEQ=ATATTTATATTTTCTCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:37,127:164,2:0.012:2,2:20.5:1:31.5:1:0.4065:3.40:60:4:0.0124:0:1 0/0:159:0:0,0:45,114:159,0:0:2,0:25.7:1:29.8:1:1:0:60:38.75:1:0:0.5 +21 31384543 . T C 76 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.52273;SOR=0.28305;LSEQ=TGAATCATGGCAAATATGTA;RSEQ=ACTTCTATAGTCAGAAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:3,6:0.6667:0,0:38.3:1:29.5:1:1:0:60:5:0.625:0:1.2 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:45:0:34:0:1:0:60:2:0.3333:0:2 +21 32273182 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50274;SOR=Inf;LSEQ=GGTTTTTGCTAAGCTGACTT;RSEQ=GCGGAGTTCTTGGCTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:17,14:31,0:0:2,0:27.3:1:29.9:1:1:0:60:30:1:0:0.9 0/1:41:2:1,1:24,15:39,2:0.0488:2,2:15.5:1:29:1:1:1.58108:60:4:0.05:0:1 +21 32273185 . G A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7664;SOR=0.78956;LSEQ=TTTTGCTAAGCTGACTTAGC;RSEQ=GAGTTCTTGGCTAAAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:27:15,12:2,3:5,27:0.8438:2,2:28.3:1:31.9:1:0.64544:1.84:60:54:0.8438:0:1 1/1:42:34:20,14:5,3:8,34:0.8095:2,2:23.6:1:29.8:1:1:1.16243:60:68:0.8095:0:1.1 +21 32273325 . G A 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41667;SOR=0;LSEQ=ATATTCCTGTACTTCCAAGC;RSEQ=ATTCAACTATCTTGAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:14.3:1:27.7:1:1:0:60:6:1:0:1.1 1/1:5:4:0,4:0,1:1,4:0.8:0,0:16.8:1:31.5:1:1:0:60:8:0.8:0:1 +21 32380890 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16075;SOR=Inf;LSEQ=CAAGGAATGCCCAAACTTGC;RSEQ=AGCAAACCACCAAAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:30,32:62,0:0:2,0:25.6:1:31.8:1:1:0:60:124:1:0:0.2 0/1:42:2:1,1:19,21:40,2:0.0476:2,2:35:1:28.5:1:1:1.10:60:4:0.0476:0:1 +21 33044256 . GGCT G 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.66723;SOR=0.5074;LSEQ=GAGGCTGTTGTGATGGTGGT;RSEQ=GCTGCTGCTGCTGCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:2,2:12,8:20,4:0.1667:2,2:31.8:1:31.8:1:1:1.47432:60:8:0.1667:0:0 0/1:22:2:1,1:10,10:20,2:0.0909:2,2:29:1:30:1:1:1:60:4:0.0909:0:0 +21 36164388 . G C 102 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00713;SOR=0;LSEQ=AGGCCCGCGCGCCCGGAGGC;RSEQ=AAGGCGGCGGCCCGCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:9,0:23,0:23,9:0.2727:1,0:7:1:32.2:1:1:0:60:18:0.3:0:1 0/0:24:0:0,0:21,3:24,0:0:2,0:9.5:1:27.9:1:1:0:58.7:11:1:0:1 +21 36164405 . G T 150 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=47.06532;LSEQ=GGCGAAGGCGGCGGCCCGCG;RSEQ=GGCCCAGCCGGGCCAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:2,0:80,8:88,2:0.0222:2,0:16.5:1:30:0:1:0:60:4:0.0225:0:1 1/0:63:33:30,3:27,3:30,33:0.5238:2,2:14.8:1:29.8:1:1:1.11:60:66:0.5323:0:1.1 +21 36164413 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51478;SOR=0;LSEQ=CGGCGGCCCGCGGGGCCCAG;RSEQ=CGGGCCAGGCCTGGCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:103,20:123,2:0.016:2,2:7:1:29:1:0.3089:5.05037:60:4:0.016:0:1 0/0:86:0:0,0:72,14:86,0:0:2,0:17.8:1:31.8:1:1:0:59.6:85:1:0:0.6 +21 36164469 . G T 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.09625;SOR=6.13596;LSEQ=CGGCCTCCTCCAGGCGCGCG;RSEQ=AGGGCGCCATGTTGGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:1:0,1:322,143:465,1:0.0021:2,0:1:0:23:0:0.30901:0:60:2:0.0022:0:1 0/1:384:5:2,3:247,132:379,5:0.013:2,2:13.2:1:27:1:0.3494:2.79874:60:10:0.0134:0:1 +21 36164889 . G A 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09817;SOR=6.01995;LSEQ=ACTGGCGCGGGTCGCTGAAC;RSEQ=CTGTCAGGTCGGGTGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:581:1:1,0:223,357:580,1:0.0017:2,0:24:0:12:0:0.38554:0:60:0:0:0:3 0/1:486:5:3,2:193,288:481,5:0.0103:2,2:20.2:1:27.2:1:0.39704:2.23:60:10:0.0104:0:1.2 +21 36164953 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.5162;SOR=0;LSEQ=CGGAAGTGAGTAGGAGGTTG;RSEQ=GGAGGCCACAGCTCTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:19,152:171,2:0.0116:2,2:10:0:32:0:0.21844:7.82:60:4:0.0118:0:1.5 0/0:118:0:0,0:14,104:118,0:0:2,0:22.3:1:28.4:1:1:0:60:15.857:1:0:0.3 +21 36165041 . T C 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=28.99651;LSEQ=GCCACCCAGGATGCTACTGC;RSEQ=GGGGAGGACGGGGACCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:0,3:0,39:39,3:0.0714:1,0:15:1:30:1:1:0:60:6:0.075:0:1.3 1/0:14:10:0,10:0,4:4,10:0.7143:0,0:21.1:1:27:1:1:0:60:9:0.6923:0:1 +21 36192484 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAGGGCTGGGGTGCCGG;RSEQ=TGGGGCTGCGGAGGGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 36193871 . T C 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0214;LSEQ=AACGTGCATTCTGAGGGCTG;RSEQ=CATCTTTCTTCTGAGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:378:376:309,67:0,1:1,376:0.9947:0,2:24.8:1:32.3:1:0.18037:0:59.9:93:0.9973:0:1.1 1/1:190:152:118,34:27,11:38,152:0.8:2,2:23.7:1:31:1:0.39916:1.41:60:37:0.7957:0:1.1 +21 36194056 . G A 102 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00026;SOR=16.5244;LSEQ=GGACAATTCTTTATAGAGCC;RSEQ=CGAATGCATTCCCCTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:637:1:1,0:199,436:635,1:0.0016:2,0:1:0:28:0:0.31447:0:60:2:0.0016:0:1 0/1:473:12:5,7:157,304:461,12:0.0254:2,2:20.5:1:28.7:1:0.55501:1.38:60:24:0.0258:0:1 +21 36206932 . G A 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGAGGGGAGGGGATGGG;RSEQ=GGAGGGAAGGAGGGAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:311:311:91,220:0,0:0,311:1:0,2:24.4:1:30.7:1:1:0:59.9:22.923:1:0:1.2 1/1:248:248:83,165:0,0:0,248:1:0,2:22.9:1:29.3:1:1:0:60:30:1:0:1.1 +21 36229637 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06923;LSEQ=ACAGCCAGACCGTTACAATC;RSEQ=CATAGACATCTTTTTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:121:115:63,52:4,2:6,115:0.9504:2,2:22.8:1:29.3:1:0.69083:1.64423:60:56.5:0.9496:0:1.1 1/1:86:82:47,35:2,2:4,82:0.9535:2,2:24.9:1:28.6:1:1:1.34:59.7:81:0.9643:0:1.1 +21 36229647 . C CT 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50992;SOR=0;LSEQ=CGTTACAATCGCATAGACAT;RSEQ=TTTTTTCCCCTCTGACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:69,59:128,2:0.0154:2,2:41.5:1:31.5:1:1:1.16808:60:4:0.0155:0:1.5 0/0:95:0:0,0:54,41:95,0:0:2,0:27.3:1:30.4:1:1:0:59.7:46.5:1:0:1 +21 36229695 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50393;SOR=0;LSEQ=AAAAGTCAGAGTCGCCACCA;RSEQ=TTGTTTTCTGAAGCTCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:90,106:196,2:0.0101:2,2:23.5:1:31.5:1:1:1.18:60:4:0.0104:0:1 0/0:161:0:0,0:76,85:161,0:0:2,0:26.3:1:29.9:1:1:0:59.7:79.5:1:0:0.5 +21 36229712 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5003;SOR=0;LSEQ=CCATTTGTTTTCTGAAGCTC;RSEQ=ATAACTTTGTTATTTCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:72,88:160,2:0.0123:2,2:34:0:33:1:1:1.22:60:4:0.0123:0:1 0/0:143:0:0,0:61,82:143,0:0:2,0:24.8:1:29.4:1:1:0:60:46.667:1:0:0.4 +21 36229760 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50129;SOR=0;LSEQ=CAGGAAATGCTGGCAGTGAG;RSEQ=CAAAACCCAGCCTTCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:20,40:60,2:0.0323:2,2:31:1:28.5:1:1:1.98:60:4:0.0345:0:1 0/0:50:0:0,0:13,36:49,0:0:2,0:22.6:1:30.4:1:1:0:60:23.5:0.9792:0:0.1 +21 36229941 . C T 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATTTCTCTAAGTTTAGT;RSEQ=ACCCTCAAAGTCGATTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:31:0:30:0:1:0:60:2:1:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:30.7:1:29.7:1:1:0:50.7:6:1:0:1.3 +21 36229995 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTCCCTCCCAGCCAGGC;RSEQ=CCTTGCCATAATTCAAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:28:1:28:1:1:0:60:4:0.6667:0:1.5 +21 36231556 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10917;SOR=Inf;LSEQ=GTCAGCCTAATTTCCTTTTG;RSEQ=CCTCTAAAAGGATGCTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:147,6:153,0:0:1,0:25.2:1:32.3:1:1:0:59.6:50:1:0:0.1 0/1:76:2:1,1:68,6:74,2:0.0263:2,2:22:1:28:1:0.17684:10.56963:60:4:0.0263:0:1 +21 36231564 . A G 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTCCTTTTGCCCTCTAA;RSEQ=AGGATGCTTCAAAAAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:174,11:185,2:0.0107:2,2:7.5:1:31:1:0.12455:15.18781:60:4:0.0108:0:1.5 0/0:93:0:0,0:85,8:93,0:0:2,0:24.5:1:29.9:1:1:0:60:186:1:0:0.1 +21 36232156 . C A 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTTAAGTCAGGATTTC;RSEQ=GGAAACCATAGAGTCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:1,5:6,2:0.25:2,0:25.5:1:33.5:1:1:0:60:4:0.25:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 36233905 . C G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTAATTTCTCACTCACCCC;RSEQ=TCTCCTCCGCATACCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 36252595 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTAGTAAAAATCTCAGGC;RSEQ=TTTCTTTGAAATTCACAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:5,0:5,2:0.2857:0,2:34.5:1:32.5:1:0.28571:0:43.5:4:0.2857:0:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:43:0:29:0:1:0:60:2:1:0:0 +21 36252622 . T C 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAATTCACAATTCCTACG;RSEQ=TGCATGTTCCAAATCAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:10,0:10,2:0.1667:0,2:39.5:1:35:0:0.16667:0:43.5:4:0.1667:0:2.5 0/0:2:0:0,0:2,0:2,0:0:0,0:18:1:27.5:1:1:0:60:4:1:0:0 +21 36252870 . G A 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTACCTCTTCCACTTCGACC;RSEQ=ACAAACCTGAGGTCATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:711:0:0,0:402,309:711,0:0:2,0:25.2:1:30.8:1:1:0:60:100.571:1:0:0.1 0/1:715:21:13,8:394,299:693,21:0.0294:2,2:18.1:1:30.1:1:0.82363:1.23:60:42:0.0295:0:1.1 +21 36253146 . ATAACT A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.03517;SOR=0.1967;LSEQ=GTTGCAGAGGAATAGCAATG;RSEQ=TAAGCAAAACAACAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:15:0,15:0,23:23,15:0.3947:1,1:24.5:1:32:1:1:0:57.9:30:0.3947:0.0526:0.1 0/1:18:2:0,2:0,16:16,2:0.1111:1,0:14.5:1:31.3:1:1:0:60:4:0.1176:0.0556:0 +21 36258839 . T C 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52857;SOR=0;LSEQ=GGGTTATAACTTTTCCTACT;RSEQ=TGTATCAAAGCTAAGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:3,1:9,0:9,4:0.3077:0,2:18.3:1:32.5:1:0.30769:0:60:8:0.3077:0:1 0/0:3:0:0,0:2,1:3,0:0:2,0:28.3:1:29.7:1:1:0:60:6:1:0:0 +21 36259498 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18877;SOR=Inf;LSEQ=TCAGCAAGCAGCTCCCGGGA;RSEQ=ACCAACATACACGTTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:10,113:123,0:0:2,0:21.6:1:32.9:1:1:0:59.9:60.5:1:0:0.2 0/1:95:2:1,1:15,77:92,2:0.0211:2,2:8:1:28:1:0.31297:5.00:60:4:0.0213:0:1 +21 36259539 . T G 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.76706;SOR=1.24863;LSEQ=GCCTTTATTACTGCGGGGGG;RSEQ=GGGGGGGGGCGGGGGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:19:0,19:3,10:13,19:0.5938:2,1:6.6:1:26.9:1:0.05766:0:46.8:5.333:0.6154:0:2.6 1/0:17:11:0,11:2,4:6,11:0.6471:2,0:7:0:25.9:1:0.11029:0:46.5:10:0.625:0:2 +21 36259549 . C G 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.38858;LSEQ=CTGCGGGGGGTGGGGGGGGG;RSEQ=GGGGGTGGTTAGGGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:0,20:4,0:4,20:0.8333:0,1:16.2:1:23.5:1:9e-05:0:47:3:0.8333:0:2.7 1/1:16:14:1,13:1,1:2,14:0.875:2,1:13.7:1:23.2:1:0.24167:9.5394:49.4:3.667:0.9167:0:1.8 +21 36260693 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGACCACAGAGCACTTTC;RSEQ=CCCCCTGTTGTAAAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:21:0:32:0:1:1.7321:60:4:0.4:0:1.5 +21 36265299 . G A 36 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.09105;LSEQ=GGAAAATAAAAGTAATGCAA;RSEQ=TTTAAAAATTAACTTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:4:0,4:84,220:304,4:0.0129:2,0:27.3:1:18:1:0.57778:0:60:0.333:0.0036:0:5.3 0/1:214:3:2,1:65,142:207,3:0.014:2,2:7:1:20.7:1:0.23929:4.34:60:2:0.0102:0:1.7 +21 36265319 . C A 35 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.27968;SOR=0;LSEQ=GTTTAAAAATTAACTTTCCC;RSEQ=CGACTTTTTTTTTTTTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:2,1:30,175:205,3:0.0144:2,2:7.7:1:22.7:1:0.06241:11.44:60:2:0.0105:0:1.3 0/0:137:0:0,0:33,104:137,0:0:2,0:25.9:1:29.1:1:1:0:59.6:10.417:1:0:0.3 +21 36265323 . CT C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.73323;SOR=1.17688;LSEQ=AAAAATTAACTTTCCCCCGA;RSEQ=TTTTTTTTTTTGCTAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:23:3,20:20,141:161,23:0.123:2,2:30.3:1:31.5:1:1:1.06:59.1:10.5:0.1257:0.0053:0.3 0/1:127:18:3,15:20,83:103,18:0.1417:2,2:30.3:1:31.3:1:1:1.20303:59.7:36:0.1513:0:0.2 +21 36421036 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18444;SOR=0.65357;LSEQ=TCACAAACAAGACAGGGAAC;RSEQ=GGCAGGCACCGAGGCATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:53:52,1:51,3:54,53:0.4953:2,1:25.5:1:30.6:1:0.61789:3.03:60:16.667:0.4808:0:1.1 0/1:82:32:31,1:48,2:50,32:0.3902:1,1:26.8:1:30.2:1:1:1.29:60:31:0.3827:0:1.3 +21 36421059 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5041;SOR=0;LSEQ=CAGGCACCGAGGCATCTCTG;RSEQ=ACCGAGGTGAAACAAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:144,25:169,2:0.0117:2,2:8:1:30:1:0.28173:5.66778:60:4:0.0119:0:1 0/0:138:0:0,0:116,22:138,0:0:2,0:22.4:1:31.5:1:1:0:60:68:1:0:0.3 +21 36421116 . T C 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00523;SOR=Inf;LSEQ=AAGCTGAGCAAAAGTAGATA;RSEQ=TACAAGACCAGCATGTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:265,162:427,0:0:2,0:27:1:30.9:1:1:0:60:105.75:1:0:0.1 0/1:385:7:6,1:232,146:378,7:0.0182:2,2:28.7:1:32.3:1:0.25902:3.77:60:14:0.0184:0:1.1 +21 36421263 . G T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09541;SOR=0;LSEQ=TGATTTCTTTTACCTTCGGA;RSEQ=CGAAAACCAAGACAGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:2,1:53,152:205,3:0.0144:2,2:25.7:1:25:1:0.17145:5.68:60:2:0.0099:0:1 0/0:246:0:0,0:61,185:246,0:0:2,0:24.8:1:31.5:1:1:0:60:492:1:0:0.1 +21 36421280 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50329;SOR=Inf;LSEQ=GGAGCGAAAACCAAGACAGG;RSEQ=CACTGTTTCAGCCTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:22,125:147,0:0:2,0:22.5:1:30.1:1:1:0:60:146:1:0:0.1 0/1:179:2:1,1:32,145:177,2:0.0112:2,2:24:1:32:1:0.33557:4.48:60:4:0.0114:0:1 +21 36421331 . T C 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.89182;LSEQ=CATCTCTCTTTCTTCTCCCC;RSEQ=CTGCTGGATACCTCTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:11:0,11:0,56:56,11:0.1642:1,0:24.2:1:31.6:1:1:0:58.4:22:0.1774:0:1.2 0/1:47:7:0,7:0,40:40,7:0.1489:1,0:31.9:1:31.4:1:1:0:60:14:0.1522:0:1.1 +21 36421412 . TA T 59 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=1.3537;LSEQ=ATATTCAAATTGTTAAAGAT;RSEQ=AAAAAAAAAAAAAAGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:0,9:9,4:0.2667:0,0:23.3:1:29.6:1:1:0:60:8:0.2857:0.0667:1 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:33:1:30:1:1:0:60:4:0.3333:0:0.5 +21 36971791 . G A 84 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAGGCAAGTTCAATCTGATT;RSEQ=GATCCTGGATCCCATCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:8,0:8,0:8,8:0.5:0,0:33.5:1:28.1:1:1:0:56.8:16:0.5:0:1.1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:6:0:30:0:1:0:60:2:0.5:0:2 +21 36971853 . G A 122 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04101;SOR=0.12689;LSEQ=CCCTGATCCTCGGTCAGAGC;RSEQ=AGCGCTTAGGTTCCCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:15,0:24,0:24,15:0.3846:1,1:20.2:1:31.3:1:1:0:60:30:0.3846:0:1.1 0/1:14:1:1,0:13,0:13,1:0.0714:1,0:33:0:26:0:1:0:60:2:0.0714:0:2 +21 36971941 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.15472;SOR=Inf;LSEQ=CCTGGGAGTCCACGACAACT;RSEQ=AAAAAACTCAAAACTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:149,6:155,0:0:1,0:22.3:1:32.7:1:1:0:59.8:50.667:1:0:0.1 0/1:101:2:1,1:95,4:99,2:0.0198:1,2:13:1:27:1:0.09703:21.35426:60:4:0.0202:0:2 +21 36972001 . A AGAG 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0;SOR=0.37463;LSEQ=AGCTGAGGCAGCTGTTTCAG;RSEQ=GAGGAGGAGGAGGAGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:171:100,71:224,120:344,171:0.3308:2,2:27.8:1:31.9:1:0.14739:1.32457:59.8:170:0.3386:0.0464:0.1 0/1:378:59:39,20:182,134:316,59:0.1561:2,2:30.8:1:30.4:1:0.25048:1.43:59.9:118:0.1582:0:0.2 +21 36972392 . A G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00084;SOR=0.26479;LSEQ=GTTTGAAATTCTGAATTTGC;RSEQ=AAGTACTATAAGAATAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:38:0,38:1,33:34,38:0.5278:1,1:24.5:1:32.9:1:0.47222:0:39.2:76:0.5352:0:1.1 0/1:53:12:0,12:1,40:41,12:0.2264:1,0:14.9:1:30.9:1:1:0:34.9:24:0.2264:0:1 +21 36972552 . A AG 34 v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAAATTGAAAAAAAAA;RSEQ=TTGAGTCTGATGGGTCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:27:0:34.5:1:0.33333:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 36972695 . A C 35 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTGCAGAAGTGTATCTG;RSEQ=TTAACTCTTGACAACTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:28:1:35:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 37555326 . C G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCACTGTAGGATGTTTT;RSEQ=TTTTGTTTAAGAGGCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:33.5:1:1:0:60:4:1:0:1.5 +21 37557225 . A T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07;SOR=Inf;LSEQ=AGGAGTTAACATCTCATTTC;RSEQ=TTAGAGCATGCCAGTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:18,0:18,0:0:1,0:28.9:1:31.6:1:1:0:60:36:1:0:0 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:17:1:32:0:1:0:60:4:0.2857:0:1 +21 37557351 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50377;SOR=0;LSEQ=GTCCCGAAGGCGTTCTTCCT;RSEQ=TTCTTCTGTCTCTGACTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:130,63:193,2:0.0103:2,2:25:1:27.5:1:0.54983:2.05522:60:4:0.0103:0:1 0/0:159:0:0,0:118,41:159,0:0:2,0:22:1:29.8:1:1:0:60:78.5:1:0:0.1 +21 37557420 . G A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35392;SOR=3.28222;LSEQ=GTTTGTTAAACAGATCATTT;RSEQ=TATGTGCAATAAAATATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:1,0:137,171:308,1:0.0032:2,0:1:0:27:0:0.4466:0:60:2:0.0033:0:1 0/1:284:3:2,1:132,149:281,3:0.0106:2,2:18.3:1:26.3:1:0.60359:2.25:60:6:0.0106:0:1 +21 37557425 . T A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24991;SOR=0;LSEQ=TTAAACAGATCATTTGTATG;RSEQ=GCAATAAAATATGTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:127,166:293,3:0.0101:2,2:17.3:1:24.3:1:0.5821:2.61:60:2:0.0069:0:1 0/0:273:0:0,0:122,151:273,0:0:2,0:25.6:1:28.9:1:1:0:60:67.25:1:0:0.3 +21 37557447 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23063;SOR=Inf;LSEQ=CAATAAAATATGTTTAAAAA;RSEQ=TAGAAAAATAACATCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:85,132:217,0:0:2,0:25.1:1:30.4:1:1:0:59.9:71.333:1:0:0.4 0/1:201:2:1,1:70,129:199,2:0.01:2,2:40.5:1:28.5:1:1:1.84:57.5:4:0.0101:0:3 +21 37557474 . T C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=0.32466;LSEQ=AATAACATCTCCCGATACTA;RSEQ=GTTATTTTATATTTTTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:49:20,29:30,71:101,49:0.2882:2,2:21.2:1:30.3:1:0.19862:1.63:60:48:0.2892:0:1 0/1:164:19:4,15:45,62:107,19:0.1159:2,2:13.2:1:29.3:1:0.12444:2.70216:60:38:0.1159:0:1.1 +21 37557492 . A T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=2.91209;LSEQ=TATGTTATTTTATATTTTTA;RSEQ=TGGTATGATTACTTTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:20:6,14:40,83:123,20:0.1399:2,2:21.9:1:31:1:1:1.12361:59.8:40:0.1408:0:2.2 0/1:149:48:16,32:40,61:101,48:0.3221:2,2:18.1:1:29.5:1:0.47641:1.30911:59.9:96:0.3265:0:1.9 +21 37558998 . C T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGGCTTTGCAGGGCGCTGG;RSEQ=GGACCTGAAATACTCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:7:0:33.5:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:30.5:1:1:0:60:4:1:0:1 +21 37954473 . A G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18502;SOR=4.36956;LSEQ=GGAAAGGATGGAGAACAGAT;RSEQ=TCAAAGGCTGACATAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:12,1:13,7:0.35:1,0:17.6:1:33.4:1:1:0:60:14:0.35:0:1 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:34.8:1:31.2:1:1:0:60:10:0.7143:0:1 +21 37954502 . G GA 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.02761;SOR=4.84794;LSEQ=TGACATAGATTTTCTGAGCA;RSEQ=AAAAAATAAGGTAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:16:16,0:23,1:24,16:0.4:1,1:25.2:1:31.2:1:1:0:60:32:0.4:0.1:0.4 1/0:13:10:10,0:3,0:3,10:0.7692:0,0:19.4:1:28.1:1:1:0:60:20:0.7692:0.1538:0.6 +21 37954611 . G A 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=TGGCCCCTGCACAAGGACTC;RSEQ=TTCCATGAGGCAGCGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:180,54:234,0:0:2,0:21.8:1:30:1:1:0:60:116:1:0:0.9 0/1:159:9:7,2:111,39:150,9:0.0566:2,2:32.9:1:27.3:1:1:1.23:60:8:0.0506:0:2 +21 37954652 . C T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=0.05635;LSEQ=GCCCACATGTGTACAGTTGA;RSEQ=TTCCACCGATTGTTCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:416:415:248,167:1,0:1,415:0.9976:0,2:26:1:30.5:1:1:0:60:68.167:1:0:1.3 1/1:365:350:213,137:8,6:14,350:0.9589:2,2:25.6:1:29.8:1:0.78629:1.17:60:86.5:0.9584:0:1.4 +21 37954722 . A T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.13032;LSEQ=TGACACAAGTTCTATCTCCA;RSEQ=CAAACCAGCTGTCAGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:201:80,121:145,178:323,201:0.3829:2,2:25.5:1:30.1:1:0.27647:1.2316:59.9:66:0.386:0:1.5 1/0:504:287:139,148:95,122:217,287:0.5694:2,2:26.9:1:28.8:1:0.32166:1.21:60:56.4:0.5663:0:1.5 +21 37954734 . T A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06191;SOR=0;LSEQ=TATCTCCAACAAACCAGCTG;RSEQ=CAGGAAATGGTCTCAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:5:3,2:188,273:461,5:0.0107:2,2:32.4:1:27.4:1:0.40445:2.17:60:10:0.011:0:1.6 0/0:455:0:0,0:209,246:455,0:0:2,0:26.5:1:28.4:1:1:0:60:64:1:0:0.9 +21 37954773 . C A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25129;SOR=0;LSEQ=CTCCAAGAACAGAAACTTCT;RSEQ=TTGACAGTGCATTCTGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:85,207:292,3:0.0102:2,2:13:1:21:1:0.20875:4.84:60:2:0.007:0:2 0/0:262:0:0,0:86,176:262,0:0:2,0:21.8:1:31:1:1:0:60:130:1:0:0.5 +21 37954982 . T C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52797;SOR=0;LSEQ=ATCATAAAAAACCTGCCCCA;RSEQ=TCCCCCACAACCCTTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:7,3:0.3:0,0:27:1:32:1:1:0:60:6:0.3:0:1.7 0/0:3:0:0,0:1,2:3,0:0:2,0:18.7:1:31.3:1:1:0:60:6:1:0:0.3 +21 37954987 . C A 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.52273;SOR=0.28305;LSEQ=AAAAAACCTGCCCCATTCCC;RSEQ=CACAACCCTTTCCCAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:3,6:0.6667:0,0:35.7:1:28.2:1:1:0:60:5:0.625:0:1.3 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:5:0:28:0:1:0:60:2:0.3333:0:1 +21 37955122 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTGGAGACAGAGTGGC;RSEQ=TCCTGGGCCCCGAATAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:45.5:1:34:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 37955134 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGGCTTCCTGGGCCCC;RSEQ=AATAACCTTTGGGGGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:30:1:30.7:1:1:0:51.7:6:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 37955163 . C T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGGGGCCTGCCTGATGAC;RSEQ=CTCCACAGCAACCATGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:30.7:1:1:0:51.7:6:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 37955178 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGACCCTCCACAGCAACCA;RSEQ=GTGGATTCTGGTACTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24:1:30.5:1:1:0:47.5:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 39625613 . A AT 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.56855;SOR=0;LSEQ=AGGATTGGAAACATTATAGC;RSEQ=TTTTTTTTTCTTTTTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:4:4,0:61,0:61,4:0.0615:1,0:35:1:30.8:1:1:0:59.5:8:0.0635:0:1.5 0/0:20:0:0,0:20,0:20,0:0:1,0:19.6:1:29:1:1:0:60:40:1:0:0.2 +21 39625779 . C A 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.60773;LSEQ=GACACAACTAAGAGTCTTTC;RSEQ=GTTAACTGTGGAGGTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:705:514:268,246:90,98:188,514:0.7291:2,2:26.7:1:30.8:1:0.34849:1.19:59.9:56.111:0.7298:0:1.2 1/0:606:376:195,181:125,105:230,376:0.6205:2,2:25:1:29.2:1:0.55848:1.10482:59.9:33.182:0.6166:0:1.1 +21 39625891 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19634;SOR=Inf;LSEQ=GGTCAGTAAAATTAACCATG;RSEQ=TCAATTATGAAATGATTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:21,186:207,0:0:2,0:23.8:1:30.3:1:1:0:59.8:68:0.9951:0:0.1 0/1:166:2:1,1:21,143:164,2:0.012:2,2:26:1:30:1:0.24819:6.68:60:4:0.0122:0:1 +21 39627712 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGCACTTGGGGTGAATTGC;RSEQ=GAGCCCAGTACTCTGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:31:0:1:0:60:4:1:0:1 +21 39739136 . A G 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGCGATGTACTAGGTTAG;RSEQ=CAGAAGTCACAGGCCGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:18:1:30.3:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 39739478 . A G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00437;SOR=0.56655;LSEQ=GAATAAGTGATGCAAAGAGA;RSEQ=GGCCACGCTGCCTTCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:121:93,28:154,34:188,121:0.3916:2,2:25.8:1:32.6:1:0.30947:1.36226:60:120:0.3896:0:1 0/1:206:55:40,15:104,47:151,55:0.267:2,2:22.8:1:30.9:1:0.73154:1.20:60:54:0.2634:0:1 +21 39739665 . T A 242 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08381;LSEQ=AGACAGAATTCTGCACAGAC;RSEQ=TTCATCAACAATAACTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:239:232:45,187:1,6:7,232:0.9707:2,2:23.1:1:30.8:1:1:1.44:59.9:45.4:0.9701:0:1.1 1/0:173:127:29,98:9,37:46,127:0.7341:2,2:19.9:1:29.4:1:0.83553:1.22:60:126:0.7368:0:1.1 +21 39740158 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTCCCTTGCTTTTCCTC;RSEQ=TTTTTTTGTTTGTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26.5:1:30.5:1:1:0:54.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 39755227 . T C 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27803;SOR=0;LSEQ=CAGCCCCAGTAAAGCTTTTT;RSEQ=CATTCCTCTTGAGGCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:2,1:230,23:253,3:0.0117:2,2:17.7:1:26.7:1:0.25661:4.94406:60:2:0.008:0:1 0/0:171:0:0,0:151,20:171,0:0:2,0:21.2:1:30.3:1:1:0:60:170:1:0:0.1 +21 39755976 . T A 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13002;SOR=0;LSEQ=TCACCAGGCCTGTCCGTCCA;RSEQ=CCCTCAGCTGCAGGGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:0,7:0,11:11,7:0.3889:0,0:33.1:1:29.6:1:1:0:60:14:0.4118:0:1 0/0:6:0:0,0:1,5:6,0:0:2,0:33.8:1:27.7:1:1:0:60:5:1:0:0 +21 39762883 . T C 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.33797;LSEQ=TAACCACTGCCAAAAAGTAA;RSEQ=TTTGTAAGAAGAAAATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:121:87,34:282,149:431,121:0.2192:2,2:25.6:1:32.7:1:0.19146:1.35:60:242:0.2208:0:1.1 0/1:462:40:22,18:262,160:422,40:0.0866:2,2:25.3:1:31.1:1:0.39858:1.33887:60:80:0.0879:0:1.1 +21 39763354 . C A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26568;SOR=0.3615;LSEQ=AAAGAAGCAGCCTGTGTGCA;RSEQ=GTAGAATTTTTTTCCCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:19:19,0:8,0:8,19:0.7037:0,1:19.6:1:30.8:1:1:0:60:38:0.7037:0:1.1 0/1:11:5:4,1:6,0:6,5:0.4545:0,2:19.6:1:31.2:1:0.45455:0:60:10:0.5:0:1 +21 39764016 . A T 82 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATGGCCAAGATTCAGGAAA;RSEQ=CACCGATTATTTAATGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:3,4:6,1:7,7:0.5:2,2:30:1:29.4:1:0.26573:6.78852:58:14:0.5385:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 39764211 . T A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00028;SOR=0.44378;LSEQ=ACATGTTGCAAAATCACAGA;RSEQ=TAACCACAGAAATTATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:194:119:108,11:65,10:75,119:0.6134:2,2:24.5:1:30.4:1:0.47723:1.51:60:38.667:0.6073:0:1.1 0/1:143:59:52,7:74,10:84,59:0.4126:2,2:23.3:1:29.7:1:1:1.00:60:118:0.4126:0:1.1 +21 39764222 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17818;SOR=Inf;LSEQ=AATCACAGATTAACCACAGA;RSEQ=ATTATTATATACTCCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:198,45:243,0:0:2,0:23.6:1:30.4:1:1:0:60:80:1:0:0.5 0/1:178:2:1,1:136,40:176,2:0.0112:2,2:19:1:27:1:0.40862:3.37054:60:4:0.0114:0:1.5 +21 39764366 . T A 47 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05989;SOR=Inf;LSEQ=TGGGGGGCTCATATGGTAAA;RSEQ=CTGTAAAGACAAATAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:129,276:405,0:0:2,0:24.6:1:30.6:1:1:0:59.9:404:1:0:0.2 0/1:398:4:3,1:145,249:394,4:0.0101:2,2:7.3:1:23.8:1:0.14715:5.13:60:3:0.0077:0:1 +21 39764401 . C G 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=3e-04;SOR=Inf;LSEQ=AAATTGACTAAAAGATCAAT;RSEQ=ATGTAATTTTTATAAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:53,183:236,0:0:2,0:23.2:1:32.3:1:1:0:59.9:117:0.9957:0:0.3 0/1:223:11:4,7:54,158:212,11:0.0493:2,2:23.7:1:30.7:1:0.48232:1.67:60:22:0.0505:0:1.5 +21 39764437 . T C 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01631;SOR=0.48678;LSEQ=GAGATGCTTTGGTTTTTTAT;RSEQ=TGATTTTGTATTTATTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:55:6,49:9,42:51,55:0.5189:2,2:21.8:1:33.5:1:0.40667:1.74076:60:110:0.5189:0:1.1 0/1:99:34:1,33:8,57:65,34:0.3434:2,1:26.6:1:30.7:1:0.15872:4.57777:60:33:0.3367:0:1.2 +21 39764588 . G A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.375;SOR=0;LSEQ=TTGTCTGAAAACTTCCATTG;RSEQ=CAGATTCTCCCAGAGCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:12.8:1:27.2:1:1:0:60:10:0.7143:0:1.2 0/0:1:0:0,0:0,1:1,0:0:0,0:20:0:33:0:1:0:60:2:1:0:0 +21 39772561 . G A 57 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09035;SOR=6.642;LSEQ=TATTTGGGAAAATAAAAGCT;RSEQ=CACCCCCTGCAGACAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:1:1,0:193,439:632,1:0.0016:2,0:1:0:24:0:0.30648:0:60:2:0.0016:0:1 0/1:480:5:4,1:183,292:475,5:0.0104:2,2:7.4:1:24.8:1:0.07819:6.36:60:10:0.0105:0:1 +21 39774197 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGAAGACTGTAATCCGG;RSEQ=AAATGTGAGCTAAGTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:16,0:16,2:0.1111:1,2:32.5:1:32:0:0.11111:0:60:4:0.1111:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:15:1:33:0:1:0:60:4:1:0:0 +21 39774348 . C G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76118;SOR=1.12269;LSEQ=GTGGTACATTCCTAAGTATC;RSEQ=GAAAGTATTCTGAATCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:40:39,1:65,1:66,40:0.3774:1,1:22:1:30.6:1:1:1.65824:60:80:0.3774:0:1.2 0/1:79:32:31,1:46,0:46,32:0.4051:1,1:22.1:1:29.8:1:0.41026:0:60:64:0.4103:0:1.3 +21 39774592 . G GA 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.10304;SOR=1.68007;LSEQ=ACAAAAAGCGACATCAAAAT;RSEQ=AAAAAAAAAAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:19:3,16:86,252:338,19:0.0522:2,2:28.8:1:31.6:1:0.42541:1.8175:59.7:38:0.0581:0:0.7 0/1:354:30:9,21:93,222:315,30:0.0847:2,2:33.4:1:29.6:1:1:1.02:58.5:60:0.0935:0:0.5 +21 39774601 . AAG A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.06172;SOR=Inf;LSEQ=GACATCAAAATGAAAAAAAA;RSEQ=AGAGAGAGAGAAAGAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:51,248:299,0:0:2,0:20.6:1:31.4:1:1:0:58.1:28.9:1:0:0.6 0/1:313:5:1,4:69,239:308,5:0.016:2,2:21.6:1:29.5:1:1:1.1543:54:10:0.0162:0.0032:1.2 +21 39774632 . T TA 66 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2978;SOR=0.39136;LSEQ=AGAAAGAGAATTACCTTTCT;RSEQ=ACAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:6:0,6:6,112:118,6:0.0462:2,0:31.3:1:25.7:1:1:0:36.5:5:0.0463:0.0077:2.3 0/1:108:2:0,2:5,100:105,2:0.0185:1,0:36:1:18:1:1:0:60:1:0.0128:0:1.5 +21 39774634 . C AAA 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.25327;SOR=0;LSEQ=AAAGAGAATTACCTTTCTTA;RSEQ=AAAAAAAAAAAAAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:3:0,3:6,112:118,3:0.0231:2,0:28:1:22.4:1:1:0:33:6:0.0278:0:4 0/0:108:0:0,0:5,100:105,0:0:1,0:18.7:1:23.8:1:1:0:54:2.75:0.9872:0:1.3 +21 39774658 . G A 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09293;SOR=Inf;LSEQ=AAAAAAAAAAAAAAAAGAAA;RSEQ=AAAAAGAAAGAAAGAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:1,63:64,0:0:1,0:23.5:1:32:1:1:0:49.4:128:1:0:1.8 0/1:54:3:1,2:0,51:51,3:0.0556:1,2:12.3:1:24.7:1:0.05556:0:48.3:2:0.0385:0:3.3 +21 39774660 . A G 32 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.21454;SOR=Inf;LSEQ=AAAAAAAAAAAAAAGAAAGA;RSEQ=AAAGAAAGAAAGAAAACCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:1,61:62,0:0:1,0:24:1:31.1:1:1:0:49.9:124:1:0:1.7 0/1:54:2:0,2:1,51:52,2:0.037:1,0:7.5:1:32.5:1:1:0:42.5:4:0.037:0:3.5 +21 39775373 . A G 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTTGAACCCTCTGAAGCTC;RSEQ=GGTCATAAGAACCATAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:232:232:200,32:0,0:0,232:1:0,2:21.5:1:29.9:1:1:0:60:37.667:1:0:1.1 1/0:145:106:92,14:33,6:39,106:0.731:2,2:22.1:1:29.9:1:0.78754:1.19:60:212:0.731:0:1.1 +21 39775417 . G T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09372;SOR=6.31732;LSEQ=CCATCTATCCTTGGAGGAAG;RSEQ=GGGAGCTTACTCTCTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:1:1,0:367,133:500,1:0.002:2,0:13:0:32:0:1:0:60:2:0.002:0:1 0/1:400:5:1,4:266,129:395,5:0.0125:2,2:9.4:1:25.6:1:0.04383:8.20368:60:10:0.0127:0:1.2 +21 39775468 . G A 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGAGAGAAGGATGTCGGC;RSEQ=TTGTAGCTGGGGGTGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:885:0:0,0:513,371:884,0:0:2,0:24.2:1:30.4:1:1:0:59.9:39.182:1:0:0.2 0/1:881:34:20,14:459,388:847,34:0.0386:2,2:26.6:1:29.9:1:0.72601:1.21:60:68:0.0389:0:1.3 +21 39775626 . T A 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00884;SOR=Inf;LSEQ=ATGGTCTGTACTCCATAGCG;RSEQ=AGGATCTGAAAGGGGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:145,310:455,0:0:2,0:24.2:1:29:1:1:0:60:226.5:1:0:0.1 0/1:382:6:5,1:130,246:376,6:0.0157:2,2:10:1:22:1:0.02245:9.41:60:2:0.0106:0:1.7 +21 39794880 . T G 69 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACAATAATCTCCAAGAAG;RSEQ=GGCAATTCCTCCCTAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:24:1:29.8:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 39795170 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06198;SOR=Inf;LSEQ=TGCTGTCGATCCGTGAACAT;RSEQ=TCCTCATGCATAGACCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:92,0:92,0:0:1,0:26.1:1:33.1:1:1:0:60:91:1:0:0.5 0/1:31:2:2,0:28,1:29,2:0.0645:1,0:22.5:1:32.5:1:1:0:47:4:0.069:0:1 +21 39795202 . T G 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45097;SOR=0.78102;LSEQ=AGACCTCTGCCAGCTCCCAT;RSEQ=TACAAGCCCTGCTCTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:57:55,2:87,0:87,57:0.3958:1,1:23.9:1:32.6:1:0.15501:0:60:114:0.3986:0:1.1 0/1:68:23:22,1:44,1:45,23:0.3382:1,1:29:1:31.8:1:1:1.9782:60:22:0.3284:0:1.2 +21 39795217 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATTTACAAGCCCTGCTC;RSEQ=GGACAAAGGAGATGTGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:164,3:167,2:0.0118:1,2:27:1:30:1:0.04691:47.48808:60:4:0.012:0:2 0/0:84:0:0,0:82,2:84,0:0:1,0:25.1:1:30.6:1:1:0:59.7:41:1:0:0.4 +21 39795279 . A T 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCTCCCTGAGGCTCAGCCT;RSEQ=GCCTTGGGGAAGTTGCGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:35:27,8:361,93:454,35:0.0716:2,2:21.6:1:31.6:1:0.67112:1.14977:60:70:0.0725:0:1.1 0/0:359:0:0,0:275,84:359,0:0:2,0:22.5:1:28:1:1:0:60:118.667:1:0:0.1 +21 39817064 . TTT C 49 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=17;MSI=19.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TTTCTTTCTTTCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTGTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,0:1,3:0.6:0,0:18:1:31.2:1:1:0:52.7:6:0.75:0.4:0.7 0/0:2:0:0,0:1,0:1,0:0:0,0:39:0:33:0:1:0:28:2:0.5:0:2 +21 39817598 . T A 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10665;SOR=Inf;LSEQ=CTCCAACAGACAGTCATGTT;RSEQ=CAAAAAGTTGTTGATTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:56,250:306,0:0:2,0:23.7:1:30:1:1:0:60:42.714:1:0:0.1 0/1:277:3:2,1:66,208:274,3:0.0108:2,2:12.3:1:24.7:1:0.15017:6.25:60:6:0.0109:0:1 +21 39818701 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CCAGTCCAAACTTGTCATCT;RSEQ=CAAATGAGAAATCTGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:18:1:31.8:1:1:0:60:8:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:27.5:1:1:0:60:4:1:0:1 +21 39870310 . G A 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=4.82778;LSEQ=AATAGTGCTGGCCATAATGC;RSEQ=ATCAAGTTTATTGATCGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:734:527:213,314:83,122:205,527:0.718:2,2:23.8:1:30.7:1:1:1.00292:59.9:57.556:0.7225:0:1.1 1/1:612:566:244,322:21,25:46,566:0.9248:2,2:24:1:29.5:1:0.75878:1.10834:59.9:55.6:0.9236:0:1.1 +21 39947487 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17187;SOR=Inf;LSEQ=TTTCTTAGCTCCTGGGCTGT;RSEQ=TTGACTGACCCCTAATTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:220,25:245,0:0:2,0:23.8:1:32.5:1:1:0:60:80.667:1:0:0.1 0/1:174:2:1,1:143,29:172,2:0.0115:2,2:7:1:26:1:0.31593:4.86516:60:4:0.0118:0:2.5 +21 39947697 . A G 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=AGACAAAAGGAACAACATAC;RSEQ=TAATAATAAACAACTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:0:0,0:77,294:371,0:0:2,0:22.2:1:31.1:1:1:0:60:122.667:1:0:0.1 0/1:250:25:7,18:64,161:225,25:0.1:2,2:23.3:1:30.2:1:1:1.02209:60:50:0.102:0:1 +21 39947747 . C A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.94012;LSEQ=TATGTTCTAGCAGGACAGGA;RSEQ=ACAATTCACCAATGGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:7:1,6:2,123:125,7:0.053:1,2:30.7:1:30.6:1:0.1519:9.80:60:6:0.0462:0:1 0/1:80:4:0,4:3,73:76,4:0.05:1,0:33.5:1:28:1:1:0:60:3:0.038:0:1 +21 41326462 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49893;SOR=Inf;LSEQ=CACGTAACCTTCACAAAGAC;RSEQ=AGCTGATTGACTAATGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:149,43:192,0:0:2,0:22.8:1:31.4:1:1:0:60:63:1:0:0.1 0/1:200:2:1,1:144,54:198,2:0.01:2,2:22.5:1:27:1:0.47538:2.65147:60:4:0.0101:0:1 +21 41326577 . G A 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.24729;LSEQ=AAGACTATCTACGGTAGGTC;RSEQ=TTAAGCAGCCAATGATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:569:484:235,249:37,48:85,484:0.8506:2,2:24.7:1:30.8:1:0.41189:1.22:60:241:0.8531:0:1.3 1/0:539:315:150,165:102,122:224,315:0.5844:2,2:25.4:1:29.7:1:0.66186:1.09:59.9:630:0.5877:0:1.2 +21 41326640 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11587;SOR=Inf;LSEQ=ATGTGCCACTTTGTTTTGCA;RSEQ=GATGCAGCAGGCCGACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:98,208:306,0:0:2,0:23.5:1:31.9:1:1:0:60:152:0.9967:0:1.1 0/1:294:3:1,2:103,188:291,3:0.0102:2,2:30:1:30.7:1:1:1.09542:60:6:0.0104:0:1.3 +21 41326645 . C T 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.10699;SOR=Inf;LSEQ=CCACTTTGTTTTGCAGGATG;RSEQ=AGCAGGCCGACAGTCATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:88,203:291,0:0:2,0:22.4:1:32.2:1:1:0:60:71.75:1:0:1.2 0/1:264:3:1,2:86,173:259,3:0.0114:2,2:7.3:1:27.3:1:1:1.01:60:6:0.0114:0:2 +21 41326658 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05005;LSEQ=CAGGATGCAGCAGGCCGACA;RSEQ=TCATAGGCGGCCTGTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:216:186:47,139:5,25:30,186:0.8611:2,2:23.2:1:30.4:1:0.36506:1.69:60:30:0.8612:0:1.4 0/1:200:47:12,35:41,112:153,47:0.235:2,2:21.5:1:30.1:1:1:1.06737:60:94:0.2362:0:1.4 +21 41326917 . T A 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGAGGAAGGGCCAGAAAC;RSEQ=CATGGAAAGCTCTAGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21:1:30.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:43:0:29:0:1:0:60:2:1:0:1 +21 41918860 . G T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22745;SOR=Inf;LSEQ=GCTGGGGTGGGAGCCTGGAG;RSEQ=ATCCTTTCTAAAGGCTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:129,24:153,0:0:2,0:24.7:1:31.4:1:1:0:59.8:152:1:0:0.1 0/1:140:2:1,1:102,36:138,2:0.0143:2,2:14:0:28:1:0.46012:2.80845:60:4:0.0146:0:1.5 +21 41918958 . A G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15536;LSEQ=AACCCCATCCAAATCCCCTC;RSEQ=TAACATCAAGCAGAGCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:466:256:135,121:103,107:210,256:0.5494:2,2:26.2:1:31:1:0.45679:1.16:60:255:0.5519:0:1.1 0/1:453:72:32,40:197,184:381,72:0.1589:2,2:26.4:1:30:1:0.30405:1.33745:60:35:0.1563:0:1.3 +21 41919040 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08015;SOR=Inf;LSEQ=CCTCACCGTCCTCTCTGTCC;RSEQ=CAACCCTGTCTATCCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:54,165:219,0:0:2,0:23.7:1:31.1:1:1:0:60:53.75:1:0:0.3 0/1:167:3:2,1:46,118:164,3:0.018:2,2:25:1:27:1:0.19876:5.07:60:6:0.0185:0:1 +21 41936517 . C G 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGCCTGGATCCTGCCAAC;RSEQ=CTGCCTCCTACAAAAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:16,19:0,0:0,35:1:0,2:27.5:1:31.5:1:1:0:60:70:1:0:1.1 1/1:7:7:4,3:0,0:0,7:1:0,2:18.1:1:28.9:1:1:0:60:14:1:0:1 +21 41936617 . T C 61 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTAAATGGAATGAGCACG;RSEQ=GAAACGGGAACCTGCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:22.8:1:30.8:1:1:0:60:8:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:32:0:1:0:60:4:1:0:1 +21 42461865 . A AG 55 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACTCCAGTGTCAGATGCT;RSEQ=TTCAGTGCCCTGATAAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:30.3:1:35:0:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42462100 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32988;LSEQ=CATTTGTGACCTGGAGGGTC;RSEQ=CTTAATGCTTTTGGCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:195:127,68:31,21:52,195:0.7895:2,2:26.3:1:30.6:1:0.51638:1.26:59.9:390:0.8025:0:1.2 1/0:248:137:87,50:70,40:110,137:0.5524:2,2:24.9:1:29.5:1:1:1.00572:60:136:0.5528:0:1.3 +21 42462148 . G T 52 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06169;SOR=Inf;LSEQ=CCAATGTTTGGAAAACCCTT;RSEQ=TTCTTTCATCATCATGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:164,172:336,0:0:2,0:26.3:1:32:1:1:0:59.9:83:0.997:0:1 0/1:346:5:1,4:164,177:341,5:0.0145:2,2:29.2:1:22.6:1:0.37406:3.69391:60:1.5:0.0088:0:2.2 +21 42462188 . A G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29794;LSEQ=TGTCACAACTAGTCATGGAC;RSEQ=TGTGTCTACCCCATCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:305:234:87,147:26,45:71,234:0.7672:2,2:25.9:1:31.3:1:1:1.02:59.9:233:0.769:0:1.8 0/1:295:146:55,91:70,78:148,146:0.4949:2,2:22.5:1:30.3:1:0.10013:1.48281:59.8:145:0.4966:0:1.9 +21 42462244 . C T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.22733;LSEQ=ACAGCCTCAGTGTGGAGTTC;RSEQ=CAGAGAGCTCTCCCTATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:122:30,92:9,24:33,122:0.7871:2,2:24.4:1:30.7:1:0.82177:1.14893:59.8:121:0.7857:0:2.6 0/1:134:61:17,44:22,51:73,61:0.4552:2,2:22.5:1:29.4:1:0.8495:1.11558:60:29.5:0.4538:0:2.6 +21 42462249 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50345;SOR=0;LSEQ=CTCAGTGTGGAGTTCCCAGA;RSEQ=AGCTCTCCCTATAAGACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:30,112:142,2:0.0139:2,2:19:1:28:1:0.38539:3.69:60:4:0.0139:0:4 0/0:117:0:0,0:32,85:117,0:0:2,0:23.2:1:30.7:1:1:0:59.9:57.5:1:0:1.4 +21 42462253 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.2167;LSEQ=GTGTGGAGTTCCCAGAGAGC;RSEQ=CTCCCTATAAGACTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:133:106:18,88:7,20:27,106:0.797:2,2:24.1:1:31.2:1:0.28284:1.70345:59.8:52:0.7939:0:2.6 0/1:107:49:13,36:14,43:57,49:0.4579:2,2:20.8:1:30.8:1:0.82705:1.11:59.8:98:0.4667:0:2.8 +21 42462562 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTCAAACCTGACTTCGTA;RSEQ=CCATTAAGTATCTCAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:26:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42837800 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATCTCAATGGGGCAGCC;RSEQ=CCACCCCTCTCCTCCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:17,2:0.1053:1,0:13.5:1:31.5:1:1:0:60:4:0.1053:0:1.5 0/0:3:0:0,0:3,0:3,0:0:0,0:19.3:1:31.7:1:1:0:60:6:1:0:0.7 +21 42837848 . C T 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=CAGTGCCCACAACCAGCCGG;RSEQ=CATCACCCCTTGCGGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:41,0:41,0:0:1,0:22.7:1:31.4:1:1:0:60:12.667:1:0:0.1 0/1:28:8:8,0:19,1:20,8:0.2857:1,0:27.9:1:29.6:1:1:0:60:16:0.2857:0:1 +21 42838093 . G GA 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.159;SOR=1.4569;LSEQ=CCGTCTGCCTGTTCAAATAG;RSEQ=AAAAAAAAAAGTGTGTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:27:11,16:196,419:615,27:0.0417:2,2:28.5:1:30.3:1:0.40005:1.47:59.3:54:0.0432:0.0046:0.3 0/1:620:37:15,22:210,370:580,37:0.0597:2,2:28.1:1:29.2:1:0.60085:1.20:59.5:36:0.0598:0.0065:0.5 +21 42838138 . A T 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAGACAAACAAAGGTGGAA;RSEQ=ATAATTTTTTCCTCTAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:26,227:253,0:0:2,0:21.6:1:31:1:1:0:59.9:125.5:1:0:0.1 0/1:253:31:8,23:37,185:222,31:0.1225:2,2:19.5:1:27.4:1:0.21523:1.73:60:14.5:0.116:0:1.4 +21 42838198 . G A 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=CCAAATAAGCAAGCTTAATA;RSEQ=CACAAAGGGATCATTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:1,74:75,0:0:1,0:21.8:1:32.9:1:1:0:60:74:1:0:0 0/1:52:9:0,9:1,42:43,9:0.1731:1,0:26:1:29.7:1:1:0:60:18:0.18:0:1.8 +21 42839299 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCACTCCAGCCTGGGCGACA;RSEQ=AGTGAGACTCCATCTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:8.5:1:31.5:1:1:0:25:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42839603 . G T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.03904;SOR=Inf;LSEQ=CAGAACCACGCCTAACAGAT;RSEQ=TCTGGCTTTGGCTCGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:335,137:472,0:0:2,0:23.3:1:31.8:1:1:0:60:66.429:1:0:0.1 0/1:380:4:2,2:239,137:376,4:0.0105:2,2:10.8:1:26:1:0.62551:1.74175:60:8:0.0106:0:1 +21 42839859 . T A 42 v3;q25;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07404;SOR=6.52401;LSEQ=AGCAGAAAATCAAGTCACAA;RSEQ=CTGCCGCACACCACTGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:1,0:49,231:280,1:0.0036:2,0:1:0:25:0:0.17794:0:60:2:0.0036:0:1 0/1:175:4:4,0:28,143:171,4:0.0229:2,0:11:1:21.3:1:0.00095:0:60:3:0.0176:0:1.3 +21 42840580 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02193;SOR=0;LSEQ=CAGATGGTCACAGCCCTATT;RSEQ=TCCAGCCCTGCCCCGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:72:0,72:0,0:0,72:1:0,1:21.3:1:33.9:1:1:0:59.8:144:1:0:1.8 1/1:29:26:1,25:1,2:3,26:0.8966:2,1:23.8:1:32:1:0.19951:10.40842:60:52:0.8966:0:1.8 +21 42840595 . G C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28;SOR=0;LSEQ=CTATTTTCCAGCCCTGCCCC;RSEQ=GTCAGCTCATCCCAGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:0,54:0,0:0,54:1:0,1:18.4:1:30.3:1:1:0:59.7:108:1:0:2 1/1:21:20:1,19:0,1:1,20:0.9524:0,1:21.8:1:30.4:1:1:0:60:40:0.9524:0:2.1 +21 42842203 . T C 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCACCATGGGTCCAGGA;RSEQ=GCCCGTCCTCACCAAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:20:1:34:0:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42842591 . C T 153 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.06689;LSEQ=TCACCTTTCTCCTCGGTGGC;RSEQ=CCCCACCCGGAAATCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:33:19,14:529,423:952,33:0.0334:2,2:25.9:1:30.5:1:0.86035:1.09:60:32:0.0331:0:1.2 0/0:868:2:1,1:475,391:866,2:0.0023:2,2:22:1:27:1:1:1.21456:60:4:0.0023:0:1 +21 42842713 . C CCTAAGGCCTCGGG 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08378;LSEQ=AGTGAGCCAGGCGGGTATCA;RSEQ=CTATGTCTCCACCTGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:694:643:215,428:20,26:46,643:0.9265:2,2:22.7:1:30.8:1:0.19735:1.53036:59.5:213.333:0.9249:0.4193:0.2 1/0:495:254:65,189:103,134:237,254:0.5131:2,2:32:1:29.9:1:4e-05:2.23128:59.8:253:0.5195:0.0404:0.1 +21 42842771 . C G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=0.30388;LSEQ=GGGCCTGGCACCCTGGCCAC;RSEQ=CTGCCCAGAGGACCCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:74:1,73:3,97:100,74:0.4253:1,1:25.8:1:31.7:1:0.63757:2.24818:59.8:17.5:0.4167:0:1.5 0/1:82:15:0,15:0,67:67,15:0.1829:1,1:24.3:1:32.3:1:1:0:60:30:0.1923:0:1.2 +21 42842834 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14;SOR=0;LSEQ=CTTTCTCCCCCTGCCAGACC;RSEQ=CTCCTTCTGGCAGGCAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:86:86:0,86:0,0:0,86:1:0,1:25.6:1:31:1:1:0:60:27.667:1:0:1.9 1/1:14:13:0,13:0,1:1,13:0.9286:0,1:16.1:1:31.6:1:1:0:60:26:0.9286:0:1.5 +21 42842854 . C A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07463;SOR=0;LSEQ=TCTCCTTCTGGCAGGCAAGA;RSEQ=GTTATGCTACTTATAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:62:1,61:0,0:0,62:1:0,1:27:1:32.5:1:1:0:60:61:1:0:2 1/1:5:4:0,4:0,1:1,4:0.8:0,0:13.5:1:32:0:1:0:60:8:0.8:0:2 +21 42842949 . T C 87 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTACATATCTCCAGGTGA;RSEQ=CAAGACGGGAAAGACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:0,8:1:0,2:23.1:1:29.1:1:1:0:59.3:7:1:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42842988 . G A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=CAGGAGGCAACAGCCAAAAA;RSEQ=CCGATGGAGTCAATGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:1,4:5,1:0.1667:2,0:37:0:24:0:1:0:60:2:0.1667:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:31:0:1:0:60:4:1:0:1 +21 42843565 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.27765;LSEQ=TGCTGCCTCCCCCAAAATGC;RSEQ=GCAGGTGCTCTTAGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:14:14,0:15,0:15,14:0.4828:1,1:25.7:1:31.2:1:1:0:59.9:28:0.4828:0:1.1 1/0:11:6:5,1:5,0:5,6:0.5455:0,2:16.2:1:29.5:1:1:0:60:12:0.5455:0:1.3 +21 42843960 . A G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=GCCATAAACACAGAGCTCTC;RSEQ=GTGGATGAACTTCCAACGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:188:188:19,169:0,0:0,188:1:0,2:23:1:31.3:1:1:0:59.9:61.667:1:0:1.5 1/1:164:153:23,130:3,7:10,153:0.9329:2,2:23.3:1:30.1:1:0.20009:2.40564:60:75.5:0.9321:0:1.7 +21 42843962 . T A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=2.2311;LSEQ=CATAAACACAGAGCTCTCAG;RSEQ=GGATGAACTTCCAACGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:74:4,70:12,88:100,74:0.4253:2,2:25.6:1:32.4:1:0.1862:2.37533:60:73:0.4269:0:2.2 1/0:154:96:13,83:9,49:58,96:0.6234:2,2:25.2:1:30.1:1:0.81341:1.17145:60:95:0.6209:0:2 +21 42844052 . T G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0678;SOR=0;LSEQ=CAGGGAGATAGTGGAAGAGG;RSEQ=GCTCGGTCTCCCCTTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:1,43:0,0:0,44:1:0,1:24.4:1:31.6:1:1:0:59.6:43:1:0:1.8 1/1:16:14:0,14:0,2:2,14:0.875:0,1:22.3:1:30.1:1:1:0:60:13:0.8667:0:1.5 +21 42844057 . G A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18029;SOR=0.27258;LSEQ=AGATAGTGGAAGAGGTGCTC;RSEQ=GTCTCCCCTTCTCCCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:1,14:1,23:24,15:0.3846:1,1:32.9:1:33.1:1:1:1.62:60:30:0.3947:0:2.1 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:23:1:31:1:1:0:60:4:0.1429:0:2 +21 42844510 . A G 28 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGGGAGCACCCTTGGGTAAC;RSEQ=GCCCTTGCTTCCTTGACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:24:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:0:28:1:1:0:60:4:1:0:1 +21 42845167 . G C 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00279;SOR=Inf;LSEQ=AACACAAGGATGCCGGGGCT;RSEQ=CAAGGGTTGAGACCTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:112,7:119,0:0:2,0:22.4:1:32:1:1:0:59.8:18.833:1:0:0.1 0/1:74:6:6,0:65,3:68,6:0.0811:1,0:30.2:1:30.2:1:1:0:60:12:0.0811:0:1 +21 42845216 . T C 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13866;SOR=0;LSEQ=GGGTGGCTGTAGGCCAGCCC;RSEQ=GAGCCCCCACCCGGCCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:4:2,2:213,56:269,4:0.0147:2,2:8:1:31.3:1:0.19915:3.77917:60:8:0.0148:0:1 0/0:205:0:0,0:157,48:205,0:0:2,0:26:0:13:0:1:0:58:0:0:0:3 +21 42845232 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08687;SOR=Inf;LSEQ=GCCCTGAGCCCCCACCCGGC;RSEQ=CGCGCCGCCCCTGGCATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:250,106:356,0:0:2,0:23.7:1:30.8:1:1:0:59.9:49.857:1:0:0.1 0/1:284:3:2,1:197,84:281,3:0.0106:2,2:18.3:1:28.7:1:1:1.17192:60:6:0.0107:0:1 +21 42845241 . C T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17527;SOR=5.12764;LSEQ=CCCCACCCGGCCCGCGCCGC;RSEQ=CCTGGCATACTTTTCCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:453:1:0,1:309,143:452,1:0.0022:2,0:1:0:29:0:0.31788:0:60:2:0.0023:0:1 0/1:356:4:1,3:233,119:352,4:0.0112:2,2:16.5:1:27.8:1:0.11834:5.84357:60:8:0.0114:0:1.3 +21 42845374 . G A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.83248;LSEQ=GCCCCCGGGAGCGCGCTCTC;RSEQ=CCGCCCACAATCCTGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:24:9,15:280,337:617,24:0.0374:2,2:26.8:1:28.9:1:0.53306:1.38408:60:48:0.038:0:1.1 0/1:550:87:40,47:212,250:462,87:0.1582:2,2:23.5:1:29.2:1:1:1.00:60:174:0.1629:0:1.3 +21 42845377 . G A 64 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05048;SOR=7.37115;LSEQ=CCCGGGAGCGCGCTCTCGCC;RSEQ=CCCACAATCCTGCTCTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:642:1:1,0:291,350:641,1:0.0016:2,0:1:0:25:0:0.45483:0:60:2:0.0016:0:1 0/1:527:6:4,2:241,280:521,6:0.0114:2,2:12.7:1:24.8:1:0.42374:2.32:60:12:0.0116:0:1.3 +21 42845383 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21096;SOR=1.16699;LSEQ=AGCGCGCTCTCGCCGCCCAC;RSEQ=ATCCTGCTCTGGCGGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:631:349:155,194:128,154:282,349:0.5531:2,2:24.9:1:31:1:0.80973:1.04026:60:115.333:0.5563:0:1.1 1/0:528:312:146,166:102,114:216,312:0.5909:2,2:25.6:1:29.8:1:0.92957:1.01727:60:77:0.5912:0:1.2 +21 42845473 . C A 55 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14755;SOR=0;LSEQ=GTGAGACCAGCAGAAGCCGC;RSEQ=CAGCCACCCAGCGCCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:4:3,1:74,219:293,4:0.0135:2,2:6.3:1:27.5:1:0.05492:8.80:60:8:0.014:0:1.3 0/0:207:0:0,0:60,147:207,0:0:2,0:23.1:1:29.4:1:1:0:60:22:1:0:0.3 +21 42845638 . C T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.60281;LSEQ=GGAAGCACCACTTCCCTGAA;RSEQ=ACTCCTGTGATCCCATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:0,11:0,9:9,11:0.55:0,0:25.5:1:28.6:1:1:0:60:22:0.5789:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:11.5:1:29:0:1:0:60:4:0.6667:0:1 +21 42845800 . G T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.1;SOR=Inf;LSEQ=GGGCAGGGCTGGAAGTGAGT;RSEQ=AGGGGGTGAGGAGACGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:28:1:30.7:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:0:30.5:1:1:0:60:4:1:0:1.5 +21 42846888 . AGGGGTGGGTGAGGTGGTGAGTGAGGGGGTGAGGGGTGAGTGAGGGGGGTGAGGGGTAAGGAGGTGAGGGGGTGGGTGAGGGGTGGGTGAGGTGGTGGGTGAGGGGGTGAAGGGGTGAGTGAG A 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAGTGAGGGGGTGGGTG;RSEQ=GGGGTGAGTGAGGGGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:25:1:30.1:1:1:0:57.3:6:1:1:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42847017 . A G 65 p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AAGGGGTGAGTGAGGGGGTG;RSEQ=GTGAGGGGATGAGGGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:1,0:1,4:0.8:0,2:7.3:1:32.5:1:1:0:58:8:0.8:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42847036 . A G 77 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGAGGGGATGAGGGAGT;RSEQ=ATTCAGAGGGTGAAGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:26:1:33.4:1:1:0:58.4:10:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42847077 . AT A 25 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAGGGAGTGAAGGCATG;RSEQ=TGAGGGGGTGAAGGGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:10.5:1:25:1:1:1.7321:55:4:0.4:0.2:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42847266 . GT G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGAGTGAGGAGGTGAAG;RSEQ=GTGAGTGAGGGCGTGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:31.5:1:1:0:60:4:1:0:0 +21 42847358 . AAGGGGTGAGTGAGGGGGTGC A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGTGGGTGAGTGGATG;RSEQ=AGGGGTGAGTGAGGGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:28:1:1:0:60:4:1:0:0 +21 42848115 . G C 39 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCACCTGGTGGCCACAC;RSEQ=GTGGTGCTGGACCACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:24:1:24.7:1:1:0:60:2:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42848187 . C T 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGGGCTCACTAACGCCA;RSEQ=CCCCCTTTGCTTTCTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1:0,2:19.7:1:30.5:1:1:0:60:12:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42848494 . A C 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATCAAAAGGGGGACTCCAG;RSEQ=TGAACTTACCTATACAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1057:0:0,0:547,510:1057,0:0:2,0:26.4:1:30.5:1:1:0:60:74.5:1:0:0.1 0/1:926:35:22,13:455,435:890,35:0.0378:2,2:22.6:1:31.3:1:0.22714:1.62:60:70:0.0382:0:1.2 +21 42848560 . CAG C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01222;LSEQ=AGGCATCACTGCAAAAAGAA;RSEQ=GGGAAATTCTGGTCACGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:627:626:214,412:0,0:0,626:0.9984:0,2:28:1:31.6:1:1:0:60:155.5:1:0.0351:0.1 1/1:656:580:228,352:31,43:74,580:0.8841:2,2:25:1:30.2:1:0.70564:1.11283:59.9:144:0.8862:0.154:0.2 +21 42848684 . C T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGTCTGCTAGTTACAACT;RSEQ=CAATAAGGTAAGTAAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:0,87:87,0:0:1,0:22.1:1:31.7:1:1:0:60:42.5:1:0:0.2 0/1:53:14:0,14:1,38:39,14:0.2642:1,1:30.1:1:28.6:1:1:0:60:28:0.2692:0:1.1 +21 42848747 . C T 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56914;SOR=0;LSEQ=AGACACTGAGCCAAGGTACG;RSEQ=GGCTCACATCCCCACAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:5:0,5:2,28:30,5:0.1429:2,0:36.8:1:29.2:1:1:0:60:10:0.1471:0:1.2 0/0:7:0:0,0:0,7:7,0:0:0,0:15.3:1:30:1:1:0:60:14:1:0:0.7 +21 42848835 . T C 96 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGACGGTTGTGAGGGTAAG;RSEQ=ATACAATAATGCTAGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:0,8:1:0,2:15.3:1:32.1:1:1:0:60:16:1:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42849097 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGCTATGCTGAGAAGG;RSEQ=AAGACGCGGCCCCTGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:33.3:1:30.7:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42849134 . T C 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCAGAGCTGGCCCGCCC;RSEQ=GATAGCTGGGCCGTGTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:23.7:1:30.3:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42849137 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGCTGGCCCGCCCTGA;RSEQ=AGCTGGGCCGTGTGCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:20.7:1:31:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42850911 . C T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02206;SOR=0;LSEQ=TAGCAGAGAAACCTCAGCCA;RSEQ=TTCCTATGAATAAACCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:14,0:1,0:1,14:0.9333:0,1:21.4:1:32.4:1:1:0:60:28:0.9333:0:2.1 0/0:2:0:0,0:2,0:2,0:0:0,0:21.5:1:33.5:1:1:0:60:4:1:0:0.5 +21 42850977 . A G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05588;LSEQ=CAGACTCTAATCTCCTCCCA;RSEQ=TGCAAAACCCATCCAGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:59:58,1:17,0:17,59:0.7763:1,1:23.7:1:33.9:1:1:0:59.9:118:0.7763:0:2.2 0/1:38:6:6,0:32,0:32,6:0.1579:1,0:20.5:1:30.7:1:1:0:60:5:0.1351:0:2 +21 42851006 . A G 199 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09142;LSEQ=CCATCCAGACCGAGTATTGC;RSEQ=GCTCAGAGAAATCAGACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:99:93,6:28,1:29,99:0.7615:1,2:24.5:1:30.1:1:1:1.79942:60:48.5:0.7698:0:1.6 0/1:85:19:18,1:61,5:66,19:0.2235:2,1:24.2:1:29.3:1:1:1.47:60:18:0.2169:0:1.3 +21 42851038 . C T 33 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.25685;SOR=0;LSEQ=TCAGACTCAGGACAACGATT;RSEQ=CCCATGGTGTCTCCTAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:1,2:190,28:218,3:0.0136:2,2:5.7:1:21.3:1:0.04911:13.28415:59:2:0.0092:0:3 0/0:178:0:0,0:151,27:178,0:0:2,0:23.9:1:30.5:1:1:0:60:177:1:0:0.2 +21 42851262 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52298;SOR=0;LSEQ=TAAGGCATAAGCAAACACAA;RSEQ=TCCTATACTATGTCATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:19,157:176,2:0.0112:2,2:20.5:1:29:1:0.21266:8.08:60:4:0.0112:0:1 0/0:114:0:0,0:24,90:114,0:0:2,0:20.4:1:29.7:1:1:0:60:56:1:0:0.1 +21 42851565 . TGG T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGGTTCCTGGACTGTGA;RSEQ=GGGGGCTTTGCTGTGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:33:1:33.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42852311 . G A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01119;SOR=Inf;LSEQ=CAATTGTCCCCAGCACTCAT;RSEQ=TGCCGGTGCTTTCACAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:111,4:115,0:0:1,0:24.5:1:33.1:1:1:0:60:230:1:0:0.3 0/1:81:5:5,0:72,4:76,5:0.0617:2,0:19.6:1:28.6:1:1:0:60:10:0.0625:0:1 +21 42852320 . C A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=3.6771;LSEQ=CCAGCACTCATGTGCCGGTG;RSEQ=TTTCACAGGGAGGCAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:27:27,0:101,4:105,27:0.203:1,1:21.3:1:30.4:1:0.5811:0:60:54:0.203:0:1.1 0/1:101:49:45,4:48,4:52,49:0.4851:2,2:21.4:1:29.6:1:1:1.06595:60:98:0.4851:0:1.1 +21 42852334 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58166;SOR=2.61652;LSEQ=CCGGTGCTTTCACAGGGAGG;RSEQ=AGAGAGAGGGTCTTCTCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:1:0,1:165,19:184,1:0.0054:2,0:1:0:27:0:0.10811:0:60:2:0.0054:0:1 0/1:143:2:1,1:125,16:141,2:0.014:2,2:21.5:1:26.5:1:0.22437:7.60942:60:4:0.014:0:1.5 +21 42852497 . C T 205 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCTCTGAGATGAGTACA;RSEQ=CTGAAGGATGAAGTTTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1071:0:0,0:472,599:1071,0:0:2,0:25.6:1:31.2:1:1:0:60:41.84:1:0:0.1 0/1:1036:137:60,77:441,456:897,137:0.1322:2,2:22.8:1:28.9:1:0.27086:1.24086:60:274:0.135:0:1.2 +21 42852565 . C CT 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.28929;SOR=0.70528;LSEQ=GATTATCCATGAGTTTCTTT;RSEQ=TTTTTTTTTCTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:651:27:9,18:180,439:619,27:0.0415:2,2:29:1:31.1:1:0.66707:1.22:59.7:54:0.0422:0:0.1 0/1:608:18:7,11:218,371:589,18:0.0296:2,2:29.1:1:29.8:1:1:1.08:55.2:36:0.0302:0:0.3 +21 42852575 . C CT 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00128;SOR=Inf;LSEQ=GAGTTTCTTTCTTTTTTTTT;RSEQ=TTTTTTTTGAGACGGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:0:0,0:143,412:555,0:0:2,0:20.8:1:32.7:1:1:0:59.9:54.5:0.9963:0:0.1 0/1:513:9:4,5:165,333:498,9:0.0175:2,2:15.6:1:29.4:1:0.48962:1.61:60:18:0.018:0.0058:0.7 +21 42860136 . G T 96 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14911;SOR=0.20277;LSEQ=CTGTCATCTCCCACCTGCTG;RSEQ=GTGAGGTTGGGCCGGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:9:9,0:34,0:34,9:0.2093:1,0:26.7:1:30.6:1:1:0:60:18:0.2093:0:1 0/1:20:1:1,0:19,0:19,1:0.05:1,0:7:0:31:0:1:0:60:2:0.05:0:1 +21 42860258 . G T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02322;SOR=Inf;LSEQ=CCAGTCACCCAAAGGCCCCT;RSEQ=GACCCGGCTGCTGTCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:0:0,0:369,144:513,0:0:2,0:23.3:1:31.7:1:1:0:60:50.3:1:0:0.9 0/1:330:4:1,3:230,96:326,4:0.0121:2,2:13.3:1:28:1:0.08243:7.13966:60:8:0.0124:0:2 +21 42860307 . C T 295 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGGAGTCCCTTCCCAAGGT;RSEQ=AAGGCTGACTCACCACACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:960:960:551,409:0,0:0,960:1:0,2:25.9:1:29.8:1:1:0:59.9:119:1:0:1.1 1/0:772:598:329,269:95,78:173,598:0.7746:2,2:24.7:1:28.4:1:1:1.00:60:53.364:0.7744:0:1.2 +21 42860485 . G C 256 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCCCTTCAGGCTGAGAAAC;RSEQ=CAATGAGCCTCATGGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:299:299:56,243:0,0:0,299:1:0,2:24.1:1:31.2:1:1:0:60:48.833:1:0:1.1 1/0:239:183:40,143:11,43:54,183:0.7657:2,2:22.7:1:30.4:1:1:1.09:60:182:0.7679:0:1.1 +21 42860494 . C G 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTGAGAAACGCAATGAGC;RSEQ=TCATGGAGTGAGGAACACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:40,221:261,0:0:2,0:24.2:1:32.5:1:1:0:60:42.5:1:0:1 0/1:207:20:4,16:35,152:187,20:0.0966:2,2:20:1:30.8:1:1:1.09:60:40:0.0985:0:1 +21 42860522 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14859;SOR=Inf;LSEQ=GTGAGGAACACCGTGGCATT;RSEQ=CTGTAGCTCGCTGCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:11,154:165,0:0:2,0:25.2:1:30.2:1:1:0:60:164:1:0:0.9 0/1:104:2:1,1:7,95:102,2:0.0192:2,2:17:1:31:1:0.14862:12.76:60:4:0.0194:0:2 +21 42860532 . G A 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05303;SOR=0;LSEQ=CCGTGGCATTACTGTAGCTC;RSEQ=CTGCAGCCTCCAACTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:8:0,8:4,124:128,8:0.0588:1,0:23.5:1:30.4:1:1:0:60:16:0.0593:0:1.8 0/0:77:0:0,0:6,70:76,0:0:2,0:25.8:1:31.5:1:1:0:60:75:0.9868:0:0.9 +21 42860593 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00124;SOR=Inf;LSEQ=TTTTGTTTTTGAGATGAAGT;RSEQ=TCATTCTGTCACCCAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:1,41:42,0:0:1,0:26.4:1:34.1:1:1:0:58.9:84:1:0:0.2 0/1:17:5:0,5:0,12:12,5:0.2941:0,0:18.4:1:29.6:1:1:0:58.6:10:0.3125:0:1 +21 42861332 . C T 223 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08809;LSEQ=TATGTAAGAGAGGAACCTCA;RSEQ=GGAGGGCCTCCAGAGGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:198:151:143,8:40,7:47,151:0.7626:2,2:25.1:1:30.9:1:0.05197:3.11:60:36.75:0.7577:0:1.1 0/1:96:21:20,1:69,6:75,21:0.2188:2,1:20.2:1:30.8:1:1:1.73:60:42:0.2211:0:1.1 +21 42861616 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51782;SOR=0;LSEQ=TTTATAGTACACCACATTAA;RSEQ=AAATAATTATTTCATATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:5,191:196,2:0.0101:1,2:8.5:1:29.5:1:0.05984:34.97:60:4:0.0103:0:1 0/0:133:0:0,0:9,124:133,0:0:2,0:21.4:1:30.7:1:1:0:60:266:1:0:0 +21 42865324 . G A 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=3.51553;LSEQ=GGGGTAGAAACGCAGGAGCG;RSEQ=CAGCACTTGTCCTGAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:24.7:1:32:0:1:0:60:6:0.5:0:1.3 1/1:5:4:4,0:1,0:1,4:0.8:0,0:31.5:1:29:1:1:0:60:8:0.8:0:1 +21 42865906 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGGACTGTATGACAAA;RSEQ=GTAAGATAGTTGATTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:34:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 42866107 . T C 48 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.63785;SOR=2.11819;LSEQ=TAGGCCTGGCAGCGACAGCT;RSEQ=TGACCCAGCAGGAAGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:23,0:23,2:0.08:1,0:33:1:34:0:1:0:60:4:0.08:0:1 0/1:19:3:3,0:16,0:16,3:0.1579:1,0:34:1:30.7:1:1:0:60:6:0.1579:0:1 +21 42866296 . TG CA 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0;LSEQ=ATCCTACTTGAGGTGCACAC;RSEQ=TCCCGGATGGGGATTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:16:13,3:330,192:522,16:0.0297:2,2:23.3:1:31:1:0.18865:2.52:60:32:0.0303:0.0074:0.9 0/0:453:0:0,0:230,172:402,0:0:2,0:25.4:1:29.9:1:1:0:60:200:0.8909:0:0.2 +21 42866730 . G A 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29047;SOR=0.36141;LSEQ=CTACAAGGCTGGGTGCGGTG;RSEQ=CTCATGCCTGTAATCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:6:4,2:127,278:405,6:0.0146:2,2:16.3:1:28:1:0.0848:4.36:52.8:12:0.0149:0:1 0/0:376:2:2,0:138,236:374,2:0.0053:2,0:1:0:25:1:0.13801:0:60:4:0.0054:0:1 +21 42866756 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07773;SOR=Inf;LSEQ=GCCTGTAATCCCAGCACTTT;RSEQ=GGAGGCCGAGGCGGGCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:53,221:274,0:0:2,0:23:1:31.2:1:1:0:41:67.5:1:0:0.1 0/1:205:3:2,1:47,155:202,3:0.0146:2,2:15.3:1:27.7:1:0.14268:6.52:43:6:0.0149:0:3.3 +21 42866763 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07478;SOR=Inf;LSEQ=ATCCCAGCACTTTGGGAGGC;RSEQ=GAGGCGGGCGGATCATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:38,201:239,0:0:2,0:23.9:1:30.1:1:1:0:38.2:78.667:1:0:0.1 0/1:175:3:1,2:30,141:171,3:0.0171:2,2:11.7:1:31:1:0.44701:2.34:44.3:6:0.0174:0:3 +21 42866768 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15802;SOR=Inf;LSEQ=AGCACTTTGGGAGGCCGAGG;RSEQ=GGGCGGATCATGAGGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:30,189:219,0:0:2,0:24.5:1:30.1:1:1:0:36.4:35.5:1:0:0.1 0/1:145:2:1,1:23,118:141,2:0.0138:2,2:10.5:1:31:1:0.30848:5.04:37:4:0.0141:0:4 +21 42866772 . C A 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15404;SOR=Inf;LSEQ=CTTTGGGAGGCCGAGGCGGG;RSEQ=GGATCATGAGGTCAGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:23,178:201,0:0:2,0:25.3:1:30.4:1:1:0:34.8:200:1:0:0.1 0/1:131:2:1,1:16,112:128,2:0.0153:2,2:6.5:1:31:1:0.24532:6.82:37:4:0.0155:0:4 +21 42866994 . CAA C 241 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0;SOR=0.14743;LSEQ=GACAGAGCAAGACTATGTCT;RSEQ=AAAAAAAAAAAAAAGTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:384:201:155,46:48,9:57,201:0.5234:2,2:19.1:1:31.5:1:0.2773:1.58019:58.4:66:0.5266:0.1589:1 0/1:259:36:28,8:87,27:114,36:0.139:2,2:27.3:1:31.6:1:1:1.09:57.3:72:0.1412:0:0.9 +21 42867003 . A T 218 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=1;SSF=0;SOR=0.00552;LSEQ=AGACTATGTCTCAAAAAAAA;RSEQ=AAAAAAAGTAATAGAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:446:142:109,33:225,79:304,142:0.3184:2,2:18.7:1:30.6:1:0.55988:1.16:59.5:141:0.3183:0:1 0/0:390:1:0,1:271,118:389,1:0.0026:2,0:1:0:22:0:0.30513:0:60:2:0.0026:0:1 +21 42867220 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01968;SOR=Inf;LSEQ=TTAATACAATATTTATTCAC;RSEQ=ATTACAGTTGAGAAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:573:0:0,0:234,339:573,0:0:2,0:25:1:31.1:1:1:0:59.6:80.857:1:0:0.1 0/1:482:5:3,2:176,301:477,5:0.0104:2,2:31.4:1:25.4:1:0.36533:2.56:55.8:4:0.0084:0:2.4 +21 42867553 . CA C 191 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.41826;SOR=0.81537;LSEQ=CAAGAGCGAAACTCCCGTCT;RSEQ=AAAAAAAAAAAAAAACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:71:59,12:82,10:92,71:0.3679:2,2:16.5:1:31.1:1:0.3555:1.66243:56.3:34.5:0.3632:0.1606:1.5 0/1:143:46:40,6:48,16:64,46:0.3217:2,2:16.5:1:30.9:1:0.15071:2.21:55.7:92:0.3239:0.1119:1.8 +21 42868206 . T C 215 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCCTAAAGGAGCATAGTCTC;RSEQ=GTGTTATCCTGCAAATACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:798:0:0,0:441,357:798,0:0:2,0:25.9:1:31.2:1:1:0:59.9:56:1:0:0.1 0/1:659:164:82,82:247,245:492,164:0.2489:2,2:26.2:1:29.3:1:1:1.00815:59.8:40:0.2458:0:1.2 +21 42868876 . G A 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2121;SOR=2.83487;LSEQ=CTCCCAGGTTCAAGTGATTC;RSEQ=TCTGCCTCAGCCGCCCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:4:1,3:19,30:49,4:0.0755:2,2:19.5:1:23:1:1:1.87902:34.8:1:0.0488:0:1.3 0/1:21:4:2,2:1,16:17,4:0.1905:1,2:15.5:1:30:1:0.0797:12.75:30:8:0.25:0:1 +21 42868888 . C T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16378;SOR=0.45008;LSEQ=AGTGATTCGTCTGCCTCAGC;RSEQ=GCCCGAGTAGCTGGGATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:51:34:15,19:10,7:17,34:0.6667:2,2:22.6:1:30:1:0.38227:1.7884:35:16:0.6667:0:1.4 0/1:17:8:1,7:2,7:9,8:0.4706:2,2:17.4:1:29.8:1:1:1.9219:33.1:16:0.6154:0:1.1 +21 42868917 . A G 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.00027;SOR=Inf;LSEQ=AGCTGGGATTACAGGCATGC;RSEQ=CCACCACACCCGGCTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:37,16:53,0:0:2,0:25.4:1:28.2:1:1:0:33.1:9.6:1:0:0.8 0/1:21:6:3,3:11,4:15,6:0.2857:2,2:8:0:31.7:1:0.35436:2.60894:52.5:12:0.3158:0:1.5 +21 42868997 . A C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08467;LSEQ=AGGCTGGTCTCGAACTCCCA;RSEQ=CCTCAGGTGATCTGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:147:95:91,4:49,3:52,95:0.6463:2,1:26.5:1:32.6:1:0.6982:1.39:50.3:94:0.6528:0:1.5 0/1:98:13:13,0:85,0:85,13:0.1327:1,1:22.1:1:31.9:1:1:0:51.7:26:0.1354:0:1.5 +21 42869063 . A G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.53468;LSEQ=AGGCATGAGCCACCACGCCC;RSEQ=GCCTGCCCCTTGTCTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:466:334:220,114:79,50:129,334:0.7167:2,2:22.9:1:29.9:1:0.38621:1.22:59.1:82.5:0.7205:0:1.3 1/0:421:242:155,87:108,69:177,242:0.5748:2,2:23.3:1:29.2:1:0.54067:1.14:59.1:47.4:0.5766:0:1.2 +21 42869606 . A G 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTAGCCACATTTGTCTCCA;RSEQ=AGGGAGTGGGCTCCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:0:0,0:319,307:626,0:0:2,0:26.7:1:30.6:1:1:0:59.8:155.5:1:0:0.1 0/1:475:55:28,27:218,201:419,55:0.1158:2,2:25.1:1:30.5:1:0.88691:1.04576:60:17.333:0.1116:0:1.2 +21 42869735 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69015;SOR=1.06264;LSEQ=TGGAACATACCCCTGTTATC;RSEQ=CCATCCTGCCTCATCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:164:81,83:288,316:604,164:0.2135:2,2:23.5:1:30.2:1:0.72489:1.07:59.9:163:0.2168:0:1.1 0/1:585:131:66,65:219,232:451,131:0.2239:2,2:26.7:1:28.7:1:0.76602:1.08:59.9:42.667:0.2218:0:1.2 +21 42870262 . A G 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACCTTTGGCCTGCATCTTC;RSEQ=CCACTGCTTCCCCACATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1062:0:0,0:500,561:1061,0:0:2,0:25.1:1:30.1:1:1:0:60:95.455:1:0:0.1 0/1:808:82:45,37:339,385:724,82:0.1015:2,2:24.6:1:29.7:1:0.19925:1.38:60:26.333:0.099:0:1.1 +21 42870522 . C T 163 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=57.49827;LSEQ=GTGCCACTAAGCCCAGGCAT;RSEQ=CTGCTGGACTTAACCCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:725:1:0,1:367,356:723,1:0.0014:2,0:2:0:30:0:0.49309:0:60:2:0.0014:0:1 0/1:583:43:21,22:280,260:540,43:0.0738:2,2:24.8:1:30.1:1:0.75253:1.12797:59.8:86:0.0748:0:1.1 +21 42871220 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0011;SOR=1.37837;LSEQ=AGCTAGAGATGCCGTCAACA;RSEQ=GAAATGCTGTATAGTAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1176:263:132,131:436,475:911,263:0.2236:2,2:24.2:1:30.7:1:0.52875:1.10:59.9:86.667:0.2224:0:1.1 0/1:1066:303:136,167:365,396:761,303:0.2842:2,2:25.9:1:29.7:1:0.3769:1.13168:60:302:0.2849:0:1.1 +21 42871273 . T C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49332;SOR=1.10048;LSEQ=TCACTCTCCATGGACAAAGA;RSEQ=TCTTCGCTTGATCAAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1170:116:58,58:492,562:1054,116:0.0991:2,2:27:1:32.4:1:0.55669:1.14:60:37.667:0.098:0:1.1 0/1:1120:121:50,71:465,533:998,121:0.108:2,2:22.9:1:31.5:1:0.28907:1.2386:59.7:242:0.1091:0:1.2 +21 42871545 . A AT 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=0.11556;LSEQ=CTTGATGTTTTCTCTTTGTG;RSEQ=TTTTTCCACCCACCAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1533:964:515,449:311,256:567,964:0.6288:2,2:26.8:1:30.7:1:0.59586:1.05908:59.5:49.737:0.6283:0.0835:0.1 0/1:1351:221:122,99:610,519:1129,221:0.1636:2,2:25.1:1:29.6:1:0.76815:1.05:59.1:220:0.1654:0.02:0.2 +21 42871730 . A AT 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.24752;SOR=0.77753;LSEQ=TTAACAAGTCTCATTGGACG;RSEQ=TTTTTTTTTCTTTAACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1181:55:22,33:470,652:1122,55:0.0466:2,2:24.5:1:29.9:1:0.88883:1.08124:59.5:54:0.0467:0.0085:0.3 0/1:1066:39:17,22:457,569:1026,39:0.0366:2,2:28.9:1:29.3:1:1:1.03936:59.6:38:0.036:0.0019:0.3 +21 42871941 . G C 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21108;LSEQ=TGTCCACTGTCTGTGACATG;RSEQ=CCACAGAAGAATATTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:595:574:266,308:10,11:21,574:0.9647:2,2:24.6:1:31.9:1:1:1.05257:60:113.8:0.9677:0:1.1 1/1:453:386:169,217:30,34:64,386:0.8521:2,2:23.9:1:30.5:1:0.68454:1.13264:60:47.25:0.8552:0:1.1 +21 42872398 . C T 204 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01192;LSEQ=TTCAGTACACCATCGCTTTC;RSEQ=TGTGTCCTAAGCAGAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1052:93:45,48:452,507:959,93:0.0884:2,2:22.7:1:31.2:1:0.82859:1.05:60:186:0.089:0:1.1 0/0:867:1:0,1:410,455:865,1:0.0012:2,0:1:0:23:0:1:0:60:2:0.0012:0:1 +21 42872751 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.76868;SOR=0.96516;LSEQ=CCTTGCCTATGTCTGCTTTG;RSEQ=GAAGAGAGAGGATCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:955:224:105,119:358,373:731,224:0.2346:2,2:25.8:1:30.9:1:0.59354:1.08766:60:43.8:0.2337:0:1.1 0/1:701:160:87,73:254,286:540,160:0.2282:2,2:25.7:1:30.6:1:0.106:1.34:60:159:0.2288:0:1.1 +21 42872897 . G C 345 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22441;LSEQ=ATGCCTCTGGTTTCTCGGCT;RSEQ=TCCTATCTCCCCAGTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1569:1502:776,726:34,33:67,1502:0.9573:2,2:25.6:1:32.7:1:0.90117:1.04:59.9:82.444:0.9568:0:1.1 1/1:1284:1071:560,511:107,104:211,1071:0.8341:2,2:25.5:1:30.8:1:0.70645:1.07:59.9:65.938:0.8333:0:1.1 +21 42873283 . T A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09897;SOR=Inf;LSEQ=CGGCGGCTCCTGCCTATAAT;RSEQ=CCAGCACTTTGGGAGGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:68,255:323,0:0:2,0:23.4:1:30:1:1:0:52.5:34.889:1:0:0.1 0/1:279:3:2,1:64,211:275,3:0.0108:2,2:10:1:26.3:1:0.14129:6.54:60:6:0.0112:0:1.3 +21 42873300 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20874;SOR=Inf;LSEQ=AATTCCAGCACTTTGGGAGG;RSEQ=CAAGGCGGGCAGATCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:35,175:210,0:0:2,0:25.1:1:31.3:1:1:0:48.5:25.25:1:0:0.1 0/1:178:2:2,0:24,152:176,2:0.0112:2,0:18.5:1:26.5:1:0.02063:0:51.5:4:0.0114:0:1 +21 42873558 . A G 210 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=28.000;MSILEN=1;SSF=0;SOR=0.15584;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AAAAAGAAACAACAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:122:82,40:114,77:191,122:0.3801:2,2:17.1:1:30.3:1:0.18964:1.38:55.6:8.385:0.372:0:1.3 0/1:207:18:14,4:91,91:182,18:0.087:2,2:18.2:1:28.9:1:0.02721:3.48:53.8:5:0.0773:0:1.4 +21 42873605 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.02601;SOR=1.51632;LSEQ=AATTGAAAATAAAACAAGGG;RSEQ=GGGAATGTCCCGCTCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:902:59:36,23:527,315:842,59:0.0654:2,2:28.2:1:31:1:0.8895:1.06879:59.6:58:0.0655:0:1.1 0/1:719:69:38,31:363,285:648,69:0.096:2,2:30.3:1:29.2:1:0.89904:1.03902:60:138:0.0969:0:1.1 +21 42875004 . C T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24044;SOR=1.27857;LSEQ=TTTTATATACCAACAACAGA;RSEQ=GATCGGAAATGTAAATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:56:18,38:250,435:685,56:0.0754:2,2:26.9:1:31.3:1:0.56511:1.21294:60:112:0.0764:0:1 0/1:625:59:28,31:229,335:564,59:0.0944:2,2:24:1:29.8:1:0.33218:1.32:60:118:0.0956:0:1.1 +21 42875652 . G T 179 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=60.28026;LSEQ=CCTAAAAATGTATGTTTCAA;RSEQ=ACTGGAGGATCATTTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1133:2:0,2:535,596:1131,2:0.0018:2,0:10.5:1:17:1:0.50111:0:60:1:9e-04:0:1 0/1:839:81:34,47:371,385:756,81:0.0965:2,2:26.2:1:28.3:1:0.24324:1.33163:60:39.5:0.0948:0:1.1 +21 42876400 . C T 298 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35161;LSEQ=TGCCAGAAAACCAGCCTCGA;RSEQ=TCCCAACCAGCGCATTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1406:858:366,492:252,295:547,858:0.6102:2,2:26.5:1:30.6:1:0.22532:1.1482:60:60.286:0.6085:0:1.1 0/1:1234:438:196,242:364,430:794,438:0.3549:2,2:25.1:1:29.6:1:0.72026:1.04517:59.9:53.75:0.3533:0:1.2 +21 42876598 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.9493;SOR=1.00864;LSEQ=CTTTTGCTCCTCCTTGGGTG;RSEQ=CCACAGGCTCGGTGGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:784:177:82,95:291,316:607,177:0.2258:2,2:24.8:1:31.5:1:0.73269:1.06676:60:43.25:0.2241:0:1.1 0/1:638:145:74,71:240,252:492,145:0.2273:2,2:28.2:1:31:1:0.63799:1.09:60:290:0.2305:0:1.1 +21 42877161 . AAAAT A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.85894;SOR=0.9063;LSEQ=AATTTTCAAGAGGGCTTAGA;RSEQ=AAATAAATAAATAAGATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:914:18:7,11:367,529:896,18:0.0197:2,2:24.7:1:31:1:1:1.09011:59.7:36:0.0199:0.0033:0.1 0/1:783:14:4,10:325,444:769,14:0.0179:2,2:28.4:1:29.4:1:0.41556:1.82863:60:28:0.018:0:0 +21 42877382 . T C 179 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=89.6257;LSEQ=ATCGTGGTGGTGGTGGTTAC;RSEQ=GGCATAAGGTACTGCACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1351:1:1,0:584,764:1348,1:7e-04:2,0:8:0:15:0:0.43365:0:60:0:0:0:4 0/1:1107:69:28,41:473,565:1038,69:0.0623:2,2:24.7:1:29.4:1:0.45519:1.22563:60:33.5:0.0615:0:1.1 +21 42877542 . C A 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00525;SOR=0.63382;LSEQ=TACTGCTAGAGGGAGCAGCA;RSEQ=GGAGCCCAGGTAGGGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:633:544:291,253:54,35:89,544:0.8594:2,2:23.7:1:31.1:1:0.25083:1.34076:59.9:107.8:0.8596:0:1.1 1/0:458:364:201,163:50,44:94,364:0.7948:2,2:22.3:1:29.6:1:0.72892:1.08:59.9:51:0.7916:0:1.1 +21 42877555 . G T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01241;SOR=Inf;LSEQ=AGCAGCACGGAGCCCAGGTA;RSEQ=GGCTGTGGGCAGGGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:0:0,0:376,310:686,0:0:2,0:23.3:1:32.2:1:1:0:60:97:1:0:0.8 0/1:490:5:2,3:269,216:485,5:0.0102:2,2:9.4:1:28:1:0.66046:1.86564:60:10:0.0104:0:1.2 +21 42878126 . A C 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0757;LSEQ=CCTGAGGCTCCAGCAACAGC;RSEQ=CAAGCTTGTTGTTAGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:801:488:251,237:167,146:313,488:0.6092:2,2:25.5:1:30.8:1:0.61235:1.07993:59.9:39.667:0.6087:0:1.1 0/1:655:69:44,25:304,280:584,69:0.1053:2,2:24.9:1:29.9:1:0.07416:1.62:60:33.5:0.1039:0:1.1 +21 42878611 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03506;SOR=1.27442;LSEQ=ACTCCCAACCCCCATCCTTC;RSEQ=TTCAGGGGAGGCTGGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:997:213:107,106:380,402:782,213:0.2136:2,2:25.5:1:31.1:1:0.69937:1.07:59.9:70:0.2136:0:1.2 0/1:762:196:95,101:282,284:566,196:0.2572:2,2:22.5:1:30:1:0.80368:1.05563:59.9:97:0.2556:0:1.1 +21 42878761 . C T 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCCATGATTCGGGAGGTT;RSEQ=TCGCGGCTGGGAGCTCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:0:0,0:322,458:780,0:0:2,0:25.3:1:32.5:1:1:0:60:64:0.9974:0:0.2 0/1:652:16:5,11:281,354:635,16:0.0245:2,2:22.6:1:30.2:1:0.44528:1.74491:60:32:0.0247:0:1 +21 42878780 . T G 181 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCGCGGCTGGGAGCTCCG;RSEQ=GAGGTCAGGCATTGCCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:52:19,33:236,369:605,52:0.0789:2,2:26.6:1:31.8:1:0.7687:1.11068:60:104:0.0804:0:1.2 0/0:528:0:0,0:219,309:528,0:0:2,0:23.8:1:28.8:1:1:0:60:51.8:1:0:0.2 +21 42878913 . G T 39 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09074;SOR=Inf;LSEQ=CTGCCCACAGGGCTCACCTC;RSEQ=GGCCGCCGTGCTATCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:180,168:348,0:0:2,0:24.3:1:30.3:1:1:0:60:86:1:0:0.1 0/1:285:3:1,2:149,133:282,3:0.0105:2,2:5.7:1:25:1:0.60483:2.23446:60:6:0.0106:0:2 +21 42879057 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04484;SOR=Inf;LSEQ=AAGGCCCTCCTCTGCCACAA;RSEQ=CGCTCAGGGCTCTCGGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:0:0,0:223,221:444,0:0:2,0:25.8:1:32.6:1:1:0:60:43.4:1:0:0.1 0/1:380:4:1,3:184,192:376,4:0.0105:2,2:12.3:1:27.8:1:0.62354:2.86798:60:8:0.0108:0:1 +21 42879101 . T A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01541;SOR=Inf;LSEQ=ACTTTCTGGACATGGGGCAG;RSEQ=TTTTCAGCTGGACCCGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:498:0:0,0:252,245:497,0:0:2,0:24.7:1:29.8:1:1:0:60:48.7:1:0:0.1 0/1:384:5:3,2:187,192:379,5:0.013:2,2:25:1:27.8:1:0.68262:1.54:60:10:0.0131:0:1.4 +21 42879231 . TC T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.07803;SOR=Inf;LSEQ=AGCGCCCAGGTGCCCCGCCT;RSEQ=CCCCCAACCCGGCACGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:124,203:327,0:0:2,0:25.9:1:31.3:1:1:0:60:45.714:1:0:0.1 0/1:245:3:2,1:98,143:241,3:0.0122:2,2:25.3:1:28.3:1:0.56947:2.91:60:6:0.0125:0.0041:0.7 +21 42879262 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15287;SOR=Inf;LSEQ=CGGCACGGAGCGCAAGCGGA;RSEQ=GAGCCAGACCGGCTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:88,162:250,0:0:2,0:23.5:1:31.7:1:1:0:60:82.333:1:0:0.1 0/1:161:2:1,1:60,99:159,2:0.0124:2,2:17:1:29.5:1:1:1.64:60:4:0.0127:0:1 +21 42879308 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16971;SOR=Inf;LSEQ=GGTTCCTGCCGGTGCCGGGT;RSEQ=TCCAGGAGGCCCCGGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:68,104:172,0:0:2,0:24:1:32.4:1:1:0:60:56.333:1:0:0.2 0/1:121:2:1,1:53,66:119,2:0.0165:2,2:7:1:28:1:1:1.24:60:4:0.0168:0:1 +21 42879403 . A T 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGACTGACTGGCCGTTCGC;RSEQ=CCTCGCCCGGGGGCCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:236,96:332,0:0:2,0:25.2:1:30.4:1:1:0:59.9:82:1:0:0.2 0/1:229:74:51,23:104,49:153,74:0.3231:2,2:23.2:1:29.9:1:1:1.04:60:73:0.3244:0:1.2 +21 42879604 . C A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0286;SOR=1.45983;LSEQ=ACAGCACTCCCAGTCCTCCT;RSEQ=CCCAAAGAGAAAAGGCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:904:71:32,39:400,433:833,71:0.0785:2,2:25.6:1:29.3:1:0.71075:1.12572:59.9:34.5:0.0773:0:1.2 0/1:777:86:45,41:322,369:691,86:0.1107:2,2:23.9:1:27.7:1:0.35977:1.26:60:85:0.1104:0:1.2 +21 42879724 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07773;SOR=0.77141;LSEQ=AACTGGCTAGGGACTCGCAG;RSEQ=ACCACCTGCCCCAACCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:664:173:79,94:199,292:491,173:0.2605:2,2:26.6:1:30.6:1:0.24527:1.23:60:85.5:0.2615:0:1.1 0/1:468:100:44,56:167,200:367,100:0.2137:2,2:22.1:1:29.2:1:0.82131:1.06262:60:24:0.211:0:1.2 +21 42879797 . C T 56 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00532;SOR=Inf;LSEQ=CGGCCGTGCGCAAGGGGTCC;RSEQ=AGGCGCCCAGCACTCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:0:0,0:232,315:547,0:0:2,0:23.1:1:31.6:1:1:0:60:48.727:1:0:0.2 0/1:395:6:1,5:177,212:389,6:0.0152:2,2:7.3:1:21.8:1:0.22894:4.16209:60:2:0.0104:0:1.2 +21 42879909 . C A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42403;LSEQ=GCTCCTCACACCCGCTTTCA;RSEQ=CTCCGGGCGGGGCAGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:668:431:183,248:110,126:236,431:0.6452:2,2:25:1:30:1:0.32775:1.1828:60:106.75:0.648:0:1.3 0/1:602:262:125,137:159,181:340,262:0.4352:2,2:25.5:1:28.8:1:0.86923:1.04:59.9:86.333:0.4353:0:1.4 +21 42879936 . G A 66 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02762;SOR=Inf;LSEQ=GCGGGGCAGGGGGCATCGGC;RSEQ=GGTCCCAGGCGCCCAGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:0:0,0:210,294:504,0:0:2,0:23.8:1:30.4:1:1:0:60:49.4:1:0:0.8 0/1:482:5:4,1:215,262:477,5:0.0104:2,2:6.2:1:28.8:1:0.1819:4.86:58.2:10:0.0105:0:1.6 +21 42879982 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49867;SOR=0;LSEQ=CCCAGCCCGGACCCCGAGCC;RSEQ=GGACCCTGGTACCGGCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:49,128:177,2:0.011:2,2:12:0:32.5:1:0.48177:2.60:60:4:0.0114:0:1.5 0/0:178:0:0,0:58,117:175,0:0:2,0:21.5:1:28.5:1:1:0:60:12.462:0.9939:0:0.5 +21 42880506 . G GA 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCTGGGCAAGGACCCAG;RSEQ=GTAGGCCTTGGGGACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:28:1:1:0:60:4:1:0:0.5 +21 43124132 . T C 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=GGGAGTGGGGGGAGCCAAGG;RSEQ=CCGGGAGACGGAGGCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:22:18,4:35,16:51,22:0.3014:2,2:28.6:1:31.8:1:0.39124:2.04:60:44:0.3099:0:2.5 0/0:45:0:0,0:26,19:45,0:0:2,0:19.6:1:28.7:1:1:0:60:90:1:0:1.7 +21 43124139 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12536;SOR=Inf;LSEQ=GGGGGAGCCAAGGTCCGGGA;RSEQ=ACGGAGGCTCACTCCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:57,26:83,0:0:2,0:24.5:1:32.4:1:1:0:60:40.5:1:0:1.9 0/1:46:2:1,1:25,19:44,2:0.0435:2,2:38.5:1:29:0:1:1.30786:60:4:0.0435:0:3 +21 43124156 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.16901;SOR=0.63571;LSEQ=GGAGACGGAGGCTCACTCCC;RSEQ=CCCCAGATGACAGACCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:60:37,23:35,24:59,60:0.5:2,2:21.8:1:28.5:1:0.8523:1.10:59.5:11:0.4825:0:2.4 0/1:67:26:12,14:24,17:41,26:0.3881:2,2:31.7:1:29.1:1:0.45113:1.63463:60:52:0.3939:0:2.1 +21 43124186 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.02155;SOR=1.84277;LSEQ=ACAGACCCCTCGCATCACAC;RSEQ=CCAGGCTGACTCCTCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:71:38,33:43,43:86,71:0.4522:2,2:28.5:1:30.3:1:0.74866:1.15:60:22.667:0.4444:0:2.3 1/0:101:61:30,31:20,20:40,61:0.604:2,2:27.4:1:30.5:1:1:1.03301:58.8:60:0.6:0:2.3 +21 43124190 . G C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39147;SOR=0;LSEQ=ACCCCTCGCATCACACACCA;RSEQ=GCTGACTCCTCCACACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:157:79,78:0,0:0,157:1:0,2:28.6:1:30.8:1:1:0:59.8:38.25:1:0:2.1 1/1:101:100:50,50:0,0:0,100:0.9901:0,2:26:1:30.6:1:1:0:58.8:99:0.99:0:2.2 +21 43124240 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGGAGGGGAAACACCCT;RSEQ=CCAGCGAGAGACCCGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:39,70:109,2:0.018:2,2:40:1:30.5:1:1:1.78:60:4:0.0192:0:3 0/0:42:0:0,0:16,24:40,0:0:2,0:23:1:30.5:1:1:0:60:80:0.9524:0:1.5 +21 43124280 . CAT TGC 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02756;SOR=0;LSEQ=CCCAACTCCCCCCACCCCAC;RSEQ=GCCCCCGCCCAGCCTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:11:0,11:2,31:33,11:0.2292:2,0:17.2:1:32.2:1:1:0:60:22:0.2391:0.0625:1.4 0/0:18:0:0,0:2,16:18,0:0:2,0:22.1:1:31.2:1:1:0:60:36:1:0:0.7 +21 43124322 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54023;SOR=0;LSEQ=CTGCAGCTGTAGTCCTAAGC;RSEQ=GGGCCACTCTGCCCGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:0,18:18,2:0.1:1,0:11:1:28.5:1:1:0:60:4:0.1:0:2 0/0:10:0:0,0:0,10:10,0:0:0,0:25.5:1:30.8:1:1:0:60:20:1:0:0 +21 43124367 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=CAGTGCCTTGGCCTCGAGGA;RSEQ=GCCCCACGTGTTGGGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:45:1:32.5:1:1:0:60:4:0.25:0:2 0/0:5:0:0,0:0,5:5,0:0:0,0:26.6:1:32.2:1:1:0:60:10:1:0:0.2 +21 43124416 . A C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCTGCAACCTGCAAA;RSEQ=CTCCCAGCTTCTCGCAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:3:0:23.5:1:1:0:60:1:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:24:0:32:0:1:0:60:4:1:0:1 +21 43174165 . A T 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=0.42987;LSEQ=TTGTATACTATTTACATTTA;RSEQ=CTGCTTCATGAAGTAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:2,10:0.8333:0,0:17.2:1:30.8:1:1:0:60:20:0.8333:0:1.1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:16:1:32.5:1:1:0:60:4:0.6667:0:1 +21 43174284 . G T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17903;SOR=2.17926;LSEQ=TGGCAACTTAGGATCTAATT;RSEQ=CAGGATTCTGGATTACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:8:8,0:43,1:44,8:0.1538:1,0:26.3:1:29.6:1:1:0:60:7:0.1373:0:1 0/1:35:10:8,2:24,1:25,10:0.2857:1,2:17.1:1:29.5:1:0.19022:5.63898:60:20:0.2941:0:1 +21 43174332 . G C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.26226;LSEQ=ATTGAATAACTGTCTACTGA;RSEQ=GACTGCCCAGAAGCCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:13:10,3:117,29:146,13:0.0813:2,2:28.1:1:31.2:1:0.72606:1.20883:60:26:0.0833:0:1 0/1:116:37:28,9:60,19:79,37:0.319:2,2:24.8:1:31.3:1:1:1.01491:60:74:0.3246:0:1.1 +21 43174337 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18848;SOR=Inf;LSEQ=ATAACTGTCTACTGAGGACT;RSEQ=CCCAGAAGCCCAGTGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:138,36:174,0:0:2,0:22.5:1:31.9:1:1:0:60:28:1:0:0.2 0/1:134:2:1,1:99,33:132,2:0.0149:2,2:39:1:29:1:0.44451:2.97043:60:4:0.0154:0:2 +21 43174348 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17988;SOR=Inf;LSEQ=CTGAGGACTGCCCAGAAGCC;RSEQ=AGTGGTCAGTCCATGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:165,57:222,0:0:2,0:22.7:1:31.1:1:1:0:60:36:1:0:0.2 0/1:164:2:1,1:117,45:162,2:0.0122:2,2:17:1:27.5:1:0.48354:2.58256:60:4:0.0123:0:1 +21 43174396 . G A 32 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30996;SOR=4.37772;LSEQ=ACTTCGTCTTCAGGAACAAA;RSEQ=GCGCTGACTCTCAGAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:1:1,0:211,178:389,1:0.0026:2,0:1:0:25:0:1:0:60:2:0.0026:0:1 0/1:269:3:3,0:155,110:265,3:0.0112:2,0:15:1:20.3:1:0.27134:0:60:2:0.0077:0:3 +21 43174436 . A C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.78078;LSEQ=CGACACACACTCCCTGCTGC;RSEQ=CTCTACGCACACCAGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:115:54,61:132,156:288,115:0.2854:2,2:27.7:1:31.3:1:0.91195:1.05:59.7:114:0.285:0:1.4 1/0:294:177:85,92:57,60:117,177:0.602:2,2:26.8:1:29.8:1:1:1.02815:60:58:0.6021:0:1.3 +21 43174491 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20119;SOR=1.36774;LSEQ=ATAAGTATGTCACGTAAAGG;RSEQ=ATTTTTCGGTTTGTTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:45:13,32:73,140:213,45:0.1744:2,2:23:1:30.9:1:0.60208:1.28231:60:44:0.1725:0:1.7 0/1:214:48:15,33:59,107:166,48:0.2243:2,2:25.2:1:31.4:1:0.61037:1.21201:60:96:0.2286:0:1.8 +21 43791944 . A T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGTAATGGAGCCCCTGG;RSEQ=ATTCAGTGGATGATTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:31:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 43792665 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCAACAGAGCGAGACTCCA;RSEQ=CTCAAAAAAACAAAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:32:0:1:0:56.5:4:1:0:1 +21 43795470 . GC G 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=CCGCACTGTCTCAGCCCCCC;RSEQ=CCCCTCCCACTTTCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:31:1:1:0:60:4:1:0:0 0/0:5:0:0,0:3,2:5,0:0:2,0:30.2:1:29.8:1:1:0:60:10:1:0:1 +21 43995829 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19501;SOR=Inf;LSEQ=AAATGAGTTGAGAATTTCAG;RSEQ=AATATCAACTCACTCAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:191,60:251,0:0:2,0:22.1:1:30.5:1:1:0:60:124.5:1:0:0.2 0/1:199:2:1,1:151,46:197,2:0.0101:2,2:40:1:31.5:1:0.41749:3.25822:60:4:0.0102:0:1 +21 43995923 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=1.6086;LSEQ=CACATACAAAATCAAATACC;RSEQ=ACTCTCAACCTATGAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:310:157,153:179,165:344,310:0.474:2,2:25.7:1:30.2:1:0.75419:1.0571:60:37.75:0.4697:0:1.7 1/0:566:335:158,177:115,114:229,335:0.5919:2,2:26.5:1:29:1:0.49332:1.12983:59.9:26.917:0.5883:0:1.8 +21 43995954 . A G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.86952;LSEQ=TATGAACTTACTAGGTTTAA;RSEQ=TGGCTGTTCTTTGGATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:238:100,138:136,156:292,238:0.4482:2,2:25.5:1:32.4:1:0.33384:1.20265:59.9:78.333:0.4502:0:1.8 1/0:451:272:110,162:81,98:179,272:0.6031:2,2:23.2:1:31:1:0.33091:1.21671:59.9:67:0.6063:0:1.9 +21 43995980 . G T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03454;SOR=Inf;LSEQ=GTTCTTTGGATCATCTGTGG;RSEQ=TTCTTTTAATGCCTGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:122,264:386,0:0:2,0:24.7:1:31.8:1:1:0:59.9:76.2:1:0:0.8 0/1:294:4:2,2:103,187:290,4:0.0136:2,2:12:1:28.8:1:0.61874:1.81:60:8:0.0139:0:1.8 +21 44513091 . C G 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01404;SOR=Inf;LSEQ=TTATCACTACAAATTTTATT;RSEQ=AGAAACCCATCTTTGTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:98,3:101,0:0:1,0:27.1:1:32.4:1:1:0:60:100:1:0:0.2 0/1:77:5:3,2:69,3:72,5:0.0649:1,2:25:1:31.2:1:0.0315:14.03092:59:10:0.0658:0:1 +21 44513110 . GT G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.82895;SOR=0.86746;LSEQ=TCAGAAACCCATCTTTGTAT;RSEQ=TTTTTTTTTTGTTGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:13:11,2:127,6:133,13:0.089:1,2:22.3:1:32.4:1:0.15101:3.79276:56.2:26:0.089:0.0205:0.1 0/1:128:10:9,1:103,14:117,10:0.0781:2,2:19.8:1:31.7:1:1:1.22:55.2:20:0.0787:0.0234:0.1 +21 44513131 . T TA 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.37521;SOR=0.27383;LSEQ=TTTTTTTTTTTGTTGTTTTT;RSEQ=AAAAAAAATTCCCCTTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:4:3,1:188,24:212,4:0.0184:2,2:22.5:1:28.8:1:0.39085:2.59493:37.8:8:0.019:0.0046:0.3 0/0:196:1:1,0:150,45:195,1:0.0051:2,0:23:0:27:0:1:0:32:2:0.0052:0:2 +21 44513287 . G A 101 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.18716;SOR=1.9917;LSEQ=CCGCCGCCACCTCCACCACC;RSEQ=CCACCGCCACCGCCACGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1047:7:5,2:480,556:1036,7:0.0067:2,2:14.6:1:24.6:1:0.26055:2.89:56.4:6:0.0059:0:1.9 0/1:1058:14:9,5:491,548:1039,14:0.0132:2,2:19.1:1:26.6:1:0.28219:2.01:49.8:13:0.013:0:1.4 +21 44513411 . G A 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57886;SOR=2.68169;LSEQ=CATCCAAACCACGGCACGCA;RSEQ=CACAGAACCACACCCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:1,0:54,203:257,1:0.0039:2,0:1:0:29:0:0.21318:0:60:2:0.004:0:1 0/1:194:2:1,1:45,146:191,2:0.0103:2,2:23:1:25.5:1:0.42082:3.22:60:4:0.0105:0:1 +21 44513420 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.15653;SOR=Inf;LSEQ=CACGGCACGCAGCACAGAAC;RSEQ=ACACCCACTCTCTCAACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:40,196:236,0:0:2,0:23.3:1:32.1:1:1:0:59.9:117:1:0:0.2 0/1:155:2:1,1:29,124:153,2:0.0129:2,2:23:1:27:1:0.35065:4.22:60:4:0.0131:0:1 +21 44513429 . T C 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.55877;SOR=3.34865;LSEQ=CAGCACAGAACCACACCCAC;RSEQ=CTCTCAACACGCGCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:18,176:194,1:0.0051:2,0:32:0:11:0:1:0:60:0:0:0:4 0/1:118:2:1,1:14,101:115,2:0.0169:2,2:28:1:31:1:0.24094:7.00:60:4:0.0183:0:1 +21 44513479 . ACTG A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.02142;SOR=3.62113;LSEQ=CGGCACTGATAAGGAAAAAC;RSEQ=CTGAAGAGACTGCACGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:6:0,6:2,80:82,6:0.0674:1,0:23:1:27.4:1:1:0:60:5:0.0568:0.0337:1.2 0/1:43:9:0,9:1,33:34,9:0.2093:1,0:28.1:1:31.3:1:1:0:60:18:0.2093:0:0.8 +21 44513500 . C T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20102;SOR=2.57907;LSEQ=CTGCTGAAGAGACTGCACGC;RSEQ=GTGACTGAGACACACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:0,5:2,52:54,5:0.0847:1,0:19:1:27:1:1:0:60:4:0.0714:0:2.2 0/1:36:7:0,7:1,28:29,7:0.1944:1,0:25.4:1:29.6:1:1:0:60:14:0.1944:0:1 +21 44514488 . G A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36918;SOR=1.30987;LSEQ=GCCTTTTAAAAAACAGAAAC;RSEQ=ACACCTATGCCAAAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:33:29,4:105,12:117,33:0.22:2,2:22:1:29.9:1:0.75351:1.20535:60:15.5:0.2109:0:1.1 0/1:100:27:24,3:67,5:72,27:0.27:2,2:26.9:1:28.9:1:0.67968:1.66549:60:26:0.2653:0:1.1 +21 44514503 . AT A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17701;SOR=0.49261;LSEQ=GAAACGACACCTATGCCAAA;RSEQ=TTTTTTTTTGGAAGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:15:12,3:161,32:193,15:0.0721:2,2:26.4:1:31.9:1:0.7219:1.25633:60:30:0.0725:0.0096:0.3 0/1:163:6:4,2:122,34:156,6:0.0368:2,2:16:1:31.6:1:0.6154:1.7867:59.2:12:0.0373:0.0123:0.7 +21 44514514 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07703;SOR=Inf;LSEQ=TATGCCAAAATTTTTTTTTT;RSEQ=GAAGGGGGAGGGTTGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:207,58:265,0:0:2,0:22.6:1:31.7:1:1:0:60:87.333:1:0:0.3 0/1:198:3:1,2:142,53:195,3:0.0152:2,2:15:1:23.3:1:0.18725:5.30498:60:2:0.0102:0:2 +21 44514969 . A ATG 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00073;SOR=2.48177;LSEQ=TCTCAATTACCAATCCAAGT;RSEQ=TATCAGAGAGAGATATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:40:3,37:6,80:86,40:0.315:2,2:24.4:1:30.6:1:1:1.08:59.1:80:0.3252:0.0866:0.1 1/0:118:63:5,58:3,52:55,63:0.5339:2,2:21.1:1:30.4:1:0.72229:1.49:59.9:62:0.5345:0.1695:0.1 +21 44515346 . T C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6457;SOR=1.83303;LSEQ=ACCGCCACATATGACGCAGC;RSEQ=GGTAGGCGCCGAGCCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:7,1:14,1:15,8:0.3478:1,2:24.9:1:29.4:1:1:1.93655:60:7:0.3182:0:1.1 1/0:6:3:2,1:3,0:3,3:0.5:0,2:22.7:1:31.3:1:1:0:60:6:0.5:0:1.3 +21 44515504 . T C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=1.83084;LSEQ=TCGCCTGTTGGCCTTGGCCC;RSEQ=GGCACACTAAGCGGCCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:111:83,28:191,66:257,111:0.3008:2,2:25.3:1:30.6:1:1:1.02:60:222:0.3016:0:1.1 0/1:338:149:110,39:139,50:189,149:0.4408:2,2:24.2:1:29.6:1:1:1.01:60:73.5:0.4414:0:1.1 +21 44515685 . T C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.25559;LSEQ=GGTTTAAGACTCGTTATACA;RSEQ=TACAAAGTGTCATTAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:159:62,97:210,235:445,159:0.2624:2,2:24.6:1:33.2:1:0.07831:1.3973:60:158:0.2655:0:1.1 0/1:631:281:130,151:151,196:347,281:0.4453:2,2:25:1:31.3:1:0.51886:1.12:60:92.667:0.4462:0:1.1 +21 44520474 . T C 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22103;SOR=Inf;LSEQ=CTCTAGTGAAACGCGGTCCT;RSEQ=GACACTAGCACGGCAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:159,14:173,0:0:2,0:21.7:1:30.8:1:1:0:59.8:85.5:1:0:0 0/1:154:2:2,0:131,21:152,2:0.013:2,0:7:1:30.5:1:1:0:60:4:0.0132:0:1 +21 44521550 . GA G 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.76151;SOR=1.25886;LSEQ=GAATCAAGATGGTCTGCGGG;RSEQ=AAAAAAAATAAAAAGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:4:2,2:67,178:245,4:0.016:2,2:17.5:1:27.6:1:0.30759:2.64:60:8:0.0164:0.004:0.5 0/1:299:6:0,6:90,202:292,6:0.0201:2,0:19.2:1:32.5:1:0.18316:0:60:12:0.0205:0:0.2 +21 44524006 . G A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CAATCACGCTAACTTGGAAG;RSEQ=TGGCTCCATCACCTCTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:3,0:0:0,0:29:1:31:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:29:1:1:0:60:4:1:0:1 +21 44524290 . A C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-04;SOR=0.08199;LSEQ=GCCTCACTATTATTTAAATA;RSEQ=AAGAACACACTTATGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:22,0:37,1:38,22:0.3667:1,1:22.2:1:32.3:1:1:0:60:44:0.3667:0:1.1 0/1:45:2:2,0:42,1:43,2:0.0444:1,0:10:1:29.5:1:1:0:60:4:0.0444:0:1 +21 44527249 . T C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGAGGCGGCTTCCGGGAG;RSEQ=CGGCGACTCGGAGGCCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:16:0:32:0:1:0:60:2:1:0:0 1/0:4:2:1,1:0,2:2,2:0.5:0,2:10:1:30:1:1:0:60:4:0.6667:0:2 +21 44527289 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTCGGGCGATCAGCCAGT;RSEQ=CGGACCCCAAGGCCGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,2:2,2:0.5:0,2:42.5:1:29:1:1:0:60:4:0.5:0:2 +21 44527361 . G T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCATTCTGCCCGCTCCA;RSEQ=TTTTCCGCCGCGCGGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:1:27.5:1:1:0:60:4:1:0:1.5 +21 44527669 . T G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.83258;LSEQ=CGCCGACCCTGCCGACGCCC;RSEQ=CGGGAGACGTCACCCGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:135:33,102:105,271:376,135:0.2642:2,2:24.6:1:31.5:1:0.49804:1.19716:60:32.75:0.2636:0:1.1 1/0:444:224:55,169:63,156:219,224:0.5045:2,2:25.5:1:30.6:1:0.33461:1.2403:60:43.8:0.5093:0:1.2 +21 44529540 . A T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGACACGGTCTGGGAAC;RSEQ=AAGACTGCTGGAGAGTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:24.5:1:28:1:1:0:60:4:0.6667:0:1 +21 44588757 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGTGTCTAACGGGGGTGTG;RSEQ=GCTCTCCCTCCTCTGGCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:29:1:1:0:60:4:1:0:2 +21 44589215 . C T 85 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67277;SOR=1.63263;LSEQ=GTACCAAAGCTGAACATGGA;RSEQ=GTGACCATCCAGCACCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:1,7:3,7:10,8:0.4444:2,2:20.5:1:28.5:1:0.58824:2.83009:60:7:0.4118:0:1 1/0:7:4:2,2:1,2:3,4:0.5714:2,2:3.5:1:29.3:1:1:1.81:60:8:0.5714:0:1 +21 44985111 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48718;SOR=Inf;LSEQ=TCGTCTCAGGCTCGTAGTTC;RSEQ=CCTTCAACATGCCGGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:25.8:1:27.3:1:1:0:43.3:11:1:0:0 0/1:15:2:2,0:13,0:13,2:0.1333:1,0:12.5:1:24:0:1:0:58.5:4:0.1333:0:1 +21 44985473 . C T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67835;SOR=0.78435;LSEQ=GTGTCCGAGGGCACCAAGGC;RSEQ=GTCACCAAGTACACCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:16:10,6:18,14:32,16:0.3333:2,2:23.8:1:31.6:1:0.76255:1.29:52.2:32:0.3333:0:1.1 0/1:64:18:9,9:26,20:46,18:0.2813:2,2:25.6:1:30.4:1:0.78123:1.29463:46.4:36:0.2857:0:1.1 +21 45648880 . C T 226 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=325.91274;LSEQ=CCTCTCACGGTGGCGTCTCA;RSEQ=GGAAGCCCTGTCCACGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:844:1:0,1:513,330:843,1:0.0012:2,0:1:0:15:0:0.39218:0:60:0:0:0:1 0/1:755:210:121,89:327,218:545,210:0.2781:2,2:21.1:1:29.3:1:0.5635:1.10316:60:34:0.2742:0:1.2 +21 45648992 . T C 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21407;LSEQ=TTCCCTTCTGCAGGCAGACG;RSEQ=CGGTTTTCTCAGGACTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:843:711:269,442:56,75:131,711:0.8434:2,2:25.9:1:31.2:1:0.32878:1.22655:59.9:43.438:0.8445:0:1.1 1/0:751:402:174,228:135,210:345,402:0.5353:2,2:26:1:30.3:1:0.26416:1.19:60:29.923:0.5351:0:1.2 +21 45649209 . A G 123 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19048;SOR=0;LSEQ=TCCACAGGTGACACCACAGC;RSEQ=TGGTGGCTGCGCACACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:4,13:0,0:0,17:1:0,2:20.8:1:30.1:1:1:0:58.7:16:1:0:1.2 1/0:4:3:0,3:0,1:1,3:0.75:0,0:23.3:1:33:0:1:0:60:6:0.75:0:1 +21 45649428 . A T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51167;SOR=0;LSEQ=CACATCTATGTTGCTCCTGG;RSEQ=ACTGAGGGGCAAACGAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:110,59:169,2:0.0117:2,2:12:0:31:1:1:1.85726:60:4:0.0119:0:1 0/0:123:0:0,0:81,42:123,0:0:2,0:26.3:1:28.8:1:1:0:60:60.5:1:0:0.6 +21 45649437 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19561;SOR=Inf;LSEQ=GTTGCTCCTGGAACTGAGGG;RSEQ=CAAACGAGAGCTGCAGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:120,66:186,0:0:2,0:29.2:1:31.6:1:1:0:60:61:1:0:0.8 0/1:148:2:1,1:91,55:146,2:0.0135:2,2:24.5:1:27.5:1:1:1.64862:60:4:0.0137:0:1.5 +21 45649481 . G T 33 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08137;SOR=Inf;LSEQ=TGCCACAGAGAGAAGCTGGC;RSEQ=GTGCCCGGACCCACTCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:135,135:270,0:0:2,0:24.7:1:29.9:1:1:0:59.7:37.571:1:0:1.4 0/1:209:3:0,3:118,88:206,3:0.0144:2,0:7.7:1:21.3:1:0.081:0:46:2:0.0097:0:3 +21 45649494 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04082;LSEQ=AGCTGGCGGTGCCCGGACCC;RSEQ=CTCCGGACACCCCACAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:272:270:134,136:1,0:1,270:0.9926:0,2:26.5:1:30.3:1:0.49815:0:58.3:37.571:0.9925:0:1.8 1/1:240:203:109,94:20,15:35,203:0.8458:2,2:24.9:1:30:1:0.71829:1.14917:58.5:66.667:0.8475:0:1.6 +21 45649496 . T C 66 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12591;SOR=0;LSEQ=CTGGCGGTGCCCGGACCCAC;RSEQ=CCGGACACCCCACAGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:4:4,0:130,139:269,4:0.0147:2,0:9:0:33:0:0.05672:0:20:8:0.0153:0:4 0/0:244:0:0,0:131,113:244,0:0:2,0:23.5:1:28.6:1:1:0:56.4:16.429:1:0:1.5 +21 45649498 . C T 106 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.002;SOR=0;LSEQ=GGCGGTGCCCGGACCCACTC;RSEQ=GGACACCCCACAGGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:10:8,2:125,137:262,10:0.0365:2,2:5.1:1:32.2:1:0.05592:4.36:35.9:20:0.037:0:3 0/0:248:0:0,0:133,115:248,0:0:2,0:23.5:1:29.9:1:1:0:56.4:247:1:0:1.5 +21 45649499 . G A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00605;SOR=0.57743;LSEQ=GCGGTGCCCGGACCCACTCC;RSEQ=GACACCCCACAGGGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:101:51,50:119,144:263,101:0.2767:2,2:28.1:1:30.7:1:0.41192:1.23:59.7:32.667:0.2753:0:2.1 0/1:271:49:27,22:120,102:222,49:0.1808:2,2:24.9:1:29.6:1:1:1.04:59.9:48:0.1805:0:2.1 +21 45649509 . CA TG 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GACCCACTCCGGACACCCCA;RSEQ=GGGGCTGGGCGCCGGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:185,206:391,0:0:2,0:21.7:1:31.5:1:1:0:57.3:42.444:0.9974:0:1.5 0/1:301:24:13,11:147,129:276,24:0.0797:2,2:19.1:1:30.3:1:1:1.04:28.4:48:0.0803:0.0166:2.3 +21 45649510 . A G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.35939;LSEQ=ACCCACTCCGGACACCCCAC;RSEQ=GGGGCTGGGCGCCGGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:111:60,51:128,153:281,111:0.2832:2,2:9.2:1:30.4:1:0.14504:1.41:53.1:110:0.285:0:1.3 0/1:298:37:21,16:129,113:242,37:0.1242:2,2:7.6:1:27:1:0.72658:1.15:56.8:17.5:0.1268:0:1.1 +21 45649543 . G C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02508;SOR=0.68134;LSEQ=CGGTGCCTGGACCCGCCCTG;RSEQ=ACACCCCACGGGGGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:128:52,76:219,144:363,128:0.2607:2,2:24.8:1:31.9:1:0.00013:2.21905:57.8:24.6:0.2579:0:1.7 0/1:346:67:26,41:158,121:279,67:0.1936:2,2:25.9:1:31.5:1:0.00967:2.0548:56.7:134:0.2018:0:1.8 +21 45649580 . A G 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61208;SOR=1.38432;LSEQ=GGGCGCCGGTGCCTGGACCC;RSEQ=CTCCGGACACCCCATGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:8:8,0:366,199:565,8:0.014:2,0:31.1:1:22.5:1:0.0556:0:27.5:3:0.0107:0:3.9 0/1:416:8:6,2:244,163:407,8:0.0192:2,2:21.6:1:27.9:1:0.48614:2.00:25.6:7:0.0172:0:3.8 +21 45649582 . T C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.30831;SOR=1.79635;LSEQ=GCGCCGGTGCCTGGACCCAC;RSEQ=CCGGACACCCCATGGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:7:7,0:367,202:569,7:0.0122:2,0:30.6:1:25.7:1:0.10267:0:24.9:6:0.0108:0:4.1 0/1:416:9:5,4:243,164:407,9:0.0216:2,2:23.2:1:27.6:1:1:1.18487:29.1:8:0.0196:0:4 +21 45649584 . C T 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59414;SOR=1.3686;LSEQ=GCCGGTGCCTGGACCCACTC;RSEQ=GGACACCCCATGGGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:7:7,0:370,205:575,7:0.012:2,0:28.6:1:25.3:1:0.05589:0:24.9:2.5:0.0088:0:4.1 0/1:427:7:4,3:250,169:419,7:0.0164:2,2:21:1:29.1:1:1:1.10919:26.1:14:0.0166:0:3.7 +21 45649595 . T C 77 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.77233;SOR=1.29518;LSEQ=GACCCACTCCGGACACCCCA;RSEQ=GGGGGCTGGGCGCCGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:6:6,0:393,212:605,6:0.0098:2,0:16.5:1:25.8:1:0.09746:0:25.7:5:0.0085:0:4.3 0/1:473:6:4,2:277,189:466,6:0.0127:2,2:13.3:1:29.8:1:1:1.36:25.3:12:0.0129:0:4 +21 45649640 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=4.60008;LSEQ=CCCGCCCTGGACACCCTGGT;RSEQ=GGGGCTGGGCACTGGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:104:60,44:408,286:694,104:0.13:2,2:23.7:1:30.2:1:0.83176:1.04606:59.3:33.667:0.1283:0:1.2 0/1:709:289:170,119:252,167:419,289:0.4076:2,2:22.1:1:29.6:1:0.75548:1.05619:58.7:95.333:0.4086:0:1.2 +21 45649666 . G A 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1e-05;SOR=0.66375;LSEQ=TGGGCACTGGGGAGCGCGGG;RSEQ=GTCTAGCACTCGTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:962:496:272,224:261,203:464,496:0.5156:2,2:27.2:1:30.9:1:0.69667:1.05874:59.8:69.857:0.5186:0:1.2 0/1:947:392:219,173:301,251:552,392:0.4139:2,2:25.1:1:29.3:1:0.69089:1.06:59.9:97:0.4163:0:1.2 +21 45649748 . C T 198 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTGCACACCAGGATGCCATC;RSEQ=CATGCCAAGGGGAGGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:88:43,45:334,377:711,88:0.11:2,2:24.4:1:30.8:1:0.82104:1.08:60:43:0.1101:0:1.9 0/0:770:0:0,0:363,407:770,0:0:2,0:23.1:1:30:1:1:0:60:50.333:1:0:0.5 +21 45649778 . A G 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13215;LSEQ=GGGAGGCTGCAGGAAATGCC;RSEQ=TGCGCACCATCGAGGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:749:635:273,362:51,62:113,635:0.8478:2,2:24.2:1:31:1:0.68143:1.09062:60:62.5:0.8503:0:1.5 0/1:654:277:115,162:172,204:376,277:0.4235:2,2:23.7:1:30.7:1:0.30016:1.18741:60:554:0.4281:0:1.4 +21 45649848 . T C 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.16238;LSEQ=AGGCAAGGGACTTTTGCCTT;RSEQ=TGAAAGTTTTTTGAAACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:891:755:399,356:71,62:133,755:0.8474:2,2:24.5:1:32.6:1:0.92521:1.02173:60:93.375:0.8518:0:1.3 0/1:705:334:177,157:184,186:370,334:0.4738:2,2:22.5:1:30.8:1:0.40666:1.14:60:110.333:0.4749:0:1.3 +21 45650007 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13782;SOR=Inf;LSEQ=AAAATGGTCAGGGCAGCAGC;RSEQ=ATGGGGGGTGTCCCTAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:30,252:282,0:0:2,0:22.6:1:31.5:1:1:0:60:30.333:1:0:1.1 0/1:167:2:1,1:21,144:165,2:0.012:2,2:17:1:27.5:1:0.24681:6.72:60:4:0.0122:0:1 +21 45650009 . T C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0;SOR=0.31925;LSEQ=AATGGTCAGGGCAGCAGCGA;RSEQ=GGGGGGTGTCCCTAAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:275:173:18,155:2,36:38,173:0.6291:2,2:20:1:30:1:0.54007:2.08:60:85.5:0.8221:0:1.2 0/1:154:54:10,44:7,72:79,54:0.3506:2,2:21.7:1:29.3:1:0.11805:2.32:60:17:0.3864:0:1.2 +21 45650085 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00205;SOR=0.1932;LSEQ=CCCTACTTGGAAGTCTCCCC;RSEQ=AGGCTCCCAGCTCCAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:53:0,53:0,12:12,53:0.8154:0,1:21.5:1:32.5:1:1:0:60:52:0.8387:0:1.5 0/1:22:10:1,9:1,11:12,10:0.4545:2,2:16.7:1:30.2:1:1:1.21:60:20:0.4545:0:1.8 +21 45650800 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTGCTCTGTCGCCCAGG;RSEQ=TGGAGTGTAGTGGCGTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:28.5:1:32:1:1:0:51.5:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 45651003 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05816;SOR=Inf;LSEQ=ATCTCGTGATCCACTCGCCT;RSEQ=GGCCTCCCAAAGTGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:30,0:0:1,0:21.8:1:33.5:1:1:0:44.9:60:1:0:0.1 0/1:20:3:3,0:17,0:17,3:0.15:1,0:21.7:1:32:0:1:0:42.7:6:0.15:0:1 +21 45651275 . G A 214 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02519;LSEQ=CACGTGGCCGCGTTTTTCTC;RSEQ=CCGGTACTGACTGGATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1140:151:71,80:454,532:986,151:0.1325:2,2:25.1:1:29.6:1:0.86099:1.04:60:29.2:0.1305:0:1.2 0/0:1044:4:3,1:523,516:1039,4:0.0038:2,2:8.8:1:26.3:1:0.62434:2.96:60:8:0.0039:0:1 +21 45651380 . C CT 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.65587;SOR=2.01678;LSEQ=GGATCTTAGAGGAAAAGGGT;RSEQ=TTTTTTTTCATCCTTGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:2:0,2:81,312:393,2:0.0051:2,0:27.5:1:29.5:1:1:0:60:4:0.0051:0:0 0/1:295:3:1,2:62,230:292,3:0.0102:2,2:34.3:1:29.7:1:0.51495:1.85:60:6:0.0103:0:0.7 +21 45651413 . A G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CTTGAGTAGAAAGTGTTGCA;RSEQ=GGAAGTATTTATTCCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:180:180:8,172:0,0:0,180:1:0,1:24.5:1:31.3:1:1:0:59.9:35:1:0:1.2 1/1:118:106:4,102:1,11:12,106:0.8983:2,1:23.9:1:30.3:1:0.42079:2.29604:60:52:0.8966:0:1.2 +21 45651497 . A G 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=0.05995;LSEQ=TGAGATGAGGGTTTTCTCTT;RSEQ=CAGAGGGGCTTCATTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:32:0,32:0,2:2,32:0.9412:0,1:20.8:1:32.8:1:1:0:60:31:0.9394:0:1.3 0/1:17:8:0,8:0,9:9,8:0.4706:0,0:26.3:1:31.8:1:1:0:60:16:0.4706:0:1.5 +21 45655124 . A T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00289;SOR=1.86859;LSEQ=CCCTGGCCCCACTGTCGGGC;RSEQ=CAGCTCAGCACGCAGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:95:63,32:88,25:113,95:0.4567:2,2:27:1:30.7:1:0.08559:1.7829:60:94:0.4585:0:1.1 1/0:175:107:75,32:53,15:68,107:0.6114:2,2:28.4:1:29.2:1:0.29591:1.50408:60:106:0.6092:0:1 +21 45655163 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34114;SOR=3.49514;LSEQ=CCGGGACCTTACCTGTCTGG;RSEQ=TGCCGACAGTCAGGTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:1:0,1:201,127:328,1:0.003:2,0:1:0:29:0:0.38906:0:60:2:0.0031:0:1 0/1:284:3:1,2:174,107:281,3:0.0106:2,2:24.7:1:28:1:0.56068:3.23848:60:6:0.0106:0:1 +21 45655658 . G A 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3;SOR=Inf;LSEQ=AGTCCCAGTAGCCAGGGACC;RSEQ=CTGAGCCTGTCGGGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:20.5:1:31.5:1:1:0:60:4:0.2857:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:46:0:32:0:1:0:60:2:1:0:1 +21 45656668 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51364;SOR=0;LSEQ=ACTGGAAGAAACAGTGAATG;RSEQ=GCCAGGGAGGGGGTTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:115,12:127,2:0.0155:2,2:16.5:1:30.5:1:0.1921:9.24732:60:4:0.0155:0:1 0/0:90:0:0,0:78,12:90,0:0:2,0:24.5:1:28.7:1:1:0:60:89:1:0:0.1 +21 45656774 . C T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01874;SOR=1.35505;LSEQ=CACATGCAGTGTAACCTCAA;RSEQ=GCTCAAAACCTCCTGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:222:136,86:182,131:313,222:0.4142:2,2:26.7:1:31.1:1:0.47631:1.14:59.9:221:0.4178:0:1.1 0/1:470:230:125,105:135,105:240,230:0.4894:2,2:27:1:29.5:1:0.71087:1.07982:60:31.857:0.4848:0:1.2 +21 45657140 . C T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20815;SOR=Inf;LSEQ=GCAAAATCTGTTTTCGGAGG;RSEQ=TGATGCCCAGGCCATGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:15,131:146,0:0:2,0:24.8:1:32.9:1:1:0:60:72:1:0:0.1 0/1:123:2:0,2:19,102:121,2:0.0163:2,0:7.5:1:30.5:1:1:0:60:4:0.0164:0:1 +21 45657142 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=AAAATCTGTTTTCGGAGGCT;RSEQ=ATGCCCAGGCCATGAAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:13,131:144,0:0:2,0:24.7:1:31.7:1:1:0:60:27.8:1:0:0.1 0/1:117:2:1,1:17,98:115,2:0.0171:2,2:9.5:1:27:1:0.28515:5.63:60:4:0.0172:0:1.5 +21 45657848 . C G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCTTGGCCTCCCAAAGT;RSEQ=CTGGGATTACAGGAGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:16:1:34:0:1:0:40.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +21 45657970 . T C 48 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAGGTTTGTGCTGCGGTGC;RSEQ=TCGTCCTTATTCCTGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:10.7:1:30.7:1:1:0:60:6:0.75:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:32:1:1:0:60:4:1:0:1 +21 45658256 . C T 60 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02145;SOR=Inf;LSEQ=AGGCTGCTCCCAGTGCCCTG;RSEQ=GGCCAGCAGTCCACACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:300,151:451,0:0:2,0:26:1:31.5:1:1:0:60:89.2:1:0:0.1 0/1:392:5:1,4:252,135:387,5:0.0128:2,2:6:1:26.2:1:0.05546:7.42883:60:10:0.013:0:1.2 +21 45658443 . C T 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTATCTTCCAAACAGGAA;RSEQ=AGGCTGGTTCCCATGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:155,350:505,0:0:2,0:24.4:1:32:1:1:0:59.9:83.167:1:0:0.3 0/1:408:22:7,15:120,265:385,22:0.0539:2,2:22.4:1:27.7:1:1:1.03:60:44:0.0549:0:1 +21 45658474 . A G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01962;SOR=1.55271;LSEQ=CCATGAGCAGGAGGTAGTTA;RSEQ=GCCCATCACAGAAATGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:114:12,102:23,131:154,114:0.4254:2,2:24.8:1:31.6:1:0.36017:1.49019:60:113:0.4297:0:1.2 1/0:200:107:12,95:12,81:93,107:0.535:2,2:23.8:1:30.5:1:0.82807:1.1719:60:52.5:0.5385:0:1.1 +21 45658538 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12288;SOR=Inf;LSEQ=CTCTGTTCTCCATGGGAATT;RSEQ=GGGGTCCGGGGCCAGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:1,86:87,0:0:1,0:22.7:1:29.9:1:1:0:59.2:86:1:0:0.3 0/1:48:2:0,2:0,46:46,2:0.0417:1,0:26.5:1:30:1:1:0:60:4:0.0426:0:1.5 +21 45660599 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=GCACCTCCAGGCGAGCCCCG;RSEQ=AGGCCCCGCGTCCGAGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:6,2:8,2:0.2:2,2:26.5:1:27.5:1:1:2.64575:60:4:0.2:0:1 0/0:7:0:0,0:4,3:7,0:0:2,0:7.3:1:29.4:1:1:0:60:6:1:0:0.1 +21 45660631 . G A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49503;SOR=Inf;LSEQ=CCGAGCCGAGCTGGGGACGC;RSEQ=CGGGCCGAGCCACCCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:25,14:39,0:0:2,0:17.5:1:30.8:1:1:0:60:38:1:0:0.2 0/1:43:2:1,1:28,13:41,2:0.0465:2,2:7.5:1:29:1:1:2.11228:60:4:0.05:0:1 +21 45660676 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.04803;SOR=Inf;LSEQ=CCGCGGCGCCTCCGCTCCTT;RSEQ=CCCGGCTCACCTGCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:198,90:288,0:0:2,0:22.2:1:32.1:1:1:0:60:56.6:1:0:0.2 0/1:255:4:2,2:168,83:251,4:0.0157:2,2:16:1:25.5:1:0.6026:2.0181:60:3:0.0119:0:2 +21 45660682 . C T 55 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.3766;SOR=0.27624;LSEQ=CGCCTCCGCTCCTTCCCCGG;RSEQ=TCACCTGCCCAGCCGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:4:1,3:229,102:331,4:0.0119:2,2:18.3:1:27.8:1:0.09293:6.69358:60:8:0.0121:0:1 0/0:302:1:0,1:190,111:301,1:0.0033:2,0:1:0:23:0:0.37086:0:60:2:0.0034:0:1 +21 45660698 . C T 50 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10702;SOR=5.59191;LSEQ=CCGGCTCACCTGCCCAGCCG;RSEQ=ATGGTGCGGGCGGAGACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:1:0,1:315,179:494,1:0.002:2,0:1:0:24:0:0.36364:0:60:2:0.0021:0:1 0/1:446:5:1,4:263,178:441,5:0.0112:2,2:9.4:1:21.8:1:0.16369:5.88843:60:4:0.0091:0:1 +21 45660835 . C A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0713;SOR=0.56185;LSEQ=GGCTCTAACTGCGCTCCCGC;RSEQ=GCGCCCGAGGCTCTGAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:68:3,65:6,58:64,68:0.5152:2,1:25.4:1:32.7:1:0.31445:2.22805:60:136:0.5231:0:1.1 0/1:67:25:2,23:4,38:42,25:0.3731:2,2:22.2:1:30.2:1:1:1.20713:60:50:0.3788:0:1.1 +21 46552894 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49025;SOR=Inf;LSEQ=AAAGCCACAGTCAGCGTTTC;RSEQ=CTGCCAGCTCCTCCAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:15,8:23,0:0:2,0:30.6:1:30.6:1:1:0:60:46:1:0:0 0/1:25:2:1,1:14,9:23,2:0.08:2,2:34:0:31.5:1:1:1.52748:60:4:0.08:0:1 +21 46552998 . T C 94 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GCGCAAAGCCCTGGTGAGCC;RSEQ=GGCTCGTTTCCCTGGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:29.9:1:31.5:1:1:0:60:16:1:0:1.9 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:27:1:30.2:1:1:0:60:10:0.7143:0:1 +21 47061267 . A G 117 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33088;SOR=0.18157;LSEQ=CAGGAACTGCAAATAATAGA;RSEQ=AGTCTTTAGGGTCTAACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:4,9:0,2:2,13:0.8667:0,2:24.2:1:31.8:1:1:0:60:26:0.8667:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:47:0:30:0:1:0:60:2:0.5:0:1 +21 47061914 . TTTC T 28 d5;v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=17.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCAGGCTTTTTTTTTTTTTT;RSEQ=TTCTATTTTAAGGTTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:23:1:21:1:1:0:49:1:1:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:28.5:1:1:0:42:4:1:0.5:1 +22 16346327 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54448;SOR=0;LSEQ=TTAACATAACTAAGCTTCTC;RSEQ=AAGCTGGTATTCATTATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:96,17:113,2:0.0174:2,0:10.5:1:30:1:1:0:28.5:4:0.0179:0:2.5 0/0:61:0:0,0:57,4:61,0:0:2,0:22.3:1:31:1:1:0:35.2:122:1:0:0.3 +22 16346383 . A T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01743;SOR=0.28478;LSEQ=TGTCTGGTTATATCTGCATT;RSEQ=GGTTATTGTTGATGCTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:21:18,3:116,15:131,21:0.1382:2,2:32.8:1:30.6:1:0.71716:1.28658:28.5:42:0.14:0:1.9 0/1:92:4:4,0:81,7:88,4:0.0435:2,0:23.8:1:25.8:1:1:0:31.5:3:0.033:0:1.8 +22 16346391 . G A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00036;SOR=0.3593;LSEQ=TATATCTGCATTAGGTTATT;RSEQ=TTGATGCTAGTGACAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:81:71,10:50,5:55,81:0.5912:2,2:34:1:28.4:1:0.78122:1.40501:27.6:162:0.5956:0:1.3 0/1:88:30:27,3:54,4:58,30:0.3409:2,2:31.6:1:26.4:1:0.68602:1.49282:26.7:60:0.3409:0:1.2 +22 16346553 . A G 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96734;LSEQ=ATTTTTTTCTTAAAAATAAG;RSEQ=TAAACGAAATGACATCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:11,107:118,2:0.0167:2,2:32:1:34:0:0.19076:9.36:34.5:4:0.0167:0:1.5 0/1:124:2:1,1:22,99:121,2:0.0161:2,2:31:1:32:1:0.34026:4.42:32.5:4:0.0164:0:1.5 +22 16347994 . C A 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCTAGGAGAGTCTCAAA;RSEQ=AGGAAGACAACCGATATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:49.5:1:30.5:1:1:0:20:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 16349168 . T C 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GAAATTGGACAGATAGTAGC;RSEQ=TTATGTTGGTCCAGATAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:4,2:5,2:7,6:0.4615:2,2:27.3:1:31.2:1:1:1.22862:22.7:5:0.4167:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:29.5:1:1:0:24:4:1:0:1 +22 16349306 . C T 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TGGACACACACACACACACA;RSEQ=GCAGTTTATTGCATTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:258,28:286,0:0:2,0:37.5:1:31.6:1:1:0:27.1:34.75:1:0:0.1 0/1:196:12:12,0:166,18:184,12:0.0612:2,0:37.3:1:30.5:1:0.6071:0:26.7:24:0.0625:0:1.3 +22 16349345 . C A 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13915;SOR=0;LSEQ=GGGTTTTATACATAAAATTA;RSEQ=CCAAGTTGCAAATATATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:4:4,0:157,16:173,4:0.0225:2,0:16.3:1:27:1:1:0:27.8:3:0.0178:0:2.3 0/0:132:0:0,0:120,12:132,0:0:2,0:16.9:1:29.3:1:1:0:26.5:43:1:0:0.3 +22 16349359 . A G 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.32327;SOR=3.85748;LSEQ=AAATTACCCAAGTTGCAAAT;RSEQ=TATGTCTACCACCCTTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:1,0:94,7:101,1:0.0098:2,0:16:0:16:0:1:0:20:0:0:0:1 0/1:81:3:3,0:68,10:78,3:0.037:2,0:9.3:1:26.7:1:1:0:27.3:6:0.037:0:2 +22 16349412 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.51754;SOR=Inf;LSEQ=CAGCAGGATGCAGCGGAACC;RSEQ=CCCTGACTTGCTGACAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:22,0:0:2,0:17:1:31.6:1:1:0:30.3:44:1:0:0.8 0/1:35:2:1,1:16,17:33,2:0.0571:2,2:19:0:31.5:1:1:1.06:31:4:0.0588:0:1.5 +22 16349415 . C G 49 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27632;SOR=Inf;LSEQ=CAGGATGCAGCGGAACCCCC;RSEQ=TGACTTGCTGACAAGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:22,0:0:2,0:20:1:32.2:1:1:0:30.3:44:1:0:0.8 0/1:35:3:1,2:16,16:32,3:0.0857:2,2:48:0:31.3:1:1:1.96199:26:6:0.0857:0:1 +22 16349432 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13975;SOR=0;LSEQ=CCCCTGACTTGCTGACAAGC;RSEQ=CAGACCAGTCTAGAAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:20,2:0.0909:2,2:24.5:1:31.5:1:1:1.21:20:4:0.1:0:1.5 0/0:36:0:0,0:16,18:34,0:0:2,0:30.2:1:31.6:1:1:0:29.4:68:0.9444:0:0.6 +22 16349433 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13975;SOR=0;LSEQ=CCCTGACTTGCTGACAAGCG;RSEQ=AGACCAGTCTAGAAGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:20,2:0.0909:2,2:17:0:32.5:1:1:1.21:20:4:0.0909:0:1.5 0/0:36:0:0,0:17,19:36,0:0:2,0:30.6:1:32.7:1:1:0:28.8:72:1:0:0.6 +22 16349445 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13975;SOR=0;LSEQ=GACAAGCGCAGACCAGTCTA;RSEQ=AAGTGGCCCTGTACATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:9,11:20,2:0.0909:2,2:15.5:1:31:1:1:1.21:21:4:0.0909:0:1 0/0:36:0:0,0:17,19:36,0:0:2,0:26.1:1:31.9:1:1:0:28.8:72:1:0:0.6 +22 16349528 . G T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32178;SOR=3.93413;LSEQ=TGTTTCCGCCACCTCTGTGA;RSEQ=GAAGCAGATACCCGGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:1:0,1:172,171:343,1:0.0029:2,0:1:0:30:0:1:0:23:2:0.003:0:1 0/1:264:3:1,2:131,130:261,3:0.0114:2,2:19:1:29:1:1:2.01023:47.7:6:0.0118:0:1.7 +22 16350172 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.16903;SOR=Inf;LSEQ=CCTACTCTGCCTTTTGGGTG;RSEQ=GCTTATCAGGTTGTCCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:71,40:111,0:0:2,0:21.6:1:31.4:1:1:0:33.7:54.5:1:0:0.3 0/1:78:2:1,1:52,24:76,2:0.0256:2,2:16:0:31.5:1:0.54113:2.14325:22:4:0.0263:0:1.5 +22 16350211 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51361;SOR=0;LSEQ=TGGCAGGCAGGGCTCTAAGT;RSEQ=CAGTAACTTGATTTGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:74,39:113,2:0.0174:2,0:24.5:1:27:1:0.54783:0:26:4:0.0177:0:1.5 0/0:80:0:0,0:55,25:80,0:0:2,0:30.8:1:31.1:1:1:0:34.5:79:1:0:0.3 +22 16350245 . C A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07175;SOR=0.39313;LSEQ=TGCTGTTGTAGTTGCTTAGG;RSEQ=ACAGCAGCACTTCCGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:16:8,8:76,72:148,16:0.0976:2,2:17.9:1:31.4:1:1:1.05523:21.3:32:0.1006:0:1 0/1:123:5:3,2:63,55:118,5:0.0407:2,2:18:1:25.6:1:1:1.31:20.8:10:0.0407:0:1 +22 16350293 . C T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00665;SOR=0.51188;LSEQ=CACTGCTGAGGCGCACTGAG;RSEQ=ATCCCACTGCAGGAAACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:863:62:25,37:352,449:801,62:0.0718:2,2:27.6:1:28.4:1:0.59811:1.16007:37.9:61:0.072:0:3.1 0/1:630:24:9,15:283,323:606,24:0.0381:2,2:25.9:1:26.3:1:0.41091:1.45941:38.1:23:0.0369:0:3.3 +22 16350323 . T C 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.61773;LSEQ=CAGGAAACACTGAGGTGTGC;RSEQ=CTAAGCAACAAAAACACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1070:757:305,452:120,192:312,757:0.7075:2,2:32.3:1:30.8:1:0.58332:1.08:39.7:26.036:0.7037:0:1.3 1/0:773:463:198,265:120,190:310,463:0.599:2,2:31.8:1:29.8:1:0.26456:1.18:39:27.938:0.5905:0:1.3 +22 16350338 . C T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0068;SOR=0.56751;LSEQ=TGTGCTCTAAGCAACAAAAA;RSEQ=ACCTCTCCCAGGCACCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1180:85:27,58:411,683:1094,85:0.072:2,2:25.3:1:29:1:0.29737:1.29239:41.6:41.5:0.0712:0:2.8 0/1:806:34:10,24:307,464:771,34:0.0422:2,2:27.4:1:27.9:1:0.28249:1.58707:42.4:68:0.0427:0:2.9 +22 16350349 . G C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.16533;LSEQ=CAACAAAAACACCTCTCCCA;RSEQ=GCACCCACGCTCGATTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1079:39:14,25:379,660:1039,39:0.0361:2,2:23.8:1:29.9:1:1:1.02541:50.5:18.5:0.035:0:1.1 0/1:697:74:25,49:238,383:621,74:0.1062:2,2:24.1:1:29.5:1:0.52637:1.21762:50.6:73:0.1072:0:1.1 +22 16350350 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62003;SOR=1.20214;LSEQ=AACAAAAACACCTCTCCCAG;RSEQ=CACCCACGCTCGATTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1066:22:7,15:379,664:1043,22:0.0206:2,2:21.3:1:29.9:1:0.82358:1.22284:39.5:44:0.0212:0:2 0/1:688:17:8,9:250,421:671,17:0.0247:2,2:23.4:1:27.1:1:0.4515:1.50:42.7:34:0.0253:0:2.1 +22 16350425 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66387;SOR=0.90381;LSEQ=TTTGAAGTAAATCCAAGATA;RSEQ=GTGCATATTACAAGTATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:140:34,106:42,68:110,140:0.56:2,2:15.1:1:31.1:1:0.01919:1.92046:41.7:69:0.5656:0:1.2 1/0:129:69:13,56:18,42:60,69:0.5349:2,2:16.6:1:29.8:1:0.15341:1.83731:39.3:68:0.5313:0:1.2 +22 16351604 . G C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTCATCAATTGAGAAAAAAA;RSEQ=CCGGTATCCTTTAGCTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19:1:32:1:1:0:28:4:0.5:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29.5:1:1:0:47:4:1:0:2 +22 17052983 . TA T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50067;SOR=Inf;LSEQ=GAACAGCTCAAAGCAATTTC;RSEQ=CACGAGATCCTCTCTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:44,100:144,0:0:2,0:20.2:1:29:1:1:0:28:288:0.9931:0:0.1 0/1:166:2:1,1:63,101:164,2:0.012:2,2:33:1:32.5:1:1:1.60:25:4:0.012:0:0.5 +22 17052988 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49937;SOR=Inf;LSEQ=GCTCAAAGCAATTTCTACAC;RSEQ=AGATCCTCTCTCTGAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:52,113:165,0:0:2,0:21.5:1:30.6:1:1:0:30.3:54:1:0:0.1 0/1:179:2:1,1:66,111:177,2:0.0112:2,2:20:1:28.5:1:1:1.68:24.5:4:0.0114:0:1 +22 17053001 . T C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11532;SOR=0;LSEQ=TCTACACGAGATCCTCTCTC;RSEQ=GAAATCACTGCGCAGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:1,2:62,138:200,3:0.0148:2,2:34:1:31.7:1:1:1.11:25.3:6:0.0149:0:1.3 0/0:213:0:0,0:76,137:213,0:0:2,0:30.8:1:29.1:1:1:0:29.7:212:1:0:0.1 +22 17053093 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21545;SOR=Inf;LSEQ=TTTTCTTTATTACAGAAAAA;RSEQ=TAACTGACTTTGGCTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:13,73:86,0:0:2,0:17.3:1:31.2:1:1:0:26.6:172:1:0:0.1 0/1:75:2:1,1:7,66:73,2:0.0267:2,2:12:1:28:1:0.20324:8.89:23.5:4:0.0267:0:1.5 +22 17053109 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51097;SOR=0;LSEQ=AAAAATAACTGACTTTGGCT;RSEQ=ATCTCAGCATGTTTTTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:5,45:50,2:0.0385:2,2:12.5:1:28.5:1:0.21946:8.31:25:4:0.0385:0:1.5 0/0:36:0:0,0:3,33:36,0:0:2,0:22.1:1:29.4:1:1:0:28.9:35:1:0:0.2 +22 17053602 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22583;SOR=Inf;LSEQ=AGGTGAAAAATATGAGCTAT;RSEQ=TTCTGTCTGTTAAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:54,36:90,0:0:2,0:31.8:1:30:1:1:0:44.2:180:1:0:0.1 0/1:82:2:1,1:46,34:80,2:0.0244:2,2:33.5:1:28.5:1:1:1.34787:45:4:0.0244:0:1 +22 17053658 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49813;SOR=0;LSEQ=GCCCAGGTAAATGTATGTTT;RSEQ=AGATTACTAGATAACTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:31,23:54,2:0.0357:2,2:11:1:31.5:1:1:1.34054:48.5:4:0.0357:0:1 0/0:48:0:0,0:21,27:48,0:0:2,0:13.9:1:30.8:1:1:0:41.1:96:1:0:0.1 +22 17053738 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14376;SOR=Inf;LSEQ=AGTCCACATAAATAAATGAA;RSEQ=TAGACTAATAATAGTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:8,19:27,0:0:2,0:32:1:32:1:1:0:36.7:54:1:0:0.1 0/1:17:2:0,2:3,12:15,2:0.1176:2,0:40:1:31:1:1:0:38.5:4:0.1176:0:1 +22 17054098 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21001;SOR=Inf;LSEQ=CTCAGTATTTAATTCAGCTA;RSEQ=TACAGGTAAAATAATGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:65,120:185,0:0:2,0:18.4:1:32.4:1:1:0:27.7:45.25:1:0:0.2 0/1:157:2:1,1:59,96:155,2:0.0127:2,2:21:1:27:1:1:1.62:40:4:0.0129:0:1 +22 17054103 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03235;LSEQ=TATTTAATTCAGCTAGTACA;RSEQ=GTAAAATAATGTAAAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:18:6,12:52,88:140,18:0.1139:2,2:19.4:1:31.9:1:0.80196:1.18057:34.6:36:0.1161:0:1 0/1:128:15:7,8:40,73:113,15:0.1172:2,2:14.5:1:29.9:1:0.40642:1.59:28.9:30:0.1172:0:1 +22 17054291 . T C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.62735;SOR=1.7038;LSEQ=CATGCAGAAACTGAACCTGA;RSEQ=TTGTTTTTTTTGAATCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:16,15:31,2:0.0606:2,0:15:0:30:1:0.48864:0:20.5:4:0.0606:0:1.5 0/1:20:2:2,0:9,9:18,2:0.1:2,0:9:1:32:1:0.47895:0:20:4:0.1:0:1 +22 17054720 . T C 33 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGTAGGTTTCACTGTGTG;RSEQ=ATGGATTAAAATATCCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:26.5:1:30:1:1:0:46.5:4:1:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:22:1:33:0:1:0:36:4:0.6667:0:1 +22 17055316 . CTA C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.21352;SOR=Inf;LSEQ=ATTTGTATACTGATTTAAGA;RSEQ=TATATATATTTTTCTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:161,27:188,0:0:2,0:23.3:1:31.8:1:1:0:32.5:187:1:0:0.1 0/1:162:2:1,1:132,28:160,2:0.0123:2,2:23:1:30:1:0.32689:4.64984:24.5:4:0.0124:0:0 +22 17055405 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23313;SOR=0;LSEQ=GAGGTTTGGCCTGCTTTTGG;RSEQ=GTCCTATTGTCGTGCATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:67,37:104,2:0.0189:2,2:8.5:1:30.5:1:1:1.80001:60:4:0.0194:0:1.5 0/0:113:0:0,0:74,39:113,0:0:2,0:12:1:27.9:1:1:0:39.5:112:1:0:0.1 +22 17055458 . G A 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=0.25548;LSEQ=AGCACCTGAATAGGCAAGTC;RSEQ=AGGCAATGGAAAAGCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:33:17,16:10,24:34,33:0.4925:2,2:8.6:1:30.5:1:0.08374:2.51:39.8:66:0.4925:0:1.1 0/1:66:13:5,8:23,30:53,13:0.197:2,2:10.2:1:28.2:1:1:1.22291:36.1:26:0.197:0:1.1 +22 17055486 . C T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.09054;SOR=0;LSEQ=GGAAAAGCTCATTAACTTAA;RSEQ=TGACATTGTCAAACAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:3:1,2:60,101:161,3:0.0183:2,2:22:1:22.7:1:1:1.18694:34.3:2:0.0123:0:1.3 0/0:200:0:0,0:85,115:200,0:0:2,0:22.8:1:30.9:1:1:0:37.3:49:1:0:0.4 +22 17055569 . T G 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=7.05675;LSEQ=TGAGACTCTTTTCACTGCAG;RSEQ=GGGGCAGAGTTGTTTAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:16:5,11:8,28:36,16:0.3077:2,2:11.3:1:31.8:1:0.50602:1.58:33.5:32:0.32:0:1.2 1/0:63:48:17,31:2,13:15,48:0.7619:2,2:13.4:1:30.3:1:0.12242:3.50:35.9:47:0.7581:0:1.1 +22 17055768 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATTGTGAGAATTAAATT;RSEQ=CATGAGATATGCAAAGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:22.5:1:31:1:1:0:24.5:4:0.2857:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:31:0:1:0:60:2:1:0:0 +22 17082880 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.51107;SOR=0;LSEQ=GGGAGGAGGAACCCGAGCAG;RSEQ=GGCGGCGGCGGCCGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:126,12:138,2:0.0143:2,2:19:1:26.5:1:0.1777:10.12807:22.5:4:0.0144:0:1 0/0:101:0:0,0:86,14:100,0:0:2,0:27.1:1:30.8:1:1:0:44.9:24:1:0:0.1 +22 17082895 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.51929;SOR=0;LSEQ=AGCAGCGGCGGCGGCGGCCG;RSEQ=GGCGGCGGGAGCCCCCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:167,32:199,2:0.01:2,2:24.5:1:27.5:1:0.30209:5.15456:26.5:4:0.0101:0:1.5 0/0:133:0:0,0:101,32:133,0:0:2,0:26.2:1:30.3:1:1:0:38.1:43.333:1:0:0.1 +22 17519358 . GT G 53 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATGTAGTCCCATATGTT;RSEQ=TTTTTTTTTTTTGCGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:30.7:1:33.7:1:1:0:26.3:6:0.3333:0:0.3 0/0:2:0:0,0:2,0:2,0:0:0,0:17:1:31:0:1:0:28:4:1:0:0.5 +22 17519531 . A G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04633;SOR=Inf;LSEQ=TACCAGAGCAGTTGTATTAT;RSEQ=TTTCAAAATGTAAGATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:83,62:145,0:0:2,0:28.2:1:29.3:1:1:0:57.3:71.5:1:0:0.3 0/1:127:4:2,2:77,46:123,4:0.0315:2,2:27.3:1:31.5:1:0.63271:1.66678:55.8:8:0.032:0:1.5 +22 17519556 . A G 33 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50104;SOR=0;LSEQ=AAAATGTAAGATGATTTTTA;RSEQ=AAGCCTGAGTACCTAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:90,79:169,2:0.0117:2,2:6:1:33.5:1:1:1.13837:60:4:0.0121:0:1 0/0:148:0:0,0:78,70:148,0:0:2,0:28.8:1:29.6:1:1:0:57.8:147:1:0:0.2 +22 17519565 . G A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.602;SOR=2.27438;LSEQ=GATGATTTTTAAAAGCCTGA;RSEQ=TACCTAAGATGCAATTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:91,80:171,1:0.0058:2,0:1:0:24:0:1:0:50:2:0.0058:0:1 0/1:152:2:1,1:78,72:150,2:0.0132:2,2:43.5:1:31:1:1:1.08274:50:4:0.0134:0:1 +22 17519579 . A G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04461;LSEQ=GCCTGAGTACCTAAGATGCA;RSEQ=TTATATGAACTCTACTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:54:25,29:63,59:122,54:0.3068:2,2:24.6:1:33.3:1:0.62412:1.23713:56.1:108:0.3086:0:1 0/1:156:3:1,2:75,78:153,3:0.0192:2,2:23:1:30.7:1:1:1.91533:57.7:6:0.0194:0:1.3 +22 18501543 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATCTATCTATCTACACACA;RSEQ=ACACACATACACACATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 18501960 . CA C 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.52128;LSEQ=GACAGAGGGAGACCCTGTCT;RSEQ=AAAAAAAAAGGACCCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:4,0:33,0:33,4:0.1081:1,0:32.8:1:32.5:1:1:0:60:8:0.1081:0:0.3 0/1:17:1:1,0:16,0:16,1:0.0588:1,0:14:0:32:0:1:0:60:2:0.0588:0:0 +22 18502110 . T G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07045;SOR=0.59195;LSEQ=TGGCAAATCATTGGATATGG;RSEQ=GGGGAAAGTGGAAATATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:38:15,23:83,116:199,38:0.1603:2,2:26.6:1:30.5:1:0.85863:1.09666:60:18:0.1558:0:1.1 0/1:207:21:11,10:80,106:186,21:0.1014:2,2:29.4:1:30.1:1:0.48904:1.45:59.5:42:0.1019:0:1.2 +22 18502135 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19277;SOR=Inf;LSEQ=AAAGTGGAAATATCTATTAT;RSEQ=TCGGTTGGAAATAAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:71,120:191,0:0:2,0:23.5:1:31.9:1:1:0:59.7:62.667:1:0:0.3 0/1:150:2:1,1:63,85:148,2:0.0133:2,2:27:1:28:1:1:1.35:60:4:0.0135:0:1.5 +22 18502211 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17354;SOR=2.34118;LSEQ=TGTCTCACGCCGGTAATCCC;RSEQ=GCACTTTGGGAGGCCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:20:4,16:3,12:15,20:0.5714:2,2:22.1:1:32.4:1:1:1:54.5:40:0.5714:0:1.4 1/0:25:19:3,16:1,5:6,19:0.76:2,2:20.8:1:30.9:1:1:1.06388:55.5:38:0.7917:0:1.3 +22 18502467 . T TA 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.79699;SOR=1.15121;LSEQ=CAAGACTCTGTCTCAAAAAT;RSEQ=AAAAAAAAAGAAAAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:12,4:6,3:9,16:0.6154:2,2:30.8:1:29.4:1:0.67288:1.48:58.8:32:0.64:0:0 1/0:37:24:14,10:8,5:13,24:0.6486:2,2:21.1:1:27.5:1:1:1.13875:59:23:0.6389:0.1892:0.1 +22 18502528 . G A 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2446;SOR=0;LSEQ=TTGGCAGAATCTTGGAATGC;RSEQ=GCTTTTTTGGAATTTTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:38,29:67,2:0.029:2,2:5:0:33:1:1:1.30515:52.5:4:0.029:0:1.5 0/0:70:0:0,0:38,32:70,0:0:2,0:27.5:1:29.8:1:1:0:58.1:69:1:0:0.4 +22 18502789 . C CAGGAT 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CGGGGTTTCACTGTGTCAGC;RSEQ=AGGATGGTCTCGATCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:7,0:7,2:0.2222:0,2:28.5:1:24.2:1:0.22222:0:48:4:0.2222:0.1111:0 0/0:3:0:0,0:3,0:3,0:0:0,0:24.7:1:29.7:1:1:0:35.3:6:1:0:0 +22 19053282 . A T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.116;SOR=Inf;LSEQ=AGCTCACCTTAGGTAACACC;RSEQ=GTGACCTCTTTTATAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:99,22:121,0:0:2,0:21.7:1:30.5:1:1:0:60:59.5:1:0:0.2 0/1:63:2:1,1:55,6:61,2:0.0317:2,2:5.5:1:29:1:0.21147:8.56132:60:4:0.0317:0:1 +22 19053290 . C G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00107;SOR=5.31352;LSEQ=TTAGGTAACACCAGTGACCT;RSEQ=TTTTATAGAATCTTTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:5:4,1:107,25:132,5:0.0365:2,2:27.2:1:33.2:1:1:1.06947:60:10:0.0368:0:1.4 0/1:83:14:12,2:58,11:69,14:0.1687:2,2:22.6:1:32.6:1:1:1.14:60:28:0.1707:0:1 +22 19053325 . C T 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30903;SOR=4.40766;LSEQ=TAACCTTCAAATGTTGGGTA;RSEQ=CTCATATTAGTACACTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:0,1:181,99:280,1:0.0036:2,0:1:0:27:0:0.35587:0:60:2:0.0036:0:1 0/1:193:3:2,1:134,56:190,3:0.0155:2,2:30.7:1:29.7:1:1:1.19525:60:6:0.0158:0:1 +22 19053390 . C T 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12718;SOR=0;LSEQ=CAGTTGTAAAATTAAAAATG;RSEQ=CATTTTTAAAGTGCAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:4:2,2:186,190:376,4:0.0105:2,2:21:1:28.3:1:1:1.02:60:8:0.0107:0:1 0/0:335:0:0,0:165,170:335,0:0:2,0:25.7:1:30.3:1:1:0:60:54.833:1:0:0.3 +22 19053406 . G T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=11.29605;LSEQ=AATGCCATTTTTAAAGTGCA;RSEQ=CTATGTCTTGTGGCACTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:11:2,9:174,195:369,11:0.0288:2,2:29.6:1:30.8:1:0.06946:4.0028:60:22:0.0294:0:1.5 0/1:330:83:36,47:113,134:247,83:0.2515:2,2:21:1:28:1:0.79889:1.10063:60:19.75:0.2438:0:1.2 +22 19053443 . T A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10635;SOR=Inf;LSEQ=TAGTAAAACTTCTAGACACG;RSEQ=ATCCCCATGTATTTATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:96,175:271,0:0:2,0:26.3:1:28.9:1:1:0:59.9:542:1:0:0.2 0/1:245:3:2,1:81,161:242,3:0.0122:2,2:12.7:1:26:1:0.26565:3.95:60:6:0.0125:0:1.7 +22 19053454 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2126;SOR=Inf;LSEQ=CTAGACACGTATCCCCATGT;RSEQ=TTTATTATGTAAGCATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:77,155:232,0:0:2,0:26.5:1:29.9:1:1:0:60:76.333:1:0:0.2 0/1:199:2:1,1:66,131:197,2:0.0101:2,2:43:1:31.5:1:1:1.98:60:4:0.0102:0:1 +22 19053467 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50393;SOR=0;LSEQ=CCCATGTATTTATTATGTAA;RSEQ=CATGTGTGTGTGTGACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:57,139:196,2:0.0101:2,2:15:1:29.5:1:0.5011:2.43:60:4:0.0102:0:1 0/0:161:0:0,0:51,110:161,0:0:2,0:23.6:1:31.6:1:1:0:60:79.5:1:0:0.3 +22 19053469 . A ATG 125 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=5e-05;SOR=11.53005;LSEQ=CATGTATTTATTATGTAAGC;RSEQ=TGTGTGTGTGTGACTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:0,2:57,134:191,2:0.0104:2,0:37.5:1:31.8:1:1:0:60:4:0.0105:0:0.5 0/1:157:17:2,15:46,94:140,17:0.1083:2,2:31.6:1:30.8:1:0.09599:3.64661:60:34:0.1097:0:0.5 +22 19053471 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.50586;SOR=0;LSEQ=TGTATTTATTATGTAAGCAT;RSEQ=TGTGTGTGTGACTTCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:53,133:186,2:0.0105:2,2:17.5:1:28.5:1:0.49306:2.50:60:4:0.0107:0:1 0/0:149:0:0,0:45,103:148,0:0:2,0:22.6:1:31.6:1:1:0:60:296:1:0:0.3 +22 19053472 . T C 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.50634;SOR=0;LSEQ=GTATTTATTATGTAAGCATG;RSEQ=GTGTGTGTGACTTCTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:53,133:186,2:0.0106:2,2:5.5:1:30.5:1:0.49306:2.50:60:4:0.0106:0:1 0/0:147:0:0,0:43,104:147,0:0:2,0:22.4:1:29.3:1:1:0:60:146:1:0:0.3 +22 19053477 . G T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.00118;SOR=Inf;LSEQ=TATTATGTAAGCATGTGTGT;RSEQ=TGTGACTTCTTCATAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:45,133:178,0:0:2,0:22.6:1:32.2:1:1:0:60:177:1:0:0.1 0/1:138:8:3,5:37,93:130,8:0.058:2,2:18.6:1:30:1:0.69053:1.50:60:16:0.0588:0:1.9 +22 19466757 . A AG 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.33484;SOR=0.24961;LSEQ=GTGCCGGACCCGAGACCCGG;RSEQ=GGGGGGGTGCCCGGGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:1,4:1,3:4,5:0.5556:2,2:34.2:1:29.8:1:1:1.29098:60:10:0.625:0.1111:0 0/1:9:2:1,1:1,6:7,2:0.2222:2,2:31.5:1:29.5:1:0.41667:4.58:60:4:0.2222:0:0 +22 19466758 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=TGCCGGACCCGAGACCCGGA;RSEQ=GGGGGGTGCCCGGGACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:9,0:0:2,0:31.7:1:32.4:1:1:0:60:18:1:0:0 0/1:9:2:1,1:1,6:7,2:0.2222:2,2:18.5:1:28:1:0.41667:4.58:60:4:0.2222:0:1.5 +22 19868218 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCCGGCCATGATCGCT;RSEQ=TGGGTGTCAGCTCAGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:45:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 20918816 . ACAG A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=1;SOR=0.71413;LSEQ=CAGCAGCAGCAGGCGGCGCT;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:12,13:25,2:0.069:2,2:38.5:1:33.5:1:1:1.08:60:4:0.069:0:0 0/1:40:2:1,1:19,19:38,2:0.05:2,2:8.5:1:28.1:1:1:1:50:4:0.0486:0.058:2 +22 20918896 . TGCA T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.06973;SOR=0;LSEQ=GCAGCAGTTCCAAGCAGTAG;RSEQ=GCAGCAGCAGCAGCTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:2,3:6,14:20,5:0.2:2,2:29.4:1:32.8:1:1:1.53:60:10:0.2:0:0.2 0/0:17:0:0,0:7,10:17,0:0:2,0:17.1:1:29.4:1:1:0:60:7.5:1:0:0.2 +22 20920760 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.19661;SOR=Inf;LSEQ=TGTTCTGTCTCTAGATACAG;RSEQ=AGCAGCAACAGCAGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:32,0:0:2,0:19.4:1:32.9:1:1:0:60:64:1:0:0.2 0/1:26:2:1,1:14,10:24,2:0.0769:2,2:24:1:27:1:1:1.38168:60:4:0.0769:0:1 +22 20920781 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50351;SOR=0;LSEQ=AGCAGCAACAGCAGCTGCAG;RSEQ=GAATAGCACAGCTGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:18,19:37,2:0.0513:2,2:28.5:1:29:1:1:1.05:60:4:0.0513:0:1 0/0:29:0:0,0:17,12:29,0:0:2,0:28.6:1:30.9:1:1:0:60:58:1:0:0.2 +22 20920799 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15884;SOR=Inf;LSEQ=AGCGAATAGCACAGCTGCAG;RSEQ=TCCAACAACAGCAACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,22:42,0:0:2,0:32.9:1:32.5:1:1:0:60:84:0.9767:0:0.1 0/1:29:2:1,1:14,13:27,2:0.069:2,2:33:1:30.5:1:1:1.07415:60:4:0.069:0:1 +22 20920898 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCACCGATGCAGCAGCCA;RSEQ=AGCCTCCGCCCTCCCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:11:1:29:1:1:1.40151:60:4:0.1053:0:1 0/0:7:0:0,0:1,5:6,0:0:2,0:22.2:1:31.3:1:1:0:60:12:0.8571:0:0 +22 21135656 . G T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10186;SOR=0;LSEQ=ACACACAACCACTTCTCTTT;RSEQ=CCACCAAGGACTACCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:2,1:129,46:175,3:0.0169:2,2:18:1:31.3:1:1:1.39932:60:6:0.0173:0:1 0/0:202:0:0,0:143,59:202,0:0:2,0:23.8:1:30.7:1:1:0:60:32.667:1:0:0.1 +22 21135659 . A T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10984;SOR=0;LSEQ=CACAACCACTTCTCTTTGCC;RSEQ=CCAAGGACTACCAGGTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:3:2,1:138,53:191,3:0.0155:2,2:25.3:1:32.3:1:1:1.30004:60:6:0.016:0:1.3 0/0:210:0:0,0:146,64:210,0:0:2,0:24.3:1:28.7:1:1:0:60:104:1:0:0.1 +22 21135741 . G A 62 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11151;SOR=0.18445;LSEQ=GCTCCCGTGGTTTTATAGCA;RSEQ=CCCAGGCGAAGGAAGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:5:4,1:221,207:428,5:0.0115:2,2:6.2:1:26.8:1:0.37404:3.74:60:10:0.0118:0:1 0/0:468:1:1,0:211,256:467,1:0.0021:2,0:1:0:24:0:0.45299:0:60:2:0.0022:0:1 +22 21135760 . AC A 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.2171;SOR=0.20133;LSEQ=AGCCCAGGCGAAGGAAGGAG;RSEQ=CCCCCCCAGCTCCTGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:5:4,1:191,215:406,5:0.0122:2,2:33.2:1:30.4:1:0.19489:4.49:59:10:0.0123:0.0024:0.2 0/0:405:1:0,1:172,232:404,1:0.0025:2,0:34:0:27:0:1:0:60:2:0.0025:0:0 +22 21135763 . C A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.6084;SOR=1.08681;LSEQ=CCAGGCGAAGGAAGGAGACC;RSEQ=CCCCCAGCTCCTGGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:146:64,82:125,137:262,146:0.3578:2,2:26.3:1:29.9:1:0.46992:1.16857:60:72:0.3564:0:1.2 0/1:395:149:54,95:108,138:246,149:0.3772:2,2:23.8:1:28.9:1:0.14082:1.37569:59.9:73.5:0.3779:0:1.1 +22 21135811 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17024;SOR=Inf;LSEQ=AAAGGGGGCCAGAGCCCCTC;RSEQ=TGATCTGTCCACACACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:70,177:247,0:0:2,0:23.1:1:32.3:1:1:0:60:60.75:1:0:0.4 0/1:174:2:1,1:45,127:172,2:0.0115:2,2:22:1:28.5:1:0.45997:2.80:60:4:0.0115:0:1.5 +22 21272141 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51332;SOR=0;LSEQ=GAGGCCCTTCCTCGGCCCCA;RSEQ=AGCCGTCTGCCGGGCTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:145,33:178,2:0.0111:2,2:27:1:30.5:1:0.34295:4.34375:60:4:0.0113:0:1 0/0:127:0:0,0:99,28:127,0:0:2,0:22.2:1:29.3:1:1:0:60:254:1:0:0.1 +22 21272175 . C T 42 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66945;SOR=1.70449;LSEQ=GCTAAGGCGTGCAGAGCAGG;RSEQ=GAGGACAGCCGCCGCCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:2:0,2:221,102:323,2:0.0062:2,0:1:0:26.5:1:0.10173:0:60:4:0.0062:0:1 0/1:287:3:1,2:175,109:284,3:0.0105:2,2:5:1:26.7:1:0.56157:3.19766:60:6:0.0107:0:1 +22 21272198 . G A 75 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13301;SOR=0.19597;LSEQ=GGACAGCCGCCGCCCCTACC;RSEQ=CCGCAGAGTCCCCGGTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:6:4,2:288,164:452,6:0.0131:2,2:33.3:1:29.3:1:1:1.14:60:12:0.0133:0:1.3 0/0:386:1:1,0:228,157:385,1:0.0026:2,0:3:0:30:0:1:0:60:2:0.0026:0:1 +22 21272718 . GT G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.49998;SOR=0.56272;LSEQ=GTCACTGGATAAGAGGATGC;RSEQ=TTTTTTTTTTTCCCTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:12:0,12:1,15:16,12:0.375:1,0:21:1:30.9:1:1:0:60:11:0.3793:0.125:0.5 0/1:12:3:0,3:1,6:7,3:0.25:2,0:37:1:31.7:1:1:0:60:6:0.25:0:0.3 +22 21272752 . C T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26632;SOR=0;LSEQ=CCTCTCACGAGGCTGTTTCT;RSEQ=AATGTGAAGAGGATGCGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:10,5:0.3333:0,0:25.2:1:28.8:1:1:0:60:10:0.3333:0:2.2 0/0:5:0:0,0:1,4:5,0:0:2,0:16.8:1:31:1:1:0:60:10:1:0:0.4 +22 21280419 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17353;SOR=Inf;LSEQ=GGTGGTAGAAGAGATGGTGG;RSEQ=AGTGCTTGCTGGTAAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:241,9:250,0:0:1,0:25.8:1:32.5:1:1:0:60:61.5:1:0:0.9 0/1:179:2:2,0:155,21:176,2:0.0112:2,0:42.5:1:31.5:1:1:0:60:4:0.0114:0:1.5 +22 21280463 . G C 284 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01725;LSEQ=TTATAATTAATGTAGATGAT;RSEQ=GGCAGGAACCTAGGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:575:571:386,185:0,0:0,571:0.993:0,2:23.2:1:31.1:1:1:0:60:94.167:0.993:0:1.1 1/0:463:329:226,103:88,45:133,329:0.7106:2,2:23.7:1:30:1:0.65972:1.12:60:328:0.713:0:1.1 +22 21287911 . A G 110 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01722;SOR=0;LSEQ=GTTTGCAGTGAGCTAAGATC;RSEQ=CGCTATTGCACTCCAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1:0,1:24.1:1:29.8:1:1:0:52.1:26:1:0:1 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:16:1:30.6:1:1:0:57.6:10:0.5556:0:1.2 +22 21288518 . G A 59 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06543;SOR=0;LSEQ=CCTGTGCTTATGACAAGACT;RSEQ=CCTTGGCATTAGAGGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:5:4,1:122,260:382,5:0.0129:2,2:6.8:1:25.6:1:0.04053:8.48:60:10:0.0131:0:1 0/0:331:0:0,0:124,207:331,0:0:2,0:42:0:14:0:1:0:60:0:0:0:6 +22 21288558 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17941;SOR=Inf;LSEQ=ATCTGTTCAGATTAGCTTTT;RSEQ=GGTCCTTTGACATTTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:59,188:247,0:0:2,0:21.3:1:31.7:1:1:0:60:122.5:1:0:0.1 0/1:182:2:1,1:52,128:180,2:0.011:2,2:16:1:29:1:0.49876:2.45:60:4:0.011:0:2 +22 21294854 . CTTTTTTT C 196 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=20.000;MSILEN=1;SSF=0.46681;SOR=0.77752;LSEQ=TTTCCTCATCTTTGGTGCTC;RSEQ=TTTTTTTTTTTTTGGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:66:63,3:17,1:18,66:0.4648:1,1:22.2:1:32.5:1:1:1.23:56.2:65:0.4745:0.1268:0.3 0/1:72:29:28,1:16,0:16,29:0.4028:1,1:22.9:1:30.5:1:1:0:57.3:58:0.4085:0.125:1.5 +22 21294878 . AT A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53115;SOR=0;LSEQ=TTTTTTTTTTTTTTTTTGGC;RSEQ=TTTTTTTCTTAGTGATACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:2,0:152,4:156,2:0.0126:1,0:19:1:31.5:1:1:0:60:4:0.0128:0:2 0/0:94:0:0,0:91,2:93,0:0:1,0:21.7:1:29.2:1:1:0:57.5:92:1:0:1 +22 21294918 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06948;SOR=Inf;LSEQ=TCAGCGTTCTTTGAGGTCAC;RSEQ=AGCATCCTCAACATTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:343,80:423,0:0:2,0:23.9:1:31.2:1:1:0:58.9:41.3:1:0:0.2 0/1:297:3:1,2:234,60:294,3:0.0101:2,2:14.7:1:26.3:1:0.11156:7.72596:60:6:0.0105:0:1 +22 21303711 . G A 53 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACTGCATTCCAGCCTGG;RSEQ=CGACAGACCCCGTCTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:9.5:1:26.8:1:1:0:60:3:1:0:1.8 1/1:1:1:1,0:0,0:0,1:1:0,0:18:0:30:0:1:0:60:2:1:0:1 +22 21303797 . G A 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46389;SOR=2.41495;LSEQ=CTATTCAAGAGGTGGAGGTG;RSEQ=AAGGATCACTTGAGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:25,0:25,2:0.0741:1,0:18:1:29.5:1:1:0:60:4:0.08:0:2 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:24:0:30:0:1:0:60:2:0.1667:0:1 +22 21303818 . C T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41121;SOR=1.93321;LSEQ=AAGGATCACTTGAGCCCAGG;RSEQ=GTTAGAGGTTACATTGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:7,0:23,0:23,7:0.2333:1,0:26.9:1:29.9:1:1:0:60:14:0.2333:0:1 0/1:8:3:3,0:5,0:5,3:0.375:0,0:17.7:1:28.3:1:1:0:60:6:0.375:0:1 +22 21304408 . A G 111 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGTGGAGAGAAGTTGAC;RSEQ=TGGAAAGGGTCTTCCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:19.9:1:32.1:1:1:0:60:22:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 21304463 . T C 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTACATGGGACTGATTCTGT;RSEQ=GTGTTCACCAGAGAAAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:31.5:1:1:0:60:4:1:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:35:0:32:0:1:0:60:2:1:0:1 +22 22123189 . A C 63 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGGACAGGCAGCAAGGAA;RSEQ=GGATGAGAACCCAAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:21.5:1:31.8:1:1:0:60:8:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:8:0:26:0:1:0:60:2:1:0:1 +22 22127080 . G C 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=ATGGCAGCAGGTATATCTCA;RSEQ=GAAAATCTAAGCAAGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:203,25:228,0:0:2,0:21.4:1:33.2:1:1:0:60:227:1:0:0.1 0/1:158:10:8,2:130,18:148,10:0.0633:2,2:26.9:1:30.7:1:0.61636:1.79741:60:20:0.0645:0:1 +22 22127095 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0873;SOR=Inf;LSEQ=TCTCAGGAAAATCTAAGCAA;RSEQ=ATATGGTTGGTCCACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:248,48:296,0:0:2,0:23.1:1:33.1:1:1:0:60:147:1:0:0.1 0/1:237:3:1,2:185,48:233,3:0.0127:2,2:27.7:1:26.3:1:0.1144:7.61748:60:6:0.0129:0:1 +22 22127490 . C T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27761;SOR=0;LSEQ=ACCGCAAACAAAAACACTGG;RSEQ=ACTACTTAATGAAGCGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:1,10:11,5:0.3125:2,0:30:1:28.2:1:1:0:60:10:0.3333:0:1.2 0/0:5:0:0,0:0,5:5,0:0:0,0:26.2:1:32.6:1:1:0:60:10:1:0:0.2 +22 22141229 . G T 27 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGGGTGGGGGGTCATTA;RSEQ=TCGGCCTATCATGGTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:27.5:1:1:0:60:4:1:0:1 +22 22142388 . CA C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.07125;SOR=2.13414;LSEQ=TACTGCACTGCCACTGTTTC;RSEQ=AAAAAAAAAAGGGGGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:20:20,0:39,0:39,20:0.3175:1,1:28.2:1:31.9:1:1:0:60:40:0.3175:0.0635:0.2 1/0:44:22:21,1:19,1:20,22:0.5:1,1:23.7:1:31.6:1:1:1.10:60:44:0.5116:0.0909:0 +22 22142450 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50698;SOR=0;LSEQ=AAAGAAAGCATTATCCAATA;RSEQ=CCATAGGCTCATTTTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:172,8:180,2:0.011:1,2:31.5:1:29.5:1:0.09672:20.32926:60:4:0.0116:0:1 0/0:140:0:0,0:125,15:140,0:0:2,0:23:1:31.4:1:1:0:59.9:45.667:1:0:0.1 +22 22142732 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.222;SOR=Inf;LSEQ=GACCAAGGTAAATGACTACA;RSEQ=ACCATCAACTCTGAGTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:25,108:133,0:0:2,0:24.3:1:32.5:1:1:0:60:132:1:0:0.1 0/1:119:2:0,2:29,88:117,2:0.0168:2,0:50:0:28:1:1:0:60:4:0.0174:0:1.5 +22 22144873 . CCTGAGTAGCTGGCACTA C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCTCACCTCAGCCAGGT;RSEQ=CTGAGTAGCTGGCACACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:30.7:1:1:0:21:4:1:1:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 22153194 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51278;SOR=0;LSEQ=AGACAGCACCTTGTCTCTGG;RSEQ=CAGACAGGCAAACTCTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:2,0:105,0:105,2:0.0187:1,0:40.5:1:31.5:1:1:0:60:4:0.0187:0:1 0/0:75:0:0,0:74,1:75,0:0:1,0:22.1:1:31.9:1:1:0:60:150:1:0:0.1 +22 22153236 . A T 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37135;SOR=0.32846;LSEQ=CAGAGGGAGACTTACGGCTT;RSEQ=CTGCAATGCATTCAGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:199,37:236,3:0.0126:2,2:28:1:27.3:1:0.07003:10.58498:60:6:0.0126:0:1.3 0/0:241:1:0,1:187,53:240,1:0.0041:2,0:1:0:22:0:0.22407:0:60:2:0.0042:0:1 +22 22153239 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02729;SOR=0.43595;LSEQ=AGGGAGACTTACGGCTTACT;RSEQ=CAATGCATTCAGAAAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:26:20,6:186,46:232,26:0.1008:2,2:17.5:1:28.5:1:0.79628:1.21211:60:52:0.1012:0:1.1 0/1:258:12:7,5:190,55:245,12:0.0465:2,2:18.2:1:27.8:1:0.15813:2.45715:60:24:0.0472:0:1 +22 22153426 . G GA 69 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.26236;SOR=0.35054;LSEQ=AAAGTCACAGATCTAAGAGA;RSEQ=AAAAAAAACAGGATAACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:5:3,2:109,270:379,5:0.013:2,2:31.8:1:30:1:0.15083:3.70:60:10:0.0133:0:0 0/0:435:2:2,0:148,285:433,2:0.0046:2,0:25.5:1:25.5:1:0.11839:0:60:4:0.0047:0.0023:0.5 +22 22153494 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49763;SOR=Inf;LSEQ=ACATCACAAAAATAAAAAAG;RSEQ=CAATAGGAATAATAATGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:4,101:105,0:0:1,0:25.4:1:32.8:1:1:0:60:104:1:0:0.1 0/1:106:2:1,1:8,96:104,2:0.0189:2,2:17:1:27.5:1:0.16334:11.37:60:4:0.0189:0:1.5 +22 22160384 . T C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97351;LSEQ=TGGTCACATTTAGCAAAGCA;RSEQ=TGAAAACAAAAATGCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:15:3,12:40,197:237,15:0.0595:2,2:22.3:1:32.8:1:0.72589:1.23:60:30:0.06:0:1.1 0/1:224:13:6,7:52,159:211,13:0.058:2,2:22:1:30:1:0.10429:2.61:60:26:0.0588:0:1.1 +22 22162126 . A G 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGAACTTTGTTGACATTATC;RSEQ=TAAGCAGAGCTTAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:107,306:413,0:0:2,0:23.6:1:30.8:1:1:0:59.9:67.833:1:0:0.1 0/1:382:52:14,38:116,214:330,52:0.1361:2,2:24.8:1:30.9:1:0.27335:1.46988:60:104:0.1376:0:1.1 +22 22162143 . AAG A 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.39475;SOR=0.56306;LSEQ=ATCATAAGCAGAGCTTAAAA;RSEQ=AGAGAGAGAGATGGCATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:8:3,5:57,231:288,8:0.027:2,2:23.5:1:30:1:0.20683:2.42:60:16:0.0272:0.0034:0 0/1:260:4:2,2:58,198:256,4:0.0154:2,2:29.3:1:30.5:1:0.22873:3.39:60:8:0.0154:0:1 +22 22162257 . G C 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00732;SOR=Inf;LSEQ=GTTTCATACCCGTGAAGGCA;RSEQ=CATGTATATTATCCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:30,0:0:1,0:19.1:1:32.6:1:1:0:60:29:1:0:0.1 0/1:20:5:1,4:0,15:15,5:0.25:1,2:25.2:1:31.2:1:0.25:0:60:10:0.25:0:1 +22 22162374 . A T 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCCCTGTTAACTGGGTGAA;RSEQ=GTCTTGCCTTTATAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:15:0:31.5:1:1:0:60:4:0.6667:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:16.5:1:28:1:1:0:60:4:1:0:1.5 +22 22221552 . T A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49637;SOR=Inf;LSEQ=GGCGCGGGCGAGGCCGAGGC;RSEQ=GCGTCCGCTGCGGCCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:50,13:63,0:0:2,0:8.5:1:31.8:1:1:0:60:126:1:0:0.3 0/1:66:2:1,1:50,14:64,2:0.0303:2,2:9:0:27.5:1:0.40559:3.48449:60:4:0.0308:0:2 +22 22221563 . C T 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19028;SOR=0.21715;LSEQ=GGCCGAGGCTGCGTCCGCTG;RSEQ=GGCCCCGGGCGGTGGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:4:2,2:91,30:121,4:0.032:2,2:10.3:1:29.8:1:0.27025:3.00103:60:8:0.0336:0:1.3 0/0:141:1:0,1:91,49:140,1:0.0071:2,0:1:0:24:0:0.35461:0:60:2:0.0071:0:1 +22 22221575 . G T 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37891;SOR=3.49185;LSEQ=GTCCGCTGCGGCCCCGGGCG;RSEQ=TGGGGGGGCCGGGCGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:1,0:148,69:217,1:0.0046:2,0:9:0:14:0:1:0:60:0:0:0:2 0/1:252:4:1,3:154,94:248,4:0.0159:2,2:13.3:1:26.5:1:0.16042:4.88418:60:8:0.0162:0:1.3 +22 22221576 . TG T 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.09315;SOR=0;LSEQ=TCCGCTGCGGCCCCGGGCGG;RSEQ=GGGGGGCCGGGCGTGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:2,1:157,74:231,3:0.0128:2,2:21.7:1:33.7:1:1:1.06054:60:6:0.0133:0:0 0/0:281:0:0,0:176,105:281,0:0:2,0:16.8:1:30.6:1:1:0:60:45.833:1:0:0.3 +22 22221584 . C T 63 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7387;SOR=0.67032;LSEQ=GGCCCCGGGCGGTGGGGGGG;RSEQ=CGGGCGTGGCCGGTCGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:5:1,4:184,94:278,5:0.0177:2,2:7.8:1:27.2:1:0.05043:7.77271:60:10:0.0184:0:1 0/1:336:4:1,3:203,129:332,4:0.0119:2,2:4.8:1:21.8:1:0.30399:4.69956:60:3:0.0091:0:1.3 +22 22221589 . C T 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38264;SOR=3.38195;LSEQ=CGGGCGGTGGGGGGGCCGGG;RSEQ=GTGGCCGGTCGCGGACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:1:1,0:212,114:326,1:0.0031:2,0:16:0:32:0:1:0:60:2:0.0032:0:1 0/1:389:4:1,3:233,152:385,4:0.0103:2,2:11:1:28:1:0.30583:4.58111:60:8:0.0104:0:1.3 +22 22221680 . C T 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCGGCCCCACGTCGAACAC;RSEQ=TGCCCGCGGACCATCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:522:0:0,0:218,303:521,0:0:2,0:25.1:1:32.4:1:1:0:59.9:64.125:0.9981:0:0.2 0/1:611:63:28,35:240,307:547,63:0.1031:2,2:25.1:1:29.7:1:1:1.02:59.8:30.5:0.1017:0:1.4 +22 22221708 . CCCG C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=1.02508;LSEQ=GGACCATCTCCGGGCCCGCG;RSEQ=CCGCCGCCGCCGCCGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:6:4,2:71,168:239,6:0.0245:2,2:27.8:1:30.5:1:0.07293:4.70:60:12:0.025:0:0.2 0/1:279:7:3,4:95,177:272,7:0.0251:2,2:27.1:1:31.3:1:0.6993:1.40:59.3:14:0.0259:0:0.4 +22 22221725 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.50049;SOR=Inf;LSEQ=GCGCCCGCCGCCGCCGCCGC;RSEQ=GCCATGTTGGCTGCCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:39,93:132,0:0:2,0:13.1:1:30.4:1:1:0:60:43:1:0:0.2 0/1:151:2:1,1:48,101:149,2:0.0132:2,2:6.5:1:28:1:0.54517:2.09:60:4:0.0135:0:1 +22 22221954 . C T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACGGGCGGGCCGGCGGG;RSEQ=GGGCGGAGGGAGGGGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:26:0:1:0:60:4:1:0:1 +22 22534324 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACTTGTGGGTACCTGCC;RSEQ=CTTCAATTGTGAAATCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:30.5:1:1:0:60:4:1:0:1 +22 22534988 . T A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04919;SOR=4.4735;LSEQ=GAGCCTTTGTTGAAGATATC;RSEQ=CTGAATACCTCTCATTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:14,0:14,4:0.2222:1,0:23.3:1:30.8:1:1:0:60:8:0.2222:0:1 1/0:21:12:11,1:9,0:9,12:0.5714:0,2:22.4:1:29.6:1:1:0:60:24:0.5714:0:1.1 +22 22535064 . CT C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49697;SOR=Inf;LSEQ=TTTGTGCTTATTTTTCTAAC;RSEQ=TTATGACTGATTATCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:52,20:72,0:0:2,0:21.7:1:31.5:1:1:0:60:35:1:0:0.1 0/1:76:2:1,1:45,29:74,2:0.0263:2,2:33:1:32:1:1:1.54245:60:4:0.0263:0:0.5 +22 22535082 . T C 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02982;SOR=Inf;LSEQ=ACCTTTATGACTGATTATCA;RSEQ=TTAAGCTTAATATGAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:55,32:87,0:0:2,0:23.5:1:30.7:1:1:0:60:86:1:0:0.1 0/1:96:6:4,2:49,41:90,6:0.0625:2,2:25.2:1:31:1:0.68815:1.66:60:12:0.0625:0:1 +22 22535137 . A G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01401;SOR=3.12668;LSEQ=GATATATAAATATGTCATCA;RSEQ=TGGTCAATATTATTAAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:7:4,3:81,66:147,7:0.0452:2,2:26.1:1:33.4:1:1:1.09:60:14:0.0464:0:1.9 0/1:116:15:7,8:47,54:101,15:0.1293:2,2:28.5:1:30.7:1:1:1.01:60:30:0.1316:0:2.1 +22 22535144 . A G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01639;SOR=2.97847;LSEQ=AAATATGTCATCAATGGTCA;RSEQ=TATTATTAAAGTTATAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:8:4,4:80,74:154,8:0.0494:2,2:23.8:1:33.1:1:1:1.08054:60:16:0.0497:0:1.8 0/1:119:16:8,8:46,57:103,16:0.1345:2,2:26.3:1:29.5:1:0.78958:1.24:60:15:0.1271:0:2 +22 22535184 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17315;SOR=Inf;LSEQ=AGTAATGCAAAATTGTAGCT;RSEQ=TATATCATTTCACTTGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:59,75:134,0:0:2,0:26.7:1:30.4:1:1:0:60:133:1:0:0.1 0/1:96:2:1,1:36,58:94,2:0.0208:2,2:19.5:1:28:1:1:1.60:60:4:0.0211:0.0104:0.5 +22 22535223 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16838;SOR=Inf;LSEQ=TCACTAACATTAATATGTGA;RSEQ=GTGAGAAGATCACTTTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:21,53:74,0:0:2,0:22.4:1:31.5:1:1:0:60:148:1:0:0 0/1:52:2:1,1:15,35:50,2:0.0385:2,2:30:1:32:1:0.52489:2.29:60:4:0.0392:0:1 +22 22820648 . G C 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19346;SOR=Inf;LSEQ=GGGGTGGAGGCTATGAAAGG;RSEQ=ACCGGAGCTCAGCGTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:21,0:0:2,0:18.1:1:30.9:1:1:0:60:20:1:0:0.1 0/1:17:2:1,1:9,6:15,2:0.1176:2,2:7:1:31:1:1:1.46382:60:4:0.125:0:1 +22 24129240 . C T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02571;SOR=0.32152;LSEQ=GCTGAGGCGCCAGTACCCGG;RSEQ=CCGGTCCGCATTTCGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:20:20,0:51,0:51,20:0.2817:1,1:20.7:1:31:1:1:0:60:40:0.2817:0:1.1 0/1:54:6:6,0:48,0:48,6:0.1111:1,0:21.5:1:29.3:1:1:0:60:12:0.1176:0:1 +22 24129493 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10421;SOR=Inf;LSEQ=CTCCCCGGGCTCGGCCCCGC;RSEQ=GGAGCCCCGGGGCGGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:54,242:296,0:0:2,0:23.6:1:31.3:1:1:0:60:73:0.9966:0:0.2 0/1:265:3:2,1:66,196:262,3:0.0113:2,2:20:1:27:1:0.16268:5.89:60:6:0.0114:0:1 +22 24129553 . GGC G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=TCCATTCATCGGGGCGGGCG;RSEQ=GCGCGCGCGCGCGCTCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:3.9:1:31.9:1:1:0:60:14:1:0:0 0/1:8:2:1,1:1,3:4,2:0.25:2,2:40.5:1:31.5:1:1:2.45:60:4:0.3333:0:0.5 +22 24134302 . T C 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22857;SOR=0;LSEQ=TCCAGCAGGGCCATTGGGTA;RSEQ=GTGAGCGGGCCGGGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:1,26:0,0:0,27:1:0,1:21.7:1:29.8:1:1:0:59.3:26:1:0:1.1 1/1:8:7:1,6:0,1:1,7:0.875:0,2:32:1:30.1:1:1:0:60:14:0.875:0:1.3 +22 24134394 . T C 79 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCGATGCTCTGCCATCTG;RSEQ=CGTGGGTGTGTCGCCATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:23.8:1:30.8:1:1:0:56.3:12:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 24135672 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15061;SOR=Inf;LSEQ=GCATGCGAGGACCTTGATGT;RSEQ=CTGCATCCACTTGGCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:172,18:190,0:0:2,0:22.7:1:32.7:1:1:0:59.9:62.333:1:0:0.1 0/1:121:2:2,0:113,6:119,2:0.0165:2,0:19:1:29:0:1:0:60:4:0.0169:0:1 +22 24135703 . A T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03024;SOR=Inf;LSEQ=TTGGCTGGCTGCTGTGTGCC;RSEQ=CCGCCACCAGCAGAGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:264,75:339,0:0:2,0:24.9:1:30.4:1:1:0:59.9:678:1:0:0.1 0/1:244:4:4,0:186,54:240,4:0.0164:2,0:20.5:1:32.3:1:0.5783:0:60:8:0.0166:0:1 +22 24135716 . G T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41072;SOR=2.67559;LSEQ=GTGTGCCACCGCCACCAGCA;RSEQ=AGTGACCCAGTGATGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:2:1,1:322,112:434,2:0.0046:2,2:12:1:29:1:0.45162:2.86669:60:4:0.0046:0:1 0/1:328:4:1,3:229,95:324,4:0.0122:2,2:15.5:1:27.3:1:0.08151:7.18289:60:8:0.0123:0:1.3 +22 24135968 . C CT 133 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.11793;SOR=1.63573;LSEQ=GTTGAAGTTAAATTGAAACA;RSEQ=TTTTTTTTTTTTTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:26:0,26:2,79:81,26:0.2031:1,1:31.2:1:30.8:1:1:0:56.2:52:0.2203:0:1.2 0/1:95:28:0,28:6,49:55,28:0.2947:2,1:30.9:1:27.7:1:0.09212:0:54.7:8.333:0.3289:0.0105:2.3 +22 24135986 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50359;SOR=0;LSEQ=CACTTTTTTTTTTTTTTTTT;RSEQ=AGATGGAATCTTGTTCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:0,2:0,72:72,2:0.027:1,0:24:1:30.5:1:1:0:41:4:0.0274:0:3.5 0/0:58:0:0,0:1,54:55,0:0:1,0:21:1:31.2:1:1:0:53.2:54:1:0:1.9 +22 24142977 . GC CT 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07403;SOR=2.46316;LSEQ=ATCTGATGACAGCCTGGGGA;RSEQ=AGGCTCCTGCAAAGTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:41:40,1:30,0:30,41:0.5694:1,1:24:1:32.2:1:1:0:58.2:82:0.5857:0.0694:1 1/0:30:23:21,2:7,0:7,23:0.7667:0,2:22.3:1:30.3:1:1:0:60:46:0.7667:0.1667:1 +22 24143502 . C G 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.02812;LSEQ=TCCTCCTCACCTCTCTGGCC;RSEQ=CTCAAGTGGAGTTACTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:660:656:242,414:0,0:0,656:0.9939:0,2:25.8:1:31.4:1:1:0:59.9:71.889:0.9939:0:1.1 1/1:622:511:202,309:47,63:110,511:0.8215:2,2:26:1:30.4:1:0.59199:1.14096:60:45.455:0.821:0:1.2 +22 24143573 . C A 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=44.30937;LSEQ=AGTTTCACATGAGTGGGCCA;RSEQ=AGCCAGTCTGATGGTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:1:1,0:93,249:342,1:0.0029:2,0:1:0:26:0:0.27405:0:60:2:0.0029:0:2 0/1:330:38:12,26:100,192:292,38:0.1152:2,2:22.6:1:29.8:1:0.85615:1.12809:60:76:0.1162:0:1.6 +22 24143607 . A T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25399;SOR=0;LSEQ=GTGCAGATGCCATCCACGTG;RSEQ=CTCCCACTGTGCCACCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:1,2:43,162:205,3:0.0144:2,2:12.7:1:23.3:1:0.51175:1.88:60:2:0.0099:0:1.3 0/0:174:0:0,0:45,129:174,0:0:2,0:22.8:1:28.6:1:1:0:60:57:1:0:0.2 +22 24143628 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19243;SOR=Inf;LSEQ=CTCCCACTGTGCCACCATTT;RSEQ=CCAGAGCCTGCTGGAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:14,121:135,0:0:2,0:25.7:1:31.7:1:1:0:59.8:134:1:0:0.1 0/1:106:2:1,1:14,90:104,2:0.0189:2,2:33.5:1:27.5:1:0.26415:6.24:60:4:0.0196:0:1 +22 24144125 . A C 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCATCTCGGCGCGTGG;RSEQ=GATCCAGCCCTCTCCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:32:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:28:1:1:0:60:4:1:0:1 +22 24145395 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03602;SOR=0;LSEQ=TCCCCAGATGGGTTTGCAGA;RSEQ=GCCTGCTGTGCAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:146:146:140,6:0,0:0,146:1:0,1:25.2:1:33.5:1:1:0:60:145:1:0:1.1 1/1:73:70:63,7:1,2:3,70:0.9589:2,2:23.5:1:31.8:1:0.03839:16.61:60:69:0.9583:0:1.1 +22 24145622 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00225;SOR=Inf;LSEQ=CATGAATGGTACAAGGCAGT;RSEQ=GGGCTTGGCTGGGCCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:150,313:463,0:0:2,0:23.6:1:30.6:1:1:0:60:76.167:0.9978:0:0.4 0/1:337:7:2,5:114,216:330,7:0.0208:2,2:21.6:1:27.4:1:1:1.31842:60:6:0.0182:0:1 +22 24145635 . G A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07102;SOR=Inf;LSEQ=AGGCAGTCGGGCTTGGCTGG;RSEQ=CCTGGCCCCAACCCCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:104,261:365,0:0:2,0:24.2:1:31.9:1:1:0:60:72:1:0:0.5 0/1:259:3:2,1:79,177:256,3:0.0116:2,2:7.3:1:26.3:1:0.2313:4.45:60:6:0.012:0:1 +22 24145675 . G C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12799;SOR=0;LSEQ=TGTTACGTGGGAACAGTCCC;RSEQ=TTTCCTGCCAGCTGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:184:184:26,158:0,0:0,184:1:0,2:23.8:1:33.1:1:1:0:60:91:1:0:1.3 1/1:103:101:16,85:0,2:2,101:0.9806:0,2:20:1:31.1:1:1:0:60:202:0.9806:0:1.3 +22 24145727 . C T 185 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGACCTGACACGCAGGACAT;RSEQ=GGGGCATAGTTTTGGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:70:1,69:0,0:0,70:1:0,1:24.9:1:30.2:1:1:0:60:22.333:1:0:1.8 1/0:29:19:0,19:0,10:10,19:0.6552:0,1:31.4:1:29.9:1:1:0:60:38:0.6552:0:1.8 +22 24158709 . A G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTATGAGTGGAATGAGGG;RSEQ=AGTGTTTATGGCCATGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:24.5:1:32.1:1:1:0:57:16:1:0:1.1 1/1:2:2:2,0:0,0:0,2:1:0,0:26.5:1:33:0:1:0:56:4:1:0:2 +22 24158755 . T G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03529;SOR=Inf;LSEQ=AGGGCATGGAGCAGGAGGTC;RSEQ=GTGCAGGATGAGGGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:26,2:28,0:0:2,0:23.2:1:32.8:1:1:0:59.1:56:1:0:0.3 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:29:1:28.5:1:1:0:56:4:0.2857:0:1.5 +22 24158826 . AC A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00056;SOR=Inf;LSEQ=TCCCAGTTTCCAGGAAGGCC;RSEQ=CCCCAGTGCCCTGGTTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:74,2:76,0:0:1,0:25:1:32.6:1:1:0:60:152:1:0:0.3 0/1:24:5:5,0:19,0:19,5:0.2083:1,0:23.6:1:32.6:1:1:0:60:10:0.2174:0:0.8 +22 24158895 . A G 146 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=21.81791;LSEQ=CAAAGAAGAAGGGGTGAGGG;RSEQ=GGCCGGTCCATGCCCAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:2:2,0:186,47:233,2:0.0085:2,0:27:1:33:0:1:0:60:4:0.0087:0:1 0/1:190:30:26,4:121,39:160,30:0.1579:2,2:20.8:1:29.9:1:0.23785:2.09:59.2:29:0.1551:0:1.1 +22 24158899 . C A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32075;LSEQ=GAAGAAGGGGTGAGGGAGGC;RSEQ=GGTCCATGCCCAAGCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:261:134:102,32:100,27:127,134:0.5134:2,2:23.8:1:30.9:1:0.65843:1.16128:60:133:0.5155:0:1.1 0/1:210:53:39,14:121,35:156,53:0.2524:2,2:25.1:1:29.6:1:0.57612:1.23967:60:106:0.2536:0:1.1 +22 24159175 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23585;SOR=Inf;LSEQ=TCCTGGCCCTCAGGGTGGGT;RSEQ=TCATCATGGAGCACTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:47,159:206,0:0:2,0:21.5:1:32.1:1:1:0:60:50.5:1:0:0.1 0/1:195:2:1,1:48,145:193,2:0.0103:2,2:27.5:1:30:0:0.44039:3.00:60:4:0.0105:0:1 +22 24159176 . T C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2367;SOR=Inf;LSEQ=CCTGGCCCTCAGGGTGGGTG;RSEQ=CATCATGGAGCACTGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:42,158:200,0:0:2,0:21.7:1:30.1:1:1:0:60:65.667:1:0:0 0/1:190:2:1,1:47,141:188,2:0.0105:2,2:7:1:29:1:0.44244:2.98:60:4:0.0108:0:1.5 +22 24159244 . G A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00294;SOR=Inf;LSEQ=TTTGGGTTCCATATCATCTG;RSEQ=AAAGTCATAACACCTGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:0,75:75,0:0:1,0:27.2:1:31.6:1:1:0:60:17.75:1:0:0.3 0/1:36:5:0,5:1,30:31,5:0.1389:1,0:26.2:1:31.8:1:1:0:53.8:10:0.1389:0:2.2 +22 24159307 . A T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCATAGGCTGAGTTCTC;RSEQ=TAGTAAAGTGTTATATTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:0,24:0,0:0,24:1:0,1:24.1:1:30.3:1:1:0:60:23:1:0:1.3 1/1:7:7:0,7:0,0:0,7:1:0,0:22:1:29.7:1:1:0:60:14:1:0:1.1 +22 24159437 . G T 94 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCTGAGTGCTCCAGGG;RSEQ=GGCCTAGTAACCCAATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:28.1:1:31.4:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 24167098 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=GCAGGAGCGAAGGGCAGAAA;RSEQ=GAAGGTCCCCACCAGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:19.3:1:33.3:1:1:0:49.3:12:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:23:1:29:1:1:0:60:4:0.6667:0:1 +22 24167329 . C A 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.17594;SOR=Inf;LSEQ=ACCCTGGTGGGCAGGGCCCA;RSEQ=CCCAGGCCTGGCAGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:159,23:182,0:0:2,0:22.9:1:31.9:1:1:0:60:90:1:0:0.1 0/1:132:2:1,1:99,31:130,2:0.0152:2,2:7:1:24.5:1:0.42748:3.15908:60:4:0.0153:0:1 +22 24167513 . G A 190 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCCCTGAAGCTGTGCTC;RSEQ=GAGCTGGGGTTGGGCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:0:0,0:293,395:688,0:0:2,0:24.1:1:30.7:1:1:0:60:136.6:1:0:0.1 0/1:649:85:37,48:275,289:564,85:0.131:2,2:26.7:1:29.7:1:0.41543:1.23405:59.6:170:0.1316:0:1.1 +22 24167657 . G GAA 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=TCCCTGCAAAACTGTTTTGA;RSEQ=AAAGACTTCTCTGTGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:9,108:117,0:0:2,0:22.8:1:32.4:1:1:0:60:234:1:0:0.1 0/1:83:8:3,5:13,62:75,8:0.0964:2,2:20.9:1:28.7:1:0.17826:2.82:60:16:0.0964:0.0361:0 +22 24167744 . GTCC G 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.00843;SOR=Inf;LSEQ=GGGGTCTGTGTGTTTGCTCC;RSEQ=TCCTCCTGCCCTATGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:17,0:0:1,0:26.6:1:28.4:1:1:0:60:4.667:1:0:0.5 0/1:9:4:1,3:0,5:5,4:0.4444:0,2:31.3:1:32.8:1:0.44444:0:60:8:0.4444:0:0.3 +22 24175440 . G T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGCATCAGCATGGTCCA;RSEQ=CCCGTGCTGTCCTGTCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:35.3:1:30.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 24175583 . A C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03254;SOR=Inf;LSEQ=TCATGGCGACAACACTTGTT;RSEQ=TGGAAAGGCCCTGGCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:49,0:49,0:0:1,0:26.2:1:28.8:1:1:0:59.5:98:1:0:0.1 0/1:24:3:3,0:20,1:21,3:0.125:1,0:32.3:1:30:1:1:0:60:6:0.1364:0:1.3 +22 24175620 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03103;SOR=Inf;LSEQ=CCTCCAGCAGCTCCCTTGAG;RSEQ=TTCAGGTGACTGGAGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:95,0:95,0:0:1,0:24.7:1:31.8:1:1:0:59.8:190:0.9896:0:0 0/1:45:3:3,0:42,0:42,3:0.0667:1,0:22.7:1:28:1:1:0:60:6:0.0698:0:1.3 +22 24175650 . C T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=Inf;LSEQ=CTGGAGCATCCACTGGGTGC;RSEQ=AGCAGTGCTGCTGGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:132,2:134,0:0:1,0:24.6:1:31.8:1:1:0:59.8:268:1:0:0 0/1:74:7:6,1:66,1:67,7:0.0946:1,2:21:1:31:1:0.18141:10.26095:59.9:14:0.0946:0:1 +22 24175923 . C A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.3145;SOR=4.17994;LSEQ=CTGTGGTCCTGGGCTCTGCC;RSEQ=ACAGGCACCTGGCTTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:1:1,0:106,310:416,1:0.0024:2,0:1:0:27:0:0.25659:0:60:2:0.0025:0:1 0/1:301:3:2,1:99,199:298,3:0.01:2,2:11.3:1:27:1:0.26148:4.00:60:6:0.0102:0:1.3 +22 24175943 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16324;SOR=Inf;LSEQ=CACAGGCACCTGGCTTTCCA;RSEQ=GCAGAGGCAGGGCCATTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:50,231:281,0:0:2,0:22.4:1:31.1:1:1:0:60:30.222:1:0:0.1 0/1:191:2:1,1:45,144:189,2:0.0105:2,2:8.5:1:29.5:1:0.42463:3.18:60:4:0.0105:0:1 +22 24176053 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00356;SOR=Inf;LSEQ=TGATAAGGCCCCATCCAAAC;RSEQ=CCAGGGTATGTTTCCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:15,39:54,0:0:2,0:22.5:1:32.5:1:1:0:59.6:108:1:0:0.1 0/1:19:4:1,3:3,12:15,4:0.2105:2,2:35:1:29.5:1:1:1.31:60:8:0.25:0:1 +22 24176164 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0103;SOR=Inf;LSEQ=TGATGAGCAGGGCCTGAGTG;RSEQ=CAGACAGGCGAGGCTGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:83,10:93,0:0:2,0:25.3:1:31.2:1:1:0:59.5:22.25:1:0:0.1 0/1:45:4:4,0:38,3:41,4:0.0889:2,0:18.5:1:28.3:1:1:0:60:8:0.0909:0:1 +22 24176232 . C T 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCACATCCTGCCTCTGTTCC;RSEQ=ACCCCTACACTTGGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:25:19,6:264,46:310,25:0.0746:2,2:19.7:1:31.7:1:0.24802:1.80851:59:50:0.0755:0:1 0/0:226:0:0,0:181,45:226,0:0:2,0:22:1:30.5:1:1:0:60:112:1:0:0.2 +22 24176275 . C T 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09493;SOR=6.23044;LSEQ=TAGAGCCTTGGGAAGGGCAG;RSEQ=GCCCAGGCTGGGAGCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:1:0,1:397,217:614,1:0.0016:2,0:1:0:26:0:0.35447:0:60:2:0.0016:0:1 0/1:497:5:1,4:309,182:491,5:0.0101:2,2:16.2:1:28.4:1:0.06821:6.766:58.6:10:0.0102:0:1 +22 24176287 . G A 192 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=144.0479;LSEQ=AAGGGCAGCGCCCAGGCTGG;RSEQ=AGCTGGCCCCGACTCATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:744:1:0,1:446,295:741,1:0.0013:2,0:47:0:31:0:0.39892:0:60:2:0.0014:0:1 0/1:627:102:59,43:312,211:523,102:0.1627:2,2:25.1:1:28.8:1:0.74202:1.07755:60:204:0.1648:0:1.2 +22 24176460 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16085;SOR=Inf;LSEQ=GGACAGAGGCGAGGGGACAG;RSEQ=CCAGCGCCATCCTGAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:79,204:283,0:0:2,0:23.4:1:31.5:1:1:0:59.9:46.167:1:0:0.2 0/1:190:2:1,1:46,142:188,2:0.0105:2,2:14.5:1:27:1:0.43453:3.06:60:4:0.0108:0:1 +22 24176480 . C CG 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAGCGCCATCCTGAGGAT;RSEQ=GGGTGGGGGTGGAGTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:71,138:209,0:0:2,0:23.4:1:31:1:1:0:59.8:103.5:1:0:0.1 0/1:140:16:5,11:30,94:124,16:0.1143:2,2:23.3:1:29.6:1:0.54689:1.42:60:15:0.1087:0.0071:0.1 +22 24176527 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16804;SOR=Inf;LSEQ=GGTGGCCCTTCCCGGCACAC;RSEQ=TTCCATTTGTTGAGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:143,65:208,0:0:2,0:24:1:30.9:1:1:0:59.9:68.333:1:0:0.6 0/1:145:2:1,1:94,49:143,2:0.0138:2,2:22:1:30.5:1:1:1.90923:60:4:0.014:0:1 +22 24176544 . C T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57227;SOR=2.84456;LSEQ=CACATTCCATTTGTTGAGCC;RSEQ=CAGTCCTGCCCCCCACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:1:0,1:185,83:268,1:0.0037:2,0:1:0:27:0:0.31227:0:60:2:0.0038:0:1 0/1:190:2:1,1:133,55:188,2:0.0105:2,2:8.5:1:31:1:0.5037:2.4055:60:4:0.0107:0:1 +22 24176677 . GCAACAGGTCATGTTCAATTTCTT G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13205;LSEQ=TAACAGTTTTTAAATAAAAG;RSEQ=CAACAGGTCATGTTCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:97:40,57:204,254:458,97:0.1745:2,2:31:1:32.5:1:0.57508:1.14421:59.8:194:0.177:0.0144:0.1 0/1:627:17:11,6:276,333:609,17:0.0271:2,2:34.1:1:31.7:1:0.14042:2.21:59.7:34:0.0276:0.0032:0.1 +22 24176763 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50053;SOR=0;LSEQ=TAATGAGAGCCAGGAGTGGG;RSEQ=CCGGGGCCTGGGGGGACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:0,2:23,124:147,2:0.0134:2,0:12.5:1:30.5:1:1:0:60:4:0.0135:0:1 0/0:130:0:0,0:22,108:130,0:0:2,0:21.9:1:31.4:1:1:0:60:260:1:0:0.1 +22 24176959 . CA C 77 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAGCTGTGAGGCTCAGGG;RSEQ=AGAGGCTCTCTGCCTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:1,0:1,5:0.8333:0,0:16:1:33.3:1:0.16667:0:60:10:0.8333:0.1667:2.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 24656854 . T C 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50758;SOR=0;LSEQ=AGGGACATCTTATTGACTGC;RSEQ=TCCTTCTCTGCCACCCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:6,12:18,2:0.1:2,0:43.5:1:35:1:1:0:23:4:0.1:0:1 0/0:13:0:0,0:6,7:13,0:0:2,0:25.3:1:27.8:1:1:0:24:12:1:0:0.3 +22 25159950 . G A 41 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCTCCGCGGGGTCAGAGGC;RSEQ=CAAAGCCCCTTTTCCAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:2,3:0.6:2,2:12:1:26.3:1:1:1.73:60:6:0.6:0:1.3 +22 25160592 . CGTGTGT C 31 v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=38;MSI=22.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCATTCTTTTTGACCTTGC;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,0:6,2:0.2222:0,0:31.5:1:31.5:1:1:0:56:4:0.2222:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:33:0:32:0:1:0:60:2:1:0:0 +22 25160668 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03348;SOR=Inf;LSEQ=CTCTCTCTTTTGCCCAGGCT;RSEQ=GAGTGCAACAATGCAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:21,1:22,0:0:1,0:23.9:1:31.4:1:1:0:56:10:1:0:0.2 0/1:18:4:4,0:14,0:14,4:0.2222:1,0:21.8:1:29:1:1:0:60:8:0.2222:0:1 +22 25160783 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20637;SOR=Inf;LSEQ=AACAAAACCCAGCGGGAAAA;RSEQ=TTTGCCTGCCATTGGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:97,91:188,0:0:2,0:25.8:1:32.8:1:1:0:60:93:1:0:0.2 0/1:157:2:1,1:79,76:155,2:0.0127:2,2:48:0:29:1:1:1.03923:60:4:0.0127:0:1 +22 25160785 . T C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=6.54893;LSEQ=CAAAACCCAGCGGGAAAAGT;RSEQ=TGCCTGCCATTGGCATGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:5:2,3:93,88:181,5:0.0269:2,2:23.4:1:34.2:1:0.67745:1.58133:60:10:0.0273:0:1 0/1:156:24:13,11:66,66:132,24:0.1538:2,2:27.6:1:31.3:1:0.82523:1.18:60:48:0.1538:0:1 +22 25160792 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50151;SOR=0;LSEQ=CAGCGGGAAAAGTTTGCCTG;RSEQ=CATTGGCATGGCTGATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:89,90:179,2:0.011:2,2:22:1:29.5:1:1:1.01:60:4:0.0116:0:1 0/0:155:0:0,0:77,78:155,0:0:2,0:29.6:1:30.7:1:1:0:60:37.75:1:0:0.3 +22 25494553 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15061;SOR=Inf;LSEQ=AGAAGCATCAAGGCTGCGTA;RSEQ=GATCTGCAGGCAGCTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:26,0:26,0:0:1,0:23.2:1:34:1:1:0:60:52:1:0:0.1 0/1:17:2:2,0:14,1:15,2:0.1176:1,0:13:1:31.5:1:1:0:60:4:0.125:0:1.5 +22 25494592 . A G 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.11014;SOR=Inf;LSEQ=GGTTGGAAACAACTGGGTGG;RSEQ=GGGGGCGGGGGGGGGTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:37,1:38,0:0:1,0:24.5:1:30:1:1:0:60:37:1:0:0.1 0/1:36:3:1,2:33,0:33,3:0.0833:1,2:11.3:1:23:1:0.00476:0:60:2:0.0606:0:2.7 +22 25494598 . CG C 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.59547;SOR=2.34533;LSEQ=AAACAACTGGGTGGAGGGGG;RSEQ=GGGGGGGGTTTGCTCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:1,0:43,2:45,1:0.0217:1,0:48:0:31:0:1:0:60:2:0.0217:0:2 0/1:40:2:1,1:34,4:38,2:0.05:2,2:25:1:28.8:1:0.23718:7.71345:60:4:0.0513:0.025:0 +22 25494629 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17339;SOR=Inf;LSEQ=TTGCTCTGATTGCCCTGATG;RSEQ=CAGGGGCTCTGGAAGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:75,21:96,0:0:2,0:21.1:1:31.5:1:1:0:60:47:1:0:0.1 0/1:69:2:1,1:50,17:67,2:0.029:2,2:27.5:1:25:1:0.45652:2.88688:60:4:0.0317:0:1.5 +22 25494682 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20441;SOR=Inf;LSEQ=GCCCAAGGTCTAGGACTCTG;RSEQ=GGCTGTGGAATGTGCATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:137,88:225,0:0:2,0:25.9:1:30.7:1:1:0:60:55.25:1:0:0.1 0/1:187:2:1,1:102,83:185,2:0.0107:2,2:14.5:1:32:0:1:1.22755:60:4:0.011:0:1 +22 25494744 . C T 183 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=119.36562;LSEQ=GGGGACCTGTGGAGTGACAC;RSEQ=CCTTTGTCAAGATGCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:1:0,1:120,148:268,1:0.0037:2,0:46:0:14:0:1:0:60:0:0:0:3 0/1:252:78:37,41:78,96:174,78:0.3095:2,2:25.5:1:29.2:1:0.78458:1.11:60:156:0.3171:0:1.2 +22 25494775 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.20524;SOR=Inf;LSEQ=GATGCCAGGGCTGCCTGGCT;RSEQ=CCCCATTCCCTGCCCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:86,142:228,0:0:2,0:24.1:1:32.3:1:1:0:59.9:75:0.9956:0:0.1 0/1:191:2:1,1:71,117:188,2:0.0105:2,2:24.5:1:28:1:1:1.64:60:4:0.0106:0:2 +22 25495049 . T C 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTTGCCTTGCCCAGAGAG;RSEQ=GGAAGCTGTTGAGCACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:20.7:1:30.7:1:1:0:60:6:0.75:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:31:0:1:0:60:2:1:0:1 +22 25495827 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAATGGTGGGATTCCAAT;RSEQ=GGGCAGTCCCCATTGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:45.5:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 25593452 . A G 69 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08908;SOR=5.00307;LSEQ=GTGAATGAATAGAGTCTCCC;RSEQ=TGCATGCAGGCCCTGACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:14,9:23,2:0.08:2,0:24.5:1:30:1:0.52:0:60:4:0.0833:0:1 0/1:16:5:3,2:6,4:10,5:0.3125:2,2:17:1:30:1:1:1:60:10:0.3125:0:1.2 +22 25593459 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.52367;SOR=0;LSEQ=AATAGAGTCTCCCATGCATG;RSEQ=AGGCCCTGACTGGGGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:16,11:27,2:0.069:2,2:19:1:28:1:1:1.43545:60:4:0.069:0:1 0/0:17:0:0,0:10,7:17,0:0:2,0:28.1:1:31.8:1:1:0:60:34:1:0:0.8 +22 25594000 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGTGCAGTAGGTCTGCAAG;RSEQ=TCCTCAAAGATGTGATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 25770400 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAACGCCAGCCTCAAGTG;RSEQ=CATCAGGGACCTCCCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:18:1:28.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 25770473 . T C 53 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACATTGGGCCCTCAGCC;RSEQ=GGCCAGACGGTCTGCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:25.5:1:26.5:1:1:0:53.3:3:1:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:3:0:30:0:1:0:25:2:1:0:1 +22 25770706 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13257;SOR=Inf;LSEQ=TGCCTGCATGGTAGTGATGG;RSEQ=AACCCCAGAGACAGTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:124,62:186,0:0:2,0:27.6:1:32.6:1:1:0:60:61:1:0:0.2 0/1:107:2:1,1:66,39:105,2:0.0187:2,2:36.5:1:30:1:1:1.68356:60:4:0.0189:0:1 +22 25770725 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15761;SOR=Inf;LSEQ=GCAACCCCAGAGACAGTGGG;RSEQ=TCCTGGGCAAAAGGCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:131,89:220,0:0:2,0:26.1:1:32.7:1:1:0:60:109:1:0:0.4 0/1:146:2:1,1:90,54:144,2:0.0137:2,2:40.5:1:29:1:1:1.66052:60:4:0.0138:0:1 +22 25770790 . T A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10824;SOR=0.74051;LSEQ=CACTGTCCCTCTTGCCAGGA;RSEQ=GGCCAAGCTTGTCACTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:303:170:85,85:65,68:133,170:0.5611:2,2:26.9:1:31.3:1:0.90792:1.05:50.9:340:0.5648:0:1.1 0/1:216:105:57,48:56,55:111,105:0.4861:2,2:24:1:29.4:1:0.58835:1.17:49.7:104:0.486:0:1.1 +22 25770879 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13661;SOR=Inf;LSEQ=CCAGCACCTCATTCTAACCA;RSEQ=GGGAAAGCTGGGGTGTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:36,103:139,0:0:2,0:26.2:1:31.6:1:1:0:54.6:138:1:0:0.2 0/1:82:2:1,1:21,59:80,2:0.0244:2,2:19.5:1:28:1:0.46703:2.77:47.5:4:0.0244:0:1.5 +22 25770897 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11373;SOR=Inf;LSEQ=CAGGGGAAAGCTGGGGTGTA;RSEQ=CAGCCCCAAAATACGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:19,94:113,0:0:2,0:24.1:1:32.3:1:1:0:59.3:112:1:0:0.2 0/1:58:2:1,1:8,48:56,2:0.0345:2,2:15.5:1:29.5:1:0.28857:5.72:60:4:0.0345:0:1 +22 26043158 . C T 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00221;SOR=Inf;LSEQ=CGGGCCTCACCTCCACCCAC;RSEQ=GCCCCCTCCCACCACCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:27,2:29,0:0:2,0:11.5:1:26:1:1:0:56.9:4.8:1:0:2.3 0/1:19:6:6,0:13,0:13,6:0.3158:1,0:28:1:29.3:1:1:0:60:12:0.3333:0:1 +22 26043803 . T C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00196;SOR=0.33443;LSEQ=GAGAGAGTGAAATGGCTGGG;RSEQ=GCAGTGGCTCATGCCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:33:3,30:28,107:135,33:0.1964:2,2:25.8:1:30.7:1:0.14073:2.60463:53.4:66:0.1976:0:1 0/1:146:11:1,10:27,106:133,11:0.0753:2,2:23.9:1:29.7:1:0.69177:2.53462:51.3:22:0.0769:0:1.3 +22 26043805 . C A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59209;SOR=2.42353;LSEQ=GAGAGTGAAATGGCTGGGTG;RSEQ=AGTGGCTCATGCCTGTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:1,0:30,128:158,1:0.0063:2,0:1:0:25:0:0.19497:0:60:2:0.0063:0:1 0/1:132:2:2,0:25,104:129,2:0.0152:2,0:8.5:1:26:1:0.04122:0:60:4:0.0154:0:2 +22 26043815 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19955;SOR=Inf;LSEQ=TGGCTGGGTGCAGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:16,106:122,0:0:2,0:23.6:1:30.8:1:1:0:54.1:121:1:0:0.3 0/1:99:2:1,1:11,86:97,2:0.0202:2,2:23.5:1:31.5:1:0.22882:7.53:57:4:0.0204:0:2.5 +22 26044080 . G A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00648;SOR=Inf;LSEQ=GCGACAAGAGCAAAAACTCC;RSEQ=TCTAAAAAACAAATAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:114,6:120,0:0:2,0:22.4:1:30.7:1:1:0:58.7:240:1:0:0 0/1:71:5:3,2:63,3:66,5:0.0704:1,2:22.8:1:29.4:1:0.03682:12.81827:60:10:0.0704:0:1.2 +22 26044112 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18219;SOR=Inf;LSEQ=AATAAGCAAACAGAACAAAA;RSEQ=AAAACAAAAACGAGAGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:201,36:237,0:0:2,0:23.2:1:32.2:1:1:0:60:78:1:0:0.1 0/1:177:2:1,1:148,27:175,2:0.0113:2,2:27:1:26.5:1:0.29212:5.40096:60:4:0.0114:0:1 +22 26045057 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1201;SOR=Inf;LSEQ=CAGGATGCCTTGCCCTCAGG;RSEQ=CTGTCCAGAATCCCTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:212,134:346,0:0:2,0:29.5:1:31.5:1:1:0:47.9:68.2:1:0:0.1 0/1:184:2:2,0:118,64:182,2:0.0109:2,0:19:1:24.5:1:0.54383:0:52:4:0.0112:0:1 +22 26045111 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1866;SOR=Inf;LSEQ=GTGTTGGAAGAAGGACCCTG;RSEQ=TGAAAGACCAACATTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:81,134:215,0:0:2,0:15.9:1:30.1:1:1:0:44.6:214:1:0:0.1 0/1:164:2:1,1:66,96:162,2:0.0122:2,2:19:0:32.5:1:1:1.45:60:4:0.0125:0:1.5 +22 26388019 . G T 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02006;SOR=0;LSEQ=AGATGGGCTGAGTATCCACT;RSEQ=TGCGTGGTGGTGCAGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:7,1:52,6:58,8:0.1212:2,2:25.8:1:31.5:1:1:1.23383:60:16:0.1231:0:1.1 0/0:46:0:0,0:39,7:46,0:0:2,0:20.1:1:31.5:1:1:0:60:92:1:0:0 +22 26388087 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19955;SOR=Inf;LSEQ=GGGAGCAGCACCCCCTGCAC;RSEQ=GGTGAGCAAGCTCTGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:138,92:230,0:0:2,0:24.2:1:30.8:1:1:0:60:114:0.9956:0:0.4 0/1:187:2:1,1:111,73:184,2:0.0107:2,2:30:1:28.5:1:1:1.51698:60:4:0.0108:0:1.5 +22 26388111 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08271;SOR=Inf;LSEQ=GAGCAAGCTCTGTGTGCCAT;RSEQ=CCCTGGAGTATCTATTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:160,133:293,0:0:2,0:25.9:1:32.3:1:1:0:60:47.833:0.9965:0:0.5 0/1:228:3:1,2:120,105:225,3:0.0132:2,2:24.7:1:26.7:1:0.60152:2.27768:60:6:0.0133:0:2.3 +22 26388119 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1674;SOR=1.4734;LSEQ=TCTGTGTGCCATGCCCTGGA;RSEQ=TATCTATTCCCTCCTCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:28:16,12:152,133:285,28:0.0895:2,2:26.5:1:30.8:1:0.84301:1.17:60:27:0.0865:0:1.9 0/1:245:31:17,14:106,107:213,31:0.1265:2,2:24.1:1:29.1:1:0.70151:1.22:60:62:0.1286:0:2 +22 26388144 . T A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.75913;LSEQ=TATTCCCTCCTCTATGAAAC;RSEQ=TGGAACACCTGGTTGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:104:53,51:113,108:221,104:0.32:2,2:27.2:1:30.6:1:1:1.00679:60:103:0.3209:0:1.3 1/0:269:172:83,89:50,47:97,172:0.6394:2,2:23.4:1:29.6:1:0.614:1.14017:60:85:0.6439:0:1.3 +22 26388180 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96054;LSEQ=AGGATCCCATAAATCTGTCC;RSEQ=CAGAGAGAGCCTCTCACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:2,1:112,143:255,3:0.0116:2,2:12.3:1:29.7:1:0.58511:2.54:60:6:0.0119:0:1.7 0/1:179:2:2,0:76,101:177,2:0.0112:2,0:1:0:24:1:0.1885:0:60:4:0.0112:0:2 +22 26388192 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15773;SOR=Inf;LSEQ=ATCTGTCCGCAGAGAGAGCC;RSEQ=CTCACGGAGAACTTACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:91,141:232,0:0:2,0:23.3:1:30.2:1:1:0:60:45.4:0.9956:0:0.4 0/1:154:2:1,1:60,92:152,2:0.013:2,2:26:0:33:0:1:1.53:60:4:0.0132:0:1 +22 26790704 . G T 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64239;SOR=1.94933;LSEQ=TGTGAGATGGAGGTCACAGT;RSEQ=AGCCGACACCATACCATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:3,1:16,0:16,4:0.2:1,2:32.8:1:30.8:1:0.2:0:60:8:0.2105:0:1 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:33.3:1:32:1:1:0:54.7:6:0.3333:0:1.3 +22 26790759 . CAA C 122 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=1;SOR=0.89749;LSEQ=GAGACAGTGAGACTCCATCT;RSEQ=AAAAAAAAAAAAATTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:14:13,1:8,2:10,14:0.3784:2,1:24.9:1:32.1:1:0.5504:3.09:59.2:28:0.3784:0.1351:0.1 0/1:34:12:7,5:10,0:10,12:0.3529:0,2:19.1:1:30.7:1:0.03964:0:60:24:0.3636:0.0588:0.3 +22 26790778 . AAAAG A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18651;SOR=0.5779;LSEQ=TCAAAAAAAAAAAAAAATTG;RSEQ=AAAGAAAGGAAAAAGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:28:23,5:28,5:33,28:0.4516:2,2:17:1:30.8:1:1:1.21345:59.4:56:0.4667:0.129:0.1 0/1:56:18:11,7:27,11:38,18:0.3214:2,2:25.7:1:29.5:1:0.54478:1.54925:59.1:36:0.3214:0.0714:0.2 +22 26790885 . G C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0673;SOR=0.62553;LSEQ=GGCAGGGCCAGAGCTCAGCT;RSEQ=ATCATTCATGGGCTTGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:63:27,36:74,72:146,63:0.3014:2,2:26.1:1:32:1:0.36565:1.36829:60:126:0.3043:0:1 0/1:146:31:14,17:58,57:115,31:0.2123:2,2:24.9:1:30.9:1:0.68722:1.2338:60:62:0.2168:0:1.2 +22 26790901 . G GTCAC 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50469;SOR=0.86015;LSEQ=AGCTGATCATTCATGGGCTT;RSEQ=TCAGTCAGTAAAAGAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:118:51,67:42,41:83,118:0.5813:2,2:28.1:1:31.2:1:0.31777:1.34375:59.9:117:0.5879:0.1034:0.6 1/0:136:74:34,40:28,34:62,74:0.5441:2,2:26.3:1:29.9:1:1:1.03:59.9:148:0.5481:0.0882:0.5 +22 26790928 . G T 30 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77385;LSEQ=AGTAAAAGAATGGGGATTCC;RSEQ=AGGAAGGACAAACAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:61,106:167,2:0.0118:2,2:18:0:30.5:1:1:1.73:60:4:0.012:0:1.5 0/0:109:1:0,1:43,65:108,1:0.0092:2,0:1:0:21:0:1:0:60:2:0.0095:0:2 +22 26790999 . G T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94474;LSEQ=CCAGATGCCTCAGAAACCCA;RSEQ=ATCCTGTTTCCCAGGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:14:1,13:2,36:38,14:0.2692:2,1:30.1:1:29:1:1:1.38:60:28:0.2692:0:1.1 0/1:31:8:1,7:1,22:23,8:0.2581:1,2:23:1:28.6:1:0.45591:3.01:60:16:0.2581:0:1.1 +22 27561447 . A T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03201;SOR=Inf;LSEQ=CAGGTAGAGTTGGAGGAGGG;RSEQ=TAAGAGATAAATTATGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:265,149:414,0:0:2,0:25.4:1:30:1:1:0:60:36.636:1:0:0.6 0/1:305:4:1,3:174,127:301,4:0.0131:2,2:17.5:1:28:1:0.31602:4.09211:60:8:0.0133:0:1.3 +22 27561500 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.48144;LSEQ=TACCAAGCCAGTCCATCCAT;RSEQ=GGCAACACTACAAAGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:502:375:184,191:58,65:123,375:0.747:2,2:25.1:1:30.1:1:0.75553:1.08:60:374:0.7525:0:1.1 1/0:334:196:93,103:62,76:138,196:0.5868:2,2:25.9:1:28.5:1:0.65764:1.11:60:97:0.5915:0:1.1 +22 27561618 . C A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52506;SOR=0;LSEQ=TAATGATTATTTTTTCCTTT;RSEQ=TACCCTACTTTCTTTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:8,92:100,2:0.0196:2,2:5.5:1:28:1:0.16948:10.90:60:4:0.0198:0:1 0/0:63:0:0,0:5,58:63,0:0:2,0:19.7:1:31.4:1:1:0:59.6:30.5:1:0:0.1 +22 27661288 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49757;SOR=Inf;LSEQ=TCTGTAGGTGATGGCTTTTG;RSEQ=TGTTGCTGCTGTTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:20,16:36,0:0:2,0:26.4:1:32.2:1:1:0:60:35:1:0:0.1 0/1:43:2:1,1:21,20:41,2:0.0465:2,2:30:0:31:0:1:1.04883:60:4:0.0476:0:1.5 +22 27661307 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49562;SOR=Inf;LSEQ=GCTGTTGCTGCTGTTGCTGT;RSEQ=GTTGTTTTGTTGTTGTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:15,22:37,0:0:2,0:25.8:1:29.8:1:1:0:60:36:1:0:0.1 0/1:42:2:1,1:18,21:39,2:0.0476:2,2:26.5:1:28.5:1:1:1.16:60:4:0.0488:0:1 +22 28194872 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06712;SOR=Inf;LSEQ=CTGCTTAATCATGAGGGCCG;RSEQ=GTTTTGGCGCTGCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:59,52:111,0:0:2,0:30.2:1:30.4:1:1:0:59.2:21.2:1:0:0.1 0/1:77:3:1,2:45,29:74,3:0.039:2,2:16:1:28.3:1:0.56138:3.05731:58.3:6:0.039:0:1.3 +22 28194880 . CGCT C 73 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.13098;SOR=3.62726;LSEQ=TCATGAGGGCCGCGTTTTGG;RSEQ=GCTGCTGCTGCTGCTGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:0,2:58,53:111,2:0.0177:2,0:39.5:1:33.5:1:0.23467:0:60:4:0.0182:0:0 0/1:81:5:4,1:44,32:76,5:0.0617:2,2:33.2:1:31.8:1:0.64357:2.88:60:10:0.0625:0:0 +22 28194912 . TTGC T 95 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.00821;SOR=7.18394;LSEQ=TGCTGCTGTTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:59,73:132,2:0.0149:2,2:39:0:30:1:1:1.24:45:4:0.015:0:0 0/1:91:9:5,4:42,38:80,9:0.0989:2,2:32.1:1:30:1:1:1.13:46.3:18:0.1:0.011:0.8 +22 28195624 . GGCT G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.20635;SOR=Inf;LSEQ=GCTGCTGCTGCTGCTGCTGG;RSEQ=GCTGCTGCTGCTGGGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:21.7:1:31.4:1:1:0:58.5:14:1:0:0.3 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:25:0:33:0:1:1.18321:56:4:0.1538:0:0.5 +22 29083926 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24969;SOR=Inf;LSEQ=AGCTGGGCGCTTTGTGGTCT;RSEQ=GGCACCCTCGGCTTCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:109,103:212,0:0:2,0:27.4:1:31.1:1:1:0:50.4:424:1:0:0.1 0/1:231:3:2,1:117,111:228,3:0.013:2,2:10:1:24.3:1:1:1.89:53.7:6:0.0131:0:1 +22 29085100 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=Inf;LSEQ=TTAAGCCCAGACTACATTTA;RSEQ=TGATCATCAGGAATACGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:8.6:1:34.6:1:1:0:36.6:10:1:0:0.2 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:15.5:1:29.5:1:1:1.29098:21:4:0.2222:0:1.5 +22 29085110 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24;SOR=Inf;LSEQ=ACTACATTTAGTGATCATCA;RSEQ=GAATACGAATACCTGGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:25,13:38,0:0:2,0:5.7:1:31.9:1:1:0:23:76:1:0:0.1 0/1:37:2:1,1:23,12:35,2:0.0541:2,2:22.5:1:30.5:1:1:1.88115:21:4:0.0541:0:1.5 +22 29089846 . C CA 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.2143;SOR=0.38015;LSEQ=GACAGAACAAGAACCTGTCT;RSEQ=AAAAAAAAAAATAAAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:10,0:27,3:30,10:0.25:2,0:24.3:1:29:1:0.55972:0:41:9:0.2308:0.075:0.8 0/1:27:3:2,1:19,2:21,3:0.1111:2,2:20.7:1:29.1:1:0.34289:4.30947:35.3:6:0.12:0.037:0.7 +22 29089858 . T A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0323;SOR=Inf;LSEQ=ACCTGTCTCAAAAAAAAAAA;RSEQ=AAAACAGGTTGTAACCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:52,3:55,0:0:2,0:20.3:1:30.7:1:1:0:44.5:17.333:1:0:0.2 0/1:42:4:3,1:33,5:38,4:0.0952:2,2:23.5:1:29.8:1:0.47373:2.14919:33.5:8:0.1026:0:2 +22 29090007 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22014;SOR=Inf;LSEQ=ATTTTATGCTAGCAGGCACT;RSEQ=TCCCACACCCACCTGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:91,77:168,0:0:2,0:13.6:1:32.3:1:1:0:43.8:167:1:0:0.2 0/1:149:2:1,1:93,53:146,2:0.0134:2,2:16.5:1:27.5:1:1:1.74763:43:4:0.0135:0:1 +22 29090074 . C A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60475;SOR=0.44677;LSEQ=GTAAAACGTGCCTTTGGATC;RSEQ=ACTACCAACAACTTCTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:98,100:198,2:0.01:2,2:38.5:1:30:1:1:1.02:34:4:0.0101:0:2 0/0:223:1:1,0:128,94:222,1:0.0045:2,0:1:0:25:0:1:0:60:2:0.0045:0:1 +22 29090092 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20149;SOR=0;LSEQ=TCCACTACCAACAACTTCTT;RSEQ=ACAAGGTCCAGAGCTAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:59,69:128,2:0.0154:2,2:13:1:28:1:1:1.17:43:4:0.0155:0:1 0/0:159:0:0,0:91,68:159,0:0:2,0:12.6:1:30:1:1:0:33.9:78.5:1:0:0.1 +22 29090099 . T A 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50168;SOR=Inf;LSEQ=CCAACAACTTCTTGACAAGG;RSEQ=CCAGAGCTAAAGCAACAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:44,67:111,0:0:2,0:9.3:1:29.2:1:1:0:28.3:54.5:1:0:0.1 0/1:132:2:2,0:67,63:130,2:0.0152:2,0:8:1:22:0:0.49722:0:42.5:4:0.0154:0:1 +22 29090363 . G A 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=CACTGCCTGTTCCCTCTCTT;RSEQ=TTGCTAGACTCAAGGTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:16.8:1:30.2:1:1:0:28.6:10:0.625:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:10:0:34:0:1:0:28:2:1:0:0 +22 29091017 . T C 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20918;SOR=Inf;LSEQ=ATAGAAAATAAGAACAGAAT;RSEQ=GACAGGAGAAAACACCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:159,16:175,0:0:2,0:21:1:31.6:1:1:0:28.5:57.333:1:0:0.7 0/1:148:2:1,1:128,18:146,2:0.0135:2,2:39:0:29.5:1:0.24104:6.94841:38:4:0.0137:0:2 +22 29091024 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23335;SOR=Inf;LSEQ=ATAAGAACAGAATTGACAGG;RSEQ=GAAAACACCATGGAATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:184,22:206,0:0:2,0:23.7:1:31:1:1:0:27.4:102:1:0:0.7 0/1:193:2:1,1:161,30:191,2:0.0104:2,2:17.5:1:31:0:0.29615:5.29588:21.5:4:0.0105:0:1 +22 29091037 . G C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17497;SOR=0.78773;LSEQ=TGACAGGAGAAAACACCATG;RSEQ=AATTTGGGAAGAAACTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:313:204:165,39:87,22:109,204:0.6518:2,2:23.5:1:32.5:1:0.88116:1.07:24.1:33:0.6513:0:1.1 1/0:282:168:137,31:90,24:114,168:0.5957:2,2:23.9:1:31.8:1:0.64671:1.18:23.5:336:0.5957:0:1.1 +22 29092639 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAGGTGTGAGCCACCAT;RSEQ=CCCAGCCCACTCGTCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:23.5:1:31.1:1:1:0:54.6:10:1:0:1.5 1/1:3:3:3,0:0,0:0,3:1:0,0:19.3:1:29.7:1:1:0:46.7:6:1:0:1.3 +22 29092720 . C T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51081;SOR=0.53198;LSEQ=ACAACAGAGCTCAATAAATG;RSEQ=TCATTCGAATCTGGATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:8,0:37,1:38,8:0.1739:1,0:30.3:1:31.6:1:1:0:60:16:0.1818:0:1.1 0/1:30:3:3,0:26,1:27,3:0.1:1,0:15.7:1:30.3:1:1:0:60:6:0.1:0:1 +22 29092998 . C A 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19724;SOR=4.43131;LSEQ=ACACAGAAAGGCAGGCATGA;RSEQ=CCTCAGATTCATGCAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:1:1,0:141,294:435,1:0.0023:2,0:1:0:25:0:0.32569:0:60:2:0.0023:0:1 0/1:396:4:1,3:118,273:391,4:0.0101:2,2:12.5:1:25.5:1:1:1.29586:60:3:0.0077:0:2.5 +22 29093029 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17421;SOR=Inf;LSEQ=ATGCAGTAGATACTTAAGTA;RSEQ=AATCAAAGTTACCAACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:38,199:237,0:0:2,0:23.6:1:31.9:1:1:0:60:46.4:0.9957:0:0.1 0/1:171:2:1,1:29,140:169,2:0.0117:2,2:10.5:1:28.5:1:0.32095:4.76:60:4:0.0117:0:1.5 +22 29093239 . A G 89 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TAATAAACAACTCTTCACAC;RSEQ=GCAGAAATGTAAGGTGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:19:1:32:1:1:0:56.4:14:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 29095634 . AC A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04194;SOR=Inf;LSEQ=TGCTGGGATTATGGGCATGA;RSEQ=CACCGCGCCTCGCCAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:30,0:0:1,0:23.8:1:31.7:1:1:0:60:14:1:0:0.1 0/1:17:3:3,0:14,0:14,3:0.1765:1,0:24.3:1:28.2:1:1:0:60:6:0.1765:0.0588:0.7 +22 29095725 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19416;SOR=Inf;LSEQ=ACAGCAAACACACAGATTCT;RSEQ=TTCTGAGTTTTAATCCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:136,3:139,0:0:1,0:24.1:1:32.2:1:1:0:60:45.333:1:0:0.1 0/1:110:2:1,1:103,5:108,2:0.0182:1,2:13.5:1:27:1:0.10659:18.88648:60:4:0.0185:0:1 +22 29099459 . G T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68629;SOR=1.91501;LSEQ=GCTTTATAAAGCATTTGAAT;RSEQ=GAAACAGAAATTTTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:2:0,2:176,79:255,2:0.0078:2,0:1:0:26.5:1:0.09849:0:60:4:0.0079:0:1 0/1:270:4:1,3:190,76:266,4:0.0148:2,2:11.8:1:26.3:1:0.07669:7.43676:60:8:0.0149:0:1 +22 29099754 . T C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07523;SOR=0.16771;LSEQ=GTGAGAACATGCAAGAAATT;RSEQ=TCCACCCCACCATGATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:0,13:0,5:5,13:0.7222:0,1:25.1:1:33.3:1:1:0:60:26:0.7222:0:1.3 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:32:1:32:1:1:0:60:4:0.2857:0:1 +22 29106174 . A G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00179;SOR=Inf;LSEQ=CCAGCTCTACTTATACAAAG;RSEQ=AATCAAAGCCCAGGTCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:0,38:38,0:0:1,0:27.2:1:31.9:1:1:0:60:76:1:0:0.1 0/1:29:7:0,7:0,22:22,7:0.2414:1,0:33.6:1:30.3:1:1:0:60:14:0.2414:0:1.1 +22 29107646 . G GA 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGACTTTGAACTTGGAAGAA;RSEQ=AAAAAAAAAAACTTCCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:8,2:0.2:0,0:7.5:1:31.3:1:1:0:57:4:0.2:0.1:0 0/0:1:0:0,0:1,0:1,0:0:0,0:35:0:28:0:1:0:60:2:1:0:0 +22 29107806 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20166;SOR=Inf;LSEQ=CCATCTAAGCAGGGGGTTAT;RSEQ=CCTGAGTTTAAAAATCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:184,8:192,0:0:1,0:24.6:1:31.3:1:1:0:59.7:191:1:0:0.1 0/1:157:2:1,1:148,7:155,2:0.0127:1,2:18.5:1:27:1:0.09962:19.84568:60:4:0.0128:0:1 +22 29108082 . G GTATTAGAATTTACAGACATTCCA 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=1.130;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=CACTCCTGGGTCCACTTCAA;RSEQ=TATTAGAATTTACAGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:7,168:175,0:0:1,0:25.7:1:32.7:1:1:0:59.9:174:1:0:0.1 0/1:141:10:0,10:5,126:131,10:0.0709:1,0:27.5:1:30.9:1:1:0:58.6:20:0.0709:0.0213:0.6 +22 29108112 . A C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00587;SOR=Inf;LSEQ=TTACAGACATTCCATATAAC;RSEQ=GCCTTTCCATTGTCCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:2,111:113,0:0:1,0:23.9:1:32.6:1:1:0:59.5:55.5:1:0:0.1 0/1:65:5:0,5:0,60:60,5:0.0769:1,0:25.6:1:31.6:1:1:0:58.2:10:0.0781:0:1 +22 29108229 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.74089;LSEQ=ATTCCATTTCTGAGCCCAGC;RSEQ=ATACAAACATGGGTCTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:4,11:0.7333:0,0:26.7:1:30.5:1:1:0:60:10:0.7143:0:1.1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:22.5:1:32.5:1:1:0:60:4:0.6667:0:1 +22 29115552 . A G 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=Inf;LSEQ=GATTCTAAAATTTATTCATC;RSEQ=TATGGAATATAAGAACTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:3,99:102,0:0:1,0:24.1:1:31.9:1:1:0:60:101:1:0:0 0/1:55:9:0,9:0,46:46,9:0.1636:1,0:18.3:1:32.6:1:1:0:60:18:0.1636:0:1 +22 29120797 . A G 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58858;SOR=2.14449;LSEQ=CTCCTGACCTCAGGTGATCC;RSEQ=TCCGCCTCAGCCTCCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:3,0:36,0:36,3:0.0769:1,0:24:1:31:1:1:0:40.7:6:0.0769:0:1 0/1:13:2:2,0:11,0:11,2:0.1538:0,0:19:1:31:0:1:0:46:4:0.1538:0:1 +22 29120913 . T A 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24863;SOR=0;LSEQ=GACAGGACAAATTTTCCTCC;RSEQ=ATGAGAGAGTGGAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:1,2:205,60:265,3:0.0112:2,2:28.3:1:24.7:1:0.13472:6.76984:60:2:0.0076:0:3 0/0:264:0:0,0:186,78:264,0:0:2,0:21.7:1:28.7:1:1:0:59.8:36.714:1:0:0.2 +22 29120915 . T A 153 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGGACAAATTTTCCTCCTA;RSEQ=GAGAGAGTGGAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:33:27,6:185,62:247,33:0.1179:2,2:24:1:30.5:1:0.51734:1.51:60:66:0.1209:0:1.1 0/0:271:0:0,0:193,78:271,0:0:2,0:5:0:17:0:1:0:35:0:0:0:5 +22 29120925 . G GA 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.3743;SOR=1.33377;LSEQ=TTTCCTCCTATGAGAGAGTG;RSEQ=AAAAAAAAAATTCCAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:22:16,6:230,93:323,22:0.0636:2,2:24:1:31.1:1:1:1.08:60:44:0.0647:0.0173:0.3 0/1:325:27:19,8:203,93:296,27:0.0831:2,2:23.4:1:28.7:1:1:1.09:58.3:54:0.0857:0.0185:0.6 +22 29121457 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52979;SOR=0;LSEQ=AGGAAAATAGCCTAAGAAGG;RSEQ=AATCAGAATTATCAATCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:0,2:0,119:119,2:0.0165:1,0:32.5:1:29.5:1:1:0:60:4:0.0165:0:1 0/0:72:0:0,0:3,69:72,0:0:1,0:24.2:1:31.9:1:1:0:60:71:1:0:0.1 +22 29130012 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTCATTTGCATAAGGCG;RSEQ=CAATCCACACCAGTCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:20:1:31.3:1:1:0:54:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 29130300 . C T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01797;SOR=0.4837;LSEQ=CAACGTGCCAAAAACCTGGA;RSEQ=AACTCCAATCAGAACCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:47:46,1:60,5:65,47:0.4196:2,1:22.2:1:31.2:1:0.39803:3.80:60:46:0.422:0:1 0/1:89:23:21,2:60,6:66,23:0.2584:2,2:24.8:1:29:1:1:1.05:60:46:0.2584:0:1 +22 29130320 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59896;SOR=2.31712;LSEQ=CAACTCCAATCAGAACCTTC;RSEQ=ACCTGGTAATACAACTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:0,1:141,17:158,1:0.0063:2,0:1:0:23:0:0.11321:0:60:2:0.0063:0:1 0/1:138:2:1,1:115,21:136,2:0.0145:2,2:25:1:30:1:0.2944:5.37359:60:4:0.0149:0:1.5 +22 29130347 . G GT 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAATACAACTTTCTGTAAGT;RSEQ=TTTTTCTGAACAAAACGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:223,74:297,0:0:2,0:23.5:1:32.4:1:1:0:59.9:98:1:0:0.2 0/1:287:27:20,7:183,77:260,27:0.0941:2,2:20.8:1:28.9:1:0.82552:1.20:59.8:54:0.0938:0.0279:0.2 +22 29130748 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17631;SOR=Inf;LSEQ=GTGTCCAACAACAAAGGTGA;RSEQ=TTTCAAGGCACAAGACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:23,149:172,0:0:2,0:25.2:1:31.7:1:1:0:60:18.111:1:0:0.3 0/1:125:2:1,1:20,103:123,2:0.016:2,2:23.5:1:29:1:0.3089:5.05:60:4:0.016:0:1 +22 29413305 . G A 56 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGCCCCCATCAGGCAGGT;RSEQ=TACACTGTCCAGTCTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:24:1:28.3:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 29413785 . A G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4754;SOR=0.50507;LSEQ=GCTTATATCCGTCAACCAGG;RSEQ=TGAGTGCAGAAAAGACTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:13:13,0:8,1:9,13:0.5909:2,1:19.4:1:31.8:1:0.40909:0:60:26:0.5909:0:1.2 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:14.4:1:31.4:1:1:0:60:10:0.4167:0:1 +22 29413894 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51273;SOR=0;LSEQ=GAGAAAGGAGGCTTTTAGAT;RSEQ=TGTCCTTAAGCATTGAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:109,36:145,2:0.0136:2,2:6.5:1:29.5:1:0.44134:3.00025:60:4:0.0137:0:1 0/0:104:0:0,0:85,19:104,0:0:2,0:21.9:1:31.5:1:1:0:60:208:1:0:0.1 +22 29413919 . G T 42 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.88917;LSEQ=CTTAAGCATTGAAGCGCTTT;RSEQ=AGAGGTAATCAAGGGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:1,2:160,72:232,3:0.0128:2,2:11.7:1:26.7:1:0.234:4.41315:60:6:0.0128:0:1 0/1:176:2:0,2:117,57:174,2:0.0114:2,0:1:0:21:0:0.1111:0:60:4:0.0116:0:1.5 +22 29414001 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.86103;LSEQ=GAAGATGTGCGTATGCCTTA;RSEQ=CTTTTCAGAAATGGGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:160:81,79:153,135:288,160:0.3571:2,2:25.6:1:32.6:1:0.62294:1.1051:60:39:0.3537:0:1.1 1/0:411:209:102,107:101,101:202,209:0.5085:2,2:26:1:31.3:1:0.84381:1.04887:60:103.5:0.5124:0:1.2 +22 29414085 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18453;SOR=Inf;LSEQ=GAGGGGAGGGCGGACGGGCA;RSEQ=ACCGGATCCAAACTGGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:61,184:245,0:0:2,0:22.6:1:32.2:1:1:0:60:80.667:1:0:0.2 0/1:185:2:1,1:59,124:183,2:0.0108:2,2:27:1:30:1:0.54465:2.09:60:4:0.0109:0:1.5 +22 29414090 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.184;SOR=Inf;LSEQ=GAGGGCGGACGGGCAGACCG;RSEQ=ATCCAAACTGGATCCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:54,160:214,0:0:2,0:23.1:1:31.9:1:1:0:60:70.333:0.9953:0:0.2 0/1:162:2:1,1:48,112:160,2:0.0123:2,2:34:1:26.5:1:0.51476:2.32:60:4:0.0124:0:1 +22 29682881 . CT C 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.56028;SOR=0;LSEQ=CAAGCCTCTTTCTAAAAAAG;RSEQ=TTTTTTTTTTTCTCTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,0:19,5:0.2:1,0:24.2:1:32.8:1:1:0:60:10:0.2:0.04:0.2 0/0:7:0:0,0:6,1:7,0:0:2,0:31.4:1:30.4:1:1:0:56.9:14:1:0:1.3 +22 29683875 . GA G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.14242;SOR=Inf;LSEQ=TTGTTTATATCCATTAAGGG;RSEQ=AAAATGGCCAGGCATGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:91,154:245,0:0:2,0:24.7:1:30.9:1:1:0:59.7:244:1:0:0.1 0/1:149:2:0,2:53,94:147,2:0.0134:2,0:17.5:1:32:0:0.53855:0:60:4:0.0136:0:0 +22 29683916 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCACACCTGTAATCCCAG;RSEQ=ACTTTGGGGGAGGCCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:76,99:175,2:0.0113:2,2:30:1:26.5:1:1:1.30:60:4:0.0114:0:1 0/0:87:0:0,0:36,51:87,0:0:2,0:22.9:1:31:1:1:0:59:42.5:1:0:0.1 +22 29683924 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTAATCCCAGCACTTTGG;RSEQ=GGAGGCCAAGGCAGGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:77,85:162,2:0.0122:2,2:28.5:1:31:1:1:1.10:60:4:0.0122:0:1 0/0:78:0:0,0:32,46:78,0:0:2,0:24.5:1:30.8:1:1:0:58.9:156:1:0:0.1 +22 29684236 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07409;SOR=Inf;LSEQ=CCCTAGCAGTGTGCTAAAGC;RSEQ=CTAAGAAACCTGGCTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:170,235:405,0:0:2,0:25.2:1:31.1:1:1:0:60:44:1:0:0.1 0/1:295:3:2,1:131,161:292,3:0.0102:2,2:22:1:27.7:1:0.59048:2.45:60:6:0.0103:0:1 +22 29684629 . T A 33 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1002;SOR=Inf;LSEQ=GACCACCCCAGTAGCATGGG;RSEQ=GTTTATGGGCAGGAGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:143,181:324,0:0:2,0:24.7:1:30.2:1:1:0:51.5:107:1:0:0.1 0/1:282:3:3,0:134,144:278,3:0.0106:2,0:6.7:1:21.3:1:0.11458:0:59.3:2:0.0073:0:3.3 +22 29685163 . A G 138 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=25.69565;LSEQ=TGTCTTGAAATACCTGGTGT;RSEQ=TATACTGCAGAAAAGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:633:1:1,0:295,337:632,1:0.0016:2,0:41:0:17:0:0.46761:0:60:0:0:0:2 0/1:511:20:11,9:238,253:491,20:0.0391:2,2:24.2:1:32:1:0.65103:1.30:60:40:0.0394:0:1.1 +22 29685604 . T A 45 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.42918;SOR=2.24727;LSEQ=TTCTGTGTGTGTTCTGTCCC;RSEQ=ATATAAACTGGTAAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:444:2:1,1:146,295:441,2:0.0045:2,2:24:1:19:1:0.55405:2.02:60:1:0.0023:0:1 0/1:397:4:3,1:157,236:393,4:0.0101:2,2:12.8:1:22.8:1:0.30724:4.49:60:3:0.0078:0:2 +22 29685620 . G GA 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.28862;SOR=1.38927;LSEQ=TCCCTATATAAACTGGTAAA;RSEQ=AAAAAAAAAAGTTATGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:23:7,16:117,234:351,23:0.0612:2,2:30.8:1:29.2:1:1:1.14248:60:22:0.063:0.0053:0.1 0/1:289:24:8,16:106,159:265,24:0.083:2,2:28.4:1:28.9:1:0.6638:1.33204:59.8:48:0.0873:0.0104:0.2 +22 29685711 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.67492;LSEQ=AAATAGCATTTTTTAAAAAA;RSEQ=AGAATGAACTTCAAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:55:26,29:122,111:233,55:0.191:2,2:20.5:1:30.7:1:0.54979:1.22505:60:110:0.1916:0:1.1 1/0:185:136:67,69:22,27:49,136:0.7351:2,2:24.7:1:28.7:1:0.62086:1.19:60:135:0.7337:0:1.3 +22 29685752 . A G 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTTGATTTTTAACTTCCAT;RSEQ=TTAGCAAATACTCTTCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:158,121:279,0:0:2,0:26.7:1:29.8:1:1:0:60:278:1:0:0.2 0/1:198:32:18,14:91,75:166,32:0.1616:2,2:23.9:1:31.2:1:1:1.06:60:64:0.1641:0:1.6 +22 29685754 . T A 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=TTGATTTTTAACTTCCATAT;RSEQ=AGCAAATACTCTTCACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:161,122:283,0:0:2,0:26.4:1:30.1:1:1:0:60:282:1:0:0.2 0/1:199:9:4,5:107,83:190,9:0.0452:2,2:18.8:1:30.1:1:0.51242:1.60752:60:18:0.0459:0:1.9 +22 29685775 . G T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26727;SOR=0;LSEQ=AGCAAATACTCTTCACTACT;RSEQ=AAAGACAGTACTATTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:175,119:294,3:0.0101:2,2:31.3:1:31.3:1:1:1.36:60:6:0.0102:0:1 0/0:216:0:0,0:122,94:216,0:0:2,0:24.4:1:31:1:1:0:60:107:1:0:0.5 +22 29686200 . C T 47 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3894;SOR=0.31255;LSEQ=CAGACTGTGAAGCAGTCTGT;RSEQ=GGATCCTGTGGGGATAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:4:1,3:223,149:372,4:0.0106:2,2:12:1:23.8:1:0.3075:4.47255:60:3:0.0082:0:1 0/0:299:1:0,1:185,113:298,1:0.0033:2,0:1:0:24:0:0.38127:0:60:2:0.0033:0:1 +22 29686918 . T C 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.62802;LSEQ=AGTCATTATTCTAACTGATA;RSEQ=GTCTATAAAGTTGCACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:957:2:1,1:517,438:955,2:0.0021:2,2:8.5:1:11.5:1:1:1.18016:60:0:0:0:1.5 0/1:842:30:17,13:450,362:812,30:0.0356:2,2:26:1:29.6:1:1:1.05:60:60:0.0359:0:1.1 +22 29687464 . C T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0618;SOR=Inf;LSEQ=GGAGATGTGTTTAGCCAGTG;RSEQ=CCTTCTTCCCCACGAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:228,219:447,0:0:2,0:26.9:1:31.9:1:1:0:60:62.857:1:0:0.1 0/1:447:5:2,3:233,209:442,5:0.0112:2,2:13.8:1:21.4:1:0.67155:1.67032:60:1.5:0.0069:0:1.4 +22 29687621 . T TA 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.88694;LSEQ=GTATTACCATAGATAGTGTT;RSEQ=AAAAAAAAATGCAGTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:7:5,2:116,136:252,7:0.027:2,2:18:1:29.8:1:0.25705:2.92:60:14:0.0275:0.0077:0.1 0/1:208:5:3,2:93,110:203,5:0.024:2,2:25:1:27.9:1:0.66376:1.77:60:10:0.0242:0.0096:0.2 +22 29688184 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15156;SOR=Inf;LSEQ=TTTGAATTCTAGTTGTGCTT;RSEQ=ATATCGTGCTTTGTAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:153,127:280,0:0:2,0:24.8:1:32.5:1:1:0:59.9:92.333:1:0:0.1 0/1:179:2:1,1:92,85:177,2:0.0112:2,2:11:1:29.5:1:1:1.08186:60:4:0.0113:0:1 +22 29688632 . T G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.22152;SOR=1.17596;LSEQ=CCAGGTCATCTGGCAGAACT;RSEQ=TAAACCACAGAGCATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:780:146:86,60:344,289:633,146:0.1872:2,2:26.2:1:32.5:1:0.35608:1.20:60:292:0.1884:0:1.1 0/1:732:156:90,66:319,257:576,156:0.2131:2,2:24.3:1:31.2:1:0.64981:1.10:60:312:0.2152:0:1.1 +22 29688849 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04132;SOR=Inf;LSEQ=ACTGCAACCTCTGTTCAAGC;RSEQ=AATCTCCTGCCTCAGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:11,59:70,0:0:2,0:28.1:1:30.6:1:1:0:58.7:16.5:1:0:0.1 0/1:38:3:0,3:1,34:35,3:0.0789:1,0:15.7:1:29.7:1:1:0:57.7:6:0.0789:0:1 +22 29688980 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2204;SOR=Inf;LSEQ=AACTCCTGACCTCAGGTGAT;RSEQ=TGCCCACCTTGGCGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:106,20:126,0:0:2,0:26:1:32.3:1:1:0:59.2:41:1:0:0.1 0/1:112:2:1,1:81,29:110,2:0.0179:2,2:18.5:1:26.5:1:0.46573:2.76306:60:4:0.0179:0:1 +22 29688993 . C T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50023;SOR=0;LSEQ=AGGTGATCTGCCCACCTTGG;RSEQ=GCCTCCCAAAGTGCTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:114,51:165,2:0.012:2,2:13:0:29:1:0.52709:2.22342:60:4:0.012:0:1 0/0:148:0:0,0:94,54:148,0:0:2,0:24.1:1:29.9:1:1:0:59.3:48.333:1:0:0.2 +22 29689130 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52796;SOR=0;LSEQ=CCACAGCCTCTTGAGGTAGC;RSEQ=GGACTTATAGGCACATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:60,108:168,2:0.0117:2,2:20:1:31:1:1:1.79:60:4:0.0118:0:1 0/0:104:0:0,0:29,75:104,0:0:2,0:22.7:1:30.1:1:1:0:60:208:1:0:0.1 +22 29689145 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.54714;SOR=0;LSEQ=GTAGCTGGACTTATAGGCAC;RSEQ=TGCCACCACACCCAACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:57,94:151,2:0.0131:2,2:27.5:1:29.5:1:1:1.64:60:4:0.0131:0:1 0/0:80:0:0,0:22,58:80,0:0:2,0:23.9:1:30.1:1:1:0:60:79:1:0:0 +22 29689509 . CT C 161 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=14.24605;LSEQ=TTTTTATGATACTGAGTGAT;RSEQ=TTTTTTCCCCATGAAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:829:3:2,1:372,451:823,3:0.0036:2,2:40.3:1:33.3:1:0.59267:2.42:60:6:0.0036:0:0 0/1:751:37:19,18:330,382:712,37:0.0493:2,2:28.5:1:31:1:0.61359:1.22:59.7:74:0.0495:0.0053:0.1 +22 29689613 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52746;SOR=0;LSEQ=CACCAGGCTGGAGTGCAGTG;RSEQ=CACGATCTCGGCTCACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:0,2:0,136:136,2:0.0145:1,0:28:0:32:0:1:0:50.5:4:0.0148:0:2.5 0/0:84:0:0,0:3,81:84,0:0:1,0:24.2:1:31.7:1:1:0:56.6:168:1:0:0.1 +22 29689837 . A G 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTTTTGTGATTGCAGAC;RSEQ=TGAGCCACTGTGCCTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:0,6:1:0,2:26.8:1:30.2:1:1:0:57.2:12:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 29689868 . G A 82 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTGGCCTGTCTCTATTT;RSEQ=TTATTTTATTTTACTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:5,2:0,0:0,7:1:0,2:15.9:1:29.4:1:1:0:58.4:14:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 29690246 . G A 209 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGTTTATTTTCAAGTTGCT;RSEQ=TGGTTAAGGGTCTTCGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1728:0:0,0:926,799:1725,0:0:2,0:25.2:1:32.4:1:1:0:60:155.818:0.9983:0:0.1 0/1:1645:168:87,81:767,710:1477,168:0.1021:2,2:26.5:1:28.4:1:1:1.00578:60:55:0.1009:0:1.1 +22 29690345 . T C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=14.80529;LSEQ=GTAGCTCACGCCTGTAATCC;RSEQ=AGCACTTTGGGAGGCCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:89:36,53:167,328:495,89:0.1519:2,2:22.4:1:32:1:0.22841:1.33:48:43.5:0.1521:0:1.1 1/0:527:383:175,208:56,86:142,383:0.7268:2,2:20.6:1:30.5:1:0.23494:1.29:49.5:75.6:0.7255:0:1.1 +22 29690370 . T A 51 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03789;SOR=Inf;LSEQ=CTTTGGGAGGCCGAGGCGGG;RSEQ=GGATCACGAGGTCAGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:45,214:259,0:0:2,0:15.6:1:30.7:1:1:0:42.3:258:1:0:0.3 0/1:206:4:3,1:51,150:201,4:0.0194:2,2:5.8:1:25.8:1:0.05684:8.71:38:8:0.0198:0:2 +22 29690593 . C CA 33 v3;MSI12;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGAGTGAGACTCCGCCT;RSEQ=AAAAAAAAAAAAAAAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,4:4,2:0.2857:0,0:25:1:33:0:1:0:55.5:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 29690886 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24844;SOR=Inf;LSEQ=CACTCCAGCCTGGCGACAGA;RSEQ=CAAGACTCCATCTCAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:125,60:185,0:0:2,0:20.3:1:31.2:1:1:0:53.9:13.231:1:0:0.3 0/1:194:3:1,2:135,56:191,3:0.0155:2,2:9.7:1:29:1:0.21338:4.77699:60:6:0.0164:0:1 +22 29690900 . C CA 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.97797;LSEQ=GACAGAGCAAGACTCCATCT;RSEQ=AAAAAAAAAAAGGAAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:28:18,10:137,81:218,28:0.1129:2,2:28:1:30.6:1:1:1.06:53.3:56:0.1181:0:0.4 0/1:262:29:20,9:143,84:227,29:0.1107:2,2:30.2:1:29.4:1:0.68235:1.30:51.4:58:0.1142:0:0.3 +22 29690905 . A C 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.12496;SOR=Inf;LSEQ=AGCAAGACTCCATCTCAAAA;RSEQ=AAAAAAGGAAATACAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:180,105:285,0:0:2,0:21.8:1:30.4:1:1:0:56.4:141.5:0.9965:0:0.3 0/1:310:4:2,2:184,122:306,4:0.0129:2,2:29:1:32.8:1:1:1.5061:54:8:0.0133:0:2.3 +22 29691109 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21857;SOR=Inf;LSEQ=CTGTTGCCCAGACTGGAGTG;RSEQ=AGTGGCACAATTTCAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:76,132:208,0:0:2,0:23.3:1:32.2:1:1:0:52.2:103:1:0:0.1 0/1:184:2:1,1:64,118:182,2:0.0109:2,2:23.5:1:26.5:1:1:1.84:59:4:0.0111:0:1 +22 29691382 . A T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=22.47157;LSEQ=CTTTGGGAGGCCAAGGCAGG;RSEQ=GGATCCCAAGGATTGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:31:9,22:81,118:199,31:0.1348:2,2:23.9:1:29.9:1:0.24096:1.67437:57.9:14.5:0.1283:0:1.1 1/0:159:124:44,80:10,25:35,124:0.7799:2,2:22.6:1:29.1:1:0.54586:1.37:58.1:123:0.7785:0:1.1 +22 29691450 . C T 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.15965;LSEQ=AACAGAGTGAGACTCTGTCT;RSEQ=ACAAAAAAGAAAAAAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:141,120:261,3:0.0114:2,2:15.3:1:22:1:0.59716:2.3426:60:2:0.0078:0:1 0/1:228:3:0,3:128,97:225,3:0.0132:2,0:1:0:21.7:1:0.08295:0:60:6:0.0132:0:1 +22 29691521 . AG A 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4231;SOR=1.71509;LSEQ=ATATTTTCTTTTCAGTTTTT;RSEQ=GGTATCACGTTCCTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:502:493:257,236:6,3:9,493:0.9821:2,2:28.4:1:32.5:1:0.50842:1.83443:60:163.333:0.982:0.1155:0.1 1/1:475:470:244,226:2,3:5,470:0.9895:2,2:27.5:1:30.8:1:0.67569:1.62:60:155.667:0.9873:0.1053:0.2 +22 29691556 . C A 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17091;SOR=5.34775;LSEQ=TTTTTTTAAGTCAGAGGTAT;RSEQ=AATATATATATCCTGTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:1:1,0:222,216:438,1:0.0023:2,0:1:0:14:0:1:0:60:0:0:0:1 0/1:331:4:3,1:159,167:326,4:0.0121:2,2:20:1:25.8:1:0.3638:3.14:60:8:0.0122:0:1 +22 29691695 . ATACAAGGTAGCTCC A 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=GTACACGTGAAGATATTCTT;RSEQ=TGAATTCAAGTCAACCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:278,242:520,0:0:2,0:25.2:1:29.9:1:1:0:59.9:103:0.9981:0:0.1 0/1:386:9:5,4:203,174:377,9:0.0233:2,2:26:1:30:1:1:1.07:60:18:0.0233:0.0026:0.1 +22 29691910 . C T 183 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAAAGTCTGACTACCCCTA;RSEQ=GAGGTGGCTGTGCTCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:60:36,24:193,160:353,60:0.1449:2,2:30:1:31.1:1:0.48422:1.24:60:120:0.146:0:1.1 0/0:366:0:0,0:194,170:364,0:0:2,0:24:1:30.1:1:1:0:59.9:71.8:0.9945:0:0.2 +22 29691920 . G A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTACCCCTACGAGGTGGCT;RSEQ=TGCTCAGTGGATACCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:240,171:411,0:0:2,0:25.4:1:32.2:1:1:0:60:44.667:1:0:0.3 0/1:368:36:23,13:174,157:331,36:0.0978:2,2:16.4:1:28.3:1:0.22086:1.59:59.9:72:0.0989:0:1.2 +22 29691922 . G A 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19287;SOR=4.53905;LSEQ=TACCCCTACGAGGTGGCTGT;RSEQ=CTCAGTGGATACCTGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:1:1,0:241,165:406,1:0.0025:2,0:1:0:24:0:1:0:60:2:0.0025:0:1 0/1:362:4:2,2:193,164:357,4:0.011:2,2:37:1:29.8:1:1:1.17629:60:8:0.0112:0:1.3 +22 29691936 . T A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04602;SOR=Inf;LSEQ=GGCTGTGCTCAGTGGATACC;RSEQ=GTCTGGGCATAGAAAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:250,169:419,0:0:2,0:24.2:1:30.9:1:1:0:60:33.917:1:0:0.3 0/1:363:4:3,1:196,163:359,4:0.011:2,2:15.8:1:29.8:1:0.62994:2.49:57.5:8:0.0111:0:1.3 +22 29692275 . A G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0416;SOR=Inf;LSEQ=GATCCACATCTACCTGGACA;RSEQ=GGAAACAGGAAAGCCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:234,227:461,0:0:2,0:26:1:31.2:1:1:0:59.9:91.2:0.9978:0:0.1 0/1:382:4:2,2:199,179:378,4:0.0105:2,2:35:1:30.3:1:1:1.11142:60:8:0.0107:0:1.3 +22 29692331 . G A 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09643;SOR=6.12565;LSEQ=CCTATGAAGACCCACCCACT;RSEQ=CCAAGGCTGCCGTGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:1:1,0:245,268:513,1:0.0019:2,0:1:0:23:0:0.4786:0:60:2:0.002:0:1 0/1:423:5:4,1:200,218:418,5:0.0118:2,2:13.2:1:25.8:1:0.20102:4.35:60:10:0.012:0:1 +22 29692488 . G T 259 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTAGATGGCCGGTCTCCCT;RSEQ=CAGTAGTAGTAGCACCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:360:360:198,162:0,0:0,360:1:0,2:26.7:1:30.5:1:1:0:59.9:39:1:0:2 1/0:273:182:94,88:44,47:91,182:0.6667:2,2:26.7:1:28.3:1:0.61059:1.14:59.8:25:0.6654:0:2.1 +22 29692497 . G T 262 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CCGGTCTCCCTGCAGTAGTA;RSEQ=TAGCACCCAGCCATTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:371:371:208,163:0,0:0,371:1:0,2:26.6:1:30.7:1:1:0:59.9:52:1:0:2 1/0:278:184:96,88:44,50:94,184:0.6619:2,2:27:1:29.4:1:0.4473:1.24:59.8:60.333:0.6606:0:2.1 +22 29692867 . CA C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.55321;SOR=0;LSEQ=ATGGCAAAACCCTGTCTCTA;RSEQ=AAAAAAATACAAAAATTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:3:1,2:47,72:119,3:0.0246:2,2:24.7:1:32.7:1:1:1.30279:58:6:0.025:0:0 0/0:55:0:0,0:11,44:55,0:0:2,0:24.8:1:30.7:1:1:0:58.3:54:1:0:0.1 +22 29693540 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04279;SOR=Inf;LSEQ=AACAATTTTGTAAAATTAGT;RSEQ=GGGCATGGTGATGCGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:37,2:39,0:0:2,0:24.7:1:32.7:1:1:0:59.2:78:1:0:0.1 0/1:22:3:3,0:19,0:19,3:0.1364:1,0:19.7:1:31.7:1:1:0:59.3:6:0.1364:0:1 +22 29693640 . G A 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGCCACTGCACTCCAGCCC;RSEQ=GGCAACAGAGTGAGACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:166,25:191,0:0:2,0:21.6:1:29.8:1:1:0:59.7:46.75:1:0:0.1 0/1:152:17:13,4:108,26:134,17:0.1118:2,2:24:1:28.6:1:0.74747:1.27591:60:16:0.1096:0:1.2 +22 29693885 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06791;SOR=Inf;LSEQ=AGCCTCCAATGAACAGTATG;RSEQ=GGGGTGGTCTGCCACCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:119,147:266,0:0:2,0:24.2:1:31.2:1:1:0:59.9:87.667:0.9962:0:0.1 0/1:185:3:1,2:77,105:182,3:0.0162:2,2:18.7:1:28.3:1:1:1.46375:60:6:0.0165:0:1 +22 29693900 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.03187;SOR=Inf;LSEQ=GTATGCGGGGTGGTCTGCCA;RSEQ=CCCGTGAGGGCAGAGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:124,135:259,0:0:2,0:24.5:1:31.6:1:1:0:59.9:50.8:1:0:0.1 0/1:191:4:3,1:87,100:187,4:0.0209:2,2:14.3:1:28.5:1:0.3444:3.43:60:8:0.0211:0:1 +22 29693990 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09383;SOR=1.43744;LSEQ=AAAGGTTTTCAGTACACTTC;RSEQ=TACCCTTGAGAAACTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:53:29,24:183,109:292,53:0.1536:2,2:24:1:30.4:1:0.28608:1.38804:60:25.5:0.15:0:1.2 0/1:285:59:36,23:145,81:226,59:0.207:2,2:22.7:1:30:1:0.65203:1.14314:60:118:0.2085:0:1 +22 29694312 . G A 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00075;SOR=13.27352;LSEQ=TTAAGACCAGCCTGGCCAAC;RSEQ=TGGTGAAACTCCCTCTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:0,4:4,25:29,4:0.1212:2,0:34.5:1:27.5:1:1:0:22.8:3:0.0938:0:1.3 1/0:12:8:1,7:1,3:4,8:0.6667:2,2:36.5:1:31.1:1:1:2.16028:24.3:16:0.6667:0:1 +22 29694479 . A G 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55608;SOR=0;LSEQ=TGCACTCCAGCCTGGGCAAC;RSEQ=GTGTGAGACTCCGTCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:3:1,2:92,7:99,3:0.0294:2,2:14.7:1:22.7:1:0.01999:24.20617:55.7:2:0.0206:0:1.7 0/0:42:0:0,0:35,7:42,0:0:2,0:22.7:1:28.6:1:1:0:45.8:41:1:0:2.3 +22 29694483 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=14.57135;LSEQ=CTCCAGCCTGGGCAACAGTG;RSEQ=GAGACTCCGTCTCCAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:11:9,2:94,8:102,11:0.0973:2,2:17:1:30:1:0.25114:2.58124:48.5:10:0.0935:0:1.5 1/0:47:29:23,6:14,4:18,29:0.617:2,2:20.9:1:27.8:1:1:1.09:46.9:6.25:0.641:0:2.4 +22 29694517 . T G 26 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.83281;LSEQ=CAAAAAAAAAAAAAAAAAAT;RSEQ=GTGGGAGCTCTGTTTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:3,0:188,52:240,3:0.0123:2,0:28:1:16.7:1:1:0:35.7:0:0:0:4.3 0/1:195:2:1,1:139,54:193,2:0.0103:2,2:12.5:1:27:1:0.48559:2.55973:52.5:4:0.0108:0:3.5 +22 29694558 . T C 49 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07387;SOR=0.38125;LSEQ=GAGCACGTGGAACACGCTCC;RSEQ=CACAGGGAAGGGGGCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:545:16:16,0:334,195:529,16:0.0294:2,1:18.8:1:12.3:1:0.00095:0:50.8:0:0:0:4.4 0/1:439:5:5,0:273,158:431,5:0.0114:2,0:20.6:1:20.8:1:0.16416:0:44.2:1.5:0.0074:0:5.4 +22 29999236 . G C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTCTAAGTGGTTTCCC;RSEQ=GGTAAGGTCAGCAGAGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:31.5:1:1:0:60:4:1:0:1 +22 29999784 . C A 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCCCTGCAGCCGTCAGGG;RSEQ=CCGTCCCCCAACTCCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:28.5:1:30.7:1:1:0:60:12:0.75:0:1.2 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:29.5:1:1:0:60:4:1:0:1 +22 29999878 . G C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.79262;SOR=0.79763;LSEQ=CCAGACCGTTCCCGGGCCGG;RSEQ=CAGCCGGCCACCATGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:44:42,2:14,0:14,44:0.7586:1,1:23.1:1:32.6:1:1:0:60:43:0.7544:0:1.1 1/0:28:20:20,0:8,0:8,20:0.7143:0,1:24.4:1:32.9:1:1:0:60:40:0.7143:0:1.1 +22 29999965 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09921;SOR=Inf;LSEQ=GCAGGCCGTGGGGCGCGAGG;RSEQ=TCCCGGGCCTGAGCCCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:273,53:326,0:0:2,0:23.7:1:31.3:1:1:0:60:64.2:1:0:0.1 0/1:282:3:1,2:231,48:279,3:0.0106:2,2:21.7:1:27:1:0.08215:9.50774:60:6:0.0107:0:1.3 +22 30000039 . C T 89 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09116;SOR=0.29787;LSEQ=TCAGCTCTCTCAAGAGGAAG;RSEQ=AACCCAAGACGTTCACCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:927:10:2,8:518,399:917,10:0.0108:2,2:14.9:1:26.8:1:0.0256:5.18519:60:20:0.011:0:1 0/0:927:3:0,3:517,407:924,3:0.0032:2,0:1:0:23.3:1:0.08617:0:60:6:0.0033:0:1 +22 30032654 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50912;SOR=0;LSEQ=TAGTGTCATCCCCACGTTTT;RSEQ=GAACCTGAGAGTGGAGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:151,19:170,2:0.0116:2,2:18.5:1:28.5:1:0.21964:7.77158:60:4:0.0118:0:1 0/0:128:0:0,0:108,20:128,0:0:2,0:22.9:1:31.3:1:1:0:60:127:1:0:0.1 +22 30032665 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=CCACGTTTTGGAACCTGAGA;RSEQ=TGGAGAGTGCAGAGAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:182,27:209,0:0:2,0:25.1:1:33:1:1:0:60:103.5:1:0:0.1 0/1:154:2:1,1:120,32:152,2:0.013:2,2:13:1:29.5:1:0.38375:3.70832:60:4:0.0133:0:1 +22 30032931 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18193;SOR=Inf;LSEQ=CCAGTTTTTCCCTGAGCAGG;RSEQ=GCCTAGCTCATCACTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:18,182:200,0:0:2,0:23.6:1:30:1:1:0:60:39:0.9949:0:0.1 0/1:150:2:1,1:25,123:148,2:0.0133:2,2:23:1:28:1:0.31758:4.84:60:4:0.0137:0:1 +22 30033036 . T A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.28327;SOR=4.19245;LSEQ=AGAGATGCTACCAGTTTCCT;RSEQ=CTCCTCACAGGCTCTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:0,5:0,15:15,5:0.25:1,0:20.6:1:30.6:1:1:0:60:10:0.25:0:1 1/0:5:3:0,3:0,2:2,3:0.6:0,0:28:1:30.7:1:1:0:60:6:0.6:0:1 +22 30034994 . G T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22302;LSEQ=TAGTGGGAAAAAAATTTAAT;RSEQ=CACGCCTTGCAAAGGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:187:117:106,11:64,5:69,117:0.6257:2,2:21.5:1:31:1:0.78826:1.32634:60:57.5:0.625:0:1 0/1:122:33:29,4:79,9:88,33:0.2705:2,2:16.7:1:29.8:1:0.74904:1.20871:60:66:0.275:0:1.1 +22 30035021 . G A 108 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=22.75419;LSEQ=TTGCAAAGGCTTCTTTGAGG;RSEQ=TAGCACAGGAGGAAGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:1:1,0:269,64:333,1:0.003:2,0:23:0:27:0:1:0:60:2:0.003:0:1 0/1:218:14:12,2:154,50:204,14:0.0642:2,2:27.2:1:28.5:1:0.52689:1.94:60:13:0.061:0:1.3 +22 30038041 . T TA 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.76926;LSEQ=TCTCCACCTGTCTGCATCAG;RSEQ=AAAAAAAAAATTGTACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:9:9,0:133,0:133,9:0.0621:1,0:22.4:1:28:1:1:0:60:18:0.0634:0.0138:0 0/1:62:3:3,0:59,0:59,3:0.0484:1,0:34.3:1:27.7:1:1:0:60:6:0.0484:0:0 +22 30038052 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09305;SOR=Inf;LSEQ=CTGCATCAGTAAAAAAAAAA;RSEQ=TGTACCCTTTGTCAGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:171,1:172,0:0:1,0:23.7:1:31.4:1:1:0:60:171:1:0:0.1 0/1:76:2:2,0:74,0:74,2:0.0263:1,0:23:1:27.5:1:1:0:60:4:0.0263:0:1 +22 30038152 . A C 228 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCCTACACACCTCACTTCC;RSEQ=CTCACAGAGTATCATGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:734:0:0,0:449,283:732,0:0:2,0:26.4:1:29.8:1:1:0:60:80.333:0.9986:0:0.1 0/1:559:178:106,72:226,153:379,178:0.3184:2,2:27.8:1:30.5:1:1:1.00332:60:356:0.3196:0:1.1 +22 30038463 . ATG A 72 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.64631;SOR=0.42865;LSEQ=TTGTATAATCTTGTGTGTGT;RSEQ=TGTGTGTGTGTGTATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:2,19:21,5:0.1923:2,0:31.6:1:31.4:1:1:0:60:10:0.1923:0:0 0/1:11:1:0,1:0,10:10,1:0.0909:0,0:49:0:29:0:1:0:60:2:0.0909:0:0 +22 30051433 . C T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32547;SOR=1.75092;LSEQ=AGAATGGTGCCTTATTTACA;RSEQ=GCCCTCTCTCTGTGTGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:10:10,0:56,0:56,10:0.1515:1,0:25:1:32:1:1:0:60:20:0.1538:0:1 0/1:46:11:11,0:35,0:35,11:0.2391:1,0:26.4:1:29.8:1:1:0:60:10:0.2222:0:1 +22 30053939 . C A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54941;SOR=0;LSEQ=GAAACTAAGGCCAAGAAACT;RSEQ=CGTGATGAGTCTGTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:5,0:15,1:16,5:0.2381:1,0:14:1:28.4:1:1:0:60:10:0.2381:0:1.6 0/0:4:0:0,0:4,0:4,0:0:0,0:24.8:1:31:1:1:0:60:8:1:0:0 +22 30054024 . G A 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0068;SOR=3.88269;LSEQ=GTTTAATAGACTCAGGGCCG;RSEQ=GCAGAGCTTTGCTGGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:10:10,0:49,1:50,10:0.1667:1,0:21:1:30.4:1:1:0:60:20:0.1667:0:1.3 0/1:34:15:15,0:19,0:19,15:0.4412:1,1:32.9:1:28.6:1:1:0:60:14:0.4242:0:1.3 +22 30056718 . AT A 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGTGCCACCATGCCCGGCTA;RSEQ=TTTTTTGTGTGTATTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:21.5:1:30:1:1:0:20.5:4:0.6667:0:0.5 1/1:1:1:1,0:0,0:0,1:1:0,0:46:0:30:0:1:0:33:2:1:0:0 +22 30056945 . G A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTCTTCCTTTAGCCATC;RSEQ=AGCCAGTGACAGAAGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:3,0:18,0:18,3:0.1429:1,0:37.7:1:31.3:1:1:0:60:6:0.1429:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:20:0:24:0:1:0:60:2:1:0:0 +22 30057124 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16315;SOR=Inf;LSEQ=GTGACAGTGTGTGCCAGATT;RSEQ=TTTGGAAGGTTGAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:195,33:228,0:0:2,0:23.6:1:32.1:1:1:0:59.9:56:1:0:0.1 0/1:155:2:1,1:130,23:153,2:0.0129:2,2:24.5:1:27.5:1:0.28655:5.55448:60:4:0.0132:0:1 +22 30057574 . A G 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCCAAAGAATAGTGAAC;RSEQ=AAAACAGTAACATTTTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:13,3:0.1875:1,0:38:1:29.7:1:1:0:60:6:0.2:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 30061225 . GT G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.03746;SOR=3.36901;LSEQ=CTAAATTATATCATGAAGAA;RSEQ=TTTTTTTTTTGTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:11:0,11:1,41:42,11:0.2075:1,0:24.4:1:32.8:1:1:0:53.5:22:0.2075:0:0.1 0/1:19:9:0,9:0,8:8,9:0.4737:0,0:30:1:33.1:1:1:0:60:18:0.4737:0:0 +22 30061237 . GT G 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.56794;SOR=0;LSEQ=ATGAAGAAGTTTTTTTTTTT;RSEQ=TTTTTTTTTGAGACAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:0,3:0,40:40,3:0.0698:1,0:12:1:31.6:1:1:0:53:6:0.0714:0.0233:0 0/0:14:0:0,0:0,14:14,0:0:1,0:17.9:1:30.8:1:1:0:60:28:1:0:0.1 +22 30064073 . A AGT 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0.58042;SOR=2.18727;LSEQ=GCACCCAGAAGACATGGTGA;RSEQ=GTGTCCTCCAGTCCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:38.3:1:32.2:1:1:0:39.3:6:0.3:0:0.7 1/0:4:2:2,0:2,0:2,2:0.5:0,0:11.5:1:31.4:1:1:0:60:4:0.5:0.25:1 +22 30064117 . C T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46506;SOR=1.9087;LSEQ=TTATGATTTTTACCTCCTGG;RSEQ=ATATCTGAGGCGCCTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:12,1:13,5:0.2778:1,0:14.2:1:30.8:1:1:0:55.2:10:0.2778:0:1 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:26.5:1:30.5:1:1:0:60:12:0.4286:0:1 +22 30064232 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51491;SOR=0;LSEQ=CACGTTTACTGCTACCTGCA;RSEQ=GAGCTCAAACTGCTATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:174,13:187,2:0.0106:2,2:26:1:30.5:1:0.14303:12.9348:60:4:0.0108:0:1 0/0:131:0:0,0:116,15:131,0:0:2,0:22:1:29.3:1:1:0:60:130:1:0:0.1 +22 30064512 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17306;SOR=Inf;LSEQ=GAGGCGAGGAGTGGTCATGG;RSEQ=CTGGCAGGAGTCTTTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:19,167:186,0:0:2,0:22.6:1:32.3:1:1:0:59.8:36.2:1:0:0.1 0/1:133:2:1,1:19,112:131,2:0.015:2,2:17:1:26.5:1:0.27911:5.77:60:4:0.0155:0:1 +22 30064731 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAAGAGTGCATGCATCT;RSEQ=TCCGTCCGGCTAGCTAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:23:1:33:1:1:0:60:4:0.2222:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:26:0:1:0:60:2:1:0:0 +22 30068066 . A T 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTAATTTCAGCTTTGAAAA;RSEQ=ATCAGTGCCTTTTCTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:0,104:104,0:0:1,0:22:1:31.3:1:1:0:60:51:1:0:0.1 0/1:53:18:0,18:0,35:35,18:0.3396:1,1:28.1:1:27.2:1:1:0:60:17:0.3269:0:1.1 +22 30069207 . C T 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00787;SOR=0.51227;LSEQ=GTGTTCAAGGCAGATCTGGG;RSEQ=GGGAGAACAGCACATGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:58:44,14:140,37:177,58:0.2458:2,2:25.3:1:29.4:1:0.58725:1.20292:59.7:57:0.2489:0:1.1 0/1:196:28:21,7:113,54:167,28:0.1429:2,2:19:1:29:1:0.51414:1.43:60:56:0.1458:0:1.2 +22 30070223 . T A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAGGCCCCTTACTGTAT;RSEQ=CGGGGGTCACTCCCTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:33:1:28.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 30070699 . CT C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54429;SOR=0;LSEQ=AATATCCCTGTCTCACTGTC;RSEQ=TTTTCACCTCTTTGGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:2,0:109,2:111,2:0.0177:1,0:22.5:1:34:0:1:0:60:4:0.018:0:0 0/0:60:0:0,0:59,1:60,0:0:1,0:21.5:1:31:1:1:0:60:120:1:0:0.2 +22 30070755 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20889;SOR=Inf;LSEQ=CCCAGGTCCCTCCTCTGCAG;RSEQ=GGTGGGGTGGTGTCTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:203,34:237,0:0:2,0:25.3:1:31.4:1:1:0:59.8:78:1:0:0.1 0/1:200:2:2,0:164,34:198,2:0.01:2,0:17.5:1:30.5:1:1:0:60:4:0.0102:0:1 +22 30070763 . T G 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25471;SOR=0;LSEQ=CCTCCTCTGCAGGGGTGGGG;RSEQ=GGTGTCTTTTCCTGCTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:3,0:233,47:280,3:0.0106:2,0:18.7:1:23:1:1:0:60:2:0.0072:0:3 0/0:236:0:0,0:190,46:236,0:0:2,0:23.6:1:28.4:1:1:0:60:20.455:1:0:0.1 +22 30070770 . T C 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10192;SOR=Inf;LSEQ=TGCAGGGGTGGGGTGGTGTC;RSEQ=TTTCCTGCTACCTGCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:254,69:323,0:0:2,0:23.4:1:31.8:1:1:0:60:646:0.9969:0:0.1 0/1:285:3:1,2:215,67:282,3:0.0105:2,2:14.3:1:24.7:1:0.14646:6.365:60:2:0.0071:0:1 +22 30071358 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTACTGCCGTGCAAGAA;RSEQ=GAGCAGCCACTCTCAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:42:1:33:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 30073959 . T TTGAGGGA 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05378;SOR=5.0336;LSEQ=CATGAAGAACGGTTAGAGAT;RSEQ=TGAGGGATGATTTTCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:5,0:33,0:33,5:0.1316:1,0:24.6:1:32.7:1:1:0:60:10:0.1316:0.0263:0.2 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:20.8:1:31.3:1:1:0:60:8:0.5:0.1111:0.3 +22 30077361 . G A 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41872;SOR=0;LSEQ=CACCAAGCAGCTTGTGGGCC;RSEQ=CAGAGCACCTGAGCCGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:118:118:108,10:0,0:0,118:1:0,2:26.1:1:30.2:1:1:0:60:28.5:1:0:1.1 1/1:85:84:73,11:0,0:0,84:0.9882:0,2:21.8:1:29.4:1:1:0:60:83:0.9881:0:1.1 +22 30077658 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17723;SOR=Inf;LSEQ=ATGAAATGTGCGGTTGGCAT;RSEQ=TGGTTTCCTCAGTAGCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:28,190:218,0:0:2,0:24.8:1:33.4:1:1:0:60:71.667:1:0:0.1 0/1:159:2:1,1:24,133:157,2:0.0126:2,2:25.5:1:30.5:1:0.29058:5.45:60:4:0.0128:0:1 +22 30077659 . T A 35 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26719;SOR=0;LSEQ=TGAAATGTGCGGTTGGCATC;RSEQ=GGTTTCCTCAGTAGCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:3:2,1:26,185:211,3:0.014:2,2:6.7:1:22.7:1:0.04569:13.91:60:2:0.0095:0:1.3 0/0:155:0:0,0:23,132:155,0:0:2,0:23.3:1:29.9:1:1:0:60:310:1:0:0.1 +22 30078935 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33411;SOR=3.6305;LSEQ=AGGCCTATCCAAGCATTTTG;RSEQ=AGATGGCACTTATGGCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:1,0:239,17:256,1:0.0039:2,0:47:0:32:0:1:0:60:2:0.004:0:1 0/1:214:3:2,1:193,17:210,3:0.014:2,2:23.7:1:28:1:0.23371:5.58848:60:6:0.0142:0:1 +22 30078942 . C T 42 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77201;LSEQ=TCCAAGCATTTTGCAGATGG;RSEQ=ACTTATGGCATTGTTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:1,2:266,28:294,3:0.0101:2,2:16.7:1:26.7:1:0.02781:18.58834:60:6:0.0104:0:1 0/0:256:2:1,1:221,32:253,2:0.0078:2,2:13:1:27.5:1:0.24252:6.81543:60:4:0.0079:0:1 +22 30078965 . C T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12147;SOR=5.10527;LSEQ=TTATGGCATTGTTGATATCA;RSEQ=AGGGTATGTTTTTGTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:1:0,1:388,111:499,1:0.002:2,0:1:0:24:0:0.224:0:60:2:0.002:0:1 0/1:494:5:2,3:360,129:489,5:0.0101:2,2:9:1:26.6:1:0.1214:4.17137:60:10:0.0102:0:1.2 +22 30079164 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28337;SOR=0;LSEQ=GCCACACTGAGCCCTTACGA;RSEQ=GGCAGGTGGTGCCTGGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:0,3:11,261:272,3:0.0109:1,0:27.7:1:24:1:1:0:60:2:0.0074:0:1 0/0:178:0:0,0:21,157:178,0:0:2,0:22.1:1:30.6:1:1:0:60:58.333:1:0:0.2 +22 30079213 . T C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00029;SOR=3.83073;LSEQ=GCATGCTTTGAGTCTAAAAG;RSEQ=AGGCACCCACCCTGTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:19:0,19:1,103:104,19:0.1545:1,1:30.5:1:32.3:1:1:0:57.9:38:0.1583:0:1.1 0/1:58:24:0,24:0,34:34,24:0.4138:1,1:23:1:31.4:1:1:0:60:48:0.4138:0:1 +22 30090900 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13352;SOR=Inf;LSEQ=AGCTGGCTGGGGGTTTCCGT;RSEQ=GGAGCTCCAGAACTTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:15,229:244,0:0:2,0:24.9:1:31.5:1:1:0:60:80.333:1:0:0.1 0/1:141:2:1,1:8,131:139,2:0.0142:2,2:14.5:1:26.5:1:0.12401:15.49:60:4:0.0145:0:1 +22 30091145 . T C 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCCAGCCTGGGAAGTCA;RSEQ=TGTAGGGAGTGAGACACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:2,2:4,2:0.3333:2,0:38.5:1:33.5:1:0.46667:0:52.5:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 30936374 . T C 32 d5;v3;p8;pSTD;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=23.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTTTTTTTTTTTTTTT;RSEQ=TTTGAGTATTGTATTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:32:1:1:0:60:4:1:0:1 +22 30937190 . T TTTG 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=11.02856;LSEQ=ACACAACTTTTAAAAAAATT;RSEQ=TTATTTATTTTTTAATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:39:35,4:75,8:83,39:0.3197:2,2:24.3:1:31:1:1:1.07082:60:78:0.3305:0.0738:0 1/1:100:84:71,13:12,3:15,84:0.84:2,2:23.3:1:30.2:1:0.70523:1.36:59.9:83:0.8469:0.21:0.1 +22 30937307 . A G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.76872;LSEQ=CATACTCCCCTCCCAGCTTT;RSEQ=TTAAGGTATGAATGGTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:131:53,78:137,178:315,131:0.2924:2,2:23.6:1:32:1:0.59965:1.1324:60:64.5:0.2919:0:1.2 1/0:384:234:102,132:71,79:150,234:0.6094:2,2:24.6:1:31:1:0.52837:1.1626:60:57.5:0.6085:0:1.2 +22 30937512 . G A 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04096;SOR=18.0326;LSEQ=AAAGATTAGCCAGGTATGGT;RSEQ=GCACACGCCTGTGATCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,9:9,1:0.1:0,0:11:0:34:0:1:0:43:2:0.1:0:1 1/0:4:3:0,3:0,1:1,3:0.75:0,0:21.3:1:32:0:1:0:47.7:6:0.75:0:1.3 +22 31327019 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49503;SOR=0;LSEQ=GCCTACAATCCATGATCAGT;RSEQ=TCCTGACGACCTCTGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:22,19:41,2:0.0465:2,2:20:0:31.5:1:1:1.15394:60:4:0.0476:0:1.5 0/0:39:0:0,0:25,14:39,0:0:2,0:25.8:1:31.1:1:1:0:60:78:1:0:0.1 +22 33131355 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGGGAAGTACTTGGCAC;RSEQ=TAGTAAATTCTCAATCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 33131486 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGCTGGAACATCATTCC;RSEQ=GTATTTGTTTGTTTGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:30:1:30:1:1:0:60:4:0.4:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:33:0:32:0:1:0:60:2:1:0:0 +22 33131697 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21531;SOR=0;LSEQ=GACTCCTGAAACACGGTCAG;RSEQ=AGCCCCTAGCAGCCAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:34,2:0.0556:2,2:25:1:28.5:1:1:1.26:60:4:0.0556:0:1.5 0/0:41:0:0,0:19,22:41,0:0:2,0:29.9:1:31.1:1:1:0:60:82:1:0:0.5 +22 33131729 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57718;SOR=1.49549;LSEQ=GCCAGAGAGGTCATTGGGTC;RSEQ=CCCAGCCCACAGGGAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:3,7:4,10:14,10:0.4167:2,2:17.3:1:29.3:1:1:1.07:60:9:0.3913:0:1 1/0:27:14:7,7:5,8:13,14:0.5185:2,2:23.2:1:30.2:1:0.70357:1.57:60:28:0.5185:0:1.1 +22 33828911 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19737;SOR=Inf;LSEQ=CAAGAGTGTTGTCTAGATAA;RSEQ=AACTGCTCCTCTGTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:147,30:177,0:0:2,0:23.2:1:32.2:1:1:0:59.8:176:1:0:0.2 0/1:142:2:1,1:108,32:140,2:0.0141:2,2:22.5:1:25.5:1:0.41205:3.33877:60:4:0.0143:0:1 +22 33828944 . T A 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCCCAGAGCTGGCGTTGA;RSEQ=GTTGGCCTCAGTCTCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:207,84:291,0:0:2,0:25.5:1:30.8:1:1:0:59.9:96:1:0:0.3 0/1:244:93:56,37:91,60:151,93:0.3811:2,2:25.5:1:29.8:1:1:1.00207:60:186:0.3859:0:1.8 +22 33828996 . G A 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07348;SOR=1.29715;LSEQ=CTTAGGCAAGTTAGCCTTGT;RSEQ=GTCAATCTCTTAGGGCGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:170:94,76:148,140:288,170:0.3704:2,2:24.3:1:29.5:1:0.43932:1.17:59.8:55.667:0.3711:0:1.2 0/1:365:158:78,80:103,104:207,158:0.4329:2,2:24.6:1:28.5:1:1:1.01574:60:38.5:0.4302:0:1.6 +22 33829087 . T C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29944;LSEQ=ATCATGCAGAAGGCCTTCTC;RSEQ=TGCAATTATTACCAATACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:79:25,54:41,113:154,79:0.3376:2,2:23.3:1:31.8:1:0.44489:1.27:60:78:0.3391:0:1.3 0/1:159:21:9,12:45,93:138,21:0.1321:2,2:22.4:1:31.5:1:0.45844:1.55:60:42:0.1355:0:1.2 +22 33829090 . C A 32 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05922;SOR=Inf;LSEQ=ATGCAGAAGGCCTTCTCTTG;RSEQ=AATTATTACCAATACCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:63,164:227,0:0:2,0:22:1:31.9:1:1:0:60:36.833:1:0:0.5 0/1:146:3:3,0:45,98:143,3:0.0205:2,0:5:1:20.7:1:0.03404:0:60:2:0.0139:0:1 +22 34729259 . T TACCAGC 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=33;MSI=6.000;MSILEN=6;SSF=0.44627;SOR=1.29567;LSEQ=TCACAATCTGCACCGGTGTC;RSEQ=ACCAGCACCAGCACCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:24:10,14:39,30:69,24:0.2581:2,2:24.2:1:31.6:1:0.24142:1.80821:59.6:48:0.2581:0.0538:0.1 0/1:119:37:14,23:52,30:82,37:0.3109:2,2:30.6:1:30.9:1:0.01618:2.82148:58.8:74:0.3109:0.0336:0.2 +22 34729300 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50598;SOR=Inf;LSEQ=CAGCACCAGCACCTGATGTA;RSEQ=GTTGGTGGGGAACCAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:28,47:75,0:0:2,0:24.9:1:30.6:1:1:0:59.9:74:1:0:0.1 0/1:98:2:1,1:40,56:96,2:0.0204:2,2:31.5:1:31:0:1:1.40:60:4:0.0204:0:1 +22 34729364 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48936;SOR=Inf;LSEQ=CAGTTGTCCGGTGTTCCCCC;RSEQ=AAGCCAGGCACCTCGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:1,22:23,0:0:1,0:26:1:31.8:1:1:0:60:46:1:0:0.3 0/1:24:2:0,2:0,22:22,2:0.0833:1,0:47.5:1:29.5:1:1:0:60:4:0.0833:0:1 +22 35397186 . GT G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22433;SOR=Inf;LSEQ=GTAGTTGCTACAGAGACCAT;RSEQ=GGCCTGCAAAACCTAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:12,23:35,0:0:2,0:26.2:1:29.6:1:1:0:60:34:1:0:0.1 0/1:32:2:1,1:9,21:30,2:0.0625:2,2:21:0:32.5:1:0.53427:2.27:60:4:0.0625:0:0 +22 35397293 . C T 70 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55944;SOR=0.29522;LSEQ=GAAACAGAATGCAGGCAGAG;RSEQ=GTCAGGAAGAATGTGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:25.6:1:30.4:1:1:0:60:10:0.5556:0:1.2 0/1:4:1:0,1:1,2:3,1:0.25:2,0:12:0:31:0:1:0:60:2:0.25:0:1 +22 36521857 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49183;SOR=0;LSEQ=GGCTATGCACTAAATCTGAC;RSEQ=AGCCATTGTGTGTAAGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:8.5:1:29.5:1:1:1.14834:60:4:0.069:0:1.5 0/0:28:0:0,0:18,10:28,0:0:2,0:27.1:1:30.8:1:1:0:60:56:1:0:0.2 +22 36521859 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2377;SOR=Inf;LSEQ=CTATGCACTAAATCTGACCA;RSEQ=CCATTGTGTGTAAGGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:31,0:0:2,0:27.3:1:32.4:1:1:0:60:30:1:0:0.1 0/1:30:2:1,1:18,10:28,2:0.0667:2,2:40:1:29.5:1:1:1.76317:60:4:0.069:0:1 +22 37627234 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14901;SOR=2.48028;LSEQ=GGCCAAGTCAGGGCCTCCCC;RSEQ=GCAGCCAGATCGCCCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:11,0:15,0:15,11:0.4231:1,0:22.7:1:32.1:1:1:0:60:22:0.4231:0:2 1/0:20:13:13,0:7,0:7,13:0.65:0,1:24.8:1:30.1:1:1:0:60:26:0.65:0:2.2 +22 37627246 . G C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.80133;SOR=1.24563;LSEQ=GCCTCCCCTGCAGCCAGATC;RSEQ=CCCCTCTGAGCCCGAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:16:14,2:18,2:20,16:0.4444:2,2:21.9:1:31.5:1:1:1.27668:60:32:0.4444:0:1.7 1/0:28:14:12,2:12,2:14,14:0.5:2,2:26:1:30:1:1:1:60:28:0.5:0:2.1 +22 37627845 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCTGCCAGCCCTGGTTG;RSEQ=CACTGGGGACCCTCTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:29.5:1:1:0:60:4:1:0:1 +22 37640107 . A T 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65298;SOR=2.12879;LSEQ=CACCAGGGCGGAAGGATCTC;RSEQ=GGGCATCCCAGTTGGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:2:0,2:150,69:219,2:0.009:2,0:2:1:26:0:0.10222:0:60:4:0.0093:0:1 0/1:157:3:1,2:104,49:153,3:0.0191:2,2:11:1:21.7:1:0.24927:4.20188:60:2:0.0132:0:1.3 +22 37640188 . T A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06219;SOR=Inf;LSEQ=CACACACTTGATGGCCTGCA;RSEQ=CGTGTCCGGAGCCTGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:176,226:402,0:0:2,0:25.8:1:30.4:1:1:0:59.5:49.25:1:0:0.2 0/1:424:5:3,2:193,226:419,5:0.0118:2,2:16.2:1:28.8:1:0.66595:1.75:60:10:0.012:0:1 +22 37640232 . C T 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00708;SOR=Inf;LSEQ=CGGTGGTGACAGCTCAGGGC;RSEQ=AGGCGCGTTTCTGCGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:76,140:216,0:0:2,0:20.4:1:30.9:1:1:0:60:71:1:0:0.1 0/1:171:6:2,4:51,114:165,6:0.0351:2,2:18.7:1:28:1:1:1.12:60:12:0.0355:0:1.3 +22 37640246 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19771;SOR=Inf;LSEQ=CAGGGCCAGGCGCGTTTCTG;RSEQ=GGGCGCAAGGGGTGTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:39,109:148,0:0:2,0:22:1:29.8:1:1:0:60:73:1:0:0.1 0/1:119:2:1,1:25,92:117,2:0.0168:2,2:28:1:27:1:0.39069:3.63:60:4:0.0171:0:1 +22 37641410 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCCACTGGTCACCCACCC;RSEQ=GGACTCGTCACTCGGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 37903975 . G A 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=GCAGGTACTGAGGGTGGCAC;RSEQ=GGGCGGGGTCAGACCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:6,5:0.4545:2,2:10.2:1:31.8:1:1:1.30:60:10:0.4545:0:1 0/0:4:0:0,0:1,3:4,0:0:2,0:20.5:1:30.3:1:1:0:60:8:1:0:0.3 +22 37912009 . C T 44 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64649;SOR=2.12446;LSEQ=CAGGTCACGGCTGCGAAGTA;RSEQ=AGCCGAGTTCTTCTCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:30,20:50,2:0.0385:2,2:44.5:1:29.5:1:1:1.48801:60:4:0.0392:0:1 0/1:38:3:1,2:20,15:35,3:0.0789:2,2:27:1:28:1:0.57681:2.59906:60:6:0.0789:0:1 +22 37912060 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52027;SOR=0;LSEQ=CAGGCGCATGGCGATCATGT;RSEQ=GTTCTCATCCTTGAGCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:23,38:61,2:0.0317:2,2:26:0:33.5:1:1:1.64:60:4:0.0323:0:1.5 0/0:40:0:0,0:16,24:40,0:0:2,0:27.2:1:29.7:1:1:0:60:80:1:0:0.2 +22 37912078 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52344;SOR=0;LSEQ=GTAGTTCTCATCCTTGAGCC;RSEQ=CAGCAGCTCCAGGCTGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:15,26:41,2:0.0465:2,2:25.5:1:30:1:1:1.71:60:4:0.0488:0:1 0/0:26:0:0,0:9,17:26,0:0:2,0:26.7:1:30.7:1:1:0:60:52:1:0:0.1 +22 38012918 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22178;SOR=Inf;LSEQ=ACTCTGGCTCTGTGTTGTTC;RSEQ=TCCCACCCAGGCCTCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:20,21:41,0:0:2,0:30.9:1:31.8:1:1:0:60:40:1:0:0.2 0/1:37:2:1,1:17,18:35,2:0.0541:2,2:14:0:28:0:1:1.06:60:4:0.0541:0:1.5 +22 38012937 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10734;SOR=Inf;LSEQ=CCTCCCACCCAGGCCTCCAC;RSEQ=CGCCACCCGGCTGCTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:18,22:40,0:0:2,0:21:1:29.4:1:1:0:60:9:1:0:0.2 0/1:20:2:1,1:9,9:18,2:0.1:2,2:35:1:29.5:1:1:1:60:4:0.1111:0:1 +22 38369976 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34438;SOR=0.50101;LSEQ=GCTGCTGAGTAGCTGCTCAC;RSEQ=TGGCCTGGGTGCCCATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:12:5,7:3,2:5,12:0.7059:2,2:25.9:1:32.3:1:0.61991:2.00863:60:24:0.7059:0:1.1 1/0:24:13:8,5:5,6:11,13:0.5417:2,2:17.5:1:29:1:0.68239:1.87:60:26:0.5417:0:1.2 +22 38374009 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52081;SOR=0;LSEQ=CTCCCCACCGGGGCACTCCG;RSEQ=CTCGCCCTGGGCGGCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:64,17:81,2:0.0241:2,2:17.5:1:29:1:0.38877:3.68736:60:4:0.0253:0:1 0/0:53:0:0,0:38,14:52,0:0:2,0:18.5:1:30.6:1:1:0:60:51:0.9808:0:0.1 +22 38374064 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49905;SOR=0;LSEQ=CTGGGCTGGTACTTGTAGTC;RSEQ=GGGTGGTCTTTCTTGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:95,76:171,2:0.0115:2,2:39:1:32:1:1:1.24837:60:4:0.0118:0:1 0/0:163:0:0,0:94,69:163,0:0:2,0:30:0:16:0:1:0:60:0:0:0:1 +22 38374085 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22072;SOR=Inf;LSEQ=GGGTGGTCTTTCTTGTGCTG;RSEQ=ATACGGAGCCGCTCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:83,97:180,0:0:2,0:27.9:1:32.4:1:1:0:60:360:1:0:0.1 0/1:160:2:1,1:82,76:158,2:0.0125:2,2:37:0:31:0:1:1.07841:60:4:0.0125:0:1 +22 38379411 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08044;SOR=Inf;LSEQ=AGCTCAGCGTTGTGCAGGTG;RSEQ=GGGTACTGGTCCGCGAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:211,155:366,0:0:2,0:26.4:1:31.1:1:1:0:59:35.6:1:0:0.2 0/1:279:3:2,1:156,120:276,3:0.0108:2,2:32.3:1:29:1:1:1.54:28.7:6:0.0108:0:1 +22 38379645 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.14728;SOR=Inf;LSEQ=TTCTTGACCTTGCCCAGCTC;RSEQ=CCTGGCCCCGGGCTGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:35,188:223,0:0:2,0:24.4:1:32:1:1:0:60:43.6:0.9954:0:0.1 0/1:140:2:1,1:27,111:138,2:0.0143:2,2:35.5:1:28.5:1:0.36115:4.06:60:4:0.0143:0:1 +22 39240008 . G A 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.54034;LSEQ=GAGCCGGAGCTGGAGCTGTC;RSEQ=CCGCGGCCGCTGCTGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:24:0:32:0:1:1.11803:60:4:0.1111:0:1 0/1:17:1:1,0:8,8:16,1:0.0588:2,0:1:0:26:0:1:0:57:2:0.0588:0:1 +22 39407399 . T C 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCAGCGATAGGTAAGCTTC;RSEQ=GTGCAGGAACGGGCGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:20.7:1:30.3:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39407410 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAGCTTCTGTGCAGGAAC;RSEQ=GGCGCTGCTGCACCCCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:24.3:1:31.7:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39408841 . G A 47 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.69379;LSEQ=ACAAGACAAAGAGATAAAGC;RSEQ=AAAACAGCTGGGCCCGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:41:1:29.7:1:1:0:50:6:0.4286:0:1.3 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:39:0:30:0:1:0:52:2:0.3333:0:1 +22 39408940 . G A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00804;SOR=Inf;LSEQ=ATTTATTGCATACAAGACAA;RSEQ=GGGGGCAGGGTAAGGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:25,9:34,0:0:2,0:19.1:1:32.1:1:1:0:38.3:33:1:0:0.1 0/1:23:5:4,1:11,7:18,5:0.2174:2,2:26:1:30:1:0.62139:2.45:43.6:10:0.2174:0:1 +22 39639257 . GTCTCTC G 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCCGTCTCTCTCTCC;RSEQ=TCTCTCTCTCTCTCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:29:1:26:1:1:0:60:4:1:0.5:1 +22 39640006 . G T 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGCGGGGCCCCGGACGC;RSEQ=TAGATCGAGCGCGCCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39640933 . G T 29 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GGGAGGCAGCGGGGGAGGCT;RSEQ=CGGGTGCGCAGGGAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:24.8:1:31.3:1:1:0:60:8:1:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:22:0:29.5:1:1:1.7321:60:4:0.4:0:2 +22 39640950 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.5;SOR=Inf;LSEQ=GCTGCGGGTGCGCAGGGAGG;RSEQ=AGGCAGGCCGCTCCCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:22.3:1:34:0:1:0:60:6:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:36:1:28:1:1:2.44949:60:4:0.3333:0:1 +22 39641035 . G T 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.88734;LSEQ=AAGGAGAAGGGAGAGTGCGA;RSEQ=AGGTGGGTGGAGACAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:23,2:0.08:2,2:14.5:1:27.5:1:1:1.0871:60:4:0.08:0:1 0/1:14:1:0,1:8,5:13,1:0.0714:2,0:1:0:22:0:0.42857:0:60:2:0.0714:0:1 +22 39641067 . C T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51711;SOR=0;LSEQ=GACAGCCTTTCCTCTTCTGG;RSEQ=CCGGAGTCAGCGCCAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:27,2:0.069:2,2:23:0:30.5:1:1:1.07415:60:4:0.0714:0:1.5 0/0:18:0:0,0:9,9:18,0:0:2,0:31.9:1:30.9:1:1:0:60:17:1:0:0.5 +22 39641096 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4958;SOR=0;LSEQ=AGCGCCAGGAGGGGGGGGAC;RSEQ=CGGGAGCTGGGGGAGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:6,12:18,2:0.1:2,2:22.5:1:30.5:1:1:1.93:60:4:0.1:0:1.5 0/0:15:0:0,0:7,8:15,0:0:2,0:18.2:1:29.7:1:1:0:60:30:1:0:0.9 +22 39641913 . G T 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCCTCGGGACACGCAG;RSEQ=CTCCTGCATCACCCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:30.5:1:30:1:1:1:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39642740 . A T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGAAGCAAGCGCCTGGA;RSEQ=CCTTCCATGCAGCCTTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39756743 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17823;SOR=Inf;LSEQ=AAATATGGAGGTGAGCACAG;RSEQ=CCCCTAGAGAGGGACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:39,0:0:2,0:21:1:29:1:1:0:60:38:1:0:0.2 0/1:29:2:1,1:18,9:27,2:0.069:2,2:21:0:33:1:1:1.94942:60:4:0.069:0:1 +22 39756854 . G C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.82263;LSEQ=AGCGAGGGCAAATGCTGAAA;RSEQ=GCCTGGCAGAGCAGAGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:1,7:0,6:6,8:0.5714:0,2:23.3:1:31.3:1:1:0:60:16:0.5714:0:1 1/0:23:12:2,10:3,8:11,12:0.5217:2,2:12.4:1:29.8:1:0.64041:1.82405:60:24:0.5455:0:1.2 +22 39756896 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18182;SOR=Inf;LSEQ=GCTGTCGCCCCTGCTGGGGT;RSEQ=TACGCTTGGAGGGCGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:6,0:0:0,0:16.2:1:27.5:1:1:0:60:5:1:0:1 1/0:6:3:0,3:0,3:3,3:0.5:0,0:21.3:1:32:0:1:0:60:6:0.5:0:1 +22 39756985 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCCAACTATGGATGGA;RSEQ=GTGGCGGGAACTGCACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:31:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39758830 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGATTCTCCTTTCTACCC;RSEQ=CCGTGCTGCCTGGCCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:31:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39758844 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACCCCCCGTGCTGCCTGG;RSEQ=CCTCTCTGACTATCAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38.5:1:32.5:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39758881 . A G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGCTGTCTACTCCCCTC;RSEQ=AAGCCTTTCCTGACCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:33:1:1:0:60:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39866646 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGAGGAGGCAGAGAGAG;RSEQ=TCCATCCTGGGAGCATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:48.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 39866891 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.69461;LSEQ=AGGGCAGGATTTGAATCCAG;RSEQ=CCCTTTTGAGTCTAGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:102,52:154,2:0.0128:2,2:20.5:1:29.5:1:1:1.95251:60:4:0.013:0:1.5 0/0:112:1:0,1:72,39:111,1:0.0089:2,0:1:0:25:0:0.35714:0:60:2:0.0091:0:2 +22 39866923 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.58639;SOR=2.52814;LSEQ=CTAGACTCCAGAGAGCTATG;RSEQ=CCCCAAAGCAGCCCTCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:1,0:140,107:247,1:0.004:2,0:37:0:12:0:1:0:60:0:0:0:3 0/1:197:2:0,2:109,86:195,2:0.0102:2,0:17.5:1:27:1:0.19828:0:60:4:0.0105:0:1 +22 39866938 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=2.61334;LSEQ=CTATGGCCCCAAAGCAGCCC;RSEQ=CGCCCCACGCTGACTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:29:12,17:135,122:257,29:0.1014:2,2:25.9:1:30.3:1:0.32754:1.56515:59.5:28:0.1011:0:1.4 0/1:228:52:26,26:90,86:176,52:0.2281:2,2:25.5:1:31.1:1:1:1.04633:60:104:0.2311:0:1.2 +22 39867018 . A G 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51464;SOR=0;LSEQ=GAGAGCCCTCTCACAGAGGC;RSEQ=GAAGCACTCAGCCCAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:21,82:103,2:0.019:2,2:7.5:1:29:1:0.37674:3.84:60:4:0.019:0:1 0/0:72:0:0,0:19,53:72,0:0:2,0:20.5:1:29.8:1:1:0:60:17:1:0:0.3 +22 40982888 . AGTGCTGCTG A 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=24;MSI=2.667;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TCTCATCTGATTTGGCCTCT;RSEQ=GTGCTGCTGGTGCTGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:35,0:0:2,0:29.5:1:32.1:1:1:0:60:34:1:0:0.3 0/1:44:15:6,9:16,13:29,15:0.3409:2,2:31.1:1:31.3:1:0.5256:1.82037:60:30:0.3409:0:0 +22 40982928 . GTGC G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.24342;SOR=Inf;LSEQ=TGCTGCTGGTGCTGGTGCTG;RSEQ=TGCTGCTGCTGCTGCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:23,23:46,0:0:2,0:25.9:1:30.1:1:1:0:59.2:45:1:0:0.3 0/1:50:3:1,2:20,27:47,3:0.06:2,2:22.3:1:31.7:1:1:1.4703:60:6:0.06:0.02:0 +22 40982971 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22092;SOR=0;LSEQ=GCCGCCGCTGCCTTATCCAC;RSEQ=TGGAGTTTGTGGTTGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:10,16:26,2:0.0714:2,2:43:1:30.5:1:1:1.57:60:4:0.0741:0:1 0/0:31:0:0,0:10,21:31,0:0:2,0:23.7:1:31.3:1:1:0:60:62:1:0:0.1 +22 41461514 . C CA 28 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAAAGCGAGGCCCTGTCT;RSEQ=AAAAAAAAAAAACAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:10.5:1:28.5:1:1:0:60:4:0.6667:0.3333:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41461721 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49859;SOR=0;LSEQ=CTCTTCCTGCACCCCTTTTC;RSEQ=TGTTTAATGGTAATATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:130,28:158,2:0.0125:2,2:14.5:1:30.5:1:0.33058:4.57964:60:4:0.0125:0:1.5 0/0:154:0:0,0:118,36:154,0:0:2,0:22.6:1:30.1:1:1:0:60:153:1:0:0.1 +22 41461836 . A G 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36361;LSEQ=ATTTCTCCTCTCTATCCCCA;RSEQ=TGACAGGTTGCCACACGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:482:344:175,169:67,68:135,344:0.7137:2,2:25:1:32.4:1:0.83937:1.05:60:67.8:0.7137:0:1.2 0/1:524:249:124,125:136,139:275,249:0.4752:2,2:24.1:1:31:1:1:1.01:59.9:34.571:0.4708:0:1.6 +22 41461865 . T G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0754;SOR=1.26904;LSEQ=TGCCACACGCTATCTTACAA;RSEQ=TTCACAATGACCCTCCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:185:77,108:121,158:279,185:0.3987:2,2:27.2:1:32.9:1:0.77376:1.07396:60:91.5:0.397:0:1.3 0/1:477:218:99,119:114,145:259,218:0.457:2,2:25.5:1:30.9:1:0.78199:1.06:59.8:42.6:0.4522:0:1.6 +22 41488906 . GC G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.22686;SOR=Inf;LSEQ=CCCCCTCGGGTGCCGTCGGA;RSEQ=CCCCCAGCCCACCCCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:112,4:116,0:0:1,0:24.2:1:32:1:1:0:60:28:1:0:0.1 0/1:106:2:2,0:101,3:104,2:0.0189:1,0:14.5:1:33:0:1:0:60:4:0.0192:0:0 +22 41489173 . A AT 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.58716;SOR=0.65733;LSEQ=CGGTGCGCCTTTATTCTTCC;RSEQ=TTTTTTTTTTCTTCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:9:2,7:22,157:179,9:0.0471:2,2:21.7:1:30.6:1:0.32234:2.03:60:18:0.0492:0.0052:0.6 0/1:159:5:0,5:17,135:152,5:0.0314:2,0:30.2:1:28.8:1:1:0:60:10:0.0331:0:0 +22 41489487 . T C 69 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATTTCGAATCCTTTCTC;RSEQ=TTACTGTACTTACTGTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:19:1:34.5:1:1:0:50.8:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41513094 . G T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2997;SOR=0.68535;LSEQ=GAAAAACATGGAGTGAGGTT;RSEQ=GGAAATGACATTTAATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:99:64:64,0:33,2:35,64:0.6465:2,1:20.4:1:31.4:1:0.12266:0:59.4:63:0.6563:0:1.1 1/0:54:30:29,1:24,0:24,30:0.5556:1,1:20.4:1:29.8:1:1:0:60:29:0.5472:0:1.1 +22 41513121 . A G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51225;SOR=0;LSEQ=GACATTTAATGCTTATTGAG;RSEQ=ACAATATAGAGCAGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:152,10:162,2:0.0122:2,2:10:0:32:0:0.13003:14.53793:60:4:0.0125:0:1.5 0/0:117:0:0,0:103,14:117,0:0:2,0:22:1:28.6:1:1:0:60:57.5:1:0:0.3 +22 41513857 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12363;SOR=Inf;LSEQ=TTTGGTTTGTGTGCACAATC;RSEQ=GCATGCATGTGAGTATTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:72,201:273,0:0:2,0:23.4:1:30.7:1:1:0:59.9:90:1:0:0.1 0/1:274:4:2,2:87,183:270,4:0.0146:2,2:23.3:1:28.5:1:0.5978:2.10:60:8:0.015:0:1.3 +22 41514155 . G A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GAGATGGCTGGCATTACACT;RSEQ=TCTTCAGATGGATACTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:23.5:1:31.5:1:1:0:60:4:0.4:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:28.5:1:1:0:60:4:1:0:1 +22 41521557 . G A 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGATTACAGGTATGAGTC;RSEQ=CCAGGCCCGGCCACTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:2,3:0.6:2,0:21.3:1:32.7:1:0.4:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41521717 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1628;LSEQ=TTAGTAGAGATGGGGTTTTG;RSEQ=CACGTTGCCCAAGCTGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:21:21,0:14,0:14,21:0.6:1,1:26.3:1:31.5:1:1:0:58.9:20:0.5882:0:1 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:41:1:30.1:1:1:0:59.3:6:0.6:0:1.7 +22 41523809 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2068;SOR=Inf;LSEQ=TTTACAGCCAGGGAGAAGAA;RSEQ=GAAAATGTGATCAAGTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:23,215:238,0:0:2,0:24.2:1:31.6:1:1:0:60:237:1:0:0.2 0/1:199:2:1,1:21,176:197,2:0.0101:2,2:16:1:24.5:1:0.20938:8.21:60:4:0.0101:0:1 +22 41523937 . A G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06465;SOR=0.14579;LSEQ=TGTGGTGTCTCACACTTACA;RSEQ=TCCCAGCACTTTGGTAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:15:0,15:0,5:5,15:0.75:0,1:28:1:31.5:1:1:0:59.3:14:0.7368:0:1 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:16.5:1:33.5:1:1:0:60:4:0.3333:0:1 +22 41525892 . A G 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATATGTTTTCTTCTCTTT;RSEQ=GTGGCACACTGTGCATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:28:17,11:314,166:480,28:0.0551:2,2:23.9:1:32.2:1:0.68406:1.22344:60:56:0.0561:0:1.1 0/0:484:0:0,0:298,184:482,0:0:2,0:24.6:1:28.2:1:1:0:60:42.818:0.9958:0:0.1 +22 41526364 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=CCCAGGAGTTCAAGACCAGC;RSEQ=TAGGCAACTTAGCAAGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:6,0:0:0,0:33:1:30.8:1:1:0:60:5:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:32:1:1:0:60:4:1:0:1 +22 41527338 . C CT 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.51014;SOR=0.5531;LSEQ=TTTTTATTAGACATGTTAGT;RSEQ=TTTTTTTTCTCACCAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:6:6,0:240,44:284,6:0.0207:2,0:28.2:1:33:1:0.59567:0:60:12:0.021:0.0034:0 0/1:260:3:2,1:198,59:257,3:0.0115:2,2:20:1:29.3:1:0.54642:1.67419:60:6:0.0116:0.0077:0 +22 41531569 . C CT 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCGCCTGGTCACATTTG;RSEQ=TTTTTTTTTTTAAGTTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:3,0:19,0:19,3:0.1364:1,0:12.7:1:32.3:1:1:0:60:6:0.1364:0.0909:0 0/0:1:0:0,0:1,0:1,0:0:0,0:34:0:33:0:1:0:60:2:1:0:1 +22 41532025 . A G 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.03433;SOR=Inf;LSEQ=GAGGATGTCTTTGAATACAG;RSEQ=TAGATGTTTGAGTCCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:0,84:84,0:0:1,0:23.5:1:31.2:1:1:0:59.8:27:1:0:0 0/1:65:4:0,4:1,60:61,4:0.0615:1,0:27.5:1:32.5:1:1:0:60:8:0.0625:0:1 +22 41533590 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16758;SOR=Inf;LSEQ=CATTACAATAATCAGTGTCA;RSEQ=CTTGAATTAAATGAGGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:221,25:246,0:0:2,0:26:1:33.4:1:1:0:59.9:245:1:0:0 0/1:171:2:1,1:138,31:169,2:0.0117:2,2:30.5:1:27:1:0.34014:4.39736:60:4:0.012:0:1 +22 41536305 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09946;SOR=Inf;LSEQ=TAATAGCCAAGATTGAACCT;RSEQ=TTGTGGTTATTTTATTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:68,232:300,0:0:2,0:23.7:1:31.9:1:1:0:60:41.857:1:0:0.1 0/1:260:3:2,1:72,185:257,3:0.0115:2,2:23.7:1:27:1:0.19589:5.10:60:6:0.0116:0:1 +22 41537234 . G T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00024;SOR=0.06129;LSEQ=GGAATGACTTCTAGTAAGTG;RSEQ=TTTTTGTTATATTTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:372:371:104,267:0,0:0,371:0.9973:0,2:24.6:1:30.4:1:1:0:59.9:122.667:1:0:1.1 1/1:379:363:119,244:6,10:16,363:0.9578:2,2:25.2:1:28.9:1:0.78686:1.22953:60:59.5:0.9571:0:1.1 +22 41542753 . A G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTACTCTAGATGGCCCTCT;RSEQ=CCTGACCCAAGTATGATCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:889:0:0,0:425,464:889,0:0:2,0:24.7:1:28.9:1:1:0:60:97.778:1:0:0.1 0/1:1035:29:15,14:481,523:1004,29:0.028:2,2:27.1:1:30.4:1:0.71005:1.16:60:13.5:0.0264:0:1.2 +22 41542838 . T A 149 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGTAAATAGTGAAAAAAA;RSEQ=TTTTTTATTTTAAAAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:30:5,25:53,228:281,30:0.0958:2,2:20.5:1:30.5:1:1:1.16174:60:29:0.0935:0:1.2 0/0:351:0:0,0:94,256:350,0:0:2,0:22.8:1:29.5:1:1:0:60:115.667:0.9971:0:0.1 +22 41544167 . C T 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7099;LSEQ=AGTGTTTAGTGGCCTGCATG;RSEQ=GTTTTCACGGTCACTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:1,3:0,14:14,4:0.2222:1,2:19.3:1:26.8:1:0.22222:0:60:3:0.1765:0:1.5 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:13:0:24:0:1:0:60:2:0.1667:0:1 +22 41545330 . TGAA T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00279;SOR=0.22215;LSEQ=GACTTAGGGTATTCTGAACA;RSEQ=GAGATTATTCTGTGACATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:25:1,24:1,20:21,25:0.5435:1,1:27.3:1:31.7:1:1:1.19523:59.2:24:0.5455:0.087:0.2 0/1:34:7:0,7:0,27:27,7:0.2059:1,0:21.3:1:31:1:1:0:60:14:0.2121:0:0.3 +22 41545452 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAATCTTAGAATTAAACA;RSEQ=AATGTAGAAGGAAATCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:16:0:32.5:1:1:1.34838:60:4:0.0714:0:1.5 0/0:2:0:0,0:0,2:2,0:0:0,0:16.5:1:33:0:1:0:60:4:1:0:0 +22 41545611 . G C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.43689;SOR=0;LSEQ=GGTGCTGTCCAAAGATACAT;RSEQ=CCCAGTAATAGGGTATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:58:56,2:0,0:0,58:1:0,1:25.4:1:32.1:1:1:0:59.7:57:1:0:1 1/1:45:44:44,0:0,0:0,44:0.9778:0,1:25.2:1:31.1:1:1:0:60:43:0.9773:0:1.1 +22 41545623 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02246;SOR=Inf;LSEQ=AGATACATGCCCAGTAATAG;RSEQ=GTATTTTACACATTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:89,2:91,0:0:1,0:22.2:1:31.9:1:1:0:59.8:182:1:0:0.6 0/1:59:4:4,0:54,1:55,4:0.0678:1,0:24.8:1:29.8:1:1:0:60:8:0.069:0:2 +22 41545666 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16326;SOR=Inf;LSEQ=GACACATTGCTACTCTTTGT;RSEQ=TAATCAGTTTGTGTCCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:184,7:191,0:0:1,0:25.9:1:31.3:1:1:0:59.8:190:1:0:0.3 0/1:130:2:1,1:118,10:128,2:0.0154:2,2:17.5:1:29:1:0.16267:11.29871:60:4:0.0156:0:1.5 +22 41546187 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20558;SOR=Inf;LSEQ=ACAGCACCGCTGCTTCCTCC;RSEQ=CAGCCTGCAACTCCAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:49,171:220,0:0:2,0:26.4:1:31.4:1:1:0:59.9:30.429:1:0:0.1 0/1:183:2:1,1:54,127:181,2:0.0109:2,2:24:1:28.5:1:0.51192:2.34:60:4:0.0111:0:1 +22 41547677 . A AG 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16113;SOR=Inf;LSEQ=CCTGTTCTTAAGCATAATTA;RSEQ=GGGAGGTGAAATGGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:41,0:41,0:0:1,0:21:1:30.4:1:1:0:60:40:1:0:0.1 0/1:28:2:2,0:25,1:26,2:0.0714:1,0:11.5:1:31.5:1:1:0:60:4:0.0714:0.0357:0 +22 41547766 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19369;SOR=Inf;LSEQ=TTCTGCTATCCTGTTGCTTA;RSEQ=CTTACATTCTGATTGTATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:192,29:221,0:0:2,0:23.6:1:32:1:1:0:59.8:43.2:1:0:0.1 0/1:175:2:1,1:147,26:173,2:0.0114:2,2:13:1:28:1:0.28552:5.56707:60:4:0.0114:0:1 +22 41547819 . C T 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGTGTGTCTCACCTACTTC;RSEQ=CTTTTTTTTCTGCCCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:0:0,0:343,182:525,0:0:2,0:24:1:31.1:1:1:0:59.9:51.5:1:0:0.2 0/1:505:25:13,12:292,188:480,25:0.0495:2,2:26.4:1:28.1:1:0.40613:1.43263:60:24:0.0477:0:1.1 +22 41547820 . C CT 99 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.42164;SOR=0.57016;LSEQ=CGTGTGTCTCACCTACTTCC;RSEQ=TTTTTTTTCTGCCCAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:527:9:7,2:334,183:517,9:0.0171:2,2:25.6:1:31.4:1:0.50417:1.92:60:8:0.0154:0:0.4 0/0:510:5:2,3:305,200:505,5:0.0098:2,2:27.8:1:29.6:1:0.39138:2.2837:60:10:0.0098:0.002:0.2 +22 41548008 . A G 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1662;LSEQ=CAGATACTCAGCCGGAGGAT;RSEQ=TTTCAGAGGTGAGAGTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:575:337:128,209:93,143:236,337:0.5861:2,2:26.1:1:32.2:1:0.79369:1.06178:59.9:111.333:0.587:0:1.2 0/1:615:117:45,72:214,284:498,117:0.1902:2,2:26.8:1:31.5:1:0.40599:1.20527:59.9:116:0.1889:0:1.1 +22 41548369 . C A 63 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45312;SOR=2.34718;LSEQ=AAAAGAGTGAGTCTCTGAAG;RSEQ=CATTCGTTCTGGAGGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:2:1,1:148,258:406,2:0.0049:2,2:17.5:1:27:0:1:1.74:60:4:0.005:0:1 0/1:437:5:4,1:163,269:432,5:0.0114:2,2:6.4:1:27.2:1:0.07287:6.57:60:10:0.0116:0:1 +22 41548421 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5061;SOR=0;LSEQ=AGACCCAGGGCAGAATTGCG;RSEQ=TCATGCCTCTTGGGCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:32,138:170,2:0.0116:2,2:21.5:1:28.5:1:0.34782:4.26:60:4:0.0117:0:1 0/0:134:0:0,0:26,108:134,0:0:2,0:21.6:1:31.1:1:1:0:60:133:1:0:0.1 +22 41548519 . CT C 60 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.25618;SOR=3.11678;LSEQ=GTTACTAATAATTTTTCTTT;RSEQ=TTTTTTTTTTTTTAATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:0,4:0,23:23,4:0.1333:1,0:23:1:30.3:1:1:0:60:8:0.1481:0.0333:0.5 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:27:1:27.5:1:1:0:60:4:0.3333:0:0 +22 41550954 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.30481;SOR=0.81923;LSEQ=AATGATTTTTTAAAGTTCTT;RSEQ=TGCTTAATTGGTAACTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:259:152:138,14:100,6:106,152:0.5869:2,2:23.8:1:30.6:1:0.35011:1.68755:60:37:0.5896:0:1.4 1/0:212:114:102,12:88,9:97,114:0.5377:2,2:22.8:1:30.2:1:0.82075:1.14957:59.9:113:0.5433:0:1.6 +22 41550956 . G A 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25407;SOR=0;LSEQ=TGATTTTTTAAAGTTCTTCT;RSEQ=CTTAATTGGTAACTAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:3,0:244,24:268,3:0.0111:2,0:8.7:1:22:1:1:0:60:2:0.0076:0:2.3 0/0:228:0:0,0:199,27:226,0:0:2,0:22.3:1:31.5:1:1:0:60:74.333:1:0:0.9 +22 41550984 . C CT 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.04953;SOR=1.54844;LSEQ=GGTAACTAATTTCAAATGCA;RSEQ=TTTTTTTTTTTAAGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:38:35,3:332,84:416,38:0.0819:2,2:27.9:1:31.8:1:0.08304:2.95:58.9:18:0.0796:0:0.9 0/1:453:55:45,10:292,95:387,55:0.1214:2,2:27:1:29.7:1:0.39692:1.46:59.3:26.5:0.1216:0:1.1 +22 41551018 . A G 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTTTCAAACCAGAAGAACT;RSEQ=CGACAGGCACTGATGCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:847:0:0,0:568,277:845,0:0:2,0:24.7:1:28.6:1:1:0:59.9:37.409:0.9988:0:0.8 0/1:942:27:19,8:581,332:913,27:0.0287:2,2:20:1:30.9:1:0.54657:1.36:60:54:0.0294:0:1 +22 41551039 . T A 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.69148;LSEQ=CGACAGGCACTGATGCCAAC;RSEQ=TTGGAGGCACTTTACCGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1088:656:390,266:251,181:432,656:0.6029:2,2:26.6:1:30:1:0.65994:1.06:60:23.296:0.5973:0:1.2 1/0:1234:632:360,272:336,263:599,632:0.5122:2,2:25.7:1:29:1:0.77383:1.04:59.9:41.133:0.5112:0:1.2 +22 41551231 . AT A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.36513;SOR=0.68652;LSEQ=TTCAAATTTGTAATTCAGTG;RSEQ=TTTTTTTTTTTCCCCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:23:0,23:0,114:114,23:0.1679:1,1:30.7:1:31.4:1:1:0:59.8:46:0.1742:0:0.1 0/1:107:13:0,13:2,90:92,13:0.1215:1,1:23.8:1:31:1:1:0:59.5:26:0.1238:0.0093:0.8 +22 41551244 . C T 68 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24482;SOR=3.24316;LSEQ=TTCAGTGATTTTTTTTTTTT;RSEQ=CCCCTGAGACAGGGTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:0,2:0,106:106,2:0.0183:1,0:13:1:31.5:1:1:0:60:4:0.0189:0:1 0/1:87:5:1,4:0,82:82,5:0.0575:1,2:7.4:1:29.5:1:0.05747:0:60:4:0.0435:0:1 +22 41552926 . T G 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAGAACCTGAAGTTGC;RSEQ=TCAGTAGAATATCAGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:40:1:32:0:1:0:60:4:0.1818:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41553123 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1169;SOR=Inf;LSEQ=ATGGATGATACTCCATCTCC;RSEQ=GTAAAAATAGTGAGACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:230,71:301,0:0:2,0:22.6:1:31:1:1:0:59.9:149.5:1:0:0.1 0/1:289:3:1,2:218,67:285,3:0.0104:2,2:12.7:1:26.3:1:0.1437:6.45368:60:6:0.0107:0:1 +22 41553469 . A G 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61216;SOR=2.14261;LSEQ=TGGGATACCTAGAATAATAT;RSEQ=GTGGTGACTGGGATAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:1:0,1:29,173:202,1:0.0049:2,0:40:0:8:0:1:0:60:0:0:0:7 0/1:193:2:1,1:44,147:191,2:0.0104:2,2:32.5:1:28.5:1:0.41289:3.31:60:4:0.011:0:1 +22 41554278 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13406;SOR=Inf;LSEQ=GTAAACTGAGAATGATTTTC;RSEQ=GGAACTGAATTAGCCCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:101,2:103,0:0:1,0:24.2:1:30.8:1:1:0:60:206:1:0:0.1 0/1:60:2:2,0:56,2:58,2:0.0333:1,0:35:1:31.5:1:1:0:60:4:0.0333:0:1 +22 41554559 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25595;SOR=0;LSEQ=GTCCACATGTCCAGGGAGTG;RSEQ=ATGCGGATGGGCCAGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:1,2:47,213:260,3:0.0114:2,2:23.7:1:28.3:1:0.45508:2.26:60:6:0.0115:0:1 0/0:216:0:0,0:35,181:216,0:0:2,0:21.1:1:31.1:1:1:0:60:26:1:0:0.1 +22 41556423 . C CA 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCACTTGGCTTTGATTG;RSEQ=AAAAAAAAAAACAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:7,0:7,2:0.2:0,0:6:1:31.8:1:1:0:60:4:0.2:0.1:0 0/0:4:0:0,0:3,0:3,0:0:0,0:9:1:30.7:1:1:0:48.7:6:0.75:0:2.3 +22 41556520 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20229;SOR=Inf;LSEQ=CATTGAATGTCCTTGTCGCC;RSEQ=TTGATGACCTGCTCTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:61,2:63,0:0:1,0:25.2:1:30:1:1:0:59.9:62:1:0:0.3 0/1:52:2:1,1:50,0:50,2:0.0385:1,2:33:1:30.5:1:0.03846:0:60:4:0.0392:0:1 +22 41556812 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19161;SOR=Inf;LSEQ=TTTCTAAATGAACTTAAGCT;RSEQ=TGCTGTTGAATATGGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:1,69:70,0:0:1,0:27.3:1:31.4:1:1:0:60:69:1:0:0.1 0/1:55:2:1,1:2,51:53,2:0.0364:1,2:28:1:32.5:1:0.10707:21.02:60:4:0.0364:0:1 +22 41558232 . A G 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTCTAGGCCATAACTAGT;RSEQ=TAAGAAACGGTTTTCAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:13:1:34.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41559963 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAGTTCTTTGGTCATGAC;RSEQ=TTGGCTGTCTTTGTCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:349,47:396,0:0:2,0:25.2:1:31.5:1:1:0:59.9:55.571:1:0:0.1 0/1:323:23:17,6:254,46:300,23:0.0712:2,2:17.1:1:29.3:1:0.2326:1.94409:60:46:0.0723:0:1.4 +22 41560212 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08971;SOR=Inf;LSEQ=GTTTTTTATTCTATGCAATT;RSEQ=ACTGTATTATATCTTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:33,215:248,0:0:2,0:23.1:1:32.1:1:1:0:60:123:1:0:0 0/1:202:3:2,1:30,169:199,3:0.0149:2,2:14:1:25.7:1:0.06597:11.05:60:6:0.015:0:1 +22 41562177 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTTATTTACTTGGTTG;RSEQ=TGAACAAGTTTATACAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:17:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41562785 . A G 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00061;SOR=0;LSEQ=TAATAGAGTAAAAATAAAAT;RSEQ=ATTCTATAATCTCCTTATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:9:0,9:1,31:32,9:0.2195:1,0:24.2:1:33.2:1:1:0:60:18:0.2195:0:1.2 0/0:47:0:0,0:0,47:47,0:0:1,0:23.9:1:29.9:1:1:0:60:22.5:1:0:0.1 +22 41564287 . T C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=0.1758;LSEQ=GCATGTTCCCTGCACTCATA;RSEQ=GACATGTAAATCTGCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:34:34,0:19,0:19,34:0.6415:1,1:25.7:1:32.6:1:1:0:60:33:0.6346:0:1 0/1:34:8:8,0:26,0:26,8:0.2353:1,0:16.8:1:33.4:1:1:0:60:16:0.2353:0:1.1 +22 41564708 . C A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.54324;LSEQ=GTTATGTTGTGGTTCCCCCA;RSEQ=CATCTCAATTGTATAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:184:104,80:288,268:556,184:0.2486:2,2:27.3:1:30.5:1:0.2696:1.21:60:183:0.2493:0:1 0/1:709:108:56,52:321,280:601,108:0.1523:2,2:25.8:1:29:1:0.83419:1.06442:60:53:0.1506:0:1.1 +22 41565051 . C T 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08021;SOR=Inf;LSEQ=AAACCCCCAAACAAAATAAC;RSEQ=GCTCAATACTGCTCTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:3,21:24,0:0:2,0:19.1:1:28.4:1:1:0:59.5:23:1:0:0.3 0/1:10:2:0,2:0,8:8,2:0.2:0,0:7:1:31.5:1:1:0:60:4:0.2:0:1 +22 41565439 . A C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50062;SOR=0;LSEQ=GAGAGGGTGTTATTAGGCAC;RSEQ=TGGAGTAAAGAACTCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:163,16:179,2:0.011:2,2:26:1:31:1:0.1795:9.91362:60:4:0.0112:0:1 0/0:159:0:0,0:134,24:158,0:0:2,0:21.2:1:29.5:1:1:0:60:157:0.9937:0:0.1 +22 41565469 . CT C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.21369;SOR=0.49451;LSEQ=GAACTCATTATGTGACCTGA;RSEQ=TTTTTTTTCCTCTTCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:11:8,3:262,76:338,11:0.0315:2,2:22.5:1:33.1:1:0.71693:1.29175:59.1:22:0.0317:0.0029:0.3 0/1:316:5:3,2:214,96:310,5:0.0158:2,2:26:1:30.8:1:0.64823:1.48413:60:10:0.0158:0:0 +22 41565827 . A G 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20156;SOR=0.22573;LSEQ=GCCCTAGTTTCACCCATCCA;RSEQ=CATTAGTTTTGTTTGTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:7,11:0.6111:0,0:21.5:1:31.6:1:1:0:57.3:10:0.5882:0:1 0/1:8:2:0,2:1,5:6,2:0.25:2,0:12:1:32:1:1:0:60:4:0.25:0:1 +22 41566595 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20081;LSEQ=GGTCAGTTGGGACATAGGGG;RSEQ=CAGGTGCTGACAATAGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:542:296:85,211:76,168:244,296:0.5461:2,2:28.6:1:29.1:1:0.5711:1.12273:59.7:17.5:0.5479:0:1.3 0/1:494:96:33,63:139,258:397,96:0.1943:2,2:24.3:1:27.9:1:1:1.02849:60:31:0.1966:0:1.2 +22 41566823 . A G 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACAGGCTCCTGCCATCAC;RSEQ=CCCGGCTAAATTTTTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:20:1:31:1:1:0:22.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41567975 . TAC T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATATAGGTTGTCTCATGA;RSEQ=AGACTTGTCTTCCTCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:30.5:1:33:0:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41568480 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00507;SOR=0.65492;LSEQ=AAAGAACATAGAAATTCCTA;RSEQ=ATGTACATGCATGTTTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:358:222:164,58:97,39:136,222:0.6201:2,2:24.3:1:32.2:1:0.62518:1.14:60:110:0.6197:0:1.1 1/0:393:203:147,56:120,70:190,203:0.5165:2,2:23:1:31.3:1:0.05232:1.53:60:202:0.5193:0:1 +22 41568714 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2048;SOR=Inf;LSEQ=CTTCTATCATGATTCTAATA;RSEQ=TTAATCCAGAAGTGCACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:33,166:199,0:0:2,0:22.1:1:30.6:1:1:0:60:65.333:1:0:0.1 0/1:165:2:1,1:30,133:163,2:0.0121:2,2:17:1:30:1:0.34139:4.38:60:4:0.0125:0:1 +22 41568720 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50503;SOR=0;LSEQ=TCATGATTCTAATATTTAAT;RSEQ=CAGAAGTGCACTTAAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:0,2:24,154:178,2:0.0111:2,0:14:1:31.5:1:1:0:60:4:0.0113:0:1 0/0:143:0:0,0:24,119:143,0:0:2,0:21:1:30.3:1:1:0:60:142:1:0:0.1 +22 41568804 . TAGAG T 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.00065;SOR=0;LSEQ=TTGGACAAGAAATATTGGCT;RSEQ=AGGTTATTAGGGTTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:0,17:0,29:29,17:0.3696:1,1:23.6:1:32.7:1:1:0:60:34:0.3778:0.087:0.1 0/0:21:0:0,0:0,21:21,0:0:1,0:19.1:1:31.4:1:1:0:60:42:1:0:0 +22 41569043 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACACTCTTTTTAAATGT;RSEQ=AAAAACCATTCTTAGCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:13.5:1:31:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41569609 . C T 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=8.69314;LSEQ=AAACCTTATTTTCTTGTCTC;RSEQ=TTTGTGCTACTCTGCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:16:13,3:254,70:324,16:0.0471:2,2:17.3:1:31.8:1:1:1.19:60:32:0.0479:0:1.1 0/1:279:84:64,20:144,51:195,84:0.3011:2,2:24.9:1:30.5:1:0.76508:1.13:59.9:83:0.3007:0:1.1 +22 41569887 . G A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0259;SOR=Inf;LSEQ=GCACTTTGGGAGGCCAAGGC;RSEQ=GGTGGATCACCTGAGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:41,0:0:1,0:14.7:1:30.2:1:1:0:39.6:19.5:1:0:0 0/1:29:4:0,4:0,25:25,4:0.1379:1,0:13:1:32.3:1:1:0:40:8:0.1379:0:1 +22 41570071 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAGTGAGCCGAGGTCAC;RSEQ=CCATTGCACTCCAGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:14:1:32.5:1:1:0:31.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 41572193 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24292;SOR=Inf;LSEQ=AAGATCACGCCACTGCATTC;RSEQ=AGCCTGGATGACAGAGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:137,23:160,0:0:2,0:20.8:1:31.8:1:1:0:59.8:159:1:0:0.1 0/1:156:2:1,1:130,24:154,2:0.0128:2,2:23:1:25:1:0.2957:5.3277:60:4:0.0132:0:1.5 +22 41572223 . CA C 90 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20585;SOR=0.38501;LSEQ=GACAGAGCGAGGCCCTGTCT;RSEQ=AAAAAAAGAGACTGTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:7:5,2:225,88:313,7:0.0218:2,2:22.3:1:32.1:1:1:1.02266:60:14:0.022:0:0.4 0/0:353:3:2,1:240,110:350,3:0.0085:2,2:19:1:30:1:1:1.09063:58.7:6:0.0086:0:0 +22 41572541 . C T 102 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00217;SOR=12.45808;LSEQ=ACTGTCTGTGAGGTAGGCAC;RSEQ=GGGTTGTGGGAAGGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:1:1,0:162,248:410,1:0.0024:2,0:40:0:16:0:0.39659:0:60:0:0:0:1 0/1:373:11:3,8:128,232:360,11:0.0295:2,2:20.5:1:29.7:1:0.75309:1.46983:60:22:0.0304:0:1 +22 41572578 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.4011;LSEQ=GAGGTGAGCTCCGCAGGGTT;RSEQ=TTCTGAGGGGCCATGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:2:2,0:75,176:251,2:0.0079:2,0:1:0:23.5:1:0.09179:0:60:4:0.0081:0:1 0/1:181:2:1,1:54,125:179,2:0.011:2,2:9.5:1:28:1:0.51657:2.30:60:4:0.0114:0:1 +22 41572582 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06619;SOR=Inf;LSEQ=TGAGCTCCGCAGGGTTGTTC;RSEQ=GAGGGGCCATGCAGCCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:71,165:236,0:0:2,0:23.5:1:30.9:1:1:0:60:46.2:0.9957:0:0.1 0/1:162:3:1,2:46,112:158,3:0.0185:2,2:36.7:1:32:1:1:1.22:60:6:0.0188:0:1 +22 41572671 . GT G 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=1.90411;LSEQ=GGGCAGAGCTGAAGAGGCTA;RSEQ=TTTTGTTCTACGAAAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:1:0,1:140,45:185,1:0.0054:2,0:10:0:34:0:0.24731:0:60:2:0.0055:0:0 0/1:196:2:2,0:163,31:194,2:0.0102:2,0:29:1:32:1:1:0:60:4:0.0103:0:0 +22 41574383 . A C 203 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0;SOR=0;LSEQ=AGTTGGCTACCCACCACAGC;RSEQ=GCAGCAGCGGATGCAGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:96:46,50:403,487:890,96:0.0974:2,2:24.1:1:30.9:1:0.66658:1.11:60:192:0.0986:0:1.1 0/0:1042:0:0,0:470,571:1041,0:0:2,0:25.7:1:29.9:1:1:0:59.9:68.4:0.999:0:0.2 +22 41574969 . TGTA T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0;SOR=0.16984;LSEQ=GACATACACTAGAGACACCT;RSEQ=GTATTTTGGGAGCAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:529:255:83,172:95,177:272,255:0.482:2,2:25.5:1:31.9:1:0.58129:1.11202:59.9:84:0.4837:0.0718:0.1 0/1:565:77:29,48:182,304:486,77:0.1363:2,2:25.5:1:30.3:1:1:1.01:59.6:76:0.1355:0.023:0.2 +22 42683520 . C T 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11888;SOR=9.76063;LSEQ=AGCACAGATCCATCCCATCA;RSEQ=GTATGCATGCATTCATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:29.3:1:27.3:1:1:0:60:2:0.2222:0:1.3 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:17.8:1:27.6:1:1:0:60:10:0.8333:0:1 +22 42684161 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTAATCCCAGCATTCTGG;RSEQ=AGGCCAACGTGGGTGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 42927816 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=CGCCGACGTATGCTGCCTTC;RSEQ=CTCTCTGCTTCAGCTACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:23,3:26,0:0:2,0:24.4:1:30.2:1:1:0:45.3:12:1:0:0.2 0/1:30:2:1,1:21,7:28,2:0.0667:2,2:25.5:1:29:1:0.46897:2.87249:44.5:4:0.0667:0:1 +22 42927873 . TGCTC T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5076;SOR=Inf;LSEQ=TGTCCTATGATCACGTGACT;RSEQ=GACCTTATCAATCACTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:36,24:60,0:0:2,0:31.5:1:31.7:1:1:0:33.5:59:1:0:0.3 0/1:81:2:1,1:44,35:79,2:0.0247:2,2:31.5:1:30.5:1:1:1.25356:41.5:4:0.0256:0:0 +22 42927912 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17744;SOR=0;LSEQ=CTTGGACGACTCACCCTCCT;RSEQ=ACCCTGCTCCCCTTGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:23,33:56,2:0.0345:2,2:35.5:1:31.5:1:1:1.43:44.5:4:0.0357:0:1 0/0:79:0:0,0:34,45:79,0:0:2,0:23.2:1:27.6:1:1:0:36.2:25.333:1:0:0.1 +22 42927983 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19861;SOR=0;LSEQ=TTGGGGTCACTACCGGTCTC;RSEQ=GTGTCTTGGTGGTAGTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:1,16:17,2:0.1053:1,2:42.5:1:32.5:1:0.20468:11.66:60:4:0.1053:0:1.5 0/0:23:0:0,0:1,22:23,0:0:1,0:21.9:1:29.4:1:1:0:57.6:46:1:0:0.1 +22 43170994 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCCTGAAGGCTGAAGGC;RSEQ=GGGCTGCCAGATCCACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:31.5:1:1:0:60:4:1:0:2 +22 43171045 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTGTGGTACCTCTTCTGG;RSEQ=TGCCCATGCACCAACTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:28:1:1:0:60:4:1:0:2 +22 43172308 . T C 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=Inf;LSEQ=GCAAGCTTGTTTCTCATAAA;RSEQ=GATGTGACTTCAAGTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:24:1:33.5:1:1:0:45.5:4:0.3333:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:32:0:1:0:21:2:1:0:1 +22 43172357 . G T 54 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTTTTTTTTTTGCTG;RSEQ=CCCTAAGTTTATTGTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:32.8:1:27.3:1:1:0:50.3:8:1:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:26:0:25:0:1:0:26:2:1:0:2 +22 43172489 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45816;SOR=0.67862;LSEQ=ATCCTTCTTCTGAGCAAGGG;RSEQ=CATTTTGGGAAGGTTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:35:17,18:3,7:10,35:0.7778:2,2:32.8:1:29.8:1:0.47283:2.17:34.4:70:0.7778:0:1.1 1/0:37:26:9,17:4,7:11,26:0.7027:2,2:38.4:1:27.7:1:1:1.07713:36.4:25:0.6944:0:1 +22 43172646 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TATTGAGAGAACTGTTTCTT;RSEQ=TAAGCATCGTCATCTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:41:0:34:0:1:0:21:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:27.5:1:1:0:22:4:1:0:1.5 +22 43523991 . C A 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCAGCTCCTGGCACTCG;RSEQ=CCCCTGCCACCTGTCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:26.5:1:1:0:60:4:1:0:2 +22 43524000 . A T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGCACTCGCCCCCTGCC;RSEQ=CCTGTCCCTGGCATTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:27:1:1:0:60:4:1:0:2 +22 43525176 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCGTCTGGCCCCATTGC;RSEQ=GGGGCCTGCCCCGAGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:24.4:1:33.2:1:1:0:60:10:1:0:1 1/1:8:8:4,4:0,0:0,8:1:0,2:11.3:1:29.1:1:1:0:60:16:1:0:1.1 +22 43525244 . CGCT C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.16585;SOR=Inf;LSEQ=CTGCGAACAGGTGCTGCTGG;RSEQ=GCTGCTGCTGCTGGCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:24,0:0:2,0:25.9:1:30.2:1:1:0:60:23:1:0:0.1 0/1:17:2:1,1:6,9:15,2:0.1176:2,2:38:1:31:1:1:1.46:60:4:0.125:0:1 +22 43525278 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11092;SOR=Inf;LSEQ=CTGGCGCTGCTGCTGCCGCT;RSEQ=CTCAGCGGGGGCCTGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,15:23,0:0:2,0:30.4:1:32.7:1:1:0:60:46:1:0:0 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:23.5:1:24:1:1:1.45:60:4:0.1667:0:1 +22 43623353 . G A 46 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCAGGTGCAGGGGAGG;RSEQ=GCCAGCAGCACAGGGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:1,3:0.75:0,2:22.3:1:29.3:1:1:0:60:6:0.75:0:2 +22 43623395 . C G 45 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACCCACGCAATCCTTCC;RSEQ=GTTCCAGTGGAGCCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:2,1:1,1:2,3:0.6:2,2:32.3:1:28.7:1:1:1.73:60:6:0.6:0:2 +22 43623612 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=TCTCCTGACCCCACCGAGTC;RSEQ=GACAGCATCACGGGATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:21,0:0:2,0:26.5:1:29.4:1:1:0:60:42:1:0:0.1 0/1:14:2:1,1:9,3:12,2:0.1429:2,2:39.5:1:29:1:0.50549:2.73861:60:4:0.1429:0:1 +22 43623759 . G C 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=GCAGCTGCACCCCAGGCTAG;RSEQ=GGGCAGAGGAGGTAGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:28:1:31.3:1:1:0:60:6:0.5:0:2 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:33.5:1:30:1:1:0:60:4:0.6667:0:2 +22 43623770 . G C 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=CCAGGCTAGGGGGCAGAGGA;RSEQ=GTAGCACACGATTAAAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:26:1:32:0:1:0:60:4:0.4:0:2.5 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:23:1:31.5:1:1:0:60:4:0.6667:0:2 +22 43788785 . GGAGA G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=12.000;MSILEN=2;SSF=0.81495;SOR=1.13131;LSEQ=AATGAGTAAAGTCTGTAAAA;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:12,3:7,1:8,15:0.4688:2,2:22.7:1:32.5:1:1:1.71054:59.7:30:0.4688:0.0938:1.2 1/0:38:19:12,7:12,1:13,19:0.5:1,2:15.8:1:30.5:1:0.10058:6.63417:59.2:38:0.5135:0.1579:1.1 +22 43788811 . CGA C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=1.12917;LSEQ=AGAGAGAGAGAGAGAGAGAA;RSEQ=GAGAGAGAGAGAACAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:6:2,4:34,18:52,6:0.1034:2,2:21.5:1:30.7:1:0.18725:3.68669:60:12:0.1091:0:0.5 0/1:52:6:3,3:28,18:46,6:0.1154:2,2:43.5:1:30:1:0.67544:1.54199:60:12:0.1154:0:0.3 +22 43788830 . C G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.86648;SOR=0.93794;LSEQ=ACGAGAGAGAGAGAGAACAA;RSEQ=AGCACACGTATGTGTGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:39:25,14:22,17:39,39:0.5:2,2:28.2:1:32.3:1:0.64391:1.37:59.5:18.5:0.4933:0:1.4 0/1:62:30:16,14:18,14:32,30:0.4839:2,2:30.6:1:31:1:1:1.12286:59.7:60:0.5:0:1.2 +22 43788833 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58116;SOR=2.60563;LSEQ=AGAGAGAGAGAGAACAACAG;RSEQ=ACACGTATGTGTGTGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:0,1:48,32:80,1:0.0123:2,0:1:0:27:0:0.40741:0:60:2:0.0127:0:1 0/1:63:2:1,1:34,27:61,2:0.0317:2,2:35:1:28:1:1:1.25461:60:4:0.0317:0:1 +22 43788936 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17534;SOR=Inf;LSEQ=GATCTACTAGAGACCCCAAG;RSEQ=CAGTCCCAGGTGGAAGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:6,28:34,0:0:2,0:18.7:1:29.9:1:1:0:60:68:1:0:0.1 0/1:25:2:0,2:6,17:23,2:0.08:2,0:26:1:32.5:1:1:0:60:4:0.08:0:1 +22 44445578 . G T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08156;SOR=Inf;LSEQ=CATGTTGCAAGGAACCCTAG;RSEQ=GGCTGCCATAGCCCTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:139,83:222,0:0:2,0:24.6:1:30.4:1:1:0:60:30.714:1:0:0.2 0/1:171:3:1,2:110,58:168,3:0.0175:2,2:6:1:26.3:1:0.28174:3.76213:60:6:0.0178:0:1 +22 44445659 . C T 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=4.72661;LSEQ=ATTAAAGCAGGAGACCTCTG;RSEQ=CCGGGAACGGGCCATTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:54:25,29:106,141:247,54:0.1794:2,2:21.7:1:29.9:1:0.65292:1.15:60:108:0.1837:0:1.1 1/0:222:113:54,59:48,61:109,113:0.509:2,2:24:1:28.5:1:0.5925:1.16:60:226:0.509:0:1.2 +22 44445727 . C A 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00117;SOR=Inf;LSEQ=GTAGGTTTTATTGCCAAAGC;RSEQ=GTCCCGGCCTTGGCCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:49,115:164,0:0:2,0:24.3:1:30.2:1:1:0:60:81:1:0:0.2 0/1:104:7:2,5:31,66:97,7:0.0673:2,2:21.9:1:28.6:1:1:1.17246:60:14:0.068:0:1.1 +22 44773398 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.01026;SOR=0.09886;LSEQ=TAAATATCCATTTCAAGAGG;RSEQ=AAAAAGAAACCCCCCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:9,8:2,1:3,17:0.85:2,2:21.5:1:28.4:1:1:1.72884:60:16:0.8421:0:1.2 0/1:9:3:3,0:2,4:6,3:0.3333:2,0:20.7:1:30:1:0.16667:0:60:6:0.3333:0:1.7 +22 44773410 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.09073;SOR=Inf;LSEQ=TCAAGAGGCAAAAAGAAACC;RSEQ=CCCAAAACCCCCAAAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,11:21,0:0:2,0:27.4:1:31:1:1:0:60:42:1:0:0.8 0/1:10:2:1,1:3,4:7,2:0.2:2,2:31:0:32.5:1:1:1.29:60:4:0.2:0:1.5 +22 44773420 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12381;SOR=Inf;LSEQ=AAAAGAAACCCCCCAAAACC;RSEQ=CCAAAACAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:23,0:0:2,0:30:1:31:1:1:0:60:46:1:0:0.9 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:19.5:1:26:0:1:1.18:60:4:0.1538:0:2 +22 44773543 . C G 62 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAATCAACAAGGTTTAA;RSEQ=GTTTATTTTTCAAATGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:25:1:31.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 45133340 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTTTCAGGCATCTGAGTC;RSEQ=GCGTTTACCCAGGGGCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 45133657 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCGCAGGTTTCCAGGGTCTG;RSEQ=GTGGAGGGGGCAGACCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:22:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 45134006 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02757;SOR=Inf;LSEQ=CTCCCCTGCAGCCTCACTAT;RSEQ=CCCAGACAGGCTTTCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:21,2:23,0:0:2,0:28.7:1:32.3:1:1:0:60:46:1:0:0.5 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:27.7:1:27.7:1:1:0:60:6:0.2727:0:2 +22 45134049 . G C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94839;LSEQ=CCTCAGGTGGGCAGGATACC;RSEQ=CATCAGCCGTAGCAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:19:17,2:16,2:18,19:0.5135:2,2:22.2:1:31.6:1:1:1.06:60:38:0.5135:0:1.1 1/0:12:6:5,1:6,0:6,6:0.5:0,2:26.2:1:31.5:1:1:0:60:12:0.5:0:2 +22 45134193 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13867;SOR=Inf;LSEQ=CAGCCTTCCCTAGCCACCCC;RSEQ=GCCGTTTTAAAGCATCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:116,109:225,0:0:2,0:24:1:30:1:1:0:60:44:1:0:0.5 0/1:134:2:1,1:74,58:132,2:0.0149:2,2:33.5:1:29.5:1:1:1.27351:60:4:0.0153:0:2 +22 45134197 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=2.65312;LSEQ=CTTCCCTAGCCACCCCCGCC;RSEQ=TTTTAAAGCATCGGGTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:68:37,31:78,80:158,68:0.3009:2,2:24.6:1:30.2:1:0.56212:1.22:60:33:0.2973:0:1.3 1/0:133:71:37,34:35,27:62,71:0.5338:2,2:23.9:1:29.7:1:0.72744:1.18962:60:142:0.5338:0:1.2 +22 45134257 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06052;SOR=Inf;LSEQ=GTGGAGGGGTCTCTAACGGC;RSEQ=GGCACCTTTCCACACCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:68,113:181,0:0:2,0:27.4:1:30.5:1:1:0:59.8:89.5:1:0:0.3 0/1:118:3:2,1:46,69:115,3:0.0254:2,2:9.3:1:26.3:1:0.56571:2.97:60:6:0.0265:0:1.7 +22 45134339 . A G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21013;SOR=0.47239;LSEQ=GCCTCTCATGGCGTTTTCTC;RSEQ=AGGTGGGAAAGGAGTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:20:2,18:1,13:14,20:0.5882:1,2:27.9:1:32.9:1:1:1.43:60:40:0.6061:0:1.1 0/1:30:12:1,11:1,17:18,12:0.4:1,2:16.7:1:31.2:1:1:1.52:60:24:0.4444:0:1.3 +22 45565915 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=AAAGTCTTTGATCTTTCTGA;RSEQ=AAGTGCATAGAAGAAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:7,0:0:2,0:23.9:1:31.9:1:1:0:43.3:14:1:0:0.6 0/1:9:2:2,0:6,1:7,2:0.2222:2,0:27:1:32.5:1:1:0:60:4:0.2222:0:1 +22 45565937 . G A 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.69217;SOR=1.75912;LSEQ=AGTGCATAGAAGAAAATGCT;RSEQ=ACGTACGCCGCCTTCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:7,2:9,5:0.3571:2,0:14:1:30:1:0.50549:0:58.2:10:0.3571:0:2 1/0:12:6:5,1:5,1:6,6:0.5:2,2:30.5:1:28.2:1:1:1:39:12:0.5:0:2.2 +22 45565946 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.79307;LSEQ=AAGAAAATGCTGACGTACGC;RSEQ=GCCTTCCTTCTCTGCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:10,0:6,1:7,10:0.5882:2,0:14.7:1:33.8:1:0.41176:0:59.1:20:0.5882:0:1.6 1/0:17:9:7,2:6,2:8,9:0.5294:2,2:25.9:1:29.9:1:1:1.16:46:18:0.5294:0:1.8 +22 45714398 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTTCTAGGACCTGGTGC;RSEQ=GAGTGCTTTTGAGATCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:0:31.5:1:1:0:60:4:1:0:1.5 +22 45714489 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTATTGTGAGATTTGACTC;RSEQ=GATGTTTAGGCTGCTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:34:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 45714765 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52663;SOR=0;LSEQ=GGAGCCAGCACCAGACCTGC;RSEQ=GTTCAGGCTGAGAAAGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:101,2:103,2:0.019:1,2:26:1:31.5:1:0.05659:41.48291:60:4:0.0194:0:1 0/0:64:0:0,0:63,1:64,0:0:1,0:22.3:1:30.5:1:1:0:59.5:128:1:0:0 +22 45714782 . A G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5172;SOR=0;LSEQ=TGCAGTTCAGGCTGAGAAAG;RSEQ=GGTTTTGAGCACTTAAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:128,7:135,2:0.0146:2,2:19.5:1:28.5:1:0.11378:17.17024:60:4:0.0147:0:1 0/0:92:0:0,0:87,4:91,0:0:1,0:22.7:1:29:1:1:0:60:44.5:1:0:0 +22 45714801 . G T 22 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50683;SOR=0;LSEQ=GAGGTTTTGAGCACTTAAGC;RSEQ=AGCCACAGACCACCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:0,2:163,28:191,2:0.0104:2,0:10.5:1:22.5:1:0.02348:0:60:4:0.0105:0:1 0/0:149:0:0,0:130,19:149,0:0:2,0:22.3:1:29.5:1:1:0:60:48.667:1:0:0 +22 45714937 . T C 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14695;LSEQ=GCCTGCAAAAGTTTAATTTG;RSEQ=TCATACTGTTTTTGAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:531:390:168,222:60,79:139,390:0.7345:2,2:25.8:1:32.3:1:1:1.00361:60:42.333:0.7299:0:1.1 0/1:596:172:78,94:192,231:423,172:0.2886:2,2:24.4:1:31.4:1:1:1.00166:60:56.333:0.2864:0:1.2 +22 47217677 . C T 72 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGAATTTACATGTTGGC;RSEQ=CGTCTTGCTAGGTTGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:20:1:31.4:1:1:0:56.8:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 47218466 . A C 42 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTGATTCACTCCCATGCCT;RSEQ=GAGATGTCACTCATGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:14:0:25:0:1:0:60:2:1:0:1 1/1:3:3:1,2:0,0:0,3:1:0,2:29.3:1:27:1:1:0:46:6:1:0:1 +22 47218730 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53202;SOR=Inf;LSEQ=GCTAAGGGTTGGTGGGGGCT;RSEQ=AGGTCACCAAATGAAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:22.6:1:31.9:1:1:0:60:20:1:0:0 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:16.5:1:28:1:1:1.40:60:4:0.1053:0:1.5 +22 47788223 . C CCA 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAATCACACACATCATACA;RSEQ=CACACACAGGATACACAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 +22 47788380 . A C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CACAAACACATCATACACCC;RSEQ=CACACACACACACACGCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:41:0:28:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:32.5:1:1:0:60:4:1:0:3.5 +22 47788382 . A C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CAAACACATCATACACCCAC;RSEQ=CACACACACACACGCGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:39:0:28:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:32.5:1:1:0:60:4:1:0:3.5 +22 47788396 . G A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCCACACACACACACACAC;RSEQ=CGATACACAGGTATCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:25:0:26:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:29:0:1:0:60:4:1:0:3.5 +22 47788564 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49269;SOR=0;LSEQ=GAAACTGTCCACTGGGAGTC;RSEQ=GCGTCAGGTCAGGATGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:36:1:29.5:1:1:1.07:60:4:0.0645:0:1 0/0:28:0:0,0:15,13:28,0:0:2,0:24.4:1:29.7:1:1:0:60:56:1:0:0.2 +22 47788629 . C T 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.59956;SOR=3.33655;LSEQ=TGGAGCCCGTGACCGGGCAG;RSEQ=CCCCAGCCTCCTCTGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:2,13:15,1:0.0625:2,0:48:0:30:0:1:0:60:2:0.0667:0:1 0/1:16:3:1,2:5,8:13,3:0.1875:2,2:28.7:1:29.7:1:1:1.23302:60:6:0.1875:0:1 +22 48775198 . T C 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21235;SOR=3.23164;LSEQ=GGGTTGAGGTCTGAAGCCCT;RSEQ=TGATGGCCATCAGACCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:2,0:30,3:33,2:0.0571:2,0:20:1:34:0:1:0:60:4:0.0571:0:1 0/1:24:4:3,1:15,5:20,4:0.1667:2,2:10.5:1:30.3:1:1:1:60:8:0.1667:0:1 +22 48775249 . G T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49902;SOR=0;LSEQ=TGCAGCCACGAAGAGCCTGG;RSEQ=CAGTGACCCTCAGTGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:43,28:71,2:0.0274:2,2:13:1:25.5:1:1:1.52641:60:4:0.0278:0:1 0/0:63:0:0,0:36,27:63,0:0:2,0:28.8:1:31.3:1:1:0:60:62:1:0:0.2 +22 48775261 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49754;SOR=0;LSEQ=GAGCCTGGGCAGTGACCCTC;RSEQ=GTGCCGGAGGAAGCGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:51,37:88,2:0.0222:2,2:38.5:1:31.5:1:1:1.37337:60:4:0.023:0:2 0/0:85:0:0,0:45,40:85,0:0:2,0:24:1:29.9:1:1:0:59.9:84:1:0:0.3 +22 48775266 . CG C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4973;SOR=0;LSEQ=TGGGCAGTGACCCTCAGTGC;RSEQ=GAGGAAGCGTGCAGATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:49,39:88,2:0.0222:2,2:11:1:30:1:1:1.25319:60:4:0.0227:0:0 0/0:87:0:0,0:44,43:87,0:0:2,0:24.6:1:30.4:1:1:0:59.9:174:1:0:0.3 +22 48775300 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=AGATAAATGGCTCCCACTGG;RSEQ=CTGAGTCCAGGGTGCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:34,51:85,2:0.023:2,2:15:1:29.5:1:1:1.49:60:4:0.0235:0:2 0/0:64:0:0,0:31,33:64,0:0:2,0:28.2:1:31:1:1:0:60:128:1:0:0.2 +22 48775314 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03225;SOR=Inf;LSEQ=CACTGGCCTGAGTCCAGGGT;RSEQ=CCCACAGTAATGCTGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:24,46:70,0:0:2,0:27.6:1:31.3:1:1:0:60:22.333:1:0:0.1 0/1:53:4:2,2:24,25:49,4:0.0755:2,2:20.3:1:28.5:1:1:1.04:60:8:0.0769:0:1 +22 49025257 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGGATGCCCCACAGTCC;RSEQ=CAGCTCCCTGGGCCCCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 49026230 . T C 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60268;SOR=2.5556;LSEQ=AGGCTTGCTCCACTGCTGCC;RSEQ=CGGCCCTGGCTTTGGGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:8,1:9,5:0.3571:2,0:24.4:1:31.6:1:1:0:60:10:0.3846:0:1 1/0:5:3:3,0:2,0:2,3:0.6:0,0:28.7:1:29.3:1:1:0:60:6:0.6:0:1.3 +22 49026292 . G A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35661;SOR=0.44058;LSEQ=TTTGTTGAGTCGTCAGCGGC;RSEQ=TGTGATGACCAGGTGTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:11:11,0:40,0:40,11:0.2157:1,0:26.4:1:31.5:1:1:0:60:22:0.2245:0:1 0/1:28:3:3,0:25,0:25,3:0.1071:1,0:28:1:30.7:1:1:0:60:6:0.1071:0:1.3 +22 49026358 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18075;SOR=Inf;LSEQ=CGCTCGGGCCCAGGGCAGGT;RSEQ=GCCACGCCTTCTTACTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:111,33:144,0:0:2,0:21.4:1:32:1:1:0:60:143:1:0:0.2 0/1:107:2:1,1:77,28:105,2:0.0187:2,2:28.5:1:28:1:0.47046:2.71966:60:4:0.0196:0:1 +22 49026397 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6362;SOR=0.43131;LSEQ=ACAGGTTCACGGGATAATTG;RSEQ=TGGGGCCAGGTGGACCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:1,2:151,119:270,3:0.011:2,2:17:1:29:1:0.58598:2.52931:60:6:0.0112:0:1.7 0/0:210:1:0,1:118,91:209,1:0.0048:2,0:1:0:26:0:0.4381:0:60:2:0.005:0:1 +22 49026453 . C G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.44068;LSEQ=GAAGTCTGTGCAGTGAGTGC;RSEQ=GCTTCCAGAACAATGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:85:40,45:122,138:260,85:0.2457:2,2:26:1:30.4:1:1:1.01:60:27.333:0.2426:0:1.2 0/1:273:121:56,65:71,81:152,121:0.4432:2,2:24.6:1:29.5:1:1:1.01736:60:59.5:0.4407:0:1.2 +22 49026497 . T C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18868;SOR=Inf;LSEQ=CACGTCTTCACCGCCCTCCA;RSEQ=CAGGGGCCGCCTAGAAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:85,124:209,0:0:2,0:23.8:1:29.9:1:1:0:60:33.833:1:0:0.3 0/1:161:2:1,1:56,101:157,2:0.0124:2,2:31:0:30:1:1:1.80:60:4:0.0132:0:1 +22 49026541 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.53746;SOR=0;LSEQ=AGGCTGCAGGGCTGGCTACC;RSEQ=GGGCCCTGAATCACGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:21,81:102,2:0.0192:2,2:12.5:1:30:1:0.37995:3.79:60:4:0.0194:0:1.5 0/0:58:0:0,0:10,48:58,0:0:2,0:23.4:1:30:1:1:0:60:116:1:0:0.3 +22 49026549 . G A 92 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00184;SOR=9.28905;LSEQ=GGGCTGGCTACCGGGGCCCT;RSEQ=AATCACGGGGGCGATGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:0,2:13,71:84,2:0.0233:2,0:18:1:33:0:1:0:60:4:0.0241:0:1 0/1:49:9:2,7:6,34:40,9:0.1837:2,2:24.8:1:29.1:1:0.62794:1.60:60:18:0.1875:0:1 +22 49026616 . G GCTT 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.50551;LSEQ=GCTGGGCACTCGGCTGTGGG;RSEQ=CTTTTGTTTCTACCTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:23:0,23:0,7:7,23:0.7667:0,1:26.3:1:31.8:1:1:0:60:46:0.7931:0.0667:0.2 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:22.2:1:31.3:1:1:0:60:10:0.8333:0.1667:0.2 +22 49026883 . T C 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGTGGCTCCCCGCCCTG;RSEQ=CCTTTCTAAGGACGGACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:17.8:1:30:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 49370602 . G C 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.81119;LSEQ=TGAGGCCCCTGCCCAGGGCT;RSEQ=CGCTCCTCCCAACAGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:26.2:1:31.8:1:1:0:60:10:0.7143:0:1 1/0:9:6:6,0:2,1:3,6:0.6667:2,0:28.7:1:30.8:1:0.33333:0:60:12:0.6667:0:1 +22 49370678 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14119;SOR=Inf;LSEQ=TATACACAGGGCCAGGGCCT;RSEQ=TTTTTGTCTTTTTGCATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:49,0:0:1,0:24.9:1:32.8:1:1:0:60:98:1:0:0.2 0/1:30:2:1,1:26,2:28,2:0.0667:2,2:39:1:28:1:0.1931:10.81688:60:4:0.069:0:1 +22 49370710 . G T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15988;SOR=4.9145;LSEQ=TTGCATAATTCCTCCTGCAG;RSEQ=GGCCCCACCCCAGCAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:0,1:100,14:114,1:0.0087:2,0:1:0:25:0:0.13043:0:60:2:0.0088:0:2 0/1:72:3:1,2:57,12:69,3:0.0417:2,2:11.7:1:21:1:0.0946:9.06976:60:2:0.0294:0:1.7 +22 49370723 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51561;SOR=0;LSEQ=CCTGCAGGGGCCCCACCCCA;RSEQ=CAGGGCCTCAGCCCAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:112,25:137,2:0.0144:2,2:19:1:28.5:1:0.34021:4.41258:60:4:0.0148:0:1 0/0:95:0:0,0:72,23:95,0:0:2,0:24.7:1:30.7:1:1:0:60:18:1:0:0.5 +22 49370754 . A G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=2.32878;LSEQ=GCCCAAGGCTCCAGTGGCTG;RSEQ=GCGGCCCCCTTCCAGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:42:29,13:130,63:193,42:0.1787:2,2:27.1:1:31:1:1:1.08:60:41:0.183:0:1.4 0/1:193:65:42,23:79,49:128,65:0.3368:2,2:25.3:1:28.6:1:0.75397:1.13:60:9.833:0.3189:0:1.5 +22 49370758 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26264;SOR=0;LSEQ=AAGGCTCCAGTGGCTGAGCG;RSEQ=CCCCCTTCCAGCTTCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:167,89:256,3:0.0115:2,2:22.3:1:28.7:1:0.2828:3.7327:60:6:0.012:0:1 0/0:197:0:0,0:122,75:197,0:0:2,0:26:1:30.5:1:1:0:60:48.25:1:0:0.7 +22 49370764 . T C 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08114;SOR=Inf;LSEQ=CCAGTGGCTGAGCGGCCCCC;RSEQ=TCCAGCTTCCCTGGTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:178,101:279,0:0:2,0:25.8:1:31:1:1:0:60:45.5:1:0:0.4 0/1:214:3:1,2:130,81:211,3:0.014:2,2:25:1:24.7:1:0.56118:3.192:60:2:0.0095:0:3.3 +22 49370800 . G A 124 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=23.8885;LSEQ=CAGGAAACACCCCCTCTTGC;RSEQ=GCTGCCCAGAGACAAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:1:1,0:180,149:329,1:0.003:2,0:1:0:26:0:1:0:60:2:0.0031:0:1 0/1:265:18:11,7:129,118:247,18:0.0679:2,2:28.2:1:29.8:1:0.62601:1.44:60:36:0.0698:0:1.9 +22 49370817 . G A 119 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=23.77757;LSEQ=TGCGGCTGCCCAGAGACAAA;RSEQ=GGTCCCCTGGGTGTGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:1,0:160,159:319,1:0.0031:2,0:1:0:28:0:1:0:37:2:0.0032:0:1 0/1:273:19:9,10:123,131:254,19:0.0696:2,2:23.5:1:28.1:1:1:1.04311:60:18:0.0672:0:1.8 +22 49370834 . C G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.97447;LSEQ=AAAGGGTCCCCTGGGTGTGG;RSEQ=ACTTGCTGTCAGGCATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:54:23,31:119,135:254,54:0.1742:2,2:23.6:1:31.8:1:0.65256:1.18742:60:108:0.1759:0:1.3 0/1:254:116:54,62:61,76:137,116:0.4567:2,2:26.6:1:29.8:1:0.80034:1.08:60:37.667:0.4538:0:1.4 +22 49370864 . G A 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=Inf;LSEQ=CAGGCATATTCTAAGCCCCA;RSEQ=GCAAGCATCCTGAATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:103,168:271,0:0:2,0:25.8:1:31.8:1:1:0:60:89.333:1:0:0.2 0/1:220:10:4,6:83,127:210,10:0.0455:2,2:28.5:1:30:1:1:1.02:60:20:0.0457:0:1.9 +22 49370962 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.09313;LSEQ=CCCAGGCCACCTGCAGCCCA;RSEQ=GAGGGGCCTACCAAGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:41:3,38:3,14:17,41:0.7069:2,2:24.8:1:29.7:1:0.34497:2.66139:60:40:0.7018:0:1.1 0/1:28:5:0,5:3,20:23,5:0.1786:2,0:21.6:1:29.6:1:1:0:60:10:0.1852:0:1 +22 49371163 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATCTGGGTCCCACCCCCT;RSEQ=GCCACGTGTCCCCCCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:28:1:28:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 49371286 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAACACTGCCCCTCCTGGA;RSEQ=TGCACCCCCGGCCATGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 49371352 . C CG 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCATCTTCAAGTGAGAAA;RSEQ=TCTTCCTCTGCCCCACTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:32.2:1:1:0:60:4:1:0.5:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 50353917 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAGGCCGCGGGACAAGCG;RSEQ=AGGTCGCCTCCCGCACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:33.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 50353919 . G A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCCGCGGGACAAGCGCA;RSEQ=GTCGCCTCCCGCACTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:33:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 50354819 . C A 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05155;SOR=5.46737;LSEQ=AAGGCGTACCAGGTGGGCGC;RSEQ=GTGCTGGGTAGCGGCGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:5,2:7,3:0.3:2,2:26.7:1:31.7:1:0.5:4.17095:60:6:0.3:0:1.3 1/0:21:15:7,8:3,3:6,15:0.7143:2,2:30.8:1:30.1:1:1:1.1356:60:30:0.7143:0:1.3 +22 50354820 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGCGTACCAGGTGGGCGCC;RSEQ=TGCTGGGTAGCGGCGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:9,0:0:2,0:30.8:1:31.8:1:1:0:60:18:1:0:0.6 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:20.5:1:29:1:1:1.11:60:4:0.0952:0:1.5 +22 50354942 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCTTGCGCCTCGCTTGGCCC;RSEQ=GCCTGACCCCCGCGTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:24.3:1:31:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:31.5:1:1:0:60:4:1:0:1.5 +22 50355381 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17096;SOR=Inf;LSEQ=ACGAAAATCTGCTTGTGGAC;RSEQ=TGCGCTCCGGAGAGCTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:24,15:39,0:0:2,0:25.3:1:30.7:1:1:0:60:12:1:0:0.2 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:13.5:1:28.5:1:1:1.34838:60:4:0.0714:0:1 +22 50356274 . C T 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=AGGGAGTTAACCAGCAGGGA;RSEQ=CTCGCCGTCTGTTGAGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:7:1:28.5:1:1:0:60:4:0.3333:0:1.5 1/0:4:2:2,0:2,0:2,2:0.5:0,0:33.5:1:29:1:1:0:60:4:0.5:0:1.5 +22 50356302 . C T 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.30579;LSEQ=TCTGTTGAGCGGCTCTGCCT;RSEQ=TGTGGTGGGCGTGCTAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:4,2:6,3:0.3333:2,2:18:1:32.7:1:1:1:60:6:0.3333:0:1.3 0/1:5:2:2,0:3,0:3,2:0.4:0,0:20.5:1:28.5:1:1:0:60:4:0.4:0:1.5 +22 50356350 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTAGGCACCCGAGTGTA;RSEQ=AGCCCCCCGGAGTGGATCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:44.5:1:28:1:1:1.19087:60:4:0.0833:0:2 0/0:11:0:0,0:6,5:11,0:0:2,0:27.5:1:31.3:1:1:0:60:22:1:0:0.4 +22 50357125 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CCAAGCCCACCTCCCGCCCT;RSEQ=AGTCCTGCGGTGTGCGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:27:1:31:1:1:0:60:6:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:15.5:1:29:1:1:0:60:4:1:0:0 +22 50358008 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGGCCCTGAGGATGCA;RSEQ=CAACCCACACTAGTCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:43:1:30.5:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 50358197 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGGGTTTTGAAGGACA;RSEQ=GGAGGAGTTTGCCAGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +22 50704661 . T C 25 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGCACCAACTCACGTGTTC;RSEQ=GAGGAGATTTTTGCCAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29:1:30:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:25.5:1:1:0:60:4:1:0:1.5 +22 50705059 . A G 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63325;SOR=2.38223;LSEQ=CACTGTGCGAGGGCGAGGGG;RSEQ=CCTCCATCAGTGTGCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:3,3:3,3:6,6:0.5:2,2:19.5:1:32.7:1:1:1:60:12:0.5455:0:1.7 1/0:7:5:2,3:0,2:2,5:0.7143:0,2:20.2:1:30.6:1:1:0:60:10:0.7143:0:1 +22 50705304 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00364;SOR=Inf;LSEQ=CTAAGACCTGGCATGCAGAG;RSEQ=CAGTCGAGGGCCAGACGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:57,1:58,0:0:1,0:26.1:1:32.7:1:1:0:60:57:1:0:0.1 0/1:30:5:5,0:25,0:25,5:0.1667:1,0:21.6:1:29.4:1:1:0:60:10:0.1667:0:1 +22 50705449 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1637;SOR=Inf;LSEQ=AGCCGGTCATCTCCTCGTCC;RSEQ=CCTGGCGCGCCAGCCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:88,132:220,0:0:2,0:23.8:1:30.5:1:1:0:60:35.667:1:0:0.8 0/1:150:2:1,1:57,91:148,2:0.0133:2,2:15.5:1:24:1:1:1.59:60:4:0.0142:0:2 +22 50705455 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17433;SOR=Inf;LSEQ=TCATCTCCTCGTCCGCCTGG;RSEQ=GCGCCAGCCCAAAATCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:71,125:196,0:0:2,0:23.2:1:30.1:1:1:0:60:48:1:0:0.9 0/1:141:2:1,1:54,85:139,2:0.0142:2,2:30.5:1:29:1:1:1.57:60:4:0.0148:0:2 +22 50705461 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50742;SOR=0;LSEQ=CCTCGTCCGCCTGGCGCGCC;RSEQ=GCCCAAAATCCAGGATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:57,114:171,2:0.0116:2,2:26:1:29:1:1:1.99:60:4:0.0118:0:1.5 0/0:132:0:0,0:47,85:132,0:0:2,0:19.6:1:28.7:1:1:0:60:32:1:0:0.9 +22 50705466 . A G 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57175;SOR=0.3518;LSEQ=TCCGCCTGGCGCGCCAGCCC;RSEQ=AAATCCAGGATCTGGGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:147:42,105:1,0:1,147:0.9932:0,2:23.8:1:31.1:1:0.29054:0:60:72.5:0.9932:0:1.1 1/1:105:103:29,74:2,0:2,103:0.981:0,2:21.2:1:29.9:1:0.08516:0:60:206:0.981:0:1.1 +22 51081636 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24085;SOR=Inf;LSEQ=GCCCATCTGTGCACTTCCTT;RSEQ=TAAAATCCAGTTTTAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:37,32:69,0:0:2,0:27.8:1:32.1:1:1:0:58.5:138:1:0:0.1 0/1:67:2:1,1:28,37:65,2:0.0299:2,2:25.5:1:28:1:1:1.32:60:4:0.0303:0:1.5 +22 51081657 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49806;SOR=0;LSEQ=TAAAATCCAGTTTTAGTAAG;RSEQ=ACCTGATCACCCTTTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:28,31:59,2:0.0328:2,2:39.5:1:29.5:1:1:1.11:60:4:0.0333:0:1 0/0:53:0:0,0:18,35:53,0:0:2,0:23:1:30.1:1:1:0:59.7:52:1:0:0.2 +3 1449822 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50237;SOR=Inf;LSEQ=AAAATCCTGACTTTTTTAAT;RSEQ=TCTTAAAATATGGAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:72,52:124,0:0:2,0:25.4:1:29.2:1:1:0:60:123:1:0:0.6 0/1:149:2:1,1:85,62:147,2:0.0134:2,2:21.5:1:30:1:1:1.368:60:4:0.0138:0:1 +3 1449841 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01111;SOR=3.07854;LSEQ=TATCTTAAAATATGGAAATT;RSEQ=TTTGCTTTCCACTTTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:7:3,4:65,61:126,7:0.0526:2,2:26.7:1:31:1:0.71404:1.41702:60:14:0.0526:0:1.9 0/1:157:23:12,11:66,68:134,23:0.1465:2,2:29.7:1:32:1:0.82503:1.12:60:46:0.1465:0:1.8 +3 1449872 . A C 218 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11907;LSEQ=ACTTTTCTATGTTAAAAATT;RSEQ=TTTCATGAAATTAAATATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:113:108:47,61:1,4:5,108:0.9558:2,2:27.4:1:32.4:1:0.39268:3.06:60:35:0.9545:0:1.1 1/0:135:97:43,54:14,24:38,97:0.7185:2,2:27.8:1:30.7:1:0.44653:1.36:60:96:0.7164:0:1.2 +3 1449979 . C A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01294;SOR=0.22572;LSEQ=ATAATTTTTATTGAAAGATA;RSEQ=ATTTATTTCTTCAGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:1,15:0,10:10,16:0.6154:0,1:18.1:1:31.9:1:1:0:60:32:0.6154:0:1 0/1:27:7:0,7:3,17:20,7:0.2593:2,0:27.9:1:31:1:0.5453:0:60:14:0.2593:0:1 +3 1808553 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04762;SOR=Inf;LSEQ=CCTTACCATATAATAATAAT;RSEQ=TCTAAGGGCTTTCTTTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:21.2:1:28.4:1:1:0:60:4:1:0:1.2 1/0:4:3:3,0:1,0:1,3:0.75:0,0:26:1:25.7:1:1:0:60:2:0.6667:0:1 +3 1808586 . A AAT 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.10865;SOR=0.21713;LSEQ=CTTTAGATCAGTGGTCAGCA;RSEQ=TTTTTTTTTTTATAAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:3,3:6,2:8,6:0.4286:2,2:20.5:1:32.1:1:0.58042:2.76:60:12:0.5:0:0.2 0/1:15:2:1,1:4,1:5,2:0.1333:2,2:33.5:1:29.3:1:1:3.1622:60:4:0.1429:0:0.5 +3 1947477 . T C 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00311;SOR=Inf;LSEQ=CATCAAGGGAATGGGCACTG;RSEQ=TCAAAAAGGAACGCCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:109,63:172,0:0:2,0:22.8:1:30.1:1:1:0:35.4:344:1:0:0.1 0/1:226:11:6,5:124,91:215,11:0.0487:2,2:26:1:31.2:1:1:1.13489:32.1:22:0.0491:0:1.2 +3 1947557 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23504;SOR=0;LSEQ=CCCAGCATGCTGTTGGCATT;RSEQ=TTGTAAACAAACAAGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:73,109:182,2:0.0109:2,2:17:1:28:1:1:1.49:34:4:0.0109:0:1 0/0:195:0:0,0:83,111:194,0:0:2,0:23.4:1:30.9:1:1:0:40.2:96:0.9948:0:0.1 +3 2001631 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04858;SOR=Inf;LSEQ=AAAATAAAGGATGTGAAAAA;RSEQ=GCTACCAATAGCTTTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:40,0:40,0:0:1,0:24.4:1:33.1:1:1:0:60:39:1:0:0.1 0/1:24:3:3,0:21,0:21,3:0.125:1,0:32.7:1:28:1:1:0:60:6:0.1304:0:1.3 +3 2001689 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20482;SOR=Inf;LSEQ=TCAGTAGCACCTGTCATTTT;RSEQ=CCTTCTGTAGTCACTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:73,28:101,0:0:2,0:21.4:1:28.3:1:1:0:59.7:100:1:0:0.1 0/1:84:2:1,1:60,22:82,2:0.0238:2,2:10.5:1:33.5:1:0.47504:2.68946:60:4:0.0238:0:1 +3 2001802 . G T 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGAAGAAAGATTCCATGC;RSEQ=TCTATTGTAGCCCCAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:137,137:274,0:0:2,0:25.9:1:30.9:1:1:0:60:53.8:1:0:0.1 0/1:278:102:47,55:89,86:175,102:0.3669:2,2:24.1:1:29.2:1:0.4573:1.21019:59.9:33:0.3613:0:1.1 +3 2001855 . G T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11626;SOR=0;LSEQ=CAGCACATAAATGGGAAATT;RSEQ=AACTTTCATTGAAGACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:3:1,2:58,124:182,3:0.0162:2,2:22:1:23:1:1:1.07:60:2:0.0112:0:1.7 0/0:193:0:0,0:71,121:192,0:0:2,0:27.4:1:30.4:1:1:0:60:31:0.9947:0:0.4 +3 2001883 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24322;SOR=0;LSEQ=ATTGAAGACTCTTGAGTAAA;RSEQ=ACAGGGAAGAATGTTAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:30,95:125,2:0.0157:2,2:29.5:1:28.5:1:0.43007:3.13:60:4:0.0163:0:1 0/0:130:0:0,0:35,95:130,0:0:2,0:22:1:30.6:1:1:0:60:64:1:0:0.3 +3 2001904 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.0787;SOR=Inf;LSEQ=ACAGGGAAGAATGTTAACCC;RSEQ=GTTGCCCATACCATGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:11,81:92,0:0:2,0:24.1:1:30.5:1:1:0:60:45:1:0:0.1 0/1:70:3:0,3:10,57:67,3:0.0429:2,0:18.7:1:30.3:1:1:0:60:6:0.0429:0:1.3 +3 2569037 . G A 54 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CTGTCACCTTAGAAGTGGTC;RSEQ=TTAAAAGCTGCCATTTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:8:1:31.7:1:1:0:24.7:6:1:0:0 1/1:5:4:3,1:1,0:1,4:0.8:0,2:9:1:27.3:1:1:0:24.5:8:0.8:0:1.3 +3 2569091 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACCAAATGAGGGAACAAT;RSEQ=TATGCTGCTGCTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:16,0:0:2,0:36.4:1:31.9:1:1:0:29.5:15:1:0:0.3 0/1:43:2:1,1:21,20:41,2:0.0465:2,2:10:0:30.5:1:1:1.04883:27.5:4:0.0476:0:2 +3 2569093 . A ATGCTGC 90 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=10.000;MSILEN=3;SSF=0.31059;SOR=0.50929;LSEQ=ACCAAATGAGGGAACAATGT;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:5,4:9,5:0.3125:2,2:39.8:1:32.1:1:1:1.18:27.6:10:0.3333:0:0 0/1:43:8:3,5:19,16:35,8:0.186:2,2:33.4:1:30:1:0.45655:1.94801:29.1:16:0.1951:0:0.3 +3 2576521 . T C 34 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07143;SOR=0;LSEQ=GTATGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTATTGTTGCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:32:0:34.5:1:1:1:21:4:0.3333:0:1.5 0/0:15:0:0,0:8,7:15,0:0:2,0:32.7:1:29.3:1:1:0:22.7:30:1:0:0.6 +3 2576692 . C G 34 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=GTCAAAGCCTTGCTTCAGCT;RSEQ=TAAAGGACCTTCTTTACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:26.5:1:34:0:1:0:30:4:0.5:0:1.5 1/0:2:1:0,1:0,1:1,1:0.5:0,0:18:0:33:0:1:0:22:2:0.5:0:2 +3 6422783 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23357;SOR=0;LSEQ=CCCCAGCCACTGGATGGATG;RSEQ=CTGACCTTGGTTATTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:77,29:106,2:0.0183:2,0:37:1:31:1:1:0:60:4:0.0187:0:1.5 0/0:116:0:0,0:88,28:116,0:0:2,0:21.9:1:30.6:1:1:0:60:115:1:0:0.8 +3 6422814 . C A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.95154;LSEQ=TTATTTGGCCTTTGATCCTG;RSEQ=ATATGTCTCTTTTGTCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:68:45,23:66,46:112,68:0.3778:2,2:23.6:1:30.5:1:0.34779:1.36:60:67:0.3807:0:1.5 1/0:207:133:89,44:44,30:74,133:0.6425:2,2:25:1:28.7:1:0.29353:1.38:60:132:0.6408:0:1.4 +3 6422825 . T C 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=TTGATCCTGCATATGTCTCT;RSEQ=TTGTCAACCAGAACAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:121,83:204,0:0:2,0:25.1:1:30.6:1:1:0:60:39.8:1:0:0.9 0/1:248:16:7,9:141,91:232,16:0.0645:2,2:30:1:31.3:1:0.19647:1.98647:60:32:0.0653:0:1.3 +3 6422885 . G C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.23781;LSEQ=TTTTCAGCCTTTTTCTACAT;RSEQ=TTTGTGTTCTCACATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:180:79,101:24,14:38,180:0.8257:2,2:26:1:32.2:1:0.03334:2.18377:60:35:0.8216:0:1.3 1/0:310:164:78,86:69,77:146,164:0.529:2,2:27.9:1:30.9:1:1:1.01:60:40:0.5246:0:1.4 +3 6422914 . G T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17634;SOR=0;LSEQ=CTCACATAAAAACGAATTTT;RSEQ=AATTGGTTCTCTATATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:75,111:186,2:0.0106:2,2:6:0:32:1:1:1.48:60:4:0.011:0:1.5 0/0:259:0:0,0:110,149:259,0:0:2,0:24.2:1:30.7:1:1:0:60:258:1:0:0.7 +3 6422931 . A G 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00155;SOR=Inf;LSEQ=TTTGAATTGGTTCTCTATAT;RSEQ=ATTTTCACCACTTACTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:60,103:163,0:0:2,0:25:1:29.7:1:1:0:60:80.5:1:0:0.6 0/1:205:12:6,6:75,118:193,12:0.0585:2,2:25.8:1:31.4:1:0.54603:1.57:60:24:0.0588:0:2 +3 6610068 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=8.52595;LSEQ=AATTTCAGGGCAACAATGTG;RSEQ=TATATTTAGTCATGACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:12:6,6:123,118:241,12:0.0474:2,2:25.1:1:32:1:1:1.04222:60:24:0.0478:0:1.6 0/1:365:109:48,61:116,140:256,109:0.2986:2,2:26.6:1:30.9:1:0.90852:1.05285:60:108:0.2975:0:1.3 +3 6610126 . G A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00049;SOR=3.61075;LSEQ=GATGAGTTGCAAAATCCTGT;RSEQ=AATTCTAATATCCTTAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:9:1,8:46,117:163,9:0.0523:2,2:31.2:1:30:1:0.4471:3.12935:60:18:0.0526:0:2.2 0/1:198:33:8,25:47,118:165,33:0.1667:2,2:26.9:1:29.5:1:0.67665:1.24333:60:32:0.1649:0:2.1 +3 6610132 . T A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50023;SOR=Inf;LSEQ=TTGCAAAATCCTGTGAATTC;RSEQ=AATATCCTTAAATCTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:42,121:163,0:0:2,0:25.3:1:29.1:1:1:0:60:162:1:0:0.2 0/1:183:2:1,1:49,132:181,2:0.0109:2,2:5:1:28:1:0.47289:2.68:60:4:0.011:0:1 +3 6610161 . T C 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04931;SOR=2.91294;LSEQ=TAAATCTCAAGAGAGAAAAA;RSEQ=ATTATTCCCTTCCTTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:5:0,5:11,78:89,5:0.0532:2,0:20.6:1:34:1:1:0:60:10:0.0543:0:2.2 0/1:92:13:3,10:14,65:79,13:0.1413:2,2:20.2:1:32.3:1:0.70165:1.39:60:26:0.1413:0:2.1 +3 9005826 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11507;SOR=Inf;LSEQ=AAAAACCCTGCTAAATCAAG;RSEQ=TACCAAGAATCCCCACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:10,28:38,0:0:2,0:27.1:1:29.7:1:1:0:60:37:1:0:0.6 0/1:38:4:1,3:13,21:34,4:0.1053:2,2:29.8:1:31.5:1:1:1.82944:60:8:0.1053:0:1.5 +3 9005863 . T G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41304;SOR=0;LSEQ=CTTTGATATGTGATCACTCT;RSEQ=GATATCTGATGTGTTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:3,24:0,0:0,27:1:0,2:23.1:1:31.4:1:1:0:60:26:1:0:1.1 1/1:19:18:4,14:0,1:1,18:0.9474:0,2:25.5:1:30.7:1:1:0:58.2:36:0.9474:0:1.2 +3 9039103 . C T 29 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCCGCTTCTCCCCACAG;RSEQ=AGCCTAGAGGGTCCTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 9040714 . A G 86 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TCTTTGCATCTGTACAGTGT;RSEQ=AATTGACTATATAGATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:27.5:1:33.5:1:1:0:60:12:1:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:5:0:31:0:1:0:60:2:0.5:0:1 +3 9040851 . C G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22586;SOR=1.90067;LSEQ=ACAGCCCAGCCCCTGAGCTA;RSEQ=AGGAGAGGTTGAGACTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:18:16,2:18,2:20,18:0.4737:2,2:17.4:1:33.3:1:1:1.12151:60:36:0.4865:0:1.9 1/0:30:19:16,3:9,2:11,19:0.6333:2,2:19.5:1:30.1:1:1:1.18:60:18:0.6207:0:1.7 +3 9040889 . G C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05263;SOR=2.05122;LSEQ=TCTCAGTAGGGGCCTGGCTG;RSEQ=AGTCACATTTTAGGAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:36:28,8:33,12:45,36:0.4444:2,2:26.1:1:32.6:1:0.79644:1.27:60:72:0.4444:0:2.5 1/0:53:33:25,8:15,5:20,33:0.6226:2,2:20.6:1:31.5:1:1:1.04:60:66:0.6226:0:2.6 +3 9040951 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07367;SOR=1.50039;LSEQ=AGTGGAGGGATTGGAGGGGA;RSEQ=AGGCTGGAGGCAGCAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:88:47,41:45,32:77,88:0.5301:2,2:28.8:1:30.4:1:0.53375:1.2252:60:87:0.537:0:2.9 1/0:159:100:62,38:31,28:59,100:0.6289:2,2:27.5:1:29.3:1:0.24943:1.47:59.8:99:0.6266:0:3 +3 9040955 . C A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04571;SOR=1.59316;LSEQ=GAGGGATTGGAGGGGAGAGG;RSEQ=TGGAGGCAGCAGTGGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:169:88:45,43:46,35:81,88:0.5207:2,2:29.3:1:30.7:1:0.53715:1.25417:60:176:0.5269:0:2.9 1/0:164:104:64,40:31,29:60,104:0.6341:2,2:27.3:1:28.5:1:0.25168:1.49:59.8:51:0.6296:0:3 +3 9040994 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01806;SOR=1.69429;LSEQ=AGAGACGGCTACACTGGTGC;RSEQ=GCCTCTGAACTAGCATGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:173:99:40,59:33,40:73,99:0.5723:2,2:24.8:1:31.3:1:0.53703:1.21547:60:98:0.5731:0:2.3 1/0:206:143:72,71:28,35:63,143:0.6942:2,2:24.3:1:29.7:1:0.45323:1.27:60:70.5:0.6912:0:2.1 +3 9040999 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50171;SOR=Inf;LSEQ=CGGCTACACTGGTGCGGCCT;RSEQ=TGAACTAGCATGGGCTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:72,99:171,0:0:2,0:25:1:32.4:1:1:0:60:56:1:0:1.3 0/1:200:2:1,1:96,102:198,2:0.01:2,2:6:0:31:1:1:1.06:60:4:0.0103:0:2.5 +3 9041094 . G C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08914;SOR=2.25824;LSEQ=TCTGAAGGTTGGACATTTAT;RSEQ=CTTCTCTACCCATCAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:26:7,19:5,17:22,26:0.5417:2,2:23:1:30.6:1:1:1.25:60:25:0.5319:0:1.1 1/0:48:35:5,30:2,10:12,35:0.7292:2,2:23.5:1:31.1:1:1:1.19517:60:70:0.7292:0:1.1 +3 9065474 . T A 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTCCTGGGGCTCCCTGG;RSEQ=TCTAAGCACCCGAGATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:28.5:1:1:0:60:4:1:0:1 +3 9066519 . T C 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18903;LSEQ=TAGCATCATTTACAGATTCA;RSEQ=ATGAATATTCCAGAGCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:26.2:1:29.6:1:1:0:60:10:0.3846:0:1 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:27.7:1:32:1:1:0:60:6:0.4286:0:1.7 +3 9066587 . C G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCAGTCCCCTGGAGAAA;RSEQ=CACCCAAAAGCAGTAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:50:39,11:0,0:0,50:1:0,2:25:1:31.9:1:1:0:60:24:1:0:1.2 1/1:63:62:49,13:0,0:0,62:0.9841:0,2:24.1:1:31.5:1:1:0:60:124:0.9841:0:1.1 +3 9066645 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.18871;SOR=0;LSEQ=TCATAGTAGTAGTAACAGTG;RSEQ=TGGTGGTGCTGGTGCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:69,57:126,2:0.0156:2,2:24.5:1:31.5:1:1:1.20871:60:4:0.016:0:1.5 0/0:166:0:0,0:92,74:166,0:0:2,0:26.1:1:30.8:1:1:0:59.4:332:1:0:0.4 +3 9066678 . G T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01762;SOR=Inf;LSEQ=TGCTGGTGCTGGTGCTGGTG;RSEQ=TAGGTAAATGTTGAACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:56,78:134,0:0:2,0:25.6:1:31.8:1:1:0:59.7:268:1:0:0.3 0/1:163:7:2,5:67,89:156,7:0.0429:2,2:29:1:27.1:1:0.69985:1.8752:60:6:0.038:0:1.3 +3 9066679 . TAGGT AGGA 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50384;SOR=Inf;LSEQ=GCTGGTGCTGGTGCTGGTGG;RSEQ=AAATGTTGAACAGTTAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:55,77:132,0:0:2,0:25.7:1:28.6:1:1:0:59.7:43:1:0:0.2 0/1:163:2:1,1:68,93:161,2:0.0123:2,2:9.5:1:27.7:1:1:1.36:60:4:0.0125:0.0061:0 +3 9066709 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19359;SOR=0;LSEQ=TTGAACAGTTAACTCTTTGG;RSEQ=AGGTAACAATTAGAACTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:31,50:81,2:0.0241:2,2:17.5:1:27.5:1:1:1.60:60:4:0.0244:0:1.5 0/0:105:0:0,0:36,69:105,0:0:2,0:24.8:1:30.8:1:1:0:60:34:1:0:0.1 +3 10183241 . C CAA 62 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAAAAAACACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:1,0:1,4:0.5714:0,0:13:1:31.1:1:1:0:60:8:0.5714:0.4286:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 10183274 . C T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACACCAAACCTTAGAGGGG;RSEQ=GAAAAAAAATTTTATAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:13,0:0,0:0,13:0.9286:0,1:21.5:1:29.1:1:1:0:60:12:1:0:2.3 1/1:2:2:2,0:0,0:0,2:1:0,0:9:1:29.5:1:1:0:60:4:1:0:2 +3 10183337 . G A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.7955;LSEQ=AGCCTCGCCTCCGTTACAAC;RSEQ=GCCTACGGTGCTGGAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:19,0:5,0:5,19:0.7917:0,1:20.5:1:29.2:1:1:0:60:18:0.7826:0:1.7 1/0:8:6:6,0:2,0:2,6:0.75:0,0:30.3:1:30.3:1:1:0:60:12:0.75:0:1.3 +3 10183832 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2579;SOR=Inf;LSEQ=AGCCGCAGCCCTACCCAACG;RSEQ=TGCCGCCTGGCACGGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:88,143:231,0:0:2,0:25.6:1:32.4:1:1:0:60:37.5:1:0:0.1 0/1:289:3:2,1:125,161:286,3:0.0104:2,2:27.7:1:28.3:1:0.584:2.57:60:6:0.0107:0:1.3 +3 10183851 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13238;SOR=Inf;LSEQ=GCTGCCGCCTGGCACGGGCC;RSEQ=CCGCATCCACAGCTACCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:62,123:185,0:0:2,0:27.1:1:31.5:1:1:0:60:91.5:1:0:0.1 0/1:231:4:2,2:86,141:227,4:0.0173:2,2:17:1:27.8:1:0.63669:1.64:60:8:0.0177:0:1.3 +3 10183867 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50312;SOR=Inf;LSEQ=GGCCGCCGCATCCACAGCTA;RSEQ=CGAGGTACGGGCCCGGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:48,114:162,0:0:2,0:24.9:1:31.7:1:1:0:60:161:1:0:0.1 0/1:196:2:1,1:67,126:193,2:0.0102:2,2:18:0:31:1:1:1.87:44:4:0.0103:0:1.5 +3 10183876 . G C 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03011;SOR=Inf;LSEQ=ATCCACAGCTACCGAGGTAC;RSEQ=GGCCCGGCGCTTAGGCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:36,108:144,0:0:2,0:23.4:1:30.9:1:1:0:60:47:1:0:0.1 0/1:153:6:2,4:45,102:147,6:0.0392:2,2:21.2:1:27.3:1:1:1.13:60:5:0.0331:0:2.7 +3 10185535 . G T 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34919;SOR=3.35581;LSEQ=GGAGGGGAAAGACTGCTGTC;RSEQ=AGGAAGCAGTTAGGTAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:1,0:226,51:277,1:0.0036:2,0:2:0:31:0:1:0:60:2:0.0036:0:1 0/1:251:3:1,2:198,50:248,3:0.012:2,2:23.3:1:22.7:1:0.10982:7.82993:60:2:0.0081:0:2 +3 10185803 . A C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1238;SOR=Inf;LSEQ=GCTCCTATTTTATATAGGAA;RSEQ=TTGTATGAATTTTGTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:0,106:106,0:0:1,0:21.9:1:32:1:1:0:60:212:1:0:0.1 0/1:118:4:0,4:1,113:114,4:0.0339:1,0:29.5:1:31.8:1:1:0:60:8:0.0339:0:1 +3 10187634 . G T 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCAGAAAGGGCATGGGATT;RSEQ=AGAGCTTTAAGTACGCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:44:0:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 10188010 . AC A 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.11084;SOR=0;LSEQ=TGGGACTACAGGCGCTCGCC;RSEQ=CACACCTGGCTAATTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:19,0:0,0:0,19:1:0,1:20.7:1:32.9:1:1:0:44.4:38:1:0.3684:0.1 1/1:10:8:8,0:2,0:2,8:0.8:0,0:19.8:1:32.1:1:1:0:40.9:16:0.8:0.2:0.1 +3 10188106 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20284;SOR=Inf;LSEQ=CTGACCTCATGATCCGCCTG;RSEQ=CTCGGCCTCCCAAAGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:104,4:108,0:0:1,0:20.8:1:32.3:1:1:0:42.8:107:1:0:0 0/1:89:2:1,1:81,6:87,2:0.0225:2,2:16:1:27:1:0.15194:12.57557:52.5:4:0.023:0:1 +3 10188360 . G T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25087;SOR=Inf;LSEQ=TAAAAAGATAAGGTTGTTGT;RSEQ=GTAAGTACAGGATAGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:52,195:247,0:0:2,0:22:1:31:1:1:0:60:48.4:1:0:0.3 0/1:276:3:1,2:65,208:273,3:0.0109:2,2:27.3:1:25:1:0.56103:1.60:60:2:0.0074:0:1.7 +3 10188428 . T G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00101;SOR=0;LSEQ=TTTGCCTGATGTCAGGCACG;RSEQ=TATCCAATCTTTTTGTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:69:1,68:0,0:0,69:1:0,1:22.7:1:32.1:1:1:0:59.8:33.5:1:0:1.1 1/1:64:55:2,53:0,9:9,55:0.8594:0,1:25.7:1:31.3:1:1:0:60:54:0.8571:0:1.3 +3 10191219 . C G 96 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTGCCAGTGTCGCTTCATC;RSEQ=ACATTCAGTTAGTTAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:9,0:2,0:2,9:0.8182:0,0:18.8:1:30.4:1:1:0:60:18:0.8182:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 10191380 . G C 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50092;SOR=0;LSEQ=ACCTAAAGTGAGATCCATCA;RSEQ=TAGTACAGGTAGTTGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:92,9:101,2:0.0194:2,2:5.5:1:30:1:0.18561:9.75023:60:4:0.0198:0:1.5 0/0:87:0:0,0:76,11:87,0:0:2,0:23.2:1:31.6:1:1:0:60:86:1:0:0.1 +3 10191397 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49913;SOR=Inf;LSEQ=TCAGTAGTACAGGTAGTTGT;RSEQ=GGCAAAGCCTCTTGTTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:114,21:135,0:0:2,0:24.5:1:30.8:1:1:0:60:44:1:0:0.1 0/1:147:2:1,1:116,29:145,2:0.0136:2,2:27:1:30.5:1:0.36763:3.94968:60:4:0.0136:0:1 +3 10191678 . A C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49883;SOR=Inf;LSEQ=GTTGAAACTTACACTGTTTC;RSEQ=TCTCAGCTTTTGATGGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:44,139:183,0:0:2,0:23.3:1:31:1:1:0:60:366:1:0:0.1 0/1:190:2:1,1:42,146:188,2:0.0105:2,2:25.5:1:30.5:1:0.40234:3.45:60:4:0.0106:0:1 +3 10192672 . G A 49 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=ACTGCAACCTCTGCCTCCTG;RSEQ=GTTCACGTAATCCTCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:22.3:1:31.3:1:1:0:56:6:0.4286:0:2.7 1/0:4:2:1,1:2,0:2,2:0.5:0,2:18:1:22.5:1:1:0:52.5:1:0.3333:0:1.5 +3 10192709 . C T 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23537;LSEQ=TGAGTAGCTGGGATTACAGG;RSEQ=GCCTGCCACCACGCTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:24.4:1:30.8:1:1:0:46.2:10:0.5:0:2.4 1/0:9:5:4,1:4,0:4,5:0.5556:0,2:21:1:27.8:1:1:0:38:10:0.5556:0:2 +3 10192762 . T C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42553;SOR=0;LSEQ=TTAGTAGAGACAGTGTTTCG;RSEQ=CATGTTGGCCAGGCTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:27,0:0,0:0,27:1:0,1:19.2:1:31.8:1:1:0:29.6:26:1:0:1.2 1/1:20:19:19,0:1,0:1,19:0.95:0,1:21.3:1:32.5:1:1:0:29.1:38:0.95:0:1.2 +3 10192866 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25673;SOR=Inf;LSEQ=GTGGGCCACCGTGCCTGGCT;RSEQ=ATTCAGCATTTTTTATCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:183,44:227,0:0:2,0:23.2:1:32.3:1:1:0:59.4:55.75:1:0:0.1 0/1:280:3:1,2:215,62:277,3:0.0107:2,2:8:1:25.3:1:0.13182:6.87292:60:6:0.0108:0:1.3 +3 10193056 . A AT 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58285;SOR=0.8049;LSEQ=CAGTTTTTTGTAACTAATAG;RSEQ=TTTTTTTTTCCACTTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:15:4,11:96,247:343,15:0.0418:2,2:23.5:1:30.8:1:1:1.06863:59.3:30:0.0425:0.0028:0.3 0/1:472:16:5,11:135,321:456,16:0.0339:2,2:28.1:1:29.2:1:1:1.08:60:32:0.0343:0.0042:0.2 +3 12027806 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17845;SOR=Inf;LSEQ=TTGGCTTGAGGACTTCCCAG;RSEQ=AACATTGTCAGGCCTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:51,2:53,0:0:1,0:23.7:1:32.4:1:1:0:59.3:52:1:0:0.1 0/1:40:2:2,0:38,0:38,2:0.05:1,0:25.5:1:30.5:1:1:0:60:4:0.05:0:1.5 +3 12027851 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22344;SOR=0;LSEQ=CACATGGTAGTTCAGGATGC;RSEQ=CCTTCTCACTCCCTTTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:102,22:124,2:0.0159:2,2:25.5:1:30:1:0.33295:4.55665:60:4:0.0161:0:1 0/0:140:0:0,0:110,30:140,0:0:2,0:20:1:29.5:1:1:0:60:45.667:1:0:0.2 +3 12027856 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50169;SOR=Inf;LSEQ=GGTAGTTCAGGATGCTCCTT;RSEQ=TCACTCCCTTTCAGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:110,31:141,0:0:2,0:22.5:1:32:1:1:0:59.8:46:1:0:0.2 0/1:166:2:1,1:119,45:164,2:0.012:2,2:28:1:29.5:1:0.47864:2.62651:60:4:0.012:0:1.5 +3 12028100 . A T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55045;SOR=0;LSEQ=AATAGCATTTTGCTGAGGAC;RSEQ=CATTTCCCTCACACTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:0,4:0,18:18,4:0.1818:1,0:23:1:30.3:1:1:0:60:8:0.1818:0:1 0/0:8:0:0,0:0,8:8,0:0:0,0:30.1:1:28.5:1:1:0:60:7:1:0:0 +3 12030034 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGTTCAGACCAGAGAGA;RSEQ=AGGATCGATTGGGGTAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 12625968 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50592;SOR=Inf;LSEQ=CAGAAAAGTGGTGCCTGCTG;RSEQ=CTTCTCCTCCTCCCCTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:113,23:136,0:0:2,0:23.7:1:31.1:1:1:0:59.6:26.2:1:0:0.1 0/1:174:2:1,1:126,46:172,2:0.0115:2,2:19:1:26:1:0.46841:2.72057:60:4:0.012:0:1 +3 12626194 . C A 39 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62343;SOR=2.95412;LSEQ=AATGCTCTCATTAGCTGTGT;RSEQ=TCAAAGACACAGGATGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:1:1,0:105,119:224,1:0.0044:2,0:1:0:25:0:0.47111:0:60:2:0.0045:0:1 0/1:230:3:3,0:101,126:227,3:0.013:2,0:7.7:1:25:1:0.09099:0:60:6:0.0132:0:1 +3 12626516 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.75657;LSEQ=CAGCTGAGCTAATGGGGGGT;RSEQ=AATGAACAACAGATAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:27:16,11:194,150:344,27:0.0728:2,2:21.7:1:29.7:1:0.84205:1.12:60:54:0.0732:0:1 0/1:385:120:60,60:131,134:265,120:0.3117:2,2:25.4:1:28.8:1:1:1.02:60:240:0.3133:0:1.1 +3 12627100 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24389;SOR=Inf;LSEQ=TCGGGGAAATGTACAGAAAC;RSEQ=CTTTAAGTTTGCACATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:92,11:103,0:0:2,0:22.8:1:29.9:1:1:0:60:102:1:0:0 0/1:101:2:1,1:89,10:99,2:0.0198:2,2:6.5:1:27:1:0.20693:8.53143:60:4:0.02:0:1.5 +3 12629181 . G A 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=AAAATAAGTTTGAGGGGCAT;RSEQ=AGTAGAAAGCAGTTTTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:62,131:193,0:0:2,0:23.1:1:32:1:1:0:60:63.333:1:0:0.1 0/1:349:16:6,10:127,206:333,16:0.0458:2,2:23.1:1:29.4:1:1:1.02743:60:32:0.0461:0:1.1 +3 12629207 . C A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29836;SOR=Inf;LSEQ=AAAGCAGTTTTAAACTACAG;RSEQ=TAAGAAGTAAAGCCACTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:29,82:111,0:0:2,0:21.7:1:32.6:1:1:0:60:110:1:0:0.1 0/1:189:3:1,2:56,130:186,3:0.0159:2,2:15:1:31.3:1:1:1.16:60:6:0.0163:0:1.3 +3 12631981 . A G 24 d5;v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATAGGCATGTGCCACCAG;RSEQ=CTTGGTTCATTCTTGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28:1:33:1:1:0:53.5:4:1:0:2 1/1:2:2:2,0:0,0:0,2:1:0,0:26:1:24:1:1:0:47.5:1:1:0:3 +3 12631983 . T C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGGCATGTGCCACCAGAC;RSEQ=TGGTTCATTCTTGTATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:30:1:32:1:1:0:53.5:4:1:0:2 1/1:2:2:2,0:0,0:0,2:1:0,0:28:1:31:1:1:0:47.5:4:1:0:3 +3 12632239 . C T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24921;SOR=0;LSEQ=GCTTTTCCTGATCCTGGTTC;RSEQ=AATTTAGGGACAAATTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:168,17:185,3:0.0159:2,2:12.7:1:22:1:0.02741:19.07513:60:2:0.011:0:1.3 0/0:174:0:0,0:141,32:173,0:0:2,0:24.1:1:30.4:1:1:0:59.8:172:1:0:0.1 +3 12632652 . G C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01204;SOR=Inf;LSEQ=CGGGTGGCATTCTGAGCAAA;RSEQ=AGAAGCCCACCATTAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:1,18:19,0:0:1,0:26.2:1:31.7:1:1:0:60:38:1:0:0 0/1:11:4:0,4:1,6:7,4:0.3636:2,0:15.5:1:33:0:1:0:60:8:0.3636:0:1 +3 12633083 . A G 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=GGAGGAGCATCCAACCACAG;RSEQ=AACTCCACAGTGAGTCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:80,0:80,0:0:1,0:23.2:1:30.5:1:1:0:60:160:1:0:0.1 0/1:79:12:12,0:64,3:67,12:0.1519:1,0:22.3:1:29.5:1:1:0:60:11:0.141:0:1 +3 12633168 . A G 154 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=8;SSF=0;SOR=32.06024;LSEQ=GTCCTTGTACTCCCCACTCC;RSEQ=GCACTCCAGAGGGACTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:1:0,1:249,113:362,1:0.0027:2,0:16:0:15:0:0.31405:0:60:0:0:0:3 0/1:455:37:26,11:283,133:416,37:0.0813:2,2:23.6:1:29.7:1:0.85546:1.11:60:74:0.0833:0:1.2 +3 12633378 . A G 28 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50043;SOR=Inf;LSEQ=TGAGGAAGATACAGTGAATC;RSEQ=TTTATCCAAAGAATCACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:11,123:134,0:0:2,0:27.4:1:30.6:1:1:0:59.5:12.4:1:0:0.3 0/1:154:2:1,1:12,140:152,2:0.013:2,2:6:0:28.5:1:0.16221:11.25:60:4:0.0132:0:1 +3 12641347 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25948;SOR=Inf;LSEQ=TTATTATACTCCATGCAATG;RSEQ=TAATAATCTTTTGATAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:33,184:217,0:0:2,0:21.9:1:32:1:1:0:60:71.333:0.9953:0:0.1 0/1:278:3:1,2:58,216:274,3:0.0108:2,2:11.3:1:27.3:1:0.51399:1.86:60:6:0.0108:0:1 +3 12641518 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=37.66665;LSEQ=AGTGTGCCAAAAATGACAGT;RSEQ=ACATTTATAATCTCCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:3:3,0:44,15:59,3:0.0484:2,0:42.3:1:33:1:1:0:60:6:0.0484:0:1 1/0:51:34:32,2:17,0:17,34:0.6667:1,2:27.7:1:31.6:1:0.54667:0:60:16:0.6667:0:1.1 +3 12641996 . G T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23101;SOR=Inf;LSEQ=AAAAAAGAGGAGGAGGATGT;RSEQ=CAAGAACAAAATAGATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:7,107:114,0:0:2,0:23.8:1:32.7:1:1:0:60:113:1:0:0.1 0/1:106:2:1,1:18,86:104,2:0.0189:2,2:6:0:31.5:1:0.32776:4.68:60:4:0.0189:0:1.5 +3 12645626 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25653;SOR=Inf;LSEQ=ACATTACCACCCCCAAGGTG;RSEQ=CCTATTACCTCAATCATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:186,59:245,0:0:2,0:23.8:1:31.9:1:1:0:60:48:1:0:0.1 0/1:301:3:1,2:214,84:298,3:0.01:2,2:26.7:1:26.7:1:0.19737:5.06325:60:6:0.01:0:1 +3 12645868 . G T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50422;SOR=Inf;LSEQ=TCAAGTACATATTTGACTAA;RSEQ=TAAGATGCTTAAGGGCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:1,106:107,0:0:1,0:22.1:1:32.8:1:1:0:60:106:1:0:0.1 0/1:134:2:1,1:14,118:132,2:0.0149:2,2:8:0:27.5:1:0.2121:8.18:60:4:0.015:0:1 +3 12647547 . T TG 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=99.86797;LSEQ=AAACAGAAATTTCTACCTTT;RSEQ=CTGTACCACCAGTATCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:1:1,0:41,0:41,1:0.0238:1,0:12:0:30:0:1:0:60:2:0.025:0:0 1/0:33:24:24,0:8,1:9,24:0.7273:2,1:19.5:1:31.7:1:0.27273:0:60:48:0.7273:0.1818:0.1 +3 12650482 . T A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGATGACAAAAGACAAC;RSEQ=TCATTTCTTGGCCTCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:94:94:17,77:0,0:0,94:1:0,2:22.9:1:30.6:1:1:0:60:30.333:1:0:1.1 1/1:99:99:16,83:0,0:0,99:1:0,2:20.3:1:30.3:1:1:0:60:98:1:0:1.1 +3 12650635 . CTA C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.94313;LSEQ=AAGAACTTTAAACAATCCAA;RSEQ=TATATATATATACATACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:8:5,3:79,9:88,8:0.0825:2,2:26:1:33.6:1:0.05902:5.1239:60:16:0.0833:0:0 0/1:64:5:5,0:54,5:59,5:0.0781:2,0:24.4:1:32.1:1:1:0:60:10:0.0794:0.0156:0 +3 12650677 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62218;SOR=2.02698;LSEQ=ATATTACCTGAGAAATCTCT;RSEQ=TTATGCCTGGCAAAGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:0,1:163,37:200,1:0.005:2,0:1:0:25:0:0.18905:0:60:2:0.0051:0:1 0/1:199:2:2,0:155,42:197,2:0.0101:2,0:24.5:1:29:1:1:0:60:4:0.0102:0:1 +3 12650688 . C T 53 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21822;SOR=4.669;LSEQ=GAAATCTCTGTTATGCCTGG;RSEQ=AAAGCCCTCAACATGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:1:0,1:180,55:235,1:0.0042:2,0:1:0:26:0:0.23729:0:60:2:0.0043:0:1 0/1:256:5:1,4:182,69:251,5:0.0195:2,2:17:1:23:1:0.02431:10.44236:60:4:0.016:0:1 +3 12653204 . G GA 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGACTCCACCTCAAAAA;RSEQ=AAAAAAAAATTACAGGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:25.5:1:31.5:1:1:0:60:4:0.5:0:0.5 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:26:0:1:0:41:2:1:0:1 +3 12653370 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50074;SOR=Inf;LSEQ=ATTCTATAGGAAGCTAGTAC;RSEQ=ATTTAATACAAACATAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:120,11:131,0:0:2,0:23.1:1:30.9:1:1:0:60:130:1:0:0.1 0/1:151:2:1,1:135,14:149,2:0.0132:2,2:16.5:1:28:1:0.1894:9.35033:60:4:0.0132:0:1 +3 12653652 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49855;SOR=Inf;LSEQ=AAATGCACCAGTCTGTATTG;RSEQ=TTGTGATGGCCCACGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:13,137:150,0:0:2,0:22.4:1:33.5:1:1:0:60:300:1:0:0 0/1:156:2:1,1:7,147:154,2:0.0128:1,2:29.5:1:28:1:0.10025:19.71:60:4:0.0129:0:1 +3 12659494 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGAAAAAATAAACTAC;RSEQ=CAGAACTAAGTGGCTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 12659889 . GA G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.73358;SOR=0.66851;LSEQ=AAAAAATAAATCTGCAGTTA;RSEQ=AAAAAAAAAATAAAGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:6,0:75,0:75,6:0.0732:1,0:25.2:1:33.8:1:1:0:60:12:0.0741:0.0122:0.2 0/1:60:3:3,0:56,1:57,3:0.05:1,0:36:1:33:1:1:0:60:6:0.05:0:0 +3 12660291 . C T 192 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACTCTAGAACAAAAGTATT;RSEQ=AACCCAAGAACACAATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:110:110:9,101:0,0:0,110:1:0,2:23.9:1:28.4:1:1:0:59.9:109:1:0:1.1 1/0:115:86:9,77:3,26:29,86:0.7478:2,2:24.1:1:27.6:1:1:1.01:60:42:0.7434:0:1.1 +3 12955982 . G A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.99229;LSEQ=GAAAATGTGGCCCAGCCTGG;RSEQ=GTGCTTAGGTTGCAAAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:206:104,102:114,117:231,206:0.4714:2,2:28.6:1:31.1:1:0.84823:1.05:60:67.667:0.4743:0:1.1 1/0:459:334:161,173:67,58:125,334:0.7277:2,2:26.9:1:29.3:1:0.34544:1.24068:60:82.5:0.7269:0:1.2 +3 13333548 . G A 31 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGAAAGTTTTTAATTGACA;RSEQ=GGAAATTTAGTTATTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:35:1:31:1:1:0:60:4:0.6667:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:26:0:14:0:1:0:60:0:0:0:1 +3 13333690 . C A 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.66927;SOR=0.51536;LSEQ=ATTAACAACATATCCACACA;RSEQ=ATATAACTTACAAACAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:7,0:7,0:7,7:0.5:0,0:31.3:1:30.9:1:1:0:60:14:0.5:0:1 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:30.7:1:26.3:1:1:0:60:6:0.3333:0:1 +3 13333844 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52609;SOR=Inf;LSEQ=ATCATTTATCATTTGACAAT;RSEQ=CCTCCCATACAATTTACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:38,42:80,0:0:2,0:28.3:1:32:1:1:0:59.8:79:1:0:0.1 0/1:130:2:1,1:59,69:128,2:0.0154:2,2:28:1:26.5:1:1:1.17:60:4:0.0157:0:1 +3 13333861 . C T 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=AATGCCTCCCATACAATTTA;RSEQ=CAAACAATTTAAATCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:29,41:70,0:0:2,0:25.2:1:31.5:1:1:0:59.8:69:0.9857:0:0.1 0/1:118:19:8,11:41,58:99,19:0.161:2,2:22.7:1:28.3:1:1:1.03:60:38:0.161:0:1.2 +3 13333862 . C A 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13886;SOR=0;LSEQ=ATGCCTCCCATACAATTTAC;RSEQ=AAACAATTTAAATCATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:28,40:68,2:0.0286:2,2:7:0:32:0:1:1.42:60:4:0.0286:0:1 0/0:117:0:0,0:48,69:117,0:0:2,0:23.6:1:30.7:1:1:0:59.9:234:1:0:0.3 +3 13334021 . A G 72 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63248;LSEQ=CACTTGCCAGTGTAAGCTCC;RSEQ=TGTGTGTTATACACAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:30.8:1:31.2:1:1:0:60:10:0.625:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:12:0:33:0:1:0:60:2:0.5:0:1 +3 14386870 . GA G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50181;SOR=0;LSEQ=GAAACCCTCCGAGGAGCTCT;RSEQ=AAGAGCAGCGGGTGCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:105,6:111,2:0.0177:2,2:21:1:30.5:1:0.12058:16.27862:60:4:0.0177:0:1.5 0/0:94:0:0,0:82,12:94,0:0:2,0:22.7:1:28.7:1:1:0:60:188:1:0:0.1 +3 14387023 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11306;SOR=Inf;LSEQ=TTCCACGAACTCAGACTCAG;RSEQ=TGGCTCTGGGTTGGGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:37,167:204,0:0:2,0:25.6:1:33.1:1:1:0:60:203:1:0:0.1 0/1:192:3:1,2:41,148:189,3:0.0156:2,2:18.7:1:30.7:1:0.52527:1.80:60:6:0.0159:0:1 +3 14387154 . T C 143 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07407;SOR=0;LSEQ=CATTTCTGTTGTTGGGACTT;RSEQ=TCCTGATGCCCTTTAGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:0,20:1:0,1:25.6:1:33.1:1:1:0:60:40:1:0:1.2 1/0:8:6:1,5:0,2:2,6:0.75:0,2:14.8:1:31.7:1:1:0:59.2:12:0.75:0:1.3 +3 14387169 . A AG 115 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=7e-04;SOR=0;LSEQ=GACTTTTCCTGATGCCCTTT;RSEQ=GTAGCCGAGCTGGCTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:0,12:1:0,0:27.1:1:32.3:1:1:0:60:24:1:0.0833:1.3 0/1:6:1:0,1:1,4:5,1:0.1667:2,0:36:0:33:0:1:0:60:2:0.1667:0:0 +3 14387203 . T C 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAAGCCAAGAACCTGAC;RSEQ=GTATTCAGCCTCCAACACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:11:1:29.5:1:1:0:60:4:0.6667:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:30:0:1:0:60:2:1:0:0 +3 16403766 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00684;SOR=0.70425;LSEQ=CACTCCAACTTCTTGTTTCC;RSEQ=ATCCTGAGAGTCTGTTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:453:259:117,142:91,102:193,259:0.5717:2,2:27:1:29.9:1:0.70331:1.0826:59.9:518:0.573:0:1.1 0/1:516:250:107,143:134,131:265,250:0.4845:2,2:26.8:1:28.6:1:0.09312:1.3662:60:500:0.4883:0:1.1 +3 16403839 . TTCCTCCCAAGTGCTTATTCCATGGCCTCCTAAGAGACATGTTTCATAGGTTATCAGGGAAAAACA GAGAACTATCTTATGTTGGGATAATATCAGGATAAG 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25629;SOR=Inf;LSEQ=TCATCTGCTTTGCTGAAATG;RSEQ=GCTGCTCTGCAGCTAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:29,131:160,0:0:2,0:25.4:1:30.6:1:1:0:60:79:0.9937:0:0.4 0/1:199:3:0,3:49,147:196,3:0.0151:2,0:22:1:30.5:1:1:0:60:6:0.0152:0.0151:0.3 +3 16403843 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.2071;SOR=0;LSEQ=CTGCTTTGCTGAAATGTTCC;RSEQ=CCCAAGTGCTTATTCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:24,128:152,2:0.0129:2,2:20:1:31:1:0.29921:5.25:60:4:0.0132:0:1 0/0:185:0:0,0:42,143:185,0:0:2,0:22.5:1:28.7:1:1:0:60:184:1:0:0.3 +3 16770096 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.15695;LSEQ=TTAGTTAGTGCAGGAGCCCA;RSEQ=ACTGGCACCCAGGGACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:181:87,94:115,109:224,181:0.4447:2,2:26.5:1:29.4:1:0.54918:1.13956:60:59.333:0.4417:0:1.1 1/0:393:249:122,127:72,71:143,249:0.6336:2,2:23.9:1:28.6:1:0.83408:1.05547:60:248:0.6343:0:1.1 +3 16770289 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00454;SOR=Inf;LSEQ=GTTCCAAGATTCTTTTTGCT;RSEQ=ATTTTATCATGGTGCCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:1,26:27,0:0:1,0:25.6:1:32.9:1:1:0:60:54:1:0:0 0/1:16:5:0,5:1,10:11,5:0.3125:2,0:32.6:1:28.2:1:1:0:60:10:0.3125:0:1 +3 16770360 . CG C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGGGTATACAGATCTAA;RSEQ=TTGTGTCTCAGGGGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:1,8:9,3:0.25:2,2:24:1:33.3:1:0.45455:3.46:60:6:0.25:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:15.5:1:32:1:1:0:60:4:1:0:1 +3 16770398 . C A 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACCTTGTTACTCTTGA;RSEQ=ATTTGGACCAGATATTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:1,7:8,2:0.2:2,2:43:1:30:1:0.37778:5.29:60:4:0.2:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 16771147 . A G 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.43328;LSEQ=GATAATCAGATATTGAAGAC;RSEQ=GAGCGTTCTGGCTAAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:36.5:1:32:0:1:0:60:4:0.4:0:2 1/0:4:2:2,0:1,1:2,2:0.5:2,0:35.5:1:30.5:1:1:0:60:4:0.5:0:2 +3 16771177 . T G 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GGCTAAACTTACTAAGCAGG;RSEQ=CCCTTTGCTAAAGCTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:3,1:3,1:4,4:0.5:2,2:20:1:32:1:1:1:60:8:0.5:0:2 1/0:8:4:2,2:3,1:4,4:0.5:2,2:26.8:1:30:1:1:2.60168:60:8:0.5:0:1.5 +3 16771252 . G C 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06993;SOR=0;LSEQ=GGTCCAGAATCCTGAGTAAA;RSEQ=TTTGGCCAAGAGAAGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,2:3,4:0.5714:2,2:20.5:1:33.3:1:1:1.41418:60:8:0.5714:0:1.8 0/0:6:0:0,0:2,4:6,0:0:2,0:23.3:1:31.5:1:1:0:60:12:1:0:0.3 +3 17744103 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49752;SOR=Inf;LSEQ=TCCCCATCAAATGAAATTGA;RSEQ=AGGACAATCATTAGGCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:53,22:75,0:0:2,0:24:1:29.6:1:1:0:60:36.5:1:0:0 0/1:81:2:1,1:60,19:79,2:0.0247:2,2:25.5:1:30.5:1:0.43519:3.10369:60:4:0.0247:0:1 +3 17744147 . G T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51129;SOR=Inf;LSEQ=GTAGATAAACTAAACGAAAT;RSEQ=ATGCATTAACTTATTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:65,49:114,0:0:2,0:26.3:1:32.3:1:1:0:60:56:1:0:0.4 0/1:158:2:1,1:93,63:156,2:0.0127:2,2:23:0:28:1:1:1.47243:60:4:0.0127:0:1.5 +3 17744159 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5061;SOR=Inf;LSEQ=AACGAAATGATGCATTAACT;RSEQ=ATTTGATTCATTGTCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:71,63:134,0:0:2,0:23.8:1:29.5:1:1:0:60:66:1:0:0.5 0/1:172:2:1,1:98,71:169,2:0.0116:2,2:34:1:32.5:1:1:1.37762:60:4:0.0118:0:1 +3 17744180 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51687;SOR=Inf;LSEQ=ATTTGATTCATTGTCATCAA;RSEQ=ATGAACGAGATTGATGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:63,70:133,0:0:2,0:25.3:1:29.6:1:1:0:60:266:1:0:0.7 0/1:196:2:1,1:98,96:194,2:0.0102:2,2:22.5:1:31:1:1:1.02073:60:4:0.0103:0:2 +3 17744193 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.51164;SOR=Inf;LSEQ=TCATCAATATGAACGAGATT;RSEQ=ATGAACAAAATTTAGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:62,75:137,0:0:2,0:24.1:1:32.4:1:1:0:60:274:1:0:0.8 0/1:190:2:1,1:91,96:187,2:0.0105:2,2:34.5:1:30:0:1:1.05:60:4:0.0106:0:1 +3 17744199 . C T 44 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.26518;SOR=Inf;LSEQ=ATATGAACGAGATTGATGAA;RSEQ=AAAATTTAGCAAGATTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:60,70:130,0:0:2,0:25.3:1:32.3:1:1:0:60:129:1:0:0.9 0/1:177:3:1,2:80,94:174,3:0.0169:2,2:6.3:1:28.3:1:1:1.69723:60:6:0.017:0:2 +3 17744210 . A G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.29739;LSEQ=ATTGATGAACAAAATTTAGC;RSEQ=AGATTACTTTTTAAATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:107:50,57:10,10:20,107:0.8425:2,2:25.1:1:31.1:1:0.81183:1.13882:59.9:106:0.8413:0:1.1 1/0:168:103:46,57:28,37:65,103:0.6131:2,2:28.4:1:30.2:1:0.87425:1.07:60:206:0.6205:0:1.1 +3 17744212 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51136;SOR=Inf;LSEQ=TGATGAACAAAATTTAGCAA;RSEQ=ATTACTTTTTAAATTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:57,65:122,0:0:2,0:26.1:1:32.6:1:1:0:60:121:1:0:1 0/1:169:2:1,1:73,94:167,2:0.0118:2,2:37:1:28.5:1:1:1.29:60:4:0.0119:0:2 +3 18391132 . CCTG C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=0.93774;LSEQ=TGGCTGTGGAGGCGGCGGTG;RSEQ=CTGCTGCTGCTGCTGCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:8:6,2:71,44:115,8:0.065:2,2:34.8:1:33:1:0.70878:1.85:60:16:0.0656:0:0.3 0/1:147:9:5,4:85,53:138,9:0.0612:2,2:27:1:31.7:1:0.73523:1.28078:60:18:0.0625:0.0136:0.1 +3 18391148 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.50496;SOR=Inf;LSEQ=GGTGCCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:83,61:144,0:0:2,0:23.4:1:32.1:1:1:0:58.6:27.8:1:0:0.2 0/1:181:2:1,1:100,79:179,2:0.011:2,2:13.5:1:28:1:1:1.26415:55.5:4:0.0112:0:1.5 +3 18391151 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.50552;SOR=Inf;LSEQ=GCCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGCTGTTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:81,64:145,0:0:2,0:23.8:1:32.3:1:1:0:58.6:28:1:0:0.2 0/1:184:2:1,1:100,82:182,2:0.0109:2,2:21:1:27.5:1:1:1.21818:60:4:0.011:0:1 +3 18391154 . T C 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.61315;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:1:1,0:79,68:147,1:0.0068:2,0:45:0:15:0:1:0:22:0:0:0:8 0/1:184:2:1,1:100,82:182,2:0.0109:2,2:27.5:1:32:1:1:1.21818:43:4:0.0111:0:1.5 +3 18391165 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.20216;SOR=0;LSEQ=CTGCTGCTGTTGCTGTTGCT;RSEQ=CTGCTGTTGCTGCAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:73,74:147,2:0.0133:2,2:22:1:30:1:1:1.01:60:4:0.0136:0:1 0/0:183:0:0,0:93,90:183,0:0:2,0:30:1:31.3:1:1:0:58.8:90.5:1:0:0.2 +3 18391213 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62437;SOR=2.67679;LSEQ=ACAATCAGAGCTCTGCTATC;RSEQ=TGGAGTTCCACACAAAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:1,0:36,59:95,1:0.0104:2,0:1:0:26:0:0.38542:0:60:2:0.0105:0:3 0/1:109:3:2,1:33,73:106,3:0.0275:2,2:11:1:26.7:1:0.24091:4.36:59:6:0.0275:0:1 +3 18391218 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5018;SOR=Inf;LSEQ=CAGAGCTCTGCTATCGTGGA;RSEQ=TTCCACACAAAGCCGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:32,55:87,0:0:2,0:22.8:1:32.2:1:1:0:60:86:1:0:0.2 0/1:105:2:1,1:31,72:103,2:0.019:2,2:11.5:1:28.5:1:0.51868:2.30:60:4:0.0194:0:1 +3 18391303 . A T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11434;SOR=0.24322;LSEQ=ATAGGGATGAAGATTTAGAA;RSEQ=GAAAAGGTAGGCCGGCGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:0,18:0,5:5,18:0.7826:0,1:20.3:1:30.9:1:1:0:60:36:0.7826:0:1.2 0/1:11:5:0,5:0,6:6,5:0.4545:0,0:14.8:1:27.8:1:1:0:60:4:0.4:0:1 +3 18392827 . G T 26 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGAGCAGCACCGAGCCAT;RSEQ=GTGCAGGGGTCGGCAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:26.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 22112060 . T A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00113;SOR=0.55904;LSEQ=GGACACACTGTGATGAAAGA;RSEQ=TATAAAAGGATGAAACTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:122:62,60:69,59:128,122:0.488:2,2:26.5:1:30.5:1:0.70406:1.1312:59.8:60:0.4858:0:1.1 0/1:285:99:52,47:98,88:186,99:0.3474:2,2:29:1:29.4:1:1:1.00653:60:48.5:0.3477:0:1.1 +3 23146580 . TA AT 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5044;SOR=Inf;LSEQ=CTTAGGCTATCACTTCAATT;RSEQ=TTCCCACATGTCAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:97,27:124,0:0:2,0:24.8:1:30.6:1:1:0:60:248:1:0:0.1 0/1:155:2:1,1:115,38:153,2:0.0129:2,2:25:1:29:1:0.44114:3.00022:60:4:0.013:0:1 +3 23146591 . G T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62855;SOR=2.53716;LSEQ=ACTTCAATTTATTCCCACAT;RSEQ=TCAAATAAATAACCATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:1,0:111,45:156,1:0.0064:2,0:43:0:33:0:1:0:60:2:0.0065:0:1 0/1:187:3:1,2:129,55:184,3:0.016:2,2:13:1:27.3:1:0.22075:4.64723:60:6:0.016:0:1 +3 23146682 . C T 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.39954;LSEQ=CAATATAGACCCTGTTACTA;RSEQ=TTTTCAACCAGGAAATATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:145:65,80:70,85:155,145:0.4833:2,2:27.9:1:30.7:1:1:1.01353:60:144:0.4832:0:1.1 0/1:390:106:49,57:131,153:284,106:0.2718:2,2:28.4:1:29.7:1:1:1.00:60:212:0.2739:0:1.1 +3 23146730 . T A 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03971;SOR=0;LSEQ=TTAGCCATTGCTTTTTCACC;RSEQ=TGTGAAAACAATGGCAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:4:2,2:38,124:162,4:0.0241:2,2:10.5:1:24.3:1:0.24514:3.23:60:3:0.0184:0:1.3 0/0:204:0:0,0:73,131:204,0:0:2,0:23.4:1:29.3:1:1:0:60:203:1:0:0.4 +3 23146734 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50552;SOR=Inf;LSEQ=CCATTGCTTTTTCACCTTGT;RSEQ=AAAACAATGGCAAATTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:31,114:145,0:0:2,0:26.9:1:32.2:1:1:0:60:290:1:0:0.5 0/1:184:2:1,1:62,120:182,2:0.0109:2,2:12:1:28:1:1:1.93:60:4:0.011:0:1 +3 23146772 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00141;SOR=0.32418;LSEQ=CACAGGATTTGCCCTTGGAG;RSEQ=CAGGAAGTTGGGAGTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:34:2,32:2,43:45,34:0.4304:1,2:27.6:1:30.4:1:1:1.34:60:33:0.4231:0:1.1 0/1:92:18:2,16:9,65:74,18:0.1957:2,2:23.3:1:29.4:1:1:1.10649:60:17:0.1868:0:1.3 +3 23317493 . A G 37 pSTD;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09779;SOR=0;LSEQ=GGCTTTAACTGAATGATACC;RSEQ=GGGGCTTTGCAGATTGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:130,126:256,3:0.0116:2,2:13:0:23.7:1:1:1.93:60:2:0.0079:0:1.3 0/0:302:0:0,0:156,145:301,0:0:2,0:26.5:1:29.6:1:1:0:60:149.5:1:0:0.3 +3 23317542 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04719;LSEQ=GTGGGGAAGAAAAGTAGAGA;RSEQ=AAGCCTATTTAAAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:180:73,107:4,11:15,180:0.9184:2,2:24:1:29.6:1:0.41168:1.87:60:179:0.9179:0:1.1 0/1:258:89:40,49:72,97:169,89:0.345:2,2:24.1:1:28.3:1:0.79178:1.10:60:88:0.3438:0:1.1 +3 23317552 . TA T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.07583;SOR=0;LSEQ=AAAGTAGAGACAAGCCTATT;RSEQ=AAAAAAATTTCTATGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:3:1,2:65,104:169,3:0.0174:2,2:13:1:30.7:1:1:1.2484:60:6:0.0174:0.0058:1 0/0:233:0:0,0:96,137:233,0:0:2,0:23.5:1:28.9:1:1:0:60:466:1:0:0.4 +3 23317674 . C T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65289;SOR=0.52623;LSEQ=TTTCCATTATTCATTTCCTT;RSEQ=AGACAGCTCCTTTAGTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:27:2,25:0,3:3,27:0.9:0,2:18:1:28.1:1:1:0:60:54:0.9:0:1.5 1/1:17:14:0,14:0,3:3,14:0.8235:0,1:24.4:1:28.4:1:1:0:60:28:0.8235:0:1.4 +3 23317706 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03931;SOR=0.1351;LSEQ=TTAGTAACTTAGGTACATCC;RSEQ=ACCTTCCCCCACCAAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:4,11:0.7333:0,0:25.5:1:33:1:1:0:60:22:0.7857:0:2.2 0/1:8:2:0,2:0,6:6,2:0.25:0,0:19:1:34:0:1:0:60:4:0.25:0:2 +3 24138093 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGACTTAATTTTGCAGTATT;RSEQ=CCCAGGACTGTTCAATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:4,6:10,0:0:2,0:28.1:1:31.7:1:1:0:60:20:1:0:0.1 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:13.5:1:27.5:1:1:1.19087:60:4:0.087:0:1.5 +3 24138327 . A G 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05311;SOR=Inf;LSEQ=TCACTGGAGCTTTTTCTTCA;RSEQ=TTTCTTCATCATCAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:33,0:0:2,0:29.1:1:30.7:1:1:0:58.9:66:1:0:0.1 0/1:33:5:3,2:14,14:28,5:0.1515:2,2:21.6:1:28.4:1:1:1.48:60:4:0.129:0:1.2 +3 24138352 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50034;SOR=Inf;LSEQ=TTCATCATCAAAATTATCAT;RSEQ=ATCATCATCTTCATCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:34,0:0:2,0:25.7:1:31.5:1:1:0:58.9:33:1:0:0.1 0/1:43:2:1,1:18,23:41,2:0.0465:2,2:20:0:31:1:1:1.27:25:4:0.0476:0:1.5 +3 24138381 . AC A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28847;SOR=Inf;LSEQ=CTTCATCAGCAGCAAGTTTT;RSEQ=TTTTTTTTCTGTGGAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:23,0:0:2,0:19.4:1:32.8:1:1:0:58.4:46:1:0:0 0/1:39:3:1,2:14,22:36,3:0.0769:2,2:13.7:1:28.7:1:1:1.26509:60:6:0.0789:0.0256:1.3 +3 24138576 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20756;SOR=0;LSEQ=GTAATCCCACGGCTGATGTT;RSEQ=TTTCAAAGCCCCCAAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:21,16:37,2:0.0513:2,2:31.5:1:32:1:1:1.30327:55.5:4:0.0513:0:1.5 0/0:46:0:0,0:25,21:46,0:0:2,0:27.8:1:28.5:1:1:0:59.7:45:1:0:0.2 +3 24138663 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49315;SOR=Inf;LSEQ=TAGGACTGCCTTCATAATTC;RSEQ=TTGCCTCTGCTTCAACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:18,18:36,0:0:2,0:22.9:1:29.4:1:1:0:60:17:1:0:0.2 0/1:37:2:1,1:19,16:35,2:0.0541:2,2:23:1:29.5:1:1:1.18197:60:4:0.0541:0:1 +3 24138699 . A T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29402;SOR=4.9693;LSEQ=CAATGTGCAATTCATCTTTT;RSEQ=CACAGCCCCTAACCTGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:0,1:22,27:49,1:0.02:2,0:1:0:26:0:1:0:60:2:0.0204:0:1 0/1:32:3:2,1:16,13:29,3:0.0938:2,2:22.3:1:28:1:1:1.60:50:6:0.0968:0:1.3 +3 24138715 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52266;SOR=0;LSEQ=TTTTACACAGCCCCTAACCT;RSEQ=ACCGTGCTTAAAGATAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:24,26:50,2:0.0385:2,2:29:1:29:1:1:1.08:60:4:0.04:0:1 0/0:32:0:0,0:16,16:32,0:0:2,0:25.8:1:30.6:1:1:0:58.8:31:1:0:0.2 +3 24138787 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21076;SOR=Inf;LSEQ=CGATCATCTTCATCGGCCTT;RSEQ=AGTTCACAACCAAAAGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,23:43,0:0:2,0:23.6:1:29.5:1:1:0:60:86:1:0:0.3 0/1:37:2:1,1:15,20:35,2:0.0541:2,2:46:0:32:1:1:1.32:60:4:0.0556:0:1.5 +3 24205123 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16903;SOR=Inf;LSEQ=ATACTATTAAATGAAATAGC;RSEQ=CATGTTCAATGTACCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:89,21:110,0:0:2,0:23:1:30.1:1:1:0:60:54:0.9908:0:0 0/1:78:2:1,1:57,19:76,2:0.0256:2,2:34.5:1:29.5:1:0.44955:2.94953:60:4:0.0256:0:1 +3 24205147 . T C 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10463;SOR=Inf;LSEQ=GTTCAATGTACCTCAAATGT;RSEQ=TCCATTAGGGGACTTACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:99,48:147,0:0:2,0:26.7:1:30.7:1:1:0:60:294:1:0:0.1 0/1:132:3:1,2:87,42:129,3:0.0227:2,2:19.7:1:25.3:1:0.25755:4.0944:60:2:0.0153:0:1 +3 24205250 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10876;SOR=Inf;LSEQ=ATAAATAAAAATCAAGATGA;RSEQ=AAACTCTAAATATATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:88,108:196,0:0:2,0:26.3:1:32.4:1:1:0:60:97:1:0:0.1 0/1:180:3:1,2:76,101:177,3:0.0167:2,2:17.3:1:25.7:1:1:1.50167:60:6:0.0168:0:1.3 +3 24205251 . A C 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAATAAAAATCAAGATGAG;RSEQ=AACTCTAAATATATTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:88,108:196,0:0:2,0:26.4:1:30.3:1:1:0:60:48:1:0:0.1 0/1:182:53:22,31:57,72:129,53:0.2912:2,2:24.9:1:31.6:1:0.86938:1.11486:60:106:0.2944:0:1.1 +3 24205268 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50131;SOR=0;LSEQ=GAGAAACTCTAAATATATTT;RSEQ=ATGCTGTAATCCCCTTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:78,109:187,2:0.0106:2,2:28.5:1:29:1:1:1.39:60:4:0.0107:0:1 0/0:163:0:0,0:66,97:163,0:0:2,0:24.9:1:31:1:1:0:60:162:1:0:0.4 +3 24205281 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19079;SOR=Inf;LSEQ=TATATTTCATGCTGTAATCC;RSEQ=CTTAATATTTCATGATTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:68,108:176,0:0:2,0:25.6:1:30.7:1:1:0:60:28.333:1:0:0.1 0/1:137:2:1,1:51,84:135,2:0.0146:2,2:34:1:29:1:1:1.64:60:4:0.015:0:1 +3 25408318 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58502;SOR=2.53213;LSEQ=TAAATATTATCCTTGCATTT;RSEQ=GAATTGTTCATGGGCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:1:0,1:68,11:79,1:0.0125:2,0:1:0:25:0:0.15:0:60:2:0.0127:0:1 0/1:64:2:0,2:56,6:62,2:0.0313:2,0:13.5:1:26:1:0.01389:0:60:4:0.0317:0:1 +3 25408324 . G A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02043;SOR=Inf;LSEQ=TTATCCTTGCATTTGGAATT;RSEQ=TTCATGGGCCTCATTTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:75,18:93,0:0:2,0:21.3:1:32.3:1:1:0:60:92:1:0:0.1 0/1:81:5:2,3:64,12:76,5:0.0617:2,2:13:1:29.8:1:0.04173:7.69371:60:10:0.0617:0:1.4 +3 25408332 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21838;SOR=Inf;LSEQ=GCATTTGGAATTGTTCATGG;RSEQ=CCTCATTTTACCTCATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:80,29:109,0:0:2,0:22:1:30.9:1:1:0:60:35.333:1:0:0.1 0/1:97:2:1,1:74,21:95,2:0.0206:2,2:23:1:30.5:1:0.40399:3.46583:60:4:0.0208:0:1 +3 25408368 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22659;SOR=0;LSEQ=TGAGGTAAAGAGATTACTTG;RSEQ=AGAGTGGTGAACATATTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:123,69:192,2:0.0103:2,2:42:1:29:1:1:1.77692:60:4:0.0107:0:1 0/0:213:0:0,0:137,76:213,0:0:2,0:25.1:1:31.3:1:1:0:59.9:212:1:0:0.3 +3 25408383 . A T 35 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09999;SOR=0;LSEQ=ACTTGCAGAGTGGTGAACAT;RSEQ=TTGTTAGGCCCAAATTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:0,3:142,89:231,3:0.0128:2,0:5.3:1:22.3:1:0.05957:0:60:2:0.0088:0:1.7 0/0:269:0:0,0:164,105:269,0:0:2,0:24.9:1:28:1:1:0:59.9:32.625:1:0:0.4 +3 25408405 . A AT 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.01839;SOR=0.39968;LSEQ=TGTTAGGCCCAAATTTAACC;RSEQ=TTTTTTTTTCTTGTGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:22:12,10:148,121:269,22:0.0756:2,2:26:1:27.7:1:1:1.01922:59.3:6.333:0.0667:0.0103:0.9 0/1:348:11:6,5:183,154:337,11:0.0316:2,2:22.1:1:28.7:1:1:1.01:60:22:0.0326:0.0057:0.2 +3 25408451 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.87279;SOR=0.96811;LSEQ=CAGGATTGTAGCAACAGGCA;RSEQ=AATGTCGTAAAGAAATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:137:65,72:74,75:149,137:0.479:2,2:25.9:1:30.6:1:0.72377:1.09258:60:274:0.4893:0:1.1 0/1:344:162:76,86:88,94:182,162:0.4709:2,2:26:1:29.5:1:0.82911:1.05915:60:53:0.4746:0:1.2 +3 25408509 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10908;SOR=0;LSEQ=AAAGGATGACCCTTAAACAG;RSEQ=CAGCCTGTCTCATACCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:2,1:59,122:181,3:0.0163:2,2:20.3:1:29.7:1:0.25561:4.10:60:6:0.0164:0:1.7 0/0:200:0:0,0:80,120:200,0:0:2,0:24.3:1:30.6:1:1:0:60:65.667:1:0:0.4 +3 25408621 . T C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38681;SOR=0.5566;LSEQ=AAAAAAGATTCTCTCCAGTA;RSEQ=TTCCTCAGGTTGGAATAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:0,14:0,10:10,14:0.5833:0,1:22.3:1:33.7:1:1:0:60:28:0.5833:0:1 0/1:23:10:0,10:0,13:13,10:0.4348:1,0:24.2:1:32.2:1:1:0:60:20:0.4348:0:1.1 +3 25408748 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAATTCCAGGCTATGGTA;RSEQ=CATTTGAGCAATCTCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:24:1:31:1:1:0:60:4:0.4:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:26:0:1:0:60:2:1:0:0 +3 25482508 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.175;SOR=Inf;LSEQ=TGCAATCATATACCTAGGTA;RSEQ=CTTTTGACTGCATTAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:9,0:9,0:0:0,0:20.8:1:32.4:1:1:0:58.7:18:1:0:0.3 0/1:7:2:1,1:5,0:5,2:0.2857:0,2:9.5:1:28.5:1:0.28571:0:60:4:0.3333:0:1.5 +3 25482570 . AT A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.23904;SOR=Inf;LSEQ=ACCAATAACAGGAAGAAGAA;RSEQ=TTTTTTTCGGGGGGGTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:27,1:28,0:0:1,0:25.3:1:30.5:1:1:0:60:27:1:0:0.7 0/1:31:3:2,1:24,4:28,3:0.0968:2,2:8.3:1:27:1:0.42158:2.86274:60:6:0.1071:0.0645:1.3 +3 25482579 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00031;SOR=0.07023;LSEQ=AGGAAGAAGAAATTTTTTTT;RSEQ=GGGGGGGTGGGTGGGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:15:15,0:11,0:11,15:0.5357:0,1:31.9:1:30.1:1:1:0:60:14:0.5385:0:1 0/1:28:2:1,1:23,1:24,2:0.0714:1,2:23:1:28.5:1:0.15077:16.61257:60:4:0.08:0:2.5 +3 25482587 . T G 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.75432;SOR=1.4381;LSEQ=GAAATTTTTTTTCGGGGGGG;RSEQ=GGGTGGGAATGAAATGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:5:0,5:32,0:32,5:0.1351:1,0:10:1:15.2:1:0:0:50:0.667:0.0625:0:2.2 0/1:38:7:0,7:27,4:31,7:0.1842:2,0:10.9:1:21.9:1:3e-05:0:60:2.5:0.1515:0:2.6 +3 25482591 . T G 63 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23836;SOR=2.22769;LSEQ=TTTTTTTTCGGGGGGGTGGG;RSEQ=GGGAATGAAATGTTTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:0,4:31,2:33,4:0.1081:2,0:14.5:1:23:1:0.00023:0:53.3:3:0.0857:0:2.3 0/1:42:9:0,9:30,2:32,9:0.2143:2,0:14.4:1:19.9:1:0:0:60:2:0.1622:0:2.6 +3 25482594 . G GGA 56 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50604;SOR=1.71727;LSEQ=TTTTTCGGGGGGGTGGGTGG;RSEQ=AATGAAATGTTTCCCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:3:0,3:32,5:37,3:0.0732:2,0:18.3:1:23.1:1:0.00567:0:60:6:0.0833:0.0488:1 0/1:50:6:0,6:31,9:40,6:0.12:2,0:14.2:1:21.8:1:0.00053:0:60:1:0.0857:0.1:0.5 +3 25482630 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4963;SOR=0;LSEQ=ATCATAGTGGACTCCTAAGC;RSEQ=CGTTCTCTACGTATGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:34,32:66,2:0.0294:2,2:37:1:31.5:1:1:1.06158:60:4:0.0299:0:1 0/0:68:0:0,0:37,31:68,0:0:2,0:28.1:1:28.9:1:1:0:60:136:1:0:0.6 +3 25482633 . T A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24453;SOR=0;LSEQ=ATAGTGGACTCCTAAGCACG;RSEQ=TCTCTACGTATGCAGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:33,33:66,2:0.0294:2,2:25:0:32.5:1:1:1:60:4:0.0299:0:1 0/0:69:0:0,0:37,32:69,0:0:2,0:28.5:1:28.6:1:1:0:60:68:1:0:0.6 +3 25482663 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22476;SOR=Inf;LSEQ=ATGCAGTGTGCTGATGTCTT;RSEQ=TGGCATAATTGTTAAACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:26,40:66,0:0:2,0:29:1:32.2:1:1:0:60:32:1:0:0.3 0/1:60:2:1,1:26,32:58,2:0.0333:2,2:44.5:1:30:1:1:1.23:60:4:0.0345:0:1 +3 25502791 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51538;SOR=0;LSEQ=TCGTCTGCCAGGACAAATCA;RSEQ=CAGGGTACCACTATGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:42,39:81,2:0.0241:2,2:38:0:33:0:1:1.07594:60:4:0.0247:0:1.5 0/0:56:0:0,0:30,26:56,0:0:2,0:29.9:1:28.5:1:1:0:60:55:1:0:0.2 +3 25502851 . G A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07228;SOR=0;LSEQ=AGGTGAGTATTCACACTTCT;RSEQ=TGCCTGATGAACTCTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:2,3:15,29:44,5:0.102:2,2:20:1:28:1:1:1.28:60:10:0.102:0:1 0/0:35:0:0,0:13,22:35,0:0:2,0:26.4:1:31.5:1:1:0:60:70:1:0:0.2 +3 25502869 . T G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05915;SOR=Inf;LSEQ=CTGTGCCTGATGAACTCTCA;RSEQ=TCTCCATGTACTTTATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:10,26:36,0:0:2,0:20.8:1:29.8:1:1:0:60:35:1:0:0.4 0/1:24:3:1,2:7,14:21,3:0.125:2,2:24:1:31.3:1:1:1:60:6:0.125:0:1.3 +3 25542781 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1249;SOR=Inf;LSEQ=GATGCCAATACTGTCGACTC;RSEQ=AGAAGTGCTTTGAAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:18,14:32,0:0:2,0:30:1:32:1:1:0:60:64:1:0:0.1 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:26.5:1:27.5:1:1:1.26772:60:4:0.1111:0:1 +3 25569355 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23774;SOR=3.04664;LSEQ=AACCTCCAAAGAAAAGCCCT;RSEQ=CCCTTCGCCCCCCACAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:23.5:1:30.8:1:1:0:60:8:0.3333:0:1 1/0:13:8:7,1:5,0:5,8:0.6154:0,2:20.5:1:29.4:1:1:0:60:16:0.6154:0:1.1 +3 25569463 . A T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49786;SOR=Inf;LSEQ=AGCAACAAGGCCCTGCACAA;RSEQ=GCCAGGCGGGAGGCCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:76,16:92,0:0:2,0:21.8:1:30.5:1:1:0:60:184:1:0:0.1 0/1:98:2:1,1:68,28:96,2:0.0204:2,2:5.5:1:28.5:1:0.50642:2.40383:60:4:0.0206:0:2.5 +3 25569471 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49787;SOR=Inf;LSEQ=GGCCCTGCACAAAGCCAGGC;RSEQ=GGAGGCCTGTGGATGAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:90,25:115,0:0:2,0:19.6:1:29.9:1:1:0:60:114:1:0:0.1 0/1:117:2:1,1:78,37:115,2:0.0171:2,2:13.5:1:32:1:0.54598:2.09353:60:4:0.0172:0:2.5 +3 25569473 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49794;SOR=Inf;LSEQ=CCCTGCACAAAGCCAGGCGG;RSEQ=AGGCCTGTGGATGAGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:94,25:119,0:0:2,0:19.6:1:31.3:1:1:0:60:238:1:0:0.2 0/1:121:2:1,1:80,39:119,2:0.0165:2,2:24:1:27.5:1:1:2.03815:60:4:0.0168:0:1 +3 25569486 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49847;SOR=Inf;LSEQ=CAGGCGGGAGGCCTGTGGAT;RSEQ=AGGTGCTCTGCAAGCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:104,44:148,0:0:2,0:21.1:1:32.2:1:1:0:60:296:1:0:0.3 0/1:153:2:1,1:100,51:151,2:0.0131:2,2:23.5:1:26.5:1:1:1.95159:60:4:0.0132:0:1 +3 25569491 . G T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10997;SOR=0;LSEQ=GGGAGGCCTGTGGATGAGGT;RSEQ=CTCTGCAAGCTGAGCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:3:1,2:101,46:147,3:0.02:2,2:11:1:27.3:1:0.24007:4.34348:60:6:0.0201:0:1.3 0/0:162:0:0,0:106,56:162,0:0:2,0:25.2:1:31.7:1:1:0:60:324:1:0:0.3 +3 25569503 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22896;SOR=0;LSEQ=GATGAGGTGCTCTGCAAGCT;RSEQ=AGCCAGAAGCCTTAGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:111,59:170,2:0.0116:2,2:23.5:1:31.5:1:1:1.87407:60:4:0.0116:0:1 0/0:188:0:0,0:113,75:188,0:0:2,0:26:1:31.1:1:1:0:60:187:1:0:0.3 +3 25569565 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=0.52099;LSEQ=TGACTAATTGGTAATGTCTG;RSEQ=GGAGTTGGCACCAGGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:129:60,69:89,88:177,129:0.4216:2,2:23.8:1:29.6:1:0.56302:1.16249:60:42:0.4186:0:1.4 0/1:320:88:41,47:127,105:232,88:0.275:2,2:26.5:1:29.2:1:0.21112:1.38508:60:176:0.2776:0:1.2 +3 25569630 . G T 173 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0;SOR=0;LSEQ=TTGAGGAAGGAAGACAGACA;RSEQ=ACTTGAAGCCAAGCCTCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:56:18,38:32,60:92,56:0.3784:2,2:24.4:1:29.8:1:0.85806:1.12503:60:112:0.3784:0:1.7 0/0:232:0:0,0:94,138:232,0:0:2,0:23.3:1:30.6:1:1:0:60:76.333:1:0:0.3 +3 25569639 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51757;SOR=Inf;LSEQ=GAAGACAGACAGACTTGAAG;RSEQ=CAAGCCTCGAGTGTTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:43,89:132,0:0:2,0:22.8:1:31.4:1:1:0:59.9:43:1:0:0.6 0/1:196:2:1,1:74,120:194,2:0.0102:2,2:23.5:1:27.5:1:1:1.62:60:4:0.0105:0:1 +3 25569761 . A C 118 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09138;SOR=0.14611;LSEQ=GCCCAGATGGCCAGCATTTG;RSEQ=TTTAGCTGTTCAGGACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:0,11:0,9:9,11:0.55:0,0:24.9:1:34.2:1:1:0:60:22:0.55:0:1.1 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:26:0:33:0:1:0:60:2:0.1429:0:1 +3 25622130 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48413;SOR=0;LSEQ=GCATTATTAAGATCGTGGAG;RSEQ=TTGCTAAACGTCTGCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:20:1:31:1:1:1.15:60:4:0.1333:0:1 0/0:13:0:0,0:5,8:13,0:0:2,0:23.4:1:27.6:1:1:0:60:26:1:0:0.1 +3 25622158 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=0;LSEQ=ACGTCTGCCTGGTTTCACTG;RSEQ=CTTGACCATCGCAGACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:16:1:28.5:1:1:1.29:60:4:0.2222:0:1 0/0:8:0:0,0:2,6:8,0:0:2,0:29.5:1:31.6:1:1:0:60:16:1:0:0.1 +3 26805252 . A C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGGAAGGGAGGAAGAA;RSEQ=GGAAGGAAGTGAGGAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:0:32:0:1:0:60:4:1:0:1.5 +3 26805488 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGGAAGGGAAGGGAAGG;RSEQ=AAGGAGGAAAAGAAGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:19:1:33:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 26806016 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=GAGTGCCATTGCCCTTCGGC;RSEQ=CATGGAGGAAGGAGTGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:99,52:151,0:0:2,0:24.7:1:31.1:1:1:0:60:36.75:1:0:0.1 0/1:160:2:1,1:106,52:158,2:0.0125:2,2:18.5:1:28:1:1:2.0287:60:4:0.0127:0:1 +3 26806092 . G T 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.32602;SOR=0.2617;LSEQ=TTCACTCCACTTGATTTCAA;RSEQ=TGTCTTTATCCTCTACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:0,3:153,144:297,3:0.01:2,0:16:1:22:1:0.11642:0:60:2:0.0068:0:2 0/0:380:1:0,1:195,184:379,1:0.0026:2,0:1:0:25:0:0.48684:0:60:2:0.0026:0:2 +3 26806108 . C G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.22142;LSEQ=TCAAGTGTCTTTATCCTCTA;RSEQ=CTGCCCTCATGGCACCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:47:22,25:123,123:246,47:0.1604:2,2:28.6:1:33:1:0.75119:1.13587:60:94:0.1604:0:1.1 1/0:404:202:98,104:97,105:202,202:0.5:2,2:26.3:1:31.3:1:1:1.02:60:404:0.5037:0:1.1 +3 26806208 . T TC 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04857;SOR=1.84203;LSEQ=TCTCACATCACTTGGCCAGT;RSEQ=ACTGGAATGTCTGAATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:50:6,44:4,32:36,50:0.5814:2,2:19.2:1:32.2:1:1:1.09:60:100:0.5814:0.2093:0 1/0:107:77:20,57:5,24:29,77:0.7196:2,2:20.2:1:30.7:1:0.44543:1.68:59.9:76:0.7379:0.243:0.1 +3 28650238 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=0.55144;LSEQ=TTCTGAGAAAGAGGATTACA;RSEQ=GTGATAAAATGATGCCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:117:48,69:105,140:245,117:0.3214:2,2:27.3:1:30.2:1:0.82013:1.07788:60:38:0.3202:0:1.1 0/1:401:83:36,47:139,178:317,83:0.207:2,2:26.3:1:29.8:1:1:1.01946:60:166:0.2075:0:1.1 +3 28650262 . T A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2489;SOR=Inf;LSEQ=ATAAAATGATGCCTTGTGTC;RSEQ=TAAATATTTAAAAAGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:94,183:277,0:0:2,0:24.3:1:30.7:1:1:0:60:68.25:1:0:0.4 0/1:287:3:2,1:103,181:284,3:0.0105:2,2:14.7:1:27.3:1:0.55642:3.50:60:6:0.0106:0:1 +3 28744027 . C T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCGCTGGGATTACAGGTG;RSEQ=CTGCCACGACACCCGACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:26:1:1:0:60:4:1:0:1 +3 28745955 . T A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00341;SOR=0;LSEQ=CATCTCTCATTGTCCAATGA;RSEQ=TAAAGACTTAAAGTGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:137:137:100,37:0,0:0,137:1:0,2:20.7:1:30.4:1:1:0:60:136:1:0:1.4 1/1:137:128:90,38:8,1:9,128:0.9343:2,2:23.2:1:29.7:1:0.4453:3.35516:60:127:0.9407:0:1.3 +3 28746022 . G T 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12877;SOR=Inf;LSEQ=GCCACCTCTGAACATTTGAT;RSEQ=TTGAATCCCCTCAATTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:151,135:286,0:0:2,0:26.2:1:32.2:1:1:0:59.9:285:0.9965:0:0.9 0/1:339:4:0,4:184,151:335,4:0.0118:2,0:10:1:22.3:1:0.04279:0:60:3:0.009:0:2.8 +3 28746030 . C T 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.87059;SOR=1.03302;LSEQ=TGAACATTTGATGTTGAATC;RSEQ=CCTCAATTTTGTGATGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:296:176:93,83:57,62:119,176:0.5946:2,2:27.6:1:31:1:0.40926:1.22:59.8:57.667:0.5966:0:1.3 1/0:332:200:108,92:70,62:132,200:0.6024:2,2:24.4:1:29:1:0.91062:1.04:60:65.667:0.6043:0:1.3 +3 28746143 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50413;SOR=Inf;LSEQ=GGCCTAGTATACTCTCACAA;RSEQ=AGAGGACACTTCTGTAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:13,61:74,0:0:2,0:22.7:1:32.8:1:1:0:60:73:1:0:0.1 0/1:94:2:1,1:19,73:92,2:0.0213:2,2:39:1:28.5:1:0.38206:3.77:60:4:0.0213:0:1 +3 29047500 . A G 69 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.30341;SOR=0.18229;LSEQ=ATCTCAGTATTTTAGAATGA;RSEQ=AATATATCCCTTAGTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:30.8:1:34.5:1:1:0:60:8:0.4444:0:1.5 0/1:10:1:1,0:8,1:9,1:0.1:2,0:5:0:34:0:1:0:60:2:0.1:0:1 +3 29047673 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.40449;LSEQ=AGTAAATAAGCCTAAGGAGC;RSEQ=ACACTCACAGCATAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:92:44,48:32,30:62,92:0.5935:2,2:25.3:1:31.1:1:0.74269:1.16249:60:45:0.5882:0:1.3 0/1:205:76:37,39:65,64:129,76:0.3707:2,2:28.5:1:29.8:1:0.88525:1.07016:60:152:0.3707:0:1.1 +3 29047705 . C A 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=0;LSEQ=ATAAGAAAATATTTAAGACT;RSEQ=TAAGAAACAAGATTAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:12:4,8:57,74:131,12:0.0839:2,2:29.8:1:31.6:1:0.55719:1.53605:60:24:0.0857:0:2.3 0/0:203:0:0,0:87,116:203,0:0:2,0:25.9:1:31.1:1:1:0:60:66.667:1:0:0.4 +3 29047750 . T A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.8016;SOR=1.20512;LSEQ=ATATTGGTACATATTTTATA;RSEQ=CCTCTATTTTCACTAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:7:2,5:20,56:76,7:0.0843:2,2:18.1:1:28.1:1:1:1.12:60:6:0.0741:0:2.6 0/1:100:10:3,7:29,61:90,10:0.1:2,2:17:1:29.3:1:1:1.10817:60:20:0.101:0:1.5 +3 29049048 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATGTGTATATATATATA;RSEQ=ACACATATATATATGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:27.5:1:1:0:46:4:1:0:1.5 +3 29049074 . T TATA 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATATATGTGTATATATA;RSEQ=GGCACATATACACCATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:29.7:1:1:0:46:4:1:0:1.5 +3 29250643 . AT A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.56797;LSEQ=CCTGGAGTTCTTTTTCTTTG;RSEQ=GGTTAGAGAATAGGTATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:39:22,17:198,133:331,39:0.1054:2,2:28.4:1:32.2:1:0.73145:1.14993:60:78:0.106:0.0162:0.7 0/1:400:93:58,35:166,141:307,93:0.2325:2,2:25.4:1:30.3:1:0.18962:1.41:59.9:45.5:0.2316:0.04:0.7 +3 29250696 . C T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50812;SOR=1.09353;LSEQ=AATCACACTTAACGGAAAAC;RSEQ=ATTTGTATGCCTTTAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:212:99,113:102,125:227,212:0.4829:2,2:25.4:1:29.8:1:0.77374:1.07:60:52:0.4815:0:1.1 1/0:473:239:105,134:110,124:234,239:0.5053:2,2:25.7:1:28.3:1:0.51898:1.13181:59.9:78.667:0.5054:0:1.1 +3 29476247 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24545;SOR=Inf;LSEQ=TTTCCAGCAGTCCTATGCAC;RSEQ=AGCTCCCCACCCCATGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:56,27:83,0:0:2,0:23.4:1:31.5:1:1:0:59.9:82:1:0:0.1 0/1:82:2:1,1:57,23:80,2:0.0244:2,2:40.5:1:28:1:0.50226:2.44728:60:4:0.0244:0:1 +3 29476286 . ACAG A 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.50426;SOR=Inf;LSEQ=TCCTCCCAGCCCCAGCACAA;RSEQ=CAGCAGCAACAACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:79,71:150,0:0:2,0:28.3:1:32.2:1:1:0:59.8:149:1:0:0.2 0/1:186:2:1,1:98,86:184,2:0.0108:2,2:30:0:33:0:1:1.13873:48.5:4:0.0109:0:0.5 +3 29476292 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.20166;SOR=0;LSEQ=CAGCCCCAGCACAAACAGCA;RSEQ=CAGCAACAACAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:78,77:155,2:0.0127:2,2:26:1:29:1:1:1.01291:60:4:0.0131:0:1 0/0:192:0:0,0:100,92:192,0:0:2,0:28.7:1:31.7:1:1:0:59.6:95:1:0:0.2 +3 29476357 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50687;SOR=Inf;LSEQ=AAACCAACCTGTACATTCGA;RSEQ=GCCTCCCACCAGGCACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:22,52:74,0:0:2,0:20.3:1:31.2:1:1:0:60:73:1:0:0.1 0/1:98:2:1,1:35,61:96,2:0.0204:2,2:39.5:1:29:1:1:1.73:60:4:0.0206:0:1 +3 29476358 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50563;SOR=Inf;LSEQ=AACCAACCTGTACATTCGAG;RSEQ=CCTCCCACCAGGCACCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:21,52:73,0:0:2,0:19.9:1:31.8:1:1:0:60:146:1:0:0.2 0/1:95:2:1,1:34,59:93,2:0.0211:2,2:8:1:26:1:1:1.72:60:4:0.0213:0:1.5 +3 29476407 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5148;SOR=Inf;LSEQ=CTAATCAAGCTGTGCCAACC;RSEQ=TAAGTGTCCTTCTGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:1,16:17,0:0:1,0:30.7:1:31.6:1:1:0:60:16:1:0:0.4 0/1:27:2:1,1:0,25:25,2:0.0741:1,2:38:1:29:1:0.07407:0:60:4:0.0741:0:2 +3 29476428 . G A 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.43375;SOR=2.16695;LSEQ=TAAGTGTCCTTCTGCTGCCC;RSEQ=TGCTGTTTCTCACTCCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:1,6:7,5:0.4167:2,0:28.2:1:32.6:1:1:0:60:10:0.4167:0:1.2 1/0:13:8:1,7:0,5:5,8:0.6154:0,2:28.9:1:30.6:1:1:0:60:16:0.6154:0:1.5 +3 30648304 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49817;SOR=0;LSEQ=AGAGGGCGCGGCGCGGAGGC;RSEQ=CAGCCAGGGGTCCGGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:101,16:117,2:0.0168:2,2:19:1:29.5:1:0.26634:6.15428:60:4:0.0171:0:1 0/0:113:0:0,0:89,24:113,0:0:2,0:18.2:1:29.9:1:1:0:60:112:1:0:0.2 +3 30686181 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49978;SOR=Inf;LSEQ=GCATAACATCTTCAGGAATT;RSEQ=ATTGGCAGGCTGCCTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:147,14:161,0:0:2,0:22.2:1:32:1:1:0:59.7:39.25:1:0:0 0/1:178:2:1,1:150,26:176,2:0.0112:2,2:21.5:1:27:1:0.28109:5.68028:60:4:0.0113:0:1 +3 30686414 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.08071;LSEQ=TGTGTGGCTGTATGGTAAGC;RSEQ=AGCCTTTTAAGAAGTTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:31:9,22:32,152:184,31:0.1442:2,2:18.7:1:31.8:1:0.1405:1.94:60:62:0.1476:0:1.1 0/1:245:100:23,77:33,112:145,100:0.4082:2,2:24.2:1:30.3:1:1:1.01:60:99:0.4074:0:1.1 +3 30686447 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20998;SOR=0;LSEQ=AGTTATTCTTTCTTTTCCCC;RSEQ=TTTTACATAATGTATTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:10,90:100,2:0.0196:2,2:29:1:34:1:0.20501:8.63:60:4:0.0202:0:1 0/0:120:0:0,0:18,102:120,0:0:2,0:24.1:1:29.5:1:1:0:60:39:1:0:0.5 +3 30691473 . G A 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGACTTAAATATGTAAA;RSEQ=TTCTCCACCAGGACTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:18.8:1:31.8:1:1:0:60:8:0.5714:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 30691871 . GA G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.6659;SOR=0.87977;LSEQ=CTCCAAAGTGCATTATGAAG;RSEQ=AAAAAAAAAGCCTGGTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:24:8,16:223,291:514,24:0.0446:2,2:27.7:1:32.4:1:0.40168:1.53147:59.8:48:0.0459:0.0019:0.2 0/1:659:26:12,14:280,351:631,26:0.0395:2,2:28.2:1:30.3:1:1:1.07:60:52:0.0399:0.003:0.2 +3 30691998 . AT A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.58524;SOR=0.39246;LSEQ=GGGACCTGAGATCTGTGCCA;RSEQ=TTTTTGTATCCTTGGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:33,133:166,2:0.0119:2,2:14.5:1:30.5:1:0.36477:3.99:60:4:0.0122:0:0.5 0/0:213:1:0,1:50,162:212,1:0.0047:2,0:27:0:26:0:1:0:60:2:0.0048:0:0 +3 30692033 . A G 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50107;SOR=Inf;LSEQ=GGTCTGCAGTGTCATAGAGC;RSEQ=CATTCCTCCTGTGGTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:3,81:84,0:0:1,0:24.3:1:29.6:1:1:0:60:41:1:0:0.1 0/1:100:2:1,1:13,85:98,2:0.02:2,2:5.5:1:28.5:1:0.26162:6.34:60:4:0.02:0:1 +3 30692219 . T C 73 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTTTCTCAAAGTGCGGCC;RSEQ=CTTGAGCAGCCAGCATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:14.2:1:31.6:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 30713126 . T A 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCTTGTTTTGTTTCCCCA;RSEQ=CAGAATATAACACCAGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:149,115:264,0:0:2,0:27.2:1:30.6:1:1:0:60:65:1:0:0.1 0/1:353:42:25,17:180,131:311,42:0.119:2,2:30.1:1:28.5:1:0.86935:1.07:60:41:0.1192:0:1 +3 30713794 . G A 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATGTGGGAGGCCCAAGAT;RSEQ=CCCATCGTGCACAGGGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:0:0,0:319,292:611,0:0:2,0:26.3:1:32.3:1:1:0:60:86.286:1:0:0.1 0/1:699:25:13,12:372,301:673,25:0.0358:2,2:22.8:1:27.9:1:0.83858:1.14059:60:50:0.0363:0:1 +3 30713834 . G A 158 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02023;LSEQ=TCAAGAGCTCCAATATCCTC;RSEQ=TGAAGAACGACCTAACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:727:37:23,14:363,327:690,37:0.0509:2,2:22.5:1:30.5:1:0.3111:1.48:60:36:0.0504:0:1.1 0/0:925:1:1,0:494,429:923,1:0.0011:2,0:1:0:27:0:1:0:60:2:0.0011:0:1 +3 30715977 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATAAACCTTTGTATAATTA;RSEQ=TCTTCTCTTGACACATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:7,3:0.3:2,0:18.7:1:31:1:1:0:60:6:0.3:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:33:0:1:0:60:2:1:0:0 +3 30729836 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49841;SOR=Inf;LSEQ=ATTTCCTTTGGCTGCACATG;RSEQ=CATTCTCAGTGACCCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:123,32:155,0:0:2,0:24:1:32.1:1:1:0:59.8:76.5:1:0:0.1 0/1:157:2:1,1:119,36:155,2:0.0127:2,2:30.5:1:29.5:1:0.41695:3.27423:60:4:0.0129:0:1 +3 30730074 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49754;SOR=Inf;LSEQ=TTAGGTGGCAGAGAATTCTG;RSEQ=AATATTGAGCTTAAATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:3,82:85,0:0:1,0:26.2:1:32.1:1:1:0:60:170:1:0:0.1 0/1:90:2:1,1:5,83:88,2:0.0222:2,2:35.5:1:29:1:0.12959:15.24:60:4:0.0225:0:1 +3 30733025 . G T 69 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01009;SOR=Inf;LSEQ=GAGCTGGAGCATCTGGACAG;RSEQ=CTCTCGGGGAGGAGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:580:0:0,0:285,295:580,0:0:2,0:24.9:1:31.7:1:1:0:60:63.444:1:0:0.2 0/1:716:8:3,5:329,378:707,8:0.0112:2,2:12.8:1:23.3:1:0.73062:1.44988:60:3:0.0086:0:1.1 +3 30733187 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.2006;SOR=Inf;LSEQ=CCCTGAACTGATGCTTCCTG;RSEQ=AAAACCAAGGGGGTCACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:1,96:97,0:0:1,0:25.2:1:32.6:1:1:0:60:194:0.9898:0:0.1 0/1:80:2:0,2:2,76:78,2:0.025:1,0:18:1:29:0:1:0:60:4:0.025:0:1.5 +3 31310597 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14773;SOR=Inf;LSEQ=ACAATGGTGTGCCCTCTACT;RSEQ=AGGAGTGAAGAAACCTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:20,0:0:2,0:23.1:1:31.1:1:1:0:60:19:1:0:0.1 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:8.5:1:26.5:1:1:1.18321:60:4:0.1667:0:1 +3 31310976 . GGA G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=ATGGCGTGAACCCGGGAGGC;RSEQ=GCTTGCTGTGAGCCAAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:3,2:0.4:0,2:16.5:1:30:1:0.4:0:34.5:4:0.4:0:0 0/0:3:0:0,0:0,3:3,0:0:0,0:34.7:1:31.7:1:1:0:24.3:6:1:0:0 +3 32071654 . G A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06271;SOR=0;LSEQ=AAATTTTACTGCTTCCTTTC;RSEQ=GCCAGAACCGCCATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:1,2:164,128:292,3:0.0102:2,2:13:1:25:1:0.58471:2.55446:60:2:0.0069:0:2.7 0/0:446:0:0,0:258,187:445,0:0:2,0:26.1:1:29:1:1:0:57.9:48.444:1:0:0.1 +3 32071729 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18083;SOR=0;LSEQ=AGGAGAGACACGTGATACAT;RSEQ=TTCTCCAGGCCTTTTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:71,128:199,2:0.01:2,2:32.5:1:29.5:1:1:1.80:59:4:0.0103:0:1 0/0:271:0:0,0:97,174:271,0:0:2,0:22.4:1:31:1:1:0:59.2:53.2:1:0:0.1 +3 32072055 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=Inf;LSEQ=GAAAGAAGCCAAAGACAAAC;RSEQ=TACCTGGGTTCAACTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:18:1:30.3:1:1:0:60:6:1:0:0 0/1:13:2:1,1:2,9:11,2:0.1538:2,2:16.5:1:28:1:0.42308:3.87:35:4:0.1538:0:1 +3 32670121 . T C 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CAGGCGCCCACCACCACACC;RSEQ=GGCCATGGTTTTCTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:28.5:1:32.5:1:1:0:58:4:0.5:0:2.5 0/0:4:0:0,0:4,0:4,0:0:0,0:16.5:1:30.3:1:1:0:60:8:1:0:0.8 +3 32670172 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84715;LSEQ=TTGTTATAGGGGCCTCAGCC;RSEQ=TGGACCTTTTAATGGGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:14,0:10,0:10,14:0.5833:0,1:26.6:1:31.1:1:1:0:59.7:28:0.6087:0:2.8 1/0:24:13:13,0:11,0:11,13:0.5417:0,1:20.7:1:30.2:1:1:0:60:26:0.5417:0:1.5 +3 32670183 . A G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01047;SOR=0.23899;LSEQ=GCCTCAGCCGTGGACCTTTT;RSEQ=ATGGGTAAGATATTATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:18:18,0:15,0:15,18:0.5455:1,1:26.1:1:33.2:1:1:0:60:36:0.5455:0:2.8 0/1:32:7:7,0:25,0:25,7:0.2188:1,0:13.1:1:32.4:1:1:0:60:14:0.2258:0:2.6 +3 32670232 . G A 167 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1699;LSEQ=CCACAATATACTCACTAAAC;RSEQ=TCCAGCAGTGGAAATGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:41:40,1:40,1:41,41:0.5:1,1:25.8:1:31.3:1:1:1:60:82:0.5:0:2.3 0/1:125:18:17,1:99,7:106,18:0.144:2,1:30.6:1:30:1:1:1.20:60:36:0.1452:0:2.2 +3 32670281 . T C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17449;LSEQ=TTTGTGATTTTGATGAAATA;RSEQ=TATTGCATTAAATTTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:99:73,26:79,25:104,99:0.4877:2,2:22.7:1:32.9:1:0.74805:1.12482:60:198:0.4877:0:1.7 0/1:324:46:30,16:205,73:278,46:0.142:2,2:22:1:31:1:0.28402:1.49573:60:92:0.1438:0:1.7 +3 32670357 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1697;LSEQ=AATGAATGTCATGGGATAAT;RSEQ=CTTGATTTGGTAAAAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:209:103,106:121,117:238,209:0.4655:2,2:27:1:29:1:0.77643:1.06415:60:103.5:0.4631:0:1.3 0/1:669:86:42,44:283,299:582,86:0.1286:2,2:26.5:1:28.2:1:1:1.01:60:172:0.1295:0:1.3 +3 32670533 . G C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=0.06423;LSEQ=AGGCCAAGGCAGGTGGATTG;RSEQ=TTGAGTCCAGGCGTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:0,16:0,9:9,16:0.64:0,1:26.2:1:34.4:1:1:0:49.3:32:0.64:0:1.4 0/1:31:3:0,3:1,27:28,3:0.0968:1,0:19.3:1:32.7:1:1:0:58.3:6:0.1:0:1 +3 32670602 . C A 68 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58042;SOR=0.27349;LSEQ=TCTTTATAAGAAATACAAAA;RSEQ=AACTGGGGCCGGACGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:17.8:1:29.6:1:1:0:53.4:10:0.5:0:2 0/1:5:1:0,1:0,4:4,1:0.2:0,0:39:0:33:0:1:0:60:2:0.2:0:1 +3 33432091 . G A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10319;SOR=0.20732;LSEQ=CTGGCCCACTATCAACGCCC;RSEQ=CATTCCAACACTGTCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:12,0:7,0:7,12:0.6316:0,0:19:1:29.5:1:1:0:60:11:0.6111:0:1.7 0/1:8:2:2,0:6,0:6,2:0.25:0,0:29.5:1:31.5:1:1:0:60:4:0.25:0:1 +3 33432214 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25833;SOR=Inf;LSEQ=GTGAAATATACTGTGTCAGG;RSEQ=CAGAGGACCTGAGGGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:113,40:153,0:0:2,0:23.6:1:31.1:1:1:0:60:50:1:0:0.2 0/1:194:3:1,2:142,49:191,3:0.0155:2,2:19.3:1:26.3:1:0.16955:5.73232:60:6:0.0158:0:1 +3 33432307 . C A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.46287;LSEQ=AGATTTCAAACATTTTAAAA;RSEQ=TGTATCATTCCTTTTGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:294:163:77,86:61,70:131,163:0.5544:2,2:23.7:1:30.4:1:1:1.03:60:39.75:0.5483:0:1.1 0/1:408:149:75,74:117,142:259,149:0.3652:2,2:24.8:1:29.3:1:0.35407:1.23:60:73.5:0.363:0:1.1 +3 33432368 . TA T 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.58421;SOR=0.38965;LSEQ=AGAAGCAATATAGGCATTCA;RSEQ=AAAAAATGATTTTTCTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:0,2:45,105:150,2:0.0132:2,0:26.5:1:33:0:1:0:60:4:0.0132:0:0 0/0:194:1:0,1:60,132:192,1:0.0052:2,0:18:0:31:0:1:0:60:2:0.0053:0:1 +3 33432401 . TA T 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.75526;SOR=1.28878;LSEQ=TTTCTCATGACGACAAAGTT;RSEQ=AAAAAAAAAACAAAACAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:4:0,4:8,66:74,4:0.0513:2,0:29.8:1:32.3:1:1:0:60:8:0.0513:0:0 0/1:92:6:1,5:14,72:86,6:0.0652:2,2:19.5:1:31.3:1:1:1.03:60:12:0.0652:0.0109:0.3 +3 34786345 . C T 38 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62343;SOR=0.33261;LSEQ=GAACCTCAAAAGCCCCTATC;RSEQ=TTGTTTCTCCAGCAATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:185,52:237,3:0.0125:2,2:10.3:1:24:1:0.12788:7.0388:60:2:0.0084:0:1.3 0/0:239:1:0,1:182,56:238,1:0.0042:2,0:1:0:28:0:0.23849:0:60:2:0.0042:0:1 +3 34786456 . T C 234 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCATCTCCTCATTCTGACAA;RSEQ=TGCTCATTTCAGAAACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:226,304:530,0:0:2,0:25.6:1:30.5:1:1:0:60:65.25:1:0:0.1 0/1:613:185:83,102:194,234:428,185:0.3018:2,2:25.1:1:31.1:1:0.92977:1.01882:60:60.667:0.3028:0:1.1 +3 35897771 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18526;SOR=0;LSEQ=ATGACCCTACCCACAAGTAG;RSEQ=TGGTTATGGAACAGGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:23,8:31,2:0.0606:2,2:25.5:1:29:1:0.47727:2.76887:60:4:0.0625:0:1 0/0:43:0:0,0:26,17:43,0:0:2,0:25.9:1:31:1:1:0:60:86:1:0:0.2 +3 35897772 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49883;SOR=Inf;LSEQ=TGACCCTACCCACAAGTAGC;RSEQ=GGTTATGGAACAGGGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:25,10:35,0:0:2,0:25.6:1:31.4:1:1:0:60:34:1:0:0.1 0/1:43:2:1,1:25,16:41,2:0.0465:2,2:34.5:1:28:1:1:1.54582:60:4:0.0476:0:1 +3 35897806 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4972;SOR=Inf;LSEQ=GGGTTGGATAGTTGCACTGT;RSEQ=ATTTTGCTGCTGCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:37,25:62,0:0:2,0:23.7:1:32:1:1:0:59.9:124:1:0:0.1 0/1:68:2:1,1:38,28:66,2:0.0294:2,2:33.5:1:29:1:1:1.35095:60:4:0.0308:0:1 +3 35897810 . TTGC T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.49761;SOR=Inf;LSEQ=TGGATAGTTGCACTGTGATT;RSEQ=TGCTGCTGCTGCTCTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:36,27:63,0:0:2,0:24.9:1:30.9:1:1:0:59.9:126:1:0:0.1 0/1:70:2:1,1:39,29:68,2:0.0286:2,2:11:1:31.5:1:1:1.33905:60:4:0.029:0:0.5 +3 35897819 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.49966;SOR=Inf;LSEQ=GCACTGTGATTTTGCTGCTG;RSEQ=TGCTGCTCTTGTTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:61,0:0:2,0:26.9:1:32.5:1:1:0:59.9:60:1:0:0.1 0/1:72:2:1,1:37,33:70,2:0.0278:2,2:30:0:31.5:1:1:1.11943:60:4:0.0278:0:1.5 +3 35897837 . TTGC T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.50049;SOR=Inf;LSEQ=TGCTGCTGCTCTTGTTGCTG;RSEQ=TGCTGCTGTGGTAGAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:26,32:58,0:0:2,0:28.9:1:30.8:1:1:0:59.9:116:1:0:0.1 0/1:70:2:1,1:28,40:68,2:0.0286:2,2:23.5:1:24.5:1:1:1.42:60:4:0.029:0.0143:1.5 +3 36107937 . A G 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCACATAGAGAGAATGTCAT;RSEQ=TGAAGATGAAGAGAGAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:27:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:30:1:1:0:60:4:1:0:1.5 +3 36109775 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.33587;LSEQ=GGAAAATTAGTATTTTCCAA;RSEQ=AGTACCCTTAGCCAGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:175:80,95:14,10:24,175:0.8794:2,2:26.6:1:32:1:0.28027:1.65822:60:350:0.8794:0:1.1 1/0:210:149:65,84:27,34:61,149:0.7095:2,2:23.6:1:31.1:1:1:1.02613:60:298:0.7095:0:1.1 +3 36109777 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23605;SOR=0;LSEQ=AAAATTAGTATTTTCCAATA;RSEQ=TACCCTTAGCCAGCAGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:91,105:196,2:0.0101:2,2:22.5:1:32.5:1:1:1.15:60:4:0.0102:0:2 0/0:209:0:0,0:89,120:209,0:0:2,0:23.6:1:31.2:1:1:0:60:51.25:1:0:0.8 +3 36515636 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.49882;SOR=Inf;LSEQ=ATCTATTATGGGTACCCACA;RSEQ=CCCTACAGCAGCTGGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:126,63:189,0:0:2,0:25.2:1:30.4:1:1:0:59.9:36.8:1:0:0.3 0/1:195:2:1,1:118,75:193,2:0.0103:2,2:11.5:1:27.5:1:1:1.5695:60:4:0.0105:0:3.5 +3 36515638 . C T 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03008;SOR=Inf;LSEQ=CTATTATGGGTACCCACATC;RSEQ=CTACAGCAGCTGGCCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:131,66:197,0:0:2,0:24.8:1:30.8:1:1:0:59.9:38.4:1:0:0.4 0/1:199:6:3,3:118,75:193,6:0.0302:2,2:19.3:1:29.8:1:0.68085:1.56958:60:12:0.0306:0:1 +3 36515716 . G A 237 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATATGTAACCCATCACAAAT;RSEQ=TGATGAGAATCACATTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:258:258:120,138:0,0:0,258:1:0,2:24.8:1:29.7:1:1:0:60:257:1:0:1.1 1/0:221:167:75,92:30,24:54,167:0.7557:2,2:25.6:1:28.8:1:0.21015:1.53032:60:166:0.758:0:1.1 +3 36515853 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10653;SOR=Inf;LSEQ=CTTGCTACTTCTCTCTCAAC;RSEQ=TCATCCTCATTGACCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:7,58:65,0:0:2,0:26.9:1:30.4:1:1:0:60:31.5:1:0:0.2 0/1:32:2:0,2:1,29:30,2:0.0625:1,0:9:1:31:1:1:0:60:4:0.0625:0:2 +3 37034946 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03755;LSEQ=GGATGGCGTAAGCTACAGCT;RSEQ=AAGGAAGAACGTGAGCACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:55:54,1:44,4:48,55:0.534:2,1:23.3:1:27.3:1:0.18155:4.84:60:17.333:0.5253:0:1.1 0/1:123:5:5,0:110,8:118,5:0.0407:2,0:19.4:1:27.2:1:1:0:60:10:0.041:0:1.4 +3 37038235 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06663;SOR=Inf;LSEQ=AAAGTAGCAGGATGTTTGTG;RSEQ=GCTTCATGGAAGAGTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:124,275:399,0:0:2,0:25:1:30.5:1:1:0:59.9:65.5:1:0:0.1 0/1:476:5:2,3:184,287:471,5:0.0105:2,2:33.8:1:29:1:1:1.04:60:10:0.0105:0:1 +3 37042325 . GA G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.52085;SOR=0;LSEQ=AAAAACAAAAACCAAGAAAA;RSEQ=AAAAAAAACTCTTCTAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:2,0:78,0:78,2:0.025:1,0:8:1:33.3:1:1:0:60:4:0.026:0.0125:0 0/0:51:0:0,0:50,1:51,0:0:1,0:20.6:1:27.6:1:1:0:58:7.5:1:0:0.4 +3 37042348 . A AT 40 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.77868;LSEQ=AAAAAAACTCTTCTAAGAGG;RSEQ=TTTTTTTTTCCTGGATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:3:3,0:110,2:112,3:0.0261:1,0:28:1:25.7:1:1:0:57.7:2:0.0196:0:1 0/1:98:2:2,0:91,5:96,2:0.0204:2,0:24:1:31.3:1:1:0:60:4:0.0206:0.0102:0 +3 37042373 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.4987;SOR=0;LSEQ=TTTTTCCTGGATTAAATCAA;RSEQ=AAAATGGGAATTCAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:159,25:184,2:0.0105:2,2:37.5:1:31:1:0.26068:6.25608:60:4:0.0118:0:1 0/0:187:0:0,0:161,25:186,0:0:2,0:32:0:14:0:1:0:60:0:0:0:4 +3 37042757 . T C 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51703;SOR=0;LSEQ=ACCTGCAGAGACCTCTGATA;RSEQ=ATGTTTCTTGATGGAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:40.7:1:34.3:1:1:0:60:6:0.2308:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:18.8:1:26.3:1:1:0:60:5:1:0:0 +3 37046012 . AT A 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.37424;SOR=3.79796;LSEQ=ATATATTCATTCTGAAATGT;RSEQ=TTTTTGCCTAGGTCTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:1:0,1:91,240:331,1:0.003:2,0:48:0:30:0:1:0:60:2:0.003:0:0 0/1:352:4:3,1:115,233:348,4:0.0114:2,2:10.5:1:27.8:1:0.11153:6.05:60:8:0.0115:0.0057:0.8 +3 37048292 . C CA 57 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.14245;SOR=5.16859;LSEQ=ACAAGAGCAAAACTCCGTCT;RSEQ=AAAAAAAAAAAAAATCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:13,1:14,2:0.125:1,0:29:1:29.5:1:1:0:50.5:4:0.125:0:1.5 0/1:9:4:3,1:3,1:4,4:0.4444:2,2:12:1:28.9:1:1:1:60:8:0.4444:0.2222:0 +3 37048417 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=TATTGTTGATATGATTTTCT;RSEQ=TTTTCCCCTTGGGATTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:137,23:160,0:0:2,0:22.8:1:32.6:1:1:0:59.8:79:1:0:0.1 0/1:179:2:1,1:145,32:177,2:0.0112:2,2:27:1:30.5:1:0.33557:4.47744:60:4:0.0114:0:1 +3 37048633 . A G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.71837;LSEQ=TAAAAAATAAAATTGCTTCT;RSEQ=AGTTTTCAGGGTAATAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:16:3,13:9,88:97,16:0.1416:2,2:25.1:1:32.4:1:0.37255:2.24:60:32:0.1416:0:1 1/0:153:86:13,73:13,54:67,86:0.5621:2,2:25.6:1:30.9:1:0.52049:1.34914:60:85:0.5592:0:1.1 +3 37050240 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24196;SOR=Inf;LSEQ=TAAGACCTCGCTTTTGCCAG;RSEQ=ACATCTTGGGTTTTATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:127,14:141,0:0:2,0:24.9:1:32:1:1:0:60:282:1:0:0.5 0/1:137:2:1,1:119,16:135,2:0.0146:2,2:17:1:30:1:0.23358:7.24458:60:4:0.0148:0:1 +3 37050254 . T C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.049;LSEQ=TGCCAGGACATCTTGGGTTT;RSEQ=ATTTTCAAGTACTTCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:67:59,8:98,22:120,67:0.3583:2,2:23:1:32.3:1:0.30266:1.65:60:66:0.3568:0:1.1 0/1:189:5:5,0:144,40:184,5:0.0265:2,0:23.2:1:30.6:1:0.586:0:60:10:0.0266:0:1 +3 37053568 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.20213;LSEQ=CCGTGGACAATATTCGCTCC;RSEQ=TCTTTGGAAATGCTGTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:94:43,51:272,413:685,94:0.1207:2,2:27.9:1:31.5:1:0.26494:1.28:60:188:0.1222:0:1.1 0/1:943:393:173,220:258,291:549,393:0.4168:2,2:28:1:30.4:1:0.3888:1.12732:60:195.5:0.4186:0:1.1 +3 37055703 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=4;SSF=0.05;SOR=Inf;LSEQ=GTGGGTGGGTGGGTGGGTGG;RSEQ=TGGATGGATGGATGGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:18.8:1:32:1:1:0:60:24:1:0:0.1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:16.5:1:30:0:1:0:55:4:0.5:0:3 +3 37055711 . AT GA 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.00585;SOR=Inf;LSEQ=GTGGGTGGGTGGGTGGATGG;RSEQ=GGATGGGAGGATGGGTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:14,0:0:1,0:21.9:1:29.8:1:1:0:60:13:1:0:0.1 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:14.8:1:30.9:1:1:0:57.5:8:0.5714:0.1429:1.5 +3 37055712 . T TGGGA 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.53333;SOR=0;LSEQ=TGGGTGGGTGGGTGGATGGA;RSEQ=GGATGGGAGGATGGGTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:39:0:28:1:1:0:60:4:0.1538:0:0 0/0:7:0:0,0:3,0:3,0:0:0,0:16:1:32:0:1:0:60:6:1:0:0 +3 37056078 . C A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25226;SOR=Inf;LSEQ=GGAAATCCACTCACAGGAAA;RSEQ=ACCCACAGGGAATTTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:44,184:228,0:0:2,0:22.7:1:32.1:1:1:0:60:113:0.9956:0:0.2 0/1:264:3:3,0:60,201:261,3:0.0114:2,0:8.3:1:21:1:0.0131:0:60:2:0.0076:0:3 +3 37056209 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTCCTAAGTCTGTGCTC;RSEQ=GCCCTCCCACATGTGCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:0,17:17,2:0.1053:1,2:21.5:1:29.5:1:0.10526:0:60:4:0.1111:0:1 0/0:9:0:0,0:0,9:9,0:0:0,0:23.8:1:31.3:1:1:0:59.3:18:1:0:0 +3 37061720 . G C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11316;LSEQ=CATCTGGCCTCAAATCTTCT;RSEQ=GCCACCACATACACCATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:56:45,11:99,12:111,56:0.3353:2,2:22.7:1:31.3:1:0.15316:2.00761:59.8:55:0.3333:0:1.1 0/1:149:8:6,2:119,22:141,8:0.0537:2,2:28.5:1:29.6:1:0.61546:1.79459:60:16:0.0552:0:1 +3 37062040 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.44994;LSEQ=GCCCAGATTTTTGCCTGTTA;RSEQ=TTAGGAACTTTCTTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:15:1,14:9,106:115,15:0.1154:2,1:28.7:1:34.1:1:1:1.18719:60:30:0.1154:0:1.1 1/0:128:77:8,69:5,46:51,77:0.6016:2,2:22.6:1:31.7:1:1:1.07:60:154:0.6063:0:1.1 +3 37067050 . A G 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.65842;LSEQ=ATTTGGGGACCTGTATATCT;RSEQ=TACTTCTTATTCTGAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:6:6,0:44,0:44,6:0.12:1,0:32:1:33.8:1:1:0:52.7:12:0.12:0:1.3 1/0:53:29:29,0:24,0:24,29:0.5472:1,1:21.4:1:31.9:1:1:0:50.4:58:0.5472:0:2 +3 37067097 . A T 121 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=2;SSF=0.00017;SOR=0.14822;LSEQ=ATATATATATATATATATAT;RSEQ=TATTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:16:16,0:17,2:19,16:0.2667:2,1:21.4:1:30.4:1:0.48908:0:40.8:32:0.3478:0:3.6 0/1:99:5:3,2:43,6:49,5:0.0505:2,2:23.4:1:22.2:1:0.15376:4.57627:43.4:1.5:0.0588:0:3.4 +3 37067099 . A T 139 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=21.000;MSILEN=1;SSF=0;SOR=0.09661;LSEQ=ATATATATATATATATATAT;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:24:22,2:9,1:10,24:0.4706:2,2:19.6:1:30.4:1:1:1.21:43.4:48:0.6667:0:3 0/1:103:8:5,3:39,7:46,8:0.0777:2,2:16.1:1:22.4:1:0.15606:3.24857:45.5:3:0.1132:0:2.3 +3 37067120 . T A 92 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01029;SOR=9.31297;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=AATACAGACTTTGCTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:1,0:114,37:151,1:0.0066:2,0:32:0:27:0:1:0:40:2:0.007:0:7 0/1:223:13:11,2:146,64:210,13:0.0583:2,2:11.1:1:25:1:0.35382:2.40:55.9:3.333:0.0485:0:2.1 +3 37067565 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50161;SOR=0;LSEQ=TAAAACTGCCTTCTAACTTT;RSEQ=GCTTTTCATGAATCACTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:19,104:123,2:0.016:2,2:26.5:1:28.5:1:0.29548:5.36:60:4:0.0164:0:1 0/0:105:0:0,0:19,86:105,0:0:2,0:20.9:1:30.5:1:1:0:60:210:1:0:0 +3 37070106 . C T 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.013;SOR=7.07658;LSEQ=TTGTCAGATAAGCAGTCTAC;RSEQ=AGAGAACAGACTGATCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:3,0:20,0:20,3:0.1304:1,0:30.3:1:31.3:1:1:0:60:6:0.1304:0:1.3 1/0:17:9:9,0:8,0:8,9:0.5294:0,0:17:1:31.8:1:1:0:60:18:0.5294:0:1.1 +3 37070208 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20369;SOR=0;LSEQ=TTGCTCCTCCAAAATGCAAC;RSEQ=CACAAAATTTGGCTAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:114,12:126,2:0.0156:2,0:11.5:1:31.5:1:1:0:60:4:0.0156:0:1 0/0:155:0:0,0:138,17:155,0:0:2,0:23:1:30.3:1:1:0:59.9:37.75:1:0:0.1 +3 37070437 . G A 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGAGGGTACGTAAACGCT;RSEQ=TGGCCTGCCTGGGATGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:85,240:325,0:0:2,0:23.5:1:32.2:1:1:0:60:80.25:1:0:0.1 0/1:385:23:8,15:111,250:361,23:0.0597:2,2:20.4:1:28.5:1:0.64987:1.20:60:22:0.0588:0:1.2 +3 37070441 . C A 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3838;SOR=3.34312;LSEQ=AGGGTACGTAAACGCTGTGG;RSEQ=CTGCCTGGGATGCATAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:1,0:70,223:293,1:0.0034:2,0:1:0:26:0:0.2415:0:60:2:0.0035:0:1 0/1:354:4:2,2:102,248:350,4:0.0113:2,2:17.5:1:24:1:0.58404:2.42:60:3:0.0087:0:2.3 +3 37070444 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13113;SOR=Inf;LSEQ=GTACGTAAACGCTGTGGCCT;RSEQ=CCTGGGATGCATAGGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:65,208:273,0:0:2,0:24.1:1:32.3:1:1:0:60:53.6:1:0:0.1 0/1:333:4:2,2:96,231:327,4:0.012:2,2:14.3:1:26.8:1:0.58473:2.40:60:8:0.0122:0:1 +3 37081627 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50754;SOR=Inf;LSEQ=TGGTCAATGAAGTGGGGTTG;RSEQ=TAGGATTCTATTACTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:127,11:138,0:0:2,0:22.1:1:31.7:1:1:0:60:276:1:0:0.1 0/1:181:2:1,1:149,30:179,2:0.011:2,2:15:1:28:1:0.314:4.90237:60:4:0.011:0:1 +3 37083740 . A G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.0084;LSEQ=TTCAGCTTTTCCTTAAAGTC;RSEQ=CTTCATTTTTATTTTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:591:71:48,23:304,216:520,71:0.1201:2,2:24.2:1:30.5:1:0.15712:1.48:60:142:0.1226:0:1.1 0/1:844:413:247,166:258,170:428,413:0.4893:2,2:24.4:1:30:1:0.94387:1.01994:60:205.5:0.4905:0:1.1 +3 37085559 . T C 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTCTTTTTTTAAGACGGAGT;RSEQ=TTGCTCTTGTCACCCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:31.5:1:1:0:56.5:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:42:1:28.5:1:1:0:60:4:1:0:0 +3 37089174 . G A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.14046;SOR=Inf;LSEQ=TTCTCTTTGGAAATTGATGA;RSEQ=GTGTGACAGCCATTCTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:80,207:287,0:0:2,0:26:1:31.9:1:1:0:60:94.667:1:0:0.1 0/1:387:4:3,1:130,253:383,4:0.0103:2,2:11:1:25.8:1:0.11934:5.81:60:8:0.0104:0:1 +3 37089840 . CT C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0.95876;LSEQ=GTTTGTCAGGATGAAAAACT;RSEQ=TTTTTAAGTGTTTAGGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:32:32,0:23,0:23,32:0.5818:1,1:19.7:1:32.4:1:1:0:59.4:31:0.5741:0.1455:0.2 1/0:35:20:20,0:15,0:15,20:0.5714:1,1:23.1:1:31.2:1:1:0:60:40:0.5714:0.1143:0.1 +3 37090274 . C T 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.97659;LSEQ=ATATTCAGCAGTCCCATTTA;RSEQ=AGTTTTAACGCCTAAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:14:12,2:68,28:96,14:0.1273:2,2:20.9:1:30.7:1:0.34295:2.45:60:28:0.1308:0:1 0/1:79:37:32,5:32,10:42,37:0.4684:2,2:22.9:1:30.5:1:0.26814:1.98:60:36:0.4615:0:1 +3 37090552 . C A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22405;SOR=Inf;LSEQ=ACCCCAGGACTAGGACAGGA;RSEQ=CTCATACAATCTTTAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:28,135:163,0:0:2,0:25.3:1:31.2:1:1:0:60:31.6:1:0:0.1 0/1:147:2:1,1:29,116:145,2:0.0136:2,2:8.5:1:24:0:0.36763:3.95:60:4:0.0138:0:3 +3 37091917 . G T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36289;SOR=3.15363;LSEQ=GTGCACATCCCATCAGCCAG;RSEQ=ACACCAGTGTATGTTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:1:1,0:202,34:236,1:0.0042:2,0:43:0:12:0:1:0:60:0:0:0:1 0/1:227:3:1,2:173,51:224,3:0.0132:2,2:15.3:1:21.3:1:0.13681:6.7105:60:2:0.009:0:3 +3 37092173 . GTTC G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0;SOR=0.11715;LSEQ=ATTTATGCACTGTGGGATGT;RSEQ=TTCTTTCTCTGTATTCCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:440:148:47,101:97,194:291,148:0.3364:2,2:25:1:32.3:1:0.82979:1.07432:59.9:296:0.3379:0.0341:0.1 0/1:447:25:8,17:145,277:422,25:0.0559:2,2:24.2:1:31.7:1:1:1.11212:60:50:0.0566:0.0045:0.1 +3 37107012 . C G 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGGTATACTAGACTATCT;RSEQ=TTTGCAGAACAGTTTGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:246,107:353,0:0:2,0:23.9:1:32.2:1:1:0:59.9:69.6:1:0:0.2 0/1:362:55:41,14:222,85:307,55:0.1519:2,2:24.4:1:31.4:1:0.86969:1.12:60:110:0.1541:0:1 +3 37107022 . C A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.35856;LSEQ=TAGACTATCTCTTTGCAGAA;RSEQ=AGTTTGTAGTTAAGTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:33:22,11:253,123:376,33:0.0807:2,2:25.8:1:29.7:1:1:1.02841:60:32:0.0794:0:1.1 1/0:434:217:148,69:150,66:216,217:0.5:2,2:24.2:1:29.4:1:0.83576:1.05941:60:107.5:0.4988:0:1.1 +3 37789382 . G C 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26573;SOR=6.78852;LSEQ=GTTACACACCACCACGCCTA;RSEQ=CTAATTTTTTTTGTGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:25:1:31:1:1:0:59:6:0.3333:0:1 1/1:5:4:4,0:1,0:1,4:0.8:0,0:20.5:1:32:1:1:0:60:8:0.8:0:1.3 +3 37789529 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22094;SOR=0;LSEQ=CTTGTTGTTGCAAAATTTTG;RSEQ=AACATTTCAATCACCCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:121,54:175,2:0.0113:2,2:12.5:1:31:1:0.52613:2.22947:60:4:0.0117:0:1 0/0:199:0:0,0:145,54:199,0:0:2,0:21.5:1:30:1:1:0:60:48.75:1:0:0.1 +3 37789630 . G C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=3.68518;LSEQ=CACAAAGGGAAAGAGGAAAG;RSEQ=CACCTGATATATGTTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:9:1,8:101,150:251,9:0.0345:2,2:21.8:1:32.3:1:0.09384:5.36114:58.4:18:0.035:0:1 0/1:309:36:15,21:108,164:272,36:0.1165:2,2:20.4:1:31:1:0.85737:1.08:57.2:72:0.1184:0:1.1 +3 37789655 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50415;SOR=Inf;LSEQ=TGATATATGTTCTCTAGGCT;RSEQ=TTTAGAAAACATGGAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:46,106:152,0:0:2,0:21.8:1:30.5:1:1:0:59.4:75:1:0:0.1 0/1:188:2:1,1:54,132:186,2:0.0106:2,2:34.5:1:29.5:1:0.50063:2.43:44:4:0.0108:0:1 +3 37789755 . AG GT 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49626;SOR=Inf;LSEQ=TGGGTACTGTTCAAAAAGGA;RSEQ=GCCCCGCAAGTATTACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:22,39:61,0:0:2,0:22.4:1:31.9:1:1:0:59.9:60:1:0:0.1 0/1:64:2:1,1:29,32:61,2:0.0313:2,2:8.5:1:27.6:1:1:1.10:60:4:0.0313:0.0156:0.5 +3 37791729 . G A 29 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGAAAGAGAATATGGTA;RSEQ=TTTCAAAGTTTGAGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 38178224 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCACTCCCCCATGCCCA;RSEQ=CCCAGGGAGACAAAGCGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:35.5:1:30:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 38179665 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCCGTTTCCCACTCCCA;RSEQ=CTCGGGGAGCACAGCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:27.5:1:1:0:60:4:1:0:1 +3 38180103 . C CGGCGG 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=4.000;MSILEN=1;SSF=0.00075;SOR=Inf;LSEQ=GCTTCTCGGAAAGCGAAAGC;RSEQ=GGCGGGGCGGGGCGGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:161,25:186,0:0:2,0:24.7:1:31.1:1:1:0:59.8:45.5:1:0:0.2 0/1:131:8:6,2:96,27:123,8:0.0611:2,2:20.9:1:29.4:1:1:1.18362:60:16:0.0615:0.0153:0.1 +3 38180548 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.23987;SOR=Inf;LSEQ=GTCCCCTTCCTGGCCTCGTA;RSEQ=CTGGGGGGTGAGGAGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:46,141:187,0:0:2,0:26.6:1:31.4:1:1:0:60:61.333:1:0:0.1 0/1:180:2:1,1:57,121:178,2:0.0111:2,2:16.5:1:28:1:0.54184:2.11:60:4:0.0112:0:1.5 +3 38181293 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1841;SOR=Inf;LSEQ=TGGGACAGCGGCTGGATCCT;RSEQ=ACTGTGGGTAAAGAGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:127,36:163,0:0:2,0:22.1:1:31.7:1:1:0:60:26.167:1:0:0.1 0/1:123:2:1,1:97,24:121,2:0.0163:2,2:16:1:26:0:0.36652:3.98037:60:4:0.0169:0:1 +3 38181876 . C T 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45531;SOR=2.27607;LSEQ=CCACCCTTGTGCTCTGCACC;RSEQ=AGGGCATATGCCTGAGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:2:0,2:233,187:420,2:0.0047:2,0:23.5:1:24:0:0.2:0:60:4:0.0048:0:2 0/1:467:5:2,3:273,189:462,5:0.0107:2,2:26.8:1:24.8:1:0.40593:2.16303:60:4:0.0087:0:1.2 +3 38182112 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24878;SOR=Inf;LSEQ=ATGCATGAAGCCCTGCCCTG;RSEQ=GGTCCAGATACTGGGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:118,174:292,0:0:2,0:22.9:1:30.8:1:1:0:59.8:35.5:1:0:0.1 0/1:297:3:2,1:118,176:294,3:0.0101:2,2:8.3:1:25.7:1:0.56757:2.97:60:6:0.0102:0:2 +3 38182407 . T A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10492;SOR=Inf;LSEQ=GGGCCTCTGGATTGTCAGCC;RSEQ=TCCCTCCCCAAGGACTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:43,189:232,0:0:2,0:24.3:1:30.7:1:1:0:59.9:115:0.9957:0:0.1 0/1:209:3:2,1:40,165:205,3:0.0144:2,2:6.7:1:27.7:1:0.10445:8.13:60:6:0.0149:0:1.3 +3 38182530 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50982;SOR=0;LSEQ=TGCCAGGGGTACTTAGATGG;RSEQ=GGATGGCTGTTGTTAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:2,0:137,28:165,2:0.012:2,0:19:1:28.5:1:1:0:60:4:0.0122:0:1 0/0:123:0:0,0:99,24:123,0:0:2,0:21.4:1:30.4:1:1:0:59.8:29.75:1:0:0.1 +3 38182539 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51388;SOR=0;LSEQ=TACTTAGATGGGGGATGGCT;RSEQ=TTGTTAACCCTGGGGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:169,27:196,2:0.0101:2,2:16.5:1:29.5:1:0.26345:6.16464:60:4:0.0102:0:1 0/0:139:0:0,0:114,25:139,0:0:2,0:23.1:1:31.7:1:1:0:59.8:68.5:1:0:0.1 +3 38183201 . C A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAGACCAGGCTTGGCTG;RSEQ=GGGAGAGCTGGCTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:24.5:1:31:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 38545856 . C CA 28 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGCAAGACCCTATCT;RSEQ=AAAAAAAAAAGTTCCTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:28.5:1:1:0:33:4:1:0:0.5 +3 38548021 . T C 232 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATCATCTTGTTGGAATGA;RSEQ=ACATAATTCTTGAAAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:130,151:281,0:0:2,0:26.9:1:29.5:1:1:0:60:139.5:1:0:0.1 0/1:347:171:89,82:87,88:175,171:0.4928:2,2:26.4:1:31.4:1:0.66881:1.10:60:170:0.4942:0:1.1 +3 38548104 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50104;SOR=Inf;LSEQ=TGAATTCCAGAATGTACTCT;RSEQ=AGCGCACATAAAGAAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:26,94:120,0:0:2,0:23.4:1:31.8:1:1:0:60:59:1:0:0.1 0/1:140:2:1,1:38,100:138,2:0.0143:2,2:6.5:1:28.5:1:0.48099:2.61:60:4:0.0145:0:2 +3 38548248 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=TGTTTAATTTCTCAAATGCA;RSEQ=TTTTTCTTGGTATCTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:20:1:32.5:1:1:0:60:4:0.3333:0:1 0/0:5:0:0,0:0,5:5,0:0:0,0:15.8:1:31:1:1:0:60:10:1:0:0 +3 38949363 . A C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAACTGAATAAATGAATT;RSEQ=TTTCAATTTGATTGGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:32.5:1:1:0:60:4:1:0:1.5 +3 38951372 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49922;SOR=Inf;LSEQ=CGTGCCTGGCCAATTTTCTT;RSEQ=AAGTTTCTAACAGAATTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:15,17:32,0:0:2,0:25:1:32.3:1:1:0:60:31:1:0:0.1 0/1:40:2:1,1:20,18:38,2:0.05:2,2:22.5:1:29:1:1:1.10818:60:4:0.0513:0:1 +3 39452917 . AT A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49669;SOR=Inf;LSEQ=TGCATAAGAATTGCCCAGAT;RSEQ=TTTTTTTAAATGCCAGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:72,4:76,0:0:2,0:23.2:1:31.8:1:1:0:60:152:1:0:0.1 0/1:76:2:2,0:66,8:74,2:0.0263:2,0:28.5:1:32.5:1:1:0:60:4:0.0263:0:0 +3 39452934 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24691;SOR=Inf;LSEQ=GATATTTTTTTTAAATGCCA;RSEQ=TGTCCAGGCATTTTTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:103,16:119,0:0:2,0:21.2:1:33.1:1:1:0:60:58.5:1:0:0.1 0/1:121:3:1,2:94,24:118,3:0.0248:2,2:12:1:25.7:1:0.11624:7.65266:60:6:0.025:0:1 +3 39452940 . A T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49833;SOR=Inf;LSEQ=TTTTTTAAATGCCAGTGTCC;RSEQ=GGCATTTTTTTTTCAATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:114,20:134,0:0:2,0:21.7:1:30.5:1:1:0:60:43.667:1:0:0.1 0/1:139:2:1,1:107,30:137,2:0.0144:2,2:5.5:1:29:1:0.39756:3.52481:60:4:0.0146:0:1.5 +3 39452944 . A AT 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.2031;SOR=0.23235;LSEQ=TTAAATGCCAGTGTCCAGGC;RSEQ=TTTTTTTTTCAATCCCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:4:3,1:110,26:136,4:0.0286:2,2:32:1:31.3:1:0.57998:1.40645:60:8:0.0299:0:0 0/0:148:1:1,0:111,36:147,1:0.0068:2,0:38:0:33:0:1:0:60:2:0.0069:0:0 +3 39453057 . C T 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.57568;LSEQ=GATGTCTGTACTTTTGGTAC;RSEQ=TAGATGATGTAAGAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:402:251:113,138:69,82:151,251:0.6244:2,2:25.7:1:31:1:0.91784:1.02757:60:124.5:0.6256:0:1.1 0/1:493:241:126,115:122,130:252,241:0.4888:2,2:26.8:1:29.5:1:0.41786:1.17:60:47.2:0.4856:0:1.1 +3 39453135 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17607;SOR=0;LSEQ=TTTAATAATCTGCCACTCTT;RSEQ=GCAGGGAGCTCACTCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:51,108:159,2:0.0124:2,2:20.5:1:30.5:1:0.54301:2.11:60:4:0.0125:0:1.5 0/0:222:0:0,0:70,150:220,0:0:2,0:23.8:1:30.5:1:1:0:57.5:219:0.991:0:0.4 +3 39453160 . G A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=GGAGCTCACTCAGTGGGTTT;RSEQ=ATGTGGTGGATGCTGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:22,70:92,0:0:2,0:23.6:1:31.9:1:1:0:55.2:29.667:1:0:0.2 0/1:110:16:5,11:19,75:94,16:0.1455:2,2:25.1:1:29.5:1:0.3355:1.78:56.8:32:0.1455:0:1 +3 41265450 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21418;SOR=Inf;LSEQ=CATTTAACAGGTATCCCAGT;RSEQ=ACTTAGGAGTATTAATCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:136,12:148,0:0:2,0:25.3:1:32.7:1:1:0:60:147:1:0:0 0/1:128:2:1,1:105,20:125,2:0.0156:2,2:16.5:1:26.5:1:0.30446:5.14794:60:4:0.0159:0:1.5 +3 41265483 . C T 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24945;SOR=Inf;LSEQ=TAATCAAGCTAAATTTAAAT;RSEQ=CTAATGACTTTTGATTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:205,54:259,0:0:2,0:24.2:1:31.9:1:1:0:60:128.5:1:0:0 0/1:277:3:1,2:202,72:274,3:0.0108:2,2:10.3:1:20:1:0.17498:5.56917:60:2:0.0074:0:2 +3 41265953 . CT C 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.34773;SOR=0.4821;LSEQ=AATGGGTCATATCACAGATT;RSEQ=TTTTTTTTAAATTAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:7:5,2:145,20:165,7:0.0407:2,2:22.1:1:32.5:1:0.22053:2.87497:60:14:0.0412:0.0116:0 0/1:150:3:3,0:125,21:146,3:0.02:2,0:40:1:31.3:1:1:0:60:6:0.0201:0:0 +3 41265962 . TA T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.50029;SOR=0;LSEQ=TATCACAGATTCTTTTTTTT;RSEQ=AATTAAAGTAACATTTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:2,0:158,33:191,2:0.0104:2,0:25:1:28.5:1:1:0:60:4:0.0106:0.0052:4.5 0/0:172:0:0,0:143,28:171,0:0:2,0:23.1:1:27.9:1:1:0:60:84.5:0.9941:0:0.2 +3 41266226 . A G 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGGATTTTCTCAGTCCTTC;RSEQ=CTCAAGAACAAGTAGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:34:14,20:221,319:540,34:0.0591:2,2:25.7:1:31.1:1:1:1.01:60:68:0.0599:0:1.1 0/0:638:0:0,0:293,344:637,0:0:2,0:26.6:1:29:1:1:0:60:158.25:1:0:0.2 +3 41266750 . G A 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTTGAAGTAAATGCTCAA;RSEQ=GGGAGTAGTTTCAGAATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:168,148:316,0:0:2,0:22.5:1:32.4:1:1:0:59.9:157:1:0:0.1 0/1:254:19:11,8:129,106:235,19:0.0748:2,2:19.5:1:28.9:1:1:1.13:60:18:0.072:0:1.1 +3 41267385 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10881;SOR=0;LSEQ=TTCTTTATGTGGTTTTCATG;RSEQ=AGCATTGGACACCTCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:2,1:53,187:240,3:0.0123:2,2:38.7:1:29.3:1:0.1293:6.98:60:6:0.0124:0:1 0/0:266:0:0,0:75,191:266,0:0:2,0:23.3:1:30.2:1:1:0:60:43.333:1:0:0.1 +3 41267525 . A G 89 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=57.77024;LSEQ=ATGACACCATTCCACCTCAG;RSEQ=TAATCAGGCATTAGATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:0,1:0,22:22,1:0.0435:1,0:1:0:31:0:1:0:60:2:0.0455:0:1 1/0:9:7:0,7:0,2:2,7:0.7778:0,0:23.7:1:32:1:1:0:60:14:0.7778:0:1 +3 41268676 . GAT G 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.3951;SOR=1.47547;LSEQ=CAAGATTCCTTGACTAACAA;RSEQ=ATATATATATATCTTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:9:7,2:228,96:324,9:0.027:2,2:25.6:1:33.1:1:1:1.47:60:18:0.0272:0:0 0/1:330:13:10,3:221,95:316,13:0.0394:2,2:24.8:1:30.9:1:0.76175:1.43:60:26:0.0399:0.0061:0.2 +3 41274764 . C A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACCTCCTAAGGCTAGAA;RSEQ=AGATATTTAGGATTGATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:217:217:196,21:0,0:0,217:1:0,2:22.9:1:30.4:1:1:0:59.8:53.25:1:0:1.1 1/1:221:220:184,36:0,0:0,220:0.9955:0,2:22.2:1:29.3:1:1:0:60:54:0.9954:0:1.1 +3 41274905 . C A 152 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.61987;LSEQ=CAGAACTGTCTTTGGACTCT;RSEQ=AGGAATCTTTCAGATGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:672:1:0,1:315,356:671,1:0.0015:2,0:38:0:29:0:1:0:60:2:0.0015:0:1 0/1:772:40:20,20:345,387:732,40:0.0518:2,2:20.2:1:28.6:1:0.74735:1.12:60:80:0.0523:0:1.1 +3 41275350 . C T 227 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ACCCACCATCCCACTGGCCT;RSEQ=TGATAAAGGTAAATTGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:168:56,112:74,130:204,168:0.4492:2,2:26.2:1:30.8:1:0.58579:1.13806:60:167:0.4514:0:1.1 0/0:424:0:0,0:178,245:423,0:0:2,0:24.7:1:30.5:1:1:0:60:37.455:0.9976:0:0.1 +3 41275402 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24079;SOR=0;LSEQ=CCTTTGTTGCAGAATTGAAA;RSEQ=TGAAGCATCTCTAGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:46,124:170,2:0.0116:2,2:26.5:1:32.5:1:0.473:2.68:60:4:0.0117:0:1 0/0:178:0:0,0:42,136:178,0:0:2,0:23.3:1:30:1:1:0:60:177:1:0:0.1 +3 41277040 . C T 82 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00109;SOR=22.39046;LSEQ=GCTGCTTTGAATTAGTGCTG;RSEQ=CAGGAGGCCTCTTTTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:1,0:28,0:28,1:0.0345:1,0:27:0:32:0:1:0:60:2:0.0345:0:1 0/1:15:7:7,0:8,0:8,7:0.4667:0,0:25.3:1:29.4:1:1:0:60:14:0.4667:0:1 +3 41278759 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATTGTTAGGTTTACAAC;RSEQ=ATGCAGCTCTTGAGACCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 41279324 . GA G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49758;SOR=0;LSEQ=TTTAATGTGAGGTGCAAAGA;RSEQ=AAAAAAAATGTATCTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:24,0:24,2:0.0769:1,0:41.5:1:31:1:1:0:60:4:0.08:0:0 0/0:20:0:0,0:20,0:20,0:0:1,0:14.2:1:28.7:1:1:0:60:40:1:0:0.2 +3 41279408 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24405;SOR=Inf;LSEQ=AATGTTGGAGTTACTTGTTC;RSEQ=TTTTGTAATCTGAAAGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:138,10:148,0:0:2,0:23.8:1:31.9:1:1:0:60:48.333:1:0:0.4 0/1:145:2:1,1:135,8:143,2:0.0138:2,2:33.5:1:29:1:0.12069:15.97515:60:4:0.0139:0:1 +3 41279440 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22362;LSEQ=GAAAGTATGCTTTAAAAAAA;RSEQ=TTAGTGTACTTTTGAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:122:104,18:129,23:152,122:0.4453:2,2:22.9:1:32.7:1:1:1.03:60:39.667:0.4474:0:1.1 0/1:303:46:35,11:205,52:257,46:0.1518:2,2:19.5:1:30.8:1:0.5581:1.23811:60:45:0.1495:0:1.1 +3 41279651 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24068;SOR=Inf;LSEQ=AGAGCCGGTTTGCTCATCTG;RSEQ=GAAACCAGTGTTGGCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:33,170:203,0:0:2,0:25.3:1:30.7:1:1:0:60:24.375:1:0:0 0/1:196:2:1,1:30,164:194,2:0.0102:2,2:14:1:31:1:0.29199:5.39:60:4:0.0103:0:1 +3 41279657 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24653;SOR=Inf;LSEQ=GGTTTGCTCATCTGGGAAAC;RSEQ=AGTGTTGGCAGAAAAGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:17,164:181,0:0:2,0:26:1:32.4:1:1:0:60:89.5:1:0:0 0/1:179:2:1,1:23,154:177,2:0.0112:2,2:30:0:31.5:1:0.25083:6.58:60:4:0.0112:0:1 +3 41280525 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21311;SOR=Inf;LSEQ=TGACAAGTTTGCTGCTGAAC;RSEQ=TTGGATGCCCTAACCTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:191,9:200,0:0:1,0:23.8:1:31.9:1:1:0:60:32.333:1:0:0.1 0/1:172:2:1,1:164,6:170,2:0.0116:1,2:8.5:1:30.5:1:0.07997:25.38307:60:4:0.0117:0:1 +3 41443220 . C A 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCCACTCAATACTTCCACC;RSEQ=CAATTTCTCAATTTCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:19:9,10:168,174:342,19:0.0526:2,2:19.8:1:30.2:1:1:1.07262:60:38:0.0534:0:1.2 0/0:450:0:0,0:234,216:450,0:0:2,0:25.6:1:30.3:1:1:0:59.5:149:1:0:0.3 +3 41443267 . C T 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCAGTTATACAAGGGATA;RSEQ=ATTTGGCATACAGACTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:137,178:315,0:0:2,0:24.6:1:32.5:1:1:0:59.8:314:0.9968:0:0.2 0/1:376:97:43,54:125,152:277,97:0.258:2,2:24.2:1:28.6:1:0.90618:1.03266:57:96:0.2588:0:1.1 +3 41443310 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21747;SOR=0;LSEQ=CATTGACTGCACTAAGTCCA;RSEQ=TTTGGCTTTAATGGAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:63,126:189,2:0.0105:2,2:11:1:27.5:1:1:1.99:60:4:0.0105:0:1 0/0:218:0:0,0:77,141:218,0:0:2,0:25.3:1:31.2:1:1:0:59.3:217:1:0:0.3 +3 43176797 . T G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1516;SOR=0.26682;LSEQ=CTTTCTTTTCTCCTTCTATT;RSEQ=TCTCATCGTGTGTGTATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:13,0:10,0:10,13:0.5652:0,1:24.3:1:33.6:1:1:0:60:26:0.5652:0:1.8 0/1:12:3:3,0:9,0:9,3:0.25:0,0:8.7:1:32.3:1:1:0:60:6:0.25:0:2 +3 43176831 . T C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00224;SOR=0.15294;LSEQ=GTATCCATTGTAGCTCAGGC;RSEQ=CATTAAAAGACTGATGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:22:22,0:11,0:11,22:0.6667:0,1:24.3:1:31.3:1:1:0:60:44:0.6667:0:1.5 0/1:22:5:3,2:17,0:17,5:0.2273:1,2:25:1:31.2:1:0.04329:0:60:10:0.2381:0:1.4 +3 43177020 . A T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.61791;SOR=1.09664;LSEQ=TAATCCCACTGAATATTAGA;RSEQ=ACATACAAGACTATCATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:263:138:57,81:51,74:125,138:0.5247:2,2:21.1:1:29.1:1:1:1.02:60:137:0.5269:0:1.1 1/0:325:178:78,100:65,82:147,178:0.5477:2,2:26.8:1:28.4:1:1:1.01621:60:88:0.55:0:1.1 +3 43177084 . TA T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23242;SOR=Inf;LSEQ=TCAAGGAAAGTCAAAATAAC;RSEQ=ATTAGAGCAGTGCTTATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:20,103:123,0:0:2,0:22.4:1:30.2:1:1:0:60:40:1:0:0.5 0/1:115:2:1,1:15,98:113,2:0.0174:2,2:22:1:28.5:1:0.25995:6.36:60:4:0.0175:0:2 +3 43177107 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22967;SOR=Inf;LSEQ=TTAGAGCAGTGCTTATGTTT;RSEQ=CTTTTTCAATTTTCATCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:4,65:69,0:0:2,0:24.6:1:31.7:1:1:0:59.9:138:1:0:0.3 0/1:64:2:1,1:4,58:62,2:0.0313:2,2:19.5:1:30:1:0.15129:13.08:60:4:0.0313:0:1.5 +3 43359194 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49492;SOR=Inf;LSEQ=AGCCCGGTCCTACCTCAGGG;RSEQ=CATCCATCTCCCTCCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,16:24,0:0:2,0:29.4:1:30.7:1:1:0:60:23:1:0:0 0/1:29:2:1,1:12,15:27,2:0.069:2,2:22:1:28:1:1:1.24:60:4:0.069:0:1 +3 43360244 . G A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTAAAGAATCGAGTCCGGC;RSEQ=TGGTGGCTCATGCCTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:31.5:1:1:0:60:4:1:0:1 +3 44585886 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51213;SOR=Inf;LSEQ=CTAGAAAGGGGAGAAGCCAT;RSEQ=TCACCCAACTCCAGAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:13,16:29,0:0:2,0:34.2:1:32.3:1:1:0:35.7:58:1:0:0.1 0/1:43:2:1,1:22,19:41,2:0.0465:2,2:43.5:1:29.5:1:1:1.15394:37.5:4:0.0465:0:1 +3 45924953 . T C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATTTCTTGGACATAATTC;RSEQ=TCTCAAACCTTTTCCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:29.3:1:30.7:1:1:0:52.4:14:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:27:1:1:0:53:4:1:0:2.5 +3 45925443 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12524;SOR=Inf;LSEQ=GCCTTGGAACCAGAAAGGTG;RSEQ=CTCAGTGACAAATGAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:130,200:330,0:0:2,0:24.7:1:31.6:1:1:0:60:35.667:1:0:0.1 0/1:359:4:3,1:158,196:354,4:0.0111:2,2:21.5:1:26.5:1:0.33032:3.71:60:8:0.0113:0:1 +3 45925498 . C A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25259;SOR=Inf;LSEQ=ATTCTGGGGTAGGTTGGGTC;RSEQ=TGAAGAAATCCTGAGATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:90,150:240,0:0:2,0:27.2:1:32.3:1:1:0:60:59:1:0:0.1 0/1:278:3:2,1:114,161:275,3:0.0108:2,2:20.3:1:26.3:1:0.57294:2.81:60:6:0.0109:0:1 +3 45925574 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49917;SOR=0;LSEQ=CTCAGCCTCCTTGGGCACCA;RSEQ=AGAGGGCACTCAGCCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:12,75:87,2:0.0225:2,2:8:1:29:1:0.27222:6.04:60:4:0.0227:0:1 0/0:78:0:0,0:12,66:78,0:0:2,0:30.1:1:31:1:1:0:60:38:1:0:0.1 +3 46183820 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23865;SOR=Inf;LSEQ=GGGGGTATAAATACACATGT;RSEQ=CTTCTAGAAATAAGGCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:49,29:78,0:0:2,0:22.7:1:31.9:1:1:0:51.6:38:1:0:0.1 0/1:75:2:1,1:50,23:73,2:0.0267:2,2:14.5:1:30:1:0.54054:2.14936:25:4:0.0274:0:2.5 +3 46183846 . A C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49935;SOR=Inf;LSEQ=AGAAATAAGGCTTCGTGTCA;RSEQ=ACTCTAGACGGGTGGAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:54,36:90,0:0:2,0:31.1:1:30.5:1:1:0:53.1:44:1:0:0.1 0/1:102:2:1,1:62,38:100,2:0.0196:2,2:22:0:33.5:1:1:1.6234:25:4:0.0206:0:2.5 +3 46183922 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52293;SOR=Inf;LSEQ=AGGGGCGGGGAGCAGCACGC;RSEQ=GTCTTCCTTTCCAGCTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:75,52:127,0:0:2,0:25.9:1:30.4:1:1:0:60:62.5:1:0:0.1 0/1:199:2:1,1:115,82:197,2:0.0101:2,2:29:1:30.5:1:1:1.39999:60:4:0.0102:0:1.5 +3 46183970 . T A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26765;SOR=Inf;LSEQ=TAGGTGAACCTGCCCTTGCC;RSEQ=TTGCTGATGTGCCCACTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:116,67:183,0:0:2,0:25.5:1:31.5:1:1:0:60:366:1:0:0.1 0/1:253:3:2,1:138,112:250,3:0.0119:2,2:20:1:27.7:1:1:1.62:60:6:0.012:0:1 +3 46184057 . CAA C 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTACTTTTGCTAGTTAGTCT;RSEQ=GTCAATCTTGAGCGAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:183,126:309,0:0:2,0:24.9:1:30.5:1:1:0:58.8:43.143:1:0:0.2 0/1:400:31:20,11:214,155:369,31:0.0775:2,2:27.8:1:30.3:1:0.57082:1.32:51.1:62:0.0783:0.005:0.3 +3 46184620 . C G 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATTTCCCACAGCAATACTC;RSEQ=CTAAGACCGCACATCGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:183,235:418,0:0:2,0:24:1:31:1:1:0:59.5:37:1:0:0.1 0/1:448:35:18,17:183,229:412,35:0.0781:2,2:31:1:30.1:1:0.4806:1.32:48.7:70:0.0797:0:2 +3 46184629 . G A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=CAGCAATACTCCCTAAGACC;RSEQ=CACATCGCTGTTGGTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:189,218:407,0:0:2,0:25.2:1:31:1:1:0:59.5:57.143:1:0:0.1 0/1:454:16:5,11:205,232:437,16:0.0352:2,2:25.5:1:28.6:1:0.30808:1.94125:46.4:32:0.0358:0:1 +3 46184639 . G C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTAAGACCGCACATCGCT;RSEQ=TTGGTGCTGTAGATTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:207,210:417,0:0:2,0:25.1:1:31.9:1:1:0:59.5:40.7:1:0:0.1 0/1:427:47:27,20:183,196:379,47:0.1101:2,2:24:1:30.6:1:0.27951:1.44:43:94:0.1111:0:2.3 +3 46184680 . C T 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGATAGATTCAAGAGCCA;RSEQ=CCATTTCAGAGGAAGTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:215,185:400,0:0:2,0:24.6:1:31.9:1:1:0:59.6:132.333:1:0:0.1 0/1:401:46:28,18:187,166:353,46:0.1147:2,2:22.2:1:29.4:1:0.34783:1.38:45.6:92:0.1165:0:2.3 +3 46184689 . G A 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TTCAAGAGCCACCCATTTCA;RSEQ=AGGAAGTCAAGTACCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:226,192:418,0:0:2,0:23.4:1:32.5:1:1:0:59.7:138.333:1:0:0.1 0/1:418:16:6,10:218,183:401,16:0.0383:2,2:19:1:30.4:1:0.20876:1.98216:57.8:32:0.0387:0:1.4 +3 46184725 . C G 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTTTCTCACATAATCGG;RSEQ=GTTCTTGTAAATATCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:0:0,0:244,237:481,0:0:2,0:25.4:1:30.7:1:1:0:59.8:47.1:1:0:0.1 0/1:517:66:36,30:245,202:447,66:0.1277:2,2:24.8:1:28.9:1:1:1.01071:43.2:15.5:0.122:0:1.5 +3 46185176 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50267;SOR=Inf;LSEQ=ACCATCAGAGGCCCTTTGTT;RSEQ=GCTGATCTGACCCCAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:57,98:155,0:0:2,0:23.9:1:30.2:1:1:0:60:37.75:1:0:0.1 0/1:186:2:1,1:65,119:184,2:0.0108:2,2:18:0:32:1:1:1.82:60:4:0.011:0:1.5 +3 46185332 . G A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2;SOR=Inf;LSEQ=AACCCCTTATCTTCTTTTTT;RSEQ=TGTTTTATTCTACACATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:25.6:1:33.1:1:1:0:57.8:16:1:0:0 0/1:7:2:0,2:1,4:5,2:0.2857:2,0:5.5:1:26.5:1:1:0:60:4:0.2857:0:1.5 +3 47058057 . A G 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACAAGGCAGCCTGCTTT;RSEQ=GAATATTTACATGATAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:30.3:1:34:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 47058479 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23128;SOR=Inf;LSEQ=TCCCCAGGGTGATGTATCAT;RSEQ=AGTAGCACAGTGCTGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:98,3:101,0:0:1,0:25.4:1:33:1:1:0:60:100:1:0:0 0/1:95:2:1,1:90,3:93,2:0.0211:1,2:25:1:29.5:1:0.08287:26.12488:60:4:0.0211:0:1 +3 47058777 . A G 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08548;SOR=0;LSEQ=CAGGAAGAGAGACCACAGCC;RSEQ=CCAATCAGAGCAGAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:79,193:272,3:0.0109:2,2:32.7:1:25.7:1:1:1.22:60:2:0.0075:0:1 0/0:348:0:0,0:99,249:348,0:0:2,0:23.1:1:29:1:1:0:60:68.6:1:0:0.2 +3 47058807 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=GCAGAAATTATATGAGGGGG;RSEQ=GGACAGGGGTGGTAATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:29,141:170,2:0.0116:2,2:17.5:1:30:1:0.31926:4.80:60:4:0.0118:0:1 0/0:159:0:0,0:31,128:159,0:0:2,0:22.1:1:29.9:1:1:0:60:52:1:0:0.1 +3 47059029 . G GA 119 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.29962;SOR=1.68426;LSEQ=CCAGCTCTGACATCTGACAA;RSEQ=AAAAAAAAAAATACTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:9:9,0:100,6:106,9:0.0763:2,0:20.9:1:30.9:1:1:0:60:18:0.0783:0.0424:0 0/1:139:17:17,0:111,11:122,17:0.1223:2,1:22.1:1:29.3:1:0.35941:0:60:34:0.1269:0.0432:0.1 +3 47059069 . G T 43 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03177;SOR=0;LSEQ=ATGATGAAAAGGGCTTCTTA;RSEQ=AAGGTACACAGTTTGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:4:2,2:257,62:319,4:0.0124:2,2:11.8:1:21.5:1:0.17698:4.12037:56.8:3:0.0095:0:2.8 0/0:440:0:0,0:310,130:440,0:0:2,0:23:1:30.8:1:1:0:60:43:1:0:0.1 +3 47059268 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24869;SOR=Inf;LSEQ=GAACACGTTGCTCAACAGTC;RSEQ=AGAGAGGGCAAGGAGTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:20,174:194,0:0:2,0:25.1:1:32.3:1:1:0:60:96:1:0:0.2 0/1:205:3:2,1:29,173:202,3:0.0146:2,2:24:1:30:1:0.06036:11.69:60:6:0.0149:0:1 +3 47059269 . A G 20 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49911;SOR=Inf;LSEQ=AACACGTTGCTCAACAGTCC;RSEQ=GAGAGGGCAAGGAGTTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:18,170:188,0:0:2,0:25.4:1:31.8:1:1:0:60:36.6:1:0:0.3 0/1:199:2:1,1:28,169:197,2:0.0101:2,2:5:1:20.5:1:0.27085:5.95:60:4:0.0101:0:1 +3 47059323 . C T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14023;SOR=1.8412;LSEQ=AGAAAAGGTAGTGAGTAAAG;RSEQ=CAGCCAATCCTTCTCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:26:0,26:0,35:35,26:0.4262:1,1:24.2:1:30.4:1:1:0:60:25:0.4167:0:1.1 1/0:57:33:1,32:0,24:24,33:0.5789:1,1:21.1:1:28.1:1:1:0:60:32:0.5926:0:1.2 +3 47059325 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23467;SOR=Inf;LSEQ=AAAAGGTAGTGAGTAAAGCC;RSEQ=GCCAATCCTTCTCCTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:0,58:58,0:0:1,0:23.1:1:32.9:1:1:0:60:116:1:0:0.5 0/1:55:2:0,2:1,51:52,2:0.0364:1,0:19.5:1:30:1:1:0:55.5:4:0.0377:0:3.5 +3 47061135 . C T 23 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23592;SOR=0;LSEQ=GACATACACACAAGGAACAC;RSEQ=TTGTGTTCCTGCCTATCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:2,0:173,4:177,2:0.0112:1,0:13.5:1:23.5:1:1:0:60:4:0.0114:0:1.5 0/0:189:0:0,0:182,7:189,0:0:1,0:22.5:1:30.9:1:1:0:60:378:1:0:0.2 +3 47061183 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33176;LSEQ=GGAGATATTCGACATACTTA;RSEQ=GACAAGAAATGAAAGGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:171:120,51:214,82:296,171:0.3662:2,2:23.9:1:30.4:1:0.67059:1.1089:59.9:33.2:0.364:0:1.1 0/1:529:85:59,26:292,152:444,85:0.1607:2,2:22.8:1:29.4:1:0.53428:1.18:60:41.5:0.159:0:1.1 +3 47061433 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49746;SOR=0;LSEQ=TTTCCCCTAGCAGGGATACC;RSEQ=GATTCTTGGTATTAGAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:2,95:97,2:0.0202:1,0:17.5:1:30.5:1:1:0:60:4:0.0206:0:1.5 0/0:99:0:0,0:7,92:99,0:0:2,0:23.7:1:29.4:1:1:0:60:23.75:1:0:0.2 +3 47061453 . C T 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGATTCTTGGTATTAGAATC;RSEQ=GTTTAGAGGCCCTGACTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:31:0,31:0,37:37,31:0.4559:1,1:23.4:1:29.8:1:1:0:60:30:0.4688:0:1.1 0/0:65:0:0,0:1,64:65,0:0:1,0:20.6:1:28.8:1:1:0:60:15.25:1:0:0.3 +3 47061700 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCCACCTCTGACACTC;RSEQ=AGGATTCCAGGACAGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:15.5:1:34.5:1:1:0:56.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 47079112 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0207;SOR=1.32296;LSEQ=CATGCGGGATGGTCTTGGAC;RSEQ=GACTCCCAAATGATCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:565:276:184,92:193,96:289,276:0.4885:2,2:25.4:1:31.2:1:1:1.0052:60:275:0.4893:0:1.1 1/0:575:321:209,112:165,89:254,321:0.5583:2,2:24.9:1:29.4:1:1:1.01:60:79.25:0.5581:0:1.1 +3 47083995 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2442;SOR=Inf;LSEQ=TAAAACTCCCCTTATAGTGG;RSEQ=AACTTCTTTGATTAAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:162,33:195,0:0:2,0:23.4:1:32.6:1:1:0:60:96.5:1:0:0.1 0/1:191:2:1,1:137,52:189,2:0.0105:2,2:12.5:1:29:1:0.47903:2.61915:60:4:0.0106:0:1 +3 47087837 . T A 116 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00202;SOR=8.76464;LSEQ=ACTCTGTCTCAAAAAAAAAA;RSEQ=AAAATAAAATAAAATAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:2,0:50,1:51,2:0.0377:1,0:19:1:32:0:1:0:60:4:0.0385:0:3 0/1:54:14:14,0:34,2:36,14:0.2593:2,1:16.6:1:30.6:1:1:0:53.2:28:0.2857:0:2 +3 47087869 . G GA 56 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.87442;LSEQ=AAATAAAACAAAGAACACGT;RSEQ=AAAAAAAAACCCAAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:4:4,0:95,2:97,4:0.0396:1,0:42.5:1:31.3:1:1:0:60:8:0.0404:0:0 0/1:115:4:3,1:106,3:109,4:0.0348:1,2:26.5:1:28.1:1:0.13597:11.07601:60:8:0.0374:0.0087:0.3 +3 47087939 . G T 42 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0724;SOR=0;LSEQ=AACCTTCCAAAGACAAAGTA;RSEQ=ACAGCCAATGAGTTTTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:199,82:281,3:0.0106:2,2:7:1:26.7:1:0.20979:4.82284:60:6:0.0109:0:1 0/0:396:0:0,0:257,138:395,0:0:2,0:24.4:1:30.4:1:1:0:60:38.5:1:0:0.1 +3 47097985 . G A 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCTTGGGAGAAATGGAG;RSEQ=CCTGCTAACAACAATGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:27:1:30.3:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 47098264 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22924;SOR=Inf;LSEQ=ACCAGATTTAACTAACATCC;RSEQ=ATGAACAGACCATAAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:176,39:215,0:0:2,0:25.9:1:31.3:1:1:0:59.9:70.667:1:0:0.3 0/1:198:2:1,1:144,52:196,2:0.0101:2,2:11.5:1:28:1:0.4647:2.75249:60:4:0.0102:0:1 +3 47098278 . A G 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACATCCCATGAACAGACCAT;RSEQ=AAGCAGAAAAGAAAAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:70:53,17:166,49:215,70:0.2456:2,2:23.4:1:32.5:1:0.87054:1.08631:59.6:140:0.2491:0:1.1 0/0:308:0:0,0:203,103:306,0:0:2,0:13:0:16:0:1:0:60:0:0:0:2 +3 47098997 . G A 42 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13515;SOR=Inf;LSEQ=ATATCTAGAAAGAAAATAAG;RSEQ=ACCACAAAAAGTTGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:69,168:237,0:0:2,0:26.3:1:31.5:1:1:0:60:58.25:1:0:0.1 0/1:304:4:3,1:96,204:300,4:0.0132:2,2:11:1:21.3:1:0.10295:6.33:60:3:0.01:0:1 +3 47103376 . C T 59 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCCCACCAACCCCCATTG;RSEQ=GCTCGAAAGAACAAATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:16.5:1:29.8:1:1:0:53.5:8:0.8:0:1.8 1/1:1:1:1,0:0,0:0,1:1:0,0:24:0:31:0:1:0:60:2:1:0:1 +3 47103861 . GTT G 217 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=14.000;MSILEN=1;SSF=1;SOR=1.00795;LSEQ=GGGAAAAGGGTGGTTTGTTT;RSEQ=TTTTTTTTTTTTAAGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:113:22,91:70,154:224,113:0.2804:2,2:27.4:1:32.1:1:0.02734:1.87679:59.8:55.5:0.2868:0.0099:0.6 0/1:500:141:49,92:90,172:262,141:0.282:2,2:28.2:1:30.4:1:1:1.02:59.8:69.5:0.2843:0.018:0.6 +3 47103876 . A T 46 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13109;SOR=Inf;LSEQ=TGTTTGTTTTTTTTTTTTTT;RSEQ=AGTTTATTTGGTGGACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:68,244:312,0:0:2,0:22:1:30:1:1:0:59.4:27.364:0.9967:0:0.8 0/1:382:4:2,2:112,266:378,4:0.0105:2,2:6:1:23:1:0.58592:2.37:57.5:3:0.0081:0:1 +3 47108330 . C T 62 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63801;SOR=0.51956;LSEQ=AGAAAAAAAGCTAGTAAAGA;RSEQ=TGAGTTCAAGGAAAGCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:26.3:1:31:1:1:0:60:8:0.4:0:1 0/1:8:2:2,0:6,0:6,2:0.25:0,0:25.5:1:22.5:1:1:0:60:1:0.1429:0:3 +3 47108361 . G A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06732;SOR=0.2937;LSEQ=GAAAGCGACAACAAAACAGT;RSEQ=TAAGAGACATTTCCTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:12,1:6,0:6,13:0.6842:0,1:23.6:1:28.9:1:1:0:58.3:26:0.6842:0:1 0/1:21:8:8,0:13,0:13,8:0.381:1,0:21.4:1:27.8:1:1:0:60:16:0.381:0:1 +3 47108704 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50074;SOR=Inf;LSEQ=CATGACAATAAAGAAATGGA;RSEQ=AGTAACAAGCTGGTACTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:17,114:131,0:0:2,0:21.8:1:31:1:1:0:59.8:64.5:1:0:0.2 0/1:151:2:1,1:21,128:149,2:0.0132:2,2:21.5:1:30:1:0.27099:5.98:60:4:0.0134:0:1 +3 47125124 . TA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.24166;SOR=0;LSEQ=TTTTCAGAAATATGCATGGC;RSEQ=AAAAAAGTAGTTAATTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:2,0:123,7:130,2:0.0152:2,0:41:1:31.5:1:1:0:60:4:0.0156:0:0 0/0:136:0:0,0:128,8:136,0:0:2,0:22.3:1:28:1:1:0:60:135:1:0:0.1 +3 47125385 . G A 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.46942;LSEQ=TTGTGCCGTTGCTCTCTTTG;RSEQ=GCTCTATTTCAGCGTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1025:423:217,206:322,279:601,423:0.4127:2,2:27:1:31.1:1:0.48492:1.09552:59.9:51.875:0.4125:0:1.1 1/0:1368:695:355,340:329,338:667,695:0.508:2,2:26.6:1:29.3:1:0.55102:1.07:60:76.222:0.5078:0:1.1 +3 47125884 . TA T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.23282;SOR=0;LSEQ=CTTTATAATCTGATTAAACA;RSEQ=AAAAAAAATTACATCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:21,81:102,2:0.0192:2,2:23.5:1:33:0:0.37995:3.79:60:4:0.0198:0:0 0/0:111:0:0,0:29,81:110,0:0:2,0:24.6:1:29.1:1:1:0:58.7:109:1:0:0.4 +3 47127855 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21522;SOR=Inf;LSEQ=AGCATTGGGAGGCAATATCA;RSEQ=AATATTACAAAGAGCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:17,113:130,0:0:2,0:22.4:1:32.4:1:1:0:59.9:129:1:0:0.1 0/1:113:2:1,1:19,92:111,2:0.0177:2,2:5:1:27:0:0.32396:4.75:60:4:0.0179:0:1 +3 47129364 . C CAGG 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.55944;SOR=3.3873;LSEQ=AGCTACTCAGGACGCTGAGG;RSEQ=AGAATTGCTTGCACCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:42.3:1:33.3:1:1:0:53.8:8:0.4444:0:0 1/0:4:3:3,0:1,0:1,3:0.75:0,0:27.7:1:31.4:1:1:0:55:6:0.75:0:0 +3 47129454 . TAAAC T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=7.000;MSILEN=4;SSF=0.04054;SOR=3.0355;LSEQ=TGACAGAACAAGACCCCATC;RSEQ=AAACAAACAAACAAACAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:8:8,0:30,0:30,8:0.2105:1,0:26.5:1:33.4:1:1:0:60:16:0.2105:0.0263:0.1 0/1:31:14:14,0:17,0:17,14:0.4516:1,1:23.8:1:31.4:1:1:0:59.6:28:0.4516:0.0323:0.5 +3 47129486 . T C 33 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=4;SSF=0.59773;SOR=2.32505;LSEQ=CAAACAAACAAACAAACAAA;RSEQ=AAATAAATAAATAAAATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:1,0:76,0:76,1:0.013:1,0:26:0:34:0:1:0:60:2:0.013:0:1 0/1:67:2:2,0:64,1:65,2:0.0299:1,0:26.5:1:33.5:1:1:0:57.5:4:0.0299:0:1 +3 47129781 . CA C 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.07668;LSEQ=TTTTTATAAAACAACAACAA;RSEQ=AAAAAAAAAACCAAAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:13:0,13:23,146:169,13:0.0714:2,1:26.1:1:32.4:1:0.37747:0:60:26:0.0734:0.0055:0.1 0/1:183:14:3,11:31,137:168,14:0.0765:2,2:26.3:1:30.8:1:0.72773:1.20:60:28:0.0778:0.0109:0.4 +3 47129903 . C T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51282;SOR=0.40465;LSEQ=GTTAAGAAGGCTGATAATAA;RSEQ=AAGTCTACTGTTGATGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:18:0,18:0,1:1,18:0.9474:0,1:22.7:1:29.7:1:1:0:57.9:36:0.9474:0:1 1/1:8:7:0,7:0,1:1,7:0.875:0,0:29:1:29:1:1:0:60:14:0.875:0:1 +3 47142907 . TCC T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.02604;SOR=1.43027;LSEQ=TTATATCTGAACAGCCTATT;RSEQ=CCATCAGAAGCAGCAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:136:107,29:135,36:171,136:0.4416:2,2:29.4:1:32.4:1:1:1.01631:60:272:0.4459:0.0065:0.1 1/0:324:172:131,41:111,41:152,172:0.5309:2,2:25.8:1:30.7:1:0.52507:1.18:60:171:0.5344:0.0216:0.1 +3 47143125 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2448;SOR=0;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GCATATATAAAGATCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:2,107:109,2:0.0168:1,2:32:1:30:1:0.05356:43.88:59.5:4:0.018:0:1 0/0:121:0:0,0:6,113:119,0:0:2,0:22.8:1:28.6:1:1:0:58.1:22.8:1:0:0.5 +3 47144731 . A G 21 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94985;LSEQ=AATAAAGTAGAATAGGAAAA;RSEQ=GGGACTAAAAAATTCATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:166,23:189,2:0.0105:2,2:23.5:1:32:1:0.2361:7.08652:60:4:0.0105:0:1 0/1:201:2:2,0:173,26:199,2:0.01:2,0:24:1:21:1:1:0:60:1:0.005:0:3.5 +3 47146932 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.46214;SOR=2.00565;LSEQ=AAAAAAGGCACTCTGGGGGT;RSEQ=ATCAATAATTTCTAAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:8,7:0.4667:0,0:20.9:1:26.1:1:1:0:59:2.5:0.4167:0:2.6 1/0:14:9:9,0:5,0:5,9:0.6429:0,0:23.4:1:30.6:1:1:0:60:18:0.6429:0:1.6 +3 47147001 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12005;SOR=Inf;LSEQ=TACATATATATATGTAAATT;RSEQ=CTCTCTCTTCCATGTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:55,10:65,0:0:2,0:24.2:1:30.5:1:1:0:59.9:12:1:0:0.3 0/1:69:4:3,1:57,8:65,4:0.058:2,2:12.3:1:30.8:1:0.43593:2.33631:60:8:0.0606:0:1.5 +3 47147076 . G A 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04635;SOR=Inf;LSEQ=CTTTTTGAAAACAAATAGAC;RSEQ=CTATTTATACTGCTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:79,80:159,0:0:2,0:27.4:1:30.8:1:1:0:60:52:1:0:0.1 0/1:251:7:4,3:122,122:244,7:0.0279:2,2:33.3:1:30.1:1:1:1.33:60:14:0.028:0:1 +3 47147087 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.143;SOR=0;LSEQ=CAAATAGACGCTATTTATAC;RSEQ=GCTCTGCCCCTCATTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:73,83:156,2:0.0127:2,2:21.5:1:30:1:1:1.14:60:4:0.0127:0:1 0/0:259:0:0,0:126,133:259,0:0:2,0:26.5:1:29.9:1:1:0:59.9:258:1:0:0.2 +3 47147131 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50642;SOR=Inf;LSEQ=TTAATATATTTTAGAAATCA;RSEQ=TCGGCAGGACACGGTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:41,73:114,0:0:2,0:25.1:1:32.3:1:1:0:60:228:0.9913:0:0.1 0/1:149:2:1,1:58,89:147,2:0.0134:2,2:31.5:1:29:1:1:1.53:60:4:0.0136:0:1.5 +3 47147150 . T C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50092;SOR=Inf;LSEQ=AGTCGGCAGGACACGGTGGC;RSEQ=CATGCCTGTAATCTCAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:25,62:87,0:0:2,0:25.7:1:30.5:1:1:0:59.1:86:1:0:0.1 0/1:103:2:1,1:37,64:101,2:0.0194:2,2:7.5:1:28:1:1:1.72:60:4:0.0196:0:1.5 +3 47155304 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15312;SOR=0;LSEQ=GTGCCACTGCACTCCAGTCT;RSEQ=GGTGAAAGAGTGAGACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:145,38:183,2:0.0108:2,2:19.5:1:29:1:0.37808:3.77952:60:4:0.011:0:1 0/0:287:0:0,0:210,77:287,0:0:2,0:22.9:1:30.9:1:1:0:59.9:94.667:1:0:0.1 +3 47162661 . A G 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42111;SOR=1.08264;LSEQ=TGAGAAAGTTCAGGCAGGCG;RSEQ=TTATCTATTTGTTTTCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:748:328:146,182:217,201:418,328:0.4385:2,2:25.4:1:31.8:1:0.04663:1.34525:60:53.667:0.4399:0:1.1 0/1:1135:520:264,256:317,290:607,520:0.4581:2,2:25.9:1:30.8:1:0.63292:1.05991:59.8:73.286:0.4597:0:1.1 +3 47164928 . G A 55 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82881;LSEQ=GTGAGATCTGCTCCGCCGTC;RSEQ=CTCTCTTTCTGATCTACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:149,133:282,3:0.0105:2,2:13.7:1:26.7:1:1:1.78:49.3:6:0.0108:0:1 0/0:461:4:3,1:231,226:457,4:0.0087:2,2:21.5:1:27.5:1:0.62354:2.93:60:8:0.0088:0:1.3 +3 47164945 . C T 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16295;SOR=Inf;LSEQ=GTCGCTCTCTTTCTGATCTA;RSEQ=ATCGGGAAGATACATACCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:162,148:310,0:0:2,0:22.4:1:32.3:1:1:0:59.7:102.333:1:0:0.1 0/1:475:5:2,3:235,235:470,5:0.0105:2,2:20.4:1:20.2:1:1:1.49873:60:1.5:0.0064:0:1 +3 47168219 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13366;SOR=Inf;LSEQ=TCATAAATACTTAAAAACGA;RSEQ=TGAAATAATAGTTATTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:34,145:179,0:0:2,0:21.2:1:30.6:1:1:0:60:58.667:1:0:0.1 0/1:227:4:1,3:44,179:223,4:0.0176:2,2:14.8:1:31.8:1:1:1.35:60:8:0.0178:0:1 +3 47204939 . G T 57 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACCGGCGCCCTCTTGCC;RSEQ=GGCCCGGCACCGGCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:33.8:1:28.8:1:1:0:60:8:1:0:1 +3 47205254 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58744;SOR=0.39869;LSEQ=GGGCCTGTTACTCCTCGCGC;RSEQ=GGCCCGCGCCGCCACCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:157,26:183,2:0.0108:2,2:24:1:29:1:0.27127:5.94445:60:4:0.011:0:1 0/0:231:1:0,1:189,41:230,1:0.0043:2,0:1:0:24:0:0.18182:0:60:2:0.0043:0:1 +3 48285282 . CA C 83 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.25241;SOR=0.35853;LSEQ=CCAAGAGTGAAAGTCTGTCT;RSEQ=AAAAAAAAAAAAAAGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:7,1:8,6:0.4:2,0:22.3:1:32.4:1:1:0:57.7:12:0.4:0.1333:0.5 0/1:16:3:3,0:12,1:13,3:0.1875:1,0:17.3:1:31:1:1:0:48.3:6:0.1875:0.0625:3 +3 48285318 . C A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51186;SOR=Inf;LSEQ=GGCAGTAACACTAAGTTGAA;RSEQ=TTTAGAAGGATAATAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:16,8:24,0:0:2,0:21:1:29.8:1:1:0:59.1:7:1:0:1 0/1:36:2:2,0:22,12:34,2:0.0556:2,0:24:1:24.5:1:0.54286:0:33:4:0.0714:0:6 +3 48456008 . G A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CATCAGGACCCGGGCCACCA;RSEQ=CCAAGCAGTCCAGCTCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:29.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:23:0:27:0:1:0:60:2:1:0:0 +3 48514994 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23436;SOR=0;LSEQ=CAGCACTCTCTCCAATCTGT;RSEQ=TCCCCATGTTCTCCCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:90,38:128,2:0.0154:2,2:9.5:1:31:1:0.51163:2.35083:60:4:0.0155:0:1 0/0:138:0:0,0:94,44:138,0:0:2,0:25.6:1:30.5:1:1:0:60:68:1:0:0.2 +3 48515064 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25871;SOR=Inf;LSEQ=CATGTCACCACCTGCTCAAA;RSEQ=GCCAGCTATGGCTCCTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:91,108:199,0:0:2,0:25:1:30.8:1:1:0:60:198:1:0:0.5 0/1:252:3:1,2:124,125:249,3:0.0119:2,2:21.7:1:28.3:1:1:1.97881:60:6:0.0121:0:2.7 +3 48515065 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58531;SOR=0.39237;LSEQ=ATGTCACCACCTGCTCAAAC;RSEQ=CCAGCTATGGCTCCTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:2,0:89,106:195,2:0.0102:2,0:24:1:29:1:0.21211:0:60:4:0.0102:0:1.5 0/0:250:1:1,0:126,122:248,1:0.004:2,0:1:0:25:0:1:0:60:2:0.0041:0:1 +3 48515079 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45084;SOR=0.85654;LSEQ=TCAAACGCCAGCTATGGCTC;RSEQ=TGTAGCTCTTGCGATTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:97:42,55:43,61:104,97:0.4826:2,2:25.3:1:30.3:1:0.88645:1.08:60:31.333:0.4796:0:1.1 0/1:259:115:57,58:61,83:144,115:0.444:2,2:21.7:1:30:1:0.26072:1.34:60:230:0.4475:0:1.2 +3 48515221 . G A 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=GGCTCACACCTGCAATCCCA;RSEQ=CACTTTGGGAGGCCGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:0,9:1,8:9,9:0.5:2,0:33.2:1:30.9:1:1:0:60:18:0.5:0:1 0/0:29:0:0,0:1,28:29,0:0:1,0:18.8:1:31.7:1:1:0:60:58:1:0:0 +3 48541446 . G T 46 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2757;SOR=Inf;LSEQ=ACGGGCCGCCCCCACCCCCG;RSEQ=CTCACCACCCGGAGGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:38,52:90,0:0:2,0:27.6:1:31.3:1:1:0:60:89:1:0:0.1 0/1:134:3:1,2:62,69:131,3:0.0224:2,2:5:1:29.3:1:1:1.78957:60:6:0.0227:0:1.3 +3 48541449 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51542;SOR=Inf;LSEQ=GGCCGCCCCCACCCCCGGCT;RSEQ=ACCACCCGGAGGCGGCGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:41,57:98,0:0:2,0:26.7:1:31.7:1:1:0:60:97:1:0:0.2 0/1:143:2:1,1:66,75:141,2:0.014:2,2:19:1:28.5:1:1:1.14:60:4:0.0141:0:1 +3 48541480 . CA C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.52389;SOR=Inf;LSEQ=GGCGGCGTTAGCAGCAGCAG;RSEQ=ACAGCAACGGCAACAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:30,67:97,0:0:2,0:30.1:1:31.3:1:1:0:60:96:1:0:0.2 0/1:154:2:1,1:60,92:152,2:0.013:2,2:28.5:1:30:1:1:1.53:60:4:0.0132:0:0 +3 48541513 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26973;SOR=Inf;LSEQ=AACAGGATCCGCGGCGCGGG;RSEQ=ACCGGCGCAGTCATGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:16,45:61,0:0:2,0:23:1:31.2:1:1:0:60:29.5:1:0:0.2 0/1:88:3:2,1:25,60:85,3:0.0341:2,2:14:1:26.7:1:0.22177:4.70:60:6:0.0345:0:1.3 +3 49259335 . A G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52425;SOR=0;LSEQ=GAAAGGCACTGTCTGATTTC;RSEQ=GAAGCCTTTTCCTATAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:13,22:35,2:0.0541:2,2:13:0:32.5:1:1:1.67:24:4:0.0541:0:1.5 0/0:22:0:0,0:8,14:22,0:0:2,0:18.1:1:30.2:1:1:0:57.4:44:1:0:0 +3 49259423 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=ACTCTTACCCTAAGAAGGTG;RSEQ=AGAGTCCTCCTTTCTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:6,0:0:2,0:11.3:1:30.8:1:1:0:48.5:5:1:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:28:1:28.5:1:1:1.73:25.5:4:0.4:0:1 +3 49396360 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGCCTCCTCAGGCTGCA;RSEQ=TCACCCTACCCCCAAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:30:1:1:0:60:4:1:0:1 +3 49397284 . T A 38 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTACCTTGCAGCTGACAGA;RSEQ=AATAGGCAGGACATGTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:28.3:1:24:1:1:0:49.3:2:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 49397824 . G GA 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.04071;SOR=2.22642;LSEQ=TTTCACCGGCTCCTAGCAAA;RSEQ=AAAAAAAAATAGTCCTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:9:1,8:107,341:448,9:0.0197:2,2:28.7:1:31.1:1:0.69255:2.5065:60:18:0.02:0.0022:0.1 0/1:655:28:4,24:195,429:624,28:0.0427:2,2:28.2:1:30.6:1:0.06049:2.72391:59.3:56:0.0439:0:0.4 +3 49397900 . A AT 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.66116;SOR=1.81738;LSEQ=TATTCAAATTCATCTAAAAG;RSEQ=TTTTTTTTTCTTTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:0,2:0,113:113,2:0.0174:1,0:27.5:1:32:0:1:0:60:4:0.0179:0:0 0/1:96:3:0,3:1,91:92,3:0.0313:1,0:28:1:31:0:1:0:60:6:0.0319:0:0 +3 49400143 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1884;SOR=Inf;LSEQ=CCTCAGTGAAATTGCAGAGA;RSEQ=ACTTTCTTTGTGGCTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:2,116:118,0:0:1,0:27.7:1:32:1:1:0:59.7:22.6:1:0:0.1 0/1:91:2:1,1:1,88:89,2:0.022:1,2:44.5:1:31:1:0.04371:62.58:60:4:0.022:0:2 +3 49406080 . T C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=20.80481;LSEQ=TACATTGAAATGGCAGACCA;RSEQ=TGAAATGGCAGACGGTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:9:0,9:1,123:124,9:0.0677:1,0:27:1:33.8:1:1:0:60:18:0.0703:0:1.2 1/0:114:69:1,68:1,44:45,69:0.6053:1,1:27:1:30.8:1:1:1.53934:59.7:16.25:0.5909:0:1.1 +3 49406095 . G A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00731;SOR=Inf;LSEQ=GACCATTGAAATGGCAGACG;RSEQ=TCTAAAACAGTAAAACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:1,105:106,0:0:1,0:26.2:1:31.2:1:1:0:59.5:12.25:1:0:0.3 0/1:86:6:0,6:1,79:80,6:0.0698:1,0:27.5:1:30.3:1:1:0:57.5:12:0.0706:0:1.5 +3 49433133 . G A 43 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTAGCCTGGGCAACAGAGC;RSEQ=AGACTCTGTCTCCAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:1,3:0.75:0,2:21.3:1:27.3:1:1:0:50.3:6:0.75:0:1 +3 49433201 . G GT 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00191;SOR=0.03302;LSEQ=AGGGCACGAAAAGTGATTGA;RSEQ=TGGTTAACTGGATAGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:10,0:1,0:1,10:0.9091:0,0:25.5:1:30.6:1:1:0:60:20:0.9091:0.0909:0.5 0/1:10:2:2,0:8,0:8,2:0.2:0,0:18:1:30:1:1:0:60:4:0.25:0.1:0 +3 49433401 . C T 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.2661;LSEQ=GTAAAAACAGCATAGTCTTC;RSEQ=AGTGTATGGAATGGAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:474:473:275,198:0,0:0,473:0.9979:0,2:24.8:1:30.2:1:1:0:59.9:58.125:1:0:1.2 1/1:600:599:344,255:0,1:1,599:0.9983:0,2:24.2:1:29:1:0.42667:0:60:148.75:0.9983:0:1.2 +3 49721532 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.87858;LSEQ=CGTGAAGACAGCTGGCCAGC;RSEQ=GGACCTTGCGCATACTCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1227:92:43,49:582,552:1134,92:0.075:2,2:28.8:1:31.6:1:0.44812:1.20128:30.9:184:0.076:0:1.1 0/1:1271:168:91,77:554,546:1100,168:0.1322:2,2:27.3:1:30:1:0.36357:1.16:30.7:83:0.1313:0:1.3 +3 49721606 . G A 68 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09461;SOR=6.24319;LSEQ=TGTGGGTAAAGCAGGCAAGT;RSEQ=GGCCCCCGTAGTCACCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:1:1,0:207,166:373,1:0.0027:2,0:1:0:23:0:1:0:60:2:0.0027:0:1 0/1:303:5:3,2:139,159:298,5:0.0165:2,2:11.4:1:29.4:1:0.66807:1.71:47.4:10:0.0168:0:1.2 +3 49721622 . C T 80 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14568;SOR=3.68129;LSEQ=AAGTGGGCCCCCGTAGTCAC;RSEQ=CTGGCAGGTAGGAGAACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:50,39:89,2:0.022:2,2:11:0:33:1:1:1.27851:55:4:0.0222:0:1 0/1:78:6:3,3:33,39:72,6:0.0769:2,2:8.7:1:31.3:1:1:1.18:52.5:12:0.0769:0:1.5 +3 49721771 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14562;SOR=0;LSEQ=CAGGCCCCCACAGGGGCCAA;RSEQ=AGTCCCTCAGTGCACATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:32,35:67,2:0.029:2,2:13.5:1:32:1:1:1.09:46:4:0.0299:0:2.5 0/0:111:0:0,0:57,54:111,0:0:2,0:14.4:1:31.4:1:1:0:50.6:222:1:0:0.5 +3 49721798 . C A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20572;SOR=2.35419;LSEQ=TCAGTGCACATCTCACTCTC;RSEQ=CGCACACGTCCTCGGTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:4:2,2:39,42:81,4:0.0471:2,2:12.3:1:32:0:1:1.08:34:8:0.0482:0:2 0/1:134:14:7,7:61,59:120,14:0.1045:2,2:20.4:1:30.7:1:1:1.03365:25.3:28:0.1061:0:1.4 +3 49722056 . G A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACCATTCAGGGGGCAGGCA;RSEQ=ATCAGGGCCACACGCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:31:2:1:0:4 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23.5:1:30.5:1:1:1:20:4:0.3333:0:1.5 +3 49722164 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.22829;SOR=Inf;LSEQ=TCACACCCTCCCAGGTTGTC;RSEQ=ACATACCTCTCCAGCTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:52,48:100,0:0:2,0:37.9:1:31.8:1:1:0:21.5:49:1:0:0.1 0/1:92:2:1,1:50,40:90,2:0.0217:2,2:39.5:1:26.5:1:1:1.24694:22:4:0.022:0:1 +3 49722185 . C T 47 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42834;SOR=2.25714;LSEQ=ACATACCTCTCCAGCTTGAG;RSEQ=AGGACAAGCTGGGAGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:2:1,1:191,191:382,2:0.0052:2,2:21:1:24:1:1:1:41.5:4:0.0053:0:1.5 0/1:343:4:1,3:189,150:339,4:0.0117:2,2:19.5:1:23.8:1:0.32779:3.76626:41:3:0.0089:0:1.3 +3 49722319 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1957;SOR=Inf;LSEQ=GCCCGTGAGAGGCATATGGC;RSEQ=GGAGAGAAGCTCTGCTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,6:16,0:0:2,0:5.1:1:31.8:1:1:0:55.1:32:0.9412:0:0 0/1:14:2:1,1:8,4:12,2:0.1429:2,2:12:1:29.3:1:1:1.89743:60:4:0.1429:0.0714:0 +3 49722323 . A T 54 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10922;SOR=Inf;LSEQ=GTGAGAGGCATATGGCTGGG;RSEQ=GAGAAGCTCTGCTAGGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:23,0:0:2,0:6.4:1:30.9:1:1:0:54.9:46:1:0:0 0/1:24:4:1,3:11,9:20,4:0.1667:2,2:7:1:27.3:1:0.59006:3.48031:56.3:8:0.1667:0:1.3 +3 49722356 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49635;SOR=Inf;LSEQ=TAGGTCATTTGTGACTCTCA;RSEQ=TCCATTGCCCCAAGGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:27,39:66,0:0:2,0:28:1:32.9:1:1:0:55.8:65:1:0:0.1 0/1:68:2:1,1:26,40:66,2:0.0294:2,2:17:0:31.5:1:1:1.53:60:4:0.0299:0:1.5 +3 49722502 . C G 82 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCTTCACTAGAGACCCC;RSEQ=CGCAGAAATGCTGGCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:0,6:1:0,2:12:0:31.8:1:1:0:55:12:1:0:1 +3 49722702 . G C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1875;SOR=Inf;LSEQ=AGTTGTGCCTCACCGATTCC;RSEQ=CAAGCTGACTGTCCAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:26,10:36,0:0:2,0:5.2:1:30.4:1:1:0:50.2:72:1:0:0.1 0/1:28:2:1,1:14,10:24,2:0.0714:2,2:17:0:32.5:1:1:1.38168:55:4:0.0714:0:1 +3 49722725 . T A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50243;SOR=Inf;LSEQ=AGCTGACTGTCCAGGGTGAG;RSEQ=TGCCCGGATGGCCCCCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:65,45:110,0:0:2,0:19:1:30.6:1:1:0:53.2:109:1:0:0.2 0/1:133:2:1,1:73,58:131,2:0.015:2,2:15:0:30:1:1:1.25642:60:4:0.0152:0:1.5 +3 49722761 . C A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=CAACCACGCGCAGCTTGGAA;RSEQ=GCCGCTGATCCAGCCGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:77,57:134,0:0:2,0:33.7:1:31.6:1:1:0:52.2:43.667:1:0:0.2 0/1:168:14:7,7:84,69:153,14:0.0833:2,2:22:1:31.1:1:0.78387:1.21595:32.4:28:0.0843:0:1.4 +3 49723075 . C T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68158;SOR=0.64431;LSEQ=AATGGGGTCCTTGGGTCCAT;RSEQ=GTGTAGCACCAGGGCCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:0,3:116,136:252,3:0.0117:2,0:12:1:28.3:1:0.25317:0:34.3:6:0.0121:0:1 0/0:264:2:0,2:125,137:262,2:0.0076:2,0:1:0:25:1:0.49951:0:22.5:4:0.0076:0:1 +3 49723147 . T C 233 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCCAGTTGTGCATGCGG;RSEQ=TCGGAGGTAAACGTGAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1339:0:0,0:610,727:1337,0:0:2,0:27.9:1:30:1:1:0:32.6:69.368:0.9992:0:0.2 0/1:1423:175:82,93:576,671:1247,175:0.123:2,2:27.3:1:31.3:1:0.87177:1.03:30.6:86.5:0.1234:0:1.2 +3 49723274 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=GTTAGGGCCCTGGCGGGGCC;RSEQ=GGAGCACCAGGGACTCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:20.5:1:30.9:1:1:0:60:20:1:0:0.3 1/0:4:2:1,1:0,2:2,2:0.5:0,2:12.5:1:31.5:1:1:0:41:4:0.5:0:1.5 +3 49723344 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03374;SOR=Inf;LSEQ=GCTGGCACTGGACACCCTTG;RSEQ=GGGTCTTGCTGACCGTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:534:0:0,0:243,291:534,0:0:2,0:17.8:1:30.5:1:1:0:25.5:52.4:1:0:0.2 0/1:402:4:1,3:197,201:398,4:0.01:2,2:13.3:1:25.5:1:0.62329:2.93333:31.8:3:0.0076:0:1.3 +3 49723504 . G T 29 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6194;SOR=2.0541;LSEQ=TTGGGCCTCACCCTGGGGCC;RSEQ=CACGTCGTCTGTACAACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:0,1:45,56:101,1:0.0098:2,0:1:0:29:0:1:0:21:2:0.0098:0:1 0/1:100:2:1,1:53,45:98,2:0.02:2,2:5:0:29:1:1:1.17584:23:4:0.02:0:1.5 +3 49723518 . C T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.92081;LSEQ=GGGGCCGCACGTCGTCTGTA;RSEQ=AACGCCGGATCTGGTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:0,1:59,70:129,1:0.0077:2,0:1:0:25:0:1:0:20:2:0.0078:0:1 0/1:136:2:1,1:71,63:134,2:0.0147:2,2:5.5:1:27:1:1:1.12599:60:4:0.0147:0:1.5 +3 49723739 . A C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.86994;SOR=0.89901;LSEQ=AACGCCCGCCCCCCCCCCCC;RSEQ=CCTCACTTGCACGCGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:29:28,1:3,196:199,29:0.1255:1,1:8.9:1:23.9:1:0:1449.28:32.9:4.8:0.1127:0:2.8 0/1:140:16:15,1:4,119:123,16:0.1143:1,1:12.6:1:20.7:1:0:371.75:32.1:1.667:0.0794:0:2.3 +3 49723750 . A G 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02;SOR=Inf;LSEQ=CCCCCCCCCACCTCACTTGC;RSEQ=CGCGTATTTTTCTGGCGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:5,173:178,0:0:1,0:23.2:1:30:1:1:0:31.6:28.667:1:0:1.6 0/1:110:4:0,4:4,100:104,4:0.0364:1,0:21:1:33:1:1:0:29:8:0.0392:0:3.3 +3 49723784 . C A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11413;SOR=0.27443;LSEQ=GGCGTAAATCGGTGCTGATG;RSEQ=GGGATTTGCGCGTCCCAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:49:0,49:2,1:3,49:0.9423:2,1:16.4:1:33.1:1:0.00226:0:22.7:48:0.9796:0:1.7 1/1:27:22:1,21:2,3:5,22:0.8148:2,1:13.5:1:31.5:1:0.07863:11.89071:26.4:44:0.88:0:2.6 +3 49723916 . T G 30 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=CGGGGCTGTGCCTCGGACCC;RSEQ=TAGATGGACCGAGATAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:6:0:30.5:1:1:1.29:60:4:0.2222:0:1.5 0/0:6:0:0,0:2,3:5,0:0:2,0:12.8:1:28:1:1:0:53.4:10:0.8333:0:2 +3 49723992 . C A 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49275;SOR=0;LSEQ=GGGACCAAACCCGCCTTTCC;RSEQ=AGGTGTACGGTACTCCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:8,4:12,2:0.1429:2,2:16:0:29.5:1:1:1.89743:60:4:0.1429:0:1 0/0:10:0:0,0:5,5:10,0:0:2,0:10:1:28.7:1:1:0:60:9:1:0:0.3 +3 49724254 . C A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5073;SOR=0;LSEQ=ACCTGGGGGCGGTAATGGGG;RSEQ=GTGAACAAGACCCTGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:20,24:44,2:0.0435:2,2:22:1:33:1:1:1.20:21.5:4:0.0435:0:1 0/0:33:0:0,0:17,16:33,0:0:2,0:32.3:1:30.3:1:1:0:58.8:32:1:0:0.2 +3 49724798 . T G 86 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06239;SOR=0.21233;LSEQ=GGGAAGGTGTTTGTCTCACT;RSEQ=GTGATCATTTGGGAACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:6:3,3:46,84:130,6:0.0441:2,2:8.5:1:33.5:1:0.6669:1.82:52.5:12:0.0441:0:1.8 0/0:207:2:1,1:73,132:205,2:0.0097:2,2:18:0:32.5:1:1:1.80:52.5:4:0.0097:0:2.5 +3 49724808 . T C 186 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02688;LSEQ=TTGTCTCACTTGTGATCATT;RSEQ=GGGAACTTGTGGCTCCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:55:7,48:0,0:0,55:0.9821:0,2:5.6:1:30.4:1:1:0:57.5:110:0.9821:0:1.1 1/0:123:73:16,57:26,24:50,73:0.5935:2,2:6.9:1:30.2:1:0.00089:3.81278:58.5:146:0.5935:0:1.2 +3 49724830 . T G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAACTTGTGGCTCCAAGCC;RSEQ=GGCAGGGCAGGCCACCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:45:2:1,1:24,19:43,2:0.0444:2,2:39.5:1:30.5:1:1:1.25655:22:4:0.0444:0:1 +3 49725284 . CT C 149 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATGTAGCAGGTGCTGTAG;RSEQ=CTGTGCCCCGGAGCACTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:25:6,19:209,245:454,25:0.0521:2,2:27.9:1:32.1:1:0.03805:2.69613:33.4:50:0.0527:0:0.1 0/0:485:0:0,0:228,257:485,0:0:2,0:19.6:1:28.8:1:1:0:36.1:59.625:1:0:0.1 +3 49725432 . AG A 27 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGGGGATCAAAGCTACA;RSEQ=GCTTCTGGGATGGACCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:6.5:1:27.5:1:1:0:45.5:4:1:0.5:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 49726061 . G T 38 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.63289;SOR=0.41513;LSEQ=TAAGCATTGAGTCAGAAGCA;RSEQ=CAGGAGTGGGAGCCACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:3:2,1:155,130:285,3:0.0104:2,2:14:1:24.3:1:1:1.67:27.7:2:0.0071:0:3.3 0/0:231:1:1,0:136,93:229,1:0.0043:2,0:3:0:27:0:1:0:24:2:0.0044:0:1 +3 49924940 . T C 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.60625;LSEQ=CACCTCCCCCACTAGTACTC;RSEQ=GAAGGTGGGTCGCACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1115:64:30,34:456,593:1049,64:0.0574:2,2:24.6:1:30:1:0.60579:1.15:59.9:20.333:0.056:0:1.2 0/1:1047:455:189,266:265,327:592,455:0.4346:2,2:24.4:1:29.6:1:0.31437:1.14041:60:112.75:0.4357:0:1.2 +3 49926904 . C A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCTCAGCACCGAACCCACC;RSEQ=CGTAGGCACTGAGGACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:24:0:31:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:30:1:1:0:60:4:1:0:1 +3 49927503 . G T 212 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAATGACCACTGTGGAAA;RSEQ=GGGGAGGTGAGGGGACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1089:0:0,0:443,643:1086,0:0:2,0:25:1:31.8:1:1:0:60:97.727:0.9972:0:0.2 0/1:1023:151:59,92:375,496:871,151:0.1476:2,2:23.7:1:29.4:1:0.3739:1.17873:60:150:0.1473:0:1.1 +3 49927593 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15077;SOR=Inf;LSEQ=AGAGTCCTTCAGCTGGAAAT;RSEQ=GAAGACCCTACCCTCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:14,242:256,0:0:2,0:26:1:31.7:1:1:0:59.8:84.333:1:0:0.1 0/1:163:2:0,2:6,155:161,2:0.0123:1,0:10:1:30.5:1:1:0:60:4:0.0123:0:1 +3 49927722 . A C 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00379;SOR=Inf;LSEQ=TGGATTATCTGTGAGGAGCC;RSEQ=GTGAGTTCCCAGCCTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:43,19:62,0:0:2,0:22:1:31.1:1:1:0:59.5:124:1:0:0 0/1:22:4:3,1:12,6:18,4:0.1818:2,2:31:1:29.5:1:1:1.47:60:8:0.1818:0:1 +3 49928160 . GA G 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20462;SOR=Inf;LSEQ=ACCTGTTCTAGGCCCTTACA;RSEQ=ATTTTTTTTTTTTTTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:12,215:227,0:0:2,0:23.9:1:31.2:1:1:0:55:31.429:1:0:0.3 0/1:188:2:0,2:14,172:186,2:0.0106:2,0:17.5:1:26.5:1:1:0:20.5:4:0.0109:0.0053:1.5 +3 49928614 . T A 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTTTGCTTCACCCCAGC;RSEQ=ACTCTGGACTCTCACATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:681:0:0,0:450,231:681,0:0:2,0:24.4:1:30.5:1:1:0:60:67.1:1:0:0.4 0/1:702:41:30,11:428,233:661,41:0.0584:2,2:26.2:1:30.3:1:0.31341:1.48:60:82:0.0591:0:1.6 +3 49928691 . T C 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.65445;SOR=0.74639;LSEQ=CTCTGCCAGGTACTCCATGC;RSEQ=GCGGGCTACCTGCAGGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1272:1264:653,611:1,3:4,1264:0.9937:2,2:25.1:1:30.6:1:0.35936:3.20:60:65.526:0.996:0:1.1 1/1:1427:1415:701,714:0,6:6,1415:0.9916:0,2:25.5:1:29.7:1:0.031:0:59.9:82.235:0.9929:0:1.2 +3 49929025 . C A 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGATGCCTGCAGAGCAG;RSEQ=GCAAGTCAGGCACAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:754:0:0,0:304,449:753,0:0:2,0:25.3:1:30.7:1:1:0:60:56.923:0.9987:0:0.1 0/1:707:119:45,74:232,353:585,119:0.1683:2,2:25.8:1:29.3:1:0.75788:1.08067:60:58.5:0.1671:0:1.2 +3 49929047 . G T 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=Inf;LSEQ=CAAGTCAGGCACAGGGCAGG;RSEQ=CGTCCCTTTATAAGGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:672:0:0,0:281,391:672,0:0:2,0:23.9:1:31.6:1:1:0:60:43.8:1:0:0.1 0/1:571:30:14,16:212,329:541,30:0.0525:2,2:26.6:1:29.2:1:0.44626:1.36:60:60:0.053:0:1.1 +3 49929321 . G A 62 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02702;SOR=8.41333;LSEQ=GAGGGGATCCAGGGCCCAAG;RSEQ=CTCACACCACACATTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:1:1,0:244,549:793,1:0.0013:2,0:1:0:27:0:0.30856:0:60:2:0.0013:0:1 0/1:666:7:5,2:225,434:659,7:0.0105:2,2:9.6:1:22.4:1:0.05164:4.81:60:6:0.0092:0:1.3 +3 49934446 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57031;SOR=2.88771;LSEQ=CCCACCTGCCCCACTCCATG;RSEQ=TCTGTCTGAAAATAAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:10,161:171,1:0.0058:2,0:28:0:14:0:0.06395:0:60:0:0:0:6 0/1:120:2:1,1:0,118:118,2:0.0167:1,2:20.5:1:29.5:1:0.01667:0:60:4:0.0172:0:1.5 +3 49934678 . C T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00702;SOR=0;LSEQ=GGTCCCCACCTGGATAGAAC;RSEQ=CTGCGGCCTCCCATGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:7:1,6:352,167:519,7:0.0133:2,2:11.6:1:27.3:1:0.00605:12.59002:60:14:0.0136:0:1 0/0:539:0:0,0:366,172:538,0:0:2,0:23.3:1:30:1:1:0:60:88.667:0.9981:0:0.2 +3 49935385 . TC T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00547;SOR=Inf;LSEQ=AACCACTGCAGCTTCCCCCA;RSEQ=CCCCCTTGCCTCTGATAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:462,247:709,0:0:2,0:24.7:1:31.5:1:1:0:59.9:63.455:0.9986:0:0.1 0/1:646:7:3,4:422,217:639,7:0.0108:2,2:13:1:27.3:1:0.2383:2.5888:60:14:0.0111:0.0062:0.6 +3 49935526 . T G 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGTGGCCGGCAGGGACTT;RSEQ=GGCCCACAGTGACCTGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1498:0:0,0:750,745:1495,0:0:2,0:24.4:1:30.7:1:1:0:60:64:0.998:0:0.1 0/1:1574:34:15,19:746,791:1537,34:0.0216:2,2:22.3:1:31:1:0.72923:1.19447:59.8:68:0.0218:0:1.3 +3 49936102 . T C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.35242;LSEQ=AGTGGCGGCAGCCAGGGCCT;RSEQ=GGATAGGTACCTGGAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1336:74:35,39:583,677:1260,74:0.0554:2,2:24.7:1:30.8:1:0.9048:1.04:60:36:0.055:0:1.1 0/1:1311:551:244,307:349,407:756,551:0.4203:2,2:23.6:1:29.6:1:0.53605:1.07883:60:41.385:0.418:0:1.2 +3 49936278 . G A 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCCACAACCCTGGCCCCAG;RSEQ=CCCTGCCCCTGCCCACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:0:0,0:478,303:781,0:0:2,0:24.7:1:31.4:1:1:0:60:36.19:1:0:0.1 0/1:738:41:25,16:444,252:696,41:0.0556:2,2:19.7:1:27.7:1:0.73978:1.12743:60:82:0.0567:0:1.1 +3 49936626 . G A 184 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=41.99761;LSEQ=CATTGAATAGGTCCACACGT;RSEQ=AGAAGCTGCTACTGACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1292:2:2,0:618,672:1290,2:0.0015:2,0:1:0:26.5:1:0.23009:0:60:4:0.0016:0:1 0/1:1504:92:49,43:693,718:1411,92:0.0612:2,2:23:1:28.3:1:0.45323:1.18:59.9:45:0.0605:0:1.2 +3 49936715 . G A 210 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=155.19755;LSEQ=GGCTGGGAAAGGTCAGGGAA;RSEQ=GGAAGGAGTCAGGGTTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:715:1:1,0:234,477:711,1:0.0014:2,0:1:0:26:0:0.33006:0:60:2:0.0014:0:1 0/1:727:130:43,87:214,383:597,130:0.1788:2,2:22.7:1:30:1:0.61297:1.13026:59.8:129:0.1787:0:1.2 +3 49936910 . T A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00923;SOR=Inf;LSEQ=GCCCAGGCTGGAAGGTCCAC;RSEQ=CCTCATTCTCCCTGCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:23,0:0:1,0:24.8:1:29:1:1:0:57.4:22:1:0:0.1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:7.5:1:30.5:1:1:0:60:4:0.6667:0:1 +3 49939587 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05303;SOR=Inf;LSEQ=GCAGGTAGGGGAAAGAGCAA;RSEQ=ATGAGGCAGCCACAAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:25,0:0:1,0:25.9:1:33.8:1:1:0:60:50:1:0:0.4 0/1:8:2:2,0:6,0:6,2:0.25:0,0:9:1:30.5:1:1:0:60:4:0.25:0:1 +3 49939704 . G A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26877;SOR=0;LSEQ=GAGAGAGAATGCTTCTTTCC;RSEQ=CCTGCCCCCCCACCGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:2,1:254,7:261,3:0.0113:1,2:25.7:1:24:1:0.08851:17.41132:60:2:0.0078:0:2 0/0:190:0:0,0:185,5:190,0:0:1,0:24.1:1:29.5:1:1:0:59.9:37:1:0:0.2 +3 49940812 . G T 154 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=19.21922;LSEQ=TCAGGCCCAAGCACATGCAG;RSEQ=CGATTGCGTATGGCTACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1357:2:0,2:662,691:1353,2:0.0015:2,0:25.5:1:20:1:0.49989:0:60:1:8e-04:0:4.5 0/1:1558:43:20,23:738,775:1513,43:0.0276:2,2:25.9:1:28.5:1:0.87731:1.09501:60:42:0.0274:0:1.1 +3 50138144 . TA T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CCAAAGGAGTGACTTTTTTT;RSEQ=AAAAAAAAGCTTTGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:29.6:1:32.1:1:1:0:60:14:1:0:0 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:13.5:1:31.5:1:1:0:60:4:0.3333:0.1667:0 +3 50153003 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53529;SOR=Inf;LSEQ=CCAGTTCCCGAACAAAGATG;RSEQ=CCTAGTCAGGCACCAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:19,0:0:2,0:33.8:1:30.8:1:1:0:60:18:1:0:0.4 0/1:35:2:1,1:13,20:33,2:0.0571:2,2:43.5:1:29:1:1:1.52:60:4:0.0588:0:2 +3 50154728 . T A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16304;SOR=0;LSEQ=GGCATTGACCACAGTAACAT;RSEQ=GGCAACAAGATGCTGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:8,2:0.2:2,2:33:0:32:1:1:1:60:4:0.2:0:1 0/0:14:0:0,0:7,7:14,0:0:2,0:30.1:1:29.7:1:1:0:60:28:1:0:0.2 +3 50231540 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4902;SOR=0;LSEQ=CGCAGGATGTTCGATGTGGG;RSEQ=GGGCAGCGCTCGGAGCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:12,12:24,2:0.0769:2,2:40:0:32.5:1:1:1:60:4:0.0769:0:1 0/0:25:0:0,0:12,13:25,0:0:2,0:28.6:1:30.6:1:1:0:60:50:1:0:0.2 +3 52167577 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50113;SOR=Inf;LSEQ=ACACCAGCACACAGGTCCAG;RSEQ=CCAGGAGACCCAGGGCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:50,94:144,0:0:2,0:24.1:1:31.4:1:1:0:60:143:1:0:0.1 0/1:167:2:1,1:63,102:165,2:0.012:2,2:19.5:1:27:1:1:1.61:60:4:0.0123:0:1.5 +3 52436262 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04216;SOR=Inf;LSEQ=GGGAAGGACCCTGGTGAGGG;RSEQ=CACACGGCAAGAGTGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:458:0:0,0:335,123:458,0:0:2,0:25.5:1:31.7:1:1:0:60:56.25:1:0:0.1 0/1:381:4:1,3:264,113:377,4:0.0105:2,2:9:1:27.8:1:0.086:6.96928:60:8:0.0106:0:1 +3 52436441 . C A 236 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGGTTGGCCAGCATGCCTG;RSEQ=GAAGAGGTAGAGACCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:188:73,115:85,163:248,188:0.4302:2,2:24.8:1:31.3:1:0.36546:1.22:59.8:61.667:0.4282:0:1.1 0/0:333:0:0,0:116,217:333,0:0:2,0:21.9:1:29.9:1:1:0:60:110:1:0:0.1 +3 52436456 . C A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06911;SOR=Inf;LSEQ=GCCTGCGAAGAGGTAGAGAC;RSEQ=CTTGAGCAGGTGCTGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:120,230:350,0:0:2,0:24.5:1:31.4:1:1:0:59.9:49:1:0:0.5 0/1:246:3:2,1:75,168:243,3:0.0122:2,2:5.7:1:27.3:1:0.2316:4.45:60:6:0.0124:0:1 +3 52436473 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13565;SOR=Inf;LSEQ=GACCCTTGAGCAGGTGCTGG;RSEQ=TGCCTCAGGCCAGGAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:117,172:289,0:0:2,0:23.5:1:32.5:1:1:0:59.9:31.111:1:0:0.4 0/1:169:2:1,1:55,111:166,2:0.0118:2,2:33.5:1:27.5:1:1:2.01:60:4:0.0121:0:1 +3 52436545 . G T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08408;SOR=Inf;LSEQ=CTGCTCAAGCCTCAGGAGAG;RSEQ=CCAGGGGAGGGGAGCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:186,108:294,0:0:2,0:23.7:1:31.5:1:1:0:59.8:48:0.9965:0:0.1 0/1:231:3:0,3:151,76:227,3:0.013:2,0:6.7:1:26.3:1:0.03951:0:60:6:0.0133:0:1 +3 52436946 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1806;SOR=Inf;LSEQ=CCAGCAACAAAGCCCCACGA;RSEQ=CAATAGGCAGCTAGAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:37,191:228,0:0:2,0:22.2:1:31.9:1:1:0:59.9:21.8:1:0:0.2 0/1:169:2:1,1:17,150:167,2:0.0118:2,2:29.5:1:28.5:1:0.20224:8.60:60:4:0.012:0:1 +3 52438183 . A T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAAGCTGCCTCCCCACC;RSEQ=CCCACATCTCCTCCATCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:9,39:48,2:0.04:2,2:5:0:32.5:1:0.36327:4.16:60:4:0.0426:0:0 0/0:18:0:0,0:3,15:18,0:0:2,0:27.7:1:27.1:1:1:0:56.9:8:1:0:0.1 +3 52438386 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0902;SOR=Inf;LSEQ=GCTCAACATTATCTGCTGCA;RSEQ=GGCATTCTCAGACACAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:168,14:182,0:0:2,0:22.8:1:33:1:1:0:60:90:1:0:0 0/1:149:3:2,1:128,18:146,3:0.0201:2,2:18.7:1:28.7:1:0.33782:3.51008:60:6:0.0203:0:1 +3 52438651 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5027;SOR=0;LSEQ=CAAGTGCTGCTCGGCCCAGG;RSEQ=TGAGCCTAGACACTCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:29,133:162,2:0.0122:2,2:26.5:1:29:1:0.33331:4.53:60:4:0.0123:0:1 0/0:136:0:0,0:23,113:136,0:0:2,0:27:1:31.7:1:1:0:59.8:67:1:0:0.1 +3 52439375 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19911;SOR=Inf;LSEQ=CAAGAAAAGCTCACAGTCTC;RSEQ=CCGGCCCTGTGAACCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:21,100:121,0:0:2,0:22.3:1:31.5:1:1:0:60:59.5:1:0:0.1 0/1:98:2:1,1:14,82:96,2:0.0204:2,2:32.5:1:28:1:0.28403:5.69:60:4:0.0215:0:1 +3 52440173 . GT G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.19536;SOR=Inf;LSEQ=AAGCCCAGATCTACAAGAGA;RSEQ=ATGTTCACGAATCAGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:168,22:190,0:0:2,0:23.5:1:29.5:1:1:0:60:30.667:1:0:0.1 0/1:151:2:1,1:129,20:149,2:0.0132:2,2:33:1:30.5:1:0.2596:6.31891:60:4:0.0133:0:0 +3 52440188 . A G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07993;SOR=Inf;LSEQ=AGAGAGTATGTTCACGAATC;RSEQ=GAGACAAATGCTGTGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:210,49:259,0:0:2,0:23.2:1:30.4:1:1:0:60:31.375:1:0:0.1 0/1:197:3:2,1:158,36:194,3:0.0152:2,2:14.3:1:28.7:1:0.46615:2.18367:60:6:0.0155:0:1 +3 52440195 . A T 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26296;SOR=0;LSEQ=ATGTTCACGAATCAGAGACA;RSEQ=ATGCTGTGGGGGAAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:0,3:229,64:293,3:0.0101:2,0:9.3:1:20.7:1:0.0112:0:60:2:0.0069:0:1.3 0/0:224:0:0,0:176,48:224,0:0:2,0:22.7:1:28.8:1:1:0:60:27:1:0:0.2 +3 52440742 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21076;SOR=Inf;LSEQ=AAGCCTGATCTTGCCAGATT;RSEQ=ACCATATGGCCTTGCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:174,21:195,0:0:2,0:23.6:1:32.4:1:1:0:59.9:64:1:0:0.1 0/1:166:2:1,1:145,19:164,2:0.012:2,2:9.5:1:28:1:0.22709:7.46392:60:4:0.0121:0:1 +3 52441559 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2224;SOR=Inf;LSEQ=AGGCAAAGCTTCAGAGAGCA;RSEQ=CCTGGAGGCATTCCAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:34,166:200,0:0:2,0:23.8:1:32.4:1:1:0:59.9:49:1:0:0.1 0/1:179:2:1,1:31,146:177,2:0.0112:2,2:26.5:1:30.5:1:0.32641:4.65:60:4:0.0112:0:1 +3 52441564 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21907;SOR=Inf;LSEQ=AAGCTTCAGAGAGCAGCCTG;RSEQ=AGGCATTCCAGGAATCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:24,154:178,0:0:2,0:24.3:1:32.2:1:1:0:60:88:0.9944:0:0.1 0/1:158:2:1,1:21,135:156,2:0.0127:2,2:19:1:30:1:0.25986:6.30:60:4:0.0127:0:1 +3 52441565 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22137;SOR=Inf;LSEQ=AGCTTCAGAGAGCAGCCTGG;RSEQ=GGCATTCCAGGAATCGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:23,152:175,0:0:2,0:24.2:1:32:1:1:0:60:57.333:1:0:0 0/1:156:2:1,1:20,134:154,2:0.0128:2,2:30:1:29:1:0.25186:6.56:60:4:0.0131:0:1 +3 52441589 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21382;SOR=Inf;LSEQ=ATTCCAGGAATCGGAAGGAA;RSEQ=ACAGACGAACTTTCTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:8,110:118,0:0:2,0:23.3:1:32.7:1:1:0:60:58:1:0:0.1 0/1:102:2:1,1:4,96:100,2:0.0196:1,2:27.5:1:26.5:1:0.0961:21.58:60:4:0.0198:0:1 +3 52441606 . A T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02849;SOR=Inf;LSEQ=GAACACAGACGAACTTTCTT;RSEQ=AAAGGCTGGTGGGGGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:5,76:81,0:0:2,0:25.5:1:31:1:1:0:60:39.5:1:0:0.1 0/1:58:4:0,4:2,52:54,4:0.069:1,0:23.5:1:24.5:1:1:0:60:8:0.069:0:1 +3 52442055 . G A 80 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09143;SOR=0.24906;LSEQ=CTGCTGCAGTTCAGGAGCAC;RSEQ=CTCAGCAAGGCATGAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:594:7:5,2:253,334:587,7:0.0118:2,2:15.3:1:28.6:1:0.24866:3.29:60:14:0.0119:0:1 0/0:676:2:2,0:320,354:674,2:0.003:2,0:1:0:24.5:1:0.22652:0:60:4:0.003:0:1 +3 52442131 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24904;SOR=Inf;LSEQ=GTCACCCATACACAGCACCC;RSEQ=TCACTGCAAGCCCCAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:73,189:262,0:0:2,0:25.1:1:32.4:1:1:0:59.9:51.4:1:0:0.1 0/1:275:3:1,2:73,199:272,3:0.0109:2,2:14.3:1:25.7:1:1:1.36:57:2:0.0074:0:2 +3 52442132 . T C 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11587;SOR=0;LSEQ=TCACCCATACACAGCACCCC;RSEQ=CACTGCAAGCCCCAAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:1,2:71,181:252,3:0.0118:2,2:22:1:24:1:1:1.27:60:2:0.0081:0:3 0/0:267:0:0,0:70,196:266,0:0:2,0:23.9:1:28.3:1:1:0:60:21.167:0.9961:0:0.2 +3 52442142 . C A 42 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05619;SOR=Inf;LSEQ=ACAGCACCCCTCACTGCAAG;RSEQ=CCCAAGCCCATATACATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:56,169:225,0:0:2,0:25.4:1:31.3:1:1:0:59.9:44:1:0:0.2 0/1:215:4:3,1:44,167:211,4:0.0186:2,2:5.8:1:21.3:1:0.03353:11.21:60:3:0.0143:0:1.8 +3 52442625 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.232;SOR=Inf;LSEQ=ATAAATCCATATACAGGGCT;RSEQ=GGGGAAGTAAGGGGCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:54,151:205,0:0:2,0:23.6:1:31.1:1:1:0:60:50.25:1:0:0.1 0/1:191:2:1,1:47,141:188,2:0.0105:2,2:9:0:31.5:1:0.44244:2.98:60:4:0.0105:0:2.5 +3 52443494 . C T 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05861;SOR=Inf;LSEQ=GGGTTCCTGGCACTGTCTTC;RSEQ=CTAAGGGGCCCTGTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:205,65:270,0:0:2,0:22.4:1:30.8:1:1:0:60:37.571:1:0:0.1 0/1:264:4:1,3:194,66:260,4:0.0152:2,2:12.5:1:22.5:1:0.05601:8.73023:60:3:0.0115:0:1.3 +3 52444117 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACAGCAGATGCGGGCATG;RSEQ=GCTCGAAGGCGAACGCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:27:1:31:1:1:0:60:4:0.25:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:31:0:1:0:60:2:1:0:0 +3 52526820 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22567;SOR=Inf;LSEQ=TCTCTTCTACACGTCCTTTC;RSEQ=TGAAGTGTCGAGTCCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:82,39:121,0:0:2,0:23.5:1:31.3:1:1:0:60:59.5:1:0:0.1 0/1:110:2:1,1:63,43:106,2:0.0182:2,2:20:1:27.5:1:1:1.45979:60:4:0.0187:0:1 +3 52526835 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21442;SOR=Inf;LSEQ=CTTTCCTGAAGTGTCGAGTC;RSEQ=AGTCCTTTGTTGCTGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:91,58:149,0:0:2,0:23.7:1:31.6:1:1:0:60:73.5:1:0:0.1 0/1:129:2:1,1:75,52:127,2:0.0155:2,2:21:0:31.5:1:1:1.4381:60:4:0.0159:0:1 +3 52526842 . TTGTTGC T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=6.000;MSILEN=6;SSF=1;SOR=1.02344;LSEQ=GAAGTGTCGAGTCCAGTCCT;RSEQ=TGTTGCTGTTGCTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:141:97:46,51:35,7:42,97:0.6879:2,2:30.6:1:31.1:1:7e-05:5.47761:60:194:0.6929:0.0213:0.1 1/0:127:88:43,45:28,11:39,88:0.6929:2,2:31.2:1:30:1:0.02021:2.6435:59.1:176:0.6929:0.0157:0.2 +3 52581999 . TC T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.61731;SOR=0.48077;LSEQ=AATTATCCTCCTTTGTTCCT;RSEQ=CCCCCACCCCCAGTAACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:135,6:141,2:0.014:1,2:23.5:1:30:1:0.09583:20.90802:60:4:0.0143:0.007:0.5 0/0:148:1:1,0:131,16:147,1:0.0068:2,0:28:0:26:0:1:0:60:2:0.007:0:0 +3 52582031 . G T 40 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32904;SOR=0.26704;LSEQ=CAGTAACTAAAATGGCTACT;RSEQ=ATCCACAACTCTTTATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:2,1:192,55:247,3:0.012:2,2:19.3:1:25.3:1:0.53434:1.74101:60:2:0.0083:0:1.7 0/0:310:1:0,1:238,71:309,1:0.0032:2,0:1:0:23:0:0.23226:0:60:2:0.0033:0:1 +3 52584415 . G T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1244;SOR=Inf;LSEQ=GAAGCATGTATTTCACAAAG;RSEQ=CTTATTTAGAAGGAATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:264,119:383,0:0:2,0:25.2:1:31.4:1:1:0:60:75.6:1:0:0.1 0/1:400:4:1,3:263,133:396,4:0.01:2,2:23.8:1:24.8:1:0.116:5.90478:55.5:3:0.0077:0:2.3 +3 52584431 . T TCTC 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.79291;SOR=0.95899;LSEQ=AAAGGCTTATTTAGAAGGAA;RSEQ=CTTACCTGCCAGTGTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:208:145,63:176,96:272,208:0.4333:2,2:24.4:1:31.4:1:0.28186:1.25:59.7:103:0.4328:0.125:0.1 0/1:468:198:124,74:178,92:270,198:0.4231:2,2:29.8:1:30.4:1:0.4941:1.15427:59.9:197:0.4255:0.0192:0.2 +3 52584477 . C T 87 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01458;SOR=0.10659;LSEQ=TTGCTAATGCTGTTGGACTC;RSEQ=GCACTGAGTCCTTCAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:703:8:2,6:399,296:695,8:0.0114:2,2:7.5:1:29:1:0.08048:4.03628:60:16:0.0115:0:1 0/0:817:1:0,1:456,359:815,1:0.0012:2,0:1:0:24:0:0.44118:0:60:2:0.0012:0:2 +3 52584715 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02666;SOR=0.79067;LSEQ=CTGCACATGTTCTGAGAAGG;RSEQ=TAACTCGAATTCTGTCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:722:293:174,119:242,187:429,293:0.4058:2,2:25.1:1:31.5:1:0.44379:1.13:60:25.636:0.3994:0:1.4 0/1:810:284:154,130:272,254:526,284:0.3506:2,2:25.1:1:30.7:1:0.5076:1.11:60:39.571:0.3476:0:1.5 +3 52584787 . T C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00752;SOR=0.77387;LSEQ=TGTCCATATGGACTTCCACC;RSEQ=GGTGCTGGAGTCCCTACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:912:383:190,193:247,281:528,383:0.42:2,2:25.6:1:30.4:1:0.42041:1.12:60:75.6:0.4209:0:1.4 0/1:933:335:158,177:282,316:598,335:0.3591:2,2:24.3:1:29.6:1:1:1.00:59.9:82.75:0.3582:0:1.5 +3 52588655 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04678;SOR=0.38313;LSEQ=GCCTGGCCACAATGGGCCAC;RSEQ=GGTGCCTCCTGGAACAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:15:13,2:101,15:116,15:0.1145:2,2:19.7:1:29.9:1:1:1.03562:60:14:0.1077:0:1 0/1:170:8:7,1:128,34:162,8:0.0471:2,2:20.6:1:29.8:1:1:1.85:60:16:0.0473:0:1 +3 52592204 . G GA 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.75793;SOR=0.9214;LSEQ=GTGGCCTACTCCTTATTGGA;RSEQ=AAAAAAAAAATGAAGGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:48:32,16:297,117:414,48:0.1021:2,2:25.1:1:29.4:1:0.50124:1.26859:60:23:0.1015:0.0255:0.3 0/1:622:59:36,23:386,171:557,59:0.0949:2,2:23.6:1:28.8:1:0.2378:1.4413:60:118:0.0975:0.0048:0.2 +3 52592427 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13454;SOR=Inf;LSEQ=CTCAGCAACTTTAGCTGCCC;RSEQ=CTCTGTAAAGGCATTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:77,219:296,0:0:2,0:22.3:1:31.9:1:1:0:59.7:97.667:1:0:0.1 0/1:376:4:3,1:123,249:372,4:0.0106:2,2:15.8:1:28.3:1:0.1115:6.04:58.8:8:0.0107:0:1 +3 52595715 . G T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.08769;SOR=0;LSEQ=TAAGAACAAGAGTAAAACCT;RSEQ=TCTGTGCGCGTGCATTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:224,57:281,3:0.0106:2,2:23:1:26:1:0.49744:1.95946:60:2:0.0072:0:1 0/0:354:0:0,0:252,102:354,0:0:2,0:22.6:1:31.2:1:1:0:60:87.5:1:0:0.1 +3 52596058 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23683;SOR=Inf;LSEQ=CTCAAAATTTCAGAAGCCAG;RSEQ=CGGGCGCGGTGGCTCACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:4,121:125,0:0:1,0:23.4:1:31.4:1:1:0:59.2:40.667:1:0:0 0/1:119:2:1,1:1,116:117,2:0.0168:1,2:17:1:30:1:0.03347:82.30:60:4:0.0168:0:1 +3 52596173 . TA T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGAAACCCCGTTTCTAC;RSEQ=AAAAAAAAAATACAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:27:1:32.5:1:1:0:29:4:0.25:0:0 0/0:2:0:0,0:0,2:2,0:0:0,0:7.5:1:25:1:1:0:52.5:1:1:0:0 +3 52596398 . T C 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGTGATTCACTAGTTAC;RSEQ=GCTTTATTGACACGTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:41.3:1:30:1:1:0:60:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 52597664 . G A 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00055;SOR=0;LSEQ=GAGTTTAAATGTGTATTTAT;RSEQ=AAATTACTTGTACTTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:3,13:1,8:9,16:0.64:2,2:22.6:1:30.2:1:1:1.80:60:32:0.64:0:1 0/0:10:0:0,0:0,10:10,0:0:0,0:16.7:1:31.4:1:1:0:60:20:1:0:0 +3 52598289 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49873;SOR=Inf;LSEQ=AGAAATTAAAGGAGTAAACT;RSEQ=TGGTCATAGTTACTAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:28,165:193,0:0:2,0:22.1:1:32.3:1:1:0:59.9:63.333:0.9948:0:0.1 0/1:196:2:1,1:33,161:194,2:0.0102:2,2:11:1:30:1:0.31758:4.82:60:4:0.0102:0:1 +3 52598290 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24805;SOR=Inf;LSEQ=GAAATTAAAGGAGTAAACTG;RSEQ=GGTCATAGTTACTAACTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:28,165:193,0:0:2,0:21.8:1:30.4:1:1:0:59.9:37.6:1:0:0.1 0/1:192:2:1,1:32,158:190,2:0.0104:2,2:8.5:1:28.5:1:0.31495:4.88:60:4:0.0105:0:1 +3 52598540 . G A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATGTTGTGGTGCATGCCTGT;RSEQ=GTCCCAGCTACTCGGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:39:0:27:0:1:0:52:2:0.3333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:27:1:1:0:55:4:1:0:1.5 +3 52610415 . T C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22159;SOR=0.5812;LSEQ=TTTATCGACTGACTCCCCAA;RSEQ=CTCTGCCCCAACATAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:31:31,0:31,1:32,31:0.4921:1,1:24.9:1:33.5:1:1:0:59:62:0.5:0:1.1 0/1:39:14:14,0:24,1:25,14:0.359:1,1:23.2:1:32:1:1:0:60:28:0.359:0:1 +3 52610651 . T A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.53933;LSEQ=GGCTCATGCTCTGTTTCTTC;RSEQ=GGGTGAATGAAGATGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:310:137,173:167,209:376,310:0.4506:2,2:25.8:1:31.1:1:1:1.009:60:61:0.4532:0:1.1 0/1:760:233:113,120:254,273:527,233:0.3066:2,2:26.7:1:29.5:1:1:1.01:60:76.667:0.3059:0:1.2 +3 52613278 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23987;SOR=0;LSEQ=AAGGAATAGAGAAGGTAAGA;RSEQ=ACGAAAGCAGACTTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:7,147:154,2:0.0128:1,2:17.5:1:30:1:0.10025:19.71:60:4:0.0128:0:1 0/0:162:0:0,0:12,150:162,0:0:2,0:24.3:1:30.6:1:1:0:60:324:1:0:0.1 +3 52620360 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17352;SOR=0;LSEQ=GTTGTTGCTCTTTTTCTAAG;RSEQ=TTGAATACTTTATTCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:133,29:162,2:0.0122:2,2:23.5:1:30.5:1:0.33331:4.52606:60:4:0.0123:0:1 0/0:229:0:0,0:172,57:229,0:0:2,0:24:1:28.9:1:1:0:60:228:1:0:0 +3 52620628 . GT G 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00523;SOR=0;LSEQ=TAATTTTCTTAAAAGATTTG;RSEQ=TTTGGCAGAATACCGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:6:2,4:197,310:507,6:0.0116:2,2:24.2:1:32:1:1:1.27038:60:12:0.0121:0:0.2 0/0:722:0:0,0:309,410:719,0:0:2,0:25.8:1:28.7:1:1:0:60:30.261:1:0:0.2 +3 52620713 . TG T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.19808;SOR=0;LSEQ=CTTAAAGTATTCCTGGGGGG;RSEQ=GGGAGGGCATAAGAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:62,136:198,2:0.01:2,2:27.5:1:33:1:0.53186:2.18:60:4:0.0103:0:0 0/0:250:0:0,0:68,182:250,0:0:2,0:23.4:1:30.4:1:1:0:59.6:49:1:0:0.4 +3 52621607 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.496;SOR=Inf;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=AAGAGACTGGGTCTCACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:1,58:59,0:0:1,0:16:1:31.3:1:1:0:53:58:0.9831:0:1.6 0/1:63:2:0,2:1,59:60,2:0.0317:1,0:19:1:27:1:1:0:54.5:4:0.0323:0:2.5 +3 52621627 . C T 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15274;SOR=2.03772;LSEQ=AAAGAGACTGGGTCTCACTA;RSEQ=GTTGCCCAGGCTGGACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:12:0,12:0,27:27,12:0.3:1,0:29.5:1:28.4:1:1:0:58.6:11:0.3056:0:1.6 0/1:32:15:0,15:0,17:17,15:0.4688:1,1:25:1:29.4:1:1:0:51.3:30:0.4688:0:2.5 +3 52623304 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50082;SOR=0;LSEQ=AATAAATAAATAAAGGAAAA;RSEQ=GGTACTCACCAAAGGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:16,130:146,2:0.0135:2,2:35:1:31:1:0.21723:7.91:60:4:0.0137:0:1.5 0/0:128:0:0,0:15,113:128,0:0:2,0:22.4:1:30.2:1:1:0:59.9:127:1:0:0.1 +3 52637486 . C G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00063;SOR=1.78309;LSEQ=CACAGCTAATTATGAGAACA;RSEQ=CTAGAAGACAGTGCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:137:99,38:113,40:153,137:0.4724:2,2:22.6:1:32.3:1:0.79173:1.08404:60:67.5:0.4704:0:1 1/0:291:179:135,44:80,32:112,179:0.6151:2,2:20.9:1:31.2:1:0.49373:1.23:60:178:0.6159:0:1.1 +3 52643258 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49843;SOR=Inf;LSEQ=AGTGGAAATAGTACATCAAA;RSEQ=CAATATTCTTTCATCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:118,18:136,0:0:2,0:24.1:1:32.8:1:1:0:59.9:44.333:1:0:0.4 0/1:142:2:1,1:113,27:140,2:0.0141:2,2:17:1:27.5:1:0.35661:4.12792:60:4:0.0143:0:1 +3 52643307 . A G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00141;SOR=0.60698;LSEQ=ATAGCACATATCCTCAAAAT;RSEQ=AAAATGGCTTTGAAAACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:139:106,33:138,41:179,139:0.4357:2,2:25.4:1:31.9:1:0.89402:1.04774:59.9:45.333:0.4317:0:1 0/1:395:126:88,38:186,83:269,126:0.319:2,2:23.7:1:31.1:1:0.90739:1.03:60:125:0.3189:0:1.1 +3 52643685 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.56091;LSEQ=AAAGACTCCGGCTCATTGTA;RSEQ=GTACAGGCATTATTAAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:197:97,100:110,90:200,197:0.4937:2,2:23.9:1:30.9:1:0.26982:1.25928:59.9:97.5:0.4924:0:1.1 0/1:464:164:79,85:167,133:300,164:0.3534:2,2:23.2:1:30.3:1:0.14437:1.3501:60:328:0.3565:0:1.1 +3 52649349 . A T 62 v3;p8;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03107;SOR=Inf;LSEQ=TAGACTAAACTAAATAATGA;RSEQ=GTGTGAGGCTGCCTTACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:302,120:422,0:0:2,0:25.7:1:30.6:1:1:0:60:83.4:1:0:0.1 0/1:446:6:0,6:281,159:440,6:0.0135:2,0:7:1:24:1:0.00242:0:60:5:0.0114:0:1 +3 52649748 . A G 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATCACTGCAGGTTTTAACA;RSEQ=AAGTCCTGAAACACATTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:19:1:30.7:1:1:0:60:6:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 52651966 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCCTCACTTCCAAGTACA;RSEQ=AAACAAAACAAAATAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:14:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 52659079 . T C 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00172;SOR=Inf;LSEQ=GTCCAAAGTACCAAAGACAA;RSEQ=ATTTGAAACATTTCAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:0,54:54,0:0:1,0:22.5:1:28.6:1:1:0:60:53:1:0:0.2 0/1:48:8:0,8:1,39:40,8:0.1667:1,0:18.1:1:32.5:1:1:0:60:16:0.1702:0:1.1 +3 52659124 . T C 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18614;SOR=0.36501;LSEQ=ACAGATGTTGGCAGAAAGAA;RSEQ=GCACCCCCAGAATGAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:15:0,15:0,12:12,15:0.5556:0,1:25.3:1:30.1:1:1:0:60:30:0.5556:0:1 0/1:13:4:0,4:0,9:9,4:0.3077:0,0:21.5:1:30.3:1:1:0:60:8:0.3077:0:1 +3 52661018 . G GA 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAAAATGCCACATTAAAA;RSEQ=AAAAAAAAAAACCCAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:18.3:1:26:1:1:0:60:3:0.4286:0:2.3 0/0:1:0:0,0:1,0:1,0:0:0,0:44:0:34:0:1:0:60:2:1:0:0 +3 52661194 . C T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50076;SOR=Inf;LSEQ=TACCATTTATTTAAAGCTTA;RSEQ=AACTTGATAGCTTAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:134,17:151,0:0:2,0:23.8:1:32.1:1:1:0:59.8:74.5:1:0:0.1 0/1:173:2:1,1:147,24:171,2:0.0116:2,2:13:1:23.5:1:0.26885:6.02165:60:4:0.0117:0:1 +3 52661422 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50169;SOR=Inf;LSEQ=TCTCAGGAGTTGAGCTCATG;RSEQ=GCCAAACACTCCTCTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:38,134:172,0:0:2,0:21.9:1:30.4:1:1:0:59.9:344:1:0:0.1 0/1:201:2:1,1:42,157:199,2:0.01:2,2:13:1:27.5:1:0.38294:3.71:60:4:0.01:0:1 +3 52661640 . G C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCATTTATGACTATAATG;RSEQ=GTGCTAACTGGTTAAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:8.7:1:31.3:1:1:0:60:6:0.4286:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:35:0:32:0:1:0:60:2:1:0:0 +3 52662722 . T A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8237;LSEQ=GGTCTTGAACTCCTGAGCTC;RSEQ=AGTGATTCTCTCACCTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:11,0:9,0:9,11:0.55:0,0:24.6:1:31.5:1:1:0:44.4:22:0.55:0:1.5 1/0:10:5:5,0:5,0:5,5:0.5:0,0:26.8:1:31.2:1:1:0:51.6:10:0.5:0:1 +3 52662814 . TG T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.17342;SOR=0;LSEQ=TGTAATATTACTGCTGAGGG;RSEQ=GGGGGGATCACACATCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:2,0:73,3:76,2:0.0253:1,0:30:1:34:0:1:0:60:4:0.026:0:0 0/0:110:0:0,0:100,9:109,0:0:2,0:21.8:1:31.8:1:1:0:60:218:0.9909:0:0.1 +3 52663039 . C A 39 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30612;SOR=0.21625;LSEQ=AAAGTTTCATATTCTTGATT;RSEQ=TTCAGTTTTGTTCTGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:2,1:91,201:292,3:0.0102:2,2:8:1:24.7:1:0.23467:4.39:60:6:0.0105:0:1 0/0:452:1:0,1:170,281:451,1:0.0022:2,0:27:0:29:0:1:0:60:2:0.0023:0:1 +3 52663084 . T A 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGAAATTGCTAGAATTTTC;RSEQ=GTCATGAAAATTATGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:15:2,13:24,118:142,15:0.0955:2,2:22.4:1:32.3:1:1:1.31985:60:30:0.0962:0:1.3 0/0:215:0:0,0:51,164:215,0:0:2,0:22.2:1:29.7:1:1:0:59.9:430:1:0:0.1 +3 52663113 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.97158;LSEQ=AATTATGAAACATTCTTCCT;RSEQ=AAAGTCCAATGCAAAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:1:0,1:7,85:92,1:0.0108:2,0:47:0:17:0:1:0:60:0:0:0:4 0/1:95:2:0,2:10,83:93,2:0.0211:2,0:24:1:28.5:1:1:0:60:4:0.0211:0:1 +3 52668499 . T TA 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22118;SOR=Inf;LSEQ=GAACAGTTAAAATTTGAGGT;RSEQ=AAAAAAAAACACCATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:55,2:57,0:0:1,0:24.5:1:29.3:1:1:0:58.2:7.143:0.9804:0:0.7 0/1:52:2:2,0:49,0:49,2:0.0385:1,0:23:1:28.2:1:1:0:60:4:0.0417:0.0192:2 +3 52668863 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22022;SOR=0;LSEQ=AAAAAAGTATTTATAAAGGG;RSEQ=CGAATGAGATGAAGAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:34,143:177,2:0.0111:2,2:18.5:1:31:1:0.35371:4.16:60:4:0.0114:0:1 0/0:203:0:0,0:43,160:203,0:0:2,0:21.1:1:28.4:1:1:0:60:49.75:1:0:0.1 +3 52676065 . C T 171 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0.10596;SOR=0.76884;LSEQ=GTACTGCTCTTTTATTACTA;RSEQ=AAAAAAAAAAAAAGCAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:113:35,78:65,121:186,113:0.3054:2,2:21.6:1:25.1:1:0.52826:1.19645:59.8:3.913:0.3147:0:1.5 0/1:388:98:44,54:91,154:245,98:0.2526:2,2:21.1:1:26:1:0.22113:1.38:59.9:7.167:0.2688:0:1.4 +3 52676079 . G A 52 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06171;SOR=0;LSEQ=TTACTACAAAAAAAAAAAAA;RSEQ=CAATTAGACAGGGAAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:5:3,2:64,235:299,5:0.0163:2,2:13.8:1:22.4:1:0.07314:5.47:60:1.5:0.0118:0:2 0/0:295:0:0,0:68,226:294,0:0:2,0:7:0:11:0:1:0:60:0:0:0:2 +3 52676190 . A C 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43029;SOR=0.5979;LSEQ=TTCTATTCAATTGCCTCCTT;RSEQ=GTTTATCTCTGTACTTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:0,15:0,16:16,15:0.4839:1,1:27.9:1:30.8:1:1:0:59.4:30:0.4839:0:1 0/1:28:10:0,10:0,17:17,10:0.3571:1,0:27:1:29.8:1:1:0:60:20:0.3571:0:1 +3 52677387 . G A 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00407;SOR=Inf;LSEQ=GAGATAAGATAAAAAGCTTA;RSEQ=AAACTTGGTAGCTGAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:24,196:220,0:0:2,0:24.6:1:32.2:1:1:0:59.9:72.333:1:0:0.1 0/1:247:9:2,7:36,201:237,9:0.0364:2,2:30.2:1:29.6:1:0.63252:1.59:60:18:0.0373:0:1 +3 52678370 . C T 64 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTTCACTACCTAGAAAA;RSEQ=TCAGCAAATATAAAGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:33.8:1:32:1:1:0:50.5:8:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 52678494 . G A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.387;SOR=0.33035;LSEQ=CACTGTAACCTCTGCCTCCC;RSEQ=GGTTCAAGCAATTCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:5,6:0.5455:0,0:22.5:1:31:1:1:0:31.2:12:0.5455:0:1 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:18.7:1:30.7:1:1:0:27:6:0.2727:0:1 +3 52678621 . G A 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTTGGCCAGGATGGTCTC;RSEQ=ATCTCTTGACCTCGTGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:50,0:50,0:0:1,0:8.2:1:31:1:1:0:39.3:100:1:0:0 0/1:72:27:26,1:45,0:45,27:0.375:1,1:10.6:1:30.4:1:0.375:0:36:54:0.375:0:1.1 +3 52678668 . A G 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88197;LSEQ=CTCAGCCTCCCAAAGTGCTG;RSEQ=GATTACAGGCATGAGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:4:1,3:185,100:285,4:0.0138:2,2:5.3:1:30.3:1:0.13109:5.51637:53.8:8:0.014:0:2 0/1:409:5:2,3:263,140:403,5:0.0122:2,2:19.6:1:27.6:1:0.34884:2.81018:43:10:0.0126:0:2.2 +3 52682205 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01704;SOR=0.15408;LSEQ=AGTGCCGGGATTACAGGCGT;RSEQ=AGCCACTGCGCCCAGCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:15:15,0:8,0:8,15:0.6522:0,1:23.1:1:28.7:1:1:0:58.8:30:0.6818:0:1 0/1:14:3:3,0:11,0:11,3:0.2143:0,0:24:1:25.7:1:1:0:52:6:0.2143:0:1 +3 52682329 . AAAC A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.57339;SOR=1.33909;LSEQ=TTATCTACTATTACCAAGGA;RSEQ=AACAACAACAACAACAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:11:8,3:231,78:309,11:0.0342:2,2:26.4:1:30.3:1:1:1.11019:60:22:0.0349:0.0093:0.2 0/1:420:19:11,8:285,116:401,19:0.0452:2,2:21.7:1:29.8:1:0.30157:1.78405:60:38:0.0456:0.0119:0.1 +3 52682516 . T A 25 v3;p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.7063;LSEQ=GAGAGTTCATCAGTACAACC;RSEQ=TTAAAAAAAGAACCCCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:21,130:151,2:0.0131:2,2:7.5:1:23.5:1:0.26772:6.07:60:4:0.0132:0:1.5 0/0:216:2:2,0:26,188:214,2:0.0093:2,0:1:0:25:0:0.01628:0:60:4:0.0094:0:1 +3 52684128 . A T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCACACCTATAATCTCT;RSEQ=TGCACTTTGGGAGGCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:27:1:1:0:34:4:1:0:1 +3 52685397 . A G 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAACAACAGGTTACCCC;RSEQ=TCTACCCTGATGTGATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:28:1:29.5:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 52686087 . A C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTATTATGCAACTAGCATA;RSEQ=AATTTAATGTTTTAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:25.3:1:32.2:1:1:0:60:18:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:23.5:1:33:1:1:0:60:4:1:0:1 +3 52692124 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13515;SOR=0.67771;LSEQ=CGGCCCAACATCTTCCTTTT;RSEQ=AACTTACTTTATTTATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:57:52,5:58,6:64,57:0.4672:2,2:19.1:1:29.1:1:1:1.08:58.9:114:0.4711:0:1 0/1:145:54:47,7:84,7:91,54:0.3724:2,2:20.7:1:28:1:0.38459:1.77981:58.8:53:0.3759:0:1.1 +3 52692359 . C G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=0.50755;LSEQ=TGTGGAGAAAAAAGTACTTT;RSEQ=TAAGAGAAATAATAAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:121:18,103:23,102:125,121:0.4899:2,2:24.1:1:32.1:1:0.49693:1.28897:60:39.333:0.5:0:1.1 0/1:281:92:28,64:48,140:188,92:0.3274:2,2:20.9:1:30.8:1:0.39399:1.27:60:45:0.3297:0:1.1 +3 52692379 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49848;SOR=Inf;LSEQ=CTAAGAGAAATAATAAAATG;RSEQ=TGAATATTACATAGCTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:20,145:165,0:0:2,0:26.9:1:32.7:1:1:0:59.9:26.5:1:0:0.7 0/1:165:2:1,1:33,129:162,2:0.0121:2,2:15:1:27:1:0.37266:3.87:60:4:0.013:0:2 +3 52692721 . T C 33 v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGCCAAAGAAAGCAACT;RSEQ=CTAAGCAGTACTTATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:45:0:33:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 52695835 . T C 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02098;SOR=0;LSEQ=CAACACTGCCTTTCCTTACA;RSEQ=GATGTCTCAATGTAGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:22.3:1:31.7:1:1:0:58:14:0.7778:0:1 0/0:4:0:0,0:3,1:4,0:0:2,0:5:1:28:1:1:0:60:8:1:0:0 +3 52696310 . G GA 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.04111;LSEQ=TGGCTGTATGTTAGCAAAGA;RSEQ=AAAAAAAAAAACACTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:20:2,18:48,180:228,20:0.0781:2,2:33.3:1:32:1:0.3824:2.3935:60:40:0.0858:0:0 0/1:296:24:3,21:77,184:261,24:0.0811:2,2:25.8:1:29.6:1:0.0965:2.92061:60:23:0.0858:0.0034:0.2 +3 52702452 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21777;SOR=0;LSEQ=GCCAGGTTTATAAATATTAA;RSEQ=AAGCCAATTATCAAATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:106,15:121,2:0.0163:2,2:7.5:1:28.5:1:0.24417:6.87422:60:4:0.0164:0:1 0/0:140:0:0,0:121,19:140,0:0:2,0:23.8:1:31.4:1:1:0:60:69:1:0:0.1 +3 52703254 . GA G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACAACCAAACTCTTCG;RSEQ=AAAAAAAAACCATGGGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42:1:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 52712629 . G A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.38048;SOR=3.455;LSEQ=GCAATCTACACATTAGCAAA;RSEQ=GAGAAAAAAATCACTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:1,0:73,254:327,1:0.003:2,0:1:0:25:0:0.22561:0:60:2:0.0031:0:1 0/1:382:4:2,2:109,268:377,4:0.0105:2,2:9.3:1:24.5:1:0.58333:2.45:60:3:0.008:0:2.3 +3 52713306 . T TC 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGAAAAATGGGCTTGTT;RSEQ=CCACATGGCTATATCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:35.5:1:34:0:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 55235124 . C G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAGAGCCCCTTCCCCACCC;RSEQ=ACAGGTGCATTAGTGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:26:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 55235377 . G A 86 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00024;SOR=60.61251;LSEQ=CCTCCTTTCTGGGAGCTCCT;RSEQ=AAAAGACAAGCCCTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:12,0:12,1:0.0769:0,0:11:0:30:0:1:0:60:2:0.0769:0:1 1/1:9:8:8,0:1,0:1,8:0.8889:0,0:20.1:1:28.9:1:1:0:60:16:0.8889:0:1 +3 55235436 . A AT 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.14414;SOR=5.41961;LSEQ=CCCAGGGGTTTATGCATTGA;RSEQ=TTTTTTTTTTAATACCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:1:1,0:38,1:39,1:0.025:1,0:13:0:33:0:1:0:60:2:0.027:0:0 0/1:24:3:3,0:21,0:21,3:0.125:1,0:26:1:31.5:1:1:0:60:6:0.1304:0.0417:0 +3 55235552 . A T 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12173;SOR=0;LSEQ=GAGATGATCTGAGGGGATGC;RSEQ=GTATTTATGAACTATGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:0,3:176,104:280,3:0.0106:2,0:5:1:27.7:1:0.05311:0:60:6:0.0107:0:1 0/0:287:0:0,0:170,117:287,0:0:2,0:23.8:1:29.4:1:1:0:60:142.5:1:0:0.4 +3 55235608 . T G 146 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=24.97286;LSEQ=GGCATTTATATGAACTAGGG;RSEQ=TTTTAATAAGGTAACCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:1:1,0:192,199:391,1:0.0025:2,0:35:0:12:0:0.49235:0:60:0:0:0:1 0/1:451:27:11,16:210,213:423,27:0.0599:2,2:26.9:1:30.9:1:0.42985:1.43291:59:54:0.0608:0:1.4 +3 55235625 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.00353;LSEQ=GGGTTTTTAATAAGGTAACC;RSEQ=CTCTGAGTTTGGCATTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:66:33,33:153,175:328,66:0.1675:2,2:25.9:1:31.1:1:0.68565:1.14:60:65:0.1688:0:1.2 1/0:451:247:119,128:96,107:203,247:0.5477:2,2:26.4:1:29.9:1:0.92447:1.04:59.9:29.875:0.5457:0:1.2 +3 55235665 . G A 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19356;SOR=0.22118;LSEQ=ATAGAAAACATGCGTATTGT;RSEQ=CTTTCCTTGCATGTGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:4:2,2:113,173:286,4:0.0138:2,2:12.3:1:27:1:0.6502:1.53:60:8:0.014:0:1 0/0:325:1:0,1:134,190:324,1:0.0031:2,0:1:0:30:0:1:0:60:2:0.0031:0:2 +3 55235685 . A T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=GCTTTCCTTGCATGTGAGGA;RSEQ=TCTCGTTGAAAGTACCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:75,144:219,0:0:2,0:24.5:1:30.8:1:1:0:60:218:1:0:0.2 0/1:232:13:4,9:76,143:219,13:0.056:2,2:20.7:1:29.3:1:1:1.19494:60:26:0.0563:0:1.5 +3 55235741 . A G 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01624;SOR=Inf;LSEQ=TTGTAAACAGTGATGATTTT;RSEQ=GTCTATGGTGAATCCTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:7,80:87,0:0:2,0:24.2:1:32.1:1:1:0:60:174:1:0:0.1 0/1:70:5:0,5:5,59:64,5:0.0714:2,0:22.8:1:31.2:1:1:0:60:10:0.0735:0:2 +3 55235828 . TTA G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00042;SOR=22.74585;LSEQ=GTTTATTTTCGTTCAAGGAG;RSEQ=ATAAATGGGAATGTCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:20,3:0.1304:1,0:18:1:30.6:1:1:0:60:6:0.1304:0.0435:1.3 1/1:10:8:0,8:0,2:2,8:0.8:0,0:23.5:1:31.9:1:1:0:60:16:0.8:0.1:0.5 +3 55235867 . G A 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TCTTTGTATCACATCACCCC;RSEQ=AAGGACTTTGCTGTGACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:37:1:30.7:1:1:0:60:6:0.375:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:9.5:1:30:1:1:0:60:4:1:0:2 +3 55487201 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23961;SOR=0;LSEQ=TCCCAATTGCTTAACAAATG;RSEQ=CAATGGTCTCTTGCTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:119,30:149,2:0.0132:2,2:15:1:30:1:0.36954:3.91853:60:4:0.0133:0:1 0/0:158:0:0,0:125,33:158,0:0:2,0:21.2:1:29.2:1:1:0:60:157:1:0:0.1 +3 55487222 . A T 100 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00415;SOR=0.08753;LSEQ=CAATGGTCTCTTGCTCTTGC;RSEQ=GCCCCAGGTCAGAAATCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:10:6,4:156,62:218,10:0.0439:2,2:29.5:1:30.3:1:0.48052:1.67328:60:20:0.0441:0:1 0/0:251:1:0,1:169,81:250,1:0.004:2,0:1:0:22:0:0.32669:0:60:2:0.004:0:1 +3 55487289 . C T 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCGTCTTTGATTTTCCTT;RSEQ=ATCCCCAAGCTTTACTATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:459:0:0,0:238,221:459,0:0:2,0:26.8:1:32.1:1:1:0:60:458:1:0:0.8 0/1:547:34:19,15:271,240:511,34:0.0622:2,2:23.6:1:28.5:1:0.85956:1.12:60:33:0.0609:0:1.1 +3 55487317 . T A 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09298;LSEQ=AGCTTTACTATAGGAAGTCA;RSEQ=GAGTCAGACTTAGATTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:428:378:163,215:22,28:50,378:0.8832:2,2:25.2:1:31.2:1:1:1.0363:60:188:0.8847:0:1.1 0/1:500:206:88,118:148,146:294,206:0.412:2,2:24.8:1:29.8:1:0.10171:1.35842:60:205:0.4141:0:1.1 +3 55487428 . G A 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05787;LSEQ=TACACAGGAAAAATTTCTTG;RSEQ=TAGTTCCCAGTCTGACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:53:2,51:1,7:8,53:0.8689:2,1:21:1:31.3:1:0.3491:3.53024:60:52:0.8667:0:1.2 0/1:70:19:2,17:2,49:51,19:0.2714:1,2:28.1:1:30.4:1:0.29591:2.83:60:38:0.2754:0:1 +3 55487515 . C T 131 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.00943;LSEQ=GTGCTATGATTCCAAACTGC;RSEQ=AAACTGCTGAGCAATCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:28:0,28:0,1:1,28:0.9655:0,1:24.5:1:27.4:1:1:0:57.6:27:0.9643:0:1.3 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:39:0:28:0:1:0:60:2:0.1429:0:1 +3 55524478 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48;SOR=0;LSEQ=TCCCTGCCCTGCCACTTTCC;RSEQ=GCTGTCACACCTTGTCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:35.5:1:29.5:1:1:2.4495:60:4:0.1538:0:1 0/0:13:0:0,0:10,3:13,0:0:2,0:22.4:1:28.4:1:1:0:60:26:1:0:0.1 +3 57775195 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02288;SOR=Inf;LSEQ=GCCAGGGTGTTCAGACATCA;RSEQ=CTGAGGGATGGTAGATAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:10,0:0:2,0:23.2:1:32.1:1:1:0:60:20:1:0:0 1/0:8:4:2,2:3,1:4,4:0.5:2,2:21.5:1:27.5:1:1:2.60168:60:8:0.5:0:1 +3 59788677 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCTTGAACTGTAGTGATACG;RSEQ=GTATACATCTTACCTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:45:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:31:1:1:0:60:4:1:0:1.5 +3 59789058 . C T 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGAGGACCTTACAGGCGAG;RSEQ=ACGGGGCCAGCGAAGGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:49,7:0,0:0,56:1:0,2:26.4:1:29.8:1:1:0:59.7:112:1:0:1.8 1/0:52:34:30,4:14,4:18,34:0.6538:2,2:19.3:1:29.3:1:0.42484:2.11:60:68:0.6538:0:1.8 +3 59789101 . G A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00736;SOR=0;LSEQ=TTTTAAGATCATCTCCTGGT;RSEQ=CTCATTAGTGCTGTTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:107:73,34:0,0:0,107:1:0,2:25:1:28.8:1:1:0:59.7:214:1:0:1.8 1/1:118:110:76,34:5,3:8,110:0.9322:2,2:24.7:1:27.9:1:0.70453:1.34:60:109:0.9316:0:1.6 +3 59789139 . CT TG 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13362;SOR=Inf;LSEQ=TCTTCACCTGGGTGAGCGGG;RSEQ=TGCTTCCATGGAGAAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:79,59:138,0:0:2,0:25.5:1:32.2:1:1:0:59.9:68:1:0:1.5 0/1:176:4:2,2:95,74:169,4:0.0227:2,2:9:1:30.9:1:1:1.2819:60:8:0.0227:0.0114:0.8 +3 59789176 . C T 211 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGACCTCCGCCAGCTCCTG;RSEQ=TGCATTAACGGTCTCCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:138:138:61,77:0,0:0,138:1:0,2:24.7:1:29.8:1:1:0:59.9:68:1:0:1.3 1/0:173:135:64,71:19,19:38,135:0.7803:2,2:26:1:28.8:1:0.85484:1.10871:60:134:0.7791:0:1.4 +3 59789419 . A G 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTGACCCAACAAAGCAAA;RSEQ=TGGCTTTGTTCCCCAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20.7:1:30.7:1:1:0:49.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 59789614 . G T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACATCCGGGGCATGTAGAT;RSEQ=CTCGGTAGCAATGAATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:23.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 59967386 . G A 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.06667;SOR=Inf;LSEQ=TGCCCGCACATTAACGCAGA;RSEQ=AGATGCCCTTGATAATTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:19.3:1:29.8:1:1:0:60:3:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:11.5:1:31:0:1:0:60:4:1:0:1 +3 59967565 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24586;SOR=0;LSEQ=TTAATCATTTTCTGGAATTC;RSEQ=AGAAAAAGTCTGATGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:71,17:88,2:0.0222:2,2:28.5:1:29.5:1:0.3618:4.08728:60:4:0.0225:0:1.5 0/0:91:0:0,0:66,25:91,0:0:2,0:23:1:29.5:1:1:0:60:182:1:0:0.9 +3 59967597 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=80.30722;LSEQ=GATGTGGTTAATTTAAAATT;RSEQ=TATTTTATGATAGAGAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:184:100:50,50:46,38:84,100:0.5435:2,2:21.3:1:29.4:1:0.55546:1.20926:60:200:0.5495:0:1.1 1/1:195:193:113,80:0,0:0,193:0.9897:0,2:25.2:1:28.3:1:1:0:60:192:0.9948:0:1.3 +3 59967673 . G A 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTGCCACTCCTTTTTGCT;RSEQ=CCAGGGTCAGCAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:51,109:160,0:0:2,0:21.7:1:31.8:1:1:0:60:31:1:0:0.4 0/1:181:81:28,53:43,57:100,81:0.4475:2,2:23.9:1:28.2:1:0.28511:1.42512:59.6:80:0.4469:0:1.6 +3 59967683 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24895;SOR=Inf;LSEQ=CCTTTTTGCTGCCAGGGTCA;RSEQ=CAAAAAGAAAAAAAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:33,96:129,0:0:2,0:19.2:1:32.1:1:1:0:60:24.8:1:0:0.3 0/1:142:3:2,1:48,91:139,3:0.0211:2,2:9.7:1:22.3:1:0.28319:3.75:56.3:2:0.0152:0:1.3 +3 59967690 . G GA 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=5.55739;LSEQ=GCTGCCAGGGTCAGCAAAAA;RSEQ=AAAAAAAAAATTATTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:9:2,7:19,61:80,9:0.1011:2,2:21.7:1:30.6:1:1:1.08913:60:18:0.1071:0.0112:0 0/1:119:46:16,30:23,44:67,46:0.3866:2,2:25.5:1:29.6:1:1:1.02:59.5:92:0.3898:0.0168:0.4 +3 60170982 . GA G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATAGTTTCATGGTGTGGG;RSEQ=AAAAAAAAAATCGCATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:30.2:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 60458418 . C G 31 d5;v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTGTTTTAAAAGCAGCGCT;RSEQ=GTCTTTGCTGCCTTTCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:34:1:31.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:31:1:1:0:60:4:1:0:1 +3 60458976 . C T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67492;SOR=0.61412;LSEQ=CCATATCCACAGATAGCTGG;RSEQ=TTCTTCGATAAAATTCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:26:1:30.2:1:1:0:60:10:0.4167:0:1 0/1:10:3:3,0:7,0:7,3:0.3:0,0:18.7:1:31:1:1:0:60:6:0.3:0:1 +3 60459187 . G C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0;SOR=0.218;LSEQ=TGTGAGAGACATTATCAAGA;RSEQ=AGAATAAATACAATGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:360:190:97,93:91,76:167,190:0.5278:2,2:25.7:1:31.9:1:0.52582:1.14755:60:94:0.5281:0:1.9 0/1:455:89:49,40:175,189:364,89:0.1956:2,2:25.2:1:31.1:1:0.28715:1.32:60:43.5:0.1942:0:1.9 +3 60459201 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.29994;LSEQ=TCAAGAGAGAATAAATACAA;RSEQ=GTGAAGAGACAACCTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:364:184:85,99:91,89:180,184:0.5055:2,2:27.1:1:31:1:0.46286:1.1903:60:183:0.5097:0:2 0/1:448:105:55,50:154,188:342,105:0.2344:2,2:24.6:1:30.5:1:0.21872:1.34:60:104:0.2348:0:1.9 +3 60459291 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01838;SOR=0.56601;LSEQ=ATTAACCAATAGGGCTAACT;RSEQ=CAAAGGTGGTGCTTTGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:73:21,52:13,46:59,73:0.553:2,2:19.8:1:31.7:1:0.42744:1.43:60:23.333:0.5469:0:1.3 0/1:158:65:16,49:26,67:93,65:0.4114:2,2:19.8:1:31.2:1:0.71591:1.18714:60:130:0.414:0:1.2 +3 60459656 . CA C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAGCGAGACTCCATTTC;RSEQ=AAAAAAAAAGAAAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:30:1:1:0:60:4:1:0:0.5 +3 61186878 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=Inf;LSEQ=CTTCCTGTATGTAGACTGCA;RSEQ=CCTTCTCTCGGAAGAAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:30.7:1:34.7:1:1:0:60:12:1:0:0.2 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:20.5:1:27:1:1:0:60:4:0.6667:0:2 +3 61187046 . A T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08159;SOR=0.55601;LSEQ=CAACAGTAATAACTTACAGT;RSEQ=TCGTGAAGCTGGTTCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:44:44,0:52,1:53,44:0.4536:1,1:22.9:1:31.2:1:1:0:60:88:0.4632:0:1 0/1:73:23:22,1:48,2:50,23:0.3151:1,1:21.8:1:30.6:1:1:1.08959:60:46:0.3151:0:1 +3 61187197 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.50106;LSEQ=GATAGACAGCTACACCACAG;RSEQ=TTTTCCATGGTTCTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:171:68,103:117,162:279,171:0.38:2,2:25.1:1:29.5:1:0.69335:1.09374:59.8:41.75:0.3813:0:1.2 0/1:494:116:48,68:170,207:377,116:0.2348:2,2:26.4:1:28.8:1:0.52191:1.16309:60:57:0.237:0:1.2 +3 61187210 . C CT 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.81372;SOR=1.18613;LSEQ=ACCACAGCTTTTCCATGGTT;RSEQ=TTTTTTTTTCCTTCAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:8:3,5:145,228:373,8:0.021:2,2:25.5:1:30.5:1:1:1.05979:60:16:0.0216:0.0026:0.4 0/1:403:10:3,7:160,233:393,10:0.0248:2,2:39.9:1:27.3:1:0.74613:1.60052:60:9:0.0226:0:0.4 +3 61187274 . T A 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=21.29835;LSEQ=CTGGGCTGTTTCCCTCCACA;RSEQ=CCCTCTATTCCATCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:1:1,0:11,106:117,1:0.0085:2,0:1:0:14:0:0.10169:0:60:0:0:0:1 0/1:129:20:4,16:18,91:109,20:0.155:2,2:22.8:1:28.1:1:0.7476:1.26:60:19:0.1496:0:1.6 +3 61187278 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23615;SOR=0;LSEQ=GCTGTTTCCCTCCACATCCC;RSEQ=CTATTCCATCAAAGAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:10,101:111,2:0.0177:2,2:38:0:33:0:0.186:9.68:60:4:0.0182:0:1.5 0/0:119:0:0,0:17,102:119,0:0:2,0:22.2:1:28.9:1:1:0:60:58.5:1:0:0.3 +3 61187340 . C T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04534;SOR=0.31343;LSEQ=CAAAGAACAGGTCAGACTTA;RSEQ=GGGCTAAGATGTAAATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:18:0,18:0,25:25,18:0.4186:1,1:26.2:1:30.9:1:1:0:60:36:0.4186:0:1.1 0/1:33:6:0,6:1,26:27,6:0.1818:1,0:20.7:1:29.7:1:1:0:60:12:0.1818:0:1.5 +3 61187422 . C T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22797;SOR=0;LSEQ=TCAGAAATTTCTCCTTCCCC;RSEQ=TGAGCTACACCGTTTACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:24.8:1:31.5:1:1:0:60:8:0.4444:0:1.3 0/0:4:0:0,0:0,4:4,0:0:0,0:21.5:1:33.3:1:1:0:60:8:1:0:0.3 +3 62110040 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50252;SOR=0;LSEQ=AGGCTGACAATAGTGGGATG;RSEQ=AAGTCCAGGGTGATCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:28,18:46,2:0.0417:2,2:13:1:26:1:1:1.54082:21.5:4:0.0417:0:1 0/0:37:0:0,0:20,17:37,0:0:2,0:18.7:1:30.2:1:1:0:27.8:74:1:0:0.2 +3 63597115 . A C 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.23316;LSEQ=GGACATTAATGAACCAAAAC;RSEQ=CAATATTTTTATTACAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:9.5:1:32.5:1:1:0:60:4:0.1667:0:1 0/1:5:1:1,0:3,0:3,1:0.2:0,0:3:0:30:0:1:0:60:2:0.2:0:1 +3 63597263 . A C 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0147;SOR=Inf;LSEQ=AGGCTGCCAGGAAGCTGGAC;RSEQ=GTTCTCATCCTCCATCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:121,43:164,0:0:2,0:21.8:1:30.4:1:1:0:60:163:1:0:0 0/1:168:7:6,1:110,50:160,7:0.0417:2,2:23.9:1:28.3:1:0.67683:2.71:60:6:0.0364:0:1 +3 63597293 . T C 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.25066;SOR=Inf;LSEQ=CTCCATCTCTCATCTCTCTT;RSEQ=CTTTCTGTGTCCCTGTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:151,116:267,0:0:2,0:25.3:1:30.4:1:1:0:60:88:1:0:0.1 0/1:296:3:2,1:172,121:293,3:0.0101:2,2:38.3:1:25.3:1:1:1.41:60:2:0.0069:0:1 +3 63597363 . C CT 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09929;SOR=0;LSEQ=TTTCAGGTGAAACTTTATTT;RSEQ=TTTTTTTTCATCCACACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:112,143:255,3:0.0116:2,2:30.7:1:32.3:1:1:1.56382:60:6:0.0118:0:0.3 0/0:298:0:0,0:130,167:297,0:0:2,0:23.7:1:30.9:1:1:0:60:147.5:0.9966:0:0.5 +3 63597382 . G A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=21.37938;LSEQ=TCTTTTTTTTCATCCACACA;RSEQ=CAGAAGATAGCCACTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:14:7,7:93,106:199,14:0.0657:2,2:22.2:1:29.2:1:1:1.14:58.4:28:0.0664:0:1.2 1/0:244:147:62,85:46,49:95,147:0.6025:2,2:24.4:1:28.6:1:0.35658:1.28567:60:35.75:0.6059:0:1.1 +3 63597468 . C G 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00327;SOR=Inf;LSEQ=TGAATGAAAATCACTCAGGT;RSEQ=CAGTTGCAAATTTCTGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:25,81:106,0:0:2,0:22.1:1:30.9:1:1:0:59.8:20.2:1:0:0.1 0/1:106:9:3,6:30,67:97,9:0.0849:2,2:22.3:1:30.9:1:1:1.12:60:18:0.0857:0:1.2 +3 65425560 . T TCTG 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=11.000;MSILEN=3;SSF=0.62726;SOR=0.7172;LSEQ=GGAAAGAGGCCAACCTTCTG;RSEQ=CTGCTGCTGCTGCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:7,5:15,10:25,12:0.3243:2,2:30:1:30.8:1:1:1.06943:58.6:5:0.2941:0:0.2 0/1:47:12:7,5:25,9:34,12:0.2553:2,2:23.6:1:30.7:1:0.46702:1.95275:54.7:24:0.2667:0.0213:0.3 +3 66687518 . CA C 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16231;SOR=0.16949;LSEQ=GACAGAGTGAGACTGTGTCT;RSEQ=AAAAAAAAGCCTTCCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:4:2,2:65,34:99,4:0.0388:2,2:25.5:1:32.8:1:0.60994:1.89904:60:8:0.0388:0:0.3 0/0:148:1:1,0:94,52:146,1:0.0068:2,0:12:0:32:0:1:0:60:2:0.0068:0:0 +3 66687528 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50747;SOR=Inf;LSEQ=GACTGTGTCTCAAAAAAAAA;RSEQ=CCTTCCTTTTGGCTGGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:81,47:128,0:0:2,0:24:1:32.3:1:1:0:59.1:41.667:1:0:0.1 0/1:168:2:1,1:101,65:166,2:0.0119:2,2:37:0:30.5:1:1:1.5496:60:4:0.0121:0:1.5 +3 66687586 . A G 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50961;SOR=Inf;LSEQ=CGCCAAAATGATGAACACAA;RSEQ=GAGAAAGAGAAGAGGCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:67,76:143,0:0:2,0:24.8:1:30.9:1:1:0:59.8:46.667:1:0:0.1 0/1:193:2:1,1:86,104:190,2:0.0104:2,2:5:0:32:1:1:1.21:54:4:0.0106:0:1.5 +3 66687723 . G C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51237;SOR=Inf;LSEQ=AATGGGTACTGTTCAAAAAG;RSEQ=AATGCCCCATAAGTGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:47,40:87,0:0:2,0:23.4:1:32:1:1:0:60:86:1:0:0.1 0/1:123:2:1,1:69,52:121,2:0.0163:2,2:5.5:1:28:1:1:1.32382:60:4:0.0165:0:1.5 +3 66687728 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17283;SOR=0;LSEQ=GTACTGTTCAAAAAGGAATG;RSEQ=CCCATAAGTGTTACCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:50,41:91,2:0.0215:2,2:21.5:1:29:1:1:1.21689:60:4:0.0215:0:1 0/0:130:0:0,0:74,56:130,0:0:2,0:20.6:1:30.6:1:1:0:59.1:260:1:0:0.2 +3 69591582 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17293;SOR=Inf;LSEQ=AGCCCGACTCCCGGGCTCTC;RSEQ=GGGCAGCCAGCGCCTGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:25,8:33,0:0:2,0:24.7:1:32.1:1:1:0:60:66:1:0:0.3 0/1:24:2:1,1:13,9:22,2:0.0833:2,2:26:0:31.5:1:1:1.42202:60:4:0.0833:0:1 +3 69788682 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=Inf;LSEQ=CTCGGGGGACCCAGGCCCAG;RSEQ=TACCTTCCCTCCGCCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:118,7:125,0:0:2,0:24.5:1:32.7:1:1:0:60:61.5:1:0:0.1 0/1:136:2:1,1:126,8:134,2:0.0147:2,2:22.5:1:29:1:0.12843:14.90803:60:4:0.015:0:1 +3 69788686 . CT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22611;SOR=0;LSEQ=GGGGACCCAGGCCCAGCTAC;RSEQ=TCCCTCCGCCCCCGGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:138,11:149,2:0.0132:2,2:18.5:1:31:1:0.15311:12.05496:60:4:0.0134:0.0066:1 0/0:166:0:0,0:147,18:165,0:0:2,0:20.8:1:30.5:1:1:0:60:81.5:0.9939:0:0.1 +3 69788697 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20066;SOR=0;LSEQ=CCCAGCTACCTTCCCTCCGC;RSEQ=CCCGGGCTCTGTTCTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:169,21:190,2:0.0104:2,2:17:1:29.5:1:0.21657:7.88555:60:4:0.0107:0:1 0/0:236:0:0,0:196,40:236,0:0:2,0:19.8:1:30.2:1:1:0:60:58:1:0:0.2 +3 69788752 . C T 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06682;SOR=0.22272;LSEQ=GACGGGAAGCGGGAGCCATG;RSEQ=AGTCCGAATCGGGGATCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:6:3,3:355,199:554,6:0.0107:2,2:24.8:1:28.8:1:0.67235:1.78188:60:12:0.0108:0:1 0/0:832:2:1,1:499,331:830,2:0.0024:2,2:20:1:28:1:1:1.50675:60:4:0.0024:0:1 +3 69915345 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50077;SOR=0;LSEQ=GGATTGGAGTTTCCAGGGCC;RSEQ=TATCAGGAGCCACCCCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:127,21:148,2:0.0133:2,2:16:1:29:1:0.27266:5.93182:60:4:0.0135:0:1 0/0:130:0:0,0:108,22:130,0:0:2,0:24.2:1:29.9:1:1:0:60:42.333:1:0:0.1 +3 69915355 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22423;SOR=Inf;LSEQ=TTCCAGGGCCTTATCAGGAG;RSEQ=CACCCCTAGTGACACAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:148,36:184,0:0:2,0:22.2:1:31.6:1:1:0:60:45:1:0:0.2 0/1:166:2:1,1:132,32:164,2:0.012:2,2:15.5:1:27:1:0.35904:4.07738:60:4:0.0123:0:1 +3 69928025 . T TA 47 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GTAGTGTGCAGCATAAAATG;RSEQ=AAAAAAAAAAAAATTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,1:7,3:0.3:2,0:25:1:30.2:1:1:0:60:6:0.3:0.1:0.7 0/0:4:0:0,0:4,0:4,0:0:0,0:22.5:1:29.5:1:1:0:60:8:1:0:0 +3 69928212 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22032;SOR=Inf;LSEQ=TTATAGTTTGGTGCAATTTA;RSEQ=GATACCCCCAAAGTGCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:180,41:221,0:0:2,0:22.5:1:32.7:1:1:0:60:72.667:1:0:0.1 0/1:196:2:1,1:152,42:194,2:0.0102:2,2:17.5:1:28:1:0.39152:3.58815:60:4:0.0104:0:1 +3 69986144 . A G 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2125;SOR=0;LSEQ=TGTGTGGCTAAACTATCTTC;RSEQ=TCAGCTCCTGTTCATTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:6,7:0.5385:0,0:20.6:1:32.1:1:1:0:51:14:0.5833:0:1.7 0/0:3:0:0,0:0,3:3,0:0:0,0:14.7:1:28:1:1:0:60:6:1:0:2.7 +3 69986691 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CCTAAGATAATTTCAAACTT;RSEQ=TAATTATTAGATATGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:18.1:1:32.9:1:1:0:56.7:14:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:22:1:29:1:1:0:60:4:0.6667:0:1 +3 69986916 . C T 36 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62368;SOR=0.33635;LSEQ=TTTGTGCCTGAAGGAAGAGC;RSEQ=GTCTGAAACTCACAAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:228,48:276,3:0.0108:2,2:16.3:1:23:1:0.08382:9.38414:60:2:0.0073:0:1.3 0/0:275:1:0,1:213,60:273,1:0.0036:2,0:1:0:25:0:0.22263:0:60:2:0.0037:0:1 +3 69987248 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23709;SOR=Inf;LSEQ=TTTTCTTATGCTAAATAACT;RSEQ=GTCTGTTGAATATGATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:53,153:206,0:0:2,0:22.9:1:30.6:1:1:0:59.8:67.667:1:0:0.1 0/1:196:2:1,1:59,134:193,2:0.0102:2,2:20.5:1:30:1:0.52181:2.26:60:4:0.0103:0:1.5 +3 69987435 . C T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68747;SOR=1.84635;LSEQ=CTCCAAGTGAAATGTGGAGG;RSEQ=GAGGACACTTTTGCCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:2:0,2:172,83:255,2:0.0078:2,0:1:0:27:1:0.10852:0:60:4:0.008:0:1 0/1:281:4:1,3:182,94:276,4:0.0142:2,2:19.8:1:27.5:1:0.12147:5.77072:60:8:0.0145:0:1.3 +3 69987707 . C T 116 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00977;SOR=0.12171;LSEQ=TATAGCACATGAGACTTTAA;RSEQ=GGAAACGCAAAGGTTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:1,13:0,13:13,14:0.5185:1,1:21.9:1:30.6:1:1:0:60:28:0.5385:0:1 0/1:18:2:0,2:0,16:16,2:0.1111:1,0:18.5:1:23:1:1:0:60:1:0.0588:0:1 +3 69988183 . G T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36231;SOR=3.16163;LSEQ=CTGTGCCATCAGCTTTGTGT;RSEQ=AACAGGTCATTAAAAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:0,1:182,82:264,1:0.0038:2,0:1:0:23:0:0.31321:0:60:2:0.0038:0:1 0/1:253:3:1,2:167,83:250,3:0.0119:2,2:23.7:1:25.3:1:0.2619:4.00019:60:6:0.0121:0:1.3 +3 69988421 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.1855;SOR=Inf;LSEQ=ACCTTCCTGAAAACTTAAGC;RSEQ=TTTTTTCCCCCATTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:3,73:76,0:0:1,0:21:1:29.8:1:1:0:58.9:24.333:1:0:0.9 0/1:58:2:0,2:4,51:55,2:0.0345:2,0:18.5:1:28.5:1:1:0:60:4:0.0364:0:0 +3 69988434 . A AT 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.24443;SOR=0;LSEQ=CTTAAGCATTTTTTTCCCCC;RSEQ=TTGTTTTTTTTTTTTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:0,3:1,42:43,3:0.0556:1,0:32:1:23.3:1:1:0:54.7:2:0.0645:0:3.7 0/0:49:0:0,0:2,44:46,0:0:1,0:20.9:1:25.5:1:1:0:59.8:2.538:1:0:0.6 +3 69990522 . T A 31 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24903;SOR=Inf;LSEQ=AAGTAGAAAATCTTGAGGTG;RSEQ=TTCCAGGGTTCTTTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:56,229:285,0:0:2,0:22.7:1:30.2:1:1:0:59.9:56:1:0:0.1 0/1:298:3:2,1:83,212:295,3:0.0101:2,2:5.3:1:20:1:0.19678:5.08:60:2:0.0068:0:1.3 +3 69998349 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24974;SOR=Inf;LSEQ=TAGTAAATGTGCCTCTTACT;RSEQ=CAGATTTCTGTCCATTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:61,200:261,0:0:2,0:23.5:1:31.9:1:1:0:60:42.5:1:0:0.1 0/1:282:3:1,2:74,204:278,3:0.0106:2,2:17.7:1:27.7:1:1:1.38:60:6:0.0109:0:1 +3 70000954 . C T 63 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.036;SOR=Inf;LSEQ=ACTTCTAATGACTTCATTCA;RSEQ=GTGCACAGCGTGTATTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:251,164:415,0:0:2,0:24.7:1:31.4:1:1:0:60:206.5:1:0:0.1 0/1:513:6:3,3:321,186:507,6:0.0117:2,2:17.5:1:24.5:1:0.67427:1.7238:60:5:0.0099:0:1.5 +3 70005281 . A G 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAATTTGGGCTTTCACCAG;RSEQ=TATTGTTGGATGTCCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:26:1:31.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 70005509 . A T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49981;SOR=0;LSEQ=TTCAGGTTTCCGTTGTCATG;RSEQ=CCTGGAGAAGTTAATATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:2,0:137,13:150,2:0.0132:2,0:31.5:1:32:0:1:0:60:4:0.0133:0:1 0/0:136:0:0,0:114,22:136,0:0:2,0:24.3:1:28.5:1:1:0:59.9:44.333:1:0:0.1 +3 70005712 . T C 145 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TCGCGTGTTAATCTGCATCA;RSEQ=ATATTTTTCGTACCTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:24:8,16:136,274:410,24:0.0552:2,2:24.7:1:31.8:1:1:1.01:60:23:0.0537:0:1.4 0/0:449:0:0,0:162,287:449,0:0:2,0:6:0:15:0:1:0:60:0:0:0:5 +3 70007486 . C T 29 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGTGGGTATCTCAGGACATT;RSEQ=CCCTGGGTTGCCATCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:35:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:29:1:1:0:60:4:1:0:1 +3 70008316 . T TA 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50183;SOR=0;LSEQ=TTCCCCCAAAACTATTGAAA;RSEQ=AAAAAAAAATTTTAAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:2,0:42,0:42,2:0.0455:1,0:32.5:1:26.5:1:1:0:50:4:0.0465:0:0 0/0:34:0:0,0:34,0:34,0:0:1,0:17.8:1:31.1:1:1:0:58.5:68:1:0:0.1 +3 70008602 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13847;SOR=Inf;LSEQ=TGAGTTGTGTAAAGTTTACT;RSEQ=CTTTTTACCGACTTCAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:26,116:142,0:0:2,0:22:1:31.8:1:1:0:60:34.5:1:0:0.1 0/1:190:4:2,2:46,140:186,4:0.0211:2,2:18.3:1:29:1:0.26507:3.02:60:8:0.0213:0:1.3 +3 70008612 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50797;SOR=Inf;LSEQ=AAAGTTTACTGCTTTTTACC;RSEQ=ACTTCAAGACAGTAGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:17,93:110,0:0:2,0:23.2:1:31.7:1:1:0:60:220:1:0:0.1 0/1:146:2:1,1:27,116:143,2:0.0137:2,2:17.5:1:31.5:1:0.35:4.24:60:4:0.014:0:1 +3 70013474 . GTGAGAGACCATCTCTATTTTTCATACATAATCAAATCTATAAAACACCTAAAAATTTATTTCACATACTGCCAGTGGTACTTCTCCTATACTTTAGAACATACAGAGCTCATTAATTTAAAAGAACAAAAAACTTTTATTTTGAGGATTTATTGTTTTCCAAGTATCTGATTTTTAAAAATAGACTTTATTTTTCAGGACAGTTTTTGGTTCACAGTAAAATTGAAATGAAGCTGCAGATATTTCCCATACACCTCATTCCCCCAAGCACGCACAGCCTTCCCCATTATCAACATTCCCTACCAGAGTGGCACATTTATTAGAATCAATGAACCCGCAGTGACATTTCATTATCCTCCAAAGTCTATACTTTACATTCCCTCTGGTATTGTACATTTTGTGGGTTTGGCCAAA G 160 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03125;SOR=Inf;LSEQ=CAGTGTGAACATTAATATCT;RSEQ=TGTCTAATGACGCGCATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:48:0:30:0:1:0:60:2:1:0:0 1/1:31:31:30,1:0,0:0,31:1:0,1:25.4:1:32.3:1:1:0:56.8:62:1:0.0645:0.1 +3 70014447 . T C 312 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01904;LSEQ=AAACTGCTTCCTTTCTTGAT;RSEQ=CGTAGATTTAATAACTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1158:992:376,616:62,101:163,992:0.8566:2,2:25.1:1:31.4:1:1:1.00568:60:75.308:0.8573:0:1.1 0/1:1374:140:61,79:511,723:1234,140:0.1019:2,2:25.3:1:30.3:1:0.65143:1.09:60:280:0.1025:0:1.1 +3 70014804 . G GA 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGTAAAGCAACCAAAAA;RSEQ=AAAAAAAAAAAGAAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,6:6,2:0.2222:0,0:25:1:32:1:1:0:60:4:0.25:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:15:0:33:0:1:0:60:2:1:0:0 +3 70348641 . A C 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01136;SOR=0;LSEQ=CCCCTAGAGACATATTAAAA;RSEQ=TTCCCATTGAATCCAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,1:3,7:0.7:2,0:22.6:1:32.4:1:0.3:0:60:14:0.7778:0:1.3 0/0:6:0:0,0:6,0:6,0:0:0,0:36.5:1:29.5:1:1:0:60:12:1:0:0.2 +3 70348685 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=TGTAATCTCTGACAACTCCT;RSEQ=TCTCTCTGATCCCTTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:28.5:1:28:1:1:1.10554:60:4:0.0952:0:1.5 0/0:21:0:0,0:13,8:21,0:0:2,0:23.4:1:31.6:1:1:0:60:42:1:0:0.2 +3 70348776 . A G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24252;SOR=Inf;LSEQ=CCTTTGTTTTCATTGCCCTG;RSEQ=AAACCAATATCTCAAATTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:19,0:0:2,0:25.7:1:31:1:1:0:60:38:1:0:0.2 0/1:24:3:1,2:8,13:21,3:0.125:2,2:28.7:1:32.3:1:1:1.22038:60:6:0.1304:0:2 +3 70348796 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23361;SOR=Inf;LSEQ=AAAACCAATATCTCAAATTC;RSEQ=GAATTCATGCCTTCTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,8:15,0:0:2,0:14:1:30.1:1:1:0:60:30:0.9375:0:0.1 0/1:19:3:1,2:5,11:16,3:0.1579:2,2:21.7:1:32:1:1:1.09:60:6:0.1667:0:2 +3 71007140 . GT G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=GCAGCTGCTCGGGGAAGCCG;RSEQ=TTTTTTTTTTGGCCATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:9,1:10,0:0:2,0:21.6:1:26.7:1:1:0:60:9:1:0:0.6 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:31.5:1:29.5:1:0.33333:0:60:4:0.4:0:0 +3 71007308 . G T 21 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.72813;LSEQ=AGTGCTGCCTATGTTTCCTT;RSEQ=TGCTGGTAGAATGTGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:3:3,0:213,2:215,3:0.0138:1,0:19.3:1:13.3:1:1:0:60:0:0:0:4.3 0/1:199:2:1,1:189,7:196,2:0.0101:1,2:11.5:1:25.5:1:0.07937:25.32322:60:4:0.0126:0:2 +3 71007361 . G T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0874;SOR=1.1861;LSEQ=TTGCTGCAAAAAAAAAAAAA;RSEQ=AAAAGAAAAGAAAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:804:291:174,117:291,169:460,291:0.3619:2,2:19.9:1:26.3:1:0.35523:1.15759:59.8:4.596:0.3905:0:1.4 0/1:987:397:229,168:337,216:553,397:0.4022:2,2:20.3:1:25.4:1:0.31565:1.14442:59.6:4.838:0.4218:0:1.4 +3 71007462 . C CT 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.27236;SOR=1.17452;LSEQ=TGTTCCTAGAGTTTGTCTCT;RSEQ=TTTTTTTTTTCTGTCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1158:100:38,62:472,573:1045,100:0.0864:2,2:28.5:1:29.7:1:0.17289:1.34364:60:15.667:0.085:0.0035:0.4 0/1:1361:136:58,78:518,686:1204,136:0.0999:2,2:28.6:1:28.9:1:1:1.01547:59.5:18.429:0.0992:0:0.5 +3 71008251 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5015;SOR=Inf;LSEQ=GGTTCTTGATGGCACTAAGA;RSEQ=TTAACACATTTCAGAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:91,1:92,0:0:1,0:23.7:1:33.3:1:1:0:60:45:1:0:0.1 0/1:110:2:2,0:107,1:108,2:0.0182:1,0:26:1:32.5:1:1:0:60:4:0.0182:0:1 +3 71015021 . G T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.40453;LSEQ=GGGTCAGATAGCAAAGACCT;RSEQ=TTGGGTGGACAATACTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:404:361:254,107:31,11:42,361:0.8936:2,2:23.1:1:30.7:1:0.72247:1.18667:60:50.571:0.8939:0:1.1 1/0:492:380:252,128:77,34:111,380:0.7724:2,2:25.4:1:29.6:1:0.56843:1.14998:60:37:0.7692:0:1.2 +3 71015640 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATCAGATTATCCTGGCC;RSEQ=CACCGCTCAAACTTATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:34:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 71019750 . T C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11965;SOR=0.51932;LSEQ=GTGTTTGCCTCCAGGGAGTA;RSEQ=GATGCTTTGTGCACTTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:26:26,0:30,0:30,26:0.4643:1,1:20.6:1:32:1:1:0:60:52:0.4727:0:1.8 0/1:55:17:16,1:38,0:38,17:0.3091:1,1:23.8:1:32.2:1:0.30909:0:60:34:0.3148:0:1.2 +3 71019797 . A T 180 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00915;LSEQ=TTTAACGGAATTAAAATTTA;RSEQ=TATCTAATTAGAGCAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:55:49,6:89,13:102,55:0.3503:2,2:23.8:1:31.2:1:0.80331:1.19:60:110:0.3503:0:1.5 0/0:206:1:0,1:175,30:205,1:0.0049:2,0:1:0:25:0:0.15049:0:60:2:0.0049:0:1 +3 71019871 . C T 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08288;SOR=0.25199;LSEQ=CCTCTGCTGCATATTCGGGA;RSEQ=GGCCGTTAATCTTACCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:6:3,3:312,234:546,6:0.0109:2,2:18.5:1:26.5:1:1:1.33262:60:5:0.0093:0:1 0/0:725:2:0,2:400,323:723,2:0.0028:2,0:1:0:23.5:1:0.20061:0:60:4:0.0028:0:1 +3 71019931 . G A 75 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31326;SOR=2.73647;LSEQ=GCAGTAGGCGTGGCTGCTCT;RSEQ=CATGTTTTTAATAAGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:2:2,0:219,324:543,2:0.0037:2,0:1:0:25:0:0.16399:0:60:4:0.0037:0:1 0/1:701:7:4,3:303,388:691,7:0.01:2,2:14.6:1:26.9:1:0.70531:1.71:60:14:0.0102:0:1.1 +3 71021128 . G GA 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.81506;SOR=1.07356;LSEQ=GCAAAGCCAAAGCAACAGCA;RSEQ=AAAAAAAAAACAAAAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:34:26,8:175,53:228,34:0.1219:2,2:24.4:1:30.5:1:1:1.0159:59.7:68:0.125:0.0143:0.6 0/1:401:52:43,9:239,91:330,52:0.1297:2,2:32.3:1:29.1:1:0.12939:1.82:59.9:104:0.1361:0:0.5 +3 71021355 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18203;SOR=Inf;LSEQ=GGATAGGAGCAGCAGCAAAG;RSEQ=AGATGGAGTGGCAACAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:52,204:256,0:0:2,0:26.3:1:31.7:1:1:0:59.9:31:1:0:0.1 0/1:191:2:1,1:34,154:188,2:0.0105:2,2:33:1:27:1:0.33528:4.48:60:4:0.0106:0:1 +3 71025935 . C T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31599;SOR=0.5448;LSEQ=GAGCATTTCAACCACAATGG;RSEQ=ACTATTTTCCCAATCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:22:22,0:10,0:10,22:0.6875:0,1:27.9:1:30.4:1:1:0:60:44:0.6875:0:1.1 1/0:35:19:19,0:16,0:16,19:0.5429:1,1:25.9:1:30:1:1:0:60:38:0.5429:0:1 +3 71026053 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09298;SOR=0;LSEQ=ACAACAAACTGTTCTATGAA;RSEQ=GTCAAGATCCAAGAATAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:203,94:297,3:0.01:2,2:23.7:1:30:1:0.24087:4.2959:60:6:0.0102:0:1 0/0:361:0:0,0:233,128:361,0:0:2,0:26.2:1:30.3:1:1:0:60:71.2:1:0:0.1 +3 71026265 . A G 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61024;SOR=2.16475;LSEQ=GTCATTCCACAGTTTCTCGA;RSEQ=AATATAAAATCACTGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:14,139:153,1:0.0065:2,0:17:0:15:0:1:0:60:0:0:0:4 0/1:143:2:1,1:14,127:141,2:0.014:2,2:26.5:1:32.5:1:0.19945:8.80:60:4:0.0141:0:1.5 +3 71036994 . A G 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02255;LSEQ=TATGACCTTCATCATAAAGG;RSEQ=TAACCAGAAACAGTCGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:65:63,2:6,0:6,65:0.9155:0,1:22.7:1:31.6:1:1:0:60:64:0.9143:0:1.1 0/1:48:9:9,0:38,1:39,9:0.1875:1,0:27.2:1:31.2:1:1:0:60:18:0.1875:0:1.2 +3 71037061 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2554;SOR=Inf;LSEQ=TCCACCAAAGTAGGCTGGTC;RSEQ=TCCTTCCTCCATTTGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:177,28:205,0:0:2,0:23.5:1:31.4:1:1:0:59.8:67.333:1:0:0.3 0/1:249:3:1,2:194,52:246,3:0.012:2,2:16.7:1:29:1:0.11953:7.38061:60:6:0.0123:0:1.3 +3 71049945 . A AAAAAT 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=53;MSI=11.000;MSILEN=5;SSF=0.60839;SOR=0.42576;LSEQ=TGAACCTGCCCAAAGAGGTA;RSEQ=AAAATAAAATAAAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:30:1:31.8:1:1:0:47.3:8:0.6667:0:0 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:8:1:29.1:1:1:0:43.5:8:0.4444:0.3333:0 +3 71050054 . A C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49919;SOR=Inf;LSEQ=TGAGTACACAGGAACTCATT;RSEQ=CAGAACACTACAGAAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:158,31:189,0:0:2,0:26.2:1:28.4:1:1:0:59.6:46.25:1:0:0 0/1:201:2:1,1:157,40:197,2:0.01:2,2:15.5:1:26.5:1:0.37044:3.88917:60:4:0.01:0:1 +3 71064654 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49902;SOR=Inf;LSEQ=GCAAAGCATGAACGGTGGGA;RSEQ=GTGTTGGCTATGTAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:127,27:154,0:0:2,0:22.1:1:33:1:1:0:60:76:1:0:0.1 0/1:165:2:2,0:125,38:163,2:0.0121:2,0:26.5:1:31.5:1:1:0:60:4:0.0123:0:1 +3 71064664 . A T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12449;SOR=Inf;LSEQ=AACGGTGGGAGGTGTTGGCT;RSEQ=TGTAAAAGAAGAAAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:147,41:188,0:0:2,0:22.8:1:28.9:1:1:0:60:93:1:0:0.1 0/1:205:4:1,3:143,58:201,4:0.0195:2,2:18.5:1:26:1:0.07983:7.31562:60:8:0.0196:0:1 +3 71096086 . C T 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09442;SOR=0.15965;LSEQ=TATGCCTTCTGTAAAATCAA;RSEQ=GCATACCTTGAGCAAGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:5:2,3:240,151:391,5:0.0126:2,2:28.8:1:26.4:1:0.38132:2.3787:60:1.5:0.0077:0:1.2 0/0:493:1:0,1:276,216:492,1:0.002:2,0:1:0:27:0:0.44016:0:60:2:0.002:0:1 +3 71096576 . A C 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTATGCACACTAGAGAGA;RSEQ=GACTGCATCACTCTAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:16:1:28.5:1:1:0:60:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 71097955 . T TG 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTGAAAGCAGACTATAA;RSEQ=GGGGGGGGTACAGCTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21:1:34.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 71101321 . GA G 31 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CCCAAGCTCTGTGAGCTGGG;RSEQ=AAAAAAAAAAAAATTAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:21.5:1:31:1:1:0:60:4:0.5:0:0 0/0:2:0:0,0:1,1:2,0:0:2,0:39.5:1:30:1:1:0:60:4:1:0:1 +3 71101450 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=CTGAAGACTCTGTCAACGAT;RSEQ=CCTCTCCTGCTCCTCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:17,0:17,2:0.1053:1,2:40:1:29.5:1:0.10526:0:60:4:0.1053:0:1 0/0:11:0:0,0:11,0:11,0:0:0,0:21.2:1:32.3:1:1:0:60:22:1:0:0.2 +3 71101580 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23422;SOR=Inf;LSEQ=TCTGAAAGCTGAGAACCGAT;RSEQ=GAGTCAGCTCAGTTGTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:179,6:185,0:0:1,0:23.6:1:28.8:1:1:0:60:184:1:0:0 0/1:174:2:2,0:162,10:172,2:0.0115:2,0:25.5:1:31.5:1:1:0:60:4:0.0115:0:1 +3 71102157 . G A 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCAGTGTGTGCATGGACA;RSEQ=CCTGGGAGCTTCCGCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:31:0:1:0:60:4:1:0:1 +3 71102941 . G A 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13105;SOR=Inf;LSEQ=GAACCTAGAATGTTAATGAA;RSEQ=GATAAATAGGAAGCCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:98,197:295,0:0:2,0:25.6:1:31.6:1:1:0:60:58:1:0:0.1 0/1:359:4:2,2:129,225:354,4:0.0111:2,2:8.8:1:24.8:1:0.62553:1.74:60:3:0.0085:0:1.8 +3 71103136 . T C 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02424;SOR=0;LSEQ=GTAAAATCTTGCAGTACTGA;RSEQ=GGGGGTTCCAGGCAGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:14.7:1:30.3:1:1:0:60:14:0.875:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:14.3:1:31:0:1:0:60:6:1:0:0 +3 71153524 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49583;SOR=Inf;LSEQ=AAGACCTCATTGTGGGATCA;RSEQ=AGCCTATCCAAGAAGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:29,20:49,0:0:2,0:29.8:1:32.1:1:1:0:60:48:1:0:0.2 0/1:53:2:1,1:32,18:50,2:0.0377:2,2:24:1:29:1:1:1.7571:60:4:0.0385:0:1 +3 71153542 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51292;SOR=Inf;LSEQ=CACAGCCTATCCAAGAAGAA;RSEQ=CCGCCCTTCTGCTGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:30,29:59,0:0:2,0:29.1:1:32.8:1:1:0:60:118:1:0:0.2 0/1:85:2:1,1:49,34:83,2:0.0235:2,2:18.5:1:30:1:1:1.43483:60:4:0.0235:0:1.5 +3 71153709 . T G 91 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAATTCTTTCACATCCTC;RSEQ=AACTGTCATCAACATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:18.3:1:32:1:1:0:60:8:1:0:1.5 1/1:8:8:0,8:0,0:0,8:1:0,0:19.5:1:30.4:1:1:0:60:16:1:0:1 +3 71161817 . C T 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01532;SOR=Inf;LSEQ=AAAAACAAGAAAATCCTTTG;RSEQ=GTTACTACACAGGTTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:74,233:307,0:0:2,0:24.3:1:30.3:1:1:0:60:60.4:1:0:0.1 0/1:323:7:2,5:88,226:314,7:0.0217:2,2:14.6:1:29:1:1:1.03:60:14:0.0221:0:1.1 +3 71161847 . TA T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.22835;SOR=Inf;LSEQ=CAGGTTCAGGGGACTCTTCA;RSEQ=AAAAAGGATTCCAGGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:21,150:171,0:0:2,0:23.9:1:30.8:1:1:0:60:41.75:1:0:0.1 0/1:157:2:0,2:29,125:154,2:0.0127:2,0:19:1:32:1:1:0:60:4:0.0132:0.0064:0.5 +3 71162001 . G A 74 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCGGCCAGTTTCATCCAC;RSEQ=GTTCCACAGGCATCTAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:3,5:0.625:0,2:29.4:1:32:1:1:0:60:10:0.7143:0:1.2 1/1:1:1:0,1:0,0:0,1:1:0,0:40:0:31:0:1:0:60:2:1:0:1 +3 71179582 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50639;SOR=Inf;LSEQ=CCTTCAGAGAATGTCTGCAC;RSEQ=AGAACGGATCCCTAGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:80,12:92,0:0:2,0:25.3:1:30.6:1:1:0:59.9:184:1:0:0.1 0/1:120:2:1,1:102,16:118,2:0.0167:2,2:23.5:1:27.5:1:0.26429:6.21491:60:4:0.0168:0:1 +3 71179882 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50057;SOR=Inf;LSEQ=TTTGCCTCCACAGTAGCTGG;RSEQ=TGGGCTCTCACTAAATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:3,62:65,0:0:1,0:22.7:1:32.9:1:1:0:60:31.5:1:0:0.1 0/1:79:2:1,1:12,65:77,2:0.0253:2,2:25.5:1:28:1:0.3038:5.24:60:4:0.0256:0:1 +3 71179921 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.20653;SOR=Inf;LSEQ=CAAAGAAACCACAAGAATTC;RSEQ=TCAAGTAATTCTTCACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:1,26:27,0:0:1,0:22.5:1:33.6:1:1:0:60:54:1:0:0 0/1:23:2:1,1:0,21:21,2:0.087:1,2:36.5:1:30:1:0.08696:0:60:4:0.087:0:1.5 +3 71246918 . C T 126 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATGTATTTATTTCAACTCT;RSEQ=CTTACTCATCTACTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:15,1:16,0:16,16:0.5:1,1:26.1:1:31.5:1:1:0:60:32:0.5:0:1.1 0/0:35:0:0,0:34,1:35,0:0:1,0:20.1:1:29.5:1:1:0:60:16.5:1:0:0.3 +3 71247014 . A T 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00055;SOR=0;LSEQ=CGTTTAATTTTTATTTTTGC;RSEQ=TGAAAGCAGTGGGAACCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:9:7,2:177,35:212,9:0.0407:2,2:24.2:1:32.7:1:0.64834:1.44222:60:18:0.0413:0:1 0/0:283:0:0,0:199,84:283,0:0:2,0:22.5:1:29:1:1:0:60:39.429:1:0:0.1 +3 71247304 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.11115;LSEQ=TAAGTGTAAAATTCAGCAGT;RSEQ=AAATTCGCACCCACCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:118:81,37:130,64:194,118:0.377:2,2:22.8:1:32.3:1:0.80375:1.08:59.9:38.333:0.3758:0:1.1 0/1:382:24:14,10:241,117:358,24:0.0628:2,2:26:1:30.8:1:0.37673:1.46978:60:48:0.0632:0:1.1 +3 71247356 . TTGC T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.84922;SOR=1.16513;LSEQ=ACTCCAAAGCCCAGTACCTG;RSEQ=TGCTGCTGCTGGGCGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:528:11:6,5:313,204:517,11:0.0208:2,2:28.5:1:30.6:1:0.75963:1.27797:60:22:0.021:0.0019:0.5 0/1:744:18:10,8:433,293:726,18:0.0242:2,2:24.2:1:28.6:1:0.80946:1.18198:60:36:0.0244:0.0067:0.2 +3 71247572 . A T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07284;LSEQ=AGGATTTCCAAGATGGGGGG;RSEQ=GGGAGGGGGGGAGAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:219:129:70,59:11,11:22,129:0.589:2,2:14.7:1:27.2:1:0.81816:1.19:59.5:8.214:0.6216:0:1.3 0/1:266:25:15,10:117,60:177,25:0.094:2,2:13.5:1:26.2:1:0.65401:1.29823:59.8:7.333:0.0978:0:1.2 +3 71247576 . A T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=19.28682;LSEQ=TTTCCAAGATGGGGGGAGGG;RSEQ=GGGGGGGAGAAAAAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:15:7,8:63,37:100,15:0.0806:2,2:14.3:1:25.5:1:0.26353:1.93427:56.7:4:0.087:0:2 1/0:230:145:101,44:14,8:22,145:0.6304:2,2:17.8:1:25.7:1:0.62361:1.31:59.4:6.632:0.7119:0:1.4 +3 71247585 . G GA 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.02572;SOR=0.28845;LSEQ=TGGGGGGAGGGAGGGGGGGA;RSEQ=AAAAAAAAAGCAGCTGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:13:5,8:44,100:144,13:0.0823:2,2:17.8:1:28.7:1:0.54559:1.42:53.8:26:0.0903:0.0127:1.6 0/1:199:5:3,2:82,109:191,5:0.0251:2,2:27.2:1:31:1:0.65415:1.99:53.4:10:0.0287:0:1.6 +3 71247595 . G A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00517;SOR=Inf;LSEQ=GAGGGGGGGAGAAAAAAAAA;RSEQ=CAGCTGTTAAAGCAGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:31,118:149,0:0:2,0:21.1:1:31.9:1:1:0:55.3:36.25:1:0:1.4 0/1:187:9:2,7:58,120:178,9:0.0481:2,2:23.6:1:29:1:0.72087:1.68736:57.8:18:0.0503:0:2.6 +3 72211513 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51153;SOR=Inf;LSEQ=AGCCCCACCCTGCTTCTCTG;RSEQ=ACCGCTGACTCCTCTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:27,0:0:2,0:30.7:1:32.1:1:1:0:60:26:1:0:0.2 0/1:40:2:1,1:21,17:38,2:0.05:2,2:20.5:1:28.5:1:1:1.22874:60:4:0.05:0:1.5 +3 72213025 . G A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGACAGACCAGGTTCCA;RSEQ=GTAATTGTGGCCAAGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:31.5:1:31:0:1:1.73:60:4:0.4:0:1 +3 72322897 . C T 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.15267;LSEQ=GGAATTGTTGGTATTCAAGC;RSEQ=GGCTCTCTGGAGGCCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,1:7,3:0.3:2,0:33.3:1:32.7:1:1:0:60:6:0.3:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:39:0:27:0:1:0:60:2:0.3333:0:1 +3 72323024 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25195;SOR=Inf;LSEQ=AGCCCCCAACAGCCAACAGA;RSEQ=CTGAGCACTGCCCTGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:77,3:80,0:0:1,0:22.4:1:33:1:1:0:60:79:1:0:0.1 0/1:96:3:1,2:82,11:93,3:0.0313:2,2:19.3:1:28.7:1:0.04731:14.14585:60:6:0.033:0:1 +3 72323061 . A G 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57592;SOR=0.36454;LSEQ=TGGCTCCACACACAGCTCTC;RSEQ=GGAACTCCAGAACTTCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:96,37:133,2:0.0148:2,2:32.5:1:31:1:0.48524:2.57353:60:4:0.0149:0:1 0/0:184:1:1,0:133,50:183,1:0.0054:2,0:4:0:27:0:1:0:60:2:0.0056:0:1 +3 72323080 . G A 131 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGGAACTCCAGAACTTCCC;RSEQ=AGCACCTTGTCTGGTGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:21:15,6:117,40:157,21:0.118:2,2:22.9:1:30:1:0.79248:1.16891:60:20:0.113:0:1.4 0/0:242:0:0,0:177,65:242,0:0:2,0:26.3:1:29.1:1:1:0:60:25.889:1:0:0.1 +3 72323171 . C T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20143;LSEQ=TTACGTTTAAAACCACAAAA;RSEQ=AGAAGGGAGGTTTGTAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:568:325:175,150:137,105:242,325:0.5722:2,2:25.2:1:29.6:1:0.55047:1.11815:59.8:53.167:0.5686:0:1.2 0/1:849:180:96,84:347,322:669,180:0.212:2,2:24.7:1:28.4:1:0.73747:1.06:59.9:89:0.2129:0:1.1 +3 72323287 . A G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08131;LSEQ=ACTTCGGGTTTCCCCAAGAC;RSEQ=CTCAGGGTTCCCCAGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:68:9,59:11,85:96,68:0.4146:2,2:25:1:31.5:1:0.81032:1.18:60:33:0.4074:0:1.1 0/1:148:8:0,8:15,125:140,8:0.0541:2,0:34.3:1:32.1:1:1:0:60:16:0.0541:0:1 +3 72323384 . T A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03722;SOR=0.24248;LSEQ=AAAGTAAGAATGTGACTCTT;RSEQ=CACAAATAGTAAATGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:0,14:0,14:14,14:0.5:1,1:29.4:1:31.1:1:1:0:60:28:0.5:0:1.1 0/1:21:4:0,4:2,15:17,4:0.1905:2,0:34.3:1:30.3:1:1:0:60:8:0.2:0:1.8 +3 72323412 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20308;SOR=Inf;LSEQ=AGTAAATGAGCACATGTCAA;RSEQ=GATCTCTTTAACCTATGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:14,0:0:1,0:22.3:1:31.6:1:1:0:60:28:1:0:0.8 0/1:12:2:1,1:0,10:10,2:0.1667:0,2:7.5:1:28:0:0.16667:0:60:4:0.1667:0:2 +3 72427252 . A AT 49 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAATTGTGCACAGCAG;RSEQ=TTTTTTTTTTTTTATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:33.3:1:31:1:1:0:49.3:6:0.6:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 72427853 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50057;SOR=Inf;LSEQ=GATCAAAAACAGCTTCTGGC;RSEQ=GAATATCATCAATACGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:5,52:57,0:0:2,0:23.8:1:32.4:1:1:0:60:114:1:0:0.1 0/1:69:2:1,1:8,59:67,2:0.029:2,2:35.5:1:29:1:0.24552:7.01:60:4:0.029:0:1 +3 72428110 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21536;SOR=0;LSEQ=TCTTAGCCTACAAACCCAAG;RSEQ=CACAAAACCACCCTGGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:165,24:189,2:0.0105:2,2:27.5:1:26.5:1:0.24525:6.75521:60:4:0.0108:0:1 0/0:220:0:0,0:183,36:219,0:0:2,0:23.9:1:30.6:1:1:0:60:53.75:0.9954:0:0.1 +3 72428323 . C CA 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.27603;SOR=2.64377;LSEQ=ATACAAAACAAACAAACAAA;RSEQ=AAAAAAAACAGGCATTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:2:1,1:262,206:468,2:0.0042:2,2:12.5:1:31.3:1:1:1.27118:60:4:0.0043:0.0021:0 0/1:449:5:2,3:254,186:440,5:0.0111:2,2:17.2:1:31.4:1:0.65468:2.04507:60:10:0.0113:0:0.2 +3 72455797 . A C 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00164;SOR=0;LSEQ=AACAAAGGTATTTTAAATAG;RSEQ=TCCCCCGAGGAGATTCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:11,0:9,0:9,11:0.55:0,0:24.3:1:33.3:1:1:0:60:22:0.55:0:1 0/0:12:0:0,0:12,0:12,0:0:0,0:14.7:1:28:1:1:0:60:24:1:0:0.1 +3 72456179 . G GA 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.67376;SOR=1.64103;LSEQ=GTAAAATCCATAAAGTGCCA;RSEQ=AAAAAAAATGAGATGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:2:1,1:23,206:229,2:0.0086:2,2:21:1:27:1:0.1974:8.79:60:4:0.0089:0.0043:0.5 0/1:213:3:1,2:27,183:210,3:0.0141:2,2:28:1:28.7:1:0.3462:3.36:50.7:6:0.0143:0.0047:0.3 +3 72456199 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23549;SOR=Inf;LSEQ=GAAAAAAAATGAGATGAGTG;RSEQ=TTTCTGTCCAACAAAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:3,162:165,0:0:1,0:24.7:1:30.9:1:1:0:59.9:19.625:1:0:0.3 0/1:157:2:1,1:7,148:155,2:0.0127:1,2:10:1:29:1:0.09962:19.85:60:4:0.0131:0:1 +3 72495593 . T TA 173 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.55596;SOR=1.15996;LSEQ=AGGCTCACTACCCTCTCACT;RSEQ=AAAAAAAAAAAAAAAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:40:30,10:55,9:64,40:0.32:2,2:29.3:1:28.4:1:0.19561:2.0225:57.7:19:0.314:0.048:2 0/1:218:77:54,23:83,29:112,77:0.3532:2,2:25.9:1:27.7:1:0.61967:1.21773:57.9:76:0.3707:0.0413:2.2 +3 72495777 . C G 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03412;LSEQ=CGCTTGTCTTTTTGGCCTTC;RSEQ=GAGGAGTGGAGAGTGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:509:507:194,313:0,0:0,507:0.9961:0,2:26.1:1:30.4:1:1:0:60:49.7:0.996:0:1.2 1/1:800:717:286,431:37,43:80,717:0.8963:2,2:27.2:1:29.7:1:0.28176:1.29627:60:88.625:0.8975:0:1.2 +3 72495945 . A G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTCCGGGGACTGGAAGAG;RSEQ=GAGCGAGGAAGGGAACCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:0,12:1:0,0:22.9:1:30.9:1:1:0:60:24:1:0:1.1 1/1:15:14:0,14:0,1:1,14:0.9333:0,1:21:1:30.3:1:1:0:60:28:0.9333:0:1.1 +3 72799703 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.41196;LSEQ=GAAAGGGACCTTGCAAAGAA;RSEQ=TGACTGTCTCAGATGGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:587:36:16,20:287,263:550,36:0.0613:2,2:23.8:1:31.1:1:0.3936:1.36334:47.7:72:0.0617:0:1.2 0/1:676:240:119,121:207,228:435,240:0.355:2,2:21.7:1:29.6:1:0.63006:1.08:47.1:119:0.3552:0:1.2 +3 72800061 . C CA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19897;SOR=0;LSEQ=ATAACAGGTTATACAGCTTC;RSEQ=AAAAAAATAAAGTTGAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:0,75:75,2:0.026:1,0:19.5:1:30.5:1:1:0:60:4:0.026:0.013:0.5 0/0:95:0:0,0:10,85:95,0:0:2,0:23.8:1:31.4:1:1:0:60:94:1:0:0.1 +3 72861740 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4987;SOR=Inf;LSEQ=TATTTATATACAGTAAAAAA;RSEQ=CAAAAATCATTATTATATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:122,8:130,0:0:2,0:22.9:1:33.1:1:1:0:60:129:1:0:0.1 0/1:139:2:1,1:116,21:137,2:0.0144:2,2:7:1:26:1:0.29246:5.42011:60:4:0.0146:0:1.5 +3 72862375 . T C 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTCATGCCTGTAAAGCACT;RSEQ=TGGGACTCCAGGCGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:28.5:1:27.5:1:1:0:54:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:31.5:1:1:0:60:4:1:0:1 +3 72866303 . G T 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50011;SOR=Inf;LSEQ=TCACCACCAGTTCTACTCTA;RSEQ=ACAAGAAAGACTGATGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:119,9:128,0:0:2,0:22.8:1:33.4:1:1:0:60:127:1:0:0.2 0/1:145:2:1,1:119,24:143,2:0.0138:2,2:5.5:1:24.5:1:0.31609:4.87862:60:4:0.0142:0:1.5 +3 72873492 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4993;SOR=Inf;LSEQ=ATAAGGCAATTACAACTATA;RSEQ=GCTTAATAATATGGAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:117,13:130,0:0:2,0:24:1:32:1:1:0:60:64:1:0:0 0/1:143:2:1,1:129,12:141,2:0.014:2,2:25:1:26:1:0.17414:10.3683:60:4:0.0142:0:1 +3 72873527 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09158;SOR=0;LSEQ=AAGGCAGTAAACGTGGTACA;RSEQ=CATGAGATTTTAAAATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:1,2:196,72:268,3:0.0111:2,2:23.3:1:28:1:0.18196:5.40403:60:6:0.0112:0:1 0/0:329:0:0,0:243,86:329,0:0:2,0:23.6:1:30.8:1:1:0:60:108.667:1:0:0.1 +3 72873748 . CT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.1922;SOR=0;LSEQ=ACTATACAGGATTTCACTGG;RSEQ=TTTACTTTTTAACATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:0,2:43,153:196,2:0.0101:2,0:25.5:1:31:1:1:0:60:4:0.0102:0.0051:1 0/0:253:0:0,0:65,188:253,0:0:2,0:20.6:1:29.5:1:1:0:59.9:62.25:1:0:0.1 +3 72873809 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0014;SOR=7.17156;LSEQ=AGAAATACAGATTTTAATTC;RSEQ=AAGTACATTTCAAGGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:0,3:1,53:54,3:0.0526:1,0:13.7:1:34:0:1:0:60:6:0.0536:0:1 0/1:52:15:0,15:0,37:37,15:0.2885:1,1:21.9:1:32.1:1:1:0:60:30:0.2885:0:1 +3 72881716 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50598;SOR=Inf;LSEQ=TTTTATACAAAATGCCAAAG;RSEQ=ACAGGAAGAACCTAACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:4,83:87,0:0:1,0:24.5:1:32.6:1:1:0:59.9:174:1:0:0 0/1:113:2:1,1:9,102:111,2:0.0177:2,2:27.5:1:28.5:1:0.16988:10.80:60:4:0.018:0:1 +3 72890370 . A AT 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.1345;SOR=Inf;LSEQ=CCTGAATGTGTTAAATTTTA;RSEQ=TTTTTTTTAAGTATTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:57,216:273,0:0:2,0:23.5:1:30.6:1:1:0:57.6:33.125:1:0:0.2 0/1:347:4:1,3:96,247:343,4:0.0115:2,2:22.5:1:29.8:1:1:1.16549:55.8:8:0.0117:0.0029:0 +3 72890421 . GA G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49939;SOR=0;LSEQ=TAGGGGAAGAAAAAGTATAG;RSEQ=AAAAATGCCCACAAAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:0,2:0,97:97,2:0.0202:1,0:26.5:1:30:1:1:0:60:4:0.0206:0:2 0/0:87:0:0,0:7,80:87,0:0:2,0:24.1:1:30:1:1:0:60:42.5:1:0:0.1 +3 72890430 . C T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20292;SOR=Inf;LSEQ=AAAAAGTATAGGAAAAAATG;RSEQ=CCACAAAGATGTACCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:0,86:86,0:0:1,0:23.9:1:31:1:1:0:60:27.667:1:0:0.3 0/1:71:2:1,1:1,68:69,2:0.0282:1,2:18.5:1:24.5:1:0.05594:48.43:60:4:0.0282:0:1 +3 72891500 . G A 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAGCAGTTAACATGTTCA;RSEQ=CCCCTCAAAATGCTGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:261,305:566,0:0:2,0:27.4:1:32.4:1:1:0:59.1:69.75:1:0:0.1 0/1:856:43:21,22:383,429:812,43:0.0502:2,2:24.9:1:29.2:1:0.87619:1.07:56.4:86:0.0509:0:1.2 +3 72897298 . G T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.65404;SOR=2.49123;LSEQ=CCTTGCATTCTCCCTCTAAA;RSEQ=CAGCTATCTAACGAATGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:0,1:178,49:227,1:0.0044:2,0:1:0:28:0:0.2193:0:60:2:0.0045:0:2 0/1:368:4:1,3:272,92:364,4:0.0109:2,2:11.5:1:26:1:0.0545:8.80535:60:8:0.011:0:1 +3 72897516 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14349;SOR=Inf;LSEQ=GCACCGGACGCAAGGGCCGG;RSEQ=GCCGCTCGCTCTCACTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:50,150:200,0:0:2,0:25.8:1:30.2:1:1:0:60:99:1:0:0.1 0/1:278:4:2,2:77,196:273,4:0.0144:2,2:10.8:1:29:1:0.32183:2.54:60:8:0.0144:0:2 +3 73129574 . G A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00559;SOR=Inf;LSEQ=TGGGAGGGCCAGCTGTCTGC;RSEQ=CTTTCTGTCAAGACCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:18,0:0:2,0:29.4:1:30.1:1:1:0:60:36:1:0:0.2 0/1:23:8:3,5:5,10:15,8:0.3478:2,2:26.3:1:28.5:1:1:1.19:60:16:0.3478:0:1 +3 74788556 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.15584;SOR=Inf;LSEQ=TTGCTATCCACTGACCTCCA;RSEQ=ACTGCTTCATGGCTATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:13,0:0:2,0:23.5:1:32.6:1:1:0:58.2:26:1:0:0 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:20:1:28:1:1:1.29:60:4:0.2222:0:1 +3 75010988 . T A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=2.29617;LSEQ=GGATGGTAGCAGGATAGAAT;RSEQ=TTTATCTTTGCAATTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:178:85,93:75,73:148,178:0.546:2,2:25.8:1:29.4:1:0.65651:1.12369:60:43.5:0.5421:0:1.1 1/0:448:329:173,156:62,57:119,329:0.7344:2,2:25.5:1:28.5:1:1:1.02:60:108.667:0.7359:0:1.2 +3 75011086 . G T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.97992;LSEQ=ATAGTAATGCAAAATTATGT;RSEQ=ATTGTTTTAAAATGATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:1:0,1:25,106:131,1:0.0076:2,0:13:0:11:0:1:0:60:0:0:0:2 0/1:134:2:1,1:20,112:132,2:0.0149:2,2:9:0:31:1:0.28987:5.49:60:4:0.0155:0:1 +3 75139687 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35096;LSEQ=GTGCTTTGAAGCAGTGGGAA;RSEQ=GCCAAATCTGAAACCATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:129:75,54:84,69:153,129:0.4574:2,2:29.3:1:30.8:1:0.63041:1.14:60:42:0.4532:0:1.1 0/1:307:70:36,34:123,111:234,70:0.228:2,2:29:1:30.5:1:0.89216:1.04641:60:140:0.2303:0:1.1 +3 75139814 . G C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07521;SOR=0.46283;LSEQ=ATCAACCTCAATGAGAATGT;RSEQ=ACAAATCAATGCTGTAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:33:3,30:2,32:34,33:0.4853:2,2:22.7:1:32.8:1:0.67284:1.59:58.9:66:0.4853:0:1.1 0/1:43:13:1,12:1,29:30,13:0.3023:1,1:28.9:1:31:1:0.51827:2.36:60:26:0.3023:0:1 +3 75164778 . C T 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.251;SOR=Inf;LSEQ=TGGAATAGGGCATTAGTTCT;RSEQ=ATTATTCATTCAATTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:67,36:103,0:0:2,0:26.1:1:32.4:1:1:0:60:206:1:0:0.2 0/1:120:3:1,2:79,38:117,3:0.025:2,2:8.3:1:20:1:0.25737:4.10424:60:2:0.0168:0:1 +3 75164797 . G A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58805;SOR=0.40132;LSEQ=TCATTATTCATTCAATTTTT;RSEQ=CTCAAAGACATTTAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:79,41:120,2:0.0164:2,2:34.5:1:31:1:1:1.91583:60:4:0.0165:0:1 0/0:151:1:1,0:99,50:149,1:0.0066:2,0:1:0:23:0:1:0:60:2:0.0066:0:1 +3 75164800 . C CA 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=3e-05;SOR=0.34613;LSEQ=TTATTCATTCAATTTTTGCT;RSEQ=AAAGACATTTAAAATCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:60:39,21:53,26:79,60:0.4317:2,2:24.4:1:30.6:1:0.85716:1.09689:60:29:0.4265:0.0863:0.6 0/1:159:33:20,13:81,45:126,33:0.2075:2,2:27.7:1:29.9:1:0.6901:1.16882:60:66:0.2089:0.0314:0.6 +3 75164849 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19391;SOR=0;LSEQ=AGCAATATCTATGTCCTGAG;RSEQ=ATTCTGAAAGTTATACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:107,89:196,2:0.0101:2,2:11:1:29:1:1:1.20112:60:4:0.0103:0:1 0/0:251:0:0,0:134,116:250,0:0:2,0:25:1:30.3:1:1:0:60:249:0.996:0:0.3 +3 75164859 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32982;LSEQ=ATGTCCTGAGGATTCTGAAA;RSEQ=TTATACACCTCAGCTCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:80:40,40:60,50:110,80:0.4211:2,2:29:1:30.7:1:0.55888:1.19884:59.9:79:0.427:0:1.1 0/1:259:50:26,24:103,106:209,50:0.1931:2,2:26.6:1:29.9:1:0.755:1.11:60:100:0.1953:0:1 +3 75164938 . A T 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATGCCCCATAATTTGAATA;RSEQ=ATAATCAAGAAAATGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:44:8,36:16,35:51,44:0.4632:2,2:24:1:28.5:1:0.16173:2.04174:60:43:0.4574:0:1.1 0/0:137:0:0,0:41,96:137,0:0:2,0:22.1:1:29.7:1:1:0:60:274:1:0:0.1 +3 75164989 . G GA 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50366;SOR=Inf;LSEQ=AAATTTCAAAAAATTAAAAG;RSEQ=AAAAAATGCAGTCACATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:1,36:37,0:0:1,0:25.5:1:32.2:1:1:0:60:74:0.9737:0:0.3 0/1:50:2:0,2:6,42:48,2:0.04:2,0:27.5:1:32.5:1:1:0:60:4:0.04:0:0 +3 76716532 . T G 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.76283;LSEQ=GTTATTGTAAAAGCAGCTAT;RSEQ=GAAAGCTAAATGCAAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:29.4:1:31.4:1:1:0:60:10:0.5:0:1 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:14:1:31.3:1:1:0:60:6:0.4286:0:1 +3 76716724 . G GA 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.1585;SOR=1.31276;LSEQ=GCAGGTTAATGATCAAATCA;RSEQ=AAAAAACAACATTAATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:87:52,35:72,44:116,87:0.4265:2,2:26.4:1:30.9:1:0.77234:1.10087:60:174:0.4286:0.0686:0.6 0/1:255:126:79,47:78,49:127,126:0.4941:2,2:25.5:1:29.2:1:0.89708:1.06:60:125:0.4941:0.0784:0.6 +3 76716794 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01704;SOR=1.43346;LSEQ=GTATTTTAGAGTAATCAGGC;RSEQ=TACTGTTTTTGGTAAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:156:78,78:83,87:170,156:0.4785:2,2:27:1:30.8:1:0.91174:1.05:60:312:0.4785:0:1.1 1/0:403:229:106,123:82,92:174,229:0.5682:2,2:23.8:1:29.6:1:0.91978:1.03418:60:75.333:0.5693:0:1.1 +3 76716827 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24945;SOR=Inf;LSEQ=TAAATATAATTGTTCTTATT;RSEQ=TTTAGGGCTATTTTTAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:103,153:256,0:0:2,0:25.5:1:32.1:1:1:0:59.9:127:1:0:0.5 0/1:274:3:1,2:108,162:270,3:0.0109:2,2:15.3:1:26.7:1:1:1.33198:60:6:0.0109:0:1.3 +3 76716837 . ATTTTTAGCAGTGATCAGACTTTTTGGCTCA CTAAACAATTGTTAGGGCTCTAAACATTG 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTCTTATTGTTTAGGGCT;RSEQ=TAAGTGCTCTAAACAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:87,141:228,0:0:2,0:25.3:1:29.8:1:1:0:59.9:113:1:0:0.4 0/1:244:51:18,33:78,114:192,51:0.209:2,2:25.8:1:29.4:1:0.52301:1.25323:59.4:102:0.2099:0.123:1.1 +3 76716955 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.08905;LSEQ=TATCTAATAAAAGATAGAAA;RSEQ=TGTTCAATATTTCATAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:0,11:0,12:12,11:0.4783:0,0:21.2:1:33.3:1:1:0:60:22:0.4783:0:1 1/0:28:14:0,14:0,14:14,14:0.5:1,1:24.9:1:32.1:1:1:0:60:28:0.5:0:1.4 +3 76716986 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10446;SOR=Inf;LSEQ=TTCATAAGATTACATAAAAA;RSEQ=GACTGTAGTTATAACAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:10,0:0:0,0:23.6:1:30.5:1:1:0:60:20:1:0:0.5 0/1:13:4:0,4:0,9:9,4:0.3077:0,0:22.8:1:29.8:1:1:0:60:8:0.3333:0:1.5 +3 76717014 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=GTTATAACAAATATTCTACA;RSEQ=CATGATTTAATAAAAATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:26:1:32.6:1:1:0:58.3:16:1:0:0.3 0/1:5:2:0,2:0,3:3,2:0.4:0,0:35.5:1:31:1:1:0:60:4:0.4:0:2 +3 76717350 . T C 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTCGACCTCCTAGACTC;RSEQ=GGTGATCCTCCCACCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:30.5:1:1:0:60:4:1:0:1.5 +3 78330200 . G A 126 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AGAAGCAGCAAGGTTCAGAG;RSEQ=CTCCCATCAGAAAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:8,13:0,0:0,21:1:0,2:22.4:1:28.8:1:1:0:60:20:1:0:1.2 0/1:24:10:3,7:6,8:14,10:0.4167:2,2:33:1:29.3:1:0.67846:1.70978:60:20:0.4167:0:1.3 +3 78330515 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TAGCATCCCAACTCCAGAAC;RSEQ=GGCAGAGCCTTACAGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:24:0:24:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:28:1:1:0:60:4:1:0:1 +3 78331073 . G T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20434;SOR=0;LSEQ=AAACACACCCTCTCCAACAA;RSEQ=GGACAAAGTGCTTAATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:17,31:48,2:0.04:2,2:20:0:33.5:1:1:1.80:60:4:0.04:0:1.5 0/0:60:0:0,0:27,33:60,0:0:2,0:21.1:1:30.5:1:1:0:60:59:1:0:0.3 +3 78331074 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24615;SOR=Inf;LSEQ=AACACACCCTCTCCAACAAG;RSEQ=GACAAAGTGCTTAATTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:17,32:49,0:0:2,0:23.9:1:30.4:1:1:0:60:15.333:1:0:0.2 0/1:56:3:3,0:24,29:53,3:0.0536:2,0:15.3:1:28:1:0.10552:0:60:6:0.0556:0:1 +3 78331221 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGGTCAGAGGTCCCAGAA;RSEQ=AAGGAGCAGGCACCCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:5,0:0:2,0:28.4:1:32.2:1:1:0:41.8:10:1:0:0 0/1:12:2:0,2:6,4:10,2:0.1667:2,0:23:1:29.5:1:0.45455:0:43:4:0.1818:0:1 +3 78331246 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.51087;SOR=Inf;LSEQ=AGCAGGCACCCATCTTTGCT;RSEQ=CTCTCCAGGCTCTTTGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:9,0:0:2,0:21.4:1:31.8:1:1:0:53.6:8:1:0:0 0/1:15:2:1,1:7,6:13,2:0.1333:2,2:18:1:30:1:1:1.1547:60:4:0.1333:0:1 +3 78331555 . C A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1009;SOR=Inf;LSEQ=GCAGAGTGCCTCTTCTCCTC;RSEQ=AAATGATTGCAATGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:5,0:0:2,0:31:1:32.4:1:1:0:60:10:1:0:0.2 1/0:10:5:2,3:1,4:5,5:0.5:2,2:17.6:1:29.4:1:1:2.41:46.8:10:0.5:0:1.2 +3 78521896 . A C 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTAGAAGCAGCTCATGTG;RSEQ=CTCACTTTTACGGAGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:25.3:1:32.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 78616968 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGCAAAGAACCCTATTAAG;RSEQ=TGGTTTAGTGAGAAACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:7,16:23,0:0:2,0:29.3:1:33.6:1:1:0:59.8:46:1:0:1.3 0/1:49:2:1,1:18,29:47,2:0.0408:2,2:29.5:1:28.5:1:1:1.59:60:4:0.0417:0:2 +3 78616977 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTATTAAGCTGGTTTAG;RSEQ=GAGAAACCCCCGTCGTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:7,15:0,0:0,22:1:0,2:24.8:1:28.9:1:1:0:59.8:10:1:0:1.4 1/1:44:44:17,27:0,0:0,44:1:0,2:21.6:1:30.2:1:1:0:59.4:88:1:0:1.2 +3 87347911 . G C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15696;SOR=0.32521;LSEQ=TTTCAATTTTCAAGAAAAAT;RSEQ=TAACAACTATTTATTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:5,8:0.6154:0,0:19.5:1:32.5:1:1:0:60:16:0.6154:0:1 0/1:18:6:6,0:12,0:12,6:0.3333:0,0:24.2:1:29.3:1:1:0:60:5:0.2941:0:1 +3 87347973 . G T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08098;SOR=0;LSEQ=GAAACCATCAATACATGAAC;RSEQ=ATTATAATATTTTTAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:3,0:41,2:43,3:0.0652:1,0:19:1:33:1:1:0:60:6:0.0652:0:1.3 0/0:59:0:0,0:56,3:59,0:0:2,0:25.1:1:29.8:1:1:0:60:118:1:0:0.2 +3 87347995 . AG A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02125;SOR=0.48399;LSEQ=TTATAATATTTTTAAAACAA;RSEQ=TTATGCTGTACTGCAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:41:35,6:30,5:35,41:0.5395:2,2:22.8:1:31.8:1:1:1.0282:60:82:0.5395:0.0789:0.7 0/1:97:35:27,8:52,10:62,35:0.3608:2,2:21.8:1:29.7:1:0.42711:1.5337:59.9:70:0.3608:0.1031:0.7 +3 87348021 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.58361;SOR=0.3884;LSEQ=GCTGTACTGCAAAGTATTTT;RSEQ=AAAATTTGCAGTACCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:92,28:120,2:0.0164:2,2:33.5:1:30.5:1:0.4204:3.24605:60:4:0.0164:0:1.5 0/0:156:1:0,1:110,45:155,1:0.0064:2,0:1:0:22:0:0.29487:0:60:2:0.0065:0:1 +3 87348032 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17223;SOR=0;LSEQ=AAGTATTTTCAAAATTTGCA;RSEQ=TACCAAAGATCACATTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:98,36:134,2:0.0147:2,2:29:1:32:1:0.47157:2.69885:60:4:0.0149:0:2 0/0:191:0:0,0:117,73:190,0:0:2,0:23.7:1:31.2:1:1:0:60:380:0.9948:0:0.4 +3 87348062 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14211;SOR=0;LSEQ=TCACATTATATATGTTTGCT;RSEQ=GCATAAGTTTTGCTGAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:105,72:177,2:0.0112:2,2:43.5:1:32:1:1:1.45516:60:4:0.0112:0:2.5 0/0:295:0:0,0:157,138:295,0:0:2,0:24.7:1:28.4:1:1:0:60:72.75:1:0:0.5 +3 87348066 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04437;LSEQ=ATTATATATGTTTGCTAGCA;RSEQ=AAGTTTTGCTGAATATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:187:172:97,75:9,6:15,172:0.9198:2,2:25.5:1:31.9:1:1:1.15888:60:344:0.9198:0:1.1 0/1:298:100:54,46:105,93:198,100:0.3356:2,2:26.9:1:30.9:1:0.90258:1.04:60:24:0.3288:0:1.1 +3 87348159 . A C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19258;SOR=0;LSEQ=ATAAACTTGTATCTCTACGT;RSEQ=CAATTGAAATAAGATATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:14,76:90,2:0.0217:2,2:25:1:30.5:1:0.301:5.28:60:4:0.022:0:1 0/0:117:0:0,0:30,87:117,0:0:2,0:21.9:1:28.7:1:1:0:60:234:1:0:0.2 +3 87348221 . C T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.76882;SOR=0.7998;LSEQ=ACCAACACCCTAGAACAACA;RSEQ=ACTAGGAAAACTCTTTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:0,8:0,11:11,8:0.4211:0,0:27.1:1:28.9:1:1:0:60:16:0.4444:0:1 0/1:30:11:0,11:1,18:19,11:0.3667:1,0:16.9:1:26.1:1:1:0:60:10:0.3448:0:1 +3 87348307 . A ATTTG 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.00466;SOR=0;LSEQ=GAACGTAGCTATGTATGTTC;RSEQ=TTTGTGTATTGTCTATGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:33.7:1:32:1:1:0:60:14:0.875:0:0.1 0/0:5:0:0,0:0,5:5,0:0:0,0:10.4:1:30.6:1:1:0:60:10:1:0:0.6 +3 87348364 . T G 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGTTGAACAACTGTGTTA;RSEQ=AGATGGGCTGGCCCACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:26:1:30.5:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:42:0:30:0:1:0:60:2:1:0:0 +3 88892593 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1535;SOR=0;LSEQ=GCATTTTCAGTGAAATTTTA;RSEQ=TGACCACGCCAGCTGGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:93,82:175,2:0.0113:2,2:11.5:1:26.5:1:1:1.13334:60:4:0.0114:0:2 0/0:274:0:0,0:148,126:274,0:0:2,0:25.1:1:31:1:1:0:60:44.667:1:0:0.5 +3 88892634 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15626;SOR=0;LSEQ=AATCTTTCTCCAAATGCAAG;RSEQ=TTTCTGCAGCATGACAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:76,98:174,2:0.0113:2,2:36.5:1:29.5:1:1:1.29:60:4:0.0116:0:1 0/0:270:0:0,0:129,141:270,0:0:2,0:25.6:1:30.5:1:1:0:60:32.75:1:0:0.8 +3 88892638 . C A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.34783;LSEQ=TTTCTCCAAATGCAAGGTTT;RSEQ=TGCAGCATGACAAAATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:175:149:68,81:9,17:26,149:0.8514:2,2:25.2:1:29.8:1:0.3925:1.58:59.8:48.667:0.8538:0:1.1 1/0:266:177:83,94:39,50:89,177:0.6654:2,2:24.2:1:28.7:1:0.69615:1.13:60:87.5:0.6629:0:1.1 +3 89156692 . A G 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.01538;SOR=0;LSEQ=ATCCCGCTCTGCTTCAGCGC;RSEQ=CGCTGAAGACGGCACTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:8,1:17,0:17,9:0.3462:1,2:33.3:1:31.3:1:0.34615:0:60:18:0.3462:0:1.3 0/0:15:0:0,0:15,0:15,0:0:1,0:27.2:1:29.8:1:1:0:60:30:1:0:0.1 +3 89156791 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50182;SOR=Inf;LSEQ=AGTGTCAAACTTGACATCAG;RSEQ=CTGCGAGCGGAGCATGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:142,9:151,0:0:2,0:25:1:32.1:1:1:0:60:36.75:1:0:0.1 0/1:179:2:1,1:164,13:177,2:0.0112:2,2:24:1:26:1:0.15071:12.19364:60:4:0.0114:0:1 +3 89156795 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50218;SOR=Inf;LSEQ=TCAAACTTGACATCAGCCTG;RSEQ=GAGCGGAGCATGGTAACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:150,12:162,0:0:2,0:24.5:1:32.2:1:1:0:60:80:1:0:0.1 0/1:192:2:1,1:170,20:190,2:0.0104:2,2:8:1:27.5:1:0.2073:8.31843:60:4:0.0107:0:1 +3 89157126 . C CT 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00595;SOR=0.18256;LSEQ=AGAGTGAAGGAAAGATGTGC;RSEQ=TTTTTTTTTTCCAACTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:19:0,19:0,40:40,19:0.3167:1,1:26.7:1:29.3:1:1:0:58.9:18:0.3103:0.0333:0.6 0/1:39:3:0,3:2,32:34,3:0.0769:2,0:25.3:1:30:1:1:0:60:6:0.0789:0:0.3 +3 89259656 . GT G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50384;SOR=0;LSEQ=TGCTGGCTATGAAGAAAGAG;RSEQ=TTTATGTGCCAAGGTAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:34,126:160,2:0.0123:2,2:47.5:1:32:1:0.38647:3.67:60:4:0.0123:0:0 0/0:132:0:0,0:40,92:132,0:0:2,0:26.4:1:29.1:1:1:0:60:65:1:0:0.1 +3 89259713 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50361;SOR=0;LSEQ=TTTGAGCAATATTTCTCACC;RSEQ=ATGAGTTTATCATAGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:5,49:54,2:0.0357:2,2:37:1:32:0:0.20455:9.04:60:4:0.0357:0:1 0/0:43:0:0,0:10,33:43,0:0:2,0:27.9:1:28.1:1:1:0:60:42:1:0:0 +3 89390828 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49982;SOR=Inf;LSEQ=GTTATTTACCTCATTCAGTT;RSEQ=CATTGTAAATTATCTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:125,10:135,0:0:2,0:24.7:1:32.5:1:1:0:60:134:1:0:0 0/1:151:2:1,1:131,18:149,2:0.0132:2,2:28.5:1:29.5:1:0.23656:7.1104:60:4:0.0134:0:1 +3 89390849 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25126;SOR=Inf;LSEQ=CATTGTAAATTATCTATTTC;RSEQ=CTTGTAGTAGAAAACAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:167,43:210,0:0:2,0:23.5:1:30.8:1:1:0:60:41:1:0:0 0/1:238:3:1,2:182,53:235,3:0.0126:2,2:11.3:1:25.7:1:0.13431:6.79581:60:6:0.0128:0:1.3 +3 89391192 . TC T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.07165;SOR=0;LSEQ=ATGGGGTGTCAGAGCTGAGC;RSEQ=CCCACCAAGACAGTTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:85,200:285,3:0.0104:2,2:16:1:31:1:1:1.18:60:6:0.0106:0.0035:1.7 0/0:404:0:0,0:138,266:404,0:0:2,0:24:1:30:1:1:0:59.9:66.333:1:0:0.1 +3 89391236 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27481;SOR=Inf;LSEQ=GTCAGCATCACAACTAATCA;RSEQ=GCTGGTGAGTACATACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:36,130:166,0:0:2,0:26.1:1:31.9:1:1:0:60:82:1:0:0.1 0/1:243:3:2,1:63,177:240,3:0.0123:2,2:22.3:1:27.7:1:0.17524:5.57:60:6:0.0124:0:1.3 +3 89444754 . C T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=AGCAGCAGAGAATCTCAGCA;RSEQ=ATTTTCCCTAGGCCTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:27.3:1:32.8:1:1:0:60:8:0.5:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:29:1:33:0:1:0:60:4:1:0:0 +3 89444882 . T C 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01894;SOR=Inf;LSEQ=CCAAAAAACTGGAACAATGA;RSEQ=AGACTCCATTTGCATGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:127,1:128,0:0:1,0:24.1:1:32.2:1:1:0:60:256:1:0:0.1 0/1:77:4:4,0:70,2:72,4:0.0519:1,0:13.8:1:32.5:1:1:0:60:8:0.0533:0:1.3 +3 89444909 . C T 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00665;SOR=Inf;LSEQ=CATTTGCATGTTCCCTTCTC;RSEQ=CTCTGTTCTTATTCGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:187,33:220,0:0:2,0:24.3:1:31.4:1:1:0:59.9:43:1:0:0 0/1:171:6:5,1:139,25:164,6:0.0351:2,2:16:1:28.8:1:1:1.11131:60:5:0.0298:0:2.8 +3 89444923 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25416;SOR=0;LSEQ=CTTCTCCCTCTGTTCTTATT;RSEQ=GCCACCCTTTCTAACCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:1,2:213,60:273,3:0.0109:2,2:10.3:1:28:1:0.12766:7.03359:60:6:0.0109:0:1 0/0:232:0:0,0:188,44:232,0:0:2,0:23.1:1:30.4:1:1:0:60:464:1:0:0.2 +3 89444939 . C A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=TATTCGCCACCCTTTCTAAC;RSEQ=CATTAATTTGCTTCCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:259,89:348,0:0:2,0:25.3:1:31.1:1:1:0:59.9:68.6:1:0:0.1 0/1:342:13:11,2:242,87:329,13:0.038:2,2:22.8:1:29.2:1:0.52675:1.97:60:12:0.0356:0:2.5 +3 89444953 . C G 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTAACCCATTAATTTGCTT;RSEQ=CTTCCACCTTCCCCTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:288,133:421,0:0:2,0:25:1:31.5:1:1:0:59.9:69.167:0.9952:0:0.1 0/1:429:18:13,5:286,123:409,18:0.042:2,2:23.1:1:31.2:1:1:1.12:60:36:0.0422:0:1.8 +3 89445155 . C T 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=TGGGCTGTGTAGGCAAGAAG;RSEQ=TGTTTCCTCATGAGCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:60,195:255,0:0:2,0:24.4:1:33:1:1:0:60:84:1:0:0.1 0/1:305:14:5,9:96,194:290,14:0.0459:2,2:26.7:1:29.3:1:1:1.12:60:28:0.0461:0:1.1 +3 89448277 . TA T 49 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.11455;SOR=5.80153;LSEQ=TGACAAAGCAAGACTTTGTC;RSEQ=AAAAAAAAAAAAATGCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:11,1:12,3:0.1875:2,0:27.7:1:32.1:1:1:0:58.7:6:0.1875:0.0625:0 1/0:5:3:3,0:2,0:2,3:0.6:0,0:5.7:1:31:1:1:0:60:6:0.6:0.4:0.3 +3 89448404 . T C 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00207;SOR=Inf;LSEQ=CAGGTTTGAGTGGTTCACTG;RSEQ=TTATCATTTTATAGCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:135,7:142,0:0:1,0:23.8:1:30.5:1:1:0:59.9:141:1:0:0.1 0/1:163:10:7,3:128,25:153,10:0.0613:2,2:21.3:1:29.7:1:0.37801:2.18129:60:9:0.0556:0:1.5 +3 89448446 . A AT 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.3807;SOR=0.65717;LSEQ=AAGATTTGATTTTAACATGA;RSEQ=TTTTTTTTTCTGACCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:12:10,2:236,81:317,12:0.0365:2,2:24.1:1:32:1:0.73714:1.71:60:24:0.0372:0.0061:0.2 0/1:371:9:7,2:242,119:361,9:0.0243:2,2:23.6:1:30:1:0.72369:1.72:60:18:0.0247:0.0027:0.4 +3 89448887 . TT ATTTG 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AATGCTTCTGTTTTTTTTTT;RSEQ=AGCCATAAATTGCTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:18:1:30.9:1:1:0:60:4:0.3333:0.1667:1 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:31:0:1:0:60:2:1:0:0 +3 89456534 . T C 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTGGGAGGTGAGTTCACAG;RSEQ=CTGTTTCACTATTCACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:724:0:0,0:273,450:723,0:0:2,0:26.4:1:30:1:1:0:60:71.3:0.9986:0:0.5 0/1:879:59:23,36:358,461:819,59:0.0671:2,2:26.4:1:30.5:1:0.49994:1.21524:59.5:58:0.0671:0:1 +3 89456555 . T A 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.52382;LSEQ=CTGTTTCACTATTCACTTTC;RSEQ=TTGTTGCTTTGTTTGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:559:315:105,210:82,162:244,315:0.5635:2,2:25.2:1:30.9:1:1:1.01233:60:156.5:0.566:0:1.1 0/1:667:269:99,170:142,256:398,269:0.4033:2,2:24.8:1:29.3:1:0.80543:1.05:60:43.833:0.3997:0:1.2 +3 89462238 . ATTGT A 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.00265;SOR=Inf;LSEQ=GCCATAAAATTTGATCTATA;RSEQ=TTGTACAAATCTAGCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:123,10:133,0:0:2,0:23.4:1:31.4:1:1:0:60:65.5:1:0:0 0/1:165:10:10,0:137,18:155,10:0.0606:2,0:29:1:31.4:1:0.60317:0:60:20:0.0606:0:0 +3 89462245 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.50209;SOR=Inf;LSEQ=AATTTGATCTATAATTGTTT;RSEQ=TACAAATCTAGCTACAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:133,18:151,0:0:2,0:23.4:1:32.4:1:1:0:60:36.75:1:0:0 0/1:179:2:1,1:152,24:176,2:0.0112:2,2:25:1:28.5:1:0.26185:6.22576:60:4:0.0112:0:1 +3 89462266 . C T 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00266;SOR=Inf;LSEQ=TACAAATCTAGCTACAATTG;RSEQ=GCCTTTCTTTCTTTCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:180,54:234,0:0:2,0:23.1:1:31.5:1:1:0:60:57.5:1:0:0.1 0/1:286:10:6,4:194,82:276,10:0.035:2,2:22.7:1:27.9:1:0.49439:1.57453:60:20:0.0353:0:1.1 +3 89462464 . G A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=TAGTACTGTATGTGAATCAC;RSEQ=ATTGCTCAGTCTCTGAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:33,157:190,0:0:2,0:23.5:1:31.6:1:1:0:59.9:94:1:0:0.1 0/1:198:13:3,10:41,144:185,13:0.0657:2,2:28.1:1:27.7:1:1:1.05:60:12:0.0615:0:1 +3 89462469 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=Inf;LSEQ=CTGTATGTGAATCACGATTG;RSEQ=TCAGTCTCTGAAACCTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:28,156:184,0:0:2,0:22.6:1:33.1:1:1:0:59.9:183:0.9946:0:0.1 0/1:186:2:1,1:36,148:184,2:0.0108:2,2:9:1:28.5:1:0.35914:4.07:60:4:0.0108:0:1 +3 89468268 . A G 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2362;SOR=Inf;LSEQ=GGCACAAATATTTTAAATGG;RSEQ=AATTTTGAAATAAAACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:45,1:46,0:0:1,0:20.3:1:30.3:1:1:0:60:45:1:0:0.2 0/1:44:2:1,1:39,3:42,2:0.0455:2,2:7:1:29.5:1:0.17548:11.40199:60:4:0.0455:0:1 +3 89468314 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21129;SOR=Inf;LSEQ=CTACTGATGAATTTTTATTA;RSEQ=AGAATTCCTTACATTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:115,29:144,0:0:2,0:25.8:1:30.5:1:1:0:60:47:1:0:0.1 0/1:123:2:1,1:90,31:121,2:0.0163:2,2:39.5:1:32.5:1:0.45422:2.87333:60:4:0.0164:0:1 +3 89468653 . C A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09029;SOR=Inf;LSEQ=TCATAAGTATCTCAGTTTTA;RSEQ=CAAAAAGAAAAGTTTAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,42:42,0:0:1,0:25:1:30.5:1:1:0:60:20:1:0:0.1 0/1:36:3:0,3:0,33:33,3:0.0833:1,0:14.7:1:30.7:1:1:0:60:6:0.0833:0:1.3 +3 89478212 . C T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1242;SOR=Inf;LSEQ=TATATGTTCATTGTATAATA;RSEQ=TTGAACTGTACTGATTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:227,96:323,0:0:2,0:23.4:1:32.4:1:1:0:59.9:106.667:1:0:0.1 0/1:337:4:1,3:235,98:333,4:0.0119:2,2:11:1:26.8:1:0.08224:7.14694:60:8:0.012:0:1.3 +3 89480226 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49966;SOR=Inf;LSEQ=GTTACAAAATTCAATATGTG;RSEQ=GATTTTAACCAATAAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:133,23:156,0:0:2,0:23.1:1:30.4:1:1:0:60:77:1:0:0.2 0/1:172:2:1,1:141,29:170,2:0.0116:2,2:17:1:32:0:0.31926:4.79733:60:4:0.0117:0:1 +3 89480265 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00282;SOR=1.72503;LSEQ=TATATCTTTAAGAAATAGGA;RSEQ=CGTATCTTAATTGTACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:54:37,17:206,80:286,54:0.1584:2,2:19.9:1:32.9:1:0.62354:1.18249:60:108:0.1593:0:1.1 0/1:465:114:75,39:226,124:350,114:0.2452:2,2:23.6:1:31:1:0.91011:1.06:59.9:37:0.2424:0:1.1 +3 89480630 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50397;SOR=0;LSEQ=TTATGCTTTCCACAATAGAA;RSEQ=ACATATCTTAAAATTAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:0,47:47,2:0.0408:1,2:27.5:1:31.5:1:0.04082:0:60:4:0.0408:0:1 0/0:37:0:0,0:0,37:37,0:0:1,0:19.5:1:29.8:1:1:0:60:11.333:1:0:0.2 +3 89498301 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50014;SOR=0;LSEQ=ACTATGAGAAATTCTGTCCG;RSEQ=TTTCAGATTATGTTATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:116,10:126,2:0.0156:2,2:13:1:29:1:0.16511:11.10804:60:4:0.0163:0:1 0/0:112:0:0,0:96,16:112,0:0:2,0:35:0:14:0:1:0:60:0:0:0:1 +3 89498305 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22095;SOR=Inf;LSEQ=TGAGAAATTCTGTCCGGTTT;RSEQ=AGATTATGTTATGTATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:131,15:146,0:0:2,0:22.2:1:31.6:1:1:0:59.9:17.25:1:0:0.2 0/1:130:2:1,1:106,22:128,2:0.0154:2,2:13.5:1:28:0:0.32367:4.7345:60:4:0.0156:0:1 +3 89498619 . A G 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.00604;SOR=0;LSEQ=AACTGGGTGGCTCCTGGTTT;RSEQ=TAACACTGAAATAAAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:96:96:2,94:0,0:0,96:1:0,1:23.1:1:32.3:1:1:0:60:47:1:0:1.1 1/1:74:68:2,66:0,6:6,68:0.9189:0,1:25.9:1:31.9:1:1:0:60:67:0.9178:0:1.1 +3 89499250 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25034;SOR=Inf;LSEQ=AAAATAAGCATATTTGTGAG;RSEQ=CCCGCCCATGAAAACGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:169,40:209,0:0:2,0:22.8:1:31.8:1:1:0:60:68.667:1:0:0.1 0/1:232:3:2,1:167,62:229,3:0.0129:2,2:31.3:1:31:1:1:1.34494:60:6:0.0132:0:1 +3 89499253 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25049;SOR=Inf;LSEQ=ATAAGCATATTTGTGAGCCC;RSEQ=GCCCATGAAAACGTAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:177,49:226,0:0:2,0:22.5:1:30.7:1:1:0:60:55.5:1:0:0.1 0/1:251:3:2,1:177,71:248,3:0.012:2,2:10:1:30.3:1:1:1.24538:60:6:0.0121:0:1.3 +3 89521509 . C A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08563;SOR=2.00945;LSEQ=TTCCACAAATGAAAGGAACA;RSEQ=CATATGAAGTCTGGAAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:14:14,0:74,0:74,14:0.1591:1,1:25.9:1:31.3:1:1:0:60:28:0.1609:0:1.1 0/1:76:21:21,0:55,0:55,21:0.2763:1,1:21.2:1:30:1:1:0:60:42:0.2763:0:1.2 +3 89521598 . G GT 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.70583;SOR=0.59198;LSEQ=CTGATCTGTCTCCCTTTGGT;RSEQ=TTTTTTTTCTTGCAGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:4:3,1:250,130:380,4:0.0104:2,2:20.8:1:31.3:1:1:1.56:53.8:8:0.0105:0:0.3 0/0:486:3:2,1:295,187:482,3:0.0062:2,2:29:1:30:1:1:1.27:60:6:0.0063:0:0.3 +3 89521602 . T TC 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=8.000;MSILEN=1;SSF=0.00268;SOR=1.65874;LSEQ=TCTGTCTCCCTTTGGTGTTT;RSEQ=TTTTCTTGCAGGCCATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:69:43,26:222,126:348,69:0.1651:2,2:26:1:32:1:0.8912:1.06517:60:68:0.1635:0.0383:0.3 0/1:510:126:74,52:233,151:384,126:0.2471:2,2:25.1:1:30.2:1:0.75319:1.08413:60:125:0.248:0.0569:0.3 +3 89521664 . G A 138 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=8.28596;LSEQ=TGTGGATATCACTACCTTCC;RSEQ=CACAACAGGTGACTGGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:3:2,1:325,300:625,3:0.0047:2,2:14:1:29:1:1:1.84:60:6:0.0048:0:1 0/1:762:29:16,13:383,347:730,29:0.0381:2,2:24.6:1:28.5:1:0.85077:1.11:60:58:0.0392:0:1.6 +3 89521693 . T C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.17924;LSEQ=GTGACTGGCTTAATGGTGTC;RSEQ=GGACAGCACACTGCAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:665:80:39,41:277,307:584,80:0.1203:2,2:25.1:1:30.4:1:0.90508:1.05:60:160:0.1216:0:1.9 0/1:752:228:122,106:254,270:524,228:0.3032:2,2:26.6:1:29.5:1:0.23399:1.22:60:44.6:0.3005:0:1.9 +3 89521725 . T C 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.93598;LSEQ=TGCAAGGAAATCTTCACGGG;RSEQ=GTGGAGTACAGTTCTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:65:24,41:193,292:485,65:0.118:2,2:21.4:1:30.3:1:0.68742:1.12886:60:31.5:0.1162:0:2 0/1:677:191:87,104:208,277:485,191:0.2821:2,2:26.1:1:29.9:1:0.54728:1.11:60:37.2:0.2797:0:2 +3 89521774 . G GA 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.58959;SOR=0.65062;LSEQ=CCAAGATTTCCACAGAGTAA;RSEQ=AAAAAAAAATTCATTAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:8:1,7:73,207:280,8:0.0278:2,2:14.5:1:28.5:1:0.68454:2.46236:60:7:0.0248:0.0139:1.4 0/1:329:6:2,4:85,238:323,6:0.0182:2,2:28:1:27.5:1:0.6569:1.40:60:12:0.0186:0.0061:0.7 +3 89521821 . TGGCTTGACATGAAAGATTTG GCTGAATAT 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00275;SOR=2.68302;LSEQ=AGGATTCTTTTGAACTTTCT;RSEQ=TAACATCTTGGCTTGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:17:0,17:3,103:106,17:0.1382:1,1:28.1:1:31.9:1:1:0:60:34:0.1393:0.0244:0.4 0/1:116:35:2,33:6,75:81,35:0.3017:2,2:23.5:1:30.5:1:1:1.31704:59.9:70:0.307:0.1034:0.7 +3 89521900 . G T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4727;SOR=1.8073;LSEQ=GATCTGAGGTACTGACTACC;RSEQ=CCTGGAACTGCTAATCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:0,5:1,21:22,5:0.1852:1,0:33.8:1:31.8:1:1:0:60:10:0.1923:0:2 0/1:17:5:0,5:0,12:12,5:0.2941:0,0:20.8:1:26.2:1:1:0:60:4:0.25:0:3.6 +3 89528461 . A T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06533;SOR=2.57853;LSEQ=GTCCACAGTACTAGAATATA;RSEQ=CATCGTGCAAATTGTGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:8:8,0:50,2:52,8:0.1333:1,0:26.6:1:29.8:1:1:0:60:7:0.1207:0:1.9 0/1:56:16:15,1:40,0:40,16:0.2857:1,1:17:1:30.8:1:0.28571:0:60:32:0.2857:0:2.1 +3 89528477 . G A 113 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12833;SOR=2.11817;LSEQ=TATAACATCGTGCAAATTGT;RSEQ=CTAATTGAAAATCTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:9:8,1:60,2:62,9:0.1268:1,2:27.3:1:28.1:1:0.33829:3.6465:60:18:0.1268:0:1.8 0/1:72:17:16,1:52,3:55,17:0.2361:2,1:28.1:1:27.7:1:1:1.08212:60:16:0.2254:0:2 +3 89528502 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5017;SOR=Inf;LSEQ=TTGAAAATCTCCTGCTTATA;RSEQ=ACTATCGAGGAAACCGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:100,18:118,0:0:2,0:23.2:1:32.3:1:1:0:59.9:236:1:0:0.2 0/1:140:2:1,1:119,19:138,2:0.0143:2,2:11.5:1:26.5:1:0.26619:6.13018:60:4:0.0143:0:1 +3 89905902 . C G 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTATAGGTGAGGTGAAAAT;RSEQ=CAGTGGTTGAGATTCTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:36:0,36:0,63:63,36:0.3636:1,1:29:1:32.1:1:1:0:60:17:0.3542:0:1.2 0/0:86:0:0,0:3,83:86,0:0:1,0:23.2:1:31.3:1:1:0:60:172:1:0:0.2 +3 89905924 . C A 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=23.7807;LSEQ=AGTGGTTGAGATTCTAACAG;RSEQ=GTATGTTTTATGTAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:1:0,1:0,77:77,1:0.0128:1,0:38:0:16:0:1:0:60:0:0:0:6 0/1:50:12:0,12:2,36:38,12:0.24:2,0:19.6:1:30.7:1:1:0:60:24:0.24:0:1 +3 94370332 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22333;SOR=Inf;LSEQ=CAAAAAACAGCTCCCAGATG;RSEQ=ATTGATTTTTTGGAGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:59,42:101,0:0:2,0:24.8:1:32.2:1:1:0:57.9:49.5:1:0:0.2 0/1:91:2:1,1:50,39:89,2:0.022:2,2:32:0:31:1:1:1.27851:60:4:0.0222:0:1.5 +3 94370362 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49772;SOR=Inf;LSEQ=TTGGAGGGCTTTTTGTATCT;RSEQ=TGTCTCCTTCAATTCTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:51,53:104,0:0:2,0:32.3:1:32:1:1:0:60:25:1:0:0.2 0/1:107:2:1,1:54,51:105,2:0.0187:2,2:26:1:27.5:1:1:1.05828:60:4:0.0189:0:1 +3 94370381 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49773;SOR=Inf;LSEQ=TCTGTCTCCTTCAATTCTAC;RSEQ=CTGATTTTACATTAATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:44,56:100,0:0:2,0:24.7:1:30.2:1:1:0:60:32.333:1:0:0.2 0/1:104:2:1,1:49,53:102,2:0.0192:2,2:20:0:32.5:1:1:1.08:60:4:0.0192:0:1 +3 94370412 . GGC CAA 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49895;SOR=Inf;LSEQ=ATTAATCCCCAAGACAATGG;RSEQ=AAATGTCCCCAGGGCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:10,37:47,0:0:2,0:21.7:1:29.9:1:1:0:60:14.667:1:0:0.1 0/1:56:2:1,1:22,32:54,2:0.0357:2,2:22:1:31.7:1:1:1.44:57.5:4:0.0357:0:2 +3 94370422 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50078;SOR=Inf;LSEQ=AAGACAATGGGGCAAATGTC;RSEQ=CCAGGGCATGTCAGAGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:4,35:39,0:0:2,0:20.8:1:30.1:1:1:0:60:8.75:1:0:0.2 0/1:49:2:1,1:17,30:47,2:0.0408:2,2:14:1:31.5:1:1:1.74:57.5:4:0.0426:0:2 +3 94370571 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCAGCCATTCCAGCCCT;RSEQ=TCTGAAAGGGGCCAAAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:12:1:28:1:1:0:60:4:1:0:1 +3 94429115 . A G 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0;LSEQ=ATTCTTAGTGGGGAACAACA;RSEQ=CCACGGAAATTAGAACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:54:33,21:386,267:653,54:0.0764:2,2:27.7:1:33.2:1:0.88559:1.09:60:108:0.0771:0:1.1 0/0:662:0:0,0:376,285:661,0:0:2,0:26.2:1:28.9:1:1:0:60:164.25:1:0:0.5 +3 94429172 . G C 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=1.69621;LSEQ=GCTACAACAAATTAAGTGTG;RSEQ=TGTCAAATATGTCACAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:810:534:240,294:123,153:276,534:0.6593:2,2:26.3:1:32.6:1:0.94066:1.02:60:88:0.66:0:1.1 1/0:681:522:229,293:77,81:158,522:0.7665:2,2:23.1:1:31.2:1:0.3155:1.21593:60:260:0.7681:0:1.1 +3 94942937 . G T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0046;LSEQ=TCTTATTCTTTATTAATCTA;RSEQ=CTAGTGGTCTATCTATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:36:27,9:36,13:49,36:0.4235:2,2:17.9:1:30.1:1:1:1.08:60:35:0.4167:0:1.1 0/1:73:31:21,10:31,11:42,31:0.4247:2,2:20.2:1:29.1:1:0.6089:1.33651:59.3:62:0.4306:0:1.1 +3 94943018 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20074;SOR=Inf;LSEQ=TTTGGAGGGTTTTTGTGTCT;RSEQ=TATCTCCTTCAGTTATACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:121,126:247,0:0:2,0:26.9:1:32.6:1:1:0:59.5:81.333:1:0:0.3 0/1:201:2:1,1:86,113:199,2:0.01:2,2:29:1:27.5:1:1:1.31:60:4:0.0101:0:1 +3 94943031 . T C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19985;SOR=Inf;LSEQ=TGTGTCTCTATCTCCTTCAG;RSEQ=TATACTCTCATCTTGGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:90,109:199,0:0:2,0:25.3:1:29.8:1:1:0:59.8:65.333:0.9899:0:0.3 0/1:163:2:1,1:64,96:160,2:0.0123:2,2:6.5:1:28:0:1:1.50:56:4:0.0123:0:1.5 +3 94943046 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5063;SOR=0;LSEQ=TTCAGTTATACTCTCATCTT;RSEQ=GTTATTTCTTGTCTTTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:64,88:152,2:0.0129:2,2:27.5:1:29.5:1:1:1.37:60:4:0.0133:0:2 0/0:120:0:0,0:49,71:120,0:0:2,0:22.8:1:30.3:1:1:0:60:119:1:0:0.1 +3 94944898 . T G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTTCTTTTCTAAACTG;RSEQ=TTATTCTGGTTAGCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:31:1:1:0:51:4:1:0:1 +3 95307592 . A G 49 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGCTGGCAGTACTGGG;RSEQ=AACTGGGCGCACCCTCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:0,3:1:0,0:20:1:31.3:1:1:0:57.7:6:1:0:1.7 +3 95307625 . G A 44 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCGCAGCTGCTGGCCCC;RSEQ=GTGCTAAGCCCCTCACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:2,1:1,0:1,3:0.75:0,2:27.3:1:28.3:1:1:0:57.7:6:0.75:0:1.7 +3 95454362 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=AAATAAGCATGTTCCAACGT;RSEQ=TGTCATGAATAAAACTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:96,28:124,0:0:2,0:23.3:1:28.9:1:1:0:60:123:1:0:0.1 0/1:133:2:1,1:96,35:131,2:0.015:2,2:32.5:1:28.5:1:0.46958:2.71854:60:4:0.0153:0:1 +3 95454378 . T C 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00219;SOR=Inf;LSEQ=ACGTATGTCATGAATAAAAC;RSEQ=TGCCATTAGCAAAGCAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:103,45:148,0:0:2,0:24.8:1:31.3:1:1:0:60:73:1:0:0.1 0/1:173:10:5,5:115,48:163,10:0.0578:2,2:20.9:1:31.5:1:0.17761:2.38234:60:20:0.0581:0:1.3 +3 95454468 . T G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.9288;SOR=0.97993;LSEQ=ATTCGCCTCCATGATAAAAT;RSEQ=GTAAGGCTGTGACTGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:88:33,55:75,90:165,88:0.3478:2,2:27.1:1:31.7:1:0.23298:1.38708:60:176:0.3492:0:1 0/1:303:104:52,52:84,114:198,104:0.3432:2,2:24.8:1:30:1:0.22496:1.36:60:25:0.3344:0:1.1 +3 95454475 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25384;SOR=Inf;LSEQ=TCCATGATAAAATTGTAAGG;RSEQ=TGTGACTGGTCACAGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:105,142:247,0:0:2,0:26.6:1:32.7:1:1:0:60:60.75:1:0:0.4 0/1:292:3:2,1:128,161:289,3:0.0103:2,2:13.7:1:28.7:1:0.58721:2.51:60:6:0.0104:0:1.7 +3 95454510 . A G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00153;SOR=Inf;LSEQ=GACCCTCAAAAGACCTTTCC;RSEQ=TTCTTTTAATTAGCTGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:57,118:175,0:0:2,0:24.2:1:31.2:1:1:0:60:350:1:0:0.3 0/1:170:9:3,6:51,110:161,9:0.0529:2,2:18.8:1:30.4:1:1:1.08:60:18:0.0536:0:1 +3 96727142 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08772;SOR=Inf;LSEQ=TGTTTTTTGGAGGCTTTGTT;RSEQ=ATTATTTTTCATTCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:13,0:0:2,0:21.3:1:29.8:1:1:0:54.4:12:1:0:0.3 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:11.5:1:27:1:1:1:55.5:4:0.3333:0:1 +3 96727580 . A T 27 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50034;SOR=Inf;LSEQ=TTTTTCATTGATTCTCATCT;RSEQ=TGTGAATTTGTGTAGTTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:34,0:0:2,0:20.4:1:29.6:1:1:0:59.6:68:1:0:0.1 0/1:43:2:1,1:22,19:41,2:0.0465:2,2:7:0:27:1:1:1.15394:60:4:0.0465:0:1 +3 96727778 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=TTTACTTCATGCCTTATTCA;RSEQ=CTGATTCGCCCCCCTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:0,6:6,2:0.25:0,2:32:1:33:0:0.25:0:60:4:0.25:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:28.8:1:30.8:1:1:0:60:8:1:0:0 +3 96728036 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2092;SOR=Inf;LSEQ=AGTCTGGGCTGCCTGGATTC;RSEQ=TCAGAACTACCAAGAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:16,0:0:2,0:25.7:1:33.1:1:1:0:60:32:1:0:0.3 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:30:1:31.5:1:1:1.37:60:4:0.1429:0:1 +3 97251336 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50077;SOR=Inf;LSEQ=TAAGAGAAGCTAGTATCATG;RSEQ=GCCAGTTTGACCATCCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:38,34:72,0:0:2,0:26.9:1:31.2:1:1:0:60:71:1:0:0.1 0/1:86:2:0,2:45,39:84,2:0.0233:2,0:25:1:26:1:0.22435:0:60:4:0.0238:0:1 +3 97439141 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53672;SOR=0;LSEQ=TAAGGTGGACAGCCCCAGAA;RSEQ=CCATCGCCTACAGAAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:55,22:77,2:0.0253:2,2:29:1:27:1:0.50016:2.46719:60:4:0.0256:0:1 0/0:44:0:0,0:29,15:44,0:0:2,0:24.8:1:31.5:1:1:0:60:88:1:0:0.2 +3 97439159 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1111;SOR=Inf;LSEQ=AAGCCATCGCCTACAGAAAA;RSEQ=TCTCCTCAGCAAGCGATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:56,33:89,0:0:2,0:23.2:1:30.9:1:1:0:59.8:178:1:0:0.1 0/1:45:2:1,1:27,16:43,2:0.0444:2,2:25.5:1:30:1:1:1.66708:60:4:0.0444:0:1 +3 97439220 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.54348;SOR=0;LSEQ=GTGGGAGGTCATGTCCTATG;RSEQ=AGAGAGACCTTATTGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:43,60:103,2:0.019:2,2:25:0:31:1:1:1.39:60:4:0.019:0:1.5 0/0:56:0:0,0:25,31:56,0:0:2,0:29.6:1:30.2:1:1:0:60:55:1:0:0.2 +3 97439237 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11422;SOR=Inf;LSEQ=ATGGAGAGAGACCTTATTGG;RSEQ=AAATGTCTAACCAAGATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:35,60:95,0:0:2,0:25.6:1:32.1:1:1:0:59.7:190:1:0:0.1 0/1:49:2:1,1:19,28:47,2:0.0408:2,2:6.5:1:28.5:1:1:1.46:60:4:0.0417:0:1.5 +3 98267289 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.97618;LSEQ=TGCAACCCTGCCCTCTGGGA;RSEQ=GATCAACTGATTTGGGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:112:53,59:130,139:269,112:0.2932:2,2:26.2:1:30.4:1:0.91053:1.04104:60:36.333:0.2899:0:1.1 0/1:355:160:80,80:91,104:195,160:0.4507:2,2:25.9:1:29.1:1:0.59365:1.14:60:159:0.4543:0:1.1 +3 98267536 . C G 52 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAGGGCATTTGAACCTGT;RSEQ=GGGGTGGGGAAGTGGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:32.3:1:33:0:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:33:0:1:0:60:2:1:0:1 +3 100629641 . C A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AACATACTTTACAAATTAAA;RSEQ=ATGCTAAGACTTATCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:27.5:1:29.5:1:1:0:60:4:0.5:0:1 0/0:3:0:0,0:1,2:3,0:0:2,0:4:1:29:1:1:0:60:6:1:0:0 +3 100629803 . TA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.52925;SOR=0;LSEQ=AAAAAAATCTCCTTTTAGGT;RSEQ=AAAGGATCAAGATGTAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:60,6:66,2:0.0294:2,2:29.5:1:31:1:0.19666:9.33504:60:4:0.0303:0:1 0/0:40:0:0,0:28,12:40,0:0:2,0:30.6:1:27.9:1:1:0:60:39:1:0:0.1 +3 100630141 . C T 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00209;SOR=2.66201;LSEQ=ATGTCTGTTTTTTAAAGACA;RSEQ=AACACACGAATGAAGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:18:4,14:57,224:281,18:0.0602:2,2:19.2:1:29.3:1:0.76896:1.12:55.1:36:0.0604:0:1.1 0/1:185:27:7,20:33,125:158,27:0.1459:2,2:16.5:1:27.4:1:0.61362:1.32:56.1:26:0.1453:0:1.3 +3 100630148 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15231;SOR=Inf;LSEQ=TTTTTTAAAGACACAACACA;RSEQ=GAATGAAGAAATTCAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:50,207:257,0:0:2,0:22.4:1:30.5:1:1:0:59.7:256:1:0:0.1 0/1:165:2:1,1:34,128:162,2:0.0121:2,2:12.5:1:30:1:0.38231:3.73:60:4:0.0123:0:1.5 +3 100630177 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13502;SOR=Inf;LSEQ=AAATTCAGAATCTGGATAAA;RSEQ=GGTCCATAATGCTTGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:37,136:173,0:0:2,0:22.7:1:32:1:1:0:59.9:172:1:0:0.1 0/1:101:2:1,1:28,71:99,2:0.0198:2,2:28.5:1:29:1:0.49386:2.51:60:4:0.0198:0:1 +3 100630266 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.16317;SOR=Inf;LSEQ=CCTGAATCTATGCTCATCTC;RSEQ=TTTTTTCCAATTTCTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:87,79:166,0:0:2,0:26:1:32:1:1:0:60:82:1:0:0.2 0/1:113:2:1,1:65,46:111,2:0.0177:2,2:28:0:32:0:1:1.40862:60:4:0.0179:0:1.5 +3 100630340 . CT C 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.28508;SOR=0;LSEQ=TGCTTGTTCATTGTTTTTCA;RSEQ=TTTTTTTGCATATACTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:0,3:126,60:186,3:0.0159:2,0:24:1:35.7:1:0.03586:0:60:6:0.0161:0:0 0/0:120:0:0,0:71,49:120,0:0:2,0:23.6:1:29.8:1:1:0:60:240:1:0:0.2 +3 100630604 . T C 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.69129;LSEQ=GTTTCAGTCGATGAGTAGCG;RSEQ=AGCTTTCTGTTATTATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:373:372:169,203:0,1:1,372:0.9973:0,2:28.4:1:32.4:1:1:0:53:73.4:1:0:1.1 1/1:258:257:138,119:0,0:0,257:0.9961:0,2:28:1:31.3:1:1:0:52.2:84.667:0.9961:0:1.1 +3 100630653 . G T 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.63728;LSEQ=TAGCAGAAAAATAAGTTCTT;RSEQ=GTTTGAAAAATGCTCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:103,64:167,2:0.0118:2,2:15:0:32.5:1:1:1.60462:22:4:0.0118:0:1.5 0/0:133:1:1,0:76,56:132,1:0.0075:2,0:28:0:26:0:1:0:26:2:0.0075:0:2 +3 100630697 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.50707;SOR=0;LSEQ=TTTTGTGAAGCAGCCTCTCT;RSEQ=TAAACGTCATGATCTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:83,96:179,2:0.011:2,2:33.5:1:30.5:1:1:1.16:27.5:4:0.011:0:1 0/0:139:0:0,0:58,81:139,0:0:2,0:23.8:1:31:1:1:0:39.5:138:1:0:0.1 +3 100631031 . G A 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02648;SOR=0.3306;LSEQ=TTACCCTTCGTGCTGCCGTC;RSEQ=GCTCAGGCTTCAGGAGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:33:1,32:1,30:31,33:0.5156:1,1:19.5:1:31.8:1:1:1.06563:60:32:0.5079:0:1.1 0/1:31:8:0,8:1,22:23,8:0.2581:1,0:21.3:1:31.8:1:1:0:60:16:0.2667:0:1.3 +3 104282289 . G A 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.34522;LSEQ=TTCACTTACTGTACATTGAG;RSEQ=TCTTTGGGAAAAGGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:10,4:0.2857:0,0:27.8:1:31.3:1:1:0:57.8:8:0.2857:0:1.8 1/0:2:1:1,0:1,0:1,1:0.5:0,0:7:0:29:0:1:0:60:2:0.5:0:2 +3 104282306 . G A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTCTTTGGGAAAAGGGA;RSEQ=GAGACTTTTCAACCCATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:0,17:1:0,1:26.5:1:30.6:1:1:0:58.2:34:1:0:1.3 1/1:5:5:5,0:0,0:0,5:1:0,0:20:1:31.2:1:1:0:60:10:1:0:1.2 +3 104282451 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21171;SOR=Inf;LSEQ=GCTTAAAGCTCTGCTTACAA;RSEQ=TCCAATGAATTTGGATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:174,45:219,0:0:2,0:24.2:1:32.3:1:1:0:60:72:1:0:0.2 0/1:188:2:1,1:126,60:186,2:0.0106:2,2:28.5:1:28.5:1:0.54483:2.09102:60:4:0.0107:0:1 +3 104282534 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15507;SOR=1.23303;LSEQ=AGGAACTTATTTTATAATTT;RSEQ=GAAGAGTAGACTACCACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:138:74,64:175,183:358,138:0.2782:2,2:26.5:1:30.9:1:0.36795:1.21:60:137:0.2779:0:1.6 0/1:450:145:74,71:161,144:305,145:0.3222:2,2:26.6:1:29.8:1:0.76236:1.07256:60:144:0.3214:0:1.6 +3 104282582 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48234;SOR=1.12894;LSEQ=TTGAGATAACAGGTACTTTT;RSEQ=CTTGGCCTGAAAATTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:115:46,69:118,195:313,115:0.2668:2,2:25.8:1:31.4:1:0.73663:1.10:60:56.5:0.2684:0:1.7 0/1:388:113:45,68:127,148:275,113:0.2912:2,2:26:1:30.2:1:0.26282:1.29583:60:55.5:0.2898:0:1.8 +3 105495432 . G T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATAAGAAATAAACACCTA;RSEQ=ATGCATGCAAATTTTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:29.5:1:29.2:1:1:0:60:12:1:0:1.2 1/1:10:10:2,8:0,0:0,10:1:0,2:28.3:1:27.2:1:1:0:60:20:1:0:1.1 +3 105822703 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGGTTCACTTCAGGCCC;RSEQ=ATTCATGATTCACTCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:5,8:0,0:0,13:1:0,2:32.8:1:31.5:1:1:0:51.4:26:1:0:1.3 1/1:8:8:3,5:0,0:0,8:1:0,2:19:1:28.6:1:1:0:47.5:16:1:0:1.1 +3 105822731 . A G 63 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.36022;SOR=0.29661;LSEQ=ATTCACTCCCTTGCCTGGAT;RSEQ=TGTCACTCAAGGAGGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:4,5:9,4:0.3077:2,2:31:1:31.8:1:1:1.23:50:8:0.3077:0:2 0/1:9:1:0,1:5,3:8,1:0.1111:2,0:28:0:33:0:0.44444:0:60:2:0.1111:0:2 +3 105823159 . G C 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22857;SOR=Inf;LSEQ=AGGATGGGTCAGGGTTGGGC;RSEQ=TGAAGAGGCCCTCTGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:33.2:1:27:1:1:0:60:5:1:0:0.3 0/1:9:3:2,1:4,2:6,3:0.3333:2,2:34:1:29.3:1:1:1:39.3:6:0.3333:0:2.7 +3 105823185 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AGGCCCTCTGGCCGCAGACT;RSEQ=CCACAGCCGGTGTGTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:24.2:1:29.3:1:1:0:60:5:1:0:0.3 0/1:10:2:1,1:5,3:8,2:0.2:2,2:40.5:1:28:1:1:1.58108:29:4:0.2:0:3 +3 105823194 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=GGCCGCAGACTGCCACAGCC;RSEQ=GTGTGTTTGGCTGTGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:18.2:1:30.3:1:1:0:60:12:1:0:0.3 0/1:10:3:2,1:4,3:7,3:0.3:2,2:31.7:1:28:1:1:1.44:39.3:6:0.3:0:2.7 +3 105823884 . A T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGCACTGAGATTTTTTTTA;RSEQ=TATCATATTTTACATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:28:1:1:0:60:4:1:0:1.5 +3 106127714 . C A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.19622;LSEQ=TTACACCTAAAGTAGTGAAA;RSEQ=AAAAATCCCCCATTTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:562:413:194,219:58,73:131,413:0.7349:2,2:24.7:1:30.5:1:0.61605:1.11:59.9:205.5:0.7555:0:1.4 0/1:574:202:100,102:170,190:360,202:0.3519:2,2:23.9:1:29.8:1:0.66008:1.10:60:100:0.3578:0:1.5 +3 106127786 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20624;LSEQ=TCTCTTTGATCATACTCAGG;RSEQ=GAGGTTTGCTGCTTAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:277:216:62,154:19,42:61,216:0.7798:2,2:22.4:1:30.3:1:0.75066:1.12317:60:42.2:0.7757:0:1.6 0/1:254:107:42,65:44,103:147,107:0.4213:2,2:21.6:1:29.9:1:0.14015:1.51:60:214:0.4246:0:1.6 +3 106128036 . A G 54 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTTGTGATAGTGAGTTC;RSEQ=TTCTCAGGAGATCTGACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:23.3:1:27:1:1:0:51.3:3:0.75:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 106128083 . T G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCCTTCCCCCTTCGCTC;RSEQ=GCATTAATTCTCTCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:33:1:34:0:1:0:57:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 106567549 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATAAAACAGGAAGTATGC;RSEQ=ACCATGAAGTGAATGCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:24:0:32.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 106567717 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14228;SOR=Inf;LSEQ=ACACAGCTGGGCCCACCTTA;RSEQ=CACATCCTGTTTGACACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:47,5:52,0:0:2,0:24.4:1:31.8:1:1:0:59.2:51:1:0:0.1 0/1:32:2:2,0:26,4:30,2:0.0625:2,0:27:1:32.5:1:1:0:52.5:4:0.0625:0:1 +3 106567782 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5165;SOR=0;LSEQ=CAAACTGGACTTAGTGTAGT;RSEQ=AATGATGGACTGTCTGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:84,62:146,2:0.0134:2,2:22.5:1:27:1:1:1.352:40.5:4:0.0136:0:1 0/0:101:0:0,0:60,41:101,0:0:2,0:26.4:1:30.4:1:1:0:39.3:49.5:1:0:0.2 +3 106567825 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5075;SOR=0;LSEQ=AAGTGTATCCCTTGTATAAC;RSEQ=GATTGTGTAATGGCTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:65,87:152,2:0.013:2,2:17.5:1:28.5:1:1:1.34:45:4:0.0132:0:1 0/0:117:0:0,0:56,61:117,0:0:2,0:28.7:1:29.6:1:1:0:37.4:57.5:1:0:0.2 +3 106567840 . TG CA 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0072;SOR=Inf;LSEQ=ATAACTGATTGTGTAATGGC;RSEQ=AAATTGGGAAATTAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:54,78:132,0:0:2,0:25.2:1:30.2:1:1:0:38.3:65:1:0:0.1 0/1:106:6:3,3:43,57:100,6:0.0566:2,2:18.2:1:29.2:1:1:1.32:33.7:12:0.0571:0.0189:0.8 +3 106567854 . T C 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21682;SOR=Inf;LSEQ=AATGGCTGAAATTGGGAAAT;RSEQ=AGGGCAGAAGTATGGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:38,67:105,0:0:2,0:23.6:1:28.6:1:1:0:40.8:51.5:1:0:0.1 0/1:92:2:1,1:36,54:90,2:0.0217:2,2:22:0:28:0:1:1.49:45:4:0.0217:0:1 +3 106567870 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22201;SOR=Inf;LSEQ=AAATTAGGGCAGAAGTATGG;RSEQ=GCAGCTGTAAGGATTGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:21,57:78,0:0:2,0:22.9:1:31.1:1:1:0:48.3:38:1:0:0.2 0/1:70:2:1,1:22,46:68,2:0.0286:2,2:33:1:29:1:1:2.07:52:4:0.0286:0:1 +3 106582908 . T C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03125;SOR=2.1422;LSEQ=AACAAGAACAAATGGGGATT;RSEQ=ACAGTCAAAGATCATCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:15:10,5:76,25:101,15:0.1293:2,2:20:1:31.4:1:0.53094:1.51412:60:30:0.1339:0:1.8 0/1:124:30:19,11:65,29:94,30:0.2419:2,2:18:1:29.6:1:0.6544:1.29481:60:60:0.2479:0:1.9 +3 106582948 . T A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07301;SOR=0.69243;LSEQ=CGGGTATGTGGATAAAAAAT;RSEQ=ACAAAGAGAAAACATCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:203:143:86,57:32,27:59,143:0.7044:2,2:26:1:29.3:1:0.53027:1.27:59.5:70.5:0.705:0:1.2 1/0:249:155:89,66:55,39:94,155:0.6225:2,2:26.7:1:28.4:1:0.89527:1.04564:58.9:76.5:0.6194:0:1.3 +3 106583010 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19499;SOR=0;LSEQ=CCAGCTCACCAGGATTCTTT;RSEQ=AGAAGACAAGACAAGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:51,93:144,2:0.0137:2,2:23.5:1:28.5:1:1:1.82:60:4:0.0139:0:2 0/0:184:0:0,0:65,116:181,0:0:2,0:25.7:1:30.3:1:1:0:60:29.167:0.9887:0:0.5 +3 106583012 . GA G 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01035;SOR=Inf;LSEQ=AGCTCACCAGGATTCTTTCA;RSEQ=AGACAAGACAAGGTGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:49,92:141,0:0:2,0:23.7:1:30.3:1:1:0:60:140:1:0:0.5 0/1:180:8:3,5:59,113:172,8:0.0444:2,2:20.8:1:31.3:1:1:1.15:60:16:0.0447:0:0.1 +3 106583022 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.51315;SOR=Inf;LSEQ=GATTCTTTCAGAAGACAAGA;RSEQ=AAGGTGATCAGATATTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:32,83:115,0:0:2,0:24.4:1:31.9:1:1:0:60:114:1:0:0.4 0/1:163:2:1,1:52,109:161,2:0.0123:2,2:12:1:28:1:0.54594:2.09:60:4:0.0126:0:1 +3 106583166 . A G 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=CTCACAGCTGTAATCCCAGC;RSEQ=CTTTGCGGGGCCAAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:36:0:34:0:1:0:60:2:0.3333:0:1 1/0:4:2:1,1:0,2:2,2:0.5:0,2:38.5:1:27.5:1:1:0:51:4:0.6667:0:1.5 +3 106584051 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGCTGCAGGGCTCTGAAT;RSEQ=CTGGCAACTGTGTGAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:27:1:1:0:60:4:1:0:1 +3 106823388 . GA G 35 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGTTAAGGTTATAAAAA;RSEQ=AAAAAAAAAAACAACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:26:1:35:0:1:0:28:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:31:0:1:0:33:2:1:0:4 +3 106823432 . T C 28 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAACTAGAATTTGAATCC;RSEQ=CATAATCTGCAAAATATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31:1:28.5:1:1:0:28:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:30:0:27:0:1:0:33:2:1:0:4 +3 106824274 . G A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06057;LSEQ=GGCACTCCGTGGTACAGCCA;RSEQ=GTCCACAAGTGGTATTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:91:52,39:78,67:145,91:0.3856:2,2:23.9:1:31.2:1:0.68704:1.14:58.2:182:0.3872:0:1.8 0/1:247:9:5,4:127,111:238,9:0.0364:2,2:24:1:29.8:1:1:1.09:59.1:18:0.0366:0:1.7 +3 106824304 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0928;LSEQ=TGGTATTGCCAGACCATTCT;RSEQ=TCCATATTCCCTTGTCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:106:62,44:80,83:163,106:0.3941:2,2:23.1:1:30.9:1:0.13607:1.46:58.4:212:0.3985:0:1.7 0/1:247:14:10,4:121,110:231,14:0.0567:2,2:20.2:1:29:1:0.18195:2.27:59.2:13:0.0535:0:1.6 +3 106824338 . A G 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3247;SOR=3.85398;LSEQ=GTCCAATCTTTGAAAGTTTA;RSEQ=GTTTTCTTAGCTTATAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:1:1,0:195,149:344,1:0.0029:2,0:14:0:15:0:1:0:60:0:0:0:1 0/1:271:3:1,2:156,112:268,3:0.0111:2,2:42:1:25.3:1:0.57444:2.77523:60:2:0.0075:0:1.3 +3 106824379 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04174;SOR=Inf;LSEQ=TGAGTGGTGCTTTCTTTGAC;RSEQ=TTCCTAACATGCACGATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:0:0,0:273,197:470,0:0:2,0:26.7:1:30.7:1:1:0:59.6:35.154:1:0:0.2 0/1:390:4:2,2:222,164:386,4:0.0103:2,2:32.3:1:25:1:1:1.35258:60:3:0.0078:0:1.3 +3 106824513 . G A 129 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=25.41994;LSEQ=GTTTTCTTGGAACACTATCC;RSEQ=CCAAAAGTCATTCACAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:1:1,0:310,308:618,1:0.0016:2,0:1:0:26:0:1:0:46:2:0.0016:0:1 0/1:556:22:8,14:264,270:534,22:0.0396:2,2:32.8:1:29:1:0.27907:1.70949:46.5:44:0.04:0:1.1 +3 106824707 . ATC A 35 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37099;SOR=2.48479;LSEQ=GCAGGATGTTTTGTTTTTAT;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:0,2:15,80:95,2:0.0206:2,0:24.5:1:31:1:1:0:60:4:0.029:0.0103:1.5 0/1:60:3:0,3:11,45:56,3:0.05:2,0:13.7:1:22.5:1:1:0:28.3:2:0.0444:0.0333:4.3 +3 106824772 . T C 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCCAGCCTGGAGTGCAGTGG;RSEQ=GATCTTGGCTCACTGCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:4,21:25,2:0.0741:2,0:8:0:34:0:0.04274:0:50:4:0.0769:0:2 0/0:6:0:0,0:0,6:6,0:0:0,0:24.8:1:28.7:1:1:0:38:12:1:0:2 +3 106824935 . C G 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0119;SOR=Inf;LSEQ=GGCCAGGGTGGTCTCGATCT;RSEQ=CTGACCTTGTGATCTGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:46,1:47,0:0:1,0:21.1:1:32.3:1:1:0:26.7:94:1:0:1.1 0/1:35:5:5,0:29,1:30,5:0.1429:1,0:18.8:1:32.2:1:1:0:37.2:10:0.1515:0:2 +3 106824950 . T C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.71629;LSEQ=GATCTCCTGACCTTGTGATC;RSEQ=GCCCGCCTTGGCCTCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:51:50,1:0,0:0,51:0.9623:0,1:26.9:1:30.7:1:1:0:31.3:24.5:0.98:0:1.3 1/1:45:44:43,1:0,0:0,44:0.9778:0,1:25.8:1:30.7:1:1:0:36.7:43:0.9773:0:1.3 +3 106824988 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=0;LSEQ=AAAGTGCTGGGATTACAAGG;RSEQ=GTGAGCTACCGCGCCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:0,2:112,17:129,2:0.0153:2,0:6:1:29.5:1:0.02008:0:55:4:0.0155:0:2 0/0:122:0:0,0:105,17:122,0:0:2,0:21:1:31:1:1:0:52.3:60:1:0:0.6 +3 106825018 . A AT 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.06151;SOR=0;LSEQ=CGCGCCCGGCCTTTATATCT;RSEQ=TTTTTGGTTTTGTTTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:5:1,4:232,73:305,5:0.0161:2,2:12.8:1:28.2:1:0.01451:12.58625:48.8:10:0.0165:0.0097:0.6 0/0:306:0:0,0:221,85:306,0:0:2,0:21.2:1:28.1:1:1:0:56.5:152:1:0:0.3 +3 106825024 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08712;LSEQ=CGGCCTTTATATCTATTTTT;RSEQ=GTTTTGTTTTCTTGCCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:344:176:130,46:124,42:166,176:0.5116:2,2:21.6:1:31.6:1:0.90183:1.04457:51:87:0.5133:0:1.3 0/1:336:28:20,8:218,90:308,28:0.0833:2,2:25.7:1:30.3:1:1:1.03:52.6:56:0.0843:0:1.3 +3 106825180 . A T 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=ACTCTGCTTTCTATTTCAGC;RSEQ=GCATTTGTACAAGTCGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:28:17,11:289,268:557,28:0.0479:2,2:24.6:1:32.1:1:0.43949:1.43:36.4:56:0.0483:0:1.1 0/0:550:0:0,0:240,310:550,0:0:2,0:30.3:1:30.1:1:1:0:37.4:109:1:0:0.1 +3 106825268 . A AC 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07913;SOR=0.37857;LSEQ=GATTCTTCTTCTAATGTTCC;RSEQ=AAGATCTGTCAAAGCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:678:672:330,342:2,4:6,672:0.9912:2,2:23.4:1:31.9:1:0.68651:1.93:38.9:133.4:0.9926:0.1976:0.1 1/1:477:466:247,219:3,1:4,466:0.9769:2,2:23.5:1:31:1:0.62647:2.65479:39.3:232:0.9872:0.2055:0.1 +3 106825838 . A G 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGGGTGAAACCATTTCC;RSEQ=TGATGTCATGTTCCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:676:675:255,420:0,0:0,675:0.9985:0,2:26.4:1:31.4:1:1:0:45:95.429:0.9985:0:1.1 1/1:608:608:251,357:0,0:0,608:1:0,2:26.5:1:30.4:1:1:0:46.1:120.6:1:0:1.1 +3 106825888 . G A 49 v3;p8;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02025;SOR=Inf;LSEQ=CCGCGATGGACCTGCTTCTT;RSEQ=CTCAGGGTCTGCTGGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:0:0,0:145,324:469,0:0:2,0:25.8:1:32.5:1:1:0:59.9:233.5:1:0:0.8 0/1:399:5:5,0:129,265:394,5:0.0125:2,0:6.4:1:21.4:1:0.00406:0:60:4:0.0101:0:2 +3 106825950 . C A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14477;SOR=Inf;LSEQ=GGAGGCCTGCTCAGGACTGG;RSEQ=CGTGGGGCAGAGCCAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:5,157:162,0:0:1,0:23.3:1:31.6:1:1:0:60:161:1:0:0.1 0/1:100:2:1,1:8,90:98,2:0.02:2,2:20:0:27:1:0.17273:10.67:60:4:0.0204:0:1 +3 106827174 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCTTTTCACCTTCCACC;RSEQ=TGATTGTGAAGCCTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:29:1:1:0:29:4:1:0:1.5 +3 109128451 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=TCCCAAAGTGCTGGGATTAC;RSEQ=GGCGTGAGCCACCGCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:47,2:49,0:0:1,0:23.8:1:31.3:1:1:0:54.9:98:1:0:0 0/1:50:2:1,1:46,2:48,2:0.04:1,2:35.5:1:29.5:1:0.11755:18.9934:38:4:0.0408:0:1 +3 109128547 . C T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.34355;SOR=0.28973;LSEQ=AAGCACGTTTTCCTTGTATG;RSEQ=GGCGTGCTAGCTGGATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:1,2:149,126:275,3:0.0108:2,2:14:1:28:1:0.59619:2.35795:49:6:0.0109:0:1 0/0:318:1:0,1:169,148:317,1:0.0031:2,0:1:0:30:0:0.46855:0:51:2:0.0032:0:1 +3 109128553 . G T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTTTTCCTTGTATGCGGCGT;RSEQ=CTAGCTGGATTTCTTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:147,136:283,0:0:2,0:27.9:1:32:1:1:0:58.5:46.167:1:0:0.1 0/1:316:18:11,7:152,146:298,18:0.057:2,2:24.3:1:29.8:1:0.47183:1.51:51.8:36:0.0581:0:1.1 +3 109128577 . ATAGT A 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=GCTGGATTTCTTTTGGCATA;RSEQ=TAGCCGTTTGGCATGGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:107,142:249,0:0:2,0:25.6:1:29:1:1:0:59.4:61.25:1:0:0.1 0/1:296:17:9,8:125,154:279,17:0.0574:2,2:22.9:1:29.2:1:0.61804:1.38:53.2:34:0.058:0.0135:0.9 +3 109128618 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50233;SOR=Inf;LSEQ=ATAGCACACAGGTTGCTGTC;RSEQ=TCAAAAAGGCCAACCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:33,105:138,0:0:2,0:25.4:1:30.6:1:1:0:59.5:68:1:0:0.2 0/1:165:2:1,1:54,109:163,2:0.0121:2,2:20.5:1:29:1:1:2.01:60:4:0.0123:0:1 +3 109128643 . T G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50073;SOR=Inf;LSEQ=AAAGGCCAACCAGGTAGGCC;RSEQ=CACTTGCCTCCTGCAAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:23,78:101,0:0:2,0:22.8:1:30.7:1:1:0:59.4:100:1:0:0.4 0/1:118:2:1,1:34,82:116,2:0.0169:2,2:9.5:1:31.5:1:0.50703:2.39:60:4:0.0171:0:2 +3 109128692 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60104;SOR=0.80555;LSEQ=TGCACTCTGGAAGCGTAGAT;RSEQ=TGTTTTCAAGTCCTGAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:35:15,20:12,17:29,35:0.5469:2,2:25.3:1:30.5:1:1:1.06:59:34:0.5484:0:1.1 0/1:67:33:12,21:10,24:34,33:0.4925:2,2:27.8:1:29.2:1:0.60875:1.36:57.7:15.5:0.4844:0:1.4 +3 109128982 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5082;SOR=0;LSEQ=ATCCTTCAGCTGGAGCTCTG;RSEQ=GAGCCAGAGGCAGCGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:10,24:34,2:0.0556:2,2:28.5:1:32:0:0.52381:2.34:60:4:0.0556:0:1.5 0/0:25:0:0,0:5,20:25,0:0:2,0:25.5:1:29.3:1:1:0:60:50:1:0:0 +3 109129029 . TGCG T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.5148;SOR=0;LSEQ=GAGTGATGGCGGCATGGCGG;RSEQ=GCGGCGGCTGCGAACACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:4,21:25,2:0.0741:2,2:35:1:31.5:1:0.34188:4.81:60:4:0.0741:0:0 0/0:17:0:0,0:3,14:17,0:0:2,0:26.4:1:32:1:1:0:60:34:1:0:0.1 +3 112352947 . C G 52 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=AGGGAAGACACTTTAAGTCT;RSEQ=AGATTATTCAAAATACTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:32.3:1:33.3:1:1:0:60:6:1:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:30:0:32:0:1:0:54:2:1:0:0 +3 112352986 . A AT 51 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=CGTTAGGCTCAAAATGCTAG;RSEQ=TTTTTTTTTACAGGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:30.3:1:32.7:1:1:0:60:6:0.75:0:0.3 1/0:4:2:2,0:1,0:1,2:0.5:0,0:8:1:31.6:1:1:0:60:4:0.5:0.25:0 +3 112353099 . T C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAATAAGTAGATGGTTGTCC;RSEQ=AATACACAGATGTCTGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:62:57,5:0,0:0,62:0.9841:0,2:24.1:1:31.6:1:1:0:60:61:1:0:1 1/1:54:54:48,6:0,0:0,54:1:0,2:19.7:1:30.9:1:1:0:60:108:1:0:1 +3 112353238 . C A 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTTGTTAATTGACAAGTGA;RSEQ=TAGATCTCAGAGCGCAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:320:320:152,168:0,0:0,320:1:0,2:25.5:1:30.5:1:1:0:60:63:1:0:1.1 1/1:261:220:108,112:18,22:40,220:0.8429:2,2:26.5:1:29.4:1:0.73149:1.18:60:54:0.8438:0:1.1 +3 112353331 . A C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.01364;LSEQ=CCTATAGTCTCACTATCGTC;RSEQ=ACCTCAAACTGACACCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:29:9,20:23,66:89,29:0.2458:2,2:21.7:1:32:1:0.63343:1.29:60:58:0.2522:0:1.7 1/0:95:54:10,44:12,29:41,54:0.5684:2,2:22.6:1:31.3:1:0.23156:1.809:60:108:0.5684:0:1.6 +3 112353355 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17223;SOR=0;LSEQ=TCAAACTGACACCAAGCAGA;RSEQ=TGAAGAATTAGGTTAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:74:74:7,67:0,0:0,74:1:0,2:21.2:1:30.4:1:1:0:60:36:1:0:1.2 1/1:53:51:6,45:0,0:0,51:0.9623:0,2:23.8:1:30.2:1:1:0:60:102:0.9623:0:1.6 +3 112547386 . T C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59703;SOR=1.96324;LSEQ=AAATTGGTGACATTGTCAAA;RSEQ=ATAGCCTTTGGATATTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:6:6,0:30,0:30,6:0.1667:1,0:13.5:1:33:1:1:0:60:12:0.1667:0:1 0/1:7:2:2,0:4,1:5,2:0.2857:2,0:40:1:29:1:1:0:60:4:0.2857:0:1.5 +3 112547496 . C A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86701;LSEQ=TCTGTATATTCAATCCAATT;RSEQ=TCAGGTGTAAATGTAGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:195:160,35:0,0:0,195:0.9949:0,2:24.5:1:28.8:1:1:0:60:96.5:0.9948:0:1.1 1/1:170:169:140,29:0,0:0,169:0.9941:0,2:22.6:1:27.9:1:1:0:60:83.5:0.994:0:1.1 +3 112547601 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.33774;LSEQ=CATAGATTCTCATGCATCTC;RSEQ=TAAGCCAACACAATGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:208:103,105:209,205:414,208:0.3344:2,2:25.8:1:30.9:1:0.86511:1.03926:60:207:0.3355:0:1.1 1/0:496:268:128,140:104,122:226,268:0.5403:2,2:25.3:1:29.7:1:0.71805:1.07:60:133:0.5429:0:1.1 +3 112547684 . G A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58296;SOR=2.59444;LSEQ=GTATCTGTCACTACTCACCT;RSEQ=TAACAAAGGTGAGTGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:1,0:56,190:246,1:0.004:2,0:1:0:23:0:0.23077:0:60:2:0.0041:0:2 0/1:192:2:1,1:53,137:190,2:0.0104:2,2:10:1:26.5:1:0.48446:2.57:60:4:0.0104:0:2 +3 112547771 . GT G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTATGTGGATGAAGTTT;RSEQ=TTTTGCTACACCCTGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:0,2:0,55:55,2:0.0351:1,0:19:1:30.5:1:1:0:60:4:0.0357:0.0175:0.5 0/0:23:0:0,0:0,23:23,0:0:1,0:23.3:1:29:1:1:0:60:46:1:0:0 +3 112649289 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.48837;SOR=Inf;LSEQ=TCCAATTATCAACACTAAAG;RSEQ=CGTAAGTTGATCCCTGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:16,6:22,0:0:2,0:25.6:1:31.5:1:1:0:60:44:1:0:0 0/1:22:2:1,1:16,4:20,2:0.0909:2,2:15.5:1:26.5:1:0.41126:3.6879:60:4:0.0952:0:1 +3 112649386 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.02874;LSEQ=ACCTCATGCATCCCATAAAT;RSEQ=GACACAATGTGTCAGTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:9:3,6:8,14:22,9:0.2903:2,2:12.8:1:30.3:1:1:1.13798:60:18:0.2903:0:1.7 0/1:27:8:2,6:6,13:19,8:0.2963:2,2:24.5:1:29.8:1:1:1.36848:60:16:0.2963:0:1.6 +3 112649401 . G T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72335;SOR=1.41685;LSEQ=TAAATCGACACAATGTGTCA;RSEQ=TGACTTGGTAAGGGTTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:6,14:20,5:0.2:2,0:26:1:30.6:1:0.28871:0:60:10:0.2:0:2 0/1:19:5:0,5:4,10:14,5:0.2632:2,0:28.2:1:30.4:1:0.53044:0:60:10:0.2632:0:2 +3 112649613 . C T 28 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGTGTCACCTGTCTCTTA;RSEQ=ATGGTTTGTACTCTAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 112760178 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14937;SOR=Inf;LSEQ=TCATGGTCAACTGGAGAACG;RSEQ=TCCAGAAATCCTTGAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:243,34:277,0:0:2,0:22.8:1:31.3:1:1:0:59.7:91.333:1:0:0.1 0/1:175:2:1,1:147,26:173,2:0.0114:2,2:28.5:1:26.5:1:0.28552:5.56707:60:4:0.0116:0:1 +3 113012189 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.19075;SOR=Inf;LSEQ=TGGAGTCAGCGTTGGAGGCA;RSEQ=ACAGACCTGAATTTCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:56,62:118,0:0:2,0:26.8:1:32.8:1:1:0:59.8:236:1:0:0.1 0/1:92:2:1,1:44,46:90,2:0.0217:2,2:20:0:32.5:1:1:1.04:60:4:0.0217:0:1.5 +3 113012193 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.19825;SOR=Inf;LSEQ=GTCAGCGTTGGAGGCAGACA;RSEQ=ACCTGAATTTCAAAACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:52,61:113,0:0:2,0:26.8:1:32.5:1:1:0:59.8:55.5:1:0:0.1 0/1:92:2:1,1:43,47:90,2:0.0217:2,2:23:1:27:1:1:1.09:60:4:0.0217:0:1 +3 113012261 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15152;SOR=Inf;LSEQ=CAGCAAGTTACTCAGCTCCT;RSEQ=TGAGCTTTAGAAAGTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:7,33:40,0:0:2,0:20.8:1:32.5:1:1:0:60:39:1:0:0.1 0/1:26:2:1,1:7,17:24,2:0.0769:2,2:24:1:29:1:0.52923:2.34:60:4:0.0769:0:1 +3 113012330 . C G 76 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1.18321;LSEQ=GAAGAGGCCATACATGTAAA;RSEQ=ATATACTGTGTAAAGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:6,5:0.4545:0,0:33.2:1:33:1:1:0:60:10:0.4545:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:38:0:33:0:1:0:60:2:0.5:0:1 +3 113012343 . A C 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=ATGTAAACATATACTGTGTA;RSEQ=AGAGACAGATAACTAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:8:1:33:1:1:0:60:4:0.3333:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:43:0:34:0:1:0:60:2:0.5:0:1 +3 113068563 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGGGCTCCCGGGGCAAG;RSEQ=GCCAGCTCATGTCATCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:32:1:1:0:46:4:1:0:2.5 +3 113069023 . AAG A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=8.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AGAAAGACCAGCAGAGAGGA;RSEQ=AGAGAGAGAGAGAGGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:32:0:25:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:28.6:1:1:0:47.5:4:1:0.5:0 +3 113070399 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CAGTGACTCTCCAAAACCGC;RSEQ=AAGACCTAGATCTCCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:26.7:1:31.7:1:1:0:35.9:14:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:42:0:31:1:1:2.44949:24:4:0.3333:0:1.5 +3 113070498 . G A 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68928;SOR=1.74976;LSEQ=AGTCAGGGATAGTACGAGAT;RSEQ=CCAACCGGCATTTACAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:4,1:14,6:20,5:0.2:2,2:14.8:1:29.2:1:1:1.68:28.6:10:0.2083:0:1 0/1:13:4:4,0:8,1:9,4:0.3077:2,0:33.3:1:27.5:1:1:0:31:8:0.3077:0:1.3 +3 113070516 . GA G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18076;SOR=Inf;LSEQ=ATGCCAACCGGCATTTACAG;RSEQ=AAAGGCTTCTGAAATCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:17,8:25,0:0:2,0:30.5:1:30.4:1:1:0:32.3:50:1:0:0.3 0/1:19:2:1,1:16,1:17,2:0.1053:1,2:11:1:29.8:1:0.20468:11.66204:28:4:0.1053:0.0526:0 +3 113070575 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20556;SOR=Inf;LSEQ=CATACCAACCTCTGGAGTTG;RSEQ=GCGACATGGCTTCTCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:22,22:44,0:0:2,0:25.5:1:31.3:1:1:0:41.8:43:1:0:0.3 0/1:37:2:1,1:22,13:35,2:0.0541:2,2:38.5:1:28:1:1:1.66733:29:4:0.0556:0:1 +3 113070611 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49772;SOR=0;LSEQ=CCCTTTCTGGTCCCGTGACA;RSEQ=CCATCTTGCTATTACTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:14,24:38,2:0.05:2,2:17.5:1:29:1:1:1.69:20:4:0.05:0:1.5 0/0:33:0:0,0:13,20:33,0:0:2,0:23.2:1:29.8:1:1:0:48.2:10:1:0:0.4 +3 113376110 . TTGC T 109 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=34;MSI=12.000;MSILEN=3;SSF=0.00144;SOR=0.20855;LSEQ=CCTGCTTGTTGTTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:13:5,8:6,9:15,13:0.3939:2,2:28.9:1:29.5:1:1:1.06419:60:26:0.3939:0:0.2 0/1:85:10:4,6:24,25:49,10:0.1176:2,2:27.5:1:29.4:1:0.73421:1.43119:57.3:20:0.1176:0:0 +3 113802083 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17143;SOR=Inf;LSEQ=AATATCCCTTCTTCAGAATG;RSEQ=TTGGAACCAGAAGTGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:12,0:0:2,0:17.6:1:31.4:1:1:0:60:24:1:0:0 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:31:1:27.5:1:1:1.29:60:4:0.2222:0:1 +3 113802161 . CTGTTGT C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=12.000;MSILEN=3;SSF=0.063;SOR=2.89479;LSEQ=TGTTGTTGCTGTTGCTGCTG;RSEQ=TGTTGTTGTTGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:4,4:12,12:24,8:0.2162:2,2:29:1:32.6:1:1:1:58.6:16:0.2162:0:0.1 0/1:29:13:7,6:6,9:15,13:0.4483:2,2:32.1:1:31.9:1:0.70508:1.71:59.6:26:0.4815:0:0.2 +3 113820868 . G A 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATTTTTTTTGCAAGACT;RSEQ=TTTCATAGGTGATGATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45:0:29:1:1:0:60:4:1:0:1 +3 113822125 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.19192;SOR=Inf;LSEQ=GCTGGTATACTTGGTGATGG;RSEQ=CTTGGTGCCCTCGGACACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:25,0:0:2,0:22.5:1:31.6:1:1:0:60:24:1:0:0.1 0/1:20:2:1,1:8,10:18,2:0.1:2,2:27:0:30.5:1:1:1.24:24:4:0.1:0:1.5 +3 113822276 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51966;SOR=Inf;LSEQ=ACGTGCTCAAAGATGTCGTT;RSEQ=ACGAAGGAGTTCATGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:50,31:81,0:0:2,0:24.8:1:31.9:1:1:0:55.9:162:1:0:0.1 0/1:124:2:1,1:63,59:122,2:0.0161:2,2:9:1:28:1:1:1.0672:60:4:0.0163:0:1 +3 113822288 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13998;SOR=0;LSEQ=ATGTCGTTGACGAAGGAGTT;RSEQ=ATGATCCCCATGGCCTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:46,35:81,2:0.0241:2,2:39.5:1:29:1:1:1.3099:59:4:0.0241:0:1 0/0:138:0:0,0:68,70:138,0:0:2,0:27:1:30.8:1:1:0:58.4:137:1:0:0.2 +3 113822432 . G GA 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10777;SOR=Inf;LSEQ=CCGTAGTCACCCACCTCTTG;RSEQ=AGCCCTAATTGGGATCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:2,20:22,0:0:2,0:23.5:1:32.3:1:1:0:60:44:1:0:0 0/1:21:3:0,3:7,11:18,3:0.1429:2,0:16.3:1:31.7:1:0.52105:0:60:6:0.15:0.0476:0 +3 113824222 . G C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGCCCTAAACAGGTGTA;RSEQ=CATTTTAAAAGGTACAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29:1:1:0:60:4:1:0:1 +3 114328765 . A T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=ATCTCTGCTAGCCACAAGAA;RSEQ=ATTAGCAGTCAACATTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:28.8:1:31.2:1:1:0:60:10:1:0:0.2 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:11.8:1:29.2:1:1:0:60:10:0.8333:0:1.2 +3 114328901 . ACAG A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.24352;SOR=Inf;LSEQ=ATGATAAAGCCATGGCAATC;RSEQ=CAGCAGCAGCAGCAGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:32,20:52,0:0:2,0:25.3:1:32:1:1:0:60:51:1:0:0 0/1:55:3:2,1:29,23:52,3:0.0545:2,2:31.3:1:32:1:1:1.57:60:6:0.0556:0:0 +3 115560700 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21315;SOR=0;LSEQ=TGGCATACTTACTGAAAAGG;RSEQ=CTAGGCTGGCATTGGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:1,1:78,38:116,2:0.0169:2,2:18:1:27.5:1:1:2.03915:60:4:0.0171:0:1 0/0:137:0:0,0:82,55:137,0:0:2,0:20.6:1:27.8:1:1:0:60:44.667:1:0:0.1 +3 115560748 . TA T 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50016;SOR=Inf;LSEQ=TGTTGGCAGCCACACAGGTG;RSEQ=GTTGCCGTAGTGCTCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:75,94:169,0:0:2,0:28.3:1:29.9:1:1:0:60:41.25:1:0:0.1 0/1:189:2:1,1:86,101:187,2:0.0106:2,2:18.5:1:33:0:1:1.17:60:4:0.0106:0:0 +3 115560763 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50066;SOR=Inf;LSEQ=AGGTGTAGTTGCCGTAGTGC;RSEQ=CCTCAGTGACGTTGGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:61,96:157,0:0:2,0:27.8:1:30.6:1:1:0:60:51.333:1:0:0.1 0/1:179:2:1,1:77,100:177,2:0.0112:2,2:19:1:29.5:1:1:1.30:60:4:0.0114:0:1 +3 116164290 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=CGGGCGGGCGGGCGAGGGAG;RSEQ=CGGCACCAAGCCTGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:12,4:16,2:0.1111:2,2:20.5:1:29.5:1:0.4902:2.79285:60:4:0.1111:0:1 0/0:11:0:0,0:10,1:11,0:0:2,0:29.1:1:31.4:1:1:0:60:22:1:0:0.1 +3 116506147 . C T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCTTTTGTTCACATCTTTT;RSEQ=GTCCATGTGTACTGAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:17.5:1:29:1:1:0:60:4:0.6667:0:2.5 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:31.5:1:1:0:60:4:1:0:1.5 +3 116506453 . C T 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGGATGTCTGTGGTGGGA;RSEQ=CTGTGGAACAGCCTCGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:246,273:519,0:0:2,0:25.9:1:31.4:1:1:0:60:73.143:1:0:0.3 0/1:451:26:11,15:202,223:425,26:0.0576:2,2:24.7:1:28.7:1:0.68789:1.23465:60:25:0.0562:0:1.8 +3 116506471 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=2.14123;LSEQ=GACCTGTGGAACAGCCTCGA;RSEQ=GTCACTGTTAGGTACAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:107:49,58:182,220:402,107:0.2102:2,2:27.5:1:31.1:1:1:1.02:60:214:0.2127:0:1.2 0/1:435:158:75,83:129,148:277,158:0.3632:2,2:23.6:1:29.7:1:0.92047:1.04:60:51.667:0.3664:0:1.2 +3 116506560 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23013;SOR=Inf;LSEQ=TTACTTATGTACTGTTTCAA;RSEQ=GATGGTTCTATCCTCCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:45,141:186,0:0:2,0:25.2:1:31.8:1:1:0:60:92:1:0:0.1 0/1:172:2:1,1:49,121:170,2:0.0116:2,2:19.5:1:27.5:1:0.4981:2.45:60:4:0.0116:0:1.5 +3 117078179 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49195;SOR=Inf;LSEQ=GGGCAGCCCAGATGAGTGAA;RSEQ=TTCTCCCCAGCAAAGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:13,0:0:2,0:24.5:1:32.2:1:1:0:60:26:1:0:0.2 0/1:17:2:1,1:9,6:15,2:0.1176:2,2:19:1:27.5:1:1:1.46382:57:4:0.1176:0:1.5 +3 117078225 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19843;SOR=Inf;LSEQ=CTTCATTAAATGGGTCCTTC;RSEQ=CCCCGGGCCACCCAACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:18,10:28,0:0:2,0:31.3:1:29.9:1:1:0:60:13:1:0:0.2 0/1:23:2:1,1:10,11:21,2:0.087:2,2:48.5:1:30:1:1:1.10:60:4:0.087:0:1.5 +3 117078556 . C G 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00032;SOR=0;LSEQ=AAAAAGGCCTCCACAAAAAA;RSEQ=CCATCCAAGGGTCAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:9:5,4:19,17:36,9:0.2:2,2:22.6:1:32.8:1:1:1.12:47.2:18:0.2045:0:1.1 0/0:59:0:0,0:30,29:59,0:0:2,0:26.8:1:31:1:1:0:54:58:1:0:0.3 +3 117078557 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50293;SOR=Inf;LSEQ=AAAAGGCCTCCACAAAAAAC;RSEQ=CATCCAAGGGTCAGCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:24,22:46,0:0:2,0:27.3:1:30.9:1:1:0:52.2:22:1:0:0.9 0/1:59:2:1,1:29,28:57,2:0.0339:2,2:23:1:31:1:1:1.03511:60:4:0.0345:0:1 +3 117078561 . C T 133 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCTCCACAAAAAACCCAT;RSEQ=CAAGGGTCAGCAGCCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:21:10,11:13,10:23,21:0.4565:2,2:26.3:1:30.3:1:0.76304:1.41833:53.7:20:0.4651:0:1.2 0/0:60:0:0,0:30,30:60,0:0:2,0:25.2:1:30.3:1:1:0:52.5:29:1:0:0.4 +3 117079025 . GA G 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=GATATGCAGAAAAGCATAGA;RSEQ=AAAAAAAAATAATGAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,1:3,3:0.5:2,0:22:1:35:0:1:0:60:6:0.5:0:0 0/0:10:0:0,0:8,2:10,0:0:2,0:17.7:1:29:1:1:0:60:20:1:0:0.1 +3 117862801 . A G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTCTTTTTATGAGGTCTC;RSEQ=TATTTCTTGGAGGCTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:30.5:1:33:1:1:0:47:4:0.6667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:6:0:30:0:1:0:60:2:1:0:0 +3 117863210 . G T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0625;SOR=0.16987;LSEQ=TTGTGGAGGCAATTTCTGCT;RSEQ=GTTTGTTTTTCTTTCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:3,5:5,6:11,8:0.4211:2,2:31.5:1:30.6:1:1:1.36508:54.9:16:0.4211:0:2 0/1:19:2:0,2:7,10:17,2:0.1053:2,0:19.5:1:31:0:0.50877:0:46.5:4:0.1053:0:1.5 +3 117863221 . C A 84 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03518;SOR=0.08879;LSEQ=ATTTCTGCTGGTTTGTTTTT;RSEQ=TTTCAATAGTCAGGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:3,5:8,7:0.4667:2,2:29.6:1:30.1:1:1:1.46001:56.6:14:0.4667:0:2.1 0/1:15:1:0,1:6,8:14,1:0.0667:2,0:19:0:32:0:1:0:52:2:0.0667:0:2 +3 117863755 . T C 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGAGTTAGGCCTGAAAAGG;RSEQ=GCTCTGGCTGCAGATTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:25.5:1:31:1:1:0:49.5:4:0.5:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:38:0:34:0:1:0:54:2:1:0:2 +3 117863938 . CG TC 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCTAGTTTCAGTGCTGG;RSEQ=GCTGCCCCTCCCCCAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:47.5:1:31:1:1:1.73:60:4:0.4:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:46:0:29:0:1:0:60:2:1:0:0 +3 118605433 . C T 56 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03082;SOR=Inf;LSEQ=AGAAATGGCTGAGTTTTGAG;RSEQ=AGAATATACTGTGATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:0:0,0:261,220:481,0:0:2,0:26.7:1:32.2:1:1:0:59.8:59.125:1:0:0.3 0/1:491:6:1,5:259,226:485,6:0.0122:2,2:7.7:1:21.7:1:0.10422:5.7124:60:5:0.0103:0:1.5 +3 118605469 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.00856;LSEQ=TTTTTACGTGTGTTTTTCAA;RSEQ=GGCCCTATACTTGGATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:166:86,80:186,187:373,166:0.3074:2,2:24.4:1:31.2:1:0.7094:1.08:60:165:0.3096:0:1.1 0/1:526:248:120,128:123,155:278,248:0.4715:2,2:23.3:1:30.1:1:0.38108:1.18:60:247:0.4759:0:1.1 +3 118605684 . T C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00182;SOR=Inf;LSEQ=TGCATTTCTTGCCTGAATTA;RSEQ=TGAAATAATCACCCAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:1,24:25,0:0:1,0:24.4:1:30.7:1:1:0:60:50:1:0:0.1 0/1:12:5:1,4:0,7:7,5:0.4167:0,2:12.8:1:32.4:1:0.41667:0:60:10:0.4167:0:1 +3 118844792 . A G 60 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATGCCACCGGGGCCTAGC;RSEQ=TCCCAGTCCTGGAATGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:22.3:1:30:1:1:0:60:8:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:31.5:1:1:0:60:4:1:0:2 +3 118845271 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48308;SOR=0;LSEQ=GCTGCAGTCTCTGCAGACCA;RSEQ=CAAACTTAGCTGATCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:14.5:1:31.5:1:1:1.37:36:4:0.1429:0:2 0/0:12:0:0,0:8,4:12,0:0:2,0:23.2:1:30.9:1:1:0:54.3:24:1:0:0.3 +3 118845275 . A G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01718;SOR=0.11454;LSEQ=CAGTCTCTGCAGACCAGCAA;RSEQ=CTTAGCTGATCCTCCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:5,6:1,2:3,11:0.7857:2,2:19.8:1:32.7:1:1:1.61:48.4:22:0.7857:0:1.2 0/1:11:3:2,1:5,3:8,3:0.2727:2,2:12:1:33.7:1:1:1.18:52.7:6:0.2727:0:1.3 +3 118845411 . G T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTCCCTGTACCACCCAACT;RSEQ=GGTGAGGCACTCCAACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:19:1:31.7:1:1:0:60:6:1:0:0 0/1:13:2:1,1:3,8:11,2:0.1538:2,2:30.5:1:31:1:1:2.45:54.5:4:0.1667:0:1.5 +3 118845663 . T C 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02424;SOR=0;LSEQ=AAAGAAAAACAAGCAGAAAG;RSEQ=GACAACAACAGCATCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:2,5:1,0:1,7:0.875:0,2:24.4:1:31.7:1:0.375:0:51.1:14:0.875:0:1 0/0:3:0:0,0:1,2:3,0:0:2,0:11:1:30.3:1:1:0:32.7:6:1:0:0.3 +3 118845677 . TCAA T 47 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.30769;SOR=Inf;LSEQ=AGAAAGTGACAACAACAGCA;RSEQ=CAACAACAACAACAAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:4,5:9,3:0.25:2,2:22.3:1:30:1:1:2.32:50.3:6:0.25:0.1667:0 1/1:1:1:0,1:0,0:0,1:1:0,0:20:0:33:0:1:0:52:2:1:0:0 +3 119545503 . T TA 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.21963;SOR=Inf;LSEQ=AATAAGAACAACAATAATAA;RSEQ=AAAAAAATTGAACACTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:88,1:89,0:0:1,0:25.7:1:31.8:1:1:0:59.7:178:1:0:0 0/1:79:2:1,1:76,1:77,2:0.0253:1,2:31.5:1:28.5:1:0.05031:54.10049:60:4:0.0253:0:0.5 +3 119545532 . A AT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50181;SOR=Inf;LSEQ=TGAACACTAAAATGAACAGG;RSEQ=TTTTTTTCTCTTTTTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:136,9:145,0:0:2,0:25.2:1:29.6:1:1:0:59.4:28:1:0:0.1 0/1:171:2:2,0:149,20:169,2:0.0117:2,0:8:1:31.5:1:1:0:48:4:0.0119:0.0058:0.5 +3 119545705 . G A 56 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11521;SOR=5.29504;LSEQ=GGTCTCCAGTATTAGCATCT;RSEQ=CAAGTCAAAAAGTCCCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:1:1,0:184,306:490,1:0.002:2,0:1:0:24:0:0.37678:0:60:2:0.0021:0:1 0/1:467:5:4,1:172,290:462,5:0.0107:2,2:6.8:1:24.4:1:0.06939:6.72:60:10:0.0108:0:1 +3 119562007 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4965;SOR=Inf;LSEQ=CCTGACCTCAGGTGATCCAC;RSEQ=CACCTCGGCCTCCCAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:69,2:71,0:0:1,0:17.8:1:31.2:1:1:0:41:70:1:0:0.1 0/1:72:2:1,1:63,7:70,2:0.0278:2,2:16.5:1:31:1:0.21127:8.48351:35:4:0.0282:0:2 +3 119562009 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.4966;SOR=Inf;LSEQ=TGACCTCAGGTGATCCACCC;RSEQ=CCTCGGCCTCCCAAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:72,2:74,0:0:1,0:18:1:30.7:1:1:0:42.4:148:1:0:0.1 0/1:74:2:1,1:64,8:72,2:0.027:2,2:18.5:1:32.5:1:0.22991:7.60108:35:4:0.0278:0:2 +3 119582218 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21481;SOR=Inf;LSEQ=GAATGTCATTTCACACCCAG;RSEQ=GTGTAGCTTTCCTAGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:170,53:223,0:0:2,0:21.1:1:31.1:1:1:0:60:110.5:1:0:0.1 0/1:194:2:1,1:143,48:191,2:0.0103:2,2:32.5:1:29:1:0.4443:2.95885:60:4:0.0106:0:1 +3 119585372 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1002;SOR=Inf;LSEQ=TAATTATTTAGCCTCTCAAA;RSEQ=AAGATTTCCCCCAAGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:233,90:323,0:0:2,0:23.3:1:32.5:1:1:0:60:52.833:1:0:0.1 0/1:282:3:2,1:193,86:279,3:0.0106:2,2:34.3:1:29.7:1:1:1.12162:60:6:0.0108:0:1.3 +3 119585415 . G GA 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.67911;SOR=0.82576;LSEQ=GACCTGCCCTGAAATTTTGG;RSEQ=AAAAAAAAATTAAGTACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:13:8,5:288,210:498,13:0.0254:2,2:27:1:30.5:1:1:1.17:60:26:0.0259:0.0039:0.2 0/1:474:10:6,4:272,188:460,10:0.0211:2,2:25.7:1:29:1:1:1.04:60:20:0.0217:0.0042:0 +3 119585581 . T TG 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.79322;LSEQ=GTTATAAGAAATCCATGGTG;RSEQ=GGGGGGGGACATAGAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:3:0,3:7,119:126,3:0.0233:2,0:22.7:1:31.7:1:1:0:60:6:0.024:0.0078:0 0/1:108:2:0,2:11,95:106,2:0.0185:2,0:19:1:30.8:1:1:0:60:4:0.0189:0.0093:0 +3 119585681 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04991;SOR=Inf;LSEQ=ATTATTTCACCACAGTGTAT;RSEQ=CAAAAAAATTTTTTTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:26,0:0:1,0:29.2:1:30.7:1:1:0:60:7.667:1:0:0.3 0/1:8:2:1,1:0,6:6,2:0.25:0,2:37:1:28:1:0.25:0:60:4:0.25:0:1 +3 119585690 . T A 73 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0.52426;LSEQ=CCACAGTGTATGCAAAAAAA;RSEQ=TTTTTTTGATTGTGCAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:0,5:0,18:18,5:0.2174:1,0:26.2:1:31.6:1:1:0:60:10:0.2273:0:1 0/1:8:1:0,1:1,6:7,1:0.125:2,0:9:0:32:0:1:0:60:2:0.125:0:1 +3 119595240 . T TA 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.64663;SOR=1.2861;LSEQ=TAACTACTGATTAATATACT;RSEQ=AAAAAAAAATCTAACTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:9:5,4:376,164:540,9:0.0163:2,2:20.4:1:28.4:1:0.46628:1.83183:58.3:8:0.0148:0.0036:0.2 0/1:479:10:7,3:309,158:467,10:0.0209:2,2:20.8:1:27.3:1:1:1.19:60:20:0.0212:0.0063:0 +3 119595503 . A G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAGCAGTGCCATGATTTGA;RSEQ=TATGTCCCCCAAAGCTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:0,36:0,0:0,36:1:0,1:26.9:1:32.4:1:1:0:60:35:1:0:1 1/1:16:16:0,16:0,0:0,16:1:0,1:20.1:1:32.3:1:1:0:60:32:1:0:1 +3 119631350 . TA T 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.37423;SOR=2.34059;LSEQ=GACACAAACCTTTGAGAGGT;RSEQ=AAAAAAAAAAAGCAGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:13,0:13,4:0.2353:1,0:28.8:1:31.5:1:1:0:60:8:0.2353:0:0.3 0/1:7:3:2,1:4,0:4,3:0.4286:0,2:15.7:1:30:1:0.42857:0:60:6:0.4286:0.1429:0 +3 119631814 . A G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01074;SOR=6.56981;LSEQ=TGTAAACTGTAACTATCTCT;RSEQ=ATAAAAGAAATTTACAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:0,5:0,26:26,5:0.1613:1,0:26.8:1:31.6:1:1:0:60:10:0.1667:0:1 1/0:14:8:0,8:0,6:6,8:0.5714:0,0:28.1:1:31:1:1:0:60:16:0.5714:0:1 +3 119632125 . C A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTGACTCACGGCGAATATTT;RSEQ=AAGGCTTATAGACTCAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:27:1:1:0:60:4:1:0:1 +3 119642101 . A G 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01206;SOR=Inf;LSEQ=ACAAAGTTCCAACAATACCT;RSEQ=CTTTACAGTTTTTCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:59,2:61,0:0:1,0:20:1:28.5:1:1:0:60:19.333:1:0:0.1 0/1:45:5:5,0:39,1:40,5:0.1111:1,0:29.4:1:31:1:1:0:60:10:0.1136:0:1 +3 119666019 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.49932;SOR=0;LSEQ=GTTTCGGAATTTTTCCATTC;RSEQ=ATTAGCAAAACTGTCTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:97,5:102,2:0.0192:1,2:20.5:1:32:1:0.11258:17.79785:60:4:0.0194:0:1 0/0:92:0:0,0:86,6:92,0:0:2,0:22.8:1:30.5:1:1:0:59.9:184:1:0:0.1 +3 119721104 . A AT 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.71133;SOR=1.15089;LSEQ=CTCCTAAAGGAAGAAAGGAA;RSEQ=TTTTTTTTTCACGAGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:14:5,9:128,349:477,14:0.0285:2,2:29.4:1:28.8:1:0.54171:1.51:60:13:0.0271:0.002:0.4 0/1:459:15:2,13:154,290:444,15:0.0327:2,2:23.2:1:30.5:1:0.10137:3.44453:60:30:0.0334:0:0.2 +3 119721117 . G A 55 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02664;SOR=Inf;LSEQ=AAAGGAAATTTTTTTTTCAC;RSEQ=AGAACTGTAAGGAATTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:88,306:394,0:0:2,0:25.6:1:31.1:1:1:0:60:77.8:1:0:0.2 0/1:372:5:4,1:103,264:367,5:0.0134:2,2:13.2:1:23.8:1:0.02551:10.18:60:4:0.0109:0:1 +3 119721171 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.96462;LSEQ=AAAATATACAAGGTAAACTA;RSEQ=ATTCTTTATTTTTTATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:30:0,30:0,121:121,30:0.1987:1,1:19.2:1:32.5:1:1:0:59.8:14:0.1918:0:1.1 0/1:114:22:0,22:3,89:92,22:0.193:1,1:25.4:1:32.8:1:1:0:60:44:0.1947:0:1 +3 119721191 . A AT 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.41854;SOR=1.61404;LSEQ=TATTCTTTATTTTTTATTTT;RSEQ=TTTTTTTTTTTGAGATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:7:0,7:0,85:85,7:0.0761:1,0:39.1:1:29.7:1:1:0:60:14:0.0778:0:0.4 0/1:68:8:0,8:0,60:60,8:0.1176:1,0:21.8:1:30.6:1:1:0:60:16:0.1176:0:0 +3 119813282 . A G 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCGCATTCGCCCGGGTCAGG;RSEQ=GCTGCTCTGTGTGAGGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:31.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:6:0:32:0:1:0:60:2:1:0:0 +3 120222544 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49456;SOR=Inf;LSEQ=CATAGACACAAGCATCAAAA;RSEQ=CTGACTCCGGCTGATTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:21,19:40,0:0:2,0:27.3:1:32.6:1:1:0:60:19:1:0:0.2 0/1:43:2:1,1:20,21:41,2:0.0465:2,2:35:1:28.5:1:1:1.05:60:4:0.0465:0:1 +3 123714862 . CT C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.12883;LSEQ=GTTTACTGAATTAAATTCTC;RSEQ=TTTTTTTCTCTCCTTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:80:61,19:75,12:87,80:0.479:2,2:22.3:1:32.1:1:0.1135:1.93896:38.2:160:0.479:0.0838:0.1 0/1:133:14:10,4:92,27:119,14:0.1053:2,2:24.2:1:31.3:1:0.73833:1.35959:38.4:28:0.1061:0:0.6 +3 123714982 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.36371;LSEQ=CTTAGGGACTAAAGTTCTAT;RSEQ=TGGCCAAGTAACCATAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:223:100,123:128,161:289,223:0.4355:2,2:26.8:1:30.6:1:0.92866:1.02:54.8:446:0.439:0:1.1 0/1:443:97:46,51:156,190:346,97:0.219:2,2:25.6:1:29.3:1:0.72975:1.10:55.7:96:0.2182:0:1.1 +3 125683874 . A C 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.22793;SOR=2.24809;LSEQ=GAAGTGAGCCACAGTATAAG;RSEQ=CACACAGGATAGGGAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:12:11,1:15,0:15,12:0.4444:1,2:25.7:1:33.2:1:0.44444:0:54.8:24:0.4444:0:1 1/0:17:11:10,1:6,0:6,11:0.6471:0,2:19.4:1:32.3:1:1:0:54.2:22:0.6471:0:1.5 +3 125683918 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15421;SOR=Inf;LSEQ=TTTCTGAGCTCATAGCTAGT;RSEQ=TGAGACAGTTGATACTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:57,18:75,0:0:2,0:22:1:28.8:1:1:0:59.2:36.5:1:0:0.3 0/1:49:2:1,1:34,13:47,2:0.0408:2,2:38.5:1:31:1:0.49405:2.55705:60:4:0.0408:0:1.5 +3 125683989 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21;SOR=Inf;LSEQ=GGATTCCCACTCTCTGGTGC;RSEQ=AGACCGGTCGTCACCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:94,64:158,0:0:2,0:26.2:1:31.5:1:1:0:59.3:157:1:0:0.2 0/1:135:2:1,1:77,56:133,2:0.0148:2,2:14.5:1:30:1:1:1.37169:60:4:0.015:0:1 +3 125684001 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50054;SOR=0;LSEQ=TCTGGTGCCAGACCGGTCGT;RSEQ=ACCTGGCCAAATAGAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:93,66:159,2:0.0124:2,2:43:1:29:1:1:1.40601:50:4:0.0125:0:1 0/0:141:0:0,0:80,61:141,0:0:2,0:26.4:1:30.9:1:1:0:59.3:282:1:0:0.1 +3 125684052 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15459;SOR=Inf;LSEQ=ATACTGAACATGCAAATCTC;RSEQ=ATGGACACTGAAGTATCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:64,105:169,0:0:2,0:25.3:1:30.4:1:1:0:59.9:55.333:1:0:0.1 0/1:110:2:1,1:45,63:108,2:0.0182:2,2:20.5:1:29.5:1:1:1.40:60:4:0.0182:0:1 +3 126249824 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGACAGTGGGCTTCAG;RSEQ=TACACGCAGCAGGGTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:29:1:1:0:60:4:1:0:1 +3 127838589 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22956;SOR=0;LSEQ=GATGACATTTAATTTGATAT;RSEQ=TGAACCTCTGGGAGGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:65,54:119,2:0.0165:2,2:47:1:31.5:1:1:1.20185:60:4:0.0167:0:1 0/0:131:0:0,0:78,53:131,0:0:2,0:26:1:31.1:1:1:0:60:64.5:1:0:0.2 +3 127838630 . G C 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=GAGTCAGCGTTCCAGGCAAA;RSEQ=AAAACAGCGAATTCAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:56,76:132,0:0:2,0:26.2:1:32.7:1:1:0:60:65:1:0:0.1 0/1:152:14:7,7:62,76:138,14:0.0921:2,2:23.4:1:30.9:1:0.78254:1.22:59.6:13:0.0872:0:1.4 +3 127838657 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50284;SOR=Inf;LSEQ=GCGAATTCAGAAAATCCAAA;RSEQ=CAGAAACAAGCTTGGCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:34,52:86,0:0:2,0:24.2:1:32.8:1:1:0:60:85:1:0:0.1 0/1:106:2:1,1:41,63:104,2:0.0189:2,2:12:1:27:1:1:1.53:60:4:0.019:0:1 +3 128199662 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01129;SOR=Inf;LSEQ=GGAAACCCCACCTGGGCAGC;RSEQ=GTCAGGTGCGGAGGCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:23,1:24,0:0:1,0:23.4:1:30.5:1:1:0:60:48:1:0:0.1 0/1:8:3:3,0:4,1:5,3:0.375:2,0:27.3:1:31:0:1:0:60:6:0.375:0:1 +3 128199913 . G T 230 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00485;LSEQ=TGGGGGTGGCCGAAGGAGAG;RSEQ=CTGGAGGAGGGGTGGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:895:223:129,94:374,296:670,223:0.2492:2,2:24.5:1:29.6:1:0.64019:1.09:59.9:43.6:0.2489:0:1.2 0/0:621:1:0,1:326,294:620,1:0.0016:2,0:1:0:22:0:0.47504:0:60:2:0.0016:0:1 +3 128200072 . C T 155 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=45.9162;LSEQ=GACAGCTCCTCGAAGCACTC;RSEQ=GCCCCTTTCTTGCTCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1324:1:1,0:616,706:1322,1:8e-04:2,0:30:0:16:0:0.46636:0:60:0:0:0:1 0/1:1131:38:19,19:536,557:1093,38:0.0336:2,2:23.4:1:29.7:1:1:1.04:60:76:0.0342:0:1.1 +3 128200152 . G A 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16901;SOR=5.47066;LSEQ=TTCCTTCTTCATGGTCAGTG;RSEQ=CCTGTTAACCTAGAGGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:1:1,0:131,354:485,1:0.0021:2,0:1:0:25:0:0.2716:0:60:2:0.0021:0:1 0/1:358:4:2,2:90,263:353,4:0.0112:2,2:17.8:1:26.8:1:0.27423:2.91:60:8:0.0113:0:1.3 +3 128200459 . T C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55309;SOR=Inf;LSEQ=CAGAGAAACCACTTCCCTAG;RSEQ=CCGAGACCCTGTCCTAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:23:21,2:8,1:9,23:0.7188:2,2:22.2:1:33.2:1:1:1.30:59.3:46:0.7188:0:1.6 1/1:4:4:3,1:0,0:0,4:1:0,2:9.5:1:32.3:1:1:0:58:8:1:0:1.8 +3 128200534 . G A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.43113;SOR=0.7294;LSEQ=TTACGGGAAGCCCTTCTGGC;RSEQ=CTCACTCAGGGCAGCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:102:71:70,1:29,2:31,71:0.6961:2,1:23.2:1:30.3:1:0.21846:4.74:60:34.5:0.69:0:1.3 1/0:40:25:24,1:15,0:15,25:0.625:1,1:21.6:1:29.9:1:1:0:59.8:24:0.6154:0:1.2 +3 128200806 . G A 182 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=142.52633;LSEQ=GACTGGGAGGGCAAGGCAGC;RSEQ=TCAGCAGGCTGGACTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:1:1,0:151,340:491,1:0.002:2,0:1:0:26:0:0.30894:0:60:2:0.002:0:1 0/1:350:79:32,47:96,175:271,79:0.2257:2,2:23.5:1:28.9:1:0.42765:1.24:60:38.5:0.2219:0:1.1 +3 128201013 . A C 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03623;SOR=Inf;LSEQ=CTCAGAAGCCTGATGTTAGA;RSEQ=TCAACGGGATTGCAAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:0,19:19,0:0:1,0:24.8:1:31.8:1:1:0:60:38:1:0:0.4 0/1:5:2:0,2:0,3:3,2:0.4:0,0:7:1:31.5:1:1:0:60:4:0.4:0:1 +3 128203006 . G T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.72596;SOR=0.70614;LSEQ=GCCTGGGCAGGAAGAGGGAC;RSEQ=AGAGGGTCTCCCACATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:20:0,20:0,10:10,20:0.6667:0,1:27.3:1:28.9:1:1:0:60:40:0.6667:0:1.6 1/0:12:7:0,7:0,5:5,7:0.5833:0,0:21.9:1:26.7:1:1:0:60:14:0.6364:0:1.4 +3 128203035 . A G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34419;SOR=0.37389;LSEQ=TCCCACATGGGAGGGGGCAC;RSEQ=GGTCCAGAGTCGTTTAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:0,14:0,5:5,14:0.7368:0,1:22.2:1:31.6:1:1:0:60:28:0.7368:0:1.8 1/0:6:3:0,3:0,3:3,3:0.5:0,0:38:1:31.3:1:1:0:60:6:0.5:0:2 +3 128204488 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14422;SOR=Inf;LSEQ=GATCTGGGAAACCAACACTG;RSEQ=CACCTCTCCCAAGTCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:191,45:236,0:0:2,0:23.5:1:32.2:1:1:0:59.9:117:1:0:0.1 0/1:145:2:1,1:116,27:143,2:0.0138:2,2:34:1:29:1:0.35:4.23703:60:4:0.0142:0:1.5 +3 128204877 . C G 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGCTGGAGACGCAGCCCC;RSEQ=GTGGTGCTAGGGTCAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1285:0:0,0:606,678:1284,0:0:2,0:23.1:1:30.2:1:1:0:60:57.364:0.9992:0:0.1 0/1:791:34:15,19:333,420:753,34:0.043:2,2:23.6:1:28:1:1:1.00428:60:33:0.0424:0:1.1 +3 128204951 . C T 191 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=96.84038;LSEQ=AAGGTGGGAGCCAGAGTGGG;RSEQ=TGCTGTAGGGGTGAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1228:2:1,1:556,670:1226,2:0.0016:2,2:31.5:1:29:1:1:1.20:60:4:0.0017:0:1 0/1:768:105:51,54:298,365:663,105:0.1367:2,2:23.5:1:28.5:1:0.5273:1.16:60:34:0.1349:0:1.2 +3 128204960 . G C 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAGAGTGGGCTGCTGTAG;RSEQ=GGTGAGGGAGGCCACTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1161:0:0,0:524,635:1159,0:0:2,0:24.2:1:31.5:1:1:0:59.9:114.9:0.9983:0:0.2 0/1:704:16:7,9:315,371:686,16:0.0227:2,2:21.3:1:29.9:1:1:1.09154:60:32:0.0231:0:1.2 +3 128205133 . G A 53 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12448;SOR=3.7457;LSEQ=CCGCAGCGGCAGAGAGGGCT;RSEQ=CTTTGCCCCCGTCCAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:2:2,0:299,384:683,2:0.0029:2,0:1:0:26:1:0.19273:0:60:4:0.003:0:1 0/1:461:5:4,1:216,240:456,5:0.0108:2,2:7:1:23.2:1:0.19725:4.43:60:10:0.0109:0:1.2 +3 128205221 . AAG A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.07157;SOR=Inf;LSEQ=GGTCAGGCGGGCTGCGGGCA;RSEQ=AGAGAGAGGATCAGGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:122,240:362,0:0:2,0:25.2:1:31.5:1:1:0:59.7:180:1:0:0.2 0/1:258:3:1,2:90,166:256,3:0.0116:2,2:16:1:28:1:1:1.08401:60:6:0.0119:0.0039:0.3 +3 128205519 . G A 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00047;SOR=Inf;LSEQ=CCGCTGCTCCCACCTCTCCC;RSEQ=CCCCAATTTTTCAGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:84,4:88,0:0:1,0:22.3:1:29.9:1:1:0:60:43:1:0:0.1 0/1:37:6:6,0:28,3:31,6:0.1622:2,0:20.2:1:31:1:1:0:60:12:0.1622:0:1 +3 128205545 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTCAGCAGCTCGATTC;RSEQ=TGCGGATCCTACATCCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:134,4:138,2:0.0143:1,2:20.5:1:29.5:1:0.0704:30.0704:60:4:0.0147:0:1 0/0:58:0:0,0:53,5:58,0:0:2,0:23.5:1:30.6:1:1:0:60:116:1:0:0.1 +3 128205831 . G A 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01572;SOR=9.54551;LSEQ=GGTGCTGCGCATTCAGCACG;RSEQ=CCGGGTGCGCCATCCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:828:1:1,0:250,576:826,1:0.0012:2,0:1:0:28:0:0.30351:0:60:2:0.0012:0:1 0/1:525:6:3,3:184,335:519,6:0.0114:2,2:21.3:1:27.2:1:0.67124:1.82:60:12:0.0117:0:1 +3 128205856 . G A 43 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07891;SOR=6.30835;LSEQ=GTGCGCCATCCAGCGCGGCT;RSEQ=CTCGGGCGCCACCTCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:1:1,0:132,410:542,1:0.0018:2,0:16:0:12:0:0.24494:0:60:0:0:0:2 0/1:347:4:3,1:95,248:343,4:0.0115:2,2:11:1:21.5:1:0.06987:7.78:60:3:0.0087:0:2 +3 128205860 . G C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00223;SOR=1.58482;LSEQ=GCCATCCAGCGCGGCTGCTC;RSEQ=GGCGCCACCTCCATGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:511:292:69,223:51,168:219,292:0.5714:2,2:23.3:1:29.9:1:1:1.02:60:35.5:0.5714:0:1.1 1/0:327:222:59,163:27,78:105,222:0.6789:2,2:22.8:1:29.4:1:0.89389:1.05:59.9:110:0.6769:0:1.1 +3 128205890 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16097;SOR=Inf;LSEQ=TCCATGGCCGGCGGCGGCGG;RSEQ=TCAGGGTCTGGGTGCAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:39,207:246,0:0:2,0:22.7:1:32.8:1:1:0:60:40:1:0:0.7 0/1:166:2:1,1:33,131:164,2:0.012:2,2:9:0:30:1:0.36867:3.93:60:4:0.0121:0:2 +3 128205930 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.16863;SOR=Inf;LSEQ=GGCAACGGCCCTGCGCGAGG;RSEQ=AGGGGGAGTGAGGCGTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:10,84:94,0:0:2,0:23.6:1:31.1:1:1:0:60:93:1:0:0.5 0/1:66:2:1,1:10,54:64,2:0.0303:2,2:26.5:1:26:1:0.30769:5.20:60:4:0.0303:0:1.5 +3 128814031 . T C 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1257;SOR=Inf;LSEQ=AGCTAAAGAAATAAGGTTCC;RSEQ=CAGTGAACCCAGTGGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:75,146:221,0:0:2,0:21.6:1:30.3:1:1:0:49.6:54.25:0.9954:0:0.1 0/1:248:4:2,2:93,149:242,4:0.0161:2,2:27.3:1:26.8:1:0.64113:1.60:51.5:3:0.0124:0:1 +3 134069661 . G A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80286;SOR=1.03942;LSEQ=CCCCTGTGAGTTGTTCTTGG;RSEQ=ACCCAAACACTACAAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:608:367:183,184:122,119:241,367:0.6036:2,2:26:1:30.4:1:0.8686:1.03077:60:121.333:0.6057:0:1.2 1/0:483:296:162,134:93,93:186,296:0.6128:2,2:25.6:1:28.7:1:0.34872:1.21:60:41.286:0.611:0:1.1 +3 134069962 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=GCTCACACACCTACCTCCAC;RSEQ=TCCACCTGCTCATTCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:1,10:11,3:0.2143:2,0:23:1:28.7:1:1:0:60:6:0.2143:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:23.5:1:33.5:1:1:0:60:4:1:0:0 +3 134512680 . A C 29 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGTAGGAGGGAGGGGAGGGG;RSEQ=GGAGGAAGGCAGCCTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134513356 . C A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGTGGAAGTTCACAATG;RSEQ=ACTGGGAAGTGAACACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:31:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134514248 . AAC A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=ACACACCCACCTCTCCCATA;RSEQ=ACACACACACACATGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:28:0:1:0:60:2:1:0:0 0/1:5:2:1,1:3,0:3,2:0.4:0,2:18:0:31:0:0.4:0:60:4:0.4:0:0 +3 134514579 . T C 317 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.40541;SOR=0.46166;LSEQ=GCTGCTGGTGCCGGCCGCCT;RSEQ=GGGACTGCTGTGCTCCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1318:1316:569,747:0,0:0,1316:0.9985:0,2:26:1:30.6:1:1:0:59.9:93:0.9985:0:1.2 1/1:914:911:387,524:0,0:0,911:0.9967:0,2:25.5:1:29.8:1:1:0:59.9:129.143:0.9967:0:1.2 +3 134516015 . T G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCCCTCAGTCTCCTGCT;RSEQ=CCCTCAGGGACTGCTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134644121 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGAGTTGATGGGAAGT;RSEQ=ACCCAAGGGTGTCAATATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134644433 . G A 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63723;SOR=1.5253;LSEQ=CACTGGACTTAGCATCAGAC;RSEQ=TGAAGTCTGTATCCAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:5,0:26,1:27,5:0.1563:1,0:20.8:1:31.4:1:1:0:60:10:0.1563:0:1.4 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:7.5:1:31.5:1:1:0:60:4:0.2222:0:2 +3 134644517 . A G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=4.91517;LSEQ=GCCTTGGGCTTCACAGAGAG;RSEQ=CCTGGGCTTGAAGATGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:33:32,1:66,2:68,33:0.3267:1,1:25.8:1:32.2:1:1:1.03097:60:66:0.3267:0:1.2 1/0:58:41:39,2:16,0:16,41:0.7069:1,1:25:1:30.9:1:1:0:60:40:0.7143:0:1.1 +3 134644553 . C T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26042;SOR=0;LSEQ=GCACAAACCTCCTTGTAGTA;RSEQ=TGTCATTTACTATCACAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:3:2,1:143,41:184,3:0.016:2,2:35.3:1:25:1:0.53598:1.73798:60:2:0.0108:0:2 0/0:144:0:0,0:111,33:144,0:0:2,0:21.4:1:31:1:1:0:60:71:1:0:0.6 +3 134644635 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCATTGTTTTTGTTTATT;RSEQ=GTTTTTTCTTTTTAATCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:0:0,0:295,250:545,0:0:2,0:24.3:1:31.6:1:1:0:60:108:1:0:0.5 0/1:475:21:11,10:264,190:454,21:0.0442:2,2:27.6:1:30.2:1:0.65453:1.26252:60:42:0.0445:0:1 +3 134644636 . G T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.53527;LSEQ=CTCATTGTTTTTGTTTATTC;RSEQ=TTTTTTCTTTTTAATCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:197:109,88:183,163:346,197:0.3621:2,2:22.5:1:31.2:1:0.59247:1.10:60:196:0.3636:0:1.1 1/0:476:343:200,143:74,59:133,343:0.7206:2,2:24.3:1:29.8:1:0.60676:1.11:60:113.333:0.7203:0:1.1 +3 134644975 . C G 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ACCTAGACAACTAGGGCCAT;RSEQ=GCTGTGTGGGGATGGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:17:1:32:1:1:0:60:8:0.5:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:28.5:1:32.5:1:1:0:60:4:1:0:1 +3 134669965 . G A 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22857;SOR=Inf;LSEQ=ATGAGCATTATGGGTTAGGC;RSEQ=AGGGACAGCTTTCTTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:6,0:6,6:0.5:0,0:27.5:1:30.7:1:1:0:60:12:0.5:0:1.3 1/1:3:3:3,0:0,0:0,3:1:0,0:21:1:30.3:1:1:0:60:6:1:0:1 +3 134670080 . A C 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00097;SOR=0;LSEQ=CTTAGATGTGTTCATTTCTC;RSEQ=AGTCAATCTGCTGGACTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:20:19,1:88,1:89,20:0.1835:1,1:25.1:1:31.5:1:0.33469:4.5399:60:19:0.1776:0:1.1 0/0:45:0:0,0:44,0:44,0:0:1,0:20.9:1:29.7:1:1:0:60:43:0.9773:0:0.1 +3 134670524 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.49979;LSEQ=ACCATTGCTGCAGATGAGAG;RSEQ=TTCTCCCAGGTGGACTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1085:390:224,166:384,311:695,390:0.3594:2,2:24.9:1:30:1:0.52393:1.09:59.9:77:0.3585:0:1.1 1/0:834:487:292,195:200,146:346,487:0.5839:2,2:23.8:1:28.9:1:0.56744:1.09:60:80.167:0.5852:0:1.1 +3 134670787 . A G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03757;SOR=Inf;LSEQ=CCCCAACGCAGAGGAAGTGG;RSEQ=CGTGCCCATCAAACTCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:499:0:0,0:190,309:499,0:0:2,0:24.6:1:30:1:1:0:60:82.167:1:0:0.1 0/1:394:4:2,2:143,247:390,4:0.0102:2,2:21.8:1:30.3:1:0.62724:1.72:60:8:0.0104:0:1 +3 134670806 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03567;SOR=Inf;LSEQ=GACGTGCCCATCAAACTCTA;RSEQ=TGCAACGGGGATGGGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:0:0,0:164,266:430,0:0:2,0:23.6:1:32.9:1:1:0:60:214:1:0:0.1 0/1:332:4:1,3:118,209:327,4:0.012:2,2:9.8:1:26.3:1:1:1.69132:60:8:0.0123:0:1 +3 134670913 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08526;SOR=Inf;LSEQ=GGGTAAGCTTTGGAGCCTCT;RSEQ=CTTCCTGCCCATCTATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:51,122:173,0:0:2,0:22.6:1:31.7:1:1:0:60:23.714:1:0:0.1 0/1:137:3:2,1:42,92:134,3:0.0219:2,2:22.7:1:26:1:0.24145:4.33:60:6:0.0224:0:1.3 +3 134670929 . T A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09628;SOR=Inf;LSEQ=CTCTGCTTCCTGCCCATCTA;RSEQ=GGCAGGGCCAGATCTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:30,100:130,0:0:2,0:23.2:1:30.5:1:1:0:60:42.333:1:0:0.1 0/1:111:3:2,1:29,79:108,3:0.027:2,2:15.3:1:30.7:1:0.18797:5.35:60:6:0.0278:0:1 +3 134825097 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGTCATTGGTACCAAGAAG;RSEQ=TATATTTCACAAAGGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:17,2:0.1053:1,0:24:1:31.5:1:1:0:60:4:0.1053:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:29:1:28.8:1:1:0:60:10:1:0:0 +3 134825512 . G C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.04146;SOR=0.6797;LSEQ=TGGTGCAAGTGGTGGGTCTG;RSEQ=GGCAAGGAAGAGAAGACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:120:22,98:29,133:162,120:0.424:2,2:21.8:1:30.4:1:1:1.03:60:59:0.4214:0:1.1 0/1:216:72:17,55:30,114:144,72:0.3333:2,2:22.5:1:29.3:1:0.72679:1.17:60:71:0.3349:0:1.1 +3 134851419 . A T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00707;SOR=Inf;LSEQ=CTTTTAAAATGAATTGAAGC;RSEQ=TAGCCATTTGGGGTTGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:100,4:104,0:0:1,0:24.3:1:30.6:1:1:0:59.5:51:1:0:0.1 0/1:44:4:4,0:39,1:40,4:0.0909:1,0:25.5:1:30.8:1:1:0:60:8:0.0909:0:1.3 +3 134851577 . A T 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGTCCCATCAGGTCCCCGCA;RSEQ=TGTTATCTCCATCGTCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:840:95:56,39:411,334:745,95:0.1131:2,2:25.4:1:30.6:1:0.51209:1.17:60:46.5:0.1122:0:1.2 0/0:707:0:0,0:388,319:707,0:0:2,0:24.7:1:29.5:1:1:0:60:87.375:1:0:0.2 +3 134852051 . C A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTTGTGATCACATAGAG;RSEQ=AGGCAGGTGTAGTGTTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:0,41:0,0:0,41:1:0,1:22.2:1:31.4:1:1:0:60:82:1:0:1 1/1:17:17:0,17:0,0:0,17:1:0,1:19.9:1:30.1:1:1:0:58.6:34:1:0:1 +3 134872920 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18069;SOR=Inf;LSEQ=AATGCCATTTTTCTCCCTAC;RSEQ=TACCTCTGGAAGATGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:225,34:259,0:0:2,0:22.2:1:30.2:1:1:0:59.9:50.8:1:0:0.1 0/1:192:2:1,1:164,26:190,2:0.0104:2,2:19:1:28.5:1:0.26211:6.20863:60:4:0.0106:0:1 +3 134873388 . A AT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGGAAGGACCAGTCCC;RSEQ=TTTTTCCAGTCACATGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:0,10:10,2:0.1667:0,0:21:1:29:1:1:0:46:4:0.1667:0:0 0/0:4:0:0,0:1,3:4,0:0:2,0:25.3:1:29:1:1:0:60:8:1:0:0 +3 134880488 . A C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGATGTTGCCTAGTTTG;RSEQ=GTCTGCTGAGGTCAGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25.5:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134880745 . G T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90061;SOR=0.9465;LSEQ=GCCTGGAGCTGATGACAACT;RSEQ=CTAGCAGATATGCAGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:85:85,0:86,1:87,85:0.4942:1,1:22.9:1:31.8:1:1:0:59.6:170:0.4971:0:1 0/1:102:49:46,3:51,2:53,49:0.4804:1,2:21.4:1:30.5:1:0.66925:1.65481:60:98:0.4804:0:1 +3 134881023 . G A 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16706;SOR=5.61929;LSEQ=CTTCCAGACTCTGACTGACG;RSEQ=TAAGGGTCGGGGAGGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:1:1,0:177,324:501,1:0.002:2,0:1:0:15:0:0.35458:0:60:0:0:0:1 0/1:360:4:3,1:133,222:355,4:0.0111:2,2:12:1:26:1:0.15439:4.99:60:8:0.0113:0:1 +3 134884473 . C T 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTAGATAAGTCCCCTT;RSEQ=ATTGGAATGTCCTTAACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:5,1:6,2:0.25:2,0:36:1:32:1:1:0:46:4:0.25:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134884541 . A G 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGAGGGAATGTAGATTGG;RSEQ=AATCATCTCTGCTCCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:24.1:1:30.9:1:1:0:56.7:14:1:0:1.1 1/1:4:4:4,0:0,0:0,4:1:0,0:18.8:1:32:1:1:0:60:8:1:0:1.5 +3 134884601 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1417;SOR=Inf;LSEQ=CAGATTCTGTCACGGCTGTT;RSEQ=TGTTTTCATTGTCCTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:23,1:24,0:0:1,0:19.9:1:30.8:1:1:0:60:23:1:0:0.5 0/1:15:2:1,1:11,2:13,2:0.1333:2,2:38:1:31.5:1:0.37143:4.69047:60:4:0.1333:0:2.5 +3 134884652 . A C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18607;SOR=0.51866;LSEQ=TTTGTTTATTTATAACTTAA;RSEQ=AATTGCTGTTTGTTTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:33:33,0:32,2:34,33:0.4925:2,1:26.1:1:32.7:1:0.49254:0:60:66:0.4925:0:1.2 0/1:30:10:10,0:17,3:20,10:0.3333:2,0:25:1:31.9:1:0.53202:0:60:20:0.3448:0:1 +3 134884695 . G C 150 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=ACTTACAACTCTGACACATA;RSEQ=AAACTATCCTCTACATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:25:24,1:93,3:96,25:0.2066:1,1:22.4:1:32.5:1:1:1.28874:60:50:0.2083:0:1.1 0/0:67:0:0,0:65,2:67,0:0:1,0:23.1:1:31.4:1:1:0:60:32.5:1:0:0.2 +3 134885042 . A C 174 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACAATCATCACTCCATCTC;RSEQ=ATCCAAGAGCAGCCTAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:40:0,40:0,90:90,40:0.3077:1,1:22.4:1:32.7:1:1:0:60:80:0.315:0:1.1 0/0:58:0:0,0:1,57:58,0:0:1,0:21.2:1:30.9:1:1:0:60:57:1:0:0.1 +3 134885561 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05319;SOR=Inf;LSEQ=CACAGTCCCGCCAGGCTTCT;RSEQ=CAAGACCTTGGCTGGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:45,0:0:1,0:24.5:1:32.8:1:1:0:59.6:44:1:0:0.1 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:25:1:31.5:1:1:0:60:4:0.1429:0:1.5 +3 134885704 . C A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGGTGAGCCCCTATCTGG;RSEQ=CTGGGGCCTAGATGGAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:0:0,0:297,136:433,0:0:2,0:25:1:31.4:1:1:0:59.9:35.083:1:0:0.1 0/1:274:31:22,9:169,74:243,31:0.1131:2,2:19.8:1:27.3:1:1:1.07:60:62:0.1152:0:1.1 +3 134885719 . G T 62 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07358;SOR=4.23356;LSEQ=TCTGGCCTGGGGCCTAGATG;RSEQ=AGGTACCTGGAACAGACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:2:0,2:334,195:529,2:0.0038:2,0:1:0:23:1:0.1372:0:60:4:0.0039:0:1 0/1:381:6:2,4:245,130:375,6:0.0157:2,2:11.8:1:24.2:1:0.19014:3.75567:60:12:0.0161:0:1 +3 134885886 . A G 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ACCCGGTGTCTGACCCCCAC;RSEQ=GGCCACTGAGTCAAGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:70,226:296,0:0:2,0:24.3:1:31.2:1:1:0:60:36:0.9965:0:0.1 0/1:232:13:5,8:61,158:219,13:0.056:2,2:25.6:1:30.6:1:0.52671:1.62:60:26:0.0568:0:1.3 +3 134898742 . C T 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0197;SOR=1.21501;LSEQ=TACATTGACCCCTTCACTTA;RSEQ=GAGGATCCCAACGAAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1252:556:260,296:349,345:694,556:0.4441:2,2:25.1:1:30.5:1:0.23187:1.15153:59.9:41.769:0.4404:0:1.1 0/1:1076:530:279,251:294,249:543,530:0.4926:2,2:25.4:1:29.4:1:0.625:1.06215:60:74.714:0.4906:0:1.2 +3 134898960 . G A 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=TCTTTCTCCTCAGAAGATGA;RSEQ=TCTGAACTATCTACATGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:1,82:83,0:0:1,0:22.4:1:32.7:1:1:0:59.5:82:1:0:0.1 0/1:42:9:0,9:1,32:33,9:0.2143:1,0:18.2:1:29.9:1:1:0:60:18:0.2143:0:1.2 +3 134911143 . A AAAAACAAACTCACATATATTCTGAAATTCCACTT 111 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAAATTAAGTGTGGGG;RSEQ=AAAACAAACTCACATATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:12,0:2,0:2,12:0.8571:0,0:18.8:1:31:1:1:0:57.5:24:0.8571:0.6429:0.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134911712 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20032;SOR=Inf;LSEQ=TGCACTTGGATGCAGGTGAA;RSEQ=GATGGCTGGGGAGAGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:63,181:244,0:0:2,0:23.8:1:30.2:1:1:0:59.9:39.667:1:0:0.2 0/1:199:2:1,1:56,140:196,2:0.0101:2,2:28.5:1:29.5:1:0.49392:2.49:60:4:0.0101:0:1 +3 134911917 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAAATGAATAGAGAGGG;RSEQ=CAAAGAATGGCCATTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:30:1:32.5:1:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:34:0:31:0:1:0:60:2:1:0:0 +3 134912008 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=TGTGATTCATGCAGACATCC;RSEQ=CGGCCATCTCTGCCTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:33.3:1:31.3:1:1:0:60:8:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:39.5:1:32:1:1:0:60:4:1:0:0 +3 134912028 . T C 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=GCGGCCATCTCTGCCTTTCA;RSEQ=CAGCACAGCCACCCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:23.5:1:33.5:1:1:0:60:8:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:37.5:1:28:1:1:0:60:4:1:0:0 +3 134920243 . G T 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41123;SOR=0.30461;LSEQ=AGAAGCTGACAAGCAGCAGG;RSEQ=CCACAACATCTCTCCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:5:3,2:282,85:367,5:0.0134:2,2:16.8:1:27.8:1:0.33301:2.2062:60:4:0.0109:0:1 0/0:243:1:1,0:188,53:241,1:0.0041:2,0:23:0:24:0:1:0:60:2:0.0042:0:1 +3 134920546 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02039;SOR=Inf;LSEQ=TCCTTGGTGAGTCCTTCTTG;RSEQ=CATTCTCAAGTAGAAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:0:0,0:169,418:587,0:0:2,0:24.8:1:32:1:1:0:60:82.857:0.9983:0:0.1 0/1:501:5:3,2:174,322:496,5:0.01:2,2:12.4:1:25.4:1:0.35126:2.77:60:10:0.01:0:1.2 +3 134920603 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50886;SOR=0;LSEQ=ACTCTACATGGCTGGGAACT;RSEQ=TGACAGGGCACACTGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:16,173:189,2:0.0105:2,0:16:0:31:1:1:0:60:4:0.0106:0:1 0/0:143:0:0,0:15,128:143,0:0:2,0:22.2:1:31.7:1:1:0:60:286:1:0:0.1 +3 134959888 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3515;SOR=0.37827;LSEQ=CTGTCATAATTCACAAGATA;RSEQ=GGGAGTGAGAGTTTGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:11:11,0:111,5:116,11:0.0866:1,0:24.2:1:33.6:1:1:0:60:22:0.0866:0:1 0/1:58:2:2,0:51,5:56,2:0.0345:2,0:26:1:30.5:1:1:0:60:4:0.0351:0:1.5 +3 134960304 . T A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09898;SOR=Inf;LSEQ=AGCATGGATGTTGGAACTAA;RSEQ=CAAAGAGCCCAGCATGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:2,47:49,0:0:1,0:22.1:1:30.1:1:1:0:60:23.5:1:0:0.1 0/1:23:2:1,1:1,20:21,2:0.087:1,2:33:0:28.5:1:0.16996:14.49:60:4:0.087:0:1 +3 134960472 . T C 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTACCCTGCTTCTAAGTG;RSEQ=TCAGGTTCTGTGTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:16.8:1:32.8:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134966964 . C T 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACTACAATGTGGCCCCTG;RSEQ=TTTCTAGGAGCCCAATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:18,0:18,2:0.1:1,0:7.5:1:32:0:1:0:60:4:0.1053:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:33.8:1:32.3:1:1:0:60:8:1:0:0 +3 134967265 . G A 151 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.0907;LSEQ=CAGAAGGACCGGAACAGCCG;RSEQ=CCCCGGTTTGCGGAGATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:918:33:19,14:463,421:884,33:0.0359:2,2:25.7:1:30.1:1:0.59805:1.23:60:66:0.037:0:1.1 0/0:891:3:2,1:456,432:888,3:0.0034:2,2:23:1:28.7:1:1:1.89:56:6:0.0034:0:1 +3 134967350 . G A 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGTGGCAACCATCACCGCC;RSEQ=TGTGAGTCTAGTGAAACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:629:0:0,0:248,380:628,0:0:2,0:24:1:31.2:1:1:0:59.9:313:1:0:0.2 0/1:543:32:12,20:197,314:511,32:0.0589:2,2:23.3:1:30.5:1:1:1.04557:59.1:64:0.0593:0:1.8 +3 134967368 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.52054;LSEQ=CCGTGTGAGTCTAGTGAAAC;RSEQ=GTGATCCCTAAATATGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:34:13,21:144,296:440,34:0.0717:2,2:24.7:1:31.2:1:0.57119:1.27:60:68:0.0722:0:1 0/1:397:85:29,56:108,204:312,85:0.2141:2,2:23.2:1:30.1:1:1:1.02226:60:170:0.2168:0:1.4 +3 134967413 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.27263;SOR=0;LSEQ=CATGGTCAGGGGCATAGCCA;RSEQ=CAGCCTCTGACCATGATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:3:2,1:28,201:229,3:0.0129:2,2:11:1:30:1:0.04475:14.05:60:6:0.013:0:1 0/0:161:0:0,0:33,128:161,0:0:2,0:21.9:1:31:1:1:0:60:160:1:0:0.2 +3 134967507 . A C 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15331;LSEQ=AGCAACATGCATGAAGAAAG;RSEQ=CAGGAGAACATTGCAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:5:0,5:0,52:52,5:0.0877:1,0:22.4:1:30.2:1:1:0:60:4:0.0714:0:1 0/1:20:2:0,2:0,18:18,2:0.1:1,0:14:1:31.5:1:1:0:60:4:0.1:0:1 +3 134967823 . A G 45 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATATCTGGGGAGGTTGTG;RSEQ=TAAAATATGCATATTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:4,1:5,3:0.375:2,0:15.7:1:29:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 134968032 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06852;SOR=2.15558;LSEQ=GCTGATTTAGGATTCCATGA;RSEQ=GAAGAAAGGTTCAGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:21:20,1:83,0:83,21:0.2019:1,1:24.4:1:32.7:1:0.20192:0:58.5:20:0.202:0:1 0/1:48:17:17,0:29,1:30,17:0.3542:1,1:23.5:1:32.9:1:1:0:60:34:0.3617:0:1 +3 134968079 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15162;SOR=Inf;LSEQ=CTATAATCCTCATTCCATCA;RSEQ=GGATGCTGCCTTCCATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:227,9:236,0:0:1,0:25.5:1:33:1:1:0:59.9:58:1:0:0.2 0/1:151:2:2,0:135,14:149,2:0.0132:2,0:13:1:32:0:1:0:60:4:0.0132:0:1.5 +3 134968084 . G T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15304;SOR=Inf;LSEQ=ATCCTCATTCCATCAGGGAT;RSEQ=CTGCCTTCCATGAAGTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:238,17:255,0:0:2,0:25.2:1:32.1:1:1:0:59.9:35.429:1:0:0.1 0/1:165:2:1,1:146,16:162,2:0.0121:2,2:9:1:23.5:1:0.19714:8.88358:60:4:0.0123:0:1 +3 134968089 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15983;SOR=Inf;LSEQ=CATTCCATCAGGGATGCTGC;RSEQ=TTCCATGAAGTCAGCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:250,27:277,0:0:2,0:24.9:1:31.1:1:1:0:59.9:38.571:1:0:0.1 0/1:185:2:1,1:159,24:183,2:0.0108:2,2:25.5:1:29:1:0.25264:6.51153:60:4:0.0109:0:1 +3 134968440 . C CGTCT 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0.82504;SOR=1.0839;LSEQ=TGGCCTCATCCCTGGAGCTC;RSEQ=GTCTCTGTATAGACCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:19:0,19:1,85:86,19:0.1792:1,1:28.9:1:31.4:1:1:0:60:38:0.1863:0.0283:0.8 0/1:47:9:0,9:0,38:38,9:0.1915:1,0:22.7:1:31.6:1:1:0:60:18:0.1957:0.0426:0.6 +3 134968465 . T C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTATAGACCAGGCCTGGA;RSEQ=GGGGAGCACCTTGGAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:72:0,72:0,0:0,72:1:0,1:24.7:1:29.7:1:1:0:60:35:1:0:1 1/1:25:25:0,25:0,0:0,25:1:0,1:19.2:1:29.6:1:1:0:60:50:1:0:1 +3 134968574 . T A 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=AGTTATAGCCATATGTCATT;RSEQ=GCCTAATCACCCAGAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:17.5:1:32:1:1:0:60:8:0.4444:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:47:1:30.5:1:1:0:60:4:1:0:1 +3 134968601 . A G 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TCACCCAGAGTCTCTTCCCC;RSEQ=TTTAAGTTTTTAAACTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:34.8:1:28.5:1:1:0:60:3:0.6:0:1.5 0/0:2:0:0,0:0,2:2,0:0:0,0:25.5:1:32:0:1:0:60:4:1:0:1 +3 134977790 . GT G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16342;SOR=Inf;LSEQ=GAACATGGCTTTAGTGATGA;RSEQ=TTTGATCTGCGAAAAGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:220,45:265,0:0:2,0:23.7:1:29.8:1:1:0:60:43.167:1:0:0.1 0/1:181:2:1,1:140,38:178,2:0.011:2,2:15.5:1:33:0:0.38734:3.65:60:4:0.0114:0:0 +3 134978060 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51543;SOR=0;LSEQ=TGTACTGGAGAGACTGGCTT;RSEQ=TCAGCTGAGGAATGCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:2,159:161,2:0.0123:1,2:13.5:1:28.5:1:0.03658:65.10:60:4:0.0125:0:1 0/0:112:0:0,0:3,109:112,0:0:1,0:21.8:1:31.6:1:1:0:60:36.333:1:0:0.1 +3 134978236 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGACAAAACAATATGCATC;RSEQ=GGAGAACAAGAGTAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:20.5:1:33:1:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:33:0:1:0:60:2:1:0:1 +3 134978264 . T C 51 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGTAAACCCAGCTCCCA;RSEQ=TCTCAGTGGGCTGCAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:24:1:32.7:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:45:0:34:0:1:0:60:2:1:0:1 +3 135644725 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=GCTCAAGTGATTCTCCCACC;RSEQ=CAGCCTCCTCTCTGTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:116,50:166,2:0.0118:2,2:21.5:1:28.5:1:0.51625:2.30705:60:4:0.0119:0:1 0/0:156:0:0,0:104,51:155,0:0:2,0:21.8:1:28.9:1:1:0:60:30:1:0:0.2 +3 135644807 . C G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00085;SOR=1.94057;LSEQ=AATATCTGGGGCCTGCAGTT;RSEQ=TTATACAGGCCTATCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:58:36,22:148,123:271,58:0.1763:2,2:22.3:1:32.9:1:0.31212:1.36:60:116:0.1785:0:1.1 0/1:269:79:48,31:101,89:190,79:0.2937:2,2:23:1:31.4:1:0.28262:1.36:60:158:0.2981:0:1.2 +3 135644964 . C T 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAATCCAGGGAAGGCTACTG;RSEQ=GGAAATCAAGAAAATGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:32:8,24:52,121:173,32:0.1561:2,2:23:1:30.3:1:0.67456:1.28769:60:31:0.1535:0:1.2 0/0:193:0:0,0:60,133:193,0:0:2,0:23:1:29.9:1:1:0:60:95.5:1:0:0.1 +3 135644998 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50325;SOR=0;LSEQ=ATGTTGGTAACCTATAAGGA;RSEQ=AAGAAAGTTTCAGCTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:44,101:145,2:0.0136:2,2:26.5:1:31.5:1:0.51999:2.28:60:4:0.0138:0:2.5 0/0:120:0:0,0:34,86:120,0:0:2,0:26.4:1:30.7:1:1:0:60:240:1:0:0.1 +3 135645021 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50777;SOR=0;LSEQ=GAAAGTTTCAGCTTAATTGT;RSEQ=CCCATGCTAAACATGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:43,89:132,2:0.0149:2,2:46:1:31.5:1:0.55056:2.06:60:4:0.015:0:1 0/0:101:0:0,0:33,67:100,0:0:2,0:27.5:1:28.7:1:1:0:60:32.333:0.9898:0:0.1 +3 135645058 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13573;SOR=Inf;LSEQ=CTTGTAACCAGTTCAGAGCT;RSEQ=AACATAATTTAGATCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:28,74:102,0:0:2,0:24.7:1:31.4:1:1:0:60:33:1:0:0.1 0/1:60:2:1,1:15,43:58,2:0.0333:2,2:23.5:1:28.5:1:0.46554:2.81:59:4:0.0333:0:1 +3 136076644 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=0;LSEQ=CAGATTAGGAGGTGGATACT;RSEQ=TTGTCCTTTCTGATTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:3,8:11,2:0.1538:2,2:25:1:27.5:1:1:2.45:60:4:0.1667:0:1 0/0:11:0:0,0:3,8:11,0:0:2,0:27.1:1:31.6:1:1:0:60:22:1:0:0.1 +3 136082119 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50758;SOR=Inf;LSEQ=TATAAAATGACCTAGTTTAA;RSEQ=TGAGATGAGATACCTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:29.3:1:30.2:1:1:0:60:26:1:0:0.2 0/1:20:2:2,0:18,0:18,2:0.1:1,0:47:1:30:0:1:0:60:4:0.1:0:1 +3 136082291 . C A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50736;SOR=Inf;LSEQ=CAGTGTTTCCTTAATAATAT;RSEQ=ACCATAGTCATTGTAATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:11,57:68,0:0:2,0:21.7:1:31.4:1:1:0:59.9:21.667:1:0:0.2 0/1:91:2:1,1:21,68:89,2:0.022:2,2:7:1:26.5:1:0.42711:3.19:60:4:0.0222:0:1 +3 136196071 . C T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41667;SOR=Inf;LSEQ=ACTACTGTCATTTTGATTCC;RSEQ=AGCATTTTAGTACTGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:30.5:1:32.8:1:1:0:60:8:0.8:0:1.3 1/1:7:7:7,0:0,0:0,7:1:0,0:25.6:1:29.9:1:1:0:60:14:1:0:1.1 +3 136196178 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52341;SOR=Inf;LSEQ=TTTTAGGTAACTGTCATTTA;RSEQ=GAAGGCATCACTATACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:18,17:35,0:0:2,0:30.9:1:31.5:1:1:0:60:34:1:0:0.1 0/1:57:2:1,1:30,25:55,2:0.0351:2,2:33:0:29.5:1:1:1.19614:60:4:0.0357:0:1 +3 137443260 . G A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01206;SOR=0;LSEQ=GCTGATGAAGATGATGATAT;RSEQ=ATGATGCAGATGATGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:2,3:18,22:40,5:0.1111:2,2:29.6:1:28.2:1:1:1.22176:52.2:4:0.093:0:1 0/0:61:0:0,0:28,33:61,0:0:2,0:25.3:1:30.7:1:1:0:54.7:19.333:1:0:0.3 +3 137483362 . G T 68 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGGTCCCAGCCCCTGGT;RSEQ=CCTGAAGCCCCCCGGCCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:18:1:29.4:1:1:0:58.2:10:1:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 137483689 . C T 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23275;SOR=0.24555;LSEQ=TTCATGGTATGGTCCCGGGG;RSEQ=CAGCGGCGCAAGATGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:5:3,2:255,206:461,5:0.0107:2,2:28.4:1:28.2:1:1:1.21:53.2:10:0.0109:0:1.4 0/0:377:1:0,1:218,158:376,1:0.0027:2,0:1:0:22:0:0.42175:0:57:2:0.0027:0:1 +3 138374293 . C T 169 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01847;LSEQ=CACTTTAGTAGTCCAGCTTT;RSEQ=CCTGAGCGCCTCATCAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:890:50:20,30:406,432:838,50:0.0562:2,2:24.2:1:30.1:1:0.30778:1.40918:60:100:0.0574:0:1 0/0:912:1:0,1:424,486:910,1:0.0011:2,0:1:0:30:0:1:0:47:2:0.0011:0:1 +3 138374926 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11008;SOR=Inf;LSEQ=CCACTTGAATAAAACAGGCA;RSEQ=CTAAAACTGAGCTCAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:168,58:226,0:0:2,0:24.8:1:32.5:1:1:0:60:36.667:1:0:0.1 0/1:209:3:1,2:148,58:206,3:0.0144:2,2:15:1:27:1:0.19866:5.05733:60:6:0.0145:0:1 +3 138376323 . T C 157 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01204;SOR=0.07558;LSEQ=ATTGGAATAAAATATAATAA;RSEQ=TATTTTAAATTTCTAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:31:31,0:11,0:11,31:0.7381:0,1:21:1:31.8:1:1:0:59.4:14.5:0.725:0:1.2 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:3:0:29:0:1:0:60:2:0.1667:0:1 +3 138376717 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=TAATTTCCTTCATTTTTCTG;RSEQ=TGGGTTCCAAATATAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:21,139:160,2:0.0123:2,2:13:1:29.5:1:0.25389:6.49:60:4:0.0123:0:1 0/0:161:0:0,0:24,137:161,0:0:2,0:24.2:1:31.3:1:1:0:60:79.5:1:0:0.1 +3 138383144 . A C 95 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGGCTGTGAGTAGACT;RSEQ=ATGTTCACAGTACTTAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:1,2:3,7:0.7:2,0:23.3:1:33.9:1:0.3:0:56.3:14:0.7:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 138383201 . C A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGATCATGCTAGGGGTTGGG;RSEQ=ACATTTTAGTTAGTTTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:23.5:1:33:0:1:0:47:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 138383765 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49802;SOR=0;LSEQ=TCTAACAAGAAATGAAGCAA;RSEQ=AGATAAAAAACACTAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:95,0:95,2:0.0206:1,2:24:1:27.5:1:0.02062:0:60:4:0.0208:0:1 0/0:90:0:0,0:88,2:90,0:0:1,0:23.3:1:30.6:1:1:0:60:180:1:0:0 +3 138401270 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52015;SOR=Inf;LSEQ=TTCACTGCGCAAAGCACAGT;RSEQ=ACTTACTAGAGGTCCGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:25,29:54,0:0:2,0:30.4:1:32.2:1:1:0:54.1:53:1:0:0.9 0/1:84:2:1,1:39,43:82,2:0.0238:2,2:37.5:1:30:1:1:1.10:22:4:0.0241:0:1.5 +3 138401299 . A C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00081;SOR=0.30705;LSEQ=GAGGTCCGAGAGGATAACAC;RSEQ=TGGGTTCAGGGGTACTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:40:14,26:9,13:22,40:0.6452:2,2:28.1:1:32.1:1:0.78446:1.28043:54.1:80:0.6452:0:1.3 0/1:87:31:12,19:24,32:56,31:0.3563:2,2:30.5:1:30.4:1:0.82117:1.18516:51.9:14.5:0.3452:0:1.1 +3 138402350 . GA G 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54682;SOR=0;LSEQ=AAATCATTTTATAAGAGGGG;RSEQ=AAAAAAAAGCATTTAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:3,0:48,0:48,3:0.0577:1,0:30.3:1:28:1:1:0:60:2:0.0408:0.0192:0 0/0:26:0:0,0:26,0:26,0:0:1,0:26.7:1:28.4:1:1:0:60:52:1:0:0 +3 138403390 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.20977;LSEQ=TTCCTGAGGCTGACAGCTGG;RSEQ=CCTACTACTCCCATAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:159:123:119,4:36,0:36,123:0.7736:1,1:26.8:1:30.7:1:0.57505:0:39.3:246:0.7736:0:1 0/1:89:37:34,3:49,3:52,37:0.4157:2,2:26.6:1:29.6:1:0.68973:1.43512:37.2:74:0.4205:0:1.1 +3 138403728 . T A 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22559;SOR=Inf;LSEQ=TCATATCAATCAATAACACC;RSEQ=GCTCCCAACATATACACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:16,157:173,0:0:2,0:22.1:1:30.4:1:1:0:60:85.5:1:0:0.1 0/1:157:2:1,1:11,144:155,2:0.0127:2,2:10:1:22.5:1:0.14748:12.58:60:4:0.0129:0:1 +3 138412084 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCTGGGACCACAGGTGCG;RSEQ=ACCTCCACGCCCAGCTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:1:28.5:1:1:0:60:4:1:0:1 +3 138413373 . C T 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTGTAAGTGACTATGTG;RSEQ=TGAGTTCTGAGTCCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:9,0:9,2:0.1818:0,2:22.5:1:28:1:0.18182:0:60:4:0.2:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 138413557 . A T 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49961;SOR=0;LSEQ=TTTCTTTCTTATGAGACATC;RSEQ=AGGAGACACCCTCATCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:0,2:126,25:151,2:0.0131:2,0:15:1:24.5:1:0.03019:0:60:4:0.0132:0:1 0/0:138:0:0,0:112,26:138,0:0:2,0:22.2:1:29.3:1:1:0:60:45:1:0:0.1 +3 138417989 . G A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15809;LSEQ=AATTGTGCAAACACCACAGC;RSEQ=AACTTTCAGTAAATTTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:123:99:7,92:4,20:24,99:0.8049:2,2:22:1:31.2:1:0.22252:2.60302:59.8:48.5:0.8083:0:1.2 0/1:107:42:4,38:7,58:65,42:0.3925:2,2:25.1:1:30.2:1:1:1.14508:60:41:0.3981:0:1.2 +3 138418082 . T C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10847;SOR=0.24333;LSEQ=CCATAAAAAAAAAAAAAAGG;RSEQ=AGATCCTTTAATAATTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:0,14:0,4:4,14:0.7778:0,1:25.9:1:32.4:1:1:0:57.9:28:0.7778:0:1.8 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:29:1:32:1:1:0:60:8:0.4444:0:1.5 +3 138423164 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20865;SOR=Inf;LSEQ=CATGTGCATACTTACCCACA;RSEQ=TCACAGACTGTTCTTGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:143,11:154,0:0:2,0:23.1:1:32.7:1:1:0:60:153:1:0:0.1 0/1:130:2:1,1:115,13:128,2:0.0154:2,2:14:1:27:1:0.20453:8.55932:60:4:0.0156:0:1 +3 138423181 . CAT C 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ACACTCACAGACTGTTCTTG;RSEQ=ATGAGTTACGGTCTTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:34:28,6:159,30:189,34:0.1525:2,2:24.8:1:31.9:1:0.80141:1.13502:59.4:33:0.1493:0.0269:0.3 0/0:204:0:0,0:153,51:204,0:0:2,0:22.7:1:29.7:1:1:0:60:101:1:0:0.1 +3 138426428 . T C 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTAATTGGAACTGCTCTC;RSEQ=CTCCATCAAAATTAGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:16.3:1:32.7:1:1:0:54:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 138433543 . G A 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12422;SOR=Inf;LSEQ=GAGCTCAGTACCATGAAAAA;RSEQ=ACCAGCCCTGACATGAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:138,250:388,0:0:2,0:26.1:1:32.6:1:1:0:60:128.333:1:0:0.6 0/1:400:4:2,2:149,247:396,4:0.01:2,2:27.3:1:23.5:1:0.63468:1.66:60:3:0.0076:0:3 +3 138433568 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16873;LSEQ=GCCCTGACATGAACCTGTAA;RSEQ=GAAGCAGACAAAAACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:295:217:58,159:22,56:78,217:0.7356:2,2:24.5:1:30.8:1:0.88204:1.0767:60:107.5:0.7338:0:1.1 0/1:273:87:30,57:53,132:185,87:0.3187:2,2:26.5:1:29.9:1:0.32784:1.31:60:86:0.3209:0:1.1 +3 138433625 . TTTTG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16578;SOR=Inf;LSEQ=GTACCACGAAAAACATCTCT;RSEQ=TTTGTTTGTTTGTTTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:3,88:91,0:0:1,0:24.4:1:30.4:1:1:0:60:29.333:1:0:0.6 0/1:63:2:0,2:8,53:61,2:0.0317:2,0:34.5:1:29:1:1:0:60:4:0.0323:0:0 +3 138452310 . T A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11875;SOR=Inf;LSEQ=AATAAAATAAATACAAATTA;RSEQ=TTTAATGAAAGAAATGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:56,244:300,0:0:2,0:22.9:1:30.5:1:1:0:59.9:74:1:0:0.1 0/1:291:3:2,1:75,212:287,3:0.0103:2,2:12.3:1:25.7:1:0.17311:5.61:60:2:0.007:0:1.3 +3 138453794 . A T 116 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=1;SSF=0.03181;SOR=0.13668;LSEQ=CAAGAAATTAAAAAAAAAAA;RSEQ=TTTTTTTTTTTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:19:0,19:0,3:3,19:0.76:0,1:15.9:1:27.4:1:1:0:58.9:3.75:0.7895:0:1.4 0/1:7:2:0,2:0,4:4,2:0.2857:0,0:6:0:31.5:1:1:0:60:4:0.2857:0:2.5 +3 138456483 . TAA T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.25254;SOR=0;LSEQ=CACATTTTTAAAGTCAGAAA;RSEQ=AATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:3:3,0:174,15:189,3:0.0156:2,0:25.3:1:30:1:1:0:58.3:6:0.0157:0.0104:0.7 0/0:164:0:0,0:136,28:164,0:0:2,0:23.3:1:28:1:1:0:59.5:81:1:0:0.2 +3 138456780 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23375;SOR=0;LSEQ=GTAAATGTTATATTTATGCT;RSEQ=AAAAATCACATTACAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:19,177:196,2:0.0101:2,2:35:1:30.5:1:0.19228:9.11:60:4:0.0102:0:1 0/0:211:0:0,0:41,170:211,0:0:2,0:23.9:1:30.7:1:1:0:59.8:104.5:1:0:0.1 +3 138461345 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22003;SOR=Inf;LSEQ=TCTAAAAATGCAGTTGTATT;RSEQ=GGGTAAAAATGAGAAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:155,21:176,0:0:2,0:23.5:1:31.6:1:1:0:60:43:1:0:0.1 0/1:156:2:1,1:124,30:154,2:0.0128:2,2:25:1:28:1:0.35897:4.08248:60:4:0.013:0:1 +3 138461381 . TA T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.04979;SOR=0;LSEQ=ATTTATTACAAAATATTTCT;RSEQ=AAAAAATATAATCCTACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:4:2,2:244,74:318,4:0.0124:2,2:26:1:30:1:0.23761:3.28205:60:8:0.0125:0.0031:0.3 0/0:358:0:0,0:253,105:358,0:0:2,0:23.5:1:28.3:1:1:0:60:357:1:0:0.1 +3 138474572 . C CT 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.72802;SOR=0.66593;LSEQ=AGATATATTAAGAATTTGTA;RSEQ=TTTTTTTTTATTTTTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:5:3,2:249,65:314,5:0.0156:2,2:17.4:1:29:1:0.28285:2.54452:60:4:0.0126:0:0.4 0/1:287:3:2,1:219,63:282,3:0.0105:2,2:29.7:1:24.7:1:0.53515:1.73424:60:2:0.0071:0:1.7 +3 138474986 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3446;SOR=0.38458;LSEQ=AATTATAGAATATTACAGAA;RSEQ=GGTGAAAATAATAGAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:0,18:0,5:5,18:0.7826:0,1:23.7:1:30.3:1:1:0:59.7:36:0.7826:0:1.1 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:28.3:1:28:1:1:0:60:8:0.5714:0:1 +3 138478246 . AT A 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.24788;SOR=Inf;LSEQ=GCAAAACAACCATCAGCCAA;RSEQ=TTTATACCAAGATATGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:14,131:145,0:0:2,0:23.5:1:30:1:1:0:60:47.333:1:0:0.1 0/1:152:3:2,1:28,121:149,3:0.0197:2,2:6:1:26.7:1:0.09956:8.47:60:6:0.0197:0.0132:0.7 +3 138661770 . CACAA C 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.29151;SOR=0;LSEQ=AATTTTCACGCTAGACAAAG;RSEQ=ACAGACATGCACACAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:4,1:18,2:20,5:0.2:2,2:17.4:1:30.8:1:0.50435:2.16466:60:10:0.2:0.04:0.2 0/0:10:0:0,0:10,0:10,0:0:0,0:13:1:29.3:1:1:0:60:9:1:0:0 +3 138661895 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.13879;SOR=Inf;LSEQ=AGCCTCTAGGGCTTCCTGCT;RSEQ=CAGCTGAGCCTCCCTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:193,14:207,0:0:2,0:24.1:1:32.2:1:1:0:60:33.5:1:0:0.1 0/1:124:2:1,1:113,9:122,2:0.0161:2,2:22.5:1:28:1:0.15539:11.96401:60:4:0.0164:0:2 +3 138661896 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14296;SOR=Inf;LSEQ=GCCTCTAGGGCTTCCTGCTC;RSEQ=AGCTGAGCCTCCCTCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:198,15:213,0:0:2,0:23.9:1:31.4:1:1:0:60:52.25:1:0:0.1 0/1:130:2:1,1:115,13:128,2:0.0154:2,2:23:1:27.5:1:0.20453:8.55932:60:4:0.0159:0:1 +3 138661897 . A ATCCT 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00837;SOR=Inf;LSEQ=CCTCTAGGGCTTCCTGCTCC;RSEQ=GCTGAGCCTCCCTCTCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:202,16:218,0:0:2,0:23.8:1:30.8:1:1:0:60:71.667:1:0:0.1 0/1:138:5:4,1:117,16:133,5:0.0362:2,2:18.2:1:30.7:1:0.48713:1.81832:60:10:0.0373:0.0145:0 +3 138661907 . C T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16591;SOR=Inf;LSEQ=TTCCTGCTCCAGCTGAGCCT;RSEQ=CCTCTCCATCCTGCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:231,36:267,0:0:2,0:22.8:1:32:1:1:0:60:65.75:1:0:0.2 0/1:184:2:1,1:149,33:182,2:0.0109:2,2:7:0:31:1:0.33624:4.46317:60:4:0.011:0:1.5 +3 138661990 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19983;LSEQ=CCTGAGAATCCCCGTGGCTT;RSEQ=GTCTCCTGCCTTGTAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:861:233:132,101:363,264:627,233:0.2706:2,2:26.3:1:29.4:1:0.75661:1.052:60:57.25:0.272:0:1.2 0/1:841:58:31,27:449,332:781,58:0.069:2,2:23.2:1:28.4:1:0.5835:1.17767:59.8:28:0.068:0:1.3 +3 138662193 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.19074;SOR=Inf;LSEQ=CCACCAGCCGGCCTGGACCT;RSEQ=CCGCCACATTGCTGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:18,189:207,0:0:2,0:20.4:1:31.1:1:1:0:59.7:14.923:1:0:0.4 0/1:161:2:0,2:14,145:159,2:0.0124:2,0:22.5:1:27.5:1:1:0:60:4:0.0126:0:2 +3 138662226 . C CG 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.20992;SOR=0.34636;LSEQ=TGGCCAGGCCCCGAGATAGA;RSEQ=GGGGGGGGGGCAGTGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:9:0,9:1,91:92,9:0.0882:1,0:32.3:1:32.2:1:1:0:60:18:0.1023:0:0.7 0/1:62:2:0,2:0,59:59,2:0.0323:1,0:45:1:30.5:1:1:0:60:4:0.0345:0:2 +3 138662227 . G GGGGGGGGGGGGT 78 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.02782;SOR=0;LSEQ=GGCCAGGCCCCGAGATAGAC;RSEQ=GGGGGGGGGCAGTGAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:9:0,9:1,99:100,9:0.0796:1,0:34.3:1:24.7:1:1:0:57.4:18:0.0857:0.0708:0.1 0/0:61:0:0,0:0,59:59,0:0:1,0:19.5:1:29.9:1:1:0:59.5:58:0.9667:0:0.5 +3 138662229 . G C 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=CCAGGCCCCGAGATAGACGG;RSEQ=GGGGGGGCAGTGAGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:1,111:112,0:0:1,0:22.9:1:31.2:1:1:0:59.1:55:1:0:0.4 0/1:55:8:0,8:0,47:47,8:0.1455:1,0:22.4:1:29.3:1:1:0:60:16:0.1455:0:1 +3 138663113 . AC A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.00722;SOR=Inf;LSEQ=GGGAATCGACAAGGCAAAAA;RSEQ=AAAAACAAAACAAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:263,53:316,0:0:2,0:21.7:1:32.6:1:1:0:60:632:1:0:0.3 0/1:312:7:6,1:236,69:305,7:0.0224:2,2:21.1:1:30.3:1:1:1.75:54.9:14:0.0225:0.0096:1.1 +3 138663179 . A G 259 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=TAGAAAATTTGGTCCCCCAA;RSEQ=CAACAAGCTACAGTACAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:791:243:149,94:314,232:546,243:0.3072:2,2:28.4:1:32.8:1:0.34749:1.17:60:120.5:0.3082:0:1.1 0/0:788:0:0,0:426,361:787,0:0:2,0:26.5:1:29:1:1:0:60:97.375:1:0:0.2 +3 138663401 . G C 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22304;SOR=Inf;LSEQ=GGACTTGCATCGAAAGATCC;RSEQ=GGGACATTTGTTTTTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:14,124:138,0:0:2,0:23.8:1:31.4:1:1:0:59.9:137:1:0:0.1 0/1:124:2:1,1:13,109:122,2:0.0161:2,2:7.5:1:27.5:1:0.21387:8.12:60:4:0.0164:0:1.5 +3 138664405 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21613;SOR=Inf;LSEQ=GCGCGTCCCTGCATCCTCGC;RSEQ=TCCGTCTGCACCGGCATGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:151,51:202,0:0:2,0:23.9:1:29.8:1:1:0:60:27.857:1:0:0.2 0/1:176:2:1,1:118,56:174,2:0.0114:2,2:18.5:1:29:1:0.54409:2.09746:60:4:0.012:0:1.5 +3 138664517 . G A 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.052;SOR=Inf;LSEQ=CATCATGGCGAGCTCGGGCT;RSEQ=CCGGGCACAAGCGAACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:109,234:343,0:0:2,0:27.6:1:32.4:1:1:0:59.9:67.6:1:0:0.2 0/1:315:4:3,1:115,196:311,4:0.0127:2,2:14:1:23.8:1:0.14972:5.09:60:8:0.0128:0:1.5 +3 138664596 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48663;SOR=0;LSEQ=GCGGTGGCTGGGCTGGCAGG;RSEQ=CTGAGCTGGCCCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:5,11:16,2:0.1111:2,2:27.5:1:32:0:1:2.10:60:4:0.125:0:1.5 0/0:16:0:0,0:6,10:16,0:0:2,0:11.4:1:31.6:1:1:0:58.1:32:1:0:0.3 +3 138664682 . G T 36 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.24891;SOR=0;LSEQ=CGCGTGCAGATGGTGTGCGT;RSEQ=CGGATGCGGGTGGGGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:0,3:91,60:151,3:0.0195:2,0:7:1:23:1:0.06653:0:60:2:0.0133:0:1 0/0:141:0:0,0:78,62:140,0:0:2,0:21.9:1:31.2:1:1:0:59.9:27:0.9926:0:0.4 +3 138664683 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24964;SOR=0;LSEQ=GCGTGCAGATGGTGTGCGTG;RSEQ=GGATGCGGGTGGGGGTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:1,2:92,62:154,3:0.0191:2,2:9.7:1:30:1:0.56727:2.94706:60:6:0.0192:0:1.3 0/0:141:0:0,0:79,62:141,0:0:2,0:1:0:17:0:1:0:60:0:0:0:2 +3 138664689 . C T 39 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.09647;LSEQ=AGATGGTGTGCGTGCGGATG;RSEQ=GGGTGGGGGTGCGGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:1,2:101,69:170,3:0.0173:2,2:8.7:1:29:1:0.56875:2.90929:60:6:0.0182:0:1.3 0/1:158:3:0,3:88,67:155,3:0.019:2,0:1:0:25:1:0.08487:0:60:6:0.0211:0:1.3 +3 138664697 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50072;SOR=0;LSEQ=TGCGTGCGGATGCGGGTGGG;RSEQ=GTGCGGCGGAGGCGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:117,80:197,2:0.0101:2,2:15.5:1:27:1:1:1.45961:60:4:0.0105:0:1 0/0:175:0:0,0:101,74:175,0:0:2,0:22.9:1:29.9:1:1:0:59.9:57.333:1:0:0.4 +3 138664700 . G A 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25012;SOR=0;LSEQ=GTGCGGATGCGGGTGGGGGT;RSEQ=CGGCGGAGGCGGGGGTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:3:3,0:116,80:196,3:0.0151:2,0:14.7:1:20.3:1:0.27516:0:60:2:0.0104:0:2.7 0/0:179:0:0,0:104,74:178,0:0:2,0:23.5:1:30.9:1:1:0:59.9:24.429:0.9942:0:0.4 +3 138664707 . A C 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0025;SOR=Inf;LSEQ=TGCGGGTGGGGGTGCGGCGG;RSEQ=GGCGGGGGTGCGGCCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:131,86:217,0:0:2,0:25:1:30.7:1:1:0:60:42.4:0.9953:0:0.3 0/1:199:8:6,2:110,79:189,8:0.0402:2,2:19.4:1:30.8:1:0.47458:2.15:60:16:0.0426:0:1.4 +3 138664718 . C T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62357;SOR=0.3412;LSEQ=GTGCGGCGGAGGCGGGGGTG;RSEQ=GGCCGGCGGGCCTCCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:139,98:237,3:0.0125:2,2:22.7:1:29.7:1:0.57236:2.82442:60:6:0.013:0:1 0/0:233:1:0,1:131,100:231,1:0.0043:2,0:1:0:23:0:0.43534:0:60:2:0.0045:0:1 +3 138664725 . C T 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.67803;LSEQ=GGAGGCGGGGGTGCGGCCGG;RSEQ=GGGCCTCCCAGGCCATTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:1,2:142,108:250,3:0.0119:2,2:15:1:31.3:1:0.58126:2.61971:60:6:0.0123:0:1 0/0:248:2:0,2:138,108:246,2:0.0081:2,0:16.5:1:20:1:0.19574:0:60:1:0.0042:0:1 +3 138664770 . C T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3725;SOR=3.95603;LSEQ=TTCACTACGCCGGGGGGCAG;RSEQ=GCCATGCTCTGCACGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:1:0,1:105,130:235,1:0.0042:2,0:1:0:26:0:1:0:60:2:0.0044:0:1 0/1:241:4:2,2:113,122:235,4:0.0166:2,2:16.5:1:29.5:1:1:1.08:60:8:0.0175:0:1.3 +3 138664804 . G A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11631;SOR=Inf;LSEQ=CGCGTGTGTACGGCCCGTAC;RSEQ=AGGCGGCCGGGCCCGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:54,97:151,0:0:2,0:23.5:1:31.4:1:1:0:60:150:1:0:0.3 0/1:145:3:2,1:56,86:142,3:0.0207:2,2:16.7:1:22:1:0.56399:3.05:60:2:0.0144:0:1.3 +3 138664810 . G A 41 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47396;LSEQ=TGTACGGCCCGTACGAGGCG;RSEQ=CCGGGCCCGCCAGCCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:43,81:124,2:0.0159:2,2:8:1:29.5:1:1:1.87:60:4:0.0161:0:1 0/1:129:3:2,1:48,78:126,3:0.0233:2,2:17.7:1:26.3:1:0.55923:3.22:60:6:0.0234:0:1 +3 138664812 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4982;SOR=Inf;LSEQ=TACGGCCCGTACGAGGCGGC;RSEQ=GGGCCCGCCAGCCCCTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:36,79:115,0:0:2,0:26.3:1:30.6:1:1:0:60:230:1:0:0.3 0/1:121:2:1,1:43,76:119,2:0.0165:2,2:29.5:1:29:0:1:1.76:60:4:0.0169:0:1 +3 138664851 . G T 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21611;SOR=Inf;LSEQ=ACCACAGCGGCCGCGCCAGG;RSEQ=CTACCGGGGCCCGCGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:46,34:80,0:0:2,0:16.7:1:32.2:1:1:0:60:39:1:0:0.2 0/1:70:2:1,1:36,32:68,2:0.0286:2,2:7:0:30.5:1:1:1.1231:60:4:0.0294:0:2 +3 138664885 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21251;SOR=Inf;LSEQ=CGGCTGCAGCCGCAGCTGCT;RSEQ=CAGCCGCTGCGGCTGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:91,23:114,0:0:2,0:25:1:32.7:1:1:0:60:113:1:0:0.1 0/1:98:2:1,1:74,21:95,2:0.0204:2,2:8:1:27.5:1:0.40399:3.46583:60:4:0.0211:0:1 +3 138664903 . G T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35615;SOR=3.24722;LSEQ=CTGCAGCCGCTGCGGCTGCC;RSEQ=CCATCTGGCAGGAGGCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:0,1:112,52:164,1:0.0061:2,0:1:0:24:0:0.32121:0:60:2:0.0063:0:1 0/1:154:3:1,2:102,49:151,3:0.0195:2,2:27:1:27:1:0.2549:4.12133:60:6:0.02:0:1.7 +3 138665029 . G C 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00551;SOR=Inf;LSEQ=AGCCGTCGGCCCCGGCGCCC;RSEQ=CCACGCCGCACCCGCCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:23,52:75,0:0:2,0:17.6:1:31.3:1:1:0:60:36.5:0.9865:0:0.2 0/1:72:7:3,4:21,44:65,7:0.0972:2,2:11.6:1:30.3:1:0.67918:1.56:60:14:0.0972:0:1.1 +3 138665051 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.15269;SOR=Inf;LSEQ=CACGCCGCACCCGCCTGCGG;RSEQ=GCCTCCGGCCCCGAAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:69,30:99,0:0:2,0:11.5:1:31.8:1:1:0:60:32:1:0:0.2 0/1:64:2:1,1:36,26:62,2:0.0313:2,2:22:0:31.5:1:1:1.37745:60:4:0.0317:0:1.5 +3 138665064 . G A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00137;SOR=Inf;LSEQ=CCTGCGGCGCCTCCGGCCCC;RSEQ=AAGAGCCCCTTGCCGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:115,22:137,0:0:2,0:16.4:1:31.1:1:1:0:60:274:0.9928:0:0.1 0/1:72:6:4,2:55,11:66,6:0.0833:2,2:21.8:1:30.5:1:0.29505:2.46054:60:12:0.087:0:1.2 +3 138665100 . C T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30815;SOR=4.46875;LSEQ=GGCTGGAAGTGCGCGGGCGG;RSEQ=GGCCGGAAGGGCCTCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:1:0,1:267,72:339,1:0.0029:2,0:1:0:26:0:0.21471:0:60:2:0.003:0:1 0/1:230:3:1,2:161,66:227,3:0.013:2,2:23.7:1:29:1:0.20942:4.84038:60:6:0.0134:0:1.3 +3 138665439 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.02388;SOR=Inf;LSEQ=GGCTTCTCCGGGGCTGTCCC;RSEQ=CCGCCACCCCCACCGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:0:0,0:163,355:518,0:0:2,0:24.5:1:30.9:1:1:0:60:33.533:1:0:0.1 0/1:337:4:1,3:116,217:333,4:0.0119:2,2:31:1:25:1:1:1.60162:60:3:0.0091:0:1.3 +3 138665454 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06107;SOR=Inf;LSEQ=GTCCCGCCGCCACCCCCACC;RSEQ=CCCTTGCCTGGGCTCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:122,309:431,0:0:2,0:24.4:1:31.3:1:1:0:60:32.154:1:0:0.1 0/1:281:3:1,2:94,183:277,3:0.0107:2,2:21.7:1:25.7:1:1:1.02722:60:2:0.0073:0:2.3 +3 138665528 . C A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05793;SOR=Inf;LSEQ=CTCTGGGGCCAGCAGGGCCC;RSEQ=CGCCGCGTCCTCGGGCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:34,107:141,0:0:2,0:23.5:1:30.6:1:1:0:60:19.143:1:0:0.2 0/1:90:3:2,1:22,65:87,3:0.0333:2,2:22:1:26.3:1:0.17228:5.77:60:6:0.0345:0:1.3 +3 138665616 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50909;SOR=0;LSEQ=TCTGCTCTCCGCTCCAGGCG;RSEQ=TGGCGCGGCAAAGAGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:8,17:25,2:0.0741:2,2:36:0:31:0:1:2.06:60:4:0.08:0:1 0/0:18:0:0,0:7,11:18,0:0:2,0:24.6:1:31:1:1:0:60:36:1:0:0.1 +3 138666413 . G T 52 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02469;SOR=Inf;LSEQ=CGAGGGGGCTGGACGGGGTA;RSEQ=GGTGGGGAGAGCTGCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:395,90:485,0:0:2,0:22.4:1:32.5:1:1:0:59.9:52.889:1:0:0.1 0/1:320:4:1,3:261,55:316,4:0.0125:2,2:5.3:1:26.3:1:0.01984:14.06352:60:8:0.0128:0:1 +3 138666707 . C T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14993;SOR=Inf;LSEQ=TAGATGCCCCTCAGCTATTG;RSEQ=ACTAACACAGGCGGGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:5,268:273,0:0:1,0:26.2:1:32.6:1:1:0:59.8:33.125:1:0:0.1 0/1:173:2:0,2:6,165:171,2:0.0116:1,0:32.5:1:23.5:1:1:0:60:4:0.0118:0:1 +3 138667669 . G T 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGGGCTCTTTGGAATTCA;RSEQ=CATCTTGAAGATGACACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:123,316:439,0:0:2,0:23.9:1:32.5:1:1:0:60:145.333:0.9977:0:0.1 0/1:335:17:6,11:97,221:318,17:0.0507:2,2:23.2:1:30.1:1:0.78783:1.24:60:34:0.0515:0:1.2 +3 138667689 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14502;SOR=Inf;LSEQ=GCATCTTGAAGATGACACCA;RSEQ=AGAGGTCAGCAGGGCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:63,263:326,0:0:2,0:21:1:32.1:1:1:0:60:107.667:1:0:0.1 0/1:201:2:1,1:43,156:199,2:0.01:2,2:6.5:1:27.5:1:0.39075:3.60:60:4:0.0101:0:1.5 +3 138667699 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14606;SOR=Inf;LSEQ=GATGACACCAGAGAGGTCAG;RSEQ=AGGGCAGCCCTTGCCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:34,219:253,0:0:2,0:22.9:1:32.3:1:1:0:60:125.5:1:0:0.1 0/1:157:2:1,1:26,129:155,2:0.0127:2,2:23:1:29.5:1:0.31529:4.89:60:4:0.0131:0:1 +3 140596681 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCTTTGGCAGCAGTGAC;RSEQ=CTCCAAAACTGCCAAAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:2,3:0.6:2,2:24:1:32:1:1:1.7321:44.3:6:0.6:0:1.7 0/0:1:0:0,0:0,1:1,0:0:0,0:20:0:33:0:1:0:20:2:1:0:1 +3 140596755 . T G 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31561;SOR=4.58929;LSEQ=GCGCCTTCTTAGGGGAAAAG;RSEQ=GTTTTTACACTAACTAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:4,2:5,0:5,6:0.5455:0,2:15.2:1:31.7:1:0.45455:0:57.3:12:0.5455:0:1.3 1/1:7:6:4,2:1,0:1,6:0.8571:0,2:25.5:1:30.7:1:1:0:48:12:0.8571:0:1.2 +3 142167976 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTAAAAGGAAATCAAT;RSEQ=GAAGTTGTAAAATGAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:16.5:1:31.5:1:1:0:53:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 142168331 . C T 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00699;SOR=1.49214;LSEQ=AAGTTTTCATCAGTAGCTTC;RSEQ=TGTATAAGGTAATGCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:707:571:335,236:75,58:133,571:0.8076:2,2:26:1:31:1:0.62721:1.10:60:70.375:0.8101:0:1.1 1/1:654:564:311,253:48,41:89,564:0.8624:2,2:26.1:1:29.6:1:0.90881:1.05:60:93:0.8611:0:1.1 +3 142171883 . G T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56263;SOR=3.17693;LSEQ=TATTTCCAAGCAGTTCTCAT;RSEQ=CATAGAGATGAGAACTATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:1,0:270,23:293,1:0.0034:2,0:6:0:34:0:1:0:60:2:0.0034:0:1 0/1:186:2:1,1:167,17:184,2:0.0108:2,2:25:1:30:0:0.18466:9.5753:60:4:0.0108:0:1 +3 142176390 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50052;SOR=0;LSEQ=AAAAACAAACATATGTAGGG;RSEQ=CCAATAATTATATTCGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:171,28:199,2:0.01:2,2:18:1:28.5:1:0.26836:6.01847:60:4:0.0101:0:1 0/0:178:0:0,0:148,30:178,0:0:2,0:23.1:1:30.9:1:1:0:60:356:1:0:0.1 +3 142177776 . G T 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37545;SOR=0.27059;LSEQ=ATTGAGAGAAAACACAATTA;RSEQ=TAAGAGTAACTCATATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:353:4:1,3:259,90:349,4:0.0113:2,2:10:1:29.5:1:0.05764:8.56986:53:8:0.0115:0:1.3 0/0:324:1:1,0:223,100:323,1:0.0031:2,0:3:0:28:0:1:0:60:2:0.0031:0:1 +3 142178144 . C T 167 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=61.2379;LSEQ=GCCTGGGCAGGAGAAATTCT;RSEQ=GGAATACTTTGAGTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:547:1:0,1:257,289:546,1:0.0018:2,0:1:0:25:0:1:0:60:2:0.0019:0:1 0/1:564:57:28,29:250,257:507,57:0.1011:2,2:24.8:1:28.7:1:1:1.00749:60:18:0.0973:0:1.1 +3 142178267 . GA G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.51853;SOR=0;LSEQ=ATTAATCACATCAGCCAAAT;RSEQ=AAAAAGGGGCAAAGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:17,145:162,2:0.0122:2,2:12:0:34:0:0.20807:8.32:60:4:0.0125:0:0.5 0/0:109:0:0,0:10,99:109,0:0:2,0:19.3:1:30.3:1:1:0:60:108:1:0:0.1 +3 142183869 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=TGAAATAAAAGCAATCTGGT;RSEQ=TTATAATAGTCAAAAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:156,11:167,0:0:2,0:23.8:1:31:1:1:0:60:40.75:1:0:0 0/1:174:2:1,1:148,24:172,2:0.0115:2,2:8:1:30:1:0.26742:6.06247:60:4:0.0118:0:1 +3 142184161 . T A 36 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6512;SOR=0.49525;LSEQ=ATATTATAAACCTTGAGTTA;RSEQ=GTAAAAAAAAAAAAAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:3:2,1:5,112:117,3:0.025:1,2:6.3:1:23.3:1:0.00857:40.00:60:2:0.0175:0:1.7 0/1:80:1:1,0:1,78:79,1:0.0125:1,0:1:0:24:0:0.025:0:60:2:0.0133:0:1 +3 142185078 . T C 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCACAAATAAGATTCACG;RSEQ=AGATTTTGTGAAATACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:112,3:115,0:0:1,0:25.2:1:30:1:1:0:60:114:1:0:0.1 0/1:104:16:15,1:84,4:88,16:0.1538:1,1:25.6:1:31.1:1:0.574:1.39498:60:15:0.1471:0:1.1 +3 142185091 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24287;SOR=Inf;LSEQ=ATTCACGTAGATTTTGTGAA;RSEQ=TACACTTTTTATCTTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:148,11:159,0:0:2,0:22.7:1:30.4:1:1:0:60:52:1:0:0.1 0/1:155:2:1,1:134,19:153,2:0.0129:2,2:9:1:29:1:0.24214:6.8995:60:4:0.0131:0:1.5 +3 142185393 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49899;SOR=0;LSEQ=AACCTGAAAAAATAAATAGT;RSEQ=CATTTTAATTTGTTTTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:27,122:149,2:0.0132:2,2:33.5:1:29:1:0.33748:4.46:60:4:0.0135:0:1 0/0:140:0:0,0:34,106:140,0:0:2,0:22.7:1:31.5:1:1:0:60:45.667:1:0:0.1 +3 142185415 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20338;SOR=Inf;LSEQ=ATTTTAATTTGTTTTTACCT;RSEQ=AAATTCCACTATAACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:15,83:98,0:0:2,0:23.1:1:28.8:1:1:0:59.7:97:1:0:0.1 0/1:81:2:1,1:15,64:79,2:0.0247:2,2:23.5:1:28.5:1:0.35802:4.16:60:4:0.0247:0:1.5 +3 142186894 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04475;SOR=Inf;LSEQ=TTTCCTTGCATCTGTTCACA;RSEQ=GCATGGGATAAGATGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:129,298:427,0:0:2,0:24:1:30.5:1:1:0:60:84.4:0.9976:0:0.1 0/1:366:4:2,2:134,228:362,4:0.0109:2,2:30.8:1:30.8:1:0.6299:1.70:60:8:0.0111:0:1.3 +3 142188088 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24919;SOR=0;LSEQ=AATACAGGAGAGACGCCCTG;RSEQ=AACTTGTATCTACATATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:2,1:73,1:74,3:0.039:1,2:16:1:30.3:1:0.0769:30.00147:60:6:0.0395:0:1 0/0:66:0:0,0:62,4:66,0:0:2,0:21.2:1:30.9:1:1:0:60:65:1:0:0 +3 142188172 . C A 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATATAAAAAGGTAAAAGACC;RSEQ=TTTTACCTTTGACACAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:47:29,18:214,101:315,47:0.1298:2,2:22:1:30.1:1:0.40842:1.31405:60:46:0.1281:0:1.2 0/0:352:0:0,0:218,133:351,0:0:2,0:24.9:1:30.6:1:1:0:60:174.5:0.9971:0:0.1 +3 142188373 . C A 52 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06186;SOR=0;LSEQ=GATAACCTTGTTTATTTTAC;RSEQ=CAAATCATTCCTCATTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:5:3,2:187,283:470,5:0.0105:2,2:20:1:22.4:1:0.39337:2.27:60:1.5:0.0065:0:2 0/0:470:0:0,0:188,282:470,0:0:2,0:26.9:1:30.1:1:1:0:60:66.143:1:0:0.1 +3 142188413 . T A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.1237;SOR=0;LSEQ=ACACGATCGGAGCGGCCAGC;RSEQ=GGGGGAAGAAATAAGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:2,1:85,200:285,3:0.0104:2,2:11.3:1:23.3:1:0.21775:4.68:60:2:0.0072:0:2.3 0/0:289:0:0,0:81,207:288,0:0:2,0:21.8:1:29.5:1:1:0:60:47:1:0:0.1 +3 142204149 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.08651;SOR=Inf;LSEQ=AAAAAAGAACATAGGATACC;RSEQ=ACCTAAGGAAATCCCACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:72,241:313,0:0:2,0:24.9:1:29.3:1:1:0:60:77.25:0.9968:0:0.1 0/1:250:3:1,2:64,183:247,3:0.012:2,2:27:1:30.7:1:1:1.43:60:6:0.0121:0:1 +3 142210992 . T C 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTACTGCCCTTCTAGTA;RSEQ=GGATATAGAGTAGTTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:26:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 142211868 . CA C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.14909;SOR=Inf;LSEQ=TTATATACTCACTGAAAAGT;RSEQ=AAAAAATTTCCTGGTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:90,3:93,0:0:1,0:21.8:1:31.2:1:1:0:60:186:1:0:0.1 0/1:59:2:2,0:57,0:57,2:0.0339:1,0:14.5:1:29.5:1:1:0:60:4:0.0339:0.0169:0.5 +3 142211899 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51616;SOR=0;LSEQ=CCTGGTTATTTTTATACATG;RSEQ=GCTTTGCCATATAGACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:155,26:181,2:0.0109:2,2:25:1:31:1:0.274:5.86897:60:4:0.011:0:1 0/0:125:0:0,0:111,14:125,0:0:2,0:24:1:29.4:1:1:0:60:250:1:0:0.1 +3 142212225 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50503;SOR=0;LSEQ=TTTTCTGCAAAAGTATTAGT;RSEQ=CATTATGTTTTTGTACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:0,2:5,135:140,2:0.0141:1,0:17.5:1:31:1:1:0:60:4:0.0144:0:1 0/0:112:0:0,0:4,108:112,0:0:1,0:23.6:1:28.8:1:1:0:60:111:1:0:0 +3 142215120 . C CAT 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36032;SOR=1.86826;LSEQ=AGGAAGTACATAATTCCCGA;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:8:8,0:117,7:124,8:0.0602:2,0:39.5:1:31.9:1:1:0:36:16:0.062:0:1.1 0/1:56:6:6,0:48,2:50,6:0.1071:1,0:33.2:1:29.8:1:1:0:34.2:12:0.1091:0:1.3 +3 142215121 . TA AT 162 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=29.000;MSILEN=2;SSF=0.11637;SOR=0.52453;LSEQ=GGAAGTACATAATTCCCGAC;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:44:44,0:22,1:23,44:0.2651:1,1:29:1:29.8:1:0.34328:0:58.7:88:0.2716:0:2 0/1:63:10:9,1:34,0:34,10:0.1587:1,2:35.8:1:29:1:0.22727:0:53.5:20:0.1613:0:2 +3 142215135 . T C 162 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=29.000;MSILEN=2;SSF=0.01493;SOR=0.38276;LSEQ=CCCGACTATATATATATATA;RSEQ=ATATATATATATATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:38:38,0:50,11:61,38:0.2695:2,1:18.7:1:30.9:1:0.00592:0:58.4:76:0.3878:0:2.2 0/1:73:9:8,1:47,9:56,9:0.1233:2,2:19.6:1:31.1:1:1:1.52:48.9:18:0.1452:0:2.7 +3 142215149 . T C 169 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=29.000;MSILEN=2;SSF=2e-05;SOR=0.08786;LSEQ=TATATATATATATATATATA;RSEQ=ATATATATATATATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:40:29,11:107,30:137,40:0.2247:2,2:24.1:1:31.9:1:0.5235:1.35047:53:39:0.2241:0:2.2 0/1:81:2:2,0:50,21:71,2:0.0247:2,0:15:1:33:0:1:0:50:4:0.0278:0:3 +3 142215178 . A C 242 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=2;SSF=0;SOR=0.35718;LSEQ=ATATATATATATATATATAT;RSEQ=TGATGACATTTCCCTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:297:228:144,84:39,27:66,228:0.7677:2,2:22.2:1:31:1:0.56641:1.19:54.6:16.538:0.7706:0:1.7 1/0:257:139:84,55:70,45:115,139:0.5409:2,2:14.2:1:30.4:1:1:1.01845:57.5:68.5:0.5437:0:1.5 +3 142215180 . G A 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04655;SOR=Inf;LSEQ=ATATATATATATATATATAT;RSEQ=ATGACATTTCCCTGGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:201,126:327,0:0:2,0:19.5:1:31:1:1:0:55.8:13.864:1:0:1.2 0/1:286:4:3,1:168,113:281,4:0.014:2,2:10.8:1:22.8:1:0.65216:2.01:50:3:0.011:0:1.5 +3 142215223 . C T 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03975;SOR=7.46879;LSEQ=CTTGGACCAGAGCCACTTTG;RSEQ=CCTTTCCACGTACAGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:743:1:0,1:419,323:742,1:0.0013:2,0:1:0:31:0:0.43607:0:51:2:0.0014:0:1 0/1:802:8:1,7:466,328:794,8:0.01:2,2:12:1:26.1:1:0.01093:9.92094:60:16:0.0102:0:1.4 +3 142217537 . A G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0547;SOR=1.62457;LSEQ=CTCACTAGTTTCAGTGAGTC;RSEQ=TAAAAAGCTGTGATATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:26:12,14:324,379:703,26:0.0357:2,2:30.1:1:29.5:1:1:1.00:60:7.667:0.032:0:1.2 0/1:829:47:27,20:389,391:780,47:0.0567:2,2:24.6:1:29.4:1:0.3681:1.36:60:46:0.0559:0:1.1 +3 142217650 . G A 119 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=16.66257;LSEQ=GAAGAGTCAAGAAATGTCAC;RSEQ=GTAGCTGGGTCCAAGAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:1,0:53,203:256,1:0.0039:2,0:2:0:28:0:0.21012:0:60:2:0.0039:0:1 0/1:261:16:3,13:50,194:244,16:0.0613:2,2:21.8:1:29.8:1:1:1.11638:60:32:0.062:0:1.1 +3 142218624 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49936;SOR=Inf;LSEQ=GGTGACATTCAGAGATTTTT;RSEQ=ATTGGTTTACATACTCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:16,161:177,0:0:2,0:25.4:1:32.6:1:1:0:60:58:1:0:0.1 0/1:191:2:1,1:13,175:188,2:0.0105:2,2:19:1:28.5:1:0.1423:13.01:60:4:0.0106:0:1 +3 142218675 . T A 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01009;SOR=0;LSEQ=ATTGAATTTGCATTATATTG;RSEQ=ATTTTGTTCTTAGATATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:8:0,8:1,71:72,8:0.1:1,0:11.3:1:30.1:1:1:0:60:7:0.0933:0:1.3 0/0:61:0:0,0:3,58:61,0:0:1,0:24.3:1:28.1:1:1:0:60:122:1:0:0.1 +3 142220845 . T C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATGATACACCCGCCTTGGCC;RSEQ=CCCAGAGTGCTGCAATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:45:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:30:1:1:0:60:4:1:0:1 +3 142221956 . A G 48 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGAGCCTCACCAATAGCC;RSEQ=GTGGGTTCTAGAAGTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:4.3:1:30.7:1:1:0:60:6:0.75:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:29.5:1:1:0:60:4:1:0:1 +3 142222056 . G GA 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54965;SOR=3.59652;LSEQ=CTGACTATGAAAAACTTGAG;RSEQ=AAAAAAAAATGTTGGTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:1:1,0:44,0:44,1:0.0222:1,0:17:0:32:0:1:0:60:2:0.0227:0:0 0/1:26:2:2,0:24,0:24,2:0.0769:1,0:44:1:28.5:1:1:0:60:4:0.0769:0:0 +3 142222074 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.15746;LSEQ=AGGAAAAAAAAATGTTGGTG;RSEQ=TTATCTCCAATACCATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:40:40,0:18,0:18,40:0.6897:1,1:22.8:1:30.4:1:1:0:59.4:80:0.6897:0:1.1 0/1:47:12:12,0:35,0:35,12:0.2553:1,0:23.1:1:28.8:1:1:0:60:24:0.2609:0:1 +3 142222090 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=GGTGCTTATCTCCAATACCA;RSEQ=GAAAACACATAAAACATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:73,0:73,2:0.0267:1,2:10:1:31:1:0.02667:0:60:4:0.0274:0:1.5 0/0:65:0:0,0:64,1:65,0:0:1,0:22.6:1:30.2:1:1:0:60:130:1:0:0.2 +3 142222124 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50023;SOR=0;LSEQ=ACATTTATTACTCTACTAAA;RSEQ=ATTAAATTACCCAATTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:133,17:150,2:0.0132:2,2:9.5:1:29.5:1:0.22351:7.63155:60:4:0.0132:0:1 0/0:134:0:0,0:119,15:134,0:0:2,0:23.6:1:31.3:1:1:0:60:133:1:0:0.1 +3 142222148 . TA T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.24884;SOR=Inf;LSEQ=AAATTACCCAATTCACTAAC;RSEQ=AAAATTCTCCATTCAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:162,49:211,0:0:2,0:26.4:1:29:1:1:0:60:422:1:0:0.1 0/1:223:3:1,2:173,47:220,3:0.0135:2,2:23.3:1:28.7:1:0.12232:7.27377:60:6:0.0135:0.0045:0.3 +3 142222284 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16395;LSEQ=ATGGACTTTACTACACCATG;RSEQ=TAATGAATGATCTAGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:429:264:96,168:72,93:165,264:0.6154:2,2:23.7:1:31.8:1:0.15466:1.35384:60:51.8:0.6123:0:1.1 0/1:458:95:30,65:141,222:363,95:0.2074:2,2:25.6:1:31.3:1:0.23343:1.37519:59.9:94:0.2084:0:1 +3 142223906 . CA C 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.63019;SOR=0.40231;LSEQ=AAAAACAAAACAAAACAAAA;RSEQ=AAAAAAACTAAGGTTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:192,26:218,3:0.0136:2,2:20:1:33:1:0.32485:3.65894:60:6:0.0138:0.0045:0 0/0:182:1:1,0:160,21:181,1:0.0055:2,0:15:0:33:0:1:0:60:2:0.0056:0:0 +3 142226705 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50638;SOR=0;LSEQ=ATAAAACATTCAATAAAATG;RSEQ=ACAACATAAACATAAAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:114,9:123,2:0.016:2,2:26:1:29:1:0.15419:12.0694:60:4:0.0161:0:1 0/0:96:0:0,0:80,16:96,0:0:2,0:23.7:1:28.5:1:1:0:60:95:1:0:0.1 +3 142226734 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21068;SOR=Inf;LSEQ=AACATAAAAGACTGGCCACA;RSEQ=TAATTTTCATTATTAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:174,47:221,0:0:2,0:23.5:1:30.6:1:1:0:59.9:72.667:1:0:0.2 0/1:188:2:1,1:138,48:186,2:0.0106:2,2:31.5:1:31:1:0.45437:2.8558:60:4:0.0106:0:1 +3 142227152 . T C 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTATAACTTACCTTTCTT;RSEQ=GGACAGTCATTTAATTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:0,4:0,10:10,4:0.2857:0,0:28.8:1:32:0:1:0:60:8:0.2857:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:30:1:31.5:1:1:0:60:4:1:0:0 +3 142230846 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGCACCTGTAATCCCA;RSEQ=CTACTTGGGAGGCTGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:11:1:34.5:1:1:0:20:4:0.4:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:30:0:31:0:1:0:28:2:1:0:0 +3 142232243 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52431;SOR=0;LSEQ=AACATACATAGCCATACATA;RSEQ=GTCTACATTTCCTACTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:110,4:114,2:0.0171:1,2:18:1:30:1:0.08471:24.70868:60:4:0.0174:0:1 0/0:73:0:0,0:71,2:73,0:0:1,0:23.4:1:31.5:1:1:0:60:146:1:0:0 +3 142233990 . T C 60 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TACAATATAAAAGGAATAAA;RSEQ=GTAATTTTACACACACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:21.5:1:30.3:1:1:0:54.3:8:1:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:22:0:33:0:1:0:60:2:0.5:0:1 +3 142234534 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01197;SOR=Inf;LSEQ=GTCATTCTTGGACACCTAAA;RSEQ=TACTTCTAAGGATTTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:0,19:19,0:0:1,0:26.4:1:32.7:1:1:0:60:38:1:0:0.5 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:16.7:1:31.7:1:1:0:60:6:0.4286:0:1.3 +3 142234589 . C A 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.36364;SOR=0;LSEQ=CCTCAGATCCTTCCAACTCT;RSEQ=TTCTTATATAAGAAAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:3,7:0.7:0,0:23.4:1:31.3:1:1:0:60:14:0.7:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 +3 142237274 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACTGAGGCAGGAGAATC;RSEQ=CTTGAACCCAGGAGGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:28.5:1:1:0:29:4:1:0:1.5 +3 142238441 . CA C 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.54725;LSEQ=CGTGAGCCACTGCACCCGGC;RSEQ=AAAAAATCGCATTATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:111,7:118,2:0.0165:2,2:23:1:27.5:1:0.12941:14.89965:54:4:0.0167:0.0083:0.5 0/0:110:1:1,0:94,15:109,1:0.0091:2,0:17:0:32:0:1:0:60:2:0.0091:0:0 +3 142238771 . GT G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.53846;SOR=0;LSEQ=ATTTATGCTTCATGGATGCT;RSEQ=TTTTTTTGTCTGTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:0,2:0,32:32,2:0.0588:1,0:21:1:34:0:1:0:60:4:0.0606:0:0.5 0/0:18:0:0,0:1,17:18,0:0:1,0:23.6:1:30.8:1:1:0:60:36:1:0:0.1 +3 142239107 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTCATATTTCCAAAGAC;RSEQ=TAAGAATATTGAAATTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:43:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 142241690 . C CA 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03087;SOR=0;LSEQ=TCTTCTACTCCAGTCTCAAT;RSEQ=AGAAAAAAAAAAAAGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:6:1,5:170,360:530,6:0.0112:2,2:26.8:1:25.6:1:0.66982:2.35799:60:5:0.01:0.0056:1.7 0/0:526:0:0,0:185,340:525,0:0:2,0:22.6:1:30:1:1:0:59.9:17.75:0.998:0:0.3 +3 142241692 . GA G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.44154;SOR=0.80043;LSEQ=TTCTACTCCAGTCTCAATCA;RSEQ=AAAAAAAAAAAGAAAATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:36:10,26:142,304:446,36:0.0738:2,2:26.7:1:32.1:1:0.71115:1.21397:59.7:72:0.0747:0.002:0.3 0/1:484:29:11,18:154,295:449,29:0.0599:2,2:29.4:1:30.3:1:0.69073:1.17:60:58:0.0608:0.0021:0.1 +3 142241705 . G A 68 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.81244;SOR=0.80873;LSEQ=TCAATCAGAAAAAAAAAAAA;RSEQ=AAAATTCCAGGATAACTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:10:9,1:89,291:380,10:0.0256:2,2:9.7:1:20.7:1:2e-05:29.15:60:1.5:0.0172:0:1.1 0/1:384:8:8,0:107,268:375,8:0.0208:2,0:11.3:1:16.1:1:6e-05:0:60:0.6:0.0091:0:1.6 +3 142242788 . C T 39 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11054;SOR=Inf;LSEQ=TAAATGAAATATATAAACCT;RSEQ=AATAGGACAGAGAACTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:237,61:298,0:0:2,0:21.9:1:32:1:1:0:59.8:58.6:1:0:0.1 0/1:276:3:1,2:206,67:273,3:0.0109:2,2:7.3:1:24.7:1:0.15522:6.09897:60:6:0.011:0:1 +3 142243092 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21578;SOR=Inf;LSEQ=GTAATTTCTACAAACTAGTA;RSEQ=GTTTTCCTGAGCTAGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:9,108:117,0:0:2,0:22:1:30.3:1:1:0:59.7:38:1:0:0.1 0/1:102:2:2,0:10,90:100,2:0.0196:2,0:10:1:28:1:0.01281:0:60:4:0.0202:0:1 +3 142255076 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49892;SOR=Inf;LSEQ=TGGAATAAAAAGAATTATTT;RSEQ=CCAAGAATATGAATACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:27,126:153,0:0:2,0:23.1:1:32.3:1:1:0:60:75.5:1:0:0.1 0/1:163:2:1,1:34,127:161,2:0.0123:2,2:41:1:30:1:0.38438:3.70:60:4:0.0123:0:2 +3 142255080 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49866;SOR=Inf;LSEQ=ATAAAAAGAATTATTTGCCA;RSEQ=GAATATGAATACTAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:24,118:142,0:0:2,0:23.3:1:32:1:1:0:60:141:1:0:0.1 0/1:150:2:1,1:28,120:148,2:0.0133:2,2:19:1:29:1:0.35034:4.23:60:4:0.0136:0:1 +3 142255090 . T C 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATTTGCCAAGAATATGAA;RSEQ=ACTAAAAAAATGTAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:17,103:120,0:0:2,0:22.9:1:29:1:1:0:60:119:1:0:0.1 0/1:124:28:6,22:17,79:96,28:0.2258:2,2:25.6:1:31.4:1:0.78251:1.26:60:56:0.2276:0:1.3 +3 142257269 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49905;SOR=0;LSEQ=TACCATCAGTAATTTTGAGA;RSEQ=ATAAAAATACAGTTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:152,21:173,2:0.0114:2,2:20.5:1:27:1:0.23626:7.09472:60:4:0.0116:0:1 0/0:164:0:0,0:142,22:164,0:0:2,0:22.2:1:31.3:1:1:0:60:53.667:1:0:0.1 +3 142259898 . C G 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TATAGAGTTAAGTAGTGCTT;RSEQ=AGAGTAAAGCTTATAAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:51,224:275,0:0:2,0:22.3:1:31.9:1:1:0:60:44.833:1:0:0.1 0/1:266:13:3,10:61,192:253,13:0.0489:2,2:22.1:1:30:1:1:1.05879:60:26:0.0494:0:1.1 +3 142259937 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22002;SOR=Inf;LSEQ=ATGCTGCCAGAAGCAGATGA;RSEQ=CCCTAAGGACAAGTGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:8,125:133,0:0:2,0:27:1:32.5:1:1:0:60:65.5:1:0:0.1 0/1:118:2:1,1:12,104:116,2:0.0169:2,2:22:1:24:1:0.20904:8.37:60:4:0.0171:0:3 +3 142261339 . G A 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57624;SOR=2.45727;LSEQ=CTAAACTAAAGAAATGAAAC;RSEQ=AATACAATTCCAATTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:39,1:40,2:0.0476:1,0:9.5:1:32.5:1:1:0:60:4:0.0476:0:1 0/1:18:2:2,0:16,0:16,2:0.1111:1,0:8.5:1:30.5:1:1:0:60:4:0.1111:0:1 +3 142261548 . G A 72 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00884;SOR=Inf;LSEQ=AACACTAGAGCTCAGTAACT;RSEQ=CATGTTAAAAAAAGCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:658:0:0,0:303,355:658,0:0:2,0:26.9:1:32.2:1:1:0:60:72.111:1:0:0.1 0/1:762:8:6,2:365,386:751,8:0.0105:2,2:13.3:1:24:1:0.1686:3.17:60:7:0.0093:0:1.3 +3 142266439 . C T 150 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCTTTTCAAAATAAAAATA;RSEQ=CAACTTAAAATTTAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:30:30,0:23,0:23,30:0.566:1,1:25.9:1:30.7:1:1:0:60:9:0.54:0:1 0/0:29:0:0,0:28,1:29,0:0:1,0:18.8:1:31.9:1:1:0:60:58:1:0:0.2 +3 142268498 . T A 47 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0838;SOR=Inf;LSEQ=TTGGCAGCAAGATCAGGTAG;RSEQ=AGAACTTGTAATGTCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:114,224:338,0:0:2,0:24.7:1:28.7:1:1:0:60:66.6:1:0:0.1 0/1:264:3:2,1:104,157:261,3:0.0114:2,2:7.3:1:29.7:1:0.56637:3.01:59:6:0.0114:0:1.7 +3 142268553 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51487;SOR=0;LSEQ=AATTACCAAAAAGTACATTT;RSEQ=TCTGGGTGAAAAAAATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:35,141:176,2:0.0112:2,2:39.5:1:31.5:1:0.3645:3.99:60:4:0.0112:0:1 0/0:124:0:0,0:38,85:123,0:0:2,0:23.6:1:31.4:1:1:0:60:122:0.9919:0:0.1 +3 142271797 . A C 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACACACACTGGGGCCTGT;RSEQ=AGGGGGGTGGGGGAAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:40:1:30:1:1:0:54.7:6:0.6:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 142272275 . A AAC 203 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=13.000;MSILEN=2;SSF=0;SOR=0.28759;LSEQ=AACATACATATGAATACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:101:28,73:103,148:251,101:0.2737:2,2:31.7:1:30.5:1:0.02078:1.81143:57.8:49.5:0.2829:0.0136:0.8 0/1:338:33:7,26:105,191:296,33:0.0976:2,2:29.5:1:28:1:0.12221:2.03791:58.5:66:0.1058:0.0118:0.8 +3 142272314 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-04;SOR=0.51045;LSEQ=ACACACATACACACACATAT;RSEQ=TATCTCCAATATCCCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:236:130:49,81:40,66:106,130:0.5508:2,2:23.4:1:30.3:1:1:1.00185:58.5:42.333:0.557:0:1.2 0/1:182:70:23,47:30,82:112,70:0.3846:2,2:22.8:1:29.6:1:0.40508:1.34:58.9:69:0.3812:0:1.1 +3 142273032 . T C 129 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00695;SOR=0.06042;LSEQ=TAGGAAATTAAAATGGATAC;RSEQ=TATAAATTAAAATTACTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:0,16:0,2:2,16:0.8889:0,1:27.9:1:32.4:1:1:0:57.6:15:0.8824:0:1.3 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:3.5:1:31.5:1:1:0:60:4:0.2857:0:1 +3 142273069 . CT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTATATTTAATAAATGTCA;RSEQ=TTTTTTTTTTGATATAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:8,2:0.2:0,0:16:1:33.5:1:1:0:55:4:0.2222:0.1:1 0/0:1:0:0,0:0,1:1,0:0:0,0:25:0:31:0:1:0:60:2:1:0:0 +3 142274534 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43315;SOR=0.42867;LSEQ=AAAATCCCAAAATCACCTCT;RSEQ=CTACCAGTTTTGTGATGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:12,0:10,0:10,12:0.5455:0,0:26.8:1:31.3:1:1:0:60:24:0.5455:0:1.1 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:12.7:1:29.3:1:1:0:60:6:0.3333:0:1.3 +3 142274660 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.26112;SOR=0;LSEQ=TTCAGTCTAATTCTTTTACT;RSEQ=ATTTGAAAAGCAGAGCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:167,49:216,3:0.0137:2,2:16:1:29:1:0.13611:6.73915:60:6:0.0138:0:1 0/0:168:0:0,0:114,54:168,0:0:2,0:23.4:1:30.7:1:1:0:60:167:1:0:0 +3 142274739 . A AT 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.63778;SOR=0.87213;LSEQ=CAAGTTTTACTGGACTAGGT;RSEQ=TTTTTTTTTTCAGTAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:47:29,18:304,156:460,47:0.0923:2,2:24.4:1:30.4:1:0.62874:1.20907:60:94:0.0944:0.0177:0.3 0/1:405:33:17,16:240,131:371,33:0.0815:2,2:20.2:1:28.2:1:0.13588:1.72194:59.6:15.5:0.0781:0.0296:0.6 +3 142277365 . AAAAT A 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=9.000;MSILEN=4;SSF=0.01752;SOR=0.44529;LSEQ=CAGAGTAAGACTCCGTCTCA;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:44:42,2:51,1:52,44:0.4583:1,1:18.4:1:31.7:1:0.59166:2.40668:49.7:88:0.4632:0.1875:0.3 0/1:77:21:21,0:53,3:56,21:0.2727:2,1:12.2:1:30.6:1:0.55789:0:53:42:0.2763:0.1169:0.2 +3 142277423 . GATAA G 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=4;SSF=0.0308;SOR=Inf;LSEQ=GATAGATAGATAGATAGATA;RSEQ=ATAAAACAAACCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:253,87:340,0:0:2,0:23.4:1:30.4:1:1:0:58.3:169:1:0:0.1 0/1:356:6:5,1:238,111:349,6:0.0169:2,2:35.3:1:30.7:1:0.66936:2.33:53.8:12:0.017:0:0 +3 142277536 . A G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.2184;LSEQ=GTGGTCAACTTTAAACAGCC;RSEQ=TCATCAGAATGGGAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:639:382:168,214:116,140:256,382:0.5978:2,2:24.7:1:31:1:0.74582:1.05533:59.9:62.667:0.5959:0:1.6 0/1:678:166:79,87:237,275:512,166:0.2448:2,2:25.3:1:30.2:1:0.78873:1.05:60:165:0.2452:0:1.6 +3 142277575 . A T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38636;LSEQ=ATCCATGGAAGTGAGAGCAT;RSEQ=CCACATAAATCTTCCAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:573:334:128,206:99,140:239,334:0.5829:2,2:27:1:30.5:1:0.4886:1.1378:60:54.667:0.5795:0:1.8 0/1:605:212:90,122:170,223:393,212:0.3504:2,2:23.8:1:29.1:1:0.8637:1.03334:60:211:0.3517:0:1.5 +3 142277643 . T A 47 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13463;SOR=Inf;LSEQ=AGAAGCACAAAATAAGTCAT;RSEQ=AATTATAACTTTTCCTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:44,184:228,0:0:2,0:24.5:1:28.7:1:1:0:60:75:1:0:0.4 0/1:291:4:3,1:93,194:287,4:0.0137:2,2:7.3:1:23.8:1:0.10655:6.22:60:8:0.0137:0:1.8 +3 142278013 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20974;SOR=Inf;LSEQ=TATTCCAAACACGCACTTAG;RSEQ=CTTCAGGCAAAAAAGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:139,19:158,0:0:2,0:22.1:1:31.8:1:1:0:60:78:1:0:0.1 0/1:134:2:1,1:120,12:132,2:0.0149:2,2:5:1:27:1:0.18528:9.64765:60:4:0.015:0:1 +3 142278101 . T C 236 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTTGTACTCACCTTGCATA;RSEQ=AAATCAAAGCATCATAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:164:100,64:270,209:479,164:0.2551:2,2:26.7:1:32.2:1:0.31532:1.21:60:53.667:0.2552:0:1.1 0/0:656:0:0,0:375,281:656,0:0:2,0:25.6:1:28.8:1:1:0:60:130.2:1:0:0.1 +3 142278201 . T C 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTACAGCTCTTAAGCACTT;RSEQ=TGTGTAAAAATCCAATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:579:0:0,0:249,330:579,0:0:2,0:23.4:1:30.5:1:1:0:60:47.25:1:0:0.1 0/1:521:50:21,29:193,278:471,50:0.096:2,2:23.1:1:31.3:1:0.88115:1.04:60:100:0.0969:0:1 +3 142278357 . T C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09904;SOR=Inf;LSEQ=AGTCAAACATAAAATTGTAG;RSEQ=AAAGCCAAAAGAAATTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:13,95:108,0:0:2,0:25.2:1:29.1:1:1:0:60:216:1:0:0.1 0/1:94:3:0,3:8,83:91,3:0.0319:2,0:12.3:1:32.3:1:1:0:60:6:0.0326:0:1 +3 142279406 . AT A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.73781;SOR=1.42309;LSEQ=AATATCAACTATTCAAAAAA;RSEQ=TTTTTTTTTTTGTGAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:0,5:1,49:50,5:0.0909:1,0:20.6:1:33.4:1:1:0:53.4:10:0.0962:0:0 0/1:40:5:0,5:0,35:35,5:0.125:1,0:19.2:1:30.6:1:1:0:52.2:10:0.1282:0.025:0.2 +3 142280321 . T G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01284;SOR=0.22213;LSEQ=AGAAAATATATTTATATTAT;RSEQ=CATAGGCAGCAAGAATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:15:2,13:6,90:96,15:0.1351:2,2:22.1:1:31.7:1:0.29475:2.29:60:30:0.1351:0:1 0/1:90:3:0,3:8,79:87,3:0.0333:2,0:18.3:1:29:1:1:0:60:6:0.0333:0:1 +3 142280359 . C G 34 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.20318;SOR=Inf;LSEQ=TATTAGATGTTAGGTGTTTT;RSEQ=TAGTGAAACTACTTTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:0,53:53,0:0:1,0:20.9:1:33.1:1:1:0:60:25.5:1:0:0.2 0/1:44:2:1,1:1,41:42,2:0.0455:1,2:6:0:34:0:0.08985:29.33:60:4:0.0455:0:1.5 +3 142280924 . AG TAGT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12483;SOR=Inf;LSEQ=AGTAAAAGTCCATAATAGTG;RSEQ=CCAGACTACACTATGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:42,1:43,0:0:1,0:25.1:1:31:1:1:0:60:86:1:0:0 0/1:24:2:2,0:22,0:22,2:0.0833:1,0:24.5:1:31.6:0:1:0:60:4:0.0833:0:0 +3 142281018 . A T 45 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63002;SOR=0.40041;LSEQ=TACATTTTGCACATATGTAT;RSEQ=CAATTAAATGATGAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:194,53:247,3:0.012:2,2:5:1:28.7:1:0.12274:7.24306:60:6:0.012:0:1 0/0:207:1:0,1:163,43:206,1:0.0048:2,0:1:0:23:0:0.21256:0:60:2:0.0049:0:1 +3 142281612 . A G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.42093;LSEQ=CAATAATACGAGTAAGAACC;RSEQ=TTAATAAAGTGACTTCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:524:330:151,179:83,111:194,330:0.6298:2,2:22.8:1:31.2:1:0.5252:1.13:60:109:0.6313:0:1.1 0/1:458:191:90,101:136,129:265,191:0.417:2,2:24.1:1:30.3:1:0.39395:1.18268:60:94.5:0.4172:0:1.1 +3 142284987 . G A 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAACTGCCTTTGGCCTCAT;RSEQ=GCTTCCACTCACATTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:868:0:0,0:470,398:868,0:0:2,0:25.4:1:31.7:1:1:0:60:143.667:1:0:0.1 0/1:872:32:18,14:452,388:840,32:0.0367:2,2:23.6:1:28.6:1:0.8577:1.10:60:64:0.0369:0:1.1 +3 142285138 . C A 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.62394;SOR=2.9146;LSEQ=TTCATTTTAAAGAGTCATGA;RSEQ=AAATTAAACAATGGTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:1,0:54,235:289,1:0.0034:2,0:1:0:29:0:0.18966:0:60:2:0.0034:0:1 0/1:300:3:2,1:74,223:297,3:0.01:2,2:10.3:1:29.3:1:0.15908:5.98:60:6:0.0102:0:1 +3 142285165 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24587;SOR=Inf;LSEQ=AACAATGGTCCTTTTGTTAA;RSEQ=AAACCAGACTGTGGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:14,138:152,0:0:2,0:24.2:1:32.3:1:1:0:59.8:151:1:0:0 0/1:150:2:1,1:13,135:148,2:0.0133:2,2:5:1:28:1:0.17852:10.04:60:4:0.0137:0:1 +3 142286851 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22933;SOR=Inf;LSEQ=TGCTACTATAATTTATACAT;RSEQ=GAAAAGAAAAGTCTAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:177,39:216,0:0:2,0:22.7:1:31.8:1:1:0:59.9:42.2:1:0:0.1 0/1:199:2:1,1:153,44:197,2:0.0101:2,2:40:1:29.5:1:0.40201:3.44952:60:4:0.0104:0:1 +3 142287047 . T A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18102;SOR=1.60787;LSEQ=TAAAGTGACTCAGTTTCATT;RSEQ=GCAAAAAAAATTTCTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:18:2,16:37,179:216,18:0.0769:2,2:21.7:1:31.8:1:0.74484:1.65054:60:36:0.0776:0:1.2 0/1:186:22:6,16:34,130:164,22:0.1183:2,2:20.7:1:29.2:1:0.57986:1.43:60:44:0.1202:0:1 +3 142287049 . CA C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20468;SOR=Inf;LSEQ=AAGTGACTCAGTTTCATTTG;RSEQ=AAAAAAATTTCTCTAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:34,176:210,0:0:2,0:24.4:1:30.9:1:1:0:60:69:1:0:0.2 0/1:174:2:0,2:36,136:172,2:0.0115:2,0:18:1:33.5:1:1:0:60:4:0.0118:0:0 +3 142297576 . G A 75 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1238;SOR=0.16567;LSEQ=GCGAGGCACTAGTCAACCAC;RSEQ=CCAACGCGGGTTCCCGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:6:4,2:187,355:542,6:0.0109:2,2:14.5:1:29.3:1:0.18992:3.79:60:12:0.0112:0:1 0/0:547:1:1,0:221,325:546,1:0.0018:2,0:1:0:24:0:0.40585:0:60:2:0.0019:0:1 +3 143592482 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11294;SOR=0;LSEQ=GACATGGAGACTGGTAGTGG;RSEQ=CCCGAATGTCTGGGTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:4,0:12,1:13,4:0.2353:1,0:29:1:29.3:1:1:0:53.8:8:0.2353:0:1 0/0:13:0:0,0:11,2:13,0:0:2,0:23.9:1:31.2:1:1:0:53.3:12:1:0:0.1 +3 143592641 . A G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13736;SOR=Inf;LSEQ=CCGAAGCAGAGAGAGAAGGC;RSEQ=GCATATGTCAGCATATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:7,21:28,0:0:2,0:23.7:1:31.2:1:1:0:54:56:1:0:0.1 0/1:40:4:2,2:9,27:36,4:0.1:2,2:25:1:30.8:1:0.30031:2.90:47.3:8:0.1026:0:1.3 +3 143592698 . CT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.16304;SOR=0;LSEQ=TAAAGACTTTAAGACTTTCA;RSEQ=TTTTTTTTTACCATTATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:2,5:7,2:0.2:2,2:28:1:31.5:1:1:2.24:57:4:0.2222:0:0 0/0:14:0:0,0:2,12:14,0:0:2,0:19.7:1:29.8:1:1:0:57.8:28:1:0:0.4 +3 143779996 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14773;SOR=Inf;LSEQ=ATAGTTTCTTCTTTATTAGG;RSEQ=CAATAATACACAGTCATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:12,8:20,0:0:2,0:22.6:1:29.7:1:1:0:60:19:1:0:0 0/1:13:2:1,1:4,7:11,2:0.1538:2,2:25:1:27:1:1:1.67:60:4:0.1538:0:1 +3 144050136 . G T 25 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=CATAGTTCACCTGAAGAACG;RSEQ=ATCTCTATAATGGAAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:0,5:5,2:0.2857:0,2:7:1:25.5:1:0.28571:0:26:4:0.2857:0:1 0/0:6:0:0,0:1,5:6,0:0:2,0:23.8:1:31:1:1:0:27.7:12:1:0:0.2 +3 144623447 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47826;SOR=Inf;LSEQ=TTGGTATAAGAGTTTGAAAG;RSEQ=TGTTGTCTGATTTCAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:11,0:0:2,0:18.1:1:32.5:1:1:0:47.1:22:1:0:0.1 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:20:1:30:1:1:1.45:41:4:0.1667:0:1 +3 144624183 . TCTGA T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTTCCTCTCTCTCTCTCTC;RSEQ=CTTTCTGTCTCTTTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:45.5:1:30.5:1:1:0:60:4:0.6667:0:0 +3 145542498 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=TAGAGAACATATATCGGGTG;RSEQ=CTCTCCTCTTTCCCTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:31,43:74,0:0:2,0:18.5:1:32:1:1:0:39:73:1:0:0.1 0/1:65:2:1,1:24,39:63,2:0.0308:2,2:8:1:30.5:1:1:1.61:47.5:4:0.0308:0:1 +3 145542567 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12326;SOR=Inf;LSEQ=TGGCGGTTCCGTCCAAAAGC;RSEQ=CCTTTTTGGTTCTGTATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:32,41:73,0:0:2,0:25.4:1:30.7:1:1:0:51.4:72:1:0:0.1 0/1:40:2:1,1:12,26:38,2:0.05:2,2:25:1:28:1:1:2.12:44:4:0.05:0:1 +3 145542604 . T A 57 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06112;LSEQ=TGATGTAATTTGGCTCTGTG;RSEQ=CACCACCCAAATCTCATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:4:0,4:11,23:34,4:0.1053:2,0:25.3:1:28.5:1:0.30258:0:60:8:0.1053:0:1 0/1:9:1:0,1:0,8:8,1:0.1111:0,0:34:0:31:0:1:0:60:2:0.1111:0:1 +3 146192553 . C G 78 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CATTCTCCCTGTCTCCTCCT;RSEQ=GTACTCCAATCAATCTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:32:0:1:0:60:2:1:0:0 1/0:8:6:3,3:1,1:2,6:0.75:2,2:23.2:1:30.2:1:1:1:57.3:12:0.75:0:1.2 +3 146194118 . TG T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCAGCCAAGGGAGGCGC;RSEQ=AGTGTTCATGCTACCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:31.5:1:1:0:60:4:1:0:0 +3 146994528 . C T 26 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58441;SOR=2.56268;LSEQ=ATACAGCCTTTTGGCTGGAA;RSEQ=CGTCATCTTCCAGTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:1:0,1:108,86:194,1:0.0051:2,0:1:0:25:0:0.44615:0:32:2:0.0052:0:1 0/1:153:2:1,1:81,70:151,2:0.0131:2,2:8:0:26.5:1:1:1.15603:36.5:4:0.0132:0:1.5 +3 146994550 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18241;SOR=Inf;LSEQ=GTCATCTTCCAGTAATTTTG;RSEQ=CAAAATGACGAACACAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:116,106:222,0:0:2,0:28.6:1:31.5:1:1:0:47.7:30.714:1:0:0.1 0/1:166:2:1,1:84,80:164,2:0.012:2,2:35:0:32:0:1:1.04971:42:4:0.0123:0:1.5 +3 146994559 . C T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07584;SOR=Inf;LSEQ=CAGTAATTTTGCCAAAATGA;RSEQ=GAACACAAAGGGAAAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:109,109:218,0:0:2,0:28.7:1:31:1:1:0:47.4:71.667:1:0:0.1 0/1:161:3:2,1:75,83:158,3:0.0186:2,2:31:1:23.7:1:0.60679:2.20:44.3:2:0.0127:0:1 +3 146994601 . GT G 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.136;SOR=Inf;LSEQ=AGGCACCCGATATATGTTCT;RSEQ=AGGCCTTTTAGAAAGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:112,72:184,0:0:2,0:22.1:1:29.5:1:1:0:47.8:183:1:0:0.1 0/1:108:2:1,1:59,47:106,2:0.0185:2,2:5.5:1:27.5:1:1:1.25265:36:4:0.0187:0.0093:0.5 +3 146994746 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18315;SOR=Inf;LSEQ=TGTTACCCAGCATGCTTTTG;RSEQ=CATTGTTGTAAACAAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:96,172:268,0:0:2,0:24.2:1:31.4:1:1:0:40.2:43.667:1:0:0.1 0/1:201:2:1,1:72,127:199,2:0.01:2,2:24:1:30.5:1:1:1.76:29:4:0.01:0:1 +3 146994748 . A C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18957;SOR=Inf;LSEQ=TTACCCAGCATGCTTTTGGC;RSEQ=TTGTTGTAAACAAACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:91,169:260,0:0:2,0:23.9:1:30.5:1:1:0:40.2:42.333:1:0:0.1 0/1:201:2:1,1:71,128:199,2:0.01:2,2:5.5:1:28.5:1:1:1.80:36:4:0.01:0:2 +3 147090929 . T TA 50 d5;v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.52381;SOR=3.76419;LSEQ=ATATTGTAGGACAAAGGAGC;RSEQ=AAAAAAAAAAAAAACCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:3,1:0.25:0,0:39:0:31:0:1:0:60:2:0.3333:0:1 1/0:5:3:0,3:0,2:2,3:0.6:0,0:23.7:1:31.7:1:1:0:60:6:0.6:0:2 +3 147308948 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTAGACGTAAGTCCTTTG;RSEQ=GCGTTTTAGGAGTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:41:0:31:0:0.4:0:60:4:0.5:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:38:0:31:0:1:0:44:2:1:0:8 +3 147309195 . G T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47913;SOR=0.67487;LSEQ=TCTTGCTACCACCTCCAGGG;RSEQ=CAGATTGCCTTCCAGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:20:7,13:6,9:15,20:0.5714:2,2:27.7:1:30.5:1:1:1.23051:60:40:0.5714:0:1.2 0/1:36:17:10,7:10,9:19,17:0.4722:2,2:29.8:1:29.3:1:0.74857:1.28:60:34:0.4722:0:1.1 +3 147309475 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=ATTCATCCTTTGCACGAGCC;RSEQ=CTAAACTCACCATTCTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:23,0:0:2,0:22:1:31.1:1:1:0:60:46:1:0:0 0/1:23:2:1,1:10,11:21,2:0.087:2,2:35.5:1:28.5:1:1:1.10:60:4:0.0909:0:1 +3 147309587 . C T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52034;SOR=0;LSEQ=GAAAAGATAGTTTAGGGTCT;RSEQ=AAGGGGCTCATGTCTATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:41,14:55,2:0.0351:2,2:7.5:1:28.5:1:0.46053:2.86356:60:4:0.0351:0:1.5 0/0:36:0:0,0:27,8:35,0:0:2,0:22.5:1:30.9:1:1:0:60:16.5:1:0:0.1 +3 148295212 . G A 45 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CTCAACTAACAACTTCTACC;RSEQ=AGGACCACTGGACCGACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:15.7:1:28.7:1:1:0:30:6:1:0:3 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:34:0:27:0:1:0:21:2:0.3333:0:3 +3 148295219 . A C 60 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAACTTCTACCGAGGACC;RSEQ=CTGGACCGACGGGCTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:22.7:1:29.7:1:1:0:30:6:1:0:3 1/1:4:4:1,3:0,0:0,4:1:0,2:29.5:1:30:1:1:0:26:8:1:0:2 +3 148295275 . C T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATTCCCCTCTGGAGGACA;RSEQ=TACAACTGCAGGGCCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:29.8:1:30.8:1:1:0:26.4:10:1:0:2.2 1/1:3:3:0,3:0,0:0,3:1:0,0:16.3:1:28:1:1:0:29:6:1:0:2 +3 149114614 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTTGTTGGCCTCGTTCA;RSEQ=TTTTCATTCAATTAATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:24:1:33.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 149140381 . A AT 31 d5;v3;pSTD;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GACTTTGGTGACGGAGTATA;RSEQ=TTTTTTTTTTTTAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:47:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:0:31.5:1:1:0:60:4:1:0:0 +3 149140532 . C G 33 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTACAGGCGTGAGCCACCAT;RSEQ=TCTGGCTAATTTTTGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:33:0:1:0:45:4:1:0:1 +3 149657050 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50084;SOR=Inf;LSEQ=TTCCTCACTGGTGCTTTTTA;RSEQ=CCAGTTTCCTCATCATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:46,52:98,0:0:2,0:22.6:1:30.9:1:1:0:60:196:1:0:0.1 0/1:115:2:1,1:55,58:113,2:0.0174:2,2:42.5:1:29.5:1:1:1.05:60:4:0.0179:0:1 +3 149657159 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49727;SOR=Inf;LSEQ=CTTTTCTGCCACCTCCGGGG;RSEQ=CAGATCGCTTTCCAGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:51,38:89,0:0:2,0:24:1:31.7:1:1:0:57.6:178:1:0:0 0/1:91:2:1,1:55,34:89,2:0.022:2,2:17.5:1:27:1:1:1.60874:60:4:0.022:0:1 +3 149657220 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23679;SOR=0;LSEQ=CTTCTTCATCTTCTGACTCT;RSEQ=CATCTTCCTCCACAGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:78,75:153,2:0.0129:2,2:26:0:32.5:1:1:1.03975:23:4:0.0129:0:1.5 0/0:163:0:0,0:85,78:163,0:0:2,0:28:1:31.3:1:1:0:37.8:162:1:0:0.2 +3 149657235 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49966;SOR=Inf;LSEQ=ACTCTGCATCTTCCTCCACA;RSEQ=CTACTAAGTGCTGTCCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:78,79:157,0:0:2,0:28.4:1:32.5:1:1:0:37.3:51.333:1:0:0.1 0/1:173:2:1,1:84,87:171,2:0.0116:2,2:43:1:29:1:1:1.04:40:4:0.0117:0:1 +3 149657237 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22271;SOR=0;LSEQ=TCTGCATCTTCCTCCACAGC;RSEQ=ACTAAGTGCTGTCCACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:75,79:154,2:0.0128:2,2:44.5:1:32.5:1:1:1.05:26:4:0.013:0:1 0/0:174:0:0,0:86,88:174,0:0:2,0:24.9:1:28.5:1:1:0:39.3:57:1:0:0.2 +3 149657240 . TA T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49952;SOR=Inf;LSEQ=GCATCTTCCTCCACAGCTAC;RSEQ=AGTGCTGTCCACTAATATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:75,81:156,0:0:2,0:28.4:1:29.5:1:1:0:37.6:155:1:0:0.1 0/1:171:2:1,1:80,89:169,2:0.0117:2,2:25.5:1:28.5:1:1:1.11:42.5:4:0.0119:0:1 +3 149657498 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49834;SOR=Inf;LSEQ=TCATTATTCACCTTAAAGTG;RSEQ=TAATCTTTGTCGGCCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:80,61:141,0:0:2,0:25.4:1:30.3:1:1:0:58.1:46:1:0:0.1 0/1:145:2:1,1:68,75:143,2:0.0138:2,2:37.5:1:30:1:1:1.10:52:4:0.0138:0:1 +3 149657503 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.85516;LSEQ=ATTCACCTTAAAGTGATAAT;RSEQ=TTTGTCGGCCTTTTGTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:1:1,0:75,57:132,1:0.0075:2,0:1:0:24:0:1:0:51:2:0.0076:0:1 0/1:144:2:1,1:69,73:142,2:0.0139:2,2:23.5:1:27.5:1:1:1.06:55.5:4:0.0139:0:1 +3 149657555 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24283;SOR=Inf;LSEQ=TAGTTCTGGGGCCTCAGAGG;RSEQ=CTCATGTCCATGTCCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:68,55:123,0:0:2,0:20.8:1:31.7:1:1:0:59.3:122:1:0:0.1 0/1:120:2:1,1:64,54:118,2:0.0167:2,2:23:1:29:1:1:1.1835:60:4:0.0168:0:1 +3 149657610 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50315;SOR=0;LSEQ=GGTGACACGCACTTAGGTGG;RSEQ=AGAGAAGGTGGACAGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:89,91:180,2:0.011:2,2:19.5:1:29:1:1:1.02:48:4:0.011:0:1.5 0/0:150:0:0,0:75,75:150,0:0:2,0:26.8:1:30.3:1:1:0:59.5:300:1:0:0.1 +3 149657626 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.5061;SOR=0;LSEQ=GTGGGAGAGAAGGTGGACAG;RSEQ=GATAAACGACTGCTGCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:81,98:179,2:0.011:2,2:22:1:33:0:1:1.21:60:4:0.0113:0:1 0/0:142:0:0,0:64,78:142,0:0:2,0:28.4:1:29:1:1:0:59.5:46.333:1:0:0.1 +3 149657634 . G T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50849;SOR=0;LSEQ=GAAGGTGGACAGAGATAAAC;RSEQ=ACTGCTGCTCCAGAGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:78,97:175,2:0.0113:2,2:23:0:29:1:1:1.24:60:4:0.0117:0:1 0/0:133:0:0,0:58,75:133,0:0:2,0:28.7:1:29.8:1:1:0:59.5:43.333:1:0:0.1 +3 150742609 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24917;SOR=Inf;LSEQ=AGTCCAGATTCAAGAGGAGG;RSEQ=CAAATAAGTTCCACCTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:183,54:237,0:0:2,0:24:1:31.4:1:1:0:60:58.25:0.9957:0:0.2 0/1:253:3:2,1:176,74:250,3:0.0119:2,2:23.3:1:26:1:1:1.18832:60:6:0.012:0:1 +3 150742677 . A G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=2.24028;LSEQ=GAGGGGAGAAACTGATGGGA;RSEQ=CCATATTTGAGGACTAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:154:82,72:190,167:357,154:0.3014:2,2:30.3:1:32.8:1:1:1.00:60:76:0.301:0:1.1 0/1:539:265:141,124:135,138:273,265:0.4917:2,2:26.7:1:31.1:1:0.38977:1.16:60:87.333:0.4916:0:1.1 +3 153741490 . C G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.68017;SOR=0.51492;LSEQ=ATGTCATCCTTTTATACCAT;RSEQ=AGATCTCAGAGAGAGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:6,0:6,8:0.5714:0,0:26.4:1:32:1:1:0:60:16:0.5714:0:1 0/1:10:4:4,0:6,0:6,4:0.4:0,0:20.3:1:31.8:1:1:0:60:8:0.4:0:1 +3 153741556 . A C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10231;SOR=Inf;LSEQ=CAACAATATAAAAATTAATA;RSEQ=CTGCAGAATCAAAGCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:48,18:66,0:0:2,0:22.6:1:30.4:1:1:0:59.8:132:1:0:1 0/1:59:3:2,1:41,15:56,3:0.0508:2,2:13:1:30.3:1:1:1.359:60:6:0.0508:0:1.7 +3 153741592 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49794;SOR=Inf;LSEQ=TACAAAAATAGCTCTTTCAG;RSEQ=CAGAACCACCATCTTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:74,47:121,0:0:2,0:26.9:1:31.5:1:1:0:57.9:59.5:1:0:1.5 0/1:122:2:1,1:68,52:120,2:0.0164:2,2:21.5:1:27.5:1:1:1.30478:60:4:0.0167:0:1.5 +3 153741599 . CA TG 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49806;SOR=Inf;LSEQ=ATAGCTCTTTCAGCCAGAAC;RSEQ=CCATCTTCCAGTAATTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:74,49:123,0:0:2,0:28.2:1:31.3:1:1:0:57.8:40:1:0:1.5 0/1:126:2:1,1:69,55:124,2:0.0159:2,2:25:1:29:1:1:1.25226:45:4:0.0159:0.0079:1.5 +3 153741618 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23914;SOR=0;LSEQ=CCACCATCTTCCAGTAATTC;RSEQ=CCAAAATGACGAACACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:64,56:120,2:0.0163:2,2:30:1:31.5:1:1:1.1416:60:4:0.0169:0:2 0/0:128:0:0,0:64,64:128,0:0:2,0:30.1:1:29:1:1:0:56.6:127:1:0:1.6 +3 153741628 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00683;SOR=3.04203;LSEQ=CCAGTAATTCACCAAAATGA;RSEQ=GAACACAAAGGGAAACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:118:96:49,47:9,13:22,96:0.8136:2,2:26.9:1:30.9:1:0.48061:1.50:57.6:192:0.8205:0:2.3 1/1:129:120:55,65:4,5:9,120:0.9302:2,2:27.5:1:29.5:1:1:1.06:56.9:119:0.9297:0:1.8 +3 153741637 . A C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1845;LSEQ=CACCAAAATGACGAACACAA;RSEQ=GGGAAACAGGAGAGTCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:117:87:43,44:12,18:30,87:0.7436:2,2:21.8:1:31:1:0.40348:1.46:58:174:0.75:0:2.4 0/1:124:43:19,24:34,47:81,43:0.3468:2,2:25.8:1:30.1:1:0.85028:1.09:58.5:42:0.3471:0:2.4 +3 153741644 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24428;SOR=0;LSEQ=ATGACGAACACAAAGGGAAA;RSEQ=AGGAGAGTCACCTGATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:51,55:106,2:0.0185:2,2:10.5:1:32.5:1:1:1.08:58:4:0.0187:0:3 0/0:110:0:0,0:45,64:109,0:0:2,0:23.8:1:31.4:1:1:0:57.1:218:0.9909:0:1.8 +3 153741680 . C T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01827;SOR=5.69485;LSEQ=TAATTGTTCTCTTGGCCTTT;RSEQ=AGAAAACATAGAATTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:65:32,33:2,9:11,65:0.8553:2,2:25.4:1:30.2:1:0.09845:4.29:59:130:0.8553:0:1.9 1/1:70:68:29,39:0,2:2,68:0.9714:0,2:19.2:1:29:1:0.50766:0:58.2:67:0.971:0:1.9 +3 153741705 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18275;SOR=Inf;LSEQ=AACATAGAATTGTTCCTTTG;RSEQ=CCACATACATGGGAATCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:42,35:77,0:0:2,0:25.4:1:32.2:1:1:0:60:76:1:0:1.1 0/1:58:2:1,1:31,25:56,2:0.0345:2,2:23:0:30.5:1:1:1.23537:60:4:0.0351:0:1 +3 153741735 . G A 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGAATCCACAAGAAAGGC;RSEQ=ATATTGTAGACATCAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:52,29:81,0:0:2,0:24.1:1:30.8:1:1:0:59.9:26:1:0:0.5 0/1:78:20:13,7:43,15:58,20:0.2564:2,2:21.7:1:30.9:1:0.56514:1.53464:58.2:40:0.2632:0:1.4 +3 153741861 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24295;SOR=Inf;LSEQ=GCATTGTTCTAAACAAACAA;RSEQ=GGCAGGATTCTTGCCAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:41,84:125,0:0:2,0:17.7:1:31.4:1:1:0:58.5:124:1:0:0.1 0/1:122:2:1,1:33,87:120,2:0.0164:2,2:34.5:1:29.5:1:0.48137:2.61:49:4:0.0164:0:1.5 +3 153741874 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21963;SOR=0;LSEQ=CAAACAAGGGCAGGATTCTT;RSEQ=CCAAGAGAATTAATGTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:17,60:77,2:0.0253:2,2:9.5:1:28:1:0.40604:3.46:60:4:0.0256:0:1 0/0:89:0:0,0:16,73:89,0:0:2,0:23.1:1:31.5:1:1:0:59.4:178:1:0:0 +3 153742413 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGTTCCCCTCTCTGTGTC;RSEQ=ATGTTTTCTCATTGTTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:27.5:1:1:0:50.5:4:1:0:3 +3 153742415 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTCCCCTCTCTGTGTCCA;RSEQ=GTTTTCTCATTGTTCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:29:1:1:0:50.5:4:1:0:3 +3 153742440 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCATTGTTCAGCTCCCAC;RSEQ=TAGACTGAGAACATGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:32:1:1:0:50.5:4:1:0:3 +3 154880370 . C T 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10467;SOR=1.2781;LSEQ=AACCTCTTTTCATATGCTTG;RSEQ=CTGGTTCTTGAACAGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:124:71,53:183,165:348,124:0.2622:2,2:27.6:1:29.8:1:0.40206:1.21:59.9:61:0.2607:0:1.1 0/1:429:134:72,62:162,133:295,134:0.3124:2,2:24.3:1:28.3:1:0.83488:1.04879:60:43.667:0.3104:0:1.1 +3 155180003 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16338;SOR=0;LSEQ=TGTTGCTACCACAATGGGGG;RSEQ=AGAGAGGAGTACATCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:17,10:27,2:0.069:2,2:25.5:1:28.5:1:1:1.66781:60:4:0.069:0:1 0/0:42:0:0,0:25,17:42,0:0:2,0:26.2:1:31:1:1:0:60:84:1:0:0.1 +3 155180082 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49543;SOR=Inf;LSEQ=CCAGTGAAACTTGTAAATGG;RSEQ=CACCTGCAGCAACTATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:11,23:34,0:0:2,0:21.7:1:31.6:1:1:0:60:33:1:0:0.1 0/1:39:2:1,1:13,24:37,2:0.0513:2,2:28:1:30:0:1:1.82:60:4:0.0513:0:1 +3 155180174 . G A 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=ACTACTGACTGAAGATGTGG;RSEQ=AAATAAGAATAGGTGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:19:1:33:0:1:0:60:4:0.5:0:1 0/1:4:1:0,1:0,3:3,1:0.25:0,0:14:0:31:0:1:0:60:2:0.25:0:1 +3 155829057 . A T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05303;SOR=Inf;LSEQ=TATTTAAACAAAGCTCTTAA;RSEQ=ATAACAACGTGGTTAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:25,0:0:1,0:22.3:1:31.6:1:1:0:58.8:50:1:0:0.1 0/1:8:2:2,0:5,1:6,2:0.25:2,0:8:1:32.5:1:1:0:60:4:0.2857:0:2 +3 155829059 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04234;SOR=Inf;LSEQ=TTTAAACAAAGCTCTTAAAA;RSEQ=AACAACGTGGTTAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:25,0:0:1,0:23.6:1:32.4:1:1:0:59.3:50:1:0:0.1 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:10:1:31:0:1:0:60:4:0.2857:0:2 +3 155829377 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=1.6102;LSEQ=TTGATGTGTCTGTGAAGTGG;RSEQ=AGGAAAAATGTCTTCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:266:111,155:125,170:295,266:0.4742:2,2:24.9:1:32.3:1:0.93178:1.02672:59.9:65.5:0.4712:0:1.1 1/0:466:276:116,160:85,101:186,276:0.5923:2,2:23.7:1:31.7:1:0.44548:1.16043:59.5:552:0.5961:0:1.1 +3 155829458 . G A 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17703;SOR=5.04797;LSEQ=AGTGACATTTTGGGAAGGCT;RSEQ=CTGTCTTGTAGATTTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:0,1:165,203:368,1:0.0027:2,0:36:0:32:0:1:0:60:2:0.0028:0:1 0/1:295:4:3,1:125,166:291,4:0.0136:2,2:10.8:1:24:1:0.31999:3.97:60:8:0.0137:0:1 +3 155829701 . C G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGTTCTGCTAAATCTATA;RSEQ=TCATAAGGTCATCAGCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:544:0:0,0:223,321:544,0:0:2,0:23.1:1:32.4:1:1:0:41.5:53.4:1:0:0.1 0/1:496:25:13,12:203,267:470,25:0.0504:2,2:25.4:1:31.7:1:0.41348:1.42:42.1:50:0.051:0:1.2 +3 155829782 . T C 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCCCTGTTAATAGCCTCA;RSEQ=GGACGTCATCATCTTCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:49,190:239,0:0:2,0:23.1:1:30.6:1:1:0:59.7:46.8:1:0:0.2 0/1:156:16:6,10:35,105:140,16:0.1026:2,2:19.6:1:29.6:1:0.36719:1.79:59.6:32:0.1039:0:1.4 +3 155829829 . T A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTGTCTGTTTTCTCTGAA;RSEQ=CGACATACTTCCTCATTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:36,102:138,0:0:2,0:22:1:30.2:1:1:0:60:45:1:0:0.6 0/1:91:13:6,7:21,57:78,13:0.1429:2,2:21.2:1:29.3:1:0.19432:2.30:60:26:0.1494:0:1.7 +3 155829855 . C T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09982;SOR=1.59785;LSEQ=TACTTCCTCATTGATTTTAT;RSEQ=TTCTAGGGCATCAATATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:48:10,38:21,47:68,48:0.4138:2,2:22.7:1:30.8:1:0.28847:1.69027:59.7:96:0.4486:0:1.8 1/0:98:52:16,36:20,26:46,52:0.5306:2,2:25.4:1:29.1:1:0.21376:1.721:60:25:0.5747:0:2 +3 155829895 . T TG 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2203;SOR=0.40135;LSEQ=CGTTCTTAAAGAAAATGCTG;RSEQ=GTTTTTTTTTTTTGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:8:2,6:23,58:81,8:0.0889:2,2:35.9:1:29.3:1:1:1.1874:53.8:7:0.0833:0:2.8 0/1:80:3:1,2:26,50:76,3:0.0375:2,2:26.3:1:30:1:1:1.03949:60:6:0.0405:0:1 +3 155829896 . GT G 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.21772;SOR=0.22304;LSEQ=GTTCTTAAAGAAAATGCTGT;RSEQ=TTTTTTTTTTTGTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:5:1,4:16,46:62,5:0.0568:2,2:27.4:1:32.3:1:1:1.3849:59.2:10:0.0575:0.0227:1.6 0/1:76:1:0,1:16,29:45,1:0.0132:2,0:48:0:32:0:1:0:60:2:0.0132:0:0 +3 155829897 . T G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.0874;SOR=1.85398;LSEQ=TTCTTAAAGAAAATGCTGTG;RSEQ=TTTTTTTTTTTGTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:21:6,15:16,46:62,21:0.2386:2,2:26.4:1:31.9:1:0.78237:1.15:57.5:20:0.2299:0:2.6 0/1:76:28:7,21:16,29:45,28:0.3684:2,2:29:1:32:1:0.44022:1.64397:59.4:56:0.3684:0:3 +3 155829917 . G T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.09087;SOR=Inf;LSEQ=TTTTTTTTTTTTGTTTTTTT;RSEQ=TTTTTTTTTGTGTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:18,51:69,0:0:2,0:17.1:1:30.2:1:1:0:54.3:7.625:0.9839:0:1.6 0/1:59:3:3,0:15,40:55,3:0.0508:2,0:10.3:1:20.7:1:0.02645:0:57.7:2:0.0392:0:2.3 +3 155829925 . T G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.67253;SOR=1.26602;LSEQ=TTTTGTTTTTTTGTTTTTTT;RSEQ=TGTGTTTTTTTGAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:18:2,16:9,23:32,18:0.3529:2,2:20.6:1:29.9:1:0.28664:3.06701:48.2:5:0.3261:0:3.2 0/1:44:18:5,13:8,18:26,18:0.4091:2,2:12.9:1:30.2:1:1:1.15178:58.6:8:0.381:0:3.4 +3 155829938 . A C 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3989;SOR=0.58756;LSEQ=TTTTTTTTTGTGTTTTTTTG;RSEQ=GACAGAGTCTCTCTCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:2,12:5,14:19,14:0.4242:2,2:17.2:1:25:1:0.66975:2.09577:47.2:3.667:0.3929:0:3.3 0/1:20:6:1,5:3,11:14,6:0.3:2,2:11.7:1:30.2:1:1:1.34348:58.8:12:0.3333:0:4 +3 155829952 . T A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.02311;SOR=Inf;LSEQ=TTTTTGAGACAGAGTCTCTC;RSEQ=CTGTCACCCAGGCTGGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:7,18:25,0:0:2,0:25.1:1:29.9:1:1:0:43.9:11.5:1:0:1.3 0/1:11:3:0,3:1,7:8,3:0.2727:2,0:11.3:1:29.3:1:1:0:47.3:6:0.3:0:2.7 +3 155830167 . C T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0263;SOR=Inf;LSEQ=TCCTGACCTTGTGATCCACC;RSEQ=GCCTCGGCCTCCCAAAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:105,4:109,0:0:1,0:24.5:1:31.5:1:1:0:43.2:218:1:0:0.1 0/1:75:4:4,0:70,1:71,4:0.0533:1,0:13:1:31.5:1:1:0:57.3:8:0.0533:0:1 +3 155830211 . G A 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=GATTAGAGATGTGAGCCTCC;RSEQ=CGCCCAGACGAAATTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:214,45:259,0:0:2,0:21.3:1:30.2:1:1:0:53.3:85.333:1:0:0.3 0/1:238:15:11,4:176,47:223,15:0.063:2,2:17:1:28.2:1:0.53404:1.3598:51.5:14:0.0593:0:1.1 +3 155830283 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.73802;LSEQ=CAATGGCATCTTTCTCCTCC;RSEQ=TGTCCACAAATTCTTGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:625:286:166,120:188,150:338,286:0.4576:2,2:26.9:1:31.8:1:0.57069:1.10:36.4:94.333:0.4587:0:1.1 1/0:597:355:185,170:133,109:242,355:0.5946:2,2:25.5:1:30.6:1:0.50497:1.12103:36.9:117.333:0.5976:0:1.1 +3 155830631 . C T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.58725;LSEQ=AAGAATTACCTAGATGTTCC;RSEQ=ATTTAGCATTTTCAAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:95:34,61:52,81:133,95:0.4148:2,2:23:1:29.9:1:0.67814:1.15107:60:46.5:0.4152:0:1.1 1/0:176:114:54,60:26,36:62,114:0.6477:2,2:23.6:1:28.9:1:0.52862:1.24:60:113:0.6532:0:1.1 +3 155830919 . G GT 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.33386;SOR=3.62994;LSEQ=GTTGTTCATTTTTGTTTTTT;RSEQ=TTTTTTTTAGATGGAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:0,1:58,106:164,1:0.0061:2,0:25:0:32:0:1:0:60:2:0.0063:0:0 0/1:138:3:2,1:42,93:135,3:0.0217:2,2:26:1:29.7:1:0.23841:4.38:54.3:6:0.0217:0.0072:0.3 +3 155831114 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10135;SOR=Inf;LSEQ=AGACGGGGTTTTACCATGTT;RSEQ=GTCAGGCTGGTCTCGAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:72,4:76,0:0:2,0:23.3:1:32.8:1:1:0:33.7:75:1:0:0.1 0/1:36:2:2,0:34,0:34,2:0.0556:1,0:10.5:1:31.5:1:1:0:51.5:4:0.0556:0:1 +3 155831221 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.10473;SOR=Inf;LSEQ=GCCTGACCTGTTGTTCATTT;RSEQ=TGGTTGGAGCTATTTTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:154,86:240,0:0:2,0:31.2:1:30.6:1:1:0:54.8:59:1:0:0.1 0/1:215:3:1,2:137,75:212,3:0.014:2,2:24.3:1:29.7:1:0.292:3.63017:45.3:6:0.014:0:1.3 +3 155831270 . C T 109 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=16.81076;LSEQ=ATGGCCCCAGATAACAAGAT;RSEQ=AATGAAGTCATCCAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:1:0,1:210,182:392,1:0.0025:2,0:27:0:11:0:0.46565:0:27:0:0:0:5 0/1:364:15:7,8:185,164:349,15:0.0412:2,2:17.8:1:28:1:0.79288:1.28829:47.3:30:0.0414:0:1.1 +3 155831386 . T C 143 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=15.39785;LSEQ=GTTCTCATCTTCTTTTGATC;RSEQ=CAACATTGTTATTTCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:541:2:1,1:261,278:539,2:0.0037:2,2:24:0:33:0:1:1.07:60:4:0.0038:0:1.5 0/1:480:26:11,15:220,234:454,26:0.0542:2,2:27.7:1:30.5:1:0.68727:1.28139:54.5:52:0.0546:0:1.3 +3 155831479 . T C 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00097;SOR=Inf;LSEQ=GCAATGTTTGTGCTTCCTTT;RSEQ=TGAAGCAAAACCAGACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:180,166:346,0:0:2,0:23.4:1:30.8:1:1:0:60:114.333:0.9971:0:0.1 0/1:303:9:5,4:139,155:294,9:0.0297:2,2:26.2:1:31.8:1:0.74053:1.39:60:18:0.0298:0:1.1 +3 155831899 . A G 167 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=54.78729;LSEQ=ATGTATCATTTCCTCTGACT;RSEQ=CATCTTTCTCCATAAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:1:0,1:110,184:294,1:0.0034:2,0:24:0:11:0:1:0:23:0:0:0:8 0/1:247:39:18,21:87,121:208,39:0.1579:2,2:25.3:1:31.7:1:0.72447:1.19:45.7:78:0.1592:0:1.2 +3 155831926 . A G 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00015;SOR=Inf;LSEQ=TCTCCATAAATCCAAGATCA;RSEQ=TATCTGTTGCAACTAAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:96,153:249,0:0:2,0:26.5:1:30.8:1:1:0:59.8:34.571:1:0:0.1 0/1:207:11:7,4:86,110:196,11:0.0531:2,2:19.9:1:32.5:1:0.22669:2.23:60:22:0.0531:0:1.1 +3 155832010 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.2163;SOR=Inf;LSEQ=TTATGGTCAGTCAAGCTCCT;RSEQ=TGGGACCAAGTTCTTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:86,117:203,0:0:2,0:29.9:1:32.9:1:1:0:58.8:49.75:1:0:0.1 0/1:177:2:1,1:75,99:174,2:0.0113:2,2:37:1:30.5:1:1:1.32:43:4:0.0115:0:1 +3 155848828 . G C 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00083;SOR=Inf;LSEQ=ATTTCAGAATTTGAGTTTAA;RSEQ=TCAGGCTTTGGCCATCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:97,2:99,0:0:1,0:23.5:1:33.5:1:1:0:60:98:1:0:0.4 0/1:73:8:7,1:55,10:65,8:0.1096:2,2:23.6:1:31.4:1:1:1.27:60:16:0.1111:0:1.9 +3 155848833 . G T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00317;SOR=2.50648;LSEQ=AGAATTTGAGTTTAAGTCAG;RSEQ=CTTTGGCCATCTCCTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:47:44,3:62,3:65,47:0.4196:1,2:23.9:1:30.5:1:0.69408:1.40468:60:94:0.4196:0:1.1 1/0:79:51:40,11:23,4:27,51:0.6456:2,2:19.1:1:29:1:0.55766:1.57241:60:102:0.6538:0:1.2 +3 155848952 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.10509;LSEQ=TGCTAATGTCCTGCCAGGGA;RSEQ=TTTTACCATTGTATTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:208:108,100:129,143:272,208:0.4324:2,2:27:1:32.6:1:0.3573:1.20:60:68.333:0.4334:0:1.1 1/0:396:244:128,116:78,74:152,244:0.6162:2,2:27:1:31.1:1:0.8368:1.05:60:243:0.6215:0:1.1 +3 155849093 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59975;SOR=1.2143;LSEQ=CCCCAGGTATGTGAAATGTC;RSEQ=TCAGATGTCAGTTTTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:50:2,48:1,37:38,50:0.5682:1,1:21.8:1:31.3:1:1:1.53:59.2:100:0.5747:0:1.2 1/0:52:32:4,28:1,19:20,32:0.6154:1,2:21.2:1:30.3:1:0.63739:2.67:60:64:0.6275:0:1 +3 155849212 . T C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.32867;SOR=0.31293;LSEQ=AAGAAACTTGCCAAATATTT;RSEQ=TTCAGTCTCCAAAAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:3,7:0.7:0,0:22:1:30.7:1:1:0:60:6:0.6667:0:1.3 0/1:5:2:0,2:0,3:3,2:0.4:0,0:24.5:1:33.5:1:1:0:60:4:0.4:0:1 +3 156800360 . A G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24222;SOR=1.23742;LSEQ=CCAGTCACCGCTTTGTTCAG;RSEQ=TGACTCAGGTAAATAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:302:213:116,97:50,39:89,213:0.7053:2,2:25.1:1:31.8:1:0.80105:1.07179:59.9:105.5:0.7057:0:2 1/0:317:237:125,112:43,37:80,237:0.7476:2,2:24.9:1:30.3:1:0.89758:1.04118:60:46.4:0.7484:0:2 +3 156800384 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27052;SOR=1.21377;LSEQ=CTCAGGTAAATAAATGAGGC;RSEQ=GCACAGGCTGTCCTGACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:337:236:119,117:49,51:100,236:0.7003:2,2:25.3:1:31.1:1:0.90506:1.06:59.8:235:0.7036:0:1.9 1/0:353:261:128,133:42,50:92,261:0.7394:2,2:27.2:1:29.6:1:0.628:1.15:60:42.5:0.737:0:1.9 +3 156800426 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1105;SOR=0;LSEQ=CACACCTCTAGAATACCCTG;RSEQ=CTGTGCTGGGAGCTATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:120,164:284,3:0.0105:2,2:29.7:1:28.7:1:0.57663:2.72:60:6:0.0108:0:1.7 0/0:310:0:0,0:134,176:310,0:0:2,0:24.7:1:31:1:1:0:59.9:102.333:1:0:1 +3 156800472 . C G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=CTGAGTATTTTCATCCCTGT;RSEQ=CAAGTCACAATGATCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:42,98:140,0:0:2,0:22.8:1:31.1:1:1:0:60:69:1:0:0.2 0/1:148:2:1,1:41,104:145,2:0.0135:2,2:27:0:33.5:1:0.49119:2.52:60:4:0.0135:0:1.5 +3 156800489 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23577;SOR=Inf;LSEQ=TGTCCAAGTCACAATGATCT;RSEQ=ACTGTACCAGCCTGTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:20,78:98,0:0:2,0:23.8:1:31.7:1:1:0:60:23.5:1:0:0.1 0/1:93:2:1,1:19,72:91,2:0.0215:2,2:23.5:1:27:1:0.38569:3.72:60:4:0.0217:0:1 +3 156800696 . GA G 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATATGCAAGACTCAGGCAG;RSEQ=AAAAAAAAAGGTAATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:3,3:0.5:0,2:30:1:31.2:1:1:0:60:6:0.5:0.1667:0.3 1/1:1:1:0,1:0,0:0,1:1:0,0:39:0:31:0:1:0:60:2:1:0:0 +3 156952051 . C CT 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22977;SOR=0.24463;LSEQ=GTCATTGCAATCTGAATCAG;RSEQ=TTTTTTTTTCCTGAGCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:5:4,1:78,7:85,5:0.0556:2,2:16.4:1:31.2:1:0.37916:2.7405:60:10:0.0562:0.0222:0 0/1:71:1:1,0:67,2:69,1:0.0141:1,0:49:0:29:0:1:0:60:2:0.0145:0:0 +3 156952194 . A T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=0.53412;LSEQ=AATAAATCTAATCTTTAGGA;RSEQ=TGTCCATGGCTTTGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:117:52,65:81,85:166,117:0.4134:2,2:25.3:1:30.6:1:0.54551:1.19044:59.8:57.5:0.4137:0:1.2 0/1:322:88:37,51:107,127:234,88:0.2733:2,2:25.3:1:29.3:1:0.61542:1.16077:59.8:87:0.2719:0:1.1 +3 158104613 . AC A 32 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49718;SOR=Inf;LSEQ=ATGTGAGTCGTATTCACTAG;RSEQ=CAAAAAAAAAAAAAAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:73,15:88,0:0:2,0:24.7:1:31.6:1:1:0:59.3:43:1:0:0.5 0/1:89:2:1,1:66,21:87,2:0.0225:2,2:6:1:32:1:0.43539:3.09405:60:4:0.0238:0.0112:1 +3 158104706 . A G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=2.10825;LSEQ=TGGTAGTACATGGAAATAAA;RSEQ=TGAATATTTTGAGCAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:69:27,42:97,108:205,69:0.2518:2,2:27.4:1:31.6:1:0.26482:1.39542:60:22:0.2435:0:1.2 0/1:207:86:36,50:56,65:121,86:0.4155:2,2:25.9:1:31:1:0.57165:1.19554:60:42:0.4118:0:1.1 +3 159246336 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15;SOR=Inf;LSEQ=CACTCCTGGCTTAATTGTGT;RSEQ=GCTTCCTGCACCTTCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:10,24:34,0:0:2,0:21.9:1:29.9:1:1:0:60:68:1:0:0.1 0/1:22:2:1,1:5,15:20,2:0.0909:2,2:28.5:1:31.5:1:0.48052:2.83:60:4:0.0909:0:1 +3 159601639 . C CT 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.64225;SOR=0.75791;LSEQ=GACTACTAAATCTCCCCCAA;RSEQ=TTTTTTTTTTCTTTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:15:11,4:161,28:189,15:0.0714:2,2:25.1:1:30.2:1:0.26215:2.08169:60:14:0.0683:0.0095:0.9 0/1:109:6:6,0:92,10:102,6:0.055:2,0:32.5:1:31:1:1:0:60:12:0.0566:0:0 +3 159601763 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0029;SOR=1.41388;LSEQ=GATCAGACTTTCTTCTGAGT;RSEQ=AAAATACATATATCTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:656:296:138,158:176,184:360,296:0.4512:2,2:24.5:1:29.9:1:0.58301:1.095:60:592:0.4526:0:1.1 1/0:571:307:152,155:122,142:264,307:0.5377:2,2:25.4:1:28.8:1:0.45031:1.14:60:306:0.5406:0:1.1 +3 160603511 . C T 26 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACTCTGTCAGCCACGGAT;RSEQ=GGAAGATCCCACTCACCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:9.5:1:32.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:26.5:1:1:0:60:4:1:0:1 +3 160603613 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAATCTGCTTAAGCCTG;RSEQ=GGAGCTCCCCTGGGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:28.5:1:32:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 160604387 . G A 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=AAGTGAATCCCCAGCAAACC;RSEQ=CAGCAGCCCTACAGAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:2,3:0.6:0,2:15:1:32:0:1:0:55:6:0.6:0:1 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:34:0:32:0:1:0:34:2:0.3333:0:1 +3 160604864 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGCATAGATAAGTATCA;RSEQ=TAGCTGAATCAATCAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:13.5:1:34.5:1:1:0:59:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 160605052 . A G 66 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAGGAGACGGGGAGAAT;RSEQ=AAAACAAGGTGGAAAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:17.8:1:33:1:1:0:58:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 162297000 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGTTTACAGGAAAAGG;RSEQ=TTCTGAAATCAGACAGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:23,15:38,2:0.0488:2,2:31:1:30:1:1:1.51653:51.5:4:0.05:0:1 0/0:12:0:0,0:10,2:12,0:0:2,0:19.8:1:30.8:1:1:0:58:11:1:0:0.1 +3 162297038 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52042;SOR=0;LSEQ=GCCTTTCAAACTCTTATACC;RSEQ=ACCTCTGGAGTTGGGTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:24,25:49,2:0.0392:2,2:32.5:1:30:1:1:1.04:60:4:0.0392:0:1.5 0/0:32:0:0,0:21,11:32,0:0:2,0:30.5:1:29.3:1:1:0:53.8:31:1:0:0.2 +3 162297058 . A G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02227;SOR=Inf;LSEQ=AACCTCTGGAGTTGGGTGAC;RSEQ=TGGTTTCTCCCCTTTCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:22,28:50,0:0:2,0:28.4:1:31.3:1:1:0:55.8:100:1:0:0.2 0/1:33:4:2,2:18,11:29,4:0.1212:2,2:40.8:1:30.8:1:1:1.61126:55.5:8:0.129:0:1 +3 162297104 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.17857;SOR=0;LSEQ=TGACAGCCATCTTACTACTA;RSEQ=TCGCCTTCAGGCCCTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:5,14:19,2:0.0952:2,2:29.5:1:31:1:0.5:2.65:51.5:4:0.0952:0:1 0/0:28:0:0,0:12,16:28,0:0:2,0:16.9:1:31.4:1:1:0:57.3:56:1:0:0.2 +3 162769145 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.61462;SOR=2.79379;LSEQ=TGAGTATACTGTAAATTGCT;RSEQ=ATTATTGTTAAATAAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:11,0:8,0:8,11:0.5789:0,0:18.2:1:33.7:1:1:0:60:22:0.5789:0:1.1 1/1:5:4:4,0:1,0:1,4:0.8:0,0:36.8:1:30.5:1:1:0:60:8:0.8:0:1 +3 162769266 . T C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0241;SOR=2.07313;LSEQ=AACAATTATTTGTCACCTGG;RSEQ=CATGAATGATTTATTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:118:71:54,17:32,15:47,71:0.6017:2,2:22.2:1:31.8:1:0.39961:1.48:59.6:142:0.6121:0:1 1/0:87:66:50,16:15,5:20,66:0.7586:2,2:22.5:1:31:1:1:1.04:60:65:0.7558:0:1.1 +3 162769378 . A T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0448;SOR=1.48241;LSEQ=AAAATGTGGTCAAATGTGCT;RSEQ=AAATTATACATATTTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:95:45,50:76,91:167,95:0.3626:2,2:25.5:1:29.9:1:0.79754:1.08:60:94:0.3615:0:1.1 0/1:201:92:40,52:44,65:109,92:0.4577:2,2:26.4:1:28.1:1:0.6694:1.14:60:45:0.4523:0:1.2 +3 162769431 . G C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06851;SOR=1.75114;LSEQ=TGAGAGGGTATTGGTATAGA;RSEQ=GAAATTTCTGTATTCTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:33:12,21:37,74:111,33:0.2276:2,2:23.5:1:30.5:1:0.83478:1.14:60:66:0.2276:0:1.3 0/1:88:30:9,21:15,43:58,30:0.3409:2,2:27:1:29.7:1:0.80136:1.23:60:29:0.3372:0:1.1 +3 162769497 . A G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.3732;SOR=2.0662;LSEQ=GTGCAAATATGACAGATTTC;RSEQ=CACAACAAAATTGACTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:28:0,28:2,16:18,28:0.6087:2,1:26.2:1:31.8:1:0.14783:0:60:27:0.6:0:1.2 1/0:17:13:1,12:0,4:4,13:0.7647:0,1:28.5:1:32.6:1:1:0:60:26:0.7647:0:1.1 +3 164564437 . CTAGT C 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CCTCGAATTATCCAGCTGAC;RSEQ=TTATTTATAAGTTTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:35,0:35,0:0:1,0:23.1:1:32.7:1:1:0:59.5:70:1:0:0.1 0/1:36:14:13,1:20,2:22,14:0.3889:2,1:27.6:1:31.6:1:1:1.29:60:28:0.3889:0.0278:0 +3 164564465 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19923;SOR=Inf;LSEQ=TTTATAAGTTTTTCATTGTT;RSEQ=TAAAAACTGCATTTTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:70,10:80,0:0:2,0:21.2:1:28.8:1:1:0:59.9:39:1:0:0.2 0/1:65:2:1,1:51,12:63,2:0.0308:2,2:25.5:1:29:1:0.3625:4.12311:60:4:0.0313:0:1 +3 164564512 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20549;SOR=Inf;LSEQ=ACAACAAACCTTTCTACTTG;RSEQ=TATGTACTTTTATAACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:129,72:201,0:0:2,0:25.9:1:29.9:1:1:0:60:99.5:1:0:0.2 0/1:168:2:1,1:101,65:166,2:0.0119:2,2:34.5:1:32:1:1:1.5496:60:4:0.012:0:1 +3 164564572 . A G 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25158;SOR=0;LSEQ=GCCAATTTAGAAGGGCATGC;RSEQ=CTACATGAAATCTGTACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:1,2:119,144:263,3:0.0113:2,2:28.7:1:26:1:1:1.64979:60:2:0.0077:0:2 0/0:234:0:0,0:110,124:234,0:0:2,0:26:1:29:1:1:0:60:77:1:0:0.6 +3 164564579 . G A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=2.96842;LSEQ=TAGAAGGGCATGCACTACAT;RSEQ=AAATCTGTACTGACTATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:58:24,34:90,109:199,58:0.2257:2,2:26.7:1:29.3:1:0.65388:1.16901:60:28:0.2222:0:1.1 0/1:239:111:51,60:58,70:128,111:0.4644:2,2:24.9:1:28.5:1:1:1.03:60:36:0.4596:0:1.2 +3 164564612 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19767;SOR=Inf;LSEQ=ACTATTGAACTATATATTAT;RSEQ=TCCATAATTACTACAATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:69,124:193,0:0:2,0:24.2:1:30.6:1:1:0:59.8:95.5:1:0:0.3 0/1:155:2:1,1:56,97:153,2:0.0129:2,2:21.5:1:28:1:1:1.73:60:4:0.013:0:1.5 +3 166228705 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=CTGCTGCAGGATCTCCAATA;RSEQ=CTCCAGAGGTTCAGGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:8,2:0.2:2,2:18:1:28.5:1:1:1.58:60:4:0.2:0:1 0/0:8:0:0,0:4,4:8,0:0:2,0:25.4:1:30.9:1:1:0:60:16:1:0:0.1 +3 166229033 . A G 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=AGGTCCCATAAGAAGGAGGA;RSEQ=GCACTCATTTTTGCTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:29.7:1:32.7:1:1:1.73:60:6:0.6:0:1 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:30:1:29:1:0.33333:0:60:4:0.6667:0:1 +3 166229202 . TCAA T 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=8.000;MSILEN=3;SSF=0.47255;SOR=0.46615;LSEQ=AGAAAGTGACAACAGCGTCA;RSEQ=CAACAACAACAACAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:6,5:3,5:8,11:0.5789:2,2:27.5:1:31.6:1:0.64992:1.93:59.5:22:0.6111:0.1053:0.4 0/1:13:5:2,3:6,2:8,5:0.3846:2,2:26.2:1:28.2:1:0.29293:3.95135:55:10:0.3846:0.0769:0.6 +3 166229248 . C T 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00427;SOR=0;LSEQ=AAAGGCCCCCACAAAAGCCC;RSEQ=ATCCAAGGGTCAGCAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:6,5:9,11:20,11:0.3548:2,2:27.9:1:30.3:1:0.71599:1.45:44:22:0.3548:0:1.2 0/0:17:0:0,0:8,9:17,0:0:2,0:26.5:1:30.6:1:1:0:56:34:1:0:0.2 +3 168576724 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=18.47959;LSEQ=CCAACAGCATGCTGTGTAAC;RSEQ=TTGTAGACCCTCCCAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:10:5,5:17,19:36,10:0.2174:2,2:27.4:1:30.9:1:1:1.11:60:20:0.2222:0:1.9 1/1:82:69:36,33:7,6:13,69:0.8415:2,2:28.4:1:30:1:1:1.0686:58.5:68:0.8395:0:2.1 +3 168576736 . C T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=22.13076;LSEQ=TGTGTAACATTGTAGACCCT;RSEQ=CCAGTTTTGCCTTCGTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:3,5:14,19:33,8:0.1951:2,2:30.1:1:29.8:1:1:1.222:60:16:0.2051:0:2.1 1/1:79:67:34,33:6,6:12,67:0.8481:2,2:29.3:1:29.3:1:1:1.03:58.4:134:0.8481:0:2.1 +3 168576801 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50321;SOR=Inf;LSEQ=AGTATTCATTCCCTGGATGT;RSEQ=TACAATATCACCTTTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:25,0:0:2,0:22:1:32.3:1:1:0:60:24:1:0:0.7 0/1:34:2:1,1:6,26:32,2:0.0588:2,2:15:1:27.5:1:0.37433:4.09:60:4:0.0588:0:1 +3 168576884 . T C 102 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02973;SOR=0;LSEQ=TAAAAGGCCTAGAGAACACG;RSEQ=ATCAAGTGCCTCTCCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:9:4,5:5,7:12,9:0.4286:2,2:21.4:1:32.3:1:1:1.11:60:18:0.4286:0:1.2 0/0:10:0:0,0:1,9:10,0:0:2,0:18.7:1:28.3:1:1:0:60:20:1:0:0.1 +3 169490890 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50099;SOR=0;LSEQ=CCGCGGTGCTGTGCTGCCGG;RSEQ=CCTCGGCGCAGAGCCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:36,18:54,2:0.0357:2,2:30:1:27.5:1:1:1.97357:60:4:0.0364:0:1 0/0:45:0:0,0:26,19:45,0:0:2,0:29.9:1:30.6:1:1:0:60:90:1:0:0.2 +3 169491012 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4873;SOR=Inf;LSEQ=AGCTCTCGTATCCATGACGC;RSEQ=TGCTGCTTCGGGGGACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:17,0:0:1,0:23.6:1:33.2:1:1:0:60:34:1:0:0 0/1:19:2:1,1:3,14:17,2:0.1053:2,2:23:1:28:1:0.38596:4.18:60:4:0.1053:0:1 +3 173189273 . T C 55 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.7746;LSEQ=TCTATCTGTGTATGTAGCTC;RSEQ=GTGTCAAAATTTCCTGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:29.8:1:27.8:1:1:0:60:8:0.6667:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:4:0:27:0:1:0:60:2:0.5:0:2 +3 177193106 . T G 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23352;SOR=0;LSEQ=TTTCCTCATCTATAATGATA;RSEQ=CTGCCTCACAGAACTCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:26.8:1:35:0:1:0:60:8:0.4:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:21.3:1:29.5:1:1:0:60:12:1:0:0.2 +3 177193276 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=CGCTGACTCCGGGGAGCAGG;RSEQ=AGAGGAACAGAGGGGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:57,58:115,0:0:2,0:27.6:1:32.4:1:1:0:60:56.5:1:0:0.1 0/1:129:2:1,1:61,66:127,2:0.0155:2,2:8:0:31:1:1:1.08:60:4:0.0156:0:1.5 +3 177418073 . A G 33 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1453;SOR=7.245;LSEQ=GGCAGTGGTGCCCACCTTGA;RSEQ=CATGCTGAGGTAGAAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:1:1,0:19,1:20,1:0.0476:1,0:21:0:14:0:1:0:56:0:0:0:6 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:17:1:33.5:1:1:0:60:4:0.2857:0:3 +3 177418088 . A G 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02291;SOR=4.91322;LSEQ=CTTGAACATGCTGAGGTAGA;RSEQ=GCTGCTGGGGCCTGCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:6,1:18,1:19,7:0.2593:1,2:26.1:1:30.4:1:0.47385:2.85369:60:6:0.25:0:1 1/0:14:9:9,0:4,1:5,9:0.6429:2,0:24.8:1:32.4:1:0.35714:0:60:18:0.6429:0:1.7 +3 177418132 . G A 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTCACCTCCAGGTGCTAC;RSEQ=TTACCGTACATCTTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:38,27:65,0:0:2,0:21.8:1:30.9:1:1:0:60:130:0.9848:0:0.3 0/1:52:15:10,5:23,14:37,15:0.2885:2,2:18:1:28.5:1:1:1.21:60:14:0.28:0:1.9 +3 177418225 . G C 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.01664;SOR=0.21516;LSEQ=GCAGAATAGACCCATGAGAA;RSEQ=ATGTTCTGGGAGTGCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:15:7,8:14,22:36,15:0.2941:2,2:15.7:1:31.9:1:0.75652:1.37:60:30:0.3:0:1.1 0/1:37:3:1,2:10,24:34,3:0.0811:2,2:23.3:1:27.3:1:1:1.19:60:2:0.0588:0:1 +3 177418320 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5098;SOR=0;LSEQ=TGGATGCTACTGAACTTGTG;RSEQ=AGGTGTAGTGGCTGCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:26,22:48,2:0.04:2,2:15.5:1:29:1:1:1.17786:60:4:0.04:0:1.5 0/0:35:0:0,0:21,14:35,0:0:2,0:22.2:1:31.5:1:1:0:60:70:1:0:0.1 +3 177418753 . A C 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00996;SOR=Inf;LSEQ=GACACCAGCTTTGCGTCATC;RSEQ=TTTTCCCAAAGAGTGAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:16,0:0:1,0:32.7:1:30.6:1:1:0:60:32:1:0:0.1 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:25:1:28.8:1:1:0:60:8:0.5:0:1.8 +3 177418774 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00625;SOR=Inf;LSEQ=TTTTCCCAAAGAGTGAGTCC;RSEQ=AGGGAACCACCTCTAGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:21,7:28,0:0:2,0:22.4:1:31:1:1:0:60:56:1:0:0.2 0/1:18:5:4,1:12,1:13,5:0.2778:1,2:21.4:1:27.6:1:0.4902:2.79285:60:10:0.2778:0:1.6 +3 177418792 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1996;SOR=Inf;LSEQ=CCCAGGGAACCACCTCTAGG;RSEQ=TAGTGGTAGCTCAGCTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:27,12:39,0:0:2,0:20.9:1:31.6:1:1:0:60:18.5:1:0:0.2 0/1:32:2:1,1:23,7:30,2:0.0625:2,2:11.5:1:27.5:1:0.44355:3.1396:60:4:0.0625:0:1.5 +3 177418817 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22911;SOR=0;LSEQ=GGTAGCTCAGCTATGTGGTG;RSEQ=CTCTGCTGCCAAAGACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:30,19:49,2:0.0392:2,2:22.5:1:32:1:1:1.56436:60:4:0.0392:0:1.5 0/0:55:0:0,0:35,20:55,0:0:2,0:26.9:1:28.8:1:1:0:60:54:1:0:0.3 +3 177418818 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22949;SOR=0;LSEQ=GTAGCTCAGCTATGTGGTGT;RSEQ=TCTGCTGCCAAAGACCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:30,20:50,2:0.0385:2,2:26.5:1:30.5:1:1:1.48801:60:4:0.0385:0:1 0/0:56:0:0,0:36,20:56,0:0:2,0:27:1:31.1:1:1:0:60:112:1:0:0.3 +3 177418846 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49677;SOR=Inf;LSEQ=CCAAAGACCAACTGCTCCTG;RSEQ=TGGCTGGGCTTGGGCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:29,31:60,0:0:2,0:28.7:1:32.8:1:1:0:60:59:1:0:0.2 0/1:65:2:1,1:34,29:63,2:0.0308:2,2:42:0:30.5:1:1:1.16953:60:4:0.0308:0:1.5 +3 177577349 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22186;SOR=Inf;LSEQ=ATGGATTCTTTTTCATCTTC;RSEQ=TGAGTTTGTCTAGTTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,15:32,0:0:2,0:27.1:1:31:1:1:0:54.2:64:1:0:0.1 0/1:29:2:1,1:15,12:27,2:0.069:2,2:20.5:1:28:1:1:1.24034:41:4:0.0714:0:1.5 +3 177577357 . G C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19989;SOR=Inf;LSEQ=TTTTTCATCTTCGTGAGTTT;RSEQ=TCTAGTTTTGGTCTTTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:34,0:0:2,0:26.9:1:32.1:1:1:0:54.4:33:1:0:0.1 0/1:28:2:1,1:13,13:26,2:0.0714:2,2:5:0:33:1:1:1:46:4:0.0714:0:0.5 +3 177577766 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49675;SOR=Inf;LSEQ=AGCACTTTGTCCCTTGGTGG;RSEQ=GAGGGTGTGTTTTGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:25,0:0:2,0:26.9:1:30.7:1:1:0:57.9:50:1:0:0.1 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:24:1:28.5:1:1:1.07:60:4:0.0667:0:1 +3 177577798 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TTGCTGGAGGGAAACCCACT;RSEQ=GTTGGGCCACCTGGATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:8,13:21,0:0:2,0:25.9:1:30.4:1:1:0:58.4:20:1:0:0.1 0/1:28:2:1,1:11,15:26,2:0.0714:2,2:18:1:28:1:1:1.35:51.5:4:0.0741:0:1 +3 177577866 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=CAGCTGGTCTGCAGAGACTT;RSEQ=GGCCACCCCTCCCCCTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:6,0:0:0,0:29.5:1:31.3:1:1:0:60:12:1:0:0 1/0:4:2:0,2:0,2:2,2:0.5:0,0:23:1:28.5:1:1:0:56:4:0.5:0:1.5 +3 177577935 . G C 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTGAGCCTCTGGCTGGA;RSEQ=TTATTGGAGTTCCTGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:32.5:1:1:0:32.5:4:1:0:1 1/0:2:1:1,0:0,1:1,1:0.5:0,0:8:0:34:0:1:0:60:2:0.5:0:1 +3 177578395 . G A 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62848;SOR=2.53692;LSEQ=TGAGTTGCACAGTTCCATGG;RSEQ=AAAAGCAGTTTCCCTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:2,2:4,6:0.6:2,2:28.5:1:30.3:1:1:1.86:60:12:0.6:0:1 1/1:10:8:4,4:1,1:2,8:0.8:2,2:32.8:1:29.8:1:1:1:54.5:16:0.8:0:1.5 +3 177578423 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13725;SOR=Inf;LSEQ=GTTTCCCTGGCTGGGTAGTG;RSEQ=ACTAACTCACCACCCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:11,0:0:2,0:17.6:1:32.5:1:1:0:60:22:1:0:0.4 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:8:0:31:1:1:1.41418:59:4:0.2857:0:2.5 +3 177899353 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23199;LSEQ=AGAAATTGTGTAGGACCAAA;RSEQ=AGTCTTCTTGGAATGATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:415:309:142,167:53,53:106,309:0.7446:2,2:25.4:1:29.4:1:0.49971:1.17559:59.9:102:0.7445:0:1.1 0/1:402:162:77,85:113,127:240,162:0.403:2,2:25.2:1:28.4:1:1:1.02:60:80:0.401:0:1.2 +3 177899380 . G A 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00089;SOR=Inf;LSEQ=CTTGGAATGATGCCATAGAA;RSEQ=TATGTCAATGTTTTTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:0:0,0:156,208:364,0:0:2,0:26:1:32.5:1:1:0:60:71.8:1:0:0.7 0/1:362:10:4,6:153,199:352,10:0.0276:2,2:32:1:30.1:1:1:1.1528:60:20:0.0277:0:1.9 +3 177899444 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50136;SOR=0;LSEQ=ATGCATTTTCAAATAAAATA;RSEQ=TAAAATTTTCTTAGTTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:28,110:138,2:0.0143:2,2:46.5:1:31:1:0.37256:3.88:60:4:0.0144:0:1 0/0:119:0:0,0:34,84:118,0:0:2,0:22.2:1:29.4:1:1:0:60:58:0.9915:0:0.3 +3 177899517 . A G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44047;SOR=0.63417;LSEQ=TAAAAATAGATCTATGAGAA;RSEQ=TACTTTGAGGTATTGTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:22:2,20:0,12:12,22:0.6471:0,2:22.7:1:31.7:1:0.52941:0:60:21:0.6364:0:1 1/0:28:15:0,15:0,13:13,15:0.5357:1,1:17.7:1:28.9:1:1:0:60:4:0.48:0:1.1 +3 177899939 . C T 26 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAGGAAAATGAGATCATTGC;RSEQ=AAATTTAACTGATAGATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:39.5:1:26:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:39:0:32:0:1:0:60:2:1:0:0 +3 178511054 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACACTTTCAGCTATGGAA;RSEQ=TGCAGACAGTTGATGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:18.5:1:34.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 178511254 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49533;SOR=0;LSEQ=GCTGGACTACAGTGATGGAG;RSEQ=GAAGGAATTGAGAGAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:39,11:50,2:0.0377:2,2:25.5:1:29:1:0.41176:3.43763:60:4:0.04:0:1 0/0:51:0:0,0:34,17:51,0:0:2,0:22.7:1:29.4:1:1:0:60:24.5:1:0:0.3 +3 178511285 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16207;SOR=Inf;LSEQ=AGAGAGCAAGCCACCAAGCG;RSEQ=AAGCTGCTCTTCACCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:52,17:69,0:0:2,0:24.9:1:31.2:1:1:0:60:68:1:0:0.1 0/1:47:2:1,1:30,15:45,2:0.0426:2,2:22:1:30.5:1:1:1.96856:60:4:0.0426:0:1.5 +3 178511302 . TG T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.27725;SOR=0;LSEQ=GCGGAAGCTGCTCTTCACCC;RSEQ=GGGGGGTGGGCAATGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:2,1:59,16:75,3:0.0385:2,2:8.7:1:30.7:1:0.52692:1.82707:60:6:0.0385:0.0128:0.3 0/0:51:0:0,0:32,19:51,0:0:2,0:24.7:1:30.9:1:1:0:60:102:1:0:0.4 +3 178511310 . T G 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00245;SOR=Inf;LSEQ=TGCTCTTCACCCTGGGGGGG;RSEQ=GGGCAATGGACAGCAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:67,20:87,0:0:2,0:26.1:1:29.6:1:1:0:60:42.5:1:0:0.1 0/1:53:6:3,3:31,16:47,6:0.1132:2,2:26.5:1:27.2:1:0.65457:1.91207:60:5:0.098:0:2.3 +3 178511403 . AC A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50348;SOR=0;LSEQ=GTTGATACACTCCCTGAAGC;RSEQ=CACGGCATGAAATGGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:125,74:199,2:0.01:2,2:38.5:1:32.5:1:1:1.68451:60:4:0.0102:0:0 0/0:165:0:0,0:103,62:165,0:0:2,0:25.6:1:31.3:1:1:0:60:330:1:0:0.1 +3 178511531 . C A 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=GGCATGGGGCTATCAGGGAT;RSEQ=CAAGCCAGCTACCTCATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:16:7,9:155,153:308,16:0.0494:2,2:23.3:1:30:1:0.79859:1.30146:59.6:32:0.0502:0:1.1 0/0:283:0:0,0:144,139:283,0:0:2,0:24.2:1:30.4:1:1:0:60:140.5:1:0:0.1 +3 178511579 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09524;SOR=Inf;LSEQ=CAGCAGGTGACTCTTCCCAT;RSEQ=CAGATGACAGCCAAGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:154,147:301,0:0:2,0:23.1:1:32.3:1:1:0:60:149.5:1:0:0.1 0/1:254:3:1,2:133,118:251,3:0.0118:2,2:26:1:27.7:1:0.60381:2.24725:60:6:0.012:0:1 +3 178511689 . A C 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAACTCTGCCTCAAAAAACA;RSEQ=AGATAAAGGGAACAAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:89,208:297,0:0:2,0:22.7:1:30.7:1:1:0:60:98:1:0:0.1 0/1:245:32:11,21:71,142:213,32:0.1306:2,2:22.5:1:31.3:1:1:1.05:60:31:0.1281:0:1.2 +3 178511724 . A C 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAAACAAACAAGCAGAG;RSEQ=CCTTTCTGCACTGAGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:4,121:125,0:0:1,0:25.7:1:30:1:1:0:60:61.5:1:0:0.1 0/1:101:28:3,25:8,65:73,28:0.2772:2,2:25.6:1:30.7:1:1:1.02539:60:56:0.28:0:1 +3 178917005 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=7.78807;LSEQ=TCTAAAATGCAAATAACCAT;RSEQ=AAGCTTAACTGTTGTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:735:17:6,11:179,539:718,17:0.0231:2,2:26.4:1:30.5:1:0.39462:1.64:60:16:0.0219:0:1.3 0/1:571:89:24,65:127,354:481,89:0.1559:2,2:23.8:1:30.3:1:0.89661:1.03:60:28.667:0.1528:0:1.2 +3 178917088 . C CATT 108 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00021;SOR=10.81083;LSEQ=ATAGCTTTCTAAATAAAAAT;RSEQ=ATAAATCTAAAGTATGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:0,2:1,145:146,2:0.0135:1,0:18.5:1:31.7:0:1:0:60:4:0.0136:0:0.5 0/1:100:13:0,13:1,86:87,13:0.13:1,1:24.2:1:29.4:1:1:0:60:26:0.1313:0.04:0.4 +3 178917412 . C CA 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.85338;LSEQ=TCTACAGAGTTCCCTGTTTG;RSEQ=AAAAAAAACATGTTCATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:3:2,1:98,12:110,3:0.0265:2,2:32.3:1:30:1:0.30938:4.00369:60:6:0.0273:0:0 0/1:88:2:2,0:77,9:86,2:0.0227:2,0:31.5:1:26:1:1:0:60:4:0.0227:0:0 +3 178917436 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=0.19297;SOR=Inf;LSEQ=AAAAACATGTTCATGCTGTG;RSEQ=ATGTAATAGAATGTTATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:159,28:187,0:0:2,0:23.1:1:30.1:1:1:0:60:92.5:1:0:0.1 0/1:147:2:1,1:115,30:145,2:0.0136:2,2:28:1:28:1:0.37844:3.78736:60:4:0.0137:0:1 +3 178917697 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20492;SOR=Inf;LSEQ=ATTAGATAAAGGTAAGAAAA;RSEQ=GACTAATCTACTCTAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:55,185:240,0:0:2,0:25:1:29.8:1:1:0:59.9:20.818:1:0:0.1 0/1:199:2:1,1:51,146:197,2:0.0101:2,2:39.5:1:28:1:0.45531:2.84:60:4:0.0103:0:1 +3 178921048 . CT C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GTGATCCTTGTTTTTAATTC;RSEQ=TTTTTTGCCTCCAGTTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:17.4:1:32.6:1:1:0:55.4:10:1:0:0.4 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:26:0:33:0:1:0:60:4:0.6667:0:0.5 +3 178921158 . G A 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16724;SOR=0;LSEQ=GATTGATCTTGTGCTTCAAC;RSEQ=TAAATCCTAAATGTTAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:6:6,0:32,0:32,6:0.1579:1,0:15:1:30.2:1:1:0:60:12:0.1622:0:1.2 0/0:15:0:0,0:12,3:15,0:0:2,0:21.6:1:30.1:1:1:0:60:30:1:0:0 +3 178921253 . G GTAAA 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00081;SOR=3.67654;LSEQ=TCACCTTTGCAGATTAATAT;RSEQ=TAGTCATAATACTCTGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:11:11,0:175,3:178,11:0.0582:1,0:30:1:29.1:1:1:0:60:22:0.0582:0.0106:0.2 0/1:113:21:19,2:84,8:92,21:0.1858:2,2:23:1:28.1:1:1:1.10428:60:42:0.1858:0.0442:0 +3 178921628 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.15972;SOR=Inf;LSEQ=ATAGAAATTATTTTAGATAA;RSEQ=CTTTTTCTTGCACTATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:26,146:172,0:0:2,0:20.7:1:31.9:1:1:0:60:344:1:0:0.6 0/1:115:2:1,1:20,93:113,2:0.0174:2,2:24.5:1:28.5:1:0.33318:4.56:60:4:0.0179:0:1.5 +3 178921639 . C A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00064;SOR=0.35627;LSEQ=TTTAGATAACCTTTTTCTTG;RSEQ=ACTATACAGTAATCTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:127:96:10,86:3,27:30,96:0.7559:2,2:22.1:1:31:1:1:1.05:60:95:0.7661:0:1 1/0:86:45:4,41:8,33:41,45:0.5233:2,2:17.7:1:30.2:1:0.21566:2.45885:60:90:0.5294:0:1.1 +3 178922222 . G T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00209;SOR=4.33049;LSEQ=TTCCGTGGTTTTATATTTGA;RSEQ=TCTATCGAGTGTGTGCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:6:6,0:171,16:187,6:0.0311:2,0:25.8:1:31.7:1:1:0:60:12:0.0313:0:1.8 0/1:147:18:15,3:119,10:129,18:0.1224:2,2:15.8:1:30.2:1:0.20008:2.36193:60:36:0.1233:0:1.9 +3 178922231 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.18513;SOR=Inf;LSEQ=TTTATATTTGAGTCTATCGA;RSEQ=TGTGTGCATATGTGTATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:212,27:239,0:0:2,0:23.9:1:33:1:1:0:60:118.5:1:0:0.7 0/1:181:2:2,0:155,24:179,2:0.011:2,0:35:1:32.5:1:1:0:60:4:0.0111:0:1.5 +3 178922274 . C A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00031;SOR=0.59734;LSEQ=GTGTATACATTAGTATATAC;RSEQ=TACTTTTTTCTTTTAGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:463:313:240,73:103,47:150,313:0.676:2,2:25.2:1:30.3:1:0.07052:1.50:60:38.125:0.6703:0:1.1 1/0:393:218:162,56:120,54:174,218:0.5547:2,2:24.5:1:29.5:1:0.25906:1.30:60:217:0.5564:0:1.2 +3 178922430 . A G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2751;SOR=0.81467;LSEQ=TTATATTAGTGTTTAGCAGT;RSEQ=TGATCCATAAAAGTAGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:317:230:40,190:15,72:87,230:0.7256:2,2:23:1:32.3:1:1:1.01:60:114:0.7238:0:1.1 1/0:268:183:39,144:13,72:85,183:0.6828:2,2:24.2:1:31.3:1:0.31932:1.50:60:60:0.6818:0:1 +3 178927259 . CCAAT C 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.01376;SOR=Inf;LSEQ=GACCTTATAAAGTGCCTTTT;RSEQ=CAATCTCTTTCCTGTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:94,1:95,0:0:1,0:25.1:1:31.2:1:1:0:60:30.667:1:0:0.1 0/1:51:4:3,1:46,1:47,4:0.0784:1,2:30:1:27.5:1:0.15216:13.42263:60:3:0.0612:0:0.5 +3 178927345 . T C 123 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00597;SOR=0.09725;LSEQ=ATATACTTTGATGAAGACTT;RSEQ=TCTTGATGTATTATTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:14:11,3:273,87:360,14:0.0374:2,2:22:1:32.5:1:1:1.17:60:28:0.0376:0:1 0/0:266:1:1,0:196,69:265,1:0.0038:2,0:16:0:25:0:1:0:60:2:0.0038:0:1 +3 178927410 . A G 205 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAATGGCTGAATTATGATAT;RSEQ=TACATTCCTGATCTTCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:0:0,0:418,374:792,0:0:2,0:26.3:1:29.5:1:1:0:60:98:0.9975:0:0.1 0/1:716:91:49,42:333,292:625,91:0.1271:2,2:25:1:31.6:1:1:1.02:60:90:0.1275:0:1.2 +3 178927645 . C T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00063;SOR=0.08553;LSEQ=AATGTATCATGGAAGAATAC;RSEQ=TTGGGAGAGCTTCAGGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:23:3,20:3,14:17,23:0.575:2,2:24.4:1:30.6:1:1:1.41565:58.3:22:0.5641:0:1 0/1:20:2:0,2:1,17:18,2:0.1:1,0:15.5:1:31:0:1:0:60:4:0.1:0:1 +3 178927848 . AT A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.89653;LSEQ=GCTTAAACCTTGAAAAATCA;RSEQ=TTTTTTTTTTTAGATATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:5,0:47,0:47,5:0.0962:1,0:21.6:1:30.5:1:1:0:60:10:0.0962:0.0192:0.4 0/1:23:2:2,0:18,2:20,2:0.087:2,0:22:1:26.5:1:1:0:60:4:0.087:0.0435:0.5 +3 178927948 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62804;SOR=0.38856;LSEQ=GTGTTTTATAATTTAGACTA;RSEQ=TGAATATTTTTCTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:1,2:184,51:235,3:0.0126:2,2:12.7:1:28.7:1:0.12546:7.13636:60:6:0.0127:0:1 0/0:203:1:0,1:166,36:202,1:0.0049:2,0:1:0:24:0:0.18227:0:60:2:0.0049:0:1 +3 178936227 . T G 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30923;SOR=0;LSEQ=ACCATACCTATTGGAATAAA;RSEQ=AAAGCAGAATTTACATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:4:0,4:0,68:68,4:0.0556:1,0:35:1:32.8:1:1:0:22:8:0.0556:0:1 0/0:32:0:0,0:1,31:32,0:0:1,0:23.6:1:28.1:1:1:0:38.4:64:1:0:0.1 +3 178937682 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13002;SOR=Inf;LSEQ=TTTCTTTCTGAAAAAATTTT;RSEQ=TTTAGATCGGCCATGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:33,16:49,0:0:2,0:24.7:1:31.7:1:1:0:37.9:23.5:1:0:0.1 0/1:63:4:2,2:40,19:59,4:0.0635:2,2:12.8:1:27.5:1:0.59528:2.07849:47.5:3:0.0492:0:2.8 +3 178937752 . C A 51 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12779;SOR=Inf;LSEQ=CCTAGGTCCTAAAATATGAA;RSEQ=AATATTTGGATAACTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:13,15:28,0:0:2,0:10.1:1:31.7:1:1:0:57.3:56:1:0:0.1 0/1:37:4:3,1:14,19:33,4:0.1081:2,2:6:1:25.8:1:0.31532:3.92:55:3:0.0857:0:2 +3 178938023 . A C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27297;SOR=0.35399;LSEQ=CTCTTTGAAATTTAAAAAGC;RSEQ=GTAAATTCAAAACTAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:15:1,14:0,9:9,15:0.625:0,1:30.9:1:28.5:1:1:0:25.4:14:0.6087:0:1 0/1:11:4:1,3:1,6:7,4:0.3636:2,2:46.5:1:31.3:1:1:1.87:23.8:8:0.3636:0:1 +3 178938749 . T A 41 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.31492;LSEQ=TTAAGACTATATATATATAT;RSEQ=TTTAATTTTGCACGATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:3:3,0:236,85:321,3:0.0093:2,0:32.3:1:27.7:1:0.56956:0:26.7:6:0.0093:0:1 0/1:247:3:2,1:172,72:244,3:0.0121:2,2:23.7:1:26:1:1:1.19353:23.7:6:0.0122:0:1 +3 178938822 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50045;SOR=0;LSEQ=CAGAGGTTTGGCCTGCTTTT;RSEQ=GAGTCCTATTGTCGTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:91,60:151,2:0.0131:2,2:10:1:30:1:1:1.51238:60:4:0.0133:0:1 0/0:134:0:0,0:86,48:134,0:0:2,0:14.1:1:29.4:1:1:0:39.5:66:1:0:0.1 +3 178938885 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23021;SOR=Inf;LSEQ=AATAGGCAAGTCGAGGCAAT;RSEQ=GAAAAGCTCATTAACTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:76,85:161,0:0:2,0:10.8:1:31.1:1:1:0:36.3:160:1:0:0.1 0/1:149:2:1,1:65,82:147,2:0.0134:2,2:9.5:1:29.5:1:1:1.26:60:4:0.0135:0:1 +3 178941853 . C CT 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.68925;SOR=0.82954;LSEQ=AGTTTCTTACTGTGACTATC;RSEQ=TTTTTTTTTAATCAGGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:470:14:8,6:307,147:454,14:0.0298:2,2:26:1:31:1:0.40051:1.56476:59.6:28:0.0304:0.0064:0.1 0/1:443:11:10,1:270,158:428,11:0.0248:2,2:29.8:1:31.5:1:0.06371:5.83:60:22:0.025:0:0 +3 178942431 . C G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00642;SOR=0.49053;LSEQ=TTATATTTTAAAATAAATTT;RSEQ=AGGGTAAAATAATAATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:169:141:111,30:24,3:27,141:0.8343:2,2:22.8:1:32.5:1:0.29543:2.15383:60:282:0.8343:0:1.1 1/0:201:143:105,38:41,17:58,143:0.7114:2,2:21.5:1:30.9:1:0.72837:1.14:60:142:0.71:0:1.1 +3 178943123 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGCATGTTGCAAAGGAA;RSEQ=AGTGTAGTCTGCTCAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:28.7:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 178943714 . G A 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCCCAAATTTGCATCTGT;RSEQ=GCATTAAATGGTGATACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:275,126:401,0:0:2,0:26.5:1:31.9:1:1:0:60:65.833:1:0:0.1 0/1:367:19:14,5:221,127:348,19:0.0518:2,2:28.3:1:26.6:1:0.46581:1.61:60:18:0.0495:0:1.1 +3 178943972 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08688;SOR=Inf;LSEQ=TGATTACACTATAGTACTTT;RSEQ=ACATATCCTCCTCTTACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:0,61:61,0:0:1,0:26.9:1:33.4:1:1:0:60:122:1:0:0 0/1:26:2:0,2:0,24:24,2:0.0769:1,0:33.5:1:27:1:1:0:60:4:0.0769:0:1 +3 178943987 . T TACTTG 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.38916;LSEQ=ACTTTGACATATCCTCCTCT;RSEQ=ACTTAGAATAGCTAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:43:0,43:0,6:6,43:0.8776:0,1:23.3:1:32.1:1:1:0:60:86:0.8776:0.2449:0 1/1:22:20:0,20:0,2:2,20:0.9091:0,1:32.9:1:30.7:1:1:0:60:40:0.9091:0.0455:0.2 +3 178947289 . C T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00029;SOR=Inf;LSEQ=TTTTTGTTAGATGAGTCTGT;RSEQ=GGTGTTTGTGTATTCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:13,133:146,0:0:2,0:25.2:1:30.2:1:1:0:60:72:1:0:0.1 0/1:138:11:4,7:20,106:126,11:0.0797:2,2:22.1:1:29.5:1:0.10183:3.00:60:22:0.0797:0:1 +3 178947344 . GA G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.23557;SOR=Inf;LSEQ=AAACAATTGTACTTTCTATG;RSEQ=AAAAAATATGCTCAACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:44,0:0:1,0:21.2:1:31.4:1:1:0:60:88:1:0:0 0/1:42:2:0,2:0,40:40,2:0.0476:1,0:10.5:1:32:0:1:0:60:4:0.0488:0:0 +3 178948196 . A G 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01505;SOR=Inf;LSEQ=CAATTAAAAACACAAAATAA;RSEQ=GAGTTCTGGCTGCTCTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:35,209:244,0:0:2,0:23.5:1:31.9:1:1:0:60:243:1:0:0 0/1:252:7:3,4:58,187:245,7:0.0278:2,2:39.3:1:29.3:1:0.36487:2.41:60:14:0.028:0:1 +3 178951818 . C T 42 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33836;SOR=3.5455;LSEQ=CTAATTTTGTGACATTTGAG;RSEQ=AAAGACCTGAAGGTATTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:0,1:209,41:250,1:0.004:2,0:1:0:22:0:0.16733:0:60:2:0.0041:0:2 0/1:214:3:1,2:147,63:210,3:0.014:2,2:7:1:26.7:1:0.22136:4.62867:60:6:0.0142:0:1 +3 178952020 . C T 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTGCATACATTCGAAAGAC;RSEQ=CTAGCCTTAGATAAAACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:0:0,0:358,372:730,0:0:2,0:24.9:1:31:1:1:0:60:44.625:1:0:0.1 0/1:711:47:25,22:310,353:663,47:0.0661:2,2:21.6:1:29.4:1:0.4505:1.29:60:94:0.0673:0:1 +3 178952201 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15609;SOR=Inf;LSEQ=TCTGGATTCCACACTGCACT;RSEQ=TTAATAACTCTCAGCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:36,173:209,0:0:2,0:22:1:32:1:1:0:59.7:51.25:1:0:0.1 0/1:137:2:1,1:28,107:135,2:0.0146:2,2:29.5:1:27.5:1:0.37978:3.77:60:4:0.0148:0:1 +3 179366819 . A G 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=GTACGTTTTGACCCCATGGG;RSEQ=AAAAAAAAATAGATAACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:3:0:30:0:1:0:33:2:0.5:0:1 1/0:5:3:2,1:1,1:2,3:0.6:2,2:25:1:21.3:1:1:1.73:60:2:0.5:0:4 +3 179367238 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24645;SOR=0;LSEQ=GCGTGAGCCACCGTGCCCAG;RSEQ=ATAGTGGATTCTTAAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:75,28:103,2:0.019:2,2:13.5:1:26:0:0.47802:2.64948:50.5:4:0.019:0:1 0/0:106:0:0,0:74,32:106,0:0:2,0:19.9:1:30.7:1:1:0:56.7:52:1:0:0.1 +3 179367265 . A C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23123;SOR=0;LSEQ=GATTCTTAAGCACATTCTTC;RSEQ=GGTATGTGGTGTGTTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:87,56:143,2:0.0138:2,2:19:1:32.5:1:1:1.54866:60:4:0.014:0:1 0/0:156:0:0,0:89,66:155,0:0:2,0:26.7:1:29.5:1:1:0:59.4:76.5:0.9935:0:0.1 +3 179367383 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22823;SOR=Inf;LSEQ=AGGCCTCACTTGCCTCCTGC;RSEQ=AAGCACCAACAGCTGCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:26,62:88,0:0:2,0:25:1:31:1:1:0:59.4:87:1:0:0.1 0/1:81:2:1,1:25,54:79,2:0.0247:2,2:26.5:1:30.5:1:0.54167:2.14:38:4:0.025:0:1.5 +3 179367608 . G GTT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.4958;SOR=Inf;LSEQ=GTAGCTAGTTGCTTCCTGGA;RSEQ=TTTTTTTTGTTTGTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:1,14:15,0:0:1,0:23.9:1:33:1:1:0:58.8:30:1:0:0.4 0/1:20:2:1,1:5,11:16,2:0.1:2,2:25:1:31.5:0:1:2.10:60:4:0.1053:0:0 +3 179367638 . GT G 50 MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.54545;SOR=0.23036;LSEQ=TTTGTTTTTTTTTGCTTTTT;RSEQ=TTTTTTTTTTTTTTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:3,3:0.5:2,0:28.7:1:32:1:1:0:54:6:0.5:0:2 0/1:6:1:0,1:2,3:5,1:0.1667:2,0:14:0:30:0:1:0:31:2:0.1667:0:0 +3 179367651 . T G 33 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCTTTTTGTTTTTTTTTTTT;RSEQ=TTTGTTTGAGACGGAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25.5:1:33.5:1:1:0:51:4:0.6667:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:17.5:1:29.5:1:1:0:45.5:4:1:0:2.5 +3 179367923 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.51377;SOR=Inf;LSEQ=CCTCGGCCTCCCAAAGTGCT;RSEQ=GGATTGCTTCCTGGGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:35,22:57,0:0:2,0:20.5:1:32:1:1:0:55.5:114:1:0:0.5 0/1:83:2:1,1:59,22:81,2:0.0241:2,2:16.5:1:26.5:1:0.47987:2.64501:60:4:0.0247:0:1 +3 179367994 . T A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=4.23828;LSEQ=TTGTACCAGCCATGGTATAG;RSEQ=GACCTCCTTACTTAGACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:85:57:22,35:9,19:28,57:0.6706:2,2:27.8:1:30.5:1:0.63633:1.32:59.7:18:0.6585:0:1.1 1/1:126:113:47,66:5,8:13,113:0.8968:2,2:28.1:1:29:1:1:1.14:59.7:112:0.896:0:1.1 +3 179368001 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.33151;LSEQ=AGCCATGGTATAGTGACCTC;RSEQ=TTACTTAGACCCGTTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:1,0:27,53:80,1:0.0123:2,0:28:0:32:0:0.34568:0:60:2:0.0123:0:2 0/1:122:2:1,1:46,74:120,2:0.0164:2,2:10.5:1:27.5:1:1:1.60:60:4:0.0165:0:2.5 +3 179368044 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.51418;SOR=Inf;LSEQ=TGGAGCGTGGCGAGTGACAG;RSEQ=CGGCGCTGGTGTTGGAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:6,33:39,0:0:2,0:23.3:1:32.3:1:1:0:60:38:1:0:0.5 0/1:58:2:1,1:9,47:56,2:0.0345:2,2:12.5:1:25:1:0.3176:5.01:60:4:0.037:0:2 +3 180017244 . T G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05714;SOR=3.40792;LSEQ=TGACTAGAGGAGCCAAACTG;RSEQ=ATGATAAGTCTGATGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:6:6,0:33,0:33,6:0.15:1,0:11.2:1:32.5:1:1:0:60:12:0.15:0:1 0/1:21:8:7,1:13,0:13,8:0.381:1,2:20.1:1:31.6:1:0.38095:0:60:16:0.381:0:1.1 +3 180017320 . AT A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19839;SOR=Inf;LSEQ=TAACACCATGTTTCAAAACA;RSEQ=GGACTGGTTTTCCAGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:121,39:160,0:0:2,0:23.2:1:31.1:1:1:0:60:320:1:0:0.2 0/1:129:2:1,1:95,32:127,2:0.0155:2,2:33:1:30:1:0.44767:2.93865:60:4:0.0155:0:0 +3 180017359 . G T 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62344;SOR=0.33849;LSEQ=TCAATTAAATCCACATAGTT;RSEQ=AGTGTTCCTGCATTCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:3:1,2:142,86:228,3:0.013:2,2:22.7:1:27.7:1:0.55939:3.28476:60:6:0.0131:0:1 0/0:226:1:0,1:132,93:225,1:0.0044:2,0:1:0:22:0:0.41593:0:60:2:0.0045:0:1 +3 180017424 . T C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.59279;LSEQ=ATTGCTGTCAAAAGCCATAT;RSEQ=ATCTCAAGTTAATTTTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:49:22,27:119,142:261,49:0.1581:2,2:25.3:1:31.9:1:1:1.0284:60:48:0.1574:0:1.1 0/1:300:121:58,63:81,98:179,121:0.4033:2,2:24.2:1:30.8:1:0.72342:1.11:60:120:0.4027:0:1.2 +3 181428123 . G GT 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.41324;SOR=0.76869;LSEQ=TAAAAAAGAAATGGCATCAG;RSEQ=TTTTTTTTTCTTTATTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:672:35:9,26:186,445:631,35:0.0521:2,2:25.9:1:29.8:1:0.70659:1.20714:60:34:0.0514:0:0.4 0/1:543:22:7,15:171,346:517,22:0.0405:2,2:23.7:1:28.5:1:1:1.05893:59.8:21:0.039:0.0018:0.4 +3 181428167 . G A 36 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0622;SOR=Inf;LSEQ=ACCCCACCCTTTGTAGTCAA;RSEQ=TGCATTTTAGCCACAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:39,217:256,0:0:2,0:23.5:1:31.4:1:1:0:60:18.692:1:0:0.2 0/1:169:3:2,1:26,140:166,3:0.0178:2,2:7.3:1:23.3:1:0.07159:10.53:60:2:0.0123:0:1.7 +3 181430117 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1908;SOR=Inf;LSEQ=CGGGCCGAGGGTCGGCGGCC;RSEQ=CCGGCGGGCCGGGCCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:22,7:29,0:0:2,0:16.3:1:30.4:1:1:0:60:58:1:0:0.3 0/1:23:2:1,1:14,7:21,2:0.087:2,2:11:0:30.5:1:1:1.93655:60:4:0.1:0:1 +3 181430130 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29658;SOR=0;LSEQ=GGCGGCCGCCGGCGGGCCGG;RSEQ=CCCGCGCACAGCGCCCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:4:1,3:68,17:85,4:0.0449:2,2:14.8:1:25.5:1:0.0342:11.55446:60:3:0.0345:0:1.5 0/0:52:0:0,0:38,14:52,0:0:2,0:14.8:1:30.5:1:1:0:60:25:1:0:0.4 +3 181430136 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1647;SOR=Inf;LSEQ=CGCCGGCGGGCCGGGCCCGC;RSEQ=CACAGCGCCCGCATGTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:88,23:111,0:0:2,0:16:1:30.1:1:1:0:60:17.5:0.9906:0:0.3 0/1:77:2:1,1:52,22:74,2:0.026:2,2:29.5:1:28:1:0.51649:2.33383:60:4:0.0267:0:1 +3 181430168 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12684;SOR=0;LSEQ=CATGTACAACATGATGGAGA;RSEQ=GGAGCTGAAGCCGCCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:4:1,3:214,55:269,4:0.0147:2,2:19.8:1:29.3:1:0.03118:11.52699:60:8:0.0148:0:1.3 0/0:239:0:0,0:175,64:239,0:0:2,0:20.8:1:31.1:1:1:0:59.9:78.667:1:0:0.2 +3 181430601 . G A 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=51.18847;LSEQ=GTGGGCGCCGGCCTGGGCGC;RSEQ=GGCGTGAACCAGCGCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:1:1,0:326,332:658,1:0.0015:2,0:48:0:14:0:0.49621:0:60:0:0:0:3 0/1:484:35:17,18:202,247:449,35:0.0723:2,2:29.8:1:30.6:1:0.72631:1.15:60:70:0.0737:0:1.1 +3 181431115 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1281;SOR=Inf;LSEQ=ACATGTGAGGGCCGGACAGC;RSEQ=AACTGGAGGGGGGAGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:38,231:269,0:0:2,0:21.1:1:31.6:1:1:0:58.6:43.833:1:0:0.1 0/1:151:2:1,1:28,121:149,2:0.0132:2,2:14.5:1:28:1:0.34826:4.26:60:4:0.0136:0:1 +3 181431127 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.03845;SOR=Inf;LSEQ=CGGACAGCGAACTGGAGGGG;RSEQ=GAGAAATTTTCAAAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:21,189:210,0:0:2,0:21.3:1:30.8:1:1:0:59.1:34:1:0:0.1 0/1:108:3:1,2:13,91:104,3:0.0278:2,2:25.3:1:29.3:1:0.34622:3.44:52:6:0.0291:0:1 +3 181431226 . GA G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACGCTCAAAAAGAAAAAG;RSEQ=AAAAAAAAAATCCCATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:0,2:2,40:42,2:0.0444:1,0:35.5:1:30.5:1:1:0:60:4:0.0455:0:0.5 0/0:7:0:0,0:0,7:7,0:0:0,0:26:1:28.3:1:1:0:58.7:14:1:0:0.1 +3 181434168 . TA T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02438;SOR=Inf;LSEQ=TGCACTCACCTCTCATTTTT;RSEQ=AAAAAAAGCCCACAGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:139,3:142,0:0:1,0:26.8:1:28.7:1:1:0:60:46.333:1:0:0.1 0/1:59:3:3,0:53,1:54,3:0.0508:1,0:41:1:31.7:1:1:0:60:6:0.0526:0:0 +3 181434222 . A T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56102;SOR=3.25648;LSEQ=CAAAATGGTCAGGTTCAAAT;RSEQ=TTTAGCAAAAGGAAAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:1:0,1:279,36:315,1:0.0032:2,0:1:0:25:0:0.11709:0:60:2:0.0032:0:1 0/1:195:2:1,1:160,33:193,2:0.0103:2,2:35.5:1:29.5:1:0.31906:4.79162:60:4:0.0103:0:1 +3 182178216 . A G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01628;SOR=Inf;LSEQ=GGTGTCTACTTAAACAACAA;RSEQ=CCTATTTTCAGTGGTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:48,2:50,0:0:1,0:21.4:1:29.6:1:1:0:57.8:15.667:1:0:0 0/1:18:3:3,0:13,2:15,3:0.1667:2,0:26.3:1:30.3:1:1:0:52:6:0.1667:0:1 +3 182178480 . C T 194 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=203.26914;LSEQ=TGTCTCTAGCCAAAAGCAAT;RSEQ=GAGGTCACTTCATCTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1002:1:0,1:497,502:999,1:0.001:2,0:1:0:26:0:1:0:60:2:0.001:0:1 0/1:615:104:55,49:262,248:510,104:0.1691:2,2:25.1:1:29:1:0.82979:1.06:54.3:33.667:0.1681:0:1.1 +3 182178717 . A G 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTGCTTTTACCATTTTT;RSEQ=AAAAACCAGAGGGCCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:675:0:0,0:263,411:674,0:0:2,0:26.6:1:29.9:1:1:0:59.9:83.25:1:0:0.1 0/1:542:79:34,45:189,274:463,79:0.1458:2,2:25.3:1:30.8:1:0.71242:1.10:58.8:158:0.1468:0:1.1 +3 182178853 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16882;SOR=Inf;LSEQ=GGGTGGTTTCCTGTTCGACA;RSEQ=TCGCCATTTTTGATGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:35,122:157,0:0:2,0:20.5:1:32.2:1:1:0:60:156:1:0:0.2 0/1:110:2:1,1:25,83:108,2:0.0182:2,2:22:1:30:1:0.41852:3.28:60:4:0.0187:0:1 +3 182664547 . G A 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGCTGAGTAGGAATTGAA;RSEQ=GAAACAGAAGAATATGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:22:1:28.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 182664889 . C CA 81 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03345;SOR=5.39324;LSEQ=AACAGAATGAGACTCTATCT;RSEQ=AAAAAAAACAAAAACAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:2,0:172,0:172,2:0.0115:1,0:39:1:32.5:1:1:0:60:4:0.0116:0:0 0/1:118:7:6,1:104,5:109,7:0.0593:1,2:25.1:1:29.1:1:0.31753:3.40715:60:14:0.0593:0.0085:0 +3 182664992 . T TA 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28388;SOR=1.48833;LSEQ=TATGGGATAAAAAGGCACAT;RSEQ=AAAAAAAAGTGGTGTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:943:13:6,7:576,353:929,13:0.0138:2,2:25:1:29.2:1:0.26114:1.90237:60:12:0.0129:0.0042:0.5 0/1:883:18:11,7:504,361:865,18:0.0204:2,2:26.7:1:27.7:1:1:1.13:60:17:0.0196:0.0023:0.3 +3 182678979 . C T 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65744;SOR=1.94879;LSEQ=GTCAATGTATTTGAATATAT;RSEQ=TGAAACACCAAATATAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:2:0,2:245,49:294,2:0.0068:2,0:1:0:28:1:0.0292:0:60:4:0.0068:0:1 0/1:229:3:2,1:187,39:226,3:0.0131:2,2:10.7:1:23:1:0.43938:2.38575:60:2:0.0088:0:2.3 +3 182681606 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50154;SOR=0;LSEQ=CTTTAAATTTACACTAAAAA;RSEQ=TTCATGACATAATTCAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:2,0:153,25:178,2:0.0111:2,0:29:1:29.5:1:1:0:60:4:0.0113:0:1 0/0:154:0:0,0:127,27:154,0:0:2,0:22.8:1:31.4:1:1:0:60:76:1:0:0.1 +3 182681740 . C T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.37759;LSEQ=GTTGCTGCTCTGAACTTCCA;RSEQ=GCAATAATCAACACACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:911:306:166,140:317,288:605,306:0.3359:2,2:24.5:1:30.6:1:0.62301:1.08:32.8:75.5:0.3348:0:1.1 1/0:835:456:225,231:194,180:374,456:0.5461:2,2:24.3:1:29.6:1:0.48581:1.10638:33.8:90.2:0.5453:0:1.1 +3 182681853 . T C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.06932;LSEQ=AGGGTCTTTAAAAATAACAA;RSEQ=GCAATATTAAAGTAGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:440:172:42,130:73,195:268,172:0.3909:2,2:24.5:1:30.3:1:0.57846:1.15834:60:85:0.3917:0:1.1 1/0:382:218:65,153:46,118:164,218:0.5707:2,2:23.6:1:29.9:1:0.73375:1.09:60:108:0.5745:0:1.1 +3 182682264 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTATCAGAAAAACTGTGA;RSEQ=CTAAACTATGCAATTCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:37.5:1:30:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 182683592 . T A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50038;SOR=Inf;LSEQ=TATGTAAAATCACATAAGAC;RSEQ=AAATATTTCTATATGGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:27,124:151,0:0:2,0:22.7:1:28.9:1:1:0:60:49.333:1:0:0.2 0/1:171:2:1,1:32,137:169,2:0.0117:2,2:7.5:1:25.5:1:0.34964:4.23:60:4:0.0118:0:2 +3 182698083 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGCTCTCGCGTAGCGGCTG;RSEQ=GCCCGGGCGGGAAGGGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:39:0:10:0:1:0:60:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:23.5:1:28:1:1:1:60:4:0.5:0:2 +3 182698221 . G T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5311;SOR=0;LSEQ=GGCGGCCGGGGCGGGGGTGC;RSEQ=CGGCAGCGCCGGCCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:34,13:47,2:0.0408:2,2:5.5:1:30.5:1:0.49405:2.55705:60:4:0.0426:0:1 0/0:28:0:0,0:21,7:28,0:0:2,0:7:1:28.3:1:1:0:60:13:1:0:0.2 +3 182698233 . G GC 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.21888;SOR=Inf;LSEQ=GGGGGTGCGCGGCAGCGCCG;RSEQ=CCCCCAGCCGGCAGGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:83,37:120,0:0:2,0:11.5:1:31.6:1:1:0:60:119:1:0:0.3 0/1:106:2:1,1:66,38:104,2:0.0189:2,2:20.5:1:30.5:1:1:1.72729:60:4:0.0192:0:0.5 +3 182698254 . C T 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50472;SOR=0.51458;LSEQ=CCCCCAGCCGGCAGGGCGGG;RSEQ=GGGCGGCCGCAGTGCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:6:1,5:158,100:258,6:0.0227:2,2:14.7:1:28.8:1:0.0382:7.84545:58.2:12:0.023:0:1 0/1:254:3:0,3:151,100:251,3:0.0118:2,0:1:0:28.3:1:0.06552:0:50.7:6:0.012:0:1 +3 182698263 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05428;SOR=Inf;LSEQ=GGCAGGGCGGGCGGGCGGCC;RSEQ=CAGTGCCTCACCATGTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:208,143:351,0:0:2,0:22.7:1:30.6:1:1:0:59.1:30.909:1:0:0.3 0/1:329:4:2,2:188,137:325,4:0.0122:2,2:22.3:1:29.5:1:1:1.3709:57.8:8:0.0123:0:1.3 +3 182698328 . G A 62 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03223;SOR=Inf;LSEQ=CTCCGGCTCCGCAGCGAATG;RSEQ=ACGGCGGCGGCGGCGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:188,216:404,0:0:2,0:26.1:1:31.4:1:1:0:59.9:49.5:1:0:0.2 0/1:453:6:6,0:210,235:445,6:0.0132:2,0:7:1:24.2:1:0.01163:0:52.3:5:0.0114:0:1 +3 182698329 . ACGG A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.55859;SOR=1.32761;LSEQ=TCCGGCTCCGCAGCGAATGG;RSEQ=CGGCGGCGGCGGCGGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:11:5,6:173,203:376,11:0.0283:2,2:29.5:1:30.5:1:1:1.0226:59.5:22:0.0286:0.0026:0.2 0/1:430:16:5,11:194,217:411,16:0.0372:2,2:31.1:1:30.1:1:0.30727:1.96385:60:32:0.0378:0.0047:0.4 +3 182698341 . G A 60 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.42813;SOR=0.44273;LSEQ=GCGAATGGACGGCGGCGGCG;RSEQ=CGGCGGCTCCTCTCACGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:4:3,1:128,178:306,4:0.0129:2,2:9.8:1:30:1:0.31429:4.15:60:8:0.0131:0:1 0/0:348:2:2,0:152,194:346,2:0.0057:2,0:1:0:23.5:1:0.19512:0:60:4:0.0059:0:1 +3 182698361 . C T 57 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37693;SOR=3.56446;LSEQ=GCGGCGGCTCCTCTCACGGG;RSEQ=TTGCCCGGCTCCCGCTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:0,1:64,129:193,1:0.0052:2,0:2:0:31:0:1:0:60:2:0.0053:0:1 0/1:220:4:2,2:78,138:216,4:0.0182:2,2:25.8:1:28.5:1:0.62296:1.76:60:8:0.0186:0:1 +3 182698375 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25044;SOR=Inf;LSEQ=CACGGGCTTGCCCGGCTCCC;RSEQ=CTCATGCGCAGTGCGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:20,85:105,0:0:2,0:16.4:1:32.1:1:1:0:60:34:1:0:0.1 0/1:121:3:2,1:31,87:118,3:0.0248:2,2:8.3:1:27:1:0.18029:5.52:60:6:0.0256:0:1 +3 182698686 . C G 71 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACGCAGGCTGGAAGCGGG;RSEQ=ACGAGCGGCGGCGGATAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:36:0:33:0:1:0:60:2:1:0:2 1/1:5:5:2,3:0,0:0,5:1:0,2:31.6:1:30.6:1:1:0:60:10:1:0:1 +3 183169595 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0.14783;SOR=0;LSEQ=CAAATCCATGAGATTTACTA;RSEQ=AAATTAAATACAAGTACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:16,2:0.1111:2,2:7.5:1:28:1:1:1.62:60:4:0.1176:0:1 0/0:28:0:0,0:10,18:28,0:0:2,0:19.9:1:31.2:1:1:0:60:27:1:0:0.2 +3 184296627 . T A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGAGGAGGTGGACTTGAGC;RSEQ=GAGCCAGGCGGGATGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 184298292 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19357;SOR=Inf;LSEQ=TGAACTATGTGCACCGCGAC;RSEQ=GGCTGCTCGCAACATCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:19,30:49,0:0:2,0:26.5:1:31.1:1:1:0:60:48:1:0:0.1 0/1:39:2:1,1:14,23:37,2:0.0513:2,2:16.5:1:29.5:1:1:1.62:60:4:0.0526:0.0256:0.5 +3 184298448 . C A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=AGACTGGGGGCGGGGCCTAT;RSEQ=AGCCAGGGGCTCGGGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:24.6:1:32:1:1:0:60:10:1:0:0 0/1:5:2:1,1:0,3:3,2:0.4:0,2:6.5:1:29.5:1:0.4:0:44:4:0.4:0:1.5 +3 184298663 . G A 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14055;SOR=0;LSEQ=TACTGGGACATGAGCAACCA;RSEQ=GATGTGAGTGAGGCTACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:6,9:15,6:0.2857:2,2:21.3:1:30.2:1:0.36146:2.84:60:12:0.2857:0:1 0/0:9:0:0,0:5,4:9,0:0:2,0:27.1:1:30.3:1:1:0:60:18:1:0:0.1 +3 184489727 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCTTGTGTGACTCTCC;RSEQ=GCTGGCGTGGCTGCCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:28:1:1:0:60:4:1:0:1.5 +3 184630256 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12;SOR=Inf;LSEQ=CCAAAGGTAGCCAGGATTTT;RSEQ=GTTTGTTTGTTTTTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:3,13:16,0:0:2,0:20.4:1:28.8:1:1:0:60:15:1:0:0.3 0/1:9:2:1,1:1,6:7,2:0.2222:2,2:15:0:31.5:1:0.41667:4.58:60:4:0.2222:0:1.5 +3 184630294 . A G 76 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TTTGTTTTTTACATGACTCA;RSEQ=TTCCGAAGCTTAACTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:31:1:32.8:1:1:0:60:10:1:0:1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:18:0:33:0:1:0:60:2:0.3333:0:1 +3 184673185 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16159;SOR=0;LSEQ=CATATGCTGCCTTCTCTATC;RSEQ=CTGCGGTGGCTACCTAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:41,18:59,2:0.0328:2,2:29.5:1:30.5:1:0.52951:2.24393:54.5:4:0.0333:0:1 0/0:90:0:0,0:54,36:90,0:0:2,0:26.6:1:28.8:1:1:0:51.7:17:1:0:0.2 +3 184673209 . A T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18948;SOR=0;LSEQ=CGGTGGCTACCTAAAAGGGA;RSEQ=GGGCCCCCTGTCCCATGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:56,35:91,2:0.0215:2,2:40:0:32:1:1:1.59159:60:4:0.022:0:1.5 0/0:120:0:0,0:67,53:120,0:0:2,0:29.4:1:29.1:1:1:0:53.2:23:1:0:0.2 +3 184673217 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50489;SOR=Inf;LSEQ=ACCTAAAAGGGAAGGGCCCC;RSEQ=TGTCCCATGATCATGTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:59,41:100,0:0:2,0:27.6:1:31.4:1:1:0:56.5:49:1:0:0.2 0/1:127:2:1,1:71,52:123,2:0.0157:2,2:36:1:31:0:1:1.36192:60:4:0.0165:0:1 +3 184673222 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50274;SOR=Inf;LSEQ=AAAGGGAAGGGCCCCCTGTC;RSEQ=CATGATCATGTGACTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:61,44:105,0:0:2,0:27.8:1:30.8:1:1:0:56.7:34:1:0:0.2 0/1:128:2:1,1:72,54:126,2:0.0156:2,2:35:1:28.5:1:1:1.33029:60:4:0.0164:0:1 +3 184673261 . A G 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10608;SOR=0;LSEQ=TTCACCTTATCACTTAGAAG;RSEQ=TTCATCCTCCTTACCCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:2,1:39,48:87,3:0.0333:2,2:21.7:1:25:1:0.58958:2.44:57.7:2:0.0235:0:1.7 0/0:99:0:0,0:41,58:99,0:0:2,0:21.5:1:28.3:1:1:0:57.3:32:1:0:0.3 +3 184673338 . T C 125 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02442;SOR=0;LSEQ=CAGTCGTTTGAGGCCACTGC;RSEQ=GGTCTCCGCGTCTTGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:1,18:0,0:0,19:1:0,1:27.6:1:29.5:1:1:0:56.5:18:1:0:1.7 1/0:23:17:1,16:1,5:6,17:0.7391:2,1:29.6:1:29.4:1:0.46245:3.01096:54.8:34:0.7391:0:1.8 +3 184673365 . T C 122 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10122;SOR=0;LSEQ=CGCGTCTTGGTGGTAGTGGT;RSEQ=CCCCGGGCCCAGCTATTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:1,15:0,0:0,16:1:0,1:20.2:1:30.6:1:1:0:52.3:15:1:0:1.9 1/0:16:12:1,11:2,2:4,12:0.75:2,2:32.1:1:30.4:1:0.13571:8.85639:52.7:11:0.7333:0:2.1 +3 185003285 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19706;SOR=Inf;LSEQ=GTACCTTAGGTCTGTACATT;RSEQ=ACATTCTTGAGGTTTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:159,17:176,0:0:2,0:23.1:1:32.3:1:1:0:60:57.667:1:0:0 0/1:141:2:1,1:122,17:139,2:0.0142:2,2:5.5:1:27:1:0.23982:7.00279:60:4:0.0142:0:1 +3 185046766 . T A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.49134;SOR=1.92252;LSEQ=TTGGTGTAAGTAGTTTTTTT;RSEQ=AAAAAAAACTATTATGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:20:20,0:9,0:9,20:0.6897:0,1:18.9:1:29:1:1:0:60:40:0.6897:0:1 1/1:16:13:13,0:3,0:3,13:0.8125:0,1:22:1:28.5:1:1:0:60:26:0.8125:0:1.1 +3 185046909 . AT A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=4e-05;SOR=1.98681;LSEQ=CAGCACTCAGCAGTAGTTTT;RSEQ=TTTTTTTTAATGGAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:381:224:167,57:112,42:154,224:0.5879:2,2:23.4:1:31.2:1:0.72175:1.10:60:223:0.5868:0.0761:0.8 1/0:307:227:160,67:58,22:80,227:0.7394:2,2:28.1:1:30.1:1:0.77603:1.10365:60:112.5:0.7377:0.0293:0.7 +3 185046975 . T C 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.51516;LSEQ=TGCTGCTAAAACAGGTCCCG;RSEQ=GTGCACGAAATGATTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:935:934:507,427:0,1:1,934:0.9989:0,2:26.8:1:30.9:1:0.45775:0:59.9:61.267:0.9989:0:1.1 1/1:964:962:496,466:0,1:1,962:0.9979:0,2:26.4:1:30.2:1:0.48494:0:59.8:52.444:0.9989:0:1.2 +3 185047301 . A G 97 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAATGTATTTTCAAAGAGG;RSEQ=AGAACTTTGTAAAACAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,0:0,9:0.9:0,0:20.2:1:30.9:1:1:0:60:18:0.9:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:24:0:32:0:1:0:60:2:1:0:1 +3 185146373 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04003;SOR=Inf;LSEQ=GTTATACTCATGGCACGATG;RSEQ=CCAACTTTCAGGAGCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:193,118:311,0:0:2,0:24.5:1:31.5:1:1:0:60:61.2:0.9967:0:0.1 0/1:254:4:2,2:149,101:250,4:0.0157:2,2:10.5:1:28.3:1:1:1.4729:60:8:0.0161:0:1.3 +3 185146499 . G A 148 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.04639;LSEQ=ACCCTTCTCCCAAGCTGCTC;RSEQ=AGGACCAGCAGGAAAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:585:1:1,0:310,274:584,1:0.0017:2,0:1:0:26:0:1:0:60:2:0.0017:0:1 0/1:544:30:18,12:280,233:513,30:0.0551:2,2:26.2:1:30.2:1:0.70643:1.25:60:60:0.0561:0:1.1 +3 185146702 . C T 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGACGGAGAGAGCACAAG;RSEQ=GGAACTGAAGACATAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:318,248:566,0:0:2,0:24.6:1:31:1:1:0:59.9:50.455:1:0:0.1 0/1:573:104:61,43:239,230:469,104:0.1815:2,2:24.5:1:28.8:1:0.16018:1.36:60:51:0.1821:0:1.1 +3 185146868 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17744;SOR=Inf;LSEQ=AGCTAGAATATGGACTTGGA;RSEQ=GATATTTCTTGTGTAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:38,210:248,0:0:2,0:23.1:1:32.2:1:1:0:60:247:1:0:0.1 0/1:181:2:1,1:39,140:179,2:0.011:2,2:16.5:1:31:0:0.39411:3.56:60:4:0.0111:0:1 +3 185155224 . T C 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTTCAAGCTTATTTCTTGCT;RSEQ=GTGTGCCTAGATACTTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:0:0,0:301,171:472,0:0:2,0:24.2:1:30.7:1:1:0:60:77.667:1:0:0.1 0/1:467:24:17,7:282,161:443,24:0.0514:2,2:23:1:30.7:1:0.52174:1.39:60:48:0.0523:0:1 +3 185155430 . C CT 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.00252;SOR=0.68969;LSEQ=CGCATTCAAGTAGGTCAAGG;RSEQ=TTTTTTTTTTTAAGAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:517:263:81,182:67,123:190,263:0.5087:2,2:28.1:1:30.3:1:0.36101:1.22337:59.7:20.917:0.5102:0.0193:0.4 0/1:593:247:79,168:106,130:236,247:0.4165:2,2:31.2:1:28.9:1:0.00374:1.73202:59.9:26.444:0.4161:0:0.5 +3 185155442 . A T 74 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00191;SOR=Inf;LSEQ=GGTCAAGGCTTTTTTTTTTT;RSEQ=AGAAGTAGACCTATTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:124,314:438,0:0:2,0:21.9:1:29.7:1:1:0:59.5:30.286:0.9976:0:0.5 0/1:471:10:9,1:140,321:461,10:0.0212:2,2:8.2:1:22.4:1:0.00019:20.51:60:2.333:0.0153:0:1.7 +3 185155807 . G A 70 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAAAACAAAGTTGGCCGGGC;RSEQ=CAGTGGCTCATGTCTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:22:1:30.2:1:1:0:47.8:10:1:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 185161145 . A G 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12789;SOR=Inf;LSEQ=TTTTAAAATAATTCGGGTAT;RSEQ=GAATTGGTTTTTATTAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:221,17:238,0:0:2,0:22.3:1:28.9:1:1:0:59.9:118:1:0:0.1 0/1:133:2:1,1:114,16:130,2:0.015:2,2:18:0:29:1:0.24185:6.94249:60:4:0.0153:0:1 +3 185165534 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=TTAGAATCATGGTTTTCGTT;RSEQ=GTACTAATGATCCAGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:180,19:199,0:0:2,0:24.1:1:28.9:1:1:0:60:398:1:0:0.1 0/1:199:2:1,1:154,43:197,2:0.0101:2,2:24.5:1:27.5:1:0.39419:3.55169:60:4:0.0101:0:1 +3 185167159 . TA T 33 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=23.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACAGAGCAAGATGCTGTC;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,1:1,2:0.5:0,0:23:1:33:1:0.33333:0:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 185167519 . AT A 160 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.67391;SOR=0.79135;LSEQ=GTGTTGATTACCCCACATAG;RSEQ=TTTTTTTTTTTTTTCAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:33:31,2:20,0:20,33:0.5:1,2:30.6:1:31.9:1:0.52104:0:59.8:66:0.5077:0.0758:0.7 0/1:34:15:12,3:10,0:10,15:0.4412:0,2:29.1:1:30.4:1:0.25:0:60:30:0.4412:0.0294:0.1 +3 185167910 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50893;SOR=0;LSEQ=TATTTGGAGTAAATATCCTG;RSEQ=TGGTGGAAAGAATAGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:17,145:162,2:0.0121:2,2:25:1:28.5:1:0.20807:8.32:60:4:0.0123:0:1 0/0:123:0:0,0:20,103:123,0:0:2,0:19.8:1:31.2:1:1:0:60:122:1:0:0 +3 185168877 . CA C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.18797;SOR=Inf;LSEQ=GACAGAGCGAGACTCCGTCT;RSEQ=AAAAAAAGAAAAAAAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:31,1:32,0:0:1,0:19:1:31.3:1:1:0:55.9:64:1:0:0.1 0/1:25:2:2,0:22,1:23,2:0.08:1,0:16.5:1:31:1:1:0:60:4:0.08:0:0 +3 185170285 . A T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCCCTGCCTCGGCCTCCC;RSEQ=AACTGCTGGGATTACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:28:1:1:0:38:4:1:0:1 +3 185180812 . T C 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCAACTCCAAATTCCCGTA;RSEQ=AGCTTCTTATATTTCTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:29.5:1:32.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 185181248 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52064;SOR=0;LSEQ=GGCTCTTCAGTAGAAGCATG;RSEQ=AGGGAAAAAAAATCTTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:2,0:161,5:166,2:0.0118:1,0:30.5:1:32:0:1:0:60:4:0.0121:0:1 0/0:110:0:0,0:106,4:110,0:0:1,0:24.4:1:31.9:1:1:0:60:109:1:0:0.1 +3 185181543 . C T 26 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57784;SOR=2.69831;LSEQ=ACCATTTCACTTTCCACACA;RSEQ=CTTTCACCTCTGCTTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:0,1:10,170:180,1:0.0055:2,0:15:0:14:0:1:0:56:0:0:0:6 0/1:135:2:1,1:9,124:133,2:0.0148:2,2:6.5:1:26.5:1:0.14317:13.12:60:4:0.015:0:1 +3 185183418 . G C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGACAAGGGAGGCTTAAA;RSEQ=TAAGAGGGCCTTGGGCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:96:96:96,0:0,0:0,96:1:0,1:25.4:1:32.5:1:1:0:60:47:1:0:1.2 1/1:55:55:53,2:0,0:0,55:1:0,1:21.4:1:31.5:1:1:0:60:110:1:0:1.1 +3 185183491 . C T 215 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01122;LSEQ=CATCAAGCGGACTTTTTTCT;RSEQ=CCGAAGTTGGTTGGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:129:85,44:192,99:291,129:0.3071:2,2:26.8:1:30.8:1:1:1.00391:60:128:0.3107:0:1.2 0/0:406:2:0,2:254,150:404,2:0.0049:2,0:1:0:24.5:1:0.13959:0:60:4:0.0051:0:1 +3 185183656 . G A 219 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00404;LSEQ=AGAAGGAGCTCATTAAGTAT;RSEQ=TATCCAGACTAGTGTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:493:162:55,107:133,198:331,162:0.3286:2,2:25.9:1:29.9:1:0.19985:1.30609:60:39.5:0.3258:0:1.1 0/0:508:1:1,0:198,309:507,1:0.002:2,0:1:0:22:0:0.39173:0:60:2:0.002:0:1 +3 185183717 . C A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32098;SOR=3.9419;LSEQ=AATCAGCAGAAACATACTAC;RSEQ=CTTCCATGTTGCTGCTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:0,1:18,168:186,1:0.0053:2,0:27:0:12:0:1:0:60:0:0:0:6 0/1:144:3:2,1:11,130:141,3:0.0208:2,2:16.7:1:27:1:0.02155:22.38:60:6:0.0211:0:1 +3 185191198 . C T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05119;SOR=Inf;LSEQ=GCTCAGAGACAGCTGCCCGG;RSEQ=TCGAGCCCTGACCTCATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:185,219:404,0:0:2,0:23.5:1:32.4:1:1:0:59.9:49.5:1:0:0.1 0/1:368:4:2,2:153,211:364,4:0.0109:2,2:28:1:24.5:1:1:1.38:60:3:0.0084:0:1.5 +3 185195227 . G GA 161 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=10.0945;LSEQ=ATTGCTTTTAGTGGAATGGG;RSEQ=AAAAAAAATCCTAAGTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:5:3,2:184,405:589,5:0.0084:2,2:29.6:1:29.4:1:0.18235:3.29:60:10:0.0085:0.0017:0.2 0/1:582:46:12,34:188,344:532,46:0.079:2,2:22.8:1:29.2:1:0.25827:1.54735:59.9:45:0.078:0.0069:0.2 +3 185197965 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19479;SOR=Inf;LSEQ=TACTATGAGTGACAGATAAG;RSEQ=AAAGAAAAGCAGTTGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:185,46:231,0:0:2,0:22.8:1:31.3:1:1:0:59.9:24.667:1:0:0.1 0/1:183:2:1,1:134,47:181,2:0.0109:2,2:23:1:30:1:0.45685:2.83172:60:4:0.0113:0:1 +3 185199743 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTATCCGGGCATGGTGGCAC;RSEQ=CGCCTGTAGTCCCAGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:37.5:1:30:1:1:0:33.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 185200783 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACATTTTAGAACACAAAG;RSEQ=ACAGCAAAAGAAAAGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:10:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 185200873 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTACGGAAATGACCTA;RSEQ=AAAAGTCTGGTGACCAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:26:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 186073482 . T C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00499;LSEQ=CTACCATCATTACCCCATTA;RSEQ=CACCATCACCAGCACCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:17:11,6:14,9:23,17:0.425:2,2:29.5:1:32.4:1:1:1.17:60:34:0.4595:0:1.3 0/1:61:26:14,12:17,18:35,26:0.4262:2,2:25.6:1:30.7:1:0.7972:1.23:60:25:0.431:0:1.2 +3 186490322 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53613;SOR=0;LSEQ=CGGCGGGCAGAGCTGGCCTG;RSEQ=GGGCCGGGTCCCGTGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:20,1:21,2:0.087:1,2:20.5:1:32:0:0.16996:14.49116:60:4:0.0909:0:1 0/0:12:0:0,0:12,0:12,0:0:0,0:19.7:1:28.8:1:1:0:60:5:1:0:0.4 +3 186490810 . G T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56342;SOR=3.11046;LSEQ=CGGAAGTCCGTGGGCTCAGC;RSEQ=GCGGCTTTTGCAGGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:0,1:89,61:150,1:0.0066:2,0:1:0:25:0:0.4106:0:60:2:0.0067:0:1 0/1:98:2:1,1:57,39:96,2:0.0204:2,2:37:0:31.5:1:1:1.45573:60:4:0.0204:0:1.5 +3 186490832 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51443;SOR=0;LSEQ=CGGCTTTTGCAGGGACCCCA;RSEQ=AGCAGGCAGCCTGGGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:88,74:162,2:0.0122:2,2:18.5:1:29.5:1:1:1.18792:60:4:0.0123:0:1.5 0/0:114:0:0,0:63,51:114,0:0:2,0:26.5:1:30.8:1:1:0:60:56:1:0:0.2 +3 186490848 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17547;SOR=Inf;LSEQ=CCCAGAGCAGGCAGCCTGGG;RSEQ=GGTGCCGCTGGGACTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:85,77:162,0:0:2,0:29.8:1:31:1:1:0:60:53:0.9938:0:0.1 0/1:118:2:1,1:57,59:116,2:0.0169:2,2:19.5:1:29:1:1:1.03:60:4:0.0172:0:1.5 +3 186491092 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22691;SOR=Inf;LSEQ=AGGTTTCCCTGGTCCATCCT;RSEQ=CCTGACCCCCATGCATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:58,14:72,0:0:2,0:23:1:32.3:1:1:0:60:71:1:0:1 0/1:66:2:1,1:52,12:64,2:0.0303:2,2:40.5:1:30:1:0.35758:4.20318:60:4:0.0303:0:2 +3 186491101 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49729;SOR=0;LSEQ=TGGTCCATCCTCCCTGACCC;RSEQ=CATGCATGCCCAGGTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:65,19:84,2:0.0233:2,2:17.5:1:33:1:0.41313:3.35992:60:4:0.0233:0:2 0/0:82:0:0,0:64,18:82,0:0:2,0:25.9:1:30.3:1:1:0:60:26.333:1:0:1.1 +3 186491116 . T C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03482;SOR=8.46071;LSEQ=GACCCCCATGCATGCCCAGG;RSEQ=TCTGCATCCAGGCCCTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:90:70,20:5,2:7,90:0.9184:2,2:26.2:1:32.4:1:0.65516:1.39:60:89:0.9271:0:1.2 1/1:97:96:73,23:1,0:1,96:0.9897:0,2:27.8:1:31.5:1:1:0:60:95:0.9896:0:1.2 +3 186491156 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2195;SOR=0;LSEQ=CTCCTTGCCTAATCCCAGCT;RSEQ=CCCGCGAAGATGCAGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:106,45:151,2:0.0131:2,2:36.5:1:29.5:1:0.5123:2.3408:60:4:0.0132:0:2 0/0:173:0:0,0:114,59:173,0:0:2,0:20.4:1:30:1:1:0:60:85.5:1:0:0.6 +3 186491189 . G A 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.35971;SOR=3.19751;LSEQ=CAGCCAGCAGGAACGTCTAG;RSEQ=TTTTGCAGCTACCAACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:1,0:158,109:267,1:0.0037:2,0:1:0:25:0:1:0:60:2:0.0038:0:1 0/1:253:3:2,1:142,108:250,3:0.0119:2,2:15.3:1:25.7:1:1:1.52:60:6:0.012:0:2 +3 186491192 . T C 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24911;SOR=0;LSEQ=CCAGCAGGAACGTCTAGGTT;RSEQ=TGCAGCTACCAACCAACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:1,2:156,112:268,3:0.0111:2,2:27.3:1:25.3:1:0.57444:2.77523:60:2:0.0075:0:2.7 0/0:257:0:0,0:142,114:256,0:0:2,0:25.2:1:28.9:1:1:0:60:35.571:1:0:0.3 +3 186491195 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36277;SOR=3.15544;LSEQ=GCAGGAACGTCTAGGTTTTG;RSEQ=AGCTACCAACCAACCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:1:0,1:157,117:274,1:0.0036:2,0:1:0:26:0:0.42909:0:60:2:0.0037:0:1 0/1:263:3:1,2:142,118:260,3:0.0114:2,2:17.3:1:28:1:0.59353:2.39894:60:6:0.0115:0:1 +3 186491296 . CCA C 75 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.21159;SOR=0.19927;LSEQ=GCTTCAATTTCGTCCTGCCC;RSEQ=CACACACACCATGGGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:5:1,4:12,80:92,5:0.0521:2,2:16.2:1:32.6:1:0.52096:1.66:60:10:0.0526:0.0313:0.6 0/1:93:1:0,1:16,76:92,1:0.0108:2,0:26:0:27:0:1:0:60:2:0.0109:0:1 +3 186501502 . C A 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.43158;LSEQ=GGAGATGATAGTGGATGGCA;RSEQ=GGAGGCAAAAACTCTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1185:535:188,347:224,426:650,535:0.4515:2,2:24.6:1:31.5:1:0.8067:1.03:59.9:534:0.4552:0:1.1 1/0:1441:961:356,605:186,292:478,961:0.6669:2,2:24.9:1:29.8:1:0.52525:1.08246:60:191.2:0.6709:0:1.1 +3 186501648 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCTAAAGGGCGTTTTTCCTC;RSEQ=CTAAGACATTACGAAACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:26:1,25:3,59:62,26:0.2955:1,1:19.3:1:30.5:1:1:1.26785:60:12:0.2857:0:1.5 1/1:43:43:0,43:0,0:0,43:1:0,1:20.6:1:29.9:1:1:0:59.4:20.5:1:0:1.2 +3 186501900 . C T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGTGAACCGTTGGCATCGC;RSEQ=CTCGCCAGGCCGCTCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:3,0:10,4:14,3:0.1765:2,0:48.3:1:25.3:1:0.54118:0:56:2:0.1333:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:34.5:1:31.5:1:1:0:48.5:8:1:0:0 +3 186502017 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07671;SOR=Inf;LSEQ=AAACGGGATCGCCATGCGCT;RSEQ=GGGCCTGGGGGGCTGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:44,2:46,0:0:1,0:23.9:1:31.9:1:1:0:60:45:1:0:0.2 0/1:35:3:3,0:31,1:32,3:0.0857:1,0:34.3:1:30:1:1:0:60:6:0.0882:0:1 +3 186502034 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23997;SOR=Inf;LSEQ=GCTCGGGCCTGGGGGGCTGC;RSEQ=TTCCGGGCATCCGCAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:60,3:63,0:0:1,0:23.6:1:31.8:1:1:0:60:20:1:0:0.2 0/1:61:2:1,1:59,0:59,2:0.0328:1,2:34:1:29.5:1:0.03279:0:60:4:0.0333:0:0 +3 186502665 . C T 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGATCACTTGATTATTTGGG;RSEQ=ATAATGTTCCAAATGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:264,53:317,0:0:2,0:24:1:32.2:1:1:0:59.6:34.222:1:0:0.1 0/1:249:36:32,4:191,22:213,36:0.1446:2,2:23.1:1:28.8:1:0.77583:1.08488:59.1:72:0.1446:0:1.1 +3 186503435 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=TGTAGGAAACGTTATTCTTG;RSEQ=ATTGTCTAGCTGATGCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:13:11,2:22,0:22,13:0.3714:1,2:24.9:1:31.2:1:0.13109:0:59.5:26:0.3714:0:1.1 1/1:8:8:8,0:0,0:0,8:1:0,0:32.4:1:28:1:1:0:55.6:7:1:0:1 +3 186503571 . TA T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.17813;SOR=Inf;LSEQ=AGTTTTGTGCTGTGCATGCA;RSEQ=AAAGCTGTTGGCAGACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:225,3:228,0:0:1,0:24.9:1:28.6:1:1:0:59.9:56:1:0:0.1 0/1:167:2:1,1:158,7:165,2:0.012:1,2:19.5:1:26.5:1:0.09379:21.18043:60:4:0.012:0.006:0.5 +3 186504148 . T C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=3.92236;LSEQ=AATACAACTGATGTGTTTTG;RSEQ=TGTCGTTCCCCCTGCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:72:10,62:48,224:272,72:0.2093:2,2:22.6:1:33.3:1:0.59529:1.32758:59.9:144:0.2136:0:1.1 1/0:249:127:24,103:21,100:121,127:0.51:2,2:24.1:1:31.1:1:0.86927:1.11:60:41.333:0.5124:0:1.1 +3 186504212 . CAG C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.02541;SOR=Inf;LSEQ=ACCTTCATTCCGTAGTAAGA;RSEQ=AGACGCTTGGCTTCAGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:147,102:249,0:0:2,0:24.7:1:31.6:1:1:0:59.8:82:1:0:0.1 0/1:167:4:2,2:101,62:163,4:0.024:2,2:33:1:33.3:1:0.63789:1.62403:60:8:0.0241:0:0 +3 186504406 . A C 203 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTGACCCTTGAAGGAATCA;RSEQ=ACAGTTTTATATTAATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1147:73:34,39:492,580:1072,73:0.0636:2,2:31.3:1:32.9:1:1:1.03:49.8:72:0.0635:0:1.1 0/0:1282:0:0,0:618,661:1279,0:0:2,0:27:1:29.8:1:1:0:55.4:126.9:0.9984:0:0.1 +3 186504901 . T C 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGACTGTTAACTTTAAC;RSEQ=TCTAAACATTACAGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1007:0:0,0:600,407:1007,0:0:2,0:25.7:1:31.2:1:1:0:52.7:142.857:1:0:0.1 0/1:1167:33:21,12:668,466:1134,33:0.0283:2,2:17.8:1:31.1:1:0.7201:1.22:43:66:0.0287:0:1.1 +3 186505706 . A C 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTTGGCTGTATTGAAAAAA;RSEQ=TTCATACGTTTTTCTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:576:0:0,0:156,420:576,0:0:2,0:24.2:1:31.1:1:1:0:59.9:114.2:1:0:0.1 0/1:573:20:7,13:174,379:553,20:0.0349:2,2:25:1:31.6:1:0.80739:1.17:60:40:0.0353:0:1.2 +3 186505900 . T G 64 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62637;SOR=0.40085;LSEQ=TTTTTCCACAATTGTTGGTC;RSEQ=TACCTTATGCTTGAGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:0,4:0,14:14,4:0.2222:1,0:23.8:1:32.3:1:1:0:60:8:0.2222:0:1 0/1:10:1:0,1:2,7:9,1:0.1:2,0:10:0:33:0:1:0:60:2:0.1111:0:1 +3 187303758 . G A 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTATATTTCCTACAAGGG;RSEQ=GGAATTTAGTTTGCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:5,0:5,3:0.3333:0,0:37.3:1:31.3:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 187304069 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.23386;LSEQ=AAAGGGGCAAAAAAGCAAAA;RSEQ=GAAGAAATCACCCTTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:218:119,99:182,154:336,218:0.3935:2,2:24.8:1:30.7:1:0.93067:1.02:60:71.667:0.3981:0:1.1 1/0:446:264:141,123:80,86:166,264:0.5919:2,2:26.3:1:29.5:1:0.32203:1.23:60:263:0.5923:0:1.1 +3 187440092 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGGCTCCCAGTCCCCCAG;RSEQ=CCCCGACCCCCACCACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:2,0:43,0:43,2:0.0444:1,0:20:1:29.5:1:1:0:60:4:0.0465:0:1 0/0:20:0:0,0:18,2:20,0:0:2,0:28.9:1:28.7:1:1:0:60:9:1:0:1.8 +3 187440126 . G C 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08579;SOR=0;LSEQ=CACCCCCAACCCCCAGCTAT;RSEQ=ATTTGCACTAGTGGATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:6:6,0:62,0:62,6:0.0882:1,0:18.8:1:26.8:1:1:0:60:2:0.0784:0:1.3 0/0:38:0:0,0:36,2:38,0:0:2,0:20.5:1:27.9:1:1:0:60:3.222:1:0:1 +3 187440458 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19706;SOR=Inf;LSEQ=GATGTCATTGCTCAAAGACC;RSEQ=AGAGAGGAAGATTCTCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:25,150:175,0:0:2,0:23.7:1:32.3:1:1:0:60:86.5:1:0:0.4 0/1:141:2:1,1:22,117:139,2:0.0142:2,2:14.5:1:26:0:0.30061:5.22:60:4:0.0144:0:1.5 +3 187440506 . C A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=0.18778;LSEQ=CTGGGGCAGCTCTTGCCTCT;RSEQ=CAAGGCCAGGTGAAGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:84:74:1,73:0,10:10,74:0.881:0,1:27:1:30.6:1:1:0:59.9:148:0.8916:0:1.1 1/0:45:26:0,26:1,18:19,26:0.5778:1,1:25.1:1:29.7:1:0.42222:0:60:52:0.5778:0:1.2 +3 187442168 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAGACCCCGCCCTAGAACA;RSEQ=TCCAATCCCAGTGAACCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 187442527 . C A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57562;SOR=0.44667;LSEQ=TGAGTCCCCTAATGCTTGGG;RSEQ=CAAGGTCAAGCAGGGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:14:14,0:3,0:3,14:0.8235:0,1:21.4:1:31.4:1:1:0:60:28:0.8235:0:1.1 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:30.3:1:28.3:1:1:0:60:8:0.6667:0:1 +3 187442662 . G GCTCCACCTCCTTCCCTGCC 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=3.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=TGCTCCACCTCCTTCCCTGC;RSEQ=CTCCACCTCCTTCCCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:182,30:212,0:0:2,0:23.9:1:30:1:1:0:59.9:52:1:0:0.1 0/1:148:8:7,1:117,23:140,8:0.0541:2,2:11.9:1:30.9:1:1:1.37:57.5:16:0.0541:0.0473:1 +3 187442666 . C T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.01227;SOR=Inf;LSEQ=CCACCTCCTTCCCTGCGCTC;RSEQ=ACCTCCTTCCCTGCCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:197,33:230,0:0:2,0:23.5:1:31.4:1:1:0:59.9:114:1:0:0.1 0/1:165:5:2,3:131,29:160,5:0.0303:2,2:12.4:1:27.4:1:0.05061:6.66257:60:10:0.0303:0:1 +3 187443210 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50897;SOR=0;LSEQ=ACTTGCCTGCCCACTCCTCC;RSEQ=CTTGCCTGCCCACTCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:2,0:110,16:126,2:0.0153:2,0:20:1:31:0:1:0:40.5:4:0.0177:0:2 0/0:97:0:0,0:83,14:97,0:0:2,0:25.2:1:28.7:1:1:0:58.8:31.333:1:0:0.5 +3 187443213 . T C 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18441;SOR=1.66123;LSEQ=TGCCTGCCCACTCCTCCGCT;RSEQ=GCCTGCCCACTCCTCCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:15:13,2:103,15:118,15:0.1119:2,2:27.5:1:31.3:1:1:1.05598:54.5:30:0.1271:0:1.7 0/1:98:17:15,2:69,12:81,17:0.1735:2,2:31.5:1:29.9:1:1:1.30:52.9:34:0.1771:0:2.1 +3 187443225 . CCTCCGCTCGCCTGCCCG C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37312;SOR=1.56911;LSEQ=CCTCCGCTTGCCTGCCCACT;RSEQ=CTCCGCTCGCCTGCCCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:10:8,2:126,22:148,10:0.0633:2,2:18:1:31.4:1:0.64957:1.4282:45.1:20:0.0671:0.0316:2.2 0/1:125:12:9,3:95,17:112,12:0.096:2,2:20.5:1:29.7:1:0.40846:1.85189:47.3:24:0.0984:0.048:2.2 +3 187443238 . G A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.33449;SOR=3.61874;LSEQ=GCCCACTCCTCCGCTCGCCT;RSEQ=CCCGCTCCGCTCGCCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:1:1,0:148,31:179,1:0.0054:2,0:6:0:29:0:1:0:58:2:0.0059:0:2 0/1:155:3:2,1:117,28:145,3:0.0194:2,2:17:1:28.3:1:0.48277:2.07677:51.3:6:0.0208:0:1.3 +3 187443241 . C T 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=CACTCCTCCGCTCGCCTGCC;RSEQ=GCTCCGCTCGCCTGCCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:149,35:184,0:0:2,0:22:1:30.3:1:1:0:59.3:29.667:0.9944:0:0.2 0/1:160:11:6,5:116,27:143,11:0.0688:2,2:15.8:1:27.5:1:0.05152:3.5418:60:10:0.0658:0:1.1 +3 187443250 . C T 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47906;SOR=1.97763;LSEQ=GCTCGCCTGCCCGCTCCGCT;RSEQ=GCCTGCCCGCTCCGCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:2,1:178,49:227,3:0.013:2,2:8.7:1:32:1:0.52242:1.81086:45.7:6:0.0136:0:2.3 0/1:196:5:5,0:142,49:191,5:0.0255:2,0:10:1:28:1:0.33401:0:48.4:10:0.0259:0:3 +3 187443267 . C T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42131;SOR=0.79779;LSEQ=GCTCGCCTGCCCGCTCCGCT;RSEQ=GCCTGCCCACTCTGCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:37:21,16:207,68:275,37:0.1186:2,2:17.1:1:29.2:1:0.02818:2.31222:55.8:8.25:0.1089:0:1.6 0/1:258:25:16,9:163,70:233,25:0.0969:2,2:19.7:1:29.6:1:0.64823:1.30844:55.8:24:0.0945:0:1.4 +3 187443268 . G A 54 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18143;SOR=4.87922;LSEQ=CTCGCCTGCCCGCTCCGCTC;RSEQ=CCTGCCCACTCTGCTCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:1:0,1:230,83:313,1:0.0032:2,0:17:0:12:0:0.26752:0:60:0:0:0:2 0/1:260:4:3,1:177,79:256,4:0.0154:2,2:6:1:27:1:1:1.34:48:8:0.0157:0:2.8 +3 187443274 . C T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33754;SOR=3.56368;LSEQ=TGCCCGCTCCGCTCGCCTGC;RSEQ=CACTCTGCTCACCTGTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:1:1,0:241,97:338,1:0.0029:2,0:2:0:32:0:1:0:60:2:0.0031:0:1 0/1:287:3:2,1:194,90:284,3:0.0105:2,2:20:1:29:1:1:1.07749:60:6:0.0107:0:1 +3 187443314 . G A 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCTGGCTCCGCAGGTTTC;RSEQ=CATTTGTAGGGCTTCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:637:0:0,0:403,234:637,0:0:2,0:25:1:30.7:1:1:0:59.8:126.4:1:0:0.2 0/1:592:21:13,8:337,230:567,21:0.0355:2,2:23.1:1:29.4:1:1:1.11:60:42:0.0361:0:1.1 +3 187444210 . T C 67 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTCTGGCTTTACAAAAAT;RSEQ=GAATCTATTTGTCTTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:34:1:33.5:1:1:0:60:8:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:28:0:32:0:1:0:60:2:1:0:1 +3 187445197 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACACAAAGCATTCCAGG;RSEQ=ATGTAAGATATAGGTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:29.5:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 187445892 . A G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAAGCTACTTTTGCTGGC;RSEQ=TGAAGCTAAAATGACTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:0,17:1:0,1:26:1:29.3:1:1:0:59.9:16:1:0:1.3 1/1:5:5:4,1:0,0:0,5:1:0,2:37:1:30:1:1:0:60:10:1:0:1.6 +3 187445909 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00706;SOR=Inf;LSEQ=GGCATGAAGCTAAAATGACT;RSEQ=TATGGTAAGTCTTGATTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:25,0:0:1,0:19.9:1:31.6:1:1:0:58.6:24:1:0:0.6 0/1:7:3:2,1:4,0:4,3:0.4286:0,2:33.3:1:28:1:0.42857:0:60:6:0.4286:0:2 +3 187446035 . A G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41335;SOR=1.58688;LSEQ=GGAGTGCCAGTGGACTTCCA;RSEQ=TTGAGGACTGCTCCAATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:8:8,0:145,4:149,8:0.051:1,0:21.5:1:33.3:1:1:0:60:16:0.0519:0:1 0/1:89:7:7,0:82,0:82,7:0.0787:1,0:17.6:1:27.3:1:1:0:60:2.5:0.0581:0:2.1 +3 187446059 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00396;SOR=Inf;LSEQ=AGGACTGCTCCAATCAGAGA;RSEQ=AACAGCATAAGTAAAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:224,16:240,0:0:2,0:23.7:1:32:1:1:0:60:39:1:0:0.1 0/1:161:6:5,1:146,9:155,6:0.0373:2,2:17.8:1:29.5:1:0.32366:3.20668:60:12:0.038:0:1 +3 187446082 . A T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07227;SOR=Inf;LSEQ=CAGCATAAGTAAAATGGAGC;RSEQ=CAAAACCTATGGAGCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:325,49:374,0:0:2,0:22.2:1:30.4:1:1:0:59.9:73.8:1:0:0.1 0/1:268:3:1,2:218,47:265,3:0.0112:2,2:10.3:1:26:1:0.08699:9.16072:60:6:0.0113:0:1 +3 187446211 . C T 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAGGGAACGTGGGGCCAG;RSEQ=GGTGTGGAGGCACATCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1165:0:0,0:534,630:1164,0:0:2,0:25.1:1:30.5:1:1:0:60:45.56:0.9991:0:0.1 0/1:1057:56:26,30:472,529:1001,56:0.053:2,2:26.1:1:28.2:1:1:1.0295:60:55:0.0529:0:1.2 +3 187446493 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCTCCAAACAGTATCTGC;RSEQ=GAAAGATCACTGACCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:6,29:0,0:0,35:1:0,2:25.1:1:31.2:1:1:0:59.4:34:1:0:1.4 1/1:7:7:0,7:0,0:0,7:1:0,0:22.7:1:31.1:1:1:0:60:14:1:0:1.1 +3 187446731 . T C 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01769;SOR=Inf;LSEQ=ACTCAATCTATAGGCACTGA;RSEQ=TCCACACCTCTAATAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:130,5:135,0:0:1,0:26.2:1:31.4:1:1:0:59.9:44:1:0:0.1 0/1:79:4:3,1:72,3:75,4:0.0506:1,2:17.5:1:32.8:1:0.19105:7.54641:60:8:0.0506:0:1 +3 187447032 . G A 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3932;LSEQ=CCCTCTGGTTTGGCATTCTG;RSEQ=TTGAGGCTGTTGAGCACGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1411:1179:571,608:104,127:231,1179:0.8356:2,2:25.7:1:30.3:1:0.35007:1.15:60:30.026:0.8335:0:1.1 1/0:1181:787:375,412:190,200:390,787:0.6664:2,2:24.9:1:29:1:0.75676:1.04372:60:36.476:0.6626:0:1.2 +3 187447581 . G T 87 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05616;SOR=4.35687;LSEQ=TCATCGGAGAAGAGGAGGCT;RSEQ=CTGACAGGGAGGTGGCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:653:2:0,2:331,320:651,2:0.0031:2,0:1:0:28:1:0.24277:0:60:4:0.0031:0:1 0/1:605:8:3,5:310,285:595,8:0.0132:2,2:22.3:1:29:1:0.49064:1.81109:60:16:0.0133:0:1.4 +3 187447926 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10103;SOR=0.25375;LSEQ=AATTAGCTAGACATAGGTGA;RSEQ=GTGGCTCTGGAGCAGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:39:0,39:0,6:6,39:0.8667:0,1:25.8:1:31.1:1:1:0:59.7:78:0.8667:0:1.1 1/0:13:8:0,8:0,5:5,8:0.6154:0,0:23.8:1:28.8:1:1:0:60:16:0.6154:0:1.3 +3 187448009 . T G 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAATTGGGAAGACTGAG;RSEQ=CCCAGAGAAGGGAAGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:29.7:1:32.9:1:1:0:53.9:20:1:0:1.1 1/1:4:4:0,4:0,0:0,4:1:0,0:14.3:1:28:1:1:0:60:3:1:0:1.5 +3 187449922 . G C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCGTTTGCTCCTTACAAC;RSEQ=CTGCAAGGTAGGTACTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:1,14:0,0:0,15:1:0,1:23.5:1:32.4:1:1:0:60:30:1:0:1.1 1/1:4:4:0,4:0,0:0,4:1:0,0:31.8:1:27.3:1:1:0:60:3:1:0:1.3 +3 187451113 . G A 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTCTATGCCCACAGAAC;RSEQ=TGGCTCTTTCTTTTCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:31,0:0,0:0,31:1:0,1:20.2:1:29.6:1:1:0:58.9:14.5:1:0:1 1/1:7:7:7,0:0,0:0,7:1:0,0:14.9:1:29.4:1:1:0:60:14:1:0:1 +3 187451349 . C A 148 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CATGAGGACCGTTTTATGGG;RSEQ=TCTAAACTGCTCACGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:961:29:14,15:460,470:930,29:0.0302:2,2:25.1:1:30.6:1:1:1.0486:60:28:0.0297:0:1.1 0/0:857:0:0,0:445,412:857,0:0:2,0:25.3:1:31.1:1:1:0:60:49.412:1:0:0.2 +3 187451469 . C T 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73875;SOR=0.62977;LSEQ=GAACTGGATACAGCTGTCAG;RSEQ=CGGCGAGGCCATTTTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:6:3,3:190,403:593,6:0.01:2,2:15.2:1:30.3:1:0.39299:2.12:60:12:0.0103:0:1.5 0/0:474:3:2,1:175,293:468,3:0.0063:2,2:26.3:1:18.3:1:0.55943:3.34:60:0.5:0.0022:0:2.7 +3 187451609 . A G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCAACTCAGGTCCCTTGT;RSEQ=TTTGATCTTTGAACAATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:2,42:0,0:0,44:1:0,1:23.1:1:31.5:1:1:0:60:21:1:0:1.1 1/1:31:31:3,28:0,0:0,31:1:0,2:24.6:1:32.1:1:1:0:60:62:1:0:1 +3 187451701 . T C 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59752;SOR=0.51822;LSEQ=TTTTATCCAACAAGTTGGGA;RSEQ=AGAAAGCCCTTTAGGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:0,12:0,3:3,12:0.8:0,0:22.8:1:33.3:1:1:0:56.1:24:0.8:0:2.1 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:20.5:1:31.8:1:1:0:60:8:0.6667:0:2 +3 187451709 . C T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58533;SOR=0.47979;LSEQ=AACAAGTTGGGATAGAAAGC;RSEQ=CTTTAGGGGAAAAGCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:0,13:0,3:3,13:0.8125:0,1:21.1:1:30.1:1:1:0:56.4:26:0.8125:0:1.9 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:20.5:1:28.8:1:1:0:60:8:0.6667:0:2 +3 187451910 . G GC 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAATCTCAGCTCACTGCAA;RSEQ=TCCGCCTTCCCAGGTTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24:1:32.5:1:1:0:50:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 188183768 . A C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.89036;LSEQ=TTGAACTATCCATTAAGTCA;RSEQ=AGGGGATAGGCTATTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:15:15,0:29,1:30,15:0.3333:1,1:27.3:1:32.1:1:1:0:58.6:30:0.3409:0:1.2 0/1:26:8:8,0:16,2:18,8:0.3077:2,0:19.1:1:32.4:1:1:0:60:16:0.3333:0:1.1 +3 188183865 . C T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.36523;SOR=0.82069;LSEQ=TCAGAATCCTAGGTACTCTC;RSEQ=TTTAGACTGCCTGGTGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:82:58,24:117,49:166,82:0.3306:2,2:25.6:1:31:1:1:1.01:60:40:0.3292:0:1.1 0/1:215:62:41,21:98,55:153,62:0.2884:2,2:22.4:1:30.1:1:0.87511:1.10:60:124:0.2925:0:1.3 +3 188183879 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09944;SOR=Inf;LSEQ=ACTCTCCTTTAGACTGCCTG;RSEQ=TGACTACTCATTTGTCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:196,111:307,0:0:2,0:24.4:1:31.1:1:1:0:60:37.375:1:0:0.4 0/1:266:3:1,2:158,105:263,3:0.0113:2,2:17.7:1:26.7:1:0.56666:2.99694:60:6:0.0115:0:1.7 +3 188183932 . T A 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAATAGTTCAGTAGAATA;RSEQ=AACTTTGTGGAAATTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:180,196:376,0:0:2,0:27.4:1:29.7:1:1:0:60:375:1:0:0.2 0/1:345:82:46,36:133,130:263,82:0.2377:2,2:26.6:1:29.7:1:0.44776:1.25:60:81:0.2362:0:1.1 +3 188184000 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21242;SOR=Inf;LSEQ=CAGTGAGATGGGAGAGTCAG;RSEQ=GTCATTCATTGGTATTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:64,159:223,0:0:2,0:26.8:1:31:1:1:0:60:30.857:1:0:0.1 0/1:192:2:1,1:64,125:189,2:0.0104:2,2:26.5:1:28:1:1:1.95:60:4:0.0106:0:1 +3 188184054 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20546;SOR=Inf;LSEQ=CTTTTTGTCTGATCTTGCCT;RSEQ=GAGAATTATTTTTAAGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:4,75:79,0:0:2,0:22.5:1:31.2:1:1:0:60:25.333:1:0:0.1 0/1:66:2:1,1:4,60:64,2:0.0303:2,2:15.5:1:31.5:1:0.14685:13.53:60:4:0.0323:0:1 +3 189348968 . GCTCCA G 69 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTCAGAGATGCCTCCA;RSEQ=AATTGCCAACAACAAGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:36.3:1:34.8:1:1:0:60:8:0.8:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 189349077 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04329;SOR=Inf;LSEQ=CCCAGCTGGTAAGAATCGAG;RSEQ=GTTTATGAAGTTTTAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:17,0:0:1,0:19.6:1:30.8:1:1:0:60:34:1:0:0.3 0/1:5:2:2,0:3,0:3,2:0.4:0,0:36:1:33.5:1:1:0:60:4:0.4:0:1 +3 189349247 . A T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.19702;LSEQ=ATCTATATATACACAGGTAT;RSEQ=TGTGTATATTTTATATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:334:305:240,65:21,7:28,305:0.9132:2,2:24.2:1:30.2:1:0.63503:1.23:60:24.417:0.9099:0:1.1 1/0:233:157:118,39:56,20:76,157:0.6738:2,2:22.4:1:29.4:1:0.87261:1.08:60:38.25:0.6711:0:1.1 +3 189349251 . G T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16632;SOR=5.65616;LSEQ=ATATATACACAGGTATATGT;RSEQ=TATATTTTATATAATTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:1:1,0:272,81:353,1:0.0028:2,0:1:0:32:0:1:0:60:2:0.0028:0:1 0/1:253:4:1,3:186,63:249,4:0.0158:2,2:12.5:1:27.3:1:0.05566:8.76466:60:8:0.016:0:1 +3 189349456 . C A 23 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57353;SOR=2.8092;LSEQ=GCTGTGTACAAAGAACAATT;RSEQ=CTCCTTGTTTAGTCAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:1:1,0:27,218:245,1:0.0041:2,0:1:0:23:0:0.11382:0:60:2:0.0042:0:1 0/1:176:2:1,1:22,152:174,2:0.0114:2,2:16:1:23.5:1:0.24494:6.78:60:4:0.0115:0:1 +3 189349472 . G A 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.79608;LSEQ=AATTCCTCCTTGTTTAGTCA;RSEQ=CACAGTGATATTATTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:0,2:6,169:175,2:0.0113:1,0:30.5:1:32:0:1:0:60:4:0.0116:0:2 0/0:111:1:1,0:8,102:110,1:0.009:2,0:1:0:27:0:0.08108:0:60:2:0.009:0:1 +3 189349501 . G A 185 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01506;LSEQ=TATTATTTTGGACTTTCTGT;RSEQ=GACTTAAAGTGGTCTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:54:0,54:0,56:56,54:0.4909:1,1:26:1:32.2:1:1:0:60:108:0.5094:0:1 0/1:71:1:0,1:0,70:70,1:0.0141:1,0:2:0:31:0:1:0:60:2:0.0143:0:1 +3 189455380 . A G 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96049;LSEQ=CACTACCTGAAGAAATGCCA;RSEQ=TTGTGCAACTTGTAACATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:4:4,0:48,0:48,4:0.0769:1,0:26:1:34.5:1:1:0:60:8:0.0769:0:1 0/1:27:2:1,1:25,0:25,2:0.0741:1,2:40:1:31.5:1:0.07407:0:60:4:0.0741:0:1 +3 189455688 . C A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27127;SOR=0;LSEQ=AACAAGCAAGAAATGTTTTG;RSEQ=TTGAGCTAAATAGGTAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:2,1:49,231:280,3:0.0106:2,2:13.3:1:28.3:1:0.08471:9.32:60:6:0.0108:0:1 0/0:199:0:0,0:43,156:199,0:0:2,0:19.9:1:31.8:1:1:0:60:98.5:1:0:0.1 +3 189456354 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17525;SOR=Inf;LSEQ=TGACTTTGAAGCAGAAAATG;RSEQ=TTGTTGTTAACAACAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:197,36:233,0:0:2,0:23:1:32.3:1:1:0:59.6:115.5:1:0:0.1 0/1:169:2:1,1:134,32:166,2:0.0118:2,2:23:1:28:1:0.35522:4.13892:60:4:0.0119:0:1 +3 189456639 . T C 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00121;SOR=Inf;LSEQ=TAAACCTGTCTTTTCAGTCA;RSEQ=GTGTGAAAAGGCAGGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:6,159:165,0:0:1,0:24.8:1:30.8:1:1:0:60:164:1:0:0.1 0/1:129:8:2,6:4,117:121,8:0.062:1,2:20:1:29:1:0.04474:9.36:60:16:0.0625:0:1 +3 189456729 . C G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.76206;SOR=1.30593;LSEQ=AAGATTTGGTGTGGATTATG;RSEQ=ATTCTGGGTCTGCCGCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:16:0,16:0,24:24,16:0.4:1,1:22.1:1:32.3:1:1:0:58.1:32:0.4:0:1.1 0/1:15:7:0,7:0,8:8,7:0.4667:0,0:25.4:1:31:1:1:0:60:14:0.5:0:1 +3 189456903 . T G 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGAATCAGAAATTTATT;RSEQ=TATTTATATATTTATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:20:1:32:1:1:0:41:4:0.2857:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 189485909 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGTGTATGAATAACTAACCA;RSEQ=CTCTAGGTTTTAGGGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:17,2:0.1053:2,2:17:1:30:1:1:1.77272:60:4:0.1176:0:1 0/0:6:0:0,0:4,2:6,0:0:2,0:13.2:1:28.3:1:1:0:60:5:1:0:0.3 +3 189485975 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11067;SOR=Inf;LSEQ=TTTTGCAAAACGGGATTAAT;RSEQ=TGACTATGGTGAAAACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:15,0:0:2,0:31.3:1:29.6:1:1:0:60:30:1:0:0.4 0/1:8:2:1,1:3,3:6,2:0.25:2,2:12:1:31:1:1:1:60:4:0.25:0:1 +3 189486023 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAATATAAAGAGCTTACC;RSEQ=CAATAGCATTGGTTCAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:5,2:0.2857:2,0:31:1:34:0:1:0:60:4:0.2857:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:45.5:1:29.5:1:1:0:60:4:1:0:0.5 +3 189507490 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=Inf;LSEQ=GACTTGAGTTCTGTTATCTT;RSEQ=TTAAGTAGATTCATATTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:186,18:204,0:0:2,0:23.6:1:32:1:1:0:59.9:28.143:1:0:0.1 0/1:137:9:8,1:111,17:128,9:0.0657:2,2:22.8:1:28.4:1:1:1.22:60:8:0.0611:0:1.1 +3 189507518 . C CAGAG 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.02685;LSEQ=GATTCATATTGTAAGGGTCT;RSEQ=GGGGTGGGGGGGTTGGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:333:258,75:15,3:18,333:0.9:2,2:23.7:1:30.9:1:0.77288:1.45205:59.6:165.5:0.9093:0.2324:0.2 0/1:228:44:37,7:129,48:177,44:0.193:2,2:26:1:30.4:1:0.17179:1.96:59.5:88:0.1973:0.0088:0.2 +3 189507519 . GGGGTG AGAGGGGGT 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=7.000;MSILEN=1;SSF=0.82652;SOR=0.84921;LSEQ=ATTCATATTGTAAGGGTCTC;RSEQ=GGGGGGTTGGCAAAATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:14:13,1:279,84:363,14:0.037:2,1:12.9:1:28.1:1:0.20658:3.90:58.2:13:0.0354:0.0291:0.5 0/1:253:8:7,1:181,64:245,8:0.0316:2,2:13.5:1:28.4:1:0.68393:2.47:60:16:0.032:0.0158:0.4 +3 189507689 . T TA 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.17703;SOR=Inf;LSEQ=CTTTTTAATTTTTATTTTTG;RSEQ=AAAAAAACTTACGTATTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:51,203:254,0:0:2,0:22.9:1:28.7:1:1:0:59.8:126:1:0:0.1 0/1:185:2:1,1:47,136:183,2:0.0108:2,2:32.5:1:28.5:1:0.45264:2.87:60:4:0.011:0:0 +3 189507711 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19044;SOR=Inf;LSEQ=AAAAAACTTACGTATTTGCG;RSEQ=TTCTCGGTCACCCAATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:11,133:144,0:0:2,0:24.7:1:32.2:1:1:0:59.7:35:1:0:0.1 0/1:112:2:0,2:16,94:110,2:0.0179:2,0:8:0:31.5:1:1:0:60:4:0.0183:0:1 +3 189525713 . G A 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAACCTCAAAATGGAATA;RSEQ=CAGGCAGTATTTATTTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:24.4:1:31:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 189526135 . C T 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTCCTCGTCCACCAGTCC;RSEQ=TATAACACAGACCACGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1250:0:0,0:664,584:1248,0:0:2,0:24.7:1:32.3:1:1:0:60:82.2:0.9984:0:0.1 0/1:1029:64:36,28:521,443:964,64:0.0622:2,2:24.3:1:30.2:1:0.79609:1.09:59.7:128:0.0634:0:1.2 +3 189581535 . TA T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAACAGATATTCCATCT;RSEQ=AAAAAAATCCCATGAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:17:1:33:0:1:0:60:4:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 189582241 . T G 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAATCTCTAACTGTTCAACC;RSEQ=CCTTGAAGGTCAAGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:77,260:337,0:0:2,0:20.9:1:29.9:1:1:0:59.6:27.083:1:0:0.1 0/1:311:23:3,20:71,216:287,23:0.074:2,2:20.4:1:30.1:1:0.30859:2.18679:60:22:0.0728:0:1 +3 189582249 . G A 159 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=48.73601;LSEQ=AACTGTTCAACCTCCTTGAA;RSEQ=GTCAAGATTCTGTGGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:1:0,1:58,226:284,1:0.0035:2,0:10:0:17:0:1:0:33:0:0:0:6 0/1:265:39:9,30:49,177:226,39:0.1472:2,2:24.6:1:30.2:1:0.83551:1.08:60:78:0.1494:0:1.2 +3 189584420 . C T 158 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03103;LSEQ=ATGCAATTTCATTTTATTTT;RSEQ=TTTATTTTTAAGGTAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:34:29,5:180,29:209,34:0.1399:2,2:23.1:1:31.1:1:1:1.06986:60:68:0.1405:0:1.1 0/0:200:1:0,1:158,41:199,1:0.005:2,0:1:0:23:0:0.21:0:60:2:0.005:0:1 +3 189584890 . G A 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGTTTTATCCAACTGGCA;RSEQ=TTGGACGGGTAGTGGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:26:1:32.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 189585208 . A G 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=AAGATGTTATTAATGGAAGT;RSEQ=TATATTCAAATCTATATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:7.5:1:34:0:0.33333:0:60:4:0.3333:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:33.5:1:1:0:60:4:1:0:1.5 +3 189585542 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17561;SOR=Inf;LSEQ=TTCATCAGAAGTGGAATTCC;RSEQ=TAAATAGAGGGAAGAACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:206,47:253,0:0:2,0:22.5:1:31.5:1:1:0:59.7:41.167:1:0:0.1 0/1:183:2:1,1:142,39:181,2:0.0109:2,2:27:0:32.5:1:0.39032:3.60751:60:4:0.0109:0:1.5 +3 189585563 . G T 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3989;SOR=0.33229;LSEQ=TAAATAGAGGGAAGAACTGA;RSEQ=AAGGAACAACGTCAGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:4:1,3:262,95:357,4:0.0111:2,2:11.3:1:28:1:0.06267:8.21647:60:8:0.0111:0:1 0/0:270:1:0,1:187,82:269,1:0.0037:2,0:1:0:23:0:0.30741:0:60:2:0.0037:0:2 +3 189585692 . G A 82 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00821;SOR=0;LSEQ=TTGTGTTGGAGGGATGAACC;RSEQ=CCGTCCAATTTTAATCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:8:6,2:331,450:781,8:0.0101:2,2:7:1:27.4:1:0.07908:4.07:60:7:0.009:0:1.3 0/0:714:0:0,0:323,390:713,0:0:2,0:25.3:1:29.9:1:1:0:60:49.929:1:0:0.1 +3 189585852 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03479;SOR=Inf;LSEQ=GAGAGCTTGTCCTTTGTGCT;RSEQ=TAAATCCTTGCTACAAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:1,65:66,0:0:1,0:25.3:1:33.7:1:1:0:60:132:1:0:0.1 0/1:33:3:0,3:2,28:30,3:0.0909:2,0:25.3:1:30.7:1:1:0:60:6:0.0968:0:1 +3 189586182 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05645;SOR=Inf;LSEQ=ATGGAATGTTATTTACTAAT;RSEQ=TTACTTGTGGCATGTTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:20,4:24,0:0:2,0:28.7:1:29.4:1:1:0:60:48:1:0:0.1 0/1:8:2:2,0:6,0:6,2:0.25:0,0:29.5:1:30:1:1:0:60:4:0.25:0:1 +3 189586310 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51353;SOR=0;LSEQ=AGTGGAAGTGGTAGATCTTC;RSEQ=GGGGACTTTCAAAATGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:98,40:138,2:0.0143:2,2:13.5:1:29:1:0.50144:2.43227:60:4:0.0145:0:1 0/0:98:0:0,0:65,33:98,0:0:2,0:24.1:1:29.4:1:1:0:60:196:1:0:0.1 +3 189586466 . G A 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAGCATCAGAAAGCAGCAA;RSEQ=TTTCGGACAGTACAAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:25:13,12:237,263:500,25:0.0476:2,2:22.9:1:29.7:1:0.68599:1.20:60:24:0.0462:0:1.1 0/0:492:0:0,0:252,239:491,0:0:2,0:25.1:1:31.3:1:1:0:60:97.2:0.9979:0:0.2 +3 189586470 . C T 219 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATCAGAAAGCAGCAAGTTT;RSEQ=GGACAGTACAAAGAACGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:150:69,81:178,191:369,150:0.289:2,2:27:1:30.3:1:0.69833:1.09382:59.9:49:0.2899:0:1.1 0/0:484:0:0,0:244,239:483,0:0:2,0:25.8:1:29.8:1:1:0:60:68:0.9979:0:0.2 +3 189586532 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11021;SOR=Inf;LSEQ=AGATGTAGTGGCCAAATGGG;RSEQ=TAGGGTTGAATCTTCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:92,212:304,0:0:2,0:24.6:1:32:1:1:0:60:151:1:0:0.3 0/1:281:3:2,1:95,183:278,3:0.0107:2,2:11:1:28.3:1:0.27446:3.83:60:6:0.0107:0:1.7 +3 189586535 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25039;SOR=0;LSEQ=TGTAGTGGCCAAATGGGGTA;RSEQ=GGTTGAATCTTCTCCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:3:0,3:88,204:292,3:0.0102:2,0:29.7:1:29.3:1:0.557:0:60:6:0.0103:0:1 0/0:268:0:0,0:88,179:267,0:0:2,0:23.2:1:30.4:1:1:0:60:132.5:0.9962:0:0.1 +3 189586553 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20407;SOR=Inf;LSEQ=TAGGGTTGAATCTTCTCCAG;RSEQ=TGTTGGAGAATGGGGTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:42,171:213,0:0:2,0:21.7:1:30.4:1:1:0:60:25.625:1:0:0.2 0/1:176:2:1,1:34,140:174,2:0.0114:2,2:26:1:29.5:1:0.35909:4.07:60:4:0.0116:0:1 +3 189586572 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20986;SOR=Inf;LSEQ=GATGTTGGAGAATGGGGTGA;RSEQ=ATTGGAGAAGCTGCATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:16,136:152,0:0:2,0:22.6:1:28.5:1:1:0:60:75:1:0:0.1 0/1:129:2:1,1:16,110:126,2:0.0155:2,2:32.5:1:30:1:0.24889:6.70:60:4:0.0155:0:1 +3 189586630 . C G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9182;LSEQ=CAGCAAGTGGGACGTCAGCC;RSEQ=TCAGAGCCAGTGAGAATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:13:0,13:2,44:46,13:0.2203:1,1:24.4:1:32.6:1:1:0:60:26:0.2203:0:1 0/1:34:7:2,5:1,26:27,7:0.2059:1,2:24.7:1:31.6:1:0.1006:9.38:60:14:0.2121:0:1.1 +3 189586876 . T C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=TTCTTTTATGTATTCTTCCC;RSEQ=ACCATCCTTCCACCTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:11,1:9,0:9,12:0.5714:0,2:19:1:31.4:1:1:0:60:24:0.5714:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:9.5:1:32:0:1:0:60:4:1:0:1 +3 189587091 . A G 214 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAGTGTTCCCAGGATGAA;RSEQ=CTTGCATTTTTCCTCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:0:0,0:461,256:717,0:0:2,0:26.4:1:30.1:1:1:0:60:64.182:1:0:0.1 0/1:507:111:68,43:243,151:394,111:0.2189:2,2:26.2:1:31.5:1:1:1.0176:60:110:0.2187:0:1.1 +3 189587235 . C T 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATGGTTGCTTCATTTTAA;RSEQ=CTTCTTTGAATGGGCTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:146,345:491,0:0:2,0:26.3:1:31.6:1:1:0:59.9:60.375:0.9979:0:0.2 0/1:382:26:8,18:134,222:356,26:0.0681:2,2:24.2:1:28.9:1:0.53548:1.35706:60:52:0.069:0:1 +3 189587274 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00586;SOR=1.72482;LSEQ=TACAGTATGATCATCATCTC;RSEQ=TTATCTGTGACAATGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:88:20,68:20,157:177,88:0.3321:2,2:21.9:1:31.8:1:0.01798:2.30:60:87:0.3321:0:1 0/1:184:85:19,66:21,78:99,85:0.462:2,2:21.5:1:30.8:1:0.85978:1.07:60:84:0.459:0:1.1 +3 189590559 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54015;SOR=0;LSEQ=AAATAAACAAATTGCAATTA;RSEQ=GGAATCCTCAAATAATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:165,0:165,2:0.012:1,2:27.5:1:31:1:0.01198:0:60:4:0.0121:0:1 0/0:92:0:0,0:90,2:92,0:0:1,0:23.5:1:31.8:1:1:0:59.6:91:1:0:0.1 +3 189590824 . G C 201 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTAGGAGGCATGAGTGA;RSEQ=GGTGACTTTATTTGGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:507:0:0,0:136,371:507,0:0:2,0:23.6:1:31.7:1:1:0:60:100.4:1:0:0.2 0/1:390:108:33,75:63,141:204,108:0.2769:2,2:23.1:1:29.8:1:1:1.01543:60:107:0.2765:0:1.1 +3 189590871 . G A 181 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGATTGATGAGCAATGTG;RSEQ=AACATAATGGGAGATAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:57:6,51:8,145:153,57:0.2714:2,2:20.7:1:31.2:1:0.21256:2.12:60:114:0.2754:0:1.1 0/0:134:0:0,0:14,119:133,0:0:2,0:23.2:1:30.8:1:1:0:59.7:43.333:1:0:0.5 +3 189591053 . G T 47 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=AACTCACACTAACAGTTCTC;RSEQ=TCTCTATATGCCTGGTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:15.7:1:30:1:1:0:50.7:6:0.4286:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:37:0:32:0:1:0:60:2:0.5:0:1 +3 189597951 . G A 245 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00873;LSEQ=ACATTCCAAGCCCCCAAACC;RSEQ=ATCAGTGTACCCATAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1065:266:110,156:331,464:795,266:0.2498:2,2:26.7:1:30.5:1:0.94286:1.01167:59.9:32.25:0.2481:0:1.2 0/0:1037:3:3,0:441,593:1034,3:0.0029:2,0:1:0:25:1:0.07819:0:60:6:0.003:0:1 +3 189598021 . AGT A 123 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.09524;SOR=0.36264;LSEQ=TATTTCCATGTGTATATGTG;RSEQ=GTGTGTGTGTGTATGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:15:1,14:38,277:315,15:0.0455:2,1:22.5:1:31.7:1:1:1.91756:60:14:0.0436:0.0152:0.3 0/1:236:4:0,4:31,201:232,4:0.0169:2,0:19.3:1:30.9:1:1:0:60:8:0.0172:0.0085:0.3 +3 189598045 . C T 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13689;SOR=Inf;LSEQ=TGTGTGTGTGTATGTGTGTG;RSEQ=GTGTGTATCTAGCCCTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:6,206:212,0:0:1,0:23.9:1:29.6:1:1:0:59.9:25.5:1:0:0.2 0/1:125:2:1,1:3,120:123,2:0.016:1,2:6.5:1:31.5:1:0.06323:34.78:58.5:4:0.016:0:2 +3 189598095 . G A 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01133;SOR=0;LSEQ=TGAAGACACTTTGGCTCAGA;RSEQ=ACCCAACTGCTCAAAGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:14:1,13:2,85:87,14:0.1386:1,1:24:1:30.8:1:0.36397:3.21:60:13:0.1383:0:1.5 0/0:38:0:0,0:1,37:38,0:0:1,0:23.6:1:30.9:1:1:0:59.9:37:1:0:0.1 +3 189604149 . T G 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.65623;LSEQ=TCCCCACTCTTCAGTGTCCC;RSEQ=TGCTCACCATTATTTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:844:433:295,138:268,142:410,433:0.513:2,2:24.9:1:30.4:1:0.42117:1.13:60:71.167:0.5126:0:2.1 1/0:615:391:244,147:138,86:224,391:0.6358:2,2:24:1:29.9:1:0.86311:1.03:59.8:64.167:0.6364:0:2.1 +3 189604160 . T C 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.76045;LSEQ=CAGTGTCCCTTGCTCACCAT;RSEQ=ATTTCCATGTTTGTCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:940:476:311,165:285,179:464,476:0.5064:2,2:26.1:1:32:1:0.22325:1.18:60:94.2:0.5059:0:2 1/0:682:439:270,169:142,101:243,439:0.6437:2,2:26.2:1:31:1:0.46211:1.14:59.7:438:0.6479:0:2 +3 189607032 . A T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.15282;SOR=Inf;LSEQ=AAAAGGAAGGCTGGTAGTTT;RSEQ=GGCCCTTGATAAAATTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:237,38:275,0:0:2,0:23.7:1:28.7:1:1:0:59.9:90.667:1:0:0.1 0/1:177:2:1,1:146,29:175,2:0.0113:2,2:16.5:1:25.5:1:0.31106:4.96692:60:4:0.0114:0:1.5 +3 189607037 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15656;SOR=Inf;LSEQ=GAAGGCTGGTAGTTTAGGCC;RSEQ=TTGATAAAATTTAACCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:247,47:294,0:0:2,0:24.3:1:31.1:1:1:0:59.9:31.667:1:0:0.1 0/1:193:2:1,1:154,37:191,2:0.0104:2,2:5.5:1:27:1:0.35584:4.12035:60:4:0.0108:0:1.5 +3 189607076 . G T 53 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02753;SOR=Inf;LSEQ=ACAAGATGGACCACTGGGAT;RSEQ=CTGGTACATGATGATGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:0:0,0:395,179:574,0:0:2,0:24.7:1:32.1:1:1:0:59.9:62.778:1:0:0.1 0/1:396:4:1,3:260,132:392,4:0.0101:2,2:7.5:1:26.8:1:0.11682:5.88146:60:8:0.0102:0:1.3 +3 189607319 . G A 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=11.22876;LSEQ=GGGCCTGCCCTAAGCATCCC;RSEQ=GGATGGTGGAGGGCGGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:507:2:2,0:102,401:503,2:0.0039:2,0:1:0:26:0:0.04209:0:60:4:0.004:0:1 0/1:328:14:3,11:79,235:314,14:0.0427:2,2:20.9:1:28.9:1:1:1.23187:60:13:0.0404:0:1.1 +3 189608731 . A T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05595;SOR=Inf;LSEQ=ATTTCTTTCCTCTGATGACA;RSEQ=CCGCCTTGTAGTTCAATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:38,272:310,0:0:2,0:23.3:1:30:1:1:0:60:76.5:1:0:0.1 0/1:193:3:1,2:27,163:190,3:0.0155:2,2:16.3:1:24.3:1:0.37681:2.99:60:2:0.0106:0:1 +3 189608961 . C A 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTATTCCCGCAATCAAAA;RSEQ=ATTCATAATTTCTAAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:0,7:0,2:2,7:0.7778:0,0:30.7:1:32.9:1:1:0:60:14:0.7778:0:1.9 1/1:1:1:0,1:0,0:0,1:1:0,0:35:0:15:0:1:0:60:0:0:0:2 +3 189612328 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18147;SOR=Inf;LSEQ=TCTTCCTATCCCTCTCCTAA;RSEQ=TGCCAGCCCCCTAAAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:28,195:223,0:0:2,0:23.8:1:33.3:1:1:0:60:110.5:1:0:0.1 0/1:166:2:1,1:30,134:164,2:0.012:2,2:31:1:28.5:1:0.33954:4.41:60:4:0.0122:0:1 +3 189612336 . C T 79 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00377;SOR=12.34665;LSEQ=TCCCTCTCCTAACTGCCAGC;RSEQ=CCCTAAAAGCACTCCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:1:0,1:24,164:188,1:0.0053:2,0:44:0:14:0:1:0:60:0:0:0:6 0/1:129:8:3,5:21,100:121,8:0.062:2,2:24.5:1:26.4:1:0.16728:2.83:60:7:0.0565:0:1 +3 190212442 . C T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86551;LSEQ=TCCAGCACCCAGAACATTAC;RSEQ=TGGCATAACAGAGTTATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:21.6:1:33.3:1:1:0:60:14:0.6364:0:1 1/0:5:3:3,0:2,0:2,3:0.6:0,0:28.3:1:30:1:1:0:60:6:0.6:0:1 +3 190212706 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01773;SOR=1.47427;LSEQ=GAAAACTCACAATTTGTTTA;RSEQ=TTTAAAATTATAAGCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:232:109,123:75,97:172,232:0.5743:2,2:25.1:1:30.7:1:0.54472:1.15:60:115:0.575:0:1.1 1/0:290:193:89,104:46,50:96,193:0.6655:2,2:25.2:1:29.8:1:0.80309:1.07479:59.9:386:0.6678:0:1.1 +3 190212795 . A AT 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.11007;SOR=1.4911;LSEQ=CATTCCCTACTTAAATATGT;RSEQ=TTTTTTTTATCCTTAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:80:19,61:16,66:82,80:0.4878:2,2:25.2:1:30.3:1:0.56943:1.28:60:79:0.4877:0.0183:0.2 1/0:109:64:12,52:13,32:45,64:0.5872:2,2:28:1:28.9:1:0.25134:1.75109:60:128:0.5872:0.0642:0.1 +3 192873634 . T C 85 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGTGAGAGTCACAGGTGT;RSEQ=GTAGCAGCCGTGGAGGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:17:0:34:0:1:0:59:2:1:0:1 1/1:7:7:7,0:0,0:0,7:1:0,0:22.4:1:30.3:1:1:0:51.1:6:1:0:1.7 +3 192873745 . ATGT A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.50583;SOR=Inf;LSEQ=TTCCCTGGCCAGCTTGTCAC;RSEQ=TGTTGTTGCTGTTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:21,19:40,0:0:2,0:27.1:1:30.5:1:1:0:58.9:80:1:0:0.3 0/1:54:2:1,1:27,25:52,2:0.037:2,2:42:1:29.5:1:1:1.07844:51.5:4:0.0377:0:0 +3 192873757 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19164;SOR=0;LSEQ=CTTGTCACATGTTGTTGTTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:22,24:46,2:0.0417:2,2:46:0:31.5:1:1:1.09:60:4:0.0417:0:1 0/0:61:0:0,0:30,31:61,0:0:2,0:24.3:1:30.2:1:1:0:54.9:19.333:1:0:0.8 +3 192873763 . T C 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACATGTTGTTGTTGCTGTTG;RSEQ=TGCTGCTGCTGCTGCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:22,26:48,0:0:2,0:26.9:1:30.2:1:1:0:57.1:96:1:0:0.3 0/1:60:29:15,14:14,17:31,29:0.4833:2,2:23.7:1:30.5:1:0.79633:1.30:55.1:28:0.4746:0:1.2 +3 193971987 . C T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39091;SOR=0;LSEQ=CCTGCACTGGCACCTCAGAG;RSEQ=CGCCACCCCTGCCATTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:67:36,31:0,0:0,67:1:0,2:21.1:1:29.9:1:1:0:59.5:32.5:1:0:2.5 1/1:43:42:22,20:1,0:1,42:0.9767:0,2:23.6:1:28.4:1:1:0:60:41:0.9762:0:2.7 +3 193972016 . A G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18513;SOR=0;LSEQ=CTGCCATTCACTATGGCACA;RSEQ=GGCACAGCGTCAGGGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:19,28:0,0:0,47:1:0,2:31.2:1:31.4:1:1:0:59.6:22.5:1:0:3.4 1/1:36:34:16,18:1,1:2,34:0.9444:2,2:30:1:29.3:1:1:1.12132:60:7.5:0.9677:0:3.2 +3 193972034 . C G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16553;SOR=0;LSEQ=CAAGGCACAGCGTCAGGGCT;RSEQ=CTCCTTCAATCCCAGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:18,25:0,0:0,43:1:0,2:31.1:1:32.1:1:1:0:60:86:1:0:3.6 1/1:30:28:13,15:1,1:2,28:0.9333:2,2:24.4:1:30.5:1:1:1.14834:60:27:0.931:0:3.4 +3 193972070 . G T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.60176;LSEQ=GGCCATCCTTACCCAGCAAG;RSEQ=CTCAGCTCGGCTGGTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:27:7,20:0,1:1,27:0.931:0,2:19.5:1:29.9:1:1:0:60:54:0.931:0:3.6 1/1:9:8:3,5:0,1:1,8:0.8889:0,2:21.1:1:27.9:1:1:0:60:16:1:0:3.5 +3 193972099 . C T 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGGTCTTCTAAGGCTGG;RSEQ=AACGAGGTAACTGAGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:22.6:1:29.5:1:1:0:60:22:1:0:3 1/1:5:5:0,5:0,0:0,5:1:0,0:15.4:1:25.6:1:1:0:60:10:1:0:2.6 +3 194238312 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24426;SOR=Inf;LSEQ=CATCAGAAGCTGAAAAAAAC;RSEQ=GTGCTGAGAAACGTGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:127,70:197,0:0:2,0:25.1:1:30.8:1:1:0:60:196:1:0:0.8 0/1:193:2:1,1:115,76:191,2:0.0104:2,2:10:1:28.5:1:1:1.50978:60:4:0.0104:0:1 +3 194238335 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30413;LSEQ=GCTGAGAAACGTGGCCTGCC;RSEQ=TCTTTCCAGCTAAGGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:262:149:93,56:67,46:113,149:0.5687:2,2:26:1:30.9:1:0.61166:1.14:59.8:298:0.5687:0:1.6 0/1:231:66:38,28:96,69:165,66:0.2857:2,2:29.5:1:29.7:1:1:1.02507:60:132:0.2882:0:1.5 +3 194238390 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.42733;SOR=0.86152;LSEQ=TGGGTTGTCCTCTGCAAACG;RSEQ=GCTGCTGCAGGTTGCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:289:169:84,85:60,58:118,169:0.5848:2,2:25.7:1:30:1:0.90466:1.04666:59.9:83.5:0.5901:0:1.5 1/0:239:131:62,69:48,60:108,131:0.5481:2,2:25.5:1:29:1:0.69664:1.12:60:130:0.5508:0:1.4 +3 194238468 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56175;SOR=3.181;LSEQ=GAACTGACTGAAATTGGATG;RSEQ=TAATAAGTTGCTAGGTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:1:1,0:32,123:155,1:0.0064:2,0:1:0:25:0:0.21154:0:60:2:0.0065:0:2 0/1:99:2:1,1:22,75:97,2:0.0202:2,2:8.5:1:28:1:0.41249:3.36:60:4:0.0206:0:1.5 +3 194238483 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53041;SOR=0;LSEQ=GGATGGTAATAAGTTGCTAG;RSEQ=TTATTTTCCACTTTTTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:20,93:113,2:0.0174:2,2:19.5:1:29.5:1:0.33318:4.56:60:4:0.0175:0:1 0/0:68:0:0,0:14,54:68,0:0:2,0:24.9:1:30.7:1:1:0:60:33:1:0:0.2 +3 195391020 . G T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTTATCAGCGTGCATTT;RSEQ=GCGGACACAGCCTCAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:31.5:1:1:0:20:4:1:0:1.5 +3 195391057 . C T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50834;SOR=0;LSEQ=GTTTGGAAAGGGCAGGCAGG;RSEQ=CCATCGGTGCTGCTGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:0,2:26,59:85,2:0.023:2,0:10:1:25.5:1:1:0:21.5:4:0.0235:0:1 0/0:64:0:0,0:24,40:64,0:0:2,0:11:1:29.5:1:1:0:21.8:63:1:0:0.2 +3 195391074 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16387;SOR=Inf;LSEQ=AGGCCCATCGGTGCTGCTGT;RSEQ=TGGCTGATCGGACCGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:38,98:136,0:0:2,0:21.7:1:31.3:1:1:0:22.4:135:1:0:0.1 0/1:93:2:1,1:31,60:91,2:0.0215:2,2:12:1:27.5:1:1:1.92:60:4:0.0217:0:1 +3 195391116 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13614;SOR=Inf;LSEQ=CAATATTGCACACCTTATAT;RSEQ=GGAGGGTAAGGCTGCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:59,183:242,0:0:2,0:31.9:1:31.6:1:1:0:25.5:241:1:0:0.1 0/1:142:2:1,1:38,102:140,2:0.0141:2,2:33:1:29.5:1:0.47528:2.66:22.5:4:0.0142:0:1 +3 195391130 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.62857;SOR=1.71168;LSEQ=TTATATGGGAGGGTAAGGCT;RSEQ=CCCCCCGTCCACCTGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:2:1,1:58,182:240,2:0.0083:2,2:29.5:1:28.5:1:0.42893:3.12:22:4:0.0084:0:1 0/1:142:2:1,1:38,102:140,2:0.0141:2,2:19:1:28:1:0.47528:2.66:22:4:0.0142:0:1.5 +3 195395145 . T TA 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=4;SSF=0.01282;SOR=0;LSEQ=TCTCAAAATAAATAAATAAA;RSEQ=AAATAAAATATAAATGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:10,1:0,0:0,11:1:0,2:29.4:1:28.6:1:1:0:22.9:22:1:0:0.1 0/0:2:0:0,0:2,0:2,0:0:0,0:25.5:1:31.5:1:1:0:25.5:4:1:0:0 +3 195395328 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCCGTTCTGTGATCTCA;RSEQ=TAGACAGGAGGTCCGGACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:34.5:1:1:0:28.5:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 195395334 . A T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTGTGATCTCATTAGAC;RSEQ=GGAGGTCCGGACGTGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:33:1:1:0:28.5:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 195395347 . G A 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64992;SOR=1.92733;LSEQ=ATTAGACAGGAGGTCCGGAC;RSEQ=TGGGCCACTGTGTGCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:3,2:3,2:5,5:0.5:2,2:16.4:1:30.6:1:1:1:30:10:0.5:0:5.2 1/0:9:6:3,3:2,1:3,6:0.6667:2,2:9.2:1:28.7:1:1:1.8525:23.3:12:0.6667:0:3.5 +3 195395354 . A G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04702;SOR=4.30492;LSEQ=AGGAGGTCCGGACGTGGGCC;RSEQ=CTGTGTGCAGTCACTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:7,8:15,4:0.2:2,2:26.5:1:31.3:1:1:1.13:27.8:8:0.2105:0:4.5 1/0:17:9:5,4:4,4:8,9:0.5294:2,2:12.4:1:30.4:1:1:1.23:22.2:18:0.5294:0:3.1 +3 195395379 . T G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3862;SOR=1.50871;LSEQ=GTGCAGTCACTGCTCTCTGT;RSEQ=GTTTCCATAGGCTACGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:11:6,5:14,16:30,11:0.2683:2,2:23.5:1:31.2:1:0.73372:1.36:27.8:10:0.2564:0:3.2 0/1:56:20:10,10:18,18:36,20:0.3571:2,2:21.5:1:31.3:1:1:1:25.3:40:0.3571:0:2.1 +3 195399620 . C G 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GGGGCCCATCTCGCAGTTGT;RSEQ=TCTTTAGATCTTAGAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:38:2,36:4,74:78,38:0.3276:2,2:40.7:1:31.7:1:1:1.03:25.7:37:0.3246:0:1.6 0/0:46:0:0,0:3,43:46,0:0:2,0:32.5:1:30.6:1:1:0:30:45:1:0:0 +3 195400488 . A T 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.74002;LSEQ=GGGGTTTCACCATGTTAGCC;RSEQ=GACAGGTCTCGAACCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:9,5:0.3571:0,0:23.4:1:31.6:1:1:0:21.8:10:0.3571:0:2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:28.5:1:29:1:1:0:21.5:4:0.5:0:2 +3 195400498 . C T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.74002;LSEQ=CATGTTAGCCAGACAGGTCT;RSEQ=GAACCCCTGAACTCAGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:9,5:0.3571:0,0:13.4:1:30.2:1:1:0:21.8:10:0.3571:0:2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:18.5:1:28.5:1:1:0:21.5:4:0.5:0:2 +3 195400889 . T G 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18701;SOR=3.82321;LSEQ=TCTTCAGGACCCAGACTATT;RSEQ=GAGAAGGCGCAGGAGGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:0,2:7,122:129,2:0.0153:2,0:10:1:15.5:1:1:0:40:0:0:0:2.5 0/1:71:4:0,4:8,59:67,4:0.0563:2,0:22:1:25.8:1:1:0:37.5:8:0.058:0:1 +3 195400918 . C CT 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00027;SOR=0.38979;LSEQ=GCAGGAGGTTAGTCTTTTTT;RSEQ=TTTTTTTTTGAGACAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:176:101:5,96:4,65:69,101:0.5739:2,1:37.8:1:29.2:1:1:1.18036:35.8:19.2:0.5783:0.0057:0.2 0/1:99:34:3,31:6,54:60,34:0.3434:2,2:37.4:1:28:1:1:1.14652:34.8:68:0.3579:0:0.1 +3 195401426 . T C 51 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAGTCATTATTTTCTG;RSEQ=TTAGAAAAAGCACTATTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20:1:32.7:1:1:0:48.7:6:1:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:38:0:32:0:1:0:43:2:1:0:2 +3 195410304 . T C 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1548;SOR=7.43427;LSEQ=TGTTTTTAATAAAAACAGGC;RSEQ=GAAAGAAAAGATGGAGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:3,0:13,0:13,3:0.1875:1,0:34:1:31.7:1:1:0:34.7:6:0.2:0:1.3 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:41:0:31:1:1:0:23:4:0.6667:0:1 +3 195410751 . C T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00741;SOR=1.83585;LSEQ=GGGAAGGTCAGTGTGGAGCT;RSEQ=GTTCTCACCACAGCCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:51:10,41:37,102:139,51:0.267:2,2:9.2:1:31.1:1:0.35014:1.48429:60:102:0.2684:0:1 0/1:172:69:16,53:20,83:103,69:0.4012:2,2:9:1:30.2:1:0.57086:1.25:59.7:138:0.4012:0:1.1 +3 195410794 . T C 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69026;SOR=1.7456;LSEQ=CACACGGCCCCGCCCAGGTC;RSEQ=GCGGGCTGGCCTTGCTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:0,4:1,22:23,4:0.1481:1,0:20.8:1:27.5:1:1:0:22.3:8:0.1538:0:3.3 0/1:17:4:2,2:1,12:13,4:0.2353:1,2:17.3:1:29.8:1:0.12059:9.64:21.5:8:0.2353:0:1.8 +3 195410820 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.04305;LSEQ=CTGGCCTTGCTGATGGTGAA;RSEQ=GCGGAGGAGCAGGCCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:11:0,11:4,62:66,11:0.1429:2,0:26:1:25.3:1:1:0:22.2:2.667:0.1081:0:2.6 0/1:27:4:1,3:4,19:23,4:0.1481:2,2:21.3:1:31.3:1:1:1.55:22.5:8:0.1481:0:1.8 +3 195410875 . A T 122 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00537;SOR=0;LSEQ=ACAGATTTGAGGCACCGCTG;RSEQ=AAAAGGCACTCTGACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:17:1,16:3,59:62,17:0.2152:1,1:26.1:1:30:1:1:1.23:23.1:34:0.2152:0:1 0/0:28:0:0,0:3,25:28,0:0:2,0:21.1:1:30.3:1:1:0:22.9:56:1:0:0.5 +3 195410876 . A C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51661;SOR=1.6341;LSEQ=CAGATTTGAGGCACCGCTGA;RSEQ=AAAGGCACTCTGACAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:9:0,9:4,64:68,9:0.1169:2,0:23.2:1:33.7:1:1:0:21.9:18:0.1169:0:2.4 0/1:28:5:0,5:3,20:23,5:0.1786:2,0:20.2:1:33:1:1:0:23:10:0.1786:0:1.8 +3 195411037 . G A 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.5;SOR=4.17095;LSEQ=CTGGTGGCAGGGGAGGAGAT;RSEQ=ATGATTGTGGACCTAGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:5,2:0.2857:2,0:42:1:32:1:1:0:35:4:0.2857:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:17.5:1:27.5:1:1:0:60:4:0.6667:0:1.5 +3 195412750 . T TC 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16129;SOR=Inf;LSEQ=CGAGGCTGACTGTGCCACTG;RSEQ=CCCCCCAGCCATTCACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:47,64:111,0:0:2,0:39.6:1:30.3:1:1:0:27.2:54.5:1:0:0.1 0/1:75:2:1,1:30,43:73,2:0.0267:2,2:41.5:1:30.5:1:1:1.43:48:4:0.0282:0:0.5 +3 195412760 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51501;SOR=0;LSEQ=TGTGCCACTGTCCCCCCAGC;RSEQ=ATTCACTCCTACTGATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:42,59:101,2:0.0192:2,2:23.5:1:30:0:1:1.40:51:4:0.0198:0:1 0/0:71:0:0,0:29,42:71,0:0:2,0:39.2:1:30.9:1:1:0:24.2:22.667:1:0:0.2 +3 195412863 . C T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52418;SOR=0;LSEQ=ATGTCATAACTGTCTTTATA;RSEQ=GCTTCTGCACTCTGGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:0,10:10,4:0.2857:0,2:8:1:27:1:0.28571:0:23:8:0.3077:0:2.3 0/0:4:0:0,0:1,3:4,0:0:2,0:7.5:1:28.8:1:1:0:23.3:8:1:0:1.8 +3 195412864 . G A 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92081;LSEQ=TGTCATAACTGTCTTTATAC;RSEQ=CTTCTGCACTCTGGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:1,10:11,4:0.2667:2,0:10.3:1:28:1:1:0:23:8:0.3077:0:1.8 0/1:4:1:1,0:0,3:3,1:0.25:0,0:2:0:30:0:0.25:0:22:2:0.25:0:1 +3 195412876 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.40748;SOR=0.42604;LSEQ=CTTTATACGCTTCTGCACTC;RSEQ=GGGGAAGAAGGAGTACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:18:3,15:2,13:15,18:0.5455:2,2:12.7:1:26.7:1:1:1.29:23.4:17:0.5484:0:2.2 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:13.5:1:30.5:1:1:1:22.5:4:0.3333:0:1.5 +3 195412920 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.44374;SOR=1.92549;LSEQ=GGGGATTGGCACCCAGTGGC;RSEQ=GGGGAGCGTGGCACTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:13:2,11:4,34:38,13:0.2549:2,2:35.8:1:28.2:1:0.63768:1.53:23.8:12:0.25:0:1.5 0/1:10:4:1,3:2,4:6,4:0.4:2,2:36.3:1:30.5:1:1:1.44135:23.3:8:0.4:0:2.3 +3 195412928 . G A 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17606;SOR=0.30974;LSEQ=GCACCCAGTGGCCGGGGAGC;RSEQ=TGGCACTTACCTTTGTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:23:2,21:4,24:28,23:0.451:2,2:31.4:1:30.4:1:0.67785:1.7315:26.3:46:0.46:0:1.7 0/1:10:2:0,2:3,5:8,2:0.2:2,0:25.5:1:29:1:1:0:26.5:4:0.2:0:1.5 +3 195412948 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGCACTTACCTTTGTCCC;RSEQ=TGCTTCATTCTTGTGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:5,46:51,2:0.0377:2,2:25.5:1:31:1:0.21553:8.49:27.5:4:0.04:0:2.5 0/0:10:0:0,0:3,7:10,0:0:2,0:27.2:1:29.3:1:1:0:24.8:20:1:0:1.4 +3 195412951 . C G 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTTACCTTTGTCCCTTG;RSEQ=TTCATTCTTGTGACAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:4:0,4:6,39:45,4:0.0816:2,0:34:1:31.5:1:1:0:29.5:8:0.0833:0:2.3 0/0:10:0:0,0:3,7:10,0:0:2,0:25.4:1:30.9:1:1:0:24.8:20:1:0:1.4 +3 195412960 . T C 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGTCCCTTGCTTCATTCT;RSEQ=GTGACAAGATAAAACTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:1,4:3,31:34,5:0.1282:2,2:10:1:32.2:1:0.43616:2.50:23.8:10:0.1282:0:2.4 0/0:7:0:0,0:3,4:7,0:0:2,0:26.4:1:28.6:1:1:0:25.3:14:1:0:1.1 +3 195494232 . T C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGATGCTGCCACTGCTGC;RSEQ=ACCACCACCACCACCATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:35.7:1:31.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 195494558 . GCCACCCCCCAAAAAA CCACCCCCAACAC 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCATCACCACCATCACTG;RSEQ=TACCACCATCGGCCACCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45:1:30.7:1:1:0:29.5:4:1:0:1.5 +3 195494583 . CG C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCCAAAAAATACCACCAT;RSEQ=GCCACCACCACCATCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:32.5:1:1:0:29.5:4:1:0:3.5 +3 195494610 . T C 31 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=CACCACCATCACCACCACCA;RSEQ=CACCATCGCCACCACCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:1:31:1:1:0:29.5:4:1:0:3.5 +3 195495721 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GACAAATGGGTGATCTTGTC;RSEQ=TGGGAAGCAGCCAGATGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:13,6:19,0:0:2,0:24.5:1:31.3:1:1:0:60:38:1:0:0.2 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:11.5:1:30:1:1:1.18321:60:4:0.1538:0:1.5 +3 195688543 . TCA T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGATCACAGGGGGCGGAGC;RSEQ=CACAGTAATGCTCTGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:32:1:1:0:38.5:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 195689449 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGATCTGTGGCCTGGGGA;RSEQ=TGGGGACCCTGATTTAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:29.5:1:1:0:22.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 195690192 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.53821;SOR=0;LSEQ=AAAGCTGATTCTGTCATCAC;RSEQ=GCATCTTGTCTCATCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:78,44:122,2:0.0161:2,2:18.5:1:30:1:1:1.76403:21.5:4:0.0161:0:1 0/0:69:0:0,0:36,29:65,0:0:2,0:13.2:1:29.7:1:1:0:21:64:0.9552:0:0.2 +3 195690235 . TGGC T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.52426;SOR=0;LSEQ=GTGAATGGCTGGGGGGACAG;RSEQ=ACAGTCAGCCTCATTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:86,53:139,2:0.0141:2,2:43.5:1:30.5:1:1:1.6168:24:4:0.0143:0:0.5 0/0:89:0:0,0:48,41:89,0:0:2,0:36.8:1:31:1:1:0:28:178:1:0:0.3 +3 195690244 . C G 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00307;SOR=Inf;LSEQ=TGGGGGGACAGTGGCACAGT;RSEQ=AGCCTCATTCAAAGTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:88,54:142,0:0:2,0:35.1:1:31.9:1:1:0:26:70:1:0:0.1 0/1:90:6:3,3:46,38:84,6:0.0667:2,2:29.5:1:30.7:1:1:1.20794:21:12:0.0674:0:2 +3 195690248 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14691;SOR=Inf;LSEQ=GGGACAGTGGCACAGTCAGC;RSEQ=TCATTCAAAGTTTTGTCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:89,55:144,0:0:2,0:31.7:1:31.6:1:1:0:26:143:1:0:0.1 0/1:90:2:1,1:48,40:88,2:0.0222:2,2:24.5:1:30.5:1:1:1.19756:20.5:4:0.0225:0:1 +3 195690264 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14691;SOR=Inf;LSEQ=CAGCCTCATTCAAAGTTTTG;RSEQ=CGATTATGGGTCTATATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:89,55:144,0:0:2,0:18.6:1:29.2:1:1:0:26:288:1:0:0.1 0/1:90:2:1,1:48,40:88,2:0.0222:2,2:13.5:1:32.5:1:1:1.19756:21:4:0.0222:0:1.5 +3 195690308 . G A 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1321;LSEQ=GTGACCTTGAAAAGAAGTCA;RSEQ=TGGTAAGTTAAGCACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:1,3:4,1:0.2:2,0:12:0:33:0:1:0:60:2:0.2:0:1 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:13.5:1:27.5:1:1:1.29:60:4:0.2222:0:1 +3 195691976 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04615;SOR=Inf;LSEQ=TGTCCCCACTACACAGATGC;RSEQ=TTCTCGCTAGGTCCATAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:19,1:20,0:0:1,0:24.8:1:31.9:1:1:0:51.3:40:1:0:0.2 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:46.5:1:32:1:1:1:49.5:4:0.3333:0:1 +3 195691993 . AATC A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.03968;SOR=Inf;LSEQ=TGCTTTCTCGCTAGGTCCAT;RSEQ=ATCATCTCTTCCCCTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:21,1:22,0:0:1,0:25.5:1:29.3:1:1:0:45:21:1:0:0.3 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:36.5:1:29.5:1:1:1:49.5:4:0.3333:0:1 +3 195692069 . A G 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTCCATCTGGCCCACACCAC;RSEQ=GAGCAACCCTTCCTTAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:9.6:1:27:1:1:0:29.6:10:0.7143:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 195692156 . CT C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.06898;SOR=Inf;LSEQ=CCCAACTGCTGTCAGAGTGC;RSEQ=TTTTCAGCGGTGCCTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:77,2:79,0:0:1,0:22.8:1:33.1:1:1:0:31.1:158:0.9875:0:0.1 0/1:29:2:1,1:26,1:27,2:0.069:1,2:31.5:1:30.5:1:0.13547:18.72551:20:4:0.069:0:0.5 +3 195692205 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTGATTTAAATCTGGCC;RSEQ=GCTCCTCTGCGTTCACCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:84,5:89,2:0.022:2,2:31:0:32:1:0.12821:15.42515:20:4:0.0222:0:1.5 0/0:28:0:0,0:26,2:28,0:0:2,0:30.8:1:30.3:1:1:0:30:56:1:0:0.1 +3 195692348 . C A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13134;SOR=Inf;LSEQ=AGGGTGTGCTTCCTCCAGTG;RSEQ=TCCTCAAAGGGCTTCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:171,136:307,0:0:2,0:19.5:1:32.2:1:1:0:29.2:75.75:1:0:0.1 0/1:175:2:1,1:86,87:173,2:0.0114:2,2:26:0:32:1:1:1.01:20:4:0.0116:0:1.5 +3 195692350 . C T 44 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30204;SOR=0;LSEQ=GGTGTGCTTCCTCCAGTGCT;RSEQ=CTCAAAGGGCTTCTTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:4:0,4:188,162:350,4:0.0113:2,0:12.5:1:22.3:1:0.04742:0:41.3:3:0.0087:0:1 0/0:202:0:0,0:99,102:201,0:0:2,0:18.2:1:29.5:1:1:0:30.9:49.25:0.9949:0:0.2 +3 195692351 . C T 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65807;SOR=0.43744;LSEQ=GTGTGCTTCCTCCAGTGCTC;RSEQ=TCAAAGGGCTTCTTCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:4:1,3:200,174:374,4:0.0106:2,2:15.8:1:29.3:1:0.34417:3.43783:32.8:8:0.0106:0:1 0/0:215:1:1,0:102,109:211,1:0.0047:2,0:2:0:31:0:0.48585:0:60:2:0.0047:0:1 +3 195697427 . C T 30 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGGGGACGGAGCTTCTC;RSEQ=GGTGGTCCTGCGGCTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:30.5:1:1:0:21:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 195697824 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAAAAAGAATGCAATCA;RSEQ=GTCTTCCGCAGCCAGACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:8,2:0.2:0,0:22:1:34:0:1:0:45:4:0.2:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:32:0:1:0:60:2:1:0:0 +3 195697927 . A G 23 d5;v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGAAGTGGGAGCTGAAC;RSEQ=GTGAGTACACATGGACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:9:1:23:1:1:0:20.5:4:1:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:32:0:1:0:35:2:1:0:0 +3 195698026 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACCTGCTGAGTACAACACA;RSEQ=ACGACTTGGGTGACGGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,1:7,3:0.3:2,0:15.7:1:28:0:1:0:26.3:6:0.3:0:1.3 0/0:2:0:0,0:2,0:2,0:0:0,0:25.5:1:28.5:1:1:0:26:4:1:0:1 +3 195701115 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07109;SOR=0.22113;LSEQ=AGCACACGAGGCTGCATAAC;RSEQ=ACCGTGAGGATCTCTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:19:18,1:33,0:33,19:0.3654:1,1:19.6:1:31.2:1:0.36538:0:47.6:38:0.3725:0:1.1 0/1:18:2:2,0:13,2:15,2:0.1111:2,0:13:0:27.5:1:1:0:59:4:0.1111:0:1 +3 195701198 . CA C 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.18265;SOR=0;LSEQ=AGGGCACTAAGACCCTGTCT;RSEQ=AAAAAAAAGAAAAAAGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:6:6,0:204,9:213,6:0.0274:1,0:31:1:30.7:1:1:0:54.7:12:0.0276:0:0 0/0:97:0:0,0:90,7:97,0:0:2,0:33.4:1:29.2:1:1:0:47.3:47.5:1:0:0.2 +3 195706971 . A G 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAGAAGAGACTTCCATTT;RSEQ=TATTTTATTTATTTATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:41:1:33:0:1:0:20:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +3 195708880 . C T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7337;SOR=1.44766;LSEQ=CCTTTACAGGTGAGGAACCA;RSEQ=GGCTGGGAAAGGCCATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:8:8,0:28,0:28,8:0.2222:1,0:42.3:1:31.3:1:1:0:21.8:16:0.2222:0:1.3 0/1:17:5:5,0:11,1:12,5:0.2941:2,0:39.8:1:28.6:1:1:0:22:10:0.2941:0:1.2 +3 195710978 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10842;SOR=Inf;LSEQ=TCAGGTGGACGGGGGGCGGC;RSEQ=TTACCCTCCCGTATAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:289,96:385,0:0:2,0:26.4:1:31.6:1:1:0:27.9:63.167:1:0:0.1 0/1:190:2:1,1:143,45:188,2:0.0105:2,2:35:1:29.5:1:0.42657:3.15401:22.5:4:0.0108:0:1 +3 195710995 . G C 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCTTACCCTCCCGTATAA;RSEQ=GTGTGCAATATTGAGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:315,115:430,0:0:2,0:27.7:1:32.3:1:1:0:28:46.778:0.9976:0:0.1 0/1:219:25:20,5:143,51:194,25:0.1142:2,2:26.6:1:30.5:1:0.62939:1.42:27.7:11.5:0.1085:0:1.2 +3 195711016 . G A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GTGTGCAATATTGAGTGGCC;RSEQ=GTCCGATCAGCCACACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:269,128:397,0:0:2,0:29.7:1:29.9:1:1:0:29.6:78.4:1:0:0.1 0/1:235:11:5,6:152,71:223,11:0.0468:2,2:31.6:1:29.5:1:0.18473:2.55764:34.6:22:0.0474:0:1.2 +3 195711497 . C G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0656;SOR=Inf;LSEQ=AGTGGGGGCCTGCTCCGTCA;RSEQ=GTAGTGGATGGCATCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:16,18:34,0:0:2,0:9.9:1:30.5:1:1:0:59.7:68:1:0:0.1 0/1:24:3:1,2:8,13:21,3:0.125:2,2:10.7:1:32.3:1:1:1.22038:60:6:0.125:0:1 +3 196248206 . T C 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28205;SOR=6.15667;LSEQ=CCGGGTTCCTCTTTGAAGTT;RSEQ=GTAGCAGATAGTGGTAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:30:1:32.5:1:1:0:42.5:8:0.3636:0:1 1/1:5:4:3,1:1,0:1,4:0.8:0,2:41:1:30.8:1:1:0:33.5:8:0.8:0:1 +3 196248332 . GC G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.54528;SOR=0;LSEQ=CGGCTACCTAAAAGGGAAGG;RSEQ=CCCCTGTCCCATGATCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:53,29:82,2:0.0238:2,2:28.5:1:30.5:1:1:1.81364:53:4:0.0244:0:0 0/0:44:0:0,0:29,15:44,0:0:2,0:24.3:1:29.8:1:1:0:32.2:43:1:0:0.1 +3 196248368 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50441;SOR=0;LSEQ=TCACGTGACTTGCTTGACCT;RSEQ=ATCAATCACTTGGACGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:48,59:107,2:0.0183:2,2:38:1:33.5:1:1:1.23:43:4:0.0187:0:1 0/0:86:0:0,0:49,37:86,0:0:2,0:26.6:1:28.8:1:1:0:28.9:85:1:0:0.2 +3 196248390 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.21244;SOR=Inf;LSEQ=TCAATCACTTGGACGACTCA;RSEQ=CCTCCTTACCCTGCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:36,64:100,0:0:2,0:32.4:1:31.5:1:1:0:32.6:200:1:0:0.1 0/1:86:2:1,1:44,40:84,2:0.0233:2,2:29:0:31.5:1:1:1.09878:27:4:0.0235:0:1.5 +3 196248551 . G A 62 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24242;SOR=6.43915;LSEQ=TTTATTTCTTACTATCTTTC;RSEQ=TCTCCGTACATGGGGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:4,1:0.2:0,0:10:0:33:0:1:0:60:2:0.2:0:1 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:27.8:1:31:1:1:0:54:8:0.6667:0:2.3 +3 196366964 . G A 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAAATACCTCCCTCCAG;RSEQ=AGCACTTAGAGCTGAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:22:1:32.5:1:1:0:60:4:0.6667:0:1 +3 196547222 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15758;SOR=Inf;LSEQ=TCCATGGAAGCCATTAACTC;RSEQ=GTTTTGTTTTGTTTTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:113,26:139,0:0:2,0:24.8:1:31.4:1:1:0:57.7:45.333:1:0:0 0/1:92:2:1,1:69,21:90,2:0.0217:2,2:20:1:28.5:1:0.42308:3.23333:50.5:4:0.0222:0:1 +3 196547446 . G C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3428;SOR=2.11345;LSEQ=AAATCCCTTGAGGGTAAGAT;RSEQ=AGTTAAACACCAGCCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:21:4,17:2,18:20,21:0.5122:2,2:22:1:30.7:1:0.6628:2.08:47.4:9.5:0.4872:0:1.3 1/0:13:9:2,7:2,2:4,9:0.6923:2,2:26.8:1:32.3:1:0.53007:3.13792:47.6:18:0.6923:0:1 +3 196547538 . G A 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.53981;LSEQ=TCCAAGAATTTAAAGTAGAA;RSEQ=GTTGATAAAACCTAATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:16.7:1:34:0:1:0:60:6:0.6:0:1.3 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:20:0:32:0:1:0:60:2:0.3333:0:1 +3 197346530 . C G 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2652;SOR=0;LSEQ=ACTGCTATTCTACAATGCCT;RSEQ=TATTTTCCTTAAAATAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:4,0:13,1:14,4:0.2222:1,0:16.5:1:30.8:1:1:0:22.5:8:0.2222:0:1 0/0:10:0:0,0:9,1:10,0:0:2,0:25.4:1:31.6:1:1:0:25.7:20:1:0:0.2 +3 197346558 . A C 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-04;SOR=Inf;LSEQ=CTTAAAATAAAGACACTCTA;RSEQ=AAGAAATTTATTCATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:115,30:145,0:0:2,0:13.7:1:30.7:1:1:0:27.3:35.25:1:0:0.1 0/1:132:10:6,4:89,33:122,10:0.0758:2,2:17.3:1:30.4:1:0.46545:1.78912:27.3:20:0.0769:0:2 +3 197346566 . T G 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGACACTCTAAAAGAAAT;RSEQ=TATTCATTTTTACAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:153,53:206,0:0:2,0:15.6:1:30.9:1:1:0:25.9:50.5:1:0:0.1 0/1:186:17:9,8:118,51:169,17:0.0914:2,2:19.6:1:31.6:1:0.17595:2.04799:25.8:34:0.0934:0:1.6 +3 197346770 . G GA 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.25489;SOR=2.07849;LSEQ=ATCTCAGAGACTAAAAGAAA;RSEQ=AAAAAAAAAGGGCAAGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:4:2,2:32,116:148,4:0.026:2,2:10.3:1:29.5:1:0.21639:3.59:24.8:8:0.0261:0.013:0.5 0/1:152:8:1,7:44,100:144,8:0.0526:2,2:14.3:1:30.4:1:0.43723:3.06239:24.9:16:0.0552:0.0197:0.5 +3 197348560 . G A 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00787;SOR=Inf;LSEQ=GTGTCCTGTCTCAGGTGGAC;RSEQ=GAGGGCGGCCTTACCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:179,34:213,0:0:2,0:25.7:1:30.3:1:1:0:32.6:105.5:1:0:0.1 0/1:174:6:5,1:127,41:168,6:0.0345:2,2:21:1:29.8:1:1:1.61:24:12:0.0347:0:2.2 +3 197348587 . G A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01007;SOR=Inf;LSEQ=GGCCTTACCCTCCCATATGA;RSEQ=GTGTGCAATATTGAGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:179,37:216,0:0:2,0:31.7:1:32.7:1:1:0:31.7:53:1:0:0.1 0/1:190:6:5,1:136,47:183,6:0.0316:2,2:41.3:1:30.3:1:1:1.72:24:12:0.0319:0:2.2 +3 197348632 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2282;SOR=Inf;LSEQ=CGATCAGCCACACAGCAGCA;RSEQ=CGATGGGCCTGCCTGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:97,26:123,0:0:2,0:17.2:1:31.1:1:1:0:23.8:246:1:0:0 0/1:113:2:1,1:76,35:111,2:0.0177:2,2:49.5:1:30:1:0.53761:2.15514:20:4:0.0182:0:2 +3 197348638 . G A 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00071;SOR=Inf;LSEQ=GCCACACAGCAGCACCGATG;RSEQ=GCCTGCCTGCCCTTTCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:74,19:93,0:0:2,0:15.6:1:30.1:1:1:0:21:186:1:0:0 0/1:92:10:6,4:57,25:82,10:0.1087:2,2:29.9:1:28.6:1:0.71963:1.51272:20.8:20:0.1111:0:1 +3 197348646 . T C 57 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.12018;SOR=Inf;LSEQ=GCAGCACCGATGGGCCTGCC;RSEQ=GCCCTTTCCAAACTTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:48,12:60,0:0:2,0:14:1:30.6:1:1:0:21:120:1:0:0 0/1:65:4:2,2:44,17:61,4:0.0615:2,2:6.3:1:28.5:1:0.574:2.5454:23:8:0.0625:0:1.5 +3 197348786 . C A 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTTATTACCTTAAAGGAGT;RSEQ=AAGATATTCACAGCTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:42,145:187,0:0:2,0:25.7:1:32.3:1:1:0:37.5:92.5:1:0:0 0/1:124:18:2,16:18,88:106,18:0.1452:2,2:27.9:1:30.3:1:0.73498:1.63072:29.8:36:0.1463:0:1.1 +3 197349042 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGACCACGAGAGCACCCAGA;RSEQ=CCTCCCGCCCATCACCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29.5:1:34.5:1:1:0:20:4:1:0:0.5 1/0:4:2:1,1:1,1:2,2:0.5:2,2:31:0:31:0:1:1:21:4:0.5:0:1.5 +3 197354659 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49988;SOR=0;LSEQ=GCAGGGACTCACAGCCTTGG;RSEQ=CAGCGCCAGCGCCAGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:120,62:182,2:0.0108:2,2:23:1:29.5:1:1:1.92811:44.5:4:0.0108:0:1 0/0:168:0:0,0:102,66:168,0:0:2,0:23.1:1:30.8:1:1:0:57:167:1:0:0.2 +3 197354663 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=0.53438;LSEQ=GGACTCACAGCCTTGGCCAG;RSEQ=GCCAGCGCCAGGCGCCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:125,66:191,2:0.0104:2,2:8.5:1:30:1:1:1.88733:60:4:0.0105:0:1 0/0:180:1:0,1:109,70:179,1:0.0056:2,0:43:0:31:0:0.39444:0:35:2:0.0056:0:1 +3 197354669 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.21688;SOR=Inf;LSEQ=ACAGCCTTGGCCAGCGCCAG;RSEQ=GCCAGGCGCCGAGCGCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:138,83:221,0:0:2,0:27.1:1:31:1:1:0:57.2:54.25:1:0:0.2 0/1:194:2:1,1:111,81:192,2:0.0103:2,2:20:1:27.5:1:1:1.36809:44.5:4:0.0104:0:1 +3 197354729 . C A 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32846;SOR=3.75492;LSEQ=ACCCCCGATACGTCTGCAGT;RSEQ=GCCTCCGCGCAGTCCCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:1:1,0:110,131:241,1:0.0041:2,0:1:0:28:0:0.45868:0:60:2:0.0042:0:1 0/1:195:3:2,1:87,105:192,3:0.0154:2,2:10.7:1:25.3:1:0.59298:2.40:33.3:6:0.016:0:1.3 +3 197354733 . T G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2033;SOR=Inf;LSEQ=CCGATACGTCTGCAGTCGCC;RSEQ=CCGCGCAGTCCCGCCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:102,127:229,0:0:2,0:29.5:1:30.2:1:1:0:50.4:24.444:1:0:0.2 0/1:191:2:1,1:84,104:188,2:0.0105:2,2:9:1:29:1:1:1.24:60:4:0.0106:0:2 +3 197354857 . C A 58 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CCGGGCCGGGGTCTAAGGGG;RSEQ=GGGGACGCCGCGCCTGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:3,1:0.25:2,0:42:0:34:0:1:0:22:2:0.25:0:1 1/1:4:4:3,1:0,0:0,4:1:0,2:45.3:1:29.3:1:1:0:21.8:8:1:0:1.5 +4 897403 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCGTGGGATGAGCAGGA;RSEQ=TGCGGGGCCTGAACTGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 899168 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACGGTTAACATCATCAC;RSEQ=GTGGAGCAATCAGTGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:26:1:32:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 899265 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=1.47399;LSEQ=CTCCGCCACGCCCCATGCCA;RSEQ=GCTACGGACTCCGCCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:7,5:1,2:3,12:0.8:2,2:35.8:1:32:1:0.56923:2.61:33.3:24:0.8:0:1 1/1:7:6:5,1:1,0:1,6:0.8571:0,2:22.7:1:31.3:1:1:0:35.8:12:0.8571:0:1.2 +4 899352 . T C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88119;LSEQ=CTCCGCCACGCCCCAGGCCA;RSEQ=GCTACGGACTTCGCCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:21:1:32.5:1:1:2.24:60:4:0.2222:0:1 0/1:10:2:1,1:4,4:8,2:0.2:2,2:9:0:32:1:1:1:60:4:0.2:0:1.5 +4 1402372 . A G 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GCACACCAGACACTTTCCAG;RSEQ=TTGCTGCGCCCCCTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:17.3:1:28:1:1:0:60:3:0.5:0:1.3 0/0:2:0:0,0:2,0:2,0:0:0,0:12.5:1:30:0:1:0:60:4:1:0:0 +4 1402580 . T C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.85985;LSEQ=CCACCCTGCCGGGTCCCAGA;RSEQ=AGTTGGAACACCTGCGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:38:25,13:131,58:189,38:0.1674:2,2:22:1:32.1:1:0.70307:1.17362:60:76:0.1704:0:1.1 0/1:175:64:40,24:75,36:111,64:0.3657:2,2:25.1:1:31:1:0.51239:1.24837:60:128:0.3699:0:1.1 +4 1402650 . A T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=0.45677;LSEQ=CTCTTAGTACAACTTTCAAA;RSEQ=CGAACACAATCACATGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:69:36,33:182,159:341,69:0.1679:2,2:26.2:1:29.6:1:0.89517:1.04917:60:12.8:0.16:0:1.1 0/1:344:29:13,16:155,160:315,29:0.0843:2,2:23.6:1:29.3:1:0.70102:1.1917:60:58:0.085:0:1.1 +4 1781058 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGTCCCCGGGCTGGCGG;RSEQ=TGACATGAGGCACAAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:28:1:1:0:60:4:1:0:1 +4 1795557 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTGCCTTCCTCCTCCTG;RSEQ=AGTCTCCCGAGCGGCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 1795701 . G T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.077;SOR=0;LSEQ=CCCTCGCGCTCTGCGTGGCC;RSEQ=TGGCCATCGTGGCCGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:5:2,3:257,111:368,5:0.0134:2,2:21.8:1:28.6:1:0.16919:3.45983:60:10:0.0139:0:1 0/0:272:0:0,0:180,92:272,0:0:2,0:23.8:1:30:1:1:0:60:53.4:1:0:0.2 +4 1795719 . G A 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.04255;SOR=0;LSEQ=CCGTGGCCATCGTGGCCGGC;RSEQ=CCTCCTCGGAGTCCTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:6:3,3:336,157:493,6:0.012:2,2:20.5:1:30.7:1:0.39093:2.13659:60:12:0.0124:0:1.2 0/0:364:0:0,0:231,131:362,0:0:2,0:27.7:1:29.6:1:1:0:60:50.714:0.9972:0:0.2 +4 1795762 . G A 178 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01973;LSEQ=GGAGCAGCGCGTCGTGGGGC;RSEQ=AGCGGCAGGTAAGAAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:65:37,28:394,281:675,65:0.0878:2,2:27:1:29.6:1:0.89537:1.06098:60:20.667:0.0854:0:1.2 0/0:528:1:1,0:277,250:527,1:0.0019:2,0:1:0:26:0:1:0:60:2:0.002:0:1 +4 1795924 . G A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55417;SOR=0;LSEQ=CCTCCTTGCCGGAGAGCGCG;RSEQ=CCAGAGCTAGCGCGGCGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:1,2:4,53:57,3:0.05:2,2:38.3:1:30.3:1:0.23334:6.24:60:6:0.05:0:1 0/0:24:0:0,0:1,23:24,0:0:1,0:28.6:1:32.1:1:1:0:60:48:1:0:0.1 +4 1801148 . C T 85 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00519;SOR=11.23976;LSEQ=GTGTCCTGGTGGGGCCCCAG;RSEQ=GGCTGCAGGTGCTGAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:862:1:0,1:398,463:861,1:0.0012:2,0:1:0:26:0:1:0:60:2:0.0012:0:1 0/1:620:8:3,5:288,324:612,8:0.0129:2,2:12.8:1:28.6:1:0.72893:1.48056:60:16:0.0132:0:1.1 +4 1801259 . T C 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04396;SOR=Inf;LSEQ=TGCGGGTGACAGGTGAGCTC;RSEQ=GGGGCCACGCCAGCTACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:0:0,0:161,312:473,0:0:2,0:25.2:1:30.9:1:1:0:60:58.125:1:0:0.1 0/1:259:3:2,1:90,165:255,3:0.0116:2,2:14.3:1:24.7:1:0.29001:3.65:60:2:0.0079:0:3.3 +4 1801278 . G A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04145;SOR=Inf;LSEQ=CTGGGGCCACGCCAGCTACA;RSEQ=AAAGGAGCCGAGTGCCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:121,255:376,0:0:2,0:25.6:1:32.6:1:1:0:59.9:124.333:1:0:0.1 0/1:200:3:3,0:69,128:197,3:0.015:2,0:14.7:1:21.3:1:0.04541:0:60:2:0.0103:0:2 +4 1801286 . C T 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01029;SOR=Inf;LSEQ=ACGCCAGCTACAGAAAGGAG;RSEQ=CGAGTGCCGGGCTCCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:119,233:352,0:0:2,0:24.4:1:31.3:1:1:0:59.9:34.2:1:0:0.1 0/1:166:4:2,2:56,105:161,4:0.0241:2,2:33.8:1:23:1:0.61333:1.87:60:3:0.0184:0:3 +4 1801295 . G A 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2332;SOR=4.40389;LSEQ=ACAGAAAGGAGCCGAGTGCC;RSEQ=GGCTCCCTGAGTCCCTGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:1:1,0:117,186:303,1:0.0033:2,0:1:0:27:0:0.38816:0:60:2:0.0033:0:1 0/1:140:2:1,1:45,93:138,2:0.0143:2,2:17:0:31.5:1:0.55077:2.06:60:4:0.0145:0:1.5 +4 1801363 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08533;SOR=Inf;LSEQ=GGTCATTGGTGGAGAGGAGG;RSEQ=CACCCCCAGGAAGTGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:158,70:228,0:0:2,0:25.5:1:31.4:1:1:0:59.9:24.333:0.9955:0:0.1 0/1:95:2:1,1:70,23:93,2:0.0211:2,2:26.5:1:28:1:0.44345:3.0006:60:4:0.0215:0:1 +4 1801408 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09649;SOR=Inf;LSEQ=TGGGGGACCCTGCCCCATCT;RSEQ=GGAGGGGCACCTGGGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:295,130:425,0:0:2,0:22:1:31.7:1:1:0:59.9:69.833:1:0:0.1 0/1:192:2:1,1:142,48:190,2:0.0104:2,2:26:1:29.5:1:0.44628:2.93815:60:4:0.0106:0:2 +4 1801511 . C T 136 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=39.60693;LSEQ=GATGACGAAGACGGGGAGGA;RSEQ=GAGGCTGAGGACACAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1199:1:0,1:610,588:1198,1:8e-04:2,0:1:0:29:0:0.49124:0:60:2:8e-04:0:1 0/1:749:24:14,10:368,356:724,24:0.032:2,2:30.3:1:29.7:1:0.53689:1.35:60:48:0.0328:0:1.2 +4 1803000 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1296;SOR=Inf;LSEQ=CAGGACGGGAAACTGAGGCT;RSEQ=GGGATGGGCAGGGGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:171,29:200,0:0:2,0:21.9:1:32:1:1:0:59.9:65.667:1:0:0.2 0/1:113:2:1,1:89,22:111,2:0.0177:2,2:26:1:29:1:0.3671:3.9787:60:4:0.0179:0:2 +4 1803013 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14123;SOR=Inf;LSEQ=TGAGGCTGGGGATGGGCAGG;RSEQ=GCAGCTCTGGGAAGGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:193,47:240,0:0:2,0:22.4:1:30.8:1:1:0:59.9:25.667:1:0:0.2 0/1:145:2:1,1:106,37:143,2:0.0138:2,2:6.5:1:28.5:1:0.4568:2.84022:60:4:0.0144:0:1 +4 1803024 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1454;SOR=Inf;LSEQ=ATGGGCAGGGGCAGCTCTGG;RSEQ=AAGGGGGTTGTTCAGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:219,68:287,0:0:2,0:22.9:1:31.2:1:1:0:59.9:40:0.9964:0:0.2 0/1:178:2:1,1:121,54:175,2:0.0112:2,2:26:1:27:1:0.52613:2.22947:60:4:0.0114:0:1 +4 1803044 . G A 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00145;SOR=Inf;LSEQ=GAAGGGGGTTGTTCAGAGGG;RSEQ=CCTCTGCTCCCACTCGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:273,139:412,0:0:2,0:23.8:1:31:1:1:0:59.9:33.333:0.9975:0:0.2 0/1:271:7:4,3:165,98:263,7:0.0258:2,2:23.9:1:26.4:1:1:1.26162:60:14:0.0263:0:1.4 +4 1803051 . C T 56 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4419;SOR=2.07852;LSEQ=GTTGTTCAGAGGGGCCTCTG;RSEQ=TCCCACTCGGGTCATGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:3:2,1:302,162:464,3:0.0064:2,2:11:1:30.7:1:1:1.07:60:6:0.0066:0:1 0/1:302:4:2,2:185,113:298,4:0.0132:2,2:23.5:1:28.3:1:0.63699:1.63433:60:8:0.0135:0:1 +4 1803307 . T C 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCTGGCAGGCGCGGTGGT;RSEQ=GCTGCCTCCGCTCACTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:389,331:720,0:0:2,0:23.4:1:30.5:1:1:0:60:89:1:0:0.1 0/1:423:72:43,29:189,162:351,72:0.1702:2,2:24.1:1:29.3:1:0.43558:1.27:60:71:0.1695:0:1.2 +4 1803457 . G A 67 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13604;SOR=2.54427;LSEQ=AGCATCCGGCAGACGTACAC;RSEQ=CTGGACGTGCTGGGTGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:999:4:3,1:451,543:994,4:0.004:2,2:19:1:27.5:1:0.33549:3.61:60:8:0.0041:0:1.3 0/1:691:7:4,3:312,372:684,7:0.0101:2,2:25.6:1:24.1:1:0.70823:1.59:60:2.5:0.0073:0:1.4 +4 1803704 . T C 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAAGCACGTGGAGGTGAA;RSEQ=GGCAGCAAGGTGGGCCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1452:0:0,0:665,786:1451,0:0:2,0:25.1:1:30.8:1:1:0:60:119.917:0.9993:0:0.2 0/1:1003:70:34,36:435,496:931,70:0.0698:2,2:27.4:1:30.5:1:0.80447:1.08:59.8:140:0.0705:0:1.3 +4 1803763 . G A 73 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0536;SOR=3.69739;LSEQ=CGTGCTCAAGGTGGGCCACC;RSEQ=TGTGCACGTGGGTGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:3:3,0:196,463:659,3:0.0045:2,0:1:0:26:1:0.02688:0:60:6:0.0046:0:1 0/1:423:7:6,1:141,275:416,7:0.0165:2,2:14.9:1:26.1:1:0.00818:11.64:60:14:0.0166:0:1.1 +4 1803801 . G A 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25882;SOR=4.02404;LSEQ=CCGCTGGGGCTCCTGGGCTG;RSEQ=CCCCAAGGGTGCCCCTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:1:0,1:32,303:335,1:0.003:2,0:10:0:32:0:1:0:60:2:0.003:0:1 0/1:168:2:1,1:24,142:166,2:0.0119:2,2:15:1:24:1:0.27623:5.82:60:4:0.012:0:1 +4 1803810 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.10906;SOR=Inf;LSEQ=CTCCTGGGCTGGCCCCAAGG;RSEQ=TGCCCCTTGGCTGCGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:20,269:289,0:0:2,0:24.5:1:32.6:1:1:0:60:288:1:0:0.1 0/1:143:2:1,1:14,127:141,2:0.014:2,2:11:1:26.5:1:0.19945:8.80:60:4:0.014:0:1 +4 1803824 . C G 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00325;SOR=Inf;LSEQ=CCAAGGGTGCCCCTTGGCTG;RSEQ=GGGTTGCGTGAGGATTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:7,216:223,0:0:1,0:25.2:1:29.8:1:1:0:60:26.875:1:0:0.1 0/1:106:5:0,5:1,100:101,5:0.0472:1,0:11.8:1:29.8:1:1:0:60:10:0.0476:0:1.2 +4 1804377 . G A 103 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CCTCGGGCCCTGTCCAGGGT;RSEQ=CAGGTTCTGCAAGAGCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:10,2:0,0:0,12:1:0,2:24.3:1:29:1:1:0:60:24:1:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:4:0:29:0:1:0:60:2:0.5:0:2 +4 1804846 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.30092;SOR=3.51047;LSEQ=GCTCCAGCTCCAAGGCCCTG;RSEQ=CCGCGCGCCCTGCACGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:1,0:43,265:308,1:0.0032:2,0:1:0:24:0:0.14239:0:60:2:0.0033:0:1 0/1:177:2:1,1:37,138:175,2:0.0113:2,2:13:1:27:1:0.38424:3.69:60:4:0.0114:0:1 +4 1804862 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25999;SOR=4.02019;LSEQ=CCTGGCCGCGCGCCCTGCAC;RSEQ=CCCCGCACGCCCAGCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:1,0:16,183:199,1:0.005:2,0:1:0:26:0:0.085:0:60:2:0.005:0:1 0/1:101:2:1,1:13,86:99,2:0.0198:2,2:12.5:1:29:1:0.25921:6.41:60:4:0.02:0:1 +4 1805279 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.10924;SOR=Inf;LSEQ=GAGGGCCCTCAGCCGCGTGG;RSEQ=GGTGACCAAGTTGGCGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:79,1:80,0:0:1,0:22:1:32.9:1:1:0:60:160:1:0:1.1 0/1:40:2:1,1:35,2:37,2:0.05:2,2:26:0:32:0:0.1498:14.49018:60:4:0.0526:0:2.5 +4 1805296 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01265;SOR=0;LSEQ=TGGCGGTGACCAAGTTGGCG;RSEQ=TGGCTGAGGAGTTGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:104:104:103,1:0,0:0,104:1:0,1:25.2:1:29.3:1:1:0:60:12:1:0:1.1 1/1:54:50:47,3:3,0:3,50:0.9259:0,2:22.4:1:28.4:1:1:0:60:11.5:0.9388:0:1.3 +4 1805573 . TCTG T 86 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.21832;SOR=2.43175;LSEQ=GGTGCTGCCAGGTACCGGCT;RSEQ=CTGCTGCTGCTGCTCCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:659:4:1,3:209,445:654,4:0.0061:2,2:21:1:31.8:1:1:1.40833:60:8:0.0061:0.0015:0 0/1:478:7:1,6:172,299:471,7:0.0146:2,2:34.4:1:30.7:1:0.43051:3.44453:60:14:0.0148:0:0 +4 1806012 . TG T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.08295;SOR=1.43918;LSEQ=GGGCATCCATGGGAGCCCCG;RSEQ=GGGGGGGGGGCCAGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:66:58,8:415,96:511,66:0.1138:2,2:20.7:1:30.8:1:0.23357:1.68:59:21:0.1135:0.0379:0.8 0/1:282:44:36,8:177,61:238,44:0.156:2,2:23.1:1:30.6:1:0.34374:1.55:59.3:43:0.1547:0.0355:0.5 +4 1806024 . C G 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27779;SOR=0.27634;LSEQ=GAGCCCCGTGGGGGGGGGGG;RSEQ=CAGGCCAGGCCTCAACGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:7:5,2:519,168:687,7:0.0101:2,2:15.7:1:25.4:1:0.68178:1.23533:60:2.5:0.0077:0:1.9 0/0:357:1:1,0:249,106:355,1:0.0028:2,0:12:0:29:0:1:0:60:2:0.0029:0:3 +4 1806028 . G T 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19172;SOR=3.73641;LSEQ=CCCGTGGGGGGGGGGGCCAG;RSEQ=CCAGGCCTCAACGCCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:724:2:2,0:523,194:717,2:0.0028:2,0:29:1:12:0:1:0:54.5:0:0:0:3 0/1:390:4:1,3:263,123:386,4:0.0103:2,2:21.8:1:26.8:1:0.10108:6.38191:60:8:0.0111:0:1.3 +4 1806478 . G A 36 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02514;SOR=Inf;LSEQ=ACGCCCCCCCTTCTGGCCCA;RSEQ=CACTGACCCCCGGCTGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:285,36:321,0:0:2,0:25.8:1:32.6:1:1:0:59.8:21.929:1:0:0.3 0/1:134:3:2,1:114,17:131,3:0.0224:2,2:7:1:23:1:0.35356:3.30902:60:2:0.0154:0:1 +4 1806519 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00059;SOR=0.41597;LSEQ=TCCACGCCCTGTCGCCCACG;RSEQ=GGCGCCAACCTGCCCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:73:48,25:375,127:502,73:0.1267:2,2:24.2:1:29.6:1:0.11827:1.53666:60:35.5:0.1259:0:1.1 0/1:334:19:13,6:213,101:314,19:0.0569:2,2:26.3:1:28.5:1:1:1.03:60:18:0.0557:0:1.2 +4 1806725 . T A 56 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.283;SOR=2.43133;LSEQ=TGCTGAGGGCCAGCGTTGGC;RSEQ=GTAGGGGGCTTGGTGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:3:3,0:221,470:691,3:0.0043:2,0:3.3:1:22:1:0.03332:0:60:2:0.003:0:1 0/1:479:5:4,1:159,314:473,5:0.0104:2,2:10:1:24.2:1:0.04827:7.86:60:4:0.0087:0:1.2 +4 1806834 . G C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGGCTGGGGTTCTGTGGA;RSEQ=ATGCTCCTGGGACGGGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:11,95:0,0:0,106:1:0,2:24.9:1:32.9:1:1:0:59.7:105:1:0:1.1 1/1:48:48:7,41:0,0:0,48:1:0,2:21.6:1:32.2:1:1:0:60:96:1:0:1.1 +4 1806937 . C T 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00213;SOR=0;LSEQ=GGTGACACTCTTCGTCCTTA;RSEQ=GAGCAGGCTGTAGGGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:22:19,3:77,9:86,22:0.2018:2,2:23:1:31.4:1:0.70669:1.34686:58.6:21:0.2:0:1.4 0/0:36:0:0,0:30,6:36,0:0:2,0:18.7:1:31.4:1:1:0:60:17:1:0:0.3 +4 1806989 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10825;SOR=Inf;LSEQ=CCTGGAGGTGGTGGCTCTGG;RSEQ=CCTCAAGGGCTGGGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:183,24:207,0:0:2,0:25.1:1:31.2:1:1:0:59.9:40.4:1:0:0.2 0/1:102:2:1,1:80,20:100,2:0.0196:2,2:8:1:26.5:1:0.371:3.92792:60:4:0.02:0:1 +4 1807008 . G T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10692;SOR=Inf;LSEQ=GGCCTCAAGGGCTGGGCCAG;RSEQ=CTGGGGTGGGGACCGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:228,55:283,0:0:2,0:23.5:1:31.4:1:1:0:59.9:55.6:1:0:0.2 0/1:138:2:1,1:104,32:136,2:0.0145:2,2:18:0:27:1:0.42241:3.21572:60:4:0.0148:0:1.5 +4 1807244 . GCGC G 101 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09958;SOR=0.17866;LSEQ=GGTGCAGAGCAGGGCTGGGG;RSEQ=CGCCGCCGCCTGACACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:9:4,5:375,358:733,9:0.0121:2,2:23.1:1:32.1:1:0.74765:1.30888:60:18:0.0123:0.0027:0.1 0/0:458:1:1,0:247,208:455,1:0.0022:2,0:14:0:33:0:1:0:60:2:0.0022:0:0 +4 1807347 . C T 145 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=9.37433;LSEQ=ATGGAGATGATGAAGATGAT;RSEQ=GGGAAACACAAAAACATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1161:4:0,4:556,600:1156,4:0.0034:2,0:1:0:26.5:1:0.12564:0:60:8:0.0035:0:1 0/1:923:29:14,15:427,466:893,29:0.0314:2,2:21.2:1:29.9:1:1:1.02:58.6:58:0.0318:0:1.2 +4 1807478 . G T 118 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=30.06594;LSEQ=GAGGAGCCCGTGTCCCCAGG;RSEQ=CCCCTGTACGTGCTGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1039:1:0,1:543,495:1038,1:0.001:2,0:1:0:25:0:0.47738:0:60:2:0.001:0:1 0/1:603:17:8,9:307,279:586,17:0.0282:2,2:20.1:1:29.1:1:0.80658:1.23746:59.1:34:0.029:0:1.3 +4 1807894 . G A 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCGACTACTACAAGAAGAC;RSEQ=ACCAACGTGAGCCCGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:973:972:460,512:0,0:0,972:0.999:0,2:24.4:1:30.5:1:1:0:60:63.8:0.999:0:1.1 1/1:628:628:282,346:0,0:0,628:1:0,2:23.8:1:29.7:1:1:0:60:103.667:1:0:1.2 +4 1807995 . C T 79 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04077;SOR=4.84289;LSEQ=CCCTCCCAGGGCCGGCTGCC;RSEQ=GTGAAGTGGATGGCGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:923:2:0,2:443,478:921,2:0.0022:2,0:1:0:27.5:1:0.50026:0:60:4:0.0022:0:1 0/1:672:7:2,5:327,336:663,7:0.0104:2,2:17.6:1:28.4:1:0.45119:2.43018:56.7:14:0.0105:0:1.1 +4 1808427 . G A 51 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24924;SOR=2.47447;LSEQ=ACCTGTGAGTGGCATCCCTG;RSEQ=CCCTCCACTGGGTCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:694:3:2,1:280,411:691,3:0.0043:2,2:12.3:1:28:1:0.56956:2.93:60:6:0.0044:0:1 0/1:376:4:3,1:142,229:371,4:0.0106:2,2:9.3:1:25.5:1:0.30302:4.82:60:8:0.0108:0:1 +4 1808438 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03439;SOR=Inf;LSEQ=GCATCCCTGGCCCTCCACTG;RSEQ=GTCCTCAGGGGTGGGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:608:0:0,0:247,361:608,0:0:2,0:24.1:1:31.1:1:1:0:60:59.8:1:0:0.1 0/1:294:3:2,1:109,182:291,3:0.0102:2,2:10:1:28.3:1:0.55907:3.33:60:6:0.0104:0:1 +4 1809127 . CGTGT C 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=9.000;MSILEN=2;SSF=0.01287;SOR=0;LSEQ=GGTCTGTGTGTGTGTGTGTG;RSEQ=GTGTGTGTGTGTGTGCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:1,11:1,21:22,12:0.2553:1,2:35:1:32.5:1:1:1.87:60:24:0.2727:0.0426:0.3 0/0:21:0:0,0:0,12:12,0:0:0,0:11.3:1:30.7:1:1:0:56.2:11:0.5789:0:1.3 +4 1809787 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAGCAGAGGACCAGGGC;RSEQ=TTTTCTGGCACCGCAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 1999836 . C CAAT 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.02601;SOR=Inf;LSEQ=AACAGCATCAACAACAACAA;RSEQ=AACAACCACAACAAAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:11,0:0:2,0:22.5:1:32.5:1:1:0:49.9:22:1:0:0.1 0/1:9:4:2,2:4,1:5,4:0.4444:2,2:12:1:28:1:0.52381:3.38757:40.8:8:0.4444:0.3333:0.8 +4 3715974 . C CTG 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=1.5077;LSEQ=TGTGGGGTGTATGTGTGTGT;RSEQ=TGTGTGTGTGTGCATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:21,29:50,2:0.0385:2,2:46.5:1:32:1:1:1.37:60:4:0.0385:0:0 0/1:35:2:1,1:17,15:32,2:0.0571:2,2:11:0:32.5:0:1:1.12916:60:4:0.0571:0:0.5 +4 3716031 . T A 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.54386;SOR=Inf;LSEQ=CTGTGGAGGGTATGTGTGTG;RSEQ=GCATATGTGCGATGTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:13,0:0:2,0:17:1:31.5:1:1:0:60:26:1:0:0.1 0/1:26:2:1,1:9,15:24,2:0.0769:2,2:5:0:29:1:1:1.63:60:4:0.0769:0:0 +4 3716037 . T A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52941;SOR=Inf;LSEQ=AGGGTATGTGTGTGTGCATA;RSEQ=GTGCGATGTGTGGATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:12,0:0:2,0:13:1:31.1:1:1:0:60:24:1:0:0.1 0/1:22:2:1,1:8,12:20,2:0.0909:2,2:26.5:1:32:1:1:1.47:60:4:0.0909:0:1.5 +4 3753097 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CAAACATGAGCCCAGAGCCC;RSEQ=GGCCCCTGCTGCCACGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:4,0:0:0,0:29.3:1:29.5:1:1:0:60:8:1:0:0.3 1/0:4:2:0,2:0,2:2,2:0.5:0,0:20:1:28.5:1:1:0:60:4:0.5:0:1.5 +4 4763704 . G A 46 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20635;SOR=0.11969;LSEQ=TGCCAGCGAGGAGCCTTAGA;RSEQ=CAAGTGACTTAACCTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:36.3:1:29.3:1:1:0:60:6:0.75:0:1 0/1:5:1:0,1:0,4:4,1:0.2:0,0:36:0:30:0:1:0:60:2:0.2:0:1 +4 4763850 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTTACCTTAGCGTAAACA;RSEQ=ATAAGAGAGCGAAAAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:29.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 4807909 . T A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12898;SOR=Inf;LSEQ=CAGTCAGCGTTCCAGTGGAG;RSEQ=GTGGTTCCTGCAGGTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:26,0:0:2,0:31.8:1:31:1:1:0:60:52:1:0:0.1 0/1:35:4:2,2:14,16:30,4:0.1143:2,2:9.5:1:28.8:1:1:1.14:60:8:0.125:0:1.5 +4 4808990 . G A 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGGGGGTCCATGTGGCC;RSEQ=GTGCTGCTGCCCAGGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 4809712 . G A 30 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGACAGCTCATGCAAACCCA;RSEQ=GCTAACCAGGCCTACAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:30.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:8.5:1:30.5:1:1:0:60:4:1:0:0 +4 4998256 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACCCAGTTTTGTCCTAAT;RSEQ=CTCTCCCTCCCCTTGCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:10,2:0.1667:2,2:15:0:31:1:1:2.16:60:4:0.1818:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:24.3:1:30.8:1:1:0:60:8:1:0:0 +4 5812778 . G A 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTAGTTTAAGACCAGTC;RSEQ=GTGGGACAAGACCTGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:21.3:1:32.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 6113431 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15293;SOR=Inf;LSEQ=GCTCCTCCCCTCTGTGACAG;RSEQ=CCGTGCTTTAATTAGACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:94,21:115,0:0:2,0:24.5:1:31.7:1:1:0:60:37.333:0.9912:0:0.2 0/1:75:2:1,1:54,19:73,2:0.0267:2,2:18:1:30.5:1:0.46486:2.79567:60:4:0.027:0:1 +4 6113451 . C G 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=CCCGTGCTTTAATTAGACTG;RSEQ=CAGCACCCAACCAGGCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:18:14,4:111,43:154,18:0.1047:2,2:22.2:1:31.3:1:0.78233:1.35:60:36:0.1078:0:1 0/0:128:0:0,0:85,42:127,0:0:2,0:24.3:1:31:1:1:0:60:254:1:0:0.1 +4 6113559 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26764;LSEQ=GCTCTGTTCCAAGCTCTTTA;RSEQ=CTAGCAGAGCCCTGAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:317:177:78,99:69,71:140,177:0.5584:2,2:25.5:1:30:1:0.36647:1.23265:59.9:43.25:0.5599:0:1.2 0/1:313:79:40,39:116,118:234,79:0.2524:2,2:25.2:1:29:1:0.89701:1.04:60:78:0.2541:0:1.1 +4 6113563 . G A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02613;SOR=Inf;LSEQ=TGTTCCAAGCTCTTTACCTA;RSEQ=CAGAGCCCTGAGTCCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:145,179:324,0:0:2,0:25.1:1:32.4:1:1:0:59.9:80:1:0:0.7 0/1:304:5:2,3:145,154:299,5:0.0164:2,2:13.4:1:28.6:1:1:1.41075:60:10:0.0168:0:1.2 +4 6113578 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11106;SOR=Inf;LSEQ=ACCTAGCAGAGCCCTGAGTC;RSEQ=AGACCACAGCCCCATCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:134,174:308,0:0:2,0:26.7:1:31.5:1:1:0:59.9:43:0.9967:0:0.6 0/1:287:3:1,2:125,159:284,3:0.0105:2,2:16:1:28.7:1:1:1.56995:52.3:6:0.0105:0:1 +4 6113869 . T C 58 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCATGCATGAGTTCCTATA;RSEQ=GATGAACTGCAACCTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:16.3:1:29.3:1:1:0:60:8:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:20:0:31:0:1:0:60:2:1:0:1 +4 6141497 . TATAAA T 66 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=6.000;MSILEN=5;SSF=0.46429;SOR=0.17288;LSEQ=AGTGAGACTCCATCTCAAAA;RSEQ=ATAAAATAAAATAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:42.8:1:33:0:1:0:44.3:8:0.8:0:0 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:45:0:33:0:1:0:43:2:0.3333:0:0 +4 6141538 . G T 79 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01862;SOR=15.429;LSEQ=ATAAAATAAAATAAGGAAAT;RSEQ=GGAGCACAGAGACACAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:12,0:12,1:0.0769:0,0:35:0:33:0:1:0:60:2:0.0769:0:1 1/0:10:6:6,0:4,0:4,6:0.6:0,0:23:1:30.7:1:1:0:60:12:0.6:0:1 +4 6141611 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50241;SOR=0;LSEQ=AGGTCACGGGGCAGATTCCA;RSEQ=GAGCCAAGGAATACCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:18,22:40,2:0.0476:2,2:9.5:1:31:1:1:1.22:60:4:0.0488:0:1.5 0/0:32:0:0,0:16,16:32,0:0:2,0:29.8:1:30.5:1:1:0:60:64:1:0:0.3 +4 6141635 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19096;SOR=Inf;LSEQ=CCAAGGAATACCAAGGACTG;RSEQ=CACCAAAGCACAGGAAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:14,24:38,0:0:2,0:27.8:1:31.3:1:1:0:60:37:1:0:0.2 0/1:30:2:1,1:11,17:28,2:0.0667:2,2:22.5:1:30.5:1:1:1.52:60:4:0.0667:0:1 +4 6141665 . C A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14634;SOR=5.52365;LSEQ=ACAGGAAGCCAGGGGAGAGG;RSEQ=CTGGGGCAGAGTCCCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:1,0:8,17:25,1:0.0385:2,0:1:0:25:0:0.34615:0:60:2:0.0385:0:1 0/1:16:3:0,3:5,8:13,3:0.1875:2,0:13:1:27.7:1:0.50893:0:60:6:0.1875:0:1 +4 6142049 . C G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACATCTTCCCACATAAAT;RSEQ=ATAATGCACACCTGATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 6926997 . A C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GAATGAGACTCCATCTCAAA;RSEQ=AAACAAACAAACAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:8,0:16,0:16,8:0.3333:1,0:28.8:1:33.3:1:1:0:60:16:0.3333:0:1 0/1:21:7:7,0:14,0:14,7:0.3333:1,0:23.1:1:32.6:1:1:0:60:14:0.3333:0:1 +4 6927011 . A G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.2795;SOR=0.33483;LSEQ=CTCAAAAAAACAAACAAACA;RSEQ=AAAAAGAATCGTGATCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:7:7,0:30,0:30,7:0.1892:1,0:17.4:1:34.3:1:1:0:59.6:14:0.1944:0:1.7 0/1:28:2:2,0:26,0:26,2:0.0714:1,0:34.5:1:30.5:1:1:0:60:4:0.0714:0:1 +4 6927079 . G T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36722;SOR=0.5835;LSEQ=GGCCGGGGCTTGGCAGGTGG;RSEQ=AACATTTCTGCAGTTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:18:18,0:130,1:131,18:0.1208:1,1:26.9:1:30.3:1:1:0:59.3:36:0.125:0:1.3 0/1:81:6:6,0:72,3:75,6:0.0741:1,0:17:1:30.8:1:1:0:60:12:0.075:0:1 +4 6927471 . T G 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCTTGTCACTATCCCTTC;RSEQ=GAGGCTGTAGCCATATCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:29:1:32:1:1:0:55.8:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 6927667 . G C 35 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGATGGGTTTTCAGAAAT;RSEQ=TGGGAAACCTTGCTTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:23.5:1:35.5:1:1:0:45:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 6959929 . G A 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.76179;SOR=0.72369;LSEQ=TGTCCAGATGACTGCTCCAG;RSEQ=TGGCCAGCCCACAGTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:5,2:11,6:17,7:0.2917:2,2:30.6:1:29.7:1:1:1.35:60:14:0.3182:0:1.3 0/1:35:8:4,4:17,10:27,8:0.2286:2,2:21.6:1:28.3:1:0.68529:1.67357:60:16:0.2286:0:1.1 +4 6959951 . C T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4955;SOR=Inf;LSEQ=GGCCAGCCCACAGTTAGAGC;RSEQ=GGAGTCTGCAGTTGCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:23,12:35,0:0:2,0:24.2:1:30.5:1:1:0:60:34:1:0:0.4 0/1:40:2:1,1:22,16:38,2:0.05:2,2:12.5:1:23:0:1:1.36391:60:4:0.05:0:1.5 +4 6960001 . T TC 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31715;SOR=0.53752;LSEQ=TTCCAACAGCCTCACCTGCT;RSEQ=CATACTGGGGGTCGAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:18:7,11:6,7:13,18:0.5806:2,2:22.6:1:30.8:1:0.72695:1.33394:60:36:0.5806:0.0968:0.3 0/1:33:14:3,11:6,13:19,14:0.4242:2,2:24.6:1:31.3:1:0.6982:1.66595:60:28:0.4242:0.0909:0.5 +4 6960010 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=CCTCACCTGCTTCATACTGG;RSEQ=GGTCGAGGGGGTTATGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:12,16:28,0:0:2,0:22.9:1:30.7:1:1:0:60:56:1:0:0.2 0/1:27:2:1,1:7,18:25,2:0.0741:2,2:19:1:31:1:0.51282:2.47:60:4:0.0741:0:1.5 +4 6960015 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49061;SOR=Inf;LSEQ=CCTGCTTCATACTGGGGGTC;RSEQ=AGGGGGTTATGTCCCTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,14:24,0:0:2,0:23.8:1:30.7:1:1:0:60:48:1:0:0.2 0/1:26:2:1,1:7,17:24,2:0.0769:2,2:40:1:30.5:1:0.52923:2.34:60:4:0.08:0:1 +4 7647801 . C T 71 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24242;SOR=0.16477;LSEQ=CCTTGCGCACCCGGCAGCCA;RSEQ=GGATTCCGGGCTACCGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:26.8:1:30.8:1:1:0:60:10:0.7143:0:1.2 0/1:4:1:0,1:0,3:3,1:0.25:0,0:21:0:31:0:1:0:60:2:0.25:0:1 +4 8042066 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCAGGGTGGCCAGGCGC;RSEQ=GTGGCTCACACCTGTACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:29.5:1:1:0:60:4:1:0:1.5 +4 8043501 . G T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAGCCATGCATGGTGGCG;RSEQ=GTGCCTGTTGTCCCAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:3,0:3,2:0.4:0,2:10:0:31:0:0.4:0:50:4:0.4:0:2 +4 8043505 . C T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATGCATGGTGGCGGGTG;RSEQ=CTGTTGTCCCAGCTACTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:3,0:3,2:0.4:0,2:14:0:30.5:1:0.4:0:50:4:0.4:0:2 +4 8043638 . G GA 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.36541;SOR=0.64112;LSEQ=GAGACTCCACTTCAAAAAAA;RSEQ=AAAAAAAAAAGAGCTCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:16:13,3:11,2:13,16:0.4706:2,2:16.2:1:31.2:1:1:1.25893:59.7:32:0.4706:0.2353:2.1 0/1:47:17:13,4:23,6:29,17:0.3617:2,2:19.1:1:29:1:1:1.1752:57.9:34:0.3696:0.1702:1.6 +4 8043682 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00045;SOR=3.32014;LSEQ=ATGAGCAGTTACTATGTGCC;RSEQ=TGCAGGTTCCAACAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:15:11,4:34,19:53,15:0.2174:2,2:27.5:1:30.3:1:0.75803:1.53:60:30:0.2174:0:1.2 0/1:108:52:30,22:32,24:56,52:0.4815:2,2:32.1:1:29.5:1:1:1.02:59.6:104:0.486:0:3 +4 8043700 . A G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=6.00701;LSEQ=CCGTGCAGGTTCCAACAACA;RSEQ=CAGCAGCAACAACAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:85:48:26,22:25,12:37,48:0.5647:2,2:27.2:1:32.8:1:0.2662:1.75109:59.3:96:0.5647:0:2.3 1/1:133:118:67,51:7,7:14,118:0.8872:2,2:27.5:1:31.3:1:0.77722:1.31:59.1:117:0.8931:0:2.6 +4 8043703 . G A 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=TGCAGGTTCCAACAACAACA;RSEQ=CAGCAACAACAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:48:25,23:25,12:37,48:0.5581:2,2:27.3:1:29.6:1:0.18513:1.90197:59.3:47:0.5663:0:2.2 0/0:135:0:0,0:7,7:14,0:0:2,0:28.4:1:31.7:1:1:0:60:28:1:0:0.1 +4 8043737 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51393;SOR=Inf;LSEQ=AACAGCAACAGCTACCACGA;RSEQ=TGAGCGCTTAGCAGGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:32,42:74,0:0:2,0:27:1:30.8:1:1:0:59.5:148:1:0:1.1 0/1:107:2:1,1:44,61:105,2:0.0187:2,2:37.5:1:30:1:1:1.38:60:4:0.019:0:2 +4 8508579 . C G 33 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGAAATGCTGCTTGGTGAG;RSEQ=TGGGCTGGCTGGGCTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:24:1:34.5:1:1:0:60:4:1:0:0 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:25:0:33:1:0.33333:0:60:4:0.3333:0:1.5 +4 8508614 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=TGCTGGCCCTCGGTCAGCCG;RSEQ=CTGCAACAGGCAGGGCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:22:1:31.1:1:1:0:60:14:1:0:0.1 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:8:1:27:1:1:1.4491:60:4:0.1667:0:1 +4 8508678 . T C 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08669;SOR=Inf;LSEQ=TGGAGGCAGCGTGGGTGGAA;RSEQ=TGTGGAATTGTCATCAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:22.6:1:30.7:1:1:0:60:20:1:0:0.1 0/1:10:4:2,2:1,5:6,4:0.4:2,2:24:1:32.3:1:0.5:4.17:60:8:0.4444:0:1 +4 8509451 . T G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGGGCTGTCGCTCCATG;RSEQ=ACAGACAGGAGTCCAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:22:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 10256323 . AT A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGTGGGAACTGTCTGGA;RSEQ=ACACCTTACTGTGTCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:18:1:30.8:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 10256455 . C G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCAGTCAGAACAGCAAG;RSEQ=CTTTCTGGGCTGAGGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:0,16:1:0,1:22.9:1:31.4:1:1:0:60:32:1:0:1.3 1/1:5:5:5,0:0,0:0,5:1:0,0:17.6:1:28.6:1:1:0:60:4:1:0:1.2 +4 10256518 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18655;SOR=Inf;LSEQ=CAATGCAGTTGGCTCCTCAG;RSEQ=AAAAACTGGTGTTTTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:32,16:48,0:0:2,0:22.4:1:30:1:1:0:60:11:1:0:0.5 0/1:37:2:1,1:24,11:35,2:0.0541:2,2:22.5:1:24:1:1:2.13205:60:4:0.0541:0:1.5 +4 10256577 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01373;SOR=3.14754;LSEQ=ACCAGCCTCTTCATTGCTTT;RSEQ=GGGCAGTTCTTGTGTATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:8:3,5:35,38:73,8:0.0988:2,2:30.8:1:30.5:1:0.71678:1.52712:60:16:0.0988:0:1.1 0/1:62:16:8,8:23,23:46,16:0.2581:2,2:35:1:29.1:1:1:1:60:32:0.2623:0:1.2 +4 10256768 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.29475;SOR=0;LSEQ=TTTTACCCTTCGTTCAGATC;RSEQ=CCTCTGGGGCCATTGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:15,1:16,4:0.2:1,2:34.8:1:31:1:0.08772:11.97303:60:8:0.2:0:2 0/0:8:0:0,0:7,1:8,0:0:2,0:20.8:1:29.5:1:1:0:60:16:1:0:0.6 +4 10256784 . C A 141 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00106;SOR=0;LSEQ=GATCGCCTCTGGGGCCATTG;RSEQ=CTGTGGGTTTCCTTAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:22,4:0,0:0,26:1:0,2:24.8:1:30.1:1:1:0:60:25:1:0:1.2 1/0:11:6:4,2:5,0:5,6:0.5455:0,2:29.2:1:27.5:1:0.45455:0:60:12:0.5455:0:1.3 +4 10256936 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03045;LSEQ=TTCTCTGCATGCCAACTAGT;RSEQ=CCTTCCCTGAGCTGTCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:212:211:152,59:0,0:0,211:0.9953:0,2:24.6:1:30.6:1:1:0:60:104.5:0.9952:0:1.1 1/1:155:134:90,44:16,5:21,134:0.8645:2,2:23.3:1:28.9:1:0.4616:1.56022:60:66:0.8627:0:1.1 +4 10257087 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15982;SOR=Inf;LSEQ=TGAACCCCAACAAGAGCAGA;RSEQ=TGTCCACATGTCCTACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:99,166:265,0:0:2,0:23.4:1:30.3:1:1:0:60:36.857:1:0:0.2 0/1:177:2:1,1:70,105:175,2:0.0113:2,2:22:1:26.5:1:1:1.50:60:4:0.0114:0:1 +4 10257145 . G A 27 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55656;SOR=3.48356;LSEQ=ATCTCTGAAGGCCTGGAACT;RSEQ=CTCTGGGGGTCAGGTTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:1:0,1:50,125:175,1:0.0057:2,0:34:0:30:0:1:0:60:2:0.0057:0:1 0/1:102:2:1,1:37,63:100,2:0.0196:2,2:39:0:27.5:1:1:1.69:60:4:0.0198:0:1 +4 10257734 . G A 135 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04685;SOR=0;LSEQ=TCCAGCCCACGTGCCTAGTG;RSEQ=GTACTTTAGTGCTATAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:16,7:0,0:0,23:1:0,2:25.3:1:30:1:1:0:60:46:1:0:1 1/0:14:11:8,3:2,1:3,11:0.7857:2,2:30.7:1:28.4:1:1:1.31:60:22:0.7857:0:1 +4 10257897 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51395;SOR=0;LSEQ=CTCAGGAAATCTACCTGAAG;RSEQ=TCTTCCCCCATCAGGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:47,51:98,2:0.02:2,2:41.5:1:31:1:1:1.08:60:4:0.0202:0:1 0/0:69:0:0,0:29,40:69,0:0:2,0:28.6:1:30.8:1:1:0:60:22:1:0:0.1 +4 10257932 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11899;SOR=Inf;LSEQ=GCAGCATCAGTATTCCAATA;RSEQ=AAATGCCTTTTTACCCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:27,48:75,0:0:2,0:22.3:1:28.5:1:1:0:60:24:1:0:0.1 0/1:40:2:1,1:14,24:38,2:0.05:2,2:26:1:33:0:1:1.69:60:4:0.05:0:1 +4 10258057 . C G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14716;SOR=0.20091;LSEQ=TTTGCACACTGACCACTGTT;RSEQ=TTTGCTTATTGGCAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:3,13:0,1:1,16:0.8889:0,2:25.4:1:32.6:1:1:0:60:32:0.9412:0:1.1 1/0:10:6:1,5:1,3:4,6:0.6:2,2:18.5:1:30:1:1:1.58108:60:12:0.6:0:1 +4 12321563 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=AGTGTAAGAGCAGTGGAAGG;RSEQ=AGCCAACGAAAAGCTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:110,50:160,2:0.0123:2,2:25:1:27.5:1:0.53186:2.18824:60:4:0.0125:0:1 0/0:161:0:0,0:118,43:161,0:0:2,0:23.6:1:30.1:1:1:0:60:160:1:0:0.2 +4 12321669 . C G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16915;SOR=0.79104;LSEQ=GATTGAAGACTTCATCACCA;RSEQ=TCTTTTCTGTTTTATGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:299:157:75,82:59,82:141,157:0.5251:2,2:26.6:1:32.7:1:0.35101:1.27:60:156:0.527:0:1.1 0/1:313:146:60,86:74,92:166,146:0.4665:2,2:23:1:30.7:1:0.56761:1.15237:59.9:28.2:0.4593:0:1.1 +4 12322014 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAGTAATTACATGGGCA;RSEQ=TTATCTGTTAACATTTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:30.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 13633615 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=TGTGTTTCAGGAAGCTATCT;RSEQ=GGCTCTTAGTGAGCTTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:19,4:23,0:0:2,0:23.4:1:31.5:1:1:0:59.1:22:1:0:0 0/1:23:2:1,1:14,7:21,2:0.087:2,2:39.5:1:31:1:1:1.93655:50.5:4:0.087:0:1 +4 13633735 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18227;SOR=Inf;LSEQ=ACATTGTAGACTCTTCTAGT;RSEQ=GTGCCATGGTAACACTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:48,52:100,0:0:2,0:30.6:1:30.6:1:1:0:59.1:99:1:0:0.2 0/1:75:2:1,1:37,36:73,2:0.0267:2,2:40.5:1:28:1:1:1.02741:41:4:0.0267:0:1 +4 13634228 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=CTTTGTGTTCGTCATTTTGG;RSEQ=GAATTACTGGAAGACAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:33,0:0:2,0:25.5:1:31.2:1:1:0:49.2:32:1:0:0.1 0/1:59:2:1,1:29,28:57,2:0.0339:2,2:36:1:29:1:1:1.03511:57:4:0.0339:0:1 +4 15499251 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.04344;LSEQ=AATTTATATTCCTACCAGCA;RSEQ=AGAAGTTTTAATTTATCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:117:56,61:211,213:424,117:0.2163:2,2:25.6:1:32:1:0.75449:1.07889:59.7:116:0.2172:0:1.1 0/1:451:206:104,102:128,117:245,206:0.4568:2,2:27:1:31.3:1:0.77668:1.07281:59.9:67.667:0.4572:0:1.2 +4 15499343 . T C 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGTGAAGTGGTACCTAA;RSEQ=TGTGGTTTTGGTTTCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:54,160:214,0:0:2,0:23.7:1:30.1:1:1:0:60:52.5:1:0:0.1 0/1:153:34:10,24:28,91:119,34:0.2222:2,2:19.7:1:30.3:1:0.50409:1.35:60:33:0.22:0:1.3 +4 15499481 . A AT 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00155;SOR=Inf;LSEQ=AAAAGCAGGATCTTTGTGGT;RSEQ=TATGGCTTATATGTCAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:12,0:0:0,0:29.7:1:31.3:1:1:0:56.8:24:1:0:0.1 1/0:9:6:0,6:0,3:3,6:0.6667:0,0:19.7:1:30.3:1:1:0:60:12:0.6667:0.2222:0 +4 16611214 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50588;SOR=Inf;LSEQ=ATCGGCTGTGGCAGTCTGCG;RSEQ=CCAGAGTGCCTCTTCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:21,0:0:2,0:31.1:1:31.9:1:1:0:59.8:42:1:0:0.4 0/1:30:2:1,1:11,17:28,2:0.0667:2,2:27.5:1:27:1:1:1.52:57:4:0.069:0:1 +4 16611273 . C A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.08684;LSEQ=CCTCAGGCAGTGCTTCCCTG;RSEQ=AGGATCTCCAATAACTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:4,7:1,3:4,11:0.7333:2,2:20.5:1:29.2:1:1:1.66:56.5:10:0.7143:0:1 1/0:8:6:3,3:0,2:2,6:0.75:0,2:14:1:29:1:0.46429:0:60:12:0.75:0:1 +4 16611787 . T C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCAGAAAGTGGCAACAA;RSEQ=AGCATCAACAACAAAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:13,18:0,0:0,31:1:0,2:23.7:1:31.7:1:1:0:57.7:30:1:0:1 1/1:24:24:11,13:0,0:0,24:1:0,2:23.3:1:31.7:1:1:0:57.5:48:1:0:1.2 +4 16611905 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.54023;SOR=0;LSEQ=AGTGAAAAAATGCTGAAAAC;RSEQ=CAAAAGGCCAGAGTGCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:18,2:0.1:2,2:28:1:31:1:1:1.54:39:4:0.1053:0:1 0/0:10:0:0,0:5,5:10,0:0:2,0:16.1:1:30:1:1:0:60:20:1:0:0.1 +4 18537350 . T C 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00135;SOR=Inf;LSEQ=ATCACCCTGGCATGGTGTAC;RSEQ=CATGGTGTACAGAGTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:13,0:0:2,0:24:1:30.9:1:1:0:60:26:1:0:0 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:23.2:1:30.2:1:1:1.41:60:10:0.7143:0:1 +4 20891259 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52005;SOR=0;LSEQ=AAATAGGAACTATTGGCCTG;RSEQ=TTGGCCCTAAATGGAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:33,115:148,2:0.0133:2,2:27:1:30.5:1:0.40313:3.45:44.5:4:0.0137:0:1 0/0:98:0:0,0:23,75:98,0:0:2,0:21.3:1:31.7:1:1:0:58.8:196:1:0:0.1 +4 20891275 . A G 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15188;SOR=Inf;LSEQ=CCTGCTTGGCCCTAAATGGA;RSEQ=GGGCTGATATTTTAAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:9,92:101,0:0:2,0:23.5:1:31.7:1:1:0:56:49.5:1:0:0.2 0/1:65:2:1,1:5,58:63,2:0.0308:2,2:6.5:1:28:1:0.1774:10.68:44:4:0.0313:0:1 +4 20891283 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14157;SOR=Inf;LSEQ=GCCCTAAATGGAAGGGCTGA;RSEQ=ATTTTAAGTTGATTATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:6,86:92,0:0:2,0:22.7:1:28.1:1:1:0:53.2:45:1:0:0.2 0/1:56:2:0,2:2,52:54,2:0.0357:1,0:8:1:31:1:1:0:42:4:0.037:0:1 +4 20891334 . A T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.28131;SOR=0;LSEQ=ATCCAACCTAATTCTTTTTA;RSEQ=TTTGGTTGAATGTTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:0,3:1,32:33,3:0.0833:1,0:9.7:1:31.7:1:1:0:47:6:0.0857:0:1 0/0:22:0:0,0:1,21:22,0:0:1,0:25:1:31.1:1:1:0:42.2:44:1:0:0.1 +4 21650176 . C T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55279;SOR=0;LSEQ=ACTACCAGACACACCTTCCA;RSEQ=AGTCTCAAGCTCTAAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:3,0:31,1:32,3:0.0857:1,0:21.7:1:33:0:1:0:60:6:0.0857:0:1 0/0:13:0:0,0:13,0:13,0:0:1,0:20.8:1:32.8:1:1:0:58.2:26:1:0:0 +4 21650368 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42334;LSEQ=AGCATTGGCCTAACTCTGAA;RSEQ=TGGCAAAGTAGGGTTGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:513:114:49,65:194,205:399,114:0.2222:2,2:25.1:1:30.7:1:0.33853:1.25479:60:113:0.2216:0:1.8 0/1:473:51:19,32:198,224:422,51:0.1078:2,2:27.4:1:29.6:1:0.23407:1.48749:59.8:102:0.1081:0:2.1 +4 21650403 . T A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39516;SOR=0.84297;LSEQ=TGTTTAGAAAGGAAAAATTC;RSEQ=GTCAAATTTAGCATATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:73:21,52:121,177:298,73:0.1968:2,2:24.1:1:31.3:1:0.08023:1.69045:60:35.5:0.1929:0:2.3 0/1:374:64:22,42:129,181:310,64:0.1711:2,2:23.7:1:30:1:0.32814:1.35952:59.8:63:0.1707:0:2.1 +4 21650441 . T A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48957;SOR=1.21944;LSEQ=TATTTTCTGTTTACATAATC;RSEQ=AGTAGAGGCCCCGCACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:30:3,27:45,122:167,30:0.1523:2,2:25.3:1:31.9:1:0.06272:3.30391:60:60:0.1546:0:2.3 0/1:178:32:11,21:46,100:146,32:0.1798:2,2:24.7:1:29.6:1:0.83477:1.14:60:64:0.1798:0:2.3 +4 21776672 . A AT 45 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.55547;SOR=0;LSEQ=TGTCCTTTTGGGTTTTCAGC;RSEQ=TTTTTTTCATTGATTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:1,2:17,16:33,3:0.0833:2,2:5.3:1:28.9:1:1:2.08218:50:6:0.0833:0.0556:0.7 0/0:13:0:0,0:8,5:13,0:0:2,0:24.5:1:28.5:1:1:0:45.5:26:1:0:0.2 +4 21776779 . G T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.52559;SOR=1.74948;LSEQ=AGGCCTTTTTTTGGTTGGTG;RSEQ=TGTTGATGCTGCTGTTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:19:7,12:3,5:8,19:0.7037:2,2:22.9:1:29.3:1:1:1.02751:59.1:38:0.7037:0:1.1 1/1:26:21:8,13:2,2:4,21:0.8077:2,2:22.7:1:29.4:1:1:1.59276:59:42:0.84:0:1.2 +4 21777782 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=CTGGGTAGCATGCTCACTCA;RSEQ=CACCTCCCTTGGCTGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:8.5:1:27.5:1:1:1:56:4:0.1667:0:1 0/0:11:0:0,0:2,9:11,0:0:2,0:19.7:1:31.3:1:1:0:56.4:22:1:0:0 +4 24030690 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.21778;SOR=Inf;LSEQ=TAACCTCAACCAATGTTAGT;RSEQ=ATTTATATAATTATTTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:107,65:172,0:0:2,0:22.5:1:30.1:1:1:0:59.7:171:1:0:0.1 0/1:151:2:1,1:90,59:149,2:0.0132:2,2:20:0:32.5:1:1:1.521:60:4:0.0134:0:1 +4 24030761 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.78092;LSEQ=CAAAAATTCAAGCAGCATCA;RSEQ=GATGATAAATTCAAGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:25:12,13:143,135:278,25:0.0825:2,2:23.5:1:32.1:1:0.83559:1.14701:60:24:0.0805:0:1.2 0/1:231:114:54,60:58,59:117,114:0.4935:2,2:25.1:1:30.5:1:0.79273:1.09186:60:113:0.5022:0:1.2 +4 25133364 . C T 112 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=ACTTAGTTTGTCCCCCAGTT;RSEQ=TTAGCTCACAAATTCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:0,12:1:0,0:25.6:1:31.3:1:1:0:60:24:1:0:1.2 1/0:4:3:3,0:1,0:1,3:0.75:0,0:28.7:1:31.3:1:1:0:60:6:0.75:0:1 +4 25133430 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTCTTATCCAATTCAGCAG;RSEQ=TATTTGCAACAATAAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:15,2:0.1176:1,0:13:1:32.5:1:1:0:60:4:0.1176:0:1.5 0/0:5:0:0,0:5,0:5,0:0:0,0:21.4:1:26:1:1:0:60:10:1:0:0.4 +4 25133516 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22395;SOR=Inf;LSEQ=TAAACAGAATAATGATCTTC;RSEQ=CCAGAAGCAAAACAGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:62,2:64,0:0:1,0:24.5:1:31.9:1:1:0:59.7:63:1:0:0.1 0/1:58:2:1,1:53,2:55,2:0.0345:1,2:16.5:1:28.5:1:0.10338:21.8405:60:4:0.0351:0:1 +4 25133641 . T C 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGTTAAATTCATGGTTA;RSEQ=TTCTCCCCTCAATGAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:281,219:500,0:0:2,0:25.2:1:30.6:1:1:0:60:82.333:1:0:0.8 0/1:431:24:12,12:209,198:407,24:0.0557:2,2:31.7:1:31.6:1:1:1.05545:60:48:0.0559:0:2 +4 25133669 . G A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15477;LSEQ=CTCAATGAAGCAAATGTGTT;RSEQ=ATCAGGAAGGGGATAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:529:485:242,243:20,23:43,485:0.9168:2,2:26.8:1:29.4:1:0.751:1.14:60:68.286:0.9175:0:1.1 1/0:427:269:125,144:73,83:156,269:0.63:2,2:23.7:1:28.6:1:1:1.01318:60:88.667:0.6274:0:1.2 +4 25134045 . A G 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAACCAATAAACTATCAC;RSEQ=ATTAAATTTTCACAGTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:9.3:1:30.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 27498143 . A G 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=4.9538;LSEQ=TTAAGATTGGGAAACAAAGA;RSEQ=AGTCTGAAAGAGCCAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:15:1:32:1:1:0:60:4:0.25:0:1 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:20.5:1:29.5:1:1:0:60:4:0.6667:0:1 +4 27498290 . G C 86 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20623;SOR=0.19007;LSEQ=GAGCAAATCAGAGGAATAGG;RSEQ=CCTGAAGTGAACCCCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:4,3:5,9:14,7:0.3333:2,2:26:1:30.9:1:0.39721:2.30:53.3:14:0.3333:0:1 0/1:12:1:0,1:6,5:11,1:0.0833:2,0:25:0:32:0:1:0:57:2:0.0909:0:1 +4 28143780 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50633;SOR=0;LSEQ=GGGGGAAGTCCCTGAAAACA;RSEQ=ACCTGGTGGTTCTAAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:130,67:197,2:0.0101:2,2:25:1:31.5:1:1:1.93344:60:4:0.0101:0:1 0/0:155:0:0,0:97,58:155,0:0:2,0:23.8:1:29.8:1:1:0:60:76.5:1:0:0.2 +4 28143801 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19741;SOR=Inf;LSEQ=ACCTGGTGGTTCTAAATGAA;RSEQ=TTTTCTTTGCCAGTACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:149,88:237,0:0:2,0:27.5:1:33.1:1:1:0:59.9:236:1:0:0.2 0/1:190:2:1,1:114,74:188,2:0.0105:2,2:44.5:1:30.5:1:1:1.53689:60:4:0.0106:0:1 +4 28143847 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09705;SOR=Inf;LSEQ=CCTTTTGAATAGGCACAGAT;RSEQ=TGTCCCTCAGTATCTCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:191,142:333,0:0:2,0:24.4:1:32.5:1:1:0:60:110:0.997:0:0.3 0/1:285:3:2,1:157,125:282,3:0.0105:2,2:12.7:1:28.3:1:1:1.59:60:6:0.0106:0:1.7 +4 28143857 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00318;SOR=1.79598;LSEQ=AGGCACAGATCTGTCCCTCA;RSEQ=TATCTCATTAGAACTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:57:35,22:158,148:306,57:0.157:2,2:21.6:1:29.5:1:0.1948:1.49:60:27.5:0.1536:0:1.1 0/1:295:74:39,35:120,100:220,74:0.2508:2,2:22.6:1:29.4:1:0.78913:1.07665:60:73:0.25:0:1.2 +4 28143921 . AT A 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.21626;SOR=4.96885;LSEQ=CTTAGAATTCCAGTTCCCGG;RSEQ=TTTTTTTACTTCACTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:0,1:95,172:267,1:0.0037:2,0:38:0:32:0:1:0:60:2:0.0038:0:0 0/1:273:5:3,2:114,154:268,5:0.0183:2,2:19.2:1:28.8:1:0.65422:2.02:60:10:0.0185:0.0037:0.2 +4 28143957 . A G 101 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.008;SOR=10.34119;LSEQ=TCACTTTTCATTGATTGAGG;RSEQ=TTGATTGATTTTTAATATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:1,0:31,117:148,1:0.0067:2,0:23:0:14:0:0.21477:0:60:0:0:0:7 0/1:137:9:2,7:40,88:128,9:0.0657:2,2:18.9:1:31.9:1:0.72148:1.58598:60:18:0.0672:0:1.2 +4 28204105 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=2.47198;LSEQ=AATCTAAAAAATTTTTCAGG;RSEQ=CAATGTAACATCTAAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:35:17,18:117,146:263,35:0.1174:2,2:24.1:1:30.2:1:0.71873:1.18:60:70:0.119:0:1.3 0/1:234:58:29,29:82,94:176,58:0.2479:2,2:22.6:1:29:1:0.76192:1.15:60:116:0.2479:0:1.1 +4 28204197 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53038;SOR=0;LSEQ=ATTTTAAGTGAGTTTATGAA;RSEQ=GGTTCTGATATGCATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:20,88:108,2:0.0182:2,2:16.5:1:30.5:1:0.34679:4.32:60:4:0.0183:0:1 0/0:65:0:0,0:11,54:65,0:0:2,0:23.3:1:30.1:1:1:0:60:130:1:0:0.1 +4 28310225 . G A 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGACAGAAAGAGAAGGAA;RSEQ=GAGAGAGATGGAAGTAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:33:1:1:0:43:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 28400060 . A G 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AATACATGCTTCTGTTTCTC;RSEQ=AGTGTGAAAAATCTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:13.6:1:31.2:1:1:0:57.8:10:1:0:2.4 0/0:1:0:0,0:1,0:1,0:0:0,0:40:0:27:0:1:0:60:2:1:0:0 +4 28400087 . C A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATCTGTTTCTGGTTAT;RSEQ=CCATGTCTAGTATTTATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:26.8:1:30:0:1:0:57.3:8:0.5:0:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:13:0:25:0:1:0:60:2:1:0:0 +4 28400119 . C T 103 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09341;SOR=0.07274;LSEQ=ATTTATGATTGTTTGCTATA;RSEQ=TGTAAGATGTTTGGATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:10,0:1,0:1,10:0.9091:0,0:31.6:1:31.3:1:1:0:58.9:20:0.9091:0:1.9 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:18:0:32:0:1:0:60:2:0.3333:0:1 +4 28400261 . G T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59335;LSEQ=TAATTTTTTGCCTAGTTATA;RSEQ=TCTGTAACTCCTACTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:129,25:154,2:0.0128:2,2:21:1:30:1:0.30645:5.07951:60:4:0.013:0:1 0/0:131:1:0,1:111,19:130,1:0.0076:2,0:1:0:24:0:0.15267:0:60:2:0.008:0:1 +4 28400383 . T C 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0.59738;LSEQ=TACTGAAATATTTCCCAGAA;RSEQ=TGAGCAACCTCTGAAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:484:244:108,136:112,127:239,244:0.5041:2,2:27.4:1:32.8:1:0.5844:1.11029:60:243:0.5052:0:1.1 0/1:458:173:76,97:126,159:285,173:0.3777:2,2:25.3:1:31.1:1:1:1.0114:60:56.667:0.3803:0:1.1 +4 28400454 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18644;SOR=Inf;LSEQ=CAGGCCTTAAAGTCTCACCT;RSEQ=GAGCATGCATAGCCTTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:55,172:227,0:0:2,0:23.4:1:30.7:1:1:0:60:112.5:1:0:0.5 0/1:173:2:1,1:46,124:170,2:0.0116:2,2:32:1:30.5:1:0.473:2.68:60:4:0.0116:0:1.5 +4 28400468 . C T 158 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCACCTTGAGCATGCATAGC;RSEQ=TTGTCCTCATCATCCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:33:7,26:20,122:142,33:0.1886:2,2:22.8:1:31.5:1:0.29599:1.64:60:66:0.1897:0:1.1 0/0:139:0:0,0:30,109:139,0:0:2,0:21.7:1:31.5:1:1:0:60:278:1:0:0.2 +4 28401647 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGATCGAGACCATCCTG;RSEQ=CTAACATAGTGAAGCCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:27.5:1:1:0:60:4:1:0:1 +4 28745882 . A G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10008;SOR=0.30822;LSEQ=TGTTCCCACAAGAAAAACGG;RSEQ=TATGGCATAGGTTTGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:25:24,1:6,0:6,25:0.8065:0,1:19.6:1:31.5:1:1:0:60:50:0.8333:0:1 1/0:18:10:10,0:7,1:8,10:0.5556:2,0:21.9:1:29.2:1:0.44444:0:60:9:0.5294:0:1.1 +4 28745978 . AT A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.16741;SOR=Inf;LSEQ=CGTTTGAGGTTTTGCATATC;RSEQ=TTTCTGTCCTTTCTGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:144,43:187,0:0:2,0:24.2:1:30.9:1:1:0:60:45.75:1:0:0.1 0/1:130:2:1,1:104,24:128,2:0.0154:2,2:13:0:32:0:0.34884:4.26615:60:4:0.0155:0:0.5 +4 28746092 . C A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.41173;LSEQ=TTTCCATCCTGCTTAGCTAC;RSEQ=ACCAAAGTAAACCTGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:476:359:158,201:55,62:117,359:0.7542:2,2:26.6:1:30.5:1:0.59352:1.12823:60:118.667:0.7591:0:1.1 1/0:466:260:130,130:102,104:206,260:0.5579:2,2:26:1:29.3:1:0.92595:1.02:60:129:0.5584:0:1.1 +4 28746179 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23643;SOR=0;LSEQ=TATATATTTATCCTATATCT;RSEQ=TATCTCTGGTTAGTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:46,138:184,2:0.0108:2,2:28.5:1:28:1:0.44255:2.98:60:4:0.0109:0:1 0/0:196:0:0,0:48,148:196,0:0:2,0:24.5:1:31.5:1:1:0:60:64.333:1:0:0.7 +4 28746194 . GT G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.22344;SOR=0;LSEQ=TATCTGTATCTCTGGTTAGT;RSEQ=TTTTTTGTGTACTGTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:0,2:25,99:124,2:0.0159:2,0:47.5:1:32:0:1:0:60:4:0.0167:0:1 0/0:140:0:0,0:31,109:140,0:0:2,0:21.7:1:29.6:1:1:0:60:280:1:0:0.9 +4 28746210 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.07305;SOR=1.84612;LSEQ=TAGTGTTTTTTTGTGTACTG;RSEQ=TTATGTGTGGCTTTTAATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:72:13,59:5,27:32,72:0.6923:2,2:21.2:1:33.2:1:1:1.19:59.7:144:0.6923:0:2 1/1:93:75:9,66:4,14:18,75:0.8065:2,2:20.2:1:32.1:1:0.26951:2.0759:60:150:0.8152:0:1.7 +4 28746238 . T G 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.03565;LSEQ=TGGCTTTTAATCGCCCTTTA;RSEQ=AATTAGGTCTTCTTGTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:37:1,36:0,20:20,37:0.6491:1,1:20.1:1:32.5:1:1:0:59.4:74:0.6491:0:3 1/0:35:23:0,23:0,12:12,23:0.6571:0,1:20.7:1:31.4:1:1:0:60:46:0.6571:0:3 +4 28746246 . T A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31489;SOR=1.84721;LSEQ=AATCGCCCTTTATAATTAGG;RSEQ=CTTCTTGTCTAGGCAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:30:0,30:0,17:17,30:0.6383:1,1:21.1:1:29.7:1:1:0:59.6:60:0.6522:0:3.2 1/0:30:23:0,23:0,7:7,23:0.7667:0,1:20.8:1:29.6:1:1:0:60:46:0.7667:0:3.1 +4 28746281 . T A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50544;SOR=0.57988;LSEQ=AGAATACTCTCAGTTGGGCC;RSEQ=AATCCAGTTCTTTAGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:0,16:0,8:8,16:0.6667:0,1:27.9:1:30.8:1:1:0:60:15:0.6522:0:3.2 1/0:15:8:0,8:0,7:7,8:0.5333:0,0:25.4:1:30.6:1:1:0:60:16:0.5333:0:3.6 +4 28746368 . A T 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTTTAAGTTCTGGGATAC;RSEQ=TGTGCAGAACATGCAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:24.3:1:31.7:1:1:0:37:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 28747068 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAGACTTTTAGGAAGAG;RSEQ=TTGTAGATAACAAGAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:31:0:1:0:60:4:1:0:1.5 +4 29722826 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14687;SOR=Inf;LSEQ=GAGTTTGTAATATCTTACAA;RSEQ=GTGATTTCTTTCTGTACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:70,0:70,0:0:1,0:25.7:1:32.4:1:1:0:59.4:140:1:0:0.1 0/1:44:2:2,0:41,1:42,2:0.0455:1,0:23:1:32:0:1:0:60:4:0.0455:0:1 +4 29722943 . G T 165 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=27.32536;LSEQ=AGCATATGGGAAAGTGAAGA;RSEQ=TTCCCAGGGTCCCTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:2:1,1:197,181:378,2:0.0053:2,2:20.5:1:30.5:1:1:1.08814:60:4:0.0053:0:2.5 0/1:387:49:30,19:188,150:338,49:0.1266:2,2:27.7:1:29.4:1:0.53834:1.26:60:48:0.1253:0:1.6 +4 29722997 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71194;SOR=1.05678;LSEQ=CTCCATATTTATTTAAGTTT;RSEQ=TATAAATCAATAAGCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:165:66,99:74,104:178,165:0.481:2,2:25:1:32.4:1:0.82612:1.06709:60:81.5:0.4808:0:1.1 0/1:390:193:91,102:93,100:193,193:0.4949:2,2:24.1:1:31:1:0.91885:1.04233:60:192:0.4936:0:1.2 +4 29723320 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATAGATTTCTATGCAAC;RSEQ=ATAGTAACAGAGAAACTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:14:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 34488836 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15103;SOR=0;LSEQ=TGCTGCTGCTGCTTCTTCTG;RSEQ=TGTTGCTGACTCTGGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:17,26:43,2:0.0444:2,2:18.5:1:30.5:1:1:1.51:60:4:0.0455:0:1 0/0:70:0:0,0:32,38:70,0:0:2,0:30.2:1:31.1:1:1:0:60:22.333:1:0:0.2 +4 34488861 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13455;SOR=0;LSEQ=GCTGACTCTGGTGGCCATGG;RSEQ=TGTGCCTCAAGAGGAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:12,23:35,2:0.0541:2,2:32:1:30.5:1:1:1.88:60:4:0.0541:0:1 0/0:63:0:0,0:26,37:63,0:0:2,0:23.5:1:28.5:1:1:0:60:62:1:0:0.2 +4 35860893 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCTGATTGGTGCGGTTT;RSEQ=TAGAGCACTGATTGGTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29.5:1:1:0:60:4:1:0:1 +4 35861432 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01003;SOR=0;LSEQ=AGAAGCCATGTCACCCAACT;RSEQ=TAGAGGTTGGTATAAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:3,1:13,10:23,4:0.1481:2,2:26.8:1:30.3:1:0.62393:2.24:41.5:8:0.1481:0:1 0/0:55:0:0,0:31,24:55,0:0:2,0:32.7:1:30.7:1:1:0:41.5:54:1:0:0.1 +4 35861468 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54648;SOR=Inf;LSEQ=GAGTTTGAAAGGCATTGTCT;RSEQ=ATTTCAGAAGCCTTTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:23,0:0:2,0:17.2:1:32:1:1:0:41.9:46:1:0:0.3 0/1:49:3:2,1:21,25:46,3:0.0612:2,2:15:1:24.3:1:0.59428:2.34:51.3:6:0.0612:0:1.3 +4 35861516 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=CGGGTGGCATCTCATACTAT;RSEQ=CCTGACTGGTTAGGAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:2,8:10,0:0:2,0:24.9:1:32.2:1:1:0:39.4:20:1:0:0.1 0/1:16:2:0,2:3,11:14,2:0.125:2,0:22.5:1:30:0:1:0:44:4:0.125:0:1.5 +4 37310266 . GT G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCCCTGGGCAGCAGGGTA;RSEQ=TCTTAGGCCCCTTGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29.1:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 37822911 . TA T 53 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.21564;SOR=0.31637;LSEQ=AAACACCCAAGAATGATCAA;RSEQ=AAAAAAAAAAGAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:4:3,1:20,15:35,4:0.1026:2,2:6.8:1:26.8:1:0.63089:2.21:60:3:0.0968:0.0513:0.5 0/1:58:2:1,1:32,24:56,2:0.0345:2,2:16.5:1:32:0:1:1.32664:60:4:0.0351:0:0.5 +4 37822922 . AG GA 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15071;SOR=0;LSEQ=AATGATCAATAAAAAAAAAA;RSEQ=AAAAAAAAAAAAGATTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:2,0:28,18:46,2:0.04:2,0:29.5:1:33.8:1:0.52128:0:60:4:0.0426:0:1 0/0:78:0:0,0:40,37:77,0:0:2,0:18.5:1:29.3:1:1:0:55.6:154:0.9872:0:0.8 +4 37822923 . G A 72 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=12.000;MSILEN=1;SSF=0.00032;SOR=0;LSEQ=ATGATCAATAAAAAAAAAAA;RSEQ=AAAAAAAAAAAAGATTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:8:1,7:24,10:34,8:0.1538:2,2:13.1:1:24.1:1:0.00433:15.63485:59.5:3:0.1622:0:1.3 0/0:84:0:0,0:34,33:67,0:0:2,0:12:0:10:0:1:0:58:0:0:0:1 +4 37823011 . G T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01675;SOR=Inf;LSEQ=CACAAAGGGAAAGAGGAGAG;RSEQ=CACCCGATATATGTTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:31,21:52,0:0:2,0:19.6:1:31.3:1:1:0:41.7:104:1:0:0.2 0/1:109:11:4,7:50,48:98,11:0.1009:2,2:19.5:1:28.2:1:0.52691:1.81305:40:22:0.1048:0:1.1 +4 37823017 . G T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05017;SOR=Inf;LSEQ=GGGAAAGAGGAGAGGCACCC;RSEQ=ATATATGTTCTCCAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:25,18:43,0:0:2,0:17.3:1:30.6:1:1:0:37.7:86:1:0:0.1 0/1:83:8:4,4:37,38:75,8:0.0964:2,2:20.8:1:29:1:1:1.03:48.3:16:0.0988:0:1.1 +4 37823139 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53177;SOR=Inf;LSEQ=GTACTGTTCGAAAAGGAATG;RSEQ=CCCGCAAGTGTTACCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:66,52:118,0:0:2,0:23.9:1:31.8:1:1:0:42.3:38.333:1:0:0.1 0/1:200:2:1,1:108,90:198,2:0.01:2,2:22.5:1:26.5:1:1:1.1989:43.5:4:0.0102:0:1 +4 37823185 . C T 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01243;SOR=Inf;LSEQ=TGGAGGAGTCTACAGTGTTA;RSEQ=CCAGCATGCTGTTGGCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:73,91:164,0:0:2,0:29.6:1:31.5:1:1:0:39.3:40:1:0:0.1 0/1:238:9:3,6:106,123:229,9:0.0378:2,2:31.9:1:28.2:1:0.5137:1.71979:36.4:8:0.0343:0:1.1 +4 37823221 . G A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14069;SOR=Inf;LSEQ=CATTGTTGTAAACAAACAAG;RSEQ=ACAAGATTCTTGCCAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:42,71:113,0:0:2,0:21.4:1:31.5:1:1:0:32.2:55.5:1:0:0.1 0/1:155:4:2,2:56,95:151,4:0.0258:2,2:32:1:30.3:1:0.63028:1.69:32.5:8:0.026:0:1.3 +4 38912621 . G A 55 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTTAACAGGACCACTCT;RSEQ=GTTCCTGGGTAGAAAATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:27.3:1:27.8:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 38912816 . C T 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17994;SOR=0.43995;LSEQ=GAACCATTAGACCAGGATGC;RSEQ=GGTCCCACCCCAGTGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:3,8:10,16:26,11:0.2973:2,2:28.7:1:30.5:1:0.71057:1.64446:60:22:0.2973:0:1.4 0/1:45:7:3,4:17,21:38,7:0.1556:2,2:17.6:1:30.3:1:1:1.07757:60:14:0.1628:0:1.4 +4 38912824 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50786;SOR=Inf;LSEQ=AGACCAGGATGCCGGTCCCA;RSEQ=CCCAGTGAAGAGAAGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:11,20:31,0:0:2,0:23.4:1:31.3:1:1:0:60:30:0.9677:0:0.6 0/1:45:2:1,1:19,24:43,2:0.0444:2,2:28:1:26:1:1:1.26:60:4:0.0455:0:1 +4 38912884 . A C 43 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTCCCAGACTGCAGTGCGGC;RSEQ=TGGGAAAGGCTGGGCGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:18:1:33:1:1:0:60:6:0.2727:0:1.7 0/1:11:3:1,2:0,8:8,3:0.2727:0,2:18:1:27.7:1:0.27273:0:60:6:0.2727:0:1.3 +4 38928641 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.59985;SOR=1.36115;LSEQ=TCTCTGCCTCCTCCCTGCGC;RSEQ=CACCTGCCTCACTCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:5,4:9,4:13,9:0.4091:2,2:26.4:1:31.4:1:0.66192:1.75137:60:18:0.4091:0:1.4 0/1:37:18:10,8:9,10:19,18:0.4865:2,2:25.7:1:30.2:1:0.74585:1.38:60:36:0.4865:0:1.2 +4 39351868 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAACAAGGCTCAATGATC;RSEQ=GTGAGACAATATCAAAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:21.5:1:32.5:1:1:0:60:4:0.4:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:42:0:28:0:1:0:60:2:1:0:0 +4 39352061 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53688;SOR=Inf;LSEQ=AGAAAACCACACTCAGGTAA;RSEQ=CCATAGTCAAACTGCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:39,33:72,0:0:2,0:30.1:1:32.7:1:1:0:59.9:144:1:0:0.2 0/1:128:2:1,1:68,58:126,2:0.0156:2,2:16.5:1:32.5:1:1:1.17095:60:4:0.0159:0:1 +4 39352073 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54687;SOR=Inf;LSEQ=TCAGGTAAGCCATAGTCAAA;RSEQ=TGCTGAAAACCAAAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:33,36:69,0:0:2,0:27.9:1:32.5:1:1:0:59.9:68:1:0:0.2 0/1:132:2:1,1:61,69:130,2:0.0152:2,2:18:0:32:1:1:1.13:57.5:4:0.0152:0:1 +4 39352099 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54819;SOR=Inf;LSEQ=AAAACCAAAAATTAAAAAAT;RSEQ=CTTTAATGAACCATGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:20,31:51,0:0:2,0:22.2:1:30.4:1:1:0:60:102:1:0:0.2 0/1:99:2:1,1:36,61:97,2:0.0202:2,2:16:0:32.5:1:1:1.68:55.5:4:0.0206:0:1 +4 39933884 . G A 32 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.55247;LSEQ=GGCCTGATAAGCATTTGTAC;RSEQ=TTGAGATTGCAATGCCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:20:1:32:0:1:0:60:4:0.5:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:4:0:29:0:1:0:60:2:0.3333:0:1 +4 39934071 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.51782;SOR=Inf;LSEQ=CAAAGTAGAGCTTCATAAAT;RSEQ=CACACAACCAAGGGGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:82,51:133,0:0:2,0:25.3:1:28.3:1:1:0:60:43.333:1:0:0.1 0/1:198:2:1,1:114,82:196,2:0.0101:2,2:31:1:31:1:1:1.38787:60:4:0.0103:0:1 +4 39934080 . C G 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTCATAAATACACACAAC;RSEQ=AAGGGGAGAAAACCTGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:91,68:159,0:0:2,0:25:1:31.1:1:1:0:59.7:38.75:0.9936:0:0.1 0/1:224:27:15,12:107,90:197,27:0.1205:2,2:21.3:1:29.2:1:1:1.05:59.8:54:0.125:0:1.1 +4 39934103 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15677;SOR=0;LSEQ=GGGGAGAAAACCTGTGGTGG;RSEQ=TGTGAAGGTCCTGATGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:89,95:184,2:0.0108:2,2:24:0:31.5:1:1:1.07:60:4:0.0109:0:2 0/0:283:0:0,0:134,148:282,0:0:2,0:28.5:1:31.3:1:1:0:59.4:55.4:1:0:0.3 +4 41332071 . CT C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCCTTGATTACCCACCC;RSEQ=TTTTTTTTTAGCTGAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 41333410 . C T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03371;SOR=0.59167;LSEQ=GGCAACTAAAGTTCTGCAGA;RSEQ=TTGTAAATAAATTATATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:50:33,17:105,67:172,50:0.2252:2,2:24.4:1:30.4:1:0.61989:1.24:60:24:0.2192:0:2.7 0/1:266:39:23,16:140,87:227,39:0.1466:2,2:23.2:1:29.1:1:0.85898:1.11896:60:38:0.1456:0:2.6 +4 41333429 . T G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00073;SOR=0.48748;LSEQ=ACTTGTAAATAAATTATATC;RSEQ=AACTGTACATAACCTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:67:45,22:102,84:186,67:0.2648:2,2:24.6:1:29.9:1:0.08505:1.68:59.9:21.333:0.2602:0:2.6 0/1:315:47:25,22:150,118:268,47:0.1492:2,2:25.6:1:29.4:1:0.75206:1.11824:60:46:0.1465:0:2.6 +4 41333444 . T C 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATCTAACTGTACATAACC;RSEQ=GGGTTACATTCTTGAGCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:155,131:286,0:0:2,0:26.2:1:31.1:1:1:0:59.9:46.667:1:0:0.9 0/1:363:40:23,17:169,154:323,40:0.1102:2,2:22.3:1:29.8:1:0.61555:1.23:60:80:0.1127:0:1.9 +4 41333461 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.39667;SOR=0.87125;LSEQ=ACCTGGGTTACATTCTTGAG;RSEQ=GAATCATATCAACATTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:301:153:76,77:75,73:148,153:0.5083:2,2:26.9:1:30.2:1:0.90838:1.0408:59.8:152:0.5067:0:1.7 0/1:382:181:87,94:97,103:200,181:0.4738:2,2:26.4:1:29:1:1:1.01748:60:180:0.4737:0:1.6 +4 41333541 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49884;SOR=Inf;LSEQ=GTTAAACAGTTTATTCTTCC;RSEQ=TCATACCAAGTTCCTTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:28,106:134,0:0:2,0:23.7:1:30.4:1:1:0:60:133:1:0:0.2 0/1:144:2:1,1:43,99:142,2:0.0139:2,2:10.5:1:29:1:0.51923:2.29:60:4:0.0144:0:0.5 +4 41333562 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49727;SOR=0;LSEQ=TTCATACCAAGTTCCTTAGG;RSEQ=ATTTGGATTCACCCTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:11,78:89,2:0.022:2,2:22:0:32.5:1:0.24762:6.83:60:4:0.0227:0:1.5 0/0:89:0:0,0:20,69:89,0:0:2,0:20.6:1:31:1:1:0:60:88:1:0:0.1 +4 41333674 . C G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=AGAACTTGCTATAAAAGCAT;RSEQ=TTAATCTTTTGTTAACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:8,2:0.2:0,0:30:1:33:1:1:0:60:4:0.2:0:1 0/0:8:0:0,0:0,8:8,0:0:0,0:23.6:1:33.3:1:1:0:60:16:1:0:0 +4 41746460 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACGTAGAGGAGACAGTCTG;RSEQ=ACTGATATTAACACGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:18.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 41746862 . GA G 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.57655;SOR=2.72824;LSEQ=GGGTAGGCGGGAGCGAGGGG;RSEQ=AAAAAAGAGTTGCGAAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:1:1,0:173,9:182,1:0.0055:1,0:23:0:33:0:1:0:60:2:0.0056:0:0 0/1:135:2:2,0:126,6:132,2:0.0148:1,0:36:1:30.5:1:1:0:60:4:0.0149:0:0 +4 41747149 . T TA 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54613;SOR=0.88208;LSEQ=GGGGGCTGGAACGGCGTCCC;RSEQ=ACTCTTCCCTGAAGAAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:54:21,33:158,320:478,54:0.1015:2,2:27.9:1:30.3:1:0.44759:1.29:60:53:0.1004:0.0113:0.1 0/1:607:55:20,35:193,354:547,55:0.0906:2,2:21.8:1:28.8:1:0.8831:1.05:59.8:26.5:0.0891:0.0297:0.2 +4 41747225 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53647;SOR=0;LSEQ=TTAGGGGTTCACAAGATCGA;RSEQ=CCTTCAGCTCCAGCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:0,2:2,141:143,2:0.0138:1,0:39.5:1:32:0:1:0:60:4:0.0143:0:1 0/0:82:0:0,0:3,79:82,0:0:1,0:25.5:1:31.5:1:1:0:59.5:40:1:0:0.1 +4 41747663 . C T 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGAAATGAGGGCGACGC;RSEQ=GTTTTCCCTTTATTCTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:6,3:9,2:0.1818:2,0:12:0:34:0:1:0:60:4:0.1818:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:31:1:23:1:1:0:60:3:1:0:0 +4 41747691 . C G 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06291;SOR=0;LSEQ=CTTTATTCTTAGCGCGATTA;RSEQ=TTTAGGCCCTCAATGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:13,2:15,5:0.25:2,2:8.2:1:32.8:1:1:1.58265:60:10:0.25:0:1.2 0/0:14:0:0,0:13,1:14,0:0:1,0:19.7:1:29.8:1:1:0:60:13:1:0:0 +4 41747763 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21453;SOR=Inf;LSEQ=GCCTACCCGCTCGCCCACTC;RSEQ=CCCGCCCGGGCCCTGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:97,15:112,0:0:2,0:19.1:1:30.3:1:1:0:60:111:1:0:0.2 0/1:98:2:1,1:82,14:96,2:0.0204:2,2:34:1:29:1:0.28403:5.69299:60:4:0.0208:0:1 +4 41747779 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49856;SOR=0;LSEQ=ACTCGCCCGCCCGGGCCCTG;RSEQ=CTCGCCCGCTGTCGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:144,25:169,2:0.0117:2,2:26.5:1:30:1:0.28173:5.66778:60:4:0.012:0:1 0/0:168:0:0,0:135,32:167,0:0:2,0:18.7:1:30.7:1:1:0:59.9:82.5:0.994:0:0.2 +4 41747783 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23628;SOR=0;LSEQ=GCCCGCCCGGGCCCTGGCTC;RSEQ=CCCGCTGTCGCCGCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:155,27:182,2:0.0109:2,2:34:1:31:1:0.2819:5.65551:60:4:0.011:0:1.5 0/0:194:0:0,0:155,39:194,0:0:2,0:19.3:1:29.6:1:1:0:59.9:37.8:1:0:0.2 +4 41747786 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21378;SOR=0;LSEQ=CGCCCGGGCCCTGGCTCGCC;RSEQ=GCTGTCGCCGCCGCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:2,0:162,30:192,2:0.0103:2,0:12:1:29:1:1:0:60:4:0.0105:0:1.5 0/0:225:0:0,0:168,56:224,0:0:2,0:19.1:1:30.2:1:1:0:59.9:73.667:0.9955:0:0.3 +4 41747791 . TCGC T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.31485;SOR=0.63652;LSEQ=GGGCCCTGGCTCGCCCGCTG;RSEQ=CGCCGCCGCCGCCGCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:15:10,5:173,49:222,15:0.0633:2,2:23.3:1:32.1:1:0.34189:1.7605:60:30:0.0647:0.0042:0.1 0/1:267:11:6,5:183,68:251,11:0.0412:2,2:22.2:1:30.2:1:0.1864:2.23481:60:22:0.042:0.0075:0.3 +4 41747797 . C T 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=3;SSF=0.67396;SOR=0.60922;LSEQ=TGGCTCGCCCGCTGTCGCCG;RSEQ=CGCCGCCGCCGCCGCAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:2,1:205,68:273,3:0.0109:2,2:16:1:29:1:1:1.5049:60:6:0.011:0:1 0/0:301:2:0,2:212,84:296,2:0.0066:2,0:1:1:26:1:0.08259:0:60:6:0.0055:0:1 +4 41748117 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=3.000;MSILEN=1;SSF=0.67105;SOR=0.59522;LSEQ=CGGAGCTCCAGCCGGGCTGG;RSEQ=CCCGCCGCCGCCGCCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:2,1:207,48:255,3:0.0116:2,2:17.3:1:29.7:1:0.46986:2.14839:60:6:0.0117:0:1 0/0:289:2:1,1:214,72:286,2:0.0069:2,2:10:0:31:1:0.44336:2.95862:60:4:0.0072:0:1.5 +4 41748118 . CCCG C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.78086;SOR=0.77091;LSEQ=GGAGCTCCAGCCGGGCTGGG;RSEQ=CCGCCGCCGCCTCCATTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:7:4,3:215,52:267,7:0.0255:2,2:29.3:1:32.1:1:0.14673:3.08421:60:14:0.0257:0.0036:0.1 0/1:303:6:5,1:219,78:297,6:0.0198:2,2:28.2:1:31.5:1:1:1.78:59.2:12:0.0202:0.0033:0.7 +4 41748217 . G A 198 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03018;LSEQ=TCAGTGCTCTTGGCCTCTTT;RSEQ=CTCTCGTCGTCCCTGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1221:118:60,58:606,497:1103,118:0.0966:2,2:25.4:1:28.8:1:0.43672:1.17851:60:38.333:0.0961:0:1.1 0/0:1555:5:5,0:844,704:1548,5:0.0032:2,0:1:0:23.8:1:0.06756:0:60:10:0.0033:0:1 +4 41748511 . T G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09684;SOR=0.19567;LSEQ=CCAAGTCTACCGCTTCTTAT;RSEQ=GCTGTGCATTTTCGGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:0,6:6,11:0.6471:0,0:22.5:1:32.6:1:1:0:60:22:0.6471:0:1.3 0/1:8:2:0,2:0,6:6,2:0.25:0,0:8.5:1:30:1:1:0:60:4:0.25:0:1 +4 41749265 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.61971;SOR=0.71005;LSEQ=CATGGGGCCCTAGGTCCTTC;RSEQ=CACTCGAGGCTCCAGGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:12:11,1:27,1:28,12:0.3:1,2:28.8:1:32.4:1:0.51538:2.39319:60:24:0.3077:0:1 0/1:43:10:9,1:31,2:33,10:0.2326:2,2:11.5:1:30.9:1:0.5579:1.69793:60:20:0.2326:0:1.1 +4 41749576 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20868;SOR=0;LSEQ=AGAGTATGACAGAGGAGACA;RSEQ=AAAGTGAGCAAATCAGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:48,133:181,2:0.0109:2,2:25:1:30:0:0.4649:2.75:60:4:0.011:0:2 0/0:217:0:0,0:64,152:216,0:0:2,0:23.8:1:30.6:1:1:0:60:71:0.9953:0:0.2 +4 41749584 . G T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=ACAGAGGAGACAGAAAGTGA;RSEQ=CAAATCAGCCGGCAGCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:40,127:167,0:0:2,0:22.2:1:32.7:1:1:0:60:334:1:0:0.1 0/1:175:2:1,1:48,124:172,2:0.0114:2,2:29:0:28.5:1:0.48508:2.57:60:4:0.0116:0:1 +4 41749668 . C T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.76104;SOR=1.2444;LSEQ=CGGCAGCCGCTACCTACACC;RSEQ=GCGCGAGAGAGTTGCCGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:16:2,14:0,20:20,16:0.4444:1,2:22.6:1:31.4:1:0.19048:0:60:32:0.4444:0:1 1/0:14:7:0,7:0,7:7,7:0.5:0,0:28.9:1:27.7:1:1:0:60:6:0.4615:0:1 +4 41750650 . G A 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03481;SOR=7.38839;LSEQ=AAAAGGTTCTGGATGGCTCA;RSEQ=CCAAGTGGAAAAATGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:1:1,0:128,219:347,1:0.0029:2,0:32:0:15:0:0.37069:0:60:0:0:0:3 0/1:335:7:5,2:120,208:328,7:0.0209:2,2:25.7:1:27.9:1:0.10705:4.31:60:14:0.0211:0:1 +4 41753130 . A C 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCTCTGCTGTAGGGTTTA;RSEQ=GCGCGTTTCCCTGCAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:0:0,0:197,405:602,0:0:2,0:24.5:1:31.2:1:1:0:60:59.2:1:0:0.1 0/1:813:63:26,37:292,456:748,63:0.0775:2,2:24.4:1:30.1:1:0.78844:1.10:60:62:0.0772:0:1.1 +4 46047034 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACGTATGAAAGTAAAAT;RSEQ=CGATGGTTGCAAACTTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:34.5:1:30:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 46047311 . T G 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00641;SOR=Inf;LSEQ=TCATAAAGTTATTGTAAATT;RSEQ=TTAATAAGCTAAAAGTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:84,28:112,0:0:2,0:24.4:1:30.6:1:1:0:60:36.333:1:0:0.1 0/1:163:10:7,3:105,48:153,10:0.0613:2,2:14.7:1:31.2:1:1:1.07:60:20:0.0625:0:1 +4 46047406 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.65426;SOR=0.91472;LSEQ=TAAAAGGAAAATCTGGAATA;RSEQ=ATGCTGAACCTAAGAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:113:48,65:47,63:110,113:0.5045:2,2:26.7:1:32.2:1:1:1.01021:60:112:0.5045:0:1.1 0/1:280:135:68,67:62,83:145,135:0.4821:2,2:27:1:31.5:1:0.23087:1.36:59.8:134:0.482:0:1.1 +4 46047625 . GA G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0.37796;LSEQ=TGGAAAGTTTCTTAAGAAAA;RSEQ=AAAAAAGTTTTATCTGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:15.8:1:33.7:1:1:0:60:12:0.8571:0:0.3 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:32.5:1:33:0:1:0:60:4:0.6667:0:0 +4 46477824 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19026;SOR=0;LSEQ=CACCAACCCCCTACCCTGAT;RSEQ=CTTGGCTACAAATCCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:35,37:72,2:0.027:2,2:14:1:27.5:1:1:1.06:60:4:0.0282:0:1 0/0:95:0:0,0:50,45:95,0:0:2,0:28.6:1:30.4:1:1:0:59.5:190:1:0:0.2 +4 46725771 . TG T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03146;SOR=Inf;LSEQ=GGCTCCACCGTTTTTTTTCT;RSEQ=GTTTTTTTTTTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:35,0:35,0:0:1,0:26.9:1:31.8:1:1:0:34.3:34:1:0:1.2 0/1:27:4:4,0:23,0:23,4:0.1481:1,0:31.3:1:32.8:1:1:0:31.5:8:0.1481:0:2 +4 46725906 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50051;SOR=Inf;LSEQ=AGGCGGGCAGAGGACTGCTC;RSEQ=GATCGCTTCGTCAAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:44,23:67,0:0:2,0:14.5:1:30.5:1:1:0:49.7:32.5:1:0:0.3 0/1:80:2:1,1:44,34:78,2:0.025:2,2:10.5:1:29.5:1:1:1.2899:60:4:0.025:0:1.5 +4 46725949 . C T 109 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00085;SOR=14.13936;LSEQ=TTGATGCCTCGCTGTGTGAG;RSEQ=GCCGAGCGCTCCAGGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:1:1,0:131,93:224,1:0.0044:2,0:20:0:32:0:1:0:59:2:0.0046:0:1 0/1:235:14:8,6:129,92:221,14:0.0596:2,2:25.1:1:28.7:1:1:1.05138:42.7:28:0.0603:0:1.1 +4 46726006 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0565;SOR=Inf;LSEQ=TTAGCCATGGCTAGACCCTG;RSEQ=GGATAGGTGATGGGAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:151,106:257,0:0:2,0:30.1:1:31.3:1:1:0:44.9:127.5:1:0:0.1 0/1:246:4:1,3:152,90:242,4:0.0163:2,2:38.3:1:30.8:1:0.15295:5.03336:33.8:8:0.0165:0:1.5 +4 46726021 . A G 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61083;SOR=2.15888;LSEQ=CCCTGCGGATAGGTGATGGG;RSEQ=GTCAGCTTCTTCTCCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:1:1,0:113,86:199,1:0.005:2,0:10:0:13:0:1:0:60:0:0:0:1 0/1:186:2:1,1:111,73:184,2:0.0108:2,2:27.5:1:30:1:1:1.51698:22.5:4:0.0109:0:1.5 +4 46726024 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23211;SOR=Inf;LSEQ=TGCGGATAGGTGATGGGAGT;RSEQ=AGCTTCTTCTCCTTCAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:112,80:192,0:0:2,0:23.2:1:31.7:1:1:0:40.1:63:1:0:0.1 0/1:179:2:1,1:108,69:177,2:0.0112:2,2:11:1:29:1:1:1.56112:52.5:4:0.0114:0:1 +4 46726267 . C T 149 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCAGCTGTATCCCATAAGCC;RSEQ=AGATTCACCGGTTTTCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:31:14,17:71,94:165,31:0.1582:2,2:20.2:1:30.2:1:0.8456:1.09:28.1:62:0.159:0:1 0/0:204:0:0,0:105,99:204,0:0:2,0:11:0:17:0:1:0:32:0:0:0:2 +4 46726302 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24436;SOR=Inf;LSEQ=TCCATCTACCATAACATTGG;RSEQ=AGAATAATTGTCAAAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:56,100:156,0:0:2,0:28.1:1:32.1:1:1:0:24.7:30.2:1:0:0.2 0/1:153:2:1,1:63,88:151,2:0.0131:2,2:37.5:1:29:1:1:1.39:30.5:4:0.0131:0:1 +4 46726431 . C A 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25428;SOR=Inf;LSEQ=CTTGATGGCCTGCATCAGGG;RSEQ=CGCTCGCTGGGCCGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:62,172:234,0:0:2,0:23.1:1:31.7:1:1:0:30.4:45.8:0.9957:0:0.2 0/1:280:3:2,1:96,181:277,3:0.0107:2,2:32:1:24.7:1:0.28101:3.75:28:2:0.0073:0:1 +4 46726444 . CGCG C 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.76031;SOR=1.43972;LSEQ=ATCAGGGCCGCTCGCTGGGC;RSEQ=GCGGCGGCGGCAGGGCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:4:1,3:32,122:154,4:0.0253:2,2:24.5:1:31.3:1:1:1.27:30.5:8:0.0263:0.0063:0.3 0/1:194:7:5,2:53,132:185,7:0.0361:2,2:11.3:1:28:1:0.02725:6.16:35.3:14:0.0372:0.0155:0.4 +4 47493210 . C G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00116;SOR=0.22596;LSEQ=TGCTTAATGTGCTCAATATG;RSEQ=ACATTAATTCTCTTGGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:21:19,2:28,3:31,21:0.4038:2,2:29.9:1:30.8:1:1:1.02:47.7:9.5:0.3958:0:1 0/1:61:8:7,1:50,3:53,8:0.1311:2,2:22.6:1:31:1:0.43888:2.33716:46.9:16:0.1311:0:1.1 +4 47493308 . G GTAACAC 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=2.000;MSILEN=2;SSF=0;SOR=0.26997;LSEQ=ACTCTTCCAGTTTTGCCATG;RSEQ=TAACACTGGTGGGGCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:52:24,28:54,60:114,52:0.3133:2,2:29:1:31.1:1:1:1.04972:48.6:51:0.3168:0.0422:0.1 0/1:247:27:14,13:102,118:220,27:0.1093:2,2:28:1:29:1:0.6841:1.24:47.2:54:0.1107:0.0162:0.1 +4 47493401 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50239;SOR=Inf;LSEQ=ATTCACAGGTATGTGGCCAA;RSEQ=GGAACAACTCCATGTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:76,22:98,0:0:2,0:23.9:1:31.4:1:1:0:48.9:196:1:0:0.2 0/1:119:2:1,1:80,37:117,2:0.0168:2,2:9:1:28.5:1:0.53853:2.14686:54:4:0.0172:0:1 +4 47493437 . C T 40 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.36762;LSEQ=TTTCTAAAAGGCCTAGAGAA;RSEQ=ATGTATGGGGTGCCGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:2:0,2:141,67:208,2:0.0095:2,0:1:0:22.5:1:0.1069:0:54:4:0.0098:0:1 0/1:308:4:1,3:196,108:304,4:0.013:2,2:8.3:1:20.3:1:0.13513:5.414:47.8:3:0.01:0:1.5 +4 48087855 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCTCCCCATGCATCCC;RSEQ=CTGAGAGCCATCTCCATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:32:0:1:0:37:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 48088069 . C T 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAACACCTCTAGACACTGT;RSEQ=GTGGGGCCAGAGCCCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 48088419 . C T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59207;SOR=0.32855;LSEQ=AGGTGTGGCTGCCTCCAAAG;RSEQ=TCATGTTGTTTCCATGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:21:1:30.8:1:1:0:60:10:0.7143:0:2 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:21.7:1:31:0:1:0:60:6:0.4286:0:1.7 +4 48088446 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13846;SOR=0;LSEQ=TGTTTCCATGACACCAGGGC;RSEQ=TGGTATGATATTTATCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:12,4:0,0:0,16:1:0,2:17.4:1:30.7:1:1:0:60:32:1:0:1.4 1/1:10:8:7,1:1,1:2,8:0.8:2,2:32.8:1:29.8:1:0.37778:5.29:60:16:0.8:0:1.3 +4 48355959 . C T 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGAGAGAAAACAGTCGA;RSEQ=ATTGGCTCAAAAATTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:28.3:1:30.5:1:1:0:53.8:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 48356063 . C T 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=TTAGAGCTCTGTGACTGACA;RSEQ=CAAGGAGAAAGATTAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:3,0:3,1:0.25:0,0:3:0:29:0:1:0:60:2:0.25:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:28:1:32.5:1:1:0:60:4:0.5:0:1.5 +4 48356096 . T G 33 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.47619;SOR=0;LSEQ=TTAGAACTATCAGAAAATTA;RSEQ=GTATGTCCAAAAACCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:6.5:1:33.5:1:1:0:60:4:0.1818:0:1 0/0:10:0:0,0:10,0:10,0:0:0,0:26.7:1:31.8:1:1:0:60:20:1:0:0.3 +4 48356153 . T TA 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.22675;LSEQ=AGCAACAAAAACTTTCAAAT;RSEQ=AAAAAAAAAAGTTATCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:3,0:32,0:32,3:0.0857:1,0:32:1:30:0:1:0:60:6:0.0857:0:0.3 0/1:29:3:3,0:25,1:26,3:0.1034:1,0:34.3:1:29.7:1:1:0:60:6:0.1034:0:0 +4 48356244 . C T 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26308;SOR=Inf;LSEQ=TGATAGAATAACAAAAAGAT;RSEQ=CTGGGCTATATAAAGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:147,66:213,0:0:2,0:24:1:31.7:1:1:0:60:70:1:0:0.2 0/1:282:3:1,2:193,85:278,3:0.0106:2,2:17.3:1:20:1:0.22734:4.51385:60:2:0.0072:0:1.7 +4 48356333 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0074;SOR=0.68677;LSEQ=TCATCACTTCTAGCTTGGGT;RSEQ=ATTAAACTGTTGTAAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:352:225:107,118:61,65:126,225:0.6392:2,2:24.9:1:29.2:1:0.91155:1.03485:59.9:55.25:0.6351:0:1.1 1/0:574:315:152,163:123,135:258,315:0.5488:2,2:24.2:1:28.5:1:0.93307:1.02:60:77.75:0.5495:0:1.1 +4 48356375 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05213;SOR=0;LSEQ=TAGAAAAAACTGATGGGAAA;RSEQ=GGAAAAAGTTAAGGGATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:102,187:289,3:0.0103:2,2:23.7:1:25.3:1:1:1.0906:60:2:0.0069:0:2 0/0:488:0:0,0:189,299:488,0:0:2,0:25.3:1:30.5:1:1:0:60:96.6:1:0:0.5 +4 48356478 . C T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45452;SOR=1.49597;LSEQ=GAGATCCTCGTTAATTGTTA;RSEQ=GGATATTTTTTTTTTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:24:0,24:0,13:13,24:0.6486:1,1:19.5:1:30.9:1:1:0:60:23:0.6765:0:1.3 1/0:34:25:0,25:0,9:9,25:0.7353:0,1:16.4:1:30.7:1:1:0:60:50:0.7353:0:1.2 +4 48356483 . AT A 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.79101;SOR=1.16822;LSEQ=CCTCGTTAATTGTTACGGAT;RSEQ=TTTTTTTTTTCCCCCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:0,13:0,17:17,13:0.4194:1,1:21.7:1:31:1:1:0:60:26:0.4483:0.0968:1.2 0/1:24:11:0,11:0,13:13,11:0.4583:1,0:18.2:1:30.8:1:1:0:60:22:0.4583:0.2083:1.5 +4 49094910 . C T 28 d5;v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCGTGTTGATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:4:0:29:0:1:0:60:2:1:0:1 1/0:4:2:1,1:0,2:2,2:0.5:0,2:5:0:28.5:1:1:0:20:4:0.5:0:0 +4 49094962 . A AG 51 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAATCCATGACATTCAACT;RSEQ=GGTTGAATCCATTGCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:44:0:32:0:1:0:60:2:1:0:1 1/0:4:3:1,2:0,0:0,3:0.75:0,2:14.7:1:32.7:1:1:0:24:6:1:0:1.3 +4 49095011 . A C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCTCTCCATTCAATT;RSEQ=CTCTCTGATTCAATCTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:29.5:1:1:0:26.5:4:1:0:2 +4 49110398 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCGTTCCATTCCATTCCATT;RSEQ=CATACCATTCCACTCGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:17:0:31.5:1:1:0:42:4:0.6667:0:3.5 +4 49110410 . A T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATACCATTCC;RSEQ=CTCGGGTTGATTCCATACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:11:0:34:0:1:0:23:2:1:0:4 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29:0:31:1:1:0:42:4:0.6667:0:3.5 +4 49110459 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCACTCGGGTTGATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:12.5:1:27:1:1:0:42:4:0.6667:0:3.5 +4 49111607 . C T 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCACT;RSEQ=GGGTTGATTCCAGTCCGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:28:1:1:0:28:4:1:0:4 +4 49111616 . T A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCACTCGGGTTGAT;RSEQ=CCAGTCCGTTCCTTTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:27.5:1:1:0:28:4:1:0:4 +4 49111620 . G C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACTCGGGTTGATTCCA;RSEQ=TCCGTTCCTTTCCATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:31:1:1:0:28:4:1:0:4 +4 49111646 . T A 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTTCCATTTCATTCTAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18:0:29.5:1:1:0:28:4:1:0:4 +4 49112043 . G T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTGGGTTGATTCCATTCC;RSEQ=TTCCTTTCCATTTCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29.5:1:29.5:1:1:0:36.5:4:0.6667:0:3.5 +4 49112051 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCCGTTCCTTT;RSEQ=CATTTCATTCCATACCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:33:0:1:0:23:2:1:0:4 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26:1:29:1:1:0:36.5:4:0.6667:0:3.5 +4 49112338 . T C 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCACTCGGGATGATT;RSEQ=CATTCAATTCCATTATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:32:0:1:0:21:4:1:0:3.5 +4 49112344 . A T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCGGGATGATTTCATTC;RSEQ=ATTCCATTATATTCCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:31:1:1:0:21:4:1:0:3.5 +4 49112349 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATGATTTCATTCAATTC;RSEQ=ATTATATTCCATTCAATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:31:1:1:0:21:4:1:0:3.5 +4 49112409 . C T 31 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCACTCGGGTTGATTC;RSEQ=ATTCCGTTCCTTTCCATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:31:1:1:0:22:4:1:0:5.5 +4 49112415 . G A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGGGTTGATTCCATTCC;RSEQ=TTCCTTTCCATTTCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:31.5:1:1:0:22:4:1:0:5.5 +4 49112452 . T A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCGT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:28.5:1:1:0:22:4:1:0:5.5 +4 49112462 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCATTCCGTTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:30:1:1:0:22:4:1:0:5.5 +4 49112755 . A G 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:34:0:30:1:1:0:21.5:4:0.6667:0:5 +4 49112760 . A G 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AATCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:39:0:30.5:1:1:0:21.5:4:0.6667:0:5 +4 49112789 . C T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCGGGTTCATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29.5:1:31:1:1:0:21.5:4:0.6667:0:5 +4 49112799 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCGGGTT;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:19.5:1:30.5:1:1:0:21.5:4:0.6667:0:5 +4 49120011 . A G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCACCAAAGTTGATTGC;RSEQ=TGCTATTCCATTCCATTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:11:0:32.5:1:1:0:39:4:0.6667:0:2.5 +4 49120056 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCAATTCCATTCC;RSEQ=TTCCACTTGGGTTGATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:8.5:1:30:1:1:0:39:4:0.6667:0:2.5 +4 49120200 . CC TA 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=TTCGGGTTAATTCCTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:28.5:1:1:0:29:4:1:0:1 +4 49120230 . C GATTGCAATCGAGTTG 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AATTCCTTTCCATTCCATTC;RSEQ=ATTCCATACCATTCCGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:31.6:1:1:0:29:4:1:1:2 +4 49120231 . A T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCTTTCCATTCCATTCC;RSEQ=TTCCATACCATTCCGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:1:31.5:1:1:0:29:4:1:1:2 +4 49120233 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCTTTCCATTCCATTCCAT;RSEQ=CCATACCATTCCGTTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10:1:32.5:1:1:0:29:4:1:1:2 +4 49120235 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTTTCCATTCCATTCCATTC;RSEQ=ATACCATTCCGTTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:1:30.5:1:1:0:29:4:1:1:2 +4 49120236 . A T 31 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTTCCATTCCATTCCATTCC;RSEQ=TACCATTCCGTTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:1:31.5:1:1:0:29:4:1:1:2 +4 49120238 . A C 32 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCGTTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:1:32.5:1:1:0:29:4:1:1:2 +4 49120405 . TT CC 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:32:1:1:0:21:4:1:0:3 +4 49120408 . C G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CACTCGGGTTCATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:33.5:1:1:0:21:4:1:0:3 +4 49120648 . C A 44 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCACTCCATTCCATT;RSEQ=CATTCCATTCCACTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:11.7:1:28.3:1:1:0:44.3:6:1:0:2 +4 49120895 . A T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATTCCATTTGACTCAGGTTG;RSEQ=TTCCGTTCCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:36:0:28:0:1:0:27:2:1:0:6 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:30.5:1:1:0:56:4:1:0:2 +4 49121013 . C G 31 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:31:1:1:0:27.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 49121030 . TT CC 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TCCACTCGGGTTGATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:31.5:1:1:0:27.5:4:1:0:4 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 49121033 . C G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCATTCCATTCCATTCCTTT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:33:1:1:0:27.5:4:1:0:4 0/0:1:0:0,0:0,1:1,0:0:0,0:19:0:32:0:1:0:24:2:1:0:1 +4 49121139 . G T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTTTTCCAATCCACTCG;RSEQ=GTTGATTCCATTCTATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:9:0:25:0:1:0:21:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:31:0:1:0:23:4:1:0:5 +4 49121153 . TA T 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACTCGGGTTGATTCCATTC;RSEQ=TTCCATTCCATTCCAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:24:0:27:0:1:0:21:2:0.5:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:32:1:1:0:23:4:1:0:5 +4 49121168 . C A 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCTATTCCATTCCATTC;RSEQ=AGTTGATTCCATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:37:0:29:0:1:0:21:2:0.5:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:32.5:1:1:0:23:4:1:0:5 +4 49121175 . T A 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCCATTCCATTCCAGTTGA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:38:0:30:0:1:0:21:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:38:0:28.5:1:1:0:23:4:1:0:5 +4 49121187 . C G 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CCAGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:26:0:33:0:1:0:21:2:0.5:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:33.5:1:1:0:23:4:1:0:5 +4 49121203 . C G 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CATTCCATTCCATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:10:0:34:0:1:0:21:2:0.5:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:31.5:1:1:0:23:4:1:0:5 +4 49121247 . C G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATTCAGTTCCTTTCCATT;RSEQ=CATTCCATTTCATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:12:0:34:0:1:0:29:2:1:0:4 1/1:2:2:2,0:0,0:0,2:1:0,0:22.5:1:32.5:1:1:0:34:4:1:0:3.5 +4 49121257 . T G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCCATTCCATTCCATT;RSEQ=CATTCCATTCCAGTTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:2:0:32:0:1:0:29:2:1:0:4 1/1:2:2:2,0:0,0:0,2:1:0,0:32.5:1:32.5:1:1:0:34:4:1:0:3.5 +4 49121284 . G A 45 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCAGTTGATTCCATTGC;RSEQ=TTCCATTCCATTCAAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:31:1:28.7:1:1:0:32:6:1:0:3 +4 49121326 . T C 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TCCATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:24:0:25:0:1:0:24:2:1:0:5 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:25.5:1:29:1:1:0:24.5:4:0.6667:0:3 +4 49122887 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TGTTCCATTCCATTCCATTC;RSEQ=ACTCGGGTTGATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:29:1:1:0:33:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 49122918 . A T 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATTCCATTCCGTTCCTTTCC;RSEQ=TTCCATTCCTTTCCGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:42:1:31:1:1:0:33:4:0.5:0:6 1/0:2:1:1,0:1,0:1,1:0.5:0,0:25:0:32:0:1:0:47:2:0.5:0:3 +4 49122928 . T A 72 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=GTTCCTTTCCATTCCATTCC;RSEQ=TTCCGTTCCATTCCATTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1:0,2:28:1:31.4:1:1:0:32.8:10:1:0:6.2 1/0:5:3:2,1:1,1:2,3:0.6:2,2:17.3:1:31.7:1:1:1.73:31.3:6:0.6:0:3.3 +4 49122930 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=0;LSEQ=TCCTTTCCATTCCATTCCTT;RSEQ=CCGTTCCATTCCATTCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:43.5:1:32.5:1:1:3.1622:33:4:0.2857:0:6 0/0:5:0:0,0:3,2:5,0:0:2,0:20.6:1:31:1:1:0:32.8:10:1:0:3.2 +4 49122932 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=CTTTCCATTCCATTCCTTTC;RSEQ=GTTCCATTCCATTCGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:20.1:1:31:1:1:0:33.5:16:1:0:5.4 0/1:5:2:1,1:2,1:3,2:0.4:2,2:14:0:32:0:1:1.7321:35.5:4:0.4:0:3.5 +4 49122942 . C T 34 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0.62174;LSEQ=CATTCCTTTCCGTTCCATTC;RSEQ=ATTCGTGTTGATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:3,3:6,2:0.25:2,0:23.5:1:34:0:0.46429:0:30:4:0.25:0:7 0/1:6:1:1,0:3,2:5,1:0.1667:2,0:46:0:30:0:1:0:23:2:0.1667:0:3 +4 49122947 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16484;SOR=Inf;LSEQ=CTTTCCGTTCCATTCCATTC;RSEQ=TGTTGATTCCATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:27:1:31.4:1:1:0:33.5:16:1:0:5.4 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:36:1:30:1:1:2.44949:35:4:0.3333:0:3 +4 49122949 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=TTCCGTTCCATTCCATTCGT;RSEQ=TTGATTCCATTCCATTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:3,3:6,2:0.25:2,0:30.5:1:33:0:0.46429:0:30:4:0.25:0:7 0/0:6:0:0,0:4,2:6,0:0:2,0:32.2:1:32.3:1:1:0:30.8:12:1:0:3 +4 49122951 . T A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=CCGTTCCATTCCATTCGTGT;RSEQ=GATTCCATTCCATTCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:6,2:0.25:2,2:24:1:32:1:1:1.8258:33:4:0.25:0:6 0/0:6:0:0,0:4,2:6,0:0:2,0:32.8:1:30.5:1:1:0:30.8:12:1:0:3 +4 49122970 . T A 60 MAF0.05;NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30769;SOR=0.22947;LSEQ=TTGATTCCATTCCATTCCAC;RSEQ=CCAATCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:2,3:5,4:0.4444:2,2:27.5:1:30:1:1:1.43:32.3:8:0.4444:0:7.3 0/1:7:1:1,0:3,3:6,1:0.1429:2,0:27:0:26:0:1:0:23:2:0.1429:0:3 +4 49122971 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.475;SOR=0;LSEQ=TGATTCCATTCCATTCCACT;RSEQ=CAATCCATTCCATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,3:6,2:0.2222:2,2:33.5:1:31.5:1:1:1:41.5:4:0.2222:0:4 0/0:7:0:0,0:3,2:5,0:0:2,0:27:1:29.2:1:1:0:27.8:10:0.7143:0:2.6 +4 49122977 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=CATTCCATTCCACTCCAATC;RSEQ=ATTCCATTCCATTCCAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:8,2:0.2:2,2:29:1:30.5:1:1:1.58:35.5:4:0.2:0:7 0/0:7:0:0,0:4,3:7,0:0:2,0:26.1:1:29.9:1:1:0:30:14:1:0:2.9 +4 49122978 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=5;SSF=0.48529;SOR=0;LSEQ=ATTCCATTCCACTCCAATCC;RSEQ=TTCCATTCCATTCCAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:8,2:0.2:2,2:25:1:29.5:1:1:1.58:43.5:4:0.2:0:4 0/0:7:0:0,0:4,3:7,0:0:2,0:25.7:1:28.9:1:1:0:30:14:1:0:2.9 +4 49122982 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.475;SOR=0;LSEQ=CATTCCACTCCAATCCATTC;RSEQ=ATTCCATTCCAATCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,3:5,2:0.2222:2,2:29:1:31:1:1:1.41:35.5:4:0.2222:0:7 0/0:7:0:0,0:4,3:7,0:0:2,0:24:1:29.9:1:1:0:30:14:1:0:2.9 +4 49122989 . TTCCAATC AAT 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18301;SOR=Inf;LSEQ=CTCCAATCCATTCCATTCCA;RSEQ=CATTCCATTCCATTCAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:22:1:30.9:1:1:0:35.9:20:1:0:5.1 0/1:8:2:1,1:4,2:6,2:0.25:2,2:33.5:1:29.9:1:1:1.8258:23:4:0.25:0:2 +4 49123003 . A G 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0.79458;LSEQ=ATTCCATTCCAATCCATTCC;RSEQ=TTCCATTCAATTCCACTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:6,5:11,2:0.1538:2,0:12.5:1:30.5:1:0.46154:0:45:4:0.1538:0:3.5 0/1:8:1:1,0:3,4:7,1:0.125:2,0:19:0:31:0:1:0:53:2:0.125:0:4 +4 49123008 . A T 80 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.15882;SOR=0.1379;LSEQ=ATTCCAATCCATTCCATTCC;RSEQ=TTCAATTCCACTCGCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:4,2:1,4:5,6:0.5:2,2:22:1:31.2:1:0.24242:6.44:34.5:12:0.5:0:6.3 0/1:9:1:0,1:3,3:6,1:0.1111:2,0:3:0:26:0:1:0:30:2:0.1111:0:4 +4 49123012 . A C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49351;SOR=0;LSEQ=CAATCCATTCCATTCCATTC;RSEQ=ATTCCACTCGCATTCAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:25:1:31:1:1:1.18:43.5:4:0.1667:0:4 0/0:9:0:0,0:4,5:9,0:0:2,0:19.8:1:30.3:1:1:0:30.8:18:1:0:3.2 +4 49123013 . A T 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.69895;LSEQ=AATCCATTCCATTCCATTCA;RSEQ=TTCCACTCGCATTCAATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:6,5:11,2:0.1538:2,0:12.5:1:29:1:0.46154:0:45:4:0.1538:0:3.5 0/1:9:1:1,0:3,5:8,1:0.1111:2,0:29:0:32:0:0.44444:0:53:2:0.1111:0:4 +4 49123019 . C G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17143;SOR=Inf;LSEQ=TTCCATTCCATTCAATTCCA;RSEQ=TCGCATTCAATCTATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:12,0:0:2,0:23.1:1:32.9:1:1:0:40:24:1:0:5 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:25.5:1:33:0:1:1.29:35:4:0.2222:0:2.5 +4 49123023 . C T 71 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17699;SOR=0.18759;LSEQ=ATTCCATTCAATTCCACTCG;RSEQ=ATTCAATCTATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:6,5:0.4545:2,2:28:1:30.8:1:1:1.30:41:10:0.4545:0:6.2 0/1:8:1:0,1:3,3:6,1:0.125:2,0:18:0:29:0:1:0:30:2:0.1429:0:4 +4 49123028 . A C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15441;SOR=Inf;LSEQ=ATTCAATTCCACTCGCATTC;RSEQ=ATCTATTCCATTCCATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:31.8:1:31.7:1:1:0:39.8:20:1:0:5.3 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:16.5:1:32:1:1:1.41:35:4:0.2857:0:2.5 +4 49123029 . AT GC 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22794;SOR=0;LSEQ=TTCAATTCCACTCGCATTCA;RSEQ=CTATTCCATTCCATTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:1,4:5,3:0.3:2,2:31:1:33.5:0:1:1.83:47.7:6:0.3:0:5.7 0/0:7:0:0,0:3,3:6,0:0:2,0:29.2:1:30.5:1:1:0:33.8:12:0.8571:0:3.3 +4 49123054 . T C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=TTCCATTCCATTTCATTCCG;RSEQ=TCTGTTCCATTCCATTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:2,5:7,3:0.3:2,2:31.3:1:33.3:1:1:1.22:47.7:6:0.3:0:5.7 0/0:5:0:0,0:2,3:5,0:0:2,0:32.2:1:30.2:1:1:0:32.6:10:1:0:3.8 +4 49123062 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.14286;SOR=Inf;LSEQ=CATTTCATTCCGTTCTGTTC;RSEQ=ATTCCATTCTATTGCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:9,0:0:2,0:30.9:1:31.6:1:1:0:39.9:18:1:0:4.8 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:0:31:1:1:1:27.5:4:0.3333:0:4.5 +4 49123071 . C T 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.21433;LSEQ=CCGTTCTGTTCCATTCCATT;RSEQ=TATTGCTTTCCATACCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:3,4:7,1:0.125:2,0:23:0:32:0:1:0:28:2:0.125:0:6 0/1:8:2:1,1:3,3:6,2:0.25:2,2:14:0:32:1:1:1:27.5:4:0.25:0:4.5 +4 49123077 . CT GA 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=TGTTCCATTCCATTCTATTG;RSEQ=TTCCATACCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:22.9:1:31.3:1:1:0:39.9:14:1:0:4.7 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:14.5:1:28:1:1:1.41418:25.5:4:0.2857:0:2 +4 49123078 . T A 83 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=GTTCCATTCCATTCTATTGC;RSEQ=TTCCATACCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:21.9:1:29.7:1:1:0:39.9:14:1:0:4.7 1/0:7:5:3,2:0,0:0,5:0.7143:0,2:14.2:1:29.8:1:1:0:33.2:10:1:0:4 +4 49123087 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CATTCTATTGCTTTCCATAC;RSEQ=ATTCCATTCCACTCGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:15.5:1:29:1:1:2.45:56.5:4:0.3333:0:5.5 0/0:4:0:0,0:2,2:4,0:0:2,0:24.3:1:31:1:1:0:27.3:8:1:0:2.8 +4 49123124 . T C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GATGATTCCATTCCATTCCA;RSEQ=TATATTCCGTTCCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:22:0:33:1:1:0:25.5:4:0.6667:0:2 +4 49149778 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTGCTTTCCATTCCATT;RSEQ=CATTCCTTTCCACTCAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:30:1:1:0:21:4:1:0:3 +4 49149781 . T A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTGCTTTCCATTCCATTCCA;RSEQ=TCCTTTCCACTCAGGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:31:0:1:0:21:4:1:0:3 +4 49149790 . A G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCTTTCC;RSEQ=CTCAGGTTGATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:32:1:1:0:21:4:1:0:3 +4 49150548 . T G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCGTTCCGTTCCGTTCG;RSEQ=TTCCATTCCATTCCATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:32.5:1:1:0:37:4:1:0:1 +4 49151206 . C CCCCTG 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CACTCGCGTTGATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:31.9:1:1:0:21:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 49152515 . G T 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGGGTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:24:0:31:1:1:0:21:4:1:0:6.5 1/0:4:2:1,1:1,1:2,2:0.5:2,2:19:0:31.5:1:1:1:23:4:0.5:0:2.5 +4 49152523 . C T 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=TTCCATTCCATTGCATTCCA;RSEQ=TCGGGGTGATTCCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:1,0:0:0,0:32:0:34:0:1:0:20:2:0.5:0:6 1/0:4:2:1,1:1,1:2,2:0.5:2,2:27:0:32:0:1:1:23:4:0.6667:0:2.5 +4 49152843 . ATG TTCAAATC 28 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=ATCCATTCCATTCCATTCCA;RSEQ=CATTCCATTTTTTTCAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36:0:28.1:1:1:0:23:4:1:0:5 +4 49155211 . C CG 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCGTTCCATTCCATTCCATT;RSEQ=ATTCCATTGCATTCCACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:27.9:1:1:0:24:4:1:0.5:3.5 +4 49155220 . GC CG 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCCATTCATTCCATT;RSEQ=ATTCCACTCGGGTTGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:28.3:1:1:0:24:4:1:0:2.5 +4 49155225 . C G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATTCATTCCATTGCATT;RSEQ=CACTCGGGTTGATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:29.5:1:1:0:24:4:1:0:2.5 +4 49155761 . A C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:33:1:1:0:26:4:1:0:3.5 +4 49155766 . A C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35:0:33:1:1:0:26:4:1:0:3.5 +4 49155812 . A T 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGACTCGGGTTGATTCCA;RSEQ=TCCATTCCATTCCAATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:28:1:1:0:26:4:1:0:3.5 +4 49156466 . T A 29 pSTD;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=5;SSF=0.06667;SOR=0;LSEQ=TTGATTCCATTCCATTCCAT;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:29.5:1:1:0:21:4:1:0:2 0/0:4:0:0,0:3,1:4,0:0:2,0:21.5:1:30.3:1:1:0:22.5:8:1:0:4.3 +4 49156480 . T C 34 p8;pSTD;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=5;SSF=0.06667;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCATTCCATTCCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:34.5:1:1:0:21:4:1:0:2 0/0:4:0:0,0:2,1:3,0:0:2,0:26.7:1:28.3:1:1:0:22.7:6:0.75:0:4 +4 49157609 . G A 25 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACGTTGAATTGCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38.5:1:25.5:1:1:0:23.5:4:1:0:1.5 +4 49637554 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GTGGAAAGGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:33.5:1:1:0:25:4:1:0:3 +4 49637557 . G C 34 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAAAGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:34:0:1:0:25:4:1:0:3 +4 49637572 . G C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:33:0:1:0:25:4:1:0:3 +4 49659235 . T A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATCCAGAGTGGAATGGAA;RSEQ=GGTATGGAATGCAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:31.5:1:1:0:23.5:4:1:0:2 +4 49659549 . A T 40 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=CCGAATCGAATCCAATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:25:0:32:0:1:0:21:2:1:0:5 1/0:4:3:1,2:1,0:1,3:0.75:0,2:11:1:25.3:1:1:0:26.7:6:0.75:0:7.3 +4 49659551 . C G 42 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGAATGGAATGGAATGGAAC;RSEQ=GAATCGAATCCAATGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,0:0,3:0.75:0,2:13:1:26.7:1:1:0:26.7:6:0.75:0:7.3 +4 49659556 . C G 43 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=3.76419;LSEQ=GGAATGGAATGGAACCGAAT;RSEQ=GAATCCAATGGAATCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,1:2,1:0.25:2,0:2:0:32:0:1:0:30:2:0.25:0:3 1/0:5:3:1,2:1,1:2,3:0.6:2,2:18:1:27.7:1:1:1.7321:26.7:6:0.6:0:7.3 +4 49659582 . G A 45 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=0.66932;SOR=0.65297;LSEQ=CAATGGAATCAACTGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:2,1:4,3:7,3:0.25:2,2:27.7:1:30.7:1:1:1.44:37.3:6:0.3:0:5 0/1:17:3:1,2:4,9:13,3:0.1765:2,2:44:1:29:1:1:1.12:26.7:6:0.1875:0:7.3 +4 49659600 . T A 87 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=0.10109;SOR=0.32536;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:4,3:5,6:11,7:0.3684:2,2:29.9:1:31.3:1:1:1.56:36.9:14:0.3684:0:3.9 0/1:32:5:2,3:11,16:27,5:0.1563:2,2:26:1:30.2:1:1:1.03026:32:10:0.1667:0:5.8 +4 49659615 . T C 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=1.19578;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGAATCCGGGTGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:9,9:18,1:0.0526:2,0:44:0:32:0:1:0:21:2:0.0556:0:4 0/1:32:2:1,1:12,18:30,2:0.0625:2,2:34.5:1:30.5:1:1:1.48:25:4:0.0625:0:5 +4 49659621 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52551;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=AATCCGGGTGGAATGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:9,9:0,0:0,18:1:0,2:33.9:1:29:1:1:0:32.2:17:1:0:3.7 1/1:31:29:12,17:0,1:1,29:0.9355:0,2:33.2:1:29.5:1:1:0:29:58:0.9355:0:4.1 +4 49659629 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52551;SOR=Inf;LSEQ=ATGGAATGGAATGAATCCGG;RSEQ=TGGAATGGAATGGAATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:18,0:0:2,0:29.7:1:32:1:1:0:32.2:36:1:0:3.7 0/1:31:2:1,1:11,17:28,2:0.0645:2,2:40:0:29:0:1:1.52:25:4:0.0645:0:5 +4 49659634 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATGGAATGAATCCGGGTGGA;RSEQ=TGGAATGGAATGTAATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:9,9:0,0:0,18:1:0,2:25.1:1:32.7:1:1:0:32.2:17:1:0:3.7 1/1:31:30:12,18:0,1:1,30:0.9677:0,2:27.7:1:32.1:1:1:0:29.6:60:0.9677:0:4.1 +4 49659651 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=GGAATGGAATGGAATGTAAT;RSEQ=GAGTGGAATGGATTGGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:10.5:1:32:1:1:0:32.7:30:1:0:3.8 0/1:28:2:1,1:10,16:26,2:0.0714:2,2:18:0:30.5:1:1:1.57:25:4:0.0714:0:5 +4 49659664 . T A 91 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTAATGGAGTGGAATGGA;RSEQ=TGGATTGGAGTGGAGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:5:0:33.5:1:1:0:28:4:1:0:3.5 1/1:8:8:4,4:0,0:0,8:1:0,2:9.1:1:30.5:1:1:0:27.5:16:1:0.125:4.5 +4 49659669 . T A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAGTGGAATGGATTGGA;RSEQ=TGGAGTGGAGTGGAATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:8:2:0,2:0,1:1,2:0.25:0,0:11:1:31:1:1:0:24.5:4:0.6667:0.125:5.5 +4 49659707 . G C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATCAACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:2,0:0,0:0,2:0.2857:0,0:10:0:33:0:1:0:21:4:1:0:2 +4 49659718 . A G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=ATCAACCCGAATGGAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:2,0:0,0:0,2:0.2857:0,0:9:0:32:0:1:0:21:4:1:0:2 +4 49659859 . A C 27 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATGCTATGGAATCAA;RSEQ=CGGAGTGTAATGTAAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:0,0:0,2:0.6667:0,0:26:0:27.5:1:1:0:25.5:4:0.6667:0:2.5 +4 49659866 . G T 27 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCTATGGAATCAAACGGAGT;RSEQ=TAATGTAAATGAATGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:33:0:27.5:1:0.33333:0:25.5:4:0.6667:0:2.5 +4 54243905 . T C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97851;LSEQ=GAGCTTTCTTCGTTCGTTCG;RSEQ=CGGCGGGTTCGCGCCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:32:29,3:29,4:33,32:0.4923:2,2:23.6:1:32.3:1:1:1.33:60:64:0.4923:0:1.2 0/1:76:37:33,4:31,8:39,37:0.4868:2,2:23.8:1:30.2:1:0.3483:2.11:60:17.5:0.4795:0:1.1 +4 54244003 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14388;SOR=Inf;LSEQ=TTTAAGTTGCGCTCGGGGCG;RSEQ=CCATGTCGGCCGGCGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:169,103:272,0:0:2,0:25.6:1:31.6:1:1:0:59.7:135:1:0:0.2 0/1:378:4:3,1:222,151:373,4:0.0106:2,2:14:1:28:1:0.65088:2.04:60:8:0.0109:0:1.3 +4 54244130 . G A 45 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30962;SOR=0.22745;LSEQ=TGTCTCTCGGGTTCTCTCAG;RSEQ=CCTCCCCTCTTGGCCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:101,170:271,3:0.0109:2,2:5:1:29:1:0.55851:3.35:60:6:0.0112:0:1 0/0:399:1:1,0:166,232:398,1:0.0025:2,0:1:0:22:0:0.41855:0:60:2:0.0025:0:1 +4 54244141 . T A 39 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.65647;SOR=0.50373;LSEQ=TTCTCTCAGGCCTCCCCTCT;RSEQ=GGCCCTCAAACGGCCGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:1,2:83,160:243,3:0.0122:2,2:19.7:1:24.7:1:1:1.03735:60:2:0.0082:0:1.7 0/0:324:2:2,0:127,195:322,2:0.0062:2,0:1:0:21:0:0.15778:0:60:4:0.0063:0:1 +4 54244144 . C A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13455;SOR=Inf;LSEQ=TCTCAGGCCTCCCCTCTTGG;RSEQ=CCTCAAACGGCCGGCGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:79,154:233,0:0:2,0:22.8:1:31.2:1:1:0:59.8:37.833:1:0:0.1 0/1:297:4:3,1:111,182:293,4:0.0135:2,2:14.8:1:26.3:1:0.15952:4.89:60:8:0.0138:0:1.8 +4 54244179 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50287;SOR=Inf;LSEQ=CGTCCCTGGCCTCTCGCGCC;RSEQ=CCGCTTCGGGCCTCTGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:8,95:103,0:0:2,0:22.7:1:32:1:1:0:60:206:1:0:0.1 0/1:126:2:1,1:4,120:124,2:0.0159:1,2:19.5:1:28:1:0.0781:26.95:60:4:0.0163:0:1 +4 54244321 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTGGCGGCCGGGCCGGG;RSEQ=TGGGGGGCTGTGACCGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:28:1:1:0:60:4:1:0:1.5 +4 54245138 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24453;SOR=Inf;LSEQ=AATCTTCATTACCTCTTAAA;RSEQ=TTAAGCTTATTTTTATAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:64,5:69,0:0:2,0:21.2:1:31.1:1:1:0:60:138:1:0:0 0/1:68:2:1,1:63,3:66,2:0.0294:1,2:23:1:30:1:0.11501:18.32472:60:4:0.0294:0:1 +4 54245169 . A AT 85 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.30674;SOR=2.90641;LSEQ=TTTTATAGCAGTAAAGTCTG;RSEQ=TTTTTTTTTCCATAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:100,20:120,2:0.0164:2,0:16.5:1:34:0:1:0:60:4:0.0164:0:0 0/1:151:7:6,1:108,35:143,7:0.0464:2,2:35.6:1:30.4:1:1:1.94:60:14:0.0473:0:0.3 +4 54245372 . T A 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01468;SOR=0;LSEQ=TTGTTTGCTTATTTATTTAT;RSEQ=TGTTTATTTTACTTGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:5:2,3:202,221:423,5:0.0117:2,2:23:1:31.8:1:1:1.37004:60:10:0.0118:0:1 0/0:565:0:0,0:285,279:564,0:0:2,0:23.1:1:29.6:1:1:0:60:93:0.9982:0:0.1 +4 54245476 . A T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATTACACAGGTTGTGTGA;RSEQ=ACAATGGTTCTGTCAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:298:298:104,194:0,0:0,298:1:0,2:23.7:1:29.1:1:1:0:60:98.333:1:0:1.1 1/1:323:323:100,223:0,0:0,323:1:0,2:23.1:1:28.2:1:1:0:60:106.667:1:0:1.2 +4 54245499 . A G 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AATGGTTCTGTCAGTTGTCA;RSEQ=AATTATTTTCTTACAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:46,142:188,0:0:2,0:22.1:1:30.6:1:1:0:60:93:1:0:1 0/1:182:16:4,12:24,142:166,16:0.0879:2,2:20.8:1:29.8:1:0.2771:1.96:60:32:0.0909:0:1.9 +4 54245749 . T G 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAGCTACTGATAAAAATA;RSEQ=TTTAACTTAATTGAAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:22.3:1:34:0:1:0:60:6:0.5:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 54245775 . A G 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAATTGAAAATGTTTTTA;RSEQ=GTAAATCAGGAACACTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:28.5:1:33:0:1:0:60:4:0.3333:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 54248276 . C A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.10003;SOR=3.45285;LSEQ=CAATGTTGAGTACTTGTCTT;RSEQ=TGCAAGTTACTAGAAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:10,0:11,0:11,10:0.4762:0,0:17.9:1:29.5:1:1:0:60:20:0.4762:0:1 1/0:17:13:13,0:4,0:4,13:0.7647:0,1:21.8:1:28.2:1:1:0:60:26:0.7647:0:1.1 +4 54248418 . A G 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCGAAAAGTAATGCCTGAC;RSEQ=TGTATACTTACTTTTGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:308:0:0,0:200,108:308,0:0:2,0:24.9:1:30.7:1:1:0:60:101.667:1:0:0.1 0/1:409:79:50,29:198,132:330,79:0.1932:2,2:25.8:1:30.1:1:0.61079:1.15:60:78:0.1926:0:1.1 +4 54248698 . A G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66685;SOR=0.54001;LSEQ=GAGGAAAAGAAATAGTAGAA;RSEQ=GACTGCAGAGGAAAATAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:1,7:0,7:7,8:0.5333:0,2:12.4:1:31:1:1:0:60:16:0.5333:0:1.1 0/1:8:3:0,3:0,5:5,3:0.375:0,0:12.3:1:31.3:1:1:0:60:6:0.375:0:1 +4 54249842 . G GA 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.35017;SOR=1.68218;LSEQ=CTGTCTCAAGACAGAAGAAA;RSEQ=AAAAAAAAAAACAGGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:10:10,0:51,0:51,10:0.1613:1,0:30.1:1:30.3:1:1:0:60:20:0.1724:0.0161:0.5 0/1:53:13:13,0:40,0:40,13:0.2453:1,1:22.2:1:29.2:1:1:0:60:26:0.2453:0.0566:0.1 +4 54249881 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22814;SOR=0;LSEQ=GTTACTTTTTTTAGTTATTA;RSEQ=TATTAGATGTTGAAATGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:115,17:132,2:0.0149:2,2:11.5:1:29.5:1:0.25149:6.60263:60:4:0.0171:0:1 0/0:146:0:0,0:129,17:146,0:0:2,0:21:0:15:0:1:0:60:0:0:0:3 +4 54250092 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50874;SOR=Inf;LSEQ=GTGTAAATGCTATATAGTAA;RSEQ=GAGAGTGTGCCTATATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:19,125:144,0:0:2,0:22.9:1:31.6:1:1:0:60:288:1:0:0.1 0/1:192:2:1,1:33,156:189,2:0.0104:2,2:9:0:31.5:1:0.3251:4.67:60:4:0.0104:0:1 +4 54250189 . T G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.02865;SOR=4.74712;LSEQ=TGTTAAAGTTTCATCATGAA;RSEQ=ATACTTCTTTGCTAAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:0,7:0,16:16,7:0.3043:1,0:17.6:1:32.1:1:1:0:60:14:0.3043:0:1 1/0:19:13:1,12:0,6:6,13:0.6842:0,1:27.5:1:31.2:1:1:0:60:26:0.6842:0:1.1 +4 54250332 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCTGTAATCCCAGGACT;RSEQ=TGGGAGGCCGAGGCGGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:30.5:1:33:1:1:2.45:42:4:0.3333:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:31:0:1:0:60:2:1:0:0 +4 54255950 . G GT 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.09181;LSEQ=AGCTTTTCAGGATAATTTCT;RSEQ=TTTTTTTTTGTTTGTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:11:8,3:167,53:220,11:0.0476:2,2:18.4:1:28.9:1:0.73041:1.18068:60:22:0.0482:0:0.5 0/1:367:19:15,4:250,93:343,19:0.0518:2,2:22.6:1:29.1:1:0.79065:1.39:59.5:18:0.0501:0.0109:0.2 +4 54256108 . CT C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.95235;LSEQ=TCTTAAATAGGTCTTAATAG;RSEQ=TTTTTTTTTAGTCGGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:14:3,11:38,150:188,14:0.069:2,2:33.7:1:32:1:1:1.08:60:28:0.0711:0.0049:0.5 0/1:258:17:4,13:53,185:238,17:0.0659:2,2:29.1:1:30.6:1:1:1.07:59.4:16:0.0643:0:0.4 +4 54256167 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00036;SOR=0.18539;LSEQ=TCAGGCTGGAGTACAGTGGC;RSEQ=CAATCTTAGTTCACTGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:27:0,27:2,35:37,27:0.4219:2,1:20.4:1:30.4:1:0.50446:0:59.7:54:0.4219:0:1.2 0/1:51:6:0,6:1,44:45,6:0.1176:1,0:28.7:1:31:1:1:0:59:12:0.1176:0:1.2 +4 54256478 . C A 79 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05668;SOR=10.23812;LSEQ=GACTGGTAAAGTTTTTCTGG;RSEQ=AAGAGTCCAGTAGCACGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:6,1:7,2:0.2222:2,2:25.5:1:32.5:1:0.41667:4.58262:60:4:0.2222:0:1 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:14.9:1:28.3:1:1:0:60:14:0.7778:0:1.1 +4 54256824 . C A 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22473;SOR=4.33966;LSEQ=ATTGTGGATTATATTAATTT;RSEQ=AATATTTTCAGTGTGAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:1:1,0:98,248:346,1:0.0029:2,0:1:0:24:0:0.2853:0:60:2:0.0029:0:1 0/1:403:5:4,1:122,276:398,5:0.0124:2,2:10.6:1:26.2:1:0.03492:9.00:60:10:0.0125:0:1 +4 54256853 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.21837;SOR=Inf;LSEQ=CAGTGTGAAGTCATCAGAAA;RSEQ=TTTTTTGAACATCAATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:31,193:224,0:0:2,0:23.2:1:30.8:1:1:0:59.9:111:1:0:0 0/1:197:2:1,1:26,169:195,2:0.0102:2,2:23:1:28.5:1:0.25593:6.40:60:4:0.0103:0.0051:0.5 +4 54257034 . A T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAATAATTTGATCAAAAATG;RSEQ=TATAGTCTTTTTGCCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:25,6:0,0:0,31:1:0,2:23.2:1:30.9:1:1:0:60:62:1:0:1 1/1:19:19:17,2:0,0:0,19:1:0,2:26.8:1:30.1:1:1:0:60:38:1:0:1 +4 54257131 . A T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25162;LSEQ=ATTTTTGATGCTGCATAAAA;RSEQ=TAGAGCTGAAATATTTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:142:80:72,8:54,8:62,80:0.5634:2,2:26.7:1:31.2:1:0.60361:1.33:59.2:25.667:0.558:0:1.1 0/1:172:42:34,8:106,24:130,42:0.2442:2,2:24.5:1:29.8:1:1:1.03898:60:84:0.2471:0:1 +4 54257507 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50262;SOR=0;LSEQ=TGATGTTCTTACTTTCAAAT;RSEQ=ACAGACTAGCCACAGCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:115,20:135,2:0.0146:2,2:12:1:28:1:0.28403:5.63583:60:4:0.0147:0:1 0/0:113:0:0,0:97,16:113,0:0:2,0:33:0:12:0:1:0:60:0:0:0:1 +4 54257719 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2481;SOR=Inf;LSEQ=ATTTTTTGTTCTTGAGTCTG;RSEQ=TCCCATGCCACTACTCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:25,157:182,0:0:2,0:25.7:1:33.4:1:1:0:60:181:1:0:0 0/1:187:3:2,1:36,147:183,3:0.016:2,2:19.3:1:27.3:1:0.10659:8.04:60:6:0.0163:0:1 +4 54265667 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=AGTTTATTCGGCTTCTAAGT;RSEQ=TTATTAATGTGAACTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:31.3:1:29:1:1:0:60:6:0.375:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:16.4:1:32:1:1:0:60:10:1:0:0 +4 54265883 . CT C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.55166;SOR=1.16553;LSEQ=AAATTCAACAAGCTAATAAC;RSEQ=TTTTTTTTTAAGGTACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:34:19,15:350,167:517,34:0.0612:2,2:23.4:1:31.7:1:0.18721:1.65301:60:68:0.0623:0.0126:0.3 0/1:581:41:26,15:334,206:540,41:0.0706:2,2:23:1:31.1:1:1:1.07:59.8:82:0.0723:0.0155:0.3 +4 54265894 . A T 83 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03529;SOR=3.81892;LSEQ=GCTAATAACCTTTTTTTTTT;RSEQ=AGGTACAGCAGGGAAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:649:3:0,3:418,227:645,3:0.0046:2,0:24.3:1:21.7:1:0.04434:0:60:2:0.0032:0:1.3 0/1:688:12:4,8:398,278:676,12:0.0174:2,2:10.5:1:23.2:1:0.08436:2.85892:60:11:0.0164:0:1.4 +4 54280705 . GA G 162 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.77245;SOR=1.10408;LSEQ=CTTTAGAAAAAGCATGTCAA;RSEQ=AAAAAAAAAAAACAGAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:30:29,1:71,3:74,30:0.2703:1,1:24.8:1:33:1:1:1.22:60:60:0.2752:0.036:0.7 0/1:124:36:30,6:76,9:85,36:0.2903:2,2:25.6:1:31.4:1:0.37484:1.68098:60:72:0.2951:0.0403:0.8 +4 54281075 . C T 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.27101;LSEQ=CCCAGCACTTGTCTTGCTAC;RSEQ=CATCTTTCTGGCTGTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:0,7:1,8:9,7:0.4375:2,0:32.1:1:30.1:1:1:0:60:14:0.4375:0:1.1 1/0:6:3:0,3:0,3:3,3:0.5:0,0:16:1:29.7:1:1:0:60:6:0.5:0:1 +4 54281140 . A AT 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTAATGGATGCTCAGTA;RSEQ=TTTTTTTTTTCGTTCTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:5,2:0.2857:2,0:35:1:31:1:1:0:60:4:0.2857:0:0.5 0/0:1:0:0,0:0,1:1,0:0:0,0:50:0:29:0:1:0:60:2:1:0:0 +4 54292133 . G GTTAATCTCCTGTAACATAAAAATTGAATCAATTCAGT 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12988;SOR=Inf;LSEQ=ATGAGAACAGCAACATACAG;RSEQ=TTTAGTATTTTAAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:92,174:266,0:0:2,0:25:1:31.4:1:1:0:60:43.333:1:0:0.1 0/1:319:4:1,3:117,197:314,4:0.0125:2,2:16.3:1:27.3:1:1:1.77878:60:8:0.0127:0.0125:0.8 +4 54292164 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23687;SOR=0;LSEQ=TAAAATAAATAATTTTCTTT;RSEQ=ACTGAAGGATGATATCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:39,115:154,2:0.0128:2,2:38:1:31:1:0.4483:2.92:60:4:0.0132:0:1 0/0:164:0:0,0:41,123:164,0:0:2,0:21.5:1:28.9:1:1:0:59.8:53.667:1:0:0.1 +4 55124831 . A C 87 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06826;SOR=7.00702;LSEQ=TTGACTAAAATGATGCTGTT;RSEQ=ATATTTTCTGTTGTGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:1,0:228,21:249,1:0.004:2,0:26:0:15:0:1:0:60:0:0:0:2 0/1:256:7:6,1:219,29:248,7:0.0273:2,2:24.1:1:31.1:1:0.58824:1.25739:60:14:0.0277:0:1 +4 55125058 . A T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-04;SOR=1.97979;LSEQ=GCTTTGTGCTGCATGGGTTT;RSEQ=TTACCAGTACTCTGCATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:42:7,35:53,308:361,42:0.1042:2,2:22.5:1:30.6:1:0.65397:1.16:59.3:41:0.1038:0:1.1 0/1:395:74:14,60:76,244:320,74:0.1873:2,2:23.3:1:29.2:1:0.44336:1.33398:59.7:73:0.1862:0:1.1 +4 55129831 . C T 241 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CTTCATTCTTTTTTAAACCA;RSEQ=AGACCCAGATGTAGCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:258:172,86:238,130:368,258:0.4115:2,2:24.3:1:30.1:1:0.66942:1.09:60:257:0.4119:0:1.1 0/0:685:0:0,0:411,274:685,0:0:2,0:24.8:1:31.4:1:1:0:60:227.333:1:0:0.1 +4 55130078 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.92838;LSEQ=TTCCAGACCATCCCATTTAA;RSEQ=GTTTATGCTTTAAAAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:583:65:26,39:187,331:518,65:0.1115:2,2:22.6:1:30.5:1:0.5852:1.18:60:130:0.114:0:1.3 0/1:662:178:74,104:202,280:482,178:0.2689:2,2:25.4:1:30.2:1:1:1.01388:60:177:0.2715:0:1.3 +4 55130125 . T A 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12171;SOR=0;LSEQ=CATCTCCTTCCTTCTTTAAA;RSEQ=AAGAGTAACAGGCAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:65,213:278,3:0.0107:2,2:16.3:1:22:1:0.14242:6.50:60:2:0.0078:0:2 0/0:285:0:0,0:80,205:285,0:0:2,0:24.2:1:27.3:1:1:0:60:22.75:1:0:0.5 +4 55130147 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21913;SOR=Inf;LSEQ=AGAGTAACAGGCAAAATCAT;RSEQ=AGGTGCGTGTAGGATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:23,173:196,0:0:2,0:20.3:1:29.9:1:1:0:59.9:14.077:1:0:0.6 0/1:173:2:1,1:22,149:171,2:0.0116:2,2:18:0:33:1:0.24889:6.65:60:4:0.0118:0:1 +4 55130154 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06892;SOR=1.81173;LSEQ=CAGGCAAAATCATAAGGTGC;RSEQ=TGTAGGATTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:21:1,20:14,122:136,21:0.1329:2,1:17.1:1:32.4:1:0.69472:2.28576:60:42:0.1489:0:1.7 0/1:147:32:3,29:11,103:114,32:0.2177:2,2:19.9:1:28.6:1:1:1.03216:59.9:7:0.209:0:1.7 +4 55130177 . A T 43 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76656;LSEQ=TAGGATTTTTTTTTTTTTTT;RSEQ=AATCATCATCACTGGTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:3:0,3:4,89:93,3:0.0313:1,0:7:1:27.3:1:1:0:60:6:0.0319:0:1.7 0/1:83:2:1,1:4,77:81,2:0.0241:1,2:2:1:18.5:1:0.11754:17.33:60:1:0.0127:0:1.5 +4 55131118 . C T 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGATCTAGAAATGGAAGCT;RSEQ=TTAAAACCGTGTATAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:722:0:0,0:400,322:722,0:0:2,0:25.4:1:32.6:1:1:0:59.9:119.333:1:0:0.1 0/1:942:49:25,24:496,397:893,49:0.052:2,2:21.3:1:29.1:1:0.55759:1.19916:60:48:0.0518:0:1.1 +4 55133252 . T C 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10086;SOR=4.74956;LSEQ=GTTTTAGGTTTACAGCAAAA;RSEQ=TGAGAGGTACAGAGATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:3,0:30,0:30,3:0.0909:1,0:39.3:1:34:0:1:0:60:6:0.0938:0:1.3 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:25.7:1:32:1:1:0:60:6:0.3333:0:1 +4 55133383 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24796;SOR=Inf;LSEQ=ACATCCATATCATCCAGAGT;RSEQ=CATAGTTTATCTTAGAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:159,25:184,0:0:2,0:23.3:1:31.6:1:1:0:59.7:35.8:1:0:0 0/1:183:2:1,1:151,30:181,2:0.0109:2,2:12.5:1:27.5:1:0.31087:4.96799:60:4:0.011:0:1 +4 55133400 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24901;SOR=Inf;LSEQ=AGTCCATAGTTTATCTTAGA;RSEQ=TTCACTCCTAGGAGCGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:193,54:247,0:0:2,0:24.4:1:32.9:1:1:0:59.8:60.75:1:0:0.1 0/1:260:3:1,2:193,64:257,3:0.0115:2,2:12.3:1:26:1:0.15951:5.97987:60:6:0.0117:0:1 +4 55133726 . T G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.26607;LSEQ=CTTCCCTGTACAGAGAAAGG;RSEQ=TTCATTGAAATCAAACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:784:93:52,41:372,317:689,93:0.1186:2,2:26.2:1:31.4:1:0.74086:1.08:60:92:0.1195:0:1.1 0/1:787:184:99,85:320,281:601,184:0.2338:2,2:26.2:1:31:1:0.93277:1.02:60:91:0.2345:0:1.2 +4 55133936 . C T 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=3.46955;LSEQ=AACTCTCTGCCCAAGTATGC;RSEQ=TTTTTTTAGTGTGCATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:31:11,20:111,184:295,31:0.0951:2,2:24.2:1:30.6:1:1:1.09655:60:62:0.0963:0:1.6 0/1:400:107:38,69:106,186:292,107:0.2675:2,2:24.4:1:29.6:1:0.9069:1.03472:60:52.5:0.2672:0:1.6 +4 55133959 . C T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.50644;LSEQ=TTTTTAGTGTGCATCAGAGG;RSEQ=GGACTGAGGTTTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:22:6,16:67,146:213,22:0.0932:2,2:27.8:1:28.3:1:0.8113:1.22276:60:10:0.0877:0:1.9 0/1:226:60:18,42:49,117:166,60:0.2655:2,2:20.7:1:29.1:1:1:1.02:60:120:0.2667:0:2 +4 55133980 . CT C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50676;SOR=0;LSEQ=GGACTGAGGTTTGTGTGTGT;RSEQ=TACAACCCAGACCCAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:35,133:168,2:0.0118:2,2:12.5:1:27:0:0.37967:3.76:60:4:0.0118:0:1 0/0:131:0:0,0:24,107:131,0:0:2,0:19.9:1:29.2:1:1:0:60:130:1:0:0.5 +4 55134183 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04545;SOR=Inf;LSEQ=TCAGCTAGGGTGGAAGAAAG;RSEQ=AAGTAAAATTGGACTCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:9,0:0:0,0:29:1:30.1:1:1:0:59.3:8:1:0:1.1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:27.5:1:28.5:1:1:0:60:4:1:0:1 +4 55134231 . G C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGATTGAATATATTCCCT;RSEQ=ATGTTCATCATCCATATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:15:1:33.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55138521 . C T 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37458;SOR=3.76624;LSEQ=TAGTCTCATATGTTCTGGGA;RSEQ=ACGAGCTATTCCATTCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:1:0,1:229,103:332,1:0.003:2,0:1:0:24:0:0.31231:0:60:2:0.003:0:1 0/1:356:4:2,2:242,110:352,4:0.0112:2,2:19:1:23.3:1:0.59296:2.19466:60:3:0.0085:0:2.8 +4 55138785 . G C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10413;SOR=0;LSEQ=TACTTATTGACTATAAGATA;RSEQ=GGTTTTGGGTGTGATAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:0,3:1,29:30,3:0.0909:1,0:20.3:1:32:0:1:0:60:6:0.0909:0:1 0/0:36:0:0,0:2,33:35,0:0:2,0:21.1:1:30.3:1:1:0:60:70:0.9722:0:0.1 +4 55139624 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50148;SOR=0;LSEQ=AAGGTCCCAACTCCTTGCCA;RSEQ=CTTAGAGTGTTCCCGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:123,3:126,2:0.0156:1,2:21.5:1:27.5:1:0.06176:35.64812:60:4:0.0159:0:1 0/0:108:0:0,0:104,4:108,0:0:1,0:23.5:1:30.3:1:1:0:60:216:1:0:0.1 +4 55139691 . T C 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00939;SOR=Inf;LSEQ=TTGGCCCTATACTTAGGCCC;RSEQ=TTTTCTCTCTAGATGTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:279,135:414,0:0:2,0:24.4:1:31.5:1:1:0:59.9:206:0.9976:0:0.1 0/1:498:8:4,4:308,182:490,8:0.0161:2,2:16.4:1:27.6:1:0.47924:1.69036:60:7:0.0142:0:1 +4 55139771 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.68572;LSEQ=ACATCATCACGGAGATCCAC;RSEQ=CCCGAGACAGGAGTACCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:732:78:40,38:326,328:654,78:0.1066:2,2:25.2:1:31.2:1:0.90473:1.06:60:25:0.1056:0:1.2 0/1:851:260:135,125:291,300:591,260:0.3055:2,2:22.5:1:30:1:0.50315:1.11:59.8:51:0.3047:0:1.2 +4 55139944 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2379;SOR=0;LSEQ=TCATCAGCTGAGCCGCATCT;RSEQ=CCCCAGGCGGAACTTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:14,94:108,2:0.0182:2,2:35:1:28.5:1:0.25521:6.52:60:4:0.0187:0:1.5 0/0:115:0:0,0:19,96:115,0:0:2,0:21.5:1:31.8:1:1:0:60:114:1:0:0.5 +4 55139978 . T C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGAATCCCAGATAGGGGT;RSEQ=ATATAGAAATGAAGGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:56:56:3,53:0,0:0,56:1:0,2:23.9:1:32.7:1:1:0:60:55:1:0:2.1 1/1:44:44:1,43:0,0:0,44:1:0,1:22.8:1:32:1:1:0:60:88:1:0:1.5 +4 55140016 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.15104;SOR=0.32935;LSEQ=CCAAGGCAGAAATTCAGTTA;RSEQ=GAATGCTCTTAAAGTCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:2,27:0,4:4,29:0.8788:0,2:30.6:1:30.7:1:1:0:60:58:0.9063:0:2.7 1/0:20:14:0,14:0,6:6,14:0.7:0,1:25.5:1:29.8:1:1:0:60:28:0.7:0:2.4 +4 55140031 . T G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTATGAATGCTCTTAAAG;RSEQ=CATGTGGGACTTTGTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:1,25:0,0:0,26:1:0,1:26.7:1:31.2:1:1:0:58.7:7.667:1:0:2.8 1/1:14:14:0,14:0,0:0,14:1:0,1:26.4:1:32.1:1:1:0:60:28:1:0:2.4 +4 55140912 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17761;SOR=Inf;LSEQ=CATGTGGAGTGAACGTTGTT;RSEQ=GACTCTACTGTGTCCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:135,62:197,0:0:2,0:22.9:1:31.7:1:1:0:60:31.833:1:0:0.1 0/1:144:2:2,0:92,50:142,2:0.0139:2,0:22.5:1:32:0:0.54351:0:60:4:0.014:0:1 +4 55141055 . A G 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36414;SOR=2.02818;LSEQ=GTCATTGAATCAATCAGCCC;RSEQ=GATGGACATGAATATATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:640:633:317,316:1,0:1,633:0.9891:0,2:24.3:1:30.7:1:1:0:60:104.5:0.9921:0:1.1 1/1:738:734:371,363:3,1:4,734:0.9946:2,2:24.6:1:29.5:1:0.62412:2.93163:59.9:65.727:0.9945:0:1.2 +4 55141293 . G A 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22539;SOR=2.81547;LSEQ=AATACATTTCTGTCTTGACA;RSEQ=TAAGTTAATTGGATCATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:3:0,3:0,26:26,3:0.1034:1,0:38:1:27.3:1:1:0:60:2:0.0769:0:2.7 0/1:16:4:0,4:0,12:12,4:0.25:0,0:29.5:1:31.3:1:1:0:60:8:0.25:0:1 +4 55143286 . G A 49 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCACGGAGCTGGTAGACAGC;RSEQ=CGCTCACACCAGGGAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:19.7:1:31.3:1:1:0:60:6:0.75:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:28:1:31.3:1:1:0:60:6:1:0:1 +4 55143321 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=AGGGCTGCACCCTCCTTTCT;RSEQ=CCGTCTGTGTTTTCTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:8.5:1:33:0:1:0:60:4:0.1818:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:20.2:1:31.5:1:1:0:60:12:1:0:0.3 +4 55143577 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.82258;LSEQ=CGGGTCTTGGGGTCTGGAGC;RSEQ=TTTGGGAAGGTGGTTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:84:44,40:336,328:664,84:0.1121:2,2:25.8:1:30.6:1:0.81711:1.07:60:41:0.1105:0:1.1 0/1:966:254:123,131:361,351:712,254:0.2629:2,2:25.5:1:29.5:1:0.55904:1.09528:59.8:126:0.2639:0:1.2 +4 55143693 . G A 95 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02201;SOR=8.29332;LSEQ=CCTGGGGATTTTTTGAGCAC;RSEQ=GGGATTTTTTGAGCATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:0,1:35,162:197,1:0.0051:2,0:34:0:29:0:1:0:60:2:0.0051:0:4 0/1:222:9:3,6:45,168:213,9:0.0405:2,2:24:1:30.1:1:0.41028:1.86:60:18:0.0413:0:1 +4 55143986 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21642;SOR=Inf;LSEQ=ATATCCAATCACAGGATTAG;RSEQ=CATATTCTTGGTTTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:170,26:196,0:0:2,0:21.8:1:30:1:1:0:60:195:1:0:0 0/1:171:2:1,1:144,25:169,2:0.0117:2,2:8.5:1:29:1:0.28173:5.66778:60:4:0.0119:0:1 +4 55144420 . A G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03306;SOR=0.37161;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=CTTTTTTGGTATCTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:55:53,2:9,0:9,55:0.8333:0,1:15.7:1:31.6:1:1:0:58.6:10:0.8475:0:2.6 1/0:54:35:32,3:18,0:18,35:0.6481:1,2:16.6:1:31.2:1:0.54282:0:57.1:16.5:0.6875:0:2.7 +4 55144447 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21789;SOR=4.64374;LSEQ=TGGTATCTTATTTTTTTCTG;RSEQ=GCCATATGGTCTGCAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:191:172,19:1,1:2,191:0.9745:2,2:21.5:1:31.2:1:0.197:8.85:59.7:12.643:0.9779:0:1.5 1/1:179:178:141,37:0,0:0,178:0.9944:0,2:19.5:1:30.6:1:1:0:59.5:21.25:0.9942:0:1.4 +4 55146389 . C T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00391;SOR=3.98279;LSEQ=CCAGTTAGCTCCCATGCCTA;RSEQ=CTCAGTACCTGGCACATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:9:9,0:63,0:63,9:0.125:1,0:18.3:1:32.2:1:1:0:59.4:18:0.125:0:1.1 0/1:41:15:15,0:26,0:26,15:0.3659:1,1:22:1:31.5:1:1:0:60:30:0.3659:0:1.1 +4 55146406 . T TTGTAGGTCCCCCAG 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.3158;LSEQ=CTACCTCAGTACCTGGCACA;RSEQ=AATCATCATCTACTGAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:128:126:112,14:1,0:1,126:0.9844:0,2:21.6:1:31.5:1:1:0:59.8:252:0.9844:0.4844:0.2 1/1:84:83:76,7:1,0:1,83:0.9881:0,2:21.6:1:30.3:1:1:0:59.6:166:0.9881:0.4405:0.3 +4 55146754 . C A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=3.15981;LSEQ=GGGATGGTAAGTGAACCTGG;RSEQ=AGCCCACGTGGTCTCTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:16:3,13:18,152:170,16:0.086:2,2:26.4:1:32.1:1:0.3982:1.94:60:32:0.0879:0:1 0/1:161:37:7,30:19,105:124,37:0.2298:2,2:22.5:1:28.9:1:0.61476:1.29:60:17.5:0.2229:0:1.1 +4 55146921 . ATT A 50 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=GGTGTGTTCCTGCAGTAAAC;RSEQ=TTTTAAAAAAAATAATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:5.3:1:31.6:1:1:0:60:6:0.375:0.25:0.3 0/0:4:0:0,0:0,4:4,0:0:0,0:10.5:1:31:1:1:0:52:8:1:0:0.5 +4 55146926 . TT AA 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.28664;LSEQ=GTTCCTGCAGTAAACATTTT;RSEQ=AAAAAAAATAATTATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,1:1,3:0.6:0,0:42:1:32.3:1:1:0:60:6:0.75:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:14.5:1:30.5:1:1:0:44:4:0.6667:0.3333:0.5 +4 55151711 . C A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12263;SOR=Inf;LSEQ=TTCAGTGAGTGGAGTGTGGA;RSEQ=GGAGATGCTAGGAGATAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:313:310:51,259:0,0:0,310:0.9904:0,2:24.4:1:31.9:1:1:0:60:50.667:0.9935:0:1.1 1/1:316:316:66,250:0,0:0,316:1:0,2:22.5:1:30.2:1:1:0:60:62.2:1:0:1.1 +4 55151934 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63392;SOR=0.42244;LSEQ=CCAAGTGCCACCATGGATCA;RSEQ=CCAGTCTTGCAGGGGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:3:2,1:162,34:196,3:0.0151:2,2:17.7:1:29:1:0.44209:2.36914:60:6:0.0152:0:1 0/0:156:1:0,1:127,28:155,1:0.0064:2,0:1:0:23:0:0.1859:0:60:2:0.0065:0:1 +4 55151958 . T TA 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23374;LSEQ=GTCTTGCAGGGGTGATGCTA;RSEQ=TCAGCTACAGATGGCTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:295:263:191,72:24,8:32,263:0.8915:2,2:24.6:1:28.9:1:1:1.13042:59.9:51.6:0.8958:0.1763:0.1 1/0:242:159:116,43:58,22:80,159:0.657:2,2:26.4:1:28:1:1:1.02:60:52:0.661:0.0496:0.2 +4 55152040 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.87274;LSEQ=GATCTGGCTGCTCGCAACGT;RSEQ=CTCCTGGCACAAGGAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:711:88:46,42:334,289:623,88:0.1238:2,2:27:1:30.1:1:0.82043:1.05517:60:28.333:0.1218:0:1.2 0/1:741:214:106,108:284,241:525,214:0.2888:2,2:23.4:1:28.8:1:0.29099:1.20035:60:34.667:0.2869:0:1.2 +4 55152199 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20771;SOR=Inf;LSEQ=ATCTCTAAAGTCAGGTGTTG;RSEQ=TTCTAGAGATTCGGTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:14,149:163,0:0:2,0:23:1:33.1:1:1:0:60:80.5:1:0:0.1 0/1:137:2:1,1:18,117:135,2:0.0146:2,2:25.5:1:27.5:1:0.25902:6.35:60:4:0.0146:0:1 +4 55152284 . T G 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05158;SOR=0;LSEQ=TGGCAGCAGATTGCCCAGGT;RSEQ=TGAGTGCCAGCTCCACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:0,32:0,0:0,32:1:0,1:24.2:1:32.9:1:1:0:60:31:1:0:1.3 1/1:20:17:0,17:0,3:3,17:0.85:0,1:23.8:1:31.9:1:1:0:58.7:34:0.85:0:1.6 +4 55153837 . A G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGCCAGTATGCTGCAGCC;RSEQ=CCTCAAACCACATGTTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:0,65:0,0:0,65:1:0,1:25:1:32.8:1:1:0:60:130:1:0:1.1 1/1:52:52:2,50:0,0:0,52:1:0,1:24.7:1:31.1:1:1:0:60:25:1:0:1.3 +4 55153921 . T C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTTGGGGGTTGCGTCT;RSEQ=ACTCCTGGCCTCTGCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:0,19:0,0:0,19:1:0,1:20.7:1:31.7:1:1:0:59.3:38:1:0:1.5 1/1:4:4:0,4:0,0:0,4:1:0,0:12:1:33:0:1:0:60:8:1:0:1.8 +4 55154527 . C G 58 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCACAATGGATCATCCCC;RSEQ=AGTGGCTTAATGGAGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:1,4:0.8:0,2:36:1:29.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55154891 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.1383;LSEQ=TCTGAAAGGTTTTCTAACAG;RSEQ=GTTCTATCATGCCAAGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:63:46,17:318,126:444,63:0.1238:2,2:23.4:1:32.1:1:0.88195:1.07:60:126:0.126:0:1.1 0/1:517:120:73,47:283,114:397,120:0.2321:2,2:21.6:1:30.6:1:0.03299:1.59681:60:240:0.2358:0:1.1 +4 55155498 . A G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCTTTCATCTTATATGT;RSEQ=CAGTACCTGTAAGCACTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:22.3:1:33.2:1:1:0:60:12:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:27.5:1:32:1:1:0:60:4:1:0:2 +4 55155693 . G A 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCTGGTTTTTTGTGGAAT;RSEQ=GGAAGCATTGTTCAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:11:1:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55156091 . T G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTCTTTTCACATCCAATGT;RSEQ=AGACCTCTCCAATGTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55156300 . C T 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.94602;LSEQ=CTCTTTACCATTGGTGGCCC;RSEQ=TTCTTCATGTTCTATGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:17,0:17,3:0.15:1,0:24:1:30.7:1:1:0:60:6:0.15:0:1.7 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:20.5:1:32:1:1:0:60:4:0.1429:0:1.5 +4 55156380 . G A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATCTTCCAGGTAGTTTGGA;RSEQ=ATATGTACAGTTAAATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:81:75,6:0,0:0,81:1:0,2:17.4:1:29.9:1:1:0:60:26:1:0:2 1/1:70:70:63,7:0,0:0,70:1:0,2:21.7:1:29.3:1:1:0:60:69:1:0:1.8 +4 55156400 . A G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.14033;LSEQ=GATATGTACAGTTAAATAAT;RSEQ=GTAAGTTCTGAGTGTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:123:119:103,16:3,1:4,119:0.9675:2,2:21.7:1:32.5:1:0.45282:2.13:60:238:0.9675:0:1.7 1/1:108:87:76,11:16,5:21,87:0.8056:2,2:22.6:1:31.3:1:0.30091:2.14:60:86:0.8037:0:1.6 +4 55156699 . C G 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTCCCTGAGGAGGAGGAC;RSEQ=TGGGCAAGAGGAACAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:112,233:345,0:0:2,0:24.3:1:32.1:1:1:0:60:48.286:1:0:0.1 0/1:338:21:5,16:115,202:317,21:0.0621:2,2:23.3:1:30.4:1:0.34698:1.81884:60:20:0.0612:0:1.2 +4 55156715 . G C 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24979;SOR=0;LSEQ=GGACCTGGGCAAGAGGAACA;RSEQ=ACACAGGTAGCTGTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:1,2:87,210:297,3:0.01:2,2:21:1:25:1:1:1.21:60:2:0.0068:0:2.3 0/0:278:0:0,0:97,181:278,0:0:2,0:25.5:1:30.7:1:1:0:60:38.714:1:0:0.3 +4 55161254 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00168;SOR=0.39258;LSEQ=AGTCTAGGTCTAGTTCTGTG;RSEQ=AGGAGTTGTAATATTTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:218:199:157,42:16,3:19,199:0.9128:2,2:23.7:1:29.6:1:0.77026:1.42459:60:98.5:0.9163:0:1.1 1/1:199:160:118,42:28,11:39,160:0.804:2,2:21.1:1:28.7:1:0.84081:1.10:60:159:0.803:0:1.1 +4 55161391 . T C 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.47165;SOR=0.49736;LSEQ=GAAGACATCGACATGATGGA;RSEQ=GACATCGGCATAGACTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:665:663:328,335:0,2:2,663:0.997:0,2:24.7:1:30.8:1:0.49934:0:60:59.273:0.9969:0:1.1 1/1:829:824:434,390:0,2:2,824:0.994:0,2:23.9:1:30.3:1:0.22492:0:59.9:136.333:0.9939:0:1.2 +4 55161516 . CA TG 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03112;SOR=0;LSEQ=AAAACCACTTTATTGCAATG;RSEQ=GAGGTTGAGAGGAGGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:6:2,4:31,174:205,6:0.0284:2,2:18.7:1:28.3:1:0.23736:2.79:60:12:0.0288:0.0047:0.8 0/0:192:0:0,0:32,160:192,0:0:2,0:21.2:1:29.7:1:1:0:60:95:1:0:1.1 +4 55161517 . A G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06239;SOR=Inf;LSEQ=AAACCACTTTATTGCAATGC;RSEQ=GAGGTTGAGAGGAGGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:203:198:28,170:0,0:0,198:0.9754:0,2:24.1:1:30.8:1:1:0:59.9:38.6:1:0:1.1 1/1:184:184:30,154:0,0:0,184:1:0,2:21.6:1:30:1:1:0:60:35.8:1:0:1.1 +4 55523938 . G A 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CTCCTCCTCCCGGCGGGCAC;RSEQ=GCCCCCCGGCATTAACACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:3:0:29:0:1:0:60:2:0.3333:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:42.3:1:30.7:1:1:0:60:6:1:0:1.3 +4 55524252 . G A 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=26.03687;LSEQ=GCTTCGCGTCCAGACAGGTG;RSEQ=GACACCGCGGCTGGCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:809:1:1,0:387,419:806,1:0.0012:2,0:1:0:25:0:0.48079:0:60:2:0.0013:0:1 0/1:864:27:12,15:376,458:834,27:0.0313:2,2:26:1:29:1:1:1.02617:60:54:0.0317:0:1.2 +4 55524304 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=28.49818;LSEQ=TACTCGGCGAAGCCTGTGCC;RSEQ=GGGAGGGTGGTACCCGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:40:14,26:106,279:385,40:0.0941:2,2:23:1:30.3:1:0.35648:1.42:60:39:0.0938:0:1.1 1/0:378:283:78,205:29,65:94,283:0.7487:2,2:22.5:1:29.4:1:0.59761:1.17206:60:282:0.752:0:1.1 +4 55524328 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17196;SOR=Inf;LSEQ=AGGGTGGTACCCGCCAGGGT;RSEQ=CATCCGGAGAGAGGACTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:52,231:283,0:0:2,0:23.6:1:32:1:1:0:60:39.429:1:0:0.2 0/1:201:2:1,1:30,169:199,2:0.01:2,2:14.5:1:28.5:1:0.28532:5.56:60:4:0.0101:0:2 +4 55524399 . T C 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAGACTCCAGGTGGCCC;RSEQ=CGGACTCTCCGGCGCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:0,2:1,74:75,2:0.026:1,0:7.5:1:31.5:1:1:0:60:4:0.027:0:1 0/0:32:0:0,0:2,30:32,0:0:2,0:19.3:1:27.9:1:1:0:60:9.667:1:0:0.4 +4 55525153 . A G 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTGCGTTCCCTGACTCC;RSEQ=ACCGCCTAGCACGCCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:31:1:1:0:60:4:1:0:1 +4 55561637 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10403;SOR=Inf;LSEQ=AAGTGCTTTATTTCGCCAAG;RSEQ=AAGAAGATCATACTCAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:176,56:232,0:0:2,0:25:1:31.5:1:1:0:60:45.4:1:0:0.1 0/1:207:3:1,2:143,61:204,3:0.0145:2,2:15.3:1:27:1:0.22029:4.64908:60:6:0.0147:0:1 +4 55561966 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25038;SOR=Inf;LSEQ=AGGTAAATGCTTGGCTTTCT;RSEQ=CAGTGCTGTGCTTTCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:63,188:251,0:0:2,0:24:1:32.3:1:1:0:60:82.667:0.992:0:0.1 0/1:279:3:1,2:77,199:276,3:0.0108:2,2:31.3:1:29:1:1:1.29:60:6:0.0108:0:1 +4 55562002 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21944;SOR=Inf;LSEQ=AAGAATTTAATATCCTGCTC;RSEQ=TAATTTTGGATGACATATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:21,118:139,0:0:2,0:24.3:1:30.8:1:1:0:60:138:1:0:0 0/1:123:2:1,1:20,101:121,2:0.0163:2,2:28.5:1:31.5:1:0.31347:4.95:60:4:0.0165:0:1 +4 55564184 . A G 68 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTATGAAATGGCAATAAT;RSEQ=ATAGTACTGATCATGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:28:1:34:0:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55566075 . A G 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01033;SOR=Inf;LSEQ=GGAGAGTGTTGGGATTGCAT;RSEQ=TTTCCCCCTTTCATACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:48,0:0:1,0:23.4:1:31.4:1:1:0:59.3:96:1:0:0.1 0/1:24:4:0,4:0,20:20,4:0.1667:1,0:23.5:1:32:1:1:0:60:8:0.1739:0:1 +4 55569859 . A AT 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.96159;LSEQ=TAAATTATATGGTAATCTTC;RSEQ=TTTTTTTTTCTCCTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:10:9,1:148,24:172,10:0.0549:2,2:24:1:32.3:1:1:1.46:59.9:20:0.0556:0.0165:0.7 0/1:170:9:7,2:131,30:161,9:0.0529:2,2:21.8:1:29.6:1:0.67777:1.2459:59.4:8:0.0479:0.0176:0.2 +4 55569877 . C T 33 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62354;SOR=0.33812;LSEQ=TCATTTTTTTTTCTCCTTTT;RSEQ=TGAAACCAGCAGACTAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:3:1,2:194,51:245,3:0.0121:2,2:6.7:1:21.3:1:0.11632:7.52349:59.7:2:0.0083:0:3 0/0:243:1:0,1:183,59:242,1:0.0041:2,0:1:0:22:0:0.24691:0:60:2:0.0042:0:1 +4 55569887 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2489;SOR=Inf;LSEQ=TTCTCCTTTTCTGAAACCAG;RSEQ=AGACTAAACTACAGGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:215,75:290,0:0:2,0:25.2:1:31.9:1:1:0:60:40.429:1:0:0.1 0/1:299:3:1,2:214,80:294,3:0.01:2,2:15.3:1:25.3:1:0.18568:5.31434:60:6:0.0102:0:1 +4 55572872 . C T 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTATTAAACATTAGGGCTC;RSEQ=CTTGTTTTCCCTTAATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:31.8:1:30.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55572970 . T A 46 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAATTCTTTTAACCTAA;RSEQ=AAACATCAAGACTAGTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:15.3:1:29.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:31:0:25:0:1:0:60:2:1:0:1 +4 55573177 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0.57538;LSEQ=ATACTGGAAATCAACCAATT;RSEQ=TTTTTGTAATTCCAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:118,6:124,2:0.0159:1,2:21:1:29:1:0.10844:18.27967:60:4:0.016:0:1 0/0:109:1:0,1:99,9:108,1:0.0092:2,0:1:0:28:0:0.09174:0:60:2:0.0094:0:1 +4 55573495 . CT C 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51271;SOR=0;LSEQ=GGGGGATTACACATTACCCC;RSEQ=TTTCCAGTGGGCTTATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:13,143:156,2:0.0127:2,2:14.5:1:25.8:1:0.16988:10.64:60:4:0.013:0.0063:0 0/0:112:0:0,0:11,101:112,0:0:2,0:22.8:1:29.5:1:1:0:60:55:1:0:0.1 +4 55575274 . C G 87 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGGGAGGAAGTGGTATG;RSEQ=GGACAGCCCAGGGTGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:0,8:1:0,2:23.8:1:29:1:1:0:58:7:1:0:1.9 1/1:2:2:1,1:0,0:0,2:1:0,2:4.5:1:27:1:1:0:60:4:1:0:0.5 +4 55575506 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50288;SOR=0;LSEQ=ATTTTTCCTCAAACAGGCAT;RSEQ=GATTTCCAGGTAGAAACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:175,18:193,2:0.0103:2,2:29:1:29:1:0.18583:9.48992:60:4:0.0103:0:1 0/0:162:0:0,0:145,17:162,0:0:2,0:22:1:28.6:1:1:0:60:324:1:0:0.1 +4 55589945 . A AT 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.50144;SOR=0;LSEQ=AATTTCAAATATGTTTTCTG;RSEQ=TTTTTTTTAAAAAAGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:0,2:8,137:145,2:0.0136:2,0:32:1:31.5:1:1:0:60:4:0.014:0:0 0/0:125:0:0,0:7,118:125,0:0:2,0:25.1:1:30:1:1:0:60:24:1:0:0.2 +4 55589953 . TA T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.50149;SOR=0;LSEQ=ATATGTTTTCTGATTTTTTT;RSEQ=AAAAAGCTTTGTTTTGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:0,2:1,116:117,2:0.0168:1,0:22.5:1:32:1:1:0:60:4:0.0172:0.0084:0.5 0/0:100:0:0,0:3,97:100,0:0:1,0:25.8:1:30.7:1:1:0:60:99:1:0:0.1 +4 55589977 . G GT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.18724;SOR=Inf;LSEQ=AAAGCTTTGTTTTGATTATT;RSEQ=TTTTTTTTCTAGCCATGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:0,78:78,0:0:1,0:22.9:1:32.5:1:1:0:59.7:77:1:0:0.2 0/1:60:2:0,2:0,58:58,2:0.0333:1,0:9.5:1:31:1:1:0:60:4:0.0351:0.0167:0 +4 55592325 . T C 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01849;SOR=Inf;LSEQ=ATGTCATTTCTGGTAATACA;RSEQ=GCATCACACCATACTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:2,69:71,0:0:1,0:24.3:1:30.8:1:1:0:59.9:70:1:0:0.3 0/1:43:4:0,4:2,37:39,4:0.093:2,0:17.5:1:28:1:1:0:60:8:0.093:0:1 +4 55593464 . A C 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GCATGATGTGCATTATTGTG;RSEQ=TGATTCTGACCTACAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:992:0:0,0:456,536:992,0:0:2,0:24.5:1:30.5:1:1:0:59.9:61:1:0:0.1 0/1:1011:52:26,26:442,517:959,52:0.0514:2,2:24.8:1:31.1:1:0.6688:1.17:60:104:0.0521:0:1.2 +4 55593481 . A G 183 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=61.78538;LSEQ=GTGATGATTCTGACCTACAA;RSEQ=TATTTACAGGTAACCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:884:1:1,0:382,501:883,1:0.0011:2,0:36:0:14:0:0.43326:0:60:0:0:0:1 0/1:855:56:25,31:359,440:799,56:0.0655:2,2:24.6:1:31.6:1:1:1.01171:60:55:0.0651:0:1.2 +4 55593865 . G A 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00178;SOR=Inf;LSEQ=GGTTTGCCATAGAGAACATC;RSEQ=TAGGAAAATGTCTCTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:77,20:97,0:0:2,0:25:1:30.6:1:1:0:59.2:47.5:1:0:0.2 0/1:69:7:5,2:53,9:62,7:0.1014:2,2:20.3:1:30.7:1:0.30864:2.31958:60:14:0.1029:0:1 +4 55593909 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23657;SOR=Inf;LSEQ=TTGTTTTTAATTCCTTTATT;RSEQ=ATTTTGAAACTGCACAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:170,28:198,0:0:2,0:23.4:1:32.2:1:1:0:59.9:48.5:1:0:0.1 0/1:188:2:1,1:150,36:186,2:0.0106:2,2:15.5:1:29:1:0.35573:4.12365:60:4:0.0109:0:1 +4 55593921 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1183;SOR=Inf;LSEQ=CCTTTATTGATTTTGAAACT;RSEQ=CACAAATGGTCCTTCAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:200,51:251,0:0:2,0:23.2:1:31.9:1:1:0:59.9:49.2:0.996:0:0.1 0/1:244:3:1,2:187,54:241,3:0.0123:2,2:17.3:1:27:1:0.13266:6.85441:60:6:0.0126:0:1 +4 55594325 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12371;SOR=Inf;LSEQ=CTGCCTTTTATTGTCTGTCA;RSEQ=GTTATCAAAACATGACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:61,230:291,0:0:2,0:22.9:1:31.4:1:1:0:60:47.5:1:0:0.1 0/1:290:3:2,1:87,199:286,3:0.0103:2,2:13.3:1:27.3:1:0.22525:4.55:60:6:0.0104:0:1 +4 55595418 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18255;SOR=Inf;LSEQ=AGCTGAATATTAATGGCCAT;RSEQ=ACCACCCTTGGGTATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:172,15:187,0:0:2,0:23.3:1:32.5:1:1:0:59.9:92.5:1:0:0.1 0/1:140:2:1,1:124,14:138,2:0.0143:2,2:24:1:29:1:0.20349:8.58908:60:4:0.0144:0:1 +4 55595429 . G T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57099;SOR=2.87928;LSEQ=AATGGCCATGACCACCCTTG;RSEQ=GTATTTTTATGGGAGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:0,1:212,42:254,1:0.0039:2,0:1:0:26:0:0.16863:0:60:2:0.004:0:1 0/1:178:2:1,1:147,29:176,2:0.0112:2,2:5.5:1:27:1:0.30946:5.00084:60:4:0.0114:0:1 +4 55595681 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=ATTTACATAAATAGTTAGCT;RSEQ=TTGACAGGCAGTTCATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:27,146:173,2:0.0114:2,2:28.5:1:28:1:0.29517:5.33:60:4:0.0117:0:1 0/0:144:0:0,0:27,117:144,0:0:2,0:24.9:1:31.2:1:1:0:60:47:1:0:0.1 +4 55597645 . T A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05845;SOR=Inf;LSEQ=AGAGAGTATGTATATCATGC;RSEQ=AATGTGGAATATAACATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:56,242:298,0:0:2,0:21:1:29.2:1:1:0:60:73.5:1:0:0.1 0/1:190:3:2,1:38,149:187,3:0.0158:2,2:11:1:20.7:1:0.11276:7.73:60:2:0.0106:0:1.7 +4 55597969 . G T 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24916;SOR=0;LSEQ=CCAGCCTTTGGTATGTCATT;RSEQ=CCACTGTCTTTTCCTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:215,17:232,3:0.0128:2,2:16.7:1:26.7:1:0.21348:6.22479:60:6:0.013:0:1 0/0:220:0:0,0:196,24:220,0:0:2,0:20.7:1:31.3:1:1:0:60:54:1:0:0.1 +4 55598449 . G T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6038;SOR=2.25091;LSEQ=GAAATTCTTTTAAAACTTTT;RSEQ=GCTTTTAGGATATAGGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:0,1:9,202:211,1:0.0047:1,0:26:0:14:0:1:0:60:0:0:0:1 0/1:190:2:0,2:7,181:188,2:0.0105:1,0:22:0:31:0:1:0:60:4:0.0108:0:1 +4 55599129 . T A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0819;SOR=Inf;LSEQ=ATACTTTAAAACAAAAGTAT;RSEQ=GGATTTTTTATAATATAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:56,0:56,0:0:1,0:26.1:1:31.4:1:1:0:60:112:1:0:0 0/1:44:3:3,0:41,0:41,3:0.0682:1,0:33.7:1:26.7:1:1:0:60:6:0.0698:0:2 +4 55599159 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50924;SOR=0;LSEQ=ATAATATAAGCAACACTATA;RSEQ=TATTAAAAAGTTAGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:111,3:114,2:0.0171:1,2:30.5:1:32.5:1:0.06807:32.17955:60:4:0.0172:0:1 0/0:86:0:0,0:50,6:56,0:0:2,0:26.8:1:30.9:1:1:0:59.8:27:0.6429:0:0.1 +4 55599268 . C T 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GACTTGGCAGCCAGAAATAT;RSEQ=CTCCTTACTCATGGTCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:586:0:0,0:329,257:586,0:0:2,0:26.6:1:31.6:1:1:0:60:82.714:1:0:0.1 0/1:586:17:10,7:315,254:569,17:0.029:2,2:23:1:26.8:1:0.81043:1.15:60:7.5:0.0262:0:1.3 +4 55599431 . T C 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.63352;LSEQ=TTTCGATAAAAATTGTTTCC;RSEQ=GTGATTTTCATAATGTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:14,133:147,2:0.0133:2,2:22.5:1:29.5:1:0.19182:9.21:60:4:0.0135:0:2 0/0:118:1:0,1:16,101:117,1:0.0085:2,0:44:0:29:0:1:0:60:2:0.0085:0:1 +4 55599436 . T C 234 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAAAAATTGTTTCCTGTGA;RSEQ=TTTCATAATGTAAATCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:127:11,116:0,0:0,127:1:0,2:24.1:1:33.5:1:1:0:60:254:1:0:1.1 0/1:97:47:7,40:4,46:50,47:0.4845:2,2:22.9:1:31.8:1:0.34711:2.00:60:94:0.4845:0:1 +4 55602765 . G C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26633;LSEQ=GGGATTTTTCTTTGGGAGCT;RSEQ=TTCTCTTTAGGTAAAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:208:84,124:184,235:419,208:0.3307:2,2:25.6:1:32.9:1:0.44051:1.15556:60:68.333:0.328:0:1.1 0/1:680:79:39,40:270,331:601,79:0.1162:2,2:23.6:1:30.2:1:0.47279:1.19:60:25.333:0.1126:0:1.1 +4 55603022 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23875;SOR=0;LSEQ=TTTTTCCTTTAGGTCACGTT;RSEQ=TCCCTTTTATTTTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:35,146:181,2:0.0109:2,2:10.5:1:28.5:1:0.35561:4.13:60:4:0.011:0:1 0/0:191:0:0,0:32,159:191,0:0:2,0:21:1:29.8:1:1:0:59.8:190:1:0:0.1 +4 55603271 . TG T 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66865;SOR=1.71332;LSEQ=GGAATTATTACTGAAGTTGC;RSEQ=GATGCCCATACATTTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:2:1,1:212,43:255,2:0.0078:2,2:22:1:31:1:0.31366:4.88546:60:4:0.0078:0:0 0/1:226:3:1,2:171,50:221,3:0.0133:2,2:18:1:31.3:1:0.13536:6.76402:60:6:0.0134:0.0044:0.3 +4 55603365 . G A 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0019;SOR=Inf;LSEQ=GACATAATGAAGACTTGCTG;RSEQ=GATGCAGATCCCCTAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:855:0:0,0:453,401:854,0:0:2,0:25.1:1:31.1:1:1:0:60:121:0.9988:0:0.1 0/1:863:10:5,5:445,407:852,10:0.0116:2,2:19.2:1:26.8:1:1:1.09325:60:9:0.0106:0:1.1 +4 55603649 . T C 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55309;SOR=0;LSEQ=TGTTCTGAGCCAAAGAAGGA;RSEQ=GTGAGATTGAGGGGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:4:0,4:0,22:22,4:0.1538:1,0:23:1:30.5:1:1:0:60:8:0.16:0:1 0/0:9:0:0,0:0,9:9,0:0:0,0:21.8:1:31.1:1:1:0:57.7:18:1:0:0 +4 55604872 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01916;SOR=Inf;LSEQ=TCTGAGCACACTTTAGTGGC;RSEQ=GATGATTTTTGTCATCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:30,0:0:1,0:25.7:1:29.7:1:1:0:60:29:1:0:0.2 0/1:12:3:0,3:0,9:9,3:0.25:0,0:19:1:30:1:1:0:60:6:0.25:0:1 +4 55943950 . G A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTGGATGGGTGTGTGGG;RSEQ=GGTGGGTGTGTGTGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:1:0:31:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:12:1:27:1:1:0:60:4:1:0:1 +4 55946081 . A G 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49146;SOR=1.81119;LSEQ=GCACCTCTCATGTGATGTCC;RSEQ=GGAGTTGGGGGTGTGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:555:550:369,181:0,0:0,550:0.991:0,2:25.4:1:30.2:1:1:0:60:109:0.9945:0:1.1 1/1:601:598:388,210:0,0:0,598:0.995:0,2:25.1:1:29.6:1:1:0:59.9:98.667:0.9966:0:1.2 +4 55946354 . G T 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAGAAGAAATGGCAAACAAA;RSEQ=GAGTTGGCAGAGAGAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:49,161:210,0:0:2,0:22:1:31.4:1:1:0:59.9:51.5:1:0:0.1 0/1:185:15:4,11:42,128:170,15:0.0811:2,2:18.6:1:28.1:1:1:1.11:60:30:0.0815:0:1.1 +4 55946366 . G T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.58304;SOR=2.5874;LSEQ=CAAACAAAGGAGTTGGCAGA;RSEQ=AGAAGACAATTCTTTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:1:0,1:30,140:170,1:0.0058:2,0:34:0:11:0:1:0:60:0:0:0:4 0/1:133:2:1,1:22,109:131,2:0.015:2,2:22:1:30.5:1:0.31704:4.87:60:4:0.0152:0:1 +4 55948108 . A G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGAAATTTGTCTTTTTAAT;RSEQ=TGGCTGAGTCTTACCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:609:609:381,228:0,0:0,609:1:0,2:24.3:1:32.1:1:1:0:60:86:1:0:1.1 1/1:577:577:346,231:0,0:0,577:1:0,2:24.8:1:31.2:1:1:0:60:95.167:1:0:1.1 +4 55948850 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5057;SOR=0;LSEQ=AGTGGTGGTATATTTGACTG;RSEQ=AGATCGGCTACCTAAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:18,136:154,2:0.0128:2,2:14.5:1:28:1:0.22945:7.38:60:4:0.0128:0:1 0/0:122:0:0,0:12,110:122,0:0:2,0:20.6:1:30.8:1:1:0:60:39.667:1:0:0.1 +4 55953330 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTAATTCCGGACACAGA;RSEQ=CCATGGCTTTCTGTATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55953380 . A G 35 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATAAGCATGTTCTCATGC;RSEQ=AGCACAGAACTCTTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:35.3:1:22.7:1:1:0:60:2:0.6667:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55953737 . C T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.09864;SOR=5.99163;LSEQ=TCCCGAGATGGCCTTGAAGT;RSEQ=ACCCTCCCCCGGGGGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:1:0,1:340,139:479,1:0.0021:2,0:1:0:23:0:0.29167:0:60:2:0.0021:0:1 0/1:404:5:2,3:270,128:398,5:0.0124:2,2:14.6:1:25.2:1:0.33489:3.15408:60:10:0.0127:0:1.2 +4 55953969 . T C 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1961;SOR=Inf;LSEQ=TGTTGTTATGGCTTCAGTTC;RSEQ=TCAAGTGCCTTTTCATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:36,175:211,0:0:2,0:23:1:30.9:1:1:0:59.9:210:0.9953:0:0.1 0/1:169:2:1,1:22,145:167,2:0.0118:2,2:11:0:29:1:0.25437:6.47:60:4:0.012:0:1 +4 55954971 . C A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08754;SOR=Inf;LSEQ=TAGCCATGAGACAGTTCAGG;RSEQ=AGTAGGAAAGTCCTTGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:238,50:288,0:0:2,0:24.1:1:32:1:1:0:60:35:1:0:0.1 0/1:231:3:2,1:181,47:228,3:0.013:2,2:29.3:1:23.7:1:0.50452:1.91899:60:2:0.0088:0:1 +4 55955232 . T C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6376;SOR=0.83473;LSEQ=AGTACACATTTGTAAAGAGC;RSEQ=GACGAGGTGAGATGCTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:85:10,75:1,28:29,85:0.7456:1,2:24.3:1:29.7:1:0.28474:3.70:59:27.333:0.7387:0:1.2 1/0:93:66:2,64:0,27:27,66:0.7097:1,1:20.5:1:29.4:1:1:0:60:132:0.7097:0:1 +4 55955737 . A AT 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.09951;LSEQ=TCCTCATCACCTATGTATCT;RSEQ=TTTTTTTTTTCAAAGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:223:118:54,64:33,65:98,118:0.5291:2,2:27.5:1:31.2:1:0.09427:1.66:60:117:0.5318:0.0628:0.2 0/1:120:12:4,8:45,60:105,12:0.1:2,2:25.6:1:29.9:1:0.7588:1.49497:58.6:24:0.1008:0:0.8 +4 55955760 . G T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25987;SOR=4.0168;LSEQ=TTTTTTTTCAAAGCTTCCGA;RSEQ=AAGTTTTGCCTGATAGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:1:0,1:143,95:238,1:0.0041:2,0:19:0:11:0:0.40167:0:60:0:0:0:4 0/1:121:2:2,0:75,43:118,2:0.0165:2,0:23:0:31.5:1:0.53627:0:60:4:0.0174:0:1 +4 55956225 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATAAGAGGATATTTCGTGC;RSEQ=GCCAGGTCCCTGTGGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:0:0,0:323,407:730,0:0:2,0:24.8:1:30.4:1:1:0:60:90.25:0.9972:0:0.1 0/1:723:24:7,17:291,408:699,24:0.0332:2,2:26.5:1:29:1:0.29251:1.7309:60:48:0.0335:0:1.2 +4 55956320 . CA C 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.77268;SOR=0.74001;LSEQ=TCTGTTGTGACCTCATGCAT;RSEQ=AAAAAAAATCCCACATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:9:0,9:8,155:163,9:0.0523:1,0:33.9:1:34:1:1:0:60:18:0.0529:0:0.1 0/1:102:4:0,4:4,94:98,4:0.0392:1,0:21:1:32.2:1:1:0:55:8:0.0396:0.0098:1 +4 55961159 . T C 233 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACAAACAAACTCCTTGAA;RSEQ=ACAAAATGAGTCTTTAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:79,286:365,0:0:2,0:22.9:1:28.8:1:1:0:60:51.143:1:0:0.1 0/1:376:180:51,129:54,142:196,180:0.4787:2,2:24.6:1:31.2:1:0.9086:1.04:60:44:0.4757:0:1.1 +4 55961665 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19764;SOR=Inf;LSEQ=AAGTTCTTCACAAAATTTCA;RSEQ=CTAAAAAACTAACCTGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:220,23:243,0:0:2,0:24.2:1:30.4:1:1:0:59.9:120.5:1:0:0.1 0/1:195:2:1,1:168,25:193,2:0.0103:2,2:21:1:27.5:1:0.24948:6.60909:60:4:0.0103:0:2 +4 55961890 . G A 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=ACTCATATTCCTCACTAAGC;RSEQ=TTTAATATAGTGATGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:25,199:224,0:0:2,0:25.3:1:32.3:1:1:0:60:448:1:0:0 0/1:183:11:2,9:27,145:172,11:0.0601:2,2:25.7:1:31.1:1:0.68701:1.19:60:22:0.0601:0:1.1 +4 55961944 . T A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15071;SOR=Inf;LSEQ=AAGAAGGCTACAACCTTTCA;RSEQ=TGGGACAGGAGTGTAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:1,77:78,0:0:1,0:24.2:1:30.9:1:1:0:60:156:1:0:0.1 0/1:50:2:0,2:0,48:48,2:0.04:1,0:25:1:32:0:1:0:60:4:0.04:0:1 +4 55962165 . AC TT 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12475;SOR=0;LSEQ=CTTCTCTGGACATCTGTTAC;RSEQ=AAGTAACAAACTGTATCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:10,1:10,2:12,11:0.4783:2,2:16.5:1:30.3:1:1:1.94:58.9:22:0.4783:0.0435:1.1 0/0:5:0:0,0:5,0:5,0:0:0,0:22.4:1:30.4:1:1:0:60:10:1:0:0.2 +4 55962358 . T C 115 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-04;SOR=14.50936;LSEQ=AACACTATCAGAGAGGCATG;RSEQ=TAAAATTGGGTGACCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:581:1:1,0:382,197:579,1:0.0017:2,0:9:0:35:0:1:0:60:2:0.0017:0:1 0/1:532:13:8,5:326,193:519,13:0.0244:2,2:20.2:1:31.3:1:1:1.05559:60:26:0.0246:0:1.2 +4 55962545 . T TG 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGAGGGAAATCATAGGTA;RSEQ=GGACATTTCCTTCAATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:66,238:304,0:0:2,0:23.7:1:30.5:1:1:0:60:100.333:1:0:0.1 0/1:237:75:17,58:40,122:162,75:0.3165:2,2:25.6:1:30.5:1:0.87033:1.11812:60:36.5:0.3133:0.0338:0.1 +4 55962556 . T A 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27321;SOR=0;LSEQ=TCATAGGTATGGACATTTCC;RSEQ=TCAATAATTGGGGTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:2,1:46,204:250,3:0.0119:2,2:10.7:1:27:1:0.09318:8.76:60:6:0.012:0:1 0/0:175:0:0,0:28,147:175,0:0:2,0:20.9:1:29.6:1:1:0:60:174:1:0:0.1 +4 55962570 . TC T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.53381;SOR=0;LSEQ=ATTTCCTTCAATAATTGGGG;RSEQ=CCTCCCTCCCTGCATGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:22,164:186,2:0.0106:2,2:20:1:30.6:1:0.23029:7.31:60:4:0.0109:0.0053:0 0/0:109:0:0,0:10,98:108,0:0:2,0:21.1:1:30.5:1:1:0:60:53:1:0:0.1 +4 55962574 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53805;SOR=0;LSEQ=CCTTCAATAATTGGGGTCCC;RSEQ=CCCTCCCTGCATGCCACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:19,161:180,2:0.011:2,2:25:1:27.5:1:0.20824:8.28:60:4:0.0112:0:1 0/0:102:0:0,0:7,95:102,0:0:2,0:20.8:1:28.6:1:1:0:60:24.5:1:0:0.1 +4 55964101 . T C 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTAATAACTCCCCCTTCAC;RSEQ=CTCCAAATGTCCTGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:19,29:48,0:0:2,0:23.4:1:30.4:1:1:0:60:15:1:0:0.1 1/0:22:11:8,3:6,5:11,11:0.5:2,2:20.8:1:29.6:1:0.65944:2.14:60:22:0.5:0:1.1 +4 55964158 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18789;SOR=Inf;LSEQ=CCTACCTCTAAGTGGCTATA;RSEQ=GAATGATTATACAAATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:56,10:66,0:0:2,0:22.8:1:31.7:1:1:0:59.3:132:1:0:0 0/1:51:2:1,1:46,3:49,2:0.0392:2,2:21:1:31.5:1:0.15216:13.42263:60:4:0.0392:0:1 +4 55964219 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17243;SOR=Inf;LSEQ=AAACCAGAATCCAACATCTG;RSEQ=ATACACCACATTTGTCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:222,35:257,0:0:2,0:23.6:1:30.7:1:1:0:60:256:1:0:0 0/1:183:2:1,1:161,20:181,2:0.0109:2,2:27:1:27:1:0.2169:7.88009:60:4:0.0112:0:1 +4 55964502 . T A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=TGGCTGTTGTTTTGTGTGCT;RSEQ=GTTATTGCTGTTTATTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:42,220:262,0:0:2,0:22.7:1:30.4:1:1:0:60:86.333:1:0:0.1 0/1:271:3:2,1:54,214:268,3:0.0111:2,2:7:1:26:1:0.10938:7.84:60:6:0.0112:0:1.3 +4 55964504 . T A 42 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11907;SOR=0;LSEQ=GCTGTTGTTTTGTGTGCTTG;RSEQ=TATTGCTGTTTATTGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:36,207:243,3:0.0122:2,2:7.7:1:26.7:1:0.0631:11.31:60:6:0.0123:0:1 0/0:253:0:0,0:46,207:253,0:0:2,0:22.3:1:29.3:1:1:0:60:506:1:0:0.2 +4 55964565 . A G 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AATAAAACTCATGGAGTTTG;RSEQ=GAGTGGTCCTATTATAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:11,94:105,0:0:2,0:23.2:1:32.7:1:1:0:59.3:210:1:0:0.2 0/1:60:24:1,23:1,35:36,24:0.4:1,1:18.3:1:31.6:1:1:1.51:60:48:0.4:0:1.1 +4 55964605 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=CTGCTTCTAGTTTCCCTTGT;RSEQ=CCCCAAAGGAGCTCAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:15,45:60,0:0:2,0:26.1:1:30.9:1:1:0:58.8:29:1:0:0.2 0/1:16:5:2,3:1,10:11,5:0.3125:2,2:11:1:29.6:1:0.21429:5.76:60:10:0.3125:0:1.4 +4 55964776 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=GCCCATTGAGCCAATAACAA;RSEQ=GGAAGAAACAACTCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:157,25:182,0:0:2,0:23.5:1:32.5:1:1:0:60:90:0.9945:0:0.1 0/1:160:2:1,1:129,28:157,2:0.0125:2,2:33.5:1:29.5:1:0.33246:4.54454:60:4:0.0128:0:0 +4 55964835 . C T 115 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00124;SOR=7.86353;LSEQ=TAATCATGAAAACCAATGTG;RSEQ=ATGGGCAGAAGGGAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:2:0,2:289,159:448,2:0.0044:2,0:7.5:1:17.5:1:0.12749:0:60:1:0.0023:0:1 0/1:471:16:11,5:275,180:455,16:0.034:2,2:27:1:28.8:1:0.60816:1.44:60:32:0.0345:0:1.1 +4 55965031 . AT A 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00017;SOR=0;LSEQ=TTATACTTTTTGTTTGTAAG;RSEQ=GACAAATTTTAGCACTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:13:2,11:5,94:99,13:0.1161:2,2:24:1:32.6:1:0.18698:3.36:60:26:0.1161:0.0268:0.2 0/0:109:0:0,0:9,100:109,0:0:2,0:23.9:1:29.8:1:1:0:60:218:1:0:0.1 +4 55967806 . A G 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TGCATTAGCTATTTTTCCTG;RSEQ=TGCTCTCCTTCTCCCCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:13:1:31.7:1:1:0:60:6:1:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:23:1:30:0:1:0:53.5:4:1:0:0 +4 55968008 . C T 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.084;SOR=Inf;LSEQ=CATGATCAGATTCCTTTTTA;RSEQ=GGCTGCATAGCATTCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:149,5:154,0:0:1,0:23.1:1:32.2:1:1:0:58.3:50.333:1:0:0.5 0/1:121:3:2,1:103,15:118,3:0.0248:2,2:7.3:1:31.7:1:0.34905:3.3822:29.3:6:0.025:0:4.3 +4 55968019 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04852;SOR=Inf;LSEQ=TCCTTTTTACGGCTGCATAG;RSEQ=ATTCCATGGTGTATATGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:170,16:186,0:0:2,0:22.8:1:32.2:1:1:0:59.4:92:1:0:0.6 0/1:166:4:2,2:130,32:162,4:0.0241:2,2:15.5:1:30.3:1:0.1864:4.0167:37:8:0.0245:0:4 +4 55968038 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24877;SOR=Inf;LSEQ=GCATTCCATGGTGTATATGT;RSEQ=CCACATTTTTTTTTATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:234,56:290,0:0:2,0:22.6:1:28.4:1:1:0:59.7:40.429:1:0:0.7 0/1:295:3:2,1:212,80:292,3:0.0102:2,2:33.7:1:31.7:1:1:1.32366:42.3:6:0.0103:0:3.3 +4 55968043 . A AT 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.96312;LSEQ=CCATGGTGTATATGTACCAC;RSEQ=TTTTTTTTTATCCCACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:6:6,0:246,66:312,6:0.0188:2,0:18.3:1:32.3:1:0.35097:0:60:12:0.0194:0.0094:0.8 0/1:331:6:5,1:230,92:322,6:0.0181:2,2:27:1:29.8:1:1:2.00:60:12:0.0185:0:0.2 +4 55968053 . A C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13042;LSEQ=TATGTACCACATTTTTTTTT;RSEQ=TCCCACTGACCTTCTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:366:218:168,50:112,36:148,218:0.5956:2,2:24.2:1:32.1:1:0.80207:1.08:59.6:26.25:0.5932:0:1.1 0/1:392:63:42,21:218,109:327,63:0.1607:2,2:23.3:1:30.8:1:1:1:60:126:0.1628:0:1.1 +4 55968745 . C G 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=ATGGTTCTGGTATCAGCAAA;RSEQ=TTTTAAACAGTTTAAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:6,142:148,0:0:1,0:23.5:1:33.8:1:1:0:60:147:1:0:0.1 0/1:144:10:0,10:12,122:134,10:0.0694:2,0:25.7:1:32.5:1:1:0:60:20:0.0694:0:1 +4 55970668 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5046;SOR=0;LSEQ=ATTATTAGCTTCTTTCTTCC;RSEQ=CAAGGACTTTCGGTGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:148,7:155,2:0.0127:1,2:21.5:1:30:1:0.09962:19.84568:60:4:0.0129:0:1 0/0:126:0:0,0:109,17:126,0:0:2,0:23.8:1:30.2:1:1:0:60:62:1:0:0.2 +4 55970680 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09659;LSEQ=TTTCTTCCTCAAGGACTTTC;RSEQ=GTGAAGAAGTGTGCACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:198:121:111,10:65,12:77,121:0.6111:2,2:23.7:1:30.9:1:0.1626:2.04:60:120:0.6218:0:1.1 0/1:168:22:18,4:117,29:146,22:0.131:2,2:20.1:1:29.3:1:1:1.11:60:44:0.1325:0:1 +4 55970782 . G A 139 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.62665;LSEQ=AAGGCATTCCAACTGCCTCT;RSEQ=CACAATGATCCAGAATTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:704:3:2,1:398,300:698,3:0.0043:2,2:23.7:1:27:1:1:1.51:60:6:0.0043:0:1.7 0/1:611:29:14,15:322,257:579,29:0.0475:2,2:22.5:1:28.7:1:0.45072:1.34174:60:28:0.0464:0:1 +4 55971846 . G T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=0.19372;LSEQ=CAGGAGATACCTGAGAAGTT;RSEQ=TAATTTATGAATGAAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:44:42,2:25,1:26,44:0.6286:1,1:25.8:1:31.1:1:1:1.18754:60:21:0.6176:0:1.1 0/1:41:10:10,0:31,0:31,10:0.2439:1,0:30:1:31.2:1:1:0:60:20:0.2439:0:1 +4 55971919 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18959;SOR=Inf;LSEQ=CCATGCCACTCACATGAATG;RSEQ=CAAAAACAACAGGGAATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:182,30:212,0:0:2,0:24.3:1:31.3:1:1:0:59.9:34.333:1:0:0.2 0/1:164:2:2,0:123,39:162,2:0.0122:2,0:35.5:1:30:1:1:0:60:4:0.0127:0:1 +4 55972782 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15417;SOR=Inf;LSEQ=TGATTATTAATCTCCAATAT;RSEQ=CCTCACATATTATTGTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:212,43:255,0:0:2,0:20.3:1:32.6:1:1:0:60:254:1:0:0.1 0/1:166:2:1,1:139,25:164,2:0.012:2,2:22:1:27.5:1:0.28952:5.47169:60:4:0.0122:0:1 +4 55972814 . AAG A 69 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.46232;SOR=0.46956;LSEQ=ATTGTACCATCCTTCCATTA;RSEQ=AGAGAGAGATTTTCAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:446:5:2,3:296,144:440,5:0.0112:2,2:33.6:1:29.8:1:0.33751:3.07477:60:10:0.0113:0.0022:0.2 0/0:378:2:2,0:252,124:376,2:0.0053:2,0:18:1:30.3:1:1:0:60:4:0.0054:0.0026:0 +4 55972946 . A G 152 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=12.84154;LSEQ=CACACTTCTCCATTCTTCAC;RSEQ=AGGGTATGGGTTTGTCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:736:3:1,2:311,422:733,3:0.0041:2,2:38.3:1:26:1:1:1.47319:60:2:0.0028:0:2 0/1:660:33:11,22:270,357:627,33:0.05:2,2:22.5:1:30.2:1:0.28581:1.51169:59:32:0.0493:0:1.6 +4 55972974 . T A 220 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=161.94481;LSEQ=GGGTTTGTCACTGAGACAGC;RSEQ=TGGCTATAAGAAAGAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:597:2:0,2:203,392:595,2:0.0034:2,0:30.5:1:32.5:1:0.55043:0:60:4:0.0034:0:1 0/1:481:170:63,107:118,193:311,170:0.3534:2,2:24.8:1:29.8:1:0.92161:1.03834:60:340:0.3556:0:1.2 +4 55973007 . T A 33 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3209;SOR=3.95932;LSEQ=AGAGATAACAGCGCATATTA;RSEQ=GATTTAATTTTTCTTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:1:1,0:74,258:332,1:0.003:2,0:1:0:28:0:0.22523:0:60:2:0.0031:0:1 0/1:254:3:3,0:70,181:251,3:0.0118:2,0:6:1:21.3:1:0.02304:0:60:2:0.0081:0:2 +4 55974095 . T C 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=AACAACTTTTGAATTGTCAG;RSEQ=CAGCTTTGAAGAATGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:20,153:173,0:0:2,0:23.9:1:29.8:1:1:0:60:33.6:1:0:0.1 0/1:139:11:3,8:15,113:128,11:0.0791:2,2:27:1:31.5:1:0.15437:2.80:60:22:0.0821:0:1.2 +4 55974106 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50855;SOR=0;LSEQ=AATTGTCAGTCAGCTTTGAA;RSEQ=AATGGGAAATAGAGGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:8,131:139,2:0.0141:2,2:24.5:1:28:1:0.12401:15.49:60:4:0.0143:0:1 0/0:106:0:0,0:10,96:106,0:0:2,0:25.3:1:30.8:1:1:0:60:212:1:0:0.2 +4 55974290 . C G 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAATCTCAGTATTTTGGGA;RSEQ=GCCAAGGTAGGTGGATCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:22.8:1:32.8:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55976168 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCTGATACATCAACTACAA;RSEQ=ATCAAACTAGAAGCTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:12:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55976451 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08009;LSEQ=ACGCCAGATGACTTTTGTAC;RSEQ=CAGGCCCAGCCATGATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:63:63,0:31,0:31,63:0.6702:1,1:24.3:1:30.7:1:1:0:60:62:0.6667:0:1 0/1:87:12:12,0:73,2:75,12:0.1379:1,0:24.9:1:29.3:1:1:0:60:24:0.1379:0:1.2 +4 55976462 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49787;SOR=Inf;LSEQ=CTTTTGTACGCAGGCCCAGC;RSEQ=ATGATATGAGTGAAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:117,0:117,0:0:1,0:23.2:1:31.2:1:1:0:60:38:1:0:0.6 0/1:118:2:2,0:115,1:116,2:0.0169:1,0:27:1:31:0:1:0:60:4:0.0171:0:1 +4 55976709 . C G 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTTTAATTGTGTGATTGGA;RSEQ=TCAAGGGGTATTCCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:880:0:0,0:392,487:879,0:0:2,0:25.5:1:32.7:1:1:0:60:42.95:0.9988:0:0.1 0/1:849:24:12,12:369,453:822,24:0.0283:2,2:32.1:1:31.8:1:0.67988:1.23:60:48:0.0284:0:1.2 +4 55976739 . A G 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCCATTTTTATACCTATG;RSEQ=AAAAAAATTCTCAGGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:707:0:0,0:337,367:704,0:0:2,0:24.7:1:30.7:1:1:0:60:87:0.9971:0:0.1 0/1:634:60:30,30:270,300:570,60:0.0946:2,2:24:1:30.2:1:0.78606:1.11:60:120:0.0954:0:1.1 +4 55976939 . G GA 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.12191;LSEQ=AGCAACAAAAGGTTTTTCTG;RSEQ=AAGAAAATAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:5:0,5:133,337:470,5:0.0104:2,0:31:1:30.8:1:0.32841:0:57.4:10:0.011:0:3.6 0/1:514:6:1,5:186,319:505,6:0.0117:2,2:27.8:1:24:1:0.42269:2.91038:52.7:5:0.0101:0.0039:4 +4 55976992 . A G 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50195;SOR=0;LSEQ=TGTAAATGGTCATTTGATTT;RSEQ=GTTTTTCATTTCAAGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:10,155:165,2:0.012:2,2:21.5:1:26.5:1:0.12777:14.83:60:4:0.0122:0:1 0/0:141:0:0,0:9,132:141,0:0:2,0:23.4:1:30.3:1:1:0:59.4:34.25:1:0:0.6 +4 55979558 . C T 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTGGTCACTCCGGGTTA;RSEQ=ACCATCTATAGTTAAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:935:0:0,0:456,479:935,0:0:2,0:24.4:1:32.2:1:1:0:60:115.875:1:0:0.1 0/1:995:101:48,53:448,444:892,101:0.1015:2,2:25.3:1:28.4:1:0.67472:1.11399:60:100:0.1018:0:1.2 +4 55979609 . G A 176 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02748;LSEQ=CTTCATCTCACTCCCAGACT;RSEQ=GGTTTTTAGGTCTCGGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:780:57:26,31:298,425:723,57:0.0731:2,2:24.9:1:30.3:1:0.57708:1.20:60:114:0.0736:0:1.1 0/0:926:2:2,0:400,524:924,2:0.0022:2,0:1:0:23.5:1:0.1882:0:60:4:0.0022:0:1 +4 55980239 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.96578;LSEQ=TATCTCTCAAGCAAACTTCA;RSEQ=TGGGGCTTATTATCTAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:119:91,28:162,53:215,119:0.3563:2,2:25.2:1:30.6:1:0.8942:1.06:60:58.5:0.3545:0:1.1 1/0:304:209:152,57:73,22:95,209:0.6875:2,2:22.7:1:29.2:1:0.48328:1.24344:60:28.857:0.6801:0:1 +4 55980456 . C T 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCAAGTAAATTGAAAAAA;RSEQ=AGAACATGAGAGAGCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:97,310:407,0:0:2,0:24.5:1:32.4:1:1:0:60:100.75:0.9975:0:0.1 0/1:299:70:23,47:57,172:229,70:0.2341:2,2:23.6:1:28.2:1:0.21728:1.47:60:69:0.2339:0:1.2 +4 55980998 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19566;SOR=Inf;LSEQ=TATCTCCAAGATCTTAATAC;RSEQ=AGGATATGTTATTAATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:146,45:191,0:0:2,0:23.7:1:30.6:1:1:0:59.9:94.5:1:0:0.1 0/1:152:2:1,1:110,40:150,2:0.0132:2,2:26:1:27:1:0.46802:2.72858:60:4:0.0134:0:1 +4 55981634 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18501;SOR=Inf;LSEQ=GTATTTACTAGAAAAGTTGG;RSEQ=CATTTTTCAGGTTCCTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:7,97:104,0:0:2,0:22.9:1:30.5:1:1:0:59.7:208:1:0:0.1 0/1:79:2:1,1:10,67:77,2:0.0253:2,2:14.5:1:27.5:1:0.26063:6.44:60:4:0.0253:0:1 +4 55981683 . G T 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.46472;SOR=1.73444;LSEQ=GACAAGTGAATGACTGGAAG;RSEQ=GACACCTCACACAACCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:0,6:0,42:42,6:0.125:1,0:18:1:31.7:1:1:0:60:12:0.1304:0:1 0/1:20:4:0,4:1,15:16,4:0.2:1,0:21.8:1:29.3:1:1:0:60:8:0.2105:0:1 +4 55985009 . G T 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05649;SOR=0;LSEQ=GGTATTAATATGAAGTGCCA;RSEQ=ACTGTGAGGCTATTTCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:4:1,3:48,233:281,4:0.014:2,2:12.3:1:24:1:0.53188:1.61:60:3:0.0106:0:2 0/0:298:0:0,0:58,240:298,0:0:2,0:24.6:1:30.4:1:1:0:60:58.6:1:0:0.1 +4 55985017 . G A 46 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24927;SOR=Inf;LSEQ=TATGAAGTGCCAGACTGTGA;RSEQ=GCTATTTCTAAGAAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:33,213:246,0:0:2,0:22.7:1:31.7:1:1:0:60:81:1:0:0.1 0/1:262:3:1,2:44,215:259,3:0.0115:2,2:6.3:1:29.3:1:0.43319:2.43:60:6:0.0115:0:1.3 +4 55985142 . A G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00452;SOR=13.25883;LSEQ=TCCCAGCACTTTGGGAGGCC;RSEQ=AGGCGGATGGATCACCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:0,4:0,15:15,4:0.2105:1,0:14.5:1:30.3:1:1:0:43.8:8:0.2105:0:1.5 1/1:10:8:0,8:0,2:2,8:0.8:0,0:12.4:1:31:1:1:0:49.8:16:0.8:0:1.4 +4 55985149 . A G 48 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.11304;SOR=5.47828;LSEQ=ACTTTGGGAGGCCAAGGCGG;RSEQ=TGGATCACCTGAGGCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:0,16:16,2:0.1111:1,0:12.5:1:31:1:1:0:32:4:0.1111:0:2.5 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:11.3:1:30.3:1:1:0:42:6:0.4286:0:2 +4 55985209 . C G 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4697;SOR=0;LSEQ=AACATGGTAAAACCCTGTCT;RSEQ=TACTAAAAATACAAAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:36.8:1:32.6:1:1:0:42:10:0.5:0:1.6 0/0:2:0:0,0:0,2:2,0:0:0,0:16.5:1:33:0:1:0:42.5:4:1:0:1 +4 55987002 . G T 50 d5 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=GTTATTGGAATGTGGGTGTG;RSEQ=GTGTGTATTTGTGTGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:31:1:25.3:1:1:0:60:3:1:0:1.3 1/0:4:2:1,1:1,1:2,2:0.5:2,2:9:0:16.5:1:1:1:60:0:0:0:1.5 +4 55987018 . C CGT 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=11.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGTGGGTGTGTATTTGTGTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:0,1:1,5:0.8333:0,0:21:1:30:1:0.16667:0:60:10:0.8333:0.3333:0.4 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:28.8:1:1:0:60:4:1:0:0.5 +4 55991042 . G T 58 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CAGACAACTTTTCACCGCCT;RSEQ=TTCTCGCCTGCGGAGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:23.8:1:29.3:1:1:0:60:3:1:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:50:0:30:0:1:0:60:2:1:0:0 +4 55991138 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTCGGCATCTCAGGACA;RSEQ=GCTCCAGCCGAGGTCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:21,0:0,0:0,21:1:0,1:24.5:1:32.5:1:1:0:60:42:1:0:1.1 1/1:7:7:5,2:0,0:0,7:1:0,2:17.9:1:31.7:1:1:0:60:14:1:0:1.1 +4 55991422 . G T 172 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=73.63081;LSEQ=GCGGCCCGGGTCTCCACGCA;RSEQ=AGCCACAGGGCGACGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:911:1:0,1:413,495:908,1:0.0011:2,0:14:0:30:0:1:0:60:2:0.0011:0:2 0/1:974:73:35,38:406,493:899,73:0.0749:2,2:25.6:1:27.9:1:0.71415:1.12:60:72:0.0748:0:1.1 +4 55991731 . T C 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=GGAAACGCAGCGACCACACA;RSEQ=TGACCGCTCTCCCGGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:1,6:0,0:0,7:0.875:0,2:25.3:1:33.1:1:1:0:60:14:1:0:1.6 0/0:1:0:0,0:0,1:1,0:0:0,0:5:0:30:0:1:0:60:2:1:0:0 +4 55991779 . T A 65 d5;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGCAGGGTGGGAGCTGG;RSEQ=GCCGAAACTCTAGAGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:7.8:1:32.5:1:1:0:60:8:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 55991885 . C G 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCACCCGGGTACCCGGCGG;RSEQ=GATCTCCAGCTCCCCAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:15.7:1:33:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 56218221 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51811;SOR=Inf;LSEQ=TTGGTGATCCTTAGAGCCAC;RSEQ=CCATACTTCTGCTCCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:21,9:30,0:0:2,0:30.7:1:31.5:1:1:0:57.1:60:1:0:0.2 0/1:47:2:1,1:30,15:45,2:0.0426:2,2:19.5:1:27.5:1:1:1.96856:48:4:0.0426:0:1 +4 56974810 . A G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.25882;SOR=Inf;LSEQ=GCTGATATTTATTGCATACA;RSEQ=GACAAGGGGGGCAGGGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:14,0:0:2,0:16.4:1:30.2:1:1:0:54.1:28:1:0:0.2 0/1:21:3:2,1:10,8:18,3:0.1429:2,2:22:1:29:1:1:1.57:60:6:0.15:0:1 +4 60522652 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13462;SOR=Inf;LSEQ=AAACCCCATCTTAGGGTCAG;RSEQ=AACCTCAAAGACCAAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:12,13:25,0:0:2,0:22.2:1:31:1:1:0:55.2:24:1:0:0.2 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:34:1:29:1:1:1.15:52.5:4:0.1333:0:1 +4 60522704 . G GA 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.52569;SOR=0;LSEQ=AAAGATGAGAAAGAATCAAT;RSEQ=AAAAAAATGTTGAAAACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:4,9:13,2:0.1333:2,2:18:0:31:1:1:2.12:35:4:0.1333:0:0 0/0:8:0:0,0:4,4:8,0:0:2,0:24:1:30.9:1:1:0:56.4:16:1:0:0.9 +4 60522757 . G A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACTTCTCCTCCAAATGA;RSEQ=CACAATGTCTCTCCATCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:32.7:1:30.6:1:1:0:60:14:1:0:1 1/1:5:5:2,3:0,0:0,5:1:0,2:24:1:28.2:1:1:0:60:10:1:0:1.2 +4 62068481 . CGT C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.24582;SOR=0;LSEQ=TGGGTGTGTGTGTGTCTGTG;RSEQ=GTGTGTGTGGTGTGTAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:3:2,1:51,33:84,3:0.0345:2,2:11.7:1:32.1:1:1:1.29:60:6:0.0345:0.023:2 0/0:84:0:0,0:58,26:84,0:0:2,0:23.5:1:29.3:1:1:0:60:41:1:0:0.1 +4 62068536 . C T 24 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6885;LSEQ=CCTCTACCAGCCTTACTTGG;RSEQ=GGCGGAGTCAGCGTTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:0,2:78,74:152,2:0.013:2,0:21:1:27:1:0.24191:0:60:4:0.0135:0:1 0/0:223:2:0,2:111,110:221,2:0.009:2,0:1:0:24:0:0.49776:0:60:4:0.0091:0:1 +4 62068561 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17446;SOR=0;LSEQ=GAGTCAGCGTTTGAGTGTGT;RSEQ=CGCATTTTTGCGCCCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:63,89:152,2:0.013:2,2:25:1:29.5:1:1:1.41:60:4:0.0133:0:1 0/0:214:0:0,0:91,121:212,0:0:2,0:25.6:1:31.5:1:1:0:59.8:105:0.9953:0:0.2 +4 62068571 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16923;SOR=0;LSEQ=TTGAGTGTGTGCGCATTTTT;RSEQ=CGCCCCAGGGACGGCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:53,71:124,2:0.0157:2,2:30.5:1:32:0:1:1.34:60:4:0.016:0:1.5 0/0:181:0:0,0:73,106:179,0:0:2,0:25:1:31.5:1:1:0:59.9:88.5:0.9888:0:0.2 +4 62707476 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13078;SOR=Inf;LSEQ=GCTGAATGCCCATAAGAATA;RSEQ=TAAATCGTCTGTACTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:44,1:45,0:0:1,0:20.4:1:33.1:1:1:0:60:90:1:0:0 0/1:26:2:2,0:23,1:24,2:0.0769:1,0:15.5:1:32:0:1:0:60:4:0.0769:0:2 +4 62707491 . T C 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02364;SOR=Inf;LSEQ=GAATACTAAATCGTCTGTAC;RSEQ=TGGCTGGAGTTTTCTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:54,1:55,0:0:1,0:25.1:1:32.7:1:1:0:60:54:1:0:0 0/1:37:4:4,0:32,1:33,4:0.1081:1,0:16.8:1:31:1:1:0:60:8:0.1081:0:1.5 +4 62707653 . C T 203 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACCGAAATTTGGCTTTAG;RSEQ=TGTCCTTAGTAAGAGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:393:0:0,0:180,213:393,0:0:2,0:25:1:32.5:1:1:0:60:38.3:1:0:0.2 0/1:489:122:58,64:177,190:367,122:0.2495:2,2:24.8:1:29.3:1:0.917:1.0279:60:244:0.2542:0:1.1 +4 62707719 . G T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00269;SOR=0.40886;LSEQ=AATCATTTGTTTAATTAGCT;RSEQ=AATCTCCTAAGGGAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:39:7,32:31,97:128,39:0.2335:2,2:24.9:1:28.9:1:0.51538:1.45784:60:18.5:0.2327:0:1.3 0/1:190:21:8,13:42,127:169,21:0.1105:2,2:17.1:1:28.7:1:0.19807:1.85:60:42:0.1123:0:1 +4 65603107 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTTCTTACAGCATGTGG;RSEQ=CTCCTTATAAAAGAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 65604616 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.17645;LSEQ=TTCATTTACAAGAACCTTTA;RSEQ=TATCAATACAATAATGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:33:15,18:65,76:141,33:0.1897:2,2:26.7:1:32.1:1:1:1.02617:60:66:0.1976:0:1.1 1/0:173:95:42,53:36,42:78,95:0.5491:2,2:23.3:1:31.8:1:0.87819:1.08114:60:190:0.5523:0:1.1 +4 65604620 . C T 170 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01172;LSEQ=TTTACAAGAACCTTTAATAT;RSEQ=AATACAATAATGCCATGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:60:27,33:51,66:117,60:0.339:2,2:25.1:1:28.9:1:0.87417:1.06:59.8:120:0.3468:0:2.9 0/0:169:1:0,1:79,89:168,1:0.0059:2,0:1:0:23:0:1:0:60:2:0.006:0:1 +4 65604632 . G GA 63 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12123;SOR=0.16637;LSEQ=TTTAATATCAATACAATAAT;RSEQ=CCATGAGCTAGACTTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:6:4,2:14,21:35,6:0.0357:2,2:26:1:24.7:1:0.37729:2.92:60:2:0.0238:0.006:2.8 0/0:164:1:1,0:49,54:103,1:0.0061:2,0:10:0:30:0:0.48077:0:60:2:0.0061:0:2 +4 65604633 . CC AGT 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.14669;LSEQ=TTAATATCAATACAATAATG;RSEQ=ATGAGCTAGACTTCTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:127:46,81:14,21:35,127:0.756:2,2:26.7:1:30.6:1:0.6964:1.17273:59.8:254:0.756:0.131:2.4 0/1:164:51:22,29:49,54:103,51:0.311:2,2:26:1:29.1:1:0.61185:1.19474:60:102:0.3129:0.061:2.1 +4 65604634 . C CT 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=7.5465;LSEQ=TAATATCAATACAATAATGC;RSEQ=ATGAGCTAGACTTCTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:32:12,20:1,0:1,32:0.2222:0,2:28.9:1:29.6:1:0.39394:0:60:64:0.8205:0.0278:1 1/0:146:100:46,54:1,0:1,100:0.6849:0,2:28.6:1:29:1:0.46535:0:60:200:0.9709:0.0616:0.9 +4 65604674 . G T 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.49876;SOR=Inf;LSEQ=TCTTTCTTGATATCCTTGAA;RSEQ=TAAGTTTTTCTAATTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:31,76:107,0:0:2,0:25:1:32.8:1:1:0:59.8:214:1:0:1.7 0/1:117:2:1,1:38,77:115,2:0.0171:2,2:22:0:26.5:1:1:2.01:60:4:0.0174:0:3.5 +4 65604715 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21572;SOR=Inf;LSEQ=GTTTTAATTTGATGAGGTAT;RSEQ=CTGATATCTTTATAGTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:9,40:49,0:0:2,0:20.9:1:32:1:1:0:59.9:98:1:0:0.6 0/1:43:2:1,1:7,34:41,2:0.0465:2,2:36:1:29.5:1:0.34109:4.61:60:4:0.0476:0:1 +4 65763540 . C A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.24859;SOR=Inf;LSEQ=GAATTCTTTTATAATTATCT;RSEQ=TCTCACCATGCTGTTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:142,82:224,0:0:2,0:24.8:1:32.7:1:1:0:60:448:0.9912:0:0.5 0/1:234:3:1,2:134,97:231,3:0.0128:2,2:25:1:23.3:1:0.57525:2.75095:60:2:0.0088:0:2.3 +4 65763592 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15016;SOR=0.79276;LSEQ=TTACAACCATTTTCATGCCT;RSEQ=TAATGCAGAAATGATCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:189:105,84:63,60:123,189:0.6058:2,2:25.8:1:32.3:1:0.48659:1.19:60:93.5:0.6032:0:1.1 1/0:326:179:84,95:70,76:146,179:0.5491:2,2:25.6:1:31.5:1:0.91118:1.04156:60:178:0.5494:0:1.1 +4 66189675 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.52325;SOR=0;LSEQ=ACTAAGAACTGGATACTTCA;RSEQ=TAAAACCATGATTACAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:70,2:72,2:0.027:1,0:15.5:1:29:1:1:0:60:4:0.027:0:1 0/0:46:0:0,0:46,0:46,0:0:1,0:21.4:1:32.2:1:1:0:60:92:1:0:0 +4 66189753 . C CT 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.14857;LSEQ=CACTGTTTTCCCTTTTCCCC;RSEQ=TTTTTTTGTTAAAATAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:64:57,7:185,38:223,64:0.2078:2,2:28.5:1:32.6:1:0.32898:1.67:60:128:0.2254:0:0.1 0/1:294:11:11,0:225,55:280,11:0.0374:2,0:25.6:1:30.4:1:0.13281:0:60:22:0.0375:0.0068:0.5 +4 66189835 . C T 180 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=76.18984;LSEQ=GCGACATTTACATGAAGTTA;RSEQ=AATGGCACCATTCCGTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:922:1:0,1:510,410:920,1:0.0011:2,0:1:0:24:0:0.44625:0:60:2:0.0011:0:1 0/1:1033:79:44,35:519,435:954,79:0.0765:2,2:27:1:28.6:1:0.90653:1.05:60:78:0.0761:0:1.2 +4 66190274 . C CTGCAGATT 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATTGAAAAGTTTTGAAA;RSEQ=TGCAGATTTACAATATTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:13:1:30.9:1:1:0:60:4:0.5:0.5:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66197804 . C T 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.25513;LSEQ=TCACCTACTGATCTGTAGGC;RSEQ=CCAGATCCTAGTGGGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:774:572:239,333:83,117:200,572:0.739:2,2:27.7:1:30.6:1:1:1.01:59.9:46.667:0.7388:0:1.1 0/1:761:319:140,179:200,240:440,319:0.4192:2,2:25:1:29.1:1:0.71168:1.06537:60:318:0.4223:0:1.1 +4 66198059 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTATCCATAATTAATGA;RSEQ=GACTTAACATGAAGACTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:26.2:1:32.7:1:1:0:60:22:1:0:1 1/1:5:5:0,5:0,0:0,5:1:0,0:25.2:1:31:1:1:0:60:10:1:0:1.4 +4 66201374 . AT A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATGAAAATACACACATTTA;RSEQ=TTTTTTTTATGCTACCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:29.2:1:33.2:1:1:0:60:12:0.8571:0:0 1/1:3:3:3,0:0,0:0,3:1:0,0:34.3:1:29.8:1:1:0:51.7:6:1:0.3333:0 +4 66213336 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTTAATTTAAAGAAAC;RSEQ=TAGACTATTCCTTTTTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:19:1:32:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66214043 . G A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.38687;SOR=0.65351;LSEQ=AAGTGAATCTGTTTGACAGC;RSEQ=CGCAGTGTCTTTTCAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:53:0,53:0,21:21,53:0.7162:1,1:20:1:30.4:1:1:0:60:106:0.7162:0:1.1 1/0:37:23:0,23:0,14:14,23:0.6216:1,1:22:1:28.7:1:1:0:60:22:0.6286:0:1 +4 66214395 . TATATATATATATATATATATAA T 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGATATATATATATATATA;RSEQ=AATATATATGTGTGTGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:22:1:29.3:1:1:0:53:6:1:1:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66216523 . C T 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATTTTCCATAGTGTAGA;RSEQ=GTAACAGTTTTTAAATAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1:0,2:21.8:1:31:1:1:0:60:10:1:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66216588 . C T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTTTTGAAGGAATAGCT;RSEQ=TTTTTTCCCTACAATGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:3,0:3,2:0.4:0,2:11.5:1:29:1:0.4:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66216749 . CTA C 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATACACAGACACATACATA;RSEQ=TATATATATATATATAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:34:1:32.3:1:1:0:60:6:0.75:0:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66216856 . A AT 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATCCATTCTGAAGTAAG;RSEQ=TTTTTTATTTTTAGTATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:2,0:8,0:8,2:0.2:0,0:44:1:30:1:1:0:49:4:0.2:0:0.5 0/0:3:0:0,0:3,0:3,0:0:0,0:13.3:1:28.7:1:1:0:60:6:1:0:0 +4 66218334 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCACTTATAGGCTCTAAC;RSEQ=TGACACCTTTATTAATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:42:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66218505 . A AT 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.66569;SOR=1.83446;LSEQ=ATTCCCTTCTACTTCTCTGC;RSEQ=TTTTTTTTTTCAAATTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:15,0:11,0:11,15:0.5172:0,1:30.2:1:31.2:1:1:0:58.7:30:0.5357:0.0345:0.6 1/0:6:4:4,0:1,0:1,4:0.6667:0,0:24:1:31.8:1:1:0:60:8:0.6667:0:0 +4 66218527 . A T 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17194;SOR=0;LSEQ=TTTTTTTTTCAAATTAAGAC;RSEQ=TACTTAAATAAAACTTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:10:10,0:28,0:28,10:0.2632:1,0:29.6:1:32.1:1:1:0:60:20:0.2632:0:1.1 0/0:9:0:0,0:9,0:9,0:0:0,0:25.4:1:29.7:1:1:0:60:18:1:0:0 +4 66218677 . C T 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTGGCCCAAATTCAACTT;RSEQ=AACATCACAGCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:28:21,7:306,93:399,28:0.0656:2,2:23:1:30.1:1:0.81929:1.09654:60:56:0.0671:0:1.9 0/0:363:0:0,0:272,91:363,0:0:2,0:24.8:1:30.4:1:1:0:60:71.6:1:0:0.6 +4 66218696 . T A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=2e-05;SOR=Inf;LSEQ=TCAACATCACAGCATCATCA;RSEQ=CACAGCACAACATCACAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:361,177:538,0:0:2,0:26.8:1:30.5:1:1:0:60:58.778:1:0:1 0/1:480:14:12,2:302,164:466,14:0.0292:2,2:16.1:1:28.4:1:0.15338:3.25:60:28:0.0294:0:1.8 +4 66218728 . C T 292 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00511;LSEQ=ATCACAATATATAAATAACA;RSEQ=CTTGAATAACTAAATTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:792:790:468,322:0,1:1,790:0.9975:0,2:24.8:1:30.4:1:0.40834:0:60:64.833:0.9987:0:1.1 1/0:696:465:265,200:134,97:231,465:0.6681:2,2:24.7:1:28.9:1:0.80768:1.04255:60:65.429:0.6686:0:1.1 +4 66218756 . C T 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTAAATTATTCCCCAATC;RSEQ=TACCTTCAAAAATGTATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:986:0:0,0:514,471:985,0:0:2,0:25.1:1:32.2:1:1:0:60:108.444:0.999:0:0.8 0/1:876:38:18,20:438,397:835,38:0.0434:2,2:23.1:1:30.2:1:0.61929:1.22557:60:37:0.0426:0:1.1 +4 66218980 . G GAAAT 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.32034;SOR=0.29281;LSEQ=AAAAATAAAATTTATTAAAT;RSEQ=AAAGATATTTAAATATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:51:0,51:0,1:1,51:0.9623:0,1:25.4:1:30.4:1:1:0:59.4:102:0.9808:0.2264:0.1 1/1:25:22:0,22:0,3:3,22:0.88:0,1:24:1:29.6:1:1:0:60:44:0.88:0.2:0.1 +4 66230452 . TA T 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AAAGTAAAAGAGCCAATAGT;RSEQ=AAAAAAAAGTTGATATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:23.5:1:31:1:1:0:60:4:0.5:0.25:0 0/0:2:0:0,0:2,0:2,0:0:0,0:19:1:28.5:1:1:0:60:4:1:0:0 +4 66232950 . CT C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGTAACAAATAGAACA;RSEQ=TTTAAAAAAAAAAAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:2,0:61,0:61,2:0.0317:1,0:20.5:1:34.5:1:1:0:60:4:0.0323:0:1 0/0:28:0:0,0:27,1:28,0:0:1,0:17.7:1:30.1:1:1:0:58.6:56:1:0:1.1 +4 66232954 . T AA 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.55059;SOR=0;LSEQ=TGTAACAAATAGAACACTTT;RSEQ=AAAAAAAAAAAAAACAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:3,0:63,0:63,3:0.0455:1,0:29.3:1:31:0:1:0:58.3:6:0.0462:0:2.7 0/0:29:0:0,0:28,1:29,0:0:1,0:17.6:1:30.1:1:1:0:58.6:58:1:0:1.2 +4 66233029 . A G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01839;SOR=1.49495;LSEQ=AGAAACTTAAATAACAATAA;RSEQ=GTGTCCCCTATTTTATTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:296:150:121,29:122,23:145,150:0.5068:2,2:24.5:1:32.2:1:0.44922:1.27025:60:20.429:0.5089:0:1.2 1/0:274:166:136,30:85,23:108,166:0.6058:2,2:21.5:1:30.9:1:0.53378:1.23:60:54.333:0.6105:0:1.1 +4 66241504 . TACAC T 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=24;MSI=14.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCACAGAAACACACACACA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:31:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66242656 . C T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12397;SOR=Inf;LSEQ=ATGGAGAAAGAAAAGGAATG;RSEQ=CGACGGTAATACATATAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:242,124:366,0:0:2,0:21.9:1:31.9:1:1:0:59.9:182:1:0:0.1 0/1:366:4:1,3:230,132:362,4:0.0109:2,2:18.3:1:26.8:1:0.14394:5.20352:60:8:0.011:0:1 +4 66270051 . G T 52 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12747;SOR=Inf;LSEQ=TCAGATCAAGGTGAGGAAGA;RSEQ=ATCAGCTGCAGAACTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:238,78:316,0:0:2,0:23.6:1:32.9:1:1:0:60:104.333:1:0:0.1 0/1:364:4:2,2:264,96:360,4:0.011:2,2:5.5:1:26:1:0.29409:2.74103:60:8:0.0111:0:1 +4 66270241 . A G 197 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTTGTGGTTAAAGTGATC;RSEQ=CATGCATTCAAAATAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:55,226:281,0:0:2,0:23.2:1:30.3:1:1:0:59.9:92.667:1:0:0.1 0/1:248:83:17,66:36,129:165,83:0.3347:2,2:19.2:1:31:1:0.87061:1.08312:60:166:0.3374:0:1.1 +4 66270271 . G A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00773;SOR=Inf;LSEQ=AAAATAAAAGTTGCTTAATA;RSEQ=ACAGTAATCAATTCATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:13,135:148,0:0:2,0:23.4:1:32.1:1:1:0:59.9:48.333:1:0:0.1 0/1:121:6:1,5:12,103:115,6:0.0496:2,2:21.3:1:30.2:1:0.50211:1.71:60:12:0.0496:0:1 +4 66270345 . G A 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17387;SOR=0;LSEQ=CCTAATATCCTTTCTTAAAA;RSEQ=TGTGTAATTGAAAAGTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:7:0,7:0,35:35,7:0.1667:1,0:24.9:1:31.7:1:1:0:60:14:0.1707:0:1 0/0:14:0:0,0:0,14:14,0:0:1,0:19.1:1:33.1:1:1:0:60:28:1:0:0.1 +4 66277927 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCACTCCAGTCTGGGCCA;RSEQ=AGAGTGAGACTCTCTCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:47.5:1:32.5:1:1:0:60:4:1:0:1.5 +4 66279935 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=AGAGTGCCCAGGGAGGGTAT;RSEQ=GATCCACTGACTCTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:160,20:180,0:0:2,0:24.1:1:31.2:1:1:0:59.8:89:0.9944:0:0.1 0/1:187:2:1,1:156,29:185,2:0.0107:2,2:15:1:27.5:1:0.29584:5.30593:60:4:0.0108:0:1 +4 66280107 . C G 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGAAGCTGGTTTCAAGCCCT;RSEQ=TGCAGTAATAGTTGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:0:0,0:231,387:618,0:0:2,0:23.9:1:32.5:1:1:0:60:76.25:1:0:0.2 0/1:716:24:9,15:292,400:692,24:0.0335:2,2:22.5:1:29.8:1:0.6809:1.21634:60:23:0.0328:0:1 +4 66280171 . C T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13174;SOR=1.47993;LSEQ=GTCTCTTGGTCCTTGGGATG;RSEQ=GCATGCATATACAATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:28:6,22:52,218:270,28:0.094:2,2:21.1:1:30:1:0.8026:1.14:60:56:0.0966:0:1.3 0/1:323:43:14,29:76,204:280,43:0.1331:2,2:22.3:1:28.5:1:0.46833:1.29:60:86:0.1348:0:1.1 +4 66285765 . T C 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGTGTCTCATCTTTTTTC;RSEQ=TATCTCCTTAACAGTATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:16:1:30.3:1:1:0:53.8:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66286088 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAACATACTCTTCTGCAA;RSEQ=TTGGATAATTGTAGTTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:237:237:207,30:0,0:0,237:1:0,2:23.4:1:30.5:1:1:0:59.1:46.4:1:0:2.2 1/1:176:176:149,27:0,0:0,176:1:0,2:21.7:1:29.7:1:1:0:59.9:352:1:0:2 +4 66286100 . T C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00729;SOR=0;LSEQ=TTCTGCAAGTTGGATAATTG;RSEQ=AGTTGCTAAAATGAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:293:293:242,51:0,0:0,293:1:0,2:24.4:1:32.1:1:1:0:59.3:28.3:1:0:2 1/1:233:227:171,56:4,2:6,227:0.9742:2,2:21.9:1:31.3:1:0.64043:1.52:59.9:55.75:0.9738:0:1.8 +4 66286113 . G GA 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.1484;LSEQ=ATAATTGTAGTTGCTAAAAT;RSEQ=AAAAAAAAAAGAAAGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:140:112,28:146,40:186,140:0.3989:2,2:28.3:1:30.3:1:0.78408:1.10:59.7:45.667:0.4018:0:1.6 0/1:302:27:17,10:197,77:274,27:0.0894:2,2:24.5:1:27.3:1:0.37419:1.50279:60:12.5:0.0842:0.0099:1.5 +4 66286376 . G A 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05177;SOR=0.15512;LSEQ=TATATTGGCATTTTGAGAAC;RSEQ=TAGCAATATAAAAAAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:9:0,9:1,89:90,9:0.0909:1,0:21.8:1:30:1:1:0:60:18:0.0928:0:1.7 0/1:66:1:0,1:1,64:65,1:0.0152:1,0:23:0:32:0:1:0:60:2:0.0154:0:1 +4 66286385 . TA T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.51589;SOR=0;LSEQ=ATTTTGAGAACGTAGCAATA;RSEQ=AAAAAAATCCCAATTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:0,2:1,79:80,2:0.0244:1,0:32:1:32:1:1:0:60:4:0.0247:0:1 0/0:55:0:0,0:1,54:55,0:0:1,0:24.5:1:31:1:1:0:60:110:1:0:0.5 +4 66286414 . T C 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAATTAAATTTTAGTTT;RSEQ=TCTATATAAGGTTTAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:46:0,46:0,0:0,46:1:0,1:22.7:1:33.4:1:1:0:59.5:45:1:0:1.2 1/1:26:26:0,26:0,0:0,26:1:0,1:19.2:1:32.1:1:1:0:60:52:1:0:1 +4 66286633 . C T 58 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGAGCTCTATATGACATAT;RSEQ=CCATTATGCTAATAGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:18.3:1:29.3:1:1:0:56:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66355888 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.0326;SOR=0.19386;LSEQ=AAATGTTTTGTTTTGTTTTG;RSEQ=TTTCCTGTAAATGGGATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:19:19,0:7,0:7,19:0.7308:0,1:26.6:1:32.6:1:1:0:60:38:0.7308:0:1.4 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:24:1:33.5:1:1:0:60:8:0.3333:0:1 +4 66355901 . G T 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=TGTTTTGTTTTCCTGTAAAT;RSEQ=GGATTGCTAACAAAGCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:30,0:0:1,0:25:1:31.9:1:1:0:59.4:29:1:0:0.9 0/1:17:7:7,0:10,0:10,7:0.4118:0,0:20.6:1:30.1:1:1:0:60:14:0.4118:0:1 +4 66360718 . GAAGAAGA G 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAGAGGAAGAAGAGGAAG;RSEQ=AAGAAGAAAGAAGAAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:24.3:1:31.5:1:1:0:54.8:8:0.8:0.2:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66361319 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.25044;SOR=Inf;LSEQ=ACAGATGCAGTGTTTGTTTT;RSEQ=TGAATAATGTCATTATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:4,101:105,0:0:1,0:23.9:1:32.8:1:1:0:60:51.5:1:0:0.1 0/1:121:3:2,1:13,105:118,3:0.0248:2,2:12.7:1:26.3:1:0.04023:15.44:60:6:0.025:0:1 +4 66468046 . TA T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.045;SOR=0.5798;LSEQ=TACAATATAAAATAGAAAGA;RSEQ=AAAAAAATTCAAAAAATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:217:186:17,169:5,26:31,186:0.8571:2,2:27.2:1:31.4:1:0.32957:1.90503:60:185:0.8605:0.0645:0.2 1/0:170:132:15,117:12,24:36,132:0.7765:2,2:27.5:1:30.5:1:0.00362:3.85996:59.7:264:0.7811:0.0529:0.1 +4 66468381 . T C 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCAAAGAAAGAAAAATA;RSEQ=GTATATTTTGAATAAAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:18.3:1:32.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 66508839 . C T 119 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03158;SOR=0;LSEQ=TGCTGAAGGAAACTTCACAT;RSEQ=TCTTTGTGGAACAATACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:0,16:1:0,1:23.7:1:29.8:1:1:0:60:15:1:0:1.4 1/0:4:2:2,0:2,0:2,2:0.5:0,0:29:1:31.5:1:1:0:60:4:0.5:0:1 +4 66508962 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.19671;SOR=Inf;LSEQ=CCCTCACCCCATCCAACACA;RSEQ=ACATAGCACCTCCTGTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:96,5:101,0:0:1,0:26.7:1:32.9:1:1:0:60:202:1:0:0.1 0/1:81:2:1,1:72,7:79,2:0.0247:2,2:25:0:32.5:1:0.18889:9.688:60:4:0.0253:0:1.5 +4 66509085 . T G 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTCATAAAACTTACCCCA;RSEQ=TTTTTGGAAAAGCAATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:0:0,0:311,281:592,0:0:2,0:26.3:1:30.6:1:1:0:59.9:97.667:0.9966:0:0.1 0/1:578:81:42,39:269,228:497,81:0.1401:2,2:25.4:1:31.5:1:0.71982:1.09538:60:162:0.1424:0:1.1 +4 66509194 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.64988;LSEQ=GAAATGTATATTATCATGAA;RSEQ=ATTGTATCTCTATTTTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:78:18,60:22,105:127,78:0.3805:2,2:22.6:1:32.3:1:0.36503:1.43:60:77:0.3812:0:1.1 1/0:200:124:32,92:16,60:76,124:0.62:2,2:22.5:1:30.9:1:0.49777:1.30:60:61:0.6162:0:1.1 +4 66535209 . G T 31 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08684;SOR=Inf;LSEQ=AGCAGCGTCCAGCGCGCTGA;RSEQ=ACCTGAACTCCCAGGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:294,52:346,0:0:2,0:22.5:1:32.4:1:1:0:60:48.429:1:0:0.2 0/1:276:3:1,2:227,46:273,3:0.0109:2,2:7.7:1:20:1:0.07919:9.74424:60:2:0.0074:0:1.7 +4 66535284 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19905;LSEQ=ACCCCCATCTCCCTACCTTC;RSEQ=TTGCTGGGGCTGGCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:217:115,102:431,356:787,217:0.2157:2,2:25.3:1:29.7:1:0.64512:1.07374:60:26.125:0.2135:0:1.1 0/1:964:50:26,24:490,421:911,50:0.0519:2,2:25.9:1:29.6:1:0.88444:1.07427:60:100:0.053:0:1.2 +4 66535316 . C T 105 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02089;SOR=4.31646;LSEQ=GGCCAGGAGGGTCCGGAGTG;RSEQ=GGCGCACAGGAGAAGGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1204:3:0,3:562,639:1201,3:0.0025:2,0:1:0:23.3:1:0.25269:0:60:2:0.0017:0:1 0/1:1218:13:5,8:576,628:1204,13:0.0107:2,2:16.1:1:28.5:1:0.58415:1.46706:54.9:26:0.0109:0:1.2 +4 66535498 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1209;SOR=0;LSEQ=CGGTGCCGCTGTCCCGAGCG;RSEQ=CTCAGTCCACCGCTTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:3:2,1:70,107:177,3:0.0167:2,2:23.3:1:28.7:1:0.56477:3.04:60:6:0.0169:0:1 0/0:183:0:0,0:75,108:183,0:0:2,0:12:0:14:0:1:0:60:0:0:0:3 +4 66535529 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=CGCTTCGGCCTCGCAGAGCG;RSEQ=CGAAGGGAGACTCGGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:27,69:96,0:0:2,0:21.4:1:32:1:1:0:60:192:1:0:0.1 0/1:106:2:1,1:30,74:104,2:0.0189:2,2:19.5:1:27:1:0.50135:2.44:60:4:0.0194:0:1 +4 67137334 . C G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTTACATTGCCAACAAACA;RSEQ=ATGAATAAAGCTCAACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:30:1:1:0:60:4:1:0:1 +4 67138143 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18202;LSEQ=CCAGATGGGAGAAACAACCC;RSEQ=AGGTAACAGAACAATTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:459:251:132,119:107,101:208,251:0.5468:2,2:25.6:1:30:1:0.85124:1.05:59.8:124.5:0.5473:0:1.1 0/1:545:98:54,44:247,200:447,98:0.1798:2,2:27.3:1:28.8:1:1:1.00629:60:97:0.18:0:1.1 +4 67138228 . A C 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACACTCAATTCCAATCCC;RSEQ=ATTGTAGTAGTATATTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:64,178:242,0:0:2,0:24.4:1:30.8:1:1:0:60:79.667:1:0:0.2 0/1:281:35:10,25:74,172:246,35:0.1246:2,2:22.6:1:30.9:1:1:1.07531:60:34:0.1245:0:1.1 +4 67138251 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50104;SOR=Inf;LSEQ=TGTAGTAGTATATTCACATT;RSEQ=TTGTGATACTTTTTAAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:25,123:148,0:0:2,0:21.5:1:30.8:1:1:0:59.8:73:1:0:0.1 0/1:171:2:1,1:30,139:169,2:0.0117:2,2:8:1:27:1:0.33058:4.57:60:4:0.012:0:1.5 +4 67138309 . G A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.00225;SOR=0.21628;LSEQ=AATCAAAAATAAGAGTCTTC;RSEQ=TAATTACAGTATTGGGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:20:0,20:0,18:18,20:0.5263:1,1:30.4:1:32.1:1:1:0:60:40:0.5263:0:1 0/1:42:8:0,8:0,34:34,8:0.1905:1,0:19.8:1:30.8:1:1:0:60:16:0.1905:0:1.3 +4 67138353 . TAA T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.48959;SOR=0.56593;LSEQ=TAATACTCATTTGACAAAAA;RSEQ=AAAAAAAAAATGATGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:0,9:0,9:9,9:0.5:0,0:23.3:1:31.1:1:1:0:60:18:0.5:0:0.6 0/1:14:5:0,5:0,7:7,5:0.3571:0,0:30.8:1:30.4:1:1:0:60:10:0.3571:0:1 +4 67191468 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50619;SOR=Inf;LSEQ=GAATGAAACCTTCATCTCAA;RSEQ=AAGTTTGGGAAAAAAATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:100,33:133,0:0:2,0:23.7:1:32.6:1:1:0:60:266:1:0:0.3 0/1:171:2:1,1:123,46:169,2:0.0117:2,2:24:0:30:1:0.47534:2.65605:60:4:0.0117:0:1.5 +4 67191491 . A C 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.38285;SOR=3.35942;LSEQ=GTTTGGGAAAAAAATAGAAA;RSEQ=ATAGAAGGAAGGAATAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:1:1,0:129,88:217,1:0.0046:2,0:47:0:13:0:1:0:60:0:0:0:4 0/1:263:4:2,2:153,106:259,4:0.0152:2,2:38.3:1:31.8:1:1:1.44131:60:8:0.0154:0:1.8 +4 67191539 . A T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20555;LSEQ=TAGCAGGGAAAATGACTACC;RSEQ=TAGGAAAATACCAGTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:286:149:75,74:70,67:137,149:0.521:2,2:27.9:1:30.8:1:0.90634:1.03075:60:23.833:0.5162:0:1.2 0/1:362:66:32,34:138,158:296,66:0.1823:2,2:25.6:1:29.9:1:0.78696:1.08:60:65:0.1836:0:1.4 +4 67191541 . A G 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=16.62405;LSEQ=GCAGGGAAAATGACTACCAT;RSEQ=GGAAAATACCAGTAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:1,0:139,141:280,1:0.0036:2,0:3:0:31:0:0.49822:0:60:2:0.0036:0:1 0/1:356:20:9,11:154,182:336,20:0.0562:2,2:30.2:1:31.9:1:1:1.0341:60:40:0.057:0:2.1 +4 67191574 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21099;SOR=0;LSEQ=TAAAAATACTATATATTGGA;RSEQ=TTGTATATTTTCTTTAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:74,124:198,2:0.01:2,2:24:1:31.5:1:1:1.67:60:4:0.0102:0:2 0/0:236:0:0,0:85,151:236,0:0:2,0:24.7:1:29.1:1:1:0:60:32.714:1:0:0.3 +4 67191597 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50581;SOR=Inf;LSEQ=GTATATTTTCTTTAAGAATT;RSEQ=AGGGTAAAGCACCCAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:36,89:125,0:0:2,0:27.3:1:28:1:1:0:59.8:24:1:0:0.4 0/1:160:2:1,1:46,112:158,2:0.0125:2,2:41:1:31.5:1:0.50252:2.42:60:4:0.0127:0:1 +4 67840231 . A G 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.01575;SOR=Inf;LSEQ=CACTTGAAGATATTTCTAAA;RSEQ=TAAAATTGTCAAAACTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:79,29:108,0:0:2,0:25.6:1:30.2:1:1:0:60:107:1:0:0.2 0/1:124:7:3,4:84,33:117,7:0.0565:2,2:29.4:1:32.3:1:0.19511:3.35535:60:14:0.0565:0:1.3 +4 67840237 . T C 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24872;SOR=Inf;LSEQ=AAGATATTTCTAAAATAAAA;RSEQ=TGTCAAAACTAAAGCATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:85,34:119,0:0:2,0:25.7:1:30.6:1:1:0:60:58.5:1:0:0.2 0/1:131:3:1,2:89,39:128,3:0.0229:2,2:33.7:1:24.7:1:0.23067:4.50517:60:2:0.0154:0:1 +4 67840314 . G T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.64873;SOR=0.91557;LSEQ=AAACAACTTTCCAATTAGTT;RSEQ=TAGAGGTATTCAGGAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:95:49,46:76,65:141,95:0.4025:2,2:24:1:29.8:1:0.79059:1.09721:60:30.667:0.3966:0:1.1 0/1:270:103:53,50:82,85:167,103:0.3815:2,2:25.4:1:29:1:0.80222:1.10:60:50.5:0.3769:0:1.3 +4 67840369 . A C 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGTTTCATGAATAATTCA;RSEQ=ATTCCAGTGTCAGTCGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:80,120:200,0:0:2,0:26.7:1:31:1:1:0:60:199:1:0:0.4 0/1:230:20:9,11:86,124:210,20:0.087:2,2:25.3:1:30.4:1:0.81348:1.18:60:19:0.0837:0:1.8 +4 67840426 . G T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02008;SOR=2.24601;LSEQ=AACTATTTCTGAATTATCTG;RSEQ=TTTGAAGCTACCTGTGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:25:2,23:6,42:48,25:0.3425:2,2:23.6:1:30.3:1:0.70702:1.63247:60:50:0.3425:0:1 1/0:74:40:11,29:7,27:34,40:0.5405:2,2:20.7:1:29.1:1:0.59084:1.46:60:39:0.5493:0:1.3 +4 68141830 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAACAGCAAGATGGCTGCC;RSEQ=TGGGACCTAGAAAGGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:30,11:41,2:0.0465:2,2:13:0:33:1:0.48505:2.65433:20:4:0.0488:0:2.5 0/0:21:0:0,0:15,6:21,0:0:2,0:23:1:28.2:1:1:0:40.7:20:1:0:0.2 +4 68141861 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53196;SOR=0;LSEQ=AAAGGGAGAAGCCATGTTGC;RSEQ=CAACTCCAGAGGTTGGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:24,25:49,2:0.0392:2,2:27.5:1:32.5:1:1:1.04:20:4:0.04:0:2.5 0/0:29:0:0,0:15,14:29,0:0:2,0:24.5:1:28.8:1:1:0:36.3:28:1:0:0.1 +4 68263831 . T G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGGCTAGGCTCAGCTGG;RSEQ=TGATTCTTCTGATCTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 68264417 . A G 34 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TTCCAAACTGCTCTATGAAA;RSEQ=GAAAGGTTAAACTCGGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:34:1:1:0:41.5:4:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:33:0:1:0:48:2:1:0:2 +4 68264432 . G T 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAAAGAAAGGTTAAACTC;RSEQ=GCGAGTTGAACGCACACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:32.5:1:1:0:41.5:4:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:19:0:32:0:1:0:48:2:1:0:2 +4 68264543 . C A 48 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCGATTGAAATCTGCA;RSEQ=CTGGAAATTCCACAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,1:1,3:0.75:0,2:21.3:1:30.3:1:1:0:57.7:6:0.75:0:1.3 +4 68264579 . TCTGTCAAAAGGAAGTTTC T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGTGTATCAAATCTGC;RSEQ=AATTCTGCTAGTTGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:27:1:31.8:1:1:0:56.5:4:0.6667:0.6667:1 +4 68264783 . T C 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GTTAAACTCTGTGAATTGAA;RSEQ=GCACACATCACAAAGTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:26:0:32:0:1:0:22:2:1:0:7 1/1:2:2:0,2:0,0:0,2:1:0,0:13:1:27.5:1:1:0:26.5:4:1:0:4.5 +4 68264989 . G C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTACTGAGAATTCTTT;RSEQ=TCCAGCAGTATATGAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:31.5:1:1:0:32:4:1:0:3.5 +4 68264994 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGAGAATTCTTTGTCCA;RSEQ=CAGTATATGAAGAAATCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:30:1:1:0:32:4:1:0:3.5 +4 68264997 . G T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAATTCTTTGTCCAGCA;RSEQ=TATATGAAGAAATCCCGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:30.5:1:1:0:32:4:1:0:3.5 +4 68265246 . TA GT 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATTCCACAAAAAGAGTG;RSEQ=TCAAATGTGCTCTGTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:31:1:1:0:29.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 68265274 . T G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTCTGTCTAAAGGAAGG;RSEQ=TCAAGTCTGTGAGTGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32:0:33.5:1:1:0:29.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 68265279 . G C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTAAAGGAAGGTTCAA;RSEQ=TCTGTGAGTGGAATACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:34.5:1:1:0:29.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 68265285 . G C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGGAAGGTTCAAGTCTGT;RSEQ=AGTGGAATACACACAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:34:0:1:0:29.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 68265408 . C G 31 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTGCGGACTATCCAAC;RSEQ=AGAGTGTTTCCACACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:31.5:1:1:0:41.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 68265462 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTTAAACTCTGTGAGTTGAA;RSEQ=GCACACATCAAAAAGTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:30.5:1:1:0:41.5:4:1:0:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:33:0:33:0:1:0:24:2:1:0:4 +4 68265492 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AAAAAGTAGTTTCTGAGAAT;RSEQ=ATTCTGTCTAATTTTTATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:10.5:1:31:1:1:0:41.5:4:1:0:2.5 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:30.5:1:28:1:1:0:39:4:0.6667:0:4 +4 68265503 . A C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.7321;LSEQ=TCTGAGAATGATTCTGTCTA;RSEQ=TTTTTATACGAAGATATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:5:0:33:0:1:0:37:2:0.5:0:3 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:30.5:1:30.5:1:1:0:39:4:0.6667:0:4 +4 68265519 . A G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAATTTTTATACGAAGAT;RSEQ=TTTCTTTTTCTACCATTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:14.2:1:34:0:1:0:24.3:12:1:0:7.7 1/1:19:17:9,8:1,1:2,17:0.8947:2,2:12.5:1:31.1:1:1:1.12:22.7:34:0.8947:0:7 +4 68265520 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTAATTTTTATACGAAGATA;RSEQ=TTCTTTTTCTACCATTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:15.2:1:32:0:1:0:24.3:12:1:0:7.7 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:30:1:29.5:1:1:1.11803:39:4:0.1053:0:4 +4 68265524 . T C 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTATACGAAGATATTTC;RSEQ=TTTTCTACCATTGGCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:19.2:1:33.2:1:1:0:24.3:12:1:0:7.7 1/1:19:17:9,8:1,1:2,17:0.8947:2,2:17.5:1:29.7:1:1:1.12:22.7:16:0.8889:0:7 +4 68265528 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATACGAAGATATTTCTTTT;RSEQ=CTACCATTGGCCTCAAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:23.2:1:33:0:1:0:24.3:12:1:0:7.7 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:22:1:30:1:1:1.10554:39:4:0.1:0:4 +4 68265534 . A T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGATATTTCTTTTTCTACC;RSEQ=TTGGCCTCAAAGCGATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:29.2:1:33.8:1:1:0:24.3:12:1:0:7.7 1/1:21:19:10,9:0,1:1,19:0.9048:0,2:24.4:1:29.3:1:1:0:23.1:18:0.9474:0:6.6 +4 68265539 . C T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTTTTTCTACCATTGG;RSEQ=CTCAAAGCGATTGAAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:34.2:1:31.3:1:1:0:24.3:12:1:0:7.7 1/1:26:23:11,12:1,2:3,23:0.8846:2,2:26:1:28.7:1:1:1.79:22.7:22:0.88:0:6.2 +4 68265545 . A T 51 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5585;SOR=0.61029;LSEQ=TTTTCTACCATTGGCCTCAA;RSEQ=GCGATTGAAATTTCCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:42:0:33:0:1:0:26:2:0.1667:0:8 0/1:28:3:2,1:12,13:25,3:0.1071:2,2:26.3:1:32.3:1:1:2.11:27:6:0.1071:0:6 +4 68265557 . T C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTCAAAGCGATTGAAAT;RSEQ=TCCACATGGAAATTCCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:47.2:1:32.3:1:1:0:24.3:12:1:0:7.7 1/1:28:24:12,12:2,2:4,24:0.8571:2,2:34.1:1:32.3:1:1:1:22.6:48:0.8571:0:6.1 +4 68265570 . T C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.56102;SOR=0;LSEQ=TTGAAATTTCCACATGGAAA;RSEQ=TCCACAAAAAGAGTGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:34.2:1:31.2:1:1:0:24.3:12:1:0:7.7 1/1:30:24:12,12:3,3:6,24:0.8:2,2:26.3:1:32.2:1:1:1:22.6:48:0.8:0:6.1 +4 68265582 . A G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CATGGAAATTCCACAAAAAG;RSEQ=GTGTTTCAAATCTGCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:22.2:1:28.2:1:1:0:24.3:12:1:0:7.7 0/1:25:3:1,2:12,10:22,3:0.12:2,2:18:1:32.3:1:0.59304:2.31861:24:6:0.12:0:5 +4 68265589 . C A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCCACAAAAAGAGTGTTT;RSEQ=AAATCTGCTCTGTCTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:15.2:1:29.8:1:1:0:24.3:12:1:0:7.7 0/1:24:3:1,2:12,9:21,3:0.125:2,2:25:1:32:1:0.57609:2.56011:24:6:0.125:0:5 +4 68265591 . A C 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCACAAAAAGAGTGTTTCA;RSEQ=ATCTGCTCTGTCTAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:13.2:1:27.8:1:1:0:24.3:12:1:0:7.7 0/1:24:3:1,2:12,9:21,3:0.125:2,2:27:1:33.7:1:0.57609:2.56011:24:6:0.125:0:5 +4 68265601 . G T 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03793;SOR=0;LSEQ=GAGTGTTTCAAATCTGCTCT;RSEQ=TCTAAAGGAAAGTTCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:3.8:1:28:1:1:0:24.4:10:1:0:8 0/1:15:6:4,2:3,3:6,6:0.4:2,2:8.2:1:29.5:1:1:1.89:23.3:12:0.4:0:7.2 +4 68265605 . A G 67 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=GTTTCAAATCTGCTCTGTCT;RSEQ=AAGGAAAGTTCAACTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:2:0:30:0:1:0:25:4:1:0:8 1/0:9:5:4,1:2,2:4,5:0.5556:2,2:5.6:1:29:1:0.52381:3.39:23:10:0.5556:0:7.2 +4 68265623 . G A 47 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAAGGAAAGTTCAACTCT;RSEQ=TGAGTTGAATGCACACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:1,0:1,3:0.75:0,2:8.7:1:29.7:1:1:0:24:6:0.75:0:5 +4 68265736 . T A 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCCATATATCCACTTGC;RSEQ=GAATTTACAAGGAGAGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:29:1:1:0:60:4:1:0:1 +4 68265873 . T A 71 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATATTTCCTTTTCTAC;RSEQ=TTTGGCGTATAAGCGCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:12:1:30.6:1:1:0:20.4:10:1:0:6.2 +4 68265880 . G C 63 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCCTTTTCTACTTTTGGC;RSEQ=TATAAGCGCTCGAAATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:4:2,2:0,1:1,4:0.8:0,2:15.8:1:31.8:1:1:0:20.5:8:0.8:0:6.5 +4 68265883 . T A 71 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTTCTACTTTTGGCGTA;RSEQ=AAGCGCTCGAAATCTCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:22:1:31:1:1:0:20.4:10:1:0:6.2 +4 68265891 . C T 87 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTGGCGTATAAGCGCT;RSEQ=GAAATCTCCAACTGCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:3,4:0,0:0,7:1:0,2:22.9:1:31.1:1:1:0:24:14:1:0:5.6 +4 68265896 . T A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGCGTATAAGCGCTCGAAA;RSEQ=CTCCAACTGCAAATATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:10:0:31:0:1:1.41:33:4:0.2857:0:4 +4 68265902 . A C 91 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGCGCTCGAAATCTCCA;RSEQ=CTGCAAATATCACAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:3,4:0,0:0,7:1:0,2:30.9:1:32.7:1:1:0:24:14:1:0:5.6 +4 68265925 . T G 89 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAATATCACAAAAAGAGG;RSEQ=TTTCACATCTGCTCCTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:3,4:0,0:0,7:1:0,2:14.9:1:31.9:1:1:0:24:14:1:0:5.6 +4 68266603 . TA GG 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAAATATCACAAAAAGAG;RSEQ=TTTCACATCTGCTCTGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:22:1:31.8:1:1:0:32.5:4:0.6667:0:2 +4 69761131 . T C 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05249;SOR=0;LSEQ=AAAATGTCACATTTGTAGTT;RSEQ=CCATTTTCTTGTCTCTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:3,10:13,5:0.2778:2,2:18:1:32:1:0.58275:2.12:55.2:10:0.2778:0:1.2 0/0:14:0:0,0:7,7:14,0:0:2,0:14.3:1:29.6:1:1:0:60:28:1:0:0.1 +4 73526628 . T C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5004;SOR=Inf;LSEQ=TAAGATGGGGGTAAGGTTCT;RSEQ=GCTAAGCTTGCTAAACTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:55,14:69,0:0:2,0:22.4:1:30.8:1:1:0:60:33.5:1:0:0.1 0/1:82:2:1,1:59,21:80,2:0.0244:2,2:7:1:28:1:0.46703:2.76809:60:4:0.0244:0:1 +4 73526674 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50618;SOR=Inf;LSEQ=GAAGGGTTCTTGTTGAAACT;RSEQ=GATATTACAAGGAAATGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:88,57:145,0:0:2,0:25.3:1:32:1:1:0:60:290:1:0:0.1 0/1:186:2:1,1:104,80:184,2:0.0108:2,2:26.5:1:28:1:1:1.29814:60:4:0.011:0:1.5 +4 73526723 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10052;SOR=0;LSEQ=CTACGAGAAGGTTCAGGAGC;RSEQ=TGACTAATGTTTGGTCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:3:2,1:57,87:144,3:0.0204:2,2:23:1:30.3:1:0.56455:3.03:60:6:0.0205:0:1 0/0:168:0:0,0:67,101:168,0:0:2,0:25.1:1:30.8:1:1:0:60:83:1:0:0.1 +4 75662382 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18171;SOR=Inf;LSEQ=ACTCTCTCACCTATTAATTT;RSEQ=TCATCCGTTTTATAGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:71,1:72,0:0:1,0:24.6:1:31.8:1:1:0:60:35:1:0:0.1 0/1:54:2:2,0:52,0:52,2:0.037:1,0:10.5:1:30:1:1:0:60:4:0.0377:0:1 +4 75662398 . AT A 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.70135;SOR=0.65729;LSEQ=ATTTCTCATCCGTTTTATAG;RSEQ=TTTTTTTTACCAATAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:4:3,1:96,5:101,4:0.0381:1,2:17.8:1:29.6:1:0.21251:6.16927:60:8:0.0381:0.0095:0.3 0/1:79:2:2,0:71,5:76,2:0.0253:2,0:21:1:31.3:1:1:0:60:4:0.0263:0.0127:0.5 +4 75662446 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.79288;LSEQ=TCTCCTCTTTCCTCCTGGGA;RSEQ=GGATCTTGTCTAAAGACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:19:12,7:143,79:222,19:0.0788:2,2:23.5:1:31:1:1:1.05567:60:38:0.0795:0:1.8 0/1:283:94:57,37:113,76:189,94:0.3322:2,2:25.1:1:30.9:1:1:1.04:60:93:0.3333:0:1.9 +4 75662515 . A T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=13.14884;LSEQ=CTGCTTTCCTAAGGTGGCCT;RSEQ=TATTAAAGATAAAGTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:29:15,14:129,178:307,29:0.0863:2,2:23:1:29.9:1:0.33194:1.48:60:28:0.0848:0:2.2 1/0:382:212:98,114:74,96:170,212:0.555:2,2:25.2:1:29.5:1:0.60662:1.11:60:69.667:0.5573:0:1.7 +4 75662524 . A G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.86522;LSEQ=TAAGGTGGCCTATATTAAAG;RSEQ=TAAAGTGATTTATAATATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:25:12,13:120,163:283,25:0.0812:2,2:24:1:32:1:0.67467:1.25:60:50:0.082:0:2.2 0/1:357:91:42,49:116,150:266,91:0.2549:2,2:23.5:1:30.6:1:0.71443:1.11:60:44.5:0.255:0:2.3 +4 75662594 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22972;SOR=Inf;LSEQ=TGTTTGCCTAACATAATAAT;RSEQ=CCAAGGTAATGGTTTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:29,103:132,0:0:2,0:23.3:1:32.3:1:1:0:60:131:1:0:0.2 0/1:122:2:1,1:29,90:119,2:0.0164:2,2:36.5:1:29:1:0.43595:3.07:60:4:0.0165:0:1 +4 75662635 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00131;SOR=5.46711;LSEQ=AAATAGACTTAAAAATTCAC;RSEQ=AATAAAAGGGATACAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:5:1,4:6,53:59,5:0.0781:2,2:30.6:1:33.2:1:0.45084:2.17:60:10:0.0806:0:1.2 0/1:50:16:0,16:5,29:34,16:0.32:2,1:23.8:1:31.6:1:0.1626:0:60:32:0.32:0:1.2 +4 75662692 . C T 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02935;SOR=8.9847;LSEQ=CAGAGAATAAATCCCTTTAA;RSEQ=GGCAAGATTTGCTTGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:0,20:20,2:0.0909:1,2:21.5:1:29.5:1:0.09091:0:60:4:0.0909:0:1.5 1/0:8:4:0,4:0,4:4,4:0.5:0,0:27.3:1:30.3:1:1:0:60:8:0.5:0:1.8 +4 75662871 . A G 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAGCTTGTGAGACAGCAG;RSEQ=AGAACCTAAGGAGTTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:34:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 76957171 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=2e-05;SOR=18.37565;LSEQ=TGCTGTTGCTGCTGGTGCTG;RSEQ=TGCTGCTACTTCAGCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:6,7:7,7:14,13:0.4815:2,2:31.5:1:30.5:1:1:1.16002:60:26:0.4815:0:1.2 1/1:38:36:16,20:1,1:2,36:0.9474:2,2:26.9:1:29.2:1:1:1.24262:60:72:0.9474:0:1.2 +4 78271425 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00183;SOR=Inf;LSEQ=TGACTATGTGAGCTTTCCTT;RSEQ=TATCTGCTTTATTGCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:39,1:40,0:0:1,0:22.1:1:32.7:1:1:0:60:39:1:0:0.2 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:22.3:1:28.5:1:1:0:60:8:0.3333:0:1 +4 78271514 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23125;SOR=Inf;LSEQ=GTGGTCTTCTACATTGTGTT;RSEQ=AAACCAGGTTGCTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:95,34:129,0:0:2,0:21.9:1:32.2:1:1:0:59.9:128:1:0:0.2 0/1:120:2:1,1:83,35:118,2:0.0167:2,2:31:1:28:1:0.51176:2.35233:60:4:0.0168:0:1 +4 78271554 . C G 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=TCCCTTTCATCTTCATTTCT;RSEQ=TTAGCAAATTCAGGGCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:11:9,2:145,92:237,11:0.044:2,2:24.3:1:33:1:0.21479:2.84:59.3:22:0.0444:0:1 0/0:305:0:0,0:177,126:303,0:0:2,0:23.5:1:31:1:1:0:60:150.5:0.9934:0:0.5 +4 78271576 . A G 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGCAAATTCAGGGCATAAC;RSEQ=TAATCTTCTAGGTTTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:200,146:346,0:0:2,0:24.8:1:30.6:1:1:0:60:33.6:1:0:0.5 0/1:377:58:34,24:170,147:317,58:0.1538:2,2:23.2:1:30.9:1:0.56669:1.22:59.5:57:0.1536:0:1.7 +4 78271612 . T A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.98997;LSEQ=GGGAGTGGGAAAGGGCAGGC;RSEQ=GGTAACAAGAAGGGAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:89:51,38:157,160:317,89:0.2192:2,2:27.6:1:31.4:1:0.23017:1.37:59.9:178:0.2225:0:2 0/1:446:97:53,44:177,172:349,97:0.2175:2,2:25.1:1:29.4:1:0.566:1.17:59.8:31.333:0.2146:0:2 +4 78271620 . A G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=2.18376;LSEQ=GAAAGGGCAGGCTGGTAACA;RSEQ=GAAGGGAAAAGCCCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:90:50,40:154,161:315,90:0.2222:2,2:26.6:1:32.5:1:0.28355:1.31:59.9:89:0.2214:0:2 0/1:424:163:90,73:132,127:259,163:0.3844:2,2:25.7:1:30.7:1:0.42381:1.19:60:53.333:0.3865:0:1.9 +4 78271705 . G A 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACCCAACCCTTTGTGTCT;RSEQ=TAGTGAAGTTTCCCACAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:58,128:186,0:0:2,0:21.4:1:32:1:1:0:60:185:1:0:0.2 0/1:197:29:13,16:62,106:168,29:0.1472:2,2:22.6:1:28.3:1:0.41662:1.39:59.9:58:0.148:0:1.4 +4 78271850 . T A 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63047;SOR=2.22221;LSEQ=TATTGCCTGTGGTGCCAACA;RSEQ=GGCCTCCCAGCTCTTCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:7,3:0.3:2,0:19.7:1:32:1:1:0:60:6:0.3:0:1 1/0:8:4:0,4:0,4:4,4:0.5:0,0:12:1:31.3:1:1:0:60:8:0.5714:0:1 +4 78271858 . C CG 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.68385;LSEQ=GTGGTGCCAACATGGCCTCC;RSEQ=AGCTCTTCAAGTATCAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:1,6:7,2:0.2222:2,0:19:1:33.5:1:1:0:60:4:0.2222:0:1 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:20.5:1:32.3:1:1:0:60:4:0.3333:0.1667:1 +4 79792217 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52273;SOR=Inf;LSEQ=GATGCTTATATGCAGCAGGT;RSEQ=ATTTTTTTGTTTCTTTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:0,21:21,0:0:1,0:30:1:30.7:1:1:0:60:42:1:0:0 0/1:35:2:1,1:5,28:33,2:0.0571:2,2:20.5:1:27:1:0.31765:5.20:60:4:0.0588:0:1 +4 82267196 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20648;SOR=0;LSEQ=ATTCTGCAGTTTCCTGGGGA;RSEQ=CCACTGTCCCCTGTGCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:22:0:32.5:1:1:1.26772:60:4:0.1333:0:1 0/0:21:0:0,0:14,7:21,0:0:2,0:22.1:1:31.5:1:1:0:60:42:1:0:0.2 +4 82267263 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.34441;LSEQ=GGTGGCGTGGCGACTCGACG;RSEQ=CAGAGAATCCCTGGCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:1,0:12,15:27,1:0.0357:2,0:1:0:30:0:0.46429:0:60:2:0.0385:0:1 0/1:42:2:1,1:16,24:40,2:0.0476:2,2:24.5:1:27.5:1:1:1.49:60:4:0.0488:0:1 +4 82267297 . T TG 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11343;SOR=0.23754;LSEQ=GCCAGGGCGGTGGCCCACTA;RSEQ=GGTGCACAACCAGTATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:2,3:6,6:12,5:0.2941:2,2:30.6:1:31.3:1:1:1.46472:60:10:0.2941:0.0588:0 0/1:23:2:0,2:6,15:21,2:0.087:2,0:25.5:1:31.5:1:1:0:60:4:0.087:0:0.5 +4 82931947 . C T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCTTTTCCTATACTTGC;RSEQ=TGCATTTTGGCTTTGATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:8,9:0,0:0,17:1:0,2:36.1:1:30.8:1:1:0:49.8:34:1:0:1.3 1/1:12:12:7,5:0,0:0,12:1:0,2:29.8:1:29.5:1:1:0:51.4:24:1:0:1.1 +4 82931981 . G T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27277;SOR=0;LSEQ=TGATATCTTCTACAGAACTA;RSEQ=GTCCTTTTGGTGTTTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:3,1:7,11:18,4:0.1818:2,2:19.3:1:31:1:0.29323:4.39:56.3:8:0.1818:0:1.5 0/0:12:0:0,0:5,7:12,0:0:2,0:25.1:1:29.8:1:1:0:55.3:24:1:0:0.8 +4 82932013 . GT G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTTTCAGGGTTTTTTTCCT;RSEQ=TTTTTTTGAATAATTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:6,5:0,0:0,11:0.9167:0,2:30.5:1:32.5:1:1:0:60:22:0.9167:0:0.5 1/1:7:7:2,5:0,0:0,7:1:0,2:30:1:31.9:1:1:0:60:14:1:0:0.4 +4 82932267 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49848;SOR=0;LSEQ=AAAAGTTGCATATCCTTCTC;RSEQ=TCTTCATCTTCTGACTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:88,49:137,2:0.0144:2,2:26.5:1:30:1:1:1.78785:60:4:0.0144:0:1 0/0:132:0:0,0:85,47:132,0:0:2,0:24.4:1:31.2:1:1:0:59.4:264:1:0:0.1 +4 82932359 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00211;SOR=0.42889;LSEQ=ACTACACTTCAACCAGAAGA;RSEQ=CACAAGTGTTATTTTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:46:18,28:45,78:123,46:0.2722:2,2:23:1:30.5:1:0.85838:1.11:59.6:45:0.2695:0:1 0/1:174:24:10,14:59,90:149,24:0.1379:2,2:27.3:1:28.8:1:1:1.09:59.6:48:0.1404:0:1.1 +4 82932384 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24383;SOR=0;LSEQ=AGTGTTATTTTAAAGTCCTC;RSEQ=AGAGACAAAAGCAAAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:28,70:98,2:0.02:2,2:14.5:1:33:1:0.49798:2.47:60:4:0.0206:0:2 0/0:102:0:0,0:31,71:102,0:0:2,0:22.2:1:29:1:1:0:60:101:1:0:0.5 +4 82932387 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00989;SOR=0.44601;LSEQ=GTTATTTTAAAGTCCTCAAG;RSEQ=GACAAAAGCAAAAATTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:43:9,34:12,33:45,43:0.4886:2,2:23.9:1:31.1:1:0.62014:1.36878:60:42:0.4828:0:1.1 0/1:94:28:6,22:20,46:66,28:0.2979:2,2:23:1:29.4:1:0.45591:1.58664:59.9:27:0.2903:0:1.1 +4 82933477 . G C 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAAGATATTTTCAAAGTTG;RSEQ=CTGTGTTATTTTAATTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:27.8:1:29.6:1:1:0:60:10:1:0:1.2 1/1:6:5:3,2:1,0:1,5:0.8333:0,2:18.2:1:32.4:1:1:0:60:10:0.8333:0:1.2 +4 82933499 . G T 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09804;SOR=0;LSEQ=TGTGTTATTTTAATTAACCT;RSEQ=CCTTCATCATTTGTTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:14:1:29.5:1:1:2.45:60:4:0.3333:0:1.5 0/0:12:0:0,0:6,6:12,0:0:2,0:22.2:1:29.9:1:1:0:60:11:1:0:1 +4 82933572 . C CT 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30888;SOR=0.29632;LSEQ=CAGTCCCTCAACTGACTATT;RSEQ=TTTTTTTTTTTGAATCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:1,4:5,3:0.375:2,2:38.7:1:33.3:1:0.46429:5.78:60:6:0.4286:0:0 0/1:14:2:0,2:6,4:10,2:0.1429:2,0:34.5:1:30.5:1:0.45455:0:60:4:0.1538:0:0 +4 82934035 . TG T 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.68017;SOR=1.62959;LSEQ=AGGCTGGGGAGGGGAGAGCA;RSEQ=GGGGGATAGGGAGAGATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:29.8:1:33.3:1:1:0:60:8:0.3333:0:0 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:10.8:1:32.1:1:1:0:60:10:0.4545:0.2727:0.6 +4 82934042 . A C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19928;SOR=Inf;LSEQ=GGAGGGGAGAGCATGGGGGG;RSEQ=TAGGGAGAGATTGGTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:12,0:12,0:0:0,0:26.8:1:29.5:1:1:0:60:24:1:0:0.1 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:35.5:1:33.5:1:1:0:60:4:0.1818:0:1 +4 83255712 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=ACCATCTGTAGCTTGATGGC;RSEQ=TCAATCCTAGAGGAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:18.5:1:32.5:1:1:2.23609:42:4:0.2222:0:1 0/0:11:0:0,0:8,3:11,0:0:2,0:20.6:1:30.5:1:1:0:33.6:22:1:0:0.1 +4 83255772 . TA T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5023;SOR=Inf;LSEQ=ATACAGGGCCCGAAGGCAAG;RSEQ=ACAGTAAGATGGCTGTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:18,9:27,0:0:2,0:21.1:1:29.8:1:1:0:53.9:54:1:0:0.1 0/1:36:2:1,1:20,14:34,2:0.0556:2,2:24:1:31:0:1:1.41419:38.5:4:0.0556:0:0 +4 83492301 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=AGTGAAACTGAGAAGCTAAG;RSEQ=AGTGAGGAGAACAGCAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:7,6:13,0:0:2,0:25.6:1:32.7:1:1:0:60:26:1:0:0.2 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:25:1:25:1:1:1.67325:60:4:0.1667:0:1.5 +4 83493197 . G C 33 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTGGCCAACATGGTGAAACC;RSEQ=CGTCTCTACTAAAAACTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:40:0:33:0:1:0:23:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:32:0:1:0:44:2:1:0:0 +4 83493495 . C G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATGTACATACATATATTCA;RSEQ=ATTTTAAAACAAAAAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32.5:1:1:0:60:4:1:0:1 +4 83501194 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49978;SOR=Inf;LSEQ=GTCTTCACATAAACTTTCTT;RSEQ=CATCTGCTCTTGATCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:92,9:101,0:0:2,0:19.7:1:31.8:1:1:0:44:100:1:0:0.1 0/1:115:2:1,1:96,17:113,2:0.0174:2,2:11:1:30:1:0.2897:5.51654:23:4:0.0177:0:1 +4 83501594 . G A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04714;SOR=0;LSEQ=GTTTGGGGAACATCAACGTC;RSEQ=CAGTCAACACCTTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:4:3,1:176,173:349,4:0.0113:2,2:16.5:1:27.8:1:0.62301:2.94:56:8:0.0115:0:1 0/0:404:0:0,0:204,200:404,0:0:2,0:25.9:1:30.3:1:1:0:55.2:100:1:0:0.1 +4 83501691 . G A 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06008;SOR=0;LSEQ=ACTGCAGTGCACCAAGACCG;RSEQ=CCCTGCATCCATGATGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:4:3,1:183,192:375,4:0.0105:2,2:17.3:1:28.5:1:0.36397:3.14:42:8:0.0107:0:1 0/0:386:0:0,0:183,203:386,0:0:2,0:24.4:1:30.7:1:1:0:54:63.333:1:0:0.2 +4 83501886 . T G 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01269;SOR=0.61412;LSEQ=GTCATGAGCGGCGCTTTCTT;RSEQ=GACGTTCCTAACACGCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:81:45,36:101,83:184,81:0.3034:2,2:15.7:1:30.3:1:1:1.03:39.2:26:0.2966:0:1.1 0/1:313:66:33,33:120,127:247,66:0.2109:2,2:16.4:1:30.3:1:0.89013:1.06:38.5:32:0.2071:0:1.2 +4 83502446 . A G 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACCCAATGTTTCCACCATT;RSEQ=GATTCTTCTTGTAATGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:195,252:447,0:0:2,0:25.3:1:30.3:1:1:0:59.1:148:0.9978:0:0.1 0/1:491:22:9,13:216,253:469,22:0.0448:2,2:17.2:1:31.1:1:0.66853:1.23268:43.4:44:0.0454:0:1.2 +4 83502533 . A T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07627;SOR=1.4728;LSEQ=ATTTCAATTCCTGACAACGA;RSEQ=TCATTTATTCAGAAATCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:52:12,40:48,142:190,52:0.2149:2,2:22.4:1:28.8:1:0.85686:1.12623:60:25:0.2101:0:1.1 0/1:247:71:21,50:51,125:176,71:0.2874:2,2:22.4:1:27.8:1:1:1.03:59.3:70:0.2846:0:1.1 +4 83502544 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=TGACAACGAATCATTTATTC;RSEQ=GAAATCATTTATTTCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:37,156:193,0:0:2,0:21.3:1:31.8:1:1:0:60:192:1:0:0.3 0/1:194:2:1,1:49,143:192,2:0.0103:2,2:22.5:1:27:1:0.45003:2.90:60:4:0.0103:0:1 +4 83680084 . AAAC A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50046;SOR=Inf;LSEQ=ACATCCCCTACAATCCTGCG;RSEQ=AACAAGCACATCCCCTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:20,0:0:2,0:19.8:1:30.9:1:1:0:60:19:1:0:0.3 0/1:27:2:1,1:13,11:24,2:0.0741:2,2:24:1:28:1:1:1.17422:60:4:0.0769:0:0 +4 84383735 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17387;LSEQ=TTGGTTACTACTACCAGTAT;RSEQ=TGCTTTAGATCGTTTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:301:146,155:191,204:395,301:0.4319:2,2:25.6:1:30.9:1:1:1.01:59.7:300:0.4329:0:1.1 0/1:909:106:50,56:406,395:801,106:0.1166:2,2:25.6:1:29.9:1:0.53569:1.15101:59.7:212:0.118:0:1.1 +4 84383810 . C T 217 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGTCATCTAAGTCTAAGG;RSEQ=TTTATGCTTAATGATTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:745:0:0,0:373,371:744,0:0:2,0:26:1:32.7:1:1:0:52:123:1:0:0.2 0/1:906:181:90,91:359,366:725,181:0.1998:2,2:25.2:1:29:1:1:1.01:43.9:180:0.2009:0:1.1 +4 84384580 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27294;SOR=Inf;LSEQ=TAGGCGACAGAGCGAGACTC;RSEQ=GTCTCAAAAATAAATAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:163,25:188,0:0:2,0:21.3:1:31.3:1:1:0:59.9:376:1:0:0.1 0/1:271:3:1,2:222,46:268,3:0.0111:2,2:8.3:1:28.7:1:0.08195:9.52964:51.7:6:0.0112:0:1 +4 84384587 . AAAAT A 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03319;SOR=7.51952;LSEQ=CAGAGCGAGACTCCGTCTCA;RSEQ=AAATAAATAAATAAAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:1:1,0:212,38:250,1:0.004:2,0:38:0:32:0:1:0:60:2:0.004:0:0 0/1:376:11:8,3:282,82:364,11:0.0293:2,2:28.3:1:28.5:1:0.71741:1.2887:60:22:0.0296:0.0053:0.4 +4 84388475 . C T 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACACATTTCTCAGAAGGTA;RSEQ=ATAGCCTTCATTAAGCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:115,1:116,0:0:1,0:23.7:1:32.2:1:1:0:60:57:1:0:0.1 0/1:93:25:24,1:68,0:68,25:0.2688:1,1:27.1:1:30.5:1:0.26882:0:60:50:0.2717:0:1 +4 84388494 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2273;SOR=0;LSEQ=ACATAGCCTTCATTAAGCAA;RSEQ=TCATAACTGTATAAATCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:134,3:137,2:0.0144:1,2:20:1:29.5:1:0.05693:38.80706:60:4:0.0145:0:1 0/0:152:0:0,0:146,6:152,0:0:1,0:21.5:1:31.7:1:1:0:60:75:1:0:0.2 +4 84388757 . TATTC T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21129;SOR=Inf;LSEQ=TAATGATAAGGTGAAAAACT;RSEQ=ATTGTCAAGGACCAATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:31,180:211,0:0:2,0:23.9:1:31.1:1:1:0:59.8:422:1:0:0.1 0/1:180:2:0,2:20,157:177,2:0.0111:2,0:14:1:32:0:1:0:60:4:0.0112:0:0 +4 84390088 . A G 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=TTTACTTGAGTAATGGATTA;RSEQ=TTTTCCCTTGAATTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:74,0:74,0:0:1,0:24.1:1:31.4:1:1:0:60:148:1:0:0 0/1:89:13:13,0:73,3:76,13:0.1461:1,1:20.8:1:32.2:1:1:0:60:26:0.1461:0:1 +4 84390446 . G A 35 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18195;LSEQ=TTTACTACTTATCCAAAATA;RSEQ=AATTTACTGACTTGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:3:0,3:1,43:44,3:0.0625:1,0:20.7:1:13.7:1:1:0:53.7:0:0:0:2 0/1:41:3:0,3:1,37:38,3:0.0732:1,0:28:1:22.3:1:1:0:40.3:2:0.0556:0:4.7 +4 84391410 . G A 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=23.56764;LSEQ=GATGAGTAGAGCAGCTTTCT;RSEQ=TTATTATACTTGGTGTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:1:1,0:230,205:435,1:0.0023:2,0:1:0:22:0:1:0:60:2:0.0023:0:1 0/1:505:26:13,13:248,231:479,26:0.0515:2,2:29.4:1:28.6:1:1:1.07342:42.8:52:0.0519:0:1.1 +4 84391486 . G A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12466;LSEQ=CTGCAAGTTTTTGTGAAGCA;RSEQ=CCTCTCTCTAAACGTCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:2,0:70,110:180,2:0.011:2,0:1:0:25.5:1:0.15518:0:60:4:0.011:0:1 0/1:243:3:2,1:101,138:239,3:0.0123:2,2:17.7:1:26:1:0.57654:2.72:45.7:6:0.0126:0:1 +4 84391576 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21816;SOR=0;LSEQ=TACAGAATAAAAAGGATATA;RSEQ=ATCTTAATAGTTACAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:33,118:151,2:0.0131:2,2:29.5:1:30.5:1:0.3962:3.54:60:4:0.0132:0:1.5 0/0:174:0:0,0:40,134:174,0:0:2,0:23.3:1:31.3:1:1:0:59.5:173:1:0:0.1 +4 84393475 . C T 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATTAAAGGTATTTCAAATA;RSEQ=GCTAAAAATATAAGTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:55,153:208,0:0:2,0:22.8:1:30.2:1:1:0:60:40.6:1:0:0.2 0/1:255:119:33,86:34,102:136,119:0.4667:2,2:22.8:1:29.4:1:0.66978:1.15:59.8:58.5:0.4643:0:1.4 +4 84393476 . G A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03751;SOR=0;LSEQ=ATTAAAGGTATTTCAAATAC;RSEQ=CTAAAAATATAAGTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:4:3,1:49,145:194,4:0.0202:2,2:13.3:1:27.5:1:0.0563:8.76:60:8:0.0207:0:1 0/0:250:0:0,0:66,184:250,0:0:2,0:24.1:1:31:1:1:0:59.9:124:1:0:0.7 +4 84393485 . A G 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATTTCAAATACGCTAAAAAT;RSEQ=TAAGTAATTTTATTAGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:35,127:162,0:0:2,0:24:1:30.6:1:1:0:60:324:1:0:0.1 0/1:214:38:9,29:41,135:176,38:0.1776:2,2:21.1:1:31.8:1:1:1.02:59.4:76:0.1784:0:2.1 +4 84397590 . A C 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0142;SOR=Inf;LSEQ=GAAAGGTAATGAAGATCAGC;RSEQ=TTAAGTAATATAAATACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:20,0:0:1,0:23.1:1:31:1:1:0:58.6:40:1:0:0 0/1:17:5:5,0:11,1:12,5:0.2941:2,0:20.8:1:30.4:1:1:0:60:10:0.2941:0:2.2 +4 84397605 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21992;SOR=Inf;LSEQ=TCAGCATTAAGTAATATAAA;RSEQ=ACAGAGAAAGAACTGCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:29,1:30,0:0:1,0:21.1:1:31.7:1:1:0:59.1:60:1:0:0 0/1:27:2:1,1:24,1:25,2:0.0741:1,2:14.5:1:28:1:0.1453:17.31852:60:4:0.0741:0:2.5 +4 84397620 . G A 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAATACAGAGAAAGAACT;RSEQ=CTAGGGTTGACAATACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:35,1:36,0:0:1,0:24.8:1:32.6:1:1:0:59.2:35:1:0:0 0/1:39:17:15,2:22,0:22,17:0.4359:1,2:25.6:1:28.4:1:0.18354:0:60:34:0.4359:0:1.4 +4 84397894 . G A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.24463;SOR=Inf;LSEQ=TTCAGAATCACCTGAATGCT;RSEQ=CATATTGAGCCTTTACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:22,142:164,0:0:2,0:23.5:1:32.5:1:1:0:59.8:163:1:0:0 0/1:161:2:1,1:26,133:159,2:0.0124:2,2:6.5:1:26.5:1:0.30815:5.04:60:4:0.0126:0:1 +4 84403178 . G T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=AAAGTGCTGGGATTACAGGT;RSEQ=TGAGCCACCTTGCCCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:83,0:83,0:0:1,0:21.5:1:32.4:1:1:0:59.6:82:1:0:0.1 0/1:53:12:12,0:41,0:41,12:0.2264:1,0:21.3:1:29.5:1:1:0:54.3:24:0.2264:0:1.4 +4 84403476 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=TAACCGTATTTCCTGAGTAT;RSEQ=TTACTATGTATACAATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:4,110:114,0:0:1,0:23.2:1:30.8:1:1:0:60:228:1:0:0.1 0/1:130:2:1,1:15,113:128,2:0.0154:2,2:11.5:1:28.5:1:0.23184:7.33:60:4:0.0156:0:1 +4 84403491 . A AG 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTATTTTACTATGTATACA;RSEQ=TATGTGCTACCAGTCGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:1,78:79,0:0:1,0:26.2:1:31.3:1:1:0:60:38.5:1:0:0.1 0/1:81:30:0,30:3,48:51,30:0.3704:2,1:24:1:32.2:1:0.29167:0:59.8:60:0.375:0.0864:0.4 +4 84406052 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22129;SOR=Inf;LSEQ=CGGCGGCGTCGGGGGAGCGG;RSEQ=CGGGGACCGGAGCAACAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:81,13:94,0:0:2,0:18.3:1:32:1:1:0:60:46:1:0:0.1 0/1:84:2:1,1:65,17:82,2:0.0238:2,2:36.5:1:28:1:0.38468:3.74436:60:4:0.0244:0:1 +4 84406085 . G T 36 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.32457;SOR=0.25938;LSEQ=CAACAGCGGGGAGGCAGGCC;RSEQ=CGCGCAGGGCTCTTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:181,53:234,3:0.0126:2,2:11.7:1:23:1:0.13535:6.75854:60:2:0.0084:0:1.3 0/0:305:1:0,1:222,81:303,1:0.0033:2,0:1:0:22:0:0.26974:0:60:2:0.0034:0:1 +4 84406267 . C T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.11432;SOR=0;LSEQ=ACAAGAGGACGAGGGCGGGG;RSEQ=GCGCGGAGGCAAGACCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:1,2:61,235:296,3:0.01:2,2:44.3:1:25.3:1:0.50331:1.92:60:2:0.0069:0:2.7 0/0:316:0:0,0:86,228:314,0:0:2,0:23:1:29.6:1:1:0:60:43.857:0.9935:0:0.2 +4 84406286 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=0;LSEQ=GCGCGCGGAGGCAAGACCCT;RSEQ=TGGTGGCAGCGAGGCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:28,161:189,2:0.0105:2,2:34.5:1:32:1:0.28129:5.67:60:4:0.0105:0:1 0/0:188:0:0,0:37,150:187,0:0:2,0:21.6:1:31.7:1:1:0:60:61.333:0.9946:0:0.2 +4 84406289 . G T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23785;SOR=Inf;LSEQ=CGCGGAGGCAAGACCCTGTG;RSEQ=TGGCAGCGAGGCGGGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:25,152:177,0:0:2,0:21.9:1:32.7:1:1:0:60:87.5:1:0:0.2 0/1:169:2:1,1:29,137:166,2:0.0118:2,2:5:1:29:1:0.32613:4.66:60:4:0.012:0:1 +4 87163499 . C T 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.96588;LSEQ=CAGTTGGGCGGCACGGGGAG;RSEQ=AGGACCCATTTAATGAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:0,1:9,9:18,1:0.0526:2,0:1:0:23:0:1:0:60:2:0.0526:0:1 0/1:20:2:1,1:11,7:18,2:0.1:2,2:20.5:1:27.5:1:1:1.53525:60:4:0.1:0:1 +4 87163541 . G T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02707;SOR=0;LSEQ=TTTGTCCCTTGATGGAGAGG;RSEQ=TGTGCTTTGCTGAGGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:2,4:17,16:33,6:0.1538:2,2:13.7:1:28.2:1:0.66142:2.08513:47.2:5:0.1316:0:2 0/0:34:0:0,0:16,18:34,0:0:2,0:27.9:1:30.8:1:1:0:56.6:68:1:0:0.2 +4 87163749 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=CCCACTGAGGAAGGATGGGT;RSEQ=AGGGTTAGACCTGAAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:21.5:1:32:1:1:0:58.8:20:1:0:0.1 0/1:10:2:1,1:5,3:8,2:0.2:2,2:8.5:1:27.5:1:1:1.58108:55:4:0.2:0:1 +4 89983727 . G C 60 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGTCAATTCAGCTGTTGATA;RSEQ=TTATGTATGCTTTACGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:9.5:1:35.5:1:1:0:47:4:1:0:1 1/1:4:4:2,2:0,0:0,4:1:0,2:9.3:1:30:1:1:0:47.8:8:1:0:1 +4 89984278 . G C 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.27218;SOR=0.19788;LSEQ=TGTCACTCAAGGAGGCTGGA;RSEQ=AGCAGCAAAGATGGGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:1,5:6,3:0.3333:2,0:19.7:1:31:1:1:0:41.3:6:0.3333:0:1.3 0/1:12:1:1,0:7,4:11,1:0.0833:2,0:44:0:29:0:1:0:44:2:0.0833:0:1 +4 89984725 . C T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.15611;LSEQ=CTGCCGACTGCCACAGCTGG;RSEQ=TTGTTGGGCTGTGGGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:0,2:2,6:0.75:0,2:17.8:1:29.5:1:0.46429:0:28.7:12:0.75:0:1.3 1/0:9:7:4,3:1,1:2,7:0.7778:2,2:24.9:1:27.7:1:1:1.29:31.4:14:0.7778:0:1.9 +4 89984747 . T C 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60839;SOR=2.12849;LSEQ=TGTTGGGCTGTGGGGACAAG;RSEQ=CGTGGGACCAAGCTGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,2:3,4:0.5714:2,2:18:1:31:1:1:1.41418:50.8:8:0.5714:0:1.5 1/0:8:6:2,4:1,1:2,6:0.75:2,2:14.5:1:29.2:1:1:1.8258:39.7:12:0.75:0:2.2 +4 94653647 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24688;SOR=0;LSEQ=CTTTAGTAGACTATCATTTT;RSEQ=TGCCTCTGCTGTTTACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:123,74:197,2:0.0101:2,2:14.5:1:32.5:1:1:1.65767:60:4:0.0101:0:1 0/0:201:0:0,0:130,70:200,0:0:2,0:24.3:1:30.8:1:1:0:60:400:1:0:0.3 +4 94653663 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25175;SOR=Inf;LSEQ=TTTTCTGCCTCTGCTGTTTA;RSEQ=AGGAATATATTTTATTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:129,87:216,0:0:2,0:24.5:1:32:1:1:0:60:107:1:0:0.2 0/1:247:3:1,2:143,101:244,3:0.0121:2,2:26.7:1:27:1:0.57258:2.81977:60:6:0.0123:0:1.3 +4 94653694 . T C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=4.79825;LSEQ=TTTATTTCAAAAGCAAGATT;RSEQ=TTCTTGGCACTCAACTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:26:15,11:114,110:224,26:0.104:2,2:24.4:1:32.4:1:0.54101:1.31:60:52:0.104:0:1.2 0/1:293:105:59,46:96,92:188,105:0.3584:2,2:25.2:1:30.8:1:0.46415:1.23:60:104:0.3599:0:1.1 +4 94653779 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23193;SOR=Inf;LSEQ=TTTGTGTGGTTAAAATGGCT;RSEQ=AGGCTCTTTTATGTTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:50,126:176,0:0:2,0:25.1:1:32.1:1:1:0:60:175:1:0:0.1 0/1:164:2:1,1:54,108:162,2:0.0122:2,2:32.5:1:29.5:1:1:1.99:60:4:0.0122:0:1.5 +4 94653783 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49848;SOR=0;LSEQ=TGTGGTTAAAATGGCTGAGG;RSEQ=TCTTTTATGTTGTTCTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:44,116:160,2:0.0123:2,2:27:1:28.5:1:0.47964:2.62:60:4:0.0125:0:1 0/0:159:0:0,0:51,108:159,0:0:2,0:25:1:31.2:1:1:0:60:78.5:1:0:0.1 +4 94741469 . T TTGC 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.00113;SOR=0.17292;LSEQ=TGCCATTGCTGTTCTTGCTG;RSEQ=TGCTGCTGCTGCTGTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:21:10,11:7,4:11,21:0.6563:2,2:28:1:31.9:1:0.47191:1.88584:60:42:0.6563:0.0938:0.6 0/1:33:8:6,2:12,13:25,8:0.2424:2,2:30.9:1:32.5:1:0.24188:3.14:60:16:0.2424:0.0303:0.8 +4 94741522 . A C 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15892;SOR=0.27953;LSEQ=GGTTCACCTTTCCTGAGCTA;RSEQ=CTCTTTTTCAACTTTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:18:7,11:1,2:3,18:0.8571:2,2:27.9:1:31.5:1:1:1.26:60:17:0.85:0:1.1 1/0:21:13:6,7:3,5:8,13:0.619:2,2:23.5:1:29.3:1:1:1.40:60:26:0.619:0:1.1 +4 96051136 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13904;SOR=0;LSEQ=TGAAAGTGTTCTTCACCACA;RSEQ=AGGAAGCCAGCTGGTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:4,7:11,2:0.1538:2,2:33.5:1:29.5:1:1:1.67:60:4:0.1538:0:1.5 0/0:21:0:0,0:9,12:21,0:0:2,0:26.9:1:31.3:1:1:0:60:42:1:0:0.1 +4 96052605 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15146;SOR=0;LSEQ=TGAAAAGTAAAAACATTCTG;RSEQ=TGAAGAAAAATGGAACTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:19,12:31,2:0.0606:2,2:45:1:30.5:1:1:1.56069:60:4:0.0606:0:1 0/0:51:0:0,0:28,23:51,0:0:2,0:26.9:1:30.3:1:1:0:60:102:1:0:0.2 +4 98947326 . G A 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=AGTTAAAAAGAGGTGGAATC;RSEQ=TCCCAAAATGTCCCTTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:24,0:0:2,0:26.9:1:31.7:1:1:0:58.8:48:1:0:0.1 0/1:52:22:15,7:18,12:30,22:0.4231:2,2:24:1:30:1:0.57552:1.42:41.3:44:0.4231:0:1.5 +4 98947401 . T C 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCCCCTCAAGAGCTCAGGAG;RSEQ=GGGCTGCTGAGAGCTAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:17,0:0:2,0:18.8:1:29.4:1:1:0:57.8:34:1:0:0.1 1/0:36:22:9,13:3,11:14,22:0.6111:2,2:20.4:1:30:1:0.29248:2.48:44.5:44:0.6111:0:1.5 +4 99802289 . C G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24045;SOR=Inf;LSEQ=TCCTAACCTTTCCTTGTATA;RSEQ=CCTCCTAGAAGAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:48,71:119,0:0:2,0:30.9:1:31.2:1:1:0:47.9:22.8:1:0:0.3 0/1:115:2:1,1:47,66:113,2:0.0174:2,2:27.5:1:31:1:1:1.40:41.5:4:0.0177:0:1.5 +4 99802300 . G GA 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.44455;SOR=0.71645;LSEQ=CCTTGTATACCCTCCTAGAA;RSEQ=AAAAAAAAAAAGAAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:18:5,13:43,60:103,18:0.1452:2,2:30.5:1:31.2:1:0.30686:1.85427:50.1:36:0.1682:0:0.1 0/1:120:13:6,7:41,62:103,13:0.1083:2,2:38.8:1:29:1:0.7669:1.29:57.5:12:0.1132:0:0.5 +4 99802309 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.49807;SOR=0;LSEQ=CCCTCCTAGAAGAAAAAAAA;RSEQ=AAGAAGAAGAAAAAAGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:47,78:125,2:0.0157:2,2:48:0:33.5:1:1:1.65:60:4:0.0159:0:1 0/0:124:0:0,0:47,77:124,0:0:2,0:27.1:1:29.5:1:1:0:51.8:61:1:0:0.4 +4 99802395 . C T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.39289;SOR=1.72957;LSEQ=TTAGTCTTTATATTAAAAAA;RSEQ=ATAGACTTGAGAATAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:0,13:0,14:14,13:0.4815:1,1:24.6:1:29.8:1:1:0:60:26:0.4815:0:1 1/0:21:13:0,13:1,6:7,13:0.619:2,1:24.6:1:26.5:1:0.35:0:60:12:0.6:0:1.1 +4 99806215 . TA T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.153;SOR=0.52112;LSEQ=TCCAATAAGGCACAGAAGCT;RSEQ=AAAAAAAATCCCAAATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:15:7,8:200,325:525,15:0.0278:2,2:29.3:1:30.6:1:0.59243:1.42:49.4:30:0.028:0.0019:0.1 0/1:682:10:6,4:267,403:670,10:0.0147:2,2:31.8:1:31.4:1:0.21131:2.26:46.2:20:0.0148:0:0.2 +4 99808136 . CTTAAA C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0;SOR=5.34465;LSEQ=CTAGTGTTGGGCATCCTTCT;RSEQ=TTAAGTAACAAATGTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:36:31,5:217,16:233,36:0.1338:2,2:23.6:1:32.7:1:0.17444:2.17951:60:72:0.1338:0.026:0.1 0/1:256:116:108,8:131,9:140,116:0.4531:2,2:26.1:1:31.1:1:1:1.07787:59.8:232:0.4531:0.0859:0.1 +4 99808254 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.07527;LSEQ=TCTAGCCAAAAGCGATCGAG;RSEQ=TCACTTCGTCTCTGCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:802:71:37,34:403,325:728,71:0.0885:2,2:31.3:1:30.5:1:0.61883:1.13927:50.8:70:0.0893:0:1.1 0/1:1006:410:216,194:307,289:596,410:0.4076:2,2:29.3:1:29:1:0.74823:1.05:49.8:57.571:0.4067:0:1.2 +4 99808693 . T C 98 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAATGAATGTCCCGTCCC;RSEQ=CTACCAACTGACAAAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:3,5:0,0:0,8:1:0,2:22.3:1:32.8:1:1:0:54.4:16:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 99808872 . T C 92 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12844;SOR=0.1878;LSEQ=TAACTCTCTCTCAATTTTTA;RSEQ=AAACAAATAGAATAAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:7,0:21,2:23,7:0.2333:2,0:23.4:1:33.1:1:1:0:60:14:0.2333:0:1 0/1:19:1:1,0:15,3:18,1:0.0526:2,0:17:0:26:0:1:0:60:2:0.0526:0:2 +4 99808940 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20349;SOR=0;LSEQ=TTAAATTATCAGCCTATTCA;RSEQ=CACACTATCAAATATTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:2,0:65,5:70,2:0.0278:2,0:30:1:33.5:1:1:0:60:4:0.0282:0:1 0/0:87:0:0,0:82,5:87,0:0:2,0:24.1:1:30.2:1:1:0:60:174:1:0:0 +4 99808952 . A T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.61601;SOR=0.47784;LSEQ=CCTATTCATCACACTATCAA;RSEQ=TATTCCTAAGTTTATGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:87,13:100,2:0.0196:2,2:18:1:29:1:0.25684:6.48583:60:4:0.0198:0:1 0/0:106:1:0,1:90,15:105,1:0.0094:2,0:1:0:28:0:0.15094:0:60:2:0.0095:0:1 +4 99809176 . A T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00154;SOR=Inf;LSEQ=AGGTGCTTACATATATATAC;RSEQ=TTTAGAACATATGATGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:31,127:158,0:0:2,0:22.5:1:31.3:1:1:0:60:78:1:0:0.1 0/1:200:12:4,8:42,146:188,12:0.06:2,2:24.7:1:29.5:1:0.47709:1.73:60:24:0.0606:0:1.2 +4 99812300 . C A 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=CATTCATTAACTGTTTAACT;RSEQ=ACACTTCATTTTGTGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:226,17:243,0:0:2,0:24.2:1:32.3:1:1:0:60:47.6:1:0:0.1 0/1:307:20:18,2:264,22:286,20:0.0651:2,2:20.5:1:27.6:1:0.66285:1.33194:60:40:0.0654:0:1.1 +4 99822587 . T G 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCAAACTCCTGACCTCAGG;RSEQ=GATCCGCCCGCCTCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:35:0:32:0:1:0:32:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:29:1:1:0:44:4:1:0:1 +4 99822905 . T C 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.46322;LSEQ=ATGGGTCATCCAAGTGAAAA;RSEQ=AGAACCCTCAACCTTAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:11:11,0:97,1:98,11:0.1009:1,0:26.3:1:32.7:1:1:0:56.8:22:0.1048:0:1.2 0/1:100:49:46,3:50,1:51,49:0.49:1,2:21.3:1:31.8:1:0.35739:3.22541:60:48:0.4848:0:1.1 +4 99823225 . AT A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30899;SOR=0.62305;LSEQ=CCTGAACTGATATGCTGATA;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:17:0,17:1,110:111,17:0.1328:1,1:32.6:1:32.5:1:1:0:57.7:34:0.1393:0.0078:0.1 0/1:115:10:0,10:1,104:105,10:0.087:1,0:21.2:1:29.4:1:1:0:56.5:9:0.0818:0.0174:0.5 +4 99849930 . T C 141 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75229;SOR=1.13592;LSEQ=CTATCATGAAGACACCATCC;RSEQ=CGCATACCCAGCCCAGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:21:21,0:166,7:173,21:0.1082:1,1:22.9:1:31.6:1:1:0:60:20:0.1064:0:1 0/1:198:24:23,1:164,10:174,24:0.1212:2,1:22.5:1:30.9:1:1:1.40:60:48:0.1231:0:1.8 +4 99850126 . A G 306 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.45879;LSEQ=GGAGGTCAGGTCCAACATGA;RSEQ=GGGGAAGGGGCGGCAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1146:426:214,212:346,373:719,426:0.3717:2,2:25:1:32.2:1:0.50154:1.09:60:141:0.3753:0:1.1 1/0:1472:989:489,500:251,230:481,989:0.6719:2,2:24:1:30.8:1:0.3447:1.11577:59.9:122.625:0.6738:0:1.2 +4 99850297 . A AG 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=39.93464;LSEQ=GATCGCACAACCGCTCCAGA;RSEQ=GGGGGGGTAAGAGGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:731:1:1,0:320,408:728,1:0.0014:2,0:22:0:35:0:0.44033:0:60:2:0.0014:0:0 0/1:1098:57:27,30:464,576:1040,57:0.0519:2,2:28:1:31.1:1:0.68429:1.12:60:114:0.0528:0.0027:0.2 +4 99850341 . A G 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATTCAAACCGGATTGGCC;RSEQ=GCTTCTGGCCACGTGACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:98,214:312,0:0:2,0:23.3:1:31:1:1:0:60:30.2:1:0:0.1 0/1:443:30:11,19:137,275:412,30:0.0677:2,2:22.8:1:30.4:1:0.69283:1.16:60:60:0.0683:0:1.2 +4 99850448 . ACCT CCC 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.06059;SOR=Inf;LSEQ=GGAAGTGGAGTCTCTCCCCC;RSEQ=TTTTTTTTTTTTTTTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:0,38:38,0:0:1,0:11.4:1:28.9:1:1:0:58.8:18:0.8571:0:0.8 0/1:34:3:0,3:1,28:29,3:0.0882:1,0:30.3:1:26.3:1:1:0:52.3:2:0.0741:0.0588:2.3 +4 100276461 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48943;SOR=0;LSEQ=CTCCCAGCATTTACAGGAAA;RSEQ=GGCTTCTGAAATCAGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:16,5:21,2:0.087:2,2:35:1:31.5:1:0.46245:3.01096:28:4:0.087:0:1 0/0:21:0:0,0:11,10:21,0:0:2,0:31.7:1:29.5:1:1:0:28.7:42:1:0:0.1 +4 100276569 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGCCATTTGCTATTACT;RSEQ=GCCTTCAGGCCCTGTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:3,13:0,0:0,16:1:0,2:14.4:1:30.1:1:1:0:24.9:32:1:0:1.1 1/1:22:22:10,12:0,0:0,22:1:0,2:19.5:1:28.4:1:1:0:23.7:21:1:0:1 +4 100276859 . A G 31 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGATGGGGGATTGAGAG;RSEQ=TGAAGCCAGCTGGGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:31:1:1:0:32.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 103165513 . G A 29 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTGACTCTCCAAAACCGCC;RSEQ=AGGCCTAGACGTCCTCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:34.5:1:29.5:1:1:0:23:4:0.6667:0:3.5 1/1:1:1:1,0:0,0:0,1:1:0,0:16:0:31:0:1:0:20:2:1:0:2 +4 103165608 . A G 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55944;SOR=3.3873;LSEQ=CCAGTCAGGGATAGTACGAG;RSEQ=TGCCACCCAGCATTTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:4,1:5,1:0.1667:2,0:37:0:29:0:1:0:45:2:0.1667:0:1 0/1:7:3:2,1:3,1:4,3:0.4286:2,2:11.3:1:31:1:1:1.41418:27.7:6:0.4286:0:1.3 +4 103165724 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49474;SOR=Inf;LSEQ=CCTTTCTAGGTCCCGTGGCA;RSEQ=CCATCTTGCTGTTACTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:1,7:8,0:0:2,0:27.3:1:31.1:1:1:0:38.5:16:1:0:0.1 0/1:12:2:1,1:2,8:10,2:0.1667:2,2:33.5:1:31.5:1:0.45455:3.46:20:4:0.1818:0:1 +4 103165885 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACCCCTGGACCAACCTG;RSEQ=TGGCACTTTCACCGGCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:13.5:1:28:1:1:1:42.5:4:0.5:0:2 +4 103165898 . C T 59 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACCTGCTGGCACTTTCAC;RSEQ=GGCCTAGAGAGCTCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:36.5:1:29.5:1:1:0:45:8:1:0:1.5 +4 103166193 . C T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTTTGCTTGTGGGGAGG;RSEQ=GTGGAGGGAGAGGCATGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:30.5:1:1:0:30:4:1:0:1.5 +4 103166437 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTCAGCTGCCTCCCTGC;RSEQ=AGGAAGGGCTCGGGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:32:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 103166444 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGCCTCCCTGCAAGGAAG;RSEQ=GCTCGGGACCTGCAGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:26.5:1:32:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 103166559 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACCAGGTCCCATCGACC;RSEQ=CCCAAGGGCTGAGGAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:39:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 103585509 . CT C 29 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCACTTTAAACATACATT;RSEQ=TTTTTTTTTTTTTGAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:29:1:1:0:52:4:1:0:0 +4 105135443 . T C 260 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCATGACTGCTAATCATAT;RSEQ=GAATGTGGTGGTTTGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:334:334:153,181:0,0:0,334:1:0,2:27.8:1:31.1:1:1:0:60:82.5:1:0:1.1 0/1:416:184:85,99:111,120:231,184:0.4423:2,2:26.2:1:29.8:1:0.76664:1.07716:60:45:0.4423:0:1.1 +4 105409654 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00578;SOR=1.59177;LSEQ=TATTTCTTTTAGCCAAATAG;RSEQ=ATTCCGCTAATAATCTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:139:75,64:64,65:129,139:0.5167:2,2:24.1:1:32.5:1:0.54092:1.19:60:138:0.5169:0:1.1 1/0:319:201:107,94:55,61:116,201:0.6301:2,2:26.4:1:31.4:1:0.35144:1.26:59.9:66:0.6306:0:1.1 +4 105409678 . G A 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10729;SOR=0;LSEQ=CCGCTAATAATCTTAGCCTT;RSEQ=AAACACAGCCCATGCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:3,0:128,137:265,3:0.0112:2,0:10.7:1:20.3:1:0.11542:0:60:2:0.0076:0:2.3 0/0:296:0:0,0:130,166:296,0:0:2,0:25.1:1:30.8:1:1:0:59.9:295:1:0:0.7 +4 105409696 . T G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12437;SOR=Inf;LSEQ=TTGAAACACAGCCCATGCTC;RSEQ=GATAGAAGGGATCTGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:108,128:236,0:0:2,0:27.3:1:31:1:1:0:60:117:1:0:0.4 0/1:253:4:2,2:99,149:248,4:0.0158:2,2:12.8:1:31.8:1:1:1.50:60:8:0.016:0:1.5 +4 106111517 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50022;SOR=0;LSEQ=TCAAACTCTGTCTTCTCTAG;RSEQ=CTGGCAAACATTCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:128,23:151,2:0.0131:2,2:24.5:1:27.5:1:0.28999:5.46937:60:4:0.0134:0:1 0/0:135:0:0,0:108,26:134,0:0:2,0:20.8:1:30.1:1:1:0:60:32.5:1:0:0.1 +4 106111673 . G T 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01852;SOR=Inf;LSEQ=TGAGCTGCTGGTAAGACAGT;RSEQ=GAGACAGTTGACACTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:0:0,0:169,249:418,0:0:2,0:26:1:31.6:1:1:0:60:58.714:1:0:0.1 0/1:510:7:2,5:224,279:503,7:0.0137:2,2:28.6:1:29.9:1:0.47112:2.00459:60:14:0.0138:0:1.1 +4 106111737 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49884;SOR=0;LSEQ=TGTAATGGTAATCTCTCTCC;RSEQ=AAACTTCAACTTCAAGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:44,135:179,2:0.011:2,2:31:1:31.5:1:0.43646:3.05:60:4:0.0111:0:1 0/0:173:0:0,0:47,126:173,0:0:2,0:22.5:1:30.9:1:1:0:60:172:1:0:0.1 +4 106111758 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20736;SOR=Inf;LSEQ=AAACTTCAACTTCAAGTTAC;RSEQ=CTGCACCCTCTCAAATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:15,104:119,0:0:2,0:23.1:1:31.9:1:1:0:59.9:238:1:0:0.1 0/1:100:2:1,1:11,87:98,2:0.02:2,2:14.5:1:31:0:0.22667:7.62:60:4:0.0202:0:1 +4 106154990 . TATAGATAG T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=4;SSF=0;SOR=0.27387;LSEQ=TTAAGATATATTAGTATTTT;RSEQ=ATAGATAGATAGATAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:134:75:73,2:57,2:59,75:0.5597:1,1:31.3:1:31.6:1:1:1.28:60:74:0.5564:0.0299:0.1 0/1:105:27:27,0:75,3:78,27:0.2571:1,1:30.8:1:31.5:1:0.56748:0:60:54:0.2621:0:0.2 +4 106155185 . C G 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCCCATTTGCCAGACAGAAC;RSEQ=TCTGGCTACAAAGCTCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:0:0,0:370,401:771,0:0:2,0:24.7:1:32.2:1:1:0:59.9:69.091:1:0:0.1 0/1:845:47:25,22:381,415:796,47:0.0556:2,2:22.7:1:29.3:1:0.54863:1.24:60:46:0.055:0:1.1 +4 106156163 . G A 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTGAAGAATTCTGTTCAG;RSEQ=TTCCAGCAGCAATTTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:227,265:492,0:0:2,0:25.3:1:31.7:1:1:0:60:48.2:1:0:0.1 0/1:541:68:31,37:209,264:473,68:0.1257:2,2:26.3:1:28.7:1:0.8963:1.06:60:67:0.1243:0:1 +4 106156187 . C T 137 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=22.20277;LSEQ=CAGCAGCAATTTGCAAGCTC;RSEQ=TGGTGGCAGCTCTGAACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:1:1,0:222,248:470,1:0.0021:2,0:21:0:27:0:0.47346:0:60:2:0.0022:0:1 0/1:509:23:8,15:216,269:485,23:0.0452:2,2:24:1:30.4:1:0.3973:1.5044:60:46:0.0455:0:1 +4 106156288 . ACAC A 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03871;SOR=7.79819;LSEQ=ATTCCTTTTCTGCCACTACC;RSEQ=CACCACCACCATCACAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:1:0,1:361,326:687,1:0.0015:2,0:49:0:32:0:0.47529:0:60:2:0.0015:0:0 0/1:712:8:3,5:353,349:702,8:0.0112:2,2:22.5:1:29.4:1:0.50441:1.68454:60:16:0.0113:0.0028:0.3 +4 106158030 . G A 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGTCTTGCCATAGTCAGAT;RSEQ=CACAGGCCAATTAAGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:613:0:0,0:304,307:611,0:0:2,0:25.2:1:31.9:1:1:0:60:37.188:0.9983:0:0.1 0/1:720:49:26,23:377,294:671,49:0.0681:2,2:18.9:1:27.7:1:0.76594:1.13415:59.8:98:0.0687:0:1.2 +4 106162473 . A T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.25216;SOR=Inf;LSEQ=TATAATTGAGGTCTAAAATA;RSEQ=TAATCTTCTATTATCTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:178,81:259,0:0:2,0:22.9:1:30.5:1:1:0:60:128.5:1:0:0.1 0/1:297:3:1,2:193,101:294,3:0.0101:2,2:13:1:26.3:1:0.27669:3.80305:60:6:0.0102:0:1 +4 106163925 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49861;SOR=0;LSEQ=TTATGCTCAAATGTTCAAAT;RSEQ=TTTTGATTGCCTCTTGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:165,13:178,2:0.0111:2,2:24.5:1:28:1:0.14991:12.26775:60:4:0.0113:0:1 0/0:180:0:0,0:159,21:180,0:0:2,0:22.7:1:27.6:1:1:0:60:59:1:0:0.1 +4 106164284 . T G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.32598;SOR=0.31895;LSEQ=TTGTATTTAATTGAAATAAT;RSEQ=TAGTGATGAGGAAGAGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:1,8:1,3:4,9:0.6923:2,2:28.9:1:33.4:1:1:2.4495:58.9:18:0.6923:0:1 0/1:5:2:0,2:0,3:3,2:0.4:0,0:24:1:30.5:1:1:0:60:4:0.4:0:1 +4 106164673 . G A 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01515;SOR=Inf;LSEQ=ATCTGCTGCAAGTGACCCTT;RSEQ=TTTTGTTTTGGTTGGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:151,42:193,0:0:2,0:25.2:1:32.4:1:1:0:59.9:95.5:1:0:0.2 0/1:206:7:6,1:154,45:199,7:0.034:2,2:22.1:1:29.3:1:1:1.75:60:14:0.035:0:1.3 +4 106164922 . G A 45 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04153;SOR=0;LSEQ=CGCTCACCAATCGCCGGTGT;RSEQ=CCTTGAATGAAGAGTAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:4:3,1:97,176:273,4:0.0144:2,2:11.5:1:22.5:1:0.13558:5.41:60:3:0.0112:0:1.3 0/0:336:0:0,0:115,221:336,0:0:2,0:23.8:1:31.1:1:1:0:60:83:1:0:0.2 +4 106164961 . CT C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23785;SOR=Inf;LSEQ=TGAAGCCCAGGGCCTCTCCC;RSEQ=CTTTGCGGCCACTGATAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:43,133:176,0:0:2,0:24:1:30.2:1:1:0:60:43:1:0:0.4 0/1:169:2:1,1:41,126:167,2:0.0118:2,2:18:0:32.5:1:0.43639:3.05:60:4:0.0123:0:1 +4 106164970 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22454;SOR=Inf;LSEQ=GGGCCTCTCCCCTCTTTGCG;RSEQ=CCACTGATAGGAAAGCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:34,122:156,0:0:2,0:23.6:1:31.6:1:1:0:60:51:1:0:0.4 0/1:141:2:1,1:31,107:138,2:0.0142:2,2:24.5:1:28:1:0.40617:3.41:60:4:0.0147:0:1 +4 106164980 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21043;SOR=0.64589;LSEQ=CCTCTTTGCGGCCACTGATA;RSEQ=GAAAGCCCAATCTTTGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:32:6,26:18,80:98,32:0.2462:2,2:27.4:1:30.5:1:1:1.03:60:15:0.24:0:1.2 0/1:115:20:5,15:18,77:95,20:0.1739:2,2:22.9:1:30.4:1:0.54564:1.42:60:40:0.1786:0:1.2 +4 106183474 . T C 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGATGTGTCAGATTTTGC;RSEQ=GATCTTCCTTTTTTGTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:25.5:1:28.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 106190740 . G A 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GAGTAAAACTAACTACTTTC;RSEQ=CATTCACACACACTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:0:0,0:296,178:474,0:0:2,0:26.1:1:30.7:1:1:0:60:78:0.9915:0:0.1 0/1:633:20:12,8:366,243:609,20:0.0316:2,2:27.6:1:29.2:1:1:1.00411:60:40:0.0321:0:1.2 +4 106190944 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5001;SOR=Inf;LSEQ=GCTTAGCAGCTGTTGAGTCT;RSEQ=TTCTCACACTGCTAATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:30,146:176,0:0:2,0:26.2:1:32.5:1:1:0:58.5:175:1:0:0.1 0/1:196:2:1,1:39,155:194,2:0.0102:2,2:25:1:31.5:1:0.36735:3.94:60:4:0.0103:0:1 +4 106193334 . T C 58 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCGTAGAAAAAACTTT;RSEQ=AGCCTGTTTTTGAAGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:23.3:1:29.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 106193588 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.18118;SOR=Inf;LSEQ=TAGGATGGTTTTATGGTAAT;RSEQ=TATATGTCACTGATCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:28,1:29,0:0:1,0:21.9:1:27.9:1:1:0:59.1:58:1:0:0 0/1:22:2:2,0:19,1:20,2:0.0909:1,0:35:1:33.5:1:1:0:60:4:0.0952:0:1 +4 106193665 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.21035;SOR=0;LSEQ=GAGAAAGATACACACACACA;RSEQ=ACACGTTTTCTTTGGGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:71,19:90,2:0.0217:2,2:33.5:1:30:1:0.38939:3.66809:60:4:0.0222:0:1 0/0:108:0:0,0:87,21:108,0:0:2,0:22.4:1:31.4:1:1:0:60:107:1:0:0.2 +4 106193666 . ACACGTTTTCTTTGGGACCTGTAGTTGAGGCTGTAATGTCTTACTTCCCTACCAGGTATGCACTCT A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.50543;SOR=Inf;LSEQ=AGAAAGATACACACACACAC;RSEQ=CACTAGAGAAGACAATCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:70,20:90,0:0:2,0:26.6:1:32.4:1:1:0:59.6:180:1:0:0.3 0/1:117:2:1,1:93,22:115,2:0.0171:2,2:17:1:30.9:1:0.35588:4.15652:60:4:0.0171:0.0171:0 +4 106193695 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22088;SOR=0;LSEQ=CTTTGGGACCTGTAGTTGAG;RSEQ=CTGTAATGTCTTACTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:126,33:159,2:0.0124:2,2:5.5:1:29.5:1:0.3788:3.77651:60:4:0.0127:0:1 0/0:181:0:0,0:134,45:179,0:0:2,0:25:1:30.6:1:1:0:60:58.667:1:0:0.1 +4 106195987 . AT A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTTGGATGTTTATTAC;RSEQ=TTTTTTTTTCACTAAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:37:1:33:1:1:0:60:4:0.1429:0:0 0/0:5:0:0,0:4,1:5,0:0:2,0:30:1:30:1:1:0:60:10:1:0:0.4 +4 106196092 . C T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74617;SOR=0.77124;LSEQ=TATCTTTGCTTAATGGGTGT;RSEQ=GTATATCACTAGTGGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:52:50,2:5,0:5,52:0.9123:0,1:23.3:1:30.5:1:1:0:59.8:25:0.9091:0:1.1 1/1:45:40:39,1:4,0:4,40:0.8889:0,1:25:1:29.3:1:1:0:60:19:0.8837:0:1.1 +4 106196829 . T G 203 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTACATCATGTAGGGAAAT;RSEQ=GCCTCCTTATCCCACTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:0:0,0:365,344:709,0:0:2,0:23.8:1:30.7:1:1:0:60:353.5:1:0:0.1 0/1:868:100:49,51:370,395:765,100:0.1152:2,2:23.6:1:30.6:1:0.91568:1.03:60:49:0.1136:0:1.1 +4 106196951 . A G 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26734;LSEQ=AACATCATTCACCTTCTCAC;RSEQ=TAATCCATAACTACAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:613:332:164,168:131,148:279,332:0.5416:2,2:25:1:31.3:1:0.56994:1.10:60:109.667:0.5465:0:1.1 0/1:738:177:81,96:295,264:559,177:0.2398:2,2:26.9:1:30.6:1:0.12035:1.32384:60:176:0.2418:0:1.1 +4 106197000 . A G 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGTTCAACAGCTCTCTTC;RSEQ=TGCCCTGCATCTCCAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:0:0,0:291,303:594,0:0:2,0:25.3:1:30.6:1:1:0:60:58.4:1:0:0.4 0/1:691:40:20,20:308,342:650,40:0.0579:2,2:29.7:1:30.7:1:0.74782:1.11:60:80:0.0582:0:1.1 +4 106197257 . G A 73 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29473;SOR=2.66088;LSEQ=CTGACATTGGGGGAGTGGCC;RSEQ=TGGCTCCAACTCATGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:2:2,0:193,211:404,2:0.0049:2,0:4.5:1:28.5:1:0.23007:0:60:4:0.005:0:1 0/1:461:6:3,3:229,226:455,6:0.013:2,2:19:1:28.3:1:1:1.01325:60:12:0.013:0:1.2 +4 107004079 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06021;SOR=Inf;LSEQ=AGCACACTACCCAGCCAGGG;RSEQ=AAACTGTGCTTTTCAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:17,0:0:2,0:29.6:1:32:1:1:0:60:34:1:0:0.1 0/1:12:3:2,1:7,2:9,3:0.25:2,2:21.3:1:28.7:1:1:1.66417:60:6:0.25:0:1 +4 107004513 . A AC 68 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.22078;SOR=Inf;LSEQ=TTCAGGTCTAACCCTGACCC;RSEQ=CCTTCCTCAGTGGGCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:32:1:31.5:1:1:0:60:8:1:0:0 1/0:10:5:2,3:3,2:5,5:0.5:2,2:21.2:1:29.4:1:1:2.06996:53.6:10:0.5:0.1:0.4 +4 107004868 . C G 27 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGGTTGGTGCCCCTCAAGGT;RSEQ=AGAGGTCCCAGAAGATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:31:0:1:0:40:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:1:27.5:1:1:0:60:4:1:0:2 +4 107005529 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19231;SOR=Inf;LSEQ=CCTTACTGAAATAAGACACA;RSEQ=AGACAAGTATAGAGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:7,0:0:2,0:28.6:1:30:1:1:0:60:6:1:0:0 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:34:1:32.5:1:0.33333:0:59:4:0.3333:0:1 +4 108124442 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23528;SOR=Inf;LSEQ=ATTGAGTGTGAAGGTTCCAC;RSEQ=GTTTTTTGAGCAAAGTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:94,18:112,0:0:2,0:23.4:1:31.7:1:1:0:59.7:224:1:0:0.7 0/1:106:2:1,1:85,19:104,2:0.0189:2,2:20.5:1:28:1:0.34322:4.38599:60:4:0.0192:0:1 +4 108124443 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.40637;SOR=0.77945;LSEQ=TTGAGTGTGAAGGTTCCACC;RSEQ=TTTTTTGAGCAAAGTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:113:74:63,11:32,7:39,74:0.6549:2,2:23.3:1:30.7:1:0.78778:1.25:59.6:148:0.6607:0:1 1/0:109:65:53,12:34,9:43,65:0.5963:2,2:24.2:1:29.6:1:0.80642:1.17:60:130:0.5963:0:1 +4 108124583 . C T 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=Inf;LSEQ=TTGGATCTCTTTGTCAAACA;RSEQ=TGTTGAGGCCTCGCTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:224,168:392,0:0:2,0:25.4:1:32.7:1:1:0:59.3:129.667:1:0:0.1 0/1:332:10:5,5:167,155:322,10:0.0301:2,2:28.4:1:30.3:1:1:1.07715:58.8:20:0.0303:0:1 +4 108124706 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00754;SOR=0.73685;LSEQ=TCTTCTCCTTCAGTTTCTCA;RSEQ=TCGTGTCTGTATCATCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:620:398:220,178:119,102:221,398:0.6419:2,2:25.2:1:30.3:1:0.73683:1.06:44.6:55.857:0.642:0:1.1 1/0:673:383:220,163:163,126:289,383:0.5691:2,2:26.8:1:29.2:1:0.81357:1.04:46:28.462:0.5649:0:1.1 +4 108124872 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00186;SOR=1.5457;LSEQ=CACATCTGTTTGCGGATAGG;RSEQ=TAGGGGGCATAATCTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:447:266:143,123:101,80:181,266:0.5951:2,2:25.9:1:30.5:1:0.69928:1.08573:33.7:65.5:0.5941:0:1.1 1/0:468:325:173,152:77,64:141,325:0.6944:2,2:25.4:1:29.2:1:0.83987:1.05699:33.9:39.625:0.6937:0:1.1 +4 108125014 . G T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06246;SOR=Inf;LSEQ=CCAGGAAATGCATTGGTTGT;RSEQ=TAACTGATCAGTAGGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:367:0:0,0:190,177:367,0:0:2,0:25.5:1:32.5:1:1:0:27.8:366:1:0:0.1 0/1:394:5:2,3:184,204:388,5:0.0127:2,2:17:1:26.6:1:1:1.35191:28.2:4:0.0103:0:1.4 +4 108125120 . G A 61 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03188;SOR=Inf;LSEQ=CGCAGGGGCAGCAGCAGGGC;RSEQ=CTGAGACCAGAAGCGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:520:0:0,0:160,360:520,0:0:2,0:27:1:31.2:1:1:0:53.8:64:1:0:0.4 0/1:572:6:3,3:211,355:566,6:0.0105:2,2:26.8:1:23.7:1:0.67628:1.68:49:2:0.0072:0:1 +4 108125157 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.04494;SOR=0.68749;LSEQ=CGGGTACAAGGAATAAAAGT;RSEQ=TCAAGGGTAAAACCTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:278:177:15,162:8,92:100,177:0.6367:2,2:23.3:1:31.1:1:1:1.06:58.3:58:0.635:0:1.1 1/0:227:124:15,109:5,98:103,124:0.5463:1,2:22.1:1:30.1:1:0.06268:2.69:58.7:248:0.5511:0:1.1 +4 108125170 . C A 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAAAGTGTCAAGGGTAAAA;RSEQ=CTCTAAAAGGTTAATTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:11,193:204,0:0:2,0:23.4:1:31.7:1:1:0:58.4:50:1:0:0.7 0/1:161:33:1,32:5,123:128,33:0.205:1,1:22.1:1:29.2:1:1:1.29884:51.5:32:0.2013:0:1.2 +4 108125279 . C G 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.07367;SOR=4.92657;LSEQ=TCTTACATCAGCCATCCCCC;RSEQ=CCAAATTGGGCATTTAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:0,4:0,21:21,4:0.16:1,0:18.5:1:32:1:1:0:59.5:8:0.1667:0:1 1/0:8:4:0,4:0,4:4,4:0.5:0,0:33.8:1:33.3:1:1:0:56:8:0.5:0:1 +4 113485894 . A T 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATTTTTAAAAAATGATC;RSEQ=CAAATGCTTAATTTCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:20.5:1:31.8:1:1:0:60:8:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 113485940 . T C 63 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ACCACTTCATGAATGTCTTC;RSEQ=ATGTGATATACATTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:31.3:1:31.8:1:1:0:60:8:1:0:1.8 0/1:4:1:1,0:3,0:3,1:0.25:0,0:22:0:32:0:1:0:60:2:0.25:0:1 +4 113486045 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49668;SOR=Inf;LSEQ=TACTGAATTGTGTTCGCAGC;RSEQ=GCCACCGCGCCGCCGTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:41,3:44,0:0:2,0:24.4:1:30.1:1:1:0:60:43:1:0:0.1 0/1:50:2:2,0:44,4:48,2:0.04:2,0:12.5:1:31:0:1:0:60:4:0.0408:0:1 +4 113486054 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49608;SOR=Inf;LSEQ=GTGTTCGCAGCCGCCACCGC;RSEQ=CCGCCGTCGCTCTCCAACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:50,3:53,0:0:2,0:22.6:1:28.8:1:1:0:59.5:16.667:1:0:0.1 0/1:57:2:1,1:52,3:55,2:0.0351:2,2:11.5:1:26:1:0.13659:15.15409:60:4:0.0357:0:1 +4 113486125 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2565;SOR=Inf;LSEQ=CCGAAGGAGAAATGAGGTAA;RSEQ=TAAGGAGGTCTCTGTACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:113,60:173,0:0:2,0:23.6:1:32.5:1:1:0:57.2:172:1:0:0.1 0/1:214:3:1,2:131,80:211,3:0.014:2,2:10.3:1:30:1:0.5598:3.25636:51:6:0.0144:0:1 +4 113486180 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25767;SOR=Inf;LSEQ=AGACTGCCCACAAATCAACC;RSEQ=GTGGTAAACCACCCAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:107,101:208,0:0:2,0:28.5:1:30.3:1:1:0:54.4:68.333:1:0:0.1 0/1:260:3:2,1:126,131:257,3:0.0115:2,2:24:1:29.3:1:0.61781:2.07:43.7:6:0.0117:0:1 +4 113486193 . C A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25673;SOR=Inf;LSEQ=ATCAACCGGTGGTAAACCAC;RSEQ=CAGGAAGCAACTGGCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:92,97:189,0:0:2,0:26.6:1:31:1:1:0:54:46.25:1:0:0.1 0/1:234:3:2,1:113,118:231,3:0.0128:2,2:25.7:1:26.3:1:0.61701:2.08:41:6:0.013:0:1 +4 113486196 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1979;SOR=0;LSEQ=AACCGGTGGTAAACCACCCA;RSEQ=GAAGCAACTGGCTACAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:84,94:178,2:0.0111:2,2:29.5:1:30:1:1:1.12:29:4:0.0112:0:1 0/0:224:0:0,0:108,115:223,0:0:2,0:26.1:1:30.4:1:1:0:54:54.75:0.9955:0:0.2 +4 113486206 . G A 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38774;SOR=3.21624;LSEQ=AAACCACCCAGGAAGCAACT;RSEQ=GCTACAAAAGCCGCTCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:1,0:70,80:150,1:0.0066:2,0:1:0:27:0:0.4702:0:60:2:0.0068:0:1 0/1:190:4:3,1:86,100:186,4:0.0211:2,2:14.8:1:26.3:1:0.34209:3.47:60:8:0.0216:0:1 +4 113486280 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TCATCGTTACAGGCCTGGTA;RSEQ=TGTGGCGCTCCGTGAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:36,0:0:2,0:12.5:1:31.3:1:1:0:60:35:1:0:0.3 0/1:45:2:1,1:20,23:43,2:0.0444:2,2:37.5:1:29.5:1:1:1.15:51:4:0.0455:0:1.5 +4 113486566 . G A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07939;SOR=0;LSEQ=TGTGCTTTAGAATCCACTAT;RSEQ=ATGGGAAACATTTCATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:3:1,2:54,146:200,3:0.0148:2,2:24.3:1:23.3:1:1:1.35:51.7:2:0.0123:0:3.3 0/0:268:0:0,0:76,190:266,0:0:2,0:22.1:1:28.4:1:1:0:44.4:5.186:1:0:0.5 +4 114756960 . C T 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=ATTTTCAGCAGTTAGCACTT;RSEQ=TAGAATTGGCATCAGCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:33:1:32.3:1:1:0:60:6:0.4286:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:31:1:32.5:1:1:0:52.5:4:0.5:0:1 +4 114757200 . A T 39 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24931;SOR=Inf;LSEQ=TTTCCACAAATATGCATGAA;RSEQ=ATCATGTTAAATATTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:97,99:196,0:0:2,0:24.6:1:30.4:1:1:0:60:195:1:0:0.6 0/1:212:3:1,2:115,94:209,3:0.0142:2,2:7.7:1:25:1:0.59101:2.43672:60:6:0.0143:0:1.3 +4 114757214 . T C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=0.1556;LSEQ=CATGAAAATCATGTTAAATA;RSEQ=TTTTTAAAGGCATTTGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:191:123:55,68:31,37:68,123:0.644:2,2:25.2:1:32.9:1:1:1.0357:60:246:0.644:0:1.2 0/1:224:49:26,23:88,87:175,49:0.2188:2,2:27.3:1:31:1:0.74918:1.12:59.5:98:0.2197:0:1.2 +4 114757257 . T G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50472;SOR=Inf;LSEQ=CTTGAGCGAAATTCTTGATA;RSEQ=TCTGCTCTTATAATATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:45,107:152,0:0:2,0:26.4:1:30.6:1:1:0:59.8:75:1:0:0.8 0/1:190:2:1,1:76,112:188,2:0.0105:2,2:17:0:33.5:1:1:1.47:60:4:0.0106:0:1.5 +4 114757297 . A G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.25225;LSEQ=CAAGGACAATAAAAAAGTAT;RSEQ=CGCTGTTTTCAAGGGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:77:47:9,38:6,24:30,47:0.6104:2,2:21.6:1:32.5:1:1:1.0548:60:94:0.6104:0:1.6 0/1:103:29:7,22:24,50:74,29:0.2816:2,2:23.6:1:31.3:1:0.47993:1.50277:59.2:28:0.2745:0:1.4 +4 114757327 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50834;SOR=Inf;LSEQ=CAAGGGCAATTGCTCATTAG;RSEQ=AGTGGAGCTGACATGTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:1,27:28,0:0:1,0:24.8:1:32.6:1:1:0:60:56:1:0:1 0/1:40:2:1,1:4,34:38,2:0.05:2,2:32:1:27:1:0.23718:7.71:60:4:0.0526:0:2 +4 114757343 . T G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.55745;SOR=1.56134;LSEQ=TTAGCAGTGGAGCTGACATG;RSEQ=CCAATTCAAAGCATTGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:15:0,15:0,9:9,15:0.625:0,1:21.3:1:32.3:1:1:0:60:30:0.625:0:1.7 1/0:29:21:2,19:1,7:8,21:0.7241:2,2:20.9:1:31.2:1:1:1.34216:60:42:0.7241:0:1.2 +4 115455964 . A G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00856;SOR=Inf;LSEQ=AAGATGAGTAGAAAACTAGA;RSEQ=TGGGGTCCAAAGACTTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:100,5:105,0:0:1,0:24.7:1:31:1:1:0:60:210:1:0:0 0/1:68:5:5,0:59,4:63,5:0.0735:2,0:38.2:1:32.8:1:1:0:60:10:0.0746:0:1.2 +4 115455999 . C T 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03512;SOR=Inf;LSEQ=TTATTAGGTGTCCATAGATC;RSEQ=ATGGATTGATCATACAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:162,43:205,0:0:2,0:23.9:1:31.5:1:1:0:60:410:1:0:0.1 0/1:158:4:1,3:120,34:154,4:0.0253:2,2:5:1:25.3:1:0.04026:10.38255:60:8:0.0265:0:1 +4 115456111 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=26.76052;LSEQ=TGCCTCACTTCCCTCCATCT;RSEQ=CAGGAACCTCACAGTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:35:17,18:181,265:446,35:0.0726:2,2:26.5:1:31.1:1:0.37636:1.38:60:70:0.0732:0:1.1 1/0:503:341:149,192:71,91:162,341:0.6779:2,2:25.1:1:28.9:1:1:1.00537:59.9:112.667:0.6828:0:1.1 +4 115456152 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.15201;LSEQ=ACTTCTTTACTCATTTAAAT;RSEQ=CCATTCTTTAAAAAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:258:178:40,138:23,57:80,178:0.6899:2,2:22.7:1:29.4:1:0.27786:1.39031:60:43.5:0.6877:0:1.1 0/1:258:65:20,45:52,141:193,65:0.2519:2,2:23.2:1:27.8:1:0.6317:1.20:60:130:0.2559:0:1.1 +4 115456182 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24497;SOR=Inf;LSEQ=AAAAAGAAAAAAAGTCCCCC;RSEQ=TTAAGACTCTCTGGCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:16,108:124,0:0:2,0:23.2:1:30.5:1:1:0:60:40.333:0.9918:0:0.8 0/1:123:2:1,1:19,101:120,2:0.0163:2,2:21.5:1:29:1:0.30213:5.21:60:4:0.0165:0:2.5 +4 115456236 . C G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=28.38371;LSEQ=GCTATGGAAAACACCAGAGT;RSEQ=AATTTATAGTTGATGTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:7:0,7:0,38:38,7:0.1556:1,0:21.6:1:32.6:1:1:0:60:14:0.1591:0:1 1/1:33:28:1,27:0,5:5,28:0.8485:0,1:25.5:1:31.1:1:1:0:60:56:0.8485:0:1 +4 115461109 . G C 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00266;SOR=0.18303;LSEQ=GACTAAACAGCTGTGAGACT;RSEQ=TGAGGTCCCTAAAGATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:13:8,5:19,9:28,13:0.3095:2,2:23.2:1:33:1:0.73374:1.31036:60:26:0.3171:0:1.4 0/1:67:5:4,1:39,23:62,5:0.0746:2,2:11.2:1:31.6:1:0.64731:2.33:60:10:0.0794:0:1.2 +4 115461155 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52065;SOR=Inf;LSEQ=TGAGGAACAGGCAGAAGGGG;RSEQ=AATAGTGAACAGCAATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:31,32:63,0:0:2,0:30.8:1:30.5:1:1:0:60:14.75:1:0:0.4 0/1:98:2:1,1:46,50:96,2:0.0204:2,2:19:1:28:1:1:1.09:60:4:0.0206:0:2 +4 115461158 . T G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.55045;LSEQ=GGAACAGGCAGAAGGGGGAA;RSEQ=AGTGAACAGCAATGACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:4:2,2:28,30:58,4:0.0645:2,2:32.5:1:32.5:1:1:1.07:60:8:0.0678:0:1 1/0:98:67:29,38:17,14:31,67:0.6837:2,2:30.6:1:30.8:1:0.38432:1.58349:60:134:0.6907:0:1.2 +4 115461170 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.519;SOR=Inf;LSEQ=AGGGGGAATAGTGAACAGCA;RSEQ=TGACAGATGATTCCACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:27,33:60,0:0:2,0:27.8:1:30.9:1:1:0:60:120:1:0:0.4 0/1:92:2:1,1:38,52:90,2:0.0217:2,2:42.5:1:31:1:1:1.36:60:4:0.0217:0:1 +4 115461265 . T C 54 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.31889;SOR=4.12333;LSEQ=TGTTACATAGGTAAATTGCA;RSEQ=GTCACTGAGGTCTGGTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:31.5:1:32:0:1:0:60:4:0.1818:0:1 1/0:8:4:0,4:0,4:4,4:0.5:0,0:24.8:1:27:1:1:0:60:8:0.5714:0:1 +4 117847288 . G C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49195;SOR=Inf;LSEQ=CTACGCGGTGCCCGGTGTCC;RSEQ=GCGGGGACGACTAGCGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:13,0:0:2,0:16.9:1:30.1:1:1:0:60:26:1:0:0.2 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:29:1:27.5:1:1:1.13389:60:4:0.1176:0:1 +4 117847340 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26667;SOR=Inf;LSEQ=CTCGCTCCCCACATCCCCGC;RSEQ=GACACAGCTGGTGGCGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:33,0:0:2,0:30.2:1:29.7:1:1:0:60:15.5:1:0:0.2 0/1:48:3:1,2:20,25:45,3:0.0625:2,2:20.7:1:29.7:1:1:1.58499:59.3:6:0.0625:0:1 +4 118610163 . T A 70 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24242;SOR=0.1257;LSEQ=ACACCTGGAAAAAGCCATCC;RSEQ=TGAGAACTAACTCCCCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:25.2:1:30.2:1:1:0:60:10:0.7143:0:1.6 0/1:5:1:1,0:4,0:4,1:0.2:0,0:11:0:31:0:1:0:60:2:0.2:0:2 +4 118610216 . C G 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54687;SOR=0.64668;LSEQ=TCACAACTGTGATTTTTCTT;RSEQ=AGAGAGAGCAAAACTATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:9,0:14,0:14,9:0.3913:1,0:24.4:1:31.6:1:1:0:60:18:0.4091:0:1.3 0/1:24:7:6,1:17,0:17,7:0.2917:1,2:22.7:1:31.9:1:0.29167:0:60:14:0.2917:0:1.1 +4 118610301 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19658;SOR=0;LSEQ=TGAGGAGCAGACATACAGAA;RSEQ=AATGATTCACAAGAAGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:72,41:113,2:0.0172:2,2:14:0:31:1:1:1.74699:60:4:0.0177:0:1 0/0:145:0:0,0:90,55:145,0:0:2,0:23.1:1:31.1:1:1:0:60:290:1:0:0.2 +4 118610383 . A C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36658;SOR=0.79874;LSEQ=ATTACTAGGGGAGAGCATCC;RSEQ=TCAGCTGACATGGTGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:57:24,33:53,64:117,57:0.3276:2,2:27.4:1:31.9:1:0.74632:1.13782:60:56:0.3256:0:1.1 0/1:200:56:27,29:65,79:144,56:0.28:2,2:25.9:1:31.1:1:0.7529:1.13:60:112:0.2814:0:1.1 +4 118610399 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50096;SOR=Inf;LSEQ=ATCCATCAGCTGACATGGTG;RSEQ=TGGCAGCATGGTCACAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:68,93:161,0:0:2,0:25.5:1:31.4:1:1:0:60:39.25:1:0:0.4 0/1:185:2:1,1:81,101:182,2:0.0108:2,2:20.5:1:26:1:1:1.25:60:4:0.011:0:2 +4 118610405 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25071;SOR=Inf;LSEQ=CAGCTGACATGGTGGTGGCA;RSEQ=CATGGTCACAACTGAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:65,92:157,0:0:2,0:24.5:1:32.3:1:1:0:60:156:1:0:0.4 0/1:178:3:2,1:76,99:175,3:0.0169:2,2:9:1:26.7:1:0.58222:2.59:60:6:0.017:0:1.7 +4 118610435 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21888;SOR=0;LSEQ=AACTGAGGTGCGGCTTCAGA;RSEQ=AGGAGAGCTTTTCAATAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:30,74:104,2:0.0189:2,2:40.5:1:32.5:1:0.50135:2.44:60:4:0.0189:0:1 0/0:120:0:0,0:38,82:120,0:0:2,0:25.5:1:30:1:1:0:60:240:1:0:0.4 +4 118610504 . A G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25579;SOR=0.46953;LSEQ=TCAAATTCCCAGGAATGTAG;RSEQ=TAATAACAATTATGCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:1,10:1,13:14,11:0.44:1,2:25.6:1:32.9:1:1:1.29:60:22:0.44:0:2.1 0/1:30:8:0,8:1,21:22,8:0.2667:1,0:28.9:1:32.3:1:1:0:60:16:0.2667:0:2.4 +4 118610508 . T C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25933;SOR=0.49155;LSEQ=ATTCCCAGGAATGTAGATAA;RSEQ=AACAATTATGCCTCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:1,10:1,13:14,11:0.44:1,2:23.1:1:32.6:1:1:1.29:60:22:0.44:0:2.1 0/1:29:8:0,8:1,20:21,8:0.2759:1,0:28.9:1:32:1:1:0:60:16:0.2759:0:2.4 +4 118862907 . T A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTGTGAGTCTCAGTGCTGG;RSEQ=TGCTGCCCCTCCCCCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:16.5:1:29:1:1:0:60:4:0.6667:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:27.5:1:1:0:60:4:1:0:1 +4 118862978 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTGTGCTGGTTGCCCCT;RSEQ=CCCGTGGGAGTTCAGTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:17.5:1:29:1:1:1.29:60:4:0.2222:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:25.5:1:32.5:1:1:0:60:4:1:0:0.5 +4 118863268 . A G 48 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ATGGGTCACGCCAGCGTTCT;RSEQ=GTCAGTTTTGGTGAGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:27:1:28.5:1:1:0:60:4:1:0:0 1/1:3:3:0,3:0,0:0,3:1:0,0:29.7:1:30.7:1:1:0:60:6:1:0:1 +4 119557567 . A C 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCTCCCACTGGACCGTC;RSEQ=CCCAACTGGCACCACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:9.3:1:27.8:1:1:0:24.7:12:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:9:0:24:0:1:0:20:2:1:0:1 +4 120258955 . T G 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=CCACAGAGGTGGGCTTCAGT;RSEQ=GGGCCTTGATGGGAGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:14.5:1:31.3:1:1:0:32:8:0.4444:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:11:1:31.7:1:1:0:24.3:6:1:0:0 +4 120259145 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50064;SOR=Inf;LSEQ=AGGGCAGAATTGTGGCAGGC;RSEQ=TAAATAGTATGATGAATTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:81,66:147,0:0:2,0:23.5:1:30.9:1:1:0:33.5:48:1:0:0.1 0/1:168:2:1,1:85,81:166,2:0.0119:2,2:26:1:28:1:1:1.0491:25:4:0.0121:0:1 +4 120259187 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25888;SOR=Inf;LSEQ=ACTTAATCCTCTGGGCAGTG;RSEQ=GATTCAGTGAAGGCTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:99,94:193,0:0:2,0:26.9:1:30.7:1:1:0:30.4:31.167:1:0:0.2 0/1:245:3:2,1:116,126:242,3:0.0122:2,2:11.7:1:25.7:1:0.61004:2.17:22.7:2:0.0083:0:2.3 +4 120259212 . CA TG 44 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19433;LSEQ=CAGTGAAGGCTTTTGGGAAA;RSEQ=GAGCATCATGCTAAGATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:2:2,0:107,120:227,2:0.0087:2,0:4:1:28.7:1:0.22547:0:20.5:4:0.0089:0.0044:0.5 0/1:288:3:3,0:129,154:283,3:0.0104:2,0:6.3:1:28.1:1:0.09711:0:20.7:6:0.0106:0.0035:1.3 +4 120324304 . C T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01989;SOR=0;LSEQ=GGAGGAGGGGGTGATGATGT;RSEQ=ATTGCTGATGACGGCTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:5,0:19,10:29,5:0.1471:2,0:17.2:1:31:1:0.2908:0:30:10:0.1471:0:1.2 0/0:38:0:0,0:21,17:38,0:0:2,0:14.8:1:30.4:1:1:0:28.9:76:1:0:0.2 +4 120324424 . A T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01828;SOR=0.2551;LSEQ=CAACAAGGGCTTTCATGGGA;RSEQ=GGTATTTGCACCTGTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:13:2,11:7,31:38,13:0.2549:2,2:29.1:1:32.1:1:1:1.23689:21.8:26:0.26:0:1 0/1:63:5:1,4:22,36:58,5:0.0794:2,2:17.4:1:28.8:1:0.64437:2.41439:22.2:10:0.0794:0:1.2 +4 120324432 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24304;SOR=Inf;LSEQ=GCTTTCATGGGAAGGTATTT;RSEQ=CACCTGTCATTCCTTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:9,39:48,0:0:2,0:20.5:1:32.6:1:1:0:24.8:23:1:0:0.4 0/1:51:3:2,1:16,32:48,3:0.0588:2,2:19:1:25.7:1:0.28163:3.88:25.7:6:0.06:0:1 +4 120324738 . CTTCTGGTGCAAGAGA C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=CTCCCAATGGATCCTGCCAC;RSEQ=CCTGAAAGTGTGGGCGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:5,7:12,0:0:2,0:12.5:1:30.4:1:1:0:21.2:24:1:0:0.1 0/1:13:2:0,2:5,6:11,2:0.1538:2,0:25:1:27.6:1:0.48718:0:22:4:0.1538:0.0769:1 +4 120324918 . A G 50 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGGGAACCCCACGGAC;RSEQ=TGGATCCCGCACTGGCGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:31.7:1:31.7:1:1:0:23:6:1:0:1 +4 120325654 . GC G 40 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0.74999;LSEQ=ATAGCGGGTCCACTGCTGCT;RSEQ=CCCTGCCCTGACTCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:5,5:10,3:0.2308:2,2:20:1:25.7:1:1:1.89792:24.3:2:0.1818:0:1 0/1:11:2:0,2:4,5:9,2:0.1818:2,0:22:1:32.5:1:0.49091:0:27:4:0.1818:0:2 +4 120325674 . C T 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22581;SOR=Inf;LSEQ=GCCCCTGCCCTGACTCCCAG;RSEQ=CCTGCCTGACCCCACCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:16,0:0:2,0:28.6:1:31.6:1:1:0:34.1:32:1:0:0.4 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:5.5:1:25.5:1:1:1.55:60:4:0.1333:0:1 +4 120325732 . C A 43 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.93553;LSEQ=GCAACTCTGGGTGCCTTGCC;RSEQ=CTGCCTCTGCCCCAGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:4,10:14,3:0.1765:2,2:5:1:27.7:1:1:1.23:24.3:6:0.1765:0:1 0/1:12:2:0,2:4,6:10,2:0.1667:2,0:3:1:25.5:1:0.51515:0:27:4:0.1667:0:2 +4 123792847 . T A 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17647;SOR=0;LSEQ=CCTTGAGTAACATCTCCAGG;RSEQ=GCAGGAGCAAATCAGATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:18:0:31:0:1:0:60:2:1:0:1 0/1:16:2:1,1:7,7:14,2:0.125:2,2:26.5:1:28.5:1:1:1:60:4:0.125:0:1 +4 123792964 . GCAA G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.48617;SOR=0;LSEQ=AAAAAAAAAACTAGCAGAAA;RSEQ=CAACAACAGCATCAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:9,2:11,2:0.1538:2,2:30:1:31.5:1:0.42308:3.87298:40.5:4:0.1818:0:1 0/0:10:0:0,0:4,6:10,0:0:2,0:23.8:1:30.6:1:1:0:60:9:1:0:0.5 +4 123793061 . G T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10256;SOR=Inf;LSEQ=AAAATAGACAAACTCACAAA;RSEQ=ATGAGAAAGAAATCAACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:18,0:0:2,0:27.3:1:32.8:1:1:0:42.8:36:1:0:0.5 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:40:0:28.5:1:1:1.29098:43:4:0.2222:0:2 +4 123793070 . GA G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTCACAAAGATGAGAAA;RSEQ=AATCAACGAAAAAATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:6,12:0,0:0,18:1:0,2:24.4:1:32.5:1:1:0:42.8:36:1:0.1111:0.5 1/1:5:5:3,2:0,0:0,5:1:0,2:21.4:1:31.1:1:1:0:42.6:10:1:0.2:1.2 +4 123793087 . G T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2451;SOR=Inf;LSEQ=AAAGAAATCAACGAAAAAAT;RSEQ=ATGAAAACCCAAAAGGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:2,6:2,4:6,8:0.5714:2,2:21.6:1:30.3:1:1:1.45647:41.6:16:0.5714:0:1.1 1/1:4:4:2,2:0,0:0,4:1:0,2:26.3:1:29.5:1:1:0:38.3:8:1:0:1.5 +4 124344600 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09994;SOR=0;LSEQ=GCTCTGTATTCCAGATATTG;RSEQ=TCCCTTAAGAGAGGAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:3:1,2:74,8:82,3:0.0353:2,2:12:1:27.7:1:0.03539:17.22203:60:6:0.0353:0:1.3 0/0:97:0:0,0:86,11:97,0:0:2,0:24.7:1:31:1:1:0:60:47.5:1:0:0.2 +4 124344636 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20034;SOR=0;LSEQ=AAGAGATTTTTCTCTTGTGA;RSEQ=ATTTGTTTATTCTACGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:143,37:180,2:0.011:2,2:14.5:1:28.5:1:0.3749:3.82698:60:4:0.0112:0:1 0/0:224:0:0,0:157,67:224,0:0:2,0:22.4:1:31:1:1:0:60:73.667:1:0:0.5 +4 124344650 . A T 168 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=55.75228;LSEQ=TTGTGAGATTTGTTTATTCT;RSEQ=CGAAACTCAAAAAGTCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:1:0,1:180,60:240,1:0.0041:2,0:33:0:27:0:0.25311:0:60:2:0.0042:0:1 0/1:280:53:34,19:149,78:227,53:0.1893:2,2:27.3:1:29.5:1:0.8732:1.06724:60:106:0.1927:0:1.1 +4 124344717 . T C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09249;SOR=0.77743;LSEQ=CAGGTCACCAAGTAGTGCAG;RSEQ=CGTCAGCTGGGGTTCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:459:355:186,169:56,47:103,355:0.7734:2,2:27.5:1:31.7:1:0.73798:1.08238:59.9:176.5:0.7741:0:1.1 1/0:537:390:198,192:68,76:144,390:0.7263:2,2:26.4:1:30.7:1:0.49554:1.15:60:64:0.7273:0:1.1 +4 124344813 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23754;SOR=Inf;LSEQ=GAGTCCTCTTCAACCAAAGG;RSEQ=TGCTAGGATTGTTTCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:42,151:193,0:0:2,0:23.5:1:32.3:1:1:0:60:37.6:1:0:0.5 0/1:184:2:1,1:48,134:182,2:0.0109:2,2:35.5:1:31:0:0.46276:2.77:60:4:0.0112:0:1 +4 124344819 . G A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10798;LSEQ=TCTTCAACCAAAGGCTGCTA;RSEQ=GATTGTTTCTGTAATCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:167:85:11,74:14,68:82,85:0.509:2,2:24:1:31.5:1:0.51868:1.38232:60:84:0.506:0:1.1 0/1:160:16:3,13:38,106:144,16:0.1:2,2:25.9:1:29.9:1:0.76332:1.54956:60:32:0.1006:0:1.1 +4 124344820 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24154;SOR=Inf;LSEQ=CTTCAACCAAAGGCTGCTAG;RSEQ=ATTGTTTCTGTAATCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:24,140:164,0:0:2,0:23.9:1:32.2:1:1:0:60:328:1:0:0.6 0/1:159:2:1,1:39,118:157,2:0.0126:2,2:35.5:1:28.5:1:0.44105:3.00:60:4:0.0127:0:1 +4 124344915 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0518;SOR=Inf;LSEQ=TCTCACTGTATTATAAGTTC;RSEQ=CCCAAAGGCTTGAGGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:0,22:22,0:0:1,0:19.9:1:30.4:1:1:0:60:21:1:0:0 0/1:25:5:0,5:0,20:20,5:0.2:1,0:28.2:1:29.2:1:1:0:60:10:0.2:0:1 +4 130070827 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51234;SOR=Inf;LSEQ=TTCAGAATTCCCCAAATTGT;RSEQ=TAAACTTCTGGCCCCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:24,10:34,0:0:2,0:24.1:1:30.6:1:1:0:60:10.333:1:0:0.5 0/1:50:2:1,1:26,20:46,2:0.04:2,2:13:1:27:1:1:1.29283:60:4:0.0426:0:2 +4 130070886 . C T 147 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGGCAATGCTGGCTAACAA;RSEQ=GTTCATTGTGTGCTTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:27:11,16:0,0:0,27:1:0,2:32.9:1:31.1:1:1:0:60:54:1:0:1.1 1/0:40:20:8,12:7,12:19,20:0.5:2,2:26.9:1:29.6:1:1:1.14:60:40:0.5128:0:1.2 +4 130125306 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10979;SOR=1.29638;LSEQ=TTCAAACTAAAACCAGTTTA;RSEQ=GTAGAGGAAATCTTTATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:335:216:108,108:62,57:119,216:0.6448:2,2:24.2:1:31.2:1:0.73305:1.08745:60:432:0.6467:0:1.1 1/0:379:266:118,148:54,59:113,266:0.7018:2,2:23.8:1:30:1:0.57364:1.14752:59.9:87.667:0.7032:0:1.1 +4 130125355 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10386;SOR=0;LSEQ=GGAAAATGTTCTTGTCATAC;RSEQ=TATCCACCTAATCTACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:100,157:257,3:0.0115:2,2:34.3:1:30.3:1:1:1.27272:60:6:0.0117:0:1.3 0/0:292:0:0,0:111,181:292,0:0:2,0:24.8:1:30.5:1:1:0:59.8:35.5:1:0:0.8 +4 130125383 . CT C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.23079;SOR=Inf;LSEQ=CTAATCTACTGATTCTCCAC;RSEQ=TTTGTTTTCTTCTTTTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:54,124:178,0:0:2,0:21.7:1:30.2:1:1:0:59.6:28.667:0.9942:0:0.9 0/1:166:2:1,1:49,114:163,2:0.012:2,2:31.5:1:32:1:0.51552:2.31:60:4:0.0127:0:0 +4 130125405 . T TA 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.98772;LSEQ=TTTGTTTTCTTCTTTTTAGC;RSEQ=AAAAAAAAAACACAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:6:1,5:23,72:95,6:0.0588:2,2:33.2:1:27.8:1:1:1.59072:55.8:5:0.0568:0:2.2 0/1:86:5:1,4:23,55:78,5:0.0581:2,2:25.4:1:31.6:1:1:1.66344:59:10:0.0725:0:1.4 +4 130125415 . AC A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.78132;SOR=1.23028;LSEQ=TCTTTTTAGCTAAAAAAAAA;RSEQ=ACAAAAAAAAAAACCTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:7:1,6:0,0:0,7:0.0921:0,2:20.3:1:30.4:1:1:0:60:14:0.0959:0.0395:0.4 0/1:63:7:0,7:3,17:20,7:0.1111:2,0:13:1:29.7:1:0.5453:0:60:14:0.1186:0.0635:0.4 +4 130125416 . C A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14086;LSEQ=CTTTTTAGCTAAAAAAAAAA;RSEQ=ACAAAAAAAAAAACCTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:67:12,55:0,0:0,67:0.8816:0,2:22.9:1:30.7:1:1:0:58.9:32.5:0.8904:0:1.6 1/0:63:32:7,25:3,17:20,32:0.5079:2,2:19.1:1:30.2:1:0.72247:1.57:57.2:64:0.5424:0:1.8 +4 130125418 . C CA 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.09252;SOR=0.31897;LSEQ=TTTTAGCTAAAAAAAAAACA;RSEQ=AAAAAAAAAAACCTAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:11:1,10:8,49:57,11:0.1447:2,2:26.9:1:28:1:1:1.62228:59.5:10:0.1563:0.0263:1.4 0/1:59:3:1,2:7,35:42,3:0.0508:2,2:27:1:31.3:1:0.45243:2.44:60:6:0.0612:0:1.3 +4 131217633 . TA T 28 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATTTTATGACTCAGTT;RSEQ=AAAAAAAAAAACAAAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:12:1:28.5:1:1:0:60:4:0.3333:0.1667:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 131217680 . T C 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20455;SOR=0;LSEQ=GTGATTAACTTTCACTCTTA;RSEQ=AGCAACATTTATTTGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:3,1:4,3:0.4286:2,2:19.3:1:30.3:1:1:1.41418:60:6:0.4286:0:1.3 0/0:5:0:0,0:5,0:5,0:0:0,0:33.6:1:31.6:1:1:0:60:10:1:0:0 +4 134134156 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22092;SOR=Inf;LSEQ=GACACAGAGTCAGACCATAT;RSEQ=GATTATAAATGTCTCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:30,1:31,0:0:1,0:19.6:1:32.8:1:1:0:60:62:1:0:0 0/1:28:2:2,0:26,0:26,2:0.0714:1,0:28:1:31:1:1:0:60:4:0.0714:0:1 +4 134134244 . T C 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25288;SOR=Inf;LSEQ=ATTACATACTTAACAATGAT;RSEQ=TATATTTTAGAAGTCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:119,59:178,0:0:2,0:25.4:1:30.5:1:1:0:60:43.5:1:0:0.7 0/1:209:3:1,2:132,74:206,3:0.0144:2,2:25.7:1:25:1:0.29961:3.54485:60:2:0.0099:0:1.7 +4 134134309 . T C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05561;LSEQ=TAATGATGTCAGTGTTTTTG;RSEQ=ATTTCCTATTTGAAGACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:239:221:107,114:8,10:18,221:0.9247:2,2:26.6:1:31.9:1:0.80976:1.17:59.8:35.833:0.9227:0:1.8 0/1:319:129:61,68:95,95:190,129:0.4044:2,2:25.8:1:31.1:1:0.64963:1.11437:60:42:0.4013:0:1.9 +4 134134331 . G A 233 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCCTATTTGAAGACTAAC;RSEQ=TGAGAATAATATTTGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:200:200:84,116:0,0:0,200:1:0,2:26.5:1:30.6:1:1:0:59.8:99:1:0:1.9 1/0:296:158:64,94:60,78:138,158:0.5338:2,2:24.4:1:29.2:1:0.63767:1.12934:59.9:51.667:0.5308:0:1.7 +4 134134348 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16468;SOR=0;LSEQ=AACGTGAGAATAATATTTGA;RSEQ=GGAAGGAGACAGATTGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:59,99:158,2:0.0124:2,2:10.5:1:29:1:1:1.67:60:4:0.0128:0:2 0/0:235:0:0,0:91,144:235,0:0:2,0:26.9:1:29.5:1:1:0:60:46:1:0:0.9 +4 134134495 . G GT 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.222;SOR=0.32577;LSEQ=CTCTTTTTAATAACATTCAT;RSEQ=TTTTTTCCAGAAAAATATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:1,15:0,5:5,16:0.7619:0,1:29.4:1:30.7:1:1:0:60:32:0.7619:0:0.1 1/0:10:5:0,5:0,5:5,5:0.5:0,0:30.4:1:30.2:1:1:0:60:10:0.5:0:0 +4 134635942 . G A 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50525;SOR=1.16577;LSEQ=TAGAAAATTTCACTGTAGTC;RSEQ=CAAGCTCTAACATTTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:42:19,23:60,77:137,42:0.2346:2,2:24.1:1:29.9:1:1:1.06:60:84:0.2346:0:1.2 0/1:262:69:30,39:87,104:191,69:0.2634:2,2:26.9:1:28.4:1:0.77974:1.08713:60:22:0.2588:0:1.2 +4 135458997 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22;SOR=Inf;LSEQ=TAGAGCATGGCAGAGTTAAT;RSEQ=CTTTCTGAGGACTGTAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:13,0:0:2,0:22.3:1:30.7:1:1:0:60:26:1:0:0 0/1:12:2:1,1:7,3:10,2:0.1667:2,2:10:1:28:1:1:2.16028:60:4:0.1667:0:1 +4 136777565 . CT C 147 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTCATCCCTCTTTACAATT;RSEQ=TTTCCTTGGGTATCTAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:24:20,4:55,7:62,24:0.2791:2,2:25.4:1:32.2:1:0.49141:1.56259:60:48:0.2791:0.0465:0 0/0:102:0:0,0:86,16:102,0:0:2,0:25.8:1:30.3:1:1:0:60:101:1:0:0 +4 136777610 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.18979;SOR=0;LSEQ=TGGAAAACAATGACAGACTT;RSEQ=CTTTCTGCCTAGTTTAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:130,53:183,2:0.0108:2,2:11:1:31:1:0.49971:2.43936:60:4:0.0111:0:1 0/0:239:0:0,0:162,77:239,0:0:2,0:23.9:1:29.8:1:1:0:60:478:1:0:0.2 +4 136777689 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0566;LSEQ=CCAGTGCAACTTAGAATCAG;RSEQ=GACAGAAAAGTGAAATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:336:304:148,156:17,15:32,304:0.9048:2,2:25.7:1:31.3:1:0.71142:1.19396:59.9:100.333:0.9066:0:1.1 0/1:436:152:71,81:132,151:283,152:0.3486:2,2:25:1:30.5:1:1:1.00:59.9:49.667:0.3457:0:1.2 +4 140810637 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11555;LSEQ=GCCTGGAGCTGTGGAGGTGG;RSEQ=GGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:80:51,29:6,4:10,80:0.8421:2,2:27.5:1:30.5:1:1:1.17:58.2:160:0.8511:0:1.5 0/1:132:50:29,21:48,31:79,50:0.3788:2,2:27.1:1:28.5:1:0.85415:1.12025:59.1:49:0.3769:0:1.6 +4 140810678 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.26414;SOR=Inf;LSEQ=CTGCTGTTGCTGTTGCTGCT;RSEQ=CTGTTGCTGCTGCTGGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:70,62:132,0:0:2,0:24.7:1:32.4:1:1:0:58.6:131:1:0:1.1 0/1:178:3:2,1:86,89:175,3:0.0169:2,2:27:1:27.3:1:0.61864:2.06:57.7:6:0.0169:0:1.3 +4 140810700 . C T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.89843;SOR=0.94178;LSEQ=TGTTGCTGCTGCTGGATATA;RSEQ=GGCATCAAGGGGTTTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:114:60:27,33:23,30:53,60:0.5263:2,2:27:1:30.3:1:1:1.07:59.5:59:0.5221:0:1.5 1/0:133:68:27,41:30,34:64,68:0.5113:2,2:26.5:1:29.3:1:0.48259:1.33687:56.4:67:0.5115:0:1.4 +4 140811050 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13816;SOR=0;LSEQ=GGGAGACCAATTTGAAGTCT;RSEQ=ATTTGAGTGCTGTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:19,15:34,2:0.0556:2,2:22.5:1:28.5:1:1:1.2583:60:4:0.0556:0:1.5 0/0:60:0:0,0:39,21:60,0:0:2,0:26.4:1:30.6:1:1:0:49.9:59:1:0:1.2 +4 140811063 . TTGCTGCTGCTGC T 140 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=47;MSI=19.000;MSILEN=3;SSF=1;SOR=1.00893;LSEQ=GAAGTCTGATTTGAGTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:18:9,9:9,10:19,18:0.4615:2,2:15.8:1:29.9:1:1:1.11:38.4:36:0.4615:0.2308:2.4 0/1:69:32:17,15:22,11:33,32:0.4638:2,2:16.3:1:28.1:1:0.3167:1.74919:41.9:31:0.4559:0.2029:2.2 +4 140811084 . C T 131 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=19.000;MSILEN=3;SSF=0.69623;SOR=1.19386;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:15:4,11:19,14:33,15:0.3125:2,2:16.1:1:31.2:1:0.06465:3.62887:59.1:30:0.3191:0:1.3 0/1:71:25:16,9:22,24:46,25:0.3521:2,2:20:1:28.3:1:0.22103:1.92:55:50:0.3571:0:1.4 +4 140811096 . C T 155 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=3;SSF=0.01071;SOR=0.36385;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:43:25,18:6,7:13,43:0.7679:2,2:22:1:30:1:0.53182:1.61:46.7:86:0.7679:0:2.3 1/0:79:43:18,25:24,12:36,43:0.5443:2,2:26.5:1:28.7:1:0.04133:2.7409:43.3:86:0.5443:0:2.3 +4 140811135 . T C 197 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03336;LSEQ=TGCTGCTGTTGCTGTTGCTG;RSEQ=TTCTGCTGCATGAGTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:70:32,38:2,0:2,70:0.9722:0,2:30.9:1:32.2:1:0.21948:0:49.1:34:0.9855:0:1.9 1/0:101:54:20,34:21,24:45,54:0.5347:2,2:29.5:1:31.2:1:0.41332:1.48145:48.3:53:0.5521:0:2 +4 140811149 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50794;SOR=Inf;LSEQ=TTGCTGTTTCTGCTGCATGA;RSEQ=TTTGGCCCTTTGTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:32,37:69,0:0:2,0:28.3:1:31.7:1:1:0:50.4:16.25:1:0:1.8 0/1:93:2:1,1:39,52:91,2:0.0215:2,2:39.5:1:29.5:1:1:1.33:53.5:4:0.0222:0:2.5 +4 142367676 . G T 36 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62427;SOR=0.35067;LSEQ=AAGTAATGTCTTCTTACTGT;RSEQ=ATAGTATAAACAAAATATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:2,1:197,95:292,3:0.0101:2,2:20:1:23:1:1:1.03669:60:2:0.0069:0:1.7 0/0:280:1:0,1:185,94:279,1:0.0036:2,0:1:0:21:0:0.33929:0:60:2:0.0036:0:1 +4 142367740 . G A 210 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGTGGCTATTTAAATAT;RSEQ=CACATGCAAACACACAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:215,242:457,0:0:2,0:25.4:1:32:1:1:0:60:64.286:1:0:0.1 0/1:584:172:85,87:211,201:412,172:0.2945:2,2:27.7:1:28.4:1:0.717:1.07431:60:171:0.2958:0:1.1 +4 142949864 . A C 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00368;SOR=Inf;LSEQ=TCATGACAATAAAAACAAAC;RSEQ=AAAAAGACCAAGGTGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:252,50:302,0:0:2,0:24.3:1:30.7:1:1:0:59.8:150:0.9967:0:0 0/1:306:9:8,1:232,64:296,9:0.0294:2,2:13.7:1:30:1:0.68985:2.20:60:18:0.0297:0:1 +4 142950186 . A AT 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.68225;LSEQ=TAACAAAGATTCAACTCTAC;RSEQ=TTTTTTTTTTCCACAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:1,36:37,2:0.05:1,0:9:1:28.3:1:1:0:60:4:0.0513:0.025:0.5 0/1:29:1:0,1:0,28:28,1:0.0345:1,0:20:0:27:0:1:0:60:2:0.037:0:1 +4 143002782 . A T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGATAATGAGTTAGTTT;RSEQ=ATTTTGCAAGTACTCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:11.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 143003015 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16763;SOR=0;LSEQ=AGATAGAGATGAAATCATTA;RSEQ=ACAGGTGGAGAAAATTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:31,0:0,0:0,31:1:0,1:24.1:1:32.7:1:1:0:60:62:1:0:1.1 1/1:22:20:20,0:2,0:2,20:0.9091:0,1:18.3:1:31.5:1:1:0:60:40:0.9091:0:1 +4 143003117 . G GA 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.85635;SOR=1.08675;LSEQ=TCCAATAAAATATGTATTTT;RSEQ=AAAAAAAAAATAAAAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:15:14,1:170,38:208,15:0.0664:2,1:24.5:1:31.7:1:0.47905:3.12:60:30:0.0685:0.0088:0.1 0/1:237:17:12,5:177,42:219,17:0.0717:2,2:17.5:1:28.5:1:0.34342:1.75115:60:34:0.0733:0.0253:0.1 +4 143003155 . G GA 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=5e-05;SOR=0.35806;LSEQ=AACTCAAAATGACCTTAAAA;RSEQ=AAAAAAACTTGAAAAACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:429:408:287,121:15,3:18,408:0.951:2,2:27.9:1:30.5:1:0.29703:2.10489:60:135:0.9597:0.1235:0.1 1/1:469:410:266,144:38,17:55,410:0.8742:2,2:28.8:1:28.8:1:0.651:1.20957:60:81:0.8824:0.0235:0.1 +4 143003396 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24773;SOR=Inf;LSEQ=TGTAATACCGTAAAGTGTCG;RSEQ=CCTCCTCCAAACACTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:26,140:166,0:0:2,0:24:1:31.3:1:1:0:60:22.714:1:0:0.2 0/1:165:2:1,1:26,137:163,2:0.0121:2,2:8.5:1:27.5:1:0.30133:5.19:60:4:0.0123:0:1 +4 143003404 . CA C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49913;SOR=0;LSEQ=CGTAAAGTGTCGGCCTCCTC;RSEQ=AACACTTCTAGTCTAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:20,127:147,2:0.0134:2,2:11:1:29:1:0.26283:6.22:60:4:0.0141:0:0 0/0:137:0:0,0:14,123:137,0:0:2,0:20.9:1:30.2:1:1:0:60:67.5:1:0:0.1 +4 143003526 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTCATTTCAAAAGCCAAC;RSEQ=CAATGGACCCAATTTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:0,13:1:0,1:24.8:1:33.2:1:1:0:60:26:1:0:1.2 1/1:6:6:0,6:0,0:0,6:1:0,0:23.3:1:29.8:1:1:0:60:12:1:0:1 +4 143003718 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAAAAACAAACAAACAA;RSEQ=CAACCAAAAAACTATATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:40.5:1:29.5:1:1:0:44.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 143007169 . C A 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71609;SOR=1.7248;LSEQ=CAAGAGTAAAAATGCCTAAT;RSEQ=CATGGACTAATAGAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:3:3,0:52,0:52,3:0.0545:1,0:23:1:30:0:1:0:60:6:0.0556:0:2 0/1:55:5:5,0:49,1:50,5:0.0909:1,0:13.2:1:28:1:1:0:60:10:0.0926:0:2 +4 143007197 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01392;SOR=0;LSEQ=TAATAGAAGATGACACCTGG;RSEQ=AACCCAAAGTGCAGAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:94:94:92,2:0,0:0,94:1:0,1:24.6:1:30.7:1:1:0:60:93:1:0:1 1/1:93:87:87,0:6,0:6,87:0.9355:0,1:25.3:1:30:1:1:0:60:174:0.9355:0:1.1 +4 143007224 . G C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49916;SOR=Inf;LSEQ=AAGTGCAGAGGTTGGACCCT;RSEQ=CACAGTAGAGAACTGATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:129,45:174,0:0:2,0:23:1:32.4:1:1:0:60:173:1:0:0.5 0/1:186:2:1,1:149,35:184,2:0.0108:2,2:5.5:1:29.5:1:0.35048:4.21166:60:4:0.0108:0:1 +4 143007419 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00482;SOR=0.52922;LSEQ=ATGTGAAATATCTGAAGGGG;RSEQ=AAAAACAAAGGAGAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:289:256:74,182:14,19:33,256:0.8858:2,2:25.8:1:31.8:1:0.15795:1.80829:60:512:0.8858:0:1.5 1/1:352:283:96,187:26,43:69,283:0.804:2,2:24.5:1:30.2:1:0.57439:1.17724:60:69.75:0.8064:0:1.5 +4 143007449 . A G 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.248;SOR=Inf;LSEQ=GGAGAAAAATAAAATGAGAC;RSEQ=GTGTTCACATTAAGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:40,148:188,0:0:2,0:23.5:1:31.8:1:1:0:59.9:187:1:0:1.5 0/1:187:2:1,1:44,141:185,2:0.0107:2,2:33:1:23.5:1:0.42436:3.18:60:4:0.011:0:1 +4 143007460 . T G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03904;SOR=0.50343;LSEQ=AAATGAGACAGTGTTCACAT;RSEQ=AAGCTGCCCATGGAGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:149:132:22,110:5,12:17,132:0.8859:2,2:22.8:1:32.4:1:0.19576:2.07123:59.8:264:0.8859:0:1.9 1/0:147:117:22,95:7,23:30,117:0.7959:2,2:22.9:1:30.4:1:0.60989:1.31167:60:28.25:0.7902:0:1.9 +4 143007466 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24347;SOR=Inf;LSEQ=GACAGTGTTCACATTAAGCT;RSEQ=CCCATGGAGGTTTTTTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:24,110:134,0:0:2,0:21.7:1:32.7:1:1:0:59.8:268:0.9926:0:1.7 0/1:132:2:1,1:23,107:130,2:0.0152:2,2:13.5:1:26:1:0.33171:4.58:60:4:0.0159:0:2.5 +4 143029211 . C T 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32862;SOR=0.26624;LSEQ=AAAGATTTATAATCAAGAAG;RSEQ=TATTATTGCTGTCTTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:1,2:193,86:279,3:0.0106:2,2:8.7:1:21.7:1:0.2305:4.46176:60:2:0.0072:0:1 0/0:351:1:0,1:245,105:350,1:0.0028:2,0:1:0:26:0:0.30199:0:60:2:0.0029:0:1 +4 143029391 . A G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.22178;SOR=0.67673;LSEQ=TGGGTTATAAAACGGTACCA;RSEQ=AAAGTAACACATTTTACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:27:8,19:30,121:151,27:0.1517:2,2:19.1:1:32.7:1:0.3069:1.69:60:54:0.1543:0:1.1 0/1:204:22:5,17:34,148:182,22:0.1078:2,2:18.4:1:29.8:1:0.57916:1.28:60:44:0.11:0:1 +4 143029543 . CACCTCAAATATCCTCACAATCATCAAATGTGAACCTAGATAAAATACCATGTATAAA C 88 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00749;SOR=0;LSEQ=ATTTCACTAATCGCTTCTAA;RSEQ=ACAACAGTCTCTGTGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:28.6:1:31.6:1:1:0:58.7:14:1:0.5714:0.3 0/1:16:6:1,5:1,9:10,6:0.375:2,2:66.5:1:30.5:1:1:1.73:60:12:0.4:0.375:0.2 +4 143033641 . T C 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACATGGGACTTCTCATCATA;RSEQ=GCTTAAAAGGAACAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:283,99:382,0:0:2,0:24.5:1:30.8:1:1:0:60:75.4:1:0:0.1 0/1:438:18:12,6:296,124:420,18:0.0411:2,2:22.6:1:31.1:1:0.79314:1.19302:60:36:0.0418:0:1.3 +4 143043164 . G GA 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49971;SOR=0;LSEQ=TTTCTTACCAAAAAGGAAAA;RSEQ=AAAAAAAACAAAAGAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:2,0:117,1:118,2:0.0167:1,0:40.5:1:31.5:1:1:0:60:4:0.0172:0:0 0/0:106:0:0,0:104,2:106,0:0:1,0:18.8:1:31.8:1:1:0:60:105:1:0:0.1 +4 143043173 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.21;SOR=Inf;LSEQ=AAAAAGGAAAAGAAAAAAAA;RSEQ=AAAAGAAATATTCCCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:145,1:146,0:0:1,0:23.3:1:32:1:1:0:60:19.857:1:0:0.1 0/1:124:2:1,1:118,4:122,2:0.0161:1,2:29.5:1:30.5:1:0.07933:26.49731:60:4:0.0163:0:1.5 +4 143043397 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11475;LSEQ=TCTAGCATTCCAATTTCATC;RSEQ=CCTAAACAATAGAAAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:93:28,65:119,219:338,93:0.2158:2,2:26.8:1:29.8:1:0.38907:1.26075:60:45.5:0.2156:0:1.2 0/1:491:15:7,8:172,303:475,15:0.0305:2,2:15.5:1:28.1:1:0.42376:1.54:60:30:0.0311:0:1.3 +4 143043404 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22608;SOR=1.32816;LSEQ=TTCCAATTTCATCGCCTAAA;RSEQ=AATAGAAAAGGCACTTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:38:9,29:119,239:358,38:0.096:2,2:29.5:1:28.9:1:0.27611:1.60259:60:76:0.0969:0:1.2 0/1:445:55:18,37:131,259:390,55:0.1236:2,2:23.9:1:28.5:1:1:1.0396:60:110:0.1259:0:1.1 +4 143043452 . C A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11667;SOR=Inf;LSEQ=AACATTTGAGGAAAATGTCA;RSEQ=TAGCTACTATGCCTCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:27,153:180,0:0:2,0:23.6:1:33.1:1:1:0:60:360:1:0:0.5 0/1:173:3:2,1:29,141:170,3:0.0173:2,2:5:1:27.7:1:0.08316:9.53:60:6:0.0175:0:1 +4 143043464 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12966;LSEQ=AAATGTCACTAGCTACTATG;RSEQ=CTCCCTGCTGGAATTTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:35:1,34:12,98:110,35:0.2414:2,1:26.4:1:30.6:1:0.18949:4.13508:60:70:0.2448:0:1.4 0/1:127:5:0,5:17,104:121,5:0.0394:2,0:22.6:1:29.2:1:1:0:60:10:0.04:0:1.8 +4 143044571 . G GA 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.04048;SOR=0.40114;LSEQ=ACAAACCAATCCAGCAAGCT;RSEQ=AAAAAAAAATATTGATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:17:6,11:104,315:419,17:0.039:2,2:22.9:1:30.1:1:0.39154:1.65:60:34:0.0394:0.0046:0.4 0/1:500:8:2,6:154,334:488,8:0.016:2,2:28.9:1:29.6:1:1:1.38242:60:16:0.0162:0:0.8 +4 143044666 . A C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35553;SOR=0.30752;LSEQ=GAGGCATCACAGATTCGATT;RSEQ=TCAGGTATGTATAACAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:59:58:1,57:0,0:0,58:0.9831:0,1:26.5:1:34.1:1:1:0:59.7:116:0.9831:0:1 1/1:56:53:2,51:0,3:3,53:0.9464:0,1:23.7:1:31.8:1:1:0:60:52:0.9455:0:1 +4 143045058 . T C 49 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCGACAGTTTGGTTAAAA;RSEQ=ATTCCCTTTTCCTAGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:40:1:31.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:1:0:29:0:1:0:60:2:1:0:1 +4 143045599 . G A 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76782;SOR=0.75405;LSEQ=ATATTCAGCTGATATTTATC;RSEQ=TGAATAAGAAACATGGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:12,0:21,0:21,12:0.3636:1,0:28.6:1:30.8:1:1:0:60:24:0.3636:0:1 0/1:20:6:6,0:13,1:14,6:0.3:1,0:25:1:30.7:1:1:0:60:12:0.3:0:1 +4 143045690 . A T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.50225;SOR=Inf;LSEQ=TATTCATCATCAAGGATAGG;RSEQ=TGTTAACAATCCGGCATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:132,28:160,0:0:2,0:24.1:1:30.5:1:1:0:60:52.333:1:0:0.1 0/1:190:2:1,1:153,35:188,2:0.0105:2,2:13:1:24:1:0.34386:4.32436:60:4:0.0106:0:1 +4 143045938 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1241;SOR=Inf;LSEQ=GGGAAGGGGGTGTAAGAACA;RSEQ=TGCAATAGATGAAGGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:115,270:385,0:0:2,0:24.3:1:32.2:1:1:0:59.8:54:0.9974:0:0.2 0/1:393:4:3,1:123,266:389,4:0.0102:2,2:22:1:27:1:0.09901:6.45:60:8:0.0103:0:1 +4 143046110 . A G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATAAGCAGCCACCCATC;RSEQ=GACCTCTCCAAGTGGATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:0,18:0,0:0,18:1:0,1:25.6:1:29.6:1:1:0:60:17:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:27.5:1:32.5:1:1:0:60:4:1:0:1 +4 143066925 . A AT 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39258;SOR=1.51628;LSEQ=GACTCCTCTTCTTCTATATC;RSEQ=TTTTTTTTTCACGAGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:9:7,2:143,18:161,9:0.0526:2,2:15.4:1:30.9:1:0.28611:2.25554:60:18:0.0533:0.0117:0.3 0/1:180:14:12,2:150,15:165,14:0.0778:2,2:26.4:1:30.9:1:0.62659:1.66103:60:28:0.0787:0.0167:0.1 +4 143066973 . G GA 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10249;SOR=0.17267;LSEQ=TTTACTCAGTAAATGATTGG;RSEQ=AAAAAAAATTATTTCTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:5:4,1:311,145:456,5:0.0108:2,2:14.6:1:27:1:1:1.86:60:4:0.0088:0.0022:0.2 0/0:530:1:1,0:352,177:529,1:0.0019:2,0:39:0:30:0:1:0:60:2:0.0019:0:0 +4 143067054 . G A 197 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.59528;LSEQ=TTTTCTCCATCATTGTTGCC;RSEQ=CCACTGCCTTCACTGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:974:3:2,1:532,437:969,3:0.0031:2,2:5:1:28:1:1:1.64:60:6:0.0031:0:1 0/1:1146:102:50,52:546,497:1043,102:0.089:2,2:25.6:1:29.6:1:0.53481:1.1424:59.8:204:0.09:0:1.1 +4 143067196 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12331;SOR=0;LSEQ=TATTTTTGTCACAAAAACAA;RSEQ=ATAAGGCAAAGTCGGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:36,182:218,3:0.0136:2,2:17.3:1:28.3:1:0.07725:9.95:60:6:0.0137:0:1 0/0:222:0:0,0:46,175:221,0:0:2,0:22.7:1:30.6:1:1:0:60:109.5:0.9955:0:0.1 +4 143081836 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12672;SOR=0;LSEQ=ATGGTGGAAAAAGTACAGAC;RSEQ=CCAAGGAGAGAAAATGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:4:0,4:1,58:59,4:0.0635:1,0:14.3:1:30.3:1:1:0:60:8:0.0645:0:1 0/0:51:0:0,0:0,51:51,0:0:1,0:24.7:1:31.6:1:1:0:60:102:1:0:0.1 +4 143094991 . C A 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0506;SOR=0;LSEQ=ACAAAGATAAAAATAAGTTA;RSEQ=ACAAACAGCATAATGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:4:3,1:69,256:325,4:0.0122:2,2:8:1:27.3:1:0.03412:11.02:60:8:0.0122:0:1 0/0:363:0:0,0:96,267:363,0:0:2,0:23.9:1:31.2:1:1:0:60:120:1:0:0.1 +4 143095139 . C T 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.05699;SOR=0;LSEQ=TATGTAAGGTGACGAAAATG;RSEQ=TTTTTAAAACTAGGTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:11,6:0.3529:0,0:19.5:1:31:1:1:0:60:12:0.375:0:1 0/0:10:0:0,0:0,10:10,0:0:0,0:26.4:1:33.3:1:1:0:60:20:1:0:0.3 +4 143095201 . C T 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=AGATTAACACTAATACTTGA;RSEQ=GTGATTACATATATGTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:42.8:1:32:0:1:0:60:10:0.625:0:1 1/1:3:3:0,3:0,0:0,3:1:0,0:36.7:1:29.7:1:1:0:60:6:1:0:1 +4 143095271 . T A 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTAATCATGTATGTCAAG;RSEQ=ATTAGTATTCAAAACAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:25:1:33:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 143113782 . A G 56 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCCCTAAGAAACAGAAC;RSEQ=TAGAATTCTGTATTGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:16.8:1:28.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 143114003 . T C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26087;SOR=0;LSEQ=AATATCACCCCTTAGTCATA;RSEQ=GACTTCCAGAAGATTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:0,17:1:0,1:26.9:1:32.5:1:1:0:60:34:1:0:2.6 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:13.6:1:32.6:1:1:0:60:10:0.8333:0:3 +4 143114011 . A G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTAGTCATATGACTTCC;RSEQ=GAAGATTTTCTGCCATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:17,0:0,0:0,17:1:0,1:28.8:1:31.2:1:1:0:60:34:1:0:2.8 1/1:6:6:5,1:0,0:0,6:1:0,2:16.8:1:30.3:1:1:0:60:12:1:0:2.8 +4 143114040 . A C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCCATCACAATGCCACT;RSEQ=ACTAAGCAAGACACTTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:34:34,0:0,0:0,34:1:0,1:22.2:1:33.1:1:1:0:60:68:1:0:1.8 1/1:10:10:9,1:0,0:0,10:1:0,2:24.1:1:31.2:1:1:0:60:20:1:0:2 +4 143114402 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23561;SOR=Inf;LSEQ=TGCAAACATTTATCTCCGTC;RSEQ=TGCTGTTTGCATTGAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:22,163:185,0:0:2,0:24.6:1:31.5:1:1:0:60:370:1:0:0 0/1:175:2:1,1:27,146:173,2:0.0114:2,2:13:1:28.5:1:0.29517:5.33:60:4:0.0117:0:1 +4 143114548 . A G 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32456;SOR=4.63479;LSEQ=AGCCACCTGTGCACCTAAAC;RSEQ=AGATATAATGTTTTCCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:0,7:0,7:7,7:0.5:0,0:28.9:1:32.3:1:1:0:55.7:14:0.5:0:3.1 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:24.4:1:32.2:1:1:0:60:10:0.8333:0:2.8 +4 143114556 . A G 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTGCACCTAAACAAGATATA;RSEQ=TGTTTTCCTGATTTATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:22.8:1:33.6:1:1:0:57:20:1:0:2.8 1/1:5:4:0,4:0,1:1,4:0.8:0,0:21:1:32.5:1:1:0:60:8:0.8:0:3.3 +4 143114558 . G A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCACCTAAACAAGATATAAT;RSEQ=TTTTCCTGATTTATGACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:21.2:1:30.8:1:1:0:57:9:1:0:2.8 1/1:5:4:0,4:0,1:1,4:0.8:0,0:19:1:31.8:1:1:0:60:8:0.8:0:3.3 +4 143114598 . G C 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATCTTAATTACATGCTACA;RSEQ=TGTAGAACAGTGTGTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:22.7:1:33:1:1:0:50:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 143129292 . G A 42 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTCAAATGAGCTTAAAT;RSEQ=TTAACTATTAGCCACCGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:31.3:1:27:1:1:0:60:6:0.375:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 143129490 . A G 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00156;SOR=Inf;LSEQ=CAACTTTATATAATTGTTAA;RSEQ=CTTTTGAATTCTGCCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:92,3:95,0:0:1,0:23.4:1:30.1:1:1:0:59.6:22.75:1:0:0.1 0/1:80:8:7,1:69,3:72,8:0.1:1,2:25.5:1:31.8:1:0.34952:3.21323:60:16:0.1013:0:1.3 +4 143129539 . A T 31 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24856;SOR=0;LSEQ=TTTACAGAAGTACACACTGT;RSEQ=ACATAATTTGCTATTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:183,58:241,3:0.0123:2,2:15:1:20:1:0.15049:6.25061:60:2:0.0083:0:1 0/0:238:0:0,0:170,68:238,0:0:2,0:23.4:1:27.8:1:1:0:60:78.333:1:0:0.1 +4 143129980 . A AT 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.27291;LSEQ=CTACATAAAATCTATTTATT;RSEQ=TTTTTTTTTTCATTTCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:57:45,12:157,21:178,57:0.2395:2,2:18.2:1:30.6:1:0.12288:1.98711:59.8:27.5:0.2371:0.0966:0.9 0/1:228:18:16,2:177,31:208,18:0.0789:2,2:31.3:1:30.8:1:1:1.40:60:36:0.0811:0:0.8 +4 143130034 . A T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACTTTGAGTAAGTAGAG;RSEQ=AATTGCTTCCACACCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:580:580:379,201:0,0:0,580:1:0,2:26.9:1:29.2:1:1:0:60:81.857:1:0:1.1 1/1:618:617:372,245:1,0:1,617:0.9984:0,2:25.8:1:28:1:1:0:59.9:60.7:1:0:1.1 +4 143130219 . T A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.22979;LSEQ=AGAGAAACTTTATTTTTATC;RSEQ=TAAATCCATAAACGCATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:264:139:24,115:22,103:125,139:0.5265:2,2:22.9:1:30.7:1:1:1.02338:59.8:68.5:0.5269:0:1.1 1/0:253:198:41,157:9,46:55,198:0.7826:2,2:22.1:1:29.5:1:0.56806:1.33:60:48.5:0.7823:0:1.1 +4 143130233 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24807;SOR=0;LSEQ=TTTATCTTAAATCCATAAAC;RSEQ=CATAACCCTTAGTCAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:1,2:24,150:174,3:0.0169:2,2:9.3:1:29:1:0.36848:3.10:60:6:0.0173:0:2 0/0:172:0:0,0:16,155:171,0:0:2,0:24:1:31.1:1:1:0:60:27.5:0.994:0:0.8 +4 143158979 . A C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.03099;LSEQ=AAAATTTTTAAATGGTATAA;RSEQ=ATAATTAATATGAGAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:98:77,21:98,22:120,98:0.4495:2,2:20.8:1:32:1:0.61003:1.21378:60:48:0.4486:0:1.1 0/1:204:5:3,2:152,46:198,5:0.0245:2,2:30.2:1:31:1:0.33834:2.19283:60:10:0.0249:0:1 +4 143159168 . G GA 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.41808;SOR=0.68976;LSEQ=TACTGGGTTCTTTAACACTG;RSEQ=AAAAAAAAAGAAAAAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:14:3,11:100,258:358,14:0.0376:2,2:28.6:1:31.6:1:0.7655:1.42:59.1:28:0.0386:0:0.4 0/1:419:11:3,8:134,273:407,11:0.0263:2,2:27.2:1:28.4:1:1:1.30815:60:22:0.0272:0:0.6 +4 143181484 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=8.04111;LSEQ=GTACATTTATCTTTCCTGTG;RSEQ=AATTGTACAATCTCCCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:31:31,0:31,0:31,31:0.5:1,1:26.7:1:30.3:1:1:0:59.7:30:0.5:0:1.1 1/1:46:41:41,0:5,0:5,41:0.8913:0,1:23.1:1:29:1:1:0:60:82:0.8913:0:1 +4 143181502 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.182;SOR=Inf;LSEQ=TGGAATTGTACAATCTCCCC;RSEQ=CATTCTGCTGGCCCCTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:84,0:84,0:0:1,0:25.4:1:28.7:1:1:0:59.9:15.8:1:0:0.5 0/1:63:2:2,0:61,0:61,2:0.0317:1,0:33:1:32.5:1:1:0:60:4:0.0323:0:1 +4 143181748 . T A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=2.95541;LSEQ=ATGTAAAAAAAAAAAAAAAA;RSEQ=TTTGAGAACAATCAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:126:28,98:40,111:151,126:0.3739:2,2:21.9:1:29.6:1:0.48366:1.26021:58.8:17:0.379:0:1.5 1/0:393:251:70,181:20,23:43,251:0.6387:2,2:24.2:1:28.8:1:0.01944:2.24162:58.2:24.1:0.7026:0:1.8 +4 143191978 . CA C 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.0999;SOR=0;LSEQ=TAAGAAGCTTCTCTCTCCCC;RSEQ=AAAATATCCAAAACACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:1,2:32,196:228,3:0.0129:2,2:13:1:27.7:1:0.37163:3.04:60:6:0.0133:0.0043:1 0/0:268:0:0,0:49,219:268,0:0:2,0:24.1:1:29.7:1:1:0:60:37.286:1:0:0.1 +4 143192000 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23477;SOR=0;LSEQ=AAAATATCCAAAACACATTT;RSEQ=TTTCTGAAAACCACCAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:13,150:163,2:0.0121:2,2:11.5:1:29.5:1:0.16297:11.16:60:4:0.0125:0:1 0/0:175:0:0,0:22,153:175,0:0:2,0:22.2:1:31.7:1:1:0:60:86.5:1:0:0.1 +4 143192178 . G A 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTGTAATGGC;RSEQ=TGATCTCAGCTCACCACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:19:0:33:0:1:0:41:2:1:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:16:1:31:0:1:0:49.5:4:1:0:1.5 +4 143192299 . G GT 49 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTACTTTTGTATTCTCCAT;RSEQ=TGGTCAGGCTGGTGTCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:35.3:1:31:1:1:0:45.3:6:1:0:0.7 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:30.5:1:1:0:34:4:1:0:1.5 +4 143226496 . A C 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01929;SOR=Inf;LSEQ=TGCAGTGGAGAACATTAGCT;RSEQ=TTTGAGAACTGACATCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:100,1:101,0:0:1,0:25:1:28.6:1:1:0:60:100:1:0:0.1 0/1:86:5:4,1:78,3:81,5:0.0581:1,2:25.2:1:32.2:1:0.21653:6.21665:60:10:0.0595:0:1.2 +4 143226512 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00171;SOR=Inf;LSEQ=AGCTATTTGAGAACTGACAT;RSEQ=TAACATCTGCAAGAATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:126,6:132,0:0:1,0:24.6:1:32.4:1:1:0:60:65:1:0:0.1 0/1:112:8:8,0:95,9:104,8:0.0714:2,0:23.5:1:30.1:1:1:0:60:16:0.0721:0:1 +4 143226521 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49957;SOR=0;LSEQ=AGAACTGACATCTAACATCT;RSEQ=CAAGAATTGTGACTTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:144,14:158,2:0.0125:2,2:29.5:1:30.5:1:0.17925:9.97142:60:4:0.0126:0:1 0/0:145:0:0,0:123,22:145,0:0:2,0:22.5:1:31.3:1:1:0:60:47.333:1:0:0.2 +4 143226768 . G T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.24018;LSEQ=TCACATCAATCAAACAAAAT;RSEQ=AGTCTTTAGAAGAATGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:343:184:89,95:94,65:159,184:0.5364:2,2:23.9:1:29.7:1:0.0512:1.54164:60:91:0.5369:0:1.9 1/1:290:241:135,106:25,24:49,241:0.831:2,2:21.7:1:29:1:0.53269:1.22:60:59.25:0.8287:0:1.9 +4 143226784 . G A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.86002;LSEQ=AAATGAGTCTTTAGAAGAAT;RSEQ=AAATATTAAATCTATTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:388:208:116,92:105,75:180,208:0.5361:2,2:24.2:1:29.7:1:0.68099:1.11004:60:68.333:0.5352:0:1.8 1/1:350:286:175,111:35,29:64,286:0.8171:2,2:21.9:1:28.6:1:0.39724:1.31:60:285:0.8213:0:1.8 +4 143235721 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12647;SOR=Inf;LSEQ=TCCATGCAATTCAGCAAATA;RSEQ=GTGACAGTGCCTCCTTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:74,3:77,0:0:1,0:23.2:1:31.6:1:1:0:59.5:154:1:0:0.1 0/1:43:2:2,0:39,2:41,2:0.0465:1,0:18:1:32.5:1:1:0:60:4:0.0465:0:1 +4 143235799 . G T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05257;SOR=Inf;LSEQ=AGTTACCAAGCAGGAGGCCA;RSEQ=AGAAAATCCAAATGATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:204,73:277,0:0:2,0:22.5:1:32.8:1:1:0:60:91.333:1:0:0.1 0/1:256:4:1,3:172,80:252,4:0.0156:2,2:15.8:1:23.5:1:0.10145:6.39976:60:8:0.0159:0:1 +4 143235865 . C G 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GAAACGTTAGAAACACTTAC;RSEQ=CCAACTTCTGGCGGGGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:572:0:0,0:286,286:572,0:0:2,0:27.2:1:31:1:1:0:60:51:1:0:0.1 0/1:603:17:8,9:310,276:586,17:0.0282:2,2:25.9:1:29.8:1:0.80627:1.26309:60:16:0.0271:0:1.4 +4 143236008 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22249;SOR=Inf;LSEQ=TTCAATTTCCTTCATCTCGC;RSEQ=TCAATTCAGACTCTGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:10,88:98,0:0:2,0:23.5:1:32.1:1:1:0:60:196:1:0:0 0/1:88:2:0,2:7,79:86,2:0.0227:2,0:31.5:1:32:0:1:0:60:4:0.0233:0:1 +4 143236139 . T C 83 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18333;SOR=0.11844;LSEQ=CTGGAACCTCACTCCATCTA;RSEQ=TTATCTAATACAGATATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:21.2:1:32.3:1:1:0:60:12:0.8571:0:1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:1:0:30:0:1:0:60:2:0.3333:0:1 +4 143323915 . T G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03286;SOR=0.23949;LSEQ=AACTTTTGCTCCTAACCAAT;RSEQ=GCCAATTTGGCAACGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:16,0:6,0:6,16:0.7273:0,1:25.4:1:33.6:1:1:0:60:32:0.7273:0:1.1 0/1:21:8:7,1:13,0:13,8:0.381:1,2:16.9:1:31.8:1:0.38095:0:60:16:0.381:0:1 +4 143324036 . T C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56508;SOR=0.85425;LSEQ=CAGTTACACAAAAAATCCAA;RSEQ=CGTGTGGAAAAGCATAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:156:104:83,21:43,9:52,104:0.6667:2,2:22.4:1:32.2:1:0.82982:1.20739:60:208:0.671:0:1.6 1/0:176:111:90,21:47,18:65,111:0.6307:2,2:22.6:1:31:1:0.19182:1.64:60:110:0.6322:0:1.6 +4 143324094 . G A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.40858;LSEQ=GAAGTACCAGTACTTACGGT;RSEQ=TCATGAGACTTATCCTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:423:266:174,92:101,54:155,266:0.6288:2,2:25:1:29.6:1:1:1.01:60:265:0.628:0:1.3 0/1:521:213:136,77:174,133:307,213:0.4088:2,2:27.2:1:28.4:1:0.10311:1.35:60:212:0.4109:0:1.4 +4 143325968 . T C 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TACAACTTTCTTTTTTTTCC;RSEQ=CAAAATAAATATTTATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:18:0:28:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:28:1:1:0:60:4:1:0:1 +4 143326120 . G T 51 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.38437;LSEQ=AAAAAAAGACAAGTTATTTT;RSEQ=TCATTTGTTCGTTCTAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:22.7:1:32.3:1:1:0:49.3:6:0.75:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:25:1:27.5:1:1:0:60:4:0.5:0:1 +4 143326265 . C G 52 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08446;SOR=7.16;LSEQ=ATTCAAATCCAGAGATGGGG;RSEQ=GGGGGTGGGGGGGAGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:1:0,1:106,0:106,1:0.0093:1,0:5:0:34:0:0.00935:0:43:2:0.0099:0:2 0/1:79:5:2,3:74,0:74,5:0.0633:1,2:10:1:22.4:1:0.00013:0:57:4:0.0541:0:4.8 +4 143326271 . T TGGGG 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=11.000;MSILEN=1;SSF=0.13163;SOR=0.37911;LSEQ=ATCCAGAGATGGGGCGGGGG;RSEQ=GGGGGGGAGGGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:14:7,7:108,0:108,14:0.112:1,2:12.1:1:30.2:1:0:0:58.1:28:0.1239:0.072:1.4 0/1:88:4:4,0:71,0:71,4:0.0455:1,0:26:1:31.3:1:1:0:60:8:0.0494:0:1.5 +4 143326299 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.2484;SOR=Inf;LSEQ=AGGGAGAGAGAGAGCAAGAG;RSEQ=GAGCGAGCCAGCAAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:149,29:178,0:0:2,0:24.9:1:30.4:1:1:0:59.8:12.692:1:0:0.4 0/1:187:3:1,2:142,41:183,3:0.016:2,2:9.3:1:23.3:1:0.13406:6.83328:51.7:6:0.0175:0:2.7 +4 143326307 . C A 15 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.89781;LSEQ=AGAGAGCAAGAGCGAGCGAG;RSEQ=CAGCAAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:149,35:184,2:0.0108:2,2:16.5:1:29:1:0.35048:4.21166:60:4:0.0115:0:1 0/0:207:2:1,1:152,53:205,2:0.0097:2,2:40:1:15:0:0.45462:2.85058:59:0:0:0:6 +4 143326312 . AAGAG A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=10.000;MSILEN=2;SSF=0.00366;SOR=0.56311;LSEQ=GCAAGAGCGAGCGAGCCAGC;RSEQ=AGAGAGAGAGAGAGAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:97:75,22:75,16:91,97:0.4597:2,2:27.3:1:30.7:1:0.46805:1.37267:59.7:47.5:0.4634:0.0711:0.3 0/1:241:78:54,24:110,38:148,78:0.3237:2,2:25.9:1:29.6:1:0.43578:1.28506:59.6:38:0.3304:0.029:0.6 +4 143326545 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23365;SOR=Inf;LSEQ=TCAGGGAAAACTTCTGCGCC;RSEQ=GGCTGAAAGTGAACTTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:4,97:101,0:0:1,0:25.7:1:31.4:1:1:0:59.8:100:1:0:0 0/1:95:2:1,1:7,86:93,2:0.0211:2,2:20:1:28.5:1:0.16215:11.56:60:4:0.0215:0:1 +4 143326714 . T G 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTGCAGTTCATGCAAGTCTT;RSEQ=ACTGGTCTGAGATCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:24.3:1:32.7:1:1:0:60:12:0.75:0:1.3 0/0:1:0:0,0:0,1:1,0:0:0,0:19:0:12:0:1:0:60:0:0:0:0 +4 143352065 . T C 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.8258;LSEQ=CTCTTAATATATATTCAAGA;RSEQ=ATTTAATCTTGTTATTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:27.5:1:29.5:1:1:0:60:4:0.3333:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:19:0:32:0:1:0:60:2:0.5:0:1 +4 143352246 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.49881;SOR=0;LSEQ=CTATGAATCTATGAATGCAT;RSEQ=TATGTATGTGTAAGTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:180,11:191,2:0.0104:2,2:20.5:1:29.5:1:0.12079:15.70575:60:4:0.0105:0:1 0/0:187:0:0,0:170,17:187,0:0:2,0:22.6:1:31.7:1:1:0:60:186:1:0:0.1 +4 143352425 . C A 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.91662;SOR=0.97105;LSEQ=ATTTCCATGATCAACCTTCA;RSEQ=AGTTTTAAAATTTTCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:49:17,32:191,338:529,49:0.0845:2,2:20.4:1:30.1:1:0.87787:1.06359:60:48:0.0845:0:1.1 0/1:608:50:20,30:206,352:558,50:0.0822:2,2:22.9:1:29.6:1:0.65064:1.14:60:100:0.0832:0:1.1 +4 143352479 . G A 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0485;SOR=Inf;LSEQ=TGTCAGTTCTAGTGATTCCT;RSEQ=GTTTAATGTAGATGTATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:12,191:203,0:0:2,0:25:1:31.2:1:1:0:60:49.75:1:0:0.1 0/1:181:4:3,1:21,156:177,4:0.0221:2,2:5.3:1:25.3:1:0.00759:21.57:60:8:0.0226:0:1.3 +4 143352599 . T A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53021;SOR=0.55628;LSEQ=TTCAGTATAAAGCTAAAAAG;RSEQ=AAAGGTAAGTAGAGACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:0,17:1,13:14,17:0.5484:1,1:18.4:1:32:1:0.45161:0:60:34:0.5667:0:1.1 0/1:15:6:0,6:0,9:9,6:0.4:0,0:21.2:1:31.3:1:1:0:60:12:0.4:0:1.2 +4 145225888 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24196;SOR=Inf;LSEQ=ATGTATTTTCCTTGTTTTAC;RSEQ=TACTGCCTTTTATGTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:110,31:141,0:0:2,0:23.1:1:30.6:1:1:0:59.8:140:1:0:0.1 0/1:137:2:2,0:96,39:135,2:0.0146:2,0:13:1:31:0:1:0:60:4:0.0147:0:1 +4 145225889 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49853;SOR=0;LSEQ=TGTATTTTCCTTGTTTTACG;RSEQ=ACTGCCTTTTATGTCAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:110,32:142,2:0.0139:2,2:26.5:1:30.5:1:0.40705:3.40028:60:4:0.0139:0:1 0/0:137:0:0,0:98,39:137,0:0:2,0:21.3:1:28.6:1:1:0:60:274:1:0:0.1 +4 145225998 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45623;SOR=0.87318;LSEQ=CTTATAGTTACAATGAATGT;RSEQ=TCAATTATTAAAATATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:131:57,74:79,100:179,131:0.4226:2,2:25.8:1:29.6:1:1:1.02554:60:42.667:0.4211:0:1.1 0/1:295:115:57,58:87,93:180,115:0.3898:2,2:24.6:1:28.7:1:0.90503:1.05:60:56.5:0.3897:0:1.1 +4 147770165 . G T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCTTGAATCTCTATCTT;RSEQ=GTGCCTAGCCTGGTCCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:20,2:22,2:0.0833:2,2:10.5:1:29.5:1:0.23913:8.36492:60:4:0.087:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 147770229 . T G 169 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCTGCCCTCAGTATGCC;RSEQ=GAGTCAGCAGTCTCACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:28,26:0,0:0,54:1:0,2:26.5:1:29.4:1:1:0:60:17:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 148756033 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14329;SOR=0;LSEQ=CCCTCCCCATTTTCTCTCAC;RSEQ=GATGTTTCCCCTAATAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:18,2:0.1:2,2:14.5:1:29.5:1:1:1.23603:60:4:0.1:0:1 0/0:32:0:0,0:15,17:32,0:0:2,0:23.4:1:30.2:1:1:0:59.5:64:1:0:0.2 +4 149116035 . A G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54337;SOR=1.72765;LSEQ=TGATTAAAATAATAAAAAAT;RSEQ=ACTGTTAAAATAGAGTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:3,5:5,6:11,8:0.4211:2,2:37.5:1:32.4:1:1:1.36508:60:16:0.4211:0:1.1 1/0:25:14:6,8:3,8:11,14:0.56:2,2:24.4:1:29.9:1:0.67662:1.95:60:28:0.56:0:1 +4 151172535 . CCCCACACA C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACCCTCCACACCACACAT;RSEQ=CCTCACACCCCCCACACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:30.5:1:1:0:56.5:4:1:0:4.5 +4 151172570 . A C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCCACACCCCCACACA;RSEQ=CCCACATCCCCCGCACCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:30:1:1:0:56.5:4:1:0:4.5 +4 151174195 . TG T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.24118;SOR=0;LSEQ=TGGTCTGGGGCATGGTTGTG;RSEQ=GGGGAACTTGCGATGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:29,11:40,2:0.0476:2,2:12.5:1:31:1:0.49477:2.56728:20:4:0.0488:0:0.5 0/0:43:0:0,0:33,10:43,0:0:2,0:25.2:1:31.5:1:1:0:59.1:86:1:0:0.1 +4 151174249 . GTCCTCCTCA G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=3.000;MSILEN=1;SSF=0.00143;SOR=0.353;LSEQ=TCGTCCTCCTCATCCTCCTC;RSEQ=TCCTCCTCATCCTCCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:69:36:17,19:19,13:32,36:0.5217:2,2:35.9:1:31.4:1:0.34148:1.62159:57.7:72:0.5217:0.029:0.2 0/1:112:31:17,14:44,37:81,31:0.2768:2,2:35.7:1:29.3:1:1:1.02:58.6:14.5:0.2685:0.0089:0.5 +4 152880761 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.21739;SOR=Inf;LSEQ=ATATCAGCAGGACATGTCTC;RSEQ=CTCTATCAGGACTAATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:3,9:12,0:0:2,0:22.2:1:29.9:1:1:0:60:11:1:0:0.4 0/1:11:2:1,1:4,5:9,2:0.1818:2,2:22.5:1:28.5:1:1:1.22:60:4:0.1818:0:1 +4 153243979 . A G 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37639;SOR=0.27659;LSEQ=TTTTTTCTTTTTGCAGGGGG;RSEQ=AGGGCAGGGAGTATATCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:4:4,0:235,41:276,4:0.0143:2,0:31.8:1:26.5:1:1:0:60:3:0.0109:0:1.5 0/0:251:1:0,1:193,56:249,1:0.004:2,0:3:0:27:0:0.228:0:60:2:0.0041:0:1 +4 153244352 . A G 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01505;SOR=Inf;LSEQ=GGTTAGAAATAATGGCTATG;RSEQ=GTTAGTTACATTATAATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:17,146:163,0:0:2,0:24.1:1:31.7:1:1:0:60:53.333:1:0:0.1 0/1:126:5:2,3:20,101:121,5:0.0397:2,2:16.4:1:30.6:1:0.20924:3.32:60:10:0.0397:0:1 +4 153245264 . CTA C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22139;SOR=Inf;LSEQ=GGTTGACTCTTTTTGTGATG;RSEQ=AGGCTCCATATTTCTCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:191,29:220,0:0:2,0:23.1:1:31.7:1:1:0:60:219:1:0:0.1 0/1:196:2:1,1:159,35:194,2:0.0102:2,2:21:1:33:0:0.33438:4.4934:60:4:0.0104:0:0 +4 153245521 . C G 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00093;SOR=0;LSEQ=GGATTGATGTATCAAGAGAT;RSEQ=CACTCACCACATGGATACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:11:4,7:190,351:541,11:0.0198:2,2:30.8:1:32:1:1:1.06:60:22:0.0203:0:1.1 0/0:550:0:0,0:214,334:548,0:0:2,0:24.8:1:30.4:1:1:0:60:77.286:0.9963:0:0.1 +4 153247036 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15745;SOR=Inf;LSEQ=TTTAACGTATATAAAAACAG;RSEQ=AGAATAATCTGATTAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:57,0:57,0:0:1,0:28.4:1:32.5:1:1:0:59.5:56:1:0:0.1 0/1:38:2:2,0:35,1:36,2:0.0526:1,0:30.5:1:30:1:1:0:60:4:0.0541:0:1 +4 153247374 . G A 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22538;SOR=4.3199;LSEQ=AGAGTGGCATCTCGAGAACC;RSEQ=CTAACAACTCTGCAGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:418:1:0,1:115,301:416,1:0.0024:2,0:39:0:31:0:1:0:60:2:0.0024:0:1 0/1:487:5:4,1:161,320:481,5:0.0103:2,2:16.6:1:25.2:1:0.04751:7.92:60:10:0.0106:0:1 +4 153248143 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACATTTGGTTCAACAT;RSEQ=AGCGCTATACTCTTCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 153249146 . T C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTTTCAAACAGGAAGC;RSEQ=GACAACACTAGCAAATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:18,0:0,0:0,18:1:0,1:30:1:31.8:1:1:0:57.4:36:1:0:1.2 1/1:5:5:5,0:0,0:0,5:1:0,0:22.6:1:32.4:1:1:0:60:10:1:0:1 +4 153250963 . AAT A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05299;SOR=Inf;LSEQ=AGAAAGATGTGCAGATTAGA;RSEQ=ATGTTAATTAAATTATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:43,208:251,0:0:2,0:21.9:1:31:1:1:0:60:61.75:1:0:0.1 0/1:233:4:1,3:53,176:229,4:0.0172:2,2:25.3:1:30.5:1:1:1.11:60:8:0.0172:0:0 +4 153251013 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50249;SOR=0;LSEQ=TACTGGTGAAGAGAAAAATG;RSEQ=AGGCATAAACAGGAACAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:0,2:2,92:94,2:0.0208:1,0:32.5:1:33.5:1:1:0:60:4:0.0211:0:1 0/0:78:0:0,0:4,74:78,0:0:2,0:23.4:1:30.9:1:1:0:60:156:1:0:0.1 +4 153251788 . G C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.09405;SOR=Inf;LSEQ=ACGGTTTTCTTTCTACAGAA;RSEQ=AGGAGTGTCATATTATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:210,13:223,0:0:2,0:24:1:33:1:1:0:59.9:36.167:1:0:0.1 0/1:187:3:3,0:161,23:184,3:0.016:2,0:12:1:32.7:1:1:0:60:6:0.0162:0:1 +4 153252061 . A G 217 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=232.02864;LSEQ=AGTAAATTGCCTTCACCAAT;RSEQ=ATAACAGTTATACATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:371:1:0,1:96,274:370,1:0.0027:2,0:31:0:33:0:1:0:60:2:0.0027:0:1 0/1:344:133:32,101:61,148:209,133:0.3866:2,2:23.9:1:30.8:1:0.3207:1.2999:60:132:0.3894:0:1.1 +4 153253991 . TA T 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.03581;SOR=0;LSEQ=TAATTCTGCACTCTGATTTC;RSEQ=AAATTATGAAAGGCAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:7:0,7:0,29:29,7:0.1892:1,0:28.6:1:32.7:1:1:0:60:14:0.1892:0:0 0/0:24:0:0,0:0,24:24,0:0:1,0:21.9:1:31.4:1:1:0:60:48:1:0:0.1 +4 153258892 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24893;SOR=0;LSEQ=GCATGACAATGTTTAAAGGT;RSEQ=GTAGCTGTTGAGTTATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:2,1:230,46:276,3:0.0108:2,2:18.3:1:29:1:0.42628:2.48933:60:6:0.0108:0:1 0/0:268:0:0,0:210,58:268,0:0:2,0:22.7:1:31.3:1:1:0:60:133:1:0:0.1 +4 153259143 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61494;SOR=2.10882;LSEQ=ACAGATGTCCCAAATTACAG;RSEQ=CTTATAAAGGAAAACTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:1:0,1:27,159:186,1:0.0053:2,0:27:0:14:0:1:0:60:0:0:0:1 0/1:179:2:1,1:33,143:176,2:0.0112:2,2:18.5:1:26.5:1:0.34641:4.28:60:4:0.0113:0:1 +4 153267968 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGCAGAATGATTTCAAA;RSEQ=TTCATCCACAGTATACTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:79:79,0:0,0:0,79:1:0,1:22.3:1:33.1:1:1:0:60:38.5:1:0:1.1 1/1:59:59:57,2:0,0:0,59:1:0,1:20.9:1:32.3:1:1:0:60:118:1:0:1.1 +4 153270964 . A G 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27778;SOR=0;LSEQ=TTTAAATTTTTGTTCACAAG;RSEQ=TAATTTCTGCTTGTGTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:9,5:0.3571:0,0:28.6:1:32.4:1:1:0:60:10:0.3571:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:27.8:1:30:1:1:0:60:8:1:0:0 +4 153271338 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=CTAACTATCAAATCTTGAGT;RSEQ=AGCATGGTTAATATTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:28,145:173,0:0:2,0:22.9:1:32.2:1:1:0:60:346:1:0:0.1 0/1:141:2:1,1:22,117:139,2:0.0142:2,2:12:1:29.5:1:0.30061:5.22:60:4:0.0143:0:2 +4 153271348 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50957;SOR=0;LSEQ=AATCTTGAGTCAGCATGGTT;RSEQ=ATATTTTAAATTCTTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:15,123:138,2:0.0143:2,2:23.5:1:31:1:0.21624:7.97:60:4:0.0143:0:1 0/0:103:0:0,0:9,94:103,0:0:2,0:23.7:1:30.2:1:1:0:60:206:1:0:0.1 +4 153273893 . A G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12461;SOR=Inf;LSEQ=GGACACACATACATACATGC;RSEQ=GCTTGACTGAGAAGAACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:62,210:272,0:0:2,0:24:1:31.5:1:1:0:60:53.4:1:0:0.1 0/1:292:4:2,2:84,204:288,4:0.0137:2,2:11.8:1:31:1:0.58386:2.42:60:8:0.0139:0:1.3 +4 153303292 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49927;SOR=Inf;LSEQ=TTTCACTAAAAGAGGCCAAG;RSEQ=TACTTCACTTAAATAAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:144,39:183,0:0:2,0:23.7:1:31.4:1:1:0:60:90.5:1:0:0.1 0/1:196:2:1,1:154,40:194,2:0.0102:2,2:13:1:27.5:1:0.37546:3.81509:60:4:0.0103:0:1 +4 153332301 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17068;SOR=Inf;LSEQ=ATTTCTACTTGTAATACTTT;RSEQ=CATTACCTTCTGTAAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:48,1:49,0:0:1,0:24.2:1:32.8:1:1:0:60:98:1:0:0.1 0/1:35:2:2,0:31,2:33,2:0.0571:2,0:23:1:32.5:1:1:0:60:4:0.0571:0:1 +4 153332604 . TCTC T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.49148;SOR=0.80022;LSEQ=ATCGTCACTCTCCTGGTCCA;RSEQ=CTCCTCCTCCTCATCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1166:29:16,13:583,551:1134,29:0.0249:2,2:29.8:1:31.9:1:0.7113:1.16:59.7:28:0.0246:0.0043:0.6 0/1:1250:25:14,11:643,578:1221,25:0.02:2,2:25.6:1:31.1:1:0.84071:1.14:60:50:0.0204:0.0016:0.1 +4 153332986 . C A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10522;SOR=Inf;LSEQ=CAGCTTGCTACTTCTTGGAC;RSEQ=TTGGCTAGACTATCAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:57,188:245,0:0:2,0:24.8:1:32.2:1:1:0:59.9:39.833:1:0:0.1 0/1:221:3:2,1:53,165:218,3:0.0136:2,2:16:1:21:1:0.15369:6.16:60:2:0.0092:0:3 +4 153333100 . T A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTCATGTTATATGTCTAC;RSEQ=TTCTAAATATCATTAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:30,0:0:1,0:28.1:1:30.5:1:1:0:60:29:1:0:0.1 1/0:11:8:0,8:0,3:3,8:0.7273:0,0:17.5:1:29:1:1:0:60:7:0.7:0:1.1 +4 155454109 . G A 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACAATTTTAAATCAAGC;RSEQ=GAAAGCACACCCATTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:22.8:1:29.8:1:1:0:60:16:1:0:1 1/1:5:5:5,0:0,0:0,5:1:0,0:16.4:1:30.2:1:1:0:60:10:1:0:1 +4 155454265 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20745;SOR=0;LSEQ=TCAAGGAAAGAAAGACAGAA;RSEQ=TTCTCCATGAGAATTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:49,39:88,2:0.0222:2,2:9.5:1:33:1:1:1.25319:60:4:0.0222:0:1.5 0/0:107:0:0,0:65,42:107,0:0:2,0:23.1:1:30.1:1:1:0:60:106:1:0:0.4 +4 155454287 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.15998;LSEQ=TCTCCATGAGAATTCTGATT;RSEQ=TCAGCTTTGTAAATTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:72:40,32:11,11:22,72:0.766:2,2:27:1:32.2:1:0.80733:1.25:60:71:0.7634:0:1 0/1:123:42:22,20:43,38:81,42:0.3415:2,2:21.3:1:30.5:1:1:1.02848:60:84:0.3443:0:1.1 +4 155454335 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51409;SOR=Inf;LSEQ=TTTCAGGAGAAACTTCCTCT;RSEQ=ACCAAGTTAAGAAAGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:27,49:76,0:0:2,0:25.2:1:32.1:1:1:0:60:152:1:0:0.6 0/1:110:2:1,1:45,63:108,2:0.0182:2,2:18.5:1:27.5:1:1:1.40:60:4:0.0185:0:1 +4 155454489 . T C 35 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCACGATTGTGCCACTGCA;RSEQ=TCCAGCCTGGGCAACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31:1:35:0:1:0:50.5:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:32:0:33:0:1:0:45:2:1:0:1 +4 155828547 . GCTGGGCCTGGGGGACCACTACCATCA G 70 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=AAAGAAATAAAGAGAAGGCA;RSEQ=AGATGCAGAGACCAGTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:14:1:32.8:1:1:0:50:8:1:0:0.5 1/0:8:5:4,1:3,0:3,5:0.625:0,2:29:1:30.5:1:1:0:32.6:10:0.625:0.25:1.4 +4 155828610 . T C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44007;SOR=2.08188;LSEQ=AGTGGCCCCGAAAGGCTGGG;RSEQ=GCACTGATATTTATTGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:6,1:3,3:6,7:0.5385:2,2:24.7:1:31.6:1:0.26573:5.17:31.7:14:0.5385:0:1.3 1/0:14:10:8,2:2,2:4,10:0.7143:2,2:22:1:31.6:1:0.52048:3.56:34.9:20:0.7143:0:2.1 +4 155828657 . G A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01178;SOR=4.01538;LSEQ=AAGGGGGGCAGGGTAAGGAG;RSEQ=GTGAATCTTCTAAGTGATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:4,3:12,8:20,7:0.2593:2,2:18.7:1:29.7:1:1:1.12007:47.1:14:0.2593:0:2.1 1/0:39:23:13,10:8,8:16,23:0.5897:2,2:25.1:1:28.4:1:0.75196:1.29:41.3:46:0.5897:0:2.4 +4 155828662 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00746;SOR=4.11049;LSEQ=GGGCAGGGTAAGGAGGGTGA;RSEQ=TCTTCTAAGTGATCGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:4,3:12,8:20,7:0.2593:2,2:22.3:1:33.4:1:1:1.12007:47.1:14:0.2593:0:2.1 1/0:42:25:14,11:8,9:17,25:0.5952:2,2:26.1:1:30.8:1:0.75395:1.42:42.8:50:0.5952:0:2.3 +4 155828714 . G GC 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.02908;SOR=3.08603;LSEQ=CACGTGATCATAGGACAGTG;RSEQ=CCCCTTCCCTTTCAGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:10:5,5:9,11:20,10:0.3333:2,2:24.1:1:30.4:1:1:1.21:49.6:9:0.3103:0.0667:1.3 1/0:36:22:7,15:6,8:14,22:0.6111:2,2:24.5:1:31.2:1:0.72296:1.58559:50.1:44:0.6111:0.1667:1.5 +4 156646905 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25341;SOR=0;LSEQ=ATCTCATGTATTTCAGCAGA;RSEQ=GACCACAACATGTTGACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:1,2:172,84:256,3:0.0116:2,2:17.3:1:24:1:0.25667:4.07103:60:2:0.0078:0:1 0/0:220:0:0,0:138,82:220,0:0:2,0:23.2:1:30.7:1:1:0:60:43:1:0:0.5 +4 156646960 . G A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16445;SOR=0.80215;LSEQ=GGACAATGCTCATGACTTAA;RSEQ=TCTTAGATTCACTGTATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:362:212:107,105:74,76:150,212:0.5856:2,2:27.3:1:30.4:1:0.91505:1.05:59.9:52:0.5843:0:1.1 1/0:320:170:85,85:81,69:150,170:0.5313:2,2:27.4:1:29:1:0.50232:1.17332:59.9:55.667:0.5318:0:1.2 +4 156647018 . A C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21128;SOR=Inf;LSEQ=CACATATAGGTTTTTATAGC;RSEQ=TAGATGGTGTTATCTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:66,165:231,0:0:2,0:23.7:1:30.6:1:1:0:60:45.2:1:0:0.5 0/1:197:2:1,1:71,124:195,2:0.0102:2,2:20.5:1:33:1:1:1.74:60:4:0.0102:0:2 +4 156647025 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22941;SOR=Inf;LSEQ=AGGTTTTTATAGCATAGATG;RSEQ=TGTTATCTTTTAAATAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:51,141:192,0:0:2,0:25.1:1:31.9:1:1:0:60:95:1:0:0.4 0/1:177:2:1,1:61,114:175,2:0.0113:2,2:28:1:30.5:1:1:1.86:60:4:0.0116:0:1.5 +4 156647054 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10123;SOR=Inf;LSEQ=TTTAAATAAATTTTTTATTA;RSEQ=TGTGGTAACACATGCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:23,94:117,0:0:2,0:23:1:32.7:1:1:0:60:116:1:0:0.1 0/1:104:3:1,2:26,75:101,3:0.0288:2,2:24.7:1:31.3:1:1:1.44:60:6:0.0291:0:1 +4 156647198 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AGTTACGTTTATATACACAT;RSEQ=CATGAATGACATTGAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:20.2:1:32.8:1:1:0:53.6:10:1:0:0 1/0:5:3:0,3:0,2:2,3:0.6:0,0:13:1:24:1:1:0:60:2:0.5:0:1 +4 157518984 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11335;SOR=Inf;LSEQ=TCCAAGAAGTCCATTTGGAT;RSEQ=CAACAAGTCACTAAAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:129,48:177,0:0:2,0:24.6:1:32:1:1:0:59.9:58:1:0:0.1 0/1:167:3:1,2:111,53:164,3:0.018:2,2:18:1:27:1:0.25258:4.14952:60:6:0.0185:0:1 +4 157519085 . T A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1241;SOR=Inf;LSEQ=CTTTATTTCATTGTATTCAC;RSEQ=GTTCATATTGAGATTGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:198,188:386,0:0:2,0:25.2:1:31.2:1:1:0:60:127.667:1:0:0.4 0/1:393:4:3,1:191,198:389,4:0.0102:2,2:11.8:1:28.5:1:0.3668:3.10:60:8:0.0102:0:1 +4 157519096 . A T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01851;SOR=0.67907;LSEQ=TGTATTCACTGTTCATATTG;RSEQ=GATTGCTTAAAGTCCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:119:58,61:130,138:268,119:0.3075:2,2:27.7:1:30.4:1:1:1.01:60:238:0.3115:0:1.1 0/1:380:88:39,49:140,151:291,88:0.2316:2,2:24.4:1:29:1:0.54496:1.16441:60:87:0.2314:0:1.1 +4 157615331 . A G 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.23365;LSEQ=CCTTTTACCTGTTTTTTCTC;RSEQ=CTTATTCCTTAAAGCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:14.3:1:30.3:1:1:0:60:8:0.4444:0:1 1/0:8:4:4,0:3,1:4,4:0.5:2,0:24.5:1:30.8:1:1:0:60:8:0.5:0:1.8 +4 157615435 . G T 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49806;SOR=0;LSEQ=AACAAGCCTCCAAATTTACA;RSEQ=TAATCCTGAGGAGCAGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:57,2:59,2:0.0328:1,2:7.5:1:31:1:0.09672:23.47392:60:4:0.0345:0:1 0/0:53:0:0,0:52,1:53,0:0:1,0:26.2:1:32.2:1:1:0:60:106:1:0:0 +4 157615446 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22327;SOR=Inf;LSEQ=AAATTTACAGTAATCCTGAG;RSEQ=AGCAGGATTCAAACCGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:68,4:72,0:0:2,0:24.3:1:31.3:1:1:0:60:23:1:0:0.2 0/1:65:2:1,1:57,5:62,2:0.0308:2,2:24:1:30.5:1:0.18006:10.49773:60:4:0.0317:0:1 +4 157615583 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25957;SOR=0.84854;LSEQ=TCAAGTTTGATAATTCACAG;RSEQ=CACTGGGAGGGGGAAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:400:211:100,111:91,97:188,211:0.5275:2,2:25.4:1:31.5:1:0.84168:1.04126:59.9:69.333:0.5253:0:1.1 0/1:405:197:99,98:104,104:208,197:0.4864:2,2:26.1:1:30.6:1:1:1.01:60:97.5:0.4912:0:1.1 +4 157615710 . G A 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60599;SOR=0.68319;LSEQ=ACTGTCAGGAACTTGGTACC;RSEQ=TGAAGAGCAGAAATTTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:11:1,10:1,45:46,11:0.193:1,2:21.7:1:31.7:1:0.3515:4.34:60:22:0.193:0:1.1 0/1:50:7:0,7:2,41:43,7:0.14:1,0:27.9:1:30.7:1:1:0:60:14:0.14:0:1.1 +4 159958815 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCTATGGTCCCAGCTACT;RSEQ=GGGAGGCTTAGGTGGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:29:1:1:0:60:4:1:0:1 +4 159959946 . T G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGTGGTGAGGGCATTTTG;RSEQ=GCAAAGGGCATAGCTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:11:1:32:0:1:0:60:4:0.6667:0:1 +4 159960118 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=GGACCCCTGATGGTTTTATA;RSEQ=TCTTATTTATTTATTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:6,9:15,0:0:2,0:17.1:1:32.5:1:1:0:60:30:1:0:0.2 0/1:28:2:1,1:11,15:26,2:0.0714:2,2:9:1:33.5:1:1:1.35:60:4:0.0714:0:1 +4 161588177 . T A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07567;SOR=Inf;LSEQ=TCTCCCCTTTCTAGGTCCCG;RSEQ=GACAGCTGTCTTGCTATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:24,0:0:2,0:29.1:1:30.5:1:1:0:45.8:48:1:0:0.1 0/1:40:6:3,3:13,21:34,6:0.15:2,2:26.5:1:27.7:1:0.6678:1.60:36.8:12:0.15:0:1.2 +4 161588273 . T A 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGGCCATCAAGCTATAGA;RSEQ=GATCTTACAAATGGAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:25.3:1:31.7:1:1:0:37.3:6:1:0:0 0/1:12:2:0,2:2,8:10,2:0.1667:2,0:36:1:32.5:1:1:0:32:4:0.1667:0:1 +4 165696972 . C T 35 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31621;SOR=0.24308;LSEQ=AGGGATGTTGGAACTTTTTC;RSEQ=AGTAAAACCCTTTTCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:1,2:172,106:278,3:0.0107:2,2:9.7:1:22.7:1:0.56081:3.23135:60:2:0.0073:0:2 0/0:383:1:0,1:233,147:380,1:0.0026:2,0:1:0:25:0:0.38845:0:60:2:0.0026:0:1 +4 165697040 . G T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.27786;LSEQ=CCATGTGTGTGCAGCTGAAA;RSEQ=GAAAGTTTCATAAACTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:107:56,51:156,146:302,107:0.2616:2,2:25.1:1:30.6:1:0.9109:1.03:60:52.5:0.2599:0:1.1 1/0:478:257:126,131:101,119:220,257:0.5377:2,2:25.6:1:29.6:1:0.52047:1.13:60:514:0.5399:0:1.1 +4 165933619 . G T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGGAGCAGGCTGGCGCTTTA;RSEQ=TTGAACCCAGGTACCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:3,0:0:0,0:7:1:33.7:1:1:0:28.7:6:1:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:12.5:1:28:1:1:0:29:4:0.5:0:1.5 +4 165933817 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53285;SOR=Inf;LSEQ=TAACATTGTAGACTCTTCCA;RSEQ=TTTTGCCATGCTAACACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:20,36:56,0:0:2,0:23.9:1:31.8:1:1:0:42.1:27:1:0:0.1 0/1:97:2:1,1:42,53:95,2:0.0206:2,2:33:1:29.5:1:1:1.26:37.5:4:0.0206:0:1 +4 165933819 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52474;SOR=Inf;LSEQ=ACATTGTAGACTCTTCCAGT;RSEQ=TTGCCATGCTAACACTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:20,40:60,0:0:2,0:24.3:1:30.4:1:1:0:42.2:120:1:0:0.1 0/1:97:2:1,1:42,53:95,2:0.0206:2,2:28.5:1:30:1:1:1.26:31.5:4:0.0208:0:1 +4 165933861 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50817;SOR=Inf;LSEQ=GGCATTCCTTTTGAACAGTA;RSEQ=CCATTCCCTTGGTGTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:26,69:95,0:0:2,0:28.1:1:31.6:1:1:0:43.7:190:1:0:0.1 0/1:127:2:1,1:46,79:125,2:0.0157:2,2:40.5:1:28.5:1:1:1.71:42:4:0.0161:0:1 +4 165934032 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50457;SOR=0;LSEQ=GGAAGATGGTGGCTCTGGCC;RSEQ=AAAGGCATAAAATTCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:17,23:40,2:0.0476:2,2:26:1:32.5:1:1:1.34:60:4:0.0476:0:1 0/0:31:0:0,0:12,19:31,0:0:2,0:26.1:1:30.1:1:1:0:59.1:62:1:0:0.1 +4 165934108 . C G 79 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.134;SOR=0.12753;LSEQ=GTTGACGGGGTTGGAGGGTG;RSEQ=GAGAGATGAACAGGAAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:4,6:0.6:0,2:24.8:1:30.8:1:1:0:60:12:0.6:0:1.2 0/1:7:1:0,1:1,5:6,1:0.1429:2,0:21:0:32:0:1:0:60:2:0.1429:0:1 +4 166144755 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21745;SOR=0;LSEQ=GAGCAGAATTGTGGCAGGCT;RSEQ=GAATAGTATGATGAATTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:96,79:175,2:0.0113:2,2:17:0:33:1:1:1.21384:23:4:0.0113:0:1.5 0/0:202:0:0,0:112,90:202,0:0:2,0:23.8:1:29.9:1:1:0:31.3:404:1:0:0.1 +4 166144830 . A G 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CTTTTGAGAAACGGAGCATC;RSEQ=TGCTAAGATTAATGATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:19:6,13:100,138:238,19:0.0739:2,2:28.6:1:31.8:1:0.47096:1.56741:22:38:0.0742:0:1.5 0/0:319:0:0,0:144,175:319,0:0:2,0:28.4:1:29.5:1:1:0:33:105.333:1:0:0.3 +4 166144875 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23699;SOR=0.743;LSEQ=TGTGAAAGGATGGCTTTTAG;RSEQ=TCAGCAGTGCATCTCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:63:20,43:26,41:67,63:0.4846:2,2:20:1:31:1:0.46447:1.36015:26.1:62:0.4806:0:1.2 0/1:163:67:28,39:36,60:96,67:0.411:2,2:15.9:1:29.2:1:0.62657:1.20:26.7:66:0.4099:0:1.1 +4 166144883 . T G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50088;SOR=Inf;LSEQ=GATGGCTTTTAGGTCAGCAG;RSEQ=GCATCTCTGGTGGGAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:33,64:97,0:0:2,0:14.9:1:30.1:1:1:0:31.1:96:1:0:0.6 0/1:114:2:1,1:40,71:111,2:0.0175:2,2:8.5:1:29.5:1:1:1.77:60:4:0.0175:0:1 +4 166310601 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50398;SOR=0;LSEQ=TCTCAAGAATGTTTTTTTCA;RSEQ=GAAGTTTTCTTGGGCTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:153,42:195,2:0.0102:2,2:13.5:1:32:1:0.38978:3.61164:60:4:0.0102:0:2 0/0:160:0:0,0:121,39:160,0:0:2,0:22.4:1:31.2:1:1:0:60:320:1:0:0.2 +4 166310679 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00194;SOR=0.65663;LSEQ=CCTTTGCTTTCAACAGAATG;RSEQ=TAACCGGATACCTTCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:197:113,84:129,122:251,197:0.4378:2,2:26.4:1:32.7:1:0.21586:1.27:60:97.5:0.4382:0:1.7 0/1:479:162:80,82:162,155:317,162:0.3382:2,2:25.8:1:31.6:1:0.77216:1.07112:60:324:0.3403:0:1.8 +4 166310721 . C A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00032;SOR=0.61018;LSEQ=AGGTTACAACTTCATGGCTT;RSEQ=AAGTATTGGTTGTGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:446:202:95,107:111,133:244,202:0.4529:2,2:25.9:1:29.5:1:0.77511:1.06:60:49.5:0.451:0:1.7 0/1:465:156:70,86:138,171:309,156:0.3355:2,2:25.9:1:28.5:1:1:1.01:59.8:51:0.3333:0:1.8 +4 166311028 . T A 61 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCTCATTTCTTAAGGAG;RSEQ=CTTTTTCAAACTTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:31.8:1:30.8:1:1:0:60:8:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 168210641 . C A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01282;SOR=0;LSEQ=GGCTTTTGTGGGGACTTTTT;RSEQ=TTTTTGTTGTTGTTGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:5,2:2,2:4,7:0.6364:2,2:25.4:1:27.3:1:0.57576:2.29:55.3:14:0.6364:0:1 0/0:7:0:0,0:5,2:7,0:0:2,0:7.7:1:28.7:1:1:0:60:6:1:0:0 +4 169529802 . G A 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCCATCTCTGATATCCAG;RSEQ=GCTGTTTGTTGTTATTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:19,0:0:2,0:29.7:1:30.6:1:1:0:58.6:18:1:0:0.3 1/0:26:17:11,6:6,2:8,17:0.6538:2,2:29.9:1:27.6:1:1:1.60542:60:16:0.6667:0:1 +4 169531708 . C A 30 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGAGCAGAAGTTTCTGC;RSEQ=TCACCACGTGCTCTTTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:30:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 171735386 . C T 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27982;SOR=0;LSEQ=AAACTCTTGGATTTTATAGC;RSEQ=TAGGCAATTTGAAGTCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:14,5:0.2632:1,0:21.4:1:32.4:1:1:0:60:10:0.2632:0:1 0/0:8:0:0,0:8,0:8,0:0:0,0:28.1:1:28.5:1:1:0:60:7:1:0:0 +4 171735486 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50537;SOR=Inf;LSEQ=AAGTCAACTATTGCACTTAC;RSEQ=AGCCTATCTTATTAAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:54,46:100,0:0:2,0:27.4:1:30.2:1:1:0:60:200:1:0:0.1 0/1:128:2:1,1:74,51:125,2:0.0156:2,2:30:0:32:0:1:1.44661:60:4:0.0156:0:1 +4 171735532 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50494;SOR=Inf;LSEQ=CCAGATTCTACTCTAGCAAC;RSEQ=CCTGCAAAAGCCAGCAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:45,59:104,0:0:2,0:25.7:1:29.6:1:1:0:59.6:33.667:1:0:0.1 0/1:132:2:1,1:60,70:130,2:0.0152:2,2:28:1:27.5:1:1:1.17:60:4:0.0153:0:1 +4 173291406 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=0;LSEQ=GTAAGACCTTCTGTATGTAG;RSEQ=TTGATGGCCTCGATTCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:8,4:12,2:0.1429:2,2:31:1:32:1:1:1.89743:51:4:0.1429:0:1 0/0:9:0:0,0:6,3:9,0:0:2,0:19.6:1:29.8:1:1:0:57.6:8:1:0:0.1 +4 173291591 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.44828;SOR=Inf;LSEQ=TTGAGACCATTCTGGCTAAC;RSEQ=TGGTGAAACCCCATCTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:4,8:0,0:0,12:0.9231:0,2:14.4:1:30.2:1:1:0:47.7:24:1:0:1.1 1/1:16:16:3,13:0,0:0,16:1:0,2:23.4:1:29.7:1:1:0:46.5:32:1:0:1.1 +4 173291655 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGCTAATTTTGGTGGTGGGC;RSEQ=CCTGTAGTCCCAGCTACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:25:1:29:1:1:0:41:2:1:0:0.7 1/0:4:2:0,2:0,2:2,2:0.5:0,0:11:1:27:1:1:0:28:4:0.5:0:2 +4 173291816 . A G 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAGAGTTTGAAAGGC;RSEQ=TTGTCTGACTTCGGAAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:20:0:34:0:1:0:32:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:27:1:1:0:53.5:4:1:0:2 +4 173291864 . A G 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATGCTGGGTGGCATCTC;RSEQ=TACTATCCGTGACTGGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:43:0:34:0:1:0:57:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:46.5:1:30.5:1:1:0:53.5:4:1:0:2 +4 173704071 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01912;SOR=2.99121;LSEQ=AGTGACTTTTCGAAGAGCTT;RSEQ=TTATGCATGGTCTAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:7:5,2:97,21:118,7:0.056:2,2:25.7:1:29.7:1:0.61161:1.83693:60:14:0.0565:0:1 0/1:119:18:15,3:75,26:101,18:0.1513:2,2:22.2:1:27:1:0.55633:1.73:60:17:0.1453:0:1.4 +4 173704096 . C T 39 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62382;SOR=2.85291;LSEQ=GCATGGTCTAGAAAAAATGT;RSEQ=ACATGTATTTCCCAGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:1:1,0:141,62:203,1:0.0049:2,0:3:0:16:0:1:0:60:0:0:0:1 0/1:216:3:1,2:136,77:213,3:0.0139:2,2:5.7:1:25:1:0.55567:3.51092:60:6:0.0141:0:1.3 +4 173704182 . G C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.29563;LSEQ=AGCTAAAGTGTGTCTTATTT;RSEQ=TAAAACACTATCTCATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:117:57,60:114,138:252,117:0.3162:2,2:24.5:1:32.1:1:0.5754:1.15:59.9:57.5:0.3142:0:1.1 1/0:379:229:115,114:72,78:150,229:0.6042:2,2:27.1:1:30.9:1:0.67603:1.09:60:228:0.6032:0:1.1 +4 173704270 . G A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09479;SOR=0.43294;LSEQ=TTCTGAATTGGACCTGCCAC;RSEQ=GCAGGTCCAATTCCTAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:20:5,15:22,84:106,20:0.1587:2,2:20.8:1:31.3:1:0.76675:1.27:60:19:0.152:0:1.2 0/1:93:7:1,6:11,75:86,7:0.0753:2,2:27.9:1:30.9:1:1:1.13:60:14:0.0769:0:1 +4 173704391 . T A 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.91151;LSEQ=AAGGACCTAAATAAATAAAG;RSEQ=AGTATACTATGTTCATGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:6,6:0.5:0,0:20:1:31.8:1:1:0:60:12:0.5:0:1.5 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:46:1:33:0:1:0:60:4:0.6667:0:2 +4 173704408 . G A 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AAGTAGTATACTATGTTCAT;RSEQ=GATTTGGAAGCTTTACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:23:1:31:1:1:0:60:8:0.6667:0:1.8 1/1:2:2:0,2:0,0:0,2:1:0,0:38:1:33:0:1:0:60:4:1:0:2 +4 175047506 . C CAT 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57673;SOR=0.7661;LSEQ=CAAACATGAAAAAATAGACA;RSEQ=CTTTCCCTTTCAGTGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:28:25,3:41,3:44,28:0.3889:2,2:22:1:30.8:1:0.67157:1.6283:60:56:0.3944:0.0556:0.2 0/1:55:18:16,2:36,1:37,18:0.3273:1,2:17.8:1:29.8:1:0.24688:4.36511:60:36:0.3273:0.1455:0.2 +4 175047525 . G T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61389;SOR=2.1173;LSEQ=ACCTTTCCCTTTCAGTGCCT;RSEQ=TTAAGAATCCAATGATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:1,0:78,24:102,1:0.0097:2,0:37:0:13:0:1:0:60:0:0:0:4 0/1:98:2:1,1:72,24:96,2:0.0204:2,2:21.5:1:31.5:1:0.44709:2.9597:60:4:0.0204:0:1 +4 175047534 . C A 29 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62173;SOR=0.49277;LSEQ=TTTCAGTGCCTGTTAAGAAT;RSEQ=CAATGATCAAAAGTAATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:82,31:113,2:0.0174:2,2:7:1:29.5:1:0.48085:2.61933:60:4:0.0179:0:1 0/0:116:1:1,0:77,38:115,1:0.0086:2,0:25:0:29:0:1:0:60:2:0.0086:0:1 +4 175047618 . G A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11129;LSEQ=CACCAGGGCCTGATAGAACC;RSEQ=TAAAAATGAGTTTTGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:97:48,49:72,88:160,97:0.3774:2,2:24.1:1:30.7:1:0.52027:1.20:60:96:0.381:0:1.1 0/1:270:17:9,8:119,134:253,17:0.063:2,2:26.4:1:30.2:1:0.80278:1.27:60:34:0.063:0:1.2 +4 175047639 . A G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00793;SOR=1.64483;LSEQ=TAAAAATGAGTTTTGCAGAG;RSEQ=CATGCCAAGAAATATTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:136:57,79:51,63:114,136:0.544:2,2:24.9:1:31.8:1:0.70123:1.12145:60:44.333:0.5407:0:1.6 1/0:249:165:70,95:38,45:83,165:0.6627:2,2:25.9:1:30.7:1:0.68423:1.1454:60:54:0.6612:0:1.6 +4 175047669 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21084;SOR=Inf;LSEQ=AAATATTTGAAATCACTGAA;RSEQ=AGAATGGAGCTTCACTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:77,125:202,0:0:2,0:24.1:1:30.9:1:1:0:60:201:1:0:1.2 0/1:172:2:1,1:67,103:170,2:0.0116:2,2:27:1:27.5:1:1:1.53:60:4:0.0119:0:3 +4 175047679 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00075;SOR=2.25345;LSEQ=AATCACTGAAAAGAATGGAG;RSEQ=TTCACTGAGCTGCCGAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:173:87:30,57:29,55:84,87:0.5029:2,2:26.6:1:30.3:1:1:1.00181:60:174:0.5058:0:1.8 1/0:138:96:31,65:13,29:42,96:0.6957:2,2:22.5:1:28.7:1:1:1.06:59.9:31:0.694:0:1.9 +4 175047700 . T C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27486;SOR=0;LSEQ=TTCACTGAGCTGCCGAGTCC;RSEQ=CCAAATAATGAAAAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:2,1:42,93:135,3:0.0216:2,2:34.3:1:31.3:1:0.23841:4.38:60:6:0.0224:0:1.7 0/0:94:0:0,0:24,70:94,0:0:2,0:23.7:1:28.7:1:1:0:60:46:1:0:1.1 +4 175304986 . G A 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.83998;LSEQ=AATGATCAATAAATAGTAAG;RSEQ=GAACTCAGAGGCCGGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:2,4:3,2:5,6:0.5455:2,2:28.8:1:33:1:0.5671:2.69977:37.3:12:0.5455:0:1 1/0:12:6:4,2:2,4:6,6:0.5:2,2:23.2:1:29.5:1:0.5671:3.53:41.3:12:0.5:0:1 +4 176934309 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACTTACAAGTGACAACATG;RSEQ=GATACTTGGTCTTCTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:31:0:1:0:53.5:4:1:0:1.5 +4 176935505 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50525;SOR=Inf;LSEQ=ACTGATGGTCTTTGCAGCCA;RSEQ=CTCTTTCCCAGTGAAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:43,7:50,0:0:2,0:24.4:1:31.7:1:1:0:59.7:100:1:0:0.1 0/1:66:2:1,1:55,9:64,2:0.0303:2,2:12.5:1:27.5:1:0.28205:5.85001:60:4:0.0303:0:1 +4 176935553 . TA T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54037;SOR=Inf;LSEQ=CAATTTCACCTTGGTGAAGT;RSEQ=CCCCCACTGATGGAGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:71,32:103,0:0:2,0:23.7:1:28.8:1:1:0:60:206:1:0:0.1 0/1:187:2:1,1:122,63:185,2:0.0107:2,2:20:0:32:0:1:1.92924:60:4:0.0108:0:0.5 +4 176935570 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.142;SOR=0;LSEQ=AGTTACCCCCACTGATGGAG;RSEQ=CAGTCGACTAAGGAGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:85,55:140,2:0.0141:2,2:22:1:29:1:1:1.54053:60:4:0.0142:0:2 0/0:234:0:0,0:146,88:234,0:0:2,0:25.5:1:30.6:1:1:0:60:45.8:1:0:0.4 +4 176935634 . G A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.38318;LSEQ=TGAATAGAGATGGCTGAGAG;RSEQ=CACTGCAGCATGTTGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:75:38,37:91,88:179,75:0.2953:2,2:26.1:1:30.4:1:1:1.00685:60:150:0.3:0:1.1 1/0:348:174:91,83:84,90:174,174:0.5:2,2:23.6:1:28.6:1:0.5201:1.17:60:86:0.4971:0:1.2 +4 176935814 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48908;SOR=Inf;LSEQ=CAAAAATAAAAAGTACCAGA;RSEQ=ATTAACAATAACTAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:0,16:16,0:0:1,0:24.4:1:32.8:1:1:0:60:32:1:0:0 0/1:19:2:1,1:0,17:17,2:0.1053:1,2:10.5:1:30:1:0.10526:0:60:4:0.1053:0:1 +4 176936014 . G A 29 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AAAAGAGAAAAAAAGCCAAA;RSEQ=AGATAAAAAGTTAACTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:15:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:29:1:1:0:60:4:1:0:1 +4 181796994 . C T 34 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TTCTCCCTGTGGAGTTTTAC;RSEQ=CCCTGCTTCTCTCCCATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:29.5:1:34:0:1:0:58:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:39:0:33:0:1:0:60:2:1:0:0 +4 181797393 . A G 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13228;SOR=0.36143;LSEQ=ACAGTCTAGTCCTGCCTCCC;RSEQ=TCCACCGTGATGATCCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:18:18,0:14,0:14,18:0.5625:1,1:25.6:1:30.8:1:1:0:60:36:0.5625:0:1.1 0/1:16:5:5,0:10,1:11,5:0.3125:2,0:27.2:1:30.4:1:1:0:60:10:0.3125:0:1 +4 181797474 . A G 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=GCAGAACAATGCCTAACCAC;RSEQ=ATGTAGGTACCATCTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:101,14:115,2:0.0171:2,2:6:1:27.5:1:0.24094:7.00406:60:4:0.0174:0:1 0/0:144:0:0,0:128,16:144,0:0:2,0:23.7:1:29.7:1:1:0:60:143:1:0:0.1 +4 181797596 . A G 301 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00908;LSEQ=TCATGATTTCCTTGTCAACA;RSEQ=TTTCAACTTGTCAACCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:582:580:299,281:1,1:2,580:0.9966:2,2:26.2:1:32.8:1:1:1.06:59.9:115:0.9965:0:1.4 1/0:780:565:278,287:107,108:215,565:0.7244:2,2:25.7:1:31.2:1:0.93615:1.02279:60:140.25:0.7286:0:1.4 +4 181797669 . C T 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=0;LSEQ=TTTTTAACTTCATTAGACGT;RSEQ=CATTTGGCGGATTCTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:350:350:105,245:0,0:0,350:1:0,2:24.1:1:30.3:1:1:0:59.9:86.5:1:0:1.8 1/1:413:398:133,265:4,11:15,398:0.9637:2,2:24.9:1:28.7:1:0.78171:1.38:60:78.6:0.9656:0:2 +4 181797677 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.27152;LSEQ=TTCATTAGACGTCCATTTGG;RSEQ=GGATTCTTCTCTTAATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:142:40,102:41,122:163,142:0.4656:2,2:23.4:1:30.2:1:0.6038:1.17:59.9:141:0.4653:0:2.3 1/0:347:257:76,181:28,60:88,257:0.7406:2,2:25.2:1:29.5:1:0.68855:1.11106:60:256:0.7464:0:2.3 +4 181797707 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49858;SOR=Inf;LSEQ=TCTTAATATTTTCTTCCATT;RSEQ=AATCAGCTGTGTCCTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:23,154:177,0:0:2,0:23.8:1:29:1:1:0:60:354:1:0:1.3 0/1:177:2:1,1:26,149:175,2:0.0113:2,2:16:1:30.5:1:0.28255:5.64:60:4:0.0115:0:1 +4 181797720 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23602;SOR=Inf;LSEQ=TTCCATTTAATCAGCTGTGT;RSEQ=CTTTCCTTATATCCCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:11,125:136,0:0:2,0:24.5:1:31.7:1:1:0:60:67:1:0:1.2 0/1:129:2:1,1:8,119:127,2:0.0155:2,2:16:1:28:1:0.13517:14.09:60:4:0.0157:0:3 +4 181797780 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22496;SOR=1.85718;LSEQ=TCCCAGGATTTCAAAGGAAA;RSEQ=TCCTAATTCCTAAACTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:12:0,12:0,24:24,12:0.3333:1,0:19.2:1:33.8:1:1:0:60:24:0.3333:0:2.1 0/1:31:15:0,15:1,15:16,15:0.4839:1,1:19.6:1:32.3:1:1:0:60:30:0.4839:0:1.6 +4 181797798 . G T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34188;SOR=0.49419;LSEQ=AATTCCTAATTCCTAAACTT;RSEQ=CACACACACAAATACAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:14,9:0.3913:1,0:24.4:1:30.3:1:1:0:60:18:0.3913:0:2.6 0/1:21:5:0,5:0,16:16,5:0.2381:1,0:26.4:1:28.8:1:1:0:60:10:0.25:0:2.2 +4 181797842 . T C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63325;SOR=2.38223;LSEQ=TGTCCCCTTCAAGTCTCATA;RSEQ=TGAAATGTAATCCCCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:6,6:0.5:0,0:25.5:1:34.3:1:1:0:60:12:0.5:0:2.8 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:21.2:1:30.8:1:1:0:60:10:0.7143:0:2.2 +4 182443806 . C T 41 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30155;SOR=Inf;LSEQ=TATGTTGTAGCCATAGTTTT;RSEQ=AGAACCAAAATGCAGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:89,36:125,0:0:2,0:25.4:1:31.8:1:1:0:59.6:40.667:1:0:0.1 0/1:228:4:1,3:149,75:224,4:0.0175:2,2:11:1:20.5:1:0.11707:5.91135:60:3:0.0133:0:2.3 +4 182443933 . G C 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGTAAATGGAGAACAACTG;RSEQ=ATCTGGATCCTGGTCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:40:23,17:148,122:270,40:0.129:2,2:30.6:1:32.5:1:0.86504:1.11:43.4:80:0.1294:0:1.1 0/0:491:0:0,0:273,217:490,0:0:2,0:24.3:1:30.2:1:1:0:57.6:60.25:0.9979:0:0.1 +4 182444038 . A G 223 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTGCTGTTATTGTGGTTGTG;RSEQ=TGATAGCAGTTGTTGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:413:0:0,0:210,201:411,0:0:2,0:25.1:1:30.4:1:1:0:59.6:67.5:1:0:0.1 0/1:773:165:90,75:314,292:606,165:0.2135:2,2:24.9:1:30.3:1:0.53977:1.12:47.8:54:0.2146:0:1.1 +4 182444093 . T A 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATTTCCAGAAAGAAGAGAA;RSEQ=GGCAAAGTATGAGAAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:37:13,24:125,198:323,37:0.1025:2,2:26.5:1:31.7:1:0.72423:1.16499:60:74:0.1048:0:1 0/0:703:0:0,0:301,402:703,0:0:2,0:24.5:1:29.5:1:1:0:58.4:99.429:1:0:0.4 +4 182444131 . A G 222 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAGATAAAGGAGATGGGT;RSEQ=GGATGCATAGGGAACTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:83,178:261,0:0:2,0:25.5:1:30.8:1:1:0:59.4:64.25:1:0:0.5 0/1:477:157:51,106:113,205:318,157:0.3291:2,2:26.2:1:30.5:1:0.53931:1.14535:59.4:38.25:0.3262:0:1.1 +4 182444132 . G T 203 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGAGATAAAGGAGATGGGTA;RSEQ=GATGCATAGGGAACTCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:95:32,63:51,111:162,95:0.3682:2,2:26.2:1:31:1:0.78254:1.11:59.1:94:0.3715:0:1.1 0/0:463:0:0,0:157,305:462,0:0:2,0:12:0:16:0:1:0:57:0:0:0:2 +4 182444208 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.5256;SOR=Inf;LSEQ=GAAATCGCAAACGGACTCAG;RSEQ=TTACAAATGTATGAGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:5,64:69,0:0:2,0:27.1:1:31.7:1:1:0:59.3:138:1:0:0.1 0/1:112:2:1,1:19,91:110,2:0.0179:2,2:16:1:30.5:1:0.32658:4.69:60:4:0.0179:0:1 +4 183806463 . G T 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCTTTTCTGATCAAAGG;RSEQ=ATAGCCAAGAGCAGAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:9.5:1:31:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:20:0:32:0:1:0:60:2:1:0:0 +4 183806775 . GA G 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49898;SOR=0;LSEQ=TCAGAGGCTGGGGAAAGGCA;RSEQ=ATAAATCAAAAGGCTGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:93,17:110,2:0.0179:2,2:15.5:1:27.6:1:0.29681:5.34506:60:4:0.0187:0.0089:0.5 0/0:101:0:0,0:84,17:101,0:0:2,0:22.5:1:29:1:1:0:60:202:1:0:0.1 +4 183806854 . G T 57 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02106;SOR=0;LSEQ=GAATGCCCATTTAAAACCTG;RSEQ=ACCAAATGGCATGTTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:5:2,3:182,155:337,5:0.0146:2,2:21.8:1:24.6:1:0.6654:1.75837:60:4:0.0119:0:1.4 0/0:397:0:0,0:228,169:397,0:0:2,0:26:1:30.3:1:1:0:60:65.167:1:0:0.4 +4 183806867 . G A 49 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04597;SOR=0;LSEQ=AAACCTGGACCAAATGGCAT;RSEQ=TTTAAGTTTCTAACAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:4:4,0:183,178:361,4:0.0109:2,0:6.5:1:24.5:1:0.1234:0:60:8:0.0109:0:1 0/0:425:0:0,0:229,196:425,0:0:2,0:25.6:1:31.2:1:1:0:60:140.667:1:0:0.5 +4 183806904 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=6.31476;LSEQ=TTTTCATTAACAAAAGTTAA;RSEQ=ATACAGAACTCCTACAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:58:22,36:122,146:268,58:0.1774:2,2:24.9:1:29.6:1:0.31074:1.36607:59.8:116:0.1779:0:1.1 1/0:421:243:115,128:87,91:178,243:0.5772:2,2:25.4:1:28.5:1:0.76783:1.06395:60:242:0.5776:0:1.1 +4 183806977 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50403;SOR=Inf;LSEQ=GGTCAAGAAATCCACTAATC;RSEQ=GATGGGTTTCAGTGGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:44,105:149,0:0:2,0:24.3:1:30.6:1:1:0:59.8:148:1:0:0.1 0/1:184:2:1,1:53,129:182,2:0.0109:2,2:8.5:1:32:1:0.50196:2.42:60:4:0.0109:0:1.5 +4 183806981 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50409;SOR=Inf;LSEQ=AAGAAATCCACTAATCGGAT;RSEQ=GGTTTCAGTGGAAACATCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:39,104:143,0:0:2,0:23.6:1:31.1:1:1:0:59.8:46.667:1:0:0.1 0/1:177:2:2,0:48,127:175,2:0.0113:2,0:8:1:25:1:0.07865:0:60:4:0.0115:0:1.5 +4 183807129 . T C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTAATCTCCTGTCTCTCT;RSEQ=AAAGATAAATGTGCCCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:30.6:1:33.7:1:1:0:56.9:18:1:0:1 1/1:5:5:0,5:0,0:0,5:1:0,0:19:1:28.2:1:1:0:60:4:1:0:1.2 +4 183807884 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCCAGGGAATTAGTGTGG;RSEQ=GATGCATGTCCATAGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29:1:1:0:49:4:1:0:2 +4 183880764 . C T 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00043;SOR=0.21323;LSEQ=GCTAACTTTACTTAGAAGGG;RSEQ=TCTTTTTCTAAAACTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:26:9,17:3,7:10,26:0.7222:2,2:26.1:1:29.2:1:1:1.23:60:52:0.7222:0:1.1 0/1:68:24:7,17:14,29:43,24:0.3529:2,2:23.2:1:28.8:1:1:1.16966:60:23:0.3485:0:1.1 +4 183881396 . ACT A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCACACACACTCTCACAC;RSEQ=CTCTCACACACTCTCACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:30.5:1:1:0:60:4:1:0:0 +4 184234224 . G C 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AAGAGAACCCATCATGGAAG;RSEQ=ATGGCTGCAAGCTCCTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:23:1:33:1:1:0:60:4:0.5:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:44:1:30:0:1:0:60:4:1:0:0 +4 184234499 . G T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04153;SOR=Inf;LSEQ=GGGGATGGGTTTTATGTAGG;RSEQ=CAGATATCAGAGGCATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:216,130:346,0:0:2,0:24.9:1:31.3:1:1:0:60:25.615:1:0:0.4 0/1:469:6:3,3:277,186:463,6:0.0128:2,2:19.7:1:27.2:1:0.6889:1.48791:60:5:0.011:0:1.7 +4 184234587 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53721;SOR=1.12442;LSEQ=GGGAGGTTTGTGGGGGGCAG;RSEQ=GGCTGCCCTGTGGTGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:412:342:142,200:31,34:65,342:0.8301:2,2:24.6:1:30.8:1:0.41183:1.28336:60:170:0.8333:0:1.2 1/1:565:478:207,271:34,48:82,478:0.846:2,2:26.7:1:30.2:1:0.80973:1.08:60:158.333:0.8482:0:1.2 +4 184234592 . G A 52 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12588;SOR=0.26927;LSEQ=GTTTGTGGGGGGCAGTGGCT;RSEQ=CCCTGTGGTGCCAGCGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:5:3,2:152,211:363,5:0.0136:2,2:13.2:1:22.8:1:0.65369:2.08:60:4:0.011:0:2.8 0/0:542:2:2,0:230,308:538,2:0.0037:2,0:1:0:23.5:1:0.18413:0:60:4:0.0037:0:2 +4 184234602 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08522;SOR=Inf;LSEQ=GGCAGTGGCTGCCCTGTGGT;RSEQ=CCAGCGCTCGAGATGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:120,199:319,0:0:2,0:22.5:1:32:1:1:0:59.9:62.8:1:0:1 0/1:471:5:3,2:186,280:466,5:0.0106:2,2:11:1:26.6:1:0.39475:2.25:60:10:0.0108:0:1.6 +4 184234645 . G A 45 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25472;SOR=Inf;LSEQ=CTGGGGAGCAGGGGTGTGGG;RSEQ=AGGATGCTGACCTCTGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:15,118:133,0:0:2,0:23.4:1:31.7:1:1:0:59.8:65.5:1:0:0.6 0/1:162:3:1,2:32,127:159,3:0.0185:2,2:7:1:29:1:0.49749:1.97:60:6:0.0189:0:2 +4 187367227 . C T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGATTTGCTTTTCAAGCA;RSEQ=TCCAAGGTTGCTAATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:10.7:1:31:1:1:0:60:6:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 187367234 . G A 48 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TGCTTTTCAAGCACTCCAAG;RSEQ=TTGCTAATTATTTTCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:17.7:1:30.7:1:1:0:60:6:1:0:4 0/0:1:0:0,0:1,0:1,0:0:0,0:7:0:31:0:1:0:60:2:1:0:0 +4 187367298 . C T 53 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=CAAACAAAACTTGTCTTTGG;RSEQ=GTATATTCTTTCTATTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:25.8:1:26.8:1:1:0:60:3:1:0:3.5 0/1:4:1:1,0:3,0:3,1:0.25:0,0:6:0:32:0:1:0:60:2:0.25:0:2 +4 187367319 . G A 59 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GTATATTCTTTCTATTCTTT;RSEQ=AAAATTTTGTACATTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:15:1:25.6:1:1:0:60:4:1:0:3.2 0/1:5:2:2,0:3,0:3,2:0.4:0,0:23.5:1:29:0:1:0:60:4:0.4:0:1.5 +4 187367404 . T C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05357;SOR=Inf;LSEQ=GGTTATTCTTACCAAAGATA;RSEQ=AGAGACCTTCCTTCAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:25,3:28,0:0:2,0:28.6:1:31.4:1:1:0:60:56:1:0:1 0/1:31:5:5,0:24,2:26,5:0.1613:2,0:11:1:32.4:1:1:0:60:10:0.1613:0:1.4 +4 187367442 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.10328;LSEQ=AAACTATAAACATTTTCAGC;RSEQ=AATAACTAATCAGAGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:59:48:39,9:8,3:11,48:0.8136:2,2:24.8:1:30:1:0.67866:1.61:59.5:47:0.8103:0:1.8 1/1:64:53:43,10:10,1:11,53:0.8281:2,2:24:1:29.5:1:0.67222:2.3006:60:106:0.8281:0:1.9 +4 187367490 . T C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.01583;SOR=0.43027;LSEQ=TTTTCCAAATATGCACAACT;RSEQ=ATAGTAGCAAAATATTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:111:97:71,26:9,5:14,97:0.8739:2,2:26.8:1:32.5:1:0.52954:1.51:59.8:194:0.8739:0:2.1 1/0:139:104:73,31:23,12:35,104:0.7482:2,2:24.4:1:30.8:1:0.67432:1.23:60:208:0.7482:0:2.1 +4 187367511 . A T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2535;SOR=Inf;LSEQ=ATAGTAGCAAAATATTTGCA;RSEQ=ACTCAGTAATCATAAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:94,57:151,0:0:2,0:23.3:1:30.2:1:1:0:59.8:302:1:0:1.5 0/1:180:3:1,2:106,71:177,3:0.0167:2,2:25.3:1:21.7:1:0.5669:2.96763:60:2:0.0112:0:2.7 +4 187367539 . T C 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0.29739;LSEQ=AATCATAAGTTAAACCATAA;RSEQ=GATGATGACATATTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:174:95,79:12,10:22,174:0.8878:2,2:23.8:1:30.8:1:1:1.00:59.9:86:0.8866:0:1.5 1/0:261:183:99,84:38,36:74,183:0.7011:2,2:24.5:1:30.2:1:0.78259:1.12:60:182:0.7027:0:1.5 +4 187367589 . C T 27 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.15461;SOR=0;LSEQ=GTTTAGTACCTTGAATATGC;RSEQ=ACACACTATCCTAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:74,104:178,2:0.0111:2,2:36:0:27:1:1:1.40:60:4:0.0113:0:1 0/0:277:0:0,0:115,162:277,0:0:2,0:27.5:1:30.6:1:1:0:60:29.778:1:0:0.6 +4 187367606 . GA G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.15684;SOR=0;LSEQ=TGCCACACACTATCCTAAAA;RSEQ=AAAAAAGTGAAGATTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:56,92:148,2:0.0133:2,2:31:1:33.5:1:1:1.64:60:4:0.0135:0:0 0/0:228:0:0,0:93,134:227,0:0:2,0:25.3:1:29:1:1:0:60:44.4:1:0:0.4 +4 187367637 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.5122;SOR=Inf;LSEQ=AAGATTCAAAAGCAGTGAGA;RSEQ=AAAATTTCCCTGTACAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:20,65:85,0:0:2,0:22.8:1:32:1:1:0:60:41.5:1:0:0.2 0/1:120:2:1,1:36,82:118,2:0.0167:2,2:35.5:1:29.5:1:0.52339:2.26:60:4:0.0171:0:1 +4 187367804 . T C 68 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGGCATGTCAGCTAGATC;RSEQ=AGCATACAGTTTTTGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:20:1:34:1:1:0:60:8:0.8:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:25:0:32:0:1:0:60:2:1:0:1 +4 187367891 . G GCCCT 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=5.000;MSILEN=4;SSF=0.33333;SOR=0;LSEQ=TTCCTTCCTTCCTTCCGCCT;RSEQ=CCCTCCCTCCCTCCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:30.9:1:1:0:43:4:1:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:21:0:34:0:1:0:60:2:1:0:1 +4 187509730 . TG T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.17383;SOR=0;LSEQ=TTCACTAAAGTCAGGCACTT;RSEQ=GGGGGAGTTGAGAGTCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:129,64:193,2:0.0103:2,2:35.5:1:32.5:1:1:2.00786:60:4:0.0103:0:0 0/0:272:0:0,0:174,98:272,0:0:2,0:23.6:1:30.6:1:1:0:60:89.667:1:0:0.2 +4 187509875 . G A 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCAGGCTGACACGTCAGA;RSEQ=CAGGAGGCGGTGGAGGCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:56:32,24:206,150:356,56:0.1353:2,2:27.4:1:29.7:1:1:1.02994:59.4:55:0.1361:0:1.4 0/0:611:0:0,0:320,289:609,0:0:2,0:26.4:1:31.2:1:1:0:60:120.8:0.9967:0:0.2 +4 187510319 . T C 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCATAGTTGGGGAACTC;RSEQ=TGTATGTCCGGCAGAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:476:0:0,0:177,298:475,0:0:2,0:24.2:1:30.6:1:1:0:60:94:0.9979:0:0.1 0/1:617:35:15,20:238,343:581,35:0.0567:2,2:21.1:1:30.9:1:0.8606:1.08:60:70:0.0569:0:1.1 +4 187510350 . C A 52 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13019;SOR=Inf;LSEQ=GCAGAGGAACGCTTGGCATC;RSEQ=AATCTGATGTATCCCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:81,232:313,0:0:2,0:24.4:1:32:1:1:0:60:77.25:1:0:0.1 0/1:376:4:3,1:127,244:371,4:0.0106:2,2:6.5:1:26.3:1:0.12211:5.74:60:8:0.0106:0:1 +4 187516655 . T A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05235;SOR=0.11439;LSEQ=CAAGTTCAAACACCTATTCA;RSEQ=TAAGAACAGTTTGGCTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:11,1:3,0:3,12:0.8:0,2:18.9:1:29.3:1:1:0:60:11:0.7857:0:1 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:19:1:31:0:1:0:60:4:0.2857:0:1 +4 187516776 . A G 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06488;SOR=Inf;LSEQ=AGGGTAGATAGTGCGTCTAC;RSEQ=TTGTGAGATAACACAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:102,11:113,0:0:2,0:22.9:1:31:1:1:0:60:112:1:0:0.1 0/1:135:5:4,1:112,18:130,5:0.037:2,2:25.2:1:29.6:1:0.53738:1.54969:60:10:0.0373:0:1 +4 187516880 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.17264;LSEQ=TCGGACTGGAAGGAGCTCAG;RSEQ=GACTGCACTTCAGACAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:456:277:171,106:116,62:178,277:0.6075:2,2:24:1:30.7:1:0.48684:1.1594:60:38.571:0.6054:0:1.1 0/1:627:132:79,53:288,207:495,132:0.2105:2,2:25.7:1:29.4:1:0.76603:1.07:60:15.5:0.2039:0:1.2 +4 187517681 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50321;SOR=Inf;LSEQ=GACACTTTAGTGAGATGAAA;RSEQ=AGTGGCTCTTACTGTCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:125,35:160,0:0:2,0:23.9:1:30.8:1:1:0:59.9:320:1:0:0.1 0/1:194:2:1,1:128,63:191,2:0.0103:2,2:39:1:32:0:1:2.02373:60:4:0.0104:0:1 +4 187518196 . C T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGACACATACTGGTTGGG;RSEQ=GCAGCATCCTCGCAGTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:130,308:438,0:0:2,0:24.8:1:30.8:1:1:0:59.9:108.5:0.9977:0:0.2 0/1:599:31:11,20:207,359:566,31:0.0518:2,2:18.8:1:29.6:1:1:1.04829:59.6:62:0.0527:0:1.1 +4 187518259 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17096;SOR=0;LSEQ=TTGCAGTGATAGGAGCCGTG;RSEQ=GTGTTCTCACAGAGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:59,139:198,2:0.01:2,2:32:1:30.5:1:0.51106:2.34:60:4:0.0102:0:1 0/0:283:0:0,0:94,189:283,0:0:2,0:24.3:1:29.6:1:1:0:60:55.6:1:0:0.2 +4 187518265 . C T 102 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05069;SOR=4.1423;LSEQ=TGATAGGAGCCGTGCGTGTT;RSEQ=TCACAGAGGGCCCCGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:58,127:185,2:0.0107:2,2:20:0:32.5:1:0.53263:2.18:60:4:0.011:0:1 0/1:256:11:3,8:83,162:245,11:0.043:2,2:24.8:1:29.5:1:0.75534:1.36467:60:22:0.0437:0:1.1 +4 187518281 . T C 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18071;SOR=0;LSEQ=TGTTCTCACAGAGGGCCCCG;RSEQ=GCAGGCAAGGGTTTCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:48,106:154,2:0.0127:2,2:47:0:28:1:0.53093:2.20:60:4:0.0132:0:1 0/0:213:0:0,0:65,148:213,0:0:2,0:24.1:1:29.1:1:1:0:60:52.25:1:0:0.2 +4 187518326 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50552;SOR=Inf;LSEQ=CGTCGATATCACTCTGACAC;RSEQ=TGCCAAGGAAGTCAGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:18,63:81,0:0:2,0:26.7:1:32.3:1:1:0:60:26:1:0:0.1 0/1:106:2:1,1:27,77:104,2:0.0189:2,2:34.5:1:31.5:1:0.46038:2.82:60:4:0.0189:0:1 +4 187518871 . G A 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCGAATCACACTGACAAAC;RSEQ=GCGCCATCCAAACTGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:667:0:0,0:380,287:667,0:0:2,0:25.9:1:30.4:1:1:0:60:73.111:1:0:0.1 0/1:870:49:26,23:442,376:818,49:0.0563:2,2:27:1:30:1:1:1.03986:60:98:0.0567:0:1.3 +4 187518976 . C T 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11125;LSEQ=AAGGAGAAACAGACATAAAC;RSEQ=TCATGATCCTATTGCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:277:83,194:37,82:119,277:0.6977:2,2:24.8:1:30.6:1:0.81279:1.05451:60:91.333:0.699:0:2 0/1:471:96:35,61:132,243:375,96:0.2038:2,2:23.3:1:29.1:1:0.81219:1.06:59.9:192:0.2065:0:2 +4 187518980 . T C 263 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAAACAGACATAAACCTCA;RSEQ=GATCCTATTGCAAATAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:370:113,257:0,0:0,370:1:0,2:24.8:1:30.9:1:1:0:60:369:1:0:1.8 1/0:441:221:69,152:84,134:218,221:0.5011:2,2:23.2:1:29.7:1:0.11049:1.37988:59.9:72.667:0.5:0:1.5 +4 187519206 . C G 297 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.2936;LSEQ=GTGCCCCCATAGAGGCATGG;RSEQ=TTGGAGGAACACGGATTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:634:633:308,325:0,0:0,633:0.9984:0,2:24.8:1:31.4:1:1:0:60:62.3:1:0:1.1 1/1:820:819:424,395:0,0:0,819:0.9988:0,2:24.5:1:30.7:1:1:0:59.9:162.8:0.9988:0:1.2 +4 187521018 . A T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24899;SOR=Inf;LSEQ=CCTTAAATGTACACACGTGC;RSEQ=GCATTTTAAAGATGGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:210,57:267,0:0:2,0:24.8:1:30.9:1:1:0:59.8:266:1:0:0.8 0/1:279:3:0,3:206,70:276,3:0.0108:2,0:17.3:1:22:1:0.01737:0:60:2:0.0072:0:2.3 +4 187521037 . C A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10541;LSEQ=CAGCATTTTAAAGATGGCAA;RSEQ=ATTACGGAGCCCACCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:212:159,53:74,26:100,212:0.6795:2,2:27.5:1:30.3:1:0.88936:1.05:60:105:0.6796:0:1.1 0/1:379:69:50,19:208,101:309,69:0.1821:2,2:26.7:1:29.8:1:0.47525:1.28:60:138:0.186:0:1.2 +4 187522325 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49873;SOR=Inf;LSEQ=TGTGGAATTCAACCATTTCA;RSEQ=TTACTTTATTATCTGTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:131,6:137,0:0:1,0:21.9:1:32.5:1:1:0:60:274:1:0:0 0/1:146:2:1,1:130,14:144,2:0.0137:2,2:17.5:1:28.5:1:0.19556:9.00529:60:4:0.0139:0:1 +4 187522658 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24631;SOR=Inf;LSEQ=AGTATGACTCCCCTGCACCC;RSEQ=TTGAGACTGATTTAGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:6,96:102,0:0:2,0:25.8:1:33.2:1:1:0:60:33:1:0:0.2 0/1:101:2:1,1:6,93:99,2:0.0198:2,2:34:1:28.5:1:0.13446:14.42:60:4:0.0198:0:1 +4 187522789 . T C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3712;SOR=0.38127;LSEQ=GAAAGAATAAATTTGACGAC;RSEQ=GCATCACAGAGAAATGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:0,11:0,4:4,11:0.7333:0,0:24:1:29.8:1:1:0:60:22:0.7333:0:1.8 1/0:8:4:1,3:0,4:4,4:0.5:0,2:11:1:30.3:1:1:0:60:8:0.5:0:1.3 +4 187525020 . A C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33208;LSEQ=TGAGTATTCTTCTCCAGAAG;RSEQ=GGTGATGAAAATCTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:460:286:111,175:78,96:174,286:0.6217:2,2:26.4:1:30.6:1:0.20594:1.28026:59.9:94.333:0.622:0:1.1 0/1:564:199:79,120:148,215:363,199:0.3528:2,2:23.8:1:29.8:1:0.85742:1.04556:60:98.5:0.3524:0:1.2 +4 187525058 . T C 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=GGGGCAAAATCGCAGGCGGA;RSEQ=AGATGCTCTCCTCAATTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:104,235:339,0:0:2,0:22.8:1:29:1:1:0:59.9:55.5:1:0:0.6 0/1:420:15:7,8:144,261:405,15:0.0357:2,2:26.2:1:31.7:1:0.41691:1.58:60:30:0.0361:0:1.1 +4 187525363 . C G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.0982;LSEQ=GAATCAACAATGAGCTCCTT;RSEQ=AAACACAGCGGGATAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:28:25,3:18,2:20,28:0.5833:2,2:24.7:1:32:1:1:1.0783:60:27:0.5745:0:1.2 0/1:34:4:4,0:28,2:30,4:0.1176:2,0:17:1:31.5:1:1:0:60:8:0.125:0:1.3 +4 187525453 . C T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24927;SOR=Inf;LSEQ=TGTATGAAATGTAAGCTGTT;RSEQ=AAATAGAAGAGGGGAACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:205,32:237,0:0:2,0:24.5:1:32.3:1:1:0:60:78:1:0:0.1 0/1:253:3:2,1:197,52:249,3:0.0119:2,2:16.3:1:21.3:1:0.50913:1.88852:60:2:0.0081:0:1.7 +4 187525910 . A T 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27761;SOR=0;LSEQ=GTGAGGAGGAGGGAAAGGAG;RSEQ=AGGGGTGTAGCGAAAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,11:11,5:0.3125:0,0:23.6:1:29.6:1:1:0:60:10:0.3125:0:1.8 0/0:5:0:0,0:0,5:5,0:0:0,0:25.8:1:31:1:1:0:60:10:1:0:0.4 +4 187525922 . G A 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56923;SOR=0.26046;LSEQ=GAAAGGAGAAGGGGTGTAGC;RSEQ=AAAAGGGAAGAAAAAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:5,7:0.5833:0,0:26.3:1:31.4:1:1:0:60:14:0.5833:0:2.3 0/1:4:1:0,1:0,3:3,1:0.25:0,0:3:0:26:0:1:0:60:2:0.25:0:2 +4 187525940 . AG CT 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAAAAGGGAAGAAAAAGG;RSEQ=GATGAAGGAAACATGGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:27.5:1:33:1:1:0:60:4:0.2222:0:2 0/0:2:0:0,0:0,2:2,0:0:0,0:14.5:1:31.5:1:1:0:60:4:1:0:0 +4 187526002 . C A 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGAGGAGGGGAAGCAGA;RSEQ=ACGAGGAGGAGTGGGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:11.5:1:31.5:1:0.33333:0:60:4:0.6667:0:4.5 0/0:1:0:0,0:0,1:1,0:0:0,0:48:0:33:0:1:0:60:2:1:0:0 +4 187527039 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.59321;SOR=1.43265;LSEQ=AAAAATCAAAGCACGGAAAG;RSEQ=AAAGAGATAAAAGCTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:13:12,1:14,1:15,13:0.4643:1,1:17.2:1:29.2:1:1:1.16024:60:12:0.4444:0:1.4 1/0:27:15:15,0:12,0:12,15:0.5556:0,1:25.4:1:29.1:1:1:0:60:30:0.5769:0:1.1 +4 187527089 . T C 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AAATGCTCATCTTTTAATAC;RSEQ=GATAGCGACTTCTTGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:13:13,0:35,2:37,13:0.26:2,1:30.6:1:32:1:1:0:60:26:0.26:0:1.4 0/0:60:0:0,0:58,2:60,0:0:1,0:23.8:1:30.8:1:1:0:60:120:1:0:0.2 +4 187527164 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15298;SOR=0;LSEQ=ATAAGAAAGAAAAGCAACAG;RSEQ=GGCCAATGGAAAAGCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:141,47:188,2:0.0105:2,2:11:0:33:0:0.44244:2.97908:60:4:0.0106:0:1.5 0/0:295:0:0,0:195,99:294,0:0:2,0:22.6:1:29:1:1:0:60:293:0.9966:0:0.1 +4 187527300 . G T 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16714;SOR=0.17817;LSEQ=CGGACACATCGATGTTCACG;RSEQ=TCGTCGTGTTGACTCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:4:2,2:148,207:355,4:0.0111:2,2:29.3:1:29:1:1:1.40:60:8:0.0112:0:1 0/0:500:1:1,0:213,285:498,1:0.002:2,0:47:0:32:0:0.42886:0:60:2:0.002:0:1 +4 187527391 . C T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22419;SOR=Inf;LSEQ=TTCAGGCAAAAGACAGAATG;RSEQ=ACGTTCATTTTCACAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:34,110:144,0:0:2,0:21.9:1:32.1:1:1:0:60:35:1:0:0.2 0/1:130:2:1,1:33,94:127,2:0.0154:2,2:8:0:29:1:0.45918:2.82:60:4:0.0155:0:1.5 +4 187527472 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00515;SOR=0.14071;LSEQ=CGGGCAGGTCCCAGTGAGCT;RSEQ=CCACTATCTGTTGCATCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:16:0,16:0,7:7,16:0.6667:0,1:27.3:1:32.7:1:1:0:60:15:0.6818:0:1.1 0/1:19:4:0,4:1,14:15,4:0.2105:1,0:23.5:1:32.3:1:1:0:60:8:0.2105:0:1 +4 187529904 . G A 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTATTTTATCTCACTCT;RSEQ=CTTTCTTCTTATGATTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:17.5:1:27.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 187530313 . C T 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGTGATTTGTAAACAA;RSEQ=GTAAATCAACCTTTTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:509:509:301,208:0,0:0,509:1:0,2:25.5:1:31:1:1:0:60:253.5:1:0:1.1 1/1:705:704:429,275:0,0:0,704:0.9986:0,2:25.7:1:29.8:1:1:0:60:87:0.9986:0:1.2 +4 187530402 . T C 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGTCAATTGTGAACGAGC;RSEQ=TCCTTGGTTGCCATCTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:0:0,0:366,350:716,0:0:2,0:24.9:1:31.1:1:1:0:60:142.2:1:0:0.2 0/1:995:58:26,32:455,481:936,58:0.0583:2,2:23.3:1:30.3:1:0.59118:1.16406:60:18.333:0.0558:0:1.3 +4 187530578 . G GT 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.75651;SOR=0.73796;LSEQ=AGCTGTTTCTTTTTGTTGTT;RSEQ=TTTTTTTTTTGAGATGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:7:0,7:2,65:67,7:0.0946:1,0:25.4:1:32:0:1:0:59.3:14:0.0959:0:0.4 0/1:56:4:0,4:0,51:51,4:0.0714:1,0:39.3:1:25:1:1:0:60:3:0.0566:0:0.3 +4 187530731 . T C 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.05371;SOR=0;LSEQ=CAGGCGCCCGCCACCACGCC;RSEQ=GGCTAATTTTTTTTTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:5,1:2,4:6,6:0.5:2,2:9.7:1:31.8:1:0.24242:7.96:51:12:0.5:0:1 0/0:6:0:0,0:4,2:6,0:0:2,0:25.8:1:29.3:1:1:0:40.5:5:1:0:0.2 +4 187531022 . A G 217 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0045;LSEQ=TGTAGGTGTCTTGGCTGAAC;RSEQ=CAGGGGTATTATCGTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:590:133:77,56:242,215:457,133:0.2254:2,2:24.6:1:30.8:1:0.32461:1.22:60:43.333:0.2241:0:1.1 0/0:767:1:1,0:399,366:765,1:0.0013:2,0:18:0:24:0:1:0:60:2:0.0013:0:1 +4 187531122 . A G 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCTCTACTGTTAGGTAAT;RSEQ=CTCATGAGAGCTCTCATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:566:0:0,0:248,318:566,0:0:2,0:24.9:1:29.1:1:1:0:60:93.333:1:0:0.1 0/1:676:27:15,12:280,369:649,27:0.0399:2,2:28.7:1:31.3:1:0.23648:1.65:59.8:54:0.0405:0:1.4 +4 187533153 . C T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TTTTGTATTTTTATTAGAGA;RSEQ=GGGGTTTCTCCATGTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:37:1:26.3:1:1:0:39:2:0.4:0:2.7 0/0:3:0:0,0:0,3:3,0:0:0,0:30:1:31.3:1:1:0:59.7:6:1:0:0 +4 187533998 . T G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAACACATCACTGATTAAT;RSEQ=CAATGGGATGTGAAGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:38.5:1:34:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 187534240 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21763;SOR=0;LSEQ=ATCTCAGTGAGCAGCGTCAG;RSEQ=CAAGAGCATTCCCGGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:149,48:197,2:0.0101:2,2:17:1:30:1:0.43277:3.08242:60:4:0.0104:0:1 0/0:227:0:0,0:176,51:227,0:0:2,0:21.6:1:30.2:1:1:0:60:55.75:1:0:0.1 +4 187534363 . G A 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12819;LSEQ=TCGGCAGAGAATTCGGGGGC;RSEQ=TTATCGTTCACATCTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:666:490:263,227:91,85:176,490:0.7357:2,2:24.4:1:30.7:1:0.66075:1.08:59.9:80.667:0.7378:0:1.7 0/1:1001:263:142,121:379,357:736,263:0.2627:2,2:24.2:1:29.2:1:0.5177:1.11:60:64.75:0.2608:0:2 +4 187534375 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39618;LSEQ=TCGGGGGCGTTATCGTTCAC;RSEQ=TCTTCTAGCGTGAGCACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:320:162,158:180,175:355,320:0.4734:2,2:24.7:1:30.7:1:1:1.00317:59.9:34.556:0.4705:0:2 0/1:1021:268:142,126:377,374:751,268:0.2625:2,2:24.5:1:29.8:1:0.47671:1.12:60:43.667:0.2607:0:2 +4 187534524 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20788;SOR=0;LSEQ=CAAAAACAAATGGACTCACT;RSEQ=GTAATTTAAGACGTGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:0,2:34,143:177,2:0.0112:2,0:10:1:30.5:1:1:0:60:4:0.0114:0:1 0/0:213:0:0,0:39,174:213,0:0:2,0:23.4:1:29.2:1:1:0:60:52.25:1:0:0.4 +4 187534542 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12215;SOR=0.68367;LSEQ=CTTGTAATTTAAGACGTGAC;RSEQ=TGCAGTTGTACATCTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:72:11,61:3,27:30,72:0.5143:2,2:25.6:1:32.9:1:0.75285:1.62:60:144:0.518:0:1 0/1:143:60:12,48:12,71:83,60:0.4196:2,2:21.6:1:31.3:1:0.49701:1.48:60:120:0.4196:0:1 +4 187534689 . G T 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00606;SOR=0;LSEQ=AGGTCTCCAACCCTGCCAGG;RSEQ=GCTAGCTCTTTAAGTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:18.6:1:31.3:1:1:0:60:16:1:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:17.3:1:30.7:1:1:0:60:6:1:0:0 +4 187535063 . T C 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03333;SOR=0;LSEQ=AAGCTTGAGTTATATTTTAA;RSEQ=TTCTGAGGGTTGTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:26.3:1:30.8:1:1:0:60:5:0.8333:0:1.2 0/0:3:0:0,0:3,0:3,0:0:0,0:28:1:31.7:1:1:0:49.3:6:1:0:0 +4 187535121 . T C 72 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.3043;SOR=0.18507;LSEQ=GCCTTCTAAATTTTAAATCC;RSEQ=TTTTTCAATTAGGTGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:25.6:1:31.4:1:1:0:60:10:0.5:0:1.8 0/1:7:1:1,0:6,0:6,1:0.1429:0,0:15:0:32:0:1:0:60:2:0.1429:0:2 +4 187535169 . T C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51213;SOR=0.54558;LSEQ=TTTTTTAAAAAATCTCACCT;RSEQ=GAATTTTACGCACTAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:11,0:13,0:13,11:0.4583:1,0:27.2:1:32.5:1:1:0:57.5:22:0.4583:0:1.5 0/1:16:5:5,0:11,0:11,5:0.3125:0,0:25.4:1:30.2:1:1:0:60:10:0.3125:0:2 +4 187535178 . C T 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29266;SOR=4.75314;LSEQ=AAATCTCACCTTGAATTTTA;RSEQ=GCACTAAATTGCTGGTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:1:1,0:31,0:31,1:0.0313:1,0:28:0:33:0:1:0:32:2:0.0313:0:3 0/1:22:3:3,0:19,0:19,3:0.1364:1,0:26:1:29.3:1:1:0:60:6:0.1429:0:2.7 +4 187535219 . C T 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21439;SOR=2.32858;LSEQ=TTTCTAAGAGATGTCAACTT;RSEQ=GGAGCATCAGAATACATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:4:4,0:51,0:51,4:0.0727:1,0:26:1:31.8:1:1:0:53:8:0.0741:0:1.5 0/1:45:7:7,0:38,0:38,7:0.1556:1,0:16.9:1:30.9:1:1:0:60:14:0.1556:0:1.7 +4 187535519 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.21435;SOR=0;LSEQ=CTGCAAAGAGTTTAAACAAA;RSEQ=ACGTTACATAAAAGCATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:37,146:183,2:0.0108:2,2:15.5:1:31.5:1:0.36951:3.91:60:4:0.0112:0:1 0/0:214:0:0,0:68,146:214,0:0:2,0:26.1:1:29.4:1:1:0:59.9:106:1:0:0.1 +4 187535528 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50183;SOR=Inf;LSEQ=GTTTAAACAAAAACGTTACA;RSEQ=AAAAGCATTAACAGGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:29,130:159,0:0:2,0:23.7:1:29.2:1:1:0:60:158:1:0:0.2 0/1:187:2:1,1:57,128:185,2:0.0107:2,2:32:1:31.5:1:0.52527:2.23:60:4:0.0108:0:1 +4 187535588 . T C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00199;SOR=0.19296;LSEQ=GGAAAAGAAATCATTCATCT;RSEQ=TGACCACAGAAAACATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:19:0,19:0,31:31,19:0.38:1,1:27.8:1:34.2:1:1:0:60:38:0.38:0:1.1 0/1:48:5:0,5:3,40:43,5:0.1042:2,0:24.4:1:32.4:1:1:0:60:10:0.1042:0:1 +4 187535765 . T C 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.375;SOR=0;LSEQ=TACAAAATGCTATTATATGT;RSEQ=ATTAAGCTGATTTCATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:24.6:1:31.8:1:1:0:60:10:0.7143:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:8:0:28:0:1:0:60:2:1:0:0 +4 187538083 . G C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49913;SOR=0;LSEQ=CATGTGAATTACACCACAGC;RSEQ=CCAAATGATGGTCCCATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:126,12:138,2:0.0143:2,2:9:0:33.5:1:0.1777:10.12807:60:4:0.0143:0:2 0/0:128:0:0,0:111,17:128,0:0:2,0:24.1:1:28.8:1:1:0:60:31:1:0:0.2 +4 187538133 . A G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0;SOR=0.14362;LSEQ=GAAATTGAAATTCATAACAC;RSEQ=CAAATGTAAGGGAAGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:319:233:181,52:59,26:85,233:0.7304:2,2:23.4:1:30.2:1:0.14194:1.53:59.9:76.667:0.7302:0:1.1 0/1:365:102:76,26:176,87:263,102:0.2795:2,2:20.7:1:29.9:1:0.16768:1.44:60:101:0.2806:0:1.1 +4 187538330 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.35642;LSEQ=TCATTCTGTATAGTTTCAAC;RSEQ=GCAAACTGTCCTAAAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:635:331:128,203:122,181:303,331:0.5213:2,2:25.2:1:31.2:1:0.68514:1.06885:60:65.2:0.5208:0:1.1 0/1:680:190:84,106:208,282:490,190:0.2794:2,2:26.1:1:29.9:1:0.72993:1.07:60:380:0.2819:0:1.1 +4 187538465 . T C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.93809;LSEQ=AATGTTATAGTTTAAAAGAA;RSEQ=TGAGTATTAAAAGAATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:6:0,6:0,60:60,6:0.0909:1,0:23.2:1:33.7:1:1:0:60:12:0.0938:0:1 0/1:35:3:0,3:0,32:32,3:0.0857:1,0:25.7:1:33:0:1:0:60:6:0.0857:0:1.3 +4 187538928 . C T 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00205;SOR=Inf;LSEQ=ATCCGTGGTACTTAAGATGG;RSEQ=AATCACCCCACCTTGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:805:0:0,0:473,332:805,0:0:2,0:25.1:1:32:1:1:0:59.9:49.313:1:0:0.7 0/1:874:10:3,7:494,369:863,10:0.0114:2,2:16.7:1:26:1:0.10999:3.11978:60:20:0.0116:0:1.5 +4 187538942 . T G 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.12968;LSEQ=AGATGGCAATCACCCCACCT;RSEQ=GGGGGTCATCCTCACTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:851:635:349,286:121,94:215,635:0.7462:2,2:25.6:1:31.7:1:0.75149:1.05482:59.9:104.833:0.7461:0:1.1 0/1:972:268:156,112:348,273:621,268:0.2757:2,2:23.1:1:30.9:1:0.55614:1.09:60:133:0.2771:0:1.2 +4 187539205 . C T 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=47.63845;LSEQ=TGTGACTGATCCAGGCTATA;RSEQ=ATAACTTGGCCGTTGGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:699:1:0,1:361,336:697,1:0.0014:2,0:1:0:25:0:0.48281:0:60:2:0.0015:0:1 0/1:766:49:22,27:365,352:717,49:0.064:2,2:23.9:1:28.7:1:0.46176:1.27219:60:48:0.0629:0:1.1 +4 187539588 . T C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.41494;LSEQ=GAGATCTATCTCTGTTCCAA;RSEQ=AGGCACGTCCTCTGACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:566:67:29,38:244,254:498,67:0.1184:2,2:22.1:1:32.2:1:0.43515:1.25824:60:32.5:0.1173:0:1.1 0/1:512:27:15,12:242,243:485,27:0.0527:2,2:20.5:1:31.3:1:0.69329:1.25:60:54:0.0538:0:1.1 +4 187540042 . G A 188 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATCCTTAGCCATTAAACG;RSEQ=ACTGAGATCACTTTCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:74:36,38:313,319:632,74:0.1048:2,2:27.1:1:30.4:1:0.90282:1.03566:53.3:36:0.1047:0:1.1 0/0:916:0:0,0:474,442:916,0:0:2,0:26:0:15:0:1:0:60:0:0:0:4 +4 187540378 . C T 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05364;SOR=Inf;LSEQ=TAAAATGGCTTCAGGGCGTG;RSEQ=CGGTGCAGGTTTGAGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:159,263:422,0:0:2,0:25.4:1:31.5:1:1:0:59.9:37.364:1:0:0.1 0/1:393:4:1,3:143,245:388,4:0.0102:2,2:30.3:1:27.3:1:1:1.74874:60:8:0.0104:0:1 +4 187540399 . G A 45 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20233;SOR=4.31654;LSEQ=CGGTGCAGGTTTGAGAGGGT;RSEQ=ATAATCCCTGTTGCACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:1:1,0:147,224:371,1:0.0027:2,0:1:0:23:0:0.39785:0:60:2:0.0027:0:2 0/1:349:4:2,2:136,209:345,4:0.0115:2,2:11.8:1:22.5:1:0.64943:1.53:60:3:0.0088:0:1 +4 187540996 . C T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18278;SOR=0.69018;LSEQ=CGTATGCTCAGCTTATATGC;RSEQ=GGGTGGGCCTCAAAGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:33:18,15:143,160:303,33:0.0982:2,2:24.5:1:31.3:1:0.46613:1.34:60:66:0.0991:0:1 0/1:415:29:14,15:204,182:386,29:0.0699:2,2:27.6:1:29.6:1:0.70169:1.20041:60:28:0.0685:0:1.1 +4 187541131 . G A 173 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=60.41817;LSEQ=TCCGGGCTGTTAGCCTGCAC;RSEQ=TGGACCACAGGGCTGTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:1:1,0:232,178:410,1:0.0024:2,0:1:0:26:0:1:0:60:2:0.0025:0:1 0/1:466:60:30,30:211,195:406,60:0.1288:2,2:23.7:1:29.3:1:0.78384:1.08186:60:29:0.1261:0:1.1 +4 187541598 . C G 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TGTCACTTCTACAACCACAT;RSEQ=AAACGCCTCCTGCTGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:14:5,9:208,273:481,14:0.0283:2,2:24.6:1:30.4:1:0.78543:1.37058:60:13:0.0269:0:1.1 0/0:555:0:0,0:267,288:555,0:0:2,0:23.8:1:31.1:1:1:0:60:68.375:1:0:0.1 +4 187541686 . G T 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTAAATCTGCGATCTGG;RSEQ=TTGAGGATGTGATAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:658:0:0,0:380,277:657,0:0:2,0:24.6:1:31.6:1:1:0:59.9:49.538:1:0:0.1 0/1:797:50:25,25:385,362:747,50:0.0627:2,2:23.3:1:29.1:1:0.88433:1.06349:60:49:0.0623:0:1.1 +4 187542094 . T C 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAGAGATGCTTCATATAA;RSEQ=GGCTTGGCAAACACAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:294,220:514,0:0:2,0:24.6:1:31:1:1:0:59.9:72.429:1:0:0.1 0/1:508:21:12,9:271,215:486,21:0.0413:2,2:26.5:1:29.6:1:1:1.06:60:20:0.0397:0:1.1 +4 187542755 . T C 244 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00368;LSEQ=ATGTAAACTTCGGAGAGGCG;RSEQ=TGTCAGCAATTGTGACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:180:90,90:289,318:607,180:0.2281:2,2:26:1:32.7:1:0.61059:1.10:59.8:59:0.2275:0:1.1 0/0:919:1:0,1:442,476:918,1:0.0011:2,0:17:0:33:0:1:0:60:2:0.0011:0:1 +4 187542899 . G A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTTTAATAGAGCCCAAGACA;RSEQ=GATCAATCATAAAAGAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:168,296:464,0:0:2,0:25.5:1:31.9:1:1:0:60:57:1:0:0.2 0/1:521:19:10,9:196,306:502,19:0.0365:2,2:26.7:1:30.8:1:0.24212:1.73:60:38:0.0368:0:1.1 +4 187542922 . A G 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAATCATAAAAGAATTTCC;RSEQ=ATATTTCCTGGAAGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:42:16,26:112,214:326,42:0.1141:2,2:23.7:1:30.7:1:0.73094:1.18:60:41:0.1139:0:1.1 0/0:402:0:0,0:147,255:402,0:0:2,0:24.5:1:29.4:1:1:0:60:99.5:1:0:0.2 +4 187542927 . T C 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=CATAAAAGAATTTCCAATAT;RSEQ=TCCTGGAAGGAGAGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:114,233:347,0:0:2,0:25.7:1:30.4:1:1:0:60:68.4:1:0:0.2 0/1:379:14:5,9:130,235:365,14:0.0369:2,2:27.6:1:29.9:1:1:1.00:60:13:0.0349:0:1.1 +4 187542986 . G C 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CACAAGGGGCAGTAGTAGTA;RSEQ=TAGTTAGAGAAACAGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:36:2,34:9,84:93,36:0.2791:2,2:27.8:1:33.4:1:0.72667:1.81396:60:72:0.2835:0:1.1 0/0:119:0:0,0:15,104:119,0:0:2,0:22.3:1:31.8:1:1:0:60:118:1:0:0.1 +4 187549364 . G A 180 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.54422;LSEQ=CTTTGTCCTTGTCCAGAGCC;RSEQ=TCACCTGCAACACAACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:841:3:2,1:442,394:836,3:0.0036:2,2:20.3:1:29:1:1:1.78:60:6:0.0036:0:1.3 0/1:1116:66:37,29:544,504:1048,66:0.0591:2,2:25.6:1:29.8:1:0.52817:1.18:60:132:0.0599:0:1.2 +4 187549586 . G A 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=ACTAATTAAAAATCACGCTC;RSEQ=AACACACAAAGGCCTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:136,118:254,0:0:2,0:23.5:1:30.6:1:1:0:60:62.5:1:0:0.1 0/1:296:16:10,6:144,136:280,16:0.0541:2,2:22.4:1:30.1:1:0.44808:1.57:60:32:0.055:0:1.1 +4 187552855 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CTCTGCTCTTCAATCCATCC;RSEQ=CGCGGTATCCTAGTGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:20.3:1:30.7:1:1:0:48.3:6:1:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:42.5:1:29:1:1:1:38.5:4:0.3333:0:1 +4 187553049 . C G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGCACCCCCCTCCCGCC;RSEQ=CCACCCAAATTCATATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:29.5:1:1:0:60:4:1:0:1 +4 187557113 . C G 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=GACTTGTGCCCAAAACTCAT;RSEQ=AAACCGTATGCAGGTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:18:12,6:161,31:192,18:0.0857:2,2:20.6:1:31.1:1:0.09839:2.58191:60:36:0.0865:0:2 0/0:193:0:0,0:151,42:193,0:0:2,0:22.8:1:30.6:1:1:0:60:63.333:1:0:0.1 +4 187557120 . T C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14659;SOR=0.60521;LSEQ=GCCCAAAACTCATCAAACCG;RSEQ=ATGCAGGTTCTCCTCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:27:20,7:180,42:222,27:0.1084:2,2:25.3:1:32.5:1:0.44095:1.49732:60:54:0.1089:0:1.7 0/1:219:15:12,3:159,45:204,15:0.0685:2,2:22.5:1:28.7:1:1:1.13:60:6.5:0.0602:0:1.1 +4 187557420 . C A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.88174;LSEQ=TGGGCAGAGGGGATTAAAAA;RSEQ=AGCAAATCAGGAGTTACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:1,0:27,153:180,1:0.0055:2,0:1:0:26:0:0.1547:0:60:2:0.0056:0:1 0/1:193:2:1,1:42,149:191,2:0.0104:2,2:30:1:30.5:1:0.39686:3.52:60:4:0.0104:0:1 +4 187557600 . G A 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15733;SOR=5.87438;LSEQ=CTGATTCTCAAACGTTATCC;RSEQ=GCATTGCCTAATGGGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:1,0:38,6:44,1:0.0217:2,0:48:0:32:0:1:0:60:2:0.0227:0:1 0/1:34:4:4,0:26,4:30,4:0.1176:2,0:27.3:1:31.5:1:1:0:60:8:0.1176:0:1.3 +4 187557642 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00376;SOR=0.23044;LSEQ=AGGTCACAAACACTTCAGCC;RSEQ=TTTACAAAATAGAAATAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:20:18,2:49,3:52,20:0.2778:2,2:27.3:1:30.8:1:0.61302:1.7982:60:40:0.2817:0:1.1 0/1:62:5:5,0:53,3:56,5:0.0806:2,0:29:1:30.6:1:1:0:60:10:0.082:0:1 +4 187557893 . T C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13026;LSEQ=CCTTGTCGGTGGCTATGACG;RSEQ=GATAGAGCGGCTCCCGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:844:635:305,330:95,107:202,635:0.7524:2,2:25.7:1:30.8:1:0.80893:1.04:59.9:51.917:0.757:0:1.1 0/1:1126:319:153,166:408,397:805,319:0.2833:2,2:24.5:1:30.4:1:0.4276:1.11492:60:158.5:0.2838:0:1.2 +4 187557908 . C T 190 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=23.34025;LSEQ=TGACGTGATAGAGCGGCTCC;RSEQ=GTCTGGCATTTCTTTCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:807:3:1,2:368,434:802,3:0.0037:2,2:8.3:1:29:1:1:1.69478:60:6:0.0038:0:1.3 0/1:1135:91:44,47:497,547:1044,91:0.0802:2,2:25.1:1:29.2:1:0.9132:1.03:60:29.333:0.0791:0:1.2 +4 187558187 . CA C 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00051;SOR=0.07257;LSEQ=CATTTTGCAGGGCACGATGA;RSEQ=ACATACACAGCAGATCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:14:1,13:0,9:9,14:0.6087:0,1:25.6:1:31.7:1:1:0:60:28:0.6087:0.0435:0.4 0/1:21:2:0,2:0,19:19,2:0.0952:1,0:34:1:28:1:1:0:60:4:0.0952:0:0 +4 187560860 . T TA 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.18268;SOR=0.74136;LSEQ=GAATCTTTAAGTATTAAAGA;RSEQ=AAAAAAAAAACTTACCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:46:24,22:249,165:414,46:0.0985:2,2:27.3:1:29.8:1:0.34301:1.38231:60:92:0.1022:0.0021:0.3 0/1:574:43:24,19:311,209:520,43:0.0749:2,2:29.7:1:28.9:1:0.63018:1.17768:60:86:0.0778:0:0.1 +4 187560995 . G A 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18041;SOR=0;LSEQ=AAGGTCAATTACAAAATACT;RSEQ=CAATTAAAATCACACTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:36,152:188,2:0.0105:2,2:16:1:24.5:1:0.35238:4.18:60:4:0.0106:0:2 0/0:258:0:0,0:59,199:258,0:0:2,0:22.4:1:30.9:1:1:0:60:35.857:1:0:0.1 +4 187561080 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09506;LSEQ=CCCAGGGGGGTGGATTACTT;RSEQ=AGGTCAGGAGTTGGAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:28:0,28:0,17:17,28:0.6222:1,1:23.3:1:32.8:1:1:0:58.1:56:0.6364:0:1.1 0/1:38:5:0,5:0,33:33,5:0.1316:1,0:31.4:1:30.8:1:1:0:58.6:10:0.1351:0:1.2 +4 187584530 . G A 185 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01325;LSEQ=TGAGCTTGTCATTAGAGCTC;RSEQ=AATCTGGATCAAATGCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:66:37,29:347,236:583,66:0.1017:2,2:26.9:1:30.7:1:0.59928:1.15217:60:65:0.1011:0:1.1 0/0:669:1:1,0:376,290:666,1:0.0015:2,0:1:0:24:0:1:0:60:2:0.0015:0:1 +4 187584771 . C G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04321;LSEQ=TGACGTCTCTATGACACCTA;RSEQ=AGAGAAAAAAGAAAAGCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:350:348:86,262:0,0:0,348:0.9943:0,2:22.4:1:32.2:1:1:0:60:86:0.9942:0:1.1 1/1:408:360:85,275:12,33:45,360:0.8824:2,2:22.4:1:30.7:1:0.71107:1.17595:60:119:0.8859:0:1.1 +4 187627096 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAAGTTAGTTCTAAGAA;RSEQ=TCATTTGCTTGTCCAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:39.5:1:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 187627576 . C CA 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49845;SOR=Inf;LSEQ=CTACAATACAGCAGCCGGGC;RSEQ=AAAAAAAATATTCACACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:73,1:74,0:0:1,0:24.5:1:30.9:1:1:0:59.3:36:1:0:0.2 0/1:83:2:2,0:76,5:81,2:0.0241:2,0:36:1:29:1:1:0:60:4:0.025:0:0 +4 187627593 . C T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35135;SOR=1.5197;LSEQ=GGCCAAAAAAAATATTCACA;RSEQ=GCACTTCTATACCGAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:12:12,0:92,1:93,12:0.1143:1,0:22.3:1:32.8:1:1:0:60:24:0.12:0:1.3 0/1:134:22:21,1:108,4:112,22:0.1642:1,1:23:1:30.2:1:1:1.28311:60:44:0.1667:0:1.2 +4 187627792 . T C 292 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01395;LSEQ=TCGGATCTCCCCATCTCTTC;RSEQ=GGCGTCCTCATCATGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:792:789:403,386:1,1:2,789:0.9962:2,2:24:1:30.4:1:1:1.04:60:86.667:0.9974:0:1.1 1/0:895:703:352,351:100,90:190,703:0.7855:2,2:24.4:1:29.4:1:0.56728:1.10783:60:45.867:0.7827:0:1.1 +4 187628054 . C G 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTGCTCCACTGAGTTTATC;RSEQ=ACATCGAAGTTTCCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:668:0:0,0:332,334:666,0:0:2,0:23.3:1:31.7:1:1:0:60:65.6:0.997:0:0.1 0/1:764:20:12,8:372,371:743,20:0.0262:2,2:15.4:1:29.9:1:0.49787:1.50:60:40:0.0264:0:1.2 +4 187628352 . A T 198 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CCAGAGGGCGTGCGATGTTA;RSEQ=CAACACCCGTCACGCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:96:55,41:123,100:223,96:0.3009:2,2:24.5:1:30.2:1:0.80597:1.09:60:31:0.2971:0:1.7 0/0:411:0:0,0:216,194:410,0:0:2,0:23:1:29.4:1:1:0:59.9:204:1:0:0.6 +4 187628398 . C G 286 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATGTGTCTGTGTCTGTAA;RSEQ=AATTGAGTACGTCACGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:422:422:265,157:0,0:0,422:1:0,2:25.7:1:32.8:1:1:0:60:69.333:1:0:1.2 1/0:478:356:211,145:71,49:120,356:0.7448:2,2:26.2:1:30.9:1:1:1.00:59.9:43.5:0.7436:0:1.1 +4 187629140 . G C 293 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGTTGGGGTTTAAACTAAA;RSEQ=AAATCCAGTTCATTTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:589:589:311,278:0,0:0,589:1:0,2:25.3:1:31.9:1:1:0:60:57.9:1:0:1.1 1/0:690:517:273,244:84,88:172,517:0.7493:2,2:25.1:1:31.4:1:0.37947:1.17:60:102.4:0.7518:0:1.1 +4 187629497 . G A 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.22463;LSEQ=ATACTGTATGTCACGTACCC;RSEQ=TTCTCACCCTCATCAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:568:489:256,233:43,35:78,489:0.8609:2,2:23.8:1:30.8:1:0.7145:1.11797:60:80.5:0.861:0:1.7 1/0:774:450:217,233:171,153:324,450:0.5814:2,2:24.1:1:29.4:1:0.21631:1.19977:60:89:0.5817:0:1.7 +4 187629538 . C T 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15984;LSEQ=TACGGCACTCAGGCTCATGA;RSEQ=AGTAGTACCAATGGGCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:618:541:284,257:37,40:77,541:0.8754:2,2:25.5:1:29.8:1:0.46794:1.19:60:89.167:0.8742:0:1.7 1/0:768:406:198,208:175,185:360,406:0.5286:2,2:24.9:1:28.5:1:1:1.01:60:49.75:0.5244:0:1.7 +4 187629770 . A C 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16385;LSEQ=AATTTAGCTTTTCCAGGTGT;RSEQ=CTTTTAAAAACATACCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:878:773:371,402:49,55:104,773:0.8804:2,2:25.2:1:31.7:1:0.91687:1.04:59.9:69.273:0.8789:0:1.1 1/0:1043:570:259,311:222,251:473,570:0.5465:2,2:25.7:1:30.1:1:0.66239:1.06196:59.9:62.333:0.5441:0:1.1 +4 187630590 . G A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14447;SOR=1.24705;LSEQ=GCACCCTGACCTTTGTTCGC;RSEQ=CCTCCACATTAGTATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:84:39,45:286,357:643,84:0.1154:2,2:22.4:1:29.9:1:0.81562:1.08:59.6:83:0.1162:0:1.1 0/1:972:136:61,75:386,449:835,136:0.1399:2,2:23.7:1:28.8:1:0.78153:1.05695:60:67:0.1397:0:1.2 +4 187630597 . C G 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GACCTTTGTTCGCGCCTCCA;RSEQ=ATTAGTATTTTTTTCAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:697:0:0,0:321,374:695,0:0:2,0:24.2:1:32.3:1:1:0:59.9:114.833:0.9971:0:0.2 0/1:923:34:19,15:404,483:887,34:0.0368:2,2:26.6:1:30.9:1:0.29293:1.51:60:68:0.0374:0:1.1 +4 187630989 . C A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02597;SOR=1.72657;LSEQ=AATGTCTCCCCATTGCTTAA;RSEQ=TGTCGGGAATCTGAAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:29:7,22:84,245:329,29:0.081:2,2:23.8:1:31.1:1:1:1.07733:60:28:0.0791:0:1.1 0/1:401:53:19,34:113,235:348,53:0.1322:2,2:24.5:1:30.1:1:0.63982:1.16:60:106:0.1332:0:1.1 +4 187631223 . C T 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54545;SOR=0.33624;LSEQ=ACTTCCTTTTCATTTTTGAA;RSEQ=GACAAGGTCCTCTCTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:18.8:1:31:1:1:0:60:10:0.625:0:1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:7:0:23:0:1:0:60:2:0.3333:0:1 +4 187631324 . A C 66 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTATATTTTTATATTTA;RSEQ=ATCGTTAAGGCAAATATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:21:1:33:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +4 189191971 . C G 107 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACACTCAGTCTCCAGCA;RSEQ=CAGCAGCAGCAGCCCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:31.7:1:33:1:1:0:52.3:6:1:0:1.3 1/1:14:13:6,7:1,0:1,13:0.9286:0,2:15.7:1:29.1:1:1:0:50.2:5.5:1:0:1.3 +4 189191998 . GCAGCAGCAGCAGCAGCAGCCC G 57 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.1819;SOR=0.26764;LSEQ=CAGCAGCCCCACCAGCACCA;RSEQ=CACCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:3,1:4,4:0.5:2,2:14.5:1:28.6:1:1:2.60168:24.8:8:0.5:0.5:2 0/1:15:3:2,1:7,5:12,3:0.2:2,2:8.4:1:26.3:1:1:1.40:35:8:-0.0579:0.0435:1 +4 189192022 . C CCAG 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=8.000;MSILEN=3;SSF=0.4074;SOR=0.46036;LSEQ=CAGCAGCAGCAGCAGCCCCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:3,1:4,1:5,4:0.4444:2,2:19:1:29.9:1:1:1.29098:32.8:8:0.5714:0.1111:2.5 0/1:19:5:4,1:7,7:14,5:0.2632:2,2:18.2:1:30:1:0.33781:3.73:36.4:10:0.2778:0.1053:1.2 +4 189192028 . G C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.05561;SOR=0;LSEQ=CAGCAGCAGCCCCACCAGCA;RSEQ=CAGCAGCAGCAGCAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:3,0:5,5:10,3:0.2143:2,0:17.3:1:33.3:1:0.23077:0:26:6:0.3:0:2.3 0/0:21:0:0,0:12,9:21,0:0:2,0:25.6:1:29.9:1:1:0:42.9:6:1:0:1 +4 189192061 . CCAG C 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.3434;SOR=0.29178;LSEQ=CAGCCCCACCAGCACCAGCA;RSEQ=CAGCAGCAGCAGCCCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:2,1:12,12:24,3:0.1111:2,2:16.7:1:33.3:1:1:1.95:34:6:0.1111:0:0.3 0/1:29:1:1,0:15,13:28,1:0.0345:2,0:30:0:33:0:1:0:34:2:0.037:0:2 +4 189192078 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49248;SOR=Inf;LSEQ=GCACCAGCAGCAGCAGCAGC;RSEQ=CCACCAGCAGCAGCACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:27,0:0:2,0:25.7:1:29.1:1:1:0:37.8:8:1:0:1 0/1:30:2:1,1:16,11:27,2:0.0667:2,2:5.5:1:27.5:1:1:1.43545:60:4:0.087:0:1.5 +4 189192088 . G C 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.35072;SOR=0.22681;LSEQ=CAGCAGCAGCCCCACCAGCA;RSEQ=CAGCACCAGCACCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:3,1:11,12:23,4:0.1481:2,2:9:1:26.8:1:0.59556:3.14:34.8:3:0.12:0:2.5 0/1:27:1:0,1:14,11:25,1:0.037:2,0:47:0:29:0:0.46154:0:34:2:0.0455:0:6 +4 189192094 . C G 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10341;SOR=6.36481;LSEQ=CAGCCCCACCAGCAGCAGCA;RSEQ=CAGCACCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:1:1,0:12,11:23,1:0.0417:2,0:26:0:14:0:1:0:27:0:0:0:8 0/1:27:6:2,4:10,10:20,6:0.2222:2,2:16.5:1:27.7:1:0.65217:1.94818:52.5:5:0.2273:0.037:2.3 +4 189192100 . C G 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28647;SOR=2.81984;LSEQ=CACCAGCAGCAGCACCAGCA;RSEQ=CAGCAGCAGCAGCAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:2,1:11,10:21,3:0.125:2,2:6:1:31.7:1:1:1.77:46.7:6:0.1364:0:2 0/1:24:7:3,4:7,9:16,7:0.2917:2,2:22.7:1:29:1:1:1.03541:50.3:6:0.2857:0:2.9 +4 189192121 . CCAG C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.1957;SOR=0;LSEQ=CAGCAGCAGCAGCAGCCCCA;RSEQ=CAGCAGCAGCAGCCTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:29.5:1:34:0:1:1:60:4:0.1667:0:1.5 0/0:17:0:0,0:8,9:17,0:0:2,0:19.2:1:29.8:1:1:0:45.8:34:1:0:1.5 +4 189192124 . G C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.23793;SOR=Inf;LSEQ=CAGCAGCAGCAGCCCCACCA;RSEQ=CAGCAGCAGCAGCCTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,5:11,0:0:2,0:16.3:1:30.4:1:1:0:46.5:10:1:0:0.2 0/1:17:3:1,2:7,7:14,3:0.1765:2,2:29.7:1:31:1:1:1.9219:50.7:6:0.1875:0:4 +4 189192127 . G C 59 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.19606;SOR=4.76459;LSEQ=CAGCAGCAGCCCCACCAGCA;RSEQ=CAGCAGCAGCCTGGCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:1,0:6,6:12,1:0.0769:2,0:11:0:14:0:1:0:45:0:0:0:1 0/1:17:5:3,2:5,7:12,5:0.2941:2,2:8.2:1:25.8:1:0.61991:2.01:36.8:4:0.2857:0:1.4 +4 190093170 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13993;SOR=Inf;LSEQ=CAGAGCAAGAGTGAGCCTTC;RSEQ=ACAGAGGTGTGCGCAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:151,99:250,0:0:2,0:24.4:1:31.2:1:1:0:60:34.714:1:0:0.5 0/1:336:4:1,3:192,140:332,4:0.0119:2,2:17.8:1:25.5:1:0.31599:4.0978:60:8:0.0121:0:1.5 +4 190093234 . C T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01137;LSEQ=TAACGGGAGAAAAAATTCCC;RSEQ=GAAGCTGACACTCATCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:323:206:98,108:58,59:117,206:0.6378:2,2:25.3:1:31.1:1:0.81686:1.08309:60:412:0.6398:0:1.1 0/1:462:9:4,5:214,236:450,9:0.0195:2,2:24.3:1:28.1:1:1:1.13317:60:8:0.0175:0:1.3 +4 190093246 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.86804;LSEQ=AAATTCCCCGAAGCTGACAC;RSEQ=CATCCAGTGCCCAGTGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:33:14,19:131,140:271,33:0.1086:2,2:22.2:1:30.6:1:0.58228:1.2689:60:32:0.1077:0:1.2 0/1:449:220:105,115:102,126:228,220:0.49:2,2:24.6:1:30.3:1:0.56978:1.13:60:219:0.4955:0:1.3 +4 190093296 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19021;SOR=0;LSEQ=TGTGTTTAAAATACTGCAGT;RSEQ=CTGTCACAACGGTTGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:67,121:188,2:0.0105:2,2:8:1:27:1:1:1.80:60:4:0.0107:0:1 0/0:245:0:0,0:90,155:245,0:0:2,0:26.4:1:31:1:1:0:60:34:1:0:0.8 +4 190093299 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26086;SOR=Inf;LSEQ=GTTTAAAATACTGCAGTGCT;RSEQ=TCACAACGGTTGTGGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:64,117:181,0:0:2,0:26.2:1:32:1:1:0:60:35.2:1:0:0.5 0/1:235:3:3,0:79,153:232,3:0.0128:2,0:9:1:25.7:1:0.04147:0:60:6:0.013:0:1.3 +4 190093329 . A G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=12.89889;LSEQ=TTGTGGTGTATGTGGCTCTG;RSEQ=GGGTTCACACGCCGAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:11:2,9:31,85:116,11:0.0866:2,2:24.3:1:29.7:1:0.72696:1.63543:60:10:0.08:0:1.4 1/0:152:84:26,58:17,51:68,84:0.5526:2,2:23.9:1:30.3:1:0.47139:1.34:60:83:0.5533:0:1.3 +4 190262203 . C T 34 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TCCTCATTTCTAACAAGCTC;RSEQ=CGTGCAATGCCATTGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:37:1:34:0:1:0:60:4:0.3333:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:6:0:30:0:1:0:60:2:1:0:1 +4 190262402 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.65258;SOR=2.01085;LSEQ=GAGACAATGCCGTACTAGTT;RSEQ=CATGGTTGACAACATGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:1:0,1:86,53:139,1:0.0071:2,0:1:0:25:0:0.38571:0:60:2:0.0072:0:2 0/1:210:3:1,2:131,76:207,3:0.0143:2,2:24.3:1:28:1:0.55677:3.42628:60:6:0.0144:0:1 +4 190262486 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33157;LSEQ=TTTATGTACATTTTATTTCC;RSEQ=AACATAAAAATATGTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:174:130:56,74:21,23:44,130:0.7471:2,2:26.2:1:30.9:1:0.6031:1.20521:60:129:0.7457:0:1.1 0/1:259:128:52,76:60,71:131,128:0.4942:2,2:25.8:1:29.7:1:0.45208:1.23409:60:127:0.4922:0:1.1 +4 190262598 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49206;SOR=Inf;LSEQ=GGATAGGGGACTTTGAATAA;RSEQ=ATTATAAAATAGGGAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:2,29:31,0:0:2,0:21.6:1:29.2:1:1:0:59.5:62:1:0:0.1 0/1:32:2:0,2:1,29:30,2:0.0625:1,0:31.5:1:33.5:1:1:0:60:4:0.0625:0:1 +5 30352 . A T 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55324;SOR=0;LSEQ=TCAAGTGTGGTGGATGCCTC;RSEQ=TCTAGGAAAGGCCCTCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:0,3:87,52:139,3:0.0211:2,0:8.7:1:20.7:1:0.05616:0:60:2:0.0147:0:2 0/0:76:0:0,0:39,37:76,0:0:2,0:24.1:1:29.6:1:1:0:59.4:75:1:0:0.2 +5 30358 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.12664;SOR=Inf;LSEQ=GTGGTGGATGCCTCATCTAG;RSEQ=AAAGGCCCTCACCACGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:99,63:162,0:0:2,0:25.7:1:31:1:1:0:60:31.4:1:0:0.2 0/1:90:2:1,1:46,42:88,2:0.0222:2,2:30.5:1:27.5:1:1:1.09413:60:4:0.0233:0:1 +5 30397 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54145;SOR=0;LSEQ=GACTCCTTCTACTCACTCAA;RSEQ=TGTACTTACTTCTCTTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:79,83:162,2:0.0121:2,2:21.5:1:29:1:1:1.05:60:4:0.0123:0:1 0/0:90:0:0,0:42,48:90,0:0:2,0:26.8:1:31.6:1:1:0:60:89:1:0:0.2 +5 30414 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12326;SOR=Inf;LSEQ=CAACTGTACTTACTTCTCTT;RSEQ=TTCCTCTATGAACACTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:55,79:134,0:0:2,0:27.3:1:29.6:1:1:0:59.8:43.667:1:0:0.2 0/1:73:2:1,1:30,41:71,2:0.0274:2,2:12.5:1:30:1:1:1.36:60:4:0.0282:0:1.5 +5 218356 . T C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71291;SOR=1.15469;LSEQ=CCACTGCAGCCCCGCTCGAC;RSEQ=CCGGCGTGGTGCGCAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:25:24,1:92,12:104,25:0.1938:2,1:26.2:1:31.4:1:0.4608:3.11:60:24:0.189:0:1.1 0/1:69:15:13,2:49,5:54,15:0.2174:2,2:24.4:1:30.4:1:0.64092:1.49792:60:30:0.2174:0:1 +5 218381 . T TC 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.7746;SOR=1.09736;LSEQ=CGTGGTGCGCAGGCGCGGTA;RSEQ=CCCCCCTCCCCCGCCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:45:38,7:142,34:176,45:0.2027:2,2:22.2:1:31.6:1:0.6704:1.30:60:90:0.2074:0.0676:0.6 0/1:110:24:19,5:69,16:85,24:0.2182:2,2:26.3:1:29.9:1:0.77728:1.13351:59.8:48:0.2222:0.0636:0.8 +5 218466 . C T 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0615;SOR=4.78674;LSEQ=GGACTGCGCGGCGGCAACAG;RSEQ=AGACATGTCGGGGGTCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:922:2:0,2:401,516:917,2:0.0022:2,0:11.5:1:20:1:0.50757:0:51:1:0.0011:0:2 0/1:582:6:2,4:262,314:576,6:0.0103:2,2:22.2:1:26.8:1:0.69398:1.66738:57.8:12:0.0108:0:1 +5 218467 . A G 164 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=78.49293;LSEQ=GACTGCGCGGCGGCAACAGC;RSEQ=GACATGTCGGGGGTCCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:925:1:1,0:401,522:923,1:0.0011:2,0:25:0:10:0:0.43506:0:24:0:0:0:6 0/1:586:46:22,24:242,296:538,46:0.0785:2,2:25.7:1:29.7:1:0.75863:1.12:52.7:92:0.082:0:1.2 +5 218598 . G A 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59207;SOR=3.04364;LSEQ=GCGGCGGTAGGAGCGGGACG;RSEQ=TCCCCAGCGGGTCCGAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:3,1:4,3:0.4286:2,2:38.3:1:23.3:1:1:1.41418:32.7:2:0.3333:0:1.7 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:28.2:1:28:1:1:1.41:36.2:10:0.7143:0:2 +5 223415 . C T 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGACCTGGGGGCTCAGTC;RSEQ=TTCCTTGCCCCTTGGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:42.5:1:32.5:1:1:0:25:4:0.5:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:36:0:27:0:1:0:21:2:1:0:0 +5 223646 . A T 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTTTTCACTTCACTGTTG;RSEQ=TGGGAACAAGAGGGCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2009:0:0,0:936,1072:2008,0:0:2,0:27.7:1:30.7:1:1:0:36:73.37:1:0:0.1 0/1:1136:31:14,17:538,566:1104,31:0.0273:2,2:31.7:1:29.3:1:0.71956:1.15407:32.3:62:0.0276:0:1.2 +5 223890 . G C 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACATTTTTACTTGTATCT;RSEQ=TTATGTATCTATAAACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:0,6:0,23:23,6:0.2069:1,0:31.5:1:29.8:1:1:0:35.3:5:0.1852:0:2.5 0/0:1:0:0,0:0,1:1,0:0:0,0:42:0:33:0:1:0:23:2:1:0:0 +5 223909 . GATTTAA G 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTATGTATCTATAAACTA;RSEQ=ATTTAGATCAAGTAAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:6:0,6:1,26:27,6:0.1818:1,0:29.3:1:32.6:1:1:0:33.8:12:0.1875:0.0303:1.7 0/0:1:0:0,0:0,1:1,0:0:0,0:39:0:33:0:1:0:23:2:1:0:0 +5 223958 . T C 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAAAATAAAATGAACAG;RSEQ=GTCTGCTGTGATAGATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:0,5:4,14:18,5:0.2174:2,0:17.4:1:28.2:1:0.53924:0:48.4:10:0.2174:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 224105 . A AT 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTGTATTTAGTGAGCCT;RSEQ=TCTCTGTTGAAAAACTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:3,3:6,4:0.4:2,2:36.5:1:30.8:1:1:1:57:8:0.4:0:0.3 0/0:1:0:0,0:1,0:1,0:0:0,0:17:0:29:0:1:0:60:2:1:0:0 +5 224196 . A T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56203;SOR=0;LSEQ=CTTGGCACCTTCTCAGGCAT;RSEQ=AGCATAGGCACGGCCCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:3,1:20,3:23,4:0.1429:2,2:37.8:1:31.3:1:0.49544:2.14404:23.5:8:0.1538:0:3 0/0:7:0:0,0:5,2:7,0:0:2,0:21.6:1:26.3:1:1:0:23.1:6:1:0:0.3 +5 224207 . C T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55508;SOR=0;LSEQ=CTCAGGCATAAGCATAGGCA;RSEQ=GGCCCTGAAGTAGAGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:3,1:21,3:24,4:0.1429:2,2:44.8:1:32:1:0.48103:2.24802:23.5:8:0.1481:0:3 0/0:8:0:0,0:6,2:8,0:0:2,0:28.8:1:32:1:1:0:23.8:16:1:0:0.3 +5 224211 . C T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55739;SOR=0;LSEQ=GGCATAAGCATAGGCACGGC;RSEQ=CTGAAGTAGAGTTGTGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:3,1:22,3:25,4:0.1379:2,2:44.8:1:32.5:1:0.46739:2.35188:23.5:8:0.1379:0:3 0/0:8:0:0,0:6,2:8,0:0:2,0:32.1:1:31.1:1:1:0:23.8:16:1:0:0.3 +5 224268 . G A 95 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43136;SOR=0.33804;LSEQ=GGATAGACCCTCTACCATTC;RSEQ=TAGAATCTGATTGTCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:9:8,1:38,1:39,9:0.1875:1,2:25.7:1:30.2:1:0.34309:4.53691:33.6:8:0.1739:0:1 0/1:14:1:1,0:12,1:13,1:0.0714:1,0:23:0:31:0:1:0:28:2:0.0714:0:1 +5 224397 . A G 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCCTTTTATCTTTGTCA;RSEQ=GCTCTTTCACTGTCACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:204,48:252,0:0:2,0:19.8:1:30.4:1:1:0:33.3:24.2:1:0:0.1 0/1:127:14:11,3:90,23:113,14:0.1102:2,2:23.9:1:31.6:1:1:1.06665:28.4:28:0.1111:0:1.1 +5 224476 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.53843;SOR=0;LSEQ=GTGAATTTTTCTTTTCCAGA;RSEQ=TTCTGCTCAGTATCCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:134,43:177,2:0.0112:2,2:18.5:1:32:1:0.43224:3.09188:60:4:0.0116:0:1.5 0/0:100:0:0,0:69,31:100,0:0:2,0:17.7:1:29.7:1:1:0:23.5:200:1:0:0.1 +5 224692 . G T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22668;SOR=1.69903;LSEQ=TGCAGGTCCCGCGCAGCCTC;RSEQ=CACTTTCTACCTGGGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:29:3,26:4,85:89,29:0.2458:1,2:28.1:1:29.4:1:0.36072:2.43:28.9:58:0.2522:0:1.3 0/1:42:15:0,15:2,25:27,15:0.3571:2,1:25.9:1:26.3:1:0.52962:0:30.7:14:0.35:0:1.5 +5 224904 . T C 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28327;SOR=4.19245;LSEQ=TGCCTACTACCTTCCCCACC;RSEQ=ACCCCCGCCACCCCAACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:1,4:1,14:15,5:0.25:1,2:19.6:1:33:1:0.44737:3.24:46.8:10:0.2632:0:1.2 1/0:5:3:1,2:1,1:2,3:0.6:2,2:12.7:1:30.7:1:1:1.7321:47.7:6:0.6:0:1 +5 225267 . C A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56006;SOR=0;LSEQ=GTAGCCTTTCACTCACTGCT;RSEQ=CAGTCAGCCCTTCCTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:5,0:21,0:21,5:0.1923:1,0:36.4:1:28:1:1:0:33.8:10:0.1923:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:16.6:1:32.2:1:1:0:52.6:10:1:0:0 +5 225328 . A AG 94 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.54795;LSEQ=AGATGAGGAGACTGAGGCTA;RSEQ=GGATGGAATCACTGGGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:7:7,0:58,3:61,7:0.1029:1,0:14.3:1:33.8:1:1:0:36.4:14:0.1077:0.0441:0.3 0/1:17:1:1,0:14,1:15,1:0.0588:1,0:11:0:33:0:1:0:25:2:0.0588:0:0 +5 225768 . G C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28365;LSEQ=AAGCAATTGAGGCGGATGTG;RSEQ=CAGCCAAAAGAATGGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:324:193:31,162:16,114:130,193:0.5957:2,2:23.5:1:31.6:1:0.42177:1.36:59.7:95.5:0.6025:0:1.1 0/1:119:35:7,28:2,82:84,35:0.2941:1,2:25.4:1:29.7:1:0.00264:10.01:59.8:16.5:0.287:0:1 +5 225774 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.19967;SOR=1.40268;LSEQ=TTGAGGCGGATGTGGCAGCC;RSEQ=AAAGAATGGTGATGAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:70:8,62:26,185:211,70:0.2491:2,2:25.4:1:32.1:1:1:1.08886:55.3:34:0.2464:0:1.8 0/1:107:34:0,34:6,67:73,34:0.3178:2,1:25.4:1:31.1:1:0.17361:0:54.7:68:0.3178:0:1.7 +5 225796 . T C 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02943;LSEQ=AAGAATGGTGATGAGCAAAG;RSEQ=TCACAAGAAGAGTCTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:55:7,48:29,128:157,55:0.2594:2,2:22.7:1:33.4:1:0.40683:1.55058:56.2:54:0.2596:0:2 0/1:83:22:0,22:6,55:61,22:0.2651:2,1:26.6:1:32.1:1:0.33387:0:56.7:21:0.2561:0:2.1 +5 225941 . C T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01647;SOR=1.94742;LSEQ=TGTTTAGTGTAGATTAGCTG;RSEQ=GAATATCTTGACTCCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:42:38,4:186,24:210,42:0.1667:2,2:32.4:1:30.3:1:1:1.22:37.2:84:0.1694:0:1.1 0/1:114:32:30,2:69,13:82,32:0.2807:2,2:32:1:29:1:0.22713:2.81:37.6:31:0.2768:0:1 +5 226064 . G T 32 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0362;SOR=Inf;LSEQ=TTTATCAGCGTGCATTTGGT;RSEQ=GACAGAGCCTCAAGTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:0:0,0:145,207:352,0:0:2,0:12.4:1:31.2:1:1:0:46.9:351:1:0:0.1 0/1:175:3:0,3:62,110:172,3:0.0171:2,0:7.3:1:20.7:1:0.55314:0:41:2:0.0117:0:1.7 +5 226160 . A C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02668;SOR=1.39272;LSEQ=TATTGCACACCTTATATGGA;RSEQ=GGGTAAGGCCGCCCCCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:150:43,107:200,456:656,150:0.1856:2,2:22.3:1:30.9:1:0.69419:1.09129:47:300:0.1873:0:1.2 0/1:390:94:39,55:90,206:296,94:0.241:2,2:26.1:1:29.8:1:0.05874:1.62:50.4:93:0.2403:0:1.2 +5 226222 . T C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.36432;SOR=0.59589;LSEQ=GCTGGGGCTTATGGTGACAG;RSEQ=GGGGAATGGGTTAGCGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:20:2,18:34,153:187,20:0.0962:2,2:9.3:1:30.3:1:0.5378:1.99439:32.2:19:0.0936:0:2 0/1:84:5:1,4:17,62:79,5:0.0595:2,2:7.6:1:28.4:1:1:1.0956:33.8:10:0.0602:0:2.2 +5 226224 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.08148;SOR=Inf;LSEQ=TGGGGCTTATGGTGACAGTG;RSEQ=GGAATGGGTTAGCGTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:34,164:198,0:0:2,0:18.7:1:31.3:1:1:0:45.6:48.5:0.9949:0:0.3 0/1:80:2:1,1:17,61:78,2:0.025:2,2:22:0:31.5:1:0.40158:3.52:21:4:0.0253:0:1.5 +5 226264 . C T 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15606;SOR=3.74736;LSEQ=AGTGAGTCAGCCAGAGATTA;RSEQ=GTAAAAAGCAACAGAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:0,2:5,61:66,2:0.0294:2,0:18.5:1:20:1:1:0:49:1:0.0152:0:1.5 0/1:29:3:0,3:4,22:26,3:0.1034:2,0:22.3:1:29.7:1:1:0:47.3:6:0.1034:0:1.3 +5 226376 . A G 106 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.75455;LSEQ=GGCAGTGTGTGACTTCTTGC;RSEQ=TCTATGTCAGAAAGTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:10:1,9:1,29:30,10:0.25:1,2:33.2:1:32:1:0.44231:3.11:60:20:0.25:0:1.7 0/1:5:1:0,1:1,3:4,1:0.2:2,0:9:0:33:0:1:0:60:2:0.2:0:1 +5 226453 . G A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0.37796;LSEQ=GTGACACTCAACATACAAGA;RSEQ=CAGAGCAAGCAGGCCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:27:1:31.3:1:1:0:55.3:12:0.8571:0:1.2 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:14:1:28.5:1:1:0:55.5:4:0.6667:0:1 +5 228129 . G A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78518;LSEQ=CCTTGTCTGTACTGCTCGGC;RSEQ=TGGAATGCCTCTCGGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:8:8,0:24,1:25,8:0.2424:1,0:30.3:1:32:1:1:0:24.6:16:0.2424:0:1 0/1:15:3:3,0:11,1:12,3:0.2:2,0:41.3:1:30.3:1:1:0:22:6:0.2:0:1 +5 228278 . CT C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09749;SOR=1.86734;LSEQ=TTGGCTTAACACTTCTTGCC;RSEQ=TTTTTTTTCCTTTCTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:18:15,3:293,82:375,18:0.045:2,2:12.6:1:32.4:1:0.77386:1.40:53.5:36:0.0451:0.0225:0.8 0/1:210:17:14,3:143,49:192,17:0.081:2,2:11.6:1:29.7:1:0.57163:1.60:57.6:34:0.0813:0.0476:1.1 +5 228279 . T C 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.10206;SOR=0;LSEQ=TGGCTTAACACTTCTTGCCC;RSEQ=TTTTTTTTCCTTTCTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:7:5,2:293,82:375,7:0.0175:2,2:8.6:1:31.1:1:0.65146:1.4278:50:14:0.0175:0:1.7 0/0:210:0:0,0:143,49:192,0:0:2,0:29.6:1:30.6:1:1:0:48.6:191:0.9139:0:0.2 +5 228293 . C T 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12689;SOR=5.58892;LSEQ=TTGCCCTTTTTTTTTCCTTT;RSEQ=TTTTAGTCTCTGCGATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:1:1,0:321,90:411,1:0.0024:2,0:22:0:13:0:1:0:25:0:0:0:4 0/1:223:3:2,1:163,57:220,3:0.0135:2,2:28.7:1:23:1:1:1.42735:36:2:0.0094:0:1 +5 228362 . T C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.46262;SOR=1.09364;LSEQ=TTGGATCTCCTGATGGAGAA;RSEQ=GGGGAGTGCCGTGGTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1112:238:141,97:448,426:874,238:0.214:2,2:26.2:1:31:1:0.03353:1.38:34.6:78.333:0.214:0:1.1 0/1:597:137:73,64:242,217:459,137:0.2295:2,2:24.6:1:29.9:1:0.92261:1.02:37.2:136:0.2309:0:1.1 +5 228687 . C A 73 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.40171;SOR=3.74166;LSEQ=AGTAGATGGTAGTGGTTGCC;RSEQ=TCAGGTTCACAGCTTACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:0,20:20,5:0.2:1,0:23.6:1:31.6:1:1:0:54:10:0.2:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:30:0:30:0:1:0:53:2:0.5:0:1 +5 228713 . A AT 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACAGCTTACCTCTCCCA;RSEQ=TTTAGATGAGGGAACTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:1,3:0,21:21,4:0.16:1,2:24.5:1:30.5:1:0.16:0:52.5:8:0.16:0.08:0.8 0/0:1:0:0,0:0,1:1,0:0:0,0:4:0:31:0:1:0:53:2:1:0:1 +5 230704 . C G 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGCCGAGATCGCACCACT;RSEQ=TACTCCAGCCTGGTCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:3,0:14,0:14,3:0.1765:1,0:27.7:1:33:1:1:0:55.3:6:0.1765:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 230749 . T TAAATA 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATCCTATCTCAAAATAAA;RSEQ=AAATAAAATACAAATGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:4,0:32,1:33,4:0.1081:1,0:29.8:1:28.3:1:1:0:47:8:0.1081:0.027:1.8 0/0:4:0:0,0:4,0:4,0:0:0,0:17.5:1:31.5:1:1:0:58.5:8:1:0:0 +5 230778 . T C 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33864;SOR=0;LSEQ=TACAAATGGAAGTCCTTTCT;RSEQ=TGATCCCAGGCTTCTATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:8,0:56,2:58,8:0.1212:1,0:23.5:1:32.4:1:1:0:32.8:16:0.1212:0:2.6 0/0:14:0:0,0:14,0:14,0:0:1,0:21.1:1:31.4:1:1:0:59.6:28:1:0:0.1 +5 230822 . G C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.80185;SOR=0.74459;LSEQ=TGTGCAGGGTAGCAGCACCA;RSEQ=TGGCGCGGCCCCTAGTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:20:20,0:108,5:113,20:0.1504:1,1:23.4:1:32.6:1:1:0:31.2:40:0.1504:0:2.4 0/1:43:5:5,0:35,3:38,5:0.1163:2,0:13.8:1:32.8:1:1:0:39.2:10:0.119:0:2 +5 230828 . C T 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.64812;SOR=0.73917;LSEQ=GGGTAGCAGCACCAGTGGCG;RSEQ=GGCCCCTAGTGATATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:24:24,0:118,5:123,24:0.1622:1,1:21.9:1:30.4:1:0.59199:0:36:48:0.1667:0:2.3 0/1:48:6:6,0:39,3:42,6:0.125:2,0:16.8:1:30.8:1:1:0:42.7:12:0.1304:0:1.8 +5 230980 . A G 342 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00883;LSEQ=GTGTGCAGTCACTGCTCTCT;RSEQ=TTGTTTCCAGAGGCTACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1601:1599:932,667:1,0:1,1599:0.9988:0,2:25.3:1:32.2:1:1:0:43.7:93.059:0.9987:0:1.1 1/1:861:754:432,322:59,46:105,754:0.8757:2,2:25.4:1:31.1:1:0.83404:1.05:42:82.778:0.8744:0:1.1 +5 231111 . T C 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3508;LSEQ=GAGTTTGTTCAGTTCCACCC;RSEQ=ACAGGTAGGGCAGGACGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:868:674:220,454:69,124:193,674:0.7765:2,2:30.3:1:31.3:1:0.43626:1.14812:43.7:38.647:0.772:0:1.3 1/0:550:302:96,206:102,142:244,302:0.5491:2,2:32.8:1:30.4:1:0.01595:1.54009:41.5:42.143:0.5463:0:1.5 +5 231143 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00858;SOR=1.43142;LSEQ=AGGACGCCTTGCCCGGCAGG;RSEQ=GTTTGGCTTGTGTGTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:935:164:38,126:217,554:771,164:0.1754:2,2:32.3:1:30.3:1:0.2102:1.2984:39.2:81:0.1761:0:1.8 0/1:514:120:34,86:115,267:382,120:0.2335:2,2:32:1:29.2:1:0.73281:1.08928:38.1:39:0.2303:0:1.9 +5 231301 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=TTTCCCACACTCCCCTTCCC;RSEQ=TAAGGCAGTTTGGGCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:0,2:2,60:62,2:0.0313:1,0:11.5:1:26:1:1:0:31:4:0.0323:0:2.5 0/0:18:0:0,0:1,17:18,0:0:1,0:16.4:1:30.9:1:1:0:43.5:17:1:0:0.1 +5 231337 . A C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCGTCTTATGTATTTCTC;RSEQ=AGAGCGCTAAACCCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:0,3:0,29:29,3:0.0938:1,0:38.7:1:32:1:1:0:34.3:6:0.0968:0:2 0/0:4:0:0,0:0,4:4,0:0:0,0:24:1:30.3:1:1:0:39.3:8:1:0:0 +5 231463 . TCAGGAGTTCGAGAC T 64 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGGCGGATCACCTGAGG;RSEQ=CAGCCTGACCAACATGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:0,4:0,6:6,4:0.4:0,0:24.3:1:32:1:1:0:40.8:8:0.4:0.1:0.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 233325 . G A 81 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACACTGGGCTGTAATCAGA;RSEQ=TATTGGCCAGAGGTCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:28.2:1:31.5:1:1:0:22.8:12:1:0:2.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 233362 . T G 89 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGGGCCGGCCTTTCTCCTC;RSEQ=CTGGGGACACCGCTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:28.1:1:29.8:1:1:0:22.1:16:1:0:1.9 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 233473 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.72332;SOR=1.13893;LSEQ=TCTTGCTGTGCAGTTTTGCA;RSEQ=ATAATGCCTTCTGCTTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:29:28,1:138,3:141,29:0.1706:1,1:21.4:1:32.2:1:0.53024:1.6373:50.1:58:0.1726:0:1.9 0/1:79:15:15,0:63,1:64,15:0.1899:1,1:25.9:1:31.2:1:1:0:48.3:30:0.1899:0:1.9 +5 233509 . CA C 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.31008;SOR=0;LSEQ=TATCTTTTTCCTCTTTCCCC;RSEQ=AAAAATGTCTTGAAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:4:3,1:326,38:364,4:0.0109:2,2:26.5:1:30.5:1:0.3624:2.8477:60:8:0.011:0:0 0/0:176:0:0,0:146,30:176,0:0:2,0:22.3:1:29.1:1:1:0:58.9:43:1:0:0.6 +5 233517 . G A 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.07145;SOR=1.45485;LSEQ=TCCTCTTTCCCCCAAAAAAT;RSEQ=TCTTGAAAAAAATAATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:77:70,7:309,56:365,77:0.1738:2,2:24.2:1:28.6:1:0.20812:1.81:53.1:24.667:0.1713:0:2.2 0/1:209:49:40,9:124,36:160,49:0.2344:2,2:21.4:1:28.3:1:0.69153:1.29:54.3:48:0.2341:0:2 +5 233572 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00092;SOR=1.517;LSEQ=TAGCAATTGTTAGGTAATAA;RSEQ=TATGTGTGGTTTTTTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:997:196:135,61:505,294:799,196:0.1966:2,2:31.1:1:33.2:1:0.15716:1.29:38:195:0.1998:0:1.4 0/1:554:150:90,60:240,162:402,150:0.2708:2,2:29.7:1:31.2:1:1:1.01:37.6:300:0.2757:0:1.4 +5 233677 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11905;SOR=Inf;LSEQ=AGTCAAGGCGAAAGGTTTAT;RSEQ=GAGCGATACGCCCCTGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:139,234:373,0:0:2,0:20.5:1:31.2:1:1:0:41.3:61.167:1:0:0.2 0/1:197:2:1,1:82,113:195,2:0.0102:2,2:25:1:31:0:1:1.38:44:4:0.0102:0:1 +5 233734 . C G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22146;SOR=1.28594;LSEQ=AGAGATGTGGTGTCTCGGTC;RSEQ=ATGACTCTGGAGATCCGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:69:24,45:248,401:649,69:0.0961:2,2:31.8:1:32:1:0.60431:1.15933:27.8:138:0.0966:0:1.2 0/1:399:48:13,35:148,203:351,48:0.1203:2,2:36:1:31.2:1:0.05903:1.95975:26.9:96:0.1224:0:1.1 +5 234989 . C G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATGCACTTACCAAGGACA;RSEQ=CTGCAGCAGGCTGTGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:15,2:0.1176:1,0:17.5:1:32.5:1:1:0:44:4:0.1176:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:33:0:1:0:35:2:1:0:0 +5 235118 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGCTTAGAAAAGATTTG;RSEQ=TGAGAGGGTGACCATACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:2,0:130,10:140,2:0.014:2,0:39.5:1:31.5:1:1:0:29:4:0.0144:0:1 0/0:59:0:0,0:56,3:59,0:0:2,0:27.2:1:29.1:1:1:0:43.3:58:1:0:0.1 +5 235548 . T C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=2.37908;LSEQ=TTAGATCTTACAGGAAAAGA;RSEQ=AGATGTTTCCTTCAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:60:5,55:9,210:219,60:0.2151:1,2:23.6:1:31.7:1:0.18958:2.11:52.2:19:0.208:0:1.3 0/1:124:49:4,45:5,70:75,49:0.3952:2,2:25.2:1:31.8:1:0.73855:1.24:53.2:48:0.3967:0:1.2 +5 235608 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02902;LSEQ=TTGCACTTTAAATTTCTATT;RSEQ=CCGGAGGATGGAGGGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:19:1,18:0,66:66,19:0.2235:1,1:19.2:1:31.8:1:0.22353:0:52.2:18:0.2143:0:1.9 0/1:35:8:0,8:1,26:27,8:0.2286:1,0:25.3:1:32:1:1:0:51.9:16:0.2286:0:1.6 +5 236142 . C T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=GATACGGTCTTTACTTCCCT;RSEQ=TCTTTTTTTTTCTTGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:42.5:1:29.5:1:1:0:26.5:4:1:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:38:0:32:0:1:0:44:2:1:0:0 +5 236144 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TACGGTCTTTACTTCCCTCT;RSEQ=TTTTTTTTTCTTGGAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:42.5:1:30:1:1:0:26.5:4:1:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:36:0:32:0:1:0:44:2:1:0:0 +5 236288 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCTGGGATTACAGGCACC;RSEQ=GCCATTATGCCCCGCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:9.3:1:32:1:1:0:26:6:0.6:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:4:0:25:0:1:0:37:2:1:0:0 +5 236405 . C G 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25205;SOR=1.44713;LSEQ=CACCTCAGCCTCCCAAAGTG;RSEQ=TGAGATTACAGGCGTGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:46:46,0:146,4:150,46:0.2347:1,1:24.1:1:31.8:1:0.57469:0:38.6:45:0.232:0:1.2 0/1:65:20:18,2:44,1:45,20:0.3077:1,2:22.6:1:30.5:1:0.22184:4.75445:43:19:0.2969:0:1 +5 236424 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57151;SOR=0;LSEQ=GCTGAGATTACAGGCGTGAG;RSEQ=CACCACGCCTGGCCTACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:3:2,1:260,9:269,3:0.011:1,2:10:1:29:1:0.10667:13.9869:42:6:0.0112:0:1.3 0/0:95:0:0,0:91,4:95,0:0:1,0:24.9:1:32.1:1:1:0:41.5:190:1:0:0.3 +5 236458 . T C 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17851;SOR=5.45548;LSEQ=CTACTTCCCTCTCTCTGACC;RSEQ=GCAGCACAGACACCCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:1:1,0:336,60:396,1:0.0025:2,0:27:0:33:0:1:0:30:2:0.0026:0:1 0/1:147:2:1,1:119,26:145,2:0.0136:2,2:28:0:31.5:1:0.33464:4.51021:60:4:0.0137:0:1.5 +5 236571 . A G 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1511;SOR=Inf;LSEQ=GCACGTGAATGGCCAGGATC;RSEQ=GATTGTGCCCGGCCTGTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:51,51:102,0:0:2,0:3.6:1:30.5:1:1:0:21:101:0.9902:0:0.1 0/1:66:2:1,1:27,37:64,2:0.0303:2,2:7.5:1:27:1:1:1.36:20:4:0.0303:0:2 +5 236587 . G T 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01054;SOR=10.78525;LSEQ=GATCAGATTGTGCCCGGCCT;RSEQ=TACGCCTGTGGGGAGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:1:0,1:190,205:395,1:0.0025:2,0:9:0:32:0:1:0:26:2:0.0026:0:1 0/1:225:6:1,5:105,113:218,6:0.0267:2,2:11.2:1:27.8:1:0.2165:4.61948:29.3:12:0.0271:0:1.2 +5 236604 . C T 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16529;SOR=0.20153;LSEQ=CCTGTACGCCTGTGGGGAGG;RSEQ=CGCCTGTGCCTCGGTACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:8:2,6:339,389:728,8:0.0109:2,2:18:1:25.4:1:0.29701:2.61119:37.3:3:0.0083:0:1.1 0/0:453:1:0,1:210,242:452,1:0.0022:2,0:1:0:24:0:1:0:60:2:0.0022:0:1 +5 236628 . C T 86 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=17.9789;LSEQ=CTGTGCCTCGGTACATGGTG;RSEQ=CAACCGCCTCGGGGCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1274:1:0,1:606,667:1273,1:8e-04:2,0:1:0:26:0:1:0:24:2:8e-04:0:1 0/1:789:11:5,6:362,416:778,11:0.0139:2,2:6.7:1:25.1:1:1:1.04418:24.2:4.5:0.0116:0:4.3 +5 236649 . C T 137 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.26174;LSEQ=CAACCGCCTCGGGGCAAACT;RSEQ=GCTCTTGGACCTGGTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1357:3:2,1:644,710:1354,3:0.0022:2,2:21:0:32.7:1:0.60762:2.20:22.3:6:0.0022:0:3 0/1:848:26:12,14:387,434:821,26:0.0307:2,2:24.2:1:29.2:1:1:1.04028:24.3:12:0.0286:0:3.5 +5 236650 . G A 143 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=51.33765;LSEQ=AACCGCCTCGGGGCAAACTC;RSEQ=CTCTTGGACCTGGTTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1357:1:0,1:646,709:1355,1:7e-04:2,0:38:0:15:0:1:0:60:0:0:0:3 0/1:850:31:13,18:388,431:819,31:0.0365:2,2:34.8:1:29:1:0.5871:1.24615:29.1:30:0.0358:0:1.1 +5 236653 . C A 133 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=14.15746;LSEQ=CGCCTCGGGGCAAACTCGCT;RSEQ=TTGGACCTGGTTGTCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1352:3:2,1:641,707:1348,3:0.0022:2,2:25:0:31:1:0.60755:2.20:22.3:6:0.0023:0:3 0/1:851:26:13,13:389,436:825,26:0.0306:2,2:25.2:1:28.3:1:0.84314:1.12:23.7:12:0.0288:0:3.5 +5 236678 . G A 133 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.21638;LSEQ=ACCTGGTTGTCTTTGGTCGG;RSEQ=CATGTGCCCTGAGCATCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1034:4:3,1:496,534:1030,4:0.0039:2,2:12.8:1:30:1:0.35775:3.23:22.8:8:0.0039:0:2.5 0/1:646:27:14,13:299,320:619,27:0.0418:2,2:36.3:1:28.1:1:0.84456:1.15:27.9:54:0.0425:0:3.4 +5 236932 . T A 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.083;SOR=0;LSEQ=CACCACACCTGGCTAATTTT;RSEQ=AAAAAAATTTATTTTGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:0,16:0,5:5,16:0.7619:0,1:28.3:1:29.6:1:1:0:23.3:7:0.7368:0:1.4 0/0:2:0:0,0:0,2:2,0:0:0,0:24:1:29:0:1:0:29:4:1:0:0 +5 240350 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10245;SOR=Inf;LSEQ=GCTGGCAGTGTGTTAGCTCA;RSEQ=GAGACTTACAGAGTTTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:163,7:170,0:0:1,0:24.1:1:33.1:1:1:0:41.2:55.667:1:0:0.1 0/1:81:2:2,0:72,7:79,2:0.0247:2,0:24.5:1:32:0:1:0:29:4:0.0247:0:1 +5 240457 . CT C 84 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04454;SOR=4.02155;LSEQ=TTTCAAAAGTTAAATTCTAG;RSEQ=TTTTTTTGTTTTAGGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:714:3:2,1:466,245:711,3:0.0042:2,2:38.3:1:34.7:1:1:1.05:26.7:6:0.0043:0:0 0/1:419:7:5,2:246,166:412,7:0.0167:2,2:27.6:1:30:1:0.70701:1.69:31:14:0.0169:0:0.1 +5 240502 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28769;SOR=3.6602;LSEQ=TCCCTCCAATTAAACCAAAC;RSEQ=CTGGGGAAGAATCTGTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:1:1,0:194,118:312,1:0.0032:2,0:1:0:27:0:1:0:21:2:0.0032:0:1 0/1:172:2:2,0:91,79:170,2:0.0116:2,0:12:1:27.5:1:0.50041:0:23:4:0.0119:0:1 +5 240581 . G A 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5441;SOR=0;LSEQ=AACATCGGAACTGCGACTCA;RSEQ=CATGCAGAAGGTAAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:24,85:109,2:0.018:2,2:40:0:29.5:1:0.40131:3.49:23:4:0.0183:0:1 0/0:59:0:0,0:13,46:59,0:0:2,0:40.8:1:31.3:1:1:0:23.7:118:1:0:0.1 +5 240584 . T G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5441;SOR=0;LSEQ=ATCGGAACTGCGACTCAGCA;RSEQ=GCAGAAGGTAAGAGCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:24,85:109,2:0.018:2,2:39.5:1:33.5:1:0.40131:3.49:21:4:0.018:0:1 0/0:59:0:0,0:13,46:59,0:0:2,0:43:1:29.4:1:1:0:23.7:58:1:0:0.1 +5 240664 . A C 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04338;SOR=0;LSEQ=TGCACTGGTTTTGTTTTTTA;RSEQ=AAACTAGATCTAGGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:1,10:11,5:0.3125:2,0:10.2:1:28.4:1:1:0:20.4:10:0.3125:0:1.2 0/0:16:0:0,0:2,14:16,0:0:2,0:31.4:1:30.8:1:1:0:46.1:15:1:0:0.1 +5 250922 . A C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12853;LSEQ=GAAACATTTATTTATTCAGA;RSEQ=GCTTTAGTCAAAACTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:6,0:16,1:17,6:0.2609:1,0:10:1:33.8:1:1:0:29.8:12:0.2727:0:1 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:5.5:1:32.5:1:1:0:35:4:0.2857:0:1 +5 251259 . C A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63449;SOR=1.65777;LSEQ=GTGCACACTGTTGGGCCCTT;RSEQ=CTTCTGCAGGGTGGGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:2:2,0:64,248:312,2:0.0064:2,0:3:1:17.5:1:0.04365:0:42.5:1:0.0032:0:2 0/1:190:2:1,1:43,145:188,2:0.0105:2,2:11.5:1:26:1:0.41047:3.34:26.5:4:0.0106:0:1 +5 251541 . A G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00338;SOR=1.48032;LSEQ=ACCATCTACGGAGCAGAGGC;RSEQ=CGGAAGGAGTCACGGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1044:163:101,62:486,391:877,163:0.1561:2,2:24.6:1:31.3:1:0.14351:1.31:25.5:326:0.1578:0:1.1 0/1:572:123:75,48:245,204:449,123:0.215:2,2:25.1:1:29.9:1:0.21964:1.30:26:122:0.214:0:1.1 +5 251704 . G C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0307;SOR=1.51783;LSEQ=CAAAAGTAAATCCAAAAAAT;RSEQ=CCTTTTTCCCCCCTGGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1758:63:26,37:759,923:1682,63:0.0358:2,2:6.8:1:30.1:1:0.60672:1.17012:23.1:11.6:0.0337:0:1.5 0/1:1011:54:23,31:411,534:945,54:0.0534:2,2:7.2:1:29.4:1:1:1.03734:24.2:53:0.0528:0:1.6 +5 251784 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12644;SOR=Inf;LSEQ=ACCTTTTCCTTGCTTTGGGT;RSEQ=GGCATCCACTGATGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:91,160:251,0:0:2,0:12.3:1:30.5:1:1:0:50:61.75:1:0:0.1 0/1:139:2:1,1:46,91:137,2:0.0144:2,2:19.5:1:30.5:1:1:1.97:60:4:0.0148:0:1.5 +5 254756 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGACAGATTCGAGGCACC;RSEQ=CTGAAAAAGGCACTCCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:0,2:6,118:124,2:0.0157:1,0:35.5:1:32:0:1:0:34:4:0.0161:0:1 0/0:37:0:0,0:1,36:37,0:0:1,0:25.4:1:31.9:1:1:0:26.7:74:1:0:0.1 +5 254861 . C G 59 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=AAGGGTTGCTCCGTGGTGTG;RSEQ=GCCAGATGGACGTCACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:5:1:29.5:1:1:0:22.5:8:0.4444:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:50:0:30.5:1:1:0:60:4:1:0:0.5 +5 256392 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09975;SOR=Inf;LSEQ=AATTTTTCAAAAGGAACACA;RSEQ=GAGATGGCTTTTTGTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:284,133:417,0:0:2,0:14.8:1:30.5:1:1:0:32.7:40.7:1:0:0.2 0/1:193:2:1,1:137,54:191,2:0.0104:2,2:20.5:1:32.5:1:0.4898:2.52303:29:4:0.0105:0:1 +5 256393 . G T 31 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.65423;SOR=1.44131;LSEQ=ATTTTTCAAAAGGAACACAA;RSEQ=AGATGGCTTTTTGTACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:3:1,2:286,138:424,3:0.007:2,2:8.3:1:20:1:0.25147:4.12985:32.3:2:0.0047:0:1 0/1:198:2:1,1:140,56:196,2:0.0101:2,2:11.5:1:27:1:0.49392:2.48682:30:4:0.0101:0:1.5 +5 256431 . C T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01806;SOR=10.00893;LSEQ=TTTTTGTGCTTAACTTACCA;RSEQ=TGACTCTTCTTTTCAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:857:1:0,1:505,351:856,1:0.0012:2,0:1:0:26:0:0.41074:0:20:2:0.0012:0:3 0/1:432:5:3,2:260,167:427,5:0.0116:2,2:10.4:1:26.4:1:1:1.03786:48.8:10:0.0117:0:1 +5 256472 . G A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.81982;SOR=1.04228;LSEQ=ACTCTGGAATATAGACCCGT;RSEQ=ATCGACAAAACTTTGAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1181:136:79,57:537,506:1043,136:0.1152:2,2:31:1:28.9:1:0.17087:1.31:22.7:67:0.115:0:1.8 0/1:653:78:40,38:300,275:575,78:0.1194:2,2:31.7:1:28.4:1:0.90434:1.03632:22.6:38:0.1176:0:1.5 +5 256509 . G A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16939;SOR=0.77798;LSEQ=ACGAGGCTGACTGTGCCACC;RSEQ=TCCCGCCAGCCATTCGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:964:110:55,55:352,502:854,110:0.1141:2,2:18.5:1:30.3:1:0.08213:1.43:23.1:109:0.1141:0:1.9 0/1:571:52:21,31:222,297:519,52:0.0911:2,2:21.4:1:29.4:1:0.77064:1.10319:23.7:51:0.0904:0:1.8 +5 256571 . G A 39 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67707;SOR=1.65165;LSEQ=TGATGACAGAATCAGCTTTT;RSEQ=TAATTATGTATAATAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:3:3,0:45,175:220,3:0.0135:2,0:1:0:24:1:0.00949:0:36.7:6:0.0135:0:1 0/1:136:3:2,1:31,102:133,3:0.0221:2,2:8:1:25:1:0.14594:6.47:36.3:6:0.0226:0:1 +5 257801 . C A 30 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTCCACCCCCTGCCAGAG;RSEQ=ATTACTGTGAGCTCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:30:1:1:0:42:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 420898 . C T 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTCCAGAAAGAGACACCTC;RSEQ=GCGCTGCACGCACGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:3,2:5,3:0.375:2,2:22.3:1:30:1:1:1.29:51.7:6:0.375:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 420915 . GCCACGCAGCCACCCAC G 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCGCGCTGCACGCACGCA;RSEQ=CCACGCAGCCACCCACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:8,2:10,3:0.2308:2,2:17.7:1:31.9:1:0.2028:6.5151:30.7:6:0.2308:0.1538:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 420932 . C G 36 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58533;SOR=2.08426;LSEQ=GCAGCCACGCAGCCACCCAC;RSEQ=CACGCAGCCACCCACCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:8,5:13,3:0.1875:2,2:7:0:23.3:1:0.55:2.96927:31.7:2:0.1429:0:2.3 0/1:6:2:2,0:2,2:4,2:0.3333:2,0:7:0:30:1:0.46667:0:38.5:4:0.3333:0:2 +5 420941 . C ACGCACAG 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.02299;SOR=Inf;LSEQ=CAGCCACCCACCCACGCAGC;RSEQ=ACCCACCCACGCAGCACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:20,0:0:2,0:19.4:1:29.9:1:1:0:44.3:9:1:0:1.4 0/1:9:3:2,1:3,3:6,3:0.3333:2,2:15:1:29.2:1:1:1.85:29.3:6:0.3333:0.2222:1.7 +5 420948 . C G 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=3.000;MSILEN=1;SSF=0.01502;SOR=15.55541;LSEQ=CCACCCACGCAGCCACCCAC;RSEQ=CACGCAGCACGCACAGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:12,10:22,1:0.0435:2,0:7:0:32:0:1:0:25:2:0.0476:0:1 0/1:9:4:2,2:3,2:5,4:0.4444:2,2:21.5:1:25.3:1:1:1.43328:32:3:0.375:0:2 +5 420961 . A C 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.70799;SOR=0.57375;LSEQ=CACCCACCCACGCAGCACGC;RSEQ=CAGACCCACGCACGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:5,8:9,2:11,13:0.5417:2,2:27.8:1:25.6:1:0.04718:6.57028:40:2.25:0.4737:0:2.2 0/1:10:4:2,2:3,2:5,4:0.4:2,2:32:1:31:1:1:1.43328:48.8:8:0.5:0:2.3 +5 421000 . A C 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0.75545;LSEQ=CACCCACCCACGCAGCACGC;RSEQ=CAGACCCACGCACGCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:2,4:10,8:18,6:0.25:2,2:17.2:1:28.3:1:0.64041:2.40592:36.2:5:0.2273:0:3.2 0/1:15:3:2,1:6,6:12,3:0.2:2,2:13:1:26.3:1:1:1.91:45.7:2:0.1667:0:2.7 +5 421057 . A C 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.50549;SOR=4.64888;LSEQ=GCACACGCAGCCACCCACCC;RSEQ=CACAGGCGCACATACGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:2,6:8,3:0.2727:2,0:13.3:1:32:1:1:0:60:6:0.3333:0:1.3 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:27.5:1:29.5:1:1:0:60:4:0.6667:0:1 +5 820725 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50183;SOR=0;LSEQ=GCTGCACTCCACTTTCTGGC;RSEQ=ATGGTGGAGACTCTGACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:17,24:41,2:0.0455:2,2:14.5:1:32.5:1:1:1.40:60:4:0.0488:0:1 0/0:34:0:0,0:13,21:34,0:0:2,0:27.3:1:31.4:1:1:0:60:68:1:0:0.3 +5 820789 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17787;SOR=Inf;LSEQ=GGGGGCTGTGATGTGGTCCC;RSEQ=TCCCAATGGAAAGTGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:19.5:1:30.1:1:1:0:60:12:1:0:0.2 0/1:10:2:1,1:3,5:8,2:0.2:2,2:10.5:1:32:1:1:1.58:60:4:0.2:0:1 +5 1096009 . C A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGTGCAGGTCCTTGGTG;RSEQ=GACCATGAGTGACTGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1097411 . T A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51652;SOR=0;LSEQ=CCAACATCCTTCCCGTCGCC;RSEQ=CCAACACTCCCAGCAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:14,7:21,2:0.087:2,2:23:1:32.5:1:1:1.93655:60:4:0.0909:0:1.5 0/0:14:0:0,0:9,5:14,0:0:2,0:27.2:1:30.5:1:1:0:60:28:1:0:0.5 +5 1097446 . G A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49979;SOR=0.5099;LSEQ=AGAAGCAACCCCTGCTCACC;RSEQ=CAGCGTCTCCTCTGCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:6,6:6,3:9,12:0.5714:2,2:22.8:1:30:1:0.66049:1.9345:60:24:0.5714:0:1.2 0/1:15:6:3,3:5,4:9,6:0.4:2,2:22.5:1:29:1:1:1.23147:60:12:0.4:0:1.2 +5 1098903 . A C 33 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCTCTGCTCACCCAGCC;RSEQ=CCCTCTAACCCTCTGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:6:0:33.5:1:1:1:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1098920 . T A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACCCTCTAACCCTCTGC;RSEQ=CACCCAGCCGCGTCCCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:23:0:32:0:1:1:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1218114 . ATCCTGG TCC 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCAGAGTTGGCGCCTCC;RSEQ=CGCCTCCTCCCGCCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:3,3:0.5:2,2:10:1:32.4:1:1:1:60:6:0.5:0.3333:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1218135 . A T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGGCGCCTCCTCCCGCC;RSEQ=CCTCCCACCACCTCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:6,2:0.25:2,2:10:1:33:1:1:1:60:4:0.25:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:15:0:31:0:1:0:60:4:1:0:0.5 +5 1219654 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06143;SOR=Inf;LSEQ=GGGACATTCCTCATTGGCTT;RSEQ=ATCTTCACGCTGAACTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:72,60:132,0:0:2,0:26.9:1:31.9:1:1:0:59.7:25.4:1:0:0.2 0/1:44:2:1,1:21,21:42,2:0.0455:2,2:23:0:30.5:1:1:1:60:4:0.0476:0:1 +5 1219710 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCTGGACAGCTATGCCG;RSEQ=CTCCATTCCCCTGCTCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:29,47:76,2:0.0256:2,2:21:1:28.5:1:1:1.61:60:4:0.026:0:2 0/0:20:0:0,0:8,12:20,0:0:2,0:23.7:1:31.3:1:1:0:60:40:1:0:0 +5 1252950 . T C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCATCATCCCTGCCACCC;RSEQ=GGCCAGGCCCTCCATCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:47:1:31:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:32:0:1:0:60:4:1:0:1.5 +5 1253641 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGCTGGACACTCAGCC;RSEQ=TTGGCTGGACACTCGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:2,0:51,2:53,2:0.0364:1,0:23.5:1:32.5:1:1:0:60:4:0.037:0:1 0/0:13:0:0,0:10,3:13,0:0:2,0:20.3:1:32.3:1:1:0:60:26:1:0:0.1 +5 1253744 . G A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.19358;LSEQ=CCTCAGACTCCCAGCGGTGC;RSEQ=GGCCTGGGTGTGGGCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:119:117,2:129,3:132,119:0.4722:1,1:25:1:31:1:1:1.36:60:58.5:0.4718:0:1.1 0/1:68:10:7,3:53,5:58,10:0.1471:2,2:24.6:1:29.5:1:0.08754:4.39917:60:20:0.1493:0:1.1 +5 1253760 . CG C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.04874;SOR=Inf;LSEQ=GTGCGGGCCTGGGTGTGGGC;RSEQ=CCCCTCCCTCCCTGGGACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:323,6:329,0:0:1,0:24.5:1:30:1:1:0:59.9:81.25:1:0:0.4 0/1:94:2:1,1:84,8:92,2:0.0213:2,2:42.5:1:30:1:0.18325:9.95828:60:4:0.0213:0:0 +5 1253818 . C T 46 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20503;SOR=3.2049;LSEQ=GGGCTGCTGGTGTCTGCTCT;RSEQ=GGCCTGGCTGTGGGCGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:874:3:0,3:684,187:871,3:0.0034:2,0:1:0:26.7:1:0.01015:0:60:6:0.0035:0:1 0/1:366:4:1,3:275,87:362,4:0.0109:2,2:12.3:1:23.3:1:0.04756:9.40931:60:3:0.0083:0:1.8 +5 1254034 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.02267;SOR=Inf;LSEQ=CGTGTGGGTGGCCGGGCAGG;RSEQ=AGGGCCTGCACCTCGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:0:0,0:94,551:645,0:0:2,0:24.1:1:32:1:1:0:59.9:45.071:1:0:0.1 0/1:256:3:1,2:46,205:251,3:0.0117:2,2:22.3:1:27:1:0.4602:2.22:60:6:0.0118:0:1.7 +5 1254201 . T C 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.01786;SOR=Inf;LSEQ=AGCAGCCAGGGAAGAGGCTG;RSEQ=GAGAGGACACAGGTCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:18,37:55,0:0:2,0:25.4:1:29.4:1:1:0:59.2:17.333:1:0:0.2 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:12:0:28.5:1:1:1.29:60:4:0.25:0:1 +5 1254335 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02935;SOR=Inf;LSEQ=GACACCAGCGTTTAATCACA;RSEQ=AGGGCTGCCAGCGTGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:123,10:133,0:0:2,0:23.5:1:31.4:1:1:0:59.3:266:1:0:0.2 0/1:28:2:2,0:26,0:26,2:0.0714:1,0:39.5:1:31.5:1:1:0:60:4:0.0714:0:1 +5 1254358 . G A 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGCCAGCGTGGCTCCAG;RSEQ=CCCCCAGGGTCAGGCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:2,1:169,5:174,3:0.0169:1,2:33.7:1:26:1:0.09883:15.98336:60:2:0.0116:0:1.7 0/0:46:0:0,0:46,0:46,0:0:1,0:23.5:1:29.7:1:1:0:60:14.333:1:0:0.2 +5 1254360 . C A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCAGCGTGGCTCCAGGC;RSEQ=CCCAGGGTCAGGCCCGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:2,1:175,6:181,3:0.0163:1,2:34:1:24:1:0.11042:13.91699:60:2:0.0111:0:1.7 0/0:48:0:0,0:48,0:48,0:0:1,0:23.5:1:30.5:1:1:0:60:96:1:0:0.2 +5 1254681 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.06485;SOR=Inf;LSEQ=AGCTCCCCTCCCAGGAGACA;RSEQ=CGGAAAGCTGCCCACACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:461:0:0,0:92,369:461,0:0:2,0:22.5:1:31.1:1:1:0:59.9:45.1:1:0:0.1 0/1:158:2:1,1:32,124:156,2:0.0127:2,2:15.5:1:27.5:1:0.37515:3.83:60:4:0.0129:0:2 +5 1255297 . C A 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04139;SOR=0;LSEQ=GGTTAAACCACTTCCTGATG;RSEQ=GAAAAGGGGTAAGAACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:13:13,0:148,5:153,13:0.0783:1,1:25.4:1:31:1:1:0:60:26:0.0807:0:1.1 0/0:53:0:0,0:50,3:53,0:0:2,0:22.4:1:31.8:1:1:0:60:52:1:0:0 +5 1255520 . G A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13698;LSEQ=GGGAGCTGCAGCACACATGC;RSEQ=TGAAACCTGAGAGGATGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:792:338:116,222:154,298:452,338:0.4268:2,2:25.1:1:30.8:1:0.93975:1.01:60:83.5:0.4277:0:1.1 0/1:357:33:8,25:129,195:324,33:0.0924:2,2:26:1:29.2:1:0.09207:2.06344:60:66:0.0935:0:1.1 +5 1260195 . T C 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTGGGACCCCGTCTCA;RSEQ=CCTGTAAGGAGTGGCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:31.2:1:29.3:1:1:0:58.7:5:0.7143:0:2.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1260515 . G A 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.76903;SOR=1.28862;LSEQ=TCAGCCTTGCAGGCACGCGC;RSEQ=CACACACACACACACATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:9:7,2:355,56:411,9:0.021:2,2:24.8:1:31.2:1:0.35941:1.8081:60:18:0.0217:0:0.8 0/1:186:5:5,0:146,27:173,5:0.0269:2,0:21.4:1:31:1:1:0:60:10:0.0275:0:1 +5 1260752 . G A 39 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07149;SOR=7.63457;LSEQ=AATGTCAGACACAGGTGCCT;RSEQ=CCCCACACCCAGCCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:1:1,0:131,456:587,1:0.0017:2,0:1:0:23:0:0.22449:0:60:2:0.0017:0:1 0/1:233:3:2,1:51,178:229,3:0.0129:2,2:11.7:1:25:1:0.13147:6.90:60:6:0.013:0:1 +5 1261052 . G A 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTGGAGCCCTGGCTCCC;RSEQ=GGCGTCCCTCGAGTGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:1,3:4,4:0.5:2,0:29.8:1:31.5:1:1:0:56.5:8:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1264152 . A G 87 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCCCCAGGGTCTCGGGTTC;RSEQ=GAGGGACTCATGCCCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:3,8:0.7273:0,0:32.1:1:29.1:1:1:0:59.6:16:0.7273:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1264465 . A G 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.08726;SOR=Inf;LSEQ=GGTGGACGCAACGGCCCTGC;RSEQ=GCAGCACCTGCCCCAGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:363,27:390,0:0:2,0:22.5:1:30.7:1:1:0:59.9:64:1:0:0.1 0/1:164:2:1,1:144,18:162,2:0.0122:2,2:26.5:1:26:1:0.21891:7.81342:60:4:0.0123:0:1 +5 1265204 . C T 62 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGAGTTCCTGCTCAGGCG;RSEQ=GGGACCTGGCTGGGCTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:14:1:31.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1265373 . G A 53 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCTGCGGCCTCTGCTGT;RSEQ=GCCCCGGGCGTCCCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:26.8:1:26.8:1:1:0:60:3:1:0:3.3 1/1:1:1:1,0:0,0:0,1:1:0,0:36:0:27:0:1:0:60:2:1:0:1 +5 1265935 . G A 61 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTTTAAAACAAGCCCACC;RSEQ=GCTCTGTGGGGCGCCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:23.3:1:30.8:1:1:0:60:8:0.8:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1266310 . A G 128 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAAAGAGCAGCAGGAGCC;RSEQ=GGTCACCGCCTGCACTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:21,2:0,0:0,23:1:0,2:21.5:1:28.5:1:1:0:60:10.5:1:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1266322 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGCCAGGTCACCGCCT;RSEQ=CACTCACCACGTGTGTAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:28,1:29,2:0.0645:1,2:41.5:1:28.5:1:0.12688:20.14946:60:4:0.069:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:2:0:31:0:1:0:44:2:1:0:0 +5 1266713 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02155;SOR=Inf;LSEQ=TTTACGTAGTATCTGTCTAC;RSEQ=AGGGACTGAATGTCAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:581:0:0,0:128,453:581,0:0:2,0:24.5:1:31.4:1:1:0:59.9:71.625:1:0:0.1 0/1:225:3:1,2:48,172:220,3:0.0133:2,2:25:1:28:1:0.52677:1.79:60:6:0.0137:0:1.3 +5 1268552 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07754;SOR=Inf;LSEQ=ACAGAGCAGTCATGGTCTCC;RSEQ=GAGCACCAGGAATATTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:504:0:0,0:394,110:504,0:0:2,0:22.5:1:30.5:1:1:0:59.9:71:1:0:0.1 0/1:195:2:1,1:155,38:193,2:0.0103:2,2:11:1:28.5:1:0.36082:4.03928:60:4:0.0103:0:1 +5 1268768 . G A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0011;SOR=Inf;LSEQ=CCTGGGGCGGGAAGACACAG;RSEQ=TGAGAGACGGGCAGGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:937:0:0,0:338,598:936,0:0:2,0:25:1:31.7:1:1:0:60:61.4:1:0:0.1 0/1:446:6:4,2:164,276:440,6:0.0135:2,2:11.2:1:26:1:0.20443:3.36:60:12:0.0137:0:1 +5 1268866 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0597;SOR=Inf;LSEQ=CAAACGACACGTCTACCATT;RSEQ=AGCCGGCAAACACCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:7,177:184,0:0:1,0:24.4:1:32.6:1:1:0:60:91:1:0:0.2 0/1:60:2:1,1:7,51:58,2:0.0333:2,2:14:1:26:1:0.25085:6.88:60:4:0.0339:0:1 +5 1271084 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01009;SOR=Inf;LSEQ=GGCCTCGGGAGCCTGCAGCC;RSEQ=AGGAGCCGGAGGGGGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:64,3:67,0:0:1,0:26.3:1:31.4:1:1:0:59.9:32.5:1:0:0.2 0/1:8:2:1,1:6,0:6,2:0.25:0,2:14:1:31.5:1:0.25:0:60:4:0.25:0:1 +5 1271150 . GA G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGCAGAAGGGCAGTGGG;RSEQ=AGGGGCAGGAGAGAGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:166,21:187,2:0.0106:2,2:16.5:1:30.5:1:0.2198:7.7461:60:4:0.0108:0.0053:0 0/0:62:0:0,0:55,7:62,0:0:2,0:23.4:1:28.7:1:1:0:60:30:1:0:0.2 +5 1271247 . G A 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00652;SOR=Inf;LSEQ=GACTCACTTGCCCCTGATGC;RSEQ=CACGGCGTGGTGGCACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:0:0,0:378,300:678,0:0:2,0:24.7:1:30.9:1:1:0:60:83.75:1:0:0.1 0/1:393:5:3,2:220,168:388,5:0.0127:2,2:22.6:1:28.2:1:1:1.15:60:10:0.0128:0:1 +5 1271524 . T C 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0482;SOR=Inf;LSEQ=GCAGAGTGTGTGACACAGAA;RSEQ=GTCTCCTCTGGGCCACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:0,12:0,14:14,12:0.4615:1,0:26.3:1:28.8:1:1:0:60:24:0.48:0:1 1/1:5:5:0,5:0,0:0,5:1:0,0:18.8:1:30.6:1:1:0:60:10:1:0:2 +5 1272019 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00833;SOR=Inf;LSEQ=GGCCTCAAGATCAAAACTGG;RSEQ=AGAGAAGACATTTAGCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:13,1:14,0:0:1,0:22.5:1:33.3:1:1:0:60:28:1:0:0.1 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:28.5:1:1:0:60:4:1:0:1 +5 1272414 . G A 226 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03278;LSEQ=ACCTGCCGGCAGAGGAGAGG;RSEQ=CATGAGCCACAAATGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:205:73,132:238,460:698,205:0.227:2,2:25.9:1:29.5:1:0.73816:1.07:60:67.333:0.2267:0:1.1 0/0:420:4:3,1:159,257:416,4:0.0095:2,2:3.3:1:23.3:1:0.16203:4.83:60:3:0.0073:0:1 +5 1277720 . TG T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCGCTGCAGCGGGGATG;RSEQ=GGGGGGGGTCTCCTGGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1278556 . CCA C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACCATGGACACACACGTG;RSEQ=CACACACACACACCACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:2,0:36,0:36,2:0.0526:1,0:38:1:32.5:1:1:0:60:4:0.0526:0:0 0/0:13:0:0,0:12,1:13,0:0:1,0:16.9:1:31.2:1:1:0:60:26:1:0:0.1 +5 1278584 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACACACCACAAATATGCA;RSEQ=GCCACAGATACATGCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:3,0:57,0:57,3:0.05:1,0:19.3:1:31.7:1:1:0:60:6:0.0526:0:1 0/0:19:0:0,0:18,1:19,0:0:1,0:29.8:1:32:1:1:0:60:38:1:0:0.1 +5 1278975 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07483;SOR=Inf;LSEQ=ACTCAGACATCACCTCTGCC;RSEQ=TCAGGGCCTGGCCTGGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:39,281:320,0:0:2,0:22.9:1:32.9:1:1:0:60:63:1:0:0.1 0/1:121:2:1,1:10,109:119,2:0.0165:2,2:28.5:1:27.5:1:0.17424:10.44:60:4:0.0171:0:1 +5 1279224 . T G 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGGTGCACAGTCGGCCCCA;RSEQ=GTGCTGCAGGAAAGGCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:4:3,1:63,8:71,4:0.0533:2,2:21.3:1:33.8:1:0.40703:2.57929:60:8:0.0541:0:1 0/0:11:0:0,0:11,0:11,0:0:0,0:22.7:1:30.5:1:1:0:60:22:1:0:0.1 +5 1279637 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07962;SOR=Inf;LSEQ=AAGTGGATCCGGCCAAGTGC;RSEQ=CACCCCACCATAGGGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:449:0:0,0:88,360:448,0:0:2,0:23.1:1:31:1:1:0:59.9:43.8:0.9977:0:0.1 0/1:177:2:1,1:39,135:174,2:0.0113:2,2:19.5:1:28:1:0.4039:3.43:60:4:0.0113:0:1 +5 1279658 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.06998;SOR=Inf;LSEQ=CACCCCACCATAGGGACCCA;RSEQ=GGGAGAAGCAGCCCCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:30,280:310,0:0:2,0:24.9:1:31.5:1:1:0:59.9:37.75:1:0:0.1 0/1:112:2:1,1:14,95:109,2:0.0179:2,2:19.5:1:26.5:1:0.25307:6.59:60:4:0.0182:0:1 +5 1279790 . C T 117 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37649;SOR=0.2696;LSEQ=CACACGGGATCCTCATGCCA;RSEQ=ACCTCTGTCCACCTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:16:3,13:2,19:21,16:0.4324:2,2:22:1:29.4:1:0.63386:2.15:60:32:0.4324:0:1.1 0/1:6:1:0,1:1,4:5,1:0.1667:2,0:38:0:30:0:1:0:60:2:0.2:0:1 +5 1279964 . G C 117 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAAGCGGAAGCGCACGGAG;RSEQ=CTGCGCACCACAGCAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:9,3:6,2:8,12:0.6:2,2:21.3:1:32.8:1:1:1:58.9:24:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1280128 . T C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26836;SOR=0.6851;LSEQ=CGGCACCTCGGCCACCTCAC;RSEQ=GTGCGCACAAATGGGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:94:93,1:71,1:72,94:0.5663:1,1:21.8:1:31.2:1:1:1.31:59.1:30.333:0.5583:0:1.4 0/1:53:25:25,0:27,0:27,25:0.4717:1,1:21.6:1:30.4:1:1:0:58.8:24:0.4615:0:1.1 +5 1280180 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.07484;SOR=Inf;LSEQ=GCCCTGGCTGTGTCCCGTGG;RSEQ=CCCTCCTCCGGGCCCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:369,19:388,0:0:1,0:24.2:1:32.1:1:1:0:60:63.667:1:0:0.5 0/1:147:2:1,1:131,14:145,2:0.0136:2,2:16:1:27.5:1:0.1943:9.0743:60:4:0.014:0:1 +5 1280190 . G A 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTCCCGTGGCCCCTCCTCC;RSEQ=GGCCCTTCATCTAAGCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:107:94,13:329,40:369,107:0.2243:2,2:25.5:1:30.4:1:0.7276:1.13716:60:20.4:0.2189:0:1.4 0/0:192:0:0,0:158,34:192,0:0:2,0:23.1:1:28.8:1:1:0:60:37.4:1:0:0.2 +5 1280434 . G A 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03726;SOR=8.69921;LSEQ=TTCCGACAGCTCCCGCAGCT;RSEQ=CACCCTCTTCAAGTGCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:705:1:0,1:188,514:702,1:0.0014:2,0:16:0:32:0:1:0:60:2:0.0015:0:1 0/1:327:4:3,1:98,225:323,4:0.0122:2,2:14:1:27:1:0.08925:6.84:60:8:0.0125:0:1.3 +5 1280477 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00686;SOR=0.42351;LSEQ=CAATAGAGAGCCCCTCAGGA;RSEQ=GCTTGCTCAGCCAGACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:72:10,62:48,226:274,72:0.2081:2,2:23.6:1:32:1:0.59496:1.31577:59.4:144:0.2156:0:1.1 0/1:130:13:3,10:18,99:117,13:0.1:2,2:22.8:1:29.5:1:0.44041:1.64:60:26:0.1008:0:1 +5 1280830 . G C 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CAGCCACTGGGGTAGCCCAA;RSEQ=GCTGGCCCCAGGCAGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:18.6:1:30:1:1:0:57.6:10:1:0:1.2 0/0:1:0:0,0:0,1:1,0:0:0,0:16:0:32:0:1:0:60:2:1:0:0 +5 1280938 . A G 32 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAGCAGAATCAGCTCTC;RSEQ=TGAGCCCACCAGTCTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1282319 . C A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.67224;SOR=1.72372;LSEQ=TGCTTTACAAACCCTAGAGA;RSEQ=CACTTGGCACAAACTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:16:15,1:14,0:14,16:0.5333:1,1:30.1:1:30:1:1:0:60:15:0.5172:0:1.1 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:30:1:30.5:1:1:0:60:8:0.6667:0:1 +5 1282414 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60707;SOR=0.83152;LSEQ=ACTTGGACCAGGCCTGTGAC;RSEQ=GGGCCCCTGGCTCCCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:73:73,0:57,1:58,73:0.5573:1,1:21.7:1:29.9:1:0.44275:0:60:17.25:0.5433:0:1.1 1/0:45:23:23,0:22,0:22,23:0.5111:1,1:22:1:29.8:1:1:0:60:46:0.5111:0:1 +5 1282755 . C G 130 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=38.26687;LSEQ=AACCCCTTAAACGAGAAGGA;RSEQ=ATGCCACATCCAGATCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:679:1:1,0:193,485:678,1:0.0015:2,0:1:0:32:0:0.28571:0:60:2:0.0015:0:1 0/1:336:18:3,15:105,211:316,18:0.0536:2,2:25.1:1:31.4:1:0.19672:2.48248:59.9:36:0.0542:0:1.2 +5 1282778 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02871;SOR=Inf;LSEQ=GCCACATCCAGATCACCGAG;RSEQ=GCCTGGTGACCTCACCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:0:0,0:113,355:468,0:0:2,0:24.5:1:31:1:1:0:59.9:28.25:1:0:0.2 0/1:208:3:2,1:56,149:205,3:0.0144:2,2:11:1:26.3:1:0.1886:5.27:60:6:0.0149:0:1 +5 1282796 . C A 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24576;SOR=2.39512;LSEQ=AGGGCCTGGTGACCTCACCC;RSEQ=GGACCTGCACCATCCGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:4:4,0:58,278:336,4:0.0118:2,0:8.3:1:23.8:1:0.00102:0:60:3:0.009:0:2.3 0/1:144:4:3,1:31,109:140,4:0.0278:2,2:13.3:1:26.3:1:0.04102:10.33:53.3:8:0.0282:0:1 +5 1283104 . T C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=GCAGGGCCTGGCGACCTCAC;RSEQ=CCGGACCTGCACCATCCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:3,7:10,2:0.1667:2,0:36:1:33:0:1:0:46.5:4:0.2222:0:3 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:32:0:1:0:48:4:1:0:2 +5 1283841 . A C 64 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCGACCTCACCCCAGAC;RSEQ=TGCACCATGCAGACACCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:29:1:32:1:1:0:39:8:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:29.5:1:1:0:33.5:4:1:0:1 +5 1284046 . T C 58 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTGCAGCAACCGGACAC;RSEQ=GCACAACCAGCTCACCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:24.8:1:31.5:1:1:0:38.5:8:1:0:1 1/1:4:4:2,2:0,0:0,4:1:0,2:28.8:1:29.3:1:1:0:40.5:8:1:0:1 +5 1284976 . C T 29 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.32198;LSEQ=CGCATATCCAGCTCACCGCA;RSEQ=GGTCTGGCACCGTCTGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:27.5:1:29:1:1:0:60:4:0.6667:0:1 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:17:0:32:0:1:0:56:2:0.3333:0:1 +5 1291522 . C G 28 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGACAGCGCCTCACTCAC;RSEQ=CTGCACGGGACAGGGACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:41:0:29:0:1:0:31:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:7:1:28.5:1:1:0:22:4:1:0:2 +5 1291591 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACAGGGACACCCGGGGA;RSEQ=GGCGCCTCACTCACCCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:31.5:1:1:0:22:4:1:0:2 +5 1291801 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACAGGGACACCCGGGGG;RSEQ=CGCGCCTCACTCACCCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:28.5:1:1:0:48.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1292983 . C A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=ATATTGGCTGACCACGTGCA;RSEQ=CTGCAAAACCCTTACCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:13.5:1:34:0:1:0:57.8:8:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:28.5:1:1:0:60:4:1:0:1 +5 1293389 . C G 228 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGAGCCCCTACTGCATTCAG;RSEQ=TCTGGGGCCTGGGCCCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:154:127,27:235,48:283,154:0.3524:2,2:22.4:1:31.4:1:0.89484:1.04073:59.9:153:0.355:0:1.1 0/0:154:0:0,0:124,30:154,0:0:2,0:25:1:31.5:1:1:0:60:37.5:1:0:0.2 +5 1293760 . G A 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02597;SOR=10.00199;LSEQ=GGGTGACCGCAGCTCGCAGC;RSEQ=GGCAGTGCGTCTTGAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:953:1:1,0:535,416:951,1:0.001:2,0:1:0:28:0:1:0:60:2:0.0011:0:1 0/1:384:4:2,2:211,167:378,4:0.0104:2,2:23:1:29:1:1:1.26269:60:8:0.0106:0:1.3 +5 1293833 . G A 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=CAGCTCCAGAAACAGGGGCC;RSEQ=CATTTGCCAGTAGCGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1581:0:0,0:800,780:1580,0:0:2,0:24.5:1:31:1:1:0:59.9:74.238:0.9994:0:0.2 0/1:665:7:4,3:354,303:657,7:0.0105:2,2:14.6:1:28.7:1:1:1.14:60:14:0.0107:0:1 +5 1294086 . C T 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35633;SOR=1.09127;LSEQ=CGCGATGTGGATGGGGGGCC;RSEQ=GCGTGGTGCTGGCGGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1437:582:271,311:395,457:852,582:0.405:2,2:26:1:31:1:0.95703:1.01:60:63.667:0.4058:0:1.2 0/1:732:312:153,159:193,223:416,312:0.4262:2,2:24.9:1:29.4:1:0.50018:1.11:60:51:0.4256:0:1.1 +5 1294166 . C T 134 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=13.85637;LSEQ=CAAAGAGGTGGCTTCTTCGG;RSEQ=GGGTCTGGCAGGTGACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1308:4:0,4:608,695:1303,4:0.0031:2,0:15.3:1:30:1:0.12806:0:60:8:0.0031:0:1 0/1:637:26:12,14:286,325:611,26:0.0408:2,2:21.2:1:28.7:1:1:1.02663:60:52:0.0411:0:1.2 +5 1294664 . CG C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.26428;SOR=3.95517;LSEQ=CACGCTGGTGGTGAAGGCCT;RSEQ=GGGGGGCCCCCGCGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:1,0:100,164:264,1:0.0038:2,0:25:0:33:0:0.38113:0:60:2:0.0038:0:0 0/1:135:2:1,1:53,80:133,2:0.0148:2,2:20.5:1:29.5:1:1:1.50:60:4:0.0152:0:0.5 +5 1294671 . GC G 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=7.000;MSILEN=1;SSF=0.55386;SOR=0;LSEQ=GTGGTGAAGGCCTCGGGGGG;RSEQ=CCCCGCGGGCCCCGTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:1,2:89,147:236,3:0.0124:2,2:27.3:1:34.3:1:1:1.2099:60:6:0.0127:0:0.3 0/0:124:0:0,0:50,73:123,0:0:2,0:26.2:1:30.1:1:1:0:59.9:23.6:0.9916:0:0.2 +5 1294709 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53628;SOR=0;LSEQ=CAGCAGCGCGAAGCCGAAGG;RSEQ=CAGCACGTTCTTCGCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:49,99:148,2:0.0133:2,2:20.5:1:31.5:1:1:2.01:60:4:0.0134:0:1 0/0:85:0:0,0:32,53:85,0:0:2,0:21.7:1:30.6:1:1:0:60:41.5:1:0:0.1 +5 1294879 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53114;SOR=0;LSEQ=CCGGACGCCGACCCCGGGGA;RSEQ=GCCCACCTGGCGGAAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:74,73:147,2:0.0134:2,2:25.5:1:30.5:1:1:1.01361:60:4:0.0138:0:1 0/0:88:0:0,0:43,45:88,0:0:2,0:18.1:1:29.6:1:1:0:60:28.333:1:0:0.3 +5 1294906 . C T 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=1;SOR=0.62546;LSEQ=CTGGCGGAAGGAGGGGGCGG;RSEQ=GGGGGGCGGCCGTGCGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:1,2:94,114:208,3:0.0142:2,2:13:1:30.3:1:1:1.64538:60:6:0.0146:0:1 0/0:112:1:0,1:53,57:110,1:0.0089:2,0:39:0:26:0:1:0:60:2:0.0095:0:1 +5 1294920 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55504;SOR=0;LSEQ=GGGCGGCGGGGGGCGGCCGT;RSEQ=CGTCCCAGGGCACGCACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:1,2:118,130:248,3:0.012:2,2:29:1:28.3:1:1:1.81125:60:6:0.012:0:1 0/0:137:0:0,0:62,74:136,0:0:2,0:25.8:1:30.6:1:1:0:60:16:1:0:0.4 +5 1294934 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30007;SOR=0;LSEQ=GGCCGTGCGTCCCAGGGCAC;RSEQ=CACACCAGGCACTGGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:129,147:276,3:0.0108:2,2:8:1:29:1:1:1.75171:60:6:0.0112:0:1 0/0:163:0:0,0:79,82:161,0:0:2,0:23.6:1:29.6:1:1:0:59.9:16.889:0.987:0:0.4 +5 1294954 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16019;SOR=Inf;LSEQ=GCACACCAGGCACTGGGCCA;RSEQ=CAGCGCGCGGAAAGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:116,135:251,0:0:2,0:24.2:1:31.7:1:1:0:60:49.2:1:0:0.4 0/1:168:2:1,1:81,85:166,2:0.0119:2,2:41.5:1:30.5:1:1:1.05:60:4:0.0123:0:1.5 +5 1294969 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57342;SOR=2.81169;LSEQ=GGCCACCAGCGCGCGGAAAG;RSEQ=CGCCGGGTCCCCGCGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:1:0,1:111,129:240,1:0.0041:2,0:1:0:31:0:1:0:60:2:0.0042:0:1 0/1:173:2:1,1:86,85:171,2:0.0116:2,2:39:1:28:1:1:1.0117:60:4:0.0121:0:1 +5 1294978 . C T 40 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.54624;LSEQ=CGCGCGGAAAGCCGCCGGGT;RSEQ=CCCGCGCTGCACCAGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:115,119:234,3:0.0127:2,2:14:1:25.3:1:1:1.92761:60:2:0.0088:0:3.7 0/0:144:1:0,1:73,70:143,1:0.0069:2,0:1:0:25:0:0.49306:0:60:2:0.0071:0:1 +5 1294987 . G T 49 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65229;SOR=0.37814;LSEQ=AGCCGCCGGGTCCCCGCGCT;RSEQ=CACCAGCCGCCAGCCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:4:2,2:120,118:238,4:0.0164:2,2:24.5:1:24.8:1:1:1.01688:60:3:0.013:0:3.3 0/0:160:1:0,1:80,78:158,1:0.0063:2,0:1:0:22:0:0.49686:0:60:2:0.0066:0:1 +5 1294996 . G T 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTCCCCGCGCTGCACCAGCC;RSEQ=CCAGCCCTGGGGCCCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:122,115:237,3:0.0125:2,2:15.7:1:30.3:1:0.61418:2.11531:60:6:0.013:0:1.3 0/1:160:2:1,1:79,77:156,2:0.0125:2,2:28:1:29.5:1:1:1.02581:60:4:0.0129:0:1 +5 1295010 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16559;SOR=Inf;LSEQ=CCAGCCGCCAGCCCTGGGGC;RSEQ=CCAGGCGCCGCACGAACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:124,107:231,0:0:2,0:23.5:1:30.4:1:1:0:60:20:1:0:0.4 0/1:159:2:1,1:84,73:157,2:0.0126:2,2:28:0:31:1:1:1.14966:60:4:0.013:0:1.5 +5 1295045 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19653;SOR=Inf;LSEQ=AACGTGGCCAGCGGCAGCAC;RSEQ=TCGCGGTAGTGGCTGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:128,120:248,0:0:2,0:25.1:1:31.7:1:1:0:60:30:1:0:0.4 0/1:198:2:1,1:96,100:196,2:0.0101:2,2:32:0:32:0:1:1.04:60:4:0.0103:0:1.5 +5 1295048 . G T 36 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63524;SOR=0.42734;LSEQ=GTGGCCAGCGGCAGCACCTC;RSEQ=CGGTAGTGGCTGCGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:127,119:246,3:0.012:2,2:6:1:23:1:0.61312:2.12816:60:2:0.0082:0:1.7 0/0:194:1:0,1:94,98:192,1:0.0052:2,0:1:0:27:0:1:0:60:2:0.0054:0:1 +5 1295061 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26318;SOR=0;LSEQ=GCACCTCGCGGTAGTGGCTG;RSEQ=GCAGCAGGGAGCGCACGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:3:1,2:123,119:242,3:0.0121:2,2:25:1:28:1:0.61887:2.06131:60:6:0.0125:0:1 0/0:186:0:0,0:89,97:186,0:0:2,0:26.3:1:30.2:1:1:0:60:45.5:1:0:0.4 +5 1295088 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1787;SOR=Inf;LSEQ=GGGAGCGCACGGCTCGGCAG;RSEQ=GGGGAGCGCGCGGCATCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:116,110:226,0:0:2,0:23.9:1:30.9:1:1:0:60:44.2:1:0:0.3 0/1:166:2:1,1:85,79:164,2:0.012:2,2:30:0:30.5:1:1:1.07545:60:4:0.0125:0:1.5 +5 1295093 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18243;SOR=Inf;LSEQ=CGCACGGCTCGGCAGCGGGG;RSEQ=GCGCGCGGCATCGCGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:117,109:226,0:0:2,0:22.3:1:30.6:1:1:0:60:24.111:1:0:0.3 0/1:169:2:1,1:86,81:167,2:0.0118:2,2:9.5:1:30.5:1:1:1.06138:60:4:0.0122:0:1.5 +5 1295110 . G C 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.13677;SOR=Inf;LSEQ=GGGAGCGCGCGGCATCGCGG;RSEQ=GGTGGCCGGGGCCAGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:126,110:236,0:0:2,0:17.1:1:31.3:1:1:0:59.6:46.2:1:0:0.3 0/1:139:2:1,1:70,67:137,2:0.0144:2,2:5.5:1:26.5:1:1:1.04446:60:4:0.0144:0:1.5 +5 1295117 . CG C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.13521;SOR=Inf;LSEQ=CGCGGCATCGCGGGGGTGGC;RSEQ=GGGCCAGGGCTTCCCACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:137,94:231,0:0:2,0:17.4:1:30.4:1:1:0:59.6:76:0.9913:0:0.3 0/1:136:2:1,1:74,60:134,2:0.0147:2,2:41.5:1:30.5:1:1:1.23141:60:4:0.0147:0:0 +5 1295123 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0517;SOR=Inf;LSEQ=ATCGCGGGGGTGGCCGGGGC;RSEQ=AGGGCTTCCCACGTGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:138,86:224,0:0:2,0:19.2:1:31.8:1:1:0:59.6:43.8:1:0:0.3 0/1:134:3:1,2:74,56:130,3:0.0224:2,2:8.7:1:26.3:1:0.5801:2.6238:60:6:0.0226:0:1.3 +5 1295127 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55802;SOR=3.41295;LSEQ=CGGGGGTGGCCGGGGCCAGG;RSEQ=CTTCCCACGTGCGCAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:1:1,0:153,85:238,1:0.0042:2,0:1:0:23:0:1:0:60:2:0.0043:0:2 0/1:141:2:1,1:81,58:139,2:0.0142:2,2:26.5:1:27:1:1:1.39317:60:4:0.0144:0:1 +5 1295161 . T C 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03649;SOR=Inf;LSEQ=CAGCAGGACGCAGCGCTGCC;RSEQ=GAAACTCGCGCCGCGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:286,119:405,0:0:2,0:23.3:1:31.4:1:1:0:60:24.313:0.9974:0:0.3 0/1:203:3:1,2:120,79:199,3:0.0148:2,2:39.7:1:23:1:0.56549:3.02108:60:2:0.0103:0:2.3 +5 1295250 . G A 236 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGCTGGGCCGGGGACCCGG;RSEQ=AGGGGTCGGGACGGGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1239:290:175,115:569,376:945,290:0.2341:2,2:25.8:1:28.9:1:1:1.01:60:17.125:0.2314:0:1.3 0/0:602:0:0,0:332,267:599,0:0:2,0:25.5:1:29.4:1:1:0:60:25.043:0.9948:0:0.4 +5 1295349 . A G 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17984;LSEQ=CAGTCCCTCCGCCACGTGGG;RSEQ=AGCGCGGTCCTGGGCGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1060:778:260,518:95,184:279,778:0.734:2,2:24.8:1:31.7:1:0.88258:1.02863:60:69.727:0.7361:0:1.2 0/1:501:166:67,99:135,199:334,166:0.3313:2,2:27:1:30.4:1:1:1.0024:60:82:0.3327:0:1.1 +5 1295373 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGGTCCTGGGCGTCTGTGC;RSEQ=CGCGAATCCACTGGGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:690:0:0,0:200,488:688,0:0:2,0:23.5:1:31:1:1:0:60:42:0.9985:0:0.9 0/1:322:11:5,6:115,196:311,11:0.0342:2,2:26.1:1:28.6:1:0.54611:1.42:60:22:0.0347:0:1.5 +5 1336626 . T A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.61782;LSEQ=TGCCCCTGTCCACCATCTCC;RSEQ=GAATGCCTGCAAGGAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:5,6:7,3:10,11:0.5238:2,2:32.2:1:31.5:1:0.387:2.66125:60:22:0.5238:0:1.1 0/1:5:2:1,1:2,1:3,2:0.4:2,2:16:1:28:1:1:1.7321:60:4:0.4:0:1 +5 1563875 . T C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCACACCCAGTTGAGGGCC;RSEQ=GGTAAAGCAGCACCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:29:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:31.5:1:1:0:60:4:1:0:1.5 +5 1564675 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAGGAGGGGCCGCTCCT;RSEQ=GTGTCACAGGGGAGGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:29:1:1:0:60:4:1:0:1 +5 1572289 . A G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45218;SOR=1.46309;LSEQ=ACATGCATGAGCTATTATAC;RSEQ=TAATTACAAAAGCTGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:14:13,1:42,6:48,14:0.2258:2,1:3.4:1:30.9:1:1:1.84:21.1:28:0.2258:0:1 0/1:30:9:8,1:15,6:21,9:0.3:2,2:5.4:1:29.1:1:0.39321:3.09:20.8:18:0.3:0:1 +5 1572302 . C T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1273;SOR=Inf;LSEQ=ATTATACATAATTACAAAAG;RSEQ=TGATTCTGTCATCACCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:152,48:200,0:0:2,0:10:1:32.9:1:1:0:33.1:400:1:0:0.2 0/1:112:2:1,1:70,40:110,2:0.0179:2,2:7:0:31:0:1:1.74074:20:4:0.018:0:2.5 +5 1572318 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.25588;SOR=1.3496;LSEQ=AAAGCTGATTCTGTCATCAC;RSEQ=GCATCTTGTCTCATCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:43:22,21:247,126:373,43:0.1034:2,2:13.3:1:31.1:1:0.06327:1.86828:26.9:86:0.1049:0:1.4 0/1:245:33:19,14:123,89:212,33:0.1347:2,2:15.3:1:30:1:1:1.01826:21:66:0.1358:0:1.4 +5 1572585 . A G 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAAAAATGATCTACATGC;RSEQ=CAACAGGGGACTGTAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:27.7:1:29.7:1:1:0:25.8:12:1:0:2 1/1:3:3:0,3:0,0:0,3:1:0,0:30.3:1:23.3:1:1:0:24.3:2:1:0:1.3 +5 1574162 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06672;SOR=Inf;LSEQ=TGTCAGAGTGCCTTTTTCAG;RSEQ=GGTGCCTCAAATCTGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:137,8:145,0:0:2,0:20.3:1:31.8:1:1:0:23:28:1:0:1 0/1:51:2:2,0:47,2:49,2:0.0392:1,0:14:1:30.5:1:1:0:25.5:4:0.04:0:2 +5 1574179 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.001;SOR=0.15959;LSEQ=CAGCGGTGCCTCAAATCTGT;RSEQ=GGGAGTTGATTTAAATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:152:146,6:4,1:5,152:0.9682:2,1:26.7:1:31.3:1:0.20633:5.94:22.8:49.667:0.9675:0:1.1 1/1:58:48:46,2:10,0:10,48:0.8276:0,1:32.4:1:30.3:1:1:0:23.8:23:0.8214:0:1.1 +5 1576000 . C G 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0923;SOR=0;LSEQ=AATAAACTGGCATTTACTTC;RSEQ=TGGTCATGCCACTCTAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:7:6,1:53,5:58,7:0.1077:2,2:35.4:1:29.9:1:0.50998:1.74827:50.7:14:0.1094:0:1 0/0:31:0:0,0:27,4:31,0:0:2,0:35.6:1:29.9:1:1:0:46.6:14.5:1:0:0 +5 1576094 . G A 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGGCATCAGTGGATGCC;RSEQ=ACCCAAAGCAAGGAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:180,84:264,0:0:2,0:11.9:1:30.6:1:1:0:49.8:51.8:1:0:0.1 0/1:149:14:9,5:93,42:135,14:0.094:2,2:11.3:1:29.1:1:0.76604:1.22837:23.6:28:0.094:0:1.1 +5 1576191 . C T 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGATTTTTTGGATTTACTT;RSEQ=TGGGGCAACGAAATAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1974:0:0,0:1072,900:1972,0:0:2,0:24.8:1:32.5:1:1:0:43.6:69.429:0.999:0:0.1 0/1:1059:45:25,20:534,479:1013,45:0.0425:2,2:26.4:1:29.7:1:0.76156:1.12:24.1:44:0.042:0:1.2 +5 1576317 . T A 149 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=66.69903;LSEQ=GTAGCCTTCCCTGGCGTGCG;RSEQ=GCCCCGTGACTCCTTCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1214:1:1,0:499,714:1213,1:8e-04:2,0:1:0:25:0:0.41186:0:37:2:8e-04:0:1 0/1:631:33:16,17:271,326:597,33:0.0523:2,2:28.5:1:29.6:1:0.72422:1.13:32.7:66:0.0527:0:1.2 +5 1576377 . G A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1129;SOR=Inf;LSEQ=CTGCAGCGCACACAGCATCA;RSEQ=GTTCTGCAGCTCCAGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:142,189:331,0:0:2,0:14.8:1:31.8:1:1:0:33.7:32.1:1:0:0.1 0/1:168:2:1,1:80,86:166,2:0.0119:2,2:6:1:28:1:1:1.07:42.5:4:0.012:0:1.5 +5 1576820 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10497;SOR=Inf;LSEQ=AAACTTTTAATCCATAGAAG;RSEQ=AGCCATATCAAGAACTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:53,309:362,0:0:2,0:23.4:1:32.4:1:1:0:55.7:89.5:1:0:0.1 0/1:174:2:1,1:33,139:172,2:0.0115:2,2:33.5:1:30:0:0.35353:4.16:49:4:0.0117:0:1 +5 1576823 . C A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5995;SOR=2.07747;LSEQ=CTTTTAATCCATAGAAGCAG;RSEQ=CATATCAAGAACTGCTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:2:0,2:44,291:335,2:0.0059:2,0:6.5:1:29:1:1:0:60:4:0.0061:0:1 0/1:163:2:1,1:31,130:161,2:0.0123:2,2:12:1:26:1:0.35507:4.14:48:4:0.0126:0:1 +5 1587545 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTAAACTGACAACCTTCCAG;RSEQ=GTGGGCATCATGGCCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:14.5:1:28.5:1:1:0:29.5:4:0.6667:0:1 +5 1587716 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08615;SOR=Inf;LSEQ=GTCAGCAGAAAAATCCCTTC;RSEQ=CCCAACGAAACACATTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:18,0:0:2,0:27.1:1:31.4:1:1:0:58.8:36:1:0:0.1 0/1:8:2:1,1:3,3:6,2:0.25:2,2:32.5:1:29:1:1:1:60:4:0.25:0:1 +5 1588404 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCACTCTCCCTCTCTTCC;RSEQ=AGTATATTTAGGGCCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1589487 . C CA 79 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.43281;SOR=0.28673;LSEQ=AGGGACTTTATCTCCTAAAA;RSEQ=AAAAAAAAGCTAGAATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:6:3,3:203,371:574,6:0.0103:2,2:44.7:1:30.8:1:0.67122:1.83:22:12:0.0105:0:0 0/0:335:1:0,1:125,209:334,1:0.003:2,0:41:0:29:0:1:0:23:2:0.003:0:0 +5 1589751 . A G 27 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTAGAAATCATCTCTAA;RSEQ=ATTAAAAAATTAAATGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:12:1:27.5:1:1:0:28.5:4:1:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:24:0:32:0:1:0:23:2:0.5:0:1 +5 1593326 . G A 133 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=41.77875;LSEQ=GCCGATTGGCACCATGTACC;RSEQ=AGGCACAGGCGGCCTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:897:1:1,0:465,431:896,1:0.0011:2,0:1:0:16:0:1:0:60:0:0:0:1 0/1:448:20:8,12:228,200:428,20:0.0446:2,2:37.5:1:30.8:1:0.26152:1.70794:32.4:40:0.0448:0:1.3 +5 1593352 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.027;SOR=Inf;LSEQ=CAGGCGGCCTCCCCACAGGC;RSEQ=TACAGGCCGGGCACAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:207,220:427,0:0:2,0:13.1:1:30.8:1:1:0:27.8:84.4:1:0:0.1 0/1:184:3:2,1:97,84:181,3:0.0163:2,2:13:1:24:1:1:1.73:35.3:2:0.0112:0:1 +5 1593401 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATTCACGTGCCTCAGGACC;RSEQ=GTGGAAAGGAAGATTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:22,7:29,2:0.0645:2,2:12.5:1:32.5:1:0.45591:3.00588:60:4:0.0667:0:1 0/0:15:0:0,0:11,4:15,0:0:2,0:23:0:9:0:1:0:60:0:0:0:2 +5 1593498 . G A 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TGCTGCAGGTCAGAGAGAGA;RSEQ=GGAAGTAGGCCCGGCGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:20,309:329,0:0:2,0:22:1:31.8:1:1:0:40.4:108.667:1:0:0.1 0/1:135:9:2,7:3,123:126,9:0.0667:1,2:24.8:1:30.3:1:0.03575:11.20:40.9:18:0.0672:0:1.1 +5 1593803 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCAAGAAAAAAAAAAAA;RSEQ=GGGAAGTAAAGACCGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:26:1:32:1:1:0:54.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 1594542 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07776;SOR=Inf;LSEQ=CGCCAGGCGCGGAGCGCTCA;RSEQ=CAGGCGCGACAGGACCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:131,72:203,0:0:2,0:28.6:1:32.6:1:1:0:56:39.6:1:0:0.2 0/1:79:2:1,1:47,30:77,2:0.0253:2,2:35:1:27.5:1:1:1.55745:60:4:0.026:0:2 +5 1594550 . G A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGGAGCGCTCAGCAGGCGC;RSEQ=ACAGGACCCAGACCGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:137,82:219,0:0:2,0:28.6:1:30.3:1:1:0:56.3:53.75:0.9954:0:0.2 0/1:89:10:5,5:46,33:79,10:0.1124:2,2:25.5:1:30.9:1:0.73857:1.38864:54.6:20:0.1136:0:1.3 +5 1594565 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07977;SOR=Inf;LSEQ=GGCGCGACAGGACCCAGACC;RSEQ=CCATGCCTGTAGTCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:142,91:233,0:0:2,0:27.3:1:29.9:1:1:0:57.7:28.125:0.9912:0:0.2 0/1:93:2:1,1:50,41:91,2:0.0215:2,2:38.5:1:30:1:1:1.21689:60:4:0.0225:0:1 +5 1594577 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.56407;SOR=0;LSEQ=CCCAGACCGCCATGCCTGTA;RSEQ=TCGCCTCCGCGCAGTCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:2,1:134,105:239,3:0.0124:2,2:18:1:27.7:1:1:1.56:56.7:6:0.0127:0:1 0/0:92:0:0,0:46,46:92,0:0:2,0:27.6:1:30.8:1:1:0:59.5:29.667:1:0:0.4 +5 1594583 . T G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07847;SOR=Inf;LSEQ=CCGCCATGCCTGTAGTCGCC;RSEQ=CCGCGCAGTCCCGCCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:127,103:230,0:0:2,0:25.2:1:30.1:1:1:0:59.8:22:1:0:0.3 0/1:90:2:1,1:43,44:87,2:0.0222:2,2:10:0:32:1:1:1.02:52.5:4:0.0235:0:1.5 +5 1594664 . C G 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TTGGGGGGCAGGAACCGCGG;RSEQ=GGGTGGGATGCCGCGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:70:10,60:0,0:0,70:1:0,2:21.9:1:31.7:1:1:0:60:140:1:0:1.1 1/0:16:10:2,8:0,6:6,10:0.625:0,2:22.6:1:31:1:0.5:0:60:20:0.625:0:1.2 +5 1594879 . C G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATCGCCCAGACCGAAAGG;RSEQ=CCCGAACGTCCAGATCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:34.5:1:1:0:53:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 2739230 . T C 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCGAGGGGACTCAACGCGCT;RSEQ=TGTAGGGCCTGTGAAATCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:1,5:6,3:0.3333:2,2:17.7:1:30:1:1:2.24:60:6:0.375:0:1.3 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:36.5:1:31:1:0.33333:0:60:4:0.3333:0:1.5 +5 2740500 . TG T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTGTTCCCTGACCTGCGAC;RSEQ=TTCGGTTCTCCCGACTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:18:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:1:31.5:1:1:0:60:4:1:0:0 +5 2958096 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGCAACCTGGAGCCTCT;RSEQ=GTGAAGCCACTGGCCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:28.5:1:1:0:60:4:1:0:2 +5 2958127 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCCTTCTGCCACCTTTT;RSEQ=CCCACACAACTTTATTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:32.5:1:1:0:60:4:1:0:2 +5 2979710 . G A 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41288;LSEQ=GCTAAGTTTAAAGCTAACAA;RSEQ=TATTTTTCTTTTTGCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:438:224,214:262,284:546,438:0.4442:2,2:25.4:1:30.6:1:0.33636:1.13:60:72:0.444:0:1.1 0/1:504:125:68,57:190,189:379,125:0.248:2,2:26.5:1:29.7:1:0.41163:1.19:60:250:0.25:0:1.2 +5 2979811 . T A 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08824;SOR=Inf;LSEQ=CGATAAGCACCTTAATCATA;RSEQ=TGTGTTTATTTCTGTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:54,268:322,0:0:2,0:22.9:1:30.5:1:1:0:60:79.5:1:0:0.1 0/1:137:2:1,1:27,108:135,2:0.0146:2,2:8.5:1:23:1:0.36818:3.95:60:4:0.0148:0:1.5 +5 2979827 . ATTTG A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0;SOR=0.20203;LSEQ=CATATTGTGTTTATTTCTGT;RSEQ=TTTGGCCTACTGAAGTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:84:8,76:13,116:129,84:0.3944:2,2:28.4:1:31.7:1:1:1.06436:60:168:0.3944:0.0469:0.2 0/1:95:11:2,9:7,77:84,11:0.1158:2,2:21.4:1:30.4:1:0.27856:2.41:60:22:0.1183:0.0316:0.1 +5 4089089 . G T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5535;SOR=0;LSEQ=TACTTCCTCTCTGACATCCA;RSEQ=GGGGCTGTAAAGCCTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:3:1,2:124,31:155,3:0.019:2,2:12:1:27.3:1:0.11079:7.85514:60:6:0.0194:0:1 0/0:73:0:0,0:52,20:72,0:0:2,0:22.4:1:30.4:1:1:0:60:23:0.9857:0:0.1 +5 4089094 . C T 39 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64832;SOR=1.48284;LSEQ=CCTCTCTGACATCCAGGGGG;RSEQ=TGTAAAGCCTCACTCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:3:0,3:132,44:176,3:0.0168:2,0:1:0:25:1:0.01725:0:60:6:0.017:0:1 0/1:81:2:1,1:54,25:79,2:0.0247:2,2:10:1:28.5:1:0.54167:2.13762:60:4:0.0256:0:1 +5 4089148 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28817;SOR=3.6525;LSEQ=AAAACCCAGCAGGGCAAAAA;RSEQ=CATGTCAGCAGAAAAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:1:0,1:195,161:356,1:0.0028:2,0:1:0:26:0:0.45378:0:60:2:0.0028:0:3 0/1:197:2:1,1:111,84:195,2:0.0102:2,2:30.5:1:29:1:1:1.31952:60:4:0.0105:0:1 +5 4089201 . T A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99815;LSEQ=GGAGTAACAGGCACATGCCC;RSEQ=GCAAGGCTTCCCTGCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:180:75,105:75,90:165,180:0.5217:2,2:25.3:1:31:1:0.51487:1.16614:59.5:35:0.5162:0:2 1/0:188:98:44,54:45,45:90,98:0.5213:2,2:26.1:1:29.7:1:0.55898:1.22592:60:196:0.5269:0:2.1 +5 4089206 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12404;SOR=Inf;LSEQ=AACAGGCACATGCCCTGCAA;RSEQ=GCTTCCCTGCAAGAAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:139,193:332,0:0:2,0:24.8:1:31.8:1:1:0:59.7:65.4:1:0:1.1 0/1:181:2:1,1:84,95:179,2:0.011:2,2:10.5:1:31:1:1:1.13:60:4:0.0114:0:1 +5 4089211 . C T 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45302;SOR=1.17089;LSEQ=GCACATGCCCTGCAAGGCTT;RSEQ=CCTGCAAGAAGGAAGACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:166:65,101:68,91:159,166:0.5092:2,2:23.6:1:29.9:1:0.57274:1.16058:59.4:26.667:0.5016:0:2.1 1/0:175:96:41,55:38,41:79,96:0.5486:2,2:25.3:1:28.9:1:0.54214:1.24175:60:31:0.5439:0:2.1 +5 4089228 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.13702;SOR=Inf;LSEQ=CTTCCCTGCAAGAAGGAAGA;RSEQ=ACCCTTGCCTTTGTTGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:99,186:285,0:0:2,0:23.5:1:32.1:1:1:0:59.8:56:1:0:0.9 0/1:168:2:1,1:68,98:166,2:0.0119:2,2:44.5:1:29:1:1:1.44:60:4:0.012:0:3.5 +5 4089499 . A G 29 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGAAAGAGGATGTGGAC;RSEQ=GAAGTAGAACAGAACTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:9:1:29:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:7:0:31:0:1:0:60:2:1:0:2 +5 4089547 . G A 31 d5;v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAGTAACACTTGGCTAAG;RSEQ=GTTTCACAAGGGTCTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:36:0:31.5:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:46:0:26:0:1:0:60:2:1:0:2 +5 4089687 . C G 52 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTCCTTCTTTCCTTCTTT;RSEQ=TTTTTCTTTCTTTCCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:19.7:1:33:1:1:0:59.7:6:0.75:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:46:0:34:0:1:0:60:2:1:0:1 +5 4112464 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCTCCACAAAGTGTCAG;RSEQ=GAATGGCCTGACTACATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 4114269 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12354;SOR=Inf;LSEQ=CCTGCGATAATTAAAATCTG;RSEQ=GTGTGGCCTCAGCTGATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:52,67:119,0:0:2,0:26.4:1:30.6:1:1:0:60:58.5:1:0:0.2 0/1:65:2:1,1:24,39:63,2:0.0308:2,2:16.5:1:28.5:1:1:1.61:60:4:0.0308:0:1 +5 4114285 . A G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00867;SOR=Inf;LSEQ=TCTGCGTGTGGCCTCAGCTG;RSEQ=TGTCTCACTCTTGAGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:35,64:99,0:0:2,0:20.9:1:30.6:1:1:0:60:98:1:0:0.2 0/1:45:4:1,3:13,28:41,4:0.0889:2,2:20:1:30.3:1:1:1.3832:60:8:0.0889:0:1.3 +5 4577774 . G T 38 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0947;SOR=6.59999;LSEQ=ATCAGCTTGTGCTGTCTGTT;RSEQ=ATTGGTGTTGTGCTGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:1:0,1:265,84:349,1:0.0029:2,0:10:0:30:0:0.24286:0:60:2:0.0029:0:1 0/1:161:3:1,2:116,42:158,3:0.0186:2,2:5.3:1:24:1:0.18154:5.45413:60:6:0.0188:0:2 +5 4577842 . G A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.94894;SOR=0.98531;LSEQ=ACTTTGGTAGCAGCATATGT;RSEQ=TGTCAGTGAATGCTGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:723:419:212,207:150,153:303,419:0.5795:2,2:24.6:1:29.3:1:0.82105:1.04:60:51.375:0.5772:0:1.1 1/0:382:220:114,106:82,80:162,220:0.5759:2,2:24.7:1:28.3:1:0.83644:1.05:60:219:0.5763:0:1.1 +5 4577917 . TTTA T 54 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.22856;SOR=2.70851;LSEQ=GCATGCAGGATCAGCTTCGT;RSEQ=TTATTATTATTATTAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:3:1,2:121,285:406,3:0.0073:2,2:25:1:31.1:1:1:1.18:60:6:0.0074:0.0024:0 0/1:204:4:1,3:63,136:199,4:0.0196:2,2:22.5:1:27.3:1:1:1.38762:60:8:0.0197:0.0049:0.5 +5 4577920 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.11342;SOR=Inf;LSEQ=TGCAGGATCAGCTTCGTTTT;RSEQ=TTATTATTATTATTAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:385:0:0,0:109,274:383,0:0:2,0:23.1:1:30.1:1:1:0:60:62.833:1:0:0.5 0/1:196:2:1,1:59,132:191,2:0.0102:2,2:27:1:28.5:1:0.52623:2.23:60:4:0.0105:0:1 +5 4577968 . A G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40238;SOR=1.30988;LSEQ=ACAAGTCAAACCACAACTGC;RSEQ=CTTTGCTTAGAATCATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:164:83:4,79:11,70:81,83:0.5061:2,1:27.2:1:33:1:0.06124:3.08324:60:166:0.5123:0:1.1 1/0:75:43:7,36:3,29:32,43:0.5733:2,2:26.3:1:30.8:1:0.50168:1.86:60:42:0.5676:0:1.2 +5 4578107 . C T 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AAACCTCATTACGAGTTCAG;RSEQ=TTAGATGCTTTCCATCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:3,6:0.6667:0,0:33.7:1:31:1:1:0:60:12:0.6667:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:27.5:1:30:1:1:0:60:4:0.6667:0:1 +5 5319835 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53007;SOR=0;LSEQ=ACCTGGAGCCACCGCCGGAG;RSEQ=CAGCGTCATCTCTAGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:22,18:40,2:0.0476:2,2:36:1:29.5:1:1:1.21636:60:4:0.0488:0:1 0/0:24:0:0,0:12,12:24,0:0:2,0:26.2:1:31:1:1:0:60:48:1:0:0.3 +5 5319934 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05455;SOR=Inf;LSEQ=ATTCCTGCTAAGGTGCTTCT;RSEQ=TCTCTTTCAGATTCATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:24.9:1:29.3:1:1:0:60:7:1:0:0.1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:9:1:30.5:1:1:0:60:4:0.6667:0:1 +5 5492597 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21465;SOR=4.72304;LSEQ=CAGCAAGTTCAATATTTAAG;RSEQ=AACATGAAATAGAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:1:0,1:216,45:261,1:0.0038:2,0:1:0:23:0:0.17557:0:60:2:0.0039:0:1 0/1:112:2:1,1:92,18:110,2:0.0179:2,2:21:1:28:1:0.31178:5.0019:60:4:0.0183:0:1 +5 5492635 . A T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03849;SOR=Inf;LSEQ=AATTCATACCTGGACTTGGA;RSEQ=AGAACTGCACTGTAGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:0:0,0:374,191:565,0:0:2,0:25:1:30.4:1:1:0:60:93.167:1:0:0.3 0/1:289:3:1,2:184,102:286,3:0.0104:2,2:14.7:1:25:1:0.29462:3.59102:60:6:0.0105:0:1.3 +5 5492718 . A T 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.53411;LSEQ=AGACAGGGAACCTTAACTGG;RSEQ=GAGGTCGTCTGGGTGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:801:532:256,276:133,136:269,532:0.6642:2,2:24.7:1:29.6:1:0.76473:1.05424:60:58.111:0.6654:0:1.2 1/0:479:246:124,122:122,111:233,246:0.5136:2,2:24.3:1:29:1:0.71468:1.08119:60:40:0.5128:0:1.1 +5 5493023 . AAAG A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAAAAGAGAAAGAAAA;RSEQ=AGAAAGGAAAGAGAAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,0:0,2:0.2857:0,0:8:1:32.5:1:1:0:60:4:0.2857:0.1429:0 0/0:3:0:0,0:0,1:1,0:0:0,0:11:1:32:1:1:0:60:2:0.3333:0:0 +5 5493025 . AG GAA 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0.81844;LSEQ=AGAAAAAGAGAAAGAAAAAA;RSEQ=AGAAAGGAAAGAGAAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,0:0,5:0.7143:0,0:27:1:31.7:1:1:0:50.8:10:0.7143:0:1.8 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:31.5:1:27.3:1:1:0:60:4:0.6667:0:1 +5 5493037 . GAGAA G 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=AGAAAAAAAGAGAAAGGAAA;RSEQ=GGAAGGAGGGAGGGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:27.3:1:31.8:1:1:0:48.5:8:0.8:0.2:2 0/0:2:0:0,0:1,1:2,0:0:2,0:23:1:26.5:1:1:0:60:4:1:0:1 +5 6482092 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09804;SOR=Inf;LSEQ=CCTGTGGCTGTGAATGTGAC;RSEQ=TTATTTGAAAATAGGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:21.7:1:31.5:1:1:0:60:24:1:0:0.1 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:8.5:1:31:1:1:0:60:4:0.3333:0:1 +5 6482179 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53112;SOR=0;LSEQ=TCCCTAATCCAATGACTGGT;RSEQ=TCACTGTAAGAAGAGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:20,22:42,2:0.0455:2,2:34:1:31:1:1:1.10:60:4:0.0455:0:1 0/0:25:0:0,0:11,14:25,0:0:2,0:29.4:1:31:1:1:0:60:50:1:0:0.3 +5 6482233 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07977;SOR=Inf;LSEQ=ACAGATTCACAGAGAACACC;RSEQ=TATGGCAATGGAGGCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:2,17:19,0:0:2,0:21:1:33:1:1:0:60:38:1:0:0.1 0/1:8:2:0,2:1,5:6,2:0.25:2,0:12.5:1:32:0:1:0:60:4:0.25:0:1 +5 6624371 . C T 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.03162;SOR=0;LSEQ=ATCCAAGGTTTTGATTAAAG;RSEQ=ATTAAGTAAGATGGGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:15:15,0:5,0:5,15:0.75:0,1:25.5:1:30.3:1:1:0:60:14:0.7368:0:1.1 0/0:3:0:0,0:3,0:3,0:0:0,0:40:1:27.3:1:1:0:60:2:1:0:0 +5 6624395 . G A 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23298;SOR=3.441;LSEQ=AAGTAAGATGGGGACATCCC;RSEQ=GCAGACAGTAACCAGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:27,0:27,3:0.1:1,0:31.7:1:30:1:1:0:60:6:0.1:0:1 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:8:1:30.5:1:1:0:60:4:0.2857:0:1 +5 6624458 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGCCAGCTTTCCATAAC;RSEQ=CAGAGGTTATTGCCATTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:66,39:105,2:0.0187:2,2:21.5:1:29:1:1:1.68356:60:4:0.0189:0:1 0/0:48:0:0,0:29,19:48,0:0:2,0:25.4:1:30.4:1:1:0:60:47:1:0:0.1 +5 6624472 . C T 33 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67294;LSEQ=CATAACCCAGAGGTTATTGC;RSEQ=ATTCATCTCAAGAGCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:1,2:78,55:133,3:0.0221:2,2:5.7:1:21.3:1:0.57171:2.81467:60:2:0.015:0:3.3 0/1:67:1:0,1:38,28:66,1:0.0149:2,0:1:0:24:0:0.43284:0:60:2:0.0149:0:1 +5 6624481 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTTATTGCCATTCATCT;RSEQ=AAGAGCTCTCATCACGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:91,66:157,2:0.0126:2,2:37:0:31:1:1:1.37594:60:4:0.0127:0:1.5 0/0:79:0:0,0:45,34:79,0:0:2,0:23.5:1:30.7:1:1:0:60:158:1:0:0.2 +5 6790378 . ATG A 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.18067;SOR=5.87068;LSEQ=GTGTGCGCGTGTGTGTTTGC;RSEQ=TGTGTGTGTGGGGGGCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:9,16:25,1:0.0385:2,0:38:0:32:0:1:0:60:2:0.04:0:0 0/1:10:2:1,1:4,4:8,2:0.2:2,2:38:0:31.5:1:1:1:60:4:0.2:0:0.5 +5 6790691 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGGTGTGGTGAGCTGTTC;RSEQ=TATGCAGGAGAGGGACGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 6830890 . C CACAT 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGCACGCACCATGCACACA;RSEQ=GCATGCACACATACACACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:20:1:32.8:0:1:0:43:4:1:0:0.5 1/1:3:3:1,2:0,0:0,3:1:0,2:20.3:1:30.1:1:1:0:52.3:6:1:0.3333:1 +5 6831048 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49872;SOR=0;LSEQ=ATGCACACGCACACACAGAC;RSEQ=CATTCTTACACATGCATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:9,12:21,2:0.087:2,2:41.5:1:31:1:1:1.32:60:4:0.087:0:1 0/0:17:0:0,0:8,9:17,0:0:2,0:14.9:1:29.6:1:1:0:60:34:1:0:0.3 +5 6831103 . ACT A 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=ATGCACGCACACACAGGCAC;RSEQ=CTCACACGTGCACGCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:6,10:16,4:0.2:2,2:16:0:34.3:1:1:1.62:60:8:0.2105:0:0.5 0/1:25:5:4,1:9,12:21,5:0.2:2,2:19.4:1:27.2:1:0.32174:5.01:55:4:0.16:0.12:1.2 +5 6831147 . T C 70 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACACACATGCACGCACA;RSEQ=ACAGGCACACTCTCACACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:28:1:31.7:1:1:0:54:6:1:0:1 1/1:5:5:2,3:0,0:0,5:1:0,2:27.8:1:30.2:1:1:0:49.8:10:1:0:1.6 +5 6831571 . T C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGACAAAATGGTAAAATGA;RSEQ=ATGCACACACCTCAGACGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36:0:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 7869455 . TC T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.11797;LSEQ=GGTTCCCACGCCCTTCGGCC;RSEQ=CGGGGGTCGCCGCGGGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:5:5,0:39,3:42,5:0.1064:2,0:27.2:1:34:0:1:0:60:10:0.1087:0:0 0/1:17:2:2,0:14,1:15,2:0.1176:1,0:21:1:32.5:1:1:0:60:4:0.1176:0:0 +5 7869518 . TC T 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.05975;SOR=Inf;LSEQ=TTTGGCCTTTGGCTTTGGTG;RSEQ=CCCGGGAGCGTGTCCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:88,60:148,0:0:2,0:26.9:1:31:1:1:0:60:28.6:1:0:0.2 0/1:96:3:1,2:57,36:93,3:0.0313:2,2:6:1:25.6:1:0.56037:3.12803:60:6:0.0313:0.0208:0.3 +5 7869546 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51244;SOR=0;LSEQ=AGCGTGTCCTTGGGCTCGGC;RSEQ=TCGGCCTCTGCCGCGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:69,81:150,2:0.0132:2,2:30.5:1:31:1:1:1.17:60:4:0.0133:0:2 0/0:108:0:0,0:57,51:108,0:0:2,0:26.7:1:30.3:1:1:0:60:107:1:0:0.3 +5 7869578 . C T 103 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00015;SOR=20.03309;LSEQ=CGCGGGAGGCCCCTGGGCGG;RSEQ=GTGGGGTCTCTCCTCATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:1:0,1:39,68:107,1:0.0091:2,0:43:0:29:0:1:0:60:2:0.0096:0:1 0/1:70:11:5,6:25,34:59,11:0.1571:2,2:23.5:1:30:1:1:1.13:60:22:0.1571:0:1.1 +5 8181426 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAGCTCAAGGCAGGGGAAG;RSEQ=GACAGAGAAAGAACAAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 8182721 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10526;SOR=Inf;LSEQ=TAATGATTTTCATCATTTGT;RSEQ=GTCATTTTAAGCCTCAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:18,8:26,0:0:2,0:19.3:1:31.8:1:1:0:60:52:1:0:0.3 0/1:13:2:1,1:9,2:11,2:0.1538:2,2:25.5:1:27.5:1:0.42308:3.87298:60:4:0.1667:0:1 +5 8182785 . AC A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50506;SOR=0;LSEQ=GGTCAGAGTTTAGAGTCGCC;RSEQ=CCCCACCCGCCACCCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:18,26:44,2:0.0435:2,2:22.5:1:31.5:1:1:1.43:60:4:0.0435:0:1.5 0/0:34:0:0,0:18,16:34,0:0:2,0:23.1:1:31:1:1:0:60:68:1:0:0.8 +5 8182799 . C T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.97009;LSEQ=GTCGCCACCCCCACCCGCCA;RSEQ=CCAGCAGGTGCACTTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:22:6,16:9,11:20,22:0.5238:2,2:23.2:1:30.1:1:0.33566:2.1407:60:21:0.5122:0:1.1 1/0:31:16:7,9:8,7:15,16:0.5161:2,2:26.6:1:29.6:1:0.72443:1.45111:60:32:0.5161:0:1.5 +5 8306347 . G A 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=8.000;MSILEN=1;SSF=0.52381;SOR=0.26566;LSEQ=CCCACCTGAGAGAGAGAGAG;RSEQ=GGGGGGCAGGGGAATCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:12.3:1:32.3:1:1:0:60:6:0.6:0:1 0/1:4:1:1,0:2,1:3,1:0.25:2,0:44:0:31:0:1:0:60:2:0.25:0:1 +5 8306754 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48052;SOR=0;LSEQ=TGCTGGAGCCAGGGAGGCTG;RSEQ=ACAGCTTGGTCCCAAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:21:0:31:1:1:1:41.5:4:0.1667:0:1.5 0/0:10:0:0,0:5,5:10,0:0:2,0:28.6:1:29.6:1:1:0:60:20:1:0:0 +5 8307486 . G GA 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AGAAGAAATAAAGAAAAGAA;RSEQ=AAAAAAAAAGGGAAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:13.3:1:32:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:28.2:1:1:0:60:4:1:0.5:0 +5 8452726 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAAGTCACATGGTTGGC;RSEQ=TGTAATGAAAGTACCTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 8453517 . CT C 53 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=1.28822;LSEQ=TCAAACGCTTTACCACATGA;RSEQ=TTTTTTAGACCATTATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:3:2,1:249,99:348,3:0.0085:2,2:30.7:1:33.7:1:1:1.25675:60:6:0.0088:0:0 0/1:182:2:1,1:130,50:180,2:0.011:2,2:17:1:30:1:0.48303:2.58427:60:4:0.0111:0:0 +5 8453614 . AG A 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TTTCAAACACTAATTATTCT;RSEQ=TCTAAGTTATAACCAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:698:0:0,0:336,359:695,0:0:2,0:26.2:1:32.5:1:1:0:60:114.833:0.9971:0:0.9 0/1:422:28:13,15:194,200:394,28:0.0664:2,2:29.9:1:29.8:1:0.84617:1.11893:60:56:0.0675:0:1.1 +5 8453623 . T C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.13893;LSEQ=CTAATTATTCTAGTCTAAGT;RSEQ=ATAACCAGCTCATCTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:680:496:220,276:90,94:184,496:0.7294:2,2:25.8:1:32:1:0.29937:1.20083:60:123:0.73:0:1.3 0/1:419:114:54,60:150,155:305,114:0.2721:2,2:24.8:1:30.4:1:0.82623:1.07507:60:113:0.2749:0:1.3 +5 8453697 . C T 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAGTCAGATGATTATAT;RSEQ=TGATCAGTGAACATGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:266:266:42,224:0,0:0,266:1:0,2:23.9:1:30.8:1:1:0:59.7:265:1:0:1.4 1/1:150:150:31,119:0,0:0,150:1:0,2:23.4:1:29.3:1:1:0:60:74:1:0:1.3 +5 8453897 . T C 120 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTTATTGTACATTTTG;RSEQ=TTTATTGAGTTTCACAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:0,12:1:0,0:25.6:1:33.6:1:1:0:58.9:24:1:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:10:0:33:0:1:0:60:2:1:0:1 +5 8453932 . CAT C 87 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGATACTGTATTTTATATA;RSEQ=ATATATATATATATAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:37.2:1:33.8:1:1:0:57.8:12:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 8726406 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2601;SOR=Inf;LSEQ=GCTGACCGGGTCGCACGCTG;RSEQ=CTCCGGCTTCACCAACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:27,0:0:2,0:23:1:32:1:1:0:60:54:1:0:0.3 0/1:38:3:2,1:17,18:35,3:0.0789:2,2:21.7:1:28.7:1:1:2.08:60:6:0.0833:0:1.7 +5 8726429 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53846;SOR=Inf;LSEQ=CCGGCTTCACCAACACCTTG;RSEQ=ATGTTGTTTCTGTGCAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:18,0:0:2,0:30.7:1:31.8:1:1:0:60:17:1:0:0.4 0/1:34:2:1,1:15,17:32,2:0.0588:2,2:21:1:28:1:1:1.13:60:4:0.0588:0:2 +5 9535516 . G C 128 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01915;SOR=0;LSEQ=AAGCTGCAACAGCCAAGATG;RSEQ=GCTGCCTGGACACGCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:9,10:0,0:0,19:1:0,2:26:1:30.2:1:1:0:60:18:1:0:1.2 1/0:8:5:3,2:2,1:3,5:0.625:2,2:18.6:1:30:1:1:1.28664:60:10:0.625:0:1 +5 9594749 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71643;LSEQ=TGGTGGAGGTGGAAGATCTT;RSEQ=ATCAAATATAGACGAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:5,2:7,2:0.2222:2,0:32.5:1:29:1:1:0:60:4:0.25:0:1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:3:0:28:0:1:0:60:2:0.1667:0:1 +5 11504369 . TTGC T 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.62107;SOR=1.78321;LSEQ=CATGGTCAGGTCTAATGCTG;RSEQ=TGCTGCTGCTGCCGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:61,66:127,2:0.0155:2,2:25:0:32.5:1:1:1.08:60:4:0.0155:0:0 0/1:73:2:1,1:40,32:72,2:0.0274:2,2:15.5:1:29:1:1:1.2462:60:4:0.0278:0.0137:0.5 +5 11504409 . C G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52394;SOR=0;LSEQ=GCTGCTGATGATGATGACGA;RSEQ=GATGACTCAGCGTAATGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:37,62:99,2:0.0198:2,2:34:1:33:1:1:1.67:60:4:0.02:0:1 0/0:63:0:0,0:27,36:63,0:0:2,0:25.3:1:29.6:1:1:0:59.5:62:1:0:0.2 +5 12856955 . A G 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57426;SOR=0;LSEQ=TAACCGGTCAGGGATAGTAC;RSEQ=CAATGCTGCCCGGCCGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:4:3,1:47,12:59,4:0.0635:2,2:18.8:1:32.3:1:1:1.29966:53.5:8:0.0656:0:1.3 0/0:25:0:0,0:19,6:25,0:0:2,0:23.6:1:29.4:1:1:0:58:50:1:0:0.2 +5 12856961 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCAGGGATAGTACACAATG;RSEQ=TGCCCGGCCGGTGTTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:49,16:65,2:0.0299:2,2:19.5:1:32.5:1:0.44595:3.00121:55:4:0.0303:0:1 0/0:27:0:0,0:21,6:27,0:0:2,0:25:1:30.9:1:1:0:57.4:26:1:0:0.3 +5 12857026 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54287;SOR=0;LSEQ=TGCCTTTCAAACTCTTACAC;RSEQ=AACCTCTGGAGTTGGGCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:98,85:183,2:0.0108:2,2:22.5:1:31:1:1:1.15205:54.5:4:0.0108:0:1 0/0:100:0:0,0:49,51:100,0:0:2,0:31.9:1:31.2:1:1:0:40.5:200:1:0:0.2 +5 12858465 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCAGCCTGACAATGAGA;RSEQ=AGAAAAGAAAAACTCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:32:1:1:0:60:4:1:0:1.5 +5 14007036 . T C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACAATGAGCTCCACTC;RSEQ=GAGCCTCCAGTGGCCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:17.6:1:29.5:1:1:0:60:16:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:27.5:1:1:0:60:4:1:0:1.5 +5 14008995 . G A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12131;LSEQ=GGTAAACAGAAAAAGAAAGC;RSEQ=TTCATTCCACCAGTTCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:88:65,23:34,8:42,88:0.6718:2,2:23.5:1:30.9:1:0.50962:1.49931:60:176:0.6769:0:1.3 0/1:66:13:9,4:35,18:53,13:0.197:2,2:26:1:29.3:1:1:1.15:60:26:0.197:0:1.2 +5 14009018 . CT C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12192;SOR=Inf;LSEQ=CATTCCACCAGTTCTATGCC;RSEQ=TCACCCCATGCATCGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:131,47:178,0:0:2,0:26:1:31.6:1:1:0:60:58.333:1:0:0.8 0/1:96:2:1,1:63,31:94,2:0.0208:2,2:23.5:1:30.7:1:1:2.01612:60:4:0.0211:0.0104:0 +5 14009050 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1157;SOR=Inf;LSEQ=CATCGGGCCTGGCCATGGGC;RSEQ=GGGCCTGCCCCTGCAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:141,85:226,0:0:2,0:25.5:1:30.5:1:1:0:60:36.667:1:0:0.7 0/1:117:2:1,1:70,45:115,2:0.0171:2,2:19.5:1:30:1:1:1.54946:60:4:0.0171:0:1 +5 14009079 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14051;SOR=Inf;LSEQ=CCCTGCAAGGACAGGACAAA;RSEQ=TGATCCATGTCCTGTCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:148,118:266,0:0:2,0:24.3:1:32.6:1:1:0:60:532:1:0:0.8 0/1:160:2:1,1:96,62:158,2:0.0125:2,2:31.5:1:28.5:1:1:1.54398:60:4:0.0125:0:1.5 +5 14009085 . C T 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19412;LSEQ=AAGGACAGGACAAACTGATC;RSEQ=ATGTCCTGTCTCGAAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:282:159:86,73:68,55:123,159:0.5638:2,2:22.8:1:30:1:0.90413:1.04932:60:38.75:0.5596:0:1.3 0/1:175:35:20,15:82,58:140,35:0.2:2,2:18.2:1:29.2:1:1:1.05998:59.9:70:0.2023:0:1.3 +5 14009089 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15465;SOR=Inf;LSEQ=ACAGGACAAACTGATCCATG;RSEQ=CCTGTCTCGAAGCTGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:155,142:297,0:0:2,0:23.6:1:29.7:1:1:0:60:48.5:1:0:0.7 0/1:193:2:1,1:107,84:191,2:0.0104:2,2:40:0:32:0:1:1.27219:60:4:0.0106:0:1 +5 14009175 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52268;SOR=0;LSEQ=GGTAGGTAACTCACTCTTGA;RSEQ=TTGAAGCCGTCGGTTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:64,129:193,2:0.0102:2,2:25.5:1:32.5:1:1:2.01:60:4:0.0102:0:1 0/0:126:0:0,0:42,84:126,0:0:2,0:22.3:1:31:1:1:0:60:252:1:0:0.1 +5 14761059 . C T 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTATCTAGCCATAAGGTCA;RSEQ=TGCAGATATAACTGGTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:32:0:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:48:0:29:0:1:0:60:2:1:0:2 +5 14761178 . T G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGATGCACACAGGGAGAAC;RSEQ=CAGTGTGAAGATGAACGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:13,3:0,0:0,16:1:0,2:30.8:1:30.9:1:1:0:60:32:1:0:2 1/1:6:6:4,2:0,0:0,6:1:0,2:20.8:1:30.5:1:1:0:60:12:1:0:1.8 +5 14761194 . C G 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACTCAGTGTGAAGATGAA;RSEQ=GCAGAAACCGGGGTGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:12,8:0,0:0,20:1:0,2:26.7:1:32.3:1:1:0:60:40:1:0:1.8 1/1:7:7:4,3:0,0:0,7:1:0,2:24.9:1:30.6:1:1:0:58.9:14:1:0:1.9 +5 14761303 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05;SOR=Inf;LSEQ=AGTCTTCCTCATATCTCTCA;RSEQ=AAGGAACCGCCCCTGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:12,0:0:2,0:25.9:1:31.3:1:1:0:60:11:1:0:0 1/0:4:2:0,2:0,2:2,2:0.5:0,0:42:1:33:0:1:0:60:4:0.5:0:1 +5 14869666 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCATGATAATCAGGTTAG;RSEQ=AATGTTTTAAGGATGAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:3,0:30,1:31,3:0.0882:1,0:24:1:31:1:1:0:60:6:0.0909:0:1 0/0:10:0:0,0:9,1:10,0:0:2,0:23.4:1:31.9:1:1:0:60:20:1:0:0.4 +5 14869709 . A G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00653;SOR=3.73918;LSEQ=ATTATTAGACCTGCGAGGAT;RSEQ=AACCATCTGGATAGTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:20:19,1:63,2:65,20:0.2353:1,1:19.5:1:33:1:0.55776:1.64688:60:40:0.2381:0:1.1 1/0:26:14:14,0:12,0:12,14:0.5385:0,1:22.4:1:32.4:1:1:0:60:28:0.5385:0:1 +5 14869915 . A G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.80446;LSEQ=TATCTCGATATGATTCTTAC;RSEQ=TGCACACAAACACACACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:191:76,115:287,376:663,191:0.2237:2,2:23.1:1:31:1:0.40701:1.1548:59.9:62.667:0.2225:0:1.1 0/1:463:207:89,118:118,136:254,207:0.4471:2,2:25.5:1:30.1:1:0.51004:1.15001:60:40.4:0.444:0:1.1 +5 14870158 . G GGAA 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.56923;SOR=3.3097;LSEQ=GCGGGTACAGGGTGGAGCAG;RSEQ=GAAGAAGCCCTTGGGGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:1,4:0,6:6,5:0.4545:0,2:23.2:1:30.6:1:0.45455:0:58:10:0.5:0.0909:1.6 1/0:4:3:1,2:0,1:1,3:0.75:0,2:16.7:1:28.5:1:1:0:60:6:0.75:0.5:0.7 +5 14870166 . C T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=AGGGTGGAGCAGGGAAGAAG;RSEQ=CCTTGGGGTACCCTTGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:10,0:0:2,0:25.6:1:31.1:1:1:0:60:20:1:0:0 1/0:4:2:1,1:0,2:2,2:0.5:0,2:8:0:27:1:1:0:60:4:0.5:0:1 +5 14870691 . G C 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGAACGCAGCTGCATCCC;RSEQ=CTGGTGGCCCTGCCAAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:32.5:1:1:0:60:4:1:0:1.5 +5 16590934 . C CAT 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.5;SOR=Inf;LSEQ=AAAACACACAGACATGCAAA;RSEQ=ACACACATGCAAACACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:38:1:33.3:1:1:0:60:6:1:0:0.3 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:29:0:31:0:1:2.44949:31:4:0.3333:0:1 +5 16590956 . C CACAA 55 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.28613;SOR=4.35427;LSEQ=CACACATGCAAACACACATG;RSEQ=ACACACAAAAAACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:5,2:0.2857:2,0:17:1:29.1:1:1:0:60:4:0.2857:0.1429:0 1/0:6:4:3,1:1,1:2,4:0.6667:2,2:3.2:1:27.6:1:1:2.45:44.8:4:0.5494:0.5055:0.8 +5 16590985 . TAC T 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=1;SOR=0.84709;LSEQ=AAAACACACACATGCAAACA;RSEQ=ACACACACGCACACACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:3,2:5,3:0.375:2,2:20.7:1:31.7:1:1:1.29:60:6:0.375:0.125:0.3 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:30:0:32:0:1:0:60:2:0.3333:0:0 +5 16591013 . A C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12644;SOR=Inf;LSEQ=CACGCACACACACATGCACA;RSEQ=ACACAAAAAAACACACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:13,6:19,0:0:2,0:16.6:1:28.8:1:1:0:57.6:18:1:0:0.2 0/1:11:2:1,1:4,5:9,2:0.1818:2,2:5:0:33.5:1:1:1.22:60:4:0.1818:0:1.5 +5 16591023 . A AC 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.76111;SOR=1.2435;LSEQ=CACATGCACAAACACAAAAA;RSEQ=ACACACACATGCAAATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:12:8,4:11,4:15,12:0.4444:2,2:15.8:1:31.7:1:1:1.3587:60:24:0.4615:0.2222:0.6 1/0:16:8:5,3:3,5:8,8:0.5:2,2:15.8:1:29.6:1:0.61927:2.60:57.6:7:0.4667:0.1875:0.9 +5 16591070 . GCA G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.10013;SOR=Inf;LSEQ=ACGCACATGCAAACACACAT;RSEQ=CACACACACATATTTGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:46,35:81,0:0:2,0:29.2:1:32.9:1:1:0:59:80:1:0:0.2 0/1:38:2:1,1:19,17:36,2:0.0526:2,2:39:1:31.5:1:1:1.11437:60:4:0.0541:0:0 +5 16591093 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03915;SOR=Inf;LSEQ=CACACACACATATTTGCTTG;RSEQ=CTCCATAGCACTTATTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:38,32:70,0:0:2,0:30.5:1:31.4:1:1:0:60:34:1:0:0.2 0/1:37:3:2,1:17,17:34,3:0.0811:2,2:44:1:28.3:1:1:1.96:60:6:0.0811:0:1.3 +5 17463005 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGGTTATTCTAGTTAGC;RSEQ=ATTCCTCTAACCTTTTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 17463384 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATGGTCAGGTCCTTCCG;RSEQ=AGGGCTGCTGCAGTTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:12.5:1:33:1:1:1.10554:60:4:0.0952:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:26.3:1:28.2:1:1:0:60:20:1:0:0.4 +5 17463669 . TG T 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=GTGAAGGGGTTGTGCTTCTC;RSEQ=GGGGGGAACCCACTTGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:22.4:1:31.6:1:1:1.41418:60:10:0.7143:0.1429:0.2 1/1:6:6:1,5:0,0:0,6:1:0,2:22.8:1:32:1:1:0:60:12:1:0.1667:0 +5 17464034 . C T 79 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCCACCCAGGGAGCTTC;RSEQ=GTGTTAGGCAGTTGCAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:24.5:1:30.7:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 17491212 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCCACTTGACACTAGT;RSEQ=CCTTGGGAGCCTCAAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:0,10:1:0,2:20.5:1:32.3:1:1:0:56.4:20:1:0:1.6 1/1:6:6:5,1:0,0:0,6:1:0,2:21.7:1:29.8:1:1:0:60:12:1:0:1.3 +5 17491269 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCACACACAAACACAAC;RSEQ=GCCACCTGATTTCTGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:23,1:0,0:0,24:1:0,1:26.8:1:32.5:1:1:0:57.5:48:1:0:1.3 1/1:9:9:5,4:0,0:0,9:1:0,2:19.6:1:30.6:1:1:0:60:18:1:0:1.2 +5 17491448 . T A 195 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTCCTCTAGAGTGCAAGGT;RSEQ=TCCCAGGAGCGTGGGCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:114:95,19:317,45:362,114:0.2395:2,2:23:1:28.6:1:0.27078:1.40781:58:113:0.2399:0:1.1 0/0:263:0:0,0:215,48:263,0:0:2,0:23.7:1:29.9:1:1:0:59:262:1:0:0.1 +5 17491543 . G A 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30269;SOR=0;LSEQ=TGACGCGCCTGGCATGGATG;RSEQ=CACACAGGTTGGTGTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:4:2,2:210,179:389,4:0.0102:2,2:14.5:1:29.5:1:1:1.1727:35.8:8:0.0104:0:1 0/0:237:0:0,0:124,113:237,0:0:2,0:13.6:1:30.3:1:1:0:42.4:117.5:1:0:0.1 +5 17491628 . G A 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11951;SOR=7.3204;LSEQ=AATGGCCGCGCTCTGGAAGC;RSEQ=CAGGTCCGGGCTGATGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:1:1,0:164,270:434,1:0.0023:2,0:1:0:26:0:0.37931:0:60:2:0.0023:0:1 0/1:120:2:1,1:40,78:118,2:0.0167:2,2:48:0:30:1:1:1.94:22:4:0.0168:0:1 +5 17502240 . C T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=0.20977;LSEQ=CAATGGTAGCGCTCTGGAAG;RSEQ=GCAGGACCAGGATGATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:37:31,6:39,17:56,37:0.3978:2,2:23.4:1:30.2:1:0.14603:2.23:40.3:36:0.4091:0:1.1 0/1:58:7:6,1:34,17:51,7:0.1207:2,2:20.3:1:30.3:1:0.41714:2.95:34:14:0.1228:0:1 +5 17502275 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17719;SOR=Inf;LSEQ=ATGGCCTAGGAGATCTTGCG;RSEQ=ACCAGGCGCTGGAAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:85,56:141,0:0:2,0:26.2:1:32:1:1:0:34.5:69.5:1:0:0.3 0/1:103:2:1,1:55,46:101,2:0.0194:2,2:18:1:28:1:1:1.19357:21.5:4:0.0196:0:1 +5 17502359 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1404;SOR=Inf;LSEQ=TCGCACATTGCCAGGCCTGT;RSEQ=GCGGTGAGGCTTCTTGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:48,83:131,0:0:2,0:23.5:1:30.3:1:1:0:48.1:42.667:1:0:0.1 0/1:79:2:1,1:31,46:77,2:0.0253:2,2:45:1:30.5:1:1:1.48:33.5:4:0.026:0:1 +5 17502367 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52973;SOR=0;LSEQ=TGCCAGGCCTGTAGCGGTGA;RSEQ=GCTTCTTGATCCCTCCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:38,76:114,2:0.0172:2,2:21.5:1:30:1:1:1.99:60:4:0.0179:0:1 0/0:69:0:0,0:28,41:69,0:0:2,0:23:1:29.9:1:1:0:49.9:22:1:0:0.2 +5 17502472 . G T 79 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGCTGGCTGTTGGCTTGG;RSEQ=GCATGCAGTGGCCTGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:16.5:1:31.8:1:1:0:21.3:8:1:0:1 1/1:6:6:0,6:0,0:0,6:1:0,0:8.7:1:30.7:1:1:0:24.3:12:1:0:1 +5 17602802 . C G 112 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.71352;LSEQ=ACAACACAGCAAAAGAGAAA;RSEQ=CATTAACAGAGAAAAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:10,0:7,0:7,10:0.5882:0,0:26.6:1:33.8:1:1:0:39.4:20:0.5882:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:13:0:34:0:1:0:60:2:0.5:0:1 +5 17602891 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05471;SOR=Inf;LSEQ=GGGCTCTTAAGCACCCTCTC;RSEQ=ACGGAGGCTGTGGGCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:49,0:0:2,0:22.7:1:31.6:1:1:0:58.9:98:1:0:0.1 0/1:31:3:2,1:18,10:28,3:0.0968:2,2:16.3:1:29:1:1:1.11:54.7:6:0.1:0:1 +5 17620724 . GT G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51332;SOR=0;LSEQ=CTGGCATGGATGACATACAG;RSEQ=TGGTGTCTTCAAAGAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:97,81:178,2:0.0111:2,2:29:1:31.5:1:1:1.19632:60:4:0.0112:0:0 0/0:127:0:0,0:67,60:127,0:0:2,0:25.4:1:29.2:1:1:0:59.3:41.333:1:0:0.1 +5 17620755 . G A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28483;SOR=0;LSEQ=CAAAGAGGCGCACCAGGTAG;RSEQ=CCTCATTGGTCCCCTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:3:3,0:82,82:164,3:0.018:2,0:14.3:1:21:1:0.24573:0:60:2:0.0122:0:1.3 0/0:106:0:0,0:52,54:106,0:0:2,0:27.9:1:30.7:1:1:0:59.1:52:1:0:0.1 +5 17620777 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18877;SOR=Inf;LSEQ=CTCATTGGTCCCCTGAAAGC;RSEQ=CCAACGGCCACGCTCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:58,65:123,0:0:2,0:23:1:30:1:1:0:60:122:1:0:0 0/1:95:2:1,1:43,50:93,2:0.0211:2,2:21.5:1:31:1:1:1.16:60:4:0.0213:0:1 +5 17620793 . TG T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50741;SOR=0;LSEQ=AAGCACCAACGGCCACGCTC;RSEQ=GAAGCCCAGGTCCCGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:45,62:107,2:0.0183:2,2:11.5:1:31:1:1:1.37:60:4:0.0187:0:1 0/0:82:0:0,0:36,46:82,0:0:2,0:24.3:1:29.9:1:1:0:60:26.333:1:0:0 +5 17625684 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCTCTCTGCCGAGTTGG;RSEQ=AGGCCAGCTGCATGTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:8,1:9,2:0.1818:2,2:22:1:27.5:1:0.34545:6:60:4:0.1818:0:1.5 0/0:3:0:0,0:2,1:3,0:0:2,0:22.3:1:32.7:1:1:0:60:6:1:0:0.7 +5 17625744 . T C 113 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08333;SOR=0;LSEQ=TGGCATGGATAACACATAGG;RSEQ=TGATGTCTTTAAAGAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:7,4:0,0:0,11:1:0,2:25.3:1:32.8:1:1:0:60:22:1:0:1.1 1/0:5:3:2,1:2,0:2,3:0.6:0,2:8:1:30.7:1:1:0:60:6:0.6:0:1 +5 17655069 . AGCTGAAGT A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTTGAAAATTGATGTAG;RSEQ=GCTGAAACTCGCTCACTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:35,2:0,0:0,37:1:0,2:23.1:1:32.7:1:1:0:59.5:74:1:0.2703:0.3 1/1:3:3:3,0:0,0:0,3:1:0,0:28:1:31.7:1:1:0:60:6:1:0:0 +5 17655589 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05812;SOR=Inf;LSEQ=CGGCTGCTTTGGTGGCCAGG;RSEQ=GCTTCCTGGGGGCCTGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:25,71:96,0:0:2,0:25.8:1:31:1:1:0:28.4:47:1:0:0.1 0/1:31:2:1,1:5,24:29,2:0.0645:2,2:39.5:1:30:1:0.35484:4.47:23:4:0.0667:0:1.5 +5 17670092 . C T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54118;SOR=0;LSEQ=ACAGTCACTACCTGTGATTT;RSEQ=TGCTTATGTTTCCACTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:10,4:0.2857:0,0:23.8:1:31.5:1:1:0:58.5:8:0.3077:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:19.3:1:31:1:1:0:60:6:1:0:0 +5 17670208 . G GA 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.13999;SOR=2.0465;LSEQ=TACCAGTAACTGAAAGAAGA;RSEQ=AAAAAAAAAACACAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:12:12,0:107,3:110,12:0.0976:1,0:24.8:1:31.7:1:1:0:60:24:0.0992:0.0163:0.9 0/1:55:10:9,1:41,4:45,10:0.1818:2,2:22.5:1:29.3:1:1:1.13613:60:20:0.1818:0.0364:0.6 +5 17670396 . G T 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=TCAAAGAGGCGCACCAGGTA;RSEQ=GCCTTGCTGGGCTCCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:23:9,14:321,477:798,23:0.028:2,2:21.9:1:30.5:1:1:1.04677:58.8:46:0.0284:0:1 0/0:487:0:0,0:200,287:487,0:0:2,0:25.5:1:30.4:1:1:0:58.9:59.875:1:0:0.2 +5 17670555 . G T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.07604;LSEQ=CTGATTTTGCAGAGTGCCAG;RSEQ=GTGCCAGACCTGTAGCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:27,127:154,2:0.0127:2,2:30:1:31:1:0.32771:4.64:60:4:0.013:0:1 0/1:73:1:0,1:19,53:72,1:0.0137:2,0:1:0:24:0:1:0:60:2:0.0137:0:1 +5 17670570 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGGGTGCCAGACCTGTA;RSEQ=CCGTGGGGCTTCTTGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:16,106:122,2:0.0161:2,2:22:1:27:1:0.25636:6.46:60:4:0.0163:0:2 0/0:55:0:0,0:10,45:55,0:0:2,0:19.5:1:31.2:1:1:0:60:54:1:0:0.1 +5 17670600 . C A 166 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0.05057;LSEQ=TTCTTGATCCCTCCTGTAGG;RSEQ=GGCGCCCTCTTGCTGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:36:5,31:5,36:41,36:0.4675:2,2:22.4:1:32.2:1:1:1.16:59.6:17:0.4722:0:1.1 0/1:24:1:0,1:5,18:23,1:0.0417:2,0:44:0:28:0:1:0:60:2:0.0417:0:1 +5 17670818 . T C 72 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGAGCCTGTGAGTTGAGATC;RSEQ=GTGCAGAAGACGCAACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:25.2:1:31.4:1:1:0:60:10:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:50:0:28:0:1:0:60:2:1:0:1 +5 18119214 . T C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTAGAAGGCTGGCATGA;RSEQ=CCATGGAGAGAAGGAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:32:0:34:0:1:0:44:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:29.5:1:1:0:49.5:4:1:0:1 +5 18119944 . T C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49;SOR=0.37048;LSEQ=TCCCCAGCAAAATACACCCT;RSEQ=TCCACCAAGGGACAAAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:11,6:1,0:1,17:0.9444:0,2:24.5:1:32.5:1:1:0:56.7:34:0.9444:0:1.1 1/1:7:6:3,3:0,1:1,6:0.8571:0,2:7.8:1:31.2:1:1:0:51.3:12:0.8571:0:1.5 +5 18119968 . G A 62 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02228;SOR=13.45809;LSEQ=ACCAAGGGACAAAGTGCTTC;RSEQ=TAAAATGGGTTCTGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:11,8:19,1:0.05:2,0:19:0:33:0:0.45:0:50:2:0.05:0:2 0/1:9:4:2,2:2,3:5,4:0.4444:2,2:22.5:1:31.3:1:1:1.43:42.8:8:0.4444:0:1.8 +5 18120256 . G GACA 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=8.000;MSILEN=3;SSF=0.07177;SOR=0.29279;LSEQ=GAAAGAAACAAGCAGAAAGT;RSEQ=ACAACAACAACAACAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:19:12,7:7,2:9,19:0.5938:2,2:22.8:1:31.1:1:0.67003:1.99246:60:38:0.5938:0.1875:0.3 0/1:17:5:2,3:5,0:5,5:0.2941:0,2:31.2:1:27.8:1:0.16667:0:54.2:10:0.2941:0:0.6 +5 18120390 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0129;SOR=Inf;LSEQ=AATGTGGAAAACCCAAAAGG;RSEQ=CAGAGTGCCTCTTGTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:10,17:27,0:0:2,0:20.7:1:29.3:1:1:0:60:54:1:0:0 1/0:4:2:1,1:0,2:2,2:0.5:0,2:12:1:32.5:1:1:0:46:4:0.5:0:1.5 +5 18120489 . C A 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTCACAGAAGTAGGCTTC;RSEQ=GAAGATGGATAATAACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:1,4:0.8:0,2:24.3:1:32.5:1:1:0:51.3:8:0.8:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 18120548 . A G 64 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGTGTTCTAACCCAATGCAA;RSEQ=GAAGCTAAGAACCATGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:14.3:1:32:1:1:0:51.3:8:1:0:1.8 1/1:1:1:1,0:0,0:0,1:1:0,0:12:0:33:0:1:0:60:2:1:0:1 +5 18123234 . CA TG 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACTGGCAAATTGAATC;RSEQ=GCAGCACATCAAAGAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37:0:32:1:1:0:55:4:1:0:1.5 +5 21758500 . C T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGAGACTCTGACTTTCTTTG;RSEQ=CTAATCATTGTAGCAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31:1:29.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:38.5:1:30.5:1:1:0:60:4:1:0:0 +5 21759524 . CTAAA C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=5.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AACCATGTCTCTCCCTCCCT;RSEQ=TAAATAAATAAATAAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:30:1:1:0:60:4:1:0:0.5 +5 21760602 . C A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2984;LSEQ=TTCAAAGAAAAGTATTGATT;RSEQ=CTCCCTTTGTGCCTTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:637:570:286,284:32,34:66,570:0.8948:2,2:26.8:1:29:1:0.89665:1.07:59.9:141.5:0.8942:0:1.1 1/0:304:218:105,113:43,42:85,218:0.7171:2,2:25.3:1:27.8:1:0.7982:1.10146:60:53.5:0.7181:0:1.2 +5 21760731 . T C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00101;SOR=Inf;LSEQ=GGTGATAATCTAAAGGAGAA;RSEQ=TGTTGCCCAGCAGGTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:3,113:116,0:0:1,0:25.7:1:30.6:1:1:0:60:232:1:0:0 0/1:41:5:0,5:1,35:36,5:0.122:1,0:27:1:32.6:1:1:0:60:10:0.122:0:1 +5 21824695 . C A 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28967;LSEQ=ACACAGCCTTGTTCTCTTTT;RSEQ=CTTTCTCTGCTGTTTTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:961:870:375,495:34,53:87,870:0.9053:2,2:24.7:1:28.8:1:0.49697:1.18:59.9:65.923:0.905:0:1.1 1/0:550:404:182,222:59,87:146,404:0.7345:2,2:22.9:1:28:1:0.3812:1.21:60:133.667:0.7385:0:1.1 +5 21825081 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACCGGCCTGGCCAACAT;RSEQ=GTGAAACTCCATCTCTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:27:1:30.7:1:1:0:50.7:6:1:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 22934322 . T G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGCTATAGGAACCAGAA;RSEQ=AGCCAGTTTATCTATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:10:1:33.5:1:1:0:50:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 22934579 . G T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.21759;LSEQ=ACACCACCTGGCATTTATAG;RSEQ=ACAGGCTTCTGAAATCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:89:71:49,22:12,6:18,71:0.7978:2,2:22.7:1:29.2:1:1:1.11:37.3:70:0.7955:0:1.2 0/1:61:28:15,13:21,12:33,28:0.459:2,2:27.1:1:28.6:1:0.44718:1.50621:39.1:56:0.459:0:1 +5 22934613 . C G 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08622;SOR=2.35016;LSEQ=ATCAGACAATGCCTTTCAAA;RSEQ=TCTTATACCAACCTCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:8:5,3:68,58:126,8:0.0593:2,2:29.6:1:31.1:1:0.7274:1.42:39.9:7:0.053:0:1.8 0/1:85:11:5,6:39,35:74,11:0.1294:2,2:30.8:1:29.7:1:0.75205:1.33256:45.5:10:0.119:0:1.7 +5 22934638 . G T 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02358;SOR=0;LSEQ=ATACCAACCTCTGGAGTTGG;RSEQ=TGACATGGCTTCTCCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:8:3,5:58,61:119,8:0.063:2,2:30.5:1:28.5:1:0.71939:1.57907:31.8:7:0.0569:0:1.8 0/0:82:0:0,0:35,47:82,0:0:2,0:28.2:1:30.1:1:1:0:35.2:81:1:0:0.5 +5 22934660 . T C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60214;SOR=1.30268;LSEQ=GACATGGCTTCTCCCCTTTC;RSEQ=AGTTCTCGTGACGGCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:9:3,6:40,64:104,9:0.0796:2,2:21.8:1:31.3:1:1:1.24759:34.3:18:0.0818:0:1.7 0/1:69:7:1,6:23,39:62,7:0.1014:2,2:24.7:1:30.3:1:0.40794:3.48638:37.6:14:0.1014:0:1.9 +5 23145691 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49365;SOR=0;LSEQ=CTAGTTTCGGTCTTTGAGGC;RSEQ=GCTGACCCTTGGATGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:31:1:29.5:1:1:1.07:60:4:0.0667:0:1 0/0:27:0:0,0:13,14:27,0:0:2,0:27.1:1:29.6:1:1:0:56.6:54:1:0:0.2 +5 23146100 . G A 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06127;SOR=0;LSEQ=AGGGTGTGTTTCGCTGGGGG;RSEQ=AAACCCACTTGTCTGTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:3,3:7,7:14,6:0.3:2,2:29.7:1:31.8:1:1:1:56.3:12:0.3:0:1 0/0:12:0:0,0:5,7:12,0:0:2,0:26.9:1:26.3:1:1:0:58.8:11:1:0:0.5 +5 23146227 . G A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGAGAGATCTGAATTCT;RSEQ=TCCCTGAGCCTCTGGCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:16,10:26,2:0.0714:2,2:6.5:1:28.5:1:1:1.57244:26:4:0.0714:0:1.5 0/0:11:0:0,0:7,4:11,0:0:2,0:18.7:1:31.4:1:1:0:51.1:22:1:0:0.3 +5 23303287 . C A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCACAATGAGGAAAAAAA;RSEQ=TTAAACTGGTTAAGGTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:27.5:1:32:0:1:0:41.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 23303312 . GA G 70 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGTTAAGGTTATAAAAA;RSEQ=AAAAAAAAAGCCTATTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:18.8:1:35:0:1:0:50.8:8:0.8:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 23303757 . G A 196 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTCTGCACAGGGTGGCGTT;RSEQ=GAGTACAAGGCAGGAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1167:92:41,51:476,597:1073,92:0.0788:2,2:26.1:1:30.1:1:1:1.01:58.7:91:0.0795:0:1.1 0/0:640:0:0,0:283,357:640,0:0:2,0:25.8:1:30.4:1:1:0:58.9:57.182:1:0:0.3 +5 23303772 . A C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=0.10966;LSEQ=GCGTTGGAGTACAAGGCAGG;RSEQ=GGGGGCTCTGATCTCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1128:673:297,376:192,258:450,673:0.5966:2,2:26.2:1:30.5:1:0.66733:1.06:53:47.071:0.5996:0:1.1 0/1:660:92:41,51:252,316:568,92:0.1394:2,2:24.1:1:29.8:1:1:1.01:54:45:0.1389:0:1.1 +5 23303943 . C A 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGCTTCTGTCTGGACCATC;RSEQ=CTGACCTCTGAGACCGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1092:59:37,22:540,493:1033,59:0.054:2,2:24.3:1:30.4:1:0.14015:1.53:53.1:118:0.0546:0:1.1 0/0:601:0:0,0:311,290:601,0:0:2,0:25.9:1:30.1:1:1:0:58.7:65.778:1:0:0.1 +5 23304111 . C T 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.16445;LSEQ=GCCCTGCATCCGTGATGCTC;RSEQ=CCTGCTTATGGTACACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:851:539:287,252:169,142:311,539:0.6334:2,2:23.7:1:31:1:0.77549:1.04497:46:58.889:0.637:0:1.1 0/1:448:99:55,44:178,169:347,99:0.221:2,2:25.6:1:29:1:0.49448:1.19:42.4:48.5:0.2235:0:1.2 +5 23304211 . G T 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12849;LSEQ=AAAGTGATATTGCCCGACCG;RSEQ=TCTCTCCATATTCCCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:971:854:452,402:61,53:114,854:0.8795:2,2:24.2:1:30.1:1:0.92078:1.02361:58.1:169.8:0.8853:0:2 0/1:515:249:124,125:145,120:265,249:0.4835:2,2:25.7:1:29.3:1:0.28928:1.2176:59:123.5:0.4881:0:1.7 +5 23304235 . T C 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15656;LSEQ=CTCCATATTCCCTGGTCCAA;RSEQ=CTTTGAAAGTTCAAGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1013:653:339,314:201,158:359,653:0.6446:2,2:24.4:1:31.6:1:0.23588:1.17814:49.4:107.833:0.6522:0:2.6 0/1:525:116:61,55:231,178:409,116:0.221:2,2:23.9:1:31.2:1:0.46084:1.16975:50.2:232:0.2235:0:2.6 +5 23304261 . G A 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.16124;LSEQ=AAAGTTCAAGTTCTCTTAGT;RSEQ=TATAGTCATGAGCTGCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1099:670:335,335:231,197:428,670:0.6096:2,2:27.5:1:29.6:1:0.21569:1.17242:42.2:73.444:0.6092:0:2.3 0/1:612:123:64,59:258,231:489,123:0.201:2,2:24.2:1:28.1:1:0.9197:1.02959:43.4:40:0.199:0:2.3 +5 23304368 . A C 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13344;LSEQ=ACACATTTACTCTTTCCTCT;RSEQ=TCCACTTCTTTTGTTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:834:474:220,254:158,201:359,474:0.5683:2,2:28.8:1:32.9:1:0.52719:1.10:38.3:473:0.5761:0:1.9 0/1:516:77:39,38:201,238:439,77:0.1492:2,2:31.1:1:31:1:0.45876:1.21:36.8:24.667:0.1474:0:1.9 +5 23304401 . G T 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14173;LSEQ=GTTGTCATGACAATCACTCG;RSEQ=GAGTTTTCTTGGAACTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:898:562:272,290:145,190:335,562:0.6258:2,2:25.4:1:30.2:1:0.14641:1.23:47.4:186.333:0.6288:0:1.8 0/1:465:89:44,45:171,205:376,89:0.1914:2,2:24.8:1:29:1:0.55482:1.17:45.9:88:0.1934:0:1.8 +5 23304501 . C T 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17204;LSEQ=TGGGCTTTGAATTGTTGCAC;RSEQ=TGGTTTCAAATTCAGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:738:450:266,184:154,133:287,450:0.6098:2,2:27.4:1:31.4:1:0.14804:1.25:34.1:63.286:0.6085:0:1.6 0/1:397:84:47,37:173,138:311,84:0.2116:2,2:25.9:1:30.1:1:1:1.01:35.7:83:0.2123:0:1.5 +5 23304559 . C T 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.147;LSEQ=GTAATCTGAAACAGGCTCAT;RSEQ=GGGATCACCGTCGTGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:872:545:294,251:151,176:327,545:0.625:2,2:27.4:1:30.5:1:0.03004:1.36:34.9:48.545:0.6238:0:2.1 0/1:463:91:45,46:182,190:372,91:0.1965:2,2:28.2:1:29.7:1:1:1.02:36:182:0.1983:0:2.1 +5 23304587 . A C 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17001;LSEQ=CCGTCGTGTAGGACAACCCT;RSEQ=GTATGATCAAAGGGTAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:665:390:197,193:122,153:275,390:0.5865:2,2:30.1:1:31:1:0.13427:1.28:38.7:31.5:0.5824:0:2.1 0/1:366:71:32,39:140,155:295,71:0.194:2,2:27.4:1:29.5:1:0.79143:1.10051:38:70:0.1961:0:2.1 +5 23304637 . C T 51 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08365;SOR=6.14127;LSEQ=TCTATTTTTGTTTTTGTTTT;RSEQ=TTGCCTTTGACCCTCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:501:1:0,1:293,206:499,1:0.002:2,0:1:0:26:0:0.414:0:29:2:0.002:0:1 0/1:329:4:1,3:189,136:325,4:0.0122:2,2:6.3:1:25.8:1:0.31443:4.15185:39:8:0.0123:0:1.3 +5 23304724 . G C 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07687;LSEQ=TTCCCAAAAGCCTTGTTTGA;RSEQ=TTTGTCTGTGGTCTCAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:692:532:289,243:77,82:159,532:0.7688:2,2:24.3:1:32.2:1:0.20542:1.27:41.7:105.4:0.7705:0:1.2 0/1:576:117:60,57:213,245:458,117:0.2031:2,2:23.7:1:31.5:1:0.40676:1.21:41.7:234:0.2038:0:1.2 +5 23304772 . T C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.09966;LSEQ=TAGTTCTCGAACTCTGCTTT;RSEQ=TATTTCAGCAGCATTTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:602:460:190,270:62,80:142,460:0.7641:2,2:24.3:1:32.4:1:0.62776:1.10114:37.9:64.714:0.7613:0:1.2 0/1:464:113:49,64:148,203:351,113:0.2435:2,2:24.7:1:30.6:1:0.82764:1.05:37.4:55.5:0.2418:0:1.3 +5 23304880 . TT CC 229 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTAATGTTCTTCAAGATCTG;RSEQ=AAAGAATCAAACCGTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:931:145:70,75:401,383:784,145:0.1557:2,2:27.8:1:32:1:0.52849:1.12164:51.7:290:0.1569:0.0054:1.7 0/0:480:0:0,0:242,238:480,0:0:2,0:26.6:1:29.1:1:1:0:55.6:79:1:0:0.7 +5 23304881 . T C 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07886;SOR=0.81502;LSEQ=TAATGTTCTTCAAGATCTGT;RSEQ=AAAGAATCAAACCGTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:932:413:213,200:192,187:379,413:0.4431:2,2:26.3:1:32.2:1:0.83105:1.04:50:136.667:0.5223:0:1.8 0/1:483:190:93,97:152,141:293,190:0.3934:2,2:26.1:1:31:1:0.57636:1.12411:49.2:94:0.3925:0:1.5 +5 23304911 . G A 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18632;LSEQ=AACCGTTCTCCTCCACCAAC;RSEQ=TCATATTTCAGTTCCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1030:611:324,287:210,205:415,611:0.5932:2,2:24.3:1:30.8:1:0.48376:1.10:53.5:151.75:0.5939:0:1.7 0/1:520:111:59,52:200,208:408,111:0.2135:2,2:24.2:1:29.7:1:0.45533:1.18:51.6:110:0.2148:0:1.8 +5 23305275 . T C 316 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14499;LSEQ=CCTCCCGCCCTCCAGCTCTG;RSEQ=GACGGACCCGCTGCTTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1885:1204:537,667:283,394:677,1204:0.6387:2,2:26.2:1:30.9:1:0.24534:1.12:46.7:79.267:0.6392:0:1.9 0/1:1123:229:108,121:390,500:890,229:0.2039:2,2:27:1:29.9:1:0.37184:1.14:47.1:44.8:0.2016:0:1.9 +5 23305303 . A G 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15462;LSEQ=CCGCTGCTTGCTCAGGCTCC;RSEQ=CTGGGCTGGGTCACATCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1408:883:357,526:200,325:525,883:0.6271:2,2:27.3:1:31.2:1:0.39828:1.10:44.3:79.273:0.6296:0:2.3 0/1:834:172:69,103:246,416:662,172:0.2062:2,2:26.4:1:29.8:1:0.48128:1.13:44:33.4:0.2049:0:2.3 +5 23305356 . G A 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13579;LSEQ=AGGCCTACTCGGGACCAGAC;RSEQ=AGGAGACAGAGCCAGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:581:388:52,336:20,172:192,388:0.6678:2,2:22.9:1:30.8:1:0.34996:1.33:58.4:54.429:0.6661:0:2.1 0/1:243:52:11,41:22,169:191,52:0.214:2,2:24.6:1:30:1:0.10702:2.05:58.1:51:0.2125:0:2.2 +5 23305427 . GC G 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.20385;LSEQ=ATCCCAGAGACTGTGCAGCC;RSEQ=CCCCCCCGGTCCGGCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:209:112:3,109:6,90:96,112:0.5359:2,1:27.5:1:32.9:1:0.30735:2.41214:60:224:0.549:0.0335:0.8 0/1:58:11:1,10:4,43:47,11:0.1897:2,2:28:1:32.6:1:1:1.07:60:22:0.193:0.0172:0.5 +5 23305435 . C GCCG 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.0113;SOR=Inf;LSEQ=GACTGTGCAGCCGCCCCCCC;RSEQ=GGTCCGGCTTGCTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:8,189:197,0:0:1,0:24.1:1:31.3:1:1:0:60:23.625:1:0:0.6 0/1:58:3:0,3:5,50:55,3:0.0517:2,0:17.7:1:27.9:1:1:0:60:6:0.0517:0.0345:1 +5 23305484 . T C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03202;SOR=0.30896;LSEQ=TTTTGTACTTTTAGTGGAGA;RSEQ=GGGGTTTCTCACTTTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:46:0,46:0,22:22,46:0.6765:1,1:22.7:1:30.8:1:1:0:60:45:0.6716:0:1 0/1:18:7:0,7:1,10:11,7:0.3889:2,0:36.4:1:29.1:1:1:0:60:14:0.3889:0:1.1 +5 23396653 . G C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50786;SOR=0;LSEQ=GCCAGGCTTTTTAATCTTCT;RSEQ=CTAGGCCCATCTGTGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:16,10:26,2:0.0714:2,2:27:0:33.5:1:1:1.57244:60:4:0.0714:0:1 0/0:19:0:0,0:11,8:19,0:0:2,0:21.9:1:30.4:1:1:0:58.2:38:1:0:0.1 +5 23396678 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1301;SOR=Inf;LSEQ=GCCCATCTGTGCAGTTCCTT;RSEQ=CAAATTCCAGTTTTAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:31,0:0:2,0:32.4:1:31.9:1:1:0:60:30:1:0:0.2 0/1:18:2:1,1:8,8:16,2:0.1111:2,2:18.5:1:28.5:1:1:1:60:4:0.1111:0:1 +5 23396822 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=TTGGCCTGTCTTCAGCAAGC;RSEQ=TCATGTTTGAGCAGTTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:44.3:1:32.7:1:1:0:60:6:1:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:12:0:31:0:1:1:60:4:0.3333:0:1.5 +5 24364917 . C A 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGAGGTAGGACAATGTTG;RSEQ=ATACCCCTAAGACAGAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:3,11:14,2:0.125:2,2:35:1:29.5:1:0.45:3.32:60:4:0.125:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 24400400 . T C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTTCTGAAATCAGACAA;RSEQ=GCCTTTCGAACTCTTATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:20.1:1:31.4:1:1:0:29:14:1:0:1 1/1:4:4:3,1:0,0:0,4:1:0,2:31:1:29.8:1:1:0:25:8:1:0:1 +5 24400471 . A G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTCTAGATCCCATGAC;RSEQ=GCCATCTTGCTATTACTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:18:0:32.5:1:1:1.13389:32:4:0.1176:0:1.5 0/0:6:0:0,0:3,3:6,0:0:2,0:25.2:1:29.7:1:1:0:55:12:1:0:0.2 +5 26148813 . A G 80 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGGGGAGGGGGTGGGGC;RSEQ=ACCAGCACTGCCTGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:0,1:1,6:0.8571:0,2:28.7:1:31.3:1:0.28571:0:60:12:0.8571:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 26149087 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11392;SOR=Inf;LSEQ=CAGGTCTAACCCTGACCCAT;RSEQ=CTTCCTCAGTGGGTGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,27:52,0:0:2,0:23.8:1:31.5:1:1:0:55.1:51:1:0:0.2 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:22.5:1:28.5:1:1:1.0801:60:4:0.0741:0:2 +5 26149197 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12797;SOR=0;LSEQ=CCCTTAGGAGTAGGGGTGGC;RSEQ=ACAGTCGCTGTGGACCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:1,4:2,6:8,5:0.3846:2,2:29.8:1:26:1:1:1.30472:55.6:4:0.3333:0:1.4 0/0:6:0:0,0:1,5:6,0:0:2,0:26.7:1:31:1:1:0:58:12:1:0:0.2 +5 26149350 . C T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19231;SOR=0;LSEQ=GGCCCTGCTCCCTATGACAC;RSEQ=CAACTGGGTGATATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:3,4:2,2:4,7:0.6364:2,2:30:1:28.9:1:1:1.29868:60:6:0.6:0:1.4 0/0:3:0:0,0:2,1:3,0:0:2,0:15:1:27.7:1:1:0:60:6:1:0:0 +5 26149627 . C CACA 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=1;SOR=0.78622;LSEQ=ACAACAGCATCATCATCAAC;RSEQ=ACAACAACAACAACAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:7,6:13,5:0.2778:2,2:22.2:1:27.8:1:1:1.69618:56.4:4:0.2353:0:0.4 0/1:13:3:0,3:6,4:10,3:0.2308:2,0:24.7:1:29.3:1:0.19231:0:60:6:0.25:0:0.3 +5 26149754 . A AGGCCCATAGTGCCTCTTCTCCTCCAAAGATCACAATGTCTGTCCATCAAG 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0119;SOR=0;LSEQ=AAAACTGCTGAAAATACAAA;RSEQ=GGCCCAGAATCGGATAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:33:1:28.8:1:1:0:54:6:1:1:0 0/0:6:0:0,0:2,4:6,0:0:2,0:3.5:1:29.2:1:1:0:60:12:1:0:0.3 +5 26150118 . A T 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.00261;SOR=0;LSEQ=ATGAACAAAGCTTCCAAGAA;RSEQ=TATGGGACTTCATAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:6,5:7,7:14,11:0.44:2,2:33.5:1:30.5:1:1:1.19:35.6:22:0.44:0:1.1 0/0:15:0:0,0:11,4:15,0:0:2,0:21.9:1:30.1:1:1:0:32.9:30:1:0:0.1 +5 26150150 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1768;SOR=Inf;LSEQ=ATAAAAAGACTGAACCTATG;RSEQ=TGACTGGAGTACCAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:31,0:0:2,0:29.4:1:31.1:1:1:0:35.6:62:1:0:0.5 0/1:23:2:1,1:11,10:21,2:0.087:2,2:24:1:28:1:1:1.09544:54:4:0.087:0:0 +5 26669768 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04195;SOR=Inf;LSEQ=GTCCCTGGGGTTTAGCAGCC;RSEQ=CTCTGGGCAGCCATGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:437,117:554,0:0:2,0:26.5:1:30.2:1:1:0:59.4:35.933:1:0:0.1 0/1:296:3:1,2:213,80:293,3:0.0101:2,2:18.3:1:27.3:1:0.1868:5.28955:60:6:0.0102:0:1 +5 26670194 . A C 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0714;SOR=0;LSEQ=AATAATATATCTTTAATTTT;RSEQ=CTTAGATTACAAAACAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:11:0,11:0,195:195,11:0.0534:1,0:31.7:1:29.2:1:1:0:60:22:0.0539:0:1.1 0/0:65:0:0,0:1,64:65,0:0:1,0:23.6:1:29.5:1:1:0:60:64:1:0:0 +5 26678490 . G T 67 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67033;SOR=0.44167;LSEQ=AGAGATCAACTAACTTATTT;RSEQ=AGGTCACATAGGTAATAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:5:2,3:164,63:227,5:0.0216:2,2:15.8:1:29:1:0.14082:3.8779:60:10:0.0217:0:1.4 0/0:104:1:0,1:69,34:103,1:0.0096:2,0:1:0:22:0:0.33654:0:60:2:0.0096:0:2 +5 26678537 . A G 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCATTCTACATTACTGTC;RSEQ=CAAAGTAGGTTTTTGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:223,171:394,0:0:2,0:27.1:1:30.1:1:1:0:60:130.333:1:0:0.1 0/1:187:26:14,12:86,75:161,26:0.139:2,2:25:1:30.6:1:1:1.02:60:52:0.1405:0:1.9 +5 26678559 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03258;SOR=Inf;LSEQ=AAAGTAGGTTTTTGAAGATA;RSEQ=ATGCTATCATACTGACATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:221,218:439,0:0:2,0:24.9:1:29.7:1:1:0:60:145.333:1:0:0.2 0/1:207:3:2,1:104,100:204,3:0.0145:2,2:26.3:1:31.3:1:1:1.92:60:6:0.0147:0:3.7 +5 26678572 . T C 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00212;SOR=8.97095;LSEQ=GAAGATATATGCTATCATAC;RSEQ=GACATTCTCATGGTCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:2:1,1:194,216:410,2:0.0048:2,2:24:0:33:1:1:1.11:60:4:0.0049:0:1.5 0/1:191:8:4,4:86,97:183,8:0.0419:2,2:28.4:1:29.4:1:1:1.13:60:16:0.0423:0:2.9 +5 26678593 . T G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.75047;LSEQ=GACATTCTCATGGTCTTAAA;RSEQ=AAATGCTATATCTTGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:22:9,13:138,195:333,22:0.062:2,2:24.4:1:32.2:1:1:1.02216:60:44:0.063:0:1.2 0/1:167:40:19,21:56,71:127,40:0.2395:2,2:27.2:1:30.6:1:0.7192:1.15:60:80:0.2395:0:1.7 +5 28498907 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=0.38343;LSEQ=CTGCCATCCTTCTGAGCTAC;RSEQ=CAATGGTGAGTAGTACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:410:374:263,111:26,10:36,374:0.9122:2,2:25.3:1:30.1:1:1:1.0971:60:92.5:0.9113:0:1.5 1/0:214:171:112,59:24,12:36,171:0.7991:2,2:23.7:1:28.5:1:1:1.05331:59.8:33.2:0.7943:0:1.5 +5 28498983 . T C 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29854;LSEQ=GTTTCAAAAACACTGTGCAT;RSEQ=AATTACATACAGTGAGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:646:583:269,314:30,32:62,583:0.9025:2,2:25:1:32.2:1:0.78934:1.09418:60:290.5:0.9022:0:1.3 1/0:406:298:146,152:54,54:108,298:0.734:2,2:26.3:1:31:1:0.91069:1.04101:60:98.333:0.732:0:1.3 +5 28499031 . A G 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATGTTGCAAAACCTAATGC;RSEQ=TGGGGAGTTTCTTCAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:189,332:521,0:0:2,0:25.3:1:30.9:1:1:0:60:129.25:1:0:0.7 0/1:303:29:11,18:107,167:274,29:0.0957:2,2:32.1:1:30:1:1:1.04829:60:28:0.0946:0:1.2 +5 28499097 . GTA G 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.7256;LSEQ=TTCCTGAGAAGCAGAAAAAA;RSEQ=TATATATATATTTGTATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:3:0,3:22,128:150,3:0.0196:2,0:28:1:34.3:1:1:0:60:6:0.0199:0:0 0/1:70:1:0,1:9,60:69,1:0.0143:2,0:43:0:31:0:1:0:60:2:0.0143:0:0 +5 28499161 . A C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03756;SOR=0.23454;LSEQ=TTATGGAAGAGGAAGCCCCA;RSEQ=AGTTGAGGTGAAAGTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:56:0,56:0,8:8,56:0.875:0,1:24.6:1:32.5:1:1:0:59.9:55:0.873:0:1.2 1/0:13:8:0,8:0,5:5,8:0.6154:0,0:25.3:1:31.3:1:1:0:60:16:0.6154:0:1 +5 28499327 . T A 63 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCTGCTCTTAAGAGTGAA;RSEQ=AAAAGCTCACAAGTGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:16.6:1:27.4:1:1:0:60:4:1:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 29070817 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21739;SOR=0;LSEQ=GTACTATTCTTGAGTGAGCT;RSEQ=GCTTAAGAATGAATATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:4,5:9,3:0.25:2,0:25.3:1:32:1:0.20455:0:60:6:0.25:0:1 0/0:12:0:0,0:9,3:12,0:0:2,0:16.3:1:28.8:1:1:0:60:24:1:0:0.1 +5 29954863 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50515;SOR=0;LSEQ=AGTTTATGAGCCAATTTTCA;RSEQ=TTATTATCTCATCATAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:74,22:96,2:0.0204:2,2:21:1:30:0:0.41616:3.31182:60:4:0.0206:0:1 0/0:76:0:0,0:57,19:76,0:0:2,0:22.3:1:29:1:1:0:60:152:1:0:0.1 +5 29954903 . A T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19467;SOR=Inf;LSEQ=GAATAAGCTTAAAAATATGA;RSEQ=GCTACTCTAATCACATTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:112,71:183,0:0:2,0:27.7:1:30.9:1:1:0:60:182:1:0:0.3 0/1:145:2:1,1:85,58:143,2:0.0138:2,2:44:0:30.5:1:1:1.46153:60:4:0.0141:0:1.5 +5 29954926 . A T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57542;SOR=2.76065;LSEQ=TACTCTAATCACATTATCTA;RSEQ=ACATTATAACATATTACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:1:0,1:135,103:238,1:0.0042:2,0:1:0:24:0:0.43515:0:60:2:0.0042:0:1 0/1:174:2:1,1:95,77:172,2:0.0115:2,2:27.5:1:29:1:1:1.23226:60:4:0.0118:0:3.5 +5 29954930 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17287;SOR=Inf;LSEQ=CTAATCACATTATCTAAACA;RSEQ=TATAACATATTACAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:139,109:248,0:0:2,0:25.3:1:31:1:1:0:60:247:1:0:0.4 0/1:177:2:1,1:95,80:175,2:0.0113:2,2:31.5:1:30.5:1:1:1.18634:60:4:0.0115:0:3.5 +5 29954963 . T C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.756;SOR=0.9234;LSEQ=CAGCAGTTCATCTATATTAG;RSEQ=TACACTTTTTAGCATCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:77:41,36:97,92:189,77:0.2884:2,2:26.1:1:32.5:1:0.78839:1.08:59.7:154:0.2917:0:1.7 0/1:202:55:31,24:71,76:147,55:0.2723:2,2:24.8:1:30.9:1:0.34477:1.38:60:110:0.2736:0:1.8 +5 29954999 . T C 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56953;SOR=1.15687;LSEQ=CAAATTAAATATAAATGACT;RSEQ=CATGAGTGAATGGAACCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:69:25,44:77,98:175,69:0.2828:2,2:25:1:31.5:1:0.31375:1.38103:59.6:138:0.2911:0:1.8 0/1:150:47:20,27:41,61:102,47:0.3133:2,2:29.9:1:29.9:1:0.85825:1.10:60:22.5:0.3103:0:1.8 +5 29955160 . GA G 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.24895;SOR=0;LSEQ=GATGTTTTAAGAATTTTTGG;RSEQ=AAGGAAAATAGAAAATGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:0,8:8,5:0.3846:0,0:33.6:1:31.8:1:1:0:60:10:0.4167:0:1.2 0/0:5:0:0,0:0,5:5,0:0:0,0:17:1:30.8:1:1:0:60:10:1:0:0.2 +5 29955205 . TGT G 51 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAATCTGTACTTTTTTTT;RSEQ=TTTTTTTTTAAAGATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:25.3:1:32.2:1:1:0:60:6:0.375:0:0.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 30031802 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.89345;SOR=0.93313;LSEQ=ATTGTGGCACTAGCATACTA;RSEQ=TATACTCTTTGTAAGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:68:63,5:104,9:113,68:0.3757:2,2:24.4:1:33.3:1:1:1.09:60:67:0.3785:0:1 0/1:89:32:31,1:48,9:57,32:0.3596:2,1:23.1:1:32.7:1:0.0881:5.73:60:64:0.3596:0:1.1 +5 30031845 . A AT 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.04473;SOR=1.76717;LSEQ=AAGCCAGGTATGTAATTTAT;RSEQ=TTTTTCTTTTCTATCAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:32:22,10:272,103:375,32:0.0784:2,2:24.2:1:30.2:1:0.68199:1.19976:60:31:0.0777:0.0172:0.9 0/1:214:28:19,9:127,59:186,28:0.1308:2,2:20.9:1:29:1:1:1.01954:60:27:0.1286:0.0327:0.9 +5 30031915 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.01493;SOR=1.35543;LSEQ=CTCTTCATGTAAGGTTATGA;RSEQ=GATTCCCCAAATATTACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:763:218:98,120:276,269:545,218:0.2857:2,2:28.6:1:31:1:0.17305:1.25597:60:108:0.2872:0:1.2 0/1:492:173:81,92:165,153:318,173:0.3516:2,2:26.8:1:29.9:1:0.29961:1.22437:60:85.5:0.3526:0:1.3 +5 30031998 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01273;SOR=1.76834;LSEQ=AATGTCTTCTTAATGATCAT;RSEQ=AGAAAGTAAAACATATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:65:10,55:30,155:185,65:0.26:2,2:23.7:1:32.6:1:1:1.06426:60:64:0.2591:0:1.5 0/1:146:56:13,43:12,78:90,56:0.3836:2,2:21.5:1:30.8:1:0.17437:1.96:60:112:0.3862:0:1.5 +5 30032075 . A C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.82648;LSEQ=CTGTTTATTAACTCATATTT;RSEQ=CACCAGACTCCTCCATTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:19:0,19:0,47:47,19:0.2879:1,1:24.9:1:32.1:1:1:0:60:38:0.2923:0:1.4 0/1:16:4:0,4:0,12:12,4:0.25:0,0:17:1:26.5:1:1:0:60:3:0.2:0:1.5 +5 30204405 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16757;SOR=Inf;LSEQ=CCTTTCAAACTCTTATACCA;RSEQ=CTACTGGAGTCAGGCGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:20,24:44,0:0:2,0:32:1:30.1:1:1:0:60:43:1:0:0.1 0/1:31:2:1,1:12,17:29,2:0.0645:2,2:35.5:1:30:0:1:1.40:60:4:0.0645:0:1 +5 30204626 . G T 26 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=ACTGACCCACTGACCCTTTG;RSEQ=CTGGCCTAGAGAGATCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:4:0:29:0:1:0:60:2:1:0:0 0/1:5:2:1,1:0,2:2,2:0.4:0,2:23:1:26.5:1:1:0:60:4:0.4:0:1 +5 30708931 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19096;SOR=Inf;LSEQ=TAGAGAGTCGCCACTGTGGC;RSEQ=CTGCCTTGGAACTGTTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:22,16:38,0:0:2,0:26.7:1:30.5:1:1:0:60:76:1:0:1.1 0/1:30:2:1,1:13,15:28,2:0.0667:2,2:20.5:1:30:0:1:1.15:60:4:0.0667:0:2 +5 30708938 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGCCACTGTGGCACTGCCT;RSEQ=GGAACTGTTGAGGTGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:37:21,16:0,0:0,37:1:0,2:28.5:1:31.3:1:1:0:60:36:1:0:1.1 1/1:29:29:12,17:0,0:0,29:1:0,2:24.9:1:29.8:1:1:0:60:28:1:0:1.3 +5 30708947 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18363;SOR=Inf;LSEQ=TGGCACTGCCTTGGAACTGT;RSEQ=GAGGTGGGAACCACTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:38,0:0:2,0:26.7:1:30.5:1:1:0:60:37:1:0:1.1 0/1:29:2:1,1:11,16:27,2:0.069:2,2:26.5:1:27.5:1:1:1.44:60:4:0.069:0:2 +5 31061347 . C T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.53602;SOR=0;LSEQ=AAAACATGAACCCTCTGATT;RSEQ=TGACAACTTCAAATATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:17,0:17,3:0.15:1,0:23:1:33:0:1:0:60:6:0.15:0:1 0/0:8:0:0,0:8,0:8,0:0:0,0:15.3:1:31.8:1:1:0:60:16:1:0:0 +5 31061463 . G A 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05397;SOR=2.36161;LSEQ=GACTTAGCAAGCATTTAAGG;RSEQ=GCCTTAACGTCAATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:12:9,3:115,14:129,12:0.0851:2,2:18.7:1:30.8:1:0.16061:2.71188:60:24:0.0863:0:1 0/1:83:15:11,4:52,16:68,15:0.1807:2,2:19.9:1:29.3:1:0.74996:1.17935:60:30:0.1829:0:1.1 +5 31061575 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=1.93169;LSEQ=TGCAGGGAATTCCTATGACA;RSEQ=GCATACATTAAACTGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:388:196:79,117:91,100:191,196:0.5052:2,2:25.7:1:30.3:1:0.15284:1.34666:60:23.5:0.496:0:1.1 1/0:229:152:69,83:38,38:76,152:0.6638:2,2:26.5:1:29.6:1:0.57395:1.20192:60:49.667:0.6622:0:1.1 +5 31061706 . G GA 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.57089;SOR=0;LSEQ=ATGGATATTGCCAACGATAG;RSEQ=AAAAAAAAACAGGGCAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:4:0,4:5,58:63,4:0.0588:2,0:29.8:1:30.3:1:1:0:60:8:0.0606:0:0 0/0:25:0:0,0:5,20:25,0:0:2,0:19.4:1:30.2:1:1:0:60:50:1:0:0.1 +5 31652486 . G A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TAAGGTTTGCCAACAATGGC;RSEQ=GTCCTGCAGATAGGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:3,0:0:0,0:38.7:1:29.3:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:30.5:1:1:0:60:4:1:0:1 +5 31652673 . G T 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20624;SOR=Inf;LSEQ=ATCCAACTAATGTTTATTTA;RSEQ=CACATGCCACATAGAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:96,26:122,0:0:2,0:24.2:1:32.9:1:1:0:60:121:1:0:0.1 0/1:102:2:1,1:74,26:100,2:0.0196:2,2:7:0:26.5:1:0.46127:2.81176:60:4:0.0198:0:1 +5 31652765 . A C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04489;SOR=0.68998;LSEQ=TGCCTTGAATTATCAATTGC;RSEQ=TCAAATTGTTTGGCTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:310:219:101,118:45,46:91,219:0.7065:2,2:26.8:1:32.2:1:0.61872:1.14242:60:53.75:0.7096:0:1.1 1/0:242:151:68,83:43,48:91,151:0.624:2,2:28:1:30.6:1:0.79046:1.09304:60:74.5:0.6234:0:1.1 +5 31652931 . A G 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTCGAGACCAGCCTGGCC;RSEQ=ACATGGTGAAACCCCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:0,13:1:0,1:36.9:1:30.9:1:1:0:43:12:1:0:1.4 1/1:4:4:0,4:0,0:0,4:1:0,0:39.5:1:32:1:1:0:28.5:8:1:0:1 +5 31840606 . T C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TAACAGTAGCTATTTTGCCA;RSEQ=GAATTCATAGGGAATGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:28:1:33:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:30.5:1:1:0:47:4:1:0:1.5 +5 31848168 . C A 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.92115;LSEQ=GTTGAAAAGCAGAGGTGGAA;RSEQ=TATCCCAAAATGTCCCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:4:3,1:32,22:54,4:0.069:2,2:23:1:31:1:1:2.04:55:8:0.069:0:1.3 0/1:47:3:2,1:26,18:44,3:0.0638:2,2:6.7:1:31.3:1:1:1.38:35:6:0.0652:0:1.3 +5 32553710 . A G 54 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57651;LSEQ=CAAGGAGGTTAAAAATACAA;RSEQ=GCCCAAAGGCGAGTAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:5,0:5,3:0.375:0,2:11.7:1:34.3:1:0.375:0:30:6:0.4286:0:1 0/1:8:2:1,1:5,1:6,2:0.25:2,2:25:1:27.5:1:0.46429:3.87298:45.5:4:0.25:0:1 +5 32553853 . A G 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66798;SOR=0.5624;LSEQ=TCCTGTAAATGCCGGGTGGC;RSEQ=TCTTGTACTATCCCTGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:4,7:11,5:0.3125:2,2:23:1:31.4:1:1:1.16:34.2:10:0.3125:0:1 0/1:10:2:0,2:3,5:8,2:0.2:2,0:20:1:26:1:1:0:32.5:4:0.2222:0:1 +5 32673983 . T A 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.55944;SOR=0.36341;LSEQ=TAAGACCATCTGTAGCATGA;RSEQ=GACCTTGATTCTAGAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:17.5:1:29:1:1:2.44949:46:4:0.3333:0:1 0/1:7:1:1,0:6,0:6,1:0.1429:0,0:46:0:32:0:1:0:60:2:0.1429:0:1 +5 33816874 . T A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGTACATCAACTGAGGA;RSEQ=GAGAAGCTGAAGAGCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,0:0,2:0.6667:0,0:25.5:1:30.5:1:1:0:60:4:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 33816914 . A C 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTCTAAGAGTGAGTAGG;RSEQ=TTGTTCTGAATCAGATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:19.8:1:26.8:1:1:0:60:3:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 33816922 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGAGTAGGATTGTTCT;RSEQ=AATCAGATTTTAACTTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:41:1:31.5:1:1:0:60:4:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 33817078 . T A 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68165;SOR=1.8784;LSEQ=CCCTCAGTAAGTGTGTAGTT;RSEQ=ACGGTGCTTCCTCTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:21:21,0:16,0:16,21:0.5676:1,1:20:1:29:1:1:0:60:42:0.5676:0:2 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:23.6:1:27.8:1:1:0:60:10:0.7143:0:2.2 +5 33817083 . T C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69184;SOR=2.05667;LSEQ=AGTAAGTGTGTAGTTTACGG;RSEQ=GCTTCCTCTCCAGGGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:23:23,0:16,0:16,23:0.5897:1,1:20.7:1:32.9:1:1:0:60:46:0.6053:0:2.1 1/0:8:6:6,0:2,0:2,6:0.75:0,0:22.8:1:31.5:1:1:0:60:12:0.75:0:2.2 +5 33817174 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26377;SOR=1.48705;LSEQ=AAGCTGTATCCTTAAAAAAT;RSEQ=TTAATCAGACTTCTACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:147:88:88,0:58,1:59,88:0.5986:1,1:25:1:32.7:1:0.40136:0:60:87:0.5959:0:1.1 1/0:58:40:40,0:18,0:18,40:0.6897:1,1:21.3:1:32.6:1:1:0:60:80:0.7018:0:1.2 +5 33817339 . A G 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.6563;LSEQ=CTACAGGTAGTAAGTAGTCT;RSEQ=TGTTTTACAAGAGACATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:890:526:230,296:152,211:363,526:0.591:2,2:24.7:1:32.2:1:0.62953:1.08:60:86.667:0.5889:0:1.3 1/0:594:419:188,231:78,95:173,419:0.7054:2,2:24.2:1:31.4:1:1:1.00883:60:418:0.7085:0:1.3 +5 33817367 . T C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41264;SOR=1.12913;LSEQ=CAAGAGACATTAACTTGAAC;RSEQ=TTAGTGGAAACTGCCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:139:50,89:206,361:567,139:0.1969:2,2:24.3:1:32.6:1:1:1.01571:59.8:278:0.1986:0:1.8 0/1:452:98:33,65:141,213:354,98:0.2168:2,2:26.9:1:31:1:0.29239:1.30313:60:48:0.2143:0:1.9 +5 33817593 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.60435;SOR=2.62691;LSEQ=GGAGTTCTTTATATTGTTAT;RSEQ=ATGGAAAATACCAAACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:0,11:0,10:10,11:0.5238:0,0:19:1:33.2:1:1:0:60:22:0.55:0:1 1/0:4:3:0,3:0,1:1,3:0.75:0,0:15.3:1:33:0:1:0:60:6:0.75:0:1 +5 33841375 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=TTGTCTGCAGCTACTCCCTC;RSEQ=TTCCTTTTCATCCTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:2,8:10,2:0.1667:2,2:25:1:32.5:1:0.45455:3.46:60:4:0.1667:0:1 0/0:6:0:0,0:2,4:6,0:0:2,0:18.7:1:27.3:1:1:0:60:5:1:0:0.7 +5 33997097 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08511;SOR=Inf;LSEQ=CATTAAATTATTTAAAATGT;RSEQ=CAGTATTTTTTTTTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:170,23:193,0:0:2,0:19.7:1:32:1:1:0:60:63.333:1:0:0.1 0/1:80:2:1,1:72,6:78,2:0.025:2,2:13:1:30:1:0.16835:11.18701:60:4:0.025:0:1 +5 33997102 . A AT 85 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.44251;SOR=0.3066;LSEQ=AATTATTTAAAATGTCCAGT;RSEQ=TTTTTTTTTAATTTTACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:7:5,2:171,28:199,7:0.034:2,2:28.6:1:30.6:1:0.27032:2.42914:60:14:0.0343:0.0049:0.7 0/1:94:1:1,0:81,12:93,1:0.0106:2,0:29:0:32:0:1:0:60:2:0.0106:0:0 +5 33997283 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09683;SOR=Inf;LSEQ=CTTAGCAATTCTGCTGTTTT;RSEQ=TCATACCCTATATGAGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:100,210:310,0:0:2,0:24.3:1:32.3:1:1:0:59.9:50.667:0.9967:0:0.1 0/1:141:2:1,1:51,88:139,2:0.0142:2,2:8.5:1:26.5:1:1:1.72:60:4:0.0144:0:1 +5 33997291 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08937;SOR=Inf;LSEQ=TTCTGCTGTTTTGTCATACC;RSEQ=TATATGAGGGTTGAGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:105,193:298,0:0:2,0:23.7:1:32.5:1:1:0:59.8:48.667:1:0:0.1 0/1:128:2:1,1:49,76:125,2:0.0156:2,2:27:0:32:1:1:1.55:60:4:0.0156:0:1.5 +5 33997307 . A C 125 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00415;SOR=0;LSEQ=TACCCTATATGAGGGTTGAG;RSEQ=GCTGTCACCAGCATTAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:16:6,10:113,148:261,16:0.0578:2,2:24.4:1:31.4:1:0.79658:1.27143:60:32:0.0597:0:1 0/0:119:0:0,0:53,66:119,0:0:2,0:23.6:1:29.5:1:1:0:60:58.5:1:0:0.1 +5 34487059 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGCACAGTATCAGTTGT;RSEQ=TGTCCTCATGACTTTGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:28:1:1:0:60:4:1:0:1.5 +5 34487707 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTATTAATACTTCAGTTG;RSEQ=AAGTTACAGAAACAGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:12,1:13,2:0.1333:1,2:28:0:32.5:1:0.25714:8.83176:60:4:0.1333:0:1.5 0/0:5:0:0,0:5,0:5,0:0:0,0:26.4:1:33:1:1:0:60:10:1:0:0 +5 34487850 . A G 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01184;SOR=Inf;LSEQ=CTACTGCAGTCCTGCCATTC;RSEQ=CGTAACTCATTGGTGACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:30,38:68,0:0:2,0:27.4:1:30:1:1:0:60:136:1:0:0.1 0/1:35:4:2,2:13,18:31,4:0.1143:2,2:22.5:1:29.3:1:1:1.37:60:8:0.1143:0:1 +5 34487998 . T C 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGAAAAGTGAGATCACA;RSEQ=AGGTTATTTCTTGTTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:18.7:1:33.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 34489182 . G C 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGATAGCAGAGCCACCCCC;RSEQ=CCCCACCACCACCCTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:27.5:1:1:0:60:4:1:0:5 +5 34489187 . A C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGCAGAGCCACCCCCGCCCC;RSEQ=CCACCACCCTGTGTTACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:29.5:1:1:0:60:4:1:0:5 +5 34605325 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.2281;LSEQ=GGATAAAAGAACATGGATCA;RSEQ=TCAGTGCACACTCATCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:93:53,40:174,149:323,93:0.222:2,2:26.1:1:30.5:1:0.63726:1.13:60:45.5:0.2203:0:1.1 0/1:371:178:96,82:103,89:192,178:0.4798:2,2:25.4:1:29.8:1:1:1.01:60:177:0.4836:0:1.1 +5 34605375 . C A 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41623;SOR=2.4736;LSEQ=AAATAACTTGAAAGCTATAT;RSEQ=ATACAAATGGTGGGTTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:2:2,0:149,225:374,2:0.0053:2,0:1:0:24:1:0.16064:0:60:4:0.0054:0:1 0/1:306:4:3,1:128,174:302,4:0.0131:2,2:22:1:27:1:0.31699:4.06:60:8:0.0133:0:1 +5 35856997 . C T 22 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30135;SOR=3.50433;LSEQ=ATCTAAGCTTCTCTGTCTTC;RSEQ=TCCCTCCCTCCCTTCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:1:0,1:309,27:336,1:0.0029:2,0:2:0:14:0:0.08309:0:60:0:0:0:1 0/1:195:2:1,1:167,26:193,2:0.0103:2,2:18:1:22:1:0.25837:6.32186:60:4:0.0106:0:1.5 +5 35857055 . ACT A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=1;SOR=1.04651;LSEQ=ACACACTGGCTCACACATCT;RSEQ=CTCTCTCTCTATCTCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:893:9:5,4:543,341:884,9:0.0101:2,2:17:1:30.6:1:0.74022:1.27353:60:18:0.0103:0.0034:0.4 0/1:664:7:6,1:402,255:657,7:0.0105:2,2:29.3:1:31.4:1:0.25873:3.80:60:14:0.0108:0:0.3 +5 35857177 . G C 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.76749;SOR=0.95934;LSEQ=AAATGGTGAGTCATTTCTAA;RSEQ=TTTTCTTATGGATTTTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:687:392:129,263:86,208:294,392:0.5706:2,2:24.5:1:32.7:1:0.31926:1.19:59.9:55:0.5678:0:1.3 1/0:505:283:98,185:77,144:221,283:0.5604:2,2:23.2:1:31.4:1:1:1.00941:60:93.333:0.5589:0:1.3 +5 35857207 . C T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.44614;LSEQ=GGATTTTGGATTATCTGTAG;RSEQ=ATGGTTTCAGGTTATTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:124:23,101:56,214:270,124:0.3147:2,2:25:1:28.4:1:0.6852:1.14869:60:40.333:0.3119:0:1 0/1:259:44:13,31:48,167:215,44:0.1699:2,2:22.9:1:27.3:1:0.33097:1.46:60:88:0.1712:0:1.1 +5 35857235 . C G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99786;LSEQ=CAGGTTATTCAGTTCCCTAA;RSEQ=AGACCTGAGTCAGGCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:240:124:11,113:10,106:116,124:0.5167:2,2:23.8:1:32.5:1:1:1.03:59.7:123:0.5146:0:2.3 1/0:124:64:6,58:5,55:60,64:0.5161:2,2:25.3:1:31:1:1:1.14:60:128:0.5161:0:2.3 +5 35857262 . A G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76696;SOR=0.88355;LSEQ=GAGTCAGGCACTGGGTTTGA;RSEQ=TGCAGTTTGAGAATTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:136:78:1,77:2,56:58,78:0.5735:1,1:25.1:1:32.8:1:0.57523:2.72969:59.6:77:0.5704:0:2.3 1/0:70:38:0,38:0,32:32,38:0.5429:1,1:24.9:1:32.1:1:1:0:60:76:0.5429:0:2.3 +5 35857294 . A AT 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.54982;SOR=0;LSEQ=AATTTCCCACATATTCAGTC;RSEQ=TTTTTTTTAATGTTTAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:3:0,3:1,75:76,3:0.038:1,0:20.7:1:30.7:1:1:0:60:6:0.038:0.0127:2 0/0:39:0:0,0:0,39:39,0:0:1,0:24.1:1:29.9:1:1:0:60:18.5:1:0:0.9 +5 35857308 . T TC 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46455;SOR=1.56721;LSEQ=TCAGTCATTTTTTTTAATGT;RSEQ=TAACCACCATGACAGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:40:1,39:0,21:21,40:0.6557:1,1:23:1:33.1:1:1:0:59.3:80:0.6557:0.1639:1.2 1/0:28:21:0,21:0,7:7,21:0.75:0,1:25.7:1:31.5:1:1:0:60:42:0.75:0.1071:0.7 +5 35860637 . A G 46 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AAAAACTCCAGTTTAAATAC;RSEQ=GAAAAGAATGTGTTCAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:22.5:1:24.5:1:1:0:60:1:0.2:0:3.5 1/1:3:3:2,1:0,0:0,3:1:0,2:16.3:1:29.3:1:1:0:60:6:1:0:1 +5 35860710 . AT A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTTACTCATTATGATGG;RSEQ=TTTTTTTTTCTATTGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:11,1:12,2:0.1429:2,0:10.5:1:32.3:1:1:0:60:4:0.1429:0.0714:0 0/0:5:0:0,0:4,1:5,0:0:2,0:14.2:1:29:1:1:0:60:10:1:0:0.4 +5 35860873 . C T 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATGTCTGCCACAGAGTCTG;RSEQ=TATTTTATTAAGGTCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:55:50,5:109,6:115,55:0.3235:2,2:22.4:1:29.9:1:0.33707:1.80989:60:54:0.3253:0:1.1 0/0:111:0:0,0:95,16:111,0:0:2,0:20:1:31.5:1:1:0:60:222:1:0:0.1 +5 35861068 . T C 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.95968;SOR=0.993;LSEQ=TGAGGACCCAGATGTCAACA;RSEQ=CACCAATCTGGAATTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:906:484:180,304:165,256:421,484:0.5342:2,2:26.4:1:31.6:1:0.53785:1.08844:59.9:79.667:0.5341:0:1.1 1/0:693:369:163,206:153,170:323,369:0.5325:2,2:25.1:1:30.7:1:0.40153:1.13721:60:72.8:0.5322:0:1.2 +5 35861149 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29984;SOR=3.5229;LSEQ=CTCTGTCTCTCTTTTCATAT;RSEQ=CTCTTTTTAATAGCCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:0,1:38,257:295,1:0.0034:2,0:39:0:30:0:1:0:60:2:0.0034:0:1 0/1:169:2:1,1:20,147:167,2:0.0118:2,2:21.5:1:27.5:1:0.23373:7.20:60:4:0.0118:0:1 +5 35861152 . C G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00037;SOR=3.25306;LSEQ=TGTCTCTCTTTTCATATGCT;RSEQ=TTTTTAATAGCCACAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:16:1,15:31,230:261,16:0.0578:2,1:21.8:1:33.4:1:0.7037:2.01771:60:32:0.0584:0:1.6 0/1:162:27:3,24:13,122:135,27:0.1667:2,2:23.1:1:31.4:1:0.73245:1.17:60:54:0.1698:0:1.3 +5 35861159 . A G 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00241;SOR=Inf;LSEQ=CTTTTCATATGCTCTTTTTA;RSEQ=TAGCCACAAAAGAAAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:25,213:238,0:0:2,0:23.7:1:31.1:1:1:0:60:38.667:1:0:0.2 0/1:140:6:1,5:9,125:134,6:0.0429:2,2:26.3:1:31.3:1:0.36436:2.75:60:12:0.0435:0:1.2 +5 35861268 . T G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.66449;SOR=0.51409;LSEQ=ACCAAAAACACTCATACAAA;RSEQ=CTCCTCTCACGGTTCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:0,12:0,6:6,12:0.6667:0,0:18.9:1:31.4:1:1:0:60:24:0.7059:0:1 1/0:8:4:0,4:0,4:4,4:0.5:0,0:33.3:1:32.8:1:1:0:60:8:0.5:0:1 +5 35867343 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14126;SOR=Inf;LSEQ=ATACATCAATGTGCATATGA;RSEQ=ACTATTCCACTGCATACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:184,46:230,0:0:2,0:23.4:1:30.7:1:1:0:59.9:114:1:0:0.1 0/1:139:2:1,1:109,28:137,2:0.0144:2,2:12:1:33.5:1:0.37493:3.84266:60:4:0.0145:0:1.5 +5 35867351 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15908;SOR=Inf;LSEQ=ATGTGCATATGATACTATTC;RSEQ=ACTGCATACAGGAACTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:199,61:260,0:0:2,0:24.3:1:31.2:1:1:0:59.9:51:1:0:0.1 0/1:173:2:1,1:128,43:171,2:0.0116:2,2:24:1:25.5:1:0.44509:2.95413:60:4:0.0118:0:1 +5 35870814 . A C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCTTCTCCCAGCAGTATT;RSEQ=GGGGCACTTTCCATCTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:26:1:29:1:1:0:59:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 35870979 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08772;SOR=Inf;LSEQ=AAGGCCACACCCCACTGCAA;RSEQ=AGAGGCTGGAGAATGCGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:24.5:1:33.2:1:1:0:60:26:1:0:0.2 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:13.5:1:27:1:0.33333:0:60:4:0.3333:0:1 +5 35871190 . G A 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19579;SOR=1.16057;LSEQ=CTCCTTTTGACCTGAGTGTC;RSEQ=TCTATCGGGAAGGAGCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:716:332:213,119:237,147:384,332:0.4637:2,2:24.6:1:30.3:1:0.53519:1.11:60:65.4:0.4671:0:1.1 1/0:567:284:172,112:170,112:282,284:0.5009:2,2:26.2:1:29.6:1:1:1.01:59.9:93.667:0.5:0:1.1 +5 35871273 . C T 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATGTAAAAGTTTTAATGCA;RSEQ=GATGTAGCTTACCGCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:843:0:0,0:336,505:841,0:0:2,0:25.7:1:30.5:1:1:0:60:63.692:0.9988:0:0.3 0/1:621:63:26,37:221,337:558,63:0.1014:2,2:28:1:29.1:1:0.78788:1.07:60:30.5:0.0997:0:1.2 +5 35871291 . G A 198 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01498;LSEQ=CACGATGTAGCTTACCGCCA;RSEQ=GAAAAGGATGAAAACAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:78:30,48:218,411:629,78:0.1103:2,2:27.3:1:31.6:1:0.53041:1.18:60:156:0.1116:0:1.1 0/0:540:1:1,0:203,336:539,1:0.0019:2,0:3:0:26:0:0.37778:0:60:2:0.0019:0:1 +5 35871460 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATCTCCCAATATTGGCC;RSEQ=CATGAAAACCTGGATCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:0,24:24,2:0.0769:1,2:24:1:32:1:0.07692:0:60:4:0.08:0:1 0/0:11:0:0,0:0,11:11,0:0:0,0:23.5:1:31.7:1:1:0:60:22:1:0:0 +5 35873872 . T G 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0.17023;LSEQ=GACACCCTTGGAGGGCACTC;RSEQ=TACACTTTCTTTGGAGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:113:57:1,56:1,55:56,57:0.5044:1,1:22:1:32.7:1:1:1.01802:60:56:0.5:0:1.1 0/1:41:6:1,5:0,35:35,6:0.1463:1,2:12.7:1:30.3:1:0.14634:0:60:12:0.1463:0:1 +5 35874575 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00068;SOR=1.60459;LSEQ=GATGGATCCTATCTTACTAA;RSEQ=CATCAGCATTTTGAGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1711:112:54,58:807,792:1599,112:0.0655:2,2:24.9:1:30.3:1:0.69607:1.09435:60:55:0.0651:0:1.1 0/1:1138:115:56,59:519,500:1019,115:0.1011:2,2:24:1:28.6:1:0.69427:1.09352:60:18.167:0.0971:0:1.1 +5 35875134 . T C 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATTACAAATACCCTAAT;RSEQ=TGAAAAGTACTGCCTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,1:3,2:0.4:2,0:26.5:1:34.5:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 35875428 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTCTCTGGTCCAACCCCT;RSEQ=CTTGAATTGATAGGGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:47,0:47,2:0.0408:1,2:29:1:32.5:1:0.04082:0:60:4:0.0408:0:1 0/0:13:0:0,0:11,2:13,0:0:2,0:23.9:1:30.6:1:1:0:60:26:1:0:0 +5 35875518 . C T 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTAGAGCCAAGACTAGAAAT;RSEQ=TGTTCTTCTGATTCCAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:35:33,2:131,9:140,35:0.2:2,2:23.1:1:30.5:1:1:1.13:60:34:0.1965:0:1.7 0/0:105:0:0,0:96,9:105,0:0:2,0:22.9:1:30.9:1:1:0:60:104:1:0:0.2 +5 35875593 . A T 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.53488;LSEQ=CTCTGCCATTCACTTCATCT;RSEQ=TCAATGTTCTCTGATTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:694:389:277,112:213,89:302,389:0.5605:2,2:24:1:30.7:1:0.86613:1.03:59.9:388:0.5681:0:1.1 0/1:444:180:123,57:176,86:262,180:0.4054:2,2:24.6:1:29.9:1:0.83641:1.05:60:179:0.4068:0:1.1 +5 35876274 . A G 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.40364;LSEQ=GCCCATCTGAGGATGTAGTC;RSEQ=TCACTCCAGAAAGCTTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1078:510:243,267:271,297:568,510:0.4731:2,2:24.8:1:30.8:1:1:1.00257:60:62.75:0.4709:0:1.1 0/1:707:188:87,101:236,283:519,188:0.2659:2,2:25.2:1:30.7:1:0.86462:1.03:59.9:376:0.2674:0:1.1 +5 35876623 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03038;SOR=Inf;LSEQ=AGACTGAACTTACCGTGAGC;RSEQ=ACAAAGATGATTTAAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:47,222:269,0:0:2,0:24:1:31.3:1:1:0:60:25.9:1:0:0.1 0/1:123:3:2,1:30,90:120,3:0.0244:2,2:17:1:26.3:1:0.16554:5.89:60:6:0.025:0:1.3 +5 36367860 . C T 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCTTAGCTGGCTGTGCTC;RSEQ=TCGGCTGTGTTTAACCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:38:1:34:0:1:0:60:4:0.4:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 36367987 . T G 124 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTTGGGGAATATTCAAT;RSEQ=GTTCATGTTTGGATCTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:14,0:3,1:4,14:0.7778:2,1:25.9:1:32.6:1:0.22222:0:60:28:0.7778:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 36368082 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03443;SOR=0.35074;LSEQ=AACAACTACTGATGATTCCT;RSEQ=TTATCTCTTTCCCAGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:50:50,0:20,0:20,50:0.7143:1,1:24.2:1:32.6:1:1:0:59.9:49:0.7206:0:1.2 0/1:28:13:13,0:15,0:15,13:0.4643:1,1:28.5:1:31.1:1:1:0:60:12:0.4444:0:1.4 +5 36368227 . G T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16515;SOR=5.80976;LSEQ=TAGCAACATTCACATGTGCT;RSEQ=TAACTCTCCCCCACCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:1:0,1:281,236:517,1:0.0019:2,0:1:0:25:0:0.45753:0:60:2:0.0019:0:2 0/1:360:4:2,2:188,168:356,4:0.0111:2,2:34:1:29.5:1:1:1.1187:60:8:0.0112:0:1.5 +5 36368254 . T C 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25699;LSEQ=TCCCCCACCATGCCTGATGC;RSEQ=GATTTCTAACCATCAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:570:439:212,227:58,73:131,439:0.7702:2,2:24.8:1:30.2:1:0.42712:1.18:60:53.875:0.7696:0:1.1 0/1:385:178:89,89:96,111:207,178:0.4623:2,2:24:1:29.8:1:0.53942:1.16:59.9:58.333:0.4617:0:1.2 +5 36368354 . T A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53893;SOR=0;LSEQ=TCCTCCTTCCCCTGTCTCTG;RSEQ=GCCTCAGTCAGGTATCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:43,140:183,2:0.0108:2,2:7:1:30:1:0.42009:3.23:60:4:0.0109:0:1 0/0:103:0:0,0:24,79:103,0:0:2,0:21.3:1:28.7:1:1:0:60:50.5:1:0:0.1 +5 36370268 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTGTGTCCATATGTACTCA;RSEQ=TGTTTAACTCCCCCTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:31:1:1:0:56:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 36391256 . ACAG A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.23881;SOR=0;LSEQ=ATATTCACCCACCAGCAGCA;RSEQ=CAGCAGCAGCCCCTAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:31,2:0.0606:2,2:33:1:31:1:1:1.06462:60:4:0.0625:0:0 0/0:34:0:0,0:16,18:34,0:0:2,0:24.3:1:31.4:1:1:0:59.2:33:1:0:0.5 +5 37743328 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCCTCCCCCAAGCTAA;RSEQ=GGAGGCGGTGAGTGAACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:25.5:1:31:1:1:1.41:60:4:0.2857:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:33:0:1:0:60:2:1:0:0 +5 37743917 . A C 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGTGGCCTTAGTCTTTGC;RSEQ=GACCAACAGACTTTGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:0,11:1:0,2:26.2:1:31.5:1:1:0:58.9:22:1:0:1.1 1/1:18:17:10,7:1,0:1,17:0.9444:0,2:20.4:1:29.7:1:1:0:59.5:34:0.9444:0:1.1 +5 37744444 . GA G 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTCAACAAAAAAATGCT;RSEQ=AAACCCACAAGGCCAGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:3,5:0.625:2,2:25:1:31:1:1:2.60168:57.6:10:0.625:0.125:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38942090 . T C 91 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTGTTCCACTGTCATTA;RSEQ=GCTTTTAAAATGAAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:24.1:1:30.4:1:1:0:57.6:7:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38942628 . T C 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17863;SOR=0;LSEQ=AATGTTGCCATCTTTGTTCA;RSEQ=TGCAACCTCTGAGTCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:6:1,5:8,41:49,6:0.1091:2,2:17.2:1:32.7:1:1:1.02:60:12:0.1154:0:1 0/0:21:0:0,0:0,21:21,0:0:1,0:22.2:1:30.1:1:1:0:59.5:42:1:0:0.2 +5 38943156 . T C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=GGTATCACTTACTTTAAAAA;RSEQ=AGATTTCCCTACAGATATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:0,147:147,0:0:1,0:25.2:1:28.8:1:1:0:60:72.5:1:0:0 0/1:56:5:1,4:2,49:51,5:0.0893:1,2:21.4:1:32.6:1:0.24874:5.77:60:10:0.0893:0:2 +5 38943260 . G GT 93 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.31889;SOR=0.23522;LSEQ=CTTAGACATTCTGAGTTTGG;RSEQ=TTTTTTTTTAAAAAAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:0,2:2,8:0.5333:0,0:31.3:1:31.3:1:1:0:60:16:0.5714:0:0 0/1:5:1:0,1:0,2:2,1:0.2:0,0:40:0:30:0:1:0:60:2:0.2:0:1 +5 38943269 . T TA 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGAGTTTGGGTTTTTTTT;RSEQ=AAAAAAAATGATTATCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:11,3:0.2143:0,0:22:1:29.3:1:1:0:60:6:0.2143:0.0714:1 0/0:3:0:0,0:0,3:3,0:0:0,0:13.7:1:30:1:1:0:60:6:1:0:2.3 +5 38944534 . C T 73 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03199;SOR=5.65196;LSEQ=AAACAAATAATACTCATGCA;RSEQ=ATAGTTTACTCACGTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1022:2:0,2:663,357:1020,2:0.002:2,0:1:0:19:1:0.12317:0:60:1:0.001:0:1 0/1:638:7:2,5:383,246:629,7:0.011:2,2:20:1:26.3:1:0.11912:3.88395:59.4:14:0.0111:0:1.1 +5 38945854 . T A 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35803;SOR=2.66144;LSEQ=TAAGTAAATATAAAACATAA;RSEQ=CCAATAAAGATAATACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:2:2,0:75,261:336,2:0.0059:2,0:1:0:26:1:0.05138:0:60:4:0.006:0:1 0/1:192:3:2,1:39,150:189,3:0.0156:2,2:9.3:1:22:1:0.1158:7.58:60:2:0.011:0:1 +5 38945855 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12932;SOR=Inf;LSEQ=AAGTAAATATAAAACATAAT;RSEQ=CAATAAAGATAATACTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:68,256:324,0:0:2,0:22.8:1:31.4:1:1:0:59.8:63.8:0.9969:0:0.1 0/1:183:2:1,1:37,144:181,2:0.0109:2,2:30:1:25:1:0.37309:3.85:60:4:0.011:0:1 +5 38945919 . C T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=6.84541;LSEQ=TTTTAAAGAAAGCTTAAGCA;RSEQ=ATTTTATGACTCAAAATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:11:0,11:1,86:87,11:0.1122:1,0:23.8:1:29:1:1:0:60:22:0.1146:0:1.1 0/1:47:22:0,22:0,25:25,22:0.4681:1,1:27.2:1:28:1:1:0:60:44:0.4783:0:1 +5 38947098 . AT A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATAAATTTCTACAGAGA;RSEQ=ATATGGATAAAGAAATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:14,2:0,0:0,16:1:0,2:25.8:1:30.8:1:1:0:58.6:32:1:0.125:0.2 1/1:3:3:2,1:0,0:0,3:1:0,2:22:1:31:1:1:0:60:6:1:0.3333:0 +5 38947185 . C G 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02056;SOR=0;LSEQ=AAGGACTAAATAAAAGAGTA;RSEQ=AGAGTAGTTGAAAAGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:9,0:25,1:26,9:0.2571:1,0:17.1:1:32.7:1:1:0:60:18:0.2647:0:1.4 0/0:18:0:0,0:17,1:18,0:0:1,0:20.2:1:31.7:1:1:0:60:36:1:0:0.1 +5 38947288 . G T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03908;SOR=Inf;LSEQ=TGGTGCCCACCCTAAATTAT;RSEQ=ATTTCTAGTAAGCAGTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:243,49:292,0:0:2,0:23.5:1:32.1:1:1:0:60:57.4:1:0:0 0/1:151:3:1,2:120,28:148,3:0.0199:2,2:8.3:1:22:1:0.1008:8.3986:60:2:0.0135:0:1.3 +5 38949632 . C T 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAGGATTTTCTTCCCCCCT;RSEQ=GCAGCTGCAAGAATCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:35:8,27:33,83:116,35:0.2318:2,2:27.9:1:29.6:1:0.66521:1.33935:60:10.667:0.2207:0:1.1 0/0:70:0:0,0:13,57:70,0:0:2,0:24.9:1:30.1:1:1:0:60:140:1:0:0.1 +5 38949775 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02928;SOR=Inf;LSEQ=TATTTAAATTTGTTAAAATG;RSEQ=AACCATTATTGGTCACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:562:0:0,0:418,144:562,0:0:2,0:23.4:1:32.3:1:1:0:60:79.286:1:0:0.1 0/1:398:4:2,2:280,114:394,4:0.0101:2,2:14.3:1:28.8:1:0.58345:2.44985:60:8:0.0101:0:1 +5 38950776 . G A 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGATATCAAGGAAAAATGT;RSEQ=CTAGTAGAGCTGCTGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:793:792:278,514:0,0:0,792:0.9987:0,2:26.1:1:29.4:1:1:0:60:98:0.9987:0:1.1 1/1:550:550:194,356:0,0:0,550:1:0,2:26.2:1:28.4:1:1:0:60:90.667:1:0:1.1 +5 38950905 . AT A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGACATCACATTTCAGGAA;RSEQ=TTTTTTTTAGTCATCTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:2,113:115,2:0.0171:1,0:39:0:31:1:1:0:60:4:0.0172:0:0 0/0:31:0:0,0:0,31:31,0:0:1,0:28.5:1:29.4:1:1:0:58.7:30:1:0:0.2 +5 38951829 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCACAAATCATTTTATATA;RSEQ=AACTATTTTTGTTACTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38952655 . GA G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.27243;SOR=0.50231;LSEQ=CCAAAATGGTTGCGTTTGTG;RSEQ=AAAAAAAAAACTTATTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:31:5,26:0,13:13,31:0.6889:1,2:27.3:1:31.4:1:0.30051:0:60:62:0.6889:0.0222:0.1 1/0:21:11:0,11:0,8:8,11:0.5238:0,0:29.7:1:30.9:1:1:0:60:22:0.5238:0:0.1 +5 38952825 . A T 135 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGAACAGCTGGGTTAC;RSEQ=GGAATACTGGAGTATCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:18,1:0,0:0,19:1:0,1:24.6:1:32:1:1:0:59.8:38:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:12:0:33:0:1:0:60:2:1:0:1 +5 38953427 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGAGATAATACACTTATAT;RSEQ=GGCAGGAACAATCCAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:101:100:93,7:0,0:0,100:0.9901:0,2:23.6:1:31.8:1:1:0:59.6:99:0.99:0:1.9 1/1:40:40:38,2:0,0:0,40:1:0,2:27:1:31:1:1:0:59.9:80:1:0:2.1 +5 38953447 . T A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCAGGAACAATCCAGTCT;RSEQ=AAATATTAATCTAATAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:125:125:117,8:0,0:0,125:1:0,2:24.2:1:28.5:1:1:0:59.7:40.667:1:0:1.7 1/1:69:69:68,1:0,0:0,69:1:0,1:20.3:1:27.9:1:1:0:59.9:68:1:0:1.7 +5 38953503 . G GA 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.65574;SOR=1.26496;LSEQ=TTTATCTATTTAGTATAAAT;RSEQ=AAAAAAAAACTTAAAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:11:8,3:256,90:346,11:0.0306:2,2:15.8:1:30.9:1:1:1.06648:60:22:0.0309:0.0111:0.5 0/1:260:10:7,3:187,60:247,10:0.0385:2,2:27.6:1:29.7:1:0.71059:1.33411:60:20:0.0398:0.0077:0.1 +5 38953661 . G GA 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.15046;SOR=0;LSEQ=TTCTGTAATAATATTCTGGA;RSEQ=AAAGAAAAAAAAATACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:4:1,3:102,283:385,4:0.0103:2,2:23:1:31:1:1:1.08106:60:8:0.011:0.0026:2.3 0/0:266:0:0,0:65,199:264,0:0:2,0:22.4:1:30.2:1:1:0:60:23:0.9961:0:0.1 +5 38953665 . G GA 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.01995;SOR=0.6481;LSEQ=GTAATAATATTCTGGAGAAA;RSEQ=AAAAAAAAATACCATGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:360:274:57,217:29,37:66,274:0.7611:2,2:27.7:1:30.9:1:0.00023:2.97252:59.9:136:0.764:0.0389:0.2 1/0:242:163:29,134:19,40:59,163:0.6736:2,2:25.2:1:30.3:1:0.02688:2.18623:59.9:162:0.6778:0.0496:0.2 +5 38954825 . G GT 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.13776;SOR=1.59658;LSEQ=TTTAGCAATGTTAAGATTTT;RSEQ=TTTTTTTTTTACTATTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:24:21,3:236,81:317,24:0.0696:2,2:24.4:1:30.6:1:0.21866:2.40:60:48:0.0714:0.0029:0.1 0/1:253:27:21,6:165,61:226,27:0.1067:2,2:24.6:1:28.8:1:0.81764:1.29:59.6:54:0.1093:0.0237:0.2 +5 38954994 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61957;LSEQ=AAAGATGATTACTATATCTC;RSEQ=TGGCTAATTTAAATATGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:287:286:52,234:1,0:1,286:0.9965:0,2:25:1:32.9:1:0.18467:0:60:94.333:0.9965:0:1 1/1:178:177:37,140:0,0:0,177:0.9944:0,2:24.6:1:31.3:1:1:0:60:87.5:0.9943:0:1.1 +5 38955796 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00244;SOR=1.39315;LSEQ=CAATCAAGTCAACATATTTG;RSEQ=AGTTGTATTCCTAGAGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:898:387:133,254:167,343:510,387:0.431:2,2:24.9:1:30.4:1:0.61764:1.08:60:42:0.43:0:1.1 1/0:557:286:95,191:106,165:271,286:0.5135:2,2:23.7:1:29.2:1:0.15838:1.291:60:56.2:0.5137:0:1.1 +5 38956039 . G T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACATTTTCAAGCCATCAC;RSEQ=TGGTTACTGCACAGACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:0,14:1:0,1:20.2:1:31:1:1:0:60:28:1:0:1.5 1/1:2:2:0,2:0,0:0,2:1:0,0:32.5:1:32:0:1:0:60:4:1:0:1.5 +5 38958167 . A G 87 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAACATGGTGAAACTCC;RSEQ=ACTCTACTAAAAATACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:23.4:1:31.1:1:1:0:38.4:14:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38958386 . T TA 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.29339;SOR=0;LSEQ=TATGAACAGACCAAAAAAAT;RSEQ=AAAAAAAAAGAAAAACCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:3,0:70,3:73,3:0.0395:1,0:22.7:1:28.7:1:1:0:60:6:0.04:0.0132:0.3 0/0:45:0:0,0:44,1:45,0:0:1,0:23.4:1:30.3:1:1:0:60:90:1:0:0.3 +5 38958750 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01176;SOR=1.44943;LSEQ=AAAAATTTAAGTATTAAATT;RSEQ=TAAAAAATGAACCTTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:139:97,42:334,168:502,139:0.2165:2,2:23.4:1:32.6:1:0.5402:1.16:60:138:0.2166:0:1.1 0/1:402:115:76,39:185,101:286,115:0.2861:2,2:20.7:1:31.4:1:0.81771:1.06:60:114:0.2843:0:1.2 +5 38958968 . A C 254 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.000;MSILEN=1;SSF=0.24486;SOR=0.7174;LSEQ=GAATACATTAAAAAAAAAAA;RSEQ=AACTTCAGCATAAATAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:296:255:51,204:6,0:6,255:0.8615:0,2:21.7:1:31.8:1:9e-05:0:59.6:22.182:0.8714:0:1.2 1/1:131:107:17,90:3,0:3,107:0.8168:0,2:23.5:1:31.4:1:0.00528:0:60:34.667:0.8254:0:1.3 +5 38959123 . T C 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTATCTAGCAGCTTCT;RSEQ=CCCCCGATACAAAAATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:67,22:89,2:0.0217:2,2:6.5:1:32:1:0.44371:3.00065:60:4:0.0227:0:1 0/0:22:0:0,0:17,5:22,0:0:2,0:29.1:1:29.9:1:1:0:60:21:1:0:0.1 +5 38959431 . G GA 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.86781;SOR=1.05645;LSEQ=AAGATTAAGGAGACTTAAAA;RSEQ=AAAAAAAAAATAAGAATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:26:3,23:96,358:454,26:0.0539:2,2:30:1:31.8:1:0.32198:2.05324:60:52:0.0571:0.0021:0.2 0/1:264:15:2,13:56,191:247,15:0.0568:2,2:27.2:1:30.4:1:0.53334:1.90191:60:30:0.0588:0.0076:0 +5 38959794 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54848;SOR=Inf;LSEQ=ATAAAACTTAACCAAACACA;RSEQ=GTACACAGAATAAAAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:223:221:205,16:0,1:1,221:0.991:0,2:25.2:1:31.8:1:0.07658:0:60:30.571:0.9953:0:1.1 1/1:116:116:107,9:0,0:0,116:1:0,2:23.6:1:31.3:1:1:0:60:37.667:1:0:1.1 +5 38960325 . T TA 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATAACTTGCCCAGTCTCA;RSEQ=AACTAGTGACTAAGTCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:39,5:0,0:0,44:1:0,2:22.4:1:29.4:1:1:0:59.1:43:0.9773:0.25:0.2 1/1:9:9:9,0:0,0:0,9:1:0,0:23.6:1:27.8:1:1:0:60:18:1:0.2222:0.1 +5 38960854 . CAT C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGTTCCCATAATCCCCA;RSEQ=GTCATGAAAGGGACCTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:0,17:0,0:0,17:1:0,1:30.9:1:31.5:1:1:0:59.9:16:1:0.1176:0.2 1/1:2:2:0,2:0,0:0,2:1:0,0:29:1:31.5:1:1:0:60:4:1:0:0 +5 38962277 . AT A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATAAGACTATATTAAAA;RSEQ=ATATATGAGTACCTATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:95:94,1:0,0:0,95:1:0,1:26.7:1:30.8:1:1:0:60:94:1:0.1474:0.1 1/1:36:36:36,0:0,0:0,36:1:0,1:24.2:1:29.7:1:1:0:60:72:1:0.1944:0.1 +5 38962325 . G T 23 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61278;SOR=1.88163;LSEQ=TTGTTAAAATGTATGTATAT;RSEQ=TCTTTAAAATTATTACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:180,17:197,2:0.01:2,2:17.5:1:29:1:0.17314:10.31853:60:4:0.0102:0:1 0/1:107:2:0,2:97,8:105,2:0.0187:2,0:1:0:23:0:0.00794:0:60:4:0.0187:0:1 +5 38962543 . A G 307 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.52914;SOR=Inf;LSEQ=TAATTACGTTATAATTAATA;RSEQ=TAAAATTAAAGACAAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:667:665:402,263:0,0:0,665:0.997:0,2:24.2:1:32.8:1:1:0:60:82.125:0.997:0:1.1 1/1:406:406:230,176:0,0:0,406:1:0,2:23.8:1:31.3:1:1:0:60:100.5:1:0:1.1 +5 38962656 . T C 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00196;SOR=0;LSEQ=TGTTGAAGGACTTGGCTATC;RSEQ=CTAAGGTTAATTAAAAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:984:12:4,8:417,554:971,12:0.0122:2,2:19.2:1:29.6:1:0.57067:1.50481:60:11:0.0114:0:1.2 0/0:706:0:0,0:306,400:706,0:0:2,0:25.5:1:29.1:1:1:0:60:57.833:1:0:0.2 +5 38964811 . A AT 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCATAACCTATCCATACT;RSEQ=TTTTTTTTAAAAAGAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:2,0:132,7:139,2:0.0142:2,0:23:1:33:0:1:0:60:4:0.0144:0:0 0/0:68:0:0,0:66,2:68,0:0:1,0:25.3:1:27.4:1:1:0:60:21.667:1:0:0 +5 38966903 . A ATT 137 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=0.04707;SOR=1.83941;LSEQ=CATCAGATTTATTTTTCAAA;RSEQ=TTTTTTTTTTTTTTTTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:31:0,31:10,82:92,31:0.1722:2,1:28:1:27.7:1:0.06421:0:57.9:6.75:0.1627:0:1.1 0/1:101:28:0,28:4,44:48,28:0.2772:2,1:25.6:1:27.5:1:0.29019:0:56.8:8.333:0.2632:0.0396:1.4 +5 38968584 . AA C 33 v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATACTTTAAAAAACAAAAC;RSEQ=AAAAAAAAAAAGCCCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,0:0,2:0.4:0,0:25.5:1:33.5:0:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38971649 . A ATT 32 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCCAGCTAATTTTTGT;RSEQ=TTTTTTTTTTTTTTAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:32.5:1:1:0:21:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38971865 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02973;SOR=1.47662;LSEQ=TTCTGTATTTTAAAAATATG;RSEQ=TCTAGATTAACAACTAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:149:144,5:194,3:197,149:0.4306:1,1:23.3:1:31.7:1:0.29756:2.24011:60:73.5:0.4324:0:1.7 1/0:216:114:109,5:97,5:102,114:0.5278:1,1:21.2:1:30.6:1:1:1.12:60:37:0.5236:0:1.8 +5 38971912 . T A 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCACCTGAAATAATTT;RSEQ=TTTTTTATAATTAATTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:908:908:649,259:0,0:0,908:1:0,2:24:1:29.1:1:1:0:60:453:1:0:1.2 1/1:643:643:434,209:0,0:0,643:1:0,2:23.8:1:28:1:1:0:60:106.167:1:0:1.2 +5 38972078 . G GA 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.99515;LSEQ=ATACCTAAAGAGGACAGAAA;RSEQ=AAAAAAAAATCACTGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:14:3,11:155,501:656,14:0.0207:2,2:25.1:1:31.4:1:1:1.13419:60:28:0.0214:0.0015:0.1 0/1:436:9:1,8:108,315:423,9:0.0206:2,2:27.2:1:30.6:1:0.45988:2.73818:60:18:0.0211:0:0.2 +5 38972335 . T C 91 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGAGTCTGACTGCCTGA;RSEQ=GAACTCTTCTCTGGGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:14.1:1:28.9:1:1:0:57.8:18:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38975458 . T C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.79189;SOR=1.15591;LSEQ=ATTAGCTAATTCCTATTGAC;RSEQ=ATTACAAATTTCCTTCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:17:17,0:32,0:32,17:0.3469:1,1:21.9:1:31.9:1:1:0:60:34:0.3469:0:1.1 0/1:21:8:8,0:13,0:13,8:0.381:1,0:19.8:1:31:1:1:0:60:16:0.381:0:1 +5 38975955 . C T 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTTCTATATTCCTGCTC;RSEQ=CTGAAAACTATTCTTAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:0,13:1:0,1:33.3:1:30.8:1:1:0:58.9:26:1:0:1.2 1/1:2:2:0,2:0,0:0,2:1:0,0:19:1:30:0:1:0:60:4:1:0:1 +5 38976082 . G C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTTTAATCACACACACT;RSEQ=TTTACTTCACAATCTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:12:1:34:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38978257 . GATA G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=ATTATACTGTCTCATTTCTA;RSEQ=ATAATATTTACTCTATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:9:1:29:1:1:0:60:4:0.6667:0.3333:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38978758 . TA T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.58017;SOR=0.85864;LSEQ=GGGTGCTAAAATTCTCTATT;RSEQ=AAAAAAAAAAGGAAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:61:14,47:183,348:531,61:0.1022:2,2:28:1:31.4:1:0.08476:1.76384:60:122:0.1039:0.0034:0.2 0/1:382:34:5,29:132,209:341,34:0.089:2,2:27.8:1:31.1:1:0.00485:3.65279:59.4:68:0.0907:0.0079:0.4 +5 38978782 . T A 38 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.70464;SOR=1.3541;LSEQ=AAAAAAAAGGAAGAAAAGAG;RSEQ=CTTTATTTTAAAATGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:4:4,0:64,327:391,4:0.0101:2,0:7.5:1:19.3:1:0.00082:0:60:1:0.0053:0:2.3 0/1:220:3:2,1:54,163:217,3:0.0136:2,2:14.3:1:20.7:1:0.16011:5.98:60:2:0.0096:0:1.3 +5 38982220 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTTTAAAACTTAATTGC;RSEQ=TTTCTGACTTGAAAAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:2,156:158,2:0.0125:1,2:20:1:32.5:1:0.03726:63.90:60:4:0.0128:0:1 0/0:58:0:0,0:0,58:58,0:0:1,0:22.6:1:32:1:1:0:60:116:1:0:0 +5 38990779 . G T 67 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATATCAGATATATATCA;RSEQ=ATATATCATATATATGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:8.5:1:33.5:1:1:0:36.5:8:0.6667:0:5.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990786 . C G 68 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGATATATATCAGATATAT;RSEQ=ATATATATGATATATATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:15.5:1:34:0:1:0:36.5:8:0.6667:0:5.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990793 . AT CA 66 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATCAGATATATCATATAT;RSEQ=GATATATATCAGATATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:2,0:2,4:0.5714:0,0:23.5:1:33:0:1:0:36.5:8:0.6667:0:4.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990810 . TG T 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATATGATATATATCAGATA;RSEQ=ATATATATGATATATATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:36.5:1:30:1:1:0:37:4:0.25:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990818 . A C 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATATCAGATATGATATAT;RSEQ=TGATATATATCATATATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:30.5:1:31:1:1:0:37:4:0.25:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990820 . G C 85 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAGATATGATATATAT;RSEQ=ATATATATCATATATATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:40.5:1:33:1:1:0:39.7:12:0.75:0:3.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990829 . C G 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGATATATATGATATATAT;RSEQ=ATATATATGATATATATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:22:1:34:0:1:0:37.5:4:0.2222:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990834 . ATA C 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATATGATATATATCATAT;RSEQ=TGATATATATGAGATATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:16.5:1:31.3:1:1:0:37:4:0.2222:0.1111:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990836 . AT CA 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATGATATATATCATATAT;RSEQ=GATATATATGAGATATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:30:1:32.5:1:1:0:37.5:4:0.2857:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990901 . GAT G 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=0.50549;SOR=Inf;LSEQ=ATGAGATATATGAGATATAT;RSEQ=ATATATGAGATATATGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:6,1:2,0:2,7:0.7778:0,2:10:1:32:1:1:0:31.4:14:0.7778:0.4444:2 1/1:5:5:4,1:0,0:0,5:1:0,2:11.4:1:31.3:1:1:0:27.6:10:1:0.6:2 +5 38990903 . T G 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGATATATGAGATATATGA;RSEQ=ATATATGAGATATATGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:0,0:0,2:0.4:0,0:33.5:1:32:1:1:0:25.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 38990927 . TGATATATGA T 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.27677;SOR=2.2909;LSEQ=TATGAGATATATGAGATATA;RSEQ=GATATATGAGATATATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:4,1:28,0:28,5:0.1515:1,2:11:1:31.8:1:0.15152:0:36.8:10:0.1515:0.1212:1.8 0/1:17:5:4,1:12,0:12,5:0.2941:0,2:10.6:1:29.2:1:0.29412:0:33.4:10:0.2941:0.2353:1.8 +5 38990946 . G TAT 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0.72079;LSEQ=TATGATATATGAGATATATG;RSEQ=ATATATGATATATATATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:46:46,0:1,1:2,46:0.9388:2,1:24.4:1:31.3:1:0.04167:0:29.8:92:0.9583:0.2857:1.7 1/1:24:22:22,0:1,1:2,22:0.9167:2,1:26.6:1:29.7:1:0.08333:0:30.5:44:0.9167:0.25:1.8 +5 38990957 . T G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=1;SOR=0.50314;LSEQ=GATATATGAGATATATGATA;RSEQ=ATATATGATAGATATATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:79:78:78,0:0,1:1,78:0.9873:0,1:21.5:1:33.9:1:0.01266:0:39.8:156:0.9873:0:1.5 1/1:40:39:39,0:0,1:1,39:0.975:0,1:22.9:1:32.5:1:0.025:0:39.1:78:0.975:0:1.6 +5 38991272 . T C 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.00218;SOR=Inf;LSEQ=TAGTTAATAACAGAATAAGA;RSEQ=CCAGAATAAGATCTAGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:1,110:111,0:0:1,0:26:1:30.5:1:1:0:59.8:36:1:0:0.1 0/1:65:6:0,6:0,59:59,6:0.0923:1,0:25.2:1:32.3:1:1:0:60:12:0.0938:0:1 +5 38996638 . A G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTCTAGTAACTTATCAA;RSEQ=GCAGTAACTACATTTACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:26.7:1:33.3:1:1:0:60:6:0.2727:0:1.3 0/0:2:0:0,0:2,0:2,0:0:0,0:24.5:1:31:1:1:0:60:4:1:0:0 +5 38996986 . T A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00518;SOR=Inf;LSEQ=CTGTTGTATGTCAATGCACC;RSEQ=AAACAATACACAAAATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:829:0:0,0:330,499:829,0:0:2,0:25.3:1:29.5:1:1:0:60:68.083:1:0:0.1 0/1:593:6:5,1:232,355:587,6:0.0101:2,2:10.7:1:26.7:1:0.04003:7.63:60:12:0.0103:0:1 +5 38997022 . C A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04678;SOR=Inf;LSEQ=TATTAATCATTGATAAAATT;RSEQ=TATTAAACAACTTTTTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:0:0,0:113,361:474,0:0:2,0:23.2:1:32.9:1:1:0:60:58.25:1:0:0.1 0/1:268:3:1,2:62,203:265,3:0.0112:2,2:7.7:1:25.7:1:0.55398:1.63:60:2:0.0075:0:2.3 +5 38997170 . G A 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32415;SOR=0;LSEQ=ATCTCGAGGGATAAATATCT;RSEQ=TCATTTAAAAGACCAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:1,28:29,8:0.2162:1,0:16.1:1:30.6:1:1:0:60:16:0.2162:0:1 0/0:9:0:0,0:1,8:9,0:0:2,0:13.3:1:32.2:1:1:0:60:18:1:0:0 +5 39002271 . CAAA C 53 d5;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATGAAATGTTACACAG;RSEQ=AAAAAAAAAAAAAAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:32:1:34:0:1:0:60:6:0.75:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 39002504 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.15973;SOR=0.36369;LSEQ=TTGTGTGTGTGTGTGTGTGT;RSEQ=TATATATATATATACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:19:19,0:37,0:37,19:0.3167:1,1:31.5:1:32:1:1:0:60:38:0.3393:0:1.8 0/1:21:3:3,0:15,0:15,3:0.1429:1,0:30.7:1:29:1:1:0:60:6:0.1667:0:1.3 +5 39002513 . TATATAC T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=2;SSF=0.56896;SOR=0;LSEQ=TGTGTGTGTGTATATATATA;RSEQ=ACACACACAAAATTCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:4:4,0:62,1:63,4:0.0588:1,0:28.3:1:32.3:1:1:0:58.8:8:0.0606:0:0.3 0/0:21:0:0,0:21,0:21,0:0:1,0:23.9:1:26.8:1:1:0:59.7:42:1:0:0.6 +5 39002515 . TATAC T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0.1466;SOR=2.65515;LSEQ=TGTGTGTGTATATATATATA;RSEQ=ACACACACAAAATTCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:7:7,0:58,1:59,7:0.0986:1,0:21.1:1:31.1:1:1:0:60:14:0.1077:0:0 0/1:22:5:5,0:17,0:17,5:0.2273:1,0:23.2:1:29:1:1:0:60:10:0.2273:0.0455:0.2 +5 39002517 . TAC T 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0.94498;LSEQ=TGTGTGTATATATATATATA;RSEQ=ACACACACAAAATTCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:6:6,0:54,2:56,6:0.0811:1,0:36.7:1:32:1:1:0:58.3:12:0.0968:0:0.7 0/1:26:2:2,0:20,0:20,2:0.0769:1,0:22.5:1:32:0:1:0:60:4:0.0909:0:0 +5 39002519 . C T 149 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGTGTATATATATATATATA;RSEQ=ACACACACAAAATTCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:32:31,1:23,2:25,32:0.4324:2,1:23.8:1:29.8:1:0.57621:2.65:60:15:0.5556:0:1.5 0/0:31:0:0,0:9,0:9,0:0:0,0:17.4:1:30.6:1:1:0:60:18:1:0:0.3 +5 39002808 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.127;SOR=Inf;LSEQ=ATACAAGTTTTGCTGCACAG;RSEQ=TTTCAAATACACACAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:65,261:326,0:0:2,0:23.7:1:31.9:1:1:0:59.9:64.2:1:0:0.1 0/1:181:2:1,1:32,147:179,2:0.011:2,2:22:1:25.5:1:0.33223:4.54:60:4:0.0112:0:3 +5 39003212 . G A 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGCCAATAGCAGGCACA;RSEQ=ACCTTTTATATCAATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:2,1:1,4:5,3:0.375:2,2:10.3:1:31.3:1:0.46429:5.78:60:6:0.375:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 39021088 . G T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03301;SOR=Inf;LSEQ=GGTCAAGAAACATTTAGTAA;RSEQ=TGTGGTAAGGAACAAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:331,95:426,0:0:2,0:24:1:32.6:1:1:0:59.9:37.727:1:0:0.1 0/1:318:4:2,2:220,94:314,4:0.0126:2,2:13.5:1:28.3:1:0.58694:2.33344:60:8:0.0127:0:1 +5 39021369 . G A 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27707;SOR=0.50685;LSEQ=TTACCCTCCACCCCAAATCT;RSEQ=TTAATTTAAATGACTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:46:1,45:0,13:13,46:0.7797:1,1:23.2:1:31:1:1:0:59.4:45:0.7759:0:1.1 1/0:25:16:1,15:0,9:9,16:0.64:0,1:25.1:1:30.7:1:1:0:60:32:0.64:0:1 +5 39021493 . G A 83 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACAAAATCTTAAATCTT;RSEQ=CTATTATTTGAATGTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:6,7:0.5385:0,0:13.3:1:29.7:1:1:0:55.6:14:0.5385:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 39074202 . C T 54 v3;p8;q25;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07977;SOR=4.04739;LSEQ=CCCTCGCGGCGCCCGCGGCG;RSEQ=CCCGCGTTACCTCGGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:792:2:0,2:550,240:790,2:0.0025:2,0:1:0:26:0:0.0931:0:60:4:0.0025:0:1 0/1:591:6:0,6:378,207:585,6:0.0102:2,0:5.8:1:21.2:1:0.00209:0:60:5:0.0085:0:1.5 +5 39074207 . C T 67 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11576;SOR=3.00387;LSEQ=GCGGCGCCCGCGGCGCCCCG;RSEQ=GTTACCTCGGGTCAGATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:870:3:0,3:595,272:867,3:0.0034:2,0:1:0:28.3:1:0.03135:0:60:6:0.0035:0:1 0/1:680:7:2,5:423,249:672,7:0.0103:2,2:7.1:1:24:1:0.1092:4.23773:60:6:0.009:0:1.7 +5 39074296 . G C 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.52282;LSEQ=ACACAGCCCCAATTAGGATT;RSEQ=GCTCGCAGGCCAGCTGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1403:593:327,266:462,342:804,593:0.4227:2,2:25.4:1:30.9:1:0.41289:1.0988:60:58.3:0.4271:0:1.1 1/0:1066:562:312,250:268,232:500,562:0.5272:2,2:25.2:1:29.7:1:0.53756:1.08:60:61.444:0.5277:0:1.2 +5 39074559 . G A 49 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.82841;LSEQ=CCTCCCCGCGCGCCGCGCCC;RSEQ=CCCCCCGCGGCACCTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:4:3,1:71,293:364,4:0.0107:2,2:12:1:24.8:1:0.02688:12.27:60:3:0.0086:0:2 0/0:226:2:2,0:45,176:221,2:0.0088:2,0:5.5:1:20:1:0.04367:0:60:1:0.0047:0:2 +5 39074575 . C T 41 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.28152;SOR=0;LSEQ=GCCCGCCCCCCGCGGCACCT;RSEQ=CCCCGCCCCCTCGGCGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:3:1,2:20,182:202,3:0.0146:2,2:13:0:26:1:0.27813:4.49:59.7:2:0.0101:0:3 0/0:134:0:0,0:23,110:133,0:0:2,0:12.8:1:30.7:1:1:0:60:132:1:0:0.2 +5 39074580 . G C 38 p8;pSTD;q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.28402;SOR=0;LSEQ=CCCCCCGCGGCACCTCCCCC;RSEQ=CCCCCTCGGCGGCGACGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:3:3,0:10,146:156,3:0.0188:2,0:6:0:24.3:1:0.00044:0:60:6:0.0195:0:5.3 0/0:102:0:0,0:11,88:99,0:0:2,0:8:0:8:0:1:0:60:0:0:0:1 +5 40456871 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAAAATAAATTGAGATAG;RSEQ=TTTCAGGGAAGAGATCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 40457232 . T A 81 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0.64552;LSEQ=CGTTGTGGAAATTCCATTTT;RSEQ=TAACACACTGTTAGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:5,8:0.6154:0,0:24.1:1:27.3:1:1:0:60:7:0.5833:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:21:0:29:0:1:0:60:2:0.5:0:1 +5 40457347 . A T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACATCCTTCTCAGACCA;RSEQ=GTGCCAGAATCTTTGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:156:156:138,18:0,0:0,156:1:0,2:24.3:1:30.9:1:1:0:59.7:155:1:0:1.5 1/1:85:85:67,18:0,0:0,85:1:0,2:23.6:1:30:1:1:0:60:170:1:0:1.2 +5 40457379 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28405;SOR=3.70455;LSEQ=TTTGGAAAGGAACATAATAT;RSEQ=CCTAATTGGAAAAGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:1:0,1:210,78:288,1:0.0035:2,0:1:0:27:0:0.27336:0:60:2:0.0035:0:1 0/1:157:2:0,2:107,48:155,2:0.0127:2,0:18.5:1:26.5:1:0.10003:0:60:4:0.0127:0:1.5 +5 40457403 . G C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12651;LSEQ=AATTGGAAAAGGCTCTGCAC;RSEQ=CACCCTGCTTCAGAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:414:207:139,68:131,76:207,207:0.5:2,2:24.6:1:30.9:1:0.47015:1.19:60:40.4:0.4963:0:1.9 0/1:250:28:23,5:133,86:219,28:0.112:2,2:23.4:1:30.2:1:0.03602:2.96:60:27:0.1089:0:2 +5 40457459 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.56966;LSEQ=TTTGGAAGACCACATAATGG;RSEQ=TCTTTAATCAACAACACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:580:311:161,150:136,132:268,311:0.5362:2,2:26.2:1:30.5:1:0.86759:1.04:60:102.667:0.5375:0:1.5 0/1:393:156:81,75:126,110:236,156:0.3969:2,2:26.9:1:28.4:1:0.83633:1.06043:60:30.2:0.3912:0:1.3 +5 40457488 . G A 149 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04799;LSEQ=CAACAACACACTGCAGGACC;RSEQ=ATATATTTTCCTTGCCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:30:15,15:240,299:539,30:0.0527:2,2:20.5:1:30.5:1:0.57653:1.25:60:60:0.0533:0:1.2 0/0:376:1:1,0:174,201:375,1:0.0027:2,0:1:0:25:0:0.46543:0:60:2:0.0027:0:1 +5 40457560 . T A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12571;SOR=Inf;LSEQ=TCTTCCCCCATATCCTGCTA;RSEQ=TCTCACAAAACGTATGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:47,176:223,0:0:2,0:23.1:1:30.4:1:1:0:60:43.6:1:0:0.1 0/1:123:2:1,1:24,97:121,2:0.0163:2,2:14:1:24.5:1:0.36652:3.98:60:4:0.0163:0:1 +5 40457629 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.2969;SOR=0;LSEQ=ACAAAATATCTCAACCAGAA;RSEQ=CAAGCAACTGAAGTTAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:4:0,4:0,56:56,4:0.0667:1,0:12:1:31:1:1:0:60:8:0.0678:0:1 0/0:30:0:0,0:1,29:30,0:0:1,0:22.1:1:32.2:1:1:0:60:60:1:0:0.1 +5 40457889 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGATATTTTATTAATT;RSEQ=TACATTTTAGTAAAGCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:18.5:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 40457892 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATATTTTATTAATTCTA;RSEQ=ATTTTAGTAAAGCATTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21.5:1:27:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 42116639 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTAAAGAAAAAAGTGTA;RSEQ=CCTATTCCTTTAAAAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:33.5:1:1:0:59:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 42384740 . A G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09388;SOR=0;LSEQ=CAGACTTTAGCATGAAGGTG;RSEQ=TGGTTAATTCAGAGGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:5,21:0,0:0,26:1:0,2:24.3:1:32.1:1:1:0:60:52:1:0:1 1/1:12:10:1,9:0,2:2,10:0.8333:0,2:22.8:1:31.7:1:1:0:60:20:0.8333:0:1 +5 42384876 . G A 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATACACATATAAGATTTAT;RSEQ=TAAGTAGGTGCAGGTTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,0:0,3:0.75:0,0:28:1:29.3:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 43981410 . G A 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTAGGTGGATACCCACAC;RSEQ=TCTGGGCTGGCCGGATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:7:1:32.5:1:1:0:60:4:1:0:0 0/1:5:2:1,1:0,3:3,2:0.4:0,2:24.5:1:31.5:1:0.4:0:60:4:0.4:0:1 +5 44273551 . TTTTG T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.19702;LSEQ=CTTAAGAGTTTGAAACTGTT;RSEQ=TTTGTTTGTTTGTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:4:3,1:172,29:201,4:0.0196:2,2:15.8:1:26.5:1:0.47164:1.96892:57.3:3:0.0151:0.0098:0.5 0/1:171:4:3,1:141,26:167,4:0.0234:2,2:22.5:1:30.3:1:0.50047:1.80019:60:8:0.0237:0.0058:0.3 +5 44273622 . G T 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00205;SOR=0.43344;LSEQ=TTTGGGAGATGAGTTGGGGA;RSEQ=ATGAAAAGACTGAATTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:54:33,21:325,224:549,54:0.0896:2,2:25.9:1:30.4:1:0.88478:1.08:60:108:0.0903:0:1.6 0/1:465:19:10,9:252,194:446,19:0.0409:2,2:24.3:1:28.8:1:0.81512:1.16867:60:38:0.041:0:1.6 +5 44273673 . A T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.60229;LSEQ=AAACTTTCACTTTGACTGTT;RSEQ=CTTTTTAACTAAAACAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:300:147,153:194,206:400,300:0.4286:2,2:24.7:1:30.7:1:0.93912:1.02:60:299:0.429:0:1.2 0/1:524:163:71,92:172,189:361,163:0.3111:2,2:26.2:1:29.1:1:0.396:1.17885:60:80.5:0.309:0:1.2 +5 44273923 . A G 63 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=2.12136;LSEQ=AATTATGTATTATGACAACA;RSEQ=CTAAGCATATTAAAAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:0,9:9,4:0.3077:0,0:28:1:31.5:1:1:0:60:8:0.3077:0:1.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:29:0:33:0:1:0:60:2:0.5:0:1 +5 44274058 . C A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGGTCAATGGATATAC;RSEQ=TGCCAAACAGGTAAGTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:19:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 44275948 . C G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTCTGAATTGCTTACA;RSEQ=GGTAAACGAATTATTAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:0:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 50979093 . G T 56 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCTCCTTTCATAATGTTA;RSEQ=AGTTTGCAGTGATATCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:32.3:1:28:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 50979220 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48649;SOR=Inf;LSEQ=GGCGATGTTCAGTTATTTAA;RSEQ=GTACCAATGCATCAGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:14,4:18,0:0:2,0:12.8:1:30.8:1:1:0:60:36:1:0:0.1 0/1:19:2:1,1:12,5:17,2:0.1053:2,2:32:1:30:0:1:2.28037:60:4:0.1053:0:1 +5 50979299 . TC T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23964;SOR=0;LSEQ=TGCTGCCCAGGAGTCAGCGT;RSEQ=CCTTTTTACTCACACAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:30,27:57,2:0.0339:2,2:19:0:33.5:1:1:1.10912:60:4:0.0351:0:0.5 0/0:61:0:0,0:28,33:61,0:0:2,0:25:1:30.7:1:1:0:60:122:1:0:0.1 +5 51977648 . G C 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24268;SOR=Inf;LSEQ=TCTCATCTTCATGAGTTTGT;RSEQ=TAGTTTGGTCTTTGAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:18,0:0:2,0:23.8:1:32.9:1:1:0:55.6:36:1:0:0.1 0/1:23:3:2,1:11,9:20,3:0.1304:2,2:11:1:29.3:1:1:1.60:54.7:6:0.1304:0:1 +5 51977894 . C G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48052;SOR=0;LSEQ=AGCAAAGATGGGTGCCTGCT;RSEQ=CTTCTTCTGGGACCTCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:20.5:1:34:0:1:1:35.5:4:0.1667:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:29.6:1:29.9:1:1:0:46.4:20:1:0:0 +5 51977947 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18347;SOR=Inf;LSEQ=CAGCCTGATGCCAATAGGAT;RSEQ=GCTCCTGTATAAGGTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:13,5:18,0:0:2,0:16.9:1:30.7:1:1:0:60:36:1:0:0.4 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:8.5:1:27.5:1:1:1.36624:60:4:0.1667:0:2 +5 51977971 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20814;SOR=Inf;LSEQ=CCTGTATAAGGTGCCTGACA;RSEQ=CCCCTATTGGAGGGTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:17,11:28,0:0:2,0:22.4:1:32.9:1:1:0:60:56:1:0:0.3 0/1:24:2:1,1:11,11:22,2:0.0833:2,2:23.5:1:32.5:1:1:1:60:4:0.087:0:1 +5 51978028 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22313;SOR=Inf;LSEQ=GAGAGCAGGACCCATTTAAC;RSEQ=AAGCACTTTGTCCCTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:43,0:0:2,0:26.6:1:30.7:1:1:0:57.6:86:1:0:0.3 0/1:39:2:1,1:17,20:37,2:0.0513:2,2:11.5:1:31.5:1:1:1.17:60:4:0.0513:0:2 +5 51978040 . C A 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49648;SOR=0;LSEQ=CATTTAACGAAGCACTTTGT;RSEQ=CCTTGGTGGAGAGAGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:19,18:37,2:0.0513:2,2:6:1:26.5:1:1:1.05412:60:4:0.0526:0:2 0/0:33:0:0,0:16,17:33,0:0:2,0:26.9:1:30.5:1:1:0:59.6:66:1:0:0.2 +5 51978302 . T C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAAGAGGCACTCTGGTTGAA;RSEQ=ACTGCCACAGCCAGTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:29.5:1:28:1:1:0:60:4:1:0:0 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:28:1:30:1:1:1.41:52:4:0.2857:0:1.5 +5 51978411 . C A 32 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCTGGAGCTATAGAAATGGG;RSEQ=ACCATCCTTCCCCCACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:32.5:1:1:0:57:4:1:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:33:0:1:0:60:2:1:0:0 +5 52074333 . A G 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGGTGTGGTGGCTCACAAA;RSEQ=TTTTTTCTAACAAATCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:1,1:0.5:0,0:1:0:31:0:1:0:60:2:0.5:0:2 1/1:2:2:2,0:0,0:0,2:1:0,0:22.5:1:33:0:1:0:60:4:1:0:1 +5 52074401 . T G 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20635;SOR=0.09168;LSEQ=ATTGCTGTTTTCCCCCCACT;RSEQ=TGTTTAGGTTATACTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:35.8:1:32.8:1:1:0:60:8:0.8:0:1.3 0/1:5:1:1,0:4,0:4,1:0.2:0,0:7:0:33:0:1:0:60:2:0.2:0:1 +5 52074527 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50561;SOR=Inf;LSEQ=CTTATTTTTATTGTTGTCTG;RSEQ=TGTTGCTGTTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:34,35:69,0:0:2,0:32.4:1:33.2:1:1:0:60:138:1:0:0 0/1:90:2:1,1:44,44:88,2:0.0222:2,2:22.5:1:28.5:1:1:1:60:4:0.0225:0:1.5 +5 52074533 . C CTGT 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=4e-05;SOR=0.15501;LSEQ=TTTATTGTTGTCTGCTGTTG;RSEQ=TGTTGTTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:22:8,14:26,24:50,22:0.3056:2,2:29.4:1:31:1:0.30632:1.87907:60:44:0.3056:0.0417:0.2 0/1:95:6:2,4:43,46:89,6:0.0632:2,2:20.2:1:27.6:1:0.67999:1.85771:60:12:0.0638:0.0316:0.5 +5 52074551 . C CTGA 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.13483;SOR=Inf;LSEQ=TGCTGTTGTTGCTGCTGCTG;RSEQ=TGATGATGATAATGATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:30,38:68,0:0:2,0:27:1:33.2:1:1:0:60:136:1:0:0.1 0/1:90:4:0,4:37,47:84,4:0.0444:2,0:25.5:1:31.8:1:0.13549:0:60:8:0.0449:0.0111:0.3 +5 52665229 . GTCT AGAC 212 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACACATTATGAATAAAACAA;RSEQ=AGATGATGCAAGAGAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:108:71,37:110,56:166,108:0.3899:2,2:26.9:1:31.5:1:1:1.02356:60:216:0.3942:0.0939:1.4 0/0:329:0:0,0:203,125:328,0:0:2,0:24.5:1:31.5:1:1:0:60:108.333:0.9969:0:0.4 +5 52665299 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.65276;LSEQ=TGTTTGTTTCCATTACATCC;RSEQ=CAGTGCCAGTTTTAGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:154:76,78:161,167:328,154:0.3182:2,2:25.8:1:30.6:1:1:1.01:60:29.8:0.3157:0:1.3 1/0:508:348:177,171:72,87:159,348:0.685:2,2:24.6:1:29.9:1:0.25206:1.25:60:57:0.6826:0:1.1 +5 52665368 . G T 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=AAGACATTAGACTTCCTATT;RSEQ=CAGTGGTTTATAACAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:15:5,10:83,196:279,15:0.051:2,2:23.1:1:30.5:1:0.77606:1.18:59.6:30:0.0523:0:1.1 0/0:312:0:0,0:122,190:312,0:0:2,0:25.3:1:31:1:1:0:60:51:1:0:0.5 +5 52665396 . A G 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTATAACAAAACCTCTTCTA;RSEQ=TGGATATTAGCATTAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:33,150:183,0:0:2,0:22.3:1:31.4:1:1:0:60:366:1:0:0.1 0/1:185:19:6,13:46,120:166,19:0.1027:2,2:17.1:1:31.6:1:0.78869:1.20:60:38:0.1027:0:1.4 +5 52665731 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCCTCCCACGAGAATTATGT;RSEQ=CACTTGACTTGGCACAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:23:1:33:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 53875170 . T TA 26 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGAGAGAGCCAGACCCTGT;RSEQ=AAAAAAAAAAGAAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:22.5:1:26.5:1:1:0:60:4:0.6667:0.3333:2 1/1:1:1:1,0:0,0:0,1:1:0,0:11:0:29:0:1:0:60:2:1:0:0 +5 53875320 . A T 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74802;LSEQ=TATAGAATCATGAGCCAACA;RSEQ=GTTGATTTAATAAATGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:63:61,2:0,0:0,63:0.9844:0,1:23.1:1:31.7:1:1:0:60:126:0.9844:0:1 1/1:48:47:43,4:1,0:1,47:0.9792:0,2:21.7:1:29.9:1:1:0:60:22.5:0.9783:0:1 +5 53875373 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2223;SOR=Inf;LSEQ=CCTCCTTCATCCATCTATTT;RSEQ=CAGAGTCACTGGTTCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:149,41:190,0:0:2,0:25.1:1:28.5:1:1:0:60:62.333:1:0:0.3 0/1:170:2:1,1:126,42:168,2:0.0118:2,2:35.5:1:30.5:1:0.44302:2.97664:60:4:0.0118:0:1 +5 53875375 . A G 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22718;SOR=Inf;LSEQ=TCCTTCATCCATCTATTTAC;RSEQ=GAGTCACTGGTTCACTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:151,45:196,0:0:2,0:25.1:1:30.8:1:1:0:60:97:1:0:0.3 0/1:179:2:1,1:129,47:176,2:0.0112:2,2:11:0:26.5:1:0.46772:2.72645:60:4:0.0114:0:1.5 +5 53875481 . G C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.03536;LSEQ=CTAGTAAACAGGAATACAGA;RSEQ=AGAAGTACACATGTGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:343:325:149,176:7,10:17,325:0.9475:2,2:25.8:1:32:1:0.80551:1.21:60:64:0.9496:0:1.2 0/1:376:146:61,85:104,125:229,146:0.3883:2,2:25.7:1:31.4:1:0.5229:1.15889:60:292:0.3904:0:1.2 +5 53875569 . G A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.05799;LSEQ=TGGAAAGAGAAGCTCATCAA;RSEQ=GATGGGAACAAATTTTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:115:20,95:1,8:9,115:0.9274:2,2:25.9:1:31.5:1:1:1.68:60:56.5:0.9262:0:1.2 0/1:109:46:9,37:13,50:63,46:0.422:2,2:25.9:1:30.5:1:1:1.06826:60:92:0.4299:0:1.2 +5 53875603 . T A 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22018;SOR=2.28635;LSEQ=TTTAGAAGGTTCCCAAGAGG;RSEQ=TAGGCATAGCAAGGTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:6:1,5:4,71:75,6:0.0741:2,2:14.3:1:31:1:0.32637:3.46:60:12:0.075:0:1.5 0/1:45:7:1,6:5,33:38,7:0.1556:2,2:27:1:30.7:1:1:1.10:60:14:0.1591:0:1.4 +5 53875646 . A G 51 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21076;SOR=3.63026;LSEQ=AGGGTGGGGCTGGCCTTAGG;RSEQ=ATATTGCAAAGTGCATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:0,3:0,34:34,3:0.0811:1,0:41.7:1:32.3:1:1:0:60:6:0.0833:0:2 0/1:8:2:0,2:0,6:6,2:0.25:0,0:3:1:30.5:1:1:0:60:4:0.25:0:2 +5 53876988 . G T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGTTGTGCTGCACCTTT;RSEQ=AATTCTGTGACTGCAGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 54380840 . G A 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGCAAGATGGCTGTCACA;RSEQ=GACCTAGAAAGAGGAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:44,28:72,0:0:2,0:24.6:1:32.2:1:1:0:54.4:144:0.9863:0:0.2 0/1:85:19:13,6:36,29:65,19:0.2235:2,2:26.6:1:29.4:1:0.42895:1.73:48.3:38:0.2235:0:1.1 +5 54380851 . G T 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50502;SOR=Inf;LSEQ=GCTGTCACAGGACCTAGAAA;RSEQ=AGGAGAAGCCATGTCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:52,38:90,0:0:2,0:24.9:1:32.7:1:1:0:51.1:89:1:0:0.2 0/1:115:2:1,1:62,51:113,2:0.0174:2,2:5:0:29.5:1:1:1.21361:34.5:4:0.0175:0:1 +5 54380854 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19258;SOR=0;LSEQ=GTCACAGGACCTAGAAAGAG;RSEQ=AGAAGCCATGTCACCCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:52,38:90,2:0.0217:2,2:13:0:31:1:1:1.36367:26:4:0.022:0:1.5 0/0:117:0:0,0:63,54:117,0:0:2,0:26.4:1:29.6:1:1:0:49.8:22.4:1:0:0.4 +5 54579474 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48485;SOR=Inf;LSEQ=TCTCTTATTTTCAGAATGCT;RSEQ=TTGTTGCTGCTGTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:16,0:0:2,0:24:1:32.8:1:1:0:60:32:1:0:0.1 0/1:17:2:1,1:7,8:15,2:0.1176:2,2:15.5:1:30.5:1:1:1.13:60:4:0.1176:0:1 +5 54914089 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTCTAGGACAATGAGTA;RSEQ=AAGTTTACTGCATTGGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:30.5:1:1:0:60:4:1:0:1 +5 56110233 . G A 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGCACCTTCTCACGTAGA;RSEQ=TCCAGGGACTAGGAGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:32:1:1:0:60:4:1:0:1.5 +5 56111307 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49967;SOR=0;LSEQ=CTCACGCAGTTGGCGCAGGA;RSEQ=GCCTTACGCTGGCGGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:155,14:169,2:0.0117:2,2:14.5:1:29.5:1:0.16821:10.73065:60:4:0.0119:0:1 0/0:155:0:0,0:139,16:155,0:0:2,0:23.4:1:31.9:1:1:0:60:154:1:0:0.1 +5 56111314 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22977;SOR=Inf;LSEQ=AGTTGGCGCAGGAGGCCTTA;RSEQ=GCTGGCGGCGCAGTGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:176,32:208,0:0:2,0:23:1:32.3:1:1:0:60:103:1:0:0.1 0/1:192:2:1,1:160,30:190,2:0.0104:2,2:37.5:1:31:1:0.29756:5.26309:60:4:0.0105:0:1.5 +5 56111330 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.06378;SOR=Inf;LSEQ=CTTACGCTGGCGGCGCAGTG;RSEQ=CCGCCCCCTGCGCTCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:225,71:296,0:0:2,0:25.5:1:31.7:1:1:0:59.9:36:1:0:0.1 0/1:334:5:3,2:233,96:329,5:0.015:2,2:14.8:1:28:1:0.63265:1.61553:60:10:0.0152:0:1 +5 56111402 . TGGC T 108 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.07282;SOR=3.32386;LSEQ=ATGTAGCCCGCGAGAGAAAA;RSEQ=GGCGGCGGCGGGGAATCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:3:1,2:370,409:779,3:0.0038:2,2:37.3:1:31.3:1:1:1.80797:60:6:0.0039:0:0 0/1:1028:13:5,8:484,529:1013,13:0.0126:2,2:25.6:1:29.3:1:0.58414:1.46336:59.3:26:0.0128:0.0039:0.5 +5 56111508 . G A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18697;SOR=0;LSEQ=GCCCTCAAGGCGAGCAGCGC;RSEQ=CCCGCGGCTGCCGCGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:44,116:160,2:0.0123:2,2:7.5:1:29:1:0.47964:2.62:60:4:0.0126:0:1 0/0:212:0:0,0:76,136:212,0:0:2,0:19.9:1:30.7:1:1:0:60:52:1:0:0.2 +5 56111553 . C T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4059;SOR=0.46228;LSEQ=CGGGAGGCGGGCAGCGGGGG;RSEQ=CGCGAGCGGGCGGACTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:1,2:132,66:198,3:0.0149:2,2:9:1:28:1:0.26482:3.97015:60:6:0.0155:0:1 0/0:288:2:0,2:177,109:286,2:0.0069:2,0:1:0:23:1:0.14772:0:60:4:0.0071:0:1 +5 56111575 . C T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=1.18328;LSEQ=GCGAGCGGGCGGACTGGCGG;RSEQ=GGCGGCAGCTGCGCAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:4:1,3:234,125:359,4:0.011:2,2:5.5:1:28.8:1:0.12773:5.58861:60:8:0.0112:0:1.3 0/1:461:6:3,3:276,179:455,6:0.013:2,2:18.2:1:27.7:1:0.6846:1.54036:60:12:0.0133:0:1.2 +5 56111730 . G A 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70493;SOR=1.81527;LSEQ=GGCTTCCAGCCTGTGGCGGT;RSEQ=CCGCCGCCCCACGGAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:2:2,0:76,181:257,2:0.0077:2,0:1:0:26:1:0.08988:0:60:4:0.008:0:1 0/1:360:5:3,2:127,228:355,5:0.0139:2,2:18.2:1:24.8:1:0.35619:2.69:60:10:0.0142:0:1.8 +5 56111734 . C A 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.40897;SOR=3.69754;LSEQ=TCCAGCCTGTGGCGGTGCCG;RSEQ=CGCCCCACGGAGCCGCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:1:1,0:66,160:226,1:0.0044:2,0:1:0:25:0:0.29515:0:60:2:0.0046:0:1 0/1:310:5:4,1:109,196:305,5:0.0161:2,2:17.4:1:24.6:1:0.061:7.15:60:10:0.0164:0:1 +5 56111749 . G A 57 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.65382;SOR=2.44821;LSEQ=TGCCGCCGCCCCACGGAGCC;RSEQ=CGAGCCGCGGCGGCGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:1:1,0:39,98:137,1:0.0072:2,0:1:0:29:0:0.28986:0:60:2:0.0076:0:1 0/1:229:4:2,2:84,141:225,4:0.0175:2,2:26.8:1:28.8:1:0.6323:1.67:60:8:0.0183:0:2.3 +5 56111751 . G C 225 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03548;LSEQ=CCGCCGCCCCACGGAGCCGC;RSEQ=AGCCGCGGCGGCGCCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:134:132:37,95:1,1:2,132:0.9851:2,2:14.9:1:32:1:0.48827:2.54687:60:65:1:0:1.2 1/0:223:156:58,98:28,38:66,156:0.6996:2,2:21.3:1:31:1:0.5468:1.24375:60:51:0.7083:0:1.3 +5 56111758 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53025;SOR=Inf;LSEQ=CCCACGGAGCCGCGAGCCGC;RSEQ=GCGGCGCCCACCTTACCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:31,74:105,0:0:2,0:13.6:1:30.1:1:1:0:60:25.25:1:0:1.2 0/1:176:2:1,1:70,103:173,2:0.0114:2,2:9.5:1:30:1:1:1.47:60:4:0.0118:0:2.5 +5 56111761 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGGAGCCGCGAGCCGCGGC;RSEQ=GCGCCCACCTTACCGAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:24,53:77,0:0:2,0:16.5:1:30.7:1:1:0:60:76:1:0:1.2 0/1:169:2:1,1:72,95:167,2:0.0118:2,2:12.5:1:28.5:1:1:1.32:60:4:0.0123:0:3 +5 56111830 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.55199;SOR=Inf;LSEQ=GTCCCGCAGCGGCCGAGCCC;RSEQ=GGGAGAAGCGGGCGCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:22,20:42,0:0:2,0:18.7:1:31.3:1:1:0:60:84:0.9767:0:0.4 0/1:77:3:2,1:38,36:74,3:0.039:2,2:15.3:1:27.7:1:1:1.88:60:6:0.04:0:1.3 +5 56111892 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12919;SOR=0;LSEQ=GCCCCCGCCGGGTGAGCAGC;RSEQ=CGGCCGGGGTCGCGGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:13,13:26,2:0.0714:2,2:46:1:31.5:1:1:1:60:4:0.0741:0:2 0/0:49:0:0,0:27,22:49,0:0:2,0:20.9:1:29.1:1:1:0:60:98:1:0:0.6 +5 56111927 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51339;SOR=1.79885;LSEQ=GCGGGGACTTGGAGAGCGGG;RSEQ=AGAGGGCAATGAATGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:4,4:4,5:9,8:0.4706:2,2:28:1:27.9:1:1:1.23:60:7:0.4375:0:1.4 1/0:21:13:6,7:5,3:8,13:0.619:2,2:18.8:1:26.2:1:0.65944:1.88324:60:26:0.619:0:1.2 +5 56152416 . C A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.1842;LSEQ=CTCATTTTATTTGTTTCTGC;RSEQ=TGCATTTTAGTCGTGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:79:65,14:78,26:104,79:0.4293:2,2:26.7:1:30.5:1:0.28059:1.54:59.6:78:0.4333:0:1.1 1/0:211:149:107,42:45,17:62,149:0.7062:2,2:25.5:1:29.6:1:1:1.03885:60:73.5:0.7136:0:1.1 +5 56155804 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20104;SOR=0;LSEQ=TTAGCTTCATTTATAACAAA;RSEQ=AAAAGACTGGCCAGCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:26,118:144,2:0.0137:2,2:17:1:31.5:1:0.3367:4.47:60:4:0.0137:0:1 0/0:179:0:0,0:37,142:179,0:0:2,0:22:1:30.2:1:1:0:60:88.5:1:0:0.1 +5 56155870 . TG T 72 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20243;SOR=5.1742;LSEQ=GATCTGCAGACCCCTGAGGA;RSEQ=GGGGGGGTGGTTCCTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:0,1:0,40:40,1:0.0244:1,0:24:0:27:0:1:0:60:2:0.025:0:0 0/1:43:5:0,5:0,38:38,5:0.1163:1,0:24.4:1:31.4:1:1:0:60:10:0.119:0:0 +5 56160541 . T TA 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.02262;SOR=0.29187;LSEQ=GAAATGAGAAACGTACCTAA;RSEQ=AAAAAAAAATGTTGTGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:12:10,2:209,56:265,12:0.0433:2,2:26.4:1:29.7:1:1:1.34:60:24:0.0446:0.0036:0.5 0/1:384:5:4,1:274,103:377,5:0.013:2,2:20.2:1:26.7:1:1:1.50:60:10:0.0134:0.0026:0.8 +5 56161787 . G A 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04104;LSEQ=TCATCATCTAGTACTTCTAC;RSEQ=TCTAGTTCAGAAAACAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:575:573:220,353:0,1:1,573:0.9965:0,2:25.9:1:30.7:1:1:0:60:113.6:0.9982:0:1.1 1/1:739:681:264,417:26,31:57,681:0.9215:2,2:25.4:1:29.8:1:0.32518:1.32424:60:112.5:0.9221:0:1.1 +5 56161975 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77608;LSEQ=GTTCGCTGGGCATGGTGGCT;RSEQ=GTGCCTGTAATCCCAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:13:2,11:0,8:8,13:0.619:0,2:15.5:1:30.3:1:0.50476:0:58.2:26:0.619:0:1.1 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:23.6:1:30.6:1:1:0:60:10:0.5556:0:1 +5 56168571 . G A 219 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAATAATTTTGAAATGATAC;RSEQ=GATATGTTTAATTTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:134:79,55:95,88:183,134:0.4227:2,2:21.1:1:31.1:1:0.25326:1.33:60:66:0.419:0:1 0/0:459:0:0,0:257,200:457,0:0:2,0:22.6:1:29.6:1:1:0:59.8:227.5:0.9956:0:0.1 +5 56168712 . C T 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGCTGCACAGCAGCAAAC;RSEQ=GTACAGCAGCAGCCTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:606:0:0,0:296,310:606,0:0:2,0:25.9:1:30.6:1:1:0:59.9:150.5:1:0:0.1 0/1:777:61:30,31:358,357:715,61:0.0785:2,2:24:1:29.7:1:1:1.03619:60:60:0.0781:0:1.1 +5 56170813 . C G 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACTCAAAATGCTCTGGGTC;RSEQ=ATAAGCTTTTCTTTACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:0:0,0:234,108:342,0:0:2,0:25.5:1:31.4:1:1:0:60:67.4:0.997:0:0.1 0/1:397:22:15,7:250,125:375,22:0.0554:2,2:23:1:29.3:1:1:1.07:60:44:0.0567:0:1.1 +5 56171171 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17192;SOR=0;LSEQ=TTCCATAATCATATCATTAT;RSEQ=GGTTTGGGGTTTTTTGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:39,154:193,2:0.0102:2,2:23:1:29:1:0.36902:3.91:60:4:0.0103:0:1 0/0:276:0:0,0:69,207:276,0:0:2,0:24.2:1:30.1:1:1:0:60:45:1:0:0.1 +5 56171191 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51097;SOR=Inf;LSEQ=GGGTTTGGGGTTTTTTGATG;RSEQ=TTCGTAGATAGTGTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:9,124:133,0:0:2,0:23.8:1:32.2:1:1:0:60:266:1:0:0 0/1:183:2:1,1:24,156:180,2:0.0109:2,2:13.5:1:31:1:0.25651:6.39:60:4:0.0111:0:1 +5 56175226 . A G 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCGATAAGAACAGTAGTTG;RSEQ=CATTTATATCTATAAGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:11:0:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 56176306 . T C 79 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55944;SOR=0.24802;LSEQ=GTACTTGCAAAGAGCCATTG;RSEQ=TGAAAATTCTGTGCTTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:6,0:4,0:4,6:0.6:0,0:20.2:1:30.7:1:1:0:57.8:5:0.5556:0:2.2 0/1:4:1:1,0:3,0:3,1:0.25:0,0:18:0:26:0:1:0:60:2:0.25:0:1 +5 56176446 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03935;SOR=Inf;LSEQ=TCCTGAAAACATTATTTCTC;RSEQ=ACTTTTTCACAAGGCATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:90,4:94,0:0:1,0:21.1:1:31.8:1:1:0:60:188:1:0:0 0/1:77:4:4,0:63,10:73,4:0.0519:2,0:24:1:32:1:1:0:60:8:0.0526:0:1 +5 56176474 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.60158;SOR=2.27967;LSEQ=CACAAGGCATTACATTACTC;RSEQ=TCTAATATTGTATAGTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:1:0,1:134,26:160,1:0.0062:2,0:1:0:27:0:0.1677:0:60:2:0.0063:0:1 0/1:142:2:1,1:108,32:140,2:0.0141:2,2:20.5:1:28.5:1:0.41205:3.33877:60:4:0.0144:0:1 +5 56176642 . C A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08956;SOR=0;LSEQ=AAAAGCTGGTAATAACTTTT;RSEQ=ACTTAAAAGGAATATAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:2,1:89,177:266,3:0.0112:2,2:13.3:1:21:1:0.26508:3.96:60:2:0.0075:0:1.7 0/0:331:0:0,0:119,212:331,0:0:2,0:24.1:1:31:1:1:0:60:109.333:1:0:0.1 +5 56177148 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.1098;LSEQ=TGTATCTTCCTACCCTCCCT;RSEQ=CACCCTCCTCAAGAATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:110:65:18,47:10,35:45,65:0.5909:2,2:22.4:1:31.4:1:0.6569:1.34:60:20.667:0.6019:0:1.1 0/1:118:16:5,11:22,80:102,16:0.1356:2,2:25.1:1:32.3:1:0.52141:1.65:60:32:0.1368:0:1 +5 56177369 . T C 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=12.42;LSEQ=TTTTCAGTAATTGGAACTTA;RSEQ=ATGGTAATGAATGTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:2:2,0:235,66:301,2:0.0066:2,0:29.5:1:13:0:1:0:60:0:0:0:5.5 0/1:327:25:18,7:219,83:302,25:0.0765:2,2:27.6:1:32.4:1:1:1.02602:60:50:0.0774:0:1 +5 56177382 . G GT 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.04896;SOR=0;LSEQ=GAACTTATATGGTAATGAAT;RSEQ=TTTTTTTCTTTCAGGTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:4:2,2:271,96:367,4:0.0108:2,2:13.5:1:29.2:1:0.28532:2.81357:60:8:0.0109:0.0054:1 0/0:416:0:0,0:288,128:416,0:0:2,0:24:1:31.3:1:1:0:60:137.667:1:0:0.5 +5 56177443 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.36843;LSEQ=CCTTTGCTTTGCAGTCCATT;RSEQ=ATAATTCCCACTCAATGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:321:179,142:226,156:382,321:0.456:2,2:27:1:29.3:1:0.39944:1.14903:60:52.5:0.4532:0:1.1 1/0:863:574:319,255:154,133:287,574:0.6651:2,2:25.4:1:28.3:1:0.61149:1.08:60:70.75:0.662:0:1.1 +5 56177743 . G A 280 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGTTCCCCTGAGTGCACA;RSEQ=TCCATTTAGAGAAAACTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:532:532:251,281:0,0:0,532:1:0,2:25.8:1:31:1:1:0:59.9:132:1:0:1.1 1/0:627:494:251,243:69,63:132,494:0.7879:2,2:24.7:1:29.4:1:0.76983:1.06026:60:69.571:0.788:0:1.1 +5 56177848 . TCAA T 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=0;SOR=0.53036;LSEQ=TTTCAGTAGGACCTTCTAGT;RSEQ=CAACAACAACAACAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:483:352:206,146:71,32:103,352:0.7288:2,2:29.4:1:32.1:1:0.06621:1.57098:59.9:69.4:0.7305:0.0518:0.2 1/0:560:329:182,147:118,82:200,329:0.5875:2,2:29.3:1:31:1:0.41692:1.16196:59.9:81.25:0.5877:0.0321:0.2 +5 56177913 . C G 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCAAACAAAAGGCAGACC;RSEQ=CACAGTCAGTGTTTGAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:767:0:0,0:403,362:765,0:0:2,0:24.5:1:31.2:1:1:0:60:108.286:0.9974:0:0.2 0/1:1047:30:14,16:546,466:1012,30:0.0287:2,2:22.9:1:30.4:1:0.46166:1.33867:60:60:0.0292:0:1.2 +5 56178111 . A G 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCGCAAGTTTTCTCTACA;RSEQ=TTCCACAGAAACTGTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:281,246:527,0:0:2,0:24.6:1:30.8:1:1:0:60:74.286:1:0:0.1 0/1:618:43:20,23:301,273:574,43:0.0696:2,2:28.7:1:31.6:1:0.52747:1.26745:60:86:0.07:0:1 +5 56178217 . A C 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02003;LSEQ=TACACAGGCCAAAGCCATCT;RSEQ=GACCTACCCCAGGTAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:718:715:350,365:0,0:0,715:0.9958:0,2:25:1:30.7:1:1:0:59.9:78.444:0.9958:0:1.1 1/1:853:705:360,345:72,75:147,705:0.8265:2,2:25:1:29.7:1:0.6515:1.09:60:87.125:0.8268:0:1.1 +5 56179212 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02233;SOR=0;LSEQ=ATTACTTTTGCATTTGCTGT;RSEQ=GGTCACAAATACCTTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:42:41,1:0,0:0,42:1:0,1:25:1:31.1:1:1:0:60:41:1:0:1.1 1/1:28:24:23,1:4,0:4,24:0.8571:0,1:23.7:1:30.5:1:1:0:60:48:0.8571:0:1 +5 56179341 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.18721;LSEQ=ACAGTAAAAAGATTGCTTTC;RSEQ=TTTAATATGTAGACACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:157:116,41:124,55:179,157:0.4673:2,2:24.2:1:30.5:1:0.39731:1.25:60:314:0.4701:0:1.1 0/1:405:57:40,17:234,114:348,57:0.1407:2,2:24.1:1:29.2:1:0.76054:1.15:60:56:0.1404:0:1.1 +5 56179573 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49968;SOR=Inf;LSEQ=TGAAGCATGTTCAGTAAAAA;RSEQ=AATAAAGGATATGTCCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:3,86:89,0:0:1,0:23.1:1:32.7:1:1:0:60:88:0.9888:0:0 0/1:103:2:0,2:6,95:101,2:0.0194:2,0:14:1:26.5:1:1:0:60:4:0.0194:0:2 +5 56180112 . T G 41 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTTTCAACAGTGTACTTG;RSEQ=GCGGTGCCATCTTGGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:22.7:1:26.3:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 56180419 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24717;SOR=Inf;LSEQ=TGCTAATAAAGTGCTAGTTT;RSEQ=CATTTGTTCATTTTAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:104,28:132,0:0:2,0:21.9:1:32:1:1:0:60:65:1:0:0.4 0/1:133:3:1,2:104,26:130,3:0.0226:2,2:14:1:24:1:0.11209:7.82851:60:6:0.0226:0:1.3 +5 56180420 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49817;SOR=Inf;LSEQ=GCTAATAAAGTGCTAGTTTG;RSEQ=ATTTGTTCATTTTAGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:107,29:136,0:0:2,0:21.7:1:32:1:1:0:60:67:1:0:0.4 0/1:137:2:2,0:106,29:135,2:0.0146:2,0:25:1:31.5:1:1:0:60:4:0.0146:0:1 +5 56180480 . A G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14326;LSEQ=AAAACTTTGTGAACGTGTTT;RSEQ=TTTGAAACAGGTGACTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:276:158:103,55:78,39:117,158:0.5725:2,2:26.5:1:32.4:1:0.89775:1.06767:60:78:0.5714:0:1 0/1:349:56:41,15:179,114:293,56:0.1605:2,2:23.3:1:31.1:1:0.09724:1.74:60:55:0.1585:0:1.1 +5 56180691 . G A 33 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11474;SOR=0;LSEQ=ATTACAAAATAGTAGTACGT;RSEQ=GATTTAACTTTCTGCAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:2,1:38,150:188,3:0.0157:2,2:6.7:1:21.3:1:0.11168:7.78:60:2:0.0107:0:1 0/0:201:0:0,0:58,143:201,0:0:2,0:22.4:1:30.5:1:1:0:60:32.5:1:0:0.1 +5 56181215 . GTTC G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTTCTCTTTACCAGTCA;RSEQ=TTAAGTATGTTATCTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:20.5:1:34:0:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 56181982 . GT AC 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17208;SOR=Inf;LSEQ=GGCTCACACCTGTAATCCCA;RSEQ=ACTTTGGGAGGTGAAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:0,67:67,0:0:1,0:22.8:1:32.3:1:1:0:59.4:66:1:0:0.1 0/1:48:2:0,2:0,46:46,2:0.0417:1,0:15:1:32.3:1:1:0:45:4:0.0417:0:2.5 +5 56182589 . C T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTAGGTCCCATTATTTT;RSEQ=CTTATCCTTTTCTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:27:0:32:0:1:0:60:2:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:23:1:29.5:1:1:0:60:4:1:0:1 +5 56183542 . C T 103 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03612;SOR=0;LSEQ=CCTTGGCAATATTCAAAAAA;RSEQ=AGGTTTTAATAGATTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:0,12:1:0,0:20.4:1:28.8:1:1:0:60:24:1:0:1.1 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:12:1:29:1:1:0:60:8:0.5714:0:1 +5 56183637 . G C 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAACTCAAAGTGCACATAA;RSEQ=AAATTTTTAAAAATATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:16.8:1:32.6:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 56183743 . T G 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16667;SOR=0;LSEQ=ATTGTTCTTCTGACTCAGCT;RSEQ=CTTCTGTCGTGTTCATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:21.6:1:32.6:1:1:1.41418:52.2:10:0.7143:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:27:1:1:0:60:4:1:0:0 +5 56183941 . C G 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=0;LSEQ=ATTAGGTAGTCCACAGAATT;RSEQ=CTGTTTGTACCAGTTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:65:63,2:0,0:0,65:1:0,1:23:1:32.2:1:1:0:59.3:20.667:1:0:1.1 1/1:45:36:36,0:9,0:9,36:0.8:0,1:22.1:1:32.7:1:1:0:60:72:0.8:0:1 +5 56184247 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.78656;LSEQ=ACAGCAGAATTTGGCAGGAG;RSEQ=CAAATTTTGATGGGTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:1:0,1:14,114:128,1:0.0078:2,0:21:0:32:0:1:0:60:2:0.0078:0:2 0/1:145:2:0,2:15,128:143,2:0.0138:2,0:42.5:1:29.5:1:1:0:60:4:0.0139:0:1.5 +5 56184444 . T C 94 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGATACACTGGTGATGC;RSEQ=AGGCAGTGGCAGCGAGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:26.3:1:31.6:1:1:0:56.6:7:1:0:1.1 1/1:1:1:1,0:0,0:0,1:1:0,0:12:0:32:0:1:0:60:2:1:0:1 +5 56184610 . C T 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTAAGCTATAATGTTTGG;RSEQ=AGGTTAGGTGTATTAACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:35.6:1:28.4:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 56188977 . G A 58 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTAATCTAAATAGCTCT;RSEQ=TATGCTGAAGAAATAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:28.3:1:29.3:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 56189554 . G GAA 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.12265;SOR=Inf;LSEQ=AAACAGGATGCTCAACAAGA;RSEQ=AAAAAAAACTTGTGGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:23,136:159,0:0:2,0:24.2:1:32:1:1:0:59.9:30.8:0.9935:0:0.2 0/1:160:4:2,2:28,128:156,4:0.025:2,2:18.5:1:28.5:1:0.15983:4.51:60:8:0.0256:0.0125:0.5 +5 56525768 . G GCGTCC 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=31;MSI=7.000;MSILEN=5;SSF=0.21644;SOR=0.37335;LSEQ=CCATCCCGTTGCATCGCATC;RSEQ=CGTCCCGTCCCGTCCCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:4,3:7,4:0.3636:2,2:38.5:1:30.6:1:1:1.29868:60:8:0.3636:0:0 0/1:52:9:5,4:26,17:43,9:0.1731:2,2:21.9:1:30.1:1:1:1.21872:51.4:18:0.1837:0.0769:0.6 +5 56527347 . A G 33 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACCTCAGGTGATCCACCT;RSEQ=CCTCAGCCTCCCAAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:33:0:1:0:60:4:1:0:1 +5 57750267 . A C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04;SOR=0;LSEQ=CTTAGCCTGTTCTGGTTCCA;RSEQ=CCAGTCCAGCAGGCCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:76:74,2:0,0:0,76:1:0,1:24.7:1:32.7:1:1:0:59.7:75:1:0:1.3 1/1:63:59:59,0:4,0:4,59:0.9365:0,1:23.5:1:31.9:1:1:0:60:118:0.9365:0:1.1 +5 57750305 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23391;SOR=Inf;LSEQ=AGGGGAATTGTTTTCGTACC;RSEQ=CCACATGTCCATCTTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:146,4:150,0:0:1,0:21.7:1:30.7:1:1:0:59.9:149:1:0:0.8 0/1:141:2:1,1:134,5:139,2:0.0142:1,2:24.5:1:26.5:1:0.08359:24.55647:60:4:0.0145:0:1.5 +5 57750350 . C G 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3343;LSEQ=ACTCTAGATCATTCTTTTGG;RSEQ=TTCCCTGTAGATCTCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:366:188:139,49:129,48:177,188:0.5137:2,2:22.9:1:31.6:1:0.90568:1.06:60:93:0.5152:0:1.1 0/1:399:104:72,32:197,98:295,104:0.2607:2,2:24.8:1:30.9:1:0.71553:1.12:60:103:0.2608:0:1 +5 57751274 . G GA 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.65026;SOR=0.74322;LSEQ=GAACGAAAGGGAGAGAAGAG;RSEQ=AAAAAAAAATAGAAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:11:7,4:126,158:284,11:0.037:2,2:30.7:1:30.9:1:0.2317:2.19:60:22:0.0378:0:0.1 0/1:324:9:4,5:124,191:315,9:0.0278:2,2:16.9:1:29.9:1:0.7433:1.23:60:18:0.0288:0.0062:0.1 +5 57751443 . A G 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTCTGAGAGCTGGTACCC;RSEQ=AAGCCATATTTGTTAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:990:0:0,0:536,454:990,0:0:2,0:24.1:1:30.6:1:1:0:59.9:81.5:1:0:0.1 0/1:996:97:50,47:470,427:897,97:0.0974:2,2:24.3:1:29.3:1:0.91496:1.03464:60:47.5:0.0966:0:1.2 +5 57751651 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20797;SOR=Inf;LSEQ=CAAGTTATACAATATTTTAG;RSEQ=AATAAAACCTCAGGCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:44,188:232,0:0:2,0:23.9:1:32.4:1:1:0:59.9:115:1:0:0.1 0/1:195:2:1,1:37,156:193,2:0.0103:2,2:9:0:30:1:0.35258:4.17:60:4:0.0104:0:1.5 +5 57751836 . G A 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00021;SOR=Inf;LSEQ=AGTTTCATTATTTAAAATAC;RSEQ=ATTGACAACCACTTACATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:598:0:0,0:436,162:598,0:0:2,0:22.8:1:30.5:1:1:0:60:148.5:1:0:0.1 0/1:589:12:10,2:413,164:577,12:0.0204:2,2:19.1:1:30.5:1:0.5243:1.98:60:24:0.0206:0:1.2 +5 57752252 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20553;SOR=Inf;LSEQ=CCATGATAATCATAGTCCAA;RSEQ=TGCTAATTAATAAAGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:173,35:208,0:0:2,0:24.2:1:33:1:1:0:60:68.333:1:0:0.1 0/1:173:2:1,1:150,21:171,2:0.0116:2,2:21.5:1:28.5:1:0.23881:7.00185:60:4:0.0118:0:1.5 +5 57752504 . T C 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=ATTTTCTCCTTCTTGCATTA;RSEQ=TGACCAACTTATGAGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:14,69:83,0:0:2,0:25:1:30.3:1:1:0:60:40.5:1:0:0.2 0/1:44:8:1,7:3,33:36,8:0.1818:2,2:24.4:1:31.9:1:0.56608:1.55:60:16:0.1818:0:1.8 +5 57752526 . G A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00158;SOR=Inf;LSEQ=GACCAACTTATGAGCATCCT;RSEQ=GGCAAAAATAGCATTTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:13,49:62,0:0:2,0:20.3:1:31.5:1:1:0:60:30:1:0:0.2 0/1:26:5:2,3:1,20:21,5:0.1923:1,2:17.6:1:28.6:1:0.08462:11.33:60:10:0.2083:0:2.4 +5 57752563 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09504;SOR=Inf;LSEQ=TACCTTTGCCTTTAGCTGCA;RSEQ=CTACCCCCAAAAGCCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:17,20:37,0:0:2,0:28.9:1:32.5:1:1:0:60:17.5:1:0:0.4 0/1:17:2:1,1:6,9:15,2:0.1176:2,2:22.5:1:32:0:1:1.46:60:4:0.1176:0:2.5 +5 57752593 . C G 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56222;SOR=0.60748;LSEQ=AAAGCCCTCTTTAGTGTTTG;RSEQ=AAAATAAAAAGCTATCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:14:9,5:15,12:27,14:0.3415:2,2:26.6:1:28.8:1:0.74171:1.43:60:13:0.325:0:1 0/1:21:5:4,1:13,3:16,5:0.2381:2,2:29.2:1:30.6:1:1:1.07915:60:10:0.2381:0:1.2 +5 57752811 . CA C 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00893;SOR=0;LSEQ=TGCTTTGTCTTTTTTGCCAC;RSEQ=AAAAGAGCAGCAGCTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:6:3,3:219,209:428,6:0.0138:2,2:30.8:1:31.7:1:1:1.04775:60:12:0.014:0:0.2 0/0:517:0:0,0:248,269:517,0:0:2,0:25.6:1:29.6:1:1:0:60:128.25:1:0:0.1 +5 57752965 . G A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=AGTAACCTGTCAGGTAACTG;RSEQ=GATCAATACCAGGTAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:267,165:432,0:0:2,0:22.6:1:31.4:1:1:0:59.8:60.714:1:0:0.1 0/1:394:14:8,6:234,146:380,14:0.0355:2,2:16.1:1:26.9:1:0.78357:1.20147:60:6:0.0316:0:1.1 +5 57752983 . TA T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.89172;SOR=1.04231;LSEQ=TGGGATCAATACCAGGTAAT;RSEQ=AAAAAAAAAGATAGTGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:545:28:17,11:329,188:517,28:0.0514:2,2:26.2:1:31.3:1:0.84075:1.13209:60:56:0.0517:0.0073:0.1 0/1:524:28:16,12:296,193:489,28:0.0534:2,2:29:1:30.5:1:0.84292:1.14994:60:56:0.0549:0.0019:0.1 +5 57753011 . C CA 105 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03026;SOR=0.25479;LSEQ=AAAGATAGTGCACCAACCTG;RSEQ=AAAAAAAAGTCATGTCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:11:7,4:428,284:712,11:0.0151:2,2:23.6:1:30.5:1:1:1.16:59.5:22:0.0157:0.0027:0.2 0/0:771:3:0,3:432,332:764,3:0.0039:2,0:31.3:1:30.7:1:0.0829:0:60:6:0.0041:0:0 +5 57753116 . C T 190 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=90.23059;LSEQ=GCAGGAGCCAGCAATGAGGA;RSEQ=GGCATTGTATACCTTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:725:1:0,1:302,421:723,1:0.0014:2,0:29:0:33:0:1:0:60:2:0.0014:0:1 0/1:802:89:36,53:320,392:712,89:0.111:2,2:23.3:1:29.4:1:0.43123:1.20154:60:43.5:0.1093:0:1.8 +5 57753149 . A G 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGCTTCCCTTATGCACCT;RSEQ=TAAGTTTCTTTGAGATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:657:0:0,0:276,381:657,0:0:2,0:25.4:1:30:1:1:0:60:130.4:1:0:0.1 0/1:675:74:31,43:248,353:601,74:0.1096:2,2:25.3:1:31.2:1:1:1.03:60:73:0.1103:0:1.9 +5 57753251 . T A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAATGGTCATAAAGCAAC;RSEQ=CTTTTCAAGTGTTAAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:144,177:321,0:0:2,0:23.5:1:30.8:1:1:0:59.9:44.857:1:0:0.1 0/1:303:21:8,13:155,127:282,21:0.0693:2,2:21.6:1:29.7:1:0.17384:1.97882:60:42:0.07:0:1.1 +5 57753413 . G A 69 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06975;SOR=6.7774;LSEQ=GGGGTACCACATATCGTTCT;RSEQ=GAAAGACAAAATATTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:1:0,1:206,304:510,1:0.002:2,0:10:0:30:0:1:0:56:2:0.002:0:6 0/1:533:7:4,3:220,304:524,7:0.0131:2,2:14.7:1:24.9:1:0.46247:1.84:60:6:0.0115:0:1.3 +5 57753437 . G A 132 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=12.57781;LSEQ=AGACAAAATATTGAGATCGT;RSEQ=TTAGGAACTATTCCACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:2:1,1:133,260:393,2:0.0051:2,2:6:0:22:1:1:1.95:60:1:0.0026:0:2 0/1:398:24:7,17:130,244:374,24:0.0603:2,2:22:1:29:1:0.66229:1.29311:60:23:0.0587:0:1.8 +5 57753456 . C T 248 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00321;LSEQ=TGTTAGGAACTATTCCACTA;RSEQ=TTAAACTTGGTTCTCTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:286:285:78,207:1,0:1,285:0.9965:0,2:24.5:1:30.5:1:0.27622:0:59.9:94:1:0:1.1 0/1:284:135:39,96:37,112:149,135:0.4754:2,2:22.6:1:29.5:1:0.50259:1.23:60:44:0.4731:0:1.2 +5 57753937 . C T 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGTTCCAAGGGTTCTAG;RSEQ=CTGGCTGCCAGACCGAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:760:0:0,0:368,391:759,0:0:2,0:26.2:1:31.6:1:1:0:59.9:93.875:0.9987:0:0.4 0/1:838:55:29,26:360,421:781,55:0.0656:2,2:27.7:1:28.3:1:0.40171:1.30:60:54:0.0653:0:1.4 +5 57754004 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=1.8426;LSEQ=TAATAAAAAAGTTCCCTAGA;RSEQ=GATAAACAAAACAAAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:182:60,122:77,150:227,182:0.4439:2,2:22.7:1:30.6:1:0.91609:1.04369:60:181:0.4469:0:1.1 1/0:440:262:87,175:62,114:176,262:0.5955:2,2:26.1:1:29.6:1:0.68158:1.09374:60:51.4:0.5922:0:1.4 +5 57754005 . G A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24224;LSEQ=AATAAAAAAGTTCCCTAGAC;RSEQ=ATAAACAAAACAAAATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:401:225:75,150:58,118:176,225:0.5611:2,2:24.9:1:30.5:1:1:1.02:60:36.5:0.5601:0:1.1 0/1:432:102:30,72:114,216:330,102:0.2361:2,2:25:1:30:1:0.40035:1.26599:60:204:0.2378:0:1 +5 57754007 . T G 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAAAAAAGTTCCCTAGACGA;RSEQ=AAACAAAACAAAATGTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:130,258:388,0:0:2,0:24.3:1:29:1:1:0:60:54.429:1:0:1.1 0/1:414:34:11,23:126,254:380,34:0.0821:2,2:25.4:1:30.1:1:1:1.03713:60:16:0.0779:0:2.6 +5 57754040 . G A 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTGAATCCCTTTGAAAAT;RSEQ=CGTTCTAACCAAGTACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:59,176:235,0:0:2,0:23.9:1:32.1:1:1:0:60:116.5:1:0:0.9 0/1:226:19:3,16:62,145:207,19:0.0841:2,2:20.8:1:29.4:1:0.28935:2.27345:60:38:0.0844:0:2.8 +5 57754132 . G C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAAAGCAAGATTGCAGACAC;RSEQ=AGATCCCAATTAAGAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:157:157:91,66:0,0:0,157:1:0,2:22.4:1:31.9:1:1:0:59.9:38.25:1:0:1.1 1/1:115:97:65,32:11,6:17,97:0.8435:2,2:20.7:1:30.5:1:1:1.11:60:96:0.8421:0:1 +5 57754159 . T TA 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.60762;SOR=0.73128;LSEQ=CAATTAAGAACATTAATATG;RSEQ=AAAAAAAAACAGAGAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:9:4,5:134,60:194,9:0.0443:2,2:21.4:1:28.7:1:0.14877:2.77597:60:18:0.0457:0.0099:0.6 0/1:183:6:3,3:136,41:177,6:0.0328:2,2:32:1:29.7:1:0.1512:3.29017:60:12:0.0331:0:0.7 +5 57754461 . C T 45 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.26123;SOR=0;LSEQ=TTAACTTTGCAGTGTAAGTG;RSEQ=TGCCACAGCTAAAATCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:3:2,1:163,75:238,3:0.0124:2,2:6.7:1:28.7:1:1:1.08628:60:6:0.0127:0:1 0/0:185:0:0,0:122,63:185,0:0:2,0:23.2:1:31.8:1:1:0:60:370:1:0:0.1 +5 57754489 . ACT A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05166;LSEQ=GCTAAAATCCCAGATAAAAT;RSEQ=CTTTGAATACCATGTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:145:108,37:127,67:194,145:0.4277:2,2:24.4:1:32.6:1:0.09539:1.54:59.6:290:0.4328:0.0619:0.1 0/1:324:12:7,5:205,107:312,12:0.037:2,2:20.2:1:29.6:1:0.75812:1.36706:59.6:24:0.0372:0.0123:0.3 +5 57754808 . G A 280 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00446;LSEQ=ACTTTACTCAAGAGTCATAC;RSEQ=CACCTTTTCCCTTTGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:621:618:361,257:0,0:0,618:0.9952:0,2:25:1:30.3:1:1:0:60:122.6:0.9951:0:1.4 0/1:768:367:206,161:215,184:399,367:0.4779:2,2:23.6:1:29:1:0.56113:1.09:60:90.75:0.4783:0:1.4 +5 57754851 . A G 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21663;LSEQ=TTAGCTACTCTGCTGTGAGG;RSEQ=ATAATTTTTGCGGCGTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:756:318:161,157:226,210:436,318:0.4206:2,2:26.3:1:31.7:1:0.76815:1.04942:59.8:62.6:0.4201:0:1.7 0/1:950:129:63,66:411,407:818,129:0.1358:2,2:27.6:1:30.5:1:0.77708:1.05788:60:128:0.136:0:1.8 +5 57754972 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23145;SOR=Inf;LSEQ=GATGGCACAAAAATGGACGG;RSEQ=AGATATTTTAAATAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:26,173:199,0:0:2,0:23.9:1:32:1:1:0:60:23.875:1:0:0.2 0/1:185:2:1,1:35,148:183,2:0.0108:2,2:10:1:29.5:1:0.35217:4.18:60:4:0.0116:0:1 +5 57755703 . C T 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31857;LSEQ=GGCCGCTTCTTCTTCGAGTC;RSEQ=GCTCCGCAACCCTTGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:735:375:184,191:165,194:359,375:0.5102:2,2:24.8:1:31.2:1:0.41659:1.13:60:124:0.5117:0:1.1 0/1:747:186:90,96:263,297:560,186:0.249:2,2:25.9:1:29.7:1:0.79935:1.06:60:92:0.2497:0:1.2 +5 57755774 . G A 68 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50663;SOR=1.94315;LSEQ=TGGCTGGTAGGTGATAGTCC;RSEQ=CAAAAGCTCCATGGTCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:3:2,1:229,329:558,3:0.0053:2,2:8:1:21.3:1:0.57157:2.87:60:2:0.0037:0:2 0/1:580:6:4,2:260,313:573,6:0.0103:2,2:17.3:1:26.5:1:0.41914:2.40:60:5:0.0087:0:1.5 +5 57755827 . G C 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00189;SOR=Inf;LSEQ=CTGCCCGCTGCCACCCCCTA;RSEQ=GCGCGGTCACACGTCCGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:91,207:298,0:0:2,0:26.4:1:31:1:1:0:60:26.091:1:0:0.1 0/1:318:10:1,9:110,198:308,10:0.0314:2,2:22.9:1:30.3:1:0.17383:4.98168:60:20:0.0323:0:1 +5 57755840 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11795;SOR=Inf;LSEQ=CCCCCTAGGCGCGGTCACAC;RSEQ=TCCGAGCCGGCCGTGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:70,195:265,0:0:2,0:23.1:1:31.2:1:1:0:60:65.25:1:0:0.1 0/1:257:3:2,1:74,180:254,3:0.0117:2,2:8.3:1:27.3:1:0.20963:4.83:60:6:0.012:0:1.7 +5 57755843 . C T 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTAGGCGCGGTCACACGTC;RSEQ=GAGCCGGCCGTGGTCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:68,190:258,0:0:2,0:22.3:1:29.9:1:1:0:60:128:0.9961:0:0.1 0/1:241:67:17,50:50,124:174,67:0.278:2,2:22.9:1:28.6:1:0.63417:1.18512:60:21.333:0.2723:0:1.2 +5 57755865 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21268;SOR=Inf;LSEQ=AGCCGGCCGTGGTCCTCGCA;RSEQ=CCTTGCCTCTGGTGCCGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:30,140:170,0:0:2,0:22.5:1:30.6:1:1:0:60:23.286:1:0:0.1 0/1:146:2:1,1:19,125:144,2:0.0137:2,2:25:0:31:0:0.25602:6.44:60:4:0.014:0:1 +5 57755901 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50456;SOR=0;LSEQ=CGACTAGCACCCAACACCCC;RSEQ=GTCCACTTGTGCGAGTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:0,2:0,89:89,2:0.022:1,0:42.5:1:30:0:1:0:60:4:0.022:0:1 0/0:71:0:0,0:1,70:71,0:0:1,0:22.1:1:30.9:1:1:0:60:70:1:0:0.6 +5 57755923 . C T 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00253;SOR=Inf;LSEQ=TCCACTTGTGCGAGTGAGAG;RSEQ=GCTCGGCGAAGTCTTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:0,64:64,0:0:1,0:22.7:1:30.4:1:1:0:60:63:1:0:0.2 0/1:40:6:0,6:0,34:34,6:0.15:1,0:20.5:1:31:1:1:0:60:12:0.1538:0:1.2 +5 57755936 . C T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00215;SOR=Inf;LSEQ=GTGAGAGCGCTCGGCGAAGT;RSEQ=TTATATACGGGGAGGCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:0,53:53,0:0:1,0:19.8:1:33.6:1:1:0:60:106:1:0:0.2 0/1:24:5:0,5:0,19:19,5:0.2083:1,0:10.6:1:31:1:1:0:60:10:0.2083:0:1.2 +5 57755944 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=GCTCGGCGAAGTCTTATATA;RSEQ=GGGGAGGCGGGAAGGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,38:38,0:0:1,0:23.1:1:30.1:1:1:0:60:76:0.9744:0:0.3 0/1:16:2:0,2:0,14:14,2:0.125:1,0:27:1:29.5:1:1:0:60:4:0.125:0:1.5 +5 57755983 . T C 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31078;SOR=5.28626;LSEQ=CGGAGACTCGATACGCGACA;RSEQ=CACGTCACGGCCTATGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:10,7:0.4118:0,0:26.6:1:33:1:1:0:60:14:0.4118:0:1.1 1/1:5:4:0,4:0,1:1,4:0.8:0,0:20:1:30.5:1:1:0:60:8:0.8:0:1.5 +5 57756109 . T G 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAAACGCCGGCCGCCGAGA;RSEQ=CTCTTGCGGCCGCGGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:18:1:32:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 58088168 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67163;SOR=0.64288;LSEQ=AACAATAACAGCCCTATGGC;RSEQ=ATGGGGGCAAAACCTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:21:21,0:4,0:4,21:0.84:0,1:23.5:1:32.4:1:1:0:60:42:0.875:0:1 1/0:13:10:9,1:3,0:3,10:0.7692:0,2:19.5:1:31.2:1:1:0:60:20:0.7692:0:1 +5 58088265 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26247;SOR=Inf;LSEQ=TGAAGAAGGAACCAAGTGCA;RSEQ=GGAAAAAAGCAAGAAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:136,49:185,0:0:2,0:24.4:1:31.4:1:1:0:60:91.5:1:0:0.3 0/1:244:3:1,2:159,82:241,3:0.0123:2,2:10.3:1:30:1:0.27308:3.85486:60:6:0.0125:0:1 +5 58088276 . A G 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.25724;SOR=Inf;LSEQ=CCAAGTGCACGGAAAAAAGC;RSEQ=AGAAATTTTACAAAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:159,78:237,0:0:2,0:22.9:1:30.2:1:1:0:60:38.5:1:0:0.4 0/1:294:3:2,1:180,111:291,3:0.0102:2,2:22.7:1:23.3:1:1:1.23:60:2:0.0069:0:1 +5 58088350 . G C 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01718;SOR=0.64653;LSEQ=GATGCAAATGCAAGGGACTA;RSEQ=TACAGTGCAGTGGAAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:362:302:139,163:28,32:60,302:0.8343:2,2:25.6:1:32.6:1:1:1.02601:60:150:0.8333:0:1.1 1/0:438:335:156,179:44,57:101,335:0.7648:2,2:24.8:1:31.3:1:0.6491:1.13:60:334:0.7696:0:1.1 +5 58088388 . G A 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35587;SOR=0.30741;LSEQ=TAGAGCCAGAGGCGGAAGCT;RSEQ=TGAACCACACATGGAAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:2,1:105,173:278,3:0.0107:2,2:12:1:29:1:0.55982:3.28:60:6:0.0109:0:1.7 0/0:303:1:1,0:120,182:302,1:0.0033:2,0:1:0:21:0:0.39934:0:60:2:0.0033:0:2 +5 58088425 . G A 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.02933;LSEQ=ACATTGATTTTGGTGAGGGA;RSEQ=GGGGGAGATGAAGGGGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:45,130:175,2:0.0113:2,2:18:1:21.5:1:0.45333:2.87:60:1:0.0057:0:2.5 0/1:172:2:1,1:52,118:170,2:0.0116:2,2:46:0:31:1:0.52258:2.26:60:4:0.0118:0:1.5 +5 58088523 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32538;SOR=0.47575;LSEQ=TAGATGGCCAAGCTATTTTC;RSEQ=TTAATAATTGTGATGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:22:0,22:0,8:8,22:0.7333:0,1:28.9:1:31.6:1:1:0:60:21:0.7241:0:1 1/0:16:9:0,9:0,7:7,9:0.5625:0,0:23.2:1:31.7:1:1:0:60:18:0.5625:0:1 +5 58205384 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=ATTCATTATCATCATTTCAT;RSEQ=AATAAAAGCCATTTGAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:18,0:18,2:0.1:1,0:11.5:1:26:1:1:0:60:4:0.1:0:1 0/0:20:0:0,0:19,1:20,0:0:1,0:22:1:32.5:1:1:0:60:40:1:0:0 +5 58205481 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4978;SOR=0;LSEQ=GGATTTAGTTTTAGAAAAAA;RSEQ=TCACCACATTTGCTTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:76,36:112,2:0.0175:2,2:17:1:29.5:1:0.54572:2.09609:60:4:0.0177:0:1 0/0:114:0:0,0:80,34:114,0:0:2,0:23.9:1:31.5:1:1:0:60:228:1:0:0.1 +5 58205509 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21426;SOR=0;LSEQ=ATTTGCTTACATTTTCATTT;RSEQ=ACCTCACATCAGCACTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:107,63:170,2:0.0116:2,2:34:1:31.5:1:1:1.69287:60:4:0.0116:0:1 0/0:199:0:0,0:115,84:199,0:0:2,0:23.2:1:28.5:1:1:0:60:198:1:0:0.3 +5 58205580 . T C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=10.61564;LSEQ=GCCCGTTTAAGCTCACGCCT;RSEQ=CTGTCATTCTCATACAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:18:8,10:82,99:181,18:0.0905:2,2:24.1:1:31.7:1:1:1.03518:60:36:0.0928:0:1.1 1/0:270:139:61,78:63,68:131,139:0.5148:2,2:26.9:1:30.7:1:0.54168:1.18392:60:68.5:0.5112:0:1.1 +5 58205668 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49803;SOR=Inf;LSEQ=AACTACCTGTCCCAAATAAA;RSEQ=GACATCCAAAGGTCATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:6,53:59,0:0:2,0:24.4:1:31.6:1:1:0:60:28.5:1:0:0 0/1:67:2:1,1:15,50:65,2:0.0299:2,2:6.5:1:27:1:0.42334:3.26:60:4:0.0303:0:3 +5 58988107 . CT C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.17516;SOR=Inf;LSEQ=GGGAGGGTCTTAAGGATCCG;RSEQ=TTTTATTGTTGTATTCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:67,24:91,0:0:2,0:23:1:31.5:1:1:0:59.5:182:1:0:0.1 0/1:66:2:1,1:47,17:64,2:0.0303:2,2:22.5:1:31:1:0.47413:2.71525:60:4:0.0303:0:0 +5 58988151 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50079;SOR=0;LSEQ=CATGTAATTTGTGCTGCTTG;RSEQ=CTTGGTTTGACCATGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:89,58:147,2:0.0134:2,2:15:1:28:1:1:1.5299:60:4:0.0134:0:1 0/0:129:0:0,0:77,52:129,0:0:2,0:24.1:1:31.2:1:1:0:59.7:258:1:0:0.1 +5 58988192 . G T 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.6987;SOR=0.81387;LSEQ=ATAGCAAAGCAGAATTCCAA;RSEQ=GGGATTGGGTGAAAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:17:5,12:77,97:174,17:0.089:2,2:6.1:1:28.1:1:0.30812:1.89907:31.6:34:0.0904:0:3 0/1:163:12:5,7:78,73:151,12:0.0736:2,2:5:1:29:1:0.56038:1.4922:34.9:24:0.0736:0:3.4 +5 58988200 . G C 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00401;SOR=Inf;LSEQ=GCAGAATTCCAAGGGGATTG;RSEQ=GTGAAAGAAGAACTCTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:81,123:204,0:0:2,0:24.7:1:30.8:1:1:0:55.7:67:1:0:0.5 0/1:173:7:1,6:77,89:166,7:0.0405:2,2:8.4:1:29.9:1:0.13011:5.15161:36.6:14:0.0407:0:3.7 +5 58988214 . T C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.90519;SOR=1.02976;LSEQ=GGATTGGGTGAAAGAAGAAC;RSEQ=CTTAAGTTATGGCTGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:48:8,40:55,89:144,48:0.2487:2,2:19.2:1:29.9:1:0.00731:3.07379:39.4:96:0.2526:0:2.4 0/1:177:45:13,32:63,69:132,45:0.2542:2,2:17.1:1:30.4:1:0.03598:2.23749:41.2:90:0.2542:0:2.5 +5 58988216 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.81291;SOR=1.06965;LSEQ=ATTGGGTGAAAGAAGAACTC;RSEQ=TAAGTTATGGCTGGTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:49:8,41:56,89:145,49:0.2526:2,2:20.8:1:31.6:1:0.00463:3.20728:39.3:98:0.2565:0:2.3 0/1:177:47:13,34:61,69:130,47:0.2655:2,2:18.3:1:31.3:1:0.02518:2.30153:40.9:94:0.2655:0:2.4 +5 58988230 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=GAACTCTTAAGTTATGGCTG;RSEQ=TTTTCCCAGAACCAGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:53,133:186,2:0.0106:2,2:34:1:29:1:0.49306:2.50:60:4:0.0108:0:1 0/0:174:0:0,0:61,113:174,0:0:2,0:25.5:1:31.3:1:1:0:50.5:348:1:0:0.7 +5 58988237 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.22629;SOR=Inf;LSEQ=TAAGTTATGGCTGGTTTTCC;RSEQ=AGAACCAGTTTCTTAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:48,130:178,0:0:2,0:28.7:1:32.2:1:1:0:51.4:177:1:0:0.8 0/1:162:2:1,1:51,109:160,2:0.0123:2,2:37.5:1:30:1:0.5403:2.13:60:4:0.0123:0:1 +5 58988316 . A C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.74491;SOR=0.76673;LSEQ=AGTAATCTCTTTAAGAGTAA;RSEQ=CCCCATCACCTCATATTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:0,7:0,16:16,7:0.3043:1,0:3.4:1:32.4:1:1:0:30.3:14:0.3182:0:1.1 0/1:20:5:0,5:1,14:15,5:0.25:1,0:5.4:1:31.2:1:1:0:25.8:10:0.25:0:1.2 +5 59017895 . A G 160 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CTTACTCCCTTTTGGATAAC;RSEQ=AAACAGCAGAAGACACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:38:33,5:0,0:0,38:1:0,2:17.7:1:30.6:1:1:0:60:37:1:0:1.1 1/0:32:19:15,4:12,1:13,19:0.5938:1,2:19.8:1:29.4:1:0.62467:3.09787:60:38:0.5938:0:1 +5 59018033 . A G 243 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAATAAGGCAAGAAAGCAC;RSEQ=ACTTTAGGACAATGCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:230:230:122,108:0,0:0,230:1:0,2:26.1:1:31:1:1:0:60:114:1:0:1.7 1/0:329:219:121,98:58,52:110,219:0.6657:2,2:24.8:1:29.9:1:0.7251:1.11:59.9:438:0.6677:0:1.5 +5 59018067 . C G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04215;LSEQ=GCCAAAAATGGCCTTCGTTT;RSEQ=TCGTCTTTTGACATAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:203:190:79,111:6,7:13,190:0.936:2,2:27.5:1:31.9:1:0.77748:1.20322:60:46.5:0.9347:0:1.9 0/1:282:107:50,57:75,98:173,107:0.3794:2,2:25:1:30.7:1:0.62154:1.15:59.7:106:0.3772:0:1.9 +5 59018098 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18442;SOR=0;LSEQ=ACATAAATAAGATGCTTTTG;RSEQ=TCATATTAATGAGTGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:47,93:140,2:0.0141:2,2:29.5:1:29.5:1:1:1.97:60:4:0.0144:0:2 0/0:188:0:0,0:65,123:188,0:0:2,0:23.8:1:29.3:1:1:0:60:187:1:0:0.8 +5 61496655 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATGCAAATTAAAGGAG;RSEQ=CACTTCTCTTTGTTTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:17:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 61496821 . T G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48988;SOR=Inf;LSEQ=ATGCTAAGACTAGATTAAGC;RSEQ=TCACACAAGAATTTTATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:13,5:18,0:0:2,0:21.3:1:30.7:1:1:0:60:36:1:0:0 0/1:21:2:1,1:15,4:19,2:0.0952:2,2:19:0:32:1:0.42857:3.46389:60:4:0.1:0:1.5 +5 62835307 . G A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCACTTTGGGAGGCCAA;RSEQ=GTGGGCAGATCAGGGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:34:1:31.8:1:1:0:57.3:8:0.5714:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:15:0:33:0:1:0:60:2:1:0:0 +5 62835401 . AT A 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.66352;SOR=0.5692;LSEQ=AGTACGGTGGGGATTAACTT;RSEQ=TTTTTTTTTTATTTTTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:3:2,1:13,9:22,3:0.12:2,2:11:1:31.4:1:1:1.37:60:6:0.1304:0.04:0.7 0/1:42:3:2,1:25,14:39,3:0.0714:2,2:16:1:30.7:1:1:1.12:60:6:0.0732:0:0.7 +5 62835420 . G A 123 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03008;LSEQ=TATTTTTTTTTTTATTTTTC;RSEQ=GAAGAAATAGGTATGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:8,8:18,10:28,16:0.3636:2,2:18.7:1:30.8:1:0.52475:1.77554:60:32:0.3636:0:1.2 0/1:61:1:1,0:35,25:60,1:0.0164:2,0:38:0:32:0:1:0:60:2:0.0167:0:1 +5 62835498 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49376;SOR=Inf;LSEQ=GGAATGCTGTGTGTTTCTAG;RSEQ=GGGAAATGGGATGTAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:13,21:34,0:0:2,0:19.5:1:30.2:1:1:0:60:68:1:0:0.3 0/1:37:2:1,1:11,24:35,2:0.0541:2,2:26:1:28.5:1:1:2.13:52:4:0.0541:0:1 +5 62836591 . T C 143 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03294;LSEQ=AGTGATATTACTTTTAAAAA;RSEQ=CACCAAGTGTAAGCACAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:22:22,0:31,0:31,22:0.4151:1,1:27.8:1:32.1:1:1:0:60:21:0.4118:0:1 0/1:45:1:1,0:41,3:44,1:0.0222:2,0:12:0:33:0:1:0:60:2:0.0227:0:1 +5 62836669 . C T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58668;SOR=0.39639;LSEQ=AAGATCTTTCAGAAAGACAG;RSEQ=ATACCTGTAACTGCTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:2,0:154,43:197,2:0.0101:2,0:24:1:31:1:1:0:60:4:0.0104:0:1.5 0/0:250:1:0,1:170,77:247,1:0.004:2,0:1:0:22:0:0.31452:0:60:2:0.0041:0:1 +5 62836715 . C G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00307;SOR=Inf;LSEQ=TGATCGTAAGTTTCCAAATC;RSEQ=ACAGTGGCACTGCAGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:358:0:0,0:223,134:357,0:0:2,0:24.6:1:31.5:1:1:0:59:70.4:0.9972:0:0.5 0/1:452:10:5,5:256,185:441,10:0.0221:2,2:23.5:1:29.7:1:0.7488:1.38275:56.9:20:0.0225:0:2 +5 62836726 . T C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03219;LSEQ=TTCCAAATCCACAGTGGCAC;RSEQ=GCAGATTCAAAGCACTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:182:110,72:118,92:210,182:0.4631:2,2:25.2:1:30.4:1:0.41285:1.19:58.1:59.667:0.4602:0:1.1 0/1:483:13:7,6:268,201:469,13:0.0269:2,2:22.5:1:30.4:1:1:1.14254:57.6:26:0.0273:0:1.8 +5 62836848 . AT A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.11434;SOR=0;LSEQ=ACCTGAATGTGCTAAATATT;RSEQ=TTTTTTAAGTATGGGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:2,1:43,153:196,3:0.015:2,2:17.7:1:29.3:1:0.12882:7.02:59.7:6:0.0152:0.005:0.3 0/0:211:0:0,0:55,155:210,0:0:2,0:22.7:1:29.3:1:1:0:59.1:69:1:0:0.1 +5 62836972 . C CA 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.5453;SOR=1.84904;LSEQ=AGCTCCCCTATTCGTGATAG;RSEQ=AAAAAAAAAAGAAAGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:0,15:15,2:0.0952:1,0:24:1:32:1:1:0:60:4:0.1111:0:0 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:33:0:32:0:1:0:60:2:0.2:0:0 +5 67151556 . A G 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.84191;LSEQ=TCTAAATTGTGTGTGGGTTG;RSEQ=GGAATGCCGCAAATAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:1:1,0:118,36:154,1:0.0064:2,0:32:0:33:0:1:0:60:2:0.0065:0:1 0/1:170:2:1,1:117,50:167,2:0.0118:2,2:18:1:28:1:0.51374:2.32685:60:4:0.0119:0:1 +5 67151565 . G A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTGGGTTGAGGAATGCC;RSEQ=CAAATAGAAAAGTTTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:132,51:183,0:0:2,0:22.9:1:30.2:1:1:0:59.9:182:1:0:0.1 0/1:211:21:15,6:125,65:190,21:0.0995:2,2:29.7:1:29.8:1:0.80825:1.30:52:42:0.1005:0:1.1 +5 67151660 . G T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22059;SOR=4.5505;LSEQ=CAAATTTAGCCCGGCTGTGA;RSEQ=AACTTACAAAGGGAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:0,1:241,120:361,1:0.0028:2,0:1:0:24:0:0.33425:0:60:2:0.0028:0:1 0/1:401:5:2,3:247,149:396,5:0.0125:2,2:21.6:1:26.6:1:0.37181:2.48069:60:10:0.0127:0:1.2 +5 67151668 . A G 224 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCGGCTGTGAGAACTTAC;RSEQ=AAGGGAAGGTCAGAGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:0:0,0:233,126:359,0:0:2,0:23.7:1:30.5:1:1:0:59.8:70.8:1:0:0.1 0/1:424:192:117,75:150,81:231,192:0.4528:2,2:23:1:29.6:1:0.41904:1.1866:59.3:95:0.4545:0:1.1 +5 67151832 . C AA 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.60801;SOR=2.19299;LSEQ=TGAAACCCCTTTTTAAAATT;RSEQ=AAAAAAAAAAAAAAAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:1:0,1:38,115:153,1:0.0064:2,0:20:0:20.5:0:1:0:60:2:0.0092:0:1 0/1:143:2:0,2:35,100:135,2:0.014:2,0:25.5:1:26.8:1:1:0:43:4:0.022:0:2.5 +5 67522441 . A G 22 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4975;SOR=Inf;LSEQ=TGAATTCACTTTTCATAAAA;RSEQ=CGTAAAATCAGACTGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:65,9:74,0:0:2,0:24.5:1:30.5:1:1:0:59.6:148:1:0:0 0/1:80:2:1,1:66,12:78,2:0.025:2,2:7:1:22:1:0.30032:5.32421:60:4:0.0253:0:1 +5 67522722 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18106;LSEQ=GGGGACTTTCCGGGAACTTA;RSEQ=GTAGAATATATTGGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:227:99,128:118,138:256,227:0.47:2,2:23.4:1:30.9:1:0.64686:1.10532:59.9:112.5:0.4717:0:1.1 0/1:666:92:43,49:284,289:573,92:0.1381:2,2:22.9:1:28.9:1:0.65395:1.11963:60:45:0.138:0:1.2 +5 67522851 . A C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2362;LSEQ=CAACAAGGTCAGTATTGATA;RSEQ=GTGGTTGCTTAATGACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:121:35,86:46,109:155,121:0.4384:2,2:23.2:1:30.8:1:1:1.03683:60:120:0.4412:0:1.1 0/1:309:48:13,35:77,184:261,48:0.1553:2,2:25.2:1:30.2:1:0.86309:1.12626:60:96:0.1558:0:1.2 +5 67569342 . T C 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTAGAGGGCATCAGTTCCT;RSEQ=TGTTCTACCCTTATTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:19:6,13:75,276:351,19:0.0514:2,2:23.2:1:33.1:1:0.39012:1.70:60:38:0.0514:0:1.2 0/0:361:0:0,0:85,275:360,0:0:2,0:24.1:1:29.4:1:1:0:60:50.429:0.9972:0:0.2 +5 67569391 . A C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00081;SOR=0.41977;LSEQ=TATTTGTCTCTTGTGCATTC;RSEQ=TTAAGTAAATTTCCTACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:62:4,58:7,79:86,62:0.4189:2,2:23.2:1:33.5:1:0.76186:1.28268:60:124:0.4276:0:1.1 0/1:151:35:3,32:13,103:116,35:0.2318:2,2:23.3:1:31.5:1:1:1.34376:60:34:0.2329:0:1.1 +5 67569479 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.75132;SOR=1.38159;LSEQ=AGTACTGGGAAAAATGTCTC;RSEQ=GTCTATAATTTCTAACTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:12:1,11:1,12:13,12:0.48:1,2:24.1:1:29.9:1:1:1.09:60:24:0.48:0:1.3 1/0:16:9:2,7:1,6:7,9:0.5625:2,2:12:1:31.4:1:1:1.66:60:18:0.5625:0:1.4 +5 67569602 . A G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02506;SOR=0.2442;LSEQ=ATGGTTTTGCCAAAATTATC;RSEQ=ACATGCCAGGTAAGATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:14:12,2:16,0:16,14:0.4667:1,2:23.4:1:29.9:1:0.2092:0:60:28:0.4828:0:1 0/1:29:5:5,0:23,1:24,5:0.1724:1,0:31:1:28.2:1:1:0:60:10:0.1724:0:1 +5 67569739 . A T 48 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18941;SOR=0.21588;LSEQ=GAGAGCTGTGTTTTGCATAC;RSEQ=TGGTCTGTGGTCTGTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:4:1,3:222,140:362,4:0.0109:2,2:8.8:1:24.3:1:0.30376:4.73724:60:3:0.0083:0:1.3 0/0:421:1:0,1:258,162:420,1:0.0024:2,0:1:0:23:0:0.38717:0:60:2:0.0024:0:1 +5 67569746 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.00034;SOR=0.60171;LSEQ=GTGTTTTGCATACATGGTCT;RSEQ=TGGTCTGTTTTGTGTCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:180:111,69:121,86:207,180:0.4627:2,2:27.3:1:29.5:1:0.53423:1.14:59.9:89:0.4611:0:1.1 0/1:466:159:97,62:181,124:305,159:0.3412:2,2:23.8:1:28.4:1:0.76509:1.07:60:52:0.3414:0:1.1 +5 67569909 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.49834;SOR=0;LSEQ=CTTTCTGTTTCAGGTAATGC;RSEQ=CACACACAAAATTGAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:20,111:131,2:0.015:2,2:28.5:1:32.5:1:0.29187:5.44:60:4:0.0152:0:1 0/0:127:0:0,0:16,111:127,0:0:2,0:21.2:1:29.5:1:1:0:60:254:1:0:0.1 +5 67569969 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19096;SOR=Inf;LSEQ=TTTAAAGGGAACTCAAATCA;RSEQ=GTACAGTTCTCCCTGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:0,38:38,0:0:1,0:26.2:1:31.5:1:1:0:60:76:1:0:0 0/1:30:2:0,2:0,28:28,2:0.0667:1,0:37:1:27.5:1:1:0:60:4:0.069:0:1 +5 67575281 . C T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.5311;LSEQ=CCTACAAGAAGTACGGCTAA;RSEQ=GAATACTTTGTGTCTTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:2,0:36,1:37,2:0.0513:1,0:9.5:1:32:1:1:0:60:4:0.0513:0:1.5 0/1:26:2:2,0:22,2:24,2:0.0769:2,0:33:1:31:1:1:0:60:4:0.0769:0:3 +5 67575323 . ATT A 141 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=0.09674;SOR=1.88492;LSEQ=TATCCTCATATTGCTTCCTT;RSEQ=TTTTTTTTTTTTTGTCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:17:17,0:31,0:31,17:0.2361:1,1:20.8:1:31.1:1:1:0:60:34:0.2361:0.0972:0.9 0/1:65:24:23,1:24,1:25,24:0.3692:1,1:23.2:1:30.9:1:1:1.04259:57.9:48:0.3692:0.0923:1.1 +5 67575344 . A G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77564;SOR=0.91802;LSEQ=TTTTTTTTTTTTTTTGTCAC;RSEQ=TGTGAGTCAAATTGTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:39:37,2:71,5:76,39:0.3362:2,2:20.1:1:27.7:1:1:1.30:59.6:8.75:0.3608:0:1.3 0/1:104:33:30,3:65,5:70,33:0.3173:2,2:22.2:1:28.5:1:0.70883:1.29652:58.8:32:0.3404:0:1.3 +5 67575642 . A G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17818;SOR=0.68581;LSEQ=ATATGTCTTGCATATATAGA;RSEQ=ATAGTGGTTAGAAAATAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:50:3,47:4,79:83,50:0.3759:1,2:21.5:1:32.9:1:1:1.26:59.8:100:0.3759:0:1.1 0/1:113:33:0,33:7,73:80,33:0.292:2,1:22.2:1:31.3:1:0.10408:0:60:66:0.2973:0:1 +5 67576345 . T A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25324;SOR=0;LSEQ=TTTCTCTTTTTTTTTTTTTT;RSEQ=AAACTTGTAGAAGTACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:2,1:191,69:260,3:0.0114:2,2:9.7:1:21:1:1:1.38223:60:2:0.0083:0:1.7 0/0:225:0:0,0:162,63:225,0:0:2,0:22.8:1:27.8:1:1:0:59.8:19.455:1:0:0.7 +5 67576346 . A T 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66434;SOR=1.78614;LSEQ=TTCTCTTTTTTTTTTTTTTT;RSEQ=AACTTGTAGAAGTACAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:2:0,2:200,72:272,2:0.0073:2,0:1:1:25:1:0.07222:0:60:6:0.0056:0:1 0/1:232:3:2,1:163,66:229,3:0.0129:2,2:25.3:1:29:1:1:1.23363:60:6:0.0133:0:1.3 +5 67576682 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50668;SOR=0;LSEQ=CAGATGCTATCACACACATT;RSEQ=ACTTGAGTGTATATAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:109,79:188,2:0.0105:2,2:24.5:1:28:1:1:1.37735:60:4:0.0107:0:1 0/0:147:0:0,0:91,56:147,0:0:2,0:23.4:1:30.6:1:1:0:60:146:1:0:0.1 +5 67576688 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.19331;SOR=Inf;LSEQ=CTATCACACACATTCACTTG;RSEQ=GTGTATATAAATGAAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:118,84:202,0:0:2,0:24.6:1:30.4:1:1:0:59.9:27.857:1:0:0.1 0/1:159:2:1,1:98,59:157,2:0.0126:2,2:19:1:29.5:1:1:1.65543:60:4:0.013:0:1 +5 67576819 . C T 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20194;SOR=0.23116;LSEQ=TCTCAACTGAATGGAATGAA;RSEQ=GACAGCCTGCACCAGGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:4:2,2:100,137:237,4:0.0166:2,2:14.5:1:28.8:1:1:1.37:60:8:0.0167:0:2.5 0/0:258:1:0,1:102,155:257,1:0.0039:2,0:10:0:31:0:1:0:60:2:0.004:0:2 +5 67576835 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22957;SOR=0;LSEQ=TGAACGACAGCCTGCACCAG;RSEQ=TAATGCTTTTTGAGCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:70,118:188,2:0.0105:2,2:8:1:31.5:1:1:1.68:60:4:0.0106:0:1 0/0:206:0:0,0:71,133:204,0:0:2,0:25.1:1:31.2:1:1:0:60:203:0.9951:0:0.2 +5 67584357 . A G 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=GGGACGAGCCGAGCCGAGCC;RSEQ=AGCGGAGCTGGGCCACTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:7,1:8,3:0.2727:2,0:28.7:1:32:0:1:0:60:6:0.2727:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:18.3:1:30.7:1:1:0:60:12:1:0:0.2 +5 67584512 . AT A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.19806;SOR=1.38669;LSEQ=GTGGAAGAACAGCTTTGGGG;RSEQ=TTTTTTTTTTTCATTGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:32:28,4:205,46:251,32:0.1103:2,2:24.3:1:32:1:0.62196:1.57:60:64:0.1131:0.0241:0.1 0/1:361:53:43,10:230,70:300,53:0.1468:2,2:23.9:1:29.7:1:0.59391:1.31:59.7:52:0.1461:0.036:0.3 +5 67584739 . G A 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00389;SOR=Inf;LSEQ=CTCCCCCTGTCCTCGAGGGG;RSEQ=ACAGTGGCTGGGAAAGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:0,104:104,0:0:1,0:25:1:33:1:1:0:60:208:1:0:0.3 0/1:89:7:0,7:0,82:82,7:0.0787:1,0:34.3:1:31.4:1:1:0:60:14:0.0795:0:1.9 +5 67584758 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37416;SOR=0.71316;LSEQ=GGACAGTGGCTGGGAAAGAT;RSEQ=GGGTTTAGGTTGGAATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:31:0,31:0,42:42,31:0.4189:1,1:23.8:1:31.5:1:1:0:60:30:0.411:0:1 0/1:59:20:0,20:0,39:39,20:0.339:1,1:23.5:1:30.3:1:1:0:60:19:0.3276:0:1.7 +5 67586680 . T A 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24859;SOR=Inf;LSEQ=CAGGTAATACTGCAGTATTA;RSEQ=TGTAGAGAGTTAGTTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:64,187:251,0:0:2,0:24.2:1:30.4:1:1:0:59.9:124.5:1:0:0.1 0/1:256:3:2,1:82,171:253,3:0.0117:2,2:7.3:1:26.3:1:0.25145:4.15:60:6:0.0118:0:1 +5 67586727 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=0;LSEQ=TTTTTAATTTTTCGAAAGCT;RSEQ=CTGTAAAAGATCCTTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:9,101:110,2:0.0179:2,2:24.5:1:30:1:0.17133:10.70:60:4:0.0179:0:1 0/0:84:0:0,0:8,76:84,0:0:2,0:23.3:1:29.4:1:1:0:60:168:1:0:0 +5 67587984 . G T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.60746;LSEQ=AACTAATGCTATATATTTCA;RSEQ=TTACTCTAACTTTTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:81,5:86,2:0.0227:2,2:16:1:31:1:0.13245:14.8795:60:4:0.023:0:1 0/1:72:1:1,0:67,4:71,1:0.0139:2,0:5:0:30:0:1:0:60:2:0.0139:0:1 +5 67587994 . C T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.074;SOR=0.60372;LSEQ=ATATATTTCAGTTACTCTAA;RSEQ=TTTTTATTTTTTTAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:55:50,5:47,6:53,55:0.5093:2,2:27.8:1:31.4:1:0.75886:1.27:60:54:0.5047:0:1.2 0/1:104:40:36,4:59,5:64,40:0.3846:2,2:20.1:1:30.7:1:0.73039:1.3076:60:80:0.3922:0:1.2 +5 67588000 . A G 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.04697;SOR=Inf;LSEQ=TTCAGTTACTCTAACTTTTT;RSEQ=TTTTTTTAAAGTAAAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:111,17:128,0:0:2,0:23.7:1:28.9:1:1:0:59.9:127:1:0:0.6 0/1:113:4:4,0:97,11:108,4:0.0354:2,0:27.3:1:33.8:1:1:0:60:8:0.036:0:2 +5 67588001 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.21549;SOR=Inf;LSEQ=TCAGTTACTCTAACTTTTTA;RSEQ=TTTTTTAAAGTAAAAGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:113,18:131,0:0:2,0:23.5:1:31.3:1:1:0:59.9:130:1:0:0.6 0/1:114:2:1,1:101,11:112,2:0.0175:2,2:20:1:29:1:0.20028:8.83537:60:4:0.0175:0:2 +5 67588025 . C T 26 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24809;SOR=Inf;LSEQ=TTTAAAGTAAAAGTATTCAT;RSEQ=TAAAGAAATTTAGTTCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:160,36:196,0:0:2,0:23.9:1:32.7:1:1:0:59.9:195:1:0:0.4 0/1:196:2:1,1:154,40:194,2:0.0102:2,2:8:0:26.5:1:0.37546:3.81509:60:4:0.0105:0:1.5 +5 67588148 . G A 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27822;SOR=1.3841;LSEQ=AACGGTATGAATAACAATAT;RSEQ=TCCTTACAAGATGCTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:23:10,13:186,248:434,23:0.0503:2,2:22:1:29.7:1:1:1.03:60:46:0.0511:0:1 0/1:512:35:15,20:206,270:476,35:0.0684:2,2:23.6:1:29.1:1:1:1.01725:60:70:0.0692:0:1.2 +5 67588162 . C T 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06404;SOR=Inf;LSEQ=CAATATGTCCTTACAAGATG;RSEQ=TGAATGGTACTGGGGAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:170,255:425,0:0:2,0:24.1:1:32.6:1:1:0:60:52.125:1:0:0.2 0/1:479:5:2,3:200,274:474,5:0.0104:2,2:17.4:1:24.2:1:1:1.09471:60:4:0.0086:0:1 +5 67589038 . G A 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=9.22839;LSEQ=TTACACTAAGGTAAGCCAGG;RSEQ=AATATAGCTGAAATTAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:2:1,1:183,218:401,2:0.005:2,2:20.5:1:22.5:1:1:1.19:60:1:0.0025:0:1.5 0/1:431:19:8,11:180,229:409,19:0.0441:2,2:19:1:28.7:1:1:1.08062:60:38:0.0445:0:1.1 +5 67589188 . C T 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CGAGATGGGAAATATGGCTT;RSEQ=TCTGACCCATTAACCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:773:0:0,0:422,350:772,0:0:2,0:25.8:1:32.5:1:1:0:60:84.778:1:0:0.1 0/1:824:25:14,11:417,382:799,25:0.0303:2,2:25.8:1:29.9:1:0.83951:1.17:60:50:0.0306:0:1.1 +5 67590558 . C A 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19685;SOR=3.3211;LSEQ=TAACCAAAATCCTCTAAAAC;RSEQ=ATTTAAAGATGATCTCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:2:2,0:47,171:218,2:0.0091:2,0:11.5:1:19.5:1:0.04882:0:60:1:0.0046:0:1.5 0/1:270:8:3,5:52,210:262,8:0.0296:2,2:18.4:1:29.4:1:0.20886:2.41:60:16:0.0299:0:1 +5 67590615 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49606;SOR=Inf;LSEQ=TCACGTGGACACAGGAAGGG;RSEQ=AATATCACTCTGGGGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:1,61:62,0:0:1,0:24.2:1:29.9:1:1:0:56.4:4.636:1:0:0.2 0/1:64:2:1,1:1,60:61,2:0.0313:1,2:27:0:30.5:1:0.06298:42.79:53:4:0.0385:0:1.5 +5 67590636 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23944;SOR=Inf;LSEQ=AATATCACTCTGGGGACTGT;RSEQ=GTGGGGTGGGGGGAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:36,0:0:1,0:21.3:1:31.9:1:1:0:53.3:72:1:0:0.5 0/1:35:2:1,1:2,31:33,2:0.0571:2,2:13.5:1:30.5:1:0.16639:12.86:50:4:0.0571:0:2 +5 67590638 . T C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.49275;SOR=Inf;LSEQ=TATCACTCTGGGGACTGTGG;RSEQ=GGGGTGGGGGGAGGAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:0,34:34,0:0:1,0:20.4:1:26.9:1:1:0:52.9:2.4:1:0:0.6 0/1:35:2:1,1:2,30:32,2:0.0571:2,2:14:0:30:1:0.17112:12.45:50:4:0.0667:0:2 +5 67591525 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=ATTTATTTTTACTCATAATG;RSEQ=TGTGAAACAACTCTCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:21.8:1:34:1:1:0:60:10:1:0:0 0/1:7:2:1,1:0,5:5,2:0.2857:0,2:28.5:1:29.5:1:0.28571:0:60:4:0.2857:0:1 +5 67592281 . G A 59 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40901;SOR=2.44954;LSEQ=ATAGTTTTAGTCTTGAATAA;RSEQ=CTTACAGTACAATAATGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:0,2:0,47:47,2:0.0408:1,0:34.5:1:27.5:1:1:0:60:4:0.0435:0:1 0/1:42:4:0,4:2,36:38,4:0.0952:2,0:21.5:1:29.5:1:1:0:60:8:0.1:0:1 +5 67592293 . A C 34 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.45929;LSEQ=TTGAATAAGCTTACAGTACA;RSEQ=TAATGTAGAAGAGAAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:0,2:0,44:44,2:0.0435:1,0:21:1:25.5:1:1:0:60:1:0.0222:0:1 0/1:32:2:0,2:2,28:30,2:0.0625:2,0:25.5:1:34:0:1:0:60:4:0.0645:0:1.5 +5 67593016 . T C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.64993;LSEQ=CAAAGTAACTGTATTACATG;RSEQ=ATTTTACTATTGTCTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:11,0:6,0:6,11:0.6111:0,0:23.5:1:33.5:1:1:0:60:22:0.6471:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:16.5:1:31.5:1:1:0:60:4:0.5:0:1 +5 67593363 . T C 170 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=48.92979;LSEQ=CATTACCAACACACCTCCCT;RSEQ=GTGCAGCACAACGACTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:847:1:0,1:348,497:845,1:0.0012:2,0:27:0:27:0:1:0:60:2:0.0012:0:1 0/1:1005:55:25,30:382,567:949,55:0.0547:2,2:26.7:1:29.5:1:0.48116:1.24:60:110:0.0556:0:1.2 +5 67593523 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1771;SOR=Inf;LSEQ=AGTCTGATCTGTGAATTGAG;RSEQ=TGCAGAAACGAAGCCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:2,73:75,0:0:1,0:21.8:1:33:1:1:0:59.6:24:1:0:0.1 0/1:55:2:0,2:1,52:53,2:0.0364:1,0:40:1:28:1:1:0:60:4:0.037:0:1.5 +5 68390203 . C G 108 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00098;SOR=0.03358;LSEQ=AAGGCAGCGACCGGCCGGGT;RSEQ=GCTCAGGATGCACTTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:6,5:2,1:3,11:0.7857:2,2:18.1:1:31.4:1:1:1.60839:60:22:0.7857:0:1.4 0/1:11:1:0,1:7,3:10,1:0.0909:2,0:49:0:29:0:0.36364:0:60:2:0.0909:0:1 +5 68390284 . C T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54505;SOR=1.61366;LSEQ=GGGTCGGCGCGCCCTCTCCC;RSEQ=CTGCCTGCCTCCCTGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:6,6:4,4:8,12:0.6:2,2:18.2:1:31.2:1:1:1:60:24:0.6:0:1.3 1/0:31:22:12,10:4,5:9,22:0.7097:2,2:27.8:1:28.8:1:0.70425:1.48:60:21:0.7:0:1 +5 72671623 . G T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.26758;SOR=0;LSEQ=AGCCTCCTGAGAGGCGAAAT;RSEQ=GGCCTCACATGAGTCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:1,2:165,29:194,3:0.0152:2,2:10.7:1:24.7:1:0.06509:11.1501:60:2:0.0103:0:1 0/0:142:0:0,0:111,31:142,0:0:2,0:22.7:1:30.8:1:1:0:60:46.333:1:0:0.1 +5 72671651 . G A 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=Inf;LSEQ=CATGAGTCTCTTCCATAGGG;RSEQ=CTCATTAAAGAGGGATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:216,78:294,0:0:2,0:23.7:1:31.2:1:1:0:60:48:1:0:0.1 0/1:253:11:7,4:166,76:242,11:0.0435:2,2:27.1:1:29.4:1:0.74605:1.24695:60:22:0.044:0:1.2 +5 72671738 . G T 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GATCTTCAGGTGATGTGTGC;RSEQ=CATTTTCTTCAGGGTATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:643:0:0,0:299,340:639,0:0:2,0:24.5:1:30.9:1:1:0:60:44.643:0.9952:0:0.1 0/1:621:75:36,39:260,283:543,75:0.1208:2,2:25.4:1:29.6:1:1:1.00:60:150:0.122:0:1.1 +5 72671819 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22681;SOR=Inf;LSEQ=GAGCAGCTTGCTTGCAATAA;RSEQ=AATAATAAAAACAACAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:45,170:215,0:0:2,0:21.3:1:32.1:1:1:0:60:70.667:1:0:0.1 0/1:196:2:1,1:47,147:194,2:0.0102:2,2:42.5:1:30:1:0.43077:3.11:60:4:0.0104:0:1 +5 72742882 . T C 59 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGCGGCGGACGAGGAGAC;RSEQ=GAGGAGGCGGCGGCGGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:33.3:1:29.8:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 72743299 . G GGC 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AAGGCGGCGGCGGCGGCGGC;RSEQ=CGCTGCGGCGGCGAAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:33.5:0:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 73011081 . T C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03543;SOR=Inf;LSEQ=TGTCCAAGGTGGAGTCTGGC;RSEQ=CTGGTGCTGTTGCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:28,0:0:2,0:24.9:1:31.3:1:1:0:60:56:1:0:0.1 0/1:23:4:2,2:10,9:19,4:0.1739:2,2:37.5:1:30.5:1:1:1.10603:60:8:0.1739:0:1 +5 75111183 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGCTCTGTCTATATGAG;RSEQ=GGGAGGTGCATTCTAGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:8:1:29.7:1:1:0:60:6:0.3:0:1.3 0/0:2:0:0,0:2,0:2,0:0:0,0:28.5:1:32:1:1:0:60:4:1:0:0 +5 75111304 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49882;SOR=0;LSEQ=ATGGGATTAAGTATAGATTT;RSEQ=TTTGCTTAATTCTCCCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:60,23:83,2:0.0235:2,2:26:1:31.5:1:0.48739:2.57497:60:4:0.0244:0:1.5 0/0:75:0:0,0:55,20:75,0:0:2,0:24:1:27.5:1:1:0:60:36.5:1:0:0.2 +5 75111343 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23262;SOR=Inf;LSEQ=TAGCCTTTTACAGTTAGCAG;RSEQ=TTGTCAGTACATGCTGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:80,59:139,0:0:2,0:25.5:1:32.3:1:1:0:59.8:33.75:1:0:0.3 0/1:130:2:2,0:86,42:128,2:0.0154:2,0:21:1:27:1:1:0:60:4:0.0156:0:1.5 +5 75111365 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23917;SOR=0;LSEQ=TGTCAGTACATGCTGCTATG;RSEQ=TGTATTAGCTGTGCAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:86,80:166,2:0.0119:2,2:45:1:31:1:1:1.07451:60:4:0.0123:0:1 0/0:175:0:0,0:105,70:175,0:0:2,0:23.1:1:28.9:1:1:0:60:174:1:0:0.3 +5 75111374 . C T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37204;SOR=3.90024;LSEQ=ATGCTGCTATGATGTATTAG;RSEQ=TGTGCAGGGGAGAAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:1:0,1:94,86:180,1:0.0055:2,0:1:0:29:0:0.48066:0:60:2:0.0057:0:1 0/1:188:4:1,3:108,76:184,4:0.0213:2,2:11.8:1:27.8:1:0.31119:4.23165:60:8:0.0217:0:1.5 +5 75111376 . G T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36155;SOR=0.3153;LSEQ=GCTGCTATGATGTATTAGCT;RSEQ=TGCAGGGGAGAAAAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:3:1,2:94,88:182,3:0.0161:2,2:12.7:1:28.3:1:0.61294:2.12789:60:6:0.0166:0:2 0/0:195:1:0,1:113,81:194,1:0.0051:2,0:1:0:24:0:0.42051:0:60:2:0.0052:0:1 +5 75111378 . GCAGGGG CAGGGGA 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24049;SOR=0;LSEQ=TGCTATGATGTATTAGCTGT;RSEQ=AGAAAAAAATTATACTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:99,91:190,2:0.0104:2,2:19.5:1:24:1:1:1.08742:54:4:0.0107:0.0052:4 0/0:199:0:0,0:115,83:198,0:0:2,0:23:1:31.1:1:1:0:60:65:0.9949:0:0.4 +5 75111397 . T C 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15415;SOR=1.42879;LSEQ=TGCAGGGGAGAAAAAAATTA;RSEQ=ACTTTTGTGTTCCCTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:38:19,19:78,83:161,38:0.19:2,2:22.8:1:32.4:1:1:1.06:60:76:0.1939:0:1.2 0/1:211:53:29,24:86,72:158,53:0.2512:2,2:25.6:1:30.9:1:1:1.01:60:25.5:0.2452:0:1.3 +5 75111451 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52031;SOR=Inf;LSEQ=CCACACAATTATAGAAGATT;RSEQ=TTGTTCATCTCCAAGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:44,75:119,0:0:2,0:22.2:1:32.1:1:1:0:60:58.5:1:0:0.3 0/1:182:2:1,1:73,106:179,2:0.011:2,2:21.5:1:31:0:1:1.45:60:4:0.0112:0:2 +5 75926812 . G A 69 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAACATAATTTGATGACAAC;RSEQ=AATTGTAATTTAATATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:24.6:1:29.8:1:1:0:60:10:0.7143:0:1.2 1/1:1:1:1,0:0,0:0,1:1:0,0:39:0:32:0:1:0:60:2:1:0:1 +5 75926863 . G A 64 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.89743;LSEQ=GTACGTGTAAGAAAAAAAGA;RSEQ=AAAGCATCCGTGTCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:12:1:32:0:1:0:60:8:0.3333:0:2.3 1/0:2:1:1,0:1,0:1,1:0.5:0,0:24:0:31:0:1:0:60:2:0.5:0:2 +5 75926873 . G A 64 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.89743;LSEQ=GAAAAAAAGAGAAAGCATCC;RSEQ=TGTCTCCCTTCTCTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:22:1:32:1:1:0:60:8:0.3333:0:2.3 1/0:2:1:1,0:1,0:1,1:0.5:0,0:34:0:31:0:1:0:60:2:0.5:0:2 +5 75927027 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTCTTACCTGGAATTAA;RSEQ=GTGGGAAATAATTCACTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:64:62,2:0,0:0,64:1:0,1:24.2:1:30.8:1:1:0:60:31:1:0:1.6 1/1:49:49:48,1:0,0:0,49:1:0,1:21.1:1:29.2:1:1:0:60:23.5:1:0:1.3 +5 75927069 . A G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00131;SOR=0.43999;LSEQ=TAACTTTCCTTAGGCAACCA;RSEQ=GAGTTTAATGTGTTTTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:145:79:69,10:56,10:66,79:0.5448:2,2:27.7:1:33.3:1:0.80963:1.23:59.5:158:0.5486:0:1.4 0/1:122:42:32,10:70,10:80,42:0.3443:2,2:23.2:1:31:1:0.12693:2.17246:60:84:0.35:0:1.3 +5 75927086 . G T 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2367;SOR=Inf;LSEQ=CCAAGAGTTTAATGTGTTTT;RSEQ=TTAATGAGGAGGGGTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:155,45:200,0:0:2,0:23.7:1:32.6:1:1:0:59.8:400:1:0:0.6 0/1:190:2:1,1:143,45:188,2:0.0105:2,2:6:0:30.5:1:0.42657:3.15401:60:4:0.0106:0:1 +5 75927188 . C T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.40962;LSEQ=CCGTTGCACATATCCACCAG;RSEQ=TCTGCCTTTCTAGAACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:174:81,93:147,160:307,174:0.3602:2,2:24.7:1:30.1:1:0.84931:1.05478:59.9:348:0.3633:0:1.8 1/0:540:311:138,173:110,119:229,311:0.5759:2,2:25.1:1:29.1:1:0.43192:1.15849:59.9:102.667:0.5768:0:1.7 +5 75927222 . T G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=2.57334;LSEQ=AACACTTGTTTAGGTTGTTT;RSEQ=TGACAATCTTGCTAAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:125:44,81:87,153:240,125:0.3425:2,2:23.8:1:31.8:1:0.90858:1.04667:59.9:61.5:0.3465:0:2.3 1/0:356:204:79,125:60,91:151,204:0.573:2,2:24.7:1:31:1:0.91248:1.04317:59.9:101:0.5771:0:2.2 +5 75927274 . T C 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.06694;LSEQ=CAAGAGAATACCAGGATTTC;RSEQ=GTAACTTAAAAAGGATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:61:6,55:15,91:106,61:0.3631:2,2:21.7:1:31:1:0.4764:1.50743:60:122:0.3653:0:2.1 1/0:124:79:16,63:7,38:45,79:0.6371:2,2:23.2:1:29.3:1:0.63358:1.38:60:78:0.6341:0:2.1 +5 75927295 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17765;SOR=Inf;LSEQ=GTAACTTAAAAAGGATTTTG;RSEQ=TTATCCTAAAGTAAACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:8,97:105,0:0:2,0:23.4:1:33.7:1:1:0:60:104:1:0:0.6 0/1:77:2:1,1:13,62:75,2:0.026:2,2:21.5:1:30.5:1:0.33254:4.63:60:4:0.0267:0:2.5 +5 75927595 . C G 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATGTTTGATACTAATG;RSEQ=ATTCCTAAAACGTTGAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:15.3:1:29.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 77168090 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=2.02904;LSEQ=GGCTCTCCCCACACTTAGCT;RSEQ=TGTTCTCCACAGAGCTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:65:31,34:139,158:297,65:0.1786:2,2:27.8:1:29.7:1:1:1.04:60:130:0.1826:0:1.5 0/1:382:117:59,58:129,135:264,117:0.3063:2,2:26.3:1:28.8:1:0.82449:1.06:60:116:0.3069:0:1.5 +5 77168145 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02014;SOR=1.71778;LSEQ=ACCCTATGTGAGCCTAGGAC;RSEQ=ATAGTAAACTTTTTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:229:36:9,27:59,133:192,36:0.1572:2,2:20.8:1:30.4:1:0.55626:1.32921:60:35:0.1549:0:1.9 0/1:280:68:25,43:78,134:212,68:0.2429:2,2:25:1:29.2:1:1:1.00119:60:136:0.2455:0:1.8 +5 77168161 . TA T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19705;SOR=0;LSEQ=GGACGATAGTAAACTTTTTT;RSEQ=AAAAAAATTATTTTCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:31,104:135,2:0.0146:2,2:46:1:31.5:1:0.41391:3.32:60:4:0.0148:0:0 0/0:171:0:0,0:57,114:171,0:0:2,0:26:1:28.3:1:1:0:60:27.5:1:0:0.5 +5 77168181 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18307;SOR=0;LSEQ=TAAAAAAAATTATTTTCAGA;RSEQ=AGTTCTTTCCTCAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:13,73:86,2:0.0227:2,2:33:1:33:1:0.29441:5.45:60:4:0.0233:0:2 0/0:117:0:0,0:31,86:117,0:0:2,0:23.4:1:29.5:1:1:0:60:38:1:0:0.4 +5 77570405 . G C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51301;SOR=Inf;LSEQ=ATAAAACTACACCAGGTACA;RSEQ=CATAGTCAAACTGCTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:23,0:0:2,0:27.4:1:32.9:1:1:0:60:46:1:0:0.1 0/1:35:2:1,1:17,16:33,2:0.0571:2,2:30:0:30:1:1:1.06069:60:4:0.0571:0:1.5 +5 78516069 . G C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAACTTCACCTCCCAGGTT;RSEQ=AAATGATTCTCCTGCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:33.5:1:1:0:43:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 78517050 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTGAGAACCAGGAAGAT;RSEQ=CACCTACTCTAAAAATTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:5,15:20,2:0.0909:2,2:40:1:28.5:1:0.48052:2.83:60:4:0.0909:0:1 0/0:10:0:0,0:3,7:10,0:0:2,0:25.1:1:29.4:1:1:0:60:9:1:0:0.1 +5 78517143 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATAGGTGAATTTTGAAGCCT;RSEQ=CGTGAATATATCCATATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:28.5:1:30:0:1:0:60:4:0.6667:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:23:1:29:0:1:0:60:4:1:0:0 +5 79172055 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.10747;SOR=Inf;LSEQ=TGGTCACTCCTCACTCTGTG;RSEQ=CCCCAAAGCCTGCTGTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:158,109:267,0:0:2,0:24.7:1:31.4:1:1:0:60:88:1:0:0.1 0/1:243:3:1,2:146,94:240,3:0.0123:2,2:19.7:1:28:1:0.56386:3.09167:60:6:0.0124:0:1.3 +5 79172136 . A G 222 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCTCAACTGGACTATAAA;RSEQ=TTCTCCAGGGTAGAGATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:143,186:329,0:0:2,0:25.5:1:30.6:1:1:0:60:53.833:1:0:0.2 0/1:294:140:62,78:69,85:154,140:0.4762:2,2:24.6:1:31.2:1:1:1.02119:60:69:0.4726:0:1.1 +5 79172158 . C T 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTCCAGGGTAGAGATTGTG;RSEQ=CTGATTCATGTAGCTTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:25:11,14:88,134:222,25:0.1012:2,2:25.6:1:29.7:1:0.67307:1.20:60:50:0.1029:0:1.2 0/0:216:0:0,0:87,129:216,0:0:2,0:26.4:1:30.2:1:1:0:60:53:1:0:0.5 +5 79172193 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18232;SOR=Inf;LSEQ=TTAGCAGAGAGGCTGGCCTG;RSEQ=AGCCTCTGTGCAGGAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:40,115:155,0:0:2,0:22.1:1:32.2:1:1:0:60:76.5:1:0:0.1 0/1:116:2:1,1:32,82:114,2:0.0172:2,2:22:1:26.5:1:0.48981:2.54:60:4:0.0175:0:2 +5 79172312 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCAGAAGCTTTGCTTCTAAT;RSEQ=TCACTTGGACAATACTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:0,19:19,2:0.0952:1,0:18.5:1:31:1:1:0:60:4:0.0952:0:1 0/0:9:0:0,0:0,9:9,0:0:0,0:28.1:1:30.4:1:1:0:60:18:1:0:0 +5 84761041 . G A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03916;SOR=Inf;LSEQ=TAAAAAGAAGAGGTGGAACC;RSEQ=TCCCAAAATGTCCCTTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:26,14:40,0:0:2,0:23.4:1:30.8:1:1:0:54.5:80:1:0:0.1 0/1:56:6:3,3:32,18:50,6:0.1071:2,2:18.2:1:29.2:1:0.66134:1.75868:33.2:12:0.1091:0:1 +5 84761079 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50938;SOR=Inf;LSEQ=CTCAGAAGAAAGATGGGGTA;RSEQ=CTCAAAAGAAGGCAAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:25,23:48,0:0:2,0:24.6:1:32.9:1:1:0:56.8:96:1:0:0.1 0/1:67:2:1,1:33,32:65,2:0.0299:2,2:22.5:1:28:1:1:1.03078:43.5:4:0.0299:0:1 +5 86564230 . C T 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.53423;LSEQ=CTGGTGGCCCCTGGGGCTCC;RSEQ=GGGCGGGCAGGGTAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:122,23:145,2:0.0136:2,2:17.5:1:32.5:1:0.30081:5.21402:60:4:0.0141:0:1 0/0:137:1:1,0:98,37:135,1:0.0073:2,0:36:0:31:0:1:0:60:2:0.0075:0:1 +5 86564237 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.20933;SOR=Inf;LSEQ=CCCCTGGGGCTCCCGGGCGG;RSEQ=CAGGGTAGGGCAGAGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:146,36:182,0:0:2,0:23.3:1:31.1:1:1:0:60:35.4:1:0:0.2 0/1:154:2:1,1:108,44:152,2:0.013:2,2:28.5:1:27.5:1:0.50038:2.43834:60:4:0.0133:0:1 +5 86564245 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24172;SOR=Inf;LSEQ=GCTCCCGGGCGGGCAGGGTA;RSEQ=GGCAGAGTAGAGCGGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:155,43:198,0:0:2,0:24.4:1:32.4:1:1:0:60:32:1:0:0.2 0/1:192:2:1,1:130,60:190,2:0.0104:2,2:20:1:27.5:1:0.53561:2.15713:60:4:0.0106:0:1 +5 86564995 . T A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26348;SOR=0.84237;LSEQ=CAGGCATACTACCTGGCGTC;RSEQ=TCCTACATTTATTGCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:138:90,48:128,91:219,138:0.3866:2,2:23:1:30.8:1:0.22105:1.33:60:276:0.3932:0:1.1 0/1:424:147:90,57:179,98:277,147:0.3467:2,2:23.9:1:29.6:1:0.52545:1.1564:60:72.5:0.3452:0:1.1 +5 86565170 . G A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.00038;SOR=Inf;LSEQ=TAGTGTATATTAACTTGTGT;RSEQ=TGTTACTTGATAAAGCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:90,263:353,0:0:2,0:23.5:1:32:1:1:0:60:116.667:1:0:0.1 0/1:423:13:5,8:99,310:409,13:0.0307:2,2:18.7:1:28.8:1:0.32273:1.95:60:26:0.0309:0:1.2 +5 86626521 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13116;SOR=0;LSEQ=TTAAACTGAGAGCAAGAAGG;RSEQ=TGAAGGGACAAAGGTGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:9,4:0.3077:0,0:15:1:30:1:1:0:60:8:0.3077:0:1 0/0:8:0:0,0:8,0:8,0:0:0,0:21.9:1:31.9:1:1:0:60:16:1:0:0 +5 86628504 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50219;SOR=Inf;LSEQ=TTCAAAACTTTATTTTTTCA;RSEQ=TACAATAATGGTTTTAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:26,102:128,0:0:2,0:25.1:1:32.3:1:1:0:60:63:1:0:0.1 0/1:153:2:1,1:33,116:149,2:0.0131:2,2:13:0:31.5:1:0.40079:3.48:60:4:0.0131:0:1.5 +5 86628891 . G A 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.04824;LSEQ=ACTGCTTATATTTAAAATAT;RSEQ=ATTTTCATAAAAACAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:6,1:4,1:5,7:0.5833:2,2:27.9:1:29:1:1:1.45:55.6:14:0.5833:0:1 1/0:4:3:3,0:1,0:1,3:0.75:0,0:40:1:27.7:1:1:0:60:6:0.75:0:1 +5 86629061 . CT C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.11363;SOR=0.67717;LSEQ=AAAAGACTATCTTTTTAAAT;RSEQ=TTTTTTTTTTATGGTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:40:27,13:179,78:257,40:0.1338:2,2:25.3:1:32.1:1:0.85399:1.10456:60:80:0.1342:0.0234:0.2 0/1:391:37:25,12:229,122:351,37:0.0946:2,2:24.4:1:30:1:0.85707:1.11:60:74:0.0951:0.023:0.1 +5 86633730 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25076;SOR=Inf;LSEQ=TCCTATTTTGTGGTATATGA;RSEQ=TATTCTAATCTCTGTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:118,13:131,0:0:2,0:23.4:1:33:1:1:0:60:262:1:0:0.1 0/1:150:3:1,2:137,10:147,3:0.02:2,2:16:1:26.3:1:0.01692:25.82876:60:6:0.0204:0:1 +5 86633973 . G A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66216;SOR=1.11803;LSEQ=TATAAATTTGGATCTTGTCC;RSEQ=TAATCAGAGAAAGTAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:81:4,77:3,70:73,81:0.526:1,1:22.4:1:30.7:1:1:1.21:59.8:26:0.5166:0:1.1 1/0:186:103:6,97:5,78:83,103:0.5538:2,2:21.3:1:30.4:1:1:1.03614:60:206:0.5538:0:1 +5 86637050 . AT A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.23045;SOR=0;LSEQ=TACGATTTTCATGAATTTTA;RSEQ=AAAAATTGATTAATAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:131,66:197,2:0.0101:2,2:37:1:30:1:1:1.97755:60:4:0.0102:0:0 0/0:215:0:0,0:151,64:215,0:0:2,0:25.1:1:29:1:1:0:60:214:1:0:0.1 +5 86637164 . G GA 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.5355;SOR=1.15412;LSEQ=TTTGTGTTAATTATTAAAAT;RSEQ=AAAAAAAAAATCTATATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:64:25,39:43,84:127,64:0.3137:2,2:29.5:1:30.3:1:0.52342:1.25:60:31:0.31:0:0.1 0/1:220:76:25,51:46,88:134,76:0.3455:2,2:25.3:1:29.4:1:0.88011:1.06607:59.7:37:0.3474:0.0136:0.3 +5 86644898 . T TA 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.12273;SOR=Inf;LSEQ=AAATTTGAAAGAAATTATCT;RSEQ=AAAAAAAAAACAAGTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:38,0:38,0:0:1,0:19:1:31.9:1:1:0:59.7:76:0.9744:0:0.3 0/1:47:4:4,0:43,0:43,4:0.0851:1,0:12:1:29.1:1:1:0:60:8:0.0851:0.0426:0.3 +5 86648120 . T TAC 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAGATAACATACTTGAAGA;RSEQ=ACACACACACACACATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:32.8:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 86648931 . GT G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.25305;SOR=Inf;LSEQ=ATATTTTTAAAGATTTTGCA;RSEQ=TTTATGAGACAGATTAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:167,64:231,0:0:2,0:25.8:1:29.6:1:1:0:60:76:1:0:0 0/1:270:3:2,1:195,71:266,3:0.0111:2,2:24.7:1:28.7:1:1:1.37151:60:6:0.0113:0:0 +5 86649101 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.10498;SOR=0;LSEQ=TTAGCATTTTATTTTAAAAT;RSEQ=CATTTTGGTGGTATGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:2,1:44,146:190,3:0.0155:2,2:12:1:28.7:1:0.14185:6.55:60:6:0.0156:0:1 0/0:215:0:0,0:54,161:215,0:0:2,0:23:1:30.8:1:1:0:59.9:70.667:1:0:0.1 +5 86649123 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49988;SOR=Inf;LSEQ=ATTTTGGTGGTATGTTTTTG;RSEQ=ACACATTTGTACAATTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:12,99:111,0:0:2,0:23.6:1:32.2:1:1:0:59.7:222:1:0:0.1 0/1:127:2:0,2:10,113:123,2:0.0157:2,0:38.5:1:27:1:1:0:60:4:0.0161:0:1 +5 86658548 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49892;SOR=0;LSEQ=CGTTGTAAATATGGAGCTCC;RSEQ=AACTTATTGTGATATATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:38,144:182,2:0.0108:2,2:19:1:32:1:0.3799:3.75:60:4:0.011:0:1.5 0/0:176:0:0,0:38,138:176,0:0:2,0:22:1:30:1:1:0:60:43:1:0:0.1 +5 86658723 . CT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTTTCTTTCTTTCTTT;RSEQ=TTTTTTTTTTTGAGGAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:1,8:9,2:0.1818:2,0:49:1:33.5:1:1:0:60:4:0.1818:0:0 0/0:2:0:0,0:0,2:2,0:0:0,0:17.5:1:30.5:1:1:0:60:4:1:0:0 +5 86659147 . A AT 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.24331;SOR=0.66581;LSEQ=TGTTTGGCTAAGAGAAAACA;RSEQ=TTTTTTTTTTTAAACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:22:18,4:200,46:246,22:0.0818:2,2:24.7:1:31.6:1:1:1.03:60:44:0.0833:0.0037:0.1 0/1:286:16:14,2:208,61:269,16:0.0559:2,2:28.8:1:30.3:1:0.53625:2.05:60:15:0.0534:0.0105:0.2 +5 86659159 . A T 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01266;SOR=0;LSEQ=AGAAAACAATTTTTTTTTTT;RSEQ=AACAGGCAAAGGAAAACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:6:5,1:247,79:326,6:0.0181:2,2:23.2:1:27.2:1:1:1.60:59.7:5:0.0156:0:2 0/0:353:0:0,0:259,94:353,0:0:2,0:24.4:1:27.9:1:1:0:59.9:69.6:1:0:0.2 +5 86665476 . CT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.4958;SOR=0;LSEQ=TCTAAAATATATATAGCTGA;RSEQ=TTTTTTTAGTAATGATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:17,1:18,2:0.1:1,0:33:1:33.5:1:1:0:60:4:0.1:0:0.5 0/0:15:0:0,0:15,0:15,0:0:1,0:19.8:1:31.1:1:1:0:60:30:1:0:0 +5 86665775 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.221;SOR=0;LSEQ=TGTTAGCCCATGTTTTCTTA;RSEQ=TAACTGGAATAGAAAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:35,164:199,2:0.01:2,2:9.5:1:29:1:0.32687:4.63:60:4:0.01:0:1 0/0:226:0:0,0:51,173:224,0:0:2,0:25:1:29.4:1:1:0:60:111:0.9955:0:0 +5 86667856 . G GA 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.29362;SOR=1.2931;LSEQ=AGGAAAAAATTGTTGAATTT;RSEQ=AAAAAAAAAACCTAACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:151:98:89,9:19,2:21,98:0.649:2,2:28.3:1:30.7:1:1:1.04:60:196:0.6533:0:0.3 1/0:190:134:114,20:21,2:23,134:0.7053:2,2:28.7:1:28.6:1:0.74426:1.83593:59.8:21.333:0.7191:0:0.3 +5 86667872 . C T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07373;SOR=Inf;LSEQ=ATTTGAAAAAAAAAACCTAA;RSEQ=TGATGATTTGGAAGCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:203,58:261,0:0:2,0:21.9:1:31.3:1:1:0:59.7:15.313:1:0:0.2 0/1:347:5:2,3:252,89:341,5:0.0144:2,2:11.2:1:21.2:1:0.11943:4.22565:60:1.5:0.0092:0:1.8 +5 86670546 . G GT 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.46504;SOR=1.49135;LSEQ=GGTTTTAGGTCTAGCACACT;RSEQ=TTTTTTTTTTTAAAGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:8:7,1:97,5:102,8:0.0714:1,2:18.5:1:29.9:1:0.37132:2.73406:58.1:7:0.0642:0.0357:0.4 0/1:97:10:10,0:83,3:86,10:0.1031:1,0:29.3:1:29.7:1:1:0:60:20:0.1042:0.0103:0.5 +5 86670582 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24861;SOR=Inf;LSEQ=CAGAAATAGGGGGTTTATTT;RSEQ=ATACTAGAACTAAAGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:169,60:229,0:0:2,0:22.3:1:31.4:1:1:0:59.9:21.9:1:0:0.1 0/1:237:3:2,1:163,70:233,3:0.0127:2,2:20.7:1:22.7:1:1:1.1635:60:2:0.0088:0:1 +5 86670643 . C G 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTTGTTAATTCTTTTTCT;RSEQ=CTTGCTCCTTTAGTGATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:0:0,0:268,234:502,0:0:2,0:25.7:1:31.7:1:1:0:60:54.778:1:0:0.1 0/1:652:28:15,13:333,289:622,28:0.0429:2,2:27.1:1:30.9:1:1:1.00:60:56:0.0433:0:1.1 +5 86672192 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49975;SOR=Inf;LSEQ=CTCTTTTTAAACAATAATTG;RSEQ=TTGTTTTTCTTCCCAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:130,36:166,0:0:2,0:23.9:1:32.5:1:1:0:60:54.333:1:0:0.1 0/1:183:2:1,1:137,44:181,2:0.0109:2,2:31.5:1:29:1:0.43235:3.08982:60:4:0.0112:0:1 +5 86675708 . T A 45 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10966;SOR=Inf;LSEQ=TTGACAAGAAATTGTGTATC;RSEQ=ATGTCTTCAGAAATTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:31,140:171,0:0:2,0:21.5:1:29:1:1:0:60:84.5:1:0:0 0/1:158:3:2,1:29,126:155,3:0.019:2,2:6:1:29:1:0.09853:8.52:60:6:0.0196:0:1 +5 86676220 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23458;SOR=Inf;LSEQ=ACTTTTTTGGGTAAAAGGCC;RSEQ=GTTTTATTGAACTGTGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:104,3:107,0:0:1,0:25.5:1:30.8:1:1:0:60:214:1:0:0 0/1:101:2:2,0:94,5:99,2:0.0198:2,0:17.5:1:27.5:1:1:0:60:4:0.0198:0:1 +5 86679466 . T C 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05073;SOR=Inf;LSEQ=TTCTGTTTATATATATTGTT;RSEQ=TAATGTAACACATTATATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:79,9:88,0:0:2,0:21.5:1:31.3:1:1:0:59.1:87:1:0:1.1 0/1:81:4:4,0:69,8:77,4:0.0494:2,0:10.3:1:32:1:1:0:58.3:8:0.05:0:3.3 +5 86679617 . T A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09014;SOR=0;LSEQ=GGTAATCAGCTTTTGATACA;RSEQ=TTTGAAATTCAAAATATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:2,1:104,185:289,3:0.0103:2,2:8:1:21.3:1:0.29901:3.54:55.7:2:0.0069:0:3.3 0/0:358:0:0,0:142,215:357,0:0:2,0:25.3:1:29.3:1:1:0:60:177.5:0.9972:0:0.1 +5 86681045 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24641;SOR=Inf;LSEQ=CAGTAAAGAAATATTAAAGT;RSEQ=CTAAATTTATAATGGTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:144,31:175,0:0:2,0:24.5:1:32:1:1:0:60:86.5:1:0:0.1 0/1:173:2:1,1:142,29:171,2:0.0116:2,2:31:1:27.5:1:0.31758:4.83125:60:4:0.0116:0:1 +5 86682545 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=ATTTGGTGCAATAGTAATTG;RSEQ=AGTTTTTGCTGTTAACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:131,6:137,0:0:1,0:23.5:1:32.6:1:1:0:59.8:136:1:0:0.1 0/1:140:2:2,0:127,11:138,2:0.0143:2,0:35.5:1:31:0:1:0:60:4:0.0146:0:1 +5 86682803 . A G 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22187;SOR=Inf;LSEQ=ATTTAAGCAGCAATCTTTAG;RSEQ=AAGATTTTCTATCCAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:4,101:105,0:0:1,0:25.7:1:31.3:1:1:0:60:104:1:0:0.1 0/1:94:2:1,1:7,85:92,2:0.0213:2,2:13:0:28.5:1:0.16381:11.43:60:4:0.0213:0:1.5 +5 86685123 . GG AA 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50453;SOR=Inf;LSEQ=ATGCCATTGCATTTCAGCCT;RSEQ=GCAACAAGAGCGAAACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:77,8:85,0:0:2,0:27.6:1:32.1:1:1:0:53.7:41.5:1:0:0.1 0/1:108:2:1,1:100,6:106,2:0.0185:2,2:8.5:1:27.5:1:0.126:15.50458:60:4:0.0185:0.0093:0.5 +5 86685148 . C CA 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.19061;SOR=0;LSEQ=ACAAGAGCGAAACTCTGTCT;RSEQ=AAAAAAAACAAAAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:149,44:193,2:0.0103:2,2:15.5:1:28.5:1:0.4092:3.35969:44:4:0.0105:0:0 0/0:251:0:0,0:195,56:251,0:0:2,0:20.2:1:30.6:1:1:0:58:124.5:1:0:0.1 +5 86685157 . C CA 79 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.15031;SOR=0.2744;LSEQ=AAACTCTGTCTCAAAAAAAA;RSEQ=AAAAAAAAAGAAGATTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:6:4,2:204,63:267,6:0.022:2,2:22:1:30.7:1:0.63068:1.61586:60:12:0.0221:0.0037:0.2 0/0:327:2:2,0:233,91:324,2:0.0061:2,0:16:1:27.5:1:1:0:52:4:0.0062:0:0 +5 86686570 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12224;SOR=Inf;LSEQ=CAGGTTCCCATCCTGAAATT;RSEQ=CTGACCGAGCTTTCATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:205,66:271,0:0:2,0:23.5:1:32.5:1:1:0:60:134.5:1:0:0.1 0/1:269:3:2,1:190,76:266,3:0.0112:2,2:24.3:1:29.3:1:1:1.24896:60:6:0.0112:0:1 +5 86686797 . A G 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24612;SOR=Inf;LSEQ=CTCTTGCCAAAAAATAGCAC;RSEQ=CTTTTCCACATTCCAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:2,89:91,0:0:1,0:23.3:1:30:1:1:0:59.6:29.333:1:0:0.1 0/1:94:3:0,3:4,87:91,3:0.0319:1,0:16.3:1:33:0:1:0:60:6:0.0319:0:1.3 +5 87428845 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49882;SOR=0;LSEQ=CAACAGTAACCGAATTGTAG;RSEQ=ACCTCAGCATTTACTAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:110,51:161,2:0.0123:2,2:17.5:1:30:1:0.53761:2.14575:60:4:0.0124:0:1 0/0:154:0:0,0:102,51:153,0:0:2,0:21.7:1:31:1:1:0:59.8:152:0.9935:0:0.2 +5 87428853 . C T 35 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6794;SOR=1.5723;LSEQ=ACCGAATTGTAGCACCTCAG;RSEQ=ATTTACTAGATGTTACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:121,70:191,2:0.0104:2,2:27.5:1:28:1:1:1.72335:60:4:0.0104:0:1 0/1:185:3:0,3:120,62:182,3:0.0162:2,0:1:0:22.7:1:0.04207:0:60:6:0.0163:0:1 +5 87428855 . TTTACTAGATG T 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00148;SOR=Inf;LSEQ=CGAATTGTAGCACCTCAGCA;RSEQ=TTACTAGATGTTACTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:129,76:205,0:0:2,0:23.8:1:30.4:1:1:0:60:50.25:1:0:0.1 0/1:197:9:5,4:119,69:188,9:0.0457:2,2:26:1:29.7:1:0.72853:1.37734:60:18:0.0464:0.0051:0.1 +5 87428894 . CTGT C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.17362;SOR=1.99632;LSEQ=TGTTACTGCTGCTGTTGCTG;RSEQ=TGTTGTTGTTGTTGCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:7:4,3:157,154:311,7:0.022:2,2:23.1:1:32.4:1:1:1.31:60:14:0.0224:0:0.1 0/1:302:13:8,5:143,145:288,13:0.043:2,2:29.6:1:31.3:1:0.57249:1.62:60:26:0.0433:0:0.1 +5 87428897 . T C 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TACTGCTGCTGTTGCTGCTG;RSEQ=TGTTGTTGTTGTTGCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:152,157:309,0:0:2,0:28.3:1:30:1:1:0:60:153.5:1:0:0.1 0/1:306:28:14,14:130,135:265,28:0.0915:2,2:25.8:1:31.5:1:1:1.04:58.1:56:0.0969:0:1.9 +5 87428912 . C T 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTGTTGTTGTTGTTGTTG;RSEQ=TTAAATTGAAGTATAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:137,170:307,0:0:2,0:26.9:1:32.7:1:1:0:60:75.75:1:0:0.1 0/1:299:23:10,13:123,153:276,23:0.0769:2,2:24.6:1:29.8:1:1:1.04495:57.7:46:0.0769:0:2.1 +5 87428969 . C A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51181;SOR=0;LSEQ=GGGTTAGAGACACCAGCCTC;RSEQ=CAGGCAGTTGAAAATTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:24,103:127,2:0.0155:2,2:6:1:29:1:0.35126:4.23:60:4:0.0156:0:1.5 0/0:92:0:0,0:17,75:92,0:0:2,0:20.9:1:30.7:1:1:0:60:91:1:0:0.2 +5 87429684 . AG GA 27 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GAAAGAAAGAAAGAAAGAAA;RSEQ=AAAGAAAAAGAAAGAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:5.5:1:27.3:1:1:0:42.5:4:0.6667:0:1 +5 87898719 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49648;SOR=Inf;LSEQ=GCTTCATTGTTACAGGCCTC;RSEQ=TAGTGAGGCACGATTCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:19,13:32,0:0:2,0:22.9:1:30.5:1:1:0:58.9:64:1:0:0.1 0/1:38:2:1,1:22,14:36,2:0.0526:2,2:18:1:28:1:1:1.55221:60:4:0.0556:0:1 +5 87898886 . A T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24854;SOR=Inf;LSEQ=CACCCACCTGTGTGCTATCC;RSEQ=TGCCAAACGTGTAACAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:138,78:216,0:0:2,0:24.1:1:30.6:1:1:0:43.8:107:1:0:0 0/1:224:3:1,2:133,88:221,3:0.0134:2,2:27:1:29:1:0.56608:3.00765:28.7:6:0.0135:0:1 +5 87898888 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24851;SOR=Inf;LSEQ=CCCACCTGTGTGCTATCCAT;RSEQ=CCAAACGTGTAACAATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:139,82:221,0:0:2,0:24.1:1:32.2:1:1:0:44.2:109.5:1:0:0 0/1:228:3:2,1:131,94:225,3:0.0132:2,2:23.7:1:29.3:1:1:1.43:47.3:6:0.0133:0:1 +5 87898894 . C T 48 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62399;SOR=2.86158;LSEQ=TGTGTGCTATCCATGCCAAA;RSEQ=GTGTAACAATTATGCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:1:0,1:141,96:237,1:0.0042:2,0:1:0:25:0:0.40756:0:60:2:0.0043:0:1 0/1:251:3:2,1:137,111:248,3:0.012:2,2:5.7:1:30.3:1:1:1.62:49.7:6:0.0121:0:1.3 +5 87898981 . G A 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2418;SOR=Inf;LSEQ=GCTTAAAAATCCACTATGAT;RSEQ=GGAAACATTTCATTCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:43,126:169,0:0:2,0:22:1:31.2:1:1:0:60:83.5:1:0:0.1 0/1:164:2:0,2:43,119:162,2:0.0122:2,0:5:1:30.5:1:1:0:60:4:0.0125:0:1 +5 87898997 . T TA 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.33276;SOR=3.64487;LSEQ=TGATGGGAAACATTTCATTC;RSEQ=AAAAAAAAATTATCTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:1:0,1:18,92:110,1:0.009:2,0:13:0:33:0:1:0:60:2:0.0092:0:0 0/1:93:3:1,2:15,75:90,3:0.0323:2,2:29.3:1:29:1:0.43629:2.47:60:6:0.0326:0.0108:0.3 +5 87899069 . C T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.14144;SOR=0;LSEQ=TTCTCCCCGCCCGCCCCCTC;RSEQ=CCCGGCCCCATGGGGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:0,5:1,22:23,5:0.1786:1,0:26.4:1:31:1:1:0:60:10:0.1786:0:1.4 0/0:16:0:0,0:1,15:16,0:0:1,0:17.7:1:30.3:1:1:0:60:32:1:0:0.1 +5 88100495 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52533;SOR=Inf;LSEQ=AAGCACTTTGTCCATGTCGG;RSEQ=GCTGGCATACTGGAACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:74,35:109,0:0:2,0:24.9:1:30.2:1:1:0:60:218:1:0:0.1 0/1:175:2:1,1:117,56:173,2:0.0114:2,2:21.5:1:29:1:0.5466:2.07976:60:4:0.0115:0:1 +5 88100578 . G C 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06675;SOR=0;LSEQ=ACAGCACGCTCAGCTCATAA;RSEQ=CCTTCTTCATCAACCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:3:1,2:69,101:170,3:0.0173:2,2:39.3:1:25.3:1:1:1.36396:60:2:0.0118:0:2.7 0/0:252:0:0,0:105,147:252,0:0:2,0:26.9:1:31:1:1:0:59.9:49.4:1:0:0.1 +5 88100618 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50749;SOR=Inf;LSEQ=TTTCCTCTTTGTAAATGTCA;RSEQ=CTAGAAAAAAGAAAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:36,74:110,0:0:2,0:24.4:1:31.6:1:1:0:60:220:1:0:0.2 0/1:145:2:1,1:35,108:143,2:0.0138:2,2:16.5:1:29.5:1:0.43621:3.06:60:4:0.0144:0:1 +5 88365778 . G A 201 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTATTGTCTTTAGCTTCA;RSEQ=TTTTGTTTTCTTTTCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:0:0,0:188,248:436,0:0:2,0:26.7:1:32.6:1:1:0:60:86.2:1:0:0.1 0/1:530:113:48,65:192,225:417,113:0.2132:2,2:26.9:1:29.6:1:0.524:1.15524:60:55.5:0.2114:0:1.2 +5 88365829 . CA C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09651;SOR=0.42815;LSEQ=CATCTCATCAGATTGACATG;RSEQ=AAAAAAAAGTCTAAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:12:2,10:57,145:202,12:0.055:2,2:27.3:1:32.6:1:0.51796:1.9602:60:24:0.0563:0.0046:0.1 0/1:247:6:2,4:72,169:241,6:0.0243:2,2:37.7:1:31:1:1:1.17:60:12:0.0246:0:0.3 +5 93018816 . AT A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52457;SOR=Inf;LSEQ=TTCTGATTTGACTTTTGTGC;RSEQ=TTTTGGCTGGAGTATCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:30,25:55,0:0:2,0:14:1:30.6:1:1:0:25.9:110:1:0:0.1 0/1:89:2:1,1:41,46:87,2:0.0225:2,2:22.5:1:32:0:1:1.12:25:4:0.023:0:1 +5 93019147 . T TA 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5249;SOR=Inf;LSEQ=AGACCACTGGTGGTGTTATT;RSEQ=CAAAGCCCCCAAGGGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:44,54:98,0:0:2,0:34.8:1:30.8:1:1:0:21.9:97:1:0:0.1 0/1:157:2:1,1:63,92:155,2:0.0127:2,2:39:0:29:0:1:1.46:32:4:0.0129:0:0.5 +5 93019388 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31455;LSEQ=AAAAGATAGTTCTGGGGCCT;RSEQ=AGGGGGCTCATGTCCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:1:1,0:42,12:54,1:0.0182:2,0:1:0:14:0:1:0:41:0:0:0:6 0/1:84:2:1,1:59,23:82,2:0.0238:2,2:44.5:1:30:0:0.49225:2.53241:28:4:0.0244:0:1 +5 93019512 . C A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02124;SOR=0;LSEQ=AGCCGCGCAGGACGGAATCA;RSEQ=ACCAGGCAAAAAGTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:4:3,1:121,239:360,4:0.011:2,2:15:1:27.5:1:0.11649:5.90:34.3:8:0.0114:0:1 0/0:587:0:0,0:202,384:586,0:0:2,0:19.9:1:30.8:1:1:0:48.5:40.857:0.9983:0:0.3 +5 93019525 . G GT 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.29852;SOR=0.69302;LSEQ=GGAATCACACCAGGCAAAAA;RSEQ=TTTTTTTTTTAAAGATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:17:3,14:54,153:207,17:0.0756:2,2:26.3:1:29.4:1:0.57043:1.64378:59.8:34:0.0762:0.0089:0.6 0/1:392:21:2,19:93,275:368,21:0.0536:2,2:26.6:1:29.6:1:0.12167:3.20591:57.6:42:0.0544:0.0026:0.6 +5 93019536 . A T 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34355;SOR=0.48641;LSEQ=AGGCAAAAAGTTTTTTTTTT;RSEQ=AAGATATATATTTTGAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:6:2,4:24,145:169,6:0.0343:2,2:12:1:28:1:0.21837:2.99:55.5:12:0.0343:0:1.5 0/1:295:5:0,5:48,242:290,5:0.0169:2,0:12.2:1:28.6:1:1:0:53.4:10:0.0169:0:1.2 +5 93019574 . T C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGAGATGAAAATGAATTC;RSEQ=TTTTAAGATGTAAAAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:83:83:0,83:0,0:0,83:1:0,1:25.8:1:33.5:1:1:0:60:82:1:0:1.1 1/1:131:131:2,129:0,0:0,131:1:0,1:23.8:1:32.3:1:1:0:60:262:1:0:1.1 +5 93019685 . TTTAA T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.63287;SOR=0.52218;LSEQ=TTGTCAATGTTATTAATTAC;RSEQ=TTATGTCTAGTACTTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:39.2:1:30.4:1:1:0:60:10:0.5:0:0.2 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:19:1:30:1:1:0:60:4:0.3333:0.1667:0 +5 93537742 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48485;SOR=0;LSEQ=TAAGATAATCAGATATTAAA;RSEQ=ATAGGGGGTTCTGGCTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:13,2:15,2:0.1176:2,2:15:1:26.5:1:0.33088:5.50762:60:4:0.1176:0:1 0/0:16:0:0,0:13,3:16,0:0:2,0:19.3:1:31.9:1:1:0:60:32:1:0:0.1 +5 96383427 . CA AG 34 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCAGAGGAGGATGTTTC;RSEQ=CTTAAAAATCCCACAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:22.5:1:34:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:25:0:32:0:1:0:60:2:1:0:0 +5 96383496 . C T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60784;SOR=2.28225;LSEQ=TTATGGCATGTGTCAACCTG;RSEQ=GTCCTCCTGTGGGATCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:20.8:1:30.8:1:1:0:60:10:0.3846:0:1.2 1/0:5:3:3,0:2,0:2,3:0.6:0,0:23.7:1:29.3:1:1:0:60:6:0.6:0:1 +5 96383670 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25098;SOR=Inf;LSEQ=ACTAAACCTCAGTGAAGAGT;RSEQ=CATGTCCTTAGGTGGATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:147,80:227,0:0:2,0:23.2:1:31.9:1:1:0:60:55.75:1:0:0.3 0/1:255:3:1,2:173,79:252,3:0.0118:2,2:22.7:1:27.3:1:0.23766:4.35166:60:6:0.0119:0:1.3 +5 96383752 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.52222;SOR=0.9047;LSEQ=TTACACACAGAAGCATTCGC;RSEQ=GAGAGTAGAAAGAGTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:183:76,107:84,114:198,183:0.4791:2,2:26:1:30.4:1:0.91732:1.03731:60:182:0.4802:0:1.1 0/1:414:188:84,104:105,121:226,188:0.4541:2,2:24.1:1:29.5:1:0.76645:1.07419:60:93:0.4559:0:1.1 +5 96383880 . T A 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5056;SOR=0.72143;LSEQ=CTCCCTCAAAGATGTCCATG;RSEQ=CCTAATCCCTGGAACCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:28:1,27:2,16:18,28:0.6087:2,1:23:1:30.5:1:0.55178:3.28381:60:56:0.6087:0:1.1 1/0:36:19:3,16:0,17:17,19:0.5278:1,2:17.1:1:27.8:1:0.23095:0:60:38:0.5278:0:1 +5 97303829 . C A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10657;SOR=Inf;LSEQ=AATTCATTGTGGTAAAATTA;RSEQ=TCAAGGGACTAAACTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:168,157:325,0:0:2,0:26:1:32.5:1:1:0:60:80.25:1:0:0.2 0/1:294:3:2,1:143,148:291,3:0.0102:2,2:23.3:1:23.7:1:0.61864:2.06:60:2:0.0069:0:2.3 +5 97303834 . G T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=27.04848;LSEQ=ATTGTGGTAAAATTACTCAA;RSEQ=GGACTAAACTCAGAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:14:9,5:156,158:314,14:0.0427:2,2:29.1:1:30.1:1:0.41377:1.82:60:13:0.0402:0:1.6 1/0:292:160:76,84:66,64:130,160:0.5479:2,2:27.4:1:29.9:1:0.63694:1.13929:60:159:0.5502:0:1.1 +5 98004209 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GAGAACCACAAGAGGAAGAT;RSEQ=ACCCCTCACCCCCAGCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:30.1:1:31.5:1:1:0:60:16:1:0:0.1 0/1:8:2:1,1:4,2:6,2:0.25:2,2:42.5:1:29.5:1:1:1.8258:60:4:0.25:0:1 +5 98004831 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTAGAGGGAGGGATGGTC;RSEQ=CAGTCTCTCTGCACCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:19:1:32:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 98005437 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02601;SOR=0;LSEQ=ACAATGTCTCTCCATGAAGG;RSEQ=CGCAGAACAACAGGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:2,2:2,3:5,4:0.4444:2,2:38.8:1:31.3:1:1:1.43:60:8:0.4444:0:1 0/0:11:0:0,0:3,8:11,0:0:2,0:25.9:1:31.4:1:1:0:57.4:22:1:0:0.1 +5 101265568 . A C 73 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8165;LSEQ=TAGTCATACAAATATCTACT;RSEQ=GTCTACTCATCTGGAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:38.8:1:31.6:1:1:0:60:10:0.5556:0:1.2 1/0:2:1:1,0:1,0:1,1:0.5:0,0:32:0:32:0:1:0:60:2:0.5:0:1 +5 101265670 . T C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10922;SOR=Inf;LSEQ=GCCTTGAGGAATGAAAAAAA;RSEQ=ACAATAATTTAAAGCCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:24,0:0:1,0:24:1:31.5:1:1:0:59.3:23:1:0:0 0/1:23:3:3,0:19,1:20,3:0.1304:1,0:11.7:1:32.3:1:1:0:60:6:0.1304:0:1.3 +5 101265723 . AT A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=TTTAAAATGCAGACTTCAAC;RSEQ=TTTTGTAGGTAATAGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:52,2:54,2:0.0357:1,2:13.5:1:31.5:1:0.10519:21.43217:60:4:0.0364:0.0179:0.5 0/0:72:0:0,0:67,5:72,0:0:2,0:25.7:1:30.2:1:1:0:60:144:1:0:0.1 +5 101265865 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.35324;SOR=0.82984;LSEQ=GACAGGATTACATTTTATAA;RSEQ=TTTCAATAAACCTCCTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:89:47,42:65,72:137,89:0.3938:2,2:27.9:1:30.7:1:0.49632:1.24:60:88:0.3929:0:1.3 0/1:277:97:37,60:77,103:180,97:0.3502:2,2:27.8:1:29.6:1:0.52251:1.21144:59.9:194:0.3514:0:1.5 +5 101265926 . C A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.90118;SOR=0.96012;LSEQ=CTTAGTTATATGATCAAGAG;RSEQ=ATTAACGCTTCAGTATCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:50:12,38:24,56:80,50:0.3846:2,2:21.9:1:30.5:1:0.54726:1.354:60:100:0.3846:0:1.6 0/1:144:54:18,36:23,67:90,54:0.375:2,2:25.1:1:29.9:1:0.34427:1.45:59.9:53:0.3732:0:1.6 +5 110749262 . A G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGCCTGGGTGACAGAGC;RSEQ=ACACTCCATCTCAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:32:1:1:0:39:4:1:0:2.5 +5 110749264 . C G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTGGGTGACAGAGCAA;RSEQ=ACTCCATCTCAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:33:1:1:0:39:4:1:0:2.5 +5 110750079 . TCAG T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.24822;SOR=Inf;LSEQ=TTTCCCCACTTCTCCACCTC;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:30,20:50,0:0:2,0:25.5:1:31.7:1:1:0:59.6:100:1:0:0.2 0/1:59:3:1,2:26,30:56,3:0.0508:2,2:38:1:30.7:1:1:1.71787:60:6:0.0517:0:0 +5 110750082 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.20885;SOR=0;LSEQ=CCCCACTTCTCCACCTCTCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:29,20:49,2:0.0392:2,2:39.5:1:32:1:1:1.43922:60:4:0.04:0:1 0/0:60:0:0,0:27,30:57,0:0:2,0:26.4:1:30.3:1:1:0:58.9:27.5:1:0:0.2 +5 110858691 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTGTTGGGATTACAGGC;RSEQ=TGAGCCACTGCAGCATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:30:1:1:0:56:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 111982886 . A G 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84735;LSEQ=TCATCAATTCTATGGCTTAG;RSEQ=TTAGCCAGTGATAGCTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:7:7,0:45,0:45,7:0.1346:1,0:19.7:1:32.3:1:1:0:60:14:0.1346:0:1 0/1:43:5:5,0:38,0:38,5:0.1163:1,0:29.6:1:29.4:1:1:0:60:10:0.119:0:1.4 +5 111982962 . TA T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.11525;SOR=0.52987;LSEQ=TTTATTTCATTTCCATTCCT;RSEQ=AAAAAAAAATACGATGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:16:13,3:140,37:177,16:0.0829:2,2:21.3:1:31:1:1:1.14:60:32:0.0829:0.0155:0.3 0/1:241:11:7,4:160,69:229,11:0.0456:2,2:30.5:1:28.8:1:0.73945:1.32346:60:22:0.0462:0:0.6 +5 111982982 . A T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07872;SOR=0;LSEQ=TAAAAAAAAAATACGATGAT;RSEQ=TAATTAGAGAACTTGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:1,2:175,75:250,3:0.0119:2,2:15:1:23.7:1:0.22051:4.63465:60:2:0.0082:0:2.3 0/0:336:0:0,0:217,119:336,0:0:2,0:22:0:15:0:1:0:60:0:0:0:3 +5 111983041 . C A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31038;SOR=1.14165;LSEQ=GATTTTTCAGGATAAGCAGA;RSEQ=ATACTCTCCACCTCCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:194:102,92:120,113:233,194:0.4501:2,2:26.8:1:30.5:1:0.84616:1.04:60:31.333:0.4476:0:1.1 0/1:592:286:147,139:153,152:305,286:0.4831:2,2:26.1:1:29.7:1:0.80504:1.05:59.9:94.333:0.4838:0:1.2 +5 111983052 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45203;SOR=0.90957;LSEQ=ATAAGCAGACATACTCTCCA;RSEQ=CTCCTAAAACAGCCCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:443:232:118,114:100,109:209,232:0.5237:2,2:26.9:1:29.9:1:0.56745:1.13:60:24.778:0.5174:0:1.2 1/0:594:297:145,152:146,151:297,297:0.5:2,2:26.4:1:28.8:1:1:1.01354:60:41.429:0.4966:0:1.1 +5 111983180 . T C 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00091;SOR=Inf;LSEQ=TAGTCTTACTCCTATCAAAG;RSEQ=CTTCTATAAGCCAGCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:0,72:72,0:0:1,0:26:1:30.5:1:1:0:59.9:144:1:0:0.1 0/1:55:8:0,8:2,45:47,8:0.1455:1,0:27.1:1:30.9:1:1:0:60:16:0.1455:0:1.3 +5 112043072 . A G 42 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCGGCTGCCTAGGCAGCA;RSEQ=TGGCTCACGGGACAGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:27.7:1:27:1:1:0:60:2:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 112043282 . CG GT 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.00523;SOR=0;LSEQ=CCGGAAGCCTAGCCGCTGCT;RSEQ=GGGGGGACCTGCGGGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:10:9,1:76,0:76,10:0.1163:1,2:26.3:1:31.7:1:0.11628:0:60:20:0.119:0:1 0/0:63:0:0,0:44,1:45,0:0:1,0:27.6:1:30.9:1:1:0:60:90:0.7258:0:0.1 +5 112043384 . T G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00145;SOR=1.96759;LSEQ=TGGTGAGGAAGGTGAAGCAC;RSEQ=CAGTTGCCTTCTCGGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:35:27,8:326,178:504,35:0.0648:2,2:25.5:1:29.8:1:0.14571:1.84:60:70:0.0659:0:1.1 0/1:658:79:53,26:351,226:577,79:0.1201:2,2:21.7:1:29.9:1:0.32445:1.31:59.9:158:0.1219:0:1.1 +5 112043548 . G A 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18419;SOR=0.20872;LSEQ=GAAGAGCCCGGGCGGCGCTC;RSEQ=TACTTCTGGCCACTGGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:4:3,1:125,271:396,4:0.01:2,2:22:1:25.8:1:0.09852:6.47:60:3:0.0077:0:1.3 0/0:476:1:1,0:174,301:475,1:0.0021:2,0:1:0:23:0:0.36765:0:60:2:0.0021:0:1 +5 112043635 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49787;SOR=0;LSEQ=GCAAAGCTTCCTCGGCTTTG;RSEQ=CCCGCCGCTGCTCGGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:0,2:23,92:115,2:0.0171:2,0:31:1:29.5:1:1:0:60:4:0.0174:0:1 0/0:115:0:0,0:21,94:115,0:0:2,0:23:1:30.6:1:1:0:60:114:1:0:0.1 +5 112089282 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTTCAACCAAAGACTT;RSEQ=TGTAGGTGATCCCTGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:0:32:1:1:0:60:4:1:0:1 +5 112090379 . CT C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATTTCATTTATCTTGAA;RSEQ=AAGACTCCACTGTTTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:3,0:16,0:16,3:0.1579:1,0:42.3:1:33:1:1:0:60:6:0.1579:0:0 0/0:2:0:0,0:2,0:2,0:0:0,0:16.5:1:32:0:1:0:41.5:4:1:0:0 +5 112090779 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49828;SOR=0;LSEQ=TTTTTATTCAGTATTCCCTC;RSEQ=TGTAAACTTGAGGTAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:17,116:133,2:0.0148:2,2:8:1:29:1:0.24975:6.66:60:4:0.0149:0:1 0/0:130:0:0,0:17,113:130,0:0:2,0:23.6:1:29.4:1:1:0:60:64:1:0:0 +5 112101793 . C A 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22797;SOR=Inf;LSEQ=AATGTATCTTAAATGTGTTT;RSEQ=TAATACCTTGCACAGAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:24.6:1:29.6:1:1:0:60:10:0.5556:0:1 1/1:4:4:3,1:0,0:0,4:1:0,2:17.5:1:28.3:1:1:0:60:8:1:0:1 +5 112101970 . T C 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=TGTCAAGAAATACAGAATCA;RSEQ=GTCTTGAAGTTATTTAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:206,56:262,0:0:2,0:23.9:1:30.8:1:1:0:60:51.4:1:0:0.1 0/1:277:14:10,4:190,73:263,14:0.0505:2,2:23.1:1:30:1:1:1.04095:60:28:0.0507:0:1.1 +5 112111070 . G A 27 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATATGAAGAAAGCCTTT;RSEQ=GTGAAGTGTAAGTATTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23.5:1:27.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:44:0:27:0:1:0:60:2:1:0:1 +5 112111450 . G A 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66133;SOR=0.54004;LSEQ=AAAATGTAAGTAACTTGGCA;RSEQ=TACAACTTATTTGAAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:3:2,1:84,196:280,3:0.0106:2,2:16.7:1:28.3:1:0.22003:4.64:60:6:0.0108:0:1 0/0:348:2:2,0:115,231:346,2:0.0057:2,0:1:0:25.5:1:0.11239:0:60:4:0.0058:0:1 +5 112116436 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12146;SOR=Inf;LSEQ=TATGCTTTTTTGCTTTTACT;RSEQ=ATTAACGTAAATACAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:130,29:159,0:0:2,0:25.6:1:32.2:1:1:0:60:78.5:1:0:0.1 0/1:157:3:1,2:117,37:154,3:0.0191:2,2:13.7:1:27.7:1:0.15264:6.23153:60:6:0.0192:0:1.3 +5 112116632 . C T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02232;SOR=2.05182;LSEQ=GTTTCTAAGTGATAAAACAG;RSEQ=GAAGAGCTATTAGGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:17:5,12:46,146:192,17:0.081:2,2:22.4:1:30.2:1:0.56857:1.32:60:34:0.0821:0:1 0/1:261:40:12,28:64,156:220,40:0.1533:2,2:23.9:1:29.2:1:1:1.04:60:80:0.1538:0:1.1 +5 112116773 . A G 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66992;SOR=0.49289;LSEQ=GCAACATAATCAATATTCAC;RSEQ=TAGTTGTGTCTTTACCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:5,7:0.5833:0,0:19.1:1:32.4:1:1:0:60:14:0.5833:0:1 0/1:10:4:0,4:0,6:6,4:0.4:0,0:17.5:1:31:1:1:0:60:8:0.4:0:1 +5 112151551 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGAGGCATGAGAATAGTT;RSEQ=GAACCCAGGAGGCAGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:30:1:27.5:1:1:0:59.5:4:0.5:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:30:0:26:0:1:0:60:2:1:0:0 +5 112154544 . C CG 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.39477;SOR=0.66918;LSEQ=GTTTTTTGTTTTTTTTTTGG;RSEQ=GGGGGGGGTTGTTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:18:18,0:28,1:29,18:0.3158:1,1:28.9:1:28.9:1:1:0:59.2:36:0.375:0.0526:0.8 0/1:51:12:12,0:31,0:31,12:0.2353:1,0:20.1:1:24.8:1:1:0:59.3:5:0.2439:0.0588:0.9 +5 112154571 . G C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.60529;SOR=1.40767;LSEQ=GGTTGTTTTGTTTTTTTAGA;RSEQ=TTATAGTAAATATCCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:6:5,1:73,3:76,6:0.0723:1,2:20.7:1:31.5:1:0.26648:4.70169:60:12:0.0857:0:1 0/1:101:10:7,3:84,7:91,10:0.099:2,2:19.5:1:29.9:1:0.05848:5.01048:58.6:9:0.0978:0:1.9 +5 112154604 . GT G 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=1.96001;LSEQ=TCCCATTCATCACTTAATTG;RSEQ=TTTTGGCTTTTGGATATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:1:1,0:122,37:159,1:0.0063:2,0:22:0:33:0:1:0:60:2:0.0063:0:0 0/1:246:3:1,2:171,71:242,3:0.0122:2,2:15:1:30:1:0.21239:4.78173:60:6:0.0123:0:1 +5 112162713 . G GT 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.32839;SOR=3.7321;LSEQ=CATATATTCTCATTGATTGA;RSEQ=TTTTTTTTTCCTAGTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:1,0:88,1:89,1:0.0111:1,0:32:0:32:0:1:0:60:2:0.0111:0:0 0/1:74:3:2,1:65,6:71,3:0.0405:2,2:22.3:1:26:1:0.261:5.20085:60:6:0.0405:0.0135:0.3 +5 112162854 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0.63704;LSEQ=CAAGTGGACTGTGAAATGTA;RSEQ=GGGCTTACTAATGACCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:588:324:181,143:150,113:263,324:0.551:2,2:25.6:1:31.1:1:0.80206:1.04869:60:161:0.5561:0:1.1 0/1:636:279:153,126:190,167:357,279:0.4387:2,2:24.8:1:30.3:1:0.68946:1.07:59.9:278:0.4406:0:1.1 +5 112163027 . C CT 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.25157;SOR=0;LSEQ=AAATACATTTTACTGATTTT;RSEQ=TTTTTTTTCACTCTCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:3:0,3:2,105:107,3:0.0273:1,0:27.7:1:32:0:1:0:60:6:0.0278:0:0 0/0:93:0:0,0:0,93:93,0:0:1,0:20.9:1:32.1:1:1:0:60:92:1:0:0.1 +5 112163238 . G GT 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGATCCATTACTAGAGAA;RSEQ=TTTAACTGTGTAGAATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:3,2:0.4:2,0:22:1:32:0:1:0:45.5:4:0.4:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 112163772 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18897;SOR=0;LSEQ=GGCAGGGTCTCACTCTGTCA;RSEQ=CCAGGCTTAGAGGGCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:9,111:120,2:0.0164:2,2:21.5:1:30.5:1:0.15784:11.75:60:4:0.0164:0:1 0/0:158:0:0,0:18,139:157,0:0:2,0:21.6:1:30.7:1:1:0:59.8:77.5:0.9936:0:0 +5 112164238 . C T 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCACAGTAACCTCAAG;RSEQ=TCCTGGGATCCTCCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:24:1:30:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 112164561 . G A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27149;SOR=1.19533;LSEQ=ATTAATTTGCAGGTTATTGC;RSEQ=AGTGTTTTGAGGAATTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:285:158:98,60:87,40:127,158:0.5544:2,2:24.2:1:30.3:1:0.26405:1.33029:60:38.5:0.552:0:1.1 1/0:398:238:156,82:100,60:160,238:0.598:2,2:24.6:1:29.5:1:0.59378:1.14:60:78.333:0.5995:0:1.1 +5 112164716 . C CT 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.08912;SOR=0.15067;LSEQ=AATATGAATTTCATGTTTGG;RSEQ=TTTTTTTTGCTGCCTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:5:1,4:7,97:104,5:0.0459:2,2:29.4:1:30.6:1:0.32201:3.40:57.6:10:0.0467:0:0 0/0:140:1:0,1:27,112:139,1:0.0071:2,0:42:0:29:0:1:0:60:2:0.0072:0:0 +5 112164747 . A G 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.02619;SOR=Inf;LSEQ=TGCCTTCTTTTAGCCATGAG;RSEQ=TTTCCTAATTTCTTACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:0,60:60,0:0:1,0:26.8:1:31.8:1:1:0:59.8:120:1:0:0 0/1:58:5:0,5:2,51:53,5:0.0862:1,0:22.4:1:33.2:1:1:0:60:10:0.0862:0:1 +5 112164862 . G A 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77001;LSEQ=AATTTCTTTTTTGAGATGGG;RSEQ=TCTCTTTCTCTCGCCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:26.5:1:32.5:1:1:0:60:4:0.4:0:1 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:45.5:1:29.5:1:1:0:60:4:0.3333:0:1 +5 112170358 . G A 61 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTTCATAATGCACATCA;RSEQ=TTGTGCCTCATATTCTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:22.5:1:30.5:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 112170490 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15556;SOR=Inf;LSEQ=TAAATACTATTTGGTATTTT;RSEQ=TGAACATTTTTCTAAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:32,1:33,0:0:1,0:25.5:1:28.4:1:1:0:58.3:66:1:0:0.1 0/1:22:2:2,0:19,1:20,2:0.0909:1,0:18.5:1:33:0:1:0:60:4:0.0909:0:1 +5 112172930 . T C 82 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAACATAGGATTTCATGATA;RSEQ=AGTTTTTAAATTGGGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:1,6:0.8571:0,2:16.5:1:32:1:1:0:60:12:0.8571:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 112173106 . T TAGAA 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.22108;SOR=2.48201;LSEQ=CATTAAACATTACATGAAAT;RSEQ=AGAACAAAAGGAGATGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:19:19,0:16,0:16,19:0.5429:1,1:18.8:1:30.3:1:1:0:58.2:38:0.5429:0.2:0 1/0:16:12:11,1:4,0:4,12:0.75:0,2:21.8:1:29.1:1:1:0:60:24:0.75:0:0.3 +5 112173849 . A T 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.04763;SOR=0.12787;LSEQ=TGAAAAAGATAGAAGTTTGG;RSEQ=GAGAGAACGCGGAATTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:6:0,6:209,226:435,6:0.0136:2,0:8.2:1:28:1:0.03146:0:60:12:0.014:0:1 0/0:569:1:0,1:286,282:568,1:0.0018:2,0:1:0:23:0:0.49736:0:60:2:0.0018:0:1 +5 112175031 . C T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05783;SOR=0;LSEQ=TGGTCAGCCTCAAAAGGCTG;RSEQ=CACTTGCAAAGTTTCTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:4:2,2:177,216:393,4:0.0101:2,2:23.5:1:29.8:1:1:1.22:60:8:0.0103:0:1 0/0:411:0:0,0:194,216:410,0:0:2,0:25:1:30.7:1:1:0:60:81:0.9975:0:0.1 +5 112175617 . T A 196 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTAAAACACCTCCACCACC;RSEQ=CCTCAAACAGCTCAAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:881:93:48,45:391,394:785,93:0.1056:2,2:27.8:1:30:1:0.82651:1.07:60:30:0.1056:0:1.1 0/0:1271:0:0,0:617,652:1269,0:0:2,0:23:0:14:0:1:0:60:0:0:0:4 +5 112175770 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.88636;SOR=0.976;LSEQ=ACTTTATTACATTTTGCCAC;RSEQ=GAAAGTACTCCAGATGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:357:209:96,113:75,73:148,209:0.5854:2,2:26.8:1:31.2:1:0.39136:1.20868:59.9:51.25:0.5824:0:1.1 1/0:459:266:128,138:91,102:193,266:0.5795:2,2:23.8:1:29.9:1:0.85034:1.04:59.8:87.667:0.578:0:1.1 +5 112176325 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06315;SOR=1.25848;LSEQ=GGAGAAGGAGTTAGAGGAGG;RSEQ=GCACAGTCAGGTGAATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:227:98,129:113,146:259,227:0.4671:2,2:23.5:1:31.1:1:0.92718:1.01877:60:36.833:0.4682:0:1.1 1/0:652:342:139,203:136,174:310,342:0.5245:2,2:23.9:1:29.4:1:0.42759:1.14125:60:67.4:0.5299:0:1.1 +5 112176559 . T G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.73115;SOR=0.9485;LSEQ=GTCCAGCAAGCATCTGCGTC;RSEQ=TCTTCTGCACCCAACAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:391:207:114,93:109,75:184,207:0.5294:2,2:24.8:1:30.8:1:0.41492:1.18509:59.9:68:0.5299:0:1.1 1/0:463:239:118,121:115,109:224,239:0.5162:2,2:24.1:1:30.4:1:0.71018:1.08168:60:238:0.5163:0:1.1 +5 112176756 . T A 265 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTGAAAAATAATTCCAAGG;RSEQ=CTTCAATGATAAGCTCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:467:467:253,214:0,0:0,467:1:0,2:25:1:29.9:1:1:0:60:50.889:1:0:1.1 1/0:574:384:206,178:107,83:190,384:0.669:2,2:22.2:1:28.4:1:0.59322:1.11372:60:75.8:0.6696:0:1.1 +5 112177171 . G A 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32534;SOR=1.12922;LSEQ=TTTGCTATTGAAAATACTCC;RSEQ=GTTTGCTTTTCTCATAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:458:246:99,147:88,124:212,246:0.5371:2,2:24.5:1:31.4:1:0.84883:1.05362:60:60.5:0.5378:0:1.1 1/0:640:363:137,226:113,164:277,363:0.5672:2,2:23.4:1:29.8:1:0.46208:1.13641:60:71.6:0.5647:0:1.1 +5 112177863 . G GA 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01351;SOR=0;LSEQ=AAGTAAAGGAATCAAAGGAG;RSEQ=AAAAAAAGTTTATAAAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:5:3,2:262,205:467,5:0.0106:2,2:20.4:1:30.6:1:1:1.17:60:10:0.0107:0.0063:0.4 0/0:643:0:0,0:353,289:642,0:0:2,0:23.6:1:30.1:1:1:0:60:63.2:0.9984:0:0.1 +5 112179789 . G A 76 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.31256;SOR=2.75217;LSEQ=TGGAACCCAAAGTCCTAAGC;RSEQ=CCATTCTGGGTCTTACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:2:2,0:156,246:402,2:0.0049:2,0:1:0:29.5:1:0.15236:0:60:4:0.005:0:1 0/1:519:7:6,1:207,304:511,7:0.0135:2,2:13.4:1:27.4:1:0.0212:8.78:58.7:14:0.0138:0:1 +5 112179909 . C A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12801;SOR=Inf;LSEQ=TCAAATGAAACTTTAAAAGA;RSEQ=TGAAAAATTTTGTAAATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:39,0:0:1,0:24.1:1:32.9:1:1:0:60:18.5:1:0:0.2 0/1:50:4:0,4:0,45:45,4:0.08:1,0:33.3:1:27:1:1:0:60:8:0.0816:0:1 +5 112213678 . CTGTGTGTG C 253 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=20.000;MSILEN=2;SSF=0;SOR=0.00814;LSEQ=ATTGAGAGTTACAGGTTACT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:764:224:124,100:172,172:344,224:0.2932:2,2:32.4:1:32.5:1:0.2293:1.24:58.3:73.667:0.2982:0.017:0.5 0/0:894:3:3,0:265,255:520,3:0.0034:2,0:29:1:32:1:0.24903:0:60:6:0.0034:0:0 +5 112213747 . GTAAC G 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=4.000;MSILEN=4;SSF=0.89171;SOR=1.01531;LSEQ=CCGATTTATCACTAGAGTGA;RSEQ=TAACTAACTAACTGCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:932:484:236,248:233,208:441,484:0.5193:2,2:26.1:1:32.6:1:0.23601:1.17694:59.2:120:0.5345:0.0579:0.8 1/0:1017:532:257,275:241,243:484,532:0.5231:2,2:28:1:31.6:1:0.66025:1.06115:59:531:0.5342:0.0206:0.8 +5 112213805 . C G 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=1.95125;LSEQ=TATTCATATGCCATATACTA;RSEQ=GGAAACAACCAGGCCAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1311:756:365,391:263,290:553,756:0.5767:2,2:26.4:1:32.2:1:0.82281:1.03:59.9:93.5:0.5754:0:1.1 1/0:1500:1090:530,560:206,202:408,1090:0.7267:2,2:24.4:1:30.8:1:0.52375:1.07747:59.9:76.857:0.7256:0:1.2 +5 112213906 . G A 51 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06242;SOR=0;LSEQ=TTATTTAGTAGACCACACCA;RSEQ=CACAATGGTTCCTCCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:5:3,2:94,323:417,5:0.0118:2,2:15:1:22.2:1:0.08221:5.13:60:1.5:0.0073:0:1 0/0:395:0:0,0:85,310:395,0:0:2,0:22.3:1:31.3:1:1:0:60:64.833:1:0:0.1 +5 112214093 . C T 91 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.51487;LSEQ=TTATATAAAATTGTACATTA;RSEQ=AGGAAGTAGAACCATAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:0,10:0,10:10,10:0.5:0,0:22.5:1:27.6:1:1:0:60:20:0.5:0:1.1 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:26:0:29:0:1:0:60:2:0.3333:0:1 +5 112227799 . A G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02695;SOR=0.81408;LSEQ=CTGAAAATGATTTAGAAAAT;RSEQ=GTACCACATGGCAAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:962:337:180,157:347,278:625,337:0.3503:2,2:31:1:31.9:1:0.54172:1.08861:51.8:83.25:0.3491:0:1.1 0/1:1213:370:203,167:455,387:842,370:0.305:2,2:31.3:1:31.1:1:0.80252:1.03:51.4:369:0.3067:0:1.1 +5 112227939 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99994;LSEQ=AAACATAATTTCCCAACATC;RSEQ=AGTCCTACCCTTCTTATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:871:250:117,133:279,341:620,250:0.287:2,2:27.1:1:31.5:1:0.65207:1.08:40.3:40.667:0.2841:0:1.1 0/1:993:285:131,154:302,402:704,285:0.287:2,2:24.8:1:31:1:0.39616:1.13:40.5:141.5:0.2888:0:1.1 +5 112227998 . G A 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=TGGAATGGAGCAGTGCAGGA;RSEQ=GGATGACTATGACCCTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:18:8,10:45,104:149,18:0.1078:2,2:9.6:1:30.7:1:0.28334:1.84:57.9:17:0.1024:0:1.1 0/0:140:0:0,0:48,92:140,0:0:2,0:10.8:1:30.4:1:1:0:58.4:139:1:0:0.2 +5 112228006 . T C 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51472;SOR=0;LSEQ=AGCAGTGCAGGAGGGATGAC;RSEQ=ATGACCCTGACGCAAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:29,84:113,2:0.0174:2,2:6.5:1:32:1:0.45538:2.86:60:4:0.0174:0:1 0/0:79:0:0,0:23,55:78,0:0:2,0:7.8:1:28.4:1:1:0:59.6:156:0.9873:0:0.1 +5 112228595 . G A 224 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=49.2292;LSEQ=CAAACGCACATCAAAGAGTC;RSEQ=GGAGAGGCACAATTCACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1061:3:3,0:483,575:1058,3:0.0028:2,0:1:0:27.3:1:0.09579:0:45:6:0.0029:0:1 0/1:1542:189:97,92:669,680:1349,189:0.1226:2,2:23.6:1:29.7:1:0.69791:1.07:48.6:93.5:0.1227:0:1.4 +5 112228667 . G A 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33665;SOR=0.91343;LSEQ=CCAGGGCCGCCGGAGCCAGA;RSEQ=CCGCAGGAGCCACCGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:855:318:172,146:260,276:536,318:0.3719:2,2:24:1:30.3:1:0.11981:1.25:56.7:317:0.3778:0:1.2 0/1:1319:463:233,230:437,416:853,463:0.351:2,2:23.9:1:29:1:0.77296:1.03694:56.9:76.167:0.3562:0:1.3 +5 112228765 . C A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00243;SOR=0.70177;LSEQ=ACAGAACTGTTCAGAGTCCC;RSEQ=AATCCAAATAAACTAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:187:76,111:171,246:417,187:0.3096:2,2:24.3:1:29.2:1:1:1.01522:31.4:14.583:0.3076:0:2 0/1:1007:241:109,132:355,411:766,241:0.2393:2,2:26.9:1:27.7:1:0.76757:1.04598:31.3:9.478:0.23:0:2 +5 112228815 . G A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69253;SOR=0.86753;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=AATGGACCAGGCCAGGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:11:10,1:15,173:188,11:0.0553:2,2:9.6:1:16.9:1:0:109.41:50.2:0.571:0.0221:0:2.5 0/1:352:17:15,2:34,298:332,17:0.0483:2,2:7.2:1:20.5:1:0:64.14:54:1.833:0.0353:0:2 +5 112675951 . C A 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTATGGAAGAGCTGTTGTG;RSEQ=ATCTTCTAGTAATTAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:177,73:250,0:0:2,0:26.3:1:32.5:1:1:0:59.9:249:1:0:0.1 0/1:219:83:58,25:96,40:136,83:0.379:2,2:25.2:1:28.6:1:1:1.03435:60:82:0.3779:0:1.5 +5 112676024 . C G 219 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGAGTCTACTCTGGTCTC;RSEQ=ATGAGAGTGAAGTCCCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:0:0,0:206,200:406,0:0:2,0:25.9:1:31.6:1:1:0:60:57:0.9975:0:0.1 0/1:460:167:85,82:150,143:293,167:0.363:2,2:26.8:1:29.7:1:1:1.01191:60:166:0.3617:0:1.4 +5 112676127 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49839;SOR=0;LSEQ=CAATAAAGAAGACAATACCC;RSEQ=ATATGTCCCCTGGAGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:16,131:147,2:0.0134:2,2:17.5:1:29:1:0.21585:7.97:60:4:0.0137:0:1 0/0:145:0:0,0:33,111:144,0:0:2,0:20.8:1:29.6:1:1:0:60:47:0.993:0:0.1 +5 112676130 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49818;SOR=0;LSEQ=TAAAGAAGACAATACCCGAT;RSEQ=TGTCCCCTGGAGCACAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:14,121:135,2:0.0146:2,2:34:1:31.5:1:0.20771:8.38:60:4:0.0149:0:1 0/0:135:0:0,0:29,106:135,0:0:2,0:20.7:1:28.8:1:1:0:60:32.75:1:0:0.1 +5 112676191 . A G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00116;SOR=Inf;LSEQ=ACAGACAGGCCGAAATATGT;RSEQ=TTCCATGAACCAAAAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:0,43:43,0:0:1,0:19.4:1:31.9:1:1:0:60:86:1:0:0.1 0/1:36:8:0,8:1,27:28,8:0.2222:1,0:24.6:1:32.1:1:1:0:60:16:0.2222:0:1 +5 113064928 . A T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTACAGCTTCGACCATAAA;RSEQ=GACGGCCGCCCCGCGAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:29:1:1:0:30:4:1:0:1 +5 113066014 . G GT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=TGGCCTTTTGGATTCTTGGT;RSEQ=TTTTTTTGGTTGATTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:9,2:0.1818:2,2:22.5:1:29.3:1:0.49091:3.05504:53.5:4:0.1818:0.0909:0 0/0:8:0:0,0:5,3:8,0:0:2,0:20.5:1:31.8:1:1:0:55:16:1:0:0.1 +5 113066133 . T G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTGTGGATGCTGTTGTT;RSEQ=TTGCTTTCTGTTTGTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:3,5:0,0:0,8:1:0,2:15:1:33:1:1:0:52.6:16:1:0:1.4 1/1:2:2:2,0:0,0:0,2:1:0,0:17.5:1:34:0:1:0:55:4:1:0:1.5 +5 113066151 . A G 50 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTGCTTTCTGTTTGTTT;RSEQ=TTTTTCTTTCAATGGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:23.3:1:31.7:1:1:0:40.3:6:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:9:0:33:0:1:0:50:2:1:0:2 +5 113066262 . G A 59 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCTGGAGATGTCACTCA;RSEQ=TAAGGCTGGAGAACAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:27:1:1:0:60:4:1:0:1 1/1:4:4:1,3:0,0:0,4:1:0,2:8.8:1:29.8:1:1:0:59.8:8:1:0:1 +5 113066568 . G C 62 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCATAGAGACTGTGGGCA;RSEQ=CTCTCCCCCTAGGGGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:33:1:1:0:57.5:4:1:0:2 1/1:4:4:2,2:0,0:0,4:1:0,2:17:1:31.3:1:1:0:57.5:8:1:0:2 +5 113066577 . C A 60 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGTGGGCAGCTCTCCCC;RSEQ=TAGGGGTCAGGCCCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:31.5:1:1:0:57.5:4:1:0:2 1/1:4:4:2,2:0,0:0,4:1:0,2:12.5:1:30:1:1:0:57.5:8:1:0:2 +5 113066747 . A G 69 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTTGGGCTGTGGGGGAC;RSEQ=TATCTTGGGACCAAGCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:22.5:1:26:0:1:0:60:4:1:0:1 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:24.6:1:29.8:1:1:1.41418:60:10:0.7143:0:1.2 +5 113697880 . AGCC A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=1.1321;LSEQ=GCGCGGCTTCTTCCCAGAGC;RSEQ=GCCGCCGCCGCCGCGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:4,1:0.2:2,0:44:0:34:0:1:0:60:2:0.2:0:0 0/1:9:2:1,1:6,1:7,2:0.2222:2,2:36.5:1:31:1:0.41667:4.58262:60:4:0.2222:0:1 +5 113698201 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTGCTCGTCGCGCCGGG;RSEQ=CAGCCAGCTCAATGTGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 113698411 . C A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCACCACCACCCGCACCCGG;RSEQ=GCACCACCAGCACCACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:3:0:29:0:1:0:60:4:1:0:0.5 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:27.5:1:27.5:1:1:1:60:4:0.3333:0:1 +5 114100938 . T G 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CACTCCAATCAATCATAGGC;RSEQ=CAGTCTTTTTATGAAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:34.5:1:31:1:1:1:25.5:4:0.5:0:1 0/0:3:0:0,0:1,2:3,0:0:2,0:32.3:1:31:1:1:0:58.3:6:1:0:0.3 +5 114725764 . C G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGAGTCGAGCAGGCCGG;RSEQ=CTTGCTTGCAGGCCGAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:30:1:1:0:60:4:1:0:1 +5 115106241 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50375;SOR=0;LSEQ=ACCTCTCACTCGCTGAGCTC;RSEQ=AGCCTAAGGAGAAGGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:78,17:95,2:0.0206:2,2:30.5:1:29.5:1:0.33827:4.48747:60:4:0.0208:0:1 0/0:77:0:0,0:56,21:77,0:0:2,0:26.1:1:30:1:1:0:60:24.667:1:0:0.2 +5 115106267 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49842;SOR=Inf;LSEQ=AAGGAGAAGGGGGGTAAGTA;RSEQ=GGAGGTCTCTATACCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:103,55:158,0:0:2,0:22.2:1:30.8:1:1:0:60:316:1:0:0.1 0/1:159:2:1,1:103,54:157,2:0.0126:2,2:21:1:30:1:1:1.89921:60:4:0.0128:0:1.5 +5 115106722 . C CA 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.95458;LSEQ=GATGGGAAACATTTCATTCT;RSEQ=AAAAAAAAAAATTATCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:19:4,15:47,163:210,19:0.0815:2,2:28.3:1:30:1:1:1.08093:39.3:18:0.08:0.0086:0.2 0/1:256:20:3,17:56,173:229,20:0.0781:2,2:25.2:1:29.4:1:0.42239:1.83044:31.9:19:0.0779:0.0117:0.5 +5 116414876 . C A 26 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TCTAAGAAAACATATCTTGC;RSEQ=TTGTCTCTAGTCCTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:3,0:0:0,0:26.7:1:31.3:1:1:0:60:6:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:26.5:1:1:0:60:4:1:0:1 +5 116415112 . TTC T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.499;SOR=0;LSEQ=AAATTGCTAGCTTTGTGTTT;RSEQ=TCTCAGTTTGGCCTCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:168,16:184,2:0.0108:2,2:21.5:1:28:1:0.17489:10.21682:60:4:0.011:0:2 0/0:176:0:0,0:160,16:176,0:0:2,0:23.8:1:30.5:1:1:0:60:87:1:0:1 +5 116415123 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99165;LSEQ=TTTGTGTTTTTCTCTCAGTT;RSEQ=GGCCTCTCCTTGGTTACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:240:239:198,41:0,0:0,239:0.9958:0,2:22.5:1:32:1:1:0:60:118.5:0.9958:0:1.1 1/1:238:237:198,39:1,0:1,237:0.9958:0,2:23.1:1:30.4:1:1:0:60:117.5:0.9958:0:1 +5 116415244 . A T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00958;SOR=0.75088;LSEQ=ACCTTTTTTCCTTTCTACCA;RSEQ=CCCAAGTAATAAGCCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:589:285:120,165:122,182:304,285:0.4839:2,2:26.7:1:30:1:0.67532:1.08:60:22.75:0.4756:0:1.1 0/1:765:316:148,168:201,246:447,316:0.4131:2,2:24.8:1:29:1:0.6581:1.08:60:78:0.4132:0:1.1 +5 117054836 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21863;SOR=Inf;LSEQ=AGTTGTTAGTTAAAAGTTAA;RSEQ=AAGGACTTCTCAAGTGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:28,9:37,0:0:2,0:25.4:1:33:1:1:0:60:74:1:0:0.1 0/1:33:2:1,1:21,10:31,2:0.0606:2,2:8.5:1:26.5:1:1:2.04944:60:4:0.0606:0:1.5 +5 117055037 . G T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28002;SOR=1.90492;LSEQ=CATTGTGTTCTGTATGTTTT;RSEQ=ATGGTCTGGAAGATATCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:6:2,4:22,16:38,6:0.1364:2,2:34.2:1:28.5:1:0.38713:2.68715:60:12:0.1364:0:1.3 0/1:43:10:6,4:12,21:33,10:0.2326:2,2:16.6:1:29.1:1:0.27535:2.56:60:20:0.2326:0:1.2 +5 117055145 . C A 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.21624;SOR=2.04029;LSEQ=TCACATTACAGTGAACTGAA;RSEQ=TGGGTCCATCTTGACCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:29:21,8:11,8:19,29:0.6042:2,2:21.8:1:30.2:1:0.35677:1.88:59.9:28:0.5957:0:1.2 1/0:29:22:11,11:4,3:7,22:0.7586:2,2:26:1:30:1:1:1.32019:60:44:0.7586:0:1.2 +5 117055315 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50458;SOR=0;LSEQ=ATGACTTTAAATTCCCTTGT;RSEQ=ATAAACTATGGCATGTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:107,72:179,2:0.011:2,2:19.5:1:28.5:1:1:1.48274:60:4:0.0112:0:1.5 0/0:145:0:0,0:86,59:145,0:0:2,0:23.4:1:31.2:1:1:0:60:290:1:0:0.1 +5 117055390 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49961;SOR=0;LSEQ=CTTGTGGATTATTCTGCTGG;RSEQ=CAGTATTGGTGACATTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:75,107:182,2:0.0108:2,2:29:1:29:1:1:1.42:60:4:0.0114:0:1 0/0:169:0:0,0:69,100:169,0:0:2,0:24.2:1:29.9:1:1:0:60:23.143:1:0:0.1 +5 117057428 . A AAT 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.04315;SOR=Inf;LSEQ=TAGAACTTAAAGTGTAATAA;RSEQ=ATATATATATATAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:19,5:24,0:0:2,0:18.3:1:31:1:1:0:53.9:48:1:0:0.1 0/1:14:3:2,1:8,3:11,3:0.2143:2,2:33.3:1:30.8:1:1:1.30524:60:6:0.2143:0:0 +5 117057746 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22552;SOR=Inf;LSEQ=TTTTTTCATGCTTGATTCTT;RSEQ=CCAACATGGCATCTATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:26,42:68,0:0:2,0:28.4:1:30.3:1:1:0:60:67:1:0:0.1 0/1:62:2:1,1:23,37:60,2:0.0323:2,2:37.5:1:26:1:1:1.60:60:4:0.0323:0:1 +5 117759448 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49368;SOR=Inf;LSEQ=GGAGCTGGCTTTTTGTAAAA;RSEQ=TTAATAAAATAGACCACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:13,24:37,0:0:2,0:17.6:1:32.6:1:1:0:59.6:74:1:0:0.1 0/1:39:2:1,1:12,25:37,2:0.0513:2,2:5:1:27.5:1:1:2.04:60:4:0.0526:0:1.5 +5 118882170 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATTTGAAGTGAGGTTGA;RSEQ=CAGCTCTATACACCTTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 118882820 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTCTTTTATTTTTTTAA;RSEQ=ACCTACTATGCCATGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:26.5:1:30:1:0.33333:0:50.5:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:31:0:1:0:55:2:1:0:0 +5 118883014 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49742;SOR=0;LSEQ=ATCTTGGCTCTTAGAGTGCT;RSEQ=AATGTGTTCAATAAGCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:44,7:51,2:0.0377:2,2:18:1:30.5:1:0.28157:5.94621:54:4:0.0377:0:1 0/0:46:0:0,0:33,13:46,0:0:2,0:27:1:29.2:1:1:0:58:45:1:0:0.1 +5 118883086 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23863;SOR=Inf;LSEQ=TTGTTTGTTTACAATAAGGC;RSEQ=AACAGCATGCCAGGTAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:115,74:189,0:0:2,0:22.9:1:31.3:1:1:0:48.5:36.8:1:0:0.1 0/1:181:2:1,1:109,70:179,2:0.011:2,2:23.5:1:28:1:1:1.55317:31:4:0.011:0:1 +5 118883091 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49891;SOR=0;LSEQ=TGTTTACAATAAGGCCAACA;RSEQ=CATGCCAGGTAACATTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:117,77:194,2:0.0102:2,2:9.5:1:29.5:1:1:1.51611:34:4:0.0103:0:1.5 0/0:188:0:0,0:117,71:188,0:0:2,0:26.6:1:31.1:1:1:0:46.8:36.6:1:0:0.2 +5 118883106 . T C 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=CAACAGCATGCCAGGTAACA;RSEQ=TGTAGACTCTTCCAGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:105,78:183,0:0:2,0:32.5:1:31:1:1:0:46.1:182:1:0:0.1 0/1:180:10:5,5:105,65:170,10:0.0556:2,2:32.1:1:31.9:1:0.51421:1.61087:38.5:20:0.0562:0:1.2 +5 118883110 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24378;SOR=Inf;LSEQ=AGCATGCCAGGTAACATTGT;RSEQ=GACTCTTCCAGTTTTGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:104,78:182,0:0:2,0:33.3:1:29.9:1:1:0:46:59.667:1:0:0.1 0/1:178:2:1,1:108,67:175,2:0.0112:2,2:24.5:1:29.5:1:1:1.60737:33:4:0.0116:0:2 +5 118883167 . C A 49 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.36613;SOR=3.10991;LSEQ=CATTCCTTTTTGAGCAGTAC;RSEQ=CATTCCCTTGATGTCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:1,0:40,59:99,1:0.01:2,0:1:0:26:0:0.41:0:36:2:0.0102:0:1 0/1:98:3:1,2:41,54:95,3:0.0306:2,2:15.3:1:31:0:1:1.51231:44.3:6:0.0313:0:1 +5 118883215 . A G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=0.19695;LSEQ=TTTCTTATAGATTTGCATAT;RSEQ=CATGGCCAAAGGAAAAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:26:4,22:7,29:36,26:0.4194:2,2:29.3:1:31.9:1:0.74792:1.32163:45:25:0.4167:0:1.1 0/1:65:8:1,7:10,47:57,8:0.1231:2,2:27.9:1:28.1:1:1:1.48113:38.9:3:0.0984:0:1.9 +5 125065999 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTGAGCTCCCTGTGGAA;RSEQ=GTGTAGCAGCCATCACTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:29:1:1:0:60:4:1:0:1 +5 125066527 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=GTAGGCTTAGTTTTCCCCCT;RSEQ=CTAGCCCTGAGGAATCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:15,0:0:2,0:24.5:1:32.9:1:1:0:60:30:1:0:0.3 0/1:28:2:1,1:14,12:26,2:0.0714:2,2:41.5:1:28.5:1:1:1.16024:60:4:0.0714:0:1 +5 125066642 . T C 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGGTCCTGGTTCCCATGC;RSEQ=CCCAACTGGGTGAGACCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:16.2:1:32.8:1:1:0:58.8:10:1:0:1 1/1:6:6:2,4:0,0:0,6:1:0,2:29.5:1:31.5:1:1:0:60:12:1:0:1 +5 125564245 . GA G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18018;SOR=0;LSEQ=ATGCCACCCTGCATTTGCAG;RSEQ=AAAGGTTTCTGAAATCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:14,2:0.125:2,2:22.5:1:32:1:1:1.73197:26:4:0.125:0:0.5 0/0:21:0:0,0:14,7:21,0:0:2,0:24.4:1:29:1:1:0:35:42:1:0:0.1 +5 125564480 . G T 43 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AACTAACGACTTCTACTGAG;RSEQ=ACCCCTGGACCAAACCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:7:0:34:0:1:0:60:2:1:0:0 1/0:4:3:0,3:0,1:1,3:0.75:0,0:29:1:27.3:1:1:0:60:6:0.75:0:1.3 +5 126841002 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49829;SOR=Inf;LSEQ=AGAGCCAGCCCTTGTTAAAT;RSEQ=ATTCCAGTGCCTGATACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:106,17:123,0:0:2,0:24.8:1:32.3:1:1:0:60:60.5:1:0:0.1 0/1:129:2:1,1:109,18:127,2:0.0155:2,2:19.5:1:26.5:1:0.27386:5.92105:60:4:0.0155:0:1 +5 126841016 . A T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=TTAAATGATTCCAGTGCCTG;RSEQ=TACTCACTTGAAATAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:131,27:158,0:0:2,0:23.7:1:30.4:1:1:0:60:78:1:0:0.1 0/1:165:2:1,1:128,35:163,2:0.0121:2,2:7:1:27:1:0.3898:3.61967:60:4:0.0122:0:1 +5 126841120 . C T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06404;LSEQ=AAAAGGAGTTGGAGAATAGA;RSEQ=GAATGCAGCATCATGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:458:392:170,222:28,36:64,392:0.8559:2,2:25.8:1:30.4:1:1:1.01566:60:48:0.8571:0:1.1 0/1:593:163:76,87:196,232:428,163:0.2749:2,2:24.5:1:29.3:1:0.92645:1.03:60:26.167:0.2712:0:1.2 +5 127195983 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1772;SOR=Inf;LSEQ=ATACTCCATAAATGTTTGTT;RSEQ=AATAGAACTAAATTATTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:124,39:163,0:0:2,0:24.2:1:32.3:1:1:0:60:162:1:0:0.1 0/1:119:2:1,1:92,25:117,2:0.0168:2,2:31:1:27:1:0.39069:3.62849:60:4:0.0168:0:1 +5 127196035 . C T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12601;SOR=0;LSEQ=AACAAGCTCTTTCTAATGAG;RSEQ=TGTATCCTCTCTTAAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:4:1,3:179,161:340,4:0.0116:2,2:17.8:1:27.3:1:0.35103:3.32464:60:8:0.0117:0:1.5 0/0:309:0:0,0:167,142:309,0:0:2,0:24.4:1:31:1:1:0:60:43.143:1:0:0.5 +5 127196066 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=14.1623;LSEQ=CTTAAAATTTTCTCTGCTTT;RSEQ=GAAAGTTTAACCCGGTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:21:12,9:171,184:355,21:0.0559:2,2:25.2:1:30.3:1:0.50314:1.43:60:42:0.0572:0:1.1 0/1:370:169:89,80:98,103:201,169:0.4568:2,2:27.6:1:28.6:1:0.46673:1.17:60:338:0.4592:0:1.1 +5 127792031 . G A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=GGAGGGGTGGCTGCAGTCTC;RSEQ=GGATCAGCAGACTTAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:35:1:33:1:1:1.7321:46.5:4:0.4:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:24:1:27.7:1:1:0:48.3:6:1:0:0.3 +5 131281244 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51538;SOR=Inf;LSEQ=ACGGGTGCCTCTGGACTCTC;RSEQ=ATGGCCTGCCTTCCTGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:42,0:0:2,0:24.2:1:30.7:1:1:0:60:84:1:0:0.1 0/1:63:2:1,1:35,26:61,2:0.0317:2,2:25.5:1:27.5:1:1:1.33971:60:4:0.0317:0:1.5 +5 131281346 . G T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22199;SOR=0;LSEQ=CTAATCGAGCGAAAGCAAAA;RSEQ=CCCCAGAACTGGAGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:6,13:19,2:0.0952:2,2:20:0:29.5:1:1:2.08:60:4:0.1:0:1 0/0:23:0:0,0:7,16:23,0:0:2,0:16.3:1:31.5:1:1:0:60:46:1:0:0.3 +5 131892979 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.05711;LSEQ=CCTCAGTTAAGCCTTTGTGG;RSEQ=CTCCAGGTCCCTGGTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:457:455:340,115:1,0:1,455:0.9956:0,2:24.7:1:29.5:1:1:0:60:40.364:0.9978:0:1.1 1/1:483:481:322,159:0,0:0,481:0.9959:0,2:23:1:28.3:1:1:0:60:119.25:0.9979:0:1.1 +5 131893329 . T C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAGTTTGCCTGAAGCAGTC;RSEQ=CGGAAGGATGTCCGGACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:0,26:0,0:0,26:1:0,1:18.3:1:31.5:1:1:0:58.8:25:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:32.5:1:30:1:1:0:60:4:1:0:1 +5 131911401 . CT C 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.58965;SOR=2.46112;LSEQ=TTGGGTAAGATTGCTTATGC;RSEQ=TTTTCTCAGAACCAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:1:1,0:114,12:126,1:0.0079:2,0:47:0:34:0:1:0:60:2:0.0079:0:0 0/1:104:2:1,1:92,10:102,2:0.0192:2,2:33.5:1:30.5:1:0.20127:8.82052:60:4:0.0194:0:0 +5 131911426 . C T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.12288;SOR=0;LSEQ=TCTCAGAACCAACACTGGTG;RSEQ=TTATTAAAGTAACATAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:4:1,3:131,39:170,4:0.023:2,2:10.8:1:27:1:0.04411:9.90643:60:8:0.0234:0:1.3 0/0:171:0:0,0:136,35:171,0:0:2,0:23.5:1:31.5:1:1:0:60:342:1:0:0.1 +5 131911847 . G C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACACAGCCTCCTCCACTAT;RSEQ=AACATTTGATTTTTTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:0,3:0,9:9,3:0.25:0,0:19.3:1:32.3:1:1:0:60:6:0.3:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:42:0:32:0:1:0:60:2:1:0:0 +5 131914904 . CT C 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.67106;SOR=1.70354;LSEQ=TAACGGGATAGGTGAAGGGC;RSEQ=TTTTTTTTATTCTTTTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:3:3,0:77,0:77,3:0.0375:1,0:20.3:1:32.7:1:1:0:60:6:0.0375:0.0125:0.3 0/1:48:3:3,0:45,0:45,3:0.0625:1,0:6.3:1:31.1:1:1:0:60:6:0.0625:0.0417:0 +5 131915213 . G A 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00076;SOR=0.49882;LSEQ=AGGTTTGTAACCCTTAAATA;RSEQ=ACTTTGTAGTCCATTAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:316:88:25,63:79,149:228,88:0.2785:2,2:25.9:1:30.7:1:0.35003:1.33491:60:28.333:0.2733:0:1.1 0/1:279:45:16,29:82,152:234,45:0.1613:2,2:24.1:1:28.2:1:1:1.02:60:14:0.1533:0:1.1 +5 131915317 . T C 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15636;SOR=0.36756;LSEQ=TCATCAGTTACTACCTCTCA;RSEQ=CCAGCAGCAACCATTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:14:1,13:2,37:39,14:0.2642:2,1:23.6:1:31.7:1:1:1.41:59.6:28:0.2692:0:1.5 0/1:26:3:0,3:1,22:23,3:0.1154:1,0:31.3:1:32.3:1:1:0:60:6:0.12:0:1.3 +5 131915526 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19664;SOR=Inf;LSEQ=CATAATTTACTTTGCCAGAA;RSEQ=TTTGATTTTTGTTTCATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:122,33:155,0:0:2,0:23.4:1:30.7:1:1:0:60:76.5:1:0:0.1 0/1:124:2:1,1:90,32:122,2:0.0161:2,2:30.5:1:33.5:1:0.46302:2.7849:60:4:0.0163:0:1 +5 131923393 . G A 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.34771;SOR=3.37993;LSEQ=AATGGAAAAGGTTTGTGGTG;RSEQ=TAGAATTTTGTTCTGCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:1,0:102,178:280,1:0.0036:2,0:1:0:25:0:0.36655:0:60:2:0.0036:0:1 0/1:251:3:1,2:102,146:248,3:0.012:2,2:30.7:1:29:1:1:1.39547:60:6:0.0121:0:1 +5 131923408 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21822;SOR=Inf;LSEQ=TGGTGGTAGAATTTTGTTCT;RSEQ=CTTCAAAATTTTGGGATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:69,154:223,0:0:2,0:25.6:1:32.5:1:1:0:60:222:1:0:0.1 0/1:196:2:1,1:65,129:194,2:0.0102:2,2:8:0:30:1:1:1.98:60:4:0.0103:0:1.5 +5 131923532 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53284;SOR=0;LSEQ=AAAATGAAGGATATTGAATA;RSEQ=GGTTTGGTTTATATTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:110,34:144,2:0.0137:2,2:17:1:34.5:1:0.42324:3.20319:60:4:0.0143:0:1 0/0:85:0:0,0:67,18:85,0:0:2,0:22.8:1:30.1:1:1:0:60:41.5:1:0:0.1 +5 131923555 . T C 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58552;SOR=2.54096;LSEQ=TTTGGTTTATATTTGATACC;RSEQ=CAAAGTGATCATATTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:1,0:145,41:186,1:0.0053:2,0:6:0:15:0:1:0:60:0:0:0:4 0/1:148:2:1,1:112,34:146,2:0.0135:2,2:19.5:1:28.5:1:0.41828:3.26116:60:4:0.0137:0:1 +5 131923604 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04774;SOR=Inf;LSEQ=ACATTAAAGCTTTTTATTTT;RSEQ=GTGTTACACAGGTTTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:372:0:0,0:260,111:371,0:0:2,0:23.9:1:31.8:1:1:0:59.9:45.375:1:0:0.1 0/1:328:4:1,3:209,115:324,4:0.0122:2,2:17.3:1:27.5:1:0.13459:5.4235:60:8:0.0123:0:1 +5 131924341 . C T 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0153;SOR=9.22635;LSEQ=TATCTCAACTTTTTAAGCAC;RSEQ=AGTTGAAAAAAAAATTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:1:1,0:109,13:122,1:0.0081:2,0:46:0:16:0:1:0:60:0:0:0:7 0/1:113:8:6,2:93,12:105,8:0.0708:2,2:18.3:1:27.9:1:0.25815:2.55455:60:16:0.0721:0:1 +5 131924346 . G GA 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.06481;LSEQ=CAACTTTTTAAGCACCAGTT;RSEQ=AAAAAAAAATTATGAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:2,0:113,18:131,2:0.015:2,0:40.5:1:29.5:1:1:0:60:4:0.0154:0:0 0/1:125:2:1,1:106,16:122,2:0.016:2,2:11:0:30.5:1:0.25636:6.45744:60:4:0.0163:0:1 +5 131924362 . G T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.24812;SOR=Inf;LSEQ=AGTTGAAAAAAAAATTATGA;RSEQ=ATTTTTTTTTTAAAAGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:144,32:176,0:0:2,0:23.8:1:32.5:1:1:0:60:34.2:1:0:0.3 0/1:183:3:1,2:141,39:180,3:0.0164:2,2:22:1:25:1:0.1265:7.12752:60:6:0.0168:0:1.7 +5 131924363 . A AT 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.63992;SOR=1.34285;LSEQ=GTTGAAAAAAAAATTATGAG;RSEQ=TTTTTTTTTTAAAAGGTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:8:7,1:138,32:170,8:0.0442:2,2:25.6:1:32:1:1:1.62:60:16:0.0471:0.0055:0 0/1:188:11:8,3:136,41:177,11:0.0585:2,2:20.5:1:30:1:0.72105:1.2424:60:22:0.0618:0.0053:0.2 +5 131924374 . A T 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00545;SOR=0;LSEQ=AATTATGAGATTTTTTTTTT;RSEQ=AAAGGTCGTCTACAGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:7:3,4:175,48:223,7:0.0304:2,2:9.7:1:25:1:0.04787:4.81737:60:6:0.0271:0:1 0/0:251:0:0,0:180,70:250,0:0:2,0:21.7:1:27.8:1:1:0:60:61.5:0.996:0:0.2 +5 131924620 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49902;SOR=Inf;LSEQ=TATTTTGTTTGCATCATATT;RSEQ=TCTACTTGAATTGTTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:39,143:182,0:0:2,0:22.6:1:32.9:1:1:0:59.9:90:1:0:0.1 0/1:192:2:1,1:46,144:190,2:0.0104:2,2:36:1:28.5:1:0.43063:3.11:60:4:0.0105:0:1 +5 131925174 . A C 103 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05485;SOR=0.12688;LSEQ=CACAATGATAAAATTGCCTA;RSEQ=TGATGCATTTCTTGGAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:13,0:13,9:0.4091:1,0:28.2:1:32.6:1:1:0:60:18:0.4091:0:2 0/1:13:1:1,0:12,0:12,1:0.0769:0,0:6:0:33:0:1:0:60:2:0.0769:0:1 +5 131925187 . T C 95 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11941;SOR=0.16676;LSEQ=TTGCCTAATGATGCATTTCT;RSEQ=GGAATATATCCCTGCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:8,0:18,0:18,8:0.3077:1,0:31.6:1:31.9:1:1:0:60:16:0.3077:0:2.1 0/1:15:1:1,0:14,0:14,1:0.0667:1,0:13:0:32:0:1:0:60:2:0.0667:0:1 +5 131925599 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52459;SOR=0;LSEQ=GAAGTATTTTGTCTATTTTT;RSEQ=ATCCTAAGATTATAGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:7,113:120,2:0.0164:2,2:6.5:1:28:1:0.12735:15.17:60:4:0.0165:0:1 0/0:76:0:0,0:5,71:76,0:0:2,0:24.5:1:31:1:1:0:60:152:1:0:0 +5 131927191 . G C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15402;SOR=Inf;LSEQ=AGACTATAAGGTATTAAGTT;RSEQ=GTATTGACTATATTTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:3,134:137,0:0:1,0:25.4:1:31.6:1:1:0:59.7:136:1:0:0 0/1:89:2:1,1:0,87:87,2:0.0225:1,2:6:1:29:1:0.02247:0:60:4:0.0225:0:1 +5 131927550 . AT A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.0639;SOR=2.07101;LSEQ=ATAGACTTTATTTTTAAAAG;RSEQ=TTTTTTTTTACCTATAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:14:10,4:174,65:239,14:0.0551:2,2:31.6:1:32.4:1:1:1.07048:60:28:0.0558:0:0 0/1:176:19:17,2:114,43:157,19:0.108:2,2:24.9:1:31.1:1:0.16332:3.19:60:38:0.1086:0.0284:0.2 +5 131931451 . TA T 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16711;SOR=1.72484;LSEQ=CAAGTCAACAGAATCAGAGC;RSEQ=AAAAAAAAGGAAAAGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:12:7,5:177,275:452,12:0.0259:2,2:31.7:1:32.5:1:0.23346:2.17:60:24:0.0265:0:0.1 0/1:525:23:8,15:217,285:502,23:0.0438:2,2:22:1:31.1:1:0.52038:1.42669:60:46:0.0442:0.0057:0.1 +5 131938959 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24955;SOR=0;LSEQ=TCTAACTGTGAGAAACATCA;RSEQ=ATACTTTATTTTTAATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:3:1,2:122,41:163,3:0.0181:2,2:9:1:28:1:0.16484:5.87312:60:6:0.0185:0:1 0/0:150:0:0,0:101,49:150,0:0:2,0:21.9:1:30.7:1:1:0:59.8:74:1:0:0.1 +5 131939240 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1676;SOR=Inf;LSEQ=CCATGGTGGCTTGAATTTGA;RSEQ=GTGTGAGAGTTAAAAATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:37,183:220,0:0:2,0:23.2:1:31.7:1:1:0:59.7:43:1:0:0.1 0/1:153:2:1,1:20,131:151,2:0.0131:2,2:23.5:1:29.5:1:0.25645:6.42:60:4:0.0133:0:1 +5 131939904 . T G 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09603;SOR=0.33029;LSEQ=CTTCTCTTTGTTCTCTTACT;RSEQ=TGCACAACAGATTTTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:16:0,16:1,25:26,16:0.381:1,1:26:1:29.2:1:1:0:60:4.333:0.3421:0:1.1 0/1:24:4:0,4:0,20:20,4:0.1667:1,0:15:1:32.5:1:1:0:60:8:0.1667:0:1 +5 131944129 . G A 55 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.76351;LSEQ=TTCTCTGTGTCTGTTTGCTC;RSEQ=TTTGAAATATAGGACTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:27.3:1:27.8:1:1:0:60:3:0.3333:0:1.5 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:22:1:31.5:1:1:0:60:4:0.4:0:1 +5 131944381 . C CA 79 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24231;SOR=2.26665;LSEQ=GAAAAAGAAGAATTAATCAA;RSEQ=AAAAAAAATACAAGCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:3:3,0:175,190:365,3:0.0082:2,0:13.7:1:28.7:1:0.11218:0:59.3:6:0.0083:0.0027:2 0/1:437:8:4,4:206,223:429,8:0.0183:2,2:17.6:1:26.4:1:1:1.08:59.9:7:0.0164:0.0069:1 +5 131944452 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22775;SOR=Inf;LSEQ=ATATATTTACTTATCAAATA;RSEQ=CTGTATTAAACTTATGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:37,118:155,0:0:2,0:25.6:1:30.3:1:1:0:60:310:1:0:0.1 0/1:142:2:1,1:33,106:139,2:0.0141:2,2:23:1:27:0:0.42543:3.18:60:4:0.0149:0:1 +5 131944592 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01829;SOR=Inf;LSEQ=TAGAACAAGGATTTGATGTA;RSEQ=ATTATTTTGCTGCTTGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:16,19:35,0:0:2,0:28.9:1:31.3:1:1:0:60:70:1:0:0 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:28:1:33:0:1:0:60:4:0.3333:0:1 +5 131944771 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49837;SOR=0;LSEQ=CTCCTGTTATGTGCCCTTAA;RSEQ=TACAACCAGTGTAAATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:2,0:100,45:145,2:0.0136:2,0:32.5:1:33:0:1:0:60:4:0.0138:0:1 0/0:143:0:0,0:96,47:143,0:0:2,0:25.3:1:31.4:1:1:0:60:70.5:1:0:0.1 +5 131944806 . C T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62473;SOR=2.77849;LSEQ=ATTTAATGAATATTTTTCTA;RSEQ=AGCTGAATGATATTAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:133,99:232,1:0.0043:2,0:1:0:23:0:0.42918:0:60:2:0.0043:0:1 0/1:253:3:1,2:145,105:250,3:0.0119:2,2:11.3:1:27.3:1:0.57535:2.75088:60:6:0.0119:0:1 +5 131944811 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24986;SOR=Inf;LSEQ=ATGAATATTTTTCTACAGCT;RSEQ=AATGATATTAAAGAGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:145,113:258,0:0:2,0:22.4:1:32.1:1:1:0:60:516:1:0:0.1 0/1:280:3:1,2:156,121:277,3:0.0107:2,2:18:1:27.7:1:0.58386:2.56993:60:6:0.0108:0:1.3 +5 131945121 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05994;SOR=Inf;LSEQ=TGCTTATGATATCACTTACA;RSEQ=CTATGACATTCTTTTCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:30,137:167,0:0:2,0:21.8:1:31.6:1:1:0:60:54.667:0.982:0:0.1 0/1:168:4:1,3:35,129:164,4:0.0238:2,2:22:1:29:1:1:1.23:60:8:0.0241:0:1 +5 131951880 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51541;SOR=0;LSEQ=CTTTATTACTGGAATGTGAA;RSEQ=AATATTAAATACCTGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:0,2:14,117:131,2:0.015:2,0:32.5:1:30:0:1:0:60:4:0.0152:0:1 0/0:91:0:0,0:13,78:91,0:0:2,0:20.4:1:30.8:1:1:0:60:182:1:0:0 +5 131951996 . T C 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.26632;SOR=0;LSEQ=CATGGCCTTAAGAACTTTAT;RSEQ=ACTGAAGAAGTGATATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:10,5:0.3333:0,0:14.8:1:32.2:1:1:0:60:10:0.3333:0:1.4 0/0:5:0:0,0:0,5:5,0:0:0,0:18.8:1:29:0:1:0:60:10:1:0:0.2 +5 131952072 . C T 70 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGTATTGAACATGCTTAG;RSEQ=CCCCATACATCTGCTAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:18.8:1:30.4:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 131953510 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAACTTTATCAGTGATC;RSEQ=CATGCTATGAGGGTTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:30.5:1:32:0:1:0:60:4:0.3333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:12:0:24:0:1:0:60:2:1:0:0 +5 131954027 . T A 42 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05266;SOR=0;LSEQ=TTTCTTATTGCAGTTAATAT;RSEQ=AACTAACATACTTTAGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:4:3,1:32,154:186,4:0.0211:2,2:8.8:1:21.3:1:0.02028:14.14:60:3:0.0161:0:1.3 0/0:205:0:0,0:45,160:205,0:0:2,0:23.2:1:28.1:1:1:0:59.9:204:1:0:0.1 +5 131972916 . A G 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTACCATGGTGTATCACAA;RSEQ=TGCTCTTTCCAAAGCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:178,314:492,0:0:2,0:25.6:1:30.8:1:1:0:60:122:1:0:0.1 0/1:424:25:11,14:156,243:399,25:0.059:2,2:24.8:1:31.6:1:0.67547:1.22:60:50:0.0594:0:1.2 +5 131973004 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1511;SOR=Inf;LSEQ=CTGGACCCCTTTCTAAGCAT;RSEQ=TCTTTGAGATTTTCTAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:1,102:103,0:0:1,0:27.1:1:33.1:1:1:0:60:206:1:0:0.1 0/1:66:2:0,2:1,63:64,2:0.0303:1,0:7:1:28:1:1:0:60:4:0.0308:0:1 +5 131973663 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69573;SOR=0.81963;LSEQ=CACACCAGCCATTGTTTTCC;RSEQ=CTGGTAATGTCAGCCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:22:22,0:37,0:37,22:0.3729:1,1:18.7:1:32:1:1:0:59.3:44:0.386:0:1 0/1:55:18:18,0:36,1:37,18:0.3273:1,1:28.3:1:30.7:1:1:0:60:17:0.3148:0:1.1 +5 131973683 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23983;SOR=Inf;LSEQ=TCTGGTAATGTCAGCCTCAT;RSEQ=TGTTGTTCCTAGGCTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:79,8:87,0:0:2,0:23.2:1:32.3:1:1:0:59.8:28:1:0:0.2 0/1:84:2:1,1:74,8:82,2:0.0238:2,2:17.5:1:30.5:1:0.20396:8.78103:60:4:0.0241:0:1 +5 131974063 . T A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10861;LSEQ=TGAATCAGGCTCAGCTACTA;RSEQ=TATTACACTCTCCTGAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:0,9:0,19:19,9:0.3103:1,0:23.3:1:30.3:1:1:0:59.1:18:0.3214:0:1.2 0/1:18:6:0,6:0,12:12,6:0.3333:0,0:24.2:1:31:1:1:0:60:12:0.3333:0:1 +5 131976302 . G T 43 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22998;LSEQ=GAAAAGATCATGTCAGGACT;RSEQ=CTTGCCTGCCATGAGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:3:2,1:230,69:299,3:0.0099:2,2:19.3:1:30.3:1:0.54801:1.66349:60:6:0.01:0:1 0/1:246:3:1,2:185,58:243,3:0.0122:2,2:18:1:27.7:1:0.14828:6.31879:60:6:0.0123:0:1 +5 131976594 . A G 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50666;SOR=0;LSEQ=CAAGAGAGTTCTGTGATGAA;RSEQ=ACGTTCTCTAGCTGTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:5,164:169,2:0.0117:1,2:6.5:1:32:0:0.06914:30.03:60:4:0.012:0:1 0/0:132:0:0,0:5,126:131,0:0:1,0:22.1:1:30.6:1:1:0:60:64.5:1:0:0 +5 131977963 . T C 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTTTTAGGACGTTCTGAATA;RSEQ=GTGGAGAAATTCTACAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:698:0:0,0:326,371:697,0:0:2,0:23.9:1:30.8:1:1:0:60:98.571:0.9986:0:0.1 0/1:629:26:16,10:299,304:603,26:0.0413:2,2:26.7:1:31:1:0.31668:1.63:59.8:52:0.0416:0:1.2 +5 131978076 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10025;SOR=Inf;LSEQ=AAAATATCCAAGATTTAAAT;RSEQ=CCATAGAAATGTAGGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:73,213:286,0:0:2,0:22.6:1:32:1:1:0:60:70.5:0.9965:0:0.1 0/1:250:3:1,2:69,177:246,3:0.012:2,2:25.3:1:28.3:1:1:1.28:60:6:0.0123:0:1 +5 133478341 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGGCACACTCTAGGCCCAC;RSEQ=CTAGAGGAGGAGGCTGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:12:1:31.7:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 133478359 . A C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=ACGCTAGAGGAGGAGGCTGC;RSEQ=ATTAGGTGGGCACTCGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:18:1:33:0:1:0:60:6:1:0:2.3 0/0:2:0:0,0:2,0:2,0:0:0,0:12:1:30.5:1:1:0:60:4:1:0:0 +5 133478475 . C T 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=CCAACCATCAAGAAGCCCCT;RSEQ=AATGCCTTCATGCTGTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:10,2:2,0:2,12:0.8571:0,2:22.8:1:30.2:1:1:0:60:24:0.8571:0:1.2 0/0:10:0:0,0:6,4:10,0:0:2,0:20.6:1:31.3:1:1:0:60:20:1:0:0 +5 133478708 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=ACGCGCTGTCGCGAGAAGAG;RSEQ=AGGCCAAGTACTATGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:11,0:0:2,0:25.3:1:32.7:1:1:0:60:22:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:28.5:1:27:1:1:2.44949:60:4:0.3333:0:1 +5 133908289 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50904;SOR=0;LSEQ=AAGACCCTGGTGGGACCCAG;RSEQ=ATTCAAGCTGAGCAGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:94,43:137,2:0.0144:2,2:35:1:32:1:0.53446:2.17257:60:4:0.0145:0:1 0/0:103:0:0,0:71,31:102,0:0:2,0:23:1:30:1:1:0:60:101:1:0:0.6 +5 133908311 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50297;SOR=0;LSEQ=TTCAAGCTGAGCAGCTTTGG;RSEQ=CAACTGTCCCTGATAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:114,70:184,2:0.0108:2,2:8:1:30:1:1:1.62408:60:4:0.011:0:2 0/0:154:0:0,0:90,64:154,0:0:2,0:23.9:1:30.4:1:1:0:60:50.333:1:0:0.9 +5 133908361 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=18.16559;LSEQ=CTGTGCTGAAGACCAAGGAA;RSEQ=TGTCTCAAGGGAGGGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:90:49,41:95,91:186,90:0.3261:2,2:25:1:30.8:1:0.60984:1.14:59.4:89:0.3248:0:1.9 1/1:207:186:89,97:9,12:21,186:0.8986:2,2:25:1:29.8:1:0.81838:1.22:60:185:0.8981:0:1.8 +5 133908378 . G C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.31452;LSEQ=GAAGTGTCTCAAGGGAGGGG;RSEQ=CTTGGTCTTGGCTTCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:91:45,46:86,95:181,91:0.3346:2,2:23.7:1:31.1:1:0.7978:1.08:59.5:21.75:0.3283:0:1.9 1/0:211:132:61,71:34,43:77,132:0.6256:2,2:25:1:31.2:1:0.88557:1.09:60:65:0.628:0:2.1 +5 133908395 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18622;SOR=Inf;LSEQ=GGGGCTTGGTCTTGGCTTCA;RSEQ=AAGTGTGGCCTGCCCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:110,137:247,0:0:2,0:26.6:1:32.7:1:1:0:59.9:246:1:0:0.7 0/1:188:2:1,1:76,110:186,2:0.0106:2,2:36:0:30.5:1:1:1.44:60:4:0.0107:0:3 +5 133908406 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17789;SOR=Inf;LSEQ=TTGGCTTCAGAAGTGTGGCC;RSEQ=GCCCTGAGAGCAGCCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:96,135:231,0:0:2,0:25.3:1:30.9:1:1:0:60:76:1:0:0.6 0/1:169:2:1,1:65,102:167,2:0.0118:2,2:16:1:27.5:1:1:1.56:60:4:0.012:0:2 +5 133908443 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1704;SOR=Inf;LSEQ=GGGAGGGATGGCCCACTGGG;RSEQ=TAAGGTGCCAGGTGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:33,99:132,0:0:2,0:23.3:1:32.2:1:1:0:60:264:0.9925:0:0.4 0/1:94:2:1,1:28,64:92,2:0.0213:2,2:33.5:1:28:1:0.52414:2.26:60:4:0.0215:0:1.5 +5 133908456 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50472;SOR=0;LSEQ=CACTGGGGTAAGGTGCCAGG;RSEQ=GGGCAGGCAGTAGCATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:17,82:99,2:0.0198:2,2:14:1:27:1:0.32614:4.72:60:4:0.0204:0:1.5 0/0:79:0:0,0:23,56:79,0:0:2,0:22.1:1:28.2:1:1:0:59.7:25.333:1:0:0.6 +5 134389581 . C T 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30842;SOR=4.43119;LSEQ=CACTGGGGTTGCGCAGAGAG;RSEQ=TGGTGGCAGATCCAAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:1,0:202,47:249,1:0.004:2,0:17:0:12:0:1:0:60:0:0:0:3 0/1:171:3:2,1:115,52:167,3:0.0175:2,2:26:1:23.7:1:1:1.1051:60:2:0.012:0:2.3 +5 134389689 . G T 206 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTAGGGGATGTGCAGGCT;RSEQ=CTGTGGTGGTGACCCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:612:0:0,0:277,334:611,0:0:2,0:27.1:1:32.1:1:1:0:60:75.375:0.9983:0:0.1 0/1:520:139:64,75:183,197:380,139:0.2673:2,2:27.5:1:29:1:0.69222:1.08841:60:68.5:0.266:0:1.1 +5 134389729 . C A 44 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18008;SOR=4.93099;LSEQ=GAGGCCAGGTGGGGGAAGCC;RSEQ=TTGTGTCTGCCTGGTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:1:1,0:124,286:410,1:0.0024:2,0:1:0:26:0:0.30414:0:60:2:0.0025:0:1 0/1:336:4:3,1:117,215:332,4:0.0119:2,2:12.8:1:22:1:0.13204:5.48:60:3:0.0091:0:1.3 +5 134389752 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.17945;SOR=Inf;LSEQ=GTGTCTGCCTGGTGCCTGTA;RSEQ=TATATTTGAATTATCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:56,209:265,0:0:2,0:23.9:1:31.1:1:1:0:60:131.5:1:0:0.1 0/1:196:2:1,1:51,143:194,2:0.0102:2,2:19:1:29.5:1:0.46122:2.79:60:4:0.0103:0:1 +5 135406459 . G C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00555;SOR=0.13968;LSEQ=CTGAGAAAGGTCACCCCTGG;RSEQ=TCAGCAGGCCCCAACTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:42:39:39,0:3,0:3,39:0.9286:0,1:24.6:1:32:1:1:0:60:38:0.9268:0:1.5 1/0:22:14:13,1:8,0:8,14:0.6364:0,1:26.1:1:32.8:1:1:0:60:28:0.6364:0:1.3 +5 135406534 . A G 221 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03341;LSEQ=TGATGAGTCACACTGCAGAA;RSEQ=GGCTGCTTCATCTTTAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:125:102,23:5,1:6,125:0.9542:2,2:21:1:31.8:1:1:1.12645:59.8:30.25:0.9528:0:1.2 0/1:123:50:38,12:56,17:73,50:0.4065:2,2:26.3:1:31.7:1:1:1.03994:60:100:0.4065:0:1.2 +5 135406560 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24808;SOR=Inf;LSEQ=CTTCATCTTTAGCAGGTGAC;RSEQ=CCACCCTCTAACCCTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:134,62:196,0:0:2,0:24.8:1:31:1:1:0:59.9:64.333:1:0:0.7 0/1:195:2:1,1:129,64:193,2:0.0103:2,2:23:0:32:0:1:2.00786:60:4:0.0103:0:1.5 +5 135406658 . G A 250 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03792;LSEQ=GAAGAAAGTCTGAGATTTGG;RSEQ=AGTAGCAGAGACAGAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:306:293:131,162:6,7:13,293:0.9575:2,2:24.5:1:30.6:1:1:1.05975:60:96.667:0.9571:0:1.1 0/1:385:177:82,95:96,110:206,177:0.4597:2,2:22.2:1:28.6:1:1:1.01106:60:58:0.4579:0:1.1 +5 135406781 . C T 136 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=75.54612;LSEQ=GTGGGGCGGGTGAGTCCCTG;RSEQ=GGCTTCTTGGCAACAGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:1:0,1:10,81:91,1:0.0109:2,0:29:0:27:0:1:0:60:2:0.0111:0:1 0/1:52:24:2,22:4,24:28,24:0.4615:2,2:19.3:1:29.8:1:0.67431:1.81273:60:48:0.4615:0:1.1 +5 135406894 . A G 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.19118;SOR=0.15819;LSEQ=CCAGAATCGGAGGGTGAGGG;RSEQ=AAAAGCCCTGCTAGAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:0,11:0,1:1,11:0.9167:0,0:28.8:1:31.5:1:1:0:57.8:10:0.9091:0:1.3 1/0:5:3:0,3:0,2:2,3:0.6:0,0:21.3:1:27.7:1:1:0:60:6:0.6:0:1.3 +5 135535192 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTAGAAAGACTTGGTCTG;RSEQ=GTCAGCAATAAGCTCTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:17,5:22,2:0.0833:2,2:15.5:1:30:1:0.44565:3.19373:60:4:0.087:0:1.5 0/0:9:0:0,0:7,2:9,0:0:2,0:35.1:1:28.9:1:1:0:60:18:1:0:0 +5 135535242 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19522;SOR=Inf;LSEQ=TGCCTTCTCTCTGCATCCTC;RSEQ=GGAGTCAGCGGTCTGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:41,18:59,0:0:2,0:29.6:1:31:1:1:0:60:58:0.9831:0:0.2 0/1:48:2:1,1:30,16:46,2:0.0417:2,2:43:0:31:1:1:1.84915:60:4:0.0417:0:1.5 +5 135535267 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50899;SOR=0;LSEQ=TCAGCGGTCTGGGCCAGCCT;RSEQ=CGGCGGGCTGAAGCTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:36,30:66,2:0.0294:2,2:35.5:1:30.5:1:1:1.19677:60:4:0.0303:0:1 0/0:49:0:0,0:26,23:49,0:0:2,0:28.6:1:30.6:1:1:0:60:23.5:1:0:0.2 +5 135535272 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17707;SOR=Inf;LSEQ=GGTCTGGGCCAGCCTGCGGC;RSEQ=GGCTGAAGCTGGGAGAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:35,29:64,0:0:2,0:25.9:1:30:1:1:0:60:63:1:0:0.1 0/1:47:2:1,1:24,21:45,2:0.0426:2,2:26.5:1:27.5:1:1:1.1396:60:4:0.0444:0:1 +5 136191507 . C T 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20567;SOR=Inf;LSEQ=GGCTTTGTATACAATGAGGA;RSEQ=TAAGAAAAGTGTTAGTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:117,27:144,0:0:2,0:23.3:1:32.4:1:1:0:59.9:71:1:0:0.1 0/1:120:2:1,1:90,28:118,2:0.0167:2,2:7:0:26.5:1:0.42647:3.17587:60:4:0.0168:0:1.5 +5 136191512 . A G 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTATACAATGAGGACTAAG;RSEQ=AAAGTGTTAGTTCATTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:121,35:156,0:0:2,0:23.5:1:30.1:1:1:0:59.9:38:0.9935:0:0.1 0/1:136:43:30,13:65,26:91,43:0.3162:2,2:25.3:1:30.7:1:0.84131:1.08268:60:86:0.3209:0:1.1 +5 136191583 . A G 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGTGAGAACAACTGAATG;RSEQ=GGTAGGGAATTTAAATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:195,168:363,0:0:2,0:26.1:1:30.6:1:1:0:59.8:35.3:1:0:0.1 0/1:327:17:10,7:150,160:310,17:0.052:2,2:33.4:1:29.8:1:0.46107:1.52:60:16:0.0494:0:1.8 +5 136191604 . T A 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04343;SOR=Inf;LSEQ=GGTAGGGAATTTAAATGCAT;RSEQ=GTTTGAAATTTCATTAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:190,187:377,0:0:2,0:25.5:1:30.6:1:1:0:59.9:74.4:1:0:0.1 0/1:319:4:3,1:149,166:315,4:0.0125:2,2:15.5:1:22.3:1:0.35062:3.33:52.5:3:0.0095:0:2.3 +5 136191624 . A G 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTTGAAATTTCATTAATG;RSEQ=GGTGCATTTAATGACAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:0:0,0:172,201:373,0:0:2,0:24.9:1:31.1:1:1:0:59.9:73.6:1:0:0.1 0/1:280:77:33,44:93,109:202,77:0.275:2,2:22.2:1:30.2:1:0.68724:1.13709:60:76:0.2754:0:1.2 +5 136191628 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.077;SOR=Inf;LSEQ=TGAAATTTCATTAATGAGGT;RSEQ=CATTTAATGACAGTGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:168,198:366,0:0:2,0:25:1:32.2:1:1:0:59.9:121:1:0:0.1 0/1:272:3:2,1:119,150:269,3:0.011:2,2:17.3:1:25.3:1:0.58688:2.51:50:2:0.0075:0:2.7 +5 136191651 . G A 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAATGACAGTGGGAACAT;RSEQ=CATAAAGGAGACTTAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:130,196:326,0:0:2,0:24.6:1:32.2:1:1:0:59.9:107.667:1:0:0.1 0/1:210:20:8,12:73,117:190,20:0.0952:2,2:21.2:1:28.2:1:1:1.07:60:40:0.0962:0:1.1 +5 137222330 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50317;SOR=0;LSEQ=ATACAAACACAGACACACCC;RSEQ=AGTGAATGACAGGGACCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:108,83:191,2:0.0103:2,2:36:0:32:1:1:1.2994:60:4:0.0105:0:1 0/0:161:0:0,0:91,70:161,0:0:2,0:25.1:1:29.3:1:1:0:60:79.5:1:0:0.2 +5 137222354 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.61177;SOR=2.14722;LSEQ=GAATGACAGGGACCATCAGG;RSEQ=GACAGATTGAAGAGCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:1:0,1:92,107:199,1:0.005:2,0:7:0:14:0:1:0:60:0:0:0:3 0/1:187:2:1,1:91,94:185,2:0.0107:2,2:35.5:1:29:1:1:1.03:60:4:0.0108:0:1.5 +5 137222379 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=0;LSEQ=GATTGAAGAGCAGAGGGAGA;RSEQ=AGCACCCAAGGGGGGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:61,115:176,2:0.0112:2,2:21:1:28.5:1:1:1.88:60:4:0.0114:0:1 0/0:172:0:0,0:72,100:172,0:0:2,0:25.7:1:31.1:1:1:0:60:85:1:0:0.2 +5 137222393 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.49836;SOR=0;LSEQ=GGGAGACAGCACCCAAGGGG;RSEQ=GATGTTTAATTCAAGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:47,100:147,2:0.0133:2,2:21:0:32:0:0.54199:2.12:60:4:0.0139:0:1.5 0/0:147:0:0,0:56,90:146,0:0:2,0:21.3:1:29.9:1:1:0:60:292:0.9932:0:0.2 +5 137431453 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19352;SOR=0;LSEQ=TTCCCTACCACTGAAGGCAA;RSEQ=CAGAGCCTGGAGGAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:100,86:186,2:0.0106:2,2:33.5:1:29.5:1:1:1.16185:60:4:0.0108:0:2.5 0/0:240:0:0,0:131,109:240,0:0:2,0:25.1:1:31.4:1:1:0:60:79:1:0:0.4 +5 137431501 . C T 229 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03963;LSEQ=CCCCTATCAGCACGTGAGAT;RSEQ=GCAGAGGAGCAAAGAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:187:178:73,105:3,6:9,178:0.9519:2,2:27:1:30.7:1:0.74053:1.39:60:58.333:0.9511:0:1.2 0/1:265:116:57,59:66,79:145,116:0.4377:2,2:25.9:1:29.5:1:0.6181:1.16:60:57:0.4335:0:1.1 +5 137431507 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17543;SOR=0;LSEQ=TCAGCACGTGAGATCGCAGA;RSEQ=GAGCAAAGAGTAGACTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:73,110:183,2:0.0108:2,2:34.5:1:29.5:1:1:1.50:60:4:0.0109:0:2 0/0:256:0:0,0:120,136:256,0:0:2,0:24.4:1:30.7:1:1:0:60:84.333:1:0:0.6 +5 137801686 . G A 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.48943;SOR=0;LSEQ=CGGCGGGGGCGGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,9:20,2:0.087:2,2:22:0:28.5:1:1:1.21106:60:4:0.0952:0:1 0/0:21:0:0,0:10,11:21,0:0:2,0:24:1:31.9:1:1:0:57.6:42:1:0:0 +5 137802404 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCGTCCTCCAGTGATTG;RSEQ=TTTCCAGTAACCAGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 138991568 . C A 35 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64499;SOR=0.49062;LSEQ=TTTTTTTTTTTTTTTTTGAA;RSEQ=ATGAAATGTTTCCCAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:3:3,0:18,6:24,3:0.1111:2,0:43:1:22.3:1:1:0:48.3:2:0.1:0:6.3 0/1:35:2:2,0:20,13:33,2:0.0571:2,0:25:1:21:1:0.51933:0:38.5:1:0.0417:0:5.5 +5 138991655 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.21271;SOR=Inf;LSEQ=CATACTTGTTACATATTTGG;RSEQ=ATGAGTTACACATAAGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:30,36:66,0:0:2,0:22.6:1:31.5:1:1:0:60:132:1:0:0.1 0/1:57:2:1,1:25,30:55,2:0.0351:2,2:15:1:26:1:1:1.20:60:4:0.0364:0:1 +5 139061857 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=CGCAAATGTCCAGAATGGTT;RSEQ=GAAAACAACAGTGGTATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:11:0:32.5:1:1:2.4495:60:4:0.1538:0:1 0/0:14:0:0,0:8,6:14,0:0:2,0:18.9:1:30.4:1:1:0:58.9:28:1:0:0.6 +5 139061927 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=6;SSF=0.50128;SOR=0;LSEQ=CAACCCCAGCCCCAGCCCCA;RSEQ=CCCCAGCCCCAGCCCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:21,15:36,2:0.0513:2,2:18.5:1:31.5:1:1:1.38742:39.5:4:0.0571:0:1.5 0/0:30:0:0,0:14,16:30,0:0:2,0:27.6:1:26.8:1:1:0:58.1:3.286:1:0:0.8 +5 139061932 . A AGCCCCC 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=5.000;MSILEN=1;SSF=0.19096;SOR=Inf;LSEQ=CCAGCCCCAGCCCCAGCCCC;RSEQ=GCCCCAGCCCTTCCATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:21,16:37,0:0:2,0:21.8:1:28.6:1:1:0:58.7:8.25:1:0:0.3 0/1:30:2:2,0:11,16:27,2:0.0667:2,0:44.5:1:24.3:1:0.19212:0:38.5:4:0.08:0:4.5 +5 139517048 . A G 213 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=223.50539;LSEQ=TGTTAGAAGGTATTCAAACT;RSEQ=ACATATGTTGTGCCAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:534:1:1,0:233,300:533,1:0.0019:2,0:37:0:32:0:0.4382:0:60:2:0.0019:0:1 0/1:422:125:60,65:134,163:297,125:0.2962:2,2:21.7:1:30.7:1:0.59457:1.12:60:124:0.2959:0:1.1 +5 139517197 . T C 102 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=72.1971;LSEQ=CCTCACTTGAATGCTTGGTA;RSEQ=GTAGTTTGGTACTTAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:0,1:1,70:71,1:0.0139:1,0:32:0:24:0:1:0:60:2:0.0141:0:1 1/0:21:11:0,11:0,10:10,11:0.5238:0,0:22:1:29.5:1:1:0:60:22:0.55:0:1 +5 139781699 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13846;SOR=Inf;LSEQ=ACCGTGAGGCTCTTTGGGGA;RSEQ=GCCGGGCCAGCGTCGGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:16,0:0:2,0:21.6:1:33.4:1:1:0:60:32:1:0:0.3 0/1:10:2:1,1:4,4:8,2:0.2:2,2:17.5:1:30.5:1:1:1:60:4:0.2:0:1.5 +5 140012528 . AGCG A 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.4878;SOR=0;LSEQ=TGGTCGCAGAGACGTGCACC;RSEQ=GCAGCAGCAGCAGCAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:11.5:1:34:1:1:1.11:43:4:0.0952:0:0.5 0/0:21:0:0,0:10,11:21,0:0:2,0:30.5:1:29.3:1:1:0:60:20:1:0:0.2 +5 140012586 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47826;SOR=Inf;LSEQ=CTGGGGAGAGAGCAGAGGTC;RSEQ=AGGAGGCCCCATCCAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:11,0:0:2,0:30.8:1:29.6:1:1:0:60:22:1:0:0.1 0/1:12:2:1,1:2,8:10,2:0.1667:2,2:25.5:1:27:1:0.45455:3.46:60:4:0.1667:0:1.5 +5 140176506 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GCCTACTCGTGCTGGTGAAG;RSEQ=ACCACGGCGAACCAGCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:13.2:1:31.4:1:1:0:60:10:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:28.5:1:28:1:1:1:60:4:0.5:0:1 +5 140188401 . A G 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GCTCGCGATGCCGGCGTGCC;RSEQ=CCTCTGGGCAGCAACGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:12.5:1:32:0:1:0:25.5:4:1:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:36.3:1:30:1:1:0:60:6:1:0:0 +5 140188575 . G C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=CGCGCGGTGGATGCTGACTC;RSEQ=GGCTACAACGCGTGGCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:11,13:0,0:0,24:1:0,2:19.3:1:31.3:1:1:0:56.2:48:1:0:1.1 1/1:24:22:9,13:1,1:2,22:0.9167:2,2:24.5:1:30.7:1:1:1.42202:56.2:44:0.9167:0:1.3 +5 140256920 . G C 247 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCGGTCGGCGCGCACATCCC;RSEQ=TTCCACGTGGGGCTGTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:218:85,133:58,102:160,218:0.5767:2,2:22.7:1:31.9:1:0.59361:1.12:59.9:71.667:0.5749:0:1.1 0/0:333:0:0,0:115,217:332,0:0:2,0:22.3:1:29.8:1:1:0:60:40.5:0.9969:0:0.1 +5 140346468 . T A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02198;SOR=0;LSEQ=CTGCTGCTGCTACCTGGCCC;RSEQ=GCGGCCTCCCAGCTGCGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:23:1:31:1:1:1.73:60:6:0.6:0:1.3 0/0:10:0:0,0:4,6:10,0:0:2,0:26.1:1:29.9:1:1:0:60:20:1:0:0.3 +5 141876089 . T C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28737;SOR=Inf;LSEQ=AGATAATTATTTGTTGGAGG;RSEQ=GGTGGCGGCGGTGGCGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:19,4:23,0:0:2,0:18:1:29.1:1:1:0:60:46:1:0:0.1 0/1:38:4:2,2:20,14:34,4:0.1053:2,2:29.8:1:30.8:1:1:1.41496:60:8:0.1053:0:1.3 +5 142328893 . T TTCCTCTC 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=2;SSF=1;SOR=0.5163;LSEQ=GAGGCCAAGTGATGAATATG;RSEQ=TCCTCTCTATGAACAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:10,4:0.2857:0,0:17.8:1:32.5:1:1:0:57.5:8:0.3333:0.1429:0.5 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:15:1:31.5:1:1:0:60:2:0.1667:0.1667:1 +5 142328966 . C T 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29915;SOR=0.60682;LSEQ=TAAGCCTTCATTTTTGCCAC;RSEQ=GTCATCTCTCTAACCCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:29:28,1:43,0:43,29:0.4028:1,1:27.8:1:33.1:1:0.40278:0:59.7:58:0.4028:0:1 0/1:38:11:11,0:26,1:27,11:0.2895:1,0:26.6:1:31:1:1:0:60:22:0.2895:0:1 +5 142329033 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05512;SOR=Inf;LSEQ=TTGCTATTCTTTGGTTGGGG;RSEQ=CAATATTAATGCATCAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:158,67:225,0:0:2,0:23.8:1:31.4:1:1:0:60:74:1:0:0.1 0/1:213:4:1,3:160,49:209,4:0.0188:2,2:19.3:1:25.8:1:0.04593:9.66329:60:8:0.0193:0:1 +5 142329054 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03052;SOR=0;LSEQ=CAATATTAATGCATCAGAAT;RSEQ=AGTGTTTGGAAGTTCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:5:2,3:195,118:313,5:0.0157:2,2:11.6:1:25.2:1:0.37254:2.47144:60:4:0.0128:0:1 0/0:319:0:0,0:216,103:319,0:0:2,0:25.2:1:30.6:1:1:0:60:78.75:1:0:0.2 +5 142329145 . A G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11668;LSEQ=TCTTTGGCTCAAGACTTTTC;RSEQ=GTACAATGTTCTAAACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:188:88,100:74,99:173,188:0.5208:2,2:26.5:1:30.5:1:0.45987:1.18:60:376:0.5251:0:1.1 0/1:401:45:20,25:138,218:356,45:0.1122:2,2:28.3:1:29.2:1:0.5181:1.26:60:21.5:0.1091:0:1 +5 142329273 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.30455;SOR=0;LSEQ=ATGAGGGGCAGAGTGGGAGG;RSEQ=AGGTAGCTGGAATGTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:0,4:2,67:69,4:0.0548:1,0:25:1:31.3:1:1:0:60:8:0.0563:0:1 0/0:34:0:0,0:1,33:34,0:0:1,0:22.2:1:30.4:1:1:0:60:68:1:0:0.1 +5 144227881 . T C 119 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00401;SOR=0;LSEQ=GAGGTTAAAAATGCAGGGCC;RSEQ=GAATGTGAGTAATAGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:10,4:0,0:0,14:1:0,2:30.5:1:31.5:1:1:0:52.9:28:1:0:1 1/0:12:6:4,2:6,0:6,6:0.5:0,2:27.8:1:32:1:0.45455:0:55.8:12:0.5:0:1 +5 144228069 . A G 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00482;SOR=Inf;LSEQ=AAAACAACACTCTTACCCTA;RSEQ=GAAGGTGCGGAGTCCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:11,0:0:2,0:19.5:1:32.5:1:1:0:53.2:22:1:0:0.1 1/0:8:5:2,3:1,2:3,5:0.625:2,2:36:1:31.6:1:1:1.29:29.2:10:0.625:0:1.2 +5 144755084 . TG T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.22;SOR=Inf;LSEQ=GTGGAGAGGGTGTGCTTTGC;RSEQ=GGGGTAAACTCGCTCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,9:13,0:0:2,0:26.3:1:31.5:1:1:0:60:26:1:0:0 0/1:12:2:1,1:3,7:10,2:0.1667:2,2:38:0:32.5:1:1:2.16:60:4:0.1667:0:0.5 +5 145123287 . G C 56 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAAACCACGCTACAGAGG;RSEQ=CTGGGGTCCCAACCCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:25.8:1:28.3:1:1:0:60:3:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 145123812 . A G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTTAGCCTTTTCTCCTGC;RSEQ=GACCAGCAGACTTAGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:0,8:1:0,2:22.6:1:31.4:1:1:0:60:16:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:32:1:1:0:60:4:1:0:1 +5 145123948 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19918;SOR=0;LSEQ=AAATGGGTCCCGTTCCCTGT;RSEQ=CCACTCAACTGGGTGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:16,22:38,2:0.05:2,2:30.5:1:32.5:1:1:1.36:36:4:0.0513:0:1.5 0/0:49:0:0,0:24,25:49,0:0:2,0:32.5:1:31.2:1:1:0:60:48:1:0:0.2 +5 145123957 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19918;SOR=0;LSEQ=CCGTTCCCTGTGCCACTCAA;RSEQ=TGGGTGAGACCCTCCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:16,22:38,2:0.05:2,2:27.5:1:29:1:1:1.36:60:4:0.0526:0:2 0/0:49:0:0,0:23,26:49,0:0:2,0:29.6:1:31.4:1:1:0:59.8:98:1:0:0.1 +5 145124401 . T C 33 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACGTTTCTCCAGCAAGGG;RSEQ=GCATAATTGGACAGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:27.5:1:33.5:1:1:0:60:4:1:0:1.5 +5 145124434 . T A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGGATGAGATGGAAGAAT;RSEQ=GACAGAAGTAGGTTTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:27:1:1:0:60:4:1:0:1.5 +5 145124755 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGAATGAACAAAGCCT;RSEQ=CAAGAAATATGGGACTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 146257931 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18995;SOR=Inf;LSEQ=CCTCCGCTGCCTCCGGGTGC;RSEQ=AAGATACGCCGTGCCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:33,0:0:2,0:28:1:31:1:1:0:60:32:1:0:0.2 0/1:26:2:1,1:10,14:24,2:0.0769:2,2:8.5:1:27.5:1:1:1.38:60:4:0.08:0:1.5 +5 146386270 . T C 28 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CTCTTTGGCAGCAGTGATTC;RSEQ=CCAAAACCACCGAGGCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:27.8:1:32.5:1:1:0:30.8:8:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:28:1:1:0:37:4:1:0:1 +5 146386506 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17321;SOR=Inf;LSEQ=ACTCTTATACCATCCTCTGG;RSEQ=GTTGGGCAACATGGCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:26,28:54,0:0:2,0:28:1:31.3:1:1:0:41.8:108:1:0:0.1 0/1:39:2:1,1:17,20:37,2:0.0513:2,2:14:0:32:0:1:1.17:60:4:0.0513:0:1.5 +5 147496166 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15235;SOR=Inf;LSEQ=AAGTTTCTCCTTAAGGTTGC;RSEQ=GGGTAAGATATCAGCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:80,2:82,0:0:1,0:26.9:1:31.1:1:1:0:60:164:1:0:0 0/1:53:2:1,1:47,4:51,2:0.0377:2,2:25:1:30.5:1:0.18142:10.62088:60:4:0.0377:0:1 +5 147496188 . TC T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.14875;SOR=Inf;LSEQ=GGTAAGATATCAGCACATTT;RSEQ=ACTGCTCTGGGGTTCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:119,14:133,0:0:2,0:22.1:1:32.2:1:1:0:60:132:1:0:0.1 0/1:84:2:1,1:66,15:81,2:0.0238:2,2:10.5:1:28.8:1:0.35028:4.29244:60:4:0.0247:0.0119:0 +5 147496226 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16245;SOR=Inf;LSEQ=TTTGGATTTCTTTACACCTT;RSEQ=AAATAATTAACAATATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:177,76:253,0:0:2,0:24.8:1:32.2:1:1:0:59.9:125.5:0.996:0:0.3 0/1:172:2:1,1:109,60:169,2:0.0116:2,2:20:1:27.5:1:1:1.80986:60:4:0.0117:0:1 +5 147496307 . G A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03152;SOR=1.34129;LSEQ=TAGACCTCATATCAATAATC;RSEQ=TTCTCATCAGTATCACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:552:306:145,161:117,127:244,306:0.5543:2,2:26.7:1:30.3:1:0.93159:1.02288:59.9:60.2:0.5574:0:1.7 1/0:387:242:123,119:69,76:145,242:0.6253:2,2:26.4:1:29.5:1:0.59962:1.14:60:120:0.6234:0:1.7 +5 147496345 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13715;SOR=1.25199;LSEQ=TGCTCTTCATTTTCTTTCAT;RSEQ=ATTCTTTCTTGCCTTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:469:266:96,170:72,131:203,266:0.5672:2,2:25.8:1:32.2:1:0.92273:1.03:60:87.667:0.5705:0:1.9 1/0:309:192:76,116:50,67:117,192:0.6214:2,2:26.1:1:31.2:1:0.63357:1.13856:60:384:0.6275:0:1.9 +5 147496415 . G T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGATCCAAGGCAGCATGATA;RSEQ=GACAAAAGAGCACAGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:19,105:124,2:0.0159:2,2:20:1:30:1:0.29333:5.41:60:4:0.0161:0:1 0/1:63:1:0,1:9,53:62,1:0.0159:2,0:9:0:31:0:1:0:60:2:0.0159:0:1 +5 147496483 . G C 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55873;SOR=1.55725;LSEQ=CCTACTACCTGGACTTGTGA;RSEQ=ACATTGAGTAAATTACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:0,16:0,16:16,16:0.5:1,1:28.1:1:32.8:1:1:0:60:32:0.5:0:1.1 1/0:18:11:0,11:0,7:7,11:0.6111:0,0:21.9:1:31.3:1:1:0:60:22:0.6111:0:1.1 +5 148140339 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAAAAACTCAGCTGTATA;RSEQ=GCTGACCAATCAAAACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:27:1:33:0:1:0:41.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 148140697 . T G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0647;LSEQ=CAAAGATCAGTGGGTAAGCC;RSEQ=GGCCCTAACCACACATAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:511:473:221,252:18,20:38,473:0.9256:2,2:26.1:1:30.6:1:1:1.0262:59.9:156.667:0.9252:0:1.1 0/1:512:228:116,112:143,138:281,228:0.4453:2,2:25.4:1:29.7:1:1:1.0005:60:113:0.4466:0:1.1 +5 148140858 . A G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06822;LSEQ=TCAAGGAACAGAAAAAATGC;RSEQ=AGCCTAAATTTGCCTGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:61:57:2,55:0,4:4,57:0.9344:0,1:20.9:1:31.9:1:1:0:60:27.5:0.9322:0:1.2 0/1:29:14:0,14:0,15:15,14:0.4828:1,1:23.4:1:31.7:1:1:0:60:28:0.4828:0:1.1 +5 148367981 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51613;SOR=0;LSEQ=TGTATAACCAATAAAATATA;RSEQ=CAGATGTGACACTGTGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:18,2:0.1:2,2:26:1:32:0:1:1:60:4:0.1111:0:1 0/0:12:0:0,0:8,4:12,0:0:2,0:32:1:31.7:1:1:0:60:24:1:0:0.1 +5 149137124 . C G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCAGAGTAGCCCTGCCAG;RSEQ=CTGTCCTGACGGATGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:5,4:2,1:3,9:0.75:2,2:27.2:1:30.9:1:1:1.53983:60:8:0.7273:0:1.3 1/1:3:3:2,1:0,0:0,3:1:0,2:31.3:1:31:1:1:0:60:6:1:0:1 +5 149433400 . G GC 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.04568;SOR=Inf;LSEQ=CCATGAGAACAGTAGGGGAG;RSEQ=GGGGGGTGAGGGCTCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:25:25,0:11,0:11,25:0.6944:0,1:23:1:31.8:1:1:0:60:24:0.7059:0.0833:0.1 1/1:11:11:11,0:0,0:0,11:1:0,0:22.4:1:30.9:1:1:0:60:22:1:0.2727:0.2 +5 149433596 . TG GA 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.24756;LSEQ=CATGGAGGAGTTGAAGTTTG;RSEQ=GGAGGGGAGAGTGGTACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:908:883:539,344:0,1:1,883:0.9725:0,2:27.5:1:31:1:0.39027:0:60:1766:0.9955:0.0099:1.1 1/1:740:664:382,282:40,28:68,664:0.8973:2,2:27.1:1:29.4:1:0.89781:1.05454:59.9:331:0.9044:0.0149:1.1 +5 149433597 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3959;SOR=0.75426;LSEQ=ATGGAGGAGTTGAAGTTTGT;RSEQ=GGAGGGGAGAGTGGTACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:908:32:16,16:0,0:0,32:0.0352:0,2:18.3:1:26.6:1:1:0:60:3:0.9231:0:2.4 0/1:746:20:9,11:42,28:70,20:0.0268:2,2:5.2:1:29.5:1:0.30742:1.82077:58.2:19:0.2159:0:1.7 +5 149433731 . ACTG A 97 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.80886;SOR=1.2114;LSEQ=GAGCTCTCCTCCTCCAGCTC;RSEQ=CTGCTGCTGCCGCTGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:862:8:4,4:382,472:854,8:0.0093:2,2:12:1:29.5:1:1:1.24:60:16:0.0094:0.0058:1 0/1:802:9:6,3:350,441:791,9:0.0112:2,2:21.6:1:30.9:1:0.19705:2.52:59.3:18:0.0113:0.0025:0.3 +5 149433752 . A G 113 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00049;SOR=15.37808;LSEQ=CTGCTGCTGCTGCCGCTGCC;RSEQ=CCGCTTCTGCTGCTGCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:825:1:1,0:377,446:823,1:0.0012:2,0:22:0:10:0:0.45874:0:60:0:0:0:1 0/1:709:13:5,8:299,396:695,13:0.0183:2,2:32:1:30.8:1:0.78627:1.20776:60:26:0.0185:0:1 +5 149433939 . G A 186 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=121.39113;LSEQ=AGGAAGGAGCAGATCTGCTG;RSEQ=AAGGTGGGTCTGTGGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:902:1:1,0:450,451:901,1:0.0011:2,0:1:0:26:0:1:0:60:2:0.0011:0:1 0/1:740:88:44,44:310,337:647,88:0.1189:2,2:27.5:1:28.8:1:0.73411:1.09:60:28.333:0.1164:0:1.1 +5 149434518 . C A 88 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTATGATTGCACACATCA;RSEQ=TGCGCTCCAGCCCGGGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:4,1:5,8:0.6154:2,0:19.9:1:29.4:1:0.38462:0:49.1:7:0.5833:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149434684 . T G 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00722;SOR=Inf;LSEQ=TGTGTCCACTATGGGAGAGA;RSEQ=AAAGTCTGACCCTGGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:234,3:237,0:0:1,0:22.6:1:31.4:1:1:0:60:46.4:1:0:0.1 0/1:143:5:5,0:136,2:138,5:0.035:1,0:20:1:33.2:1:1:0:60:10:0.0355:0:1 +5 149434722 . C T 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03217;SOR=Inf;LSEQ=CATTTTGGACAGGGAAAGAT;RSEQ=AGGGCCACACGGCCTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:0:0,0:384,103:487,0:0:2,0:24.3:1:32.1:1:1:0:59.9:47.7:1:0:0.1 0/1:360:4:2,2:286,70:356,4:0.0111:2,2:20.8:1:24:1:0.17994:4.06412:60:3:0.0085:0:1.5 +5 149434954 . C T 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTGTCTTCTCCCCATTCC;RSEQ=GCACACCCACACACATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:37,289:326,0:0:2,0:21.5:1:30:1:1:0:60:107.667:1:0:0.1 0/1:161:17:2,15:23,121:144,17:0.1056:2,2:22.5:1:29.7:1:1:1.42276:60:34:0.1063:0:1.1 +5 149435293 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTAGTAGTAGAGAGCTGC;RSEQ=TCTTCAAGGGTCTGTAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:38:1:30.5:1:1:1.55:60:4:0.1333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:29:0:1:0:60:2:1:0:0 +5 149435759 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.91577;LSEQ=TTCACCCCCTCCCCAGCCTG;RSEQ=CCCAAGCCCTCCCAGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:993:527:268,259:242,223:465,527:0.5307:2,2:24.8:1:29.8:1:0.75032:1.04874:59.9:42.917:0.5337:0:1.2 1/0:833:570:279,291:119,140:259,570:0.6843:2,2:24.3:1:28.4:1:0.45345:1.13:60:50.818:0.6901:0:1.2 +5 149435996 . G A 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28471;SOR=0;LSEQ=GAGGGCCCCACATGGCTTTG;RSEQ=AGTCCCTGCTGGAGTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:3:1,2:5,131:136,3:0.0216:1,2:18.7:1:22:1:0.12485:12.40:59.7:2:0.015:0:2.7 0/0:88:0:0,0:11,77:88,0:0:2,0:24.8:1:31:1:1:0:60:176:1:0:0.1 +5 149436545 . G A 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTATCATCCCCACCAGACC;RSEQ=CGTGCTTTATGAGCAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:32.5:1:32:0:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149436598 . A T 91 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATACACTATTTAGTAAAA;RSEQ=CGAATGAAGAAAGCCTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:8,0:8,0:8,8:0.5:0,0:24.3:1:30.5:1:1:0:60:16:0.5:0:1.4 0/0:1:0:0,0:1,0:1,0:0:0,0:23:0:31:0:1:0:60:2:1:0:0 +5 149437190 . C G 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01972;LSEQ=GGGTTGGGGGGCAGAGGTCA;RSEQ=TCATCATCACTGCACTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:452:451:108,343:0,0:0,451:0.9978:0,2:24.3:1:32.5:1:1:0:60:149.333:0.9978:0:1.1 1/1:316:284:78,206:11,21:32,284:0.8987:2,2:23.8:1:31.1:1:0.41216:1.3819:60:283:0.9042:0:1.1 +5 149438822 . G T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACCTTGTTGGTAAGGCTG;RSEQ=TCTCGAACTCCCATCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:30:1:31:1:1:0:43:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149439044 . C T 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25881;SOR=3.36185;LSEQ=CCCTCCACACTCCCAGAACA;RSEQ=GGTAGGTGTTCAAATATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:15:15,0:13,0:13,15:0.5357:1,1:27.9:1:30.8:1:1:0:60:30:0.5357:0:1.2 1/1:10:8:8,0:2,0:2,8:0.8:0,0:28.3:1:30.8:1:1:0:60:16:0.8:0:1.1 +5 149439045 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCACACTCCCAGAACAC;RSEQ=GTAGGTGTTCAAATATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:26,0:26,2:0.0714:1,0:23:1:31.5:1:1:0:60:4:0.0714:0:1 0/0:12:0:0,0:12,0:12,0:0:0,0:21.5:1:31.2:1:1:0:60:24:1:0:0.8 +5 149439458 . T G 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGTGTGGGGTGAGGGAGG;RSEQ=GCTGAGTGCTCCCCTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:0:0,0:165,356:521,0:0:2,0:24.6:1:29.9:1:1:0:59.9:103.2:1:0:0.3 0/1:385:25:10,15:128,232:360,25:0.0649:2,2:17.8:1:29.9:1:0.67012:1.21:60:24:0.0633:0:1.2 +5 149439494 . C A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22737;LSEQ=CCATGAACAGGAGCATGAGA;RSEQ=TGGGGGCAGTGAGGCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:95:11,84:25,130:155,95:0.38:2,2:24.8:1:30.8:1:0.35828:1.46635:59.6:22.75:0.3792:0:1.1 0/1:164:20:5,15:30,114:144,20:0.122:2,2:20.8:1:29.5:1:0.77081:1.26:60:40:0.1258:0:1.3 +5 149439588 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22973;SOR=0;LSEQ=TTGTGCCTCAGTAGTTCCAT;RSEQ=TGTTTAAAACAGATGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:57:0,57:0,0:0,57:1:0,1:24:1:33.8:1:1:0:58.1:56:1:0:1.2 1/1:17:16:0,16:0,1:1,16:0.9412:0,1:16.5:1:31.7:1:1:0:58.8:32:0.9412:0:1.1 +5 149440114 . C T 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCTTCATAAGAGGTAGG;RSEQ=GGGGGGCTTCACTCCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:19.5:1:31.3:1:1:0:55.5:8:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149440334 . G A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00016;SOR=Inf;LSEQ=ACTTGGAGCAGTAGGATCCT;RSEQ=AGAAGGAGAAGACGGAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:261,13:274,0:0:1,0:24.4:1:32.8:1:1:0:60:273:1:0:0.1 0/1:142:8:7,1:114,20:134,8:0.0563:2,2:19.6:1:29:1:1:1.23:60:16:0.058:0:1.1 +5 149440343 . A G 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13243;SOR=Inf;LSEQ=AGTAGGATCCTGAGAAGGAG;RSEQ=AGACGGAACAAGGTAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:286,33:319,0:0:2,0:24.3:1:30.2:1:1:0:60:52.167:1:0:0 0/1:183:2:1,1:147,34:181,2:0.0109:2,2:5:1:29.5:1:0.34678:4.27579:60:4:0.0112:0:1 +5 149440644 . C T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.86503;SOR=0.89735;LSEQ=AGGGGAGAAAGCAGGGCATA;RSEQ=CCCAAGACCCGGAGTGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:64:2,62:2,42:44,64:0.5926:1,1:24.3:1:30.3:1:1:1.47071:59.8:20.333:0.581:0:1.2 1/0:53:30:1,29:2,12:14,30:0.566:2,1:21:1:28.8:1:0.23362:4.64088:60:60:0.566:0:1.1 +5 149440721 . AGG A 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.37045;SOR=3.44446;LSEQ=CAGATGGCAGAGAGAGAGAG;RSEQ=AGGGATGAGCCTGTCACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:2,0:13,15:28,2:0.0645:2,0:20.5:1:31.5:1:0.48276:0:60:4:0.069:0:0 0/1:5:1:0,1:0,4:4,1:0.2:0,0:11:0:32:0:1:0:60:2:0.2:0:1 +5 149440723 . G A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36907;SOR=0.39713;LSEQ=GATGGCAGAGAGAGAGAGAG;RSEQ=AGGGATGAGCCTGTCACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:19:7,12:7,2:9,19:0.6333:2,2:24.1:1:29.3:1:0.10319:5.60516:56.6:18:0.6923:0:1.7 0/1:5:2:0,2:0,2:2,2:0.4:0,0:26:1:32:1:1:0:60:4:0.5:0:1.5 +5 149441015 . CA C 103 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.83353;SOR=0.87149;LSEQ=AGCCCACCCCCAGCATCTAC;RSEQ=CCCCCCATCCCTTCCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:769:14:14,0:464,266:730,14:0.0182:2,1:28.7:1:27.3:1:0.00313:0:59.1:13:0.0236:0:3.6 0/1:566:9:8,1:340,202:542,9:0.0159:2,2:23.1:1:27.8:1:0.16464:4.74:56.6:18:0.0205:0:3.7 +5 149441016 . AC A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00303;SOR=1.38946;LSEQ=GCCCACCCCCAGCATCTACC;RSEQ=CCCCCATCCCTTCCCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:366:218,148:290,122:412,366:0.4698:2,2:27.6:1:30.4:1:0.00195:1.61273:59.9:14.25:0.5015:0.0128:0.6 1/0:578:319:192,127:170,86:256,319:0.5519:2,2:27.1:1:30.1:1:0.13978:1.30692:59.6:23.538:0.5965:0.0173:0.7 +5 149447628 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77629;LSEQ=CAGAGGCCACCCAGCAGCTG;RSEQ=CTCATGTTGGCATACAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:13,0:10,0:10,13:0.5652:0,1:24.2:1:29.1:1:1:0:60:12:0.5455:0:1 1/0:6:3:3,0:3,0:3,3:0.5:0,0:29.3:1:30.7:1:1:0:60:6:0.5:0:1 +5 149447720 . G C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52499;SOR=0;LSEQ=TGAATCCATGCAGCCTGGGG;RSEQ=TACCATCCAAATCTGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:148,15:163,2:0.0121:2,2:43:1:33.5:1:0.18507:9.58559:60:4:0.0124:0:1 0/0:103:0:0,0:89,14:103,0:0:2,0:23.9:1:31.6:1:1:0:60:102:1:0:0.2 +5 149447744 . A G 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18918;SOR=Inf;LSEQ=CATCCAAATCTGGCTCACTC;RSEQ=GGCACCTGGCAGCCCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:184,31:215,0:0:2,0:26.6:1:30.3:1:1:0:59.7:52.75:1:0:0.1 0/1:166:2:1,1:137,27:164,2:0.012:2,2:24:0:28.5:1:0.30975:5.00094:60:4:0.0123:0:1 +5 149447771 . G A 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCAGCCCCACTCCGCTCC;RSEQ=GCTCACCTGCTTATACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:360:0:0,0:278,81:359,0:0:2,0:22:1:29.5:1:1:0:59.7:28.917:1:0:0.1 0/1:263:18:14,4:186,58:244,18:0.0684:2,2:21.3:1:29.2:1:1:1.09:59.1:36:0.07:0:1.1 +5 149447775 . C T 52 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40911;SOR=0.28099;LSEQ=AGCCCCACTCCGCTCCGGCT;RSEQ=ACCTGCTTATACTTGTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:5:1,4:303,94:397,5:0.0124:2,2:12:1:22.8:1:0.01367:12.79359:60:4:0.0101:0:1 0/0:284:1:0,1:206,77:283,1:0.0035:2,0:1:0:20:0:0.27465:0:60:2:0.0036:0:1 +5 149447805 . GAGC G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.08367;SOR=0.44961;LSEQ=TACTTGTACAATAGCAGCAG;RSEQ=AGCAGCAGCAGCAAGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:673:22:13,9:439,208:647,22:0.0327:2,2:24.9:1:31.8:1:0.48731:1.46033:58.9:44:0.0336:0.0119:0.3 0/1:468:7:5,2:282,179:461,7:0.015:2,2:19.3:1:29.6:1:0.7115:1.59:60:14:0.0153:0.0043:0.1 +5 149447970 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1377;SOR=Inf;LSEQ=GTCAGGCCTGCACACTGCCT;RSEQ=GAACACAGTGGGTGCTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:51,260:311,0:0:2,0:22.9:1:31.4:1:1:0:60:102.667:1:0:0.1 0/1:184:2:2,0:36,146:182,2:0.0109:2,0:23:1:25.5:1:0.04176:0:60:4:0.011:0:1 +5 149448427 . T C 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTATACTACTAGTTCTAG;RSEQ=GATGTTTTGGAGAACATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:28.3:1:30:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149449389 . C G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.69528;SOR=1.16637;LSEQ=GCCGCCTAAAGGAGCAGGGG;RSEQ=GGGGGGCGGGCGGGGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:15:0,15:170,0:170,15:0.0806:1,1:5.1:1:23.4:1:0:0:57.3:2.75:0.0629:0:2.5 0/1:140:13:0,13:122,4:126,13:0.0929:1,1:5.2:1:22.8:1:0:0:57.3:3.333:0.0781:0:2.6 +5 149449396 . C G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20551;SOR=1.50415;LSEQ=AAAGGAGCAGGGGCGGGGGG;RSEQ=GGGCGGGGGGGCGGTGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:21:0,21:190,4:194,21:0.0972:1,1:10.6:1:26.1:1:0:0:58:6:0.0909:0:2.3 0/1:172:24:0,24:142,4:146,24:0.1395:1,1:8.5:1:20.4:1:0:0:57.8:2:0.1046:0:2.5 +5 149449400 . C G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.2655;SOR=1.37615;LSEQ=GAGCAGGGGCGGGGGGCGGG;RSEQ=GGGGGGGCGGTGCGGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:29:2,27:202,6:208,29:0.1213:1,2:12.6:1:25.4:1:0:405.82493:58.6:3.833:0.105:0:2.1 0/1:194:31:0,31:156,5:161,31:0.1598:1,1:11.8:1:25.4:1:0:0:58.5:6.75:0.1467:0:2.3 +5 149449762 . G T 71 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.00447;SOR=Inf;LSEQ=TACCTATCAGTGTGGCCACT;RSEQ=CACTGCAGCCATGTCACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:693:0:0,0:419,274:693,0:0:2,0:24.6:1:31.7:1:1:0:59.9:33.65:1:0:0.1 0/1:476:6:2,4:297,173:470,6:0.0126:2,2:5.7:1:27.5:1:0.20141:3.42428:60:12:0.0129:0:1.3 +5 149449923 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05864;SOR=Inf;LSEQ=CCCGCCACCTCCCAATCTCC;RSEQ=AGTACCTACTTCCCTGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:165,281:446,0:0:2,0:22.4:1:32:1:1:0:60:62.714:0.9977:0:0.1 0/1:285:3:2,1:106,176:282,3:0.0105:2,2:26.3:1:28.3:1:0.55936:3.31:60:6:0.0106:0:1 +5 149450027 . G T 63 v3;p8;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01397;SOR=Inf;LSEQ=CCCAGCACTCACATCGAAGG;RSEQ=TGAGCTCAAACGTCAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:614:0:0,0:362,252:614,0:0:2,0:25:1:31.6:1:1:0:60:46.231:1:0:0.2 0/1:457:5:0,5:278,174:452,5:0.0109:2,0:6.8:1:27.4:1:0.00891:0:60:10:0.0112:0:1 +5 149450132 . T C 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=44.51942;LSEQ=GCAGAGAGAGGGTGAAGGTG;RSEQ=GCCTGCAGGAGAGAATCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:823:2:1,1:347,473:820,2:0.0024:2,2:42:1:21:1:1:1.36:60:1:0.0012:0:1 0/1:664:65:27,38:263,334:597,65:0.0979:2,2:25.6:1:30.1:1:0.79259:1.10803:60:64:0.0977:0:1.1 +5 149450142 . A G 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGTGAAGGTGTGCCTGCAGG;RSEQ=GAGAATCAGGTGGTGTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:0:0,0:283,447:730,0:0:2,0:25.9:1:30.8:1:1:0:59.9:47.667:1:0:0.1 0/1:618:40:19,21:240,338:578,40:0.0647:2,2:21.1:1:29.7:1:0.50885:1.27:60:80:0.0657:0:1.2 +5 149450187 . G A 114 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03328;SOR=0.2203;LSEQ=CCCAGCCTAGTATGGCCCCT;RSEQ=CCAGGATTGCAGTCAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:13:2,11:90,316:406,13:0.031:2,2:25.4:1:30.9:1:0.7421:1.56494:58.5:26:0.0316:0:1 0/0:286:2:2,0:76,208:284,2:0.007:2,0:1:0:18:1:0.07368:0:60:1:0.0036:0:1 +5 149450258 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06832;SOR=Inf;LSEQ=TAAAATATTCAGGGCCCAAC;RSEQ=GCCTTGGGTAAGCCAGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:1,88:89,0:0:1,0:23.6:1:31.1:1:1:0:60:43.5:1:0:0.1 0/1:32:2:0,2:0,30:30,2:0.0625:1,0:25.5:1:29.5:1:1:0:60:4:0.0645:0:1 +5 149452793 . C T 174 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=29.7791;LSEQ=AGGTTGGGACATGAGCCAAG;RSEQ=GTCCTGATGCTTGCTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:4:2,2:372,54:426,4:0.0093:2,2:14.3:1:27.5:1:0.08411:6.83519:60:8:0.0094:0:1 0/1:292:64:54,10:186,42:228,64:0.2192:2,2:22.9:1:29:1:0.713:1.22:60:63:0.2188:0:1.1 +5 149453450 . T C 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCTTCTGGTCATAAAT;RSEQ=AGTCAATGCGGCTTCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:9.7:1:32.7:1:1:0:58.3:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149454981 . G A 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTTTTTCTCACTCTCTCCCC;RSEQ=CAGCCACACTGGCCCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:27:0:33:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:30.5:1:1:0:60:4:1:0:2.5 +5 149455029 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACATGGCAAGCACAGTCCC;RSEQ=CTGCAGGATGGAGCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:28:1:1:0:60:4:1:0:2.5 +5 149456771 . CT AA 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=3e-05;SOR=0.63488;LSEQ=TCCCTGACATCAGCTTCCTC;RSEQ=CAAAACCCTTCTGCTCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:749:420:231,189:182,136:318,420:0.5607:2,2:27.4:1:30.5:1:0.55021:1.09478:59.9:840:0.5683:0:1.1 0/1:639:286:169,117:190,152:342,286:0.4476:2,2:25.4:1:29.2:1:0.37471:1.16:60:285:0.4538:0.0391:1 +5 149456772 . T A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.84035;SOR=1.12776;LSEQ=CCCTGACATCAGCTTCCTCC;RSEQ=CAAAACCCTTCTGCTCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:751:13:6,7:181,137:318,13:0.0173:2,2:10.7:1:27.9:1:0.57043:1.53929:60:12:0.037:0:1.8 0/1:616:12:6,6:190,152:342,12:0.0195:2,2:14.4:1:26.4:1:0.77258:1.2492:60:11:0.0315:0:2.2 +5 149456811 . G A 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCCTGCAGGATCCCTACC;RSEQ=ACTGTCCACCACCACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:859:0:0,0:466,392:858,0:0:2,0:25.7:1:30.8:1:1:0:59.9:56.2:1:0:0.5 0/1:742:89:48,41:362,291:653,89:0.1199:2,2:19.9:1:29.7:1:0.82072:1.06246:60:88:0.1221:0:1.2 +5 149457019 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08597;SOR=Inf;LSEQ=CTGCAGCCAGAAGGAATGGA;RSEQ=ATGTTATACCAAGGTAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:64,298:362,0:0:2,0:24.1:1:32.4:1:1:0:60:71.4:1:0:0.1 0/1:287:3:2,1:54,230:284,3:0.0105:2,2:20:1:27.3:1:0.09835:8.43:60:6:0.0106:0:1.7 +5 149457041 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17573;SOR=Inf;LSEQ=TGTTATACCAAGGTAGTTTA;RSEQ=GGATTAGAAAGATCTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:20,219:239,0:0:2,0:25.6:1:31.8:1:1:0:59.8:238:1:0:0.1 0/1:173:2:1,1:13,158:171,2:0.0116:2,2:22:1:28:1:0.15573:11.75:60:4:0.0116:0:1 +5 149457493 . A G 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=CGGCACAAGCATGAGTCCTG;RSEQ=TTCTGTGTCAGCTACTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:60,0:60,0:0:1,0:24:1:29.6:1:1:0:59.6:19:1:0:0.4 0/1:18:6:5,1:12,0:12,6:0.3333:0,2:13.7:1:32:1:0.33333:0:60:12:0.3529:0:1.2 +5 149457678 . G A 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.58633;LSEQ=GATCTGCAGGGACTGACCTT;RSEQ=GTGTTGTTGTGTTGGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:947:534:272,262:212,200:412,534:0.5639:2,2:26.9:1:30.1:1:0.89572:1.02101:59.9:58.333:0.5639:0:1.1 0/1:835:360:184,176:261,209:470,360:0.4311:2,2:26.9:1:28.5:1:0.20725:1.19425:60:39:0.4301:0:1.1 +5 149458110 . C T 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTGCCTCCCTCCAAGCCCCC;RSEQ=ACACCTAGATTCTTCACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:32:0:30:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:27:1:1:0:60:4:1:0:2 +5 149458128 . T C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACACCTAGATTCTTCAC;RSEQ=AAAGTGACCTCTTACAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27.5:1:32.5:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:30:1:1:0:60:4:1:0:2 +5 149459381 . T C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39148;SOR=0.40125;LSEQ=TTTGTAGCATGTCCAATGAC;RSEQ=TGAGATGACCTTGCCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:18:18,0:7,0:7,18:0.72:0,1:19.4:1:31.3:1:1:0:60:36:0.72:0:1.5 1/0:8:4:4,0:4,0:4,4:0.5:0,0:31.5:1:32.5:1:1:0:60:8:0.5:0:1 +5 149459538 . C T 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8401;LSEQ=CCCCCATCACACCCAGTCCC;RSEQ=AGTCACCACCCATGTGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:3:1,2:247,44:291,3:0.0102:2,2:15.3:1:21.7:1:0.06485:11.07471:60:2:0.0071:0:2.7 0/0:233:2:1,1:187,44:231,2:0.0086:2,2:23.5:1:14.5:1:0.34964:4.21374:60:0:0:0:5.5 +5 149459574 . C T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15281;LSEQ=GGCCGCCGGCTCTCTGTCCC;RSEQ=ACTCTTCAGGCCTGGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:203:131,72:221,109:330,203:0.3809:2,2:25.3:1:30:1:0.57319:1.11413:59.9:28:0.3769:0:1.3 0/1:443:38:26,12:248,156:404,38:0.0858:2,2:30.2:1:29:1:0.48527:1.36:60:76:0.087:0:1.1 +5 149459915 . G A 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37901;SOR=0.28492;LSEQ=AGGGTCTAGAGTAGAGGAGG;RSEQ=CACAGGGTTACAACTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:4:3,1:120,235:355,4:0.0111:2,2:17:1:28.8:1:0.11828:5.84:60:8:0.0116:0:1.3 0/0:313:1:1,0:119,193:312,1:0.0032:2,0:1:0:26:0:0.38339:0:60:2:0.0033:0:1 +5 149460176 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00158;SOR=Inf;LSEQ=CCGACTTGCAGGGTTGTTGT;RSEQ=AGGACTGCATTACATTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:47,7:54,0:0:2,0:23.9:1:31.7:1:1:0:59.8:17:1:0:0.1 0/1:15:4:4,0:10,1:11,4:0.2667:2,0:23.8:1:29:1:1:0:60:8:0.2667:0:1 +5 149460271 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13492;SOR=Inf;LSEQ=TTACGATTGTTAATTTTAGG;RSEQ=CCCATTGTAGTGGGGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:196,14:210,0:0:2,0:24.8:1:31.5:1:1:0:60:41:1:0:0 0/1:123:2:2,0:109,12:121,2:0.0163:2,0:28.5:1:31.5:1:1:0:60:4:0.0164:0:1 +5 149460291 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14545;SOR=Inf;LSEQ=GCCCATTGTAGTGGGGCCTG;RSEQ=CGGGTCAGGCCTCTTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:279,30:309,0:0:2,0:23.6:1:32.5:1:1:0:60:308:1:0:0.1 0/1:191:2:1,1:164,25:189,2:0.0105:2,2:23:1:27:1:0.25434:6.45219:60:4:0.0105:0:1 +5 149460334 . G T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01404;SOR=Inf;LSEQ=GGCTCAGACTCCTCACCTTT;RSEQ=ACATAGAGGTGGATGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:621:0:0,0:420,201:621,0:0:2,0:25.1:1:32.1:1:1:0:60:68:1:0:0.1 0/1:463:5:2,3:300,158:458,5:0.0108:2,2:13.4:1:24.6:1:0.34734:2.84118:60:4:0.0088:0:1.2 +5 149460553 . A G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29168;SOR=0.88451;LSEQ=CCTGGCTTCACGACCAGCTC;RSEQ=GGGACACTGGGCTCTATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:705:403:148,255:121,179:300,403:0.5716:2,2:25.6:1:30.7:1:0.34701:1.16443:59.9:99.75:0.5725:0:1.1 1/0:617:334:139,195:105,177:282,334:0.5413:2,2:26.1:1:29.7:1:0.28307:1.20:60:110.333:0.5417:0:1.2 +5 149460627 . G A 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=0;LSEQ=GCAGACAGAAGTGAGGTCTA;RSEQ=GATGCGCCCCTTGGGCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:22:5,17:44,201:245,22:0.0824:2,2:23.5:1:32:1:0.56881:1.34:60:44:0.0827:0:1.2 0/0:152:0:0,0:34,118:152,0:0:2,0:22.8:1:30.9:1:1:0:60:151:1:0:0.4 +5 149460645 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11725;SOR=Inf;LSEQ=TAGGATGCGCCCCTTGGGCC;RSEQ=TCCTGACTCTGAGATGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:23,170:193,0:0:2,0:23.8:1:32.1:1:1:0:60:192:1:0:0.3 0/1:101:2:1,1:18,81:99,2:0.0198:2,2:11:1:31.5:1:0.34238:4.41:60:4:0.0202:0:1 +5 149460953 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AACCCTGTGTACAAAGTGGA;RSEQ=GTATTTCTACCACCGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:16.7:1:29.7:1:1:0:60:6:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:9:0:32.5:1:1:0:60:4:1:0:0 +5 149466072 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13612;SOR=Inf;LSEQ=TCAGCTACTAGCTCCGCAGG;RSEQ=ATCGGGACACTGGACACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:38,281:319,0:0:2,0:24:1:31.8:1:1:0:59.9:62.8:1:0:0.1 0/1:187:2:1,1:35,150:185,2:0.0107:2,2:22:1:28:1:0.3488:4.24:60:4:0.0107:0:1 +5 149495050 . T C 97 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAAGCCTAACTTTCCCAT;RSEQ=TTACATATGGGAAAACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:31.1:1:32.5:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149495253 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23375;LSEQ=CTGGCTGACAGGAAGCCCGG;RSEQ=CAGGCCAGGCCAGGAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:190:160:129,31:24,6:30,160:0.8421:2,2:23.3:1:32.2:1:1:1.04:60:79:0.8404:0:1.5 1/0:112:62:44,18:38,12:50,62:0.5536:2,2:23.7:1:30.8:1:0.66868:1.29247:60:124:0.5536:0:1.4 +5 149495285 . A AG 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.63242;SOR=1.67663;LSEQ=AGGAGATGCTGGGTGCTGGC;RSEQ=GGGGGGGAGCTTCAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:2:1,1:248,86:334,2:0.006:2,2:49:1:32.5:1:0.45139:2.87287:60:4:0.0062:0:2 0/1:201:2:2,0:132,66:198,2:0.01:2,0:13:1:32.3:1:1:0:60:4:0.0103:0.005:1.5 +5 149495287 . G C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=0.26513;LSEQ=GAGATGCTGGGTGCTGGCAG;RSEQ=GGGGGAGCTTCAGGCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:118:97,21:158,68:226,118:0.343:2,2:24.8:1:32.5:1:0.01391:1.98:60:117:0.3482:0:1.6 0/1:206:25:20,5:114,59:173,25:0.1214:2,2:25.9:1:31.2:1:0.17827:2.06:60:50:0.1225:0:1.8 +5 149495395 . T C 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14063;LSEQ=TCCGGCAACTGTTCCAGCTC;RSEQ=GGCTCCGGCTCCACCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1009:881:552,329:80,45:125,881:0.8731:2,2:24.2:1:30.6:1:0.84333:1.05953:59.9:61.929:0.8731:0:1.1 0/1:828:407:248,159:249,171:420,407:0.4915:2,2:22.9:1:29.8:1:0.67009:1.07:59.9:80.4:0.4896:0:1.2 +5 149495770 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCAGCTGGCTCCAAAGCTC;RSEQ=TTTCTCACCCACCAGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:1,12:0,2:2,13:0.8667:0,1:30.2:1:30.4:1:1:0:55.6:12:0.8571:0:1.2 1/1:2:2:0,2:0,0:0,2:1:0,0:37.5:1:31.5:1:1:0:60:4:1:0:1.5 +5 149496321 . A G 25 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCTGCACTTCACTCCTCTGC;RSEQ=CCATCCACTGGGACTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:27:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:1:25.5:1:1:0:60:4:1:0:1 +5 149497099 . GCGCGCGCGCACACA G 184 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=17.000;MSILEN=2;SSF=0.00605;SOR=0.42723;LSEQ=GCAAACCTGGCAGCGCGCGC;RSEQ=CACACACACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:60:51,9:156,11:167,60:0.239:2,2:22.3:1:31.3:1:0.06267:2.49095:57.3:120:0.2429:0.0996:0.6 0/1:127:15:12,3:99,4:103,15:0.1181:1,2:24.1:1:31.5:1:0.04304:6.02921:57.3:30:0.124:0:0.5 +5 149497109 . A G 178 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=2;SSF=0.0465;SOR=0.58246;LSEQ=CAGCGCGCGCGCGCGCGCGC;RSEQ=CACACACACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:65:59,6:57,6:63,65:0.2621:2,2:15.6:1:29.6:1:1:1.03:59:64:0.4638:0:2.6 0/1:146:25:23,2:57,4:61,25:0.1712:2,2:17.7:1:27.5:1:1:1.23589:59:11.5:0.2738:0:2.1 +5 149497177 . T C 294 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17248;LSEQ=TTGGCCCCAGGCCAGGGTGG;RSEQ=TACCTGGCTAGGCTGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:739:641:391,250:53,44:97,641:0.8674:2,2:25.6:1:31.6:1:0.26583:1.30:59.2:19.677:0.864:0:1.7 1/0:555:294:173,121:144,115:259,294:0.5297:2,2:25.6:1:30.8:1:0.49075:1.14:59.6:35.75:0.5306:0:1.5 +5 149497184 . G T 56 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04684;SOR=8.05045;LSEQ=CAGGCCAGGGTGGTTACCTG;RSEQ=CTAGGCTGGGGGAACCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:791:1:1,0:469,321:790,1:0.0013:2,0:15:0:13:0:1:0:51:0:0:0:5 0/1:594:6:2,4:332,256:588,6:0.0101:2,2:15.3:1:22:1:0.41213:2.58965:58.8:5:0.0088:0:2.3 +5 149497228 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.32999;LSEQ=GGGCCCTCGTCAGCAACCTC;RSEQ=GGTTTGGGGTCAGGCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1010:350:186,164:330,328:658,350:0.3465:2,2:24.9:1:31:1:0.38976:1.13:59.9:49:0.3458:0:1.5 0/1:786:117:61,56:318,348:666,117:0.1489:2,2:26.3:1:29.4:1:0.42258:1.19:60:22.4:0.1449:0:1.6 +5 149497419 . C A 40 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22753;SOR=2.97899;LSEQ=CACCTGCTGGTACTTCTGCT;RSEQ=CCGGGGCAGGGAGAACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:2:1,1:174,345:519,2:0.0038:2,2:24:1:18.5:1:1:1.98:60:1:0.002:0:2 0/1:352:4:3,1:127,221:348,4:0.0114:2,2:9:1:20.3:1:0.14437:5.20:60:3:0.0086:0:2 +5 149497672 . C T 60 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTAACTCTTCCCCCACTT;RSEQ=AGAGCAGACAGGCACAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:12.5:1:30.3:1:1:0:60:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149497815 . A G 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGTGGGGGTGAGAAATG;RSEQ=ACCCAAAGAAGGAGCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:32.3:1:31.5:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149498064 . C G 93 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCAGCAGGACAGACAGTGCT;RSEQ=TAGGCCCCCTCCCTGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:6,1:12,0:12,7:0.3684:0,2:31.3:1:33.3:1:0.36842:0:60:14:0.3684:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149498151 . G A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53412;SOR=0.71672;LSEQ=TGCTAAAATAAACTCACAGC;RSEQ=CCAGCCCATCCCCTCCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:28:28,0:32,0:32,28:0.4667:1,1:25.4:1:30.3:1:1:0:60:27:0.4576:0:1.1 0/1:39:15:15,0:24,0:24,15:0.3846:1,1:21.1:1:30.3:1:1:0:60:30:0.3947:0:1.2 +5 149498193 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13082;SOR=Inf;LSEQ=CCAGCAGGGAAACTGAGGCC;RSEQ=AGAGAGGACAAAGGGTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:133,2:135,0:0:1,0:24.3:1:31.6:1:1:0:60:270:1:0:0.3 0/1:77:2:1,1:75,0:75,2:0.026:1,2:20.5:1:28:1:0.02597:0:60:4:0.026:0:1 +5 149498759 . A T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTGGGACTTTTGCTGGC;RSEQ=CTATGGAGCAAGCAGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:11,2:13,2:0.1333:2,2:21.5:1:29.5:1:0.37143:4.69047:53:4:0.1429:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149498821 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCATTTGGGCAATGCTGG;RSEQ=CTGAAAATGAGGCCACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:22,2:24,2:0.0769:2,0:23:1:30:1:1:0:60:4:0.08:0:1.5 0/0:6:0:0,0:6,0:6,0:0:0,0:29.7:1:31.5:1:1:0:60:12:1:0:0.3 +5 149498871 . AG A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09599;SOR=0.42631;LSEQ=GAGCTCAGGGCTAGAACAAG;RSEQ=GTTCCTGATGCCATCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:32:31,1:26,1:27,32:0.5424:1,1:21.7:1:33:1:1:1.19:60:64:0.5517:0.1356:0 0/1:24:8:7,1:16,0:16,8:0.3333:1,2:24.6:1:30.5:1:0.33333:0:60:16:0.3478:0.0417:0 +5 149499672 . T C 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.29807;LSEQ=CTCTCCGGAGCCATCCACTT;RSEQ=AAAGGCAAAAAGGTCTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:761:432:170,262:119,209:328,432:0.5677:2,2:25.6:1:32.1:1:0.40714:1.14:59.9:85.4:0.5671:0:1.1 0/1:683:192:83,109:196,294:490,192:0.2811:2,2:27.6:1:30.6:1:0.48856:1.14:60:47:0.2781:0:1.2 +5 149499733 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07779;SOR=Inf;LSEQ=AGTGCAAGGAAGGACCTCAG;RSEQ=CCCACTCTGCACCTGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:51,239:290,0:0:2,0:24.7:1:31.4:1:1:0:59.9:71.5:1:0:0.4 0/1:217:3:1,2:44,170:214,3:0.0138:2,2:17:1:27.7:1:0.50384:1.92:60:6:0.0142:0:1 +5 149499796 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11721;SOR=Inf;LSEQ=CCACCCACAACCACTTCTCC;RSEQ=TCCCATTCCCTGTGAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:1,96:97,0:0:1,0:22.6:1:32.4:1:1:0:59.5:47.5:1:0:0.1 0/1:51:2:0,2:1,48:49,2:0.0392:1,0:43.5:1:30:1:1:0:60:4:0.0392:0:1 +5 149500236 . C T 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.69682;SOR=0.66946;LSEQ=CCATTATAGCCAGCCCTCCC;RSEQ=GCCGCTATACTTGCTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:10,0:11,0:11,10:0.4762:0,0:25.8:1:30.9:1:1:0:60:9:0.45:0:2.2 0/1:8:3:2,1:5,0:5,3:0.375:0,2:27.3:1:32.3:1:0.375:0:60:6:0.375:0:1 +5 149500363 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51679;SOR=0;LSEQ=GCCCCACACAGATTTCCTAT;RSEQ=AGCTGCAGCCACACTGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:167,8:175,2:0.0113:1,2:17:1:28.5:1:0.09938:19.74323:60:4:0.0114:0:1 0/0:120:0:0,0:107,13:120,0:0:2,0:21.3:1:31.7:1:1:0:59.8:119:1:0:0.1 +5 149500402 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06869;SOR=Inf;LSEQ=CAGGAGGGAATCTGTTCCTG;RSEQ=GGTCACAGGCACTGTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:298,110:408,0:0:2,0:23.4:1:31.5:1:1:0:59.9:203:1:0:0.1 0/1:284:3:1,2:207,74:281,3:0.0106:2,2:17.3:1:26:1:0.17554:5.55392:60:6:0.0106:0:1 +5 149500423 . C T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.08744;SOR=7.11319;LSEQ=GGTCACAGGCACTGTGACTG;RSEQ=CCTGCAGGGGCCAGGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:1:0,1:381,192:573,1:0.0017:2,0:1:0:27:0:0.33624:0:60:2:0.0018:0:1 0/1:407:5:2,3:262,140:402,5:0.0123:2,2:20.6:1:25.6:1:0.34942:2.79952:60:10:0.0126:0:1 +5 149500434 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00579;SOR=Inf;LSEQ=CTGTGACTGCCCTGCAGGGG;RSEQ=CAGGGAAGGTACTCACGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:671:0:0,0:428,243:671,0:0:2,0:25.5:1:31.4:1:1:0:60:28.174:1:0:0.1 0/1:496:6:1,5:298,191:489,6:0.0121:2,2:12.7:1:25:1:0.03822:7.77004:60:12:0.0124:0:1 +5 149500514 . C T 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAGGCCAAAGTCACAGAT;RSEQ=TTGACCAGCTTGCCTTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1019:0:0,0:507,509:1016,0:0:2,0:26.1:1:32.5:1:1:0:60:58.765:0.998:0:0.2 0/1:827:32:14,18:382,413:795,32:0.0387:2,2:29.8:1:30.3:1:0.71941:1.18896:60:64:0.0393:0:1.2 +5 149500934 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16425;SOR=Inf;LSEQ=ATCTTATATCTCCTTCTGGC;RSEQ=CACAGGACCCCTGCCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:52,207:259,0:0:2,0:23.8:1:31.1:1:1:0:60:42.167:1:0:0.1 0/1:177:2:1,1:48,127:175,2:0.0113:2,2:14.5:1:29.5:1:0.47817:2.63:60:4:0.0115:0:1 +5 149501751 . A C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73297;SOR=0.79716;LSEQ=AGGAAAGCCTGTGGATCAAG;RSEQ=CTTTTCAACCAACCTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:34:0,34:0,18:18,34:0.6538:1,1:22:1:29.7:1:1:0:60:10.333:0.6327:0:1.4 1/0:10:6:0,6:0,4:4,6:0.6:0,0:27.2:1:31.5:1:1:0:60:12:0.6:0:1.3 +5 149501803 . C T 83 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19087;LSEQ=CACTGAGGCTACCAAAATGA;RSEQ=AGTTAGAACCCAGAGAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:0,10:1,11:12,10:0.4545:2,0:20.9:1:25.1:1:1:0:60:4:0.4211:0:1.9 1/0:2:1:0,1:0,1:1,1:0.5:0,0:21:0:29:0:1:0:60:2:0.5:0:2 +5 149502529 . C A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03276;SOR=Inf;LSEQ=TCACAGCCTCAGCTTCCCCT;RSEQ=CTGGACAAAAGGAGGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:95,7:102,0:0:2,0:25.3:1:32.5:1:1:0:60:204:1:0:0 0/1:49:3:3,0:40,6:46,3:0.0612:2,0:27.7:1:25:1:1:0:60:6:0.0625:0:1 +5 149502576 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15666;SOR=Inf;LSEQ=TGCTCCTCAGGTATCCCAAA;RSEQ=ATTCAGTCCCTGGCCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:197,48:245,0:0:2,0:22.3:1:33.2:1:1:0:59.9:490:1:0:0.1 0/1:161:2:1,1:128,31:159,2:0.0124:2,2:32:1:30:1:0.35901:4.07985:60:4:0.0126:0:1 +5 149502838 . G C 211 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAGGCCATGAGGCTAATCA;RSEQ=GGGCTGGATGTGGGAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:220:121:11,110:6,93:99,121:0.55:2,2:24.4:1:30.5:1:0.45585:1.55:60:120:0.5556:0:1.1 0/0:104:0:0,0:16,88:104,0:0:2,0:21.8:1:30.5:1:1:0:60:208:1:0:0.1 +5 149502881 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09545;SOR=Inf;LSEQ=TTTGGCATGACGGCTAGGAG;RSEQ=CTTTAGTGCCTTGCAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:0,104:104,0:0:1,0:22.7:1:32.6:1:1:0:60:51:1:0:0.5 0/1:47:2:1,1:1,44:45,2:0.0426:1,2:30.5:1:27.5:1:0.08418:31.47:60:4:0.0426:0:1 +5 149503670 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=0.26543;LSEQ=CCCCACCGCCCTCTGGGACC;RSEQ=CGCAGTGAGGGCGCTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:81:76,5:53,1:54,81:0.6:1,2:24.5:1:30.7:1:0.40133:3.46039:59.8:39.5:0.6031:0:1.1 0/1:60:17:17,0:42,1:43,17:0.2833:1,1:22.1:1:30:1:1:0:60:34:0.2931:0:1 +5 149503739 . AG A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.57521;SOR=0.63907;LSEQ=GTGCTGTTGTGCAAGGCCTG;RSEQ=GGGGGGGTAGGCGGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:9:5,4:346,88:434,9:0.0203:2,2:22.9:1:32.2:1:0.09397:3.13484:60:18:0.0206:0.0045:0.3 0/1:306:4:4,0:216,86:302,4:0.0131:2,0:36.3:1:32.8:1:0.57971:0:60:8:0.0132:0:0 +5 149503974 . A G 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55644;SOR=0;LSEQ=CAGTCATGGAGGCTCCATGG;RSEQ=GGCCCCACCACAGGAGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:3:2,1:37,236:273,3:0.0108:2,2:20.3:1:24.7:1:0.0533:12.55:60:2:0.0074:0:1 0/0:157:0:0,0:24,133:157,0:0:2,0:20.9:1:30.2:1:1:0:60:77.5:1:0:0.1 +5 149504115 . A T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00165;SOR=0.24646;LSEQ=GCAGGCCGAGGAGGCCAGGG;RSEQ=GAGGAACGCTCTTTCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:78:63,15:39,11:50,78:0.6094:2,2:20.7:1:30.8:1:0.82236:1.18:59.7:156:0.624:0:1.8 0/1:29:8:8,0:18,3:21,8:0.2759:2,0:25.8:1:28.3:1:0.54023:0:60:16:0.2857:0:1.6 +5 149504155 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGACCCAGACTCGGGAG;RSEQ=AGTGCCTGCTGCAGTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:172,12:184,2:0.0108:2,2:28.5:1:29:1:0.13525:13.811:60:4:0.0109:0:3 0/0:75:0:0,0:70,5:75,0:0:2,0:20.9:1:32.2:1:1:0:60:150:1:0:0.6 +5 149504158 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08558;SOR=0.62126;LSEQ=AGACCCAGACTCGGGAGCAG;RSEQ=GCCTGCTGCAGTGTGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:195:117:107,10:74,4:78,117:0.6:2,2:25.2:1:32.1:1:0.41229:1.72441:60:38:0.6:0:1.6 0/1:83:40:39,1:39,4:43,40:0.4819:2,1:18.8:1:32.3:1:0.36118:3.94:60:80:0.4819:0:1.4 +5 149504167 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09489;SOR=Inf;LSEQ=CTCGGGAGCAGTGCCTGCTG;RSEQ=AGTGTGATGGCCCCTCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:214,14:228,0:0:2,0:24.3:1:32.3:1:1:0:60:44.6:1:0:0.9 0/1:102:2:1,1:96,4:100,2:0.0196:1,2:29.5:1:30.5:1:0.0961:21.5779:60:4:0.0198:0:2 +5 149504192 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1159;SOR=Inf;LSEQ=TGATGGCCCCTCTAGTGCCT;RSEQ=CAAATCAGCATCAGGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:259,49:308,0:0:2,0:24.2:1:32.1:1:1:0:60:43:1:0:0.6 0/1:160:2:2,0:138,20:158,2:0.0125:2,0:21.5:1:29.5:1:1:0:60:4:0.0125:0:1 +5 149504348 . C T 130 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00045;SOR=4.60535;LSEQ=GAATGGCTCAGGCCATGAGC;RSEQ=GTGGCCTCCACCACCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:985:6:1,5:462,515:977,6:0.0061:2,2:7.8:1:24.3:1:0.22205:4.4797:60:5:0.0052:0:1 0/1:728:20:8,12:320,386:706,20:0.0275:2,2:31.6:1:30.2:1:0.82048:1.24315:60:40:0.0278:0:1.1 +5 149505174 . G A 72 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=CCCAGGAATTAGTTATCAGA;RSEQ=GGAGTCTCAGGCCCTGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:858:0:0,0:286,572:858,0:0:2,0:24.7:1:31.8:1:1:0:59.9:121.571:1:0:0.1 0/1:620:8:6,2:216,395:611,8:0.0129:2,2:7.9:1:24.1:1:0.02788:5.47:60:7:0.0115:0:1.5 +5 149505259 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.03294;SOR=Inf;LSEQ=AGGCCCAGAGAGGGGCAGGG;RSEQ=CATATTTGAAGTCACACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:3,139:142,0:0:1,0:25.4:1:32.7:1:1:0:60:70:1:0:0.3 0/1:68:3:0,3:2,63:65,3:0.0441:1,0:15:1:29.3:1:1:0:60:6:0.0441:0:1 +5 149505291 . T C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08475;SOR=Inf;LSEQ=TCACACAGCAAGTGCTCAAC;RSEQ=GAGCCAAGGTCTTCGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:2,82:84,0:0:1,0:23.5:1:30.4:1:1:0:60:20:1:0:0.6 0/1:35:2:1,1:1,32:33,2:0.0571:1,2:18:1:26.5:1:0.11261:22.98:60:4:0.0571:0:1.5 +5 149505306 . G A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63372;SOR=1.29608;LSEQ=TCAACTGAGCCAAGGTCTTC;RSEQ=TGGGCTCGGAGGGAACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:32:0,32:0,32:32,32:0.5:1,1:19:1:31.5:1:1:0:60:64:0.5161:0:1 1/0:23:13:1,12:0,10:10,13:0.5652:0,1:27.3:1:30.9:1:1:0:60:26:0.5652:0:1.2 +5 149505327 . A G 130 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05041;SOR=0.14775;LSEQ=TGGGCTCGGAGGGAACAGGG;RSEQ=CCAAGGGGCCCCAGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:16:0,16:0,30:30,16:0.3478:1,1:21.3:1:32.6:1:1:0:60:32:0.3478:0:1.4 0/1:14:1:0,1:1,12:13,1:0.0714:1,0:1:0:30:0:1:0:60:2:0.0714:0:1 +5 149509111 . C T 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04513;SOR=8.1767;LSEQ=ATATTCATATCCATGGCTTA;RSEQ=AGACTTGTGTTTGTACACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:3,0:26,1:27,3:0.1:1,0:31.7:1:31.3:1:1:0:60:6:0.1034:0:1 1/0:6:3:3,0:3,0:3,3:0.5:0,0:23.7:1:31.3:1:1:0:60:6:0.5:0:1 +5 149509243 . A T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03736;SOR=Inf;LSEQ=TCCTTTGGCCTGCTGTGGGT;RSEQ=CATGGGCACATTACCAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:196,33:229,0:0:2,0:22.7:1:28.5:1:1:0:59.8:458:1:0:0.2 0/1:116:3:1,2:86,27:113,3:0.0259:2,2:8:1:25.7:1:0.15378:6.24361:60:6:0.0259:0:1.7 +5 149509270 . A G 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.83349;LSEQ=CACATTACCAATTAGGCAGG;RSEQ=TTAAGGTAGGGATTGGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:41:30,11:245,92:337,41:0.1085:2,2:22.4:1:31:1:1:1.02:60:40:0.1096:0:1 1/0:240:131:84,47:69,36:105,131:0.5458:2,2:22.7:1:30.8:1:0.89099:1.07208:60:64.5:0.5536:0:1.2 +5 149509290 . C A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATTAAGGTAGGGATTGGGAT;RSEQ=GTCAGGGGCCACTGAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:314,147:461,0:0:2,0:27:1:31.5:1:1:0:60:152.667:0.9978:0:0.2 0/1:344:14:8,6:214,116:330,14:0.0407:2,2:32.1:1:30:1:0.57637:1.38221:60:28:0.0417:0:1.8 +5 149509619 . C T 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=ACTGGTGGAAGGAGGCAGGA;RSEQ=GTGTCCAGTTCCTATGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:2,106:108,0:0:1,0:25:1:30.8:1:1:0:59.6:216:1:0:0.1 0/1:53:6:1,5:0,47:47,6:0.1132:1,2:23.7:1:30.7:1:0.11321:0:60:12:0.1154:0:1 +5 149510290 . A C 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=AGTTAACAGGACAGGTCCTC;RSEQ=GGGGAGGACCTGGCCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:39,206:245,0:0:2,0:24:1:31.7:1:1:0:60:121.5:1:0:0.1 0/1:165:11:3,8:37,117:154,11:0.0667:2,2:19.1:1:26.8:1:0.72881:1.18:60:10:0.0613:0:1.1 +5 149511666 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03984;SOR=Inf;LSEQ=TCTGACACATACCTGGGGAG;RSEQ=AGGAAAGGCAGCTGTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:121,366:487,0:0:2,0:25:1:32:1:1:0:60:33.786:0.9916:0:0.1 0/1:398:4:2,2:120,274:394,4:0.0101:2,2:15.3:1:28.8:1:0.58937:2.28:60:8:0.0102:0:1 +5 149511792 . G A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5646;SOR=0;LSEQ=TCGGCATTGGTAGCAGAGCC;RSEQ=GGACTCAAACCAGGTCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:4:0,4:1,44:45,4:0.0816:1,0:20.3:1:32.5:1:1:0:60:8:0.0833:0:1 0/0:16:0:0,0:1,15:16,0:0:1,0:18.1:1:30.3:1:1:0:60:32:1:0:0.1 +5 149512042 . G A 32 v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCCCAGTCATCTGCCC;RSEQ=TTTACTTCTTGGCTGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:6,0:6,2:0.25:0,2:30:0:32.5:1:0.25:0:60:4:0.25:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 149512258 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16158;SOR=Inf;LSEQ=CTGAAAGCCGAGGGCTGCCT;RSEQ=GCGGCTGCAAAGAAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:129,22:151,0:0:2,0:25.4:1:32.4:1:1:0:60:150:1:0:0.2 0/1:102:2:1,1:85,15:100,2:0.0196:2,2:20.5:1:26.5:1:0.29043:5.51898:60:4:0.0198:0:1 +5 149512501 . G A 55 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4902;SOR=1.81977;LSEQ=CCCAGGAGCCGCACGTAGCC;RSEQ=CTCTCTGCAAGGGGTGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:3:1,2:126,251:377,3:0.0079:2,2:24.7:1:29:1:1:1.00397:60:6:0.008:0:1 0/1:350:5:3,2:125,220:345,5:0.0143:2,2:8.6:1:24:1:0.35978:2.63:60:1.5:0.0087:0:1 +5 149513072 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=20.49877;LSEQ=AAAATGCAACTCTCACCATC;RSEQ=CTCTGCACCCAGCAAAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:6:6,0:214,37:251,6:0.0233:2,0:25:1:30.5:1:0.59773:0:60:12:0.0237:0:1 0/1:209:69:59,10:116,23:139,69:0.3301:2,2:20.8:1:30:1:0.84085:1.17:60:68:0.3333:0:1.1 +5 149513626 . T G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15421;SOR=2.04902;LSEQ=TCACCACCAGCCACTAGCAC;RSEQ=TCAGCTTGGGGATAGGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:9:1,8:30,180:210,9:0.0411:2,2:29.2:1:33.1:1:1:1.33174:60:18:0.0415:0:1 0/1:136:11:2,9:24,100:124,11:0.0809:2,2:27.4:1:31:1:1:1.0794:59:22:0.0809:0:1.1 +5 149514660 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54823;SOR=0;LSEQ=TGCTGTGTGGCAAGTCATTT;RSEQ=CCATCTCTGGCCCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:12,182:194,2:0.0102:2,2:24.5:1:28:1:0.12857:14.61:60:4:0.0104:0:1 0/0:102:0:0,0:11,91:102,0:0:2,0:24.4:1:31.4:1:1:0:60:101:1:0:0.1 +5 149514958 . T G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCCAGACCAAGGAGTGGG;RSEQ=GCGAACACACTCCCCGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:53:50,3:0,0:0,53:1:0,2:22.6:1:31.5:1:1:0:59.7:106:1:0:1 1/1:16:16:16,0:0,0:0,16:1:0,1:24.3:1:32:1:1:0:60:32:1:0:1 +5 149515074 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=12.78334;LSEQ=TTCCCCTGATGCCTCCAGTT;RSEQ=ACAAGAGGGGTAAGGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:16:13,3:312,86:398,16:0.0386:2,2:25.3:1:28.6:1:1:1.19:60:32:0.0391:0:1 0/1:315:107:79,28:157,51:208,107:0.3397:2,2:24.7:1:27.4:1:0.78437:1.09078:60:25.75:0.3411:0:1.1 +5 149515397 . T A 135 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=39.1857;LSEQ=GACGACCAGGCCCTGAGAGA;RSEQ=CTGTGGTTCCAGAAGTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:664:1:1,0:269,393:662,1:0.0015:2,0:23:0:14:0:0.40724:0:60:0:0:0:3 0/1:483:27:13,14:190,266:456,27:0.0559:2,2:21.7:1:28.4:1:0.55046:1.30:60:26:0.0552:0:1.2 +5 149515468 . A G 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29077;SOR=3.62878;LSEQ=GAGAGGAGGTATCAGACATC;RSEQ=GGAAACAGGGGCTTCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:0,1:39,205:244,1:0.0041:2,0:47:0:31:0:1:0:51:2:0.0041:0:1 0/1:136:2:1,1:38,96:134,2:0.0147:2,2:31:1:28.5:1:0.49281:2.51:60:4:0.0149:0:1 +5 149515577 . G A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10204;SOR=Inf;LSEQ=CCTTTATCCGACAGACTGGG;RSEQ=CTCTCCAGCCATGGCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:0,33:33,0:0:1,0:23:1:32.2:1:1:0:58.7:32:1:0:0.2 0/1:16:2:1,1:1,13:14,2:0.125:1,2:5.5:1:25.5:1:0.24167:9.54:60:4:0.1333:0:1.5 +5 149516480 . C T 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.64214;LSEQ=GCAGTGTGCCTGGTGCTTCA;RSEQ=GCCCTGCCACCAGCACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:25:20,5:371,104:475,25:0.05:2,2:27.4:1:30.9:1:1:1.12:60:50:0.0505:0:1.1 0/1:370:96:70,26:184,90:274,96:0.2595:2,2:19.9:1:30.2:1:0.30975:1.32:60:192:0.263:0:1.2 +5 149516738 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11872;SOR=Inf;LSEQ=CCAGCCTTCATGTCCGAGGG;RSEQ=CTGAAGTCAAAAGCCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:8,206:214,0:0:1,0:25:1:32:1:1:0:59.9:25.75:1:0:0.1 0/1:113:2:1,1:11,100:111,2:0.0177:2,2:16.5:1:26.5:1:0.20196:8.75:60:4:0.0177:0:1 +5 149516774 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10036;SOR=Inf;LSEQ=ACCACGTCCCAAGCCTGAAA;RSEQ=GGCACTCATGACCACAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:2,122:124,0:0:1,0:24:1:31.1:1:1:0:59.6:19.667:1:0:0.2 0/1:58:2:0,2:3,53:56,2:0.0345:2,0:13:1:30.5:1:1:0:60:4:0.0351:0:1 +5 149782814 . C T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26202;SOR=0;LSEQ=CCGTTCTCGTCGCACTTGGG;RSEQ=CTGAATGAACCCGGGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:2,1:267,31:298,3:0.01:2,2:8.3:1:29.3:1:0.28708:4.27215:60:6:0.0103:0:1 0/0:230:0:0,0:193,37:230,0:0:2,0:23.2:1:31.1:1:1:0:60:75.667:1:0:0.1 +5 149783188 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04444;SOR=Inf;LSEQ=TCTTAGCACTTTGGGAGGCC;RSEQ=AGGTGGGCGGATCACTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:42,226:268,0:0:2,0:24.4:1:32.3:1:1:0:51.2:267:1:0:0.1 0/1:229:4:2,2:36,189:225,4:0.0175:2,2:10:1:29.3:1:0.12939:5.19:55.5:8:0.0176:0:1.5 +5 149783361 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1803;SOR=Inf;LSEQ=GAACCCGGGAGGCTGAGGTT;RSEQ=CAGTGAGCTGAGATCGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:192,16:208,0:0:2,0:25.3:1:32.3:1:1:0:33:28.714:1:0:0.1 0/1:154:2:1,1:148,4:152,2:0.013:1,2:20.5:1:30:1:0.06409:33.18104:28:4:0.0131:0:2.5 +5 149783694 . G A 200 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=73.25062;LSEQ=CCTTTGACCTTCTACTTCAG;RSEQ=ACCCTGAATCCTAGAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1813:2:2,0:873,938:1811,2:0.0011:2,0:1:0:20.5:1:0.23279:0:60:1:6e-04:0:1 0/1:1682:126:67,59:771,784:1555,126:0.0749:2,2:23.3:1:28.8:1:0.45955:1.15:59.9:62:0.0744:0:1.2 +5 149783879 . G A 210 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=49.81109;LSEQ=TGGCGCCCTCACTGGATTGC;RSEQ=GGCAGCACTGGGGCAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1594:3:2,1:765,822:1587,3:0.0019:2,2:4:1:29:1:0.61201:2.15:60:6:0.0019:0:1 0/1:1512:130:63,67:659,723:1382,130:0.086:2,2:26.1:1:30:1:0.92688:1.03:60:129:0.0861:0:1.2 +5 149784087 . G GGA 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.69138;SOR=1.20487;LSEQ=AAACCAAGAAGGAACAGACA;RSEQ=GAGAGAGAGAGAAGTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1078:11:6,5:512,555:1067,11:0.0102:2,2:20.7:1:31.2:1:0.76624:1.30:60:22:0.0104:0.0019:0.4 0/1:1141:14:7,7:554,570:1124,14:0.0123:2,2:20.9:1:28.8:1:1:1.03:60:13:0.0116:0.0026:0.4 +5 149784414 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13664;SOR=Inf;LSEQ=TTTGCCCCTGGGGACAGAAA;RSEQ=ATGCAGGGCCAAATAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,23:23,0:0:1,0:21.3:1:32.7:1:1:0:60:46:1:0:0.2 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:9.5:1:29:0:1:0:60:4:0.1429:0:1 +5 150229723 . C A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.026;SOR=Inf;LSEQ=GCTGCTGAAGGGTCCTATTT;RSEQ=TTTTCCTTTCTTTCATTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:96,18:114,0:0:2,0:20.5:1:32.1:1:1:0:60:113:1:0:0.1 0/1:78:4:4,0:61,13:74,4:0.0513:2,0:21:1:28:1:1:0:60:8:0.0513:0:1 +5 150229801 . A C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=5.03583;LSEQ=CATACGTAATTTAAAAAAAT;RSEQ=TGTATGGCAGTAAAAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:7:4,3:159,146:305,7:0.0224:2,2:22:1:33.4:1:1:1.22:60:14:0.0224:0:1.1 0/1:260:27:14,13:127,106:233,27:0.1038:2,2:27.5:1:31.1:1:0.84009:1.11208:60:54:0.1042:0:1 +5 150777720 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=CAGTCGTTGGATTAACTGAC;RSEQ=CAGCAACCATTGCCCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:26.1:1:30:1:1:0:60:14:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:12.5:1:28:1:1:0:60:4:0.6667:0:1.5 +5 150777953 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.36879;LSEQ=CCCGCAGTAATGCAGGTGTG;RSEQ=GGGCTGAAATATAATTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:42:19,23:153,133:286,42:0.128:2,2:29.3:1:30.1:1:0.32655:1.39114:60:41:0.1265:0:1.7 0/1:341:113:62,51:124,104:228,113:0.3314:2,2:27.7:1:28.7:1:1:1.02:59.9:55.5:0.3333:0:1.8 +5 150777997 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=3.28099;LSEQ=CCTTTTGCTTGGGGTGTTAA;RSEQ=AAGAAAGTATCATATGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:37:14,23:128,155:283,37:0.1156:2,2:21.4:1:32.7:1:0.48237:1.35541:60:74:0.1167:0:1.9 0/1:366:110:56,54:120,135:255,110:0.3005:2,2:23.8:1:31.2:1:0.56831:1.17:60:220:0.3064:0:1.9 +5 150778076 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00245;SOR=2.86762;LSEQ=AGTAGATACTGTACTGGAAC;RSEQ=AGAACTGAAGAAACCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:15:4,11:11,87:98,15:0.1327:2,2:26.8:1:28.3:1:0.1127:2.84:60:14:0.1261:0:1.3 0/1:98:30:3,27:12,56:68,30:0.3061:2,2:25.4:1:27.8:1:0.54328:1.9169:60:29:0.3021:0:1.6 +5 150778145 . A T 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27572;SOR=2.70643;LSEQ=AGAAAAAGCTCCAATTGCTC;RSEQ=TCCTTTATTCCAGCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:0,4:0,24:24,4:0.1429:1,0:32:1:31.5:1:1:0:60:8:0.1429:0:1.5 0/1:19:6:0,6:1,12:13,6:0.3158:1,0:16.8:1:31.3:1:1:0:60:12:0.3158:0:1.8 +5 151755922 . C T 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00111;SOR=Inf;LSEQ=TCAACCAGGAGGGTCTCCTC;RSEQ=GTGGAGAACAGTCAGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:101,13:114,0:0:2,0:25.6:1:31.2:1:1:0:60:113:1:0:0.2 0/1:105:9:8,1:85,11:96,9:0.0857:2,2:21.9:1:31.3:1:1:1.03:60:18:0.0874:0:1.2 +5 151755945 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49866;SOR=0;LSEQ=GGAGAACAGTCAGAAGTGGG;RSEQ=GCAGCAAGAGTGGAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:131,48:179,2:0.011:2,2:33:1:29:1:0.46924:2.71147:60:4:0.0111:0:1.5 0/0:177:0:0,0:126,51:177,0:0:2,0:23.8:1:30:1:1:0:60:28.5:1:0:0.5 +5 151755961 . TA T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.24984;SOR=Inf;LSEQ=TGGGGGCAGCAAGAGTGGAA;RSEQ=AAAAAATAAAAACCGGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:181,81:262,0:0:2,0:22.1:1:28.9:1:1:0:60:86.333:1:0:0.7 0/1:284:3:1,2:190,89:279,3:0.0106:2,2:15:1:28.7:1:0.24436:4.2455:60:6:0.0107:0.0035:0.3 +5 151756016 . G T 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16211;LSEQ=AGACCAGGTGGGAGAAGAAG;RSEQ=TAGCTTGGATTAGAGTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:563:495:275,220:41,27:68,495:0.8792:2,2:26.7:1:29.8:1:0.51552:1.2144:60:81.5:0.8779:0:1.1 1/0:599:324:172,152:149,125:274,324:0.5409:2,2:26.5:1:28.7:1:0.80504:1.05327:59.9:63.8:0.5379:0:1.2 +5 151756225 . G C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0018;SOR=0.07592;LSEQ=GTGGCTTTCCTGGAGCAATG;RSEQ=AAAGAAAAGCCTGAGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:25:1,24:0,4:4,25:0.8621:0,1:22.6:1:32.2:1:1:0:60:50:0.8621:0:1.2 0/1:10:3:0,3:1,6:7,3:0.3:2,0:37.7:1:32.7:1:1:0:60:6:0.3:0:1 +5 151756309 . G T 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAGATTGATGCAATTTT;RSEQ=CTAGTAAAAAAGAAGCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:15.8:1:31.3:1:1:0:60:8:0.5714:0:1.8 0/0:1:0:0,0:0,1:1,0:0:0,0:5:0:31:0:1:0:60:2:1:0:0 +5 151756408 . A G 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATATTATTTTTAAAACAAC;RSEQ=CACAAAAGATAGGAAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:9:1:34.3:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 153690374 . T C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02679;SOR=0.47953;LSEQ=CTTAAATCAGCTCTTCTCCT;RSEQ=TGAAATTAAATGACTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:131:115:88,27:11,5:16,115:0.8779:2,2:21.9:1:32.4:1:0.5382:1.48:59.7:230:0.8779:0:1.5 1/0:142:110:77,33:20,12:32,110:0.7746:2,2:23.1:1:30.7:1:0.51766:1.40:59.9:220:0.7746:0:1.7 +5 153690415 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24961;SOR=Inf;LSEQ=CTGAACAGTGGTGTTTCTTC;RSEQ=ACGATAACAGTTATTGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:164,107:271,0:0:2,0:25.3:1:31.4:1:1:0:60:53.2:1:0:1.2 0/1:291:3:2,1:169,119:288,3:0.0103:2,2:32:1:28.3:1:1:1.41:60:6:0.0104:0:2 +5 153690417 . C A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01322;SOR=1.51639;LSEQ=GAACAGTGGTGTTTCTTCCA;RSEQ=GATAACAGTTATTGATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:140:84,56:89,59:148,140:0.4861:2,2:25.1:1:30.9:1:1:1.00563:60:280:0.4878:0:2 1/0:302:178:106,72:70,54:124,178:0.5894:2,2:24.9:1:29.4:1:0.63575:1.14:60:58.333:0.5853:0:2 +5 153690473 . C G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.05991;LSEQ=GATTTAAAGGTGCTCATATA;RSEQ=CTTAAAATAAAATGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:177:90,87:100,103:203,177:0.4634:2,2:25.1:1:33.1:1:0.83708:1.07:60:176:0.4668:0:1.6 1/0:367:235:118,117:69,62:131,235:0.6403:2,2:27.1:1:31.3:1:0.66415:1.10317:59.9:77.333:0.6409:0:1.5 +5 153690516 . C A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11499;SOR=Inf;LSEQ=AACATTTCTTACATTGACTT;RSEQ=TTTTCTCTAATTTTTAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:113,168:281,0:0:2,0:25.1:1:32.5:1:1:0:60:55.2:1:0:0.4 0/1:267:3:1,2:109,155:264,3:0.0112:2,2:31.7:1:29.3:1:1:1.40472:60:6:0.0113:0:2.7 +5 154109263 . T A 62 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGTGGCATAATAGGTATT;RSEQ=AAAAAATACCTCTAGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:28.3:1:31.3:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 154193735 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGTGCCCAGTCCCAGGA;RSEQ=AGGGGACAATGAAGGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21:1:31.5:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 154194093 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2044;SOR=Inf;LSEQ=CAGCCCACAAGAAGGCCCTG;RSEQ=GGGCCCCCCCATTGCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:77,46:123,0:0:2,0:25.2:1:30.6:1:1:0:59.8:29.75:1:0:0.1 0/1:102:2:1,1:54,46:100,2:0.0196:2,2:24.5:1:26.5:1:1:1.17206:60:4:0.0204:0:1.5 +5 154194111 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50268;SOR=0;LSEQ=TGCGGGCCCCCCCATTGCCC;RSEQ=GCACTGTCTCATAGAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:80,54:134,2:0.0147:2,2:10.5:1:30.5:1:1:1.47706:60:4:0.0154:0:1 0/0:112:0:0,0:58,54:112,0:0:2,0:26.2:1:29:1:1:0:60:36.333:1:0:0.3 +5 154194208 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23456;SOR=Inf;LSEQ=ATCACCATATTTTCTCCCTG;RSEQ=TGTTCCCACCATGCCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:89,100:189,0:0:2,0:26.9:1:32.8:1:1:0:54.6:188:1:0:0.1 0/1:178:2:1,1:93,82:175,2:0.0112:2,2:25:1:27.5:1:1:1.13334:60:4:0.0116:0:1 +5 154194283 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50691;SOR=0;LSEQ=AAACTGGGGTTTGGGGGAAG;RSEQ=TTTCAGCCTCTCCCCACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:40,84:124,2:0.0159:2,2:22.5:1:28.5:1:0.54667:2.09:43.5:4:0.0164:0:1 0/0:96:0:0,0:36,58:94,0:0:2,0:22.3:1:30.4:1:1:0:50.3:46:0.9787:0:0.1 +5 154194290 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50741;SOR=0;LSEQ=GGTTTGGGGGAAGGTTTCAG;RSEQ=CTCTCCCCACTCCCCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:32,75:107,2:0.0183:2,2:18:1:29:1:0.5158:2.32:54:4:0.0185:0:1 0/0:82:0:0,0:27,54:81,0:0:2,0:21.6:1:29.7:1:1:0:52.5:19.25:0.9872:0:0.1 +5 154504661 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08276;SOR=Inf;LSEQ=CTCTGGAAAGGAGAACTTAA;RSEQ=GCCTTGGCTCTGTCTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:20,1:21,0:0:1,0:18.9:1:30.1:1:1:0:60:20:1:0:0.2 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:33.5:1:31:1:1:0:60:4:0.2222:0:2 +5 154504680 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09677;SOR=Inf;LSEQ=AAGCCTTGGCTCTGTCTTTT;RSEQ=AGTGGGTGGGTTGAGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:20,1:21,0:0:1,0:29.2:1:31:1:1:0:60:42:1:0:0.2 0/1:10:2:2,0:8,0:8,2:0.2:0,0:33.5:1:29:1:1:0:60:4:0.2222:0:2 +5 154504784 . C T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51628;SOR=0;LSEQ=AAATTTCCCAGGAAATTAGG;RSEQ=TAGCTGAGTCAGGTGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:114,24:138,2:0.0143:2,2:5:1:30.5:1:0.32631:4.67443:60:4:0.0144:0:1 0/0:95:0:0,0:74,21:95,0:0:2,0:20.5:1:31.1:1:1:0:60:94:1:0:0.1 +5 154504827 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25571;SOR=0;LSEQ=AGTGTTCTCTTTTGCTTTCT;RSEQ=CATTTTCCCCAGCGACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:190,94:284,3:0.0105:2,2:18.7:1:28.3:1:1:1.0106:60:6:0.0105:0:1.7 0/0:236:0:0,0:142,94:236,0:0:2,0:25.6:1:31.4:1:1:0:60:58:1:0:0.4 +5 154504902 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.07699;LSEQ=ACTTCTCAATTTCATCCACT;RSEQ=TCTGGAAGCTCACCTTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:379:359:165,194:8,11:19,359:0.9472:2,2:26.2:1:30:1:0.81626:1.17:60:50.286:0.9488:0:1.1 1/0:328:190:89,101:66,71:137,190:0.5793:2,2:24.4:1:29.4:1:0.82327:1.05472:60:94:0.5802:0:1.2 +5 154504947 . C T 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCTCAGGGCACATAAGCACC;RSEQ=ACATGTTGTCAGACATCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:65,171:236,0:0:2,0:24.3:1:31.6:1:1:0:60:46.2:1:0:0.8 0/1:169:19:7,12:50,100:150,19:0.1124:2,2:19.7:1:28.3:1:0.79928:1.17:60:38:0.1145:0:1.2 +5 154504952 . G A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2758;SOR=0;LSEQ=GGGCACATAAGCACCCACAT;RSEQ=TTGTCAGACATCAATTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:3:1,2:57,159:216,3:0.0136:2,2:32.7:1:23.3:1:1:1.39:60:2:0.0094:0:1.7 0/0:149:0:0,0:47,102:149,0:0:2,0:24.7:1:30.8:1:1:0:60:73.5:1:0:0.7 +5 154505054 . CAGA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.0494;SOR=0;LSEQ=GTGTGCGCATGTGAGTGAAT;RSEQ=TGTTAATCTGCTTTGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:9:0,9:0,27:27,9:0.2308:1,0:21.2:1:33.3:1:1:0:60:18:0.2432:0.1026:1.4 0/0:15:0:0,0:1,14:15,0:0:1,0:15.3:1:30.1:1:1:0:58.5:30:1:0:0.3 +5 154505097 . G T 71 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06061;SOR=0;LSEQ=AACCTTTTTCAAACACAACC;RSEQ=AATTCCTAAAGAACCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:22.7:1:27.8:1:1:0:60:12:1:0:1.8 0/1:5:2:0,2:0,3:3,2:0.4:0,0:18:1:29.5:1:1:0:58:4:0.4:0:1 +5 154505672 . T C 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTTGCTTCCTTCCTTGC;RSEQ=TCCTTCCTTCCTTCCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:33.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:25:0:27:0:1:0:60:2:1:0:1 +5 154936066 . C A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68795;LSEQ=ACCAATGGTAAACAAAGATG;RSEQ=CTCTTTGTGAGCCTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:2,0:120,5:125,2:0.0157:1,0:26.5:1:29.5:1:1:0:60:4:0.0161:0:1 0/1:92:1:1,0:81,10:91,1:0.0109:2,0:50:0:31:0:1:0:60:2:0.0112:0:1 +5 154936095 . TA T 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.81322;SOR=1.18691;LSEQ=GAGCCTTTAAAATTTCAAGT;RSEQ=AAAAAAAAAGACCCAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:10:9,1:163,25:188,10:0.05:2,2:31.7:1:31.7:1:1:1.38:60:20:0.0508:0:0 0/1:153:9:8,1:112,30:142,9:0.0588:2,2:18.8:1:30.6:1:0.68639:2.13:60:18:0.0596:0.0065:0.2 +5 154936207 . T C 216 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCAAAGTGGGTACTGTCAT;RSEQ=TGACCCCCACCCAAATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:812:0:0,0:426,386:812,0:0:2,0:25.3:1:30.6:1:1:0:60:134.333:1:0:0.1 0/1:757:127:65,62:331,298:629,127:0.1678:2,2:26.3:1:31:1:0.77114:1.05936:60:254:0.1689:0:1.2 +5 154936211 . C T 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGTGGGTACTGTCATTTGA;RSEQ=CCCCACCCAAATGTTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:809:0:0,0:412,397:809,0:0:2,0:25.8:1:31.6:1:1:0:60:100.125:1:0:0.1 0/1:770:18:7,11:390,362:752,18:0.0234:2,2:23.8:1:27.4:1:0.34254:1.69182:60:8:0.0211:0:1.9 +5 154936212 . C T 203 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTGGGTACTGTCATTTGAC;RSEQ=CCCACCCAAATGTTGTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:808:0:0,0:407,401:808,0:0:2,0:25.9:1:31:1:1:0:60:56.714:1:0:0.1 0/1:777:130:64,66:333,313:646,130:0.1673:2,2:24:1:29:1:0.63229:1.09701:59.8:42.333:0.1658:0:1.1 +5 154936488 . T TC 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00714;SOR=Inf;LSEQ=TTTCAGAAATATTTGCTGTT;RSEQ=CCTTTAATCCTTGCTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:12,0:0:0,0:16.4:1:30.5:1:1:0:60:24:1:0:0.2 1/0:4:3:1,2:0,1:1,3:0.75:0,2:24:1:30:1:1:0:60:6:0.75:0.25:0 +5 161253208 . A G 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAGGGTGTTCCTACTATT;RSEQ=CATGTTTCCTGTGGGTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:32.3:1:32:1:1:0:60:8:0.5:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:40:0:29:0:1:0:60:2:1:0:0 +5 161253295 . A G 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.68913;SOR=0.59337;LSEQ=TACATTCATTCCTAATCCCC;RSEQ=GGTACCAAAGGGTATGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:10,1:3,0:3,11:0.7333:0,2:18.1:1:28.4:1:1:0:60:10:0.7143:0:1.9 1/0:13:8:8,0:5,0:5,8:0.6154:0,0:27.1:1:28.3:1:1:0:60:16:0.6154:0:1.8 +5 161253358 . A G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01441;SOR=0.35314;LSEQ=TTTTCCGTTCTGAGCCATTT;RSEQ=AGGGCCAATATCCAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:37:30,7:17,2:19,37:0.6607:2,2:26.1:1:30.7:1:0.70265:1.9612:59.1:8.25:0.6346:0:1.6 0/1:42:17:15,2:21,3:24,17:0.4048:2,2:20.1:1:28.9:1:1:1.07:58.8:7.5:0.375:0:2 +5 161253422 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50051;SOR=Inf;LSEQ=AAAAAAAAAAAGTAGACAGA;RSEQ=GAGGCAACCAGCTGAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:87,79:166,0:0:2,0:19.2:1:29.1:1:1:0:59.5:10.857:0.9935:0:1.1 0/1:189:2:1,1:93,94:187,2:0.0106:2,2:18.5:1:29:1:1:1.01:60:4:0.0115:0:2.5 +5 161253451 . A T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.46401;LSEQ=CAGCTGAGACTTTCAGGCTC;RSEQ=TGGATTCCAGAAATGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:131:62,69:41,52:93,131:0.5848:2,2:28.9:1:31.1:1:0.68396:1.14:59.9:64.5:0.5972:0:1.3 0/1:233:92:45,47:63,78:141,92:0.3948:2,2:31.3:1:29.6:1:0.59128:1.18:59.6:91:0.4081:0:1.3 +5 161253677 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCATTTACAGGGATTCA;RSEQ=TTCTAGATGTTTCCCTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:12:1:33.5:1:1:0:60:4:0.4:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:28:1:1:0:60:4:1:0:0.5 +5 161322652 . G GT 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.56375;SOR=0;LSEQ=TATGAACTGGCATCATGTAT;RSEQ=TTTTTTTTTTTCTTTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:4:4,0:34,0:34,4:0.1053:1,0:33.5:1:30.4:1:1:0:60:8:0.1053:0.0263:0 0/0:14:0:0,0:14,0:14,0:0:1,0:18.8:1:32.4:1:1:0:60:28:1:0:0.4 +5 161322654 . T C 53 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=11.000;MSILEN=1;SSF=0.62655;SOR=1.64973;LSEQ=TGAACTGGCATCATGTATGT;RSEQ=TTTTTTTTTCTTTACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:3:3,0:35,0:35,3:0.0789:1,0:21.7:1:34:0:1:0:60:6:0.0789:0:1 0/1:16:2:2,0:14,0:14,2:0.125:1,0:5:1:31:1:1:0:60:4:0.125:0:1 +5 161322889 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.12325;LSEQ=GAAAAGGTAAATGCTTTAAT;RSEQ=GTCACTGTAGTACATCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:764:380:170,210:179,205:384,380:0.4974:2,2:24.2:1:30.3:1:0.61184:1.07852:60:94:0.5007:0:1.1 1/0:698:473:220,253:107,117:224,473:0.6777:2,2:25:1:29:1:0.80745:1.0516:60:156.667:0.6802:0:1.2 +5 161323930 . G A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGTGTTGTACTTCTTGAT;RSEQ=GCAAAAGGCTATTAAATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:31:1:1:0:60:4:1:0:1 +5 162712457 . A G 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTAAAGGTCCTGAGGCA;RSEQ=GAATAAGCTTGGTGTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:1,0:1,4:0.6667:0,0:17.3:1:35.3:1:1:0:60:8:0.6667:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:33:1:1:0:60:4:1:0:1 +5 162712583 . G A 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTGGAATCTAGGATGTTA;RSEQ=TGGTTGTCTGCATCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:57,0:57,0:0:1,0:24.2:1:33.8:1:1:0:59:114:1:0:0.1 0/1:53:18:17,1:34,1:35,18:0.3396:1,1:22.4:1:28.2:1:1:1.97209:60:17:0.3269:0:1.1 +5 162712737 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03754;SOR=0.74741;LSEQ=GGTGGTTAAACTTATATTGA;RSEQ=TTAAATGTACTATGAATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:162:78,84:123,139:262,162:0.3821:2,2:24.1:1:30.7:1:0.84165:1.05:60:53:0.3786:0:1.1 0/1:500:158:72,86:167,175:342,158:0.316:2,2:28.3:1:29.7:1:0.50222:1.13954:60:316:0.3198:0:1.1 +5 165332375 . A AT 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10502;SOR=0;LSEQ=TTGTTGTAAACAAGCAAGTT;RSEQ=AGGGCAAGGTTCCTGCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:2,2:6,9:15,4:0.2105:2,2:18.3:1:30:1:1:1.47:60:8:0.2105:0.1053:0 0/0:18:0:0,0:8,10:18,0:0:2,0:32.5:1:29.5:1:1:0:60:36:1:0:0.4 +5 165332462 . A G 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07895;SOR=Inf;LSEQ=ATAGCTTCCTGAAACCCATG;RSEQ=AGGAAAATGATCAGAAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:14,0:0:2,0:25:1:28.1:1:1:0:58.6:6:1:0:0.1 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:5:1:29.5:1:1:2.45:60:4:0.3333:0:1 +5 165488576 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49245;SOR=Inf;LSEQ=ATCCTGCTAAAAGGAAAACT;RSEQ=TGATTTGGGTAGGTCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:12,7:19,0:0:2,0:21.8:1:30.8:1:1:0:60:18:1:0:0.5 0/1:23:2:1,1:14,7:21,2:0.087:2,2:9.5:1:27:1:1:1.93655:60:4:0.087:0:1.5 +5 167024749 . CTT C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGCTATCTTACTTTCAAA;RSEQ=ATATATGCATGTCATATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:45.5:1:33.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 169531898 . G T 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCGTGTGCGCGTGTGTGGGC;RSEQ=TGCGCGTGTGCGTGTGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:1 +5 169531949 . T G 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGCGCGTACGCGTGTGTGCG;RSEQ=GTATGTGTGTGTTGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:27.5:1:21:1:1:0:60:1:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:30:1:1:0:60:4:1:0:2 +5 169533195 . C T 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCCACCCTACCTGCCCGG;RSEQ=CCCAACGCCAGCCCCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44:0:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 169533606 . T C 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64663;SOR=1.75443;LSEQ=TCCTCCCCAAGACCCCATTC;RSEQ=AGAAAGTTCTGACTAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:0,5:0,12:12,5:0.2941:0,0:26:1:34:0:1:0:60:10:0.2941:0:1 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:26.7:1:33.7:1:1:0:60:6:0.4286:0:1 +5 170187643 . T C 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CTACCTACAGAGACCCCTAC;RSEQ=ACTCCCCAGGCTCAACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:32.5:1:30.5:1:1:0:60:4:0.4:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:13:0:25:0:1:0:60:2:1:0:1 +5 170448963 . A G 91 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=0;LSEQ=TGAATGGGGTTTTTCTGTGG;RSEQ=CTTTTTTGTTGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:23:1:32.6:1:1:0:60:14:1:0:2.4 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:41.8:1:30.2:1:1:1.41:60:10:0.7143:0:2.8 +5 170448971 . G T 85 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.46154;SOR=0;LSEQ=GTTTTTCTGTGGACTTTTTT;RSEQ=TTGTTGTTGTTGATGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:21.4:1:30.6:1:1:0:60:14:1:0:2.4 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:38:1:29.2:1:1:1.41:60:10:0.7143:0:2.8 +5 170449000 . A G 57 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGATGCTCCTGTTGTTGC;RSEQ=TTGTTTGTTTGTTTGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:22.3:1:33:1:1:0:60:8:1:0:2.5 1/1:4:4:2,2:0,0:0,4:1:0,2:13.5:1:28.8:1:1:0:60:8:1:0:3 +5 170449265 . A T 149 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00065;SOR=0;LSEQ=TGCCAACCCCTGTTGGAGGG;RSEQ=CTCACCCAGTTGGGTGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:16,16:0,0:0,32:1:0,2:26.6:1:29.8:1:1:0:54.7:64:1:0:1.2 1/0:25:17:8,9:5,3:8,17:0.68:2,2:29.6:1:27.9:1:0.67277:1.82828:57.2:16:0.6667:0:1.1 +5 170449442 . G C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=AGACTGTGGCCATCCTTCCC;RSEQ=CTAGGGGCTCAGGCCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:33.7:1:31.3:1:1:0:52.7:6:1:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:22.5:1:33.5:1:1:0:60:4:1:0:0 +5 170449872 . C G 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCTGAGAGGCGGTTGA;RSEQ=AATCTGTAGGGCTCTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:20.2:1:32.8:1:1:0:58.8:10:1:0:1 1/1:8:7:4,3:1,0:1,7:0.875:0,2:18.3:1:30.1:1:1:0:55.6:14:0.875:0:1.3 +5 170814849 . C T 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.74857;LSEQ=ATATAAGCGCGGGGAGCCTG;RSEQ=GTCCTTTCCCTGGTGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:5:1,4:344,131:475,5:0.0104:2,2:6.4:1:26:1:0.02362:10.4463:60:10:0.0106:0:1 0/1:438:37:23,14:279,122:401,37:0.0845:2,2:18.5:1:28.5:1:0.35739:1.39094:58.6:74:0.0847:0:1.2 +5 170815125 . G T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00283;SOR=0.50611;LSEQ=GTGGAGACCGCCAGACCGAC;RSEQ=GGAGGCCTGAGCGGGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:189:121:5,116:3,65:68,121:0.6402:1,1:25.4:1:30.5:1:1:1.07038:60:39.333:0.6344:0:1.4 0/1:150:71:4,67:5,74:79,71:0.4733:2,2:22.5:1:29.5:1:1:1.13083:60:142:0.4797:0:1.5 +5 170816401 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGGAGTGAGAGTAGACA;RSEQ=ATGTATTCAAAACATTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:47.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170816498 . G C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTGATAACTATCGGAAA;RSEQ=AACCCTCCTTGTCTTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:32:1:34.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170816969 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.10659;SOR=Inf;LSEQ=AGTGAAAAACTAGTTCAAAA;RSEQ=TTAGACCTGACCTTTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:235,70:305,0:0:2,0:20.4:1:32.4:1:1:0:60:42.571:1:0:0.1 0/1:276:3:1,2:204,69:273,3:0.0109:2,2:13.3:1:26.7:1:0.16346:5.86644:60:6:0.011:0:2 +5 170817555 . C T 30 v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGCCAAGATCACAAAA;RSEQ=CTGAGGACAACATTGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:41:0:30:1:1:0:49:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170817947 . C CA 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGTTGTCCAGGCTGGTCT;RSEQ=AAACTCCTGACCTCATGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:28.3:1:31:1:1:0:49.7:6:0.6:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170818290 . AT A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.12012;SOR=0.79104;LSEQ=AACTCAAAAGTTGAAGTAGT;RSEQ=TTTTTTTTTGTTCACAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1595:99:48,51:775,708:1483,99:0.0621:2,2:27.1:1:31.7:1:0.46947:1.16293:59:198:0.0634:0.005:0.2 0/1:1930:96:53,43:931,894:1825,96:0.0497:2,2:30:1:30.6:1:0.46393:1.18:59.9:192:0.0505:0:0.2 +5 170818897 . A G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00197;SOR=0.3864;LSEQ=TAAAGCATGGGTATAGTACT;RSEQ=CTGTCTTTTTAATAGGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:118:76:1,75:0,42:42,76:0.6441:1,1:22.9:1:32.6:1:1:0:60:75:0.6579:0:1.9 0/1:78:32:1,31:1,45:46,32:0.4103:1,1:23.9:1:31.6:1:1:1.44:60:31:0.4133:0:1.9 +5 170818906 . T A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.32315;SOR=0.69355;LSEQ=GGTATAGTACTACTGTCTTT;RSEQ=TAATAGGTTCCAATGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:61:0,61:0,34:34,61:0.6421:1,1:25.6:1:31.8:1:1:0:60:122:0.6489:0:2.2 1/0:65:36:0,36:1,28:29,36:0.5538:1,1:24.9:1:30.9:1:0.44615:0:60:72:0.5714:0:1.8 +5 170818966 . GGGA TGGGGG 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.19302;SOR=0.38302;LSEQ=AAATAAATTTTTGGGGCGGG;RSEQ=GAGGAAATCTTGCTGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:20:0,20:0,14:14,20:0.5714:1,1:21.8:1:31.6:1:1:0:59.9:40:0.5714:0.1429:2.2 0/1:12:4:0,4:1,7:8,4:0.3333:2,0:18.8:1:30.2:1:1:0:60:8:0.3333:0.0833:2.3 +5 170819590 . CTTT C 178 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=17.000;MSILEN=1;SSF=0.26245;SOR=0.67954;LSEQ=AGTTCCTTTTCCCATGTGCT;RSEQ=TTTTTTTTTTTTTTAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:48:47,1:18,0:18,48:0.5053:1,1:23.1:1:32:1:1:0:59:47:0.5109:0.1368:1.8 0/1:66:27:27,0:28,0:28,27:0.4091:1,1:24.7:1:31.4:1:1:0:60:54:0.4091:0.0606:1.2 +5 170819607 . T A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06077;SOR=0.54378;LSEQ=GCTCTTTTTTTTTTTTTTTT;RSEQ=AAATAGAATAGAAGTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:78:73,5:29,2:31,78:0.7156:2,2:26.5:1:27.7:1:1:1.01:59.2:14.6:0.7157:0:1.7 1/0:78:45:43,2:30,3:33,45:0.5769:2,1:25.4:1:27.6:1:0.6451:2.13:60:90:0.6081:0:1.2 +5 170819654 . C CT 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17086;SOR=0.48012;LSEQ=GAGTATTTACTATCAGTGTT;RSEQ=TTTTTTTTTCTGACTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:13:8,5:200,69:269,13:0.0436:2,2:16:1:29.3:1:0.33612:1.80726:60:26:0.0504:0.0134:0.1 0/1:327:7:5,2:204,109:313,7:0.0214:2,2:36.4:1:28.9:1:1:1.33:60:14:0.0233:0:0.1 +5 170819887 . G A 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.49452;LSEQ=TTGGTGATAGAACAGCTCTT;RSEQ=TTCATGAGTACGTATCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:674:437:192,245:99,137:236,437:0.6484:2,2:23.6:1:30.2:1:0.62579:1.08:58.3:108.25:0.6463:0:1.1 0/1:755:360:156,204:185,210:395,360:0.4768:2,2:24.3:1:28.8:1:0.3421:1.1518:58.3:179:0.4773:0:1.1 +5 170820024 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.55502;LSEQ=TGATATACTTCCGGAATCTT;RSEQ=ACAAAAAAAGGAATTTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:413:272:89,183:44,97:141,272:0.6586:2,2:22.8:1:30.1:1:0.8244:1.07:59.7:544:0.6602:0:1.1 1/0:385:199:74,125:64,122:186,199:0.5169:2,2:23.1:1:28.8:1:0.59595:1.13:59.8:65.333:0.5158:0:1.1 +5 170826687 . A ATT 72 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTCTATTTAGGTCTTTA;RSEQ=TTTTTTTTTTTAACACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,0:1,5:0.7143:0,2:31.6:1:31.3:1:1:0:60:10:0.7143:0:0.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170827115 . C A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00165;SOR=0.57956;LSEQ=TCAATTCTTGTGTCTACTCC;RSEQ=AAATTTTGAAAGTGCTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:293:169:123,46:86,38:124,169:0.5768:2,2:26.7:1:30.7:1:0.60116:1.18:59.7:83.5:0.5759:0:2.1 0/1:263:116:87,29:108,39:147,116:0.4411:2,2:25.9:1:29.4:1:0.88731:1.08:59.7:232:0.4411:0:2.1 +5 170827118 . A G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00197;SOR=0.58913;LSEQ=ATTCTTGTGTCTACTCCCAA;RSEQ=TTTTGAAAGTGCTTAATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:295:171:125,46:85,39:124,171:0.5797:2,2:27.4:1:33:1:0.43534:1.25:59.6:56:0.5813:0:2.1 0/1:279:125:93,32:113,41:154,125:0.448:2,2:25.3:1:31.1:1:0.89155:1.05:59.5:61.5:0.4473:0:2 +5 170827156 . GTGA G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=1;SOR=1.02264;LSEQ=GTCTTGACATTTCATTTGTA;RSEQ=TGATGATGATGATTTTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:543:7:5,2:323,212:535,7:0.0129:2,2:23.9:1:34.1:1:0.70918:1.64:53.1:14:0.0131:0:0.1 0/1:607:8:5,3:373,226:599,8:0.0132:2,2:26:1:32.1:1:1:1.01:57.9:16:0.0134:0.0033:0 +5 170827311 . T TGGGAGATCATCTCATACTGA 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06845;SOR=0.68478;LSEQ=GTAGTTAAGGGAAGCTGGTG;RSEQ=GGGAGATCATCTCATACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:77:1,76:28,140:168,77:0.3105:2,1:26.8:1:31.1:1:0.00019:15.10519:58.8:154:0.3117:0.1048:0.1 0/1:242:57:0,57:34,149:183,57:0.2355:2,1:26.4:1:30.6:1:6e-05:0:59.9:114:0.2355:0.0785:0.1 +5 170827459 . C T 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=CCAAGTGGTTGCTGCTTTTT;RSEQ=CTTCCTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:1,10:2,6:8,11:0.55:2,2:22.1:1:27.5:1:0.54592:3.12168:57.8:4.5:0.5294:0:1.6 0/0:1:0:0,0:0,1:1,0:0:0,0:25:0:32:0:1:0:60:2:1:0:0 +5 170827464 . CT C 76 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTTGCTGCTTTTTCCTTC;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:0,6:6,5:0.3125:0,2:34.2:1:33:1:0.18182:0:48:10:0.3125:0:3.2 0/0:1:0:0,0:0,1:1,0:0:0,0:19:0:31:0:1:0:60:2:1:0:0 +5 170827654 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0418;SOR=Inf;LSEQ=CATTTTTAGTAGACCACCAT;RSEQ=TCGGCCAGGCTGGTCTCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:47,0:47,0:0:1,0:26.1:1:32.8:1:1:0:44.8:94:1:0:0.1 0/1:26:3:3,0:23,0:23,3:0.1154:1,0:20:1:29:0:1:0:36:6:0.1154:0:1 +5 170828123 . G A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05146;SOR=0;LSEQ=TCCCAGCACTTTGGGAGGGA;RSEQ=GCCAAGGTGGGTGGGATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:0,4:0,23:23,4:0.1481:1,0:22:1:33.3:1:1:0:60:8:0.1481:0:1 0/0:28:0:0,0:0,28:28,0:0:1,0:17.2:1:31:1:1:0:59.5:27:1:0:0.1 +5 170828170 . C T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61752;SOR=0.44089;LSEQ=TCAGGAGTTTGAGACTAGCC;RSEQ=GGCCAACATCGTGAAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:7,11:0.6111:0,0:17.5:1:31.2:1:1:0:54.9:22:0.6111:0:1 0/1:5:2:0,2:0,3:3,2:0.4:0,0:37.5:1:31.5:1:1:0:53.5:4:0.4:0:1 +5 170831912 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTTGAACTGACTTAGTA;RSEQ=TGTGCATAAAAGCAAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:32.5:1:30.5:1:1:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170831942 . C CT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAAACTCCCAAGTTACT;RSEQ=TTTTTTTTTTTATTTAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:21:1:29.5:1:1:0:60:4:0.2857:0:2 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 +5 170832092 . C A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01474;SOR=Inf;LSEQ=GCTGGGATTACAGGCATGCA;RSEQ=CACCATGCCTAGCTAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:42,0:42,0:0:1,0:22.9:1:32.6:1:1:0:59.5:41:1:0:0.1 0/1:24:4:4,0:20,0:20,4:0.1667:1,0:21:1:29.5:1:1:0:50.5:8:0.1667:0:1.5 +5 170832187 . G A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3099;SOR=1.37913;LSEQ=TATTGATGATAATTCCAGTT;RSEQ=TATAATTAGCTTTATAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:27:26,1:274,2:276,27:0.0891:1,1:27.7:1:29:1:0.24495:5.21617:60:54:0.0894:0:1.1 0/1:227:27:27,0:200,0:200,27:0.1189:1,1:26:1:26.7:1:1:0:60:26:0.1161:0:1.1 +5 170832243 . A G 297 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.63147;LSEQ=TTTGAGGAAATCCAGATAGA;RSEQ=TGGGTTTTAATTAGGAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:860:543:364,179:200,115:315,543:0.6314:2,2:24.3:1:32.7:1:0.29709:1.17:60:134.75:0.6297:0:1.1 1/0:870:452:285,167:262,154:416,452:0.5195:2,2:24:1:31.1:1:1:1.00:60:904:0.5207:0:1.1 +5 170832637 . C T 73 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTCCATTATGCAAGGAA;RSEQ=GTAGTGCACTGGTTGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:26:1:31.8:1:1:0:60:10:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170832767 . TACAA T 71 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATGAGACTTCATTAAAAT;RSEQ=ACAGCTGGAAAAGTAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:21.8:1:30.6:1:1:0:60:10:0.8333:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170833005 . A G 27 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGAAGAGGGTTAGGTCTCTC;RSEQ=TCTGCTTGACTGGGGGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:32.5:1:27.5:1:1:0:60:4:1:0:3 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 170834890 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52167;SOR=0;LSEQ=TTAAAAAGTTCCTAACCACA;RSEQ=ATAATATTTCATTTAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:0,2:0,129:129,2:0.0153:1,0:25.5:1:30:0:1:0:60:4:0.0155:0:1 0/0:84:0:0,0:1,83:84,0:0:1,0:25:1:31.1:1:1:0:60:168:1:0:0 +5 170837222 . C CAG 50 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GCCAACTCTAAAGCTGATCT;RSEQ=GGGAGATGAAGTTGGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:18:1:31.8:1:1:0:60:6:1:0.6667:0 0/0:1:0:0,0:1,0:1,0:0:0,0:19:0:32:0:1:0:60:2:1:0:0 +5 170837279 . T G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14229;SOR=Inf;LSEQ=TCTCTGTTCTTTCTGTTGAT;RSEQ=TCCTTAAGTAAATAATGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:14,0:0:1,0:14.5:1:31.4:1:1:0:60:28:1:0:0 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:17:1:33:0:1:0:60:4:0.2222:0:1 +5 170837457 . A G 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02259;SOR=1.64924;LSEQ=AATAGATGTTGAACTATGCA;RSEQ=AGAGACATTTAATTTATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:37:22,15:203,145:348,37:0.0956:2,2:25.8:1:32.4:1:1:1.05:60:36:0.0942:0:1.2 0/1:478:71:46,25:234,173:407,71:0.1485:2,2:26:1:30.9:1:0.2965:1.36:59.9:34.5:0.1465:0:1.2 +5 170837509 . A AT 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.09069;SOR=0.3926;LSEQ=TGTTGTGGTTCCTTAACCAC;RSEQ=TTTCTTTTTTTTTTTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:12:0,12:172,197:369,12:0.0305:2,0:38:1:28:1:7e-04:0:52.1:11:0.0334:0:2.3 0/1:493:6:0,6:226,246:472,6:0.0122:2,0:36.2:1:26.8:1:0.03165:0:53.2:5:0.0121:0:1.8 +5 170883125 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51153;SOR=Inf;LSEQ=CTCCTGAACCTTCTCTTATG;RSEQ=CCATCTGTGCACTTCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,15:27,0:0:2,0:33.4:1:31.5:1:1:0:57.9:26:1:0:0 0/1:40:2:1,1:18,20:38,2:0.05:2,2:33.5:1:27.5:1:1:1.11:60:4:0.05:0:1 +5 172084989 . C G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23;SOR=Inf;LSEQ=GCTGACATATGCTGCCTTCT;RSEQ=TGTCTGCTTCAGCTACCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:11,0:0:2,0:19.5:1:31.3:1:1:0:54.3:10:1:0:0.2 0/1:14:3:2,1:8,3:11,3:0.2143:2,2:15.7:1:30.3:1:1:1.30524:44:6:0.2143:0:1 +5 172123916 . A T 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.498;SOR=0;LSEQ=CCCAGGAAAGAAACACCAGG;RSEQ=TGTTCCCAGGAACCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:74,31:105,2:0.0187:2,2:18.5:1:24:1:0.51067:2.36534:60:4:0.0187:0:1 0/0:101:0:0,0:69,32:101,0:0:2,0:16.5:1:28.9:1:1:0:60:49.5:1:0:0.2 +5 172123938 . G T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09845;SOR=0;LSEQ=GTTCCCAGGAACCCTCTCTG;RSEQ=CTTCCCCATCTGCCCGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:3:1,2:110,57:167,3:0.0176:2,2:21:1:27.7:1:0.2765:3.82675:60:6:0.018:0:2 0/0:197:0:0,0:121,75:196,0:0:2,0:22.2:1:31.1:1:1:0:60:64.333:1:0:0.2 +5 172123950 . G A 19 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.85313;LSEQ=CCTCTCTGGCTTCCCCATCT;RSEQ=CCCGCAGTTTCCCACGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:121,76:197,2:0.0101:2,2:17.5:1:27:1:1:1.5882:60:4:0.0101:0:1 0/0:233:2:2,0:137,94:231,2:0.0086:2,0:36.5:1:19:1:0.51658:0:60:1:0.0044:0:1 +5 172124010 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50192;SOR=Inf;LSEQ=TGCCACCCCACCCCTGATCA;RSEQ=CACAAAAAGAGTTCCCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:57,89:146,0:0:2,0:24.5:1:31.7:1:1:0:60:35.5:0.9793:0:0.1 0/1:176:2:1,1:76,98:174,2:0.0114:2,2:18:1:29.5:1:1:1.29:60:4:0.0118:0:1 +5 172573673 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50198;SOR=Inf;LSEQ=CTTTTATATTAATTCAACAT;RSEQ=AATCTAAAAAGGAATGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:85,41:126,0:0:2,0:25.4:1:29.3:1:1:0:60:20:1:0:0.1 0/1:150:2:1,1:103,45:148,2:0.0133:2,2:27:1:30.5:1:0.52072:2.27487:60:4:0.0134:0:1 +5 172573767 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11084;SOR=1.35964;LSEQ=AGGATGAATTATAGTTAGTA;RSEQ=GTTAATATTAGTTGGTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:246:143:71,72:49,54:103,143:0.5813:2,2:23.9:1:30.7:1:0.7965:1.09:59.8:70.5:0.5802:0:1.1 1/0:234:153:63,90:30,51:81,153:0.6538:2,2:25.1:1:29.7:1:0.57624:1.19:60:50:0.6494:0:1.2 +5 172573834 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18004;SOR=Inf;LSEQ=GTCATTTCATTTCATTGCCT;RSEQ=GAGAAAGGCCTTTCATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:26,90:116,0:0:2,0:24.6:1:30.6:1:1:0:59.8:115:1:0:0.4 0/1:86:2:1,1:22,62:84,2:0.0233:2,2:22.5:1:29:1:0.46566:2.78:60:4:0.0233:0:1 +5 172658139 . C A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATAGAGGAGCTGGAGGTC;RSEQ=GGTCCCAGCACCTGCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:29:1:32:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 172659905 . AGGC A 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.64137;SOR=1.59275;LSEQ=GGCACCGCGATCCTGCGGGC;RSEQ=GGCGGCGGCGGCGGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:2,0:62,2:64,2:0.0303:1,0:20:1:35.5:1:1:0:60:4:0.0308:0:0.5 0/1:42:2:2,0:39,1:40,2:0.0476:1,0:13:1:32:1:1:0:60:4:0.0476:0.0238:0.5 +5 172659907 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.52458;SOR=0;LSEQ=CACCGCGATCCTGCGGGCAG;RSEQ=CGGCGGCGGCGGCGGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:62,1:63,2:0.0299:1,2:27.5:1:30.5:1:0.06106:44.19295:60:4:0.0323:0:1 0/0:41:0:0,0:39,1:40,0:0:1,0:24.9:1:30.2:1:1:0:60:39:1:0:0.2 +5 172659915 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.14609;SOR=Inf;LSEQ=TCCTGCGGGCAGGCGGCGGC;RSEQ=GCGGCGGGGGCAGCCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:75,5:80,0:0:2,0:22.6:1:29.2:1:1:0:60:25.667:1:0:0.2 0/1:50:2:1,1:42,6:48,2:0.04:2,2:11:1:29:1:0.26286:6.55744:60:4:0.0408:0:1.5 +5 172659920 . CG C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.16159;SOR=Inf;LSEQ=CGGGCAGGCGGCGGCGGCGG;RSEQ=GGGGCAGCCCCACCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:80,10:90,0:0:2,0:21.7:1:29.4:1:1:0:60:29:1:0:0.1 0/1:61:2:1,1:46,13:59,2:0.0328:2,2:12.5:1:30.8:1:0.40929:3.44648:60:4:0.0328:0.0164:0 +5 172660010 . G T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59692;SOR=2.35079;LSEQ=AACCAGATCTTGACCTGCGT;RSEQ=GACGTGAGTTTCAGCACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:0,1:108,123:231,1:0.0043:2,0:27:0:15:0:1:0:58:0:0:0:1 0/1:199:2:1,1:89,108:197,2:0.0101:2,2:22.5:1:31.5:1:1:1.21:60:4:0.0103:0:1 +5 172660050 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50564;SOR=0;LSEQ=TGGCCAGCTGGTCGCGTTCG;RSEQ=GGGCCGACAGGTACCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:63,102:165,2:0.012:2,2:32:1:29:1:1:1.61:60:4:0.0121:0:1 0/0:131:0:0,0:52,79:131,0:0:2,0:21.2:1:29.5:1:1:0:59.4:31.75:1:0:0.1 +5 172660056 . G A 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17965;SOR=Inf;LSEQ=GCTGGTCGCGTTCGGGGGCC;RSEQ=ACAGGTACCGCTGCTGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:59,98:157,0:0:2,0:25:1:30.5:1:1:0:60:51.333:1:0:0.1 0/1:116:2:1,1:45,69:114,2:0.0172:2,2:6:0:26.5:1:1:1.53:60:4:0.0175:0:1 +5 172660089 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51206;SOR=0;LSEQ=GCTGCTTGAAGCGCCGCTCC;RSEQ=GCTCATAGACCTGCGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:25,75:100,2:0.0196:2,2:29.5:1:32:0:0.44671:2.96:60:4:0.02:0:1 0/0:72:0:0,0:25,47:72,0:0:2,0:24.9:1:30.1:1:1:0:58.9:71:1:0:0.1 +5 172774626 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AGGTACCCCTTTTGTACTTA;RSEQ=TGGGCTCTCCCTCAGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:1 +5 172775066 . GCAA G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=2e-05;SOR=16.49369;LSEQ=ATCTCCAACAAACAACAACA;RSEQ=CAGCAGCAGCAGCAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:1,2:10,9:19,3:0.1364:2,2:43.7:1:34:0:1:2.1446:58.7:6:0.1364:0:0.3 1/0:34:25:10,15:4,5:9,25:0.7353:2,2:28.5:1:31.5:1:1:1.19352:59.3:50:0.7353:0.0294:0.7 +5 172775097 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCAGCAACAACAACAACAA;RSEQ=GAAACAGTAATCTAAACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:21.6:1:30.5:1:1:0:57.6:14:1:0:0.3 0/1:33:2:1,1:11,20:31,2:0.0606:2,2:36:1:28.5:1:1:1.78:60:4:0.0645:0:1 +5 173763325 . A C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCAGGATCAGGAGGCTGAG;RSEQ=CGTGATCTGGAAGTGAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:196:195:118,77:0,0:0,195:0.9949:0,2:24.6:1:31.5:1:1:0:60:38:0.9948:0:1.7 1/1:121:121:68,53:0,0:0,121:1:0,2:24:1:30.7:1:1:0:60:242:1:0:2.6 +5 173763340 . G T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20513;LSEQ=CTGAGACGTGATCTGGAAGT;RSEQ=AGTGCCCATCCATACACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:249:150:81,69:48,42:90,150:0.6024:2,2:25.2:1:29.8:1:1:1.03:60:300:0.6098:0:1.8 0/1:165:39:24,15:8,7:15,39:0.2364:2,2:22:1:28.8:1:0.75818:1.39:60:78:0.2364:0:1.7 +5 173763344 . G T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56597;SOR=3.03956;LSEQ=GACGTGATCTGGAAGTGAGT;RSEQ=CCCATCCATACACCTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:1:0,1:138,118:256,1:0.0039:2,0:1:0:26:0:0.46304:0:60:2:0.0039:0:2 0/1:170:2:1,1:96,72:168,2:0.0118:2,2:35:0:31.5:1:1:1.33103:60:4:0.0119:0:3.5 +5 173763356 . A C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=22.06199;LSEQ=AAGTGAGTGCCCATCCATAC;RSEQ=CCTTCCCCAGCTTTGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:14:10,4:128,131:259,14:0.0513:2,2:24.8:1:29.3:1:0.16859:2.55:60:13:0.05:0:2.2 1/0:196:107:58,49:49,40:89,107:0.5459:2,2:25:1:29.7:1:1:1.03475:59.9:34.667:0.5445:0:2.5 +5 173763567 . G A 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1033;SOR=Inf;LSEQ=ACAGCATCATCCTGAGTCAT;RSEQ=TTTGAACCTGAGGTAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:6,5:0.4545:0,0:22.6:1:32.2:1:1:0:60:10:0.4545:0:1 1/1:4:4:1,3:0,0:0,4:1:0,2:22.3:1:26.8:1:1:0:60:8:1:0:1 +5 173764643 . C G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGGGAACAGGCCTCCCC;RSEQ=CTTCTGTTTCCAGAAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:31.5:1:1:0:60:4:1:0:1 +5 174291096 . T C 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATTGATTCTTTCTCATCTT;RSEQ=GCGAGTTTGTCTGTTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:44:0:33:0:1:0:60:2:1:0:0 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:36:1:29:1:1:1.41:60:4:0.2857:0:1 +5 174291231 . T C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40097;SOR=2.88728;LSEQ=TTCTTTCAATAGTCAGGTCC;RSEQ=TCTTCTGTAGTGCTTCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:6,4:3,3:6,10:0.625:2,2:20:1:32.5:1:1:1.46:43.8:20:0.625:0:1.1 1/1:12:10:5,5:1,1:2,10:0.8333:2,2:22.3:1:31.4:1:1:1:45.4:20:0.8333:0:1.1 +5 174291450 . T C 76 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04977;SOR=11.63911;LSEQ=ACCTCTGCTGGAGGGTCTCA;RSEQ=CCAGTTGGGTGGCACAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:4,3:7,1:0.125:2,0:17:0:34:0:1:0:53:2:0.125:0:1 1/0:9:6:4,2:3,0:3,6:0.6667:0,2:22.5:1:29.7:1:0.5:0:47.3:12:0.6667:0:1.2 +5 174291455 . T G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=TGCTGGAGGGTCTCATCCAG;RSEQ=TGGGTGGCACAGGGAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:37.6:1:31.6:1:1:0:58.6:14:1:0:0.3 0/1:9:2:2,0:5,2:7,2:0.2222:2,0:34.5:1:33:0:1:0:60:4:0.2222:0:1 +5 174291542 . G A 59 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14861;SOR=6.08068;LSEQ=TGCTAGGCGGAAACCCACTT;RSEQ=TCTGGGTTGCCTGGATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:3,7:10,1:0.0909:2,0:14:0:32:0:1:0:60:2:0.0909:0:1 0/1:10:4:1,3:2,4:6,4:0.4:2,2:23.5:1:29.8:1:1:1.44135:58.3:8:0.4:0:1.5 +5 174291575 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.45455;SOR=Inf;LSEQ=GGATTCCTCAGAACTACCAG;RSEQ=AGGAGAGGCTAAGTCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:5,0:0:2,0:25.2:1:31.2:1:1:0:54.4:10:1:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:29.5:1:24.5:1:1:1:58:4:0.3333:0:1.5 +5 174914787 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49202;SOR=Inf;LSEQ=CTGCCTCCTGGGTGCCTCAC;RSEQ=CTTACTCCGTGCAAATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:25,0:0:2,0:30.8:1:31.1:1:1:0:60:50:1:0:0.4 0/1:28:2:1,1:11,15:26,2:0.0714:2,2:22:0:31.5:1:1:1.35:60:4:0.0741:0:1.5 +5 174914837 . A T 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2031;SOR=3.82314;LSEQ=CTTCTCCCTCGGCCCTCTCC;RSEQ=CCTCCAGTTTTTCCAACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:2,4:2,5:7,6:0.4615:2,2:24.8:1:31.3:1:1:1.23:60:12:0.4615:0:1 1/0:9:7:1,6:0,2:2,7:0.7778:0,2:32.3:1:28.6:1:1:0:60:14:0.7778:0:1 +5 176295825 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACCTGGTGGACCCGTCCC;RSEQ=GGACCCCAATGTATACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:6,0:6,2:0.25:0,2:20:1:29.5:1:0.25:0:60:4:0.25:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:14:1:30.5:1:1:0:60:4:1:0:0 +5 176516631 . G A 227 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00819;LSEQ=TGCTGCTGGCCCTGTTGGGG;RSEQ=TCCTGCTGAGTGTGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:739:171:80,91:291,277:568,171:0.2314:2,2:23:1:30.7:1:0.33749:1.1947:60:170:0.2326:0:1.1 0/0:815:2:2,0:395,418:813,2:0.0025:2,0:13:1:28:1:0.23698:0:60:4:0.0025:0:1 +5 176516760 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18545;SOR=Inf;LSEQ=GGCACCAGGAGGGGGCTGCT;RSEQ=GGCTGAGCAAAGCTGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:44,192:236,0:0:2,0:22.9:1:30.6:1:1:0:60:20.455:1:0:0.1 0/1:179:2:1,1:44,133:177,2:0.0112:2,2:7:1:27:1:0.44065:3.00:60:4:0.0115:0:1 +5 176516953 . A G 91 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTGGTGGTGAGCTCCTT;RSEQ=CCTGGGTGTGTGTGCGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:29.3:1:32.7:1:1:0:60:14:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:50:0:34:0:1:0:60:2:1:0:1 +5 176517136 . C CGTGT 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=12.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CGTATGTGTGTGTGTGTATG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:2,0:2,3:0.375:0,0:16.3:1:32.2:1:1:0:60:6:0.375:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 176517170 . G A 108 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGTGTCTTGGCCACTGTC;RSEQ=TGTGCACTAAATGCTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:0,12:1:0,2:29.5:1:30.3:1:1:0:58.8:11:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 176517292 . A G 179 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=0.03731;LSEQ=GCTCCTTCAGCATGCGTTGC;RSEQ=AAGTGCTTGTGCCCTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:64:63:57,6:1,0:1,63:0.9844:0,2:27.9:1:30.1:1:1:0:60:62:0.9841:0:2 1/0:26:18:17,1:8,0:8,18:0.6923:0,1:24.9:1:30.6:1:1:0:58.7:36:0.6923:0:2.1 +5 176517326 . T C 220 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01571;LSEQ=CTGCATGTGCGGTGTGTTCT;RSEQ=TGTACACAGGAGGCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:121:109,12:1,0:1,121:0.9918:0,2:20.4:1:31.9:1:1:0:59.8:120:1:0:1.6 1/0:60:39:31,8:20,1:21,39:0.65:1,2:23.2:1:30.7:1:0.14166:5.05196:59.4:78:0.65:0:1.5 +5 176517383 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14739;SOR=Inf;LSEQ=TCTGCTGACCTCTGCCCTCT;RSEQ=CCCACAGAGCCCTGCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:200,72:272,0:0:2,0:25.8:1:31.9:1:1:0:59.8:37.857:1:0:0.7 0/1:170:2:1,1:121,47:168,2:0.0118:2,2:18.5:1:27:1:0.48618:2.55802:60:4:0.012:0:1.5 +5 176517461 . T G 286 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01139;LSEQ=GCCCTTGGGCAGCCTGTGCG;RSEQ=CTGTGCTGTGGGCGGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:536:532:312,220:0,4:4,532:0.9925:0,2:24.2:1:31.6:1:0.03003:0:59.8:75:0.9924:0:1.1 1/0:485:292:159,133:109,84:193,292:0.6021:2,2:25.1:1:31.1:1:0.70921:1.08525:59.7:145:0.6029:0:1.2 +5 176517797 . C T 316 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.00698;LSEQ=CCCCAAGTCCCATAGGGACC;RSEQ=CTCGAATAGGCACAGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1179:1175:520,655:1,2:3,1175:0.9966:2,2:25.8:1:31:1:1:1.59:60:60.842:0.9983:0:1.2 1/0:1002:673:293,380:153,174:327,673:0.6717:2,2:24.8:1:29:1:0.34296:1.14025:59.9:83.125:0.6786:0:1.1 +5 176517801 . G A 176 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAGTCCCATAGGGACCCCTC;RSEQ=AATAGGCACAGTTACCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1169:52:24,28:504,612:1116,52:0.0445:2,2:26.3:1:30.9:1:0.88779:1.04:60:104:0.045:0:2.1 0/0:993:0:0,0:443,550:993,0:0:2,0:25:1:29.8:1:1:0:60:75.385:1:0:0.8 +5 176518315 . A C 134 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=CTCTCAGCCTCAGCAACTCC;RSEQ=TTTGTAAAGGGAGAAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:2,16:0,0:0,18:1:0,2:23.7:1:32.3:1:1:0:58.4:17:1:0:1.4 1/0:4:3:0,3:0,1:1,3:0.75:0,0:26:1:32.3:1:1:0:60:6:0.75:0:1.3 +5 176518426 . T C 93 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCTGTCATGAGGCAACTGAG;RSEQ=CTCAGAGAAGGCAAGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:0,8:1:0,2:25.9:1:31.1:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 176518633 . G T 19 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.17022;LSEQ=ATCTAGCCTCCTGGTCCTCT;RSEQ=GCCCCCTTGGTGGACATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:2,0:110,27:137,2:0.0144:2,0:39.5:1:32:1:1:0:60:4:0.0146:0:1 0/1:119:2:1,1:92,25:117,2:0.0168:2,2:5.5:1:19.5:1:0.39069:3.62849:60:1:0.0088:0:1 +5 176518642 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19167;SOR=Inf;LSEQ=CCTGGTCCTCTGGCCCCCTT;RSEQ=GTGGACATGGTCCGGTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:133,41:174,0:0:2,0:22.2:1:31.7:1:1:0:60:42.5:1:0:0.1 0/1:136:2:1,1:102,32:134,2:0.0147:2,2:31:0:32:0:0.42778:3.15418:60:4:0.015:0:1.5 +5 176518651 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.25273;SOR=0;LSEQ=CTGGCCCCCTTGGTGGACAT;RSEQ=GTCCGGTGGTCCCGGACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:3:1,2:147,46:193,3:0.0153:2,2:18.7:1:30:1:0.14909:6.31524:60:6:0.0157:0:1 0/0:167:0:0,0:124,43:167,0:0:2,0:23.8:1:30.8:1:1:0:60:40.75:1:0:0.1 +5 176518784 . C T 273 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01933;LSEQ=AACGCTGTGGGCAGCATCCG;RSEQ=TATAACTACCTGCTAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:562:557:264,293:0,0:0,557:0.9911:0,2:25.9:1:30:1:1:0:60:78.571:0.9946:0:1.2 1/0:532:363:169,194:75,94:169,363:0.6823:2,2:24.9:1:29.1:1:0.70863:1.09:59.9:180.5:0.6811:0:1.2 +5 176519285 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03201;SOR=Inf;LSEQ=ACAGGGTGCTTCTATGGGTG;RSEQ=CGGTGGTCAGGGTTGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:247,92:339,0:0:2,0:25.6:1:32:1:1:0:59.9:36.667:1:0:1.1 0/1:250:4:2,2:160,86:246,4:0.016:2,2:21.5:1:29:1:0.61477:1.85563:60:8:0.0164:0:1.8 +5 176519287 . G A 259 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00819;LSEQ=AGGGTGCTTCTATGGGTGCC;RSEQ=GTGGTCAGGGTTGACTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:348:347:252,95:1,0:1,347:0.9971:0,2:25.7:1:30.8:1:1:0:59.9:42.375:0.9971:0:1.1 1/0:260:192:128,64:41,25:66,192:0.7385:2,2:26.1:1:29.4:1:0.54916:1.22:59.9:63:0.7383:0:1.2 +5 176519730 . C T 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGCGAGTACACCTGCCT;RSEQ=GCAGGCAATTCCATCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:0:0,0:345,218:563,0:0:2,0:24.8:1:31.1:1:1:0:59.9:45.917:1:0:0.1 0/1:534:31:19,12:285,218:503,31:0.0581:2,2:27.8:1:28.7:1:0.70999:1.21:60:30:0.0575:0:1.3 +5 176520223 . C T 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05769;SOR=6.70456;LSEQ=GTCGGGCTCCCTGGCCTTGG;RSEQ=TGTGCTCCTGCTGCTGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:660:1:1,0:335,322:657,1:0.0015:2,0:26:0:27:0:1:0:60:2:0.0016:0:2 0/1:595:6:2,4:306,282:588,6:0.0101:2,2:17.2:1:27.7:1:0.43527:2.16749:60:12:0.0104:0:1.7 +5 176520243 . G A 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.24574;LSEQ=CTGTGCTCCTGCTGCTGGCC;RSEQ=GGCTGTATCGAGGGCAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:613:450:225,225:80,82:162,450:0.7341:2,2:25.8:1:30.7:1:0.9271:1.02:59.9:33.615:0.7357:0:1.1 0/1:562:227:117,110:169,165:334,227:0.4039:2,2:25.8:1:29.1:1:0.86351:1.04:60:36.833:0.3982:0:1.2 +5 176520839 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50309;SOR=0;LSEQ=CACTTTAGGAGGCTGAGGGT;RSEQ=GGAGGATCGCTTGAATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:25,162:187,2:0.0105:2,2:27:1:29:1:0.25684:6.37:60:4:0.0107:0:1 0/0:157:0:0,0:23,134:157,0:0:2,0:22.9:1:30.5:1:1:0:59.8:77.5:1:0:0.1 +5 176520848 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49949;SOR=0;LSEQ=AGGCTGAGGGTGGGAGGATC;RSEQ=CTTGAATCCAGGAATTCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:7,133:140,2:0.0141:2,2:8:1:27.5:1:0.10988:17.84:60:4:0.0144:0:1 0/0:128:0:0,0:14,113:127,0:0:2,0:23.3:1:31:1:1:0:60:126:1:0:0.1 +5 176520904 . C CA 53 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.18984;SOR=3.64191;LSEQ=ATGGCAAGACTTCATCTCTA;RSEQ=AAAAAAAAAATAAGAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:0,2:0,50:50,2:0.0385:1,0:36.5:1:30.5:1:1:0:60:4:0.0408:0:0 0/1:31:4:0,4:1,26:27,4:0.129:1,0:25:1:26.5:1:1:0:52.5:3:0.1034:0:1 +5 176522036 . C T 76 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCCTGCTCCGAGCTCTTCCC;RSEQ=TCTCTCCTGTGTCCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:37.4:1:33:1:1:0:60:10:0.625:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:35:0:32:0:1:0:60:2:1:0:1 +5 176522260 . T A 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=TGGTCCAGTGCTGCTTGTCC;RSEQ=GCACCTGCCTCTGCATGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:161,14:175,0:0:2,0:24:1:32.3:1:1:0:60:350:1:0:0.1 0/1:141:8:7,1:115,18:133,8:0.0567:2,2:20.3:1:30:1:1:1.10:60:16:0.0576:0:2 +5 176522263 . A T 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00173;SOR=Inf;LSEQ=TCCAGTGCTGCTTGTCCTGC;RSEQ=CCTGCCTCTGCATGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:162,16:178,0:0:2,0:24.5:1:30.6:1:1:0:60:177:1:0:0.1 0/1:151:8:7,1:121,21:142,8:0.053:2,2:22.5:1:30.8:1:1:1.21:60:16:0.0537:0:2 +5 176522273 . G T 31 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34142;SOR=3.48699;LSEQ=CTTGTCCTGCACCTGCCTCT;RSEQ=CATGCTCCCTCGTGCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:1:1,0:181,29:210,1:0.0047:2,0:43:0:15:0:1:0:60:0:0:0:1 0/1:184:3:1,2:146,35:181,3:0.0163:2,2:12:1:20:1:0.10346:8.20767:60:2:0.0109:0:3 +5 176522728 . C T 268 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTGGAGTCCCGGAAGGTA;RSEQ=AGGCGCTAGGGCTCTGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:619:619:218,401:0,0:0,619:1:0,2:23.4:1:28.9:1:1:0:59.9:46.615:1:0:1.1 1/0:574:353:141,212:85,135:220,353:0.615:2,2:24:1:28.1:1:0.7923:1.06:59.9:69.6:0.6127:0:1.1 +5 176522903 . A G 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5618;SOR=0;LSEQ=CACCCTTCCCCAGAGGGGAG;RSEQ=GGGGACGCAGGAGAAGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:3:2,1:33,29:62,3:0.0455:2,2:31.3:1:24.7:1:1:1.74:54.7:2:0.0317:0:3.3 0/0:24:0:0,0:12,12:24,0:0:2,0:23.5:1:29.8:1:1:0:60:23:1:0:0.2 +5 176523067 . C T 64 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.32132;SOR=2.23827;LSEQ=GCTCCCTGCAGTGTATCCAC;RSEQ=GGGACCTGGCTGCCCGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:3:0,3:344,235:579,3:0.0052:2,0:1.3:1:27.7:1:0.06788:0:49:6:0.0052:0:1 0/1:523:6:1,5:322,195:517,6:0.0115:2,2:19.8:1:24.8:1:0.03264:8.22775:55.8:5:0.0097:0:1 +5 176523422 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32386;SOR=3.87715;LSEQ=AAGGCACTGCCCAAAGTCAC;RSEQ=TGGCCCCAGGAGTCATGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:361:1:1,0:130,230:360,1:0.0028:2,0:1:0:29:0:0.36288:0:60:2:0.0028:0:1 0/1:281:3:2,1:96,181:277,3:0.0107:2,2:21.3:1:27.7:1:0.28101:3.75:60:6:0.0109:0:1 +5 176523545 . G A 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=TCATGTCTGTGGGGTCCCCC;RSEQ=TCCTAGCCCCGGTCGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:464:0:0,0:344,119:463,0:0:2,0:21.5:1:30.2:1:1:0:60:56.875:1:0:1.7 0/1:357:10:6,4:250,97:347,10:0.028:2,2:24.5:1:29.3:1:0.47766:1.71532:60:20:0.0284:0:2.5 +5 176523562 . C A 272 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCGTCCTAGCCCCGGTCGT;RSEQ=GGGAGGGCGCTGAGCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:647:647:450,197:0,0:0,647:1:0,2:21.3:1:29.2:1:1:0:59.9:63.7:1:0:1.9 1/0:517:377:243,134:88,48:136,377:0.7292:2,2:21.5:1:28.2:1:1:1.01095:60:74.4:0.7266:0:1.9 +5 176523597 . A G 317 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00555;LSEQ=CCACACTGAGCCCTGGCCCT;RSEQ=CCTCCAGGTGGTCTTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:958:955:548,407:2,1:3,955:0.9969:2,2:26.7:1:32.1:1:1:1.48481:59.9:62.667:0.9979:0:1.7 1/0:848:541:297,244:170,137:307,541:0.638:2,2:28.1:1:31.3:1:0.94275:1.01942:60:59.111:0.6364:0:1.7 +5 176523778 . GTCC G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.60212;SOR=1.43966;LSEQ=GCCCTCGACCCCACTTTCCA;RSEQ=TCCTCCTCCTCTGCCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:7:2,5:124,336:460,7:0.015:2,2:22.6:1:32.3:1:1:1.08:60:14:0.0156:0.0043:0 0/1:373:8:3,5:113,247:360,8:0.0214:2,2:22:1:29.5:1:0.71082:1.31:60:16:0.0225:0.0054:0.3 +5 176523876 . TTCC T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0.93918;LSEQ=TCCTCCTCCTCCTCTTCCTC;RSEQ=TCCTCCTCCTCTTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:0,2:2,90:92,2:0.0213:1,0:11.5:1:30.9:1:1:0:43.5:4:0.0227:0.0106:2 0/1:50:1:0,1:3,46:49,1:0.02:2,0:19:0:30:0:1:0:27:2:0.0208:0:2 +5 176523918 . T C 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.31034;SOR=0;LSEQ=TCCTCCTCTTCCTCCTCCTC;RSEQ=TCCTCCTCCTCCTCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:1,19:0,0:0,20:1:0,1:15.3:1:34:1:1:0:38.8:40:1:0:2 1/1:9:8:0,8:0,1:1,8:0.8889:0,0:11.1:1:32.8:1:1:0:40.8:16:0.8889:0:1.8 +5 176523921 . C T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.50725;SOR=0.39295;LSEQ=TCCTCTTCCTCCTCCTCTTC;RSEQ=TCCTCCTCCTCTTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:0,16:1,0:1,16:0.9412:0,1:13.8:1:29.5:1:0.05882:0:35.4:7:1:0:2.1 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:11:1:30.2:1:1:0:35:12:0.8571:0:2 +5 176524086 . T C 47 d5;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTCTCTTCCTCCTCCTTCTC;RSEQ=TCCTCCTCCTCCTCCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:1,3:0.75:0,2:6.7:1:29.7:1:1:0:42:6:0.75:0:4.3 0/0:2:0:0,0:2,0:2,0:0:0,0:23:1:30.5:1:1:0:50.5:4:1:0:0.5 +5 176524101 . C T 110 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.02692;SOR=0.04568;LSEQ=TTCTCTTCCTCCTCCTCCTC;RSEQ=TGCTCCTCTTCCTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:10,1:1,0:1,11:0.9167:0,2:13:1:32:1:1:0:51.8:10:0.9091:0:3.4 0/1:4:1:1,0:3,0:3,1:0.25:0,0:4:0:31:0:1:0:60:2:0.25:0:3 +5 176524103 . G C 115 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04603;SOR=0.10781;LSEQ=CTCTTCCTCCTCCTCCTCCT;RSEQ=CTCCTCTTCCTCCTCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:10,1:0,0:0,11:0.8462:0,2:15:1:33.5:1:1:0:51.8:22:0.8462:0:3.4 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:3.5:1:32:1:1:0:60:4:0.3333:0:2.5 +5 176524110 . T C 138 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05419;SOR=0;LSEQ=TCCTCCTCCTCCTGCTCCTC;RSEQ=TCCTCCTCCTCCTCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:17,1:0,0:0,18:1:0,1:16.6:1:33.1:1:1:0:54.9:36:1:0:2.5 1/0:12:9:8,1:3,0:3,9:0.75:0,2:7.9:1:31.6:1:1:0:60:18:0.75:0:1.4 +5 176524465 . C T 160 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05654;LSEQ=GGCCTCATCTGGCCTGACCG;RSEQ=GTGGACATGCGCCCCGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:902:42:20,22:435,424:859,42:0.0466:2,2:26.7:1:29.7:1:0.75331:1.12839:60:41:0.0464:0:1.1 0/0:727:2:0,2:381,344:725,2:0.0028:2,0:4.5:1:25.5:1:0.22616:0:60:4:0.0028:0:1 +5 176524734 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13861;SOR=Inf;LSEQ=GCCTTGGGCCTTGGGGCTCA;RSEQ=CCACAGCCTGACACAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:40,207:247,0:0:2,0:23.4:1:32.6:1:1:0:59.9:81.333:1:0:0.1 0/1:147:2:1,1:25,120:145,2:0.0136:2,2:26:1:27:1:0.32346:4.73:60:4:0.0138:0:1 +5 176525029 . G C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03571;SOR=Inf;LSEQ=CCCCTGCTGCTGCTGCCCCA;RSEQ=CGTCTTGACGGGAGCATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:6,0:0:0,0:28:1:28:1:1:0:59.2:5:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:32:1:1:0:60:4:1:0:1.5 +5 176562558 . C A 54 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27007;SOR=2.72616;LSEQ=CTATCAAGAATGGCTTTCTG;RSEQ=ACTTTGAGAATTTTACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:2:2,0:210,327:537,2:0.0037:2,0:1:0:26:1:0.15426:0:60:4:0.0038:0:1 0/1:497:5:4,1:198,294:492,5:0.0101:2,2:13.4:1:23.6:1:0.16363:5.92:60:4:0.0082:0:2 +5 176619202 . GT G 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.9594;LSEQ=ATGATTTAAACCTTCTCTCA;RSEQ=TTTTTTTTTTTGTTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:0,2:0,23:23,2:0.08:1,0:22.5:1:32:1:1:0:50:4:0.08:0:3.5 0/1:13:1:0,1:0,12:12,1:0.0769:0,0:36:0:28:0:1:0:58:2:0.0769:0:0 +5 176621075 . G C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGTGAGCCACCACACCTG;RSEQ=CTGATATTAATATATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:33:0:1:0:40:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 176630984 . T C 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00033;SOR=0.14865;LSEQ=TTTTCCTTGTGTATGATCTA;RSEQ=TCTAGGTTGTCTAGTTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:69:62:61,1:6,0:6,62:0.8986:0,1:22.4:1:32.3:1:1:0:60:61:0.9104:0:1.1 1/0:32:18:18,0:14,0:14,18:0.5625:1,1:24.1:1:31.9:1:1:0:60:36:0.5806:0:1.1 +5 176636546 . G A 133 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09246;LSEQ=TCTCAAAAAAAAAAAAAAAA;RSEQ=GAATAAAAAAAAAAGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:28:26,2:30,1:31,28:0.3043:1,2:8.6:1:27.7:1:0.5995:2.27599:56.1:4.6:0.3651:0:1.3 0/1:104:4:2,2:87,10:97,4:0.0385:2,2:22:1:19.8:1:0.06822:8.35858:40.5:1:0.0225:0:2.3 +5 176636547 . G T 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.80068;LSEQ=CTCAAAAAAAAAAAAAAAAG;RSEQ=AATAAAAAAAAAAGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:1:1,0:84,4:88,1:0.0106:1,0:11:0:15:0:1:0:28:0:0:0:2 0/1:105:2:2,0:88,12:100,2:0.019:2,0:19:1:24:1:1:0:21:4:0.0238:0:2 +5 176636550 . T TA 49 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.41918;SOR=0.42304;LSEQ=AAAAAAAAAAAAAAAAGGAA;RSEQ=AAAAAAAAAAGCTTCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:4:4,0:94,5:99,4:0.0377:2,0:19.5:1:24.8:1:1:0:47.5:3:0.037:0:2 0/1:123:2:2,0:102,17:119,2:0.0163:2,0:28.5:1:18.5:1:1:0:52:1:0.0116:0:2 +5 176636882 . C T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03826;LSEQ=GATGAGAAGGAAAAGCCTTG;RSEQ=GCTAAATCTCGAGCCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:468:337:160,177:57,72:129,337:0.7201:2,2:24.8:1:30.1:1:0.53531:1.14:60:111.333:0.7277:0:1.1 0/1:437:39:15,24:192,205:397,39:0.0892:2,2:20.4:1:28.9:1:0.24572:1.49716:60:78:0.0901:0:1.1 +5 176637149 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01352;LSEQ=ACTGCAAAGAAAGAATTTGA;RSEQ=ACTTCAAATGGTGACTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:254:134,120:68,56:124,254:0.672:2,2:25.9:1:30.6:1:0.74236:1.08718:60:30.75:0.6685:0:1.1 0/1:448:12:7,5:226,210:436,12:0.0268:2,2:22.5:1:28.8:1:0.77359:1.30:60:11:0.0249:0:1.3 +5 176637240 . G T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.01743;LSEQ=ATAAACCCCAACGAAGCCTG;RSEQ=TGTGTGGTTCAAAAGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:612:389:199,190:107,114:221,389:0.6356:2,2:24.5:1:29.9:1:0.55558:1.12:59.9:76.8:0.6379:0:1.2 0/1:646:19:10,9:298,329:627,19:0.0294:2,2:28.4:1:29.5:1:0.81645:1.23:60:38:0.0296:0:1.1 +5 176637576 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02042;LSEQ=CAGAGCCTGGAACCGAGACG;RSEQ=CTCAGGTTAATCTCTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:431:263:145,118:88,79:167,263:0.6102:2,2:23.4:1:32.1:1:0.6913:1.10:59.8:86.667:0.6176:0:1.1 0/1:454:14:7,7:250,190:440,14:0.0308:2,2:24.7:1:30.2:1:0.78532:1.31497:60:28:0.031:0:1 +5 176639031 . G T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02907;SOR=Inf;LSEQ=CAGAGCATAGAACTCCTTCA;RSEQ=CAAGCATACTTGAGGAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:0:0,0:193,300:493,0:0:2,0:24.2:1:32.4:1:1:0:59.9:60.625:0.9979:0:0.2 0/1:482:5:3,2:215,261:476,5:0.0104:2,2:26.6:1:29.4:1:0.6626:1.82:60:10:0.0106:0:1.4 +5 176639105 . T C 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=TCAGCTGGGCCACGGTTAAA;RSEQ=GTTTGTGATAAATCCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:109,188:297,0:0:2,0:23.6:1:30.5:1:1:0:60:36.125:1:0:0.1 0/1:339:15:4,11:139,183:322,15:0.0442:2,2:22.5:1:28.7:1:0.28697:2.08457:60:14:0.0426:0:1.3 +5 176639170 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49862;SOR=0;LSEQ=GCCAGGAATTCCCAGTTTGA;RSEQ=ACCACAGGCTGAGCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:46,123:169,2:0.0117:2,2:25.5:1:28.5:1:0.47534:2.66:60:4:0.012:0:1 0/0:166:0:0,0:54,112:166,0:0:2,0:26.6:1:31.1:1:1:0:60:54.333:1:0:0.2 +5 176639304 . C G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.77743;LSEQ=TAAAGTGAAGTATAAACTAG;RSEQ=GGGGAAGAATCATCACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,1:1,13:0.9286:0,1:24.5:1:28.1:1:1:0:60:5.5:0.9167:0:1.2 1/1:11:10:0,10:0,1:1,10:0.9091:0,0:27.4:1:31:1:1:0:60:20:0.9091:0:1 +5 176662828 . G A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05781;SOR=Inf;LSEQ=TTATCATCTTTTAGCTGTGC;RSEQ=GTCAGAGAAGAAACGCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:247,162:409,0:0:2,0:24.6:1:30.5:1:1:0:60:135.333:1:0:0.1 0/1:395:4:2,2:230,160:390,4:0.0101:2,2:22.3:1:32:1:1:1.43612:58.8:8:0.0103:0:1.3 +5 176666691 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19787;SOR=Inf;LSEQ=TTCATTTTGTGTGGTATACA;RSEQ=ATTTTTTAAAAATTAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:210,34:244,0:0:2,0:23:1:33.2:1:1:0:60:488:1:0:0.1 0/1:196:2:1,1:160,33:193,2:0.0102:2,2:24.5:1:27:1:0.31906:4.79162:60:4:0.0103:0:1 +5 176671142 . A T 42 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12442;SOR=Inf;LSEQ=AGACTTTGGCATATAAAGTA;RSEQ=AGGGTTTATTTTTTCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:247,73:320,0:0:2,0:24.9:1:30.5:1:1:0:60:105.667:1:0:0.1 0/1:338:4:1,3:234,99:333,4:0.0118:2,2:8.3:1:21.3:1:0.08448:7.04523:60:3:0.0091:0:1.8 +5 176675110 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50137;SOR=0;LSEQ=TAATGGCTAGACAAATAGCA;RSEQ=CCCAGAGGGAGGGGGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:134,13:147,2:0.0134:2,2:11.5:1:29:1:0.17967:9.96976:60:4:0.0136:0:1 0/0:127:0:0,0:113,14:127,0:0:2,0:23.5:1:31.9:1:1:0:60:41.333:1:0:0.2 +5 176675394 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50271;SOR=0;LSEQ=AAGGGAAACCCACTCCATCT;RSEQ=TTTATGATGGTTTCTTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:21,162:183,2:0.0108:2,2:20.5:1:31.5:1:0.22427:7.56:60:4:0.011:0:1.5 0/0:154:0:0,0:17,136:153,0:0:2,0:25:1:31.4:1:1:0:60:37.25:0.9933:0:0.1 +5 176675423 . A G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04268;SOR=Inf;LSEQ=GGTTTCTTGGTAGAATAACA;RSEQ=TGCTTTTGGATGATTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:2,103:105,0:0:1,0:27.9:1:31.8:1:1:0:60:51.5:1:0:0.1 0/1:89:4:0,4:2,83:85,4:0.0449:1,0:20.3:1:31.8:1:1:0:60:8:0.0455:0:1 +5 176678609 . G T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.58316;SOR=2.55514;LSEQ=ATCTACAACTACGGGCCCTT;RSEQ=CCTCTTTCTCACCTCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:1,0:56,2:58,1:0.0169:1,0:41:0:15:0:1:0:60:0:0:0:1 0/1:47:2:2,0:45,0:45,2:0.0426:1,0:12:1:31.5:1:1:0:60:4:0.0435:0:1 +5 176678625 . C T 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50488;SOR=0;LSEQ=CCTTGCCTCTTTCTCACCTC;RSEQ=TTTTCTGCCACTTTTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:83,4:87,2:0.0225:1,2:7.5:1:31.5:1:0.10981:18.66298:60:4:0.0225:0:1 0/0:69:0:0,0:68,1:69,0:0:1,0:19.9:1:30.3:1:1:0:60:68:1:0:0.1 +5 176687248 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50497;SOR=0;LSEQ=ATTGGAACAAAAATACTTTT;RSEQ=ATCATATTGCCACTGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:0,2:10,147:157,2:0.0126:2,0:14:1:30:1:1:0:60:4:0.0126:0:1 0/0:126:0:0,0:9,117:126,0:0:2,0:21.1:1:31.1:1:1:0:60:125:1:0:0.1 +5 176691923 . C T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.6239;SOR=0.35921;LSEQ=GTACTCTTCAAAAAGGAATG;RSEQ=CCCACAAGTGTTATCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:3:1,2:101,58:159,3:0.0185:2,2:17.3:1:28.7:1:0.55564:3.45488:22.7:6:0.0189:0:1 0/0:149:1:0,1:95,53:148,1:0.0067:2,0:1:0:24:0:0.36242:0:22:2:0.0068:0:1 +5 176691954 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5002;SOR=Inf;LSEQ=TTATCATGGCAAAACTGGAA;RSEQ=AGTCTACAGTGTTACCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:79,86:165,0:0:2,0:22.1:1:32:1:1:0:29.6:54:1:0:0.2 0/1:185:2:0,2:91,92:183,2:0.0108:2,0:20.5:1:26:1:0.49741:0:40.5:4:0.0112:0:1 +5 176691965 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.77868;LSEQ=AAACTGGAAGAGTCTACAGT;RSEQ=TTACCCAGCATGCTGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:1:1,0:64,83:147,1:0.0068:2,0:1:0:24:0:0.43919:0:28:2:0.0068:0:1 0/1:167:2:1,1:74,91:165,2:0.012:2,2:16:1:29.5:1:1:1.23:20.5:4:0.012:0:1 +5 176692006 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4994;SOR=Inf;LSEQ=ATTGTTGTAAACAAACAAGG;RSEQ=CAAGATTCTTGCCAAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:26,84:110,0:0:2,0:24.8:1:32.1:1:1:0:36.4:109:1:0:0 0/1:124:2:1,1:35,87:122,2:0.0161:2,2:41.5:1:28.5:1:0.49803:2.46:27:4:0.0165:0:1 +5 176694479 . AAT A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.76676;SOR=0.67587;LSEQ=CTTTTAGTGAAGAGAAAGAA;RSEQ=ATATATATATATGTGTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:8:7,1:153,9:162,8:0.0471:2,2:22:1:31.9:1:0.3908:2.41046:60:16:0.0473:0.0176:0.3 0/1:124:4:3,1:103,18:121,4:0.0323:2,2:25.3:1:30:1:0.48741:1.89532:60:8:0.0323:0.0081:0.3 +5 176696503 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.5082;SOR=0;LSEQ=AAGATGGACTTTAATGTGGA;RSEQ=AGACAGACATTGCTAATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:96,7:103,2:0.019:2,2:15.5:1:27.5:1:0.14725:12.89524:60:4:0.0192:0:1.5 0/0:78:0:0,0:74,4:78,0:0:2,0:23.8:1:31.7:1:1:0:60:77:1:0:0.1 +5 176696836 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50027;SOR=Inf;LSEQ=TATCCTTTTTGTTTCTCAGG;RSEQ=AAACACAGACCTCTGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:40,134:174,0:0:2,0:25.2:1:32.4:1:1:0:60:173:1:0:0.1 0/1:195:2:1,1:54,139:193,2:0.0103:2,2:28.5:1:30.5:1:0.48559:2.56:60:4:0.0104:0:1.5 +5 176697155 . A AGTCTT 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=36;MSI=8.000;MSILEN=5;SSF=0.33333;SOR=Inf;LSEQ=GAGCTACATTTGCTCCAAGG;RSEQ=GTCTTGTCTTGTCTTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:26:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:30.8:1:1:0:60:4:1:0:0 +5 176700613 . G T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24872;SOR=Inf;LSEQ=GGAAAAAGTAAAAAATAAGT;RSEQ=AATAAATAAGTAATTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:225,65:290,0:0:2,0:22.9:1:32.5:1:1:0:60:144:1:0:0.1 0/1:292:3:2,1:199,90:289,3:0.0103:2,2:17.7:1:21.3:1:1:1.10516:60:2:0.0069:0:3.3 +5 176700812 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19393;SOR=Inf;LSEQ=AGAAAATCTTGGGGGACCTT;RSEQ=TCTAGAAGAGAAATGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:56,181:237,0:0:2,0:22.7:1:32.4:1:1:0:60:32.857:1:0:0.1 0/1:187:2:1,1:51,134:185,2:0.0107:2,2:13:1:30.5:1:0.4799:2.61:60:4:0.0109:0:1 +5 176700885 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=35.95033;LSEQ=CGGAAGCACAAGCATAGTTC;RSEQ=TTTTAGGTAGAGGTATGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:20:0,20:0,44:44,20:0.3125:1,1:28.4:1:31.3:1:1:0:59.8:19:0.3016:0:1 1/1:36:34:0,34:0,2:2,34:0.9444:0,1:22.1:1:30.8:1:1:0:59.9:68:0.9444:0:1.1 +5 176707483 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50268;SOR=0;LSEQ=AAATGTGGCTGCAACTTCAA;RSEQ=GAAAAAAAGTTTGCCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:2,0:128,6:134,2:0.0147:1,0:17.5:1:32:1:1:0:60:4:0.0149:0:1 0/0:112:0:0,0:100,12:112,0:0:2,0:23.1:1:31.1:1:1:0:59.8:36.333:1:0:0.1 +5 176707544 . G A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=GCTGACTTGTTTTATGCGGT;RSEQ=TACTTTGTGTTACTTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:303,158:461,0:0:2,0:25.7:1:32.2:1:1:0:60:152.667:0.9978:0:0.1 0/1:397:14:12,2:243,140:383,14:0.0353:2,2:21.3:1:28.4:1:0.1526:3.45:60:28:0.0356:0:1 +5 176710547 . C G 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.24176;SOR=5.20669;LSEQ=ACGCAGAATGCTGCACCCCA;RSEQ=AGTCTCTGCTTTAGTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:9,0:9,3:0.25:0,0:28:1:31.3:1:1:0:60:6:0.25:0:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:25.5:1:33.5:1:1:0:60:4:0.6667:0:1 +5 176710684 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21066;SOR=Inf;LSEQ=TCTTTTCTCTGAGAGGTTCA;RSEQ=TCTTTACAAATAGAAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:121,1:122,0:0:1,0:22.6:1:33.2:1:1:0:60:60:1:0:0.1 0/1:104:2:2,0:98,4:102,2:0.0192:1,0:26.5:1:31:1:1:0:60:4:0.0196:0:1 +5 176710956 . C A 57 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10388;SOR=5.72642;LSEQ=ATCATTTCAGGATTCTGCAG;RSEQ=TGACATCTGAATTTCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:1:1,0:129,362:491,1:0.002:2,0:1:0:26:0:0.26423:0:60:2:0.0021:0:1 0/1:433:5:4,1:126,301:427,5:0.0115:2,2:6.4:1:24.8:1:0.03034:9.50:60:10:0.0117:0:1 +5 176719227 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1969;SOR=Inf;LSEQ=CTCAGGGTCTCATGCCATTT;RSEQ=CATCAGCCTTGAAGAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:13,118:131,0:0:2,0:24.3:1:32:1:1:0:59.9:42.667:1:0:0.1 0/1:105:2:0,2:13,90:103,2:0.019:2,0:25.5:1:31.5:1:1:0:60:4:0.0194:0:1 +5 176720766 . A G 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=2.38564;LSEQ=CCACACCTTCGGACTGTAGC;RSEQ=TAGCCTTGGCCCATGTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:66:61,5:139,17:156,66:0.2973:2,2:22.3:1:30.4:1:0.6239:1.49:60:65:0.3009:0:1 1/0:173:87:77,10:74,11:85,87:0.5029:2,2:22.2:1:29.9:1:0.81904:1.14:60:86:0.5:0:1 +5 176720770 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20605;SOR=Inf;LSEQ=ACCTTCGGACTGTAGCATAG;RSEQ=CTTGGCCCATGTGATATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:209,31:240,0:0:2,0:23.3:1:32.3:1:1:0:60:47:1:0:0.3 0/1:200:2:1,1:166,32:198,2:0.01:2,2:26:1:28.5:1:0.30347:5.12379:60:4:0.0101:0:1 +5 176721119 . G A 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGCTCAGGCACCCAAAAT;RSEQ=TCAGATAAACCTCCTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:196,251:447,0:0:2,0:23.8:1:32.3:1:1:0:60:62.857:1:0:0.2 0/1:311:16:6,10:140,155:295,16:0.0514:2,2:25.5:1:29.9:1:0.6084:1.50343:60:32:0.0525:0:1.5 +5 176721151 . T C 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TCCTGCTGACACCAACCAGA;RSEQ=GCTGTCGCTCTCCAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:202,221:423,0:0:2,0:23.8:1:30.9:1:1:0:59.9:140:1:0:0.3 0/1:287:11:5,6:145,131:276,11:0.0383:2,2:19.7:1:29.3:1:0.76214:1.32692:60:22:0.04:0:2 +5 176721198 . T C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=55.37497;LSEQ=CAGGGACTTGTCAGAGGCCA;RSEQ=TGCTACCTGAAAGACCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:162:82,80:155,144:299,162:0.3514:2,2:26.3:1:32.6:1:0.84541:1.05006:60:80:0.3509:0:1.2 1/1:405:392:214,178:7,6:13,392:0.9679:2,2:25.1:1:31.4:1:1:1.03:59.9:97:0.9676:0:1.3 +5 176721272 . G C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.68299;LSEQ=AAGGTCAGAGACCTCGCTGG;RSEQ=TCAGGGACCAAATCCCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:25:15,10:248,169:417,25:0.0563:2,2:23.7:1:33.2:1:1:1.02:60:50:0.0573:0:1.2 0/1:445:192:107,85:147,105:252,192:0.4315:2,2:22.8:1:31.3:1:0.62858:1.11188:60:63:0.4305:0:1.4 +5 176722005 . G A 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=TTTCTCAGCCTCCTGCCAAG;RSEQ=CCTTTTTATATGAGCCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:581:0:0,0:303,277:580,0:0:2,0:25.2:1:31.5:1:1:0:59.9:43.615:0.9982:0:0.1 0/1:598:15:7,8:283,299:582,15:0.0251:2,2:21.1:1:29.1:1:1:1.08153:60:30:0.0255:0:1.2 +5 176722514 . AG A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18157;SOR=Inf;LSEQ=CCCCAGGGTACCATTTGGGG;RSEQ=GGGAAATCTTTTCTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:0:0,0:27,239:266,0:0:2,0:23.7:1:31.5:1:1:0:60:43.333:1:0:0.1 0/1:198:2:1,1:33,163:196,2:0.0101:2,2:6:1:28:1:0.31467:4.88:60:4:0.0103:0.0051:0.5 +5 176722542 . T TA 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.63594;SOR=1.28989;LSEQ=TCTTTTCTTTCTTTCCCCCT;RSEQ=AAAAAAAAACACATCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:11:0,11:4,126:130,11:0.0775:1,0:24.7:1:30.3:1:1:0:60:10:0.0719:0.007:0.4 0/1:92:9:0,9:3,80:83,9:0.0978:1,0:28.6:1:31.7:1:1:0:60:18:0.0989:0:0.2 +5 178012665 . CA TG 53 MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15267;LSEQ=CCTGGATGGCGCTGGGGTAA;RSEQ=CTCCACAGCCCTGGATGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:3,3:6,3:0.3:2,0:27:0:33.5:0:0.46429:0:25.7:6:0.3333:0:3.7 0/1:3:1:1,0:0,2:2,1:0.3333:0,0:19:0:32.5:0:0.33333:0:36:2:0.3333:0:3 +5 178012668 . T C 66 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.6004;SOR=0.39896;LSEQ=GGATGGCGCTGGGGTAACAC;RSEQ=CCACAGCCCTGGATGGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:3,1:3,3:6,4:0.4:2,2:28.8:1:33:1:0.57143:2.69:26.3:8:0.4:0:4.5 0/1:5:1:1,0:1,3:4,1:0.2:2,0:21:0:32:0:0.4:0:36:2:0.2:0:3 +5 178012670 . C T 62 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.6004;SOR=0.39896;LSEQ=ATGGCGCTGGGGTAACACTC;RSEQ=ACAGCCCTGGATGGCGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:3,1:3,3:6,4:0.4:2,2:30.8:1:31:1:0.57143:2.69:26.3:8:0.4:0:4.5 0/1:5:1:1,0:1,3:4,1:0.2:2,0:23:0:32:0:0.4:0:36:2:0.2:0:3 +5 178095692 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49795;SOR=Inf;LSEQ=GCCTGCCTGGCTTCTCGTGG;RSEQ=TTGCTGGCAAGCTTTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:54,52:106,0:0:2,0:26.2:1:30.2:1:1:0:60:105:1:0:0.2 0/1:111:2:1,1:61,48:109,2:0.018:2,2:36:1:29:0:1:1.26806:60:4:0.0182:0:1 +5 178095709 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24205;SOR=0;LSEQ=TGGTTTGCTGGCAAGCTTTG;RSEQ=CATTCCTCGGCTTCTAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:51,55:106,2:0.0185:2,2:36:1:31.5:1:1:1.08:60:4:0.0187:0:1 0/0:111:0:0,0:53,58:111,0:0:2,0:28.2:1:30.8:1:1:0:58.6:54.5:1:0:0.2 +5 178095757 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50015;SOR=Inf;LSEQ=CCAATCTCCACCCTCATCTT;RSEQ=ATGTGGTATTCTCCCTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:18,35:53,0:0:2,0:23.5:1:31.6:1:1:0:60:25.5:1:0:0.1 0/1:64:2:1,1:18,44:62,2:0.0313:2,2:32.5:1:28:1:0.50893:2.41:60:4:0.0313:0:1 +5 178095779 . C CA 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.03182;LSEQ=TGTGGTATTCTCCCTATCTC;RSEQ=AACTTCCCCTTTTTATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:1,6:9,19:28,7:0.2:2,2:27.3:1:31.9:1:0.64446:2.77057:60:14:0.2188:0.0286:0.1 0/1:39:8:2,6:5,26:31,8:0.2051:2,2:20.1:1:30.8:1:0.61704:1.71:60:16:0.2051:0.0769:0.1 +5 178267705 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGAAAAAGGTTCTTCAG;RSEQ=CCAGGCTCCAGTATCCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:22:1:34.5:1:1:0:40.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 178267755 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGGAGGAGGAGTTTCCT;RSEQ=TAATCCAGAAGGGGAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:29:1:29:0:1:0:40.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 178268093 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49855;SOR=Inf;LSEQ=CTGAGAAGCGGGACACCCTG;RSEQ=CCCTGCTGCAGAAGCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:39,21:60,0:0:2,0:25.9:1:31.3:1:1:0:60:59:1:0:1.6 0/1:69:2:1,1:43,24:67,2:0.029:2,2:44:0:30:1:1:1.77567:60:4:0.0294:0:1 +5 178268107 . G C 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=0.20541;LSEQ=ACCCTGCCCCTGCTGCAGAA;RSEQ=CAGCCATCCCAGCAGCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:51:30,21:11,6:17,51:0.75:2,2:25.8:1:31.4:1:0.77852:1.27869:60:102:0.7727:0:2.4 0/1:74:28:15,13:28,18:46,28:0.3784:2,2:28:1:30.4:1:0.62933:1.34264:60:56:0.3889:0:2.2 +5 178268132 . A G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24184;SOR=0.65798;LSEQ=CATCCCAGCAGCCAGCAGGC;RSEQ=AGGTCTGAGCTCAGGACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:54:29,25:11,10:21,54:0.72:2,2:29.7:1:30.8:1:1:1.05:60:108:0.7397:0:2.4 1/0:86:54:27,27:19,13:32,54:0.6279:2,2:28.7:1:29.7:1:0.50328:1.45507:60:26:0.619:0:1.9 +5 178268174 . C T 23 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49991;SOR=Inf;LSEQ=CCGAGGCCCTCTATGGCCAG;RSEQ=AACCATGTCAGACACAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:25,43:68,0:0:2,0:25.8:1:31.9:1:1:0:60:21.667:1:0:1.5 0/1:80:2:1,1:32,46:78,2:0.025:2,2:7.5:1:23:1:1:1.43:60:4:0.025:0:1.5 +5 178268179 . A G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00266;SOR=0.35265;LSEQ=GCCCTCTATGGCCAGCAACC;RSEQ=TGTCAGACACAGCACCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:40:13,27:11,17:28,40:0.5882:2,2:22.9:1:30.7:1:0.61269:1.33798:60:39:0.6:0:2.2 0/1:78:26:9,17:21,31:52,26:0.3333:2,2:22.9:1:30.1:1:0.8054:1.27556:60:52:0.3377:0:2.4 +5 178268227 . T C 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00078;SOR=Inf;LSEQ=GCCAGATGCCTCTGCTGGAG;RSEQ=CAGCACTCCAAACCTATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:9,26:35,0:0:2,0:24.6:1:30.6:1:1:0:60:70:1:0:0.6 0/1:33:9:2,7:4,20:24,9:0.2727:2,2:19.3:1:29.7:1:1:1.41:60:8:0.25:0:2.1 +5 178268271 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=AAAATGGTGACCCCCACCCT;RSEQ=GCCAGGGCTCCTGGGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:0,12:12,2:0.1429:0,2:12.5:1:29:1:0.14286:0:60:4:0.1429:0:1.5 0/0:7:0:0,0:0,7:7,0:0:0,0:15.1:1:31.6:1:1:0:60:14:1:0:0.9 +5 178268295 . G A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=AGGGCTCCTGGGCCTTTGAC;RSEQ=TCTTTTAGGCTGGTCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:0,1:0,7:7,1:0.125:0,0:5:0:31:0:1:0:60:2:0.125:0:1 1/0:4:2:0,2:0,2:2,2:0.5:0,0:14:1:28:1:1:0:60:4:0.5:0:2 +5 178268306 . T C 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.63248;LSEQ=GCCTTTGACGTCTTTTAGGC;RSEQ=GGTCTGTGTGGGACAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:25.4:1:30.4:1:1:0:60:10:0.8333:0:1 1/0:4:3:0,3:0,1:1,3:0.75:0,0:15.3:1:21.3:1:1:0:60:2:0.6667:0:1.7 +5 178996349 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.25008;SOR=0;LSEQ=TGATGGAGGAAGAAGGGATG;RSEQ=TGATTGTTGGTCTGCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:1,2:149,90:239,3:0.0124:2,2:15.7:1:29:1:0.5593:3.29425:60:6:0.0124:0:1 0/0:220:0:0,0:138,82:220,0:0:2,0:22.6:1:30.6:1:1:0:60:72.333:1:0:0.2 +5 178996435 . A G 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGATTCTCAGGTAAAATG;RSEQ=AATTTTGGCTCTAGATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:119,167:286,0:0:2,0:25.5:1:30.8:1:1:0:60:94.333:1:0:0.1 0/1:332:81:36,45:111,140:251,81:0.244:2,2:25.8:1:30.2:1:1:1.01:60:80:0.2439:0:1.1 +5 178996554 . G A 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CACTGGTAGAGGACCCCAGG;RSEQ=ATGCAGCTGGGGAAGGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:28:0,28:1,16:17,28:0.6222:1,1:23.1:1:31.6:1:0.37778:0:60:56:0.6222:0:1 0/0:28:0:0,0:2,26:28,0:0:2,0:19.8:1:30.9:1:1:0:60:27:1:0:0.1 +5 179545228 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17557;SOR=Inf;LSEQ=CCAAAGGGCCCCAAGTGGGG;RSEQ=GGAGCCTGGAAACTGTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:72,41:113,0:0:2,0:23.9:1:30.4:1:1:0:60:55.5:1:0:0.7 0/1:82:2:1,1:44,36:80,2:0.0244:2,2:33.5:1:29.5:1:1:1.21921:60:4:0.0253:0:1.5 +5 179545252 . C T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15565;LSEQ=GCCTGGAAACTGTAGTGTGG;RSEQ=AGGGCAGGTCTGGGGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:79,69:148,2:0.0133:2,2:12.5:1:31:1:1:1.14389:60:4:0.0133:0:3 0/1:130:2:1,1:66,62:128,2:0.0154:2,2:6:0:31:1:1:1.06404:60:4:0.0156:0:2 +5 179545299 . TG CA 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.3915;SOR=1.521;LSEQ=GGAGAAGAGAGGAGAGGCCA;RSEQ=GGGGCTCTGAAGAACTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:120:105:44,61:7,7:14,105:0.875:2,2:27.2:1:32.2:1:0.57909:1.38248:60:210:0.8898:0.1:1 1/1:105:96:43,53:4,5:9,96:0.9143:2,2:25.9:1:30.6:1:1:1.01:60:192:0.9231:0.0667:1.1 +5 179545318 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50327;SOR=0;LSEQ=ATGGGGGCTCTGAAGAACTG;RSEQ=TGAGCAGAAGACGAAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:34,59:93,2:0.0211:2,2:12.5:1:29:1:1:1.72:60:4:0.0211:0:2.5 0/0:76:0:0,0:29,47:76,0:0:2,0:21.4:1:30.4:1:1:0:60:75:1:0:1 +5 179545346 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12783;SOR=Inf;LSEQ=AAGACGAAGTGGCCTCACTC;RSEQ=TGTGGCCCCCCAAGAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:6,47:53,0:0:2,0:19.7:1:31.2:1:1:0:60:52:1:0:0.7 0/1:30:2:1,1:2,26:28,2:0.0667:2,2:16:1:28:1:0.1931:10.82:60:4:0.0667:0:2.5 +5 180029879 . G A 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGTGATGAAAGGAGGTC;RSEQ=CCAAAGAGACATTCCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:23.3:1:29.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180030038 . C G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCCTTGGGCCTGGAGTC;RSEQ=TGCTCTTCCTAGCTGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:2,0:50,0:50,2:0.0385:1,0:10:1:32:0:1:0:60:4:0.04:0:1 0/0:24:0:0,0:23,1:24,0:0:1,0:24.6:1:30.5:1:1:0:60:48:1:0:0 +5 180030313 . C A 312 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03862;LSEQ=CCTGGCCTCCTCGGGCCCCC;RSEQ=GCTCAGGCCGCCGCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1334:1121:538,583:104,103:207,1121:0.8403:2,2:23.9:1:30.8:1:0.59631:1.09409:60:45.708:0.8387:0:1.2 0/1:1097:185:92,93:458,453:911,185:0.1686:2,2:23.2:1:29.4:1:0.93577:1.02201:60:45.25:0.1677:0:1.2 +5 180035262 . TTC T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=1.19479;LSEQ=AAATGCTGACGTATGCTGCC;RSEQ=TCTCTCTCTGCTTCAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:5:2,3:97,42:139,5:0.0347:2,2:11.2:1:30.9:1:0.17631:3.43066:54.8:10:0.0352:0.0208:0.4 0/1:97:4:2,2:65,28:93,4:0.0412:2,2:8.5:1:28.3:1:0.58522:2.29911:58.8:8:0.0426:0.0309:0.3 +5 180035274 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16236;SOR=Inf;LSEQ=ATGCTGCCTTCTCTCTCTCT;RSEQ=CTTCAGCTACCTAAGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:117,66:183,0:0:2,0:23.5:1:31.7:1:1:0:52.4:35.6:1:0:0.2 0/1:124:2:1,1:76,46:122,2:0.0161:2,2:13:1:27.5:1:1:1.64515:41:4:0.0163:0:1 +5 180035347 . C T 160 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=59.05652;LSEQ=CACCTTATCAATCACTTGAA;RSEQ=GACTCACCCTCCTGACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:1,0:131,155:286,1:0.0035:2,0:14:0:34:0:0.45993:0:60:2:0.0036:0:1 0/1:250:43:20,23:98,108:206,43:0.172:2,2:27:1:29.6:1:1:1.04335:54.3:86:0.1734:0:1.4 +5 180035504 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29032;SOR=0;LSEQ=TCTTGTGTCTTTCTTTCTTA;RSEQ=GATCTCTTATCTCCACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:1,21:0,0:0,22:1:0,1:19.1:1:30.6:1:1:0:54.1:21:1:0:1.5 1/1:9:8:1,7:0,0:0,8:0.8889:0,2:26.4:1:30.6:1:1:0:53.6:16:1:0:1.3 +5 180035792 . C T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.04236;SOR=0.27526;LSEQ=ATGTGACAGGGAGGGGCTCC;RSEQ=GCGGTGCTGTAGGTCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:19:19,0:45,4:49,19:0.2754:2,1:27.2:1:31.2:1:0.57016:0:60:18:0.2769:0:1.1 0/1:32:3:3,0:27,2:29,3:0.0938:2,0:28.7:1:32:1:1:0:60:6:0.0938:0:1 +5 180036791 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54602;SOR=0;LSEQ=TCACCCTGGACTTGCACTTT;RSEQ=AAAGGACAGTCGTTGGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:172,4:176,2:0.0112:1,2:16.5:1:31.5:1:0.05554:38.5548:60:4:0.0115:0:1 0/0:94:0:0,0:93,1:94,0:0:1,0:20.6:1:30.9:1:1:0:60:93:1:0:0 +5 180037058 . G A 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23631;SOR=2.87085;LSEQ=ATCAGAAGGTGCTGAGGAAC;RSEQ=CGCTGCAGCAACCCTCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:2:2,0:141,418:559,2:0.0036:2,0:1:0:25.5:1:0.06464:0:60:4:0.0036:0:1 0/1:393:4:3,1:121,268:389,4:0.0102:2,2:17.3:1:26.3:1:0.09481:6.61:60:8:0.0102:0:1 +5 180037231 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGCCCCAGCAGCACCCT;RSEQ=GGCTGTGTTTCCTCCCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:0,20:20,2:0.0909:1,2:20:1:27.5:1:0.09091:0:60:4:0.0952:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:34.5:1:31.5:1:1:0:60:4:1:0:0.5 +5 180038248 . T TC 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=0.08871;LSEQ=GACGTCGCATGATTTGCTTT;RSEQ=CCCCGATGACGCAGAGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:195:191:163,28:3,0:3,191:0.9795:0,2:21.4:1:31.9:1:1:0:60:94.5:0.9844:0.1744:0.2 1/1:104:84:68,16:18,2:20,84:0.8077:2,2:21.9:1:30.4:1:0.51412:2.10472:60:83:0.8058:0.1538:0.2 +5 180038678 . CCT C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTGCTTGGGCTCCTGACC;RSEQ=GAGATAGGGCCCTAACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:2,12:0,0:0,14:1:0,2:27.9:1:33:1:1:0:60:28:1:0.2143:0.6 1/1:2:2:0,2:0,0:0,2:1:0,0:35:1:32.5:1:1:0:60:4:1:0:0 +5 180039187 . A G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCACCAGGTGAAGGAAT;RSEQ=CATCATGACGATGCCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:24.2:1:33.3:1:1:0:60:22:1:0:1.1 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:31:1:1:0:60:4:1:0:1 +5 180039606 . C T 170 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=21.48471;LSEQ=ACCAGCAGTTCAGCATGATG;RSEQ=GGCGTCTGCAGGATCACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1006:4:2,2:424,578:1002,4:0.004:2,2:18.8:1:28.5:1:1:1.36:60:8:0.004:0:1 0/1:784:62:28,34:306,415:721,62:0.0791:2,2:27.2:1:28.7:1:0.68997:1.12:60:124:0.0802:0:1.3 +5 180039715 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.03379;SOR=Inf;LSEQ=TCACCCACTCTGCCCTCCTC;RSEQ=TGACACGTCTCCCACTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:5,175:180,0:0:1,0:25.6:1:33.6:1:1:0:60:89:1:0:0.2 0/1:87:3:0,3:3,81:84,3:0.0345:1,0:14.3:1:28.7:1:1:0:60:6:0.0345:0:1 +5 180040270 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACCCGACTGTGCTCTAC;RSEQ=TGGGACCTGTGGGCAAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:2,72:74,2:0.0263:1,2:28:1:29.5:1:0.07789:29.59:60:4:0.0282:0:1 0/0:22:0:0,0:0,22:22,0:0:1,0:25.7:1:30.9:1:1:0:60:21:1:0:0.2 +5 180040457 . T C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAACAAAGCCTCTCTTGC;RSEQ=TCTCGCTGCTTCTCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9:1:33.5:1:1:0:52.5:4:1:0:5.5 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:32.5:1:1:0:60:4:1:0:1 +5 180040918 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00269;SOR=8.96819;LSEQ=CCAGGCTGGGGAGAGGTGGG;RSEQ=GGCCCTTGGTGGCCCACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:13:13,0:52,0:52,13:0.2:1,1:24.5:1:31.1:1:1:0:60:26:0.2031:0:1.5 1/0:10:7:7,0:3,0:3,7:0.7:0,0:32.9:1:29.4:1:1:0:60:14:0.7:0:1.7 +5 180041001 . G C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.34398;LSEQ=AGTCCCTTACTCCAGCAGGG;RSEQ=CGGTCATGTAACCTGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:231:229:212,17:0,0:0,229:0.9913:0,2:24.8:1:32.6:1:1:0:60:458:0.9913:0:2.1 1/1:155:154:139,15:0,0:0,154:0.9935:0,2:23:1:31.8:1:1:0:60:308:1:0:2.1 +5 180041008 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41595;SOR=0;LSEQ=TACTCCAGCAGGGGCGGTCA;RSEQ=GTAACCTGCCGCCAGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:271:271:241,30:0,0:0,271:1:0,2:23.4:1:32:1:1:0:60:66.75:1:0:2 1/1:193:192:167,25:0,0:0,192:0.9948:0,2:22.6:1:31.3:1:1:0:60:191:0.9948:0:1.9 +5 180041208 . T C 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10944;LSEQ=ACAGAGGGAAGCTTGTCCCG;RSEQ=GGTGGATGGGGAGACGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:558:544:182,362:2,9:11,544:0.9749:2,2:24.9:1:30.1:1:0.35253:2.26:54:27.632:0.9795:0:1.3 1/1:409:331:111,220:28,48:76,331:0.8093:2,2:24.8:1:29.2:1:0.59355:1.15573:54.2:32.1:0.8127:0:1.3 +5 180041242 . T C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=0.28749;LSEQ=ACGGAGGGAAGCGTGTCCCG;RSEQ=GGTGGATGGGGAGACGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:45:7,38:55,195:250,45:0.151:2,2:20.6:1:26.1:1:0.42749:1.52912:29:10.25:0.1486:0:2.1 0/1:206:10:4,6:49,145:194,10:0.0485:2,2:19.7:1:28.7:1:0.28893:1.97:28.9:20:0.0508:0:2.2 +5 180041258 . G A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00846;SOR=Inf;LSEQ=CCCGTGGTGGATGGGGAGAC;RSEQ=GAGGGAAGCGTGTCCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:30,184:214,0:0:2,0:24:1:31:1:1:0:39.1:34.667:1:0:1.8 0/1:136:5:4,1:27,104:131,5:0.0368:2,2:24.4:1:26.2:1:0.00965:15.00:27.2:10:0.0373:0:3 +5 180041268 . G T 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01606;SOR=Inf;LSEQ=ATGGGGAGACGGAGGGAAGC;RSEQ=TGTCCTGCGGTGGATGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:22,157:179,0:0:2,0:23:1:31.6:1:1:0:37.1:28.833:1:0:1.9 0/1:101:4:2,2:17,80:97,4:0.0396:2,2:41:1:24:1:0.1595:4.61:27.8:3:0.03:0:3.3 +5 180041274 . T C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGACGGAGGGAAGCGTGTCC;RSEQ=GCGGTGGATGGGGAGACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:163:162:19,143:0,0:0,162:0.9939:0,2:22.8:1:29.9:1:1:0:36:39.5:0.9937:0:2 1/1:94:94:18,76:0,0:0,94:1:0,2:21.1:1:29.8:1:1:0:37.5:188:1:0:2 +5 180041276 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04779;SOR=Inf;LSEQ=ACGGAGGGAAGCGTGTCCTG;RSEQ=GGTGGATGGGGAGACGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:18,140:158,0:0:2,0:22.6:1:29.7:1:1:0:36.6:21.571:1:0:1.9 0/1:91:3:0,3:17,70:87,3:0.033:2,0:17:1:30.3:1:1:0:23:6:0.0337:0:2 +5 180041316 . A G 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59753;SOR=2.073;LSEQ=GGAAGCGTGTCCCGTGGTGG;RSEQ=TGGGAAGAGAGGGCTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:0,2:11,60:71,2:0.0274:2,0:24:0:34:0:1:0:39:4:0.0278:0:3 0/1:36:2:0,2:10,24:34,2:0.0556:2,0:44:1:32.5:1:1:0:60:4:0.0556:0:2 +5 180041637 . G A 42 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCTGAGGCATCTCCGCC;RSEQ=CCGGCTGTCTCTCTCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:25.3:1:27:1:1:0:60:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180041662 . G A 55 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCTCTCTCCCTCTCATG;RSEQ=TCTCTACCTGGGAGCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:31:1:27.5:1:1:0:60:3:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180041999 . G T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCACATACTGCACCAAGC;RSEQ=GGTCCATCTCCAGGACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:28.5:1:1:0:60:4:1:0:1 +5 180043388 . G A 213 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=122.81601;LSEQ=CTGCCCTTGCGGACGTAGTC;RSEQ=GGGTCTTTGTAGATGTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1085:2:2,0:549,533:1082,2:0.0018:2,0:1:0:29:0:0.49968:0:60:4:0.0019:0:1 0/1:810:150:79,71:336,321:657,150:0.1852:2,2:25.4:1:29.6:1:0.78609:1.06:59.7:74:0.1864:0:1.1 +5 180043538 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14582;SOR=Inf;LSEQ=TGTCAGTGCAGGCCCCTGGG;RSEQ=TAATACCCACACCCGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:48,194:242,0:0:2,0:23:1:31.9:1:1:0:60:79.667:1:0:0.1 0/1:150:2:1,1:31,117:148,2:0.0133:2,2:8:1:28.5:1:0.38228:3.73:60:4:0.0135:0:1 +5 180043731 . C A 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=GCTGCTGACCAGCCAAGAGA;RSEQ=CTTGGGAGGTCAACTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:100,7:107,0:0:2,0:26.7:1:32.9:1:1:0:59.8:214:1:0:0.1 0/1:45:7:7,0:37,1:38,7:0.1556:1,0:31:1:30.7:1:1:0:60:14:0.1556:0:1 +5 180045700 . G GGGTTACCCTA 245 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.03254;LSEQ=CCCGCTGAGGACCCCAGGCT;RSEQ=GGGTGCCTGATCACGGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:290:287:244,43:3,0:3,287:0.9897:0,2:21:1:30.1:1:1:0:59.8:94.667:0.9861:0.4414:0.2 1/0:176:133:107,26:30,10:40,133:0.7557:2,2:22.2:1:29.3:1:0.50652:1.37:59.8:266:0.7688:0.3466:0.1 +5 180045715 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05453;SOR=Inf;LSEQ=AGGCTGGGGTGCCTGATCAC;RSEQ=GGATATAACCGGGCCCGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:305,119:424,0:0:2,0:18.1:1:29.7:1:1:0:59.9:59.571:1:0:0.2 0/1:260:3:2,1:185,72:257,3:0.0115:2,2:15:1:26.3:1:1:1.28345:60:6:0.0117:0:1 +5 180045944 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12277;SOR=Inf;LSEQ=CGGATGCACGAAGCTGGCTC;RSEQ=AGGGCGCCCAGTCGTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:53,238:291,0:0:2,0:25.9:1:32:1:1:0:59.9:96:0.9965:0:0.1 0/1:158:2:1,1:30,126:156,2:0.0127:2,2:24:1:27:1:0.35491:4.15:60:4:0.0128:0:1 +5 180046002 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20776;SOR=Inf;LSEQ=CCCCCGCCGCCCGCGGCGCC;RSEQ=CGCAGGCCGCCCGCTCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:78,79:157,0:0:2,0:19.9:1:31.5:1:1:0:60:156:1:0:0.1 0/1:132:2:1,1:61,69:130,2:0.0152:2,2:25:1:27.5:1:1:1.13:60:4:0.0155:0:1.5 +5 180046012 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49975;SOR=0;LSEQ=CCGCGGCGCCCCGCAGGCCG;RSEQ=CCGCTCACCGCGCAGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:95,85:180,2:0.0109:2,2:42:1:30:1:1:1.11696:60:4:0.0112:0:1 0/0:166:0:0,0:90,76:166,0:0:2,0:22.6:1:30.7:1:1:0:60:40.5:1:0:0.3 +5 180046031 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.4458;LSEQ=GCCCGCTCACCGCGCAGGGG;RSEQ=TGAAGGCGTCCCGCTTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:2:1,1:139,106:245,2:0.0081:2,2:31.5:1:30:1:1:1.30985:60:4:0.0082:0:1 0/1:257:3:1,2:141,113:254,3:0.0117:2,2:21.7:1:26.3:1:0.58827:2.48687:60:6:0.012:0:1 +5 180046107 . G A 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.62662;SOR=0.37626;LSEQ=CTCCACGATCACCATGAGGG;RSEQ=GCCTGCGGCGGGACCGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:3:3,0:124,169:293,3:0.0101:2,0:8.7:1:21.7:1:0.07792:0:60:2:0.0069:0:2 0/0:261:1:0,1:122,138:260,1:0.0038:2,0:7:0:31:0:1:0:60:2:0.0039:0:1 +5 180046111 . T G 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25327;SOR=0;LSEQ=ACGATCACCATGAGGGGGCC;RSEQ=GCGGCGGGACCGGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:116,158:274,3:0.0108:2,2:20:1:24.3:1:1:1.4664:60:2:0.0074:0:1.3 0/0:238:0:0,0:108,128:236,0:0:2,0:22.4:1:29.6:1:1:0:59.9:46.2:0.9914:0:0.3 +5 180046126 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18266;SOR=Inf;LSEQ=GGGCCTGCGGCGGGACCGGG;RSEQ=GGCGGCCGTGCGTTCGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:82,125:207,0:0:2,0:24.3:1:30.6:1:1:0:60:33.5:1:0:0.3 0/1:155:2:1,1:64,89:153,2:0.0129:2,2:33.5:1:30.5:1:1:1.39:60:4:0.014:0:1.5 +5 180046127 . G T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18472;SOR=Inf;LSEQ=GGCCTGCGGCGGGACCGGGC;RSEQ=GCGGCCGTGCGTTCGGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:79,121:200,0:0:2,0:24.3:1:30.6:1:1:0:60:39:0.9949:0:0.3 0/1:152:2:1,1:62,88:150,2:0.0132:2,2:7:1:29:1:1:1.42:60:4:0.0137:0:1 +5 180046137 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51027;SOR=0;LSEQ=GGGACCGGGCGGCGGCCGTG;RSEQ=GTTCGGAACCCGGGGCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:60,105:165,2:0.0119:2,2:11.5:1:29:1:1:1.74:60:4:0.0122:0:1.5 0/0:123:0:0,0:46,76:122,0:0:2,0:19.9:1:29.6:1:1:0:59.9:39.667:1:0:0.3 +5 180046209 . C T 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=0;LSEQ=CCCTCCCGCCCGCGGCGCCC;RSEQ=GCGCCCGGGGTCTCGCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:122:108,14:0,0:0,122:1:0,2:15.8:1:32.7:1:1:0:60:121:1:0:1.2 1/1:92:79:63,16:10,3:13,79:0.8587:2,2:14.4:1:30.4:1:0.72747:1.18:60:78:0.8667:0:1.3 +5 180046234 . C T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.66948;SOR=1.70081;LSEQ=CCGGGGTCTCGCCGTCCCAG;RSEQ=GGGCCGCCCGCTCCGTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:2:0,2:193,59:252,2:0.0079:2,0:1:0:25:0:0.05695:0:60:4:0.0081:0:1 0/1:225:3:1,2:150,72:222,3:0.0133:2,2:11:1:27:1:0.25234:4.13785:60:6:0.0136:0:1 +5 180046238 . C T 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62867;SOR=0.39111;LSEQ=GGTCTCGCCGTCCCAGCGGG;RSEQ=CGCCCGCTCCGTACCCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:2,1:211,76:287,3:0.0103:2,2:30:1:30.7:1:1:1.38648:60:6:0.0105:0:2 0/0:246:1:0,1:161,84:245,1:0.0041:2,0:1:0:28:0:0.34553:0:60:2:0.0041:0:1 +5 180046344 . G C 298 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0081;LSEQ=AGCTCCGACATCAGCGCGCG;RSEQ=TGCTCGCTGGCCGTGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:583:581:295,286:0,0:0,581:0.9966:0,2:25.7:1:32.5:1:1:0:59.8:63.556:1:0:1.2 1/0:478:335:168,167:76,65:141,335:0.7008:2,2:25.5:1:31.2:1:0.48287:1.1619:59.9:82.75:0.7058:0:1.2 +5 180046426 . C CTGGCCGCTTAGCTAAGGCACAG 277 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.03865;LSEQ=CAGGTCCCCGTTCCCCGCCA;RSEQ=CCGGCGCTTTTGGGAGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:498:492:269,223:0,0:0,492:0.988:0,2:23.4:1:31:1:1:0:59:491:0.9919:0.5703:0.4 1/0:341:259:125,134:40,40:80,259:0.7595:2,2:24.6:1:30.2:1:0.79933:1.07176:59.2:518:0.764:0.434:0.5 +5 180046492 . CAG C 304 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0788;LSEQ=TCCTGCCGGCCCCACTGAGG;RSEQ=AGGGGGTTCGGGTGGTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:720:694:377,317:16,10:26,694:0.9639:2,2:26.3:1:32.3:1:0.54977:1.34481:59.8:137.8:0.9636:0.1333:0.2 1/0:502:340:187,153:86,75:161,340:0.6773:2,2:27:1:31.4:1:0.77353:1.07:59.7:339:0.6794:0.0837:0.2 +5 180046495 . A G 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCGGCCCCACTGAGGCAG;RSEQ=GGGGGTTCGGGTGGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:0:0,0:373,303:676,0:0:2,0:26.4:1:31.2:1:1:0:59.8:74.111:0.9881:0:0.2 0/1:489:17:11,6:249,210:459,17:0.0348:2,2:14.5:1:27.3:1:0.4634:1.54:59.4:7.5:0.0313:0:3.1 +5 180046499 . GGT T 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0049;SOR=Inf;LSEQ=GGCCCCACTGAGGCAGAGGG;RSEQ=TCGGGTGGTCCCTCGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:718:0:0,0:398,320:718,0:0:2,0:26.5:1:31.4:1:1:0:59.8:78.778:1:0:0.2 0/1:506:6:5,1:267,224:491,6:0.0119:2,2:11:1:25.6:1:0.22852:4.18:59.2:12:0.0121:0.002:2 +5 180046784 . GG A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.03023;SOR=Inf;LSEQ=CTCTCCCTGTCGGGGCAGGG;RSEQ=CCAGTTGCAGGTGAGCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:117,254:371,0:0:2,0:25.3:1:31.3:1:1:0:60:52:0.9918:0:0.1 0/1:269:4:3,1:74,189:263,4:0.0149:2,2:13.5:1:26.1:1:0.07367:7.60:60:8:0.015:0.0074:1 +5 180046839 . G A 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGACAGGTGGGCGGCGGGG;RSEQ=AGCCCCGTGCAGAGGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:18,123:141,0:0:2,0:22.8:1:32.1:1:1:0:59.7:69.5:1:0:0.1 0/1:66:14:2,12:5,47:52,14:0.2121:2,2:20.7:1:30.6:1:0.63402:1.55:60:28:0.2188:0:1.2 +5 180046846 . G A 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGGCGGCGGGGGAGCCCC;RSEQ=TGCAGAGGTCCAGGAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:0,2:17,109:126,2:0.0156:2,0:5.5:1:32.5:1:1:0:60:4:0.016:0:1 0/0:52:0:0,0:6,46:52,0:0:2,0:20.8:1:31.2:1:1:0:60:25:1:0:0.5 +5 180046934 . G T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.22214;LSEQ=AGAGGTGGACAGGAGGCCGC;RSEQ=CATCCTCCCGGGTAGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:25:9,16:9,14:23,25:0.5208:2,2:28:1:30.6:1:1:1.13968:60:24:0.5217:0:1.4 1/0:7:4:1,3:0,3:3,4:0.5714:0,2:17.8:1:30.5:1:1:0:60:8:0.5714:0:1 +5 180047412 . T C 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGATGGCACTTCCTGCGGGG;RSEQ=TCTCAGTCAAGGAGGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:183:181:17,164:0,0:0,181:0.9891:0,2:26.3:1:33.6:1:1:0:59.8:44.25:1:0:1.1 1/1:85:85:5,80:0,0:0,85:1:0,2:25:1:31.3:1:1:0:60:41.5:1:0:1.1 +5 180047615 . C T 57 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04972;SOR=7.47281;LSEQ=GGAGGGACACTCACCCTCCT;RSEQ=ATGTTACAGAAGATGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:677:1:0,1:420,256:676,1:0.0015:2,0:1:0:24:0:0.37962:0:60:2:0.0015:0:1 0/1:548:6:1,5:326,215:541,6:0.0109:2,2:5.3:1:22.2:1:0.04113:7.55469:57:5:0.0092:0:1.8 +5 180047793 . G C 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGCAGCACCCCTTCTGGT;RSEQ=GCCACGACTTGCCCAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:162,227:389,0:0:2,0:23.2:1:31.7:1:1:0:59.9:37.9:1:0:0.4 0/1:295:53:20,33:96,146:242,53:0.1797:2,2:19.1:1:29.3:1:0.87706:1.08466:60:16.667:0.1761:0:1.4 +5 180047863 . C G 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.46277;LSEQ=AAGGGAGTTGAGGGGTGCAG;RSEQ=CTGAGGCCAGACCTTCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:561:559:305,254:0,1:1,559:0.9964:0,2:24.5:1:31.5:1:0.45536:0:59.9:42:0.9964:0:1.1 1/1:410:409:227,182:0,0:0,409:0.9976:0,2:25.7:1:30.6:1:1:0:60:57.429:1:0:1.2 +5 180048056 . C T 197 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=159.68041;LSEQ=CCACCTGGGTTTGGGATCGT;RSEQ=GGCCTCGCGGGCCTCCGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:667:1:0,1:331,335:666,1:0.0015:2,0:1:0:27:0:1:0:60:2:0.0015:0:1 0/1:547:106:55,51:228,213:441,106:0.1938:2,2:21.5:1:29.3:1:1:1.01:60:34.333:0.1914:0:1.1 +5 180048315 . G T 50 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30117;SOR=0;LSEQ=AGCAGGAGGACCCTCTTTGG;RSEQ=CTGGGAGCAGAGGTAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:3:1,2:23,171:194,3:0.0152:2,2:7.3:1:32:0:0.32421:3.68:60:6:0.0155:0:1.3 0/0:114:0:0,0:12,100:112,0:0:2,0:22.5:1:31.7:1:1:0:60:111:0.9823:0:0.1 +5 180048487 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52831;SOR=0;LSEQ=CCACGCCGGGGCAAAGGCAG;RSEQ=GGCAGCTACTGCTAGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:67,18:85,2:0.023:2,2:25:1:30.5:1:0.39107:3.65023:60:4:0.0241:0:1 0/0:52:0:0,0:45,7:52,0:0:2,0:21.1:1:29.1:1:1:0:60:51:1:0:0.1 +5 180048581 . G T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08801;SOR=Inf;LSEQ=CTTGTGGCAGTGCTTGTCAT;RSEQ=GCTGCGCCGGTCTTGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:204,133:337,0:0:2,0:27.4:1:31.7:1:1:0:60:83.25:1:0:0.1 0/1:271:3:2,1:160,108:268,3:0.0111:2,2:11.7:1:23.7:1:1:1.35:60:2:0.0075:0:3.7 +5 180048954 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.15339;SOR=Inf;LSEQ=CTGCCCTGGGAGTTTGCTCC;RSEQ=CCATCCACCTGCCGCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:25,201:226,0:0:2,0:22.9:1:31.1:1:1:0:59.9:27.25:1:0:0.1 0/1:146:2:1,1:24,119:143,2:0.0137:2,2:7.5:1:27:1:0.31609:4.88:60:4:0.0142:0:2 +5 180048958 . T C 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0717;SOR=6.64131;LSEQ=CCTGGGAGTTTGCTCCCCCA;RSEQ=CCACCTGCCGCCCCGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:1:0,1:20,187:207,1:0.0048:2,0:23:0:14:0:1:0:60:0:0:0:1 0/1:128:4:2,2:20,104:124,4:0.0313:2,2:16.5:1:23:1:0.13649:5.10:58.8:3:0.0242:0:1.5 +5 180048972 . C A 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.06412;SOR=4.16578;LSEQ=CCCCCATCCACCTGCCGCCC;RSEQ=GGGGTCTCCTCCTGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:3:0,3:8,143:151,3:0.0195:2,0:27:1:33.3:1:1:0:60:6:0.02:0:1 0/1:78:6:1,5:4,68:72,6:0.0769:2,2:17.2:1:29.7:1:0.33724:3.32:60:12:0.0779:0:1 +5 180048986 . G GCCTC 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=5.000;MSILEN=4;SSF=0.02586;SOR=0.46374;LSEQ=CCGCCCCGGGGTCTCCTCCT;RSEQ=CCTCCCTCCCTCCCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:80:2,78:0,40:40,80:0.6667:1,1:29.3:1:30.5:1:0.55182:0:59.4:19:0.6552:0.1417:0.3 0/1:50:24:1,23:0,26:26,24:0.48:1,1:29.5:1:30.6:1:0.48:0:59.8:48:0.4898:0.06:0.3 +5 180049003 . T C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00114;SOR=Inf;LSEQ=CCTGCCTCCCTCCCTCCCTC;RSEQ=CTCCTGGAGGGGCCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:2,76:78,0:0:1,0:24.7:1:29.7:1:1:0:59.4:25:1:0:0.2 0/1:33:5:0,5:1,27:28,5:0.1515:1,0:11.2:1:26.2:1:1:0:60:4:0.125:0:1 +5 180049212 . C T 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TCTTGTCTCTCTGGTCACTT;RSEQ=TGGTCAGGCTCCTGTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:16:1:33:1:1:0:60:6:1:0:0.7 1/0:4:2:1,1:1,1:2,2:0.5:2,2:16:0:31.5:1:1:1:60:4:0.5:0:1.5 +5 180049525 . T C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGGGAGGAGCCCCAGGG;RSEQ=TGGGGACAGAGGATGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:28,1:0,0:0,29:1:0,1:26.2:1:31.8:1:1:0:60:28:1:0:1.4 1/1:7:7:6,1:0,0:0,7:1:0,2:19.9:1:32.9:1:1:0:60:14:1:0:1.1 +5 180049618 . A G 248 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0902;LSEQ=TTTTCCTGTCTACAACCGGT;RSEQ=GGCCTTGGATCTCTCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:215:205:205,0:9,0:9,205:0.9535:0,1:21.6:1:32.3:1:1:0:59.9:28.286:0.9519:0:1.1 1/0:119:77:74,3:42,0:42,77:0.6471:1,1:22.1:1:30.9:1:0.55119:0:60:24.667:0.6379:0:1.1 +5 180049923 . GCAC G 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.40505;SOR=0.27958;LSEQ=TTCTGCAAGGAGGTCGCTGT;RSEQ=CACCCCCCCCAATCATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:5:0,5:9,125:134,5:0.0357:2,0:30.8:1:32.2:1:1:0:60:10:0.0455:0:0 0/1:98:1:0,1:3,90:93,1:0.0102:1,0:48:0:34:0:1:0:60:2:0.0128:0:0 +5 180049926 . CCA C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=9.000;MSILEN=1;SSF=1;SOR=1.44572;LSEQ=TGCAAGGAGGTCGCTGTGCA;RSEQ=CCCCCCCCAATCATGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:0,2:5,84:89,2:0.0156:2,0:35.5:1:33:0:1:0:60:4:0.023:0:0 0/1:89:2:0,2:2,68:70,2:0.0225:1,0:33.5:1:32:1:1:0:60:4:0.0278:0:0 +5 180049927 . CA C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.34842;SOR=1.56238;LSEQ=GCAAGGAGGTCGCTGTGCAC;RSEQ=CCCCCCCCAATCATGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:10:0,10:0,5:5,10:0.0775:0,0:29.9:1:33.4:1:1:0:60:20:0.1124:0:0.5 0/1:86:10:0,10:0,1:1,10:0.1163:0,0:27.9:1:30.5:1:1:0:60:20:0.1538:0:0.4 +5 180049928 . A C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.32135;SOR=1.34215;LSEQ=CAAGGAGGTCGCTGTGCACC;RSEQ=CCCCCCCCAATCATGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:129:75:5,70:0,5:5,75:0.5814:0,2:20.4:1:31.5:1:1:0:59.4:150:0.8427:0:2.2 1/0:86:56:2,54:0,1:1,56:0.6512:0,1:22.4:1:30.2:1:1:0:60:27:0.8308:0:2 +5 180050148 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTCTGGCCGTGGCTATG;RSEQ=TGAGGGGGCACCAGCGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:28:1:31:1:1:0:53.7:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180050208 . A G 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGCCTGGGTCACAGCAAA;RSEQ=GCCAGTCACTTCTGGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:27.3:1:30.7:1:1:0:48.7:6:1:0:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180051003 . T C 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.04916;LSEQ=GGGGTTCACGGCATCCTGCG;RSEQ=GGTCACCGCCCTCCAGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1065:925:409,516:64,73:137,925:0.8685:2,2:26.4:1:30.8:1:0.58216:1.10597:60:70.154:0.8702:0:1.1 0/1:915:224:96,128:320,369:689,224:0.2448:2,2:26:1:29.9:1:0.35531:1.15609:60:43.8:0.2436:0:1.2 +5 180051120 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.15139;SOR=Inf;LSEQ=CAGGCAGGAAGGGCCCACAT;RSEQ=GGGGGCGGGGTCAAGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:41,211:252,0:0:2,0:24.3:1:31.5:1:1:0:59.9:83:1:0:0.2 0/1:161:2:1,1:30,129:159,2:0.0124:2,2:6:1:27:1:0.34899:4.25:60:4:0.0127:0:1 +5 180053307 . A G 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0.81607;LSEQ=GGGCCCATACAGATCCCACC;RSEQ=CAGCCCCAACCTCATGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:431:429:117,312:1,0:1,429:0.9954:0,2:24.7:1:31.2:1:0.27442:0:60:38:0.9952:0:1.1 1/1:352:350:113,237:2,0:2,350:0.9943:0,2:23.8:1:30:1:0.10611:0:60:57.333:0.9942:0:1.3 +5 180053387 . C T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=8.6397;LSEQ=GGCAGGAGTGCAGGGTAGGA;RSEQ=GGGGAACACTGGTCTGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:7:0,7:0,95:95,7:0.0686:1,0:14.9:1:31.3:1:1:0:60:14:0.0707:0:1.7 0/1:56:22:0,22:0,34:34,22:0.3929:1,1:17.5:1:29.1:1:1:0:60:44:0.3929:0:1.5 +5 180054220 . T C 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGATACACCACTGTGTCC;RSEQ=GGGAGAGGCACAGCCCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:20:1:30.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180055773 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53487;SOR=0;LSEQ=CCCCCGCCATGCCTGGTCTC;RSEQ=GTGTGCAGGTCCTGACGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:174,5:179,2:0.011:1,2:14.5:1:32:1:0.06538:31.8554:60:4:0.0114:0:2 0/0:104:0:0,0:98,5:103,0:0:1,0:23.1:1:30.4:1:1:0:60:33.333:0.9901:0:0.2 +5 180055862 . T G 298 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.01351;LSEQ=AAGGGTATCGGCGGGGTCGG;RSEQ=GGGGAGCCAGGGCTGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:799:793:488,305:1,0:1,793:0.9925:0,2:27.6:1:31:1:1:0:59.8:38.65:0.9936:0:2.2 1/0:693:444:260,184:138,111:249,444:0.6407:2,2:27.2:1:30.1:1:0.42474:1.14:59.8:33.154:0.658:0:2.3 +5 180055864 . G A 278 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.04767;LSEQ=GGGTATCGGCGGGGTCGGTG;RSEQ=GGAGCCAGGGCTGTTACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:813:791:479,312:11,1:12,791:0.9729:2,2:27.4:1:28.9:1:0.03441:7.15447:59.8:9.273:0.9903:0:2.2 1/0:713:450:261,189:147,112:259,450:0.6311:2,2:26.7:1:27.8:1:0.75291:1.05:59.8:9.714:0.6172:0:2.2 +5 180055946 . C T 88 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01316;SOR=4.62835;LSEQ=CTTCACCAGCTCGTCTCCTG;RSEQ=CGTGGCCTCCAGGATGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1242:3:0,3:594,645:1239,3:0.0024:2,0:1:0:26.7:1:0.25081:0:60:6:0.0025:0:1 0/1:992:11:3,8:463,517:980,11:0.0111:2,2:23.6:1:25.5:1:0.23312:2.38609:60:4.5:0.0092:0:1.1 +5 180056044 . G A 203 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=306.94057;LSEQ=AAATCCAGGACTGACCCGTC;RSEQ=TGGACTGACCAGGGACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:1:0,1:217,392:609,1:0.0016:2,0:2:0:30:0:1:0:60:2:0.0017:0:1 0/1:351:118:42,76:86,147:233,118:0.3362:2,2:23:1:29.5:1:0.9066:1.05848:60:58:0.3362:0:1.1 +5 180056071 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09675;SOR=Inf;LSEQ=GACCAGGGACTCCCCCCACG;RSEQ=CCCCTGCAGCCCCGGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:109,292:401,0:0:2,0:22.8:1:31.6:1:1:0:59.9:29.846:1:0:0.1 0/1:182:2:1,1:46,133:179,2:0.011:2,2:10:1:28:1:0.45298:2.87:60:4:0.0114:0:1.5 +5 180056103 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07409;SOR=Inf;LSEQ=CCGGCAGCCGGACATCCGCA;RSEQ=ACTGGGGCTGGCCATGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:81,169:250,0:0:2,0:23.5:1:32.5:1:1:0:59.9:61.5:1:0:0.2 0/1:94:2:1,1:18,74:92,2:0.0213:2,2:15.5:1:28.5:1:0.36513:4.03:60:4:0.0215:0:2 +5 180056192 . T C 272 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGCTGGACTCCTGAGTGC;RSEQ=CAAGGGCACCGTGAGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:402:402:303,99:0,0:0,402:1:0,2:24.1:1:31.5:1:1:0:60:79.4:1:0:1.1 1/0:211:141:116,25:57,13:70,141:0.6682:2,2:23.3:1:30.4:1:1:1.06:60:46:0.6667:0:1.1 +5 180056215 . C T 57 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.71877;SOR=1.54908;LSEQ=AGGGCACCGTGAGCTCTGGG;RSEQ=CCAGGCCCACAGGGCACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:579:4:2,2:405,170:575,4:0.0069:2,2:11.3:1:23:1:0.58604:2.37834:60:3:0.0053:0:1.5 0/1:375:4:2,2:264,107:371,4:0.0107:2,2:25.5:1:28.5:1:0.58307:2.46054:60:8:0.0109:0:1.3 +5 180056434 . G A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16266;SOR=0;LSEQ=TTACCCCGCTCTGCCTGCCC;RSEQ=CACCCAGGGAAGCCCCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:5:3,2:122,333:455,5:0.0109:2,2:26.4:1:28.8:1:0.12658:4.08:60:10:0.0112:0:1 0/0:284:0:0,0:92,192:284,0:0:2,0:24.8:1:30.5:1:1:0:60:70:1:0:0.1 +5 180056457 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14457;SOR=Inf;LSEQ=CCCAGGGAAGCCCCGCGTCA;RSEQ=CAGGCGGGCTCCTGCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:58,246:304,0:0:2,0:24.1:1:32.3:1:1:0:59.8:42.429:1:0:0.1 0/1:187:2:1,1:51,134:185,2:0.0107:2,2:25:1:26.5:1:0.4799:2.61:60:4:0.0109:0:1 +5 180056620 . G A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGGCCCACACATCCTCCAC;RSEQ=CGGAGGCCCAGTGTGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:292:291:244,47:1,0:1,291:0.9966:0,2:24:1:30.5:1:1:0:60:71.75:1:0:1.1 1/1:174:174:147,27:0,0:0,174:1:0,2:23.7:1:29.2:1:1:0:59.8:57:1:0:1.1 +5 180056863 . C T 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CACGCACACAGTGACTCCCA;RSEQ=GCCCTCACAGGACGACACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:786:0:0,0:373,413:786,0:0:2,0:24.4:1:31:1:1:0:59.9:97.25:1:0:0.1 0/1:489:11:5,6:236,242:478,11:0.0225:2,2:23.8:1:30.3:1:1:1.16987:60:22:0.0228:0:1 +5 180056924 . C T 79 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13688;SOR=2.53476;LSEQ=GACAGCCCCGTTACTGGGAA;RSEQ=GGGGCACAGCCCTGTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:975:4:2,2:492,478:970,4:0.0041:2,2:14.5:1:29:1:1:1.02926:60:8:0.0041:0:1.3 0/1:677:7:2,5:358,312:670,7:0.0103:2,2:21.1:1:28.4:1:0.26157:2.86435:60:14:0.0105:0:1.4 +5 180057167 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02366;SOR=Inf;LSEQ=CTCCTGGCCAGACAGGCGGC;RSEQ=GCCTTTCCCAGGGGTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:492:0:0,0:238,254:492,0:0:2,0:23.6:1:29.6:1:1:0:59.9:22.429:1:0:0.2 0/1:319:4:1,3:152,163:315,4:0.0125:2,2:8.5:1:27.5:1:0.62389:2.78916:60:8:0.0134:0:1.3 +5 180057293 . T C 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACATGGCGTCCTTCCTGT;RSEQ=GACCAAGAGCGTGTCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:0:0,0:426,455:881,0:0:2,0:26:1:30.4:1:1:0:59.9:47.944:0.9988:0:0.2 0/1:645:65:35,30:291,287:578,65:0.1008:2,2:26.9:1:30:1:0.60363:1.15:59.8:64:0.0997:0:1.4 +5 180057375 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.06943;SOR=Inf;LSEQ=GCTGTTGGGGAAGGGACGTG;RSEQ=CGGCCAGGCTGGGGGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:167,250:417,0:0:2,0:24:1:31.4:1:1:0:59.8:25.063:1:0:0.1 0/1:292:3:1,2:99,188:287,3:0.0103:2,2:8:1:22.7:1:1:1.05301:60:2:0.007:0:3 +5 180057504 . G A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=4.000;MSILEN=1;SSF=0;SOR=10.96734;LSEQ=ACAGGCTGGGGGCGGTGTGG;RSEQ=CCCCAGCTGCCCGGGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:25:18,7:366,140:506,25:0.047:2,2:18.1:1:29.1:1:1:1.01664:60:24:0.0464:0:1.2 0/1:364:128:97,31:166,69:235,128:0.3516:2,2:23.9:1:27.9:1:0.32647:1.30:60:41.667:0.3501:0:1.1 +5 180058008 . C A 97 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGGGGCTGGCCTGTGG;RSEQ=CAAGCACAGGCCTTGGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1:0,2:24.3:1:29.3:1:1:0:60:9:1:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180058189 . G A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=CCATATGAAATGCTGATGGG;RSEQ=TGGGCTGGGCACAGTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:21:1:31.8:1:1:0:51:8:1:0:1 0/0:4:0:0,0:1,3:4,0:0:2,0:27:1:31:1:1:0:60:8:1:0:0 +5 180058451 . T C 95 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACTGCACTCCAGCCTGGG;RSEQ=GACAGAGTGAGACTCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:31.7:1:33.9:1:1:0:37.3:14:1:0:1.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180058474 . GA G 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGTGAGACTCCATCTCA;RSEQ=AAAAAAAAAAGAAATGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:18,0:18,2:0.1:1,0:15.5:1:35:0:1:0:40.5:4:0.1:0:0 0/0:3:0:0,0:3,0:3,0:0:0,0:17.3:1:30.3:1:1:0:60:6:1:0:0 +5 180058591 . G A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79493;SOR=1.19579;LSEQ=CTGCCCTGACTCTGCCCTGG;RSEQ=AGGGGGCTGCCATCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:9:8,1:152,8:160,9:0.0533:2,2:14.8:1:25.4:1:0.39646:2.35805:60:2:0.0368:0:1.1 0/1:111:7:7,0:97,7:104,7:0.0631:2,0:26.6:1:28.6:1:1:0:60:14:0.066:0:1.3 +5 180058913 . GCGTGGCCTGGCCTCA C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0;SOR=10.90074;LSEQ=CTCAGGTTCTCAGCCAGCAC;RSEQ=CCATGTGCGCCGTGAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:11:1,10:1,61:62,11:0.1507:1,2:22.4:1:31.3:1:0.28044:5.86:59.5:22:0.1549:0.0548:0.8 1/0:27:18:1,17:1,5:6,18:0.6667:2,1:26.4:1:30.5:1:0.44565:3.19373:60:36:0.72:0.1111:0.7 +5 180058928 . A C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00213;SOR=Inf;LSEQ=GCACCGCGTGGCCTGGCCTC;RSEQ=CCATGTGCGCCGTGAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:1,45:46,0:0:1,0:25.6:1:30.3:1:1:0:59.2:92:1:0:0.3 0/1:8:3:0,3:1,4:5,3:0.375:2,0:33:1:30.7:1:1:0:54.7:6:0.375:0:3 +5 180058963 . G A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=18.72485;LSEQ=AGCAGCACCAGCTCCCAGGC;RSEQ=CCAAGACAGCCACGAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:0,8:2,25:27,8:0.2286:2,0:17:1:29.5:1:1:0:60:16:0.2353:0:1.6 1/1:14:12:0,12:0,2:2,12:0.8571:0,0:24.2:1:29:1:1:0:58.7:24:0.8571:0:2.4 +5 180059042 . T C 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAGCTACACACCGGCCC;RSEQ=GGACCTAACCCCAACCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:20.5:1:29.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180059230 . A C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATCCCAGGTCCTCCCCG;RSEQ=ACCACGCAGGCCTCGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180073373 . A G 50 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCTGCTGGCACTGCCGC;RSEQ=TCTCCAGCCTCGTTTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:35.3:1:32:1:1:0:60:6:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:29.5:1:1:0:60:4:1:0:2.5 +5 180073385 . G A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=ACTGCCGCATCTCCAGCCTC;RSEQ=TTTCCCCTACCTCCCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:47.3:1:24.3:1:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:30:1:1:0:60:4:1:0:2.5 +5 180074544 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50337;SOR=0;LSEQ=AGGCTTCTGGCCTGCTCCCA;RSEQ=CGGACCAGCTGCCCTGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:7,14:21,2:0.087:2,2:17:1:28:1:1:1.94:60:4:0.0909:0:1.5 0/0:16:0:0,0:8,8:16,0:0:2,0:23.3:1:31.3:1:1:0:60:32:1:0:0.3 +5 180074627 . T C 66 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TGCAGCTGAGGGCTTGTGCT;RSEQ=CCGCCATGGCATCCCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:14.8:1:33:0:1:0:60:8:1:0:1.5 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:28:0:32:0:1:0:60:2:0.3333:0:1 +5 180075730 . A AT 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTCCCCGCCAGAGCCAC;RSEQ=TCCCAACACAAACCGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:27.5:1:1:0:60:4:1:0:0 +5 180076403 . C T 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4648;SOR=1.7628;LSEQ=CCCGCCCGTACCCGGCGGAG;RSEQ=GGTCTCAGCGCCCGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:4:3,1:47,8:55,4:0.0678:2,2:13.5:1:30.8:1:0.49399:1.93153:60:8:0.069:0:1 0/1:35:4:3,1:26,5:31,4:0.1143:2,2:11.3:1:30.8:1:0.54639:1.7024:60:8:0.1176:0:1.3 +5 180076445 . G T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.66637;SOR=1.74444;LSEQ=TGCGCGGTACCCCCTCCCCG;RSEQ=CCAGCCCCACGCTCGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:0,2:118,80:198,2:0.01:2,0:15:1:16.5:1:0.16688:0:60:0:0:0:1.5 0/1:173:3:1,2:103,66:169,3:0.0173:2,2:27.7:1:21:1:0.56295:3.10023:60:2:0.012:0:1 +5 180076468 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09773;SOR=Inf;LSEQ=AGCCCCACGCTCGGGCGGGT;RSEQ=GCCCGTTCGCCGCGCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:172,143:315,0:0:2,0:25.8:1:31.5:1:1:0:60:77.75:1:0:0.2 0/1:270:3:1,2:146,121:267,3:0.0111:2,2:22.3:1:29.7:1:0.59314:2.40554:60:6:0.0113:0:1.3 +5 180076529 . G A 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.67099;SOR=1.68075;LSEQ=GCCACAGTCGCAGGCACAGC;RSEQ=CGGCGCCCCGCTGCATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:2:2,0:127,159:286,2:0.0069:2,0:1:0:26:0:0.19977:0:60:4:0.0071:0:1 0/1:258:3:2,1:114,141:255,3:0.0116:2,2:21.7:1:28.7:1:0.58952:2.47:60:6:0.0118:0:1.3 +5 180076550 . G A 47 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17889;SOR=4.96194;LSEQ=CGGCGCCCCGCTGCATCTCC;RSEQ=GCCGCTGCGCGTGGGTCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:1:1,0:80,117:197,1:0.005:2,0:2:0:26:0:0.40909:0:60:2:0.0052:0:1 0/1:163:4:3,1:66,93:159,4:0.0245:2,2:16:1:23.5:1:0.31187:4.19:60:3:0.0186:0:1.3 +5 180076574 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2047;SOR=Inf;LSEQ=GCTGCGCGTGGGTCCGACCC;RSEQ=AGCGGCCGCGGCTCGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:31,64:95,0:0:2,0:17.2:1:31.3:1:1:0:60:22.75:1:0:0.3 0/1:79:2:1,1:27,50:77,2:0.0253:2,2:26:1:27:1:1:1.84:60:4:0.0263:0:1 +5 180525809 . G GT 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCAGACAATCTGAAGTT;RSEQ=TTTTTTTTTTCTTTGAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,0:1,2:0.5:0,0:29:1:32:0:1:0:47:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180525845 . T G 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGGAGTCTTGCTTTGTT;RSEQ=CCAGGCTGGAGTGCAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:32:1:27.9:1:1:0:36.6:2.5:1:0:1.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180525899 . C G 97 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAATCTCCGCCTCCCA;RSEQ=GTTCAAGCGATTCTTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:28.5:1:32.4:1:1:0:31.6:16:1:0:1.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +5 180526117 . A T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25896;SOR=0;LSEQ=CCAGCCGATGAAGTACTTTT;RSEQ=AGTGTAGCGGGCTCACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:2,1:176,60:236,3:0.0126:2,2:40:1:23:1:1:1.46411:60:2:0.0085:0:1 0/0:188:0:0,0:139,49:188,0:0:2,0:21.7:1:27.9:1:1:0:59.2:376:1:0:0.1 +5 180526302 . G A 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16839;SOR=5.5184;LSEQ=TCCAAGGGCTCAGTGAGCAT;RSEQ=CCGTCCAAGTCACTTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:1:0,1:297,235:532,1:0.0019:2,0:12:0:32:0:0.44278:0:60:2:0.0019:0:1 0/1:389:4:3,1:199,186:385,4:0.0103:2,2:16.8:1:25.8:1:0.62419:2.80:60:8:0.0104:0:1.3 +5 180526819 . T C 313 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16272;LSEQ=TCTGGGGCAAAGGGCTCATG;RSEQ=TGGACTGGCCCTACGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:841:794:468,326:27,19:46,794:0.9441:2,2:24.7:1:32.5:1:1:1.01:59.9:78.4:0.9446:0:1.1 1/0:603:442:250,192:105,56:161,442:0.733:2,2:24:1:31.2:1:0.06152:1.43913:59.9:39.182:0.728:0:1.2 +5 180526837 . T C 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTGGACTGGCCCTACGTC;RSEQ=GTTTTTTGCAGTTTGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:939:0:0,0:560,379:939,0:0:2,0:23.8:1:31.3:1:1:0:60:103.333:1:0:0.8 0/1:712:22:14,8:402,288:690,22:0.0309:2,2:29:1:28.8:1:0.66669:1.25:60:21:0.0299:0:2.9 +5 180526839 . T G 130 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=26.13128;LSEQ=TTGGACTGGCCCTACGTCTG;RSEQ=TTTTTGCAGTTTGGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:939:1:1,0:551,386:937,1:0.0011:2,0:6:0:13:0:1:0:60:0:0:0:2 0/1:737:20:12,8:416,297:713,20:0.0271:2,2:29.3:1:30.3:1:1:1.07:60:40:0.0277:0:2.9 +5 180527070 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13808;SOR=Inf;LSEQ=TGGCGGGTACCCCACAGAAT;RSEQ=TGCGTCCCCATCTCCAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:334:0:0,0:185,149:334,0:0:2,0:25.2:1:32.6:1:1:0:59.9:333:1:0:0.1 0/1:198:2:1,1:110,85:195,2:0.0101:2,2:29.5:1:29.5:1:1:1.2924:60:4:0.0102:0:1 +5 180527309 . C A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19427;LSEQ=AGCTTGACTTAGGCTCCGAG;RSEQ=GCATTTGCTGCTGCTGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:260:242:74,168:5,13:18,242:0.9308:2,2:24.3:1:31.7:1:1:1.14:60:59.5:0.9297:0:2 1/0:144:104:22,82:6,34:40,104:0.7222:2,2:25.1:1:30.5:1:0.4862:1.52:60:208:0.7222:0:1.8 +5 180527344 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14244;LSEQ=TGTCCATGGATGCAGCTCTT;RSEQ=TCCTAAGAGATCTCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:224:207:97,110:6,10:16,207:0.9241:2,2:25.9:1:30.1:1:0.60499:1.47:60:206:0.9321:0:2.6 1/0:128:81:34,47:21,26:47,81:0.6328:2,2:21.3:1:29.4:1:0.85351:1.11555:60:162:0.6328:0:2.4 +5 180527367 . G A 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.11567;LSEQ=CTAAGAGATCTCCCACCCTT;RSEQ=CCGCCCTCTGGATCCAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:256:236:122,114:11,8:19,236:0.9219:2,2:23.2:1:28.6:1:0.64098:1.28358:59.9:58:0.9243:0:2.3 1/0:139:80:49,31:34,25:59,80:0.5755:2,2:24.1:1:28.2:1:0.72765:1.16:60:79:0.5725:0:2.2 +5 180527433 . C T 54 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03394;SOR=Inf;LSEQ=TCATTCTGCGCGCGAGTCAG;RSEQ=TTGCTGTGTAGGGACAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:0:0,0:233,136:369,0:0:2,0:25.2:1:32.6:1:1:0:59.9:45.125:1:0:1.1 0/1:279:4:2,2:178,97:275,4:0.0143:2,2:6.8:1:27.3:1:0.617:1.83089:60:8:0.0145:0:1.5 +5 180527440 . T C 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03229;SOR=Inf;LSEQ=GCGCGCGAGTCAGCTTGCTG;RSEQ=GTAGGGACAGAAGATGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:388:0:0,0:244,144:388,0:0:2,0:24.9:1:30:1:1:0:59.9:63.667:1:0:1.1 0/1:287:4:2,2:180,102:282,4:0.0139:2,2:28.8:1:28.8:1:0.62347:1.76093:60:8:0.0141:0:1 +5 180527455 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16247;LSEQ=TGCTGTGTAGGGACAGAAGA;RSEQ=GACGAAGTGAATTCCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:415:387:238,149:13,15:28,387:0.9325:2,2:25.2:1:31.2:1:0.15996:1.84:59.9:63.5:0.9338:0:1.2 1/0:311:215:137,78:55,41:96,215:0.6913:2,2:25.7:1:30.4:1:0.313:1.31:60:214:0.6948:0:1.2 +5 180527614 . G A 34 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25076;SOR=0;LSEQ=CGGCGTGGGACAGGCTGCGC;RSEQ=ACGCGGTGCGACGGGACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:2,1:70,226:296,3:0.01:2,2:6.7:1:21.7:1:0.14507:6.41:60:2:0.0068:0:1.3 0/0:270:0:0,0:70,200:270,0:0:2,0:25:1:30:1:1:0:60:66.5:1:0:0.2 +5 180527742 . C T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09797;SOR=0.43294;LSEQ=CCTGCAGCAGGCTCGGGTTG;RSEQ=TCATGAAGTCGGCGCTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:19:10,9:6,7:13,19:0.5938:2,2:29.4:1:29.4:1:1:1.29:60:38:0.5938:0:1.7 0/1:39:15:8,7:13,11:24,15:0.3846:2,2:32.3:1:27.9:1:1:1.03322:60:14:0.3684:0:2.1 +5 180527769 . A G 149 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTCGGCGCTGACGGGCGGG;RSEQ=CTGGAGGTGGCCGCGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:10,14:0,0:0,24:1:0,2:19.7:1:32.5:1:1:0:60:48:1:0:1.6 0/1:39:14:7,7:11,14:25,14:0.359:2,2:24.4:1:29.1:1:0.74957:1.26:60:13:0.3514:0:2.1 +5 180527792 . C CGCGGAGCTCCCGCCCGGGCG 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGAGGTGGCCGCGTGGGACC;RSEQ=GCGACTGGAAATCCGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:3,7:0,1:1,10:0.7692:0,2:15.6:1:31.2:1:1:0:60:20:0.7692:0.6923:1.4 0/0:24:0:0,0:5,8:13,0:0:2,0:12.7:1:29.9:1:1:0:60:26:0.5417:0:0.3 +6 393170 . C T 79 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0102;SOR=10.05999;LSEQ=GGCATGAACCTGGAGGGCGG;RSEQ=GGCCGAGGCGGAGAGTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:955:1:0,1:593,361:954,1:0.001:2,0:47:0:32:0:0.37906:0:60:2:0.0011:0:1 0/1:670:7:4,3:394,268:662,7:0.0104:2,2:24.7:1:28.3:1:1:1.10245:60:14:0.0106:0:1.3 +6 393205 . G C 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCGGCATGAGCGCGGTGA;RSEQ=CTGCGGCAACGGGAAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1168:0:0,0:659,505:1164,0:0:2,0:25.5:1:32.5:1:1:0:60:54.429:0.9974:0:0.1 0/1:850:31:17,14:442,373:815,31:0.0365:2,2:22.2:1:31:1:1:1.02:60:62:0.0371:0:1.2 +6 393409 . GC G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19942;SOR=Inf;LSEQ=GCGGGGGCGCGCCGGGGAGG;RSEQ=CCAGAGACAGAGCCCGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:40,205:245,0:0:2,0:25.8:1:31.6:1:1:0:60:29.625:0.9958:0:0.1 0/1:199:2:1,1:35,161:196,2:0.0101:2,2:12:1:29.5:1:0.33133:4.55:60:4:0.0103:0.005:0.5 +6 394711 . T A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00165;SOR=Inf;LSEQ=GCTGCGGTGAGCTATCATCG;RSEQ=GCCACTGTACTCTAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:75,6:81,0:0:2,0:21.7:1:30:1:1:0:60:162:1:0:0.1 0/1:45:6:5,1:37,2:39,6:0.1333:2,2:27:1:28.3:1:0.35595:3.54565:60:12:0.1333:0:1 +6 394950 . C T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10812;SOR=5.54759;LSEQ=AACTGGTTGAGCGGAGCCAG;RSEQ=TGGACATCTCAGACCCGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:1:1,0:241,309:550,1:0.0018:2,0:39:0:32:0:0.4392:0:60:2:0.0018:0:1 0/1:500:5:2,3:222,273:495,5:0.01:2,2:19:1:26.6:1:1:1.2193:60:10:0.0102:0:1 +6 394967 . G A 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01369;SOR=Inf;LSEQ=CAGCTGGACATCTCAGACCC;RSEQ=TACAAAGTGTACAGGATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:206,299:505,0:0:2,0:25.3:1:31.3:1:1:0:60:504:1:0:0.1 0/1:486:6:3,3:210,270:480,6:0.0123:2,2:30.7:1:29.8:1:1:1.29:60:12:0.0126:0:1.2 +6 395000 . CA C 69 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.48827;SOR=1.84182;LSEQ=AGGATTGTTCCTGAGGGAGC;RSEQ=AAAAAGGTAGGGGCTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:3:0,3:113,231:344,3:0.0086:2,0:19.7:1:31.1:1:0.55378:0:60:6:0.0088:0.0029:0.3 0/1:316:5:2,3:118,193:311,5:0.0158:2,2:36.8:1:29.8:1:1:1.09:60:10:0.0161:0:0 +6 395031 . T C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58759;SOR=2.50545;LSEQ=GGGGCTCTCCTGAATTTGGG;RSEQ=CACCTAACAGAGGCAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:1,0:55,176:231,1:0.0043:2,0:46:0:14:0:0.24138:0:60:0:0:0:2 0/1:186:2:1,1:55,128:183,2:0.0108:2,2:25.5:1:29:1:0.51492:2.32:60:4:0.0109:0:1 +6 395042 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50258;SOR=0;LSEQ=GAATTTGGGTCACCTAACAG;RSEQ=GGCAGCCAGATCCTTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:36,143:179,2:0.011:2,2:33.5:1:29:1:0.36796:3.93:60:4:0.0112:0:1 0/0:151:0:0,0:38,113:151,0:0:2,0:22.8:1:29.6:1:1:0:60:36.75:1:0:0.1 +6 395980 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05453;SOR=Inf;LSEQ=CTGAGGGCGAGGCTGTGTGG;RSEQ=CCAGCTGCCCACATGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:460:0:0,0:97,363:460,0:0:2,0:23.9:1:31.7:1:1:0:60:45:1:0:0.1 0/1:282:3:2,1:63,216:279,3:0.0106:2,2:16:1:26.7:1:0.13387:6.80:60:6:0.0108:0:1 +6 395988 . C A 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05124;SOR=Inf;LSEQ=GAGGCTGTGTGGGCCAGCTG;RSEQ=CCACATGGCCAGAGAACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:66,329:395,0:0:2,0:24.4:1:31.4:1:1:0:60:64.833:0.9974:0:0.1 0/1:235:3:2,1:46,185:231,3:0.0128:2,2:16:1:20:1:0.10772:7.94:60:2:0.0087:0:1 +6 396003 . A G 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12477;SOR=Inf;LSEQ=AGCTGCCCACATGGCCAGAG;RSEQ=ACCACAGCAGCCCAGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:325:0:0,0:28,297:325,0:0:2,0:23.3:1:31.2:1:1:0:60:107.333:1:0:0.1 0/1:178:2:0,2:26,150:176,2:0.0112:2,0:26:1:25.5:1:1:0:60:4:0.0114:0:2.5 +6 396121 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08081;SOR=Inf;LSEQ=ACGGTGCTGCCATTGGTGTG;RSEQ=ATTTTAAGTTGGGGAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:0,39:39,0:0:1,0:22.4:1:32.5:1:1:0:59.1:78:1:0:0.1 0/1:16:2:0,2:0,14:14,2:0.125:1,0:26:1:33:0:1:0:60:4:0.125:0:1 +6 397038 . TCTCCTGCACTCCTTTAC T 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGTGCTTCCTATCTCAGCC;RSEQ=CCCCGTCTCAATGCCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:76,19:95,0:0:2,0:13:1:32.7:1:1:0:39.3:46.5:1:0:0.2 0/1:73:16:12,4:42,15:57,16:0.2192:2,2:14.1:1:30.6:1:1:1.07:52.4:32:0.2222:0.0959:0.2 +6 397290 . T C 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGAAATAGAAGAGCTAA;RSEQ=TGCTAATGTGGCCATGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:53,292:345,0:0:2,0:22.4:1:30.2:1:1:0:59.8:114:1:0:0.1 0/1:232:20:6,14:42,169:211,20:0.0862:2,2:24.8:1:31.6:1:0.38442:1.72:60:40:0.0873:0:1.1 +6 398775 . G A 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACACCCCAGGAAGCCCCGC;RSEQ=GTGCGTCGGACTCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:604:0:0,0:419,183:602,0:0:2,0:22.6:1:30.1:1:1:0:59.9:149.5:0.9967:0:0.1 0/1:554:52:34,18:325,175:500,52:0.0939:2,2:22:1:29.3:1:1:1.02:60:104:0.0945:0:1.1 +6 399079 . T A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.02267;SOR=0;LSEQ=AGATGTAGACACATCCTGTG;RSEQ=GTGAGGTGACCAGGGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:0,43:0,0:0,43:1:0,1:21.5:1:31:1:1:0:60:9.75:1:0:1.2 1/1:18:15:1,14:0,3:3,15:0.8333:0,1:26.5:1:30.4:1:1:0:60:30:0.8333:0:1 +6 401509 . C T 187 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=130.30253;LSEQ=CCCGAGGGCTGCCGGATCTC;RSEQ=CATGGACATACGTATGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:711:1:0,1:401,309:710,1:0.0014:2,0:2:0:26:0:0.43601:0:60:2:0.0014:0:1 0/1:547:85:47,38:243,219:462,85:0.1554:2,2:27.1:1:29.3:1:0.72302:1.11:60:84:0.1556:0:1.2 +6 401878 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.15888;SOR=Inf;LSEQ=CACCCCAGGCTGAGGTCTTC;RSEQ=TCCTGTTGACTTCGGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:17,112:129,0:0:2,0:22.7:1:32.5:1:1:0:59.8:42:1:0:0.1 0/1:86:2:1,1:9,75:84,2:0.0233:2,2:25.5:1:29.5:1:0.22025:7.96:60:4:0.0235:0:1 +6 404973 . G A 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TTTAACCTGGTGTGTTCGGT;RSEQ=ATGAGGGTTTCTGAACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:514:0:0,0:376,138:514,0:0:2,0:23.3:1:32.2:1:1:0:60:72.429:1:0:0.1 0/1:362:28:18,10:233,99:332,28:0.0773:2,2:26.9:1:28.9:1:0.52468:1.30655:60:56:0.0791:0:1.1 +6 405162 . G A 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00323;SOR=Inf;LSEQ=GTTACACTCCTACCATAGTG;RSEQ=CTTCCTGTTCTTTGTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:529:0:0,0:152,376:528,0:0:2,0:23.7:1:31.8:1:1:0:59.9:57.667:1:0:0.1 0/1:420:7:5,2:121,288:409,7:0.0167:2,2:13.6:1:25.7:1:0.02889:5.92:60:6:0.0146:0:1 +6 407652 . A T 22 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58345;SOR=2.58252;LSEQ=TTTTTTTTTTTTTTTTTGAT;RSEQ=CGGGGATACGGGGTCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:1:0,1:31,180:211,1:0.0047:2,0:18:0:16:0:1:0:40:0:0:0:4 0/1:165:2:1,1:35,128:163,2:0.0121:2,2:9.5:1:22:1:0.3898:3.62:39.5:4:0.0145:0:4.5 +6 407656 . G A 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTTTTTTTTTGATACGG;RSEQ=GATACGGGGTCTTGCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:25,159:184,0:0:2,0:18.8:1:29.1:1:1:0:54.5:9.222:0.994:0:1.8 0/1:144:53:10,43:18,72:90,53:0.3681:2,2:20.6:1:26.4:1:1:1.07448:48.4:2.786:0.325:0:3.2 +6 407882 . T C 88 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTACTGTTTTGAGGAA;RSEQ=TCAGAAGTGGAGATTTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:36.5:1:34.2:1:1:0:60:12:1:0:1.5 1/1:1:1:0,1:0,0:0,1:1:0,0:18:0:33:0:1:0:60:2:1:0:1 +6 408012 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGCATTTCTTGTGTTCT;RSEQ=TAGACTGCCATCATTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:33:1:31:1:1:0:47.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 408385 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGGGTCCCTCTGCCCC;RSEQ=CCCTCCTTCCCATTGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 432393 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.53846;SOR=0;LSEQ=AGAAAAGTCAGAGCGCCACA;RSEQ=AACAGAACCAATGCAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:7,9:16,2:0.1111:2,2:32.5:1:31.5:1:1:1.27:60:4:0.1111:0:1.5 0/0:9:0:0,0:6,3:9,0:0:2,0:31.7:1:32.2:1:1:0:60:18:1:0:0.4 +6 432451 . G A 42 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.11403;LSEQ=TATCAGGAGATGTGGGCTTG;RSEQ=AGAGCCACATCTTTTTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:35.5:1:31.5:1:1:1.73:60:4:0.4:0:1 0/1:7:3:2,1:1,3:4,3:0.4286:2,2:20.3:1:26.7:1:0.48571:4.45:60:6:0.4286:0:1 +6 1313117 . A C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGCGGCGGCGCCAGAGAT;RSEQ=CGCAGGGCGACGGCGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:32:0:1:0:60:4:1:0:2 +6 1313121 . A C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCGGCGCCAGAGATACGC;RSEQ=GGGCGACGGCGAACAGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:31.5:1:1:0:60:4:1:0:2 +6 1390276 . CCCGCCGCCG C 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=9.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=CCGCCCTGATGAGCCCGCCG;RSEQ=CCGCCGCCGCCGCCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:29:1:1:0:60:4:1:0:0 +6 1390636 . C A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49701;SOR=Inf;LSEQ=AGAACTCGGTGCGCCACAAT;RSEQ=TCTCGCTCAACGAGTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:52,32:84,0:0:2,0:25.8:1:32.7:1:1:0:55.3:168:1:0:0.1 0/1:84:2:1,1:45,37:82,2:0.0238:2,2:16:0:27:1:1:1.21336:46.5:4:0.0244:0:1 +6 1390652 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49732;SOR=0;LSEQ=CAATCTCTCGCTCAACGAGT;RSEQ=CTTCATCAAGCTGCCTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:43,42:85,2:0.023:2,2:21.5:1:29.5:1:1:1.02354:60:4:0.0233:0:1.5 0/0:83:0:0,0:42,41:83,0:0:2,0:28.2:1:30.8:1:1:0:52.8:26.667:1:0:0.3 +6 1390668 . TA T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23591;SOR=Inf;LSEQ=GAGTGCTTCATCAAGCTGCC;RSEQ=AGGGCCTCGGGCGGCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:36,45:81,0:0:2,0:26.4:1:29.1:1:1:0:46.9:39.5:1:0:0.1 0/1:77:2:1,1:34,41:75,2:0.026:2,2:27:1:32:0:1:1.20:48.5:4:0.0267:0:0 +6 1390718 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19312;SOR=Inf;LSEQ=CTACTGGACCATCGACCCGG;RSEQ=CAGCGAGTTCATGTTCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:12,32:44,0:0:2,0:22.4:1:31.2:1:1:0:35.3:43:1:0:0.1 0/1:35:2:1,1:8,25:33,2:0.0571:2,2:20.5:1:27.5:1:0.45378:3.00:49.5:4:0.0571:0:1 +6 1390722 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16812;SOR=Inf;LSEQ=TGGACCATCGACCCGGCCAG;RSEQ=GAGTTCATGTTCGAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:10,31:41,0:0:2,0:21.6:1:29.2:1:1:0:34.7:12.667:1:0:0.1 0/1:29:2:1,1:4,23:27,2:0.069:2,2:11.5:1:31:0:0.3202:5.25:25:4:0.069:0:1 +6 1391252 . C G 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCAGCCGCCTGCCCTGACGC;RSEQ=CAGCAGCAACCCCGCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:30.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:38.5:1:32:1:1:0:60:4:1:0:0.5 +6 1611183 . TGCG T 47 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.67266;SOR=1.76916;LSEQ=GTTCGAGAACGGCAGCTTCC;RSEQ=GCGGCGGCGGCGCTTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:3:0,3:81,252:333,3:0.0089:2,0:35.7:1:31.7:1:1:0:46:6:0.009:0:0 0/1:191:3:1,2:44,142:186,3:0.0157:2,2:33.3:1:30:1:0.55993:1.61:47:6:0.0159:0:0 +6 1611190 . G A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.55511;SOR=0;LSEQ=AACGGCAGCTTCCTGCGGCG;RSEQ=CGGCGGCGCTTCAAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:3:2,1:68,230:298,3:0.01:2,2:11:1:27.7:1:0.13614:6.71:27:6:0.0101:0:1 0/0:163:0:0,0:39,124:163,0:0:2,0:24.4:1:30.7:1:1:0:40.5:53.333:1:0:0.1 +6 1611220 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09839;SOR=Inf;LSEQ=TTCAAGAAGAAGGACGCGGT;RSEQ=AAGGACAAGGAGGAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:16,146:162,0:0:2,0:23.2:1:32.5:1:1:0:52:80:0.9938:0:0.2 0/1:75:2:1,1:8,65:73,2:0.0267:2,2:33.5:1:27.5:1:0.22703:7.72:54.5:4:0.0267:0:1 +6 2872045 . G A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGGGTTGCAGTGAGCTGA;RSEQ=ATCACGCCACCGCAATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:31:0:1:0:59.5:4:1:0:1 +6 2873722 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52862;SOR=Inf;LSEQ=CGCCCTGCCCAGCACTCAGC;RSEQ=CCTTCCCTTACGCTGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:13,7:20,0:0:2,0:27.5:1:29.9:1:1:0:60:40:1:0:0.2 0/1:35:2:1,1:18,15:33,2:0.0571:2,2:28:0:32.5:1:1:1.19373:60:4:0.0571:0:1.5 +6 2873791 . C T 42 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12821;SOR=0.15773;LSEQ=CCAGAACCATCGCCTCTGCC;RSEQ=CAAACACCTGCATTAACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:7,3:0.3:2,0:14:1:26.7:1:1:0:60:6:0.3:0:1.3 0/1:17:1:0,1:4,12:16,1:0.0588:2,0:42:0:28:0:1:0:60:2:0.0588:0:1 +6 3797630 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.08615;SOR=Inf;LSEQ=ACAATGGGCTCCCACAAGCC;RSEQ=GGGAAAGCCAGCTATGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:18,0:18,0:0:1,0:22.6:1:29.6:1:1:0:60:17:1:0:0.2 0/1:8:2:2,0:6,0:6,2:0.25:0,0:16.5:1:30.5:1:1:0:60:4:0.25:0:1 +6 3797857 . A G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41781;LSEQ=ACACTCAAGCTTAGTCCCAA;RSEQ=GGGAACACACCCCTCCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:387:254:121,133:60,73:133,254:0.6563:2,2:23.3:1:31.8:1:0.66865:1.11:60:62.5:0.6579:0:1.1 0/1:354:157:74,83:102,94:196,157:0.4435:2,2:25.8:1:30.7:1:0.3921:1.21639:60:38.25:0.4397:0:1.2 +6 4289703 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19615;SOR=Inf;LSEQ=TGGCAGAGTTGGTTCCTTCT;RSEQ=AGGGCTGGGAGGGAGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:22,0:0:2,0:26.4:1:31.3:1:1:0:60:21:1:0:0.3 0/1:18:2:1,1:10,6:16,2:0.1111:2,2:37.5:1:29.5:1:1:1.61828:60:4:0.1111:0:1.5 +6 4289773 . G A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24026;SOR=0;LSEQ=GATTGCTGGCAAGCTTTGAC;RSEQ=TTCCTTGGCTAGCAGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:2,8:10,3:0.2308:2,2:15:1:32.7:1:1:1.89:60:6:0.2308:0:1 0/0:9:0:0,0:3,6:9,0:0:2,0:23.2:1:30.8:1:1:0:60:18:1:0:0.4 +6 4291026 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAGGTCACTGCAACCTC;RSEQ=GCCTCCTGGGTTCAAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:29:1:1:0:30:4:1:0:1.5 +6 4405966 . A AG 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACATTCTCAACAGCCCCTC;RSEQ=CTGGAATCTGCTTAAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:0,7:1:0,2:23.1:1:33.1:1:1:0:60:14:1:0:0 1/1:4:4:1,3:0,0:0,4:1:0,2:31.3:1:32.5:1:1:0:59.3:8:1:0:0.3 +6 4406121 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=AACACACTAAGCTCCCTGAG;RSEQ=GGGGGAAGGGCAGAAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:35:1:31.8:1:1:0:58.8:8:1:0:1.3 0/1:8:2:2,0:3,3:6,2:0.25:2,0:18:1:29:0:0.46429:0:60:4:0.25:0:1 +6 4406129 . G A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02857;SOR=0;LSEQ=AAGCTCCCTGAGCGGGGGAA;RSEQ=GGCAGAAGCCATTTCTATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:31:1:32.8:1:1:0:58.8:8:1:0:1.3 0/0:4:0:0,0:2,2:4,0:0:2,0:19:1:31.8:1:1:0:59:8:1:0:0.5 +6 4406150 . T TTC 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGAAGCCATTTCTATAG;RSEQ=CAGGCCGCACTTTTCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:15.2:1:30.8:1:1:0:57:10:1:0.6:1.2 1/1:4:4:2,2:0,0:0,4:1:0,2:21.3:1:28.7:1:1:0:57:8:1:0.5:0.8 +6 4406229 . T C 88 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCCCCCACAGCCCAACA;RSEQ=ACCAGCTGTGGCAGACTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:0,7:1:0,2:27.3:1:31.6:1:1:0:41.9:14:1:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:14:0:33:0:1:0:50:2:1:0:1 +6 4406310 . T C 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTGGGCAGGGCTTCCC;RSEQ=GCAGGAACTCCAACAACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:8,2:0.2:2,2:8.5:1:24.5:1:1:1:47.5:4:0.2222:0:2.5 0/0:1:0:0,0:0,1:1,0:0:0,0:38:0:32:0:1:0:44:2:1:0:0 +6 4406601 . A G 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84709;LSEQ=CAGGGGTTGTCAGAGAGCCT;RSEQ=TACAGGAGTGATACTACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:31.5:1:33:1:1:1.41:54:4:0.2857:0:3 0/1:4:1:0,1:1,2:3,1:0.25:2,0:33:0:28:0:1:0:60:2:0.25:0:3 +6 4406607 . G A 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.15267;LSEQ=TTGTCAGAGAGCCTATACAG;RSEQ=AGTGATACTACTGGCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:25.5:1:32:0:1:1.29:54:4:0.2222:0:3 0/1:4:1:0,1:1,2:3,1:0.25:2,0:39:0:27:0:1:0:60:2:0.25:0:3 +6 4406615 . C T 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.66417;LSEQ=GAGCCTATACAGGAGTGATA;RSEQ=TACTGGCATCAGGTTAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:17.5:1:30:1:1:1.29098:54:4:0.2222:0:3 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:47:0:28:0:1:0:60:2:0.3333:0:3 +6 4407325 . A G 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.5321;LSEQ=AGACATGCAGACAAGATTAC;RSEQ=GAGAAAAGAATGCAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:13.8:1:25.5:1:1:0:60:3:0.75:0:1 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:18:1:31:0:1:0:60:8:0.6667:0:1 +6 4407421 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49206;SOR=Inf;LSEQ=ACTGGAGTACCTGAAGGAGA;RSEQ=GGGGAGAATGGAAACAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:4,8:12,0:0:2,0:24.3:1:30.9:1:1:0:49.4:24:1:0:0.2 0/1:16:2:0,2:7,7:14,2:0.125:2,0:27.5:1:32.5:1:0.475:0:42:4:0.125:0:1.5 +6 4407450 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=Inf;LSEQ=TGGAAACAAGCTGGAAAACA;RSEQ=ACTTCAGGATATTATCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:26.8:1:30.2:1:1:0:46.8:12:1:0:0 0/1:8:2:1,1:4,2:6,2:0.25:2,2:11:1:29.5:1:1:1.8258:26.5:4:0.25:0:1.5 +6 5042052 . G T 59 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTAATAAACTATAAGAA;RSEQ=CAAGGAAAATTAGGGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:24.3:1:29.8:1:1:0:41:8:1:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:28.5:1:1:0:33:4:1:0:1 +6 5042179 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03917;SOR=Inf;LSEQ=GTGCCACACAATGATTTAAG;RSEQ=TATTTGTTTTCTATAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:55,3:58,0:0:2,0:26.7:1:32.1:1:1:0:33.7:116:1:0:0.1 0/1:48:4:3,1:42,2:44,4:0.0833:1,2:26.5:1:29.5:1:0.23427:6.47588:26:8:0.0833:0:1 +6 5042363 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.23564;LSEQ=AGACTTTTATTTTTGTGTGT;RSEQ=ATCAAATATAGGTAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:134:49,85:4,10:14,134:0.9054:2,2:22.7:1:29.7:1:0.77083:1.44:45.2:133:0.9048:0:1.6 1/0:146:101:39,62:15,30:45,101:0.6918:2,2:24.6:1:28.3:1:0.58205:1.26:46.1:100:0.6897:0:1.5 +6 5042388 . C T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.19085;LSEQ=AATATAGGTAAAAATAATTG;RSEQ=GCAATTCTGCTGTTTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:65:25,40:3,8:11,65:0.8553:2,2:18.4:1:30.8:1:0.73677:1.66:31.8:130:0.8553:0:2.1 1/0:91:48:17,31:9,34:43,48:0.5275:2,2:18.6:1:29.6:1:0.16473:2.06:30:96:0.5275:0:2 +6 5042389 . G A 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00416;SOR=Inf;LSEQ=ATATAGGTAAAAATAATTGC;RSEQ=CAATTCTGCTGTTTAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:27,48:75,0:0:2,0:19:1:31.8:1:1:0:34:17.75:1:0:1.7 0/1:90:9:3,6:22,59:81,9:0.1:2,2:22.6:1:29.9:1:0.70427:1.34:47:18:0.1011:0:1.2 +6 5042420 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49309;SOR=Inf;LSEQ=GTTTAAACAGGAACTATTGG;RSEQ=CTCCTTGGCCCTAAATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:7,23:30,0:0:2,0:15.6:1:30.6:1:1:0:39:60:1:0:1.1 0/1:33:2:1,1:4,27:31,2:0.0606:2,2:19:1:27:1:0.28409:6.15:24.5:4:0.0645:0:2.5 +6 5042488 . A G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59705;SOR=0.51177;LSEQ=ATTGTAAAATAATCCAACCT;RSEQ=ATTTTTTTTAATTTGGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:21:3,18:0,3:3,21:0.875:0,2:22.8:1:31.5:1:1:0:41.5:20:0.8696:0:1.3 1/0:9:7:0,7:0,2:2,7:0.7778:0,0:28.1:1:32.1:1:1:0:42.4:14:0.7778:0:1 +6 5042668 . C A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGCTGCTGTGTTCTGTT;RSEQ=ATTGCCTCCTTCAACAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:9:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 5043276 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCCTAGTGACTTCTACT;RSEQ=TATGCTCCAGCTTTCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:26.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 5106731 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13793;SOR=Inf;LSEQ=TGGTGGGGCTTGAGATTAAC;RSEQ=GGAGAGGCTGTGGATGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:55,0:55,0:0:1,0:24.9:1:30.1:1:1:0:60:54:1:0:0.1 0/1:33:2:2,0:31,0:31,2:0.0606:1,0:25.5:1:32:0:1:0:60:4:0.0606:0:1.5 +6 5106788 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07871;SOR=Inf;LSEQ=CTACTTAGTTAGCAGCAGGA;RSEQ=GGAGTATACCTAAAGCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:131,33:164,0:0:2,0:21.1:1:31.4:1:1:0:60:53.667:1:0:0.3 0/1:124:3:2,1:86,35:121,3:0.0242:2,2:22:1:27.3:1:1:1.22641:60:6:0.0246:0:1 +6 5106807 . T C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.24106;SOR=1.33994;LSEQ=ACGGAGTATACCTAAAGCAA;RSEQ=CTAGCCAATTCTTTCAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:50:37,13:122,54:176,50:0.2212:2,2:24.7:1:32:1:0.60058:1.26:60:100:0.2283:0:1.2 0/1:174:48:30,18:78,48:126,48:0.2759:2,2:24.8:1:30.9:1:1:1.03:60:47:0.2733:0:1.3 +6 5106899 . T G 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.08139;LSEQ=GTGCAAGATCTCCCAGCTAT;RSEQ=ATGTCATGACAGCCAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:149:55,94:91,116:207,149:0.4185:2,2:24.3:1:32:1:0.1916:1.33964:60:48.667:0.4171:0:1.1 1/0:265:159:72,87:47,57:104,159:0.6:2,2:26.1:1:30.7:1:1:1.00:60:30.8:0.5923:0:1.2 +6 5106916 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08204;SOR=Inf;LSEQ=TATTATGTCATGACAGCCAG;RSEQ=CCAGCCCAGAGCTGTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:101,182:283,0:0:2,0:23.9:1:31.1:1:1:0:60:30.444:0.9964:0:0.5 0/1:220:3:1,2:92,125:217,3:0.0136:2,2:8:1:25:1:1:1.46951:59:2:0.0093:0:4 +6 5106962 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58168;SOR=2.60936;LSEQ=CTAGGATATAGCCTTGCTCG;RSEQ=CCAATGAGTTCTGCCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:1:0,1:27,104:131,1:0.0076:2,0:38:0:31:0:1:0:60:2:0.0077:0:1 0/1:102:2:1,1:29,71:100,2:0.0196:2,2:38:1:28:1:0.50379:2.42:60:4:0.0202:0:1 +6 5603804 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15766;SOR=0;LSEQ=CTTCTGAGGATCTGTTTTGT;RSEQ=CCTCCTTCACCTCCAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:8,5:13,2:0.1333:2,2:30.5:1:31.5:1:1:1.54914:60:4:0.1333:0:2 0/0:22:0:0,0:13,9:22,0:0:2,0:24:1:31.6:1:1:0:60:44:1:0:1.1 +6 5603835 . A G 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.163;LSEQ=CTCCAGTGGTTTGCTGGCAC;RSEQ=CTTTGGCATTCCTGGGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:18:10,8:4,3:7,18:0.72:2,2:27.2:1:31.3:1:1:1.06395:60:36:0.72:0:1.7 1/0:24:18:9,9:3,3:6,18:0.75:2,2:35.8:1:31.6:1:1:1:60:36:0.75:0:1.8 +6 5603872 . G C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.75264;SOR=1.2615;LSEQ=CTTGCAGGAGCGTTATCCCA;RSEQ=CCTCTGGCTTCATCTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:13:4,9:3,6:9,13:0.5909:2,2:28.1:1:31:1:1:1.11896:60:26:0.5909:0:1.6 1/0:17:11:5,6:3,3:6,11:0.6471:2,2:19.8:1:31:1:1:1.18716:60:22:0.6471:0:2.1 +6 6269168 . C G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00036;SOR=Inf;LSEQ=CCTGACCTCAGGTGTTCCCC;RSEQ=CCGCCTCAGCCTCCCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:65,0:65,0:0:1,0:28.5:1:30.5:1:1:0:57.9:31.5:1:0:0.1 0/1:34:7:7,0:27,0:27,7:0.2059:1,0:14.6:1:30.6:1:1:0:55.7:14:0.2059:0:1.4 +6 6269225 . A AT 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.2064;SOR=Inf;LSEQ=TGAGCCACCATGCCTGGCAA;RSEQ=TTGTTTTTTTTTTTTAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:159,53:212,0:0:2,0:21.1:1:30.3:1:1:0:59:41.4:1:0:0.4 0/1:177:2:0,2:133,42:175,2:0.0113:2,0:13.5:1:24:1:0.06073:0:60:4:0.0114:0.0056:3 +6 6269228 . GT G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.93146;LSEQ=GCCACCATGCCTGGCAAATT;RSEQ=TTTTTTTTTTTAAGTATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:15:13,2:164,62:226,15:0.0602:2,2:22.1:1:32.3:1:0.36581:2.45:59.7:30:0.0615:0.0241:0.1 0/1:213:12:9,3:143,56:199,12:0.0563:2,2:18.6:1:30.5:1:1:1.17:56.6:24:0.0566:0.0141:1.4 +6 6269298 . G C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.28163;LSEQ=GAAGGGGTGATTTCTTTTTT;RSEQ=CTCTCTGGTTCTGAATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:113:69,44:264,226:490,113:0.1874:2,2:29.2:1:31.2:1:0.17398:1.34:60:36.667:0.189:0:1.1 1/0:535:294:154,140:121,119:240,294:0.5495:2,2:24.7:1:30.3:1:0.66426:1.08:59.8:72.5:0.5556:0:1.2 +6 6270236 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTACAGGCATGAGCCACTG;RSEQ=GCCCAGCCTACCTACTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:28:1:1:0:36.5:4:1:0:1 +6 6728508 . GC G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10686;SOR=Inf;LSEQ=AGGAGCCCTTCCTTGTGAGG;RSEQ=CCAGCTCTGATATTCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:37,25:62,0:0:2,0:26.2:1:31.9:1:1:0:60:61:1:0:0 0/1:57:3:2,1:25,29:54,3:0.0526:2,2:22:1:29.9:1:0.5986:2.29:60:6:0.0545:0.0175:0 +6 6728616 . G A 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TAGCCTAGGCCTTCACAGCA;RSEQ=GGGGCAAGGGGGATGTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:20:5,15:2,10:12,20:0.625:2,2:23:1:31.4:1:0.68332:1.64:60:40:0.625:0:1.1 0/0:29:0:0,0:13,16:29,0:0:2,0:19.7:1:29.9:1:1:0:60:58:1:0:0.2 +6 7516670 . GTA G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.15;SOR=Inf;LSEQ=TCACAACGGTGGCAATAACT;RSEQ=TATATATATATGTCTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:34,0:34,0:0:1,0:21.1:1:30.9:1:1:0:58.4:68:1:0:0.4 0/1:22:2:2,0:19,1:20,2:0.0909:1,0:16:1:33:0:1:0:60:4:0.0909:0:0 +6 7516674 . A ATATATACATATATATATATATATATG 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=4e-05;SOR=0;LSEQ=AACGGTGGCAATAACTGTAT;RSEQ=TATATATATGTCTATAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:18,0:21,0:21,18:0.4286:1,1:18.6:1:31.3:1:1:0:60:36:0.439:0.1905:1.1 0/0:26:0:0,0:21,1:22,0:0:1,0:17.7:1:28:1:1:0:59.9:44:0.8462:0:0 +6 7516700 . T A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02048;SOR=0.41618;LSEQ=ATATGTCTATAAACTTACAA;RSEQ=AAAGATAAACTCTAGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:51:51,0:45,0:45,51:0.5313:1,1:17.7:1:31.1:1:1:0:59.3:102:0.5313:0:1.2 0/1:47:15:15,0:30,2:32,15:0.3191:2,1:15.5:1:29.5:1:1:0:59.4:30:0.3191:0:1.1 +6 7516833 . G T 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42129;LSEQ=TCCTCAGCCCAGGTATGAAC;RSEQ=TAAAGTTTGGCCTGAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:753:470:263,207:175,108:283,470:0.6242:2,2:27.3:1:31.1:1:0.12717:1.27493:37.4:57.75:0.6252:0:1.1 0/1:661:272:158,114:222,167:389,272:0.4115:2,2:28.1:1:29.9:1:0.81084:1.04:37.1:89.667:0.4101:0:1.1 +6 7517131 . A T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.47656;LSEQ=GGCCTTTCTGGTACATGCAG;RSEQ=AGTGACGGGTTACAGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:796:477:234,243:143,176:319,477:0.5992:2,2:26:1:29:1:0.24737:1.18:47.6:67.143:0.598:0:1.1 0/1:589:245:126,119:180,164:344,245:0.416:2,2:26:1:28:1:0.86722:1.03654:46.2:60.25:0.417:0:1.2 +6 7517239 . G A 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCCATACCCTTGGGCCACA;RSEQ=AGTCTGACTGCATGTCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:658:0:0,0:322,335:657,0:0:2,0:25.6:1:32.6:1:1:0:59.1:92.857:0.9985:0:0.1 0/1:550:75:39,36:229,244:473,75:0.1364:2,2:24.3:1:28.8:1:0.61954:1.15:54.5:36.5:0.1347:0:1.2 +6 7517509 . T C 216 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGTGTGCAAAATCTTCGA;RSEQ=TGACTTATCTTGATTATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:796:0:0,0:412,384:796,0:0:2,0:23.7:1:30.6:1:1:0:59.5:78.6:1:0:0.1 0/1:635:119:66,53:256,260:516,119:0.1874:2,2:24.1:1:31.4:1:0.26438:1.26:49.4:58.5:0.1863:0:1.1 +6 7518105 . A AT 204 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.01136;SOR=0.60697;LSEQ=TAAACCTTGAAAGTGAATCA;RSEQ=TTTTTTTTTTTTTCTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:107:15,92:45,138:183,107:0.3282:2,2:25:1:30.4:1:0.03568:1.99548:53.8:34.667:0.3312:0.0215:0.5 0/1:245:56:9,47:44,124:168,56:0.2286:2,2:25.9:1:29.6:1:0.14764:1.84836:55.3:55:0.2292:0.0245:0.4 +6 7518127 . G A 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5159;SOR=0;LSEQ=TTTTTTTTTTTTCTGAGACG;RSEQ=AGTTTTGCTCTTGTTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:12,157:169,2:0.0117:2,2:6:1:27:1:0.14668:12.61:47:4:0.012:0:1 0/0:117:0:0,0:7,109:116,0:0:2,0:20:1:30.7:1:1:0:51.7:57:1:0:0.4 +6 7518144 . C A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGGAGTTTTGCTCTTGTTG;RSEQ=CCAGGCTGGAGTGCAATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:0,108:108,0:0:1,0:24.4:1:31.8:1:1:0:41.6:107:1:0:0.3 0/1:63:12:0,12:0,51:51,12:0.1905:1,0:20.5:1:29.8:1:1:0:38.9:24:0.1905:0:1.3 +6 7518659 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAAAAAGCTATGCAACT;RSEQ=TAATTCTTTTCCAAACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21:1:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 8313973 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTGTAGGTGACCTGGG;RSEQ=TTTCTCTGTGGCTGCCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19:1:31.5:1:1:0:45.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 8314164 . G A 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.71314;SOR=0.61042;LSEQ=TGAAGTGTGTTTTCCACCTT;RSEQ=TTTCCATTATCCCCATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:5,2:5,2:7,7:0.5:2,2:20.7:1:30.9:1:1:1:43.3:14:0.5:0:1.1 0/1:16:6:4,2:4,6:10,6:0.375:2,2:28.5:1:29.3:1:0.60839:2.79:58.3:12:0.375:0:1.3 +6 8314545 . G T 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTTTTTTTATTACCCAT;RSEQ=TTCTGAAGCCTACTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:19.3:1:32.8:1:1:0:55.5:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 8314616 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCTCTTGAAGGAGAGAC;RSEQ=TTGCAGTCATTTGGAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:3,1:4,4:0.5:2,0:25:1:30.3:1:1:0:40.8:8:0.5714:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:31:0:1:0:52:2:1:0:0 +6 8314742 . GT G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.48276;SOR=0;LSEQ=GCTGCTGACTCTTGCATGGG;RSEQ=TTTTTTTTTGGCAGCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:25:1:29.5:1:1:1.55:50.5:4:0.1333:0.0667:1 0/0:14:0:0,0:9,5:14,0:0:2,0:28.7:1:29.3:1:1:0:52.9:28:1:0:0.4 +6 8314762 . T TTTG 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.4467;LSEQ=GTTTTTTTTTTGGCAGCTTT;RSEQ=TTGTTGTTGATGCTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:3,7:1,3:4,10:0.7143:2,2:21.8:1:30.1:1:1:1.26:49.5:20:0.7143:0.0714:0.8 1/0:14:11:6,5:2,1:3,11:0.7857:2,2:31.2:1:29.5:1:1:1.60839:53.1:22:0.7857:0.0714:0.5 +6 8315463 . T C 42 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGATCTATGGAGATGGCTG;RSEQ=CACCCTTCCCCCACCTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:26.7:1:31.3:1:1:0:60:6:1:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:27:1:27:1:1:0:60:2:1:0:1.7 +6 8315773 . C G 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.07395;SOR=0.15127;LSEQ=CTGGCTGTGTAGCGTGCTCA;RSEQ=TCACCACCTCCCTTGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:1,1:2,9:0.8182:2,0:24.7:1:32.1:1:0.18182:0:60:18:0.8182:0:1.2 0/1:8:3:1,2:1,4:5,3:0.375:2,2:29.3:1:32.3:1:1:1.83:60:6:0.375:0:1 +6 8909370 . CT AC 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=TTTTCTTAGTTTAGATTCCC;RSEQ=TGAAATAGACCCTCAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:11,0:0:2,0:21.4:1:28.5:1:1:0:60:10:1:0:1.3 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:6.5:1:29.5:1:1:2.44949:60:4:0.3333:0.1667:0.5 +6 8909371 . T C 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=0;LSEQ=TTTCTTAGTTTAGATTCCCC;RSEQ=TGAAATAGACCCTCAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:8,3:0,0:0,11:1:0,2:21.8:1:28.5:1:1:0:60:10:1:0:1.3 0/0:5:0:0,0:3,1:4,0:0:2,0:15.3:1:31.3:1:1:0:60:8:1:0:0.3 +6 10214590 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49503;SOR=Inf;LSEQ=CTTCTCTTTCCCTTTGTGTT;RSEQ=GTCATCTTGGCAAATTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,17:38,0:0:2,0:25.3:1:31.1:1:1:0:51.6:37:1:0:1 0/1:43:2:1,1:21,20:41,2:0.0465:2,2:29.5:1:28.5:1:1:1.04883:57:4:0.0465:0:1 +6 10214600 . G A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05578;LSEQ=CCTTTGTGTTCGTCATCTTG;RSEQ=CAAATTACTGGAAGATGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:34:19,15:1,2:3,34:0.9189:2,2:26.7:1:29.7:1:0.5843:2.47:53.3:33:0.9167:0:1.2 0/1:45:17:9,8:13,15:28,17:0.3778:2,2:28.2:1:29.1:1:0.7631:1.29:57.6:34:0.3864:0:1.1 +6 10575131 . T C 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.63512;SOR=0.45507;LSEQ=TTTCTTTTTCTGATCGTTTT;RSEQ=CTTCAAGCGTTTCAGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:4,4:1,1:2,8:0.8:2,2:32.6:1:31.3:1:1:1:25.9:16:0.8:0:1.1 1/0:11:7:4,3:3,1:4,7:0.6364:2,2:19.6:1:30:1:1:2.09375:24.3:14:0.6364:0:1 +6 10575346 . T C 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16809;SOR=0.30774;LSEQ=CATTCCCTTGATGCCTGCAA;RSEQ=GTCACCTTTCTTATAGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:5,3:11,5:16,8:0.3333:2,2:30.6:1:31.3:1:1:1.30452:48:16:0.3333:0:1 0/1:23:3:2,1:13,7:20,3:0.1304:2,2:38:1:31.7:1:1:1.07:46:6:0.1364:0:1 +6 12518463 . T G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25178;SOR=0.31741;LSEQ=TTTTACATTGCATGCCTGTA;RSEQ=CAAAACATCTCATGTACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:13,0:5,0:5,13:0.4815:0,1:22.8:1:33.5:1:1:0:43.2:12:0.4615:0:2.4 0/1:9:2:2,0:0,0:0,2:0.2222:0,0:17:1:29.5:1:1:0:41:4:0.2222:0:2 +6 12518500 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.21897;LSEQ=CCCCATAAATATATACACCT;RSEQ=CTATGTACCTATGAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:42:42,0:7,0:7,42:0.8571:0,1:26.1:1:32.7:1:1:0:51.6:41:0.8542:0:2.5 1/1:25:22:22,0:3,0:3,22:0.88:0,1:15.9:1:32.1:1:1:0:54.7:44:0.88:0:2 +6 12518544 . A T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.70532;SOR=1.18077;LSEQ=ATTAAAAAAAATTAAAAATT;RSEQ=AACAAACACTTGCAGATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:138:117:112,5:21,0:21,117:0.8478:1,1:21.2:1:31.2:1:1:0:58.8:38:0.8444:0:1.5 1/1:91:79:71,8:12,0:12,79:0.8681:0,2:23.8:1:30.2:1:0.5907:0:59.7:158:0.8681:0:1.2 +6 12518585 . C T 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04466;SOR=Inf;LSEQ=ATCAAATGTGTGTTCTCCCA;RSEQ=CATGTGTAAATCATCAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:208,77:285,0:0:2,0:26.4:1:31.7:1:1:0:60:94:1:0:0.5 0/1:244:4:1,3:162,78:240,4:0.0164:2,2:7.8:1:25:1:0.10807:6.18137:60:8:0.0165:0:1 +6 12518688 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2793;LSEQ=GAAAATGTTTCTGGAGTTAG;RSEQ=TTAGAAGAATGTGTGGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:434:373:149,224:24,36:60,373:0.8594:2,2:25.2:1:29.9:1:1:1.00223:60:92.25:0.8601:0:1.1 1/0:376:237:98,139:64,75:139,237:0.6303:2,2:24.8:1:29.2:1:0.38974:1.20971:60:117.5:0.6317:0:1.1 +6 12518742 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07458;SOR=Inf;LSEQ=TGAGTGTACTTCTTTTTCTG;RSEQ=TCATGTGACAATAAATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:69,180:249,0:0:2,0:25.3:1:31.6:1:1:0:59.9:61.25:1:0:0.7 0/1:182:3:2,1:61,118:179,3:0.0165:2,2:13.3:1:26.7:1:0.27535:3.84:60:6:0.0168:0:1 +6 13521823 . G T 62 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCAAGGGTCACTTTGCT;RSEQ=TACATTGTATTACACCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:14.5:1:31:1:1:0:30.3:8:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:27.5:1:31.5:1:1:0:42.5:4:1:0:1.5 +6 13686333 . C T 32 d5;v3;pSTD;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAATTTCCAAAATTTCTT;RSEQ=CCCCCCCCCCCCCCGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:32.5:1:1:0:58:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 16463818 . G A 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AGTAGTGAATATCCAAAACC;RSEQ=CCAAGGCCTAGACCTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:3,0:0:0,0:19:1:28.7:1:1:0:51:6:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:16:1:31:0:1:2.44949:24.5:4:0.3333:0:1.5 +6 16945029 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20789;SOR=0;LSEQ=TTTTTCTAGCAGCTTTCAAG;RSEQ=TGTTTTTGTTTTAATCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:20,6:26,2:0.069:2,2:16:0:34.5:1:0.44444:3.16227:60:4:0.0714:0:1.5 0/0:34:0:0,0:20,14:34,0:0:2,0:25.3:1:29:1:1:0:60:68:1:0:0.1 +6 16945103 . G T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01044;SOR=0.17912;LSEQ=TGGTTTTCTTTGTGTTTATT;RSEQ=TTTATCATCTTTGGGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:14:5,9:9,13:22,14:0.3889:2,2:18.5:1:29.5:1:1:1.23859:60:28:0.3889:0:1.3 0/1:30:3:1,2:11,16:27,3:0.1:2,2:20.7:1:28:1:1:1.36092:60:6:0.1034:0:1 +6 17627494 . T C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.13997;LSEQ=ATTAGACCCTATCATGTTTT;RSEQ=GTTGCTTTCCAAATAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:43:33,10:23,9:32,43:0.5733:2,2:21.6:1:30.6:1:0.78908:1.29:60:13.333:0.5714:0:1 0/1:64:10:8,2:42,12:54,10:0.1563:2,2:24.7:1:30.6:1:1:1.14:60:20:0.1563:0:1 +6 17627535 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24234;SOR=Inf;LSEQ=TAATTTTAGTTTTGATTTTG;RSEQ=CTTTATATTTCTAAGTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:106,42:148,0:0:2,0:23.5:1:30.1:1:1:0:60:48.333:1:0:0.5 0/1:144:2:1,1:99,43:142,2:0.0139:2,2:13.5:1:28.5:1:0.51923:2.28751:60:4:0.0139:0:2 +6 17627590 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.3974;LSEQ=AAACTGCTCATAGCTATTTG;RSEQ=TGAATTCCATACTTTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:72:38,34:97,78:175,72:0.2915:2,2:24.6:1:31.9:1:0.77879:1.1122:60:23:0.2887:0:1.1 1/0:284:214:116,98:37,32:69,214:0.7535:2,2:26.2:1:31.1:1:1:1.02:60:106:0.7544:0:1.1 +6 17729006 . G T 28 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAGGGAGAGGCGCCGCG;RSEQ=GGAACTGGGGCTGTGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44:0:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 17729816 . T C 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01945;SOR=Inf;LSEQ=AATCTGGTTGGGTTGCTTTC;RSEQ=GTGTTATGAGGGCTTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:21,0:0:2,0:34.6:1:31:1:1:0:60:20:1:0:0.5 0/1:36:9:4,5:10,17:27,9:0.25:2,2:21:1:28:1:0.71151:1.35:60:8:0.2353:0:1.9 +6 17729829 . C G 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07079;SOR=Inf;LSEQ=TGCTTTCTGTGTTATGAGGG;RSEQ=TTTGTGTTTTTTTGTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:20,0:0:2,0:31.9:1:31.8:1:1:0:60:19:1:0:0.6 0/1:32:6:3,3:9,17:26,6:0.1875:2,2:14.2:1:30.8:1:0.64713:1.85:60:12:0.2:0:2.3 +6 17729851 . C T 88 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05246;SOR=0.12258;LSEQ=TTGTGTTTTTTTGTTCTTTA;RSEQ=GTTAAAACTTGTTGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:7,7:14,8:0.3636:2,2:16.1:1:29.6:1:0.67492:1.62835:60:16:0.3636:0:1.9 0/1:16:1:1,0:4,10:14,1:0.0625:2,0:26:0:32:0:0.33333:0:60:2:0.0667:0:2 +6 17729871 . C G 69 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36898;SOR=0.30006;LSEQ=CGTTAAAACTTGTTGCTGCT;RSEQ=CCTTTGTGAGTTACATCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:2,3:3,7:10,5:0.3333:2,2:23.8:1:30:1:1:1.51:60:10:0.3333:0:2 0/1:8:1:1,0:0,7:7,1:0.125:0,0:6:0:33:0:0.125:0:60:2:0.1429:0:2 +6 18657237 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15766;SOR=Inf;LSEQ=TCCCCCAGCAAAGCACACCC;RSEQ=CCTCCACCAGGGGACATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,8:21,0:0:2,0:21.1:1:30.7:1:1:0:54.6:20:1:0:0 0/1:15:2:1,1:5,7:12,2:0.1333:2,2:36.5:1:30.5:1:1:1.37:60:4:0.1429:0:1.5 +6 18657579 . A G 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CAGAAAGCAACAACAATAGC;RSEQ=TCAACAATAACAAAAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:43.5:1:30.5:1:1:1:60:4:0.5:0:1 0/0:5:0:0,0:1,4:5,0:0:2,0:22:1:30.6:1:1:0:60:10:1:0:0.2 +6 19144021 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51334;SOR=0;LSEQ=CCTTTGGCCACATATATGCG;RSEQ=ATCTATAAGAAAGGTGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:30,91:121,2:0.0163:2,2:24.5:1:28.5:1:0.44209:3.00:49:4:0.0167:0:1 0/0:86:0:0,0:17,69:86,0:0:2,0:25.7:1:30.1:1:1:0:58:172:1:0:0.1 +6 19144202 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48791;SOR=Inf;LSEQ=GTGCGTATTGAGCACATTAA;RSEQ=CACTCTAAGAGCTGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:18,0:0:2,0:30.3:1:33.7:1:1:0:60:36:1:0:0 0/1:20:2:1,1:6,12:18,2:0.1:2,2:46:0:30.5:1:1:1.93:46:4:0.1:0:1.5 +6 19349172 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02767;SOR=Inf;LSEQ=ATCCAGTCTATGAGAAGAAG;RSEQ=CCGAGAAAGAAGTTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:13,3:16,0:0:2,0:22.6:1:30.3:1:1:0:60:32:1:0:0 0/1:8:3:3,0:4,1:5,3:0.375:2,0:19:1:30.7:1:1:0:60:6:0.4286:0:1.7 +6 19349215 . T C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00949;SOR=Inf;LSEQ=GAAGTGGAACCATCTGAAAA;RSEQ=GTCCCTTGCCCAGAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:26,17:43,0:0:2,0:22.4:1:30.5:1:1:0:58.4:42:1:0:0.1 0/1:30:5:3,2:15,10:25,5:0.1667:2,2:11.8:1:28.8:1:1:1:45.6:10:0.1667:0:2 +6 19349227 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17068;SOR=Inf;LSEQ=TCTGAAAATGTCCCTTGCCC;RSEQ=GAAGAAAGATCAGGTAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:27,22:49,0:0:2,0:25.1:1:30.7:1:1:0:58:48:1:0:0.1 0/1:35:2:1,1:19,14:33,2:0.0571:2,2:22.5:1:29:1:1:1.34517:60:4:0.0571:0:2.5 +6 19728835 . G C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02401;SOR=0.33518;LSEQ=TAACCAACTGGCAACCATGG;RSEQ=TGTTTTCATTACTTGGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:34:34,0:25,0:25,34:0.5763:1,1:22:1:31:1:1:0:60:10.333:0.5536:0:1.1 0/1:29:9:9,0:19,1:20,9:0.3103:1,0:16:1:31.3:1:1:0:60:18:0.3103:0:1 +6 19729003 . T G 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.52003;LSEQ=CAATATGTGGAATCAAGAAC;RSEQ=TTGGTTATTTGTCGGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:535:377:184,193:79,78:157,377:0.7047:2,2:26.8:1:30.8:1:0.77612:1.06221:59.9:52.857:0.7088:0:1.1 1/0:448:248:119,129:97,102:199,248:0.5536:2,2:24.9:1:30:1:0.92419:1.03084:60:123:0.5553:0:1.1 +6 19729078 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17995;SOR=Inf;LSEQ=ATCACTTGGTTTGCAAAATT;RSEQ=CCAAGGGACTAAATGACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:56,170:226,0:0:2,0:24.1:1:31.9:1:1:0:60:36.667:1:0:0.4 0/1:167:2:1,1:42,123:165,2:0.012:2,2:10:1:28.5:1:0.44982:2.91:60:4:0.0123:0:1 +6 19729381 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGCACTGTATTGAGAAG;RSEQ=AAGCCGATTTCACTAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:33:1:34:0:1:0:32:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 20402239 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03158;SOR=Inf;LSEQ=CATCCCCGCTTGGGGCCCGA;RSEQ=ATCCGTGCGGCCGGGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:14,2:16,0:0:2,0:24.1:1:32:1:1:0:60:32:1:0:0 1/0:4:2:2,0:1,1:2,2:0.5:2,0:25.5:1:30.5:1:1:0:60:4:0.5:0:1.5 +6 20402594 . TCGC T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.00614;SOR=2.7541;LSEQ=ACTGCTAGCCAGCCCCGGCT;RSEQ=CGCCGCCGCCGCCGCTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:831:11:7,4:508,310:818,11:0.0132:2,2:26.5:1:32.5:1:1:1.07:60:22:0.0134:0:0.3 0/1:589:21:14,7:349,217:566,21:0.0357:2,2:22.8:1:30.8:1:0.81978:1.24:59.5:42:0.036:0.0034:0.4 +6 20402610 . C T 129 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.08067;SOR=0.38896;LSEQ=GGCTTCGCCGCCGCCGCCGC;RSEQ=GCTGCCGCCGCCCCGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1052:17:11,6:639,395:1034,17:0.0162:2,2:27.6:1:31.8:1:1:1.13:59.9:34:0.0163:0:1.1 0/0:788:5:3,2:477,306:783,5:0.0063:2,2:24.4:1:28.6:1:1:1.03919:60:10:0.0064:0:1 +6 20402765 . C A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01429;SOR=Inf;LSEQ=CGCCGGCAGCCTCCTCTACA;RSEQ=CACGCCGCACGGACCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:0:0,0:94,395:489,0:0:2,0:23.9:1:31.8:1:1:0:58.6:121.25:0.9979:0:0.2 0/1:368:5:4,1:89,274:363,5:0.0136:2,2:16.4:1:27:1:0.01562:12.21:49.6:10:0.0138:0:1 +6 20402799 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06723;SOR=Inf;LSEQ=CCCTCCAGCAGAGCCGGGCT;RSEQ=CTGCAGCAGCCACCAGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:32,164:196,0:0:2,0:21:1:33.1:1:1:0:58.4:64.333:0.9948:0:0.2 0/1:136:3:1,2:21,112:133,3:0.0221:2,2:9.3:1:29:1:0.41356:2.64:60:6:0.0224:0:1.3 +6 20402836 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.15349;SOR=Inf;LSEQ=CGCTGGGACGCGGCGGCAGC;RSEQ=GCGGCGGCGGCGGCCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:17,35:52,0:0:2,0:20.5:1:30.7:1:1:0:60:104:1:0:0.3 0/1:34:2:1,1:11,20:31,2:0.0588:2,2:30:0:31.5:1:1:1.78:60:4:0.0625:0:1.5 +6 20403936 . AC A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.53578;SOR=0;LSEQ=ACCCTCCCTCTCCTCTCCCC;RSEQ=CCCCCCACCGGCGCCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:2,0:155,8:163,2:0.0121:1,0:8:1:32.9:1:1:0:60:4:0.0125:0.0061:0 0/0:94:0:0,0:88,5:93,0:0:2,0:19.4:1:31.3:1:1:0:59.2:22.25:0.9889:0:1.1 +6 20403953 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16354;SOR=Inf;LSEQ=CCCACCCCCCCACCGGCGCC;RSEQ=GCCCTCGCCCTGCGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:232,25:257,0:0:2,0:22.8:1:31:1:1:0:60:41.833:1:0:0.6 0/1:175:2:1,1:157,16:173,2:0.0114:2,2:25.5:1:26.5:1:0.18535:9.5498:60:4:0.0116:0:1 +6 20403978 . G T 61 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47706;SOR=0.42883;LSEQ=TCGCCCTGCGCCGCCGGTCT;RSEQ=TTCGGCCCTCCGGGCCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:6:2,4:353,128:481,6:0.0123:2,2:17.8:1:23.8:1:0.04874:5.49252:60:2:0.0088:0:1.8 0/0:377:2:0,2:279,96:375,2:0.0053:2,0:1:0:26:0:0.06706:0:60:4:0.0056:0:1 +6 20404345 . A AG 42 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGGGCGATAGAAAACCGG;RSEQ=GGGGGCTTCTCGCCAATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:14.7:1:27:1:1:0:46:2:0.3333:0.25:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 20481404 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03036;SOR=Inf;LSEQ=TTCTTTACCTTTCCCCCTAT;RSEQ=CCCCACCCGCTCGGTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:202,60:262,0:0:2,0:25.9:1:32.1:1:1:0:60:86.333:1:0:0.1 0/1:261:5:2,3:182,74:256,5:0.0192:2,2:15.6:1:27.8:1:0.15449:3.66834:60:10:0.0195:0:1 +6 20481678 . G C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=2.57415;LSEQ=TGAGTAGGAGTCCTCCCCAT;RSEQ=CCCCGGCTCTGAGGGGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:68:23,45:128,295:423,68:0.1385:2,2:24.3:1:30.9:1:0.57257:1.18:59.9:67:0.1396:0:1.1 0/1:437:128:45,83:112,194:306,128:0.2929:2,2:23.8:1:29.1:1:0.82691:1.0647:60:31:0.2925:0:1.3 +6 20481758 . C G 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16803;SOR=Inf;LSEQ=CCACGCCCACACGTTCTTTT;RSEQ=TTTTCTCTCCTACTGTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:2,111:113,0:0:1,0:23.6:1:33.8:1:1:0:60:226:1:0:0.2 0/1:79:2:1,1:4,73:77,2:0.0253:2,2:5:0:33:0:0.12334:16.43:60:4:0.0263:0:1.5 +6 20481825 . T C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00392;SOR=7.2757;LSEQ=CAGCTTCTAAGCCAGAAGTT;RSEQ=GAAGTCTCTTTACAAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:15:0,15:1,19:20,15:0.4286:1,1:18.5:1:30.8:1:1:0:60:30:0.4412:0:1 1/1:20:17:1,16:1,2:3,17:0.85:2,1:19.8:1:30.6:1:0.28421:6.73285:58.6:34:0.85:0:1.1 +6 20482573 . G GT 28 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGATGGGTTGTTTTTTT;RSEQ=TTTTTTTTTTTTTTTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:15:1:28.8:1:1:0:60:4:0.5:0.25:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 20482821 . G GAA 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.05983;SOR=Inf;LSEQ=AAGTGCAGAACTGTATTTAT;RSEQ=AAAAAAAAAATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:19,0:19,0:0:1,0:18.2:1:33.1:1:1:0:57.4:38:0.95:0:1.1 0/1:7:2:2,0:4,0:4,2:0.2857:0,0:16.5:1:30.8:1:1:0:60:4:0.2857:0.1429:2 +6 20482830 . A T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=1;SSF=0.69944;SOR=0.63235;LSEQ=ACTGTATTTATGAAAAAAAA;RSEQ=ATATATATATATATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:8:8,0:17,0:17,8:0.2857:1,0:21.5:1:32.9:1:1:0:57.5:16:0.2963:0:1.6 0/1:10:2:2,0:6,0:6,2:0.2:0,0:13:1:32.5:1:1:0:60:4:0.2:0:1.5 +6 20482851 . A G 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=11.000;MSILEN=2;SSF=0.00085;SOR=Inf;LSEQ=ATATATATATATATATATAT;RSEQ=TGTGTAAATGTTCTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:21,0:21,0:0:1,0:19.9:1:29.2:1:1:0:60.2:42:0.7241:0:0.7 0/1:14:5:5,0:9,0:9,5:0.3571:0,0:24.4:1:29.6:1:1:0:60:4:0.3077:0:1.4 +6 20482958 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10146;SOR=Inf;LSEQ=CTCCTTCCCCTCCCTCCCAT;RSEQ=AGTAGCCATGAAGAGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:224,45:269,0:0:2,0:22.8:1:32:1:1:0:60:37.429:0.9962:0:0.1 0/1:237:3:2,1:171,63:234,3:0.0127:2,2:10:1:27.7:1:1:1.35528:60:6:0.0129:0:1 +6 20483230 . A G 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01583;SOR=Inf;LSEQ=TGACAATCTGACTTATGCAC;RSEQ=AGGTAGATTATTATTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:21,174:195,0:0:2,0:21.4:1:31.2:1:1:0:60:96.5:1:0:0.1 0/1:153:5:1,4:14,134:148,5:0.0327:2,2:13.6:1:30.6:1:0.40736:2.37:60:10:0.0329:0:1.2 +6 20483265 . T A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51357;SOR=0;LSEQ=TCTGATGTCATGCAAATGAG;RSEQ=ACCTGTGTGCCTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:0,92:92,2:0.0213:1,2:29.5:1:32:0:0.02128:0:60:4:0.0215:0:1.5 0/0:65:0:0,0:0,65:65,0:0:1,0:25.7:1:27.5:1:1:0:60:31.5:1:0:0.1 +6 20483286 . ATG A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.51597;SOR=0;LSEQ=ACCTGTGTGCCTGTGTGTGT;RSEQ=TGTGTGTGTGTGCACGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:0,2:1,69:70,2:0.0278:1,0:16.5:1:31.8:1:1:0:60:4:0.0278:0.0139:0 0/0:48:0:0,0:0,48:48,0:0:1,0:21.4:1:28.9:1:1:0:60:15:1:0:0.1 +6 20483407 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10839;SOR=12.42446;LSEQ=ATTTTGATACCAGGTGGGAA;RSEQ=TGTTTTTTAAAGCATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:0,9:9,1:0.1:0,0:47:0:32:0:1:0:60:2:0.1111:0:1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:5.5:1:30:0:1:0:60:4:0.6667:0:1 +6 20486754 . C T 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00135;SOR=Inf;LSEQ=ACCTCATGATCCACCCGCCT;RSEQ=GGCCTCCCAAAGTGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:28,0:28,0:0:1,0:17.2:1:32.2:1:1:0:39.9:27:1:0:0.3 0/1:21:7:7,0:14,0:14,7:0.3333:1,0:12.4:1:30.1:1:1:0:49.6:14:0.3333:0:1 +6 20486794 . C T 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04032;SOR=0;LSEQ=ATTACAGGTGTGAGCCACCG;RSEQ=GCCCGGCCACATATGCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:7:7,0:60,0:60,7:0.1045:1,0:26.9:1:28.3:1:1:0:45.7:6:0.0923:0:1.4 0/0:45:0:0,0:45,0:45,0:0:1,0:27.9:1:32.2:1:1:0:51.8:90:1:0:0.6 +6 20486798 . C T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04247;SOR=2.32515;LSEQ=CAGGTGTGAGCCACCGCGCC;RSEQ=GGCCACATATGCATACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:15:15,0:60,1:61,15:0.1974:1,1:20:1:32.1:1:1:0:52.5:30:0.2055:0:1 0/1:52:19:19,0:33,0:33,19:0.3654:1,1:25.2:1:31.4:1:1:0:50.4:38:0.3654:0:1.1 +6 20487054 . G A 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTAAGGAGACAGCGTCTTT;RSEQ=TTCATCTGCAAAGATCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:111,312:423,0:0:2,0:23.6:1:32.1:1:1:0:59.6:83.6:0.9976:0:0.1 0/1:414:23:5,18:130,260:390,23:0.0556:2,2:23.4:1:29:1:0.36019:1.7977:59:22:0.0541:0:1.3 +6 20487250 . T G 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.64992;SOR=1.80535;LSEQ=TGACCTAGCAGGATGTTCAG;RSEQ=TCAAAGTGGTATATGATGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:1,6:7,5:0.4167:2,0:24.2:1:33.8:1:1:0:60:10:0.4545:0:1.2 1/0:7:4:0,4:1,2:3,4:0.5714:2,0:29.5:1:33.5:1:0.42857:0:60:8:0.5714:0:1 +6 20488234 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00121;SOR=2.95286;LSEQ=GTTGGACTAGTAGGGAAAAA;RSEQ=CAAGTGAAAAACGAACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:32:31,1:72,0:72,32:0.3077:1,1:20.7:1:30.7:1:0.30769:0:59.6:64:0.3077:0:1 1/0:65:37:37,0:28,0:28,37:0.5692:1,1:19.9:1:29.9:1:1:0:60:74:0.5692:0:1.1 +6 20488897 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTTATTTTCCCCCCCA;RSEQ=TGAGATGGGGAGAGGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:22:1:33.5:1:1:0:43.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 20490321 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17286;SOR=Inf;LSEQ=TACATGCTTTTTTCTAACAG;RSEQ=AACATATACATTCTTCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:186,3:189,0:0:1,0:22.6:1:32.7:1:1:0:59.8:62:1:0:0.1 0/1:135:2:1,1:126,7:133,2:0.0148:2,2:16.5:1:27:1:0.11542:16.9034:60:4:0.0152:0:1 +6 20490390 . T G 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0;SOR=Inf;LSEQ=TTTTGTTTCCATCAATGTTT;RSEQ=CTTTTCAGACTTGGCTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:0:0,0:453,227:680,0:0:2,0:25.4:1:30.7:1:1:0:59.9:96.143:1:0:0.1 0/1:612:23:15,8:371,218:589,23:0.0376:2,2:21.2:1:31.3:1:1:1.10:60:46:0.0381:0:1.1 +6 22054082 . AGTG A 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.04336;SOR=Inf;LSEQ=TAAAATTAGAGGATGACAGC;RSEQ=GTGGTGGTGGTGGTGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:24,0:0:2,0:25.5:1:32.7:1:1:0:60:48:1:0:0.1 0/1:44:8:5,3:21,15:36,8:0.1818:2,2:30:1:32.6:1:1:1.19:60:16:0.186:0:0.3 +6 22054141 . G GGCCCTTTCATCTATTTCTTCACTATCTCCC 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14132;SOR=0;LSEQ=TTTGTCTTCTTCCTTTTCCT;RSEQ=ATTAGCTTGATAGATTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:9,13:22,2:0.0833:2,2:22:1:30.6:1:1:1.42:60:4:0.087:0.0833:0 0/0:39:0:0,0:16,23:39,0:0:2,0:22.1:1:30:1:1:0:60:18.5:1:0:0.3 +6 22054191 . G T 91 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05361;SOR=10.0407;LSEQ=GGCATTTTCCACATCAGGCT;RSEQ=TAGTTCTTTATTTTTTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:35:1:31:1:1:0:60:4:0.25:0:1 1/1:10:8:0,8:0,2:2,8:0.8:0,0:27.8:1:30.4:1:1:0:60:16:0.8:0:1.1 +6 23515364 . G A 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29644;SOR=0;LSEQ=AAAACTTTAGTCAGGTTTCT;RSEQ=AACCTTCTCCTAGGTCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:5,2:12,7:19,7:0.2692:2,2:22.7:1:27.4:1:1:1.44:60:14:0.2692:0:1 0/0:6:0:0,0:4,2:6,0:0:2,0:26.7:1:30.8:1:1:0:60:12:1:0:0 +6 25092335 . A G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2031;SOR=3.82314;LSEQ=GTAAGACTCAAATGCTCTTA;RSEQ=ATGATAGATGATAGGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:7,0:7,6:0.4615:0,0:27.5:1:34.3:1:1:0:60:12:0.4615:0:1.2 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:29.1:1:31.1:1:1:0:60:14:0.7778:0:1 +6 25092425 . T C 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAGTCTATATTAGCAAAAC;RSEQ=GCTTCATGTCACTAACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:34:25,9:36,4:40,34:0.4595:2,2:23.4:1:31.4:1:0.07485:3.18828:60:68:0.4595:0:1.8 1/1:58:58:54,4:0,0:0,58:1:0,2:23.4:1:30.5:1:1:0:60:57:1:0:1.9 +6 25092465 . C T 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGTATACAGCTGGTTAT;RSEQ=GCTATCTGAAGTACTATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:117,44:161,0:0:2,0:23.8:1:32:1:1:0:60:79.5:1:0:0.8 0/1:129:30:21,9:74,25:99,30:0.2326:2,2:24.3:1:29.7:1:0.63955:1.26621:60:60:0.2362:0:1.6 +6 25092466 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.07476;LSEQ=AATGTATACAGCTGGTTATC;RSEQ=CTATCTGAAGTACTATTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:67:47,20:71,27:98,67:0.4061:2,2:25.9:1:30.5:1:0.86075:1.11822:60:66:0.4024:0:1.8 1/0:133:98:72,26:24,11:35,98:0.7368:2,2:25.1:1:28.9:1:0.66124:1.27:60:48:0.7442:0:1.9 +6 25092479 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19557;SOR=Inf;LSEQ=GGTTATCGCTATCTGAAGTA;RSEQ=TATTAGTAATGAGACATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:141,69:210,0:0:2,0:23.3:1:32.7:1:1:0:60:420:1:0:0.7 0/1:167:2:1,1:107,58:165,2:0.012:2,2:9:1:28:1:1:1.83773:60:4:0.0122:0:2.5 +6 25092539 . A C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.88557;LSEQ=GGTGAGGAAATAAATGTGAG;RSEQ=TGTTTCTCATTGTCATATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:110:51,59:100,104:204,110:0.3503:2,2:26.1:1:32.3:1:0.72266:1.11199:60:54:0.3462:0:1.3 1/0:295:214:94,120:39,42:81,214:0.7254:2,2:28.3:1:31.4:1:0.51591:1.18472:60:70.333:0.7301:0:1.4 +6 25092612 . GT G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.5076;SOR=0;LSEQ=TTTATAAAAAACTGTCAAAA;RSEQ=TTTTCTCTTTTTCATACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:28,86:114,2:0.0171:2,2:44.5:1:30:1:0.43913:3.04:60:4:0.0171:0:0.5 0/0:88:0:0,0:15,73:88,0:0:2,0:22.6:1:29.3:1:1:0:60:43:1:0:0.4 +6 25261412 . CA C 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.13563;SOR=0;LSEQ=AGAAGCAAGAAAATGTGACC;RSEQ=AAAACAAAACCAGCCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:4:2,2:119,86:205,4:0.0191:2,2:28.8:1:30.8:1:1:1.38152:60:8:0.0194:0:0.3 0/0:161:0:0,0:98,63:161,0:0:2,0:24.1:1:29.4:1:1:0:60:52.667:1:0:0.1 +6 25261601 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22515;SOR=Inf;LSEQ=ATTGCAGACATCAAGGGAAG;RSEQ=GGTACTGTTCAAAAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:99,71:170,0:0:2,0:22.4:1:31.3:1:1:0:57.2:84:1:0:0.3 0/1:154:2:1,1:90,62:152,2:0.013:2,2:32:1:31:1:1:1.44799:53:4:0.0131:0:1 +6 25261662 . A T 189 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCAAAACTGGAAGAGTCTAC;RSEQ=ATTTTACCCAGCATGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:80:36,44:63,75:138,80:0.367:2,2:27.5:1:29.9:1:1:1.02655:43.6:79:0.3657:0:1.1 0/0:224:0:0,0:104,120:224,0:0:2,0:28.5:1:29.4:1:1:0:56.8:73.667:1:0:0.1 +6 25261697 . C A 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.89425;LSEQ=GCTTTTGGCATTGTTTTAAA;RSEQ=AAACAAGTTAAGGGCAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:1:1,0:39,92:131,1:0.0076:2,0:1:0:25:0:0.30303:0:41:2:0.0076:0:2 0/1:140:2:1,1:50,88:138,2:0.0143:2,2:13:1:25:1:1:1.75:42.5:4:0.0143:0:1 +6 25261964 . TAAAAT G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=8;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAATAGGTGTTAAAGAAA;RSEQ=AAAAGACCTCTGGACTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:1,4:5,2:0.2857:2,0:21:1:32.4:0:1:0:60:4:0.2857:0:0.5 0/0:1:0:0,0:0,1:1,0:0:0,0:24:0:32:0:1:0:60:2:1:0:0 +6 25606558 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15114;SOR=Inf;LSEQ=AGGTGGCTTCCCAGAGCCAG;RSEQ=TGGATCAGACTCTGCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:125,22:147,0:0:2,0:25.7:1:32.5:1:1:0:59.8:146:1:0:0.1 0/1:94:2:1,1:73,19:92,2:0.0213:2,2:11.5:1:27.5:1:0.38206:3.77038:60:4:0.0215:0:1 +6 25606644 . G T 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38546;SOR=0.30317;LSEQ=GGGGATCACAAGAAACCTAT;RSEQ=CAAAGCTGTGAAAGTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:4:2,2:202,177:379,4:0.0104:2,2:22.3:1:31:1:1:1.14085:60:8:0.0105:0:1.3 0/0:314:1:0,1:164,149:313,1:0.0032:2,0:1:0:26:0:0.47771:0:60:2:0.0032:0:1 +6 25606672 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.13043;LSEQ=GTGAAAGTGATGAGAGCTGA;RSEQ=GGATTCTTTTATTTAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:128:55,73:127,121:248,128:0.3404:2,2:24.3:1:30.2:1:0.15679:1.39184:60:41.667:0.3369:0:1.9 0/1:302:19:9,10:131,150:281,19:0.0629:2,2:16:1:28.6:1:1:1.03:60:18:0.0608:0:2 +6 25606678 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.67074;SOR=0.91772;LSEQ=GTGATGAGAGCTGACGGATT;RSEQ=TTTTATTTAATGCAGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:119:51,68:125,120:245,119:0.326:2,2:25.1:1:30.4:1:0.14813:1.38762:60:118:0.3278:0:2 0/1:283:87:44,43:86,109:195,87:0.3074:2,2:24.6:1:29.1:1:0.36552:1.30:60:28:0.3:0:1.3 +6 25727517 . G A 82 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12159;SOR=6.31813;LSEQ=ACTAAGTACACCAGCTCCAA;RSEQ=TAAGCCTGCTAAGTAAACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:1:0,1:9,16:25,1:0.0385:2,0:36:0:32:0:1:0:60:2:0.0385:0:1 0/1:34:7:4,3:12,15:27,7:0.2059:2,2:34.1:1:29.4:1:0.68146:1.64:60:14:0.2059:0:1.3 +6 25727527 . T A 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27677;SOR=0.36841;LSEQ=CCAGCTCCAAGTAAGCCTGC;RSEQ=AAGTAAACGTCATTTCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:1,5:8,13:21,6:0.2222:2,2:28:1:31.5:1:0.62785:2.96583:60:12:0.2222:0:1.2 0/1:32:3:1,2:13,16:29,3:0.0938:2,2:37.7:1:29:1:1:1.60139:60:6:0.0938:0:1 +6 25732302 . G C 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTTTGCGGCATCTCTT;RSEQ=CGCTTTTTGTCCTCCTTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:36.5:1:33.5:1:1:0:60:4:0.3333:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 25732331 . A G 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCTCCTTCGAGTTTTAGC;RSEQ=ACTGCCTTCTTAAAGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:8.7:1:28.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 25795460 . A T 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51342;SOR=0;LSEQ=CAACCAGGTAAACAAAGGAG;RSEQ=ATGGAGGAAATTCTACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:103,39:142,2:0.0139:2,2:20.5:1:24:0:0.4798:2.62044:60:4:0.0139:0:4.5 0/0:101:0:0,0:75,26:101,0:0:2,0:24.5:1:28.3:1:1:0:60:32.667:1:0:0.1 +6 25795577 . A T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00301;SOR=1.9361;LSEQ=TTGATATTTTGGAAGGAGAA;RSEQ=AAAAGCAGAAAAAGAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:41:15,26:107,134:241,41:0.1454:2,2:26.6:1:29:1:0.39658:1.38251:60:40:0.1429:0:1.1 0/1:250:62:28,34:83,105:188,62:0.248:2,2:24.4:1:28.4:1:1:1.04:60:124:0.249:0:1 +6 25795612 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.50043;SOR=0;LSEQ=AATATAGCATGTAAATAGAA;RSEQ=AAATGAACACATTTTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:60,133:193,2:0.0103:2,2:30.5:1:31.5:1:0.52889:2.21:60:4:0.0104:0:1 0/0:173:0:0,0:61,112:173,0:0:2,0:25.9:1:30:1:1:0:60:172:1:0:0.3 +6 25795614 . A T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.222;SOR=Inf;LSEQ=TATAGCATGTAAATAGAAAA;RSEQ=ATGAACACATTTTCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:60,128:188,0:0:2,0:24.4:1:31.1:1:1:0:60:376:1:0:0.3 0/1:168:2:1,1:59,107:166,2:0.0119:2,2:10.5:1:26.5:1:1:1.81:60:4:0.0119:0:1 +6 25795682 . C A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51489;SOR=0;LSEQ=ATTTAAAATATTCTACAAAT;RSEQ=TAAATTGCTAGAGTCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:5,50:55,2:0.0351:2,2:6.5:1:28.5:1:0.20113:9.22:60:4:0.0357:0:1.5 0/0:38:0:0,0:4,34:38,0:0:2,0:20:1:31.9:1:1:0:60:76:1:0:0.1 +6 26020431 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGCTGAGGCGGGAAGATC;RSEQ=TTTGAGCCCAAGTTTAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:12,0:12,3:0.2:0,0:19.3:1:31.3:1:1:0:60:6:0.2:0:1 0/0:3:0:0,0:2,1:3,0:0:2,0:17.3:1:30.7:1:1:0:60:6:1:0:0.3 +6 26021044 . C T 219 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=95.16819;LSEQ=GGGCTATTTGAGGACACTAA;RSEQ=CTGTGCGCCATCCACGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2983:2:0,2:1566,1413:2979,2:7e-04:2,0:1:0:28:1:0.22523:0:60:4:7e-04:0:1 0/1:3031:182:95,87:1483,1360:2843,182:0.06:2,2:21.6:1:29.3:1:1:1.00:58.1:90:0.06:0:1.2 +6 26021124 . C T 200 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=33.31921;LSEQ=CCGCATCCGCGGAGAGAGGG;RSEQ=GTGATTACTGTGGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2519:4:0,4:1030,1479:2509,4:0.0016:2,0:1:0:27:1:0.1492:0:60:8:0.0016:0:1 0/1:2405:121:54,67:1006,1274:2280,121:0.0503:2,2:25.9:1:29:1:0.92538:1.02:59.4:120:0.0506:0:1.2 +6 26021147 . C T 183 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=87.8035;LSEQ=GATTACTGTGGTCTCTCTGA;RSEQ=GGTCCAAGCAAAGGCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1994:1:0,1:680,1313:1993,1:5e-04:2,0:12:0:32:0:1:0:60:2:5e-04:0:1 0/1:1776:75:23,52:624,1074:1698,75:0.0422:2,2:22.8:1:29.4:1:0.32743:1.31337:60:150:0.0425:0:1.1 +6 26021327 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11453;SOR=2.09587;LSEQ=GCCTGTAATTCAAGCACTTT;RSEQ=AGAGGCTGAGGCGGGCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:21:0,21:0,56:56,21:0.2692:1,1:25.6:1:31:1:1:0:59.9:20:0.2597:0:1 0/1:32:14:0,14:0,18:18,14:0.4375:1,1:15.3:1:30.2:1:1:0:59.8:28:0.4375:0:1.3 +6 26021456 . C G 51 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAGCGCTTGTAATCCCAG;RSEQ=TACACTCTGAAGGCTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:0,3:0,8:8,3:0.2727:0,0:23.3:1:32.3:1:1:0:60:6:0.2727:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 26026599 . G C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.71703;SOR=0.95443;LSEQ=TAACCGCCAGTCCTACTCCA;RSEQ=AGAAGGGGGAGGTGACGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:193:74,119:211,325:536,193:0.2644:2,2:26.2:1:32.6:1:0.86346:1.04398:60:386:0.2673:0:1.2 0/1:693:177:74,103:215,298:513,177:0.2554:2,2:25.9:1:31.3:1:1:1.00421:60:176:0.2577:0:1.2 +6 26031613 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTAATCATAGCAAGCTA;RSEQ=AGGCCTGAATGATAGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:2,0:25,0:25,2:0.0741:1,0:9:1:31:1:1:0:60:4:0.0741:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:15.5:1:30.5:1:1:0:60:4:1:0:0 +6 26031720 . C G 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00441;SOR=0;LSEQ=AAACCGTTATTTCTGTTAAT;RSEQ=AACTTTAAGACCATAGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:14:14,0:61,0:61,14:0.1842:1,1:22.7:1:31.6:1:1:0:60:13:0.1757:0:1.1 0/0:36:0:0,0:36,0:36,0:0:1,0:24.4:1:30.9:1:1:0:59.1:35:1:0:0.2 +6 26031855 . C T 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGCCTTTGGGTTTTAAGA;RSEQ=TGATGAAAAAGTGACTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:791:0:0,0:594,197:791,0:0:2,0:23.3:1:32.5:1:1:0:60:130.833:1:0:0.4 0/1:770:37:26,11:539,194:733,37:0.0481:2,2:22:1:29.6:1:0.7034:1.17517:60:36:0.0471:0:2.2 +6 26031868 . G A 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.07375;LSEQ=TTTAAGACTGATGAAAAAGT;RSEQ=ACTTTACATTTACGCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1005:362:250,112:456,187:643,362:0.3602:2,2:23.7:1:29:1:0.56547:1.09235:60:180:0.3604:0:1.1 1/0:1004:777:534,243:159,63:222,777:0.7739:2,2:23.6:1:28.2:1:0.45758:1.14828:59.9:128.5:0.7749:0:1.2 +6 26032428 . T A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.67499;SOR=1.71993;LSEQ=GCCCTTCTTGGATTGGTCCA;RSEQ=CTCTGTGCCTGGTTGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:5:0,5:2,50:52,5:0.0877:1,0:24.8:1:30.4:1:1:0:60:10:0.0877:0:1 0/1:21:3:0,3:3,15:18,3:0.1429:2,0:33:1:31.3:1:1:0:60:6:0.1579:0:1 +6 26032847 . G C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTTATCACGCCGCTGCACT;RSEQ=CAGCTTGGGCGAGAGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:11:0:33:0:1:0:60:2:0.5:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:31:1:1:0:60:4:1:0:2 +6 26036092 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07692;SOR=0;LSEQ=CACTCCAGCCTGGGCAAGAG;RSEQ=GAAACTCCATTTCAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:14.3:1:30.7:1:1:0:53:6:0.4286:0:1.7 0/0:8:0:0,0:6,2:8,0:0:2,0:23.4:1:28:1:1:0:51.6:7:1:0:0.6 +6 26036105 . CAA C 75 MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=20.000;MSILEN=1;SSF=0.35753;SOR=0.24661;LSEQ=GCAAGAGCGAAACTCCATTT;RSEQ=AAAAAAAAAAAAAAAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:5,0:8,0:8,5:0.2778:0,0:10.2:1:32.5:1:1:0:58.8:10:0.2778:0.1667:0.4 0/1:12:1:1,0:6,1:7,1:0.0833:2,0:29:0:33:0:1:0:41:2:0.0833:0:0 +6 26036476 . T C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=8.68466;LSEQ=AGCAGTGCACGTTCTGCATA;RSEQ=AAAATAAAGATTTTGAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:50:8,42:14,91:105,50:0.3226:2,2:20.9:1:32.4:1:0.63227:1.24:60:100:0.3247:0:1 1/1:119:96:14,82:3,20:23,96:0.8067:2,2:23.9:1:31.3:1:1:1.14:60:95:0.8051:0:1.1 +6 26043661 . C T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.55701;LSEQ=GCCAGGCGAGAAGCCTCGCC;RSEQ=GCGATGCGCTCGAAGATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:0,2:134,64:198,2:0.01:2,0:22.5:1:28:1:0.10779:0:23.5:4:0.0102:0:1 0/0:179:1:0,1:118,60:178,1:0.0056:2,0:34:0:32:0:0.34078:0:33:2:0.0057:0:1 +6 26043670 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11202;SOR=Inf;LSEQ=GAAGCCTCGCCCGCGATGCG;RSEQ=TCGAAGATGTCGTTGACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:146,85:231,0:0:2,0:25.6:1:32.3:1:1:0:55.4:37.5:1:0:0.1 0/1:216:3:1,2:135,78:213,3:0.0139:2,2:9.7:1:27.3:1:0.55662:3.44086:31.7:6:0.014:0:1 +6 26043834 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16104;SOR=Inf;LSEQ=CTTCTGCGCCTTAGTGATAG;RSEQ=CTTCTTAGAACCCTTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:64,74:138,0:0:2,0:25.6:1:31.5:1:1:0:60:45:1:0:0 0/1:93:2:1,1:34,57:91,2:0.0215:2,2:17:1:27:1:1:1.67:60:4:0.022:0:1 +6 26044064 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.21219;LSEQ=GGTGGGGTTTATGCAAATAT;RSEQ=GAATTTATGTTATCTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:53:17,36:260,356:616,53:0.079:2,2:25.9:1:30.7:1:0.19059:1.54562:60:52:0.0785:0:1.2 0/1:674:179:74,105:216,277:493,179:0.2656:2,2:24.4:1:28.7:1:0.59763:1.10628:60:88.5:0.2662:0:1.1 +6 26044155 . A C 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0441;SOR=Inf;LSEQ=CAGCCTTGCAGTTTGTATAA;RSEQ=AGGATTTGTTCAGGCGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:15,144:159,0:0:2,0:23:1:31.1:1:1:0:60:78.5:1:0:0.1 0/1:136:4:0,4:18,114:132,4:0.0294:2,0:16:1:32:1:1:0:60:8:0.0296:0:2 +6 26044174 . A G 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03679;SOR=Inf;LSEQ=AAAGGATTTGTTCAGGCGCC;RSEQ=TTCCAGCTTGCTTGTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:6,105:111,0:0:2,0:24.4:1:31.4:1:1:0:60:110:1:0:0.1 0/1:88:4:0,4:6,78:84,4:0.0455:2,0:21.5:1:32.5:1:1:0:60:8:0.0465:0:1.8 +6 26044729 . T C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTTTTGAGACAGTCTAG;RSEQ=TCTGTCACCCAGGCTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:18.3:1:33.7:1:1:0:60:6:0.4286:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:26:0:31:0:1:0:41:2:1:0:0 +6 26044812 . T A 49 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.59564;LSEQ=CTTCACGCGGTTCTCATGCC;RSEQ=CAGCCTCCTGTGTACTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:21.3:1:31.3:1:1:0:60:6:0.375:0:1.3 1/0:4:2:2,0:2,0:2,2:0.5:0,0:17:1:23.5:1:1:0:58.5:1:0.3333:0:3.5 +6 26044956 . C CA 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00394;SOR=Inf;LSEQ=ATCGTCCCATCTCGCCCTCC;RSEQ=AAAATGCTGGGATTACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:154,40:194,0:0:2,0:22.6:1:31.3:1:1:0:59.9:96:1:0:0.1 0/1:164:7:6,1:119,37:156,7:0.0427:2,2:20.7:1:29.7:1:1:1.86:60:14:0.0427:0.0122:0.3 +6 26044967 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21427;SOR=Inf;LSEQ=TCGCCCTCCCAAAATGCTGG;RSEQ=ATTACAGGCGTGAGCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:166,62:228,0:0:2,0:23.4:1:31.2:1:1:0:59.9:56:1:0:0.1 0/1:197:2:1,1:140,55:195,2:0.0102:2,2:8.5:1:26.5:1:0.48876:2.53163:60:4:0.0104:0:1 +6 26044975 . G T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02539;SOR=Inf;LSEQ=CCAAAATGCTGGGATTACAG;RSEQ=CGTGAGCCACCGCCCCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:179,77:256,0:0:2,0:24.3:1:31:1:1:0:59.9:31:1:0:0.1 0/1:238:5:1,4:161,72:233,5:0.021:2,2:9.4:1:27.6:1:0.0371:8.85817:59.2:10:0.0214:0:1 +6 26044987 . G GC 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00063;SOR=Inf;LSEQ=GATTACAGGCGTGAGCCACC;RSEQ=CCCCCCTAGCCTAATGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:212,106:318,0:0:2,0:24.8:1:30.6:1:1:0:60:78.5:0.9968:0:0.1 0/1:297:10:6,4:181,104:285,10:0.0337:2,2:21.1:1:30.4:1:1:1.15965:60:20:0.0342:0.0067:0.1 +6 26045737 . C G 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTAAGAGCGCTCCGGCCAC;RSEQ=GGTGGCGTGAAGAAACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2294:0:0,0:1179,1111:2290,0:0:2,0:24.4:1:30.7:1:1:0:59.8:103.091:0.9987:0:0.1 0/1:2095:87:46,41:985,1014:1999,87:0.0415:2,2:22.8:1:30:1:0.51376:1.15:59.3:174:0.0419:0:1.1 +6 26045905 . G C 216 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCGTTTCCAGAGCTCTGC;RSEQ=GTGATGGCGCTGCAGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2636:0:0,0:1329,1305:2634,0:0:2,0:25:1:30.6:1:1:0:57.7:83.968:0.9992:0:0.4 0/1:2516:171:84,87:1158,1184:2342,171:0.068:2,2:23.9:1:29.2:1:0.93707:1.01297:54:41.75:0.0672:0:1.9 +6 26045929 . T C 329 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=6.5983;LSEQ=ATGGCGCTGCAGGAGGCTTG;RSEQ=GAGGCCTACCTGGTGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2630:914:449,465:857,857:1714,914:0.3475:2,2:26.1:1:31:1:0.6822:1.03564:56.8:59.933:0.3444:0:1.1 1/0:2398:1867:916,951:270,252:522,1867:0.7786:2,2:25.2:1:30.3:1:0.2985:1.11232:55.7:97.263:0.7794:0:1.2 +6 26046158 . T C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12612;SOR=1.56716;LSEQ=ATGTTAGTTTCCAGGAGATA;RSEQ=AAAGGTGATAACTACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:31:0,31:4,247:251,31:0.1099:1,1:22.4:1:33.2:1:1:0:60:62:0.1111:0:1.1 0/1:191:31:1,30:4,156:160,31:0.1623:1,1:24.5:1:32:1:0.59173:1.30:60:62:0.164:0:1 +6 26046265 . T TA 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTACTGTTTTGCCCTTGT;RSEQ=AAAAAATTCCTAGGGGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:0,2:2,53:55,2:0.0351:1,0:22:1:33:0:1:0:60:4:0.0351:0:0 0/0:9:0:0,0:0,9:9,0:0:0,0:22.6:1:29:1:1:0:60:18:1:0:0.1 +6 26046565 . G A 43 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATAGATTTATGTAACAA;RSEQ=TACACAAGACTTGCGTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:26:1:27.3:1:1:0:60:2:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 26049819 . A C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACACACCAGATTTCAAAGA;RSEQ=CTAGTAAAATAACAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:32.5:1:31.5:1:1:0:60:4:0.25:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:18:1:30.5:1:1:0:60:4:1:0:0 +6 26049924 . T C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68166;SOR=1.95409;LSEQ=ATTAAAATAGATTTCTTTTT;RSEQ=CACTTTTTAAAATGTGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:10,0:12,0:12,10:0.4545:0,0:24.2:1:32.7:1:1:0:60:20:0.4545:0:1 1/0:8:5:5,0:3,0:3,5:0.625:0,0:23.2:1:31.2:1:1:0:60:10:0.625:0:1 +6 26050295 . GT CC 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.23946;LSEQ=TGTAGTTTTCATCAGTATGT;RSEQ=ATGTTCAAATGGAGATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:48:1,47:3,85:88,48:0.3453:1,1:23.7:1:32.5:1:1:1.65316:59.3:96:0.3478:0.0288:0.9 1/0:117:81:6,75:2,29:31,81:0.6923:2,2:19.6:1:31.1:1:1:1.16:59.6:80:0.6957:0.1282:0.9 +6 26055865 . G GTC 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.57326;SOR=0.41067;LSEQ=CCAACCCCGTCACCCAATTC;RSEQ=TCTGATACCTCAGTAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:25:24,1:2,0:2,25:0.9259:0,1:29.2:1:31.1:1:1:0:60:50:0.9259:0.037:0 1/1:12:10:9,1:2,0:2,10:0.8333:0,2:21.1:1:30.3:1:1:0:59.5:20:0.8333:0.25:0.6 +6 26055962 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59606;SOR=2.36256;LSEQ=TTATCCAGCTCTTTTATTGA;RSEQ=ATCAGTGGTGGCTCTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:1:1,0:157,36:193,1:0.0052:2,0:22:0:14:0:1:0:60:0:0:0:1 0/1:165:2:1,1:127,36:163,2:0.0121:2,2:12:1:27.5:1:0.39926:3.49328:60:4:0.0123:0:1 +6 26055968 . TG T 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22497;SOR=Inf;LSEQ=AGCTCTTTTATTGAGATCAG;RSEQ=GTGGCTCTGAAAAGAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:173,47:220,0:0:2,0:25.5:1:32.1:1:1:0:59.8:54:1:0:0.1 0/1:199:2:1,1:143,50:193,2:0.0101:2,2:19:1:33:0:0.45567:2.84171:60:4:0.0103:0:0.5 +6 26056065 . C T 67 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21731;SOR=0.20161;LSEQ=CTTGACAACCTTGGGCTTAG;RSEQ=GGCCTTGGGCTTCACAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:5:2,3:278,183:461,5:0.0107:2,2:22.8:1:29.2:1:0.3924:2.27457:60:10:0.0109:0:1 0/0:459:1:0,1:261,197:458,1:0.0022:2,0:1:0:24:0:0.43137:0:60:2:0.0022:0:2 +6 26056072 . G C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.94761;LSEQ=ACCTTGGGCTTAGCGGCCTT;RSEQ=GGCTTCACAGCCTTAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:23:10,13:281,191:472,23:0.0465:2,2:29.3:1:31.8:1:0.13471:1.91003:60:46:0.0482:0:1 0/1:465:130:74,56:192,141:333,130:0.2796:2,2:26.3:1:29.6:1:0.91688:1.03043:60:64:0.2783:0:1.1 +6 26056399 . G A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGTGCCCTTGCTCACCAG;RSEQ=CTCTTGAGACCAAGTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:0:0,0:230,362:592,0:0:2,0:27.2:1:32.1:1:1:0:59.8:64.778:0.9966:0:0.1 0/1:567:26:12,14:238,303:541,26:0.0459:2,2:22.8:1:28.8:1:0.84232:1.09:60:52:0.0465:0:1.3 +6 26056477 . A C 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCAACGCTTTTTTCAGAGC;RSEQ=GCCAGAGAAACTCCGCTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:162,185:347,0:0:2,0:23.8:1:31:1:1:0:60:56.833:1:0:0.2 0/1:316:17:12,5:130,169:299,17:0.0538:2,2:25.5:1:29.9:1:0.04262:3.11:60:34:0.054:0:1.5 +6 26056541 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.05602;SOR=0;LSEQ=TGGTGATGAGCTCTGACACC;RSEQ=GGGGACCAGACGCCTTACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:4:2,2:145,186:331,4:0.0119:2,2:18.3:1:25.5:1:1:1.28:60:3:0.0091:0:1.8 0/0:352:0:0,0:164,187:351,0:0:2,0:23.7:1:29.5:1:1:0:60:57.5:1:0:0.8 +6 26056549 . A G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.66326;LSEQ=AGCTCTGACACCGGGGGACC;RSEQ=GACGCCTTACGAGGCGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:107:48,59:102,132:234,107:0.3129:2,2:24.7:1:30.5:1:0.90646:1.05:60:52.5:0.3144:0:1.1 1/0:355:256:121,135:41,58:99,256:0.7211:2,2:24.9:1:29.2:1:0.34344:1.27:59.9:84.333:0.7208:0:1.2 +6 26056637 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=GAGGCGCGGCAGCGGGAGCG;RSEQ=CAGGAGCAGTCTCGGACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:54,134:188,2:0.0105:2,2:25:1:30.5:1:0.49624:2.47:60:4:0.0106:0:1 0/0:176:0:0,0:60,116:176,0:0:2,0:22.7:1:30.9:1:1:0:60:175:1:0:0.3 +6 26056646 . G A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10606;SOR=Inf;LSEQ=CAGCGGGAGCGGCAGGAGCA;RSEQ=TCTCGGACATGTTGAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:43,125:168,0:0:2,0:24.8:1:32.1:1:1:0:60:55:1:0:0.1 0/1:152:3:3,0:49,100:149,3:0.0197:2,0:14:1:21.3:1:0.03852:0:60:2:0.0134:0:1.7 +6 26056708 . C T 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00026;SOR=7.60176;LSEQ=AAAGCGCCGATGAAGCAGCG;RSEQ=CTGGGCAGGGCCGCTGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:4:0,4:6,54:60,4:0.0625:2,0:28:1:30.8:1:1:0:60:8:0.0656:0:1 0/1:44:15:3,12:8,21:29,15:0.3409:2,2:29.4:1:28.1:1:0.72221:1.50978:60:14:0.3333:0:1.1 +6 26061649 . CT C 85 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.02757;SOR=8.30143;LSEQ=CCTGGCTTCAGCCCCATAAA;RSEQ=TTTTTTTAACATATAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:602:1:0,1:181,419:600,1:0.0017:2,0:17:0:35:0:1:0:60:2:0.0017:0:0 0/1:513:7:3,4:160,345:505,7:0.0136:2,2:16.6:1:30.3:1:0.68483:1.62:59.7:14:0.0139:0.0039:0.3 +6 26061769 . G C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00056;SOR=6.53198;LSEQ=CTCACCTCAAGGGCTGAGAC;RSEQ=AAAGTTACTGCATCTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:21:1,20:0,37:37,21:0.3621:1,1:25.6:1:32.4:1:0.36207:0:60:42:0.3621:0:1.1 1/0:24:19:0,19:0,5:5,19:0.7917:0,1:19.3:1:31.4:1:1:0:60:18:0.7826:0:1.1 +6 26065976 . AAC A 85 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.2089;SOR=0.39122;LSEQ=TTGTAAACCACATTCCCTTA;RSEQ=ACACACACACCTCAAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:683:7:5,2:453,222:675,7:0.0102:2,2:25.9:1:30.6:1:1:1.22:60:14:0.0103:0.0029:0 0/0:744:3:3,0:446,295:741,3:0.004:2,0:13.3:1:27.6:1:0.28117:0:60:6:0.0041:0.0027:0 +6 26066088 . TA T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.85906;SOR=1.09153;LSEQ=TTGTGTATTAATCTGTGAAC;RSEQ=AAAAAAAATTTCATTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:731:16:8,8:251,463:714,16:0.0219:2,2:27.6:1:31.5:1:0.29:1.84:60:32:0.0221:0.0014:0.1 0/1:671:16:6,10:263,392:655,16:0.0238:2,2:25.1:1:29.3:1:1:1.11804:60:15:0.0226:0.003:0.3 +6 26066198 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12649;SOR=1.7094;LSEQ=TTAACTTTTAGATTTTTCAA;RSEQ=GCTAGCAGAACTGCTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:22:1,21:3,71:74,22:0.2292:1,1:23.8:1:32:1:1:1.13:60:44:0.2292:0:1 0/1:77:26:0,26:1,50:51,26:0.3377:1,1:21.2:1:30.7:1:1:0:60:52:0.3377:0:1 +6 26123539 . G C 52 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACAACGAATTGACCCCAAA;RSEQ=CCATTTTTAATGGCTGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:29.3:1:32.3:1:1:0:60:6:0.75:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:25:1:33:1:1:0:60:6:1:0:1.7 +6 26123629 . T C 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19794;SOR=2.68522;LSEQ=CCACCCCTCTCCAGTTCCTA;RSEQ=ATTCTAATACCCCTCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:17:17,0:10,0:10,17:0.6296:0,1:16.8:1:32.1:1:1:0:59.9:34:0.6538:0:1.1 1/1:17:14:14,0:3,0:3,14:0.8235:0,1:23.8:1:30.8:1:1:0:60:13:0.8125:0:1.1 +6 26123737 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09537;SOR=0;LSEQ=TTGGGGTTAGGTGTTAAGAC;RSEQ=CTTACTTGGAATGTTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:153,92:245,3:0.012:2,2:32.7:1:28.3:1:0.55906:3.30948:55.3:6:0.0124:0:1 0/0:296:0:0,0:178,116:294,0:0:2,0:26:1:29.5:1:1:0:55.5:48:0.9931:0:0.2 +6 26123802 . C A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12755;SOR=Inf;LSEQ=CTTGGTGCCCTCCGACACGG;RSEQ=GTGCTTGGCCAGCTCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:94,124:218,0:0:2,0:25.9:1:30.6:1:1:0:41.5:71.667:1:0:0.1 0/1:253:4:3,1:112,136:248,4:0.0158:2,2:30.5:1:25:1:0.33392:3.63:33.8:3:0.0122:0:1.3 +6 26123809 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12404;SOR=Inf;LSEQ=CCCTCCGACACGGCGTGCTT;RSEQ=GCCAGCTCTCCGGGAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:81,107:188,0:0:2,0:23.8:1:31.5:1:1:0:39.7:46:0.9946:0:0.1 0/1:205:4:3,1:87,114:201,4:0.0195:2,2:18.3:1:25:1:0.32159:3.91:40:8:0.0202:0:1 +6 26124018 . A T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59962;SOR=2.30974;LSEQ=CACCTTGTACACGTACACAG;RSEQ=GTAACTCTCCTTGCGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:0,1:111,95:206,1:0.0048:2,0:1:0:27:0:0.46377:0:60:2:0.005:0:1 0/1:180:2:1,1:106,72:178,2:0.0111:2,2:17:1:26.5:1:1:1.46895:60:4:0.0112:0:1 +6 26124032 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50159;SOR=0;LSEQ=ACACAGAGTAACTCTCCTTG;RSEQ=GGCTGCGCTTGCGCTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:100,94:194,2:0.0102:2,2:23.5:1:30:1:1:1.06353:55.5:4:0.0105:0:1 0/0:168:0:0,0:98,70:168,0:0:2,0:27:1:30.6:1:1:0:59.4:336:1:0:0.1 +6 26124046 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49883;SOR=0;LSEQ=TCCTTGCGGCTGCGCTTGCG;RSEQ=TTCTTGCCATCTTTCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:92,95:187,2:0.0106:2,2:20.5:1:29.5:1:1:1.03:60:4:0.0108:0:1 0/0:182:0:0,0:94,88:182,0:0:2,0:24.7:1:31.2:1:1:0:59.5:90:1:0:0.1 +6 26124243 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00386;SOR=0.08541;LSEQ=AGTTAATTGGAAGACAAACT;RSEQ=CACAGTTGTCATCCGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:0,14:1,5:6,14:0.7:2,1:26.1:1:31.1:1:0.3:0:60:28:0.7:0:1 0/1:13:2:0,2:0,11:11,2:0.1538:0,0:23:1:31:0:1:0:60:4:0.1538:0:1 +6 26124303 . T C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02424;SOR=Inf;LSEQ=ATGAAAGTACAGCTTTTCTA;RSEQ=TGGCTATCTGACTAGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:18.7:1:31.1:1:1:0:60:14:1:0:0.3 1/0:4:3:0,3:0,1:1,3:0.75:0,0:12.7:1:32.7:1:1:0:60:6:0.75:0:1 +6 26127759 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00027;SOR=0.56507;LSEQ=AGCATAGAACTTGGCATACA;RSEQ=GAGACACTTGGCTGTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:344:217:163,54:95,32:127,217:0.6308:2,2:24.2:1:32.5:1:1:1.02:60:107.5:0.6287:0:1.1 0/1:334:164:118,46:119,51:170,164:0.491:2,2:24:1:31.2:1:0.71881:1.10:59.9:81:0.4954:0:1.1 +6 26127813 . CT C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00645;SOR=1.38467;LSEQ=TGAACTGAATGAATCAATGA;RSEQ=TAGGCAGCCAGGAAGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:683:433:232,201:127,121:248,433:0.634:2,2:26.4:1:32.4:1:0.57702:1.10:59.9:143.333:0.6333:0.101:0.4 1/0:605:427:224,203:100,78:178,427:0.7058:2,2:25.8:1:31:1:0.4217:1.16157:59.9:854:0.7093:0.1041:0.4 +6 26128007 . G GGT 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.08403;SOR=Inf;LSEQ=GAGGTGGGTAGATCACCTGA;RSEQ=GTCAGGAGTTTGAGACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:7,102:109,0:0:2,0:22.9:1:32.1:1:1:0:47.9:218:1:0:0 0/1:45:2:0,2:2,41:43,2:0.0444:1,0:37:1:32:1:1:0:54.5:4:0.0455:0:0 +6 26128226 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCGACAAAGTGAAACTC;RSEQ=GTCTCAAAAAAAAACCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:10.5:1:28.5:1:1:0:42:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 26128632 . C A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCTAAGCAAAGGACATT;RSEQ=CTCGTAGCTCTGTCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:30.5:1:1:0:46:4:1:0:1.5 +6 26153159 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07848;SOR=Inf;LSEQ=CCAATATATGGTCATATTCA;RSEQ=CATGGATATCTTTTCTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:88,294:382,0:0:2,0:22:1:32.4:1:1:0:59.9:75.4:1:0:0.1 0/1:287:3:2,1:71,213:284,3:0.0105:2,2:18.7:1:26.3:1:0.1602:5.95:60:6:0.0106:0:1 +6 26156918 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50056;SOR=Inf;LSEQ=GTGCAGACCAAGGGCACCGG;RSEQ=GCGTCGGGTTCCTTCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:32,63:95,0:0:2,0:27:1:30.2:1:1:0:59.9:46.5:1:0:0.1 0/1:112:2:1,1:43,67:110,2:0.0179:2,2:5.5:1:27.5:1:1:1.55:60:4:0.0187:0:1 +6 26156981 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=GAAGCCAAGCCTAAGGCTAA;RSEQ=AAGGCAGGCGCGGCCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:6,21:27,0:0:2,0:23.4:1:31.3:1:1:0:60:54:1:0:0 0/1:28:3:0,3:2,23:25,3:0.1071:2,0:27.7:1:31:1:1:0:60:6:0.1111:0:1 +6 26158328 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18817;SOR=Inf;LSEQ=TGAATACCGCATCTATAAAT;RSEQ=AACAGGGCCTCGGCGGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:166,20:186,0:0:2,0:22.3:1:32.5:1:1:0:59.9:92:1:0:0.1 0/1:143:2:1,1:118,22:140,2:0.014:2,2:23.5:1:25:1:0.29867:5.26803:60:4:0.0142:0:1 +6 26158562 . C T 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTCCATCCCGACACCGGCAT;RSEQ=TCTTCCAAGGCAATGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:268,331:599,0:0:2,0:26.9:1:32.6:1:1:0:56.1:65.556:1:0:0.1 0/1:622:65:28,37:251,306:557,65:0.1045:2,2:24.8:1:29.6:1:0.79335:1.08381:43.8:64:0.1036:0:1.2 +6 26158615 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05888;SOR=Inf;LSEQ=CGTCAACGACATCTTCGAGC;RSEQ=CATCGCAGGCGAGGCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:130,196:326,0:0:2,0:24.5:1:31.6:1:1:0:53.8:325:1:0:0.2 0/1:318:4:1,3:128,184:312,4:0.0126:2,2:24.5:1:29.3:1:0.64776:2.08256:47.3:8:0.0127:0:1 +6 26158636 . G A 30 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61324;SOR=0.46975;LSEQ=CATCGCAGGCGAGGCTTCCC;RSEQ=CCTGGCGCATTACAACAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:71,94:165,2:0.012:2,2:7.5:1:30:1:1:1.32:48.5:4:0.0125:0:1 0/0:177:1:1,0:75,101:176,1:0.0056:2,0:1:0:25:0:0.42938:0:22:2:0.0057:0:1 +6 26158643 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49801;SOR=Inf;LSEQ=GGCGAGGCTTCCCGCCTGGC;RSEQ=CATTACAACAAGCGCTCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:53,72:125,0:0:2,0:14.7:1:31:1:1:0:54.1:40.667:1:0:0.2 0/1:126:2:1,1:46,78:124,2:0.0159:2,2:7.5:1:27:1:1:1.69:33:4:0.0161:0:1 +6 26158690 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50043;SOR=Inf;LSEQ=CTCCAGGGAGATCCAGACGG;RSEQ=CGTGCGCCTGCTGCTTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:59,30:89,0:0:2,0:12:1:31.6:1:1:0:33.5:43.5:1:0:0.1 0/1:104:2:0,2:63,39:102,2:0.0192:2,0:7:1:27.5:1:0.1531:0:28.5:4:0.0196:0:1 +6 26158993 . T C 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9643;LSEQ=TAGAAATTGAGTGCTATGGG;RSEQ=ACGTATTAGATCGTTAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:13,3:0.1875:1,0:18.3:1:33:1:1:0:60:6:0.1875:0:1 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:16.5:1:32:1:1:0:60:4:0.1818:0:1 +6 26165446 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGGGAATCCGAAATACC;RSEQ=AAATGTCTGTTTTCCACGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:38.5:1:30:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 26172150 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19012;SOR=Inf;LSEQ=TCAACCCTCGCCAAAAACGC;RSEQ=GGCCCCCTCATAGGGCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:43,184:227,0:0:2,0:24.1:1:30.3:1:1:0:60:44.4:1:0:0.1 0/1:176:2:1,1:39,134:173,2:0.0114:2,2:36.5:1:30:1:0.40591:3.41:60:4:0.0116:0:1.5 +6 26172219 . C T 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.39779;SOR=2.07787;LSEQ=AGAGCCACACGTTACGCCGC;RSEQ=GCCCCGTTACGCCCATCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:0,3:3,64:67,3:0.0429:1,0:16:1:32:0:1:0:60:6:0.0441:0:1 0/1:35:3:0,3:1,31:32,3:0.0857:1,0:30:1:30:1:1:0:60:6:0.0857:0:1 +6 26184082 . C G 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01378;SOR=Inf;LSEQ=GGGCTCCAAGAAGGCCGTGA;RSEQ=CAAGGCGCAGAAGAAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:83,57:140,0:0:2,0:28.8:1:31.5:1:1:0:42.2:27:1:0:0.2 0/1:106:5:4,1:55,46:101,5:0.0472:2,2:42.2:1:29.6:1:0.37946:3.31:49:10:0.0481:0:1 +6 26184086 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18164;SOR=Inf;LSEQ=TCCAAGAAGGCCGTGACCAA;RSEQ=GCGCAGAAGAAGGACGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:81,57:138,0:0:2,0:29.6:1:32.3:1:1:0:41.9:68:1:0:0.2 0/1:103:2:1,1:56,45:101,2:0.0194:2,2:28.5:1:28.5:1:1:1.24178:22:4:0.0202:0:1 +6 26184098 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.178;SOR=Inf;LSEQ=GTGACCAAGGCGCAGAAGAA;RSEQ=GACGGCAAGAAGCGCAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:68,56:124,0:0:2,0:30.7:1:32.2:1:1:0:39.9:61:1:0:0.2 0/1:91:2:1,1:45,44:89,2:0.022:2,2:27.5:1:29.5:1:1:1.02248:44:4:0.0225:0:1 +6 26184102 . G A 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00894;SOR=3.84435;LSEQ=CCAAGGCGCAGAAGAAGGAC;RSEQ=GCAAGAAGCGCAAGCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:6:3,3:61,52:113,6:0.0504:2,2:21.2:1:28.8:1:1:1.1715:49:5:0.0435:0:1.7 0/1:88:15:7,8:36,37:73,15:0.1705:2,2:28.9:1:29.4:1:1:1.11063:41.5:14:0.1609:0:1.3 +6 26184183 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18367;SOR=0;LSEQ=AACAGGTCCACCCCGACACC;RSEQ=GCATCTCCTCTAAAGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:35,61:96,2:0.0204:2,2:26.5:1:30.5:1:1:1.73:20:4:0.0213:0:1.5 0/0:130:0:0,0:60,70:130,0:0:2,0:29.2:1:29.5:1:1:0:52:129:1:0:0.1 +6 26184188 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50422;SOR=Inf;LSEQ=GTCCACCCCGACACCGGCAT;RSEQ=TCCTCTAAAGCCATGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:40,67:107,0:0:2,0:28.9:1:31.6:1:1:0:53.7:25.75:1:0:0.1 0/1:134:2:1,1:60,72:132,2:0.0149:2,2:14:0:31:0:1:1.20:57:4:0.0152:0:1.5 +6 26184268 . C T 28 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49505;SOR=Inf;LSEQ=CGGCGAGGCTTCCCGCCTGG;RSEQ=GCATTACAACAAGCGCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:16,34:50,0:0:2,0:19.9:1:29.6:1:1:0:41:24:1:0:0.2 0/1:51:2:1,1:14,34:48,2:0.0392:2,2:5:0:28.5:1:0.51429:2.38:60:4:0.0392:0:1 +6 26184412 . C T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49782;SOR=Inf;LSEQ=CAGCTCCAAGTAAACTTGTC;RSEQ=CTGCAACTGCCTTAGTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:40,49:89,0:0:2,0:23.6:1:31:1:1:0:59.4:88:0.9888:0:0.1 0/1:96:2:1,1:36,57:93,2:0.0208:2,2:12:0:27.5:1:1:1.58:60:4:0.0213:0:1 +6 26197493 . C A 193 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=55.2242;LSEQ=AGCCATTGCGAACTTCTAAA;RSEQ=CCTGCTAAATGACGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1599:2:1,1:587,1010:1597,2:0.0013:2,2:17.5:1:30.5:1:1:1.72:60:4:0.0013:0:1 0/1:1637:106:41,65:601,930:1531,106:0.0648:2,2:26.3:1:28.7:1:1:1.02451:59.9:105:0.0648:0:1.2 +6 26198064 . A ACT 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTCATCCTCATATGAAAGC;RSEQ=CTCTTATCTTTTACAAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:32.5:1:33:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 26199822 . A G 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=AAGTCCGCTCCTGCTCCAAA;RSEQ=AAGGGCTCCAAAAAGGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:80,55:135,0:0:2,0:27.6:1:30.7:1:1:0:60:270:1:0:0.1 0/1:184:17:10,7:105,62:167,17:0.0924:2,2:25.6:1:31.4:1:0.79529:1.18436:59.2:34:0.0939:0:1.2 +6 26199887 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50054;SOR=Inf;LSEQ=TAAGAAGCGCAAGCGTAGCC;RSEQ=CAAGGAGAGCTATTCCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:91,86:177,0:0:2,0:24.9:1:30.9:1:1:0:58.3:58:1:0:0.1 0/1:200:2:1,1:95,103:198,2:0.01:2,2:37.5:1:28:1:1:1.08:28:4:0.0101:0:1.5 +6 26199903 . C T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=AGCCGCAAGGAGAGCTATTC;RSEQ=GTGTACGTGTACAAGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:89,84:173,0:0:2,0:26.9:1:30.8:1:1:0:57.9:172:1:0:0.1 0/1:180:13:6,7:71,96:167,13:0.0722:2,2:28.6:1:29.2:1:1:1.16:50.7:26:0.0722:0:1 +6 26199939 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50626;SOR=0;LSEQ=GTGCTAAAGCAGGTCCACCC;RSEQ=GACACCGGCATCTCATCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:91,97:188,2:0.0105:2,2:25:1:33:1:1:1.07:29:4:0.0106:0:1 0/0:148:0:0,0:60,87:147,0:0:2,0:24.3:1:28.8:1:1:0:56.6:23.5:0.993:0:0.3 +6 26200080 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06716;SOR=2.48071;LSEQ=TCCAGGGAGATCCAGACGGC;RSEQ=GTACGCCTGCTGCTGCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:9:6,3:56,37:93,9:0.0882:2,2:29.6:1:31.7:1:1:1.32:38:18:0.09:0:1.4 0/1:72:14:8,6:30,28:58,14:0.1944:2,2:22.1:1:29.6:1:0.7728:1.24:39.2:28:0.1972:0:1.1 +6 26200083 . A G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00115;SOR=6.89088;LSEQ=AGGGAGATCCAGACGGCCGT;RSEQ=CGCCTGCTGCTGCCCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:2,1:63,43:106,3:0.0275:2,2:15.3:1:32:1:1:1.36:25:6:0.0278:0:1 0/1:79:13:7,6:34,31:65,13:0.1646:2,2:16.1:1:28:1:1:1.06:28.6:5.5:0.1429:0:1.1 +6 26200106 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21268;SOR=Inf;LSEQ=CCTGCTGCTGCCCGGGGAGC;RSEQ=GGCTAAGCACGCCGTGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:89,80:169,0:0:2,0:23.8:1:31:1:1:0:57.9:83.5:1:0:0.2 0/1:146:2:1,1:75,69:144,2:0.0137:2,2:12.5:1:28:1:1:1.08632:60:4:0.0139:0:1 +6 26200117 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49875;SOR=0;LSEQ=CCGGGGAGCTGGCTAAGCAC;RSEQ=CCGTGTCAGAGGGCACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:97,90:187,2:0.0106:2,2:38.5:1:31:1:1:1.07733:27:4:0.011:0:2 0/0:184:0:0,0:95,89:184,0:0:2,0:24.3:1:29.7:1:1:0:54.9:35.8:1:0:0.3 +6 26200175 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23301;SOR=0;LSEQ=CAGCTCTAAGTAATTCTAAC;RSEQ=TCTTCATACCCAATCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:67,106:173,2:0.0114:2,2:31.5:1:32:1:1:1.58:60:4:0.0115:0:1 0/0:187:0:0,0:85,102:187,0:0:2,0:25.3:1:29.5:1:1:0:59.1:22.375:1:0:0.2 +6 26200215 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.229;SOR=Inf;LSEQ=AGGCTCTTTTAAGAGCCACC;RSEQ=ACTTTTTCAGCTATAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:20,59:79,0:0:2,0:19.2:1:32.1:1:1:0:60:158:1:0:0 0/1:73:2:1,1:18,53:71,2:0.0274:2,2:12:1:27.5:1:0.45548:2.89:60:4:0.0286:0:1 +6 26200256 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49183;SOR=Inf;LSEQ=GTAATTACCTGCATATTTTC;RSEQ=GTGTTTACCACCAACAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:28,0:0:1,0:26.3:1:30.7:1:1:0:60:56:1:0:0 0/1:30:2:0,2:1,27:28,2:0.0667:1,0:30:1:30:1:1:0:60:4:0.0667:0:1.5 +6 26216656 . T C 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00269;SOR=Inf;LSEQ=GAAGCCTCGCCTGCGATGCG;RSEQ=TCGAAGATGTCGTTAACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:48,27:75,0:0:2,0:23:1:30.4:1:1:0:59.3:150:1:0:0.1 0/1:72:8:4,4:37,27:64,8:0.1111:2,2:31.1:1:31.3:1:0.71856:1.36428:49.8:16:0.1127:0:1.1 +6 26216806 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50388;SOR=Inf;LSEQ=TTCTTGCCATCCTTCTTCTG;RSEQ=GCCTTGGTCACAGCCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:31,40:71,0:0:2,0:26.5:1:31.5:1:1:0:59.9:142:1:0:0.1 0/1:90:2:1,1:44,44:88,2:0.0222:2,2:10:1:27:1:1:1:60:4:0.0222:0:2 +6 26216819 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50064;SOR=Inf;LSEQ=TCTTCTGCGCCTTGGTCACA;RSEQ=CCTTCTTGGAACCCTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:27,38:65,0:0:2,0:25.9:1:32.6:1:1:0:59.9:64:1:0:0.1 0/1:78:2:1,1:37,39:76,2:0.0256:2,2:20:1:27:1:1:1.05:59.5:4:0.026:0:1 +6 26216866 . A C 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49521;SOR=Inf;LSEQ=GGAGCTGACTTAGCTGGTTC;RSEQ=GGCATGCTGTCAGAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:9,32:41,0:0:2,0:21.2:1:30.8:1:1:0:60:40:1:0:0 0/1:45:2:1,1:10,33:43,2:0.0444:2,2:7.5:1:30.5:1:0.43333:3.19:60:4:0.0444:0:1 +6 26219312 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19615;SOR=Inf;LSEQ=CCACACGGAAGTCCACTGGT;RSEQ=GCAGACAGCCTCCTAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:22,0:0:2,0:26.1:1:30.8:1:1:0:60:44:1:0:0 0/1:18:2:1,1:11,5:16,2:0.1111:2,2:34:1:31.5:1:1:2.09766:60:4:0.1176:0:1 +6 26219319 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18937;SOR=Inf;LSEQ=GAAGTCCACTGGTGGCAGAC;RSEQ=GCCTCCTAAGCAGCTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:24,0:0:2,0:25.2:1:30.9:1:1:0:60:48:1:0:0.1 0/1:19:2:1,1:11,6:17,2:0.1053:2,2:38:0:31.5:1:1:1.77272:60:4:0.1053:0:1.5 +6 26219337 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20854;SOR=Inf;LSEQ=ACAGCCTCCTAAGCAGCTGG;RSEQ=CACCAAGGCAGCCAGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:22,0:0:2,0:28.5:1:32.6:1:1:0:60:44:1:0:0.1 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:27:1:27:1:1:1.40151:60:4:0.1053:0:1 +6 26219384 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48276;SOR=Inf;LSEQ=TGGCCACCAGCAGCTTGAAG;RSEQ=TGTCCCTCAGATATAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:14,0:0:2,0:25.4:1:31.9:1:1:0:60:28:1:0:0.1 0/1:15:2:1,1:3,10:13,2:0.1333:2,2:40:1:29:1:0.47619:3.03:60:4:0.1333:0:1 +6 26225381 . C G 217 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATTTACTTTGCAGATGAA;RSEQ=TATGGCGCGTACTAAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1789:0:0,0:1045,742:1787,0:0:2,0:25.1:1:32.7:1:1:0:60:80.227:0.9989:0:0.1 0/1:2089:118:71,47:1121,846:1967,118:0.0565:2,2:27.3:1:31.6:1:0.5657:1.14:60:236:0.0571:0:1.1 +6 26226032 . C G 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25953;SOR=2.88708;LSEQ=GCTGTTCTCCATTGGTTTAG;RSEQ=TGGCTTTGTTTTGCTGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:3:0,3:3,50:53,3:0.0536:2,0:29.7:1:33:1:1:0:60:6:0.0536:0:1.3 0/1:14:2:0,2:1,11:12,2:0.1429:2,0:14:1:32.5:1:1:0:60:4:0.1538:0:1 +6 26234734 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49652;SOR=Inf;LSEQ=TCTTCGGGGTAGCGGCGCCA;RSEQ=CCACCTTCTTGGGCTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:25,12:37,0:0:2,0:28.4:1:33.3:1:1:0:59:74:1:0:0 0/1:43:2:1,1:21,20:41,2:0.0465:2,2:16.5:1:27.5:1:1:1.04883:60:4:0.0476:0:1 +6 26234883 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51216;SOR=Inf;LSEQ=GTACCTTTGGTCTGCACCAG;RSEQ=GTACCTTTGCTCACCAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:35,34:69,0:0:2,0:28:1:31:1:1:0:60:68:1:0:0.1 0/1:98:2:1,1:48,48:96,2:0.0204:2,2:20:0:32.5:1:1:1:60:4:0.0206:0:1.5 +6 26249518 . G T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CTACTCGGGAGGCTGAGGCA;RSEQ=GAGAATCGCTTGAACCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:44.5:1:30.5:1:1:0:32:4:0.6667:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:36.5:1:31.5:1:1:0:44.5:4:1:0:0 +6 26250254 . C G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.94641;LSEQ=TTTGAAGACAATGGCCAAGA;RSEQ=ACAAAAGCCTAGTTTAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:13:13,0:120,3:123,13:0.0956:1,1:18.8:1:33.5:1:1:0:60:26:0.097:0:1 0/1:66:6:6,0:59,1:60,6:0.0909:1,0:22.2:1:29.2:1:1:0:60:5:0.0769:0:1.2 +6 26251905 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23311;SOR=Inf;LSEQ=GATCCAGCTAAGTCCGCTCC;RSEQ=GCCCCGAAGAAGGGCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:83,60:143,0:0:2,0:27.1:1:30.6:1:1:0:57.4:70.5:1:0:0.1 0/1:134:2:1,1:77,55:132,2:0.0149:2,2:37.5:1:30.5:1:1:1.3964:60:4:0.0149:0:1 +6 26251911 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49828;SOR=0;LSEQ=GCTAAGTCCGCTCCCGCCCC;RSEQ=AAGAAGGGCTCCAAGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:82,62:144,2:0.0137:2,2:40:0:31.5:1:1:1.32001:60:4:0.0138:0:2 0/0:145:0:0,0:83,62:145,0:0:2,0:26.9:1:29.2:1:1:0:55.2:28:1:0:0.1 +6 26251944 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49874;SOR=0;LSEQ=AAGAAGGCGGTGACCAAGGC;RSEQ=CAGAAGAAGGATGGCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:78,83:161,2:0.0123:2,2:18:1:29.5:1:1:1.06:37:4:0.0123:0:1 0/0:155:0:0,0:75,80:155,0:0:2,0:25.3:1:29.8:1:1:0:56.2:154:1:0:0.1 +6 26251959 . C A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49869;SOR=0;LSEQ=AAGGCGCAGAAGAAGGATGG;RSEQ=AAGAAGCGTAAACGCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:2,0:79,74:153,2:0.0129:2,0:8.5:1:25.5:1:0.49778:0:35.5:4:0.0131:0:1 0/0:147:0:0,0:72,75:147,0:0:2,0:25.1:1:30.8:1:1:0:56.6:72.5:1:0:0.2 +6 26251979 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24166;SOR=Inf;LSEQ=CAAGAAGCGTAAACGCAGCC;RSEQ=CAAGGAGAGCTACTCCGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:70,66:136,0:0:2,0:24.9:1:31.1:1:1:0:59.2:135:1:0:0.1 0/1:132:2:1,1:64,66:130,2:0.0152:2,2:39.5:1:28:1:1:1.03:60:4:0.0152:0:1 +6 26252035 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50332;SOR=0;LSEQ=TGAAGCAAGTCCACCCCGAC;RSEQ=CCGGCATCTCCTCCAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:77,80:157,2:0.0126:2,2:28:1:30:1:1:1.04:48:4:0.0127:0:1 0/0:130:0:0,0:62,68:130,0:0:2,0:23.5:1:28.5:1:1:0:59.7:64:1:0:0.1 +6 26252104 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24292;SOR=Inf;LSEQ=ATATCTTCGAGCGCATCGCC;RSEQ=GCGAGGCTTCCCGCCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:35,54:89,0:0:2,0:24.1:1:29.8:1:1:0:59.6:43.5:1:0:0.1 0/1:87:2:1,1:37,48:85,2:0.023:2,2:16.5:1:28:1:1:1.29:56.5:4:0.023:0:1 +6 26252240 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22209;SOR=0;LSEQ=GGGCACTAAGGCCGTCACCA;RSEQ=GTACACCAGCTCCAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:48,53:101,2:0.0194:2,2:30.5:1:32.5:1:1:1.10:60:4:0.0194:0:1 0/0:115:0:0,0:57,58:115,0:0:2,0:27.1:1:29.3:1:1:0:59.7:56.5:1:0:0.1 +6 26270961 . T C 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32152;SOR=4.34789;LSEQ=TTCCACTACCAAATCGAAGC;RSEQ=CCAAACCCCTAAAAGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:2,0:27,1:28,2:0.0667:1,0:19.5:1:30:1:1:0:60:4:0.0714:0:1 0/1:4:1:0,1:2,1:3,1:0.25:2,0:16:0:32:0:1:0:60:2:0.25:0:1 +6 26271241 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.62197;LSEQ=ATGCGGCGAGCGAGCTGAAT;RSEQ=TCCTTGGGCATGATAGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2568:183:103,80:1313,1069:2382,183:0.0713:2,2:25.1:1:29.5:1:0.81709:1.05:58.8:182:0.0715:0:1.1 0/1:2629:291:163,128:1190,1147:2337,291:0.1107:2,2:25.3:1:28.3:1:0.10603:1.23:59.5:71.75:0.11:0:1.1 +6 26271713 . A T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.44076;LSEQ=GCCTTGTTGATTTTCAAAAG;RSEQ=CCCGCGCAACAAAACCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:348:46:1,45:8,294:302,46:0.1322:1,1:23.3:1:29.6:1:1:1.22383:60:22:0.1275:0:1.3 0/1:241:83:2,81:10,147:157,83:0.3444:2,1:23.1:1:29:1:0.22626:2.74547:60:166:0.3458:0:1.1 +6 26273285 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21869;SOR=0;LSEQ=AGGCACAGAAGAAGGATGGC;RSEQ=AGAAGCGCAAGCGCAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:89,101:190,2:0.0104:2,2:25:1:30.5:1:1:1.13:32.5:4:0.0104:0:1 0/0:218:0:0,0:113,105:218,0:0:2,0:29.7:1:29.7:1:1:0:58.8:436:1:0:0.1 +6 26273347 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49875;SOR=0;LSEQ=GTGTACAAGGTGCTGAAGCA;RSEQ=GTCCACCCCGACACCGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:77,120:197,2:0.0101:2,2:17:0:32.5:1:1:1.55:60:4:0.0103:0:1.5 0/0:197:0:0,0:87,110:197,0:0:2,0:23.2:1:30.3:1:1:0:44.7:97.5:1:0:0.1 +6 26273378 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2456;SOR=0;LSEQ=ACACCGGCATCTCGTCCAAG;RSEQ=CTATGGGGATTATGAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:72,123:195,2:0.0102:2,2:17:0:32:0:1:1.70:33:4:0.0103:0:1.5 0/0:200:0:0,0:87,113:200,0:0:2,0:28.3:1:30.8:1:1:0:44.9:49:1:0:0.2 +6 26273435 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49971;SOR=Inf;LSEQ=TCGAGCGCATTGCAGGCGAG;RSEQ=CTTCCCGCCTGGCGCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:32,74:106,0:0:2,0:22.8:1:32:1:1:0:59.6:105:1:0:0 0/1:120:2:1,1:38,80:118,2:0.0167:2,2:30.5:1:31:1:0.54622:2.09:44:4:0.0172:0:2 +6 26273522 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12163;SOR=Inf;LSEQ=GCCTGCTGCTACCCGGGGAG;RSEQ=TGGCCAAACACGCGGTGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:51,50:101,0:0:2,0:24.1:1:32.4:1:1:0:58.7:49.5:1:0:0.1 0/1:105:4:1,3:59,42:101,4:0.0381:2,2:8:1:25.5:1:0.31129:4.15912:60:8:0.0381:0:1 +6 26273525 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49795;SOR=Inf;LSEQ=TGCTGCTACCCGGGGAGCTG;RSEQ=CCAAACACGCGGTGTCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:53,53:106,0:0:2,0:24:1:31.4:1:1:0:58.8:52:1:0:0.1 0/1:111:2:1,1:62,47:109,2:0.018:2,2:10:0:27:1:1:1.31581:60:4:0.0182:0:1 +6 26273560 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49913;SOR=Inf;LSEQ=TCGGAGGGCACCAAGGCGGT;RSEQ=ACCAAGTACACCAGCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:60,71:131,0:0:2,0:27:1:32.2:1:1:0:58.5:42.667:1:0:0.1 0/1:143:2:1,1:71,70:141,2:0.014:2,2:30:0:30.5:1:1:1.01419:20:4:0.0141:0:1.5 +6 26273574 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49932;SOR=Inf;LSEQ=GGCGGTCACCAAGTACACCA;RSEQ=CTCCAAGTAAACTAGTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:53,72:125,0:0:2,0:27:1:32.6:1:1:0:58.4:40.667:1:0:0.2 0/1:138:2:1,1:60,76:136,2:0.0145:2,2:35.5:1:29:1:1:1.26:60:4:0.0145:0:1 +6 26322023 . G GA 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.49763;SOR=0;LSEQ=GGTACCTTTTGACCCCATGG;RSEQ=AAAAAAAATAACGTTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:2,0:94,7:101,2:0.0194:2,0:34.5:1:31:1:1:0:60:4:0.0198:0:0.5 0/0:100:0:0,0:90,9:99,0:0:2,0:23.3:1:30.5:1:1:0:55.6:48.5:0.9898:0:0.1 +6 26322115 . C T 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTGGATTCTTAAGCACGTT;RSEQ=TCCACGTATGCGGCGTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:200,75:275,0:0:2,0:33.3:1:32.2:1:1:0:43.6:90.667:1:0:0.1 0/1:267:27:17,10:150,90:240,27:0.1011:2,2:33.7:1:29.4:1:1:1.02:45.7:26:0.0985:0:1.7 +6 26322153 . A G 123 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAGCTGGATGTCTTTTGGC;RSEQ=TAATTGTTACACGTTTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:115,102:217,0:0:2,0:10:1:29.6:1:1:0:37.6:35.167:1:0:0.1 0/1:175:20:9,11:64,91:155,20:0.1143:2,2:7.3:1:28.5:1:0.81182:1.16:31.8:19:0.1092:0:1.8 +6 26322444 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21851;SOR=Inf;LSEQ=TCTTGCGAGAGGCTTTTGTA;RSEQ=CCAGTTGCTTCCCGGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:102,123:225,0:0:2,0:22.4:1:32.6:1:1:0:58.2:74:1:0:0.3 0/1:198:2:1,1:102,93:195,2:0.0101:2,2:11.5:1:24.5:1:1:1.09626:30:4:0.0102:0:1 +6 26322473 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.62501;LSEQ=TTCCCGGGTGCTTTGCCACC;RSEQ=GTCGATTTGCCGGTCGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:8:5,3:108,123:231,8:0.0333:2,2:32.1:1:31.1:1:0.48145:1.89:60:16:0.034:0:1 0/1:212:53:27,26:78,79:157,53:0.25:2,2:29.3:1:29.6:1:1:1.05:60:106:0.2524:0:1.2 +6 26322500 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20385;SOR=Inf;LSEQ=TTGCCGGTCGATTTGCGGGC;RSEQ=GTCGGCTTTCTACGAGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:98,131:229,0:0:2,0:27.8:1:30.8:1:1:0:60:37.167:1:0:0.4 0/1:189:2:1,1:85,102:187,2:0.0106:2,2:40:1:30.5:1:1:1.20:60:4:0.0106:0:3 +6 26322501 . G A 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCCGGTCGATTTGCGGGCA;RSEQ=TCGGCTTTCTACGAGCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:57:22,35:76,93:169,57:0.2522:2,2:26.6:1:30.5:1:0.44195:1.2986:60:56:0.25:0:1.1 0/0:188:0:0,0:84,104:188,0:0:2,0:26.5:1:31.7:1:1:0:59.7:187:1:0:0.4 +6 26322526 . A G 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTTTCTACGAGCCGTGGTAT;RSEQ=GAGACCTCCTTACTTACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:59,111:170,0:0:2,0:21.8:1:30.7:1:1:0:59.8:84:1:0:0.4 0/1:126:16:7,9:43,67:110,16:0.127:2,2:19.6:1:29.8:1:0.78752:1.21:60:15:0.12:0:1.1 +6 26322624 . G T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97535;LSEQ=AGCGACGGCAGGACGGCTGC;RSEQ=GCTACGAACACAATTGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:0,5:4,35:39,5:0.1136:2,0:17.8:1:26.2:1:1:0:60:1.5:0.0732:0:1 0/1:27:3:0,3:1,23:24,3:0.1111:1,0:20.7:1:31:1:1:0:60:6:0.1111:0:1 +6 27100347 . G T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25225;SOR=Inf;LSEQ=TTCACAAACGAATTCATGAT;RSEQ=CCCATGGCCTTGGACGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:62,15:77,0:0:2,0:25.8:1:32.1:1:1:0:59.6:37.5:1:0:0.1 0/1:93:3:1,2:63,27:90,3:0.0323:2,2:11.7:1:24.7:1:0.2284:4.5803:60:6:0.0333:0:1 +6 27100413 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24072;SOR=Inf;LSEQ=AGAACCTTGTACACATAGAT;RSEQ=GAATAGCTCTCCTTGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:126,78:204,0:0:2,0:26.7:1:32:1:1:0:58.7:101:1:0:0.1 0/1:197:2:1,1:113,82:195,2:0.0102:2,2:17.5:1:31:0:1:1.37575:59:4:0.0103:0:1 +6 27100458 . C A 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24875;SOR=0;LSEQ=TTGCGCTTCTTGCCGTCTTT;RSEQ=TTCTGCGCCTTAGTCACCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:3:2,1:129,111:240,3:0.0123:2,2:5.3:1:27.3:1:1:1.72:47.7:6:0.0125:0:1 0/0:233:0:0,0:118,115:233,0:0:2,0:27.6:1:30.5:1:1:0:58.5:37.833:1:0:0.1 +6 27101644 . G C 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-04;SOR=Inf;LSEQ=TGTTCCACGCGGGCCAGGGC;RSEQ=GCATGAAGAAGTCCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:124,28:152,0:0:2,0:20.8:1:30.1:1:1:0:60:75:1:0:0.1 0/1:156:12:11,1:105,37:142,12:0.0769:2,2:24.1:1:30.2:1:0.29569:3.85:60:24:0.0789:0:1 +6 27101761 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24024;SOR=Inf;LSEQ=TCCTGCGAGAGCTCGGCGGT;RSEQ=ACGCCGCTGCACGAGAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:54,140:194,0:0:2,0:22.3:1:31.9:1:1:0:60:63.667:1:0:0.1 0/1:187:2:1,1:52,133:185,2:0.0107:2,2:21.5:1:27:1:0.48761:2.54:60:4:0.0108:0:1 +6 27114052 . G T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87078;LSEQ=CTGCATGCATTACTCAGTGT;RSEQ=ATAAGATCATGATAATCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:13,0:13,9:0.4091:1,0:30:1:31:1:1:0:55.8:18:0.4091:0:1.1 0/1:8:3:3,0:5,0:5,3:0.375:0,0:10:1:31:1:1:0:60:6:0.375:0:1 +6 27114150 . T C 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4982;SOR=0;LSEQ=ATCGATAATTTAAGTGGCTC;RSEQ=TAAAAGAGCCTTTGGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:84,35:119,2:0.0165:2,2:18:0:34.5:1:0.50826:2.3805:60:4:0.0168:0:1.5 0/0:115:0:0,0:84,31:115,0:0:2,0:20.8:1:29.9:1:1:0:59.4:114:1:0:0.1 +6 27114223 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50096;SOR=Inf;LSEQ=AGCGCTGGTGTACTTGGTGA;RSEQ=GGCCTTGGTGCCCTCGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:62,70:132,0:0:2,0:25:1:31.1:1:1:0:48.4:131:1:0:0.3 0/1:153:2:1,1:78,73:151,2:0.0131:2,2:30:0:31.5:1:1:1.068:36:4:0.0131:0:1.5 +6 27114233 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5995;SOR=0.4335;LSEQ=TACTTGGTGACGGCCTTGGT;RSEQ=CCCTCGGACACGGCGTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:49,59:108,2:0.0182:2,2:10:1:29:1:1:1.20:43:4:0.0183:0:1 0/0:126:1:0,1:62,63:125,1:0.0079:2,0:3:0:28:0:1:0:60:2:0.0079:0:1 +6 27775248 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21943;SOR=Inf;LSEQ=GAGCGAACCAGCTCTTCTTT;RSEQ=GATAATAGTGAGTGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:67,13:80,0:0:2,0:22:1:28.4:1:1:0:60:39:1:0:0 0/1:71:2:2,0:54,15:69,2:0.0282:2,0:25.5:1:32:1:1:0:60:4:0.0294:0:1 +6 27775315 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19496;SOR=0;LSEQ=CTTGAGAATTTACTTGGAGC;RSEQ=GGTGTACTTGGTGACGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:109,84:193,2:0.0103:2,2:33.5:1:30:1:1:1.29586:53:4:0.0104:0:1 0/0:246:0:0,0:130,115:245,0:0:2,0:27.3:1:29.5:1:1:0:46.7:39.833:1:0:0.1 +6 27775370 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50318;SOR=Inf;LSEQ=ACCGCGTGCTTGGCCAGCTC;RSEQ=CCCGGAAGCAGCAGGCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:61,77:138,0:0:2,0:26.5:1:31.1:1:1:0:42.3:137:1:0:0.1 0/1:168:2:1,1:70,96:166,2:0.0119:2,2:24.5:1:31.5:1:1:1.37:40:4:0.0122:0:1 +6 27775446 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.85717;LSEQ=GCTTGTTGTAGTGCGCCAGG;RSEQ=GGGAAGCCTCGCTTGCGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:0,1:61,47:108,1:0.0092:2,0:1:0:26:0:0.44037:0:33:2:0.0092:0:1 0/1:118:2:1,1:60,56:116,2:0.0169:2,2:12:1:27.5:1:1:1.07077:52:4:0.0172:0:1 +6 27775486 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49844;SOR=Inf;LSEQ=GCGCTCGAAGATGTCGTTGA;RSEQ=GAAGGAGTTCATGATTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:91,70:161,0:0:2,0:27.6:1:30.9:1:1:0:51:39.25:1:0:0.1 0/1:161:2:1,1:93,66:159,2:0.0124:2,2:21:0:31.5:1:1:1.40601:21:4:0.0125:0:1.5 +6 27775672 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.07993;SOR=0;LSEQ=CGGGGCGGGAGCAGACTTGG;RSEQ=CAGCTCGGGCATAATGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:3:1,2:44,94:138,3:0.0213:2,2:29.7:1:28.3:1:1:1.07:60:6:0.0221:0:1 0/0:185:0:0,0:64,121:185,0:0:2,0:24.9:1:30.6:1:1:0:57.6:184:1:0:0.4 +6 27775674 . A G 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGGCGGGAGCAGACTTGGCC;RSEQ=GCTCGGGCATAATGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:42,94:136,0:0:2,0:25.3:1:31.3:1:1:0:57.3:44.333:1:0:0.2 0/1:178:20:9,11:49,109:158,20:0.1124:2,2:27.4:1:29.7:1:0.21551:1.81:57.4:40:0.1136:0:2.1 +6 27775697 . G C 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCGGGCATAATGAAACAATA;RSEQ=TGGCAAAACCAAAACAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:16,73:89,0:0:2,0:21.5:1:32.9:1:1:0:59.4:178:0.9889:0:0.2 0/1:116:20:7,13:22,74:96,20:0.1724:2,2:25:1:30.9:1:0.26648:1.80:58.1:40:0.1739:0:2.1 +6 27775707 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25404;SOR=Inf;LSEQ=TGAAACAATAGTGGCAAAAC;RSEQ=AAAACAAGAAGTCGGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:12,57:69,0:0:2,0:20.3:1:32.5:1:1:0:59.6:138:0.9857:0:0.1 0/1:87:3:2,1:14,70:84,3:0.0345:2,2:16.7:1:28.3:1:0.08566:9.61:60:6:0.0349:0:2 +6 27778097 . C T 255 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=464.24528;LSEQ=GCGCAGGACTTCAAGACCGA;RSEQ=TTGCGCTTCCAGAGCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2826:1:0,1:1453,1372:2825,1:4e-04:2,0:1:0:25:0:0.48585:0:60:2:4e-04:0:1 0/1:2780:394:198,196:1230,1154:2384,394:0.1417:2,2:24.7:1:29.6:1:0.62486:1.0551:55.7:77.8:0.1412:0:1.2 +6 27783042 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50136;SOR=0;LSEQ=CAACGACATCTTTGAGCGTA;RSEQ=CGCCGGAGAAGCGTCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:41,125:166,2:0.0119:2,2:12.5:1:28.5:1:0.43862:3.02:60:4:0.012:0:1 0/0:144:0:0,0:54,90:144,0:0:2,0:23.7:1:28.8:1:1:0:59.6:35:1:0:0.2 +6 27783144 . C T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.64208;LSEQ=ACTGCTACCCGGGGAATTGG;RSEQ=CAAGCACGCCGTGTCCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:1:1,0:34,36:70,1:0.0141:2,0:22:0:32:0:0.49296:0:60:2:0.0145:0:1 0/1:87:2:1,1:43,42:85,2:0.023:2,2:21:0:31:0:1:1.02354:43.5:4:0.023:0:1 +6 27783199 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.521;SOR=Inf;LSEQ=ACCAAGTATACCAGCTCCAA;RSEQ=TGAGCCTCTCGCTGCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:32,42:74,0:0:2,0:27:1:31.6:1:1:0:58.6:23.667:1:0:0.2 0/1:115:2:1,1:52,59:111,2:0.0174:2,2:42.5:1:30:1:1:1.13:60:4:0.0174:0:1 +6 27806434 . C A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01325;SOR=Inf;LSEQ=CAATTTTCCGGCAGTTACTC;RSEQ=CAGTCATGCCCGAGCCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:56,11:67,0:0:2,0:23:1:31.1:1:1:0:60:134:1:0:0 0/1:66:6:5,1:51,9:60,6:0.0909:2,2:18:1:29.2:1:1:1.13114:60:12:0.0923:0:1 +6 27806492 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6202;SOR=2.04774;LSEQ=GAAGAAAGGCTCCAAGAAGG;RSEQ=AGTGACAAAGGCCCAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:0,1:101,56:157,1:0.0063:2,0:1:0:27:0:0.36076:0:24:2:0.0065:0:1 0/1:155:2:1,1:88,65:153,2:0.0129:2,2:33.5:1:28:1:1:1.35115:37.5:4:0.013:0:1 +6 27806519 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23726;SOR=Inf;LSEQ=AAAGGCCCAGAAGAAGGACG;RSEQ=CAAGAAGCGCAAGCGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:94,55:149,0:0:2,0:29.1:1:31.7:1:1:0:39.8:73.5:1:0:0 0/1:142:2:1,1:75,65:140,2:0.0141:2,2:20.5:1:26.5:1:1:1.15268:40:4:0.0142:0:1 +6 27806523 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23708;SOR=Inf;LSEQ=GCCCAGAAGAAGGACGGCAA;RSEQ=AAGCGCAAGCGCAGCCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:92,55:147,0:0:2,0:28.4:1:32.5:1:1:0:38.5:35.75:1:0:0 0/1:140:2:1,1:72,66:138,2:0.0143:2,2:22:1:28:1:1:1.09022:22.5:4:0.0143:0:1 +6 27806748 . GC G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.24233;SOR=Inf;LSEQ=ACGGCCGTGCGCCTGCTGCT;RSEQ=CAGGGGAGCTGGCCAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:66,48:114,0:0:2,0:24.5:1:31.8:1:1:0:34.7:56:0.9912:0:0.1 0/1:112:2:1,1:67,43:110,2:0.0179:2,2:10:1:30.8:1:1:1.55174:45:4:0.0182:0.0089:0 +6 27806755 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49823;SOR=0;LSEQ=TGCGCCTGCTGCTGCCAGGG;RSEQ=AGCTGGCCAAGCACGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:73,60:133,2:0.0148:2,2:28.5:1:28:1:1:1.21489:37.5:4:0.015:0:1 0/0:131:0:0,0:76,55:131,0:0:2,0:25:1:29.5:1:1:0:36.9:17.714:1:0:0.1 +6 27806839 . G A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.89973;LSEQ=GAGCCCGCCCACCGCGGAAC;RSEQ=TTCGGTCAGTCTCGGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:2,0:68,102:170,2:0.0116:2,0:1:0:28:1:0.16422:0:44:4:0.0118:0:1 0/1:191:2:1,1:80,109:189,2:0.0105:2,2:25.5:1:26.5:1:1:1.36:52:4:0.0105:0:1.5 +6 27835012 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50632;SOR=0;LSEQ=CAGAAGCACCAGTGCCCTTG;RSEQ=TCTGCACCAGGGTGCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:43,56:99,2:0.0198:2,2:37:1:30.5:1:1:1.30:60:4:0.0202:0:1 0/0:77:0:0,0:36,41:77,0:0:2,0:48:0:14:0:1:0:60:0:0:0:1 +6 27835026 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0452;SOR=Inf;LSEQ=CCCTTGGTCTGCACCAGGGT;RSEQ=CCCTTGCTCACCAAGCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:41,62:103,0:0:2,0:28.1:1:31.6:1:1:0:59.9:50.5:1:0:0.1 0/1:58:3:1,2:26,29:55,3:0.0517:2,2:29.7:1:28.7:1:1:1.77582:56.7:6:0.0517:0:1 +6 27835094 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52314;SOR=0;LSEQ=CTTCTCCACGTCGTAGCCAC;RSEQ=GGCCGCTAAGGCCTTCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:0,2:1,29:30,2:0.0625:1,0:28.5:1:32:1:1:0:60:4:0.0645:0:1 0/0:19:0:0,0:3,16:19,0:0:2,0:26.1:1:28.8:1:1:0:59.5:38:1:0:0.2 +6 27839184 . C T 43 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTAGCTGGGACTACAGGCG;RSEQ=GTGCCACCACGGCCGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:10.7:1:27.7:1:1:0:47:2:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 27839746 . T C 267 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAGGCATAATAGTGACGCG;RSEQ=TTGGCGTGAATGGCGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2728:0:0,0:1433,1290:2723,0:0:2,0:24.7:1:30.1:1:1:0:59.9:99.852:0.9993:0:0.2 0/1:2822:367:197,170:1262,1190:2452,367:0.13:2,2:23.4:1:31.4:1:0.43363:1.09:53.4:51.429:0.129:0:1.2 +6 27840221 . C A 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00252;SOR=0;LSEQ=CGTCTCACACACGGAATTGG;RSEQ=TCCCAGTTTAATCTGCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:13:0,13:5,192:197,13:0.0619:1,1:23.9:1:31.8:1:1:0:60:26:0.0644:0:1 0/0:125:0:0,0:2,123:125,0:0:1,0:23.1:1:31.6:1:1:0:60:61.5:1:0:0.1 +6 27840322 . CA C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAAAACAAAAACGGAAA;RSEQ=AAAAAAAATCCCCCAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:0,3:1,40:41,3:0.0682:1,0:12:1:32.5:1:1:0:60:6:0.0714:0.0227:0 0/0:13:0:0,0:2,11:13,0:0:2,0:29:1:30.7:1:1:0:60:26:1:0:0.2 +6 27858040 . A G 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00144;SOR=Inf;LSEQ=CCAGTTTATCCCTGCTTTAA;RSEQ=GTTGATTTAAGACAGTCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:219,3:222,0:0:1,0:23:1:30.6:1:1:0:60:110:1:0:0.1 0/1:179:8:7,1:164,7:171,8:0.0447:1,2:21.8:1:31.8:1:0.31155:3.30993:60:16:0.0449:0:1.1 +6 27858421 . A G 264 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTGATAACGGCGGATCTC;RSEQ=CGCAAGGCCACGGTGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2203:0:0,0:1086,1117:2203,0:0:2,0:25:1:30.3:1:1:0:60:121.389:1:0:0.1 0/1:2063:438:209,229:799,823:1622,438:0.2123:2,2:26.1:1:30.2:1:0.59026:1.06368:59.4:86.6:0.2122:0:1.2 +6 27858837 . T C 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=CTCCCGGGTTCAAGCGATTC;RSEQ=GCCTCAGCCTCCGGAGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:36:1:26:1:1:0:49:4:0.2222:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:13.5:1:30:1:1:0:40.5:4:1:0:1 +6 27858904 . C T 45 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGGCTAATTTTTTTTTAG;RSEQ=AGAGAAGGGGTTTCACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:0,5:5,3:0.375:0,2:28:1:29:1:0.375:0:45:6:0.4286:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 27861326 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19792;SOR=Inf;LSEQ=CCAGAAAAAGGACGGCAAGA;RSEQ=GCGCAAGCGCAGCCGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:41,27:68,0:0:2,0:28.3:1:30.1:1:1:0:58.9:21.667:1:0:0.1 0/1:55:2:1,1:29,24:53,2:0.0364:2,2:25.5:1:29:1:1:1.20416:55.5:4:0.0364:0:1 +6 27861643 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22804;SOR=Inf;LSEQ=CTCTCGCAGCTGCCAGCAAT;RSEQ=CAAAGGCTCTTTTCAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:25,39:64,0:0:2,0:24.3:1:30.9:1:1:0:60:31:1:0:0.1 0/1:59:2:1,1:21,36:57,2:0.0339:2,2:8.5:1:26.5:1:1:1.70:60:4:0.0339:0:1 +6 27861670 . G A 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45239;SOR=0.47638;LSEQ=CTCTTTTCAGAGCCACTCAC;RSEQ=CTTCCAGAGAAAGAGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:5:0,5:9,24:33,5:0.1316:2,0:15.6:1:28.2:1:0.31207:0:60:10:0.1316:0:1 0/1:30:2:1,1:5,23:28,2:0.0667:2,2:20.5:1:27.5:1:0.36552:4.29:60:4:0.069:0:1 +6 28067099 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54247;SOR=0;LSEQ=CCCAACTGGGTAAGACCCTG;RSEQ=AAGAGGGGTAGTCAGACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:1,3:5,11:16,4:0.2:2,2:21.3:1:29.3:1:1:1.34348:60:8:0.2:0:1.3 0/0:6:0:0,0:3,3:6,0:0:2,0:26.2:1:29.8:1:1:0:60:12:1:0:0.2 +6 28067196 . T C 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAGAGGAAGGAGCAGACACC;RSEQ=ATCTTGTGCTCTCCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:36.5:1:33.5:1:1:0:60:4:0.6667:0:1 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:22:1:33.5:1:0.33333:0:60:4:0.6667:0:1 +6 28067537 . G A 43 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATACTAGACAAATTCATGA;RSEQ=GATGAGAAAGAATCAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:19:0:35:0:1:0:29:2:1:0:0 1/0:5:3:2,1:1,1:2,3:0.6:2,2:18:1:27.7:1:1:1.73:53:6:0.6:0:1.3 +6 28954286 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49496;SOR=0;LSEQ=TTCCTCCTAGCTGTGAAGGT;RSEQ=AGGACCGCCGGTGTCAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:24,23:47,2:0.0408:2,2:20.5:1:26:1:1:1.04259:60:4:0.0408:0:1 0/0:47:0:0,0:23,24:47,0:0:2,0:27:1:30.3:1:1:0:60:46:1:0:0.1 +6 29230100 . T TA 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTTCTTTTTTTATTTT;RSEQ=TTTTTTGTTTGTTTTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:23:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:30:1:1:0:60:4:1:0:0.5 +6 29230520 . A C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=3e-05;SOR=0.13465;LSEQ=TGGGAGTAACAATGGAGTAA;RSEQ=ATATATGGAGAAGTTTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:36:35,1:72,0:72,36:0.3333:1,1:24.3:1:32.8:1:0.33333:0:60:72:0.3429:0:1.1 0/1:64:4:4,0:60,0:60,4:0.0625:1,0:14.3:1:30.8:1:1:0:60:8:0.0625:0:1 +6 29230577 . C A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05138;SOR=0.71219;LSEQ=TGTTTCCTGGCTCTATATAC;RSEQ=TATATCTAACAGTCCCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:316:184:136,48:107,24:131,184:0.5823:2,2:23.6:1:30.5:1:0.134:1.5713:56.6:60.333:0.582:0:1.1 0/1:253:126:87,39:98,28:126,126:0.498:2,2:23.7:1:29.5:1:0.15362:1.56613:56.8:125:0.5:0:1.1 +6 29230683 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25353;LSEQ=CTTGATCTTGAGTACAGCCA;RSEQ=AGCAATGAAGCCATATGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:297:227:69,158:29,41:70,227:0.7643:2,2:27.7:1:31.9:1:0.1093:1.61696:43.8:74.667:0.7645:0:1.1 0/1:324:146:56,90:75,102:177,146:0.4506:2,2:27.2:1:30.3:1:0.49559:1.18111:44.9:35.5:0.4494:0:1.1 +6 29236102 . TTTTTATTATAA T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATTCGGCTTAATTATAA;RSEQ=TTTTATTATATTTTTAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:34.5:1:30:1:1:0:50.5:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29236155 . TAGACAATTTAT A 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TATTATCTTTATCTCAGGTG;RSEQ=TTACAAAATAAATTGTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:22.7:1:33:0:1:0:60:6:0.6:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29236581 . C A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=0;LSEQ=AGAGGAACAAGAACTATAAT;RSEQ=AGGCACATGGCAAATGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:12,124:136,2:0.0145:2,2:5:1:29.5:1:0.18015:9.97:60:4:0.0147:0:1 0/0:126:0:0,0:23,103:126,0:0:2,0:47:0:15:0:1:0:60:0:0:0:7 +6 29236588 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12518;LSEQ=CAAGAACTATAATCAGGCAC;RSEQ=TGGCAAATGTGGTTACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:36:1,35:6,78:84,36:0.3:2,1:25.5:1:32.5:1:0.67305:2.67444:60:72:0.3:0:1.1 0/1:99:5:1,4:11,83:94,5:0.0505:2,2:20.6:1:31.2:1:0.48339:1.87:60:10:0.051:0:1 +6 29236645 . G T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.00495;SOR=Inf;LSEQ=CACATGCAATCTTGAATCTT;RSEQ=ATCATTGCAGACATTTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:1,38:39,0:0:1,0:18:1:31.8:1:1:0:60:38:1:0:0.4 0/1:30:6:0,6:0,24:24,6:0.2:1,0:23.2:1:26.3:1:1:0:60:12:0.2:0:1 +6 29236722 . G A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.12732;SOR=7.15885;LSEQ=CGAGGAAGACTCGTGGCATA;RSEQ=GGGGAAGGTATGATGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,9:9,5:0.3333:0,0:16.2:1:30.6:1:1:0:60:10:0.3571:0:1 1/1:5:4:0,4:0,1:1,4:0.8:0,0:22:1:30.5:1:1:0:53.3:8:0.8:0:1 +6 29491195 . G GC 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.19087;LSEQ=TTCCTGTTTTATCCTAAACA;RSEQ=CTTCTTTCCTAAATAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:3,2:6,3:9,5:0.3571:2,2:20.2:1:29.6:1:1:1.30579:60:10:0.3571:0.2143:0 0/1:10:4:3,1:5,1:6,4:0.4:2,2:33:1:31.6:1:1:1.58108:60:8:0.4:0.1:0 +6 29491263 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.18149;SOR=Inf;LSEQ=AAGATTTCTTTGTTGTTGCT;RSEQ=CTGTTGTTGCTGCTGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:15,18:33,0:0:2,0:26.6:1:32.6:1:1:0:60:32:1:0:0.2 0/1:25:2:1,1:10,13:23,2:0.08:2,2:37:1:30.5:1:1:1.29:60:4:0.08:0:1 +6 29491297 . GTC G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.50046;SOR=0;LSEQ=TGTTGTTTCCTTGAGACAAG;RSEQ=TCTCTCTCTGTGTCACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:24:1:30.5:1:1:1.0801:60:4:0.0769:0:0 0/0:20:0:0,0:8,12:20,0:0:2,0:29.9:1:29.4:1:1:0:59.2:40:1:0:0.2 +6 29691019 . G A 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64241;SOR=2.05177;LSEQ=GAGGCGGTGTCTGGGGTTGG;RSEQ=AGGCTCAGTATTGAGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:36.7:1:24.3:1:1:0:60:2:0.2222:0:1.7 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:24.3:1:25.8:1:1:0:60:3:0.375:0:1.8 +6 29691090 . T A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=9.71141;LSEQ=CAACCCGTGTCAGGTCCTTC;RSEQ=TCCTGGATACTCATAACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:6:6,0:58,2:60,6:0.0909:1,0:25.3:1:30.8:1:1:0:60:12:0.0909:0:1.2 1/0:34:17:16,1:14,2:16,17:0.5:2,1:19.4:1:29.9:1:0.60117:2.23:60:34:0.5152:0:1.2 +6 29691097 . A T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01518;SOR=Inf;LSEQ=TGTCAGGTCCTTCTTCCTGG;RSEQ=TACTCATAACGCGGCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:70,3:73,0:0:1,0:22.8:1:30.1:1:1:0:60:23.333:1:0:0.2 0/1:41:4:3,1:34,3:37,4:0.0976:2,2:22:1:29.3:1:0.34783:3.59822:60:8:0.1053:0:2 +6 29691140 . C G 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=Inf;LSEQ=CTCACTCCCATTGGGCGTCG;RSEQ=GTTTCTAGAGAAGCCAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:123,6:129,0:0:1,0:25.3:1:32.2:1:1:0:59.9:42:1:0:0.1 0/1:96:12:10,2:77,7:84,12:0.125:2,2:28.3:1:31.6:1:0.31257:2.17739:60:24:0.1304:0:1.4 +6 29691166 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19133;SOR=Inf;LSEQ=TAGAGAAGCCAATCAGTGTC;RSEQ=CCGCAGTTCCCAGGTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:179,21:200,0:0:2,0:22.7:1:29.7:1:1:0:59.9:39:1:0:0.2 0/1:156:2:1,1:136,18:154,2:0.0128:2,2:12:1:26:1:0.22945:7.38177:60:4:0.0133:0:1.5 +6 29691303 . G A 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=46.98423;LSEQ=GCCCTGACCGATACTTGGGC;RSEQ=GGTGAGTGCGGGGTCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:544:1:1,0:230,311:541,1:0.0018:2,0:1:0:29:0:0.4262:0:39:2:0.0019:0:2 0/1:438:35:13,22:162,241:403,35:0.0799:2,2:21.5:1:30:1:0.85758:1.1372:58.3:70:0.0805:0:1.1 +6 29691390 . CT GC 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=5.50281;LSEQ=CGCAGGACTCAGGGAGCCGC;RSEQ=CCGGAGGAGGGTCTGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:103:41,62:74,101:175,103:0.364:2,2:23.8:1:31.5:1:0.70687:1.10754:54.5:206:0.3718:0.0601:1 1/0:154:117:62,55:17,18:35,117:0.7597:2,2:23.4:1:30.3:1:0.70202:1.19:52.4:234:0.7748:0.0714:1.1 +6 29691391 . T C 41 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.46062;SOR=1.85525;LSEQ=GCAGGACTCAGGGAGCCGCC;RSEQ=CCGGAGGAGGGTCTGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:4:1,3:73,103:176,4:0.015:2,2:18.3:1:27.8:1:0.64463:2.11816:56:3:0.0173:0:2.5 0/1:145:4:1,3:17,18:35,4:0.0276:2,2:12.8:1:20.8:1:0.60937:2.7643:50:1:0.0556:0:1.8 +6 29691396 . A G 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30188;SOR=0;LSEQ=ACTCAGGGAGCCGCCTCCGG;RSEQ=GGAGGGTCTGGCGGGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:4:2,2:113,161:274,4:0.0143:2,2:15.3:1:31.5:1:1:1.42:43:8:0.0148:0:2 0/0:167:0:0,0:85,82:167,0:0:2,0:22.6:1:29.1:1:1:0:54:32.4:1:0:0.9 +6 29691408 . C T 23 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5654;SOR=3.0651;LSEQ=GCCTCCGGAGGAGGGTCTGG;RSEQ=GGGTCTCAGCCCCTCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:1:0,1:136,162:298,1:0.0033:2,0:1:0:26:0:1:0:60:2:0.0034:0:1 0/1:196:2:1,1:107,87:194,2:0.0102:2,2:6.5:1:23.5:1:1:1.22857:60:4:0.0105:0:1.5 +6 29691487 . G A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26603;SOR=0;LSEQ=GTGTCGCGGCCCGGCCGCGG;RSEQ=GAGCCCCGCTACATCGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:2,1:125,147:272,3:0.0109:2,2:15:1:28:1:0.59704:2.34:60:6:0.0111:0:1.3 0/0:202:0:0,0:89,113:202,0:0:2,0:23.6:1:29.7:1:1:0:60:39.4:1:0:0.2 +6 29691524 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16943;SOR=Inf;LSEQ=CCGTGGAGTACGTAGACGAC;RSEQ=CGCAATTCCTGCGGTTCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:95,143:238,0:0:2,0:22.9:1:29.7:1:1:0:60:58.5:1:0:0.2 0/1:167:2:1,1:71,94:165,2:0.012:2,2:29.5:1:30:1:1:1.32:60:4:0.0123:0:1.5 +6 29691551 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21714;SOR=Inf;LSEQ=TCCTGCGGTTCGACAGCGAC;RSEQ=CCGCGATTCCGAGGATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:82,126:208,0:0:2,0:28.9:1:31.3:1:1:0:59.9:40.6:1:0:0.1 0/1:182:2:1,1:88,92:180,2:0.011:2,2:27:0:31:1:1:1.05:60:4:0.0113:0:1.5 +6 29691592 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=CCGCGGGAGCCGTGGGTGGA;RSEQ=CAAGAGGGGCCGCAGTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:75,103:178,0:0:2,0:22.5:1:32.8:1:1:0:59.9:177:1:0:0.1 0/1:181:2:1,1:96,83:179,2:0.011:2,2:30.5:1:28.5:1:1:1.15569:58:4:0.0111:0:3 +6 29691604 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49915;SOR=Inf;LSEQ=TGGGTGGAGCAAGAGGGGCC;RSEQ=CAGTATTGGGAGTGGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:76,90:166,0:0:2,0:22.3:1:31.1:1:1:0:59.9:165:1:0:0.1 0/1:178:2:1,1:95,80:175,2:0.0112:2,2:33.5:1:28.5:1:1:1.18634:60:4:0.0114:0:1 +6 29691648 . A G 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19985;SOR=0;LSEQ=GTACGCCAAGGCCAACGCAC;RSEQ=GACTGACCGAGTGGCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:74,87:161,2:0.0123:2,2:20:1:26.5:1:1:1.17:60:4:0.0123:0:1 0/0:201:0:0,0:90,111:201,0:0:2,0:26.1:1:29.6:1:1:0:60:49.25:1:0:0.2 +6 29691713 . A C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02413;SOR=Inf;LSEQ=AGAGCGAGGCTGGTGAGTGA;RSEQ=CCCGGCCGGGGGCGCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:32,62:94,0:0:2,0:22.2:1:29.7:1:1:0:60:188:1:0:0.2 0/1:87:5:1,4:23,59:82,5:0.0575:2,2:24:1:28.8:1:1:1.55213:60:10:0.0581:0:2 +6 29691736 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50041;SOR=0;LSEQ=CGGCCGGGGGCGCAGGTCAC;RSEQ=ACCACCCCCCATCCGCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:14,45:59,2:0.0328:2,2:37:1:30.5:1:0.43443:3.14:60:4:0.0333:0:2 0/0:50:0:0,0:13,37:50,0:0:2,0:23.4:1:29.9:1:1:0:60:100:1:0:0.7 +6 29691740 . AC A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.18733;SOR=Inf;LSEQ=CGGGGGCGCAGGTCACGACC;RSEQ=CCCCCATCCGCCACGGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:11,46:57,0:0:2,0:22.2:1:32:1:1:0:60:114:1:0:0.2 0/1:44:2:0,2:11,31:42,2:0.0455:2,0:38.5:1:30.5:1:1:0:60:4:0.0488:0:0.5 +6 29691744 . C G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.07371;SOR=Inf;LSEQ=GGCGCAGGTCACGACCACCC;RSEQ=CCATCCGCCACGGACCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:9,45:54,0:0:2,0:22.9:1:31.8:1:1:0:60:108:1:0:0.2 0/1:40:3:0,3:9,28:37,3:0.075:2,0:39.3:1:31.3:1:1:0:60:6:0.0769:0:2.3 +6 29691772 . T C 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00034;SOR=7.64131;LSEQ=CCACGGACCGCCCGGGTCCC;RSEQ=CAGAGTCTCCGGATCCGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:6:1,5:9,29:38,6:0.1364:2,2:17.8:1:32.3:1:1:1.5377:60:12:0.1395:0:1.3 1/0:27:15:4,11:0,12:12,15:0.5556:0,2:26.9:1:30:1:0.10598:0:60:14:0.5385:0:1.7 +6 29691774 . A C 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00074;SOR=Inf;LSEQ=ACGGACCGCCCGGGTCCCTC;RSEQ=GAGTCTCCGGATCCGAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:11,32:43,0:0:2,0:24.2:1:31.9:1:1:0:60:86:1:0:0.3 0/1:27:7:3,4:1,19:20,7:0.2593:1,2:34.3:1:31.1:1:0.04188:12.39:60:14:0.2593:0:2.1 +6 29691857 . C G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-04;SOR=15.66999;LSEQ=GAGTCCCAGGCGCCTTTACC;RSEQ=AGGTTCATTTTCAGTTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:2,1:19,15:34,3:0.0811:2,2:22.7:1:29:1:1:1.56:60:6:0.0833:0:1.3 1/0:15:9:4,5:5,1:6,9:0.6:2,2:27.8:1:30.2:1:0.28671:5.514:60:18:0.6:0:1.1 +6 29691936 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14012;SOR=Inf;LSEQ=TAGCTGGGCGGGGCTGACTG;RSEQ=GGGGACCGGCTAGGGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:43,18:61,0:0:2,0:24.8:1:30.9:1:1:0:60:29.5:1:0:0 0/1:37:2:1,1:26,9:35,2:0.0541:2,2:46.5:1:29.5:1:0.47297:2.79285:60:4:0.0541:0:1 +6 29691992 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20006;SOR=Inf;LSEQ=GAATGGCTGCGACATGGGGC;RSEQ=CGACGGACGCCTCCTCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:51,46:97,0:0:2,0:24.6:1:31:1:1:0:59.8:96:1:0:0.1 0/1:79:2:1,1:47,30:77,2:0.0253:2,2:24:0:31:1:1:1.55745:60:4:0.026:0:1.5 +6 29692000 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.21282;SOR=Inf;LSEQ=GCGACATGGGGCCCGACGGA;RSEQ=GCCTCCTCCGCGGGTATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:54,47:101,0:0:2,0:25.7:1:30.7:1:1:0:59.8:49.5:1:0:0.1 0/1:87:2:1,1:52,33:85,2:0.023:2,2:11.5:1:27.5:1:1:1.56722:60:4:0.0241:0:1 +6 29692050 . C A 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24428;SOR=0;LSEQ=TACGACGGCAAGGATTACAT;RSEQ=TCCCTGAACGAGGACCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:44,62:106,2:0.0185:2,2:36:0:30:1:1:1.40:45:4:0.0187:0:1.5 0/0:110:0:0,0:52,58:110,0:0:2,0:26.6:1:30.9:1:1:0:58.8:220:1:0:0.2 +6 29692305 . A G 66 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52381;SOR=4.91839;LSEQ=CAAGGTTGGGAGGAAAGTGG;RSEQ=CCCAATGCTAGGATATCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:1,2:3,1:0.25:2,0:12:0:33:0:1:0:60:2:0.25:0:1 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:30.5:1:33:1:1:0:60:8:0.6667:0:1 +6 29692433 . T C 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACAATTAAGGGATGAAAT;RSEQ=TCTGAGGGAATGGAGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:25:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:32:1:1:0:60:4:1:0:1 +6 29692562 . A G 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTCACACTCAATGTGTTTG;RSEQ=GGCTCTGATTCCAGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:28.5:1:31.5:1:1:0:56.5:4:0.5:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:14:0:25:0:1:0:38:2:1:0:1 +6 29692634 . T G 36 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03333;SOR=Inf;LSEQ=TGCTCCCCCCTCAGAGACTC;RSEQ=AACTTTCCAAGGAATAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:4,2:6,1:0.1429:2,0:17:0:26:0:1:0:53:2:0.1429:0:2 1/1:3:3:3,0:0,0:0,3:1:0,0:12.7:1:23.3:1:1:0:34.3:2:1:0:1.3 +6 29692852 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49701;SOR=0;LSEQ=ACCACCCCATCTCTGACCAT;RSEQ=AGGCCACCCTGAGGTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:39,43:82,2:0.0238:2,2:18.5:1:31:1:1:1.10:60:4:0.0247:0:1 0/0:84:0:0,0:34,50:84,0:0:2,0:22:1:30.8:1:1:0:53.9:168:1:0:0.1 +6 29693011 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.57756;LSEQ=GGGCCGCTGTGGTGGTGCCT;RSEQ=CTGGAGAGGAACAGAGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:117:86,31:121,44:165,117:0.4149:2,2:21.4:1:30:1:1:1.01:27.8:57.5:0.4197:0:1.1 1/0:202:145:106,39:38,19:57,145:0.7178:2,2:22.3:1:29.7:1:0.3901:1.36:27:144:0.7236:0:1 +6 29693113 . C T 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGATGGGTAAAGAGGGGAA;RSEQ=GAGGGGTCATGTCTTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:188,225:413,0:0:2,0:23.2:1:30.7:1:1:0:59.9:50.625:0.9975:0:0.1 0/1:347:24:14,10:134,187:321,24:0.0692:2,2:19.1:1:29.8:1:0.13576:1.95:59.6:23:0.0673:0:1.2 +6 29693183 . G A 203 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGCAGGGTCAGGGCTGAG;RSEQ=CCTGGAGATCAGGGCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:115:62,53:166,111:277,115:0.2926:2,2:22.5:1:29.7:1:0.31164:1.27758:59.8:56.5:0.2974:0:1.2 0/0:326:0:0,0:192,132:324,0:0:2,0:21.5:1:30.5:1:1:0:59.9:63.8:0.9969:0:0.2 +6 29693370 . T A 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04884;SOR=Inf;LSEQ=GGTGAGGAGTGGAGTCTGAG;RSEQ=TTTCTTGTCCCACTGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:81,207:288,0:0:2,0:22.2:1:29.9:1:1:0:59.4:71:1:0:0.1 0/1:257:4:3,1:79,174:253,4:0.0156:2,2:9.3:1:24.8:1:0.09714:6.56:37.3:3:0.0119:0:4.8 +6 29693392 . G A 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17308;SOR=5.19327;LSEQ=TTCTTGTCCCACTGGGGGTT;RSEQ=CAAGCCCCAAGTAGAAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:1:0,1:32,134:166,1:0.006:2,0:39:0:31:0:1:0:52:2:0.006:0:1 0/1:132:4:2,2:27,101:128,4:0.0303:2,2:13.5:1:26.8:1:0.20962:3.69:57.8:8:0.031:0:1 +6 29693499 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03805;SOR=Inf;LSEQ=CAGCACCTACTCATTTGTAA;RSEQ=GCTCCTGTGAAAATGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:4,31:35,0:0:2,0:21.9:1:31.6:1:1:0:60:34:1:0:0.1 0/1:9:2:0,2:1,6:7,2:0.2222:2,0:29:1:29:1:1:0:60:4:0.2222:0:2 +6 29693680 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1369;SOR=Inf;LSEQ=GATCCTGCCCTGGATCTACA;RSEQ=TTACACTTTTCTGGAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:33,7:40,0:0:2,0:24.7:1:33.4:1:1:0:60:80:1:0:0 0/1:24:2:2,0:20,2:22,2:0.0833:2,0:32.5:1:31.5:1:1:0:60:4:0.0909:0:1 +6 29693726 . G T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01092;SOR=Inf;LSEQ=GGATCAAAGACTAGGGGTTT;RSEQ=CTCTAGGACCTTATGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:79,33:112,0:0:2,0:23.2:1:32.3:1:1:0:60:55:1:0:0 0/1:79:5:4,1:54,20:74,5:0.0633:2,2:18.4:1:30.2:1:1:1.47:60:10:0.0641:0:1 +6 29693811 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23213;SOR=Inf;LSEQ=GAAACAGAGGGAGCTACTCT;RSEQ=AGGCTGCAGGTAAGATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:84,94:178,0:0:2,0:24.8:1:32.2:1:1:0:59.6:177:1:0:0.1 0/1:166:2:1,1:89,75:164,2:0.012:2,2:33:1:27.5:1:1:1.18544:60:4:0.0123:0:1 +6 29693815 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2334;SOR=Inf;LSEQ=CAGAGGGAGCTACTCTCAGG;RSEQ=TGCAGGTAAGATGAAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:82,94:176,0:0:2,0:25.5:1:32.5:1:1:0:59.6:57.667:1:0:0.1 0/1:165:2:1,1:87,76:163,2:0.0121:2,2:5.5:1:27.5:1:1:1.1438:60:4:0.0123:0:1 +6 29693833 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49865;SOR=0;LSEQ=GGCTGCAGGTAAGATGAAGG;RSEQ=GGCTGATCCCTGAGATTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:72,86:158,2:0.0125:2,2:26.5:1:29:1:1:1.19:60:4:0.0131:0:1 0/0:153:0:0,0:73,80:153,0:0:2,0:27.8:1:28.7:1:1:0:59.9:16:1:0:0.2 +6 29693938 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02152;SOR=2.7053;LSEQ=GTGGGCTCTGACCAGGTCCT;RSEQ=TTTTTGTTCTACCCCAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:9:3,6:51,77:128,9:0.0657:2,2:24.1:1:30.2:1:1:1.32204:60:18:0.0667:0:1 0/1:106:17:4,13:40,49:89,17:0.1604:2,2:27:1:28.2:1:0.11553:2.63066:60:7.5:0.1456:0:1.2 +6 29693952 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18367;SOR=Inf;LSEQ=GGTCCTGTTTTTGTTCTACC;RSEQ=CAATCACTGACAGTGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:50,84:134,0:0:2,0:26.5:1:31.1:1:1:0:60:43.667:1:0:0.4 0/1:101:2:1,1:39,60:99,2:0.0198:2,2:49.5:1:29:1:1:1.53:60:4:0.0198:0:2 +6 29693966 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19524;SOR=Inf;LSEQ=TCTACCCCAATCACTGACAG;RSEQ=GCCCAGGGCTCTGGGGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:43,65:108,0:0:2,0:25:1:29.9:1:1:0:60:53:1:0:0.5 0/1:86:2:1,1:34,50:84,2:0.0233:2,2:26:0:32.5:1:1:1.46:60:4:0.0233:0:1 +6 29693969 . C T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00723;SOR=0.34209;LSEQ=ACCCCAATCACTGACAGTGC;RSEQ=CAGGGCTCTGGGGTGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:31:12,19:29,48:77,31:0.287:2,2:26.4:1:30.5:1:1:1.04:60:62:0.2925:0:1.2 0/1:83:10:2,8:31,42:73,10:0.1205:2,2:28.9:1:29.1:1:0.30187:2.9184:60:20:0.1235:0:1.1 +6 29759729 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CAGAAGTAGCGGGGTCAGGG;RSEQ=GAAGTCCCAGGGCCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:18.5:1:32:0:0.33333:0:60:4:0.3333:0:2.5 0/0:3:0:0,0:3,0:3,0:0:0,0:24:1:32.7:1:1:0:56.7:6:1:0:1 +6 29759750 . G A 81 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.60277;LSEQ=GAAGTCCCAGGGCCTCAGGC;RSEQ=TGGCTCTCAGGATCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:5,1:7,0:7,6:0.4615:0,2:19.2:1:31.5:1:0.46154:0:54.3:12:0.4615:0:3.5 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:31:0:32:0:1:0:50:2:0.5:0:3 +6 29759811 . C G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52868;SOR=1.58697;LSEQ=TGGGGAGGCCCAGCGCTGGG;RSEQ=ATTCCCCATCTTTGCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:12:12,0:31,1:32,12:0.2727:1,0:30.2:1:31.5:1:1:0:52.2:24:0.2791:0:3.6 0/1:16:6:5,1:9,1:10,6:0.375:2,2:24.5:1:31.7:1:1:1.73197:52.2:12:0.375:0:4.2 +6 29759823 . TT CC 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.38892;SOR=1.65448;LSEQ=GCGCTGGGCATTCCCCATCT;RSEQ=GCAGGGTTTCTCTTCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:12:12,0:37,2:39,12:0.2308:2,0:24:1:31:1:1:0:50.5:24:0.2449:0.0192:2.4 0/1:21:7:6,1:11,2:13,7:0.3333:2,2:27.4:1:31.1:1:1:1.09:48.7:14:0.3333:0:3.3 +6 29759824 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTGGGCATTCCCCATCTT;RSEQ=GCAGGGTTTCTCTTCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:2,0:37,2:39,2:0.0385:2,0:10.5:1:32.5:1:1:0:51:4:0.0513:0:3 0/0:21:0:0,0:11,2:13,0:0:2,0:19.4:1:29.2:1:1:0:60:26:1:0:0.2 +6 29759876 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26656;SOR=1.42733;LSEQ=TGTCGGGTCCTTCTTCCTGG;RSEQ=TACTCACCGGGCTGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:37:34,3:98,10:108,37:0.2552:2,2:32:1:30.1:1:1:1.16:52:36:0.2571:0:1.4 0/1:73:24:22,2:42,6:48,24:0.3288:2,2:22.3:1:28.8:1:0.71044:1.56:54.4:48:0.338:0:3.1 +6 29759885 . G A 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCTTCCTGGGTACTCACC;RSEQ=GGCTGCCCCAGTTCTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:153,15:168,0:0:2,0:25.7:1:30.1:1:1:0:58.2:83:1:0:0.4 0/1:100:34:31,3:58,7:65,34:0.34:2,2:19.8:1:29.6:1:1:1.24:56.1:68:0.3434:0:2.8 +6 29759894 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15519;SOR=Inf;LSEQ=GGGTACTCACCGGGCTGCCC;RSEQ=AGTTCTCACTCCCATTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:173,17:190,0:0:2,0:26:1:31.8:1:1:0:58.4:380:1:0:0.3 0/1:124:2:1,1:112,10:122,2:0.0161:2,2:21:1:28:1:0.17021:10.72653:60:4:0.0167:0:1 +6 29759920 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17429;SOR=Inf;LSEQ=TCACTCCCATTGAGTGTCGG;RSEQ=TTTCTAGAGAAGCCAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:242,28:270,0:0:2,0:23.8:1:31.2:1:1:0:59:66.5:1:0:0.4 0/1:194:2:1,1:172,20:192,2:0.0103:2,2:16:1:27:1:0.20528:8.41571:60:4:0.0105:0:1 +6 29759923 . T C 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCCCATTGAGTGTCGGGTT;RSEQ=CTAGAGAAGCCAATCAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:246,31:277,0:0:2,0:23.9:1:31:1:1:0:59.2:91.333:1:0:0.4 0/1:206:69:60,9:123,14:137,69:0.335:2,2:25.5:1:30.4:1:0.63998:1.31599:58.8:22:0.3267:0:2.1 +6 29759996 . T C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00597;SOR=1.30624;LSEQ=CCCACCGGGACTCCGATTCT;RSEQ=CCCAGTCGCCGAGGATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:294:170,124:370,306:676,294:0.3031:2,2:26.9:1:31.6:1:0.39897:1.13:59.1:48:0.3035:0:1.2 0/1:966:350:191,159:338,278:616,350:0.3623:2,2:27.1:1:30:1:0.94644:1.01212:58.5:57.333:0.361:0:1.3 +6 29760029 . G C 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATGGTGTCATGGCGCCCC;RSEQ=AACCCTGCTTCTGCTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1128:0:0,0:551,573:1124,0:0:2,0:25.3:1:30.7:1:1:0:59.7:47.87:0.9964:0:0.4 0/1:1113:48:21,27:508,555:1063,48:0.0431:2,2:30:1:30.8:1:0.65843:1.17666:60:96:0.044:0:1.1 +6 29760050 . CG C 99 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.01961;SOR=5.26683;LSEQ=AACCCTGCTTCTGCTGCTCT;RSEQ=GGGGCCCTGGTCCTGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:955:2:1,1:431,519:950,2:0.0021:2,2:19:1:33.5:1:1:1.20:60:4:0.0021:0:0 0/1:914:10:5,5:391,511:902,10:0.0109:2,2:24:1:30:1:0.75386:1.31:60:20:0.0111:0.0011:0.1 +6 29760111 . G C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76129;SOR=0.94975;LSEQ=GGGGTCGGGAGGGAAACGGC;RSEQ=TCTGTGGGGAGTAGCTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:150:41,109:88,207:295,150:0.3371:2,2:24.6:1:32.5:1:0.65859:1.12988:58.6:49:0.3349:0:1.9 0/1:347:113:32,81:70,163:233,113:0.3256:2,2:23.6:1:30.8:1:0.80198:1.08681:58.8:55.5:0.3246:0:1.3 +6 29760132 . G T 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTGTGGGGAGTAGCTAGGG;RSEQ=CCTGCCCGGCGGGGGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:108:25,83:59,168:227,108:0.3224:2,2:25.2:1:29.9:1:0.5931:1.16541:59.6:53:0.3242:0:2.3 0/0:239:0:0,0:69,168:237,0:0:2,0:23.4:1:30.6:1:1:0:59.9:78:1:0:0.5 +6 29760149 . G T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00937;SOR=Inf;LSEQ=GGGGCCTGCCCGGCGGGGGC;RSEQ=CAGGAACCCGGTTGCGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:74,199:273,0:0:2,0:24.4:1:31.4:1:1:0:59.7:33.125:0.9925:0:0.7 0/1:180:5:2,3:51,123:174,5:0.0278:2,2:35:1:29.6:1:0.63351:1.60:60:10:0.0281:0:2.4 +6 29760188 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.6224;SOR=1.13376;LSEQ=GCCGGGAGGAGGGTCGGGAG;RSEQ=GTCTCAGCCCCCTCCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:61:23,38:44,89:133,61:0.3112:2,2:22.9:1:32.1:1:0.62588:1.22:60:122:0.3228:0:1.8 0/1:121:41:10,31:20,60:80,41:0.3388:2,2:21:1:30.2:1:1:1.03306:60:82:0.3388:0:1.5 +6 29760299 . C A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.6624;LSEQ=CTCTCCGTGGGCGACGTGGA;RSEQ=GACACGCAGTGCGTGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:90,82:172,2:0.0115:2,2:19:1:29.5:1:1:1.09697:60:4:0.0117:0:1 0/0:131:1:1,0:74,56:130,1:0.0076:2,0:1:0:23:0:1:0:60:2:0.0079:0:1 +6 29760311 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50429;SOR=0;LSEQ=GACGTGGACGACACGCAGTG;RSEQ=GTGCGGCTCGACAGCGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:84,82:166,2:0.0119:2,2:13:1:30.5:1:1:1.02425:60:4:0.0121:0:2 0/0:135:0:0,0:75,60:135,0:0:2,0:26:1:29.9:1:1:0:60:44:1:0:0.2 +6 29760317 . G C 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACGACACGCAGTGCGTGCG;RSEQ=CTCGACAGCGACGCCACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:39:12,27:74,53:127,39:0.2349:2,2:24.4:1:30.7:1:0.00327:3.11956:59.6:18.5:0.2298:0:1.1 0/0:141:0:0,0:80,61:141,0:0:2,0:25.4:1:29.6:1:1:0:60:14.667:1:0:0.2 +6 29760341 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50223;SOR=0;LSEQ=GACAGCGACGCCACGAGTCC;RSEQ=AGGATGGAGCCGCGGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:85,96:181,2:0.0109:2,2:25:1:29.5:1:1:1.13:60:4:0.0113:0:1 0/0:154:0:0,0:89,65:154,0:0:2,0:34:0:14:0:1:0:60:0:0:0:2 +6 29760351 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50288;SOR=0;LSEQ=CCACGAGTCCCAGGATGGAG;RSEQ=CGCGGGCGCCGTGGATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:80,99:179,2:0.011:2,2:49.5:1:30.5:1:1:1.24:60:4:0.0113:0:1.5 0/0:150:0:0,0:82,68:150,0:0:2,0:25.7:1:30.7:1:1:0:59.5:49:1:0:0.2 +6 29760352 . CGCGGGCGCCGTGGATGGAGCA C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33066;SOR=1.35795;LSEQ=CACGAGTCCCAGGATGGAGC;RSEQ=GGAGGGGCCGGAATATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:31:12,19:65,80:145,31:0.1761:2,2:28.6:1:31.5:1:0.5571:1.28464:59.5:62:0.1782:0.0227:0.9 0/1:151:34:21,13:63,54:117,34:0.2252:2,2:25.5:1:30.7:1:0.43988:1.38:59.9:68:0.2267:0.053:0.2 +6 29760364 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21837;SOR=Inf;LSEQ=GATGGAGCCGCGGGCGCCGT;RSEQ=GATGGAGCAGGAGGGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:65,75:140,0:0:2,0:25.9:1:31.5:1:1:0:60:69:1:0:0.2 0/1:147:2:1,1:67,52:119,2:0.0136:2,2:28:0:31:1:1:1.28573:60:4:0.0167:0:1.5 +6 29760365 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.22566;SOR=Inf;LSEQ=ATGGAGCCGCGGGCGCCGTG;RSEQ=ATGGAGCAGGAGGGGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:62,74:136,0:0:2,0:26.7:1:32:1:1:0:60:272:1:0:0.2 0/1:148:2:1,1:67,53:120,2:0.0135:2,2:20:1:27:1:1:1.2617:60:4:0.0164:0:1 +6 29760399 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.20683;SOR=Inf;LSEQ=GGCCGGAATATTGGGAAGAG;RSEQ=AGACAGGGACCGCCAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:102,106:208,0:0:2,0:21.6:1:31.7:1:1:0:60:103:1:0:0.3 0/1:174:2:1,1:95,77:172,2:0.0115:2,2:23:1:31:1:1:1.23226:60:4:0.0115:0:1 +6 29760462 . T C 160 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=ACCTGCGGACCCTGAGCGGC;RSEQ=ACTACAACCAGAGTGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:35:18,17:88,107:195,35:0.1522:2,2:30.7:1:31.3:1:0.58142:1.29:60:34:0.1491:0:1.5 0/0:243:0:0,0:107,136:243,0:0:2,0:29.8:1:28.5:1:1:0:60:59.75:1:0:0.4 +6 29760504 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23182;SOR=0;LSEQ=GTGAGTGACACCGGCCGGGG;RSEQ=CGCAGGTCACTACCCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:47,75:122,2:0.0161:2,2:22.5:1:28.5:1:1:1.59:60:4:0.0165:0:1 0/0:133:0:0,0:50,83:133,0:0:2,0:21.6:1:30.4:1:1:0:60:43.333:1:0:0.8 +6 29760510 . G A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=3.54799;LSEQ=GACACCGGCCGGGGGCGCAG;RSEQ=TCACTACCCCTCCACATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:17:4,13:39,52:91,17:0.1574:2,2:20.3:1:30.9:1:0.18012:2.41886:60:34:0.1619:0:1.9 0/1:115:46:17,29:24,45:69,46:0.4:2,2:22.9:1:29.2:1:0.84433:1.10:60:92:0.4035:0:2 +6 29760523 . C T 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGCGCAGGTCACTACCCCTC;RSEQ=ACATCCCCCACGGACCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:28,58:86,0:0:2,0:22.4:1:31.6:1:1:0:59.5:27.667:1:0:0.4 0/1:81:35:12,23:17,29:46,35:0.4321:2,2:22.3:1:27.9:1:0.81993:1.12195:60:34:0.425:0:2.3 +6 29760536 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19119;SOR=Inf;LSEQ=ACCCCTCCACATCCCCCACG;RSEQ=ACCGCCCGGGTCTCCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:25,49:74,0:0:2,0:22.2:1:31.8:1:1:0:59.5:73:1:0:0.3 0/1:58:2:0,2:16,40:56,2:0.0345:2,0:18.5:1:32.5:1:1:0:60:4:0.0345:0:1 +6 29760590 . G A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03325;SOR=2.69944;LSEQ=GATCCACGCCGAGGCAGCGG;RSEQ=ACCTGGAGACCCTTGACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:13:10,3:33,27:60,13:0.1781:2,2:32.3:1:28.4:1:0.21568:2.69:60:5.5:0.1571:0:2.3 0/1:35:13:7,6:11,11:22,13:0.3714:2,2:23.1:1:28.7:1:1:1.16:60:26:0.3824:0:2.6 +6 29760605 . G T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22119;SOR=1.81323;LSEQ=AGCGGGACCTGGAGACCCTT;RSEQ=ACCCGGGAGAGGCCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:13:11,2:40,24:64,13:0.1688:2,2:27.6:1:28.8:1:0.19865:3.26:60:12:0.1579:0:2.3 0/1:37:10:6,4:16,11:27,10:0.2703:2,2:26.8:1:28.3:1:1:1.03:60:20:0.2857:0:2.4 +6 29760677 . A G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30855;SOR=1.30995;LSEQ=CCCGCAGGTTGGTCCTGGCG;RSEQ=GGGCGGGGCTCGGTGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:43:33,10:138,20:158,43:0.2129:2,2:20.9:1:30.1:1:0.09414:2.08213:55.7:13.333:0.2073:0:1.6 0/1:149:39:35,4:93,17:110,39:0.2617:2,2:22.2:1:31.1:1:0.59367:1.59:57.6:78:0.2708:0:1.3 +6 29760730 . AC A 212 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGGCGGGGCCAGGGTCTCAC;RSEQ=CCATCTAGAGGATGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:99:62,37:224,163:387,99:0.2037:2,2:27.7:1:32:1:0.42428:1.22:57.8:198:0.2054:0.0226:1.6 0/0:469:0:0,0:266,202:468,0:0:2,0:25:1:30.7:1:1:0:59.7:45.8:0.9978:0:0.3 +6 29760765 . C A 205 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTCTGTCTGCGACGTGGGGT;RSEQ=GGACGGGCGCCTACTCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:118:64,54:228,251:479,118:0.1977:2,2:25.6:1:29.8:1:0.21769:1.30:58.9:236:0.2014:0:2 0/0:573:0:0,0:277,295:572,0:0:2,0:27.6:1:29.7:1:1:0:59.9:94.333:0.9982:0:0.3 +6 29760799 . T C 198 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCGCGGGTATCACCAGCT;RSEQ=GCTTACGATGGCAAGGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:93:45,48:119,204:323,93:0.2236:2,2:25.1:1:30.3:1:0.05385:1.61:59.9:30:0.2217:0:2.3 0/0:423:0:0,0:181,241:422,0:0:2,0:24.8:1:29.5:1:1:0:60:421:0.9976:0:0.3 +6 29760819 . A C 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTTACGATGGCAAGGATT;RSEQ=CATCGTCCTGAACGAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:0:0,0:117,229:346,0:0:2,0:22.3:1:29.1:1:1:0:59.8:68.2:0.9971:0:0.6 0/1:307:74:25,49:93,140:233,74:0.241:2,2:20.4:1:30:1:0.41081:1.3009:60:36:0.2361:0:1.1 +6 29760854 . G A 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56846;SOR=2.95263;LSEQ=AGGACCTGTGCTCCTTGACA;RSEQ=CCGCAGACACGGCGGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:54,174:228,1:0.0044:2,0:1:0:29:0:0.24017:0:60:2:0.0044:0:2 0/1:156:2:1,1:40,114:154,2:0.0128:2,2:41:0:31:1:0.45782:2.83:53:4:0.0128:0:2 +6 29760856 . C T 188 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACCTGTGCTCCTTGACAGC;RSEQ=GCAGACACGGCGGCTCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:77:21,56:31,117:148,77:0.3422:2,2:23.9:1:30.1:1:0.31871:1.41:58.8:37.5:0.3363:0:1.7 0/0:153:0:0,0:38,115:153,0:0:2,0:24.8:1:29:1:1:0:59.9:37.25:1:0:0.3 +6 29760900 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05871;SOR=Inf;LSEQ=CCAGCTCAAGTGGGAGGCGG;RSEQ=CCGGGGGGCGGAGGTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:40,122:162,0:0:2,0:25.2:1:31.5:1:1:0:59.5:53:1:0:0.4 0/1:104:3:1,2:26,75:101,3:0.0288:2,2:15.7:1:27:1:1:1.44:55.3:6:0.0291:0:1.7 +6 29761062 . A G 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=CGCGGGACACACCTCAGAGG;RSEQ=AAGGGGATGAAGCGTGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:20.3:1:32.7:1:1:0:59.7:6:0.5:0:2.3 1/0:4:2:0,2:0,2:2,2:0.5:0,0:25.5:1:29.5:1:1:0:60:4:0.5:0:3.5 +6 29761080 . T G 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22619;SOR=7.11489;LSEQ=GGAAAGGGGATGAAGCGTGG;RSEQ=CCATGACCATGGCACCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:29:0:34:0:1:0:59:2:0.2:0:5 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25.5:1:29.5:1:1:0:60:4:0.6667:0:3.5 +6 29761835 . A G 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69794;SOR=1.54582;LSEQ=AGTGACTGGTCACAGCAGGC;RSEQ=TTAAGGCAAGCCATTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:7,4:11,5:0.3125:2,2:27.6:1:32:1:1:1.15538:60:10:0.3125:0:2.6 0/1:12:5:2,3:4,3:7,5:0.4167:2,2:35.6:1:31.6:1:1:1.88578:60:10:0.4167:0:2.2 +6 29761880 . T C 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09463;SOR=5.21634;LSEQ=CACGGGACTCCTCTGATGGC;RSEQ=AACTGTAGCTGGAAGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:6,8:14,5:0.2632:2,2:28.6:1:31.6:1:1:1.11808:60:10:0.2632:0:3.2 1/0:9:6:3,3:1,2:3,6:0.6667:2,2:16:1:31.7:1:1:1.85:53.3:12:0.6667:0:2.5 +6 29761896 . A G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12874;SOR=5.91384;LSEQ=TGGCTAACTGTAGCTGGAAG;RSEQ=CTCCTCCACGGCCTTGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:4,6:10,3:0.2308:2,2:39:1:32.7:1:1:1.30472:60:6:0.2308:0:4 1/0:6:4:1,3:0,2:2,4:0.6667:0,2:17.8:1:32.5:1:1:0:50:8:0.6667:0:2.8 +6 29761906 . G A 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53044;SOR=0;LSEQ=TAGCTGGAAGACTCCTCCAC;RSEQ=GCCTTGCTCAACTCTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:5,6:11,3:0.2143:2,2:33.3:1:26.7:1:1:1.60839:60:2:0.1538:0:4 0/0:5:0:0,0:2,3:5,0:0:2,0:28.6:1:31.8:1:1:0:52:10:1:0:1 +6 29762440 . T TC 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTATTTTTGAACATTT;RSEQ=AAATTTTGTCTTTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:31:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29768344 . T C 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GAAAAGGCGGCTCAGATGTT;RSEQ=TGGAGGAGGAACATGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:41:1:29:0:1:0:60:4:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:11:1:33:1:1:0:60:4:0.6667:0:1.5 +6 29768816 . C T 32 d5;v3;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGCTCTTCTGAGTCCCT;RSEQ=GGCCTCCACTCAGGTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:16.5:1:32:1:1:0:33:4:0.5:0:8 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:31:0:1:0:60:2:1:0:0 +6 29768831 . T C 34 d5;v3;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TCCCTCGGCCTCCACTCAGG;RSEQ=CAGGACCAGAAATCTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:31.5:1:34:0:1:0:33:4:0.5:0:8 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:29.5:1:1:0:60:4:1:0:0 +6 29768835 . GA AG 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=TCGGCCTCCACTCAGGTCAG;RSEQ=CCAGAAATCTCTGTTTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:36.5:1:33.8:1:1:0:33:4:0.5:0:7 0/0:2:0:0,0:1,1:2,0:0:2,0:17.5:1:32.5:1:1:0:60:4:1:0:0 +6 29768852 . T A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CAGGACCAGAAATCTCTGTT;RSEQ=CCGCCTCAGACACTAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:38:1:29.5:1:0.33333:0:33:4:0.6667:0:7 0/0:3:0:0,0:2,1:3,0:0:2,0:25.7:1:31.7:1:1:0:60:6:1:0:0 +6 29768861 . G A 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=AAATCTCTGTTTCCGCCTCA;RSEQ=ACACTAGAACTTTCCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:38:1:31:1:0.33333:0:33:4:0.6667:0:7 0/0:5:0:0,0:3,2:5,0:0:2,0:21:1:31.4:1:1:0:60:10:1:0:0.2 +6 29768885 . A G 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07353;SOR=0;LSEQ=CTAGAACTTTCCAAGGAATA;RSEQ=GAGATTATCCCAGGTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:15.5:1:30:0:1:0:33:4:0.4:0:7 0/0:12:0:0,0:7,5:12,0:0:2,0:20.5:1:29.7:1:1:0:53.4:24:1:0:0.7 +6 29768908 . T C 34 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05848;SOR=0;LSEQ=GATTATCCCAGGTGCCTGTG;RSEQ=CCAGAATGTTGTCTGGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:1,1:2,2:0.4:2,0:21.5:1:34:0:1:0:37.5:4:0.4:0:3 0/0:14:0:0,0:8,6:14,0:0:2,0:26.9:1:29.3:1:1:0:54.4:28:1:0:0.6 +6 29768917 . T C 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGTGCCTGTGTCCAGAATG;RSEQ=TGTCTGGGTTCTGTGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:32.3:1:31.8:1:1:0:48.8:8:1:0:1.5 0/1:15:2:1,1:7,6:13,2:0.1333:2,2:39:1:32.5:1:1:1.1547:20.5:4:0.1333:0:3 +6 29768951 . A G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53044;SOR=Inf;LSEQ=TGCTCCCTTCCCCACCCCAG;RSEQ=TGTCCCATCCATTCTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:31:1:28.8:1:1:0:38.6:10:1:0:2.2 0/1:15:4:2,2:5,6:11,4:0.2667:2,2:21.5:1:31.3:1:1:1.19:28.8:8:0.2667:0:2.5 +6 29768957 . CA TG 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00387;SOR=0;LSEQ=CTTCCCCACCCCAGATGTCC;RSEQ=TCCATTCTCAGGATGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:2,0:2,4:0.6667:0,2:32.5:1:31.1:1:1:0:33.3:8:0.6667:0:1.8 0/0:13:0:0,0:6,7:13,0:0:2,0:29.6:1:30.4:1:1:0:50.4:26:1:0:0.8 +6 29768958 . A G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.25542;SOR=Inf;LSEQ=TTCCCCACCCCAGATGTCCC;RSEQ=TCCATTCTCAGGATGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,0:2,0:0:0,0:12:1:29.5:1:1:0:60:4:1:0:0 0/1:13:4:2,2:4,5:9,4:0.3077:2,2:21.5:1:30.5:1:1:1.23:28.8:8:0.3077:0:2.5 +6 29769063 . T A 78 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03512;SOR=7.18247;LSEQ=CCTGAAGGCACAGGTAACCC;RSEQ=CCACCCCATCTCCAACTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:13,5:18,2:0.1:2,0:3.5:1:27.5:1:1:0:60:4:0.1:0:1.5 0/1:13:6:5,1:4,3:7,6:0.4615:2,2:23.5:1:30.2:1:0.55944:3.39:60:12:0.4615:0:1 +6 29769226 . A G 29 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50361;SOR=0;LSEQ=AGAACCTTCCAGAAGTGGGC;RSEQ=GCTGCAGTGGTGTCTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:61,23:84,2:0.0233:2,2:5:0:29:1:0.48263:2.61753:60:4:0.0238:0:0 0/0:68:0:0,0:48,20:68,0:0:2,0:22.9:1:29.8:1:1:0:60:136:1:0:0.4 +6 29769246 . G A 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGCTGCAGTGGTGTCTTCTG;RSEQ=AGAGAAGCAGAGGTACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:45:28,17:59,23:82,45:0.3543:2,2:22:1:29.9:1:0.31871:1.5518:57.8:90:0.3571:0:1.2 0/0:109:0:0,0:69,40:109,0:0:2,0:21.1:1:30.6:1:1:0:60:218:1:0:0.8 +6 29769280 . C T 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACACATGCCATGTGCAGCA;RSEQ=GAGGGGTTGCCTGAGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:99,70:169,0:0:2,0:31:1:30.9:1:1:0:59.6:32.8:1:0:0.4 1/0:139:74:39,35:40,25:65,74:0.5324:2,2:32.1:1:29.8:1:0.3088:1.43213:60:148:0.5362:0:1.7 +6 29769332 . G A 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGTAAGGAGACGAATGAG;RSEQ=GGTCATGTCTCTTCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:88,74:162,0:0:2,0:21.4:1:31:1:1:0:60:80:1:0:0.3 1/0:116:63:26,37:27,26:53,63:0.5431:2,2:18.1:1:28.9:1:0.35116:1.47277:60:62:0.5536:0:1.8 +6 29769497 . A C 196 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTGCTGGCCTGGTTCTTCT;RSEQ=GTTGCTGTAATCACTGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:89,183:272,0:0:2,0:24.1:1:30.1:1:1:0:59.9:26.2:1:0:0.6 0/1:212:103:42,61:43,66:109,103:0.4858:2,2:24.3:1:29.4:1:0.88893:1.06:59.8:102:0.488:0:2.5 +6 29769507 . A T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00201;SOR=1.902;LSEQ=TGGTTCTTCTAGTTGCTGTA;RSEQ=TCACTGTAGCTGTAGTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:71:25,46:38,121:159,71:0.3074:2,2:23.6:1:30:1:0.08073:1.73:59.6:34.5:0.308:0:1.9 0/1:179:82:30,52:35,62:97,82:0.4581:2,2:23.9:1:29.4:1:1:1.02:59.7:81:0.4551:0:2.7 +6 29769521 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=6;SSF=0;SOR=3.3765;LSEQ=GCTGTAATCACTGTAGCTGT;RSEQ=GTCGCTGCTGTGATGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:79:16,63:17,82:99,79:0.4438:2,2:21.6:1:31.1:1:0.69856:1.22:59.7:38.5:0.4425:0:1.8 1/0:126:92:30,62:7,27:34,92:0.7302:2,2:21.4:1:30.1:1:0.27038:1.86:59.6:29.667:0.7295:0:2.3 +6 29769529 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50588;SOR=0;LSEQ=CACTGTAGCTGTAGTCGCTG;RSEQ=TGTGATGTGGAGGAATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:20,117:137,2:0.0144:2,2:16.5:1:32:0:0.28026:5.73:60:4:0.015:0:2 0/0:108:0:0,0:26,82:108,0:0:2,0:18.7:1:31.4:1:1:0:59.7:216:1:0:1.7 +6 29769621 . A T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.74857;SOR=1.27674;LSEQ=TTCAAGCCCCAGGTAGGAGT;RSEQ=GGCTCATATCTTGCCTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:0,10:0,9:9,10:0.5263:0,0:31.8:1:30.7:1:1:0:60:20:0.5556:0:1.3 1/0:17:10:0,10:0,7:7,10:0.5882:0,0:18.5:1:29.7:1:1:0:60:20:0.5882:0:1.3 +6 29769696 . G A 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CAGAGGCCCTGTCTATCAAC;RSEQ=CTTACTCTTTTGTAAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:3,3:0.5:2,0:6:1:31.3:1:1:0:60:6:0.5:0:2 1/0:4:2:0,2:0,2:2,2:0.5:0,0:24:1:28:1:1:0:60:4:0.5:0:3 +6 29770158 . C G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TGTTCCACCCCAAACAGGAA;RSEQ=AGTACCCAGGGCTCTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:3,0:3,3:0.5:0,2:23:1:31:1:0.4:0:26.3:6:0.5:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:46.5:1:29.5:1:1:0:24:4:1:0:1 +6 29770187 . A C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06593;SOR=Inf;LSEQ=GGGCTCTGATGTGTCTCTCA;RSEQ=GGCTTGTAAAAGTGACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:30.6:1:31.5:1:1:0:44:20:1:0:0.5 1/0:4:2:0,2:1,1:2,2:0.5:2,0:25.5:1:31:0:1:0:24:4:0.5:0:1 +6 29770255 . A G 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCAGAGGGGACACAACTA;RSEQ=GCTCTGGAGATTCTTTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:0,3:3,4:0.5714:0,2:16.5:1:32.3:1:0.42857:0:38.5:8:0.5714:0:1.3 0/0:1:0:0,0:0,1:1,0:0:0,0:18:0:29:0:1:0:60:2:1:0:0 +6 29770423 . A G 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.11403;LSEQ=CTCCTCTTTGTGACATTAAG;RSEQ=GCCTCTGGCTTCTCTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:0,3:3,4:0.5714:0,2:23.8:1:32:1:0.42857:0:50.5:8:0.5714:0:1.5 1/0:5:3:1,2:1,1:2,3:0.6:2,2:19:1:30.3:1:1:1.7321:54:6:0.6:0:1.7 +6 29770450 . G C 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GGCTTCTCTTTCTGCCAAAG;RSEQ=GTCTGAATGTGTCTATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:2,3:0.6:0,2:21.3:1:30.3:1:1:0:52.3:6:0.6:0:1.7 0/0:4:0:0,0:1,1:2,0:0:2,0:21:1:28.5:1:1:0:60:4:0.5:0:0 +6 29794443 . A G 47 d5;v3;q25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGAAAGAATTCCAAAGCAGC;RSEQ=GAACTCTTAGGTTTAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:9.8:1:23.8:1:1:0:43.8:3:1:0:1.8 +6 29795222 . G A 40 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GGAGTCCAGTTCAGGGACAG;RSEQ=GATTCCGGGATGAAAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:22.3:1:25.3:1:1:0:43.7:2:1:0:3.3 0/0:1:0:0,0:0,1:1,0:0:0,0:16:0:25:0:1:0:60:2:1:0:1 +6 29795231 . G A 48 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TTCAGGGACAGGGATTCCGG;RSEQ=ATGAAAAGTGAAGGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:25.3:1:30.3:1:1:0:43.7:6:1:0:3.3 0/0:1:0:0,0:0,1:1,0:0:0,0:25:0:26:0:1:0:60:2:1:0:1 +6 29795253 . C A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TGAAAAGTGAAGGGAGAGGG;RSEQ=CAGGGACCTTGCCGAGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:2,0:2,4:0.6667:0,2:22.8:1:30:1:0.46667:0:41:8:0.6667:0:2.8 0/0:1:0:0,0:0,1:1,0:0:0,0:47:0:29:0:1:0:60:2:1:0:1 +6 29795421 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00094;SOR=Inf;LSEQ=GCCCCACAGGCGGTGTATGG;RSEQ=TTGGGGAGGCCCCGCGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:35,1:36,0:0:1,0:24.5:1:31.7:1:1:0:60:35:1:0:0 0/1:14:5:5,0:8,1:9,5:0.3571:2,0:29.2:1:26.6:1:1:0:52.6:4:0.3077:0:1 +6 29795551 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07947;SOR=Inf;LSEQ=AGGTTTTTAGAGAAGCCAAT;RSEQ=AGCGTCGCCGCGGTCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:268,29:297,0:0:2,0:24.5:1:32.3:1:1:0:59.9:98:1:0:0.4 0/1:225:3:1,2:185,37:222,3:0.0133:2,2:15.3:1:24:1:0.07846:9.84496:60:6:0.0135:0:1.3 +6 29795566 . C T 212 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01514;LSEQ=CCAATCAGCGTCGCCGCGGT;RSEQ=CTGGTTCTAAAGTCCTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:140:107,33:271,87:358,140:0.2811:2,2:21.4:1:29.8:1:0.90761:1.04:59.7:22.333:0.2752:0:1.1 0/0:341:2:0,2:243,96:339,2:0.0059:2,0:1:0:23:0:0.08199:0:60:4:0.006:0:2 +6 29795636 . G A 252 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAGGATGGTGGTCATGGC;RSEQ=CCCCGAACCCTCTTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1085:0:0,0:537,547:1084,0:0:2,0:27:1:30.7:1:1:0:59:50.619:1:0:0.3 0/1:967:405:203,202:270,291:561,405:0.4188:2,2:27:1:29.1:1:0.55756:1.08:52.2:100.25:0.423:0:2.1 +6 29795657 . G A 241 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=802.99986;LSEQ=CCCCGAACCCTCTTCCTGCT;RSEQ=CTCTCGGGGGCCCTGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1063:1:1,0:478,582:1060,1:9e-04:2,0:1:0:24:0:0.45146:0:60:2:0.001:0:1 0/1:904:393:179,214:229,280:509,393:0.4347:2,2:24.3:1:28:1:0.89275:1.02:50.3:97.25:0.4361:0:2.2 +6 29795720 . A G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.87102;LSEQ=TGCGGGGTCAGGAGGGAAAC;RSEQ=GCCCCTGCGCGGAGGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:182:57,125:136,236:372,182:0.3273:2,2:25.9:1:30.5:1:0.25472:1.26322:50.7:35.4:0.3248:0:1.4 1/0:367:272:97,175:30,65:95,272:0.7411:2,2:23.7:1:29.6:1:0.53169:1.20:48.5:53.4:0.7417:0:2.2 +6 29795747 . G C 175 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCGGAGGAGGGAGGGGCC;RSEQ=GCCCGGCGGGGGCGCAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:0:0,0:174,256:430,0:0:2,0:23.4:1:30.5:1:1:0:59.2:46.778:1:0:0.6 0/1:237:67:24,43:62,108:170,67:0.2827:2,2:25:1:28.9:1:1:1.02843:57.5:32.5:0.2778:0:2.9 +6 29795751 . C T 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGAGGGAGGGGCCGGCC;RSEQ=GGCGGGGGCGCAGGACTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:180,250:430,0:0:2,0:22.4:1:29.9:1:1:0:59.1:25.875:1:0:0.6 0/1:228:66:26,40:63,98:161,66:0.2895:2,2:24:1:29.7:1:1:1.01:58.4:32:0.2883:0:2.7 +6 29795768 . T C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=2.10921;LSEQ=GCCCGGCGGGGGCGCAGGAC;RSEQ=CGGCAGCCGCGCCGGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:417:96:44,52:143,177:320,96:0.2302:2,2:20.5:1:31.2:1:0.90698:1.05:53.9:47:0.2344:0:1.7 0/1:217:84:45,39:57,75:132,84:0.3871:2,2:22.4:1:30.8:1:0.16241:1.52:48.7:168:0.3907:0:2.1 +6 29795809 . C T 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTCGGGCGGGTCTCAACC;RSEQ=CTCCTCGCCCCCAGGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:282,248:530,0:0:2,0:25.5:1:31.2:1:1:0:56.8:52:1:0:0.3 0/1:329:113:68,45:128,88:216,113:0.3435:2,2:22.4:1:29.2:1:0.90619:1.04:44.2:36.667:0.3406:0:1.6 +6 29795913 . A T 221 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00782;LSEQ=CCATGGGCTACGTGGACGAC;RSEQ=CGCAGTTCGTGCGGTTCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:140:89,51:215,153:368,140:0.2756:2,2:25.9:1:31.1:1:0.31208:1.24:46.6:45.667:0.2745:0:1.2 0/0:338:1:0,1:173,164:337,1:0.003:2,0:1:0:23:0:0.48817:0:60:2:0.003:0:1 +6 29795931 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01946;SOR=Inf;LSEQ=ACACGCAGTTCGTGCGGTTC;RSEQ=ACAGCGACTCGGCGTGTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:556:0:0,0:344,211:555,0:0:2,0:25.1:1:30.8:1:1:0:55.4:91.5:0.9982:0:0.4 0/1:333:4:2,2:180,148:328,4:0.012:2,2:19.3:1:28.3:1:1:1.21549:53.8:8:0.0122:0:1.3 +6 29795993 . G A 223 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGTGGAGCAGGAGGGGCC;RSEQ=GAGTATTGGGAAGAGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:919:0:0,0:519,400:919,0:0:2,0:24.8:1:30.4:1:1:0:59.1:182.8:1:0:0.2 0/1:613:184:102,82:238,191:429,184:0.3002:2,2:26.5:1:29.7:1:1:1.00174:59.9:60.333:0.2987:0:1.1 +6 29796103 . T C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.07212;LSEQ=GAGCGAGGCCAGTGAGTAAC;RSEQ=CCGGCCCAGGGAGCAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:625:168:56,112:159,297:456,168:0.2688:2,2:25.5:1:30.9:1:0.77593:1.07061:59.1:55:0.2718:0:3.5 0/1:467:202:85,117:88,172:260,202:0.4325:2,2:22.8:1:29.9:1:0.08111:1.42:57.7:49.5:0.4333:0:2 +6 29796106 . G T 224 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGAGGCCAGTGAGTAACTCC;RSEQ=GCCCAGGGAGCAGATCACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:160:51,109:145,273:418,160:0.2759:2,2:25.9:1:30.7:1:0.55656:1.13491:59.2:79:0.2787:0:3.6 0/0:427:0:0,0:157,269:426,0:0:2,0:23.7:1:29.6:1:1:0:59:105.5:0.9976:0:1 +6 29796115 . A C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00055;SOR=1.66259;LSEQ=TGAGTAACTCCGGCCCAGGG;RSEQ=GCAGATCACGACCCCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:143:43,100:111,245:356,143:0.2866:2,2:25.7:1:30.4:1:0.83111:1.05353:59.5:142:0.291:0:3.8 0/1:357:143:59,84:65,149:214,143:0.4006:2,2:23.4:1:29.6:1:0.04112:1.61:57.6:46.667:0.4046:0:2.4 +6 29796126 . A AC 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCCAGGGAGCAGATCACG;RSEQ=CCCCCACCTCCATGCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:107,298:405,0:0:2,0:24.4:1:29.7:1:1:0:59.8:56.857:1:0:1.3 0/1:280:97:30,67:57,123:180,97:0.3464:2,2:23.8:1:30.2:1:1:1.03484:58:47.5:0.3493:0.0357:2.4 +6 29796128 . C A 202 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCAGGGAGCAGATCACGAC;RSEQ=CCCACCTCCATGCCCCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:123:29,94:74,204:278,123:0.306:2,2:25:1:29.2:1:0.53854:1.17532:59.4:23.6:0.3041:0:3.9 0/0:275:0:0,0:84,191:275,0:0:2,0:20.8:1:29.5:1:1:0:59.2:33.375:1:0:1.1 +6 29796132 . A C 55 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.01719;SOR=9.34427;LSEQ=GGGAGCAGATCACGACCCCC;RSEQ=CCTCCATGCCCCACGGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:1:1,0:90,284:374,1:0.0027:2,0:4:0:7:0:0.24267:0:60:0:0:0:1 0/1:246:6:3,3:67,172:239,6:0.0244:2,2:8.2:1:21.3:1:0.35712:2.56:59.8:2:0.0173:0:3.3 +6 29796152 . G C 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTCCATGCCCCACGGACG;RSEQ=CCCGGGTACTCCCGAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:49,213:262,0:0:2,0:21.3:1:31.5:1:1:0:60:28.111:1:0:1.1 0/1:150:62:11,51:14,73:87,62:0.4133:2,2:22.3:1:30.5:1:0.82641:1.12:58.4:61:0.4266:0:2.4 +6 29796234 . CA C 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTCTACCTGGGAGAACCC;RSEQ=AGGCGCCTTTACCAAAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:64,63:127,0:0:2,0:23.5:1:31:1:1:0:59.8:62.5:1:0:0.5 0/1:47:18:6,12:16,13:29,18:0.383:2,2:18.2:1:31.6:1:0.2293:2.41392:60:36:0.383:0.1064:1.4 +6 29796257 . C T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07886;SOR=1.87363;LSEQ=GGCGCCTTTACCAAAATCCC;RSEQ=GCGGGTGGGTCCGGGCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:34:27,7:52,41:93,34:0.2677:2,2:24.5:1:32.2:1:0.0222:3.02:60:68:0.2742:0:2 0/1:54:22:15,7:26,6:32,22:0.4074:2,2:19.2:1:30.5:1:0.33828:1.99504:60:21:0.3962:0:2 +6 29796265 . G T 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACCAAAATCCCCGCGGGTG;RSEQ=GTCCGGGCGAGGGCGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:41:32,9:65,49:114,41:0.2645:2,2:22.5:1:30.7:1:0.02328:2.66:60:82:0.268:0:1.9 0/0:59:0:0,0:46,13:59,0:0:2,0:23.8:1:30.5:1:1:0:60:118:1:0:0.8 +6 29796306 . G A 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGTGGGCGGGGCTGACCGA;RSEQ=GGGGTGGGGCCAGGTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:139,117:256,0:0:2,0:26.8:1:32:1:1:0:59.6:63:0.9921:0:0.4 0/1:135:38:24,14:61,36:97,38:0.2815:2,2:22.9:1:28.5:1:1:1.01:60:37:0.2803:0:2.2 +6 29796312 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.11706;SOR=Inf;LSEQ=GCGGGGCTGACCGAGGGGGT;RSEQ=GGGCCAGGTTCTCACACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:148,126:274,0:0:2,0:27.7:1:31.5:1:1:0:59.6:67.5:1:0:0.3 0/1:143:2:1,1:88,53:141,2:0.014:2,2:6.5:1:27:1:1:1.65418:60:4:0.0142:0:1.5 +6 29796327 . C T 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGGTGGGGCCAGGTTCTCA;RSEQ=ACCCTCCAGTGGATGATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:149,150:299,0:0:2,0:28.8:1:32.1:1:1:0:59.7:58.8:1:0:0.3 0/1:163:17:10,7:87,59:146,17:0.1043:2,2:26.6:1:28.7:1:1:1.03202:60:34:0.1049:0:2.2 +6 29796369 . A T 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCGACCTGGGGTCCGACGG;RSEQ=CGCCTCCTCCGCGGGTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:123,126:249,0:0:2,0:23.9:1:29.5:1:1:0:59.8:34.571:1:0:0.2 0/1:162:17:7,10:72,73:145,17:0.1049:2,2:23.1:1:28.7:1:0.61141:1.40604:60:34:0.1076:0:1.7 +6 29796376 . C A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1e-05;SOR=Inf;LSEQ=TGGGGTCCGACGGACGCCTC;RSEQ=TCCGCGGGTATGAACAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:114,120:234,0:0:2,0:22.5:1:32:1:1:0:59.8:57.5:1:0:0.2 0/1:156:12:5,7:72,72:144,12:0.0769:2,2:22.6:1:29.3:1:0.76548:1.397:59.4:24:0.0779:0:1.3 +6 29796434 . AC A 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0027;SOR=Inf;LSEQ=TTACCTCGCCCTGAACGAGG;RSEQ=CTGCGCTCCTGGACCGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:172,63:235,0:0:2,0:25.1:1:32:1:1:0:59.4:38.167:1:0:0.1 0/1:180:7:4,3:111,61:172,7:0.0389:2,2:25.1:1:30.3:1:0.70176:1.36225:60:14:0.0393:0.0111:0 +6 29796640 . T C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0467;SOR=2.11186;LSEQ=CCTGATCTCCTGTAGACCTC;RSEQ=CAGCCTGGCCTAGCACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:30:1,29:6,63:69,30:0.303:2,1:22.2:1:31.2:1:0.67161:2.73907:59.3:29:0.2959:0:1.5 0/1:50:24:1,23:3,23:26,24:0.48:2,1:26.9:1:30.3:1:0.61051:2.93967:60:48:0.48:0:1.5 +6 29796656 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTCAGCCTGGCCTAGCA;RSEQ=AAGGAGAGGAGGAAAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:5,76:81,2:0.0241:2,2:24.5:1:29:1:0.14017:13.97:60:4:0.0244:0:1 0/0:40:0:0,0:4,36:40,0:0:2,0:28.1:1:31.5:1:1:0:60:39:1:0:0.8 +6 29796675 . G T 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00169;SOR=0;LSEQ=ACAAGGAGAGGAGGAAAATG;RSEQ=GACCAACACTAGAATATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:15:1,14:2,39:41,15:0.2679:1,1:23.5:1:30.1:1:1:1.38:54.9:30:0.2679:0:1.8 0/0:28:0:0,0:2,26:28,0:0:2,0:27.5:1:30.6:1:1:0:60:27:1:0:1 +6 29796685 . T C 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGAAAATGGGACCAACAC;RSEQ=AGAATATCGCCCTCCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:3,41:44,0:0:2,0:24.6:1:28.4:1:1:0:58.5:88:1:0:0.5 0/1:25:12:1,11:2,11:13,12:0.48:2,2:26.4:1:32.8:1:1:1.94684:60:24:0.48:0:2 +6 29796877 . GGCACC G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGACCCCACAGCAGCCTT;RSEQ=AGGACTTTTCCCCTCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:31:1:33:1:1:3.1622:57:4:0.2857:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:43:0:31:0:1:0:60:2:1:0:2 +6 29796986 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.01587;SOR=Inf;LSEQ=CCTCCACTCAGGTCAGAACC;RSEQ=GAGGTCCCTGCTCCCCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:22,2:24,0:0:2,0:26.8:1:30.9:1:1:0:58.3:48:1:0:0.2 1/0:4:2:1,1:2,0:2,2:0.5:0,2:29.5:1:32:1:1:0:35:4:0.5:0:1 +6 29797155 . G C 217 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GCTGCTGGAGTGTCCCATGA;RSEQ=AGATGCAAAGTGCTTGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:111:77,34:142,95:237,111:0.3181:2,2:22.4:1:32:1:0.09645:1.51:51.7:54.5:0.3187:0:2.7 0/0:237:0:0,0:143,94:237,0:0:2,0:23.6:1:30.4:1:1:0:59.5:38.5:1:0:0.5 +6 29797173 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12832;SOR=1.26169;LSEQ=GAGAGATGCAAAGTGCTTGA;RSEQ=TTTTCTGACTCTTCCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:148:90,58:190,143:333,148:0.3071:2,2:24.6:1:32.6:1:0.48362:1.17:51.8:73:0.3074:0:2.7 0/1:329:118:64,54:122,89:211,118:0.3587:2,2:27:1:31.1:1:0.56297:1.15608:58.3:236:0.362:0:1.2 +6 29797211 . C T 232 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAGACCCCCCCAAGACACA;RSEQ=GTGACCCACCACCCTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:542:180:87,93:166,196:362,180:0.3321:2,2:27.9:1:31:1:0.64772:1.10:46.4:360:0.3352:0:2.2 0/0:384:0:0,0:171,211:382,0:0:2,0:27.5:1:30.1:1:1:0:57.3:94.5:0.9947:0:0.4 +6 29797302 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55116;SOR=0;LSEQ=AGATCATACTGACCTGGCAG;RSEQ=GGGATGGGGAGGACCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:39,93:132,2:0.0149:2,2:32:1:27.5:1:0.50948:2.37:22:4:0.0152:0:1 0/0:68:0:0,0:27,41:68,0:0:2,0:22.8:1:29.5:1:1:0:42.6:21.667:1:0:0.1 +6 29797420 . C T 91 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02066;SOR=5.66413;LSEQ=TGGAGAGGAGCAGAGATACA;RSEQ=GTGCCATGTGCAGCATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:0,2:94,91:185,2:0.0107:2,0:1:0:25:0:0.24599:0:60:4:0.0109:0:1 0/1:138:8:3,5:74,56:130,8:0.058:2,2:25.6:1:30.4:1:0.4658:2.18977:46.9:16:0.0593:0:1 +6 29797452 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19436;SOR=Inf;LSEQ=AGCATGAGGGGCTGCCGGAG;RSEQ=CCCTCATGCTGAGATGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:113,121:234,0:0:2,0:31.9:1:31.6:1:1:0:51.1:45.8:1:0:0.1 0/1:185:2:1,1:89,94:183,2:0.0108:2,2:34.5:1:28.5:1:1:1.06:60:4:0.0111:0:1.5 +6 29797456 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.19032;SOR=Inf;LSEQ=TGAGGGGCTGCCGGAGCCCC;RSEQ=CATGCTGAGATGGAGTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:118,123:241,0:0:2,0:30.5:1:30.8:1:1:0:51.6:39.167:1:0:0.1 0/1:187:2:1,1:89,96:185,2:0.0107:2,2:12:1:32:0:1:1.08:25.5:4:0.011:0:1 +6 29797553 . G C 198 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAACAGGGTCGGTGGTGAGG;RSEQ=CTGGGGGTCAGAGACCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:109,72:181,0:0:2,0:23.1:1:31.4:1:1:0:60:35.2:0.9944:0:0.2 1/0:150:85:46,39:41,24:65,85:0.5667:2,2:22.1:1:31:1:0.31774:1.44477:60:84:0.5753:0:1.3 +6 29797554 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1971;SOR=Inf;LSEQ=AACAGGGTCGGTGGTGAGGG;RSEQ=TGGGGGTCAGAGACCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:115,76:191,0:0:2,0:22.3:1:31.8:1:1:0:60:26.286:1:0:0.2 0/1:153:2:1,1:86,65:151,2:0.0131:2,2:21.5:1:30.5:1:1:1.32061:60:4:0.0136:0:1 +6 29797558 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.502;SOR=0;LSEQ=GGGTCGGTGGTGAGGGCTGG;RSEQ=GGTCAGAGACCCTCACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:119,77:196,2:0.0101:2,2:12:1:28:1:1:1.54191:60:4:0.0103:0:1.5 0/0:168:0:0,0:93,75:168,0:0:2,0:22.2:1:29.9:1:1:0:60:55:1:0:0.8 +6 29797564 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09432;SOR=Inf;LSEQ=GTGGTGAGGGCTGGGGGTCA;RSEQ=AGACCCTCACCTTCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:133,92:225,0:0:2,0:22.8:1:32.3:1:1:0:60:44:1:0:0.2 0/1:189:3:1,2:104,82:186,3:0.0159:2,2:16.7:1:27.3:1:0.58585:2.52432:60:6:0.0162:0:2 +6 29797639 . C T 188 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=210.03178;LSEQ=ATCATGGGTATCGTTGCTGG;RSEQ=CTGGTTGTCCTTGCAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:1:1,0:147,153:300,1:0.0033:2,0:4:0:13:0:0.49169:0:60:0:0:0:2 0/1:249:103:59,44:73,73:146,103:0.4137:2,2:21.1:1:28.2:1:0.30257:1.34:58.1:50.5:0.4156:0:1.7 +6 29797642 . G A 42 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25417;SOR=0;LSEQ=ATGGGTATCGTTGCTGGCCT;RSEQ=GTTGTCCTTGCAGCTGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:3,0:144,150:294,3:0.0101:2,0:7.7:1:27:1:0.12:0:60:6:0.0102:0:1 0/0:250:0:0,0:132,117:249,0:0:2,0:22.4:1:30.5:1:1:0:58.9:82:0.996:0:0.8 +6 29797653 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09675;SOR=Inf;LSEQ=TGCTGGCCTGGTTGTCCTTG;RSEQ=AGCTGTAGTCACTGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:141,162:303,0:0:2,0:21.5:1:31.9:1:1:0:59.2:49.5:0.9966:0:0.3 0/1:259:3:1,2:132,124:256,3:0.0116:2,2:13.7:1:26.3:1:0.61358:2.12302:55:6:0.0119:0:1.7 +6 29797696 . A G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=2.14556;LSEQ=GTCGCTGCTGTGCTGTGGAG;RSEQ=AAGAAGAGCTCAGGTAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:92:37,55:53,96:149,92:0.3817:2,2:30:1:31.6:1:0.49506:1.22:56.6:91:0.3808:0:1.1 1/0:242:138:63,75:37,67:104,138:0.5702:2,2:29:1:30:1:0.14678:1.52:55.9:68:0.5763:0:1.5 +6 29797719 . G A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24826;SOR=0;LSEQ=GAAGAGCTCAGGTAAGGAAG;RSEQ=GGTGACAAGTGGGGTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:3:2,1:70,137:207,3:0.0143:2,2:8.7:1:22.3:1:0.27102:3.89:60:2:0.0098:0:1 0/0:206:0:0,0:73,133:206,0:0:2,0:26.7:1:29.9:1:1:0:57.6:205:1:0:0.9 +6 29797763 . C A 31 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25512;SOR=0;LSEQ=TCTTGTCCCACTGGGGGTTT;RSEQ=AAGCCCCAGGTAGAAGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:3:2,1:16,81:97,3:0.03:2,2:10:1:20:1:0.08263:9.77:55.3:2:0.0204:0:2.3 0/0:80:0:0,0:12,68:80,0:0:2,0:22.3:1:31.2:1:1:0:56.2:39:1:0:0.9 +6 29797782 . T C 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCAAGCCCCAGGTAGAAGTG;RSEQ=GCCCTGCCTGGTTACTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:8,56:64,0:0:2,0:25:1:30.7:1:1:0:53:31:1:0:0.3 1/0:42:24:2,22:0,18:18,24:0.5714:1,2:25:1:29.2:1:0.49826:0:51.3:23:0.561:0:1.3 +6 29797899 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00395;SOR=Inf;LSEQ=ACAATGAAGGACAGATTTAT;RSEQ=ACCTTGATGATTGTAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:12,9:21,0:0:2,0:28.9:1:30.7:1:1:0:58.2:42:1:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:44:1:32.5:1:1:0:33.5:4:1:0:2 +6 29797933 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00342;SOR=Inf;LSEQ=TAGTGATGGGGACCTGATCC;RSEQ=AGTAATCACAGGTCAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:17,5:22,0:0:2,0:27.5:1:32.2:1:1:0:57.7:44:1:0:0 1/0:5:3:1,2:2,0:2,3:0.6:0,2:8:1:28.7:1:0.4:0:29:6:0.6:0:2.3 +6 29798039 . G A 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTTCCTGATCCCGCCCTG;RSEQ=GTCTGCAGTCACACATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:77,1:78,0:0:1,0:22.5:1:31.1:1:1:0:48.4:18.5:1:0:0.1 1/0:29:16:13,3:13,0:13,16:0.5517:1,2:28.6:1:29.3:1:0.23153:0:44.4:32:0.5517:0:1.4 +6 29798083 . C T 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00041;SOR=21.77179;LSEQ=AACTTCTCGAGGGTCCAAGA;RSEQ=TAGGAGGTTCCTCTAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:0,1:158,28:186,1:0.0053:2,0:1:0:27:0:0.15508:0:60:2:0.0054:0:1 0/1:66:7:7,0:50,9:59,7:0.1061:2,0:24.1:1:30:1:0.58064:0:32.7:14:0.1061:0:2.1 +6 29798092 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08912;SOR=Inf;LSEQ=AGGGTCCAAGACTAGGAGGT;RSEQ=CCTCTAGGACCTCATGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:177,38:215,0:0:2,0:24.6:1:30.7:1:1:0:52.7:70.667:1:0:0.1 0/1:92:2:1,1:76,14:90,2:0.0217:2,2:30.5:1:31.5:1:0.301:5.279:30:4:0.022:0:1.5 +6 29798140 . A G 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCTGGCCTCTCACAGGAC;RSEQ=TTTTCTTCCCACAGATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:254,154:408,0:0:2,0:25.3:1:30.5:1:1:0:41.7:80.6:1:0:0.1 0/1:230:64:49,15:108,57:165,64:0.2783:2,2:33:1:29.7:1:0.11493:1.72:23.3:128:0.2857:0:1.1 +6 29798232 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15272;SOR=Inf;LSEQ=TGAGATCCTTGGGATCTTGT;RSEQ=TTTGGGAGCCCATGGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:121,190:311,0:0:2,0:20.8:1:32:1:1:0:39.9:102.667:1:0:0.1 0/1:200:2:1,1:87,111:198,2:0.01:2,2:6.5:1:27:1:1:1.27:24:4:0.0101:0:1.5 +6 29798280 . G A 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16509;SOR=5.75602;LSEQ=ACCCCACAATTCCTCCTCTG;RSEQ=CCACATCTCCTGTGGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:1:0,1:128,178:306,1:0.0033:2,0:8:0:13:0:1:0:24:0:0:0:5 0/1:216:4:2,2:90,122:212,4:0.0185:2,2:25.8:1:29.3:1:1:1.35:58.8:8:0.019:0:1 +6 29798312 . G A 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=GTGGTCTCTGACCAGGTGCT;RSEQ=TTTTTGTTCTACTCTAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:0:0,0:150,196:346,0:0:2,0:25.7:1:32.2:1:1:0:58.6:85.5:1:0:0.1 0/1:238:10:4,6:103,124:227,10:0.042:2,2:16.2:1:29.2:1:1:1.24483:55.9:20:0.0424:0:1 +6 29798419 . G A 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTGTGGGTTGTTGAGGG;RSEQ=AACAGGGGACATAGCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:24,89:113,0:0:2,0:24.1:1:31.8:1:1:0:59.3:55.5:1:0:0.7 0/1:74:27:6,21:12,35:47,27:0.3649:2,2:17.2:1:29.1:1:1:1.19708:56.1:26:0.3611:0:2.1 +6 29798425 . G T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.62812;SOR=1.20111;LSEQ=TGGGTTGTTGAGGGGAACAG;RSEQ=GGACATAGCTGTGCTATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:38:10,28:9,57:66,38:0.3654:2,2:25.8:1:30.8:1:0.12102:2.24:58.4:76:0.3762:0:1.6 0/1:66:27:8,19:8,31:39,27:0.4091:2,2:20.9:1:29:1:0.56001:1.62:53.7:54:0.4219:0:2.3 +6 29798459 . C G 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29989;SOR=1.56457;LSEQ=CTATGAGGTTTCTTTGACTT;RSEQ=AATGTATTGAGCATGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:28:12,16:11,33:44,28:0.3889:2,2:24.6:1:32.1:1:0.12821:2.22:44.6:27:0.3857:0:1.8 1/0:34:17:5,12:3,14:17,17:0.5:2,2:29.9:1:31.1:1:0.68802:1.91:41.9:34:0.5:0:2.4 +6 29798581 . G GTATTTGTTCATGCCT 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50409;SOR=1.4424;LSEQ=TGTGTGGGACTGAGTGGCAA;RSEQ=TCCCTTTGTGACTTCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:20:6,14:23,26:49,20:0.2899:2,2:9:1:29.1:1:0.28314:2.04293:44.5:40:0.2899:0.2899:2.1 0/1:35:13:6,7:13,9:22,13:0.3714:2,2:12.5:1:27.2:1:0.50306:1.65991:35.2:26:0.3714:0.3714:1.2 +6 29798610 . C T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04942;SOR=2.42969;LSEQ=TGACTTCAAGAACCCTGACT;RSEQ=CTCTTTGTGCAGAGACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:22:2,20:15,24:39,22:0.3607:2,2:25.4:1:30:1:0.01752:6.08755:54.4:44:0.3607:0:2.6 1/0:31:18:4,14:5,8:13,18:0.5806:2,2:21.8:1:27.8:1:0.43277:2.13085:54:36:0.5806:0:2.1 +6 29798617 . G C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33501;SOR=1.69752;LSEQ=AAGAACCCTGACTCCTCTTT;RSEQ=TGCAGAGACCAGCCCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:16:0,16:15,26:41,16:0.2807:2,1:35:1:33.3:1:0.0055:0:52.3:32:0.2807:0:3.2 0/1:30:12:0,12:7,11:18,12:0.4:2,0:26.4:1:30.5:1:0.02419:0:51:11:0.3929:0:2.6 +6 29798634 . C A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00438;SOR=Inf;LSEQ=TTTGTGCAGAGACCAGCCCA;RSEQ=CCCTGTGCCCACCATGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:8,39:47,0:0:2,0:29.4:1:31.4:1:1:0:57.4:46:1:0:1.2 0/1:26:5:0,5:2,19:21,5:0.1923:2,0:33.8:1:27.6:1:1:0:52:10:0.1923:0:3.6 +6 29798642 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11091;SOR=0.36934;LSEQ=GAGACCAGCCCACCCCTGTG;RSEQ=CCACCATGACCCTCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:21:0,21:5,21:26,21:0.4468:2,1:29.3:1:30:1:0.05615:0:54.1:20:0.4444:0:2.7 0/1:22:5:0,5:0,17:17,5:0.2273:1,0:32.2:1:26.8:1:1:0:52:10:0.2273:0:3.6 +6 29798749 . C G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62848;SOR=0.39418;LSEQ=CTCTGTCTCAAATTTGTGGT;RSEQ=CACTGAGCTATAACTTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:0,2:2,8:0.8:0,0:27.5:1:33.3:1:1:0:60:16:0.8:0:1.3 1/0:10:6:1,5:0,4:4,6:0.6:0,2:25.5:1:31.5:1:1:0:60:12:0.6:0:1.3 +6 29855241 . C T 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCTTGGCACAGGAGGAG;RSEQ=GGGGTCAGGGCGAAGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:15,1:16,2:0.1111:1,2:35:1:32:0:0.21569:10.95468:26.5:4:0.1111:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29855320 . T G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00244;SOR=9.81798;LSEQ=GGCGGTGTATGGATTGGGGA;RSEQ=GCCCCGCCTTAGGGATTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:9:9,0:38,2:40,9:0.1837:2,0:32:1:34:1:1:0:45.7:18:0.1875:0:2.7 1/0:10:7:7,0:3,0:3,7:0.7:0,0:21.6:1:32:1:1:0:51:14:0.7:0:4 +6 29855331 . A G 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=5e-04;SOR=16.99456;LSEQ=GATTGGGGATGCCCCGCCTT;RSEQ=GGGATTCGCCACCTCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:28:26,2:34,1:35,28:0.4444:1,2:23.1:1:32.1:1:0.58047:2.57615:55.4:27:0.4355:0:1.6 1/1:15:14:14,0:1,0:1,14:0.9333:0,1:23.6:1:32.4:1:1:0:55.5:28:0.9333:0:3.6 +6 29855355 . CTCT C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.33843;SOR=0.52468;LSEQ=ATTCGCCACCTCCGCAGTTT;RSEQ=TCTTCTCACAACCTGCGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:21:20,1:78,1:79,21:0.21:1,1:24:1:32.6:1:0.37758:3.83033:60:42:0.2165:0.05:0.7 0/1:41:5:5,0:35,1:36,5:0.122:1,0:22.8:1:31.3:1:1:0:60:10:0.125:0.0244:0.4 +6 29855376 . A T 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCTTCTCACAACCTGCG;RSEQ=CGGGTCCTTCTTCCTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:136,3:139,2:0.0141:1,0:33:0:28.5:1:1:0:22.5:4:0.0147:0:6.5 0/0:70:0:0,0:67,3:70,0:0:1,0:22.8:1:29:1:1:0:60:69:1:0:2.7 +6 29855378 . G T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTCTCACAACCTGCGAC;RSEQ=GGTCCTTCTTCCTTGATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:2,0:143,3:146,2:0.0133:1,0:35:0:30:1:1:0:22.5:4:0.0137:0:6.5 0/0:74:0:0,0:71,3:74,0:0:1,0:22.8:1:29.8:1:1:0:60:148:1:0:2.8 +6 29855386 . C T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=17.79081;LSEQ=ACAACCTGCGACGGGTCCTT;RSEQ=TTCCTTGATACTCACGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:19:18,1:152,3:155,19:0.1086:1,1:22.3:1:31.4:1:0.373:2.79079:59.9:38:0.1138:0:3.2 1/0:96:66:62,4:29,1:30,66:0.6875:1,2:22:1:30.5:1:1:1.86021:60:65:0.6842:0:3.8 +6 29855392 . T G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=21.73424;LSEQ=TGCGACGGGTCCTTCTTCCT;RSEQ=GATACTCACGAAGCGGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:19:18,1:171,4:175,19:0.0964:1,1:25.2:1:33.1:1:0.4061:2.36039:60:38:0.0979:0:3.1 1/0:104:73:69,4:28,1:29,73:0.7019:1,2:23.1:1:31.8:1:1:1.61626:60:35.5:0.6961:0:3.6 +6 29855401 . C G 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTCTTCCTTGATACTCA;RSEQ=GAAGCGGACACAGTTCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:220,6:226,0:0:1,0:24:1:32.5:1:1:0:59.7:112:1:0:0.5 0/1:129:41:38,3:84,4:88,41:0.3178:1,2:24.5:1:31.9:1:0.6786:1.65096:60:82:0.3228:0:3.7 +6 29855409 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=18.00649;LSEQ=CCTTGATACTCACGAAGCGG;RSEQ=CACAGTTCTCATTCCCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:28:27,1:232,5:237,28:0.1057:1,1:24.1:1:31.2:1:0.49176:1.71423:60:27:0.1063:0:2.3 1/0:148:101:95,6:45,2:47,101:0.6824:1,2:25:1:30.4:1:1:1.41789:60:32.667:0.6759:0:3 +6 29855431 . G T 39 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05645;SOR=Inf;LSEQ=ACAGTTCTCATTCCCACTAG;RSEQ=TGTCGGGTTTCTAGAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:338,38:376,0:0:2,0:24.4:1:31.2:1:1:0:59.9:30.333:1:0:0.3 0/1:235:3:1,2:208,23:231,3:0.0128:2,2:6:1:24.7:1:0.03083:17.61527:60:6:0.0131:0:1 +6 29855492 . C A 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00171;SOR=0.39333;LSEQ=CCGGTTCTAAAGTCCCCACG;RSEQ=ACCCACCGGGACTCAGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1141:50:22,28:642,447:1089,50:0.0438:2,2:27.5:1:30.8:1:0.04026:1.8269:24.9:49:0.0437:0:4.8 0/1:791:14:7,7:433,340:773,14:0.0177:2,2:26.9:1:30.5:1:0.78751:1.27313:28.2:28:0.0179:0:3.9 +6 29855500 . G C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00249;SOR=0.40548;LSEQ=AAAGTCCCCACGCACCCACC;RSEQ=GGACTCAGATTCTCCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1252:49:21,28:678,523:1201,49:0.0391:2,2:35.4:1:31.2:1:0.07729:1.72769:24.2:98:0.0395:0:4.7 0/1:862:14:7,7:460,386:846,14:0.0162:2,2:33.9:1:28.4:1:0.79163:1.19146:28.2:6:0.0141:0:3.9 +6 29855533 . T C 169 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00026;SOR=0.28734;LSEQ=TCCCCAGACGCCGAGGATGG;RSEQ=GCTCATGGCGCCCCGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1503:42:17,25:734,726:1460,42:0.0279:2,2:26.8:1:31.5:1:0.27312:1.4864:22.6:84:0.0284:0:5.1 0/0:1099:9:4,5:526,563:1089,9:0.0082:2,2:18.2:1:30.6:1:1:1.16769:26.6:18:0.0083:0:4.9 +6 29855535 . C G 171 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.22957;LSEQ=CCCAGACGCCGAGGATGGTG;RSEQ=TCATGGCGCCCCGAACCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1510:41:17,24:729,736:1465,41:0.0272:2,2:25.4:1:32.1:1:0.34308:1.39802:22.6:82:0.0274:0:5.1 0/0:1100:7:3,4:528,565:1093,7:0.0064:2,2:21.1:1:29:1:1:1.24577:23.3:6:0.0055:0:5.3 +6 29855538 . A G 167 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0.23315;LSEQ=AGACGCCGAGGATGGTGCTC;RSEQ=TGGCGCCCCGAACCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1522:41:17,24:729,750:1479,41:0.0269:2,2:22.4:1:31.3:1:0.34572:1.37195:22.6:82:0.0273:0:5.1 0/0:1092:7:3,4:520,565:1085,7:0.0064:2,2:18.1:1:30.4:1:1:1.22691:23.3:14:0.0065:0:5.3 +6 29855570 . AG A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0.21014;LSEQ=ACCCTCCTCCTGCTGCTCTC;RSEQ=GGGCCCTGGCCCTGACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1161:66:38,28:476,618:1094,66:0.0568:2,2:15.6:1:32.3:1:0.02979:1.76:42.7:132:0.0576:0.0043:0.7 0/1:800:10:5,5:360,430:790,10:0.0125:2,2:13.3:1:30.1:1:1:1.19:42.3:20:0.0126:0.0025:0.6 +6 29855571 . GGGGCCCT G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1525;LSEQ=CCCTCCTCCTGCTGCTCTCA;RSEQ=GGCCCTGACCCTGACCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1157:271:114,157:389,495:884,271:0.2342:2,2:29.9:1:32.1:1:0.62408:1.08218:51.3:270:0.2377:0.032:1.1 0/1:786:35:16,19:336,410:746,35:0.0445:2,2:30.2:1:31.1:1:1:1.03:48.1:70:0.0461:0.0064:1.3 +6 29855574 . GCCCTGGCCCTGA G 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00338;SOR=0.56119;LSEQ=TCCTCCTGCTGCTCTCAGGG;RSEQ=CCCTGACCCAGACCTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1088:97:43,54:327,430:757,97:0.0892:2,2:28.5:1:31.8:1:0.82872:1.05:54.7:96:0.1139:0.0083:0.2 0/1:730:38:18,20:289,369:658,38:0.0521:2,2:28.7:1:30.8:1:0.73791:1.15:56.3:76:0.0552:0.0027:0.1 +6 29855580 . GCCCTGA G 260 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=2.000;MSILEN=6;SSF=0;SOR=1070.46798;LSEQ=TGCTGCTCTCAGGGGCCCTG;RSEQ=CCCTGACCCAGACCTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1032:1:0,1:386,555:941,1:0.001:2,0:49:0:34:0:1:0:60:2:0.0011:0:0 1/0:665:344:150,194:125,160:285,344:0.5173:2,2:28.7:1:30.9:1:1:1.0104:47.3:56.333:0.5514:0.0812:0.3 +6 29855586 . A G 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.27121;LSEQ=TCTCAGGGGCCCTGGCCCTG;RSEQ=CCCTGACCCAGACCTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:977:265:103,162:252,370:622,265:0.2712:2,2:29.9:1:32:1:0.65417:1.07116:51.5:264:0.3021:0:1.1 0/1:633:58:22,36:112,131:243,58:0.0916:2,2:19.7:1:30.2:1:0.30421:1.39748:53:57:0.1939:0:1.7 +6 29855662 . G C 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGCGAGGGGCCCGCCCGGC;RSEQ=GGGGCGCAGGACCCGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:0:0,0:180,242:422,0:0:2,0:23.9:1:30.8:1:1:0:59.4:59.286:0.9976:0:0.4 0/1:244:23:7,16:92,129:221,23:0.0943:2,2:28.5:1:28.3:1:0.37479:1.62701:55:22:0.0917:0:3.1 +6 29855677 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=18.70186;LSEQ=CCGGCGGGGGCGCAGGACCC;RSEQ=GGGATCCGCGCAGGGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:45:20,25:186,213:399,45:0.1014:2,2:24.3:1:31:1:0.87505:1.09131:51.2:44:0.1007:0:2.7 1/0:256:174:77,97:42,39:81,174:0.6797:2,2:21.4:1:30.1:1:0.28228:1.35499:48.9:348:0.6797:0:3 +6 29855682 . T G 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=20.16935;LSEQ=GGGGGCGCAGGACCCGGGGA;RSEQ=CCGCGCAGGGAGGAGGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:44:19,25:195,210:405,44:0.098:2,2:25:1:32.6:1:0.63402:1.22126:50.1:43:0.0989:0:2.7 1/0:250:172:79,93:41,37:78,172:0.688:2,2:21.9:1:31.1:1:0.34233:1.30308:47.8:171:0.6951:0:3 +6 29855706 . C G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=17.24615;LSEQ=CGCAGGGAGGAGGGTCGGGC;RSEQ=GGTCTCAGCTCCTCCTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:56:27,29:257,232:489,56:0.1026:2,2:24.1:1:30.8:1:0.57393:1.18943:44:112:0.1051:0:2.2 1/0:304:202:104,98:60,41:101,202:0.6645:2,2:23.8:1:29.6:1:0.22171:1.37751:42:404:0.6667:0:2.5 +6 29855733 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTCCTCCTCGCTCCCAGG;RSEQ=TCCCACTCCATGAGGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:0:0,0:342,321:663,0:0:2,0:26.8:1:32.7:1:1:0:57.5:81.875:1:0:0.3 0/1:413:23:13,10:199,191:390,23:0.0557:2,2:22.7:1:29.3:1:0.67141:1.25:46.2:46:0.0565:0:2.9 +6 29855818 . G T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01457;SOR=0.42062;LSEQ=TCTCCGTCGGCTACGTGGAC;RSEQ=ATACGCAGTTCGTGCGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:41:20,21:204,206:410,41:0.0909:2,2:23.2:1:28.9:1:1:1.03973:52.1:40:0.0903:0:1.1 0/1:248:10:4,6:104,134:238,10:0.0403:2,2:16.6:1:29.6:1:1:1.16347:49.3:20:0.0413:0:1.3 +6 29855901 . A G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=17.78459;LSEQ=TGGATGGAGCGGGAGGGGCC;RSEQ=GAGTATTGGGACCGGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:35:11,24:217,208:425,35:0.0754:2,2:26.2:1:31.3:1:0.03379:2.27231:30.5:34:0.0749:0:2 1/0:268:159:79,80:47,62:109,159:0.5933:2,2:22.8:1:29.5:1:0.31996:1.30:36.3:158:0.5962:0:1.7 +6 29855902 . G A 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATGGAGCGGGAGGGGCCA;RSEQ=AGTATTGGGACCGGAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:229,234:463,0:0:2,0:25.2:1:32.4:1:1:0:57:153.333:1:0:0.3 0/1:273:14:4,10:126,133:259,14:0.0513:2,2:22.5:1:29.9:1:0.1753:2.36154:52.6:28:0.0524:0:1.2 +6 29855930 . G T 71 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0036;SOR=Inf;LSEQ=GGACCGGAACACACAGATCT;RSEQ=CAAGGCCCAGGCACAGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:190,260:450,0:0:2,0:27.6:1:31.9:1:1:0:58:89:1:0:0.2 0/1:292:6:1,5:127,159:286,6:0.0205:2,2:27:1:27.5:1:0.23539:3.97817:35:12:0.0208:0:8 +6 29855935 . G A 84 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00065;SOR=Inf;LSEQ=GGAACACACAGATCTGCAAG;RSEQ=CCCAGGCACAGACTGAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:173,266:439,0:0:2,0:27.4:1:31.5:1:1:0:58.2:61.714:1:0:0.2 0/1:296:8:2,6:124,164:288,8:0.027:2,2:32.9:1:28:1:0.47379:2.26259:38.6:16:0.028:0:7.9 +6 29855938 . C A 88 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00064;SOR=Inf;LSEQ=ACACACAGATCTGCAAGGCC;RSEQ=AGGCACAGACTGAACGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:0:0,0:168,267:435,0:0:2,0:27.1:1:31.5:1:1:0:58.6:53.375:1:0:0.2 0/1:293:8:2,6:121,164:285,8:0.0273:2,2:35.9:1:29.4:1:0.47494:2.20796:38.6:16:0.0276:0:7.9 +6 29855940 . G A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.2724;LSEQ=ACACAGATCTGCAAGGCCCA;RSEQ=GCACAGACTGAACGAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:17:4,13:158,254:412,17:0.0394:2,2:27.4:1:32.8:1:0.30829:2.01867:38.6:34:0.0401:0:3 0/1:286:51:17,34:97,128:225,51:0.1783:2,2:28.9:1:29.2:1:0.21215:1.51339:47.2:24.5:0.175:0:2.8 +6 29855945 . A G 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.11343;LSEQ=GATCTGCAAGGCCCAGGCAC;RSEQ=GACTGAACGAGAGAACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:17:4,13:146,255:401,17:0.0407:2,2:24.8:1:30.8:1:0.31612:1.85828:38.6:16:0.039:0:3 0/1:316:47:16,31:104,165:269,47:0.1487:2,2:30.3:1:29.3:1:0.62636:1.22045:49.2:22.5:0.1447:0:2.9 +6 29855950 . G T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GCAAGGCCCAGGCACAGACT;RSEQ=AACGAGAGAACCTGCGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:143,271:414,0:0:2,0:25.4:1:31.9:1:1:0:58.7:58.143:1:0:0.3 0/1:321:14:3,11:113,194:307,14:0.0436:2,2:29.3:1:26.9:1:0.39372:2.13129:37.4:13:0.0415:0:5.2 +6 29855952 . A C 165 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=23.66442;LSEQ=AAGGCCCAGGCACAGACTGA;RSEQ=CGAGAGAACCTGCGGATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:3:1,2:141,270:411,3:0.0072:2,2:14:1:26.7:1:1:1.04434:28.7:2:0.0049:0:4 0/1:325:48:12,36:103,173:276,48:0.1477:2,2:16.5:1:29.7:1:0.10544:1.78314:33.7:47:0.1478:0:2.9 +6 29855960 . A G 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28333;SOR=0.49268;LSEQ=GGCACAGACTGAACGAGAGA;RSEQ=CCTGCGGATCGCGCTCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:10:4,6:125,254:379,10:0.0257:2,2:9:1:32.9:1:0.73613:1.35:24.6:20:0.0261:0:2.6 0/1:312:4:0,4:103,205:308,4:0.0128:2,0:7.3:1:28.5:1:0.3063:0:23.5:8:0.0131:0:2.8 +6 29855978 . G T 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GAACCTGCGGATCGCGCTCC;RSEQ=CTACTACAACCAGAGCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:94,210:304,0:0:2,0:24.7:1:31.2:1:1:0:55.5:42.429:1:0:0.3 0/1:244:14:4,10:70,160:230,14:0.0574:2,2:27.3:1:29.3:1:1:1.09335:52.5:28:0.0591:0:1.7 +6 29855999 . G A 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07416;SOR=0.24453;LSEQ=CTACTACAACCAGAGCGAGG;RSEQ=CGGTGAGTGACCCCGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:10:4,6:47,159:206,10:0.0463:2,2:35.3:1:28.3:1:0.25131:2.25:24.2:9:0.0429:0:2.7 0/1:171:2:1,1:31,93:124,2:0.0117:2,2:21.5:1:26:1:0.44495:2.97:41:4:0.0121:0:2 +6 29856022 . G A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=26.37006;LSEQ=GTGAGTGACCCCGGCCCGGG;RSEQ=CGCAGGTCACGACCCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:3:0,3:44,119:163,3:0.0181:2,0:22.3:1:29.3:1:0.56621:0:53.7:6:0.0185:0:2.3 0/1:91:30:3,27:14,47:61,30:0.3297:2,2:23.9:1:29.7:1:0.16323:2.65522:50.7:60:0.3448:0:1.4 +6 29856039 . TCCC T 88 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00772;SOR=7.46725;LSEQ=GGGGCGCAGGTCACGACCCC;RSEQ=CATCCCCCACGGAGGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:0,2:31,92:123,2:0.016:2,0:10:0:34.5:1:1:0:22:4:0.0164:0:2 0/1:64:7:0,7:13,43:56,7:0.1094:2,0:7.7:1:31.5:1:0.32792:0:30.6:14:0.1148:0.0625:2.3 +6 29856058 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCATCCCCCACGGAGG;RSEQ=CCGGGTCGCCTCGAGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:43,66:109,2:0.018:2,2:11:0:32:0:1:1.53:60:4:0.0183:0:1.5 0/0:39:0:0,0:14,25:39,0:0:2,0:24.2:1:31.7:1:1:0:50.7:78:1:0:0.8 +6 29856092 . A T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=20.29012;LSEQ=AGTCTCTGGGTCCGAGATCC;RSEQ=CCCCGAAACCGCGGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:8:6,2:71,44:115,8:0.065:2,2:16.6:1:31.6:1:0.70878:1.85:40.1:16:0.0672:0:1.5 1/0:32:19:12,7:8,5:13,19:0.5938:2,2:27.3:1:30.2:1:1:1.07:49:38:0.5938:0:1.3 +6 29856151 . CG C 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00521;SOR=Inf;LSEQ=GAGGCCCAGGCGCCTTTACC;RSEQ=GTTTCATTTTCAGTTTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:182,18:200,0:0:2,0:25.2:1:29.9:1:1:0:46.1:49:1:0:0.4 0/1:75:4:4,0:67,4:71,4:0.0533:2,0:28:1:32.1:1:1:0:29:8:0.0541:0.0133:2 +6 29856178 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=4.14412;LSEQ=ATTTTCAGTTTAGGCCAAAA;RSEQ=CCCCGCGGGTTGGTCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:101:90,11:171,29:200,101:0.3355:2,2:20.7:1:31:1:0.47304:1.39:43.2:100:0.3356:0:1.2 1/0:155:105:94,11:44,5:49,105:0.6774:2,2:21.6:1:29.9:1:1:1.02959:42.9:104:0.6753:0:1.5 +6 29856194 . G C 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAACCCCCGCGGGTTGGTC;RSEQ=GGGCAGGGCGGGGCTCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:332,89:421,0:0:2,0:22:1:30:1:1:0:54.2:83.2:1:0:0.4 0/1:234:37:23,14:153,44:197,37:0.1581:2,2:21.3:1:27.4:1:0.06062:2.10897:49:6.4:0.1404:0:1.6 +6 29856197 . G A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00602;SOR=Inf;LSEQ=ACCCCCGCGGGTTGGTCGGG;RSEQ=CAGGGCGGGGCTCGGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:0:0,0:336,102:438,0:0:2,0:22.6:1:31.4:1:1:0:54.8:61.571:1:0:0.4 0/1:248:5:4,1:179,64:243,5:0.0202:2,2:19.6:1:26:1:1:1.43:43:4:0.0167:0:2.4 +6 29856198 . C T 59 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09148;SOR=0;LSEQ=CCCCCGCGGGTTGGTCGGGG;RSEQ=AGGGCGGGGCTCGGGGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:6:3,3:337,102:439,6:0.0135:2,2:15.5:1:23.2:1:0.14647:3.29283:50.5:5:0.0115:0:1.2 0/0:255:0:0,0:186,69:255,0:0:2,0:22.8:1:31:1:1:0:52.5:41.5:1:0:0.8 +6 29856199 . A G 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCGCGGGTTGGTCGGGGC;RSEQ=GGGCGGGGCTCGGGGGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:0:0,0:350,113:463,0:0:2,0:22.4:1:30.7:1:1:0:55.1:76.167:1:0:0.4 0/1:261:17:13,4:177,67:244,17:0.0651:2,2:15.2:1:29.1:1:1:1.23:47.1:16:0.0632:0:2.5 +6 29856204 . G T 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGTTGGTCGGGGCAGGGC;RSEQ=GGGCTCGGGGGACCGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:507:0:0,0:361,145:506,0:0:2,0:22.7:1:30.1:1:1:0:55.9:49.6:1:0:0.3 0/1:293:22:15,7:186,85:271,22:0.0751:2,2:15:1:30.4:1:1:1.02112:50.3:44:0.0767:0:2.1 +6 29856248 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=0.35868;LSEQ=GCGGGGGCGGGGCCAGGTTC;RSEQ=CACACCATGCAGGTGATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:73:41,32:516,381:897,73:0.0753:2,2:26.7:1:31:1:0.90214:1.05696:57.1:23.333:0.0735:0:1.3 0/1:635:18:10,8:338,278:616,18:0.0283:2,2:25.5:1:29.8:1:1:1.03:59.4:36:0.0289:0:1.3 +6 29856279 . G T 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTGATGTATGGCTGCGAC;RSEQ=TGGGGCCCGACGGGCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1126:0:0,0:556,569:1125,0:0:2,0:25.9:1:30.9:1:1:0:57.4:55.25:0.9991:0:0.4 0/1:782:38:18,20:367,375:742,38:0.0486:2,2:25.6:1:29.7:1:0.8686:1.08727:56.7:37:0.0479:0:1.4 +6 29856285 . C T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTATGGCTGCGACGTGGGG;RSEQ=CCGACGGGCGCTTCCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1103:0:0,0:527,575:1102,0:0:2,0:26.3:1:31.6:1:1:0:56.9:43.08:0.9991:0:0.4 0/1:750:14:6,8:356,380:736,14:0.0187:2,2:14.6:1:27:1:0.79035:1.24875:27.9:13:0.0177:0:2.4 +6 29856287 . C G 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TATGGCTGCGACGTGGGGCC;RSEQ=GACGGGCGCTTCCTCCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1102:0:0,0:522,579:1101,0:0:2,0:26.2:1:30.3:1:1:0:56.5:60.167:0.9991:0:0.4 0/1:737:13:6,7:349,374:723,13:0.0176:2,2:17.7:1:29.5:1:1:1.08853:25.8:26:0.0179:0:2.3 +6 29856303 . C T 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGCCCGACGGGCGCTTCCTC;RSEQ=GCGGGTATGAACAGCACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1056:0:0,0:500,556:1056,0:0:2,0:25.6:1:30.3:1:1:0:54.6:54.579:1:0:0.4 0/1:712:93:47,46:294,325:619,93:0.1306:2,2:28.4:1:29.5:1:0.65633:1.13:54:45.5:0.1293:0:1.6 +6 29856330 . G A 198 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=47.04727;LSEQ=ATGAACAGCACGCCTACGAC;RSEQ=GCAAGGATTACATCGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:857:4:4,0:389,463:852,4:0.0047:2,0:5.3:1:27.8:1:0.04406:0:55.8:8:0.0048:0:1.3 0/1:580:105:47,58:220,252:472,105:0.181:2,2:21.1:1:29.5:1:0.74668:1.07717:53.7:104:0.1821:0:1.9 +6 29856347 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.44664;LSEQ=GACGGCAAGGATTACATCGC;RSEQ=CTGAACGAGGACCTGCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:739:291:118,173:198,248:446,291:0.3938:2,2:24.7:1:30.2:1:0.32263:1.17026:52.2:21.385:0.3872:0:1.1 1/0:487:299:140,159:78,110:188,299:0.614:2,2:23.2:1:29:1:0.26239:1.24:51.7:98.667:0.6141:0:1.7 +6 29856368 . C T 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00339;SOR=Inf;LSEQ=CTGAACGAGGACCTGCGCTC;RSEQ=TGGACCGCGGCGGACATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:0:0,0:282,369:651,0:0:2,0:23.6:1:31.9:1:1:0:47.7:49.077:1:0:0.4 0/1:415:6:2,4:187,222:409,6:0.0145:2,2:16:1:30:1:0.69274:1.68265:25:12:0.0146:0:2 +6 29856426 . CG GT 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03298;SOR=0.51023;LSEQ=GCAAGTGGGAGGCGGCCCGT;RSEQ=GGCGGAGCAGCTGAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:598:41:18,23:239,317:556,41:0.0686:2,2:30.4:1:31.1:1:1:1.04:35.1:82:0.0694:0.0084:1.2 0/1:387:14:4,10:174,198:372,14:0.0362:2,2:22.6:1:30.9:1:0.2747:2.1927:31.7:28:0.0366:0.0026:1.5 +6 29856427 . G A 196 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=218.74767;LSEQ=CAAGTGGGAGGCGGCCCGTC;RSEQ=GGCGGAGCAGCTGAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:1:1,0:242,315:557,1:0.0017:2,0:1:0:27:0:0.43548:0:24:2:0.0018:0:1 0/1:389:105:51,54:125,146:271,105:0.2699:2,2:24.6:1:29.2:1:0.7299:1.10:45.2:25.25:0.276:0:1.4 +6 29856439 . T G 192 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=183.89887;LSEQ=GGCCCGTCGGGCGGAGCAGC;RSEQ=GAGAGCCTACCTGGAGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:576:1:1,0:251,324:575,1:0.0017:2,0:31:0:9:0:0.4375:0:24:0:0:0:3 0/1:362:88:41,47:116,157:273,88:0.2431:2,2:28.1:1:29.8:1:0.53733:1.18:47.7:176:0.2458:0:2.2 +6 29856445 . C T 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGGGCGGAGCAGCTGAGAG;RSEQ=CTACCTGGAGGGCGAGTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:0:0,0:246,319:565,0:0:2,0:26:1:31.4:1:1:0:52.8:34.313:1:0:0.2 0/1:359:92:43,49:115,152:267,92:0.2563:2,2:26.2:1:28.4:1:0.54533:1.16:47.2:91:0.2563:0:2.1 +6 29856468 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05363;SOR=Inf;LSEQ=ACCTGGAGGGCGAGTTCGTG;RSEQ=AGTGGCTCCGCAGATACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:187,292:479,0:0:2,0:24.3:1:31.4:1:1:0:51:42.545:1:0:0.2 0/1:291:3:2,1:117,171:288,3:0.0103:2,2:19:1:26.3:1:0.56947:2.91:51.3:6:0.0104:0:1.7 +6 29856531 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12463;SOR=Inf;LSEQ=AGCGCGCGGGTACCAGGGGC;RSEQ=ACAGGGCGCCTCCCGGATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:31,165:196,0:0:2,0:24.4:1:32.1:1:1:0:52.7:48:1:0:0.1 0/1:108:2:1,1:24,82:106,2:0.0185:2,2:10:1:28:1:0.41104:3.37:37:4:0.0192:0:1 +6 29856546 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03892;SOR=Inf;LSEQ=GGGGCCACAGGGCGCCTCCC;RSEQ=GATCGCCTGTAGATCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:17,140:157,0:0:2,0:25.5:1:31.5:1:1:0:56.9:156:0.9936:0:0.1 0/1:82:3:1,2:16,63:79,3:0.0366:2,2:24.7:1:30:1:0.50678:1.95:46.3:6:0.037:0:1.3 +6 29856550 . C G 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACAGGGCGCCTCCCGGAT;RSEQ=GCCTGTAGATCTCCGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:17,134:151,0:0:2,0:25.2:1:30.3:1:1:0:57.2:36.75:1:0:0.1 0/1:73:33:2,31:9,31:40,33:0.4521:2,2:25.2:1:30.7:1:0.09718:4.41758:56.4:66:0.4648:0:1.3 +6 29856552 . C T 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00119;SOR=Inf;LSEQ=ACAGGGCGCCTCCCGGATCG;RSEQ=CTGTAGATCTCCGGGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:16,128:144,0:0:2,0:25.8:1:31.3:1:1:0:57.8:27.8:1:0:0.1 0/1:72:6:0,6:11,55:66,6:0.0833:2,0:24.7:1:30:1:0.58115:0:52:12:0.0833:0:2 +6 29856633 . T C 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=36.6935;LSEQ=ATATCGCCCTCCCTCTGGTC;RSEQ=TGAGGGAGAAGAATCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:3,23:26,1:0.037:2,0:32:0:35:0:1:0:25:2:0.0385:0:1 1/0:18:11:1,10:2,5:7,11:0.6111:2,2:20.5:1:32:1:0.52819:3.68244:53.4:22:0.6111:0:1.7 +6 29856655 . G C 103 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05911;SOR=0.13365;LSEQ=GAGGGAGAAGAATCCTCCTG;RSEQ=GTTTCCAGAGAGTGACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:3,7:3,11:14,10:0.4167:2,2:20.5:1:31.2:1:0.66533:1.54:56.5:20:0.4167:0:1 0/1:12:1:0,1:2,8:10,1:0.0833:2,0:28:0:25:0:1:0:60:2:0.0909:0:1 +6 29856843 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02372;SOR=Inf;LSEQ=CTGCTTCACACTCAATGTGC;RSEQ=TGGGGGTCTGAGTCCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:16,3:19,0:0:2,0:16.9:1:30.8:1:1:0:30.9:38:1:0:0.2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:29:1:33:0:1:0:27.5:4:0.5:0:1.5 +6 29856862 . T A 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.31736;LSEQ=CGTGGGGGTCTGAGTCCAGC;RSEQ=CTTCTGAGTCCCTCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:2,0:15,1:16,2:0.1111:1,0:14.5:1:33:0:1:0:40:4:0.1111:0:1.5 0/1:7:1:1,0:6,0:6,1:0.1429:0,0:7:0:29:0:1:0:55:2:0.1429:0:1 +6 29856917 . T C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=15.44446;LSEQ=CCAGAAGTCGCTGTTCCCTC;RSEQ=TCAGGGACTAGAATTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:3:3,0:68,4:72,3:0.04:2,0:11.3:1:33.3:1:1:0:54.7:6:0.0405:0:2 0/1:30:12:12,0:14,4:18,12:0.4:2,0:24.6:1:30.7:1:0.12972:0:50.9:24:0.4:0:1.3 +6 29856930 . A G 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.98298;LSEQ=TTCCCTCTTCAGGGACTAGA;RSEQ=TTTTCCACGGAATAGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:5:5,0:82,4:86,5:0.0549:1,0:19.2:1:35.4:1:1:0:55.4:10:0.0556:0:2 0/1:37:2:2,0:31,4:35,2:0.0541:2,0:16:1:31.5:1:1:0:57:4:0.0541:0:2.5 +6 29856965 . G C 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00266;SOR=Inf;LSEQ=GGAGATTATCCCAGGTGCCT;RSEQ=TGTCCAGGCTGTTGTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:170,5:175,0:0:1,0:25.1:1:32.6:1:1:0:50.1:57.333:1:0:0.3 0/1:79:5:5,0:70,4:74,5:0.0633:2,0:10:1:31.4:1:1:0:37.2:10:0.0633:0:4 +6 29856977 . T G 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.80677;SOR=1.16418;LSEQ=AGGTGCCTGTGTCCAGGCTG;RSEQ=TGTCTGGGTTCTGTGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:14:12,2:201,4:205,14:0.0639:1,2:22.4:1:30.1:1:0.04922:8.19401:42:13:0.0599:0:1.4 0/1:95:7:5,2:86,2:88,7:0.0737:1,2:15.6:1:27.3:1:0.02623:15.91255:51:6:0.0645:0:1.3 +6 29857005 . C T 71 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.67932;SOR=0.43915;LSEQ=GTTCTGTGCTCCCTTCCCCA;RSEQ=CCCAGGCATCCTGTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:6:6,0:284,8:292,6:0.0201:1,0:5.3:1:27.5:1:1:0:27.3:12:0.0207:0:2 0/0:112:1:1,0:110,1:111,1:0.0089:1,0:2:0:26:0:1:0:34:2:0.0092:0:2 +6 29857013 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=8.67582;LSEQ=CTCCCTTCCCCACCCCAGGC;RSEQ=TCCTGTCCATTCTCAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:17:16,1:256,6:262,17:0.0609:1,1:35:1:29.4:1:0.3592:2.65251:30.4:34:0.0625:0:1.7 0/1:105:38:38,0:66,1:67,38:0.3619:1,1:35.9:1:27.7:1:1:0:30.5:37:0.3627:0:1.8 +6 29857021 . C A 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCACCCCAGGCATCCTGTC;RSEQ=ATTCTCAAGATGGCCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:262,7:269,0:0:1,0:30.8:1:30.9:1:1:0:41.9:23.455:1:0:0.3 0/1:102:10:10,0:91,1:92,10:0.098:1,0:33.8:1:29.7:1:1:0:32.8:20:0.101:0:2.8 +6 29857050 . A T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.03522;LSEQ=GATGGCCACATGCGTGCTGG;RSEQ=GGAGTGTCCCATGACAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:10:9,1:201,13:214,10:0.0446:2,2:10.1:1:25.9:1:0.48273:1.7128:23.3:9:0.0421:0:2 0/1:80:29:29,0:45,6:51,29:0.3625:2,1:18.3:1:25.4:1:0.08167:0:25.4:28:0.3784:0:2.4 +6 29857098 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGAATTTTCTGACTCTTC;RSEQ=CGTCAGACCCCCCCCAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:36,11:47,2:0.0408:2,2:33:0:32:0:0.43367:3.17661:20:4:0.0426:0:1 0/0:16:0:0,0:10,6:16,0:0:2,0:19.9:1:29.9:1:1:0:20.9:32:1:0:0.5 +6 29857359 . C A 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGCAGCATGAGGGTCTGCC;RSEQ=GAGCCCCTCACCCTGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:71,78:149,0:0:2,0:10.9:1:29.7:1:1:0:22.8:48.667:1:0:0.3 0/1:94:40:23,17:23,31:54,40:0.4255:2,2:11.3:1:29:1:0.21059:1.81:21.9:39:0.4239:0:2.7 +6 29857410 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=11.69485;LSEQ=GGAGATGGGGGTGTCATGTC;RSEQ=CTTAGGGAAAGCCGGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:57:26,31:141,239:380,57:0.1304:2,2:30.9:1:31.5:1:0.24309:1.42:29.7:114:0.1338:0:1.2 1/0:290:185:87,98:36,68:104,185:0.6379:2,2:29:1:30:1:0.04746:1.67:31.3:45.25:0.6373:0:1.8 +6 29857424 . G A 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGTCTCTTAGGGAAAGCC;RSEQ=GAGCCTCTCTGGAGAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:513:0:0,0:203,310:513,0:0:2,0:29.8:1:30.5:1:1:0:33.6:41.75:1:0:0.3 0/1:356:81:35,46:116,159:275,81:0.2275:2,2:27.8:1:29.1:1:0.89862:1.04:31.7:19.25:0.22:0:2.7 +6 29857473 . C T 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGGGTCCCTCACCTTCCCC;RSEQ=CTTTTCCCAGAGCCATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:0:0,0:206,327:533,0:0:2,0:25.1:1:31.2:1:1:0:50.7:58.222:1:0:0.4 0/1:429:20:11,9:181,228:409,20:0.0466:2,2:16.9:1:29.4:1:0.36596:1.54:24.5:40:0.0472:0:2.7 +6 29857502 . A C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.48366;LSEQ=AGAGCCATCTTCCCAGCCCA;RSEQ=CGTCCCCATCGTGGGCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:43:14,29:169,269:438,43:0.0892:2,2:26.3:1:30.7:1:0.51175:1.30069:29.7:13.333:0.0849:0:2.6 1/0:382:270:119,151:58,54:112,270:0.7068:2,2:26.8:1:30.9:1:0.17778:1.36177:39.4:44:0.704:0:2.2 +6 29857504 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=17.99289;LSEQ=AGCCATCTTCCCAGCCCAAC;RSEQ=TCCCCATCGTGGGCATCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:39:13,26:172,268:440,39:0.0814:2,2:27.2:1:30.9:1:0.60714:1.28293:27.6:38:0.0815:0:2.6 1/0:385:237:106,131:70,76:146,237:0.6156:2,2:26.7:1:29.3:1:0.59779:1.13789:37.8:32.857:0.615:0:2.4 +6 29857522 . G A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.43448;SOR=0.74465;LSEQ=ACGTCCCCATCGTGGGCATC;RSEQ=TTGCTGGCCTGGTTCTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:28:9,19:160,279:439,28:0.06:2,2:26.7:1:30.9:1:0.69107:1.21015:31.9:56:0.0613:0:2.8 0/1:353:16:7,9:149,188:337,16:0.0453:2,2:22.9:1:28.4:1:1:1.01894:33.1:32:0.0461:0:2.7 +6 29857570 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01956;SOR=0.44527;LSEQ=TGGTCACTGGAGCTGTGGTC;RSEQ=CTGCTGTAATGTGGAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:34:11,23:105,210:315,34:0.0974:2,2:27.4:1:29.9:1:1:1.04533:47.9:33:0.0962:0:1.7 0/1:262:12:3,9:93,157:250,12:0.0458:2,2:28:1:28.3:1:0.54425:1.7735:37.8:24:0.0463:0:2.1 +6 29857646 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14792;SOR=Inf;LSEQ=CTGAGATTTCTTGTCTCACT;RSEQ=AGAGTTCCAAGCCCCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:30,94:124,0:0:2,0:23.8:1:32.1:1:1:0:56.4:40.333:1:0:0.2 0/1:78:2:1,1:12,64:76,2:0.0256:2,2:14.5:1:28.5:1:0.30736:5.16:60:4:0.0267:0:1 +6 29857671 . T G 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48917;SOR=0.50086;LSEQ=TTCCAAGCCCCAGGTAGAAG;RSEQ=GCCCTGCCTGGTTACTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:7:1,6:14,54:68,7:0.0933:2,2:20.7:1:30.9:1:1:1.54735:52:14:0.0933:0:1.4 0/1:41:2:0,2:3,36:39,2:0.0488:2,0:23:1:26:0:1:0:50:4:0.0488:0:2 +6 29857730 . G C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.36917;SOR=2.76471;LSEQ=GGGCCTACCCAGCCTGGGCC;RSEQ=TGTGTGCCAGCACTTACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:0,6:1,12:13,6:0.3158:1,0:8.2:1:33:1:1:0:31.7:12:0.3158:0:1.5 1/0:7:4:0,4:1,2:3,4:0.5714:2,0:12.3:1:29.5:1:0.42857:0:27.3:8:0.6667:0:1.5 +6 29857753 . T C 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53216;SOR=0;LSEQ=TGTGCCAGCACTTACTCTTT;RSEQ=GTAAAGCACCTGTTACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:3,1:3,9:12,4:0.25:2,2:8.8:1:31.3:1:0.11813:7.64:60:8:0.25:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:15.6:1:29.4:1:1:0:38.4:10:1:0:0.6 +6 29857852 . A G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00374;SOR=9.03157;LSEQ=AGTCACAGGGGAAGGTCCCC;RSEQ=AGGACAGACCTCAGAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:16,1:22,7:29,17:0.3696:2,1:26.4:1:28.9:1:0.2263:4.95:42.8:16:0.3556:0:2.2 1/1:13:11:9,2:1,1:2,11:0.8462:2,2:21.4:1:30.3:1:0.42308:3.87:32.5:22:0.8462:0:2.5 +6 29857890 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.90315;LSEQ=GGCGGTTGGTCCAGGACCCA;RSEQ=ATCTGCTTTCTTCATGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:4:4,0:72,10:82,4:0.0465:2,0:33.5:1:34.3:1:1:0:27.5:8:0.0471:0:3.8 1/0:34:19:17,2:15,0:15,19:0.5588:1,2:26.2:1:31.8:1:0.49198:0:26.5:38:0.5588:0:2.8 +6 29857901 . T C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00026;SOR=8.9264;LSEQ=CAGGACCCATATCTGCTTTC;RSEQ=TCATGTTTCCTGATCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:4:4,0:92,9:101,4:0.0377:2,0:38.8:1:31.8:1:1:0:27.5:8:0.0377:0:3.8 0/1:38:10:9,1:27,1:28,10:0.2632:1,2:40.3:1:30.9:1:0.4623:2.89808:26.5:20:0.2632:0:3.5 +6 29857905 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01679;SOR=0.27297;LSEQ=ACCCATATCTGCTTTCTTCA;RSEQ=GTTTCCTGATCCCACCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:33:30,3:70,6:76,33:0.3028:2,2:21.6:1:32.6:1:1:1.16496:58:66:0.3056:0:1.3 0/1:38:4:4,0:32,2:34,4:0.1053:2,0:26.8:1:33:1:1:0:60:8:0.1053:0:1.5 +6 29857919 . A G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=18.58052;LSEQ=TCTTCATGTTTCCTGATCCC;RSEQ=CCCTGGGTCTGCAGTTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:6:5,1:117,9:126,6:0.0455:2,2:20:1:30.7:1:0.38262:2.57311:27.8:12:0.0458:0:3 0/1:59:28:24,4:31,0:31,28:0.4746:1,2:23.1:1:29.4:1:0.04499:0:27.3:56:0.4746:0:2.6 +6 29857965 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=10.57009;LSEQ=TGGAAACTTCTCTGGGGTCC;RSEQ=AGACTTGGAGGTTCCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:23:18,5:234,60:294,23:0.0726:2,2:22:1:30.9:1:0.79432:1.08307:39.4:46:0.0735:0:1.2 0/1:174:79:54,25:68,26:94,79:0.454:2,2:21.5:1:29.5:1:0.61728:1.20948:39.8:78:0.4509:0:1.3 +6 29857986 . G T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05652;SOR=Inf;LSEQ=AGACTTGGAGGTTCCTCTAG;RSEQ=ACCTTATGGCCCTGGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:310,138:448,0:0:2,0:24.2:1:31.2:1:1:0:58.3:36.333:1:0:0.2 0/1:280:3:2,1:171,106:277,3:0.0107:2,2:12.7:1:21.3:1:1:1.24:51:2:0.0073:0:1.7 +6 29857993 . T A 58 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02331;SOR=Inf;LSEQ=GAGGTTCCTCTAGGACCTTA;RSEQ=GGCCCTGGCTTCTTTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:506:0:0,0:339,167:506,0:0:2,0:24.5:1:30.7:1:1:0:57.1:100.2:1:0:0.2 0/1:326:4:2,2:193,129:322,4:0.0123:2,2:5:1:29:1:1:1.49419:27.8:8:0.0124:0:4 +6 29858001 . G A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01016;SOR=Inf;LSEQ=TCTAGGACCTTATGGCCCTG;RSEQ=CTTCTTTCTGGCATCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:0:0,0:353,204:557,0:0:2,0:25.5:1:31.5:1:1:0:54.2:78.571:1:0:0.2 0/1:373:5:3,2:215,153:368,5:0.0134:2,2:13.2:1:28.8:1:1:1.07:34.2:10:0.0135:0:3.4 +6 29858004 . T C 108 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.81868;SOR=1.20259;LSEQ=AGGACCTTATGGCCCTGGCT;RSEQ=CTTTCTGGCATCTCACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:577:11:8,3:357,209:566,11:0.0191:2,2:3.9:1:31.3:1:0.75389:1.56:24.3:22:0.0192:0:3.1 0/1:394:9:5,4:221,164:385,9:0.0228:2,2:8.6:1:30.7:1:1:1.07784:26.3:18:0.0229:0:3.3 +6 29858013 . C T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26535;SOR=1.43831;LSEQ=TGGCCCTGGCTTCTTTCTGG;RSEQ=ATCTCACAGGACATTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:21:13,8:364,236:600,21:0.0338:2,2:11.3:1:29.6:1:1:1.05:25:42:0.0345:0:2.3 0/1:438:21:12,9:230,187:417,21:0.0479:2,2:12.8:1:28.9:1:1:1.08:25.6:42:0.0485:0:2.4 +6 29858090 . C A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.81506;SOR=0.86625;LSEQ=GCAAGTAAGTATGAAGGAGG;RSEQ=TGATCCCTGAAATCCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:11:8,3:253,369:622,11:0.0174:2,2:7.2:1:28.7:1:0.0585:3.88:23.2:22:0.0176:0:3.1 0/1:464:7:5,2:206,251:457,7:0.0151:2,2:6.7:1:27.1:1:0.2536:3.04:23.3:14:0.0153:0:2.6 +6 29858201 . T C 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07318;SOR=Inf;LSEQ=GGATCTGACCAGGTCCTGTT;RSEQ=TTATTCTACTCGAGGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:134,197:331,0:0:2,0:24.3:1:30.3:1:1:0:57.6:46.286:1:0:0.5 0/1:239:3:2,1:102,134:236,3:0.0126:2,2:9:1:24.3:1:0.58133:2.62:57.7:2:0.0086:0:3.3 +6 29858213 . G C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.79402;LSEQ=GTCCTGTTTTTATTCTACTC;RSEQ=AGGCAGCAACAGTGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:117:54,63:87,104:191,117:0.3799:2,2:25.7:1:31.7:1:1:1.02:54.9:57.5:0.3808:0:1.3 1/0:221:165:74,91:25,30:55,165:0.7466:2,2:27.5:1:30.4:1:1:1.02467:53.5:54:0.757:0:2.5 +6 29858218 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.58189;LSEQ=GTTTTTATTCTACTCGAGGC;RSEQ=GCAACAGTGCCCAGGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:21:8,13:135,153:288,21:0.068:2,2:26.8:1:31:1:0.50153:1.43218:52.8:42:0.0695:0:2.5 1/0:213:120:53,67:42,47:89,120:0.5634:2,2:28:1:29.3:1:0.67599:1.129:52.4:39:0.5735:0:3 +6 29858253 . G A 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCTCTGATGTGTCTCTCAC;RSEQ=GCTTGAAAGGTGAGACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:119,130:249,0:0:2,0:26:1:30.2:1:1:0:57.4:26.667:1:0:0.9 0/1:145:32:13,19:50,63:113,32:0.2207:2,2:29.3:1:27.4:1:0.84041:1.15877:44.9:4.333:0.194:0:4.3 +6 29858256 . T G 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=29.66623;LSEQ=TCTGATGTGTCTCTCACGGC;RSEQ=TGAAAGGTGAGACCTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:9:3,6:117,113:230,9:0.0375:2,2:19.7:1:27.6:1:0.33328:2.06469:52.2:3.5:0.0313:0:3.4 1/0:141:76:30,46:31,33:64,76:0.539:2,2:25.3:1:30.8:1:0.30879:1.43659:49.6:152:0.5547:0:3.6 +6 29858294 . A G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.96632;LSEQ=GGGGGCCTGATGTGTGGGGG;RSEQ=TGTTGGGGGGGAACAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:13:8,5:100,62:162,13:0.0703:2,2:18:1:26.6:1:1:1.00802:57.7:2.25:0.0692:0:2 0/1:90:43:21,22:22,21:43,43:0.4778:2,2:17.7:1:30.5:1:1:1.09632:58.3:42:0.5676:0:2.7 +6 29858296 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54248;SOR=0;LSEQ=GGGCCTGATGTGTGGGGGAT;RSEQ=TTGGGGGGGAACAGTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:103,74:177,2:0.0112:2,2:12:1:27.5:1:1:1.38926:60:4:0.0126:0:1.5 0/0:97:0:0,0:44,53:97,0:0:2,0:16.3:1:29.1:1:1:0:57.9:7.818:1:0:1.8 +6 29858357 . A G 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00074;SOR=Inf;LSEQ=TTGAATTTGATGTTTTGAGC;RSEQ=TGCGATGGGCTGCCAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:144,52:196,0:0:2,0:24:1:30.2:1:1:0:59.6:27:1:0:0.4 0/1:112:7:6,1:77,28:105,7:0.0625:2,2:22.3:1:29.6:1:0.67462:2.17:59:14:0.0631:0:1.4 +6 29858407 . G C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06266;SOR=2.26878;LSEQ=ACTGGGACAGATATGAATTT;RSEQ=TTCATGAATATTTTTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:11:6,5:217,74:291,11:0.0364:2,2:5.8:1:32.1:1:0.16329:2.43526:21.5:22:0.0372:0:3.2 0/1:139:11:3,8:99,29:128,11:0.0791:2,2:5.4:1:29.2:1:0.00117:8.92069:21:22:0.0803:0:3.1 +6 29858468 . G T 102 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGGGACTGAGAGGCAAGA;RSEQ=TTGTTCCTGCCTTCCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:0:0,0:267,285:552,0:0:2,0:25.1:1:32.4:1:1:0:40:68:1:0:0.3 0/1:172:11:6,5:73,87:160,11:0.064:2,2:5.7:1:29.6:1:0.75629:1.43:26.8:22:0.0647:0:1 +6 29858471 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05484;SOR=Inf;LSEQ=GGGACTGAGAGGCAAGAGTT;RSEQ=TTCCTGCCTTCCCTTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:259,292:551,0:0:2,0:26.3:1:31.9:1:1:0:40.5:67.875:1:0:0.3 0/1:169:2:1,1:76,91:167,2:0.0118:2,2:14.5:1:28:1:1:1.20:29:4:0.0118:0:1.5 +6 29858476 . T C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0016;SOR=2.70094;LSEQ=TGAGAGGCAAGAGTTGTTCC;RSEQ=GCCTTCCCTTTGTGACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:29:14,15:225,285:510,29:0.0538:2,2:32:1:30:1:0.70338:1.18:21.3:28:0.0529:0:3.2 0/1:165:22:9,13:65,78:143,22:0.1333:2,2:30.9:1:30:1:0.81896:1.20236:21.2:44:0.135:0:3.1 +6 29858480 . T A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05608;SOR=Inf;LSEQ=AGGCAAGAGTTGTTCCTGCC;RSEQ=TCCCTTTGTGACTTGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:0:0,0:231,312:543,0:0:2,0:29.4:1:30.7:1:1:0:41.5:66.875:1:0:0.3 0/1:169:2:1,1:74,93:167,2:0.0118:2,2:46:0:29:1:1:1.26:25:4:0.0118:0:1 +6 29858483 . C T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00226;SOR=2.52313;LSEQ=CAAGAGTTGTTCCTGCCTTC;RSEQ=CTTTGTGACTTGAAGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:29:14,15:208,295:503,29:0.0545:2,2:25:1:30.1:1:0.56194:1.32:21.3:13.5:0.0521:0:3.2 0/1:173:22:9,13:63,86:149,22:0.1272:2,2:24.2:1:29.4:1:1:1.05781:21.2:44:0.1287:0:3.1 +6 29858506 . ACTTT A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0;SOR=10.80292;LSEQ=TTGTGACTTGAAGAACCCTG;RSEQ=CTTTCTACAAAGGCACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:10:0,10:175,318:493,10:0.0192:2,0:22.5:1:32:1:0.01751:0:33.4:20:0.0197:0.0019:1.2 0/1:171:30:4,26:50,80:130,30:0.1754:2,2:21.6:1:30.2:1:0.00956:4.03262:35.4:60:0.1765:0.0058:1.1 +6 29858507 . C A 118 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06632;SOR=2.16284;LSEQ=TGTGACTTGAAGAACCCTGA;RSEQ=TTTCTTTCTACAAAGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:16:7,9:175,318:493,16:0.0308:2,2:5.5:1:29.5:1:0.59741:1.41:20.9:32:0.0315:0:3.3 0/1:171:11:6,5:50,80:130,11:0.0643:2,2:4.7:1:27.3:1:0.34485:1.91:21.5:22:0.0647:0:3.1 +6 29858517 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.62094;LSEQ=AGAACCCTGACTTTCTTTCT;RSEQ=CAAAGGCACCTGAATGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:10:0,10:171,336:507,10:0.0193:2,0:28.6:1:32.4:1:0.03509:0:33.4:20:0.0196:0:1.2 0/1:174:37:4,33:51,86:137,37:0.2126:2,2:23.6:1:30.3:1:0.00239:4.85612:35.6:36:0.2093:0:1.2 +6 29858567 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.54555;SOR=0;LSEQ=GTAGGCATAATGTGTGGAGG;RSEQ=GGGGAGACCAACCCACCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:0,2:5,176:181,2:0.0109:1,0:20:1:30:1:1:0:45:4:0.011:0:1 0/0:97:0:0,0:14,83:97,0:0:2,0:23.7:1:30.2:1:1:0:49.2:194:1:0:0.6 +6 29858660 . A C 68 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00227;SOR=16.71209;LSEQ=TCTTTCCTGTTCCAGAGAGG;RSEQ=GGGGCTGAGATGTCTCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:1,36:37,2:0.0513:1,0:14:0:32:0:1:0:52.5:4:0.0513:0:1 1/0:10:5:1,4:0,5:5,5:0.5:0,2:25.4:1:29.4:1:1:0:54.6:10:0.5:0:1 +6 29858842 . A C 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGACAAAATAAATGGAACAC;RSEQ=TGAGAACCTTCCAGAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28.5:1:32:1:1:0:25:4:1:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:32:0:1:0:60:2:1:0:1 +6 29864315 . T G 71 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06061;SOR=Inf;LSEQ=AGGAGGTGTCTGGGTTCTGT;RSEQ=CTCCCTTCCCCACCCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:20.8:1:30.8:1:1:0:60:8:1:0:0 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:35:1:30.8:1:1:1.41:36.4:10:0.7143:0:1.2 +6 29864404 . G C 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=ATGAGGAATGCAAAGTGCCT;RSEQ=AATTTTCTTACTCTTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:13,0:0:2,0:14:1:30.5:1:1:0:48:12:1:0:0.2 1/1:4:4:3,1:0,0:0,4:1:0,2:23.5:1:32.3:1:1:0:60:8:1:0:4 +6 29864423 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.001;SOR=Inf;LSEQ=TGAATTTTCTTACTCTTCCC;RSEQ=TCAGAATCCCAGAATACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:10,0:0:2,0:27.3:1:33.2:1:1:0:60:20:1:0:0 1/1:4:4:3,1:0,0:0,4:1:0,2:35.5:1:30.5:1:1:0:60:8:1:0:4 +6 29864446 . G T 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=AGAATCCCAGAATACATGTG;RSEQ=GATCCACTACCCCATCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,4:14,0:0:2,0:27.7:1:32.6:1:1:0:60:28:1:0:0 1/1:7:6:4,2:1,0:1,6:0.8571:0,2:25.7:1:29.3:1:1:0:60:12:0.8571:0:3.3 +6 29864478 . A G 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00058;SOR=Inf;LSEQ=CCATCTCGGACCATGAGGCC;RSEQ=CCCTGAGGTGCTGGGTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:11,3:14,0:0:2,0:27.4:1:30.1:1:1:0:60:28:1:0:0 1/0:13:8:6,2:4,1:5,8:0.6154:2,2:22.3:1:29:1:1:1.30472:60:16:0.6154:0:2.8 +6 29864562 . A G 129 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=28.44986;LSEQ=GGGAGGACCAAATTTAGGAC;RSEQ=CAGAGCTTGTGGGGACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:28,12:40,2:0.0476:2,0:28:1:32:0:1:0:60:4:0.0488:0:1 1/0:35:21:14,7:11,3:14,21:0.6:2,2:18.1:1:29.4:1:0.70412:1.80255:60:20:0.5882:0:1.8 +6 29864599 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21899;SOR=Inf;LSEQ=CAGACCTGCAGGGTATAGAA;RSEQ=CTTCCAGAAGTGGGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:42,12:54,0:0:2,0:26.2:1:32.3:1:1:0:59.6:53:1:0:0.2 0/1:48:2:1,1:36,10:46,2:0.0417:2,2:26:0:31:1:0.40957:3.47963:60:4:0.0426:0:2.5 +6 29864613 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2446;SOR=Inf;LSEQ=ATAGAACCTTCCAGAAGTGG;RSEQ=CAGCTGTGGTGCTGTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:57,13:70,0:0:2,0:22.2:1:31.7:1:1:0:59.7:34:1:0:0.2 0/1:69:2:1,1:44,23:67,2:0.029:2,2:8.5:1:28:1:1:1.89399:60:4:0.0294:0:4 +6 29864622 . G A 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCAGAAGTGGGCAGCTGTG;RSEQ=TGCTGTCTTCTAGAGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:65,21:86,0:0:2,0:20.5:1:31.4:1:1:0:59.8:85:1:0:0.1 1/0:78:41:27,14:21,16:37,41:0.5256:2,2:24:1:29:1:0.48721:1.46:59.4:40:0.5263:0:1.5 +6 29864650 . A C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20935;SOR=Inf;LSEQ=TTCTAGAGACAAGTAGAGAT;RSEQ=CACATGCCATGTGCAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:83,48:131,0:0:2,0:24.9:1:28.9:1:1:0:60:130:1:0:0.1 0/1:111:2:1,1:65,44:109,2:0.018:2,2:27:1:32:0:1:1.47193:60:4:0.0182:0:1 +6 29864686 . C T 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00196;SOR=Inf;LSEQ=GCAGGAGGCACTGCCAGAGC;RSEQ=CCTCACACTGAGATGGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:78,80:158,0:0:2,0:29.6:1:30.9:1:1:0:58:78:1:0:0.6 0/1:113:7:3,4:49,57:106,7:0.0619:2,2:23.1:1:29.7:1:1:1.14482:60:14:0.0631:0:2.4 +6 29864693 . A C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20189;SOR=0.43082;LSEQ=GCACTGCCAGAGCCCCTCAC;RSEQ=CTGAGATGGGCTAAGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:13:4,9:70,78:148,13:0.0807:2,2:14.7:1:31.2:1:0.38503:2.01083:34.2:26:0.0828:0:6 0/1:110:4:1,3:46,60:106,4:0.0364:2,2:17.5:1:28.8:1:0.63431:2.28424:35.8:8:0.0374:0:6.3 +6 29864704 . C G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14148;SOR=0.3958;LSEQ=GCCCCTCACACTGAGATGGG;RSEQ=TAAGGAGATGAATGAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:15:4,11:64,81:145,15:0.0938:2,2:23.3:1:31.7:1:0.27399:2.16299:33.9:30:0.0962:0:6 0/1:102:4:1,3:41,57:98,4:0.0392:2,2:28.5:1:30:1:0.64138:2.14318:35.8:8:0.0396:0:6.3 +6 29864724 . C T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07669;SOR=0.38353;LSEQ=CTAAGGAGATGAATGAGGGG;RSEQ=CATGTCTCTTCTCAGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:20:4,16:35,75:110,20:0.1538:2,2:34.1:1:29.2:1:0.42691:1.85854:31.4:40:0.1626:0:6.1 0/1:77:5:1,4:29,43:72,5:0.0649:2,2:41.4:1:29.2:1:0.643:2.66771:34:10:0.0658:0:6.2 +6 29864730 . C G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0226;SOR=0.32228;LSEQ=AGATGAATGAGGGGCCATGT;RSEQ=TCTTCTCAGGGAAAGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:25:4,21:30,71:101,25:0.1984:2,2:28.9:1:31.5:1:0.21279:2.20592:29.4:50:0.2016:0:6.5 0/1:68:5:1,4:26,37:63,5:0.0735:2,2:39.8:1:33:1:0.64106:2.77393:34:10:0.0746:0:6.2 +6 29864736 . T A 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01292;SOR=0.29026;LSEQ=ATGAGGGGCCATGTCTCTTC;RSEQ=CAGGGAAAGCAGGAGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:26:4,22:24,63:87,26:0.2301:2,2:29.2:1:29.6:1:0.30101:2.08297:29.2:52:0.243:0:6.5 0/1:63:5:1,4:21,37:58,5:0.0794:2,2:36.2:1:30:1:0.64966:2.24457:34:10:0.082:0:6.2 +6 29864745 . G A 44 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35329;SOR=2.71426;LSEQ=CATGTCTCTTCTCAGGGAAA;RSEQ=CAGGAGCCTTTCTGGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:19,83:102,2:0.0192:2,0:40:1:31:1:1:0:60:4:0.0194:0:2 0/1:59:3:2,1:14,42:56,3:0.0508:2,2:24.7:1:28:1:0.17595:5.78:60:6:0.0517:0:2 +6 29864754 . T C 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01188;SOR=2.60017;LSEQ=TCTCAGGGAAAGCAGGAGCC;RSEQ=TTCTGGAGGCCTTCAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:35:4,31:7,48:55,35:0.3889:2,2:24.9:1:32.8:1:1:1.12865:33.2:70:0.3933:0:6.2 1/0:48:30:5,25:3,15:18,30:0.625:2,2:22.2:1:31.6:1:1:1:51.6:60:0.6383:0:2.4 +6 29864792 . G A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.06658;SOR=0.37626;LSEQ=AGGGTCAGGGCTGAGGCCTG;RSEQ=GGGTCAGGACCCCTCACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:26:0,26:8,34:42,26:0.3824:2,1:31.5:1:33.2:1:0.01992:0:34.7:52:0.3824:0:6.5 0/1:32:6:1,5:5,21:26,6:0.1875:2,2:26.5:1:28.2:1:1:1.18422:44:12:0.1875:0:6.2 +6 29864801 . A G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22989;SOR=0.50629;LSEQ=GCTGAGGCCTGGGGGTCAGG;RSEQ=CCCCTCACGTTCCCCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:25:0,25:11,33:44,25:0.3623:2,1:29.5:1:33.4:1:0.00535:0:35.8:50:0.3623:0:6.6 0/1:27:6:1,5:6,15:21,6:0.2222:2,2:26.7:1:29.8:1:1:1.95426:44:12:0.2222:0:6.2 +6 29864810 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13402;SOR=0.41526;LSEQ=TGGGGGTCAGGACCCCTCAC;RSEQ=TTCCCCTCCTTTCTTAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:0,22:10,28:38,22:0.3667:2,1:28.9:1:32.3:1:0.00951:0:37.1:44:0.3667:0:6.7 0/1:26:5:1,4:5,16:21,5:0.1923:2,2:32.8:1:30:1:1:1.2397:47.4:10:0.2:0:6.2 +6 29864814 . CC TG 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29669;SOR=0.47903;LSEQ=GGTCAGGACCCCTCACGTTC;RSEQ=CTCCTTTCTTAGGGCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:20:0,20:10,28:38,20:0.3448:2,1:28:1:32.5:1:0.01088:0:38.8:40:0.3448:0:5.7 0/1:25:5:1,4:5,15:20,5:0.2:2,2:33.8:1:29.1:1:1:1.31882:47.4:10:0.2:0:5.2 +6 29864846 . C T 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.78475;LSEQ=AGGGCCATCTTCCCAGCCCA;RSEQ=ATTCCCCATCGTGGGCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:7:0,7:9,21:30,7:0.1842:2,0:21.1:1:29.1:1:0.15996:0:49.9:14:0.1892:0:5.3 0/1:20:3:1,2:4,13:17,3:0.15:2,2:31.3:1:30.3:1:1:1.58:51.3:6:0.15:0:5.3 +6 29864852 . C T 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00044;SOR=23.74803;LSEQ=ATCTTCCCAGCCCACATTCC;RSEQ=CATCGTGGGCATTGTTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:1:0,1:9,26:35,1:0.0278:2,0:13:0:32:0:1:0:60:2:0.0278:0:2 0/1:19:8:2,6:3,8:11,8:0.4211:2,2:25.4:1:28.1:1:1:1.11808:60:16:0.4211:0:4.1 +6 29864857 . G A 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=24.47975;LSEQ=CCCAGCCCACATTCCCCATC;RSEQ=TGGGCATTGTTACTGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:9,24:33,1:0.0294:2,0:8:0:33:0:1:0:60:2:0.0303:0:2 0/1:18:8:2,6:3,7:10,8:0.4444:2,2:25:1:29.5:1:1:1.26799:60:16:0.4706:0:4.1 +6 29864865 . T C 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00051;SOR=Inf;LSEQ=ACATTCCCCATCGTGGGCAT;RSEQ=GTTACTGTCCTGGTTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:9,18:27,0:0:2,0:26.1:1:30.2:1:1:0:59.9:26:1:0:0.7 0/1:17:7:2,5:3,7:10,7:0.4118:2,2:26.3:1:29.3:1:1:1.06713:60:14:0.4375:0:4.4 +6 29864871 . T C 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=CCCATCGTGGGCATTGTTAC;RSEQ=GTCCTGGTTGTTCTAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,17:26,0:0:2,0:23.1:1:30.9:1:1:0:59.8:52:1:0:0.7 0/1:17:8:2,6:3,6:9,8:0.4706:2,2:22.6:1:28.4:1:1:1.46472:60:16:0.4706:0:4 +6 29864879 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=GGGCATTGTTACTGTCCTGG;RSEQ=TGTTCTAGGTGCTGTGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:8,13:21,0:0:2,0:22:1:29.6:1:1:0:60:42:1:0:0.4 0/1:14:2:1,1:4,8:12,2:0.1429:2,2:47:0:32.5:1:1:1.90:60:4:0.1429:0:5.5 +6 29865725 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTGTTCATGACTATTTT;RSEQ=TTTCTAAGACTGCCTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:30.5:1:1:0:25.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29865903 . C T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCCACCATGACCCCTGATA;RSEQ=TGTTTGGATCTGTGTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:17:0:35:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:35.5:1:30.5:1:1:0:23:4:0.6667:0:1.5 +6 29892834 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGAAAGGGACAGAGGGAA;RSEQ=GGCTGGAGAAGCAGGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:1:29:1:1:0:43:4:1:0:2 +6 29892854 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCTGGAGAAGCAGGAGGT;RSEQ=AGGAAAAGGAGCAGAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:29.5:1:1:0:43:4:1:0:2 +6 29893919 . G C 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGACTCAGGGAGACATTGA;RSEQ=ACAGAGCGCTTGGCACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:4,0:9,0:9,4:0.3077:0,0:25.3:1:32.3:1:1:0:42:8:0.3077:0:4 0/0:1:0:0,0:1,0:1,0:0:0,0:35:0:33:0:1:0:60:2:1:0:0 +6 29893922 . A T 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTCAGGGAGACATTGAGAC;RSEQ=GAGCGCTTGGCACAGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:23.8:1:30.2:1:1:0:41.8:10:0.3846:0:4.2 0/0:1:0:0,0:1,0:1,0:0:0,0:38:0:30:0:1:0:60:2:1:0:0 +6 29893960 . T C 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60268;SOR=0.35166;LSEQ=GGAGCGGGGTCAGGGCGAAG;RSEQ=CCTATGGCCCCAGGCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:27.8:1:29.3:1:1:0:44:5:0.3846:0:4.5 0/1:5:1:1,0:4,0:4,1:0.2:0,0:10:0:33:0:1:0:60:2:0.2:0:4 +6 29893982 . C T 91 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20112;SOR=0.20713;LSEQ=CTATGGCCCCAGGCGTGGCT;RSEQ=TCAGGGTTTCAGGCCCCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:11,0:11,8:0.4211:0,0:18.4:1:30.5:1:1:0:51:16:0.4211:0:4 0/1:8:1:1,0:6,1:7,1:0.125:2,0:32:0:32:0:1:0:60:2:0.125:0:4 +6 29894007 . A T 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44628;SOR=0.45077;LSEQ=GGTTTCAGGCCCCGAAGGCG;RSEQ=TGTATTGATTGGGGAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:11:10,1:16,1:17,11:0.3929:1,2:18.9:1:30.5:1:1:1.57244:55.1:22:0.3929:0:2.6 0/1:9:2:2,0:5,2:7,2:0.2222:2,0:24.5:1:28:1:1:0:60:4:0.2222:0:3 +6 29894016 . T C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0.65525;LSEQ=CCCCGAAGGCGATGTATTGA;RSEQ=TGGGGAGGCCCAGGGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:6,1:24,1:25,7:0.2188:1,2:24.4:1:32.4:1:0.39516:3.77964:59.3:14:0.2188:0:2.7 0/1:13:2:2,0:8,3:11,2:0.1538:2,0:24.5:1:30.5:1:1:0:60:4:0.1538:0:3 +6 29894030 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10345;SOR=Inf;LSEQ=TATTGATTGGGGAGGCCCAG;RSEQ=GTTGGGGATTCCCCATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:37,2:39,0:0:2,0:24.7:1:31.7:1:1:0:59.3:38:1:0:0.7 0/1:19:2:2,0:12,5:17,2:0.1053:2,0:9.5:1:33.5:1:1:0:60:4:0.1053:0:1 +6 29894128 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=5.30103;LSEQ=GATGTGGACTCAGTTCTCAC;RSEQ=CCCATTTGGTGTCGGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:17:17,0:215,4:219,17:0.072:1,1:29.6:1:32.2:1:1:0:60:34:0.0739:0:1.2 0/1:147:43:42,1:100,4:104,43:0.2925:1,1:24.1:1:30.4:1:1:1.67:60:86:0.2945:0:1.5 +6 29894152 . C A 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTTGGTGTCGGGTTTCTAG;RSEQ=GAAGCCAATCGGCGTCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:319,36:355,0:0:2,0:23.5:1:31.9:1:1:0:59.9:43.375:1:0:0.3 0/1:243:24:17,7:186,33:219,24:0.0988:2,2:16:1:27.3:1:0.0861:2.31095:60:48:0.0992:0:1.4 +6 29894205 . T C 217 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAAGTCCCCGCGAACCCA;RSEQ=TGGGACTCAGATTCTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:963:0:0,0:558,405:963,0:0:2,0:26:1:30.6:1:1:0:58.8:59.188:1:0:0.5 0/1:769:128:80,48:378,263:641,128:0.1664:2,2:22.6:1:31.1:1:0.49072:1.16:55.8:256:0.1684:0:2.9 +6 29894211 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.64371;LSEQ=TCCCCGCGAACCCATTGGGA;RSEQ=TCAGATTCTCCCCAGACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1036:340:195,145:395,299:694,340:0.3282:2,2:27.6:1:30.7:1:0.94669:1.02:57.4:84:0.3294:0:1.4 0/1:832:199:113,86:364,269:633,199:0.2392:2,2:25.4:1:29.2:1:0.86975:1.02982:56.7:65.333:0.2393:0:1.4 +6 29894226 . G T 215 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=281.5521;LSEQ=TGGGACTCAGATTCTCCCCA;RSEQ=ACGCCGAGGATGGGGTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1201:1:1,0:623,577:1200,1:8e-04:2,0:45:0:13:0:1:0:60:0:0:0:7 0/1:949:180:98,82:404,365:769,180:0.1897:2,2:26:1:28.8:1:0.67867:1.08:50.9:179:0.1919:0:2.8 +6 29894243 . C T 220 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=316.52981;LSEQ=CCAGACGCCGAGGATGGGGT;RSEQ=ATGGCGTCCCGAACCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1290:1:0,1:632,656:1288,1:8e-04:2,0:28:0:13:0:1:0:49:0:0:0:2 0/1:1019:200:99,101:398,421:819,200:0.1963:2,2:27.7:1:28.8:1:0.87465:1.04:48.3:65.667:0.1958:0:2.6 +6 29894250 . T A 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=24.72813;LSEQ=CCGAGGATGGGGTCATGGCG;RSEQ=CCCGAACCCTCCTCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1263:4:2,2:606,651:1257,4:0.0032:2,2:5.5:1:19.8:1:1:1.07:43.3:1:0.0016:0:3 0/1:1015:74:37,37:450,490:940,74:0.0729:2,2:27.9:1:27.9:1:0.80922:1.09:49.3:23.667:0.0714:0:2.2 +6 29894254 . G A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33011;LSEQ=GGATGGGGTCATGGCGTCCC;RSEQ=AACCCTCCTCCTGCTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1237:106:50,56:531,599:1130,106:0.0857:2,2:23.9:1:30.7:1:1:1.01:50.3:212:0.087:0:1.8 0/1:1000:30:14,16:456,512:968,30:0.03:2,2:26.4:1:30.6:1:1:1.01784:52.4:60:0.0305:0:1.9 +6 29894269 . T C 179 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=89.13111;LSEQ=GTCCCGAACCCTCCTCCTGC;RSEQ=GCTCTTGGGGGCCCTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1126:1:0,1:504,621:1125,1:9e-04:2,0:29:0:26:0:1:0:31:2:9e-04:0:4 0/1:925:68:32,36:386,469:855,68:0.0735:2,2:22.4:1:29.5:1:0.80077:1.08:46.4:136:0.0747:0:2.4 +6 29894297 . G A 67 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0245;SOR=9.24667;LSEQ=GGGGCCCTGGCCCTGACCGA;RSEQ=ACCTGGGCGGGTGAGTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:862:1:1,0:362,499:861,1:0.0012:2,0:1:0:29:0:0.42111:0:60:2:0.0012:0:1 0/1:658:7:3,4:261,390:651,7:0.0106:2,2:8.9:1:24:1:1:1.12:50.9:6:0.0093:0:2.4 +6 29894299 . C A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25481;LSEQ=GGCCCTGGCCCTGACCGAGA;RSEQ=CTGGGCGGGTGAGTGCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:226:100,126:243,369:612,226:0.2697:2,2:25.3:1:29.8:1:0.23643:1.20:46.7:74.333:0.271:0:1.7 0/1:640:55:23,32:230,355:585,55:0.0859:2,2:22.5:1:28.8:1:0.77344:1.11:45.6:110:0.0883:0:1.7 +6 29894324 . GA G 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGGGTGAGTGCGGGATCCG;RSEQ=GGGAAATGGCCTCTGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:220,389:609,0:0:2,0:25.1:1:30.9:1:1:0:50:32.833:1:0:0.8 0/1:441:22:6,16:143,275:418,22:0.0499:2,2:28.5:1:30.9:1:0.64566:1.38569:49.2:44:0.0512:0.0068:2.2 +6 29894332 . T A 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=25.77705;LSEQ=GTGCGGGATCCGGAGGGAAA;RSEQ=GGCCTCTGCGGGGAGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:2:1,1:185,370:555,2:0.0036:2,2:5:1:29:1:1:2.00:35:4:0.0036:0:3 0/1:388:33:11,22:119,236:355,33:0.0851:2,2:22.5:1:30.4:1:1:1.00845:37.3:66:0.0868:0:4.3 +6 29894334 . G A 144 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=17.22498;LSEQ=GCGGGATCCGGAGGGAAATG;RSEQ=CCTCTGCGGGGAGGAGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:3:2,1:174,366:540,3:0.0055:2,2:3:1:28:1:0.24664:4.19:31.3:6:0.0056:0:2 0/1:377:33:11,22:115,229:344,33:0.0875:2,2:22.5:1:28.6:1:1:1.00436:37.5:32:0.0872:0:4.3 +6 29894344 . G C 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGGAAATGGCCTCTGCGG;RSEQ=GAGGAGGTAGGGGCCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:468:0:0,0:150,318:468,0:0:2,0:25.2:1:31.1:1:1:0:53.9:57.5:1:0:1 0/1:317:20:7,13:97,199:296,20:0.0631:2,2:22.6:1:30.6:1:0.81036:1.10:50.3:40:0.0643:0:2.4 +6 29894349 . AGGTAGGGGCCC A 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGGCCTCTGCGGGGAGG;RSEQ=GCGCACTGGGGCGCAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:133,309:442,0:0:2,0:24.5:1:31.9:1:1:0:55.9:48.111:1:0:1.1 0/1:282:26:8,18:80,176:256,26:0.0922:2,2:28.2:1:31.9:1:1:1.02265:40.3:52:0.0949:0.0071:5 +6 29894351 . G C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.20891;LSEQ=ATGGCCTCTGCGGGGAGGAG;RSEQ=TAGGGGCCCGCGCACTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:171:47,124:82,179:261,171:0.394:2,2:24.9:1:32.6:1:0.39228:1.20808:54.4:33.2:0.3934:0:2.4 1/0:275:186:60,126:17,48:65,186:0.6764:2,2:21.9:1:30.9:1:0.43519:1.34:53.3:30:0.7407:0:1.9 +6 29894389 . A C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.87887;LSEQ=GGGCGCAGGACCCGGGGAGC;RSEQ=GCGCAAGGAGGAGGGTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:107:29,78:52,123:175,107:0.3794:2,2:25.1:1:30.7:1:0.68536:1.13657:56.3:106:0.3799:0:2.9 1/0:141:90:26,64:12,39:51,90:0.6383:2,2:26.3:1:30.4:1:0.5568:1.32:49.9:89:0.6357:0:3.7 +6 29894392 . G T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0713;SOR=1.47699;LSEQ=CGCAGGACCCGGGGAGCAGC;RSEQ=CAAGGAGGAGGGTCGGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:105:28,77:48,119:167,105:0.386:2,2:24.9:1:31.1:1:0.78183:1.10881:56.3:210:0.3903:0:2.9 0/1:137:66:18,48:18,53:71,66:0.4818:2,2:25:1:29.7:1:0.84746:1.10:52.6:32:0.4776:0:3 +6 29894393 . C G 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAGGACCCGGGGAGCAGCG;RSEQ=AAGGAGGAGGGTCGGACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:77,195:272,0:0:2,0:23.3:1:32:1:1:0:58.5:29.222:1:0:1.2 0/1:139:23:8,15:29,86:115,23:0.1655:2,2:25.8:1:30.7:1:0.43902:1.58:38.8:46:0.1691:0:5.8 +6 29894406 . CG AA 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAGCGCAAGGAGGAGGGT;RSEQ=GACGGGTCTCAGCCCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:85,182:267,0:0:2,0:23.2:1:30.7:1:1:0:58.5:132.5:1:0:1 0/1:130:19:5,14:36,73:109,19:0.1462:2,2:27.6:1:31:1:0.79044:1.37749:35.6:38:0.1484:0.0231:5.5 +6 29894410 . C T 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=146.32729;LSEQ=GCGCAAGGAGGAGGGTCGGA;RSEQ=GGGTCTCAGCCCCTCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:1,0:87,170:257,1:0.0039:2,0:30:0:33:0:0.34109:0:60:2:0.004:0:3 0/1:131:48:20,28:27,56:83,48:0.3664:2,2:22.8:1:29.9:1:0.34593:1.48:48.4:23:0.3594:0:3.8 +6 29894439 . A T 173 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=249.56594;LSEQ=GCCCCTCCTCGCCCCCAGGT;RSEQ=CCCACTCCATAAGGTATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:1,0:113,146:259,1:0.0038:2,0:42:0:33:0:0.43846:0:60:2:0.0039:0:3 0/1:123:61:29,32:30,31:61,61:0.4959:2,2:24.4:1:29.2:1:1:1.06727:51.9:60:0.4959:0:3.2 +6 29894449 . T A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=GCCCCCAGGTACCCACTCCA;RSEQ=AAGGTATTTCAGCACCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:113,147:260,0:0:2,0:26.7:1:29.3:1:1:0:58.7:31.5:1:0:0.3 0/1:116:6:2,4:57,53:110,6:0.0517:2,2:25.2:1:29.3:1:0.43462:2.13721:58:12:0.0526:0:1.3 +6 29894456 . T G 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=224.0673;LSEQ=GGTACCCACTCCATAAGGTA;RSEQ=TTCAGCACCGCCGTGTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:1,0:107,151:258,1:0.0039:2,0:25:0:35:0:0.41699:0:60:2:0.004:0:3 0/1:117:55:27,28:35,27:62,55:0.4701:2,2:30.7:1:31.4:1:0.46194:1.34088:53.3:110:0.4701:0:3 +6 29894495 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04808;SOR=Inf;LSEQ=CGGCCGGGTCGCGGGGAGCC;RSEQ=CGGTACATCGCAGTGGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:124,120:244,0:0:2,0:23.7:1:31.1:1:1:0:59:60:1:0:0.2 0/1:141:3:1,2:81,57:138,3:0.0213:2,2:10:1:24.3:1:0.57154:2.82109:42:2:0.0144:0:2 +6 29894505 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13523;SOR=Inf;LSEQ=GCGGGGAGCCCCGGTACATC;RSEQ=CAGTGGGCTACGTGGACGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:134,111:245,0:0:2,0:23.9:1:30.8:1:1:0:58.5:39.833:1:0:0.2 0/1:143:2:1,1:80,61:141,2:0.014:2,2:29:1:29:1:1:1.30895:47:4:0.0143:0:2.5 +6 29894523 . G A 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGCAGTGGGCTACGTGGAC;RSEQ=ACACGCAGTTCGTGCGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:142,115:257,0:0:2,0:24.3:1:30.5:1:1:0:58.3:35.714:1:0:0.3 0/1:154:20:12,8:72,62:134,20:0.1299:2,2:25.5:1:28.7:1:0.63856:1.29:50.3:19:0.1275:0:2.8 +6 29894548 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15808;SOR=Inf;LSEQ=GCAGTTCGTGCGGTTCGACA;RSEQ=CGACGCGGCGACTCCGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:168,107:275,0:0:2,0:25:1:32.8:1:1:0:58.4:54:1:0:0.5 0/1:182:2:1,1:106,74:180,2:0.011:2,2:9:1:27.5:1:1:1.42952:60:4:0.0112:0:1 +6 29894567 . G A 126 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=46.94111;LSEQ=AGCGACGCGGCGACTCCGAG;RSEQ=ATGTAGCCGCAGTCGCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:1:1,0:207,117:324,1:0.0031:2,0:1:0:26:0:1:0:57:2:0.0032:0:1 0/1:213:27:14,13:110,76:186,27:0.1268:2,2:22.1:1:26.5:1:0.53348:1.34207:51.1:8:0.1165:0:3.1 +6 29894569 . T C 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGACGCGGCGACTCCGAGGA;RSEQ=GTAGCCGCAGTCGCCGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:205,127:332,0:0:2,0:23.1:1:30.6:1:1:0:59.3:46.429:1:0:0.6 0/1:224:16:8,8:118,89:207,16:0.0714:2,2:24.7:1:30:1:0.60989:1.32413:56.3:32:0.0717:0:1.4 +6 29894580 . T G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.69182;LSEQ=CTCCGAGGATGTAGCCGCAG;RSEQ=CGCCGTGGTTGGAGCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:150:85,65:128,94:222,150:0.4032:2,2:22.7:1:31.1:1:0.91497:1.04122:59.3:36.5:0.4044:0:1.3 1/0:252:180:102,78:41,31:72,180:0.7143:2,2:22.6:1:29.7:1:1:1.01134:57.8:21.5:0.7078:0:1.7 +6 29894584 . C A 103 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=21.57;LSEQ=GAGGATGTAGCCGCAGTCGC;RSEQ=GTGGTTGGAGCAGGAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:1:1,0:214,170:384,1:0.0026:2,0:2:0:21:0:1:0:60:2:0.0027:0:2 0/1:263:14:9,5:137,112:249,14:0.0532:2,2:15.4:1:27.2:1:0.58759:1.47:58.5:6:0.0469:0:2.5 +6 29894595 . C T 80 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0088;SOR=7.10435;LSEQ=CGCAGTCGCCGTGGTTGGAG;RSEQ=AGGAGGGACCGGAGTATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:2:0,2:234,187:421,2:0.0047:2,0:1:0:18:1:0.19905:0:60:1:0.0025:0:1.5 0/1:275:9:5,4:146,119:265,9:0.0327:2,2:24.9:1:25.4:1:1:1.02:59.6:18:0.0332:0:2.6 +6 29894600 . G T 103 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=18.58692;LSEQ=TCGCCGTGGTTGGAGCAGGA;RSEQ=GGACCGGAGTATTGGGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:1:0,1:227,191:418,1:0.0024:2,0:1:0:28:0:0.45823:0:60:2:0.0024:0:1 0/1:281:12:7,5:146,123:269,12:0.0427:2,2:19.3:1:28.8:1:1:1.18:59.9:24:0.0432:0:2.3 +6 29894603 . A G 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGTGGTTGGAGCAGGAGGG;RSEQ=CCGGAGTATTGGGACCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:420:0:0,0:226,194:420,0:0:2,0:27:1:29.8:1:1:0:59.8:51.5:1:0:0.5 0/1:287:37:20,17:135,115:250,37:0.1289:2,2:24.3:1:29.7:1:1:1.00:53.4:17.5:0.1254:0:2.5 +6 29894629 . G C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.8786;SOR=0.90834;LSEQ=GTATTGGGACCGGAGCACAC;RSEQ=GAACATCAGGCCCGCGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:30:9,21:183,203:386,30:0.0721:2,2:29.5:1:30.2:1:0.08617:2.09987:60:60:0.0732:0:1.9 0/1:273:18:6,12:120,135:255,18:0.0659:2,2:30.3:1:28.6:1:0.33074:1.77416:60:36:0.0664:0:1.6 +6 29894630 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06233;SOR=Inf;LSEQ=TATTGGGACCGGAGCACACG;RSEQ=AACATCAGGCCCGCGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:0:0,0:188,223:411,0:0:2,0:28.4:1:31.2:1:1:0:59.9:57.714:0.9951:0:0.4 0/1:273:3:2,1:124,146:270,3:0.011:2,2:16.3:1:26:1:0.59686:2.35:60:2:0.0074:0:1.7 +6 29894636 . C CA 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACCGGAGCACACGGAACAT;RSEQ=AGGCCCGCGCACAGACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:171,225:396,0:0:2,0:27.8:1:31.8:1:1:0:59.9:65:1:0:0.4 0/1:266:35:14,21:104,126:230,35:0.1316:2,2:27.7:1:30:1:0.58947:1.23711:59.6:70:0.1341:0.015:1.5 +6 29894756 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07485;SOR=Inf;LSEQ=ACGACCCCTCCTCATCCCCC;RSEQ=CGGACGTCCCGGGTCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:22,50:72,0:0:2,0:21.6:1:29.7:1:1:0:59.9:17:0.9855:0:0.6 0/1:28:2:0,2:5,21:26,2:0.0714:2,0:29.5:1:33:0:1:0:60:4:0.08:0:2 +6 29894763 . T C 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.88658;LSEQ=CTCCTCATCCCCCACGGACG;RSEQ=CCCGGGTCCCCCCCGCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:18:7,11:15,36:51,18:0.2609:2,2:22.8:1:32.4:1:0.55876:1.52:60:36:0.2727:0:1.8 0/1:21:5:1,4:5,11:16,5:0.2381:2,2:30.2:1:32.4:1:1:1.77078:60:10:0.2381:0:1.8 +6 29894794 . A G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00013;SOR=8.6892;LSEQ=CCCCGCGAGTCTCCGGCTCC;RSEQ=AGATCCACCCCGAGGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:14:6,8:20,22:42,14:0.25:2,2:26.1:1:31.9:1:1:1.20797:60:28:0.2593:0:2.4 1/0:20:15:11,4:2,2:4,15:0.75:2,2:15.3:1:29.5:1:0.55728:2.59:59.8:30:0.75:0:2.4 +6 29894798 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06507;SOR=Inf;LSEQ=GCGAGTCTCCGGCTCCAAGA;RSEQ=CCACCCCGAGGCTGCGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:27,27:54,0:0:2,0:26.4:1:30.2:1:1:0:60:12.5:1:0:0.8 0/1:19:2:1,1:12,5:17,2:0.1053:2,2:11.5:1:32.5:1:1:2.28037:58.5:4:0.1111:0:2.5 +6 29894813 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08606;SOR=Inf;LSEQ=CAAGATCCACCCCGAGGCTG;RSEQ=GGGACCCGCCAGATCCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:34,25:59,0:0:2,0:25.4:1:31.1:1:1:0:60:28.5:1:0:0.7 0/1:25:2:1,1:17,6:23,2:0.08:2,2:14:1:28.5:1:0.49:2.69921:60:4:0.0833:0:4 +6 29894851 . C A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05273;SOR=2.13867;LSEQ=CGACCCGGGAGAGGCCCAGG;RSEQ=GCCTTTACCAGGTTTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:17:12,5:48,15:63,17:0.2099:2,2:22.5:1:30.8:1:0.75334:1.32837:59.9:34:0.2152:0:1.6 0/1:55:20:16,4:27,8:35,20:0.3636:2,2:27.6:1:27.7:1:1:1.18:59.8:19:0.3654:0:2.1 +6 29894853 . C T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACCCGGGAGAGGCCCAGGCG;RSEQ=CTTTACCAGGTTTCATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:62,18:80,0:0:2,0:23:1:32.2:1:1:0:59.6:39:1:0:0.6 0/1:56:12:11,1:33,11:44,12:0.2143:2,2:30.8:1:27.1:1:0.4274:3.60:59.7:11:0.2075:0:2.6 +6 29894863 . G A 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGCCCAGGCGCCTTTACCAG;RSEQ=TTTCATTTTCCGTTTAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:78,18:96,0:0:2,0:22.1:1:31.2:1:1:0:58.8:23:1:0:0.6 0/1:68:12:9,3:47,9:56,12:0.1765:2,2:24.5:1:28.3:1:0.4319:1.72487:49.4:11:0.1719:0:2.8 +6 29894874 . C A 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTACCAGGTTTCATTTTC;RSEQ=GTTTAGGCCAAAATCCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:96,17:113,0:0:2,0:23.1:1:30.5:1:1:0:59:15.143:0.9907:0:0.5 0/1:78:32:27,5:39,7:46,32:0.4103:2,2:25.8:1:28.3:1:1:1.03135:49.4:7:0.3836:0:2.3 +6 29894909 . G A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00686;SOR=Inf;LSEQ=CCCCGCGGGTTGGTCGGGGC;RSEQ=GGGGCGGGGCTCGGTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:193,40:233,0:0:2,0:24.3:1:30:1:1:0:58.9:45.6:0.9956:0:0.6 0/1:139:5:4,1:96,38:134,5:0.036:2,2:9.6:1:29.6:1:1:1.58:53.6:10:0.0365:0:4.8 +6 29894914 . C T 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGTTGGTCGGGGCGGGGG;RSEQ=GGGGCTCGGTGGGCGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:202,39:241,0:0:2,0:25.5:1:29.5:1:1:0:59:6.531:0.9952:0:0.5 0/1:153:19:14,5:93,29:122,19:0.1242:2,2:21.9:1:26.3:1:0.77869:1.14417:57.1:3.75:0.124:0:2.2 +6 29894933 . C T 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16652;SOR=2.206;LSEQ=GCGGGGCTCGGTGGGCGGGG;RSEQ=TGACCGCGGGGGCGGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:6:2,4:260,126:386,6:0.0153:2,2:13.8:1:27.8:1:0.09678:4.11071:60:12:0.0161:0:2.5 0/1:241:8:5,3:147,86:233,8:0.0332:2,2:21.1:1:28.5:1:1:1.02549:57.4:16:0.0351:0:4.8 +6 29894938 . C A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=12;MSI=2.000;MSILEN=2;SSF=0;SOR=8.33068;LSEQ=GCTCGGTGGGCGGGGCTGAC;RSEQ=GCGGGGGCGGGGCCAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:36:27,9:256,133:389,36:0.0843:2,2:24.3:1:28.8:1:0.35572:1.56:58.3:6.2:0.0769:0:1.5 0/1:269:117:71,46:91,59:150,117:0.4349:2,2:20.3:1:27.9:1:1:1.00:57.1:5.5:0.4024:0:2.5 +6 29894953 . A T 109 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGACCGCGGGGGCGGGGCC;RSEQ=GGGTCTAACACCCTCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:331,202:533,0:0:2,0:24.6:1:30.4:1:1:0:59.4:43.417:0.9962:0:0.4 0/1:379:14:6,8:201,164:365,14:0.0369:2,2:23.8:1:28.8:1:0.41984:1.63199:57.6:28:0.0373:0:3.6 +6 29894964 . C A 110 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=5e-05;SOR=19.74056;LSEQ=GGCGGGGCCAGGGTCTAACA;RSEQ=CCTCCAGATAATGTATGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:586:1:0,1:338,247:585,1:0.0017:2,0:25:0:13:0:0.42321:0:60:0:0:0:5 0/1:428:14:8,6:219,194:413,14:0.0327:2,2:26.6:1:28.9:1:0.79307:1.18:57.6:28:0.033:0:3.6 +6 29894966 . C T 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGGCCAGGGTCTAACACC;RSEQ=TCCAGATAATGTATGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:0:0,0:342,258:600,0:0:2,0:26:1:31.5:1:1:0:59.6:53.545:1:0:0.4 0/1:437:37:20,17:211,189:400,37:0.0847:2,2:22.6:1:29.8:1:1:1.05:58.8:74:0.0855:0:2.6 +6 29894991 . T C 191 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=144.23624;LSEQ=GATAATGTATGGCTGCGACT;RSEQ=GGGGCTGGAAGGGCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:594:1:0,1:292,301:593,1:0.0017:2,0:25:0:32:0:1:0:60:2:0.0017:0:6 0/1:464:91:46,45:190,183:373,91:0.1961:2,2:28.5:1:29.5:1:1:1.01565:60:44.5:0.1943:0:2.7 +6 29894998 . G A 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09267;SOR=6.4064;LSEQ=TATGGCTGCGACTTGGGGCT;RSEQ=GAAGGGCGCCTCCTCCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:1:1,0:267,299:566,1:0.0018:2,0:1:0:27:0:0.47266:0:60:2:0.0018:0:1 0/1:446:5:3,2:224,216:440,5:0.0112:2,2:33.8:1:28:1:1:1.45:60:10:0.0114:0:2.6 +6 29895002 . G C 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGCGACTTGGGGCTGGAA;RSEQ=GGCGCCTCCTCCGCGGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:0:0,0:266,297:563,0:0:2,0:27:1:31.8:1:1:0:59.8:61.556:0.9964:0:0.3 0/1:435:83:42,41:162,162:324,83:0.1908:2,2:28.7:1:30.3:1:1:1.02:60:166:0.1939:0:2.7 +6 29895005 . C T 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGACTTGGGGCTGGAAGGG;RSEQ=GCCTCCTCCGCGGGTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:255,296:551,0:0:2,0:26.7:1:30.7:1:1:0:59.8:90.833:0.9963:0:0.3 0/1:425:26:14,12:200,199:399,26:0.0612:2,2:32.3:1:29.2:1:0.84017:1.16:58.9:52:0.0628:0:2.8 +6 29895032 . G C 158 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.5564;LSEQ=TCCGCGGGTATGAACAGCAC;RSEQ=CCAACGATGGCAAGGATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:1:1,0:194,245:439,1:0.0023:2,0:21:0:14:0:0.44318:0:52:0:0:0:8 0/1:321:39:19,20:138,142:280,39:0.1215:2,2:19.1:1:29.9:1:1:1.02291:58.3:78:0.1254:0:1.5 +6 29895039 . A C 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTATGAACAGCACGCCAACG;RSEQ=TGGCAAGGATTACATAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:417:0:0,0:182,235:417,0:0:2,0:21.6:1:30.8:1:1:0:58:58.571:1:0:0.1 0/1:299:24:11,13:136,139:275,24:0.0803:2,2:19.5:1:30.4:1:0.83255:1.15575:57.5:23:0.0788:0:2.8 +6 29895099 . C A 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGACCGCGGCGGACATGG;RSEQ=GGCTCAGATCACCAAGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:487:0:0,0:253,233:486,0:0:2,0:26:1:31.1:1:1:0:54.8:68.429:0.9979:0:0.2 0/1:372:48:24,24:173,147:320,48:0.129:2,2:26.1:1:29.4:1:0.64316:1.17635:54.5:96:0.1304:0:1.4 +6 29895111 . C T 125 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=31.46401;LSEQ=GGACATGGCGGCTCAGATCA;RSEQ=CAAGCGCAAGTGGGAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:1:0,1:266,251:517,1:0.0019:2,0:49:0:16:0:0.48649:0:48:0:0:0:3 0/1:400:23:11,12:195,182:377,23:0.0575:2,2:22.7:1:27.7:1:0.83071:1.16837:59.1:22:0.0563:0:1.2 +6 29895215 . C T 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGAGAACGGGAAGGAGA;RSEQ=GCTGCAGCTCACGGGTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:52,157:209,0:0:2,0:25.1:1:30.6:1:1:0:59.7:103.5:0.9952:0:0.2 1/0:135:78:20,58:13,44:57,78:0.5778:2,2:24.6:1:29.8:1:0.83973:1.17:59:156:0.5778:0:1.3 +6 29895228 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16782;SOR=Inf;LSEQ=AAGGAGACGCTGCAGCTCAC;RSEQ=GGTACCAGGGAACACAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:30,135:165,0:0:2,0:25:1:31.1:1:1:0:60:54:1:0:0.3 0/1:115:2:0,2:28,85:113,2:0.0174:2,0:41.5:1:31:1:1:0:60:4:0.0175:0:2 +6 29895235 . A G 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00101;SOR=Inf;LSEQ=CGCTGCAGCTCACGGGTACC;RSEQ=GGGAACACAAGACGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:24,132:156,0:0:2,0:23.2:1:31.8:1:1:0:60:51:1:0:0.3 0/1:96:7:1,6:19,70:89,7:0.0729:2,2:24.9:1:29.4:1:1:1.62126:60:14:0.0745:0:1 +6 29895250 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00044;SOR=3.004;LSEQ=GTACCAGGGAACACAAGACG;RSEQ=CTCCCTGATCGCCTGTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:38:5,33:9,80:89,38:0.2992:2,2:18.9:1:30.3:1:0.75766:1.34:60:76:0.3089:0:1.1 1/0:71:40:2,38:8,23:31,40:0.5634:2,2:20.8:1:27.8:1:0.017:6.43642:60:19:0.5507:0:1.6 +6 29895682 . A G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46007;SOR=0.5205;LSEQ=GAATTCGGAGATTATCCCAG;RSEQ=TACCTGTGTCCAGGTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:8,1:6,2:8,9:0.5294:2,2:7.4:1:30:1:0.57647:2.52:35.8:8:0.5333:0:2.3 0/1:11:4:4,0:5,2:7,4:0.3636:2,0:5.3:1:30.5:1:0.49091:0:35.3:8:0.3636:0:2.3 +6 29895701 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0362;LSEQ=GATACCTGTGTCCAGGTTGG;RSEQ=GTCTGGGTTCTGTGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:12:11,1:13,3:16,12:0.4286:2,2:22.1:1:31.9:1:0.61319:2.46:39.2:11:0.4231:0:2 0/1:16:7:7,0:5,4:9,7:0.4375:2,0:18.3:1:32.7:1:0.08846:0:40.6:14:0.4375:0:1.7 +6 29895816 . A T 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.72218;SOR=1.09812;LSEQ=AAGTGCCTGAATTTTCTGAC;RSEQ=CTTCCTGTTAGACCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:264:218:126,92:27,19:46,218:0.8258:2,2:29.1:1:30.1:1:1:1.03746:50:10.474:0.8189:0:3.8 1/1:242:203:107,96:20,18:38,203:0.8388:2,2:27.9:1:28.7:1:1:1.00:45.5:28:0.8376:0:4.4 +6 29895822 . T C 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24946;SOR=0;LSEQ=CTGAATTTTCTGACACTTCC;RSEQ=GTTAGACCTCTCCCCCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:1,2:147,113:260,3:0.0114:2,2:15:1:24.7:1:0.58265:2.59245:34.7:2:0.0079:0:5.7 0/0:245:0:0,0:126,119:245,0:0:2,0:28.9:1:29.6:1:1:0:47.6:39.833:1:0:3.8 +6 29895830 . CTCTCCCCC ACCCCCCTCCA 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=Inf;LSEQ=TCTGACACTTCCTGTTAGAC;RSEQ=AGACACATATGATCCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:144,117:261,0:0:2,0:31.2:1:31.9:1:1:0:51.8:16.4:1:0:3.2 0/1:244:19:10,9:111,113:224,19:0.0779:2,2:34.7:1:30.9:1:0.81612:1.13:46.5:38:0.0795:0:5.7 +6 29895831 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.19164;LSEQ=CTGACACTTCCTGTTAGACC;RSEQ=CTCCCCCAGACACATATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:251:198:103,95:30,22:52,198:0.7888:2,2:32.2:1:31.3:1:0.53316:1.25657:50.5:48.5:0.7886:0:4.2 0/1:233:97:41,56:17,17:34,97:0.4163:2,2:31.4:1:30.4:1:0.54768:1.36255:46.7:194:0.7348:0:4.6 +6 29895833 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.74363;SOR=0.91423;LSEQ=GACACTTCCTGTTAGACCTC;RSEQ=CCCCCAGACACATATGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:195:100,95:32,22:54,195:0.78:2,2:32.3:1:31.1:1:0.35583:1.38002:50.3:31.5:0.7842:0:4.2 1/0:229:175:78,97:12,13:25,175:0.7642:2,2:31.5:1:29.8:1:0.83096:1.14713:46.5:24:0.8705:0:4.2 +6 29895836 . CCC ACCA 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=Inf;LSEQ=ACTTCCTGTTAGACCTCTCC;RSEQ=AGACACATATGATCCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:132,123:255,0:0:2,0:31.1:1:31.4:1:1:0:52.1:126.5:1:0:3.3 0/1:230:58:24,34:68,77:145,58:0.2522:2,2:31.3:1:29.6:1:0.53377:1.2497:44.1:116:0.2829:0.0174:4.9 +6 29895837 . CC GCA 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.09635;LSEQ=CTTCCTGTTAGACCTCTCCC;RSEQ=AGACACATATGATCCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:255:128:67,61:64,60:124,128:0.502:2,2:31.9:1:31.8:1:1:1.03:50.9:256:0.51:0.0157:4.4 0/1:227:20:9,11:61,67:128,20:0.0881:2,2:34.9:1:31.3:1:1:1.11197:56.5:40:0.137:0:4.2 +6 29895838 . C CCA 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00017;SOR=0.27094;LSEQ=TTCCTGTTAGACCTCTCCCC;RSEQ=AGACACATATGATCCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:37:16,21:34,23:57,37:0.1451:2,2:30.5:1:29.5:1:0.14173:1.92633:48.3:17.5:0.2756:0.0078:3.9 0/1:228:10:4,6:18,17:35,10:0.0439:2,2:35.7:1:28.2:1:0.72224:1.57201:37.3:9:0.0709:0:4.7 +6 29895862 . G A 205 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=452.9593;LSEQ=CACATATGATCCACCATTCC;RSEQ=TCTCTGACTATAAGGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:1:1,0:103,130:233,1:0.0043:2,0:1:0:28:0:0.44444:0:27:2:0.0045:0:4 1/0:199:132:45,87:29,37:66,132:0.6633:2,2:23.6:1:29.2:1:0.21287:1.51201:43:25.4:0.6615:0:5 +6 29895877 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09094;SOR=Inf;LSEQ=ATTCCGTCTCTGACTATAAG;RSEQ=CCACCCTGAGGTGCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:76,110:186,0:0:2,0:21:1:31.4:1:1:0:51.6:30:1:0:2.7 0/1:153:3:2,1:50,99:149,3:0.0196:2,2:13.3:1:26:1:0.26961:3.92:43.3:6:0.02:0:4.3 +6 29895878 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19827;SOR=Inf;LSEQ=TTCCGTCTCTGACTATAAGG;RSEQ=CACCCTGAGGTGCTGGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:76,109:185,0:0:2,0:20.9:1:31.4:1:1:0:51.5:60.667:1:0:2.7 0/1:149:2:1,1:49,98:147,2:0.0134:2,2:25:1:30:1:1:1.99:60:4:0.0136:0:2 +6 29895888 . G C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12425;LSEQ=GACTATAAGGCCACCCTGAG;RSEQ=TGCTGGGCCCTGGGCTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:81:34,47:25,23:48,81:0.4939:2,2:20.1:1:32.4:1:0.27899:1.49774:49:162:0.5094:0:3.6 0/1:121:13:2,11:33,70:103,13:0.1074:2,2:28.8:1:31.2:1:0.33855:2.57504:55.4:26:0.1102:0:3.2 +6 29895913 . G A 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCCTGGGCTTCTACCCT;RSEQ=TGGAGATCACACTGGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:61,69:130,0:0:2,0:28.5:1:32.6:1:1:0:52.1:129:1:0:1.5 0/1:74:17:2,15:17,40:57,17:0.2297:2,2:23.2:1:29.4:1:0.20727:3.1458:45.3:16:0.2192:0:4.6 +6 29895928 . G A 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97229;LSEQ=ACCCTGTGGAGATCACACTG;RSEQ=CCTGGCAGCAGGATGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:73:23,50:39,16:55,73:0.5703:2,2:27.3:1:29.3:1:1e-05:5.22243:45:13.6:0.5574:0:2.5 1/0:71:40:15,25:9,6:15,40:0.5634:2,2:20.6:1:29.2:1:0.22159:2.45704:43.1:39:0.5735:0:2.5 +6 29895939 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10793;SOR=Inf;LSEQ=ATCACACTGGCCTGGCAGCA;RSEQ=GATGGAGAGGACCAGACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:78,62:140,0:0:2,0:24.2:1:32.7:1:1:0:51:139:1:0:1.4 0/1:69:2:0,2:33,34:67,2:0.029:2,0:9:1:31.5:1:0.49361:0:31.5:4:0.0294:0:3 +6 29895944 . G A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTGGCCTGGCAGCAGGATG;RSEQ=AGAGGACCAGACTCGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:85,58:143,0:0:2,0:23.4:1:32.3:1:1:0:50.8:286:1:0:1.3 0/1:71:11:4,7:34,26:60,11:0.1549:2,2:24.2:1:30.5:1:0.32531:2.26177:39.5:22:0.1571:0:3.3 +6 29895958 . C A 76 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00505;SOR=13.46101;LSEQ=AGGATGGAGAGGACCAGACT;RSEQ=GGGACATGGAGCTTCTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:1:1,0:109,51:160,1:0.0062:2,0:43:0:27:0:1:0:60:2:0.0063:0:3 0/1:77:6:4,2:45,26:71,6:0.0779:2,2:20.7:1:29.5:1:1:1.15:38.7:12:0.0779:0:2.3 +6 29895959 . G A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28079;SOR=0.43282;LSEQ=GGATGGAGAGGACCAGACTC;RSEQ=GGACATGGAGCTTCTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:14:4,10:107,40:147,14:0.087:2,2:18.4:1:31.6:1:0.0014:6.59585:34.5:28:0.0875:0:3.3 0/1:76:3:3,0:47,26:73,3:0.0395:2,0:44.3:1:31.3:1:0.54694:0:26:6:0.0395:0:4 +6 29895973 . C G 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.78948;LSEQ=AGACTCGGGACATGGAGCTT;RSEQ=TAGAGACCAGGCCTGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:49:24,25:95,14:109,49:0.3101:2,2:26.6:1:32.5:1:0:6.95893:42.9:48:0.3097:0:2.7 1/0:76:48:34,14:22,6:28,48:0.6316:2,2:26.5:1:32.1:1:0.59177:1.50184:38.2:96:0.64:0:2.4 +6 29896001 . C A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01766;LSEQ=CAGGCCTGCAGGGGATGGAA;RSEQ=CTTCCAGAAGTGGGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:50:29,21:112,25:137,50:0.2674:2,2:21.4:1:29.9:1:0.00182:3.22059:33.3:49:0.2692:0:2.9 0/1:96:26:21,5:54,15:69,26:0.2708:2,2:21.6:1:29.1:1:1:1.16:36.3:52:0.2766:0:2.8 +6 29896015 . G A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04995;SOR=Inf;LSEQ=ATGGAACCTTCCAGAAGTGG;RSEQ=CAGCTGTGGTGGTGCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:178,79:257,0:0:2,0:20.8:1:31.4:1:1:0:42.2:127.5:1:0:0.9 0/1:152:3:2,1:108,40:148,3:0.0197:2,2:31:1:23:1:1:1.34715:38.3:2:0.0135:0:1.7 +6 29896016 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55889;SOR=3.3658;LSEQ=TGGAACCTTCCAGAAGTGGG;RSEQ=AGCTGTGGTGGTGCCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:1,0:182,83:265,1:0.0038:2,0:38:0:28:0:1:0:26:2:0.0039:0:3 0/1:159:2:1,1:114,43:157,2:0.0126:2,2:20.5:1:27:1:0.47815:2.63234:54:4:0.0129:0:1 +6 29896045 . CAG C 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGGTGCCTTCTGGAGAGGAA;RSEQ=AGATACCCGTGCCATGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:475:0:0,0:269,205:474,0:0:2,0:23.6:1:30.6:1:1:0:49.5:58.25:0.9979:0:1 0/1:294:28:19,9:157,108:265,28:0.0952:2,2:20.1:1:31.2:1:0.42294:1.45:28.6:56:0.0972:0.0374:4.4 +6 29896054 . CC AT 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.02384;SOR=1.40846;LSEQ=CTGGAGAGGAACAGAGATAC;RSEQ=GTGCCATGTGCAGCATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:156:83,73:197,153:350,156:0.3077:2,2:28.8:1:30.9:1:0.56155:1.13217:41.1:312:0.3101:0.0059:2 0/1:322:124:73,51:93,70:163,124:0.3851:2,2:26:1:29.9:1:0.80967:1.08:36.8:248:0.3949:0.0435:2.8 +6 29896055 . C T 59 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0924;SOR=3.27199;LSEQ=TGGAGAGGAACAGAGATACC;RSEQ=GTGCCATGTGCAGCATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:506:3:1,2:196,154:350,3:0.0059:2,2:7:1:30.3:1:0.58567:2.53884:60:6:0.0086:0:1.3 0/1:313:6:2,4:113,84:197,6:0.0192:2,2:22.2:1:23:1:0.4063:2.67747:42.5:2:0.0202:0:3.2 +6 29896084 . A G 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCAGCATGAGGGGTTGCCC;RSEQ=AGCCCCTCACCCTGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:0:0,0:344,339:683,0:0:2,0:27.6:1:30.7:1:1:0:53.9:74.889:1:0:0.7 0/1:450:73:39,34:194,182:376,73:0.1622:2,2:26.3:1:29.6:1:0.79912:1.08:41.2:35.5:0.1606:0:3.4 +6 29896105 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=6e-05;SOR=0.56734;LSEQ=AGCCCCTCACCCTGAGATGG;RSEQ=GTAAGGCAGGAGATGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:221:100,121:181,219:400,221:0.3547:2,2:27.3:1:30.9:1:1:1.00006:51.2:30.571:0.3526:0:1.7 0/1:425:101:49,52:149,174:323,101:0.2376:2,2:25.5:1:28.9:1:0.73204:1.10:49.1:19.2:0.2319:0:2.5 +6 29896108 . A T 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=70.10162;LSEQ=CCCTCACCCTGAGATGGGGT;RSEQ=AGGCAGGAGATGAGTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:1:0,1:272,346:618,1:0.0016:2,0:42:0:14:0:1:0:60:0:0:0:4 0/1:401:41:19,22:162,198:360,41:0.1022:2,2:24.9:1:28:1:0.87021:1.06:46.7:40:0.101:0:3.5 +6 29896112 . C T 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACCCTGAGATGGGGTAAGG;RSEQ=AGGAGATGAGTGGAGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:609:0:0,0:264,344:608,0:0:2,0:25.1:1:32.1:1:1:0:57.4:59.8:1:0:0.6 0/1:388:39:18,21:151,198:349,39:0.1005:2,2:24.7:1:27.5:1:0.73664:1.12:48.6:38:0.1005:0:3.6 +6 29896114 . G A 188 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=152.87404;LSEQ=CCCTGAGATGGGGTAAGGCA;RSEQ=GAGATGAGTGGAGGGGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:605:1:1,0:260,344:604,1:0.0017:2,0:3:0:27:0:0.4314:0:60:2:0.0017:0:1 0/1:385:78:33,45:132,175:307,78:0.2026:2,2:28:1:30:1:1:1.0285:46.2:156:0.2053:0:3.3 +6 29896120 . G T 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=45.75645;LSEQ=GATGGGGTAAGGCAGGAGAT;RSEQ=AGTGGAGGGGGGGTCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:571:3:1,2:236,332:568,3:0.0053:2,2:16:1:26.7:1:1:1.42084:56.3:6:0.0053:0:1.3 0/1:369:72:30,42:124,173:297,72:0.1951:2,2:29.1:1:28.2:1:1:1.00346:48.1:71:0.1951:0:3.3 +6 29896125 . G A 147 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=53.64272;LSEQ=GGTAAGGCAGGAGATGAGTG;RSEQ=AGGGGGGGTCATGTCTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:1,0:226,308:534,1:0.0019:2,0:1:0:27:0:0.4243:0:60:2:0.0019:0:1 0/1:350:32:10,22:137,181:318,32:0.0914:2,2:24.8:1:29.5:1:0.25961:1.66287:54.7:64:0.093:0:2.3 +6 29896126 . A AG 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=6e-04;SOR=Inf;LSEQ=GTAAGGCAGGAGATGAGTGG;RSEQ=GGGGGGGTCATGTCTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:223,304:527,0:0:2,0:23.1:1:30.8:1:1:0:58.9:51.7:1:0:0.6 0/1:349:8:2,6:145,196:341,8:0.0229:2,2:25.1:1:30.9:1:0.47563:2.21478:46.6:16:0.0234:0:2.8 +6 29896128 . G T 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCAGGAGATGAGTGGAG;RSEQ=GGGGGTCATGTCTCTTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:519:0:0,0:220,299:519,0:0:2,0:22.8:1:30.9:1:1:0:59:102.8:1:0:0.6 0/1:340:31:9,22:132,176:308,31:0.0912:2,2:24.6:1:29.4:1:0.18059:1.83023:54.5:62:0.0925:0:2.3 +6 29896145 . A AG 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.09103;SOR=1.31438;LSEQ=GAGGGGGGGTCATGTCTCTT;RSEQ=GGAAAGCAGGAGCCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:151:66,85:104,159:263,151:0.3647:2,2:21.5:1:31.4:1:0.40886:1.19:58.5:74.5:0.3634:0.0894:0.9 0/1:265:114:41,73:61,86:147,114:0.4302:2,2:25.1:1:30.8:1:0.374:1.26177:56.6:228:0.4318:0.0377:1.2 +6 29896147 . G GT 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGGGGTCATGTCTCTTAG;RSEQ=AAAGCAGGAGCCTCTCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:163,235:398,0:0:2,0:22.3:1:31.8:1:1:0:59.4:98.5:1:0:0.4 0/1:255:53:18,35:78,123:201,53:0.2078:2,2:23:1:28.3:1:0.63314:1.23206:57.5:106:0.2103:0.0431:2.4 +6 29896210 . G GCT 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGGGCTGAGGGTCAGGGAC;RSEQ=CTCACCTTCCCCTTTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:187,189:376,0:0:2,0:24.2:1:31:1:1:0:60:187:0.992:0:0.1 0/1:270:18:9,9:127,125:252,18:0.0667:2,2:19.5:1:29.4:1:1:1.01594:59.8:36:0.0674:0.0185:2.1 +6 29896257 . C T 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTCTTCTCAGCCCACCATC;RSEQ=CCATCGTGGGTATCGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:175,229:404,0:0:2,0:26.6:1:31.2:1:1:0:59.4:100:1:0:0.2 0/1:301:21:11,10:127,153:280,21:0.0698:2,2:26.7:1:29.3:1:0.65101:1.32:51.2:42:0.0712:0:2.8 +6 29896268 . T C 211 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=125.94611;LSEQ=CCCACCATCCCCATCGTGGG;RSEQ=ATCGTTGCTGGCCTGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:2:1,1:155,216:371,2:0.0054:2,2:8:1:32:1:1:1.39:52:4:0.0054:0:2 0/1:273:111:51,60:69,93:162,111:0.4066:2,2:28.2:1:31.1:1:0.62049:1.15:42.4:54.5:0.4037:0:2.2 +6 29896272 . G A 140 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=42.84476;LSEQ=CCATCCCCATCGTGGGTATC;RSEQ=TTGCTGGCCTGGTTCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:1,0:150,211:361,1:0.0028:2,0:1:0:26:0:0.41713:0:60:2:0.0028:0:1 0/1:263:28:11,17:100,135:235,28:0.1065:2,2:25.3:1:29.2:1:0.84072:1.14419:36:27:0.1038:0:2 +6 29896275 . G A 165 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=46.9244;LSEQ=TCCCCATCGTGGGTATCGTT;RSEQ=CTGGCCTGGTTCTCCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:346:2:1,1:141,203:344,2:0.0058:2,2:15:1:27:1:1:1.44:52:4:0.0059:0:2 0/1:265:57:25,32:87,119:206,57:0.2151:2,2:27.8:1:28.4:1:0.88011:1.07:42.8:56:0.2162:0:2.1 +6 29896280 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07504;SOR=Inf;LSEQ=ATCGTGGGTATCGTTGCTGG;RSEQ=CTGGTTCTCCTTGGAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:133,196:329,0:0:2,0:25.5:1:31.2:1:1:0:59.3:46:1:0:0.1 0/1:241:3:0,3:99,139:238,3:0.0124:2,0:14.3:1:25:1:0.27085:0:49.7:6:0.0128:0:1.7 +6 29896291 . T C 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTTGCTGGCCTGGTTCTCC;RSEQ=TGGAGCTGTAGTCACTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:105,178:283,0:0:2,0:25:1:30.5:1:1:0:59.5:39.429:1:0:0.1 0/1:231:20:10,10:84,126:210,20:0.0866:2,2:25.4:1:30.2:1:0.47648:1.50:50.9:40:0.0885:0:2.7 +6 29896336 . GGAA G 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.80618;SOR=1.13525;LSEQ=GGTTTCTGCTGTGATGTGCA;RSEQ=GAAGAACTCAGGTAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:9:2,7:39,99:138,9:0.0612:2,2:32.7:1:32.2:1:1:1.37602:60:18:0.0621:0:0 0/1:116:8:2,6:33,75:108,8:0.069:2,2:31.9:1:31.4:1:1:1.31704:60:16:0.0702:0:0 +6 29896457 . C A 25 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09059;SOR=Inf;LSEQ=ACTGGGAAGCACCATCCACA;RSEQ=TCATGGGCCTACCCAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:3,26:29,0:0:2,0:24.2:1:34.2:1:1:0:38.6:58:1:0:0.1 0/1:13:2:0,2:2,9:11,2:0.1538:2,0:22:0:25:0:1:0:22:4:0.1667:0:2 +6 29896467 . T G 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09244;SOR=Inf;LSEQ=ACCATCCACACTCATGGGCC;RSEQ=ACCCAGCCTGGGCCCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:2,22:24,0:0:2,0:20.2:1:28.9:1:1:0:34.1:23:1:0:0 0/1:11:2:0,2:2,7:9,2:0.1818:2,0:32:0:27:0:1:0:22:4:0.2:0:2 +6 29896636 . C T 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22857;SOR=0;LSEQ=ACCTCAGGAGGGCAGTTGGT;RSEQ=CAGGACCCACACCTGCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:5,1:6,6:0.5:2,0:22.2:1:32:1:1:0:56.8:12:0.5:0:1.3 0/0:3:0:0,0:1,2:3,0:0:2,0:14:1:25:1:1:0:60:2:1:0:0 +6 29896713 . G A 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12837;SOR=0.23307;LSEQ=CACTTTCAGGAAACTTCTCT;RSEQ=GGATCAAAGGCTAGGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:10,0:9,1:10,10:0.5:2,0:19.1:1:28.7:1:1:0:58.9:20:0.5:0:1.9 0/1:11:2:2,0:8,1:9,2:0.1818:2,0:32.5:1:29.5:1:1:0:60:4:0.2:0:1.5 +6 29896773 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=0.16834;LSEQ=CTGACTCCTTTCTGGCCTCT;RSEQ=ATAGGACATTTTCTTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:29:23,6:26,6:32,29:0.4754:2,2:24.2:1:30.4:1:1:1.12816:60:58:0.4754:0:1.7 0/1:46:6:5,1:32,8:40,6:0.1304:2,2:24.2:1:30.5:1:1:1.24:60:12:0.1364:0:1.5 +6 29896847 . T TGA 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=32.06031;LSEQ=GTATGAAGTGGGCTGATCCC;RSEQ=GATCCTTGGGATATTGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:9:5,4:46,33:79,9:0.0657:2,2:21.2:1:29.7:1:1:1.11376:53.3:18:0.0662:0.0365:1.9 1/0:122:85:47,38:0,6:6,85:0.6967:0,2:23.5:1:29.7:1:0.01059:0:51.4:170:0.9551:0.3934:0.9 +6 29896850 . TCC GATCT 181 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=TGAAGTGGGCTGATCCCTGA;RSEQ=TTGGGATATTGTGGTCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:49:30,19:46,33:79,49:0.3577:2,2:30.7:1:32.3:1:0.85339:1.13:57:98:0.3603:0.0073:1.3 0/0:122:0:0,0:0,6:6,0:0:0,0:36:1:27.5:1:1:0:99.8:8:0.0449:0:-9.5 +6 29896852 . C T 97 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00125;SOR=0;LSEQ=AAGTGGGCTGATCCCTGATC;RSEQ=TTGGGATATTGTGGTCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:11:7,4:44,31:75,11:0.0821:2,2:18.3:1:28.2:1:1:1.23:54.5:4.5:0.1084:0:1.9 0/0:110:0:0,0:38,39:77,0:0:2,0:26.1:1:30.3:1:1:0:53:37.5:1:0:0.4 +6 29896872 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22357;SOR=Inf;LSEQ=CTTGGGATATTGTGGTCGGG;RSEQ=GCCCATGGGGGAGCTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:76,55:131,0:0:2,0:24.3:1:30.1:1:1:0:58.7:25.2:1:0:0.9 0/1:118:2:1,1:62,54:116,2:0.0169:2,2:40:0:32:1:1:1.1468:40:4:0.0172:0:1.5 +6 29896883 . G A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00745;SOR=Inf;LSEQ=GTGGTCGGGAGCCCATGGGG;RSEQ=AGCTCACCCAACCCCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:81,56:137,0:0:2,0:22.2:1:31:1:1:0:58.7:33.25:1:0:1 0/1:111:6:4,2:55,48:103,6:0.0541:2,2:26:1:27.8:1:0.68535:1.74:60:12:0.0561:0:1.3 +6 29896914 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20567;SOR=Inf;LSEQ=ACCCCAGATTCCTCCTCTAG;RSEQ=CGCATCTCCTCTGGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:84,60:144,0:0:2,0:26:1:31.7:1:1:0:60:47:1:0:1.3 0/1:120:2:1,1:72,46:118,2:0.0167:2,2:35.5:1:27.5:1:1:1.55914:60:4:0.0171:0:2 +6 29896922 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0128;SOR=0.38152;LSEQ=TTCCTCCTCTAGCCGCATCT;RSEQ=CTCTGGGCTCTGACCAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:27:16,11:66,50:116,27:0.1888:2,2:35.6:1:31.7:1:1:1.10:60:54:0.1929:0:3 0/1:123:10:7,3:65,48:113,10:0.0813:2,2:21.9:1:29.2:1:0.52065:1.72:60:20:0.0826:0:2.7 +6 29896925 . C G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.39755;SOR=1.24756;LSEQ=CTCCTCTAGCCGCATCTCCT;RSEQ=TGGGCTCTGACCAAGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:75:49,26:35,39:74,75:0.4967:2,2:29.9:1:32.4:1:0.03213:2.09:59.8:74:0.4933:0:2.4 1/0:125:69:44,25:31,25:56,69:0.552:2,2:26.2:1:31.1:1:0.36374:1.42:59.9:138:0.552:0:2.1 +6 29896959 . C A 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.59635;SOR=2.35819;LSEQ=AGTCCTGTTTTTGTTCTACC;RSEQ=CAGGCAGCGACCATGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:1,0:101,93:194,1:0.0051:2,0:47:0:30:0:1:0:60:2:0.0053:0:3 0/1:167:2:1,1:86,79:165,2:0.012:2,2:48:0:30.5:1:1:1.08804:60:4:0.0124:0:3 +6 29896967 . C T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02374;SOR=0.59924;LSEQ=TTTTGTTCTACCCCAGGCAG;RSEQ=GACCATGCGCAGGGTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:81:42,39:67,60:127,81:0.3894:2,2:23.1:1:29.3:1:1:1.03674:59.2:80:0.3902:0:2.2 0/1:181:50:27,23:65,65:130,50:0.2762:2,2:22.9:1:29.7:1:0.73947:1.17:57.9:100:0.2809:0:3 +6 29896968 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.21006;LSEQ=TTTGTTCTACCCCAGGCAGC;RSEQ=ACCATGCGCAGGGTTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:41:23,18:83,81:164,41:0.2:2,2:22.3:1:28.9:1:0.60153:1.25:59:12.667:0.19:0:2.9 0/1:181:9:4,5:89,83:172,9:0.0497:2,2:34.4:1:29.9:1:0.74184:1.33819:59.4:18:0.0503:0:2.7 +6 29896977 . C T 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=CCCCAGGCAGCGACCATGCG;RSEQ=AGGGTTCTGATGTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:105,107:212,0:0:2,0:23.5:1:31.5:1:1:0:59.1:29.286:1:0:1.5 0/1:189:9:4,5:91,89:180,9:0.0476:2,2:26.1:1:28.7:1:0.74718:1.27643:58.2:18:0.0497:0:4.7 +6 29896980 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2282;SOR=Inf;LSEQ=CAGGCAGCGACCATGCGCAG;RSEQ=GTTCTGATGTGTCTCTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:98,107:205,0:0:2,0:24.5:1:30.5:1:1:0:59:28.286:1:0:1.5 0/1:188:2:1,1:94,92:186,2:0.0106:2,2:34.5:1:28:1:1:1.02163:60:4:0.0109:0:2 +6 29896991 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23904;SOR=Inf;LSEQ=CATGCGCAGGGTTCTGATGT;RSEQ=TCTCTCACGGCTTGTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:92,104:196,0:0:2,0:26.8:1:31.1:1:1:0:58.9:18.6:1:0:1.6 0/1:188:2:0,2:98,87:185,2:0.0106:2,0:15.5:1:29:1:0.22517:0:48:4:0.011:0:2 +6 29896999 . C T 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTTCTGATGTGTCTCTCA;RSEQ=GGCTTGTAAAGGTGAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:95,103:198,0:0:2,0:26.9:1:29.9:1:1:0:59:27.286:1:0:1.6 0/1:191:25:10,15:83,82:165,25:0.1309:2,2:26.4:1:29.2:1:0.39405:1.51497:58.3:50:0.1374:0:4.4 +6 29897017 . CA AG 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACGGCTTGTAAAGGTGAGA;RSEQ=CTGGGGGACCTGATGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:85,105:190,0:0:2,0:27.1:1:30:1:1:0:58.9:14.833:1:0:1.7 0/1:168:43:19,24:59,62:121,43:0.256:2,2:28.1:1:30.9:1:0.72254:1.20069:56.7:86:0.2792:0.006:2.7 +6 29897018 . A G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.44392;SOR=0.83237;LSEQ=ACGGCTTGTAAAGGTGAGAC;RSEQ=CTGGGGGACCTGATGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:187:119:48,71:35,33:68,119:0.6364:2,2:27.3:1:30.1:1:0.16894:1.56494:58.3:13.875:0.6236:0:2.5 1/0:167:99:45,54:12,13:25,99:0.5928:2,2:28.7:1:30:1:0.82645:1.10678:57.4:98:0.8167:0:2 +6 29897030 . G A 93 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGTGAGACACTGGGGGACCT;RSEQ=ATGTGGGGGGGTGTTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:77,102:179,0:0:2,0:25.6:1:31.1:1:1:0:58.9:13.917:1:0:1.7 0/1:151:15:7,8:59,77:136,15:0.0993:2,2:26.1:1:24:1:1:1.14:58.4:2:0.0725:0:2.7 +6 29897035 . G GT 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00292;SOR=2.04097;LSEQ=GACACTGGGGGACCTGATGT;RSEQ=GGGGGGTGTTGGGGGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:176:96:31,65:41,38:79,96:0.5455:2,2:26.9:1:28.7:1:0.01326:2.25144:58.6:8.6:0.5276:0.0284:2.5 1/0:152:108:39,69:21,20:41,108:0.7105:2,2:23.3:1:27.8:1:0.13401:1.84976:57.1:12.5:0.7143:0.1118:2.5 +6 29897036 . G T 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00057;SOR=0;LSEQ=ACACTGGGGGACCTGATGTG;RSEQ=GGGGGTGTTGGGGGCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:12:6,6:65,95:160,12:0.069:2,2:10.1:1:29.7:1:0.55532:1.46:57.8:24:0.0719:0:2.6 0/0:149:0:0,0:54,80:134,0:0:2,0:23.5:1:29.4:1:1:0:57.8:15.75:0.9921:0:2.1 +6 29897050 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51111;SOR=0;LSEQ=GATGTGGGGGGGTGTTGGGG;RSEQ=CAATAGTGGACGCAGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:67,89:156,2:0.0126:2,2:8:1:29:1:1:1.33:55:4:0.0131:0:2.5 0/0:115:0:0,0:47,68:115,0:0:2,0:30:0:15:0:1:0:60:0:0:0:7 +6 29897051 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18232;SOR=Inf;LSEQ=ATGTGGGGGGGTGTTGGGGG;RSEQ=AATAGTGGACGCAGCTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:65,90:155,0:0:2,0:22.8:1:31.6:1:1:0:59.2:16.222:1:0:1.6 0/1:116:2:0,2:48,66:114,2:0.0172:2,0:7:1:26:1:0.51064:0:60:4:0.0182:0:2 +6 29897061 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.03234;LSEQ=GTGTTGGGGGCAATAGTGGA;RSEQ=GCAGCTGTGCTATGGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:143:77:29,48:37,28:65,77:0.5385:2,2:23.7:1:30.1:1:0.02819:2.17485:57.9:37.5:0.5357:0:2.7 1/0:97:53:17,36:22,20:42,53:0.5464:2,2:21.1:1:29.4:1:0.05946:2.30803:58.2:25.5:0.5484:0:3.1 +6 29897102 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01095;SOR=2.09996;LSEQ=CTTTGAATTGGATGTATTGA;RSEQ=CATGTGATGGGCTGTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:57:31,26:50,18:68,57:0.456:2,2:24.4:1:30.3:1:0.0381:2.31352:51.7:56:0.4516:0:2.5 1/0:83:53:28,25:21,9:30,53:0.6386:2,2:24.5:1:30.1:1:0.16503:2.0651:51:52:0.642:0:2.5 +6 29897112 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52248;SOR=0;LSEQ=GATGTATTGAGCATGTGATG;RSEQ=GCTGTTTAAAGTGTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:2,0:91,39:130,2:0.0152:2,0:47.5:1:30:0:1:0:48.5:4:0.0155:0:2.5 0/0:84:0:0,0:56,28:84,0:0:2,0:24.8:1:30.3:1:1:0:50.5:20:1:0:1.4 +6 29897129 . C T 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00019;SOR=2.58536;LSEQ=ATGGGCTGTTTAAAGTGTCA;RSEQ=CCCTCACTGTGACGGATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:55:33,22:84,27:111,55:0.3313:2,2:23.4:1:31.1:1:0.04689:2.06444:48.7:110:0.3354:0:1.9 1/0:112:63:42,21:33,16:49,63:0.5625:2,2:21.8:1:28.9:1:1:1.03098:46.5:20:0.5505:0:1.9 +6 29897138 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08166;SOR=Inf;LSEQ=TTAAAGTGTCACCCCTCACT;RSEQ=TGACGGATATGAATTTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:127,57:184,0:0:2,0:21.8:1:31.9:1:1:0:45.7:35.8:1:0:0.6 0/1:142:3:1,2:92,47:139,3:0.0211:2,2:19.7:1:28.3:1:0.27354:3.87461:37.3:6:0.0213:0:1 +6 29897196 . G C 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02475;SOR=0.41958;LSEQ=TAGTGTGAGACAGCTGCCTT;RSEQ=TGTGGGACTGAGAGGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:413:27:13,14:220,166:386,27:0.0654:2,2:26.3:1:32.7:1:0.42429:1.42598:47.5:54:0.0668:0:1.1 0/1:316:9:6,3:169,138:307,9:0.0285:2,2:33:1:31.7:1:0.73606:1.63:43.1:18:0.0288:0:1.1 +6 29897227 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08321;SOR=Inf;LSEQ=AGAGGCAAGATTTGTTCACG;RSEQ=CTTCCCTTTGTGACTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:0:0,0:173,209:382,0:0:2,0:29.7:1:31.3:1:1:0:44.9:75.4:1:0:0.1 0/1:297:3:2,1:135,158:293,3:0.0101:2,2:19.3:1:24:1:0.59781:2.33:45.3:2:0.0068:0:1.7 +6 29897259 . T A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GACTTCAAAAACCCTGACTC;RSEQ=CTTTCTGCAAAGGCACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:93,183:276,0:0:2,0:24:1:30.3:1:1:0:53.4:38.429:1:0:0.1 0/1:192:33:10,23:60,99:159,33:0.1719:2,2:25.5:1:29:1:0.5515:1.3916:48.2:32:0.1684:0:1.1 +6 29897301 . C T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00106;SOR=Inf;LSEQ=TGTGCCTGTGTTCCTGTAGG;RSEQ=ATAATATGAGGAGGTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:1,93:94,0:0:1,0:26:1:33.2:1:1:0:59.1:188:1:0:0.1 0/1:73:8:0,8:2,63:65,8:0.1096:1,0:18.1:1:29:1:1:0:60:16:0.1096:0:1.5 +6 29897322 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04413;SOR=Inf;LSEQ=ATAATATGAGGAGGTGGGGA;RSEQ=ACCAACCCACCCCCATGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:1,73:74,0:0:1,0:23.6:1:32.4:1:1:0:58.9:36:1:0:0.1 0/1:42:3:0,3:1,38:39,3:0.0714:1,0:19:1:28.7:1:1:0:60:6:0.075:0:2 +6 29897350 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01033;SOR=Inf;LSEQ=CACCCCCATGTCCACCATGA;RSEQ=CCTCTTCCCTCATGCTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:1,47:48,0:0:1,0:24.6:1:31.2:1:1:0:59.1:23:1:0:0.3 0/1:24:4:0,4:0,20:20,4:0.1667:1,0:15.3:1:28.5:1:1:0:60:8:0.1739:0:2 +6 29897379 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06388;SOR=Inf;LSEQ=CTCATGCTGACCTGTGTTCC;RSEQ=TCTCCAATAATTAATCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:1,30:31,0:0:1,0:27.5:1:32.8:1:1:0:60:62:1:0:0.4 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:38.5:1:33.5:1:1:0:60:4:0.1818:0:2 +6 29897412 . G C 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.47778;LSEQ=AATCATTCCTGCTCCATAGA;RSEQ=GTGAGGCTGAGATGTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:0,11:1,10:11,11:0.5:2,0:21.3:1:30.5:1:1:0:60:22:0.5:0:1.2 1/0:5:3:0,3:0,2:2,3:0.6:0,0:18.3:1:30.3:1:1:0:60:6:0.6:0:1 +6 29901783 . A T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00438;SOR=Inf;LSEQ=GCTTACAGAGGCCAGGGAAT;RSEQ=AACCTGGACAAATTATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:33,0:0:1,0:25.2:1:28.1:1:1:0:58.6:66:1:0:0.5 0/1:13:4:4,0:9,0:9,4:0.3077:0,0:30.3:1:30.8:1:1:0:58.5:8:0.3077:0:1 +6 29901806 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02056;LSEQ=CCTGGACAAATTATGCCCCA;RSEQ=GGTGGAATCACTGGGTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:12,0:35,0:35,12:0.2553:1,0:24.2:1:31.3:1:1:0:56.1:24:0.2609:0:1.7 0/1:27:7:7,0:20,0:20,7:0.2593:1,0:19.3:1:31.1:1:1:0:56.6:14:0.2692:0:1.9 +6 29901865 . G C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31003;SOR=1.30649;LSEQ=CTCCCCATTCTCTGTAAAAA;RSEQ=GATTCTCTGTAAAAAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:62:62,0:97,7:104,62:0.3735:2,1:23.3:1:33:1:0.0464:0:58.2:124:0.3758:0:2.6 0/1:105:46:45,1:52,7:59,46:0.4381:2,1:22.6:1:31.7:1:0.0765:5.98:58.5:92:0.4466:0:2.8 +6 29901898 . CC GG 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAGATTACATCGCCCTAAA;RSEQ=AGGACCTGAGCTCTTGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:326:0:0,0:253,73:326,0:0:2,0:23.1:1:31.6:1:1:0:53.7:64.2:1:0:1.1 0/1:207:49:40,9:124,34:158,49:0.2367:2,2:25.5:1:31.1:1:0.69218:1.22:45.6:98:0.2402:0:2.1 +6 29901899 . C G 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00113;SOR=1.78209;LSEQ=AAGATTACATCGCCCTAAAC;RSEQ=AGGACCTGAGCTCTTGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:131:103,28:158,47:205,131:0.3899:2,2:21.9:1:30.2:1:0.7891:1.09:44.1:130:0.3904:0:2.7 1/0:214:114:88,26:40,11:51,114:0.5327:2,2:23.6:1:29.1:1:1:1.07393:44.6:56:0.6914:0:2.8 +6 29901917 . A G 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCAGGACCTGAGCTCTTGG;RSEQ=CTGCGGCGGCCATGGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:424:0:0,0:287,137:424,0:0:2,0:24.8:1:29.4:1:1:0:51.4:37.545:1:0:1.1 0/1:311:23:16,7:199,89:288,23:0.074:2,2:26.6:1:30:1:1:1.02:42.9:22:0.0721:0:3.7 +6 29901919 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=4.68372;LSEQ=CAGGACCTGAGCTCTTGGAC;RSEQ=GCGGCGGCCATGGCGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:176:118,58:169,86:255,176:0.4084:2,2:25.4:1:30.2:1:0.91738:1.04:39.3:57.667:0.41:0:2.6 1/0:318:243:168,75:51,23:74,243:0.7642:2,2:24.5:1:29.8:1:1:1.01:39:80:0.7668:0:2.6 +6 29901921 . C T 128 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=29.55343;LSEQ=GGACCTGAGCTCTTGGACTG;RSEQ=GGCGGCCATGGCGGCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:1:0,1:290,156:446,1:0.0022:2,0:1:0:29:0:0.35123:0:28:2:0.0023:0:3 0/1:337:21:12,9:216,100:316,21:0.0623:2,2:20.3:1:29.3:1:0.33634:1.61756:40.1:42:0.0638:0:3 +6 29901987 . C G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=3.28543;LSEQ=CCATGAGGCGGAGCAGCAGA;RSEQ=AGCCTACCTGGAGGGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:565:195:96,99:152,217:369,195:0.3451:2,2:27.4:1:33:1:0.07461:1.38:31.4:96.5:0.3471:0:2.5 1/0:421:267:142,125:70,83:153,267:0.6342:2,2:27:1:30.9:1:0.15624:1.35:28.3:65.75:0.6368:0:2.4 +6 29901997 . G A 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00087;SOR=Inf;LSEQ=GAGCAGCAGACAGCCTACCT;RSEQ=GAGGGCAGGTGCGTGGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:510:0:0,0:209,301:510,0:0:2,0:25.9:1:31.4:1:1:0:50.7:84:1:0:0.8 0/1:364:8:4,4:170,186:356,8:0.022:2,2:29.3:1:27.8:1:1:1.09:26.9:16:0.0222:0:4 +6 29902005 . G C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.73239;LSEQ=GACAGCCTACCTGGAGGGCA;RSEQ=GTGCGTGGAGTGGCTCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:33:12,21:163,265:428,33:0.0716:2,2:15.7:1:31:1:1:1.07626:23.9:66:0.0725:0:2.5 0/1:310:116:63,53:81,113:194,116:0.3742:2,2:18.3:1:30.1:1:0.03471:1.66:23.5:115:0.377:0:2.5 +6 29902011 . T A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00173;SOR=Inf;LSEQ=CTACCTGGAGGGCAGGTGCG;RSEQ=GGAGTGGCTCCGCAGATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:158,261:419,0:0:2,0:22.6:1:30.1:1:1:0:52.4:58.857:1:0:0.7 0/1:286:7:4,3:127,152:279,7:0.0245:2,2:18.3:1:27:1:0.70635:1.59:26:14:0.0246:0:4.1 +6 29902016 . T A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.34616;LSEQ=TGGAGGGCAGGTGCGTGGAG;RSEQ=GGCTCCGCAGATACCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:76:34,42:104,205:309,76:0.1969:2,2:17.7:1:31:1:0.08272:1.59:35.4:37:0.1953:0:2.3 0/1:256:20:11,9:106,130:236,20:0.0781:2,2:12.6:1:29.1:1:0.48457:1.50:35.7:40:0.0791:0:2.3 +6 29902040 . A G 116 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07176;SOR=0.17187;LSEQ=TCCGCAGATACCTGGAGAAC;RSEQ=GGAAGGAGACACTGCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:13:5,8:44,134:178,13:0.0681:2,2:14:1:31.5:1:0.32398:1.90:21.6:26:0.0688:0:3.1 0/1:81:1:0,1:21,59:80,1:0.0123:2,0:2:0:30:0:1:0:24:2:0.0127:0:2 +6 29902051 . A G 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGGAGAACAGGAAGGAGAC;RSEQ=CTGCAGCACACCTGTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:27,108:135,0:0:2,0:22.9:1:30.1:1:1:0:57:44:1:0:0.3 0/1:59:28:7,21:5,26:31,28:0.4746:2,2:28.7:1:30.8:1:0.52137:1.72:50.4:27:0.4737:0:1.5 +6 29902135 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09619;SOR=Inf;LSEQ=GCCTCCCACAAGGATGGGAG;RSEQ=CAGATGGGACCAACACTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:30,0:0:1,0:25.2:1:30.3:1:1:0:59.9:60:1:0:0.1 0/1:14:2:1,1:1,11:12,2:0.1429:2,2:33:1:31.5:1:0.27473:8.12:46:4:0.1429:0:1 +6 29902168 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0154;SOR=Inf;LSEQ=ACACTAGAATATCACCCTCC;RSEQ=TCTGGTCCTGAGGGAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:0,24:24,0:0:1,0:24.7:1:33.8:1:1:0:58.2:48:1:0:0.2 0/1:9:3:0,3:1,5:6,3:0.3333:2,0:10.3:1:31.3:1:1:0:60:6:0.3333:0:1 +6 29902197 . CA GG 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGGAGAAGAATCCTCCT;RSEQ=GTTTCCAGATCCTGTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:14,2:0.125:1,0:26:1:27.5:1:1:0:23.5:4:0.1333:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:43:0:31:0:1:0:60:2:1:0:0 +6 29902294 . G T 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TGAGGCAATGACGGGAAGAC;RSEQ=CAATTAAGGGATAAAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:19.5:1:32:0:1:0:57:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:17:0:34:0:1:0:60:2:1:0:0 +6 29909745 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCTCATGCACTCAGGC;RSEQ=CAACTTTTCCGGATTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:27:1:30:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29909756 . G C 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTCAGGCACAACTTTTCC;RSEQ=GATTAAAAACAAAAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:27:0:30.5:1:1:0:60:4:0.5:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29910057 . C A 69 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.57203;LSEQ=CAGAGGGGTCAGGGCGAAGT;RSEQ=CCAGGGCCCCAGGCGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:13,1:14,5:0.2632:1,0:13.2:1:30:0:1:0:30.8:10:0.2632:0:2 0/1:6:1:1,0:4,1:5,1:0.1667:2,0:12:0:29:0:1:0:34:2:0.1667:0:2 +6 29910083 . A G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.35223;LSEQ=GCCCCAGGCGTGGCTCTCAG;RSEQ=GTCTCAGGCCCCGAAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:9,2:20,0:20,11:0.3548:1,2:28.3:1:31.2:1:0.11828:0:39.5:10:0.3448:0:2 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:37.7:1:32:1:1:0:32:6:0.4286:0:1.3 +6 29910167 . C G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69487;SOR=1.18549;LSEQ=GCAGTTTCTTTTCTCCCTCT;RSEQ=CCAACCTACGTAGGGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:21:21,0:162,2:164,21:0.1135:1,1:22.4:1:33.4:1:1:0:57.3:42:0.1148:0:3 0/1:91:12:12,0:78,1:79,12:0.1319:1,0:24.6:1:32.3:1:1:0:56.3:24:0.1319:0:3 +6 29910176 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99669;LSEQ=TTTCTCCCTCTCCCAACCTA;RSEQ=GTAGGGTCCTTCATCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:89:88,1:131,2:133,89:0.3991:1,1:20.7:1:31.2:1:1:1.34:57.9:28.667:0.3963:0:2.2 0/1:118:47:46,1:70,1:71,47:0.3983:1,1:21.7:1:30.7:1:1:1.51614:58.5:94:0.4017:0:2.4 +6 29910189 . A T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00966;LSEQ=CAACCTACGTAGGGTCCTTC;RSEQ=TCCTGGATACTCACGACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:126:123,3:161,2:163,126:0.436:1,1:21.2:1:32.9:1:0.6561:1.95877:54:125:0.4417:0:2.8 0/1:146:64:60,4:81,1:82,64:0.4384:1,2:22.4:1:30.7:1:0.16867:5.34332:56.5:31:0.4336:0:2.5 +6 29910194 . G A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13965;SOR=0.38696;LSEQ=TACGTAGGGTCCTTCATCCT;RSEQ=GATACTCACGACGCGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:16:15,1:299,8:307,16:0.0495:1,1:11.6:1:29.8:1:0.37071:2.48125:24.8:32:0.0502:0:6.4 0/1:152:3:3,0:145,4:149,3:0.0197:1,0:12:0:28:1:1:0:26:6:0.0199:0:6 +6 29910195 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10169;SOR=Inf;LSEQ=ACGTAGGGTCCTTCATCCTG;RSEQ=ATACTCACGACGCGGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:321,9:330,0:0:1,0:23.4:1:31.8:1:1:0:57.8:46.143:1:0:1.2 0/1:155:2:2,0:149,4:153,2:0.0129:1,0:39:1:29:1:1:0:60:4:0.0133:0:2 +6 29910245 . C T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03369;SOR=0.34825;LSEQ=CCCATTGGGTGTCGGGTTTC;RSEQ=AGAGAAGCCAATCAGTGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:618:18:16,2:470,130:600,18:0.0291:2,2:26.2:1:29.8:1:0.38851:2.21:28.7:36:0.0294:0:5.8 0/1:484:5:4,1:356,123:479,5:0.0103:2,2:19.8:1:28.6:1:1:1.38:39.6:10:0.0104:0:4.2 +6 29910265 . G T 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAGAAGCCAATCAGTGTC;RSEQ=TCGCGGTCGCTGTTCTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:867:0:0,0:587,267:854,0:0:2,0:22.1:1:29.9:1:1:0:53.4:46.444:0.9847:0:0.9 0/1:689:61:39,22:399,226:625,61:0.0885:2,2:23.9:1:30:1:1:1.00:50.8:122:0.0896:0:3.5 +6 29910276 . T G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39035;SOR=1.08655;LSEQ=ATCAGTGTCGTCGCGGTCGC;RSEQ=GTTCTAAAGCCCGCACGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1062:399:250,149:420,242:662,399:0.3757:2,2:23.2:1:30.2:1:0.84379:1.03437:39.6:98.75:0.3791:0:2.2 0/1:822:325:199,126:287,210:497,325:0.3954:2,2:26.6:1:29.2:1:0.34572:1.16:39.6:161.5:0.3953:0:2.3 +6 29910277 . G C 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAGTGTCGTCGCGGTCGCT;RSEQ=TTCTAAAGCCCGCACGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1079:0:0,0:675,398:1073,0:0:2,0:22.5:1:31.8:1:1:0:51.5:81.538:0.9944:0:0.9 0/1:832:66:38,28:454,311:765,66:0.0793:2,2:26.8:1:30.6:1:0.79506:1.07555:48.1:65:0.0787:0:3.6 +6 29910286 . C T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.4182;LSEQ=TCGCGGTCGCTGTTCTAAAG;RSEQ=CCGCACGCACCCACCGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1203:451:263,188:452,300:752,451:0.3749:2,2:24.2:1:29.7:1:0.54477:1.07694:37.6:55.375:0.3748:0:2.1 1/0:952:640:371,269:179,133:312,640:0.6723:2,2:26:1:28.5:1:0.88889:1.02:42:70.111:0.6713:0:2.1 +6 29910302 . G C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0256;SOR=0.60421;LSEQ=AAAGCCCGCACGCACCCACC;RSEQ=GGACTCAGATTCTCCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1507:62:29,33:790,649:1439,62:0.0411:2,2:8.4:1:30.1:1:0.24121:1.38484:28.4:124:0.0419:0:3.7 0/1:1227:31:19,12:638,554:1192,31:0.0253:2,2:8.5:1:30.2:1:0.4671:1.37:28.7:62:0.0256:0:3.7 +6 29910324 . G C 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTCAGATTCTCCCCAGAC;RSEQ=CCGAGGATGGCCGTCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1964:0:0,0:996,961:1957,0:0:2,0:25.8:1:31:1:1:0:50.3:66.483:0.9974:0:0.9 0/1:1500:100:48,52:695,700:1395,100:0.0667:2,2:26.1:1:30.1:1:0.75675:1.07551:47.6:49:0.066:0:2.5 +6 29910336 . C G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.5428;LSEQ=CCCCAGACGCCGAGGATGGC;RSEQ=GTCATGGCGCCCCGAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2121:198:97,101:961,953:1914,198:0.0934:2,2:27.4:1:30.7:1:0.76556:1.04997:42.8:197:0.094:0:2.7 0/1:1625:86:42,44:749,786:1535,86:0.0529:2,2:27:1:30.2:1:1:1.00:42.3:172:0.0536:0:2.8 +6 29910340 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.54485;LSEQ=AGACGCCGAGGATGGCCGTC;RSEQ=TGGCGCCCCGAACCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2154:212:100,112:965,976:1941,212:0.0984:2,2:28.8:1:31.3:1:0.51518:1.10732:43.9:105:0.0994:0:2.6 0/1:1639:92:46,46:749,797:1546,92:0.0561:2,2:28.8:1:30.6:1:0.83019:1.06:42.7:91:0.0562:0:2.7 +6 29910358 . C G 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=207.64025;LSEQ=TCATGGCGCCCCGAACCCTC;RSEQ=TCCTGCTACTCTCGGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2161:4:2,2:1025,1130:2155,4:0.0019:2,2:26.5:1:30.3:1:1:1.10:42:8:0.0019:0:2.3 0/1:1592:443:209,234:557,589:1146,443:0.2783:2,2:25.5:1:30.3:1:0.61486:1.05878:44.5:72.833:0.2778:0:2.3 +6 29910371 . C T 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.27497;LSEQ=AACCCTCCTCCTGCTACTCT;RSEQ=GGGGGCCCTGGCCCTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2035:583:263,320:665,784:1449,583:0.2865:2,2:25.4:1:30.5:1:0.7678:1.03204:50.2:52:0.2867:0:1.9 0/1:1489:148:71,77:634,703:1337,148:0.0994:2,2:26.8:1:29.6:1:0.93097:1.02:49.4:73:0.0988:0:1.8 +6 29910378 . C T 227 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=98.64005;LSEQ=CTCCTGCTACTCTCGGGGGC;RSEQ=CTGGCCCTGACCCAGACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1945:4:2,2:871,1067:1938,4:0.0021:2,2:34.5:1:27.8:1:1:1.22:53.8:3:0.0016:0:2.5 0/1:1395:236:108,128:558,600:1158,236:0.1692:2,2:25.6:1:28.9:1:0.5203:1.10214:48.5:46.2:0.1694:0:2.9 +6 29910402 . G A 155 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=55.54377;LSEQ=GCCCTGACCCAGACCTGGGC;RSEQ=GGTGAGTGCGGGGTCGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1609:1:1,0:696,912:1608,1:6e-04:2,0:1:0:27:0:0.43319:0:49:2:6e-04:0:1 0/1:1136:38:16,22:512,585:1097,38:0.0335:2,2:22.2:1:29.7:1:0.62263:1.20322:37:76:0.0337:0:3.1 +6 29910419 . GGA TG 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.20057;LSEQ=GGCGGGTGAGTGCGGGGTCG;RSEQ=GGGAAACCGCCTCTGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1304:379:159,220:391,527:918,379:0.2906:2,2:24.1:1:30.5:1:0.85311:1.02656:53.9:53.143:0.2906:0.0613:3.4 0/1:896:68:33,35:369,437:806,68:0.0759:2,2:23.9:1:29.7:1:0.70469:1.12:51:67:0.0762:0.0056:3.8 +6 29910420 . GA G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01131;SOR=0.46115;LSEQ=GCGGGTGAGTGCGGGGTCGG;RSEQ=GGGAAACCGCCTCTGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:950:38:22,16:388,520:908,38:0.04:2,2:8:1:29.1:1:0.0682:1.84:57.1:37:0.04:0.0347:2.3 0/1:796:15:4,11:353,425:778,15:0.0188:2,2:11.4:1:28.9:1:0.19302:2.28187:55.7:30:0.0194:0.0138:2.9 +6 29910429 . C G 217 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=316.83475;LSEQ=TGCGGGGTCGGGAGGGAAAC;RSEQ=GCCTCTGCGGGGAGAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1153:1:0,1:486,666:1152,1:9e-04:2,0:41:0:14:0:1:0:57:0:0:0:8 0/1:755:163:68,95:269,320:589,163:0.2159:2,2:24.4:1:29.6:1:0.37529:1.17415:37.2:80.5:0.2176:0:4.6 +6 29910437 . C T 192 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=202.37836;LSEQ=CGGGAGGGAAACCGCCTCTG;RSEQ=GGGGAGAAGCAAGGGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1041:1:0,1:439,601:1040,1:0.001:2,0:1:0:26:0:1:0:60:2:0.001:0:1 0/1:668:109:46,63:265,291:556,109:0.1632:2,2:26.2:1:28.5:1:0.34484:1.24678:35.4:26.25:0.1608:0:5.1 +6 29910439 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00351;SOR=0.61329;LSEQ=GGAGGGAAACCGCCTCTGCG;RSEQ=GGAGAAGCAAGGGGCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1016:136:50,86:384,496:880,136:0.1339:2,2:18.7:1:31.5:1:0.13716:1.33124:49.1:33:0.1321:0:3.2 0/1:647:56:24,32:278,313:591,56:0.0866:2,2:13.8:1:29.6:1:0.57767:1.18393:48.6:112:0.0882:0:2.3 +6 29910444 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=9e-04;SOR=0.43041;LSEQ=GAAACCGCCTCTGCGGGGAG;RSEQ=AGCAAGGGGCCCTCCTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:915:67:25,42:377,471:848,67:0.0732:2,2:29.3:1:32.1:1:0.30652:1.34428:42.6:134:0.0749:0:6.1 0/1:578:19:9,10:263,295:558,19:0.0329:2,2:28.5:1:30.4:1:1:1.01:43.4:38:0.0335:0:6 +6 29910448 . AA GG 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00268;SOR=0.40781;LSEQ=CCGCCTCTGCGGGGAGAAGC;RSEQ=GGGGCCCTCCTGGCGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:871:52:19,33:374,444:818,52:0.0597:2,2:32.3:1:31.8:1:0.25015:1.46239:37.8:104:0.0605:0:6.2 0/1:555:14:7,7:256,285:541,14:0.0252:2,2:33.1:1:29.8:1:1:1.11:37.5:13:0.0237:0:6.3 +6 29910450 . G C 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTCTGCGGGGAGAAGCAA;RSEQ=GGGCCCTCCTGGCGGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:851:0:0,0:376,473:849,0:0:2,0:24.2:1:32:1:1:0:56.1:52.063:0.9988:0:1.7 0/1:536:78:28,50:223,233:456,78:0.1455:2,2:26.8:1:30:1:0.03702:1.70737:33.3:77:0.1467:0:5.7 +6 29910451 . G C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00395;SOR=0.42028;LSEQ=CCTCTGCGGGGAGAAGCAAG;RSEQ=GGCCCTCCTGGCGGGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:843:52:19,33:355,435:790,52:0.0617:2,2:30.4:1:31.7:1:0.25249:1.41685:37.8:104:0.0634:0:6.2 0/1:521:14:7,7:239,266:505,14:0.0269:2,2:31.1:1:30.8:1:1:1.11:37.5:28:0.0273:0:6.3 +6 29910457 . T G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41346;SOR=0.89528;LSEQ=CGGGGAGAAGCAAGGGGCCC;RSEQ=CCTGGCGGGGGCGCAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:802:232:91,141:269,300:569,232:0.2893:2,2:25.5:1:31.7:1:0.04177:1.38876:46.3:76.333:0.2936:0:5.4 0/1:513:137:58,79:181,194:375,137:0.2671:2,2:27.8:1:30.5:1:0.27109:1.2702:35.9:274:0.2724:0:5.8 +6 29910460 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28724;LSEQ=GGAGAAGCAAGGGGCCCTCC;RSEQ=GGCGGGGGCGCAGGACCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:225:89,136:269,294:563,225:0.2848:2,2:24:1:30.8:1:0.03952:1.39755:45.9:450:0.2896:0:5.5 0/1:507:52:23,29:213,241:454,52:0.1026:2,2:29.1:1:29.9:1:0.77015:1.11413:42.7:104:0.104:0:5.9 +6 29910468 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.15831;SOR=0.64644;LSEQ=AAGGGGCCCTCCTGGCGGGG;RSEQ=CGCAGGACCGGGGGAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:762:39:20,19:334,389:723,39:0.0512:2,2:25.3:1:30.1:1:0.62168:1.23:44.8:38:0.0511:0:6.2 0/1:475:16:8,8:217,242:459,16:0.0337:2,2:26.7:1:28.9:1:1:1.11:44.3:32:0.0342:0:6.3 +6 29910473 . G A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCCTCCTGGCGGGGGCGCA;RSEQ=GACCGGGGGAGCCGCGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:0:0,0:353,408:761,0:0:2,0:22.3:1:31.6:1:1:0:56.3:35.238:0.9987:0:1.4 0/1:466:13:8,5:215,237:452,13:0.0279:2,2:23.7:1:28.6:1:0.40292:1.76:28.3:26:0.0286:0:6.2 +6 29910478 . G C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.09689;SOR=1.32385;LSEQ=CCTGGCGGGGGCGCAGGACC;RSEQ=GGGGAGCCGCGCCGGGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:104:44,60:309,330:639,104:0.1389:2,2:21:1:30.3:1:0.28982:1.27644:43.3:208:0.1415:0:6 0/1:449:79:31,48:185,183:368,79:0.1759:2,2:19.6:1:29.1:1:0.08295:1.56373:35:38.5:0.1734:0:6.4 +6 29910482 . G T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00081;SOR=0.47322;LSEQ=GCGGGGGCGCAGGACCGGGG;RSEQ=AGCCGCGCCGGGACGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:750:89:39,50:314,347:661,89:0.1187:2,2:20.2:1:29.1:1:0.57208:1.1599:40.5:178:0.1216:0:6.3 0/1:451:27:12,15:186,194:380,27:0.0599:2,2:19.6:1:27.7:1:0.69419:1.19792:39.6:26:0.0595:0:6.4 +6 29910491 . C A 94 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.9569;LSEQ=CAGGACCGGGGGAGCCGCGC;RSEQ=GGGACGAGGGTCGGGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:741:9:4,5:345,385:730,9:0.0121:2,2:5.1:1:29.9:1:1:1.11995:42.9:18:0.0124:0:6 0/1:430:5:4,1:207,218:425,5:0.0116:2,2:2.6:1:26.6:1:0.20813:4.20:44.2:10:0.0118:0:5.8 +6 29910496 . C G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.09103;LSEQ=CCGGGGGAGCCGCGCCGGGA;RSEQ=GAGGGTCGGGCAGGTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:748:59:26,33:328,359:687,59:0.0789:2,2:13.4:1:31.9:1:0.68394:1.1594:33.1:118:0.0802:0:6.8 1/0:446:236:117,119:109,100:209,236:0.5291:2,2:23.3:1:30.4:1:0.63498:1.10837:43.9:38.333:0.5239:0:2.7 +6 29910506 . G T 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCGCCGGGACGAGGGTCGG;RSEQ=CAGGTCTCAGCCACTGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:770:0:0,0:378,392:770,0:0:2,0:24.7:1:31.4:1:1:0:57.6:44.294:1:0:0.5 0/1:462:64:34,30:211,187:398,64:0.1385:2,2:22.8:1:29:1:1:1.00:44.3:128:0.1419:0:3 +6 29910507 . CA TG 99 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00887;SOR=0;LSEQ=GCGCCGGGACGAGGGTCGGG;RSEQ=GGTCTCAGCCACTGCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:776:11:7,4:371,389:760,11:0.0142:2,2:7.7:1:28.9:1:0.37594:1.83:27:22:0.0144:0.0052:6.7 0/0:475:0:0,0:253,221:474,0:0:2,0:24.2:1:31:1:1:0:51.8:51.667:0.9979:0:1.2 +6 29910508 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05229;SOR=1.80218;LSEQ=CGCCGGGACGAGGGTCGGGC;RSEQ=GGTCTCAGCCACTGCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:773:24:10,14:367,374:741,24:0.031:2,2:8.2:1:29.8:1:0.53576:1.37323:24.4:48:0.0318:0:6.8 0/1:476:26:14,12:242,206:448,26:0.0546:2,2:5.3:1:28.2:1:1:1.00692:30.5:25:0.054:0:6 +6 29910510 . G A 142 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00593;SOR=0.25089;LSEQ=CCGGGACGAGGGTCGGGCAG;RSEQ=TCTCAGCCACTGCTCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:788:25:14,11:379,384:763,25:0.0317:2,2:7.5:1:30.6:1:0.54998:1.29:24.4:50:0.0327:0:6.1 0/0:491:4:3,1:264,223:487,4:0.0081:2,2:6.3:1:28.5:1:0.62924:2.53:24.8:8:0.0083:0:6 +6 29910522 . G C 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01654;SOR=1.57482;LSEQ=TCGGGCAGGTCTCAGCCACT;RSEQ=CTCGCCCCCAGGCTCCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:857:63:34,29:395,398:793,63:0.0735:2,2:11:1:31.5:1:0.60094:1.18:23.4:30.5:0.0728:0:3.9 0/1:558:62:33,29:259,234:493,62:0.1111:2,2:10.8:1:30.5:1:1:1.03:29.4:61:0.1119:0:3.8 +6 29910527 . C T 155 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=13.09465;LSEQ=CAGGTCTCAGCCACTGCTCG;RSEQ=CCCCAGGCTCCCACTCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:886:5:2,3:440,441:881,5:0.0056:2,2:18.6:1:26.2:1:1:1.49592:42.2:4:0.0046:0:3.8 0/1:563:39:21,18:274,250:524,39:0.0693:2,2:16.4:1:29.4:1:0.86973:1.06:30.6:38:0.0688:0:4 +6 29910538 . C T 180 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=54.65993;LSEQ=CACTGCTCGCCCCCAGGCTC;RSEQ=CACTCCATGAGGTATTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:956:2:0,2:481,473:954,2:0.0021:2,0:1:0:28:1:0.24661:0:28.5:4:0.0021:0:1 0/1:632:65:37,28:288,279:567,65:0.1028:2,2:17.4:1:29.9:1:0.3623:1.28:28.2:64:0.1026:0:3.1 +6 29910557 . TT AC 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32633;LSEQ=CCCACTCCATGAGGTATTTC;RSEQ=CACATCCGTGTCCCGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1001:173:96,77:413,409:822,173:0.1728:2,2:28:1:31.2:1:0.24139:1.23:25.8:172:0.175:0.014:1.5 0/1:674:43:22,21:331,298:629,43:0.0638:2,2:31.6:1:30.5:1:0.87573:1.06019:25.2:86:0.0645:0.003:1.6 +6 29910558 . T C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=7.86948;LSEQ=CCACTCCATGAGGTATTTCT;RSEQ=CACATCCGTGTCCCGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:16:4,12:412,401:813,16:0.0162:2,2:24.4:1:29.3:1:0.04627:3.07852:27.6:7:0.0172:0:3 0/1:662:76:40,36:279,251:530,76:0.1148:2,2:24.8:1:29.7:1:1:1.0004:36:24.333:0.1193:0:3.5 +6 29910562 . A C 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TCCATGAGGTATTTCTTCAC;RSEQ=TCCGTGTCCCGGCCCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1005:0:0,0:527,478:1005,0:0:2,0:25.9:1:30.8:1:1:0:50.4:42.696:1:0:0.5 0/1:659:11:6,5:347,301:648,11:0.0167:2,2:12:1:31.4:1:1:1.04:22.4:22:0.0171:0:2.6 +6 29910581 . C A 148 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=18.75019;LSEQ=CATCCGTGTCCCGGCCCGGC;RSEQ=GCGGGGAGCCCCGCTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:996:3:2,1:563,428:991,3:0.003:2,2:30.7:1:32.3:1:1:1.52:36.7:6:0.0031:0:5 0/1:652:35:21,14:337,278:615,35:0.0537:2,2:20.9:1:29:1:0.60305:1.24:36.6:34:0.0532:0:4.8 +6 29910583 . C T 145 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=16.97466;LSEQ=TCCGTGTCCCGGCCCGGCCG;RSEQ=GGGGAGCCCCGCTTCATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:991:3:2,1:566,422:988,3:0.003:2,2:31:1:31.3:1:1:1.49:36.7:6:0.0031:0:5 0/1:652:32:18,14:341,279:620,32:0.0491:2,2:21.3:1:29:1:1:1.05:35.3:64:0.05:0:5 +6 29910586 . G A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=4.86169;LSEQ=GTGTCCCGGCCCGGCCGCGG;RSEQ=GAGCCCCGCTTCATCGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:11:7,4:575,416:991,11:0.0109:2,2:14.9:1:30.6:1:0.76922:1.27:29:10:0.0101:0:3.3 0/1:666:34:19,15:349,283:632,34:0.0511:2,2:18:1:29.1:1:1:1.03:35.2:33:0.0505:0:4.9 +6 29910604 . C A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.35161;LSEQ=GGGGAGCCCCGCTTCATCGC;RSEQ=GTGGGCTACGTGGACGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1068:45:17,28:625,398:1023,45:0.0421:2,2:12.7:1:30:1:0.00273:2.5841:32.5:21.5:0.041:0:2.1 0/1:700:153:92,61:303,243:546,153:0.2186:2,2:22.4:1:29.5:1:0.31209:1.21:29.9:75.5:0.2201:0:2.3 +6 29910607 . G C 96 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00157;SOR=13.75755;LSEQ=GAGCCCCGCTTCATCGCCGT;RSEQ=GGCTACGTGGACGACACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1057:1:1,0:641,413:1054,1:9e-04:2,0:35:0:14:0:1:0:37:0:0:0:2 0/1:699:9:8,1:384,304:688,9:0.0129:2,2:15.8:1:30.6:1:0.08542:6.32:22.1:18:0.0132:0:3.6 +6 29910622 . C T 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=22.98398;LSEQ=GCCGTGGGCTACGTGGACGA;RSEQ=ACGCAGTTCGTGCGGTTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1102:2:0,2:657,443:1100,2:0.0018:2,0:1:0:23.5:1:0.16284:0:55:4:0.0019:0:1 0/1:747:30:19,11:409,308:717,30:0.0402:2,2:14.6:1:28.4:1:0.57431:1.30:30.4:60:0.0408:0:3.1 +6 29910640 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.87242;SOR=0.96194;LSEQ=GACACGCAGTTCGTGCGGTT;RSEQ=GACAGCGACGCCGCGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1211:103:65,38:637,471:1108,103:0.0851:2,2:25.4:1:30.6:1:0.29734:1.26:49.7:206:0.0868:0:2.3 0/1:865:71:41,30:440,353:793,71:0.0821:2,2:21.9:1:29.1:1:0.80329:1.10:50.3:70:0.0824:0:2 +6 29910663 . G A 214 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCGACGCCGCGAGCCAGA;RSEQ=GATGGAGCCGCGGGCGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1517:0:0,0:833,684:1517,0:0:2,0:24.3:1:32.1:1:1:0:52.6:93.813:1:0:1 0/1:1160:155:85,70:519,481:1000,155:0.1336:2,2:22.1:1:29.5:1:0.54538:1.13:49.4:310:0.1353:0:2 +6 29910679 . G A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30299;LSEQ=CAGAGGATGGAGCCGCGGGC;RSEQ=CCGTGGATAGAGCAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1641:162:88,74:756,720:1476,162:0.0987:2,2:25.7:1:30:1:0.45764:1.13:55.5:39.5:0.0978:0:3.4 0/1:1339:43:20,23:652,642:1294,43:0.0321:2,2:27.8:1:29.4:1:0.64473:1.16778:54.9:86:0.0326:0:3.5 +6 29910688 . A G 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05899;SOR=1.3969;LSEQ=GAGCCGCGGGCGCCGTGGAT;RSEQ=GAGCAGGAGGGGCCGGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1788:68:25,43:886,834:1720,68:0.038:2,2:22.5:1:31.3:1:0.01865:1.82662:32.9:33:0.0373:0:2.4 0/1:1452:76:36,40:692,682:1374,76:0.0523:2,2:23.3:1:30.5:1:0.63873:1.12731:31.1:24.333:0.0509:0:2.6 +6 29910693 . A G 151 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=25.42368;LSEQ=GCGGGCGCCGTGGATAGAGC;RSEQ=GGAGGGGCCGGAGTATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1851:2:1,1:941,906:1847,2:0.0011:2,2:34:1:21:1:1:1.03862:55:1:6e-04:0:2.5 0/1:1531:41:22,19:744,744:1488,41:0.0268:2,2:20.5:1:28.3:1:0.75198:1.16:30.7:9.25:0.0246:0:2.9 +6 29910698 . G A 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.44956;LSEQ=CGCCGTGGATAGAGCAGGAG;RSEQ=GGCCGGAGTATTGGGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1938:518:272,246:699,720:1419,518:0.2673:2,2:25.2:1:31.1:1:0.21799:1.14:57.6:85.333:0.269:0:3.2 0/1:1576:222:109,113:673,675:1348,222:0.1409:2,2:25.3:1:29.4:1:0.82834:1.03361:57.5:221:0.1415:0:2.8 +6 29910699 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.38041;SOR=0.81087;LSEQ=GCCGTGGATAGAGCAGGAGG;RSEQ=GCCGGAGTATTGGGACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1958:52:18,34:960,944:1904,52:0.0266:2,2:15.9:1:30.9:1:0.03404:1.92027:32.4:25:0.026:0:2.5 0/1:1571:34:13,21:771,766:1537,34:0.0216:2,2:14.6:1:29.9:1:0.22441:1.62542:32.9:68:0.0219:0:2.4 +6 29910700 . G T 225 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=175.95192;LSEQ=CCGTGGATAGAGCAGGAGGG;RSEQ=CCGGAGTATTGGGACCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1968:2:0,2:980,984:1964,2:0.001:2,0:24:1:26:1:0.49975:0:60:4:0.001:0:3 0/1:1573:239:125,114:661,673:1334,239:0.1519:2,2:25.4:1:28.5:1:0.44059:1.12:48.8:238:0.1529:0:4.9 +6 29910703 . G T 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.44717;LSEQ=TGGATAGAGCAGGAGGGGCC;RSEQ=GAGTATTGGGACCAGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2007:541:276,265:727,737:1464,541:0.2696:2,2:24.9:1:31.2:1:0.61492:1.06:57.9:107.2:0.2706:0:3.3 0/1:1617:229:115,114:695,693:1388,229:0.1416:2,2:25.6:1:29.8:1:1:1.01:57.9:228:0.142:0:2.8 +6 29910716 . CA GG 241 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGCCGGAGTATTGGGAC;RSEQ=GGAGACACGGAATGTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2148:0:0,0:1053,1089:2142,0:0:2,0:24.2:1:31.8:1:1:0:57.6:75.5:0.9986:0:1.4 0/1:1725:262:139,123:685,700:1385,262:0.1519:2,2:26.3:1:30:1:0.31225:1.15:50.3:261:0.1536:0.0081:4.3 +6 29910717 . A T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33237;LSEQ=GGGGCCGGAGTATTGGGACC;RSEQ=GGAGACACGGAATGTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2131:200:97,103:955,966:1921,200:0.0939:2,2:26.8:1:31.1:1:0.76661:1.04976:56.5:39:0.0928:0:3.9 0/1:1683:56:26,30:630,626:1256,56:0.0333:2,2:26.8:1:29.9:1:0.68236:1.16109:57.4:112:0.0396:0:3.9 +6 29910719 . G C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.34499;LSEQ=GGCCGGAGTATTGGGACCAG;RSEQ=AGACACGGAATGTGAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2143:200:99,101:969,972:1941,200:0.0933:2,2:26.8:1:32.4:1:0.94086:1.01705:55.9:65.667:0.093:0:3.9 0/1:1721:59:31,28:783,772:1555,59:0.0343:2,2:26.6:1:31.3:1:0.79153:1.09:55.8:28.5:0.0334:0:3.9 +6 29910721 . G C 212 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCGGAGTATTGGGACCAGGA;RSEQ=ACACGGAATGTGAAGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2183:0:0,0:1080,1098:2178,0:0:2,0:24.3:1:32.6:1:1:0:58.3:71.6:0.9981:0:1.4 0/1:1758:108:55,53:826,820:1646,108:0.0614:2,2:28.4:1:31.5:1:0.92102:1.03:35.9:107:0.0614:0:5.4 +6 29910725 . C G 189 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=86.39667;LSEQ=AGTATTGGGACCAGGAGACA;RSEQ=GGAATGTGAAGGCCCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2231:1:0,1:1100,1124:2224,1:4e-04:2,0:26:0:33:0:1:0:56:2:5e-04:0:3 0/1:1768:66:36,30:837,859:1696,66:0.0373:2,2:28.3:1:31.4:1:0.45235:1.23:42.7:132:0.0378:0:4.1 +6 29910730 . T A 255 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=307.76907;LSEQ=TGGGACCAGGAGACACGGAA;RSEQ=GTGAAGGCCCAGTCACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2227:2:1,1:1105,1120:2225,2:9e-04:2,2:25:1:23.5:1:1:1.01:58:1:5e-04:0:2 0/1:1759:380:199,181:677,700:1377,380:0.216:2,2:24.1:1:29.8:1:0.27157:1.14:49.5:94:0.2156:0:4.3 +6 29910731 . G A 232 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=194.45762;LSEQ=GGGACCAGGAGACACGGAAT;RSEQ=TGAAGGCCCAGTCACAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2223:2:2,0:1105,1116:2221,2:9e-04:2,0:1:0:24.5:1:0.24787:0:50:4:9e-04:0:3 0/1:1757:262:128,134:746,747:1493,262:0.1491:2,2:23.4:1:29:1:0.7888:1.04547:50.3:261:0.1497:0:3.8 +6 29910742 . G C 309 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.13127;LSEQ=ACACGGAATGTGAAGGCCCA;RSEQ=TCACAGACTGACCGAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2151:580:279,301:765,805:1570,580:0.2696:2,2:26.2:1:33:1:0.8081:1.02524:57.1:144:0.2707:0:3.5 1/0:1682:902:447,455:383,395:778,902:0.5363:2,2:24:1:31.5:1:0.92205:1.01:48.9:111.75:0.5376:0:4.1 +6 29910750 . C T 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23711;LSEQ=TGTGAAGGCCCAGTCACAGA;RSEQ=TGACCGAGTGGACCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2098:562:267,295:748,786:1534,562:0.2679:2,2:26.5:1:30.8:1:0.62202:1.05145:54.9:69.25:0.2676:0:3.6 0/1:1629:130:59,71:742,753:1495,130:0.0798:2,2:26:1:29.2:1:0.36195:1.18568:54.6:129:0.0804:0:3.6 +6 29910752 . G C 259 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAAGGCCCAGTCACAGACT;RSEQ=ACCGAGTGGACCTGGGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2096:0:0,0:1010,1085:2095,0:0:2,0:25.8:1:32.2:1:1:0:57.6:73.821:0.9995:0:1.4 0/1:1584:327:167,160:614,640:1254,327:0.2064:2,2:25.3:1:31.1:1:0.53466:1.09:47.6:326:0.2087:0:4.1 +6 29910759 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.23227;LSEQ=CCAGTCACAGACTGACCGAG;RSEQ=GGACCTGGGGACCCTGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2047:150:75,75:898,997:1895,150:0.0733:2,2:28.1:1:30.9:1:0.55305:1.11:53:49:0.0727:0:3.9 0/1:1439:293:140,153:555,576:1131,293:0.2036:2,2:27.5:1:30.8:1:0.74306:1.053:46.5:292:0.2052:0:4.9 +6 29910761 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.33634;LSEQ=AGTCACAGACTGACCGAGTG;RSEQ=ACCTGGGGACCCTGCGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2007:147:72,75:875,984:1859,147:0.0732:2,2:28:1:30.4:1:0.66865:1.08:52.2:35.75:0.0723:0:3.9 0/1:1399:292:141,151:546,561:1107,292:0.2087:2,2:26.9:1:29.5:1:0.79246:1.04227:46.1:96.333:0.2097:0:4.9 +6 29910801 . C A 197 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.98588;LSEQ=CTACTACAACCAGAGCGAGG;RSEQ=CGGTGAGTGACCCCGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1295:4:3,1:530,761:1291,4:0.0031:2,2:2.3:1:26.8:1:0.31194:4.30:50:8:0.0031:0:2 0/1:824:131:65,66:300,391:691,131:0.159:2,2:12.9:1:28.1:1:0.2126:1.28:42.9:262:0.1615:0:4.2 +6 29910816 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.37082;LSEQ=CGAGGCCGGTGAGTGACCCC;RSEQ=GCCGGGGGCGCAGGTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:998:234:83,151:273,490:763,234:0.2345:2,2:22.2:1:31.4:1:1:1.01358:37.9:233:0.2378:0:4.7 0/1:569:58:25,33:184,327:511,58:0.1019:2,2:23.6:1:29.2:1:0.31534:1.35:37.3:28:0.1004:0:4.1 +6 29910820 . G C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=2.82073;LSEQ=GCCGGTGAGTGACCCCGGCC;RSEQ=GGGGCGCAGGTCAGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:262:81,181:214,426:640,262:0.2901:2,2:22.6:1:29.9:1:0.48251:1.12237:34.6:64.5:0.2905:0:4.7 1/0:504:270:88,182:82,148:230,270:0.5357:2,2:22.5:1:28.7:1:0.50768:1.14557:34.5:89:0.5361:0:3.8 +6 29910834 . G C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.13657;LSEQ=CCGGCCGGGGGCGCAGGTCA;RSEQ=GACCCCTCATCCCCCACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:737:220:57,163:150,367:517,220:0.2985:2,2:22.9:1:30.6:1:0.42083:1.16854:34.5:72.333:0.2985:0:4.8 1/0:384:245:69,176:41,98:139,245:0.638:2,2:24.8:1:29.3:1:0.81472:1.06696:36.8:80.667:0.6385:0:3.3 +6 29910839 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00051;SOR=1.60079;LSEQ=CGGGGGCGCAGGTCAGGACC;RSEQ=CTCATCCCCCACGGACGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:210:49,161:127,339:466,210:0.3107:2,2:22.7:1:30.6:1:0.29876:1.23056:35.8:104:0.3133:0:4.8 0/1:365:153:44,109:57,154:211,153:0.4192:2,2:22.4:1:28.2:1:0.72346:1.09:34.1:37.25:0.4209:0:3.8 +6 29910852 . G C 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75984;SOR=0.66337;LSEQ=CAGGACCCCTCATCCCCCAC;RSEQ=GACGGGCCAGGTCGCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:9:6,3:111,442:553,9:0.016:2,2:23.1:1:31.9:1:0.00352:7.92:45.1:18:0.0162:0:3.6 0/1:281:3:2,1:58,219:277,3:0.0107:2,2:22.7:1:23.7:1:0.11704:7.48:48.3:2:0.0072:0:3.7 +6 29910856 . G A 222 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCCTCATCCCCCACGGAC;RSEQ=GGCCAGGTCGCCCACAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:129:28,101:71,317:388,129:0.2495:2,2:24.9:1:31.7:1:0.43838:1.24:45.3:128:0.2485:0:4.6 0/0:263:0:0,0:52,211:263,0:0:2,0:23.7:1:29.9:1:1:0:48.1:86.667:1:0:2 +6 29910861 . A G 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47493;SOR=0.78207;LSEQ=TCATCCCCCACGGACGGGCC;RSEQ=GGTCGCCCACAGTCTCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:43:12,31:79,360:439,43:0.0892:2,2:28.2:1:31.6:1:0.15006:1.76:38.6:86:0.0898:0:3.6 0/1:239:17:4,13:37,184:221,17:0.0711:2,2:32.8:1:29.8:1:0.50416:1.53:38.5:34:0.0726:0:3.5 +6 29910865 . C G 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCCACGGACGGGCCAGGT;RSEQ=GCCCACAGTCTCCGGGTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:0:0,0:76,370:446,0:0:2,0:26:1:31.1:1:1:0:55.4:222:1:0:1.5 0/1:226:16:6,10:26,184:210,16:0.0708:2,2:26.9:1:31.1:1:0.01431:4.21:52.9:32:0.0721:0:2.4 +6 29910866 . G A 206 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.20691;LSEQ=CCCCACGGACGGGCCAGGTC;RSEQ=CCCACAGTCTCCGGGTCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:114:19,95:55,262:317,114:0.2645:2,2:28.4:1:30.2:1:1:1.0495:50.7:56:0.2654:0:4.3 0/1:217:15:1,14:29,173:202,15:0.0691:2,1:16.1:1:28.2:1:0.6998:2.33986:47.4:14:0.0648:0:3.4 +6 29910892 . A G 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=144.30819;LSEQ=AGTCTCCGGGTCCGAGATCC;RSEQ=CCCCGAAGCCGCGGGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:382:1:1,0:94,287:381,1:0.0026:2,0:35:0:26:0:0.24869:0:49:2:0.0027:0:1 0/1:188:52:14,38:40,95:135,52:0.2766:2,2:22.9:1:31.3:1:0.85728:1.14202:45.8:51:0.2742:0:2.5 +6 29910910 . C T 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACCCCGAAGCCGCGGGAC;RSEQ=CCGAGACCCTTGCCCCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:131,209:340,0:0:2,0:24:1:31.4:1:1:0:51.9:47.571:1:0:1 0/1:166:20:9,11:61,85:146,20:0.1205:2,2:28.8:1:30.1:1:0.81277:1.14:44.5:40:0.1242:0:2.3 +6 29910923 . C A 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.78665;SOR=1.25498;LSEQ=GCGGGACCCCGAGACCCTTG;RSEQ=CCCGGGAGAGGCCCAGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:10:8,2:152,164:316,10:0.0307:2,2:26.6:1:29.7:1:0.0574:4.30:41.8:20:0.0312:0:3.3 0/1:157:6:4,2:63,68:131,6:0.0382:2,2:25.7:1:29.3:1:0.43425:2.15:28.2:12:0.0392:0:2.3 +6 29910947 . T A 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGAGAGGCCCAGGCGCCTT;RSEQ=ACCCGGTTTCATTTTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:0:0,0:256,109:365,0:0:2,0:22.8:1:30.7:1:1:0:46.3:181.5:1:0:0.8 0/1:184:12:7,5:125,47:172,12:0.0652:2,2:22.6:1:27.4:1:0.32414:1.89245:38.8:11:0.0615:0:1.6 +6 29910970 . G A 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99049;LSEQ=CCGGTTTCATTTTCAGTTTA;RSEQ=GCCAAAAATCCCCCCGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:7:7,0:375,92:467,7:0.0147:2,0:39.6:1:27.9:1:0.35497:0:20.9:6:0.013:0:3.1 0/1:274:4:3,1:213,57:270,4:0.0146:2,2:41:1:25:1:1:1.24455:21.8:3:0.0111:0:3 +6 29910980 . C T 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTCAGTTTAGGCCAAAAAT;RSEQ=CCCCCGGGTTGGTCGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:0:0,0:446,136:582,0:0:2,0:23.1:1:31.8:1:1:0:48.8:43.769:1:0:1.2 0/1:311:14:12,2:227,69:296,14:0.045:2,2:23.1:1:29.2:1:0.7444:1.82:45.9:28:0.0459:0:1.2 +6 29910984 . C G 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.06983;LSEQ=AGTTTAGGCCAAAAATCCCC;RSEQ=CGGGTTGGTCGGGGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:7:7,0:469,145:614,7:0.0112:2,0:32.3:1:24.7:1:0.20913:0:20.9:6:0.0099:0:3.1 0/1:333:4:3,1:254,75:329,4:0.012:2,2:32.3:1:24.8:1:1:1.12849:21.8:3:0.0091:0:3 +6 29910986 . G A 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAGGCCAAAAATCCCCCC;RSEQ=GGTTGGTCGGGGCTGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:0:0,0:488,159:647,0:0:2,0:23.2:1:29.9:1:1:0:49.5:45.214:1:0:1.3 0/1:348:44:37,7:227,77:304,44:0.1264:2,2:27.4:1:29.8:1:0.19228:1.79:26.4:88:0.1272:0:3.8 +6 29911000 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.08845;SOR=0.80073;LSEQ=CCCCCCGGGTTGGTCGGGGC;RSEQ=GGGCGGGGCTCGGGGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:819:287:204,83:357,170:527,287:0.3504:2,2:25.2:1:30.3:1:0.34226:1.17:38.5:40:0.3487:0:3.5 0/1:431:130:92,38:122,54:176,130:0.3016:2,2:24.9:1:29.9:1:0.80219:1.07:42.4:64:0.304:0:3.3 +6 29911003 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35317;LSEQ=CCCGGGTTGGTCGGGGCTGG;RSEQ=CGGGGCTCGGGGGACTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:857:310:220,90:362,185:547,310:0.3617:2,2:24.6:1:29.5:1:0.17043:1.25:38.5:43.286:0.3616:0:3.5 0/1:450:75:53,22:262,112:374,75:0.1667:2,2:26.3:1:28.8:1:1:1.03:37.9:150:0.1689:0:3.6 +6 29911005 . G A 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGTTGGTCGGGGCTGGGC;RSEQ=GGGCTCGGGGGACTGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:917:0:0,0:598,316:914,0:0:2,0:23.7:1:29.7:1:1:0:50.4:38.739:0.9966:0:1.4 0/1:471:46:32,14:290,134:424,46:0.0977:2,2:25.8:1:29.7:1:1:1.06:51.9:92:0.0981:0:3.2 +6 29911011 . C T 169 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=55.66599;LSEQ=GGTCGGGGCTGGGCGGGGCT;RSEQ=GGGGGACTGGGCTGACCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1006:2:0,2:638,365:1003,2:0.002:2,0:1:0:26:0:0.13312:0:40:4:0.002:0:3 0/1:520:52:35,17:311,157:468,52:0.1:2,2:25.6:1:29.8:1:1:1.04:51.5:104:0.1018:0:3.1 +6 29911019 . T C 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGGGCGGGGCTCGGGGGAC;RSEQ=GGGCTGACCGCGGGGTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1127:0:0,0:700,427:1127,0:0:2,0:24.9:1:31:1:1:0:50.8:44.08:1:0:1.3 0/1:628:75:51,24:349,203:552,75:0.1194:2,2:21.1:1:28.9:1:0.4452:1.24:26.4:36.5:0.1176:0:4.9 +6 29911029 . G T 125 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.07357;LSEQ=CTCGGGGGACTGGGCTGACC;RSEQ=CGGGGTCGGGGCCAGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1281:4:1,3:751,526:1277,4:0.0031:2,2:2:1:27:1:0.31246:4.2786:60:3:0.0024:0:1.3 0/1:751:23:15,8:434,294:728,23:0.0306:2,2:14:1:27.7:1:0.66985:1.27:28.6:10.5:0.0284:0:5.1 +6 29911030 . C T 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.34432;LSEQ=TCGGGGGACTGGGCTGACCG;RSEQ=GGGGTCGGGGCCAGGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1294:498:301,197:457,336:793,498:0.3849:2,2:24.9:1:29.7:1:0.32414:1.12:39.3:44.273:0.385:0:3.1 0/1:762:135:88,47:367,260:627,135:0.1772:2,2:23.3:1:28.4:1:0.17566:1.33:38.4:32.75:0.1765:0:3.3 +6 29911037 . G C 204 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGGGCTGACCGCGGGGTC;RSEQ=GGGCCAGGTTCTCACACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1395:0:0,0:799,593:1392,0:0:2,0:26.1:1:30:1:1:0:52.2:50.556:0.9985:0:1.3 0/1:860:128:76,52:428,300:728,128:0.1488:2,2:15.6:1:29.2:1:0.92271:1.02:28.2:127:0.1496:0:5.5 +6 29911056 . A G 209 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=67.81361;LSEQ=CGGGGCCAGGTTCTCACACC;RSEQ=TCCAGATAATGTATGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1597:3:2,1:851,741:1592,3:0.0019:2,2:21:1:23:1:1:1.74:35.3:2:0.0013:0:5 0/1:1111:126:65,61:507,425:932,126:0.1134:2,2:22.3:1:30:1:0.56872:1.11941:28.5:125:0.1139:0:6.2 +6 29911063 . TA GG 221 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=115.86116;LSEQ=AGGTTCTCACACCATCCAGA;RSEQ=ATGTATGGCTGCGACGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1664:2:1,1:856,803:1659,2:0.0012:2,2:17.5:1:30.8:1:1:1.066:29:4:0.0012:0:6 0/1:1159:142:70,72:531,479:1010,142:0.1225:2,2:29.5:1:31:1:0.47423:1.1401:28.1:284:0.1235:0:5.3 +6 29911064 . A G 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.45883;LSEQ=GGTTCTCACACCATCCAGAT;RSEQ=ATGTATGGCTGCGACGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1692:663:336,327:537,489:1026,663:0.3918:2,2:25.5:1:32:1:0.5171:1.06869:42:54.25:0.3922:0:2.8 0/1:1166:266:143,123:395,362:757,266:0.2281:2,2:25.6:1:30.8:1:0.66904:1.07:39.2:265:0.2606:0:3.3 +6 29911069 . A T 167 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=38.26312;LSEQ=TCACACCATCCAGATAATGT;RSEQ=TGGCTGCGACGTGGGGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1747:2:0,2:885,860:1745,2:0.0011:2,0:1:0:26:0:0.24332:0:52:4:0.0012:0:2 0/1:1213:51:24,27:602,560:1162,51:0.042:2,2:30:1:29.6:1:0.56778:1.20918:36.3:50:0.0418:0:4.8 +6 29911086 . T C 263 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=184.82077;LSEQ=TGTATGGCTGCGACGTGGGG;RSEQ=CGGACGGGCGCTTCCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1740:4:3,1:848,885:1733,4:0.0023:2,2:28.5:1:32.5:1:0.36478:3.13:43.5:8:0.0023:0:1.3 0/1:1254:375:185,190:433,443:876,375:0.299:2,2:27.4:1:30.8:1:1:1.00384:42.3:61.5:0.2981:0:2 +6 29911092 . G T 224 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=73.65802;LSEQ=GCTGCGACGTGGGGTCGGAC;RSEQ=GGCGCTTCCTCCGCGGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1713:4:1,3:841,863:1704,4:0.0023:2,2:23.3:1:28.3:1:0.62471:2.92208:40.3:8:0.0024:0:4 0/1:1249:184:86,98:516,547:1063,184:0.1473:2,2:26.5:1:29.8:1:0.68975:1.07486:27.8:91:0.1472:0:5.1 +6 29911098 . T C 160 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=18.54295;LSEQ=ACGTGGGGTCGGACGGGCGC;RSEQ=TCCTCCGCGGGTACCGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1655:3:1,2:816,836:1652,3:0.0018:2,2:22.7:1:20:1:1:1.95138:39:0.5:6e-04:0:4 0/1:1227:40:20,20:570,616:1186,40:0.0326:2,2:25.8:1:30.2:1:0.87279:1.08:27.7:39:0.0322:0:4.3 +6 29911114 . G A 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.61061;LSEQ=GCGCTTCCTCCGCGGGTACC;RSEQ=GCAGGACGCCTACGACGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1502:444:203,241:537,516:1053,444:0.2956:2,2:27.3:1:31.2:1:0.0701:1.23533:45:48.333:0.2949:0:2.5 0/1:1064:217:104,113:310,347:657,217:0.2039:2,2:23.7:1:29.5:1:0.87554:1.03:38.1:53.25:0.2032:0:3.1 +6 29911119 . G T 207 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=141.90278;LSEQ=TCCTCCGCGGGTACCGGCAG;RSEQ=ACGCCTACGACGGCAAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1464:2:1,1:704,757:1461,2:0.0014:2,2:28.5:1:30:1:1:1.08:29:4:0.0014:0:5 0/1:989:161:78,83:386,441:827,161:0.1628:2,2:28.5:1:28.3:1:0.73006:1.07:27.4:160:0.1631:0:4.6 +6 29911124 . C T 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCGGGTACCGGCAGGACGC;RSEQ=TACGACGGCAAGGATTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1412:0:0,0:681,726:1407,0:0:2,0:25.8:1:32:1:1:0:53.8:53.115:0.9978:0:0.9 0/1:945:50:25,25:418,476:894,50:0.0529:2,2:23.7:1:29.9:1:0.66519:1.14:27.5:100:0.0536:0:3.7 +6 29911149 . C T 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50219;LSEQ=ACGGCAAGGATTACATCGCC;RSEQ=TGAACGAGGACCTGCGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1103:352:160,192:351,399:750,352:0.3191:2,2:24.5:1:30.8:1:0.69775:1.05562:43.4:57.667:0.3192:0:2.4 0/1:630:120:48,72:230,279:509,120:0.1905:2,2:26.5:1:29.9:1:0.3093:1.23614:43.9:119:0.191:0:2.4 +6 29911154 . C A 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=55.95476;LSEQ=AAGGATTACATCGCCCTGAA;RSEQ=GAGGACCTGCGCTCTTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1067:4:3,1:496,566:1062,4:0.0037:2,2:16.5:1:29.5:1:0.3455:3.42:53.8:8:0.0038:0:1.3 0/1:597:104:51,53:214,278:492,104:0.1742:2,2:14.9:1:29.1:1:0.32894:1.25:26.4:51:0.1735:0:4.1 +6 29911190 . G A 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGACCGCGGCGGACATGGC;RSEQ=GCTCAGATCACCAAGCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:852:0:0,0:397,455:852,0:0:2,0:23.6:1:30.3:1:1:0:50.9:55.8:1:0:0.6 0/1:423:95:44,51:150,178:328,95:0.2246:2,2:17.4:1:29.5:1:1:1.02:29.5:46.5:0.2214:0:4.3 +6 29911198 . T C 198 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCGGACATGGCGGCTCAGA;RSEQ=CACCAAGCGCAAGTGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:826:0:0,0:377,448:825,0:0:2,0:25:1:30.3:1:1:0:51.5:40.25:1:0:0.6 0/1:399:93:44,49:138,167:305,93:0.2331:2,2:23.8:1:30.3:1:0.81215:1.09:27.9:30:0.2314:0:4.8 +6 29911203 . A C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.85703;SOR=0.95786;LSEQ=ACATGGCGGCTCAGATCACC;RSEQ=AGCGCAAGTGGGAGGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:831:110:59,51:328,393:721,110:0.1324:2,2:29.3:1:31.1:1:0.12388:1.39:26.4:54:0.1324:0:3.3 0/1:400:51:25,26:166,183:349,51:0.1275:2,2:28.3:1:30.2:1:0.88146:1.06:29:24.5:0.1253:0:3 +6 29911207 . G A 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=99.66126;LSEQ=GGCGGCTCAGATCACCAAGC;RSEQ=CAAGTGGGAGGCGGCCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:805:3:1,2:374,428:802,3:0.0037:2,2:9.7:1:24:1:1:1.7465:46.3:2:0.0025:0:1 0/1:386:105:48,57:138,143:281,105:0.272:2,2:27.7:1:29:1:0.56897:1.14557:27.9:210:0.2742:0:4.6 +6 29911218 . G A 111 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=38.4603;LSEQ=TCACCAAGCGCAAGTGGGAG;RSEQ=CGGCCCATGAGGCGGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:813:1:1,0:368,442:810,1:0.0012:2,0:3:0:17:0:0.45499:0:29:0:0:0:2 0/1:375:17:11,6:169,189:358,17:0.0453:2,2:25.9:1:27.3:1:0.21448:2.05:30:16:0.0438:0:2.8 +6 29911225 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00206;SOR=0.38636;LSEQ=GCGCAAGTGGGAGGCGGCCC;RSEQ=TGAGGCGGAGCAGTTGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:820:65:33,32:340,415:755,65:0.0793:2,2:32.4:1:31.5:1:0.43633:1.26:22.1:130:0.0803:0:3.7 0/1:373:12:7,5:168,193:361,12:0.0322:2,2:28.4:1:28.2:1:0.5592:1.61:22.4:11:0.0301:0:3.6 +6 29911228 . A T 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.67706;LSEQ=CAAGTGGGAGGCGGCCCATG;RSEQ=GGCGGAGCAGTTGAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:816:67:34,33:341,408:749,67:0.0821:2,2:29.3:1:30.6:1:0.44394:1.23:22.5:134:0.0834:0:3.7 0/1:372:182:82,100:87,101:188,182:0.4892:2,2:31.6:1:29.4:1:0.83516:1.0503:30.8:90:0.4918:0:4 +6 29911239 . TT CA 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGCCCATGAGGCGGAGCAG;RSEQ=GAGAGCCTACCTGGATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:812:0:0,0:372,439:811,0:0:2,0:25.1:1:30.1:1:1:0:47.7:114.857:1:0:0.5 0/1:352:59:27,32:134,159:293,59:0.1676:2,2:25.3:1:30.7:1:1:1.00:37.9:118:0.1691:0.0085:2.5 +6 29911240 . T G 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCCATGAGGCGGAGCAGT;RSEQ=GAGAGCCTACCTGGATGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:810:0:0,0:372,437:809,0:0:2,0:25:1:30.6:1:1:0:47.6:79.9:1:0:0.5 0/1:347:15:9,6:124,150:274,15:0.0432:2,2:9.3:1:29.8:1:0.29682:1.81:30.3:30:0.0526:0:3.4 +6 29911256 . T G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.83639;LSEQ=CAGTTGAGAGCCTACCTGGA;RSEQ=GGCACGTGCGTGGAGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:741:69:36,33:281,388:669,69:0.0931:2,2:8.2:1:31.4:1:0.12502:1.51:26.8:138:0.0949:0:2.7 0/1:318:142:61,81:75,100:175,142:0.4465:2,2:17:1:30.6:1:1:1.00:27:141:0.4519:0:3.7 +6 29911260 . AC CG 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGAGCCTACCTGGATGGC;RSEQ=GTGCGTGGAGTGGCTCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:727:0:0,0:314,413:727,0:0:2,0:24.4:1:30:1:1:0:46.3:144.4:1:0:0.4 0/1:318:13:2,11:125,180:305,13:0.0409:2,2:14.4:1:27.1:1:0.08376:3.80648:28.5:26:0.0417:0.022:1.4 +6 29911267 . T A 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03484;SOR=8.93657;LSEQ=CTACCTGGATGGCACGTGCG;RSEQ=GGAGTGGCTCCGCAGATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:684:1:1,0:286,397:683,1:0.0015:2,0:1:0:25:0:0.41959:0:60:2:0.0015:0:1 0/1:309:4:3,1:117,188:305,4:0.0129:2,2:8:1:26.8:1:0.30276:4.80:35:8:0.013:0:3.8 +6 29911271 . GT CG 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTGGATGGCACGTGCGTGGA;RSEQ=GGCTCCGCAGATACCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:676:0:0,0:277,396:673,0:0:2,0:24.4:1:32.3:1:1:0:45.5:60.182:0.9955:0:0.3 0/1:297:10:2,8:110,176:286,10:0.0337:2,2:8.6:1:28.6:1:0.32862:2.49334:29.7:20:0.0341:0.0135:3.1 +6 29911272 . T A 101 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12402;SOR=0.18877;LSEQ=TGGATGGCACGTGCGTGGAG;RSEQ=GGCTCCGCAGATACCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:12:3,9:273,389:662,12:0.0178:2,2:8.3:1:28.3:1:0.37683:2.10328:31:11:0.0166:0:4.3 0/0:294:1:0,1:108,179:287,1:0.0034:2,0:17:0:26:0:1:0:25:2:0.0035:0:6 +6 29911296 . G A 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=62.60948;LSEQ=TCCGCAGATACCTGGAGAAC;RSEQ=GGAAGGAGACGCTGCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:1:1,0:166,354:520,1:0.0019:2,0:1:0:29:0:0.32054:0:43:2:0.0019:0:1 0/1:241:26:5,21:63,152:215,26:0.1079:2,2:31.5:1:28.7:1:0.35962:1.73719:36.9:25:0.105:0:3.5 +6 29911306 . C T 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGAGAACGGGAAGGAGA;RSEQ=GCTGCAGCGCACGGGTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:138,348:486,0:0:2,0:26.3:1:29.9:1:1:0:40.3:29.375:1:0:0.5 0/1:232:24:4,20:53,155:208,24:0.1034:2,2:34.5:1:27.8:1:0.45586:1.70616:38.7:23:0.1:0:3.5 +6 29911307 . G A 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00801;SOR=0.23266;LSEQ=CTGGAGAACGGGAAGGAGAC;RSEQ=CTGCAGCGCACGGGTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:26:4,22:130,324:454,26:0.0541:2,2:31.3:1:28.9:1:0.17959:2.20375:37.8:52:0.0556:0:3.7 0/1:229:3:0,3:56,170:226,3:0.0131:2,0:35.3:1:27.7:1:1:0:40.3:6:0.0134:0:4 +6 29911319 . G T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00011;SOR=2.2921;LSEQ=AAGGAGACGCTGCAGCGCAC;RSEQ=GGTACCAGGGGCCACGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:54:9,45:96,278:374,54:0.1262:2,2:33.5:1:29.9:1:0.17735:1.72465:39.9:26:0.1241:0:3.1 0/1:229:57:10,47:38,130:168,57:0.2489:2,2:31.5:1:29.4:1:0.46065:1.37199:38.6:114:0.25:0:3.2 +6 29911326 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.68073;SOR=0.80704;LSEQ=CGCTGCAGCGCACGGGTACC;RSEQ=GGGGCCACGGGGCGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:18:6,12:79,304:383,18:0.0449:2,2:25.4:1:29.9:1:0.23459:1.92:43.3:17:0.0428:0:1.8 0/1:219:8:4,4:42,169:211,8:0.0365:2,2:22.3:1:27.4:1:0.06238:3.99:34.9:16:0.0369:0:2 +6 29911329 . G A 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00152;SOR=0.1859;LSEQ=TGCAGCGCACGGGTACCAGG;RSEQ=GCCACGGGGCGCCTCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:27:3,24:70,289:359,27:0.0699:2,2:37.3:1:32.1:1:0.44312:1.93488:37.4:54:0.0714:0:3.9 0/1:218:3:0,3:46,169:215,3:0.0138:2,0:39:1:27.3:1:1:0:40.3:2:0.0093:0:4 +6 29911344 . C A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00033;SOR=Inf;LSEQ=CCAGGGGCCACGGGGCGCCT;RSEQ=CCTGATCGCCTGTAGATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:42,274:316,0:0:2,0:24.4:1:31.1:1:1:0:50.1:34.111:1:0:0.7 0/1:187:8:0,8:28,143:171,8:0.0428:2,0:26:1:29.3:1:0.36053:0:37.1:16:0.0428:0:2.8 +6 29911360 . A G 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00077;SOR=Inf;LSEQ=GCCTCCCTGATCGCCTGTAG;RSEQ=TCTCCCGGGCTGGCCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:6,217:223,0:0:1,0:25.8:1:31.4:1:1:0:53.9:43.6:1:0:0.8 0/1:128:7:0,7:13,108:121,7:0.0547:2,0:23.1:1:28.6:1:1:0:40.7:6:0.048:0:2.4 +6 29911365 . C G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.12591;SOR=Inf;LSEQ=CCTGATCGCCTGTAGATCTC;RSEQ=CGGGCTGGCCTCCCACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:5,205:210,0:0:1,0:24.6:1:31.5:1:1:0:55:51.5:1:0:0.8 0/1:116:2:0,2:12,102:114,2:0.0172:2,0:10:1:33:0:1:0:32.5:4:0.0174:0:4 +6 29911367 . G A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00985;SOR=3.00695;LSEQ=TGATCGCCTGTAGATCTCCC;RSEQ=GGCTGGCCTCCCACAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:11:0,11:3,190:193,11:0.0539:1,0:29.2:1:32.9:1:1:0:50.9:22:0.055:0:3.7 0/1:109:16:2,14:8,85:93,16:0.1468:2,2:28.1:1:30.6:1:0.63904:1.51:44.9:32:0.1509:0:4.3 +6 29911388 . G A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.35453;SOR=1.55985;LSEQ=GGCTGGCCTCCCACAAGGAG;RSEQ=GGAGACAATTGGGACCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:13:0,13:4,121:125,13:0.0935:1,1:14:1:33.5:1:1:0:44.2:26:0.0956:0:4.5 0/1:72:10:1,9:7,55:62,10:0.1389:2,2:20.3:1:31.7:1:1:1.14338:43:20:0.1389:0:4.5 +6 29911396 . AT GA 116 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01425;SOR=3.29407;LSEQ=TCCCACAAGGAGGGGAGACA;RSEQ=TGGGACCAACACTAGAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:9:0,9:3,105:108,9:0.0769:1,0:9.9:1:32.8:1:1:0:40.1:18:0.0769:0.0171:4 0/1:60:13:1,12:7,40:47,13:0.2167:2,1:14.2:1:31.6:1:0.67266:2.07821:38.5:26:0.2167:0.0167:3.3 +6 29911419 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00118;SOR=6.59675;LSEQ=GGGACCAACACTAGAATATC;RSEQ=CCCTCCCTCTGGTCCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:0,6:4,57:61,6:0.0896:2,0:27.3:1:34:1:1:0:46.8:12:0.0923:0:1.2 0/1:25:10:2,8:0,15:15,10:0.4:1,2:20.4:1:31.8:1:0.15:0:43.6:20:0.4:0:1.5 +6 29911457 . G GT 68 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00107;SOR=21.55529;LSEQ=AGGGAGAGGAATCCTCCTGG;RSEQ=TTCCAGATCCTGTACCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:5,34:39,2:0.0488:2,0:25.5:1:32:0:1:0:22.5:4:0.0513:0:1 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:28.6:1:29.6:1:1:0:30.4:10:0.5556:0:1 +6 29911505 . C G 34 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=1.66053;LSEQ=CTGAGGTTCCGCCCTGCTCT;RSEQ=TGACACAATTAAGGGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:2,15:17,2:0.1053:2,0:14:1:34:0:1:0:37.5:4:0.1176:0:1.5 0/1:6:1:0,1:1,3:4,1:0.1667:2,0:9:0:33:0:1:0:25:2:0.2:0:1 +6 29911538 . G A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42308;SOR=3.87298;LSEQ=GGGATAAAATCTCTGAAGGA;RSEQ=TGACGGGAAGACGATCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:0,2:3,6:9,2:0.1818:2,0:36.5:1:30.5:1:1:0:55:4:0.2:0:1.5 1/0:2:1:0,1:1,0:1,1:0.5:0,0:5:0:30:0:1:0:47:2:0.5:0:1 +6 29911583 . G GACAC 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTGATGAGTGGTTCCCTTT;RSEQ=ACACCGGCAGCAGCCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:8,2:10,4:0.2857:2,2:20.8:1:32.5:1:0.09491:9.51263:42.8:8:0.3077:0.0714:0.8 0/0:1:0:0,0:1,0:1,0:0:0,0:19:0:26:0:1:0:60:2:1:0:0 +6 29911684 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01136;SOR=Inf;LSEQ=GAGTCCAGCACTTCTGAGTC;RSEQ=CTCAGCCTCCACTCAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:28,1:29,0:0:1,0:24.2:1:31.9:1:1:0:45.2:58:1:0:0 1/0:4:2:2,0:1,1:2,2:0.5:2,0:25.5:1:31:1:1:0:45.5:4:0.5:0:2 +6 29911836 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19416;SOR=Inf;LSEQ=ATTCTCAAGATGGCCACATG;RSEQ=GTGCTGGTGGAGTGTCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:134,5:139,0:0:1,0:32.8:1:31.3:1:1:0:39.9:33.75:1:0:0.2 0/1:110:2:2,0:101,7:108,2:0.0182:2,0:45.5:1:28.5:1:1:0:44:4:0.0183:0:1 +6 29911837 . G A 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=TTCTCAAGATGGCCACATGC;RSEQ=TGCTGGTGGAGTGTCCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:134,5:139,0:0:1,0:32.4:1:28.9:1:1:0:39.9:22.167:1:0:0.2 0/1:111:10:9,1:94,7:101,10:0.0901:2,2:27.5:1:28.2:1:0.54228:1.48589:38.2:20:0.0917:0:1.1 +6 29911893 . C T 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06702;SOR=Inf;LSEQ=CTGAATTTTCTGACTCTTCC;RSEQ=GTCAGACCCCCCCAAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:15,3:18,0:0:2,0:7.7:1:28.9:1:1:0:22.2:36:1:0:0.3 0/1:27:6:3,3:18,3:21,6:0.2222:2,2:27.7:1:30.2:1:0.10093:5.49418:20.3:12:0.2222:0:1 +6 29912149 . G C 143 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=0.14251;LSEQ=CATGTGCAGCATGAGGGTCT;RSEQ=CCCAAGCCCCTCACCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:28:12,16:58,55:113,28:0.1972:2,2:5.1:1:29.8:1:0.52743:1.40266:22.7:56:0.1986:0:2.1 0/1:119:4:2,2:51,64:115,4:0.0336:2,2:3:1:30:1:1:1.25:22.3:8:0.0339:0:2 +6 29912188 . T C 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATGGGGTAAGGAGGGAGA;RSEQ=GGGGGTGTCATGTCTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:595:0:0,0:273,322:595,0:0:2,0:24.9:1:30.2:1:1:0:31.5:53.091:1:0:0.9 0/1:391:60:29,31:147,182:329,60:0.1535:2,2:22.2:1:29.8:1:0.67267:1.16:33.7:120:0.1583:0:2.4 +6 29912204 . C T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10559;SOR=0.82999;LSEQ=GAGATGGGGGTGTCATGTCT;RSEQ=TTAGGGAAAGCAGGAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:395:178,217:198,198:396,395:0.4975:2,2:28.6:1:30.4:1:0.17634:1.21879:35.8:55.429:0.4974:0:1.9 0/1:541:244:121,123:136,159:295,244:0.451:2,2:26.8:1:29.4:1:0.43642:1.15:37.5:33.857:0.4506:0:2.2 +6 29912208 . G C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGGTGTCATGTCTCTTA;RSEQ=GGAAAGCAGGAGCCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:862:0:0,0:403,459:862,0:0:2,0:28.5:1:31.9:1:1:0:38:46.889:1:0:1 0/1:588:22:16,6:264,299:563,22:0.0374:2,2:28.7:1:30.2:1:0.02743:3.01:34:21:0.0365:0:2.4 +6 29912227 . TGGA T 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.02636;SOR=1.24341;LSEQ=AGGGAAAGCAGGAGCCTCTC;RSEQ=GACCTTTAGCAGGGTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1150:369:173,196:369,411:780,369:0.3209:2,2:26.7:1:32.2:1:0.89945:1.01716:37.4:183.5:0.3219:0.0417:1.5 0/1:816:302:152,150:241,271:512,302:0.3701:2,2:25.9:1:30.7:1:0.38413:1.14:40.3:604:0.3747:0.0515:1.7 +6 29912234 . C G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.48302;LSEQ=GCAGGAGCCTCTCTGGAGAC;RSEQ=TTTAGCAGGGTCAGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1219:233:104,129:474,510:984,233:0.1911:2,2:26.4:1:31.7:1:0.3436:1.15269:39.6:466:0.1935:0:2.5 0/1:869:89:34,55:389,388:777,89:0.1024:2,2:24.2:1:31:1:0.04343:1.62091:37.6:88:0.1023:0:2.7 +6 29912280 . T C 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5211;SOR=1.05859;LSEQ=TTCCCCTCTTTTCCCAGAGC;RSEQ=GTCTTCCCAGCCCACCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1271:561:272,289:349,359:708,561:0.4414:2,2:29.2:1:30.7:1:0.77774:1.03289:38:111.2:0.4427:0:2.5 0/1:977:445:231,214:266,249:515,445:0.4555:2,2:27.8:1:29.9:1:0.94843:1.01:36.7:88:0.4541:0:2.2 +6 29912297 . A G 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTGTCTTCCCAGCCCACC;RSEQ=TCCCCATCGTGGGCATCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1174:0:0,0:571,601:1172,0:0:2,0:25:1:30.5:1:1:0:42.7:44.077:1:0:1.1 0/1:919:19:12,7:462,438:900,19:0.0207:2,2:31.3:1:30:1:0.35888:1.62:23.8:38:0.0211:0:2.4 +6 29912315 . A C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00024;SOR=0.52416;LSEQ=CCATCCCCATCGTGGGCATC;RSEQ=TTGCTGGCCTGGTTCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1016:111:46,65:446,458:904,111:0.1093:2,2:19.9:1:32.1:1:0.13123:1.37558:26.8:110:0.111:0:3.5 0/1:828:50:24,26:394,384:778,50:0.0604:2,2:21.6:1:30.8:1:0.77135:1.1114:25.4:49:0.06:0:3.7 +6 29912326 . G A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33067;LSEQ=GTGGGCATCATTGCTGGCCT;RSEQ=GTTCTCCTTGGAGCTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:943:138:65,73:386,418:804,138:0.1463:2,2:14.6:1:29.6:1:0.85421:1.03707:28:45:0.1453:0:3.4 0/1:802:43:23,20:383,375:758,43:0.0536:2,2:13.4:1:27.7:1:0.75529:1.13:27.6:20.5:0.0519:0:3.3 +6 29912333 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.67023;LSEQ=TCATTGCTGGCCTGGTTCTC;RSEQ=TTGGAGCTGTGATCACTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:941:193:81,112:355,393:748,193:0.2051:2,2:14.3:1:30.2:1:0.19519:1.24872:23.3:31.167:0.2026:0:3.8 0/1:810:244:118,126:280,286:566,244:0.3012:2,2:21.8:1:29.7:1:0.81831:1.04536:26.4:488:0.3031:0:3 +6 29912345 . A T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17435;LSEQ=TGGTTCTCCTTGGAGCTGTG;RSEQ=TCACTGGAGCTGTGGTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:887:70:27,43:368,449:817,70:0.0789:2,2:8.2:1:28.8:1:0.31812:1.3049:26.7:34:0.0781:0:4.9 0/1:816:12:6,6:390,413:803,12:0.0147:2,2:10.4:1:27.8:1:1:1.06:25.3:24:0.0149:0:4.8 +6 29912348 . A G 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=0.52537;LSEQ=TTCTCCTTGGAGCTGTGATC;RSEQ=CTGGAGCTGTGGTCGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:870:116:41,75:347,407:754,116:0.1333:2,2:17.4:1:30.9:1:0.03501:1.55881:27.4:115:0.1333:0:4.5 0/1:816:61:29,32:358,394:752,61:0.0748:2,2:26.6:1:30:1:1:1.00262:25.4:60:0.0746:0:4.1 +6 29912368 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.10082;LSEQ=ACTGGAGCTGTGGTCGCTGC;RSEQ=GTGATGTGGAGGAGGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:938:154:47,107:359,424:783,154:0.1642:2,2:21.1:1:30.4:1:5e-04:1.92627:33.8:50.333:0.164:0:4.3 0/1:859:251:109,142:280,328:608,251:0.2922:2,2:24.8:1:29.6:1:0.49825:1.11197:36.9:34.857:0.2888:0:3 +6 29912373 . T G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.23999;LSEQ=AGCTGTGGTCGCTGCCGTGA;RSEQ=GTGGAGGAGGAAGAGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:937:85:22,63:384,468:852,85:0.0907:2,2:22.2:1:31.4:1:0.00079:2.34754:35.6:84:0.0916:0:4.9 0/1:856:20:6,14:377,459:836,20:0.0234:2,2:19.9:1:28.8:1:0.25506:1.91509:34.9:9:0.0214:0:4.9 +6 29912386 . G C 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCGTGATGTGGAGGAGGAA;RSEQ=AGCTCAGGTGGAGAAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:985:0:0,0:411,572:983,0:0:2,0:25.6:1:32.5:1:1:0:54.7:64.533:0.9979:0:1 0/1:878:69:32,37:349,456:805,69:0.0786:2,2:26.4:1:32:1:0.7046:1.13:51.5:138:0.0793:0:2.1 +6 29912398 . A GGT 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0.25489;LSEQ=GGAGGAGGAAGAGCTCAGGT;RSEQ=GAAGGGGTGAAGGGTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:967:106:28,78:366,493:859,106:0.1096:2,2:33.6:1:31.5:1:0.00158:2.06664:34.5:212:0.1122:0.0031:4.6 0/1:855:26:9,17:358,469:827,26:0.0304:2,2:31.7:1:30.6:1:0.42649:1.44124:33.9:52:0.0309:0.0035:4.6 +6 29912405 . G A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00743;SOR=2.27538;LSEQ=AGAGCTCAGGTGGAGAAGGG;RSEQ=TGAAGGGTGGGGTCTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:916:16:5,11:368,532:900,16:0.0175:2,2:39.4:1:30.9:1:0.60918:1.52114:38.4:32:0.0178:0:5.3 0/1:797:31:10,21:329,434:763,31:0.0389:2,2:34.6:1:29.8:1:0.26917:1.59104:33.3:62:0.0394:0:4.6 +6 29912410 . G A 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=81.26417;LSEQ=TCAGGTGGAGAAGGGGTGAA;RSEQ=GGTGGGGTCTGAGATTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:880:1:1,0:352,527:879,1:0.0011:2,0:1:0:25:0:0.40114:0:60:2:0.0012:0:1 0/1:755:64:23,41:293,397:690,64:0.0848:2,2:24.7:1:29.7:1:0.35487:1.31516:60:63:0.0848:0:1.2 +6 29912413 . TG T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.07801;SOR=0.78792;LSEQ=GGTGGAGAAGGGGTGAAGGG;RSEQ=GGGTCTGAGATTTCTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:848:169:48,121:286,392:678,169:0.1993:2,2:32.3:1:32.4:1:0.0011:1.8379:34.7:338:0.2024:0.0012:4.2 0/1:732:120:41,79:264,346:610,120:0.1639:2,2:29.2:1:30.7:1:0.06879:1.46942:35.2:119:0.1653:0.0096:3.7 +6 29912451 . C A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17434;SOR=0.75531;LSEQ=GTCTCACTGAGGGTTCCAAG;RSEQ=CCCAGCTAGAAATGTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:81:20,61:139,266:405,81:0.1663:2,2:16.3:1:30.4:1:0.119:1.59235:36.5:162:0.1698:0:4.6 0/1:359:47:13,34:108,204:312,47:0.1309:2,2:16:1:28.9:1:0.40955:1.38341:36.7:46:0.1322:0:4.5 +6 29912457 . C G 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08272;SOR=0.66382;LSEQ=CTGAGGGTTCCAAGCCCCAG;RSEQ=TAGAAATGTGCCCTGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:67:18,49:121,248:369,67:0.1533:2,2:12.7:1:31.6:1:0.39359:1.32735:35:66:0.1538:0:4.8 0/1:317:34:10,24:97,186:283,34:0.1073:2,2:14.9:1:31.6:1:0.70185:1.25073:32.9:68:0.1086:0:4.8 +6 29912463 . A G 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75099;SOR=0.87119;LSEQ=GTTCCAAGCCCCAGCTAGAA;RSEQ=TGTGCCCTGTCTCATTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:26:5,21:112,253:365,26:0.0665:2,2:10.1:1:32.5:1:0.27143:1.85668:30.1:52:0.0675:0:5.3 0/1:291:17:4,13:88,186:274,17:0.0584:2,2:11.5:1:32.1:1:0.59531:1.53553:28:34:0.0586:0:5.4 +6 29912473 . T C 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.57795;SOR=0.76328;LSEQ=CCAGCTAGAAATGTGCCCTG;RSEQ=CTCATTACTGGGAAGCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:21:2,19:64,218:282,21:0.0689:2,2:8.3:1:32.4:1:0.26983:2.78205:29.7:42:0.07:0:5.2 0/1:206:11:2,9:49,146:195,11:0.0534:2,2:9.3:1:31:1:1:1.50747:28.3:22:0.0542:0:5.5 +6 29912477 . A G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96869;LSEQ=CTAGAAATGTGCCCTGTCTC;RSEQ=TTACTGGGAAGCACCGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:12:0,12:51,196:247,12:0.0463:2,0:8.3:1:32.8:1:0.13136:0:25.5:24:0.0467:0:5.4 0/1:178:8:2,6:42,128:170,8:0.0449:2,2:7.8:1:31.8:1:1:1.02:25.5:16:0.0455:0:5.8 +6 29912493 . G T 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=93.67092;LSEQ=TCTCATTACTGGGAAGCACC;RSEQ=TCCACAATCATGGGCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:0,1:19,152:171,1:0.0058:2,0:29:0:32:0:1:0:60:2:0.0058:0:1 0/1:104:37:6,31:3,41:44,37:0.3558:2,2:22.6:1:29.5:1:0.28802:2.61:54.2:36:0.3495:0:2.3 +6 29912510 . T G 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCGTCCACAATCATGGGCC;RSEQ=ACCCAGTCTGGGCCCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:9,140:149,0:0:2,0:26:1:28.7:1:1:0:59.4:73.5:1:0:0.1 0/1:66:31:1,30:0,35:35,31:0.4697:1,1:26.5:1:31.4:1:0.4697:0:46:62:0.4697:0:3 +6 29912517 . T C 160 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=89.42854;LSEQ=ACAATCATGGGCCTACCCAG;RSEQ=CTGGGCCCTGTGTGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:11,125:136,2:0.0145:2,2:10:1:31.5:1:0.16693:10.92:28.5:4:0.015:0:2 1/0:59:34:1,33:0,25:25,34:0.5763:1,1:22.4:1:31.6:1:1:0:45.1:68:0.5763:0:2.9 +6 29912594 . C T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70296;SOR=1.35801;LSEQ=CAGATTTATCACCTTGATTA;RSEQ=GGCGGTGATGGGACCTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:11:8,3:30,25:55,11:0.1667:2,2:22.9:1:30.9:1:0.33076:2.20:33.4:22:0.1667:0:3.1 0/1:14:3:2,1:2,9:11,3:0.2143:2,2:31.3:1:31.7:1:0.17582:7.30:41.7:6:0.2308:0:3.7 +6 29912595 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0046;SOR=Inf;LSEQ=AGATTTATCACCTTGATTAC;RSEQ=GCGGTGATGGGACCTGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:40,25:65,0:0:2,0:21.7:1:30.9:1:1:0:51.2:64:1:0:0.9 0/1:14:3:2,1:2,9:11,3:0.2143:2,2:19.3:1:31.7:1:0.17582:7.30:34.7:6:0.25:0:4.3 +6 29912649 . G C 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00085;SOR=Inf;LSEQ=TCACAGGGGAAGGTCCCTGA;RSEQ=GACAGACCTCAGGAGGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:71,13:84,0:0:2,0:25.9:1:33.3:1:1:0:49.4:83:1:0:1.3 0/1:29:5:3,2:22,2:24,5:0.1724:2,2:13.6:1:31.2:1:0.12652:6.60213:36.2:10:0.1786:0:4.6 +6 29912652 . CAGA C 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11284;SOR=0;LSEQ=CAGGGGAAGGTCCCTGAGGA;RSEQ=CCTCAGGAGGGCTATTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:9:8,1:47,9:56,9:0.09:2,2:8.3:1:30:1:1:1.52:43.2:18:0.0909:0.08:3.1 0/0:37:0:0,0:22,2:24,0:0:2,0:20.6:1:30.2:1:1:0:55:48:0.6486:0:1.2 +6 29912653 . AGACC CT 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.00591;LSEQ=AGGGGAAGGTCCCTGAGGAC;RSEQ=TCAGGAGGGCTATTGGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:35:29,6:47,9:56,35:0.35:2,2:23.1:1:32.4:1:1:1.07953:35.6:70:0.3535:0.02:2.1 0/1:37:13:11,2:22,2:24,13:0.3514:2,2:19.4:1:31.3:1:0.6016:1.96044:34.8:26:0.3514:0.0811:2.5 +6 29912656 . C T 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00175;SOR=Inf;LSEQ=GGAAGGTCCCTGAGGACAGA;RSEQ=CTCAGGAGGGCTATTGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:58,11:69,0:0:2,0:21.2:1:31.9:1:1:0:56:68:1:0:0.6 0/1:29:5:3,2:24,0:24,5:0.1724:1,2:12.2:1:28.6:1:0.02463:0:36.2:10:0.1724:0:4.6 +6 29912668 . TA GG 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32135;SOR=0.69425;LSEQ=AGGACAGACCTCAGGAGGGC;RSEQ=TTGGTCCAGGACCCACACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:59:52,7:59,10:69,59:0.4538:2,2:18.9:1:31.4:1:0.79565:1.26:35.6:118:0.4683:0.0462:2.1 0/1:52:19:17,2:29,0:29,19:0.3654:1,2:18.1:1:30.4:1:0.1516:0:35.1:38:0.3725:0.0385:2.1 +6 29912680 . A G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00696;SOR=Inf;LSEQ=AGGAGGGCTATTGGTCCAGG;RSEQ=CCCACACCTGCTTTCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:133,11:144,0:0:2,0:22.6:1:30.1:1:1:0:47.2:35:1:0:1 0/1:60:4:3,1:54,2:56,4:0.0667:1,2:29.3:1:31.5:1:0.18995:8.30053:30.5:8:0.0667:0:5 +6 29912687 . C T 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00107;SOR=Inf;LSEQ=CTATTGGTCCAGGACCCACA;RSEQ=CTGCTTTCTTCATGTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:141,9:150,0:0:2,0:24.5:1:32.3:1:1:0:45.8:49:1:0:1 0/1:73:6:5,1:65,2:67,6:0.0822:1,2:22.5:1:30.2:1:0.22977:6.18583:32.2:12:0.0822:0:4 +6 29912713 . C T 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=TTCTTCATGTTTCCTGATCC;RSEQ=GCCCTGGGTCTGCAGTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:236,9:245,0:0:1,0:24.4:1:31.7:1:1:0:43.9:244:1:0:0.9 0/1:129:8:7,1:116,5:121,8:0.062:1,2:25.8:1:30.8:1:0.32433:3.26551:37.9:16:0.0625:0:3.3 +6 29912754 . G A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05525;SOR=1.40551;LSEQ=CATTTCTGGAAACTTCTCTG;RSEQ=GGTCCAAGACTAGGAGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:478:109:94,15:286,82:368,109:0.228:2,2:28.5:1:30.1:1:0.05792:1.79:32.2:53.5:0.2286:0:2.1 0/1:276:81:66,15:142,53:195,81:0.2935:2,2:31.3:1:29.1:1:0.16702:1.64:33.8:162:0.2956:0:2.5 +6 29912766 . A T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01006;SOR=1.55755;LSEQ=CTTCTCTGGGGTCCAAGACT;RSEQ=GGAGGTTCCTCTAGGACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:102:86,16:339,134:473,102:0.1774:2,2:30.9:1:30.6:1:0.00875:2.12:32:50:0.1779:0:2.1 0/1:330:83:64,19:170,77:247,83:0.2515:2,2:32.2:1:29.7:1:0.16455:1.52:33.7:40.5:0.2508:0:2.4 +6 29912767 . G C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00091;SOR=0.48537;LSEQ=TTCTCTGGGGTCCAAGACTA;RSEQ=GAGGTTCCTCTAGGACCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:578:95:72,23:354,127:481,95:0.1644:2,2:27.5:1:31.8:1:0.70279:1.12:38.2:190:0.1664:0:1.6 0/1:333:29:19,10:216,87:303,29:0.0871:2,2:28.7:1:28.1:1:0.52522:1.30565:39.8:8.667:0.0793:0:1.6 +6 29912796 . G A 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.08515;LSEQ=TCTAGGACCTTAAGGCCCTG;RSEQ=CTCCTTTCTGGTATCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:742:2:1,1:472,263:735,2:0.0027:2,2:10.5:1:29.5:1:1:1.79308:46.5:4:0.0028:0:1 0/1:485:32:23,9:275,177:452,32:0.066:2,2:21.3:1:27.8:1:0.26103:1.64:32.5:31:0.0653:0:3.1 +6 29912830 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=10.44917;LSEQ=TCTCACAGGACATTTTCTTC;RSEQ=CACAGATAGAAAAGGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:852:53:28,25:447,352:799,53:0.0622:2,2:13.1:1:31.1:1:0.67077:1.13366:27.1:52:0.0628:0:2.3 0/1:566:232:122,110:180,152:332,232:0.4099:2,2:24.6:1:29.9:1:0.7318:1.0676:30.1:57:0.4093:0:1.3 +6 29912935 . C T 159 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=11.09426;LSEQ=TTGGGAGCCCATGGGGGAGC;RSEQ=CACCCACCTCACAATTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:15:8,7:379,347:726,15:0.0202:2,2:1.4:1:28.3:1:1:1.05:23.3:30:0.0207:0:2.9 0/1:252:47:22,25:95,110:205,47:0.1865:2,2:8:1:28.7:1:1:1.02:29.9:94:0.1903:0:1.8 +6 29912938 . C A 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00149;SOR=17.73774;LSEQ=GGAGCCCATGGGGGAGCCCA;RSEQ=CCACCTCACAATTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:754:1:1,0:399,352:751,1:0.0013:2,0:1:0:29:0:1:0:49:2:0.0013:0:1 0/1:260:6:1,5:119,135:254,6:0.0231:2,2:26.8:1:30.5:1:0.2217:4.38659:23.3:12:0.0235:0:3.2 +6 29912944 . T C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.39427;LSEQ=CATGGGGGAGCCCACCCACC;RSEQ=CACAATTCCTCCTCTAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:760:67:39,28:364,328:692,67:0.0882:2,2:6.3:1:30.4:1:0.44213:1.25:23.1:32.5:0.087:0:2.7 0/1:283:70:36,34:95,118:213,70:0.2473:2,2:7.7:1:30.5:1:0.33634:1.31:25:140:0.2491:0:2 +6 29912961 . G T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72604;SOR=0.89447;LSEQ=ACCTCACAATTCCTCCTCTA;RSEQ=CCACATCTTCTGTGGGATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:879:63:37,26:441,375:816,63:0.0717:2,2:16.1:1:30.5:1:0.51311:1.21:25.3:62:0.0717:0:2.2 0/1:418:27:16,11:206,185:391,27:0.0646:2,2:12.4:1:28.8:1:0.55462:1.31:27.5:26:0.0633:0:2 +6 29912968 . C G 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATTCCTCCTCTAGCCACAT;RSEQ=TTCTGTGGGATCTGACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:911:0:0,0:500,409:909,0:0:2,0:23:1:32.8:1:1:0:52.1:128.857:0.9978:0:0.6 0/1:486:16:9,7:260,209:469,16:0.0329:2,2:10.8:1:31:1:1:1.03:30.4:32:0.0334:0:3.8 +6 29913001 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.58518;LSEQ=TGACCAGGTTCTGTTTTTGT;RSEQ=CTACCCCAGGCAGTGACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1270:264:155,109:547,459:1006,264:0.2079:2,2:27.4:1:32:1:0.21148:1.19:34:65:0.2077:0:4.2 0/1:834:111:58,53:405,318:723,111:0.1331:2,2:26.2:1:29.7:1:0.47399:1.16358:33.5:14.857:0.1273:0:4.5 +6 29913007 . C T 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTCTGTTTTTGTTCTACC;RSEQ=CAGGCAGTGACAGTGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1345:0:0,0:747,598:1345,0:0:2,0:25.9:1:31.3:1:1:0:49.2:63.048:1:0:1.4 0/1:900:40:23,17:481,379:860,40:0.0444:2,2:26.9:1:30:1:0.87219:1.07:35.4:80:0.0448:0:2.8 +6 29913037 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.54668;LSEQ=ACAGTGCCCAGGGCTCTGAT;RSEQ=TGTCCCTCACAGCTTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1808:486:266,220:680,641:1321,486:0.2688:2,2:24.2:1:29.8:1:0.22234:1.14:45.3:120.5:0.2699:0:5.1 0/1:1285:215:109,106:579,489:1068,215:0.1673:2,2:24.6:1:28.6:1:0.36868:1.15133:44.7:214:0.1677:0:5.2 +6 29913042 . C T 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.1349;LSEQ=GCCCAGGGCTCTGATGTGTC;RSEQ=CTCACAGCTTGTAAAGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1833:763:406,357:545,524:1069,763:0.4163:2,2:24.7:1:31:1:0.36754:1.09:43.2:49.867:0.4144:0:4.9 1/0:1314:908:483,425:217,189:406,908:0.691:2,2:24.7:1:29.3:1:0.95233:1.01027:44.4:63.857:0.6888:0:3.6 +6 29913067 . T C 308 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.88602;SOR=0.98718;LSEQ=CAGCTTGTAAAGGTGAGAGC;RSEQ=TGGAGGACCTAATGTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1918:777:374,403:536,559:1095,777:0.4051:2,2:28.2:1:32.1:1:0.74266:1.0332:48.4:58.769:0.4038:0:5.3 0/1:1398:562:271,291:425,411:836,562:0.402:2,2:27.3:1:30.8:1:0.35388:1.11029:48.9:55.2:0.4003:0:4.8 +6 29913070 . G C 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CTTGTAAAGGTGAGAGCTTG;RSEQ=AGGACCTAATGTGTGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1888:0:0,0:822,834:1656,0:0:2,0:26.4:1:31.7:1:1:0:57:91:0.9994:0:1.8 0/1:1402:76:34,42:664,662:1326,76:0.0542:2,2:31.9:1:31.3:1:0.40951:1.23883:43.7:37:0.0534:0:5.8 +6 29913074 . A G 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.48356;LSEQ=TAAAGGTGAGAGCTTGGAGG;RSEQ=CCTAATGTGTGTTGGGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1857:751:353,398:540,562:1102,751:0.4044:2,2:29.2:1:31.6:1:0.42088:1.0833:49.5:56.769:0.4059:0:5.3 1/0:1373:862:435,427:250,252:502,862:0.6278:2,2:27.7:1:30.8:1:0.82249:1.03:51:52.875:0.6304:0:4.3 +6 29913078 . A G 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.61659;LSEQ=GGTGAGAGCTTGGAGGACCT;RSEQ=ATGTGTGTTGGGTGTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1843:753:351,402:527,560:1087,753:0.4086:2,2:28.8:1:32.2:1:0.4477:1.07776:49.8:93.125:0.4107:0:5.2 1/0:1376:886:444,442:241,249:490,886:0.6439:2,2:27.2:1:31:1:0.77835:1.04:51.5:62.286:0.6421:0:4.3 +6 29913098 . C A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.46549;LSEQ=AATGTGTGTTGGGTGTTGGG;RSEQ=GGAACAGTGGACACAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1697:240:92,148:646,808:1454,240:0.1414:2,2:23.7:1:31:1:0.07942:1.28597:50:47:0.1412:0:5 0/1:1250:89:41,48:461,541:1002,89:0.0712:2,2:22.7:1:29.4:1:1:1.00:50.4:43.5:0.0706:0:4.8 +6 29913111 . A G 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.58761;LSEQ=TGTTGGGCGGAACAGTGGAC;RSEQ=CAGCTGTGCTATGGGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1447:383:162,221:427,636:1063,383:0.2647:2,2:26:1:31.3:1:0.46751:1.09:52.5:62.833:0.2636:0:4.7 0/1:1077:188:85,103:372,517:889,188:0.1746:2,2:25.2:1:30.1:1:0.41711:1.15:51.8:46:0.1724:0:4.6 +6 29913135 . G C 203 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTGCTATGGGGTTTCTTT;RSEQ=CATTGGATGTATTGAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:964:0:0,0:337,625:962,0:0:2,0:24.1:1:32:1:1:0:57:52.444:0.9979:0:1.5 0/1:709:105:36,69:237,366:603,105:0.1481:2,2:22.9:1:30.3:1:0.38492:1.24075:55.8:34:0.1457:0:3.6 +6 29913137 . A G 204 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGCTATGGGGTTTCTTTGC;RSEQ=TTGGATGTATTGAGCATGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:942:0:0,0:323,619:942,0:0:2,0:23.9:1:30.5:1:1:0:57:39.957:1:0:1.5 0/1:677:103:39,64:215,359:574,103:0.1521:2,2:25.6:1:30.6:1:1:1.02:59.1:102:0.1529:0:3.1 +6 29913171 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07158;SOR=1.30368;LSEQ=GCATGCGATGGGCTGTTTAA;RSEQ=GTGTGACCCCTCACTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:153:44,109:135,260:395,153:0.2787:2,2:21.2:1:31.7:1:0.26407:1.28569:42.4:37.25:0.2764:0:3.8 0/1:391:131:60,71:90,170:260,131:0.335:2,2:19.5:1:30:1:0.03643:1.59:43.6:31.75:0.3325:0:3.5 +6 29913179 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00737;SOR=0.58241;LSEQ=TGGGCTGTTTAAGGTGTGAC;RSEQ=CCTCACTGTGATGGATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:94:30,64:139,264:403,94:0.1891:2,2:27.6:1:30.8:1:0.71709:1.12301:38.6:30.333:0.19:0:4.4 0/1:343:41:18,23:118,184:302,41:0.1195:2,2:27:1:30.3:1:0.61085:1.22:39:82:0.1224:0:4.3 +6 29913191 . TG CA 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08488;SOR=1.37684;LSEQ=GGTGTGACCCCTCACTGTGA;RSEQ=GATATGAATTTGTTCATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:84:27,57:160,230:390,84:0.1732:2,2:27.8:1:31.7:1:0.14112:1.46744:37:168:0.1761:0.0454:3.5 0/1:326:73:36,37:109,139:248,73:0.2239:2,2:27.1:1:30.9:1:0.42568:1.24:37.4:146:0.2281:0.0491:3.3 +6 29913197 . T C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2623;SOR=1.21537;LSEQ=ACCCCTCACTGTGATGGATA;RSEQ=GAATTTGTTCATGAATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:96:39,57:173,216:389,96:0.1975:2,2:23.9:1:30.8:1:0.56591:1.17021:35.8:192:0.2013:0:3.3 0/1:343:79:46,33:127,137:264,79:0.2303:2,2:24.2:1:30.3:1:0.12497:1.50:33.8:78:0.2301:0:3 +6 29913201 . T G 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1673;SOR=5.59913;LSEQ=CTCACTGTGATGGATATGAA;RSEQ=TTGTTCATGAATATTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:1:1,0:230,271:501,1:0.002:2,0:45:0:16:0:0.46016:0:39:0:0:0:5 0/1:362:4:3,1:189,169:358,4:0.011:2,2:22.3:1:29.5:1:0.62571:2.68:36.5:8:0.0112:0:3.3 +6 29913266 . G T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38671;LSEQ=TGTGGGACTGAGAGGCAAGA;RSEQ=TTGTTCCTGCCCTTCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:268:131,137:240,232:472,268:0.3622:2,2:31.6:1:30.5:1:0.64641:1.08175:29:28.778:0.3563:0:2 0/1:678:122:55,67:271,285:556,122:0.1799:2,2:30.1:1:29.7:1:0.48488:1.15809:30.7:121:0.1814:0:1.7 +6 29913298 . A T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18816;LSEQ=CTTCCCTTTGTGACTTGAAG;RSEQ=ACCCTGACTTTGTTTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:683:209:80,129:197,277:474,209:0.306:2,2:23.7:1:28.3:1:0.44716:1.14657:33.9:103.5:0.309:0:2.2 0/1:575:44:19,25:217,314:531,44:0.0765:2,2:27.2:1:27.5:1:0.75296:1.10:34.1:43:0.0758:0:2.3 +6 29913344 . G T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00046;SOR=0.52128;LSEQ=ACCTGCATGTGTCTGTGTTC;RSEQ=TGTAGGCATAATGTGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:121:16,105:44,204:248,121:0.3193:2,2:25:1:30.5:1:0.29609:1.41416:49.2:59.5:0.3182:0:2 0/1:270:53:13,40:42,155:197,53:0.1963:2,2:24.5:1:29.2:1:0.70882:1.20:52.4:52:0.1948:0:1.7 +6 29913353 . T C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26684;SOR=0.46125;LSEQ=TGTCTGTGTTCGTGTAGGCA;RSEQ=AATGTGAGGAGGTGGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:10:0,10:36,288:324,10:0.0299:2,0:28.6:1:31.6:1:0.60836:0:34.2:20:0.0302:0:7.1 0/1:214:3:0,3:36,175:211,3:0.014:2,0:19.3:1:30.7:1:1:0:36.7:6:0.0141:0:6.7 +6 29913355 . A G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38775;SOR=0.46777;LSEQ=TCTGTGTTCGTGTAGGCATA;RSEQ=TGTGAGGAGGTGGGGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:10:0,10:30,283:313,10:0.031:2,0:30.2:1:32.2:1:0.60724:0:34.2:20:0.0314:0:7.1 0/1:204:3:0,3:31,169:200,3:0.0147:2,0:21.3:1:30.7:1:1:0:36.7:6:0.0148:0:6.7 +6 29913367 . G A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.58739;SOR=0.64445;LSEQ=TAGGCATAATGTGAGGAGGT;RSEQ=GGGAGACCACCCCACCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:11:0,11:9,229:238,11:0.044:1,0:33:1:31.5:1:1:0:34.8:22:0.0444:0:6.8 0/1:139:4:0,4:7,128:135,4:0.0288:2,0:27:1:31.3:1:1:0:38:8:0.0292:0:6 +6 29913374 . C G 114 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=24.02889;LSEQ=AATGTGAGGAGGTGGGGAGA;RSEQ=CACCCCACCCCCATGTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:1:0,1:2,210:212,1:0.0047:1,0:18:0:27:0:1:0:60:2:0.0049:0:3 0/1:117:12:0,12:2,103:105,12:0.1026:1,0:23.8:1:31.8:1:1:0:51.5:24:0.1034:0:1.6 +6 29913377 . C T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.43382;SOR=0.59417;LSEQ=GTGAGGAGGTGGGGAGACCA;RSEQ=CCCACCCCCATGTCCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:12:0,12:2,192:194,12:0.0583:1,0:33.4:1:30.3:1:1:0:36.9:24:0.0591:0:6.6 0/1:113:4:0,4:0,109:109,4:0.0354:1,0:32:1:29:1:1:0:38:8:0.0374:0:6 +6 29913383 . C T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.58981;SOR=0.615;LSEQ=AGGTGGGGAGACCACCCCAC;RSEQ=CCCATGTCCACCATGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:12:0,12:2,173:175,12:0.0642:1,0:34.2:1:30.7:1:1:0:36.9:24:0.0659:0:6.6 0/1:99:4:0,4:0,94:94,4:0.0404:1,0:35:1:28.8:1:1:0:38:8:0.0417:0:6 +6 29913386 . C G 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=Inf;LSEQ=TGGGGAGACCACCCCACCCC;RSEQ=ATGTCCACCATGACCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:2,184:186,0:0:1,0:25.2:1:32.7:1:1:0:56:61:1:0:0.9 0/1:94:8:0,8:0,85:85,8:0.0851:1,0:29.6:1:29.9:1:1:0:58.4:16:0.087:0:1.6 +6 29913396 . A C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.84565;LSEQ=ACCCCACCCCCATGTCCACC;RSEQ=TGACCCTCTTCCCACGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:12:0,12:3,141:144,12:0.0769:1,0:28.8:1:34.4:1:1:0:38:24:0.0774:0:6.1 0/1:76:5:0,5:0,71:71,5:0.0658:1,0:30.4:1:32:1:1:0:42.4:10:0.0667:0:5.4 +6 29913430 . C T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGCTGACCTGTGCTCCCTC;RSEQ=CCAATCATCTTTCCTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:1,74:75,0:0:1,0:21.8:1:31.4:1:1:0:55.6:74:1:0:0.8 0/1:34:11:0,11:0,23:23,11:0.3235:1,0:19.4:1:29.5:1:1:0:57.5:22:0.3333:0:1.9 +6 29913449 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07991;SOR=Inf;LSEQ=CCCCAATCATCTTTCCTGTT;RSEQ=CAGAGAGGTGGGGCTGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:1,51:52,0:0:1,0:24.2:1:31:1:1:0:53.6:51:1:0:0.6 0/1:21:2:0,2:0,19:19,2:0.0952:1,0:11:1:32.5:1:1:0:60:4:0.1:0:1 +6 29913468 . G A 71 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.54391;LSEQ=TCCAGAGAGGTGGGGCTGAG;RSEQ=TGTCTCCATCTCTGTCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:0,5:1,34:35,5:0.125:1,0:30:1:30.6:1:1:0:33.8:10:0.1282:0:3 0/1:14:1:0,1:0,13:13,1:0.0714:1,0:28:0:32:0:1:0:60:2:0.0769:0:3 +6 29913483 . T C 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17924;SOR=0;LSEQ=CTGAGGTGTCTCCATCTCTG;RSEQ=CTCAACTTCATGGTGCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:9:1,8:0,28:28,9:0.2432:1,2:21.8:1:31.8:1:0.24324:0:55:18:0.2432:0:1 0/0:8:0:0,0:0,8:8,0:0:0,0:20.9:1:29.1:1:1:0:57:16:1:0:1.8 +6 29913495 . G A 53 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53476;SOR=1.7662;LSEQ=CATCTCTGTCTCAACTTCAT;RSEQ=GTGCACTGAGCTGTAACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:0,27:27,3:0.1:1,0:30.3:1:33.7:1:1:0:25.3:6:0.1:0:3 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:1:0:31:0:1:0:60:2:0.2:0:3 +6 29913518 . C A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGAGCTGTAACTTCTT;RSEQ=CTTCCCTATTAAAATTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:0,4:0,21:21,4:0.16:1,0:9.8:1:30.3:1:1:0:40.3:8:0.1739:0:3.3 0/0:1:0:0,0:0,1:1,0:0:0,0:34:0:32:0:1:0:60:2:1:0:0 +6 29913526 . A G 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTAACTTCTTCCTTCCCT;RSEQ=TTAAAATTAGAACCTTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:0,3:0,19:19,3:0.1364:1,0:13:1:32.3:1:1:0:46.7:6:0.1364:0:3.3 0/0:1:0:0,0:0,1:1,0:0:0,0:26:0:18:0:1:0:60:0:0:0:0 +6 29913542 . T G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTATTAAAATTAGAACCT;RSEQ=AGTATAAATTTACTTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:32.5:1:31.5:1:1:0:60:4:0.1429:0:3 0/0:1:0:0,0:0,1:1,0:0:0,0:10:0:29:0:1:0:60:2:1:0:0 +6 29915102 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACACTGGGGCTTACAGA;RSEQ=GCCAGGGAATAAACCTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:30.5:1:30.5:1:1:1:60:4:0.5:0:2.5 +6 29915122 . T C 61 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCAGGGAATAAACCTAGA;RSEQ=ACATTATGCCCCATGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:16.3:1:30.5:1:1:0:41.5:8:1:0:2.5 +6 29915124 . C A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGGAATAAACCTAGATA;RSEQ=ATTATGCCCCATGGTGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:22:1:29:1:1:1:23:4:0.5:0:2.5 +6 29917701 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TTCCCTTGTCCGTTGTGTGA;RSEQ=CGGAATCATCCAGCAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:31:1:32.5:1:1:0:60:8:1:0:0.8 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:26.5:1:28.5:1:1:0:29:4:0.6667:0:2.5 +6 29917703 . G A 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.81007;LSEQ=CCCTTGTCCGTTGTGTGAGC;RSEQ=GAATCATCCAGCAACCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:29.5:1:30.5:1:1:0:60:4:0.5:0:1.5 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:28.5:1:28.5:1:1:0:29:4:0.6667:0:2.5 +6 29917801 . G A 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14256;SOR=0;LSEQ=ACTCCTAGGTAATGTCCCAC;RSEQ=TCTCTGCTTCTGTGCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:4,1:21,0:21,5:0.1923:1,2:27.4:1:30:1:0.19231:0:49.2:10:0.2083:0:1.4 0/0:14:0:0,0:14,0:14,0:0:1,0:24.5:1:29.6:1:1:0:59.4:28:1:0:0.2 +6 29917881 . C T 125 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=22.96964;LSEQ=AGTTGTTCCCAGCCAGTGAC;RSEQ=GGTCACAGCAAGCACACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:1,0:63,36:99,1:0.01:2,0:5:0:34:0:1:0:60:2:0.0102:0:5 0/1:100:19:14,5:52,29:81,19:0.19:2,2:20.7:1:29.5:1:0.59208:1.55:59.5:38:0.1939:0:1.1 +6 29917899 . T C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00205;SOR=0.27961;LSEQ=ACCGGTCACAGCAAGCACAC;RSEQ=AAGGCAGGCCATTACTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:23:13,10:59,41:100,23:0.187:2,2:25:1:30.1:1:0.81942:1.10602:60:22:0.1849:0:1 0/1:133:8:7,1:73,52:125,8:0.0602:2,2:32.3:1:31.8:1:0.1445:4.94:60:16:0.0615:0:1 +6 29917940 . G A 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=GACATGGGACTCCTCTGATG;RSEQ=CCAAATGTGGCTCCAGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:52,69:121,0:0:2,0:26.6:1:31.5:1:1:0:59.9:120:1:0:0.2 0/1:128:14:8,6:48,66:114,14:0.1094:2,2:27.1:1:28.9:1:0.39313:1.82:60:28:0.112:0:1 +6 29917941 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23897;SOR=0;LSEQ=ACATGGGACTCCTCTGATGG;RSEQ=CAAATGTGGCTCCAGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:51,68:119,2:0.0165:2,2:33.5:1:31:1:1:1.33:60:4:0.0167:0:1.5 0/0:126:0:0,0:56,70:126,0:0:2,0:27.5:1:30.4:1:1:0:60:125:1:0:0.4 +6 29917974 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23132;SOR=0;LSEQ=CAGGACTCCTCCATGCCCTT;RSEQ=CTCAACTCTCCTTAGACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:21,46:67,2:0.0286:2,2:17:1:31.5:1:0.53922:2.16:51.5:4:0.029:0:3.5 0/0:75:0:0,0:25,50:75,0:0:2,0:21.9:1:29.7:1:1:0:60:74:1:0:0.2 +6 29918022 . C T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11742;SOR=Inf;LSEQ=CTAGGATGCGTCGAACAGAC;RSEQ=TTGTCTCCTTCTGTCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:1,19:20,0:0:1,0:20.6:1:33.5:1:1:0:59.2:40:1:0:0.3 0/1:25:4:0,4:0,21:21,4:0.16:1,0:24.8:1:28:1:1:0:53.8:8:0.16:0:2 +6 29918059 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21053;SOR=Inf;LSEQ=AGCACTTGGGGTCACACTTG;RSEQ=ATCATTGTCTGCCGCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:0,10:10,0:0:0,0:15.8:1:31.9:1:1:0:58.9:20:1:0:0.3 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:27:1:29:0:1:0:47.5:4:0.2222:0:3 +6 29918072 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20588;SOR=Inf;LSEQ=ACACTTGCATCATTGTCTGC;RSEQ=GCCTTTTCCAGGGATTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:23.8:1:29.3:1:1:0:58.6:16:1:0:0.6 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:10.3:1:30.3:1:1:0:51.7:6:0.3333:0:2.3 +6 29918684 . G T 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAGTAAAGAAAAGGAAG;RSEQ=TATTAATGGAATATGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:32:0:1:0:42.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29924822 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCCTGCACTCTGGGACA;RSEQ=TTAAAGGATGTAGTCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:24:1:30:1:1:0:44:4:0.4:0:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:31:0:1:0:36:2:1:0:1 +6 29924833 . T A 48 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGGGACAGTTAAAGGATG;RSEQ=AGTCTCTGAGGGAAAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,1:2,3:0.6:2,0:29.3:1:30.7:1:0.4:0:42:6:0.6:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:43:0:26:0:1:0:36:2:1:0:1 +6 29925086 . T G 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.73779;SOR=1.2499;LSEQ=AAGATTGCCCCAGGTGCCTG;RSEQ=GTCTAGACTGGTGTCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:5:5,0:71,1:72,5:0.0649:1,0:18.6:1:32.6:1:1:0:60:10:0.0649:0:1 0/1:50:4:4,0:45,1:46,4:0.08:1,0:27.5:1:31.3:1:1:0:60:8:0.08:0:1 +6 29925127 . G A 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCTCCCTTCCCCACTTCAG;RSEQ=TGTCCCGTCAATTTTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:140,2:142,0:0:1,0:27.3:1:31.3:1:1:0:60:27.4:1:0:0.5 0/1:112:22:22,0:89,1:90,22:0.1964:1,1:25.4:1:28.1:1:1:0:60:21:0.1892:0:1.1 +6 29925134 . G A 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14578;LSEQ=TTCCCCACTTCAGGTGTCCC;RSEQ=TCAATTTTCAGGATGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:59:58,1:97,3:100,59:0.3711:1,1:26.9:1:31:1:1:1.79:60:118:0.3806:0:1 0/1:127:10:10,0:114,3:117,10:0.0787:1,0:21.2:1:30.8:1:1:0:60:20:0.0794:0:1 +6 29925221 . C CA 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.02579;SOR=1.30369;LSEQ=GACTCTTCCCCTCAGAACCC;RSEQ=AAAGACTCACATGACCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:251:124,127:201,197:398,251:0.3867:2,2:30.8:1:30.2:1:0.80919:1.04494:49.1:30.375:0.3827:0.0324:0.2 0/1:554:250:124,126:151,148:299,250:0.4513:2,2:32.5:1:29.7:1:0.86408:1.03668:50:61.5:0.4522:0.0235:0.2 +6 29925268 . C A 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=61.43431;LSEQ=TCTCTGACCATGAGGCCACC;RSEQ=TGAGGTGCTGGGCTCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:460:1:1,0:165,294:459,1:0.0022:2,0:1:0:25:0:0.36087:0:60:2:0.0022:0:1 0/1:329:39:12,27:98,192:290,39:0.1185:2,2:24.4:1:29.7:1:0.85678:1.14799:51.5:78:0.1207:0:1.3 +6 29925281 . C G 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=GGCCACCCTGAGGTGCTGGG;RSEQ=TCTGGGCTTCTACCCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:94,247:341,0:0:2,0:23.8:1:32.9:1:1:0:47.3:55.833:1:0:0.2 0/1:247:12:1,11:62,173:235,12:0.0486:2,2:30.1:1:30.4:1:0.30555:3.92723:45.9:11:0.0456:0:1 +6 29925331 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60634;SOR=0.66394;LSEQ=TGACCCAGTAGTGGGATGGA;RSEQ=AGGACCAAATGTAGGATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:12:4,8:42,98:140,12:0.0789:2,2:16:1:29.2:1:0.75487:1.17:54:11:0.0748:0:1.7 0/1:93:5:2,3:23,65:88,5:0.0538:2,2:19.6:1:30:1:0.60825:1.87:60:10:0.0543:0:1 +6 29925438 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08012;LSEQ=TCTGGAGAGGAGCAGAGATA;RSEQ=ACATGCCATGTGCAGCACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:105:63,42:131,100:231,105:0.3125:2,2:24.1:1:29.3:1:0.63403:1.14:58.7:104:0.3114:0:1.2 0/1:257:9:6,3:144,104:248,9:0.035:2,2:29.1:1:30:1:0.73902:1.44:56:18:0.0353:0:1 +6 29925456 . C T 129 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.13993;LSEQ=TACACATGCCATGTGCAGCA;RSEQ=GATGGGCTGCCAGAGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:1:0,1:189,169:358,1:0.0028:2,0:1:0:28:0:0.47354:0:60:2:0.0028:0:1 0/1:293:20:11,9:144,129:273,20:0.0683:2,2:31.3:1:30:1:1:1.09:50.4:40:0.069:0:1.2 +6 29925473 . C T 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00214;SOR=0.38742;LSEQ=GCACGATGGGCTGCCAGAGC;RSEQ=CCTCACCCTGAGATGGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:43:21,22:157,158:315,43:0.1201:2,2:32.6:1:31.1:1:1:1.04089:58.9:86:0.1239:0:2.1 0/1:299:15:5,10:143,141:284,15:0.0502:2,2:33:1:28.2:1:0.28959:2.02372:60:14:0.0483:0:1.7 +6 29925500 . G A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00349;SOR=0.41194;LSEQ=CCTGAGATGGGTAAGGAAGG;RSEQ=GATGAGGGGTCATGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:44:20,24:133,159:292,44:0.131:2,2:25.6:1:30:1:1:1.00376:58.9:13.667:0.125:0:2.1 0/1:257:15:4,11:101,141:242,15:0.0584:2,2:24.7:1:29.5:1:0.29095:1.96504:60:30:0.0593:0:1.7 +6 29925533 . AGGAGCCCTTCT A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=1.000;MSILEN=1;SSF=0.01802;SOR=0.29854;LSEQ=TGTCTCTTCTCACGGGAACT;RSEQ=GGAGCCCTTCAGCAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:19:9,10:82,99:181,19:0.095:2,2:30.9:1:33.1:1:1:1.09:57.4:38:0.0974:0.005:1.4 0/1:165:5:0,5:77,83:160,5:0.0303:2,0:35.4:1:31.6:1:0.06147:0:60:10:0.0305:0:1.4 +6 29925558 . AAGGTCAGGG A 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTTCTGGAGCCCTTCAGC;RSEQ=TTTGAGGCCTGATGGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:113,111:224,0:0:2,0:21.8:1:30.8:1:1:0:59.8:43.8:0.9955:0:0.4 0/1:165:23:13,10:74,68:142,23:0.1394:2,2:29.6:1:30.4:1:0.82275:1.19:59.8:46:0.142:0.0242:0.7 +6 29925584 . C G 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00451;SOR=Inf;LSEQ=AGGGTTTGAGGCCTGATGGT;RSEQ=AGGGCCCCTCACGTTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:164,128:292,0:0:2,0:24:1:32.2:1:1:0:60:57.4:1:0:0.5 0/1:254:7:5,2:132,113:245,7:0.0276:2,2:16.6:1:30.7:1:0.45927:2.13:60:14:0.0278:0:2.1 +6 29925596 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.112;SOR=Inf;LSEQ=CTGATGGTCAGGGCCCCTCA;RSEQ=GTTCCCCTCCTTTCTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:174,142:316,0:0:2,0:27.4:1:31.2:1:1:0:59.9:62.2:1:0:0.6 0/1:296:3:1,2:158,135:293,3:0.0101:2,2:21.3:1:26.7:1:0.59781:2.3342:58.3:6:0.0102:0:1.7 +6 29925636 . G T 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=4.6225;LSEQ=GCTGTCTTCCCAGCCCACCA;RSEQ=CCCCATCATGGGCATCGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:347:186:86,100:71,90:161,186:0.536:2,2:28.4:1:29.8:1:0.74583:1.09:59.7:25.571:0.5375:0:1.1 1/1:324:273:127,146:23,28:51,273:0.8426:2,2:27.1:1:28.9:1:0.87952:1.06:58.8:33.125:0.8439:0:1.2 +6 29925653 . G A 57 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19091;SOR=4.59016;LSEQ=CCAGCCCCATCATGGGCATC;RSEQ=TTACTGTCCTGGTTGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:1:1,0:122,184:306,1:0.0033:2,0:1:0:27:0:0.40065:0:45:2:0.0033:0:2 0/1:270:4:2,2:113,153:266,4:0.0148:2,2:34:1:28.8:1:1:1.35:60:8:0.015:0:2 +6 29925682 . TT GG 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.70142;SOR=1.36299;LSEQ=CTGGTTGTTCTTGGTGCTGT;RSEQ=TCACCAGAGCTGTGGTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:3:2,1:42,149:191,3:0.0155:2,2:29.3:1:33.8:1:0.12949:7.00:22.3:6:0.0158:0:3.7 0/1:143:3:1,2:42,98:140,3:0.021:2,2:28.7:1:28.3:1:1:1.17:32:6:0.021:0:3.3 +6 29925686 . A C 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.69004;SOR=1.46862;LSEQ=TTGTTCTTGGTGCTGTTTTC;RSEQ=CCAGAGCTGTGGTCACTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:3:2,1:33,142:175,3:0.0169:2,2:32.3:1:33:0:0.09915:8.46:22.3:6:0.0172:0:3.7 0/1:122:3:1,2:28,91:119,3:0.0246:2,2:31.7:1:28.3:1:0.56047:1.62:32:6:0.0246:0:3.3 +6 29925689 . A T 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68397;SOR=1.53881;LSEQ=TTCTTGGTGCTGTTTTCACC;RSEQ=GAGCTGTGGTCACTGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:3:2,1:31,137:168,3:0.0175:2,2:35.3:1:33.3:1:0.09565:8.68:22.3:6:0.0179:0:3.7 0/1:112:3:1,2:23,86:109,3:0.0268:2,2:34.7:1:28:1:0.51853:1.86:32:6:0.0268:0:3.3 +6 29925713 . T TG 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01218;SOR=2.26903;LSEQ=CTGTGGTCACTGCTGTGATG;RSEQ=GAAGAATAAGAGCCCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:50:5,45:8,39:47,50:0.4673:2,2:27.1:1:32:1:0.37879:1.83453:54.9:49:0.5104:0.1589:0.9 1/0:66:44:3,41:0,18:18,44:0.6667:1,2:21.9:1:30.6:1:0.54976:0:56.7:88:0.7097:0.2424:1 +6 29925719 . A G 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55259;SOR=0;LSEQ=TCACTGCTGTGATGTGAAGA;RSEQ=TAAGAGCCCAGGTAGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:0,3:9,68:77,3:0.0333:2,0:30.7:1:32.3:1:1:0:54.3:6:0.038:0:2 0/0:50:0:0,0:2,44:46,0:0:1,0:25.5:1:30.7:1:1:0:57:92:1:0:0.6 +6 29925817 . A G 42 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94642;LSEQ=GGCTTGTATCCTGCCTAGTC;RSEQ=TGAGGCACCATCTCTGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:0,17:17,3:0.15:1,0:23.3:1:27:1:1:0:60:2:0.1053:0:1 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:10:0:33:0:1:0:60:2:0.1429:0:1 +6 29926300 . AGGGACAGTACCCAGG A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03612;SOR=Inf;LSEQ=GTTTTTGTTCCACCCGAAAC;RSEQ=GCTCTGATGTGTCTCTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:12,0:0:2,0:24.7:1:33.8:1:1:0:57.3:24:1:0:0.1 0/1:7:3:1,2:3,1:4,3:0.4286:2,2:21.3:1:30.2:1:0.48571:4.4496:35.7:6:0.4286:0.1429:0 +6 29926597 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02407;SOR=Inf;LSEQ=GTCTTCTCTTTCTGCCAAGG;RSEQ=GTCTGAATGTGTCTACATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:9,18:27,0:0:2,0:25.1:1:29.7:1:1:0:60:54:1:0:0.1 0/1:12:3:0,3:2,7:9,3:0.25:2,0:28:1:31.3:1:1:0:36:6:0.25:0:1 +6 29926668 . C G 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=CCCACCCTCATGTCCACCAT;RSEQ=ACCCCTGATATTGTTTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:4,1:0.2:0,0:1:0:32:0:1:0:60:2:0.2:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:19.5:1:32.5:1:1:0:35.5:4:1:0:1 +6 29973526 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACAGAAACTCAGGGCTA;RSEQ=GGAATAAAGGTAAATTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:29.5:1:1:0:59.5:4:1:0:1 +6 29973978 . A G 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCCGGATGAAAAGTGAA;RSEQ=GGAGAGGGACGGGGCCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,1:5,2:0.2857:2,0:31.5:1:34:1:1:0:31:4:0.2857:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29973989 . G C 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGTGAAAGGAGAGGGAC;RSEQ=GGGCCCAAGCTGAGGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:34:1:31.5:1:1:0:31:4:0.3333:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29974000 . T C 38 q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGGGACGGGGCCCAAGC;RSEQ=GAGGGTTTCTTCCTGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:25.3:1:24.3:1:1:0:34.3:2:0.3333:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 29974083 . CG C 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGTTTGTCACAGGAGGAG;RSEQ=GGGTCAGGGCGAAGTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:5,1:6,1:7,6:0.4615:2,2:31:1:29.7:1:1:1.18321:53.5:5:0.4545:0:0.7 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:25:0:1:0:60:2:1:0:1 +6 29974191 . CAG C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.11579;SOR=Inf;LSEQ=TTGGGGATTCCCCATCTCCG;RSEQ=AGTTTCTCTTCTCCCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:61,2:63,0:0:1,0:19.8:1:30.6:1:1:0:60:62:1:0:0.1 0/1:33:2:2,0:27,3:30,2:0.0606:2,0:10.5:1:32.1:1:1:0:60:4:0.0625:0.0303:0 +6 29974294 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14053;SOR=Inf;LSEQ=CTGAGTGTCGGGTTTCTAGG;RSEQ=AAGCCAATCAGCGTCGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:282,37:319,0:0:2,0:24.1:1:31.2:1:1:0:59.9:28:0.9968:0:0.3 0/1:193:2:1,1:161,29:190,2:0.0104:2,2:32.5:1:28:1:0.28878:5.47542:60:4:0.0107:0:1 +6 29974346 . G C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.34247;LSEQ=AAAGTCCCCACGCACCCACC;RSEQ=GGACTCGGAGTCTCCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:942:301:179,122:392,246:638,301:0.3195:2,2:24.2:1:30.7:1:0.56744:1.08597:57.5:149.5:0.3222:0:1.2 0/1:650:90:52,38:319,239:558,90:0.1385:2,2:28.5:1:29.2:1:1:1.03:57.1:89:0.1384:0:1.2 +6 29974500 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07486;SOR=0.72876;LSEQ=CCGTGAGGAGCGAAAGGTCC;RSEQ=CCTGGCTGGGGCGCAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:131:54,77:141,191:332,131:0.2817:2,2:23.5:1:31.7:1:0.83499:1.05255:55.1:130:0.2832:0:1.1 0/1:297:66:26,40:94,137:231,66:0.2222:2,2:20.9:1:30.4:1:0.88767:1.05541:54.3:65:0.2211:0:1.1 +6 29974506 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0574;SOR=Inf;LSEQ=GGAGCGAAAGGTCCACCTGG;RSEQ=TGGGGCGCAGGACCCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:203,254:457,0:0:2,0:23.9:1:32.8:1:1:0:54.9:64.286:1:0:0.4 0/1:288:3:1,2:117,168:285,3:0.0104:2,2:19:1:28.3:1:1:1.39131:60:6:0.0105:0:2 +6 29974608 . C G 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=ATGAGGTATTTCAGCACCGC;RSEQ=GTTTCCTGGCCGGGCCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:567:0:0,0:296,271:567,0:0:2,0:26.2:1:30.7:1:1:0:51.7:93.5:1:0:0.1 0/1:333:21:12,9:156,156:312,21:0.0631:2,2:27.5:1:29.3:1:0.65336:1.33:45:20:0.0612:0:1.2 +6 29974672 . T G 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTACGTGGACGACACGCAG;RSEQ=TCGTGCGGGTCGACAGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:348,201:549,0:0:2,0:25:1:30.2:1:1:0:59.9:136.25:1:0:0.1 0/1:309:33:19,14:160,114:274,33:0.1068:2,2:19.9:1:30.5:1:1:1.03407:59:66:0.1082:0:1.2 +6 29974675 . G A 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00208;SOR=Inf;LSEQ=ACGTGGACGACACGCAGTTC;RSEQ=TGCGGGTCGACAGTGACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:0:0,0:362,202:564,0:0:2,0:25:1:30.7:1:1:0:59.9:50.273:1:0:0.1 0/1:316:6:4,2:181,129:310,6:0.019:2,2:27.2:1:30.8:1:1:1.42:60:12:0.0194:0:1.3 +6 29975047 . G T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06931;SOR=3.00874;LSEQ=ATCTCCGCAGGTTGCTAGGG;RSEQ=CCGGGCCAGGGCTCGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:6:5,1:54,28:82,6:0.0682:2,2:18.8:1:31.2:1:0.65903:2.57:60:12:0.0706:0:1 0/1:44:8:7,1:27,9:36,8:0.1818:2,2:15.5:1:29.6:1:0.65852:2.30:60:16:0.2:0:1 +6 29975049 . C G 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00354;SOR=Inf;LSEQ=CTCCGCAGGTTGCTAGGGGC;RSEQ=GGGCCAGGGCTCGGTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:61,31:92,0:0:2,0:22.4:1:29.9:1:1:0:59.4:17.4:1:0:0.2 0/1:46:5:4,1:31,10:41,5:0.1087:2,2:14.4:1:29.8:1:1:1.28:60:10:0.1136:0:4 +6 29975055 . A G 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00529;SOR=Inf;LSEQ=AGGTTGCTAGGGGCCGGGCC;RSEQ=GGGCTCGGTGGGCGGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:67,33:100,0:0:2,0:21.6:1:30.4:1:1:0:59.5:24:1:0:0.2 0/1:56:5:4,1:38,13:51,5:0.0893:2,2:20.4:1:30:1:1:1.36:60:10:0.0909:0:4 +6 29975093 . A T 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=CTGACCGCGGGAACTGGGCC;RSEQ=GGGTATCACATCCTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:95,50:145,0:0:2,0:26.4:1:30.4:1:1:0:59.9:47.333:1:0:0.2 0/1:96:10:6,4:60,26:86,10:0.1042:2,2:30.9:1:29.9:1:0.49819:1.53117:60:20:0.1075:0:3.1 +6 29975095 . G C 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=GACCGCGGGAACTGGGCCAG;RSEQ=GTATCACATCCTCCAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:95,52:147,0:0:2,0:26.6:1:31:1:1:0:59.9:48:1:0:0.2 0/1:100:10:6,4:62,28:90,10:0.1:2,2:31.7:1:30.6:1:0.72222:1.47018:60:20:0.102:0:3.1 +6 29975105 . C A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50981;SOR=0;LSEQ=ACTGGGCCAGGGTATCACAT;RSEQ=CTCCAGGGAATGTTTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:98,63:161,2:0.0123:2,2:6.5:1:28.5:1:1:1.55116:60:4:0.0125:0:1 0/0:120:0:0,0:77,43:120,0:0:2,0:26.5:1:30.1:1:1:0:60:39:1:0:0.4 +6 29975193 . ATCGCCCTGAA CGT 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00218;SOR=0.3758;LSEQ=CCTACGACGGCAAGGATTAC;RSEQ=CGAGGACCTGCGCTCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:40:16,24:93,97:190,40:0.1739:2,2:23.4:1:31.4:1:0.38404:1.43588:52.1:80:0.177:0.0478:0.3 0/1:205:15:10,5:92,98:190,15:0.0732:2,2:29.3:1:30.4:1:0.19184:2.12:48.1:30:0.0743:0.0049:0.3 +6 29975213 . G A 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.57307;LSEQ=ATCGCCCTGAACGAGGACCT;RSEQ=CGCTCCTGGACCGCCGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:2,0:95,103:198,2:0.01:2,0:25.5:1:25:1:0.23397:0:60:4:0.0101:0:1 0/0:174:1:1,0:87,86:173,1:0.0057:2,0:1:0:21:0:1:0:34:2:0.0058:0:1 +6 29975230 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24786;SOR=Inf;LSEQ=CCTGCGCTCCTGGACCGCCG;RSEQ=GGATACCGCGGCTCAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:89,85:174,0:0:2,0:24.3:1:30.8:1:1:0:41.7:42.5:0.9942:0:0.2 0/1:176:3:1,2:85,86:171,3:0.017:2,2:19.3:1:26.7:1:1:1.9693:47.7:6:0.0171:0:1 +6 29975231 . G A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36572;SOR=3.11571;LSEQ=CTGCGCTCCTGGACCGCCGC;RSEQ=GATACCGCGGCTCAGATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:1:1,0:90,85:175,1:0.0057:2,0:1:0:27:0:1:0:21:2:0.0057:0:1 0/1:171:3:2,1:83,85:168,3:0.0175:2,2:19:1:26.3:1:0.62058:2.04:42:6:0.0176:0:1 +6 29975304 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51093;SOR=0;LSEQ=AGCAAAGGAGAGCCTACCTG;RSEQ=AGGGCACCTGCATGGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:84,105:189,2:0.0105:2,2:16:1:28.5:1:1:1.25:52:4:0.0105:0:1 0/0:139:0:0,0:58,81:139,0:0:2,0:26.2:1:30.5:1:1:0:56.8:278:1:0:0.2 +6 29975453 . C A 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0.75739;LSEQ=AGGAGGGGAAGAAAATGGAA;RSEQ=CACCACCAGAATATCGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:1,7:1,11:12,8:0.4:2,2:24.5:1:30.5:1:1:1.54:60:16:0.4211:0:1.1 0/1:9:3:1,2:1,5:6,3:0.3333:2,2:16:1:28.7:1:1:2.24:60:6:0.3333:0:1 +6 29975719 . T C 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATGTGTCGGAGTCTGAC;RSEQ=CCAGCTCCTCTGAGTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:3,1:3,1:4,4:0.5:2,2:27.3:1:31.3:1:1:1:51:8:0.5:0:3.3 0/0:1:0:0,0:0,1:1,0:0:0,0:37:0:29:0:1:0:60:2:1:0:0 +6 29975766 . G C 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=CACTCAGATCAGGACCAGAA;RSEQ=TCCCTGCTACCCTGCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:9,2:6,1:7,11:0.6111:2,2:24.3:1:32.1:1:1:1.3127:38.5:22:0.6471:0:2.5 0/0:2:0:0,0:1,1:2,0:0:2,0:10.5:1:33.5:1:1:0:60:4:1:0:0 +6 29975775 . A C 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18947;SOR=0;LSEQ=CAGGACCAGAAGTCCCTGCT;RSEQ=CCCTGCTCAGAGACTAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:9,2:6,1:7,11:0.6111:2,2:26.5:1:30.7:1:1:1.3127:38.5:10:0.625:0:2.3 0/0:2:0:0,0:1,1:2,0:0:2,0:10.5:1:27:1:1:0:60:4:1:0:0 +6 29975950 . C T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16769;SOR=0.69698;LSEQ=TGCAAAGTGCCTGAGTTTTC;RSEQ=GACTCTTCCTTTCAGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:53:37,16:59,36:95,53:0.3581:2,2:28.2:1:31.4:1:0.37449:1.41:47.8:106:0.3655:0:1.4 0/1:143:40:28,12:61,42:103,40:0.2797:2,2:24.8:1:29.9:1:0.25503:1.60:45.2:80:0.2817:0:1.9 +6 29975957 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24757;SOR=0;LSEQ=TGCCTGAGTTTTCCGACTCT;RSEQ=CCTTTCAGACCCCCCCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:90,62:152,2:0.013:2,2:25:1:32.5:1:1:1.44799:58.5:4:0.0133:0:1 0/0:155:0:0,0:91,63:154,0:0:2,0:26.1:1:28.8:1:1:0:55.3:76:1:0:0.9 +6 29975966 . AC A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=0.22743;LSEQ=TTTCCGACTCTTCCTTTCAG;RSEQ=CCCCCCCAAGACACACGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:49:24,25:57,46:103,49:0.3182:2,2:19.3:1:31.7:1:0.49059:1.28857:41.5:98:0.3427:0.0195:1.7 0/1:157:15:8,7:78,64:142,15:0.0955:2,2:19.2:1:29.9:1:1:1.06595:39.3:30:0.1027:0.0064:1.8 +6 29975968 . C A 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.12264;SOR=Inf;LSEQ=TCCGACTCTTCCTTTCAGAC;RSEQ=CCCCCCAAGACACACGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:85,74:159,0:0:2,0:24:1:30.6:1:1:0:53.7:25.5:1:0:1.1 0/1:158:3:2,1:83,72:155,3:0.019:2,2:26.3:1:24.7:1:1:1.73:60:2:0.0136:0:1.3 +6 29975994 . C A 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.14295;SOR=0.66741;LSEQ=CAAGACACACGTGACCCACC;RSEQ=CCCTCTCTGAACATGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:43:15,28:42,56:98,43:0.3028:2,2:22.9:1:29:1:0.45688:1.39669:42.9:42:0.3043:0:2.1 0/1:147:33:10,23:50,64:114,33:0.2245:2,2:25.2:1:28.4:1:0.22734:1.78993:43.4:66:0.2357:0:2.5 +6 29975997 . C CTG 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.2608;SOR=0.71193;LSEQ=GACACACGTGACCCACCCCC;RSEQ=TCTCTGAACATGAGGCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:37:10,27:50,59:109,37:0.2534:2,2:29.4:1:30.6:1:0.05368:2.27564:46.7:74:0.2587:0.0342:2.1 0/1:144:28:9,19:49,66:115,28:0.1944:2,2:30.1:1:29.4:1:0.39242:1.56255:45.9:56:0.2044:0.0347:2.5 +6 29976024 . C G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96288;LSEQ=AACATGAGGCATAACGAGGT;RSEQ=CTGGGTTCTGGGCTTCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:45:12,33:41,47:88,45:0.3383:2,2:31:1:31.1:1:0.03888:2.38343:47.9:10.25:0.328:0:1.9 0/1:97:32:11,21:20,45:65,32:0.3299:2,2:25.9:1:31.1:1:0.8177:1.18:48.7:64:0.3368:0:2.2 +6 29976161 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1505;SOR=Inf;LSEQ=AGAAGTGGGCGGTTGTGGTA;RSEQ=TGCCTTCTGGAGAGGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:196,71:267,0:0:2,0:21.9:1:32.7:1:1:0:58.8:65.75:0.9925:0:0.1 0/1:171:2:1,1:129,40:169,2:0.0117:2,2:13:1:29:1:0.42312:3.19774:52:4:0.012:0:1 +6 29976193 . C T 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16704;SOR=5.61393;LSEQ=GAGGAACAGAGATACACATG;RSEQ=CATGTGCAGCACAAGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:1:0,1:271,179:450,1:0.0022:2,0:9:0:14:0:0.39911:0:60:0:0:0:1 0/1:324:4:1,3:196,124:320,4:0.0123:2,2:9.3:1:25.8:1:0.30368:4.71959:57.5:8:0.0127:0:1.5 +6 29976253 . TG T 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGATGGGGTAAGGAGAGAGA;RSEQ=GGGGCGGCCATGTCTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:495:0:0,0:214,281:495,0:0:2,0:24.6:1:31.6:1:1:0:58.9:122.75:1:0:0.4 0/1:362:14:6,8:144,204:348,14:0.0387:2,2:20.4:1:31.1:1:1:1.06:59:28:0.0393:0.0055:0.2 +6 29976262 . C T 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25383;SOR=0.82147;LSEQ=AAGGAGAGAGATGGGGGCGG;RSEQ=CATGTCTCTTAGGGAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:129:57,72:130,183:313,129:0.2912:2,2:24.3:1:30.1:1:0.672:1.11:57.4:63.5:0.294:0:1.1 0/1:329:83:31,52:98,148:246,83:0.2523:2,2:21.6:1:28.6:1:0.79497:1.11035:56.3:82:0.2539:0:1.2 +6 29976312 . C G 107 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00021;SOR=18.11768;LSEQ=CTGGAGACCTTTAGCAGGGT;RSEQ=GGGGCTGGGTCCTGGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:1,0:117,142:259,1:0.0038:2,0:49:0:34:0:0.45385:0:60:2:0.004:0:1 0/1:168:11:5,6:59,97:156,11:0.0655:2,2:22.8:1:31:1:0.75031:1.37:58.3:22:0.0663:0:1.8 +6 29976419 . TTGGAGCTGTGGTCAC T 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTGCTGGCCTGGTTCTCC;RSEQ=TGGAGCTGTGGTCACTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:0:0,0:293,245:538,0:0:2,0:23.8:1:30.6:1:1:0:59.5:133.5:1:0:0.2 0/1:428:17:7,10:228,182:410,17:0.0397:2,2:28.4:1:30.3:1:0.32052:1.78716:47.2:34:0.0402:0.0093:0.8 +6 29976432 . C T 52 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09886;SOR=5.98009;LSEQ=GTTCTCCTTGGAGCTGTGGT;RSEQ=ACTGGAGCTGTGGTCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:564:1:0,1:302,261:563,1:0.0018:2,0:1:0:26:0:0.46454:0:28:2:0.0018:0:1 0/1:475:5:1,4:241,216:457,5:0.0105:2,2:17.2:1:22.6:1:0.19646:4.44973:48.2:4:0.0088:0:1.2 +6 29976499 . C G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.38514;LSEQ=GTGGGGAAGGGGTGAGGAGT;RSEQ=GGGTTTGAGTTTTCTTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:149:54,95:100,179:279,149:0.3481:2,2:23.9:1:31.4:1:1:1.02:56.8:148:0.3491:0:1.1 0/1:311:53:17,36:87,169:256,53:0.1704:2,2:21.3:1:30.4:1:0.8737:1.08987:51.7:52:0.1716:0:1.3 +6 29976741 . A G 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60927;SOR=1.80741;LSEQ=AAGGTCCCTGCTGAGGACAG;RSEQ=CCTTAGGAGGGCAGTTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:4:2,2:23,10:33,4:0.1081:2,2:22.5:1:33.8:1:0.5821:2.24385:56.5:8:0.1081:0:1 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:26.5:1:32:0:1:0:51.5:4:0.2:0:1 +6 29976789 . T C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00246;SOR=Inf;LSEQ=CACATCTGCTTTCCTTGTTT;RSEQ=TCCTGATCCTGCCCTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:37,7:44,0:0:2,0:23.8:1:31.1:1:1:0:50.1:88:1:0:0.3 0/1:21:5:5,0:15,1:16,5:0.2381:1,0:25:1:32.6:1:1:0:45.8:10:0.25:0:1.4 +6 29976838 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=4.23115;LSEQ=CACATTTCTGGAAACTTCTC;RSEQ=AGGTTCCAAGACTAGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:25:24,1:62,3:65,25:0.2778:1,1:19.9:1:30.6:1:1:1.16:32.3:50:0.2841:0:1.3 1/0:45:28:24,4:16,1:17,28:0.6222:1,2:18.9:1:27.7:1:0.63533:2.61607:30.6:13:0.6047:0:1.4 +6 29976842 . T G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTTCTGGAAACTTCTCAAGG;RSEQ=TCCAAGACTAGGAGGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:8:8,0:84,4:88,8:0.0833:1,0:14.6:1:32.4:1:1:0:26.5:16:0.0851:0:1.9 0/1:48:4:3,1:38,6:44,4:0.0833:2,2:7.3:1:30.8:1:0.47955:2.07091:27.5:8:0.0833:0:2.5 +6 29976857 . G C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0376;SOR=Inf;LSEQ=CAAGGTTCCAAGACTAGGAG;RSEQ=TTCCTCTAGGACCTCATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:124,7:131,0:0:2,0:23.8:1:31.7:1:1:0:48.9:64.5:1:0:0.4 0/1:67:3:3,0:55,9:64,3:0.0448:2,0:16.7:1:33:0:1:0:48.7:6:0.0462:0:2 +6 29976904 . G T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07196;SOR=Inf;LSEQ=ACCTTCCTGGCCTCTCACAG;RSEQ=ACGTTTTCTTCCCGCAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:233,104:337,0:0:2,0:24.1:1:31.3:1:1:0:38.9:41.125:1:0:0.2 0/1:241:3:1,2:156,82:238,3:0.0124:2,2:16:1:25:1:0.27891:3.78203:28.7:6:0.0129:0:1 +6 29977068 . G C 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACATCTCCTGTGGGATCT;RSEQ=ACCAGGTTCTGTTTTTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:0:0,0:264,309:573,0:0:2,0:25.3:1:32.2:1:1:0:56.1:56.3:0.9982:0:0.2 0/1:411:28:12,16:201,181:382,28:0.0681:2,2:22.5:1:31.2:1:0.33453:1.47923:47.4:56:0.0691:0:1.1 +6 29977145 . G C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00158;SOR=2.1687;LSEQ=GTCTCTCACGGCTTGTAAAG;RSEQ=TGAGACCCTGGGGAGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:30:15,15:161,245:406,30:0.0688:2,2:23.3:1:32.3:1:0.33506:1.52:60:29:0.0681:0:1.1 0/1:340:47:14,33:128,165:293,47:0.1382:2,2:24.2:1:30.9:1:0.08092:1.82546:58.9:14.667:0.1333:0:1.3 +6 29977276 . G C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06468;SOR=Inf;LSEQ=GGTGTGACCCCTCACTGTGA;RSEQ=TGATATGAATTTGTTCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:173,82:255,0:0:2,0:26.2:1:32.7:1:1:0:49.2:50:1:0:0.1 0/1:172:3:2,1:115,54:169,3:0.0174:2,2:15:1:33:0:1:1.06442:51.7:6:0.0175:0:5.7 +6 29977299 . AT A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=ATATGAATTTGTTCATGAAT;RSEQ=TTTTTCTATAGTGTGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:197,107:304,0:0:2,0:23.1:1:30.7:1:1:0:38.8:151:0.9967:0:0.1 0/1:237:12:5,7:142,83:225,12:0.0506:2,2:12:1:28.5:1:0.22011:2.38593:32.4:24:0.0508:0.038:4.6 +6 29977308 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02398;SOR=2.17629;LSEQ=TGTTCATGAATATTTTTTCT;RSEQ=TAGTGTGAGACAGCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:15:9,6:198,124:322,15:0.0445:2,2:5.7:1:32.4:1:1:1.06432:32.1:30:0.0453:0:4.3 0/1:293:27:12,15:165,101:266,27:0.0922:2,2:11:1:30.3:1:0.09775:2.03694:32.8:54:0.0931:0:4.4 +6 29977317 . G A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12853;SOR=1.55434;LSEQ=ATATTTTTTCTATAGTGTGA;RSEQ=ACAGCTGCCTTGTGTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:24:14,10:209,136:345,24:0.065:2,2:11.1:1:30.9:1:0.83203:1.09741:32.8:48:0.0654:0:3.8 0/1:338:33:16,17:179,124:303,33:0.0976:2,2:15.9:1:28.7:1:0.26796:1.53174:32.8:32:0.0964:0:4.2 +6 29977327 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23924;SOR=1.3315;LSEQ=TATAGTGTGAGACAGCTGCC;RSEQ=TGTGTGGGACTGAGAGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:36:20,16:205,158:363,36:0.09:2,2:16:1:32.7:1:1:1.0379:32.5:72:0.0925:0:3.3 0/1:378:44:23,21:187,147:334,44:0.1164:2,2:19.7:1:30.2:1:0.74721:1.16103:34.7:43:0.1162:0:3.6 +6 29977342 . A T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21795;SOR=1.34136;LSEQ=CTGCCTTGTGTGGGACTGAG;RSEQ=GGCAAGATTTGTTCATGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:40:23,17:188,214:402,40:0.0905:2,2:29.2:1:31.3:1:0.24526:1.54:32:80:0.0922:0:3 0/1:416:49:24,25:178,189:367,49:0.1178:2,2:30.4:1:29.2:1:1:1.02:35.7:98:0.1186:0:3.4 +6 29977350 . T G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00051;SOR=0.38951;LSEQ=TGTGGGACTGAGAGGCAAGA;RSEQ=TTGTTCATGCCTTCCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:432:47:14,33:179,206:385,47:0.1088:2,2:12.1:1:30.7:1:0.03052:2.04495:33.9:22.5:0.1066:0:2.1 0/1:419:19:5,14:184,216:400,19:0.0453:2,2:11.3:1:29.8:1:0.10347:2.38053:34.8:38:0.0458:0:2.1 +6 29977357 . A C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00114;SOR=0.38766;LSEQ=CTGAGAGGCAAGATTTGTTC;RSEQ=TGCCTTCCCTTTGTGACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:43:14,29:168,212:380,43:0.1012:2,2:19.2:1:31.5:1:0.19313:1.63965:34.8:42:0.1007:0:2.1 0/1:407:17:5,12:174,215:389,17:0.0418:2,2:18.3:1:29.4:1:0.31839:1.93931:36.2:34:0.0422:0:2 +6 29977359 . G GC 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00025;SOR=0.37296;LSEQ=GAGAGGCAAGATTTGTTCAT;RSEQ=CCTTCCCTTTGTGACTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:433:51:16,35:164,213:377,51:0.1178:2,2:19.7:1:30.6:1:0.13013:1.6823:38.6:50:0.1182:0.0185:1.9 0/1:401:19:5,14:169,211:380,19:0.0474:2,2:20.7:1:29.5:1:0.15581:2.23842:36.7:38:0.0479:0.0025:2 +6 29977400 . G A 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32659;SOR=3.8055;LSEQ=GAACCCTGACTTCTCTTTCT;RSEQ=CAAAGGCATCTGAATGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:1:1,0:100,246:346,1:0.0029:2,0:1:0:23:0:0.29107:0:27:2:0.0029:0:1 0/1:276:3:2,1:87,185:272,3:0.0109:2,2:20:1:25.7:1:0.24558:4.23:49:6:0.0111:0:1 +6 29977402 . AAAGGCATCTGAATGTGTCTGTGTCCCTATAGGCATAATGTGAGGTGGTGGG A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.8843;SOR=0.94204;LSEQ=ACCCTGACTTCTCTTTCTGC;RSEQ=GAGACCAGCCCACACCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:30:18,12:72,226:298,30:0.0915:2,2:60.4:1:30.6:1:0.00012:4.68:32.7:60:0.0929:0.0915:2.6 0/1:254:22:13,9:64,168:232,22:0.0866:2,2:58.8:1:29.4:1:0.00348:3.77:35.6:44:0.0876:0.0866:2.8 +6 30227246 . T A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18673;SOR=2.00935;LSEQ=TTTTGGTTCTCCCAACCTTC;RSEQ=TCCTGGATACTTGTGACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:10:10,0:53,1:54,10:0.1563:1,0:19.2:1:31:1:1:0:60:20:0.1563:0:1 0/1:33:9:9,0:24,0:24,9:0.2727:1,0:21.7:1:29.9:1:1:0:60:18:0.2813:0:1 +6 30227322 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1355;SOR=Inf;LSEQ=TAGAGAAGCCAATCAGCTTC;RSEQ=CCGCGATCCCGGCACTACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:207,5:212,0:0:1,0:25.6:1:29.8:1:1:0:60:69.667:1:0:0.1 0/1:124:2:2,0:116,6:122,2:0.0161:1,0:28.5:1:29:1:1:0:60:4:0.0171:0:1 +6 30227340 . C A 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0014;SOR=Inf;LSEQ=TCGCCGCGATCCCGGCACTA;RSEQ=GATCCCGGCACTACAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:246,48:294,0:0:2,0:22.9:1:31.8:1:1:0:60:293:1:0:0.2 0/1:192:7:6,1:150,34:184,7:0.0365:2,2:12.7:1:29.1:1:1:1.36:60:14:0.0372:0:1 +6 30227397 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=2.92891;LSEQ=CTCAGATTCTCCCCAAACGC;RSEQ=AAGGATGGGGGTCATGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:58:31,27:357,282:639,58:0.0832:2,2:25.3:1:29.1:1:0.78296:1.10245:54.1:18.333:0.0814:0:1.2 0/1:571:120:69,51:253,197:450,120:0.2102:2,2:25.7:1:28.5:1:0.83626:1.05:52.8:29:0.2094:0:1.2 +6 30227399 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00535;SOR=0.5351;LSEQ=CAGATTCTCCCCAAACGCCA;RSEQ=GGATGGGGGTCATGGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:65:38,27:353,289:642,65:0.0919:2,2:31.3:1:31.4:1:0.60376:1.15:54.5:15.25:0.0883:0:1.2 0/1:584:30:15,15:310,244:554,30:0.0514:2,2:27.4:1:29.9:1:0.57386:1.26996:53.6:29:0.0508:0:1.2 +6 30227425 . C G 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGTCATGGCTCCCCGAAC;RSEQ=CTCCTCCTGCTGCTCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:850:0:0,0:421,429:850,0:0:2,0:25.1:1:30.9:1:1:0:49.7:35.957:1:0:0.3 0/1:733:48:23,25:333,350:683,48:0.0655:2,2:26.1:1:30.2:1:1:1.03412:50.2:47:0.0651:0:1.2 +6 30227442 . T G 87 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16083;SOR=2.5708;LSEQ=AACCCTCCTCCTGCTGCTCT;RSEQ=GGGGGCCCTGGCCCTGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:794:4:2,2:364,426:790,4:0.005:2,2:22:1:33.3:1:1:1.17:20:8:0.0052:0:2.8 0/1:700:9:4,5:321,369:690,9:0.0129:2,2:20.2:1:27.6:1:1:1.0873:25.1:8:0.0116:0:6.3 +6 30227449 . CC AG 94 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03044;SOR=5.06726;LSEQ=CTCCTGCTGCTCTTGGGGGC;RSEQ=TGGCCCTGACCGAGACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:746:2:1,1:335,409:744,2:0.0027:2,2:26:0:33.8:1:1:1.22:20:4:0.0027:0:3.5 0/1:669:9:4,5:303,352:655,9:0.0135:2,2:30:1:29.7:1:1:1.0759:24.6:18:0.0137:0:5.2 +6 30227499 . G T 88 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00759;SOR=10.50117;LSEQ=GTGCGGGGTCGGGAGGGAAA;RSEQ=GGCCTCTGCGGGGAGAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:1:0,1:168,273:441,1:0.0023:2,0:1:0:31:0:1:0:20:2:0.0023:0:4 0/1:387:9:4,5:149,228:377,9:0.0233:2,2:19.4:1:27.9:1:0.74457:1.22:24.6:8:0.0209:0:5.2 +6 30227508 . C T 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00093;SOR=Inf;LSEQ=CGGGAGGGAAAGGGCCTCTG;RSEQ=GGGGAGAAGCGAGTGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:141,236:377,0:0:2,0:23.4:1:30.5:1:1:0:53.3:74.4:1:0:0.2 0/1:326:9:4,5:122,194:316,9:0.0276:2,2:10.4:1:25.7:1:0.739:1.27:24.6:3.5:0.0219:0:5.2 +6 30227527 . C T 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=GCGGGGAGAAGCGAGTGGCC;RSEQ=GCCCGGCCCGGGGAGCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:113,197:310,0:0:2,0:23.4:1:30.1:1:1:0:59.5:61:1:0:0.2 0/1:232:23:9,14:81,128:209,23:0.0991:2,2:24.9:1:29.1:1:1:1.02:58.7:22:0.0969:0:1 +6 30227583 . C G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11697;SOR=1.5702;LSEQ=GGCGGGTCTCAGCCTCTCCT;RSEQ=GCCTCCAGGCTCCCACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:26:17,9:149,167:316,26:0.0758:2,2:23:1:32.5:1:0.10133:2.11:51.7:52:0.0772:0:1.1 0/1:254:29:13,16:113,112:225,29:0.1142:2,2:23.4:1:30.5:1:0.69403:1.2407:54.6:28:0.1116:0:1.1 +6 30227838 . G T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0248;SOR=Inf;LSEQ=GAACCTGCGGACCCTGCTCC;RSEQ=CTATTACAACCAGAGCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:108,289:397,0:0:2,0:20.9:1:31.3:1:1:0:59.8:48.625:0.9949:0:0.1 0/1:264:4:1,3:74,185:259,4:0.0152:2,2:21.3:1:30.5:1:1:1.19919:60:8:0.0153:0:1 +6 30227912 . CG TT 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04422;SOR=Inf;LSEQ=CGATCCCTCCCCATCCCCCA;RSEQ=GACAGCCCAGGTCCCGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:19,86:105,0:0:2,0:20.5:1:30.7:1:1:0:60:51.5:0.9904:0:0.1 0/1:59:3:2,1:12,43:55,3:0.0508:2,2:29.7:1:29.3:1:0.14156:6.86:60:6:0.0508:0:2 +6 30227915 . A T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01588;SOR=Inf;LSEQ=TCCCTCCCCATCCCCCACGG;RSEQ=CAGCCCAGGTCCCGGGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:20,79:99,0:0:2,0:21.2:1:30.4:1:1:0:60:98:1:0:0.2 0/1:56:4:2,2:12,40:52,4:0.0714:2,2:28.5:1:29:1:0.25767:3.25:60:8:0.0714:0:2 +6 30227955 . AC A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.52027;SOR=0;LSEQ=GAGTCTCCGGTCTGAGATCC;RSEQ=CCCGAGGCTGCGGGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:2:1,1:21,40:61,2:0.0317:2,2:34:1:31:1:1:1.88:60:4:0.0317:0:0 0/0:40:0:0,0:18,22:40,0:0:2,0:24:1:30.5:1:1:0:60:39:1:0:0.5 +6 30228038 . CA C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.57048;SOR=2.87635;LSEQ=GGTTTAATTTCAGTTTAGGC;RSEQ=AAATCCCCGCGGGTTGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:1:1,0:116,26:142,1:0.0069:2,0:40:0:31:0:1:0:60:2:0.007:0:0 0/1:101:2:1,1:80,19:99,2:0.0198:2,2:35.5:1:29:0:0.35842:4.12948:47.5:4:0.0202:0:3.5 +6 30228063 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18245;SOR=Inf;LSEQ=TCCCCGCGGGTTGGTCGGGG;RSEQ=GGGAGCGGGGCTCGGTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:161,69:230,0:0:2,0:22.9:1:31.1:1:1:0:59.9:75.667:1:0:0.2 0/1:172:2:1,1:115,55:170,2:0.0116:2,2:19:1:28:1:0.54644:2.0812:60:4:0.0117:0:1 +6 30228073 . G A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.26509;SOR=0;LSEQ=TTGGTCGGGGCGGGAGCGGG;RSEQ=CTCGGTGTTCGGGGCTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:3:1,2:196,91:287,3:0.0103:2,2:25:1:25.3:1:0.24175:4.28378:60:2:0.0071:0:1.7 0/0:215:0:0,0:140,75:215,0:0:2,0:22.9:1:30.1:1:1:0:59.8:29.714:1:0:0.2 +6 30228138 . G A 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06541;SOR=0.5032;LSEQ=CACCATCCAGAGGAAGCATG;RSEQ=CTGCGACGTGGGCCCGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:26:11,15:175,191:366,26:0.0663:2,2:24.6:1:31.2:1:0.68597:1.2487:60:52:0.0675:0:1.2 0/1:348:12:8,4:159,177:336,12:0.0345:2,2:29.8:1:28.1:1:0.24364:2.22:60:24:0.0346:0:1.1 +6 30228224 . A T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50185;SOR=0;LSEQ=TTACATCGCCCTGAACGAGG;RSEQ=CCTGCACTCCTGGACCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:54,122:176,2:0.0112:2,2:25.5:1:26:0:0.52371:2.25:60:4:0.0113:0:1 0/0:151:0:0,0:54,97:151,0:0:2,0:25.8:1:28.6:1:1:0:58.9:49.333:1:0:0.4 +6 30228225 . C A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.59625;SOR=2.35879;LSEQ=TACATCGCCCTGAACGAGGA;RSEQ=CTGCACTCCTGGACCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:1:1,0:53,122:175,1:0.0057:2,0:1:0:25:0:0.30682:0:60:2:0.0058:0:1 0/1:150:2:1,1:52,96:148,2:0.0133:2,2:30:1:31:0:1:1.84:60:4:0.0136:0:1 +6 30228230 . A C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00655;SOR=2.23213;LSEQ=CGCCCTGAACGAGGACCTGC;RSEQ=CTCCTGGACCGCCGCGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:24:6,18:45,102:147,24:0.1404:2,2:19.3:1:31.8:1:0.63943:1.32142:56.7:48:0.1404:0:1.2 0/1:142:38:13,25:37,67:104,38:0.2676:2,2:25.1:1:29.8:1:1:1.06157:57.1:37:0.2624:0:1.2 +6 30228379 . A G 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2233;SOR=1.8557;LSEQ=CGGGAAGGAGACGCTGCAGC;RSEQ=CGCGGGTACCAGGGGCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:12:2,10:17,38:55,12:0.1791:2,2:20.8:1:32:1:0.48512:2.21327:41:24:0.1791:0:2 0/1:38:11:4,7:11,16:27,11:0.2895:2,2:20:1:30.3:1:1:1.19733:35.8:22:0.2973:0:1.3 +6 30228384 . G C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53824;SOR=0;LSEQ=AGGAGACGCTGCAGCACGCG;RSEQ=GTACCAGGGGCCACGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:18,44:62,2:0.0313:2,2:22:1:27.5:1:0.50893:2.41:54.5:4:0.0323:0:1.5 0/0:35:0:0,0:12,23:35,0:0:2,0:26.2:1:29.9:1:1:0:47.3:70:1:0:0.4 +6 30228395 . CCACGGGGGCG TCACGGGGCA 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5481;SOR=0;LSEQ=CAGCACGCGGGTACCAGGGG;RSEQ=CCTCCCTCATTTCCTGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:3:2,1:13,41:54,3:0.0517:2,2:29:1:29.1:1:0.16627:6.06:32.3:6:0.0556:0.0172:2.3 0/0:30:0:0,0:9,21:30,0:0:2,0:24.5:1:29.9:1:1:0:49:29:1:0:0.3 +6 30228398 . CG C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52687;SOR=1.70212;LSEQ=CACGCGGGTACCAGGGGCCA;RSEQ=GGGGCGCCTCCCTCATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:7:1,6:12,32:44,7:0.1373:2,2:21.4:1:31.4:1:0.66183:2.21983:39.6:14:0.1373:0.0392:1.9 0/1:28:6:1,5:7,15:22,6:0.2143:2,2:21.3:1:30.5:1:0.63991:2.27148:32.3:12:0.2143:0:1.5 +6 30228416 . T C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.9693;LSEQ=CACGGGGGCGCCTCCCTCAT;RSEQ=TCCTGTAGATTTCCCGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:6:2,4:5,26:31,6:0.1622:2,2:38:1:33.5:1:0.3155:2.52:37:12:0.1714:0:2.7 0/1:19:3:0,3:4,12:16,3:0.1579:2,0:35.3:1:31:1:1:0:35.3:6:0.1579:0:2 +6 30228712 . AG A 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=Inf;LSEQ=TTGTTCTCTCCCTCACACTC;RSEQ=TGTGTCCGTGGCTCCGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:2,3:5,3:0.375:2,0:9.3:1:31.9:1:0.19643:0:60:6:0.375:0.125:1.3 1/1:3:3:2,1:0,0:0,3:1:0,2:21.3:1:28.9:1:1:0:60:6:1:0.3333:1.3 +6 30228721 . G A 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=CCCTCACACTCAGTGTGTCC;RSEQ=TGGCTCCGATTCCAGCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:4,3:0.4286:2,0:14.3:1:31.7:1:1:0:60:6:0.4286:0:1.3 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:31:0:1:0:60:4:1:0:1 +6 30228879 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12412;SOR=2.52892;LSEQ=GGGTTCTGTGCTCCCTTCCC;RSEQ=ATCCCAGGTGTCCTGTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:7:7,0:68,6:74,7:0.0864:2,0:25.4:1:32.6:1:1:0:45.1:14:0.0864:0:2.6 0/1:36:7:6,1:24,5:29,7:0.1944:2,2:19:1:31.3:1:1:1.24:46.3:14:0.1944:0:2.9 +6 30228881 . T C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07152;SOR=2.90403;LSEQ=GTTCTGTGCTCCCTTCCCCA;RSEQ=CCCAGGTGTCCTGTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:7:7,0:71,6:77,7:0.0833:2,0:26.4:1:33.7:1:1:0:45.1:14:0.0843:0:2.6 0/1:38:8:7,1:25,5:30,8:0.2105:2,2:18.1:1:32.4:1:1:1.39:48:16:0.2162:0:2.8 +6 30228938 . T C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01157;SOR=1.90417;LSEQ=TATGCTGCTGGAGTGTCCTA;RSEQ=GAGGAATGCAAAGTGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:32:22,10:136,62:198,32:0.1391:2,2:23.4:1:29.3:1:1:1.00:57.3:7:0.1267:0:2 0/1:191:45:30,15:93,53:146,45:0.2356:2,2:21.2:1:30.9:1:0.85886:1.14:56.9:90:0.2406:0:1.9 +6 30228957 . G T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04601;SOR=Inf;LSEQ=ATGAGGAATGCAAAGTGCCT;RSEQ=AATTTTCTGACTCTTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:0:0,0:198,125:323,0:0:2,0:23.9:1:32:1:1:0:58.7:34.889:1:0:0.4 0/1:281:4:1,3:164,113:277,4:0.0142:2,2:14:1:26.5:1:0.30972:4.33204:60:8:0.0146:0:1.3 +6 30229013 . A G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03986;SOR=1.59296;LSEQ=CACATGTGACCCAGCACCCC;RSEQ=TCTCTGACCATGAGGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:46:24,22:114,151:265,46:0.1474:2,2:23.3:1:30.3:1:0.26401:1.44:51.2:92:0.1489:0:1.6 0/1:273:59:24,35:90,124:214,59:0.2161:2,2:23.7:1:30.4:1:0.88246:1.05827:51.2:58:0.2189:0:1.5 +6 30229027 . G A 45 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04607;SOR=Inf;LSEQ=CACCCCATCTCTGACCATGA;RSEQ=GCCACCCTGAGGTGCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:92,153:245,0:0:2,0:21.8:1:31.7:1:1:0:56.8:39.833:1:0:0.3 0/1:213:4:3,1:85,124:209,4:0.0188:2,2:5.5:1:22.5:1:0.30875:4.35:59.8:3:0.0144:0:2.5 +6 30229034 . C CT 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00555;SOR=2.02347;LSEQ=TCTCTGACCATGAGGCCACC;RSEQ=TGAGGTGCTGGGCCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:32:15,17:72,124:196,32:0.1404:2,2:22.3:1:30.4:1:0.32721:1.52:43.9:64:0.1416:0.0307:1.2 0/1:185:46:19,27:52,86:138,46:0.2486:2,2:17.7:1:29.1:1:0.72739:1.16:44:92:0.2527:0.0865:0.9 +6 30229102 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17851;SOR=Inf;LSEQ=TGGCAGCAGGATGGGGAGGA;RSEQ=CAGACCCAGGACACGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:65,71:136,0:0:2,0:24.6:1:31.6:1:1:0:57.6:33:1:0:0.1 0/1:100:2:1,1:42,56:98,2:0.02:2,2:15.5:1:28:1:1:1.33:27:4:0.0202:0:1.5 +6 30229267 . G C 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGAGATGGGGTAAGGAGGG;RSEQ=TGTAAGTTGTCTCCTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:409:0:0,0:186,223:409,0:0:2,0:25.1:1:31.6:1:1:0:59.9:67.167:1:0:0.5 0/1:393:22:11,11:179,192:371,22:0.056:2,2:24.7:1:30.9:1:1:1.07:55:21:0.0538:0:1.5 +6 30229280 . CC AT 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.21933;LSEQ=AGGAGGGGTGTAAGTTGTCT;RSEQ=TCTCAGGGAAAGCAGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:60:27,33:142,156:298,60:0.1676:2,2:22.8:1:30.8:1:0.77736:1.1122:59.6:120:0.1681:0.0112:1.7 0/1:330:102:46,56:115,113:228,102:0.3091:2,2:22.1:1:29.1:1:0.40506:1.23813:59.9:204:0.311:0.0303:1.6 +6 30229306 . A G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=3.57373;LSEQ=AGGGAAAGCAGGAGACCTTC;RSEQ=GCAGGGCAGGGCTGAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:47:22,25:109,132:241,47:0.1632:2,2:21.6:1:30.6:1:0.87373:1.07:60:94:0.1661:0:1.7 0/1:248:102:55,47:70,76:146,102:0.4113:2,2:22.3:1:29.8:1:0.36907:1.27:60:50:0.4098:0:1.7 +6 30229401 . C T 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=32.40103;LSEQ=ACCATCCCCATCGTGGGCAT;RSEQ=GTTGCTGGCCTGTTTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:1:0,1:219,230:449,1:0.0022:2,0:1:0:28:0:1:0:42:2:0.0022:0:1 0/1:431:29:14,15:188,214:402,29:0.0673:2,2:22.4:1:30:1:1:1.06:53.6:58:0.0682:0:1.2 +6 30229457 . C T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01835;SOR=1.60282;LSEQ=TGGAGCTGTGGTTGCTGCTG;RSEQ=GATGTGGAGGAAGAAAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:57:20,37:103,175:278,57:0.1701:2,2:26:1:30.1:1:0.88036:1.08861:44.3:114:0.1727:0:2.5 0/1:299:74:27,47:95,130:225,74:0.2475:2,2:29.8:1:28.8:1:0.41547:1.27106:43.9:73:0.25:0:2.4 +6 30229463 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02031;SOR=1.61863;LSEQ=TGTGGTTGCTGCTGCGATGT;RSEQ=GAGGAAGAAAAGCTCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:53:19,34:89,165:254,53:0.1726:2,2:27.3:1:30.7:1:1:1.04:44.6:106:0.1773:0:2.5 0/1:285:72:25,47:86,127:213,72:0.2526:2,2:29.6:1:28.7:1:0.48475:1.272:44.4:35:0.2509:0:2.5 +6 30229504 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0287;SOR=1.83604;LSEQ=GGGAAGGGGTGAGAGGTGGG;RSEQ=TCTGGGTTTTCTTGTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:33:7,26:31,106:137,33:0.1941:2,2:21.5:1:31.7:1:1:1.08574:53.3:66:0.1988:0:2.6 0/1:127:39:11,28:29,59:88,39:0.3071:2,2:17.8:1:29.4:1:0.68118:1.24898:53.6:38:0.3016:0:2.8 +6 30229583 . G C 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13418;SOR=2.26856;LSEQ=CATCACTGGGAAGCACCGTC;RSEQ=ACACACAGGCCGACCTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:12:0,12:0,36:36,12:0.25:1,0:25.6:1:32.5:1:1:0:60:24:0.25:0:1.3 0/1:30:13:1,12:0,17:17,13:0.4333:1,1:21.6:1:32.8:1:0.43333:0:60:26:0.4333:0:1.5 +6 30229869 . T C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGCTGTTTCCTTAAGGAC;RSEQ=TCATGCCCCATGTCCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:1,1:0.5:0,0:33:0:35:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:30.5:1:1:0:60:4:1:0:1 +6 30229989 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05276;SOR=Inf;LSEQ=AGAGGGCTGCTCCCTGAGAT;RSEQ=GTTGGGACAGTGTAGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:19,6:25,0:0:2,0:21.5:1:31.8:1:1:0:60:50:1:0:0.2 0/1:28:5:4,1:17,6:23,5:0.1786:2,2:16.4:1:29:1:1:1.40:60:10:0.1786:0:1 +6 30229990 . G A 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.21233;SOR=2.7122;LSEQ=GAGGGCTGCTCCCTGAGATC;RSEQ=TTGGGACAGTGTAGACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:4:4,0:15,6:21,4:0.16:2,0:38.5:1:30.8:1:0.5404:0:60:8:0.16:0:1 0/1:29:10:8,2:14,5:19,10:0.3448:2,2:21.3:1:29.6:1:1:1.41:60:20:0.3448:0:1.5 +6 30230066 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49745;SOR=Inf;LSEQ=CAGTTCCTATTTTTGTTCTA;RSEQ=CCCAGGCAGCAATTGTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:19,22:41,0:0:2,0:26.4:1:31.5:1:1:0:60:82:1:0:0.3 0/1:48:2:1,1:20,26:46,2:0.0417:2,2:12.5:1:29:1:1:1.29:47.5:4:0.0435:0:1 +6 30230085 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00898;SOR=4.76351;LSEQ=ACCCCAGGCAGCAATTGTGC;RSEQ=CAGTACTCTGATGCATCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:0,4:15,13:28,4:0.125:2,0:36.5:1:32:1:0.10414:0:60:8:0.125:0:1.5 0/1:39:16:4,12:8,15:23,16:0.4103:2,2:17.4:1:27.8:1:0.72618:1.58106:60:7:0.3784:0:2 +6 30230128 . T C 51 v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.10577;SOR=4.74507;LSEQ=ATACTTGTAAAGGTGAGACA;RSEQ=GGGGGGGCCTGAAGTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:2,13:15,2:0.1176:2,0:14.5:1:30.5:1:1:0:60:4:0.1429:0:2 0/1:15:6:0,6:0,9:9,6:0.4:0,0:31.7:1:20:1:1:0:60:1:0.3333:0:3 +6 30457216 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12531;SOR=Inf;LSEQ=TCATTCCCAATGGGTGTCGG;RSEQ=TTTCTAGAGAAGCCAATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:45,7:52,0:0:2,0:25.4:1:31.2:1:1:0:60:51:1:0:0.1 0/1:29:2:1,1:18,9:27,2:0.069:2,2:9.5:1:27:1:1:1.94942:60:4:0.069:0:1 +6 30457589 . G A 40 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62489;SOR=0.3593;LSEQ=TCTCTGTGGGCTACGTGGAC;RSEQ=ACACCCAGTTCGTGCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:3,0:148,149:297,3:0.01:2,0:13.7:1:25.7:1:0.24753:0:54.7:2:0.0068:0:1 0/0:277:1:1,0:128,148:276,1:0.0036:2,0:1:0:23:0:0.4657:0:60:2:0.0037:0:1 +6 30457604 . C T 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1095;SOR=Inf;LSEQ=TGGACGACACCCAGTTCGTG;RSEQ=GCTTCGACAACGACGCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:136,154:290,0:0:2,0:26:1:30.6:1:1:0:59.3:47.333:1:0:0.1 0/1:267:3:0,3:120,144:264,3:0.0112:2,0:11:1:23.7:1:0.25488:0:59:2:0.0077:0:1 +6 30457732 . T C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.45004;LSEQ=GCACAGATTTTCCGAGTGAA;RSEQ=CTGCGGACGCTGCGCGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:102:39,63:62,95:157,102:0.3938:2,2:26.9:1:31.7:1:0.89653:1.05406:59.6:101:0.3961:0:1.1 1/0:273:203:86,117:29,41:70,203:0.7436:2,2:26:1:30.6:1:1:1.04:59.6:49.75:0.7425:0:1.1 +6 30457792 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24239;SOR=0;LSEQ=GGTGAGTGACCCCGGCCAGG;RSEQ=GAGCAGGTCACGACCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:44,99:143,2:0.0138:2,2:25.5:1:30:1:0.52586:2.24:60:4:0.0141:0:1 0/0:149:0:0,0:50,99:149,0:0:2,0:22.1:1:29.9:1:1:0:59.9:73.5:1:0:0.6 +6 30458015 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.54724;SOR=0;LSEQ=ACTGACTAAGGGGCGGGGCC;RSEQ=GGGTCTCACACCCTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:103,50:153,2:0.0129:2,2:23:1:30:1:0.55124:2.04964:60:4:0.0135:0:1 0/0:81:0:0,0:58,22:80,0:0:2,0:24.1:1:29.6:1:1:0:60:79:0.9875:0:0.5 +6 30458039 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5188;SOR=0;LSEQ=TCTCACACCCTGCAGTGGAT;RSEQ=CATGGCTGCGAGCTGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:111,87:198,2:0.01:2,2:30.5:1:31:1:1:1.27429:60:4:0.0102:0:2 0/0:133:0:0,0:81,52:133,0:0:2,0:26.3:1:31.1:1:1:0:59.8:65.5:1:0:0.7 +6 30458058 . C T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1437;SOR=0;LSEQ=TGCATGGCTGCGAGCTGGGG;RSEQ=CCGACGGGCGCTTCCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:4:0,4:105,109:214,4:0.0183:2,0:11.8:1:27:1:0.12256:0:60:8:0.0193:0:1.5 0/0:156:0:0,0:89,66:155,0:0:2,0:28.8:1:29.8:1:1:0:59.8:18.375:1:0:0.7 +6 30458064 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=8.58128;LSEQ=GCTGCGAGCTGGGGCCCGAC;RSEQ=GGCGCTTCCTCCGCGGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:33:16,17:91,102:193,33:0.1454:2,2:25.7:1:31.1:1:1:1.05:60:66:0.1507:0:1.1 1/0:163:97:55,42:37,29:66,97:0.5951:2,2:30.2:1:29.2:1:1:1.03:59.7:23.25:0.6:0:1.1 +6 30458099 . C T 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.64317;LSEQ=GGGTATGAACAGTTCGCCTA;RSEQ=GACGGCAAGGATTATCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:73,120:193,2:0.0102:2,2:20.5:1:32.5:1:1:1.64:60:4:0.0104:0:1 0/0:152:1:1,0:70,81:151,1:0.0066:2,0:7:0:32:0:0.46711:0:60:2:0.0068:0:1 +6 30458100 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50532;SOR=0;LSEQ=GGTATGAACAGTTCGCCTAC;RSEQ=ACGGCAAGGATTATCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:72,118:190,2:0.0104:2,2:9.5:1:29:1:1:1.63:60:4:0.0105:0:2 0/0:152:0:0,0:70,82:152,0:0:2,0:25.1:1:29.3:1:1:0:59.3:29.4:1:0:0.6 +6 30458160 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50118;SOR=Inf;LSEQ=CCTGGACCGCGGTGGACACG;RSEQ=CGGCTCAGATCTCCGAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:16,50:66,0:0:2,0:21.6:1:32.3:1:1:0:60:132:1:0:0.1 0/1:80:2:1,1:28,50:78,2:0.025:2,2:21:1:29.5:1:1:1.77:60:4:0.026:0:1.5 +6 30458172 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50323;SOR=Inf;LSEQ=TGGACACGGCGGCTCAGATC;RSEQ=CCGAGCAAAAGTCAAATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:14,41:55,0:0:2,0:23.7:1:30.9:1:1:0:60:110:1:0:0.1 0/1:70:2:1,1:24,44:68,2:0.0286:2,2:13:1:28.5:1:1:1.82:60:4:0.0299:0:1 +6 30458248 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21601;SOR=Inf;LSEQ=AGACACATGCGTGGAGTGGC;RSEQ=CCACAAATACCTGGAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:18,39:57,0:0:2,0:28.7:1:30.5:1:1:0:60:56:1:0:0.1 0/1:50:2:1,1:17,31:48,2:0.04:2,2:33:1:29.5:1:1:1.80:60:4:0.0408:0:1 +6 30458260 . T A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22697;SOR=Inf;LSEQ=GGAGTGGCTCCACAAATACC;RSEQ=GGAGAAGGGGAAGGAGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:16,34:50,0:0:2,0:27.2:1:31:1:1:0:60:100:1:0:0.1 0/1:46:2:1,1:16,28:44,2:0.0435:2,2:24.5:1:32:1:1:1.73:60:4:0.0444:0:1 +6 30458322 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=0;LSEQ=TCCACAGGGCTACTCTCCCA;RSEQ=CTCCTTCTTGGGCTAGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:1,11:12,2:0.1429:2,0:25:1:30.5:1:1:0:60:4:0.1429:0:1 0/0:8:0:0,0:1,7:8,0:0:2,0:28:1:29.8:1:1:0:60:16:1:0:0 +6 30458735 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5148;SOR=0;LSEQ=TGGGCTAGCTCATCCCGATT;RSEQ=TAGAACTTTCCAAGGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:23,2:25,2:0.0741:2,2:41.5:1:29.5:1:0.21368:9.59167:60:4:0.0769:0:1 0/0:17:0:0,0:17,0:17,0:0:1,0:18.9:1:31.6:1:1:0:60:34:1:0:0.1 +6 30458802 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20202;SOR=Inf;LSEQ=GGCTGGTGTCAAGGTTTTGT;RSEQ=CTCTTCTCCTACTATAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:79,0:79,0:0:1,0:24.5:1:31.5:1:1:0:60:25.333:1:0:0.1 0/1:65:2:1,1:59,4:63,2:0.0308:2,2:24:1:28:1:0.14904:13.30416:60:4:0.0313:0:1 +6 30458838 . G T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21215;SOR=Inf;LSEQ=AATTGTCCTCTTCCTTCTCA;RSEQ=GATGGTCACATGGGTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:137,17:154,0:0:2,0:22.2:1:32.3:1:1:0:59.6:29.8:1:0:0.1 0/1:132:2:1,1:110,20:130,2:0.0152:2,2:6.5:1:30:1:0.29389:5.39189:60:4:0.0154:0:1 +6 30458974 . G A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35098;SOR=3.32652;LSEQ=CCATGAGGCCACCCTGAGGT;RSEQ=CTGGGCCCTGGGCTTCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:1:1,0:74,155:229,1:0.0043:2,0:25:0:11:0:0.32609:0:30:0:0:0:5 0/1:209:3:2,1:70,136:206,3:0.0144:2,2:22.7:1:28:1:0.27325:3.86:47.3:6:0.0147:0:1 +6 30458979 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22212;SOR=Inf;LSEQ=AGGCCACCCTGAGGTGCTGG;RSEQ=CCCTGGGCTTCTACCCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:60,137:197,0:0:2,0:17.6:1:31.1:1:1:0:38.1:27.143:1:0:0.1 0/1:177:2:1,1:59,116:175,2:0.0113:2,2:10.5:1:28:1:1:1.96:52:4:0.0114:0:1 +6 30459130 . A T 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10214;SOR=0;LSEQ=GGTGCCTTCTGGAGAGGAGC;RSEQ=GAGATACACGTGCCATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:3:0,3:158,77:235,3:0.0126:2,0:5:1:27.7:1:0.03703:0:59.7:6:0.0128:0:1 0/0:270:0:0,0:154,116:270,0:0:2,0:23.7:1:29.6:1:1:0:44.4:89:1:0:0.2 +6 30459165 . C T 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGTGCAGCATGAGGGGCTA;RSEQ=CCGAGCCCGTCACCCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:42:21,21:218,175:393,42:0.0966:2,2:30.1:1:30.6:1:0.51779:1.24507:53.3:84:0.0981:0:1.2 0/0:457:0:0,0:236,221:457,0:0:2,0:29.8:1:30.7:1:1:0:50.7:75.167:1:0:0.2 +6 30459450 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.24964;SOR=Inf;LSEQ=GGTGGGGAAGGGAGAAGGGT;RSEQ=GGGTCTGAGTTTTCTTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:63,197:260,0:0:2,0:25.3:1:31.1:1:1:0:59.9:36.143:1:0:0.1 0/1:280:3:2,1:97,180:277,3:0.0107:2,2:9.3:1:24:1:0.28591:3.69:60:6:0.0108:0:1 +6 30459475 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=CTGAGTTTTCTTGTCCCACT;RSEQ=GGTGTTTCAAGCCCTAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:32,136:168,2:0.0118:2,2:23.5:1:29.5:1:0.35148:4.20:60:4:0.0119:0:1.5 0/0:157:0:0,0:40,117:157,0:0:2,0:23:1:30.4:1:1:0:59.8:156:1:0:0.1 +6 30460232 . C T 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00068;SOR=Inf;LSEQ=GTGTAAGTGCGGGGCGGGAG;RSEQ=GTGGAGGAGCTCGCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:51,15:66,0:0:2,0:24:1:30.4:1:1:0:60:12.2:1:0:0.2 0/1:57:9:7,2:40,8:48,9:0.1579:2,2:25.7:1:27.4:1:0.65047:1.41894:60:8:0.1429:0:1.3 +6 30460300 . GT G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.05221;SOR=Inf;LSEQ=GTGGGCTCTGACCAGGTCTT;RSEQ=TTTTGTTCTACCCCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:95,88:183,0:0:2,0:27.9:1:29.6:1:1:0:60:60:1:0:0.2 0/1:170:4:2,2:91,75:166,4:0.0235:2,2:29.5:1:31.1:1:1:1.21194:60:8:0.0241:0.0059:0 +6 30460318 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.60614;SOR=2.21879;LSEQ=TTGTTTTTGTTCTACCCCAG;RSEQ=GAGCGACAGTGCCCAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:1,0:86,103:189,1:0.0053:2,0:34:0:32:0:0.45789:0:60:2:0.0053:0:1 0/1:172:2:0,2:84,86:170,2:0.0116:2,0:21.5:1:26.5:1:0.49735:0:60:4:0.0118:0:1 +6 30460323 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23346;SOR=Inf;LSEQ=TTTGTTCTACCCCAGGGAGC;RSEQ=ACAGTGCCCAGGGGTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:87,105:192,0:0:2,0:27.5:1:30.7:1:1:0:59.9:95:1:0:0.2 0/1:180:2:1,1:84,93:177,2:0.0111:2,2:38.5:1:28:0:1:1.11:60:4:0.0112:0:1 +6 30460341 . G T 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.06157;LSEQ=GCGACAGTGCCCAGGGGTCT;RSEQ=AGTCTCACAGCTTGTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:69,102:171,2:0.0115:2,2:23.5:1:29:1:1:1.47:60:4:0.0118:0:1 0/1:164:2:1,1:68,93:161,2:0.0122:2,2:31:1:27.5:1:1:1.36:60:4:0.0123:0:1 +6 30545661 . GAGC G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.20777;SOR=0;LSEQ=AGAAAGTGCTCAAGGAGAAG;RSEQ=AGCAGCAGCAGCAACAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:34,29:63,2:0.0308:2,2:16.5:1:33.5:1:1:1.16953:60:4:0.0313:0:0 0/0:77:0:0,0:38,39:77,0:0:2,0:24.9:1:29.4:1:1:0:59.9:76:1:0:0.2 +6 30545707 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50051;SOR=Inf;LSEQ=GCAGGTACAAGTGCCACAGG;RSEQ=CCCACCAATCCTGGGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:20,29:49,0:0:2,0:26.3:1:31.6:1:1:0:60:98:1:0:0.1 0/1:60:2:1,1:23,35:58,2:0.0333:2,2:27.5:1:29.5:1:1:1.51:60:4:0.0339:0:1.5 +6 30545737 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49514;SOR=0;LSEQ=CCTGGGAGGCATCTGGGTTC;RSEQ=ACCAACCCCTTTCCAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:7,25:32,2:0.0588:2,2:31:1:28:1:0.42068:3.41:60:4:0.0606:0:1 0/0:29:0:0,0:10,19:29,0:0:2,0:21.6:1:30.3:1:1:0:60:58:1:0:0.1 +6 30668071 . C G 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01632;SOR=Inf;LSEQ=AACAAACAAACAAAAAACAA;RSEQ=CTGTGGCTTCCAAATCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:44,3:47,0:0:2,0:27.1:1:32.1:1:1:0:59.4:46:1:0:0.3 0/1:17:3:3,0:13,1:14,3:0.1765:1,0:14.7:1:33.3:1:1:0:60:6:0.1765:0:1 +6 30668143 . A C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06777;SOR=Inf;LSEQ=CCCACCCATGTTCCAGGACA;RSEQ=GTTGTATCAATATACCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:122,15:137,0:0:2,0:23.1:1:30.5:1:1:0:59.6:67.5:0.9926:0:0.2 0/1:96:3:3,0:81,12:93,3:0.0313:2,0:27:1:33.3:1:1:0:60:6:0.033:0:1 +6 30668159 . C T 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00718;SOR=Inf;LSEQ=GACAAGTTGTATCAATATAC;RSEQ=CCAATCCTTTCTAACGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:147,26:173,0:0:2,0:24.9:1:31.2:1:1:0:59.9:42.25:1:0:0.1 0/1:138:6:3,3:107,25:132,6:0.0435:2,2:22.5:1:29.2:1:0.09788:4.21934:60:12:0.0444:0:1.5 +6 30668226 . A G 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCGTGGTCTGGGAGGGAA;RSEQ=AGGGTAGTGGAGTTCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:662:0:0,0:466,195:661,0:0:2,0:25:1:30.7:1:1:0:60:93.429:1:0:0.1 0/1:526:25:17,8:314,185:499,25:0.0475:2,2:26.7:1:31.2:1:0.67596:1.25:60:24:0.0465:0:1.4 +6 30668374 . G A 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=86.15569;LSEQ=AGTGGAATGGAGCAATGAGG;RSEQ=AAGTCCTGAGGGCATGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1260:1:1,0:573,684:1257,1:8e-04:2,0:1:0:24:0:0.45628:0:60:2:8e-04:0:1 0/1:1076:69:37,32:495,511:1006,69:0.0641:2,2:22.9:1:29.7:1:0.5343:1.19:59.9:138:0.0648:0:1.2 +6 30668447 . A G 136 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=8.54738;LSEQ=AAGGCAAAATCAGGTGAAAA;RSEQ=GAATCCTAGAAATGGGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:3:1,2:160,447:607,3:0.0049:2,2:25.7:1:33.3:1:1:1.40:60:6:0.005:0:1 0/1:542:22:7,15:171,349:520,22:0.0406:2,2:26.3:1:30.5:1:1:1.04985:60:44:0.0406:0:1.4 +6 30668488 . C G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.43378;SOR=0.84529;LSEQ=GGACCCACTAACCAGTCTTA;RSEQ=CATCACTAAAATAATACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:101:8,93:16,156:172,101:0.37:2,2:23:1:32.2:1:0.82608:1.19153:59.8:49.5:0.368:0:1.1 0/1:196:65:5,60:11,120:131,65:0.3316:2,2:22.4:1:32:1:1:1.09948:60:130:0.3368:0:1.1 +6 30668679 . C CA 28 v3;MSI12;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=22.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGTCTCTACTAAAAATA;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,2:2,2:0.2857:0,0:35:1:28.5:1:1:0:27.5:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 30669956 . T C 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AGGCTGAGGCAGGAGAATGG;RSEQ=GTGAACCCAGGAGGCGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:27:1:18.5:1:1:0:44.5:1:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:32:1:1:0:24:4:1:0:1 +6 30670292 . C T 144 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07962;LSEQ=AGCCACCTCTTTAACTGCCA;RSEQ=TGCCACCTCACCCAGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:744:28:17,11:466,250:716,28:0.0376:2,2:23.7:1:30.1:1:0.68773:1.20579:60:56:0.0379:0:1 0/0:645:2:0,2:382,261:643,2:0.0031:2,0:12:1:27.5:1:0.16589:0:60:4:0.0031:0:1 +6 30670674 . G A 86 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39685;SOR=0.56479;LSEQ=ACTAAGGACGGCAGCAGTCA;RSEQ=CATCAAAGCTCAGCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:8:4,4:227,368:595,8:0.0133:2,2:19.5:1:28.9:1:0.4899:1.62:60:7:0.0119:0:1 0/0:531:4:3,1:198,329:527,4:0.0075:2,2:20.3:1:26.8:1:0.15449:4.97:60:8:0.0076:0:1.3 +6 30670700 . A C 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCTCAGCCCAGCCCCTCA;RSEQ=TCAGCTCTGCTGCCTAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:0:0,0:137,308:445,0:0:2,0:24.2:1:30.6:1:1:0:60:36.083:1:0:0.1 0/1:357:62:19,43:99,196:295,62:0.1737:2,2:20.4:1:31.2:1:0.76674:1.14274:60:61:0.1723:0:1.1 +6 30670842 . G A 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCACTATATGAGCAGTCTT;RSEQ=CCACTATATCGGTCTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:636:0:0,0:400,236:636,0:0:2,0:24.2:1:31.9:1:1:0:60:36.412:1:0:0.1 0/1:524:33:23,10:314,176:490,33:0.063:2,2:26.5:1:27.7:1:0.57723:1.29:60:66:0.0643:0:1.2 +6 30671312 . A C 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGGTTTTGGAGTCACGAC;RSEQ=TCCTGAGATTGAGAAAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:826:0:0,0:343,483:826,0:0:2,0:22.5:1:30.8:1:1:0:59.9:81.6:1:0:0.1 0/1:613:27:11,16:230,356:586,27:0.044:2,2:17.8:1:30.7:1:1:1.06:60:54:0.0444:0:1 +6 30671452 . T C 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCTTCCTTGATAATCAC;RSEQ=GTCTTCTGGGAGACTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1107:0:0,0:576,530:1106,0:0:2,0:25.2:1:31.2:1:1:0:60:84.077:1:0:0.1 0/1:997:38:25,13:512,446:958,38:0.0381:2,2:26.9:1:29.8:1:0.13974:1.67:60:76:0.0385:0:1.1 +6 30671588 . A T 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGATCTACCTGCTGGTTCC;RSEQ=CCTTTTGGATCTGGGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1070:0:0,0:514,556:1070,0:0:2,0:24.6:1:30:1:1:0:60:61.941:1:0:0.2 0/1:979:48:20,28:454,473:927,48:0.049:2,2:25.3:1:29:1:0.37508:1.34335:60:47:0.0489:0:1.2 +6 30671650 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27422;LSEQ=TGGGGAGAGGCAGGCTCAGG;RSEQ=ATGGCTGTAAGGGATTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:942:219:105,114:357,365:722,219:0.2325:2,2:25.5:1:31.6:1:0.7005:1.06182:60:35.5:0.2323:0:1.1 0/1:822:63:27,36:378,381:759,63:0.0766:2,2:20.8:1:30.2:1:0.29769:1.32238:59.9:30.5:0.0758:0:1.1 +6 30671726 . G C 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=44.67725;LSEQ=CCTGGGATTTAGGTTCCAAG;RSEQ=GTGCAGAGCAAGGCTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:861:1:0,1:427,432:859,1:0.0012:2,0:19:0:8:0:1:0:60:0:0:0:8 0/1:707:35:17,18:326,345:671,35:0.0495:2,2:24.9:1:30.6:1:1:1.00051:60:34:0.0489:0:1.1 +6 30671760 . C T 141 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.30023;LSEQ=CTTATGGTCAATGGGAGCTG;RSEQ=GAGGGAGCCAGGGTTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:842:3:1,2:412,427:839,3:0.0036:2,2:7.3:1:29.3:1:1:1.92829:60:6:0.0036:0:1 0/1:682:31:13,18:325,325:650,31:0.0455:2,2:23.9:1:28.6:1:0.46308:1.38395:60:30:0.0446:0:1.3 +6 30671969 . G C 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACGGACTGGTCTGTGGGG;RSEQ=TAAAAGGCTCAAGATCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1330:0:0,0:695,632:1327,0:0:2,0:24.8:1:31.5:1:1:0:60:50.038:0.9977:0:0.2 0/1:1188:38:20,18:601,547:1148,38:0.032:2,2:27.9:1:30.8:1:1:1.01:60:76:0.0323:0:1.1 +6 30671989 . G C 218 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAAAAGGCTCAAGATCAGA;RSEQ=GCTGCTGGTTCAACTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1465:0:0,0:767,694:1461,0:0:2,0:25.5:1:32.1:1:1:0:60:51.179:0.9986:0:0.2 0/1:1295:149:82,67:572,573:1145,149:0.1151:2,2:25.1:1:30.2:1:0.25816:1.23:59.9:73.5:0.1143:0:1.1 +6 30672326 . T C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0968;LSEQ=TGGGCTCAGGGGTGACAGGT;RSEQ=GGTCTGTGGAGGTGGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1793:654:313,341:553,584:1137,654:0.3648:2,2:25.3:1:30.2:1:0.76838:1.03162:45.4:35.333:0.3653:0:2 0/1:1558:82:37,45:741,734:1475,82:0.0526:2,2:24.5:1:29.5:1:0.42724:1.22765:44.6:81:0.0532:0:2 +6 30672342 . A G 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.50679;LSEQ=AGGTTGGTCTGTGGAGGTGG;RSEQ=AGGCTGGAGCTCAGGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1738:649:299,350:526,559:1085,649:0.3734:2,2:26.5:1:31.3:1:0.34532:1.1014:46.3:37.176:0.3707:0:2 0/1:1522:353:173,180:573,594:1167,353:0.2319:2,2:25.3:1:30.4:1:1:1.00368:52:69.6:0.2342:0:1.4 +6 30672433 . C A 201 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=54.70159;LSEQ=CTAGTGGTCCGAGATGTGGG;RSEQ=TCAGAGGTGACAGGCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1297:3:1,2:658,633:1291,3:0.0023:2,2:33.3:1:32:1:0.61787:2.07784:59.3:6:0.0023:0:1 0/1:1073:121:66,55:491,461:952,121:0.1128:2,2:24.6:1:29.1:1:0.56316:1.13:58.7:39.333:0.112:0:1.2 +6 30672463 . G A 187 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=97.0295;LSEQ=ACAGGCTGGTCTGTGGAGGC;RSEQ=GAAGCCTGTAGCTCAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1458:1:1,0:746,711:1457,1:7e-04:2,0:1:0:30:0:1:0:26:2:7e-04:0:1 0/1:1264:79:42,37:600,584:1184,79:0.0625:2,2:24.7:1:29.8:1:0.72776:1.10:53.6:158:0.0633:0:1.1 +6 30672718 . G A 176 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=19.80057;LSEQ=TCTGTGGAAGTGGAAGGCTC;RSEQ=AGCTTAGGGGCTGTGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2059:4:3,1:978,1074:2052,4:0.0019:2,2:14.8:1:28:1:0.35336:3.29:60:8:0.002:0:1.3 0/1:1778:66:35,31:832,878:1710,66:0.0371:2,2:29:1:29.2:1:0.53127:1.19:60:65:0.037:0:1.1 +6 30672757 . G A 189 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=47.87718;LSEQ=ACAAGTGTTTCAGGGGTCTT;RSEQ=CCAGAGGATCTATTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1788:3:3,0:874,908:1782,3:0.0017:2,0:1:0:24.7:1:0.11839:0:60:6:0.0017:0:1.3 0/1:1461:109:61,48:650,700:1350,109:0.0746:2,2:16.9:1:28:1:0.13494:1.37:58.2:53.5:0.0738:0:1.2 +6 30673013 . A G 193 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CAGGGGTCTTGACAGAGGAC;RSEQ=TATTTGTCCTGCTCCTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1584:0:0,0:816,762:1578,0:0:2,0:23.4:1:30.3:1:1:0:57.5:32.574:0.9974:0:0.2 0/1:1402:88:46,42:673,638:1311,88:0.0628:2,2:23.7:1:30:1:0.91247:1.04:50.6:87:0.0635:0:1.2 +6 30673064 . C T 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=40.75421;LSEQ=TGGGCTTGGGGGTGACAGGT;RSEQ=GGTCTGTGGAGGTGGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1824:2:0,2:872,949:1821,2:0.0011:2,0:1:0:26:0:0.50067:0:26.5:4:0.0011:0:1 0/1:1562:67:39,28:770,723:1493,67:0.0429:2,2:29.9:1:29.4:1:0.31844:1.31:28.2:32.5:0.0428:0:1.6 +6 30673113 . G T 166 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=73.78355;LSEQ=AGGGGCTGTGGGCACAACTG;RSEQ=TTCAGGGGTCTTGACAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1574:1:0,1:740,830:1570,1:6e-04:2,0:6:0:32:0:1:0:60:2:6e-04:0:1 0/1:1226:55:34,21:550,618:1168,55:0.0449:2,2:22.9:1:28.8:1:0.03795:1.82:28.7:110:0.0456:0:1.7 +6 30673288 . G T 189 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=57.08744;LSEQ=CTTCCCCTAGTAGCCTGAGA;RSEQ=GTGGGTTCAGAGGTGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2265:2:0,2:1170,1091:2261,2:9e-04:2,0:38:1:15.5:1:0.23317:0:37.5:0:0:0:3.5 0/1:1955:94:50,44:954,903:1857,94:0.0481:2,2:31.8:1:28.9:1:0.75199:1.08:34.3:17.8:0.0465:0:1.7 +6 30673340 . A G 167 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=30.39454;LSEQ=AGGTGGAAGGCTGGAGCTCA;RSEQ=GGGCTGTGGGCACAACTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2364:2:1,1:1145,1215:2360,2:8e-04:2,2:14.5:1:23.5:1:1:1.06:55.5:1:4e-04:0:1 0/1:1952:49:26,23:933,965:1898,49:0.0251:2,2:13.3:1:29.9:1:0.66485:1.17:31.2:15.333:0.0241:0:2.3 +6 30673351 . C G 127 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00037;SOR=4.62355;LSEQ=TGGAGCTCAAGGGCTGTGGG;RSEQ=ACAACTGTTTCAGGGGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2202:6:3,3:1057,1138:2195,6:0.0027:2,2:33.3:1:17.2:1:1:1.08:39.2:0.2:5e-04:0:2.3 0/1:1763:22:11,11:840,894:1734,22:0.0125:2,2:12.3:1:28.5:1:1:1.06:31.5:10:0.0116:0:2.5 +6 30673422 . A G 208 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=151.62401;LSEQ=AACCTGAGATGTGGGCTCAG;RSEQ=GGTGACAGGCTGGTCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1437:1:1,0:706,730:1436,1:7e-04:2,0:45:0:31:0:0.492:0:29:2:7e-04:0:1 0/1:1203:115:58,57:521,567:1088,115:0.0956:2,2:26.5:1:30.5:1:0.6246:1.11:33.8:114:0.0967:0:1.3 +6 30673489 . G C 202 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGGGGACAACTGGTTCAGG;RSEQ=GTCTTGACAGAGGACCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1463:0:0,0:741,722:1463,0:0:2,0:25.2:1:31.1:1:1:0:44.9:53.185:1:0:0.1 0/1:1110:114:59,55:503,491:994,114:0.1027:2,2:25.8:1:29.7:1:0.84363:1.05:42.7:37:0.1023:0:1.3 +6 30673625 . G A 194 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=113.67533;LSEQ=GAAAGGGTGTCATTCTGGAG;RSEQ=ACTTCCGAGTTCTAATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1596:1:1,0:691,902:1593,1:6e-04:2,0:1:0:25:0:0.43413:0:60:2:6e-04:0:1 0/1:1532:102:51,51:684,746:1430,102:0.0666:2,2:23.2:1:29.2:1:0.68289:1.09:60:101:0.0668:0:2 +6 30673662 . G C 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAGGCTTTGGGTGGAAAG;RSEQ=CTCCAGCTCTGAGGACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1240:0:0,0:511,728:1239,0:0:2,0:24.7:1:31.7:1:1:0:59.9:50.625:0.9992:0:0.1 0/1:1098:64:29,35:478,552:1030,64:0.0583:2,2:23.9:1:31.3:1:0.89781:1.04507:60:128:0.0593:0:2.7 +6 30673681 . G A 174 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=67.41048;LSEQ=GGCTCCAGCTCTGAGGACAA;RSEQ=GGAGCCTCTGGAGCTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1134:1:1,0:461,670:1131,1:9e-04:2,0:1:0:26:0:0.40813:0:60:2:9e-04:0:1 0/1:978:55:24,31:395,527:922,55:0.0562:2,2:20.9:1:30.1:1:1:1.03:60:110:0.0568:0:2.6 +6 30673888 . A G 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04324;SOR=Inf;LSEQ=TGATCGCCCTAGGGAGAAAC;RSEQ=GAAGCAAGTGAGGGGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:76,229:305,0:0:2,0:26:1:31.9:1:1:0:60:100.667:0.9967:0:0.2 0/1:258:4:2,2:79,174:253,4:0.0155:2,2:24:1:29.8:1:0.59253:2.20:60:8:0.0158:0:1 +6 30675036 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12244;SOR=Inf;LSEQ=GAATAGAAGCCAATCAAGGC;RSEQ=TGACAAAAATGGAAGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:193,3:196,0:0:1,0:24.8:1:30.7:1:1:0:59.9:392:1:0:0 0/1:106:2:2,0:102,2:104,2:0.0189:1,0:13.5:1:30.5:1:1:0:60:4:0.0189:0:1 +6 30675135 . T C 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATAGAGATGACTTGTGGAA;RSEQ=AGGAGGTAGAAAAAGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:947:0:0,0:560,387:947,0:0:2,0:25.8:1:29.9:1:1:0:60:156.833:1:0:0.1 0/1:826:81:49,32:410,334:744,81:0.0981:2,2:26.3:1:30.9:1:0.41003:1.25:60:39.5:0.0974:0:1.2 +6 30675605 . T G 221 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0;SOR=185.24352;LSEQ=GCTACTGGTCTCTCTACTTC;RSEQ=CTCTCAAATGCTTTGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1517:1:1,0:739,774:1513,1:7e-04:2,0:15:0:9:0:0.48877:0:53:0:0:0:2 0/1:1480:161:79,82:646,670:1316,161:0.1088:2,2:24.9:1:30.2:1:1:1.00079:60:79.5:0.1085:0:1.1 +6 30676046 . C G 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTCCATAGGCCTCAAGGTG;RSEQ=GTGTCAAAAGGCTGGGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:832:0:0,0:330,502:832,0:0:2,0:24.7:1:30.5:1:1:0:60:42.789:1:0:0.1 0/1:705:62:30,32:272,369:641,62:0.0879:2,2:22.7:1:29.9:1:0.42051:1.27:60:61:0.0884:0:1.2 +6 30676152 . AAG A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.63328;SOR=0.71403;LSEQ=TACCTGGAAGGGGAGGAAGG;RSEQ=AGAGAGAGAGGGAGAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:13:2,11:57,212:269,13:0.0461:2,2:29.9:1:31.1:1:1:1.47691:60:26:0.0473:0.0071:0.2 0/1:180:6:1,5:46,128:174,6:0.0333:2,2:29:1:30.3:1:1:1.79186:60:12:0.0343:0:0.5 +6 30676173 . A G 23 v3;pSTD;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13253;SOR=Inf;LSEQ=AGAGAGAGAGAGGGAGAGGG;RSEQ=GAGAAAAGAGGGAGAGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:35,172:207,0:0:2,0:22.2:1:31.5:1:1:0:60:68:1:0:0.1 0/1:119:2:1,1:18,99:117,2:0.0168:2,2:17:0:23.5:1:0.29497:5.38:60:4:0.0171:0:1.5 +6 30679134 . G GA 96 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01143;SOR=9.88528;LSEQ=ATCCAGCCTGAGTGACAGAG;RSEQ=AAAAAAAAGAGAATGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:592:1:1,0:476,114:590,1:0.0017:2,0:34:0:27:0:1:0:60:2:0.0017:0:0 0/1:607:10:7,3:421,173:594,10:0.0165:2,2:17.3:1:28.9:1:1:1.04287:60:20:0.0167:0.0066:0 +6 30679289 . G C 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGCTCTGGACTGCTGTACA;RSEQ=GAAAAGATGGCCTAAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1030:0:0,0:373,657:1030,0:0:2,0:25.5:1:31.8:1:1:0:60:63.375:1:0:0.1 0/1:833:59:23,36:286,488:774,59:0.0708:2,2:23.5:1:30:1:0.78061:1.09:60:118:0.0713:0:1.5 +6 30679333 . T C 202 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=174.34118;LSEQ=CCTCCATACTACTGTAGGGT;RSEQ=CCATTCCTGGTCTCCTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:675:1:0,1:269,405:674,1:0.0015:2,0:29:0:15:0:1:0:60:0:0:0:1 0/1:466:96:41,55:142,227:369,96:0.206:2,2:17.5:1:30.8:1:0.48243:1.19:60:192:0.2073:0:1.4 +6 30679628 . T A 303 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=78.86946;LSEQ=CCTGGTTGATTTCAGAGGTC;RSEQ=AGGAAGGAAGGCCAGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1153:985:547,438:90,76:166,985:0.8543:2,2:26.6:1:30.5:1:0.80024:1.05:60:88.545:0.8544:0:1.1 1/1:928:926:497,429:0,1:1,926:0.9978:0,2:26.3:1:29.3:1:0.46386:0:60:53.471:0.9978:0:1.1 +6 30680562 . G A 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTCCAGAGGGACAGCCTGT;RSEQ=GGGCCTTGCCTTCTTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:780:0:0,0:424,354:778,0:0:2,0:23.7:1:31.8:1:1:0:60:85.444:0.9987:0:0.1 0/1:617:59:29,30:292,264:556,59:0.0956:2,2:24.7:1:29.1:1:0.68165:1.14395:60:118:0.097:0:1.8 +6 30680608 . C T 186 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=116.86249;LSEQ=ATCACTACCAGCCTGGCTCT;RSEQ=CTGCAGATGGGCCAGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:882:1:1,0:495,386:881,1:0.0011:2,0:13:0:13:0:1:0:60:0:0:0:2 0/1:699:82:43,39:327,290:617,82:0.1173:2,2:22.7:1:29.3:1:1:1.02267:60:81:0.1179:0:1.5 +6 30680916 . C T 187 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=88.07102;LSEQ=TGACTTTTGTATCATTGTCC;RSEQ=TCTCCTTCACTAAAGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1480:1:0,1:667,809:1476,1:7e-04:2,0:2:0:28:0:1:0:60:2:7e-04:0:1 0/1:1440:81:37,44:634,721:1355,81:0.0563:2,2:24.4:1:29.6:1:0.9089:1.04567:60:162:0.0568:0:1.2 +6 30681315 . G T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05785;LSEQ=CTGAGTGAATGAATATGTAT;RSEQ=GTTCCCCAGCCCCAACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:19:16,3:118,11:129,19:0.1284:2,2:14.9:1:31.1:1:0.39195:1.9998:58.2:38:0.1301:0:1 0/1:89:12:11,1:73,4:77,12:0.1348:2,2:25.7:1:29.3:1:0.524:1.64805:60:11:0.1279:0:1 +6 30681359 . T C 93 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01592;SOR=9.01487;LSEQ=ATAATCATCTCTTTTAGAGA;RSEQ=TGATCCTCCAGCCCCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:1,0:233,62:295,1:0.0034:2,0:22:0:13:0:1:0:60:0:0:0:5 0/1:269:8:6,2:194,67:261,8:0.0297:2,2:22.8:1:31.3:1:1:1.04:60:16:0.03:0:1 +6 30681477 . G A 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=44.1215;LSEQ=CCTTGATTTTTTTACCATAC;RSEQ=CCTTTCAGAAAGAAAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:1:1,0:450,432:882,1:0.0011:2,0:1:0:25:0:1:0:60:2:0.0012:0:1 0/1:796:38:22,16:375,383:758,38:0.0477:2,2:27.6:1:28.6:1:0.324:1.40:60:76:0.0481:0:1.2 +6 30681980 . A G 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTAAGAATTAGAGAGGTAG;RSEQ=TAAGCTCCAAGATCAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:24,119:143,0:0:2,0:25.1:1:31.2:1:1:0:60:142:1:0:0 0/1:110:16:5,11:23,71:94,16:0.1455:2,2:32.7:1:30.3:1:0.54767:1.40:60:32:0.1455:0:1.8 +6 30682007 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0675;SOR=Inf;LSEQ=CCAAGATCAGAGTCCTGGCC;RSEQ=GTCATTAGGAAAAAGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:13,86:99,0:0:2,0:24.4:1:30.6:1:1:0:60:98:1:0:0 0/1:69:3:1,2:13,53:66,3:0.0435:2,2:12.3:1:30.3:1:0.49927:2.01:60:6:0.0455:0:2.7 +6 30682700 . G GA 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.21519;SOR=0.46531;LSEQ=GCCCCATCTCTTCCATTCAT;RSEQ=AAAAAAAAAAATTCACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:14:14,0:177,2:179,14:0.0714:1,1:24.5:1:30.1:1:1:0:60:28:0.0725:0.0153:0.1 0/1:116:4:3,1:109,2:111,4:0.0345:1,2:20.3:1:29.3:1:0.10162:16.66065:60:8:0.0351:0:0 +6 30683058 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02495;SOR=Inf;LSEQ=GTAAACTGGATCATTATGAA;RSEQ=GTTGATGCTTCTCTTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:1,154:155,0:0:1,0:26.2:1:30.6:1:1:0:59.8:310:1:0:0.1 0/1:65:3:1,2:2,60:62,3:0.0462:1,2:27.3:1:31:1:0.13416:13.33:60:6:0.0462:0:1 +6 30683117 . A AT 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00962;SOR=Inf;LSEQ=CCTTCTGAAGCACTTAAAAC;RSEQ=TTTTTTTCTTTTTTGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:48,0:0:1,0:19.2:1:31.9:1:1:0:59.7:47:1:0:0.1 0/1:14:3:0,3:0,11:11,3:0.2143:0,0:15:1:28.7:1:1:0:49.3:6:0.2143:0.1429:0 +6 30865058 . C T 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66992;SOR=0.61559;LSEQ=ATGTACGCTGGGGGTGGGGA;RSEQ=GCCTGGTCTGCCTGAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:27.4:1:32.8:1:1:0:60:10:0.4545:0:1.6 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:28.3:1:25:1:1:0:60:2:0.25:0:1 +6 30865115 . G A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17058;SOR=0.26506;LSEQ=CGCGGGGGAAGGTGCAGGCC;RSEQ=CCCACTCGGCATTCCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:10:8,2:19,3:22,10:0.3125:2,2:21.9:1:30.8:1:0.63675:1.55946:60:20:0.3226:0:1.3 0/1:19:2:2,0:13,4:17,2:0.1053:2,0:16.5:1:30:1:1:0:60:4:0.1053:0:1 +6 30865204 . A C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=0.18322;LSEQ=ATGTCGAGGCTCAAGGACCC;RSEQ=AACATCATTCGGCTGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:22:9,13:39,37:76,22:0.2245:2,2:25.3:1:32.7:1:0.47085:1.516:58.2:44:0.2245:0:1.3 0/1:120:6:3,3:55,59:114,6:0.05:2,2:16.2:1:31:1:1:1.07:60:12:0.0504:0:1.3 +6 30865225 . CGT C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=0.50634;SOR=Inf;LSEQ=AACATCATTCGGCTGCTGGG;RSEQ=GTGTGTGCAGGACGACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:31,42:73,0:0:2,0:27:1:31.2:1:1:0:60:146:1:0:0.3 0/1:96:2:1,1:41,52:93,2:0.0208:2,2:23:0:33.5:1:1:1.27:60:4:0.0211:0:0.5 +6 30865230 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.17382;SOR=0;LSEQ=CATTCGGCTGCTGGGCGTGT;RSEQ=TGTGCAGGACGACCCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:26,39:65,2:0.0299:2,2:31.5:1:28:1:1:1.49:60:4:0.0303:0:1 0/0:93:0:0,0:40,53:93,0:0:2,0:23.6:1:31.2:1:1:0:60:186:1:0:0.2 +6 30865279 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01478;SOR=Inf;LSEQ=ACTGACTACATGGAGAACGG;RSEQ=GACCTCAACCAGTTCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:5,28:33,0:0:2,0:23.5:1:29.7:1:1:0:60:66:1:0:0.1 0/1:27:5:1,4:1,21:22,5:0.1852:1,2:32.6:1:29.2:1:0.34188:4.81:60:10:0.1852:0:1 +6 30865991 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10638;SOR=Inf;LSEQ=ATCAAAATCGCAGACTTTGG;RSEQ=ATGAGCCGGAACCTCTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:21,11:32,0:0:2,0:21.8:1:32.2:1:1:0:60:64:1:0:0.1 0/1:16:2:1,1:9,5:14,2:0.125:2,2:23.5:1:27:1:1:1.73197:60:4:0.125:0:1.5 +6 30866035 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54338;SOR=0;LSEQ=GGACTATTACCGTGTGCAGG;RSEQ=CCGGGCAGTGCTGCCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:26,20:46,2:0.0417:2,2:11:0:32:0:1:1.29283:60:4:0.0426:0:1 0/0:25:0:0,0:11,14:25,0:0:2,0:33.4:1:31.1:1:1:0:60:50:1:0:0.2 +6 30954245 . T C 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACTCTGAGTTCAGCACAG;RSEQ=GTCCAGTGGGATCAGCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:2,0:2,5:0.7143:0,2:33:1:32.4:1:1:0:55.4:10:0.7143:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 30954873 . G A 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=0;LSEQ=ACCAACTCTGAGTCCAGTAC;RSEQ=ACCTCCAGTGGGGCCAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:25.5:1:30:1:1:0:29:4:0.4:0:1.5 0/0:9:0:0,0:4,5:9,0:0:2,0:26.8:1:30.6:1:1:0:57.3:18:1:0:0.4 +6 31052539 . C CT 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATGTCCTGCCTCCTCCT;RSEQ=TTTTTTTTTCTTCTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:28.6:1:1:0:60:4:1:0.5:0.5 +6 31053131 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22873;SOR=0;LSEQ=AGAGTAAAGGATGAAGTCCC;RSEQ=TTTAGAGAGATACACTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:2,0:93,10:103,2:0.019:2,0:29:1:32.5:1:1:0:60:4:0.0192:0:1 0/0:114:0:0,0:99,15:114,0:0:2,0:23.7:1:30.3:1:1:0:60:56:1:0:0.1 +6 31053257 . A C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01688;SOR=1.33208;LSEQ=AAATGCCACTGGTTTAAATT;RSEQ=GGTAGAAAATGTTTTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:242:128,114:160,146:306,242:0.4416:2,2:26.3:1:31.1:1:0.9314:1.02:60:79.667:0.4401:0:1.1 1/0:573:294:140,154:132,147:279,294:0.5131:2,2:27.2:1:30:1:1:1.01:60:588:0.514:0:1.2 +6 31053348 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58224;SOR=2.60696;LSEQ=GACCTGCTCTATCATTCCCC;RSEQ=AACTTATAGGACAAAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:1:1,0:44,169:213,1:0.0047:2,0:1:0:26:0:0.21028:0:60:2:0.0047:0:1 0/1:165:2:1,1:35,128:163,2:0.0121:2,2:19.5:1:27.5:1:0.3898:3.62:60:4:0.0123:0:1 +6 31053360 . CA C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.17137;SOR=Inf;LSEQ=CATTCCCCCAACTTATAGGA;RSEQ=AAAAGTCCGAGAAGCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:22,150:172,0:0:2,0:23.6:1:30.8:1:1:0:60:85:1:0:0.1 0/1:122:2:1,1:18,102:120,2:0.0164:2,2:12.5:1:32.5:1:0.28831:5.54:60:4:0.0165:0:0.5 +6 31053516 . G C 84 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTCCTCCTGGGGCCATC;RSEQ=TCCCAGGGGTTATGCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:11,6:0.3529:0,0:23.2:1:32.8:1:1:0:60:12:0.375:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31053521 . A G 82 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTGGGGCCATCGTCCC;RSEQ=GGGGTTATGCCTCGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:11,6:0.3529:0,0:22.3:1:31.8:1:1:0:60:12:0.3529:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31162154 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAGAAATTCATGTTCTG;RSEQ=ATTCTGAGCAATGCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:28:1:1:0:60:4:1:0:1 +6 31162384 . G A 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAACCTTGAGCGCAAGGG;RSEQ=GGTTTGGTTCCTCTTACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:36.5:1:32:0:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31162520 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00057;SOR=0.092;LSEQ=GAAAGCGGAATGAAAGCAGG;RSEQ=CAAAAGTGGCTGGGAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:14:14,0:5,1:6,14:0.7:2,1:26.5:1:33.3:1:0.3:0:60:28:0.7:0:1 0/1:24:4:4,0:14,6:20,4:0.1667:2,0:20:1:32:1:0.53924:0:60:8:0.1667:0:1 +6 31162648 . C A 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00557;SOR=Inf;LSEQ=CATCCCTGCCCTCCAGAGCC;RSEQ=ACTTAGTCACACACTACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:23,34:57,0:0:2,0:24.4:1:31:1:1:0:60:27.5:1:0:0.1 0/1:44:6:2,4:17,21:38,6:0.1364:2,2:33.2:1:30.8:1:0.68428:1.60194:60:12:0.1364:0:1.2 +6 31162839 . C T 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGATTAGGGAAATAGTGT;RSEQ=TACATTTCAAAAGAGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:38.5:1:31.5:1:1:0:60:4:0.5:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:33:0:33:0:1:0:60:2:1:0:0 +6 31193144 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAACCCTGAGAAGAAAGAG;RSEQ=AACTTGACTGTCTGAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:14,2:0.125:2,2:15:1:28:1:1:1.73197:60:4:0.1333:0:3.5 0/0:5:0:0,0:3,2:5,0:0:2,0:27:1:26.2:1:1:0:60:4:1:0:1.6 +6 31193155 . T C 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07849;SOR=0.1408;LSEQ=AAGAAAGAGGAACTTGACTG;RSEQ=CTGAAGGCTCTTGGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:9,7:2,0:2,16:0.8889:0,2:23.1:1:30.2:1:0.49673:0:60:15:0.8824:0:3.1 1/0:6:3:2,1:2,1:3,3:0.5:2,2:30.7:1:30:1:1:1:60:6:0.5:0:2.3 +6 31193164 . T C 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05619;SOR=0.19946;LSEQ=GAACTTGACTGTCTGAAGGC;RSEQ=CTTGGGTGGTGTTTAAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:16:9,7:2,1:3,16:0.8421:2,2:28.9:1:31.1:1:1:1.52085:60:32:0.8421:0:3.1 1/0:12:6:4,2:3,3:6,6:0.5:2,2:16.2:1:29.3:1:1:1.89:60:12:0.5:0:2.5 +6 31193211 . C T 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53488;SOR=Inf;LSEQ=CACTGTGTCCTGGCTGAATG;RSEQ=ATACATGCAGATGGAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:26:13,13:1,1:2,26:0.9286:2,2:26.8:1:29.3:1:1:1:56.5:52:0.9286:0:2.7 1/1:15:15:7,8:0,0:0,15:1:0,2:37.9:1:28.9:1:1:0:60:30:1:0:1.8 +6 31193239 . CT C 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.57307;SOR=2.63458;LSEQ=CAGATGGAATCTCTTTCTTT;RSEQ=TTTTTTTTTTGAGACGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:6,9:15,1:0.0625:2,0:26:0:30:0:1:0:25:2:0.0625:0:1 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:34.5:1:33:0:1:1.18321:60:4:0.1538:0:2 +6 31193255 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.21733;SOR=0.27015;LSEQ=CTTTCTTTTTTTTTTTGAGA;RSEQ=GGAGTCTCGCTCTGTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:9:4,5:1,3:4,9:0.6923:2,2:15.4:1:30.6:1:1:2.25:52.1:18:0.6923:0:2.6 0/1:11:4:2,2:3,3:6,4:0.3636:2,2:13.3:1:30:1:1:1:60:8:0.3636:0:2.5 +6 31234911 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTGGAGTTGTCTGCCCA;RSEQ=CTGCCACCCCAGCTCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:31.5:1:1:0:34.5:4:1:0:3.5 +6 31234948 . C A 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACCTGCATTCCTAGTAG;RSEQ=CATGTCCTCCACTGAGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:26.5:1:1:0:34.5:4:1:0:3.5 +6 31234952 . G C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCATTCCTAGTAGCCAT;RSEQ=TCCTCCACTGAGTGCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:30.5:1:1:0:34.5:4:1:0:3.5 +6 31236034 . T C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCCCACACCAACCGCCC;RSEQ=GCACACTGCAGCACACGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:49:0:34:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:18:0:30:1:1:0:60:4:1:0:1 +6 31236853 . G A 56 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59207;SOR=2.46629;LSEQ=AGGAACGCAGACACATTCAG;RSEQ=TGCCTTTGCAGAAAGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:2,2:4,3:0.4286:2,0:24:1:31.3:1:0.42857:0:35:6:0.4286:0:1.3 1/0:6:4:3,1:1,0:1,4:0.6667:0,2:21.5:1:28:1:1:0:36.3:8:0.6667:0:1.3 +6 31236998 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15528;SOR=0.14089;LSEQ=TTCAGGTCAGTCATGGTAAG;RSEQ=GATGACACTCTGAACGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:11,5:0,1:1,16:0.9412:0,2:19.9:1:29.8:1:0.35294:0:42.6:32:0.9412:0:4.8 1/0:6:4:3,1:1,1:2,4:0.6667:2,2:24.3:1:29:1:1:2.45:44.3:8:0.6667:0:3.8 +6 31237002 . G C 41 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08079;SOR=8.59451;LSEQ=GGTCAGTCATGGTAAGCGAT;RSEQ=ACACTCTGAACGGCCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:1:1,0:11,5:16,1:0.0588:2,0:14:0:34:0:1:0:60:2:0.0588:0:7 0/1:8:3:3,0:3,2:5,3:0.375:2,0:11.7:1:26:1:0.46429:0:55.3:2:0.2857:0:6 +6 31237014 . G A 122 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=TAAGCGATGACACTCTGAAC;RSEQ=GCCCACCACACACTCGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:11,4:0,0:0,15:1:0,2:26.7:1:31.3:1:1:0:43.6:30:1:0:5.3 1/0:7:5:5,0:1,1:2,5:0.7143:2,0:21:1:30:1:0.28571:0:52.4:10:0.7143:0:5.2 +6 31237016 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AGCGATGACACTCTGAACGG;RSEQ=CCACCACACACTCGAAACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:10,4:14,0:0:2,0:29.2:1:33.1:1:1:0:44.6:28:1:0:5.6 0/1:7:2:2,0:4,1:5,2:0.2857:2,0:29:1:31:0:1:0:48:4:0.2857:0:4 +6 31237017 . C T 123 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02632;SOR=0;LSEQ=GCGATGACACTCTGAACGGC;RSEQ=CACCACACACTCGAAACGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:10,4:0,0:0,14:1:0,2:29.5:1:32.4:1:1:0:44.6:28:1:0:5.6 1/0:7:4:4,0:2,1:3,4:0.5714:2,0:13:1:30.3:1:0.42857:0:56.5:8:0.5714:0:5.5 +6 31237027 . C T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=0.12397;LSEQ=TCTGAACGGCCCACCACACA;RSEQ=TCGAAACGTCCCAATCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:15:12,3:1,0:1,15:0.9375:0,2:31.2:1:31.8:1:1:0:48.2:30:0.9375:0:5.5 1/0:8:5:5,0:2,1:3,5:0.625:2,0:15.2:1:30:1:0.375:0:57.2:10:0.625:0:5.2 +6 31237048 . A G 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1256;SOR=0.29144;LSEQ=TCGAAACGTCCCAATCAAAG;RSEQ=ATCCCCATTACCCAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:20:18,2:4,0:4,20:0.8333:0,2:25.6:1:32.3:1:1:0:54.8:40:0.8333:0:4.8 1/0:12:7:7,0:4,1:5,7:0.5833:2,0:30.9:1:32:1:0.41667:0:56.6:14:0.5833:0:4.6 +6 31237061 . C T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27541;SOR=0.43678;LSEQ=ATCAAAGAATCCCCATTACC;RSEQ=AGGCCTTTTCCCTCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:28:25,3:5,0:5,28:0.8235:0,2:18.6:1:32.3:1:1:0:57.3:56:0.8485:0:3.8 1/0:15:10:7,3:5,0:5,10:0.6667:0,2:20.8:1:29.3:1:0.50549:0:60:20:0.6667:0:3.5 +6 31237087 . C A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55246;SOR=0.62018;LSEQ=TTTTCCCTCTGCCCCACCCC;RSEQ=GACCACTTCAGCTCCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:9:5,4:33,17:50,9:0.1525:2,2:18.6:1:30.7:1:0.7078:1.54098:60:18:0.1525:0:3.4 0/1:40:4:2,2:22,14:36,4:0.1:2,2:31.8:1:28.3:1:1:1.55321:60:8:0.1:0:3.5 +6 31237110 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50322;SOR=0;LSEQ=CCACTTCAGCTCCCCAGAAT;RSEQ=TCACCTTTACAAGTGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:48,39:87,2:0.0225:2,2:18.5:1:30:0:1:1.22788:53:4:0.0227:0:3.5 0/0:71:0:0,0:42,29:71,0:0:2,0:23.7:1:30.6:1:1:0:59.9:70:1:0:1.6 +6 31237124 . T C 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05386;SOR=0.48756;LSEQ=CAGAATCTCACCTTTACAAG;RSEQ=GATGAGAGACTCATCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:77:37,40:11,7:18,77:0.8105:2,2:30.5:1:30.5:1:0.43347:1.6894:59.2:37.5:0.8152:0:2.3 1/0:80:54:29,25:17,9:26,54:0.675:2,2:28.5:1:30.8:1:0.34649:1.61851:59.9:108:0.6835:0:2.2 +6 31237148 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24315;SOR=Inf;LSEQ=GAGAGACTCATCAGAGCCCT;RSEQ=GGCACTGTTGCTGCCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:41,51:92,0:0:2,0:28.5:1:31.8:1:1:0:59.2:45:1:0:1.8 0/1:90:2:1,1:43,45:88,2:0.0222:2,2:20.5:1:29:1:1:1.05:60:4:0.0225:0:2.5 +6 31237162 . C G 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03943;SOR=0.47435;LSEQ=AGCCCTGGGCACTGTTGCTG;RSEQ=CTGGGGTAGAACAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:83:66:22,44:9,8:17,66:0.7952:2,2:24:1:31.8:1:0.16506:2.22679:57.5:65:0.7927:0:2.4 1/0:85:55:27,28:15,15:30,55:0.6471:2,2:25:1:31.3:1:1:1.03661:58.4:110:0.6548:0:2.2 +6 31237174 . CA C 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.03009;LSEQ=TGTTGCTGCCTGGGGTAGAA;RSEQ=AAAAAAAAGACCTGGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:24,44:68,2:0.0286:2,2:33:1:32.5:1:1:1.82:60:4:0.029:0:1.5 0/1:68:2:1,1:32,34:66,2:0.0294:2,2:42.5:1:31.5:1:1:1.06:60:4:0.0294:0:2 +6 31237230 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34621;SOR=0.47543;LSEQ=TGGGACAAGAGGAATTATGG;RSEQ=GTAGGTGAGCTCCTCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:15:2,13:2,5:7,15:0.6818:2,2:27.9:1:32:1:0.56459:2.4775:37.1:30:0.6818:0:3.3 1/0:20:10:3,7:1,9:10,10:0.5:2,2:23.3:1:30.7:1:0.58204:3.61:40.6:20:0.5:0:3.2 +6 31237233 . A G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20566;SOR=0.40988;LSEQ=GACAAGAGGAATTATGGAGT;RSEQ=GGTGAGCTCCTCCACACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:14:2,12:2,5:7,14:0.6667:2,2:27.2:1:32.3:1:0.57427:2.29323:35.5:28:0.6667:0:3.4 0/1:18:8:3,5:1,9:10,8:0.4444:2,2:27.3:1:31.3:1:0.27451:4.90:35.8:16:0.4444:0:3.5 +6 31237255 . G A 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71163;SOR=0.70851;LSEQ=GTGAGCTCCTCCACACGCCC;RSEQ=CCGCCATCACTTACACGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:3,9:1,5:6,12:0.6667:2,2:13.6:1:30.4:1:1:1.62:33.1:24:0.6667:0:3.3 1/0:12:7:3,4:0,5:5,7:0.5833:0,2:18.7:1:28.6:1:0.20455:0:31.1:14:0.6364:0:3.7 +6 31237323 . A G 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31561;SOR=4.58929;LSEQ=CTGTGGGAAGAAAATGCCCT;RSEQ=TGAGGGGACTGGGAGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:3,3:1,4:5,6:0.5455:2,2:21.2:1:30.8:1:0.54545:3.52:43:12:0.5455:0:3.2 1/1:7:6:2,4:0,1:1,6:0.8571:0,2:25.5:1:33:1:1:0:42:12:0.8571:0:3.7 +6 31237333 . T A 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58462;SOR=2.80823;LSEQ=AAAATGCCCTATGAGGGGAC;RSEQ=GGGAGGAGGCAGGGCCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:0,3:3,6:0.6667:0,2:21.2:1:30.2:1:0.46429:0:43:12:0.6667:0:3.2 1/1:7:6:2,4:0,1:1,6:0.8571:0,2:25.5:1:31.7:1:1:0:42:12:0.8571:0:3.7 +6 31237342 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=TATGAGGGGACTGGGAGGAG;RSEQ=CAGGGCCATGTGATCTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:9,0:0:2,0:23.2:1:32.1:1:1:0:55.3:18:1:0:1.9 0/1:11:2:0,2:3,6:9,2:0.1818:2,0:11:1:26.5:1:1:0:45.5:4:0.1818:0:3.5 +6 31237353 . T C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.31198;LSEQ=TGGGAGGAGGCAGGGCCATG;RSEQ=GATCTTAGGGGAACCTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:0,2:2,6:0.75:0,2:23.3:1:31:1:0.46429:0:57.3:12:0.75:0:3 1/1:10:8:2,6:1,1:2,8:0.8:2,2:21.3:1:28.6:1:1:2.64575:46.5:16:0.8:0:3.4 +6 31237405 . C T 85 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=AAGAGAAGTTTCCAGAACTA;RSEQ=GACTGCAGACCCAGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:35.3:1:31.7:1:1:0:60:6:1:0:2.7 1/0:11:7:3,4:2,2:4,7:0.6364:2,2:21.6:1:30.4:1:1:1.29868:52.3:14:0.6364:0:3.7 +6 31237437 . T C 52 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCAGGATCAGGAAACA;RSEQ=GGGGAAAGCAGTTGTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:28:0:1:0:60:2:1:0:4 1/0:5:3:2,1:1,1:2,3:0.6:2,2:37.7:1:33:1:1:1.73:42:6:0.6:0:4.3 +6 31237449 . T C 53 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAACATGGGGAAAGCAG;RSEQ=TGTGGGTTCTGGACCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:3:0:29:0:1:0:60:2:1:0:4 1/1:3:3:2,1:0,0:0,3:1:0,2:25.7:1:33.7:1:1:0:42:6:1:0:4.3 +6 31237463 . C G 52 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAGTTGTGGGTTCTGGA;RSEQ=CAACTGCCCTCCTAAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:11.7:1:33:0:1:0:42:6:1:0:4.3 +6 31237526 . C CA 47 d5;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTCATGAATGCTGGAAT;RSEQ=AGGACCCCAACACCATAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:36.7:1:30:1:1:0:27.7:6:1:0:1.3 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:6.5:1:30.5:1:1:0:32.5:4:0.6667:0.3333:2.5 +6 31237563 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59764;LSEQ=AATCATCAAGGTGATACATC;RSEQ=GTCCTTCATTGTCACATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:6,1:1,0:1,7:0.875:0,2:21.7:1:31.1:1:1:0:39.7:14:0.875:0:2.4 1/1:5:4:3,1:1,0:1,4:0.8:0,2:32.5:1:29.3:1:1:0:40.3:8:0.8:0:2.3 +6 31237575 . TCA T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0.4714;LSEQ=GATACATCCGTCCTTCATTG;RSEQ=CATGTGCTTCACAAAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:8,1:1,0:1,9:0.9:0,2:20.6:1:31.1:1:1:0:44.2:18:0.9:0.1:2.6 1/1:5:4:3,1:1,0:1,4:0.8:0,2:39.5:1:29.5:1:1:0:40.3:8:0.8:0:2.3 +6 31237592 . A C 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTGTCACATGTGCTTCACAA;RSEQ=AGAGTAAGTGCTGGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:13,1:1,0:1,14:0.9333:0,1:19.8:1:31.5:1:1:0:54.6:13:0.9286:0:3.1 1/1:6:6:4,2:0,0:0,6:1:0,2:24.2:1:31:1:1:0:46.8:12:1:0:2.5 +6 31237605 . G A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55829;SOR=2.71122;LSEQ=TTCACAAAAGAGTAAGTGCT;RSEQ=GCACACAGGGTCCCAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:17,2:0.1053:1,0:31:1:28:1:1:0:48:4:0.1053:0:5 0/1:8:2:2,0:4,2:6,2:0.25:2,0:7:1:28:1:1:0:60:4:0.25:0:4 +6 31237660 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.21429;SOR=0;LSEQ=TGGATGGTGCTTCCAGTAAC;RSEQ=AGGCGGGGCACACTTCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:32,1:0,0:0,33:1:0,1:28.2:1:28.5:1:1:0:51.5:32:1:0:3.5 1/1:9:8:7,1:1,0:1,8:0.8889:0,2:24.9:1:30.5:1:1:0:43.1:16:0.8889:0:4 +6 31237664 . C T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21951;SOR=0;LSEQ=TGGTGCTTCCAGTAACAAGG;RSEQ=GGGGCACACTTCTACCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:31,1:0,0:0,32:1:0,1:29.2:1:29.1:1:1:0:51.3:31:1:0:3.5 1/1:9:8:7,1:1,0:1,8:0.8889:0,2:24.9:1:30.1:1:1:0:43.1:16:0.8889:0:4 +6 31237703 . G A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2357;SOR=0.29876;LSEQ=GGGCTTGAAACTCCCAGTGG;RSEQ=ACAAGAAAACCCAGACCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:15:14,1:13,0:13,15:0.5357:1,1:24.6:1:27.3:1:1:0:46.3:14:0.56:0:4.1 0/1:8:2:2,0:6,0:6,2:0.25:0,0:38:0:25:0:1:0:31:4:0.25:0:5 +6 31237723 . G A 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94581;LSEQ=GACAAGAAAACCCAGACCCC;RSEQ=CTCTTCACCCCTTCCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:12:11,1:16,1:17,12:0.4138:1,2:12.2:1:25.7:1:1:1.43545:37.9:5:0.3704:0:4.7 0/1:10:4:4,0:6,0:6,4:0.4:0,0:20.8:1:25.8:1:1:0:26.3:8:0.4:0:4.5 +6 31237727 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.08381;LSEQ=AGAAAACCCAGACCCCGCTC;RSEQ=TCACCCCTTCCCTACCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:15:13,2:18,1:19,15:0.4412:1,2:7.3:1:29.9:1:0.57136:2.68744:35.2:30:0.4412:0:5.6 0/1:13:6:6,0:7,0:7,6:0.4615:0,0:12.5:1:28:1:1:0:26.5:12:0.4615:0:5.7 +6 31237760 . CAC TGT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1427;SOR=Inf;LSEQ=TACCTGAGCTCTTCCTCCTA;RSEQ=ATCATAGCGGTGACCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:65,5:70,0:0:2,0:25.8:1:32.5:1:1:0:47.3:34:1:0:5 0/1:43:2:1,1:36,5:41,2:0.0465:2,2:27:1:31.7:1:0.26246:6.66447:24:4:0.0465:0:6 +6 31237765 . C A 29 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14589;SOR=Inf;LSEQ=GAGCTCTTCCTCCTACACAT;RSEQ=ATAGCGGTGACCACAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:67,5:72,0:0:2,0:28.5:1:32.3:1:1:0:47.7:23:1:0:4.8 0/1:45:2:2,0:37,6:43,2:0.0444:2,0:37:1:29:1:1:0:44:4:0.0455:0:8 +6 31237767 . T C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34784;SOR=0.68404;LSEQ=GCTCTTCCTCCTACACATCA;RSEQ=AGCGGTGACCACAGCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:44:40,4:29,1:30,44:0.5946:1,2:30.8:1:32.9:1:0.64236:2.86397:39.8:43:0.589:0:7.9 1/0:46:23:19,4:21,2:23,23:0.5:2,2:31.4:1:31.7:1:0.66515:2.17346:39.4:22:0.4889:0:7.7 +6 31237769 . G A 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19793;SOR=0.5994;LSEQ=TCTTCCTCCTACACATCATA;RSEQ=CGGTGACCACAGCTCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:43:40,3:31,1:32,43:0.5658:1,2:33.2:1:30.7:1:0.6315:2.30131:40:42:0.5753:0:7.9 0/1:48:21:18,3:23,4:27,21:0.4375:2,2:33.3:1:29.7:1:1:1.04:40.9:42:0.4375:0:7.9 +6 31237771 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20634;SOR=0.62193;LSEQ=TTCCTCCTACACATCATAGC;RSEQ=GTGACCACAGCTCCAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:44:40,4:31,1:32,44:0.5789:1,2:34.8:1:31:1:0.39046:3.06009:39.8:43:0.5811:0:7.9 0/1:50:23:19,4:24,3:27,23:0.46:2,2:35.4:1:29.5:1:0.68883:1.66656:39.4:22:0.449:0:7.7 +6 31237773 . TG CC 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03049;SOR=0.44162;LSEQ=CCTCCTACACATCATAGCGG;RSEQ=ACCACAGCTCCAAGGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:42:38,4:30,1:31,42:0.5676:1,2:37.7:1:32.8:1:0.38694:3.11483:39.5:84:0.5915:0:6.9 0/1:52:19:16,3:24,5:29,19:0.3654:2,2:37.4:1:31.3:1:1:1.11:41.3:38:0.3878:0:6.9 +6 31237774 . G C 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73917;SOR=0.61929;LSEQ=CTCCTACACATCATAGCGGT;RSEQ=ACCACAGCTCCAAGGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:7:6,1:29,1:30,7:0.0886:1,2:12:1:28.4:1:0.34685:4.55132:33.4:6:0.1667:0:6.3 0/1:53:3:3,0:25,6:31,3:0.0566:2,0:31:1:24.7:1:1:0:33.3:2:0.0606:0:7.7 +6 31237776 . C T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17716;SOR=2.70946;LSEQ=CCTACACATCATAGCGGTGA;RSEQ=CACAGCTCCAAGGACAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:4:4,0:122,34:156,4:0.025:2,0:44.8:1:32.5:1:0.57911:0:44:8:0.0253:0:7.3 0/1:92:6:6,0:65,21:86,6:0.0652:2,0:37.8:1:29.8:1:0.33041:0:46.2:12:0.0659:0:6.7 +6 31237779 . C T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00449;SOR=0.43944;LSEQ=ACACATCATAGCGGTGACCA;RSEQ=AGCTCCAAGGACAGCTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:54:41,13:100,29:129,54:0.2951:2,2:11.2:1:30.9:1:0.84822:1.09281:34.4:108:0.2967:0:4.6 0/1:129:20:17,3:78,31:109,20:0.155:2,2:6.4:1:30.1:1:0.2757:2.24:33.7:40:0.1563:0:4.6 +6 31237786 . A T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00329;SOR=0.47397;LSEQ=ATAGCGGTGACCACAGCTCC;RSEQ=AGGACAGCTAGGACAACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:228:192:141,51:31,5:36,192:0.8421:2,2:16.7:1:31.2:1:0.1393:2.23576:35.1:95:0.8407:0:4.9 1/0:155:111:76,35:33,11:44,111:0.7161:2,2:15.9:1:29.3:1:0.55886:1.37878:39.3:222:0.7255:0:4.5 +6 31237800 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18832;SOR=Inf;LSEQ=AGCTCCAAGGACAGCTAGGA;RSEQ=AACCAGGACAGCCAGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:182,73:255,0:0:2,0:24.3:1:32.4:1:1:0:38.3:254:1:0:4 0/1:196:2:1,1:128,65:193,2:0.0102:2,2:17.5:1:31:0:1:1.96194:60:4:0.0104:0:1 +6 31237802 . A G 254 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCAAGGACAGCTAGGACA;RSEQ=CCAGGACAGCCAGGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:259:215:152,63:33,11:44,215:0.8301:2,2:25.7:1:32.9:1:0.7144:1.24237:34.1:42:0.83:0:4.8 0/0:199:0:0,0:37,19:56,0:0:2,0:26:1:28.5:1:1:0:60:112:0.9825:0:0.1 +6 31237821 . C A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02492;SOR=Inf;LSEQ=AACCAGGACAGCCAGGCCAG;RSEQ=AACGATGCCCATGATGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:198,97:295,0:0:2,0:30.5:1:32.1:1:1:0:39.5:72.75:1:0:3.7 0/1:272:5:4,1:164,103:267,5:0.0184:2,2:10.6:1:28.8:1:0.65229:2.50:24.8:10:0.0187:0:7 +6 31237833 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00059;SOR=0.54184;LSEQ=CAGGCCAGCAACGATGCCCA;RSEQ=GATGGGGATGGTGGGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:344:271:178,93:39,34:73,271:0.7878:2,2:27.5:1:30.9:1:0.05721:1.67:33.2:66.75:0.7853:0:4.2 1/0:313:209:127,82:50,45:95,209:0.6677:2,2:27.5:1:30.3:1:0.20997:1.39:37.2:51.25:0.6634:0:3.6 +6 31237835 . A T 93 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00774;SOR=10.41676;LSEQ=GGCCAGCAACGATGCCCATG;RSEQ=TGGGGATGGTGGGCTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:1:0,1:233,136:369,1:0.0027:2,0:1:0:26:0:0.37027:0:60:2:0.0028:0:2 0/1:327:9:6,3:182,135:317,9:0.0275:2,2:14.8:1:29.6:1:0.73832:1.48:27.6:18:0.0277:0:6.7 +6 31237858 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30612;LSEQ=GGGATGGTGGGCTGGGAAGA;RSEQ=GGCTCTGGGAAAGGAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:435:291:165,126:72,72:144,291:0.669:2,2:19.1:1:30.5:1:0.21955:1.31:33.8:47.5:0.6754:0:4.1 0/1:385:147:77,70:114,123:237,147:0.3818:2,2:21.1:1:29.3:1:0.46258:1.19:32.6:48:0.378:0:4.3 +6 31237862 . T C 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGTGGGCTGGGAAGATGGC;RSEQ=CTGGGAAAGGAGGAGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:0:0,0:220,197:417,0:0:2,0:23.6:1:30.3:1:1:0:40.5:25.063:1:0:3.1 0/1:380:27:14,13:171,182:353,27:0.0711:2,2:32.9:1:30.2:1:0.84232:1.15:44.4:54:0.0726:0:3.1 +6 31237876 . A G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01903;SOR=0.65343;LSEQ=GATGGCTCTGGGAAAGGAGG;RSEQ=GAAGGTGAGGGGCCCTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:411:343:172,171:27,41:68,343:0.8345:2,2:26.8:1:30.8:1:0.14373:1.53:38.2:84.75:0.835:0:3.4 1/0:365:280:125,155:35,50:85,280:0.7671:2,2:27.6:1:29.6:1:0.61862:1.15:40.1:45.667:0.7654:0:3.2 +6 31237893 . G T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGAGAAGGTGAGGGGCCCT;RSEQ=ACCCCCAAGCCTCAGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:155,202:357,0:0:2,0:31.3:1:31.9:1:1:0:44.4:50:1:0:2.5 0/1:319:18:8,10:121,180:301,18:0.0564:2,2:34.5:1:27.7:1:0.8063:1.19:40.2:36:0.057:0:5.3 +6 31237896 . C A 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAGGTGAGGGGCCCTGAC;RSEQ=CCCAAGCCTCAGCCCTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:155,201:356,0:0:2,0:30.7:1:31.7:1:1:0:44.6:49.857:1:0:2.5 0/1:310:18:8,10:115,177:292,18:0.0581:2,2:33.2:1:28.2:1:0.80472:1.23:40.2:36:0.0586:0:5.3 +6 31237897 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.16157;LSEQ=GAAGGTGAGGGGCCCTGACC;RSEQ=CCAAGCCTCAGCCCTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:354:218:93,125:62,74:136,218:0.6158:2,2:34.4:1:31.1:1:0.65966:1.12575:40.5:108:0.6225:0:3.2 0/1:307:63:22,41:100,144:244,63:0.2052:2,2:35.7:1:28.1:1:0.47047:1.29312:37.5:20:0.2:0:3.4 +6 31237917 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00015;SOR=2.96392;LSEQ=CCCAAGCCTCAGCCCTGACC;RSEQ=GGCTGAAGGGCTCCAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:19:10,9:123,168:291,19:0.0611:2,2:19.2:1:30.1:1:0.4743:1.52:33.2:18:0.0586:0:3.3 0/1:247:40:15,25:78,129:207,40:0.1619:2,2:22.1:1:29.4:1:1:1.00772:33.2:80:0.1639:0:3.5 +6 31237931 . CAGA C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17188;SOR=0.72964;LSEQ=CTGACCCGGCTGAAGGGCTC;RSEQ=AGGACTTCTGCTTTCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:238:186:69,117:21,30:51,186:0.7815:2,2:15.9:1:31.9:1:0.6271:1.18608:44.8:61:0.7888:0.1723:2.9 1/0:184:133:39,94:21,30:51,133:0.7228:2,2:18.3:1:31:1:0.15959:1.68224:45.5:266:0.7228:0.1739:3.1 +6 31237943 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18811;SOR=Inf;LSEQ=AAGGGCTCCAGAAGGACTTC;RSEQ=GCTTTCTCTGATAAGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:56,117:173,0:0:2,0:13.6:1:31.3:1:1:0:47.3:85.5:1:0:2.3 0/1:133:2:1,1:37,94:131,2:0.015:2,2:24.5:1:29.5:1:0.49134:2.52:30:4:0.0152:0:6 +6 31237950 . T C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.656;SOR=0.86881;LSEQ=CCAGAAGGACTTCTGCTTTC;RSEQ=CTGATAAGAGATGTGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:150:119:36,83:10,21:31,119:0.7933:2,2:6.2:1:32.1:1:0.82962:1.09719:45.2:238:0.7933:0:2.7 1/0:117:90:19,71:15,12:27,90:0.7692:2,2:10.6:1:30.8:1:0.00126:4.59733:45.2:89:0.7672:0:3.3 +6 31237955 . T G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36112;SOR=1.44325;LSEQ=AGGACTTCTGCTTTCTCTGA;RSEQ=AAGAGATGTGACCCCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:26:4,22:11,20:31,26:0.4561:2,2:6.5:1:31.7:1:0.13152:2.96766:42.8:52:0.4561:0:5.2 1/0:62:34:6,28:16,12:28,34:0.5484:2,2:15.6:1:30.9:1:0.00158:6.01755:40.3:68:0.5484:0:5.8 +6 31237960 . G C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16281;SOR=2.11936;LSEQ=TTCTGCTTTCTCTGATAAGA;RSEQ=ATGTGACCCCCCATTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:9:2,7:11,20:31,9:0.225:2,2:9:1:31.8:1:0.69039:1.89579:42.2:18:0.2308:0:5.8 0/1:47:18:4,14:17,12:29,18:0.383:2,2:21.7:1:31.8:1:0.0185:4.78402:36.9:36:0.3913:0:6.9 +6 31237962 . TG CA 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01344;SOR=5.23931;LSEQ=CTGCTTTCTCTGATAAGAGA;RSEQ=TGACCCCCCATTCCCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:1,2:11,20:31,3:0.0882:2,2:20.7:1:31.5:1:1:1.09697:40.7:6:0.0909:0:6 0/1:44:15:4,11:18,11:29,15:0.3409:2,2:22.8:1:31:1:0.05461:4.33997:36.5:30:0.3409:0:6.2 +6 31237971 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01573;SOR=4.74348;LSEQ=CTGATAAGAGATGTGACCCC;RSEQ=CATTCCCCTCCTTACCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:1,2:10,19:29,3:0.0938:2,2:12.7:1:29.3:1:1:1.05096:40.7:6:0.0968:0:6 0/1:45:15:4,11:19,11:30,15:0.3333:2,2:14.8:1:28.9:1:0.02868:4.57753:36.5:30:0.3333:0:6.2 +6 31237975 . T C 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02845;SOR=4.27892;LSEQ=TAAGAGATGTGACCCCCCAT;RSEQ=CCCCTCCTTACCCCAGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:1,2:10,17:27,3:0.1:2,2:8.7:1:30.7:1:1:1.17019:40.7:6:0.1111:0:6 0/1:46:15:4,11:19,12:31,15:0.3261:2,2:10.8:1:30.5:1:0.05736:4.21034:36.5:30:0.3261:0:6.2 +6 31237992 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50502;SOR=Inf;LSEQ=CATTCCCCTCCTTACCCCAG;RSEQ=TCAGGGTGAGGGGCTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:9,17:26,0:0:2,0:28.7:1:32.3:1:1:0:60:25:1:0:0.2 0/1:36:2:1,1:20,14:34,2:0.0556:2,2:18:1:26:1:1:1.41419:60:4:0.0556:0:1 +6 31238053 . G C 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0873;SOR=0.21284;LSEQ=GCACGTGTATCTCTGCTCTT;RSEQ=TCCAGAAGGCACCACCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:2,2:3,11:14,4:0.2222:2,2:22.5:1:31.5:1:0.53268:3.37:20.8:8:0.2353:0:1.8 0/1:36:2:1,1:10,23:33,2:0.0556:2,2:22.5:1:29:1:0.53613:2.24:22:4:0.0556:0:1 +6 31238068 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=CTCTTGTCCAGAAGGCACCA;RSEQ=CACAGCTGCCCACTTCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:1,2:6,12:18,3:0.1429:2,2:38:1:29:1:1:1:21:6:0.15:0:2 0/0:36:0:0,0:10,26:36,0:0:2,0:24.4:1:30.5:1:1:0:54.7:72:1:0:0.3 +6 31238230 . G C 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03485;SOR=0.64865;LSEQ=GGTGGCCTCATGGTCAGAGA;RSEQ=GGGGTGGTGGGTCACGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:174:107:56,51:36,31:67,107:0.6149:2,2:22.3:1:30.5:1:0.87717:1.05723:32.7:52.5:0.6213:0:4.7 1/0:234:119:66,53:56,58:114,119:0.5085:2,2:23.1:1:30.1:1:0.36001:1.29:34.4:118:0.513:0:4.4 +6 31238232 . G A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03887;SOR=Inf;LSEQ=TGGCCTCATGGTCAGAGAGG;RSEQ=GGTGGTGGGTCACGTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:97,84:181,0:0:2,0:24.1:1:30.6:1:1:0:40.8:35.2:1:0:3.1 0/1:238:6:2,4:120,111:231,6:0.0252:2,2:31.5:1:26:1:0.43499:2.15537:33.7:5:0.0213:0:5.2 +6 31238234 . G A 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01386;SOR=0.607;LSEQ=GCCTCATGGTCAGAGAGGGG;RSEQ=TGGTGGGTCACGTGTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:182:114:61,53:36,32:68,114:0.6264:2,2:24:1:29.7:1:1:1.02:34.1:21.8:0.6193:0:4.8 1/0:246:124:67,57:60,62:122,124:0.5041:2,2:25.4:1:28.8:1:0.52361:1.21:34.9:123:0.5062:0:4.5 +6 31238242 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17205;SOR=0;LSEQ=GTCAGAGAGGGGGTGGTGGG;RSEQ=CACGTGTGTCTTTGGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:102,90:192,2:0.0103:2,2:43.5:1:28.5:1:1:1.1326:42:4:0.0105:0:1.5 0/0:273:0:0,0:136,137:273,0:0:2,0:29.4:1:28.1:1:1:0:44.7:38:1:0:2.4 +6 31238259 . G T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00011;SOR=0.49652;LSEQ=GGGTCACGTGTGTCTTTGGG;RSEQ=GTTCTGACGGGAAGAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:225:141:70,71:42,42:84,141:0.6267:2,2:33:1:30.4:1:1:1.01422:37.7:282:0.6295:0:4.7 0/1:306:139:66,73:64,77:141,139:0.4542:2,2:32.1:1:28.9:1:0.81065:1.09:38.1:68.5:0.4536:0:4.5 +6 31238267 . C T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.19778;LSEQ=TGTGTCTTTGGGGGTTCTGA;RSEQ=GGGAAGAGTCAGAAAATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:27:13,14:98,105:203,27:0.1174:2,2:36.5:1:30.2:1:1:1.00511:29.7:26:0.1145:0:5.8 0/1:313:8:3,5:139,166:305,8:0.0256:2,2:38.6:1:26.1:1:0.73258:1.39413:30.9:3:0.0199:0:5.8 +6 31238297 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01727;SOR=0.5997;LSEQ=CAGAAAATTCAGACACTTTG;RSEQ=ATCTCTCTTGGGACACTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:186:134:51,83:23,28:51,134:0.7204:2,2:24.7:1:28.9:1:0.40476:1.33468:41.4:66:0.7253:0:4.9 1/0:234:142:53,89:31,60:91,142:0.6068:2,2:24.5:1:27.4:1:0.67558:1.15:43.4:70:0.6114:0:4.7 +6 31238308 . G C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.13653;SOR=0.70078;LSEQ=GACACTTTGCATCTCTCTTG;RSEQ=GACACTCCAGCAGCGCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:118:42,76:18,28:46,118:0.7152:2,2:21.1:1:30.7:1:0.71973:1.16218:42.8:236:0.7239:0:4.9 1/0:182:116:38,78:20,45:65,116:0.6374:2,2:22.4:1:29.8:1:0.86861:1.10:45.3:115:0.6461:0:4.8 +6 31238318 . G A 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02222;SOR=0.56865;LSEQ=ATCTCTCTTGGGACACTCCA;RSEQ=CAGCGCCCATGTGACCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:92:29,63:14,29:43,92:0.6815:2,2:21.7:1:30:1:1:1.04837:44.5:91:0.6894:0:4.8 1/0:155:85:21,64:24,45:69,85:0.5484:2,2:21.4:1:28.5:1:0.21279:1.62015:43.8:84:0.5526:0:4.8 +6 31238322 . C T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00098;SOR=Inf;LSEQ=CTCTTGGGACACTCCAGCAG;RSEQ=GCCCATGTGACCATCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:39,86:125,0:0:2,0:20.5:1:30.5:1:1:0:50.1:124:1:0:3.2 0/1:142:11:1,10:35,95:130,11:0.0775:2,2:16.4:1:29.7:1:0.28948:3.65918:40.8:22:0.078:0:5.4 +6 31238345 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01769;SOR=4.14534;LSEQ=CCATGTGACCATCCTGAGAA;RSEQ=GGACAGGACACCTGGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:4:1,3:10,57:67,4:0.0563:2,2:23.3:1:31.3:1:0.49813:1.88:50.3:8:0.0563:0:4.8 0/1:65:13:4,9:4,48:52,13:0.2:2,2:28:1:30.2:1:0.04445:5.15:38.4:26:0.2:0:4.8 +6 31238364 . G A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21711;SOR=Inf;LSEQ=ATGGACAGGACACCTGGGGT;RSEQ=GGGAAGGCGGCAGAGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:5,46:51,0:0:2,0:24.4:1:31:1:1:0:46:16:1:0:2.6 0/1:45:2:0,2:4,39:43,2:0.0444:2,0:7.5:1:29.5:1:1:0:43:4:0.0444:0:4.5 +6 31238372 . C G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62025;SOR=1.39223;LSEQ=GACACCTGGGGTGGGGAAGG;RSEQ=GGCAGAGAACCCAGACGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:31:4,27:0,13:13,31:0.7045:1,2:22:1:31.5:1:0.30236:0:37.7:62:0.7045:0:3.7 1/0:39:30:3,27:1,8:9,30:0.7692:2,2:25.6:1:31.2:1:1:1.12151:32.5:60:0.7692:0:4.2 +6 31238377 . G C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00215;SOR=13.74382;LSEQ=CTGGGGTGGGGAAGGCGGCA;RSEQ=AGAACCCAGACGCCAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:28:5,23:0,12:12,28:0.7:0,2:21.8:1:31.9:1:0.29801:0:37.9:56:0.7:0:3.4 1/1:34:33:3,30:0,1:1,33:0.9706:0,2:22.5:1:32.2:1:1:0:37.2:66:0.9706:0:3.4 +6 31238490 . T C 113 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09701;SOR=0.08933;LSEQ=GTCCTGACCTGAGTGGAGGC;RSEQ=GCAGGACTCAGAAAAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:0,14:0,2:2,14:0.875:0,1:24.6:1:29.8:1:1:0:57.2:13:0.8667:0:3.1 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:2:0:28:0:1:0:55:2:0.3333:0:1 +6 31238492 . C A 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05;SOR=0;LSEQ=CCTGACCTGAGTGGAGGCTG;RSEQ=AGGACTCAGAAAAGCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:0,12:0,2:2,12:0.8571:0,0:27.3:1:32:1:1:0:58.2:24:0.8571:0:2.9 0/0:2:0:0,0:0,2:2,0:0:0,0:15:1:33:0:1:0:60:4:1:0:0 +6 31238524 . G A 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCTGGAATCAAACCTTCA;RSEQ=ACACATTGAGTGTGAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:19.8:1:32:1:1:0:59.8:10:0.8333:0:4.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31238535 . T C 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACCTTCAGACACATTGAG;RSEQ=GTGAGGCAGAGAACAAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:1,4:0.8:0,2:14.5:1:32.8:1:1:0:59.8:8:0.8:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31238613 . A G 98 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGGTCAAAGTGGTCAAAGG;RSEQ=GACCCCTGATCAGTATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:9,1:1,0:1,10:0.9091:0,2:16.4:1:29.6:1:1:0:39.9:9:0.9:0:2.9 1/1:1:1:1,0:0,0:0,1:1:0,0:16:0:32:0:1:0:31:2:1:0:3 +6 31238632 . C T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACCCCTGATCAGTATTC;RSEQ=AGGGACTGTCTTCCCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:8,1:9,3:0.25:2,0:28.7:1:33.3:1:1:0:24:6:0.25:0:4 0/0:1:0:0,0:1,0:1,0:0:0,0:35:0:31:0:1:0:31:2:1:0:3 +6 31238661 . GA AG 123 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCTTCCCCTCCATTTCCTCA;RSEQ=GACTTCATCCCTTAATTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:14,0:0,0:0,14:0.875:0,1:29.4:1:32.5:1:1:0:37.3:28:1:0.0625:2.1 1/1:1:1:1,0:0,0:0,1:1:0,0:36:0:26.5:0:1:0:31:2:1:0:2 +6 31238728 . G C 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3696;SOR=0.43572;LSEQ=GGAAACTCAGGAAAACTCAT;RSEQ=CCATTCTCCATTCAAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:22:22,0:4,0:4,22:0.8462:0,1:18:1:31.8:1:1:0:35.3:44:0.8462:0:3.5 1/0:10:7:6,1:3,0:3,7:0.7:0,2:25:1:30.1:1:1:0:34.3:14:0.7:0:3.6 +6 31238759 . C T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87244;LSEQ=TTCAAGGGAGGGCGATATTC;RSEQ=AGTGCTGATCCCATTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:28:27,1:13,0:13,28:0.6829:1,1:24.1:1:32.3:1:1:0:34.4:56:0.6829:0:4.3 1/0:23:15:14,1:7,1:8,15:0.6522:2,1:18.3:1:30.4:1:1:1.94:35:30:0.6522:0:3.6 +6 31238762 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78821;SOR=1.30528;LSEQ=AAGGGAGGGCGATATTCCAG;RSEQ=GCTGATCCCATTTTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:29:28,1:13,1:14,29:0.6744:1,1:24.9:1:33.2:1:1:2.11:34.3:58:0.6744:0:4.3 1/0:26:19:17,2:7,0:7,19:0.7308:0,2:19.8:1:31.8:1:1:0:37.3:38:0.7308:0:3.4 +6 31238797 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.15957;SOR=Inf;LSEQ=CCTCCCCTCCTCGTGGGAGG;RSEQ=CATCCCGGGAGATCTATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:104,8:112,0:0:2,0:23.4:1:32.3:1:1:0:47.1:36.333:1:0:3.1 0/1:75:2:1,1:67,6:73,2:0.0267:2,2:18:1:26.5:1:0.1791:10.41528:40.5:4:0.027:0:2.5 +6 31238801 . C G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0.15308;LSEQ=CCCTCCTCGTGGGAGGCCAT;RSEQ=CCGGGAGATCTATAGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:30:29,1:82,7:89,30:0.25:2,1:22.1:1:32.2:1:0.67768:2.46:42.5:29:0.25:0:4.3 0/1:83:4:4,0:72,7:79,4:0.0482:2,0:28:1:32:1:1:0:41.8:8:0.0488:0:4.5 +6 31238814 . TA CG 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18179;LSEQ=AGGCCATCCCGGGAGATCTA;RSEQ=GGAGATGGGGAAGGCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:188:110:97,13:48,4:52,110:0.5851:2,2:23.9:1:31.7:1:0.58515:1.60388:40.7:220:0.5978:0.0691:2.4 0/1:128:26:21,5:45,10:55,26:0.2031:2,2:22.3:1:30.3:1:1:1.07051:39.7:52:0.2031:0.0313:2.3 +6 31238815 . A G 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00625;SOR=0;LSEQ=GGCCATCCCGGGAGATCTAT;RSEQ=GGAGATGGGGAAGGCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:10:8,2:70,7:77,10:0.0543:2,2:8.9:1:27.1:1:0.27524:2.46602:34.5:9:0.1059:0:3.2 0/0:130:0:0,0:90,17:107,0:0:2,0:20.6:1:28.6:1:1:0:43.7:52.5:1:0:1.6 +6 31238851 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31513;LSEQ=TCCCCACTGCCCCTGGTACC;RSEQ=GCGCGCTGCAGCGTCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:278:235:187,48:31,11:42,235:0.8453:2,2:33.5:1:30.6:1:0.41557:1.38:34.9:32.571:0.8444:0:2 1/0:212:134:102,32:55,23:78,134:0.6321:2,2:32.2:1:30.2:1:0.41757:1.33:34.2:133:0.6364:0:2.1 +6 31238868 . C T 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00049;SOR=Inf;LSEQ=ACCTGCGCGCTGCAGCGTCT;RSEQ=CTTCCCGTTCTCCAGGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:209,61:270,0:0:2,0:33.5:1:31.2:1:1:0:35.2:37.571:1:0:1.6 0/1:241:10:7,3:160,71:231,10:0.0415:2,2:31.5:1:28.5:1:1:1.04:29.4:20:0.0418:0:2.3 +6 31238875 . G A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60789;SOR=0.72496;LSEQ=CGCTGCAGCGTCTCCTTCCC;RSEQ=TTCTCCAGGTATCTGCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:9:8,1:200,63:263,9:0.0331:2,2:23:1:27.7:1:0.69031:2.51:38.4:18:0.0336:0:4.1 0/1:248:6:5,1:162,80:242,6:0.0242:2,2:26.2:1:28.3:1:0.6669:2.46:36.2:12:0.0243:0:4.3 +6 31238880 . C T 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5775;SOR=0.64831;LSEQ=CAGCGTCTCCTTCCCGTTCT;RSEQ=CAGGTATCTGCGGAGCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:8:7,1:192,64:256,8:0.0303:2,2:20.5:1:28.9:1:0.68377:2.33:37.1:16:0.0308:0:4.3 0/1:252:5:4,1:159,88:247,5:0.0198:2,2:25.4:1:29.4:1:0.65901:2.21:33.8:10:0.02:0:4.6 +6 31238886 . A G 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CTCCTTCCCGTTCTCCAGGT;RSEQ=TCTGCGGAGCCACTCCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:186,64:250,0:0:2,0:26.1:1:28.1:1:1:0:33.7:49:1:0:1.4 0/1:247:16:10,6:145,85:230,16:0.0648:2,2:23:1:32:1:1:1.02345:25.5:32:0.0664:0:2.8 +6 31238897 . C G 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06174;SOR=Inf;LSEQ=TCTCCAGGTATCTGCGGAGC;RSEQ=ACTCCACGCACGTGCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:172,73:245,0:0:2,0:20.2:1:30.6:1:1:0:34.4:60.25:1:0:1.2 0/1:259:5:4,1:149,105:254,5:0.0193:2,2:20.2:1:27.6:1:0.65136:2.81:26.8:10:0.0193:0:3.2 +6 31238909 . GT AG 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09148;SOR=0.58486;LSEQ=TGCGGAGCCACTCCACGCAC;RSEQ=GCCCTCCAGGTAGGCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:27:20,7:113,65:178,27:0.1317:2,2:7.3:1:30.4:1:0.3873:1.64:25.9:54:0.1324:0.0537:1.8 0/1:258:21:16,5:124,112:236,21:0.0814:2,2:7.4:1:27.4:1:0.04121:2.88:27.1:42:0.0827:0.031:2.5 +6 31238925 . C T 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09214;SOR=Inf;LSEQ=GCACGTGCCCTCCAGGTAGG;RSEQ=TCTCAGCTGCTCCGCCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:64,47:111,0:0:2,0:24.7:1:32:1:1:0:43.5:54.5:1:0:0.3 0/1:200:6:2,4:93,101:194,6:0.03:2,2:24.8:1:28.8:1:0.68514:1.83618:22:12:0.0309:0:3 +6 31238930 . A T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00052;SOR=Inf;LSEQ=TGCCCTCCAGGTAGGCTCTC;RSEQ=GCTGCTCCGCCGCACGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:54,42:96,0:0:2,0:27.4:1:30.8:1:1:0:46.7:192:0.9897:0:0.2 0/1:188:18:8,10:78,91:169,18:0.0957:2,2:27.8:1:29.9:1:1:1.07106:27.8:36:0.0963:0:2 +6 31238942 . G A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08512;SOR=3.03799;LSEQ=AGGCTCTCAGCTGCTCCGCC;RSEQ=CACGGGCCGCCTCCAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:3:2,1:45,38:83,3:0.0341:2,2:5:1:28:1:1:1.68:25.3:6:0.0353:0:1 0/1:175:17:8,9:69,83:152,17:0.0971:2,2:31.5:1:29.9:1:1:1.07:25.8:34:0.1:0:2.9 +6 31238945 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55383;SOR=Inf;LSEQ=CTCTCAGCTGCTCCGCCGCA;RSEQ=GGGCCGCCTCCAACTTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:47,39:86,0:0:2,0:28.5:1:31:1:1:0:48.9:85:1:0:0.2 0/1:172:2:1,1:76,94:170,2:0.0116:2,2:41:0:31.5:1:1:1.24:58:4:0.0117:0:1.5 +6 31238951 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30109;SOR=Inf;LSEQ=GCTGCTCCGCCGCACGGGCC;RSEQ=CCTCCAACTTGCGCTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:41,36:77,0:0:2,0:29.1:1:30.9:1:1:0:51.4:37.5:1:0:0.2 0/1:146:4:3,1:61,81:142,4:0.0274:2,2:10.8:1:25.3:1:0.31936:3.95:38:3:0.0208:0:1 +6 31238957 . A C 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGCCGCACGGGCCGCCTCC;RSEQ=ACTTGCGCTGGGTGATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:36,35:71,0:0:2,0:28.2:1:30.9:1:1:0:52.9:70:1:0:0.1 0/1:132:27:13,14:44,61:105,27:0.2045:2,2:14.7:1:30.8:1:0.66407:1.28:25.4:54:0.2045:0:2.8 +6 31239016 . G A 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02172;SOR=Inf;LSEQ=GTCCAGGAGCGCAGGTCCTC;RSEQ=TTCAGGGCGATGTAATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:33,34:67,0:0:2,0:16.4:1:31.2:1:1:0:33.9:134:1:0:1.1 0/1:98:8:1,7:44,46:90,8:0.0816:2,2:11.5:1:27:1:0.06636:6.5925:26.6:16:0.0825:0:3.6 +6 31239038 . C T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60475;SOR=0.44706;LSEQ=TCAGGGCGATGTAATCCTTG;RSEQ=CGTCGTAGGCGGACTGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:75,82:157,2:0.0126:2,2:8:1:28:1:1:1.09:24.5:4:0.0127:0:5 0/0:177:1:0,1:83,93:176,1:0.0056:2,0:1:0:23:0:1:0:26:2:0.0057:0:5 +6 31239049 . GG TA 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05873;SOR=Inf;LSEQ=TAATCCTTGCCGTCGTAGGC;RSEQ=ACTGGTCATACCCGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:99,114:213,0:0:2,0:22.4:1:30.5:1:1:0:33:52.25:1:0:2.8 0/1:209:4:1,3:95,110:205,4:0.0191:2,2:24:1:27.4:1:0.62641:2.58014:29:8:0.0192:0.0048:3 +6 31239050 . G A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05912;SOR=0.68112;LSEQ=AATCCTTGCCGTCGTAGGCG;RSEQ=ACTGGTCATACCCGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:92:42,50:46,46:92,92:0.4201:2,2:20:1:30.6:1:0.65807:1.18934:25.2:184:0.4201:0:4.3 0/1:212:70:30,40:63,68:131,70:0.3302:2,2:25.5:1:28.3:1:0.55302:1.23399:26.9:69:0.3333:0:3.9 +6 31239057 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13804;SOR=0.75306;LSEQ=GCCGTCGTAGGCGGACTGGT;RSEQ=ATACCCGCGGAGGAGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:104:46,58:65,84:149,104:0.4111:2,2:24.1:1:29.3:1:1:1.02:25.7:103:0.412:0:4.3 0/1:241:83:34,49:76,82:158,83:0.3444:2,2:28.1:1:27.3:1:0.34112:1.33411:28:40.5:0.3403:0:3.9 +6 31239060 . A G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.56763;SOR=1.31213;LSEQ=GTCGTAGGCGGACTGGTCAT;RSEQ=CCCGCGGAGGAGGCGCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:13:8,5:106,150:256,13:0.0483:2,2:24.8:1:31.4:1:0.16367:2.26:22.3:12:0.0456:0:4.3 0/1:256:16:7,9:111,127:238,16:0.0625:2,2:36.2:1:31.4:1:1:1.12321:23.7:32:0.0635:0:3.6 +6 31239082 . G C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.27742;LSEQ=CCGCGGAGGAGGCGCCCGTC;RSEQ=GGCCCCAGGTCGCAGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:140:57,83:71,102:173,140:0.4473:2,2:33.8:1:30.6:1:1:1.01355:25.1:139:0.4484:0:4.3 0/1:306:56:24,32:113,137:250,56:0.183:2,2:31.7:1:29.9:1:0.76854:1.0994:25.4:112:0.1873:0:4.1 +6 31239090 . G C 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75229;SOR=0.68394;LSEQ=GAGGCGCCCGTCGGGCCCCA;RSEQ=GTCGCAGCCAGACATCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:6:2,4:128,195:323,6:0.0182:2,2:41.3:1:31.2:1:1:1.31177:24.2:12:0.0185:0:4.7 0/1:320:4:3,1:137,178:315,4:0.0125:2,2:38.8:1:32.3:1:0.32311:3.88:23.3:8:0.0127:0:5.3 +6 31239101 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28026;LSEQ=CGGGCCCCAGGTCGCAGCCA;RSEQ=ACATCCTCTGGAGGGTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:159:61,98:18,27:45,159:0.4862:2,2:30.1:1:31:1:0.86362:1.07068:25.5:158:0.4922:0:4.2 0/1:301:63:27,36:12,21:33,63:0.2093:2,2:29.2:1:29.8:1:0.66254:1.31:26:62:0.2088:0:4 +6 31239108 . T A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79164;SOR=1.05575;LSEQ=CAGGTCGCAGCCAGACATCC;RSEQ=CTGGAGGGTGTGAGACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:96:33,63:89,134:223,96:0.3009:2,2:29:1:29.4:1:0.38091:1.26704:40.3:23:0.2977:0:3.5 0/1:288:90:38,52:91,107:198,90:0.3125:2,2:25.9:1:29:1:0.60977:1.16318:42.5:89:0.3123:0:3.1 +6 31239114 . G T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01304;SOR=2.08956;LSEQ=GCAGCCAGACATCCTCTGGA;RSEQ=GGTGTGAGACCCTGGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:20:10,10:102,186:288,20:0.0647:2,2:23.9:1:31.2:1:0.23047:1.82:24.5:40:0.066:0:4.7 0/1:253:32:14,18:98,122:220,32:0.1265:2,2:17.5:1:29.8:1:1:1.03266:25.8:64:0.127:0:4.4 +6 31239116 . G A 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.73248;SOR=1.17858;LSEQ=AGCCAGACATCCTCTGGAGG;RSEQ=TGTGAGACCCTGGCCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:19:9,10:97,183:280,19:0.0635:2,2:23.5:1:30.6:1:0.3223:1.69:24.6:18:0.0612:0:4.7 0/1:243:18:9,9:98,127:225,18:0.0741:2,2:16.2:1:29.4:1:0.62866:1.29:24.5:36:0.075:0:4.3 +6 31239124 . C A 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=ATCCTCTGGAGGGTGTGAGA;RSEQ=CCTGGCCCCGCCCCCGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:83,180:263,0:0:2,0:24.8:1:31.9:1:1:0:33.9:86.667:1:0:3.5 0/1:209:10:3,7:88,111:199,10:0.0478:2,2:8.3:1:28.1:1:0.51887:1.84471:28.5:20:0.049:0:4.9 +6 31239135 . C G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.68222;LSEQ=GGTGTGAGACCCTGGCCCCG;RSEQ=CCCCGCGGTCAGCCCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:4:1,3:58,141:199,4:0.0197:2,2:9.3:1:32.8:1:1:1.2328:30.3:8:0.0199:0:5.3 0/1:148:2:1,1:61,85:146,2:0.0135:2,2:18:0:33:0:1:1.39:23:4:0.0137:0:3.5 +6 31239141 . C T 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02212;SOR=0.55413;LSEQ=AGACCCTGGCCCCGCCCCCG;RSEQ=GGTCAGCCCAGTCCCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:177:134:35,99:14,29:43,134:0.7571:2,2:21.3:1:30.6:1:0.43675:1.36306:33.5:66:0.7674:0:4.3 1/0:128:81:29,52:23,24:47,81:0.6328:2,2:20:1:28.5:1:0.19123:1.71101:35.7:39.5:0.627:0:4 +6 31239151 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00035;SOR=0.33355;LSEQ=CCCGCCCCCGCGGTCAGCCC;RSEQ=GTCCCCCGAGCCCCGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:58:14,44:7,21:28,58:0.4328:2,2:18:1:31.3:1:1:1.04704:25.4:57:0.4385:0:4.3 0/1:94:19:9,10:16,20:36,19:0.2021:2,2:16.5:1:29.5:1:1:1.12:26:18:0.1978:0:4.1 +6 31239157 . C G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02461;SOR=Inf;LSEQ=CCCGCGGTCAGCCCAGTCCC;RSEQ=CGAGCCCCGCCCCGCCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:23,86:109,0:0:2,0:17.5:1:31.3:1:1:0:31.4:53.5:1:0:3.3 0/1:73:4:0,4:28,41:69,4:0.0548:2,0:12.3:1:31.3:1:0.29114:0:28.5:8:0.0556:0:5 +6 31239170 . C CA 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=22.80281;LSEQ=CAGTCCCCCGAGCCCCGCCC;RSEQ=GCCCCGACCAACCCGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:11:3,8:8,18:26,11:0.1158:2,2:10.1:1:28.6:1:1:1.17983:32.5:10:0.1087:0.0737:3.5 1/0:41:31:7,24:0,3:3,31:0.7561:0,2:12.1:1:29.3:1:1:0:31:30:0.9091:0.5366:4.2 +6 31239171 . GC AGT 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=AGTCCCCCGAGCCCCGCCCC;RSEQ=CCCGACCAACCCGCGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:58:13,45:8,18:26,58:0.6105:2,2:10.8:1:30.6:1:0.42597:1.53029:31.3:57:0.6196:0.2842:4 0/0:41:0:0,0:0,3:3,0:0:0,0:9:1:34.9:1:1:0:42.7:6:0.0909:0:-6.7 +6 31239205 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28823;SOR=0.57032;LSEQ=GCGGGGATTTTGGCCTAAAC;RSEQ=GAAAATGAAACCGGGTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:83:67:36,31:9,7:16,67:0.8072:2,2:22.6:1:31:1:1:1.10578:37.8:134:0.8171:0:3.5 1/0:27:19:7,12:3,5:8,19:0.7037:2,2:27.9:1:29.9:1:1:1.02751:39.9:38:0.7037:0:3.4 +6 31239227 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03452;SOR=0.35857;LSEQ=AAAATGAAACCGGGTAAAGG;RSEQ=GACTGGGGCTCTCTCCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:115:99:65,34:14,2:16,99:0.8609:2,2:26.6:1:30.5:1:0.0907:3.62851:40:48.5:0.8584:0:3.7 1/0:32:22:11,11:4,6:10,22:0.6875:2,2:28:1:29.9:1:0.71195:1.48:40:44:0.6875:0:3.9 +6 31239232 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04563;SOR=Inf;LSEQ=GAAACCGGGTAAAGGCGACT;RSEQ=GGGCTCTCTCCGGTCGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:91,36:127,0:0:2,0:26:1:32.2:1:1:0:43.6:30.75:1:0:3.2 0/1:35:2:0,2:18,15:33,2:0.0571:2,0:38.5:1:32.5:1:0.22857:0:46.5:4:0.0571:0:3 +6 31239246 . T C 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=Inf;LSEQ=GCGACTGGGGCTCTCTCCGG;RSEQ=CGAGGGTCTGGGCGGGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:113,37:150,0:0:2,0:26.9:1:30.2:1:1:0:45:29:1:0:3.2 0/1:50:6:3,3:29,15:44,6:0.12:2,2:18.2:1:32.5:1:0.65377:1.90656:40.8:12:0.12:0:4.2 +6 31239270 . GATCCA G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95167;LSEQ=GGGTCTGGGCGGGTTCCGCA;RSEQ=CCTTGGGGTGGATCTCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:18:15,3:26,3:29,18:0.1059:2,2:17.8:1:31.2:1:0.66157:1.71226:46.2:36:0.1071:0.0529:3.7 0/1:79:8:7,1:12,3:15,8:0.1013:2,2:11.6:1:31.9:1:1:1.71:49.3:16:0.1111:0.0886:3.5 +6 31239271 . ATCCACCTT CCTC 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37449;SOR=0.75863;LSEQ=GGTCTGGGCGGGTTCCGCAG;RSEQ=GGGGTGGATCTCAGACGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:170:122:98,24:26,3:29,122:0.7176:2,2:28.8:1:32.6:1:0.29226:2.11347:44.8:244:0.7262:0.0471:2.7 1/0:79:52:43,9:12,3:15,52:0.6582:2,2:21.6:1:30.5:1:1:1.19:42.2:16.333:0.6806:0.1899:3 +6 31239279 . T C 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGGGTTCCGCAGATCCACCT;RSEQ=GGGGTGGATCTCAGACGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:26:23,3:27,3:30,26:0.4561:2,2:12.1:1:28.8:1:1:1.17054:43.2:5.5:0.4314:0:3.9 0/0:28:0:0,0:15,3:18,0:0:2,0:24:1:30.8:1:1:0:59.8:36:1:0:0.6 +6 31239296 . G C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23993;SOR=1.38165;LSEQ=CCTTGGGGTGGATCTCAGAC;RSEQ=GGGAGACTCTGGGCGACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:79:71,8:90,12:102,79:0.4365:2,2:24.8:1:30.9:1:0.81378:1.18:37.4:78:0.4407:0:4.7 1/0:87:45:38,7:39,1:40,45:0.5172:1,2:28.6:1:30.3:1:0.06123:7.04979:36.2:44:0.5176:0:3.9 +6 31239305 . CT TG 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05675;SOR=0.53297;LSEQ=GGATCTCAGACGGGGAGACT;RSEQ=GGGCGACCCGGGCCGTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:54:49,5:110,13:123,54:0.3017:2,2:26.6:1:30.9:1:1:1.16:38:108:0.3103:0.0168:4.1 0/1:91:17:14,3:68,5:73,17:0.1868:2,2:27.1:1:30.5:1:0.17059:2.87017:38.7:34:0.1932:0:4.1 +6 31239306 . T G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00171;SOR=2.37108;LSEQ=GATCTCAGACGGGGAGACTC;RSEQ=GGGCGACCCGGGCCGTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:175:91:81,10:29,4:33,91:0.52:2,2:24.6:1:30.2:1:1:1.12:46.6:182:0.7398:0:2.2 1/0:93:67:61,6:9,0:9,67:0.7204:0,2:28:1:29.7:1:1:0:42.1:134:0.8816:0:2.1 +6 31239314 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12282;SOR=Inf;LSEQ=ACGGGGAGACTCTGGGCGAC;RSEQ=CGGGCCGTCCGTGGGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:154,23:177,0:0:2,0:25.2:1:30.6:1:1:0:44.3:43.25:1:0:2.2 0/1:96:2:1,1:86,8:94,2:0.0208:2,2:30.5:1:30.5:1:0.17961:10.19401:38.5:4:0.0213:0:3 +6 31239335 . G A 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24108;SOR=0.6358;LSEQ=CGGGCCGTCCGTGGGGGATG;RSEQ=GGAGGGGTCGTGACCTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:31:28,3:170,39:209,31:0.1286:2,2:23.9:1:28.2:1:0.3119:2.14:35.8:9.333:0.1197:0:4.3 0/1:140:12:11,1:107,21:128,12:0.0857:2,2:25.8:1:27.8:1:0.69111:2.15:38.2:24:0.087:0:4 +6 31239350 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13955;SOR=Inf;LSEQ=GGATGGGGAGGGGTCGTGAC;RSEQ=TGCGCCCCGGGCCGGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:229,72:301,0:0:2,0:21.7:1:31.5:1:1:0:41.1:74.25:1:0:1.6 0/1:180:2:1,1:136,42:178,2:0.0111:2,2:14.5:1:28.5:1:0.42173:3.21196:22:4:0.0114:0:3.5 +6 31239376 . C T 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00041;SOR=Inf;LSEQ=CCCGGGCCGGGGTCACTCAC;RSEQ=GTCCTCGCTCTGGTTGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:509:0:0,0:347,162:509,0:0:2,0:23.4:1:30.8:1:1:0:44:83.833:1:0:1.7 0/1:374:9:7,2:248,117:365,9:0.0241:2,2:14.6:1:30.2:1:0.72478:1.65:35.9:18:0.0243:0:2.8 +6 31239378 . T G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22836;SOR=1.21376;LSEQ=CGGGCCGGGGTCACTCACCG;RSEQ=CCTCGCTCTGGTTGTAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:108:64,44:298,131:429,108:0.2007:2,2:9.3:1:30.3:1:0.05074:1.56261:33.9:26:0.1977:0:2.3 0/1:398:93:66,27:200,105:305,93:0.2337:2,2:10.2:1:30.8:1:0.37927:1.28:37.1:186:0.2354:0:2.5 +6 31239407 . G T 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.60817;LSEQ=TGGTTGTAGTAGCCGCGCAG;RSEQ=TTCCGCAGGCTCACTCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:963:552:334,218:225,185:410,552:0.5732:2,2:24.4:1:29.7:1:0.08594:1.26:52.5:77.857:0.5713:0:2.2 0/1:723:325:186,139:222,176:398,325:0.4495:2,2:25.4:1:29:1:0.70678:1.06:52.2:107.333:0.4503:0:2.3 +6 31239417 . C T 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.65877;LSEQ=AGCCGCGCAGGTTCCGCAGG;RSEQ=TCACTCGGTCAGCCTGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1054:581:347,234:249,222:471,581:0.5512:2,2:25.7:1:29.8:1:0.02854:1.32:54.5:82:0.553:0:2.2 0/1:805:360:200,160:245,200:445,360:0.4472:2,2:26.9:1:29.1:1:0.94318:1.02:53.8:179:0.4497:0:2.3 +6 31239430 . C T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.67195;SOR=0.95901;LSEQ=CCGCAGGCTCACTCGGTCAG;RSEQ=CTGTGCCTGGCGCTTGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1158:382:188,194:432,343:775,382:0.3299:2,2:29.8:1:29.8:1:0.03868:1.29936:49.3:46.75:0.3284:0:1.4 0/1:923:296:158,138:328,299:627,296:0.3207:2,2:28.4:1:29:1:0.77789:1.04:50:147:0.3217:0:1.6 +6 31239449 . C G 212 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=145.74478;LSEQ=GCCTGTGCCTGGCGCTTGTA;RSEQ=TTCTGTGTCTCCCGGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1223:1:1,0:618,599:1217,1:8e-04:2,0:42:0:29:0:1:0:60:2:8e-04:0:3 0/1:1003:107:50,57:459,434:893,107:0.1067:2,2:26.7:1:31.5:1:0.41316:1.20544:55:214:0.1083:0:1.2 +6 31239501 . G T 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.35008;LSEQ=CCTCCTGCTCCACCCACGGC;RSEQ=CCCGCGGCTCCCCTCTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:905:351:149,202:238,313:551,351:0.3878:2,2:23.9:1:30.4:1:0.83632:1.03083:49.2:34.1:0.3849:0:2.4 0/1:722:131:62,69:269,321:590,131:0.1814:2,2:24.2:1:29.3:1:0.7714:1.07:47.1:42.667:0.1816:0:2.3 +6 31239506 . C G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00023;SOR=1.80887;LSEQ=TGCTCCACCCACGGCGCCCG;RSEQ=GGCTCCCCTCTCGGACTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:843:76:31,45:324,441:765,76:0.0902:2,2:24.2:1:31.5:1:0.80904:1.06643:51.1:152:0.0916:0:1.3 0/1:684:104:44,60:256,324:580,104:0.152:2,2:24:1:30:1:0.74867:1.07736:53:103:0.153:0:1.2 +6 31239518 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.81779;SOR=1.03255;LSEQ=GGCGCCCGCGGCTCCCCTCT;RSEQ=GGACTCGCGGCGTCGCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:732:260:101,159:195,276:471,260:0.3552:2,2:27.1:1:30.4:1:0.52931:1.11209:45.7:31.5:0.351:0:2.4 0/1:593:215:89,126:166,210:376,215:0.3626:2,2:24.6:1:29.7:1:0.54612:1.11889:47.2:52.75:0.3613:0:2 +6 31239543 . C T 149 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=40.83084;LSEQ=TCGCGGCGTCGCTGTCGAAC;RSEQ=GCACGAACTGCGTGTCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:526:1:1,0:219,306:525,1:0.0019:2,0:10:0:16:0:0.41825:0:42:0:0:0:4 0/1:429:31:11,20:186,212:398,31:0.0723:2,2:22.2:1:30.2:1:0.26407:1.5935:45.5:62:0.0729:0:2.5 +6 31239577 . A C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.38074;LSEQ=GTCGTCCACGTAGCCCACTG;RSEQ=GATGAAGCGGGGCTCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:58:21,37:132,164:296,58:0.1629:2,2:11:1:30.7:1:0.25022:1.41674:32.5:116:0.1648:0:3.2 0/1:325:103:46,57:106,115:221,103:0.3169:2,2:16.8:1:29.2:1:0.63302:1.14169:33.5:33.333:0.3155:0:2.3 +6 31239585 . C T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18378;SOR=1.96778;LSEQ=CGTAGCCCACTGAGATGAAG;RSEQ=GGGGCTCTCCGCGGCCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:7:1,6:145,180:325,7:0.0211:2,2:11.3:1:31:1:0.14014:4.81527:29.6:14:0.0215:0:2.9 0/1:344:14:4,10:159,171:330,14:0.0407:2,2:10.4:1:29.6:1:0.17909:2.31907:30.8:28:0.0413:0:2.9 +6 31239593 . T C 111 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25778;SOR=0.56849;LSEQ=ACTGAGATGAAGCGGGGCTC;RSEQ=CCGCGGCCGGGCCGGGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:12:2,10:132,150:282,12:0.0408:2,2:3.3:1:31:1:0.07164:4.38144:25.1:24:0.0414:0:3.7 0/1:339:8:3,5:160,171:331,8:0.0236:2,2:7.3:1:29.8:1:0.72494:1.55745:26.4:16:0.024:0:3.4 +6 31239602 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08253;LSEQ=AAGCGGGGCTCTCCGCGGCC;RSEQ=GGCCGGGACACGGCGGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:80:41,39:87,105:192,80:0.2941:2,2:16.8:1:30.7:1:0.42422:1.27:35.8:79:0.2959:0:3.3 0/1:332:11:5,6:156,165:321,11:0.0331:2,2:20:1:29.7:1:1:1.13411:39.9:22:0.0333:0:3.4 +6 31239616 . CG AT 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09495;LSEQ=GCGGCCGGGCCGGGACACGG;RSEQ=GTGTCGAAATACCTCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:39:21,18:90,103:193,39:0.1681:2,2:39.2:1:31:1:0.48306:1.33:36.6:78:0.1696:0.0172:4.8 0/1:320:6:2,4:149,164:313,6:0.0188:2,2:39.2:1:29.2:1:0.68724:1.8138:43.8:12:0.0189:0.0031:4.5 +6 31239621 . TC AA 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08866;LSEQ=CGGGCCGGGACACGGCGGTG;RSEQ=GAAATACCTCATGGAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:36:21,15:95,104:199,36:0.1532:2,2:44:1:31:1:0.27927:1.53:38.8:72:0.1538:0.0043:4.2 0/1:318:5:1,4:146,167:313,5:0.0157:2,2:45.2:1:31:1:0.37823:3.48504:47.2:10:0.0159:0:4 +6 31239622 . C A 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCGGGACACGGCGGTGT;RSEQ=GAAATACCTCATGGAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:94,102:196,0:0:2,0:27.4:1:31:1:1:0:50.6:97:1:0:0.1 0/1:316:60:30,30:114,137:251,60:0.1899:2,2:36.8:1:29:1:0.56569:1.20:29.6:120:0.1954:0:2.1 +6 31239630 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08925;LSEQ=ACACGGCGGTGTCGAAATAC;RSEQ=TCATGGAGTGGGAGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:35:20,15:92,99:191,35:0.1549:2,2:42.9:1:31.4:1:0.36186:1.43:38.2:34:0.1532:0:4.3 0/1:312:5:1,4:139,168:307,5:0.016:2,2:38.6:1:31:1:0.38421:3.29855:47.2:10:0.0162:0:4 +6 31239652 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19152;LSEQ=CATGGAGTGGGAGCCTGGGG;RSEQ=CGAGGAGGGGCTGAGACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:45:19,26:105,130:235,45:0.1601:2,2:11.9:1:29:1:0.87014:1.10485:23.6:44:0.1612:0:4.5 0/1:313:11:8,3:132,170:302,11:0.0351:2,2:14.3:1:28.4:1:0.06879:3.42:30.2:22:0.0362:0:3.5 +6 31239660 . G T 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.18365;LSEQ=GGGAGCCTGGGGGCGAGGAG;RSEQ=GGCTGAGACCCGCCCGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:67:25,42:111,123:234,67:0.2226:2,2:14.6:1:28.7:1:0.16451:1.51401:23.8:21.333:0.2207:0:4.7 0/1:301:15:8,7:126,158:284,15:0.0498:2,2:14.2:1:29.1:1:0.59727:1.43:25.2:30:0.0507:0:4.5 +6 31239662 . G A 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11275;SOR=Inf;LSEQ=GAGCCTGGGGGCGAGGAGGG;RSEQ=CTGAGACCCGCCCGACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:137,168:305,0:0:2,0:19.2:1:31.3:1:1:0:38.8:60:1:0:2.2 0/1:287:3:2,1:128,156:284,3:0.0105:2,2:7.3:1:27:1:0.59168:2.43:34:6:0.0105:0:1.3 +6 31239681 . A T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.33273;LSEQ=GGCTGAGACCCGCCCGACCC;RSEQ=CCTCCCTGCGCGGCTCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:298:180:87,93:48,70:118,180:0.604:2,2:24.4:1:30.3:1:0.23411:1.36:33.3:24.714:0.5986:0:4.5 0/1:232:78:51,27:70,84:154,78:0.3362:2,2:22:1:29.9:1:0.00528:2.26:39.8:77:0.3348:0:3.3 +6 31239722 . A C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11342;SOR=1.50513;LSEQ=GGTCCTGCGCCCTCGCCGGG;RSEQ=GGGCCCCTCGCTCCTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:440:385:209,176:21,31:52,385:0.875:2,2:26.4:1:31.1:1:0.07527:1.75:39.6:76:0.8796:0:4.3 1/1:277:253:157,96:12,11:23,253:0.9134:2,2:25.9:1:30.4:1:0.37705:1.50:45.8:125.5:0.9161:0:3 +6 31239727 . C A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.14492;LSEQ=TGCGCCCTCGCCGGGAGGGC;RSEQ=CCTCGCTCCTCTCCGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:143:85,58:171,159:330,143:0.3011:2,2:27:1:30.2:1:0.13293:1.36:45.9:46.667:0.307:0:4.7 0/1:307:18:12,6:177,112:289,18:0.0586:2,2:25.9:1:29.2:1:0.80427:1.26:45.4:36:0.06:0:4.8 +6 31239733 . C T 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16243;LSEQ=CTCGCCGGGAGGGCCCCTCG;RSEQ=TCCTCTCCGCAGAGGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:156:93,63:175,158:333,156:0.319:2,2:26.7:1:30.2:1:0.17227:1.33:44.5:155:0.3229:0:4.7 0/1:340:24:15,9:196,120:316,24:0.0706:2,2:22.5:1:28.5:1:1:1.02:41.7:48:0.0721:0:4.6 +6 31239742 . G C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30983;LSEQ=AGGGCCCCTCGCTCCTCTCC;RSEQ=CAGAGGCCGCTTCCCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:506:190:98,92:178,136:314,190:0.3755:2,2:27.2:1:31.2:1:0.26946:1.22818:33.4:62.333:0.3809:0:4.7 0/1:357:56:33,23:191,109:300,56:0.1569:2,2:29.1:1:29.9:1:0.5475:1.22058:35.6:55:0.1558:0:4.5 +6 31239752 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.45066;LSEQ=GCTCCTCTCCGCAGAGGCCG;RSEQ=TTCCCTCCCAACCCCGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:498:422:244,178:33,25:58,422:0.8474:2,2:26.1:1:29.7:1:0.88839:1.04:39.1:45.889:0.848:0:4.3 1/0:371:265:167,98:46,29:75,265:0.7143:2,2:25.2:1:28.8:1:0.78849:1.07:41.9:65.25:0.717:0:3.9 +6 31239766 . C T 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGCCGCTTCCCTCCCAACC;RSEQ=CGCACTCACAGGCCCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:0:0,0:299,219:518,0:0:2,0:25.8:1:31.3:1:1:0:40.9:85.333:1:0:3.7 0/1:415:42:24,18:228,145:373,42:0.1012:2,2:26.9:1:29.2:1:0.62085:1.17883:40.2:84:0.1022:0:4.1 +6 31239776 . A C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45774;SOR=0.88737;LSEQ=CCTCCCAACCCCGCACTCAC;RSEQ=GGCCCAGGTCTCGGTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:133:76,57:237,166:403,133:0.2481:2,2:28.2:1:30.2:1:0.76137:1.07065:36.2:43.333:0.2486:0:4.6 0/1:468:106:61,45:209,151:360,106:0.2265:2,2:26:1:29.4:1:1:1.02102:36.2:52:0.2291:0:4.5 +6 31239790 . G A 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCACAGGCCCAGGTCTCG;RSEQ=TCAGGGCCAGGCCTCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:558:0:0,0:315,242:557,0:0:2,0:24:1:31.5:1:1:0:37.6:49.636:0.9982:0:3.7 0/1:497:44:24,20:258,194:452,44:0.0885:2,2:24.2:1:28.6:1:0.75239:1.10802:33.2:21:0.0868:0:4.8 +6 31239802 . C G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.50397;LSEQ=AGGTCTCGGTCAGGGCCAGG;RSEQ=CTCCCGAGAGCAGCAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:635:537:304,233:51,45:96,537:0.8457:2,2:21.7:1:31.5:1:0.57701:1.15:31.1:43.75:0.8454:0:4.7 1/0:564:414:227,187:81,68:149,414:0.734:2,2:23.4:1:30.1:1:0.92388:1.02:32.2:28.571:0.7313:0:4.7 +6 31239821 . G T 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=0.34251;LSEQ=GCCTCCCGAGAGCAGCAGGA;RSEQ=GAGGGCTCGGGGCGCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:817:695:363,332:66,56:122,695:0.8507:2,2:21.3:1:30.6:1:0.76823:1.07779:35:56.917:0.8506:0:4.5 1/0:705:466:242,224:130,108:238,466:0.661:2,2:21.7:1:29:1:0.52364:1.114:33.7:37.833:0.6561:0:4.8 +6 31239827 . C T 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32914;LSEQ=CGAGAGCAGCAGGAGGAGGG;RSEQ=TCGGGGCGCCATGACCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:845:724:364,360:63,56:119,724:0.8568:2,2:22.5:1:29.9:1:0.62154:1.1125:36.8:54.692:0.8608:0:4.4 1/0:742:492:246,246:132,116:248,492:0.6631:2,2:22.1:1:28.6:1:0.43623:1.13773:35.2:48.2:0.6648:0:4.7 +6 31239829 . C T 185 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=91.78958;LSEQ=AGAGCAGCAGGAGGAGGGCT;RSEQ=GGGGCGCCATGACCCGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:861:1:1,0:430,427:857,1:0.0012:2,0:21:0:33:0:1:0:45:2:0.0012:0:5 0/1:735:71:38,33:335,329:664,71:0.0966:2,2:23.7:1:30.1:1:0.70818:1.13:42:142:0.0981:0:4.7 +6 31239855 . C G 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.50203;LSEQ=GCCATGACCCGCATCTCGGC;RSEQ=TCTGGGGAGAATGTGAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:928:815:365,450:49,61:110,815:0.8782:2,2:30:1:31.3:1:1:1.01:42.8:115.429:0.8811:0:3.9 1/0:716:561:244,317:72,83:155,561:0.7835:2,2:29.6:1:30.4:1:0.5235:1.12681:40.6:92.5:0.785:0:4.5 +6 31239868 . G C 311 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24037;LSEQ=TCTCGGCCTCTGGGGAGAAT;RSEQ=TGAGTCCGGGTGGGTGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:877:715:311,404:42,62:104,715:0.8153:2,2:31.3:1:32.8:1:0.5968:1.14:44.8:101.143:0.8166:0:3.8 1/0:655:337:147,190:60,73:133,337:0.5145:2,2:30:1:30.8:1:0.83664:1.06219:45.3:47.143:0.5124:0:4.2 +6 31239888 . GGGGACTTT TC 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGAGTCCGGGTGGGTGACT;RSEQ=AGAACCGGGACTGCGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:860:0:0,0:334,526:860,0:0:2,0:25.6:1:31.9:1:1:0:48.8:70.667:1:0:3 0/1:603:48:20,28:219,333:552,48:0.0796:2,2:27.9:1:30.3:1:0.87801:1.09:52.5:96:0.0807:0.0033:3.5 +6 31239896 . T C 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.11215;LSEQ=GGGTGGGTGACTGGGGACTT;RSEQ=AGAACCGGGACTGCGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:764:31:10,21:258,472:730,31:0.0406:2,2:22.2:1:32.1:1:0.84854:1.1477:50.9:62:0.0412:0:4.4 0/1:427:76:29,47:121,229:350,76:0.178:2,2:24.6:1:31:1:0.59671:1.17:52:152:0.1792:0:4.2 +6 31239912 . G T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTTTAGAACCGGGACTGCG;RSEQ=AGACGCTGATTGGCTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:145,404:549,0:0:2,0:21.5:1:31.6:1:1:0:57.7:67.625:0.9963:0:1.8 0/1:332:37:12,25:74,221:295,37:0.1114:2,2:24.7:1:28.2:1:0.32656:1.43:51.5:74:0.1118:0:4.2 +6 31239937 . C T 128 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=4.65347;LSEQ=GCTGATTGGCTTCTCTAGAA;RSEQ=CCGACACCCAATGGGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:11:2,9:34,272:306,11:0.0347:2,2:23.6:1:30.3:1:0.36117:1.77:59.7:22:0.0351:0:2.8 0/1:160:23:0,23:14,123:137,23:0.1438:2,1:21.3:1:28.4:1:0.22366:0:58.1:22:0.141:0:2.7 +6 31239951 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10822;SOR=Inf;LSEQ=CTAGAACCCGACACCCAATG;RSEQ=GAGTGGGAATTGGGGACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:18,238:256,0:0:2,0:26.1:1:31.3:1:1:0:57.4:84.333:1:0:0.3 0/1:126:2:1,1:8,116:124,2:0.0159:2,2:36.5:1:28:1:0.13829:13.73:60:4:0.0159:0:1 +6 31240010 . G GAGA 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.82868;SOR=0.87051;LSEQ=AAGGACCCGACGCAGGTTGG;RSEQ=AGAAGTGAAACTCAGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:91:69:4,65:1,21:22,69:0.7582:1,2:25:1:31.9:1:1:1.29:43.4:68:0.764:0.1319:0.6 1/0:41:30:3,27:2,8:10,30:0.7317:2,2:29.7:1:30.4:1:0.58352:2.19818:39.8:60:0.7317:0.0732:1.1 +6 31240034 . A GAGTGGG 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.0229;SOR=Inf;LSEQ=AGTGAAACTCAGGGGAGTGG;RSEQ=GAATCCCCAACGCGGCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:0,51:51,0:0:1,0:19.7:1:31.7:1:1:0:40.3:24.5:1:0:1.1 0/1:34:4:0,4:4,26:30,4:0.1176:2,0:11.5:1:32:1:1:0:31.5:8:0.1176:0.1176:0 +6 31240035 . G A 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15485;SOR=Inf;LSEQ=GTGAAACTCAGGGGAGTGGA;RSEQ=AATCCCCAACGCGGCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:0,47:47,0:0:1,0:20.3:1:31.4:1:1:0:40:14.667:1:0:1.2 0/1:31:2:0,2:4,25:29,2:0.0645:2,0:7:1:31:1:1:0:31.5:4:0.0645:0.0645:0 +6 31240037 . A T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14631;SOR=Inf;LSEQ=GAAACTCAGGGGAGTGGAGA;RSEQ=TCCCCAACGCGGCGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:0,46:46,0:0:1,0:19.9:1:30:1:1:0:39.9:10.5:1:0:1.3 0/1:29:2:0,2:4,23:27,2:0.069:2,0:5:1:29.5:1:1:0:31.5:4:0.069:0.069:0 +6 31240041 . C T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09524;SOR=2.30505;LSEQ=CTCAGGGGAGTGGAGAATCC;RSEQ=CAACGCGGCGCCTCCCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:0,16:0,28:28,16:0.3636:1,1:18.7:1:29.1:1:1:0:37.6:15:0.3659:0:2.8 1/0:28:16:2,14:2,10:12,16:0.5714:2,2:20.8:1:29.7:1:1:1.38301:38.4:32:0.5714:0:1.8 +6 31240060 . A G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42436;SOR=0.47681;LSEQ=CCCAACGCGGCGCCTCCCCA;RSEQ=TGCAGACACGGCCCTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:24:0,24:0,3:3,24:0.8889:0,1:24.8:1:30.9:1:1:0:37.9:23:0.8846:0:2.2 1/0:19:15:2,13:1,3:4,15:0.7895:2,2:16.3:1:31.2:1:0.53044:2.06666:33.6:30:0.7895:0:1.8 +6 31240096 . G A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.17928;SOR=5.13198;LSEQ=TGGAGCCTGAGACCCTGAGA;RSEQ=CCCCGCCCGGGACCTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:0,14:14,2:0.1053:1,0:24.5:1:27.5:1:1:0:26:4:0.125:0:2.5 0/1:5:2:1,1:0,3:3,2:0.4:0,2:12:1:28.5:1:0.4:0:29.5:4:0.4:0:3 +6 31240128 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50909;SOR=0;LSEQ=ACCTGGGACTTCGTCCTGAT;RSEQ=CCTCTTCTCCTACACCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:38:1:32:0:1:0:37.3:6:0.3333:0:1.7 0/0:3:0:0,0:0,3:3,0:0:0,0:25:1:32:0:1:0:35.7:6:1:0:0.7 +6 31240180 . A C 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTGTGCCTGAGTCCTGG;RSEQ=CAAGGATCTGTCTGTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:10.5:1:33:0:1:0:22:4:0.6667:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:15:0:31:0:1:0:60:2:1:0:0 +6 31240307 . TACCTC T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TCCCACCCTTTGCCTTACCT;RSEQ=ACCTCAGGTAATATTAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21.5:1:28.5:1:1:0:45.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31241032 . A G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCTGCCAGGCTCTTCT;RSEQ=CTGCTTTAGAATTCTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:19.7:1:32.3:1:1:0:58:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31241092 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTGCTTCTCCAGCCCTTCT;RSEQ=TCTGCCCCTCTCATCCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:25.5:1:31.5:1:1:0:43.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31320467 . C T 32 d5;v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CATCCCACTCAGAGCAAAGG;RSEQ=CAGATCCAACCCCACTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:7:0:32:0:1:0:24:4:0.6667:0:3.5 0/0:2:0:0,0:1,1:2,0:0:2,0:5:0:32.5:1:1:0:60:4:1:0:0.5 +6 31320473 . C G 34 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACTCAGAGCAAAGGCCAGAT;RSEQ=CAACCCCACTCCCCTCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:13:0:34:0:1:0:24:4:0.6667:0:3.5 0/0:2:0:0,0:1,1:2,0:0:2,0:11:0:32:0:1:0:60:4:1:0:0.5 +6 31320538 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACCTCACCTCAGTTTCTCTC;RSEQ=GTCCAGCCCTCCTGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:30:1:1:0:24:4:1:0:3.5 0/0:2:0:0,0:1,1:2,0:0:2,0:14.5:1:28.5:1:1:0:60:4:1:0:0.5 +6 31321807 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTGCAGCTCAGTGCAC;RSEQ=TAAAGTTGAGACAGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:31.5:1:32.5:1:1:0:32:4:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31321845 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGAGACATCCAGCCCCACC;RSEQ=CTCTGGAACAAGAAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:31.5:1:31:1:1:0:32:4:0.5:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31321856 . A G 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCCACCTCTCTGGAACA;RSEQ=GAAAGATGACTGGGGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:20.5:1:31:1:1:1.73:32:4:0.4:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31321883 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTGGGGAGGAAACACAG;RSEQ=TCAGCATGGGAACAGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:40.5:1:30:1:1:0:60:4:0.5:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31321916 . AG CA 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGGTCACAGTGGACACA;RSEQ=GGTGGGCTGTCTCTCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26.5:1:33.5:1:1:0:60:4:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31321919 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTCACAGTGGACACAAGG;RSEQ=TGGGCTGTCTCTCCACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:24.5:1:32:0:1:0:60:4:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31322121 . C T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13804;SOR=5.07211;LSEQ=TTCTGGTTAGTCATGGTAAG;RSEQ=GATGACACTCTAAACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:23:23,0:8,0:8,23:0.7419:0,1:22.4:1:29.9:1:1:0:58:46:0.7419:0:3.3 1/1:16:15:14,1:1,0:1,15:0.9375:0,1:31.4:1:30.5:1:1:0:58.1:30:0.9375:0:3 +6 31322129 . C G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13158;SOR=Inf;LSEQ=AGTCATGGTAAGCGATGACA;RSEQ=TCTAAACAGCCCACCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:36,0:36,0:0:1,0:23.5:1:32.9:1:1:0:57.2:72:1:0:3.1 0/1:21:2:2,0:18,1:19,2:0.0952:1,0:33:1:33:0:1:0:60:4:0.1:0:5.5 +6 31322133 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.87812;LSEQ=ATGGTAAGCGATGACACTCT;RSEQ=AACAGCCCACCACACACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:15:15,0:23,0:23,15:0.3947:1,1:25:1:33.3:1:1:0:55.9:30:0.4054:0:4.9 0/1:22:8:7,1:14,0:14,8:0.3636:1,2:25.3:1:32.1:1:0.36364:0:56.4:16:0.3636:0:3.4 +6 31322143 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02182;SOR=Inf;LSEQ=ATGACACTCTAAACAGCCCA;RSEQ=CACACACGCGAAACATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:44,0:44,0:0:1,0:23.9:1:32.2:1:1:0:57.7:43:1:0:2.9 0/1:29:4:4,0:24,1:25,4:0.1379:1,0:18:1:29.5:1:1:0:60:8:0.1379:0:2.8 +6 31322144 . C G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01512;SOR=0.20603;LSEQ=TGACACTCTAAACAGCCCAC;RSEQ=ACACACGCGAAACATCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:16,0:28,0:28,16:0.3636:1,1:27.5:1:29.6:1:1:0:56.1:32:0.3721:0:4.9 0/1:29:3:3,0:25,1:26,3:0.1034:1,0:23.7:1:30.7:1:1:0:60:6:0.1034:0:3.7 +6 31322174 . CC GT 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.72848;SOR=0.61378;LSEQ=AAACATCCCAATCAAAGAAT;RSEQ=CCATTACCCAGGCCTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:6:6,0:55,0:55,6:0.0984:1,0:25.8:1:31.3:1:1:0:58:12:0.1034:0.0164:2.3 0/1:48:3:3,0:45,0:45,3:0.0625:1,0:26.7:1:28.3:1:1:0:60:6:0.0625:0:1.3 +6 31322175 . C T 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21689;SOR=1.96603;LSEQ=AACATCCCAATCAAAGAATC;RSEQ=CCATTACCCAGGCCTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:46:46,0:8,0:8,46:0.7797:0,1:26.2:1:32.1:1:1:0:56:45:0.8654:0:3.5 1/1:48:42:42,0:3,0:3,42:0.875:0,1:23.1:1:30.6:1:1:0:55.5:84:0.9333:0:3 +6 31322197 . T A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=32.69587;LSEQ=CATTACCCAGGCCTTTCCCC;RSEQ=CTGCCCCACCCACCCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:3:2,1:69,5:74,3:0.0385:2,2:10.3:1:24.3:1:0.21866:6.56169:56.3:2:0.0299:0:3.7 1/0:61:35:32,3:25,1:26,35:0.5738:1,2:19.3:1:26.3:1:0.62945:2.31407:58.3:10.667:0.5714:0:3.5 +6 31322204 . C CCT 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0399;SOR=0;LSEQ=CAGGCCTTTCCCCTCTGCCC;RSEQ=ACCCACCCCCAGACCCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:6:6,0:41,5:46,6:0.0625:2,0:23.7:1:27.1:1:1:0:51.2:12:0.0659:0:5.5 0/0:70:0:0,0:57,13:70,0:0:2,0:13.8:1:29:1:1:0:56.8:22.333:1:0:2.4 +6 31322205 . A CTC 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=0;LSEQ=AGGCCTTTCCCCTCTGCCCC;RSEQ=CCCACCCCCAGACCCGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:26:19,7:41,5:46,26:0.2708:2,2:19.2:1:29.1:1:0.10386:2.97087:58:52:0.2857:0.125:4.3 0/0:70:0:0,0:57,13:70,0:0:2,0:13.8:1:29:1:1:0:56.8:22.333:1:0:2.4 +6 31322208 . CACCCCCAGACCCGCCACCCCA ACCCCCCCCG 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.1271;SOR=0;LSEQ=CCTTTCCCCTCTGCCCCACC;RSEQ=CCCACTCTAGACCCCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:4:4,0:41,11:52,4:0.058:2,0:15.3:1:28.3:1:0.57502:0:60:8:0.0755:0.0435:2 0/0:56:0:0,0:41,14:55,0:0:2,0:17.6:1:27.1:1:1:0:58.8:5.875:1:0:2.5 +6 31322220 . C T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22772;LSEQ=GCCCCACCCACCCCCAGACC;RSEQ=GCCACCCCACCCACTCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:90:58:39,19:15,12:27,58:0.6444:2,2:20:1:27.7:1:0.33854:1.63:58.9:3.833:0.6389:0:3.4 0/1:93:27:15,12:41,25:66,27:0.2903:2,2:16.4:1:28.4:1:0.64263:1.3081:60:26:0.2921:0:1.6 +6 31322221 . G C 31 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.72083;SOR=1.64382;LSEQ=CCCCACCCACCCCCAGACCC;RSEQ=CCACCCCACCCACTCTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:3:3,0:52,31:83,3:0.0326:2,0:15.7:1:21:1:0.55018:0:57.3:2:0.0317:0:5 0/1:95:5:5,0:51,38:89,5:0.0526:2,0:19.6:1:13.4:1:0.07873:0:54.2:0:0:0:4.6 +6 31322224 . A C 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.45949;SOR=1.60329;LSEQ=CACCCACCCCCAGACCCGCC;RSEQ=CCCCACCCACTCTAGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:7:6,1:53,34:87,7:0.0722:2,2:17.3:1:18.4:1:0.25167:3.81:57.6:0.75:0.0417:0:5 0/1:99:11:5,6:51,35:86,11:0.1111:2,2:14.5:1:22.9:1:0.51926:1.73824:60:1.75:0.0843:0:3.9 +6 31322229 . A G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00311;SOR=0.37381;LSEQ=ACCCCCAGACCCGCCACCCC;RSEQ=CCCACTCTAGACCCCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:37:15,22:55,36:91,37:0.2846:2,2:5.9:1:28.8:1:0.05068:2.22627:59.8:17.5:0.3153:0:1.1 0/1:124:16:7,9:59,45:104,16:0.129:2,2:8.4:1:31.1:1:0.42082:1.67827:60:32:0.1538:0:1.9 +6 31322253 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.60685;SOR=2.2102;LSEQ=ACTCTAGACCCCAAGAATCT;RSEQ=ACCTTTTCAAGCTGTGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:1,0:112,105:217,1:0.0046:2,0:26:0:11:0:1:0:47:0:0:0:7 0/1:198:2:1,1:104,92:196,2:0.0101:2,2:32:1:28:1:1:1.12973:60:4:0.0106:0:1 +6 31322299 . G A 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.71003;LSEQ=TCAGAGCCCTGGGCACTGTC;RSEQ=CTGCCTGGAGTAGAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:130,151:281,3:0.0106:2,2:26.3:1:31:1:0.59898:2.32:49:6:0.011:0:2 0/0:266:2:2,0:114,150:264,2:0.0075:2,0:1:0:23.5:1:0.18925:0:60:4:0.0077:0:1.5 +6 31322303 . C G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21754;LSEQ=AGCCCTGGGCACTGTCGCTG;RSEQ=CTGGAGTAGAACAAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:193:82,111:38,39:77,193:0.7096:2,2:28.8:1:31.8:1:0.34319:1.31757:58.7:63.333:0.7116:0:1.3 0/1:257:89:38,51:72,94:166,89:0.3463:2,2:29.7:1:30.9:1:1:1.02789:56.4:88:0.3492:0:1.4 +6 31322340 . G A 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=ACAGGACCTGGTCAGAGCCC;RSEQ=CAGGAGACGTGGGACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:61,119:180,0:0:2,0:23.3:1:30.9:1:1:0:59.9:59:1:0:0.7 0/1:153:12:7,5:46,91:137,12:0.0784:2,2:21:1:28.2:1:0.11596:2.75:56.9:11:0.0738:0:2.2 +6 31322341 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0892;SOR=Inf;LSEQ=CAGGACCTGGTCAGAGCCCG;RSEQ=AGGAGACGTGGGACAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:63,119:182,0:0:2,0:22.6:1:31.4:1:1:0:59.9:35.4:1:0:0.7 0/1:148:3:2,1:49,96:145,3:0.0203:2,2:16:1:28:1:0.27295:3.88:60:6:0.0204:0:1.3 +6 31322367 . T G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00412;SOR=Inf;LSEQ=ACGTGGGACAGGAGGAATTA;RSEQ=GGGGTGGGTGAGCTCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:24,86:110,0:0:2,0:22.9:1:30.5:1:1:0:60:109:1:0:0.4 0/1:76:6:2,4:14,56:70,6:0.0789:2,2:24.3:1:29.5:1:0.60029:1.98:49.5:12:0.08:0:1.8 +6 31322395 . A G 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00521;SOR=Inf;LSEQ=GTGAGCTCCTCCACACTCCC;RSEQ=CCCCCACCACTTACACGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:14,66:80,0:0:2,0:22.8:1:30.5:1:1:0:58.9:160:1:0:0.3 0/1:45:5:1,4:9,31:40,5:0.1111:2,2:17:1:31:1:1:1.15756:54.6:10:0.1136:0:2 +6 31322402 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCTCCACACTCCCACCCCCA;RSEQ=CACTTACACGCAGCCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:16,64:80,0:0:2,0:21.8:1:32.3:1:1:0:57.7:160:0.9877:0:0.4 0/1:44:10:1,9:9,25:34,10:0.2273:2,2:22.6:1:29.7:1:0.41055:3.1702:49.4:20:0.2381:0:2 +6 31322459 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08105;SOR=Inf;LSEQ=CCACCTGTGGGAAGAAAATG;RSEQ=CCTGTGAGGGCACTGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:18,36:54,0:0:2,0:26.2:1:30.4:1:1:0:51.2:108:1:0:0.9 0/1:22:2:0,2:6,14:20,2:0.0909:2,0:26.5:1:31.5:1:1:0:24.5:4:0.0952:0:2.5 +6 31322470 . C G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.74022;SOR=1.51839;LSEQ=AAGAAAATGTCCTGTGAGGG;RSEQ=ACTGGGAGGAAGCAGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:36:13,23:3,7:10,36:0.766:2,2:26.8:1:32.2:1:1:1.31:46.8:72:0.766:0:1.5 1/1:18:15:6,9:0,3:3,15:0.8333:0,2:27.5:1:30.5:1:0.51471:0:46.3:14:0.8235:0:1.5 +6 31322487 . G A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.17457;LSEQ=GGGCACTGGGAGGAAGCAGG;RSEQ=CCATGAGATCTTAGAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:0,2:12,21:33,2:0.0571:2,0:21.5:1:31.5:1:0.53613:0:56:4:0.0588:0:3 0/1:15:1:0,1:5,9:14,1:0.0667:2,0:13:0:24:0:1:0:60:2:0.0714:0:3 +6 31322513 . A C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19368;SOR=0.26156;LSEQ=AGATCTTAGAGGAACCTCCT;RSEQ=GTCTTGGACCCAAAAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:13:2,11:1,3:4,13:0.7647:2,2:25.1:1:30:1:1:1.76214:48.8:26:0.7647:0:2.3 0/1:9:4:1,3:1,4:5,4:0.4444:2,2:25.3:1:28.5:1:1:1.29:54.5:8:0.5:0:2.5 +6 31322559 . G A 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.55811;LSEQ=GAAGTATGACTACAGACCCA;RSEQ=GGCAGGATCAGGAAACACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:1,3:4,5:0.5556:2,0:21.8:1:31.6:1:0.44444:0:60:10:0.5556:0:2 0/1:5:2:1,1:1,2:3,2:0.4:2,2:24.5:1:28.5:1:1:1.73:60:4:0.4:0:2 +6 31322704 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCATCAAGGTGATACATCC;RSEQ=TCCTTCATTGTCACATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:20.5:1:33:1:1:0:25.5:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31322767 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11497;SOR=0;LSEQ=CACACAGGGTCCCAGGCTGC;RSEQ=TTAGCCCCTGTGTGCATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:3,1:8,1:9,4:0.3077:2,2:24:1:30:1:1:2.4495:46.3:8:0.3077:0:2.3 0/0:9:0:0,0:8,1:9,0:0:2,0:27.1:1:30.1:1:1:0:58.1:18:1:0:0.9 +6 31322782 . C G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.296;SOR=0.42821;LSEQ=GCTGCGTTAGCCCCTGTGTG;RSEQ=ATGCTGCTTCCCAGTAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:11,1:8,0:8,12:0.6:0,2:16.3:1:30.7:1:1:0:51.4:11:0.5789:0:1.4 0/1:13:5:5,0:6,2:8,5:0.3846:2,0:31.6:1:31.2:1:0.48718:0:56.6:10:0.3846:0:1 +6 31322803 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04163;SOR=Inf;LSEQ=ATGCTGCTTCCCAGTAATGA;RSEQ=GCAGGGAACACTTCTACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:30,2:32,0:0:2,0:22.8:1:34:1:1:0:55.5:64:1:0:0.6 0/1:18:3:2,1:13,2:15,3:0.1667:2,2:28:1:27.3:1:0.4424:2.98763:60:6:0.1765:0:1 +6 31322854 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16291;SOR=Inf;LSEQ=CCCCCAGTGGGACAAGAAAA;RSEQ=CCAGACCCCACCCCTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:66,16:82,0:0:2,0:24:1:31.2:1:1:0:52.5:19.5:1:0:1.4 0/1:56:2:1,1:39,15:54,2:0.0357:2,2:17.5:1:31.5:1:0.49351:2.54952:60:4:0.0357:0:1 +6 31322855 . C T 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=CCCCAGTGGGACAAGAAAAC;RSEQ=CAGACCCCACCCCTCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:67,17:84,0:0:2,0:23.7:1:30.5:1:1:0:52.7:20:0.9877:0:1.4 0/1:57:11:7,4:33,13:46,11:0.193:2,2:24.1:1:30.6:1:0.71657:1.4407:43.3:22:0.193:0:2.1 +6 31322888 . A G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51218;SOR=0.77131;LSEQ=CTCACCCCTTCCCTACCTGA;RSEQ=CTCTTCCTCCTACACATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:125:102:86,16:16,7:23,102:0.816:2,2:27.5:1:32.7:1:0.13385:2.33:54.5:19.4:0.8083:0:2.1 1/0:106:82:57,25:18,6:24,82:0.7736:2,2:25.7:1:31.3:1:0.79923:1.31249:52.8:81:0.7864:0:1.6 +6 31322911 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.14549;LSEQ=CTTCCTCCTACACATCACAG;RSEQ=AGCGACCACAGCTCCGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:174:134:108,26:28,12:40,134:0.7701:2,2:24.3:1:29.8:1:0.19047:1.77:56:66:0.7719:0:2.4 0/1:138:45:33,12:65,28:93,45:0.3261:2,2:23.8:1:28.7:1:0.84158:1.18:53.2:90:0.3261:0:2.4 +6 31322980 . C T 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.20682;LSEQ=AACAATGCCCACGATGGGGA;RSEQ=GGTGGACTGGGAAGACGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:370:283:162,121:47,40:87,283:0.7649:2,2:29.8:1:30.4:1:0.62221:1.14:46.3:39.429:0.7645:0:2.9 0/1:264:106:58,48:80,78:158,106:0.4015:2,2:28.9:1:29.3:1:0.53204:1.18:45.5:105:0.4086:0:2.6 +6 31322987 . C T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0108;SOR=Inf;LSEQ=CCCACGATGGGGACGGTGGA;RSEQ=TGGGAAGACGGCTCTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:209,180:389,0:0:2,0:28.7:1:32:1:1:0:48.3:31.417:1:0:2.2 0/1:266:5:3,2:132,129:261,5:0.0188:2,2:22:1:27.4:1:1:1.46:44.6:10:0.0192:0:2 +6 31322996 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0.25095;LSEQ=GGGACGGTGGACTGGGAAGA;RSEQ=GGCTCTGGGAAAGGAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:387:315:164,151:36,36:72,315:0.814:2,2:28.1:1:30.7:1:0.79447:1.09:44.1:156.5:0.8151:0:2.8 1/0:264:138:72,66:59,67:126,138:0.5227:2,2:29.5:1:29.1:1:0.3917:1.24:46.3:22:0.5136:0:2.2 +6 31323012 . G A 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGACGGCTCTGGGAAAGGA;RSEQ=GGGAAGATGAGGGGCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:191,192:383,0:0:2,0:25.1:1:31.9:1:1:0:44.4:46.875:1:0:2.1 0/1:267:43:18,25:105,118:223,43:0.161:2,2:28.9:1:30:1:0.61707:1.2349:59.1:86:0.1648:0:1 +6 31323020 . T C 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04878;LSEQ=TCTGGGAAAGGAGGGGAAGA;RSEQ=GAGGGGCCCTGACCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:364:266:129,137:41,56:97,266:0.7308:2,2:23.2:1:30.7:1:0.34183:1.29:39.8:52.2:0.7291:0:2.7 0/1:258:30:13,17:109,119:228,30:0.1163:2,2:20.8:1:30.1:1:0.70021:1.19697:38:60:0.1176:0:2.6 +6 31323027 . C T 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGAGGGGAAGATGAGGGG;RSEQ=CCTGACCCTGCTGAAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:154,188:342,0:0:2,0:22.5:1:31.1:1:1:0:43.5:30.091:1:0.0029:1.9 0/1:242:14:8,6:105,122:227,14:0.0579:2,2:21.4:1:29.4:1:0.58273:1.55:41.8:28:0.0593:0:2.4 +6 31323039 . T TGAAGGGCTCCA 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29169;LSEQ=ATGAGGGGCCCTGACCCTGC;RSEQ=GAAGGGCTCCTGCTTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:383:249:122,127:59,74:133,249:0.6501:2,2:23.1:1:31.2:1:0.39222:1.20:44.8:248:0.6544:0.2742:1.5 0/1:245:86:42,44:78,79:157,86:0.351:2,2:21.9:1:30.1:1:1:1.03423:47.8:172:0.3539:0.151:1.4 +6 31323045 . G A 78 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77534;SOR=1.33386;LSEQ=GGCCCTGACCCTGCTGAAGG;RSEQ=CTCCTGCTTTCCCTGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:7:3,4:186,197:383,7:0.0179:2,2:3.7:1:27.9:1:1:1.25814:21:14:0.0182:0:8 0/1:252:6:4,2:125,121:246,6:0.0238:2,2:7.7:1:28.7:1:0.68427:1.93:35.5:12:0.0241:0:5.7 +6 31323048 . C CCAGGACTT 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59223;SOR=0.84055;LSEQ=CCTGACCCTGCTGAAGGGCT;RSEQ=CTGCTTTCCCTGAGAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:41:19,22:182,190:372,41:0.099:2,2:12.1:1:30.7:1:0.86949:1.10886:23.9:82:0.0998:0.0797:6.2 0/1:272:23:8,15:127,122:249,23:0.0846:2,2:10.3:1:28.8:1:0.19042:1.94714:28.7:46:0.0868:0.0699:5.5 +6 31323065 . G C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.92408;LSEQ=GCTCCTGCTTTCCCTGAGAA;RSEQ=AGATATGACCCCTCATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:413:9:5,4:198,206:404,9:0.0218:2,2:12.1:1:33.7:1:0.74749:1.30:53.7:18:0.022:0:1.4 0/1:291:34:15,19:130,127:257,34:0.1168:2,2:21.9:1:31.6:1:0.58468:1.29543:51.4:68:0.1168:0:1.2 +6 31323067 . G C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35424;SOR=0.76305;LSEQ=TCCTGCTTTCCCTGAGAAGA;RSEQ=ATATGACCCCTCATCCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:41:19,22:190,188:378,41:0.0979:2,2:25.4:1:32.4:1:0.74268:1.16977:23.9:40:0.0971:0:6.2 0/1:301:23:9,14:144,133:277,23:0.0764:2,2:22.8:1:32.3:1:0.28081:1.68129:26.5:46:0.0774:0:5.7 +6 31323069 . T C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.29293;SOR=0.74507;LSEQ=CTGCTTTCCCTGAGAAGAGA;RSEQ=ATGACCCCTCATCCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:41:19,22:195,194:389,41:0.0953:2,2:27.4:1:32.4:1:0.74312:1.16345:23.9:40:0.0941:0:6.2 0/1:316:23:9,14:156,137:293,23:0.0728:2,2:24.8:1:31.7:1:0.20222:1.76808:26.5:22:0.0703:0:5.7 +6 31323072 . G C 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01871;SOR=0.49229;LSEQ=CTTTCCCTGAGAAGAGATAT;RSEQ=ACCCCTCATCCCCCTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:42:19,23:208,197:405,42:0.0933:2,2:28.7:1:32.8:1:0.51768:1.27741:24:84:0.0942:0:6.2 0/1:332:16:7,9:171,145:316,16:0.0482:2,2:26.3:1:31.9:1:0.45098:1.51433:24.3:32:0.0486:0:6.3 +6 31323115 . T C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48126;SOR=0.83616;LSEQ=CCATCTCAGGGTGAGGGGCT;RSEQ=CGGCAGCCCCTCATGCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:49:22,27:250,267:517,49:0.0864:2,2:23.5:1:32:1:0.6571:1.14885:23.8:98:0.0878:0:5.8 0/1:423:31:14,17:193,198:391,31:0.0733:2,2:27.2:1:29.6:1:0.71127:1.18315:25:14.5:0.0694:0:5.3 +6 31323116 . C T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CATCTCAGGGTGAGGGGCTT;RSEQ=GGCAGCCCCTCATGCTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:0:0,0:267,295:562,0:0:2,0:28:1:30.9:1:1:0:55.6:139.5:1:0:0.6 0/1:420:14:7,7:199,206:405,14:0.0333:2,2:28.5:1:28.5:1:1:1.04:46.6:13:0.0315:0:1.5 +6 31323128 . A G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99444;LSEQ=AGGGGCTTCGGCAGCCCCTC;RSEQ=TGCTGTACATGGCATGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:36:17,19:217,259:476,36:0.0703:2,2:18.2:1:30.7:1:0.86392:1.07:22.9:35:0.0694:0:6.3 0/1:386:27:14,13:167,192:359,27:0.0699:2,2:21.6:1:29.5:1:0.69036:1.24:24.4:54:0.0709:0:5.6 +6 31323134 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.89167;SOR=1.04333;LSEQ=TTCGGCAGCCCCTCATGCTG;RSEQ=ACATGGCATGTGTATCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:34:17,17:207,256:463,34:0.0683:2,2:13.1:1:31.9:1:0.59465:1.24:22.4:68:0.0687:0:6.4 0/1:352:25:14,11:143,182:325,25:0.071:2,2:20.6:1:30.2:1:0.29814:1.62:24.5:50:0.0712:0:5.4 +6 31323143 . T C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55073;SOR=1.34665;LSEQ=CCCTCATGCTGTACATGGCA;RSEQ=GTGTATCTCTGCTCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:14:7,7:183,244:427,14:0.0317:2,2:14.6:1:29:1:0.59685:1.33:21.4:13:0.0299:0:5.9 0/1:308:13:8,5:122,172:294,13:0.0422:2,2:20:1:29.4:1:0.1645:2.25:22.5:26:0.0433:0:5.2 +6 31323203 . A G 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=GCCCACTTCTGGAAGGTTCT;RSEQ=TCTCCTGCTGGTCTGGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:67,121:188,0:0:2,0:25.7:1:30.2:1:1:0:58:46:1:0:0.2 0/1:107:10:2,8:35,62:97,10:0.0935:2,2:22.5:1:31.5:1:0.48846:2.24298:46.3:20:0.0962:0:1.8 +6 31323225 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.09787;SOR=Inf;LSEQ=CTCCTGCTGGTCTGGTCTCC;RSEQ=CAAGCTCAGTGTCCTGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:103,87:190,0:0:2,0:22.7:1:30.8:1:1:0:49.1:189:1:0:0.4 0/1:87:2:1,1:42,43:85,2:0.023:2,2:49:0:31:1:1:1.02:60:4:0.023:0:1 +6 31323233 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.81135;LSEQ=GGTCTGGTCTCCACAAGCTC;RSEQ=GTGTCCTGAGTTTGGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:4:1,3:102,76:178,4:0.022:2,2:34.5:1:31.3:1:0.31812:3.99711:52.3:8:0.0225:0:1 0/1:83:30:15,15:31,22:53,30:0.3614:2,2:32.1:1:29.5:1:0.49676:1.4032:37.6:60:0.3614:0:1.4 +6 31323296 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.67081;SOR=0.86569;LSEQ=GTGATCTCCGCAGGGTAGAA;RSEQ=CCCAGGGCCCAGCACCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:169:112:82,30:34,23:57,112:0.6627:2,2:14.2:1:32.2:1:0.08145:1.84:24.9:111:0.6687:0:1.1 1/0:81:51:37,14:21,9:30,51:0.6296:2,2:13.7:1:31:1:0.80437:1.13:23.8:50:0.6329:0:1.1 +6 31323303 . GC G 34 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12672;SOR=Inf;LSEQ=CCGCAGGGTAGAAACCCAGG;RSEQ=CCAGCACCTCAGGGTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:144,74:218,0:0:2,0:13.9:1:30.4:1:1:0:30.8:15.769:1:0:0.7 0/1:121:2:1,1:73,45:118,2:0.0165:2,2:24:1:34:0:1:1.61538:22.5:4:0.0167:0:1 +6 31323321 . G A 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCCAGCACCTCAGGGTG;RSEQ=CCTCATGGTCAGAGATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:205,171:376,0:0:2,0:17.3:1:31.4:1:1:0:41.8:93:0.9947:0:0.9 0/1:272:28:14,14:131,110:241,28:0.1029:2,2:9.9:1:27.8:1:0.69267:1.19013:33.9:27:0.1015:0:2.6 +6 31323337 . T C 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.39644;LSEQ=GGTGGCCTCATGGTCAGAGA;RSEQ=GGGGTGGTGGGTCACGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:547:144:73,71:216,187:403,144:0.2633:2,2:19.7:1:30.3:1:0.5609:1.12319:45.5:27.8:0.2603:0:1.9 0/1:492:61:36,25:231,200:431,61:0.124:2,2:16.6:1:29.3:1:0.49292:1.25:47.9:19.333:0.1193:0:1.9 +6 31323353 . G A 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=14.77101;LSEQ=GAGATGGGGTGGTGGGTCAC;RSEQ=TGTGTCTTTGGGGGGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:672:30:17,13:327,313:640,30:0.0446:2,2:29.1:1:30.6:1:0.58025:1.25:49.7:60:0.0453:0:1.9 0/1:604:247:124,123:197,159:356,247:0.4089:2,2:27:1:29.7:1:0.2453:1.22857:47.4:60.75:0.4077:0:2 +6 31323409 . T C 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05917;SOR=1.40639;LSEQ=AATTCAGGCGCTTTGCATCT;RSEQ=TCATGGGACACCCTAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:579:483:174,309:36,59:95,483:0.8342:2,2:23.1:1:32.3:1:0.72772:1.08342:54.9:59.375:0.8333:0:1.7 1/1:517:453:192,261:26,37:63,453:0.8762:2,2:21.6:1:30.3:1:0.89261:1.05:53.9:36.75:0.8733:0:1.8 +6 31323414 . G A 220 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01492;LSEQ=AGGCGCTTTGCATCTTTCAT;RSEQ=GGACACCCTAGGACCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:160:55,105:125,245:370,160:0.3019:2,2:21.5:1:30.1:1:0.92057:1.03:57.2:39:0.3012:0:2.1 0/0:470:3:3,0:194,273:467,3:0.0064:2,0:6.7:1:15.7:1:0.07299:0:48.3:0.5:0.0022:0:3.3 +6 31323416 . G C 185 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGCTTTGCATCTTTCATGG;RSEQ=ACACCCTAGGACCACCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:0:0,0:166,336:502,0:0:2,0:22.4:1:31.3:1:1:0:56.2:44.636:1:0:1.5 0/1:447:73:29,44:152,221:373,73:0.1633:2,2:20.7:1:30:1:0.89706:1.04344:58.4:23.333:0.1602:0:2.1 +6 31323455 . A G 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00579;SOR=Inf;LSEQ=TGTGACCAGCCTGAGAATGG;RSEQ=CAGGACACCTGGGGTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:10,215:225,0:0:1,0:23:1:30.4:1:1:0:58:224:1:0:1.2 0/1:168:6:0,6:11,151:162,6:0.0357:2,0:28.8:1:31.3:1:1:0:56.8:12:0.0361:0:1.8 +6 31323468 . G T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=0.26442;LSEQ=AGAATGGACAGGACACCTGG;RSEQ=GTGGGGAAGGGGCACAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:59:2,57:2,114:116,59:0.3371:1,1:27.9:1:31.3:1:0.60389:1.99:55.2:118:0.345:0:1.6 0/1:127:15:1,14:4,108:112,15:0.1181:1,1:27.7:1:28.9:1:0.47232:1.92:50.1:30:0.1181:0:1.5 +6 31323480 . G A 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=ACACCTGGGGTGGGGAAGGG;RSEQ=CACAGAACCCAGACACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:4,146:150,0:0:1,0:24.3:1:32.5:1:1:0:56.9:49:1:0:0.9 0/1:111:11:0,11:4,96:100,11:0.0991:1,0:27.3:1:30.1:1:1:0:46.5:22:0.1:0:1.7 +6 31323501 . CTGGAC GGAT 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CACAGAACCCAGACACCAGC;RSEQ=GCAGGCACCTGGGATAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:2,105:107,0:0:1,0:25.9:1:33.5:1:1:0:55.8:52.5:1:0:0.6 0/1:72:12:0,12:1,59:60,12:0.1667:1,0:21.3:1:31.7:1:1:0:51:24:0.1739:0.0417:0.8 +6 31323524 . TCTC T 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=GACGCAGGCACCTGGGATAA;RSEQ=CTATTCATTGGAAAGTTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:2,67:69,0:0:1,0:25.7:1:33.7:1:1:0:55.6:68:1:0:0.3 0/1:37:7:1,6:0,30:30,7:0.1892:1,2:14.4:1:32.7:1:0.18919:0:49.4:14:0.1892:0.027:0.7 +6 31323707 . G A 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTGCTGCAGGGGTCAAAG;RSEQ=GGACCCCTGATCAGTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:0,4:3,6:9,4:0.3077:2,0:25.5:1:32.8:1:0.4965:0:59.3:8:0.3077:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31323766 . T C 53 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCCTCAGAGACGTCAT;RSEQ=CCTTAATTGTCTAGAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:2,1:3,3:0.4286:2,0:9.7:1:34:0:0.4:0:59:6:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31323838 . C G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65932;SOR=2.3761;LSEQ=TCATGCCATTCTCCATTCAA;RSEQ=GGAGGGCGACATTCTAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:29:27,2:6,1:7,29:0.8056:2,2:23.7:1:33.6:1:0.48824:2.19:44.2:58:0.8056:0:1.1 1/1:11:10:9,1:1,0:1,10:0.9091:0,2:23.4:1:33:1:1:0:42:20:0.9091:0:1.5 +6 31323875 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01391;SOR=Inf;LSEQ=GCGCTGATCCCATTTTCCTC;RSEQ=TCTTCTCGTGGGAGGCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:61,3:64,0:0:1,0:28.3:1:31.4:1:1:0:46.5:128:1:0:0.9 0/1:35:4:4,0:29,2:31,4:0.1143:2,0:12.5:1:32.3:1:1:0:24.5:8:0.1143:0:3.3 +6 31323945 . A C 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21261;SOR=1.75347;LSEQ=TCCCCACTGCCCCTGGTACC;RSEQ=GCGCGCTCCAGCTTGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:15:14,1:32,15:47,15:0.2419:2,1:9.9:1:28.1:1:0.08751:6.42:37:14:0.2295:0:1.7 0/1:50:18:17,1:25,7:32,18:0.36:2,1:22.2:1:28.4:1:0.23072:4.64:34.5:36:0.36:0:2.6 +6 31323949 . C A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50695;SOR=0;LSEQ=CACTGCCCCTGGTACCAGCG;RSEQ=GCTCCAGCTTGTCCTTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:45,17:62,2:0.0308:2,2:24:0:33:1:0.48661:2.60091:36:4:0.0317:0:1.5 0/0:48:0:0,0:40,8:48,0:0:2,0:23.6:1:30.6:1:1:0:50.9:96:1:0:0.9 +6 31323953 . C G 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.78425;SOR=1.21109;LSEQ=GCCCCTGGTACCAGCGCGCT;RSEQ=CAGCTTGTCCTTCCCGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:8:8,0:39,22:61,8:0.1159:2,0:6.6:1:27.4:1:0.04825:0:25.9:3:0.0896:0:2.3 0/1:51:7:7,0:31,13:44,7:0.1373:2,0:8.3:1:30.1:1:0.1695:0:29.9:14:0.1429:0:3.6 +6 31323958 . T G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00053;SOR=7.99179;LSEQ=TGGTACCAGCGCGCTCCAGC;RSEQ=TGTCCTTCCCGTTCTCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:3:3,0:42,23:65,3:0.0441:2,0:5:1:24:1:0.54565:0:23.3:2:0.0299:0:3.7 0/1:55:15:14,1:25,15:40,15:0.2727:2,1:12.5:1:26.7:1:0.04259:8.15:33.3:30:0.283:0:2.9 +6 31324003 . TC GT 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01615;SOR=0.36776;LSEQ=TGCGGAGCCACTCCACGCAC;RSEQ=GCCCTCCAGGTAGGCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:27:20,7:51,49:100,27:0.1901:2,2:7.6:1:30.9:1:0.04816:2.72:48.3:54:0.1929:0.0282:1.1 0/1:101:8:5,3:36,33:69,8:0.0792:2,2:9.1:1:29.2:1:0.71651:1.52:54.3:16:0.0842:0.0099:1.1 +6 31324024 . C A 89 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01203;SOR=10.81933;LSEQ=CGCCCTCCAGGTAGGCTCTC;RSEQ=GCTGCTCCGCCTCACGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:1:0,1:119,112:231,1:0.0043:2,0:1:0:25:0:0.48707:0:20:2:0.0043:0:2 0/1:178:8:5,3:81,89:170,8:0.0449:2,2:31.5:1:29.8:1:0.48534:1.83:29.8:16:0.0457:0:2.1 +6 31324025 . G A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00054;SOR=2.23791;LSEQ=GCCCTCCAGGTAGGCTCTCC;RSEQ=CTGCTCCGCCTCACGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:44:20,24:104,95:199,44:0.1811:2,2:21.1:1:29.7:1:0.50546:1.3122:30.9:88:0.1818:0:2 0/1:178:59:30,29:56,63:119,59:0.3315:2,2:22.2:1:27.8:1:0.75017:1.16:32.6:18.667:0.3218:0:1.9 +6 31324036 . T A 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00231;SOR=Inf;LSEQ=AGGCTCTCCGCTGCTCCGCC;RSEQ=CACGGGCCGCCTCCCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:138,131:269,0:0:2,0:25:1:31.1:1:1:0:43.5:88.667:1:0:0.8 0/1:198:7:4,3:91,100:191,7:0.0354:2,2:44.7:1:29.6:1:0.71221:1.46:25.4:14:0.0363:0:2.1 +6 31324077 . C G 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0396;SOR=4.93497;LSEQ=CGCTGGGTGATCTGAGCCGC;RSEQ=GTGTCCGCGGCGGTCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:2:1,1:109,109:218,2:0.0091:2,2:3:0:31:1:1:1:23.5:4:0.0092:0:1 0/1:161:7:6,1:74,80:154,7:0.0435:2,2:12.4:1:30:1:0.06359:6.42:25.9:14:0.0438:0:2.7 +6 31324078 . G T 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GCTGGGTGATCTGAGCCGCC;RSEQ=TGTCCGCGGCGGTCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:109,108:217,0:0:2,0:29.5:1:31.3:1:1:0:39.1:107.5:1:0:0.9 0/1:161:16:7,9:73,72:145,16:0.0994:2,2:36.6:1:29.8:1:0.79317:1.30143:32.4:32:0.0994:0:1.8 +6 31324086 . G C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00041;SOR=3.38705;LSEQ=ATCTGAGCCGCCGTGTCCGC;RSEQ=GCGGTCCAGGAGCGCAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:14:5,9:97,95:192,14:0.068:2,2:24.6:1:30.8:1:0.40762:1.83257:35.9:28:0.0693:0:2.9 0/1:146:29:19,10:52,65:117,29:0.1986:2,2:17.7:1:29.6:1:0.06084:2.36:33.6:28:0.1944:0:2.7 +6 31324089 . G A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-04;SOR=Inf;LSEQ=TGAGCCGCCGTGTCCGCGGC;RSEQ=GTCCAGGAGCGCAGGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:98,102:200,0:0:2,0:23.1:1:30.3:1:1:0:36.9:65.667:1:0:0.9 0/1:146:8:3,5:67,71:138,8:0.0548:2,2:22:1:30.8:1:0.72075:1.56799:33.4:16:0.0559:0:1.6 +6 31324100 . G T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=4.05869;LSEQ=GTCCGCGGCGGTCCAGGAGC;RSEQ=CAGGTCCTCGTTCAGGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:11:4,7:74,81:155,11:0.0663:2,2:15.7:1:30.8:1:0.54344:1.59435:34:22:0.0667:0:2.9 0/1:156:35:23,12:59,62:121,35:0.2244:2,2:17.7:1:29.9:1:0.08644:2.01:31.7:70:0.2244:0:2.7 +6 31324104 . G A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19413;LSEQ=GCGGCGGTCCAGGAGCGCAG;RSEQ=TCCTCGTTCAGGGCGATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:75:32,43:40,43:83,75:0.4747:2,2:19:1:30.9:1:0.52469:1.24822:32.2:36.5:0.474:0:1.1 0/1:175:26:15,11:80,69:149,26:0.1486:2,2:19.2:1:28.9:1:0.83177:1.18:28.5:52:0.1494:0:1.1 +6 31324109 . C A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50634;SOR=Inf;LSEQ=GGTCCAGGAGCGCAGGTCCT;RSEQ=GTTCAGGGCGATGTAATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:65,82:147,0:0:2,0:15.2:1:30.4:1:1:0:33.6:48:1:0:0.9 0/1:189:2:1,1:104,82:186,2:0.0106:2,2:8:0:28:1:1:1.26667:25:4:0.0108:0:2 +6 31324110 . G A 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00626;SOR=Inf;LSEQ=GTCCAGGAGCGCAGGTCCTC;RSEQ=TTCAGGGCGATGTAATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:64,75:139,0:0:2,0:15.6:1:30.2:1:1:0:32.9:22.167:1:0:0.9 0/1:196:10:3,7:108,78:186,10:0.051:2,2:13.2:1:29.5:1:0.10508:3.21171:28.7:20:0.0513:0:2.1 +6 31324128 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03455;SOR=Inf;LSEQ=TCGTTCAGGGCGATGTAATC;RSEQ=TTGCCGTCGTAGGCGTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:46,59:105,0:0:2,0:18.1:1:32.1:1:1:0:39.8:51.5:1:0:0.6 0/1:232:10:5,5:115,107:222,10:0.0431:2,2:22.6:1:29.7:1:1:1.07441:41.1:20:0.0437:0:3.4 +6 31324143 . GT TA 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00058;SOR=0;LSEQ=TAATCCTTGCCGTCGTAGGC;RSEQ=ACTGGTCATGCCCGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:6:3,3:53,53:106,6:0.0531:2,2:14:1:30.4:1:1:1:39.8:12:0.0536:0:4.7 0/0:272:0:0,0:142,130:272,0:0:2,0:26.4:1:30:1:1:0:38.6:135:1:0:2.2 +6 31324144 . T G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99154;LSEQ=AATCCTTGCCGTCGTAGGCG;RSEQ=ACTGGTCATGCCCGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:16:9,7:44,45:89,16:0.1429:2,2:19.6:1:30.7:1:0.78697:1.31:26.1:15:0.1429:0:2.6 0/1:275:39:20,19:117,108:225,39:0.1418:2,2:24.8:1:29.6:1:1:1.02906:24:18.5:0.1355:0:2.4 +6 31324145 . A C 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCCTTGCCGTCGTAGGCGT;RSEQ=CTGGTCATGCCCGCGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:56,57:113,0:0:2,0:25.5:1:29.6:1:1:0:45.4:112:1:0:0.8 0/1:280:82:43,39:101,95:196,82:0.2929:2,2:23.8:1:30.2:1:0.89619:1.04:28.6:164:0.295:0:4 +6 31324151 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=8.22475;LSEQ=GCCGTCGTAGGCGTACTGGT;RSEQ=ATGCCCGCGGAGGAGGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:8:4,4:56,59:115,8:0.065:2,2:17:1:30.5:1:1:1.05:38.4:16:0.0667:0:4.3 0/1:307:112:59,53:95,98:193,112:0.3648:2,2:28.9:1:28.9:1:0.63479:1.15:44.6:111:0.3639:0:2 +6 31324154 . G A 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCGTAGGCGTACTGGTCAT;RSEQ=CCCGCGGAGGAGGCGCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:64,67:131,0:0:2,0:26.7:1:32.3:1:1:0:45.5:42.667:1:0:0.9 0/1:315:83:39,44:118,114:232,83:0.2635:2,2:30.2:1:27.8:1:0.60929:1.16721:29.3:82:0.2654:0:4.2 +6 31324169 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08187;SOR=0;LSEQ=GTCATGCCCGCGGAGGAGGC;RSEQ=CCCGTCCGGCCCCACGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:73,75:148,2:0.0133:2,2:39.5:1:31.5:1:1:1.03:60:4:0.0135:0:1 0/0:373:0:0,0:181,192:373,0:0:2,0:28.5:1:30.1:1:1:0:42.3:92.25:1:0:2.2 +6 31324177 . G A 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20776;SOR=0.20664;LSEQ=CGCGGAGGAGGCGCCCGTCC;RSEQ=GCCCCACGTCGCAGCCGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:76,83:159,2:0.0124:2,2:18.5:1:32:0:1:1.09:47:4:0.0125:0:1.5 0/0:387:1:1,0:186,200:386,1:0.0026:2,0:1:0:22:0:0.4832:0:33:2:0.0026:0:1 +6 31324184 . C G 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00243;SOR=0.19482;LSEQ=GAGGCGCCCGTCCGGCCCCA;RSEQ=GTCGCAGCCGTACATGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:10:5,5:71,82:153,10:0.0613:2,2:16.2:1:33.6:1:1:1.15:37.5:20:0.0625:0:3.8 0/1:399:5:3,2:185,209:394,5:0.0125:2,2:12.2:1:31.2:1:0.66985:1.69:39.2:10:0.0127:0:5 +6 31324194 . G A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.01427;LSEQ=TCCGGCCCCACGTCGCAGCC;RSEQ=TACATGCTCTGGAGGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:10:5,5:68,73:141,10:0.0658:2,2:6.2:1:31.6:1:1:1.07:37.5:20:0.0671:0:3.8 0/1:390:26:14,12:165,199:364,26:0.0667:2,2:12.2:1:28.6:1:0.42194:1.41:38.6:25:0.0646:0:4.7 +6 31324200 . G C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.44634;LSEQ=CCCACGTCGCAGCCGTACAT;RSEQ=CTCTGGAGGGTGTGAGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:32:15,17:48,56:104,32:0.2336:2,2:30.1:1:31.8:1:1:1.03:30.9:15:0.2256:0:2.9 1/0:349:179:80,99:70,92:162,179:0.5129:2,2:25.2:1:30.4:1:0.82735:1.06:32.4:178:0.5174:0:3.6 +6 31324206 . GAGG CCAA 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18797;SOR=Inf;LSEQ=TCGCAGCCGTACATGCTCTG;RSEQ=GTGTGAGACCCTGGCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:60,68:128,0:0:2,0:26.4:1:31.8:1:1:0:48.1:127:1:0:0.9 0/1:314:6:3,3:129,178:307,6:0.0191:2,2:13:1:29.6:1:0.69951:1.38:45.2:12:0.0192:0:3.7 +6 31324208 . G T 190 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=23.91629;LSEQ=GCAGCCGTACATGCTCTGGA;RSEQ=GGTGTGAGACCCTGGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:0,2:60,65:125,2:0.0157:2,0:5:1:27:1:0.49756:0:21.5:4:0.0163:0:3 0/1:299:83:31,52:89,120:209,83:0.2776:2,2:26.3:1:29.9:1:0.43181:1.24316:35.7:166:0.2842:0:4.7 +6 31324210 . G A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=17.45333;LSEQ=AGCCGTACATGCTCTGGAGG;RSEQ=TGTGAGACCCTGGCCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:3:0,3:60,75:135,3:0.0217:2,0:5.3:1:29.3:1:0.25738:0:21.7:6:0.0221:0:2.7 0/1:289:81:30,51:88,120:208,81:0.2803:2,2:25.5:1:29.8:1:0.42761:1.24572:35.5:80:0.2778:0:4.7 +6 31324227 . C A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02696;SOR=0.46599;LSEQ=AGGGTGTGAGACCCTGGCCC;RSEQ=GGCCCCGCGGTCAGCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:23:10,13:34,78:112,23:0.1704:2,2:19.3:1:31.4:1:0.23134:1.76:32.4:46:0.1769:0:3 0/1:218:19:7,12:75,124:199,19:0.0872:2,2:22.7:1:29.9:1:1:1.0367:29.5:38:0.088:0:3.1 +6 31324245 . A C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.72571;LSEQ=CCCGGCCCCGCGGTCAGCCC;RSEQ=GTCCCCCGAGCCCCGCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:125:68:9,59:17,39:56,68:0.544:2,2:23.5:1:28.1:1:0.02642:2.83277:26.6:33:0.55:0:1.7 1/1:164:134:38,96:13,17:30,134:0.8171:2,2:18.4:1:29.2:1:0.1284:1.92359:38.4:133:0.821:0:2.4 +6 31324247 . T TC 175 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGCCCCGCGGTCAGCCCAG;RSEQ=CCCCCGAGCCCCGCCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:26,100:126,0:0:2,0:22.5:1:27.9:1:1:0:33:14.75:1:0:1 0/1:154:55:16,39:32,65:97,55:0.3571:2,2:21.9:1:30.4:1:0.71732:1.19857:38.8:54:0.3649:0.0325:1.4 +6 31324254 . A AGCCCC 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=16;MSI=4.000;MSILEN=1;SSF=0.49979;SOR=Inf;LSEQ=GCGGTCAGCCCAGTCCCCCG;RSEQ=GCCCCGCCCCGCCCCGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:22,95:117,0:0:2,0:27:1:29.9:1:1:0:31.7:12:0.9908:0:0.9 0/1:133:2:0,2:35,95:130,2:0.015:2,0:32.5:1:25.1:1:1:0:25:4:0.0159:0:2 +6 31324269 . C T 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.00348;SOR=Inf;LSEQ=CCCCGAGCCCCGCCCCGCCC;RSEQ=GACCAACCCGCGGGGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:19,103:122,0:0:2,0:30.3:1:29.5:1:1:0:32.7:29.5:1:0:0.8 0/1:101:7:0,7:22,71:93,7:0.0693:2,0:34.3:1:29.4:1:0.34235:0:37.6:6:0.0606:0:2.1 +6 31324271 . A C 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03785;SOR=Inf;LSEQ=CCGAGCCCCGCCCCGCCCCG;RSEQ=CCAACCCGCGGGGATTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:19,102:121,0:0:2,0:30.6:1:29.3:1:1:0:32.7:29.25:1:0:0.8 0/1:97:4:1,3:19,74:93,4:0.0412:2,2:15:1:27.8:1:1:1.29:45.5:8:0.043:0:1.3 +6 31324290 . G T 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52407;SOR=0;LSEQ=GACCAACCCGCGGGGATTTT;RSEQ=GCCTCAACTGAAAATGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:22,99:121,2:0.0163:2,2:6:0:33:1:0.34026:4.42:60:4:0.0165:0:1.5 0/0:77:0:0,0:13,64:77,0:0:2,0:29.1:1:30.3:1:1:0:39.3:24.667:1:0:1 +6 31324348 . C T 55 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15606;SOR=2.87021;LSEQ=GGCTCTCGCCGGTCGAGGGT;RSEQ=TGGGCGGGTCCCGCGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:2,1:74,30:104,3:0.028:2,2:18.3:1:32.3:1:1:1.23078:52.7:6:0.0288:0:1.3 0/1:65:5:2,3:32,28:60,5:0.0769:2,2:26.2:1:24:1:0.66312:1.70016:60:4:0.0635:0:1.6 +6 31324369 . AGGGA GGG 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGCGGGTCCCGCGGCCTC;RSEQ=GGCGGATCTCGGACCCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:110,19:129,0:0:2,0:25:1:30.6:1:1:0:59.7:24.8:0.992:0:0.2 0/1:67:14:8,6:39,12:51,14:0.209:2,2:24.1:1:29.7:1:0.18471:2.40038:59:28:0.209:0.0448:0.4 +6 31324373 . A G 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=10.36987;LSEQ=CGGGTCCCGCGGCCTCAGGG;RSEQ=GGCGGATCTCGGACCCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:3,0:116,16:132,3:0.0222:2,0:26:1:32.7:1:1:0:58.7:6:0.0233:0:2 0/1:57:11:7,4:38,8:46,11:0.193:2,2:17.3:1:29.1:1:0.21852:2.65847:60:10:0.1786:0:1.5 +6 31324415 . A C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=23.0717;LSEQ=CTCGGGGCGACCCGGGCCGT;RSEQ=CGTGGGGGATGGGGAGTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:7:7,0:211,41:252,7:0.027:2,0:33.3:1:29.3:1:0.60107:0:49.1:6:0.0235:0:1.9 0/1:94:37:31,6:51,6:57,37:0.3936:2,2:25.6:1:30.5:1:0.53014:1.63611:47.1:74:0.3978:0:1.1 +6 31324448 . G A 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06463;SOR=2.22036;LSEQ=GGAGTCGTGACCTGCGCCCC;RSEQ=GGCCGGGGTCACTCACCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:12:8,4:291,102:393,12:0.0296:2,2:20.8:1:30.7:1:0.52116:1.42512:37.6:24:0.0306:0:1.8 0/1:173:11:7,4:108,53:161,11:0.0636:2,2:21.8:1:29.4:1:1:1.16336:37.5:22:0.0655:0:1.8 +6 31324506 . CT TC 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=AGCCGCGCAGGTTCCGCAGG;RSEQ=CTCTCGGTCAGTCTGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:861:0:0,0:482,378:860,0:0:2,0:25.6:1:32.6:1:1:0:52:85:0.9988:0:1.5 0/1:390:11:8,3:205,172:377,11:0.0282:2,2:11.1:1:30.7:1:0.35782:2.23:28.3:22:0.0284:0:5.7 +6 31324516 . C A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.44176;LSEQ=GTTCCGCAGGCTCTCTCGGT;RSEQ=AGTCTGTGCCTGGGCCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:913:265:154,111:348,299:647,265:0.2903:2,2:24.9:1:29.5:1:0.24152:1.19:38.9:36.857:0.2905:0:5 0/1:425:65:33,32:190,170:360,65:0.1529:2,2:22.3:1:28.8:1:0.78851:1.08357:35.2:130:0.1563:0:4.6 +6 31324525 . CC TG 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=1.82131;LSEQ=GCTCTCTCGGTCAGTCTGTG;RSEQ=TGGGCCTTGTAGATCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:844:180:109,71:348,308:656,180:0.2133:2,2:34.4:1:31.6:1:0.07641:1.36:41.9:360:0.2158:0:5.7 0/1:372:123:65,58:129,118:247,123:0.3306:2,2:31.3:1:30.2:1:1:1.03:42.5:246:0.3361:0:4.8 +6 31324526 . C G 47 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07682;SOR=4.51664;LSEQ=CTCTCTCGGTCAGTCTGTGC;RSEQ=TGGGCCTTGTAGATCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:841:2:0,2:345,311:656,2:0.0024:2,0:29:1:31:0:0.2259:0:30.5:4:0.0031:0:7.5 0/1:375:4:4,0:127,121:248,4:0.0107:2,0:35.3:1:23.5:1:0.1232:0:44.3:3:0.0121:0:5.5 +6 31324528 . G T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.46815;LSEQ=CTCTCGGTCAGTCTGTGCCT;RSEQ=GGCCTTGTAGATCTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:849:182:109,73:346,321:667,182:0.2144:2,2:34.4:1:30.9:1:0.06491:1.38:41.7:59.667:0.2146:0:5.7 0/1:380:153:83,70:114,113:227,153:0.4026:2,2:30.2:1:29.5:1:0.46481:1.17:40.1:37.25:0.3984:0:4.8 +6 31324531 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=1.84339;LSEQ=TCGGTCAGTCTGTGCCTGGG;RSEQ=CTTGTAGATCTGTGTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:861:195:117,78:341,322:663,195:0.2265:2,2:32.3:1:29.9:1:0.04107:1.42:41.7:47.75:0.2255:0:5.6 0/1:385:135:74,61:128,122:250,135:0.3506:2,2:30.1:1:28.2:1:0.52228:1.16:41.7:32.75:0.3447:0:4.7 +6 31324536 . T A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33867;SOR=0.88204;LSEQ=CAGTCTGTGCCTGGGCCTTG;RSEQ=AGATCTGTGTGTTCCGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:280:153,127:358,327:685,280:0.2875:2,2:22.4:1:30.5:1:0.52287:1.10:38.1:92.333:0.2876:0:5.2 0/1:442:116:66,50:115,111:226,116:0.2624:2,2:23.9:1:29.1:1:0.30514:1.27:44.8:115:0.2632:0:3.6 +6 31324547 . G C 151 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=8.70283;LSEQ=TGGGCCTTGTAGATCTGTGT;RSEQ=TTCCGGTCCCAATACTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1015:9:6,3:527,475:1002,9:0.0089:2,2:23.9:1:31.8:1:0.51171:1.80:26.9:18:0.009:0:7 0/1:470:34:18,16:227,208:435,34:0.0723:2,2:34.6:1:29.8:1:1:1.03:29.3:16:0.0688:0:5 +6 31324549 . T C 152 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=9.96111;LSEQ=GGCCTTGTAGATCTGTGTGT;RSEQ=CCGGTCCCAATACTCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1006:9:6,3:521,476:997,9:0.0089:2,2:21.9:1:31.1:1:0.51036:1.83:26.9:18:0.0091:0:7 0/1:472:39:20,19:227,206:433,39:0.0826:2,2:30.7:1:28.9:1:1:1.04676:29.5:12:0.0774:0:5 +6 31324562 . C T 162 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=94.89484;LSEQ=TGTGTGTTCCGGTCCCAATA;RSEQ=TCCGGCCCCTCCTGCTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:968:1:0,1:492,475:967,1:0.001:2,0:1:0:26:0:0.49174:0:36:2:0.001:0:7 0/1:502:45:19,26:231,226:457,45:0.0896:2,2:25.2:1:29.6:1:0.34884:1.39776:33.2:90:0.0902:0:2.9 +6 31324574 . C T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCCCAATACTCCGGCCCCTC;RSEQ=TGCTCTATCCACGGCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:895:0:0,0:442,453:895,0:0:2,0:25:1:32.3:1:1:0:48.3:178:1:0:1.9 0/1:490:16:7,9:225,248:473,16:0.0327:2,2:26.2:1:28.9:1:0.80459:1.16611:36.9:15:0.0309:0:5.8 +6 31324586 . C T 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30904;LSEQ=GGCCCCTCCTGCTCTATCCA;RSEQ=GGCGCCCGCGGCTCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:775:268:131,137:247,259:506,268:0.3458:2,2:26.6:1:30.5:1:1:1.00:33.8:43.667:0.3434:0:5.4 0/1:449:63:29,34:179,204:383,63:0.1403:2,2:26.4:1:30.1:1:1:1.02868:31.8:126:0.1419:0:5.1 +6 31324595 . C G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.40074;LSEQ=TGCTCTATCCACGGCGCCCG;RSEQ=GGCTCCTCTCTCGGACTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:665:234:113,121:207,223:430,234:0.3519:2,2:27.1:1:30.9:1:1:1.01:31.3:32.429:0.3503:0:5.4 0/1:392:70:32,38:151,170:321,70:0.1786:2,2:28.6:1:30:1:0.89517:1.05466:31.5:34:0.1757:0:5.3 +6 31324599 . T G 78 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18701;SOR=2.55919;LSEQ=CTATCCACGGCGCCCGCGGC;RSEQ=CCTCTCTCGGACTCGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:641:4:1,3:310,325:635,4:0.0062:2,2:44:1:26.5:1:0.62436:2.85752:27.3:3:0.0048:0:5.5 0/1:379:6:3,3:172,200:372,6:0.0158:2,2:44.8:1:30.2:1:1:1.16:32.2:12:0.0163:0:6.2 +6 31324602 . TCT GTC 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0;SOR=0.31248;LSEQ=TCCACGGCGCCCGCGGCTCC;RSEQ=CTCGGACTCGCGGCGTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:667:252:122,130:197,205:402,252:0.3778:2,2:23.2:1:30.6:1:0.93596:1.02396:29.6:251:0.3856:0.1154:3.3 0/1:364:58:26,32:136,162:298,58:0.1593:2,2:29.8:1:30:1:1:1.03315:31.3:116:0.1629:0.0192:3.5 +6 31324603 . CT TC 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.20647;SOR=3.31938;LSEQ=CCACGGCGCCCGCGGCTCCT;RSEQ=CTCGGACTCGCGGCGTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:2:1,1:195,204:399,2:0.0034:2,2:28.5:1:29.5:1:1:1.05:43.5:4:0.005:0:4 0/1:353:4:3,1:134,157:291,4:0.0113:2,2:31.8:1:27.8:1:0.34049:3.50:23:8:0.0137:0:4.3 +6 31324641 . T A 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CGCTGTCGAACCTCACGAAC;RSEQ=GGGTGTCGTCCACGTAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:180,209:389,0:0:2,0:22.9:1:30.9:1:1:0:38.6:47.625:1:0:1.6 0/1:247:12:6,6:111,124:235,12:0.0486:2,2:20.3:1:30.7:1:1:1.12:33.7:24:0.0498:0:2.4 +6 31324643 . G C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02843;SOR=1.57407;LSEQ=CTGTCGAACCTCACGAACTG;RSEQ=GTGTCGTCCACGTAGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:62:30,32:148,169:317,62:0.1636:2,2:15.9:1:30.3:1:0.8895:1.07:30:30:0.1609:0:1.3 0/1:242:57:25,32:90,95:185,57:0.2355:2,2:16.2:1:30.8:1:0.54759:1.21166:28.2:114:0.2385:0:1.5 +6 31324647 . T C 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.00139;SOR=Inf;LSEQ=CGAACCTCACGAACTGGGTG;RSEQ=CGTCCACGTAGCCCACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:162,195:357,0:0:2,0:24.2:1:29.8:1:1:0:38.8:43.625:1:0:1.5 0/1:232:7:4,3:105,120:225,7:0.0302:2,2:19.6:1:31.3:1:0.70906:1.52:28.4:14:0.0306:0:2.9 +6 31324664 . T G 39 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15258;SOR=5.01138;LSEQ=GTGTCGTCCACGTAGCCCAC;RSEQ=GAGATGAAGCGGGGCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:1:1,0:134,161:295,1:0.0034:2,0:44:0:29:0:0.45608:0:22:2:0.0034:0:5 0/1:179:3:1,2:80,96:176,3:0.0168:2,2:21.7:1:25:1:1:1.66211:29.7:2:0.0115:0:2.7 +6 31324666 . A C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.22072;LSEQ=GTCGTCCACGTAGCCCACTG;RSEQ=GATGAAGCGGGGCTCCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:290:150:75,75:51,86:137,150:0.5172:2,2:27.4:1:31.2:1:0.03251:1.68:25.4:49:0.5213:0:2.5 0/1:173:33:19,14:55,79:134,33:0.1908:2,2:31.5:1:30.5:1:0.1171:1.94:27:32:0.1905:0:2.7 +6 31324702 . C T 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26394;LSEQ=CCCGCGGCCGGGCCGGGACA;RSEQ=GGAGGTGTAGAAATACCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:58:38,20:63,75:138,58:0.2944:2,2:21.2:1:30:1:0.01251:2.25:26.4:57:0.2938:0:3 0/1:182:18:11,7:74,89:163,18:0.0989:2,2:21.1:1:28.9:1:0.22355:1.88:27.7:36:0.1:0:3.1 +6 31324705 . A C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.26745;LSEQ=GCGGCCGGGCCGGGACACGG;RSEQ=GGTGTAGAAATACCTCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:51:34,17:65,80:145,51:0.2602:2,2:19.3:1:30.5:1:0.00905:2.45:26.2:102:0.2615:0:3.1 0/1:175:15:8,7:72,88:160,15:0.0857:2,2:21.9:1:29.2:1:0.59469:1.39:28.7:14:0.0819:0:3.2 +6 31324711 . A G 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00207;SOR=Inf;LSEQ=GGGCCGGGACACGGAGGTGT;RSEQ=GAAATACCTCATGGAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:109,92:201,0:0:2,0:23.1:1:29.6:1:1:0:48.1:49.25:1:0:0.9 0/1:176:8:3,5:77,91:168,8:0.0455:2,2:22.4:1:31.3:1:0.7296:1.40756:24.9:16:0.046:0:1.6 +6 31324732 . A C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21599;SOR=Inf;LSEQ=GAAATACCTCATGGAGTGGG;RSEQ=GCCTGGGGGTGAGGAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:89,97:186,0:0:2,0:21.7:1:30.6:1:1:0:50.1:25.571:1:0:0.4 0/1:162:2:1,1:69,91:160,2:0.0123:2,2:40:1:30:1:1:1.32:43:4:0.0126:0:1 +6 31324741 . GTG CA 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.19739;SOR=Inf;LSEQ=CATGGAGTGGGAGCCTGGGG;RSEQ=AGGAGGGGCTGAGACCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:90,101:191,0:0:2,0:21.6:1:31.6:1:1:0:50.7:190:1:0:0.5 0/1:154:2:1,1:63,89:152,2:0.013:2,2:31:1:27.6:1:1:1.41:23.5:4:0.0131:0.0065:1.5 +6 31324742 . T C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54474;SOR=0.85972;LSEQ=ATGGAGTGGGAGCCTGGGGG;RSEQ=GAGGAGGGGCTGAGACCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:59:28,31:59,71:130,59:0.3122:2,2:18.5:1:30.2:1:0.87509:1.09:35.9:28.5:0.3081:0:1.5 0/1:139:39:15,24:41,58:99,39:0.2806:2,2:24.1:1:30.1:1:0.84804:1.13003:33.5:78:0.2868:0:2.1 +6 31324749 . G T 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=GGGAGCCTGGGGGTGAGGAG;RSEQ=GGCTGAGACCCGCCCGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:92,113:205,0:0:2,0:22.7:1:30.9:1:1:0:50.6:50.25:1:0:0.9 0/1:148:11:3,8:59,77:136,11:0.0743:2,2:32.6:1:30.1:1:0.35734:2.03403:25.7:22:0.0759:0:2.9 +6 31324756 . G A 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=9e-05;SOR=Inf;LSEQ=TGGGGGTGAGGAGGGGCTGA;RSEQ=ACCCGCCCGACCCTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:102,124:226,0:0:2,0:22.8:1:32.1:1:1:0:51.1:55.5:1:0:1.1 0/1:151:10:5,5:60,81:141,10:0.0662:2,2:30:1:30.6:1:0.74586:1.35:37.8:20:0.0671:0:1.9 +6 31324764 . C A 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.07624;SOR=0.48627;LSEQ=AGGAGGGGCTGAGACCCGCC;RSEQ=GACCCTCCTCCCGGCGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:28:12,16:99,119:218,28:0.1134:2,2:11.1:1:31:1:0.84254:1.10876:44.5:56:0.1152:0:5.1 0/1:154:9:5,4:69,76:145,9:0.0584:2,2:12.3:1:29.7:1:0.73855:1.37:38.3:18:0.0592:0:5.1 +6 31324776 . C A 95 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00087;SOR=15.72251;LSEQ=GACCCGCCCGACCCTCCTCC;RSEQ=GGCGCGGCTCCTCAGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:1:1,0:118,141:259,1:0.0038:2,0:14:0:32:0:0.45769:0:60:2:0.0039:0:6 0/1:157:9:2,7:76,72:148,9:0.0573:2,2:7.4:1:30.1:1:0.16703:3.66674:24:18:0.0584:0:3 +6 31324788 . T C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00752;SOR=1.85969;LSEQ=CCTCCTCCCGGCGCGGCTCC;RSEQ=CAGGTCCTGCGCCCCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:60:31,29:112,132:244,60:0.1974:2,2:24.7:1:31:1:0.47144:1.26:49.7:59:0.2:0:4.7 0/1:156:49:29,20:56,51:107,49:0.3141:2,2:28.5:1:30.7:1:0.48985:1.32:38.3:48:0.3179:0:5 +6 31324790 . A G 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00569;SOR=1.87956;LSEQ=TCCTCCCGGCGCGGCTCCTC;RSEQ=GGTCCTGCGCCCCCGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:61:32,29:113,135:248,61:0.1974:2,2:26.3:1:30.1:1:0.39062:1.32:49.9:60:0.1987:0:4.7 0/1:158:50:31,19:57,50:107,50:0.3165:2,2:28.9:1:30.2:1:0.38838:1.43:39.4:100:0.3205:0:5 +6 31324819 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0214;SOR=Inf;LSEQ=GCCCCCGCCTGCGGTCCCCT;RSEQ=GCTCCTCCCGGCAGAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:167,168:335,0:0:2,0:28.3:1:31.1:1:1:0:51.2:46.857:1:0:2.1 0/1:209:4:2,2:119,85:204,4:0.0191:2,2:25:1:28.8:1:1:1.39767:40.3:8:0.0193:0:6.5 +6 31324820 . G T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCCGCCTGCGGTCCCCTC;RSEQ=CTCCTCCCGGCAGAGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:166,164:330,0:0:2,0:28.7:1:30.9:1:1:0:51.6:32:1:0:2.1 0/1:207:18:10,8:112,77:189,18:0.087:2,2:33.7:1:29.9:1:0.80509:1.16277:33.7:17:0.0829:0:4.9 +6 31324829 . GG CA 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23865;LSEQ=GCGGTCCCCTCGCTCCTCCC;RSEQ=CAGAGGCCATTTCCCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:316:230:112,118:45,35:80,230:0.7278:2,2:30.9:1:31.2:1:0.29904:1.35325:49.9:229:0.7435:0.038:1.9 0/1:216:84:49,35:73,50:123,84:0.3889:2,2:28.7:1:30.3:1:0.88672:1.04268:38.9:168:0.4:0.0046:3.2 +6 31324830 . G A 55 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.74153;SOR=0.69906;LSEQ=CGGTCCCCTCGCTCCTCCCG;RSEQ=CAGAGGCCATTTCCCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:6:3,3:45,36:81,6:0.0197:2,2:29.8:1:21.5:1:1:1.24677:41.5:1:0.0366:0:3.8 0/1:217:3:1,2:75,51:126,3:0.0138:2,2:30:1:24.7:1:0.56782:2.91649:42.3:2:0.0161:0:5.3 +6 31324847 . C G 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=6.23255;LSEQ=CCGGCAGAGGCCATTTCCCT;RSEQ=CCGACCCGCACTCACCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:9:5,4:154,126:280,9:0.0311:2,2:28.8:1:27.7:1:1:1.02:38.4:3.5:0.0254:0:4 0/1:251:42:26,16:115,93:208,42:0.1673:2,2:25.4:1:31:1:0.49664:1.31:37.3:84:0.1694:0:3.9 +6 31324851 . A AC 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=0.3931;LSEQ=CAGAGGCCATTTCCCTCCCG;RSEQ=CCCGCACTCACCGGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:106:52,54:105,72:177,106:0.3593:2,2:22.8:1:30.9:1:0.1084:1.51214:46.1:52:0.3688:0.078:2.7 0/1:255:46:32,14:108,88:196,46:0.1804:2,2:25.3:1:30.3:1:0.09662:1.86:35.5:45:0.1786:0.0353:4.3 +6 31324864 . G A 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCCCGACCCGCACTCACC;RSEQ=GCCCAGGTCTCGGTCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:178,150:328,0:0:2,0:18.1:1:29.9:1:1:0:48.8:45.857:1:0:2.5 0/1:302:18:12,6:150,133:283,18:0.0596:2,2:18.8:1:28.1:1:0.33223:1.77:38.3:17:0.0584:0:3.7 +6 31324887 . GG CT 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.39236;LSEQ=CCAGGTCTCGGTCAGGGCCA;RSEQ=GCCGCCGAGAGCAGCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:143:68,75:124,103:227,143:0.3844:2,2:22.7:1:31.9:1:0.20062:1.32677:43:286:0.3886:0:6 0/1:412:81:39,42:169,159:328,81:0.1966:2,2:18.1:1:30.8:1:0.62079:1.14427:35.5:162:0.198:0.0097:6.6 +6 31324891 . CG TC 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1082;SOR=1.75988;LSEQ=GTCTCGGTCAGGGCCAGGGC;RSEQ=CCGAGAGCAGCAGGAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:14:6,8:192,175:367,14:0.0366:2,2:24.9:1:31.9:1:0.58968:1.46139:34.1:28:0.0369:0.0052:3.9 0/1:430:27:12,15:207,196:403,27:0.0628:2,2:23.3:1:28.8:1:0.55341:1.3193:33.2:54:0.064:0.007:4.2 +6 31324892 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.2295;LSEQ=TCTCGGTCAGGGCCAGGGCC;RSEQ=CCGAGAGCAGCAGGAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:205:103,102:86,72:158,205:0.5423:2,2:21.6:1:30.7:1:0.45905:1.1823:40:40:0.5602:0:6 0/1:431:92:48,44:161,153:314,92:0.2135:2,2:20:1:30.1:1:0.906:1.04:35.9:29.667:0.2225:0:6.4 +6 31324895 . G C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.23894;LSEQ=CGGTCAGGGCCAGGGCCGCC;RSEQ=AGAGCAGCAGGAGGACGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:399:221:114,107:95,81:176,221:0.5539:2,2:22.9:1:31.5:1:0.68592:1.10056:40.5:54.25:0.5522:0:5.9 0/1:464:106:50,56:185,173:358,106:0.2284:2,2:20.1:1:30.7:1:0.44005:1.19722:36.6:52:0.2266:0:6.3 +6 31324911 . C G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06035;SOR=1.29362;LSEQ=CGCCGAGAGCAGCAGGAGGA;RSEQ=GGTTCGGGGCGCCATGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:125:59,66:222,239:461,125:0.2133:2,2:23.4:1:32.3:1:0.91965:1.03902:34.1:250:0.2166:0:6.2 0/1:643:167:79,88:234,242:476,167:0.2597:2,2:21.1:1:30.5:1:0.7192:1.07696:35.1:54.667:0.2571:0:5.4 +6 31324921 . C T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34309;LSEQ=AGCAGGAGGACGGTTCGGGG;RSEQ=GCCATGACCAGCATCTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:71:27,44:259,293:552,71:0.114:2,2:29.7:1:30:1:0.16604:1.43969:36.7:70:0.1142:0:6.5 0/1:663:28:16,12:301,333:634,28:0.0422:2,2:27.7:1:29.3:1:0.33953:1.47:53:56:0.0431:0:4.4 +6 31324925 . A G 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3842;LSEQ=GGAGGACGGTTCGGGGCGCC;RSEQ=TGACCAGCATCTCGGCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:641:453:192,261:93,94:187,453:0.7067:2,2:29.7:1:31.3:1:0.09685:1.34426:47.4:74.5:0.7062:0:5.2 0/1:668:321:148,173:168,179:347,321:0.4805:2,2:29.6:1:30.2:1:0.58735:1.09693:42.9:44.857:0.4765:0:5.1 +6 31324931 . A C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35478;LSEQ=CGGTTCGGGGCGCCATGACC;RSEQ=GCATCTCGGCGTCTGAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:671:488:196,292:90,93:183,488:0.7273:2,2:29.6:1:30.3:1:0.04365:1.4409:48.3:53.222:0.728:0:5.1 0/1:677:329:152,177:164,180:344,329:0.486:2,2:30.8:1:29.6:1:0.75733:1.06085:43.2:46:0.4871:0:5 +6 31324938 . C T 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCGCCATGACCAGCATCT;RSEQ=GGCGTCTGAGGAGACTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:676:0:0,0:277,399:676,0:0:2,0:29.1:1:30.7:1:1:0:51.3:111.667:1:0:3.8 0/1:673:60:26,34:281,331:612,60:0.0892:2,2:25.3:1:30.6:1:0.78629:1.10997:59.8:120:0.09:0:1.4 +6 31324941 . C T 196 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01918;LSEQ=CGCCATGACCAGCATCTCGG;RSEQ=GTCTGAGGAGACTCTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:678:92:29,63:244,340:584,92:0.1357:2,2:32.4:1:30.1:1:0.06776:1.55803:42.2:184:0.1375:0:5.9 0/0:668:2:0,2:304,362:666,2:0.003:2,0:25.5:1:30.5:1:0.50329:0:48.5:4:0.003:0:1 +6 31324953 . C T 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01952;SOR=0.76457;LSEQ=CATCTCGGCGTCTGAGGAGA;RSEQ=TCTGAGTCCGGGTGGGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:644:402:156,246:88,153:241,402:0.6242:2,2:27.4:1:30.3:1:0.61458:1.10:51.1:66:0.6256:0:4.9 1/0:631:353:148,205:124,154:278,353:0.5594:2,2:27.6:1:29.7:1:0.51782:1.11511:42.4:352:0.5623:0:5.1 +6 31324955 . C T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02782;SOR=2.07638;LSEQ=TCTCGGCGTCTGAGGAGACT;RSEQ=TGAGTCCGGGTGGGTGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:630:14:4,10:235,380:615,14:0.0222:2,2:28.9:1:31.3:1:0.58353:1.54505:41.7:28:0.0225:0:5.5 0/1:621:28:10,18:259,333:592,28:0.0451:2,2:28.7:1:29.7:1:0.44111:1.39926:42.1:56:0.0455:0:4.7 +6 31324996 . G C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00276;LSEQ=GGGACTTTAGAACTGGGACC;RSEQ=CGGCGACGCTGATTGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:326:251:48,203:17,56:73,251:0.7699:2,2:22.2:1:31.2:1:0.50649:1.28284:52.4:34.857:0.7673:0:4.9 1/0:257:198:61,137:14,38:52,198:0.7704:2,2:22.6:1:29.6:1:0.734:1.21:49.9:27.286:0.764:0:4.4 +6 31325004 . G A 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31508;LSEQ=AGAACTGGGACCGCGGCGAC;RSEQ=CTGATTGGCTTCTCTAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:267:206:32,174:11,50:61,206:0.7715:2,2:21.8:1:30.4:1:0.69215:1.19538:52:205:0.7707:0:5 1/0:202:104:27,77:21,77:98,104:0.5149:2,2:22.4:1:29.5:1:0.50965:1.28:42.7:208:0.52:0:5.6 +6 31325023 . T C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=3.93398;LSEQ=CGCTGATTGGCTTCTCTAGA;RSEQ=ATCCAATACCCAATGGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:20:0,20:17,125:142,20:0.1235:2,1:19.6:1:32.5:1:0.13365:0:32.6:40:0.1266:0:6.9 0/1:109:39:7,32:6,63:69,39:0.3578:2,2:25.6:1:32.2:1:0.21803:2.28:26.5:78:0.3578:0:6.8 +6 31325025 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.67022;LSEQ=CTGATTGGCTTCTCTAGATA;RSEQ=CCAATACCCAATGGGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:15:0,15:16,119:135,15:0.1:2,1:24.9:1:29.6:1:0.37112:0:27.9:6.5:0.0884:0:7 0/1:102:35:5,30:6,61:67,35:0.3431:2,2:27.2:1:31.4:1:0.50479:1.69:23.8:70:0.3571:0:6.9 +6 31325028 . A G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02352;SOR=2.0848;LSEQ=ATTGGCTTCTCTAGATATCC;RSEQ=ATACCCAATGGGAGTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:134:90:10,80:3,41:44,90:0.6716:2,2:25.7:1:31.9:1:0.54462:1.70:45.4:44:0.6718:0:5.6 1/1:95:77:7,70:2,16:18,77:0.8105:2,2:25.4:1:30.7:1:0.67765:1.2469:41.4:24.667:0.8043:0:5.4 +6 31325030 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06249;SOR=1.86934;LSEQ=TGGCTTCTCTAGATATCCAA;RSEQ=ACCCAATGGGAGTGGGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:128:89:10,79:3,36:39,89:0.6953:2,2:25.2:1:32.2:1:0.75305:1.51:45:28.667:0.6935:0:5.6 1/1:95:77:6,71:2,16:18,77:0.8105:2,2:24.1:1:31.6:1:0.64388:1.47246:41.1:18.25:0.8022:0:5.5 +6 31325049 . G A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04965;SOR=0.51972;LSEQ=ATACCCAATGGGAGTGGGAA;RSEQ=TGGGGACGCGTCACGAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:111:77:7,70:3,29:32,77:0.6937:2,2:22.5:1:30.9:1:1:1.03414:43.8:37.5:0.6944:0:5.5 1/0:63:34:6,28:0,27:27,34:0.5397:1,2:16.2:1:29.2:1:0.02955:0:35.1:33:0.5323:0:6.2 +6 31325056 . C T 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATGGGAGTGGGAAGTGGGGA;RSEQ=GCGTCACGAGTATCCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:8,94:102,0:0:2,0:22.7:1:29.7:1:1:0:49.1:50:1:0:3.7 0/1:58:19:0,19:5,34:39,19:0.3276:2,1:19.7:1:28.8:1:0.16118:0:59.5:18:0.3158:0:3.6 +6 31325090 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42865;SOR=0.60032;LSEQ=CCTGGAAGAAGGACCCGACA;RSEQ=AAGTTGGGAGAAGAAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:46:3,43:0,13:13,46:0.7797:1,2:27:1:28.8:1:1:0:39.5:92:0.7797:0:5.7 1/0:28:19:2,17:0,9:9,19:0.6786:0,2:32.3:1:28:1:1:0:45.9:38:0.6786:0:5.1 +6 31325092 . A G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.78482;SOR=0.80952;LSEQ=TGGAAGAAGGACCCGACACA;RSEQ=GTTGGGAGAAGAAGTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:46:3,43:0,13:13,46:0.7797:1,2:26.4:1:32.1:1:1:0:39.5:92:0.7797:0:5.7 1/0:27:20:2,18:0,7:7,20:0.7407:0,2:32.1:1:30.8:1:1:0:46.7:40:0.7407:0:5.1 +6 31325115 . AG GT 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24449;SOR=0.49118;LSEQ=TGGGAGAAGAAGTGAAACTC;RSEQ=GGGAGTGGGGAATCCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:35:2,33:0,8:8,35:0.814:0,2:24.6:1:31.9:1:1:0:40.6:70:0.814:0.093:4.7 1/0:25:17:1,16:0,6:6,17:0.68:0,1:24.8:1:29.5:1:1:0:51.1:34:0.7083:0.04:3.9 +6 31325151 . T A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02556;SOR=0.16938;LSEQ=CCCAACGCTGCGCCTCCCCA;RSEQ=TGCAGACGCGGCCCTCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:18:1,17:0,4:4,18:0.8182:0,1:20.1:1:32:1:1:0:36.5:36:0.8182:0:4.8 0/1:12:5:0,5:0,7:7,5:0.4167:0,0:5.2:1:29.8:1:1:0:55.4:10:0.4167:0:4 +6 31325159 . GC AA 111 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00241;SOR=0;LSEQ=TGCGCCTCCCCATTGCAGAC;RSEQ=GGCCCTCGGAGCCTGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:1,5:6,11:0.6471:2,0:14.2:1:32.3:1:0.35294:0:32:22:0.6471:0.2353:5.4 0/0:9:0:0,0:0,8:8,0:0:0,0:25:1:31:1:1:0:52:16:0.8889:0:0.9 +6 31325164 . C T 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01796;SOR=0;LSEQ=CTCCCCATTGCAGACGCGGC;RSEQ=CTCGGAGCCTGAGACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:1,5:6,7:0.5385:2,0:13.9:1:31.3:1:0.46154:0:28.4:14:0.5385:0:5.4 0/0:8:0:0,0:0,8:8,0:0:0,0:24.1:1:29.8:1:1:0:52:16:1:0:0.9 +6 31325201 . C A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=CTGAGAGCCCCGTCCGGGAC;RSEQ=TGGGACTTCGTCCTGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:16.3:1:33.3:1:1:0:28.7:6:0.6:0:2.3 0/0:7:0:0,0:1,6:7,0:0:2,0:30.6:1:31.3:1:1:0:46.1:14:1:0:0.6 +6 31325235 . CA C 52 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=2.60168;LSEQ=TGATCCCTCTTCTCCTACAC;RSEQ=AGCCTCTTTGTCACACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:27:0:29:0:1:0:22:2:0.3333:0:1 1/0:5:3:0,3:1,1:2,3:0.6:2,0:21.7:1:33:0:0.4:0:37.3:6:0.6:0:0 +6 31325403 . AC A 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTCCTTACCTCTCCTCTTGG;RSEQ=TCTTGTGTAGGGAAACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:31.5:1:30:1:1:0:50.5:4:1:0:6 0/0:1:0:0,0:0,1:1,0:0:0,0:25:0:33:0:1:0:60:2:1:0:0 +6 31326099 . A T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCCTGCTCCTTTTCCTC;RSEQ=CCTCCTGCCTCTCCAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:32:0:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31326131 . C T 29 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCCAGCCCTTCTGTCTGCCC;RSEQ=TCTCATCCCTCACACCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:29.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31326140 . C T 29 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCTGCCCCTCTCATCC;RSEQ=TCACACCCCCGCTCCCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:29.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31345229 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTTTGTATGGCTGTGGCT;RSEQ=TTCAGCCCCTACTTCTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:2,0:2,2:0.5:0,2:32.5:1:28.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31345237 . C G 48 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGCTGTGGCTGTTCAGCC;RSEQ=CTACTTCTGATCCCCTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:22:1:24.3:1:1:0:52.5:3:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31345270 . C T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTAGGACTGGGAGCAGCC;RSEQ=GCCTGGGGGAGACCATCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:29:1:30.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31345441 . TGG T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00548;SOR=0.03659;LSEQ=GTCTGGCAGGACCCAGGCTC;RSEQ=GAGCTGATCCTCCCTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:1,8:0.8889:0,0:27.8:1:32.5:1:1:0:60:16:0.8889:0:0.6 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:28:1:32.8:1:1:0:60:4:0.1818:0.0909:1 +6 31345484 . G A 113 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00023;SOR=0.04088;LSEQ=AAGGCCTGCTGCAGCCTCCC;RSEQ=CTGAGGTCTTGAAACCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:12,0:10,0:10,12:0.5455:0,0:21.8:1:31.7:1:1:0:60:24:0.5455:0:1 0/1:23:1:1,0:22,0:22,1:0.0435:1,0:41:0:29:0:1:0:60:2:0.0455:0:1 +6 31345486 . T A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70078;SOR=1.81893;LSEQ=GGCCTGCTGCAGCCTCCCGC;RSEQ=GAGGTCTTGAAACCATCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:3,0:21,0:21,3:0.125:1,0:20.3:1:32:1:1:0:60:6:0.125:0:1 0/1:24:5:5,0:19,0:19,5:0.2083:1,0:24.4:1:30.2:1:1:0:60:10:0.2083:0:1.2 +6 31345513 . T G 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=TTGAAACCATCAGGAGCAGT;RSEQ=GTTCTTTGGCCTCCGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:40,13:53,0:0:2,0:20.9:1:30.6:1:1:0:60:25.5:1:0:0.3 0/1:46:11:10,1:25,9:34,11:0.2391:2,2:20.2:1:32.3:1:0.40874:3.52:60:22:0.2444:0:2.7 +6 31345523 . C T 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=CAGGAGCAGTTGTTCTTTGG;RSEQ=CTCCGGGACACCGCAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:48,21:69,0:0:2,0:22.6:1:32.2:1:1:0:60:138:1:0:0.3 0/1:52:11:9,2:27,14:41,11:0.2115:2,2:25.1:1:30.2:1:0.46794:2.30:60:22:0.22:0:2.8 +6 31345535 . C T 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTTTGGCCTCCGGGACAC;RSEQ=GCAGGGCTGAGTTGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:61,30:91,0:0:2,0:24.8:1:30.8:1:1:0:59.6:90:1:0:0.3 0/1:64:16:9,7:31,17:48,16:0.25:2,2:24.4:1:29.3:1:0.56532:1.41035:60:32:0.254:0:2.2 +6 31345596 . G A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00068;SOR=0.23533;LSEQ=GGCCCACTGTCTGGGTCAAG;RSEQ=ATGGTGCAGAGCTGGTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:33:19,14:70,64:134,33:0.1976:2,2:28.9:1:29.8:1:0.69757:1.24:60:32:0.1951:0:1.1 0/1:110:6:3,3:49,55:104,6:0.0545:2,2:30.3:1:25.7:1:1:1.12:60:5:0.0459:0:1 +6 31345602 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15609;SOR=Inf;LSEQ=CTGTCTGGGTCAAGGATGGT;RSEQ=CAGAGCTGGTGTCCTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:87,73:160,0:0:2,0:27.7:1:32.3:1:1:0:58.8:159:1:0:0.3 0/1:105:2:1,1:45,58:103,2:0.019:2,2:30:1:28.5:1:1:1.29:60:4:0.0194:0:1 +6 31345640 . C G 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATGCATCCTGGTGGAGCC;RSEQ=CAGCAGCTGCAGGTGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:43,60:103,0:0:2,0:22.6:1:30.7:1:1:0:60:50.5:1:0:0.3 0/1:61:13:5,8:14,34:48,13:0.2131:2,2:23.2:1:30.6:1:0.51965:1.51:60:26:0.2167:0:1.1 +6 31345728 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13277;SOR=Inf;LSEQ=AGCATGAGCGGTGCCACTCA;RSEQ=TGTGCACATGACAGATGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:5,29:34,0:0:2,0:27.4:1:32.1:1:1:0:59.9:33:1:0:0.3 0/1:20:2:0,2:5,13:18,2:0.1:2,0:22.5:1:30:0:1:0:60:4:0.1:0:1.5 +6 31345771 . C CG 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.01485;SOR=4.65572;LSEQ=TCCTCAGGAGATGACAAAGA;RSEQ=GGGAGGACAAGGTGAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:4,4:4,23:27,8:0.2286:2,2:30.3:1:29.9:1:0.05958:5.39:60:16:0.2286:0.0286:0.1 1/0:17:10:4,6:3,4:7,10:0.5882:2,2:28:1:30.9:1:1:1.11721:60:20:0.625:0:0.2 +6 31345772 . G GT 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03872;SOR=0.24988;LSEQ=CCTCAGGAGATGACAAAGAC;RSEQ=GGAGGACAAGGTGAAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:19:4,15:4,11:15,19:0.5588:2,2:25.4:1:29.9:1:1:1.3511:59.7:38:0.5938:0.0882:1.4 0/1:17:4:2,2:5,8:13,4:0.2353:2,2:33.8:1:27.3:1:1:1.56:60:8:0.25:0:1.8 +6 31345783 . G GC 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20924;SOR=0.36337;LSEQ=GACAAAGACGGGAGGACAAG;RSEQ=TGAAGACACAGGTGCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:4,11:4,12:16,15:0.4839:2,2:27.8:1:33.2:1:1:1.09:60:30:0.4839:0.0968:1.7 0/1:16:4:2,2:5,7:12,4:0.25:2,2:33.8:1:31.8:1:1:1.37:60:8:0.25:0:1.8 +6 31345794 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20644;SOR=0.39767;LSEQ=GAGGACAAGGTGAAGACACA;RSEQ=GTGCATCATCTCCTACTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:2,10:4,10:14,12:0.4615:2,2:29.3:1:32.1:1:0.65217:1.94818:60:24:0.48:0:2 0/1:16:4:2,2:5,7:12,4:0.25:2,2:28.8:1:29.5:1:1:1.37:60:8:0.25:0:1.8 +6 31345801 . C A 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48753;SOR=0.54293;LSEQ=AGGTGAAGACACAGGTGCAT;RSEQ=ATCTCCTACTCACCTCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:2,8:4,8:12,10:0.4545:2,2:28.9:1:31.4:1:0.64617:1.93862:60:20:0.4545:0:2.2 0/1:13:4:1,3:4,5:9,4:0.3077:2,2:24.3:1:29:1:1:2.24915:60:8:0.3077:0:2 +6 31349805 . C A 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTGAAGTCACAAAGGGG;RSEQ=GGCATGAAGAAATCCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:1,0:1,3:0.6:0,0:12.3:1:32:0:1:0:60:6:0.75:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31349819 . C A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=AAGGGGCGGCATGAAGAAAT;RSEQ=CTGCATCTCAGTCCCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:22.8:1:28.8:1:1:0:52.4:10:0.8333:0:2.6 0/0:3:0:0,0:2,1:3,0:0:2,0:6:1:31.3:1:1:0:60:6:1:0:0 +6 31349922 . C T 57 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23944;SOR=2.47577;LSEQ=AGCGTAACACTCTGAACTCC;RSEQ=CACTACACACTCAAAGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:4:4,0:68,2:70,4:0.0541:1,0:7.5:1:32:1:1:0:60:8:0.0548:0:1.3 0/1:32:4:3,1:27,1:28,4:0.125:1,2:15:1:28.5:1:0.2379:7.93681:60:8:0.125:0:1 +6 31349980 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1465;SOR=Inf;LSEQ=TCCAGTCTTGTCCCCTGTAC;RSEQ=CCATCCCCCTTCCACATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:169,35:204,0:0:2,0:22:1:31.1:1:1:0:60:50:1:0:0.2 0/1:127:2:1,1:99,26:125,2:0.0157:2,2:13:1:28.5:1:0.38133:3.75541:60:4:0.0161:0:1 +6 31349993 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18794;SOR=Inf;LSEQ=CCTGTACCCCATCCCCCTTC;RSEQ=ACATAAGGCCCTCCAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:186,59:245,0:0:2,0:23.4:1:31.4:1:1:0:60:80.667:1:0:0.2 0/1:188:2:1,1:131,55:186,2:0.0106:2,2:27:1:27.5:1:0.50814:2.36947:60:4:0.011:0:1 +6 31350090 . C T 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.45854;LSEQ=GGTAGAACAAAAACAGGACC;RSEQ=GGTCAGAGCCTGCAGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:366:295:107,188:25,45:70,295:0.806:2,2:26.2:1:30.8:1:1:1.02:59.2:72.75:0.8039:0:1.1 1/0:299:196:77,119:40,63:103,196:0.6555:2,2:26.1:1:29.5:1:1:1.02:58.7:64.333:0.6542:0:1.2 +6 31350114 . G A 47 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07085;SOR=Inf;LSEQ=CAGAGCCTGCAGGAGATGTG;RSEQ=GAGAGGAGGAATTATGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:69,186:255,0:0:2,0:23.6:1:31.2:1:1:0:59.7:126.5:1:0:0.8 0/1:181:3:1,2:52,126:178,3:0.0166:2,2:6:1:30:1:1:1.21:60:6:0.0168:0:1.3 +6 31350154 . C T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TAGGTGAGCTCCTCCACATC;RSEQ=GTCTCCCATAGTTACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:11,103:114,0:0:2,0:23.8:1:30.3:1:1:0:60:56:1:0:0.5 0/1:70:10:1,9:4,56:60,10:0.1429:2,2:18.5:1:29.3:1:0.54875:1.54:60:20:0.1493:0:1.1 +6 31350232 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.63035;SOR=0.63189;LSEQ=ATCCTGTGAGGGGCTAGGGA;RSEQ=GAGACAGGGCCATGAGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:32:3,29:0,5:5,32:0.8649:0,2:26.6:1:31.4:1:1:0:60:64:0.8649:0:1.1 1/1:10:8:0,8:0,2:2,8:0.8:0,0:25:1:31.3:1:1:0:60:16:0.8:0:1 +6 31350303 . T G 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.55841;LSEQ=GAAGTTTCCAAAACTGTGAC;RSEQ=GCAGACCCAGGGCAGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:1,4:0,6:6,5:0.4545:0,2:19.4:1:31.2:1:0.45455:0:60:10:0.4545:0:2 1/0:7:4:2,2:1,2:3,4:0.5714:2,2:34.5:1:30:1:1:1.81:58.5:8:0.5714:0:2.5 +6 31350328 . A G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06993;SOR=Inf;LSEQ=ACCCAGGGCAGGAAACATGA;RSEQ=GAAAGCAGGTGTGAGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:0,3:3,3:0.5:0,2:33.3:1:31.7:1:1:0:60:6:0.5:0:1.7 1/1:7:7:3,4:0,0:0,7:1:0,2:28:1:31.6:1:1:0:58.9:14:1:0:2.1 +6 31358749 . T C 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03194;SOR=5.21146;LSEQ=CCCAGCTCCTCTTAAAACAA;RSEQ=GCCCTGCACACAGTAGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:4:4,0:37,2:39,4:0.093:2,0:36:1:34.3:1:1:0:36.3:8:0.0976:0:1 0/1:14:5:5,0:9,0:9,5:0.3571:0,0:34.8:1:32.4:1:1:0:36.6:10:0.3571:0:1 +6 31358847 . CA C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.53445;SOR=0;LSEQ=CAGAATGAAAACCCACAGGC;RSEQ=AAAGTGGCTGGGAAAAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:105,58:163,2:0.0121:2,2:10.5:1:28.5:1:1:1.80337:57:4:0.0123:0:1 0/0:95:0:0,0:59,35:94,0:0:2,0:20.1:1:29.9:1:1:0:56.2:93:0.9894:0:0.1 +6 31358899 . C A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.6827;SOR=1.14025;LSEQ=TAGTGATGGGCACAGGGCCC;RSEQ=CTAAAGTTCACTTTTGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:36:18,18:311,225:536,36:0.0628:2,2:10.6:1:30.2:1:0.38576:1.38141:30.7:35:0.0621:0:7 0/1:352:25:12,13:178,147:325,25:0.071:2,2:9.4:1:28.9:1:0.53822:1.31076:30.9:50:0.072:0:7.2 +6 31358902 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.59768;SOR=1.16306;LSEQ=TGATGGGCACAGGGCCCCCT;RSEQ=AAGTTCACTTTTGGAACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:593:38:20,18:319,236:555,38:0.0641:2,2:13:1:32.2:1:0.61269:1.21611:30.9:37:0.0632:0:7 0/1:366:27:13,14:185,154:339,27:0.0738:2,2:11.7:1:30.9:1:0.55208:1.29278:33:54:0.0742:0:7.1 +6 31358905 . G A 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.41963;SOR=1.21682;LSEQ=TGGGCACAGGGCCCCCTAAA;RSEQ=TTCACTTTTGGAACCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:50:25,25:321,249:570,50:0.0801:2,2:12.2:1:29.9:1:0.45812:1.28861:37.6:24:0.0784:0:6.4 0/1:386:37:18,19:188,160:348,37:0.0959:2,2:11.2:1:29:1:0.60422:1.23958:40.1:36:0.0945:0:6.6 +6 31358914 . T C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9784;LSEQ=GGCCCCCTAAAGTTCACTTT;RSEQ=GGAACCTTCCCATCTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:710:49:21,28:351,310:661,49:0.069:2,2:12.3:1:30.5:1:0.18364:1.50879:45.7:98:0.0697:0:5 0/1:488:33:12,21:236,219:455,33:0.0676:2,2:11.7:1:29.1:1:0.10459:1.88341:49:15.5:0.0643:0:4.9 +6 31358918 . A G 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70588;SOR=1.07362;LSEQ=CCCTAAAGTTCACTTTTGGA;RSEQ=CCTTCCCATCTGTCTTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:755:75:37,38:356,323:679,75:0.0993:2,2:15.5:1:32.4:1:0.62795:1.13177:50.8:150:0.1004:0:5.1 0/1:510:54:30,24:223,217:440,54:0.1059:2,2:14.3:1:31.4:1:0.56475:1.22:51.4:53:0.1047:0:4.8 +6 31358943 . T C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08935;SOR=1.20684;LSEQ=CCCATCTGTCTTGTTCTCCT;RSEQ=TCATCAGGGACATCCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:869:307:138,169:281,281:562,307:0.3533:2,2:27.1:1:32.9:1:0.15642:1.22435:49:614:0.3566:0:3.7 0/1:604:240:110,130:183,180:363,240:0.3974:2,2:27.8:1:31.2:1:0.28024:1.20114:49.9:79:0.3963:0:3.8 +6 31358955 . A T 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=1.45834;LSEQ=GTTCTCCTTTCATCAGGGAC;RSEQ=TCCATGCCCCTCAAAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:870:370:160,210:245,255:500,370:0.4253:2,2:30.1:1:31.1:1:0.09915:1.26068:48.3:122.333:0.4262:0:3.3 1/0:628:326:150,176:146,156:302,326:0.5191:2,2:30.1:1:29.9:1:0.5761:1.09795:49.3:80.5:0.5177:0:3.2 +6 31358975 . C A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.05729;SOR=1.24787;LSEQ=ATCCATGCCCCTCAAAGCCC;RSEQ=CCTAGTCACACACTACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:771:261:113,148:212,298:510,261:0.3385:2,2:30.8:1:30.2:1:0.64483:1.07:44.6:86:0.3399:0:4 0/1:567:221:101,120:154,191:345,221:0.3898:2,2:30.8:1:29.3:1:0.86255:1.04:45.7:109.5:0.3883:0:4 +6 31359023 . G A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36784;SOR=0.69792;LSEQ=ACCTTCCAGATCAGCCAGGT;RSEQ=CAAATCCCACAGACTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:23:9,14:78,147:225,23:0.0924:2,2:7.7:1:28.3:1:0.6539:1.21:35.1:22:0.0913:0:3.8 0/1:166:11:4,7:68,87:155,11:0.0663:2,2:6.9:1:28.7:1:0.75812:1.36529:31.2:22:0.0667:0:4.1 +6 31359024 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1614;SOR=Inf;LSEQ=CCTTCCAGATCAGCCAGGTG;RSEQ=AAATCCCACAGACTTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:84,155:239,0:0:2,0:20:1:32:1:1:0:48.5:46.8:1:0:1.1 0/1:161:2:1,1:69,90:159,2:0.0124:2,2:28.5:1:29.5:1:1:1.30:37:4:0.0127:0:1.5 +6 31359025 . A T 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCAGATCAGCCAGGTGC;RSEQ=AATCCCACAGACTTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:79,153:232,0:0:2,0:19.6:1:30.7:1:1:0:48.5:115:1:0:1 0/1:160:21:12,9:57,82:139,21:0.1313:2,2:15.4:1:28.7:1:0.23673:1.91:33.7:42:0.1329:0:3.5 +6 31360946 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCATGCCCGGCCGCATGAA;RSEQ=ATTTTTAAGCCTTCTCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:34:0:1:0:44:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 31430010 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=GACACTCCAGCAGCACTCAC;RSEQ=TGACCATCCTGAGAATGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:23.1:1:30:1:1:0:60:16:1:0:0.4 0/1:5:2:2,0:2,1:3,2:0.4:2,0:31.5:1:31.5:1:1:0:60:4:0.4:0:2 +6 31430065 . C T 55 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07619;SOR=Inf;LSEQ=GGGGAAGGGAGCACAGAACC;RSEQ=AGACACCAGCCTGGACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:27:1:32.3:1:1:0:60:8:1:0:0 1/0:6:4:2,2:1,1:2,4:0.6667:2,2:28.5:1:27.5:1:1:1:49.3:8:0.6667:0:1.5 +6 31430143 . G C 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GTATCTGAGGGAGGAACAGT;RSEQ=ACTTCTGGTCCTGACCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:20:1:30.7:1:1:0:60:6:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29.5:1:29:1:1:0:60:4:0.6667:0:1 +6 31430721 . A G 64 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01282;SOR=26.16533;LSEQ=AGCCAAGTCCCAGGGCCCGG;RSEQ=GCTTGGCTCTCTGGGCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:10,0:10,1:0.0909:0,0:3:0:14:0:1:0:60:0:0:0:6 1/1:5:4:4,0:1,0:1,4:0.8:0,0:12.8:1:32.3:1:1:0:60:8:0.8:0:2.3 +6 31430752 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01722;SOR=Inf;LSEQ=CTGGGCTTCAGGCCCCGAGG;RSEQ=CGGTGCCTGGGATGGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:28:1:32:1:1:0:58.2:26:1:0:0.8 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:33.8:1:28.5:1:1:0:60:8:0.4444:0:1.8 +6 31430799 . G T 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37752;SOR=1.82687;LSEQ=TTTGGGGTTTCCCGAGCTCC;RSEQ=CTCTCTCTCTTCCACCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:13:13,0:30,0:30,13:0.3023:1,1:13.8:1:32.5:1:1:0:58.2:26:0.3095:0:1 0/1:18:8:8,0:10,0:10,8:0.4444:0,0:31.8:1:31.1:1:1:0:60:16:0.4444:0:1 +6 31430951 . C T 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTAAAGTCCTCGCCGGCC;RSEQ=ACCGGGACTCAGATTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:0:0,0:461,256:717,0:0:2,0:24.4:1:31.1:1:1:0:59.9:36.737:1:0:0.1 0/1:527:36:23,13:305,186:491,36:0.0683:2,2:25.5:1:29.9:1:1:1.08:60:72:0.0694:0:1.1 +6 31431082 . A G 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.87476;SOR=1.03213;LSEQ=TGCGGGGTCGGGAGGGAAAA;RSEQ=GCCTCTGCGGGAAGGAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:510:388:98,290:36,86:122,388:0.7608:2,2:26.2:1:31.7:1:0.3483:1.23816:59.9:54.429:0.7605:0:1.1 1/0:394:302:85,217:32,60:92,302:0.7665:2,2:25.3:1:30.5:1:0.24168:1.36051:59.6:301:0.7659:0:1.1 +6 31431091 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03241;SOR=Inf;LSEQ=GGGAGGGAAAAAGCCTCTGC;RSEQ=GGAAGGAGCGAGGGGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:462:0:0,0:116,346:462,0:0:2,0:25.3:1:30.8:1:1:0:59.9:76:1:0:0.9 0/1:342:4:1,3:98,240:338,4:0.0117:2,2:28.8:1:29.8:1:1:1.22429:60:8:0.0119:0:1.5 +6 31455630 . G C 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68659;LSEQ=AGGGCAAGGAGGGTTTATTT;RSEQ=CTCTTACCTCAGTTCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:5,1:3,1:4,6:0.6:2,2:19:1:30.8:1:1:1.58:27.3:5:0.5556:0:1.7 1/0:4:2:2,0:1,1:2,2:0.5:2,0:29.5:1:32.5:1:1:0:26.5:4:0.5:0:1 +6 31455671 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCTTAAAACAATGCCCCA;RSEQ=GCACAGTAGGTATTTGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:12,2:14,2:0.125:2,0:29.5:1:30.5:1:1:0:28.5:4:0.125:0:2.5 0/0:5:0:0,0:4,1:5,0:0:2,0:22.2:1:30.8:1:1:0:38.8:10:1:0:0.4 +6 31455743 . A C 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.12035;LSEQ=GGCTTGGCAGACAGGAAAGC;RSEQ=GAATGAAAACCCACAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:2,0:15,3:18,2:0.1:2,0:14:1:32:1:1:0:21.5:4:0.1:0:2.5 0/1:9:1:1,0:5,2:7,1:0.1111:2,0:15:0:32:0:1:0:23:2:0.1111:0:2 +6 31455767 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.07598;LSEQ=TGAAAACCCACAGGCCAAAA;RSEQ=TGGCTGGGAAAAGATTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:30:23,7:11,3:14,30:0.6667:2,2:19.8:1:33.9:1:1:1.11322:25:60:0.6667:0:2.2 1/0:41:28:18,10:9,4:13,28:0.6829:2,2:15.8:1:30.7:1:1:1.2433:27:56:0.6829:0:2.3 +6 31455804 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21777;SOR=Inf;LSEQ=TTCCAAATCCTAGTGCTGGG;RSEQ=ACAGGGCCCACTGAAATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:69,31:100,0:0:2,0:32:1:32.7:1:1:0:38.1:49:1:0:1.6 0/1:88:2:1,1:45,41:86,2:0.0227:2,2:24.5:1:29.5:1:1:1.0964:43:4:0.0233:0:1.5 +6 31455829 . C T 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90151;LSEQ=GGCCCACTGAAATTCACTTT;RSEQ=GGAAACTTCCCATCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:5:3,2:71,35:106,5:0.0446:2,2:12.2:1:31.2:1:1:1.34861:51.8:10:0.045:0:3.6 0/1:99:4:2,2:49,46:95,4:0.0404:2,2:21.3:1:30.5:1:1:1.06457:60:8:0.0408:0:4 +6 31455833 . AA GC 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.05184;LSEQ=CACTGAAATTCACTTTCGGA;RSEQ=CTTCCCATCTGTCTCGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:4:2,2:67,34:101,4:0.0381:2,2:9.8:1:33.4:1:0.60542:1.95703:59.8:8:0.0385:0:2.8 0/1:100:4:2,2:48,48:96,4:0.04:2,2:16.3:1:31.8:1:1:1:60:8:0.0404:0:3 +6 31455834 . A C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.77012;SOR=1.10443;LSEQ=ACTGAAATTCACTTTCGGAA;RSEQ=CTTCCCATCTGTCTCGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:106:69:48,21:19,13:32,69:0.6509:2,2:27.8:1:32.1:1:0.36798:1.56:32.3:138:0.6765:0:2 1/0:101:68:32,36:17,12:29,68:0.6733:2,2:27.6:1:30.6:1:0.37626:1.58605:42.3:136:0.701:0:1.6 +6 31455849 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0013;SOR=0.3381;LSEQ=CGGAAACTTCCCATCTGTCT;RSEQ=GTTCTCCTCTCATCAGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:37:27,10:33,26:59,37:0.3814:2,2:17.1:1:30.1:1:0.12949:2.11:23.9:36:0.375:0:2.4 0/1:99:17:8,9:38,44:82,17:0.1717:2,2:13.4:1:28.9:1:1:1.03:30.8:34:0.1771:0:2.8 +6 31455922 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49123;SOR=0;LSEQ=CCACCTTCCAGATCAGCCAG;RSEQ=TACAAATCCCACAGACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:13,14:27,2:0.069:2,2:19:0:31.5:1:1:1.07:58.5:4:0.069:0:3 0/0:29:0:0,0:8,21:29,0:0:2,0:19.1:1:31.3:1:1:0:51.7:58:1:0:0.5 +6 31455935 . A C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03277;SOR=5.68015;LSEQ=CAGCCAGGTACAAATCCCAC;RSEQ=GACTTCCTGCCTGTGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:7,9:16,3:0.1579:2,2:16.3:1:30:1:1:1.52085:42:6:0.1667:0:1 1/0:17:9:2,7:0,7:7,9:0.5294:0,2:10:1:28.7:1:0.475:0:44.2:18:0.5294:0:1 +6 31457417 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTATACTGGTATTTCCTTG;RSEQ=TGGAATTTGACATCCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:19:1:31:1:1:1:29:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 32163274 . G A 165 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=54.13595;LSEQ=TGGAGGGCTGGGGGACCACA;RSEQ=TCAAGTTGAGGTGATCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1918:1:1,0:999,918:1917,1:5e-04:2,0:1:0:29:0:1:0:60:2:5e-04:0:1 0/1:1673:46:22,24:816,808:1624,46:0.0275:2,2:24.8:1:29.9:1:0.76701:1.10164:60:45:0.0273:0:1.1 +6 32163541 . A C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00296;SOR=1.58994;LSEQ=CCCGAGAGGCTCCGGCAATG;RSEQ=GAATAGGCCCCGCCCCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:90:40,50:340,407:747,90:0.1074:2,2:26.3:1:30.9:1:0.91091:1.04418:60:180:0.1102:0:1.1 0/1:635:102:41,61:254,279:533,102:0.1606:2,2:24.3:1:30.1:1:0.19353:1.35384:60:204:0.1632:0:1.1 +6 32163799 . T C 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAGATCCCAGTGGTTACG;RSEQ=TGGTGAGCGACGTCCGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:795:0:0,0:390,405:795,0:0:2,0:25.7:1:29.8:1:1:0:60:40.842:1:0:0.2 0/1:665:18:8,10:306,340:646,18:0.0271:2,2:23:1:31.7:1:1:1.1248:60:36:0.0276:0:1.3 +6 32164265 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20468;SOR=Inf;LSEQ=CCTGGGTTCCGGTTTCCCAC;RSEQ=GGTTCTGGCCTTGGGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:15,149:164,0:0:2,0:24.3:1:31.6:1:1:0:60:81:1:0:0.1 0/1:136:2:1,1:19,115:134,2:0.0147:2,2:30.5:1:28:1:0.27342:5.92:60:4:0.0148:0:1 +6 32164535 . TG T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.20055;SOR=5.07536;LSEQ=GTGGTGTTGAGGGTGGGAGT;RSEQ=GGGGGGGAAACTCACGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:1,0:78,2:80,1:0.0123:1,0:28:0:35:0:1:0:60:2:0.0128:0:0 0/1:33:2:2,0:29,2:31,2:0.0606:2,0:10.5:1:31.7:1:1:0:60:4:0.0606:0.0303:0.5 +6 32164587 . C T 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00263;SOR=Inf;LSEQ=ACCGCATCTCAGATTGACCG;RSEQ=CGTAACAGCAGGATGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:164,3:167,0:0:1,0:25.9:1:32.3:1:1:0:59.8:40.75:1:0:0.1 0/1:128:7:7,0:114,7:121,7:0.0547:2,0:33:1:30.6:1:1:0:60:14:0.0551:0:1.1 +6 32164615 . C T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09255;SOR=Inf;LSEQ=GCAGGATGAGAGGGAATGCC;RSEQ=CTCTGCTGCACCTATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:264,29:293,0:0:2,0:23.1:1:30.9:1:1:0:60:25.636:1:0:0.1 0/1:243:3:1,2:207,33:240,3:0.0123:2,2:21.3:1:21.3:1:0.05517:12.32029:60:2:0.0084:0:1 +6 32164665 . CT C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16282;LSEQ=CTCCCACCCCATCTGCTCAA;RSEQ=TCTCTATAGCATACATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:241:164,77:367,214:581,241:0.2932:2,2:25:1:32.3:1:0.2001:1.24:59.7:482:0.2979:0.0608:0.2 0/1:712:45:27,18:403,264:667,45:0.0632:2,2:22.8:1:31:1:1:1.01766:60:90:0.0644:0.014:0.2 +6 32164869 . G C 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.89449;LSEQ=GCTGGGGAGACAGAGGGCCA;RSEQ=TGACCCCTGGGGTACCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:331:12:3,9:80,239:319,12:0.0363:2,2:27.8:1:33.8:1:1:1.00417:60:24:0.0368:0:2.2 0/1:257:59:15,44:41,157:198,59:0.2296:2,2:22.8:1:31.5:1:0.47374:1.30:60:58:0.2292:0:1.8 +6 32164874 . C A 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=5.37716;LSEQ=GGAGACAGAGGGCCAGTGAC;RSEQ=CCTGGGGTACCTTGGACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:12:3,9:71,215:286,12:0.0403:2,2:26.9:1:30.8:1:1:1.01:60:24:0.041:0:2.2 0/1:233:43:8,35:38,152:190,43:0.1845:2,2:19.6:1:29.5:1:1:1.09333:60:86:0.1861:0:2.2 +6 32165018 . G T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.31673;SOR=4.0806;LSEQ=AAACTCTAGGGGATGCTTCT;RSEQ=TCCAGCTTTACTTGTAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:1,0:170,62:232,1:0.0043:2,0:2:0:14:0:1:0:60:0:0:0:3 0/1:173:3:1,2:131,38:169,3:0.0173:2,2:27.7:1:28:1:0.13541:6.79458:60:6:0.0174:0:1 +6 32165215 . AG A 91 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.07118;SOR=3.35015;LSEQ=AGAATCGGGCAGCCAGGTGC;RSEQ=GGGGGTCTCCCCAGTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:922:3:2,1:518,400:918,3:0.0033:2,2:21:1:34.7:1:1:1.54:60:6:0.0033:0:0 0/1:739:8:3,5:372,354:726,8:0.0108:2,2:30.9:1:30.6:1:0.49681:1.75009:60:16:0.0109:0.0027:0.4 +6 32165444 . A G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01222;SOR=2.11406;LSEQ=GGGACAACATGTAAGCTCAG;RSEQ=GAGAATCAAAACCTGAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:28:2,26:9,168:177,28:0.1359:2,2:19.3:1:31.5:1:0.64916:1.43:60:27:0.1324:0:1.1 0/1:128:32:2,30:5,91:96,32:0.25:2,2:20.4:1:29.9:1:1:1.21:60:31:0.248:0:1.2 +6 32166380 . C G 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAAGGTTGATTTGCCCTTT;RSEQ=ATCCCTTCCATCACCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1167:0:0,0:630,537:1167,0:0:2,0:24.1:1:32.3:1:1:0:59.9:96.25:1:0:0.1 0/1:836:43:25,18:422,370:792,43:0.0514:2,2:23.6:1:30.4:1:0.6382:1.22:60:13.333:0.0483:0:1.2 +6 32166992 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53746;SOR=0;LSEQ=ATTACTATTGGGAGACCTTT;RSEQ=GACAAGTTTAGTAGCCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:8,94:102,2:0.0192:2,0:13.5:1:31:1:1:0:60:4:0.0192:0:1 0/0:58:0:0,0:9,49:58,0:0:2,0:22.7:1:30.6:1:1:0:60:57:1:0:0.6 +6 32167009 . G T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.61393;SOR=0.76405;LSEQ=TTTGGACAAGTTTAGTAGCC;RSEQ=GTCTTTGCCTCGGTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:62:2,60:1,13:14,62:0.8158:1,1:21.7:1:30.2:1:0.46202:2.27628:59.4:124:0.8267:0:1 1/0:35:27:2,25:0,8:8,27:0.7714:0,2:22.6:1:30:1:1:0:60:54:0.7941:0:1.1 +6 32168565 . G T 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.39192;SOR=0.31797;LSEQ=TGTTGCTAGCATGAGAGCTG;RSEQ=CCTGGGAACAGAGGTCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:4:2,2:297,98:395,4:0.01:2,2:9:1:30.5:1:0.26225:3.02039:60:8:0.0103:0:1.3 0/0:312:1:0,1:209,102:311,1:0.0032:2,0:1:0:22:0:0.33013:0:60:2:0.0033:0:1 +6 32168771 . G T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.87648;LSEQ=CGGGACAAATCCACACCCAT;RSEQ=ACCACCACAAACCTGTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1335:132:60,72:590,610:1200,132:0.0989:2,2:25.4:1:28.7:1:0.46323:1.16052:60:25.4:0.0972:0:1.1 0/1:1054:180:83,97:411,461:872,180:0.1708:2,2:26.3:1:28.3:1:0.80632:1.04189:60:59:0.1704:0:1.2 +6 32168932 . C T 152 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.68999;LSEQ=GTCTCCTTGCCCAGGGGCTG;RSEQ=GTTTGAGGGGCTGCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1729:8:1,7:887,834:1721,8:0.0046:2,2:11.3:1:28.5:1:0.03408:7.43798:60:16:0.0047:0:1.3 0/1:1303:45:26,19:654,604:1258,45:0.0345:2,2:22.6:1:27.8:1:0.54402:1.26:60:21.5:0.0333:0:1.1 +6 32169621 . T A 44 MAF0.05;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17241;SOR=Inf;LSEQ=GGCTTGAGACCTGAGTTCCT;RSEQ=CAACTCTTAGAGAGGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:4,0:21,3:24,4:0.1429:2,0:26:1:22.3:1:1:0:60:3:0.1111:0:3.3 1/1:1:1:1,0:0,0:0,1:1:0,0:39:0:30:0:1:0:60:2:1:0:1 +6 32169795 . TTCC T 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.000;MSILEN=3;SSF=0.043;SOR=0;LSEQ=ACTCAGAGCCATCTACGTCC;RSEQ=TCCTCCTCTCACCCACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:6:1,5:418,113:531,6:0.0111:2,2:11.8:1:26:1:0.00237:18.36814:60:5:0.0094:0.0074:0.7 0/0:391:0:0,0:288,101:389,0:0:2,0:21.1:1:29.3:1:1:0:59.9:63.833:0.9974:0:0.1 +6 32170433 . C T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.47586;LSEQ=GCATTATTCTTCCCGCTCTC;RSEQ=ATCAAGCAAACTCTTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:21:6,15:28,116:144,21:0.1273:2,2:27:1:28.2:1:0.38606:1.65:60:20:0.1235:0:1.1 1/0:105:55:12,43:12,38:50,55:0.5238:2,2:22.6:1:27.9:1:0.8197:1.13024:59.9:54:0.5243:0:1 +6 32170464 . AG A 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=7.43912;LSEQ=CTCTTGGGTTAAGACGGTGC;RSEQ=AGGGTCCTAGATTCTCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:13:1,12:3,70:73,13:0.1512:1,1:19.8:1:31.1:1:0.48745:1.93:60:12:0.1412:0.0349:1.1 1/0:54:31:1,30:2,21:23,31:0.5741:2,1:22.9:1:30.4:1:0.56882:2.80191:59.8:30:0.5769:0.1667:0.9 +6 32171415 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAGACACTTCCCACTGT;RSEQ=AGCTTGGCATGGCTTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:2,0:133,2:135,2:0.0144:1,0:37:1:31.5:1:1:0:60:4:0.0147:0:1 0/0:60:0:0,0:58,2:60,0:0:1,0:26.3:1:31.7:1:1:0:60:120:1:0:0.2 +6 32171427 . G A 39 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67212;LSEQ=CCCACTGTGAGCTTGGCATG;RSEQ=CTTTTTCCAATAATTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:3:2,1:151,2:153,3:0.0192:1,2:33.3:1:24.7:1:0.05695:33.36202:48.3:2:0.0132:0:1.3 0/1:77:1:1,0:72,4:76,1:0.013:2,0:43:0:26:0:1:0:60:2:0.0132:0:1 +6 32171476 . G A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07226;SOR=Inf;LSEQ=TCACCCACAGTCCCTTCTGG;RSEQ=ATTCCAACTGAGGTATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:284,55:339,0:0:2,0:23.2:1:31.2:1:1:0:59.8:41.375:1:0:0.1 0/1:243:3:2,1:186,54:240,3:0.0123:2,2:26:1:23.7:1:0.5386:1.71784:60:2:0.0084:0:1.7 +6 32171538 . G A 173 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAGAGAAGGCAGATTTGTG;RSEQ=TCACTTGCCTTGGGGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:887:0:0,0:551,336:887,0:0:2,0:25.4:1:31.4:1:1:0:59.9:45.684:1:0:0.1 0/1:678:64:37,27:364,247:611,64:0.0944:2,2:27.5:1:28.9:1:0.79043:1.07527:60:128:0.0958:0:1.1 +6 32171683 . T C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.55082;LSEQ=TAATTATGGGGGAGATTAGA;RSEQ=GTCACACACTGCATCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:631:88:21,67:151,391:542,88:0.1395:2,2:23.8:1:30.7:1:0.51911:1.23177:60:87:0.1401:0:1.1 1/0:419:216:67,149:61,139:200,216:0.5155:2,2:21.9:1:29.4:1:0.91578:1.02:60:53:0.5171:0:1.1 +6 32171831 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACCAGGTGACGGCTGCC;RSEQ=CATGGGTGGAGACTATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:2,0:107,42:149,2:0.0132:2,0:25:1:32.5:1:1:0:60:4:0.0136:0:1 0/0:73:0:0,0:57,16:73,0:0:2,0:22.9:1:29.6:1:1:0:59.8:72:1:0:0.2 +6 32172065 . T G 328 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2142;SOR=0.86353;LSEQ=GGAGGGCAGGCACAGTGGAA;RSEQ=CCTCCAGGTTTGGGAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1253:1081:559,522:84,85:169,1081:0.8627:2,2:25.1:1:32.6:1:0.67916:1.08:60:76.214:0.8633:0:1.1 1/1:1054:890:454,436:84,78:162,890:0.8444:2,2:25:1:31.4:1:0.86461:1.0342:59.9:147.333:0.8476:0:1.2 +6 32178414 . TA T 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.36244;SOR=2.58923;LSEQ=GTTAGTTGGGTGTGTGGGGT;RSEQ=AAAAAAATAAAAGGAGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:2,0:112,6:118,2:0.0167:2,0:25.5:1:32:1:1:0:60:4:0.0171:0:0 0/1:71:3:2,1:64,4:68,3:0.0423:2,2:22.3:1:28.6:1:0.19937:7.51513:60:6:0.0423:0.0141:0 +6 32178773 . T C 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.76707;LSEQ=GGGGGCCGGGCGCCATGGCT;RSEQ=ACGCCTGTAATCCCAGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:23:1,22:18,114:132,23:0.1484:2,1:21.1:1:31.5:1:0.31073:3.45434:50.6:22:0.1429:0:1.1 0/1:90:41:5,36:7,41:48,41:0.4556:2,2:24.8:1:30.7:1:1:1.22644:52.9:19.5:0.4483:0:1.1 +6 32180146 . A G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72065;SOR=0.87351;LSEQ=TGTGTGGTTTTGATTCTCAG;RSEQ=TGGTTGTTTTGGCCAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:148:126:116,10:20,1:21,126:0.8514:1,2:23.3:1:31.8:1:1:1.71875:59.5:62:0.8552:0:1.1 1/1:96:80:77,3:15,1:16,80:0.8333:1,1:21.4:1:31.2:1:0.5239:1.70:60:160:0.8333:0:1.2 +6 32180172 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18206;SOR=Inf;LSEQ=GTTTTGGCCAAAAGCTGTGT;RSEQ=GAAGCCCACAGGAACGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:173,43:216,0:0:2,0:25:1:31.9:1:1:0:59.8:107:0.9953:0:0.6 0/1:162:2:1,1:131,29:160,2:0.0123:2,2:25:1:27:1:0.33701:4.45825:60:4:0.0126:0:1.5 +6 32180241 . C T 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTCTCCAGTCAGTGCCGG;RSEQ=GTTGGTTACCTTGGCTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:689:0:0,0:438,248:686,0:0:2,0:26.5:1:31.4:1:1:0:59.9:56.167:0.9985:0:0.2 0/1:572:60:36,24:299,212:511,60:0.1049:2,2:24.4:1:28.6:1:0.89021:1.06:60:29:0.1028:0:1.1 +6 32180684 . A C 125 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=25.12758;LSEQ=GCAGGTTGCCCTATTCCTAC;RSEQ=GGGGCTGAACAAGACAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:870:1:0,1:385,484:869,1:0.0011:2,0:2:0:10:0:1:0:60:0:0:0:2 0/1:782:22:8,14:345,415:760,22:0.0281:2,2:27.4:1:28.2:1:0.51586:1.45414:60:21:0.0272:0:1.1 +6 32181113 . AC A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.15682;SOR=Inf;LSEQ=ACACTGTACATAGGACATAC;RSEQ=CCCCCACCCCCATCAAAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:13,244:257,0:0:2,0:27.4:1:31.2:1:1:0:59.8:31.125:1:0:0.2 0/1:169:2:0,2:15,152:167,2:0.0118:2,0:35.5:1:32.5:1:1:0:60:4:0.0122:0:0 +6 32181182 . G A 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00325;SOR=14.57428;LSEQ=TATTTATATGATATTTTATT;RSEQ=TTTTTAGATAGGGTCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:1:0,1:11,51:62,1:0.0159:2,0:35:0:17:0:1:0:60:0:0:0:1 0/1:36:7:2,5:1,28:29,7:0.1944:1,2:17.9:1:30:1:0.0902:10.09:60:14:0.2121:0:1 +6 32181399 . A G 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07123;SOR=Inf;LSEQ=ATTTTAAAAAATATGACACA;RSEQ=GCATACCCTCCTTAGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:254,44:298,0:0:2,0:20.8:1:30.8:1:1:0:60:98.333:1:0:0.1 0/1:212:3:1,2:158,51:209,3:0.0142:2,2:16.3:1:26.3:1:0.15491:6.1298:60:2:0.0097:0:2.3 +6 32181517 . A C 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGCCCTGTGTGGCTTGG;RSEQ=GGGCAGGTGCAGTAGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:812:0:0,0:440,371:811,0:0:2,0:25.6:1:30.8:1:1:0:59.9:46.706:1:0:0.1 0/1:609:16:8,8:325,268:593,16:0.0263:2,2:30.8:1:29.4:1:0.80113:1.2123:60:15:0.0252:0:1.4 +6 32181669 . G A 61 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0405;SOR=7.57577;LSEQ=TGTCCTCCTTCCCTCCCTCC;RSEQ=CTCTCCTTCTCTTTCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:1:1,0:136,347:483,1:0.0021:2,0:1:0:26:0:0.28306:0:60:2:0.0021:0:1 0/1:323:5:4,1:94,222:316,5:0.0155:2,2:7.8:1:26.4:1:0.03173:9.38:60:10:0.0156:0:0.6 +6 32181738 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10919;SOR=Inf;LSEQ=ATTCTTTCCCATCAACCTCC;RSEQ=TTCTCACCACCTCCCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:118,114:232,0:0:2,0:23.3:1:31:1:1:0:59.9:45.4:1:0:0.2 0/1:115:2:1,1:61,52:113,2:0.0174:2,2:24:1:26:1:1:1.17144:60:4:0.0174:0:1.5 +6 32182175 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.07439;LSEQ=GTGACTTTGCTCTCAGCACC;RSEQ=CCCCCATCCTCCCCAACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:0,2:2,84:86,2:0.0227:1,0:25.5:1:29:1:1:0:60:4:0.023:0:1.5 0/1:41:1:0,1:2,38:40,1:0.0244:2,0:45:0:32:0:1:0:60:2:0.025:0:1 +6 32182243 . G GAT 89 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=10.000;MSILEN=2;SSF=0.1591;SOR=0;LSEQ=CATCTATATATCTAGTTGGA;RSEQ=ATATATATATATATATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:0,8:0,19:19,8:0.2759:1,0:36.9:1:29.7:1:1:0:60:16:0.2759:0.0345:0.1 0/0:9:0:0,0:0,9:9,0:0:0,0:16.3:1:31.1:1:1:0:60:18:1:0:0.2 +6 32182261 . T TATAC 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=9.000;MSILEN=2;SSF=0.01709;SOR=Inf;LSEQ=GAGATATATATATATATATA;RSEQ=ACACACATATATATTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:0,18:18,0:0:1,0:23.6:1:28.7:1:1:0:60:36:0.7826:0:0.1 1/0:4:2:0,2:0,1:1,2:0.5:0,0:35:1:30:1:1:0:60:4:0.5:0:0.5 +6 32182914 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54964;SOR=0;LSEQ=TCCCCATTGGTCATTTCTCA;RSEQ=AGACCTACATCTCACTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:167,27:194,2:0.0102:2,2:24.5:1:28.5:1:0.26593:6.09191:60:4:0.0105:0:1 0/0:101:0:0,0:80,21:101,0:0:2,0:22.3:1:31.3:1:1:0:60:100:1:0:0.1 +6 32183175 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.86682;LSEQ=GAGCTGGCCTGGGGTGGGAA;RSEQ=ATGGGTCAAAAAGAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:593:85:31,54:155,353:508,85:0.1433:2,2:23.6:1:30.4:1:0.31222:1.31:60:84:0.1429:0:1.1 0/1:512:230:77,153:90,190:280,230:0.4492:2,2:25.6:1:29.4:1:0.77647:1.06:60:75.667:0.4504:0:1.2 +6 32183193 . C G 61 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03546;SOR=Inf;LSEQ=AAGATGGGTCAAAAAGAAAA;RSEQ=AGCTCCTCCACATCCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:0:0,0:110,342:452,0:0:2,0:22.2:1:32.3:1:1:0:60:225:1:0:0.2 0/1:348:4:2,2:80,263:343,4:0.0115:2,2:6:1:30.5:1:0.23814:3.27:60:8:0.0116:0:2.3 +6 32183195 . G A 59 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01414;SOR=Inf;LSEQ=GATGGGTCAAAAAGAAAACA;RSEQ=CTCCTCCACATCCTTCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:0:0,0:106,328:434,0:0:2,0:22.2:1:32.2:1:1:0:59.9:47.222:1:0:0.2 0/1:325:5:4,1:70,249:319,5:0.0154:2,2:6.2:1:25.8:1:0.01053:14.08:60:10:0.0158:0:1 +6 32183200 . T A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07597;SOR=Inf;LSEQ=GTCAAAAAGAAAACAGCTCC;RSEQ=CCACATCCTTCATTGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:85,306:391,0:0:2,0:22.3:1:29.9:1:1:0:59.9:54.857:1:0:0.2 0/1:289:3:2,1:60,226:286,3:0.0104:2,2:13:1:21.7:1:0.11732:7.46:60:2:0.0071:0:2.3 +6 32184526 . T C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53947;SOR=0;LSEQ=CACCATTTACACTGGGCCCA;RSEQ=GTGGGCCCTACGGTAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:2,0:197,1:198,2:0.01:1,0:25:1:27.5:1:1:0:60:4:0.0101:0:1 0/0:111:0:0,0:108,3:111,0:0:1,0:22:1:30.2:1:1:0:60:222:1:0:0.2 +6 32184543 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06558;SOR=Inf;LSEQ=CCATGTGGGCCCTACGGTAA;RSEQ=CCCTGCCCTTGTCCCCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:247,8:255,0:0:1,0:23.2:1:32.1:1:1:0:60:62.75:0.996:0:0.1 0/1:174:3:2,1:159,12:171,3:0.0172:2,2:20:1:23:1:0.20892:6.47866:60:2:0.0116:0:1.3 +6 32184574 . G A 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCCCATGGTTGTACAATT;RSEQ=TGCAGGTTTTACACTAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:328,99:427,0:0:2,0:21.9:1:32.1:1:1:0:60:60:0.9976:0:0.1 0/1:389:56:41,15:253,80:333,56:0.144:2,2:22.3:1:28.7:1:0.73675:1.15655:60:112:0.1443:0:1.1 +6 32184705 . G A 291 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04598;SOR=0.8004;LSEQ=TATTCTGCCAGTTCTTTCCA;RSEQ=TGCCTCCCCTGTGAACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:970:773:366,407:94,100:194,773:0.7969:2,2:23.5:1:30.4:1:0.80964:1.04528:59.9:34.136:0.7939:0:1.2 1/0:915:694:308,386:112,108:220,694:0.7585:2,2:23.7:1:29.4:1:0.10297:1.29928:60:42.375:0.7575:0:1.1 +6 32185246 . T G 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00743;SOR=0;LSEQ=TGTGACTTTGGGCAAGCTGG;RSEQ=CAACCCTCTAGGCCCCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:2,7:0,19:19,9:0.3214:1,2:29.1:1:32.9:1:0.09524:0:60:18:0.3333:0:1.3 0/0:18:0:0,0:1,17:18,0:0:1,0:27.5:1:27.5:1:1:0:59.2:17:1:0:0.3 +6 32185593 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGATGAGAATGGGCAAG;RSEQ=AAGCAAGGGAAGATTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:57,0:57,2:0.0339:1,2:17.5:1:29:1:0.0339:0:60:4:0.0339:0:1 0/0:25:0:0,0:22,3:25,0:0:2,0:20.5:1:29.7:1:1:0:58.6:50:1:0:0.2 +6 32185796 . C T 160 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.01311;LSEQ=CAGGCAGATGCACTGGAAGC;RSEQ=GTTGAGCAGGTCATGGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1072:3:0,3:565,503:1068,3:0.0028:2,0:1:0:26.7:1:0.10513:0:60:6:0.0028:0:1 0/1:965:44:22,22:488,433:921,44:0.0456:2,2:28:1:29.4:1:0.75814:1.12688:60:13.667:0.0434:0:1.3 +6 32185818 . C T 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTGAGCAGGTCATGGCAATC;RSEQ=GCGTGGTTCAGGCAGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1135:0:0,0:577,557:1134,0:0:2,0:25.4:1:30.3:1:1:0:60:48.304:1:0:0.2 0/1:996:82:41,41:458,455:913,82:0.0823:2,2:24.5:1:29.4:1:1:1.00659:59.9:81:0.0831:0:1.4 +6 32185922 . CAG C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.39471;LSEQ=CATGAGGGCTGTGGCTCAGC;RSEQ=GTCTGCCTGGGAGACCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:53:14,39:94,306:400,53:0.1165:2,2:22.9:1:31:1:0.61094:1.17:59.8:52:0.1163:0.0308:0.2 0/1:346:144:40,104:65,137:202,144:0.4162:2,2:25.9:1:30.9:1:0.40784:1.23283:60:143:0.4194:0.0289:0.1 +6 32185973 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51976;SOR=0;LSEQ=TCGGCCCTGCTCCTGACTTG;RSEQ=CCCACTCAGGCGGTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:7,178:185,2:0.0107:1,2:17.5:1:28.5:1:0.08395:23.85:60:4:0.011:0:1 0/0:123:0:0,0:12,111:123,0:0:2,0:25.2:1:30.4:1:1:0:60:40:1:0:0.2 +6 32186050 . G A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01839;SOR=4.27922;LSEQ=CCCTGAGGCCCTGCTGCTTC;RSEQ=CAGTGTGTGGCCCTGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:10:1,9:0,32:32,10:0.2381:1,2:24.6:1:29.3:1:0.2381:0:60:20:0.2439:0:1 1/0:19:11:1,10:1,7:8,11:0.5789:2,2:30.3:1:30.5:1:1:1.40151:60:22:0.5789:0:1.2 +6 32186147 . C A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=AAGGCTTTCTGGTGGCCATT;RSEQ=CTGTGTATACAGAGGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:33.5:1:29:1:1:0:60:4:0.2222:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:26.5:1:31:1:1:0:60:4:1:0:1 +6 32187202 . T C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=24.48247;LSEQ=ATCTGTGGTAACCCCTCTCC;RSEQ=AGGGGTCTTGGGTGTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:4:3,1:35,1:36,4:0.1:1,2:34.3:1:31.5:1:0.19231:10.24701:60:8:0.1:0:1 1/0:16:12:12,0:4,0:4,12:0.75:0,0:20.6:1:30.4:1:1:0:60:24:0.75:0:1.1 +6 32187605 . A G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=3.81178;LSEQ=GAGTCCACAGGGGTCAGGGC;RSEQ=GGAAGGGCAAGGAGGTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:53:20,33:49,189:238,53:0.1821:2,2:21.1:1:30.4:1:0.01186:2.33:60:25.5:0.1809:0:1.4 0/1:224:103:22,81:33,88:121,103:0.4598:2,2:22.5:1:29.5:1:0.35131:1.3787:60:33.333:0.4587:0:1.3 +6 32187637 . G T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16505;SOR=1.64444;LSEQ=GAGGTGAGACTGTCAGGGAA;RSEQ=GTGTGGGGGCCTGCGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:22:3,19:17,128:145,22:0.1317:2,2:23.4:1:30.3:1:0.73063:1.19:60:44:0.1341:0:1.9 0/1:100:20:2,18:9,71:80,20:0.2:2,2:26.6:1:29.2:1:1:1.13939:60:19:0.1959:0:2.1 +6 32187721 . AC TT 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56273;SOR=1.45117;LSEQ=GAAAGGAAATAAGGGACCAA;RSEQ=TCATGGGGACTGAGGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:12:4,8:29,37:66,12:0.1519:2,2:21.6:1:31:1:0.5443:1.55881:60:11:0.1486:0.0253:1 0/1:29:6:2,4:7,15:22,6:0.2069:2,2:22.5:1:28.1:1:1:1.07:60:12:0.2143:0:1 +6 32187722 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.06402;LSEQ=AAAGGAAATAAGGGACCAAA;RSEQ=TCATGGGGACTGAGGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:4:2,2:28,33:61,4:0.0533:2,2:22.8:1:32.5:1:1:1.18:60:8:0.0625:0:1.3 1/0:30:15:5,10:3,6:9,15:0.5:2,2:19.8:1:29.9:1:1:1:60:30:0.625:0:1.1 +6 32187836 . G GCC 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0;SOR=5.10023;LSEQ=TTTAATTGGAAAAGCAATCT;RSEQ=CCCTTTTCTGTCTTCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:20:18,2:209,21:230,20:0.08:2,2:20.4:1:30.8:1:1:1.1054:59.4:19:0.0776:0.024:0.4 0/1:146:45:43,2:90,11:101,45:0.3082:2,1:21:1:31:1:0.34526:2.61:60:90:0.3125:0.0822:0.1 +6 32188099 . C T 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=7.98268;LSEQ=GGTGAGGCTCTCAAAGGCCA;RSEQ=TTGAAGCTCCTAGCAGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:27:14,13:230,318:548,27:0.047:2,2:19.5:1:30:1:0.32504:1.49:60:26:0.0457:0:1.1 0/1:428:121:45,76:119,186:305,121:0.2827:2,2:23.4:1:30.1:1:0.74189:1.08037:60:242:0.2827:0:1.2 +6 32188297 . G C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=5.87396;LSEQ=TTCTCCTCACAGCTTGTGCC;RSEQ=CCCCAGCCACTCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1500:77:37,40:728,688:1416,77:0.0513:2,2:26.5:1:30.7:1:0.6399:1.14383:59.5:24.667:0.0504:0:1.3 0/1:1293:312:153,159:490,485:975,312:0.2413:2,2:24:1:30:1:0.74508:1.04991:59.9:61.4:0.2412:0:1.3 +6 32188383 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.16161;LSEQ=GCAGTGAGGGGGACCCTGGG;RSEQ=CTCACACTCATCCACATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:825:123:46,77:252,447:699,123:0.1491:2,2:24.3:1:31.8:1:0.76156:1.06:60:246:0.1517:0:1.2 0/1:646:307:129,178:135,203:338,307:0.4752:2,2:25.3:1:30.6:1:0.63064:1.09:60:75.75:0.4742:0:1.2 +6 32188603 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.90114;LSEQ=CAAGTGCCCCCATTCTGACA;RSEQ=TGGTGGCTGACACAGTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1181:38:19,19:566,576:1142,38:0.0322:2,2:26.4:1:31.1:1:1:1.02:60:76:0.0326:0:1.9 0/1:1040:295:143,152:373,371:744,295:0.2837:2,2:24.8:1:29.5:1:0.6309:1.06858:59.8:146.5:0.2842:0:2.3 +6 32188640 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.01169;LSEQ=TGTCTGGATTCACCTCACAG;RSEQ=CTGGGCCTATGAAACCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:956:31:12,19:411,513:924,31:0.0324:2,2:19.8:1:30.7:1:0.58456:1.26821:60:30:0.0321:0:2.6 0/1:823:222:102,120:270,330:600,222:0.2697:2,2:26.6:1:30.7:1:0.81335:1.04:59.7:36:0.2693:0:2.9 +6 32188642 . T C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=11.65872;LSEQ=TCTGGATTCACCTCACAGTC;RSEQ=GGGCCTATGAAACCTGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:947:29:12,17:403,514:917,29:0.0306:2,2:20.7:1:30.3:1:0.85084:1.11058:60:58:0.0309:0:2.6 0/1:813:219:101,118:271,323:594,219:0.2694:2,2:26.4:1:29.7:1:0.9368:1.02:59.9:53.75:0.2671:0:2.9 +6 32188678 . G A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20155;SOR=1.24219;LSEQ=GACAGGGTCATGGATCAGCT;RSEQ=TGGGAGGAGGCTCCAACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:86:36,50:262,357:619,86:0.1218:2,2:25.1:1:29.4:1:1:1.01927:60:42:0.121:0:1.1 0/1:517:76:33,43:199,242:441,76:0.147:2,2:23.2:1:28.6:1:0.80406:1.07139:60:152:0.1484:0:1.1 +6 32188713 . C G 240 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACGGAGACATCCTGCCCTG;RSEQ=CCAGAGAGAGGGGCGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:191:88,103:188,251:439,191:0.3013:2,2:22:1:31.8:1:0.48488:1.14:59.8:46.75:0.3031:0:1.1 0/0:443:0:0,0:213,227:440,0:0:2,0:23.7:1:30.7:1:1:0:60:54:0.9931:0:0.3 +6 32188823 . G A 251 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTGGCAGGTGCCCCCATTC;RSEQ=AACAGCCCCTAGGAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:306:181,125:311,254:565,306:0.3505:2,2:25.1:1:30.5:1:0.25268:1.18:60:50:0.3509:0:1.1 0/0:680:0:0,0:361,319:680,0:0:2,0:25.4:1:29.7:1:1:0:60:96.143:1:0:0.2 +6 32189032 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=7.33127;LSEQ=TGGCACTGGATCTGGGGGTA;RSEQ=GTGGCCAGACACACCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1057:53:23,30:434,567:1001,53:0.0501:2,2:24.2:1:30.4:1:1:1.00:60:52:0.0501:0:1.1 0/1:881:246:104,142:290,343:633,246:0.2792:2,2:24.7:1:29.9:1:0.36505:1.15422:59.8:60.5:0.2785:0:1.2 +6 32189192 . G A 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTCACTCTGGATTATCTCT;RSEQ=GGTCTCATTTTCATATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:36:0,36:2,101:103,36:0.259:1,1:22.1:1:32.8:1:1:0:58.9:72:0.2609:0:1.3 0/0:76:0:0,0:6,70:76,0:0:2,0:25.7:1:30.4:1:1:0:60:75:1:0:0.1 +6 32190028 . A G 89 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAGATTAAAGGGGCTAG;RSEQ=ACAGGCATCAGGATGGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:25.6:1:29.9:1:1:0:55.5:7:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 32190217 . T C 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=10.48006;LSEQ=AGTTTCTCAGGCTCCAGTTC;RSEQ=ATCTTCCCCACCCACAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:8:8,0:80,6:86,8:0.0851:2,0:28.5:1:31.3:1:1:0:60:16:0.086:0:1.1 1/0:36:18:16,2:17,1:18,18:0.5:1,2:25.6:1:29.8:1:1:2.08218:60:17:0.4857:0:1.3 +6 32190302 . A T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06649;SOR=Inf;LSEQ=GCTTACCTGTCCATCCAGGC;RSEQ=TGCAGGAGCACTGTGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:0:0,0:289,105:394,0:0:2,0:24.5:1:30.5:1:1:0:59.9:130.333:1:0:0.2 0/1:270:3:1,2:178,89:267,3:0.0111:2,2:12.7:1:26.3:1:0.26339:3.97778:60:6:0.0115:0:1.7 +6 32190304 . G A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06643;SOR=Inf;LSEQ=TTACCTGTCCATCCAGGCAT;RSEQ=CAGGAGCACTGTGGGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:292,112:404,0:0:2,0:24.8:1:32:1:1:0:59.9:49.5:1:0:0.2 0/1:276:3:2,1:181,92:273,3:0.0109:2,2:6:1:25.7:1:1:1.02:60:6:0.0109:0:1 +6 32190390 . T G 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.13709;LSEQ=AGGACAAGGGTCTTCAAGCT;RSEQ=GGCCTGGCATCTCTCACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:943:137:79,58:449,356:805,137:0.1453:2,2:24.7:1:31.8:1:0.71021:1.08:60:136:0.1462:0:1.9 0/1:799:278:158,120:287,233:520,278:0.3479:2,2:23.8:1:30.8:1:0.70846:1.07:60:45.333:0.3483:0:2 +6 32190406 . A G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.18674;LSEQ=AGCTTGGCCTGGCATCTCTC;RSEQ=CCAGTGAAGCCAGGGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:991:110:60,50:481,400:881,110:0.111:2,2:23.9:1:30.4:1:1:1.00208:60:26.5:0.1091:0:2 0/1:834:328:189,139:269,237:506,328:0.3933:2,2:24.7:1:30.3:1:0.22596:1.20:60:108.333:0.393:0:1.9 +6 32190484 . G A 288 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00067;LSEQ=CTGGGGAGCCCTAGGGGAGC;RSEQ=GGAAGCAGGGCTTGGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:954:626:297,329:154,174:328,626:0.6562:2,2:25.8:1:31.1:1:0.89162:1.02:59.9:77.25:0.6581:0:1.1 0/0:803:1:1,0:383,417:800,1:0.0012:2,0:1:0:25:0:0.4794:0:60:2:0.0013:0:1 +6 32190620 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=10.98747;LSEQ=AGGAAAACTCACATCACTGG;RSEQ=CCCTCTTCCTATTCTTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:37:12,25:136,224:360,37:0.0927:2,2:27.9:1:31.5:1:0.59475:1.26415:59.2:36:0.0921:0:1.2 1/0:232:123:38,85:29,80:109,123:0.5302:2,2:21.7:1:31:1:0.56177:1.23:59.7:60.5:0.5261:0:1.1 +6 32190941 . G A 34 p8;q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.26485;SOR=0;LSEQ=TCTTCTAGGTGCTCCTGAGA;RSEQ=ACCTGCCCACAGCAGCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:3:3,0:51,246:297,3:0.01:2,0:7:1:21.7:1:0.00557:0:60:2:0.0068:0:1 0/0:223:0:0,0:60,163:223,0:0:2,0:22.5:1:30.5:1:1:0:60:54.75:1:0:0.1 +6 32190994 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53312;SOR=0;LSEQ=AACCACCTCTTCTTCACATC;RSEQ=GTCCCCACTCTCCACATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:0,2:2,121:123,2:0.0159:1,0:22.5:1:31:1:1:0:60:4:0.0163:0:2 0/0:73:0:0,0:2,71:73,0:0:1,0:24.6:1:29.5:1:1:0:60:72:1:0:0.2 +6 32191041 . G A 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19218;SOR=3.39216;LSEQ=CCCCAGCCCCAGTGCCCTCC;RSEQ=TCCCAGTTACTAATCCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:0,3:2,60:62,3:0.0462:1,0:12.7:1:32.7:1:1:0:60:6:0.0476:0:1 0/1:28:4:1,3:2,22:24,4:0.1429:2,2:28.8:1:31.3:1:0.38217:3.44:60:8:0.1429:0:1.5 +6 32191457 . G A 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCACCCCTGGCACCAGGCCC;RSEQ=AAGCAGCTCCATGGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:195,0:195,0:0:1,0:24.3:1:29.5:1:1:0:60:23.375:1:0:0.1 0/1:82:25:24,1:55,2:57,25:0.3049:1,1:26.2:1:29.7:1:1:1.14387:60:50:0.3086:0:1 +6 32191544 . C T 159 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=72.44028;LSEQ=TCCATCCAGCATCCCTCACA;RSEQ=GGCCTGGGGCTTGGCCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:964:1:0,1:675,288:963,1:0.001:2,0:1:0:29:0:0.29979:0:60:2:0.001:0:1 0/1:656:46:28,18:413,197:610,46:0.0701:2,2:19.1:1:28.9:1:0.3338:1.34713:60:45:0.069:0:1.2 +6 32191581 . T A 260 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=536.16388;LSEQ=CTCTTCCCCCACCCCACTGA;RSEQ=CATCCTCCTAAGGGAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1594:2:1,1:877,711:1588,2:0.0013:2,2:38:1:31:1:1:1.2333:60:4:0.0013:0:1 0/1:1252:501:286,215:407,342:749,501:0.4002:2,2:25.9:1:29:1:0.35313:1.12:59.9:70.571:0.4026:0:1.5 +6 32191607 . C T 240 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=175.38493;LSEQ=TCCTAAGGGAGCTGGGTCCC;RSEQ=TCACCTCACCCACGCCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1919:2:0,2:952,963:1915,2:0.001:2,0:1:0:27:1:0.49976:0:57.5:4:0.0011:0:1.5 0/1:1628:252:137,115:702,672:1374,252:0.1548:2,2:26.4:1:30.2:1:0.37279:1.14:58.9:251:0.1553:0:1.9 +6 32191620 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.68615;LSEQ=GGGTCCCCTCACCTCACCCA;RSEQ=GCCATGCCTCACCTCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1938:210:103,107:812,912:1724,210:0.1084:2,2:25.2:1:30.7:1:0.60891:1.08:59.2:209:0.109:0:1.2 0/1:1690:416:201,215:645,628:1273,416:0.2462:2,2:26:1:29.7:1:0.42922:1.09855:59.6:137.667:0.2473:0:1.2 +6 32191658 . TAGC T 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=10.000;MSILEN=3;SSF=0;SOR=0.52712;LSEQ=GGTCTGACCACTGAGACACA;RSEQ=AGCAGCAGCAGCAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1512:488:203,285:435,550:985,488:0.3228:2,2:34.8:1:31.7:1:0.37153:1.11031:59.9:121:0.3248:0.0053:0.3 0/1:1355:272:125,147:444,460:904,272:0.2007:2,2:34.8:1:30.7:1:0.36914:1.13497:59.8:544:0.2021:0:0.5 +6 32191730 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.72371;LSEQ=CAGCCCCTTCTCCAAGCCCC;RSEQ=GTCCCTGTCCCTCTTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:321:116,205:185,348:533,321:0.3759:2,2:24.9:1:31.2:1:0.71166:1.06:59.7:39.125:0.374:0:1.2 1/0:689:351:122,229:125,213:338,351:0.5094:2,2:23.7:1:29.8:1:0.57826:1.1014:59.9:42.875:0.5052:0:1.2 +6 32191822 . G A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01047;SOR=Inf;LSEQ=TGCCCCTCTTCTTCCTCCTC;RSEQ=GCCTGCTGCAAGCCTCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:4,199:203,0:0:1,0:24.1:1:31.2:1:1:0:59.7:49.75:1:0:0.2 0/1:97:4:1,3:3,90:93,4:0.0412:1,2:28.8:1:29.8:1:0.15732:9.42:60:8:0.0412:0:1 +6 32877073 . A G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=0.21684;LSEQ=AATTTACTGAATGTTCATTC;RSEQ=TTTTAACTTTTTTAAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:32:20,12:126,34:160,32:0.1667:2,2:22.8:1:30.1:1:0.06797:2.21301:60:64:0.1675:0:1.1 0/1:169:7:5,2:111,50:161,7:0.0414:2,2:28.3:1:30.7:1:1:1.13:60:14:0.0414:0:1 +6 32877076 . T C 25 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.21274;SOR=Inf;LSEQ=TTACTGAATGTTCATTCATT;RSEQ=TAACTTTTTTAAGTGGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:154,51:205,0:0:2,0:22.5:1:30.8:1:1:0:60:410:1:0:0.3 0/1:176:2:1,1:119,55:174,2:0.0114:2,2:10:0:25:1:0.53636:2.15327:60:4:0.0114:0:1 +6 32877173 . A G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01561;SOR=0.70456;LSEQ=CATTCTTGAATATTCACTAT;RSEQ=AGCCTGATGCTATGCGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:202:107,95:121,106:227,202:0.4698:2,2:23.5:1:31.8:1:1:1.01346:60:32.667:0.4656:0:1.2 0/1:380:146:74,72:116,118:234,146:0.3842:2,2:24.4:1:30.8:1:0.91603:1.05:60:72:0.384:0:1.2 +6 32877176 . C T 57 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06386;SOR=0;LSEQ=TCTTGAATATTCACTATAAG;RSEQ=CTGATGCTATGCGAGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:5:0,5:225,206:431,5:0.0115:2,0:6.4:1:24.6:1:0.0259:0:60:4:0.0094:0:2 0/0:388:0:0,0:191,197:388,0:0:2,0:23.5:1:30.5:1:1:0:60:54.429:1:0:0.5 +6 32877266 . G A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38394;SOR=0.80889;LSEQ=TATGGCTGAGTTTTTAAAAT;RSEQ=TAATTCAAGCTTTTCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:90:18,72:37,91:128,90:0.4128:2,2:21.6:1:31.5:1:0.15563:1.62281:60:180:0.4186:0:1.2 0/1:149:54:15,39:24,71:95,54:0.3624:2,2:19.8:1:29.4:1:0.84653:1.14:60:108:0.3624:0:1.2 +6 32942572 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.50198;SOR=Inf;LSEQ=GACATTGGAGCCGGGGAGGT;RSEQ=TGGGATGAGCAAGAATGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:9,0:0:0,0:32.1:1:32.7:1:1:0:60:18:1:0:0 0/1:14:2:1,1:4,8:12,2:0.1429:2,2:9:1:28:1:1:1.90:60:4:0.1429:0:1 +6 32944987 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAAGTTATAGGGTGGAAA;RSEQ=ACAGGCATAGGCCACCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:10.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 32945230 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15698;SOR=Inf;LSEQ=CTTCTGCAGCGGAAGATGGA;RSEQ=AACCGTGATTACCGGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:56,24:80,0:0:2,0:21.2:1:32.1:1:1:0:60:25.667:1:0:0.2 0/1:53:2:1,1:37,14:51,2:0.0377:2,2:29.5:1:27:1:0.48984:2.58752:60:4:0.0377:0:2 +6 32945235 . G T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56298;SOR=3.09216;LSEQ=GCAGCGGAAGATGGAGAACC;RSEQ=TGATTACCGGGATGCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:1:0,1:63,32:95,1:0.0104:2,0:1:0:26:0:0.34375:0:60:2:0.011:0:1 0/1:63:2:1,1:41,20:61,2:0.0317:2,2:25:1:31:0:1:2.0249:60:4:0.0323:0:1 +6 32945243 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1641;SOR=Inf;LSEQ=AGATGGAGAACCGTGATTAC;RSEQ=GGGATGCACAGGAGTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:68,36:104,0:0:2,0:22.3:1:30.3:1:1:0:60:33.667:0.9902:0:0.2 0/1:72:2:1,1:45,24:69,2:0.0278:2,2:41:1:29.5:1:1:1.85749:60:4:0.0286:0:2 +6 32945254 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19012;SOR=Inf;LSEQ=CGTGATTACCGGGATGCACA;RSEQ=GAGTTTGCTGCTGATGTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:67,41:108,0:0:2,0:26.8:1:32.1:1:1:0:60:26:1:0:0.2 0/1:84:2:1,1:48,34:82,2:0.0238:2,2:11:0:30.5:1:1:1.40585:60:4:0.0238:0:1 +6 32945296 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5021;SOR=0;LSEQ=CTTATGTTCTCCAACTGCTA;RSEQ=AAGTACAATCCCCCAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:50,64:114,2:0.0172:2,2:10.5:1:30.5:1:1:1.28:60:4:0.0177:0:1 0/0:96:0:0,0:40,56:96,0:0:2,0:25.1:1:27.8:1:1:0:59.7:47:1:0:0.2 +6 33286403 . A T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28606;SOR=0;LSEQ=TTAAGCTTTTTTTTTTTTTT;RSEQ=AAGAAACACCACCAAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:3:3,0:55,2:57,3:0.0484:1,0:21.3:1:24.7:1:1:0:53.3:2:0.0357:0:2.7 0/0:38:0:0,0:36,1:37,0:0:1,0:24.8:1:26.1:1:1:0:59:11.333:1:0:0.7 +6 33286430 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50419;SOR=0;LSEQ=CACCACCAAAAGGGGATTAG;RSEQ=TTAGTCCATCCCTTCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:2,0:99,10:109,2:0.018:2,0:19.5:1:30:1:1:0:55:4:0.0204:0:3.5 0/0:88:0:0,0:80,8:88,0:0:2,0:37:0:16:0:1:0:46:0:0:0:8 +6 33286460 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=CCCTTCCTCAGTCATCTGCT;RSEQ=CCCACCTTCCTCCAAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:136,41:177,0:0:2,0:26.7:1:30.2:1:1:0:59.7:34.4:1:0:0.2 0/1:179:2:1,1:133,44:177,2:0.0112:2,2:29.5:1:27:1:0.44065:3.00017:60:4:0.0114:0:3 +6 33286501 . C T 50 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37452;SOR=3.76209;LSEQ=ATCCCAGAACATTCTGGAGG;RSEQ=AGGGAGAAGGGGAGGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:1:0,1:199,111:310,1:0.0032:2,0:1:0:23:0:0.36013:0:60:2:0.0033:0:1 0/1:333:4:1,3:210,119:329,4:0.012:2,2:7.3:1:25:1:0.14126:5.26739:60:8:0.0123:0:1 +6 33287100 . C T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07381;SOR=Inf;LSEQ=AGTTCCCCAGTATTGCTCTC;RSEQ=GAAAGTCCCCTGCAATCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:206,122:328,0:0:2,0:22.9:1:30.9:1:1:0:60:64.6:1:0:0.1 0/1:238:3:1,2:156,79:235,3:0.0126:2,2:9:1:24.7:1:0.26773:3.92486:60:6:0.0127:0:1 +6 33287183 . T C 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTAATGGCCCTGATCCTGT;RSEQ=TGCTTCTTCTCCTTCCGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:807:0:0,0:440,367:807,0:0:2,0:26:1:30.8:1:1:0:60:88.667:1:0:0.1 0/1:785:46:28,18:396,342:738,46:0.0586:2,2:25.5:1:30.3:1:0.36401:1.34:60:45:0.0583:0:1.1 +6 33287796 . G C 201 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CCCTTGACATACCTGCTGCT;RSEQ=CTTCTTCCTCTTCGTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1437:0:0,0:793,643:1436,0:0:2,0:25.1:1:32.3:1:1:0:59.9:88.75:0.9993:0:0.1 0/1:1464:104:52,52:738,616:1354,104:0.071:2,2:27.8:1:30.1:1:0.41423:1.1979:60:33.667:0.0699:0:1.1 +6 33287897 . TTCC T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.89443;SOR=0.95123;LSEQ=GTGGCCTCCTCCTCTTCTTC;RSEQ=TCCTCCTCCTCCTCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:987:30:12,18:409,547:956,30:0.0304:2,2:25.1:1:29.9:1:0.85236:1.12141:59.8:60:0.0312:0.0071:0.3 0/1:967:28:15,13:431,505:936,28:0.029:2,2:21.8:1:30.7:1:0.44828:1.35:59.1:56:0.0296:0.0052:0.4 +6 33288067 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06872;SOR=Inf;LSEQ=GTTTGGTTCTTGCTTTCCTT;RSEQ=TCATGCTCCCCCATCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:0:0,0:146,223:369,0:0:2,0:23.5:1:32.6:1:1:0:60:45.125:1:0:0.5 0/1:257:3:1,2:91,162:253,3:0.0117:2,2:17:1:25.7:1:1:1.12297:60:2:0.008:0:2 +6 33288075 . C A 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.30527;LSEQ=CTTGCTTTCCTTCTCATGCT;RSEQ=CCCCATCAGTCAACCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:163:73,90:71,109:180,163:0.4752:2,2:22.5:1:29:1:0.32634:1.24:60:39.75:0.4718:0:1.1 0/1:222:48:21,27:63,111:174,48:0.2162:2,2:22.7:1:28.8:1:0.40108:1.37:60:96:0.2222:0:1.1 +6 33288086 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1547;SOR=Inf;LSEQ=TCTCATGCTCCCCCATCAGT;RSEQ=AACCTGGACTCCCTGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:130,170:300,0:0:2,0:24.5:1:32.2:1:1:0:59.9:49:1:0:0.6 0/1:195:2:1,1:78,115:193,2:0.0103:2,2:7.5:1:28:1:1:1.47:60:4:0.0104:0:1 +6 33288271 . A G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21658;LSEQ=CTTTTGTCTTGCAACATTGC;RSEQ=TATTTGGAGATGACCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:830:386:194,192:218,224:442,386:0.4651:2,2:26.8:1:30.8:1:0.83448:1.04:59.9:54.143:0.4662:0:1.1 0/1:859:136:68,68:361,359:720,136:0.1583:2,2:28.4:1:29.8:1:1:1.00556:60:33:0.1562:0:1.1 +6 33288506 . C A 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAGAGGCATCCCACCAAC;RSEQ=CCCTACCTGGCCTATAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:400:0:0,0:239,161:400,0:0:2,0:25.6:1:31.2:1:1:0:60:132.333:1:0:0.1 0/1:400:30:16,14:216,153:369,30:0.075:2,2:24.8:1:27.9:1:0.57123:1.23462:60:29:0.0734:0:1.3 +6 33289316 . G A 60 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.45258;SOR=0.42286;LSEQ=GGACCACCTCAGGGTGGTCT;RSEQ=CTGTCTGCATCTTACAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:5:4,1:161,234:395,5:0.0125:2,2:9.8:1:26:1:0.16436:5.79:60:10:0.0127:0:1 0/0:377:2:2,0:156,219:375,2:0.0053:2,0:1:0:22.5:1:0.175:0:60:4:0.0053:0:1 +6 33289356 . A G 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13192;SOR=0;LSEQ=TTCAAGGAACTAGAAGGTTC;RSEQ=GGGGAAGAAGGAAGGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:4:3,1:140,184:324,4:0.0122:2,2:25.5:1:30.5:1:0.32149:3.93:60:8:0.0126:0:1 0/0:266:0:0,0:115,151:266,0:0:2,0:24.1:1:30.2:1:1:0:60:87.667:1:0:0.1 +6 33289411 . T A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07627;SOR=Inf;LSEQ=GGGTTGAGAGAAAGGGGAGG;RSEQ=GGGGTTAGTGGGAAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:330:0:0,0:225,103:328,0:0:2,0:22.7:1:29.6:1:1:0:60:24.231:1:0:0.1 0/1:244:3:2,1:169,72:241,3:0.0123:2,2:20.3:1:23.3:1:1:1.1728:60:2:0.0084:0:1 +6 33289707 . G A 60 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72805;SOR=1.51239;LSEQ=TGTTAGCGGTGGCCATAGGG;RSEQ=ATCAAATCCCCCGGAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:3:2,1:143,260:403,3:0.0074:2,2:14:1:19:1:0.29106:3.62:60:0.5:0.0025:0:2.7 0/1:450:5:4,1:172,273:445,5:0.0111:2,2:10.2:1:26:1:0.07922:6.32:60:10:0.0114:0:1 +6 33289739 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11506;SOR=Inf;LSEQ=CGGAGGGAGGAAGTGGTGGG;RSEQ=ATTTCAGAATTCCTGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:70,194:264,0:0:2,0:24.3:1:31.7:1:1:0:60:131:1:0:0.1 0/1:251:3:1,2:70,178:248,3:0.012:2,2:20:1:27.7:1:1:1.27:60:6:0.0122:0:1 +6 33289931 . T TG 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGGGCCCTTCAAGTGGTG;RSEQ=GGGGGGGGGGCAAACCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:1,6:7,2:0.1818:2,2:30:1:33.5:1:0.41667:4.58:60:4:0.2:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:33:0:30:0:1:0:60:2:1:0:0 +6 33290402 . G A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4025;SOR=0.38064;LSEQ=AACTGATCAAAAGTCCCCCC;RSEQ=CACCGCGCTACGCTCTCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:13,0:12,0:12,13:0.52:0,1:22.1:1:27.8:1:1:0:60:3.333:0.5:0:1.2 0/1:7:2:1,1:5,0:5,2:0.2857:0,2:40:1:28.5:1:0.28571:0:60:4:0.2857:0:2 +6 33290547 . T A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.08244;SOR=0.75337;LSEQ=GGACAGGAAGGTACCACAGC;RSEQ=TTCCCCTCAGACTCAGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:358:206:164,42:116,35:151,206:0.5754:2,2:24.4:1:28.7:1:0.6026:1.18:60:8.81:0.5799:0:1.7 1/0:295:149:123,26:120,25:145,149:0.5051:2,2:21.2:1:29.2:1:1:1.01459:60:20.286:0.5145:0:1.6 +6 33290825 . A G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54479;SOR=0.81377;LSEQ=GCTTCCTGTGGCCGGAGGTG;RSEQ=CAGTAGGCCCGCCCCGCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:112:61:3,58:1,50:51,61:0.5446:1,1:22.4:1:33:1:0.62432:2.57:60:122:0.5446:0:1.4 0/1:71:35:1,34:1,35:36,35:0.493:1,1:22.8:1:31.4:1:1:1.03:60:34:0.4857:0:1.3 +6 33290827 . A T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15806;SOR=0;LSEQ=TTCCTGTGGCCGGAGGTGAC;RSEQ=GTAGGCCCGCCCCGCGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:5:0,5:4,101:105,5:0.0455:1,0:17.8:1:31.2:1:1:0:60:10:0.0463:0:1 0/0:68:0:0,0:2,66:68,0:0:1,0:25.4:1:30.7:1:1:0:60:33:1:0:0.7 +6 33290872 . G A 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0318;SOR=0.25766;LSEQ=CAGTGCGGCCCACATAGTCA;RSEQ=CGGTCTCTTCCAGGTCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:20:0,20:0,24:24,20:0.4545:1,1:24.5:1:29.8:1:1:0:60:40:0.4762:0:2 0/1:23:4:0,4:0,19:19,4:0.1739:1,0:24:1:29.8:1:1:0:60:8:0.1818:0:3 +6 34294906 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49607;SOR=Inf;LSEQ=GTCATCCAAATGATTGATAA;RSEQ=GTCAAGCAAGTCACATGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:29,32:61,0:0:2,0:28.6:1:32:1:1:0:44.4:60:1:0:0.1 0/1:63:2:1,1:28,33:61,2:0.0317:2,2:42:1:29:1:1:1.18:44:4:0.0317:0:1 +6 34617036 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22835;SOR=0;LSEQ=TAGGTCACGTAACTCTGAAA;RSEQ=GGTCAAAGATATTGATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:115,39:154,2:0.0127:2,2:26.5:1:32:1:0.4483:2.92406:60:4:0.0129:0:1 0/0:171:0:0,0:121,50:171,0:0:2,0:23.3:1:29.6:1:1:0:60:170:1:0:0.1 +6 34617144 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.05235;LSEQ=GAGAAGTATAATAGAACTGG;RSEQ=CTCCAAATTAAGTCTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:273:240:108,132:15,18:33,240:0.8791:2,2:24.3:1:31.6:1:1:1.01845:59.9:79:0.8778:0:1.1 0/1:248:68:25,43:79,100:179,68:0.2742:2,2:27.2:1:31.5:1:0.31565:1.35712:60:136:0.2753:0:1.1 +6 34617243 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51198;SOR=0;LSEQ=GTTTTATGACGTTCCTAGTT;RSEQ=AGTATCACAATCAAGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:6,72:78,2:0.025:2,2:34:1:28.5:1:0.16835:11.19:60:4:0.025:0:1 0/0:56:0:0,0:9,47:56,0:0:2,0:23.1:1:29.1:1:1:0:60:112:1:0:0 +6 34803947 . C T 93 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00022;SOR=0;LSEQ=ATGTAGATCACTCCACCAGC;RSEQ=CCCAGTGCCCAGCAGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:0,8:1:0,2:19.1:1:31.1:1:1:0:60:16:1:0:1.1 0/1:19:4:3,1:10,5:15,4:0.2105:2,2:20:1:30:1:1:1.47:60:8:0.2222:0:1 +6 34804012 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.53529;SOR=Inf;LSEQ=GGGCAACAGCAACAGCAGCA;RSEQ=CAGCCGCCTCAGCCAGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:35.8:1:33.2:1:1:0:60:38:1:0:0.3 0/1:35:2:1,1:14,19:33,2:0.0571:2,2:38.5:1:28.5:1:1:1.35:60:4:0.0571:0:1 +6 35758334 . C G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAAGGAAGTTAGAATTTG;RSEQ=GGGTTATGTACCATCTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:33:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 35758979 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=Inf;LSEQ=TGGTCATTGGTAGAGGCTGC;RSEQ=GTTGTCAGAATCCAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:37:1:29.2:1:1:0:60:5:1:0:0 0/1:8:2:1,1:3,3:6,2:0.25:2,2:12:1:31.5:1:1:1:60:4:0.25:0:1.5 +6 35759063 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57158;SOR=1.46714;LSEQ=GCTACATCCTGATAAACACA;RSEQ=TGTTTAAGTTGAAAATATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:1,5:6,9:15,6:0.2857:2,2:30.8:1:33.8:1:0.61262:3.16415:60:12:0.3158:0:1.2 0/1:35:13:6,7:12,10:22,13:0.3714:2,2:29.5:1:31.6:1:0.73322:1.38652:60:26:0.3714:0:1.2 +6 35759082 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51429;SOR=Inf;LSEQ=ATTGTTTAAGTTGAAAATAT;RSEQ=GTAAGTTGAAAATACGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:5,17:22,0:0:2,0:21.2:1:30.5:1:1:0:59.4:44:1:0:0.5 0/1:34:2:1,1:16,16:32,2:0.0588:2,2:12.5:1:28:1:1:1:60:4:0.0588:0:1 +6 36104803 . T C 35 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=8.000;MSILEN=1;SSF=1;SOR=0.57733;LSEQ=ACTTTATTTAAATAACTGTC;RSEQ=TTTTTTTCTTAATGTGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:33:1:35:0:1:0:60:4:0.6667:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:14:0:26:0:1:0:60:2:0.5:0:1 +6 36645466 . G A 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51422;SOR=1.62192;LSEQ=GGCATTTTTGTCATTTTGGA;RSEQ=CCACAGAAATAAAGGATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:6:6,0:84,0:84,6:0.0667:1,0:14.5:1:30.3:1:1:0:60:12:0.0674:0:2 0/1:48:5:5,0:43,0:43,5:0.1042:1,0:23.2:1:30.4:1:1:0:60:10:0.1064:0:1 +6 36645549 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.03177;SOR=Inf;LSEQ=ACTATAGTCATTTCTTTGCT;RSEQ=CATGATCTGAGTTAGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:347,93:440,0:0:2,0:22.7:1:31.9:1:1:0:60:54:1:0:0.2 0/1:323:4:2,2:245,74:319,4:0.0124:2,2:16:1:27.5:1:0.2364:3.29547:60:8:0.0125:0:1.5 +6 36645588 . A C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.22022;LSEQ=ACCAGACTTCTCTGAGCCCC;RSEQ=GTTTCCCCAGCAGTGTATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:791:35:22,13:481,272:753,35:0.0442:2,2:32.1:1:30.7:1:1:1.04488:60:70:0.045:0:1.1 0/1:642:161:96,65:307,174:481,161:0.2508:2,2:24.8:1:29.4:1:0.34762:1.19428:60:52.667:0.2496:0:1.2 +6 36645696 . A G 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.76032;LSEQ=AAGCTGCTGCAACCACAGGG;RSEQ=TTTCTTCTGTTCAGGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:984:146:55,91:353,484:837,146:0.1484:2,2:26.1:1:31.3:1:0.31831:1.2065:60:47.667:0.1482:0:1.2 0/1:905:294:133,161:261,349:610,294:0.3249:2,2:25.3:1:30.8:1:0.51947:1.10:60:293:0.3281:0:1.2 +6 36648084 . C CGTGT 92 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=38;MSI=21.000;MSILEN=2;SSF=0.55045;SOR=0;LSEQ=CGCGTGCGTGTCTGCGCGGG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:8,0:13,0:13,8:0.3077:1,0:11:1:30.9:1:1:0:52.9:16:0.32:0.2308:1.3 0/0:4:0:0,0:4,0:4,0:0:0,0:25:1:29.3:1:1:0:51.8:8:1:0:0.8 +6 36648117 . G GTC 46 v3;MSI12;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=18.000;MSILEN=2;SSF=0.01437;SOR=Inf;LSEQ=GTGTGTGTGTGTGTGTGTGT;RSEQ=TGTGTCTGTGTCAGAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:31,0:0:1,0:18.2:1:32.5:1:1:0:56.7:30:1:0:0.5 0/1:11:3:3,0:8,0:8,3:0.2727:0,0:22:1:29.2:1:1:0:54:6:0.2727:0.1818:1 +6 36648275 . C CAG 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=5.95748;LSEQ=ACGCGCAGCCGGAGTGGAAG;RSEQ=AGTTTTGGCGGGCGAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:863:111:65,46:471,279:750,111:0.1286:2,2:26.5:1:30.9:1:0.40252:1.19445:59.9:110:0.1305:0.022:0.2 0/1:786:368:217,151:247,169:416,368:0.4682:2,2:26.2:1:30:1:0.942:1.017:59.9:367:0.4699:0.0814:0.3 +6 36648364 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.58723;LSEQ=TCTGCCCACGCACCTCCCAC;RSEQ=CCGCGCGTGATTTCCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1222:111:57,54:517,593:1110,111:0.0908:2,2:25.1:1:30.9:1:0.36974:1.21:60:26.75:0.0901:0:1.2 0/1:1063:381:176,205:326,356:682,381:0.3584:2,2:26.5:1:30.1:1:0.6539:1.06653:59.9:41.333:0.3612:0:1.2 +6 36650267 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48538;SOR=0;LSEQ=CCCTTTAAACTTGGTGTGAA;RSEQ=TTACCAAGAGCCTCCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:9,0:9,2:0.1818:0,0:23.5:1:32:0:1:0:60:4:0.1818:0:1 0/0:8:0:0,0:7,1:8,0:0:2,0:20.8:1:30.8:1:1:0:55.1:16:1:0:0 +6 36650436 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0652;SOR=Inf;LSEQ=GAAACTGCAAGTTGGGACTT;RSEQ=TCCCTAGGAAAATCCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:249,39:288,0:0:2,0:23.7:1:32.3:1:1:0:60:71:1:0:0.1 0/1:195:3:1,2:164,28:192,3:0.0154:2,2:26:1:29.7:1:0.06232:11.46954:60:6:0.0155:0:1 +6 36650467 . C T 75 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00298;SOR=Inf;LSEQ=AATCCAGTTGCTGCCAAGGT;RSEQ=GTGCAGTCACTCAGCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:491:0:0,0:373,118:491,0:0:2,0:24.1:1:31.4:1:1:0:60:69.143:1:0:0.1 0/1:382:7:2,5:257,118:375,7:0.0183:2,2:5.3:1:26.9:1:0.03765:5.41829:60:14:0.0185:0:1.4 +6 36650547 . G A 226 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CATGGGCAAACTCACTCTCC;RSEQ=TTTTCCCTCTCCTGAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1074:163:79,84:442,468:910,163:0.1518:2,2:26.1:1:30.8:1:1:1.00422:60:162:0.1524:0:1.1 0/0:938:0:0,0:470,465:935,0:0:2,0:25.4:1:30.3:1:1:0:60:132.571:0.9968:0:0.4 +6 36650565 . G C 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=4.60672;LSEQ=CCGTTTTCCCTCTCCTGAAG;RSEQ=GGGAGGAGAGGAGCCAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1100:56:25,31:482,559:1041,56:0.0509:2,2:26.4:1:30.4:1:0.89082:1.06915:60:55:0.0508:0:1.1 0/1:1029:204:99,105:409,410:819,204:0.1983:2,2:22.7:1:30.1:1:0.75445:1.05799:60:101:0.1992:0:1.2 +6 36650659 . G A 54 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10421;SOR=5.71163;LSEQ=GGCAACACGAGGCAGGGGCT;RSEQ=CCAGGTGTCTAGACTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:1:1,0:189,343:532,1:0.0019:2,0:1:0:21:0:0.35647:0:60:2:0.0019:0:1 0/1:470:5:4,1:156,309:465,5:0.0106:2,2:5.8:1:23.4:1:0.04795:7.89:60:10:0.0107:0:1 +6 36650706 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16537;SOR=Inf;LSEQ=GATGTGCCTGGCAGGATGTG;RSEQ=CTCAGCCTGGGAGAAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:8,197:205,0:0:1,0:25.2:1:32.4:1:1:0:59.9:33.167:1:0:0.1 0/1:141:2:0,2:8,131:139,2:0.0142:2,0:20:1:29.5:1:1:0:60:4:0.0144:0:1 +6 36651971 . C A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.49362;LSEQ=GTGGACAGCGAGCAGCTGAG;RSEQ=CGCGACTGTGATGCGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:34:20,14:301,278:579,34:0.0555:2,2:25.1:1:30.4:1:0.48311:1.32:60:68:0.0576:0:1.2 0/1:579:121:72,49:256,200:456,121:0.209:2,2:24.5:1:28.4:1:0.53663:1.15:59.9:120:0.2109:0:1.1 +6 36652339 . C G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.43773;LSEQ=GACAGGTGCGGACATGTGCA;RSEQ=GGAAGGACTTTGTAAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:81:33,48:130,200:330,81:0.1971:2,2:23.9:1:32.1:1:0.89922:1.06:59.7:80:0.198:0:1.2 0/1:347:130:51,79:84,133:217,130:0.3746:2,2:23.4:1:30.5:1:1:1.02:60:129:0.3772:0:1.2 +6 36652366 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17917;SOR=Inf;LSEQ=ACTTTGTAAGGGACCAGGAT;RSEQ=CTCAGAATCCATGGTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:96,169:265,0:0:2,0:24:1:30.1:1:1:0:59.9:65.25:1:0:0.3 0/1:195:2:1,1:55,138:193,2:0.0103:2,2:21.5:1:28.5:1:0.49294:2.50:60:4:0.0105:0:2 +6 36653438 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18918;SOR=Inf;LSEQ=CCATTGGCCCCAGGGAAGGG;RSEQ=GTCCTGGCCCCCCACTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:191,37:228,0:0:2,0:24.8:1:30.1:1:1:0:59.8:227:1:0:0.1 0/1:176:2:1,1:140,33:173,2:0.0114:2,2:26:1:28.5:1:0.35172:4.19447:60:4:0.0116:0:1.5 +6 36653471 . C T 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43508;SOR=2.17228;LSEQ=CACTGTCTTCCTCAGTTGGG;RSEQ=AGCTCCGCCGCGTCCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:2:0,2:284,115:399,2:0.005:2,0:1:0:24.5:1:0.08461:0:60:4:0.005:0:1 0/1:371:4:1,3:254,113:367,4:0.0108:2,2:10:1:25.8:1:0.09244:6.70559:60:8:0.011:0:1.3 +6 36653597 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=7.99734;LSEQ=ATCCGCCCACAGGAAGCCTG;RSEQ=AGTCCTGGAAGCGCGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:17:6,11:229,386:615,17:0.0269:2,2:29.7:1:29.2:1:1:1.08752:60:34:0.0273:0:1.1 0/1:651:118:45,73:221,311:532,118:0.1813:2,2:26.1:1:27.8:1:0.5354:1.15252:59.9:58:0.181:0:1.2 +6 37137426 . C A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGAGCCCTTGACCCAAAA;RSEQ=CCTCAGCGAAACGGAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:10:1:27:1:1:0:60:4:1:0:1 +6 37138023 . GGCA G 79 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=10.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCAGCGGCGGCGGCGGGACC;RSEQ=GCAGCAGCAGCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38.5:1:33:0:1:0:60:4:1:0:0.5 1/1:6:6:2,4:0,0:0,6:1:0,2:30:1:30.7:1:1:0:60:12:1:0:0.2 +6 37138220 . C G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23955;SOR=1.42231;LSEQ=CCTTCCGCGCCAGCCGCAGC;RSEQ=ACAGCCGCAACGCCACCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:39:39,0:60,1:61,39:0.39:1,1:25:1:30.9:1:1:0:60:78:0.3939:0:1.1 0/1:86:41:37,4:40,5:45,41:0.4767:2,2:26:1:30:1:1:1.15:60:82:0.4767:0:1.1 +6 37139322 . T C 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20271;SOR=2.12812;LSEQ=CTCGGCCCGGCCCGGCCCAG;RSEQ=CCGGAGGCCTCGGCCAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:13:3,10:3,23:26,13:0.3333:2,2:23.3:1:32.2:1:0.38049:2.25:57.1:26:0.3333:0:1.1 1/0:27:14:4,10:2,11:13,14:0.5185:2,2:18.9:1:30.2:1:0.64831:2.14:60:28:0.5185:0:1.1 +6 37140501 . C T 80 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21416;SOR=2.76979;LSEQ=GGCCTCAAGTTTTGGGTCTG;RSEQ=GGCCAGCTGTGTTTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:2:1,1:240,261:501,2:0.004:2,2:31:1:20.5:1:1:1.09:60:1:0.002:0:4.5 0/1:731:8:2,6:352,371:723,8:0.0109:2,2:15.5:1:26.8:1:0.28832:2.84291:57.1:16:0.0111:0:1.5 +6 37140599 . C T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11492;SOR=0;LSEQ=TGCTTTGGGTTGGAGAGATG;RSEQ=CGTAAGGTGCGCCTCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:3:2,1:83,178:261,3:0.0113:2,2:27.7:1:23.7:1:0.24335:4.26:60:2:0.0078:0:3 0/0:279:0:0,0:82,197:279,0:0:2,0:24.7:1:30.3:1:1:0:60:38.857:1:0:0.2 +6 37140684 . T A 59 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.41506;SOR=2.45637;LSEQ=GAAGGGATTTTTTTTTTTTT;RSEQ=AAAAGAAAGAGTTATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:2:1,1:97,56:153,2:0.0128:2,2:10:1:29:1:1:1.72563:60:4:0.0129:0:1 0/1:129:4:1,3:86,34:120,4:0.031:2,2:7.8:1:29.5:1:0.0791:7.44867:60:4:0.0259:0:1.5 +6 37140733 . C A 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=Inf;LSEQ=CTTCTTTGTGCTTGTTTTTG;RSEQ=TAAAAGTGTGTTTTCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:224,81:305,0:0:2,0:25.3:1:31.7:1:1:0:60:29.5:1:0:0.2 0/1:352:12:9,3:234,105:339,12:0.0341:2,2:26.1:1:28.8:1:0.76173:1.35:60:24:0.0354:0:1.3 +6 37141622 . T C 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00117;SOR=Inf;LSEQ=TCCCTGGGACCCCAGACTTG;RSEQ=GGGCCTCTGAGAAGCAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:122,15:137,0:0:2,0:22.6:1:30.1:1:1:0:60:67.5:1:0:0.1 0/1:107:8:7,1:89,10:99,8:0.0748:2,2:23.6:1:31:1:0.59319:1.26834:60:7:0.066:0:1.1 +6 37141696 . C A 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATTCATAACCTCGTCTAT;RSEQ=CTCCTTTCTGCAGAATGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:502:0:0,0:305,195:500,0:0:2,0:25.9:1:31.8:1:1:0:59.9:82.333:0.996:0:0.1 0/1:568:21:11,10:338,209:547,21:0.037:2,2:20.8:1:29.1:1:0.49377:1.46913:60:42:0.0371:0:1.2 +6 37141734 . G T 93 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04962;SOR=7.22707;LSEQ=TCAGCATCTCATTAGATGGT;RSEQ=CTTGGCCCTGAGACCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:632:1:0,1:355,276:631,1:0.0016:2,0:34:0:32:0:0.43829:0:60:2:0.0016:0:1 0/1:794:9:5,4:434,351:785,9:0.0113:2,2:22:1:29.6:1:1:1.01:60:18:0.0114:0:1.2 +6 37141962 . C A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02135;SOR=Inf;LSEQ=AGTACCAGTGACACGTCTCG;RSEQ=CAAGCAGGACAGTGCTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:2,64:66,0:0:1,0:26.5:1:31.1:1:1:0:60:15.5:1:0:0.2 0/1:59:5:0,5:0,54:54,5:0.0847:1,0:28.8:1:29:1:1:0:60:10:0.0862:0:1.2 +6 39189959 . C G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=AATCTGGGAAGGTCACCAAA;RSEQ=GGGAGACGGAATGTCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:20:1:33:1:1:0:60:6:0.6:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:21.3:1:27:1:1:0:58.8:3:1:0:1.3 +6 39190287 . T A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06196;SOR=1.29596;LSEQ=CTACTTGAAAATTGCAAAAA;RSEQ=TTGATGGAGTTCAAATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:148:74,74:161,186:347,148:0.299:2,2:26.2:1:30.7:1:0.49199:1.15:60:48.333:0.2984:0:1.1 0/1:455:162:85,77:143,150:293,162:0.356:2,2:24.7:1:29.4:1:0.49344:1.16:59.8:161:0.3546:0:1.1 +6 39338315 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50014;SOR=0;LSEQ=CATATATTGGAGTCAAAAGT;RSEQ=AGTTCTGAGACAGACCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:167,23:190,2:0.0104:2,2:17.5:1:31.5:1:0.23495:7.12893:60:4:0.0106:0:1 0/0:172:0:0,0:143,29:172,0:0:2,0:23.2:1:31.3:1:1:0:60:85:1:0:0.1 +6 39338368 . C T 64 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75207;SOR=1.26046;LSEQ=ACATTTTCAAAGTGAAATGG;RSEQ=GAGAGCTGGCTAGACAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:4:1,3:277,191:468,4:0.0085:2,2:2.5:1:27.5:1:0.31042:4.33774:60:8:0.0086:0:2 0/1:469:5:1,4:278,186:464,5:0.0107:2,2:10.2:1:27.6:1:0.16328:5.95741:60:10:0.0108:0:1.6 +6 39338435 . A G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0852;LSEQ=GGCCAAAATAAATGTTTGAC;RSEQ=AGAATTCCTTTAAAAAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:597:563:257,306:13,21:34,563:0.943:2,2:26.4:1:31.2:1:0.4791:1.36:60:92.833:0.9441:0:1.1 1/0:602:352:161,191:112,138:250,352:0.5847:2,2:26.1:1:29.8:1:0.8681:1.04:60:87:0.5859:0:1.2 +6 39338532 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51204;SOR=0;LSEQ=TGCTTCTTCCTCCCTCAGGG;RSEQ=CAGTGAAGGAGCCCGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:20,131:151,2:0.013:2,2:24:1:29.5:1:0.25645:6.42:60:4:0.0135:0:1 0/0:110:0:0,0:19,91:110,0:0:2,0:20.9:1:30.9:1:1:0:60:35.667:1:0:0.2 +6 40588076 . A G 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.36185;SOR=3.12593;LSEQ=TTACAGCTAGCTCCATTGCA;RSEQ=TGAGGAAGCCCTCGGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:4,0:8,0:8,4:0.3333:0,0:27.5:1:35:0:1:0:60:8:0.3333:0:1 1/0:8:5:5,0:3,0:3,5:0.625:0,0:16:1:32.2:1:1:0:60:10:0.625:0:1.2 +6 40588223 . G A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=6.63174;LSEQ=ACACAGGATAATCGTCCCCA;RSEQ=GTGACTCTTAGCATAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:206:130:100,30:56,19:75,130:0.6311:2,2:24.4:1:30.7:1:0.73597:1.13:59.9:64:0.6275:0:1.5 1/1:124:114:78,36:7,3:10,114:0.9194:2,2:24:1:30.1:1:1:1.07629:60:113:0.9262:0:1.5 +6 40588276 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05881;SOR=Inf;LSEQ=CCAGATTGCTTTGAGAGGCT;RSEQ=TTGCCTCAGGTGGGACCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:374:0:0,0:211,163:374,0:0:2,0:27.7:1:32.1:1:1:0:60:186:1:0:0.9 0/1:239:3:2,1:135,101:236,3:0.0126:2,2:17:1:26:1:1:1.49:60:6:0.0127:0:2.7 +6 40588295 . G T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.23869;LSEQ=TGTTGCCTCAGGTGGGACCC;RSEQ=TGATCTCCCCAGTAAGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:167:89,78:102,101:203,167:0.4489:2,2:26.5:1:31:1:0.60164:1.13:59.9:166:0.4523:0:1.8 1/0:260:168:89,79:46,45:91,168:0.6462:2,2:26.1:1:29.6:1:0.79455:1.10:60:167:0.6473:0:1.7 +6 40588343 . C T 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.99225;LSEQ=AGGGATTTGGTGAGGCACCA;RSEQ=CCCTACCCACTATGCTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:108:36,72:58,93:151,108:0.417:2,2:25.8:1:29.8:1:0.43343:1.24625:60:26:0.4143:0:1.8 0/1:212:88:38,50:47,77:124,88:0.4151:2,2:25.2:1:28.8:1:0.47847:1.24:60:43:0.4095:0:1.7 +6 40588380 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=0;LSEQ=TCACAACCCAAGGGATGCAG;RSEQ=TGACAGAGCTGGTGAAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:31,121:152,2:0.013:2,2:36:1:30.5:1:0.37348:3.86:60:4:0.0133:0:2 0/0:139:0:0,0:50,89:139,0:0:2,0:22.2:1:30.7:1:1:0:60:45.333:1:0:0.8 +6 40588404 . G A 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGAGCTGGTGAAGGTGATG;RSEQ=TGACCATGTCTGGCTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:11,99:110,0:0:2,0:22.2:1:32.4:1:1:0:60:109:1:0:0.4 0/1:79:24:5,19:16,39:55,24:0.3038:2,2:19.7:1:30:1:0.58273:1.55059:60:48:0.3038:0:1.1 +6 40588579 . C T 74 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTTTCAGGTCCCCACTTG;RSEQ=GGGGGGCGGATGGGGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:19.2:1:32.2:1:1:0:60:10:0.5556:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:39:0:31:0:1:0:60:2:1:0:1 +6 41311545 . CT C 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGAAGGTGAGATAAACAA;RSEQ=TGGTTTTGGCTTGGTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:10.5:1:32.5:1:1:0:46:4:0.4:0.2:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 41311635 . T C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62114;LSEQ=GTGCAGGAGCTCAGTCTAAA;RSEQ=CAATGGCCTCTTATTACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:2,10:0.8333:0,0:20.3:1:32.7:1:1:0:57.2:20:0.8333:0:3.4 1/0:4:3:3,0:1,0:1,3:0.75:0,0:24.7:1:32.7:1:1:0:60:6:0.75:0:3 +6 41311638 . A G 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82769;LSEQ=CAGGAGCTCAGTCTAAATCA;RSEQ=TGGCCTCTTATTACTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:11,0:3,0:3,11:0.7857:0,0:20.2:1:29.4:1:1:0:57.5:4.5:0.75:0:3.3 1/0:4:3:3,0:1,0:1,3:0.75:0,0:27.7:1:32.7:1:1:0:60:6:0.75:0:3 +6 41311656 . G T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72102;SOR=1.46437;LSEQ=CAATGGCCTCTTATTACTCT;RSEQ=ATTTAACACCCCAAATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:13,0:11,0:11,13:0.5417:0,1:25.7:1:29.9:1:1:0:60:12:0.5217:0:2.6 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:22.7:1:29.6:1:1:0:60:14:0.6364:0:2.7 +6 41311790 . G T 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02688;SOR=Inf;LSEQ=AAGCCCCTTCACCTCACACT;RSEQ=GCACTCGGACCACTGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:220,81:301,0:0:2,0:23.7:1:31.2:1:1:0:59.9:26.364:1:0:0.6 0/1:207:4:1,3:138,65:203,4:0.0193:2,2:10.3:1:22:1:0.10471:6.30861:60:3:0.0146:0:2 +6 41311821 . A G 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=3.34886;LSEQ=CACTGTGTCAGCCACCTAAC;RSEQ=GGGGGTCCTGTCTTCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:425:216:133,83:121,85:206,216:0.5082:2,2:26.4:1:29.7:1:0.61899:1.13:60:29.857:0.5061:0:1.4 1/0:335:260:161,99:42,33:75,260:0.7761:2,2:25.6:1:29.3:1:0.42108:1.28:60:51:0.7774:0:1.5 +6 41311892 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=2.98137;LSEQ=CCTTCCCAACAATACCTCTG;RSEQ=GCATTTCTGCCACCCAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:515:268:120,148:107,140:247,268:0.5204:2,2:26.8:1:30.7:1:0.78995:1.06:60:43.667:0.5198:0:1.4 1/0:462:353:162,191:52,56:108,353:0.7641:2,2:25.9:1:29.8:1:0.74103:1.09458:59.9:43.125:0.7616:0:1.4 +6 41312937 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCAGAGAATCTAGGAGT;RSEQ=TAAGTGATTCTTAAAGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:30.5:1:1:0:60:4:1:0:1 +6 41460161 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50666;SOR=0;LSEQ=GCCCCACCCGGCCCCGTGAT;RSEQ=GATGGCATCTGTCTTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:96,25:121,2:0.0163:2,2:19:1:28.5:1:0.37945:3.78499:60:4:0.0164:0:1 0/0:94:0:0,0:68,26:94,0:0:2,0:21.3:1:30.8:1:1:0:60:93:1:0:0.1 +6 41460186 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22835;SOR=Inf;LSEQ=GCATCTGTCTTCTGCTTTAT;RSEQ=AAACTCACGCCGCGGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:120,51:171,0:0:2,0:24.4:1:29.7:1:1:0:59.9:41.75:1:0:0.2 0/1:157:2:1,1:103,52:155,2:0.0127:2,2:23.5:1:27:1:1:1.97156:60:4:0.0129:0:1 +6 41460195 . G T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10848;SOR=Inf;LSEQ=TTCTGCTTTATTAAACTCAC;RSEQ=CCGCGGTTCAGCCCTGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:140,64:204,0:0:2,0:24.5:1:30.4:1:1:0:60:67:1:0:0.3 0/1:187:3:2,1:115,69:184,3:0.016:2,2:34.3:1:31.7:1:1:1.20:60:6:0.0161:0:1.7 +6 41460287 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=1.81163;LSEQ=TTTCAGGGGGTTACCAAGAC;RSEQ=CAGACAGGAAACGGCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:120:60,60:139,163:302,120:0.2844:2,2:26:1:30.2:1:0.51681:1.17:60:23:0.2785:0:1.2 0/1:320:134:63,71:90,96:186,134:0.4188:2,2:26.3:1:29.1:1:0.82145:1.05634:60:66:0.4177:0:1.3 +6 41460300 . G A 136 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=33.0186;LSEQ=CCAAGACCCAGACAGGAAAC;RSEQ=GCTTTCACCCTGAGTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:1:1,0:177,226:403,1:0.0025:2,0:1:0:25:0:0.44059:0:60:2:0.0025:0:1 0/1:316:24:12,12:134,158:292,24:0.0759:2,2:28.4:1:29.8:1:0.8319:1.18:60:48:0.0764:0:1.3 +6 41634511 . A G 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=CTGGTATAACATATTTGAAA;RSEQ=TTATTTTATAACTTTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:15.5:1:35:0:1:0:60:4:0.1429:0:1 0/0:7:0:0,0:7,0:7,0:0:0,0:28:1:28.7:1:1:0:60:14:1:0:0 +6 41634620 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16491;SOR=Inf;LSEQ=TCTCCATCTGCCTTCTCTCC;RSEQ=ACCTAAGTGCGTGGCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:35,33:68,0:0:2,0:28.5:1:31.4:1:1:0:59.1:33:1:0:0.2 0/1:47:2:1,1:23,22:45,2:0.0426:2,2:30:1:28:1:1:1.04448:60:4:0.0426:0:1 +6 41634789 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2282;SOR=Inf;LSEQ=TCTTTAAGAACAGTCAGTTA;RSEQ=GGGGCTGGAGCAAAGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:81,42:123,0:0:2,0:26.4:1:31.3:1:1:0:58:122:1:0:0.1 0/1:113:2:1,1:61,50:111,2:0.0177:2,2:28:1:32.5:1:1:1.21784:51.5:4:0.0179:0:1 +6 41634834 . C A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57966;LSEQ=CACATTGTTGAAGCAGAGGC;RSEQ=ATGAATTACAAAGGCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:94,46:140,2:0.0141:2,2:24:1:30:1:1:2.0324:23:4:0.0141:0:1 0/0:122:1:1,0:72,49:121,1:0.0082:2,0:1:0:27:0:1:0:22:2:0.0083:0:1 +6 41634890 . C T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13857;SOR=0;LSEQ=GGCAACTTTGAAAATGTCTG;RSEQ=ACAACCAATGGTTTCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:4:1,3:140,96:236,4:0.0167:2,2:11.3:1:26:1:0.30901:4.34908:48.8:8:0.0172:0:1 0/0:180:0:0,0:103,77:180,0:0:2,0:27.8:1:31.4:1:1:0:58:59:1:0:0.1 +6 41635041 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50841;SOR=0;LSEQ=GGTGAAGAGGAGGAGGATGT;RSEQ=AAACTCTTAAGTACATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:44,58:102,2:0.0192:2,2:32:1:28.5:1:1:1.31:25.5:4:0.0196:0:1 0/0:77:0:0,0:36,41:77,0:0:2,0:22.5:1:31.3:1:1:0:37.3:76:1:0:0.1 +6 41635054 . A T 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51707;SOR=0;LSEQ=AGGATGTGAAACTCTTAAGT;RSEQ=CATCTGGAAAGCAGTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:44,53:97,2:0.0202:2,2:34:0:30.5:1:1:1.20:22:4:0.0202:0:1 0/0:66:0:0,0:34,32:66,0:0:2,0:27.5:1:28.4:1:1:0:41.2:132:1:0:0.1 +6 41635073 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27944;SOR=0;LSEQ=TACATCTGGAAAGCAGTCTG;RSEQ=CCCTGGAAGTGGTAGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:3:2,1:53,56:109,3:0.0268:2,2:34.7:1:30:1:0.61486:2.10:45.7:6:0.0273:0:1 0/0:73:0:0,0:39,34:73,0:0:2,0:26:1:30.5:1:1:0:49.4:72:1:0:0.1 +6 41635118 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17534;SOR=Inf;LSEQ=ACAGAAAAGAAGTAAAACTT;RSEQ=CTGCTGATGAAGATGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:79,73:152,0:0:2,0:25.6:1:32.2:1:1:0:58.5:151:1:0:0.1 0/1:110:2:1,1:57,50:107,2:0.0182:2,2:14:0:30.5:1:1:1.13863:44:4:0.0187:0:1.5 +6 41635129 . AGAT A 54 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.6404;SOR=0.45275;LSEQ=GTAAAACTTGCTGCTGATGA;RSEQ=GATGATGATGATGATGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:3:1,2:77,72:149,3:0.0197:2,2:30.7:1:34.3:1:0.61272:2.12855:59:6:0.0197:0:0 0/0:111:1:0,1:57,53:110,1:0.009:2,0:50:0:29:0:0.48649:0:50:2:0.0091:0:0 +6 41635148 . G A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.51185;SOR=0;LSEQ=AAGATGATGATGATGATGAT;RSEQ=AAGAAGATGATTTTGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:79,74:153,2:0.0129:2,2:7.5:1:28:1:1:1.06708:59:4:0.013:0:1.5 0/0:111:0:0,0:55,56:111,0:0:2,0:26.7:1:31.2:1:1:0:55.9:110:1:0:0.2 +6 41635181 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50336;SOR=0;LSEQ=TTGATGATGAGGAAACTGAA;RSEQ=AAGCGCCAGTGAAGAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:66,58:124,2:0.0159:2,2:18.5:1:32:1:1:1.13676:60:4:0.0163:0:1.5 0/0:102:0:0,0:54,48:102,0:0:2,0:21.6:1:30.3:1:1:0:59.1:50:1:0:0.1 +6 41635226 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50052;SOR=0;LSEQ=AAGACACTCCAGCCAGAAAT;RSEQ=CACAAAAGTCAGATCAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:67,68:135,2:0.0146:2,2:43:1:29.5:1:1:1.01:42.5:4:0.0147:0:1 0/0:119:0:0,0:62,57:119,0:0:2,0:24.4:1:31.3:1:1:0:57:58.5:1:0:0.1 +6 41635266 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21103;SOR=Inf;LSEQ=TGGAAAAGTCTCAAAACCAT;RSEQ=ATCAACACCAAGATCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:93,90:183,0:0:2,0:26.7:1:31.9:1:1:0:57.9:44.75:1:0:0.1 0/1:156:2:1,1:82,72:154,2:0.0128:2,2:39:0:30.5:1:1:1.13794:57:4:0.0129:0:1 +6 41635420 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50195;SOR=0;LSEQ=GTCCTGGGCACTACTGGTAA;RSEQ=TTAAGCCCAAAGATGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:36,57:93,2:0.0211:2,2:25.5:1:31.5:1:1:1.58:20:4:0.0215:0:1.5 0/0:78:0:0,0:32,46:78,0:0:2,0:27.6:1:29.4:1:1:0:56.8:156:1:0:0.1 +6 41658829 . TTGC T 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.17621;SOR=0.20011;LSEQ=GGCCCTCCGAGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:2,2:14,15:29,4:0.1212:2,2:38.3:1:30.8:1:1:1.07:60:8:0.125:0:0.3 0/1:38:1:1,0:19,18:37,1:0.0263:2,0:45:0:33:0:1:0:60:2:0.0263:0:0 +6 41658889 . C T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.04275;SOR=0.19037;LSEQ=TGTTGCTGCATGCGCTCCCG;RSEQ=TGCTCCTCCTGCTGCGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:15:5,10:1,2:3,15:0.8333:2,2:15.7:1:30.3:1:1:1:60:30:0.8333:0:1.1 0/1:21:10:4,6:3,8:11,10:0.4762:2,2:22.3:1:29.6:1:0.65944:1.73:60:20:0.4762:0:1 +6 41903614 . C T 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66063;SOR=1.86537;LSEQ=TGTGGTGTGGTTCCTGGAGG;RSEQ=AGGGAGGTGGGTGGCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:2:0,2:266,44:310,2:0.0064:2,0:1:0:24.5:1:0.02133:0:60:4:0.0066:0:1.5 0/1:252:3:1,2:203,46:249,3:0.0119:2,2:11.7:1:23.3:1:0.09388:8.71676:60:6:0.0121:0:1 +6 41903782 . A C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.56911;LSEQ=TGGGCTGGAGCTGGTCTGAG;RSEQ=GGCTTCCCTGAGGCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:929:165:67,98:329,434:763,165:0.1776:2,2:26:1:30.9:1:0.60272:1.10867:59.9:164:0.1796:0:1.1 0/1:846:302:134,168:236,289:525,302:0.357:2,2:25.7:1:29.9:1:0.88472:1.02379:59.9:74.5:0.3595:0:1.1 +6 41903959 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11109;SOR=Inf;LSEQ=GTCTGGGGAGGTTAGGCCAC;RSEQ=GCCCGGCCCCAGGAATCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:5,70:75,0:0:2,0:22.3:1:31.9:1:1:0:60:74:1:0:0.1 0/1:38:2:1,1:1,35:36,2:0.0526:1,2:17:0:32:1:0.10384:25.10:60:4:0.0526:0:1.5 +6 41904258 . A T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25177;SOR=0;LSEQ=TCAGGGCATAGCACTACTTT;RSEQ=TGAATGGAGAGGCTGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:3:1,2:127,34:161,3:0.0182:2,2:14.3:1:27.7:1:0.12162:7.34812:60:6:0.0188:0:1 0/0:142:0:0,0:107,35:142,0:0:2,0:24.3:1:27.5:1:1:0:60:34.5:1:0:0.1 +6 41904483 . C T 148 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=21.9282;LSEQ=GAAGGAAACCTGAAGGATAA;RSEQ=GGCCAGCATGGACTTCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:2:1,1:81,223:304,2:0.0065:2,2:30:1:30:1:0.46478:2.74:60:4:0.0066:0:1 0/1:245:31:6,25:60,154:214,31:0.1265:2,2:21.5:1:29.9:1:0.3892:1.62044:60:62:0.1292:0:1.1 +6 41905174 . T A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46892;SOR=1.14725;LSEQ=GGGGTCAGTGGCTGGAGAAG;RSEQ=GAAGAGGAGGGAGCAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:288:183:43,140:23,81:104,183:0.6354:2,2:22.8:1:31.6:1:0.8842:1.08:59.9:366:0.6489:0:1.1 1/0:249:166:43,123:17,64:81,166:0.6667:2,2:21.9:1:29.7:1:0.43308:1.31:60:165:0.6707:0:1.1 +6 41905187 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1954;SOR=Inf;LSEQ=GGAGAAGTGAAGAGGAGGGA;RSEQ=CAAAGCAGAAGTCTCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:39,180:219,0:0:2,0:23.3:1:32.3:1:1:0:59.9:218:1:0:0.7 0/1:174:2:1,1:33,139:172,2:0.0115:2,2:29.5:1:28:1:0.35353:4.16:60:4:0.0116:0:2 +6 41905275 . G A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.97653;LSEQ=CTGTTTCTGATTTTAAGGCC;RSEQ=GGCACCATGGAGTTCAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:7:1,6:1,40:41,7:0.1458:1,2:18.9:1:31.3:1:0.27305:6.25:60:6:0.1333:0:1.1 0/1:21:3:0,3:0,18:18,3:0.1429:1,0:14:1:29:1:1:0:60:6:0.15:0:1 +6 41908032 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52032;SOR=0;LSEQ=TCCAGGGGGCAGAAAGCCTC;RSEQ=GATATCTCAAGCTTTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:163,11:174,2:0.0114:2,2:33:1:31:1:0.13208:14.23649:60:4:0.0115:0:1 0/0:115:0:0,0:99,16:115,0:0:2,0:22.9:1:30:1:1:0:60:37.333:1:0:0.1 +6 41908366 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16955;SOR=Inf;LSEQ=TGCTGGGTCTGGAGCGTGGG;RSEQ=AACACAGCAGCGGGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:22,202:224,0:0:2,0:23.1:1:31.4:1:1:0:60:19.364:0.9953:0:0.3 0/1:158:2:1,1:20,136:156,2:0.0127:2,2:30:1:28:1:0.24889:6.66:60:4:0.0133:0:1 +6 41908377 . CG C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.26866;SOR=0;LSEQ=GAGCGTGGGGAACACAGCAG;RSEQ=GGGGGGTGGGAGCGCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:3:0,3:15,156:171,3:0.0172:2,0:24.7:1:31.7:1:1:0:60:6:0.0175:0:0 0/0:124:0:0,0:13,109:122,0:0:2,0:24.8:1:29:1:1:0:60:29.5:0.9833:0:0.4 +6 41908561 . C A 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.55392;SOR=0;LSEQ=GGAGTGGTAAAGCCAAGGAG;RSEQ=CCTTGCTCACGGAGGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:2,1:165,16:181,3:0.0163:2,2:16.3:1:26:1:0.25361:5.0739:60:6:0.0167:0:1 0/0:85:0:0,0:82,3:85,0:0:1,0:24.5:1:32.2:1:1:0:60:170:1:0:0 +6 41908563 . C A 33 v3;p8;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05792;LSEQ=AGTGGTAAAGCCAAGGAGCC;RSEQ=TTGCTCACGGAGGATTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:166,16:182,2:0.0109:2,2:5:0:33:0:0.1767:10.09554:60:4:0.0111:0:1.5 0/1:87:1:1,0:83,3:86,1:0.0115:1,0:13:0:31:0:1:0:60:2:0.0116:0:1 +6 41908717 . G A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=GAAGGGAGGAGGCTCCTGCC;RSEQ=CTGCCTCCTGCACTTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:904:0:0,0:418,485:903,0:0:2,0:23.5:1:31:1:1:0:59.9:63.5:1:0:0.1 0/1:856:10:6,4:402,444:846,10:0.0117:2,2:21.7:1:27.6:1:0.53146:1.66:60:20:0.0119:0:1.1 +6 41908810 . G A 58 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01429;SOR=Inf;LSEQ=GAACCCCGCGAAAGACACAG;RSEQ=AACCGGCTCCCGGGCGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:84,248:332,0:0:2,0:20.3:1:31.4:1:1:0:60:54.333:1:0:0.2 0/1:250:5:4,1:69,175:244,5:0.02:2,2:7.6:1:25:1:0.02697:10.04:60:10:0.0203:0:1.2 +6 41909028 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGGGCTCGGGAAAGCAAG;RSEQ=GAGGCAGCTGGCGTGGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:71,6:77,2:0.0247:2,2:39:0:31.5:1:0.1704:11.03273:60:4:0.0274:0:1.5 0/0:39:0:0,0:37,2:39,0:0:2,0:22.8:1:29.9:1:1:0:60:12:1:0:0.2 +6 41909422 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24929;SOR=Inf;LSEQ=CAGGCAGGGCGGGAGTGCGG;RSEQ=CTCGCGAGTCCCAAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:34,120:154,0:0:2,0:24.2:1:32.6:1:1:0:60:308:1:0:0.2 0/1:170:3:2,1:54,113:167,3:0.0176:2,2:24:1:26.7:1:0.2527:4.15:60:6:0.0182:0:2 +6 41909426 . G T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=CAGGGCGGGAGTGCGGGCTC;RSEQ=CGAGTCCCAAGGCAGGCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:31,112:143,0:0:2,0:22.8:1:32.3:1:1:0:60:142:1:0:0.2 0/1:150:15:6,9:42,91:133,15:0.1:2,2:29.2:1:29.8:1:0.56483:1.44:60:30:0.1014:0:1.2 +6 41909432 . C A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50216;SOR=Inf;LSEQ=GGGAGTGCGGGCTCGCGAGT;RSEQ=CCAAGGCAGGCGACGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:24,91:115,0:0:2,0:22.1:1:32.1:1:1:0:60:56.5:1:0:0.2 0/1:138:2:1,1:43,93:136,2:0.0145:2,2:9:0:28:0:0.53761:2.15:60:4:0.0149:0:2.5 +6 41909521 . CCG C 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCCCCAGCCCGCCCGCCGC;RSEQ=CGCGCGCGCGCCGCTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:33:0:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 42699907 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGTGCTGAAATTACAGT;RSEQ=TGAGCCACCACGCCCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:33.5:1:1:0:60:4:1:0:2 +6 42699921 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGTATGAGCCACCACGC;RSEQ=CAGCTGAGACTATTATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:31.5:1:1:0:60:4:1:0:2 +6 42701641 . G A 69 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GACAAAGAGATAAAGAGAAA;RSEQ=CAGCTGGGCCTGGGGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1:0,2:16:1:30:1:1:0:30:10:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 42701676 . T C 64 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACCACTACCACCAAGACG;RSEQ=GGAGACGTAGTGGCCTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:31.3:1:32:1:1:0:30.3:8:1:0:1.8 1/0:4:3:3,0:1,0:1,3:0.75:0,0:14:1:32.7:1:1:0:38:6:0.75:0:1 +6 42702973 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTCGCTCTGTTGCCCAG;RSEQ=CTGGAGTGAAGCGATACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 42703256 . A G 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATCTACTTTCAATGTTCC;RSEQ=TAACTTTCTTCATTTTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:41:0:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 43738350 . C G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.15502;LSEQ=GGGCGTGCGAGCAGCGAAAG;RSEQ=GACAGGGGCAAAGTGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:98:83:80,3:13,1:14,83:0.8469:1,1:24.1:1:31.1:1:0.46964:2.03:60:26.667:0.8421:0:1 0/1:35:16:14,2:18,1:19,16:0.4571:1,2:25.1:1:28.9:1:0.58197:2.50361:60:15:0.4545:0:1.2 +6 43738423 . TC T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06181;SOR=Inf;LSEQ=GTGAGCCCTCCCCCTTGGGA;RSEQ=CCGCAGCTGACCAGTCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:0:0,0:173,142:315,0:0:2,0:23.1:1:30.9:1:1:0:60:62:1:0:0.3 0/1:207:3:1,2:120,84:204,3:0.0145:2,2:25.7:1:27.7:1:0.57146:2.84265:60:6:0.0151:0.0048:0.3 +6 43738436 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07288;SOR=Inf;LSEQ=CTTGGGATCCCGCAGCTGAC;RSEQ=AGTCGCGCTGACGGACAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:180,195:375,0:0:2,0:25.1:1:30.9:1:1:0:60:36.5:1:0:0.2 0/1:270:3:1,2:143,124:267,3:0.0111:2,2:29.3:1:27.3:1:0.60011:2.29952:60:6:0.0114:0:1 +6 43738449 . GGACA G 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=4.000;MSILEN=4;SSF=1;SOR=1.01491;LSEQ=AGCTGACCAGTCGCGCTGAC;RSEQ=GACAGACAGACACCGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:5:2,3:177,248:425,5:0.0116:2,2:20.4:1:31.8:1:1:1.07041:60:10:0.0118:0.0047:0.8 0/1:339:4:2,2:159,175:334,4:0.0118:2,2:13.5:1:29.3:1:1:1.10:60:8:0.012:0.0029:0.3 +6 43738513 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65652;SOR=1.9795;LSEQ=TCCCCGGCCGGCGGCGGACA;RSEQ=TGGACGCGGCGGCGAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:2:2,0:86,210:296,2:0.0067:2,0:1:0:28:0:0.0865:0:60:4:0.0068:0:1 0/1:227:3:2,1:84,140:224,3:0.0132:2,2:14:1:27:1:0.55879:3.32:60:6:0.0135:0:1.3 +6 43738527 . G A 35 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63489;SOR=0.42521;LSEQ=CGGACAGTGGACGCGGCGGC;RSEQ=AGCCGCGGGCAGGGGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:3,0:117,152:269,3:0.011:2,0:6.3:1:22.7:1:0.08467:0:60:2:0.0076:0:1.3 0/0:213:1:1,0:97,115:212,1:0.0047:2,0:1:0:24:0:0.46009:0:60:2:0.0048:0:1 +6 43738530 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57444;SOR=2.78801;LSEQ=ACAGTGGACGCGGCGGCGAG;RSEQ=CGCGGGCAGGGGCCGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:0,1:132,146:278,1:0.0036:2,0:1:0:25:0:1:0:60:2:0.0037:0:1 0/1:201:2:1,1:90,108:198,2:0.01:2,2:11.5:1:26.5:1:1:1.20:60:4:0.0102:0:1 +6 43738535 . G T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14646;SOR=0;LSEQ=GGACGCGGCGGCGAGCCGCG;RSEQ=GCAGGGGCCGGAGCCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:4:1,3:170,136:306,4:0.0129:2,2:18:1:29.3:1:0.32904:3.73503:60:8:0.0132:0:1.3 0/0:218:0:0,0:111,106:217,0:0:2,0:12.8:1:30.2:1:1:0:59.8:35.167:0.9953:0:0.3 +6 43738977 . C T 317 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03614;LSEQ=GCCGGCCCCGGTCGGGCCTC;RSEQ=GAAACCATGAACTTTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1457:1163:631,532:157,135:292,1163:0.7982:2,2:24.7:1:31.2:1:0.8956:1.02:60:76.533:0.7967:0:1.2 0/1:1097:137:70,67:509,451:960,137:0.1249:2,2:25.7:1:29.9:1:0.7147:1.08015:59.9:136:0.1244:0:1.3 +6 43740595 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAGGAGGGGGAGGAGTG;RSEQ=CTGCCTGGCCACAGTGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 43740840 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=Inf;LSEQ=CAGGGGGTCCCTGCAGGAGC;RSEQ=GCAGTGGTAAGCTGTCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:35.6:1:30.4:1:1:0:60:16:1:0:0.1 0/1:10:2:1,1:4,4:8,2:0.2:2,2:18:0:31:0:1:1:60:4:0.2222:0:1.5 +6 43742166 . C A 176 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=38.52298;LSEQ=GTTGGATGGGGTTCCCTGTC;RSEQ=TCTCAGGGGATGGGTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1920:2:2,0:848,1069:1917,2:0.001:2,0:1:0:30:1:0.19607:0:58:4:0.0011:0:1 0/1:1528:59:29,30:668,801:1469,59:0.0386:2,2:28.4:1:30:1:0.5961:1.16:60:118:0.0392:0:1.2 +6 43742419 . G C 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28783;SOR=4.57254;LSEQ=GAGCAGGAAGACAGTGTTCA;RSEQ=GGATCCTAGGTGTTGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:0,8:0,13:13,8:0.381:1,0:32.5:1:31.4:1:1:0:57.1:16:0.381:0:1.1 1/0:4:3:0,3:0,1:1,3:0.75:0,0:17:1:28:1:1:0:60:6:0.75:0:1.3 +6 43745095 . C A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07246;LSEQ=TACGTTAGATTTTGGAAGGA;RSEQ=TTGCCTGATTCGGAAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:282:219:216,3:61,1:62,219:0.7766:1,1:24.2:1:30.7:1:1:1.18:60:53.75:0.7847:0:1.1 0/1:170:34:34,0:132,4:136,34:0.2:1,1:24.4:1:29.1:1:0.5849:0:60:33:0.1953:0:1 +6 43745107 . G A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.98843;LSEQ=TGGAAGGACTTGCCTGATTC;RSEQ=GAAGCTCCAAAGAGTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:71:69,2:285,6:291,71:0.1961:1,1:25:1:30.8:1:0.65788:1.37548:60:70:0.195:0:1.1 1/0:211:116:110,6:93,2:95,116:0.5498:1,2:24.8:1:29.7:1:0.29948:2.52611:60:57:0.5455:0:1.1 +6 43745577 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.71767;LSEQ=TGGAGAAGATGCTTCATTCC;RSEQ=AGCCCAGGTTCCCAGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:700:137:25,112:111,452:563,137:0.1957:2,2:21.5:1:28.7:1:0.80975:1.10004:60:44.667:0.1951:0:1.1 1/0:395:230:40,190:39,126:165,230:0.5823:2,2:23.6:1:27.9:1:0.1285:1.46874:60:114:0.5831:0:1 +6 43746169 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=4.02309;LSEQ=TGGCTGGCTGGGTCACTAAC;RSEQ=TCTGTGATCTGCTTCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1018:194:124,70:505,317:822,194:0.1906:2,2:24.3:1:31.5:1:0.5653:1.11:60:96:0.192:0:1.1 0/1:787:383:225,158:233,171:404,383:0.4867:2,2:25.3:1:29.6:1:0.77282:1.05:60:53.714:0.487:0:1.2 +6 43746352 . CT C 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.09435;SOR=0;LSEQ=CCAGGGTTAAGCATGCTGTA;RSEQ=TTTTGGCCCCCGTCCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:2,4:84,367:451,6:0.0131:2,2:25.7:1:33:1:0.31546:2.18:60:12:0.0133:0.0022:0.2 0/0:252:0:0,0:61,189:250,0:0:2,0:23:1:29.7:1:1:0:60:124:0.992:0:0.1 +6 43746360 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12368;SOR=5.6737;LSEQ=AAGCATGCTGTACTTTTTGG;RSEQ=CCCCGTCCAGCTTCCCGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:1:0,1:72,331:403,1:0.0025:2,0:37:0:32:0:1:0:60:2:0.0026:0:1 0/1:216:3:1,2:49,163:212,3:0.0139:2,2:25.3:1:26:1:0.54993:1.66:60:2:0.0095:0:1 +6 43747783 . G A 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCCCAAGCCTCTCCTCCCCA;RSEQ=ACCTCCTTAACTCCCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:26:0:35:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:42.5:1:31:1:1:0:60:4:1:0:1.5 +6 43747962 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGTCGCAGTTGCAAATGA;RSEQ=GGCACAAGGCCTGATACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:28.5:1:34:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 43748328 . C G 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATGCCTCCCCAGAGACCA;RSEQ=CTGCCTCCTGACACTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:56:54,2:81,4:85,56:0.3944:1,1:23.6:1:32.9:1:1:1.33:59.8:27:0.3857:0:1.2 0/0:65:0:0,0:63,2:65,0:0:1,0:23:1:31.3:1:1:0:60:31.5:1:0:0.2 +6 43748350 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04943;SOR=Inf;LSEQ=TGCCTCCTGACACTTCCTCC;RSEQ=GGAAGCGGCCCTGTGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:180,7:187,0:0:1,0:25.8:1:30.3:1:1:0:60:92.5:0.9946:0:0.7 0/1:110:3:3,0:104,3:107,3:0.0273:1,0:13.7:1:31.3:1:1:0:60:6:0.0283:0:2 +6 43748357 . G A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=Inf;LSEQ=TGACACTTCCTCCGGGAAGC;RSEQ=GCCCTGTGTGGCTTTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:195,6:201,0:0:1,0:26.5:1:30.5:1:1:0:59.9:200:1:0:0.8 0/1:124:8:8,0:112,3:115,8:0.0645:1,0:25.3:1:30.5:1:1:0:60:16:0.065:0:2.3 +6 43748643 . T C 312 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=5.5959;LSEQ=CTGCCTCCCTCCCCTGGTCC;RSEQ=TCCCTGGCTCTCATCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1028:835:205,630:50,141:191,835:0.8123:2,2:24.2:1:32.2:1:0.64327:1.08968:59.9:51.188:0.8133:0:1.1 1/1:656:630:177,453:7,17:24,630:0.9604:2,2:22.8:1:30.9:1:1:1.05376:60:62:0.9612:0:1.1 +6 43748697 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10828;SOR=Inf;LSEQ=CTCTCACTCTCTCACTCCAC;RSEQ=AATTGGCACCAACGGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:18,348:366,0:0:1,0:23.1:1:28.4:1:1:0:59.9:29.5:1:0:0.7 0/1:180:2:1,1:13,165:178,2:0.0111:2,2:18:1:29.5:1:0.14991:12.27:60:4:0.0115:0:1.5 +6 43748795 . C T 53 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02998;SOR=7.21367;LSEQ=GGAGGATTAAGGGAGGGGAC;RSEQ=CTGGCTTGGCTGGGCACCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:0,2:1,55:56,2:0.0345:1,0:38.5:1:32:0:1:0:60:4:0.0357:0:1 0/1:19:4:0,4:0,15:15,4:0.2105:1,0:33:1:26.5:1:1:0:60:3:0.1875:0:2.8 +6 43749163 . T C 51 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGGGCAGCCTCTTCCTC;RSEQ=GGGTCGGAGGCTGTGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:24:1:32.3:1:1:0:60:6:1:0:1.7 1/1:1:1:0,1:0,0:0,1:1:0,0:16:0:24:0:1:0:60:2:1:0:2 +6 43749230 . C T 42 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCCTGGCCTGGGGACAC;RSEQ=GCCTCCGGGCTTAGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16:1:32:1:1:0:60:4:1:0:4.5 1/1:3:3:1,2:0,0:0,3:1:0,2:24.7:1:27:1:1:0:60:2:1:0:2 +6 43749612 . AG A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.05913;SOR=Inf;LSEQ=GGTGCAGCTGCGGACATGTT;RSEQ=GGGGTGTTGCATGGTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:362,24:386,0:0:2,0:22.2:1:32.8:1:1:0:59.9:47.25:0.9974:0:0.2 0/1:248:3:1,2:224,21:245,3:0.0121:2,2:19.3:1:27.2:1:0.02337:20.72187:60:6:0.0122:0.0081:0.3 +6 43749615 . G T 54 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.0353;SOR=7.9789;LSEQ=GCAGCTGCGGACATGTTAGG;RSEQ=GGTGTTGCATGGTGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:1:1,0:371,26:397,1:0.0025:2,0:11:0:12:0:1:0:60:0:0:0:4 0/1:253:5:1,4:226,22:248,5:0.0198:2,2:11:1:23.6:1:0.00042:39.74444:60:4:0.0163:0:1 +6 43749876 . GGA G 121 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.63834;SOR=0.7349;LSEQ=GGGGCATCACACAGAGATGG;RSEQ=GAGAGAGAGAGAAAGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:637:13:1,12:142,482:624,13:0.0204:2,1:28.2:1:32.9:1:0.31624:3.53055:58.5:26:0.0206:0.0016:0.3 0/1:398:6:1,5:84,307:391,6:0.0151:2,2:34:1:31.5:1:1:1.36708:60:12:0.0152:0:0 +6 43749914 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.30227;SOR=0;LSEQ=AGAGTGAGCGAGCGAGCGAG;RSEQ=GGGAGAGCGCCTGAGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:3:0,3:12,256:268,3:0.011:1,0:20:1:31:1:1:0:53.3:6:0.0115:0:2 0/0:157:0:0,0:6,151:157,0:0:1,0:24.4:1:29.4:1:1:0:60:30.4:1:0:0.2 +6 43751669 . G C 39 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATGAGGCCTACAGCCACA;RSEQ=TGGGAGGGGACATGGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:31:1:25:1:1:0:60:2:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 43751976 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTTGGTATCCGTTCATTT;RSEQ=TTGCTTTGTAAAGTGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:2,0:20,0:20,2:0.0909:1,0:33:1:31.5:1:1:0:60:4:0.0952:0:1.5 0/0:4:0:0,0:4,0:4,0:0:0,0:22.8:1:31.5:1:1:0:60:8:1:0:0 +6 43752536 . C T 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCGGGCGGGTGACCCAGCA;RSEQ=GGTCCCTCTTGGAATTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:2,208:210,0:0:1,0:23.6:1:30.5:1:1:0:60:104:1:0:0.1 0/1:107:21:0,21:1,85:86,21:0.1963:1,1:31:1:28.9:1:1:0:60:20:0.1905:0:1 +6 43752551 . T C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03059;SOR=Inf;LSEQ=CAGCACGGTCCCTCTTGGAA;RSEQ=TGGATTCGCCATTTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:2,154:156,0:0:1,0:22.5:1:30.5:1:1:0:60:51:1:0:0.1 0/1:72:3:0,3:1,68:69,3:0.0417:1,0:19.7:1:33.3:1:1:0:60:6:0.0417:0:1 +6 45390281 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.18076;SOR=Inf;LSEQ=TTTCCACCCTCCTCCCCCTC;RSEQ=CCCGGCCACTTCGCTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:19,6:25,0:0:2,0:20.5:1:31.7:1:1:0:58.3:50:1:0:0.6 0/1:19:2:1,1:11,6:17,2:0.1053:2,2:12:0:30.5:1:1:1.77272:60:4:0.1053:0:1.5 +6 45390400 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17289;SOR=Inf;LSEQ=GGCAAAATGAGCGACGTGAG;RSEQ=CCGGTGGTGGCTGCGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:36,49:85,0:0:2,0:26:1:30.9:1:1:0:59.5:27.333:1:0:0.2 0/1:61:2:1,1:25,33:58,2:0.0328:2,2:28.5:1:28.5:1:1:1.31:60:4:0.0339:0:1 +6 45390430 . ACAG A 34 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.15854;SOR=Inf;LSEQ=GCTGCGCAACAGCAGCAGCA;RSEQ=CAGCAGCAGCAACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:37,62:99,0:0:2,0:27.4:1:32.5:1:1:0:57.8:198:1:0:0.3 0/1:66:2:1,1:26,38:64,2:0.0303:2,2:21:0:34:0:1:1.45:37:4:0.0317:0:0.5 +6 45390433 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.51753;SOR=0;LSEQ=GCGCAACAGCAGCAGCAACA;RSEQ=CAGCAGCAGCAACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:35,61:96,2:0.0204:2,2:14.5:1:28.5:1:1:1.73:60:4:0.0208:0:1 0/0:65:0:0,0:25,38:63,0:0:2,0:25.4:1:30.6:1:1:0:58.5:20:1:0:0.4 +6 45390445 . ACAG A 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.08015;SOR=6.41043;LSEQ=CAGCAACAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:1:0,1:30,56:86,1:0.0115:2,0:25:0:34:0:1:0:60:2:0.0116:0:0 0/1:57:4:2,2:21,32:53,4:0.0702:2,2:25.5:1:29.8:1:1:1.51:46.5:8:0.0741:0.0351:0.8 +6 45390448 . G A 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.64324;SOR=1.57951;LSEQ=CAACAGCAGCAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:2:1,1:28,55:83,2:0.0233:2,2:25.5:1:29:1:1:1.95:60:4:0.0241:0:1 0/1:55:2:1,1:20,31:51,2:0.0364:2,2:1.1:1:27.6:1:1:1.54:41:4:0.0365:0:1.5 +6 45390461 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.15219;SOR=Inf;LSEQ=AGCAACAGCAGCAGCAGCAG;RSEQ=AGCAACAGCAGCAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:21,47:68,0:0:2,0:23.9:1:32.4:1:1:0:57:67:1:0:0.3 0/1:44:2:1,1:15,27:42,2:0.0455:2,2:9:0:30.5:1:1:1.77:60:4:0.0465:0:1.5 +6 45390466 . ACAG A 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=1;SOR=0.77823;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:0,2:17,42:59,2:0.0328:2,0:47:1:33:1:1:0:60:4:0.0339:0:0 0/1:39:1:0,1:13,25:38,1:0.0256:2,0:45:0:29:0:1:0:60:2:0.0256:0:0 +6 45390501 . C G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22;SOR=0;LSEQ=GCAGGAGGCGGCGGCGGCGG;RSEQ=TGCGGCGGCGGCGGCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:1,9:10,2:0.1667:2,2:14:0:32.5:1:0.31818:6.71:60:4:0.1667:0:1.5 0/0:13:0:0,0:3,10:13,0:0:2,0:15:1:31.7:1:1:0:56.3:26:1:0:0.7 +6 45390595 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50315;SOR=0;LSEQ=ATGGTGGAGATCATCGCCGA;RSEQ=CACCCGGCCGAACTCGTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:142,38:180,2:0.011:2,2:22.5:1:32.5:1:0.38358:3.70183:60:4:0.0112:0:1 0/0:150:0:0,0:110,40:150,0:0:2,0:19.4:1:31.1:1:1:0:60:74:1:0:0.1 +6 45390711 . C A 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.62406;SOR=0.35211;LSEQ=CAAGGTAAGAGGCTACACCG;RSEQ=CCCCCGCCCCCGGCCGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:2,1:83,151:234,3:0.0127:2,2:16.7:1:27.3:1:0.29279:3.62:60:6:0.0128:0:1 0/0:223:1:1,0:86,136:222,1:0.0045:2,0:1:0:25:0:0.39013:0:60:2:0.0046:0:1 +6 45390727 . G A 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36764;SOR=3.09094;LSEQ=ACCGCCCCCCGCCCCCGGCC;RSEQ=GGAGCGGCGGAACCTGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:38,115:153,1:0.0065:2,0:9:0:27:0:1:0:60:2:0.0066:0:1 0/1:151:3:2,1:44,104:148,3:0.0199:2,2:16.7:1:24.3:1:0.2202:4.67:60:2:0.0136:0:1 +6 45390733 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50116;SOR=0;LSEQ=CCCCGCCCCCGGCCGGGAGC;RSEQ=GCGGAACCTGCCCGCCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:32,111:143,2:0.0137:2,2:14.5:1:26.5:1:0.4046:3.43:60:4:0.0141:0:1 0/0:125:0:0,0:26,87:113,0:0:2,0:22.3:1:29.8:1:1:0:60:226:0.904:0:0.1 +6 45390808 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51637;SOR=0;LSEQ=TCCAAGACCTCCTGCCTTGG;RSEQ=GGCTCTAACCCCAGAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:1,36:37,2:0.0513:1,0:11:1:32.5:1:1:0:60:4:0.0526:0:1 0/0:25:0:0,0:2,22:24,0:0:2,0:21.4:1:29.4:1:1:0:59.8:48:1:0:0.4 +6 45390838 . C CCT 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.11997;SOR=Inf;LSEQ=CCCAGAAACCCCCGGCCGGG;RSEQ=CTCCCTCCGGATGCCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:0,14:0,4:4,14:0.7778:0,1:24:1:31.5:1:1:0:60:28:0.7778:0.2222:0 1/1:13:13:2,11:0,0:0,13:1:0,2:25.6:1:27.8:1:1:0:59.6:12:1:0.1538:1 +6 45391943 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTGCTCCGCAGGTTGAGG;RSEQ=TTTAGGATCTGGAGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29:1:1:0:60:4:1:0:1.5 +6 45459414 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=CAGAGAAGGTGTCTAGTATC;RSEQ=TGCCTCTCTATTGATGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:11,0:11,0:0:0,0:20.5:1:28:1:1:0:59.7:4.5:1:0:0.9 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:32.5:1:32:0:1:0:60:4:0.3333:0:1 +6 45459534 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52126;SOR=0;LSEQ=AAAGCAATTTGAAATGGAAG;RSEQ=CATTATGTAGACAAGTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:83,9:92,2:0.0213:2,2:23.5:1:32:0:0.20247:8.80272:60:4:0.0215:0:1 0/0:60:0:0,0:53,7:60,0:0:2,0:26.7:1:31.4:1:1:0:60:120:1:0:0 +6 45459915 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10328;SOR=Inf;LSEQ=CTGGGGGTGAGGGGCTACCA;RSEQ=AGGAGATGTGTTCACTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:104,163:267,0:0:2,0:25.4:1:32.5:1:1:0:60:132.5:1:0:0.1 0/1:237:3:1,2:92,142:234,3:0.0127:2,2:24.7:1:26:1:1:1.2944:60:6:0.0129:0:1 +6 45459967 . A G 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21661;SOR=Inf;LSEQ=CTGTGAAGCGGCTTATTATT;RSEQ=AAGAATCAAGACTTGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:45,98:143,0:0:2,0:25.1:1:30:1:1:0:60:70.5:1:0:0.1 0/1:125:2:1,1:31,92:123,2:0.016:2,2:13.5:1:24.5:1:0.448:2.94:60:4:0.016:0:1 +6 45556069 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.01914;LSEQ=TAGACACATATATATTATCT;RSEQ=ATAATACCTAAACACATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:49:24,25:206,237:443,49:0.0996:2,2:24.7:1:29.9:1:0.76464:1.10:60:48:0.0994:0:1.3 0/1:377:165:79,86:103,108:211,165:0.4377:2,2:23.9:1:28.3:1:0.91724:1.03812:60:81.5:0.437:0:1.1 +6 45556152 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17027;SOR=Inf;LSEQ=AGGCAAAATGTGTGTATCTT;RSEQ=CATGGTGCTTAGCTCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:61,176:237,0:0:2,0:25.9:1:31.4:1:1:0:60:58.25:1:0:0.1 0/1:167:2:1,1:54,111:165,2:0.012:2,2:27.5:1:27.5:1:0.55155:2.05:60:4:0.0121:0:1 +6 45556263 . C A 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08537;SOR=6.10095;LSEQ=TACACATTATGAATGTATAG;RSEQ=AAATTTAGAACATGTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:0,22:22,2:0.0833:1,0:32:1:30:1:1:0:60:4:0.0909:0:2 0/1:8:3:0,3:0,5:5,3:0.375:0,0:29.7:1:29.7:1:1:0:60:6:0.375:0:1.7 +6 45556291 . G A 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.24871;SOR=3.95518;LSEQ=GAACATGTACATTATAGAGA;RSEQ=AATCTAGAAAATACACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:13,3:0.1875:1,0:23.7:1:30:1:1:0:60:6:0.2:0:1.7 1/0:4:2:0,2:0,2:2,2:0.5:0,0:14:1:32:0:1:0:60:4:0.5:0:2 +6 45768791 . A G 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGCAGAGAGACCTCATAA;RSEQ=CTCATTTGCTAGCGTAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:44.3:1:34:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 45768796 . T TC 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGAGACCTCATAAACTCA;RSEQ=TTGCTAGCGTAACATGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:38.3:1:32.7:1:1:0:60:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 45768804 . C T 40 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCATAAACTCATTTGCTAG;RSEQ=GTAACATGCGTCCAATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:30.3:1:25.7:1:1:0:60:2:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 45768935 . C T 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAATGGCAGGAATAAAATC;RSEQ=GTCTGGCCAGGGTGTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:27:1:32.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 45769257 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55768;SOR=0;LSEQ=GTTCCAAGTACCATGAATAG;RSEQ=CCCACCCGAGGGGAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:3:3,0:153,6:159,3:0.0185:1,0:36:1:29:1:1:0:60:6:0.0186:0:1 0/0:67:0:0,0:66,1:67,0:0:1,0:22.4:1:31.6:1:1:0:60:66:1:0:0 +6 45769293 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11452;SOR=Inf;LSEQ=CAGTTTATGTGTGCAGAAAG;RSEQ=GCCCTGGGGTGAGTAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:253,51:304,0:0:2,0:23.2:1:31.5:1:1:0:60:59.8:1:0:0.1 0/1:156:2:1,1:131,23:154,2:0.0128:2,2:25.5:1:27.5:1:0.28486:5.59704:60:4:0.0131:0:1.5 +6 45769418 . G C 304 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34071;LSEQ=ATGTCCCTTGCGAATGCATC;RSEQ=TATTTTCTCGTTCAACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:686:658:286,372:12,16:28,658:0.9592:2,2:26.7:1:32.5:1:1:1.03:60:130.6:0.9603:0:1.8 1/1:576:512:225,287:31,32:63,512:0.8889:2,2:25.7:1:30.4:1:0.50207:1.23523:60:35.571:0.8877:0:1.8 +6 45769439 . G A 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00051;SOR=0.42566;LSEQ=TATTTTCTCGTTCAACCAGC;RSEQ=TCAAATGCAATCCTGGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:556:528:210,318:10,18:28,528:0.9496:2,2:24.9:1:30.7:1:0.84318:1.19:60:74.429:0.949:0:2 1/1:451:401:153,248:23,27:50,401:0.8891:2,2:25.1:1:29.5:1:0.28643:1.37973:60:79.2:0.8879:0:2 +6 45769869 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCCTTCGATGAGTGAAAC;RSEQ=TAGATTTGAGGGGGCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 46910123 . C T 107 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAATCCCTAACGCAGCA;RSEQ=GCTATTAGAGATGCTTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:24.3:1:31.2:1:1:0:60:10:1:0:2.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 46910144 . G A 123 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTATTAGAGATGCTTAAGA;RSEQ=GGTAAAAGCATGGGCTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:0,16:1:0,1:29.1:1:30.8:1:1:0:60:32:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 46910415 . C T 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.00519;LSEQ=TCTGTCATGAGAAGCCTGCA;RSEQ=ATAGGACACTTTTCATTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:439:437:215,222:0,0:0,437:0.9954:0,2:26.9:1:29.4:1:1:0:60:61.429:0.9954:0:1.1 1/0:357:189:94,95:80,87:167,189:0.5294:2,2:24.9:1:29:1:0.75079:1.08:60:188:0.5311:0:1.1 +6 46910536 . A C 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTTTTTCTCTTTCTTTGAC;RSEQ=TACTACTTTACAAGTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:12,94:106,0:0:2,0:22.2:1:30.4:1:1:0:60:25.5:1:0:0.1 0/1:67:21:1,20:3,43:46,21:0.3134:2,1:20:1:32.1:1:1:1.38884:60:42:0.3134:0:1.1 +6 47074474 . A G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37071;SOR=2.72696;LSEQ=AGACTTCCAACCACCAAAAC;RSEQ=GTGAAACAATACATTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:1,9:10,7:0.4118:2,0:20.4:1:32.6:1:1:0:60:14:0.4118:0:1 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:39.3:1:31.5:1:1:0:60:8:0.6667:0:1 +6 50726648 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49344;SOR=Inf;LSEQ=GGAGAAGGTTCAGAAGCCTG;RSEQ=CTAAAGTTTACTCAAGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:12,20:32,0:0:2,0:25.7:1:31.1:1:1:0:60:31:1:0:0.1 0/1:35:2:1,1:11,21:32,2:0.0571:2,2:35.5:1:30.5:1:1:1.87:60:4:0.0588:0:1 +6 51716715 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07792;SOR=Inf;LSEQ=TAACTCCTTCAATTCTTCTC;RSEQ=GATCTTAGTTATTTCTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:12,0:0:2,0:21.3:1:30.7:1:1:0:59.2:24:1:0:0.3 0/1:10:3:1,2:4,3:7,3:0.3:2,2:8.3:1:31:0:1:2.41422:27.3:6:0.3:0:1.3 +6 51716738 . C A 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.14286;SOR=0;LSEQ=TCTTAGTTATTTCTTGTCTT;RSEQ=TGCTGGCTTTTGGATTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:14.5:1:31.5:1:1:2.45:58:4:0.3333:0:1 0/0:9:0:0,0:5,4:9,0:0:2,0:21.8:1:30.1:1:1:0:52.4:18:1:0:0.3 +6 51719074 . A T 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45;SOR=0;LSEQ=GAGATGTCACTCAAGGAGAC;RSEQ=GGAGTGCAGCAAAGATGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:2,9:0,0:0,11:1:0,2:26.1:1:29.2:1:1:0:37.3:10:1:0:1 1/1:9:8:5,3:0,1:1,8:0.8889:0,2:20:1:29.5:1:0.44444:0:32.8:16:0.8889:0:1.1 +6 51719409 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GGAGATATGAATTCTGTCCC;RSEQ=GAGCCTCTGGCTGGAGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:9.8:1:32:1:1:0:60:10:1:0:0.2 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:15.5:1:28.5:1:1:0:51.5:4:0.6667:0:1 +6 51719595 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCCAACAGGGAAAAAA;RSEQ=GCAGCCTAGAGCTATAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:14:1:30:1:1:1.41:53:4:0.2857:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:12:0:33:0:1:0:60:2:1:0:0 +6 54479334 . G A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=ACTAGAAGCAGCACCGTTTC;RSEQ=AGGCTTCCACCGAAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:2,1:3,3:0.5:2,2:24.3:1:32.3:1:1:1:60:6:0.5:0:1.3 0/0:5:0:0,0:3,2:5,0:0:2,0:20:1:25.4:1:1:0:60:4:1:0:0 +6 54479426 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=CATCAAAATTGACTAGAAGG;RSEQ=TGGTGTGACCCACAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:2,3:0.6:2,2:24:1:29:1:1:1.7321:51.7:6:0.6:0:2 0/0:7:0:0,0:3,4:7,0:0:2,0:30.6:1:31.6:1:1:0:49.4:14:1:0:0.3 +6 54479457 . A G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02424;SOR=0;LSEQ=CACAGAGAGAAGGAAGAACA;RSEQ=TGTGGTGTGGCAACCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:32.7:1:31:1:1:0:51.7:6:0.75:0:2 0/0:7:0:0,0:3,4:7,0:0:2,0:17.1:1:29.4:1:1:0:52:14:1:0:0.3 +6 54479836 . T G 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=GCTTCCTGGGCAGGGGAAGG;RSEQ=TGGCACCCATTTCTGTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:6:0:33.5:1:1:0:60:4:0.3333:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:30.2:1:29.2:1:1:0:60:10:1:0:0.2 +6 54480057 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=ACCAGAGGCTCAGAGAGAGA;RSEQ=TTCAGATCTCCTTGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:23.2:1:30.7:1:1:0:55.1:18:1:0:0.1 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:41.5:1:30:1:1:1.29:60:4:0.2222:0:1 +6 54480148 . A G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=CTCTCCTCCTGGTATTTCTG;RSEQ=GAAATCCAGGCAGCCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:1,2:8,1:9,3:0.25:2,2:20.7:1:31:1:0.12727:11.0937:56:6:0.25:0:1 0/0:6:0:0,0:4,2:6,0:0:2,0:23.7:1:30.8:1:1:0:56.2:12:1:0:0.3 +6 54480190 . AAC A 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0.71951;LSEQ=AGTGGTTTTGCCCCAAGCAA;RSEQ=ACACTCTCTTCACCAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:5,2:15,10:25,7:0.2188:2,2:23.3:1:30:1:0.68332:1.64:60:14:0.2188:0.0313:0.9 0/1:12:2:2,0:7,3:10,2:0.1667:2,0:30:1:31.5:1:1:0:60:4:0.1667:0:1 +6 54480220 . G C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91427;LSEQ=CTTCACCAAGGGACAAAGTG;RSEQ=TTCGTTAAATGGGTCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:3,2:21,14:35,5:0.125:2,2:33.6:1:33.2:1:1:1:60:10:0.1282:0:1.2 0/1:26:3:2,1:13,10:23,3:0.1154:2,2:30.7:1:31.3:1:1:1.51:60:6:0.12:0:1 +6 54480393 . T G 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.32397;LSEQ=TGCTGTTCTCTAGCCTCCTT;RSEQ=AGTGACATCTCCAGGCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:4,2:13,15:28,6:0.1765:2,2:23.3:1:32.3:1:0.65618:2.25:48.3:12:0.1765:0:2.2 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:6.5:1:28.5:1:1:1.29:41.5:4:0.2222:0:2 +6 54480396 . T G 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60588;SOR=1.83492;LSEQ=TGTTCTCTAGCCTCCTTTAG;RSEQ=GACATCTCCAGGCACGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:4,2:13,15:28,6:0.1765:2,2:24.3:1:31.3:1:0.65618:2.25:48.3:12:0.1765:0:2.2 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:9.5:1:28:1:1:1.41:41.5:4:0.2857:0:2 +6 54480521 . A G 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05856;SOR=0;LSEQ=ACAAGCAGAAAGCATCAGCA;RSEQ=CAGCAAAAACATCAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:7,5:12,3:0.2:2,0:20.3:1:34:0:0.2:0:60:6:0.2:0:1 0/0:22:0:0,0:11,11:22,0:0:2,0:25.8:1:29.2:1:1:0:60:44:1:0:0 +6 54480573 . G T 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.48775;LSEQ=CACAAAAACCCCATCCAAGG;RSEQ=TCAGCAGCTTCAAAGACCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:9,13:22,2:0.0833:2,0:24.5:1:26.5:1:0.51087:0:45.5:4:0.087:0:1.5 0/1:25:3:2,1:9,13:22,3:0.12:2,2:18:1:28.7:1:0.56478:2.77:44.7:6:0.12:0:1 +6 54480935 . CAA C 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACCTTGTGAAGCCAAATCGA;RSEQ=AGTGGAAGAAAGGATATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,2:2,2:0.6667:0,2:26:1:32:1:1:0:60:4:0.6667:0.3333:1.5 0/0:2:0:0,0:2,0:2,0:0:0,0:15:1:30:1:1:0:60:4:1:0:0 +6 54635157 . T C 79 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATAAAATGAATCTTTAGTG;RSEQ=TTGACATTATCCTGCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:1,6:0.8571:0,2:20:1:30.8:1:1:0:55.2:12:0.8571:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:14:0:33:0:1:0:60:2:1:0:1 +6 54635275 . G C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19858;SOR=0.36062;LSEQ=ATACTGGTTTAGATGAAGCT;RSEQ=GGCCAGTACTCCCGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:31:31,0:4,0:4,31:0.8857:0,1:21.6:1:33.1:1:1:0:55.7:62:0.8857:0:1.3 1/0:30:22:22,0:8,0:8,22:0.7333:0,1:25.5:1:30.4:1:1:0:55.9:21:0.7241:0:1.1 +6 54635342 . G A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=1;SOR=0.85915;LSEQ=CGCAGGCACTGAAGGCGGCG;RSEQ=CAGGGCCAGAGGCTCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:73,18:91,2:0.0215:2,2:26.5:1:29:1:0.36863:3.97433:55.5:4:0.0217:0:1.5 0/1:108:2:1,1:87,19:106,2:0.0185:2,2:41:1:28.5:1:0.33749:4.4886:59.5:4:0.0187:0:1 +6 54635362 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19639;SOR=0;LSEQ=GCAGGGCCAGAGGCTCAGCG;RSEQ=CTCCCAGACCTGCTGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:99,34:133,2:0.0148:2,2:26:1:29.5:1:0.45274:2.88435:60:4:0.0149:0:1.5 0/0:169:0:0,0:122,46:168,0:0:2,0:22.2:1:30.1:1:1:0:58.3:83:0.994:0:0.5 +6 54635398 . T TG 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.24914;LSEQ=AAAATGACTGAATATAAACT;RSEQ=GCGGTAGTTGGAGCTGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:264:237:151,86:14,12:26,237:0.8977:2,2:26.1:1:31.8:1:0.39338:1.50:47.2:58.25:0.8996:0.1364:1.1 1/0:315:216:129,87:67,32:99,216:0.6857:2,2:24.3:1:30.7:1:0.21075:1.41053:46.9:215:0.6891:0.127:1.1 +6 54635417 . G A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18499;LSEQ=TTGCGGTAGTTGGAGCTGGT;RSEQ=GCGTAAGCAAAAGTGTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:325:298:189,109:14,12:26,298:0.9169:2,2:25.7:1:29.7:1:0.3986:1.48:49.1:98.333:0.9219:0:1.1 1/0:407:273:156,117:82,52:134,273:0.6708:2,2:25.3:1:28.4:1:0.45531:1.1822:49.3:90:0.6716:0:1.2 +6 54635439 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06893;SOR=Inf;LSEQ=CGTAAGCAAAAGTGTCTTGA;RSEQ=GATACAGCTAATTCAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:238,159:397,0:0:2,0:24.7:1:31.3:1:1:0:51.5:197.5:0.9975:0:0.8 0/1:493:5:2,3:268,220:488,5:0.0101:2,2:19.8:1:29:1:0.66232:1.82501:51.6:10:0.0102:0:1.6 +6 54635573 . A G 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CAACAGGTCAAGAAGAGTAC;RSEQ=ATGCAATGAGGACCAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:446:0:0,0:231,215:446,0:0:2,0:25.7:1:30.6:1:1:0:47:110.5:1:0:0.7 0/1:330:12:8,4:176,142:318,12:0.0364:2,2:30.3:1:28.1:1:0.55949:1.61:49.4:11:0.0344:0:1.1 +6 54635601 . T TG 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.63615;SOR=0.72744;LSEQ=GAGGACCAGTACATGAGGAC;RSEQ=GGGCGGGGGGGGGGGGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:13:5,8:200,197:397,13:0.0317:2,2:12.1:1:31.8:1:0.57479:1.62246:39.5:26:0.033:0:0.2 0/1:258:6:3,3:154,97:251,6:0.0233:2,2:13:1:31.3:1:0.68045:1.58462:40.3:12:0.0253:0:0.5 +6 54635605 . CGGGGGGGG GC 255 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=16.000;MSILEN=1;SSF=0;SOR=0.1641;LSEQ=AGGACCAGTACATGAGGACT;RSEQ=GGGGGGGGCTTTCTTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:412:264:119,145:27,16:43,264:0.6408:2,2:30:1:31.7:1:0.03341:2.05139:46.6:528:0.6471:0.0413:0.1 0/1:270:61:25,36:45,15:60,61:0.2259:2,2:23.8:1:28.8:1:0.00021:4.26339:49.6:11.2:0.2188:0.0741:0.4 +6 54635613 . G C 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=16.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATGAGGACTGGGCGGGGGGG;RSEQ=GGGGGGGGCTTTCTTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:47:19,28:58,54:112,47:0.2938:2,2:12.9:1:26.1:1:0.22499:1.57825:55.8:3.7:0.2552:0:1.4 0/0:254:0:0,0:131,107:238,0:0:2,0:16.7:1:28.8:1:1:0:48.4:18.833:1:0:0.9 +6 54635879 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19717;SOR=Inf;LSEQ=AGTTTGAGAAATAAAAGATG;RSEQ=GCAAAGATGGTAAGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:78,151:229,0:0:2,0:23.8:1:31.3:1:1:0:59.8:37.167:1:0:0.1 0/1:185:2:1,1:72,110:182,2:0.0108:2,2:28.5:1:28:1:1:1.52:60:4:0.0112:0:1.5 +6 54870777 . C CA 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.0345;SOR=Inf;LSEQ=GTCTATTGTGTTAATTTTTT;RSEQ=AAAAAAAAAAACAACTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:1,0:1,4:0.4:0,2:24.3:1:30:1:1:0:50:8:0.4:0:0.3 1/1:7:7:4,3:0,0:0,7:1:0,2:34:1:26.9:1:1:0:60:6:1:0.1429:0 +6 54872205 . A T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCCCCACATATGTGTGAAT;RSEQ=TGATCCTGTCATCATTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:31:0:1:0:46.5:4:1:0:2 +6 54872251 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGTTTTGCACACTACTC;RSEQ=ATGCAGTTTCTTCGTAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:28.5:1:1:0:46.5:4:1:0:2 +6 54872899 . T C 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77722;LSEQ=TTTCATTCATTTTTCTCTAT;RSEQ=CTTGTCTGTATGTCTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:34.5:1:33:0:1:0:35.5:4:0.4:0:2.5 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:42:0:32:0:1:0:46:2:0.3333:0:2 +6 54872912 . T C 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.32198;LSEQ=TCTCTATTCTTGTCTGTATG;RSEQ=CTTATTTCAGTAAGGTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:34.5:1:33:0:1:0:35.5:4:0.6667:0:2.5 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:46:0:33:0:1:0:46:2:0.3333:0:2 +6 54873271 . G A 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.2634;LSEQ=AACAGAAACTCTGGCCTTTT;RSEQ=GGTTTTCAGCATTTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:3,1:0.25:2,0:26:0:29:0:1:0:60:2:0.25:0:1 0/1:10:3:3,0:4,3:7,3:0.3:2,0:21.7:1:30:1:0.475:0:60:6:0.3:0:1 +6 54873564 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23588;SOR=Inf;LSEQ=AGCAAAGATGGGTGCCTCCT;RSEQ=CTTCTTCCGGGACCTCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:6,14:20,0:0:2,0:20:1:31.2:1:1:0:44.5:40:1:0:0.2 0/1:23:3:0,3:4,16:20,3:0.1304:2,0:9.7:1:30:0:1:0:29.7:6:0.1304:0:1 +6 54873667 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48791;SOR=0;LSEQ=GTTGGAGGGTCTCACCCAGT;RSEQ=GGGAGGCACAGGGAGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:18,2:0.1:2,2:31:0:32:0:1:1.54:42:4:0.1:0:1.5 0/0:18:0:0,0:9,9:18,0:0:2,0:25.9:1:29.6:1:1:0:51.5:36:1:0:0.3 +6 54873715 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAAGCACTTTGTCCCTT;RSEQ=GTGGAGAGGGTGTGTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:20,16:36,2:0.0526:2,2:33:1:32.5:1:1:1.24262:55.5:4:0.0541:0:1 0/0:12:0:0,0:4,8:12,0:0:2,0:32.6:1:30.5:1:1:0:42.3:24:1:0:0.4 +6 54873758 . G A 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.39396;SOR=2.46486;LSEQ=GGGGGAAACCCACTTGTCTG;RSEQ=GCTGCCTGGATTCCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:10:7,3:8,11:19,10:0.3448:2,2:31.5:1:29.6:1:0.24508:3.08:28.8:9:0.3333:0:1.7 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:9.8:1:29.8:1:1:0:34.8:8:0.5714:0:1 +6 54873784 . A G 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGATTCCTCAGAACTACC;RSEQ=GGAGTAGAGGCTAAGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:6,8:14,5:0.2632:2,0:18.8:1:28.8:1:0.04455:0:31.2:10:0.2632:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:32:0:1:0:31:2:1:0:1 +6 54873908 . G A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GAGTTATTGGAGATCCTGCA;RSEQ=GAAAGCCCCACCCACTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:2,4:4,4:8,6:0.4286:2,2:29.2:1:31.7:1:0.62704:1.90258:59.5:12:0.4286:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:15.5:1:32:0:1:0:60:4:1:0:0 +6 54874109 . C T 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.3705;LSEQ=TTCCCCCCGCCCAGGGAGCT;RSEQ=AGCGTGTTAGGCAGTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:3,2:3,4:7,5:0.4167:2,2:24.8:1:29.6:1:1:1.89:46.6:10:0.4167:0:2 1/0:4:2:0,2:1,1:2,2:0.5:2,0:18:1:29:0:1:0:59.5:4:0.5:0:1 +6 54874135 . A G 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAGGCAGTTGCAAGTCCC;RSEQ=GTGCTGGCTGCTACCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:6,5:0.4545:2,2:17.8:1:29.6:1:1:1.30:43.8:10:0.5:0:2.2 0/0:1:0:0,0:0,1:1,0:0:0,0:5:0:30:0:1:0:60:2:1:0:0 +6 54874302 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=0;LSEQ=TTGGGAAGCTAGGTCCCAGT;RSEQ=GCGTGGGTTCGTGAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:25.5:1:28.5:1:1:1.73:60:4:0.4:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:21.6:1:31.6:1:1:0:60:10:1:0:0.2 +6 54874413 . G T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52381;SOR=0.2952;LSEQ=CCGCCTTCCTTGGCTTGTGG;RSEQ=GACAGGGTACCCCTTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:22.3:1:30:1:1:0:60:8:0.8:0:1 1/0:4:2:1,1:2,0:2,2:0.5:0,2:27:1:31:0:1:0:60:4:0.5:0:1 +6 54874576 . T C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.94088;LSEQ=CGCTTATTATGTTTTTTTTT;RSEQ=CTATGGTAGACTCCAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:4,4:2,1:3,8:0.6154:2,2:12.4:1:29.6:1:1:1.87936:60:7:0.5833:0:1 1/0:5:3:1,2:1,1:2,3:0.6:2,2:22.3:1:31:1:1:1.7321:60:6:0.6:0:1 +6 54874637 . A AT 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGGCCCCACCCGAAGTTA;RSEQ=TTTTTTTTTTCTTTTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:24.3:1:29.7:1:1:0:46:6:0.6:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 55804858 . A AT 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49939;SOR=Inf;LSEQ=TTCTGATTTGACTTTTGTGC;RSEQ=TTTTTGGCTGGAATATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:22,19:41,0:0:2,0:25.1:1:30.9:1:1:0:55.7:82:1:0:0.1 0/1:50:2:1,1:27,21:48,2:0.04:2,2:26.5:1:29.5:1:1:1.2792:59.5:4:0.04:0:0 +6 55804954 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.49591;SOR=Inf;LSEQ=TCTTCATTATCATCATCATC;RSEQ=TCTTCAGCAGCATCAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:21,21:42,0:0:2,0:30.3:1:30.6:1:1:0:60:84:1:0:0 0/1:47:2:1,1:20,25:45,2:0.0426:2,2:27:1:31.5:1:1:1.24:60:4:0.0426:0:1 +6 55805131 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.2414;SOR=0;LSEQ=CACACTTCAACTGTAAGACC;RSEQ=TGGGTGGTGTTATTTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:71,55:126,2:0.0156:2,2:26:0:33.5:1:1:1.2883:42:4:0.0159:0:1.5 0/0:132:0:0,0:75,57:132,0:0:2,0:27.7:1:29.7:1:1:0:53.8:65:1:0:0.2 +6 55805151 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.49966;SOR=Inf;LSEQ=ATGGGTGGTGTTATTTCAAA;RSEQ=CCCCCAAGGGAAACTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:67,64:131,0:0:2,0:29.8:1:32.7:1:1:0:56.1:64.5:1:0:0.1 0/1:146:2:1,1:74,70:144,2:0.0137:2,2:36.5:1:30:1:1:1.05677:45:4:0.0141:0:1.5 +6 55805211 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49674;SOR=Inf;LSEQ=GTTGCCAGTGTTACTTAATT;RSEQ=GACTGCCTTCATAACTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:23,48:71,0:0:2,0:22.9:1:30.4:1:1:0:59.4:142:1:0:0.1 0/1:74:2:1,1:27,44:71,2:0.027:2,2:19.5:1:28:1:1:1.62:40:4:0.0274:0:1 +6 55805272 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49543;SOR=0;LSEQ=CAATTCATCTTTTCCACAGG;RSEQ=CCCTAAACTTACCATTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:16,21:37,2:0.0513:2,2:9.5:1:30:1:1:1.30:60:4:0.0526:0:1 0/0:34:0:0,0:16,18:34,0:0:2,0:20:1:31.4:1:1:0:60:33:1:0:0.2 +6 55805282 . T G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20658;SOR=Inf;LSEQ=TTTCCACAGGGCCCTAAACT;RSEQ=ACCATTCTTAAAGATAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:21,24:45,0:0:2,0:22.8:1:29.7:1:1:0:60:44:1:0:0.2 0/1:38:2:1,1:19,17:36,2:0.0526:2,2:25.5:1:33:1:1:1.11437:60:4:0.0541:0:1 +6 55805422 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.49738;SOR=Inf;LSEQ=CATGTCCATTGAATCTTCCA;RSEQ=GGGTGGTGGCACTCACTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:45,38:83,0:0:2,0:21.5:1:32:1:1:0:59.2:166:1:0:0.1 0/1:89:2:1,1:48,39:87,2:0.0225:2,2:17.5:1:29:1:1:1.22788:60:4:0.0225:0:0 +6 58774984 . T A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGCAGTTTCCAAACACTC;RSEQ=TTTGTAGAATTTGCAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:30.5:1:1:0:32:4:1:0:4 +6 58775010 . T G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATTTGCAAGGGTACATT;RSEQ=AGAGCGCATTCAGTCCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:33:1:1:0:32:4:1:0:4 +6 58775018 . A T 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGGTACATTTAGAGCGC;RSEQ=TTCAGTCCTATGGTACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:32:1:1:0:32:4:1:0:4 +6 58775024 . T G 33 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATTTAGAGCGCATTCAG;RSEQ=CCTATGGTACAAAAGGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:33:1:1:0:32:4:1:0:4 +6 58776492 . G C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACCTTCCTTTGGATACA;RSEQ=CAGTTTTGAAACACTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:32:0:1:0:60:4:1:0:2.5 +6 58776555 . T C 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.67735;LSEQ=TTAGAGCGCCTTGAAGCCTA;RSEQ=GCTAGAAATGGAAATATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:5,3:8,3:0.2727:2,2:16.3:1:29.7:1:0.54545:2.97405:28.3:6:0.3:0:1 0/1:15:3:1,2:5,7:12,3:0.2:2,2:39:1:30.3:1:1:1.39581:22:6:0.2143:0:1.3 +6 58776575 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51087;SOR=Inf;LSEQ=TGCTAGAAATGGAAATATCT;RSEQ=CCCATAAAACCAAGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:9,0:0:2,0:40.1:1:30.9:1:1:0:21.4:18:1:0:0.9 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:24:0:30:0:1:1.55:22:4:0.1429:0:1.5 +6 58776735 . C T 32 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=CTAGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTCCATCTAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:26:0:32:1:1:1:20:4:0.5:0:4 0/0:2:0:0,0:1,1:2,0:0:2,0:32.5:1:30.5:1:1:0:60:4:1:0:1 +6 58776745 . C T 61 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGTTGGAAACGGGATTTCT;RSEQ=CATCTAAACCTACAGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:28.3:1:30.8:1:1:0:20.5:8:1:0:2.8 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:30.5:1:1:0:60:4:1:0:1 +6 58776821 . C G 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61079;SOR=0.41858;LSEQ=CTCACAGAATGGAACATTCC;RSEQ=TTTGATAGAGCAGTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:4,2:6,3:0.3333:2,2:25:1:31.3:1:0.52381:3.38757:36:6:0.375:0:1.7 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:35:1:33:1:1:1.45:24.5:4:0.1667:0:1.5 +6 58776855 . A G 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26316;SOR=Inf;LSEQ=TTTTGAGACACCGTTTTTGT;RSEQ=GAATTCCCAAGTGGATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:41:1:29.9:1:1:0:21.3:14:1:0:0.7 0/1:12:3:1,2:4,5:9,3:0.25:2,2:38.3:1:29.3:1:1:1.53983:24:6:0.25:0:1.7 +6 58776887 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54117;SOR=Inf;LSEQ=TGGATATTTAGAGCACTTTG;RSEQ=AGTCTCTGCTAGAAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:6,10:16,0:0:2,0:17.5:1:30.6:1:1:0:29.5:32:1:0:1.1 0/1:31:3:1,2:16,11:27,3:0.0968:2,2:14:1:32:1:0.56453:2.80646:25.7:6:0.0968:0:1.7 +6 58776909 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTCTCTGCTAGAAAAGGAAA;RSEQ=ATCTTCATGTAAAAAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:17,0:0:2,0:29.1:1:33.1:1:1:0:31.2:34:1:0:1.4 0/1:42:2:1,1:24,16:40,2:0.0476:2,2:46:1:30:1:1:1.48518:26:4:0.0513:0:2 +6 58776910 . A T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08227;SOR=0;LSEQ=TCTCTGCTAGAAAAGGAAAC;RSEQ=TCTTCATGTAAAAAGTAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:6,9:15,2:0.1176:2,2:47:0:32:1:1:1.46:21:4:0.1176:0:1 0/0:41:0:0,0:25,16:41,0:0:2,0:29.3:1:29.7:1:1:0:32.3:82:1:0:1.3 +6 58776918 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGAAAAGGAAACATCTTCAT;RSEQ=TAAAAAGTAGATAGAATCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:9,11:20,0:0:2,0:30:1:31.8:1:1:0:33.3:19:1:0:1.5 0/1:49:2:1,1:28,19:47,2:0.0408:2,2:12:1:27.5:1:1:1.46176:22:4:0.0408:0:1.5 +6 58776930 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53352;SOR=Inf;LSEQ=ATCTTCATGTAAAAAGTAGA;RSEQ=AGAATCGTTCTCAGAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:31,0:0:2,0:24.2:1:30.2:1:1:0:33.5:62:1:0:1.7 0/1:55:2:1,1:30,23:53,2:0.0364:2,2:18.5:1:32.5:1:1:1.29798:22.5:4:0.0377:0:3 +6 58776932 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13258;SOR=0;LSEQ=CTTCATGTAAAAAGTAGATA;RSEQ=AATCGTTCTCAGAAAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:15,15:30,2:0.0625:2,2:40:1:30.5:1:1:1:49.5:4:0.0625:0:3 0/0:55:0:0,0:31,22:53,0:0:2,0:28.9:1:31.2:1:1:0:32.4:52:0.963:0:1.5 +6 58776942 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13258;SOR=0;LSEQ=AAAGTAGATAGAATCGTTCT;RSEQ=AGAAAGTGCTTAGTGACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:15,15:30,2:0.0625:2,2:30:1:29:1:1:1:49.5:4:0.0645:0:3 0/0:55:0:0,0:31,24:55,0:0:2,0:29.5:1:30.6:1:1:0:32.3:26.5:1:0:1.5 +6 58776950 . G A 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52954;SOR=Inf;LSEQ=TAGAATCGTTCTCAGAAAGT;RSEQ=CTTAGTGACGTGTGCGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:16,15:31,0:0:2,0:28.8:1:33.2:1:1:0:33.3:62:1:0:1.5 0/1:55:2:1,1:30,23:53,2:0.0364:2,2:6:0:30.5:1:1:1.29798:60:4:0.0377:0:1.5 +6 58776958 . A T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53026;SOR=Inf;LSEQ=TTCTCAGAAAGTGCTTAGTG;RSEQ=CGTGTGCGTTCAACTCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:30,0:0:2,0:29.9:1:29.5:1:1:0:33.9:14:1:0:1.7 0/1:52:2:1,1:29,20:49,2:0.0385:2,2:17:0:30.5:1:1:1.43922:29:4:0.0392:0:1.5 +6 58776965 . C T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46933;SOR=0.64421;LSEQ=AAAGTGCTTAGTGACGTGTG;RSEQ=GTTCAACTCACAGAGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:18:8,10:7,4:11,18:0.6207:2,2:27.8:1:28.8:1:0.44973:2.1283:34.2:8:0.5926:0:2.2 1/0:43:22:12,10:12,9:21,22:0.5116:2,2:26.5:1:28.4:1:1:1.10839:33.1:21:0.5:0:2.2 +6 58776982 . G T 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31857;SOR=0.44094;LSEQ=GTGCGTTCAACTCACAGAGT;RSEQ=TAACGTTTCTTTTGATAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:10,9:2,1:3,19:0.8636:2,2:23.7:1:29.2:1:1:1.75399:34.3:8.5:0.8947:0:1.7 1/0:30:22:13,9:4,4:8,22:0.7333:2,2:21.2:1:28.8:1:0.69763:1.43:32.2:21:0.7241:0:2 +6 58776992 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49024;SOR=Inf;LSEQ=CTCACAGAGTGTAACGTTTC;RSEQ=TTTGATAGAGCGTTTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:11,8:19,0:0:2,0:19.7:1:30.2:1:1:0:31:38:1:0:1.7 0/1:22:2:1,1:11,9:20,2:0.0909:2,2:9.5:1:28:1:1:1.21106:37.5:4:0.0909:0:3 +6 58777056 . G T 85 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.81102;LSEQ=AGTGGATATTTGGACCTATT;RSEQ=GAGGCCTTCTTTGGAAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,0:0,5:0.8333:0,2:6.8:1:29.8:1:1:0:43:10:1:0:2.4 1/1:10:8:6,2:0,1:1,8:0.8:0,2:4.9:1:28.4:1:0.33333:0:49.3:16:0.8:0:2.8 +6 58777071 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51337;SOR=Inf;LSEQ=CTATTGGAGGCCTTCTTTGG;RSEQ=AACGGGATTTCTTCATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:13,0:0:2,0:16.4:1:28.9:1:1:0:49.1:12:1:0:2 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:18:1:30:1:1:1.11:32.5:4:0.0952:0:3 +6 58777094 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49675;SOR=Inf;LSEQ=CGGGATTTCTTCATGTAACT;RSEQ=TAGATTGAAGAATTCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:8,17:25,0:0:2,0:25.8:1:32.4:1:1:0:46.9:24:1:0:1.8 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:33.5:1:28:1:1:1.07:60:4:0.0667:0:3.5 +6 58777098 . A T 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.56765;SOR=1.5921;LSEQ=ATTTCTTCATGTAACTCTAG;RSEQ=TTGAAGAATTCTCAGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:1,5:9,12:21,6:0.2222:2,2:32.7:1:29.5:1:0.36252:3.59095:49.3:12:0.2222:0:2.8 0/1:35:11:7,4:10,14:24,11:0.3143:2,2:24.4:1:28.8:1:0.28899:2.39:42.4:22:0.3235:0:3.2 +6 58777108 . TC CT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49796;SOR=Inf;LSEQ=GTAACTCTAGATTGAAGAAT;RSEQ=TCAGAAACTCCTTTGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:12,18:30,0:0:2,0:30.8:1:30.5:1:1:0:43.3:29:1:0:1.8 0/1:37:2:1,1:17,18:35,2:0.0541:2,2:18.5:1:31.5:1:1:1.06:28:4:0.0541:0:1.5 +6 58777109 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.25489;LSEQ=TAACTCTAGATTGAAGAATT;RSEQ=TCAGAAACTCCTTTGTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:27:11,16:1,2:3,27:0.9:2,2:32.3:1:30.9:1:1:1.36:44.6:54:0.9:0:2 1/1:37:34:17,17:0,1:1,34:0.9189:0,2:31.4:1:29.5:1:1:0:44.9:33:0.9706:0:2.4 +6 58777121 . T G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49556;SOR=Inf;LSEQ=GAAGAATTCTCAGAAACTCC;RSEQ=TTGTGATGTGTGCATTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:16,20:36,0:0:2,0:28.6:1:31.3:1:1:0:42.1:35:1:0:1.8 0/1:41:2:1,1:19,20:39,2:0.0488:2,2:40.5:1:31.5:1:1:1.05:60:4:0.0488:0:3.5 +6 58777135 . A C 33 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60772;SOR=0.45856;LSEQ=AACTCCTTTGTGATGTGTGC;RSEQ=TTCAATTCAAAGAGTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:18,22:40,2:0.0476:2,2:16:0:33.5:1:1:1.22:27:4:0.0476:0:2.5 0/1:45:1:0,1:22,22:44,1:0.0222:2,0:19:0:34:0:1:0:54:2:0.0227:0:4 +6 58777156 . C G 84 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07768;SOR=4.43614;LSEQ=TTCAATTCAAAGAGTGAAAC;RSEQ=TCCCTTTTCACAGAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:2,0:20,20:40,2:0.0476:2,0:45:1:31:1:0.48897:0:24:4:0.0488:0:3 0/1:38:7:3,4:15,16:31,7:0.1842:2,2:19.6:1:30:1:1:1.24271:38.1:14:0.1842:0:2.9 +6 58777164 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23557;SOR=0;LSEQ=AAAGAGTGAAACCTCCCTTT;RSEQ=CACAGAGCAGTTTGGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:20,20:40,2:0.0476:2,2:8:1:30.5:1:1:1:42.5:4:0.0476:0:2 0/0:44:0:0,0:22,22:44,0:0:2,0:19.1:1:29:1:1:0:41.8:88:1:0:1.9 +6 58777178 . G T 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.65395;LSEQ=CCCTTTTCACAGAGCAGTTT;RSEQ=GAAACACTGTTTTTGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:42:24,18:0,0:0,42:0.9545:0,2:21.4:1:30.4:1:1:0:38.4:41:0.9535:0:1.6 1/1:44:41:22,19:1,2:3,41:0.9318:2,2:21.4:1:29.4:1:0.59884:2.27:39.7:82:0.9318:0:1.9 +6 58777185 . C G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4953;SOR=Inf;LSEQ=CACAGAGCAGTTTGGAAACA;RSEQ=TGTTTTTGTAGGATTTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:25,17:42,0:0:2,0:23.8:1:32.8:1:1:0:36.4:84:1:0:1.5 0/1:46:2:1,1:23,21:44,2:0.0435:2,2:31.5:1:31:1:1:1.09307:46:4:0.0435:0:3.5 +6 58777231 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22788;SOR=0;LSEQ=TATTTATAGCGCATTGAGCC;RSEQ=ACGGCAGAAAAAGAAACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:28,18:46,2:0.0417:2,2:18.5:1:32:1:1:1.54082:54.5:4:0.0426:0:1 0/0:52:0:0,0:27,25:52,0:0:2,0:26.5:1:29.1:1:1:0:48.2:51:1:0:1.3 +6 58777233 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55748;SOR=1.55474;LSEQ=TTTATAGCGCATTGAGCCTA;RSEQ=GGCAGAAAAAGAAACATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:4,1:24,17:41,5:0.1087:2,2:34.2:1:31.4:1:0.63434:2.78:40.2:10:0.1087:0:2.2 0/1:50:8:5,3:21,21:42,8:0.16:2,2:28.8:1:29:1:0.70411:1.65:48.1:7:0.1458:0:2.6 +6 58777237 . A G 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49744;SOR=Inf;LSEQ=TAGCGCATTGAGCCTACGGC;RSEQ=GAAAAAGAAACATCTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:27,15:42,0:0:2,0:23.1:1:31.3:1:1:0:45:84:1:0:1.2 0/1:49:2:1,1:25,22:47,2:0.0408:2,2:7.5:1:28:1:1:1.13339:34:4:0.0417:0:2.5 +6 58777245 . A G 34 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18045;SOR=0;LSEQ=TGAGCCTACGGCAGAAAAAG;RSEQ=AACATCTTCCTATAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:22,9:31,2:0.0606:2,2:6:0:34:1:0.52083:2.37114:42:4:0.0606:0:2.5 0/0:44:0:0,0:22,22:44,0:0:2,0:25.3:1:28.9:1:1:0:48.6:13.667:1:0:1.3 +6 58777295 . T C 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.40625;SOR=0;LSEQ=AATTCTCAGAATCTGCTTTG;RSEQ=GATGTGTGCGTTCAACTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:11,8:0,0:0,19:1:0,2:13.1:1:30.7:1:1:0:38.2:38:1:0:2.6 1/1:13:12:6,6:1,0:1,12:0.9231:0,2:11.3:1:29.9:1:1:0:31.8:24:0.9231:0:2.4 +6 58777300 . T G 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00723;SOR=0;LSEQ=TCAGAATCTGCTTTGTGATG;RSEQ=GTGCGTTCAACTCATAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:2,5:5,5:10,7:0.4118:2,2:24.3:1:30.9:1:0.62207:2.36758:44.6:14:0.4118:0:4.4 0/0:16:0:0,0:8,8:16,0:0:2,0:9.1:1:29:1:1:0:32.6:32:1:0:2.6 +6 58777312 . T C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.69739;SOR=0.55139;LSEQ=TTGTGATGTGTGCGTTCAAC;RSEQ=CATAGAGTAAAACTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:4,8:1,2:3,12:0.8:2,2:23.8:1:31.4:1:1:1:49.4:24:0.8:0:4.1 1/0:19:13:7,6:3,3:6,13:0.6842:2,2:10.4:1:30.4:1:1:1.16:44.3:26:0.6842:0:3.4 +6 58777315 . T C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGTGTGCGTTCAACTCA;RSEQ=AGAGTAAAACTTTTCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:0,15:1:0,2:26.6:1:32.3:1:1:0:43.9:30:1:0:3.9 1/1:22:21:10,11:0,1:1,21:0.9545:0,2:14.2:1:31.1:1:1:0:42.1:42:0.9545:0:3.1 +6 58777334 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52087;SOR=Inf;LSEQ=ATAGAGTAAAACTTTTCTTT;RSEQ=GATAGAGCAGTTTTGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:22,0:0:2,0:27.3:1:31.6:1:1:0:43.3:44:1:0:3.5 0/1:36:2:1,1:16,18:34,2:0.0556:2,2:18:1:26.5:1:1:1.12:47:4:0.0556:0:3 +6 58777335 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14294;SOR=0;LSEQ=TAGAGTAAAACTTTTCTTTT;RSEQ=ATAGAGCAGTTTTGAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:10,11:21,2:0.087:2,2:43:1:32:1:1:1.10:38:4:0.087:0:5.5 0/0:37:0:0,0:17,20:37,0:0:2,0:23.8:1:30.4:1:1:0:42.8:36:1:0:2.5 +6 58777365 . AATATTTGCATGTGT GGAAAATGCAAGTGG 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07331;SOR=0;LSEQ=TTTTGAAACACTCTTTTTGT;RSEQ=ATATTTAGAGCGCATTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:1,2:17,16:33,3:0.0811:2,2:22:1:32.3:1:1:2.08218:42.7:6:0.0833:0.0541:1.7 0/0:50:0:0,0:25,25:50,0:0:2,0:30.4:1:29:1:1:0:44.6:100:1:0:2.2 +6 58777366 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.15714;SOR=Inf;LSEQ=TTTGAAACACTCTTTTTGTA;RSEQ=TATTTGCATGTGTATATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:32:17,15:0,0:0,32:0.9412:0,2:25.3:1:32.9:1:1:0:43.6:64:1:0:2.8 1/1:51:51:26,25:0,0:0,51:1:0,2:29.9:1:31.6:1:1:0:44.4:102:1:0:2.2 +6 58777393 . A T 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.80484;LSEQ=CATGTGTATATTTAGAGCGC;RSEQ=TTGAAGCCCACAGTAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:2,0:25,24:49,2:0.0392:2,0:21.5:1:34:0:0.49176:0:46.5:4:0.0392:0:2.5 0/1:63:2:1,1:35,26:61,2:0.0317:2,2:31.5:1:28:1:1:1.33971:40.5:4:0.0323:0:4 +6 58777397 . A G 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.54264;LSEQ=TGTATATTTAGAGCGCATTG;RSEQ=AGCCCACAGTAGAAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:1,0:26,22:48,1:0.0204:2,0:30:0:33:0:1:0:33:2:0.0204:0:4 0/1:64:2:1,1:35,27:62,2:0.0313:2,2:27.5:1:28.5:1:1:1.29098:40.5:4:0.0317:0:4 +6 58777401 . C A 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40431;SOR=0.38408;LSEQ=TATTTAGAGCGCATTGAAGC;RSEQ=CACAGTAGAAAAGGAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:4:3,1:27,21:48,4:0.0769:2,2:26:1:31:1:0.62883:2.30:32.8:8:0.0816:0:2 0/1:65:2:1,1:37,26:63,2:0.0308:2,2:4.5:1:26:1:1:1.4152:23:4:0.0313:0:2 +6 58777419 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09406;LSEQ=GCCCACAGTAGAAAAGGAAA;RSEQ=AACTTCACCTAAAACCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:32:16,16:16,8:24,32:0.5714:2,2:21.5:1:32.3:1:0.27854:1.97518:45.9:31:0.5741:0:1.7 0/1:55:6:4,2:28,21:49,6:0.1091:2,2:23.5:1:32.2:1:1:1.49:37.5:12:0.1091:0:2.3 +6 58777461 . C T 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40356;SOR=0.37794;LSEQ=AGAAGCAATCTCAGAAACTA;RSEQ=TTTGTGATGTGTACATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:4:3,1:25,26:51,4:0.0727:2,2:10.8:1:29.8:1:0.61098:3.06:32.5:8:0.0727:0:2 0/1:70:2:1,1:40,28:68,2:0.0286:2,2:15:0:28.5:1:1:1.42114:21:4:0.029:0:1 +6 58777486 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51234;SOR=Inf;LSEQ=TGATGTGTACATTCAACTCA;RSEQ=AGAGTGGAACTTTCCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:34,0:0:2,0:33.4:1:33:1:1:0:33:68:1:0:0.8 0/1:50:2:1,1:26,22:48,2:0.04:2,2:14.5:1:28.5:1:1:1.17786:27:4:0.04:0:1.5 +6 58777500 . C T 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70875;SOR=0.66227;LSEQ=AACTCACAGAGTGGAACTTT;RSEQ=CTCTTTATAGAGCAGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:3,1:13,14:27,4:0.129:2,2:29.5:1:31.8:1:0.59956:3.12:31:8:0.129:0:1.5 0/1:45:4:2,2:21,19:40,4:0.0889:2,2:17:1:31:1:1:1.10275:35:8:0.0909:0:1.3 +6 58777508 . T G 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03099;SOR=0;LSEQ=GAGTGGAACTTTCCTCTTTA;RSEQ=AGAGCAGTGTTGAAACACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:2,2:12,13:25,4:0.1379:2,2:23.3:1:34.5:1:1:1.08:38:8:0.1379:0:1.5 0/0:38:0:0,0:19,18:37,0:0:2,0:24.4:1:28.5:1:1:0:26.6:74:0.9737:0:0.5 +6 58777546 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.39474;SOR=0;LSEQ=CTCTTTTTGTAGAAACTGCA;RSEQ=GTGGATATTTGGACCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:14,9:0,0:0,23:1:0,2:18.6:1:31.1:1:1:0:27.2:46:1:0:2.1 1/1:15:14:5,9:1,0:1,14:0.9333:0,2:14.6:1:28.5:1:0.4:0:24.4:13:0.9286:0:1.7 +6 58777573 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.58199;LSEQ=ATTTGGACCTCTTTGAGGCC;RSEQ=TCGTTGGAAACGGGATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:33:20,13:1,0:1,33:0.9706:0,2:28.5:1:31.1:1:1:0:38.2:66:0.9706:0:1.7 1/1:20:19:10,9:1,0:1,19:0.95:0,2:20.7:1:28.6:1:1:0:43.4:38:0.95:0:1.5 +6 58777575 . C T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27143;SOR=0;LSEQ=TTGGACCTCTTTGAGGCCCT;RSEQ=GTTGGAAACGGGATTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:2,1:19,12:31,3:0.0882:2,2:37:1:32:1:1:1.25:31.7:6:0.0882:0:2.7 0/0:22:0:0,0:12,10:22,0:0:2,0:20.8:1:29.5:1:1:0:44.1:44:1:0:1.5 +6 58777634 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50788;SOR=0;LSEQ=GAATTTTCAGAAACCTCATT;RSEQ=TGATGTGTGCGTTCATCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:26,30:56,2:0.0345:2,2:21.5:1:29:1:1:1.15:60:4:0.0345:0:1 0/0:42:0:0,0:21,21:42,0:0:2,0:21.8:1:31.8:1:1:0:57:84:1:0:0.6 +6 58777666 . C G 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17379;SOR=5.09312;LSEQ=TTCATCTCACAGAGTGGAGT;RSEQ=TTCCGTTTGATAGAGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:1:0,1:25,28:53,1:0.0185:2,0:47:0:31:0:1:0:60:2:0.0185:0:1 0/1:45:4:2,2:20,21:41,4:0.0889:2,2:27.3:1:32.5:1:1:1.05:52:8:0.0909:0:1.3 +6 58777684 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49821;SOR=0;LSEQ=GTCTTCCGTTTGATAGAGAA;RSEQ=TTTTGAAACCCTGTTCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:23,28:51,2:0.0377:2,2:24.5:1:34.5:1:1:1.21:59:4:0.0377:0:1 0/0:45:0:0,0:27,18:45,0:0:2,0:24.3:1:32.1:1:1:0:55:90:1:0:0.4 +6 58777685 . T C 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.59393;LSEQ=TCTTCCGTTTGATAGAGAAG;RSEQ=TTTGAAACCCTGTTCTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:24,28:52,2:0.037:2,2:26:1:32:1:1:1.16:60:4:0.037:0:1 0/1:45:1:0,1:27,17:44,1:0.0222:2,0:39:0:32:0:0.4:0:60:2:0.0227:0:1 +6 58777715 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49317;SOR=Inf;LSEQ=CTGTTCTTGTAGGATTTCCA;RSEQ=GTGGATATTTAGACCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:14,20:34,0:0:2,0:29.2:1:31.5:1:1:0:50.5:68:1:0:0.3 0/1:36:2:0,2:23,11:34,2:0.0556:2,0:22:1:27.5:1:0.12381:0:60:4:0.0556:0:2 +6 58777766 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0;LSEQ=ATAGAAAAGGAAACATCTTC;RSEQ=TGGAAAACATAGATAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:23:1:30:1:1:1.45:25:4:0.1667:0:1 0/0:9:0:0,0:8,1:9,0:0:2,0:11.4:1:27.2:1:1:0:35.7:18:1:0:0.2 +6 58777785 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGAAAACATAGATAGAA;RSEQ=CATTCTCAGAAACAACTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,3:3,2:0.4:0,2:8:0:33.5:1:0.4:0:20:4:0.4:0:2.5 0/0:2:0:0,0:0,2:2,0:0:0,0:3.5:1:27.5:1:1:0:23:4:1:0:0.5 +6 58777836 . A C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51417;SOR=Inf;LSEQ=GTTGAACTCACCGTCTTTAA;RSEQ=CTTTCTTTTGGTAGAGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:8,14:1,1:2,22:0.9167:2,2:24:1:31.2:1:1:1.70775:31.8:44:0.9167:0:1.5 1/1:15:15:6,9:0,0:0,15:1:0,2:29.5:1:31.5:1:1:0:31.5:30:1:0:1.5 +6 58777960 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49673;SOR=0;LSEQ=TAAAAGGCAGACAGAAGTGT;RSEQ=CTCAGAAACTGCTTTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:7,2:9,2:0.1818:2,0:11.5:1:34:0:1:0:28:4:0.2:0:4.5 0/0:7:0:0,0:3,4:7,0:0:2,0:8.7:1:28.7:1:1:0:36:14:1:0:3.6 +6 58777995 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23585;SOR=Inf;LSEQ=TGTGATGTCTGTGTTCAACT;RSEQ=ACAGAGTTTAACATTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:27,0:0:2,0:28.8:1:31.4:1:1:0:36.4:12.5:1:0:3.3 0/1:26:2:1,1:13,11:24,2:0.0769:2,2:44:1:29:1:1:1.17422:34.5:4:0.0769:0:5 +6 58778001 . G A 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58173;SOR=0.39135;LSEQ=GTCTGTGTTCAACTCACAGA;RSEQ=TTTAACATTTCCTTTGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:16,11:27,2:0.069:2,2:23:1:30:1:1:1.43545:43:4:0.069:0:1.5 0/1:36:1:1,0:16,18:34,1:0.0278:2,0:33:0:31:0:0.48571:0:45:2:0.0286:0:3 +6 58778003 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50311;SOR=Inf;LSEQ=CTGTGTTCAACTCACAGAGT;RSEQ=TAACATTTCCTTTGATAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:18,12:30,0:0:2,0:30.1:1:30.5:1:1:0:36.2:29:1:0:3.5 0/1:40:2:1,1:18,20:38,2:0.05:2,2:49:1:32:1:1:1.11:34.5:4:0.0526:0:5 +6 58778019 . T G 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3985;SOR=0.56843;LSEQ=GAGTTTAACATTTCCTTTGA;RSEQ=AGAGCAGTTTAGTAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:31:19,12:2,3:5,31:0.8611:2,2:30.8:1:33.3:1:0.62957:2.32:34:62:0.8611:0:4.1 1/0:45:35:15,20:6,4:10,35:0.7778:2,2:29.9:1:30.9:1:0.47637:1.96904:37.8:34:0.7727:0:3.9 +6 58778025 . A G 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45592;SOR=2.23527;LSEQ=AACATTTCCTTTGATAGAGC;RSEQ=GTTTAGTAACACTGTCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:31:19,12:2,3:5,31:0.8611:2,2:30.8:1:30.4:1:0.62957:2.32:34:62:0.8611:0:4.1 1/1:45:42:20,22:1,2:3,42:0.9333:2,2:28.2:1:30:1:1:1.80:36.9:41:0.9318:0:3.6 +6 58778039 . G C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGCAGTTTAGTAACACT;RSEQ=TCTTTGTAGAATTTGGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:22,21:0,0:0,43:1:0,2:25.5:1:32.3:1:1:0:32.9:20.5:1:0:4 1/1:46:46:23,23:0,0:0,46:1:0,2:27.7:1:31.2:1:1:0:36.2:92:1:0:3.8 +6 58778081 . TT GC 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=TATACTAAGAGCGCTTTGAG;RSEQ=CTATGGTAGAAAAGGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:28:13,15:0,0:0,28:1:0,2:28:1:32.2:1:1:0:28.2:56:1:0:3.5 1/1:27:26:13,13:0,0:0,26:0.963:0,2:22:1:30.4:1:1:0:31.8:25:0.9615:0.1481:3.5 +6 58778086 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4949;SOR=0;LSEQ=TAAGAGCGCTTTGAGTTCTA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:12,14:26,2:0.0714:2,2:29:1:31.5:1:1:1.16:26:4:0.0714:0:4.5 0/0:23:0:0,0:10,13:23,0:0:2,0:23.7:1:29.8:1:1:0:30.2:46:1:0:3.6 +6 58778100 . A T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.23787;SOR=2.862;LSEQ=GTTCTATGGTAGAAAAGGAA;RSEQ=TATCTTTGCATAAAAGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:1,2:7,9:16,3:0.1579:2,2:21:1:30:1:1:1.52085:25:6:0.1579:0:4.3 0/1:14:5:2,3:5,4:9,5:0.3571:2,2:27:1:30.2:1:1:1.79176:27.6:10:0.3571:0:3.8 +6 58778108 . G C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGAAAAGGAAATATCTTT;RSEQ=CATAAAAGCTAGACAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:0,15:1:0,2:26.3:1:31.7:1:1:0:22.9:30:1:0:3.1 1/1:9:9:6,3:0,0:0,9:1:0,2:36.2:1:28.2:1:1:0:23.8:8:1:0:3.1 +6 58778142 . C A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48276;SOR=Inf;LSEQ=CAGAAGCAATCTCAGAAACT;RSEQ=CTTTGTGATGTCTGCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:4,11:15,0:0:2,0:13.1:1:29.7:1:1:0:26.5:30:1:0:1.4 0/1:15:2:1,1:7,6:13,2:0.1333:2,2:7.5:1:25:1:1:1.1547:29:4:0.1333:0:4 +6 58778193 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50101;SOR=0;LSEQ=TGGAACATTCCTCTTGATAG;RSEQ=GCAGTTTGGAAACGCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:15,23:38,2:0.05:2,2:29.5:1:30.5:1:1:1.52:58:4:0.0513:0:3 0/0:31:0:0,0:17,14:31,0:0:2,0:29.7:1:29.7:1:1:0:44.2:62:1:0:1.8 +6 58778202 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19444;SOR=Inf;LSEQ=CCTCTTGATAGAGCAGTTTG;RSEQ=AAACGCTCTTTCTGTAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:18,27:45,0:0:2,0:30.5:1:31.8:1:1:0:47.4:44:1:0:2 0/1:36:2:1,1:18,16:34,2:0.0556:2,2:19.5:1:29:1:1:1.12132:60:4:0.0556:0:2.5 +6 58778207 . G A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47126;SOR=0;LSEQ=TGATAGAGCAGTTTGGAAAC;RSEQ=CTCTTTCTGTAGAATCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:46:19,27:0,0:0,46:1:0,2:31:1:30.8:1:1:0:47.7:92:1:0:2 1/1:41:40:20,20:0,0:0,40:0.9756:0,2:25.3:1:29.3:1:1:0:47.8:80:0.9756:0:1.9 +6 58778244 . A T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.47368;SOR=0;LSEQ=AGCTTGTTTGTATTTGGACC;RSEQ=CCTTGAGGCCTTCGTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:50:25,25:0,0:0,50:1:0,2:21:1:31.7:1:1:0:54.9:100:1:0:2 1/1:45:44:25,19:0,0:0,44:0.9778:0,2:25:1:29.1:1:1:0:58.2:21:1:0:1.8 +6 58778284 . AC A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20024;SOR=0;LSEQ=AACGGGTTTTCATCTTATAA;RSEQ=CCAGACAGAAGAATTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:21,18:39,2:0.0488:2,2:25:1:30:1:1:1.16227:60:4:0.0488:0:0.5 0/0:50:0:0,0:24,26:50,0:0:2,0:25:1:31.1:1:1:0:60:100:1:0:1.1 +6 58778289 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50311;SOR=Inf;LSEQ=GTTTTCATCTTATAAACCCA;RSEQ=ACAGAAGAATTCTCAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:21,19:40,0:0:2,0:23.2:1:32.9:1:1:0:59.8:80:1:0:0.8 0/1:52:2:1,1:25,25:50,2:0.0385:2,2:28:1:27.5:1:1:1:60:4:0.0385:0:1 +6 58778308 . T A 44 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.28571;SOR=Inf;LSEQ=AGACAGAAGAATTCTCAGAG;RSEQ=CTTCTTTGTGATGTGTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:22,18:40,0:0:2,0:26.8:1:30.4:1:1:0:59.9:80:1:0:0.4 0/1:65:3:2,1:30,32:62,3:0.0462:2,2:7.7:1:28:1:0.61319:2.11:60:6:0.05:0:2.7 +6 58778325 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52085;SOR=Inf;LSEQ=GAGTCTTCTTTGTGATGTGT;RSEQ=CTTTCAACTCACCGAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:51,0:0:2,0:24.7:1:32.4:1:1:0:59.6:102:1:0:0.7 0/1:80:2:1,1:40,38:78,2:0.025:2,2:21.5:1:28:1:1:1.05198:60:4:0.0256:0:1.5 +6 58778338 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00539;SOR=Inf;LSEQ=GATGTGTGCTTTCAACTCAC;RSEQ=GAGATAAAGATTTCTCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:51,0:0:2,0:25.5:1:30.3:1:1:0:59.6:50:1:0:0.9 0/1:74:10:5,5:30,34:64,10:0.1351:2,2:27.3:1:29.8:1:1:1.13:58.2:20:0.1389:0:2.2 +6 58778339 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5106;SOR=Inf;LSEQ=ATGTGTGCTTTCAACTCACC;RSEQ=AGATAAAGATTTCTCTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:51,0:0:2,0:25.5:1:30.3:1:1:0:59.6:24.5:1:0:0.9 0/1:72:2:1,1:34,36:70,2:0.0278:2,2:28.5:1:28:1:1:1.06:60:4:0.029:0:2.5 +6 58778354 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52375;SOR=Inf;LSEQ=TCACCGAGATAAAGATTTCT;RSEQ=TTGATAGAGCAATTTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:23,26:49,0:0:2,0:25.7:1:32.1:1:1:0:59.6:23.5:1:0:1 0/1:79:2:1,1:39,38:77,2:0.0253:2,2:15:1:32:0:1:1.02598:39:4:0.0256:0:3 +6 58778360 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53635;SOR=Inf;LSEQ=AGATAAAGATTTCTCTTGAT;RSEQ=GAGCAATTTGGAAACACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:22,25:47,0:0:2,0:25.4:1:29.9:1:1:0:60:46:1:0:1.1 0/1:84:2:1,1:41,41:82,2:0.0238:2,2:30:1:29:1:1:1:60:4:0.0247:0:2.5 +6 58778392 . T C 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACACTCTTTTTGTAGAAT;RSEQ=TGCAAGGGTACCCTGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:18,15:33,0:0:2,0:23.5:1:30.5:1:1:0:57.5:32:1:0:2.6 0/1:74:2:1,1:36,36:72,2:0.027:2,2:7:0:30:1:1:1:34:4:0.027:0:1 +6 58778394 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACTCTTTTTGTAGAATTT;RSEQ=CAAGGGTACCCTGAGAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:18,16:34,0:0:2,0:22.3:1:32.6:1:1:0:57.5:33:1:0:2.8 0/1:71:2:1,1:33,36:69,2:0.0282:2,2:20:1:28.5:1:1:1.09:60:4:0.0286:0:2.5 +6 58778404 . CC AT 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGAATTTGCAAGGGTAC;RSEQ=TGAGAGTGCTTTCAGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:15,16:0,0:0,31:1:0,2:22.1:1:31.4:1:1:0:57.3:62:1:0.0645:2.3 1/1:60:60:31,29:0,0:0,60:1:0,2:23.7:1:29.2:1:1:0:53.9:120:1:0.1333:2.3 +6 58778412 . T C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCAAGGGTACCCTGAGAG;RSEQ=GCTTTCAGGCCTATGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:29:14,15:0,0:0,29:1:0,2:22.4:1:31.1:1:1:0:56.4:58:1:0:2.7 1/1:59:59:31,28:0,0:0,59:1:0,2:23.8:1:29.1:1:1:0:52.6:18.667:1:0:2.5 +6 58778452 . A C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.06822;LSEQ=AAAAGGGAATATCTTTCCAT;RSEQ=AAAGGTAGACAGAAGCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:24:13,11:4,3:7,24:0.7742:2,2:29:1:32.2:1:1:1.12384:53.5:48:0.7742:0:2.8 0/1:60:11:4,7:24,25:49,11:0.1833:2,2:32.9:1:30.8:1:0.51874:1.66572:53.2:22:0.1864:0:2.9 +6 58778456 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.54834;SOR=Inf;LSEQ=GGGAATATCTTTCCATAAAA;RSEQ=GTAGACAGAAGCAATCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:17,14:31,0:0:2,0:27.7:1:32.6:1:1:0:54.8:62:1:0:2.7 0/1:60:3:2,1:27,30:57,3:0.05:2,2:18:1:29.3:1:0.60593:2.19:60:6:0.0536:0:2 +6 58778468 . C A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCATAAAAGGTAGACAGAAG;RSEQ=AATCTCAGAAACTGCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:28,0:0:2,0:30.4:1:32.5:1:1:0:54.4:56:1:0:2.6 0/1:62:2:1,1:26,34:60,2:0.0323:2,2:15:0:27.5:1:1:1.30:25:4:0.0333:0:5 +6 58778482 . G A 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53895;SOR=0;LSEQ=CAGAAGCAATCTCAGAAACT;RSEQ=CTTTGTGATGTGTGCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:32:16,16:0,0:0,32:1:0,2:24.9:1:29.4:1:1:0:54.9:64:1:0:2.3 1/1:59:57:25,32:1,1:2,57:0.9661:2,2:27.8:1:27.5:1:1:1.2746:52.9:18:0.9818:0:2 +6 58778489 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55048;SOR=Inf;LSEQ=AATCTCAGAAACTGCTTTGT;RSEQ=ATGTGTGCATTCAACTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:16,17:33,0:0:2,0:22.4:1:32.2:1:1:0:56.6:66:0.9706:0:2 0/1:61:3:1,2:25,33:58,3:0.0492:2,2:28:1:22.3:1:1:1.50525:54.7:2:0.0339:0:3 +6 58778519 . A G 85 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.71377;SOR=1.79863;LSEQ=TTCAACTCACCGAGTGCAAC;RSEQ=TTCCTCTTGATAGAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:2,0:14,17:31,2:0.0606:2,0:19.5:1:32:0:0.22727:0:60:4:0.0606:0:2 0/1:67:7:4,3:27,32:59,7:0.1045:2,2:9.7:1:30.4:1:0.69779:1.57:36.9:14:0.1077:0:3.6 +6 58778530 . TA CC 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56896;SOR=1.61721;LSEQ=GAGTGCAACATTCCTCTTGA;RSEQ=GAGCAGTTTGGAAACATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:2,2:13,13:26,4:0.1333:2,2:27:1:31.9:1:1:1:53.3:8:0.1379:0:1.8 0/1:65:13:7,6:26,25:51,13:0.2:2,2:25.2:1:29.6:1:1:1.12:45.8:26:0.2031:0.0154:2.3 +6 58778577 . T A 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40054;SOR=1.46069;LSEQ=TAGAATCTGCAAGTGGATAT;RSEQ=TGGACCTCTTTGAGGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:7,5:10,11:21,12:0.3636:2,2:23.8:1:29.6:1:0.72068:1.52:57.3:24:0.375:0:2 0/1:68:31:16,15:19,18:37,31:0.4559:2,2:22.9:1:28.2:1:1:1.01:47.7:62:0.4627:0:2.7 +6 58778582 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10225;SOR=0;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=CTCTTTGAGGCCTTCGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:17,13:30,2:0.0625:2,2:30:1:30.5:1:1:1.29665:51.5:4:0.0645:0:1.5 0/0:67:0:0,0:35,32:67,0:0:2,0:22.9:1:29.8:1:1:0:46.3:21.333:1:0:1.7 +6 58778584 . T G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.98416;LSEQ=TGCAAGTGGATATTTGGACC;RSEQ=CTTTGAGGCCTTCGTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:20:11,9:7,5:12,20:0.625:2,2:26.5:1:31.6:1:1:1.14061:55.1:40:0.625:0:1.7 1/0:66:41:23,18:12,13:25,41:0.6212:2,2:22.8:1:29.8:1:0.61415:1.38:46.4:82:0.6308:0:2.4 +6 58778598 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.92145;LSEQ=TGGACCTCTTTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:1,0:16,13:29,1:0.0333:2,0:1:0:26:0:1:0:60:2:0.0345:0:2 0/1:65:2:1,1:32,31:63,2:0.0308:2,2:12.5:1:29:1:1:1.03176:30:4:0.0313:0:2 +6 58778606 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54257;SOR=Inf;LSEQ=TTTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCCTATAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:35,0:0:2,0:23:1:31.1:1:1:0:55:70:1:0:1 0/1:66:2:1,1:32,32:64,2:0.0303:2,2:30:0:28.5:1:1:1:37:4:0.0308:0:3 +6 58778610 . A T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=AGGCCTTCGTTGGAAACGGG;RSEQ=TTTCTTCCTATAAACCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:23,17:40,0:0:2,0:20.9:1:29.2:1:1:0:52.6:19:1:0:1 0/1:60:2:1,1:29,29:58,2:0.0333:2,2:35:0:29.5:1:1:1:24:4:0.0345:0:2 +6 58778617 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50979;SOR=Inf;LSEQ=CGTTGGAAACGGGATTTCTT;RSEQ=CTATAAACCCAGACAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:24,17:41,0:0:2,0:22:1:30.9:1:1:0:52.1:19.5:1:0:0.9 0/1:58:2:1,1:26,30:56,2:0.0345:2,2:30.5:1:29.5:1:1:1.15:26:4:0.0345:0:4 +6 58778624 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50747;SOR=Inf;LSEQ=AACGGGATTTCTTCCTATAA;RSEQ=CCCAGACAGAAGAATTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:25,18:43,0:0:2,0:22.5:1:30:1:1:0:53.1:86:1:0:0.8 0/1:59:2:1,1:26,31:57,2:0.0339:2,2:24:1:27:0:1:1.19:26:4:0.0357:0:4 +6 58778647 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49643;SOR=Inf;LSEQ=CAGACAGAAGAATTCTCAGA;RSEQ=ACTTCTTTGTGATGTGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:30,21:51,0:0:2,0:25.6:1:32.6:1:1:0:52.2:50:0.9804:0:0.6 0/1:57:2:1,1:23,32:55,2:0.0351:2,2:22.5:1:27.5:1:1:1.38:47:4:0.0351:0:2.5 +6 58778649 . C T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00512;SOR=3.32893;LSEQ=GACAGAAGAATTCTCAGAGA;RSEQ=TTCTTTGTGATGTGTGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:11:5,6:25,16:41,11:0.2115:2,2:26.4:1:31.5:1:0.49459:1.85187:45.3:22:0.2157:0:1.6 0/1:59:28:12,16:14,17:31,28:0.4746:2,2:21:1:29.4:1:1:1.0963:42.6:56:0.4746:0:2 +6 58778655 . T A 48 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24472;SOR=0;LSEQ=AGAATTCTCAGAGACTTCTT;RSEQ=GTGATGTGTGAATTCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:3:1,2:33,22:55,3:0.0517:2,2:6.7:1:30.7:1:0.56365:2.94302:42:6:0.0517:0:1.3 0/0:53:0:0,0:25,28:53,0:0:2,0:23:1:30:1:1:0:45.8:106:1:0:1.5 +6 58778664 . T G 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.0096;SOR=Inf;LSEQ=AGAGACTTCTTTGTGATGTG;RSEQ=GAATTCAACTCACAGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:34,25:59,0:0:2,0:26.8:1:30.5:1:1:0:52.1:118:1:0:0.6 0/1:53:6:4,2:19,28:47,6:0.1132:2,2:17.8:1:31.8:1:0.38479:2.89:39:12:0.1132:0:1.5 +6 58778666 . AA CT 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21831;SOR=Inf;LSEQ=AGACTTCTTTGTGATGTGTG;RSEQ=TTCAACTCACAGTGTGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:61,0:0:2,0:26.3:1:30.7:1:1:0:51.5:122:1:0:0.6 0/1:54:2:1,1:23,27:50,2:0.037:2,2:7:0:32.3:1:1:1.17:40:4:0.037:0:1.5 +6 58778686 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22077;SOR=Inf;LSEQ=AATTCAACTCACAGTGTGGA;RSEQ=CCTTCCTTTTGATAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:34,32:66,0:0:2,0:26.4:1:30.7:1:1:0:52.1:65:1:0:0.5 0/1:59:2:1,1:29,27:56,2:0.0339:2,2:22.5:1:30:1:1:1.07272:60:4:0.0339:0:2 +6 58778690 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49613;SOR=0;LSEQ=CAACTCACAGTGTGGATCCT;RSEQ=CCTTTTGATAGAGCAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:32,30:62,2:0.0313:2,2:38:0:33:0:1:1.06563:60:4:0.0313:0:1 0/0:62:0:0,0:32,30:62,0:0:2,0:24.5:1:29.6:1:1:0:47.1:124:1:0:0.9 +6 58778699 . T C 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23715;SOR=0;LSEQ=GTGTGGATCCTTCCTTTTGA;RSEQ=AGAGCAGTTTTGAAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:32,32:64,2:0.0303:2,2:5:0:32:1:1:1:37:4:0.0303:0:2.5 0/0:69:0:0,0:34,35:69,0:0:2,0:24.2:1:28.9:1:1:0:45.9:68:1:0:0.9 +6 58778707 . T G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49642;SOR=Inf;LSEQ=CCTTCCTTTTGATAGAGCAG;RSEQ=TTTGAAACACTGTTTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:31,33:64,0:0:2,0:26.3:1:29.5:1:1:0:48.1:63:1:0:0.8 0/1:67:2:1,1:29,34:63,2:0.0299:2,2:21:1:33:1:1:1.17:60:4:0.0299:0:2 +6 58778715 . C A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4963;SOR=Inf;LSEQ=TTGATAGAGCAGTTTTGAAA;RSEQ=ACTGTTTTTGTAGTATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:35,32:67,0:0:2,0:24.7:1:32.1:1:1:0:46.8:134:1:0:0.9 0/1:68:2:1,1:34,32:66,2:0.0294:2,2:29:1:32:1:1:1.06158:60:4:0.0294:0:2 +6 58778716 . A C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24444;SOR=Inf;LSEQ=TGATAGAGCAGTTTTGAAAC;RSEQ=CTGTTTTTGTAGTATTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:35,33:68,0:0:2,0:24.3:1:29.8:1:1:0:46.6:67:1:0:0.9 0/1:67:2:0,2:35,30:65,2:0.0299:2,0:27:1:32.5:1:0.22433:0:45.5:4:0.0299:0:1 +6 58778718 . T C 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42553;SOR=1.7181;LSEQ=ATAGAGCAGTTTTGAAACAC;RSEQ=GTTTTTGTAGTATTTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:6:4,2:28,31:59,6:0.0923:2,2:29.8:1:30.8:1:0.42665:2.19:38.3:12:0.0938:0:1.7 0/1:67:10:5,5:30,27:57,10:0.1493:2,2:30.3:1:29.3:1:1:1.10936:39.9:20:0.1493:0:2.5 +6 58778727 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22166;SOR=0;LSEQ=TTTTGAAACACTGTTTTTGT;RSEQ=GTATTTCCAAGCGGATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:28,31:59,2:0.0328:2,2:15:1:29:1:1:1.11:28.5:4:0.0328:0:3.5 0/0:68:0:0,0:36,32:68,0:0:2,0:26:1:28.9:1:1:0:43.4:67:1:0:1.1 +6 58778739 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.84011;LSEQ=GTTTTTGTAGTATTTCCAAG;RSEQ=GGATATTTGGAACGCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:1:1,0:29,31:60,1:0.0161:2,0:36:0:27:0:0.4918:0:46:2:0.0161:0:1 0/1:68:2:1,1:33,33:66,2:0.0294:2,2:25.5:1:28:1:1:1:23.5:4:0.0294:0:2 +6 58778740 . G A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1006;SOR=0;LSEQ=TTTTTGTAGTATTTCCAAGC;RSEQ=GATATTTGGAACGCCTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:1,2:28,30:58,3:0.0492:2,2:27:1:31:1:1:1.84836:31:6:0.0492:0:2.3 0/0:69:0:0,0:35,34:69,0:0:2,0:24.7:1:29.7:1:1:0:42.6:68:1:0:1.2 +6 58778752 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22395;SOR=0;LSEQ=TTCCAAGCGGATATTTGGAA;RSEQ=GCCTTGAAGCGTATGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:2:1,1:27,29:56,2:0.0345:2,2:36.5:1:32.5:1:1:1.07:54:4:0.0345:0:1.5 0/0:64:0:0,0:31,33:64,0:0:2,0:25.1:1:30.9:1:1:0:43:128:1:0:1.2 +6 58778764 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21831;SOR=0;LSEQ=ATTTGGAACGCCTTGAAGCG;RSEQ=ATGGTAGAAAAGGAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:26,25:51,2:0.037:2,2:33:1:29.5:1:1:1.03924:27.5:4:0.0377:0:2.5 0/0:61:0:0,0:29,32:61,0:0:2,0:24.5:1:27.8:1:1:0:39.1:60:1:0:1.4 +6 58778765 . A G 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59408;SOR=0.42114;LSEQ=TTTGGAACGCCTTGAAGCGT;RSEQ=TGGTAGAAAAGGAAATATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:26,25:51,2:0.0377:2,2:47.5:1:33:1:1:1.03924:28.5:4:0.0377:0:3.5 0/1:62:1:0,1:30,31:61,1:0.0161:2,0:5:0:33:0:1:0:36:2:0.0161:0:2 +6 58778766 . T A 71 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12357;SOR=5.39856;LSEQ=TTGGAACGCCTTGAAGCGTA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:1:1,0:26,25:51,1:0.0192:2,0:42:0:32:0:1:0:29:2:0.0196:0:2 0/1:62:6:4,2:26,30:56,6:0.0968:2,2:22.2:1:27.7:1:0.41797:2.28:37:12:0.0968:0:2 +6 58778769 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22118;SOR=0;LSEQ=GAACGCCTTGAAGCGTATGG;RSEQ=AGAAAAGGAAATATCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:27,23:50,2:0.0385:2,2:8.5:1:32:1:1:1.17028:37:4:0.0392:0:2.5 0/0:58:0:0,0:28,29:57,0:0:2,0:25.2:1:28.1:1:1:0:36.6:56:0.9825:0:1.5 +6 58778787 . CT GC 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.49881;SOR=Inf;LSEQ=GGTAGAAAAGGAAATATCTT;RSEQ=CATAAAACCTAGACAGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:26,24:50,0:0:2,0:23.2:1:31.5:1:1:0:34.4:49:1:0:1.9 0/1:59:2:1,1:28,29:57,2:0.0339:2,2:40.5:1:30.8:1:1:1.04:60:4:0.0345:0:1 +6 58778788 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49634;SOR=0;LSEQ=GTAGAAAAGGAAATATCTTC;RSEQ=CATAAAACCTAGACAGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:50:50:24,26:0,0:0,50:1:0,2:23.1:1:31.2:1:1:0:34.5:100:1:0:2 1/1:55:53:27,26:0,0:0,53:0.9636:0,2:23.4:1:30.6:1:1:0:34.7:106:1:0:1.8 +6 58778799 . A T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=AATATCTTCTCATAAAACCT;RSEQ=GACAGAACCAATCTCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:51,0:0:2,0:22.4:1:29.4:1:1:0:35.9:24.5:1:0:2.1 0/1:60:2:1,1:31,27:58,2:0.0333:2,2:27:0:31.5:1:1:1.1455:29:4:0.0339:0:2 +6 58778809 . A C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.97961;LSEQ=CATAAAACCTAGACAGAACC;RSEQ=ATCTCAGAAACGACTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:27:13,14:10,11:21,27:0.5625:2,2:27.4:1:30.8:1:1:1.02:37.6:26:0.5532:0:2.3 1/0:61:34:18,16:15,12:27,34:0.5574:2,2:23.6:1:31:1:1:1.10919:39:68:0.5574:0:1.9 +6 58778828 . T A 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01528;SOR=0.15247;LSEQ=CAATCTCAGAAACGACTTTG;RSEQ=GATGTCTGCATTCAACTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:8:3,5:17,21:38,8:0.1702:2,2:30.1:1:31.3:1:1:1.34057:47.4:16:0.1739:0:1.8 0/1:67:2:1,1:31,34:65,2:0.0299:2,2:5:1:27.5:1:1:1.10:35:4:0.0299:0:2 +6 58778836 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1682;SOR=0;LSEQ=GAAACGACTTTGTGATGTCT;RSEQ=CATTCAACTCACAGAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:18,25:43,2:0.0444:2,2:32.5:1:29.5:1:1:1.38:47:4:0.0455:0:1.5 0/0:64:0:0,0:31,33:64,0:0:2,0:28.3:1:30.8:1:1:0:42.9:63:1:0:1.3 +6 58778844 . C G 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07791;SOR=Inf;LSEQ=TTTGTGATGTCTGCATTCAA;RSEQ=TCACAGAGTTGAACATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:21,26:47,0:0:2,0:25.5:1:32.8:1:1:0:45.1:94:1:0:1.7 0/1:68:5:2,3:29,34:63,5:0.0735:2,2:41.6:1:30.8:1:1:1.27484:53.2:10:0.0735:0:1.4 +6 58778864 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50476;SOR=Inf;LSEQ=CTCACAGAGTTGAACATTTC;RSEQ=CTTGATAGAGCAGTTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:23,29:52,0:0:2,0:23:1:31.2:1:1:0:50.4:51:1:0:1.5 0/1:68:2:1,1:32,34:66,2:0.0294:2,2:15:1:28.5:1:1:1.06:56:4:0.0299:0:2.5 +6 58778865 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18571;SOR=0;LSEQ=TCACAGAGTTGAACATTTCT;RSEQ=TTGATAGAGCAGTTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:21,29:50,2:0.0385:2,2:22.5:1:31:1:1:1.37:45:4:0.0385:0:3 0/0:68:0:0,0:33,35:68,0:0:2,0:24.6:1:30.6:1:1:0:48.5:136:1:0:1.1 +6 58778872 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12624;SOR=Inf;LSEQ=GTTGAACATTTCTCTTGATA;RSEQ=AGCAGTTTTGAAACCCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:23,31:54,0:0:2,0:22.7:1:32.9:1:1:0:52.6:108:1:0:1.5 0/1:66:4:2,2:28,34:62,4:0.0606:2,2:24.8:1:30.5:1:1:1.21:32.5:8:0.0606:0:1.3 +6 58778897 . A T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.7726;LSEQ=GTTTTGAAACCCTCTTTCTG;RSEQ=AGGATCTGCAAGTGGATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:1,0:23,26:49,1:0.02:2,0:45:0:28:0:0.48:0:40:2:0.02:0:2 0/1:57:2:1,1:23,32:55,2:0.0351:2,2:12.5:1:26:1:1:1.38:42.5:4:0.0351:0:4 +6 58778902 . T G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07621;SOR=0.21598;LSEQ=GAAACCCTCTTTCTGAAGGA;RSEQ=CTGCAAGTGGATATTTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:7:3,4:20,21:41,7:0.1458:2,2:40.1:1:32.7:1:1:1.26356:53.3:14:0.1489:0:2.4 0/1:57:2:0,2:24,31:55,2:0.0351:2,0:14.5:1:30:1:0.50376:0:34.5:4:0.037:0:3 +6 58778906 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.22436;SOR=0;LSEQ=CCCTCTTTCTGAAGGATCTG;RSEQ=AAGTGGATATTTGGACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:24,24:48,2:0.04:2,2:40:1:29:1:1:1:59.5:4:0.04:0:2 0/0:55:0:0,0:22,32:54,0:0:2,0:25.4:1:31.8:1:1:0:54.8:53:1:0:1.5 +6 58778908 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21601;SOR=0;LSEQ=CTCTTTCTGAAGGATCTGCA;RSEQ=GTGGATATTTGGACCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:24,24:48,2:0.04:2,2:31.5:1:32.5:1:1:1:59.5:4:0.0417:0:2.5 0/0:57:0:0,0:24,33:57,0:0:2,0:24.9:1:30.2:1:1:0:54.4:114:1:0:1.6 +6 58778919 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22744;SOR=0;LSEQ=GGATCTGCAAGTGGATATTT;RSEQ=GACCTCCTTTGGGTCTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:25,19:44,2:0.0426:2,2:35.5:1:31:1:1:1.30786:60:4:0.0426:0:2 0/0:51:0:0,0:23,28:51,0:0:2,0:29.2:1:31.2:1:1:0:54.3:50:1:0:1.9 +6 58778922 . C A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23217;SOR=Inf;LSEQ=TCTGCAAGTGGATATTTGGA;RSEQ=CTCCTTTGGGTCTTCGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:45:25,20:0,0:0,45:0.9574:0,2:29.5:1:29.8:1:1:0:53.8:44:0.9565:0:2 1/1:50:50:22,28:0,0:0,50:1:0,2:30.1:1:29.4:1:1:0:54:100:1:0:2 +6 58778948 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23411;SOR=Inf;LSEQ=TTGGGTCTTCGTTGGAAACG;RSEQ=GATTTCTTCGTATAAATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:30,26:56,0:0:2,0:19.1:1:30.7:1:1:0:48.3:55:1:0:2.4 0/1:53:2:1,1:26,25:51,2:0.0377:2,2:25.5:1:28.5:1:1:1.03924:60:4:0.0385:0:3 +6 58778961 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21406;SOR=0;LSEQ=GGAAACGGGATTTCTTCGTA;RSEQ=AAATCTAGACAGAAGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:23,22:45,2:0.0426:2,2:28:1:32.5:1:1:1.04448:42:4:0.0435:0:4.5 0/0:54:0:0,0:26,24:50,0:0:2,0:21.9:1:28.5:1:1:0:50.1:100:0.9259:0:2.7 +6 58778967 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93812;LSEQ=GGGATTTCTTCGTATAAATC;RSEQ=AGACAGAAGAATTCTCCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:35:19,16:8,7:15,35:0.7:2,2:22.1:1:31.2:1:1:1.04:46.4:34:0.6939:0:3.1 1/0:51:35:18,17:8,8:16,35:0.6863:2,2:23.3:1:31:1:1:1.06:48.4:70:0.6863:0:3.1 +6 58778989 . T C 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAAGAATTCTCCGAAA;RSEQ=TTCTTTGGTTGTGTGCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:44:44:21,23:0,0:0,44:1:0,2:30.7:1:32.3:1:1:0:44.3:43:1:0:3.1 1/1:43:43:23,20:0,0:0,43:1:0,2:27.4:1:31.4:1:1:0:45.6:42:1:0:3 +6 58779007 . C T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTTCTTTGGTTGTGTGCA;RSEQ=TCAAGTCACAGAGTGGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:46:46:24,22:0,0:0,46:1:0,2:26.7:1:30.5:1:1:0:46.3:45:1:0:2.8 1/1:53:53:28,25:0,0:0,53:1:0,2:23.8:1:29.6:1:1:0:49:106:1:0:2.7 +6 58779019 . A G 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.03886;LSEQ=TGTGTGCACTCAAGTCACAG;RSEQ=GTGGAACCTTCCTTTGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:3:1,2:30,22:52,3:0.0536:2,2:38.7:1:32:1:0.57461:2.67813:52.7:6:0.0556:0:4.7 0/1:54:3:2,1:25,26:51,3:0.0556:2,2:21.3:1:30:1:1:2.05:49:6:0.0588:0:4.7 +6 58779032 . T G 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06193;SOR=0;LSEQ=GTCACAGAGTGGAACCTTCC;RSEQ=TTGGATAGAGCAGTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:2,3:31,24:55,5:0.0833:2,2:10.2:1:31.8:1:0.64935:1.91607:53.2:10:0.0862:0:2.6 0/0:50:0:0,0:25,25:50,0:0:2,0:24.1:1:29.6:1:1:0:54.2:49:1:0:2.1 +6 58779037 . A G 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70457;SOR=1.54079;LSEQ=AGAGTGGAACCTTCCTTTGG;RSEQ=TAGAGCAGTTTGAAACGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:1,2:30,28:58,3:0.0492:2,2:26.3:1:33.7:1:0.61239:2.11706:52.7:6:0.0508:0:4.7 0/1:54:4:1,3:24,25:49,4:0.0741:2,2:26.3:1:29.5:1:0.61274:2.82767:57.5:8:0.0769:0:3.5 +6 58779057 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4956;SOR=0;LSEQ=ATAGAGCAGTTTGAAACGCT;RSEQ=TGGTTGTAGTATTTCCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:27,25:52,2:0.037:2,2:19.5:1:34:1:1:1.07844:57.5:4:0.037:0:4.5 0/0:51:0:0,0:23,28:51,0:0:2,0:24.3:1:30.4:1:1:0:58.6:16:1:0:1.4 +6 58779077 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11056;SOR=Inf;LSEQ=GTGGTTGTAGTATTTCCAAG;RSEQ=GGATATTAGAGCGCCTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:25,27:52,0:0:2,0:28.2:1:31:1:1:0:55.8:104:1:0:0.8 0/1:49:3:1,2:19,27:46,3:0.0612:2,2:22.7:1:30.3:1:1:1.39796:44.7:6:0.0625:0:1.3 +6 58779089 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49619;SOR=0;LSEQ=TTTCCAAGCGGATATTAGAG;RSEQ=GCCTTGAAGCCTATGGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:23,25:48,2:0.0385:2,2:25.5:1:31.5:1:1:1.09:42:4:0.0408:0:1.5 0/0:47:0:0,0:16,21:37,0:0:2,0:26.1:1:30.2:1:1:0:51.1:74:0.7872:0:1 +6 58779097 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.22196;LSEQ=CGGATATTAGAGCGCCTTGA;RSEQ=GCCTATGGTAGAAAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:2,2:19,24:43,4:0.0851:2,2:36.8:1:32.8:1:1:1.26:60:8:0.0909:0:2 1/0:45:26:14,12:8,11:19,26:0.5778:2,2:22.5:1:30.7:1:0.5499:1.59:52.3:25:0.5682:0:1.6 +6 58779103 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49474;SOR=0;LSEQ=TTAGAGCGCCTTGAAGCCTA;RSEQ=GGTAGAAAAGGAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:21,25:46,2:0.0417:2,2:26.5:1:28.5:1:1:1.19:44:4:0.0426:0:1 0/0:48:0:0,0:24,24:48,0:0:2,0:21.5:1:29.8:1:1:0:50.4:47:1:0:1 +6 58779121 . C T 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12406;SOR=0;LSEQ=TATGGTAGAAAAGGAAATAT;RSEQ=TTCCCATAAAACCTAGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:4:0,4:20,26:46,4:0.08:2,0:27.8:1:28.8:1:0.14003:0:55:8:0.0816:0:1.3 0/0:41:0:0,0:22,19:41,0:0:2,0:24:1:31.9:1:1:0:48.3:82:1:0:0.8 +6 58779157 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.20979;SOR=Inf;LSEQ=GACGGAAGCAATCTCAGAAA;RSEQ=TACTGTGTGATGGCTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:18,24:42,0:0:2,0:28:1:32.9:1:1:0:50:41:1:0:0.3 0/1:36:2:1,1:21,13:34,2:0.0556:2,2:25.5:1:29.5:1:1:1.5932:34:4:0.0556:0:1 +6 58779214 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50906;SOR=0;LSEQ=ACATTTCTCTTGATAGAGCA;RSEQ=TTTTGAAACACTCTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:17,16:33,2:0.0571:2,2:14:1:32.5:1:1:1.06069:23.5:4:0.0571:0:1 0/0:24:0:0,0:13,10:23,0:0:2,0:21.2:1:31.4:1:1:0:36.4:46:0.9583:0:0.7 +6 58779308 . T C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29066;SOR=0.2151;LSEQ=TTTCTTCATGTTACTCTAGA;RSEQ=AGAAGAATTCTCAAACACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:21:10,11:1,0:1,21:0.9545:0,2:18.5:1:32:1:1:0:43.6:20:0.9524:0:1.4 1/1:16:13:5,8:2,1:3,13:0.8125:2,2:23.8:1:31.8:1:0.55:2.96927:36.8:26:0.8125:0:2 +6 58779328 . A G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.40909;SOR=Inf;LSEQ=TAGAAGAATTCTCAAACACT;RSEQ=CTATGTGATGTTTGCATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:2,6:1,0:1,8:0.8889:0,2:11.4:1:33.1:1:0.33333:0:28.3:16:0.8889:0:2 1/1:13:13:5,8:0,0:0,13:1:0,2:10.2:1:31.2:1:1:0:31:26:1:0:1.9 +6 58779802 . C T 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTGGAAACGGGATTTCT;RSEQ=CATCTAAACCTACAGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:32.5:1:1:0:25:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 58779807 . T G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAACGGGATTTCTCCATC;RSEQ=AAACCTACAGAGAAGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:33:1:1:0:25:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 63788281 . G A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3322;SOR=3.29271;LSEQ=AGAAGCCTTTTCCTGTAAAC;RSEQ=GCCGGTGGCATCTCATACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:2,2:4,3:0.4286:2,2:8.3:1:33:1:1:1.81007:42:6:0.4286:0:1 1/0:11:8:3,5:1,2:3,8:0.7273:2,2:13.1:1:29.4:1:1:1.18:46.9:16:0.7273:0:1 +6 64740380 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=AACTGCCGAGGACTAGACCT;RSEQ=CTCACTGCTGAGAAAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:22.8:1:32.2:1:1:0:60:10:1:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:5.5:1:26:1:1:0:26:4:0.5:0:1.5 +6 64740517 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4955;SOR=Inf;LSEQ=AATCAGATGCCTTTCAAATT;RSEQ=TTATACCAACCTCTGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:11,5:16,0:0:2,0:26.3:1:32.5:1:1:0:36.4:32:1:0:0 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:32:1:28:1:1:1.11:55:4:0.0952:0:1 +6 64741118 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCATGAGTTCTGGGTGGGC;RSEQ=TGGGCTTGGCCAGCTCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 65096797 . T G 273 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01047;LSEQ=CACTTTGGTTGCTATCAGAG;RSEQ=GAACATAGCATGATGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:459:456:207,249:0,0:0,456:0.9935:0,2:26:1:31:1:1:0:60:64.143:0.9956:0:1.1 1/0:465:285:128,157:85,95:180,285:0.6129:2,2:26.5:1:29.9:1:0.63412:1.09723:60:27.5:0.6057:0:1.1 +6 65096877 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18442;SOR=Inf;LSEQ=GTATGTAATGTATAGTATAT;RSEQ=TATATGGCAGCAATATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:40,148:188,0:0:2,0:23.8:1:31.6:1:1:0:60:22.5:1:0:1 0/1:142:2:1,1:31,109:140,2:0.0141:2,2:20:1:31.5:1:0.40116:3.48:60:4:0.0141:0:2 +6 65096906 . C T 193 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCAATATGTAAATATATAC;RSEQ=ATTTTGCATTTTACATAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:112:112:13,99:0,0:0,112:1:0,2:25.3:1:28.4:1:1:0:60:27:1:0:1.1 1/0:65:40:8,32:2,23:25,40:0.6154:2,2:29.3:1:28.2:1:0.29393:2.83:60:80:0.6154:0:1.1 +6 65097066 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACCTTTCCATTACCTAAG;RSEQ=CTGTGTATATGTAATATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:31.3:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 68164879 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.17058;SOR=Inf;LSEQ=GGCATTAGAAAAGTCAGTGA;RSEQ=CATTAAGGTGTTGATTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:139,82:221,0:0:2,0:26.2:1:30.6:1:1:0:60:35.833:1:0:0.1 0/1:156:2:1,1:93,61:154,2:0.0128:2,2:47:0:31:1:1:1.52031:60:4:0.013:0:1 +6 68164889 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19472;SOR=Inf;LSEQ=AAGTCAGTGATCATTAAGGT;RSEQ=TTGATTTGGCAACAAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:141,104:245,0:0:2,0:27.3:1:32.2:1:1:0:60:121.5:1:0:0.2 0/1:194:2:1,1:108,84:192,2:0.0103:2,2:41:1:29.5:1:1:1.28402:60:4:0.0104:0:1 +6 68164958 . T G 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.25256;LSEQ=ACTCACATCCCTTCTAGAGA;RSEQ=AAATATTTAATAATGTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:44:18,26:95,130:225,44:0.163:2,2:22.6:1:31.7:1:1:1.05536:60:43:0.161:0:1.1 0/1:206:80:34,46:57,69:126,80:0.3883:2,2:25.9:1:30.9:1:0.77382:1.11704:60:39:0.3824:0:1.2 +6 68431386 . G C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTATTCATGAGGGATTTTA;RSEQ=TCTGTAGTTTTTTTATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 68433219 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTGCACCCCACCATGCC;RSEQ=GAACCTCCCCCATGCCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:41:1:29.5:1:1:1:60:4:0.5:0:2 +6 68433236 . G A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCGAACCTCCCCCATGCC;RSEQ=TGGGCTCCTGCGCGGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:43:1:31:1:1:1:60:4:0.5:0:2 +6 70415267 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2102;SOR=0;LSEQ=TCATATAATTGATGAACTTG;RSEQ=CTTCCACTTTGGGAAGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:2,0:35,27:62,2:0.0313:2,0:20.5:1:29:1:0.50446:0:30.5:4:0.0317:0:1 0/0:75:0:0,0:41,34:75,0:0:2,0:30.7:1:31.1:1:1:0:37.8:150:1:0:0.1 +6 70415352 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24427;SOR=Inf;LSEQ=TACAGAACTAGGTCCTTTTG;RSEQ=TGTTTTAGGAGATTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:37,29:66,0:0:2,0:22.4:1:31.8:1:1:0:49.9:132:1:0:0 0/1:65:2:1,1:36,27:63,2:0.0308:2,2:38:1:30.5:1:1:1.32735:40:4:0.0308:0:1 +6 70415435 . T C 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=ATGGTTTTGAGTCTTTTCCA;RSEQ=TCTGATTTGGCTTTTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:70,76:146,0:0:2,0:27:1:30.7:1:1:0:47.7:72:1:0:0.4 0/1:160:13:8,5:80,67:147,13:0.0813:2,2:25:1:30.4:1:0.77373:1.34:43.8:26:0.0813:0:2 +6 70415453 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=CATTCTGATTTGGCTTTTGT;RSEQ=CATTTTTGGCTGGAGTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:83,76:159,0:0:2,0:23:1:32.6:1:1:0:45.2:318:1:0:0.6 0/1:166:2:1,1:86,78:164,2:0.012:2,2:15.5:1:27.5:1:1:1.10191:27:4:0.0122:0:1.5 +6 70415473 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24425;SOR=Inf;LSEQ=GCATTTTTGGCTGGAGTATC;RSEQ=CATATAGATTTCTTCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:74,79:153,0:0:2,0:23.2:1:31.1:1:1:0:44.9:50:1:0:0.7 0/1:150:2:1,1:70,78:148,2:0.0133:2,2:35:1:29.5:1:1:1.11:41:4:0.0134:0:2 +6 70415475 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=3.23936;LSEQ=ATTTTTGGCTGGAGTATCTC;RSEQ=TATAGATTTCTTCACTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:104:52,52:23,28:51,104:0.671:2,2:21.8:1:31.4:1:0.61034:1.22:40.7:208:0.6753:0:1.1 1/1:145:126:59,67:9,10:19,126:0.869:2,2:24.7:1:29.9:1:1:1.02189:36.9:252:0.869:0:1.2 +6 70415528 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.19984;SOR=Inf;LSEQ=TTTCCTTATTATCAAAATCA;RSEQ=CATTATCACCATCTTCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:74,80:154,0:0:2,0:24.8:1:30.7:1:1:0:54.6:76:1:0:0.5 0/1:125:2:1,1:59,64:123,2:0.016:2,2:9:1:28.5:1:1:1.08:34.5:4:0.0163:0:2 +6 70415550 . TATC T 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.72873;SOR=0.69094;LSEQ=ATTATCACCATCTTCATCAT;RSEQ=ATCATCATCATCATCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:5:3,2:61,77:138,5:0.035:2,2:36.6:1:31.8:1:0.65664:1.88:53:10:0.036:0:0 0/1:123:3:1,2:56,63:119,3:0.0244:2,2:20.3:1:30:1:1:1.76975:47.3:6:0.0244:0.0081:0.7 +6 70415581 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49849;SOR=0;LSEQ=TCATCATCTTCATCAGTAGC;RSEQ=AGTTTTACTTTTTTCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:71,87:158,2:0.0125:2,2:29:1:30:1:1:1.22:45:4:0.0129:0:1 0/0:156:0:0,0:71,84:155,0:0:2,0:24.2:1:29.3:1:1:0:43:50.667:0.9935:0:0.2 +6 70415615 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50154;SOR=Inf;LSEQ=TCTGTGGAACCTTGCTACCA;RSEQ=CTCCAGGGACAGACCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:72,74:146,0:0:2,0:29:1:31.9:1:1:0:42.8:72:1:0:0.1 0/1:171:2:1,1:78,91:169,2:0.0117:2,2:26.5:1:27.5:1:1:1.17:43.5:4:0.0118:0:1.5 +6 70415637 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50075;SOR=Inf;LSEQ=TCCAGGGACAGACCACTTTC;RSEQ=AGATATACTTAAGAGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:66,75:141,0:0:2,0:26.7:1:32.2:1:1:0:43.4:140:1:0:0.1 0/1:162:2:1,1:73,87:160,2:0.0123:2,2:20.5:1:29:1:1:1.19:28:4:0.0126:0:1 +6 70415662 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.50003;SOR=Inf;LSEQ=ATACTTAAGAGTTTCACATC;RSEQ=TCCTCCTCTTCATCTACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:59,59:118,0:0:2,0:21.8:1:31.6:1:1:0:52.9:28.5:1:0:0.1 0/1:134:2:1,1:60,72:132,2:0.0149:2,2:24:1:27.5:1:1:1.20:43:4:0.0152:0:1 +6 70415663 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50008;SOR=Inf;LSEQ=TACTTAAGAGTTTCACATCC;RSEQ=CCTCCTCTTCATCTACTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:57,58:115,0:0:2,0:22.1:1:30.4:1:1:0:53.5:27.75:1:0:0.1 0/1:131:2:1,1:60,69:129,2:0.0153:2,2:27.5:1:27.5:1:1:1.15:54.5:4:0.0153:0:1 +6 70415667 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.49939;SOR=Inf;LSEQ=TAAGAGTTTCACATCCTCCT;RSEQ=CTCTTCATCTACTGACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:57,55:112,0:0:2,0:21.8:1:31.4:1:1:0:54.6:55:1:0:0.1 0/1:125:2:1,1:57,65:122,2:0.016:2,2:22.5:1:29:1:1:1.14:50.5:4:0.0163:0:1 +6 70415731 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22794;SOR=Inf;LSEQ=TTGTTCACTAATATGCACTG;RSEQ=CCCTGAACCACACTTCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:48,62:110,0:0:2,0:27.5:1:31.5:1:1:0:50.7:35.667:1:0:0.1 0/1:101:2:0,2:47,52:99,2:0.0198:2,0:11.5:1:26:1:0.49743:0:54:4:0.0204:0:1 +6 70415946 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18691;SOR=Inf;LSEQ=ATAACTAGTGCTCATTTTCA;RSEQ=CATTATCCACCTTAAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:42,44:86,0:0:2,0:24.5:1:31:1:1:0:58.3:85:1:0:0.1 0/1:66:2:1,1:32,32:64,2:0.0303:2,2:26.5:1:29.5:1:1:1:60:4:0.0308:0:1 +6 70416053 . C G 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.8383;LSEQ=ATGTCCATCAAATCTTCCAT;RSEQ=AGGTGGCAGCACACACTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:2,1:17,24:41,3:0.0682:2,2:22.3:1:31.7:1:0.56962:2.76:60:6:0.0682:0:1 0/1:52:3:1,2:24,25:49,3:0.0577:2,2:31.7:1:31.3:1:1:1.8969:60:6:0.0588:0:1 +6 72501165 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00311;SOR=Inf;LSEQ=TCTGGAGTTGGGCAACGTGG;RSEQ=TTCTCCCCTTTCTAGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:19,27:46,0:0:2,0:31.1:1:32:1:1:0:41.4:45:1:0:0.1 0/1:31:6:3,3:10,15:25,6:0.1935:2,2:34.8:1:29.7:1:0.67583:1.48:42.5:12:0.1935:0:1.2 +6 72501263 . T C 68 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=0.35973;LSEQ=AAATTTGTTTCCTGTAGAAT;RSEQ=GAGGCCATCAAGCTACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:23.8:1:29.6:1:1:0:37.8:10:0.5:0:1 0/1:4:1:0,1:1,2:3,1:0.25:2,0:8:0:30:0:1:0:60:2:0.25:0:1 +6 72558460 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.5052;SOR=0;LSEQ=AAAATAAAGCTGCATTTTGA;RSEQ=GAGAGAATAGATTTTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:134,31:165,2:0.012:2,2:38:1:32:1:0.34745:4.27035:60:4:0.0121:0:1 0/0:132:0:0,0:107,25:132,0:0:2,0:20.7:1:29.5:1:1:0:60:131:1:0:0.1 +6 72558580 . G C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.55455;LSEQ=AAATATAACGATGAAAATTA;RSEQ=GTACCTCATGTGATAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:112:53,59:171,191:362,112:0.2358:2,2:24.1:1:31.4:1:1:1.00:60:224:0.2383:0:1.1 1/0:431:252:117,135:83,91:174,252:0.5847:2,2:25.2:1:30.4:1:0.84357:1.05225:59.9:504:0.586:0:1.2 +6 72558584 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=0.54536;LSEQ=ATAACGATGAAAATTAGGTA;RSEQ=CTCATGTGATAAATTATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:163:77,86:142,167:309,163:0.3446:2,2:26.6:1:30.5:1:0.84616:1.05:60:53.333:0.3441:0:1.1 0/1:431:96:46,50:153,182:335,96:0.2227:2,2:25:1:29:1:0.72837:1.09:60:95:0.2241:0:1 +6 72558773 . A T 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00136;SOR=7.54043;LSEQ=TTATGCAATGATTATTAAAG;RSEQ=TATACTGTGAATTATTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:0,4:0,29:29,4:0.1212:1,0:38.5:1:28.3:1:1:0:60:8:0.129:0:2 1/0:25:13:1,12:1,11:12,13:0.52:2,1:15.2:1:30.5:1:1:1.0871:60:26:0.5417:0:1.5 +6 72558820 . A C 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37148;SOR=2.87218;LSEQ=GCAATTGAGTTTTAAAACTG;RSEQ=TAAAACTAAACTAATAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:4:0,4:0,15:15,4:0.2105:1,0:15.5:1:35:0:1:0:60:8:0.2105:0:1.8 0/1:9:4:1,3:0,5:5,4:0.4444:0,2:37.5:1:33:1:0.44444:0:60:8:0.4444:0:2.5 +6 76277769 . T C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGTGGTGTGGCAGCCCA;RSEQ=CTGAAAGCCACACAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:33:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29:1:1:0:60:4:1:0:1 +6 76295861 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=TCATACAAAGCAAACTGCCT;RSEQ=CAAATCGACCAGTGACAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:30.8:1:33.1:1:1:0:60:16:1:0:0.4 0/1:18:2:1,1:8,8:16,2:0.1111:2,2:6.5:1:27:1:1:1:60:4:0.1111:0:1 +6 76295914 . C T 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06978;SOR=0.12265;LSEQ=AAATGGCTAAAAAAGCCACT;RSEQ=GAGAGGGAGTGTACCCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:3,4:1,1:2,7:0.7778:2,2:21.6:1:30.3:1:1:1.29098:60:14:0.7778:0:1 0/1:11:3:1,2:4,4:8,3:0.2727:2,2:31.7:1:30.7:1:1:1.87936:60:6:0.2727:0:1 +6 76296115 . G A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00105;SOR=0.14226;LSEQ=AGCACAGCTATTGGTGTTTT;RSEQ=CAGGAGGCAAGTGAAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:22:18,4:7,2:9,22:0.7097:2,2:25.5:1:28:1:1:1.27:58:44:0.7097:0:1.3 0/1:24:6:4,2:14,4:18,6:0.25:2,2:31:1:26.3:1:0.61806:1.70678:55:12:0.25:0:1.5 +6 76296176 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18831;SOR=Inf;LSEQ=ACACCAAATTGTGTGCTATC;RSEQ=ATGTGTAACAAATTATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:44,31:75,0:0:2,0:23.1:1:31.1:1:1:0:60:36.5:1:0:0.2 0/1:58:2:1,1:36,20:56,2:0.0345:2,2:18.5:1:25.5:1:1:1.78076:60:4:0.0345:0:1 +6 76296999 . C CTCTTT 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCCTTTTTCTTTTCTCTT;RSEQ=TCTTTTCTTTTCTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:28.8:1:1:0:60:4:1:0:0 +6 76598904 . A G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=1.84276;LSEQ=TGGAGGAAAATGAAAATGCT;RSEQ=TAAATAGACTCAGCTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:121:59,62:167,138:305,121:0.284:2,2:26.9:1:31.9:1:0.28272:1.27095:60:39.333:0.2816:0:1.1 0/1:400:169:85,84:114,115:229,169:0.4225:2,2:28.6:1:31.3:1:1:1.02:60:83.5:0.4239:0:1.1 +6 76598991 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.15676;SOR=Inf;LSEQ=ATTAAAATTAACCCACCCAC;RSEQ=TTTTTGAAGGCTAATTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:40,153:193,0:0:2,0:23.4:1:30.4:1:1:0:60:95.5:1:0:0.1 0/1:127:2:1,1:29,96:125,2:0.0157:2,2:21.5:1:28.5:1:0.41807:3.27:60:4:0.0161:0:0 +6 79720867 . T A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.43137;LSEQ=TCCTGCCAATGCCAAACAAA;RSEQ=GTGGGCTTACTAAGTTATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:535:302:135,167:111,122:233,302:0.5645:2,2:27.1:1:31:1:0.54046:1.12525:60:49.333:0.5638:0:1.1 0/1:452:162:79,83:131,159:290,162:0.3584:2,2:25.5:1:29.6:1:0.49185:1.15:60:324:0.3657:0:1.1 +6 79720958 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57819;SOR=2.68647;LSEQ=AAATATCCAAATATATACTA;RSEQ=ATTTCCTCTGAATACTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:1,0:22,129:151,1:0.0066:2,0:1:0:28:0:0.15132:0:60:2:0.0066:0:1 0/1:114:2:1,1:20,92:112,2:0.0175:2,2:9:1:27.5:1:0.33582:4.51:60:4:0.0177:0:1 +6 80346379 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51923;SOR=0;LSEQ=TCAGGGAGTTGGTGGGGTTG;RSEQ=TTCCTTCTGAGGGCTGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:16,7:23,2:0.08:2,2:27.5:1:28.5:1:1:2.20393:60:4:0.08:0:1 0/0:15:0:0,0:12,3:15,0:0:2,0:24.4:1:31.1:1:1:0:60:30:1:0:0.1 +6 80346398 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49796;SOR=0;LSEQ=GCTTCCTTCTGAGGGCTGTG;RSEQ=GGGAGAGTCCTTTCCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:22,12:34,2:0.0541:2,2:40.5:1:30.5:1:1:1.8009:60:4:0.0541:0:1 0/0:30:0:0,0:19,10:29,0:0:2,0:20.5:1:28.9:1:1:0:60:58:0.9667:0:0.1 +6 80346560 . A G 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58042;SOR=0.27349;LSEQ=CCCAAATGTTCTGTTTTTAT;RSEQ=AGGACACAGCCATACTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:24:1:32.8:1:1:0:60:8:0.4444:0:1 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:50:0:29:0:1:0:60:2:0.1667:0:1 +6 80563236 . A C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCTTCAGCAATACCCCA;RSEQ=AAGCACAGGCAACCAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:32.5:1:1:0:53.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 80564836 . C T 79 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00466;SOR=0;LSEQ=CAGTTTCCCAAGCAGGACTT;RSEQ=CCCTAAACCAGAAGAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:0,6:1:0,2:15:1:30.8:1:1:0:60:12:1:0:1.3 0/1:7:1:1,0:5,1:6,1:0.1429:2,0:22:0:32:0:1:0:60:2:0.1667:0:1 +6 80564945 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48617;SOR=Inf;LSEQ=CTTTCTACAGAATCTGAGAT;RSEQ=TGGCCCATCAGATGAAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:19.9:1:30.6:1:1:0:60:20:1:0:0 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:8:0:32.5:1:1:1.18:60:4:0.1538:0:1 +6 80565248 . T C 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68277;SOR=1.68366;LSEQ=AAAGACTTTCATACCAAATG;RSEQ=GATGAAATTTTTCTAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:11,4:15,5:0.25:2,2:37.2:1:31.8:1:1:1.43:60:10:0.25:0:1 0/1:11:4:4,0:5,2:7,4:0.3636:2,0:22.5:1:32.8:1:0.49091:0:60:8:0.3636:0:1 +6 82466944 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13742;SOR=Inf;LSEQ=CAACATTCCTGTCCTGCTTT;RSEQ=GGTCTTTCCACACCAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:101,0:101,0:0:1,0:23.9:1:31.4:1:1:0:59.9:100:1:0:0.2 0/1:60:2:1,1:55,3:58,2:0.0333:2,2:24:1:30:0:0.12994:16.02469:60:4:0.0333:0:1 +6 82466991 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17305;SOR=Inf;LSEQ=TGTCTCTCTTGATTTTCCAC;RSEQ=TCTACCACTTCTGCTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:237,14:251,0:0:2,0:24:1:32:1:1:0:60:49.2:0.996:0:0.1 0/1:180:2:1,1:160,18:178,2:0.0111:2,2:19.5:1:29.5:1:0.2005:8.68078:60:4:0.0111:0:0 +6 82467107 . T C 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=0.66388;LSEQ=ATTTGAGTACTCCCCCACCC;RSEQ=TGTCTGTCCCCCACCTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1306:328:163,165:487,490:977,328:0.2511:2,2:27.1:1:31.4:1:1:1.00607:60:31.8:0.2508:0:1.1 0/1:1049:191:94,97:427,431:858,191:0.1821:2,2:24.2:1:30.8:1:0.93626:1.02232:60:190:0.1839:0:1.2 +6 82609926 . C G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65394;SOR=0.43997;LSEQ=TTGATGTGCCTTGACATTTT;RSEQ=CTTTATTAGAAAATATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:14:14,0:12,0:12,14:0.5385:0,1:22.1:1:32.6:1:1:0:60:28:0.5833:0:1 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:37:1:29.5:1:1:0:60:4:0.3333:0:1 +6 82610040 . A T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.24311;LSEQ=TGGGATGAGACATACTACTC;RSEQ=GTGTGAATTCCTAAGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:69:67,2:34,2:36,69:0.6571:2,1:24.4:1:32.3:1:0.60542:1.96:60:68:0.6538:0:1.1 0/1:57:18:17,1:39,0:39,18:0.3158:1,1:15.2:1:29.7:1:0.31579:0:60:17:0.3091:0:1.1 +6 82610066 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14532;SOR=Inf;LSEQ=AATTCCTAAGACTGAATGAG;RSEQ=GCTTTGAATTTGAATAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:149,19:168,0:0:2,0:23:1:31.3:1:1:0:60:55:1:0:0.4 0/1:104:2:2,0:87,15:102,2:0.0192:2,0:31.5:1:30.5:1:1:0:60:4:0.0198:0:2 +6 82610188 . A T 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43274;LSEQ=GAGGGCTTCGTGGTTTATGA;RSEQ=CAGATTAGTCTATTTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:630:369:172,197:126,135:261,369:0.5857:2,2:25.9:1:30.6:1:0.68632:1.06887:60:51.714:0.5886:0:1.1 0/1:651:247:119,128:197,207:404,247:0.3794:2,2:25:1:29:1:0.93562:1.02364:60:48.4:0.3799:0:1.2 +6 82610327 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.17715;LSEQ=AAAATCTAATAAAGGCAGTC;RSEQ=GTTTGAGAGACACTAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:83:55:0,55:0,28:28,55:0.6627:1,1:26:1:32.1:1:1:0:60:54:0.6585:0:1 0/1:47:12:0,12:1,34:35,12:0.2553:1,0:17.4:1:30.7:1:1:0:60:24:0.2553:0:1 +6 82679396 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCCATAAAAAAAAAAAAAAA;RSEQ=CACTTATAATAAGCATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:22:1:20:1:1:0:60:1:1:0:2 1/1:2:2:0,2:0,0:0,2:1:0,0:20.5:1:29.5:1:1:0:49:4:1:0:3 +6 82679654 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCGGAAGATCCCACTCGC;RSEQ=AACCCACGCCACCAGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:32.4:1:31:1:1:0:60:10:1:0:0.2 0/1:19:2:1,1:6,11:17,2:0.1053:2,2:39.5:1:29:0:1:1.77:60:4:0.1053:0:1 +6 82679990 . G GGGCTGTGGCA 48 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=ACAGCCCAAAAAAACCACAC;RSEQ=GGCTGTGGCAGGCTGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:16.5:1:28:1:1:0:60:4:1:0:0 1/0:5:3:0,3:1,1:2,3:0.6:2,0:23.3:1:30.4:1:0.4:0:60:6:0.75:0.4:0 +6 82680358 . T C 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATACCCTATAAAGGAGTGA;RSEQ=CCTACTGACATCAGGTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1:0,2:14.8:1:31.7:1:1:0:58:12:1:0:1.2 1/1:9:9:5,4:0,0:0,9:1:0,2:20.4:1:29.3:1:1:0:54:8:1:0:1.1 +6 82680523 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CAGAAAACTGAAGCAGCCCT;RSEQ=CAGAAGAGGGTCCTGACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:3,1:1,0:1,4:0.8:0,2:17.8:1:30.3:1:1:0:60:8:0.8:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:30:0:1:0:60:2:1:0:0 +6 82680878 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAACCCAATGCAAAGAAG;RSEQ=TAAGAACCTTGATAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:32:1:1:0:45.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 82852407 . AAAAT A 158 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=37;MSI=10.000;MSILEN=4;SSF=0;SOR=50.15357;LSEQ=GTGAGACCCTGTCCCCCCAA;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:41,2:43,2:0.0377:1,2:20:1:25.4:1:0.1303:16.94013:60:1:0.0196:0.0189:1.5 1/0:55:37:30,7:17,1:18,37:0.6727:1,2:20.6:1:30.5:1:0.24975:3.88783:59.7:74:0.6727:0.2:0.3 +6 82852449 . G T 31 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50956;LSEQ=AATAAATAAATAAATAAATA;RSEQ=AGTCTCAGTTGGTGTTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:132,45:177,2:0.0112:2,2:13:0:31.5:1:0.449:2.91248:60:4:0.0113:0:1.5 0/0:175:1:0,1:116,58:174,1:0.0057:2,0:1:0:22:0:0.33714:0:60:2:0.0058:0:1 +6 82852544 . A G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=2.08596;LSEQ=AGAGAAAGTACATTGAGATG;RSEQ=GGCAAAACCAATCAGATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:50:18,32:88,123:211,50:0.1916:2,2:25.1:1:31.1:1:0.52333:1.27075:60:100:0.1931:0:1.1 0/1:296:98:48,50:93,105:198,98:0.3311:2,2:23.9:1:29.8:1:0.80494:1.08:60:196:0.3356:0:1.1 +6 85805288 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5078;SOR=0;LSEQ=ACCCACCTCTGGAGTTGGAC;RSEQ=ACATGGCTTCTCCCCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:33,32:65,2:0.0299:2,2:10:0:32.5:1:1:1.03078:28:4:0.0303:0:1.5 0/0:49:0:0,0:22,27:49,0:0:2,0:34.1:1:30.4:1:1:0:43.9:98:1:0:0.1 +6 85805584 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAGCTAGAGTGGTCATC;RSEQ=CCCAGTTCCCAATAGCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26:1:29:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 85995785 . G A 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=AAGAAGGAAGCGGGGGAGGA;RSEQ=GAAGAAGGATGCGGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:6:0:33:0:1:0:60:2:0.1667:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:16.7:1:31:1:1:0:60:6:1:0:1 +6 85995875 . G GGACACAGCA 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48059;SOR=0.54461;LSEQ=GGTGGTGGAGCGGACACAGC;RSEQ=GACACAGCAGACACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:12:8,4:3,0:3,12:0.8:0,2:24.5:1:30.5:1:0.51648:0:50.3:24:0.8:0.4:0.8 1/0:22:15:8,7:3,1:4,15:0.6818:2,2:31.5:1:30:1:0.60268:2.50209:57.8:30:0.6818:0.1818:0.3 +6 86578833 . G A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00815;SOR=Inf;LSEQ=TCTGGGTGTATGAGATACAA;RSEQ=TGGACAAGAAGATTACACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:25,6:31,0:0:2,0:26.2:1:33:1:1:0:60:62:1:0:0.3 0/1:41:9:6,3:22,10:32,9:0.2195:2,2:27.1:1:29:1:1:1.09742:60:18:0.225:0:1 +6 86578870 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.53963;SOR=Inf;LSEQ=ACAGGTGGACAGATTATGAC;RSEQ=CCCACCCCCGTTCCTATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:27,11:38,0:0:2,0:24.6:1:30.5:1:1:0:60:18:1:0:0.1 0/1:70:2:1,1:42,26:68,2:0.0286:2,2:14.5:1:28:1:1:1.60389:60:4:0.0299:0:1.5 +6 86578881 . T G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.55191;SOR=Inf;LSEQ=GATTATGACCCCCACCCCCG;RSEQ=TCCTATCCACAAACAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:27,14:41,0:0:2,0:24.9:1:29.6:1:1:0:60:82:1:0:0 0/1:82:2:1,1:50,30:80,2:0.0244:2,2:22.5:1:29.5:1:1:1.65581:60:4:0.0253:0:1 +6 86578949 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51493;SOR=Inf;LSEQ=TCCTGCGTCATTAGAAAATG;RSEQ=CCATGCCAAGTGGTGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:61,46:107,0:0:2,0:24.8:1:30:1:1:0:60:214:1:0:0.1 0/1:155:2:1,1:93,60:153,2:0.0129:2,2:31:0:31:0:1:1.54544:60:4:0.0129:0:1 +6 86578969 . G T 18 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75953;LSEQ=TCCATGCCAAGTGGTGTCCT;RSEQ=AAGTGCAGCACCATTGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:69,59:128,2:0.0153:2,2:20:1:30:1:1:1.16808:60:4:0.0154:0:1.5 0/1:172:2:0,2:97,73:170,2:0.0116:2,0:1:0:18:1:0.1887:0:60:1:0.006:0:1 +6 87383938 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGATACAAAGCCAACAG;RSEQ=AATTTGCCAGGGAAGGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:29:1:1:0:35.5:4:1:0:1 +6 87821903 . C T 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGTTTTTTTGTTTTTTATG;RSEQ=TTTTGAGACAGAGTCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:32:0:1:0:59.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 87821941 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCTTTCACCCAGGCTGCA;RSEQ=TGCAGTGGCATGACTATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38.5:1:31:1:1:0:59.5:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 87822418 . A T 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.87089;LSEQ=CAGGATCAAAATCCTAAATT;RSEQ=AGTGGTTTTGGCCTGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:2,1:5,1:6,3:0.3333:2,2:25.3:1:31.3:1:1:2.23609:60:6:0.3333:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:40:0:32:0:1:0:60:2:0.5:0:1 +6 87822526 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49306;SOR=Inf;LSEQ=GTAAATGATTAGGCTTATTT;RSEQ=GTAAATTGAATGGGAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:23,0:0:2,0:24:1:32.5:1:1:0:59.7:46:1:0:0.1 0/1:27:2:1,1:12,13:25,2:0.0741:2,2:31.5:1:28.5:1:1:1.08:60:4:0.0741:0:1 +6 89786309 . G GA 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAAAGTCTATATAAAGAG;RSEQ=AAAAAAGACATTCAGGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35:0:29.5:1:1:0:60:4:1:0:0.5 +6 89787305 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50629;SOR=0;LSEQ=AGGGCAAACATGAAGCCTAC;RSEQ=CTTAAGGCCTCAAAATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:3,160:163,2:0.0121:1,2:27.5:1:30:1:0.04804:46.34:60:4:0.0126:0:1.5 0/0:128:0:0,0:2,126:128,0:0:1,0:22.7:1:29.5:1:1:0:59.7:63:1:0:0.2 +6 89787349 . C T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08587;SOR=0.506;LSEQ=TATACACATAATTACTCCAA;RSEQ=AATCACCCAAGAAATACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:42:0,42:0,21:21,42:0.6563:1,1:27.2:1:28.4:1:1:0:60:41:0.6613:0:1.1 0/1:49:24:1,23:1,24:25,24:0.4898:1,1:23.4:1:26.5:1:1:1.04:58.5:11:0.4783:0:1.1 +6 89790201 . A G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCAGGGGCGTGCTGGGGAGG;RSEQ=GTAAAGAGGGTGGGGCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:28:1:32:0:1:0:60:4:1:0:1 +6 89790559 . CTTCA C 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=0.00329;SOR=1.58449;LSEQ=CGCCACCCTATCTTCACTGG;RSEQ=TTCACCTTCTCCTTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:456:340:261,79:100,16:116,340:0.7456:2,2:25.3:1:32.4:1:0.03394:1.88936:59.9:112.333:0.7506:0.1162:0.1 1/1:559:460:348,112:78,21:99,460:0.8229:2,2:24.2:1:31.1:1:0.6029:1.19506:59.9:114:0.8261:0.161:0.1 +6 89790979 . G A 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49969;SOR=Inf;LSEQ=CAGTACCAGCAGCACCGGCC;RSEQ=AGTCTGGAGGGCGGCCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:32,120:152,0:0:2,0:25.2:1:31.9:1:1:0:60:75:1:0:0.2 0/1:168:2:1,1:46,119:165,2:0.0119:2,2:5:0:30.5:1:0.48489:2.57:60:4:0.0122:0:1.5 +6 89790991 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22416;SOR=0;LSEQ=CACCGGCCGAGTCTGGAGGG;RSEQ=GGCCGGAGCCCCGCGACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:25,84:109,2:0.0179:2,2:8:1:31.5:1:0.41523:3.31:60:4:0.018:0:1 0/0:124:0:0,0:36,88:124,0:0:2,0:25.6:1:29.8:1:1:0:60:123:1:0:0.2 +6 89791003 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49877;SOR=Inf;LSEQ=CTGGAGGGCGGCCGGAGCCC;RSEQ=GCGACCGGCCCGAGCGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:15,68:83,0:0:2,0:23.5:1:30:1:1:0:60:26.667:1:0:0.2 0/1:93:2:1,1:26,65:91,2:0.0215:2,2:47:1:30:1:0.4986:2.47:60:4:0.0217:0:1 +6 89791012 . C T 33 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24584;SOR=Inf;LSEQ=GGCCGGAGCCCCGCGACCGG;RSEQ=CCGAGCGGAGCGCAGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:11,52:63,0:0:2,0:21.3:1:31.2:1:1:0:60:20:1:0:0.2 0/1:69:3:1,2:17,49:66,3:0.0435:2,2:7:1:21.3:1:1:1.43:60:2:0.0303:0:1 +6 89791015 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49803;SOR=Inf;LSEQ=CGGAGCCCCGCGACCGGCCC;RSEQ=AGCGGAGCGCAGGAGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:10,48:58,0:0:2,0:20.3:1:31.9:1:1:0:60:28:1:0:0.2 0/1:66:2:1,1:17,47:64,2:0.0303:2,2:12.5:1:26.5:1:0.47413:2.72:60:4:0.0308:0:2 +6 89791123 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14282;SOR=0;LSEQ=CTTGCCCCGCTGCGGCCCGC;RSEQ=GCTCCCGGCCAAACCCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:33,22:55,2:0.0351:2,2:36.5:1:30:1:1:1.48905:60:4:0.0357:0:1 0/0:93:0:0,0:55,38:93,0:0:2,0:28.2:1:29.8:1:1:0:59.8:92:1:0:0.4 +6 89791128 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52492;SOR=Inf;LSEQ=CCCGCTGCGGCCCGCGGCTC;RSEQ=CGGCCAAACCCCCCTCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:33,25:58,0:0:2,0:27.9:1:31:1:1:0:60:28:1:0:0.3 0/1:94:2:1,1:53,38:91,2:0.0213:2,2:10:0:31.5:1:1:1.38965:54:4:0.0217:0:1.5 +6 89791134 . A T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52543;SOR=Inf;LSEQ=GCGGCCCGCGGCTCCCGGCC;RSEQ=AACCCCCCTCAGGAAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:33,26:59,0:0:2,0:27.2:1:30.8:1:1:0:60:58:1:0:0.3 0/1:96:2:1,1:53,40:93,2:0.0208:2,2:25:0:31:1:1:1.32102:60:4:0.0213:0:1.5 +6 89791136 . AC A 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.13972;SOR=0;LSEQ=GGCCCGCGGCTCCCGGCCAA;RSEQ=CCCCCTCAGGAAAGAGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:32,25:57,2:0.0339:2,2:22.5:1:34:1:1:1.2746:60:4:0.0345:0:1 0/0:98:0:0,0:54,44:98,0:0:2,0:26.4:1:30.7:1:1:0:59.8:31.667:1:0:0.3 +6 89792120 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=CATTGAATTAGAGATTTGCG;RSEQ=TTTATCTGTGCCCTTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:142,17:159,2:0.0124:2,0:23.5:1:28.5:1:1:0:60:4:0.0126:0:3 0/0:159:0:0,0:138,21:159,0:0:2,0:25:1:30.4:1:1:0:60:78.5:1:0:0.1 +6 89792138 . GA G 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.25114;SOR=Inf;LSEQ=CGGTTTATCTGTGCCCTTGG;RSEQ=AAAAATTTGCCCACCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:186,52:238,0:0:2,0:21.9:1:30.4:1:1:0:59.9:78.333:0.9958:0:0.1 0/1:269:3:2,1:204,61:265,3:0.0112:2,2:12:1:29.3:1:0.54739:1.66851:60:6:0.0113:0.0037:0.3 +6 89792392 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50018;SOR=0;LSEQ=TGCAGTGATCTAGTGGATTA;RSEQ=CTTACGCTTTTCCATCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:10,159:169,2:0.0117:2,2:10:1:29:1:0.12487:15.21:60:4:0.012:0:1 0/0:152:0:0,0:15,137:152,0:0:2,0:21.6:1:30.3:1:1:0:60:37:1:0:0.1 +6 89793894 . G C 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGCAGTACACTTAAAAAC;RSEQ=CTCCTCAAAGTTCAAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:67,164:231,0:0:2,0:26.2:1:31.3:1:1:0:59.9:32:0.9956:0:0.1 0/1:279:59:16,43:81,139:220,59:0.2115:2,2:25.8:1:30.2:1:0.21782:1.56368:60:58:0.2101:0:1.1 +6 89795085 . T C 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.98283;LSEQ=ATTTTAGCTTTTGTTAGTAA;RSEQ=GTGTTGTAAATATTAATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:63:61,2:57,0:57,63:0.525:1,1:26.2:1:33:1:0.49706:0:60:126:0.5294:0:1 1/0:121:63:63,0:58,0:58,63:0.5207:1,1:25.7:1:31.8:1:1:0:60:126:0.5207:0:1 +6 89795288 . G C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8391;SOR=0.97871;LSEQ=TCCAACATTTCTCAGCTCTT;RSEQ=TCATTTTGAGCAGTATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:711:366:140,226:141,202:343,366:0.5148:2,2:26.1:1:32.5:1:0.44343:1.12661:60:44.75:0.5136:0:1.9 1/0:852:434:169,265:184,232:416,434:0.5094:2,2:24.9:1:30.8:1:0.1258:1.24329:60:71.333:0.5089:0:1.5 +6 89795303 . A G 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34079;LSEQ=CTCTTGTCATTTTGAGCAGT;RSEQ=TGTCTGCAGTTTAATGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:615:316:115,201:108,189:297,316:0.5138:2,2:25.2:1:32.2:1:1:1.00:60:104.333:0.514:0:2 0/1:718:190:65,125:207,321:528,190:0.2646:2,2:23.8:1:30.9:1:0.25694:1.23975:59.9:62.333:0.2638:0:2 +6 89795551 . G C 78 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACACCTTAGAAAGTAACA;RSEQ=TGAGTTGAGCTGGGCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:15:1:33.6:1:1:0:60:10:0.5:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 90009187 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50044;SOR=0;LSEQ=TTTGTGTCCTGATTCTCCTT;RSEQ=CCTGCTCTTATATTTGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:112,14:126,2:0.0156:2,2:36:1:27.5:1:0.22146:7.76299:60:4:0.016:0:2 0/0:111:0:0,0:93,18:111,0:0:2,0:20.9:1:31.5:1:1:0:60:222:1:0:0.9 +6 90009199 . A T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=3.65959;LSEQ=TTCTCCTTGCCTGCTCTTAT;RSEQ=TTTGTAGGACAAAAAAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:166:108:87,21:48,9:57,108:0.6506:2,2:23.9:1:31.2:1:0.67307:1.28544:60:216:0.6626:0:1.1 1/1:149:130:101,29:12,7:19,130:0.8725:2,2:21.7:1:29.8:1:0.24836:2.02:60:260:0.8725:0:1.1 +6 90009220 . G A 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTGTAGGACAAAAAAGTTG;RSEQ=CAGCTGCAGGGCCTGTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:21:12,9:150,68:218,21:0.0879:2,2:17.3:1:28.4:1:0.32887:1.65073:60:20:0.0858:0:1.7 0/0:217:0:0,0:142,75:217,0:0:2,0:25.5:1:30.4:1:1:0:60:71.333:1:0:0.8 +6 90009311 . T C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22216;SOR=1.19391;LSEQ=CCCTCTCCACTACTTCCTGC;RSEQ=CTTTTCTCCTTGGGAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:417:236:108,128:70,110:180,236:0.5659:2,2:25.5:1:31:1:0.16337:1.32:60:77.667:0.5697:0:1.1 1/0:381:232:102,130:64,83:147,232:0.6089:2,2:25.8:1:30:1:1:1.02:60:76.333:0.6123:0:1.1 +6 90009410 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52474;SOR=0;LSEQ=AGCGCTGTGCCAGAGGGAGC;RSEQ=AGAGAGGGCAGCACATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:10,85:95,2:0.0206:2,2:14.5:1:29.5:1:0.21499:8.15:60:4:0.0208:0:1.5 0/0:60:0:0,0:9,51:60,0:0:2,0:23.6:1:31.9:1:1:0:59.4:59:1:0:0.2 +6 90009427 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15472;SOR=Inf;LSEQ=AGCCAGAGAGGGCAGCACAT;RSEQ=ACATCCCTGGGGCCAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:4,60:64,0:0:2,0:25:1:32.9:1:1:0:60:128:1:0:0.1 0/1:42:2:0,2:4,36:40,2:0.0476:2,0:37.5:1:27.5:1:1:0:60:4:0.0488:0:1 +6 90012435 . G A 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.37616;SOR=0.39312;LSEQ=GGCAGTGGCCACCGTGTTCC;RSEQ=GGGCTGCCTGTCCATGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:24.3:1:30.3:1:1:0:40.5:8:0.4444:0:1.5 0/1:13:3:3,0:8,2:10,3:0.2308:2,0:14.7:1:31:0:1:0:34.3:6:0.2308:0:1.3 +6 90012463 . C A 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.65879;SOR=0.59813;LSEQ=CTGTCCATGAAGGAGGTGGA;RSEQ=GAGCAGATGCTGTCCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:7,3:10,3:0.2308:2,2:26:1:31:1:1:1.15267:33.3:6:0.2308:0:1.7 0/1:20:3:1,2:10,7:17,3:0.15:2,2:27.3:1:30:1:0.56579:2.70974:22.7:6:0.15:0:1.3 +6 90012496 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49826;SOR=Inf;LSEQ=TCCATCCAGAGCAAGAACAG;RSEQ=AGCTACTTCGTGGAGTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:18,0:0:2,0:24.9:1:31.8:1:1:0:40.8:36:1:0:0.3 0/1:24:2:1,1:11,10:21,2:0.0833:2,2:44:0:30:1:1:1.09544:20:4:0.0833:0:1 +6 92525675 . C T 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCTGAACACTTCATGTA;RSEQ=CCCAAAGAGCCAATTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:0:0,0:366,350:716,0:0:2,0:26.9:1:31.7:1:1:0:58.7:64.091:1:0:0.2 0/1:660:33:17,16:326,299:625,33:0.05:2,2:27.1:1:28.8:1:1:1.02613:59.8:66:0.0505:0:1.1 +6 92525884 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.93363;SOR=0.9798;LSEQ=TAAACTCTCAGGGTTGTCAA;RSEQ=GGAGAACACATAACATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:102:44,58:134,203:337,102:0.2323:2,2:24.3:1:30.8:1:0.56612:1.15:59.9:101:0.2343:0:1.1 0/1:376:86:37,49:120,168:288,86:0.2287:2,2:20.9:1:29.3:1:0.90099:1.06:60:85:0.2297:0:1.1 +6 92525977 . A G 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.16692;LSEQ=TCCCACAAAGTCAGCTCTAC;RSEQ=CTTTCCCATCCACCTCGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:330:161:78,83:77,91:168,161:0.4879:2,2:24.7:1:30.5:1:0.65959:1.11:60:31.2:0.4921:0:1.1 0/1:358:49:24,25:154,155:309,49:0.1369:2,2:23.5:1:30.1:1:1:1.03486:60:98:0.1392:0:1.2 +6 92526096 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49904;SOR=0;LSEQ=GTCTTGCCACAGACTCTGTC;RSEQ=CCGACAATTACCAGCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:56,140:196,2:0.0101:2,2:40:1:28:1:0.49392:2.49:60:4:0.0101:0:2 0/0:188:0:0,0:68,120:188,0:0:2,0:24.1:1:28.7:1:1:0:60:376:1:0:0.2 +6 92526109 . A T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5008;SOR=0;LSEQ=CTCTGTCACCGACAATTACC;RSEQ=GCTTCTTCTGGACGGGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:47,122:169,2:0.0117:2,2:33.5:1:32:1:0.4838:2.58:60:4:0.0121:0:2 0/0:149:0:0,0:51,98:149,0:0:2,0:21.9:1:29.3:1:1:0:60:48.667:1:0:0.1 +6 92526266 . A AGC 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.30975;LSEQ=CCGCAAGTCGCAAGCTGGGA;RSEQ=AGCAGGGCTGATAACTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:4,6:0.6:0,0:25.2:1:32.2:1:1:0:56.8:12:0.6:0.3:0 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:14.5:1:32:1:1:0:60:8:0.6667:0.3333:0 +6 93108565 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1448;SOR=Inf;LSEQ=TTGAGATTCCATACATATGG;RSEQ=TTAGGAATGAAGTCATCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:96,9:105,0:0:2,0:24.9:1:32.4:1:1:0:60:104:1:0:0.1 0/1:65:2:1,1:54,9:63,2:0.0308:2,2:33:1:28:1:0.28606:5.74461:60:4:0.0313:0:1 +6 93108691 . A T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.03967;SOR=0.69519;LSEQ=CCACTATGTTTCTATGCTAG;RSEQ=ACTGTGTTATAAGTGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:279:158:63,95:49,72:121,158:0.5663:2,2:27.8:1:29.3:1:1:1.02615:60:157:0.5668:0:1.1 0/1:267:127:60,67:62,78:140,127:0.4757:2,2:24.8:1:28:1:0.71221:1.13:60:126:0.4773:0:1.1 +6 93108758 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20837;SOR=Inf;LSEQ=AATAATTCTAAAATTGAAGT;RSEQ=CCATTCATTTGATTAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:31,97:128,0:0:2,0:24.3:1:32.2:1:1:0:60:41.667:1:0:0.3 0/1:108:2:1,1:28,78:106,2:0.0185:2,2:16.5:1:27:1:0.46677:2.75:60:4:0.0189:0:1 +6 93108854 . T TTTAA 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.8378;LSEQ=TCACTTATTTTGTTTTCTAT;RSEQ=TTAAAGTTAACATTTTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:12,8:0.4:0,0:24:1:30.7:1:1:0:60:16:0.4:0.05:0 0/1:14:5:0,5:0,9:9,5:0.3571:0,0:26.2:1:29.8:1:1:0:60:10:0.3571:0.0714:0 +6 93589500 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTTGGGGAGGGCAGCAGCCA;RSEQ=CACTGGGACTCAAAACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24:1:32.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 93590442 . G C 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGCTTCTCTGCAGGAACT;RSEQ=CAATAACCCCAGCCAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:32.5:1:1:0:60:4:1:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:50:0:29:0:1:0:33:2:1:0:1 +6 93590467 . G A 62 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=AACCCCAGCCAGAGGCTCAG;RSEQ=GACAGAACCCCGATCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:23:1:31.3:1:1:0:60:8:1:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:26:0:33:0:1:0:33:2:1:0:1 +6 93591455 . T G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAACACTCCAAGAAATAT;RSEQ=GGACTTATTAAAAAGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:30.5:1:1:0:60:4:1:0:1.5 +6 93592984 . T C 30 d5;v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=TAACTAAGATTAGAGCAGAA;RSEQ=TGAAGGAGATAGAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:30:1:1:0:56:4:1:0:1.5 0/0:2:0:0,0:2,0:2,0:0:0,0:11.5:1:26.5:1:1:0:49.5:4:1:0:0.5 +6 93954830 . A G 118 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.65232;SOR=0.44051;LSEQ=TATTGTTGTGAAGGTTAAAA;RSEQ=GGTAATATGTTTAAAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:12:12,0:26,0:26,12:0.3158:1,0:23.4:1:33:1:1:0:60:24:0.3243:0:1.8 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:19:0:33:0:1:0:60:2:0.1667:0:1 +6 93954871 . C T 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28528;SOR=0.47689;LSEQ=ATTTAGTATAATGCCTGGTA;RSEQ=GCAGTAAGAACTTGTTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:23:23,0:49,0:49,23:0.3194:1,1:23.7:1:32.7:1:1:0:60:46:0.3239:0:1.5 0/1:22:4:4,0:18,0:18,4:0.1818:1,0:16:1:31.5:1:1:0:60:8:0.1818:0:1 +6 93954896 . AT A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGAACTTGTTAAAGAAGT;RSEQ=TTTTTTTATCTTGATTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:2,0:106,0:106,2:0.0185:1,0:19.5:1:31:1:1:0:60:4:0.0187:0:1.5 0/0:53:0:0,0:52,1:53,0:0:1,0:22.4:1:31:1:1:0:60:106:1:0:0.1 +6 93955304 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52935;SOR=0;LSEQ=GTACATAATAAAAAATACAT;RSEQ=GATATGCTAATAAAAACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:0,2:1,152:153,2:0.0129:1,0:21.5:1:30.5:1:1:0:60:4:0.0132:0:1 0/0:93:0:0,0:2,91:93,0:0:1,0:21.7:1:29.6:1:1:0:60:92:1:0:0.1 +6 93956769 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00014;SOR=0.542;LSEQ=TTATAATAAACCAAATTTCC;RSEQ=GGTAGGCAAAATGATTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:479:372:59,313:16,91:107,372:0.7766:2,2:22.4:1:30.2:1:0.88105:1.07:60:185:0.7757:0:1 1/0:320:209:32,177:15,95:110,209:0.6531:2,2:22.7:1:29.3:1:0.74203:1.14:60:103.5:0.653:0:1.1 +6 93957161 . C T 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATATGAATGTACTATGA;RSEQ=AGAAAATATTACCAAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:1,6:7,3:0.3:2,0:36.3:1:29.7:1:1:0:60:6:0.3:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 93964187 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0.98378;LSEQ=TGATTATTCAAAATGAAAGC;RSEQ=AAAATAATAAAATTAGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:70:61:61,0:9,0:9,61:0.8714:0,1:23:1:32.4:1:1:0:60:60:0.8696:0:1.1 1/1:23:20:20,0:3,0:3,20:0.8696:0,1:28.1:1:31.2:1:1:0:60:40:0.8696:0:1.1 +6 93964319 . C T 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.56359;LSEQ=CATGTTCCAGTAATACTGGC;RSEQ=ATTAATGTATTCAATCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:698:546:431,115:118,34:152,546:0.7822:2,2:26:1:31.1:1:0.73764:1.08:60:67.25:0.782:0:1.1 1/0:514:344:244,100:129,40:169,344:0.6693:2,2:24.4:1:29.2:1:0.20735:1.32102:59.8:85:0.6719:0:1 +6 93964787 . T C 59 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7746;LSEQ=ACAAACAATGACAGGCTGGG;RSEQ=GCTGTGGCTCACATCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:17.3:1:29.5:1:1:0:56.5:8:0.5714:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:17:0:31:0:1:0:60:2:0.5:0:1 +6 93965458 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15436;SOR=Inf;LSEQ=GCTCAATTTGCTTCATTTCT;RSEQ=CTGTTTAGTTTTACATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:292,7:299,0:0:1,0:26.8:1:32.3:1:1:0:59.9:58.8:1:0:0.1 0/1:194:2:1,1:178,14:192,2:0.0103:2,2:22:1:27.5:1:0.14903:12.31775:60:4:0.0104:0:1.5 +6 93965492 . G A 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTATTAGGTCCTGCTTTC;RSEQ=TGGTAGAAAAATCTTAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:0:0,0:457,87:544,0:0:2,0:23.2:1:30.2:1:1:0:59.9:180.333:0.9982:0:0.1 0/1:418:28:22,6:302,88:390,28:0.067:2,2:24.6:1:29.5:1:1:1.07:60:56:0.068:0:1 +6 93966205 . G T 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAACGGGGGAAATATTTGAG;RSEQ=CAAAATGAAGAGAAACTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:19.3:1:31.7:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 93967249 . TA T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.20615;SOR=1.23869;LSEQ=ATGACTGGTTTCCCTAAAAT;RSEQ=AAAAAAAAAAGTTTCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:81:21,60:268,532:800,81:0.0911:2,2:28.8:1:31.6:1:0.1745:1.43875:59.6:80:0.0923:0.0022:0.3 0/1:697:77:27,50:214,397:611,77:0.1105:2,2:27.1:1:30.3:1:1:1.00:59.5:154:0.1132:0.0057:0.4 +6 93967319 . C T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01898;SOR=Inf;LSEQ=TTTCTCATCCCCCAATAAAA;RSEQ=ACATGGTGTTCTTTTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:5,233:238,0:0:1,0:25.9:1:32.7:1:1:0:60:78.333:1:0:0.1 0/1:142:4:0,4:2,136:138,4:0.0282:1,0:26:1:28.3:1:1:0:60:8:0.0284:0:1 +6 93967851 . C T 324 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.48716;LSEQ=CCTTCCAAATGGACAACATT;RSEQ=GGGTGGTCAAACTGCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1965:1536:862,674:246,180:426,1536:0.7817:2,2:27:1:30.7:1:0.58085:1.06859:59.9:101.4:0.7808:0:1.1 1/0:1800:1144:613,531:350,305:655,1144:0.6356:2,2:26.1:1:29.9:1:0.96085:1.01:59.9:162.429:0.6356:0:1.1 +6 93968070 . G T 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1637;SOR=5.99349;LSEQ=ATTTTCTTTTAAGAGTAAAT;RSEQ=CGTTGAATTATTTTTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:1:0,1:56,390:446,1:0.0022:2,0:29:0:32:0:1:0:60:2:0.0023:0:1 0/1:301:4:2,2:50,247:297,4:0.0133:2,2:11.3:1:30:1:0.13935:4.90:60:8:0.0134:0:1 +6 93968162 . C T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00189;SOR=0.24441;LSEQ=GTAAAGCCCTGTGAGTTACA;RSEQ=TGAATACATTCCCATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:59:0,59:0,15:15,59:0.7973:1,1:29:1:30.5:1:1:0:59.7:118:0.831:0:1 0/1:37:18:0,18:0,19:19,18:0.4865:1,1:21.3:1:30.4:1:1:0:60:36:0.5:0:1 +6 93968294 . A ACTGT 80 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAAGTTACGCTTTCCTAA;RSEQ=CTGTTAAACAGGCTACTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:12,6:0.3333:0,0:25.3:1:31.1:1:1:0:58:12:0.3333:0.1111:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 93973569 . A G 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCATAATAAAGAAAAGCCA;RSEQ=ACACTTACAATGAAAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1640:0:0,0:912,726:1638,0:0:2,0:25.4:1:30.5:1:1:0:60:62:0.9988:0:0.1 0/1:1296:33:18,15:705,558:1263,33:0.0255:2,2:24.5:1:31:1:1:1.05279:60:66:0.0258:0:1.2 +6 93973658 . A G 159 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=35.71222;LSEQ=AAGAAAGCAAATTTGTGACA;RSEQ=TCTCAGTCATTTTACTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1196:1:0,1:434,761:1195,1:8e-04:2,0:48:0:33:0:1:0:60:2:9e-04:0:1 0/1:1103:32:13,19:423,648:1071,32:0.029:2,2:23.5:1:31.9:1:1:1.05:60:64:0.0295:0:1.4 +6 93973686 . A C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.68967;LSEQ=CATTTTACTTTATATATTTA;RSEQ=TATTCAGTACAATGTACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:722:199:49,150:139,384:523,199:0.2756:2,2:21.1:1:33:1:0.63569:1.10797:60:198:0.2762:0:1.2 1/0:670:339:101,238:103,227:330,339:0.506:2,2:23.6:1:31.3:1:0.73702:1.0691:60:338:0.5113:0:1.1 +6 93973735 . T C 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACAACTTACTAGAGTTAAA;RSEQ=TTACTGTTCATAGTTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:43:1,42:8,239:247,43:0.1483:1,1:22.8:1:33.1:1:1:1.40438:59.2:86:0.1498:0:1.8 0/0:192:0:0,0:9,183:192,0:0:1,0:22.7:1:29.8:1:1:0:60:384:1:0:0.5 +6 93973784 . G T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1796;SOR=0;LSEQ=GTAATAATATAGCGATTCAC;RSEQ=ATTAAAATTGCAAAGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:6:0,6:3,126:129,6:0.0444:1,0:27.2:1:25:1:1:0:60:5:0.0379:0:1.5 0/0:61:0:0,0:1,60:61,0:0:1,0:21.9:1:31.7:1:1:0:60:122:1:0:0.1 +6 93979090 . A T 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=2.28126;LSEQ=TACATATATATTTATTTGTA;RSEQ=ATGTAAAAATTATGATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:68:66,2:194,2:196,68:0.2576:1,1:24.1:1:30.8:1:0.27382:2.92487:59.5:33:0.2548:0:1 0/1:156:69:69,0:87,0:87,69:0.4423:1,1:23:1:30.6:1:1:0:60:68:0.4416:0:1.1 +6 93979780 . A G 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAAGTTATTCAGCAAGA;RSEQ=AAAAAGCCAGATGCTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:32:1:32.5:1:1:0:59.8:8:0.5714:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 93982124 . A G 320 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03632;LSEQ=ACTCTCTCCTTCATTACTCC;RSEQ=CTCACTTGCGAGGGAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1233:1225:517,708:3,0:3,1225:0.9935:0,2:24.7:1:31.2:1:0.07568:0:60:71.059:0.9983:0:1.1 1/1:1121:950:407,543:78,90:168,950:0.8475:2,2:25.7:1:30.3:1:0.39929:1.15611:60:58.375:0.8499:0:1.1 +6 94065703 . T C 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATTACAAAGATCATAGTC;RSEQ=ATGTAGTAAAAAATTGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16:1:28:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 94065942 . A G 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTCCTGTTTTTTTTTTTCC;RSEQ=GAGACAAGAGTCTTAGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:34.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 94066172 . C T 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52632;SOR=0;LSEQ=ACCTTGTGATCTGCCCGCCT;RSEQ=GGCCTCCCAAAATGCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:12,6:0.3333:0,0:23.3:1:33:0:1:0:46.7:12:0.3333:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:21.7:1:30.7:1:1:0:58.7:6:1:0:0.7 +6 94066191 . G A 104 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59826;SOR=0.34684;LSEQ=TCGGCCTCCCAAAATGCTGG;RSEQ=ATTACAGGTGTGAGCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:11,0:11,0:11,11:0.5:0,0:25.6:1:30.1:1:1:0:51.8:22:0.5:0:1 0/1:4:1:1,0:3,0:3,1:0.25:0,0:39:0:29:0:1:0:60:2:0.25:0:1 +6 94066446 . G T 191 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0274;LSEQ=AAAACATACCTGCTTGACCA;RSEQ=TGGTGATACTGACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1532:77:48,29:866,589:1455,77:0.0503:2,2:24.5:1:30.6:1:0.72088:1.13:60:76:0.0501:0:1.2 0/0:1382:2:1,1:820,560:1380,2:0.0014:2,2:7:1:29.5:1:1:1.46384:60:4:0.0015:0:1 +6 94066811 . G GA 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.97502;LSEQ=TAAGTAAATAAGCAAAAATA;RSEQ=AAAAAAAAACATACAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:845:34:6,28:183,621:804,34:0.0402:2,2:24.6:1:30.7:1:0.67492:1.3747:60:33:0.04:0:0.2 0/1:713:28:7,21:197,478:675,28:0.0393:2,2:25:1:29.8:1:0.83192:1.23602:60:56:0.0403:0.0014:0 +6 94066934 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAACATTTCATTACCTTT;RSEQ=CTAGAGAAGCTGTATAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:0,85:85,2:0.023:1,2:26:1:29.5:1:0.02299:0:60:4:0.0233:0:1 0/0:29:0:0,0:0,29:29,0:0:1,0:21.8:1:29:1:1:0:60:28:1:0:0.2 +6 94067373 . C CT 31 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATGCAAGACCCTAATAA;RSEQ=TTTTTTTTTTTTTTTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:2,0:2,2:0.5:0,0:12:1:31.5:1:0.33333:0:60:4:0.5:0.25:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 94067497 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTCCTGCTTCAGTCTTCC;RSEQ=CGTAGCTGGGATTACAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:41.5:1:30.5:1:1:0:42:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 94067846 . A C 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATTTTATCTTAATATTTT;RSEQ=AAATAATTTTAATATTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:121,0:121,0:0:1,0:22.2:1:28.7:1:1:0:59.8:120:1:0:0.5 0/1:69:15:15,0:54,0:54,15:0.2174:1,1:22.3:1:30.8:1:1:0:60:30:0.2174:0:1 +6 94067861 . T G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25999;LSEQ=ATTTTAAAATAATTTTAATA;RSEQ=TTAAGTATAATTAAGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:86:86,0:89,0:89,86:0.4914:1,1:22.3:1:33.5:1:1:0:60:27.667:0.4826:0:1 0/1:100:20:20,0:79,1:80,20:0.2:1,1:21.7:1:31.7:1:1:0:60:40:0.202:0:1 +6 94067981 . C T 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01798;SOR=1.21563;LSEQ=TAATACAACTCACTTGTGCA;RSEQ=GCAACGTATGGTGGGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1382:795:476,319:358,227:585,795:0.5753:2,2:25:1:30.7:1:0.65592:1.05691:59.9:60.154:0.5742:0:1.1 1/0:1138:708:417,291:246,182:428,708:0.6221:2,2:25.9:1:29.7:1:0.66388:1.06:60:77.667:0.6208:0:1.1 +6 94068181 . T TA 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.67021;SOR=1.22177;LSEQ=CATGAGAGCAAATCGATCTT;RSEQ=AAAAAAAAATTGTATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:611:11:2,9:116,480:596,11:0.018:2,2:27.5:1:31.2:1:1:1.08734:60:22:0.0185:0.0016:0 0/1:502:11:1,10:111,373:484,11:0.0219:2,2:24.9:1:30.3:1:0.46952:2.97121:60:22:0.022:0.004:0.1 +6 94068208 . G C 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATTGTATTATTTAGCAAG;RSEQ=AATCAAATATTAAATGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:28:6,22:32,297:329,28:0.0784:2,2:25.7:1:32.3:1:0.09997:2.52:60:56:0.0795:0:1.1 0/0:259:0:0,0:22,237:259,0:0:2,0:23.8:1:30.7:1:1:0:60:50.8:1:0:0.1 +6 94068364 . G C 118 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07552;SOR=0.13317;LSEQ=TGCACCTGCAGTTGGCACCA;RSEQ=GCCAAAGTCTGGAGCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:16:1,15:0,10:10,16:0.6154:0,1:26:1:29.7:1:1:0:58.1:32:0.6154:0:1.1 0/1:6:1:0,1:0,5:5,1:0.1667:0,0:40:0:27:0:1:0:60:2:0.1667:0:1 +6 94119750 . A G 59 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATTCTAAAAGTTTGTAAAT;RSEQ=TATTCGTTTATGCCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:23.5:1:29.5:1:1:0:60:8:0.4:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 94120192 . G A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.82128;SOR=1.02317;LSEQ=GAAATTTAAAAAGGCAAAGT;RSEQ=GAGTTTTAATAGGACACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1105:609:404,205:319,177:496,609:0.5511:2,2:26.3:1:29.3:1:0.48503:1.09:59.9:42.5:0.5519:0:1.1 1/0:898:500:313,187:236,158:394,500:0.5568:2,2:25.6:1:28.3:1:0.44663:1.12:60:124:0.5567:0:1.1 +6 94124157 . G T 70 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.18321;LSEQ=GTAATTAGTTAGCATTTACA;RSEQ=CCTGGACCCTGAGGTATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:16.2:1:30.4:1:1:0:53.4:10:0.4545:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:35:0:32:0:1:0:60:2:0.5:0:1 +6 94124370 . G T 64 v3;p8;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04778;SOR=7.80217;LSEQ=ACCCTGGAGGGAAGGGAAAC;RSEQ=TTTTGTTTCTTATTTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:686:1:0,1:525,159:684,1:0.0015:2,0:1:0:26:0:0.23358:0:60:2:0.0015:0:1 0/1:532:6:0,6:391,135:526,6:0.0113:2,0:6.5:1:25:1:0.00032:0:60:12:0.0115:0:1 +6 94124530 . C A 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41576;SOR=0.91219;LSEQ=TATGTTACATGAAACACTTA;RSEQ=GCACACATGTAGACATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:818:432:112,320:102,284:386,432:0.5281:2,2:24.6:1:31.4:1:0.87377:1.02613:60:143:0.5316:0:1.1 1/0:582:294:68,226:90,194:284,294:0.5052:2,2:24.1:1:30:1:0.02495:1.54065:60:48:0.5017:0:1.1 +6 94128872 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=0.50469;SOR=0;LSEQ=GGGTCGCCCGGCGCCGGAGG;RSEQ=GCGGCCGGCAGCGCCGCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:124,3:127,2:0.0155:1,2:17:1:31:1:0.06129:35.9361:60:4:0.0157:0:1 0/0:102:0:0,0:93,8:101,0:0:2,0:16.8:1:31.6:1:1:0:60:32.667:0.9899:0:0.2 +6 94129194 . T C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52756;SOR=0;LSEQ=CTCGGTCCCCGATCGGCTGC;RSEQ=CCACGTTTAGCTTTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:0,2:3,188:191,2:0.0104:1,0:13:1:27.5:1:1:0:60:4:0.0107:0:1 0/0:118:0:0,0:2,116:118,0:0:1,0:19.6:1:28.6:1:1:0:60:38.333:1:0:0.1 +6 95221894 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=GACAAGTGGATTTCCTCCCA;RSEQ=TGAAGCATACCCCCTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:4,1:5,0:0:2,0:24:1:33.2:1:1:0:60:10:1:0:1 0/1:5:2:1,1:2,1:3,2:0.4:2,2:20.5:1:29:1:1:1.7321:60:4:0.4:0:2 +6 95221943 . A G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCAAGGTGCTTCGTTAAAT;RSEQ=TGTCCTGTTTCCCGTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:12,10:0,0:0,22:1:0,2:24.5:1:32.5:1:1:0:59.1:44:1:0:1 1/1:8:8:4,4:0,0:0,8:1:0,2:34.4:1:32:1:1:0:60:16:1:0:1.3 +6 96823954 . ACAG A 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.0652;SOR=0;LSEQ=ATTAAATCAATGATGCTGGC;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:3:2,1:15,14:29,3:0.0938:2,2:23.3:1:34.7:1:1:1.83:60:6:0.0938:0:0 0/0:46:0:0,0:24,22:46,0:0:2,0:27.8:1:30.2:1:1:0:60:14.333:1:0:0.2 +6 97729953 . C A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.59726;LSEQ=AAAAATTAGTGCCCAGCTCC;RSEQ=TACAGTAAGGGAACATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:501:246:133,113:136,118:254,246:0.491:2,2:24.9:1:30.7:1:0.92867:1.02:60:245:0.493:0:1.1 0/1:602:220:121,99:191,190:381,220:0.3654:2,2:28.1:1:29.7:1:0.27093:1.22:60:219:0.3656:0:1.2 +6 98417064 . A G 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18703;SOR=Inf;LSEQ=AGTCTTTTACAAAAGTATCT;RSEQ=ATCCTATTCTAGTGTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:153,55:208,0:0:2,0:22.5:1:29.2:1:1:0:59.9:103:1:0:0.2 0/1:159:2:1,1:108,49:157,2:0.0126:2,2:5:0:26:1:0.53141:2.19205:60:4:0.0127:0:1.5 +6 98417147 . A T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.21902;LSEQ=CAGCCAGCTACCTGAGGAGA;RSEQ=GGGAAGTGGGAGAGACTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:87:41,46:180,169:349,87:0.1995:2,2:27:1:30.5:1:0.47425:1.19449:60:86:0.2005:0:1.1 0/1:376:134:71,63:115,127:242,134:0.3564:2,2:24.1:1:29.4:1:0.33339:1.24:60:43.667:0.3531:0:1.1 +6 98417252 . AT A 143 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.03607;LSEQ=CGGCATCACACTGGGATTCA;RSEQ=TTTTTTTTTCTCTCTATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:23:4,19:11,88:99,23:0.1885:2,2:29.7:1:31.8:1:0.47991:1.68:60:46:0.1917:0.0082:0.3 0/1:67:13:1,12:10,44:54,13:0.194:2,1:31.5:1:29.2:1:0.67722:2.69504:60:26:0.194:0.0299:0.3 +6 99282579 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.47059;SOR=0;LSEQ=GGCGGCGGCGGCAGCAGCAG;RSEQ=AGTAATAGCAGGAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:18.5:1:29:1:1:1.29:60:4:0.25:0:1.5 0/0:8:0:0,0:4,4:8,0:0:2,0:17:1:31.3:1:1:0:60:16:1:0:0 +6 99282584 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=CGGCGGCAGCAGCAGCAGTA;RSEQ=TAGCAGGAGCAGCAACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:3,5:8,2:0.2:2,2:23.5:1:32:1:1:1.58:60:4:0.2222:0:1.5 0/0:7:0:0,0:3,4:7,0:0:2,0:15.7:1:29.9:1:1:0:60:14:1:0:0 +6 99282962 . CG C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTCCCACGGCGGCGGCGG;RSEQ=GGGGCGGTGGCGGCGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:33:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:10:0:32.5:1:1:0:60:4:0.6667:0:0.5 +6 99283061 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50416;SOR=0;LSEQ=CTGGGCCAGCCGGACATCAA;RSEQ=CCCTCGGTGGTGGTGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:2,0:82,4:86,2:0.0227:1,0:46:0:31:0:1:0:60:4:0.023:0:1 0/0:69:0:0,0:65,4:69,0:0:2,0:24.6:1:31.9:1:1:0:59.7:33.5:1:0:0.2 +6 99283107 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02956;SOR=Inf;LSEQ=GCCGCGGAGACGAGCTGCAC;RSEQ=GGCCAGGCGCCCTGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:161,91:252,0:0:2,0:24.3:1:29.5:1:1:0:59.9:30.5:1:0:0.2 0/1:180:4:2,2:109,67:176,4:0.0222:2,2:17.8:1:29.3:1:0.63815:1.62224:60:8:0.023:0:1 +6 99283111 . C G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18448;SOR=Inf;LSEQ=CGGAGACGAGCTGCACGGGC;RSEQ=AGGCGCCCTGCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:162,98:260,0:0:2,0:25.1:1:30.7:1:1:0:59.9:27.889:0.996:0:0.2 0/1:197:2:1,1:118,75:193,2:0.0102:2,2:11.5:1:27.5:1:1:1.5695:60:4:0.0104:0:1 +6 99283120 . TGCA T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=0.09598;SOR=Inf;LSEQ=GCTGCACGGGCCAGGCGCCC;RSEQ=GCAGCAGCATCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:163,119:282,0:0:2,0:27.4:1:31.7:1:1:0:59.8:30.333:0.9964:0:0.2 0/1:240:3:1,2:135,102:237,3:0.0125:2,2:27.3:1:29:1:0.58039:2.63645:60:6:0.0128:0.0042:0.7 +6 99283127 . G T 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.66011;SOR=1.87743;LSEQ=GGGCCAGGCGCCCTGCAGCA;RSEQ=CAGCATCAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:2:1,1:175,132:307,2:0.0065:2,2:32.5:1:32:0:1:1.32452:60:4:0.0066:0:1 0/1:248:3:2,1:133,111:244,3:0.0121:2,2:47.7:1:30.7:1:1:1.67:60:6:0.0123:0:1 +6 99283133 . T C 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0955;SOR=Inf;LSEQ=GGCGCCCTGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:187,142:329,0:0:2,0:27.6:1:30.1:1:1:0:58.6:24.308:1:0:0.2 0/1:278:3:2,1:148,127:275,3:0.0108:2,2:24.3:1:24.7:1:1:1.71:56.7:2:0.0074:0:1.3 +6 99283172 . ACAG A 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.69553;SOR=1.22857;LSEQ=CAGCAGCAGCAACAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:13:8,5:182,196:378,13:0.0331:2,2:26.3:1:32.5:1:0.4052:1.72:57.7:26:0.0333:0.0076:0.2 0/1:347:14:6,8:159,174:333,14:0.0403:2,2:31.1:1:31.9:1:0.78987:1.2177:53:28:0.0407:0:0.2 +6 99283175 . G A 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.01104;SOR=Inf;LSEQ=CAGCAGCAACAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:176,192:368,0:0:2,0:23.9:1:32.8:1:1:0:58.9:91:1:0:0.2 0/1:342:6:3,3:155,167:322,6:0.0175:2,2:20:1:29.7:1:1:1.08:60:12:0.0189:0:1.2 +6 99283182 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.04975;SOR=Inf;LSEQ=AACAGCAGCAACAGCAGCAG;RSEQ=AGCAGCAGCAACAGCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:161,176:337,0:0:2,0:26.4:1:32.4:1:1:0:59:66.4:0.997:0:0.2 0/1:304:4:2,2:142,157:299,4:0.0132:2,2:32:1:29:1:1:1.11:42:8:0.0133:0:1.3 +6 99283198 . G A 34 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35546;SOR=3.25894;LSEQ=GCAGCAGCAGCAGCAACAGC;RSEQ=GCCGCCGCATCTGGTGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:1:1,0:129,154:283,1:0.0035:2,0:1:0:27:0:0.45775:0:48:2:0.0036:0:1 0/1:263:3:3,0:118,142:260,3:0.0114:2,0:14.7:1:22:1:0.09608:0:43.3:2:0.0078:0:2.3 +6 99283376 . T G 77 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGGCGGGCAGCCGGCCGG;RSEQ=CTGCACCACCACGGCCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:16.2:1:29.8:1:1:0:60:5:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:4:0:31:1:1:0:60:4:1:0:1.5 +6 99708653 . T A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGAACTGACCACATATA;RSEQ=TTCACAAATCAGACAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 99710546 . AACTTT A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACACTATTAACTTTTAGCA;RSEQ=ACTTTAGTTGAAAACCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:36.5:1:28.5:1:1:0:40.5:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 100302134 . T A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CTCTTTTCTTTTTCTTTCTT;RSEQ=TTTTCTCCCCTTCCTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:15.5:1:26.5:1:1:0:60:4:0.3333:0:2 0/0:6:0:0,0:5,1:6,0:0:2,0:22.2:1:31.8:1:1:0:60:12:1:0:0.2 +6 100302409 . A G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00036;SOR=0.602;LSEQ=ACATTTATGTTGTTTGAGGT;RSEQ=GAAAATAGACTTTCAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:472:329:148,181:68,73:141,329:0.697:2,2:25.6:1:31.8:1:0.54532:1.13889:60:163.5:0.6972:0:1.1 1/0:422:245:116,129:87,89:176,245:0.5806:2,2:25:1:30.5:1:0.69328:1.08686:60:80.667:0.5776:0:1.1 +6 100302494 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23863;SOR=Inf;LSEQ=TATTATCTCTTGGTAATTCA;RSEQ=CATTTTTTTTAAGAGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:60,129:189,0:0:2,0:24.1:1:32.3:1:1:0:60:30.5:1:0:0.3 0/1:181:2:1,1:56,123:179,2:0.011:2,2:25:1:27:1:0.53186:2.19:60:4:0.0113:0:1.5 +6 100302496 . A AT 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.06417;LSEQ=TTATCTCTTGGTAATTCAGC;RSEQ=TTTTTTTTAAGAGGCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:0,2:58,124:182,2:0.0109:2,0:18.5:1:32:0:1:0:60:4:0.0111:0:0 0/1:173:2:0,2:51,119:170,2:0.0116:2,0:10:1:28.9:1:1:0:60:4:0.0117:0.0058:0 +6 100302541 . T C 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=0;LSEQ=CTCTGTCACCCAGGCTGGAG;RSEQ=GCAGTGGTGCTCACTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:7,55:62,2:0.0313:2,2:29:1:25.5:1:0.23611:7.42:60:4:0.0317:0:1 0/0:55:0:0,0:4,51:55,0:0:2,0:22.5:1:29.3:1:1:0:60:54:1:0:0.1 +6 100303613 . A C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCATCAGTCTACTCCCTCTC;RSEQ=CACCCCGCTGCCTCCTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:45:0:30:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:30:1:1:0:60:4:1:0:1 +6 100314801 . CA C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.08772;SOR=Inf;LSEQ=AGTTCAGTAGATACTACCTA;RSEQ=AAAAAAAGTTTAGCATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:25.7:1:30.8:1:1:0:60:26:1:0:0.2 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:26:1:32.5:1:1:0:60:4:0.3333:0:0 +6 100314973 . A G 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTATATAATAAGAAATAGA;RSEQ=GTATAGGCATAAAATTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:246:245:158,87:0,0:0,245:0.9959:0,2:23.1:1:32.5:1:1:0:60:244:0.9959:0:1.2 1/1:183:183:121,62:0,0:0,183:1:0,2:24.8:1:30.8:1:1:0:60:44.75:1:0:1.4 +6 100315027 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.89712;LSEQ=GCTAAGATAGACTATAGCAC;RSEQ=TAACCTCAAGACAGGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:68:30,38:163,152:315,68:0.1775:2,2:28.1:1:31.4:1:0.2856:1.35724:60:67:0.1754:0:1.5 0/1:352:161:83,78:90,101:191,161:0.4574:2,2:25:1:30:1:0.45405:1.19:60:79.5:0.4556:0:1.5 +6 100315078 . G T 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10988;SOR=Inf;LSEQ=CCTTTAGTGATGTTGGTTTT;RSEQ=TATCACATGTTCAAGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:106,179:285,0:0:2,0:24.4:1:32:1:1:0:60:56:1:0:0.2 0/1:263:3:2,1:103,157:260,3:0.0114:2,2:22.3:1:24.7:1:0.56552:3.04:60:2:0.0077:0:2.3 +6 100498318 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50644;SOR=0;LSEQ=TCATCCACAAGCAATTCTTC;RSEQ=CATAATTGATGAACTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:78,30:108,2:0.0182:2,2:32:0:33:1:0.48607:2.57407:47.5:4:0.0182:0:1 0/0:84:0:0,0:57,27:84,0:0:2,0:24.7:1:29.4:1:1:0:54.8:83:1:0:0.1 +6 100498343 . C A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.20548;SOR=Inf;LSEQ=ATTGATGAACTTGGCTTCCA;RSEQ=TTTGAGAAGAGAACCACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:83,37:120,0:0:2,0:23.2:1:32.6:1:1:0:59.4:119:1:0:0 0/1:100:2:1,1:71,27:98,2:0.02:2,2:23:1:32:1:0.48364:2.60037:60:4:0.02:0:1 +6 100498364 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.23751;SOR=Inf;LSEQ=TTTGAGAAGAGAACCACCTT;RSEQ=TTCTATACTTGCATTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:98,54:152,0:0:2,0:21:1:31.1:1:1:0:59.8:151:1:0:0 0/1:145:2:1,1:103,40:143,2:0.0138:2,2:14:1:30:1:0.48697:2.55573:60:4:0.0138:0:1 +6 100498524 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24655;SOR=Inf;LSEQ=CAAAAGGCTTTGAGTCTTTT;RSEQ=CATTCTAGTTTGACTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:66,116:182,0:0:2,0:24.4:1:31.7:1:1:0:59.7:181:1:0:0.1 0/1:180:2:0,2:58,119:177,2:0.0111:2,0:24.5:1:25:1:1:0:60:4:0.0113:0:1 +6 100498557 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23434;SOR=Inf;LSEQ=ACTTTTGTGCATTTTTGGCT;RSEQ=GAGTATCTCCTATAGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:60,94:154,0:0:2,0:27.7:1:31.8:1:1:0:59.7:153:1:0:0.1 0/1:145:2:1,1:52,91:143,2:0.0138:2,2:28:1:31.5:1:1:1.74:56:4:0.0139:0:1 +6 100498638 . G T 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0286;SOR=0.11955;LSEQ=CACCATCATCATCATCTTCG;RSEQ=CATTATCATCATCATCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:11:4,7:29,57:86,11:0.1134:2,2:26.5:1:27.7:1:1:1.12:59.6:4.5:0.0947:0:1.5 0/1:67:1:0,1:31,35:66,1:0.0149:2,0:28:0:30:0:1:0:60:2:0.0152:0:1 +6 100498642 . TATC T 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=1e-05;SOR=4.63077;LSEQ=ATCATCATCATCTTCGGCAT;RSEQ=ATCATCATCTTATTCATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:25:9,16:26,49:75,25:0.25:2,2:28.7:1:31.2:1:1:1.06:58.4:50:0.2525:0.01:0.6 1/0:64:39:21,18:11,14:25,39:0.6094:2,2:30.4:1:30.6:1:0.60884:1.48:58.1:78:0.619:0.0156:0.8 +6 100498662 . T C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16745;SOR=Inf;LSEQ=TATCATCATCATCTTATTCA;RSEQ=CAGCAGCAAGTTTTACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:42,67:109,0:0:2,0:24.7:1:30.1:1:1:0:57.9:35.333:1:0:0.8 0/1:76:2:1,1:39,35:74,2:0.0263:2,2:11:1:26:1:1:1.1127:60:4:0.0263:0:2 +6 100498693 . G T 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTACTTTTCTCTGTGGAA;RSEQ=CTTGCTACCACCTCCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:110:110:45,65:0,0:0,110:1:0,2:25.8:1:30.4:1:1:0:51.6:35.667:1:0:1.1 1/1:85:85:45,40:0,0:0,85:1:0,2:22.9:1:29.3:1:1:0:52.4:41.5:1:0:1.3 +6 100498754 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22709;SOR=Inf;LSEQ=CTTAAGAGTTTCACATCCTC;RSEQ=TCCTCTTCATCTTCTGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:54,52:106,0:0:2,0:22.4:1:32.4:1:1:0:44.2:105:1:0:0.5 0/1:97:2:1,1:51,44:95,2:0.0206:2,2:11.5:1:25:0:1:1.15732:60:4:0.0211:0:1.5 +6 100498976 . C T 157 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTGCTTCAACAATGTGCAA;RSEQ=TTATCCTTCGCACCAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:33:17,16:93,73:166,33:0.1658:2,2:25.1:1:31.3:1:0.70296:1.19793:44.4:66:0.1667:0:1.3 0/0:226:0:0,0:114,112:226,0:0:2,0:27.7:1:31.6:1:1:0:56.2:452:1:0:0.1 +6 100499087 . GA G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0.83073;LSEQ=TTGGCCTTCAGTTCACAATT;RSEQ=AAAAGATAGTTCTGGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:38:15,23:1,2:3,38:0.9268:2,2:29.5:1:31.4:1:1:1.30:46.6:37:0.925:0.2195:0 1/1:46:42:16,26:2,2:4,42:0.913:2,2:27.3:1:30.7:1:0.63864:1.60729:45.8:84:0.9333:0.1739:0.1 +6 100977863 . AT A 61 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCATCATTAAATCGTG;RSEQ=TTTTTTTTTTTTCTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:11.3:1:30.5:1:1:0:60:8:0.4:0.1818:0.5 0/0:2:0:0,0:2,0:2,0:0:0,0:36:1:31.5:1:1:0:60:4:1:0:0.5 +6 100977940 . T C 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00192;SOR=0;LSEQ=TATTCTGGTATAATTTGGTA;RSEQ=TTAACATACATTAATTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:16,0:11,0:11,16:0.5714:0,1:29.4:1:30.4:1:1:0:60:7:0.5385:0:1.3 0/0:10:0:0,0:10,0:10,0:0:0,0:10:0:15:0:1:0:60:0:0:0:5 +6 100978351 . C T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19495;LSEQ=TGGAAAGGAAGAAGTTAGAA;RSEQ=AACTGTACAATAGAGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:376:224:109,115:70,82:152,224:0.5957:2,2:23.7:1:29.7:1:0.67408:1.11:52.1:55:0.593:0:1.1 0/1:238:53:28,25:92,93:185,53:0.2227:2,2:23.2:1:29.1:1:0.75613:1.13:51.9:106:0.2236:0:1.1 +6 100978570 . C T 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18713;LSEQ=GCATAGAAAAACTAAAGGCC;RSEQ=AGATACCCAAGATGTAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:766:372:193,179:198,195:393,372:0.4856:2,2:26.1:1:30.4:1:0.7176:1.06:48.6:123:0.4868:0:1.1 0/1:720:108:57,51:320,291:611,108:0.15:2,2:23.9:1:28.8:1:1:1.02:48.4:107:0.1505:0:1.1 +6 100978829 . C T 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=26.00472;LSEQ=AGTACAGTGATTGCAAATCA;RSEQ=GTGTCTAATTATGATGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:677:1:1,0:365,309:674,1:0.0015:2,0:28:0:14:0:1:0:26:0:0:0:8 0/1:512:19:12,7:269,224:493,19:0.0371:2,2:20.6:1:28.7:1:0.49214:1.43:50.8:38:0.0375:0:1.5 +6 100979222 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00833;SOR=Inf;LSEQ=CCATAAGTCCTAGAAGCTTT;RSEQ=TGGTGATTATTTTGAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:0,14:14,0:0:1,0:31.2:1:32.3:1:1:0:52.1:28:1:0:0.1 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:30:1:1:0:60:4:1:0:1 +6 100979445 . A AT 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTATTTTGGTTTGGGGGGA;RSEQ=TTTTTTTTTTTCCTGGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:23.5:1:29.5:1:1:0:36:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 101337371 . G A 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23913;SOR=0;LSEQ=CTGCTGGTGCTGTTGCCGCC;RSEQ=CTGCTCTCGCTGCAGTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:3:2,1:18,14:32,3:0.0857:2,2:22:1:28.7:1:1:1.54:60:6:0.0857:0:1 0/0:35:0:0,0:16,19:35,0:0:2,0:27.7:1:29.8:1:1:0:59.5:34:1:0:0.2 +6 104473752 . T C 47 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23361;SOR=Inf;LSEQ=GGAGTTTTCTTCAGTTTCCT;RSEQ=ATCATCAAAATTATTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:16,0:0:2,0:16.6:1:30.2:1:1:0:60:32:1:0:0.1 0/1:19:3:2,1:9,7:16,3:0.1579:2,2:6.3:1:30:1:1:1.52:60:6:0.1579:0:1 +6 104473941 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17612;SOR=Inf;LSEQ=AAAGTGCTGTCTACTAATAT;RSEQ=CACAAGGTCTGAACTACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:30,26:56,0:0:2,0:23.5:1:30.9:1:1:0:60:27:1:0:0.2 0/1:41:2:1,1:17,22:39,2:0.0488:2,2:33:1:27:1:1:1.29:60:4:0.0488:0:1 +6 104474026 . AT A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03476;SOR=Inf;LSEQ=AAACAGTTGGCTGTACAGAC;RSEQ=TTTTTTTTAACATTGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:2,17:19,0:0:2,0:21.3:1:29.6:1:1:0:60:18:1:0:0.5 0/1:16:4:2,2:4,8:12,4:0.25:2,2:21:1:29.1:1:0.6044:1.91:58.8:8:0.25:0.0625:0.3 +6 106051185 . A C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATTCCTAAGCATGGTAA;RSEQ=AATTTGGTGCCCCAAAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:13:1:32:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 106051358 . AG A 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACTTTGATAGCAGAACA;RSEQ=TATTCTTAGTAATTAGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:42.5:1:32:1:1:0:60:8:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 106051478 . G A 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10131;SOR=0;LSEQ=GCTGAAATATATCAGTAACA;RSEQ=TATTAAATAATGTGTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:6,1:6,0:6,7:0.5385:0,2:28.1:1:31.6:1:1:0:60:14:0.5385:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:22.2:1:33.2:1:1:0:60:10:1:0:0 +6 106051695 . A G 217 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTTCAGAAGACTTTTGATC;RSEQ=TAATTTTGGGGTTAATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:136:74,62:116,98:214,136:0.3886:2,2:25.1:1:30.7:1:1:1.01:60:135:0.3879:0:1.7 0/0:390:0:0,0:205,183:388,0:0:2,0:25.7:1:29.5:1:1:0:60:76.6:0.9948:0:0.4 +6 106051738 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.21162;LSEQ=TAAAATCAATATATGGTAGC;RSEQ=TTGAGTAAGAGACAAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:346:270:119,151:35,41:76,270:0.7803:2,2:25.9:1:32:1:0.7946:1.08296:60:53:0.7794:0:1.4 0/1:378:162:70,92:99,116:215,162:0.4286:2,2:23.4:1:30.9:1:0.60223:1.12133:60:39.5:0.427:0:1.1 +6 106534362 . C T 64 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.9832;LSEQ=CGCCGAGGTGCGCGTCTGTG;RSEQ=GGCTCAGCCTGGCGGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:4:0,4:269,70:339,4:0.0117:2,0:1:0:27:1:0.00203:0:60:8:0.0118:0:1 0/1:436:5:2,3:334,97:431,5:0.0115:2,2:16.4:1:27.6:1:0.08178:5.13966:60:10:0.0116:0:1 +6 106534484 . AT A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.14857;SOR=0.72537;LSEQ=GACCTTGGTAAGGAACTTGA;RSEQ=TTTTTTTTTTTAATTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:45:14,31:202,332:534,45:0.0769:2,2:28.6:1:30.8:1:0.42451:1.34658:59.9:90:0.078:0.0103:0.4 0/1:737:42:18,24:267,423:690,42:0.057:2,2:28.4:1:29.8:1:0.62651:1.19:60:41:0.0569:0.0054:0.1 +6 106534554 . AT A 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=2.00911;LSEQ=CTTTATTGTTATTATTATTA;RSEQ=TTTTTTTGGCTAATGTCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:1:0,1:1,145:146,1:0.0068:1,0:25:0:27:0:1:0:60:2:0.0068:0:0 0/1:148:2:0,2:1,145:146,2:0.0135:1,0:26.5:1:32:0:1:0:60:4:0.0135:0:0 +6 106535812 . CT C 53 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATTGTTCAGAGGTGATT;RSEQ=TTTTTTTTTTTTCCTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:22:1:34:0:1:0:50.7:6:0.3333:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:11:0:32:0:1:0:60:2:1:0:0 +6 106535936 . C T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96539;LSEQ=CAGTTTACTTTATACGGCTT;RSEQ=TTGGCTCTTTCTCAACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:38:36,2:5,0:5,38:0.8837:0,2:24.4:1:31.6:1:1:0:59.2:76:0.9048:0:1.2 1/1:25:22:22,0:3,0:3,22:0.88:0,1:21.6:1:29.3:1:1:0:60:21:0.875:0:1.3 +6 106536046 . G T 56 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06177;SOR=Inf;LSEQ=ACAGGAACGGCGGGACAATG;RSEQ=GGATTAAAGGCCTTTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:0:0,0:289,119:408,0:0:2,0:24.4:1:31.2:1:1:0:59.9:50:1:0:0.2 0/1:414:5:1,4:278,131:409,5:0.0121:2,2:18.4:1:24.4:1:0.04083:8.44338:60:4:0.0099:0:1.2 +6 106536253 . G A 175 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=63.46204;LSEQ=GGGATTCTGGTGCTGATGGC;RSEQ=GTACTTCGGTTCAGGCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:768:1:0,1:314,453:767,1:0.0013:2,0:42:0:32:0:1:0:60:2:0.0013:0:1 0/1:797:61:24,37:322,413:735,61:0.0765:2,2:23.1:1:29.6:1:0.59117:1.2017:60:122:0.0771:0:1.1 +6 106543405 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49905;SOR=Inf;LSEQ=CATTGTTAGTTGTATTACTA;RSEQ=TTGACAGTCCAATTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:87,1:88,0:0:1,0:24.9:1:33:1:1:0:59.9:176:1:0:0 0/1:99:2:1,1:88,9:97,2:0.0202:2,2:18:1:30:1:0.19274:9.32857:60:4:0.0208:0:1 +6 106543620 . G A 182 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01293;LSEQ=TTTTTGGAGGGTAAGTAAGG;RSEQ=AAATTTCTTCAGACCCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:61:19,42:88,183:271,61:0.1837:2,2:26.2:1:30.8:1:0.88068:1.0628:60:60:0.1835:0:1.2 0/0:346:1:1,0:134,211:345,1:0.0029:2,0:1:0:22:0:0.39017:0:60:2:0.0029:0:2 +6 106543695 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23715;SOR=Inf;LSEQ=TGGCTCACCTTTCTCATCCT;RSEQ=TGCTGAGAAATGCTGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:2,67:69,0:0:1,0:25.2:1:32.6:1:1:0:59.4:138:1:0:0.1 0/1:66:2:1,1:2,62:64,2:0.0303:1,2:12.5:1:27:1:0.08951:25.52:60:4:0.0308:0:1 +6 106546865 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50647;SOR=Inf;LSEQ=AGTAGCAAAAGTAGTACTCT;RSEQ=TGGTGGGTTAATCGGTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:98,32:130,0:0:2,0:25.3:1:32.2:1:1:0:60:129:1:0:0.1 0/1:168:2:1,1:123,43:166,2:0.0119:2,2:25:0:30:1:0.45637:2.83924:60:4:0.012:0:1 +6 106546886 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19473;SOR=0;LSEQ=TGGTGGGTTAATCGGTTTGA;RSEQ=GCAGCTCCTTAAATGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:124,53:177,2:0.0112:2,2:20:1:31:1:0.51353:2.32721:60:4:0.0113:0:1 0/0:226:0:0,0:157,69:226,0:0:2,0:25.1:1:31.4:1:1:0:60:225:1:0:0.1 +6 106547372 . C G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00379;SOR=0.542;LSEQ=CTTGTGTGGTATTGTCGGGA;RSEQ=TTTGCAGAAAGGCTTCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:62:26,36:248,365:613,62:0.0919:2,2:26.4:1:33:1:0.8922:1.06:60:124:0.0935:0:1.2 0/1:770:40:16,24:327,402:729,40:0.0519:2,2:29.2:1:31.5:1:0.62535:1.21984:60:80:0.0524:0:1.1 +6 106547453 . T A 68 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.06665;SOR=Inf;LSEQ=TGGATTACAGAACAAAAAAA;RSEQ=AAAAAATGCCAGTAATGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:46,195:241,0:0:2,0:24:1:28.6:1:1:0:60:39.167:1:0:0.1 0/1:290:5:3,2:59,226:285,5:0.0172:2,2:5.8:1:29.4:1:0.06737:5.70:60:10:0.0175:0:1 +6 106547470 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23211;SOR=0;LSEQ=AAATAAAAAATGCCAGTAAT;RSEQ=TCGGTTCTGCCCCTTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:27,149:176,2:0.0112:2,2:19.5:1:30.5:1:0.29061:5.44:60:4:0.0114:0:1 0/0:192:0:0,0:29,163:192,0:0:2,0:23.4:1:31.5:1:1:0:60:384:1:0:0.1 +6 106553096 . G A 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=CAAGAGCTCCAGCCCTCACA;RSEQ=CAGCCCTGGGAATACGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:92:40,52:381,474:855,92:0.097:2,2:27.8:1:29.6:1:0.9122:1.0449:60:29.667:0.0957:0:1.2 0/0:919:0:0,0:421,498:919,0:0:2,0:24.4:1:31:1:1:0:60:60.267:1:0:0.2 +6 106553383 . C T 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00125;SOR=Inf;LSEQ=TGTGCCCTGTCTACAGCAAT;RSEQ=TCCTCGGTGGGGGCAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:165,256:421,0:0:2,0:24.5:1:32.2:1:1:0:59.9:29.071:1:0:0.1 0/1:386:9:3,6:162,215:377,9:0.0233:2,2:23:1:30.1:1:0.73812:1.50544:60:18:0.0237:0:1.1 +6 106553385 . C A 42 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05458;SOR=Inf;LSEQ=TGCCCTGTCTACAGCAATCT;RSEQ=CTCGGTGGGGGCAGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:161,250:411,0:0:2,0:24.7:1:31.3:1:1:0:59.9:50.375:1:0:0.1 0/1:386:4:3,1:164,218:382,4:0.0104:2,2:8.8:1:21:1:0.32004:3.97:60:3:0.0079:0:1 +6 106553911 . GC G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.53009;SOR=0;LSEQ=TTGCATTTGCAGTAGTATGA;RSEQ=CCCCGGTTGGGGATAGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:2:0,2:5,111:116,2:0.0169:1,0:38:1:33.5:1:1:0:60:4:0.0175:0:0 0/0:70:0:0,0:1,69:70,0:0:1,0:22.6:1:30.6:1:1:0:60:34:1:0:0 +6 106554163 . A G 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=GCTTTTCTTAAGATATTTGC;RSEQ=TCAACACTTGAGTCTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:186,11:197,0:0:2,0:23.8:1:30.4:1:1:0:60:31.833:1:0:0.1 0/1:140:8:8,0:129,3:132,8:0.0571:1,0:24:1:28.3:1:1:0:60:16:0.0576:0:1 +6 106554191 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07987;SOR=Inf;LSEQ=TTGAGTCTTGGAGCAGAAAT;RSEQ=TTAGGTCTCAGAGCCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:266,46:312,0:0:2,0:24:1:32.6:1:1:0:60:311:1:0:0.1 0/1:237:3:1,2:202,32:234,3:0.0127:2,2:16:1:29:1:0.05472:12.39144:60:6:0.0128:0:1.7 +6 106554732 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5187;SOR=0;LSEQ=CCTCCCGTTGGCAACTCTTA;RSEQ=TCTTCTGGCCTTCCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:135,11:146,2:0.0135:2,2:21.5:1:31.5:1:0.15609:11.79388:60:4:0.0139:0:1 0/0:98:0:0,0:91,7:98,0:0:2,0:24.5:1:29.8:1:1:0:60:97:1:0:0.2 +6 106554760 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17119;SOR=Inf;LSEQ=GCCTTCCTGTCTCCCTTCCC;RSEQ=GCTGTCTCTCTCCCCTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:190,52:242,0:0:2,0:25.9:1:31.4:1:1:0:60:47.4:1:0:0.1 0/1:172:2:1,1:132,38:170,2:0.0116:2,2:28:1:29.5:1:0.4031:3.44171:60:4:0.0118:0:1 +6 106554762 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18598;SOR=Inf;LSEQ=CTTCCTGTCTCCCTTCCCTG;RSEQ=TGTCTCTCTCCCCTACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:189,52:241,0:0:2,0:26.8:1:32.2:1:1:0:60:59.25:1:0:0.1 0/1:184:2:1,1:135,47:182,2:0.0109:2,2:34:1:28:1:0.45474:2.85277:60:4:0.011:0:1 +6 106554806 . C T 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.43992;SOR=2.11909;LSEQ=GTCTGCCACAAGAGATTTAG;RSEQ=AGCACCAGCAATCTCAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:2:0,2:268,135:403,2:0.0049:2,0:1:0:23.5:1:0.11387:0:60:4:0.0051:0:1 0/1:384:4:1,3:234,146:380,4:0.0104:2,2:15.5:1:24.3:1:0.30334:4.78886:60:8:0.0104:0:1.3 +6 106555025 . G A 209 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=157.28537;LSEQ=GGGAACTGCGCTGCGGCCCC;RSEQ=GCGCCTGGGCTGCCCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:1:1,0:251,251:502,1:0.002:2,0:1:0:25:0:1:0:60:2:0.002:0:1 0/1:569:136:65,71:215,218:433,136:0.239:2,2:22.7:1:29.6:1:0.76815:1.07712:60:272:0.242:0:1.1 +6 107090222 . C T 33 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0.77722;LSEQ=ATTACAGGCGTGAGCCACCC;RSEQ=GCCCCGCCGACTCTTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:21.5:1:33.5:1:1:0:60:4:0.4:0:2 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:23:0:32:0:1:0:60:2:0.3333:0:2 +6 107090228 . G A 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.43328;LSEQ=GGCGTGAGCCACCCCGCCCC;RSEQ=CCGACTCTTGTTTCTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:21.5:1:32.5:1:1:0:60:4:0.4:0:2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:16.5:1:30:1:1:0:60:4:0.5:0:1.5 +6 107090369 . A G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10736;SOR=0.50118;LSEQ=GGGAAAGAGGAGAGGCACCC;RSEQ=ATATGTGTTTTCTAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:26:22,4:16,2:18,26:0.5909:2,2:21.7:1:30.1:1:1:1.44256:49.8:25:0.5814:0:2.1 0/1:55:23:18,5:24,8:32,23:0.4182:2,2:20.6:1:30.1:1:1:1.20:49.1:46:0.4259:0:2 +6 107090393 . C G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.27837;SOR=0.6601;LSEQ=TGTGTTTTCTAGGCCTTTTA;RSEQ=AAAACAGGGAGTTGTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:29:24,5:28,3:31,29:0.4833:2,2:29.7:1:33.1:1:0.46527:1.92307:51.4:58:0.4915:0:2 0/1:63:24:20,4:31,8:39,24:0.381:2,2:30.7:1:31.8:1:1:1.29:50.8:48:0.381:0:2 +6 107090441 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49813;SOR=0;LSEQ=TGTGAACCTATAAGAAAGGT;RSEQ=ATGTGGACATCAAGGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:94,37:131,2:0.015:2,2:18.5:1:29:1:0.49134:2.5202:54:4:0.0152:0:2 0/0:131:0:0,0:90,41:131,0:0:2,0:20.6:1:30.8:1:1:0:57.7:130:1:0:0.3 +6 107090462 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24804;SOR=0;LSEQ=ATGTGGACATCAAGGGAATG;RSEQ=GTATTGTTCAAAAAGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:117,72:189,2:0.0105:2,2:20.5:1:29.5:1:1:1.62065:49:4:0.0106:0:1.5 0/0:192:0:0,0:110,82:192,0:0:2,0:21.7:1:29.8:1:1:0:56.2:63:1:0:0.2 +6 107090513 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24919;SOR=Inf;LSEQ=GTTACCATGGCAAAACTGGA;RSEQ=AGTACACAGTGTTCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:131,138:269,0:0:2,0:28.8:1:32.6:1:1:0:53.9:88.667:1:0:0.2 0/1:284:3:2,1:132,149:281,3:0.0106:2,2:29.3:1:28:1:0.60359:2.25:25:6:0.0107:0:1 +6 107090588 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24551;SOR=Inf;LSEQ=AGATTCTTGCCAAGAGAATG;RSEQ=ATGTGCATATTGAGCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:3,81:84,0:0:1,0:26.3:1:31.1:1:1:0:56.3:41:1:0:0.2 0/1:83:2:1,1:7,74:81,2:0.0241:2,2:30:1:30:1:0.18454:9.96:57:4:0.0247:0:1 +6 107090614 . C A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05548;SOR=0.36311;LSEQ=CATATTGAGCACAGTAAGTA;RSEQ=TGTAAGAGCCGAGATAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:15:1,14:1,44:45,15:0.25:1,1:24.9:1:32:1:0.44068:3.07:56.4:30:0.2542:0:1.1 0/1:56:6:0,6:5,45:50,6:0.1071:2,0:17.2:1:30.7:1:1:0:55.7:12:0.1071:0:1 +6 108424797 . AG A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATAATAAAAAGAAAAAA;RSEQ=AAACAAGTTCACTTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:28.5:1:1:0:60:4:1:0:0 +6 108425786 . A G 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CCAAAGTGCTGGGATTACAG;RSEQ=CATGAGCCACTGCGCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:39.5:1:33:0:1:0:38:4:1:0:1 0/0:3:0:0,0:2,1:3,0:0:2,0:15.3:1:30.3:1:1:0:47.7:6:1:0:0.3 +6 108425807 . CTTA C 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=CATGAGCCACTGCGCCCGGC;RSEQ=TTATTATTATTTTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:19.2:1:33.8:1:1:0:51.2:10:1:0:0.8 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:22:0:29.5:1:1:1.67325:60:4:0.1538:0:0 +6 108425822 . T G 51 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.29551;SOR=0.25881;LSEQ=CCGGCCTTATTATTATTATT;RSEQ=TTTTTGAGATAGGGTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:6,1:7,3:0.3:2,0:14.3:1:32.7:1:1:0:60:6:0.3:0:1 0/1:21:2:1,1:13,6:19,2:0.0952:2,2:4.5:1:30.5:1:1:2.08171:60:4:0.0952:0:1 +6 108425901 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.52344;SOR=Inf;LSEQ=AGTAGGAGCTCTGGAAAGAG;RSEQ=AAATAGGAGGTAAGAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:12,14:26,0:0:2,0:23.3:1:30.9:1:1:0:60:25:1:0:0.2 0/1:43:2:1,1:18,23:41,2:0.0465:2,2:5.5:1:27:1:1:1.27:60:4:0.0465:0:1 +6 108883054 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25115;SOR=0;LSEQ=TGCGTACCCACCCCGGGCTG;RSEQ=CAGCAGGACCCGCCGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:73,180:253,3:0.0117:2,2:12.7:1:29.7:1:1:1.23:60:6:0.0121:0:1 0/0:227:0:0,0:76,150:226,0:0:2,0:23.9:1:30.2:1:1:0:59.9:44.2:0.9955:0:0.2 +6 108883133 . A T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02218;SOR=Inf;LSEQ=GCGCTTGCGGGCTCCAGGGC;RSEQ=AGGGGTTGGCAGGGGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:0,66:66,0:0:1,0:22.3:1:31.6:1:1:0:60:132:1:0:0.1 0/1:43:4:0,4:0,39:39,4:0.093:1,0:24.3:1:25.5:1:1:0:60:3:0.0769:0:1.3 +6 110255274 . T C 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCCCCATGTGTTGTTCTGCA;RSEQ=TGACCTGTGACCCTGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:28:1:32.5:1:1:0:60:4:0.4:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:26.5:1:27:1:1:0:60:4:1:0:1 +6 110699712 . C T 27 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CCTTGGGCCCCCTCACTCAC;RSEQ=GCCTCCCTCCTCCAGCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:30:0:32.5:1:1:0:60:4:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:9:0:27.5:1:1:1:60:4:0.5:0:1 +6 110699863 . T C 100 pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01099;SOR=0;LSEQ=AGCATCCTAACCGTGGAACA;RSEQ=GCAGATTTTTGAGGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:0,9:1:0,2:26.6:1:31.8:1:1:0:60:18:1:0:1.1 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:38:0:32:0:1:1:60:4:0.3333:0:1 +6 110700046 . A G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCTCCTGGGCAGGGGAAT;RSEQ=GCGGCACCCATCTCTATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:24:1:32.5:1:1:0:54.4:16:1:0:1.3 1/1:5:5:2,3:0,0:0,5:1:0,2:22.8:1:30.6:1:1:0:60:10:1:0:1 +6 110700201 . T G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22711;SOR=Inf;LSEQ=CAGGTCTAACCCATCTTTCC;RSEQ=AATTGGGCGGGGCTACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:14,14:28,0:0:2,0:24.4:1:28.5:1:1:0:59.3:13:1:0:0.5 0/1:26:2:1,1:12,12:24,2:0.0769:2,2:29:1:28:1:1:1:60:4:0.0769:0:1 +6 110700229 . T C 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.01522;LSEQ=CGGGGCTACCCTGCAGGATC;RSEQ=CCAATAATGCCAGCCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:7,9:0,0:0,16:0.9412:0,2:24.6:1:29.4:1:1:0:60:15:0.9375:0:1.1 0/1:13:2:0,2:5,6:11,2:0.1538:2,0:22:1:28.5:1:0.48718:0:60:4:0.1538:0:1 +6 110700656 . A G 80 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00466;SOR=0;LSEQ=ATGAATAGGGCCTGAAGTGA;RSEQ=CCCCCAGCAACCTGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1:0,2:27.8:1:31.3:1:1:0:45.5:12:1:0:1.2 0/1:7:1:1,0:4,2:6,1:0.1429:2,0:47:0:34:0:1:0:36:2:0.1429:0:1 +6 110700703 . G GA 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.52923;SOR=Inf;LSEQ=AGAAGAGGGGCCTGACTATT;RSEQ=AAAAAAAAACAAGCCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,4:8,0:0:2,0:19.8:1:31.3:1:1:0:55.9:16:1:0:0.6 0/1:17:2:1,1:11,4:15,2:0.1176:2,2:19.5:1:27.5:1:0.51471:2.56905:60:4:0.1176:0:0 +6 110700892 . T C 30 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TCTCCTCCAAATGATTGCAA;RSEQ=GTCTCTCCATCAGGGGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:30:0:30:1:1:0:30:4:0.6667:0:1.5 0/0:5:0:0,0:2,3:5,0:0:2,0:27:1:30.2:1:1:0:46:10:1:0:0 +6 110701451 . A G 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAACACCATTAAGATGCTCT;RSEQ=TGAGAAGATCAATCCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:30.5:1:1:0:42.5:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:43:0:30:0:1:0:60:2:1:0:0 +6 111995666 . A G 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGTGTCAAAAAAGCCTCC;RSEQ=ATCTCAGGCCCATGTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:792:0:0,0:581,211:792,0:0:2,0:23.9:1:30.5:1:1:0:60:131:1:0:0.1 0/1:782:32:23,9:508,241:749,32:0.0409:2,2:24.1:1:28:1:0.70267:1.21:60:15:0.039:0:1.1 +6 111996251 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACTGAGCTGCTCCCAGG;RSEQ=TGGGGACAACTGGATACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:0,3:0,2:2,3:0.6:0,0:35:1:32:0:1:0:60:6:0.6:0:1.7 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:33:0:1:0:60:2:1:0:1 +6 112015373 . T C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00013;SOR=0.10592;LSEQ=ACCCACCCACCAAAAACCAA;RSEQ=ATCTCATCCCTCCACTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:46:45,1:7,0:7,46:0.8679:0,1:23.7:1:32.8:1:1:0:59.3:45:0.8654:0:1.1 0/1:20:8:7,1:11,1:12,8:0.4:2,2:12:1:31.6:1:1:1.53525:60:16:0.4:0:1.1 +6 112017435 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.63013;SOR=0.94203;LSEQ=ATTTCTCTCCCCTAAACAAC;RSEQ=CCTTAAGGCACTGTGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:241:170,71:303,127:430,241:0.3592:2,2:23.3:1:30.9:1:1:1.00:60:39.167:0.3577:0:1.1 0/1:547:189:132,57:251,107:358,189:0.3455:2,2:23.1:1:28.8:1:1:1.01294:60:16.182:0.334:0:1.2 +6 112021529 . A G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00037;SOR=Inf;LSEQ=AGCAGAACACATGTAATGAC;RSEQ=ACACTCATAAGTGTAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:370:0:0,0:48,322:370,0:0:2,0:23.6:1:30.7:1:1:0:59.9:40.111:1:0:0.2 0/1:312:10:2,8:41,261:302,10:0.0321:2,2:15.9:1:28.4:1:0.63336:1.59:60:9:0.029:0:1.1 +6 112024350 . TAC T 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.5613;SOR=3.20148;LSEQ=CAAGGATGCACACACACATG;RSEQ=ACACACACAGCATCTCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:0,1:2,154:156,1:0.0064:1,0:25:0:32:0:1:0:60:2:0.0064:0:0 0/1:99:2:0,2:2,94:96,2:0.0202:1,0:10:1:31:1:1:0:60:4:0.0204:0.0101:0.5 +6 112025063 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51665;SOR=0;LSEQ=TAGAGCCTGGAGGGAAGACT;RSEQ=AAAACAGGACTCCACTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:2,0:137,3:140,2:0.0141:1,0:40:1:32.5:1:1:0:60:4:0.0143:0:1 0/0:96:0:0,0:94,2:96,0:0:1,0:20.9:1:32.3:1:1:0:60:192:1:0:0.1 +6 112025352 . C A 55 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09976;SOR=5.92943;LSEQ=TATTTTGAAATAGTCATTTA;RSEQ=AAAATGCAACAGCATAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:1:1,0:77,416:493,1:0.002:2,0:1:0:26:0:0.15789:0:60:2:0.0021:0:1 0/1:420:5:3,2:79,336:415,5:0.0119:2,2:9:1:24:1:0.05325:6.34:60:4:0.0096:0:1.6 +6 112025371 . CT C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.37842;SOR=1.88003;LSEQ=ACAAAATGCAACAGCATAGG;RSEQ=TTTTTTTTGCCCATGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:5:0,5:13,311:324,5:0.0152:1,0:25:1:31.8:1:1:0:60:10:0.0156:0.003:0 0/1:248:7:0,7:14,227:241,7:0.0282:2,0:20.4:1:32.3:1:1:0:60:14:0.0288:0.0081:0.3 +6 112029020 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08797;SOR=Inf;LSEQ=CTGAAAAACTCAGCCTTAAT;RSEQ=ACTGCTGTGAATTTCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:204,2:206,0:0:1,0:26.1:1:32:1:1:0:59.7:67.667:1:0:0.1 0/1:166:3:3,0:157,6:163,3:0.0181:1,0:29.7:1:29.7:1:1:0:60:6:0.0183:0:3 +6 112029331 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=3.03088;LSEQ=ACCTAATCATCCTGCCACCC;RSEQ=ATTTCTCCAACCTATTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:34:0,34:3,135:138,34:0.1977:1,1:30.6:1:31.6:1:1:0:59.3:68:0.2:0:1.1 0/1:105:45:1,44:1,59:60,45:0.4286:1,1:29.9:1:30.9:1:1:1.34:60:90:0.4286:0:1.2 +6 112029402 . C T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01216;SOR=4.03628;LSEQ=AAGGTCAGAAGGTTCCAGTT;RSEQ=GAGTCAGCCATGAGATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:8:0,8:1,41:42,8:0.16:1,0:21:1:30.6:1:1:0:60:16:0.1633:0:1.5 0/1:25:11:1,10:0,14:14,11:0.44:1,2:14:1:30.7:1:0.44:0:60:22:0.4583:0:1.7 +6 112029505 . G C 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=CTCTTGGTAGGGGGCATTTT;RSEQ=CTTGGTTAGTGTCCTTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:24:1:30.4:1:1:0:60:10:0.8333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:41:0:34:0:1:0:60:2:1:0:0 +6 112035002 . A G 66 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTCATTCAAGAGTGGGT;RSEQ=AAATCACTTCTTCTAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:25.8:1:33:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 112041359 . T C 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.54042;LSEQ=GAGTAATTGACAAGGCTCAC;RSEQ=GTTGGCTATTTCAGGCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:48:0,48:5,227:232,48:0.1714:1,1:21.1:1:28.9:1:0.59198:0:60:11:0.1618:0:1.1 1/0:185:99:1,98:2,84:86,99:0.5351:1,1:24.4:1:29.2:1:0.59817:2.32295:60:98:0.5385:0:1 +6 112042878 . C G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGCCTCCCAAAGTACTGG;RSEQ=ATTACAGGCGTGAACCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:32:0:1:0:23.5:4:1:0:1 +6 112111363 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24556;SOR=Inf;LSEQ=AAGATATCCAGCTAGCACAC;RSEQ=ACATACCTGGAGAATCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:32,53:85,0:0:2,0:27.4:1:31.2:1:1:0:60:20.25:1:0:0.1 0/1:84:2:1,1:31,51:82,2:0.0238:2,2:26:1:31.5:1:1:1.63:60:4:0.0241:0:1 +6 112111450 . TACAC T 32 v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=47;MSI=25.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGTAGTTCTGAACCTTAGA;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,3:3,2:0.2222:0,0:31:1:32:0:1:0:57.5:4:0.2222:0:0 0/0:2:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:0.5:0:0 +6 115553830 . C T 114 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00062;SOR=0.05376;LSEQ=AAGGGAGAGGCAATGTTGCC;RSEQ=AACTCCAGAGGTTGGTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:7,7:10,8:18,14:0.4375:2,2:30.9:1:30.1:1:1:1.24128:29.7:28:0.4375:0:1.1 0/1:26:1:1,0:14,11:25,1:0.0385:2,0:43:0:30:0:1:0:44:2:0.04:0:1 +6 116233469 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21438;SOR=Inf;LSEQ=AAAATTATTAAGAAGAAACA;RSEQ=CAAGGGTAAGGGGGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:51,47:98,0:0:2,0:26.8:1:31.1:1:1:0:59.2:31.667:1:0:0.2 0/1:85:2:1,1:40,43:83,2:0.0235:2,2:9:1:31:1:1:1.07:60:4:0.0241:0:1 +6 116417095 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49857;SOR=Inf;LSEQ=AAAGGCTTCTGATATCAGAC;RSEQ=ATGCCTTTCAAACTCTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:81,48:129,0:0:2,0:23.9:1:30.5:1:1:0:52:42:1:0:0.2 0/1:137:2:1,1:77,57:134,2:0.0146:2,2:37.5:1:31:1:1:1.34783:50.5:4:0.0152:0:1 +6 116417316 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=ACAACTTCTACCGAGGACCC;RSEQ=TGGACAAACCCACTGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:0,5:5,2:0.2857:0,2:44:1:31:1:0.28571:0:56:4:0.2857:0:1 0/0:4:0:0,0:1,3:4,0:0:2,0:23.5:1:29.3:1:1:0:60:8:1:0:0 +6 116470561 . A G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07917;SOR=1.28517;LSEQ=TAGACAGTGTGTCTTTACCA;RSEQ=ACTGGCTCTGCATTTTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:152:75,77:139,144:283,152:0.3494:2,2:26.5:1:32.1:1:1:1.01:60:37:0.3507:0:1.1 0/1:426:174:84,90:126,125:251,174:0.4085:2,2:25.8:1:30.6:1:0.76731:1.0798:60:57:0.4091:0:1.1 +6 117609387 . T C 95 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAGGGAGAAGGGAGAGCAG;RSEQ=GTTTCCCTTCCAGACTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:1,0:1,7:0.875:0,0:40.3:1:33.9:1:1:0:57.3:14:0.875:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:42:0:34:0:1:0:60:2:1:0:1 +6 117609529 . A G 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0.17702;LSEQ=CAGAACCAAGATTAGAAATC;RSEQ=GGAACGTTGCATTGTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:48:48,0:20,0:20,48:0.7059:1,1:22.3:1:30.4:1:1:0:60:96:0.7059:0:1 0/1:34:10:10,0:24,0:24,10:0.2941:1,0:19.6:1:30.8:1:1:0:60:20:0.303:0:1 +6 117609569 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.50831;SOR=0;LSEQ=TTGGAGTTATAGACCACCAT;RSEQ=ACATTTATCATTCTAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:2:1,1:134,12:146,2:0.0135:2,2:23:1:28.5:1:0.16851:10.76875:60:4:0.0137:0:1.5 0/0:111:0:0,0:101,10:111,0:0:2,0:21.2:1:31.8:1:1:0:60:222:1:0:0.2 +6 117622028 . A G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08168;SOR=1.88152;LSEQ=ATGATGACAAAGGTGCCAGT;RSEQ=TATTATTCTTTTTGCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:22:22,0:115,2:117,22:0.1583:1,1:16.2:1:33.1:1:1:0:60:44:0.1594:0:1.1 0/1:84:22:22,0:59,3:62,22:0.2619:1,1:21.6:1:31.9:1:0.56339:0:60:44:0.2651:0:1.1 +6 117622184 . G C 209 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=136.98844;LSEQ=TGTTGTTTGCTTCATCTCTG;RSEQ=ACTTATAAATGCTATTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:876:1:1,0:483,391:874,1:0.0011:2,0:23:0:14:0:1:0:60:0:0:0:5 0/1:745:101:58,43:361,283:644,101:0.1356:2,2:26.2:1:31.5:1:0.82977:1.06:60:202:0.1369:0:2.6 +6 117622188 . T G 209 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GTTTGCTTCATCTCTGGACT;RSEQ=ATAAATGCTATTTAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:872:0:0,0:470,399:869,0:0:2,0:23.9:1:29.7:1:1:0:60:85.9:0.9965:0:0.1 0/1:751:106:61,45:356,286:642,106:0.1411:2,2:25.1:1:31.2:1:0.75175:1.09:60:212:0.1423:0:2.6 +6 117622233 . C T 213 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=240.67423;LSEQ=TCTGAATAACTGAAGTTGGT;RSEQ=CTGAATTCTATGAAAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1111:1:0,1:560,549:1109,1:9e-04:2,0:1:0:26:0:0.4955:0:60:2:9e-04:0:1 0/1:1006:179:90,89:424,402:826,179:0.1779:2,2:24.3:1:28.5:1:0.80517:1.04298:60:34.8:0.1765:0:1.8 +6 117622521 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.03623;SOR=Inf;LSEQ=CTTTTGAAAAGCTGACATTA;RSEQ=TTTAACAGTTATTATTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:1,18:19,0:0:1,0:21.7:1:29.3:1:1:0:60:18:1:0:0.3 0/1:5:2:0,2:0,3:3,2:0.4:0,0:21.5:1:27.5:1:1:0:60:4:0.4:0:1 +6 117629650 . A T 84 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTGTATACTCTCTCTCTC;RSEQ=CACACACACACATACACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:28.7:1:32.8:1:1:0:60:12:0.75:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 117629661 . CAT C 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCACACACACACA;RSEQ=ACACTCGGAGTGCTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:6,0:6,4:0.3636:0,0:25.3:1:32.8:1:1:0:60:8:0.4:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 117629663 . T C 87 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTCACACACACACACA;RSEQ=ACACTCGGAGTGCTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:0,0:0,6:0.5455:0,0:19.7:1:33.8:1:1:0:60:12:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 117630188 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10597;SOR=Inf;LSEQ=TTTCCTGGGGCTAGCAGGGT;RSEQ=TACTTTGTCAGTGTATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:3,170:173,0:0:1,0:25.8:1:33.4:1:1:0:60:33.6:1:0:0.1 0/1:84:2:1,1:3,79:82,2:0.0238:1,2:26.5:1:29.5:1:0.09352:22.95:60:4:0.0241:0:1.5 +6 117631157 . TA T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.19836;SOR=Inf;LSEQ=GGTCTTCTGTTTTCTCACAT;RSEQ=AAAAAGCAAGATTAGATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:205,25:230,0:0:2,0:21.9:1:28.8:1:1:0:59.9:75.667:0.9956:0:0.1 0/1:186:2:1,1:157,27:184,2:0.0108:2,2:15:1:27:1:0.2791:5.72824:60:4:0.0108:0.0054:0.5 +6 117631431 . T G 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30277;LSEQ=CACGGAAACAAGGCAATTTC;RSEQ=AGCTGCCAGATCCCTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:767:239:100,139:209,318:527,239:0.3116:2,2:24:1:31:1:0.57869:1.09:60:238:0.3152:0:1.1 0/1:631:76:36,40:233,321:554,76:0.1204:2,2:23.4:1:29.3:1:0.38924:1.24:60:152:0.1222:0:1.2 +6 117631463 . TTAA T 171 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0;SOR=42.34187;LSEQ=CCCTGTGGCAGAAGTTATAT;RSEQ=TAATAATAATAATAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:2:1,1:108,336:444,2:0.0045:2,2:39:1:31:0:0.42948:3.10:60:4:0.0045:0:0 0/1:350:56:14,42:91,202:293,56:0.16:2,2:31.6:1:29.6:1:0.42811:1.35036:60:112:0.1609:0.0171:0.2 +6 117631479 . T C 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.01225;SOR=0;LSEQ=ATATTTAATAATAATAATAA;RSEQ=AACAACAATAAAGTTCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:9:1,8:64,286:350,9:0.025:2,2:17.1:1:32.9:1:1:1.78778:60:18:0.0265:0:1.3 0/0:270:0:0,0:60,202:262,0:0:2,0:28.6:1:27.1:1:1:0:59.8:22.818:0.9921:0:0.2 +6 117631500 . A T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17265;SOR=Inf;LSEQ=AACAACAATAAAGTTCCAGA;RSEQ=ATCAAAGAAGTAGCCCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:20,255:275,0:0:2,0:26.2:1:30.8:1:1:0:59.9:67.75:1:0:0.4 0/1:196:2:1,1:29,165:194,2:0.0102:2,2:24.5:1:25:1:0.28336:5.61:60:4:0.0102:0:1 +6 117631558 . AC TT 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTATTTTTTTTTTTTTT;RSEQ=TTTAAGTTCTGGATTACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:0,2:1,90:91,2:0.0211:1,0:5:0:32.5:1:1:0:60:4:0.0217:0:1 0/0:40:0:0,0:0,39:39,0:0:1,0:19.9:1:30.2:1:1:0:57.7:78:1:0:0.9 +6 117631666 . T C 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTCATCTAGATTTTAAGCCC;RSEQ=GCCTGCATTAGGTATTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:0,5:5,3:0.375:0,2:16.7:1:30.7:1:0.375:0:51.3:6:0.375:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:24.5:1:31:0:1:0:31:4:1:0:0 +6 117632139 . G T 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGCACTACAGGTGATTATT;RSEQ=TGCCAATATCCGTAATAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:509:0:0,0:358,151:509,0:0:2,0:25:1:32.2:1:1:0:59.9:71.714:1:0:0.1 0/1:357:24:15,9:231,102:333,24:0.0672:2,2:24.9:1:29.3:1:0.4979:1.35764:60:48:0.0682:0:1 +6 117638124 . G A 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35153;SOR=0.44647;LSEQ=CGGGCTCACATGACCAGAAA;RSEQ=TGCCAGAATGTTAGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:13:13,0:20,0:20,13:0.3939:1,1:29.5:1:29.7:1:1:0:60:26:0.3939:0:1.1 0/1:18:4:4,0:13,1:14,4:0.2222:1,0:29.5:1:30.8:1:1:0:60:8:0.2222:0:1 +6 117638493 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16545;SOR=Inf;LSEQ=GAAGCAGGAGTCCTAGCCGA;RSEQ=GGTCTTTATGGAGTACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:22,215:237,0:0:2,0:23.9:1:31.4:1:1:0:60:38.5:1:0:0 0/1:163:2:0,2:21,140:161,2:0.0123:2,0:12:1:31.5:1:1:0:60:4:0.0125:0:1.5 +6 117638495 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16447;SOR=Inf;LSEQ=AGCAGGAGTCCTAGCCGAGG;RSEQ=TCTTTATGGAGTACAGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:16,209:225,0:0:2,0:24.3:1:32.5:1:1:0:60:111.5:1:0:0 0/1:154:2:1,1:17,135:152,2:0.013:2,2:21:1:27:1:0.22078:7.75:60:4:0.0132:0:1 +6 117638546 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04724;SOR=Inf;LSEQ=TAGTTTCCTTCAAAACCCCT;RSEQ=ACTTAGTGTCTCTAACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:1,82:83,0:0:1,0:24.1:1:32.6:1:1:0:60:82:1:0:0.1 0/1:48:3:0,3:0,45:45,3:0.0625:1,0:17:1:32:0:1:0:60:6:0.0625:0:1 +6 117639026 . C T 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCATTTGAGAGAACTCTCT;RSEQ=TTACTGGGTATACTTGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:5,1:6,3:0.3333:2,0:30.7:1:33:0:1:0:60:6:0.375:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 117639104 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAACAGCTTCAGAATTCA;RSEQ=TTGCAAAACATGCTCCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:14,1:0,0:0,15:1:0,1:25.4:1:32.3:1:1:0:59.6:30:1:0:1.2 1/1:4:4:4,0:0,0:0,4:1:0,0:28:1:33.3:1:1:0:60:8:1:0:1 +6 117639153 . T C 133 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08176;SOR=0.15516;LSEQ=AAAGAAAGGAGAACCTTTTG;RSEQ=CTGAGGATTGCCTGTACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:18:18,0:29,1:30,18:0.375:1,1:24.1:1:31.9:1:1:0:59.7:17:0.3617:0:1.3 0/1:12:1:1,0:11,0:11,1:0.0833:0,0:14:0:29:0:1:0:60:2:0.0909:0:1 +6 117639262 . G A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=0.10787;LSEQ=TGTTGTTTTAGTCATGATCC;RSEQ=TTAAGTCATGTCATTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:22:19,3:191,36:227,22:0.0884:2,2:28.9:1:29.6:1:1:1.19:60:44:0.0894:0:1.1 0/1:194:2:2,0:157,35:192,2:0.0103:2,0:27:1:28.5:1:1:0:60:4:0.0103:0:1 +6 117639266 . A T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31399;LSEQ=GTTTTAGTCATGATCCGTTA;RSEQ=GTCATGTCATTTTGGGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:89:76,13:143,31:174,89:0.3384:2,2:23.3:1:31.5:1:0.60167:1.27:60:88:0.3424:0:1 0/1:210:29:23,6:144,37:181,29:0.1381:2,2:22.4:1:29.9:1:1:1.0152:60:28:0.1359:0:1.1 +6 117639301 . C T 121 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=21.0034;LSEQ=GGTGTTAAAAATAAGTCAAG;RSEQ=GGACTTAAAACTTCTTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:1:0,1:336,148:484,1:0.0021:2,0:1:0:26:0:0.30722:0:60:2:0.0021:0:1 0/1:456:19:14,5:277,160:437,19:0.0417:2,2:22.3:1:28.7:1:0.46768:1.62:60:38:0.042:0:1.1 +6 117639419 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.28159;LSEQ=GAACCCTTCTTCAAAGTCTA;RSEQ=ACAACATAAAAACAAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:796:259:110,149:213,323:536,259:0.3254:2,2:25:1:32.1:1:0.48833:1.12:60:85.333:0.3249:0:1.1 0/1:703:84:29,55:273,346:619,84:0.1195:2,2:23.6:1:31.3:1:0.10131:1.49557:60:83:0.1189:0:1.2 +6 117639516 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13465;SOR=Inf;LSEQ=TTGTTCTGTAATATCTACCC;RSEQ=GAAAGCTGGAAACAGATCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:13,169:182,0:0:2,0:24.1:1:30.5:1:1:0:60:90:1:0:0.1 0/1:106:2:1,1:10,94:104,2:0.0189:2,2:24.5:1:31.5:1:0.19766:9.01:60:4:0.0194:0:2 +6 117639620 . G T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07761;SOR=0.21476;LSEQ=AAGAATATGCAAAATAAGAG;RSEQ=TCTAGTAATGTTTACACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:14:0,14:0,13:13,14:0.5185:1,1:24.1:1:31.3:1:1:0:60:28:0.5185:0:1 0/1:11:2:0,2:0,9:9,2:0.1818:0,0:29.5:1:31:0:1:0:60:4:0.1818:0:1 +6 117640388 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATACATTAAGTATACTAT;RSEQ=ATAAATAATCATGTAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:25:1:30:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 117641246 . C A 289 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28449;LSEQ=CTCCACATATATAGGGTGTA;RSEQ=AAGTTTGTGTTGGTATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2154:693:352,341:753,708:1461,693:0.3217:2,2:24.6:1:30.7:1:0.74697:1.03032:59.9:137.6:0.3236:0:1.2 0/1:1977:235:122,113:903,838:1741,235:0.1189:2,2:24.3:1:29.9:1:1:1.00:60:470:0.12:0:1.2 +6 117641330 . C T 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26377;LSEQ=ATTGTGTGTTTTATGTGACA;RSEQ=GGTGATGTGGAACTTTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1878:605:283,322:585,688:1273,605:0.3222:2,2:23.6:1:30.6:1:0.76639:1.03:59.9:59.5:0.3208:0:1.3 0/1:1850:206:101,105:768,874:1642,206:0.1114:2,2:24.3:1:29.5:1:0.55421:1.09:59.9:67.667:0.1107:0:1.3 +6 117641474 . G A 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30193;LSEQ=ATTGCCTCAACACTTTTATT;RSEQ=TAGCTTGTTGAGTCAAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1196:395:220,175:419,382:801,395:0.3303:2,2:25:1:29.8:1:0.2948:1.15:59.9:130.667:0.3311:0:1.1 0/1:965:125:57,68:451,388:839,125:0.1295:2,2:24.7:1:28.8:1:0.10244:1.3862:60:40.667:0.1282:0:1.1 +6 117641819 . T G 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.28632;LSEQ=CTCTAAACAGCTGATTTAGA;RSEQ=CACCTTTGTGTCTACTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1500:482:236,246:491,525:1016,482:0.3213:2,2:25.3:1:32.6:1:0.82504:1.03:59.8:119.5:0.3238:0:1.1 0/1:1324:158:82,76:569,597:1166,158:0.1193:2,2:25.5:1:31.7:1:0.49789:1.13:60:316:0.1209:0:1.1 +6 117642070 . TA T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27493;LSEQ=TTGACTTAAGGCTGACCACG;RSEQ=ACACAAGGCTCTCAAAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1669:516:243,273:532,621:1153,516:0.3092:2,2:26.2:1:30.2:1:0.75006:1.04:59.9:257:0.31:0.0318:0.1 0/1:1397:153:72,81:564,676:1240,153:0.1095:2,2:24.1:1:29.5:1:0.7313:1.07:59.9:306:0.1106:0.0172:0.2 +6 117643433 . T C 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.33621;LSEQ=TTTTCCAACTTGAAATGTTC;RSEQ=CACCACCTCGCTTCACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1412:432:226,206:498,482:980,432:0.3059:2,2:24.2:1:31.3:1:0.64399:1.06:59.9:107:0.3062:0:1.1 0/1:1178:152:75,77:500,524:1024,152:0.129:2,2:24.1:1:29.9:1:0.93085:1.02:59.8:49.667:0.1278:0:1.1 +6 117643659 . C G 293 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.31135;LSEQ=GTCTTCCCACACAGGCATGT;RSEQ=TTAACTCCCTCATTAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1674:531:278,253:597,540:1137,531:0.3172:2,2:25.2:1:32.4:1:0.95808:1.00613:59.9:58:0.3171:0:1.1 0/1:1417:179:94,85:605,632:1237,179:0.1263:2,2:25.5:1:31.3:1:0.37983:1.16:60:178:0.1267:0:1.1 +6 117643865 . A C 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACAATACAAATTTTAAAAT;RSEQ=ATTGTGACTGTTTTGTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:757:0:0,0:395,362:757,0:0:2,0:24:1:30:1:1:0:60:188.25:1:0:0.2 0/1:583:30:15,15:284,269:553,30:0.0515:2,2:22.8:1:31.7:1:1:1.05569:60:60:0.052:0:1.1 +6 117643897 . A G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.44291;LSEQ=TTTGTTATTTTAATTACTCA;RSEQ=TCTTTTCTCATGCACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:888:184:113,71:413,291:704,184:0.2072:2,2:24.4:1:32.9:1:0.55546:1.12:60:91:0.2071:0:1.1 0/1:675:70:43,27:354,250:604,70:0.1037:2,2:25.9:1:31.6:1:0.70134:1.12:60:140:0.1062:0:1.1 +6 117644018 . C A 168 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=63.65506;LSEQ=ATTTCAAACAGAATAAAGAC;RSEQ=TTTAAGTCCTGAGAAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1423:1:1,0:693,727:1420,1:7e-04:2,0:1:0:27:0:0.48839:0:60:2:7e-04:0:1 0/1:1142:49:24,25:529,563:1092,49:0.0429:2,2:21.3:1:30:1:1:1.02:60:98:0.0433:0:1.1 +6 117644054 . T C 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.20386;LSEQ=AGTCAGATATCCATAGGATG;RSEQ=CTTGGAAGCACAATAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1430:467:226,241:507,455:962,467:0.3266:2,2:24.9:1:31.6:1:0.12814:1.18809:59.9:50.889:0.3251:0:1.3 0/1:1101:99:48,51:484,518:1002,99:0.0899:2,2:25.5:1:30.9:1:1:1.01:59.8:98:0.0896:0:1.3 +6 117644065 . C CAAT 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CATAGGATGTCTTGGAAGCA;RSEQ=AATAGGTTGTCTGAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1452:0:0,0:742,708:1450,0:0:2,0:24.4:1:32.3:1:1:0:60:110.538:0.9986:0:0.5 0/1:1116:48:26,22:518,547:1065,48:0.043:2,2:25.8:1:29.2:1:0.46484:1.25:59.6:96:0.0434:0.0081:1.3 +6 117644132 . C T 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21882;LSEQ=GTTTAAACAATGGTGATGTA;RSEQ=AAGAAAGCAAGCAAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1553:507:263,244:541,504:1045,507:0.3265:2,2:24.8:1:29.9:1:1:1.00:59.9:252.5:0.3275:0:1.3 0/1:1325:127:65,62:611,585:1196,127:0.0958:2,2:23.8:1:28.7:1:1:1.00:60:126:0.0958:0:1.2 +6 117644797 . T C 173 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=53.98409;LSEQ=AAATAAACAAGAATGTATGA;RSEQ=CACTGTGATAACTCTAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1659:1:0,1:802,856:1658,1:6e-04:2,0:17:0:19:0:1:0:60:0:0:0:1 0/1:1457:46:24,22:707,703:1410,46:0.0316:2,2:27.2:1:31.4:1:0.88115:1.08:60:45:0.0313:0:1.3 +6 117644841 . C T 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25928;LSEQ=AATCAGTACTTGACCATTCC;RSEQ=TTTGAGGTTTTTACTGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1547:473:203,270:482,589:1071,473:0.3058:2,2:26.3:1:31:1:0.47021:1.08836:60:117.25:0.3065:0:1.8 0/1:1269:130:57,73:541,597:1138,130:0.1024:2,2:25.6:1:29.9:1:0.45863:1.16043:60:260:0.1032:0:1.8 +6 117644866 . T C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.35372;LSEQ=AGGTTTTTACTGCATTTTAT;RSEQ=ATCATTAAAGTAAATCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1285:397:172,225:393,494:887,397:0.3089:2,2:22.7:1:32.1:1:0.76125:1.04067:60:98.25:0.3082:0:1.9 0/1:1033:141:66,75:404,486:890,141:0.1365:2,2:24.6:1:31.1:1:0.78516:1.06:60:140:0.1363:0:1.8 +6 117645041 . C T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25129;LSEQ=CTTCTGCAAAAGAGGCCCTA;RSEQ=TCATTCCAAACCAGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1761:546:287,259:646,569:1215,546:0.3101:2,2:26.3:1:30.7:1:0.83648:1.02456:60:59.667:0.3088:0:1.1 0/1:1400:142:78,64:657,598:1255,142:0.1014:2,2:24.7:1:29.7:1:0.59518:1.11:59.9:141:0.1014:0:1.1 +6 117645120 . T C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTGGCCTCCCATTAATTCTA;RSEQ=ACTTTTTTCTGTACCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1709:0:0,0:773,936:1709,0:0:2,0:24.9:1:29.6:1:1:0:59.9:84.45:1:0:0.2 0/1:1396:41:18,23:647,707:1354,41:0.0294:2,2:26.7:1:31.6:1:0.63833:1.16921:59.4:82:0.0297:0:1.1 +6 117645239 . C T 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.28399;LSEQ=AAGAAACCTAAAAGTTGGTG;RSEQ=CCTTGCAAGTAGTTTTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1313:394:180,214:455,464:919,394:0.3001:2,2:25.4:1:30.2:1:0.20643:1.16569:60:97.5:0.3014:0:1.1 0/1:1060:115:55,60:449,494:943,115:0.1085:2,2:23.7:1:28.5:1:1:1.01:60:230:0.1107:0:1.1 +6 117645778 . C CT 137 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.09025;SOR=0.53771;LSEQ=TCAAAAGCAAGGTGTTTTTG;RSEQ=TTTTTTTTGCAGAGAGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1401:24:12,12:664,712:1376,24:0.0171:2,2:26.8:1:29.9:1:1:1.07:60:23:0.0167:0.005:0.3 0/0:1185:11:6,5:564,607:1171,11:0.0093:2,2:29.1:1:30.5:1:0.76682:1.29:60:22:0.0094:0:0.2 +6 117646289 . A G 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27126;LSEQ=GTAGCAAACTTCTGTACACA;RSEQ=CTAACTAGATAACTAACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1113:350:173,177:374,387:761,350:0.3145:2,2:25.3:1:32.5:1:0.94855:1.01:60:37.889:0.3131:0:1.1 0/1:859:95:43,52:386,378:764,95:0.1106:2,2:24.9:1:31.1:1:0.38425:1.23459:60:190:0.1116:0:1.1 +6 117646772 . T C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.40919;LSEQ=CTGTCAGCAGTATGCGTAAG;RSEQ=CAAGGGCACAGGCAAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1574:477:245,232:548,549:1097,477:0.303:2,2:24.9:1:31.9:1:0.62181:1.06:60:94.4:0.3031:0:1.1 0/1:1384:209:103,106:584,589:1173,209:0.151:2,2:26.3:1:31.2:1:0.94017:1.02038:59.9:103.5:0.1512:0:1.1 +6 117647124 . A G 176 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=73.08154;LSEQ=TTGGAAGCCTAATTAGGAGC;RSEQ=TGGAATTGATGTGGTAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2048:1:1,0:958,1087:2045,1:5e-04:2,0:1:0:31:0:0.46872:0:60:2:5e-04:0:1 0/1:1739:60:33,27:804,870:1674,60:0.0345:2,2:23.8:1:29.9:1:0.29624:1.32:60:59:0.0343:0:1.2 +6 117647253 . AT A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01214;SOR=0.29918;LSEQ=TTAATAGTTTGGATAATAAG;RSEQ=TATATATATATATATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:542:25:23,2:184,185:369,25:0.0461:2,2:19.4:1:31:1:3e-05:11.51:57.2:50:0.066:0:0.2 0/1:351:5:3,2:142,143:285,5:0.0142:2,2:12.6:1:29:1:1:1.51:60:10:0.0169:0:0 +6 117647581 . C CA 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTTGAAGTGCTCTTTCTG;RSEQ=AAAAAATAATAAATACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1526:0:0,0:766,759:1525,0:0:2,0:25:1:32.2:1:1:0:59.9:94.313:0.9993:0:0.1 0/1:1285:49:30,19:584,647:1231,49:0.0381:2,2:26.4:1:29.6:1:0.07921:1.75:60:98:0.0385:0.0078:0.1 +6 117647643 . GATC G 166 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTATTTCTAGTTGTTCATA;RSEQ=TTCTTAGTGACTGAACGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1695:0:0,0:890,805:1695,0:0:2,0:25.5:1:30.7:1:1:0:59.9:83.75:1:0:0.1 0/1:1249:39:17,22:636,572:1208,39:0.0312:2,2:30.8:1:31.5:1:0.32861:1.43848:60:78:0.0317:0.0016:0.2 +6 117647938 . T G 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTTTCCATTTTCTCAAT;RSEQ=TTCAGTCTTTTACATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1429:0:0,0:699,728:1427,0:0:2,0:25.7:1:30.9:1:1:0:60:157.556:0.9993:0:0.1 0/1:1161:37:17,20:584,538:1122,37:0.0319:2,2:26.5:1:30.9:1:0.50624:1.27679:60:36:0.0312:0:1.1 +6 117648064 . C T 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24602;LSEQ=TTATATCTGAGATTCTGAGG;RSEQ=TCGTTGCTTCCTTTTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1661:483:227,256:592,585:1177,483:0.2908:2,2:24.8:1:30.2:1:0.23456:1.14116:59.9:160:0.2913:0:1.1 0/1:1463:134:63,71:665,662:1327,134:0.0916:2,2:24.9:1:29.3:1:0.52624:1.13199:60:268:0.0924:0:1.1 +6 117648215 . T C 208 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAAAGGCAAGCTCAAGGTCT;RSEQ=CCATTATGTCTTCTCTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1399:101:57,44:665,632:1297,101:0.0722:2,2:24.4:1:31.3:1:0.35259:1.23:60:32.667:0.071:0:1.1 0/0:1205:0:0,0:639,564:1203,0:0:2,0:23.8:1:29.3:1:1:0:59.9:91.538:0.9992:0:0.1 +6 117648340 . C T 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.23904;LSEQ=TGGGAGAATCTGGTTCTATT;RSEQ=CTGCTAATTGACTCATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2026:649:330,319:710,662:1372,649:0.3203:2,2:25.5:1:30.6:1:0.73867:1.03676:60:80.125:0.3202:0:1.1 0/1:1719:174:90,84:771,772:1543,174:0.1012:2,2:25.6:1:29.3:1:0.68961:1.07:60:173:0.1017:0:1.2 +6 117648481 . A C 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGAGCTGAGGGTCCCTTT;RSEQ=AGGACCATCCTGAGCAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1732:0:0,0:845,882:1727,0:0:2,0:24.8:1:29.6:1:1:0:60:77.5:0.9971:0:0.1 0/1:1542:68:32,36:732,739:1471,68:0.0441:2,2:24.8:1:30.6:1:0.71058:1.11426:60:67:0.0439:0:1.2 +6 117649173 . C T 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23589;LSEQ=TCCCGCTGATACGTTGGTTT;RSEQ=AGACTTCTAACCTCTAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1804:621:318,303:583,594:1177,621:0.3442:2,2:24.2:1:29.9:1:0.51917:1.07:59.9:1242:0.3465:0:1.1 0/1:1607:177:90,87:704,725:1429,177:0.1101:2,2:23.8:1:28.8:1:0.74999:1.07:60:176:0.1101:0:1.2 +6 117649988 . T C 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29324;LSEQ=TTTCAGTCCCTGGGAACACA;RSEQ=TGCAAACTGTAATCTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1838:578:284,294:609,647:1256,578:0.3145:2,2:24.1:1:32.8:1:0.8017:1.03:59.9:191.667:0.317:0:1.1 0/1:1662:197:100,97:714,748:1462,197:0.1185:2,2:23.3:1:31.4:1:0.64896:1.08:60:97.5:0.1183:0:1.2 +6 117650131 . A T 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23799;LSEQ=GAGAGTATTCACCTTGCTAA;RSEQ=GCAAATTATCATCAGGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1650:572:291,281:525,552:1077,572:0.3467:2,2:25.3:1:30.8:1:0.43771:1.09:60:189.667:0.3489:0:1.1 0/1:1383:155:76,79:605,621:1226,155:0.1121:2,2:25.8:1:29.6:1:1:1.01268:60:310:0.1128:0:1.1 +6 117650800 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41652;LSEQ=AAACCATAATAAGTGTGTGA;RSEQ=TCCTTCACCGGCAAGGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:153:68,85:198,234:432,153:0.2611:2,2:23.8:1:30.6:1:0.77772:1.05762:58.2:152:0.2634:0:1.1 0/1:468:60:31,29:187,221:408,60:0.1282:2,2:23.8:1:29.2:1:0.40912:1.26:58.3:29:0.1258:0:1.2 +6 117650964 . G T 53 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01752;SOR=Inf;LSEQ=GCGAGCGAGCAGGCTACCCA;RSEQ=CCGGGGAAATTGCTTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:309,290:599,0:0:2,0:25.7:1:32.5:1:1:0:59.8:38.933:1:0:0.1 0/1:483:5:1,4:241,237:478,5:0.0104:2,2:13:1:23.2:1:0.21583:4.05692:60:4:0.0084:0:1.6 +6 117651024 . G A 123 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=10.64167;LSEQ=GATTGGAAGATCCCACTCTC;RSEQ=ATCCCATGCCACCGAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:619:2:1,1:296,320:616,2:0.0032:2,2:7.5:1:30:1:1:1.08:60:4:0.0033:0:1 0/1:539:18:8,10:237,284:521,18:0.0334:2,2:23:1:29.5:1:1:1.04306:60:36:0.0338:0:1.2 +6 117651145 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53252;SOR=0;LSEQ=GGGGTGACCAGCACAGGCTT;RSEQ=TGCTGCCTGCTGTCTAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:57,122:179,2:0.011:2,2:13:1:29:1:0.53941:2.13:60:4:0.0112:0:1 0/0:106:0:0,0:36,70:106,0:0:2,0:20.8:1:31.2:1:1:0:59.9:105:1:0:0.2 +6 117651172 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12431;SOR=Inf;LSEQ=CTGCTGTCTAAGCCCTTTGA;RSEQ=CTCCTTGAGGGAGGGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:59,98:157,0:0:2,0:23.3:1:32.6:1:1:0:59.5:77.5:1:0:0.1 0/1:86:2:1,1:38,46:84,2:0.0233:2,2:23.5:1:27:1:1:1.21:60:4:0.0235:0:1 +6 117651192 . C A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00211;SOR=Inf;LSEQ=GCTCCTTGAGGGAGGGGCAG;RSEQ=AGCCAGCACTGGGACTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:76,97:173,0:0:2,0:24.4:1:32.2:1:1:0:59.1:85.5:1:0:0.1 0/1:99:6:2,4:46,47:93,6:0.0606:2,2:26.5:1:29.3:1:0.67855:1.94464:59.8:12:0.0619:0:1 +6 117651240 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16653;SOR=Inf;LSEQ=AACACGCTAATCTCCCTGGG;RSEQ=GGCGGGGAGAAATGCAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:118,109:227,0:0:2,0:24.9:1:31.3:1:1:0:59:74.667:1:0:0.2 0/1:157:2:1,1:82,72:154,2:0.0127:2,2:39:0:31:0:1:1.13794:60:4:0.013:0:1.5 +6 117651285 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50248;SOR=0;LSEQ=TTCTATAGCTCCAGGCTGTG;RSEQ=TTTTCCCCTGCGGGAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:102,86:188,2:0.0105:2,2:28:1:30:1:1:1.18497:54:4:0.0106:0:1.5 0/0:160:0:0,0:88,72:160,0:0:2,0:23.3:1:30.8:1:1:0:59.5:31:1:0:0.2 +6 117651307 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19228;SOR=Inf;LSEQ=TTTCCCCTGCGGGAGCCAGC;RSEQ=AGGCTGGACAGCTTGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:97,97:194,0:0:2,0:23.4:1:30.5:1:1:0:59.3:47.5:1:0:0.3 0/1:152:2:1,1:82,67:149,2:0.0132:2,2:25.5:1:25:1:1:1.22223:60:4:0.0135:0:1 +6 117651314 . G T 26 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.62661;LSEQ=TGCGGGAGCCAGCGAGGCTG;RSEQ=ACAGCTTGGTCCCAAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:94,99:193,2:0.0102:2,2:15.5:1:26:1:1:1.05:60:4:0.0104:0:1 0/0:156:1:0,1:81,74:155,1:0.0064:2,0:1:0:21:0:0.48077:0:25:2:0.0067:0:2 +6 117651344 . A G 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.25239;LSEQ=TCCCAAGACTTGTCGCCACA;RSEQ=CCCAACACACCAGCTGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:49:21,28:58,73:131,49:0.2707:2,2:26.3:1:32.8:1:1:1.05905:54:98:0.2784:0:1.2 0/1:164:14:9,5:70,79:149,14:0.0854:2,2:22.9:1:30.2:1:0.26862:2.02:52.3:28:0.0859:0:1.1 +6 117651345 . C T 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.55612;LSEQ=CCCAAGACTTGTCGCCACAA;RSEQ=CCAACACACCAGCTGTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:78,103:181,2:0.0109:2,2:37.5:1:27:1:1:1.32:60:4:0.011:0:1.5 0/0:164:1:0,1:78,85:163,1:0.0061:2,0:1:0:25:0:1:0:60:2:0.0062:0:1 +6 117651372 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21025;SOR=Inf;LSEQ=CACCAGCTGTGGTAGTCAGC;RSEQ=GCCAGAGTGCCTCTTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:76,97:173,0:0:2,0:24.3:1:30.5:1:1:0:57:33.6:1:0:0.4 0/1:147:2:1,1:63,82:145,2:0.0136:2,2:21.5:1:29.5:1:1:1.30:47.5:4:0.0139:0:1.5 +6 117651379 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21615;SOR=Inf;LSEQ=TGTGGTAGTCAGCGGCCAGA;RSEQ=TGCCTCTTCAGGTCTAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:74,90:164,0:0:2,0:23.6:1:32.7:1:1:0:56.9:81:1:0:0.4 0/1:143:2:1,1:61,80:141,2:0.014:2,2:7.5:1:27.5:1:1:1.31:60:4:0.0141:0:1.5 +6 117651651 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20586;SOR=Inf;LSEQ=ACAAAGTGCTTCGTTAAATG;RSEQ=GTCCTCCTCCTGGTGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:239:0:0,0:120,119:239,0:0:2,0:24.8:1:31.4:1:1:0:58.7:78.667:1:0:0.2 0/1:199:2:1,1:87,110:197,2:0.0101:2,2:30:1:27.5:1:1:1.26:60:4:0.0105:0:1 +6 117651724 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15507;SOR=Inf;LSEQ=AGGACACCCTATACAGGAGC;RSEQ=ATCCTACTGGCATCAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:62,65:127,0:0:2,0:23.1:1:30.9:1:1:0:58:254:1:0:0.1 0/1:83:2:1,1:41,40:81,2:0.0241:2,2:11.5:1:29:1:1:1.0247:49.5:4:0.0244:0:1 +6 117651762 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52392;SOR=0;LSEQ=TTGGTGCCCCTTGAAGTCAG;RSEQ=GGTCCCAGAAGAAGGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:66,72:138,2:0.0143:2,2:15:1:30:1:1:1.09:60:4:0.0145:0:1 0/0:88:0:0,0:53,35:88,0:0:2,0:19.6:1:28.8:1:1:0:57.9:176:1:0:0.1 +6 117651764 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15897;SOR=Inf;LSEQ=GGTGCCCCTTGAAGTCAGAG;RSEQ=TCCCAGAAGAAGGAGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:69,72:141,0:0:2,0:25:1:31.8:1:1:0:58.6:69.5:1:0:0.1 0/1:94:2:1,1:55,37:92,2:0.0213:2,2:30.5:1:27:1:1:1.48004:59:4:0.0213:0:1 +6 117651772 . A T 36 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.98672;LSEQ=TTGAAGTCAGAGGTCCCAGA;RSEQ=GAAGGAGCAGACACCCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:3:0,3:77,71:148,3:0.0199:2,0:14.3:1:23:1:0.11525:0:55:2:0.0137:0:1 0/1:102:2:0,2:58,42:100,2:0.0196:2,0:1:0:25.5:1:0.18365:0:60:4:0.0198:0:1 +6 117651880 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23942;SOR=Inf;LSEQ=AAGTGAACCCCAGCAAACTG;RSEQ=AGCAGCCCTACAGAAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:97,105:202,0:0:2,0:24.2:1:32.3:1:1:0:54.4:100:0.995:0:0.3 0/1:195:2:1,1:101,91:192,2:0.0103:2,2:25:1:26.5:1:1:1.10929:60:4:0.0104:0:1 +6 117651888 . C G 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11218;SOR=Inf;LSEQ=CCCAGCAAACTGCAGCAGCC;RSEQ=TACAGAAGAGGGAAGTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:87,102:189,0:0:2,0:23.4:1:32.1:1:1:0:53.6:188:0.9947:0:0.4 0/1:178:3:2,1:89,86:175,3:0.0169:2,2:14.3:1:21.7:1:1:1.93:54.7:2:0.0114:0:1.3 +6 117651926 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.35298;LSEQ=ACTATTGAAAGAAAAACAAA;RSEQ=AAGCAGAAAGTGACAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:171:90:51,39:43,38:81,90:0.5263:2,2:22.9:1:32.3:1:0.64785:1.15:40:180:0.5325:0:1.1 0/1:153:43:15,28:59,49:108,43:0.281:2,2:24.9:1:30.5:1:0.03176:2.23552:40.9:20.5:0.2733:0:1.1 +6 117651947 . A G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=AAGCAGAAAGTGACAACAAC;RSEQ=GCATCATCATCAACAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:131,87:218,0:0:2,0:22.6:1:31.1:1:1:0:52.4:35.333:0.9953:0:0.5 0/1:181:12:6,6:92,77:169,12:0.0663:2,2:21.8:1:27.5:1:0.77411:1.19362:60:11:0.0632:0:1.2 +6 117651957 . TCAA T 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=1;SOR=0.93604;LSEQ=TGACAACAACAGCATCATCA;RSEQ=CAACAACAACAAGGGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:5:2,3:137,104:241,5:0.0203:2,2:25:1:32.4:1:0.65534:1.97042:60:10:0.0208:0:0.4 0/1:210:4:2,2:111,94:205,4:0.019:2,2:27.5:1:33:1:1:1.17991:60:8:0.0193:0:0 +6 117651975 . G T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.34712;SOR=3.38994;LSEQ=CATCAACAACAACAACAAGG;RSEQ=CCCCCACAAAAAACCCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:1:0,1:162,128:290,1:0.0034:2,0:1:0:16:0:0.4433:0:60:0:0:0:3 0/1:260:3:1,2:131,126:257,3:0.0115:2,2:14:1:27.3:1:0.61781:2.07371:49.3:6:0.0119:0:1 +6 117652005 . C T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.19859;SOR=4.39982;LSEQ=AAAACCCATACAAGGGTCAG;RSEQ=AGCCTCAAAGACCACAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:1:0,1:168,166:334,1:0.003:2,0:1:0:23:0:0.49851:0:60:2:0.003:0:1 0/1:307:4:1,3:154,149:303,4:0.013:2,2:23:1:27.5:1:0.36768:3.09033:57.3:8:0.0131:0:1 +6 117652037 . G A 87 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03291;SOR=7.58139;LSEQ=CCACAACTAGACAAACTCAC;RSEQ=AAGGTGAGAAAGAACCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:1:1,0:136,154:290,1:0.0034:2,0:1:0:26:0:0.47079:0:60:2:0.0035:0:1 0/1:274:7:6,1:133,134:267,7:0.0255:2,2:26.6:1:31:1:0.12047:6.01:49.3:14:0.0259:0:1 +6 117652187 . T C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07161;LSEQ=CAGAAGTAGGCTTCACAAGA;RSEQ=GGGTAGAAAAAACTATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:48:21,27:26,60:86,48:0.3582:2,2:25:1:30.4:1:0.13333:1.79:59:47:0.3588:0:1.2 0/1:105:4:1,3:37,64:101,4:0.0381:2,2:20.3:1:27:1:1:1.72606:60:8:0.0396:0:1 +6 117652632 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02915;SOR=Inf;LSEQ=CTAGCAAGACAGGCCAACAT;RSEQ=CAAATTCGGCAAACACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:62,342:404,0:0:2,0:23.2:1:32:1:1:0:43.2:43.889:1:0:0.1 0/1:286:4:0,4:45,236:281,4:0.014:2,0:11:1:29.5:1:1:0:42.3:8:0.0141:0:1.3 +6 117653900 . G A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATTGAACAACTTGCTCCT;RSEQ=AATGGCTCCTGGGTAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:4,1:11,0:11,5:0.3125:0,2:27.2:1:28.6:1:0.3125:0:36.2:10:0.3125:0:1.2 0/0:1:0:0,0:1,0:1,0:0:0,0:2:0:28:0:1:0:41:2:1:0:4 +6 117654044 . TT AG 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10298;SOR=Inf;LSEQ=CATAGCACTAAATGCCCACA;RSEQ=AGAAAGCCAGAAAGATCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:164,0:164,0:0:1,0:22.8:1:31.8:1:1:0:48.8:81:1:0:0 0/1:78:2:2,0:76,0:76,2:0.0256:1,0:9.5:1:30.9:1:1:0:32:4:0.0263:0.0128:1.5 +6 117654053 . CA AG 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0037;SOR=Inf;LSEQ=AAATGCCCACATTAGAAAGC;RSEQ=GAAAGATCTCAAATCGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:192,0:192,0:0:1,0:23.3:1:32.1:1:1:0:47.5:191:1:0:0 0/1:95:5:5,0:90,0:90,5:0.0526:1,0:8.2:1:30.9:1:1:0:33.8:10:0.0532:0.0316:0.6 +6 117654130 . G A 97 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00305;SOR=7.51625;LSEQ=AGCAAACTAATCCAAAAGCT;RSEQ=GCAGAAGACAAGAAATAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:849:2:2,0:603,244:847,2:0.0024:2,0:5:1:29.5:1:1:0:59:4:0.0024:0:1.5 0/1:630:11:7,4:432,184:616,11:0.0175:2,2:7.5:1:28.3:1:0.74105:1.34098:46.9:22:0.0178:0:1.6 +6 117654196 . C CA 122 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0096;SOR=2.74791;LSEQ=CAAAGACACAAAAAGCCCTC;RSEQ=AAAAAAAATCAACACATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2094:9:5,4:1020,1062:2082,9:0.0043:2,2:30.6:1:31:1:0.74897:1.30:55.6:18:0.0044:0:0.2 0/1:1791:21:10,11:879,885:1764,21:0.0117:2,2:27.9:1:28:1:1:1.09247:58.4:20:0.0113:0.0022:0.4 +6 117654231 . T A 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATCCAGGAGCCGTTTTTTT;RSEQ=AAAAAATAAAATAAATAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1600:0:0,0:676,920:1596,0:0:2,0:26:1:29.5:1:1:0:59.9:144.091:0.9994:0:0.2 0/1:1351:61:30,31:561,719:1280,61:0.0452:2,2:25.5:1:28.8:1:0.43047:1.24:59.5:122:0.0456:0:1.2 +6 117654308 . C CA 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.56204;SOR=3.20681;LSEQ=AGAGAAGAATCAAATAGACA;RSEQ=AAAAAAAATGATAAAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:1:0,1:4,309:313,1:0.0032:1,0:31:0:33:0:1:0:57:2:0.0033:0:0 0/1:198:2:0,2:1,195:196,2:0.0101:1,0:37.5:1:32.5:1:1:0:50:4:0.0102:0:0 +6 117657368 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52116;SOR=0;LSEQ=CTGGGGTACATGTGCAGGAC;RSEQ=TGAAGGTTTGTTACATGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:23,155:178,2:0.011:2,2:20:1:34:1:0.24953:6.62:60:4:0.011:0:1 0/0:118:0:0,0:21,96:117,0:0:2,0:22.6:1:31.2:1:1:0:59.9:116:0.9915:0:0.1 +6 117657686 . A G 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.27249;SOR=0;LSEQ=TCATTCCTTTTTATGGCTGC;RSEQ=TAGTATGCCATGGTGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:3,2:11,1:12,5:0.2941:2,2:25.2:1:29.8:1:0.19118:6.32143:52.4:10:0.2941:0:1 0/0:6:0:0,0:5,1:6,0:0:2,0:26.5:1:30.2:1:1:0:54.7:12:1:0:0.2 +6 117658193 . G C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.18952;LSEQ=CAAGGTCTCCTATATTTTCT;RSEQ=AATTTCTTCATTCAAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:233:136,97:248,192:440,233:0.3457:2,2:24.2:1:32.4:1:0.62444:1.09:60:115.5:0.3479:0:1.1 0/1:484:44:26,18:238,202:440,44:0.0909:2,2:26:1:30.6:1:0.63429:1.23:60:43:0.0905:0:1.1 +6 117659005 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTTTTCCTCCTAACAC;RSEQ=CTCTTCAGACATGTAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:26.5:1:29.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 117662453 . C T 203 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03304;LSEQ=ACTCTCTGTACACCACATTT;RSEQ=CTCAGAGTGGCAGGCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:945:103:53,50:386,456:842,103:0.109:2,2:30:1:30.4:1:0.29646:1.25:60:102:0.1093:0:1.1 0/0:746:3:0,3:355,388:743,3:0.004:2,0:1:0:23:1:0.25074:0:60:6:0.0041:0:1 +6 117662944 . C T 104 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22933;SOR=0.23263;LSEQ=AAGTCAGCCTCTTCTATAAT;RSEQ=GTAGGTTAACAGACTGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:10:0,10:2,16:18,10:0.3571:2,0:28.1:1:31.4:1:0.52381:0:60:20:0.3571:0:1.3 0/1:9:1:0,1:0,8:8,1:0.1111:0,0:1:0:31:0:1:0:60:2:0.1111:0:1 +6 117663364 . A G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30762;SOR=0.36273;LSEQ=TCCTAGTTGCTTTCTATTTT;RSEQ=ATAGAATATTATTAGTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:14:14,0:30,0:30,14:0.3182:1,1:26.7:1:32.6:1:1:0:57.1:28:0.3182:0:1.1 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:30.5:1:32:1:1:0:60:4:0.1429:0:1 +6 117663499 . A G 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.3397;LSEQ=GATTTTAAAAAATAAACATC;RSEQ=ACATACACAGCACATATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:188:138,50:278,103:381,188:0.3304:2,2:22.8:1:30.4:1:1:1.02:59.8:93:0.3316:0:1.1 0/1:495:71:45,26:298,125:423,71:0.1434:2,2:21.6:1:28.7:1:0.26534:1.37653:60:22.667:0.1391:0:1.1 +6 117665115 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06562;LSEQ=ATTAGCTGTAAAAAAGTTGC;RSEQ=TACTAGTCCATTTCAGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:35:35,0:52,0:52,35:0.4023:1,1:21.8:1:31:1:1:0:60:34:0.3953:0:1 0/1:48:2:2,0:44,2:46,2:0.0417:1,0:37.5:1:29.5:1:1:0:60:4:0.0417:0:1 +6 117665635 . G C 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1049;SOR=0;LSEQ=CTTGATACTGTGTGTAGTAT;RSEQ=TGTAGTATGTACTGCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:30.3:1:27.8:1:1:0:60:3:0.4286:0:1 0/0:5:0:0,0:1,4:5,0:0:2,0:10.4:1:30.8:1:1:0:60:10:1:0:0 +6 117674087 . G A 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGGACAGCCTTGGAGAAGGA;RSEQ=ATGTTATGAGATTTTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:200,17:217,0:0:2,0:23:1:33:1:1:0:59.9:42.4:0.9953:0:0.1 0/1:137:43:40,3:84,10:94,43:0.3139:2,2:18.7:1:29.2:1:0.75441:1.58:60:86:0.3139:0:1.1 +6 117674434 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51786;SOR=0;LSEQ=ATTATAATTGCTAAATTTTG;RSEQ=ATCTATTATTTCAACATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:0,111:111,2:0.0177:1,2:27:1:34:0:0.0177:0:60:4:0.0179:0:1 0/0:75:0:0,0:2,73:75,0:0:1,0:22.5:1:30.9:1:1:0:60:150:1:0:0 +6 117678083 . A G 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.11047;LSEQ=TGTCCAATACAAGCGACTAT;RSEQ=GAGGAAAAAAAAGTCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:522:474:80,394:12,34:46,474:0.908:2,2:24:1:31.4:1:0.1537:1.73611:59.9:42.091:0.9132:0:1.1 1/0:357:186:42,144:41,130:171,186:0.521:2,2:23.4:1:30.4:1:0.80244:1.08108:59.9:92:0.5212:0:1.1 +6 117678087 . G GA 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.16404;SOR=5.95068;LSEQ=CAATACAAGCGACTATAGAG;RSEQ=AAAAAAAAGTCCCCCCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:1:0,1:79,395:474,1:0.0021:2,0:28:0:33:0:1:0:60:2:0.0021:0:1 0/1:326:4:1,3:71,251:322,4:0.0123:2,2:13.5:1:30.8:1:1:1.18:60:8:0.0124:0.0061:0.5 +6 117678900 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5247;SOR=0;LSEQ=GTCTTCTACTATTAAACCAA;RSEQ=GACATTACATTAAATATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:140,10:150,2:0.0132:2,2:15:1:31:1:0.13994:13.39609:60:4:0.0137:0:1 0/0:95:0:0,0:86,9:95,0:0:2,0:25.1:1:30:1:1:0:60:190:1:0:0 +6 117680945 . T C 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAATACTTCACTTCCTTTA;RSEQ=TTCGGAAGAATTACATAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:253,63:316,0:0:2,0:23.8:1:30.9:1:1:0:60:51.667:1:0:0.1 0/1:240:22:15,7:152,66:218,22:0.0917:2,2:26.5:1:31.2:1:1:1.07442:60:44:0.0924:0:1.1 +6 117681423 . A C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1771;SOR=Inf;LSEQ=AGACAGTGTTCATATCCCTA;RSEQ=AGACACCAATGGGACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:183,31:214,0:0:2,0:23.6:1:30:1:1:0:58.9:25.75:1:0:0.3 0/1:156:2:2,0:126,28:154,2:0.0128:2,0:27:1:32:1:1:0:57.5:4:0.0132:0:1 +6 117681436 . G GACAC 214 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=15.000;MSILEN=2;SSF=0.00012;SOR=0.44072;LSEQ=ATCCCTAAAGACACCAATGG;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:216:113:93,20:43,7:50,113:0.5231:2,2:30.8:1:31.4:1:0.65197:1.31887:58.8:226:0.528:0.0185:0.4 0/1:169:55:45,10:43,12:55,55:0.3254:2,2:25.6:1:30.3:1:0.81207:1.25:59.6:110:0.3374:0.0296:0.3 +6 117681655 . C G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.50044;SOR=0;LSEQ=TGAGAGATTACTAAATGTTT;RSEQ=ATTTCATACTCCTGATACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:18,173:191,2:0.0103:2,2:21:0:34:0:0.18766:9.38:60:4:0.0104:0:1.5 0/0:172:0:0,0:30,142:172,0:0:2,0:20.7:1:31.6:1:1:0:60:171:1:0:0.1 +6 117681661 . A C 104 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.00046;SOR=Inf;LSEQ=ATTACTAAATGTTTCATTTC;RSEQ=TACTCCTGATACACAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:10,158:168,0:0:2,0:24.4:1:31.6:1:1:0:60:336:1:0:0.1 0/1:150:10:2,8:23,117:140,10:0.0667:2,2:19.5:1:31.6:1:0.67316:1.27:60:20:0.0671:0:1.1 +6 117683821 . G A 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGTTGAAAAGACATCACT;RSEQ=AGGGAGTGACATTGACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:757:0:0,0:438,318:756,0:0:2,0:25.8:1:32.1:1:1:0:60:150.2:1:0:0.1 0/1:650:55:32,23:331,260:591,55:0.0846:2,2:23.9:1:28.1:1:0.77835:1.09:60:54:0.084:0:1.2 +6 117686192 . T C 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00421;SOR=Inf;LSEQ=AAAGTGAGATTCTGCTTTTT;RSEQ=AAGAAAAAAGACAGATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:256,97:353,0:0:2,0:24:1:30.1:1:1:0:59.9:87.25:1:0:0.1 0/1:301:7:4,3:206,88:294,7:0.0233:2,2:21.4:1:31.7:1:0.43551:1.75204:60:14:0.0234:0:1 +6 117686693 . A T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06863;SOR=Inf;LSEQ=AGTGTGGGCAAGGCTGACAC;RSEQ=GATGGTACAGTCTGTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:289,112:401,0:0:2,0:22.9:1:30.6:1:1:0:60:132.667:1:0:0.1 0/1:279:3:1,2:188,88:276,3:0.0108:2,2:24.3:1:29.3:1:0.2442:4.24827:60:6:0.0108:0:1 +6 117686701 . C T 49 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03262;SOR=Inf;LSEQ=CAAGGCTGACACAGATGGTA;RSEQ=AGTCTGTTTGGGAAATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:297,138:435,0:0:2,0:24.6:1:32.1:1:1:0:60:107.75:1:0:0.1 0/1:323:4:1,3:213,106:319,4:0.0124:2,2:5.3:1:24.5:1:0.11342:5.99317:60:8:0.0124:0:1.3 +6 117686781 . A G 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATTCTACACTGTAGAAAACT;RSEQ=CACCCCAGTCTACCGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:803:0:0,0:446,357:803,0:0:2,0:25.4:1:29:1:1:0:60:88.222:1:0:0.1 0/1:636:27:14,13:344,264:608,27:0.0425:2,2:29.2:1:30.4:1:0.69346:1.20958:60:54:0.0427:0:1.1 +6 117686918 . CA C 124 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.01096;SOR=0.10738;LSEQ=AAGTTCCCTACAGGATGAAA;RSEQ=AAAAAAAGAAATAGGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:13:3,10:184,382:566,13:0.0225:2,2:37.3:1:33.7:1:0.56332:1.60439:57:26:0.0226:0:0.1 0/0:407:1:1,0:134,272:406,1:0.0025:2,0:12:0:33:0:0.3317:0:60:2:0.0025:0:0 +6 117686943 . A T 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.75166;LSEQ=AAAAGAAATAGGAGAAAAAA;RSEQ=TGGGGATTATTGACCAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:26:5,21:79,275:354,26:0.0684:2,2:23.3:1:30.1:1:0.81167:1.20597:60:52:0.0697:0:1 0/1:242:88:21,67:38,115:153,88:0.3636:2,2:23.7:1:29.4:1:1:1.05403:60:87:0.3625:0:1.1 +6 117687002 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11796;SOR=Inf;LSEQ=ATAGCAATTACTAATAATTA;RSEQ=AACTGAAACAAAATTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:10,98:108,0:0:2,0:24.7:1:32.8:1:1:0:60:216:1:0:0.1 0/1:57:2:0,2:3,52:55,2:0.0351:2,0:11.5:1:30:1:1:0:60:4:0.0351:0:2 +6 117687159 . G GA 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.02252;LSEQ=TCTTAAAACTTAATTCTTAA;RSEQ=AAAAAAAAATATCCCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:7:6,1:227,44:271,7:0.0251:2,2:25.3:1:31.1:1:1:1.16:60:14:0.0252:0:0 0/1:234:6:6,0:189,39:228,6:0.0256:2,0:12.8:1:28.8:1:0.59289:0:60:12:0.026:0.0128:0.3 +6 117687535 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.02229;SOR=Inf;LSEQ=AAGTAGTCATGAGAATATAT;RSEQ=TTTGTGAGTATCTGTACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:4,154:158,0:0:1,0:24:1:32:1:1:0:59.5:21.571:1:0:0.1 0/1:101:4:0,4:6,91:97,4:0.0396:2,0:17.3:1:30.5:1:1:0:60:8:0.04:0:1 +6 117687553 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.13506;SOR=Inf;LSEQ=ATGTTTGTGAGTATCTGTAC;RSEQ=CATTTGTGTACATTAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:1,110:111,0:0:1,0:23.9:1:32.3:1:1:0:59.6:21.2:1:0:0.1 0/1:65:2:0,2:0,63:63,2:0.0308:1,0:14:1:31:0:1:0:60:4:0.0313:0:1 +6 117699831 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02778;SOR=Inf;LSEQ=GATCAGGACAGGGGGATAAG;RSEQ=TTGAGGACACAGATCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:7,0:7,0:0:0,0:34.4:1:31.7:1:1:0:55.7:14:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:31.5:1:1:0:60:4:1:0:1 +6 117699988 . A G 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACACTTCCTGGGCTCTTA;RSEQ=GCAGCATTCTCCTGAGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,1:20,5:0.2:1,0:27.8:1:34.2:1:1:0:60:10:0.2:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:26:0:31:0:1:0:60:2:1:0:0 +6 117700393 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15091;SOR=Inf;LSEQ=AACTTTGTGAACAGGTCACA;RSEQ=TTAAGCTATAGATTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:12,195:207,0:0:2,0:25.7:1:32.9:1:1:0:59.9:50.75:1:0:0.1 0/1:132:2:1,1:10,120:130,2:0.0152:2,2:12:1:29:1:0.16031:11.49:60:4:0.0153:0:1 +6 117704316 . GC TT 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.0189;SOR=5.57781;LSEQ=TTGTGACCATCAAATAAGGC;RSEQ=TTTTTTTTCAAATAACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:5,0:33,1:34,5:0.1282:1,0:28.6:1:31.3:1:1:0:60:10:0.1316:0:1 0/1:13:6:5,1:7,0:7,6:0.4615:0,2:30.3:1:30.2:1:0.46154:0:60:12:0.4615:0:1 +6 117704607 . T C 176 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=59.79749;LSEQ=CTGAATCCACCACCATGTCA;RSEQ=TCACCAATAGCTTCACGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1079:1:0,1:458,620:1078,1:9e-04:2,0:47:0:14:0:1:0:60:0:0:0:2 0/1:988:52:28,24:423,513:936,52:0.0526:2,2:20.7:1:30.9:1:0.25324:1.41:60:104:0.0531:0:1.2 +6 117706683 . G GA 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.93613;LSEQ=GAAATTGTGTCTCAAAAAAA;RSEQ=AAAAAAAAAATGTTTAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:4:4,0:57,0:57,4:0.0645:1,0:16.8:1:31.3:1:1:0:60:8:0.0656:0.0323:0.3 0/1:33:2:2,0:30,1:31,2:0.0606:1,0:24.5:1:30.3:1:1:0:60:4:0.0606:0.0303:0 +6 117706757 . AT A 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.4075;SOR=0.28832;LSEQ=AGCATAAGTGGTGCACAGGT;RSEQ=TTAAAAAAAAAAAAGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:5:4,1:191,15:206,5:0.0236:2,2:16.8:1:29.4:1:0.3285:3.15585:60:10:0.0244:0.0142:0.6 0/0:145:1:1,0:138,6:144,1:0.0069:1,0:27:0:32:0:1:0:60:2:0.007:0:0 +6 117706760 . TA T 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.25164;SOR=0.70485;LSEQ=ATAAGTGGTGCACAGGTATT;RSEQ=AAAAAAAAAAAGAAATTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:38:36,2:161,19:180,38:0.1667:2,2:22.2:1:31.8:1:0.54345:2.12:60:76:0.1696:0.0307:0.6 0/1:162:20:18,2:130,6:136,20:0.1235:1,2:25.5:1:30.5:1:0.27264:2.38958:60:40:0.125:0.0123:0.2 +6 117707038 . G A 215 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01123;LSEQ=TCCATGTCTCAAAATAAAGT;RSEQ=AATGATTAGCAGTTATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:152:42,110:88,264:352,152:0.301:2,2:23.4:1:29.8:1:0.57937:1.15:60:37:0.2996:0:1.1 0/0:417:2:2,0:119,296:415,2:0.0048:2,0:1:0:23.5:1:0.0837:0:60:4:0.0048:0:1.5 +6 117707912 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03064;SOR=Inf;LSEQ=TTTCTTAACAGAATCACTGG;RSEQ=AGTAGAGTTCAGTCAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:90,0:90,0:0:1,0:28.9:1:32:1:1:0:59.7:29:1:0:0 0/1:42:3:3,0:38,1:39,3:0.0714:1,0:16.3:1:30:0:1:0:60:6:0.075:0:1 +6 117708692 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATCAATTATAGTGTTTC;RSEQ=TTAAAAAATATCTTGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:13,1:14,2:0.125:1,0:29:1:32.5:1:1:0:60:4:0.125:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:13:1:32:0:1:0:60:4:1:0:0 +6 117708971 . C T 186 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=92.53109;LSEQ=AGGGTAGTACCCACTGAGGG;RSEQ=TCTGACCAGGGGCCTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:815:1:1,0:461,353:814,1:0.0012:2,0:21:0:32:0:1:0:60:2:0.0012:0:1 0/1:861:88:52,36:426,347:773,88:0.1022:2,2:26.6:1:28.8:1:0.49888:1.18:60:87:0.1026:0:1.1 +6 117710369 . C CT 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54987;SOR=0;LSEQ=ATGCAGAACAAATGTATAAA;RSEQ=TTTTTTTTTAGCTAAGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:3,0:59,1:60,3:0.0476:1,0:18.7:1:32.3:1:1:0:60:6:0.0484:0.0317:0 0/0:28:0:0,0:26,2:28,0:0:2,0:18.2:1:32.6:1:1:0:60:56:1:0:0 +6 117710447 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49937;SOR=0;LSEQ=TCAAAATTGAATCACAACGC;RSEQ=AAGCAGTTCAAACCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:153,32:185,2:0.0107:2,2:16:1:28.5:1:0.32258:4.72366:60:4:0.0109:0:2 0/0:173:0:0,0:133,40:173,0:0:2,0:20.7:1:30:1:1:0:60:42.25:1:0:0.1 +6 117710476 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11997;SOR=Inf;LSEQ=CAAACCTTCCTCTTATTCCA;RSEQ=CAAGGCCAGTAACCACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:215,83:298,0:0:2,0:22.2:1:32.1:1:1:0:60:32.111:1:0:0.1 0/1:291:3:1,2:191,97:288,3:0.0103:2,2:21:1:28:1:0.26772:3.91818:60:6:0.0104:0:1 +6 117711059 . G A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13045;SOR=Inf;LSEQ=GATTCAGTCCAAAGGTTGAT;RSEQ=AGTAACCTCCTCAGCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:12,95:107,0:0:2,0:21.9:1:32:1:1:0:60:106:1:0:0.1 0/1:61:2:0,2:6,53:59,2:0.0328:2,0:5.5:1:29.5:1:1:0:60:4:0.0339:0:1 +6 117714346 . C G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.72246;LSEQ=TTTCTCAAAGATTATTTATT;RSEQ=CCAATGGAAGAGAATTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:49:35,14:266,104:370,49:0.1169:2,2:20:1:32:1:1:1.02302:60:98:0.1186:0:1.1 0/1:353:136:100,36:155,60:215,136:0.3853:2,2:24.4:1:30.9:1:0.80665:1.08:59.8:272:0.3864:0:1.1 +6 117717021 . AG T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATAGGGATTAGGGCAGAAA;RSEQ=TTATATGTATCCCTTAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:4,0:4,2:0.2857:0,0:19.5:1:30.8:1:1:0:60:4:0.2857:0.1429:0 0/0:3:0:0,0:2,1:3,0:0:2,0:10.3:1:28.3:1:1:0:60:6:1:0:0.7 +6 117717342 . G GA 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTAGCTAAAGGAAGAAGCCT;RSEQ=ACCCATACCTGCTGAAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:735:0:0,0:414,321:735,0:0:2,0:24.8:1:32.1:1:1:0:60:72.5:1:0:0.1 0/1:686:44:28,16:376,265:641,44:0.0641:2,2:25.4:1:29:1:0.635:1.23:60:88:0.0649:0.0131:0.1 +6 117718303 . A G 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06688;SOR=1.6366;LSEQ=GAAGAGATAATGGTGACATA;RSEQ=TGAGCAGAAAAATGTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:31:7,24:80,243:323,31:0.0876:2,2:30.8:1:32.3:1:1:1.12837:60:62:0.0888:0:1.2 0/1:265:36:9,27:74,155:229,36:0.1358:2,2:26.6:1:31.8:1:0.4432:1.43042:60:72:0.1364:0:1.1 +6 117718359 . G GT 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.79999;SOR=0.77796;LSEQ=ATAAGATGGAAAAAAGTCTT;RSEQ=TTTTTTTTTTTGAAAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:12:1,11:4,96:100,12:0.1062:1,2:26:1:29.4:1:0.4388:2.16:58.3:24:0.1143:0.0088:0.9 0/1:71:6:0,6:1,62:63,6:0.0845:1,0:28.2:1:30.5:1:1:0:60:12:0.0938:0:0.2 +6 117724207 . G A 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0069;SOR=0;LSEQ=TTGAATGGATCGATTAATAG;RSEQ=AAGGAATAGATTTATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:8:7,1:92,5:97,8:0.0762:2,2:11.1:1:31.1:1:0.38598:2.59429:60:16:0.0777:0:1.1 0/0:100:0:0,0:90,10:100,0:0:2,0:21.2:1:30.6:1:1:0:60:99:1:0:0.1 +6 117724277 . C T 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17093;SOR=5.35229;LSEQ=GCTTTGGAATAATGTCCTTT;RSEQ=ATAAGAAATGTGTGCACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:525:1:0,1:398,126:524,1:0.0019:2,0:1:0:27:0:0.2419:0:60:2:0.0019:0:1 0/1:395:4:1,3:269,122:391,4:0.0101:2,2:8.5:1:25.8:1:0.09558:6.58052:60:8:0.0103:0:1 +6 117724379 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.27231;LSEQ=CTGTGAAGATCCAAACCACT;RSEQ=GGAAAATGTACTCAGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:963:91:41,50:395,475:870,91:0.0945:2,2:28.2:1:30.2:1:1:1.01411:60:44.5:0.0933:0:1.2 0/1:869:24:8,16:405,440:845,24:0.0276:2,2:30:1:29.6:1:0.21334:1.83966:59.7:23:0.0267:0:1.3 +6 117724462 . C A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=3.49816;LSEQ=TAGATCAAGGAGTGATCAAT;RSEQ=ATCAGCATTATAGAATCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:37:12,25:81,288:369,37:0.0911:2,2:17.5:1:30.2:1:0.15406:1.70:60:74:0.092:0:1.6 0/1:350:91:25,66:79,180:259,91:0.26:2,2:23.5:1:29.1:1:0.68931:1.15816:60:90:0.2594:0:1.4 +6 117724489 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17159;SOR=Inf;LSEQ=ATTATAGAATCAGCACCCCA;RSEQ=ATTGGGACTAAAAAGCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:28,223:251,0:0:2,0:22.9:1:32.5:1:1:0:59.9:124.5:1:0:0.2 0/1:178:2:1,1:25,151:176,2:0.0112:2,2:6.5:1:28:1:0.2715:5.94:60:4:0.0114:0:1.5 +6 117724498 . TA T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=TCAGCACCCCACATTGGGAC;RSEQ=AAAAGCATAGATTAATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:7,180:187,2:0.01:1,2:11:0:33.5:1:0.08308:24.12:60:4:0.0101:0:0.5 0/0:130:0:0,0:8,81:89,0:0:2,0:21.3:1:30.2:1:1:0:60:88:0.6875:0:0.2 +6 117724499 . A C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=7.86127;LSEQ=CAGCACCCCACATTGGGACT;RSEQ=AAAAGCATAGATTAATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:11:0,11:7,180:187,11:0.055:1,0:29.2:1:32.5:1:1:0:60:22:0.0553:0:1.9 0/1:130:41:5,36:8,81:89,41:0.3154:2,2:23.7:1:30.9:1:0.54672:1.40:60:40:0.3125:0:1.8 +6 117724504 . G T 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=CCCCACATTGGGACTAAAAA;RSEQ=CATAGATTAATTTGTAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:6,170:176,0:0:1,0:23.5:1:32.5:1:1:0:59.9:34.2:1:0:0.2 0/1:120:9:2,7:11,100:111,9:0.075:2,2:16.1:1:28.2:1:0.25188:2.57:60:18:0.0769:0:1.1 +6 117725448 . T G 208 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GGCAGCCTTTCATACCTTAG;RSEQ=ATAAGTCCAGCTTCCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:895:0:0,0:497,398:895,0:0:2,0:27.3:1:28.6:1:1:0:59.8:37.913:1:0:0.2 0/1:948:120:61,59:425,401:826,120:0.1266:2,2:26:1:30.2:1:0.92236:1.02508:59.2:59:0.128:0:1.4 +6 117725578 . T A 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.60527;LSEQ=GAAGCAAAGGGAGCAGTTGG;RSEQ=AGGTCTGCATTTTCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:63:26,37:213,321:534,63:0.1055:2,2:26.2:1:30.4:1:0.89205:1.06:60:62:0.1054:0:1.5 0/1:529:158:67,91:147,220:367,158:0.2987:2,2:26.1:1:29.1:1:0.62927:1.10:60:78:0.2989:0:1.2 +6 117725622 . G A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04861;SOR=0.44714;LSEQ=AACAAGATTTCACTCACCAC;RSEQ=CACTCCTGTCCATCAGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:25:4,21:94,195:289,25:0.0796:2,2:21.1:1:29.8:1:0.11476:2.52451:60:24:0.0777:0:1.9 0/1:242:9:4,5:75,158:233,9:0.0372:2,2:13.4:1:27.4:1:0.47885:1.68:60:18:0.0386:0:2.1 +6 117725763 . ATCAG A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.01862;SOR=Inf;LSEQ=CAGTTTATTTTAAAAAATCA;RSEQ=TCAGTCTGTCAGTCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:41,0:0:1,0:23.7:1:29.6:1:1:0:60:19.5:1:0:0.4 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:12:1:31:1:1:0:60:4:0.2857:0.1429:0.5 +6 117730403 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.5;SOR=0;LSEQ=AAATAAATAAATAAAAAAGA;RSEQ=AGAAAAAAAACTGGCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:8.5:1:30.5:1:1:0:44.5:4:0.3333:0:2.5 0/0:3:0:0,0:1,2:3,0:0:2,0:37.7:1:28:1:1:0:60:6:1:0:0 +6 117730592 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=4.62432;LSEQ=TTTATCAGAATGGCCTATAC;RSEQ=TTTGAAATTATTGAATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:17:17,0:139,3:142,17:0.1069:1,1:25.6:1:30.8:1:1:0:60:34:0.1076:0:1.1 0/1:81:29:29,0:52,0:52,29:0.358:1,1:20.6:1:29:1:1:0:60:28:0.35:0:1.1 +6 117730673 . G A 186 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=110.44941;LSEQ=GATGTTTTGAGAGGTGTTTC;RSEQ=TTATCTTTACATAAGTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:773:1:1,0:527,244:771,1:0.0013:2,0:48:0:30:0:1:0:60:2:0.0013:0:1 0/1:638:80:54,26:365,189:554,80:0.1254:2,2:23.7:1:29.5:1:0.80212:1.08:60:160:0.1268:0:1.1 +6 117730819 . G A 189 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCCCGCTGTGGAAGACAG;RSEQ=GAGCATGACAGTCAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:687:0:0,0:207,480:687,0:0:2,0:24.5:1:30.7:1:1:0:59.9:35.158:1:0:0.1 0/1:514:78:19,59:149,287:436,78:0.1518:2,2:23.6:1:30.2:1:0.11519:1.61073:60:77:0.1522:0:1.1 +6 117730899 . T G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15763;SOR=0.43685;LSEQ=TAAAATCCGAATGCCTAATA;RSEQ=GCAAGTATATCTTTGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:15:0,15:8,141:149,15:0.0915:2,1:22.2:1:30.7:1:1:0:60:14:0.0875:0:1 0/1:119:5:0,5:10,103:113,5:0.042:2,0:23.4:1:28.8:1:1:0:60:10:0.0424:0:1 +6 117737337 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20927;SOR=Inf;LSEQ=CAAACTAGTTGAAAGCCAAT;RSEQ=GAAATGCAAATGGGAATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:179,40:219,0:0:2,0:24.4:1:32.2:1:1:0:60:72:0.9954:0:0.1 0/1:186:2:1,1:151,33:184,2:0.0108:2,2:12.5:1:26.5:1:0.33298:4.52288:60:4:0.0108:0:2 +6 117737390 . G A 183 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCTTGAAAGAAACATCA;RSEQ=TATCAAAATAGAAATCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:308,181:489,0:0:2,0:23.9:1:33:1:1:0:60:488:1:0:0.1 0/1:463:80:47,33:234,148:382,80:0.1728:2,2:20.9:1:29.1:1:0.70639:1.10987:60:160:0.1735:0:1.1 +6 117739772 . G A 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5657;SOR=3.03292;LSEQ=GAAATAACGTTGCCTCCTCC;RSEQ=CATTTTGTAACTCTAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:8,161:169,1:0.0059:1,0:48:0:32:0:1:0:60:2:0.006:0:1 0/1:113:2:1,1:15,96:111,2:0.0177:2,2:7:1:27:1:0.26422:6.23:60:4:0.0179:0:1 +6 117746637 . C T 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1707;SOR=5.35123;LSEQ=AACAATTCTATCAGTTATAA;RSEQ=AAGCTGAATGCTACATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:1:0,1:278,72:350,1:0.0028:2,0:1:0:23:0:0.20798:0:60:2:0.0029:0:1 0/1:265:4:1,3:205,56:261,4:0.0151:2,2:8.8:1:23.3:1:0.03561:10.8488:60:8:0.0153:0:1 +6 117746851 . G A 102 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00082;SOR=14.29581;LSEQ=TGGCAGATTTTTAGATGGCC;RSEQ=GTCTAATTTTCTCCATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:470:1:0,1:138,329:467,1:0.0021:2,0:35:0:19:0:1:0:60:0:0:0:5 0/1:371:11:4,7:115,245:360,11:0.0296:2,2:22.7:1:29.7:1:0.75028:1.22:60:22:0.0298:0:1 +6 117746919 . A T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00516;SOR=Inf;LSEQ=TTCAATTGGAGGAGTAGCTG;RSEQ=TGGATTTTGCTTTGTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:1,138:139,0:0:1,0:25.4:1:31.3:1:1:0:60:68.5:1:0:0.1 0/1:77:5:0,5:0,72:72,5:0.0649:1,0:22.8:1:27:1:1:0:60:4:0.0533:0:1.8 +6 117747602 . CCT C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTTCCTGCCTGCCTTCCTT;RSEQ=CTCTCTCTCTCTCTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:42.5:1:33:1:1:1:60:4:0.6667:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 118629787 . G T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36364;SOR=3.14348;LSEQ=GCCAAAGAGTTAAAAATATG;RSEQ=GAAAGTTTAATTACATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:0,1:159,71:230,1:0.0043:2,0:1:0:27:0:0.31169:0:60:2:0.0043:0:1 0/1:222:3:1,2:152,67:219,3:0.0135:2,2:11:1:25.7:1:0.22865:4.50281:60:6:0.0136:0:1 +6 118629865 . G T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1244;LSEQ=CATGGTTATTATGGTCACCT;RSEQ=ATGGCCACATATCCTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:411:364:174,190:24,23:47,364:0.8856:2,2:26.1:1:29.5:1:0.7569:1.13907:59.9:120.333:0.8848:0:1.1 0/1:400:196:91,105:102,102:204,196:0.49:2,2:24.3:1:28.4:1:0.48524:1.15343:60:64.333:0.4886:0:1.1 +6 119108265 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21847;SOR=Inf;LSEQ=ATCTCAGATCCTTCATAGTT;RSEQ=TTGACATTGTTCTCTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:112,30:142,0:0:2,0:23.5:1:31.8:1:1:0:60:34.5:0.9928:0:0.2 0/1:126:2:1,1:99,25:124,2:0.0159:2,2:11.5:1:32.5:1:0.37143:3.90266:60:4:0.0161:0:1 +6 119108363 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.163;LSEQ=ATAAAGATAAAGGCACATCA;RSEQ=GTGGCTAATGTGAGATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:399:334:174,160:28,36:64,334:0.8371:2,2:26.3:1:31:1:0.27488:1.40:60:166:0.8363:0:1.1 0/1:503:229:115,114:140,133:273,229:0.4553:2,2:26.8:1:30.2:1:0.85784:1.04342:60:113.5:0.4577:0:1.2 +6 119748114 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49811;SOR=Inf;LSEQ=CAGGCAGTCTACAAAGACTG;RSEQ=TGTTTTGTCAGTACCCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:114,18:132,0:0:2,0:21.8:1:32.2:1:1:0:60:32:1:0:0 0/1:133:2:0,2:110,21:131,2:0.015:2,0:7:1:27:1:0.02882:0:60:4:0.0152:0:1 +6 119748232 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00653;SOR=1.42756;LSEQ=TTAGTTTTTGAAAACGAAAT;RSEQ=TAACATGATAAACTGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:209:100,109:135,113:248,209:0.4573:2,2:24.5:1:31.8:1:0.18842:1.30144:60:51.25:0.4545:0:1.8 1/0:498:272:134,138:108,116:224,272:0.5462:2,2:26.2:1:30.9:1:0.85688:1.04:60:23.727:0.5426:0:1.8 +6 119748259 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04529;SOR=1.32382;LSEQ=GATAAACTGGAAGAAGAGAG;RSEQ=GTCCTACACGTATATCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:192:80,112:110,106:216,192:0.4694:2,2:25:1:30.7:1:0.07343:1.45146:60:31:0.465:0:1.9 1/0:430:232:103,129:82,114:196,232:0.5395:2,2:23.1:1:29.2:1:0.62501:1.11:60:115:0.5463:0:1.9 +6 120904528 . A T 59 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAAACCCTGATATCCTT;RSEQ=CTTCTACTTGGTTGATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:20.8:1:29.8:1:1:0:57.8:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 120905648 . G T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CAGCCTGGAGCTATAGAAAA;RSEQ=GGTGCCACCCTTCCCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:22.8:1:33:1:1:0:60:8:1:0:0.3 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:17.5:1:28.5:1:1:1:60:4:0.3333:0:1.5 +6 121788574 . T A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02411;SOR=4.62141;LSEQ=CAAGGAAAGAAATTACTTTA;RSEQ=AGTAAACCACTGGGACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:5,0:24,0:24,5:0.1724:1,0:16.2:1:31:1:1:0:60:10:0.1724:0:1 1/0:18:9:9,0:9,0:9,9:0.5:0,0:25.9:1:30.3:1:1:0:60:18:0.5:0:1 +6 121788627 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49897;SOR=0;LSEQ=TAAATACTGTGAAGGAGAAT;RSEQ=GCACTTCTGTGATTTAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:58,15:73,2:0.0267:2,2:14.5:1:29.5:1:0.38342:3.77602:60:4:0.0274:0:1 0/0:65:0:0,0:51,14:65,0:0:2,0:23:1:30:1:1:0:60:130:1:0:0.2 +6 121788731 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=0.43616;LSEQ=TGAAGCTAGAGATAAAAATG;RSEQ=TTATGAAATCAAGGTAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:180:101:49,52:39,40:79,101:0.5611:2,2:25.6:1:29.5:1:1:1.03451:59.7:19.2:0.5486:0:1.2 0/1:207:74:36,38:68,65:133,74:0.3575:2,2:26:1:28.7:1:0.77284:1.10374:60:148:0.3575:0:1.1 +6 121788786 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=ATTGATTTAGAAACCTTGAT;RSEQ=AAGAAGGAACAGAATAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:49,83:132,0:0:2,0:25.9:1:32:1:1:0:60:65:1:0:0.4 0/1:141:2:2,0:47,92:139,2:0.0142:2,0:47:1:32:1:0.11915:0:60:4:0.0143:0:1.5 +6 122329143 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49896;SOR=Inf;LSEQ=TACTCTGTACCTATTATACA;RSEQ=TCACCAAAAGCAGAGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:105,12:117,0:0:2,0:23.5:1:33:1:1:0:60:116:1:0:0.1 0/1:128:2:1,1:107,19:126,2:0.0156:2,2:24:1:28:1:0.28912:5.51465:60:4:0.0159:0:1 +6 122329217 . C T 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ATTTAAGTATTAAAATTAAC;RSEQ=TTGAGCATCAAATAGCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:242,139:381,0:0:2,0:23.8:1:31.8:1:1:0:60:62.5:1:0:0.8 0/1:433:19:13,6:255,159:414,19:0.0439:2,2:21.5:1:29.6:1:0.63497:1.35:60:38:0.0443:0:1 +6 122329267 . A G 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08828;LSEQ=CACAGAGTGAGGTTGTTTGG;RSEQ=TGGAAATTGAGGAAGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:596:540:276,264:23,29:52,540:0.906:2,2:27.5:1:31.3:1:0.38488:1.32:60:48.091:0.9074:0:1.2 0/1:638:293:140,153:173,171:344,293:0.4592:2,2:29.6:1:30.8:1:0.57786:1.10546:60:145.5:0.4619:0:1.2 +6 122329438 . C CT 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.03476;SOR=Inf;LSEQ=AGTTCTGGGATTTGATAACA;RSEQ=TTTTTTTTTCTTTTTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:0,48:48,0:0:1,0:23.7:1:33.4:1:1:0:60:96:1:0:0.1 0/1:38:4:0,4:0,34:34,4:0.1053:1,0:12.8:1:31:0:1:0:60:8:0.1053:0:0 +6 122329923 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24259;SOR=Inf;LSEQ=CACATTGTTATGTAGCAGAG;RSEQ=CAAACAGCAGTGAGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:122,31:153,0:0:2,0:22.4:1:29.7:1:1:0:60:152:1:0:0.7 0/1:149:2:1,1:104,43:147,2:0.0134:2,2:11.5:1:29.5:1:0.50481:2.40245:60:4:0.0135:0:1.5 +6 122329938 . G GA 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.95178;LSEQ=CAGAGACAAACAGCAGTGAG;RSEQ=AAAAAAAAAATTAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:8:6,2:147,48:195,8:0.039:2,2:24:1:29.6:1:1:1.02073:60:16:0.04:0.0049:1.1 0/1:215:8:5,3:136,70:206,8:0.0372:2,2:25.6:1:29.1:1:1:1.16485:60:16:0.0381:0:0.3 +6 122329970 . C A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08616;LSEQ=TAAAAAATTCATTCCACTAG;RSEQ=CTTCATTGTTGTGTAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:376:336:216,120:24,16:40,336:0.8936:2,2:24.4:1:29.6:1:0.60481:1.20:60:36.333:0.8934:0:1.1 0/1:439:184:121,63:155,99:254,184:0.4191:2,2:22.8:1:28.3:1:0.31808:1.23:60:29.667:0.4159:0:1.1 +6 122330162 . T C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00172;SOR=0.15846;LSEQ=GAATATAATAAGGAAATAGA;RSEQ=ACATTTCCTATGGTATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:42:0,42:0,6:6,42:0.875:0,1:23.5:1:33.3:1:1:0:60:84:0.875:0:1.1 1/0:27:14:0,14:0,13:13,14:0.5185:1,1:21:1:32.8:1:1:0:60:28:0.5185:0:1 +6 125257962 . A G 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GATGAAATTCTGTTGCTTTT;RSEQ=TAACTAAATTCTTGAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:54,2:56,0:0:1,0:25.1:1:29.1:1:1:0:60:112:1:0:0.3 0/1:34:10:9,1:23,1:24,10:0.2941:1,2:24.8:1:32.7:1:0.50802:2.47657:60:20:0.2941:0:1.1 +6 125258040 . G T 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.34512;LSEQ=TATAACACCTCAAACATTAT;RSEQ=ATATGGGACGGAACTGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:194:146:108,38:35,13:48,146:0.7526:2,2:25.5:1:30:1:1:1.06:60:35.5:0.7474:0:1.1 1/0:133:68:49,19:47,18:65,68:0.5113:2,2:23.9:1:29.3:1:1:1.01238:60:136:0.5113:0:1.1 +6 125258137 . C T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.49677;LSEQ=CAACTGTTTCAAATTATTAA;RSEQ=GGGAGACTTTAAAAACCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:443:298:139,159:73,72:145,298:0.6727:2,2:25.9:1:30.5:1:0.47946:1.15938:59.9:48.667:0.6713:0:1.1 1/0:402:203:100,103:93,103:196,203:0.505:2,2:26.9:1:29.7:1:0.76395:1.08:60:66.667:0.5025:0:1.2 +6 128960860 . T A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20908;SOR=Inf;LSEQ=TAATTTTTTAATTTAAAAAT;RSEQ=TCTAATGATTCTACTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:68,151:219,0:0:2,0:21.7:1:30.3:1:1:0:60:72:1:0:0.1 0/1:185:2:1,1:61,122:183,2:0.0108:2,2:15:1:24:1:1:1.99:60:4:0.011:0:1 +6 129478995 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0.34002;LSEQ=TAGATATCAGCCATGATGTA;RSEQ=GGCTGGAAGTGGTTTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:124:49,75:109,123:232,124:0.3483:2,2:28.7:1:30.9:1:0.18146:1.35523:22:61:0.3466:0:1.1 0/1:280:43:17,26:109,128:237,43:0.1536:2,2:28.6:1:30:1:0.50627:1.30117:22:86:0.1552:0:1.1 +6 129479232 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11506;SOR=0;LSEQ=GTGCCATACGTTTCTGTGTG;RSEQ=AGGTGGCACAGACCACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:3:2,1:56,67:123,3:0.0238:2,2:26:1:30.3:1:0.59409:2.38:20.7:6:0.0246:0:1 0/0:132:0:0,0:53,79:132,0:0:2,0:27.3:1:31.2:1:1:0:22.4:43:1:0:0.2 +6 129479237 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49816;SOR=Inf;LSEQ=ATACGTTTCTGTGTGCAGGT;RSEQ=GCACAGACCACAGGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:58,68:126,0:0:2,0:33.2:1:31.4:1:1:0:21.7:24.2:1:0:0.1 0/1:130:2:1,1:50,76:126,2:0.0154:2,2:32:1:31.5:1:1:1.51:22:4:0.0155:0:1 +6 129479376 . T G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22531;SOR=Inf;LSEQ=TGAGTCCAGGAACCTGTACC;RSEQ=TTAATATCTGCCGCTATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:26,0:0:2,0:34:1:31.8:1:1:0:49.2:52:1:0:0.4 0/1:24:2:1,1:8,14:22,2:0.0833:2,2:14:0:31:1:1:1.71:22:4:0.0833:0:1.5 +6 129480349 . T A 44 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25651;SOR=0;LSEQ=TTTAAATGACTGTCATTCAG;RSEQ=GAGATTTTCTTGTAAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:60,214:274,3:0.0108:2,2:5.7:1:28.3:1:0.12682:7.07:50:6:0.0109:0:1.3 0/0:226:0:0,0:60,166:226,0:0:2,0:16.2:1:28.8:1:1:0:53.2:55.5:1:0:0.1 +6 131790227 . G T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0142;SOR=0;LSEQ=CACAAAGGGAAAGAGGAGAG;RSEQ=CACCGATACGTGTTCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:3,2:39,2:41,5:0.1087:1,2:22:1:28.4:1:0.05279:11.59891:59.2:10:0.1163:0:1 0/0:59:0:0,0:52,7:59,0:0:2,0:23.3:1:31:1:1:0:59:118:1:0:0.1 +6 131790416 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.65036;LSEQ=GTTACCCAGCATGCTATTGG;RSEQ=TTTGTTGTAAACAAACAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:1,0:58,99:157,1:0.0063:2,0:1:0:26:0:0.37342:0:21:2:0.0064:0:1 0/1:192:2:1,1:65,125:190,2:0.0104:2,2:10.5:1:27:1:1:1.92:31.5:4:0.0106:0:1 +6 132626885 . G C 66 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=4.91839;LSEQ=TGAAGTGAACACCCAGCAAA;RSEQ=TGCAGCAGCCCTACAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:1,2:3,1:0.25:2,0:11:0:35:0:1:0:60:2:0.25:0:1 1/0:6:4:2,2:1,1:2,4:0.6667:2,2:9.5:1:33.3:1:1:1:45.5:8:0.6667:0:1.3 +6 132627132 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATCGCTCCATCAAGGGTG;RSEQ=AGAACTAGATGGAGGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:33.5:1:27:1:1:1.41418:45:4:0.2857:0:1 +6 132840195 . G C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18494;SOR=0.35928;LSEQ=ATCTTGGCAAGAATCATGCC;RSEQ=TTAACTTGTTTGTTTACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:20:15,5:5,2:7,20:0.7407:2,2:25:1:32.1:1:1:1.19:60:40:0.7407:0:1.1 1/0:16:8:5,3:4,4:8,8:0.5:2,2:33.6:1:30.8:1:1:1.61:60:16:0.5:0:1.6 +6 132840197 . T A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00319;SOR=Inf;LSEQ=CTTGGCAAGAATCATGCCGT;RSEQ=AACTTGTTTGTTTACAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:23,7:30,0:0:2,0:23.2:1:30.4:1:1:0:60:60:1:0:0.7 0/1:16:5:3,2:6,5:11,5:0.3125:2,2:38.8:1:29.2:1:1:1.23:60:10:0.3125:0:2 +6 132840201 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54667;SOR=0;LSEQ=GCAAGAATCATGCCGTTAAC;RSEQ=TGTTTGTTTACAACAGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:23,9:32,2:0.0588:2,2:11:1:30.5:1:0.50802:2.47657:60:4:0.0588:0:1.5 0/0:17:0:0,0:10,7:17,0:0:2,0:26.3:1:30.7:1:1:0:60:34:1:0:0.9 +6 132840339 . G A 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00056;SOR=Inf;LSEQ=ACGGTATAACCTTTCTTGTA;RSEQ=ATTCGCATGTATGTGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:8,14:22,0:0:2,0:28.3:1:32:1:1:0:60:44:0.9565:0:0 0/1:23:10:5,5:6,7:13,10:0.4348:2,2:26.7:1:29.1:1:1:1.16:56.9:20:0.4348:0:1.2 +6 132840396 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50175;SOR=Inf;LSEQ=TTTCTAAAAGGCCTAGAGAA;RSEQ=ATGTATCAGGTGCCTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:23,0:0:2,0:24.5:1:33.2:1:1:0:57.6:46:1:0:0 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:16:1:26.5:1:1:1.07:60:4:0.0645:0:1.5 +6 133309056 . C T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12449;SOR=0;LSEQ=AGTCCTGTAGCTGAAGTCAG;RSEQ=CATAAGTGAAGTCCAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:4:1,3:84,58:142,4:0.0274:2,2:16.5:1:29.8:1:0.30862:4.30279:60:8:0.0278:0:1 0/0:131:0:0,0:73,58:131,0:0:2,0:21.1:1:30.7:1:1:0:60:262:1:0:0.2 +6 134758313 . A T 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATACTTAAGATTTGTTAA;RSEQ=CCTTATCCCTGGTCAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:465:0:0,0:236,229:465,0:0:2,0:25.5:1:30:1:1:0:60:65.429:1:0:0.1 0/1:492:34:14,20:232,225:457,34:0.0691:2,2:24.6:1:29.7:1:0.29259:1.47185:60:68:0.0697:0:1.1 +6 134758428 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17765;SOR=Inf;LSEQ=ATTTTTGTAATTCCTTTTAT;RSEQ=TAATGGAACTATTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:7,98:105,0:0:2,0:22.1:1:33:1:1:0:60:104:1:0:0 0/1:77:2:1,1:6,69:75,2:0.026:2,2:28.5:1:26:1:0.17464:10.72:60:4:0.0263:0:1 +6 136294983 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01082;LSEQ=TTAGAAGATGCCCATTTGAA;RSEQ=GGTAACACTTTAGTTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:110:59,51:129,117:246,110:0.309:2,2:27.4:1:30.7:1:0.9086:1.05:60:109:0.307:0:1.1 0/1:363:113:55,58:120,130:250,113:0.3113:2,2:26.3:1:29.7:1:0.91023:1.03:60:226:0.3156:0:1.1 +6 136295052 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19496;SOR=Inf;LSEQ=CATCAGCTGCATGTGCTGCC;RSEQ=TGCTATTCATGCCCCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:57,146:203,0:0:2,0:22.2:1:30.8:1:1:0:60:202:1:0:0.3 0/1:161:2:1,1:47,112:159,2:0.0124:2,2:23.5:1:28.5:1:0.5087:2.37:60:4:0.0126:0:1 +6 136359280 . C CG 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.54747;SOR=0.36853;LSEQ=CGAAGCTGGAGAGGATCTTA;RSEQ=GGGGGTTCGCTTTTCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:2,2:0.5:2,0:11:1:31.5:1:1:0:60:4:0.5:0.25:0.5 0/1:8:2:2,0:5,1:6,2:0.25:2,0:25.5:1:31.3:1:1:0:60:4:0.25:0.125:0 +6 136359300 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47826;SOR=0;LSEQ=CGGGGGTTCGCTTTTCCCTG;RSEQ=CTGGGAAGAATTTCCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:7,3:10,2:0.1667:2,2:10.5:1:28.5:1:1:2.16028:60:4:0.1667:0:1.5 0/0:12:0:0,0:8,4:12,0:0:2,0:14.2:1:30.2:1:1:0:60:24:1:0:0.1 +6 136359323 . TAGCAGC T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=6.000;MSILEN=3;SSF=0.22857;SOR=Inf;LSEQ=GGGAAGAATTTCCCCTGTGG;RSEQ=AGCAGCAGCAGCAGAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:12,5:17,0:0:2,0:26.1:1:29.3:1:1:0:60:34:1:0:0.3 0/1:18:3:1,2:8,7:15,3:0.1667:2,2:13.3:1:27.3:1:1:2.18465:58.3:6:0.1667:0.0556:0.3 +6 136359367 . ACAG A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.23765;SOR=Inf;LSEQ=CAGAAACAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,10:23,0:0:2,0:26.3:1:33.4:1:1:0:60:46:0.9583:0:0.3 0/1:27:3:1,2:12,12:24,3:0.1111:2,2:38.3:1:33:1:1:1.95076:60:6:0.1111:0:0 +6 136359446 . A C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23636;SOR=0;LSEQ=AGAATGCCTGTGCTAGAGCG;RSEQ=TATTTCCACCCAGCAGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:0,4:4,3:0.4286:0,2:19.7:1:33.7:1:0.42857:0:60:6:0.4286:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:22.8:1:28.3:1:1:0:60:8:1:0:0 +6 137519127 . C T 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=Inf;LSEQ=AATTAAAGCAGAAAACTGTC;RSEQ=AGGAAAATCAGACTTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:275,121:396,0:0:2,0:25.4:1:31.4:1:1:0:60:55.571:1:0:0.1 0/1:417:14:9,5:269,134:403,14:0.0336:2,2:25.4:1:29.1:1:1:1.11496:60:28:0.0341:0:1 +6 137519154 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03252;SOR=Inf;LSEQ=ATCAGACTTCAAAGTTGGTG;RSEQ=AACTTAGCTGATCTCATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:524:0:0,0:334,189:523,0:0:2,0:25.5:1:32.3:1:1:0:60:73.714:0.9981:0:0.1 0/1:591:6:2,4:356,229:585,6:0.0102:2,2:17.5:1:26:1:0.21875:3.1031:60:12:0.0103:0:1 +6 137519504 . ACT A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.07265;SOR=2.27686;LSEQ=TTACTACTTAAAGGTGAAGA;RSEQ=CTCTCTCTCTATTGGAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:8:4,4:380,266:646,8:0.0122:2,2:29.1:1:32.6:1:0.72344:1.42775:60:16:0.0124:0.0015:0.1 0/1:656:18:10,8:357,279:636,18:0.0274:2,2:24.8:1:29.6:1:1:1.02363:60:17:0.0264:0.0076:0.5 +6 137519588 . A C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31567;LSEQ=GTCACCACTTCTGTTATACT;RSEQ=GAAAGTTCTTCTGTATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:270:129,141:360,339:699,270:0.2784:2,2:25.2:1:31:1:0.31606:1.16055:60:540:0.2818:0:1.1 0/1:931:101:51,50:429,400:829,101:0.1085:2,2:23.3:1:29.9:1:0.83354:1.05144:60:100:0.1087:0:1.1 +6 137519780 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.04488;LSEQ=CTTCTTACCACAGAGATCTA;RSEQ=GGGGAGAAAAATTGATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:124:38,86:37,112:149,124:0.4542:2,2:25.5:1:30.4:1:0.34061:1.34:60:61:0.4569:0:1.2 0/1:307:11:3,8:106,190:296,11:0.0358:2,2:19.3:1:30:1:0.75207:1.48591:60:22:0.0364:0:1 +6 137519834 . C CA 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.06049;SOR=0;LSEQ=TAAGCTTAAGTGCCTACCCT;RSEQ=AAAAAAAACAAAGGTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:0,5:15,94:109,5:0.0439:2,0:32.4:1:31.8:1:1:0:60:10:0.0446:0.0088:0.4 0/0:106:0:0,0:20,85:105,0:0:2,0:23:1:31.5:1:1:0:60:210:1:0:0.1 +6 137521825 . TA T 101 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.57738;LSEQ=ACCGTGTTTTTCCCTGAGAA;RSEQ=AAAAAAAAAACAAAATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:9,0:4,0:4,9:0.6429:0,0:22.7:1:32.1:1:1:0:59.4:18:0.6429:0:0.1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:19:0:32:0:1:0:60:2:0.5:0:1 +6 137522190 . T C 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10513;SOR=Inf;LSEQ=TTACAATTAAGATGGAATAC;RSEQ=GCTATTATCTATCAAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:52,173:225,0:0:2,0:22.3:1:30.5:1:1:0:60:55.25:1:0:0.1 0/1:203:3:1,2:54,146:200,3:0.0148:2,2:10.7:1:22.7:1:1:1.35:60:2:0.0101:0:2.3 +6 137524613 . G GA 77 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.31895;SOR=2.26738;LSEQ=TACTGCTCCCTCTATATTTA;RSEQ=AAAAAAAATGGCAAGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:373:3:2,1:264,105:369,3:0.008:2,2:16.3:1:32:1:1:1.25637:60:6:0.0081:0.0027:1 0/1:332:6:4,2:218,105:323,6:0.0181:2,2:38.5:1:29.8:1:1:1.03796:60:12:0.0183:0:0 +6 137524760 . C T 141 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=28.65406;LSEQ=TTCAGTGAGGATACTGGAAT;RSEQ=GCTAACTGGCACTGAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:704:1:0,1:281,421:702,1:0.0014:2,0:1:0:29:0:1:0:60:2:0.0014:0:1 0/1:663:26:15,11:295,341:636,26:0.0392:2,2:23:1:30.2:1:0.3171:1.58:60:52:0.0395:0:1.1 +6 137524803 . G A 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06197;SOR=Inf;LSEQ=CACAATCATCTTCCTTCTGC;RSEQ=TGAGTATTTTATACTGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:479:0:0,0:148,331:479,0:0:2,0:26.4:1:31.5:1:1:0:60:46.9:1:0:0.1 0/1:492:5:2,3:172,315:487,5:0.0102:2,2:19.6:1:28.2:1:1:1.22:55.2:4:0.0083:0:1.4 +6 137524851 . G A 37 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62371;SOR=0.34193;LSEQ=AAAAAGAAAACAGTGAAAAT;RSEQ=CACAGCTTCTTTTAATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:1,2:64,193:257,3:0.0115:2,2:15.3:1:23.7:1:1:1.51:60:2:0.0082:0:3.3 0/0:252:1:1,0:70,181:251,1:0.004:2,0:1:0:22:0:0.28175:0:60:2:0.0041:0:1 +6 137525423 . G T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01793;SOR=Inf;LSEQ=TACAGAAAGGAACAACTTTT;RSEQ=CTAGCTACACAAGAATTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:0:0,0:314,75:389,0:0:2,0:23.1:1:32.3:1:1:0:59.9:76.8:1:0:0.1 0/1:317:5:2,3:228,83:311,5:0.0158:2,2:27.4:1:26.4:1:0.12653:4.09838:60:10:0.0159:0:1 +6 137527446 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11151;SOR=Inf;LSEQ=TCCATTCTGAATTCTTAACA;RSEQ=TAAAAAGAATAAAAAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:44,206:250,0:0:2,0:25.9:1:33.2:1:1:0:59.9:82.333:1:0:0.1 0/1:233:3:1,2:48,182:230,3:0.0129:2,2:32.3:1:24:1:0.50922:1.89:60:2:0.0087:0:1.7 +6 137527456 . TA T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.0481;SOR=Inf;LSEQ=ATTCTTAACACTAAAAAGAA;RSEQ=AAAAAATGCGAAGATAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:36,178:214,0:0:2,0:25.2:1:31:1:1:0:59.9:428:1:0:0.1 0/1:190:4:2,2:37,149:186,4:0.0211:2,2:12.5:1:32:0:0.18733:3.99:60:8:0.0211:0:0.3 +6 137536262 . T G 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2437;SOR=Inf;LSEQ=TCCCGTGAGGGAGACAATGT;RSEQ=ACCATACATATTTTACCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:59,0:0:1,0:25.1:1:31.5:1:1:0:60:58:1:0:0.1 0/1:60:3:3,0:56,1:57,3:0.05:1,0:21.3:1:33:0:1:0:60:6:0.05:0:1 +6 137536455 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.50506;LSEQ=ATTTTCTGGTGACTTCAAAA;RSEQ=CATCTGCTTCAGGTAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:173:73,100:181,217:398,173:0.303:2,2:26.2:1:29.8:1:0.52137:1.14234:60:172:0.306:0:1.1 0/1:578:104:52,52:210,263:473,104:0.1799:2,2:23.8:1:29.1:1:0.32813:1.25:60:103:0.1807:0:1.1 +6 137536517 . G A 49 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18517;SOR=4.75443;LSEQ=ACAATTATATTATGGCCACT;RSEQ=CAAAAGTTGAACAATGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:1:0,1:40,202:242,1:0.0041:2,0:46:0:29:0:1:0:60:2:0.0042:0:5 0/1:207:4:2,2:42,161:203,4:0.0193:2,2:11:1:24.8:1:0.19897:3.80:60:8:0.0196:0:1 +6 137536519 . A G 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.60123;SOR=2.28717;LSEQ=AATTATATTATGGCCACTGC;RSEQ=AAAGTTGAACAATGCATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:0,1:33,195:228,1:0.0044:2,0:44:0:15:0:1:0:60:0:0:0:5 0/1:201:2:1,1:42,157:199,2:0.01:2,2:41:1:29.5:1:0.38294:3.71:60:4:0.01:0:1 +6 137539423 . AAAAAG A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0;SOR=0.12258;LSEQ=GAATCATAAATCATAATAAA;RSEQ=AAAACTGAATTGAAAAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:48:48,0:45,1:46,48:0.5161:1,1:22.8:1:30.8:1:0.48936:0:59.8:96:0.5161:0.1183:0.8 0/1:70:8:8,0:62,0:62,8:0.1143:1,0:17:1:30.2:1:1:0:60:16:0.1143:0.0429:0.8 +6 137539505 . C G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26622;LSEQ=TGCACTTCAGAAAAGCCACC;RSEQ=TCAACATTTGTTTTCTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:172:125,47:140,61:201,172:0.4611:2,2:24.3:1:30.6:1:0.56753:1.16:60:171:0.4647:0:1.1 0/1:421:78:59,19:229,113:342,78:0.1853:2,2:24.8:1:29.6:1:0.17608:1.53:60:156:0.1875:0:1.1 +6 137539726 . TC T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.21997;SOR=1.97154;LSEQ=CCTACCCTAAGCACTTTGAG;RSEQ=CCCCCCCCCACCCCCGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:8:0,8:1,92:93,8:0.0777:1,0:35.3:1:32.8:1:1:0:58.5:16:0.0879:0:0.6 0/1:77:11:0,11:3,63:66,11:0.1429:1,0:25.4:1:30.2:1:1:0:58.2:22:0.1528:0:1.5 +6 137539810 . G A 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.39513;SOR=2.458;LSEQ=TGCTGATCAGGACACTCACA;RSEQ=TCATGCGTCACTTAACGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:19,5:0.2083:1,0:18:1:31.2:1:1:0:60:10:0.2083:0:1.2 0/1:10:4:0,4:0,6:6,4:0.4:0,0:22.8:1:29.8:1:1:0:60:8:0.4:0:1.5 +6 137539947 . C A 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTCATGAACCTGTACAGC;RSEQ=TGTCACTGCACTGAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:27:1:31:1:1:1.7321:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 137540335 . C T 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.13883;LSEQ=CTGGGGCGGATCCCTCCCTC;RSEQ=CTCTCGTCCCGACCCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:262:183,79:235,100:335,262:0.4389:2,2:23.2:1:30.6:1:1:1.01446:59.8:20.833:0.431:0:2 0/1:450:44:36,8:281,125:406,44:0.0978:2,2:21.9:1:30.2:1:0.08506:2.00:60:43:0.0971:0:2.2 +6 137540370 . A G 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.42903;LSEQ=CGGCCGCAGCCCTGCCGCGA;RSEQ=CGACGGTACCTGAGGACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:920:649:373,276:160,109:269,649:0.7054:2,2:26.2:1:32.4:1:0.60725:1.08604:59.9:48.923:0.7051:0:1.5 1/0:902:457:259,198:251,190:441,457:0.5067:2,2:25.5:1:30.9:1:0.94639:1.00991:60:34.154:0.504:0:1.3 +6 137540481 . G A 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15447;SOR=3.5003;LSEQ=CCATGCTGCTACCGACGGTC;RSEQ=CTGGCTCCAACCCCGAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:2:2,0:166,362:528,2:0.0038:2,0:1:0:25:0:0.10007:0:60:4:0.0038:0:1 0/1:458:6:4,2:153,299:452,6:0.0131:2,2:15:1:25.7:1:0.18747:3.90:60:5:0.011:0:1 +6 137540520 . A G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=0.45481;LSEQ=GCCTGCGGGACCAGCCCAGC;RSEQ=CTGCCCTCCAGCCCCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:273:189:27,162:9,75:84,189:0.6923:2,2:24.4:1:31.7:1:0.56122:1.39:60:36.8:0.6891:0:1.4 1/0:188:95:20,75:12,80:92,95:0.5053:2,2:26.2:1:31:1:0.17559:1.77:60:46.5:0.5:0:1.1 +6 137540536 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08232;LSEQ=CAGCACTGCCCTCCAGCCCC;RSEQ=GCCTTACGTCACTTCCGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:67:5,62:22,125:147,67:0.3131:2,2:26.1:1:31.4:1:0.18184:2.17539:60:21.333:0.3048:0:2.1 0/1:139:5:0,5:14,120:134,5:0.036:2,0:20.6:1:31:1:1:0:60:10:0.0362:0:1.8 +6 137723086 . C T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGATCCCTTTCTTTGTTA;RSEQ=AGGAATGTTGTTGCCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:19.7:1:30.7:1:1:0:59.7:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 137723110 . T C 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTTGTTGCCTTAAATTA;RSEQ=TCTTGTTAATGCTATGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:27.7:1:32.7:1:1:0:59.7:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 137723291 . C T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AATTATATCTTCTTATAATC;RSEQ=TTGTCTTTATTTTTTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:7,0:7,0:7,7:0.5:0,0:18.9:1:33.4:1:1:0:60:14:0.5:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:17:0:32:0:1:0:60:4:0.5:0:1 +6 137723535 . G GT 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0077;SOR=0.55436;LSEQ=TTTATGTTTAAACAAACACG;RSEQ=TTTTTTTTAATAATGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:65:27,38:112,130:242,65:0.205:2,2:27.6:1:30.3:1:0.57493:1.21178:59.4:64:0.2051:0:1.2 0/1:328:41:20,21:118,113:231,41:0.125:2,2:30.2:1:28.6:1:0.8659:1.09609:60:40:0.1238:0.003:1.3 +6 137723544 . A T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17953;LSEQ=AAACAAACACGGTTTTTTTT;RSEQ=ATAATGAAATTGAGTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:273:116,157:14,20:34,273:0.8806:2,2:24.8:1:29.5:1:1:1.06:59.8:135.5:0.8827:0:1.2 1/0:311:177:81,96:33,32:65,177:0.5691:2,2:26.6:1:28.8:1:0.56156:1.2212:60:176:0.5714:0:1.3 +6 137723575 . T C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGTTTCCTCCTGCACATA;RSEQ=TTGATTTTTATGTTCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:91,154:245,0:0:2,0:24.1:1:30.5:1:1:0:60:80.667:1:0:0.7 0/1:236:22:10,12:86,128:214,22:0.0932:2,2:26.7:1:30.2:1:0.65402:1.24:60:21:0.0913:0:2.2 +6 137723595 . G T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23086;SOR=Inf;LSEQ=TTTGATTTTTATGTTCATCT;RSEQ=TGCACTTGCCTAAACTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:63,130:193,0:0:2,0:25.5:1:32:1:1:0:59.8:31.167:1:0:0.6 0/1:179:2:1,1:65,111:176,2:0.0112:2,2:18:0:28:1:1:1.70:60:4:0.0114:0:3.5 +6 137723722 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04435;SOR=Inf;LSEQ=TTCAGAAAAAAAGGTTTGAA;RSEQ=AGACAAGCACTATTGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:1,19:20,0:0:1,0:21.6:1:28.5:1:1:0:60:40:1:0:0.1 0/1:12:3:0,3:0,9:9,3:0.25:0,0:22:1:31:1:1:0:60:6:0.25:0:1.3 +6 138026354 . G A 61 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGAGAGGTCTAGCTACCCT;RSEQ=CCAGCCAGCCACTGAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1:0,2:30:1:26.6:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 138026532 . T C 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49761;SOR=0;LSEQ=GAAAGTCCACATCTGTGGAC;RSEQ=TTCTGTGCTGAAGTTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:58,25:83,2:0.0235:2,2:6.5:1:31.5:1:0.52073:2.2945:60:4:0.0238:0:1.5 0/0:79:0:0,0:56,22:78,0:0:2,0:24:1:29.8:1:1:0:60:77:0.9872:0:0.1 +6 138026552 . A G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50006;SOR=0;LSEQ=TTTCTGTGCTGAAGTTTTCC;RSEQ=GGTTTTCTCATGTGAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:80,35:115,2:0.0171:2,2:29:0:32.5:1:0.52255:2.26782:60:4:0.0175:0:1.5 0/0:102:0:0,0:69,33:102,0:0:2,0:26.7:1:29.3:1:1:0:60:204:1:0:0.1 +6 138026868 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19134;SOR=Inf;LSEQ=CACTGTGTGGATGGTTTTGA;RSEQ=AAGGTCAATGTTGCAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:101,153:254,0:0:2,0:22.2:1:32.7:1:1:0:59.9:126:1:0:0.1 0/1:198:2:1,1:81,114:195,2:0.0101:2,2:12:1:29.5:1:1:1.40:60:4:0.0102:0:1 +6 138026895 . T A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.19094;SOR=Inf;LSEQ=AATGTTGCAGTTAATACCTT;RSEQ=CTCTCTGATGATGTCAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:118,112:230,0:0:2,0:24.3:1:30.7:1:1:0:59.8:56.5:1:0:0.1 0/1:179:2:1,1:82,94:176,2:0.0112:2,2:21:0:27:1:1:1.15:60:4:0.0114:0:1 +6 138027115 . C A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49558;LSEQ=ACCGTTCTCGCCATATTCCC;RSEQ=TGGAGTACAGCTTGTCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:407:237:105,132:72,97:169,237:0.5823:2,2:26.4:1:30.8:1:0.76129:1.07:59.4:58.25:0.5825:0:1.7 0/1:382:156:64,92:90,135:225,156:0.4084:2,2:23.9:1:29.3:1:0.91549:1.04:59.3:51:0.408:0:1.8 +6 138027145 . C T 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCTTGTCCAACCTTTGAAAA;RSEQ=TTAAGTTCTCTTAGCATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:329:329:144,185:0,0:0,329:1:0,2:25.5:1:30.8:1:1:0:60:81.25:1:0:1.5 1/0:280:159:70,89:42,79:121,159:0.5679:2,2:24:1:29.5:1:0.13949:1.48:59.7:25.5:0.5604:0:1.7 +6 138027229 . C T 195 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCATATTCTTGTAGAGCATC;RSEQ=TCTTCAGACCAGTATTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:121,135:256,0:0:2,0:24.1:1:32.5:1:1:0:59.8:127:1:0:0.2 0/1:230:90:52,38:82,58:140,90:0.3913:2,2:22.1:1:30.1:1:1:1.03303:59.2:89:0.3904:0:1 +6 138027662 . A G 305 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAATTTGCTTAGTTCTCAA;RSEQ=CTCTGCTTTCTATTTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:664:664:302,362:0,0:0,664:1:0,2:25.4:1:32.6:1:1:0:46.6:59.364:1:0:1.1 1/0:682:382:176,206:147,151:298,382:0.5601:2,2:25.5:1:31.1:1:0.43906:1.13923:47.1:75.4:0.5635:0:1.1 +6 138027772 . G A 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.43138;LSEQ=TTCTTCTTGTAATGTTCCAC;RSEQ=AGATCCGTCAAAGAATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:597:594:290,304:0,0:0,594:0.995:0,2:26.2:1:30.8:1:1:0:42.9:98:0.9949:0:1.1 1/1:569:567:264,303:0,1:1,567:0.9965:0,2:26.2:1:30:1:1:0:42.4:282.5:0.9965:0:1.1 +6 138027910 . A G 216 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGTGCGCACAGAGAGAAC;RSEQ=AAATCTCCAGGGTGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:134:62,72:226,266:492,134:0.2137:2,2:28.8:1:30.7:1:1:1.01:54.6:32.5:0.2124:0:1.1 0/0:586:0:0,0:281,304:585,0:0:2,0:26.7:1:29.7:1:1:0:58.1:145.25:0.9983:0:0.2 +6 138028127 . G T 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATACTGGACCAACTCAGCC;RSEQ=AAGTGGCAAACTTTTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:734:0:0,0:376,358:734,0:0:2,0:25.9:1:31:1:1:0:59.7:103.857:1:0:0.1 0/1:652:58:31,27:294,299:593,58:0.089:2,2:27.3:1:28.8:1:0.58535:1.17:51.1:116:0.0902:0:1.9 +6 138028152 . C T 213 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=72.30981;LSEQ=GGCAAACTTTTCCCCCCAAA;RSEQ=GGGTCCTAGTAATCACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:713:3:1,2:361,348:709,3:0.0042:2,2:12.7:1:27.7:1:0.61823:2.07265:60:6:0.0043:0:1 0/1:635:149:71,78:250,235:485,149:0.2346:2,2:26.8:1:29.6:1:0.45372:1.16842:56.5:298:0.2365:0:1.4 +6 138028543 . A C 77 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTAACCGGGAGTGGAGGCTG;RSEQ=GGCGGGAGGATCACTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1:0,2:24.2:1:29.8:1:1:0:60:12:1:0:1.2 1/0:2:1:0,1:0,1:1,1:0.5:0,0:50:0:29:0:1:0:60:2:0.5:0:2 +6 138192324 . CT C 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.08828;SOR=2.07391;LSEQ=AAGTCAGGCTAATAGAATGG;RSEQ=TTTTTTTTTTCCTTTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:11:10,1:115,6:121,11:0.0833:1,2:32.5:1:31.5:1:0.46423:1.90476:60:10:0.0775:0:0.2 0/1:88:14:12,2:68,5:73,14:0.1591:2,2:24.6:1:32.1:1:0.31331:2.24031:60:28:0.1628:0.0114:0.3 +6 138192335 . TC T 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.1507;SOR=0;LSEQ=ATAGAATGGCTTTTTTTTTT;RSEQ=CTTTCCTTTTCAGGTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:4:3,1:140,19:159,4:0.0245:2,2:17.3:1:24.3:1:0.41072:2.4378:60:3:0.0195:0.0123:2.8 0/0:110:0:0,0:95,14:109,0:0:2,0:24.8:1:29.9:1:1:0:59.9:17.167:1:0:0.2 +6 138192670 . T C 186 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=54.631;LSEQ=AAAACGAACGGTAAGACTTG;RSEQ=TCTGTTGTGTTTCTTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:1:1,0:128,233:361,1:0.0028:2,0:24:0:13:0:0.35635:0:56:0:0:0:4 0/1:510:67:22,45:173,266:439,67:0.1314:2,2:26.7:1:30.8:1:0.34653:1.32958:60:32.5:0.1305:0:1.1 +6 138192728 . A T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49857;SOR=Inf;LSEQ=CTGCTGGATCCCCATTCATG;RSEQ=AGCTTTAATAGGACAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:24,118:142,0:0:2,0:24.6:1:30.4:1:1:0:60:46.333:1:0:0.2 0/1:149:2:1,1:20,127:147,2:0.0134:2,2:7:1:27.5:1:0.26283:6.22:60:4:0.0136:0:1 +6 138192730 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23157;SOR=0;LSEQ=GCTGGATCCCCATTCATGAA;RSEQ=CTTTAATAGGACAAGCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:20,113:133,2:0.0148:2,2:24.5:1:29:1:0.28789:5.54:60:4:0.015:0:1 0/0:145:0:0,0:20,125:145,0:0:2,0:21.7:1:31:1:1:0:60:28:1:0:0.3 +6 138192745 . G A 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24684;SOR=Inf;LSEQ=ATGAAGCTTTAATAGGACAA;RSEQ=CCCAAACTCAAATCAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:6,88:94,0:0:2,0:28.3:1:32.2:1:1:0:60:30.333:1:0:0.1 0/1:100:3:0,3:6,91:97,3:0.03:2,0:29:1:29.3:1:1:0:60:6:0.03:0:2 +6 138192761 . A G 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.33903;SOR=3.51729;LSEQ=ACAAGCCCAAACTCAAATCA;RSEQ=TCTTGAGATTTAGTATTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:1:1,0:1,77:78,1:0.0127:1,0:1:0:31:0:0.02532:0:60:2:0.0132:0:1 0/1:69:3:0,3:1,65:66,3:0.0435:1,0:13:1:32.7:1:1:0:60:6:0.0441:0:2 +6 138195402 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTAATTCCGTGTTGTCAA;RSEQ=ACGACTTTCCACACCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:31.5:1:1:0:60:4:1:0:2.5 +6 138195418 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATACGACTTTCCACACC;RSEQ=GGAGAGGAAACTCCCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:28:1:1:0:60:4:1:0:2.5 +6 138195693 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGAACTTAAGGAATTTCC;RSEQ=CCAGGTCACCTAAACTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:14:1:32.5:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 138195961 . TCTC T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=0.26951;LSEQ=TAACTTGACTTTCCTTCTCT;RSEQ=CTCCTTTCTGTCCTCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:289:244:180,64:36,11:47,244:0.8443:2,2:25.5:1:32.4:1:0.8556:1.16307:60:243:0.8438:0.1453:0.2 1/0:354:210:145,65:102,43:145,210:0.5932:2,2:24.7:1:30.7:1:0.81541:1.0632:59.9:420:0.5949:0.096:0.3 +6 138196066 . T G 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTACTGAGGAAGGCGCTGT;RSEQ=CAGCACGCTCAAGGAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:713:0:0,0:387,325:712,0:0:2,0:24.3:1:30.4:1:1:0:60:78.111:0.9986:0:0.1 0/1:804:40:22,18:417,347:764,40:0.0498:2,2:29.1:1:30.9:1:1:1.02:60:19:0.0483:0:1.2 +6 138196723 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19889;SOR=Inf;LSEQ=TGAAAGGGGAAAAAATAAGC;RSEQ=GAGTTATATAAATGAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:129,12:141,0:0:2,0:24.9:1:31.6:1:1:0:60:19.143:1:0:0 0/1:114:2:1,1:107,5:112,2:0.0175:1,2:15.5:1:30:1:0.10293:19.63123:60:4:0.0179:0:1 +6 138196799 . CT C 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=1.06877;LSEQ=GAGTACAGGATACATTCAAG;RSEQ=TTTTTTTCACCCCGCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:541:7:3,4:345,189:534,7:0.0129:2,2:23.4:1:33.4:1:0.25435:2.42961:60:14:0.013:0:0.1 0/1:579:8:5,3:362,209:571,8:0.0138:2,2:22.6:1:31.3:1:1:1.03914:60:16:0.0139:0.0035:0.5 +6 138196993 . G A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTGAGATGCCTGCAGATCAC;RSEQ=GATCTGTACTTAAATGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:0:0,0:119,235:354,0:0:2,0:24.2:1:31:1:1:0:60:117:1:0:0.1 0/1:337:17:6,11:114,206:320,17:0.0504:2,2:16.4:1:29:1:1:1.01452:60:16:0.0489:0:1.1 +6 138197331 . A C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1452;LSEQ=AACTGCATTAATTCACATCT;RSEQ=TAACTAGACACTGAAACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:338:312:68,244:4,22:26,312:0.9231:2,2:24.5:1:32.6:1:0.61888:1.53:60:103:0.9224:0:1.1 1/0:323:205:53,152:33,85:118,205:0.6347:2,2:24.8:1:31.3:1:0.69634:1.11305:60:204:0.6335:0:1.1 +6 138197824 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCATTTTTATCCTTTTAGCA;RSEQ=TCTTGTGAGATGTAGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 138198413 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12156;SOR=0;LSEQ=AGTAAGCAGTTTATGTTCAG;RSEQ=TCTCTCCTGTGTCATCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:3:2,1:58,154:212,3:0.014:2,2:15.7:1:30.3:1:0.18892:5.26:60:6:0.0142:0:1 0/0:218:0:0,0:70,148:218,0:0:2,0:23.3:1:31.2:1:1:0:60:53.5:1:0:0.1 +6 138199417 . G T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42884;SOR=0.4984;LSEQ=TCATGTTGCGTGAAAAGTGT;RSEQ=AGCTCTTCATCACAGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:23:23,0:5,0:5,23:0.8214:0,1:25.9:1:31.2:1:1:0:60:22:0.8148:0:1.3 1/0:13:9:9,0:4,0:4,9:0.6923:0,0:20.3:1:29.9:1:1:0:60:18:0.6923:0:1.2 +6 138199768 . A T 259 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00198;LSEQ=CGCCCAACTGCCCCTTCTTC;RSEQ=TGTCTGTGAACACCCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1125:328:160,168:388,408:796,328:0.2916:2,2:25.3:1:31.1:1:1:1.00:60:45.857:0.2887:0:1.1 0/0:1240:1:0,1:621,617:1238,1:8e-04:2,0:1:0:24:0:0.49879:0:60:2:8e-04:0:1 +6 138199922 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02823;SOR=Inf;LSEQ=AGAAGCCTATGAGCCCTTGG;RSEQ=GTGGAACCCTGAGGAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:178,253:431,0:0:2,0:24.9:1:30.5:1:1:0:60:46.889:1:0:0.1 0/1:416:5:3,2:188,223:411,5:0.012:2,2:15.8:1:28:1:0.66462:1.78:60:4:0.0097:0:1.6 +6 138200369 . G T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0309;SOR=Inf;LSEQ=CTGCCTGTCTCAAGCTGCAC;RSEQ=GACTCCTGGGGACAGGACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:224,262:486,0:0:2,0:25.9:1:30.2:1:1:0:59.9:39.5:1:0:0.2 0/1:502:6:4,2:247,247:494,6:0.012:2,2:24.8:1:25:1:0.68563:2.00:60:2:0.0082:0:1.5 +6 138200522 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.23973;SOR=Inf;LSEQ=TTGACTTCCTAACACAGCGG;RSEQ=TGCTGTCCAGAAGGGGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:49,160:209,0:0:2,0:22.8:1:32.7:1:1:0:60:33.833:1:0:0.1 0/1:201:2:1,1:44,154:198,2:0.01:2,2:24:1:27.5:1:0.40025:3.47:60:4:0.0101:0:1 +6 138200529 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60602;SOR=2.21996;LSEQ=CCTAACACAGCGGCTGCTGT;RSEQ=CAGAAGGGGTTTTGTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:1:0,1:37,141:178,1:0.0056:2,0:25:0:32:0:1:0:60:2:0.0057:0:1 0/1:162:2:1,1:28,132:160,2:0.0123:2,2:30.5:1:27:1:0.32689:4.65:60:4:0.0127:0:1 +6 138201076 . CAT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=5.000;MSILEN=2;SSF=0.54783;SOR=0;LSEQ=TTTATAGACTTAAACATATA;RSEQ=ATATATATTTCTATACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:2,0:73,1:74,2:0.0263:1,0:37.5:1:33.5:1:1:0:60:4:0.027:0:2.5 0/0:39:0:0,0:39,0:39,0:0:1,0:24.7:1:30.3:1:1:0:60:78:1:0:0.1 +6 138201452 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50994;SOR=Inf;LSEQ=ATGCTTTTTGCTGGAGCGTT;RSEQ=TCTACCGACAGTGACAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:10,97:107,0:0:2,0:24.1:1:30.6:1:1:0:59.8:34.667:1:0:0.1 0/1:146:2:1,1:28,116:144,2:0.0137:2,2:18:1:29:1:0.3589:4.09:60:4:0.014:0:1 +6 138201783 . GGCCT G 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGACAGAGCTTCCCAGG;RSEQ=GCCTCCACCTAATGGCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:28.7:1:29:1:1:0:53:6:1:0:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 138202155 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12587;SOR=Inf;LSEQ=CTGACTTTTTAATGATCTGC;RSEQ=TGTTCTTTCCACTCAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:251,100:351,0:0:2,0:23.7:1:31.8:1:1:0:59.9:86.75:1:0:0.1 0/1:388:4:1,3:261,122:383,4:0.0103:2,2:12.5:1:25.5:1:0.101:6.38503:60:8:0.0105:0:1 +6 138202350 . AC A 92 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.11899;SOR=3.43994;LSEQ=GGGTGAGCCTGCCCCCGAAG;RSEQ=CCCCCCAAGCAGCGTTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:626:2:1,1:287,335:622,2:0.0032:2,2:43.5:1:31.5:1:1:1.17:60:4:0.0034:0:0 0/1:733:8:4,4:366,356:722,8:0.0109:2,2:29:1:30.9:1:1:1.02806:60:16:0.0115:0.0014:0.4 +6 138202447 . G A 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCTTTCAGTTCAAGCAGAT;RSEQ=TATGGCTAACCGGAAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:505:0:0,0:202,303:505,0:0:2,0:24.4:1:32.3:1:1:0:59.9:100:1:0:0.1 0/1:588:21:7,14:233,334:567,21:0.0357:2,2:23.5:1:29.9:1:0.65206:1.39445:60:42:0.0361:0:1.1 +6 138202498 . G A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11417;SOR=Inf;LSEQ=CCTGCAAGAAGTGGGGCCTC;RSEQ=AGCTGTCAGTCATCATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:72,205:277,0:0:2,0:24:1:31.3:1:1:0:59.9:54.4:1:0:0.1 0/1:262:3:3,0:78,181:259,3:0.0115:2,0:8:1:20.7:1:0.02879:0:60:2:0.0077:0:1.3 +6 139292582 . T G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00726;SOR=0.31616;LSEQ=CCAGGCACACTGGAACTCTG;RSEQ=AGAAGTTTTGCCTCATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:20:17,3:31,10:41,20:0.3226:2,2:26.6:1:31.3:1:0.51589:1.81:60:19:0.3167:0:1 0/1:77:10:9,1:52,15:67,10:0.1299:2,2:21.1:1:30.5:1:0.67787:2.57:60:20:0.1299:0:1 +6 139292609 . GA G 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.03245;LSEQ=TTTGCCTCATTATATTTTAT;RSEQ=AAAAAAAAAGTATACGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:5:3,2:74,37:111,5:0.0431:2,2:27.6:1:31.6:1:1:1.32985:60:10:0.0442:0.0086:0.8 0/1:180:8:7,1:114,58:172,8:0.0444:2,2:14.4:1:30.9:1:0.27578:3.54:60:16:0.0452:0.0222:0.1 +6 139292620 . G T 49 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14057;SOR=Inf;LSEQ=ATATTTTATGAAAAAAAAAA;RSEQ=TATACGCTATAGTGCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:96,61:157,0:0:2,0:21:1:31.8:1:1:0:60:21.429:0.9934:0:0.4 0/1:215:4:2,2:141,70:211,4:0.0186:2,2:5.8:1:24.5:1:0.60311:2.00726:52.5:3:0.0147:0:3.3 +6 139292658 . A T 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=27.03141;LSEQ=AGGTGTCCAGATTCTACCAT;RSEQ=ATTTATTTCTTTAGTTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:1:0,1:137,96:233,1:0.0043:2,0:13:0:12:0:0.41453:0:60:0:0:0:1 0/1:355:37:21,16:177,141:318,37:0.1042:2,2:24.4:1:28:1:1:1.05:58.9:36:0.102:0:1.5 +6 139292683 . A G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.37907;LSEQ=ATTTCTTTAGTTGCCAATAA;RSEQ=TTATCAGTTTTTAAAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:65:37,28:100,94:194,65:0.25:2,2:25.5:1:32.9:1:0.47588:1.24:60:64:0.251:0:1 0/1:366:41:19,22:174,151:325,41:0.112:2,2:25.7:1:31.5:1:0.41023:1.3332:60:82:0.1136:0:1.1 +6 139292727 . T TA 134 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=22.44095;LSEQ=TACAATTACTCTGCTATAGA;RSEQ=AAAAAAAAGTGGGGGTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:77,115:192,1:0.0052:2,0:33:0:33:0:1:0:60:2:0.0053:0:0 0/1:238:25:9,16:71,141:212,25:0.105:2,2:26:1:29:1:0.82502:1.12:59.8:50:0.1064:0:0.6 +6 139292767 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2448;SOR=Inf;LSEQ=TAAGGGAAAAAGATCCTGAA;RSEQ=GGGAGGGAGGGGAAAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:29,91:120,0:0:2,0:24.9:1:31.7:1:1:0:60:59:1:0:0.1 0/1:119:2:1,1:21,96:117,2:0.0168:2,2:18.5:1:29.5:1:0.33685:4.49:60:4:0.0168:0:1 +6 139309070 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49491;SOR=Inf;LSEQ=TGCGGCTGCGGCTGCGACTA;RSEQ=GGCTCCGGCTCCGGCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:14,7:21,0:0:2,0:23.8:1:30.6:1:1:0:60:20:1:0:0.1 0/1:26:2:1,1:14,10:24,2:0.0769:2,2:31.5:1:28.5:1:1:1.38168:60:4:0.08:0:1.5 +6 139320432 . GT G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51637;SOR=Inf;LSEQ=GCACTTCCTTGTAAAATCCA;RSEQ=TTTAGCAAAGAACATGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:11,14:25,0:0:2,0:24.5:1:29.5:1:1:0:57.8:24:1:0:0.3 0/1:39:2:1,1:17,20:37,2:0.0513:2,2:17.5:1:31:1:1:1.17:30:4:0.0513:0:0.5 +6 139320458 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51052;SOR=Inf;LSEQ=GCAAAGAACATGCTAAGTCA;RSEQ=TTTAGCAAGAAGCCCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:17,0:0:2,0:20.2:1:32.4:1:1:0:56.7:34:1:0:0.5 0/1:26:2:1,1:9,15:24,2:0.0769:2,2:32.5:1:29.5:1:1:1.63:37:4:0.0769:0:2 +6 139320470 . G C 102 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.02734;SOR=9.39347;LSEQ=CTAAGTCAGTTTAGCAAGAA;RSEQ=CCCCCACCCTCAATATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:4,7:11,1:0.0833:2,0:38:0:33:0:1:0:60:2:0.0833:0:7 0/1:21:10:3,7:5,6:11,10:0.4762:2,2:24.8:1:31:1:0.65944:1.88324:52.6:20:0.4762:0:1.4 +6 139320493 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CCCACCCTCAATATGTGATC;RSEQ=ACCTGGAAAATCTGACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:0,6:6,0:0:0,0:35.7:1:33:1:1:0:60:12:1:0:1.3 0/1:10:2:0,2:2,6:8,2:0.2:2,0:22.5:1:32:0:1:0:60:4:0.2:0:2 +6 143236425 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19843;SOR=0;LSEQ=GATGTAATTAGTTAGGATGA;RSEQ=ATCACACTGTAGTAGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:10,11:21,2:0.087:2,2:14.5:1:29:1:1:1.10:60:4:0.087:0:1 0/0:28:0:0,0:13,15:28,0:0:2,0:24.4:1:30.1:1:1:0:60:13:1:0:0.3 +6 147728025 . A G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00833;SOR=Inf;LSEQ=TGTCAGGGGTGGGAGAAGCC;RSEQ=TGGATCCCGGGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:55,67:122,0:0:2,0:25.1:1:30.5:1:1:0:59.6:121:1:0:0.1 0/1:143:8:3,5:66,69:135,8:0.0559:2,2:30:1:31.4:1:0.72004:1.5891:60:16:0.0571:0:1.3 +6 147728034 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50096;SOR=Inf;LSEQ=TGGGAGAAGCCATGGATCCC;RSEQ=GGCAGCAGCAACTGCCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:53,78:131,0:0:2,0:24.2:1:29.6:1:1:0:59.6:25.2:0.9921:0:0.2 0/1:153:2:2,0:68,83:151,2:0.0131:2,0:18.5:1:28.5:1:0.20769:0:60:4:0.0132:0:1 +6 147728037 . C A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.09711;SOR=0;LSEQ=GAGAAGCCATGGATCCCGGG;RSEQ=AGCAGCAACTGCCTCAACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:1,2:48,81:129,3:0.0227:2,2:27:1:28.3:1:1:1.18373:60:6:0.0236:0:1.3 0/0:154:0:0,0:66,88:154,0:0:2,0:26.8:1:31.5:1:1:0:59.2:153:1:0:0.2 +6 147728079 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60103;SOR=2.28263;LSEQ=CCCCCCAGGGCCAAGGGCAG;RSEQ=CACCGGCGCAGCGCCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:1:0,1:35,67:102,1:0.0097:2,0:43:0:14:0:1:0:60:0:0:0:6 0/1:91:2:1,1:31,58:89,2:0.022:2,2:25:1:30.5:1:1:1.86:60:4:0.022:0:1 +6 147728092 . GC G 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.57284;SOR=2.79404;LSEQ=AGGGCAGCCACCGGCGCAGC;RSEQ=CCCCCAGGGGCAGGGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:1:0,1:33,57:90,1:0.011:2,0:42:0:34:0:1:0:60:2:0.0114:0:0 0/1:66:2:1,1:20,44:64,2:0.0303:2,2:27:1:30:1:0.53846:2.17:60:4:0.0303:0:0 +6 147728099 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51299;SOR=0;LSEQ=CCACCGGCGCAGCGCCCCCC;RSEQ=GGGGCAGGGCCCGCGGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:35,55:90,2:0.0217:2,2:18.5:1:32:1:1:1.56:60:4:0.0227:0:1.5 0/0:64:0:0,0:26,38:64,0:0:2,0:20.3:1:30.1:1:1:0:60:63:1:0:0.1 +6 147728117 . C T 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCAGGGGCAGGGCCCGCGGT;RSEQ=CAGACCAGGGCACCCGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:21:11,10:44,29:73,21:0.2234:2,2:20.4:1:31:1:0.6172:1.3745:60:42:0.2234:0:1.2 0/0:69:0:0,0:42,27:69,0:0:2,0:15.4:1:31.1:1:1:0:60:68:1:0:0.1 +6 147728866 . C A 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11341;SOR=5.35518;LSEQ=CAGTGAAACAGCCACCACCC;RSEQ=TGGTTCCCCAGAGCCCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:1:1,0:235,252:487,1:0.002:2,0:1:0:26:0:0.48361:0:60:2:0.0021:0:1 0/1:459:5:3,2:198,256:454,5:0.0109:2,2:12.8:1:29:1:0.65767:1.94:60:10:0.0111:0:1.2 +6 147729477 . T G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00713;SOR=0.19272;LSEQ=CTGTTCATAGTTGTAGCTTG;RSEQ=GGTGGTTATTGTAGTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:24:0,24:2,16:18,24:0.5714:2,1:18:1:31.5:1:0.1777:0:36.5:48:0.5714:0:1 0/1:20:4:0,4:1,15:16,4:0.2:1,0:15:1:30:1:1:0:43.5:8:0.2:0:1 +6 148266173 . G T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCATCTAAACTCCATAGTG;RSEQ=TCCACTGGAAGCCTTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:17.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 148266417 . T C 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCTGCCTTGCTCAAGATA;RSEQ=CCACAGCCAGAACTGACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:13:1:32.5:1:1:0:60:8:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 148266419 . C A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCTGCCTTGCTCAAGATATC;RSEQ=ACAGCCAGAACTGACCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:13.3:1:31.7:1:1:0:60:6:0.75:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 148266575 . C T 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5841;SOR=2.52788;LSEQ=TCAGATTTTTAACCCCCAAA;RSEQ=GTTATTTATCCGTGTATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:1,0:46,0:46,1:0.0213:1,0:13:0:33:0:1:0:60:2:0.0213:0:2 0/1:38:2:2,0:34,2:36,2:0.0526:2,0:22.5:1:32:0:1:0:60:4:0.0541:0:2 +6 148266586 . C T 169 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01357;LSEQ=ACCCCCAAACGTTATTTATC;RSEQ=GTGTATAAATACATGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:35:35,0:20,0:20,35:0.6364:1,1:25.9:1:33.1:1:1:0:60:70:0.6364:0:2.1 0/1:45:1:1,0:41,2:43,1:0.0222:1,0:11:0:32:0:1:0:60:2:0.0227:0:2 +6 148266603 . C A 181 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCCGTGTATAAATACATGT;RSEQ=AGATGCTCATTTAAAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:82:82:82,0:0,0:0,82:1:0,1:24.6:1:28.6:1:1:0:60:164:1:0:1.5 1/0:61:44:42,2:16,1:17,44:0.7213:1,1:26.6:1:27.6:1:1:1.31:60:21:0.7119:0:1.2 +6 148266753 . C T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.69687;LSEQ=AGGGTGATGAATAAAAGTGA;RSEQ=GCTATTGGAGAGGGATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:742:245:122,123:262,235:497,245:0.3302:2,2:22.9:1:30.7:1:0.48232:1.12385:60:121.5:0.3302:0:1.1 1/0:657:459:231,228:102,96:198,459:0.6986:2,2:25.3:1:29.6:1:0.79906:1.04865:60:64.571:0.6954:0:1.2 +6 148266755 . C T 137 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=5.89948;LSEQ=GGTGATGAATAAAAGTGACG;RSEQ=TATTGGAGAGGGATGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:741:5:0,5:379,357:736,5:0.0067:2,0:1:0:26.8:1:0.02743:0:60:10:0.0069:0:1 0/1:674:26:12,14:329,318:647,26:0.0386:2,2:25.9:1:29.2:1:0.69224:1.20668:60:52:0.0392:0:2.3 +6 148266965 . A G 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0;LSEQ=GTTCCTACCTTGTGCCAGGC;RSEQ=CTAGGGTTATGCAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:23:0,23:0,15:15,23:0.6053:1,1:24.5:1:31.8:1:1:0:60:22:0.5946:0:1.2 0/0:15:0:0,0:0,15:15,0:0:1,0:26.4:1:30.2:1:1:0:60:30:1:0:0 +6 148267180 . T A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTATAAAAGACTCCTAA;RSEQ=TTAAAATTAGCTACCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 149159629 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19521;SOR=0.74594;LSEQ=GGAAGCCTGGCAGGGCCTGA;RSEQ=ATTCTGCATTTCTAACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:82:56,26:60,33:93,82:0.4686:2,2:24.1:1:32.3:1:0.63325:1.18:59.7:40:0.4651:0:1.1 0/1:174:69:41,28:67,37:104,69:0.3966:2,2:22:1:30.1:1:0.52502:1.23511:60:22:0.3905:0:1.1 +6 149159687 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24873;SOR=Inf;LSEQ=TGTTGCTGTTGCTGTTGCTG;RSEQ=TGGTCCATAGACGTCACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:107,148:255,0:0:2,0:27.9:1:32.6:1:1:0:59.8:41.5:1:0:0.4 0/1:263:3:2,1:115,145:260,3:0.0114:2,2:19:1:29:1:0.58683:2.51:60:6:0.0116:0:1.3 +6 149159725 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=TGTCAGTGTCAAGGCTCTCC;RSEQ=TCTCCTTTAAAATGATCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:55,116:171,0:0:2,0:23.5:1:30.5:1:1:0:60:170:1:0:0.2 0/1:143:2:1,1:49,92:141,2:0.014:2,2:11.5:1:28.5:1:1:1.87:60:4:0.0145:0:1 +6 149215481 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23469;SOR=0;LSEQ=ATGAAGATGAGGTCATACTG;RSEQ=AGAAGGGTGGACCCTAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:15,7:22,2:0.0833:2,2:18:0:31:1:1:2.07024:60:4:0.0833:0:1.5 0/0:25:0:0,0:14,11:25,0:0:2,0:20.4:1:30:1:1:0:60:24:1:0:0.1 +6 149307085 . C G 34 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=AAGGAGGCAGGAAGAGCCAT;RSEQ=AAACCCATAGTAGATCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:28.5:1:34:0:1:0:60:4:0.5:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:33.2:1:31:1:1:0:60:12:1:0:0 +6 149982813 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21225;SOR=0;LSEQ=CTCTCAGAACCTCAAAACAC;RSEQ=TCGCATTTCAGGCCCTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:127,21:148,2:0.0133:2,2:41.5:1:31:1:0.27266:5.93182:60:4:0.0136:0:1 0/0:175:0:0,0:124,50:174,0:0:2,0:22.9:1:30.2:1:1:0:60:28:0.9941:0:0.2 +6 149983216 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.56676;LSEQ=TGTCTCAGGTCACTGGAGAA;RSEQ=TCAATTGTTTTAAAAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:504:157:69,88:162,185:347,157:0.3115:2,2:26:1:30.7:1:0.62948:1.11656:60:77.5:0.3094:0:1.1 0/1:598:122:66,56:223,253:476,122:0.204:2,2:22.4:1:29.6:1:0.15677:1.34:60:60:0.2034:0:1.1 +6 149997233 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16776;SOR=Inf;LSEQ=CCTAGGCTCAAGCAATCCTC;RSEQ=TGCCTCAGCCTCCCAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:79,1:80,0:0:1,0:24.7:1:31.9:1:1:0:60:160:1:0:0 0/1:56:2:2,0:54,0:54,2:0.0357:1,0:10.5:1:28:1:1:0:60:4:0.0357:0:1 +6 149997283 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.97487;LSEQ=TGGGTGTGAGCCACTGCACC;RSEQ=GGCCCAAGTTCATTCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:1:0,1:146,37:183,1:0.0054:2,0:1:0:26:0:0.20652:0:60:2:0.0056:0:1 0/1:187:2:1,1:149,36:185,2:0.0107:2,2:8:1:29.5:1:0.35743:4.09625:60:4:0.0108:0:1 +6 149997343 . C A 160 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGTACTAATAAATAAAAGT;RSEQ=AATGATGTAGCAACTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:0:0,0:353,201:554,0:0:2,0:24.1:1:32.2:1:1:0:60:91.333:0.9982:0:0.1 0/1:657:51:27,24:366,238:604,51:0.0776:2,2:20.9:1:28.3:1:0.29989:1.36625:60:50:0.0769:0:1.2 +6 149997512 . C A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12442;SOR=Inf;LSEQ=CTGTGTGTATCCTAAAATAA;RSEQ=AAAGTTATTTATAAGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:86,232:318,0:0:2,0:24.3:1:32.4:1:1:0:60:317:1:0:0.1 0/1:336:4:2,2:106,225:331,4:0.0119:2,2:12.5:1:26.8:1:0.59689:2.12:60:8:0.012:0:1 +6 149997620 . A G 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22362;SOR=Inf;LSEQ=TTATTATAAGCCTGAAAAAT;RSEQ=AGGCATATTCTAGTGTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:148,61:209,0:0:2,0:22.4:1:29.6:1:1:0:60:418:1:0:0.4 0/1:188:2:1,1:122,64:186,2:0.0106:2,2:26:0:29.5:1:1:1.89933:60:4:0.0106:0:1 +6 149997657 . T C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06341;SOR=0.72435;LSEQ=CGTTTTGGCTGGTCTAAAGG;RSEQ=CTACTGAGAATATATATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:113:68,45:134,58:192,113:0.3705:2,2:26.6:1:31.6:1:0.10316:1.52667:60:55.5:0.3725:0:1.1 0/1:328:98:66,32:140,90:230,98:0.2988:2,2:28.1:1:30.8:1:0.31819:1.32:60:31.667:0.295:0:1.2 +6 149997665 . G T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12541;SOR=Inf;LSEQ=CTGGTCTAAAGGTCTACTGA;RSEQ=AATATATATGAAAGAAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:215,117:332,0:0:2,0:26.3:1:32.7:1:1:0:60:109.667:1:0:0.4 0/1:363:4:2,2:223,136:359,4:0.011:2,2:26.5:1:28.3:1:0.63671:1.63732:60:8:0.0111:0:1.5 +6 149997936 . T A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16678;SOR=Inf;LSEQ=CAGTAAACCTGAAGTCTATT;RSEQ=AATCTTCTGACATCGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:16,118:134,0:0:2,0:21.4:1:28.7:1:1:0:60:268:1:0:0.1 0/1:93:2:1,1:10,81:91,2:0.0215:2,2:5:1:26:1:0.2237:7.77:60:4:0.0215:0:1.5 +6 150000946 . T C 30 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49809;SOR=0;LSEQ=AGTGATGATACCATCTTATA;RSEQ=TTTACTACATCAATAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:115,11:126,2:0.0156:2,2:5:0:30.5:1:0.17938:10.05293:60:4:0.0157:0:1 0/0:125:0:0,0:108,17:125,0:0:2,0:21:1:29.9:1:1:0:59.8:40.667:1:0:0.1 +6 150004027 . A C 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.75222;SOR=0.74905;LSEQ=ATAGGAAATTCTGAATAAAT;RSEQ=TTGAAATACTAAAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:7:7,0:24,0:24,7:0.2258:1,0:24.3:1:33.9:1:1:0:54.7:14:0.2258:0:1.1 0/1:28:5:5,0:21,2:23,5:0.1786:2,0:17.2:1:30.6:1:1:0:60:10:0.1852:0:1 +6 150004779 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01007;SOR=0.7027;LSEQ=ATTGCAGTGACTGTTGTAGC;RSEQ=GAAGGCTGAGAATTAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:176:90,86:158,190:348,176:0.3359:2,2:25:1:30.6:1:0.22917:1.26:59.8:175:0.3385:0:1.1 0/1:515:135:54,81:164,216:380,135:0.2621:2,2:25.7:1:29.2:1:0.54427:1.1386:60:26:0.2574:0:1.1 +6 150005615 . T C 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ATCTGTCTGTGAGTTGGGAC;RSEQ=CTCAGAATGATAGGCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:0:0,0:176,255:431,0:0:2,0:24.4:1:30.8:1:1:0:60:42.1:1:0:0.1 0/1:537:26:13,13:216,294:510,26:0.0484:2,2:25.9:1:30.8:1:0.54288:1.36:60:52:0.0493:0:1.3 +6 150005739 . A G 103 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01472;SOR=9.05601;LSEQ=TGCACATTCCCTATGGTTAT;RSEQ=AGAGAGATAAAGAGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:38,113:151,1:0.0065:2,0:30:0:34:0:1:0:60:2:0.0066:0:1 0/1:196:11:3,8:58,127:185,11:0.0561:2,2:14:1:30:1:1:1.21664:60:22:0.0561:0:1.1 +6 150016376 . TA T 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.5454;SOR=1.7187;LSEQ=TCCTGATATGAATTGAAGTT;RSEQ=AAAAAAAAGAAACAAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:4:0,4:64,223:287,4:0.0137:2,0:19.5:1:32.5:1:0.5793:0:60:8:0.014:0:0 0/1:301:7:1,6:80,214:294,7:0.0233:2,2:23.4:1:30.3:1:0.67894:2.23809:60:14:0.0233:0:0 +6 150016576 . G A 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51648;SOR=0;LSEQ=TCAAGCCACTTTGGGAGGCC;RSEQ=AGGTGGTCAGATCACTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:0,7:7,4:0.3636:0,0:33.8:1:29.8:1:1:0:60:8:0.3636:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:17.3:1:32:0:1:0:60:8:1:0:0.3 +6 150022869 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22925;SOR=Inf;LSEQ=CACCCAAAAAGTGTTATGTA;RSEQ=CATAAGGTAAGAAGAATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:137,29:166,0:0:2,0:21.3:1:33.2:1:1:0:60:54.333:1:0:0.1 0/1:153:2:1,1:121,30:151,2:0.0131:2,2:28:1:28.5:1:0.36524:3.98411:60:4:0.0133:0:1 +6 150023348 . C G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06556;SOR=0.28083;LSEQ=TGAGCAAAAGTGAAAATGAT;RSEQ=CTTCAAGGAAGTCCCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:18:0,18:0,50:50,18:0.2647:1,1:25.1:1:33:1:1:0:60:36:0.2769:0:1.2 0/1:33:3:0,3:0,30:30,3:0.0909:1,0:15.3:1:32.7:1:1:0:60:6:0.0938:0:1 +6 151176771 . C T 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=0;LSEQ=TTTGGGCCCTGTATTTTTAA;RSEQ=CTTCTTGTCAAATTTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:1,5:0.8333:0,2:25:1:31.8:1:1:0:42.6:10:0.8333:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:46.5:1:31:1:1:0:21:4:1:0:0 +6 152128937 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16144;SOR=Inf;LSEQ=TCGCGTGTCGGCGGGACATG;RSEQ=GCTGCGTCGCCTCTAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:160,6:166,0:0:1,0:23.1:1:31.9:1:1:0:60:32.2:1:0:0.1 0/1:112:2:2,0:102,8:110,2:0.0179:2,0:27.5:1:31.5:1:1:0:60:4:0.0179:0:1 +6 152129063 . C T 191 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=105.16001;LSEQ=GGACCATGACCATGACCCTC;RSEQ=ACACCAAAGCATCTGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1293:1:0,1:712,578:1290,1:8e-04:2,0:1:0:24:0:0.44849:0:60:2:8e-04:0:2 0/1:1261:95:58,37:619,545:1164,95:0.0753:2,2:24.8:1:29.1:1:0.16398:1.38:60:46.5:0.0749:0:2.1 +6 152129077 . T C 301 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.64457;LSEQ=ACCCTCCACACCAAAGCATC;RSEQ=GGGATGGCCCTACTGCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1393:994:529,465:213,183:396,994:0.7136:2,2:25.2:1:30.3:1:0.85836:1.02311:60:44.182:0.7131:0:1.2 1/0:1334:822:440,382:266,244:510,822:0.6162:2,2:24.2:1:29.7:1:0.65153:1.06:59.9:90.333:0.6168:0:1.3 +6 152129308 . G C 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.03415;LSEQ=GGCCCCGGGTCTGAGGCTGC;RSEQ=GCGTTCGGCTCCAACGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1053:801:355,446:111,136:247,801:0.7607:2,2:25:1:30.3:1:0.88369:1.02538:60:56.214:0.7663:0:1.2 0/1:870:85:37,48:357,423:780,85:0.0977:2,2:22.8:1:29.2:1:0.73168:1.09474:60:41.5:0.0971:0:1.2 +6 152129488 . G A 57 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19161;SOR=4.57091;LSEQ=GTGCGCGAGGCCGGCCCGCC;RSEQ=GCATTCTACAGGTACCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:0,1:71,188:259,1:0.0038:2,0:8:0:34:0:1:0:60:2:0.0039:0:1 0/1:230:4:2,2:76,150:226,4:0.0174:2,2:7:1:28.8:1:0.60596:1.97:60:8:0.0178:0:1 +6 152129545 . AGGAG A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=6.000;MSILEN=4;SSF=0.60042;SOR=2.28004;LSEQ=GGGTGGCCGCCGCGCCCGGC;RSEQ=GGAGGGAGGGAGGGAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:1:0,1:7,47:54,1:0.0182:2,0:44:0:34:0:1:0:60:2:0.0182:0:0 0/1:49:2:1,1:12,34:46,2:0.0408:2,2:39.5:1:31:1:0.47252:2.76:60:4:0.0417:0:1 +6 152129588 . C T 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0068;SOR=Inf;LSEQ=AGAAGGGAGAGCCTAGGGAG;RSEQ=TGCGGGAGCCGCGGGACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:0,16:16,0:0:1,0:18.8:1:34.1:1:1:0:60:32:1:0:0.1 0/1:16:7:1,6:1,8:9,7:0.4375:2,2:29:1:30:1:1:1.31:60:14:0.4375:0:1.1 +6 152163335 . T C 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGTTCCAAATGTCCCAGC;RSEQ=GTTTTATGCTTTGTCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:31:1:32.3:1:1:0:55.3:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 152164026 . A G 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00374;SOR=0;LSEQ=GAATCAGCCATTTGTACAAA;RSEQ=CATGAATCCCTAGTAGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:12:0,12:2,97:99,12:0.1081:1,0:25.8:1:32.5:1:1:0:60:24:0.1101:0:1 0/0:73:0:0,0:0,73:73,0:0:1,0:22.8:1:29.5:1:1:0:60:72:1:0:0.1 +6 152164239 . C T 44 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGTTGTCTGTGCCCTGA;RSEQ=TGGGGAATGCCAGATGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:26:1:28:1:1:0:47.3:6:0.75:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 152201853 . G T 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00799;SOR=0;LSEQ=TGATAAAAACAGGAGGAAGA;RSEQ=CTGCCAGGCCTGCCGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:589:8:4,4:287,293:580,8:0.0136:2,2:23.9:1:30:1:1:1.02:60:16:0.0137:0:1.8 0/0:542:0:0,0:254,288:542,0:0:2,0:24.6:1:31.1:1:1:0:59.9:53.2:1:0:0.9 +6 152201875 . T C 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=93.91628;LSEQ=TGCCAGGCCTGCCGGCTCCG;RSEQ=AAATGCTACGAAGTGGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:484:401:194,207:39,44:83,401:0.8285:2,2:25.5:1:32.4:1:0.90402:1.06:60:132.667:0.8292:0:1.1 1/1:456:455:211,244:0,0:0,455:0.9978:0,2:24.8:1:31.1:1:1:0:60:112.75:0.9978:0:1.2 +6 152201963 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50098;SOR=0;LSEQ=CCTGGCCACCGCCCAGTGCT;RSEQ=GCTCTACCCATTGGAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:35,158:193,2:0.0103:2,2:23:1:32:1:0.33592:4.47:60:4:0.0103:0:1 0/0:170:0:0,0:42,128:170,0:0:2,0:23.8:1:30.4:1:1:0:60:340:1:0:0.5 +6 152202007 . T C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64156;SOR=1.28817;LSEQ=ATGGGAATTTTGTGTTTTTT;RSEQ=CTTTTAATTGTTTTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:68:0,68:0,13:13,68:0.8395:1,1:22.8:1:31.9:1:1:0:60:67:0.8375:0:1 1/1:62:54:0,54:0,8:8,54:0.871:0,1:24.8:1:30.5:1:1:0:60:53:0.8689:0:1 +6 152265282 . A AT 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.12387;SOR=0.77718;LSEQ=CACGGGAAAAAAATAAACTA;RSEQ=TTTTTTTTTCCACCTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:356:251:185,66:70,28:98,251:0.7051:2,2:22.5:1:31.1:1:0.68819:1.12:60:124.5:0.7094:0.1517:0.1 1/0:340:221:155,66:84,32:116,221:0.65:2,2:23:1:29.5:1:0.70599:1.11736:60:43.2:0.6448:0.1676:0.2 +6 152265522 . G C 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04115;SOR=0.73458;LSEQ=TTGTTGGATGCTGAGCCCCC;RSEQ=ATACTCTATTCCGAGTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:538:435:200,235:43,58:101,435:0.8086:2,2:23.6:1:31.8:1:0.57978:1.15:60:71.5:0.8094:0:1.1 1/0:566:428:204,224:59,76:135,428:0.7562:2,2:24.8:1:30.9:1:0.4306:1.17:60:141.667:0.7576:0:1.1 +6 152332921 . C G 180 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGTTTGCTCCTAACTTGCT;RSEQ=TTGGACAGGTAAGTGACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:50:16,34:167,370:537,50:0.085:2,2:25.1:1:31.9:1:0.87446:1.04:60:49:0.0848:0:1.1 0/0:528:0:0,0:179,347:526,0:0:2,0:25:1:31.2:1:1:0:60:525:0.9962:0:0.1 +6 152333032 . A G 118 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00353;SOR=0;LSEQ=GTGAAGCTTCAGAGAACTTT;RSEQ=TTAGGTATGTTTACTTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:12:0,12:1,74:75,12:0.1379:1,0:23.6:1:33:1:1:0:60:24:0.1379:0:1 0/0:53:0:0,0:1,52:53,0:0:1,0:18.2:1:29.8:1:1:0:60:52:1:0:0.1 +6 152381781 . C G 29 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=TTTAGAATATAGTAGCAGAT;RSEQ=AATATACGTGTATTAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:33.5:1:32.3:1:1:0:41.8:8:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:29:1:1:0:60:4:1:0:1.5 +6 152382089 . TTTTA T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.21925;SOR=Inf;LSEQ=GATTTTCTGTTTTTTAATCT;RSEQ=TTTATTTATTTATTTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:162,18:180,0:0:2,0:21.3:1:31:1:1:0:60:29:1:0:0.1 0/1:159:2:1,1:136,21:157,2:0.0126:2,2:16:1:25:1:0.25834:6.35052:60:4:0.0127:0.0063:1 +6 152382382 . G A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00152;SOR=Inf;LSEQ=GAAAGAAACTACTGACACAC;RSEQ=TTTTAAAATAACCTACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:2,45:47,0:0:1,0:21.4:1:31.7:1:1:0:60:22.5:1:0:0.1 0/1:54:10:0,10:0,44:44,10:0.1852:1,0:27.5:1:30.8:1:1:0:56.4:20:0.1887:0:1.3 +6 152414420 . CA C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCTGTCTCAAAAAAAAAA;RSEQ=AAAAAAAAAAACTAAGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:30.8:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 152415753 . C A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25773;SOR=0;LSEQ=AGACATAAAGAAAACATGCC;RSEQ=CCAAACCTATGTGACAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:1,2:45,168:213,3:0.0139:2,2:17.3:1:25:1:0.51433:1.86:60:2:0.0093:0:1.7 0/0:172:0:0,0:47,125:172,0:0:2,0:22.1:1:30.4:1:1:0:60:85:1:0:0.1 +6 152415776 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52416;SOR=0;LSEQ=AAACCTATGTGACAGCTGGC;RSEQ=GGGAAGGACTGGTGCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:0,2:11,132:143,2:0.0138:2,0:8:1:29.5:1:1:0:60:4:0.0138:0:1 0/0:91:0:0,0:13,77:90,0:0:2,0:22.3:1:29.6:1:1:0:60:44:0.9888:0:0.1 +6 152419807 . A G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06812;SOR=Inf;LSEQ=CTTCCCCTTCTAGGGATTTC;RSEQ=GCACTCCTGGGGCTCGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:169,28:197,0:0:2,0:26.7:1:30.6:1:1:0:60:196:1:0:0.1 0/1:137:3:2,1:113,20:133,3:0.0219:2,2:31.3:1:29.7:1:0.39785:2.79596:60:6:0.0221:0:1 +6 152420095 . G A 202 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=59.53514;LSEQ=GCAGAGGGTTTCCCTGCCAC;RSEQ=GTCTGAGAGCTCCCTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:627:2:2,0:233,392:625,2:0.0032:2,0:1:0:27:0:0.1401:0:60:4:0.0032:0:1 0/1:661:106:45,61:237,318:555,106:0.1604:2,2:22.4:1:30.1:1:1:1.01026:60:212:0.1621:0:1.2 +6 153023013 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05141;SOR=Inf;LSEQ=ATAATTTTCAATATTGTCCC;RSEQ=TAACCCTAGAGCTGCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:46,0:46,0:0:1,0:24.2:1:30.2:1:1:0:59.7:45:1:0:0.1 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:35:1:30:1:1:0:60:4:0.1429:0:1 +6 153023151 . G A 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00385;SOR=1.67015;LSEQ=GATACCCAAGGGTTCTCAGA;RSEQ=CGGCTTGCCATCTTTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:90:48,42:94,88:182,90:0.3309:2,2:25.6:1:29.9:1:0.79811:1.07:59.9:89:0.3333:0:1.7 0/1:274:124:73,51:83,67:150,124:0.4526:2,2:27.8:1:29.2:1:0.62418:1.15:60:61:0.4552:0:1.9 +6 153023184 . A G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00039;SOR=1.83722;LSEQ=TTTCCCAGGAAGCTGGAAAT;RSEQ=AGTACCAGTTCCTCTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:90:40,50:85,105:190,90:0.3214:2,2:25.4:1:32.6:1:1:1.01186:60:180:0.3226:0:1.7 0/1:305:142:74,68:82,80:162,142:0.4656:2,2:24.5:1:30.6:1:0.81879:1.06:60:141:0.4653:0:1.8 +6 153023257 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11471;SOR=Inf;LSEQ=GGCTGGAGAGTGATGCTTCC;RSEQ=TTCTCCAAAACCCTTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:46,118:164,0:0:2,0:23.3:1:32.1:1:1:0:60:53.667:1:0:0.2 0/1:156:3:2,1:51,102:153,3:0.0192:2,2:12.7:1:29:1:0.26644:3.96:60:6:0.0195:0:1.3 +6 153023277 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49789;SOR=Inf;LSEQ=CTTCTCCAAAACCCTTACAG;RSEQ=TCGTATTCTATATAGCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:22,90:112,0:0:2,0:24.2:1:31.8:1:1:0:60:36.333:0.9909:0:0.1 0/1:116:2:1,1:28,86:114,2:0.0172:2,2:25:1:25.5:1:0.43913:3.04:60:4:0.018:0:1 +6 153082870 . C G 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.10294;SOR=0;LSEQ=AGGCACCGCAGACCAGGTGT;RSEQ=TCAAACAAAGAAATCAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:19.8:1:33.3:1:1:0:60:8:0.4444:0:1 0/0:7:0:0,0:6,1:7,0:0:2,0:29.4:1:31.9:1:1:0:60:14:1:0:0 +6 153269698 . G A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20705;SOR=0.36195;LSEQ=CAGCAGGCTGTAGATGCCTC;RSEQ=CACGCTGACTCCACACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:7,2:11,9:20,9:0.3103:2,2:19.2:1:31.8:1:0.41183:2.77:60:18:0.3103:0:2.6 0/1:29:4:2,2:12,13:25,4:0.1379:2,2:32:1:30.8:1:1:1.08:60:8:0.1379:0:2.5 +6 153269715 . A G 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.2231;SOR=0.406;LSEQ=CTCGCACGCTGACTCCACAC;RSEQ=GCAGAGCCTTCAGAGTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:10:7,3:11,12:23,10:0.303:2,2:23.2:1:31:1:0.2828:2.47:60:20:0.303:0:2.5 0/1:27:4:2,2:10,13:23,4:0.1481:2,2:31.8:1:31.8:1:1:1.29:60:8:0.1481:0:2.5 +6 153269782 . T A 121 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03162;SOR=0;LSEQ=ATCTCAAGGGATAATATCAG;RSEQ=GTTAGCAATCTTAGTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:5,10:0,0:0,15:1:0,2:19.9:1:31.1:1:1:0:60:30:1:0:1.9 1/0:8:5:0,5:0,3:3,5:0.625:0,0:21.8:1:30.4:1:1:0:60:10:0.625:0:1.4 +6 153269819 . C T 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATAATTTTAAGTAAAAA;RSEQ=ATATTTATCAGCGTGCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:29.2:1:28.3:1:1:0:60:12:1:0:2.2 1/1:4:4:1,3:0,0:0,4:1:0,2:31:1:24.8:1:1:0:60:3:1:0:1.5 +6 153412390 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17977;SOR=Inf;LSEQ=AGGAAAACAATCTAAAGGCA;RSEQ=AAGTGATTCTAAAATACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:178,74:252,0:0:2,0:23.3:1:32:1:1:0:60:125:1:0:0.1 0/1:186:2:1,1:129,55:184,2:0.0108:2,2:19.5:1:29.5:1:0.51264:2.33343:60:4:0.0108:0:1.5 +6 153412476 . CA TG 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.02426;LSEQ=TAATGGCTAGTTTGGAGAAC;RSEQ=TCTCAAATGATTTTGCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:68:29,39:214,225:439,68:0.1336:2,2:28.1:1:31.4:1:0.36416:1.27846:60:136:0.1371:0.0098:1 0/1:421:134:68,66:135,151:286,134:0.3183:2,2:24.4:1:30.8:1:0.5304:1.15:60:268:0.3183:0.0333:1 +6 155699472 . TA T 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03278;SOR=0;LSEQ=AATAAGTAAAATGCAAATAT;RSEQ=AAAAAAAATCTGAAATCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:5,1:75,1:76,6:0.0732:1,2:19.2:1:30.6:1:0.14182:13.78406:60:12:0.0741:0.0244:0 0/0:67:0:0,0:61,5:66,0:0:2,0:19.8:1:28:1:1:0:60:65:1:0:0.1 +6 155699620 . T C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.96399;LSEQ=TTCATGATATTTAGTGTATG;RSEQ=TCTTTCAGGTCAAAAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:28:11,17:165,194:359,28:0.072:2,2:30.8:1:32.6:1:0.5579:1.31352:60:27:0.0703:0:1.1 0/1:345:24:12,12:148,172:320,24:0.0696:2,2:26.7:1:30.3:1:0.83274:1.16:60:23:0.0676:0:1.1 +6 155699667 . AAT A 46 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04606;SOR=Inf;LSEQ=TTTTGATTTTTTATTCTCAA;RSEQ=GACTTGTAAGAGTAATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:94,180:274,0:0:2,0:25.4:1:30.7:1:1:0:60:273:1:0:0.2 0/1:238:4:4,0:94,140:234,4:0.0168:2,0:7.3:1:23.3:1:0.02771:0:60:3:0.0128:0.0126:1.5 +6 155699732 . A G 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.78869;LSEQ=TTCCTCTGGGTCCTCAGAAC;RSEQ=AGCCTTTTTTTTTTTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:5:0,5:10,74:84,5:0.0562:2,0:8.8:1:33.2:1:1:0:60:10:0.0575:0:1 0/1:67:3:1,2:10,54:64,3:0.0448:2,2:13.7:1:31:0:0.42135:2.65:60:6:0.0462:0:1.3 +6 155699736 . CT C 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.97554;LSEQ=TCTGGGTCCTCAGAACAAGC;RSEQ=TTTTTTTTTTAATTTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:7:0,7:5,61:66,7:0.0959:2,0:23.9:1:33.1:1:1:0:60:14:0.1:0.0137:0.1 0/1:64:6:0,6:7,50:57,6:0.0938:2,0:30.2:1:32.2:1:1:0:60:12:0.1:0:0.3 +6 156983276 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18947;SOR=0;LSEQ=AGCCGCTCGCAGAGTGCGCC;RSEQ=TCTACCGGAGGGGTGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:33:1:29.5:1:1:2.23609:60:4:0.2222:0:1 0/0:11:0:0,0:7,4:11,0:0:2,0:30.1:1:29.7:1:1:0:60:10:1:0:0.4 +6 156983504 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14154;SOR=0;LSEQ=TGAAGACATTAACTTGTGTG;RSEQ=TGTCTATGCCAAACGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:16,2:0.1111:2,2:10.5:1:28.5:1:1:1.62:60:4:0.1111:0:1 0/0:29:0:0,0:9,20:29,0:0:2,0:23.6:1:31.8:1:1:0:60:58:1:0:0.1 +6 156983856 . G A 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAAAATGTTTCAGTGAAC;RSEQ=AGTTTCAGCAGTTCAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:18.5:1:26.5:1:1:0:43.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 157098952 . CGCG C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGGAGGCGGGGGCGCGCGG;RSEQ=GCGGCGGCGGCGGCGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:32.5:1:1:0:60:4:1:0:0.5 +6 157099165 . GTCC G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.53177;SOR=0.86692;LSEQ=GGTGGAAGCGCCGCCGCGCT;RSEQ=TCCTCCTCCTCCTCCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:784:53:34,19:459,269:728,53:0.0676:2,2:28.8:1:32.3:1:1:1.05:59:106:0.0685:0.0064:0.3 0/1:761:45:28,17:440,267:707,45:0.0591:2,2:25.8:1:30.6:1:1:1.00053:59.7:90:0.0605:0.0105:0.2 +6 157099282 . C T 108 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00865;SOR=3.98063;LSEQ=CACAAACTGAAAACCGTTGG;RSEQ=GAAGCCCCCGCCGCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1450:4:0,4:727,709:1436,4:0.0028:2,0:4.3:1:29.3:1:0.05985:0:58:8:0.003:0:1 0/1:1652:18:6,12:837,793:1630,18:0.0109:2,2:13.5:1:26:1:0.15697:2.11003:60:17:0.0109:0:1.3 +6 157099312 . GCAC G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.8068;SOR=0.9191;LSEQ=GCCGCGCCGCCCCACCAGCA;RSEQ=CACCACCACCACCATGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1215:33:15,18:538,642:1180,33:0.0272:2,2:33:1:32.4:1:1:1.0056:60:66:0.0278:8e-04:0.3 0/1:1439:36:20,16:654,746:1400,36:0.025:2,2:27.6:1:32:1:0.31416:1.43:59.9:72:0.0257:0:0.3 +6 157099332 . CCCA C 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.04543;SOR=0.57687;LSEQ=GCACCACCACCACCACCATG;RSEQ=CCACCACCACCACCATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1003:35:12,23:411,557:968,35:0.0349:2,2:31.6:1:30.4:1:0.38641:1.4138:59.7:34:0.035:0.001:0.3 0/1:1126:23:8,15:496,600:1096,23:0.0204:2,2:34.5:1:30.5:1:0.39885:1.54941:60:46:0.0209:9e-04:0.4 +6 157099402 . CCAG C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.11582;SOR=1.54113;LSEQ=CAGCAGCAGCTAAACCAGTT;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:24:8,16:273,321:594,24:0.0385:2,2:26.4:1:31.3:1:0.29631:1.69952:60:23:0.0379:0.0048:0.2 0/1:637:37:20,17:285,312:597,37:0.0581:2,2:30.6:1:30.4:1:0.50016:1.29:57.2:17.5:0.0565:0.0063:0.5 +6 157099426 . ACAG A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.134;SOR=1.55127;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:765:22:13,9:364,378:742,22:0.0288:2,2:22.5:1:32.1:1:0.39273:1.50:59.9:44:0.0291:0.0065:0 0/1:774:34:12,22:384,354:738,34:0.0439:2,2:26.6:1:31.4:1:0.07798:1.98695:57:68:0.0446:0.0078:0.2 +6 157099429 . G A 89 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.79905;SOR=0.83618;LSEQ=CAGCAGCAGCAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:760:8:3,5:357,378:735,8:0.0105:2,2:11.4:1:29.9:1:0.72614:1.57313:59.4:16:0.0109:0:1.3 0/0:794:7:3,4:392,364:756,7:0.0088:2,2:11.7:1:27.3:1:0.71676:1.43521:60:6:0.008:0:1.3 +6 157099563 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06318;SOR=Inf;LSEQ=AGGCGCCAAGGACAGTGCTG;RSEQ=GGGCGGCCAGGCCGACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:154,284:438,0:0:2,0:21.4:1:30.6:1:1:0:59.9:47.667:0.9954:0:0.3 0/1:483:5:1,4:175,302:477,5:0.0104:2,2:8.2:1:25.2:1:0.65704:2.31441:60:10:0.0106:0:1 +6 157099591 . G T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13108;SOR=Inf;LSEQ=CAGGCCGACCCCCCGGGCCC;RSEQ=CCGCTGCTGAGCAAGCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:137,140:277,0:0:2,0:24.5:1:30.2:1:1:0:60:22.083:0.9925:0:0.4 0/1:340:4:1,3:166,168:334,4:0.0118:2,2:13.3:1:26.8:1:0.62287:2.9558:60:3:0.009:0:1 +6 157099646 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14825;SOR=0;LSEQ=CGCCGCCCAAGATGGGGGAG;RSEQ=CGGCGGGCGGCCGCTACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:65,75:140,2:0.0141:2,2:14:0:32:0:1:1.15:60:4:0.0145:0:1.5 0/0:226:0:0,0:105,121:226,0:0:2,0:25.3:1:30.5:1:1:0:60:27.25:1:0:0.4 +6 157099697 . C A 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16075;SOR=0;LSEQ=TGGGCGCCCTGGGCACGCAG;RSEQ=AGCCGCCGGTCGCCGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:17,21:38,2:0.0476:2,2:5.5:1:28:1:1:1.23:60:4:0.0488:0:1 0/0:62:0:0,0:26,34:60,0:0:2,0:9.1:1:30.5:1:1:0:60:29:0.9667:0:0.4 +6 157099712 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.50695;SOR=Inf;LSEQ=CGCAGCAGCCGCCGGTCGCC;RSEQ=TGCCCGGGGGCGGCGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:68,23:91,0:0:2,0:8.4:1:30.1:1:1:0:60:44.5:0.9889:0:0.3 0/1:121:2:1,1:80,38:118,2:0.0165:2,2:10.5:1:30:1:0.54622:2.0911:60:4:0.0168:0:1.5 +6 157099715 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19435;SOR=0;LSEQ=AGCAGCCGCCGGTCGCCGTG;RSEQ=CCGGGGGCGGCGGCGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:77,23:100,2:0.0194:2,2:11:1:29.5:1:0.41701:3.29852:60:4:0.0196:0:1 0/0:130:0:0,0:90,40:130,0:0:2,0:10.6:1:31:1:1:0:60:129:1:0:0.3 +6 157099725 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.20036;SOR=0;LSEQ=GGTCGCCGTGCCCGGGGGCG;RSEQ=CGGCGGCCCGGCGGCCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:2,0:131,31:162,2:0.0121:2,0:18:1:26:1:1:0:60:4:0.0123:0:1 0/0:203:0:0,0:139,64:203,0:0:2,0:14.7:1:31.1:1:1:0:60:100.5:1:0:0.3 +6 157099726 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.19869;SOR=0;LSEQ=GTCGCCGTGCCCGGGGGCGG;RSEQ=GGCGGCCCGGCGGCCGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:137,32:169,2:0.0117:2,2:17.5:1:31.5:1:0.34964:4.23125:60:4:0.0118:0:1.5 0/0:212:0:0,0:145,67:212,0:0:2,0:15.1:1:31:1:1:0:60:52:1:0:0.3 +6 157099732 . C T 54 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06717;SOR=Inf;LSEQ=GTGCCCGGGGGCGGCGGCGG;RSEQ=CCGGCGGCCGTCCCGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:174,43:217,0:0:2,0:17:1:32.8:1:1:0:60:53.25:1:0:0.2 0/1:264:5:1,4:175,84:259,5:0.0189:2,2:7.6:1:23.4:1:0.0437:8.26487:60:4:0.0156:0:1.2 +6 157099871 . TCCG T 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.00022;SOR=2.66381;LSEQ=TGGGGATGATGCACTCCGCC;RSEQ=CCGCCGCCGCCGGGGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1516:18:11,7:731,764:1495,18:0.0119:2,2:26:1:31.7:1:0.34867:1.64:60:36:0.0121:0.002:0.1 0/1:1644:51:28,23:782,803:1585,51:0.031:2,2:30.9:1:30.2:1:0.4783:1.25:59.9:102:0.0316:0.0012:0.3 +6 157099945 . G A 201 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=49.5206;LSEQ=GAAGGGTACCCCAACAGCCA;RSEQ=TGCAACCATTATCCGGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1317:2:1,1:556,759:1315,2:0.0015:2,2:17.5:1:19.5:1:1:1.36:60:1:8e-04:0:3 0/1:1541:108:51,57:659,770:1429,108:0.0701:2,2:22.7:1:29.8:1:0.84184:1.05:59.1:216:0.0714:0:1.3 +6 157100054 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.50344;SOR=Inf;LSEQ=GAGGAGGAGGAGGAGCAGGA;RSEQ=CAGGAGGAGCAGGAGCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:22,133:155,0:0:2,0:24:1:33.3:1:1:0:58.4:310:1:0:0.2 0/1:189:2:1,1:40,147:187,2:0.0106:2,2:46:1:29:1:0.38771:3.64:60:4:0.0108:0:1 +6 157100092 . CGCG C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.17498;SOR=0;LSEQ=GGAGCTGTGGCGGCGGCGGC;RSEQ=GCGGCGGCGGCAGCAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:15,36:51,2:0.0377:2,2:49.5:1:32.5:1:0.51669:2.36:60:4:0.0377:0:1 0/0:73:0:0,0:31,42:73,0:0:2,0:12.7:1:30.8:1:1:0:60:72:1:0:0.5 +6 157100100 . C T 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=1.60558;LSEQ=GGCGGCGGCGGCCGCGGCGG;RSEQ=GGCGGCAGCAGCAGGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:26,32:58,1:0.0169:2,0:1:0:26:0:1:0:60:2:0.0175:0:1 0/1:74:2:1,1:34,38:72,2:0.027:2,2:10:0:30.5:1:1:1.12:60:4:0.0274:0:2 +6 157100103 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.10846;SOR=Inf;LSEQ=GGCGGCGGCCGCGGCGGCGG;RSEQ=GGCAGCAGCAGGAGGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:34,34:68,0:0:2,0:8.7:1:30.1:1:1:0:59.8:21.667:1:0:0.5 0/1:63:3:1,2:32,28:60,3:0.0476:2,2:9:1:29:1:0.60112:2.25667:60:6:0.0476:0:1.7 +6 157100116 . AGGC A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.52976;SOR=0.621;LSEQ=GCGGCGGCGGCAGCAGCAGG;RSEQ=GGCGGCGGCGGCGGCTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:6:2,4:49,42:91,6:0.0612:2,2:14.2:1:31:1:0.41835:2.31347:60:12:0.0612:0.0204:0.7 0/1:103:4:2,2:55,42:97,4:0.0388:2,2:8:1:29.8:1:1:1.30598:55:8:0.04:0.0291:1 +6 157100139 . G T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.32495;SOR=0.26032;LSEQ=CGGCGGCGGCGGCGGCTATG;RSEQ=GGGCTCGTCCGCGGGGTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:1,2:102,88:190,3:0.0155:2,2:27:1:30:1:0.59922:2.30837:60:6:0.0155:0:1.3 0/0:245:1:0,1:130,114:244,1:0.0041:2,0:1:0:28:0:0.46939:0:60:2:0.0041:0:1 +6 157100164 . G T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03849;SOR=Inf;LSEQ=TCGTCCGCGGGGTACGGGGT;RSEQ=CTGAGCTCCCCCCGGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:136,134:270,0:0:2,0:26.9:1:32.2:1:1:0:59.9:32.75:0.9962:0:0.4 0/1:352:6:1,5:174,172:346,6:0.017:2,2:9.5:1:26.2:1:0.21478:5.03849:60:12:0.0171:0:1.2 +6 157100170 . C T 42 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.78291;LSEQ=GCGGGGTACGGGGTGCTGAG;RSEQ=TCCCCCCGGCAGCAGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:0,3:145,143:288,3:0.0103:2,0:9:1:21.7:1:0.24742:0:60:2:0.007:0:1 0/0:371:3:0,3:185,183:368,3:0.0081:2,0:1:0:26.7:1:0.24798:0:59.3:6:0.0082:0:1 +6 157100171 . TC T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.13599;SOR=Inf;LSEQ=CGGGGTACGGGGTGCTGAGC;RSEQ=CCCCCGGCAGCAGGGCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:148,147:295,0:0:2,0:26.2:1:31.4:1:1:0:59.9:31.778:1:0:0.4 0/1:382:4:2,2:190,188:378,4:0.0105:2,2:34.8:1:31.8:1:1:1.01061:60:8:0.0106:0:0.3 +6 157100178 . G A 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.39015;SOR=3.18242;LSEQ=CGGGGTGCTGAGCTCCCCCC;RSEQ=GCAGCAGGGCGGCGGCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:1:1,0:149,149:298,1:0.0033:2,0:1:0:27:0:1:0:60:2:0.0034:0:1 0/1:378:4:3,1:188,185:373,4:0.0106:2,2:16.3:1:27.5:1:0.62313:2.94:60:8:0.0107:0:1 +6 157100229 . G T 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3787;SOR=3.50875;LSEQ=CGGGGGCGGCGGGGCCGCGA;RSEQ=CCTCAGCAAGGCGGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:1:0,1:152,92:244,1:0.004:2,0:1:0:27:0:0.37959:0:60:2:0.0041:0:1 0/1:285:4:1,3:166,115:281,4:0.014:2,2:12:1:28:1:0.31026:4.30902:60:8:0.0142:0:1.3 +6 157100246 . G T 51 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.14422;LSEQ=CGAGCCTCAGCAAGGCGGCC;RSEQ=CCGGCTCGGCGGCGGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:3:0,3:209,97:306,3:0.0096:2,0:1:0:25.3:1:0.03321:0:60:6:0.0098:0:1 0/1:364:4:1,3:222,138:360,4:0.011:2,2:5:1:25.5:1:0.30307:4.80552:60:8:0.0111:0:1 +6 157100255 . G T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.02237;SOR=0;LSEQ=GCAAGGCGGCCGCCGGCTCG;RSEQ=CGGCGGGGGGCTTCCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:5:1,4:245,127:372,5:0.0132:2,2:14.6:1:27.2:1:0.05146:7.67479:60:10:0.0135:0:1.2 0/0:428:0:0,0:271,157:428,0:0:2,0:20.8:1:31.2:1:1:0:59.9:52.5:1:0:0.3 +6 157100260 . G T 62 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.06427;LSEQ=GCGGCCGCCGGCTCGGCGGC;RSEQ=GGGGGCTTCCAGCGCTTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:4:1,3:266,140:406,4:0.0097:2,2:9.3:1:28.5:1:0.12421:5.67505:60:8:0.01:0:1 0/1:483:5:1,4:299,178:477,5:0.0104:2,2:12:1:27:1:0.0699:6.69365:60:10:0.0104:0:1 +6 157100396 . GCGC G 83 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.50837;SOR=1.85128;LSEQ=CCGAGTACAGCAGCCCCAGC;RSEQ=CGCCGCCGCCGCCGTCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:3:1,2:104,207:311,3:0.0094:2,2:13:1:30.3:1:1:1.00482:60:6:0.0096:0.0063:1 0/1:346:6:2,4:122,216:338,6:0.0173:2,2:30:1:32.3:1:1:1.12926:60:12:0.0175:0:0 +6 157100398 . G A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.12524;SOR=Inf;LSEQ=GAGTACAGCAGCCCCAGCGC;RSEQ=CCGCCGCCGCCGCCGTCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:102,208:310,0:0:2,0:22:1:31.7:1:1:0:60:154:1:0:0.2 0/1:339:4:3,1:119,210:329,4:0.0118:2,2:11.3:1:26.3:1:0.14126:5.27:60:8:0.0122:0:1 +6 157100410 . G A 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.72464;SOR=1.6052;LSEQ=CCCAGCGCGCCGCCGCCGCC;RSEQ=CCGTCGCAGCCCCAGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:3:1,2:59,156:215,3:0.0138:2,2:16.7:1:24:1:1:1.32:60:2:0.0094:0:2 0/1:228:5:4,1:67,155:222,5:0.0219:2,2:8.8:1:28:1:0.03426:9.16:58.4:10:0.022:0:1 +6 157100469 . C T 29 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60332;SOR=0.44372;LSEQ=GGCGGCGGGCGGCCAGCAGG;RSEQ=GGCCGCGGGCATGGGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:86,29:115,2:0.0171:2,2:6:1:29.5:1:0.44872:2.93244:60:4:0.0177:0:1 0/0:131:1:0,1:92,38:130,1:0.0076:2,0:1:0:24:0:0.29771:0:60:2:0.0079:0:1 +6 157100470 . G T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22217;SOR=0;LSEQ=GCGGCGGGCGGCCAGCAGGC;RSEQ=GCCGCGGGCATGGGCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:94,32:126,2:0.0156:2,2:34:0:33:1:0.45066:2.90822:60:4:0.0159:0:1.5 0/0:143:0:0,0:103,40:143,0:0:2,0:11.4:1:29.4:1:1:0:59.8:27.6:1:0:0.3 +6 157100482 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25244;SOR=Inf;LSEQ=CAGCAGGCGGCCGCGGGCAT;RSEQ=GGCTTGGGCAAGGACATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:167,71:238,0:0:2,0:15.7:1:32.3:1:1:0:60:78.333:1:0:0.3 0/1:275:3:1,2:187,85:272,3:0.0109:2,2:9.7:1:22.3:1:0.23606:4.37371:60:2:0.0073:0:1.3 +6 157100505 . C T 52 v3;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.07041;SOR=Inf;LSEQ=CTTGGGCAAGGACATGGGCG;RSEQ=CCAGTACGCCGCTGCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:267,128:395,0:0:2,0:24.5:1:32.2:1:1:0:60:78:0.9974:0:0.2 0/1:501:5:0,5:323,172:495,5:0.01:2,0:9.2:1:22.4:1:0.00536:0:60:4:0.0082:0:1.2 +6 157150145 . G A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.38002;LSEQ=TTTAGTCTAGAGCTCTCTTA;RSEQ=TTGTTAAAAACTCCTAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:10,0:4,0:4,10:0.7143:0,0:17.7:1:30.6:1:1:0:60:20:0.7143:0:1.2 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:31:1:29.9:1:1:0:60:14:0.7778:0:1 +6 157150230 . A G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.08219;LSEQ=GTCTTGCTGGATGTTTTGTC;RSEQ=GGTCATTGTTTTTAATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:32:31,1:59,2:61,32:0.3441:1,1:23.4:1:30:1:1:1.05:60:64:0.3441:0:1.1 0/1:49:2:2,0:47,0:47,2:0.0408:1,0:23.5:1:28:1:1:0:60:4:0.0426:0:1 +6 157150529 . G A 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02135;SOR=Inf;LSEQ=GTCGGACTCCCGGGGCCATG;RSEQ=CCGGAATGCAGTACCCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:527:0:0,0:175,352:527,0:0:2,0:26.1:1:31.7:1:1:0:60:46.909:1:0:0.1 0/1:457:5:3,2:172,279:451,5:0.0109:2,2:23.6:1:27.2:1:0.37658:2.43:60:10:0.0112:0:1 +6 157150546 . T A 56 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19311;SOR=4.5331;LSEQ=ATGGCCGGAATGCAGTACCC;RSEQ=CAGCAGCAGGTTTGTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:1:1,0:119,309:428,1:0.0023:2,0:1:0:27:0:0.27972:0:60:2:0.0024:0:1 0/1:381:4:3,1:123,254:377,4:0.0105:2,2:6:1:28.3:1:0.10762:6.16:60:8:0.0108:0:1 +6 157150583 . T C 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.00038;SOR=Inf;LSEQ=CTGGTCCCCCGACCCGCTGC;RSEQ=TTTTTGTAATAGTTTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:31,184:215,0:0:2,0:23:1:31:1:1:0:60:106.5:0.9953:0:0.1 0/1:185:10:4,6:33,142:175,10:0.0541:2,2:27.5:1:31:1:0.11495:2.85:59.8:20:0.0556:0:1.1 +6 157222269 . A T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03636;SOR=Inf;LSEQ=CCACCTTTATGATATTATCA;RSEQ=TAGTTTCTATCTGATAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:14,0:14,0:0:1,0:26.1:1:30.3:1:1:0:60:28:1:0:0 0/1:8:3:3,0:5,0:5,3:0.375:0,0:13.7:1:27.7:1:1:0:60:6:0.4286:0:1 +6 157222396 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50553;SOR=0;LSEQ=AAGAGAGGATTAGAAATATT;RSEQ=AGTTTAGTTGCTTAGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:2,0:134,1:135,2:0.0146:1,0:24.5:1:30.5:1:1:0:60:4:0.0146:0:1 0/0:107:0:0,0:103,4:107,0:0:1,0:20.9:1:31.6:1:1:0:60:106:1:0:0.1 +6 157222436 . A T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24881;SOR=Inf;LSEQ=GAACCCCCTTCATGTTGCTG;RSEQ=ATTGAAACCATATTTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:236,40:276,0:0:2,0:21.6:1:30.2:1:1:0:60:137:1:0:0.1 0/1:284:3:1,2:228,53:281,3:0.0106:2,2:27:1:25:1:0.09697:8.51026:60:6:0.0106:0:1 +6 157222761 . G GA 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.51134;SOR=0;LSEQ=TTAAAAATTATGTTCTGGTG;RSEQ=AAAAAAAATTAGTTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:3,87:90,2:0.0215:1,0:30.5:1:33:0:1:0:60:4:0.022:0:0 0/0:66:0:0,0:1,65:66,0:0:1,0:24.1:1:30.7:1:1:0:59.5:65:1:0:0 +6 157256508 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19346;SOR=Inf;LSEQ=ACAGGCATGAGCCACTGTGC;RSEQ=CAGCCAAGCTTTTGTTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:136,6:142,0:0:1,0:25.1:1:31.8:1:1:0:59.5:284:1:0:0.1 0/1:112:2:2,0:101,9:110,2:0.0179:2,0:41:1:28:1:1:0:60:4:0.018:0:1 +6 157256511 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50367;SOR=0;LSEQ=GGCATGAGCCACTGTGCCCA;RSEQ=CCAAGCTTTTGTTTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:2,0:138,7:145,2:0.0136:1,0:20.5:1:30:1:1:0:60:4:0.0141:0:1 0/0:119:0:0,0:106,13:119,0:0:2,0:22.4:1:31.3:1:1:0:59.6:58.5:1:0:0.1 +6 157256588 . G GT 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50144;SOR=1.24688;LSEQ=ATGAAGTGCTTTGTGTTTGT;RSEQ=TTTTTTTTTAGGACATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:24:15,9:385,215:600,24:0.0383:2,2:24.7:1:30.4:1:0.83223:1.07429:60:48:0.0397:0.0032:0.3 0/1:719:34:19,15:418,264:682,34:0.0473:2,2:28.5:1:29:1:0.58991:1.24959:60:33:0.0467:0.0028:0.1 +6 157403542 . A G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06672;SOR=Inf;LSEQ=GTCCAGTAATCAAGTTAAAT;RSEQ=TAAAGTTTCACCAGCTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:18.2:1:30.1:1:1:0:60:38:1:0:0.1 0/1:14:3:1,2:4,7:11,3:0.2143:2,2:12.3:1:30.3:1:1:1.1321:60:6:0.2143:0:1.3 +6 157405270 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGTGAGACTTCATCACC;RSEQ=CCCCCCCAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:33.5:1:1:0:57:4:1:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 157405495 . GC TT 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCTGTCTGTGTTGTGTG;RSEQ=ATTTTGAACAGGTCTAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:13.5:1:32.5:0:1:0:60:4:0.5:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:19:1:29:1:1:0:60:4:1:0:0 +6 157405761 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.11147;SOR=1.30303;LSEQ=GATGAGATATTCATCCAAAC;RSEQ=TGTCACTCTATAAATACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:116:87,29:156,45:201,116:0.3636:2,2:22.8:1:30.4:1:0.67943:1.15502:60:115:0.3662:0:1 0/1:342:146:104,42:139,57:196,146:0.4269:2,2:25.5:1:29.8:1:1:1.02:60:292:0.4294:0:1.1 +6 157405930 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02776;SOR=1.23929;LSEQ=TCGCCTTTCTCCCCACATGC;RSEQ=TCCCCTCATCTCTCCAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:929:317:171,146:349,261:610,317:0.3412:2,2:24:1:30.7:1:0.36462:1.14151:60:38.625:0.3414:0:1.1 0/1:954:373:211,162:325,251:576,373:0.391:2,2:24.2:1:29.5:1:1:1.01:60:73.6:0.3907:0:1.1 +6 157406462 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTCTAAAACATTTCTAC;RSEQ=GTCTATACTTATCAGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 157431259 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCCCACCTGGAGACTCA;RSEQ=GTAAGAGTCAGGAGGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:29.5:1:31:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 157431876 . T G 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64045;SOR=2.02759;LSEQ=GAGGAGGGAGGATGCTTTCT;RSEQ=GTAGGTTGGGTGAAGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:0,2:1,21:22,2:0.0833:1,0:26:1:31:1:1:0:60:4:0.087:0:1 0/1:19:3:0,3:0,16:16,3:0.1579:1,0:22.7:1:32:1:1:0:60:6:0.1579:0:1 +6 157454046 . T C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6516;SOR=0.7539;LSEQ=TTAGCTATTTTTTAGGAGAA;RSEQ=CTTATGGTACCAGCCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:14:14,0:109,3:112,14:0.1111:1,1:23.2:1:32.5:1:1:0:60:28:0.1138:0:1.1 0/1:93:8:8,0:84,1:85,8:0.086:1,0:23.5:1:31.8:1:1:0:60:16:0.0879:0:1 +6 157454082 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20566;SOR=Inf;LSEQ=TTCTCCCCTGCCACCTGCCA;RSEQ=ATCAGTCCATGTCCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:212,26:238,0:0:2,0:24.7:1:32.4:1:1:0:59.8:118:1:0:0.1 0/1:198:2:1,1:172,24:196,2:0.0101:2,2:21.5:1:31.5:1:0.23714:7.0422:60:4:0.0102:0:1 +6 157469563 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52314;SOR=0;LSEQ=GGGGCTGTCTGTATTTGAGT;RSEQ=ACTCTCTGAGGGCCTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:42,2:44,2:0.0435:1,2:24.5:1:28:1:0.12754:17.3476:60:4:0.0435:0:1 0/0:28:0:0,0:27,1:28,0:0:1,0:22.6:1:31.3:1:1:0:60:56:1:0:0.2 +6 157470120 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15035;SOR=0;LSEQ=AGCACGCCCCGGGCAGGTAC;RSEQ=CTGTGTGTCTACCCGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:4:1,3:9,80:89,4:0.043:2,2:11.8:1:30.3:1:0.37062:2.91:60:8:0.0435:0:1 0/0:62:0:0,0:9,53:62,0:0:2,0:20.4:1:31.1:1:1:0:59.7:61:1:0:0.2 +6 157488140 . C T 81 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59287;SOR=1.49628;LSEQ=CCACTGCTAATGTGCATGGT;RSEQ=GGTATATGTGTGCTGTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:849:6:0,6:517,326:843,6:0.0071:2,0:1:0:26.5:1:0.00348:0:60:12:0.0072:0:1 0/1:759:8:2,6:446,305:751,8:0.0105:2,2:9.5:1:27:1:0.06953:4.37863:60:16:0.0106:0:1.3 +6 157495331 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17262;SOR=Inf;LSEQ=TTCTCTCTTCACTGGTGTTG;RSEQ=CCGACACTTTTTTTTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:21,164:185,0:0:2,0:24.4:1:31.7:1:1:0:60:45.25:1:0:0.2 0/1:132:2:1,1:12,118:130,2:0.0152:2,2:11:0:27:1:0.18795:9.49:60:4:0.0155:0:1.5 +6 157495338 . CT C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50965;SOR=0;LSEQ=TTCACTGGTGTTGGCCGACA;RSEQ=TTTTTTTCATTTGGTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:0,2:13,145:158,2:0.0125:2,0:36.5:1:32.5:1:1:0:60:4:0.0128:0:0 0/0:118:0:0,0:8,110:118,0:0:2,0:21.7:1:29.3:1:1:0:59.7:38.333:1:0:0.1 +6 157496153 . G GT 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.15408;SOR=1.6374;LSEQ=AAGCCCTGTAAGTGGCTCTG;RSEQ=TTTTTTTTTGTTTTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:593:18:3,15:144,430:574,18:0.0304:2,2:28.1:1:31.1:1:0.5823:1.67322:60:36:0.031:0:0 0/1:492:24:8,16:147,320:467,24:0.0488:2,2:28.4:1:29.1:1:0.825:1.09:58.3:23:0.0475:0.002:0.5 +6 157496163 . G GT 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14938;SOR=3.72907;LSEQ=AGTGGCTCTGGTTTTTTTTT;RSEQ=TTTTTTTTGTTTTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:480:2:0,2:117,360:477,2:0.0042:2,0:18.5:1:32:0:1:0:60:4:0.0042:0:0.5 0/1:390:6:1,5:112,272:384,6:0.0154:2,2:29:1:26.8:1:0.67696:2.05562:60:5:0.0131:0:0.5 +6 157502370 . T C 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTGGATAAGTTCTTACAG;RSEQ=GGCTTTCTTTGAATGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:40,180:220,0:0:2,0:22.6:1:29.6:1:1:0:59.9:30.429:1:0:0.1 0/1:145:31:2,29:14,100:114,31:0.2138:2,2:25.6:1:29.5:1:0.52334:2.02167:60:62:0.2153:0:1.1 +6 157510619 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08124;SOR=Inf;LSEQ=AATAGAAAAGCAACGAATTT;RSEQ=ACAACATCATTATCAGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:77,2:79,0:0:1,0:25.8:1:31.3:1:1:0:59.7:78:1:0:0.1 0/1:32:2:2,0:30,0:30,2:0.0625:1,0:25:1:29.5:1:1:0:60:4:0.0625:0:1.5 +6 157511319 . G A 130 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=0.10393;LSEQ=ATGCCCTATGAGCCCAACAA;RSEQ=GACCCCTTTGGGGGAATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:18:5,13:135,329:464,18:0.0373:2,2:21.4:1:31.2:1:1:1.06673:60:36:0.0382:0:1 0/0:500:2:2,0:181,317:498,2:0.004:2,0:1:0:26.5:1:0.13349:0:56.5:4:0.004:0:1 +6 157517575 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13078;SOR=Inf;LSEQ=GTGTCCCCTTTCCTGTGAAA;RSEQ=TAAAGAGGCAATGGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:0,45:45,0:0:1,0:22.4:1:32.9:1:1:0:59:90:1:0:0.1 0/1:26:2:0,2:1,23:24,2:0.0769:1,0:25:1:29.5:1:1:0:60:4:0.0769:0:1 +6 157519832 . A G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00089;SOR=Inf;LSEQ=TTGTCGGAGGGGTGCGCAGT;RSEQ=AAAGCCACACAGAGCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:97,2:99,0:0:1,0:23.8:1:28.4:1:1:0:59.8:98:1:0:0.1 0/1:74:8:8,0:66,0:66,8:0.1081:1,0:30.4:1:32.9:1:1:0:60:16:0.1096:0:1 +6 157519938 . A G 200 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGTTTTCTTTGAATGCCTC;RSEQ=TTCCAGGCATGAACCTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:743:0:0,0:466,276:742,0:0:2,0:27.6:1:30.7:1:1:0:60:81.444:1:0:0.1 0/1:642:96:56,40:337,208:545,96:0.1495:2,2:24:1:30.4:1:0.57011:1.15701:60:192:0.1517:0:1.3 +6 157522360 . G A 168 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=14.88362;LSEQ=CCGTCCTACCAGACGCCACC;RSEQ=TCACTGCCAAATCACATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:879:5:3,2:425,449:874,5:0.0057:2,2:13:1:27.6:1:0.67899:1.58:60:10:0.0058:0:1 0/1:751:59:32,27:345,344:689,59:0.0786:2,2:23.7:1:28.6:1:0.58851:1.18:60:18.667:0.0758:0:1.1 +6 157522675 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50213;SOR=0;LSEQ=ATTCCAGTTGCAGTGTAGAA;RSEQ=TTTAATTTTAGTAAAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:1,167:168,2:0.0118:1,2:17.5:1:29.5:1:0.02346:118.34:60:4:0.0121:0:1 0/0:143:0:0,0:7,136:143,0:0:1,0:21.6:1:29.6:1:1:0:60:46.667:1:0:0.2 +6 157524934 . G T 138 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=32.11547;LSEQ=TTATTTTTTCTTACTCTTTC;RSEQ=TTAACTTTCGTTCTTTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:0,1:354,76:430,1:0.0023:2,0:1:0:27:0:0.17865:0:60:2:0.0024:0:1 0/1:374:26:21,5:277,70:347,26:0.0695:2,2:27.3:1:29.5:1:1:1.06:60:12:0.0647:0:1.1 +6 157527280 . TCTC T 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.11762;SOR=0.19136;LSEQ=TGTACCTGTTCTTTCTTTCT;RSEQ=CTCCTCCTCCTCTCCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:5:5,0:205,46:251,5:0.0196:2,0:25.2:1:32.8:1:0.58886:0:60:10:0.0199:0.0039:0.2 0/0:263:1:0,1:193,66:259,1:0.0038:2,0:15:0:33:0:0.25769:0:60:2:0.0038:0:0 +6 157527482 . A C 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGAGGAGGAAGATGCTG;RSEQ=ATGTATTGATGACGACGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:818:0:0,0:379,438:817,0:0:2,0:23.9:1:30.5:1:1:0:59.9:73.273:1:0:0.1 0/1:854:39:20,19:372,443:815,39:0.0457:2,2:23.9:1:30.9:1:0.51417:1.25:60:18.5:0.044:0:1.2 +6 157527492 . TGAC T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GAAGATGCTGAATGTATTGA;RSEQ=GACGAGGAAGACGAGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:805:0:0,0:366,439:805,0:0:2,0:25.2:1:32.1:1:1:0:59.9:88.444:1:0:0.1 0/1:845:28:13,15:363,449:812,28:0.0331:2,2:24.8:1:30.5:1:0.84972:1.07:60:56:0.0337:0.0059:0.2 +6 158190377 . C A 50 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48571;SOR=0.22474;LSEQ=AATTTTTGCAGAGTTCTACT;RSEQ=TGATGCAGGCGCAGGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:19.3:1:31.7:1:1:0:60:6:0.75:0:1.3 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:20:0:32:0:1:0:60:2:0.3333:0:1 +6 158411364 . T C 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.43328;LSEQ=CTGCCCACTCTCTCATGCCT;RSEQ=CTTCTCCTTCTCCTTGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:19.5:1:28.5:1:1:0:60:4:0.4:0:1 1/0:4:2:2,0:1,1:2,2:0.5:2,0:8.5:1:31:1:1:0:60:4:0.5:0:1 +6 158411645 . A G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=13.68192;LSEQ=TGTTAGCGGCTGCTGCTCAG;RSEQ=CCCAGCGGAGGACCGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:19:9,10:103,130:233,19:0.0748:2,2:30.4:1:31.9:1:0.81421:1.14:60:38:0.0769:0:1.1 1/0:283:149:68,81:58,76:134,149:0.5265:2,2:25.9:1:30.2:1:0.72032:1.10:60:36.25:0.5216:0:1.1 +6 159215375 . G T 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02277;SOR=0;LSEQ=ACCACCACCACCAGGCTTTG;RSEQ=CAATTGAGAAAACACATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:14,14:28,5:0.1515:2,2:29.4:1:30:1:1:1.48182:60:10:0.1515:0:1 0/0:35:0:0,0:15,20:35,0:0:2,0:28.6:1:30.9:1:1:0:57.2:34:1:0:0.3 +6 159215408 . C T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.04885;SOR=0.23444;LSEQ=CACATCTAAATCCCAACTTT;RSEQ=CATTTTATTATCAGGGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:6,6:3,4:7,12:0.6316:2,2:17.5:1:30.4:1:1:1.31:60:24:0.6316:0:1.5 0/1:18:5:2,3:6,7:13,5:0.2778:2,2:27.6:1:29.4:1:1:1.26799:60:10:0.2778:0:1 +6 159215413 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=CTAAATCCCAACTTTCCATT;RSEQ=TATTATCAGGGTGTTAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,8:14,2:0.125:2,2:9.5:1:31.5:1:1:1.31:60:4:0.125:0:2.5 0/0:16:0:0,0:7,9:16,0:0:2,0:16.3:1:29.4:1:1:0:60:32:1:0:0.4 +6 159947173 . G T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TCTCTGGGTGGAGCAGGCTG;RSEQ=CGCTTTAGCTGAACCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:49:0:33:0:1:0:60:2:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:39.5:1:29:1:1:0:39:4:0.6667:0:3 +6 159947207 . G T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCAGGTACCTTTCTCTTTG;RSEQ=CTTCTTTCTTTTTCTGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:15:0:34:0:1:0:60:2:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:27.5:1:31:1:1:0:39:4:0.6667:0:3 +6 159947377 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13885;SOR=Inf;LSEQ=TGGGGAACATCGTAGACTCC;RSEQ=AGTTTTGCCATGGTGACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:74,75:149,0:0:2,0:32.7:1:31.7:1:1:0:36.1:48.667:1:0:0.1 0/1:89:2:1,1:40,47:87,2:0.0225:2,2:39:0:31:1:1:1.17:57.5:4:0.0225:0:1 +6 159947467 . G A 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCACCTTTCTTATAGATTC;RSEQ=CATATACGTGGCCAAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:33,35:68,0:0:2,0:24.5:1:31.6:1:1:0:41.8:136:1:0:0.1 0/1:54:14:7,7:19,21:40,14:0.2593:2,2:27.5:1:29.4:1:1:1.10:23.7:28:0.2642:0:1.1 +6 159947476 . T TG 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTATAGATTCGCATATACG;RSEQ=GGCCAAAGGAGCAACTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:41,37:78,0:0:2,0:22.6:1:30.1:1:1:0:44.6:38:1:0:0.1 0/1:57:15:9,6:23,19:42,15:0.2632:2,2:26.7:1:31.3:1:0.77078:1.23:23.7:30:0.2679:0.0351:1.1 +6 159947526 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20425;SOR=Inf;LSEQ=AAGGCCTAGAGAACATATGT;RSEQ=AGGTGCCTCTCCTCTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:74,59:133,0:0:2,0:23.5:1:32.1:1:1:0:52.3:132:0.9925:0:0.3 0/1:111:2:1,1:63,46:109,2:0.018:2,2:38.5:1:28:1:1:1.36561:26:4:0.0182:0:1.5 +6 159947566 . C T 135 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=36.3813;LSEQ=CTTTGTGTTCGTCATTTTGG;RSEQ=GAATTACCGGAAGATGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:1:1,0:94,92:186,1:0.0053:2,0:10:0:29:0:1:0:24:2:0.0054:0:1 0/1:158:26:12,14:70,62:132,26:0.1646:2,2:31:1:28.8:1:0.52932:1.31489:42.1:25:0.1603:0:1.8 +6 159947590 . C T 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14789;SOR=1.43803;LSEQ=TTACCGGAAGATGGCGGTTC;RSEQ=GGCCAAAAGACCAAAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:47:21,26:56,77:133,47:0.2597:2,2:28.6:1:31.1:1:0.86402:1.11:44.3:94:0.2626:0:1.2 0/1:152:51:22,29:44,57:101,51:0.3355:2,2:28.3:1:29.4:1:1:1.01743:41.5:102:0.34:0:1.1 +6 159947592 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21758;SOR=Inf;LSEQ=ACCGGAAGATGGCGGTTCCG;RSEQ=CCAAAAGACCAAAATATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:74,97:171,0:0:2,0:27.7:1:31.5:1:1:0:53.9:41.75:1:0:0.4 0/1:150:2:1,1:63,85:148,2:0.0133:2,2:17:1:26.5:1:1:1.35:39.5:4:0.0135:0:1.5 +6 159947597 . A G 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.59472;SOR=2.38191;LSEQ=AAGATGGCGGTTCCGGCCAA;RSEQ=AGACCAAAATATGATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:72,94:166,1:0.006:2,0:34:0:15:0:1:0:44:0:0:0:3 0/1:141:2:1,1:59,80:139,2:0.0142:2,2:42:1:30:1:1:1.35:51:4:0.0146:0:3 +6 159947617 . T A 115 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=23.10072;LSEQ=AAGACCAAAATATGATTTTT;RSEQ=AATAAGCAGTATACATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:1,0:43,81:124,1:0.008:2,0:1:0:23:0:0.352:0:43:2:0.008:0:1 0/1:101:16:5,11:33,52:85,16:0.1584:2,2:16.6:1:28.9:1:0.77937:1.39169:52.9:32:0.1584:0:2.2 +6 159947648 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.01631;SOR=Inf;LSEQ=ATACATCTCCTCTGGGAAAA;RSEQ=AAAAGGGGACTTTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:2,51:53,0:0:1,0:24.8:1:32.7:1:1:0:60:106:1:0:0.2 0/1:31:4:0,4:2,25:27,4:0.129:2,0:30.5:1:27.5:1:1:0:60:8:0.129:0:2.3 +6 159947789 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01786;SOR=Inf;LSEQ=AAATTCTGCTTACATGTCTC;RSEQ=TATACACCTGGGTAGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:29.8:1:32.8:1:1:0:60:10:1:0:0.2 1/1:3:3:2,1:0,0:0,3:1:0,2:38:1:29.7:1:1:0:60:6:1:0:3.7 +6 159947800 . G T 43 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=ACATGTCTCCTATACACCTG;RSEQ=GTAGGAGACCTGAGAGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:0,3:3,1:0.25:0,0:45:0:16:0:1:0:60:0:0:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:27:1:27.7:1:1:0:60:6:1:0:3.7 +6 159947807 . G A 43 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02857;SOR=Inf;LSEQ=TCCTATACACCTGGGTAGGA;RSEQ=ACCTGAGAGTAGCCTAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:4,0:0:0,0:32.8:1:32.5:1:1:0:60:8:1:0:0.3 1/1:3:3:2,1:0,0:0,3:1:0,2:20:1:27.3:1:1:0:60:6:1:0:3.7 +6 159948256 . CA TG 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGGTGGGAGGATTGCTTG;RSEQ=CTAAGGTGGTTGAGGTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:28.5:1:1:0:44.5:4:1:0:2.5 +6 159948268 . T C 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGCTTGCACTAAGGTGGT;RSEQ=GAGGTTGCAGTGAGCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:29:1:1:0:44.5:4:1:0:2.5 +6 160639440 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53772;SOR=Inf;LSEQ=TAGCAGCAATAGTAGCAACA;RSEQ=CAGCAACAACAGTAATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:34,0:0:2,0:27.3:1:32.8:1:1:0:60:68:1:0:0 0/1:62:2:1,1:32,26:58,2:0.0323:2,2:10:0:30.5:1:1:1.22648:59:4:0.0323:0:1 +6 160639443 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53608;SOR=Inf;LSEQ=CAGCAATAGTAGCAACAGCA;RSEQ=CAACAACAGTAATTACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:35,0:0:2,0:25.5:1:32.9:1:1:0:60:70:1:0:0 0/1:63:2:1,1:34,27:61,2:0.0317:2,2:16:1:27:1:1:1.25461:60:4:0.0317:0:1.5 +6 160639492 . C G 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00709;SOR=Inf;LSEQ=AATAGCAACAGTAGAAGCAT;RSEQ=AGTGACAACAGCAGCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,18:39,0:0:2,0:27.1:1:32.6:1:1:0:60:78:1:0:0.1 0/1:33:6:4,2:14,13:27,6:0.1818:2,2:18.7:1:30.7:1:0.66478:1.82:60:12:0.1818:0:1 +6 160639494 . GTGACAACAGCAGCAGTAA G 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.31336;SOR=2.20188;LSEQ=TAGCAACAGTAGAAGCATCA;RSEQ=CAACAACAAAAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:3:2,1:22,18:40,3:0.0698:2,2:7:1:29.6:1:1:1.62:22:6:0.0714:0.0698:7 0/1:42:6:3,3:20,16:36,6:0.1429:2,2:6.2:1:29.4:1:1:1.24333:22:12:0.1429:0.1429:7.2 +6 160639499 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4953;SOR=0;LSEQ=ACAGTAGAAGCATCAGTGAC;RSEQ=ACAGCAGCAGTAACAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:21,20:41,2:0.0435:2,2:40:1:31.5:1:1:1.04883:60:4:0.0476:0:1 0/0:42:0:0,0:20,17:37,0:0:2,0:22.5:1:28.7:1:1:0:60:36:1:0:0.3 +6 160639530 . GC AT 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.48968;SOR=2.02719;LSEQ=TAACAACAACAAAAGCAACA;RSEQ=AGCAACAATAGTAATAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:3:2,1:26,25:51,3:0.0556:2,2:19:0:30.8:1:1:1.90:22:6:0.0577:0:6 0/1:56:6:3,3:22,28:50,6:0.1071:2,2:19.2:1:28.9:1:1:1.27:22:12:0.1071:0:6.2 +6 160639536 . A G 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31315;SOR=2.22926;LSEQ=CAACAAAAGCAACAGCAGCA;RSEQ=CAATAGTAATAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:3:2,1:30,25:55,3:0.0517:2,2:24:0:33.7:1:1:1.65:22:6:0.0517:0:6 0/1:55:6:3,3:22,27:49,6:0.1091:2,2:24.2:1:31.2:1:1:1.22:22:12:0.1091:0:6.2 +6 160639540 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23055;SOR=Inf;LSEQ=AAAAGCAACAGCAGCAACAA;RSEQ=AGTAATAGCAACAGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:33,25:58,0:0:2,0:24.8:1:29.7:1:1:0:58:28:1:0:0.4 0/1:55:2:1,1:23,30:53,2:0.0364:2,2:13:0:33:1:1:1.30:36:4:0.0364:0:4.5 +6 160639543 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2389;SOR=Inf;LSEQ=AGCAACAGCAGCAACAATAG;RSEQ=AATAGCAACAGCAACAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:31,26:57,0:0:2,0:26:1:29.3:1:1:0:58:27.5:1:0:0.4 0/1:55:2:1,1:23,30:53,2:0.0364:2,2:16:0:33:1:1:1.30:36:4:0.0364:0:4.5 +6 160639545 . AT GC 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48932;SOR=2.10621;LSEQ=CAACAGCAGCAACAATAGTA;RSEQ=AGCAACAGCAACAGTAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:3:2,1:29,24:53,3:0.0536:2,2:32:0:33.7:1:1:1.64:22:6:0.0536:0:5 0/1:56:6:3,3:22,28:50,6:0.1071:2,2:32:0:31:1:1:1.27:22:12:0.1071:0:5.2 +6 160639546 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4955;SOR=Inf;LSEQ=AACAGCAGCAACAATAGTAA;RSEQ=AGCAACAGCAACAGTAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:29,24:53,0:0:2,0:26.1:1:29.8:1:1:0:60:52:1:0:0.1 0/1:56:2:1,1:21,27:48,2:0.0357:2,2:19:0:32.5:1:1:1.28:36:4:0.04:0:4.5 +6 160639551 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.49625;SOR=Inf;LSEQ=CAGCAACAATAGTAATAGCA;RSEQ=CAGCAACAGTAACAGTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:31,25:56,0:0:2,0:25.6:1:30.4:1:1:0:58:112:1:0:0.4 0/1:60:2:1,1:26,32:58,2:0.0333:2,2:24:0:32.5:1:1:1.23:36:4:0.0333:0:4.5 +6 160639553 . AG CA 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.49407;SOR=1.91683;LSEQ=GCAACAATAGTAATAGCAAC;RSEQ=CAACAGTAACAGTAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:3:2,1:29,24:53,3:0.0536:2,2:24:0:32.3:1:1:1.64:22:6:0.0545:0:4 0/1:61:6:3,3:25,30:55,6:0.0984:2,2:24:0:29.9:1:1:1.20:22:12:0.1:0:4.2 +6 160639597 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49656;SOR=Inf;LSEQ=AGATATGGCAACAGTAATAC;RSEQ=ATCAGCAGCAACAGCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:39,23:62,0:0:2,0:23.5:1:31.4:1:1:0:60:30:1:0:0.1 0/1:66:2:1,1:38,26:64,2:0.0303:2,2:32.5:1:29.5:1:1:1.45294:60:4:0.0308:0:1 +6 160639684 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24166;SOR=Inf;LSEQ=ACGAGCAACAGCAGCAGCAA;RSEQ=AATAGTATCAGTAATAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:73,63:136,0:0:2,0:23.4:1:32.3:1:1:0:60:135:1:0:0.1 0/1:132:2:1,1:77,53:130,2:0.0152:2,2:29.5:1:27.5:1:1:1.4486:60:4:0.0153:0:1 +6 160639780 . T A 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.87983;LSEQ=AACAAAAGCAACAGAAACAG;RSEQ=AACAACAAAACCAACAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:1:1,0:53,75:128,1:0.0076:2,0:48:0:16:0:0.4186:0:60:0:0:0:1 0/1:140:2:1,1:55,82:137,2:0.0143:2,2:6:1:28.5:1:1:1.49:59:4:0.0144:0:1 +6 160639821 . T G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00219;SOR=Inf;LSEQ=CAACAACAGCAGCAACAATT;RSEQ=TAGCAATAGCAGCAACAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:28,53:81,0:0:2,0:23:1:30.3:1:1:0:60:39.5:1:0:0.1 0/1:74:8:4,4:23,43:66,8:0.1081:2,2:20.3:1:32.1:1:0.45223:1.85:60:16:0.1111:0:1 +6 160639881 . G A 49 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.6182;SOR=2.91211;LSEQ=CACAATTAAGAGCAACAACA;RSEQ=CAGCAACAATAGCCACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:1,0:19,30:49,1:0.02:2,0:5:0:32:0:0.4:0:22:2:0.02:0:7 0/1:53:3:3,0:22,28:50,3:0.0566:2,0:5:0:31:0:0.09818:0:22:6:0.0577:0:7 +6 160639900 . A C 52 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61746;SOR=3.03152;LSEQ=AGCAGCAACAATAGCCACAG;RSEQ=AATAGCAAAATCAGCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:1,0:20,29:49,1:0.02:2,0:24:0:34:0:0.42:0:22:2:0.02:0:7 0/1:51:3:3,0:22,26:48,3:0.0588:2,0:24:0:33:1:0.11044:0:22:6:0.0588:0:7 +6 160639903 . T C 52 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6193;SOR=2.79392;LSEQ=AGCAACAATAGCCACAGAAA;RSEQ=AGCAAAATCAGCAGTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:1:1,0:20,27:47,1:0.0208:2,0:27:0:34:0:0.4375:0:22:2:0.0208:0:7 0/1:53:3:3,0:22,28:50,3:0.0566:2,0:27:0:33:1:0.09818:0:22:6:0.0566:0:7 +6 160639909 . A C 51 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61753;SOR=2.90255;LSEQ=AATAGCCACAGAAATAGCAA;RSEQ=ATCAGCAGTAGCAACAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:1:1,0:19,25:44,1:0.0222:2,0:33:0:34:0:0.44444:0:22:2:0.0227:0:7 0/1:48:3:3,0:21,24:45,3:0.0625:2,0:33:0:32.7:1:0.23404:0:22:6:0.0625:0:7 +6 160639911 . T G 51 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61716;SOR=2.96809;LSEQ=TAGCCACAGAAATAGCAAAA;RSEQ=CAGCAGTAGCAACAACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:1,0:20,25:45,1:0.0217:2,0:35:0:35:0:0.45652:0:22:2:0.0227:0:7 0/1:48:3:3,0:21,24:45,3:0.0625:2,0:35:0:32.7:1:0.23404:0:22:6:0.0625:0:7 +6 160639920 . GCAA G 49 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.62542;SOR=2.49797;LSEQ=AAATAGCAAAATCAGCAGTA;RSEQ=CAACAGAAGTCGCAGCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:1:1,0:19,23:42,1:0.0233:2,0:35:0:35:0:0.46512:0:22:2:0.0238:0:7 0/1:53:3:3,0:25,25:50,3:0.0566:2,0:35:0:31.3:1:0.23803:0:22:6:0.0566:0:7 +6 160639932 . G A 46 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62946;SOR=2.37975;LSEQ=CAGCAGTAGCAACAACAGAA;RSEQ=TCGCAGCAATAACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:1,0:21,19:40,1:0.0244:2,0:27:0:32:0:1:0:22:2:0.0244:0:7 0/1:53:3:3,0:24,26:50,3:0.0566:2,0:27:0:29.3:1:0.23585:0:22:6:0.0566:0:7 +6 160639939 . C T 45 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62416;SOR=2.52929;LSEQ=AGCAACAACAGAAGTCGCAG;RSEQ=AATAACAGCAGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:1:1,0:22,18:40,1:0.0244:2,0:20:0:32:0:1:0:22:2:0.025:0:7 0/1:50:3:3,0:24,23:47,3:0.06:2,0:20:0:28.7:1:0.23959:0:22:6:0.06:0:7 +6 160639944 . ACAG A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.21263;SOR=0;LSEQ=CAACAGAAGTCGCAGCAATA;RSEQ=CAGCAGCAGCAACAGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:0,2:25,18:43,2:0.0444:2,0:33.5:1:32.5:1:0.19192:0:60:4:0.0465:0:0 0/0:52:0:0,0:29,23:52,0:0:2,0:27.3:1:31.3:1:1:0:57:104:1:0:1 +6 160639948 . C T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.36536;SOR=3.78773;LSEQ=AGAAGTCGCAGCAATAACAG;RSEQ=AGCAGCAGCAACAGAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:1:1,0:26,20:46,1:0.0213:2,0:11:0:32:0:1:0:22:2:0.0213:0:7 0/1:52:4:3,1:25,23:48,4:0.0769:2,2:18.5:1:29:1:0.61463:2.71:31.5:8:0.0769:0:5.5 +6 160639954 . C T 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=1;SOR=0.91747;LSEQ=CGCAGCAATAACAGCAGCAG;RSEQ=AGCAACAGAAGTAGCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:4:1,3:26,18:44,4:0.0833:2,2:12:0:28.8:1:0.3055:4.20628:54.5:8:0.0833:0:6 0/1:52:4:3,1:26,22:48,4:0.0769:2,2:11.5:1:29.8:1:0.62058:2.50:50:8:0.0769:0:5.8 +6 160639956 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.49505;SOR=Inf;LSEQ=CAGCAATAACAGCAGCAGCA;RSEQ=CAACAGAAGTAGCAGTAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:29,21:50,0:0:2,0:23.8:1:32.7:1:1:0:58.3:100:1:0:0.9 0/1:51:2:1,1:29,20:49,2:0.0392:2,2:21.5:1:27:1:1:1.43922:60:4:0.04:0:1 +6 160639965 . G A 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70966;SOR=1.44905;LSEQ=CAGCAGCAGCAGCAACAGAA;RSEQ=TAGCAGTAGTAATAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:3:1,2:28,18:46,3:0.0588:2,2:23:0:26.7:1:0.55927:3.03852:56.3:2:0.04:0:5.7 0/1:48:4:3,1:24,20:44,4:0.0833:2,2:22.5:1:30.8:1:0.62118:2.46:50:8:0.0833:0:5.8 +6 160639966 . TAGCAGTAGTAATAGCAGCAACAGCAGCAGC T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=7.000;MSILEN=3;SSF=0.11027;SOR=Inf;LSEQ=AGCAGCAGCAGCAACAGAAG;RSEQ=AGCAGCAGCAGCAATCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:29,18:47,0:0:2,0:26.2:1:29.3:1:1:0:59.4:46:0.9388:0:0.3 0/1:48:3:1,2:24,17:41,3:0.0625:2,2:7:1:26.5:1:0.56962:2.75752:60:6:0.0625:0.0625:2 +6 160639974 . GTAATAGCAGCAAC ATAACAGT 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21957;SOR=Inf;LSEQ=CAGCAACAGAAGTAGCAGTA;RSEQ=AGCAGCAGCAGCAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:30,23:53,0:0:2,0:24.8:1:32.5:1:1:0:59.1:106:0.9636:0:0.7 0/1:49:2:1,1:22,20:42,2:0.0408:2,2:34:0:31.3:1:1:1.09762:40:4:0.0435:0:4.5 +6 160639980 . G A 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12315;SOR=0;LSEQ=CAGAAGTAGCAGTAGTAATA;RSEQ=CAGCAACAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:4:1,3:31,23:54,4:0.0667:2,2:20.5:1:29:1:0.3161:3.9511:54.5:8:0.0727:0:6 0/0:51:0:0,0:22,20:42,0:0:2,0:18.2:1:30.8:1:1:0:59.5:84:0.9333:0:0.3 +6 160639984 . C T 91 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42078;SOR=0.60886;LSEQ=AGTAGCAGTAGTAATAGCAG;RSEQ=AACAGCAGCAGCAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:10:4,6:33,23:56,10:0.1493:2,2:12.4:1:27.6:1:0.31463:2.12683:57.8:20:0.1515:0:4.8 0/1:52:5:3,2:22,18:40,5:0.0962:2,2:2.6:1:26.6:1:1:1.22:60:10:0.1111:0:4 +6 160639986 . A G 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03135;SOR=0;LSEQ=TAGCAGTAGTAATAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:6:2,4:68,38:106,6:0.0526:2,2:21.2:1:32.2:1:0.19487:3.53638:56.3:12:0.0541:0:5.3 0/0:99:0:0,0:56,34:90,0:0:2,0:9.2:1:29:1:1:0:56.8:180:1:0:1.3 +6 160639989 . G A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=3;SSF=0.33486;SOR=0.58375;LSEQ=CAGTAGTAATAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:12:5,7:82,49:131,12:0.0822:2,2:3.8:1:28.3:1:0.21675:2.32833:60:11:0.0791:0:3.3 0/1:121:6:3,3:67,46:113,6:0.0496:2,2:9.3:1:29.8:1:0.68927:1.45179:60:12:0.0504:0:2.5 +6 160639990 . C T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.13116;SOR=1.49185;LSEQ=AGTAGTAATAGCAGCAACAG;RSEQ=AGCAGCAGCAGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:50:36,14:54,48:102,50:0.3247:2,2:6:1:29.2:1:0.03456:2.27:56.2:24:0.3288:0:2.4 0/1:122:51:35,16:35,33:68,51:0.418:2,2:5.8:1:28.6:1:0.06382:2.05:54.8:102:0.4322:0:2.2 +6 160639992 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.20689;SOR=Inf;LSEQ=TAGTAATAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:94,65:159,0:0:2,0:13.9:1:32.5:1:1:0:57.8:52:1:0:1.6 0/1:134:2:1,1:77,52:129,2:0.0149:2,2:24:0:31.5:1:1:1.47619:60:4:0.0153:0:1.5 +6 160639993 . C T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=1;SOR=1;LSEQ=AGTAATAGCAGCAACAGCAG;RSEQ=AGCAGCAGCAGCAGCAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:22:11,11:85,57:142,22:0.1333:2,2:5.2:1:29:1:0.48626:1.48748:60:44:0.1401:0:2.9 0/1:135:18:12,6:67,47:114,18:0.1333:2,2:5.7:1:28.2:1:0.61119:1.40:60:36:0.1364:0:2.3 +6 160640012 . C A 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22744;SOR=0.74766;LSEQ=GCAGCAGCAGCAGCAGCAAT;RSEQ=ATTACCATAGTAGCAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:56:36,20:191,103:294,56:0.1595:2,2:15.6:1:28.4:1:1:1.03014:58.8:27:0.1593:0:1.5 0/1:330:41:25,16:177,110:287,41:0.1242:2,2:16.6:1:28:1:1:1.02974:57.8:82:0.125:0:1.4 +6 160640055 . G A 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63971;SOR=0.93391;LSEQ=TAGCAGCAACACCAGCAGCA;RSEQ=TAGCAGCAGCAATAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:564:413:254,159:80,70:150,413:0.7323:2,2:24.9:1:30.6:1:0.09883:1.40:59.7:81.6:0.7405:0:2.6 1/0:558:401:244,157:79,76:155,401:0.7186:2,2:25.2:1:29.6:1:0.03553:1.49:59.7:79.2:0.7187:0:2.5 +6 160640059 . C T 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.09982;SOR=1.22374;LSEQ=AGCAACACCAGCAGCAGTAG;RSEQ=AGCAGCAATAGCAACAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:593:194:117,77:225,173:398,194:0.3272:2,2:23.1:1:29.3:1:0.42512:1.17:59.8:193:0.3294:0:3.4 0/1:587:219:131,88:206,162:368,219:0.3731:2,2:23.6:1:28.3:1:0.38859:1.17:59.5:72:0.375:0:3.4 +6 160640107 . T C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57217;SOR=0.9222;LSEQ=AGCAACAGCAATAGCAACAG;RSEQ=AGCAGCATCAGCAACAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:786:119:61,58:351,316:667,119:0.1514:2,2:21.7:1:32.5:1:0.84217:1.05609:32.4:58.5:0.1512:0:3.3 0/1:814:115:61,54:357,338:695,115:0.1413:2,2:21.7:1:31.7:1:0.76323:1.07:33.4:114:0.1418:0:2.8 +6 160640117 . A G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0087;SOR=0.42464;LSEQ=ATAGCAACAGTAGCAGCATC;RSEQ=GCAACAATAACAGCAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:723:30:10,20:358,335:693,30:0.0415:2,2:6.7:1:31.3:1:0.06148:2.13515:58.6:60:0.042:0:2.3 0/1:776:14:6,8:391,370:761,14:0.018:2,2:5.7:1:29.6:1:0.59642:1.40838:58.5:28:0.0183:0:2.7 +6 160640125 . T CAGC 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.07001;SOR=1.21555;LSEQ=AGTAGCAGCATCAGCAACAA;RSEQ=AACAGCAACAGAAGCAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:331:169,162:167,177:344,331:0.4875:2,2:30.5:1:32.8:1:0.53829:1.11:54.1:662:0.4933:0:5 1/0:731:392:197,195:167,163:330,392:0.5363:2,2:29.2:1:31.6:1:0.94054:1.01412:54:784:0.5429:0.0068:5.1 +6 160640127 . A G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1394;SOR=0.79019;LSEQ=TAGCAGCATCAGCAACAATA;RSEQ=CAGCAACAGAAGCAATAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:106:52,54:228,221:449,106:0.191:2,2:13.1:1:31.8:1:0.82909:1.0712:32.9:20.2:0.1853:0:3.5 0/1:598:94:51,43:250,253:503,94:0.1572:2,2:10.7:1:31:1:0.43345:1.20:33.3:46:0.1565:0:3.1 +6 160640128 . C G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00911;LSEQ=AGCAGCATCAGCAACAATAA;RSEQ=AGCAACAGAAGCAATAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:45:25,20:251,252:503,45:0.0817:2,2:8.4:1:32.9:1:0.53464:1.25:55.4:44:0.0809:0:2.2 0/1:595:49:25,24:270,269:539,49:0.0824:2,2:9.9:1:31.6:1:1:1.04:55.1:98:0.0831:0:2.3 +6 160640133 . AC GT 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11044;SOR=0.57539;LSEQ=CATCAGCAACAATAACAGCA;RSEQ=AGAAGCAATAACAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:25:11,14:98,80:178,25:0.0464:2,2:31.2:1:31:1:0.39214:1.55564:25:50:0.1256:0:7 0/1:588:16:11,5:87,85:172,16:0.0272:2,2:29.4:1:29.2:1:0.19701:2.14:24.7:32:0.0274:0:7 +6 160640136 . G A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06035;SOR=0.54411;LSEQ=CAGCAACAATAACAGCAACA;RSEQ=AAGCAATAACAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:26:11,15:207,188:395,26:0.061:2,2:28.1:1:30.9:1:0.41826:1.49999:26.4:52:0.0624:0:6.7 0/1:498:17:12,5:239,235:474,17:0.0341:2,2:25.9:1:29.1:1:0.13822:2.36:26.8:34:0.0348:0:6.8 +6 160640137 . A C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.39107;SOR=1.14348;LSEQ=AGCAACAATAACAGCAACAG;RSEQ=AGCAATAACAGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:423:318:162,156:56,45:101,318:0.7518:2,2:19:1:32.4:1:0.49295:1.19783:53.9:52:0.7554:0:5.1 1/0:491:381:187,194:60,43:103,381:0.776:2,2:18.7:1:31.5:1:0.11969:1.44646:53.5:46.625:0.7836:0:5.2 +6 160640139 . G A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.86735;SOR=0.96266;LSEQ=CAACAATAACAGCAACAGAA;RSEQ=CAATAACAGCAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:419:336:168,168:48,32:80,336:0.8019:2,2:18:1:30.2:1:0.13488:1.49853:51.6:66.2:0.8073:0:5.3 1/0:475:378:189,189:53,40:93,378:0.7958:2,2:18:1:29.2:1:0.24785:1.3242:52.3:93.5:0.8043:0:5.4 +6 160640142 . AT GC 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10355;SOR=0.56368;LSEQ=CAATAACAGCAACAGAAGCA;RSEQ=AACAGCAGCAGCAACAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:24:11,13:195,176:371,24:0.06:2,2:22.2:1:32.7:1:0.53571:1.3085:24.5:48:0.0609:0:6 0/1:461:16:10,6:226,214:440,16:0.0347:2,2:19.3:1:30.5:1:0.45097:1.58:24.9:32:0.0355:0:5.8 +6 160640145 . A AGAG 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.29284;LSEQ=TAACAGCAACAGAAGCAATA;RSEQ=CAGCAGCAGCAACAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:177:90,87:83,68:151,177:0.4609:2,2:15.6:1:31.4:1:0.5059:1.1793:51.3:176:0.5382:0.2604:5.2 0/1:435:87:48,39:69,51:120,87:0.2:2,2:19.3:1:30.2:1:0.77734:1.09876:47.2:174:0.2033:0.0092:5 +6 160640146 . C G 213 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACAGCAACAGAAGCAATAA;RSEQ=AGCAGCAGCAACAACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:88:42,46:110,83:193,88:0.2604:2,2:7.7:1:33:1:0.15763:1.44955:56.7:176:0.3154:0:4.9 0/0:387:0:0,0:117,90:207,0:0:2,0:15.8:1:31.2:1:1:0:51:102.5:1:0:2.7 +6 160640155 . C T 53 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.68959;SOR=1.77163;LSEQ=AGAAGCAATAACAGCAGCAG;RSEQ=AACAACAGCAGTACGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:2:0,2:144,121:265,2:0.0075:2,0:8.5:1:20:1:0.21129:0:45.5:1:0.0038:0:6 0/1:304:4:3,1:159,139:298,4:0.0132:2,2:11:0:26.5:1:0.62652:2.61:60:8:0.0133:0:4.3 +6 160640160 . A G 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00513;SOR=2.04523;LSEQ=CAATAACAGCAGCAGCAACA;RSEQ=CAGCAGTACGAACACCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:28:14,14:108,86:194,28:0.1256:2,2:6.3:1:32.7:1:0.68524:1.25451:49.1:56:0.1267:0:7 0/1:242:55:29,26:103,82:185,55:0.2273:2,2:6.2:1:31:1:0.7583:1.1256:48.7:54:0.2278:0:7.1 +6 160640164 . CAGTACGAACACCAGCAGT C 122 NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AACAGCAGCAGCAACAACAG;RSEQ=AACAACAGCAGCAGCAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:17:6,11:103,83:186,17:0.0825:2,2:24.7:1:30:1:0.13193:2.26597:23.4:34:0.0837:0.0825:7.8 0/0:188:0:0,0:101,87:188,0:0:2,0:17:1:29.6:1:1:0:53.1:187:1:0:2.5 +6 160640179 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24421;SOR=Inf;LSEQ=AACAGCAGTACGAACACCAG;RSEQ=AGTAACAACAGCAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:77,57:134,0:0:2,0:23.6:1:32.3:1:1:0:58.4:133:1:0.0066:0.4 0/1:149:2:1,1:79,68:147,2:0.0134:2,2:20.5:1:28:1:1:1.16059:60:4:0.0136:0:1.5 +6 160640205 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49827;SOR=Inf;LSEQ=CAACAGCAGCAGCAACATCA;RSEQ=CAACAACAGCAGCAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:74,65:139,0:0:2,0:23.6:1:32.7:1:1:0:58.5:68.5:1:0:0.4 0/1:142:2:1,1:68,72:140,2:0.0141:2,2:34:0:30.5:1:1:1.06:52.5:4:0.0145:0:1.5 +6 160640215 . C CAGCAACAACAGT 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.00189;SOR=0.40384;LSEQ=AGCAACATCAGCAACAACAG;RSEQ=AGCAACAACAGTAGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:136:113:55,58:13,9:22,113:0.8309:2,2:25.2:1:30.4:1:0.4855:1.51849:58.1:112:0.8296:0.2132:0.4 1/0:131:87:42,45:21,21:42,87:0.6641:2,2:27.3:1:29.6:1:1:1.07084:58.7:86:0.6667:0.1298:0.3 +6 160640308 . T C 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20183;SOR=Inf;LSEQ=AGAAATAAGTACAATAGCAA;RSEQ=AACAACAGTAATAGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:35,22:57,0:0:2,0:21.4:1:30.2:1:1:0:60:114:1:0:0.2 0/1:47:2:1,1:28,17:45,2:0.0426:2,2:5:0:31:1:1:1.62892:57:4:0.0426:0:0 +6 160640350 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50307;SOR=Inf;LSEQ=AAAAACAATAGCAGCAGTAA;RSEQ=AATAACAACAGCAATAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:53,36:89,0:0:2,0:24.6:1:32.4:1:1:0:60:178:1:0:0.1 0/1:110:2:1,1:69,39:108,2:0.0182:2,2:32:0:30:1:1:1.7595:42.5:4:0.0183:0:3 +6 160640353 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50274;SOR=Inf;LSEQ=AACAATAGCAGCAGTAACAA;RSEQ=AACAACAGCAATAGCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:56,37:93,0:0:2,0:24.7:1:30:1:1:0:59.8:186:1:0:0.1 0/1:114:2:1,1:71,41:112,2:0.0175:2,2:29:0:32.5:1:1:1.72289:42.5:4:0.0177:0:3 +6 160640355 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50407;SOR=Inf;LSEQ=CAATAGCAGCAGTAACAATA;RSEQ=CAACAGCAATAGCAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:57,37:94,0:0:2,0:25.3:1:30.6:1:1:0:59.9:188:1:0:0.1 0/1:118:2:1,1:71,45:116,2:0.0169:2,2:27:0:32.5:1:1:1.57143:42.5:4:0.0172:0:3 +6 160640362 . CAAT C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.50687;SOR=Inf;LSEQ=AGCAGTAACAATAACAACAG;RSEQ=AGCAGCAACAACAGCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:60,40:100,0:0:2,0:26.4:1:30.9:1:1:0:59.9:99:1:0:0.1 0/1:131:2:1,1:80,49:129,2:0.0153:2,2:19:0:33.5:1:1:1.62625:42.5:4:0.0153:0:3 +6 160640420 . A T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.18294;SOR=0;LSEQ=GCAGCAGCAACAACAGCAGC;RSEQ=GCAGCAACAACATCAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:70,72:142,2:0.0139:2,2:38:0:29:1:1:1.03:60:4:0.0139:0:1 0/0:192:0:0,0:95,97:192,0:0:2,0:27.3:1:29.6:1:1:0:59.7:95:1:0:0.2 +6 160640424 . G A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.26186;SOR=Inf;LSEQ=CAGCAACAACAGCAGCAGCA;RSEQ=CAACAACATCAGCCACCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:67,78:145,0:0:2,0:28.7:1:32.5:1:1:0:60:47.333:1:0:0.1 0/1:191:3:2,1:91,97:188,3:0.0157:2,2:15.7:1:28.3:1:0.61332:2.12:60:6:0.0158:0:1.7 +6 160640426 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18731;SOR=0;LSEQ=GCAACAACAGCAGCAGCAGC;RSEQ=ACAACATCAGCCACCGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:66,79:145,2:0.0136:2,2:36.5:1:30:1:1:1.20:60:4:0.0137:0:1 0/0:192:0:0,0:91,101:192,0:0:2,0:26.2:1:29.5:1:1:0:59.7:95:1:0:0.2 +6 160640435 . A C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50525;SOR=Inf;LSEQ=GCAGCAGCAGCAACAACATC;RSEQ=GCCACCGGTGAGTGACTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:62,78:140,0:0:2,0:27.3:1:31.2:1:1:0:60:139:1:0:0.1 0/1:177:2:1,1:76,99:175,2:0.0113:2,2:14:1:28:1:1:1.30:60:4:0.0115:0:1.5 +6 160640437 . C A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50618;SOR=Inf;LSEQ=AGCAGCAGCAACAACATCAG;RSEQ=CACCGGTGAGTGACTACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:60,77:137,0:0:2,0:27.3:1:31.9:1:1:0:60:136:1:0:0.1 0/1:176:2:1,1:75,99:174,2:0.0114:2,2:30:0:28.5:1:1:1.32:60:4:0.0117:0:1.5 +6 160640476 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49674;SOR=0;LSEQ=AACTAAATACCAAGCACTGC;RSEQ=ACGGGTGCTTCGTCGCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:18,54:72,2:0.027:2,2:12.5:1:27.5:1:0.4502:2.95:60:4:0.0274:0:1 0/0:71:0:0,0:19,52:71,0:0:2,0:24.9:1:29.5:1:1:0:60:34.5:1:0:0.2 +6 160640494 . C T 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00701;SOR=Inf;LSEQ=GCGACGGGTGCTTCGTCGCA;RSEQ=TGTCCCATTCATGAGCCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:4,40:44,0:0:2,0:25.5:1:32.9:1:1:0:60:43:1:0:0 0/1:52:8:3,5:7,37:44,8:0.1538:2,2:21.1:1:29.8:1:0.17097:3.08:60:16:0.1538:0:1 +6 161771025 . C T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.22142;SOR=4.43818;LSEQ=AAACTTGAAGAGTGTGTGTG;RSEQ=GCGCGCGCGCGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:153,18:171,1:0.0058:2,0:3:0:24:0:1:0:60:2:0.006:0:1 0/1:197:5:4,1:171,20:191,5:0.0254:2,2:18.2:1:26.6:1:0.43609:2.12663:60:10:0.0265:0:1 +6 161771035 . CGTGT C 134 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=7.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGTGTGTGTGCGCGCGCGCG;RSEQ=GTGTGTGTGTTTGAAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:19:14,5:158,30:188,19:0.0884:2,2:8.4:1:31.6:1:0.33012:1.87431:60:38:0.0896:0.0372:0.1 0/0:261:0:0,0:202,39:241,0:0:2,0:22.7:1:29.6:1:1:0:60:78.667:0.9183:0:0.2 +6 161771037 . T C 175 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGTGTGTGCGCGCGCGCGCG;RSEQ=GTGTGTGTGTGTTTGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:53:46,7:117,25:142,53:0.2477:2,2:24.3:1:30.6:1:0.52185:1.40:59.9:12.25:0.2649:0:2 0/0:269:0:0,0:207,43:250,0:0:2,0:22.3:1:28.3:1:1:0:60:34.714:1:0:0.2 +6 161771039 . T C 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TGTGTGCGCGCGCGCGCGTG;RSEQ=GTGTGTGTGTTTGAAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:55:48,7:122,28:150,55:0.2535:2,2:23.3:1:31:1:0.40392:1.57:59.9:26.5:0.2718:0:2 0/0:272:0:0,0:222,49:271,0:0:2,0:23.1:1:28.2:1:1:0:60:26.1:1:0:0.3 +6 161771361 . T C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36621;SOR=1.85657;LSEQ=GAGCGAATAATCACAAGCAA;RSEQ=ACAAGGGCAGAGAGAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:5:0,5:1,59:60,5:0.0769:1,0:26.2:1:33.4:1:1:0:60:10:0.0833:0:1 0/1:52:7:0,7:1,44:45,7:0.1346:1,0:28.4:1:32.4:1:1:0:60:14:0.1346:0:1.1 +6 161807664 . G C 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00203;SOR=Inf;LSEQ=ACACTGTGCCCCAAGGAGGG;RSEQ=AGTCATTCTGGGAGAAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:74,1:75,0:0:1,0:25.6:1:31.7:1:1:0:58.6:74:1:0:0.1 0/1:44:6:6,0:37,1:38,6:0.1364:1,0:31.8:1:32.5:1:1:0:60:12:0.1429:0:1 +6 161807855 . C G 259 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTCCTGAGGCTTCAAATA;RSEQ=GGCACTGCACTCCCCTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:977:0:0,0:467,509:976,0:0:2,0:25.7:1:31:1:1:0:59.9:96.6:0.999:0:0.1 0/1:1078:341:174,167:354,381:735,341:0.3163:2,2:24.2:1:30.8:1:0.39471:1.12:60:169.5:0.3168:0:1.1 +6 161807975 . CT C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.24378;SOR=0;LSEQ=TTGGCAATAACACATTTTTC;RSEQ=TTTCCAAATTCATTATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:14,162:176,2:0.0112:2,2:28:1:28:1:0.16187:11.21:60:4:0.0114:0:0 0/0:182:0:0,0:24,158:182,0:0:2,0:23.7:1:29.1:1:1:0:60:29.333:1:0:0.1 +6 161966036 . T C 67 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGCGGAAGACCACCCAGG;RSEQ=ACATGGTCGTGGGTGAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:28.8:1:33.8:1:1:0:53:8:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:33:0:1:0:60:2:1:0:1 +6 161966374 . T A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.2502;SOR=0;LSEQ=CTGGAACTCTGTAATTCTTC;RSEQ=ATAGCTTTGCTACCAATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:2,1:219,44:263,3:0.0113:2,2:32.3:1:30.3:1:0.42783:2.47754:60:6:0.0114:0:1 0/0:242:0:0,0:183,59:242,0:0:2,0:22.5:1:29.4:1:1:0:60:484:1:0:0.1 +6 161966410 . G T 68 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4515;SOR=0.40561;LSEQ=ATGACTTTTCCTTGAACGAT;RSEQ=TATTGAATGAGGCACTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:5:1,4:293,169:462,5:0.0107:2,2:9.8:1:29.4:1:0.06521:6.9071:60:10:0.0108:0:1.2 0/0:458:2:0,2:280,176:456,2:0.0044:2,0:1:0:25:1:0.15053:0:60:4:0.0044:0:1 +6 161970150 . ATGTG A 156 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=11.000;MSILEN=2;SSF=0.22865;SOR=0.68201;LSEQ=CAGTTTCAGTAAAATAATGC;RSEQ=TGTGTGTGTGTGTGTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:37:0,37:5,99:104,37:0.227:1,1:35.2:1:30.1:1:0.3259:0:59.9:36:0.2264:0.0123:0.3 0/1:114:19:2,17:2,77:79,19:0.1667:1,2:32.7:1:29.9:1:0.16811:4.43:60:38:0.1696:0.0175:0.4 +6 161970231 . T A 166 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=ACGAATATGGTTCAATGCAG;RSEQ=AAAAGTCTACCAAATTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:43:43:1,42:0,0:0,43:1:0,1:22.1:1:30.6:1:1:0:60:20.5:1:0:1.1 1/0:19:11:1,10:0,8:8,11:0.5789:0,2:21.5:1:30.9:1:1:0:60:22:0.5789:0:1.4 +6 161990286 . A G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02226;SOR=Inf;LSEQ=TTCCCCATTTCAGGGCACCC;RSEQ=GGGTCAGGAGACATACTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:103,9:112,0:0:2,0:24.1:1:30.8:1:1:0:60:55:1:0:0.1 0/1:72:4:4,0:64,4:68,4:0.0556:2,0:24.8:1:30.5:1:1:0:60:8:0.058:0:1 +6 161990339 . G A 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=GCCCAAACTGTCTCATTAGC;RSEQ=TCTATCTTTCATGACAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:0:0,0:237,73:310,0:0:2,0:24.5:1:30.9:1:1:0:60:154:0.9968:0:0.1 0/1:238:11:11,0:170,57:227,11:0.0462:2,0:35.4:1:29.9:1:0.07065:0:60:22:0.0474:0:1.1 +6 161990401 . G A 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTCACCTGCTCTTCTCCCA;RSEQ=AATCCTGAAGTGATGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:671:0:0,0:382,289:671,0:0:2,0:24.6:1:32.4:1:1:0:60:94.857:1:0:0.2 0/1:568:38:25,13:300,230:530,38:0.0669:2,2:22.7:1:30:1:0.31071:1.47:60:76:0.0677:0:1.2 +6 161990483 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.26757;SOR=0.86854;LSEQ=AATTAATCACAAAAACGTCA;RSEQ=TTTCACTCTGTGTGGTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:228:76,152:124,172:296,228:0.4343:2,2:25.3:1:30.3:1:0.04668:1.44084:60:113:0.4371:0:1.6 0/1:560:224:84,140:141,195:336,224:0.4:2,2:25.5:1:29.5:1:0.3332:1.20472:60:111:0.4007:0:1.6 +6 161990516 . G C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7398;SOR=1.06229;LSEQ=TGGTTATATGTTCTTACACA;RSEQ=AGTTATGACTATCAACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:130:24,106:42,113:155,130:0.4545:2,2:23.6:1:32.2:1:0.09228:1.63875:60:64:0.4523:0:1.9 0/1:296:139:34,105:49,107:156,139:0.4696:2,2:23.3:1:31.4:1:0.19685:1.41257:60:138:0.4726:0:1.8 +6 161990678 . C T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61957;SOR=2.35237;LSEQ=AGAAAACAGTTGCATGTGAC;RSEQ=CTGGCCAGGCTTTCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:0,8:0,13:13,8:0.381:1,0:20.1:1:30.1:1:1:0:60:16:0.4:0:1 1/0:5:3:0,3:1,1:2,3:0.6:2,0:27.7:1:29.3:1:0.4:0:60:6:0.6:0:1 +6 162136980 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53201;SOR=0;LSEQ=AGAAACTCAAATTATGATAC;RSEQ=CCACCCTAGACAGACTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:189,1:190,2:0.0104:1,2:22.5:1:29.5:1:0.02078:133.93733:60:4:0.0105:0:1 0/0:113:0:0,0:109,4:113,0:0:1,0:21.3:1:30.8:1:1:0:60:226:1:0:0.1 +6 162137099 . CATCTT C 222 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=194.72422;LSEQ=CCACCATGCTGTGCTGGGCC;RSEQ=ACCGACTCCTCTCCTGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1150:1:1,0:640,507:1147,1:9e-04:2,0:45:0:30:0:1:0:60:2:9e-04:0:0 0/1:1146:166:90,76:544,435:979,166:0.1449:2,2:27.8:1:30.2:1:0.80012:1.05596:59.9:82:0.1445:0.0096:0.5 +6 162137107 . C A 204 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01856;LSEQ=CTGTGCTGGGCCCATCTTAC;RSEQ=GACTCCTCTCCTGAATCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1196:99:47,52:604,491:1095,99:0.0828:2,2:26.8:1:30.8:1:0.17043:1.36064:60:98:0.0829:0:1.1 0/0:1198:2:2,0:643,552:1195,2:0.0017:2,0:1:0:25.5:1:0.5026:0:60:4:0.0017:0:1 +6 162137147 . C T 191 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCAGAGCTCCTCTAAGCAC;RSEQ=ACTGTGTCTCCAGTTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1195:0:0,0:544,650:1194,0:0:2,0:25.5:1:31.6:1:1:0:59.9:58.7:0.9991:0:0.2 0/1:1197:103:46,57:518,573:1091,103:0.086:2,2:22.6:1:28.6:1:0.60694:1.12008:59.8:102:0.0861:0:1.2 +6 162138301 . C A 27 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCAGCCCATGATGGAATG;RSEQ=GGACGGGCAAGAGGACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:27.5:1:1:0:60:4:1:0:1.5 +6 162169954 . T C 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00127;SOR=Inf;LSEQ=AGAAATTCCCTTGCCTGTCA;RSEQ=GTGTATTCCACAACGCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:179,89:268,0:0:2,0:25.2:1:30.8:1:1:0:60:52.6:1:0:0.1 0/1:248:9:6,3:153,86:239,9:0.0363:2,2:26.8:1:28.8:1:1:1.12:60:8:0.0331:0:1.3 +6 162169968 . C T 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGTCATGTGTATTCCACAA;RSEQ=GCATGAAAAGACCAGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:303:0:0,0:193,110:303,0:0:2,0:27.7:1:31.4:1:1:0:60:74.75:1:0:0.1 0/1:314:26:18,8:178,110:288,26:0.0828:2,2:25.2:1:27.7:1:0.53017:1.39:60:7.667:0.0754:0:1 +6 162170039 . C T 213 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCAGCTGGGAAACATTT;RSEQ=GAAGGGCTGGGAGAGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:229,228:457,0:0:2,0:25.5:1:30.9:1:1:0:60:75.167:1:0:0.1 0/1:475:157:72,85:153,165:318,157:0.3305:2,2:24.1:1:29.2:1:0.69619:1.09449:59.9:38.25:0.3269:0:1.2 +6 162170045 . G T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06281;SOR=Inf;LSEQ=GCTGGGAAACATTTCGAAGG;RSEQ=CTGGGAGAGATGGAAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:222,225:447,0:0:2,0:26.4:1:31.6:1:1:0:60:43.7:0.9977:0:0.1 0/1:485:5:1,4:226,254:480,5:0.0103:2,2:15.8:1:27.2:1:0.37755:3.55089:60:10:0.0105:0:1 +6 162170083 . G T 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGCAAAACCAAGGGGAGG;RSEQ=GGTCCTTGTACTTGGTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:156,245:401,0:0:2,0:25.9:1:30.9:1:1:0:60:35.455:1:0:0.3 0/1:367:29:8,21:135,203:338,29:0.079:2,2:26.9:1:29.5:1:0.23554:1.7432:60:58:0.0803:0:1.2 +6 162170097 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09855;SOR=Inf;LSEQ=GGGAGGGGGTCCTTGTACTT;RSEQ=GTGAACAGATGACTCTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:121,218:339,0:0:2,0:25.8:1:31.6:1:1:0:60:83.75:1:0:0.3 0/1:292:3:2,1:101,188:289,3:0.0103:2,2:14.3:1:27.3:1:0.2848:3.71:60:6:0.0104:0:2.3 +6 162170141 . C T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=4e-05;SOR=0.33673;LSEQ=AAGGATTCAGGGCCGGGAGG;RSEQ=GGGCAAGCAGGTACGCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:84:11,73:10,54:64,84:0.5676:2,2:24.6:1:30.7:1:0.81263:1.22722:60:168:0.5753:0:1 0/1:108:33:7,26:15,60:75,33:0.3056:2,2:24.8:1:28.9:1:1:1.08:60:32:0.3107:0:1.1 +6 162206873 . A T 199 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCATTGAGTCTTGTCACAC;RSEQ=GTATAAGTGGAAACAGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:82:34,48:262,325:587,82:0.1222:2,2:26.1:1:31.4:1:0.63582:1.13788:60:164:0.1239:0:1.1 0/0:795:0:0,0:360,435:795,0:0:2,0:23.9:1:29.7:1:1:0:60:87.333:1:0:0.2 +6 162206881 . T C 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GTCTTGTCACACAGTATAAG;RSEQ=GGAAACAGTCTAAGCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:649:0:0,0:280,367:647,0:0:2,0:24.9:1:30.2:1:1:0:59.9:128.4:1:0:0.2 0/1:762:18:8,10:319,424:743,18:0.0236:2,2:24.5:1:31.2:1:1:1.06:60:36:0.0237:0:1.2 +6 162394272 . GCTATTTTTAGATCCTTACCTCACGTCCGTGGAGGGAAGTGACA G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=1.000;MSILEN=1;SSF=0.21408;SOR=Inf;LSEQ=AGTAAGGAGGGGGGAGTGAT;RSEQ=CTATTTTTAGATCCTTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:171,27:198,0:0:2,0:21.9:1:32.1:1:1:0:59.9:38.6:1:0:0.1 0/1:171:2:1,1:139,30:169,2:0.0117:2,2:19.5:1:27.9:1:0.33058:4.57438:59.5:4:0.0118:0.0117:0 +6 162394295 . C T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35631;SOR=3.24649;LSEQ=ATTTTTAGATCCTTACCTCA;RSEQ=GTCCGTGGAGGGAAGTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:1:0,1:204,79:283,1:0.0035:2,0:1:0:28:0:0.28169:0:60:2:0.0036:0:1 0/1:264:3:1,2:195,64:259,3:0.0114:2,2:26.3:1:29:1:0.15732:6.04173:60:6:0.0116:0:1.3 +6 162394500 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.23519;SOR=0;LSEQ=TGGATCCCGGCTGCTCATTT;RSEQ=TCCTCTAAATGTTTCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:19,165:184,2:0.0108:2,2:13.5:1:28:1:0.20401:8.49:60:4:0.0108:0:1 0/0:197:0:0,0:37,160:197,0:0:2,0:22:1:29.4:1:1:0:60:196:1:0:0.1 +6 162473060 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.18947;SOR=Inf;LSEQ=CCAAAGATACCAGGAATGAC;RSEQ=GTGTTATTAGATGAGATCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:11,0:0:2,0:24.9:1:31.3:1:1:0:60:22:1:0:0.2 0/1:9:2:1,1:6,1:7,2:0.2222:2,2:12.5:1:29:1:0.41667:4.58262:51:4:0.2222:0:1.5 +6 162474893 . A G 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06462;SOR=Inf;LSEQ=GTTTAAATTGGCACATTTCC;RSEQ=CACGGTCCCCCCAAATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:18,1:19,0:0:1,0:27.3:1:31.3:1:1:0:60:38:1:0:0.1 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:33.5:1:26.5:1:1:0:60:4:0.2857:0:1 +6 162475245 . T A 43 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.68852;SOR=1.81818;LSEQ=ATATATGCTTATATGAGTTA;RSEQ=AATAGAAATGTACTCCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:2:2,0:71,272:343,2:0.0058:2,0:1:0:25.5:1:0.04429:0:60:4:0.0059:0:1 0/1:381:4:3,1:103,274:377,4:0.0105:2,2:6.3:1:21.8:1:0.06714:7.93:56.3:3:0.008:0:2.5 +6 162475434 . A C 116 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATATTTGACATTTTGCTCC;RSEQ=AACCTGTTCGTTTTCCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:0,13:0,6:6,13:0.6842:0,1:24.7:1:31.5:1:1:0:60:12:0.6667:0:1.5 1/1:1:1:0,1:0,0:0,1:1:0,0:14:0:33:0:1:0:60:2:1:0:1 +6 162622197 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGTTGCCTGCCTGCAGGTG;RSEQ=TGCACTGTACCCTGAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:833:0:0,0:437,395:832,0:0:2,0:25.4:1:32.5:1:1:0:60:63:1:0:0.2 0/1:800:18:9,9:414,367:781,18:0.0225:2,2:27.6:1:29.8:1:0.81601:1.12789:60:36:0.023:0:1.2 +6 162622304 . A G 276 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GCTGGAGAAGAAAAAGCAGA;RSEQ=GAAGTGGCTAATAATGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:427:427:123,304:0,0:0,427:1:0,2:25.4:1:31.6:1:1:0:60:141.333:1:0:1.1 1/0:393:295:89,206:35,63:98,295:0.7506:2,2:23.3:1:30.6:1:0.31746:1.28501:60:146.5:0.7494:0:1.1 +6 162683474 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17904;SOR=Inf;LSEQ=ACGTATCATAAACTAAATAT;RSEQ=CACCCGGTGAGGCCATGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:170,27:197,0:0:2,0:22.4:1:32.6:1:1:0:60:394:1:0:0.1 0/1:145:2:1,1:122,21:143,2:0.0138:2,2:15.5:1:27.5:1:0.28132:5.69922:60:4:0.014:0:1 +6 162683876 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1592;LSEQ=GCGAGATAGAGTTTAACTTG;RSEQ=CCTCCGTGGTAGAAGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:88:78:1,77:0,10:10,78:0.8864:0,1:23.8:1:30.4:1:1:0:59.5:156:0.8864:0:1.7 1/0:69:38:0,38:0,31:31,38:0.5507:1,1:25.1:1:28.4:1:1:0:59.1:37:0.5522:0:1.6 +6 162864276 . G T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.356;SOR=3.25038;LSEQ=CAGGCATGAATGTCAGATTG;RSEQ=CAGCGCAGGCGGCATGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:0,1:201,26:227,1:0.0044:2,0:2:0:15:0:0.11842:0:60:0:0:0:2 0/1:212:3:1,2:175,34:209,3:0.0142:2,2:19.7:1:27:1:0.07538:10.11791:60:6:0.0144:0:1 +6 162864289 . C T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05335;SOR=Inf;LSEQ=CAGATTGGCAGCGCAGGCGG;RSEQ=ATGAGCAATGGAGCTGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:236,52:288,0:0:2,0:23.5:1:31.9:1:1:0:59.9:71:1:0:0.1 0/1:268:4:1,3:211,53:264,4:0.0149:2,2:13.5:1:23.8:1:0.02971:11.79678:60:8:0.015:0:1 +6 162864317 . A G 198 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=102.50521;LSEQ=ATGGAGCTGGCGGCATCCCA;RSEQ=GAACGGCCGCCAAGGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:1:0,1:308,141:449,1:0.0022:2,0:14:0:25:0:0.31556:0:60:2:0.0023:0:5 0/1:484:90:63,27:259,135:394,90:0.186:2,2:20.6:1:30.5:1:0.4606:1.22:60:89:0.185:0:1.1 +6 162864566 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=CACTCGAAGCCCTTAAATGG;RSEQ=GATAGCAACATTTCTCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:22,184:206,0:0:2,0:23.3:1:30.4:1:1:0:59.6:205:0.9951:0:0.1 0/1:173:2:1,1:28,143:171,2:0.0116:2,2:28:1:27:1:0.30797:5.04:60:4:0.0116:0:1 +6 162992355 . CAA C 92 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.17532;SOR=2.94642;LSEQ=CAACAGAGAAAAACTCATTT;RSEQ=AAAAAAAAAAAAAAGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:3,0:14,0:14,3:0.15:1,0:23:1:33:1:1:0:53.3:6:0.15:0:1.3 0/1:23:8:7,1:8,0:8,8:0.3478:0,2:12.4:1:30.7:1:1:0:60:16:0.3478:0.087:1 +6 162992419 . G T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.52949;LSEQ=TGTATCCTATAAATATACAC;RSEQ=CATACTATGTACCCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:89,23:112,2:0.0174:2,2:23.5:1:30:1:0.3782:3.80931:60:4:0.0183:0:1.5 0/0:108:1:0,1:89,18:107,1:0.0093:2,0:1:0:23:0:0.17593:0:60:2:0.0102:0:1 +6 162992532 . C G 191 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=34.77311;LSEQ=ATTAAAACTGCTTTGACAAA;RSEQ=TTTTGGCAGATAAAATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:2:1,1:102,150:252,2:0.0079:2,2:24.5:1:32:1:1:1.47:60:4:0.008:0:1.5 0/1:332:72:30,42:108,152:260,72:0.2169:2,2:24.4:1:31.1:1:1:1.01:60:144:0.2182:0:1.2 +6 162992556 . T A 21 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21012;SOR=0;LSEQ=TGGCAGATAAAATTTGTGAT;RSEQ=GGTTGAATGTAGGCACTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:54,129:183,2:0.0108:2,2:14.5:1:21.5:1:0.50734:2.38:60:4:0.0109:0:1.5 0/0:218:0:0,0:70,148:218,0:0:2,0:23.2:1:28.9:1:1:0:60:53.5:1:0:0.3 +6 162992560 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50112;SOR=Inf;LSEQ=AGATAAAATTTGTGATTGGT;RSEQ=GAATGTAGGCACTCAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:47,125:172,0:0:2,0:23.3:1:30.3:1:1:0:60:171:1:0:0.1 0/1:198:2:1,1:58,136:194,2:0.0101:2,2:21.5:1:29:1:0.51251:2.33:60:4:0.0103:0:1.5 +6 162992704 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47712;SOR=Inf;LSEQ=GGATGTAAAGTACCCGTGGG;RSEQ=TGTCCAAGTTGAGGGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:22.8:1:32:1:1:0:60:16:1:0:0 0/1:10:2:0,2:1,7:8,2:0.2:2,0:20:1:29.5:1:1:0:60:4:0.2222:0:1 +6 163092643 . G A 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTTTGAAACATTTGTGCA;RSEQ=TAATCAAAAATTCCGAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:86,166:252,0:0:2,0:19.2:1:32.1:1:1:0:59.9:504:1:0:0.1 0/1:294:40:13,27:82,172:254,40:0.1361:2,2:21.9:1:29:1:1:1.01:60:80:0.1365:0:1.1 +6 163092678 . C G 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12618;SOR=Inf;LSEQ=GAAATCATAGAAGAATTTAC;RSEQ=AGTCAATCATACCAGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:1,108:109,0:0:1,0:27.5:1:33.1:1:1:0:59.8:218:1:0:0.1 0/1:127:4:1,3:2,121:123,4:0.0315:1,2:11.3:1:28.3:1:0.09225:18.48:60:8:0.0315:0:1 +6 163092867 . C T 69 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCAGATGTCAAATTGTA;RSEQ=AGTCAAAGAATAAATGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,1:1,5:0.8333:0,2:21.4:1:30:0:1:0:60:10:0.8333:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 163092968 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGGTGACGGAGGCAGAC;RSEQ=CCAGGGCTGCAGACTGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:29.5:1:1:0:60:4:1:0:1.5 +6 163148559 . CG C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51098;SOR=0;LSEQ=GGGAGCCCGGCGGCGCGGGC;RSEQ=GGGACGGCACGGGCACTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:2,0:145,5:150,2:0.0132:1,0:28:1:33:0:1:0:60:4:0.0136:0:0 0/0:110:0:0,0:105,4:109,0:0:1,0:23.1:1:30.1:1:1:0:60:108:0.9908:0:0.1 +6 163148803 . G A 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03935;SOR=Inf;LSEQ=TCCTGGGTTAAATCCTCCAG;RSEQ=CCTCCCCGCCCCCGCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:71,292:363,0:0:2,0:23.7:1:32.3:1:1:0:60:71.6:1:0:0.1 0/1:293:4:3,1:64,223:287,4:0.0137:2,2:6:1:25:1:0.03928:10.34:60:8:0.0139:0:1 +6 163516710 . G A 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTCCCGCCCCATCTTCAT;RSEQ=TGGCCTTTTTTCCTGTGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:20.3:1:30:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 163517035 . T A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21648;LSEQ=TCACATTGCTGTAACTAGTG;RSEQ=TACTGAGCCTGCTCTGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:516:288:133,155:104,122:226,288:0.5581:2,2:26.4:1:30.7:1:1:1.01:59.9:143:0.5619:0:1.1 0/1:471:101:52,49:172,198:370,101:0.2144:2,2:27.2:1:28.8:1:0.4315:1.22:60:49.5:0.2115:0:1.1 +6 163528662 . G A 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCATTTGGCTGTCTGGACC;RSEQ=GGCCTCTCTGCTTCATGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:25.3:1:29.3:1:1:0:60:8:0.4444:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:30:0:1:0:60:2:1:0:0 +6 163528776 . C T 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.13904;LSEQ=AAAATCAGGTACAAGGCAGA;RSEQ=CTTTTCTTTGTTGGATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:29:29,0:27,0:27,29:0.5179:1,1:23.9:1:31.4:1:1:0:59:58:0.5179:0:2 0/1:47:6:6,0:39,2:41,6:0.1277:1,0:32:1:31.5:1:1:0:56.7:12:0.1277:0:2 +6 163528806 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09384;LSEQ=GTTGGATTCCAAATGTACAA;RSEQ=GACTCAATCTTGATTACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:107:82:76,6:24,1:25,82:0.7664:1,2:23.1:1:30.9:1:1:1.88519:58.5:81:0.7714:0:1.4 0/1:86:20:20,0:63,3:66,20:0.2326:1,1:23.6:1:29.9:1:1:0:59:40:0.2326:0:1.4 +6 163528910 . C T 191 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTATAAATTTCTCCAAAAT;RSEQ=CTAACATGTTGTTTGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:76:41,35:183,171:354,76:0.1763:2,2:25.6:1:30.7:1:0.80042:1.09:59.8:152:0.178:0:1.8 0/0:543:0:0,0:271,271:542,0:0:2,0:27.2:1:30.2:1:1:0:59.9:66.75:0.9981:0:0.3 +6 163528948 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10039;LSEQ=ATTTGGTTGTTTCTTCTTAT;RSEQ=CAAGTTTGCATTTCAAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:398:320:128,192:35,42:77,320:0.804:2,2:25.5:1:29.2:1:0.43907:1.24928:60:159:0.8051:0:1.2 0/1:481:140:65,75:138,203:341,140:0.2911:2,2:22.7:1:27.8:1:0.26364:1.27:60:45.667:0.2878:0:1.2 +6 163529076 . T C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00165;SOR=0.21959;LSEQ=TAGGTTTGACATAAGGGAGG;RSEQ=GGTTTGAGGCTGAAGCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:38:4,34:0,15:15,38:0.717:1,2:24:1:30.4:1:0.56786:0:60:76:0.717:0:1.6 0/1:34:12:2,10:2,20:22,12:0.3529:2,2:23:1:28.8:1:0.60152:1.96:60:11:0.3333:0:2 +6 163529109 . G T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.09804;SOR=0.30953;LSEQ=AAGCCGTCTGATGTGGTTTG;RSEQ=CTTTGTGTCCCTACCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:20:0,20:0,8:8,20:0.7143:0,1:23.3:1:30:1:1:0:60:19:0.7037:0:2.1 0/1:14:6:0,6:0,8:8,6:0.4286:0,0:21.8:1:29.2:1:1:0:60:12:0.4615:0:2.2 +6 163529169 . C G 89 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86755;LSEQ=ACCCATGTTGGAGGAGGGGC;RSEQ=AGGTGGGAGGTGATTGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:3,7:0.7:0,0:12.9:1:32:1:1:0:54.3:14:0.7:0:2.1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:4:1:30:0:1:0:60:4:0.6667:0:3.5 +6 163529226 . A G 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.28571;SOR=0;LSEQ=TTCTTTCTGTTCTCATGATG;RSEQ=TGAGTGAGCTCTCACGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:28.4:1:32.8:1:1:0:52:10:0.8333:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:7:0:32:0:1:0:60:2:1:0:1 +6 163529269 . A C 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTGTTTAAAAATCTGTAG;RSEQ=ACCACCCACTTTGCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:34.5:1:31.5:1:1:0:60:4:0.6667:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:27:0:1:0:37:2:1:0:0 +6 163529910 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGATCTTTATGTATTCATC;RSEQ=AAATCAATACATCAAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:16:1:33:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 164341042 . C A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.28818;LSEQ=AATGAAGTGTTTCTATGTGC;RSEQ=TATTTCTCTAGGGTTTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:14:14,0:43,1:44,14:0.2414:1,1:24.4:1:31:1:1:0:60:28:0.2414:0:1.1 1/0:33:26:26,0:7,0:7,26:0.7879:0,1:24.3:1:29.9:1:1:0:60:52:0.7879:0:1 +6 164341106 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.4995;SOR=0;LSEQ=CCTGATGAACATATCACTTC;RSEQ=TTTGAACTCTGTGGGTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:132,44:176,2:0.0112:2,2:8.5:1:29:1:0.44277:2.97768:60:4:0.0113:0:1 0/0:163:0:0,0:127,36:163,0:0:2,0:19:1:30.4:1:1:0:60:80.5:1:0:0.2 +6 164341214 . T C 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.3417;LSEQ=CCCCGTGACCTGTTACCTGT;RSEQ=GCTGAACCTTGTTCCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:102:50,52:161,188:349,102:0.2262:2,2:28.2:1:30.6:1:0.65235:1.12:60:50:0.2237:0:2.4 1/0:416:284:125,159:66,66:132,284:0.6827:2,2:25.2:1:29.4:1:0.29062:1.27125:59.9:93.667:0.6804:0:2.6 +6 164341220 . A C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=7.34035;LSEQ=GACCTGTTACCTGTTGCTGA;RSEQ=CCTTGTTCCAGTGCACAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:97:46,51:153,187:340,97:0.222:2,2:27.9:1:31.6:1:0.72908:1.10:60:96:0.2222:0:2.5 1/0:403:273:118,155:66,62:128,273:0.6774:2,2:25.1:1:30.2:1:0.13267:1.3971:59.9:33.125:0.6726:0:2.7 +6 164341228 . C T 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTGTTGCTGAACCTTGTT;RSEQ=CAGTGCACAGCGGCCTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:411:0:0,0:169,242:411,0:0:2,0:25.8:1:31.4:1:1:0:60:40.1:1:0:0.7 0/1:381:18:5,13:165,196:361,18:0.0472:2,2:26.7:1:27.8:1:0.15259:2.1845:60:36:0.0481:0:3.8 +6 164341235 . A G 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCTGAACCTTGTTCCAGTGC;RSEQ=CAGCGGCCTCTCGCGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:159,238:397,0:0:2,0:24.9:1:29.8:1:1:0:60:55.714:1:0:0.7 0/1:367:17:5,12:147,203:350,17:0.0463:2,2:24.6:1:30.8:1:0.45032:1.73546:60:34:0.047:0:3.5 +6 164341262 . A C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.45037;LSEQ=CCTCTCGCGCATCCCCACCC;RSEQ=CCCGTCGGGTTGGGAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:64:20,44:85,142:227,64:0.2192:2,2:23.8:1:30.9:1:0.38111:1.31568:60:31:0.2191:0:2.4 1/0:279:189:60,129:31,58:89,189:0.6774:2,2:24.5:1:30.2:1:0.68131:1.14855:60:62:0.6813:0:2.6 +6 164341291 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.49926;SOR=0;LSEQ=GTTGGGAACTGGTCAAAACC;RSEQ=TCATCCTTCCGTTTTGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:51,134:185,2:0.0107:2,2:26:1:30:1:0.4799:2.61:60:4:0.0109:0:1.5 0/0:174:0:0,0:43,131:174,0:0:2,0:24.4:1:29.9:1:1:0:60:86:1:0:1.5 +6 164341302 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.22591;SOR=Inf;LSEQ=GTCAAAACCATCATCCTTCC;RSEQ=TTTTGCCATCATGGCATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:36,118:154,0:0:2,0:24.2:1:31.6:1:1:0:60:50.333:1:0:0.4 0/1:140:2:1,1:30,108:138,2:0.0143:2,2:34:1:30:1:0.39507:3.56:60:4:0.0146:0:2.5 +6 164341347 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22528;SOR=Inf;LSEQ=TATTTAGGGTTTGGAGTTCG;RSEQ=TGAATTTAAACTGATACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:2,55:57,0:0:1,0:25.3:1:30.7:1:1:0:60:114:1:0:0.1 0/1:52:2:0,2:5,45:50,2:0.0385:2,0:25.5:1:33:1:1:0:60:4:0.04:0:1 +6 165677269 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=TATAGGGTGACAGAAGGCAG;RSEQ=GCAGAGTCTGCGGCCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:20,10:30,2:0.0625:2,2:10.5:1:28.5:1:1:1.95408:60:4:0.0625:0:1.5 0/0:31:0:0,0:21,10:31,0:0:2,0:19.9:1:30:1:1:0:60:62:1:0:0.2 +6 165677286 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22761;SOR=0;LSEQ=CAGCGCAGAGTCTGCGGCCA;RSEQ=AGGCCAAGCTGAACCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:21,14:35,2:0.0541:2,2:32.5:1:30.5:1:1:1.4832:60:4:0.0556:0:1 0/0:40:0:0,0:23,17:40,0:0:2,0:24.3:1:30.7:1:1:0:60:39:1:0:0.2 +6 165677365 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51637;SOR=Inf;LSEQ=ACACTCTGCTCTAGGTGTGC;RSEQ=CCTTTTCAAGGAAGCTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:8,17:25,0:0:2,0:23.4:1:31.2:1:1:0:60:50:1:0:0.1 0/1:39:2:1,1:14,23:37,2:0.0513:2,2:34:1:30:1:1:1.62:60:4:0.0526:0:1 +6 166653608 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCTCTCTTTTGAATATTC;RSEQ=CTCGATCATAAGACACCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:11.5:1:32.5:1:1:0:45.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 166653638 . A G 55 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGACACCAATAACACACAA;RSEQ=CAGTTTCATCTTCATAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:33:1:35:0:1:0:37.3:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 166653737 . T TA 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.52941;SOR=0;LSEQ=ATTGTACACAAATGTACAAT;RSEQ=AAAAAAAAAAGTTTGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:8:1:29.7:1:1:0:60:4:0.1667:0.0833:2.5 0/0:6:0:0,0:6,0:6,0:0:0,0:14.2:1:30.2:1:1:0:55:12:1:0:0.2 +6 166653792 . A C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11793;SOR=0.42304;LSEQ=ATTTTACTACAAAAAGGAAT;RSEQ=GAATTTCTGGGTCTGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:24:24,0:13,0:13,24:0.6486:1,1:25.9:1:32.6:1:1:0:59.5:23:0.6389:0:1.1 0/1:23:10:10,0:13,0:13,10:0.4348:1,0:23.7:1:31.6:1:1:0:58.7:20:0.4348:0:1 +6 166653885 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.79246;LSEQ=AGACAATTGTTTAAAGTCTG;RSEQ=AGCTGCCTGGGAAACTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:1:0,1:108,50:158,1:0.0063:2,0:1:0:22:0:0.32075:0:60:2:0.0063:0:3 0/1:178:2:1,1:123,53:176,2:0.0112:2,2:18.5:1:28:1:0.5159:2.30852:60:4:0.0114:0:1 +6 166653963 . C T 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38239;LSEQ=CACTTTCTTCATAGCTGCGA;RSEQ=GCTGGAGGAAGCCAACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:261:144:69,75:66,51:117,144:0.5517:2,2:26.1:1:31:1:0.21291:1.40478:60:143:0.5564:0:1.1 0/1:366:117:53,64:125,124:249,117:0.3197:2,2:26.7:1:29.4:1:0.43271:1.21663:59.2:57.5:0.323:0:1.1 +6 166654047 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2315;SOR=Inf;LSEQ=GTCATAGGGGGCCAGAAAAT;RSEQ=GAGAGCATTCTCACATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:47,124:171,0:0:2,0:25.2:1:31.2:1:1:0:59.8:56:0.9941:0:0.7 0/1:160:2:1,1:39,118:157,2:0.0125:2,2:5.5:1:27:1:0.44105:3.00:60:4:0.0127:0:2 +6 166654085 . T C 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13254;SOR=0.58049;LSEQ=CCTACCATGGGCTGGACGTT;RSEQ=CCAAAGCAGGCAGAAATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:45:3,42:2,41:43,45:0.5114:1,2:23.2:1:31.7:1:1:1.46:60:44:0.5057:0:2 0/1:61:23:1,22:3,35:38,23:0.377:2,1:24.2:1:30.4:1:1:1.86785:60:46:0.3898:0:2 +6 166654087 . C G 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22582;SOR=0.63776;LSEQ=TACCATGGGCTGGACGTTTC;RSEQ=AAAGCAGGCAGAAATTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:43:3,40:2,39:41,43:0.5119:1,2:23.8:1:32.8:1:1:1.46:60:86:0.5119:0:2 0/1:55:22:1,21:2,31:33,22:0.4:2,1:25.2:1:30.3:1:1:1.34762:60:44:0.4:0:2 +6 167630110 . C G 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCCTTGATCCCGACGAG;RSEQ=CAGAGTGTGGCGCTGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:40.5:1:32:1:1:0:22:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:33:0:1:0:21:2:1:0:0 +6 167630297 . A C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=3.76737;LSEQ=ACCAGGAAGACAAGAAAGGA;RSEQ=GTGCCTGGAGTGTTCAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:43:41,2:25,3:28,43:0.4175:2,1:23.9:1:32.9:1:0.37631:2.43:23.1:42:0.42:0:2.1 1/0:67:49:46,3:9,1:10,49:0.7313:2,2:23.4:1:31.9:1:0.53447:1.69:22.9:98:0.7313:0:2.1 +6 167630301 . C G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02897;SOR=2.4334;LSEQ=GGAAGACAAGAAAGGAAGTG;RSEQ=CTGGAGTGTTCAGTCCACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:111:81:74,7:26,4:30,81:0.7297:2,2:26:1:32.4:1:0.48425:1.62:26.2:80:0.7477:0:2 1/1:76:66:61,5:9,1:10,66:0.8684:2,2:23.9:1:29.8:1:0.5844:1.35:25:12.2:0.8592:0:1.9 +6 167630896 . C A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCACCAATAAATGTTATC;RSEQ=TCAATAAATGTTAATTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:19.3:1:30.3:1:1:0:26.7:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 167721910 . A T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGACGGGGCTCTGGGGC;RSEQ=TCCTGGGCAGTGGTGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 167723142 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1852;SOR=Inf;LSEQ=TGAGATGACAGACCTGGCTG;RSEQ=TGTCCCTGCACTGAGGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:25,112:137,0:0:2,0:33:1:32.8:1:1:0:37.2:274:1:0:0.1 0/1:104:2:1,1:23,79:102,2:0.0192:2,2:29.5:1:30.5:1:0.41001:3.38:46.5:4:0.0198:0:1 +6 167723177 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17749;SOR=Inf;LSEQ=GGATAAAGAGCACATGTGAC;RSEQ=TCAGATCGCGGACAGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:25,157:182,0:0:2,0:27.6:1:33.1:1:1:0:39.1:90:1:0:0 0/1:133:2:1,1:23,108:131,2:0.015:2,2:40.5:1:28.5:1:0.32946:4.62:48:4:0.0154:0:1 +6 167723184 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GAGCACATGTGACCTCAGAT;RSEQ=GCGGACAGAACACTCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:25,164:189,0:0:2,0:24.4:1:30.4:1:1:0:38.7:93.5:1:0:0 0/1:136:22:4,18:20,94:114,22:0.1618:2,2:30.6:1:28:1:1:1.04:42.9:21:0.1579:0:1.2 +6 167723225 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52211;SOR=0;LSEQ=ACGTCCTTTCTTGTCTTCCT;RSEQ=GTGGGTTGCGTATCCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:3,79:82,2:0.0238:1,2:23.5:1:31.5:1:0.09352:22.95:25:4:0.0238:0:1 0/0:53:0:0,0:0,53:53,0:0:1,0:24.3:1:30.8:1:1:0:45.1:52:1:0:0.3 +6 168672824 . C T 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18354;SOR=0;LSEQ=CCACAGGCGTGTGGCAAATG;RSEQ=AGGCAGGCCTGGGCTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:6.5:1:27.5:1:1:1.13389:60:4:0.1176:0:2 0/0:22:0:0,0:8,14:22,0:0:2,0:20.8:1:31.2:1:1:0:60:44:1:0:0.3 +6 169642695 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATTCCCACCTTCCCAC;RSEQ=TTCCCACCTTCCCACCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:33.5:1:1:0:55:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +6 169643879 . T C 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0.08819;LSEQ=GCTCTGACAGGAATGTAGTT;RSEQ=TACCTGGTAGTAAAACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:39:38,1:76,4:80,39:0.3277:2,1:23.9:1:32.6:1:1:1.99:60:78:0.3277:0:1.1 0/1:49:2:2,0:45,2:47,2:0.0408:1,0:37:1:33:0:1:0:60:4:0.0408:0:1 +6 169643986 . C T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0216;SOR=1.35652;LSEQ=TCTTCACAAGGTTACTCTCA;RSEQ=TTTTAACAAACAGTGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:195:115,80:199,159:358,195:0.3526:2,2:25.6:1:30.6:1:0.47281:1.15:60:47.75:0.3505:0:1.8 0/1:440:187:105,82:138,115:253,187:0.425:2,2:25:1:29.6:1:0.7715:1.07:59.9:45.75:0.4207:0:1.8 +6 169644032 . C T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=1.66802;LSEQ=TGTCATTACCAAGAACCAAT;RSEQ=CATGAACTAGCTGTTTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:226:101,125:198,235:433,226:0.3429:2,2:28.1:1:30.3:1:0.80533:1.04272:60:55.5:0.3442:0:1.7 0/1:522:243:121,122:130,148:278,243:0.4655:2,2:24.8:1:29.2:1:0.53853:1.13:59.9:47.6:0.463:0:1.7 +6 169644086 . TGAA T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=0.00097;SOR=Inf;LSEQ=CTTAAGTCTGACATAACCAG;RSEQ=GAAGAAGTCTTTGTTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:127,255:382,0:0:2,0:23.3:1:32.1:1:1:0:60:75.4:0.9869:0:0.4 0/1:284:8:2,6:109,167:276,8:0.0282:2,2:21:1:32.4:1:0.48846:1.95388:60:16:0.0289:0:0.4 +6 169644148 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.14542;SOR=1.58516;LSEQ=GGACATTGGCATCCACCTGG;RSEQ=TTTGAGTAGACTAACTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:45:6,39:5,72:77,45:0.3689:2,2:21:1:30.5:1:0.32546:2.20:60:90:0.3689:0:1.2 0/1:81:39:4,35:7,35:42,39:0.4815:2,2:21.7:1:29.5:1:0.52197:1.73813:60:78:0.4815:0:1.1 +6 169644190 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05062;SOR=Inf;LSEQ=GTGATTGCCACATATGGTCC;RSEQ=GTAGATATATGTATATAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:0,63:63,0:0:1,0:26:1:32.2:1:1:0:60:126:1:0:0.5 0/1:38:3:0,3:0,35:35,3:0.0789:1,0:31:1:31:1:1:0:60:6:0.0833:0:1.7 +6 170137581 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51036;SOR=Inf;LSEQ=TTGGTCTTTGAGGCTGCTGA;RSEQ=CCTTAGATGGGGTTTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:37,0:0:2,0:33:1:32.1:1:1:0:51.3:74:1:0:0.1 0/1:53:2:1,1:25,26:51,2:0.0377:2,2:40.5:1:29:1:1:1.04:60:4:0.0377:0:1 +6 170137584 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51209;SOR=Inf;LSEQ=GTCTTTGAGGCTGCTGACCC;RSEQ=TAGATGGGGTTTTTGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:37,0:0:2,0:33.2:1:30.9:1:1:0:51.3:36:1:0:0.1 0/1:54:2:1,1:25,27:52,2:0.037:2,2:28.5:1:32:1:1:1.08:53.5:4:0.037:0:1 +6 170138104 . G GA 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTCCCTGAGCCTCTGGCTG;RSEQ=AGTTATTGGAGATCCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:16.7:1:30.3:1:1:0:54.7:6:1:0:0 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:20.5:1:29.2:1:1:1.29098:40:4:0.2222:0.1111:0 +6 170508532 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20979;SOR=Inf;LSEQ=CAACCCAGAAACACCAACGG;RSEQ=CACAAATAGAAGCAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:23,19:42,0:0:2,0:29.1:1:31.6:1:1:0:60:41:1:0:0.1 0/1:36:2:1,1:21,13:34,2:0.0556:2,2:35:1:27.5:1:1:1.5932:60:4:0.0588:0:1 +6 170508585 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23944;SOR=0;LSEQ=CTCTGCAGCCAAGGCCCTGG;RSEQ=GGGGCCGCCCAGAAGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:14,19:33,2:0.0571:2,2:37.5:1:30.5:1:1:1.35:60:4:0.0606:0:1 0/0:36:0:0,0:14,22:36,0:0:2,0:25.8:1:29.2:1:1:0:60:35:1:0:0.1 +6 170508601 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22273;SOR=Inf;LSEQ=CTGGAGGGGCCGCCCAGAAG;RSEQ=AGCCCCGGCAAACGCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:12,21:33,0:0:2,0:21.6:1:31.8:1:1:0:60:66:1:0:0.2 0/1:30:2:1,1:9,19:28,2:0.0667:2,2:20.5:1:30:1:1:2.05:60:4:0.0667:0:1 +6 170798799 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=CAAGGGGCGTATAAGTCCAG;RSEQ=TAATCGAACTCTTACTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:125,66:191,0:0:2,0:24.7:1:29.8:1:1:0:59.9:94.5:1:0:0.2 0/1:192:2:1,1:118,72:190,2:0.0104:2,2:32.5:1:30:1:1:1.63444:60:4:0.0105:0:1 +6 170798821 . G A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18697;SOR=0.56969;LSEQ=AATCGAACTCTTACTCCACC;RSEQ=CTTTTTCATTCTTAAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:19:14,5:140,90:230,19:0.0763:2,2:30.9:1:31.1:1:0.33147:1.80:60:38:0.0772:0:1.5 0/1:245:11:6,5:137,97:234,11:0.0449:2,2:22.9:1:29.1:1:1:1.17618:60:22:0.0462:0:1.7 +6 170798856 . G T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24875;SOR=Inf;LSEQ=AGGCCTGAAGTTGGAGAAAA;RSEQ=GAGGAAAGCGGAGCAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:155,130:285,0:0:2,0:26.1:1:32.2:1:1:0:59.9:141.5:1:0:0.7 0/1:290:3:1,2:146,141:287,3:0.0103:2,2:10:1:25:1:0.61855:2.0659:60:6:0.0105:0:1.7 +6 170798891 . C T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.46823;LSEQ=AGCCATGGGTCTTTGCAAAA;RSEQ=GAACAGAGCTCAGAGATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:130:59,71:74,74:148,130:0.4659:2,2:24.5:1:30.3:1:0.47163:1.20258:60:64:0.4655:0:1.9 0/1:283:82:41,41:89,111:200,82:0.2898:2,2:23.7:1:29.5:1:0.43143:1.25:59.9:81:0.2914:0:2 +6 170798912 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=0.44292;LSEQ=GAACAGAGCTCAGAGATAGC;RSEQ=AGATCCCAGGCACAGGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:125:45,80:67,78:145,125:0.463:2,2:24.4:1:30.8:1:0.1074:1.52463:60:124:0.4662:0:1.9 0/1:250:69:32,37:76,104:180,69:0.276:2,2:26.5:1:29.8:1:0.57043:1.18:59.9:33.5:0.2724:0:2 +6 170798941 . T TA 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.21116;SOR=Inf;LSEQ=GGCACAGGCGCAGCCATTAG;RSEQ=AACAAAAACAGCTCACAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:81,136:217,0:0:2,0:27.4:1:29.1:1:1:0:60:434:1:0:0.7 0/1:185:2:1,1:68,115:183,2:0.0108:2,2:8.5:1:29.6:1:1:1.69:57.5:4:0.011:0.0054:3 +6 170871004 . G GCAA 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.21421;SOR=0;LSEQ=GAGCAACAAAGGCAGCAGCA;RSEQ=CAACAACAACAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:2,0:22,17:39,2:0.0488:2,0:33:1:31.2:1:0.50244:0:50.5:4:0.0488:0.0244:1 0/0:47:0:0,0:27,20:47,0:0:2,0:28.7:1:30.6:1:1:0:53.4:22.5:1:0:0.4 +6 170871013 . A ACAG 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=9.000;MSILEN=3;SSF=0.00886;SOR=0.29748;LSEQ=AGGCAGCAGCAGCAACAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:24:14,10:8,7:15,24:0.6154:2,2:37:1:32.4:1:1:1.22:51:48:0.6154:0:0.1 0/1:47:15:7,8:17,12:29,15:0.3191:2,2:38.1:1:30.9:1:0.53159:1.60113:53.5:30:0.3261:0.0213:0.1 +6 170871046 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.21142;SOR=Inf;LSEQ=CAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:20,17:37,0:0:2,0:20.4:1:29.2:1:1:0:49:74:1:0:0.2 0/1:32:2:1,1:15,15:30,2:0.0625:2,2:10:1:31.5:1:1:1:55:4:0.0625:0:3.5 +7 58384 . C A 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTGCATTTGGGGGAAC;RSEQ=AGAAGTGAGCTGATCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:3,0:3,3:0.5:0,2:19.7:1:30.7:1:1:0:60:6:0.5:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 58414 . C G 83 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGATCTGCATATAGGCCAG;RSEQ=CTTTCTGCATAGGGCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:4,2:2,1:3,6:0.6667:2,2:20.3:1:32.2:1:1:1:60:12:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 58421 . G T 32 v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATATAGGCCAGCCTTTCT;RSEQ=CATAGGGCACAGCGTATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:11:0:32.5:1:1:2.23609:60:4:0.2222:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 59118 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATACCAGGCAAGGCCATG;RSEQ=GGGAAAGCACCAGCTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 60033 . C T 101 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01562;SOR=0.09863;LSEQ=ACTCCAAGCTCCCCCAGACC;RSEQ=GGTGGAAACGCAGACTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:4,6:9,8:17,10:0.3704:2,2:27.7:1:30.6:1:0.69458:1.65488:60:9:0.3462:0:1.6 0/1:19:1:0,1:11,7:18,1:0.0526:2,0:21:0:31:0:0.42105:0:60:2:0.0556:0:1 +7 60046 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16944;SOR=Inf;LSEQ=CCAGACCCGGTGGAAACGCA;RSEQ=ACTCCTTGGCTAACACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:10,15:25,0:0:2,0:23.3:1:32.9:1:1:0:60:50:1:0:1.8 0/1:18:2:1,1:8,8:16,2:0.1111:2,2:21:1:29.5:1:1:1:60:4:0.1111:0:2 +7 60055 . G T 117 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=0.04495;LSEQ=GTGGAAACGCAGACTCCTTG;RSEQ=CTAACACTGCCATGGGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:7,8:3,7:10,15:0.6:2,2:19.9:1:30.1:1:0.67846:1.98:60:30:0.6:0:1.9 0/1:17:1:0,1:8,8:16,1:0.0588:2,0:39:0:30:0:1:0:60:2:0.0625:0:2 +7 60061 . A G 133 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=0;LSEQ=ACGCAGACTCCTTGGCTAAC;RSEQ=CTGCCATGGGAGTAGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:8,12:0,0:0,20:1:0,2:18.4:1:30.9:1:1:0:60:40:1:0:2 0/1:15:5:2,3:5,5:10,5:0.3333:2,2:40.2:1:30.8:1:1:1.46001:60:10:0.3333:0:1.6 +7 60086 . C G 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00272;SOR=Inf;LSEQ=CATGGGAGTAGAACCCACCA;RSEQ=AAGCCCCCTACACTCCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:24:1:32.1:1:1:0:60:20:1:0:1.3 1/0:13:8:3,5:2,3:5,8:0.6154:2,2:30.6:1:30.6:1:1:1.10211:60:16:0.6154:0:1 +7 173163 . G T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCAGTGCGGAGGGAGAG;RSEQ=GCCCAGGTCAGCCCAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:17.5:1:27.5:1:1:0:51:4:0.6667:0:1.5 +7 330676 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54221;SOR=0;LSEQ=CCCGCGGGGAGGGTGACCCT;RSEQ=TCCGGCATCTACGACTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:118,34:152,2:0.0129:2,2:22.5:1:28.5:1:0.40404:3.435:60:4:0.0132:0:1 0/0:84:0:0,0:69,15:84,0:0:2,0:20.1:1:30.9:1:1:0:60:27:1:0:0.1 +7 330781 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03754;SOR=Inf;LSEQ=CTGTCCCTCAACAGCTGCTT;RSEQ=GTCAAGGTGAGCGCCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:99,197:296,0:0:2,0:24.3:1:30.3:1:1:0:60:73:1:0:0.5 0/1:150:3:2,1:50,97:147,3:0.02:2,2:14:1:24:1:0.2758:3.84:60:6:0.0205:0:1.7 +7 330808 . GC G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.09951;SOR=Inf;LSEQ=GTGAGCGCCGCCCCCGACGG;RSEQ=CCCGGGTGTCCCAGCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:40,125:165,0:0:2,0:22.5:1:31.2:1:1:0:59.9:54:0.9939:0:1 0/1:77:2:1,1:11,62:73,2:0.026:2,2:19:1:29.5:1:0.29622:5.44:60:4:0.026:0:2.5 +7 330822 . A C 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00019;SOR=0.10237;LSEQ=CGACGGGCCCCGGGTGTCCC;RSEQ=GCGTGGCGACACCTGCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:119:18,101:0,3:3,119:0.9754:0,2:22.5:1:29.4:1:1:0:59.9:22.8:0.9744:0:1.4 1/1:55:44:5,39:1,10:11,44:0.8:2,2:21.7:1:29.5:1:1:1.28:60:21:0.7925:0:1.3 +7 330834 . C T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09486;SOR=Inf;LSEQ=GGTGTCCCAGCGTGGCGACA;RSEQ=CTGCGCCAGGGCCTCGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:3,79:82,0:0:1,0:25.1:1:31.9:1:1:0:59.8:81:1:0:1.4 0/1:37:2:0,2:2,33:35,2:0.0541:2,0:6:1:30:0:1:0:60:4:0.0588:0:2.5 +7 330882 . T G 130 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=GGGAGGGCACCGCGGCGGCT;RSEQ=CAGGGAGGTCCGTCCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:0,15:1:0,1:20.1:1:33.5:1:1:0:58.9:30:1:0:2.9 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:19:1:32:1:1:0:60:10:0.7143:0:2.8 +7 330884 . A G 124 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=GAGGGCACCGCGGCGGCTTC;RSEQ=GGGAGGTCCGTCCTCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:0,14:1:0,1:19.7:1:32.6:1:1:0:58.9:28:1:0:2.9 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:17.8:1:30.6:1:1:0:60:10:0.7143:0:2.8 +7 331086 . G A 61 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTACTGGACGTTCGCGGGC;RSEQ=GCTGCGAGTCGCTGCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:19.5:1:30.8:1:1:0:60:8:1:0:1.3 1/1:3:3:1,2:0,0:0,3:1:0,2:30.7:1:28.7:1:1:0:60:6:1:0:1 +7 384385 . G A 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.23443;SOR=4.80832;LSEQ=AGATGGGGAGGGCCAGAGTC;RSEQ=CCCCCACAGCGGCCACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:10,8:18,1:0.0526:2,0:26:0:32:0:1:0:60:2:0.0526:0:2 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:43.5:1:30.5:1:1:1.29:60:4:0.2857:0:1.5 +7 384439 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=GGACAGTGGCTGAACCCAGT;RSEQ=CCAGGTGCCAGGTGCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:4,2:6,2:0.2222:2,2:11.5:1:29.5:1:1:1.8258:60:4:0.2222:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:29.4:1:30.2:1:1:0:60:10:1:0:0 +7 385269 . T G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTGGCTGTGGATATGTTAG;RSEQ=GGGTAACGATTACTCTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:32:0:1:0:54:4:1:0:1.5 +7 385345 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTATGTGATCTCCTGAGCT;RSEQ=GTGATCCACCCACCTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:30:1:1:0:37:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 602992 . C G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGGCTGCCTCTGCAGACA;RSEQ=CATTCCTTAGGCCAGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:32:1:1:0:60:4:1:0:2 +7 603002 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCAGACACCATTCCTTA;RSEQ=GCCAGAAGGGAAAGGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:29:1:1:0:60:4:1:0:2 +7 604190 . T C 34 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.32198;LSEQ=CAGGTCCCCGCCCCACCGCA;RSEQ=TCAGGCCCTCGACTCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:16:1:34:0:1:0:60:4:0.6667:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:12:0:33:0:1:0:60:2:0.3333:0:2 +7 606189 . T C 42 d5;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCACCACCATCACCATCA;RSEQ=TGTCATCACCTTCACATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:6:1:27:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 1055639 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51515;SOR=0;LSEQ=ATCTAGTGTCTGAGGTGTCA;RSEQ=ATGAGGATCCCAGACAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:4,2:6,2:0.25:2,2:21:1:31.5:1:1:1.8258:60:4:0.25:0:1 0/0:4:0:0,0:3,1:4,0:0:2,0:27.5:1:32.8:1:1:0:60:8:1:0:1 +7 1056124 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.45455;SOR=0;LSEQ=CATAGCAGCACAGCAGCACA;RSEQ=AGCAGCGCACAGCAGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:12.5:1:30.5:1:1:2.45:60:4:0.3333:0:2 0/0:5:0:0,0:3,2:5,0:0:2,0:40:1:31.4:1:1:0:60:10:1:0:0 +7 1056145 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.19231;SOR=0;LSEQ=AGCAGCGCACAGCAGCACAG;RSEQ=AGCGCACAGCAGCACACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:33.5:1:28:1:1:2.45:60:4:0.3333:0:2 0/0:7:0:0,0:4,3:7,0:0:2,0:25:1:29.3:1:1:0:60:6:1:0:0.9 +7 1056183 . G A 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23516;SOR=6.81231;LSEQ=ACCAGCACAAAGCAGCGCAC;RSEQ=CCAGCGCACAGCAGCGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:4,4:8,1:0.1111:2,0:13:0:32:0:1:0:60:2:0.1111:0:2 1/0:6:3:2,1:1,2:3,3:0.5:2,2:32.3:1:29.7:1:1:3.11:50.7:6:0.5:0:3.3 +7 1056188 . C T 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.11813;SOR=7.63506;LSEQ=CACAAAGCAGCGCACGCCAG;RSEQ=GCACAGCAGCGCACACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:0,1:4,5:9,1:0.1:2,0:8:0:33:0:1:0:60:2:0.1111:0:2 1/0:6:3:2,1:1,2:3,3:0.5:2,2:30.7:1:29.7:1:1:3.11:50.7:6:0.5:0:3.3 +7 1056203 . A G 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05779;SOR=Inf;LSEQ=GCCAGCGCACAGCAGCGCAC;RSEQ=CCAGTACACAGCAGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:11,0:0:2,0:18.6:1:30.4:1:1:0:60:22:1:0:0.9 0/1:8:3:2,1:2,3:5,3:0.375:2,2:25.7:1:29.3:1:1:2.60:50.7:6:0.375:0:3.3 +7 1056239 . G A 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59993;LSEQ=ACACAGCACCACACAGCAGC;RSEQ=TACAGCAGCGCACGCCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:2,2:4,3:7,4:0.3636:2,2:14.8:1:31.8:1:1:1.29868:60:8:0.4:0:1.5 0/1:8:2:1,1:2,3:5,2:0.25:2,2:34.5:1:31.5:1:1:1.41:60:4:0.2857:0:3 +7 1056265 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05495;SOR=Inf;LSEQ=CAGCGCACGCCAGAGCACAG;RSEQ=AGCGCACGCCAGCGCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:17.3:1:28.8:1:1:0:60:16:1:0:0.3 1/0:6:3:2,1:1,2:3,3:0.5:2,2:10:1:31:1:1:3.11:50.7:6:0.5:0:3.3 +7 1056349 . GCACAGCAGCA G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCATGCCAGCACACGCCAGC;RSEQ=CACAGCAGCACACGCCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:6,5:11,2:0.1429:2,0:16.5:1:34:0:0.48718:0:39.5:4:0.1538:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:6:0:33:0:1:0:60:2:1:0:2 +7 1056463 . G A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACACCAGCGCACAGCAGC;RSEQ=CACAGCAGCGCACGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:7,8:15,3:0.1667:2,2:16:1:31.3:1:1:1.69794:23:6:0.1765:0:5.3 0/0:3:0:0,0:1,2:3,0:0:2,0:24:1:31:1:1:0:50.3:6:1:0:0.7 +7 1056477 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGCGCACAGCAGCGCAC;RSEQ=CCAGCACACAGCAGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:14,2:0.125:2,2:18.5:1:30.5:1:1:1:24:4:0.125:0:5.5 0/0:4:0:0,0:1,3:4,0:0:2,0:23.8:1:20.8:1:1:0:43:1:1:0:1.5 +7 1056524 . A G 52 MAF0.05;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=0.87218;LSEQ=AGCAGCGCACAGCAGCACAC;RSEQ=CCAGCGCACAGCAGCACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:3,2:5,8:13,5:0.2778:2,2:27.6:1:22.4:1:0.60784:2.28:27.4:1.5:0.2143:0:3.8 0/1:4:1:0,1:1,2:3,1:0.25:2,0:37:0:29:0:1:0:21:2:0.25:0:4 +7 1056530 . GC AT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCACAGCAGCACACACCAGC;RSEQ=ACAGCAGCACACGCCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,9:15,2:0.1111:2,2:24:1:29.8:1:1:1.46:24:4:0.125:0:4.5 0/0:4:0:0,0:1,2:3,0:0:2,0:22.7:1:31.7:1:1:0:43.7:6:0.75:0:2 +7 1056540 . A G 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53947;SOR=0;LSEQ=ACACACCAGCGCACAGCAGC;RSEQ=CACGCCAGCGCACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:5,7:12,3:0.2:2,2:15.7:1:30:1:0.56923:2.61:23.3:6:0.2:0:4.3 0/0:5:0:0,0:1,4:5,0:0:2,0:16.8:1:26.8:1:1:0:38.8:4:1:0:2.4 +7 1056565 . GCAGCACACGC G 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCGCACAGCAGCACACA;RSEQ=CAGCACACGCCAGCGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:1,2:3,5:8,3:0.2727:2,2:19.3:1:33:1:1:1.18052:20.7:6:0.2727:0.2727:0.3 0/0:2:0:0,0:1,1:2,0:0:2,0:38.5:1:33:1:1:0:41:4:1:0:3.5 +7 1056600 . A G 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=ACACGCCAGCGCACAGCAGC;RSEQ=CACGCCAGCACACACCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:3,0:0:0,0:23.7:1:28:1:1:0:52.3:6:1:0:0.7 1/0:4:2:1,1:1,1:2,2:0.5:2,2:30.5:1:28:1:1:1:45:4:0.6667:0:3 +7 1056610 . ACACACCAGCG A 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.00794;SOR=Inf;LSEQ=GCACAGCAGCACACGCCAGC;RSEQ=CACAGCAGCGCACAGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:17.4:1:32.8:1:1:0:60:10:1:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:23.5:1:29.8:1:1:0:43:8:1:0.5:3.3 +7 1056636 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02222;SOR=Inf;LSEQ=CAGCGCACAGCAGCGCACAG;RSEQ=AGCACACAGCAGCACACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:22.8:1:31.1:1:1:0:60:16:1:0:0.1 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:32:1:1:0:45:4:1:0:3 +7 1056645 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02222;SOR=Inf;LSEQ=GCAGCGCACAGGAGCACACA;RSEQ=CAGCACACAGCAGCGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:27.3:1:32.6:1:1:0:60:16:1:0:0.1 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:32.5:1:1:0:45:4:1:0:3 +7 1056911 . A T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATAAGGAGCTCCCTGCTCA;RSEQ=ATTGGAGCTGCGGGGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:36:1:29:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 1270880 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1489;SOR=Inf;LSEQ=GCGCCGTCCCCTCCTCTCCC;RSEQ=CAAGGAGAGACAAGAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:41,33:74,0:0:2,0:27.6:1:30.8:1:1:0:60:73:1:0:0.1 0/1:47:2:1,1:25,20:45,2:0.0426:2,2:26.5:1:28.5:1:1:1.24403:60:4:0.0435:0:1 +7 1270955 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54198;SOR=0;LSEQ=ACGACCTTCAGTTAGGAACA;RSEQ=GGCCAGACTGTGGGTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:22,29:51,2:0.0377:2,2:44.5:1:31:1:1:1.31:60:4:0.0392:0:1 0/0:28:0:0,0:9,19:28,0:0:2,0:23.6:1:30.1:1:1:0:60:56:1:0:0.1 +7 1345000 . T C 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24195;SOR=2.80936;LSEQ=TAGCTTAAAATTGGCCTTGG;RSEQ=GGGAGTATTTACACCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:6,8:14,3:0.1765:2,2:22.7:1:31:1:1:1.46561:60:6:0.1875:0:1 0/1:13:5:3,2:4,4:8,5:0.3846:2,2:26.2:1:30.2:1:1:1.45:60:10:0.3846:0:1.2 +7 1672522 . G T 52 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42391;SOR=0.34545;LSEQ=GTGGCTTCTGCCTCAGTGGG;RSEQ=AGGTGGACAGAGCTGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:5:1,4:268,184:452,5:0.0109:2,2:8.2:1:22.8:1:0.16443:5.80554:60:4:0.0089:0:1.4 0/0:263:1:0,1:155,107:262,1:0.0038:2,0:1:0:21:0:0.41065:0:60:2:0.0038:0:2 +7 1672540 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06594;SOR=0.75249;LSEQ=GGGAGGTGGACAGAGCTGAG;RSEQ=ACAAAGAAATCAATGGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:512:341:183,158:86,83:169,341:0.666:2,2:25.5:1:29.1:1:0.57279:1.12:60:340:0.6693:0:1.1 1/0:290:174:103,71:65,51:116,174:0.6:2,2:26.4:1:28.1:1:0.62816:1.14:59.9:173:0.5986:0:1.1 +7 1672759 . C G 52 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.94642;LSEQ=GCAAGGGTTGGACCATGGGG;RSEQ=GGGGGCAGGGAAAGGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:0,16:16,3:0.15:1,0:34.7:1:33.3:1:1:0:60:6:0.1579:0:1 0/1:7:1:0,1:1,4:5,1:0.1429:2,0:49:0:29:0:1:0:60:2:0.1667:0:1 +7 2020877 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCAAAGTGCTGGGATGA;RSEQ=AAGCGTGAGCCGGTGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:2:1,1:80,16:96,2:0.0204:2,2:15.5:1:29:1:0.31833:4.88103:60:4:0.0206:0:1.5 0/0:43:0:0,0:34,9:43,0:0:2,0:25.1:1:29.7:1:1:0:60:13.333:1:0:0.3 +7 2020882 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1023;SOR=Inf;LSEQ=AAAGTGCTGGGATGACAAGC;RSEQ=TGAGCCGGTGTGCCCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:83,18:101,0:0:2,0:23.6:1:30.2:1:1:0:59.9:100:1:0:0.2 0/1:48:2:1,1:34,12:46,2:0.0417:2,2:17:1:27.5:1:0.47252:2.76192:60:4:0.0435:0:3 +7 2020904 . G C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53314;SOR=1.31673;LSEQ=GAGCCGGTGTGCCCGGCCAG;RSEQ=AGTGTGGATTCTAACTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:21:14,7:109,42:151,21:0.1221:2,2:22.6:1:31.7:1:0.61115:1.29561:60:20:0.1183:0:1 0/1:71:11:7,4:37,23:60,11:0.1549:2,2:30.3:1:30.8:1:1:1.09:60:22:0.1594:0:1.4 +7 2020995 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.69814;SOR=0.92785;LSEQ=CAGGAGCCAGAACGGACTGC;RSEQ=GGCTCAAGGAAGAGCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:361:219:109,110:67,75:142,219:0.6066:2,2:25.8:1:30.8:1:0.667:1.11:60:108.5:0.6045:0:1.1 1/0:158:93:40,53:30,35:65,93:0.5886:2,2:24.7:1:29.6:1:0.74605:1.1348:59.9:45.5:0.5871:0:1.1 +7 2021162 . T C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACAGGATCCGATGGGTT;RSEQ=AGGGAGGTAAATCCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:0,20:1:0,1:20.4:1:33.1:1:1:0:60:40:1:0:1.1 1/1:4:4:0,4:0,0:0,4:1:0,0:25.3:1:33.3:1:1:0:60:8:1:0:1 +7 2021248 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCAGCTCACTCCGTCA;RSEQ=GAAGGGAGGAGGAAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:31.5:1:32:0:1:0:60:4:0.3333:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:24:1:28.5:1:1:0:60:4:1:0:0 +7 2160931 . T C 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGCCTCTCCCAACCTCTG;RSEQ=TCAGCGTCAGAGCGAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:39.5:1:34:0:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2160997 . G C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACCGTGGGGACAGGCAG;RSEQ=GATGAGGGAGGCTGCGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:12,0:12,2:0.1429:0,0:27:1:33.5:1:1:0:60:4:0.1429:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:38:0:27:0:1:0:60:2:1:0:0 +7 2161099 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47484;SOR=0.64191;LSEQ=CCCACGGGAGGGTCGTTAAC;RSEQ=GAGTCCCGGTGGCCAGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:23:18,5:25,6:31,23:0.4259:2,2:21.3:1:29.9:1:1:1.15425:60:46:0.434:0:1 0/1:28:9:8,1:15,4:19,9:0.3214:2,2:22.7:1:29.8:1:1:2.08:60:18:0.3214:0:1 +7 2161239 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGGGCAGGACTATGCTG;RSEQ=AGATCACGGCATCCTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:9,43:52,2:0.0364:2,2:35.5:1:30:1:0.33892:4.59:60:4:0.0377:0:1 0/0:14:0:0,0:0,14:14,0:0:1,0:21.7:1:31.8:1:1:0:60:28:1:0:0 +7 2166233 . T C 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGATGCCGCCAGCCTTCC;RSEQ=TGGGACCAAGCACAACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,2:5,2:0.2857:2,0:26:1:30.5:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2166259 . G C 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAGCACAACCCAGGCCCA;RSEQ=CCCAGCTCTGAAAGGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:5,2:7,2:0.2222:2,0:38.5:1:32.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2166319 . T G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04923;SOR=6.0033;LSEQ=CTCTGGGGACCGGCCTCTTC;RSEQ=GTCACTCAGAGTTTTTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:6,1:15,0:15,7:0.3182:1,2:17.9:1:31.4:1:0.31818:0:60:14:0.3182:0:1 1/0:8:6:6,0:2,0:2,6:0.75:0,0:19.2:1:29.7:1:1:0:60:12:0.75:0:1.2 +7 2166451 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09328;SOR=Inf;LSEQ=CCGCCAGGCAGGTGCTCACT;RSEQ=ACACTGTCCCCATGGGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:230,110:340,0:0:2,0:23.1:1:32:1:1:0:59.4:339:1:0:0.3 0/1:150:2:1,1:102,45:147,2:0.0133:2,2:16.5:1:30.5:1:0.52358:2.25289:60:4:0.0134:0:1 +7 2166514 . T C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.55606;SOR=0.9117;LSEQ=TCAGAATGAATAACCCCCTC;RSEQ=CACACTGCCAGGCAAATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:230:113,117:160,177:337,230:0.4035:2,2:26.9:1:31.2:1:0.73234:1.07:59.9:75.667:0.4112:0:1.2 0/1:291:111:54,57:86,93:179,111:0.3814:2,2:26.1:1:29.7:1:1:1.02:59.3:26.75:0.3808:0:1.2 +7 2166580 . C T 174 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGTAGGGCATTTTAAACAA;RSEQ=GGCAGATTACAACTGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:56:20,36:73,166:239,56:0.1886:2,2:26.1:1:30:1:0.52294:1.26:60:27:0.1862:0:1.1 0/0:135:0:0,0:42,93:135,0:0:2,0:22.1:1:29.5:1:1:0:60:44:1:0:0.4 +7 2166583 . C T 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00931;SOR=Inf;LSEQ=TAGGGCATTTTAAACAACGG;RSEQ=AGATTACAACTGAGAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:85,195:280,0:0:2,0:23.1:1:32:1:1:0:60:45.667:0.9928:0:0.6 0/1:129:4:1,3:39,86:125,4:0.031:2,2:31.8:1:22.8:1:1:1.35745:60:3:0.0236:0:2.3 +7 2166601 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09179;SOR=Inf;LSEQ=GGCAGATTACAACTGAGAAC;RSEQ=TGGGATAAAGCCAGCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:40,159:199,0:0:2,0:23.5:1:32.4:1:1:0:60:48.75:1:0:0.5 0/1:87:2:1,1:16,68:84,2:0.023:2,2:35:1:28.5:1:0.35814:4.15:60:4:0.0235:0:1 +7 2166654 . C A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTCAGTCACGAAGCACAT;RSEQ=CGAGGCCTCGTTCCCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:2,75:77,2:0.025:1,2:21:1:25.5:1:0.07498:30.85:60:4:0.0256:0:1 0/0:27:0:0,0:1,26:27,0:0:1,0:20.5:1:30.7:1:1:0:60:54:1:0:0.2 +7 2166714 . A G 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGATGAAGACATCTGAAC;RSEQ=CTCTCCTGGAGGGGGCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:0,25:0,0:0,25:1:0,1:26:1:32.6:1:1:0:59.2:50:1:0:1 1/1:4:4:0,4:0,0:0,4:1:0,0:24.8:1:32.5:1:1:0:60:8:1:0:1 +7 2640196 . C G 130 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11208;SOR=0.17318;LSEQ=ACTCCTCGTCCTCCCGAAAG;RSEQ=GTGGGAGAAAACTTAGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:16:16,0:61,2:63,16:0.2025:1,1:23.9:1:32.5:1:1:0:60:32:0.2078:0:1 0/1:24:1:1,0:21,2:23,1:0.0417:2,0:22:0:32:0:1:0:60:2:0.0417:0:1 +7 2640258 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.23321;SOR=4.40801;LSEQ=ATGCTGGCTTGTCTGTCTGT;RSEQ=TCACTCTTATTCAGTGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:1:0,1:205,54:259,1:0.0038:2,0:1:0:27:0:0.21154:0:60:2:0.0039:0:1 0/1:119:2:1,1:94,23:117,2:0.0168:2,2:14.5:1:29:1:0.36405:4.02213:60:4:0.0168:0:1 +7 2640306 . G T 55 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01021;SOR=Inf;LSEQ=TTGCTTCCATCGTATATTCT;RSEQ=CTGGTCCTTGTACTCAGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:0:0,0:326,189:515,0:0:2,0:25:1:32.4:1:1:0:59.9:127.75:1:0:0.1 0/1:345:5:2,3:216,124:340,5:0.0145:2,2:24:1:24:1:0.36172:2.60524:60:4:0.0118:0:1.8 +7 2640378 . A C 214 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=124.46251;LSEQ=TACAGTAGTACAAATGTGGG;RSEQ=CGTGCACTCTGATGTACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:731:3:1,2:342,386:728,3:0.0041:2,2:20.7:1:30.7:1:1:1.77069:60:6:0.0042:0:1 0/1:411:140:66,74:116,155:271,140:0.3406:2,2:24.1:1:30.1:1:0.40438:1.19:60:69:0.345:0:1.2 +7 2640450 . T TGGCATC 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=6;SSF=0.00148;SOR=Inf;LSEQ=TAAGTGCACATTGATTAACT;RSEQ=GGCATCAACATCTGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:0:0,0:107,249:356,0:0:2,0:25:1:30.5:1:1:0:59.9:177:1:0:0.1 0/1:184:6:2,4:57,119:176,6:0.0326:2,2:21:1:28.7:1:1:1.04:60:12:0.0331:0.0109:0 +7 2640485 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGAGGACTTCGCTCACATC;RSEQ=ATAAGAACACATGCTCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:21,154:175,2:0.0113:2,2:30.5:1:31:1:0.23376:7.19:60:4:0.0114:0:1 0/0:81:0:0,0:12,69:81,0:0:2,0:22.3:1:27.8:1:1:0:60:80:1:0:0.2 +7 2640533 . C T 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00481;SOR=5.36026;LSEQ=CTCTACTGATTGTGACGCTG;RSEQ=GTGTCAGCTGCAGCCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:10:0,10:1,54:55,10:0.1538:1,0:26.3:1:30.2:1:1:0:60:20:0.1563:0:1.1 1/0:20:10:0,10:1,9:10,10:0.5:2,0:18.2:1:30:1:1:0:60:20:0.5:0:1 +7 2641473 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAATTACAGGCGTGAGCCAC;RSEQ=GCGCCCGGCAAGTCCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2642115 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAGGAGAGGACCCCGCC;RSEQ=CAGTCACTCAGAGCTGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:30.5:1:1:0:60:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2642142 . A G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCAGAGCTGGCGCTGGGCC;RSEQ=CAGGGCTTCTCACGCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:39.5:1:32:1:1:0:60:4:0.6667:0:3 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:32:1:1:0:60:4:1:0:2 +7 2642187 . A C 62 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCTCACCCACAGCTGCTTCT;RSEQ=AGTGGCAGGGCAGACTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:16.5:1:30.5:1:1:1:60:4:0.5:0:3 1/1:4:4:2,2:0,0:0,4:1:0,2:32.5:1:31:1:1:0:60:8:1:0:1.8 +7 2732326 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.53247;SOR=0;LSEQ=TCTGAGAGGTTGCAGGGGGT;RSEQ=CTGCCTCCACACGCTGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:19,15:34,2:0.0556:2,2:9:0:31:1:1:1.2583:60:4:0.0606:0:1.5 0/0:20:0:0,0:13,7:20,0:0:2,0:22.3:1:31.2:1:1:0:60:40:1:0:0.3 +7 2732378 . C A 61 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.28545;SOR=0;LSEQ=AGGGCAGGAGTACCCCACCC;RSEQ=TTGGCCACAAGCCCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:2,2:14,15:29,4:0.1212:2,2:7:1:30.5:1:1:1.07:60:8:0.125:0:1.3 0/0:17:0:0,0:8,9:17,0:0:2,0:22.5:1:28.8:1:1:0:60:16:1:0:0.3 +7 2732414 . C T 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05491;SOR=9.05283;LSEQ=GCAGCGGTTCCCCACCTCAC;RSEQ=CAGAGCAAAGGTTAAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:4,11:15,1:0.0625:2,0:23:0:32:0:1:0:60:2:0.0625:0:1 0/1:10:4:0,4:0,6:6,4:0.4:0,0:29.5:1:30:1:1:0:60:8:0.4:0:1 +7 2770789 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08339;SOR=Inf;LSEQ=AGCCGTGGGGGCTGCTCAAC;RSEQ=ACGACAAACCCCGGGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:18,0:18,0:0:1,0:17.8:1:31.1:1:1:0:60:36:1:0:0.1 0/1:15:3:2,1:10,2:12,3:0.2:2,2:9:1:29.7:1:0.51648:2.32631:60:6:0.2308:0:1.3 +7 2770861 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50464;SOR=0;LSEQ=TCTCCTGCAGGATGGTGTCT;RSEQ=TCACAGCATGGAACACGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:40,32:72,2:0.027:2,2:20.5:1:32:1:1:1.2462:60:4:0.027:0:1 0/0:57:0:0,0:32,25:57,0:0:2,0:31.7:1:28.9:1:1:0:60:27.5:1:0:0.2 +7 2772261 . T C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCACTCAGGCAGCTTCT;RSEQ=GCCAAAACACCAAACACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:0:31.5:1:1:0:60:4:1:0:2.5 +7 2772290 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAAACACGGACATGATCA;RSEQ=GCCTCGATCTAGAGGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:32:1:1:0:60:4:1:0:2.5 +7 2881639 . G GAGGGAGGGAGGAAGGAAGAA 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAGGGTAGAGAGGTAGG;RSEQ=AGGGAGGGAGAAAGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:27.1:1:1:0:46.5:4:1:0.5:0.5 +7 2883502 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10414;SOR=Inf;LSEQ=GTCACCTTGAGGATGTTGTC;RSEQ=AAGATGGTGTCGCGGAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:43,21:64,0:0:2,0:20.5:1:30.5:1:1:0:60:63:1:0:0.3 0/1:31:2:1,1:22,7:29,2:0.0645:2,2:9.5:1:30:1:0.45591:3.00588:60:4:0.0667:0:1 +7 2883515 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55294;SOR=0;LSEQ=TGTTGTCGAAGATGGTGTCG;RSEQ=GGAACTCCAGCAGCGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:1,2:46,28:74,3:0.039:2,2:20:1:27.7:1:0.55666:3.23384:60:6:0.04:0:1 0/0:44:0:0,0:28,16:44,0:0:2,0:20.4:1:30.4:1:1:0:60:43:1:0:0.1 +7 2883523 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52815;SOR=0;LSEQ=AAGATGGTGTCGCGGAACTC;RSEQ=AGCAGCGCCTTCTGGTCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:59,34:93,2:0.0211:2,2:49.5:1:30:0:1:1.72467:60:4:0.0211:0:2 0/0:57:0:0,0:33,24:57,0:0:2,0:21.5:1:30.7:1:1:0:60:114:1:0:0.2 +7 2944263 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAAAAAGCAGCATTGCTCA;RSEQ=GGGCTCTTGGAGGGAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:28:1:1:0:60:4:1:0:1.5 +7 2946179 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02001;SOR=Inf;LSEQ=GGGCAGCTCTGTGGGCCACA;RSEQ=GATCCCCCCGCACCCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:245,26:271,0:0:2,0:24.3:1:33.1:1:1:0:60:53.2:1:0:0.1 0/1:102:3:1,2:90,9:99,3:0.0294:2,2:10.7:1:26.7:1:0.03011:18.74937:60:6:0.0294:0:1 +7 2946188 . C T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00252;SOR=Inf;LSEQ=TGTGGGCCACAGGATCCCCC;RSEQ=GCACCCACTGCATCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:262,45:307,0:0:2,0:24.6:1:30.9:1:1:0:60:50.167:1:0:0.1 0/1:135:5:4,1:109,21:130,5:0.037:2,2:17:1:29.6:1:1:1.29491:60:10:0.037:0:1.4 +7 2946461 . T C 318 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04996;LSEQ=AACTCCTCCTCCGTCTCAGG;RSEQ=CGGGGCAGCAGCTTTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1209:1148:470,678:23,33:56,1148:0.9495:2,2:24.3:1:31.3:1:1:1.00541:59.9:40:0.9532:0:1.2 0/1:721:349:149,200:163,206:369,349:0.484:2,2:25.2:1:30.4:1:0.7069:1.06199:60:42.625:0.4837:0:1.2 +7 2946552 . C A 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=5e-04;SOR=0.39658;LSEQ=GGCACCACCTGTCCGGCCAC;RSEQ=CCTGACTGCCGTGGTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:84:8,76:21,202:223,84:0.2727:2,2:24:1:30.1:1:1:1.01:60:83:0.2776:0:1.3 0/1:147:19:3,16:17,111:128,19:0.1293:2,2:24.2:1:29.8:1:0.72482:1.22:60:38:0.1329:0:1.2 +7 2946741 . T C 63 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAGTGCAGTGGCACTTTCT;RSEQ=GGCTCACTGCAACCTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:29.5:1:31.8:1:1:0:40.8:8:0.8:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:25:0:29:0:1:0:52:2:1:0:1 +7 2948456 . TTTTTG T 29 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCGTCCTTTCGTTTTTTTT;RSEQ=TTTTTTTTTTTCTGAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25.5:1:29.5:1:1:0:53.5:4:1:0.5:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2949143 . G C 63 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54545;SOR=2.97405;LSEQ=CCCCTCCGCCCCTCACCCCT;RSEQ=CGCCCCTCACCCCTCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:28:0:26:0:1:0:34:2:0.3333:0:2 1/0:8:5:3,2:1,2:3,5:0.625:2,2:9:1:27.4:1:1:2.60:46.8:4:0.6667:0:1.6 +7 2950020 . C T 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07977;SOR=Inf;LSEQ=GGCAGAGATGAGGCCCCGGA;RSEQ=GGGGTGAACCAGGTGGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:0,6:0,19:19,6:0.24:1,0:21.3:1:31.7:1:1:0:60:12:0.24:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:28.5:1:1:0:60:4:1:0:1 +7 2950622 . A C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAATCCCAGCACTTTGGG;RSEQ=GGTGGGAGGATTGCTTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2951244 . G A 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAAGGTCAGCGTCCACCAC;RSEQ=GAGCCAGCCCCCGGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:33.5:1:30.5:1:1:0:60:4:0.6667:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:11:0:32:0:1:0:60:2:1:0:1 +7 2951256 . C G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACCACGGAGCCAGCCCC;RSEQ=GGCAGCTGGGGGAGCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:21.5:1:29.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2951346 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTCAACGCTTAGGTCAC;RSEQ=TTGTCTGGCTCCAAAGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:41:1:32:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2951650 . C G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06902;SOR=2.26291;LSEQ=GGGTGCAGAGAGGGAGTTAA;RSEQ=ACGGGGCAGCTGCTGGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:26:26,0:82,0:82,26:0.2407:1,1:21.5:1:32.7:1:1:0:60:25:0.2381:0:1 0/1:31:13:13,0:16,2:18,13:0.4194:2,1:23.6:1:32.4:1:0.49677:0:60:26:0.4194:0:1.1 +7 2951726 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10014;SOR=Inf;LSEQ=AAACAACTCTTCATCCCACC;RSEQ=TTGTCCCTGGCCCAGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:355,50:405,0:0:2,0:22.1:1:31.5:1:1:0:60:100.25:1:0:0.2 0/1:188:2:1,1:164,22:186,2:0.0106:2,2:9.5:1:27.5:1:0.23029:7.31445:60:4:0.0107:0:1.5 +7 2951763 . C T 148 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.87954;LSEQ=TGGCCTCATGAGGATCATCA;RSEQ=GGAGGGTCCTGGCCCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:754:5:0,5:516,231:747,5:0.0066:2,0:5:1:26.6:1:0.00296:0:60:10:0.0068:0:1 0/1:412:35:24,11:259,118:377,35:0.085:2,2:23.4:1:29:1:1:1.00599:60:34:0.0842:0:1.3 +7 2951934 . C T 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0;LSEQ=ATCTCTTGTGACGATATCTG;RSEQ=AGAGAGAGGGGCCAGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:22:5,17:255,426:681,22:0.0313:2,2:27.3:1:29:1:0.18408:2.03337:60:44:0.0318:0:1 0/0:477:0:0,0:161,315:476,0:0:2,0:24:1:31.1:1:1:0:59.9:78.333:0.9979:0:0.1 +7 2952037 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01097;SOR=Inf;LSEQ=GCTCTACAGAACTCGATGTC;RSEQ=GATCCCCTTCCAGCCATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:4,143:147,0:0:1,0:24.8:1:30.1:1:1:0:60:146:1:0:0.1 0/1:43:3:0,3:0,40:40,3:0.0698:1,0:21.7:1:30.7:1:1:0:60:6:0.0732:0:1 +7 2952241 . C T 60 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCACCAGTCTAAATAAAT;RSEQ=TCCTGTTCCACCCACCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:1,3:0,5:5,4:0.4444:0,2:15:1:30.3:1:0.44444:0:60:8:0.4444:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2952624 . GGGA G 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGGGGGAGGAGGGGTGATG;RSEQ=GGAGGAGGAGGGAAGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:30:1:32.5:1:1:0:48:4:0.2857:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2952796 . G A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGAAAGGAAAGAGGGAAGAG;RSEQ=AGGAAAGAGGGAAGAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:5:5,0:75,0:75,5:0.0625:1,0:14.8:1:30.6:1:1:0:26:10:0.0676:0:3 0/0:14:0:0,0:13,1:14,0:0:1,0:13.6:1:30.9:1:1:0:58.4:28:1:0:0.1 +7 2952799 . GAAA AGGGGAG 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=AAGGAAAGAGGGAAGAGGAG;RSEQ=GAGGGAAGAGAAGAGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:5:5,0:76,0:76,5:0.0617:1,0:16.8:1:33:1:1:0:26:10:0.0676:0:3 0/0:14:0:0,0:13,1:14,0:0:1,0:14.6:1:29.4:1:1:0:58.4:28:1:0:0.1 +7 2952802 . A AGAGGGAAGAGAAGAGGGGAG 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00045;SOR=0;LSEQ=GAAAGAGGGAAGAGGAGGAA;RSEQ=GAGGGAAGAGAAGAGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:41:41,0:70,1:71,41:0.3504:1,1:13.6:1:30.4:1:1:0:58.1:40:0.3704:0.2735:0.2 0/0:21:0:0,0:18,1:19,0:0:1,0:14.4:1:30.7:1:1:0:60:38:0.9048:0:0.2 +7 2952879 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08198;SOR=Inf;LSEQ=GGAAGTCGTCCTGGTTCATG;RSEQ=CTCCCGCGGGGCTCCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:338,87:425,0:0:2,0:25.5:1:31.3:1:1:0:59.5:46.222:1:0:0.3 0/1:171:2:1,1:136,33:169,2:0.0117:2,2:18:0:27:1:0.35906:4.07505:60:4:0.012:0:1 +7 2952886 . C T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01709;SOR=1.69934;LSEQ=GTCCTGGTTCATGGCTCCCG;RSEQ=GGGGCTCCCCAGGTGGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:70:52,18:315,98:413,70:0.1446:2,2:22.2:1:30.2:1:0.7624:1.11238:59.1:140:0.1452:0:1.2 0/1:197:44:34,10:114,39:153,44:0.2234:2,2:28.7:1:28.5:1:0.84373:1.16:57.2:13.667:0.2135:0:1.1 +7 2952915 . G A 127 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00025;SOR=0;LSEQ=CCAGGTGGCCGTGGCTCGCC;RSEQ=CTCACCTGACTTGCAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:21:13,8:417,237:654,21:0.0311:2,2:29.7:1:29:1:0.82262:1.08264:60:20:0.0303:0:1 0/0:336:0:0,0:208,127:335,0:0:2,0:23.1:1:29.6:1:1:0:59.6:166.5:0.997:0:0.3 +7 2953168 . GC G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GACCTTCCACGGAGGACGGG;RSEQ=CCCTGGGCTGGGTCCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:18,219:237,0:0:2,0:24.4:1:31.3:1:1:0:60:28.625:1:0:0.1 0/1:83:2:1,1:8,73:81,2:0.0241:2,2:22:1:28.2:1:0.20629:8.66:60:4:0.0244:0.012:0 +7 2954801 . T C 284 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09857;SOR=0;LSEQ=CTCACAAGGACCGATGTTCC;RSEQ=CCAGGTGAGGGTGAGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:543:543:434,109:0,0:0,543:1:0,2:22.7:1:31.3:1:1:0:60:107.6:1:0:1.1 1/1:249:247:186,61:2,0:2,247:0.992:0,2:22.2:1:29.8:1:1:0:60:40.167:0.9918:0:1.2 +7 2955084 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03907;SOR=Inf;LSEQ=CAGGGTGCTGCCCTCAACCC;RSEQ=GCAAAGCCAGACCTTGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:13,243:256,0:0:2,0:25.3:1:30.8:1:1:0:59.9:24.6:1:0:0.3 0/1:133:3:1,2:5,125:130,3:0.0226:1,2:16:1:29:1:0.13026:11.84:60:6:0.0226:0:1 +7 2955097 . C T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01152;SOR=0.46141;LSEQ=TCAACCCGGCAAAGCCAGAC;RSEQ=TTGTTCAAATCCCTGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:60:1,59:2,143:145,60:0.2927:1,1:25.4:1:29.8:1:1:1.21:60:19:0.2953:0:1.2 0/1:100:16:0,16:0,84:84,16:0.16:1,1:27.1:1:30:1:1:0:60:32:0.16:0:1.3 +7 2956759 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01911;SOR=Inf;LSEQ=GTCTACCCACCTGTCACTGA;RSEQ=AGGATAAAACGGGACAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:50,2:52,0:0:1,0:26.6:1:33.4:1:1:0:60:104:1:0:0.1 0/1:20:3:3,0:17,0:17,3:0.15:1,0:32.3:1:31:1:1:0:60:6:0.1579:0:1 +7 2956858 . TG T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.23103;SOR=4.43463;LSEQ=ATTCGGGTGTCTCTTCTCAG;RSEQ=GGGAGAGGGCAGGGCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:1:1,0:289,78:367,1:0.0027:2,0:19:0:35:0:1:0:60:2:0.0028:0:6 0/1:167:2:1,1:128,36:164,2:0.012:2,2:23.5:1:28.5:1:0.39715:3.52065:60:4:0.012:0:0 +7 2956918 . C A 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCGGTAGGTGCTCCGGAGAG;RSEQ=CTTACCTGAAGGAGCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:814:0:0,0:477,334:811,0:0:2,0:25.9:1:31.8:1:1:0:60:80.1:0.9963:0:0.2 0/1:424:80:48,32:197,145:342,80:0.1887:2,2:25.3:1:28.3:1:0.7081:1.10:60:160:0.1923:0:1.3 +7 2956926 . G T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10449;SOR=4.58044;LSEQ=TGCTCCGGAGAGCCTTACCT;RSEQ=AAGGAGCTGGCCAAAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:844:2:1,1:473,369:842,2:0.0024:2,2:8.5:1:27.5:1:1:1.28145:60:4:0.0024:0:3.5 0/1:464:5:2,3:255,204:459,5:0.0108:2,2:20.8:1:25:1:0.6601:1.87243:57.2:4:0.0088:0:2.6 +7 2957005 . T C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.70021;LSEQ=CTTGTTGAAAGCGCTTCTTC;RSEQ=GGCTGCAGGGTGTTCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:763:91:37,54:287,384:671,91:0.1193:2,2:26.2:1:30.2:1:0.73565:1.0907:60:44.5:0.1185:0:1.1 0/1:449:150:60,90:121,178:299,150:0.3341:2,2:24.5:1:29.7:1:1:1.01962:59.7:149:0.3341:0:1.3 +7 2957113 . G GC 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00823;SOR=Inf;LSEQ=AACTGGAGACCTGTCCTCAA;RSEQ=CCCCTCCATGCTAACGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:9,156:165,0:0:2,0:22.9:1:32.5:1:1:0:59.8:164:0.9939:0:0.1 0/1:43:3:0,3:2,38:40,3:0.0698:2,0:21.3:1:32:1:1:0:60:6:0.0732:0:0 +7 2958013 . C T 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00181;SOR=Inf;LSEQ=TTCCCTAGAATTCATCATCC;RSEQ=AATACGGATGGATTGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:149,3:152,0:0:1,0:28.6:1:31.8:1:1:0:59.9:304:1:0:0.1 0/1:62:5:5,0:54,3:57,5:0.0806:2,0:35.6:1:31.4:1:1:0:60:10:0.0806:0:1 +7 2958194 . C T 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01804;SOR=6.04957;LSEQ=CCTCGGTGCATCAGGCGCTG;RSEQ=AGTTTCACCAGGAGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1042:2:1,1:465,574:1039,2:0.0019:2,2:29.5:1:26.5:1:1:1.23:60:4:0.0019:0:1 0/1:695:8:4,4:327,360:687,8:0.0115:2,2:19:1:28.3:1:1:1.10:60:16:0.0118:0:1.3 +7 2958274 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04361;SOR=Inf;LSEQ=AAATTCAGGGGCCAAGCACC;RSEQ=GGAAGCCAGCGGGGCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:405:0:0,0:89,316:405,0:0:2,0:23.1:1:31:1:1:0:60:80:1:0:0.2 0/1:221:3:2,1:51,167:218,3:0.0136:2,2:16.3:1:27:1:0.14365:6.48:60:6:0.014:0:1 +7 2958298 . C T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00786;SOR=1.94377;LSEQ=AGCCAGCGGGGCCGCAGCAC;RSEQ=GCACTGGCATGGGTGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:46:9,37:20,189:209,46:0.1804:2,2:22.4:1:30.8:1:0.07033:2.29:60:92:0.1818:0:1.3 0/1:140:42:1,41:14,84:98,42:0.3:2,1:22.2:1:29.9:1:0.03913:6.77225:60:84:0.3022:0:1.1 +7 2958337 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06645;SOR=Inf;LSEQ=CGCGTGTCCGACTCTGCGTA;RSEQ=GGATGGCCCTGTGGCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:9,122:131,0:0:2,0:26.6:1:31.3:1:1:0:60:42.667:1:0:0.2 0/1:46:2:0,2:1,43:44,2:0.0435:1,0:21:1:31:0:1:0:60:4:0.0435:0:1 +7 2958484 . TCTC T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CGAACCCCTCTGAGCCACGG;RSEQ=CTCCTCTGTAAATCTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:0,3:0,12:12,3:0.2:0,0:33.3:1:33.3:1:1:0:47.3:6:0.2:0:0.3 0/0:1:0:0,0:0,1:1,0:0:0,0:45:0:34:0:1:0:60:2:1:0:1 +7 2959172 . G A 208 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCTGGCTGGAGATGTTCA;RSEQ=GTTCAGCCGGATGTAGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1510:0:0,0:714,795:1509,0:0:2,0:24.4:1:32:1:1:0:59.9:67.591:0.9993:0:0.2 0/1:852:139:62,77:356,356:712,139:0.1631:2,2:24.2:1:29.3:1:0.26612:1.24162:60:138:0.1643:0:1.2 +7 2959278 . C A 38 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12782;SOR=5.55921;LSEQ=AAGATGCTCCAGCTGTCTAT;RSEQ=AGTATGGGGTCCCCCGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:521:1:1,0:114,406:520,1:0.0019:2,0:1:0:25:0:0.22073:0:60:2:0.0019:0:1 0/1:283:3:2,1:87,193:280,3:0.0106:2,2:6.3:1:24.3:1:0.23365:4.41:60:2:0.0072:0:1.7 +7 2959287 . G A 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05234;SOR=7.58296;LSEQ=CAGCTGTCTATCAGTATGGG;RSEQ=TCCCCCGACCATCAGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:408:1:1,0:63,344:407,1:0.0025:2,0:1:0:25:0:0.15686:0:60:2:0.0025:0:1 0/1:218:4:3,1:54,159:213,4:0.0183:2,2:17:1:26.8:1:0.0565:8.73:60:8:0.0186:0:1 +7 2961066 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCGCAGCTCCGGGCTTTGG;RSEQ=GGTGCTGCCCACATCATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:29.5:1:1:0:60:4:1:0:1 +7 2961909 . A C 100 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAAGCCCGAGAGAGGAGG;RSEQ=AACTTCCACTTACCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:27.5:1:33.5:1:1:0:59.3:16:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2962014 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07326;SOR=12.4481;LSEQ=TGTGACCCGGCGGGCAGCCC;RSEQ=AGACACCTGGGCAGGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:1:1,0:22,0:22,1:0.0435:1,0:22:0:30:0:1:0:60:2:0.0455:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:12:1:27:1:1:0:60:4:0.4:0:1 +7 2962036 . C T 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57187;SOR=0;LSEQ=GACACCTGGGCAGGTGAGTG;RSEQ=AGACGTGGCCAAAGAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:8:8,0:31,0:31,8:0.2051:1,0:17.3:1:30:1:1:0:60:16:0.2162:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:31.7:1:33.3:1:1:0:60:12:1:0:0.3 +7 2962183 . G T 39 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03612;SOR=Inf;LSEQ=GAACAGACGAGCAAGCAGAG;RSEQ=CTCTAGGCGGCGAGGTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:0:0,0:393,91:484,0:0:2,0:22.5:1:31.2:1:1:0:60:36.231:1:0:0.2 0/1:240:3:1,2:183,53:236,3:0.0125:2,2:6.7:1:24.7:1:0.13329:6.83308:60:6:0.0126:0:1 +7 2962201 . A C 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGGCTCTAGGCGGCGAGGTC;RSEQ=CTTGTCCAGGTCAGAGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:37:27,10:504,187:691,37:0.0508:2,2:25.1:1:31.6:1:1:1.00:60:74:0.0515:0:1.1 0/0:387:0:0,0:267,118:385,0:0:2,0:22:1:29.2:1:1:0:60:76:0.9948:0:0.2 +7 2962241 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04319;SOR=0.73323;LSEQ=CGCCTCCCTGGCCAAGGGTC;RSEQ=CTCCAGACGGTGGAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1261:161:102,59:669,430:1099,161:0.1277:2,2:25.7:1:30.5:1:0.60354:1.11:60:79.5:0.1278:0:1.1 0/1:743:72:43,29:380,290:670,72:0.0969:2,2:23.2:1:28.9:1:0.70739:1.13:60:144:0.0976:0:1.2 +7 2962293 . C G 219 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=358.03598;LSEQ=TGGTTGACCTTGTAGTGCAG;RSEQ=GTGACGGGGCCGCTGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1640:1:0,1:841,793:1634,1:6e-04:2,0:1:0:15:0:0.48563:0:60:0:0:0:1 0/1:939:168:84,84:393,373:766,168:0.1789:2,2:23.1:1:29.7:1:0.7984:1.05359:60:23:0.1754:0:1.2 +7 2962556 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTCAGGGGGGTGCACCT;RSEQ=CCTCCTGCCTGCACCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:37,64:101,2:0.0194:2,2:9.5:1:31.5:1:1:1.72:60:4:0.0206:0:1 0/0:19:0:0,0:7,12:19,0:0:2,0:20.8:1:30.9:1:1:0:60:38:1:0:0.1 +7 2962753 . G A 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=0.57081;LSEQ=TTGCAGCCACCTCCCTTGCC;RSEQ=CCATCCCCTCACCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:799:611:373,238:117,68:185,611:0.7647:2,2:24.8:1:30.3:1:0.60589:1.09769:59.9:121.2:0.7671:0:1.1 1/0:431:280:181,99:93,58:151,280:0.6497:2,2:26.6:1:29.2:1:0.53113:1.14:59.8:279:0.6503:0:1.1 +7 2963056 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04409;SOR=Inf;LSEQ=CGGGGGTTGGTGGTGGGCGC;RSEQ=AGGACCCCGGTGGCATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:3,105:108,0:0:1,0:24.5:1:32.4:1:1:0:59.8:53:1:0:0.1 0/1:60:3:0,3:1,56:57,3:0.05:1,0:32.3:1:27:1:1:0:60:6:0.0508:0:1 +7 2963120 . C T 72 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.78333;LSEQ=GTGTCCTGGCTCCGAGAAGG;RSEQ=CCTTAATGGCTAAGGGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:0,5:0,37:37,5:0.1136:1,0:19.6:1:31.2:1:1:0:60:10:0.122:0:1 0/1:11:1:0,1:1,9:10,1:0.0909:2,0:13:0:30:0:1:0:60:2:0.0909:0:1 +7 2963521 . G T 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTGGGCTCAAGTGATCC;RSEQ=CCTGCCTCAGCCTCCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:22:1:32.3:1:1:0:39.8:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2963744 . T C 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07503;SOR=0;LSEQ=CTGACTCGGGAATGCTACAA;RSEQ=TCTGGTTCTGGCTCTAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:12:12,0:180,2:182,12:0.0619:1,0:20:1:32.7:1:1:0:60:24:0.0628:0:1.2 0/0:53:0:0,0:53,0:53,0:0:1,0:24.2:1:30.7:1:1:0:60:52:1:0:0 +7 2963940 . GGGA G 143 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.22809;SOR=0.52613;LSEQ=ATCCAGGCCCTCGGATTGGT;RSEQ=GGAGGAGGAGGAGTGGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1999:22:10,12:992,983:1975,22:0.011:2,2:25.5:1:32.1:1:0.67495:1.21087:60:44:0.0112:0.003:0.2 0/0:1031:6:4,2:509,512:1021,6:0.0058:2,2:36.2:1:32:1:0.45152:2.01:60:12:0.0059:0:0 +7 2964011 . C T 218 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACTGTCATCTGCAGAGGGA;RSEQ=GAGGGCCCATCAGTACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1818:0:0,0:812,1006:1818,0:0:2,0:25.1:1:30.7:1:1:0:60:52.471:1:0:0.2 0/1:977:166:68,98:379,429:808,166:0.1699:2,2:23.3:1:29.6:1:0.17183:1.27289:59.7:40.5:0.1695:0:1.2 +7 2964267 . AT A 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGTATCTGGTTTTTAAG;RSEQ=TTTTTTTTTTTGAGAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:0,2:0,34:34,2:0.0556:1,0:24.5:1:31:1:1:0:60:4:0.0556:0.0278:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2966138 . G A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47171;SOR=1.7108;LSEQ=TAAAAGCCCAGACCTAGCTC;RSEQ=CACCCTCTGCACAGCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:9:9,0:61,0:61,9:0.1268:1,0:19.9:1:31.4:1:1:0:60:18:0.1343:0:1 0/1:20:4:3,1:15,1:16,4:0.2:1,2:7.3:1:29:1:0.36842:4.47215:60:8:0.2:0:1 +7 2966334 . G A 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGTGACCCTCTGTGACCC;RSEQ=TCCTACCCAGGACCCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1787:0:0,0:998,782:1780,0:0:2,0:25.3:1:30.3:1:1:0:59.9:31.364:0.9988:0:0.2 0/1:962:50:28,22:506,404:910,50:0.052:2,2:26.8:1:29.7:1:1:1.02:60:49:0.0524:0:1.3 +7 2966445 . T G 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00079;SOR=1.36303;LSEQ=GCTGCAAGACACAAGGGAGG;RSEQ=GGGGGAAAGCATGCATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1451:488:191,297:368,581:949,488:0.3363:2,2:26.7:1:30.6:1:0.90909:1.02:60:29.5:0.3388:0:1.2 0/1:793:324:140,184:177,245:422,324:0.4086:2,2:24.6:1:30.1:1:0.76516:1.05:59.9:80:0.4188:0:1.3 +7 2966465 . AGT A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.59507;SOR=1.14271;LSEQ=TGGGGGAAAGCATGCATGTG;RSEQ=GTGTGTGTGTGTGCACACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1099:40:9,31:364,690:1054,40:0.0364:2,2:26.9:1:32.9:1:0.12825:1.81618:59.4:80:0.037:0.0036:0.5 0/1:580:24:9,15:203,352:555,24:0.0414:2,2:24:1:30.7:1:1:1.04:59.2:23:0.0402:0.0052:0.7 +7 2966520 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09394;SOR=Inf;LSEQ=GAGAAGCTTCTGGAAGGTTC;RSEQ=AGGCTTCCGAGTGGCCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:22,357:379,0:0:2,0:22.8:1:32.3:1:1:0:59.8:53.143:1:0:0.3 0/1:168:2:1,1:11,154:165,2:0.0119:2,2:13.5:1:29:0:0.13895:13.45:60:4:0.012:0:1 +7 2968093 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCAGCCTCCTCATCTGTA;RSEQ=AATGAGCAGTACCCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:2,0:189,7:196,2:0.0101:1,0:14:0:31:1:1:0:60:4:0.0102:0:1.5 0/0:64:0:0,0:62,2:64,0:0:1,0:22.2:1:32:1:1:0:60:128:1:0:0.2 +7 2968105 . C A 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATCTGTACAATGAGCAGTA;RSEQ=CCTGCCTTTCAGGGTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:239,9:248,0:0:1,0:24.1:1:32.6:1:1:0:60:81.667:1:0:0.1 0/1:85:10:9,1:72,3:75,10:0.1176:1,2:25.7:1:28.7:1:0.39971:2.62452:60:20:0.1176:0:1 +7 2968195 . G A 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGGCTTGGCATGGTGGCAC;RSEQ=GGGCAAAAGCCCAGTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1149:0:0,0:707,437:1144,0:0:2,0:24.5:1:30:1:1:0:60:44.76:0.9956:0:0.1 0/1:579:54:35,19:318,204:522,54:0.0933:2,2:22.1:1:29.1:1:0.6605:1.18:60:108:0.0947:0:1.1 +7 2968289 . T C 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TGGAGTCGTTTCCCGGGGGC;RSEQ=CGGCGGTGATTGACATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1596:26:8,18:661,905:1566,26:0.0163:2,2:22:1:30.7:1:0.3171:1.64288:60:25:0.0162:0:1.3 0/0:937:0:0,0:418,517:935,0:0:2,0:23.9:1:28.9:1:1:0:59.9:45.75:0.9978:0:0.2 +7 2968359 . C T 106 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=3e-05;SOR=14.04928;LSEQ=ACACAGACACACACACGTTA;RSEQ=GGGTGCATAAATATTACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:664:2:0,2:166,494:660,2:0.003:2,0:33:1:30:1:1:0:60:4:0.0031:0:1 0/1:294:12:3,9:74,207:281,12:0.0408:2,2:15.3:1:29.8:1:1:1.07221:60:24:0.0408:0:1.1 +7 2968361 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.23722;SOR=1.28084;LSEQ=ACAGACACACACACGTTACG;RSEQ=GTGCATAAATATTACACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:76:18,58:137,413:550,76:0.1212:2,2:22.1:1:31.2:1:0.88789:1.06876:59.7:75:0.123:0:1.2 0/1:273:41:9,32:58,174:232,41:0.1502:2,2:16.1:1:30.2:1:0.84417:1.18445:60:40:0.1481:0:1.1 +7 2968486 . G C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48247;SOR=1.89614;LSEQ=GGCTGGAGGAGGCTTGTGCT;RSEQ=AGCCCGGAGCGGCCGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:23:0,23:1,43:44,23:0.3433:1,1:24.2:1:32.8:1:1:0:60:46:0.3594:0:1.1 1/0:10:5:0,5:0,5:5,5:0.5:0,0:12.4:1:31.6:1:1:0:60:10:0.5:0:1 +7 2968548 . G A 112 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCGCACATCTGCTCACAGG;RSEQ=AGGACGCAGGCGGGAGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:0,12:0,11:11,12:0.5217:0,0:21.2:1:31.3:1:1:0:60:24:0.5455:0:1.3 0/0:1:0:0,0:0,1:1,0:0:0,0:39:0:32:0:1:0:23:2:1:0:1 +7 2969496 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03266;SOR=Inf;LSEQ=TCCCTGGATGGCATTCTGCA;RSEQ=GGGGAGAGGGTGGTGGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:163,7:170,0:0:1,0:22.4:1:33:1:1:0:59.9:33:1:0:0.3 0/1:38:2:2,0:35,1:36,2:0.0526:1,0:22:1:30:0:1:0:60:4:0.0541:0:1 +7 2969508 . G A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00499;SOR=2.66542;LSEQ=ATTCTGCAGGGGGAGAGGGT;RSEQ=GTGGGGATGAGCTCTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:35:32,3:157,7:164,35:0.1759:1,2:24.7:1:27.4:1:0.38518:2.09314:60:16.5:0.1701:0:1.1 0/1:55:20:19,1:33,2:35,20:0.3636:2,1:21.1:1:27.7:1:1:1.15:60:40:0.3774:0:1.1 +7 2969583 . A T 42 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00865;SOR=Inf;LSEQ=ACACTCTTCTGCAGGGGGAG;RSEQ=CAATGGAGGGGACCTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:744:0:0,0:562,181:743,0:0:2,0:24:1:29.8:1:1:0:59.9:48.533:1:0:0.2 0/1:328:4:1,3:228,96:324,4:0.0122:2,2:7.5:1:21.3:1:0.08381:7.07765:60:3:0.0096:0:1.3 +7 2969660 . C A 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGTTGGTGATGGGCAGAGAT;RSEQ=CGCAGGAGCTAGGGCTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1601:76:41,35:738,787:1525,76:0.0475:2,2:26.5:1:28.7:1:0.34992:1.25:60:75:0.0474:0:1.2 0/0:862:0:0,0:440,421:861,0:0:2,0:25.3:1:30.3:1:1:0:60:85.1:0.9988:0:0.4 +7 2969680 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.95331;LSEQ=CCGCAGGAGCTAGGGCTGGC;RSEQ=TCCGTGCCTTCTTCCTCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1588:247:114,133:618,718:1336,247:0.1555:2,2:24.6:1:30.6:1:1:1.00418:59.9:48.4:0.1539:0:1.1 0/1:888:235:112,123:320,333:653,235:0.2646:2,2:25.1:1:29.5:1:0.76096:1.05531:60:46:0.2635:0:1.2 +7 2969983 . C T 110 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCTCCTCTTGCTTTTTAT;RSEQ=AAATTTTTTATAGAGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:0,14:0,4:4,14:0.7778:0,1:22.8:1:29.1:1:1:0:57.9:28:0.7778:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2971977 . T TG 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.54849;SOR=Inf;LSEQ=AGAGGGGACCTTTCAGCAGT;RSEQ=GGGCTCCTGCCTGCTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:61:59,2:2,0:2,61:0.9683:0,1:23.5:1:31.4:1:1:0:58.9:19.333:0.9831:0.2063:0.2 1/1:32:32:31,1:0,0:0,32:1:0,1:21.7:1:30.8:1:1:0:60:15:1:0.2813:0.3 +7 2972031 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.08688;SOR=Inf;LSEQ=TAATTGCTATTTGGATGGAC;RSEQ=CCCACCACTCCGAGACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:191,4:195,0:0:1,0:25.7:1:31.4:1:1:0:59.8:31.5:1:0:0.3 0/1:82:2:1,1:77,3:80,2:0.0244:1,2:37.5:1:29:1:0.09575:22.37217:60:4:0.0247:0:2.5 +7 2972072 . A G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=2.09339;LSEQ=GAGAACCCGCCACGTTTACC;RSEQ=CGCAGGATTGTTCGTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:70:56,14:285,54:339,70:0.1711:2,2:25:1:29.5:1:0.38373:1.3185:60:34:0.1692:0:1.1 0/1:192:58:45,13:98,35:133,58:0.3021:2,2:23.2:1:28.1:1:0.71701:1.23:60:18.333:0.2957:0:1.1 +7 2973685 . TTTTTC T 69 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCACAATGCCTGGCTGTTT;RSEQ=TTTTCTTTTCTTTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:37.6:1:29.8:1:1:0:57:10:1:0.1667:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 2973920 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03887;SOR=Inf;LSEQ=AAATGAGTAAGAAGCGAGTC;RSEQ=CAGGATTTCCAGCTTACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:59,0:0:1,0:23.7:1:30.4:1:1:0:59.8:118:1:0:0 0/1:15:2:2,0:12,1:13,2:0.1333:1,0:24.5:1:31:0:1:0:43:4:0.1429:0:1 +7 2973979 . C T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTCTGGGCACCCAAGAC;RSEQ=CACCCAGAAGCAGGCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:2,0:151,7:158,2:0.0125:1,0:20.5:1:34:0:1:0:60:4:0.0132:0:1 0/0:61:0:0,0:54,7:61,0:0:2,0:25.8:1:31.1:1:1:0:60:122:1:0:0.1 +7 2974165 . C T 177 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=66.22565;LSEQ=CTGTCTTCAGGTGACTCCTC;RSEQ=GAGGTGGAAGAATCGTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1702:2:0,2:914,786:1700,2:0.0012:2,0:1.5:1:28.5:1:0.21421:0:60:4:0.0012:0:1 0/1:952:69:33,36:459,419:878,69:0.0725:2,2:28.6:1:29.1:1:0.53208:1.19483:59.5:22:0.0705:0:1.1 +7 2974494 . C A 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.21839;SOR=4.17601;LSEQ=GGTCCAGTCTCCCAAACAAG;RSEQ=CCCGGTCTTCTTGTACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:0,4:0,18:18,4:0.1818:1,0:17:1:32:0:1:0:59.5:8:0.1818:0:1 1/0:4:2:1,1:0,2:2,2:0.5:0,2:39:1:26.5:1:1:0:60:4:0.5:0:1 +7 2976520 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06167;SOR=Inf;LSEQ=GGTTTGGGGCCCCACAGGGA;RSEQ=GTGGCGACTGGTCACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:59,0:0:1,0:22.3:1:32.5:1:1:0:59.2:28.5:1:0:0.1 0/1:20:2:1,1:16,2:18,2:0.1:2,2:9:0:31.5:1:0.28421:6.73285:29:4:0.1:0:3 +7 2976522 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06013;SOR=Inf;LSEQ=TTTGGGGCCCCACAGGGAGG;RSEQ=GGCGACTGGTCACAGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:59,1:60,0:0:1,0:22.4:1:30.2:1:1:0:59.2:120:1:0:0.1 0/1:20:2:1,1:16,2:18,2:0.1:2,2:11:0:32:1:0.28421:6.73285:29:4:0.1053:0:3 +7 2976572 . G A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=CAGGGGGCACCTGGCTTCAG;RSEQ=TGTGGGTCTCCACGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:135,0:135,0:0:1,0:24:1:31.5:1:1:0:59.7:44:1:0:0.1 0/1:53:9:7,2:40,4:44,9:0.1698:2,2:19.6:1:29.3:1:0.26677:2.78562:53.1:18:0.1765:0:1.4 +7 2976767 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=1.64107;LSEQ=ACCATCTCGATCCTCATCTC;RSEQ=TCGTTCTTCTCCTCCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1875:271:127,144:815,788:1603,271:0.1445:2,2:25.9:1:30.5:1:0.23737:1.17261:59.9:32.875:0.143:0:1.2 0/1:1239:269:141,128:491,479:970,269:0.2171:2,2:25.1:1:29.4:1:0.62969:1.07:60:66.25:0.2165:0:1.2 +7 2977488 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17127;SOR=0;LSEQ=GGAGCCGGTGGTCTGGGGTG;RSEQ=GGGCCCCGCTGTGCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:5:3,2:383,99:482,5:0.0103:2,2:9.8:1:26.2:1:0.27756:2.57285:60:10:0.0104:0:1 0/0:254:0:0,0:187,67:254,0:0:2,0:21.6:1:30.5:1:1:0:60:41.333:1:0:0.2 +7 2977732 . T C 154 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=64.76218;LSEQ=AGGTCAGGACTGAAAGCTGT;RSEQ=CTCTGCTCGTGCCTTCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:1:0,1:20,271:291,1:0.0034:2,0:40:0:13:0:1:0:60:0:0:0:2 0/1:186:34:2,32:13,139:152,34:0.1828:2,2:20.1:1:30.3:1:1:1.49348:60:33:0.1833:0:1.1 +7 2977768 . G T 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05018;SOR=0;LSEQ=CCCGCCAGCTGGCTGGAGCT;RSEQ=GCCTGTCCCTCCCTAAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:7:0,7:2,147:149,7:0.0446:1,0:35.7:1:30.7:1:1:0:60:14:0.0467:0:1 0/0:90:0:0,0:0,90:90,0:0:1,0:21.1:1:30.2:1:1:0:60:21.5:1:0:0.2 +7 2978226 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10329;SOR=Inf;LSEQ=TGGAAAGGAGTGTGGGGTCA;RSEQ=GGAGGTCCTGCTGACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:245,20:265,0:0:2,0:22.8:1:33.1:1:1:0:59.8:264:1:0:0.1 0/1:126:2:1,1:119,5:124,2:0.0159:1,2:29.5:1:28.5:1:0.09333:21.8176:60:4:0.0161:0:1 +7 2978506 . G A 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04803;SOR=7.84182;LSEQ=TTCAGAGGGTCAGGGTCGGG;RSEQ=TGGGGAGCCAGGTGGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:665:1:1,0:201,463:664,1:0.0015:2,0:1:0:25:0:0.30376:0:60:2:0.0015:0:1 0/1:342:4:2,2:108,230:338,4:0.0117:2,2:10.3:1:27.8:1:0.59652:2.12:60:8:0.0119:0:1.8 +7 2978543 . A T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09793;SOR=Inf;LSEQ=CCTGGAGGGCAGGGGACAGA;RSEQ=GAACCAGCAACAGATACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:29,319:348,0:0:2,0:22.5:1:32.2:1:1:0:59.8:173:1:0:0.1 0/1:159:2:1,1:21,136:157,2:0.0126:2,2:20:0:30:1:0.25834:6.35:60:4:0.0126:0:1.5 +7 2985351 . C A 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05689;SOR=0;LSEQ=TCACAGCTTAAGAACCATGC;RSEQ=ACTACTGAGGACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:8:8,0:232,5:237,8:0.0327:1,0:24.8:1:31.4:1:1:0:60:16:0.0343:0:1.3 0/0:120:0:0,0:113,5:118,0:0:1,0:22.4:1:30.4:1:1:0:59.8:28.5:0.9828:0:0.3 +7 2985361 . GAC G 213 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=13.000;MSILEN=2;SSF=0.00151;SOR=0.48124;LSEQ=AGAACCATGCCACTACTGAG;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:103:101,2:115,3:118,103:0.3872:1,1:32.2:1:32:1:1:1.32:59.8:206:0.4008:0:0.3 0/1:146:34:34,0:91,9:100,34:0.2329:2,1:25.1:1:31.2:1:0.11104:0:60:68:0.2378:0.0274:0.1 +7 2985391 . C G 75 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.08684;SOR=0;LSEQ=CACACACACACACACACAGA;RSEQ=ACACACACACACACGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:6:5,1:331,78:409,6:0.014:2,2:6.8:1:29.3:1:1:1.18:60:5:0.0123:0:1.5 0/0:273:0:0,0:203,60:263,0:0:2,0:22.6:1:30.9:1:1:0:59.7:51.6:1:0:0.4 +7 2985393 . C G 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=7.000;MSILEN=2;SSF=0.11585;SOR=3.98215;LSEQ=CACACACACACACACAGACA;RSEQ=ACACACACACACGCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:460:2:2,0:367,88:455,2:0.0043:2,0:14:1:35:0:1:0:52.5:4:0.0044:0:2.5 0/1:292:5:3,2:216,70:286,5:0.0171:2,2:22.8:1:24.8:1:0.60037:2.05131:54:1.5:0.0104:0:2.2 +7 2985639 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12602;SOR=Inf;LSEQ=GAATACATATCTGATGGAAC;RSEQ=CAAGTCTCTGTGGCTGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:30,238:268,0:0:2,0:25.5:1:32.3:1:1:0:60:66:1:0:0.1 0/1:148:2:1,1:19,127:146,2:0.0135:2,2:9.5:1:24:0:0.2528:6.54:60:4:0.0135:0:1 +7 2985643 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12408;SOR=Inf;LSEQ=ACATATCTGATGGAACGCAA;RSEQ=TCTCTGTGGCTGGTCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:26,225:251,0:0:2,0:25.3:1:32.5:1:1:0:60:49.2:1:0:0.1 0/1:137:2:1,1:16,119:135,2:0.0146:2,2:26.5:1:28:1:0.23358:7.24:60:4:0.0147:0:1 +7 2985857 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01818;SOR=Inf;LSEQ=ATTGCCGCCCCAGTTTTGAA;RSEQ=AGTTTCCCAACTGACCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:0,9:9,0:0:0,0:21.7:1:32.9:1:1:0:59:18:1:0:0.2 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:32.5:1:1:0:60:4:1:0:1 +7 2987515 . TA T 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.92359;LSEQ=ACCTCTAGAATATATTAAGT;RSEQ=AAAAAAAGTCCTGTACACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:0,3:3,238:241,3:0.0123:1,0:28.3:1:33:0:1:0:60:6:0.0124:0:0.3 0/1:88:1:0,1:1,86:87,1:0.0114:1,0:42:0:28:0:1:0:60:2:0.0114:0:0 +7 2998044 . A G 112 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.21338;LSEQ=CTGCAGTATGTTATGATCAC;RSEQ=TCACTGCACTCCAGCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:368:1:1,0:318,49:367,1:0.0027:2,0:22:0:26:0:1:0:60:2:0.0027:0:1 0/1:175:15:12,3:137,23:160,15:0.0857:2,2:15.3:1:28.7:1:0.47061:1.48534:60:30:0.0877:0:1 +7 3371961 . T G 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCTAGCAGGGCTCCATCC;RSEQ=TTAATGTCAGTGCCGTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:23.3:1:32:0:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 3372172 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11177;SOR=Inf;LSEQ=AAGGCATGATAATGGAGTCT;RSEQ=TTATCTATTTGGAAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:138,86:224,0:0:2,0:25.8:1:32:1:1:0:60:55:1:0:0.3 0/1:113:2:1,1:67,44:111,2:0.0177:2,2:19:1:28:1:1:1.51687:60:4:0.018:0:1 +7 3372198 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0981;SOR=Inf;LSEQ=TATTTGGAAAAACAACTTTT;RSEQ=TTGCCATTTATAATAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:153,120:273,0:0:2,0:25.3:1:29.3:1:1:0:60:38:1:0:0.4 0/1:125:2:1,1:63,60:123,2:0.016:2,2:19.5:1:29:1:1:1.04961:60:4:0.0163:0:2 +7 3372228 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22707;SOR=4.50538;LSEQ=ATAATAAATGTAAATGGCCT;RSEQ=CCATTTATTTTAGAATTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:0,1:149,135:284,1:0.0035:2,0:1:0:28:0:0.47719:0:60:2:0.0036:0:1 0/1:128:2:1,1:63,62:125,2:0.0156:2,2:21.5:1:28:1:1:1.016:60:4:0.016:0:2.5 +7 3372238 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.10576;SOR=Inf;LSEQ=TAAATGGCCTGCCATTTATT;RSEQ=TAGAATTACTCTGTTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:140,137:277,0:0:2,0:25:1:30.6:1:1:0:60:68.25:1:0:0.8 0/1:134:2:1,1:62,70:132,2:0.0149:2,2:11.5:1:29:1:1:1.13:60:4:0.0153:0:2.5 +7 3372249 . C G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=7e-05;SOR=0.40905;LSEQ=CCATTTATTTTAGAATTACT;RSEQ=TGTTTCTAGGCCCTAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:284:146:70,76:67,71:138,146:0.5141:2,2:24.5:1:32.6:1:1:1.02447:60:292:0.5252:0:1.5 0/1:126:38:16,22:39,48:87,38:0.3016:2,2:26.1:1:31.1:1:0.84597:1.1162:60:37:0.296:0:1.5 +7 3372308 . G C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26817;SOR=0.71756;LSEQ=AAAGTTAGTAGAGGCTAGAA;RSEQ=AACTTATAGGAATGTCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:81:25,56:24,64:88,81:0.4765:2,2:25.4:1:32.1:1:0.61561:1.19:60:162:0.4821:0:1.7 0/1:76:30:11,19:17,29:46,30:0.3947:2,2:25.2:1:31.5:1:1:1.01237:60:29:0.3867:0:1.4 +7 3372409 . T C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.08567;SOR=0.23051;LSEQ=TAGTTCCAGATAACTTCTTT;RSEQ=CCCCCCAGGAATAGATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:14,9:0.3913:1,0:23:1:32.3:1:1:0:60:18:0.3913:0:1 0/1:16:2:0,2:1,13:14,2:0.125:1,0:21:1:31:1:1:0:60:4:0.1333:0:1 +7 3377718 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.49833;SOR=0;LSEQ=CTTAAAAAGTGGGGAAGGGC;RSEQ=TTTTGGCTGGAACCAACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:37,11:48,2:0.04:2,2:34.5:1:30:1:0.42612:3.26364:60:4:0.0426:0:1 0/0:42:0:0,0:25,17:42,0:0:2,0:22.6:1:29.8:1:1:0:60:41:1:0:0.2 +7 3377771 . A G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01308;SOR=Inf;LSEQ=TGCCAAAATGATGAACGACA;RSEQ=AGAGAAAAGGGAGAGGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:60,29:89,0:0:2,0:22.6:1:30.4:1:1:0:60:88:1:0:0.2 0/1:47:4:3,1:18,25:43,4:0.0851:2,2:28.3:1:30:1:0.31124:4.05:60:8:0.0889:0:1 +7 3377822 . T C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGGCCTTTTAGAAAACA;RSEQ=GGACTTGTTCTTTTGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:93,42:135,2:0.0146:2,2:12:1:27:1:0.53081:2.20016:60:4:0.0147:0:1 0/0:51:0:0,0:30,21:51,0:0:2,0:26.2:1:30.2:1:1:0:60:102:1:0:0.3 +7 3377882 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13165;SOR=Inf;LSEQ=AAAGATGATATTGGAGACAT;RSEQ=AAGGGAATGGGTACTGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:169,82:251,0:0:2,0:23.4:1:31.9:1:1:0:59.6:34.857:0.9959:0:0.1 0/1:144:2:2,0:91,51:142,2:0.0139:2,0:15.5:1:25:1:0.53934:0:60:4:0.014:0:1 +7 3377886 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12677;SOR=Inf;LSEQ=ATGATATTGGAGACATCAAG;RSEQ=GAATGGGTACTGTTCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:0:0,0:183,91:274,0:0:2,0:23:1:30.9:1:1:0:59.6:29.444:1:0:0.1 0/1:152:2:1,1:94,56:150,2:0.0132:2,2:33.5:1:29.5:1:1:1.67254:56:4:0.0136:0:1 +7 3377896 . C T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55891;SOR=3.37526;LSEQ=AGACATCAAGGGAATGGGTA;RSEQ=TGTTCAGAAAGGAAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:1:0,1:194,119:313,1:0.0032:2,0:1:0:28:0:0.38217:0:40:2:0.0032:0:1 0/1:187:2:1,1:113,72:185,2:0.0107:2,2:13:0:31:0:1:1.56549:47:4:0.0109:0:1.5 +7 3378162 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.175;SOR=Inf;LSEQ=GCCAGCCTGTTCCCAGAGAA;RSEQ=CACACTTTGTGAGAAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:9,0:0:2,0:28.2:1:32.9:1:1:0:60:18:1:0:0.1 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:36:1:29:1:1:1.41:60:4:0.3333:0:1.5 +7 4382226 . G T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCCTCCACCCAGTCTT;RSEQ=AGGACCGAGAGCAACCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 4407814 . A G 47 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02692;SOR=21.88909;LSEQ=CTGCTCCTCCTGGGAGCCAG;RSEQ=AACCCCTCCTGGGAAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:0,1:5,6:11,1:0.0833:2,0:21:0:34:0:1:0:60:2:0.0833:0:1 1/0:4:3:1,2:0,1:1,3:0.75:0,2:12.3:1:29.7:1:1:0:60:6:0.75:0:1 +7 4798533 . G C 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=AGGCTGGGTTCAGGTTACGG;RSEQ=GGCGTTTCTCACCGTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:509:0:0,0:220,288:508,0:0:2,0:25.8:1:30.7:1:1:0:60:49.8:0.998:0:0.1 0/1:331:11:4,7:137,183:320,11:0.0332:2,2:29.2:1:31.1:1:0.76431:1.30906:60:22:0.0335:0:1.2 +7 4798579 . G A 117 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=24.68932;LSEQ=AGGACAGAGACGAGCTCCAG;RSEQ=GAGCGTGGGCGGGTGACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:1:0,1:97,222:319,1:0.0031:2,0:47:0:13:0:1:0:60:0:0:0:2 0/1:194:14:4,10:63,117:180,14:0.0722:2,2:24.6:1:30.9:1:0.77448:1.34418:60:28:0.0729:0:1.1 +7 4799576 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCTGAGGGAGGAGAAT;RSEQ=GCTTGAAGCCTGGAGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:31.5:1:1:0:40:4:1:0:1.5 +7 6017523 . A G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97141;LSEQ=CACTTTGGGAGGCTGAGGCC;RSEQ=GCGGATCATGAGGTCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:11:0,11:1,46:47,11:0.1897:1,0:25.4:1:29.8:1:1:0:32.5:10:0.1786:0:1.2 0/1:27:5:0,5:0,22:22,5:0.1852:1,0:15.6:1:29.6:1:1:0:29.8:10:0.1852:0:1 +7 6026222 . C CTGA 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.05121;SOR=Inf;LSEQ=AATCCCAGCTACTCAGGAGG;RSEQ=TGAGGCAGGAGAAACGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:29,0:0:1,0:32.2:1:32.7:1:1:0:25.7:58:1:0:0 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:20.5:1:31.3:1:1:0:48:4:0.2222:0.1111:1 +7 6026384 . C T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAAAGTAAAAAATTAAAA;RSEQ=TTTACCTTATCTCTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:346,75:421,0:0:2,0:36.8:1:32.3:1:1:0:45.5:69.167:1:0:0.1 0/1:284:31:25,6:187,66:253,31:0.1092:2,2:37.4:1:29.5:1:0.51519:1.47:47.1:62:0.1103:0:1.1 +7 6026421 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15026;SOR=Inf;LSEQ=TCTTAGTTCATCTTCGGCTG;RSEQ=TTGATTTTCTCCAGGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:244,67:311,0:0:2,0:16:1:31:1:1:0:40.9:76.75:0.9968:0:0.1 0/1:198:2:0,2:132,64:196,2:0.0101:2,0:13:1:31:0:0.10998:0:44.5:4:0.0104:0:1.5 +7 6026530 . C T 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTCGTTTAGCTAAAGAACT;RSEQ=ATAGAAAAGTCCAGGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:70:27,43:653,639:1292,70:0.0514:2,2:26.1:1:29.2:1:0.06498:1.6269:30.2:69:0.0513:0:1 0/0:949:0:0,0:475,474:949,0:0:2,0:27.3:1:31.1:1:1:0:36.3:85.273:1:0:0.1 +7 6026896 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11669;SOR=Inf;LSEQ=CTGAACCCCTCAGAATCCAC;RSEQ=GAAGTGCTGCCGTGCCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:292:0:0,0:110,182:292,0:0:2,0:18:1:31:1:1:0:24.7:291:1:0:0.1 0/1:152:2:1,1:59,91:150,2:0.0132:2,2:25.5:1:27.5:1:1:1.54:30:4:0.0134:0:1.5 +7 6026958 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=GTCCGTAGGGTCACTGGGTC;RSEQ=GTGACTGGAACTCACTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:83,94:177,0:0:2,0:10.3:1:29.9:1:1:0:27.3:43.25:1:0:0.8 0/1:132:11:5,6:55,66:121,11:0.0833:2,2:9.6:1:29.3:1:1:1:25.7:22:0.0833:0:1.1 +7 6026988 . G A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.37665;LSEQ=ACTCACTGCCTCTTTCTGAG;RSEQ=TCTCAGGACGCCTTTGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:487:345:184,161:72,69:141,345:0.7084:2,2:24.1:1:30.7:1:0.68923:1.10:29.5:42.125:0.7095:0:1.1 0/1:356:170:88,82:92,94:186,170:0.4775:2,2:25:1:29.3:1:0.67273:1.10:29.1:169:0.4788:0:1.1 +7 6029348 . C CA 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.61676;SOR=1.83424;LSEQ=AAGAGACTTTGTTTTCATGT;RSEQ=AAAAAAAAGTTTACTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:2,0:180,13:193,2:0.0103:2,0:22.5:1:32.5:1:1:0:60:4:0.0104:0:0 0/1:107:2:2,0:92,13:105,2:0.0187:2,0:35.5:1:30:1:1:0:60:4:0.0189:0:3.5 +7 6029690 . G GT 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00024;SOR=0.18199;LSEQ=ACTCTGTCGCCTAGGCTGGA;RSEQ=TGCAGTGGCGCGATCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:79:41:1,40:0,38:38,41:0.519:1,1:22.5:1:31.4:1:1:0:50:82:0.519:0.1392:0.3 0/1:37:6:0,6:1,30:31,6:0.1622:1,0:17.2:1:31:1:1:0:53.3:12:0.1622:0.027:0.2 +7 6029748 . C T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16152;SOR=0.31942;LSEQ=TCCTGGGTTCAAGTGATTCT;RSEQ=CCTGCCTCAGCCTCCGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:22:1,21:0,16:16,22:0.5789:1,1:25.8:1:29.9:1:1:0:31:21:0.5676:0:1.1 0/1:10:3:0,3:1,6:7,3:0.3:2,0:20:1:30:0:1:0:20.3:6:0.3:0:1 +7 6031101 . TA T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTCCCTTGGTTGACAT;RSEQ=AAAAAAATTACATTTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:33.5:1:31.5:1:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6031469 . C CA 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.64504;SOR=1.50732;LSEQ=GACAGAGCAAGACCCCGTCT;RSEQ=AAAAAAAAACAAAAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:3,0:141,4:145,3:0.0203:1,0:13.7:1:32:1:1:0:47:6:0.0204:0.0068:0 0/1:66:2:2,0:63,1:64,2:0.0303:1,0:11:1:26.2:1:1:0:32:4:0.0303:0.0152:0.5 +7 6031524 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54857;SOR=0;LSEQ=TAAATTGTTATCTCATTCCA;RSEQ=TCATAGCAGAGCTGTAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:2,0:140,3:143,2:0.0138:1,0:31.5:1:28:1:1:0:46.5:4:0.0142:0:1 0/0:75:0:0,0:74,1:75,0:0:1,0:34.6:1:31.1:1:1:0:39.3:150:1:0:0 +7 6031744 . G A 42 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6742;SOR=1.73395;LSEQ=ACAAATGTTCCCAGCCCCCC;RSEQ=CATTCTAACAACATTCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:423:3:1,2:78,338:416,3:0.0071:2,2:16.3:1:16.3:1:0.46658:2.16:41.7:0.5:0.0025:0:4 0/1:245:3:1,2:49,191:240,3:0.0122:2,2:11.3:1:27:1:0.50059:1.94:41:6:0.0131:0:2 +7 6031957 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=TACAGGCAGGATTTTTTTTT;RSEQ=TTTTTTTTTTTCAACGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,3:3,0:0:0,0:41:1:35:1:1:0:60:6:0.75:0:0 1/0:3:2:0,2:0,0:0,2:0.6667:0,0:8:1:29.5:1:1:0:55.5:4:0.6667:0:3.5 +7 6034818 . AA GC 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTGGGATTACAGGCGTGG;RSEQ=CACCATGCCTGGTTATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:2,0:2,3:0.6:0,2:18.7:1:31.8:1:1:0:52:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6035065 . A C 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTTAAAGCCATGTTTCTCA;RSEQ=AGTCCCGAGCTCCACGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:194,3:197,0:0:1,0:25.2:1:30.9:1:1:0:60:394:1:0:0.1 0/1:78:13:13,0:65,0:65,13:0.1667:1,1:28.5:1:32.8:1:1:0:60:26:0.1667:0:2 +7 6035081 . G A 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTCAAAGTCCCGAGCTCCAC;RSEQ=TAAACTGCCTATTATCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:240,4:244,0:0:1,0:26:1:30.2:1:1:0:60:60:1:0:0.1 0/1:124:18:18,0:106,0:106,18:0.1452:1,1:27.8:1:30.4:1:1:0:60:36:0.1463:0:1.7 +7 6035373 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01274;SOR=Inf;LSEQ=AAACAAAACACCAGGTGACA;RSEQ=GCTGATAAGGATCACTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:4,163:167,0:0:1,0:25.6:1:30.7:1:1:0:60:82.5:1:0:0.3 0/1:86:4:0,4:4,77:81,4:0.0465:1,0:32:1:25.3:1:1:0:60:8:0.0471:0:1 +7 6035428 . A C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.61166;SOR=0.72734;LSEQ=CTGTGCTCCAAATCTTGATG;RSEQ=GTCATCAAAGAACCAAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:46:1,45:0,20:20,46:0.697:1,1:24.8:1:30:1:1:0:60:45:0.6923:0:1.1 1/0:24:15:1,14:0,9:9,15:0.625:0,1:20.6:1:29.7:1:1:0:57.7:30:0.625:0:1.1 +7 6036802 . A G 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04533;SOR=4.56742;LSEQ=TTGCAGTGAGCCAAGATAGC;RSEQ=CCATTGCACTCCAGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:3:3,0:67,0:67,3:0.0429:1,0:9.7:1:32:0:1:0:48.7:6:0.0435:0:2.3 0/1:29:5:5,0:24,0:24,5:0.1724:1,0:16.4:1:29:1:1:0:37:10:0.1724:0:1.4 +7 6036895 . TA T 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.34865;SOR=1.60712;LSEQ=AGCCTTAGAATCACTATCTT;RSEQ=AAAAAAAAGCTCTCAGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:9:7,2:362,77:439,9:0.02:2,2:34:1:30.8:1:0.66231:1.34226:60:8:0.0185:0.0022:0.2 0/1:314:10:7,3:230,74:304,10:0.0318:2,2:28:1:28.7:1:0.71145:1.33075:60:20:0.0332:0.0064:0.3 +7 6036980 . G C 302 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00036;SOR=0.56309;LSEQ=AAAAGATTATGCAGAGCATC;RSEQ=GAACAGCTCAAACCGTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1138:1064:555,509:40,32:72,1064:0.935:2,2:25.3:1:30.1:1:0.62662:1.14626:59.9:37:0.935:0:1.2 1/1:873:777:406,371:48,42:90,777:0.89:2,2:25.6:1:29.6:1:0.91136:1.0443:59.9:76.7:0.8919:0:1.2 +7 6037057 . GA G 244 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=0.1325;SOR=0.81275;LSEQ=AGGAATGAGGCTTTGCAACT;RSEQ=AAAAAAAAAAAAAAAATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:738:209:54,155:156,246:402,209:0.2832:2,2:28.1:1:31.7:1:0.00164:1.81848:59.1:103.5:0.2936:0.0136:0.9 0/1:502:122:33,89:132,170:302,122:0.243:2,2:31.4:1:30:1:0.00142:2.09059:59.2:39.667:0.2464:0.006:0.7 +7 6037075 . T A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57714;SOR=0.64932;LSEQ=CTGAAAAAAAAAAAAAAAAA;RSEQ=TCACAGTTACTTCCTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:9:4,5:133,437:570,9:0.0155:2,2:8.7:1:22.7:1:0.2263:2.62:53.9:2:0.0111:0:2.9 0/1:395:4:3,1:99,291:390,4:0.0101:2,2:6.3:1:28.3:1:0.055:8.76:60:8:0.0107:0:1.8 +7 6037153 . CA C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.55352;SOR=0;LSEQ=AGCTATTGACATTACAAGCG;RSEQ=AAAAAAATTAAAAGAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:0,3:0,132:132,3:0.0222:1,0:48.3:1:33.3:1:1:0:60:6:0.0224:0:0 0/0:61:0:0,0:2,58:60,0:0:1,0:22.3:1:30.1:1:1:0:60:29:1:0:0.1 +7 6037232 . A G 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29187;SOR=3.2706;LSEQ=ATTGCCCAGGCTGGAGTACA;RSEQ=TGGCTCAATCATACCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:14,2:0.125:1,0:13.5:1:33.5:1:1:0:60:4:0.125:0:1.5 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:10:1:33.5:1:1:0:60:4:0.3333:0:1 +7 6038324 . CAA C 33 v3;pSTD;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=14.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=AACAGAGCAAGACTCCAGCT;RSEQ=AAAAAAAAAAAACCGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:10.8:1:29.6:1:1:0:49.2:10:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:33:0:1:0:42:4:1:0:0.5 +7 6038620 . CA C 199 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.78528;SOR=1.08149;LSEQ=AGCAGTGCGAGACTCCCTCT;RSEQ=AAAAAAAAAAAAAAATCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:75:72,3:70,2:72,75:0.4167:1,1:22.9:1:32.1:1:1:1.45464:58.9:74:0.4181:0.0944:0.5 0/1:78:34:33,1:27,0:27,34:0.4359:1,1:22.6:1:30.4:1:1:0:58.6:68:0.4416:0.1154:0.6 +7 6038703 . G A 126 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=18.45357;LSEQ=AACCCGCTATAATCACTAGA;RSEQ=CAATAAGAGGCGTTGAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:946:2:2,0:625,314:939,2:0.0021:2,0:3.5:1:20:1:0.55485:0:60:1:0.0011:0:1.5 0/1:637:24:14,10:374,237:611,24:0.0377:2,2:26.4:1:27.6:1:0.83223:1.12697:60:23:0.0373:0:1.2 +7 6038722 . T C 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.34709;LSEQ=AGCAATAAGAGGCGTTGAAG;RSEQ=AACCGGCCATCACTACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1189:791:486,305:232,166:398,791:0.6653:2,2:26.1:1:32.2:1:0.31486:1.14:60:78.1:0.6647:0:1.1 0/1:816:333:192,141:279,204:483,333:0.4081:2,2:25.8:1:31.2:1:1:1.00436:60:46.571:0.4055:0:1.2 +7 6038919 . C A 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00971;SOR=Inf;LSEQ=GCATACTCCTGTTTAAAAAA;RSEQ=ACAAACACAATATTCTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:748:0:0,0:245,503:748,0:0:2,0:25.4:1:32.3:1:1:0:60:92.5:1:0:0.1 0/1:492:5:4,1:180,307:487,5:0.0102:2,2:12.2:1:20.2:1:0.06754:6.80:60:1.5:0.0061:0:2 +7 6039129 . T C 93 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCACTTCCCAATGTGCCA;RSEQ=GCATCCTGGTAAAACAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:12,8:0.4:0,0:20.4:1:31:1:1:0:57.6:16:0.4444:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6041836 . T A 45 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGCCCAGTAAATTTTTTTT;RSEQ=AAAATTTTTCATAGAGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:30:1:29:1:1:0:53.7:6:0.6:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:19:0:29:0:1:0:42:2:1:0:2 +7 6042522 . C T 37 MAF0.05;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=1.29098;LSEQ=TCGTTTTTCAGGTTGAACTG;RSEQ=AAAACCATAAATGATCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:16.7:1:23.7:1:1:0:47:2:0.3333:0:1.3 1/0:2:1:0,1:0,1:1,1:0.5:0,0:34:0:29:0:1:0:45:2:0.5:0:1 +7 6043112 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.12195;SOR=0.23043;LSEQ=GTTTTAATAAGGGTAACCAT;RSEQ=TTTTTAACAATACTATTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:13:12,1:10,0:10,13:0.5652:0,1:35.9:1:32.2:1:1:0:29.5:26:0.5909:0:1 0/1:9:2:1,1:7,0:7,2:0.2222:0,2:41:1:30.5:1:0.22222:0:30:4:0.2222:0:1 +7 6043386 . G A 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08905;SOR=6.63539;LSEQ=GTTTCAACCTGAGTTAGGTC;RSEQ=GCAAACTCTTGAATCTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:1:1,0:66,65:131,1:0.0076:2,0:1:0:25:0:1:0:21:2:0.0077:0:1 0/1:103:5:2,3:47,51:98,5:0.0485:2,2:8.4:1:27.4:1:1:1.37807:21.4:10:0.0485:0:1 +7 6043576 . TA T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09286;SOR=Inf;LSEQ=CATGTGACCCAATTATTTTA;RSEQ=ATAGGATTAGAAAAAGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:316:0:0,0:226,90:316,0:0:2,0:13:1:28.6:1:1:0:49.5:104.333:1:0:0 0/1:139:2:1,1:105,32:137,2:0.0144:2,2:16.5:1:27:1:0.41977:3.24648:33:4:0.0144:0.0072:1 +7 6043797 . C G 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTAAGAGTCATAACTATAC;RSEQ=TTTAGTTAAACATACTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:8,203:211,0:0:1,0:24.8:1:33.4:1:1:0:55.6:210:1:0:0.1 0/1:92:17:3,14:4,71:75,17:0.1848:2,2:25.2:1:31.1:1:0.11476:3.73:56.2:34:0.1889:0:1 +7 6043964 . CTG C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAAGGAACAAAAAAAAT;RSEQ=TAACTGGTGGTGATCAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:0,2:2,17:19,2:0.0952:2,0:23.5:1:32.2:1:1:0:60:4:0.1:0.0476:0 0/0:1:0:0,0:0,1:1,0:0:0,0:13:0:31:0:1:0:60:2:1:0:0 +7 6044650 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTCAAGCAATTCTCCTCC;RSEQ=TCAGCGTCCTGAGGAGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:31:1:1:0:54:4:1:0:1 +7 6045385 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.31059;SOR=0.50929;LSEQ=GCTAAGTACTAGGCACATAA;RSEQ=AGGTGCTAACTTCAACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:35:34,1:10,1:11,35:0.7609:2,1:28.6:1:31.4:1:0.42512:3.29:28.4:34:0.7727:0:1 1/0:13:8:7,1:4,1:5,8:0.6154:2,2:23.6:1:30.1:1:1:1.67:30.6:16:0.6154:0:1 +7 6045627 . C T 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51644;SOR=0.87771;LSEQ=AAATCTGATGGACTGACTTC;RSEQ=GATCAATAGGTTTGATGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:549:92:36,56:187,270:457,92:0.1676:2,2:18.2:1:31.2:1:0.8163:1.07725:30.1:91:0.1673:0:1 0/1:353:53:28,25:130,169:299,53:0.1501:2,2:17.2:1:29.3:1:0.23198:1.45:31:52:0.1486:0:1.2 +7 6048359 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATGGGATGTGGGCAAGG;RSEQ=CTGTCTGGGACAGGCCGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:4,0:20,0:20,4:0.1667:1,0:12.3:1:30.3:1:1:0:54:8:0.1739:0:1.5 0/0:4:0:0,0:4,0:4,0:0:0,0:12:1:31.8:1:1:0:53.8:8:1:0:0 +7 6048510 . G T 49 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17366;SOR=0;LSEQ=GCCACTCCGGGGCCTCCAGG;RSEQ=GGCTGCCTCGCCACGCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:5:3,2:234,42:276,5:0.0177:2,2:13:1:21.4:1:0.17577:3.68937:40.8:1.5:0.011:0:2.8 0/0:142:0:0,0:113,29:142,0:0:2,0:22.7:1:30.2:1:1:0:53.4:70:1:0:0.3 +7 6048556 . G A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00191;SOR=1.72301;LSEQ=ATGTTCCCCCCATTTCCAGG;RSEQ=AGGTTGGAATGCCGTGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:75:48,27:340,182:522,75:0.1256:2,2:24.3:1:29.6:1:0.89714:1.05073:57.5:24:0.1244:0:1.2 0/1:408:81:59,22:216,111:327,81:0.1985:2,2:24.8:1:29:1:0.28981:1.38:54.3:80:0.2005:0:1.2 +7 6048804 . G C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01534;SOR=Inf;LSEQ=ACTTCCCGTCTCTCCTTTTC;RSEQ=CCTATTGGCTCTGTCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:2,125:127,0:0:1,0:23.3:1:32.5:1:1:0:47.8:62.5:1:0:0.1 0/1:43:3:0,3:0,40:40,3:0.0698:1,0:20.7:1:31.3:1:1:0:27.7:6:0.0714:0:1 +7 6048845 . A G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.01559;SOR=Inf;LSEQ=TCGACTTCGTGACGTCAAAG;RSEQ=GCCTGGGCCAATCAGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:2,58:60,0:0:1,0:24.6:1:31.4:1:1:0:60:14:1:0:0.1 0/1:21:3:0,3:0,18:18,3:0.1429:1,0:30.7:1:32.3:1:1:0:56.7:6:0.1429:0:1.3 +7 6048973 . C A 46 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCTTTGGCACGCGCTAC;RSEQ=CCCTTTTGCTTTGGTTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:22.7:1:29.3:1:1:0:60:6:0.75:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6348257 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03931;SOR=0.1351;LSEQ=GTTAGAGCCTCTGGGAACCC;RSEQ=TACAATAGAATATTAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:6,5:1,3:4,11:0.7333:2,2:26.3:1:30.5:1:0.56923:3.31:59.3:22:0.7333:0:1 0/1:8:2:0,2:4,2:6,2:0.25:2,0:24.5:1:30.5:1:0.42857:0:60:4:0.25:0:1 +7 6348344 . G T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02158;SOR=Inf;LSEQ=TTTCTCCAAATTCCTTTTCA;RSEQ=GAAACTTTTGTTCACATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:20,0:0:2,0:32.8:1:31.9:1:1:0:60:40:1:0:0.1 0/1:14:4:2,2:4,6:10,4:0.2857:2,2:24.3:1:30:1:1:1.46:60:8:0.2857:0:1.5 +7 6414333 . TGCC T 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.22068;SOR=1.97696;LSEQ=CGCTTCCTATCTCAGCGCCC;RSEQ=GCCGCCGCCGCGGCCCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:7:2,5:78,60:138,7:0.0476:2,2:10.4:1:29:1:0.2431:3.22444:32.1:14:0.0493:0.0272:0.4 0/1:122:11:5,6:67,43:110,11:0.0902:2,2:9.4:1:29.9:1:0.34947:1.85985:46.8:22:0.0917:0.041:0.3 +7 6414344 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.20584;SOR=Inf;LSEQ=TCAGCGCCCTGCCGCCGCCG;RSEQ=CGCGGCCCAGCGAGCGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:130,103:233,0:0:2,0:14.7:1:31.4:1:1:0:42.9:45.6:1:0:0.2 0/1:194:2:1,1:108,84:192,2:0.0103:2,2:9:0:30:1:1:1.28402:28:4:0.0104:0:1.5 +7 6414355 . C T 51 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.42213;SOR=2.34967;LSEQ=CCGCCGCCGCCGCGGCCCAG;RSEQ=GAGCGGCCCTGATGCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:2:0,2:174,146:320,2:0.0062:2,0:1:0:26:1:0.21048:0:60:4:0.0063:0:1 0/1:276:4:0,4:146,125:271,4:0.0145:2,0:6.3:1:25.8:1:0.04722:0:58.5:8:0.0147:0:1.3 +7 6414424 . G A 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25977;SOR=2.91057;LSEQ=GAGTGCGCGGCCGGGGCCGG;RSEQ=CTGGAGGCCGCGGGATCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:580:2:2,0:256,321:577,2:0.0034:2,0:1:0:24:1:0.19813:0:49:4:0.0035:0:1 0/1:501:5:4,1:223,273:496,5:0.01:2,2:14.2:1:26.4:1:0.18125:4.88:60:10:0.0102:0:1 +7 6414442 . G A 60 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.37883;SOR=0.28402;LSEQ=GGGCTGGAGGCCGCGGGATC;RSEQ=GGCGCGGAGGGGGGTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:4:3,1:148,232:380,4:0.0104:2,2:15.8:1:30.3:1:0.30445:4.68:60:8:0.0105:0:1 0/0:336:1:1,0:139,196:335,1:0.003:2,0:1:0:24:0:0.41667:0:60:2:0.003:0:1 +7 6414450 . AG A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.05191;SOR=Inf;LSEQ=GGCCGCGGGATCGGGCGCGG;RSEQ=GGGGGTTGGGCCCGGACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:103,190:293,0:0:2,0:20:1:32.3:1:1:0:60:292:0.9966:0:0.2 0/1:270:4:2,2:106,160:266,4:0.0148:2,2:18.3:1:30.3:1:1:1.51:60:8:0.0152:0.0037:0.3 +7 6414482 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14791;SOR=Inf;LSEQ=CCCGGACTGGGGCCCAGGCA;RSEQ=GCCGGCGTCCGCCGCGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:12,48:60,0:0:2,0:10.6:1:32.2:1:1:0:60:120:1:0:0.2 0/1:38:2:1,1:5,31:36,2:0.0526:2,2:6.5:1:27.5:1:0.29445:5.75:60:4:0.0541:0:2 +7 6415128 . G A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CTCAGCCTCCAAAAGCGCTG;RSEQ=GGTGACACCGCGCCCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:24:0:32:0:1:0:60:2:1:0:0 +7 6415498 . A G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTCCCATAGAAACAAGA;RSEQ=TCTCAGTGTAACCCGAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:49:0:32:1:1:0:60:4:1:0:1 +7 6426318 . G A 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCTACTTGGGAGGCTGA;RSEQ=GCAGGAGAATCGCTTGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:26:1:32:0:1:0:35:4:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:30:0:33:0:1:0:34:2:1:0:3 +7 6426419 . CA C 63 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GACAGCACGAGACTCGGTCT;RSEQ=AAAAAAAAAAAAAAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:17.5:1:31.6:1:1:0:47.8:8:0.8:0.2:3 0/0:1:0:0,0:0,1:1,0:0:0,0:43:0:30:0:1:0:60:2:1:0:1 +7 6426892 . C T 169 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GTTACACAACCAATGCATTT;RSEQ=CTGGAGAATATATCCCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1063:49:19,30:460,553:1013,49:0.0461:2,2:25.2:1:30.1:1:0.38183:1.31308:48.3:23.5:0.0451:0:1.1 0/0:724:0:0,0:355,368:723,0:0:2,0:24:0:15:0:1:0:39:0:0:0:1 +7 6426908 . C G 190 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTTCCTGGAGAATATATCC;RSEQ=TACTGTGTAAGTATCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:962:73:30,43:366,523:889,73:0.0759:2,2:26.3:1:30.8:1:1:1.00306:46.8:72:0.076:0:2 0/0:683:0:0,0:305,377:682,0:0:2,0:25.8:1:30.8:1:1:0:46.7:84.25:1:0:0.5 +7 6426941 . C T 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43036;LSEQ=ATCTTAAATTGGGAATTAAC;RSEQ=TGTTTGTGTTACGGGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:641:465:126,339:53,123:176,465:0.7254:2,2:23.9:1:30.6:1:0.48998:1.15903:55:76.5:0.7263:0:1.8 1/0:502:267:100,167:88,147:235,267:0.5319:2,2:23.6:1:29.2:1:1:1.00:53.8:43.5:0.5273:0:1.3 +7 6426954 . G A 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14287;LSEQ=AATTAACCTGTTTGTGTTAC;RSEQ=GGTTTCACATTTCTTTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:522:306:75,231:54,161:215,306:0.5862:2,2:24.7:1:31.7:1:0.91799:1.033:58.7:305:0.5899:0:2.1 0/1:375:63:19,44:107,204:311,63:0.168:2,2:26.2:1:30.1:1:0.56125:1.21402:58.8:126:0.1698:0:1.9 +7 6429994 . A G 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAATTCCAGCACTTTGGG;RSEQ=AGCTGAGGTGGGCGCATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6431256 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTACCCTTATTTCTTCTGG;RSEQ=GATAAAAGTCTTAAACTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:12.5:1:31:1:1:0:60:4:0.2857:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:34:0:32:0:1:0:60:2:1:0:0 +7 6431404 . G T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00018;SOR=0.24101;LSEQ=CCGCAAGTTTTGCCCGTGCC;RSEQ=CCTTCCTCCTTGTGCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:83:63:62,1:20,0:20,63:0.759:1,1:22.7:1:32:1:1:0:60:62:0.7561:0:1.3 0/1:49:21:20,1:28,0:28,21:0.4286:1,1:20.7:1:30.8:1:0.42857:0:60:42:0.4468:0:1.1 +7 6431420 . C A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37096;SOR=2.48553;LSEQ=TGCCGCCTTCCTCCTTGTGC;RSEQ=TGCAGGGACATTTGCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:2,0:99,1:100,2:0.0196:1,0:20.5:1:19:1:1:0:60:1:0.0102:0:2 0/1:63:3:3,0:59,1:60,3:0.0476:1,0:23.7:1:26.7:1:1:0:60:2:0.0328:0:1.3 +7 6431457 . C G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=0.17114;LSEQ=GGTGTGGCAGCCTCCAGGCC;RSEQ=GTCCCCAGCCTTTTTCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:35:33,2:160,10:170,35:0.1707:2,2:19.9:1:29.9:1:1:1.03:60:70:0.1716:0:1.4 0/1:118:4:4,0:104,10:114,4:0.0339:2,0:27.3:1:31.5:1:1:0:60:8:0.0342:0:1.5 +7 6431477 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12013;SOR=Inf;LSEQ=CGTCCCCAGCCTTTTTCTTG;RSEQ=CACACCTTCTCTAGGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:277,35:312,0:0:2,0:23:1:31.4:1:1:0:60:30.2:1:0:0.3 0/1:166:2:1,1:134,29:163,2:0.012:2,2:24.5:1:27:1:0.33149:4.55997:60:4:0.0125:0:1 +7 6431523 . C CT 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=CAGTGACTTAGCTTCTACAC;RSEQ=TGTGACTAACCATTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:23:15,8:455,199:654,23:0.034:2,2:25.1:1:30.5:1:0.6498:1.21903:55.9:22:0.0329:0.0103:0.2 0/0:452:0:0,0:289,163:452,0:0:2,0:23.7:1:30.3:1:1:0:58.3:36.667:1:0:0.2 +7 6431690 . C T 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.24693;LSEQ=ACAGTAAGGATTGCAGCTGA;RSEQ=TTTTAATGTGTCTTTTAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:823:605:198,407:68,148:216,605:0.7351:2,2:24.1:1:30.4:1:0.79952:1.06:49.3:66.222:0.7331:0:1.1 0/1:566:230:87,143:124,212:336,230:0.4064:2,2:24.5:1:29.4:1:0.85965:1.04:48.9:75.667:0.4054:0:1.1 +7 6431759 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13689;SOR=Inf;LSEQ=CATGTTACCTATGGACTTGC;RSEQ=TATATTGCCATCATTTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:6,206:212,0:0:1,0:25.5:1:30.5:1:1:0:60:105:1:0:0.5 0/1:125:2:1,1:9,114:123,2:0.016:2,2:13.5:1:28.5:1:0.15419:12.07:60:4:0.0161:0:1 +7 6431933 . C G 93 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.59764;LSEQ=AGAATAACCGTATGAAAGAG;RSEQ=TACTTTTTGTTTTTGCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:0,7:0,4:4,7:0.6364:0,0:17.4:1:33.4:1:1:0:60:14:0.6364:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:38:0:32:0:1:0:60:2:0.5:0:1 +7 6432217 . C G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCAGAAAAAAAAGTTTA;RSEQ=TTTTGCTTCTGTATCAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:15:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6433607 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAAGAACTGGATCTGGTA;RSEQ=TAACATGCTGGCACCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:28.5:1:1:0:60:4:1:0:1 +7 6437843 . T TTGTC 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATGTTCTGGGAGAGCCCT;RSEQ=TGGCAGGCATCATTTACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:16:1:30.9:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6438217 . A G 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAAAATTCTAATAAAGA;RSEQ=TCGATAAGAGGTTATATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:482:0:0,0:407,75:482,0:0:2,0:23.5:1:30.2:1:1:0:60:47.2:1:0:0.1 0/1:284:26:19,7:207,51:258,26:0.0915:2,2:17.5:1:30.2:1:0.44281:1.49303:60:52:0.0925:0:1.1 +7 6438388 . C T 129 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00013;SOR=0;LSEQ=CCACTTCAGTTTCAAGCTTT;RSEQ=TCTGTTCTCTCATTTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:886:18:6,12:278,588:866,18:0.0203:2,2:26.9:1:31.1:1:1:1.06:60:36:0.0206:0:1 0/0:581:0:0,0:212,368:580,0:0:2,0:25.3:1:30.9:1:1:0:60:115:0.9983:0:0.1 +7 6439448 . A T 119 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTTATACTTGATTTTTTC;RSEQ=TTTTAGATAGTTAGGCGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:13:13,0:5,0:5,13:0.7222:0,1:20:1:32.2:1:1:0:60:26:0.7222:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:46:0:32:0:1:0:60:2:1:0:1 +7 6439945 . A G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05822;SOR=0.52183;LSEQ=TTTTAGCAATTTGCTACTTA;RSEQ=GTACATGATTGGGTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:96:0,96:0,41:41,96:0.7007:1,1:23.7:1:30:1:1:0:59.8:8.6:0.6935:0:1.3 1/0:51:28:0,28:0,23:23,28:0.549:1,1:21.7:1:30.4:1:1:0:60:27:0.5625:0:1 +7 6439958 . G GT 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.08309;LSEQ=CTACTTAAGTACATGATTGG;RSEQ=TTTTTTTTTTTCTTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:14:0,14:0,85:85,14:0.1373:1,1:18.4:1:30:1:1:0:57.2:28:0.1429:0.049:0.9 0/1:34:5:0,5:0,29:29,5:0.1471:1,0:24.2:1:27.7:1:1:0:60:10:0.1563:0.0588:1 +7 6439994 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0479;SOR=Inf;LSEQ=TGAGACGGAGGTCTCACTCT;RSEQ=TTGTGTCCAGGCTGGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:0,41:41,0:0:1,0:25.5:1:32.4:1:1:0:58.8:40:1:0:0.7 0/1:12:2:0,2:0,10:10,2:0.1667:0,0:11:1:30.5:1:1:0:60:4:0.1818:0:3 +7 6441229 . T TC 114 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTTTGTTTCTCTTCCCT;RSEQ=CCCCCCTTCCCCTGCGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:12,0:7,0:7,12:0.6316:0,0:31:1:32:1:1:0:60:24:0.6316:0:0.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6441688 . T C 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTGTGTTTTTCCTCCTCCT;RSEQ=GTACCTCTTTTATTGTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:0:0,0:110,374:484,0:0:2,0:23.3:1:30.8:1:1:0:56.3:79.667:1:0:0.1 0/1:325:21:7,14:83,220:303,21:0.0646:2,2:25.4:1:29:1:0.61535:1.32:55:20:0.0623:0:1.2 +7 6441799 . G C 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00123;SOR=0.3317;LSEQ=GAACCAGCTGGCAAGGCCCT;RSEQ=TGGGTCTTAACGTCAGCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:120:85:45,40:19,16:35,85:0.7083:2,2:24.8:1:33.3:1:1:1.05511:59.8:170:0.7143:0:1.1 0/1:54:24:13,11:13,17:30,24:0.4444:2,2:16.4:1:31.6:1:0.5843:1.53:60:48:0.4444:0:1.1 +7 6441887 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02397;SOR=Inf;LSEQ=AGGAGCTGCCTCCCGCTGGT;RSEQ=GTGTGATCAGAAGAGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:265,98:363,0:0:2,0:22:1:31.9:1:1:0:59.8:89.75:1:0:0.2 0/1:237:4:1,3:171,62:233,4:0.0169:2,2:11.3:1:27.8:1:0.06391:8.18757:60:8:0.0172:0:1 +7 6441993 . C G 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00044;SOR=0;LSEQ=GCGCTCACACAGCGAGGCCT;RSEQ=AAGACAGTGTTTGACGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:13:7,6:279,212:491,13:0.0257:2,2:26.6:1:30.7:1:1:1.12776:45.6:12:0.0243:0:1.2 0/0:410:0:0,0:225,183:408,0:0:2,0:21.7:1:30.5:1:1:0:55.8:39.8:0.9975:0:0.2 +7 6442014 . G A 34 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25815;SOR=0;LSEQ=AAGACAGTGTTTGACGAAGC;RSEQ=ATCCGAGCAGTCCTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:3:3,0:131,125:256,3:0.0116:2,0:7.3:1:22:1:0.248:0:50.7:2:0.0078:0:1.3 0/0:206:0:0,0:105,101:206,0:0:2,0:11.5:1:29:1:1:0:52:102:1:0:0.3 +7 6442143 . C A 112 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.45016;SOR=0.62041;LSEQ=ACGCTTTGCTCAAAAAAAAA;RSEQ=AAAAAAAAAAAACAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:21:0,21:2,17:19,21:0.4773:2,1:14.2:1:25.7:1:0.21923:0:28:6:0.6429:0:2.3 0/1:25:9:0,9:2,14:16,9:0.36:2,0:25.3:1:18.1:1:0.52:0:35:0.8:0.3333:0:2.7 +7 6442156 . C A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.02585;SOR=0.28221;LSEQ=AAAAAAACAAAAAAAAAAAA;RSEQ=AAAAAAAAAAAACAACGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:21:0,21:2,24:26,21:0.4286:2,1:22.8:1:28.5:1:0.49491:0:25.5:20:0.4651:0:2.1 0/1:29:5:1,4:1,18:19,5:0.1724:1,2:17.6:1:29.2:1:0.38043:4.14:30.2:10:0.1923:0:1.4 +7 6442371 . G A 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAAGCGCCCCCCCCATTCTT;RSEQ=TTCAGATTAAGAGTTGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:1,3:0,1:1,4:0.8:0,2:18.3:1:28:1:1:0:60:8:0.8:0:1.3 0/0:1:0:0,0:0,1:1,0:0:0,0:17:0:33:0:1:0:60:2:1:0:0 +7 6661256 . C G 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58252;SOR=2.52477;LSEQ=AGCAACAGCAGGAACAGTTA;RSEQ=AGCAGCAGCAGCTGCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:1:0,1:17,10:27,1:0.0357:2,0:16:0:34:0:0.39286:0:60:2:0.0357:0:1 0/1:23:2:1,1:11,10:21,2:0.087:2,2:38:1:30:1:1:1.09544:60:4:0.087:0:1 +7 6661979 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGGTGCTGCCCGCCGTG;RSEQ=CAGCGCCGGCCGTGGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6774643 . C CA 32 v3;MSI12;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAAGAGCGAGACTCCGTCT;RSEQ=AAAAAAAAAAAAAAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,0:3,2:0.3333:0,0:27:1:32:1:1:0:40:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 6774808 . CA C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.02789;SOR=Inf;LSEQ=GACAAGGCGAGACCTTGTCT;RSEQ=AAAAAAAAACCAAAAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:60,1:61,0:0:1,0:18.8:1:30.7:1:1:0:46.7:29.5:0.9833:0:0.3 0/1:28:3:2,1:24,1:25,3:0.1071:1,2:18:1:32.3:1:0.20635:10.00004:41.7:6:0.1071:0:0 +7 6774871 . GT G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1426;SOR=Inf;LSEQ=GTTGGTTAGAATAGTATGTT;RSEQ=TAGAATGCAGGGGGTCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:241,40:281,0:0:2,0:26.3:1:30:1:1:0:51.8:69.25:1:0:0.1 0/1:171:2:1,1:143,26:169,2:0.0117:2,2:9:1:28.8:1:0.29164:5.41612:60:4:0.0119:0.0058:0.5 +7 6775132 . G GT 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.6059;SOR=1.31348;LSEQ=AACAATTTATGGTCATGTAA;RSEQ=TTTTTTTTTTTCTTTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:12:0,12:2,103:105,12:0.1017:1,0:33.6:1:29.2:1:1:0:46.7:11:0.0991:0.0085:0.4 0/1:54:7:0,7:1,43:44,7:0.1296:1,0:38.4:1:29.4:1:1:0:38.1:14:0.1346:0:1.3 +7 6775144 . C T 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=7e-05;SOR=Inf;LSEQ=TCATGTAAGTTTTTTTTTTT;RSEQ=TTTTTGAGACGGGGTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:2,120:122,0:0:1,0:25.2:1:34.1:1:1:0:44.8:121:1:0:0.2 0/1:56:8:0,8:1,47:48,8:0.1429:1,0:34.5:1:30.5:1:1:0:44.8:16:0.1481:0:2.1 +7 6776906 . A G 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02059;SOR=Inf;LSEQ=CCAAGAAGGAGCCCTCTAGG;RSEQ=CAGAAAAGGGGTATGTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:601:0:0,0:290,310:600,0:0:2,0:29.9:1:29.8:1:1:0:24.7:45.154:0.9983:0:0.1 0/1:368:4:1,3:181,183:364,4:0.0109:2,2:31:1:26.3:1:0.62304:2.95942:21.8:3:0.0083:0:1 +7 6776956 . A G 203 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=229.25224;LSEQ=TTCAGATGCCATCTCTGACA;RSEQ=AGGCGTCCTGAGACCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:596:1:1,0:280,315:595,1:0.0017:2,0:10:0:29:0:0.47148:0:21:2:0.0017:0:1 0/1:362:101:48,53:126,135:261,101:0.279:2,2:27.6:1:30.6:1:0.90723:1.03048:23.8:49.5:0.2773:0:1.1 +7 6777218 . T C 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTTCAGATGTGGACTGCCA;RSEQ=TCAAACCAGGAAGATACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:645:0:0,0:264,380:644,0:0:2,0:29.3:1:30.5:1:1:0:33.1:127.8:1:0:0.1 0/1:424:22:7,15:173,229:402,22:0.0519:2,2:34.5:1:30.4:1:0.37802:1.61708:29.1:21:0.0506:0:1 +7 6777369 . T C 224 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=149.17688;LSEQ=AATACTCAGAACGTGTCAGC;RSEQ=TCTCAGGTTGATGTAGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1079:2:1,1:646,431:1077,2:0.0019:2,2:25.5:1:23.5:1:1:1.49822:38:1:9e-04:0:2.5 0/1:727:158:91,67:328,239:567,158:0.2173:2,2:28.1:1:30.8:1:1:1.01042:29.7:157:0.2175:0:1.1 +7 6777418 . A G 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAAGAAAGTTGTGCCCCTG;RSEQ=ACTTTTCTGAGTTCTTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:764:0:0,0:401,363:764,0:0:2,0:27.1:1:30.6:1:1:0:47:83.889:1:0:0.1 0/1:510:26:17,9:252,232:484,26:0.051:2,2:22.3:1:29.9:1:0.22775:1.74:24.7:25:0.0499:0:1 +7 6786286 . A AT 32 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTTTCAGATGTTCACT;RSEQ=TTTTTTTTTTTTTTCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:21.5:1:32.5:1:1:0:42.5:4:0.6667:0:0 0/0:1:0:0,0:0,1:1,0:0:0,0:47:0:27:0:1:0:60:2:1:0:0 +7 6786731 . C T 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AAAAGCTGGACCTTCGGACC;RSEQ=CAGGACGTCGATGAACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:16.3:1:33:0:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:17:0:31:1:1:0:44:4:1:0:1 +7 9291444 . A G 54 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTCCCCACAAAATCCCC;RSEQ=TCCAAGGATCAGCAGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:30.3:1:34.3:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:40:0:33:0:1:0:44:2:1:0:1 +7 10556727 . T C 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77151;LSEQ=TAAAAGAATGTCTATGAGTT;RSEQ=AGAGCACAGCAGTACTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:2,0:15,8:23,2:0.08:2,0:14.5:1:30.5:1:1:0:51:4:0.087:0:2 0/1:16:1:1,0:9,6:15,1:0.0625:2,0:13:0:32:0:1:0:60:2:0.0625:0:1 +7 10556795 . A T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06264;SOR=0.22838;LSEQ=CAAAACACACCCTCTCCACC;RSEQ=AAGGACAAAGTGCTTCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:25:13,12:1,2:3,25:0.8929:2,2:26.9:1:29.3:1:1:2.11:42.6:11.5:0.8846:0:2.1 1/0:17:11:5,6:4,2:6,11:0.6471:2,2:25.4:1:28.5:1:0.61991:2.27808:42.8:22:0.6471:0:2.1 +7 10556797 . A C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04495;SOR=0.16716;LSEQ=AAACACACCCTCTCCACCAA;RSEQ=GGACAAAGTGCTTCATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:23:11,12:0,2:2,23:0.92:0,2:28.4:1:31:1:0.48667:0:39.6:46:0.92:0:2.2 1/0:17:11:5,6:4,2:6,11:0.6471:2,2:23.7:1:29.8:1:0.61991:2.27808:42.8:22:0.7333:0:2.1 +7 10557265 . T C 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1321;LSEQ=GAGTCCCTCTTCTCTCCAAA;RSEQ=GATCGCAACATCTCTCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:1,6:1,3:4,7:0.6364:2,2:20.4:1:29.7:1:1:1.87089:60:14:0.6364:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:21.5:1:29:1:1:0:60:4:0.6667:0:1 +7 10557347 . GA G 53 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=AGAGCTTAGATATAATCCGT;RSEQ=AATGCGAAGCAATTGAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:13.7:1:34:0:1:0:60:6:1:0:0.7 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:32:0:1:0:60:2:1:0:1 +7 10563778 . G A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGAGGCCAGGAAGGAGAGG;RSEQ=AGGAGGAGACCTGATGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:31:1:1:0:60:4:1:0:1 +7 10567455 . C T 45 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49255;SOR=2.02157;LSEQ=TGGGACTCACAACTGCCTAA;RSEQ=AGGCTAAGCTCCCTGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:1,2:19,12:31,3:0.0882:2,2:38.3:1:29:1:0.55548:3.05869:56:6:0.0882:0:1 0/1:6:1:1,0:3,2:5,1:0.1667:2,0:45:0:29:0:1:0:60:2:0.1667:0:1 +7 10567691 . G T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31025;SOR=0.29158;LSEQ=TCTACAGGGAAGAGGCTAAC;RSEQ=ACAGCCAGAGGCTCAGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:25:8,17:1,2:3,25:0.8929:2,2:23.2:1:28.4:1:1:1.06018:58.6:24:0.8889:0:1.8 1/0:10:7:3,4:2,1:3,7:0.7:2,2:31.4:1:27.4:1:1:2.41422:60:14:0.7:0:2 +7 10567706 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30923;SOR=0.29892;LSEQ=CTAACGACAGCCAGAGGCTC;RSEQ=GGGACAGAATTCAGATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:21:7,14:1,2:3,21:0.875:2,2:22.9:1:30.1:1:1:1:60:42:0.875:0:1.9 1/0:9:6:2,4:2,1:3,6:0.6667:2,2:27:1:30.2:1:0.52381:3.38757:60:12:0.6667:0:2.2 +7 10568077 . G A 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATCTCCAGGCATGGGAGC;RSEQ=AATCAGATGAATAGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:1,0:1,5:0.8333:0,2:10:1:30.6:1:1:0:24:10:0.8333:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:6:0:25:0:1:0:24:2:1:0:1 +7 10711288 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=AATATTCAGGTCCCTCTTCT;RSEQ=TTGGGCTGCTGCAGTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:15.2:1:32.2:1:1:0:53.4:20:1:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:13:0:31.5:1:1:1:28:4:0.3333:0:1.5 +7 10711493 . C CA 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.72467;SOR=1.63137;LSEQ=GACAACCCCTGTTGGAGGGT;RSEQ=CGTCCAGTTGAGTGGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:7,4:5,2:7,11:0.6111:2,2:25.4:1:31:1:1:1.40086:56.6:22:0.6111:0.1667:0.3 1/0:18:13:9,4:4,1:5,13:0.7222:2,2:24.7:1:28.7:1:1:1.7252:57.8:26:0.7222:0.1111:0.3 +7 10711573 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19481;SOR=Inf;LSEQ=GGATTGGGGTGTGTGTTTTG;RSEQ=TAGGGGGAACCCACTTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:15,16:31,0:0:2,0:26.8:1:31.8:1:1:0:56.9:14.5:1:0:0.2 0/1:25:2:1,1:11,12:23,2:0.08:2,2:25:1:27:1:1:1.09:58.5:4:0.08:0:1 +7 10711893 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.48;SOR=Inf;LSEQ=TGGCCCCAGCAGGGGAAAAG;RSEQ=ACAGCCTGGAGCTATGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:12,0:0:2,0:26.2:1:32.6:1:1:0:54.7:24:1:0:0.1 0/1:13:2:1,1:6,5:11,2:0.1538:2,2:30.5:1:28:1:1:1.18321:60:4:0.1667:0:1 +7 11297357 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02597;SOR=Inf;LSEQ=CTTGAACAGCTTCCTGGTCG;RSEQ=TCATCCAGAAGCAGTCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:15,3:18,0:0:2,0:21.6:1:30.6:1:1:0:60:17:1:0:0.5 1/0:4:2:1,1:1,1:2,2:0.5:2,2:32.5:1:26.5:1:1:1:60:4:0.5:0:1 +7 11297388 . T C 93 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05728;SOR=0.0964;LSEQ=GCAGTCCTTCACGTGATTGA;RSEQ=AAATTTGGCTTCCACTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:7,1:3,1:4,8:0.6667:2,2:24.9:1:31.1:1:1:2.16:60:16:0.6667:0:1.1 0/1:7:1:0,1:3,3:6,1:0.1429:2,0:48:0:34:0:1:0:60:2:0.1429:0:1 +7 11297492 . G GT 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.11098;SOR=Inf;LSEQ=AAGGTCCTTTTGGTGTTTTA;RSEQ=TTTTTTTTTTCCCTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:27,0:0:2,0:22.3:1:31:1:1:0:58.8:12.5:1:0:1.5 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:35.5:1:28.5:1:1:1.36624:60:4:0.1667:0:0.5 +7 11297507 . T G 72 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.000;MSILEN=1;SSF=0.27207;SOR=0;LSEQ=TTTTAGTTTTTTTTTTCCCT;RSEQ=TTTTTTTTTTTTGAGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:2,3:4,6:10,5:0.2941:2,2:14.4:1:31.4:1:1:1:60:10:0.3571:0:1 0/0:7:0:0,0:2,3:5,0:0:2,0:25.8:1:27.8:1:1:0:60:10:1:0:1 +7 11297736 . C G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01527;SOR=0.30112;LSEQ=TTTCCTTTTTTTCTGTGGAA;RSEQ=CTCACTACCATTTCTAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:32:25,7:27,7:34,32:0.4848:2,2:23.3:1:31.8:1:1:1.07873:60:15:0.4688:0:1 0/1:32:7:4,3:19,6:25,7:0.2188:2,2:17:1:30.7:1:0.37018:2.30456:60:14:0.2258:0:1.3 +7 11297820 . C T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16342;SOR=5.87853;LSEQ=CTCTTCATCTTCTCACTCTG;RSEQ=CTCTTCCTCCACAGCTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:0,1:131,85:216,1:0.0046:2,0:1:0:25:0:0.39631:0:60:2:0.0046:0:1 0/1:151:4:1,3:85,62:147,4:0.0265:2,2:10:1:29:1:0.31507:4.07626:40:8:0.0268:0:1.3 +7 11297830 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCTCACTCTGCCTCTTCCTC;RSEQ=ACAGCTACTAAGTGCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:146,107:253,0:0:2,0:26.3:1:31.3:1:1:0:58:62.25:1:0:0.2 0/1:175:25:13,12:84,66:150,25:0.1429:2,2:18.8:1:28.6:1:0.82855:1.17373:47:50:0.1445:0:1.2 +7 11297892 . C T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01966;SOR=Inf;LSEQ=ACCACGCTTCAACCATAAGA;RSEQ=CACGGGTGGTGGTATTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:86,142:228,0:0:2,0:22.9:1:30.8:1:1:0:59.7:31.571:1:0:0.2 0/1:138:4:1,3:55,79:134,4:0.029:2,2:31:1:23.8:1:0.64639:2.07853:60:3:0.0222:0:1 +7 11297904 . G A 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.12728;SOR=Inf;LSEQ=CCATAAGACCACGGGTGGTG;RSEQ=TATTTCAAAGCCCCTAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:61,122:183,0:0:2,0:23.1:1:31.8:1:1:0:60:90.5:1:0:0.1 0/1:102:2:1,1:33,67:100,2:0.0196:2,2:5:0:30:0:1:2.02:47.5:4:0.0196:0:2 +7 11297930 . A G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01623;SOR=Inf;LSEQ=CAAAGCCCCTAAGGGAAACC;RSEQ=CTGGCTGTATAGACATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:23,95:118,0:0:2,0:26.3:1:29.7:1:1:0:60:38.333:1:0:0.1 0/1:67:4:0,4:17,46:63,4:0.0597:2,0:8.5:1:31.8:1:0.56529:0:60:8:0.0597:0:1 +7 11298043 . G C 86 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00464;SOR=10.60442;LSEQ=CCTATGTATCAGCCCCTAAA;RSEQ=TGACTATTCTTAAAGATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:4,22:26,2:0.0714:2,2:28:1:34.5:1:0.33069:5.03:60:4:0.0714:0:1 0/1:15:7:3,4:3,5:8,7:0.4667:2,2:20.9:1:30.9:1:1:1.23:60:14:0.4667:0:1.1 +7 11691113 . A ACTAT 129 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=39;MSI=10.000;MSILEN=4;SSF=0.27673;SOR=0.47451;LSEQ=TATTATCTATCTATCTATCA;RSEQ=CTATCTATCTATCTATCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:17:17,0:42,0:42,17:0.2881:1,1:22.6:1:31.8:1:1:0:48:34:0.2881:0.0847:0.4 0/1:25:4:4,0:18,0:18,4:0.16:1,0:36.5:1:32.1:1:1:0:47.3:8:0.16:0:0 +7 11691169 . T C 73 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00554;SOR=14.79053;LSEQ=TCTAGCACTACAATGAACTA;RSEQ=AGCCCACCCTTTTTTAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:1:1,0:143,19:162,1:0.0061:2,0:46:0:34:0:1:0:24:2:0.0062:0:2 0/1:59:5:5,0:47,7:54,5:0.0847:2,0:28.6:1:31.6:1:1:0:47.6:10:0.0847:0:1 +7 11691177 . C A 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACAATGAACTATAGCCCAC;RSEQ=CTTTTTTAGTCATGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:152,26:178,0:0:2,0:21.5:1:31.7:1:1:0:59:177:1:0:0.1 0/1:73:16:14,2:48,9:57,16:0.2192:2,2:18.4:1:28.9:1:1:1.31:58.8:32:0.2192:0:1 +7 11691247 . G T 56 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05087;SOR=7.65287;LSEQ=ATATAGCAACATTACCTCAA;RSEQ=GTTCTAAGGAGTTAATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:693:1:1,0:425,267:692,1:0.0014:2,0:38:0:14:0:1:0:60:0:0:0:7 0/1:365:4:1,3:210,150:360,4:0.011:2,2:7.3:1:28.3:1:0.31371:4.18417:60:8:0.0111:0:1.3 +7 11691296 . C T 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=2.34804;LSEQ=GCCTTGGGGAACTTTTAAAC;RSEQ=CCTTAGACCTAAAGGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:896:305:159,146:288,303:591,305:0.3404:2,2:25.6:1:30.7:1:0.35951:1.15:60:42.571:0.3394:0:1.1 1/0:458:251:129,122:98,109:207,251:0.548:2,2:24.8:1:28.6:1:0.39948:1.18:60:24.1:0.544:0:1.2 +7 12252540 . C G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41825;SOR=1.74633;LSEQ=TAATCTATTTTTAGGAACCG;RSEQ=TAAAAGACATATCAAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:16:16,0:31,0:31,16:0.3404:1,1:21.7:1:31.9:1:1:0:60:32:0.3404:0:1.1 0/1:21:10:9,1:10,1:11,10:0.4762:2,2:29.6:1:31:1:1:1.10554:60:20:0.4762:0:1 +7 12252659 . G A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.94207;LSEQ=GCAGGGTGTATTATATGACT;RSEQ=TTAAGTTCTTTTCAGCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:103:75,28:247,124:371,103:0.2168:2,2:26:1:28.6:1:0.28278:1.34:59.7:33.333:0.2128:0:1.3 1/0:268:140:90,50:85,43:128,140:0.5224:2,2:25.1:1:28.2:1:0.79739:1.09781:60:139:0.5206:0:1.4 +7 12252741 . T G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.63395;LSEQ=CTGCAGAAGTTATTTTTGTG;RSEQ=AGGCACTAGTACTAATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:150:58,92:217,282:499,150:0.2311:2,2:28.3:1:31.5:1:0.30186:1.22022:60:49:0.2297:0:1.2 1/0:402:210:95,115:83,109:192,210:0.5224:2,2:26.5:1:30.3:1:0.68912:1.08:59.9:51.5:0.5176:0:1.6 +7 12252744 . G A 163 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=93.40423;LSEQ=CAGAAGTTATTTTTGTGTAG;RSEQ=CACTAGTACTAATTATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:648:1:0,1:272,374:646,1:0.0015:2,0:7:0:25:0:1:0:60:2:0.0016:0:1 0/1:395:50:24,26:147,197:344,50:0.1266:2,2:28.7:1:29:1:0.54214:1.24:60:100:0.1292:0:2.3 +7 12252893 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02132;SOR=3.31125;LSEQ=TATTTTGGAACATTGGCTTC;RSEQ=TAATTTTAACTGTCAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:17:0,17:0,44:44,17:0.2787:1,1:25.3:1:32.6:1:1:0:60:34:0.2787:0:1.3 1/0:23:13:0,13:0,10:10,13:0.5652:0,1:20.2:1:31.8:1:1:0:60:26:0.5652:0:1.2 +7 12252902 . A ACT 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.04552;SOR=3.1961;LSEQ=ACATTGGCTTCATAATTTTA;RSEQ=CTGTCAACTGTTGAATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:14:0,14:0,41:41,14:0.2545:1,1:25.6:1:31.8:1:1:0:60:28:0.2593:0.0182:1 1/0:19:10:0,10:0,9:9,10:0.5263:0,0:22.7:1:29.6:1:1:0:60:20:0.5263:0.1579:1.3 +7 12253050 . A C 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAAAGGTGCGTGAATTTTC;RSEQ=GAGGCTGAAACGTACTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:18.5:1:27:0:1:0:40:4:0.25:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:5:0:30:0:1:0:60:2:1:0:0 +7 12462917 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.02464;SOR=Inf;LSEQ=CAAAATATTAGCCATACCCA;RSEQ=TAATCCTTCTGTGGCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:92,3:95,0:0:1,0:24.4:1:30.4:1:1:0:60:94:1:0:0.2 0/1:40:3:3,0:37,0:37,3:0.075:1,0:24.3:1:31.3:1:1:0:60:6:0.0811:0:3 +7 12462931 . G GCC 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.01125;SOR=0;LSEQ=TACCCAATAATCCTTCTGTG;RSEQ=CCCCCCCCTTATTTCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:13:13,0:98,3:101,13:0.1121:1,1:22.7:1:32.3:1:1:0:59.2:26:0.115:0.0259:1.4 0/0:48:0:0,0:43,0:43,0:0:1,0:25.2:1:30.6:1:1:0:60:20.5:0.8913:0:0.3 +7 12462937 . C A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.00271;SOR=Inf;LSEQ=ATAATCCTTCTGTGGCCCCC;RSEQ=CCTTATTTCATTTGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:119,3:122,0:0:1,0:28.3:1:31.6:1:1:0:59.9:121:1:0:0.2 0/1:56:5:5,0:49,2:51,5:0.0893:1,0:28:1:26.8:1:1:0:60:4:0.0727:0:2.2 +7 12463056 . G A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.85936;SOR=1.03931;LSEQ=CATTTACCCTCAAACTCTTC;RSEQ=TTGAATCCTTACTCTACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:92:55,37:384,313:697,92:0.1165:2,2:25.5:1:30.6:1:0.43522:1.21:60:91:0.1162:0:1.5 0/1:498:60:33,27:231,206:437,60:0.1205:2,2:29:1:30:1:0.78409:1.09:60:59:0.1204:0:1.6 +7 12463109 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.98413;LSEQ=CTGTATGGCCACACTGCTTA;RSEQ=GAGGAAAGCACTCAGCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:823:107:48,59:309,406:715,107:0.13:2,2:28.3:1:30.4:1:0.75481:1.07:60:52.5:0.1298:0:1.5 0/1:515:220:102,118:135,160:295,220:0.4272:2,2:23.4:1:29.3:1:0.92887:1.02:60:54:0.4252:0:1.3 +7 12463189 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.9996;LSEQ=GTTACAGTGTCAGCATTCTC;RSEQ=TGAATTTTCAATGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:48:13,35:65,228:293,48:0.1399:2,2:24.9:1:30:1:0.46104:1.30:60:47:0.1378:0:1.4 0/1:193:27:6,21:53,113:166,27:0.1399:2,2:19:1:30:1:0.37322:1.63769:60:54:0.1414:0:1.6 +7 12463400 . C G 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACATAGATTGTGAAAGA;RSEQ=ATTTTTATATTGCTGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:0,3:0,7:7,3:0.3:0,0:13.7:1:33.3:1:1:0:60:6:0.3:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 13860395 . T C 28 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CCTTCCTTCCTTCCTTCCTT;RSEQ=CTTTCTTTCTTTTCTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:28.5:1:1:0:41:4:1:0:1 +7 13861917 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1777;SOR=Inf;LSEQ=GCAGAATCTGTTCCATGTCT;RSEQ=TCCCCTGGCTTCTGGTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:24,0:0:2,0:29.5:1:32.3:1:1:0:60:23:1:0:0.1 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:21.5:1:28.5:1:1:1.26772:60:4:0.1111:0:1 +7 13935307 . C T 136 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=7e-05;SOR=0;LSEQ=TTTAGATTACTCCCACCCAC;RSEQ=CTCAAATAAAGTGCACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:22:20,2:7,0:7,22:0.7586:0,2:22.9:1:30.7:1:1:0:58.5:10:0.7407:0:1.2 0/0:9:0:0,0:9,0:9,0:0:0,0:19:1:30.7:1:1:0:60:18:1:0:0.1 +7 13935468 . G T 52 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07462;SOR=0;LSEQ=AAAAGGAAAAGCGCAAAAAC;RSEQ=CCCTGCTTGACTGTCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:5:2,3:321,161:482,5:0.0102:2,2:17.4:1:22.6:1:0.34096:2.98336:60:1.5:0.0063:0:1.4 0/0:366:0:0,0:240,125:365,0:0:2,0:25.4:1:29.5:1:1:0:60:35.5:1:0:0.2 +7 13935763 . GA G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11888;SOR=Inf;LSEQ=CCTCACCATCGCCAGATGGG;RSEQ=AGGACAGGAAGGAAAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:52,234:286,0:0:2,0:20.4:1:30.8:1:1:0:59.9:56.2:1:0:0.1 0/1:151:2:1,1:33,116:149,2:0.0132:2,2:31.5:1:29.5:1:0.40079:3.48:60:4:0.0134:0:1 +7 13935772 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11747;SOR=Inf;LSEQ=CGCCAGATGGGGAAGGACAG;RSEQ=AAGGAAAAAGCCAAAAACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:34,199:233,0:0:2,0:20.7:1:32.1:1:1:0:60:232:1:0:0.1 0/1:122:2:1,1:18,100:118,2:0.0164:2,2:24.5:1:26:1:0.29272:5.43:60:4:0.0168:0:1 +7 13935783 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5408;SOR=0;LSEQ=GAAGGACAGGAAGGAAAAAG;RSEQ=CAAAAACGTGGTTTAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:0,2:12,161:173,2:0.0114:2,0:32:1:30.5:1:1:0:60:4:0.0117:0:1 0/0:96:0:0,0:9,87:96,0:0:2,0:21.4:1:30.3:1:1:0:60:18.2:1:0:0.1 +7 13935861 . T TA 71 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.05047;SOR=4.07036;LSEQ=CAACTAATAGCAGATACACA;RSEQ=AAAAAAAAAAAAGTCTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:5:0,5:0,41:41,5:0.098:1,0:35.6:1:32.2:1:1:0:52.6:10:0.1282:0:0 0/1:16:5:0,5:0,11:11,5:0.3125:0,0:27:1:31:1:1:0:60:10:0.4167:0:0 +7 13945864 . C T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.39974;LSEQ=TTTGTAGGATTGTATACAAC;RSEQ=GGAAGGAACACGCAATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:8:8,0:17,0:17,8:0.32:1,0:13.4:1:32.5:1:1:0:60:16:0.3333:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:32.5:1:32.5:1:1:0:60:4:0.5:0:1 +7 13946266 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09043;SOR=Inf;LSEQ=TTTCTATTATTAGCAATACT;RSEQ=TGCTATCTTACATAAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:22,221:243,0:0:2,0:22.9:1:31.3:1:1:0:60:120.5:1:0:0 0/1:105:2:1,1:13,90:103,2:0.019:2,2:18.5:1:29.5:1:0.25:6.71:60:4:0.019:0:1.5 +7 13946316 . C T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=CAATCACTAATATGGTTAAA;RSEQ=CACAATCAACCACTTTATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:0,90:90,0:0:1,0:24:1:31.4:1:1:0:60:44:1:0:0 0/1:30:6:0,6:0,24:24,6:0.2:1,0:28.3:1:27.2:1:1:0:60:5:0.1724:0:1.2 +7 13950777 . A T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.56341;SOR=3.14438;LSEQ=AATGATTTTTCCCAAATAAT;RSEQ=TAATGATTAATTAAATGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:0,1:246,55:301,1:0.0033:2,0:1:0:27:0:0.18543:0:60:2:0.0033:0:1 0/1:193:2:1,1:149,42:191,2:0.0104:2,2:38.5:1:29:1:0.39686:3.51767:60:4:0.0104:0:1 +7 13950838 . C T 170 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=86.55322;LSEQ=TATTCTGAACGGTATTTACA;RSEQ=GGAATTTCAGTGGTGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:819:1:0,1:484,333:817,1:0.0012:2,0:1:0:25:0:0.40831:0:60:2:0.0012:0:1 0/1:563:54:33,21:298,211:509,54:0.0959:2,2:25.2:1:29.6:1:0.7724:1.11:60:108:0.0969:0:1.2 +7 13970739 . C T 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTAAATGTTATAAGCAA;RSEQ=ATGTGACCTAGTTCAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:8.8:1:30:1:1:0:60:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 13971151 . G T 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05731;SOR=5.24334;LSEQ=GTCATATGCAAAATCTCTGG;RSEQ=TTCCTGTTTAATCATCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1036:2:0,2:649,384:1033,2:0.0019:2,0:23:1:19:1:0.13886:0:60:1:0.001:0:1 0/1:597:6:2,4:366,225:591,6:0.0101:2,2:21.7:1:27.3:1:0.21012:3.24673:60:12:0.0101:0:1.2 +7 13971669 . C CCA 48 MSI12;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=14.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTTTGAGGATTTTACACAC;RSEQ=CACACACACACACACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:29.7:1:30.7:1:1:0:54.3:6:0.3333:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 13975472 . TG T 72 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.20274;SOR=2.34386;LSEQ=CACTGGCGTGCTGGATGGTG;RSEQ=GGGGGGTTGGAGGGCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:753:4:1,3:295,453:748,4:0.0053:2,2:31:1:30.8:1:1:1.95206:60:8:0.0054:0.0013:0.3 0/1:485:6:1,5:204,273:477,6:0.0124:2,2:16.8:1:27.9:1:0.2479:3.72793:60:12:0.0126:0.0041:0.8 +7 13975575 . A T 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00036;SOR=Inf;LSEQ=TTTCTTTGGAGCAATTTTTT;RSEQ=AAAAAGTTTCTAATCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:27,164:191,0:0:2,0:23.7:1:30.2:1:1:0:60:30.833:1:0:0.1 0/1:94:7:2,5:15,72:87,7:0.0745:2,2:18.9:1:27:1:0.60623:1.90:60:14:0.0745:0:1.3 +7 13978645 . C T 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=16.08921;LSEQ=AGCTTGTTACATATTAAAGA;RSEQ=GTTACTCATAAAATATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:6:6,0:252,8:260,6:0.0226:1,0:28.7:1:31.2:1:1:0:60:12:0.0233:0:2.2 0/1:99:27:27,0:66,6:72,27:0.2727:2,1:22.6:1:30.4:1:0.18492:0:60:54:0.2784:0:2.3 +7 13978648 . T A 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=16.8342;LSEQ=TTGTTACATATTAAAGACGT;RSEQ=ACTCATAAAATATGACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:6:6,0:275,9:284,6:0.0207:1,0:29.7:1:28.8:1:1:0:60:12:0.0209:0:2.2 0/1:106:28:28,0:72,6:78,28:0.2642:2,1:23.2:1:28:1:0.33742:0:60:56:0.2667:0:2.3 +7 13978683 . C G 106 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.57703;LSEQ=ACTTGAGATTTCATATTATT;RSEQ=TGGACTTTTTGATTCAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:1:1,0:443,131:574,1:0.0017:2,0:9:0:16:0:1:0:60:0:0:0:6 0/1:244:12:10,2:176,55:231,12:0.0492:2,2:23.1:1:29.8:1:0.73716:1.56:60:11:0.0456:0:1.8 +7 13978734 . G A 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTACATACATACACCTGGT;RSEQ=GCTTTACCTGACATTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1185:0:0,0:708,475:1183,0:0:2,0:26.7:1:31.9:1:1:0:60:83.5:0.9983:0:0.1 0/1:622:33:19,14:345,243:588,33:0.0531:2,2:28.4:1:28.4:1:1:1.04602:60:66:0.0538:0:1.6 +7 13978809 . T C 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.22267;LSEQ=TTCTTGACTGCAGGCAGAGC;RSEQ=GATTTCTGAACATGGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1228:31:15,16:512,684:1196,31:0.0252:2,2:25.6:1:29.5:1:0.5837:1.25:60:14.5:0.024:0:1.2 0/1:698:168:70,98:239,291:530,168:0.2407:2,2:26.3:1:29.3:1:0.47606:1.1496:60:83:0.2416:0:1.2 +7 14016939 . T C 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGCTGTAAGTTAAAAAGG;RSEQ=GCTGGTACAATGTAAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:164,11:175,0:0:2,0:22.1:1:30.3:1:1:0:60:174:1:0:0.1 1/0:87:56:54,2:30,1:31,56:0.6437:1,1:23.4:1:32.3:1:1:1.1098:60:112:0.6437:0:2.2 +7 14017007 . CC TG 233 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAAAGAAGAAAGAAGGAAA;RSEQ=AGAAAGACAGAAAAATACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:552:0:0,0:349,202:551,0:0:2,0:25.6:1:31.6:1:1:0:60:54.1:0.9982:0:0.1 1/0:340:204:136,68:83,46:129,204:0.6:2,2:26:1:30.4:1:0.72235:1.11:59.8:408:0.6108:0.0382:1.2 +7 14017008 . C G 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00089;SOR=Inf;LSEQ=GAAAGAAGAAAGAAGGAAAC;RSEQ=AGAAAGACAGAAAAATACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:0:0,0:351,209:560,0:0:2,0:25.5:1:31.5:1:1:0:60:69:0.9982:0:0.1 0/1:328:7:3,4:83,47:130,7:0.0213:2,2:22:1:25.3:1:0.42377:2.33911:60:2.5:0.0373:0:2.1 +7 14017126 . T TA 190 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTGAAGAAGAAAAAGAAAAT;RSEQ=AAAAAAAATTAAGAGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:57,211:268,0:0:2,0:22.5:1:28.7:1:1:0:60:43.667:1:0:0.2 1/0:171:88:14,74:19,63:82,88:0.5146:2,2:27.3:1:29.5:1:0.25009:1.58969:60:28.333:0.506:0.0117:0.3 +7 14025411 . T G 32 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05455;SOR=Inf;LSEQ=TCCAAAAGAAAAATTTCAAA;RSEQ=TATGAATGCCAACAGAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:8,0:0:0,0:18.8:1:30.3:1:1:0:60:16:1:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:5:1:32:1:1:0:60:4:0.6667:0:2 +7 14025474 . A G 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=AGTTGTATAAAGCTTTATGA;RSEQ=GCAATCTCATTTTCCTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:23,0:23,0:0:1,0:24.4:1:30.6:1:1:0:58.8:22:1:0:0.4 1/0:7:5:4,1:2,0:2,5:0.7143:0,2:27.2:1:32:1:1:0:60:10:0.7143:0:1.4 +7 14025528 . C A 147 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00019;SOR=0.03931;LSEQ=AAAAGATATAACAGATTGCA;RSEQ=CACAAAATTTTAACAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:30:30,0:11,0:11,30:0.7317:0,1:28.5:1:30:1:1:0:60:29:0.725:0:1.1 0/1:11:1:1,0:9,1:10,1:0.0909:2,0:4:0:29:0:1:0:60:2:0.0909:0:1 +7 14025640 . G A 188 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATAGCAAAGGTCAATTTCA;RSEQ=CAAACATAACATGAATAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:226,23:249,0:0:2,0:24.5:1:33:1:1:0:60:82:1:0:0.1 1/0:122:83:73,10:39,0:39,83:0.6803:1,2:23.8:1:29.6:1:0.02955:0:59.5:82:0.6833:0:1.2 +7 14025727 . C T 246 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1657.00449;LSEQ=AAACCCATAGATTTCCTAAG;RSEQ=ATTAGATACACACCTAACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1148:1:0,1:654,493:1147,1:9e-04:2,0:1:0:23:0:0.43031:0:60:2:9e-04:0:1 1/0:696:418:241,177:157,119:276,418:0.6006:2,2:25.3:1:28.3:1:0.87547:1.03:60:138.333:0.605:0:1.9 +7 14025766 . T A 261 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTCTGTGTTGTGAACAAGG;RSEQ=GGAAAGAAGACACTTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1385:0:0,0:697,687:1384,0:0:2,0:25.3:1:29.8:1:1:0:60:105.462:1:0:0.1 1/0:841:500:247,253:172,168:340,500:0.5945:2,2:26.9:1:29.2:1:0.77862:1.04865:60:124:0.5976:0:1.7 +7 14026134 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21886;SOR=4.67043;LSEQ=ATCAGAGGCTCTAATGTATG;RSEQ=ATGACACATGAGGTGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:1:0,1:145,8:153,1:0.0065:2,0:1:0:24:0:0.05844:0:60:2:0.0066:0:1 0/1:67:2:2,0:62,3:65,2:0.0299:1,0:27:1:30:1:1:0:60:4:0.0299:0:1.5 +7 14026357 . A G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00221;SOR=1.8936;LSEQ=ATAAGATTTGCAAATCTTTA;RSEQ=TCTTCATTAAATGGAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:347:239:51,188:28,80:108,239:0.6888:2,2:23.3:1:32.2:1:0.4068:1.28918:59.8:46.8:0.6903:0:1.1 1/1:213:172:55,117:16,25:41,172:0.8075:2,2:22.1:1:30.9:1:0.46123:1.35937:60:56.333:0.8048:0:1.1 +7 14026421 . C T 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00585;SOR=0;LSEQ=ATAAATTTAATTTCAAGAGA;RSEQ=GCAGTCAACATAAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:15:0,15:0,99:99,15:0.1316:1,1:17.3:1:31:1:1:0:60:30:0.1351:0:1.9 0/0:49:0:0,0:1,48:49,0:0:1,0:19.9:1:29.1:1:1:0:60:98:1:0:0.6 +7 14026438 . TA T 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACGCAGTCAACATAAAAA;RSEQ=AAAAAAAGAGGCATAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:1,75:76,0:0:1,0:19.4:1:31.8:1:1:0:60:75:1:0:0.6 1/0:30:16:0,16:0,14:14,16:0.5333:1,1:25.8:1:30.1:1:1:0:60:32:0.5333:0:0.3 +7 14027477 . G A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=Inf;LSEQ=CAAAACAATGATTAAAAGAA;RSEQ=GTTGTCATTGAGAAGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:38,0:0:1,0:20.8:1:33.3:1:1:0:59.1:37:1:0:0.5 1/0:6:4:3,1:2,0:2,4:0.6667:0,2:17.5:1:31:1:1:0:60:8:0.6667:0:1.5 +7 14027557 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.71225;SOR=0.86517;LSEQ=AGTCTCCCATGCAAACTGCC;RSEQ=CATTATGTAAATCGTTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:152:116:115,1:35,0:35,116:0.7632:1,1:25.8:1:30.9:1:1:0:59.8:115:0.7667:0:1.1 1/0:53:39:39,0:14,0:14,39:0.7358:1,1:22.6:1:30.2:1:1:0:60:78:0.7358:0:1.3 +7 14027867 . G A 56 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=1;SOR=1.23074;LSEQ=ACACACACGCACACGCGCGC;RSEQ=CACACACACACACACAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:4:0,4:8,192:200,4:0.0194:1,0:34:1:28.3:1:1:0:60:8:0.0201:0:1 0/1:84:2:0,2:2,49:51,2:0.0238:1,0:21.5:1:31.5:1:1:0:60:4:0.0244:0:0.5 +7 14027991 . T C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00081;SOR=Inf;LSEQ=TTTGACAGTGAAAGCTTATG;RSEQ=TAAGCAGGCAGGGAGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:0,28:28,0:0:1,0:25.4:1:30:1:1:0:59:27:1:0:0.1 1/0:4:3:0,3:0,1:1,3:0.75:0,0:29.7:1:33:1:1:0:60:6:0.75:0:1 +7 14028220 . G GA 29 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAAAAAGAGTAGAGAAAT;RSEQ=AAAAAAAAAAAAAAGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:17:1:29.4:1:1:0:60:4:0.6667:0.3333:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 14028544 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGTATCTGCAATCCCAACC;RSEQ=CCGTGCCCCCTCCCTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:0:0,0:385,82:467,0:0:2,0:23.2:1:30.9:1:1:0:60:41.455:1:0:0.4 0/1:282:21:14,7:200,61:261,21:0.0745:2,2:25.5:1:28.4:1:0.29805:1.63617:60:20:0.0719:0:1.2 +7 14028575 . C T 201 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=0.01291;LSEQ=TCCCTTCTCATTTTCTCCCT;RSEQ=TCCCCACCCCCGACGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:804:100:65,35:475,228:703,100:0.1244:2,2:23.3:1:30.4:1:0.64901:1.12163:60:200:0.1292:0:1.1 0/0:547:1:0,1:342,204:546,1:0.0018:2,0:1:0:28:0:0.37477:0:60:2:0.0019:0:1 +7 14028707 . TA T 237 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCGCAAATCTCAGCTCAG;RSEQ=TTTTATATTTTGAGCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:658:0:0,0:189,469:658,0:0:2,0:24:1:30.3:1:1:0:60:72.111:1:0:0.1 1/0:429:258:87,171:60,111:171,258:0.6014:2,2:23:1:29.7:1:0.83547:1.06229:59.9:516:0.6028:0.1305:0.2 +7 14028794 . TA T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAAGATGGCTTTTAGGCT;RSEQ=AAAAAAAATCATGAATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:0,2:2,131:133,2:0.0148:1,0:17.5:1:33:0:1:0:60:4:0.0149:0:0 0/0:52:0:0,0:3,49:52,0:0:2,0:26.8:1:29.5:1:1:0:60:51:1:0:0.3 +7 14028860 . CA C 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CCCTCCGACAGTCCCATTCA;RSEQ=AAAATAACCCTCCCTACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:0,52:52,0:0:1,0:24.1:1:31.7:1:1:0:59.6:104:1:0:0.1 0/1:14:6:0,6:1,7:8,6:0.4286:2,0:21.2:1:31.8:1:1:0:60:12:0.4286:0:0 +7 14030093 . T G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGGGAGGAGGAGGGAG;RSEQ=GCTTGGGGTTGCTCGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 15146113 . A G 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03284;SOR=7.40131;LSEQ=TGTAAAATAGTAAGTGCTCA;RSEQ=AGATATTTCCTGTAATCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:2,1:12,8:20,3:0.1304:2,2:26.7:1:32.3:1:1:1.32:60:6:0.1304:0:1 1/0:11:6:5,1:4,1:5,6:0.5455:2,2:28:1:30.8:1:1:1.22:60:12:0.5455:0:1 +7 16584291 . A T 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85937;LSEQ=CACATACATATAATCTTCTG;RSEQ=CTTTGCTCGTTACTTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:28:28,0:18,0:18,28:0.6087:1,1:28.3:1:30.3:1:1:0:60:56:0.6087:0:1 1/0:14:8:8,0:6,0:6,8:0.5714:0,0:24.1:1:30.8:1:1:0:60:16:0.5714:0:1 +7 16584370 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10597;SOR=Inf;LSEQ=ATAATATTGGTGCCACAATG;RSEQ=TAATATCCTTCTATTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:138,35:173,0:0:2,0:23.9:1:29.8:1:1:0:59.8:85.5:1:0:0.1 0/1:84:2:1,1:62,20:82,2:0.0238:2,2:17.5:1:31:1:0.43976:3.04948:60:4:0.0244:0:1 +7 16584389 . G T 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.27387;LSEQ=GTTAATATCCTTCTATTTCT;RSEQ=GAAGTACGACAGTAGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:3:2,1:153,65:218,3:0.0136:2,2:8.3:1:32:1:1:1.17601:60:6:0.0138:0:2.3 0/1:116:2:1,1:73,41:114,2:0.0172:2,2:1:0:27:1:1:1.77108:60:4:0.0179:0:1.5 +7 16584413 . A G 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04354;SOR=Inf;LSEQ=GTACGACAGTAGCTTGGTAT;RSEQ=TTACATTTTGTCTCAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:184,120:304,0:0:2,0:25.2:1:29.3:1:1:0:59.9:151:1:0:0.5 0/1:166:3:2,1:98,65:163,3:0.0181:2,2:23:1:22.3:1:1:1.32:60:2:0.0121:0:1.3 +7 16584470 . A G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00023;SOR=0.52544;LSEQ=CTCACCAAGCAAGTATTCAA;RSEQ=ATGGAATCTGGGTTTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:393:256:110,146:65,72:137,256:0.6514:2,2:26.8:1:32.4:1:0.39687:1.19767:60:63:0.6478:0:1.2 0/1:206:102:46,56:48,56:104,102:0.4951:2,2:26.6:1:30.7:1:0.88969:1.04329:60:101:0.4975:0:1.2 +7 16584588 . GAAT G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=8e-05;SOR=Inf;LSEQ=TATAAACATCATTATCTAAA;RSEQ=AATTGAGATATTTATAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:7,69:76,0:0:2,0:22:1:30.5:1:1:0:60:24.333:1:0:0.2 0/1:30:7:1,6:1,22:23,7:0.2333:1,2:31.7:1:30.3:1:0.41839:3.47:60:14:0.2333:0.0333:0.1 +7 16584598 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATTATCTAAAGAATAATTGA;RSEQ=ATATTTATAATAACATCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:5,57:62,2:0.0313:2,2:13.5:1:28.5:1:0.18006:10.50:60:4:0.0317:0:1 0/0:22:0:0,0:2,20:22,0:0:2,0:27.6:1:30.7:1:1:0:60:44:1:0:0.1 +7 16603332 . G C 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTATAGAAGGAAAAAATAGA;RSEQ=TTAAAAATATGATTGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:34.5:1:30.5:1:1:0:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 16603629 . G T 43 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20952;SOR=3.25943;LSEQ=AGTTTTTAAATTTCCATATA;RSEQ=AAGTTACTTAACCAAGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:2:0,2:335,227:562,2:0.0035:2,0:1:0:24.5:1:0.16443:0:60:4:0.0036:0:1.5 0/1:349:4:0,4:191,153:344,4:0.0115:2,0:19.5:1:21.8:1:0.04056:0:60:3:0.0087:0:1.8 +7 16603660 . C G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=10.70973;LSEQ=ACCAAGGATTAGCAGAAAAA;RSEQ=CCAAGAAATGAAATGAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:84:42,42:274,288:562,84:0.1296:2,2:23.4:1:32.8:1:0.90694:1.05:60:168:0.1302:0:1.1 1/0:364:224:106,118:71,68:139,224:0.6154:2,2:25.2:1:31:1:0.51776:1.16183:60:55:0.6128:0:1.1 +7 16603759 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52084;SOR=0;LSEQ=ATTGAAAGATGTTGGTATAT;RSEQ=TTCCATTAACGTCATATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:24,163:187,2:0.0106:2,2:14.5:1:28:1:0.24766:6.68:60:4:0.0106:0:1.5 0/0:123:0:0,0:26,96:122,0:0:2,0:20.9:1:29.4:1:1:0:60:121:0.9918:0:0.1 +7 18170622 . A T 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTCTTTCTAGTTTCTTAT;RSEQ=ATCGAGTGTTTAGAAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:19.3:1:32.3:1:1:0:49.3:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 18170626 . G C 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCTAGTTTCTTATAATC;RSEQ=AGTGTTTAGAAATCTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:23:1:33:0:1:0:49.3:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 18170898 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13547;SOR=Inf;LSEQ=TGCTTTAAAAATAGAACATT;RSEQ=ATGATTCAGTGCCCAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:167,20:187,0:0:2,0:21.4:1:32.2:1:1:0:60:186:0.9947:0:0.7 0/1:110:2:1,1:95,13:108,2:0.0182:2,2:15.5:1:33:0:0.23937:7.07866:60:4:0.0187:0:1 +7 18170920 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14183;LSEQ=TGATTCAGTGCCCAATATTT;RSEQ=TTAGTATGAACTTAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:289:192:154,38:77,19:96,192:0.6644:2,2:22.1:1:28.7:1:1:1:60:47:0.6643:0:1.1 0/1:174:38:29,9:107,29:136,38:0.2184:2,2:28.3:1:27.9:1:0.82472:1.14414:60:76:0.2184:0:1.2 +7 18171029 . G T 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17755;LSEQ=AAATGTTATGGTTAAAGAAC;RSEQ=AGTTTAGTAGCACTAATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:876:541:267,274:165,169:334,541:0.6176:2,2:25.7:1:30:1:1:1.00193:59.9:179.333:0.6191:0:1.1 0/1:566:126:57,69:215,224:439,126:0.2226:2,2:27.9:1:28.6:1:0.48017:1.16158:60:252:0.2254:0:1.1 +7 18171348 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGAACAAGAGAGGAGGGTG;RSEQ=AGGTGAGGCGGTGAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:22.5:1:34:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 18182755 . T C 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19572;LSEQ=CTAGGGCAAAGATCTCCCCC;RSEQ=GCTTTTGTAAACTGGTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:939:621:280,341:152,163:315,621:0.6613:2,2:25.6:1:30.2:1:0.36776:1.13551:60:76.625:0.6634:0:1.4 0/1:561:155:76,79:202,204:406,155:0.2763:2,2:26.4:1:29.1:1:0.92485:1.02924:60:76.5:0.2772:0:1.9 +7 18182771 . T C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24403;SOR=1.17221;LSEQ=CCCCTGCTTTTGTAAACTGG;RSEQ=CTATCCTGTGCACCTACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:848:157:64,93:298,392:690,157:0.1851:2,2:25.6:1:31.5:1:0.59304:1.10452:60:51.333:0.184:0:2.2 0/1:561:118:48,70:214,229:443,118:0.2103:2,2:25.6:1:30.5:1:0.14726:1.36205:60:117:0.2108:0:2.2 +7 18182840 . G C 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14134;LSEQ=GGCATATTTGTATTTTGTAG;RSEQ=AATTGCTGATAGTAATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:290:197:42,155:18,75:93,197:0.6793:2,2:23.1:1:32.2:1:0.75773:1.13:60:48.25:0.6772:0:1.5 0/1:196:45:12,33:40,111:151,45:0.2296:2,2:25.6:1:31.7:1:1:1.01:60:44:0.2292:0:1.6 +7 18988498 . C G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01754;SOR=Inf;LSEQ=TGAAATAAGACAGAAATTTT;RSEQ=TAACAAGCTGTTTAAACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:14,2:16,0:0:2,0:20.9:1:32.6:1:1:0:60:32:1:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:20:1:33:1:1:0:60:4:0.6667:0:1 +7 18988707 . G GT 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTTAGCGTTTTGGGAGG;RSEQ=TTTTTTTTCTGTTTTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:7,9:16,2:0.1111:2,0:9.5:1:32:1:0.49673:0:58:4:0.1111:0.0556:0.5 0/0:7:0:0,0:4,3:7,0:0:2,0:28.7:1:30.9:1:1:0:60:14:1:0:0 +7 18988818 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.3971;SOR=1.72395;LSEQ=AATTTTGGCTGGAGTATCTT;RSEQ=TATAGATTTCTTCACTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:23:13,10:5,5:10,23:0.697:2,2:25.4:1:32.3:1:1:1.29:57.3:46:0.697:0:2 1/1:30:24:13,11:4,2:6,24:0.8:2,2:27.9:1:31.7:1:0.67247:1.66358:56.4:48:0.8:0:1.9 +7 18988836 . A G 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.57856;SOR=1.56038;LSEQ=TTATATAGATTTCTTCACTG;RSEQ=GCTTTTTCTTCATCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:23:12,11:5,6:11,23:0.6765:2,2:29.2:1:30.9:1:1:1.30:57.3:22:0.6667:0:2 1/0:30:23:12,11:4,3:7,23:0.7667:2,2:25.1:1:30.5:1:1:1.2141:56.3:46:0.7667:0:2 +7 18988889 . CATT C 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=3;SSF=0.28118;SOR=0;LSEQ=GTCATCTTCATTGTCATCAT;RSEQ=ATCTTCATTAGCAGCAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:2,2:12,12:24,4:0.1429:2,2:33.8:1:32.8:1:1:1:60:8:0.1429:0:0 0/0:17:0:0,0:8,9:17,0:0:2,0:25.7:1:28:1:1:0:60:16:1:0:1.1 +7 18988916 . A T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02126;SOR=Inf;LSEQ=TTCATTAGCAGCAAGTTTTT;RSEQ=CTTTTTTTCTGTGGAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,8:24,0:0:2,0:26.2:1:28.2:1:1:0:60:23:1:0:0.2 0/1:17:4:1,3:6,7:13,4:0.2353:2,2:37.3:1:28.8:1:0.60294:2.43937:60:8:0.2353:0:1.3 +7 18989094 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTCAACCATAAGACCATA;RSEQ=GTGGTGGTATTTCAAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:18,34:52,2:0.037:2,2:28:0:31.5:1:1:1.87:58:4:0.037:0:1.5 0/0:17:0:0,0:9,8:17,0:0:2,0:16.3:1:32.1:1:1:0:54.4:34:1:0:0.4 +7 18989154 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50913;SOR=0;LSEQ=GTACAGACATTTTCAAAGTT;RSEQ=CCAGTGTTACTTTTATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:17,24:41,2:0.0465:2,2:10:1:30:1:1:1.40:60:4:0.0476:0:1 0/0:30:0:0,0:14,15:29,0:0:2,0:23.9:1:31.4:1:1:0:52.8:58:0.9667:0:0.5 +7 18989156 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17505;SOR=Inf;LSEQ=ACAGACATTTTCAAAGTTGC;RSEQ=AGTGTTACTTTTATTTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:18,23:41,0:0:2,0:17.2:1:31.7:1:1:0:58:82:1:0:0.3 0/1:30:2:1,1:14,14:28,2:0.0667:2,2:20.5:1:28:1:1:1:49:4:0.0667:0:1.5 +7 18989222 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.2092;SOR=Inf;LSEQ=TTCAACGATGTGCAATTCAT;RSEQ=ATAGGTACCAGCTCCTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:9,7:16,0:0:2,0:25.1:1:31.2:1:1:0:60:15:1:0:0.6 0/1:14:2:1,1:6,6:12,2:0.1429:2,2:28.5:1:27:1:1:1:60:4:0.1429:0:2 +7 18989232 . A G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15195;SOR=3.3402;LSEQ=TGCAATTCATCATAGGTACC;RSEQ=GCTCCTGAACTGGCCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:4,6:5,3:8,10:0.5556:2,2:20.7:1:29.9:1:0.63719:2.37182:60:20:0.5556:0:1.1 1/1:16:13:8,5:2,1:3,13:0.8125:2,2:17.4:1:30.5:1:1:1.23302:60:26:0.8125:0:1.2 +7 18989402 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=ATGGGTTTGTGGCACCCACT;RSEQ=TGGTGGGAGAGAAGGCGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:17.2:1:32.7:1:1:0:60:12:1:0:0 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:18:1:29.5:1:0.33333:0:60:4:0.3333:0:1 +7 19616137 . A C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23636;SOR=0;LSEQ=TTTATATCAATGTAGAAGAG;RSEQ=AACATTTGGGTTGAAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:38:1:34:0:1:0:60:6:0.4286:0:1.3 0/0:4:0:0,0:4,0:4,0:0:0,0:13.3:1:30:0:1:0:60:8:1:0:0 +7 19616316 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19678;SOR=0.71368;LSEQ=GAAAATGGCATATTTCTCTA;RSEQ=GTTTGAATTTGCATGTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:165:111:89,22:46,8:54,111:0.6727:2,2:21.8:1:30.9:1:0.52198:1.41844:60:36:0.6708:0:2 1/0:106:63:42,21:29,14:43,63:0.5943:2,2:21.7:1:29.8:1:1:1.03538:60:62:0.5962:0:2 +7 19616327 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06621;SOR=Inf;LSEQ=ATTTCTCTACGTTTGAATTT;RSEQ=CATGTGTTACACATGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:158,51:209,0:0:2,0:23:1:32.3:1:1:0:60:68.667:1:0:1.2 0/1:143:3:1,2:92,48:140,3:0.021:2,2:9:1:29.3:1:0.27981:3.79474:60:6:0.0211:0:1.3 +7 19616340 . A G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30582;SOR=0.80037;LSEQ=TGAATTTGCATGTGTTACAC;RSEQ=TGTGTAAGCAAGGGTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:266:177:124,53:61,26:87,177:0.6654:2,2:23.4:1:30.6:1:1:1.00278:60:58:0.6641:0:1.7 1/0:171:105:64,41:44,22:66,105:0.614:2,2:25.6:1:29.3:1:0.51602:1.2794:60:25.25:0.6159:0:1.7 +7 19616437 . T G 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01453;SOR=0.64863;LSEQ=TTTGTTTTAGATATTACACA;RSEQ=AGTAAAAGAAAAATCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:267:120,147:56,80:136,267:0.6609:2,2:24.8:1:32.4:1:0.52421:1.17:60:266:0.6683:0:1.1 1/0:215:120:56,64:45,50:95,120:0.5581:2,2:24.4:1:30.7:1:1:1.02845:60:59:0.5592:0:1.3 +7 19616522 . C T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATCTTTAAAAAGTGTCAT;RSEQ=GATTTCCTAGCAGCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:42,131:173,0:0:2,0:22.2:1:30.5:1:1:0:60:346:1:0:0.5 0/1:92:34:12,22:12,46:58,34:0.3696:2,2:21.1:1:28.7:1:0.1448:2.07:60:68:0.3778:0:1.6 +7 19616550 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13372;SOR=Inf;LSEQ=TAGCAGCTTTTTTAAAAAGT;RSEQ=TCACTACAAACATATACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:9,89:98,0:0:2,0:22.1:1:33.2:1:1:0:60:97:1:0:0.5 0/1:57:2:1,1:7,48:55,2:0.0351:2,2:19.5:1:27:1:0.26316:6.48:60:4:0.0364:0:2.5 +7 19616566 . A T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00283;SOR=0.24324;LSEQ=AAGTCTCACTACAAACATAT;RSEQ=CACCAATTATAAAAAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:52:1,51:0,14:14,52:0.7879:1,1:24.6:1:29.7:1:1:0:60:16.333:0.7778:0:1.1 0/1:34:16:0,16:1,17:18,16:0.4706:1,1:29:1:27.8:1:1:0:60:15:0.4545:0:1.8 +7 19616651 . G GT 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATCATGGAAGTATAGGAG;RSEQ=TTTTTTTTTGCTTTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:0,11:11,2:0.1538:0,0:36:1:32:0:1:0:60:4:0.1667:0:0 0/0:2:0:0,0:0,2:2,0:0:0,0:19.5:1:30.5:1:1:0:60:4:1:0:0.5 +7 19694243 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0094;SOR=Inf;LSEQ=ATACAGGGCCCAAAGGCGAG;RSEQ=AATAGCAAGATGGCTGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:69,36:105,0:0:2,0:19.8:1:28.8:1:1:0:49.9:210:1:0:0.1 0/1:49:4:3,1:30,15:45,4:0.0816:2,2:13.3:1:31.5:1:1:1.49:60:8:0.0816:0:1 +7 19694269 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53897;SOR=0;LSEQ=CAAGATGGCTGTCAGGGGAC;RSEQ=TAGAAAGGGGAGAAGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:81,62:143,2:0.0137:2,2:45:1:31.5:1:1:1.30401:36:4:0.014:0:1 0/0:81:0:0,0:50,31:81,0:0:2,0:24.6:1:30.7:1:1:0:49.7:162:1:0:0.2 +7 19694292 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53873;SOR=0;LSEQ=GAAAGGGGAGAAGCCATGTC;RSEQ=CCCAACTACAGAGGTTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:84,81:165,2:0.012:2,2:31.5:1:29.5:1:1:1.03682:30.5:4:0.0123:0:1 0/0:93:0:0,0:51,42:93,0:0:2,0:29.9:1:29.9:1:1:0:51.5:45.5:1:0:0.2 +7 19694293 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12591;SOR=Inf;LSEQ=AAAGGGGAGAAGCCATGTCG;RSEQ=CCAACTACAGAGGTTGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:86,84:170,0:0:2,0:30.2:1:31.3:1:1:0:51.9:27.333:1:0:0.1 0/1:94:2:1,1:50,42:92,2:0.0213:2,2:31.5:1:29:1:1:1.18826:37:4:0.0215:0:1.5 +7 19694393 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03066;SOR=Inf;LSEQ=CCTCGTACTATCCTTGACTG;RSEQ=TTAGTGTAAAAACAACACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:6,28:34,0:0:2,0:28.1:1:31.7:1:1:0:58.8:33:1:0:0.1 0/1:26:4:1,3:1,21:22,4:0.1538:1,2:10:1:29.8:1:0.28923:6.21:57.8:8:0.1538:0:1.5 +7 19695194 . T C 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCTCTTTGACTGTCTTT;RSEQ=CCCTCCTCCCCACCACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:26:1:1:0:60:4:1:0:1 +7 20042316 . G T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30343;SOR=4.66971;LSEQ=TCTGCAAATCTGACAAGTTG;RSEQ=CATCCAAGCAAAATTTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:1:0,1:111,30:141,1:0.007:2,0:1:0:25:0:0.21831:0:45:2:0.0071:0:1 0/1:93:3:1,2:63,27:90,3:0.0323:2,2:18.7:1:26.3:1:0.2284:4.5803:52:6:0.0326:0:1 +7 20042378 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51378;SOR=0;LSEQ=GGAACCGCCATCTTCCAGTA;RSEQ=TTCGCCAAAATGACGAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:2:1,1:82,76:158,2:0.0125:2,2:43.5:1:33.5:1:1:1.07841:32:4:0.0127:0:1.5 0/0:112:0:0,0:62,50:112,0:0:2,0:30.6:1:29.4:1:1:0:46.6:224:1:0:0.2 +7 22987360 . A AGT 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.45011;SOR=0.69165;LSEQ=CTTTGTACTCTTAAAATTCT;RSEQ=TTTTTTATGAGGCTACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:83:68:64,4:13,2:15,68:0.8193:2,2:21.6:1:32.1:1:0.29576:2.43:59.9:136:0.8293:0.2289:0 1/0:33:25:24,1:8,0:8,25:0.7576:0,1:23.8:1:29.8:1:1:0:60:24:0.75:0.2121:0.2 +7 22987500 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28423;SOR=1.18013;LSEQ=TCATCTATTATTAACAGTAA;RSEQ=TATTAATGTGGCTGTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:157:77,80:167,161:328,157:0.3237:2,2:28.5:1:30.5:1:0.77099:1.07751:60:51.333:0.3222:0:1.1 0/1:313:113:58,55:103,97:200,113:0.361:2,2:22.6:1:29.4:1:1:1.00691:60:112:0.3601:0:1.1 +7 23293746 . A G 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=16.95646;LSEQ=AATGTTTATGAACGAAAGGA;RSEQ=AAAGATGCTGGATCATCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:15:7,8:302,303:605,15:0.0242:2,2:28.6:1:32.9:1:1:1.13885:60:30:0.0244:0:1.1 0/1:364:108:56,52:118,137:255,108:0.2967:2,2:22.8:1:30.8:1:0.35887:1.25:59.9:53:0.2969:0:1.2 +7 23293803 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05844;SOR=Inf;LSEQ=CCTAGGAGGCCGTGTGCAGG;RSEQ=GGTCCTGACCAGTGACTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:102,226:328,0:0:2,0:25.2:1:30.8:1:1:0:59.9:163:1:0:0.2 0/1:209:3:2,1:76,130:206,3:0.0144:2,2:25.7:1:27:1:0.55716:3.40:60:6:0.0148:0:1 +7 23293814 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15845;SOR=Inf;LSEQ=GTGTGCAGGCGGTCCTGACC;RSEQ=GTGACTCACCAGCCCTCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:77,202:279,0:0:2,0:24.6:1:31.7:1:1:0:59.9:68.75:1:0:0.1 0/1:185:2:1,1:64,119:183,2:0.0108:2,2:38.5:1:29.5:1:1:1.85:60:4:0.0109:0:1 +7 23662013 . G A 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.375;SOR=Inf;LSEQ=GTTTATAGTATTCTCTGGTG;RSEQ=TAGTTTGTATTTCTGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:18:1:31.5:1:1:0:45.5:4:0.2857:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:16:0:30:0:1:0:47:2:1:0:1 +7 23662135 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53508;SOR=0;LSEQ=AAAGCGAAACTGGATTTAGT;RSEQ=CAGTCAACGATGGACTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:103,35:138,2:0.0143:2,2:15.5:1:29.5:1:0.44954:2.9155:60:4:0.0147:0:1.5 0/0:80:0:0,0:60,20:80,0:0:2,0:26:1:31.6:1:1:0:58.6:79:1:0:0.1 +7 23662148 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52927;SOR=0;LSEQ=ATTTAGTGCAGTCAACGATG;RSEQ=ACTGTCTGTATGCCAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:113,53:166,2:0.0119:2,2:29.5:1:30:0:0.54085:2.12161:48.5:4:0.0122:0:1 0/0:101:0:0,0:68,33:101,0:0:2,0:26.6:1:30.3:1:1:0:53.2:100:1:0:0.1 +7 23662173 . C A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28783;SOR=0;LSEQ=TCTGTATGCCAGGTGTATCC;RSEQ=TTGTGTAACTGATTGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:3:2,1:115,90:205,3:0.0144:2,2:30.3:1:24:1:1:1.56:56:2:0.0098:0:1.3 0/0:130:0:0,0:74,56:130,0:0:2,0:26.8:1:30.3:1:1:0:45.1:129:1:0:0.1 +7 23895077 . A C 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.39581;LSEQ=CAAATTTGACGAGGAGGTTA;RSEQ=AAATACAGGGCCCGAAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:3,4:1,1:2,7:0.7778:2,2:32.4:1:31.7:1:1:1.29098:21.7:14:0.7778:0:1 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:18.2:1:31.2:1:1:0:21:10:0.8333:0:1 +7 23895205 . CT C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.13816;SOR=Inf;LSEQ=CATTGTCTGATTTCAGAAGC;RSEQ=TTTCCTGTAAACGCTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:22,38:60,0:0:2,0:21.7:1:30.9:1:1:0:50.4:120:1:0:0.2 0/1:36:2:1,1:13,21:34,2:0.0556:2,2:29:1:33:1:1:1.59:45:4:0.0556:0:0.5 +7 24164485 . A AT 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02308;SOR=6.42475;LSEQ=TAAAATGCTTGTATAGTCAG;RSEQ=TTTTTTTTAACTTTCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:2:2,0:194,8:202,2:0.0098:1,0:30:1:33:0:1:0:60:4:0.0101:0:0 0/1:83:5:5,0:73,5:78,5:0.0602:2,0:21:1:30.1:1:1:0:60:10:0.061:0.0241:0 +7 24164624 . T C 219 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=420.64974;LSEQ=TTTTGAGGCTGCAACCAGTA;RSEQ=GTACATGTTTTGGATTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:810:1:0,1:328,481:809,1:0.0012:2,0:1:0:31:0:1:0:60:2:0.0012:0:1 0/1:452:155:64,91:118,176:294,155:0.3429:2,2:25.6:1:30.1:1:0.84011:1.05:60:154:0.343:0:1.2 +7 24164678 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03029;SOR=Inf;LSEQ=CCTTACTTCATATCAGGCTT;RSEQ=CACAGCTGGACACAGTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:329:0:0,0:74,255:329,0:0:2,0:21.5:1:31.5:1:1:0:60:81.25:1:0:0.1 0/1:150:3:0,3:32,115:147,3:0.02:2,0:27.3:1:29.7:1:1:0:60:6:0.0204:0:1 +7 26196963 . G A 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCACCACTGCTTCTGGCT;RSEQ=ATTTTTTTTTTTTTTAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40:0:31:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 26196964 . A AT 32 d5;v3;pSTD;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCACCACTGCTTCTGGCTG;RSEQ=TTTTTTTTTTTTTTAATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38:0:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 27134260 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49971;SOR=0;LSEQ=CAGATCTTCACTTGGGTCTC;RSEQ=TTGAGCTGCAGGGATGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:28,41:69,2:0.0282:2,2:22.5:1:29.5:1:1:1.46:60:4:0.0286:0:1 0/0:60:0:0,0:30,30:60,0:0:2,0:29.1:1:29.6:1:1:0:59.6:19:1:0:0.1 +7 27135314 . C T 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTAGCCGGCTGGGGGTGG;RSEQ=GATGGTGGTGGTGGTGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:21.7:1:30.3:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:28:0:28:0:1:0:60:2:1:0:1 +7 27141657 . C G 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCCACTCTCCCCTCCCCC;RSEQ=ACAGCCACTCTCGGGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:5,2:7,2:0.2222:2,0:16.5:1:30:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 27141768 . TGGC T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.05;SOR=Inf;LSEQ=AGGGCCGGTGGCTGCGGCGG;RSEQ=GGCGGCGGCGGCGGCCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:19,0:0:2,0:27:1:31.5:1:1:0:60:38:1:0:0.3 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:38.5:1:30:1:1:1:60:4:0.3333:0:0 +7 27141771 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCCGGTGGCTGCGGCGGTGG;RSEQ=GGCGGCGGCGGCGGCCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:6,11:17,2:0.1053:2,2:29.5:1:29:1:1:1.77:60:4:0.1053:0:1 0/0:6:0:0,0:2,2:4,0:0:2,0:15:1:32:1:1:0:60:8:1:0:0.3 +7 27201532 . C A 32 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGACTCCGCGGGGGTGG;RSEQ=GGGCGGTGCGAGGATGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:32:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:10:0:15:0:1:0:60:0:0:0:2 +7 27203139 . G A 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.56488;SOR=3.5981;LSEQ=AGGCTAGGGTGGGGGTGAGA;RSEQ=AAGGGAGAAGGCGGAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:20.5:1:32.3:1:1:0:60:8:0.5:0:1 1/1:5:4:4,0:1,0:1,4:0.8:0,0:16.5:1:29:1:1:0:60:8:0.8:0:1 +7 27203259 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.14697;SOR=Inf;LSEQ=GGTCTTTGTTGATTTTCTTC;RSEQ=TTTTCATCCTGCGGTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:64,50:114,0:0:2,0:26.6:1:30.3:1:1:0:60:56:1:0:0.1 0/1:72:2:1,1:38,31:69,2:0.0278:2,2:21.5:1:29:1:1:1.22227:60:4:0.0299:0:1 +7 27203278 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51256;SOR=0;LSEQ=CATTTTCATCCTGCGGTTCT;RSEQ=GAACCAGATCTTGACCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:53,59:112,2:0.0174:2,2:44.5:1:31.5:1:1:1.11:60:4:0.0174:0:1 0/0:81:0:0,0:38,43:81,0:0:2,0:27.8:1:30.8:1:1:0:60:80:1:0:0.2 +7 27203334 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15063;SOR=Inf;LSEQ=GCAGTCGAGCCACCTCGTAC;RSEQ=TGCGGTCCCTGGTGAGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:21,46:67,0:0:2,0:22.4:1:32.4:1:1:0:60:134:1:0:0 0/1:43:2:1,1:14,27:41,2:0.0465:2,2:34:1:29.5:1:1:1.90:60:4:0.0476:0:1 +7 27203413 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=GTGTTTTGTATAGGGGCACC;RSEQ=CTTTTTCCGAGTGGAGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:13,0:0:1,0:16.4:1:32.8:1:1:0:60:26:1:0:0 0/1:8:2:1,1:0,6:6,2:0.25:0,2:35.5:1:28:1:0.25:0:60:4:0.25:0:1 +7 28996220 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGCCGACTCAGCCTTAG;RSEQ=GCGCTGCGGTTGCCTACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:42.5:1:29.5:1:1:0:60:4:1:0:1 +7 28996940 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCGCGGCCCGAGGTGCTG;RSEQ=AGGTTGTTGGCCGAGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:17,21:38,2:0.05:2,2:24.5:1:30.5:1:1:1.23:60:4:0.0513:0:2.5 0/0:4:0:0,0:2,2:4,0:0:2,0:32.3:1:30.5:1:1:0:60:8:1:0:1.3 +7 28996944 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCCCGAGGTGCTGCAGG;RSEQ=TGTTGGCCGAGAGGATGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:40:18,22:0,0:0,40:1:0,2:28.3:1:33:1:1:0:59.9:39:1:0:1.5 1/1:4:4:2,2:0,0:0,4:1:0,2:32.3:1:30.8:1:1:0:60:8:1:0:1.3 +7 28997596 . G GC 51 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTCCGGGCACACGGGCTCG;RSEQ=CAGCGGCGGGAGCGCGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:1,0:1,3:0.75:0,0:29.7:1:32.7:1:0.25:0:60:6:0.75:0:0 1/1:1:1:0,1:0,0:0,1:1:0,0:15:0:32:0:1:0:60:2:1:0:0 +7 28997974 . G T 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AGCAAGACCCGGCGCTTTTT;RSEQ=TTTGCAGCTGAGTCCGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:47.5:1:31:1:1:1:60:4:0.5:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:15.5:1:30:1:1:0:60:4:1:0:0.5 +7 29880530 . T G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGATCGGACATACCCTGG;RSEQ=GGTTGGTGAAGGATAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:36:1:33:0:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:34:1:27:1:1:0:60:4:1:0:0 +7 31287159 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05603;SOR=Inf;LSEQ=AAAAAGCAGCCCCAGGCCAA;RSEQ=GGCATTGGGAGTGCTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:223,140:363,0:0:2,0:24.4:1:32:1:1:0:60:71.6:1:0:0.2 0/1:226:3:1,2:130,93:223,3:0.0133:2,2:22.3:1:29.3:1:0.57389:2.78303:60:6:0.0133:0:1 +7 31287173 . C T 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04149;SOR=7.5154;LSEQ=GGCCAAGGGCATTGGGAGTG;RSEQ=TGGGGCAGGTGAGGTAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:414:1:0,1:237,176:413,1:0.0024:2,0:1:0:15:0:0.42754:0:60:0:0:0:1 0/1:279:5:1,4:151,123:274,5:0.0179:2,2:15.2:1:24.8:1:0.18086:4.88612:60:4:0.0147:0:1 +7 31287246 . C A 140 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=60.76058;LSEQ=GCCCCAGGAGAAGATGAAAT;RSEQ=TTAAGCCCAGATTTGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:1:1,0:96,167:263,1:0.0038:2,0:1:0:26:0:0.36742:0:60:2:0.0038:0:1 0/1:175:33:14,19:50,92:142,33:0.1886:2,2:20.8:1:27.9:1:0.54763:1.35:60:32:0.185:0:1.1 +7 32159902 . G A 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=GGCCGCAGTCTCTGCAGACC;RSEQ=TCATACTTAGCCTTTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:5,2:6,2:8,7:0.4667:2,2:20.1:1:29.7:1:1:1.18545:47.9:14:0.4667:0:1.1 0/0:2:0:0,0:1,1:2,0:0:2,0:14:1:30:1:1:0:54:4:1:0:0 +7 32161232 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCAACCCAGAGTTTCAT;RSEQ=TCCAGCCAAACTAAGCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:31:1:1:0:22:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 32894331 . G T 56 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01844;SOR=6.55712;LSEQ=TTCGAATCACCCCATAAGGG;RSEQ=CAGAAGCATGTCTCAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:3,0:49,0:49,3:0.0577:1,0:28:1:31.3:1:1:0:39.7:6:0.0612:0:1 0/1:17:5:5,0:12,0:12,5:0.2941:0,0:25.4:1:24.2:1:1:0:31.8:1.5:0.2:0:1.8 +7 32894398 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53438;SOR=0;LSEQ=AGAGAAAATCTAGGTTTCAT;RSEQ=TGAAGAACTGCCATTTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:150,41:191,2:0.0103:2,2:32.5:1:29.5:1:0.38876:3.62636:40:4:0.0104:0:1 0/0:112:0:0,0:81,31:112,0:0:2,0:24.8:1:29.2:1:1:0:41.6:36.333:1:0:0.1 +7 32894503 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.18497;LSEQ=AGAAGAGCTTGGAAAAATGC;RSEQ=TGGCAGCCTGATGTCACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:187:83,104:130,131:261,187:0.4174:2,2:28:1:30.5:1:0.29142:1.24283:30:61.333:0.4153:0:1.1 1/1:265:222:106,116:17,25:42,222:0.8377:2,2:27.1:1:29.3:1:0.40465:1.34:31:54.5:0.8385:0:1.1 +7 32894601 . G A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02063;SOR=4.63197;LSEQ=AGACTCAGACTCCTCAGACT;RSEQ=GGAACCAGGGGAGACTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:4:1,3:19,33:52,4:0.0714:2,2:6.3:1:30.5:1:1:1.71181:53.5:8:0.0727:0:1 0/1:30:8:3,5:4,18:22,8:0.2667:2,2:5.4:1:29.5:1:0.3446:2.60:46.6:16:0.2667:0:1.3 +7 33716528 . T C 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATGAAATACTAGACATGAGA;RSEQ=TTTTTTTCTCTTTATTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:32.5:1:32:1:1:0:60:4:1:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:32:0:1:0:60:2:1:0:0 +7 33716674 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=GTCAGCGGGCCTGGATGCAC;RSEQ=TCCCAGTTCTGCCTCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:24:1:30:1:1:1.12:60:4:0.1053:0:1.5 0/0:11:0:0,0:4,7:11,0:0:2,0:23.6:1:29.5:1:1:0:60:10:1:0:0.2 +7 34959604 . C T 119 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0762;SOR=0.14039;LSEQ=TTTTAGTCTCCCCTGGTTCC;RSEQ=AGTCTGAGGAGTCTGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:13:11,2:23,0:23,13:0.3611:1,2:12.8:1:32.4:1:0.12381:0:51.2:26:0.3611:0:2.1 0/1:14:1:1,0:11,2:13,1:0.0714:2,0:10:0:33:0:1:0:60:2:0.0833:0:3 +7 34959617 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.00915;SOR=0.29408;LSEQ=TGGTTCCCAGTCTGAGGAGT;RSEQ=TGAGTCTGGGCTGCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:36:30,6:17,3:20,36:0.6429:2,2:18.2:1:31.8:1:1:1.13087:43.7:72:0.6429:0:1.4 0/1:35:12:9,3:17,6:23,12:0.3429:2,2:13.3:1:30.1:1:1:1.06:39.3:24:0.3636:0:1.3 +7 34959661 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15621;SOR=Inf;LSEQ=AGTGTTTCAGCCCCTCTGCC;RSEQ=TGCTCACCTCTTGACCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:150,91:241,0:0:2,0:23.7:1:31.8:1:1:0:37.4:59.25:1:0:0.4 0/1:158:2:1,1:94,62:156,2:0.0127:2,2:32.5:1:28.5:1:1:1.51199:26.5:4:0.0131:0:2.5 +7 34959774 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51865;SOR=0;LSEQ=CTGAGTACTGTCTTGTGCTT;RSEQ=CCCAGCCTAGGAGTCTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:59,118:177,2:0.0112:2,2:17:1:30.5:1:1:1.99:21:4:0.0115:0:1 0/0:119:0:0,0:32,87:119,0:0:2,0:29.3:1:30.3:1:1:0:28.8:118:1:0:0.2 +7 34959828 . C G 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29499;SOR=0.49045;LSEQ=ATGAAACCTAGATTTTCTCT;RSEQ=CCCATTTGAAACGAAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:14:0,14:3,42:45,14:0.2373:2,1:25.6:1:33:1:1:0:40.4:28:0.2414:0:2.2 0/1:38:5:0,5:4,29:33,5:0.1316:2,0:21.4:1:30.8:1:1:0:47.4:10:0.1389:0:1.6 +7 34959833 . TTT A 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.48405;SOR=1.90415;LSEQ=ACCTAGATTTTCTCTCCCCA;RSEQ=GAAACGAAAGCTCCACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:5:0,5:3,45:48,5:0.0943:2,0:16.8:1:33.6:1:1:0:20.4:10:0.098:0.0189:0 0/1:30:5:0,5:2,23:25,5:0.1667:2,0:14:1:31.4:1:1:0:20.6:10:0.1667:0.0667:0 +7 34959845 . G C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52213;SOR=0.58209;LSEQ=TCTCCCCATTTGAAACGAAA;RSEQ=CTCCACCAGAGGGTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:12:0,12:1,29:30,12:0.2857:1,0:21:1:30.9:1:1:0:43.9:11:0.2683:0:2.4 0/1:16:3:0,3:1,12:13,3:0.1875:1,0:23.3:1:29.7:1:1:0:39:6:0.1875:0:2 +7 35458399 . A T 51 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48571;SOR=0.15605;LSEQ=GAATTCCCAGAGGAGTGAGA;RSEQ=GATTGGGGTTGGAGTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:46.7:1:32.3:1:1:0:60:6:0.75:0:1 0/1:4:1:1,0:3,0:3,1:0.25:0,0:35:0:31:0:1:0:60:2:0.3333:0:3 +7 35458489 . G A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03118;SOR=Inf;LSEQ=TGGCGGTGGTGATGGCGGTG;RSEQ=CGGTGACGGTGGCGGTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:10,10:20,0:0:2,0:23.1:1:31.2:1:1:0:58.3:19:1:0:0.8 0/1:27:6:3,3:11,10:21,6:0.2222:2,2:33.8:1:27.8:1:1:1.09612:60:12:0.25:0:1.2 +7 35458520 . TGGC T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.1996;SOR=0;LSEQ=GGCGGTGGCGGTGGCGGTGG;RSEQ=GGCGGCGGCGGTGGCGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:17,13:30,2:0.0625:2,2:33.5:1:31.5:1:1:1.29665:60:4:0.0625:0:0.5 0/0:39:0:0,0:21,18:39,0:0:2,0:21.9:1:30.2:1:1:0:57.2:18.5:1:0:0.7 +7 35458532 . C A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.01329;SOR=0.22866;LSEQ=GGCGGTGGTGGCGGCGGCGG;RSEQ=GGTGGCGGTGGCGGGCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:7,6:11,7:18,13:0.4194:2,2:25.8:1:27.8:1:0.72695:1.33394:58.2:3.333:0.3846:0:1 0/1:36:5:2,3:16,15:31,5:0.1389:2,2:28.8:1:29.8:1:1:1.57936:60:10:0.1429:0:1.2 +7 35458551 . GT G 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01355;SOR=5.31402;LSEQ=GCGGTGGCGGTGGCGGGCTA;RSEQ=AAGACCTCTGCGTGTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:10,3:6,5:11,13:0.5417:2,2:30.7:1:32.1:1:0.39045:2.66:60:26:0.5652:0.0417:0.7 1/1:30:26:12,14:3,1:4,26:0.8667:2,2:24.3:1:30.4:1:0.5977:3.36376:59.7:25:0.8621:0.1:0.7 +7 36858427 . G T 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21842;SOR=0;LSEQ=TCCACGTGCAAAAGAATGAA;RSEQ=TTGGACCCCTGCCTCACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:7,2:7,1:8,9:0.5294:2,2:14.3:1:31.7:1:1:1.9219:60:18:0.5294:0:1.1 0/0:3:0:0,0:3,0:3,0:0:0,0:27:1:31.3:1:1:0:60:6:1:0:0 +7 36858494 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52425;SOR=0;LSEQ=TGTGATTCCGTCCTGCATGG;RSEQ=TGTTCTCTTGAGCAGTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:23,12:35,2:0.0541:2,2:37.5:1:29:1:1:1.88115:60:4:0.0556:0:1.5 0/0:22:0:0,0:13,9:22,0:0:2,0:21.6:1:31.6:1:1:0:60:44:1:0:0.2 +7 36858643 . A G 152 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=110.48124;LSEQ=TTGTGAACTAAAGGCTGACA;RSEQ=TCACTTTCAAGTGGATAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:1:1,0:102,34:136,1:0.0073:2,0:46:0:35:0:1:0:60:2:0.0074:0:1 0/1:66:30:23,7:26,10:36,30:0.4545:2,2:22.2:1:31.1:1:0.78099:1.26:55.4:29:0.4603:0:1 +7 36858858 . C T 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=TAACACCACCAGTAGTCTTA;RSEQ=GGTTGAAGTGTGGTTCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:210,194:404,0:0:2,0:25.1:1:30.4:1:1:0:32:30.077:1:0:0.1 0/1:254:9:3,6:132,113:245,9:0.0354:2,2:8.3:1:28.2:1:0.31221:2.32868:30:18:0.0361:0:1.1 +7 36859014 . C A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5665;SOR=3.01253;LSEQ=GAGGTGGTAGCAAGGTGCCA;RSEQ=AGAAAAAAGTAAAACTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:0,1:79,122:201,1:0.005:2,0:30:0:16:0:1:0:60:0:0:0:1 0/1:135:2:1,1:55,78:133,2:0.0148:2,2:37.5:1:29:1:1:1.41:60:4:0.0152:0:1 +7 36859286 . A G 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04323;SOR=0;LSEQ=AAAATGCAAGCAAGTATACA;RSEQ=AAAGCATATTGAACAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:7:1,6:13,33:46,7:0.1321:2,2:23.4:1:33.4:1:0.6601:2.33155:46.9:14:0.14:0:1 0/0:31:0:0,0:7,24:31,0:0:2,0:24.8:1:30:1:1:0:51.8:62:1:0:0.1 +7 36859510 . T C 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=Inf;LSEQ=CACTTTTCTTCTGACTGCTG;RSEQ=GATTCAATGAACCTTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:10:0:25:0:1:0:21:2:0.3333:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:28.3:1:30.3:1:1:0:39.7:6:1:0:1 +7 37220821 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16373;SOR=Inf;LSEQ=TAAAGTGTTAGATGGCAAAC;RSEQ=ATCAGCATGCCCAGTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:295:0:0,0:221,74:295,0:0:2,0:22:1:31.2:1:1:0:60:294:1:0:0.1 0/1:201:2:1,1:146,53:199,2:0.01:2,2:16.5:1:26.5:1:0.46612:2.73842:60:4:0.0102:0:1.5 +7 37220826 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07796;SOR=Inf;LSEQ=TGTTAGATGGCAAACCATCA;RSEQ=CATGCCCAGTGGCCACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:214,84:298,0:0:2,0:24.2:1:32.7:1:1:0:60:98.333:0.9966:0:0.1 0/1:224:3:2,1:153,68:221,3:0.0134:2,2:16.3:1:26:1:1:1.12439:60:6:0.0136:0:1 +7 37220932 . G A 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.06469;LSEQ=GTACTCCAGGCTAAGTCACC;RSEQ=AGAAGGAGGATGCCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:597:556:242,314:19,19:38,556:0.9313:2,2:25.6:1:30.4:1:0.50024:1.29693:60:60.778:0.9366:0:1.1 0/1:388:181:75,106:90,114:204,181:0.4665:2,2:24.4:1:29.6:1:0.60745:1.11547:60:89.5:0.4723:0:1.2 +7 37220996 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13102;SOR=Inf;LSEQ=CACACCTGCCCTCTCTGTGG;RSEQ=CTACTCTTCACATTTTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:46,214:260,0:0:2,0:23.1:1:32.3:1:1:0:59.9:51:1:0:0.7 0/1:148:2:1,1:33,113:146,2:0.0135:2,2:16.5:1:27.5:1:0.40789:3.39:60:4:0.0136:0:2 +7 37221055 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13415;SOR=0.3916;LSEQ=TGAGGCAGCTCTGTCTTGTA;RSEQ=TTGCAGATTGGATGGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:18:1,17:2,61:63,18:0.2222:1,1:23.1:1:33.3:1:0.53456:1.78:60:36:0.2222:0:1.1 0/1:40:4:0,4:3,33:36,4:0.1:2,0:24.8:1:32:1:1:0:60:8:0.1:0:1 +7 39479901 . A G 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCGTGTTTCCATTCTCCCT;RSEQ=TCTCATTCTGGTACTCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:47.5:1:30:0:1:0:60:4:1:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:36:1:30.5:1:1:1:52:4:0.3333:0:1.5 +7 39480448 . C T 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTCTTTGAGGCTGCTGAT;RSEQ=GTTGGAGGGTTTTTGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:10:0:33:0:1:1.10554:60:4:0.1:0:1 0/0:9:0:0,0:4,5:9,0:0:2,0:29.7:1:30.2:1:1:0:54.9:18:1:0:0.1 +7 39480470 . CTTG C 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.52923;SOR=0;LSEQ=TTGGAGGGTTTTTGTGAGGG;RSEQ=TTGTTGTTGTTGATGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:1,2:7,7:14,3:0.1765:2,2:34.3:1:34.7:1:1:1.9219:60:6:0.1875:0:0.7 0/0:9:0:0,0:5,4:9,0:0:2,0:29.1:1:29:1:1:0:54.9:8:1:0:0.6 +7 39480486 . A T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.52727;SOR=4.02871;LSEQ=AGGGCTTGTTGTTGTTGTTG;RSEQ=TGATGATGATGTTGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:6,7:13,1:0.0714:2,0:17:0:26:0:1:0:60:2:0.0769:0:3 0/1:8:2:2,0:2,4:6,2:0.25:2,0:31.5:1:30.5:1:0.42857:0:37:4:0.25:0:2 +7 39480585 . C T 48 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=GTTTGCTGGGAGGTTCACTT;RSEQ=AGGCCCTACTCATCCGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:26:1:33.8:1:1:0:60:8:1:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:39:1:30.3:1:1:0:59.3:6:1:0:2.3 +7 39480601 . G A 48 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=ACTTCAGGCCCTACTCATCC;RSEQ=ATTCACTCCCGTGCCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:21.8:1:32.8:1:1:0:60:8:1:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:33.3:1:30.7:1:1:0:59.3:6:1:0:2.3 +7 39480649 . A C 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TCAAGAAGTCTGGAGAACAG;RSEQ=AAAAATGGGTGCCTCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:2,2:4,1:0.2:2,0:28:0:34:0:1:0:38:2:0.2:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:31:1:1:0:50.5:4:1:0:2 +7 39480827 . CT C 26 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGTATTTTTAAAGCTTAG;RSEQ=TTTTTTTTTTTTTCAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:26:1:26.5:1:0.33333:0:60:4:0.6667:0.3333:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 39520306 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTATCGAAAGGACATAGC;RSEQ=GTGGCTCAGCTCTGACCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 39520802 . C G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCATGATGCACACCACCAC;RSEQ=CCAGGGGAGCTTAAGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 39521781 . A C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAAAGGATAATTTCACTGC;RSEQ=TCAAGAATTCCATGTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:37:1:33:0:1:0:60:6:0.3333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:32:0:1:0:60:2:1:0:0 +7 39521940 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1199;SOR=Inf;LSEQ=CTGGTTGCTTTCAAGATTTT;RSEQ=TCTCACTGATTTTCTGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:49,52:101,0:0:2,0:26.7:1:32.7:1:1:0:59.6:49.5:1:0:0.2 0/1:54:2:1,1:27,25:52,2:0.037:2,2:38:0:32.5:1:1:1.07844:60:4:0.0385:0:1.5 +7 39835950 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=TCGGTCTCCAGTTCCCTGAG;RSEQ=CCGTCCTCGGCTTCTTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:25.4:1:30.1:1:1:0:31:14:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:12:1:30.5:1:1:0:21.5:4:0.6667:0:1 +7 39835960 . GCTT G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=GTTCCCTGAGCCCGTCCTCG;RSEQ=CTTCACCTGTACAGGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:15.4:1:32.4:1:1:0:31:14:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:23:1:33.5:1:1:1:21.5:4:0.5:0:1 +7 39836043 . C T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12482;SOR=4.15212;LSEQ=AGATGGAGCATCTTCTCATC;RSEQ=TGCATTTGGGCATGGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:4,1:8,3:11,5:0.3125:2,2:34.2:1:31.2:1:1:1.46:37.6:10:0.3333:0:1 1/0:12:8:4,4:3,1:4,8:0.6667:2,2:38.4:1:31.1:1:0.57576:2.74155:37.3:16:0.6667:0:1.3 +7 39836727 . G T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34121;SOR=0;LSEQ=ATCACCCCCTCCTCCTCATG;RSEQ=ATGACCATGTGCTCCTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:7:5,2:22,32:54,7:0.1148:2,2:19.9:1:29.9:1:0.22448:3.56:27.4:14:0.1167:0:1 0/0:18:0:0,0:11,7:18,0:0:2,0:23.7:1:29.4:1:1:0:25.7:17:1:0:0.1 +7 40117685 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16149;SOR=Inf;LSEQ=AACACCATGAAACCAAAGAA;RSEQ=CAATATCGTCGAAAGTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:40,55:95,0:0:2,0:25.1:1:32.2:1:1:0:60:46.5:0.9894:0:0.2 0/1:65:2:1,1:24,39:63,2:0.0308:2,2:17:1:31.5:1:1:1.61:60:4:0.0313:0:1 +7 40117692 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.27034;SOR=0;LSEQ=TGAAACCAAAGAAGCAATAT;RSEQ=GTCGAAAGTTAAGAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:3:1,2:30,54:84,3:0.0345:2,2:32:1:31.3:1:1:1.1098:60:6:0.0353:0:1 0/0:60:0:0,0:23,37:60,0:0:2,0:20.4:1:29.7:1:1:0:59.9:120:1:0:0.1 +7 40117696 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51697;SOR=0;LSEQ=ACCAAAGAAGCAATATCGTC;RSEQ=AAAGTTAAGAGAAGAATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:27,51:78,2:0.025:2,2:25:1:30:1:1:1.87:60:4:0.0263:0:1 0/0:53:0:0,0:19,34:53,0:0:2,0:20.1:1:30.1:1:1:0:59.8:106:1:0:0.1 +7 41461200 . G A 246 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1576.6671;LSEQ=AACCACCCAGGGCCCTTTTA;RSEQ=TTCATGTAAGACCTAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:913:1:1,0:447,464:911,1:0.0011:2,0:1:0:28:0:0.49123:0:60:2:0.0011:0:1 1/0:539:337:149,188:92,109:201,337:0.6252:2,2:24.4:1:29.4:1:0.78811:1.06483:59.9:83.25:0.6271:0:1.1 +7 41461291 . C T 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCTCTCAGAAGACAAGGAT;RSEQ=GAATCCTTCTAAGGGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:38,272:310,0:0:2,0:22.8:1:30.4:1:1:0:60:102.333:1:0:0.1 0/1:129:12:2,10:22,95:117,12:0.093:2,2:22.8:1:30.1:1:1:1.15663:60:24:0.0945:0:1 +7 41461425 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTCTACTTTCCAGGTTG;RSEQ=AATCTCCCATCCTCCCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:0,23:23,2:0.08:1,2:45.5:1:29.5:1:0.08:0:60:4:0.08:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:33:1:27.5:1:1:0:60:4:1:0:1.5 +7 41726288 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAGTTTCAAATAAAATAT;RSEQ=GAATTACATTTCTCTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:0,91:91,2:0.0215:1,0:18:1:32:0:1:0:60:4:0.0217:0:1 0/0:19:0:0,0:0,19:19,0:0:1,0:21.9:1:31.1:1:1:0:60:38:1:0:0.1 +7 41729111 . G GT 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.00049;SOR=0.36419;LSEQ=TTTGTTTTTAATTTACTTTT;RSEQ=TTTTTTTTTGTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:80:79,1:166,5:171,80:0.3101:1,1:20.4:1:30.8:1:0.66768:2.37:57.3:160:0.315:0.0814:1.1 0/1:114:16:14,2:91,4:95,16:0.1404:1,2:29.8:1:29.3:1:0.20673:3.20199:57.6:32:0.1455:0:1.1 +7 41729121 . GT G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.3967;SOR=0.62638;LSEQ=ATTTACTTTTGTTTTTTTTT;RSEQ=TTTTTTTTTTGTTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:22:22,0:281,6:287,22:0.0692:1,1:21.7:1:32.2:1:1:0:58.5:44:0.071:0.022:0.5 0/1:135:6:6,0:117,7:124,6:0.0444:2,0:23.7:1:31.3:1:1:0:60:12:0.0469:0.0074:0.5 +7 41729159 . G A 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00885;SOR=Inf;LSEQ=TTTTTAATTTCTATTTTTCT;RSEQ=GTTAACTCAGAAACCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:704:0:0,0:676,23:699,0:0:1,0:23.4:1:31:1:1:0:59.4:9.13:0.9984:0:0.3 0/1:313:4:4,0:285,22:307,4:0.0128:2,0:27.8:1:23.5:1:1:0:55.8:3:0.0103:0:2.3 +7 41729740 . TTTC T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.76389;SOR=1.06532;LSEQ=TTCCCTTCCCCCTCCTCTTC;RSEQ=TTCTTCTTCTTGCCCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2907:64:34,30:1354,1485:2839,64:0.022:2,2:28:1:30.8:1:0.44812:1.24:59.8:63:0.022:0.0034:0.4 0/1:1836:43:22,21:898,890:1788,43:0.0234:2,2:28.1:1:30:1:1:1.04:59.8:86:0.0237:0.0027:0.2 +7 41729758 . CA AG 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTTTCTTCTTCTTCTTGCC;RSEQ=GGAGAACCAAGCTGGCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2531:28:13,15:1250,1245:2495,28:0.0111:2,2:25.9:1:32.4:1:0.70924:1.15841:60:56:0.0113:4e-04:1.1 0/0:1565:0:0,0:781,781:1562,0:0:2,0:24.8:1:30.5:1:1:0:60:56.852:0.9987:0:0.1 +7 41730289 . G C 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACAGCCCATGGGCTGAAACT;RSEQ=TTTCTGTACTGCCTGCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:44:0,44:0,157:157,44:0.2189:1,1:25.5:1:32.8:1:1:0:60:21:0.2121:0:1.2 0/0:71:0:0,0:1,70:71,0:0:1,0:25.2:1:32:1:1:0:60:70:1:0:0.1 +7 41735034 . C T 346 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.69741;LSEQ=CAGGGTGCATTCTCTGAAGC;RSEQ=CTAACTTTGCATTTGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2914:2270:1195,1075:325,318:643,2270:0.779:2,2:25.6:1:31.1:1:0.34815:1.09:60:65.765:0.7799:0:1.1 1/0:1487:1057:553,504:224,203:427,1057:0.7108:2,2:25.4:1:29.4:1:1:1.00567:59.9:104.7:0.7113:0:1.2 +7 41735646 . T TC 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATCTCTTTTCCCATCTT;RSEQ=CCCACCATTTCTCTCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,2:3,2:0.3333:2,0:8.5:1:33:1:1:0:60:4:0.4:0.1667:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 41739141 . G C 108 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCATTCCACTCCAATCCT;RSEQ=GTACATTCACCCCTCTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:0,10:1:0,2:35.4:1:32.7:1:1:0:60:20:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 41740059 . A AT 100 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.57336;SOR=0.55999;LSEQ=AGGTTTTTTTGTGTGTGTGG;RSEQ=TTTTTTTATTTTTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:715:12:0,12:58,639:697,12:0.0168:2,0:35.9:1:28.1:1:0.61274:0:51.6:24:0.0182:0:4 0/0:317:3:0,3:42,268:310,3:0.0095:2,0:39.3:1:21.3:1:1:0:57.3:2:0.0069:0:3.3 +7 41740067 . AT A 149 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.05187;SOR=1.83552;LSEQ=TTGTGTGTGTGGATTTTTTT;RSEQ=TTTTTTTTTTGGTGTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:582:27:0,27:25,528:553,27:0.0464:1,1:26.2:1:31.5:1:0.62244:0:58.9:54:0.0475:0.0034:0.4 0/1:256:21:0,21:14,221:235,21:0.082:2,1:22.1:1:30.4:1:0.6134:0:57.7:42:0.0843:0.0117:0.7 +7 41740079 . G T 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18526;SOR=0;LSEQ=ATTTTTTTATTTTTTTTTTT;RSEQ=GTGTTTTTTTTTTCCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:6:0,6:14,462:476,6:0.0124:1,0:9:1:25.8:1:1:0:60:2:0.009:0:1.7 0/0:212:0:0,0:6,201:207,0:0:1,0:21.8:1:29.9:1:1:0:59.2:16.25:1:0:0.6 +7 41740082 . G GT 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.86919;SOR=1.08938;LSEQ=TTTTTATTTTTTTTTTTGGT;RSEQ=TTTTTTTTTTCCTTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:32:1,31:12,414:426,32:0.0693:1,1:22.8:1:30.2:1:1:1.11:58:31:0.0723:0.0108:1.2 0/1:200:15:0,15:6,178:184,15:0.075:1,1:27.9:1:28.6:1:1:0:57.9:30:0.0806:0.005:1.1 +7 41740390 . G C 33 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=AGAGGGAAAGAAGGGGGAGA;RSEQ=AGAGGGAGAGAGGGAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:33.5:1:1:0:48:4:1:0:1.5 +7 41741672 . G T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAGCGTTCCTTCCCTCTC;RSEQ=GTTTCTTTCCCACACATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:9.5:1:34:0:1:0:60:4:0.1667:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:25.5:1:31:0:1:0:60:4:1:0:0 +7 41742179 . A G 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTCACATATACAGTACCCA;RSEQ=AATGTTTTGCAGTTCAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:605:0:0,0:59,546:605,0:0:2,0:23.9:1:31.3:1:1:0:60:85.429:1:0:0.1 0/1:233:15:3,12:23,195:218,15:0.0644:2,2:16.7:1:29.9:1:0.22615:2.11:60:30:0.0647:0:1 +7 42426790 . G GGACCCTTCCTT 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTGCAGGTTTTAGGGAG;RSEQ=GACCCTTCCTTGCCCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:30.7:1:1:0:60:4:1:0:0 +7 42427292 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTAGGGCCCACCCTAAT;RSEQ=TAGTATGACCTCATCTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:9,15:24,2:0.0769:2,2:23.5:1:30.5:1:1:1.63:60:4:0.08:0:1 0/0:11:0:0,0:4,7:11,0:0:2,0:31.7:1:31.8:1:1:0:60:22:1:0:0 +7 43288295 . TTCC T 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=28;MSI=10.000;MSILEN=3;SSF=0.00857;SOR=7.82576;LSEQ=TCCTCCTCCTCCTCCTCCTT;RSEQ=TCCTCCTCCTCCTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:5,0:14,0:14,5:0.1923:1,0:17.6:1:32.6:1:1:0:53.8:10:0.2381:0.0385:2.4 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:20:1:31.3:1:1:0:60:16:0.6667:0:1.3 +7 43288365 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCTCTTCCCCCATCTCC;RSEQ=CGTTCTCCTCCTGTTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:2,0:140,41:181,2:0.0109:2,0:16:1:32:0:1:0:60:4:0.0112:0:1 0/0:85:0:0,0:68,17:85,0:0:2,0:26.5:1:30.1:1:1:0:59.9:41.5:1:0:0.4 +7 43288484 . A G 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28669;LSEQ=CTGTGTGCATGTGAGGCCAC;RSEQ=ACCTCTAGACCCCAGTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:565:374:179,195:97,94:191,374:0.6619:2,2:26.6:1:30.9:1:0.53411:1.12392:59.9:61.333:0.6595:0:1.6 0/1:348:125:56,69:106,117:223,125:0.3592:2,2:24.4:1:29.4:1:0.65506:1.11595:60:30.25:0.3517:0:1.3 +7 43288513 . T G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1401;LSEQ=ACCCCAGTGACTTAGGGGCC;RSEQ=CCCTGCCTCCCCTCTAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:216:87,129:129,164:293,216:0.4244:2,2:27.9:1:31:1:0.41516:1.16596:60:53:0.424:0:2 0/1:289:27:10,17:115,146:261,27:0.0934:2,2:23.7:1:29.8:1:0.54487:1.33771:60:26:0.0919:0:2 +7 43299455 . A G 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAAATGTGAGTAGTTGCA;RSEQ=TCCTAGAATAATGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:42.3:1:32.8:1:1:0:60:8:0.5714:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:31:0:1:0:60:2:1:0:1 +7 43299616 . T C 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AACCACACCCAGGCACATCA;RSEQ=AGTCAAACTTCTGAAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:51:26:12,14:12,13:25,26:0.5098:2,2:30.5:1:32.9:1:1:1.07536:60:52:0.5098:0:1.1 0/0:68:0:0,0:32,36:68,0:0:2,0:30:1:28.3:1:1:0:60:33:1:0:0.1 +7 43299667 . GA G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.20139;SOR=0;LSEQ=AAATATAAAAGCAACCACAG;RSEQ=AAAAATGATATGTTGCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:7,20:27,2:0.069:2,2:15.5:1:29.8:1:0.48276:2.74:60:4:0.0714:0.0345:1 0/0:35:0:0,0:13,22:35,0:0:2,0:21.2:1:28.6:1:1:0:60:70:1:0:0.1 +7 43316879 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5125;SOR=0;LSEQ=GCTTCCACTGACTCCCACTG;RSEQ=CACCTGCCGCCATGACGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:18,19:37,2:0.0513:2,2:37.5:1:29.5:1:1:1.05:60:4:0.0541:0:1 0/0:26:0:0,0:11,15:26,0:0:2,0:28.2:1:31.2:1:1:0:60:52:1:0:0.1 +7 43774515 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16374;SOR=Inf;LSEQ=GAGAAGGCAGCATACGTCAG;RSEQ=GTTTTCTTCTATGCACTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:11,0:0:2,0:21.1:1:30.8:1:1:0:39.5:22:1:0:0 0/1:8:2:1,1:2,4:6,2:0.25:2,2:20:1:31.5:1:1:1.83:43.5:4:0.25:0:1 +7 43975601 . G A 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26354;SOR=2.75183;LSEQ=CTTGTGCCTCAGCCTCCTGA;RSEQ=TAGCTGGTTATAGGCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:0,4:0,10:10,4:0.2857:0,0:24.5:1:32.8:1:1:0:60:8:0.2857:0:1 1/0:15:8:0,8:0,7:7,8:0.5333:0,0:16.8:1:30.4:1:1:0:58.4:16:0.5333:0:1 +7 44664306 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50026;SOR=Inf;LSEQ=ACCAACCACCGTATCTGTAT;RSEQ=GGACCCAGCATAGCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,15:27,0:0:2,0:24.5:1:31:1:1:0:60:54:1:0:0 0/1:35:2:1,1:16,17:33,2:0.0571:2,2:38.5:1:28:1:1:1.06:60:4:0.0606:0:1 +7 45127176 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55298;SOR=0;LSEQ=TTTCTCATCTACAAAGCAGA;RSEQ=CCAGGATTAGAGTTGAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:2,1:75,15:90,3:0.0323:2,2:14:1:29.3:1:0.43629:2.46845:60:6:0.0326:0:1 0/0:52:0:0,0:40,12:52,0:0:2,0:21.3:1:31.4:1:1:0:60:104:1:0:0.1 +7 45127225 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15646;SOR=Inf;LSEQ=GGGGACCCTGTTGCCAGGCT;RSEQ=CTCCAGCTCCCCTCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:204:0:0,0:116,88:204,0:0:2,0:28.5:1:32.2:1:1:0:60:203:1:0:0.5 0/1:134:2:1,1:79,53:132,2:0.0149:2,2:14.5:1:24:0:1:1.48598:60:4:0.015:0:1.5 +7 45127231 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16598;SOR=Inf;LSEQ=CCTGTTGCCAGGCTGCTCCA;RSEQ=CTCCCCTCAGCAGCATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:119,96:215,0:0:2,0:28.6:1:32.5:1:1:0:60:106.5:0.9953:0:0.5 0/1:149:2:1,1:84,63:147,2:0.0134:2,2:12.5:1:31:0:1:1.33071:60:4:0.0135:0:1 +7 45127263 . T A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=7;SSF=0.15593;SOR=Inf;LSEQ=AGCATCAGAGCCCTGAGCCC;RSEQ=GAACCACCAGCCAAAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:138,132:270,0:0:2,0:24.1:1:31:1:1:0:60:89:0.9926:0:0.7 0/1:178:2:1,1:86,90:176,2:0.0112:2,2:21:0:32:1:1:1.05:60:4:0.0112:0:1.5 +7 45127282 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.31437;LSEQ=CTGAACCACCAGCCAAAACT;RSEQ=GTCACCCAAGGGCTTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:257:209:97,112:25,23:48,209:0.8132:2,2:24.6:1:31:1:0.52337:1.25392:60:103.5:0.8118:0:1.1 1/0:175:101:45,56:37,37:74,101:0.5771:2,2:28.1:1:30:1:0.54038:1.24288:60:202:0.5805:0:1.4 +7 45127332 . G A 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=3.9442;LSEQ=TGGGACATCCAGGGGGTCCT;RSEQ=AGACAAGGGGGTCCTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:18:8,10:79,108:187,18:0.0878:2,2:24.9:1:30.2:1:1:1.09:60:36:0.0891:0:1.7 0/1:105:29:12,17:31,45:76,29:0.2762:2,2:18.8:1:28.2:1:1:1.02:60:28:0.2718:0:1.8 +7 45381731 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49413;SOR=0;LSEQ=AGAACAGCAATACAGACTTG;RSEQ=AATGGGGTTACTTCCTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:24,16:40,2:0.0476:2,2:25.5:1:31:1:1:1.48518:51:4:0.0488:0:1.5 0/0:40:0:0,0:23,17:40,0:0:2,0:22.3:1:31.1:1:1:0:58.3:80:1:0:0.2 +7 45549709 . TT GG 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCCAGGTCTCAAGTAGG;RSEQ=CAGAAAATGCAAAACCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:33.5:1:27.8:1:1:0:60:4:0.6667:0:3 +7 45549712 . A T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGTCTCAAGTAGGTTC;RSEQ=GAAAATGCAAAACCCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:33.5:1:28:0:1:0:60:4:0.6667:0:3 +7 45551574 . A T 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54067;SOR=0;LSEQ=CCTCTTGTGATTTTCCATCC;RSEQ=CTGACCCTTGCAACCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:2,4:7,5:12,6:0.3333:2,2:26.2:1:29.7:1:0.61991:2.64037:60:12:0.3333:0:1 0/0:4:0:0,0:1,3:4,0:0:2,0:26.8:1:29:1:1:0:60:8:1:0:0 +7 45553520 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATCTCAGACTCCCAGCC;RSEQ=CTGGAACTGTGAGAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 45856117 . AG CC 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00794;SOR=Inf;LSEQ=CCAGCCTCTGGGACCCATGC;RSEQ=CGGCTCCCAGCGGCCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:26,31:57,0:0:2,0:32.1:1:30.9:1:1:0:41.2:114:1:0:0.1 0/1:37:5:3,2:18,14:32,5:0.1351:2,2:9.8:1:29.4:1:1:1.16:52.4:10:0.1351:0.027:0.8 +7 45856916 . G A 27 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GTCTCTTGCACCAGAAGGTG;RSEQ=CAGGATCCATTGGGAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:10.5:1:27:1:1:1:35:4:0.5:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:15.2:1:31:1:1:0:28.2:10:1:0:0 +7 45857752 . C T 24 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACACCCCAGGGGCAGTGG;RSEQ=AGTGCCCGTCTCTGATATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:44:1:24.5:1:1:1.14834:22:4:0.0667:0:1.5 0/0:13:0:0,0:9,4:13,0:0:2,0:40.8:1:32.1:1:1:0:21.5:26:1:0:0.2 +7 45857848 . G A 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.63903;SOR=0.76469;LSEQ=CTCTGAGCTGGACTTCTTTC;RSEQ=GTCCTTGTTGCAAGTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:17:6,11:20,27:47,17:0.2656:2,2:25.2:1:31:1:0.77456:1.35162:24.5:34:0.2656:0:3.1 0/1:37:8:3,5:14,15:29,8:0.2162:2,2:31.6:1:29.4:1:0.70133:1.53728:23.5:16:0.2286:0:3.3 +7 45857884 . GC TT 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3715;SOR=0.69135;LSEQ=GGGCCACCTTCACTTGGAAG;RSEQ=CAGGTCGTAGCACTTCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:31:10,21:28,39:67,31:0.3163:2,2:28.6:1:30.5:1:0.50406:1.50147:24.5:62:0.3163:0.0204:1.7 0/1:62:15:6,9:19,27:46,15:0.2419:2,2:25.7:1:30.1:1:1:1.05464:25.5:30:0.2586:0.0161:1.5 +7 45857885 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14866;SOR=Inf;LSEQ=GGCCACCTTCACTTGGAAGG;RSEQ=CAGGTCGTAGCACTTCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:30,39:69,0:0:2,0:32.6:1:31.8:1:1:0:21.9:68:1:0:0.1 0/1:62:2:0,2:19,27:46,2:0.0323:2,0:36.5:1:28.5:1:0.51152:0:24.5:4:0.0426:0:3.5 +7 45858486 . T C 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCCGGGCCTCGTGTGGC;RSEQ=GCAGGGAGGGGTCAGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:97,90:187,2:0.0106:2,2:8:0:29.5:1:1:1.07733:60:4:0.0109:0:1.5 0/0:83:0:0,0:46,37:83,0:0:2,0:21.2:1:29.5:1:1:0:29.7:40.5:1:0:0.1 +7 45858615 . AC A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19018;SOR=Inf;LSEQ=CGCAGGCCTGTGGGCCGAGT;RSEQ=TTGGTCCGGGCAGGGGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:42,97:139,0:0:2,0:23.4:1:33.1:1:1:0:30:138:1:0:0.1 0/1:108:2:2,0:46,60:106,2:0.0185:2,0:15:1:24:1:0.19522:0:21.5:4:0.0187:0.0093:0.5 +7 46780610 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28527;SOR=0.8423;LSEQ=CTGCATCCAGAGAGAAATTT;RSEQ=AAGCATATTTGAAAGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:171:95,76:148,128:276,171:0.3826:2,2:24.8:1:32:1:0.69724:1.08:60:170:0.3855:0:2 0/1:315:108:54,54:101,106:207,108:0.3429:2,2:26.8:1:30.3:1:0.90559:1.05:60:107:0.3429:0:2.1 +7 46780614 . C A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10577;SOR=1.27628;LSEQ=ATCCAGAGAGAAATTTTAAG;RSEQ=ATATTTGAAAGCAGGTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:220:126,94:121,115:236,220:0.4825:2,2:24.4:1:30.3:1:0.22168:1.27:60:54:0.4811:0:1.8 1/0:311:169:87,82:63,79:142,169:0.5434:2,2:27.1:1:28.7:1:0.25462:1.33:60:41.25:0.55:0:1.8 +7 46780714 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54277;SOR=0;LSEQ=CAGAGGGACATTGTCGAAAT;RSEQ=GTTTCCTACAGACAGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:2:1,1:44,147:191,2:0.0103:2,2:20:1:29.5:1:0.41289:3.31:60:4:0.0104:0:1 0/0:105:0:0,0:28,77:105,0:0:2,0:19:1:29.4:1:1:0:59.6:20:1:0:0.1 +7 46859675 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTTCCCTTTTAGGTAGC;RSEQ=GAAGCAGAGAGGAAAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:18,31:49,2:0.0392:2,2:27.5:1:30:1:1:1.70:40.5:4:0.0392:0:1 0/0:19:0:0,0:8,11:19,0:0:2,0:18.8:1:29.1:1:1:0:45.4:38:1:0:0.1 +7 47092258 . G GC 81 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAGAGCGCTCCCTGCGGA;RSEQ=TCGGCCGCCCGCCTCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:6,0:59,2:61,6:0.0896:1,0:6.3:1:31.7:1:1:0:23.7:12:0.0909:0.0746:0.8 0/0:6:0:0,0:6,0:6,0:0:0,0:26:1:30.3:1:1:0:29.8:5:1:0:0.5 +7 47092291 . G T 134 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04674;SOR=0;LSEQ=CTCTCCCCCAGGTCTCTCCC;RSEQ=ACGTCCCCACGCGGGGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:16:16,0:144,2:146,16:0.0988:1,1:23.8:1:33.5:1:1:0:35.3:32:0.1:0:1.1 0/0:42:0:0,0:42,0:42,0:0:1,0:18.5:1:29.6:1:1:0:40.6:41:1:0:0.1 +7 47092580 . T G 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.98397;LSEQ=TCGCCTTCGTCCGGTTTCAC;RSEQ=ACCGGAGCGACGCGCAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:70:24,46:138,253:391,70:0.1515:2,2:14.5:1:30.2:1:1:1.04536:25.7:69:0.1527:0:1.1 0/1:158:55:28,27:39,64:103,55:0.3481:2,2:14.5:1:28.9:1:0.13014:1.70:26.7:26.5:0.3419:0:1.1 +7 47092608 . C T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08225;SOR=7.10085;LSEQ=CGACGCGCAAGACGCCGAGG;RSEQ=CGCCATGGACTGGGCGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:1:0,1:194,333:527,1:0.0019:2,0:1:0:27:0:1:0:60:2:0.0019:0:1 0/1:225:3:0,3:102,120:222,3:0.0133:2,0:8.3:1:21.3:1:0.25321:0:50.3:2:0.0091:0:1.3 +7 47092671 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60234;SOR=2.03265;LSEQ=GCAGATGGCGCGCTATGGCC;RSEQ=CCGGGACCTGCCTCGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:407:2:2,0:132,273:405,2:0.0049:2,0:1:0:26.5:1:0.10785:0:60:4:0.0051:0:1 0/1:201:2:1,1:83,116:199,2:0.01:2,2:15.5:1:28.5:1:1:1.40:22.5:4:0.01:0:1.5 +7 47092673 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11149;SOR=Inf;LSEQ=AGATGGCGCGCTATGGCCGC;RSEQ=GGGACCTGCCTCGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:394:0:0,0:125,268:393,0:0:2,0:25.1:1:30.2:1:1:0:39.7:77.6:0.9974:0:0.2 0/1:198:2:1,1:78,116:194,2:0.0101:2,2:12:0:30:1:1:1.48:60:4:0.0103:0:1.5 +7 47092677 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10953;SOR=Inf;LSEQ=GGCGCGCTATGGCCGCCGGG;RSEQ=CCTGCCTCGCAGCAGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:120,255:375,0:0:2,0:24.2:1:29.9:1:1:0:40:92.75:1:0:0.1 0/1:186:2:1,1:71,113:184,2:0.0108:2,2:38.5:1:30.5:1:1:1.59:44.5:4:0.0109:0:3 +7 47092710 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCAGGAAGAGCCAAGCG;RSEQ=CAGGTCCTGGGGCGGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:37,147:184,2:0.0108:2,2:11.5:1:31:1:0.36774:3.93:31.5:4:0.011:0:1 0/0:77:0:0,0:22,55:77,0:0:2,0:17.7:1:30.9:1:1:0:34.1:154:1:0:0.2 +7 47093009 . T C 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00018;SOR=10.25673;LSEQ=CTCGCTACAGGAGGTCTCCC;RSEQ=ACATCCGGTCTTCCCGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:3,2:42,2:44,5:0.102:1,2:13.8:1:31.2:1:0.04675:12.48045:38:10:0.1042:0:1.2 1/0:20:11:11,0:9,0:9,11:0.55:0,0:21.7:1:31.1:1:1:0:45.5:22:0.55:0:1 +7 47093211 . G A 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56063;SOR=3.27626;LSEQ=CAAGAGGGAATCCAAGTCCA;RSEQ=GTCGCGATCCAAGAGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:1:1,0:204,108:312,1:0.0032:2,0:1:0:26:0:1:0:60:2:0.0033:0:1 0/1:192:2:1,1:106,84:190,2:0.0104:2,2:20:0:31.5:1:1:1.26036:20:4:0.0105:0:1.5 +7 47272406 . C T 114 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00879;SOR=0;LSEQ=CACCCTAAGGGGCCCTAATC;RSEQ=GATATGACCATGTCCTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:18.2:1:33.1:1:1:0:60:22:1:0:1.1 0/1:4:1:1,0:3,0:3,1:0.25:0,0:15:0:33:0:1:0:60:2:0.25:0:1 +7 47272496 . AC A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52561;SOR=0;LSEQ=AAGGTCAGAGTTATGCCACC;RSEQ=AAGCCAAGGAATGCCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:36,28:64,2:0.0303:2,2:24:1:30.1:1:1:1.28077:60:4:0.0308:0.0152:1 0/0:40:0:0,0:22,18:40,0:0:2,0:30.1:1:31.9:1:1:0:58.8:80:1:0:0.1 +7 47467864 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTCAGCCCCATGCAGGC;RSEQ=CAGCTTTTAGCACCTCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:28.5:1:33:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 47468573 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCACAGACCAGCAACAC;RSEQ=AGCAGGAGAAGCAGAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:32:1:31.5:1:1:1.12:60:4:0.1053:0:1 0/0:7:0:0,0:2,5:7,0:0:2,0:26.9:1:29:1:1:0:60:6:1:0:0.6 +7 47800327 . T C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAAACAATCCAATTATAC;RSEQ=TTTAATTATTTTAAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13:1:34:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 47802173 . GC G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATATTGGCAATACCATTT;RSEQ=ACAGGAACTCCTTGCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:33.1:1:1:0:60:4:1:0.5:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 47802311 . C G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00838;SOR=0.12304;LSEQ=AAAAATCTTTCCAACTCCCA;RSEQ=CTGATTTCTGAAGGTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:29,0:3,1:4,29:0.8788:2,1:21.9:1:30.7:1:0.12121:0:60:8.667:0.8667:0:1.3 0/1:11:5:4,1:5,1:6,5:0.4545:2,2:20.6:1:33.2:1:1:1.22474:60:10:0.4545:0:1.2 +7 47802407 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12639;SOR=Inf;LSEQ=GCCTCCTTTAGTGAAGTCAG;RSEQ=TGCCTGAGGCTGGGCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:127,57:184,0:0:2,0:23.5:1:32.3:1:1:0:60:60.333:1:0:0.6 0/1:102:2:1,1:70,30:100,2:0.0196:2,2:29.5:1:27.5:1:0.51757:2.31175:60:4:0.0196:0:1 +7 47802472 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.09104;LSEQ=GGGGGGCTGGGGTGGGTCAC;RSEQ=CTTATTCTACTGGATATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:324:287:139,148:17,19:36,287:0.8858:2,2:26.4:1:30.5:1:1:1.05:59.9:30.889:0.8825:0:1.8 0/1:223:92:45,47:66,65:131,92:0.4126:2,2:25.1:1:30.2:1:0.89201:1.06021:59.8:184:0.4163:0:1.8 +7 47802508 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.09651;LSEQ=ATCACTGTTCCTGGGCCCTG;RSEQ=CACCACTCTCAGCCCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:295:266:114,152:12,17:29,266:0.9017:2,2:26.1:1:29.6:1:1:1.06:60:52.2:0.9:0:1.9 0/1:188:88:39,49:40,59:99,88:0.4681:2,2:27.4:1:28.6:1:0.65694:1.17:59.1:43:0.4674:0:1.8 +7 47802516 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56404;SOR=3.11571;LSEQ=TCCTGGGCCCTGCCACCACT;RSEQ=TCAGCCCTGGTGCTGTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:1,0:111,167:278,1:0.0036:2,0:1:0:27:0:0.40143:0:53:2:0.0036:0:3 0/1:180:2:1,1:72,106:178,2:0.0111:2,2:19.5:1:27:1:1:1.47:60:4:0.0112:0:1 +7 47802635 . C T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01094;SOR=0.13204;LSEQ=CTCACGGTAGCAGGTGGTGA;RSEQ=AGAGGACATGTCATTGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:27:2,25:0,4:4,27:0.871:0,2:24.1:1:27.6:1:1:0:60:12.5:0.8621:0:1.8 0/1:11:5:0,5:0,6:6,5:0.4545:0,0:37:1:28.6:1:1:0:60:10:0.4545:0:2 +7 47802663 . G A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.04916;SOR=0.14346;LSEQ=ATGTCATTGTCGCAGTCACT;RSEQ=AGGACACTGGTTCTCATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:19:2,17:0,2:2,19:0.9048:0,2:22.7:1:31.1:1:1:0:60:38:0.9048:0:2.2 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:15.8:1:29.6:1:1:0:60:10:0.5556:0:2 +7 47802710 . A G 110 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TCTGTGCCTGGACCTCAGCT;RSEQ=TAGGCCTGGCCCCATTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:21.8:1:33.3:1:1:0:60:20:1:0:2.4 1/0:2:1:0,1:0,1:1,1:0.5:0,0:50:0:30:0:1:0:60:2:0.5:0:2 +7 47802771 . C T 77 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTTGAGCTACCTGACT;RSEQ=TTCCCAGTTGGCCAGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:19:1:29.8:1:1:0:60:12:1:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 47802808 . T C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CACATCCCAGTGAATGATCA;RSEQ=CATCCTGCTCTCATCTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:41.3:1:32:1:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 47802835 . T C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTCATCTCATAGCCAGC;RSEQ=GATCAGTCTGTTCACCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:17.7:1:32:0:1:0:60:6:1:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 48114609 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07977;SOR=Inf;LSEQ=ACTTGCTGAAGACAAGGCAA;RSEQ=GTGATAAGGTATCTAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:19,0:0:2,0:24.3:1:30.1:1:1:0:60:18:1:0:0 0/1:8:2:1,1:2,4:6,2:0.25:2,2:31:1:29:1:1:1.83:60:4:0.25:0:1 +7 49852999 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26667;SOR=0;LSEQ=CTGATCCAGAGGCTTGGCTG;RSEQ=GGCCTGAGAATTTGCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:1,2:24,6:30,3:0.0909:2,2:17.3:1:29.7:1:0.13856:7.35065:60:6:0.0938:0:1 0/0:22:0:0,0:17,5:22,0:0:2,0:21.5:1:29.6:1:1:0:60:21:1:0:0 +7 50358752 . G T 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17642;SOR=Inf;LSEQ=ATGAGAAAAGCTTCCCTGGG;RSEQ=CCGGAAGTCACAGTGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:72,179:251,0:0:2,0:25:1:31.5:1:1:0:59.8:82.667:0.996:0:0.1 0/1:183:2:1,1:61,119:180,2:0.0109:2,2:6.5:1:24:1:1:1.94:60:4:0.0112:0:1 +7 50367232 . A T 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08752;SOR=7.12221;LSEQ=CACACTTCTTCTTTCTCATC;RSEQ=GGGAAGGAAAGCCCCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:683:1:0,1:402,280:682,1:0.0015:2,0:1:0:26:0:0.41142:0:60:2:0.0015:0:1 0/1:483:5:1,4:285,190:475,5:0.0104:2,2:8.8:1:28.4:1:0.16318:5.97925:59.2:10:0.0107:0:1.2 +7 50367388 . A C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12508;SOR=Inf;LSEQ=AGCGGCCTCTGTGCCTGTGA;RSEQ=ACCTTTATCTCTTTGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:62,277:339,0:0:2,0:22.9:1:30.8:1:1:0:59.9:55.5:1:0:0.1 0/1:186:2:1,1:43,141:184,2:0.0108:2,2:10:0:33:0:0.41813:3.25:60:4:0.0108:0:1 +7 50444040 . G A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13002;SOR=0;LSEQ=TGTAACCCCAGGTGCATCCC;RSEQ=AGGCCTGCCACCGAAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:7,0:11,0:11,7:0.3889:0,0:31.7:1:29.1:1:1:0:55:6:0.3529:0:1.1 0/0:6:0:0,0:5,1:6,0:0:2,0:17.7:1:30.8:1:1:0:60:12:1:0:0 +7 50444181 . G GT 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.39369;SOR=1.37173;LSEQ=CTGCTGTGTTGTTTTGTTGA;RSEQ=TTTTTTTTTTGCAATGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:22:19,3:213,36:249,22:0.0809:2,2:22.7:1:31.2:1:1:1.07:59.1:44:0.0824:0:0.5 0/1:167:18:13,5:119,30:149,18:0.1078:2,2:20.2:1:28.5:1:0.53882:1.52141:60:36:0.1084:0.0419:0.2 +7 50450446 . C T 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGGGCTGTCTGGGTGTCC;RSEQ=GGGATTCCTCCACTCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:0:0,0:130,422:552,0:0:2,0:24:1:30.1:1:1:0:60:109.4:0.9982:0:0.2 0/1:296:38:12,26:82,176:258,38:0.1284:2,2:19.4:1:29.1:1:1:1.00944:60:76:0.1306:0:1.2 +7 50450456 . C A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04042;SOR=Inf;LSEQ=CTGGGTGTCCCGGGATTCCT;RSEQ=CACTCTGCCCGCCTGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:0:0,0:98,369:467,0:0:2,0:23.6:1:31.3:1:1:0:60:65.714:1:0:0.1 0/1:245:3:2,1:69,172:241,3:0.0122:2,2:10.7:1:23.3:1:0.20367:4.95:60:6:0.0124:0:3.3 +7 50454452 . G A 26 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTATTATATAATGCAAAT;RSEQ=TAAGATATATTTATATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:30:1:26.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 50454648 . A G 50 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGCATAGACTGAGGCCT;RSEQ=CTCTGGAGGCAAATCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:38.3:1:31.7:1:1:0:56.3:6:0.6:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 50454736 . A G 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGCATCCACGTTATAACAC;RSEQ=GCAGTGGCTCGTTTTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:2,1:4,0:4,3:0.4286:0,2:38:1:31.3:1:0.42857:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 50454939 . AT A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.50592;SOR=0.66058;LSEQ=TTTTAGCTCTCAAGGGTAGA;RSEQ=TTTTTTTTTAACTTTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:18:17,1:277,22:299,18:0.0568:2,1:24.2:1:31.3:1:1:1.35:60:36:0.0573:0.0063:0.6 0/1:157:6:5,1:142,9:151,6:0.0382:2,2:21.5:1:30:1:0.33071:3.1193:60:12:0.0382:0.0127:0.8 +7 50454980 . A T 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28054;LSEQ=GTAATAATTGTATTGCATGC;RSEQ=TTCCCCTTACACAGAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:253:188,65:306,129:435,253:0.3677:2,2:23.9:1:31.3:1:0.292:1.22:60:83.333:0.3693:0:1.2 0/1:421:59:44,15:249,113:362,59:0.1401:2,2:22.5:1:29.5:1:0.44604:1.33:60:18.667:0.1369:0:1.2 +7 50455179 . C A 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.02674;SOR=0;LSEQ=CTGTACCCAGGTAAGCGCTG;RSEQ=TGCTCGGAGGCCAGCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:8:2,6:142,308:450,8:0.0175:2,2:20.3:1:32:1:1:1.38223:60:16:0.0177:0:1.1 0/0:284:0:0,0:89,193:282,0:0:2,0:24:1:31.8:1:1:0:60:564:0.993:0:0.1 +7 50455209 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.13649;SOR=Inf;LSEQ=GCCAGCCTGGTGGGCTCTCC;RSEQ=CCCAGCACGGTGGGGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:60,231:291,0:0:2,0:23.2:1:31.1:1:1:0:60:40.571:1:0:0.1 0/1:171:2:1,1:37,132:169,2:0.0117:2,2:19.5:1:31:1:0.39608:3.53:60:4:0.0118:0:1 +7 50459320 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00012;SOR=0.22689;LSEQ=TAGAATTAATCTCTAGGAAG;RSEQ=GCCTGGCTCTTGTAGGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:56:56,0:118,3:121,56:0.3164:1,1:25.7:1:30.4:1:0.55254:0:60:112:0.32:0:1.1 0/1:74:7:7,0:63,4:67,7:0.0946:2,0:14:1:28.7:1:1:0:60:14:0.0986:0:1 +7 50459588 . T TA 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.36814;SOR=1.53148;LSEQ=GTTAAATGTTTGCTGTCTCT;RSEQ=AAAAAAAAACTATGTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:12:5,7:147,365:512,12:0.0229:2,2:21.6:1:28.9:1:0.34271:1.77:60:24:0.0234:0.0057:0.3 0/1:289:10:2,8:82,196:278,10:0.0346:2,2:25.7:1:27.1:1:0.72881:1.6708:60:9:0.0316:0.0035:0.2 +7 50459624 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11603;SOR=Inf;LSEQ=GGGTGTTTTAGATGCAAGTA;RSEQ=AAATGAGTTGAGGGTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:33,268:301,0:0:2,0:23.7:1:32.2:1:1:0:59.8:36.625:1:0:0.1 0/1:156:2:1,1:24,129:153,2:0.0128:2,2:19:1:28:1:0.29744:5.29:60:4:0.013:0:1.5 +7 50467583 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGACCGGTTCCGGAGGTGGC;RSEQ=GCGCCCCACTCACTGTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:294,63:357,0:0:2,0:24.4:1:30.8:1:1:0:60:34.7:1:0:0.1 0/1:194:18:14,4:143,33:176,18:0.0928:2,2:21.4:1:29.9:1:0.75351:1.23666:60:17:0.0904:0:1.1 +7 50467767 . C A 266 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0;SOR=0.4872;LSEQ=CGCCCGCTGGTGCAGACGCC;RSEQ=CCGGGCGGTTCCGAGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1356:498:226,272:389,467:856,498:0.3673:2,2:25:1:29.7:1:1:1.00252:60:54.333:0.366:0:1.1 0/1:726:160:72,88:254,311:565,160:0.2204:2,2:24.8:1:29:1:1:1.00:60:159:0.2236:0:1.1 +7 50468384 . C T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09689;SOR=Inf;LSEQ=CAGGAAAAGCACAAGGACTG;RSEQ=CGCCTTCTCGCTCCCGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:12,217:229,0:0:2,0:25.6:1:31:1:1:0:60:27.625:1:0:0.1 0/1:104:2:1,1:19,83:102,2:0.0192:2,2:7.5:1:26.5:1:0.34914:4.28:60:4:0.0198:0:1.5 +7 50493201 . C A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15143;SOR=Inf;LSEQ=TGTTATTTTGGTAGAGCCAC;RSEQ=TGCTCCCCACACCTGCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:27,35:62,0:0:2,0:22.5:1:31.8:1:1:0:60:124:1:0:0.1 0/1:40:2:1,1:18,20:38,2:0.05:2,2:28:0:32:0:1:1.11:60:4:0.05:0:1.5 +7 50493208 . C A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.5175;SOR=0;LSEQ=TTGGTAGAGCCACCTGCTCC;RSEQ=CACACCTGCTACCCCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:24,31:55,2:0.0351:2,2:6.5:1:29:1:1:1.29:60:4:0.0357:0:1.5 0/0:37:0:0,0:18,19:37,0:0:2,0:25.3:1:30.1:1:1:0:60:74:1:0:0.2 +7 50738265 . C T 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAGTTTTGTTGTCCTGGGTG;RSEQ=GTGCTCATCTCAGGCAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:42:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:30.5:1:1:0:60:4:1:0:1 +7 50739151 . G A 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50877;SOR=0;LSEQ=GATCCAGCTAACTATCCCAC;RSEQ=TAGACCAGCAAATGATGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:7,0:10,0:10,7:0.4118:0,0:23.3:1:31.4:1:1:0:57.9:14:0.4375:0:1.1 0/0:2:0:0,0:2,0:2,0:0:0,0:18:1:29.5:1:1:0:60:4:1:0:0 +7 50739320 . T G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCATAACAGCTTCAGCCT;RSEQ=GGCAAGGCGTCCAACTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:185,11:196,2:0.0101:2,2:22.5:1:30.5:1:0.11783:16.14892:60:4:0.0104:0:1 0/0:61:0:0,0:56,5:61,0:0:2,0:24.5:1:30.3:1:1:0:60:122:1:0:0.1 +7 50739383 . G T 55 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07958;SOR=4.45963;LSEQ=AGGAGATGGATAAAACGGGT;RSEQ=GCCAGTGCCACTTTCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:516:2:0,2:363,151:514,2:0.0039:2,0:34:1:15:1:0.08751:0:60:0:0:0:4 0/1:234:4:1,3:161,69:230,4:0.0171:2,2:5.3:1:27.5:1:0.08781:6.93598:60:8:0.0175:0:1.8 +7 50739455 . T C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=2.33991;LSEQ=AAGATAATCTGACGTTTTAG;RSEQ=GTCCACAAAAGCTTCTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1032:403:197,206:297,327:624,403:0.3905:2,2:26.2:1:31.1:1:0.70149:1.05:60:402:0.393:0:1.3 1/0:565:339:176,163:117,105:222,339:0.6:2,2:25.5:1:30.1:1:0.86321:1.03194:60:66.8:0.5996:0:1.4 +7 50739472 . C T 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TAGTGTCCACAAAAGCTTCT;RSEQ=TATTTATTGGGTTGTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1038:0:0,0:464,574:1038,0:0:2,0:26.8:1:32.7:1:1:0:60:128.75:1:0:0.6 0/1:563:26:13,13:253,284:537,26:0.0462:2,2:25.5:1:28.4:1:0.8419:1.12:58.9:12:0.0432:0:2.5 +7 50739526 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00036;SOR=1.71671;LSEQ=TCCTGTGTTGACTTTAAAGC;RSEQ=GCTCAGAGACATCGCCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:522:216:65,151:89,215:304,216:0.4138:2,2:24.1:1:31.9:1:0.84605:1.04:59.9:432:0.4186:0:1.6 1/0:281:154:46,108:38,89:127,154:0.548:2,2:21.9:1:29.8:1:1:1.00243:59.8:153:0.5543:0:1.8 +7 50739588 . C G 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00972;SOR=2.35664;LSEQ=CAAAGACAAAAAATCCCCAC;RSEQ=AAAGAGGCTCACAATAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:56:0,56:4,83:87,56:0.3916:1,1:26.9:1:32.1:1:0.15526:0:59.3:55:0.3873:0:1.6 1/0:53:32:1,31:2,19:21,32:0.6038:2,1:22.8:1:31.1:1:0.55537:3.1891:60:64:0.6154:0:1.7 +7 50741391 . C T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTACCACTGCCCCCACGAC;RSEQ=CCTGGCAACCAGAATGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:19:1:29.5:1:1:1.73:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 50825947 . C A 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00783;SOR=Inf;LSEQ=CCAACACCCCGAGAGTAGAC;RSEQ=AGCACACTTCACACGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:4,3:7,4:11,7:0.3889:2,2:31.6:1:31.1:1:1:1.29262:60:14:0.3889:0:1.4 1/1:7:7:4,3:0,0:0,7:1:0,2:19.7:1:30:1:1:0:60:14:1:0:1.1 +7 50825976 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACACGCTGACCCGGACCA;RSEQ=TGGACAGAAGTTACAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:20:0:32:1:1:1.13389:60:4:0.1176:0:2.5 0/0:7:0:0,0:4,3:7,0:0:2,0:39.1:1:31.7:1:1:0:60:14:1:0:1.1 +7 50826694 . C CA 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTTCAAGACCAGTTATGG;RSEQ=ATATAGCGTGACCCTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:0:32.5:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 50826889 . C CA 29 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACAGAGTGAGACTCTGCCT;RSEQ=AAAAAAAAAAAAAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:29.5:1:1:0:39:4:1:0:0.5 +7 51449823 . T G 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=TGCACTCCAGCCTGCCAAAC;RSEQ=GCATCTCAAAACAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:16,1:17,0:0:1,0:18.4:1:31.1:1:1:0:48.5:16:1:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:24:0:27:1:1:0:32.5:4:0.5:0:1 +7 51449830 . C CAAAACAAAAAACAA 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=29;MSI=6.000;MSILEN=1;SSF=0.02849;SOR=Inf;LSEQ=CAGCCTGCCAAACTGCATCT;RSEQ=AAAACAAAAAACAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:20,2:22,0:0:2,0:18.9:1:32.8:1:1:0:44.4:44:1:0:0 0/1:5:2:1,1:3,0:3,2:0.4:0,2:32:0:28.1:1:0.4:0:32.5:4:0.4:0:1 +7 51450099 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGTTCTCCTGGTACTCTG;RSEQ=CCCCTTCCTGACCCCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:69,94:163,2:0.012:2,2:35:1:32.5:1:1:1.36:22:4:0.0122:0:1 0/0:71:0:0,0:31,40:71,0:0:2,0:12.7:1:28.7:1:1:0:31.3:142:1:0:0.2 +7 51450101 . C A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0798;SOR=7.30646;LSEQ=TGTTCTCCTGGTACTCTGTC;RSEQ=CCTTCCTGACCCCTCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:1:1,0:67,88:155,1:0.0064:2,0:1:0:25:0:0.4359:0:60:2:0.0065:0:1 0/1:66:3:2,1:27,36:63,3:0.0455:2,2:21:1:26:1:0.57793:2.63:24:6:0.0455:0:1 +7 51450113 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09783;SOR=Inf;LSEQ=ACTCTGTCCCCTTCCTGACC;RSEQ=CTCCCTGCAGCCGCGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:25,41:66,0:0:2,0:6.3:1:30.7:1:1:0:24.1:132:0.9851:0:0.1 0/1:31:2:1,1:12,17:29,2:0.0645:2,2:8:0:31:1:1:1.40:22:4:0.0645:0:1 +7 51450416 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGACCACGATGATGCTTTC;RSEQ=TCTCCGTCATGTCTCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:19,14:33,2:0.0571:2,2:12:0:32.5:1:1:1.34517:60:4:0.0571:0:1.5 0/0:13:0:0,0:10,3:13,0:0:2,0:12.7:1:30.5:1:1:0:36.2:26:1:0:0 +7 51450476 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.5352;SOR=0;LSEQ=TCAGATGATGTCAGGCCCAG;RSEQ=CCCTCAGTGCCCTGTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:2:1,1:41,42:83,2:0.0235:2,2:40:1:32.5:1:1:1.02:21:4:0.0247:0:1 0/0:48:0:0,0:27,21:48,0:0:2,0:35:1:28.1:1:1:0:35.4:23:1:0:0.1 +7 51450572 . A G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.52768;SOR=0;LSEQ=ACCACATCTGGTGGCCCATG;RSEQ=GTGGCGGTCACGATCTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:17,19:36,2:0.0526:2,2:9:0:32.5:1:1:1.11:22:4:0.0526:0:2 0/0:22:0:0,0:9,13:22,0:0:2,0:18.2:1:30.1:1:1:0:33.5:44:1:0:0.3 +7 51450578 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13269;SOR=Inf;LSEQ=TCTGGTGGCCCATGAGTGGC;RSEQ=GTCACGATCTTCAGCAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:20,21:41,0:0:2,0:23.2:1:31:1:1:0:30:40:1:0:0.3 0/1:24:2:0,2:10,12:22,2:0.0833:2,0:35.5:1:29.5:1:0.49275:0:22:4:0.0833:0:1 +7 51450625 . G C 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.43106;SOR=0.55334;LSEQ=GGCCCTGGCAGGGCGCACCA;RSEQ=GGTCACCCCTACCAGGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:16:8,8:53,33:86,16:0.1569:2,2:30.3:1:31.3:1:0.41548:1.59835:30.3:32:0.1569:0:1.1 0/1:43:4:3,1:22,17:39,4:0.093:2,2:34.3:1:32.3:1:0.62807:2.28:28.8:8:0.0952:0:1 +7 51450658 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11898;SOR=Inf;LSEQ=CAGGATAACTGGACCATCAG;RSEQ=CAGATCCTGAGCGAGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:57,37:94,0:0:2,0:31:1:31.5:1:1:0:29.5:93:1:0:0.2 0/1:50:2:1,1:30,18:48,2:0.04:2,2:25.5:1:27.5:1:1:1.64896:27.5:4:0.0426:0:1 +7 51450765 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCAACAAGGACCGAAAG;RSEQ=AGTCCAGCTCAGAGGCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:36,46:82,2:0.0238:2,2:16.5:1:28:1:1:1.27:21:4:0.0247:0:1 0/0:41:0:0,0:15,26:41,0:0:2,0:15.1:1:28.7:1:1:0:21.6:82:1:0:0.1 +7 51450917 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=24.917;LSEQ=GCCCAGACACTCCTGAGCTC;RSEQ=GATACCAAGGAGCAGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:4:2,2:100,93:193,4:0.0203:2,2:29.5:1:30.3:1:1:1.07485:26.3:8:0.0204:0:1.3 0/1:102:35:15,20:37,30:67,35:0.3431:2,2:27.2:1:30.2:1:0.29795:1.63633:27.2:70:0.3431:0:1.1 +7 51451068 . G A 23 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.54946;SOR=3.36612;LSEQ=CACTACAGGAACTGACACAG;RSEQ=TGGTGTCTGGCACTGCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:1,0:19,7:26,1:0.037:2,0:27:0:27:0:1:0:26:2:0.0385:0:1 0/1:17:2:2,0:10,5:15,2:0.1176:2,0:15:1:23.5:1:1:0:29:4:0.1333:0:1 +7 51452216 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.07143;SOR=Inf;LSEQ=CCCCTCCAAGGTTTGTTCTG;RSEQ=CCCTGCCCTGATTCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:8,7:15,0:0:2,0:33.7:1:31.8:1:1:0:32.1:30:1:0:0.1 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:36:1:28:1:1:2.44949:28.5:4:0.3333:0:1 +7 52528708 . C T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTGCAGTGAGCCGAGATCG;RSEQ=GTCACTGCACTCTGGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:16.5:1:30.5:1:1:0:50.5:8:0.5:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:16:0:31:0:1:0:60:2:1:0:1 +7 52528757 . C CA 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.28268;SOR=0;LSEQ=ACGACTCCATCCCCCGCCCA;RSEQ=AAAAAAAAAAAGAAATTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:4:4,0:18,0:18,4:0.1818:1,0:12.8:1:30.9:1:1:0:60:8:0.1905:0.1364:0.3 0/0:10:0:0,0:10,0:10,0:0:0,0:17.8:1:32.2:1:1:0:60:20:1:0:0.1 +7 52528898 . T C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.69266;LSEQ=AATCAGATTTTCAGGTGGGT;RSEQ=TCTTTAGTCTAGTGGTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:144:109,35:85,40:125,144:0.5353:2,2:27.4:1:31.9:1:0.17453:1.46:60:23:0.5328:0:1.2 1/0:189:143:96,47:26,20:46,143:0.7566:2,2:26.9:1:30.7:1:0.21657:1.57:60:142:0.7676:0:1.3 +7 52528952 . A AT 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.91007;SOR=1.03181;LSEQ=AACTCTGAAATATAATTTTG;RSEQ=TTTTTTTTTTTCTGGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:55:37,18:254,173:427,55:0.1132:2,2:26.6:1:31.1:1:0.30656:1.40:60:54:0.1154:0:0.8 0/1:318:37:25,12:146,129:275,37:0.1164:2,2:29.7:1:31:1:0.1142:1.84:60:74:0.1201:0:0.8 +7 52528964 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29815;SOR=1.54318;LSEQ=TAATTTTGATTTTTTTTTTT;RSEQ=TGGAGACAGTGTAATCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:12:8,4:320,240:560,12:0.0209:2,2:12.5:1:25.8:1:0.56998:1.50:59.8:5:0.0189:0:2.3 0/1:376:12:6,6:189,175:364,12:0.0319:2,2:30:1:24.7:1:1:1.07976:60:3:0.0255:0:2.4 +7 52528967 . G T 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12359;SOR=3.76733;LSEQ=TTTTGATTTTTTTTTTTCTG;RSEQ=AGACAGTGTAATCCGACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:592:2:0,2:334,255:589,2:0.0034:2,0:1:0:25:1:0.18868:0:60:4:0.0035:0:1.5 0/1:396:5:1,4:206,185:391,5:0.0126:2,2:8.6:1:24.8:1:0.19693:4.43875:60:10:0.013:0:1.6 +7 52528988 . A C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=2.90718;LSEQ=AGACAGTGTAATCCGACCAT;RSEQ=TTTAAAAACAACGTTCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:708:366:200,166:173,168:341,366:0.5169:2,2:26.8:1:31.6:1:0.32717:1.17:59.9:13.64:0.509:0:1.3 1/0:469:355:186,169:57,56:113,355:0.7569:2,2:26.2:1:30.5:1:0.7464:1.08:59.9:28.583:0.7522:0:1.2 +7 52529160 . G A 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGAATGTATGGGAGATAC;RSEQ=TGGAATAAATGGGAACTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:1,54:55,0:0:1,0:23.6:1:31.9:1:1:0:60:54:1:0:0.7 0/1:33:12:0,12:1,19:20,12:0.3636:1,0:18.7:1:29.9:1:1:0:60:11:0.3548:0:1.8 +7 52529181 . C T 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26531;SOR=0;LSEQ=TGGAATAAATGGGAACTTCG;RSEQ=TGAGGCCTGAAGATGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:36:36:1,35:0,0:0,36:1:0,1:28:1:29.8:1:1:0:60:17:1:0:1.1 1/1:13:12:1,11:0,1:1,12:0.9231:0,2:25.4:1:29.7:1:1:0:60:24:0.9231:0:1.4 +7 53722738 . A G 137 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=54.83213;LSEQ=TTAATCAGAATAAAAATATA;RSEQ=AATATCAATACTTATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:65,7:72,2:0.027:2,0:15.5:1:35:0:1:0:60:4:0.027:0:1 1/0:34:21:19,2:11,2:13,21:0.6176:2,2:21.3:1:31.4:1:0.62718:1.70:60:42:0.6176:0:1 +7 53722820 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5562;SOR=0;LSEQ=ACAAATTCAAATATAGTCTA;RSEQ=AAATAGACTGGCATATTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:0,3:160,90:250,3:0.0119:2,0:17:1:25.7:1:0.04865:0:60:6:0.0121:0:1 0/0:143:0:0,0:81,62:143,0:0:2,0:26.1:1:30.6:1:1:0:60:46.667:1:0:0.4 +7 53722880 . T A 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=69.25689;LSEQ=AAAACAATTCAAAAAATTCT;RSEQ=TAATTTTCTAGACTTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:5:3,2:132,156:288,5:0.0171:2,2:19.4:1:28.6:1:0.66451:1.77:60:10:0.0174:0:1 1/0:164:90:40,50:33,41:74,90:0.5488:2,2:24.3:1:29.1:1:1:1.00606:60:180:0.5488:0:1 +7 53722906 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12318;SOR=Inf;LSEQ=TTCTAGACTTACTTTAGGGA;RSEQ=ACTGAGCAATACAGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:119,163:282,0:0:2,0:26.2:1:32.1:1:1:0:60:39.286:1:0:0.1 0/1:153:2:1,1:64,86:150,2:0.0131:2,2:36:1:29:1:1:1.34:60:4:0.0132:0:2 +7 53854866 . G A 134 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0;LSEQ=TTAACTCAGTTAGGGATTTG;RSEQ=ATCCTGCTCCTAATCCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:723:21:15,6:436,265:701,21:0.029:2,2:16.6:1:30.7:1:0.49538:1.52:39.7:42:0.0295:0:1.2 0/0:439:0:0,0:277,161:438,0:0:2,0:27:1:30.4:1:1:0:49.4:86.6:0.9977:0:0.1 +7 54023644 . C T 31 d5;v3;MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGAGTAAGGATAGATTT;RSEQ=GTTATTTCTTGCAAACTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:5:1:31:1:1:0:40:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:9:0:31:0:1:0:36:2:1:0:1 +7 55086755 . G T 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCGCGGCCGCAGCAGCCTCC;RSEQ=CCCCCCGCACGGTGTGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:13:0:33.5:1:1:0:60:4:1:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:31.5:1:1:0:60:4:1:0:1.5 +7 55086780 . A C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCACGGTGTGAGCGCCCG;RSEQ=CGCGGCCGAGGCGGCCGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:30.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55086848 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCAGACCGGACGACAGG;RSEQ=CACCTCGTCGGCGTCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:67,2:69,2:0.0282:1,2:14.5:1:27:1:0.0833:27.55605:60:4:0.029:0:1 0/0:19:0:0,0:19,0:19,0:0:1,0:19.5:1:31.8:1:1:0:60:18:1:0:0.2 +7 55086908 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23986;SOR=4.30156;LSEQ=AACGCCACAACCACCGCGCA;RSEQ=GGCCCCCTGACTCCGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:1,0:238,47:285,1:0.0035:2,0:18:0:33:0:1:0:60:2:0.0036:0:1 0/1:134:2:1,1:97,35:132,2:0.0149:2,2:22.5:1:27:1:0.46661:2.74672:60:4:0.0149:0:1 +7 55086974 . C T 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19171;SOR=3.73612;LSEQ=CTCTTCGGGGAGCAGCGATG;RSEQ=GACCCTCCGGGACGGCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:2:1,1:379,327:706,2:0.0028:2,2:13.5:1:31.5:1:1:1.15878:60:4:0.0029:0:1 0/1:382:4:2,2:206,172:378,4:0.0105:2,2:25.5:1:30.3:1:1:1.1971:60:8:0.0107:0:1 +7 55087083 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14268;SOR=Inf;LSEQ=GGGCGTGTCTCGCCGGCTCC;RSEQ=GCGCCGCCCCCGGATCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:0:0,0:78,247:325,0:0:2,0:20.4:1:30.7:1:1:0:60:80.25:0.9969:0:0.2 0/1:199:2:1,1:66,130:196,2:0.0101:2,2:42:1:29.5:1:1:1.96:60:4:0.0104:0:1 +7 55087092 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15649;SOR=Inf;LSEQ=TCGCCGGCTCCCGCGCCGCC;RSEQ=CCGGATCGCGCCCCGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:54,178:232,0:0:2,0:19:1:31.6:1:1:0:60:45.4:0.9956:0:0.2 0/1:153:2:1,1:47,104:151,2:0.0131:2,2:24.5:1:28.5:1:0.53044:2.20:60:4:0.0133:0:1 +7 55087102 . GC G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.14196;SOR=Inf;LSEQ=CCGCGCCGCCCCCGGATCGC;RSEQ=CCCGGACCCCGCAGCCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:30,123:153,0:0:2,0:15.4:1:31.5:1:1:0:60:29.6:1:0:0.2 0/1:93:2:1,1:24,66:90,2:0.0215:2,2:43:0:31.5:1:0.47181:2.71:60:4:0.0222:0:1 +7 55087139 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.2;SOR=Inf;LSEQ=CCGCCCAACCGCGCACCGGC;RSEQ=CACCGGCTCGGCGCCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:1,6:7,0:0:2,0:6.1:1:32.1:1:1:0:60:14:1:0:0.1 0/1:8:3:1,2:2,3:5,3:0.375:2,2:9:1:27.7:1:1:1.28664:60:6:0.375:0:1 +7 55088415 . T C 63 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=GGAAGGTTTAATTGCACAAT;RSEQ=CCAACCTTGAGCTGCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:4,4:0.5:2,2:33.8:1:31.8:1:1:1:60:8:0.5:0:1.3 1/1:2:2:1,1:0,0:0,2:1:0,2:3:0:31.5:1:1:0:60:4:1:0:1.5 +7 55209637 . C A 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.36364;SOR=Inf;LSEQ=ATTTTCATCTACCACCCACC;RSEQ=CTTTAAATTTCAACATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:3,0:7,0:7,3:0.3:0,0:25.3:1:31.7:1:1:0:60:6:0.3:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:20:0:30:0:1:0:60:2:1:0:1 +7 55209936 . G T 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03074;SOR=9.38629;LSEQ=TGTTTTATTTTAGTTTTTCT;RSEQ=CATTTCTCAGTATTTCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:709:1:0,1:606,102:708,1:0.0014:2,0:29:0:13:0:0.14528:0:60:0:0:0:2 0/1:305:4:1,3:236,65:301,4:0.0131:2,2:11:1:25.3:1:0.0359:10.77779:60:8:0.0132:0:1 +7 55210188 . G A 84 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00082;SOR=18.29263;LSEQ=AGAAAATCTAAGTGGAGAAA;RSEQ=GCCTGGGCAGAATTCCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:463:1:1,0:55,407:462,1:0.0022:2,0:1:0:25:0:0.12095:0:60:2:0.0022:0:1 0/1:183:7:1,6:26,150:176,7:0.0383:2,2:24:1:30:1:1:1.03979:60:14:0.0387:0:1 +7 55210733 . G C 112 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAGAGTGTTGAACCCCGT;RSEQ=AGGCATGAGAGCACAGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:11,0:9,1:10,11:0.5238:2,0:21:1:32.6:1:0.47619:0:60:22:0.5238:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55213918 . A C 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54747;SOR=0.36853;LSEQ=CAGGGCTGTAGCACTCAGGA;RSEQ=CTGCCTCCCTGCCCTGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:2,0:2,6:0.75:0,2:27.2:1:30.3:1:1:0:60:12:0.75:0:1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:15:1:29:1:1:1:60:4:0.5:0:1 +7 55214348 . C T 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.33966;LSEQ=AACAACCCTGCCCTGTGCAA;RSEQ=GTGGAGAGCATCCAGTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1625:1143:647,496:258,222:480,1143:0.7034:2,2:25.3:1:30.6:1:0.2985:1.12:59.9:53.429:0.7034:0:1.1 0/1:852:380:215,165:261,211:472,380:0.446:2,2:23.8:1:29.6:1:0.72885:1.05:60:189:0.45:0:1.2 +7 55214443 . G A 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.23471;LSEQ=CCTGGGCAGCTGTAAGTGTC;RSEQ=CATACACACTATCTCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1280:158:50,108:419,703:1122,158:0.1234:2,2:24.1:1:29.8:1:0.1859:1.28715:60:51.667:0.1229:0:1.1 0/1:688:22:7,15:271,395:666,22:0.032:2,2:25.1:1:30.2:1:0.5099:1.46937:60:44:0.0325:0:1.1 +7 55214535 . A T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00622;SOR=Inf;LSEQ=ATGTTTAGTAAGTCACATTA;RSEQ=TCAGAAACAAAAAGTAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:8,275:283,0:0:1,0:22.2:1:31.2:1:1:0:59.8:93.333:1:0:0.1 0/1:112:4:0,4:6,102:108,4:0.0357:2,0:25:1:29.5:1:1:0:60:8:0.0364:0:1 +7 55214647 . G T 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.53807;LSEQ=CAGCCCAGCTGGTTGGCAGT;RSEQ=CAGGCCACCGGAGGCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:18:0,18:0,14:14,18:0.5625:1,1:25.1:1:30.3:1:1:0:60:17:0.5484:0:1.1 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:8:1:26:1:1:0:60:3:0.6:0:1 +7 55215018 . A C 85 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGTCAGCGTGGCGCCCTG;RSEQ=CTCAGGCCAGCACTGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:0,6:1:0,2:29.8:1:33.2:1:1:0:60:12:1:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:29:0:32:0:1:0:60:2:1:0:4 +7 55217047 . C G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCTCTCTCACTCTCACTGT;RSEQ=TCTCTTTCTGTCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:32.5:1:30:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55218903 . T C 257 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.33285;LSEQ=GATTGTCTTCATTTATTGAA;RSEQ=GTGCTTAACTCAGGCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:397:271:237,34:100,24:124,271:0.6826:2,2:23.5:1:31.9:1:0.09167:1.67:60:44.167:0.683:0:1.1 0/1:144:60:44,16:65,19:84,60:0.4167:2,2:21.2:1:30.6:1:0.69393:1.2421:60:120:0.4196:0:1.1 +7 55218915 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07809;SOR=Inf;LSEQ=TTATTGAATGTGCTTAACTC;RSEQ=GGCCCGGGAAAGGGCGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:517:0:0,0:404,113:517,0:0:2,0:23.6:1:30.6:1:1:0:60:50.7:1:0:0.6 0/1:201:2:1,1:139,58:197,2:0.01:2,2:21.5:1:27.5:1:0.50612:2.38471:60:4:0.0102:0:1 +7 55219159 . C T 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.26178;LSEQ=CTGAAGACTCCAAAGAGTTA;RSEQ=TTTATTACAGGGTCAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:351:247:20,227:11,92:103,247:0.7037:2,2:21.4:1:30.5:1:0.41802:1.35585:59.8:48.4:0.7076:0:1.1 0/1:115:44:4,40:6,65:71,44:0.3826:2,2:19.3:1:29.6:1:1:1.08:60:88:0.3894:0:1 +7 55219290 . T C 135 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00167;SOR=0.04312;LSEQ=AAGTGAACATCAGCAGGGGC;RSEQ=GGGCGCGGTGGCTCACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:26:0,26:0,6:6,26:0.8125:0,1:25:1:28.9:1:1:0:53.4:25:0.8065:0:1.7 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:17:0:25:0:1:0:60:2:0.1429:0:1 +7 55219307 . C G 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.01129;SOR=0;LSEQ=GGCTGGGCGCGGTGGCTCAC;RSEQ=CCTATAATCCCAGCACTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:0,3:3,17:0.85:0,1:25.9:1:33.2:1:1:0:48.6:34:0.85:0:1.9 0/0:3:0:0,0:0,3:3,0:0:0,0:16.7:1:31.7:1:1:0:60:6:1:0:0 +7 55219568 . AAAC A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=CAGAGCGAGACTCCGTCTCA;RSEQ=AACAACAACAACAACAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:28:1:30.5:1:1:0:43:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:28.9:1:1:0:48:4:1:0.5:0 +7 55220177 . A G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32242;LSEQ=GTCTGCAAGTGCTCTGCGAC;RSEQ=TCCCTGGGAAATGATCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1181:854:575,279:224,102:326,854:0.7231:2,2:23:1:30.4:1:0.67649:1.06553:60:84.4:0.7238:0:1.1 0/1:569:260:173,87:197,112:309,260:0.4569:2,2:23.1:1:29.6:1:0.5369:1.13:60:520:0.4602:0:1.1 +7 55220349 . G A 64 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01535;SOR=10.53806;LSEQ=GCACAGGCCCCCGGGAGAGC;RSEQ=ACTGCCTGGTAAGATGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:926:1:1,0:307,615:922,1:0.0011:2,0:1:0:25:0:0.33369:0:60:2:0.0011:0:1 0/1:443:5:3,2:157,281:438,5:0.0113:2,2:13.8:1:27.6:1:0.35679:2.68:60:4:0.0092:0:1.2 +7 55220905 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCTGAGCTGCACCCTGC;RSEQ=CTCAAGGGGTCCTGAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:32:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55221447 . C G 135 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCATCTATACGTTAGTAAA;RSEQ=AGACGTATTTTTATCATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:18,0:5,0:5,18:0.7826:0,1:27.6:1:32.6:1:1:0:57.6:17:0.7727:0:1.6 1/1:1:1:1,0:0,0:0,1:1:0,0:6:0:34:0:1:0:60:2:1:0:1 +7 55221469 . C T 89 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.61579;LSEQ=GACGTATTTTTATCATAATC;RSEQ=ATAAATTATGATAGGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:7,0:23,0:23,7:0.2333:1,0:25.7:1:31.9:1:1:0:60:14:0.2414:0:1.7 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:9:0:32:0:1:0:60:2:0.3333:0:1 +7 55221550 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00829;SOR=Inf;LSEQ=CTTTCTGACTCTGCAGAGGG;RSEQ=GCCAGCTGGGTTTTCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:130,0:130,0:0:1,0:24.1:1:32.4:1:1:0:60:42.333:1:0:0.2 0/1:34:3:2,1:31,0:31,3:0.0882:1,2:17:1:28.7:1:0.08824:0:60:6:0.0938:0:1 +7 55221619 . G T 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17216;SOR=5.61427;LSEQ=TAACTTGGGCTTTCTGACGG;RSEQ=AGTCAACACCGTGCTGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:1:0,1:320,24:344,1:0.0029:2,0:1:0:26:0:0.07246:0:60:2:0.003:0:4 0/1:124:2:1,1:107,15:122,2:0.0161:2,2:10:0:30:1:0.24233:6.93899:60:4:0.0165:0:1.5 +7 55221627 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07167;SOR=Inf;LSEQ=GCTTTCTGACGGGAGTCAAC;RSEQ=CCGTGCTGCGCTTCCTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:358,38:396,0:0:2,0:22.4:1:30.5:1:1:0:60:98:0.9949:0:0.3 0/1:146:2:1,1:124,20:144,2:0.0137:2,2:8.5:1:28.5:1:0.26783:6.07495:60:4:0.0138:0:1 +7 55221643 . T C 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28736;SOR=2.7848;LSEQ=CAACACCGTGCTGCGCTTCC;RSEQ=CCGTGTGTGGCGCTGAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:2:1,1:450,80:530,2:0.0038:2,2:30:1:29.5:1:0.28157:5.59645:60:4:0.0038:0:1 0/1:192:2:1,1:154,36:190,2:0.0104:2,2:33:0:32:0:0.34909:4.23325:60:4:0.0105:0:1 +7 55221655 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00746;SOR=1.53955;LSEQ=GCGCTTCCTCCGTGTGTGGC;RSEQ=CTGAGTGTACTTACCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:651:170:147,23:387,94:481,170:0.2611:2,2:24.5:1:30.8:1:0.08241:1.55:60:169:0.2649:0:1.1 0/1:261:92:76,16:126,40:166,92:0.3525:2,2:23.3:1:29.3:1:0.26974:1.51:60:184:0.3525:0:1.1 +7 55222033 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02517;SOR=Inf;LSEQ=CTGGCTTGCTACCGAGGAGC;RSEQ=GGCAGGTGGTGGCCATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:603:0:0,0:229,374:603,0:0:2,0:24.7:1:30.2:1:1:0:59.9:32.5:1:0:0.1 0/1:251:3:1,2:96,152:248,3:0.012:2,2:16:1:29.7:1:1:1.262:59.3:6:0.0121:0:1.3 +7 55222094 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17037;SOR=5.64573;LSEQ=GCACAGGGCAGATCTGGGTG;RSEQ=CCAGGCCACCTCACAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:553:1:0,1:268,284:552,1:0.0018:2,0:41:0:31:0:1:0:60:2:0.0018:0:1 0/1:197:2:1,1:99,95:194,2:0.0102:2,2:8.5:1:27:1:1:1.0419:60:4:0.0103:0:1 +7 55222433 . G T 80 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00298;SOR=13.61712;LSEQ=CCAGGGTTTAGGGAAATTGT;RSEQ=ACATAAAATAATTCCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1335:1:1,0:649,681:1330,1:7e-04:2,0:6:0:13:0:0.48835:0:60:0:0:0:1 0/1:692:7:3,4:335,350:685,7:0.0101:2,2:23.9:1:28.6:1:1:1.27574:60:14:0.0103:0:1.7 +7 55222593 . A C 137 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=4.000;MSILEN=1;SSF=0.00054;SOR=0;LSEQ=CAGATTTGTGTACATGAAAA;RSEQ=TTTTACATTCCGTATGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:21:12,9:301,373:674,21:0.0301:2,2:20.3:1:31.2:1:0.27375:1.65:59:9.5:0.0278:0:1.2 0/0:308:0:0,0:135,172:307,0:0:2,0:23.2:1:29.8:1:1:0:59.9:75.75:1:0:0.3 +7 55222610 . G GA 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.29835;LSEQ=AAAATTTTACATTCCGTATG;RSEQ=AAAAAAAAAACACAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:668:304:142,162:148,158:306,304:0.4551:2,2:26.3:1:30.7:1:0.68612:1.06852:59.8:303:0.4683:0.0659:0.4 0/1:276:55:28,27:91,108:199,55:0.1993:2,2:25.3:1:29.6:1:0.54293:1.23:59.6:110:0.206:0.0036:0.3 +7 55222755 . G A 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21641;LSEQ=TAGGAAAACACTTCGAGCCT;RSEQ=AGATACCAAGAGCAGATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1137:661:368,293:271,205:476,661:0.5814:2,2:25:1:29.4:1:0.71626:1.05251:60:329.5:0.5847:0:1.1 0/1:537:124:68,56:225,187:412,124:0.2309:2,2:21.3:1:28.5:1:1:1.01:60:123:0.2316:0:1.1 +7 55222954 . G A 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15942;LSEQ=GGACCAGCCTGGCCAACAGG;RSEQ=TGAAACCTCGTCTCTACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:127:13,114:8,64:72,127:0.6382:2,2:27.1:1:31.7:1:0.81568:1.09564:50.7:62.5:0.6345:0:1 0/1:55:12:1,11:2,41:43,12:0.2182:1,2:28:1:30.9:1:0.5296:1.84:49.7:24:0.2222:0:1 +7 55223101 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09858;SOR=Inf;LSEQ=GCTGAGATCACACCACTGCA;RSEQ=TCCAGCCTGGGTGACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:192,56:248,0:0:2,0:22.5:1:32.1:1:1:0:44.8:48.6:1:0:0.4 0/1:114:2:1,1:78,34:112,2:0.0175:2,2:20.5:1:28.5:1:0.52166:2.27558:48.5:4:0.0179:0:3.5 +7 55223176 . G A 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34558;LSEQ=ATAGAGCTCCTAAAAATAAC;RSEQ=CAGAAGTCTGCTATTAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:925:644:395,249:160,120:280,644:0.6962:2,2:26.1:1:30.4:1:0.2427:1.19:59.8:213.667:0.699:0:1.1 0/1:498:220:126,94:159,119:278,220:0.4418:2,2:26.3:1:29.4:1:1:1.00:59.7:440:0.4462:0:1.2 +7 55223790 . T C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22428;SOR=0.46859;LSEQ=AGAAGATAAAGCTGTAAAGC;RSEQ=AGGTTAGGCAATGGGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:41:4,37:3,16:19,41:0.6833:2,2:25:1:32.8:1:0.66819:1.71731:59:82:0.6949:0:1 1/0:14:7:0,7:0,7:7,7:0.5:0,0:32:1:31.7:1:1:0:60:14:0.5:0:1 +7 55224143 . C T 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15126;SOR=3.67807;LSEQ=TCCGGTGACCGGAATTCCTT;RSEQ=CTGCTTCCCTCTGCCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:2:1,1:403,64:467,2:0.0043:2,2:17:1:19.5:1:0.25823:6.25601:60:1:0.0022:0:1.5 0/1:193:3:1,2:157,33:190,3:0.0155:2,2:14:1:28:1:0.08524:9.34854:60:6:0.0159:0:1 +7 55224152 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02844;SOR=Inf;LSEQ=CGGAATTCCTTCCTGCTTCC;RSEQ=TCTGCCTGTGGATCCCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:544:0:0,0:437,107:544,0:0:2,0:22.5:1:31.5:1:1:0:59.9:107.8:1:0:0.1 0/1:240:3:1,2:184,52:236,3:0.0125:2,2:10:1:26.3:1:0.12887:7.00083:60:6:0.0128:0:1 +7 55225140 . G C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.61126;LSEQ=GGCGGGAGACATGCGGAATC;RSEQ=CAGCGGAAGGCGGGAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:11:10,1:18,0:18,11:0.3793:1,2:12.5:1:31.5:1:0.37931:0:58.1:22:0.3793:0:2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:7.5:1:27.5:1:1:0:60:4:0.5:0:1.5 +7 55225170 . G C 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGGAGGCAGCTGTGAACT;RSEQ=TGGCTCGGCCTGCGTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:45,2:0,0:0,47:1:0,1:24.5:1:32.9:1:1:0:59.6:94:1:0:1.3 1/1:4:4:4,0:0,0:0,4:1:0,0:30:1:31:1:1:0:60:8:1:0:1.5 +7 55227781 . A T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02962;SOR=Inf;LSEQ=GAAACAAAGTTTTCAGGGAT;RSEQ=CATTGTTTTTATAATTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:310,65:375,0:0:2,0:22.9:1:28.7:1:1:0:60:374:1:0:0.1 0/1:169:3:1,2:132,34:166,3:0.0178:2,2:15.7:1:25:1:0.11507:7.63666:60:6:0.0178:0:1 +7 55228053 . A T 293 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0885;LSEQ=TAAGTCACCGCTTTCTGTTT;RSEQ=GTTTATGGAGTTGGTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:801:776:247,529:9,14:23,776:0.9688:2,2:25.8:1:30.6:1:0.49855:1.37627:60:154.2:0.9686:0:1.1 1/0:389:285:94,191:37,66:103,285:0.7326:2,2:24.1:1:29.6:1:0.62735:1.13871:60:284:0.7339:0:1.1 +7 55228085 . T A 29 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19265;SOR=5.13465;LSEQ=TGGTTCTAATGGGTCCTTTA;RSEQ=TTGTATTTAGAATATTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:503:1:0,1:105,396:501,1:0.002:2,0:13:0:19:0:1:0:60:0:0:0:3 0/1:197:2:1,1:57,138:195,2:0.0102:2,2:6.5:1:29:1:0.50321:2.41:60:4:0.0103:0:2 +7 55228160 . T G 161 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00127;SOR=0;LSEQ=TTAAGAAGCAAATTAAAATC;RSEQ=TAAGATTCCTAACTGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:31:2,29:1,87:88,31:0.2605:1,2:22.2:1:32.5:1:0.16586:5.89:60:62:0.2605:0:1.7 0/0:28:0:0,0:2,26:28,0:0:2,0:22.9:1:30.4:1:1:0:60:56:1:0:0.5 +7 55228173 . C T 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=0.04407;LSEQ=TAAAATCTTAAGATTCCTAA;RSEQ=TGTGAAATTACCATGTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:91:89:3,86:0,2:2,89:0.978:0,1:24.8:1:30:1:1:0:59.5:21.25:0.977:0:1.3 1/0:23:15:0,15:1,7:8,15:0.6522:2,1:18.6:1:30.3:1:0.34783:0:60:30:0.6522:0:1 +7 55228217 . A T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04407;SOR=Inf;LSEQ=ATTAAAACTTTTTCCAGATC;RSEQ=TTACCATTCAATGGGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:2,44:46,0:0:1,0:23.1:1:31.3:1:1:0:60:45:0.9783:0:0.7 0/1:13:2:1,1:0,11:11,2:0.1538:0,2:26:1:25:1:0.15385:0:60:4:0.1538:0:1 +7 55229015 . A G 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1633;SOR=3.16638;LSEQ=CACAACTACTTTGTCCTTCC;RSEQ=GTCACGGTCGGCCTCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:7:7,0:38,0:38,7:0.1556:1,0:9.1:1:29.9:1:1:0:60:14:0.1556:0:1 0/1:8:3:2,1:5,0:5,3:0.375:0,2:36.3:1:30:1:0.375:0:60:6:0.375:0:1 +7 55229255 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00257;SOR=1.47852;LSEQ=CTGCTGGGGCCCGGAGCCCA;RSEQ=GGACTGCGTCTCTTGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1666:165:97,68:839,657:1496,165:0.099:2,2:25.8:1:30.5:1:0.56276:1.12:60:40.25:0.098:0:1.1 0/1:894:125:74,51:428,340:768,125:0.1398:2,2:24.3:1:29.4:1:0.49712:1.15:60:61.5:0.1393:0:1.2 +7 55229414 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08876;SOR=Inf;LSEQ=ACAGGCATTCTGTTTGATTT;RSEQ=CTCTTCCTTTTATTCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:25,431:456,0:0:2,0:22.9:1:30.5:1:1:0:60:113:1:0:0.1 0/1:194:2:1,1:13,178:191,2:0.0103:2,2:9:0:31:1:0.14017:13.23:60:4:0.0104:0:1 +7 55229543 . T C 121 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.16833;LSEQ=AATAAGCAAGTATTATTGCC;RSEQ=AATATAATCCAATAATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:14:0,14:0,41:41,14:0.2545:1,1:13.4:1:32:1:1:0:60:28:0.2545:0:1.1 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:31:1:22.5:1:1:0:60:1:0.1667:0:1 +7 55230840 . A G 39 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTGCTGGAGGGTAGAACT;RSEQ=TGCTTGACTACTAGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:29.3:1:25:1:1:0:60:2:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55231357 . A T 46 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.03265;SOR=9.16879;LSEQ=CAAGTTATTTGGAATTTTGA;RSEQ=GAGGTGATTTGTGTTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:1:0,1:520,165:685,1:0.0015:2,0:1:0:25:0:0.24198:0:60:2:0.0015:0:1 0/1:303:4:1,3:217,82:299,4:0.0132:2,2:8.5:1:23.3:1:0.06842:7.87618:60:3:0.0101:0:1 +7 55231575 . G A 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34286;SOR=2.93734;LSEQ=GAAGGGCCTTCACAGAAGCC;RSEQ=AACAGTGATGATGGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:2:2,0:57,261:318,2:0.0063:2,0:1:0:27.5:1:0.03352:0:60:4:0.0063:0:1 0/1:165:3:3,0:39,123:162,3:0.0182:2,0:8:1:24.3:1:0.01562:0:60:6:0.0188:0:1 +7 55232333 . A G 36 d5;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGAGTGGACAAAACCAAC;RSEQ=TGAGAGAACTTAGCCAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:1,3:0.75:0,2:23:1:23:1:1:0:60:2:0.6667:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55232726 . G T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.34756;SOR=0.3626;LSEQ=GCAGAATGCAATAATGTAGA;RSEQ=AATATCATTTCTTTCATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:19:19,0:10,0:10,19:0.6552:0,1:25.9:1:31.4:1:1:0:58:18:0.6429:0:1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:19.5:1:30.5:1:1:0:60:4:0.4:0:1 +7 55233159 . AT A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.04714;SOR=Inf;LSEQ=AAAGTGAAGGAGAACAGAAC;RSEQ=TTCCTCTCTTGCAAATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:95,340:435,0:0:2,0:22.8:1:30.4:1:1:0:59.9:61.143:1:0:0.1 0/1:247:3:2,1:69,175:244,3:0.0121:2,2:27.3:1:29.7:1:0.19931:5.03:60:6:0.0122:0.004:0.7 +7 55235215 . G A 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGTGGTGGTGGTGATGGTG;RSEQ=TGAGGAGGTGGGAGTCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:41:0:31.5:1:1:0:43.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55235345 . C T 27 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGTCACAATGGTAGTGG;RSEQ=GATGATGGTGTTGGTGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:27.5:1:1:0:60:4:1:0:1 +7 55235804 . C A 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTCGCCTTTGGGTATA;RSEQ=CAACATGCCAGCTCTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:28:1:31:1:1:0:59.8:8:0.5:0:2.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55236020 . T C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00182;SOR=Inf;LSEQ=TCTCTGCATCAATATCTCTA;RSEQ=ATCAGTATCTCTGTGTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:93,1:94,0:0:1,0:26.1:1:31.6:1:1:0:60:93:1:0:0.1 0/1:26:4:4,0:21,1:22,4:0.1538:1,0:34.8:1:33:1:1:0:60:8:0.1538:0:1 +7 55236175 . G A 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCAAGATTTAAATTAAAAAT;RSEQ=TTAGTGGTCATTTTTCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1268:0:0,0:752,516:1268,0:0:2,0:25.7:1:32.4:1:1:0:59.9:139.889:1:0:0.1 0/1:666:18:11,7:361,284:645,18:0.027:2,2:23.6:1:27.7:1:0.81104:1.24:60:36:0.0274:0:1.2 +7 55236774 . A G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCCAGACGAGGGGGAGG;RSEQ=ACCCTGGAGGAATAGCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:39:1:32.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55236796 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGAGGAATAGCTATTT;RSEQ=TTTTTTTTTTTTGTCGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:8:1:29.5:1:1:0:56:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55237913 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05367;SOR=Inf;LSEQ=GAGACCTGGAGAGCAGAGAT;RSEQ=GAAACTGTTAGGATCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:0:0,0:427,29:456,0:0:2,0:22.7:1:28.9:1:1:0:59.8:151:1:0:0.1 0/1:138:2:1,1:127,9:136,2:0.0145:2,2:33.5:1:30.5:1:0.14017:13.4396:60:4:0.0145:0:1 +7 55237977 . T C 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=56.41443;LSEQ=AGGCCTCTCACATATTGAAA;RSEQ=GTACTTGTCCATCTTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1418:1:1,0:910,507:1417,1:7e-04:2,0:15:0:34:0:1:0:60:2:7e-04:0:1 0/1:652:25:15,10:414,213:627,25:0.0383:2,2:23.5:1:30.1:1:0.526:1.2952:60:50:0.0388:0:1.1 +7 55238087 . C T 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30156;LSEQ=AATGATGGCAGCGTGTCCCA;RSEQ=CAGAGCGGGAGCCCAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2220:300:143,157:999,918:1917,300:0.1351:2,2:25.2:1:30.4:1:0.15369:1.19468:59.9:36.5:0.1336:0:1.2 0/1:1067:48:20,28:500,518:1018,48:0.045:2,2:24.4:1:28.7:1:0.37573:1.35097:60:96:0.0457:0:1.1 +7 55238253 . G T 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTGAGCCTCATGCCTTCAC;RSEQ=TGTCTGTTCCCCCCGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1384:0:0,0:478,902:1380,0:0:2,0:26.5:1:31.4:1:1:0:59.9:64.714:0.9971:0:0.2 0/1:732:53:21,32:271,408:679,53:0.0724:2,2:23.7:1:29.8:1:1:1.01212:60:52:0.0721:0:1.8 +7 55238268 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00202;SOR=1.59622;LSEQ=TTCACGTGTCTGTTCCCCCC;RSEQ=CTTTTCCTTTCTGCCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1165:124:43,81:331,710:1041,124:0.1064:2,2:23.4:1:30.1:1:0.54188:1.14:60:248:0.1084:0:1.1 0/1:582:93:31,62:186,303:489,93:0.1598:2,2:24.5:1:28.9:1:0.4149:1.2273:60:92:0.16:0:1.5 +7 55238464 . T G 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGTCAGAAACCTGCAGGGAC;RSEQ=CCATGCTGCCAGCCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:0,7:2,26:28,7:0.2:2,0:18.1:1:33.1:1:1:0:60:14:0.2:0:1 0/1:5:1:0,1:0,4:4,1:0.2:0,0:4:0:30:0:1:0:60:2:0.2:0:1 +7 55238874 . T A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=1.91889;LSEQ=TTCACTTCCTACAGATGCAC;RSEQ=GGGCCAGGTCTTGAAGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1295:136:74,62:694,464:1158,136:0.105:2,2:25.8:1:31.1:1:0.23065:1.25291:60:135:0.1054:0:1.1 0/1:631:116:66,50:275,240:515,116:0.1838:2,2:25.6:1:29.6:1:0.53664:1.15:59.9:57:0.183:0:1.1 +7 55238941 . G A 112 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=8.78025;LSEQ=CTCTGTGTCACATGGACCTC;RSEQ=TCAAGAATGACCACACTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1097:4:4,0:421,672:1093,4:0.0036:2,0:2.3:1:24.3:1:0.02233:0:60:3:0.0028:0:1 0/1:449:14:6,8:182,253:435,14:0.0312:2,2:28.5:1:29.6:1:1:1.04:60:28:0.0315:0:1.5 +7 55238990 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.08361;SOR=Inf;LSEQ=AGATGCTTTCCTGCATTTCT;RSEQ=ACTGTCCTCTGTCCTGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:429:0:0,0:46,383:429,0:0:2,0:24.2:1:32.4:1:1:0:60:84.8:1:0:0.1 0/1:175:2:1,1:33,140:173,2:0.0114:2,2:30.5:1:27:1:0.35172:4.19:60:4:0.0114:0:1 +7 55240461 . G C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06312;SOR=0.2645;LSEQ=ATTTTAAAAAATGAGGAAAA;RSEQ=TGTGCCTGGTAGGGGACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:82:46:45,1:33,3:36,46:0.561:2,1:25.2:1:32.8:1:0.31476:4.02:59.3:92:0.561:0:1.1 0/1:12:3:3,0:9,0:9,3:0.25:0,0:27.3:1:31.7:1:1:0:60:6:0.25:0:1 +7 55241755 . G A 122 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=45.24055;LSEQ=AGGTAAGGTCCCTGGCACAG;RSEQ=CCTCTGGGCTGGGCCGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:831:1:1,0:292,537:829,1:0.0012:2,0:1:0:30:0:0.35301:0:60:2:0.0012:0:1 0/1:386:20:7,13:126,238:364,20:0.0518:2,2:25.7:1:28.3:1:1:1.02:60:40:0.0525:0:1.1 +7 55242609 . A G 230 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16645;LSEQ=CTCTGCTCTAGACCCTGCTC;RSEQ=TCTCCACATCCTAAATGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:229:136:4,132:3,90:93,136:0.5939:1,1:26:1:32.5:1:1:1.09954:60:44.333:0.5938:0:1.1 0/1:118:23:1,22:5,90:95,23:0.1949:2,1:22.8:1:31:1:1:1.22026:60:22:0.1913:0:1 +7 55242782 . T C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TAGTTTCTTGACACGCATGA;RSEQ=GAGTGAGTGCTCTTGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:2,12:0,0:0,14:1:0,2:18.6:1:30.4:1:1:0:60:28:1:0:1.3 1/1:2:2:1,1:0,0:0,2:1:0,2:13:1:29.5:1:1:0:60:4:1:0:1 +7 55248231 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATAGGGAGCCTGGGGGC;RSEQ=CAGCACAGAGAGACCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55248787 . T C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00805;SOR=0.11498;LSEQ=GATGCACCCAGGAGGGGCCC;RSEQ=CTCCCACTGCATCTGTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:28:28,0:3,0:3,28:0.9032:0,1:21.9:1:29.9:1:1:0:60:13:0.8966:0:1.1 1/0:12:6:6,0:6,0:6,6:0.5:0,0:22.2:1:32.2:1:1:0:60:12:0.5:0:1 +7 55248893 . C A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTATTTTGAAACTCAAGAT;RSEQ=GCATTCATGCGTCTTCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:306,14:320,0:0:1,0:23.7:1:32.3:1:1:0:60:105.667:1:0:0.4 0/1:88:11:11,0:70,7:77,11:0.125:2,0:29.3:1:26.7:1:0.58918:0:60:22:0.131:0:1.1 +7 55248926 . T C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.14437;LSEQ=CTTCACCTGGAAGGGGTCCA;RSEQ=GTGCCCCTCCTTCTGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:253:204,49:270,57:327,253:0.4355:2,2:24:1:31.7:1:0.58856:1.13751:59.8:252:0.436:0:1.1 0/1:220:22:18,4:147,50:197,22:0.1:2,2:21.5:1:30.9:1:0.60511:1.53:58.5:44:0.1009:0:1.5 +7 55249063 . G A 310 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1861;LSEQ=TGCCTCACCTCCACCGTGCA;RSEQ=CTCATCACGCAGCTCATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1526:1294:655,639:119,111:230,1294:0.848:2,2:24.8:1:30:1:0.77495:1.04587:59.9:70.889:0.8495:0:1.1 1/0:823:419:225,194:193,208:401,419:0.5091:2,2:24.8:1:29.1:1:0.12422:1.25:59.9:138.667:0.5111:0:1.1 +7 55249208 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00356;SOR=Inf;LSEQ=GATACGGGGAGGGGAGATAA;RSEQ=GAGCCAGGATCCTCACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:973:0:0,0:322,651:973,0:0:2,0:22.9:1:31.3:1:1:0:60:59.813:1:0:0.1 0/1:468:5:4,1:157,306:463,5:0.0107:2,2:9.8:1:25.4:1:0.04983:7.76:60:10:0.0108:0:1 +7 55249229 . G A 39 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07875;SOR=7.25731;LSEQ=GAGCCAGGATCCTCACATGC;RSEQ=GTCTGCGCTCCTGGGATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:663:1:0,1:138,524:662,1:0.0015:2,0:50:0:16:0:1:0:60:0:0:0:3 0/1:276:3:2,1:59,213:272,3:0.0109:2,2:11.3:1:25:1:0.12472:7.15:60:6:0.011:0:1 +7 55251103 . C T 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTGCATTTAGGACCCAC;RSEQ=CTAAATCCAGGATGATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:27:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55259622 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10485;SOR=Inf;LSEQ=CTGACACCAGGGACCAGGCT;RSEQ=CCTTCCCACTAGCTGTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:402:0:0,0:83,319:402,0:0:2,0:22.8:1:32.2:1:1:0:60:66:1:0:0.1 0/1:193:2:1,1:49,142:191,2:0.0104:2,2:23:1:25:1:0.45202:2.88:60:4:0.0104:0:1 +7 55259763 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24482;SOR=3.57184;LSEQ=GCCAGAGCTGCTTTGGGAAC;RSEQ=GTACTTGCTGGGACAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:18:2,16:0,22:22,18:0.45:1,2:25.7:1:31.8:1:0.19615:0:60:36:0.4615:0:1.2 1/0:8:6:0,6:0,2:2,6:0.75:0,0:20.5:1:30.3:1:1:0:60:12:0.75:0:1.2 +7 55260334 . A G 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57618;SOR=0;LSEQ=GGAGGCGCCGGGCCTGGGGG;RSEQ=CGGGTCCTGGGGTGATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:3,0:264,6:270,3:0.011:1,0:12:1:27:1:1:0:60:2:0.0077:0:2.3 0/0:91:0:0,0:88,3:91,0:0:1,0:25.4:1:28.5:1:1:0:60:29.333:1:0:0 +7 55265940 . G C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTATCAAATGGAACTTAA;RSEQ=CTTTTTCATTTCCAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:13.7:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55266336 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07644;SOR=Inf;LSEQ=CAAGAAACAGTAACCAGTAA;RSEQ=GATGACTAAAGCAAGGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:509:0:0,0:447,62:509,0:0:2,0:23.5:1:31.3:1:1:0:60:83.833:1:0:0.4 0/1:195:2:2,0:166,27:193,2:0.0103:2,0:18.5:1:32.5:1:1:0:60:4:0.0104:0:1.5 +7 55266417 . T C 322 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.30097;LSEQ=TTCATCCTCTCAGGGGTGAC;RSEQ=GTTTGGGAGTTGATGACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1625:1572:881,691:29,20:49,1572:0.9674:2,2:25.6:1:30.4:1:0.77038:1.13718:60:86.333:0.9688:0:1.1 1/1:893:803:463,340:44,43:87,803:0.8992:2,2:26:1:29.6:1:0.2117:1.33:60:60.769:0.8977:0:1.1 +7 55266757 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69421;SOR=0.61348;LSEQ=CATTGGGCAGTATGACCTGA;RSEQ=ATTTGCCCATGTTTGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:0,11:1,19:20,11:0.3548:1,0:22.4:1:25.5:1:1:0:57.1:4.5:0.3103:0:1.3 0/1:8:2:0,2:0,6:6,2:0.25:0,0:10:1:29:0:1:0:60:4:0.25:0:1 +7 55268916 . C T 201 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=243.95239;LSEQ=CATTTGCCAAGTCCTACAGA;RSEQ=TCCAACTTCTACCGTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1539:1:0,1:849,689:1538,1:6e-04:2,0:1:0:28:0:0.44834:0:60:2:7e-04:0:1 0/1:890:122:64,58:421,345:766,122:0.1371:2,2:26:1:29.1:1:0.62538:1.10576:59.6:29.5:0.1344:0:1.1 +7 55269675 . C CAG 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07644;SOR=0.12843;LSEQ=CCAGTAGTAGCATCGCCTGG;RSEQ=CTTGTTAGAAACGCCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:83:81:4,77:0,2:2,81:0.9759:0,1:23.3:1:32.3:1:1:0:59:162:0.9878:0.2892:0.2 1/1:12:10:0,10:0,2:2,10:0.8333:0,0:23.8:1:31.6:1:1:0:60:20:0.8333:0.25:0 +7 55270119 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAACCTACTAATCAGAAC;RSEQ=AGCATCTCAAGGAGATCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:157,7:164,2:0.012:1,2:7.5:1:29:1:0.09434:21.04679:60:4:0.0121:0:1 0/0:63:0:0,0:61,2:63,0:0:1,0:20.9:1:31.2:1:1:0:60:126:1:0:0.1 +7 55270463 . C T 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGCAGACACAGTGAAGGG;RSEQ=GTAAGGAGCAGATAAACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:909:0:0,0:263,645:908,0:0:2,0:24.2:1:30.3:1:1:0:59.9:32.63:0.9989:0:0.1 0/1:455:19:5,14:145,291:436,19:0.0418:2,2:27.4:1:29.2:1:0.62481:1.39423:60:38:0.042:0:1.1 +7 55272496 . TAC T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACACCATACATACACACGTA;RSEQ=ACACACCACATATACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:26:1:31.3:1:1:0:60:6:0.75:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 55272826 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56906;SOR=0.71374;LSEQ=AACAGCAAGAGGGCCCTCCC;RSEQ=AGGCTCCTGCTCCCTGTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:122:118:117,1:4,0:4,118:0.9672:0,1:22.1:1:30.7:1:1:0:59.8:117:0.9669:0:1.1 1/1:22:21:21,0:1,0:1,21:0.9545:0,1:21.4:1:30.5:1:1:0:60:42:0.9545:0:1 +7 55804335 . CA C 32 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.04412;SOR=Inf;LSEQ=CAGCCTGCCAAACTGCATCT;RSEQ=AAAAAAAAAAAACAAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:17.1:1:30.7:1:1:0:42.1:26:1:0:1.3 1/0:4:2:2,0:2,0:2,2:0.5:0,0:27:1:32:1:1:0:39.5:4:0.5:0:3 +7 55804944 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19287;SOR=Inf;LSEQ=CTGACACCCAGTTGCCTCCA;RSEQ=CACTCAGATGATGTCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:20,10:30,0:0:2,0:26.8:1:31.8:1:1:0:35.1:60:1:0:0.1 0/1:24:2:1,1:15,7:22,2:0.0833:2,2:20.5:1:27.5:1:1:2.07024:52:4:0.087:0:1 +7 55805070 . G A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01684;SOR=0.36201;LSEQ=TCCGGTGGCCCATGAGTGGC;RSEQ=TTCATGATCTTCAGCAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:29:13,16:72,72:144,29:0.1667:2,2:29.2:1:30.6:1:0.68605:1.22929:28.6:28:0.1637:0:1.1 0/1:104:7:2,5:52,45:97,7:0.0673:2,2:25.3:1:29.3:1:0.25695:2.86078:24:14:0.0673:0:1.3 +7 55805089 . C T 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54761;SOR=1.56152;LSEQ=CGTTCATGATCTTCAGCAAG;RSEQ=GGCACTAGGCCCTGGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:6:3,3:64,69:133,6:0.0432:2,2:28:1:30.7:1:1:1.08:26:12:0.0438:0:1.2 0/1:91:6:2,4:43,42:85,6:0.0659:2,2:23.5:1:30.7:1:0.67684:2.03203:28:12:0.0674:0:1.2 +7 55805107 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04708;SOR=Inf;LSEQ=AGCGGCACTAGGCCCTGGCA;RSEQ=GGCGCACCAGGGTCACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:55,60:115,0:0:2,0:27.7:1:32.1:1:1:0:33.1:230:1:0:0.4 0/1:66:3:2,1:34,29:63,3:0.0455:2,2:38:1:27:1:1:1.69:39:6:0.0462:0:1.7 +7 55805114 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15136;SOR=Inf;LSEQ=CTAGGCCCTGGCAGGGCGCA;RSEQ=CAGGGTCACCCCAACCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:49,46:95,0:0:2,0:27.8:1:31.7:1:1:0:32.5:190:1:0:0.3 0/1:61:2:1,1:33,26:59,2:0.0328:2,2:31.5:1:28.5:1:1:1.26423:39.5:4:0.0339:0:2 +7 55806087 . G T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21224;SOR=0.3424;LSEQ=CAGGAGCCTTCAAAGCCCAG;RSEQ=AATCTGGTCAGGGCAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:13:10,3:24,20:44,13:0.2281:2,2:29.2:1:30.2:1:0.20428:2.73:25:26:0.2321:0:1 0/1:22:2:2,0:11,9:20,2:0.0909:2,0:36.5:1:29:1:0.49351:0:22:4:0.0909:0:1 +7 55806116 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.08356;SOR=Inf;LSEQ=CAGGGCAGCAGAGCGGGCCC;RSEQ=CTATGGCCCCTACCCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:43,32:75,0:0:2,0:30.1:1:31:1:1:0:26.5:36.5:1:0:0.3 0/1:31:2:1,1:18,11:29,2:0.0645:2,2:43:1:28:1:1:1.60957:22.5:4:0.0645:0:2.5 +7 55806150 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGGGATGGGGGCCCAG;RSEQ=GATGCCTTCCAAGGCGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:25,20:45,2:0.0426:2,2:11:1:29:1:1:1.24403:37:4:0.0435:0:1 0/0:23:0:0,0:13,10:23,0:0:2,0:28.7:1:30.2:1:1:0:27:46:1:0:0.4 +7 55806991 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAGGGCCGCTGGGAGCC;RSEQ=CTGCATGGGTCCCAGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:10,35:45,2:0.0426:2,2:32.5:1:30.5:1:0.41721:3.38:21:4:0.0435:0:1 0/0:20:0:0,0:5,15:20,0:0:2,0:18.2:1:28.3:1:1:0:27.5:40:1:0:0.1 +7 55807008 . G A 120 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05641;SOR=0.14746;LSEQ=GCCGCTGCATGGGTCCCAGA;RSEQ=GCTGGACTGCGGCAGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:13:3,10:11,40:51,13:0.2031:2,2:38.5:1:32.5:1:1:1.09:28.5:26:0.2063:0:1.1 0/1:28:1:0,1:8,19:27,1:0.0357:2,0:31:0:26:0:1:0:22:2:0.0357:0:1 +7 55865547 . A G 59 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52381;SOR=0.20333;LSEQ=GTGGCAGCTGCTGAGATTGC;RSEQ=CCACTGCACTCCAGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:20.3:1:29.8:1:1:0:60:8:0.6667:0:1 0/1:4:1:1,0:2,1:3,1:0.25:2,0:16:0:26:0:1:0:60:2:0.25:0:2 +7 55865699 . G C 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.52679;SOR=0;LSEQ=AGGGGGCTGAGGAAGTGTGA;RSEQ=CCCCTGCCAGGAACCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:97,35:132,2:0.0149:2,2:7:0:33.5:1:0.46661:2.74672:60:4:0.0156:0:1.5 0/0:82:0:0,0:58,24:82,0:0:2,0:21.6:1:30.1:1:1:0:60:12.667:1:0:0 +7 55865719 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16348;SOR=Inf;LSEQ=GCCCCTGCCAGGAACCCCTG;RSEQ=CCAGACCATGTACTCGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:116,63:179,0:0:2,0:25.6:1:31.2:1:1:0:59.9:24.571:1:0:0.2 0/1:122:2:1,1:78,42:120,2:0.0164:2,2:16:0:30.5:1:1:1.84722:60:4:0.0167:0:1 +7 55865734 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00226;SOR=Inf;LSEQ=CCCTGCCCAGACCATGTACT;RSEQ=GGCCCACAGGCCCCTGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:130,83:213,0:0:2,0:26.3:1:31:1:1:0:60:70:0.9906:0:0.2 0/1:158:7:4,3:89,62:151,7:0.0443:2,2:16:1:27.4:1:1:1.07611:60:6:0.0387:0:1.1 +7 55865867 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12767;SOR=Inf;LSEQ=TCCTTCCTGACCCCTCCCTG;RSEQ=AGCCACGCAAAGCCCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:52,82:134,0:0:2,0:25.6:1:31.9:1:1:0:59.5:66:1:0:0.1 0/1:75:2:1,1:37,36:73,2:0.0267:2,2:17.5:1:27:1:1:1.02741:60:4:0.027:0:1.5 +7 55865896 . A T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17879;SOR=2.19199;LSEQ=AAAGCCCAGCAACCTGCCAG;RSEQ=CACTCAGTGGCCTCCAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:7:2,5:42,71:113,7:0.0583:2,2:23.4:1:30.7:1:1:1.47431:46.4:14:0.0593:0:1 0/1:75:9:3,6:29,37:66,9:0.12:2,2:32.1:1:29.2:1:0.72439:1.55849:47.6:18:0.12:0:1.1 +7 55865957 . C A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27753;SOR=0;LSEQ=TGGCAGCTGTTGCTCATGAG;RSEQ=GTCCACCAGGTGGGACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:3:1,2:36,48:84,3:0.0345:2,2:26:1:33.3:1:1:1.49329:51.7:6:0.0349:0:1 0/0:57:0:0,0:25,32:57,0:0:2,0:27.9:1:30.8:1:1:0:48.3:114:1:0:0.2 +7 55866158 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08512;SOR=Inf;LSEQ=AGAGAATGACCACAATGATG;RSEQ=TTTCCTCTCCGTCATGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:25,17:42,0:0:2,0:18.2:1:32.5:1:1:0:42.6:41:1:0:0.1 0/1:34:3:2,1:18,13:31,3:0.0882:2,2:26.7:1:30.3:1:1:1.43:24:6:0.0882:0:1 +7 55866192 . G C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53026;SOR=Inf;LSEQ=ATGTCTCCTGACACCCAGTT;RSEQ=CCTCTACCACCCAAATGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:19,11:30,0:0:2,0:26.9:1:32.2:1:1:0:44.1:29:1:0:0 0/1:52:2:1,1:29,21:50,2:0.0385:2,2:7:1:28:1:1:1.37225:60:4:0.0385:0:1 +7 55866274 . C T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02476;SOR=Inf;LSEQ=CATCTTCTGAGAAGGATGGA;RSEQ=GCAGCCCCAACAAATGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:76,62:138,0:0:2,0:28.7:1:31.1:1:1:0:43.7:276:1:0:0.8 0/1:128:5:3,2:60,63:123,5:0.0391:2,2:30.6:1:30.8:1:0.67756:1.57:32.6:10:0.0394:0:1 +7 55866295 . AAGG A 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01015;SOR=Inf;LSEQ=GCAGCCCCAACAAATGGGAC;RSEQ=ACCACATCCGGCAGCCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:95,78:173,0:0:2,0:22.8:1:30.6:1:1:0:47.3:85.5:1:0:0.9 0/1:117:5:1,4:61,51:112,5:0.0427:2,2:36.2:1:29.8:1:0.18559:4.72756:49.6:10:0.0435:0:0 +7 55866297 . G A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19812;LSEQ=AGCCCCAACAAATGGGACAA;RSEQ=GACCACATCCGGCAGCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:173:128:72,56:23,22:45,128:0.7399:2,2:22.7:1:30.9:1:0.60322:1.23:47.3:127:0.7384:0:1.2 0/1:117:42:24,18:37,33:70,42:0.359:2,2:27.4:1:29.5:1:0.69863:1.19:46.5:20:0.3704:0:1.2 +7 55866313 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15836;SOR=Inf;LSEQ=ACAAGGACCACATCCGGCAG;RSEQ=CCGTGAGTGGCACTCATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:107,98:205,0:0:2,0:21.4:1:31.2:1:1:0:54.2:40:1:0:0.7 0/1:136:2:1,1:70,64:134,2:0.0147:2,2:18:1:26.5:1:1:1.09302:52:4:0.0152:0:1.5 +7 55866443 . A G 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00098;SOR=Inf;LSEQ=GTGGTACACTCTGGGGCCCA;RSEQ=TGAGAGGCAGAAGTACCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:67,107:174,0:0:2,0:26.3:1:30.8:1:1:0:59.4:57:1:0:0.1 0/1:106:7:3,4:40,59:99,7:0.066:2,2:25.3:1:31.3:1:1:1.11:55.9:14:0.0673:0:1.3 +7 55866455 . A T 75 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0156;SOR=9.75702;LSEQ=GGGGCCCAATGAGAGGCAGA;RSEQ=GTACCATGACCTGACCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:1:0,1:58,101:159,1:0.0063:2,0:37:0:32:0:1:0:60:2:0.0063:0:1 0/1:103:6:2,4:39,58:97,6:0.0583:2,2:14.8:1:29.3:1:1:1.34108:45.7:12:0.0588:0:1.2 +7 56430156 . G T 27 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11719;SOR=Inf;LSEQ=CCTGCCCAGACCAAGTACTT;RSEQ=GCCCACAGGCCTGCGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:189,79:268,0:0:2,0:23.4:1:31.8:1:1:0:30.2:66:1:0:0.1 0/1:140:2:1,1:92,45:137,2:0.0143:2,2:7:0:27:1:1:2.03312:25:4:0.0147:0:1 +7 56430192 . C T 53 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26512;SOR=2.33726;LSEQ=TCCAGCGAGGCCTCCCGTGG;RSEQ=GTCAGCATGTTCATGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:561:3:0,3:324,234:558,3:0.0053:2,0:1:0:25.7:1:0.07485:0:35.7:6:0.0054:0:1 0/1:322:4:1,3:180,138:318,4:0.0124:2,2:10.5:1:26.8:1:0.32255:3.89741:27.5:8:0.0127:0:1 +7 56430650 . C T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00706;SOR=0.08174;LSEQ=CCCAGTCCCTCAGTGCACTG;RSEQ=GCAAGGAACAGGACTCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:27:13,14:2,0:2,27:0.931:0,2:26.8:1:30.2:1:0.48276:0:24.4:54:0.931:0:1 1/0:10:5:2,3:3,2:5,5:0.5:2,2:24.8:1:24.8:1:1:2.06996:22.4:4:0.4444:0:1 +7 56430693 . C A 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.32315;SOR=0;LSEQ=TAAGAAGGATGGACACAGCC;RSEQ=CAACAAATGGGACAAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:4,2:25,17:42,6:0.125:2,2:34.3:1:30.7:1:1:1.35:27.8:12:0.125:0:1 0/0:16:0:0,0:8,8:16,0:0:2,0:26.4:1:30.4:1:1:0:23.9:32:1:0:0.4 +7 56430843 . C T 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09642;SOR=0;LSEQ=CCTGAGCAAGCGGTGGTACA;RSEQ=CCTGGGGCCCAATGAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:7:7,0:70,31:101,7:0.0648:2,0:32.3:1:33:0:0.18875:0:22.7:14:0.066:0:1.1 0/0:54:0:0,0:31,23:54,0:0:2,0:24.7:1:30.8:1:1:0:25.8:53:1:0:0.2 +7 56430879 . T A 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00048;SOR=Inf;LSEQ=GACACAGAAGTACCACGACC;RSEQ=GGCCTTCCAAGTGAAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:97,56:153,0:0:2,0:27.7:1:31.2:1:1:0:22:75.5:1:0:0.1 0/1:62:6:3,3:31,25:56,6:0.0968:2,2:21.7:1:29.8:1:1:1.23567:24.2:12:0.0968:0:1.2 +7 56431767 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=AGCCCAGGAGTCTGGTCAGG;RSEQ=CAGCAGAGCCGGCCCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:14,12:26,0:0:2,0:19.1:1:30.5:1:1:0:25.4:12:1:0:0.6 0/1:30:2:1,1:13,15:28,2:0.0667:2,2:36:1:27.5:1:1:1.15:25.5:4:0.0667:0:1 +7 56431807 . G A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.77398;SOR=1.27439;LSEQ=TGGCCCCTACCCCTGGGGAC;RSEQ=GGGGCCCAGGGATGCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:10:6,4:14,10:24,10:0.2941:2,2:32.3:1:31:1:1:1.07:28.8:20:0.3125:0:1 0/1:23:8:5,3:6,9:15,8:0.3478:2,2:30.4:1:30.6:1:0.40032:2.40:29.8:16:0.3478:0:1.1 +7 56432708 . T C 135 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCAGGGGCCAACTGAAGCTG;RSEQ=TGGGGCAGCATGAGCAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:16:1,15:1,3:4,16:0.8:2,1:42.7:1:33.9:1:0.36842:4.47215:23.9:32:0.8:0:2.1 0/0:31:0:0,0:8,23:31,0:0:2,0:22.3:1:28.6:1:1:0:31.7:62:1:0:0.1 +7 56432714 . C A 128 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=GCCAACTGAAGCTGTTGGGG;RSEQ=AGCATGAGCAGGATGTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:16:1,15:1,3:4,16:0.8:2,1:46.4:1:32.1:1:0.36842:4.47215:23.9:32:0.8:0:2.1 0/0:27:0:0,0:7,20:27,0:0:2,0:24.1:1:31.1:1:1:0:33:54:1:0:0 +7 56434776 . A C 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.42857;SOR=0;LSEQ=GCGGGAGCTGAGTCCAAAGA;RSEQ=GTTGTTGGGAGGCCGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:2,3:0.6:2,2:32.3:1:30.3:1:1:1.7321:22.7:6:0.6:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:33.5:1:31:1:1:0:29:4:1:0:0.5 +7 56442996 . G C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGCCTGCGGAAGTGGC;RSEQ=GAGAGGCAGGAGTTTTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:29.5:1:1:0:28:4:1:0:2.5 +7 56443001 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGCGGAAGTGGCGGAGA;RSEQ=GCAGGAGTTTTGGACTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:30.5:1:1:0:28:4:1:0:2.5 +7 56747708 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTTAATATTAACCATTA;RSEQ=GGCCAGCCCCCTCTCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:29.5:1:1:0:29.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 56748760 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGTGATTACAATATTAATA;RSEQ=CATCATCTAGATAGAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:36.5:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 56748814 . T C 68 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGAAATTGCTTCAACTTA;RSEQ=AATAATTTAGAAACTAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:35.8:1:34:0:1:0:49:8:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:33:0:1:0:41:2:1:0:2 +7 56748878 . T C 73 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=AAAAATGTATCAATGCATTT;RSEQ=CCTCAGTTTTTCTGTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:22.8:1:31.6:1:1:0:42.6:10:1:0:1.4 1/0:2:1:1,0:1,0:1,1:0.5:0,0:22:0:25:0:1:0:41:2:0.5:0:2 +7 56748970 . A G 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39422;SOR=0.43249;LSEQ=TATTCTGGGTCCAGCAGCAC;RSEQ=TGGGAGGAGCCAATATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:12,0:4,0:4,12:0.75:0,0:26.3:1:31.1:1:1:0:46.7:24:0.75:0:1.2 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:21.6:1:29.2:1:1:0:49.4:10:0.5556:0:1 +7 56749207 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3253;LSEQ=AATGACCAAAATGTTGGCTA;RSEQ=GCTTAGGTGACTAAGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:383:284:110,174:42,57:99,284:0.7415:2,2:27.1:1:30.7:1:0.55171:1.16507:42:283:0.7428:0:1.1 0/1:282:136:57,79:68,78:146,136:0.4823:2,2:27:1:29.5:1:0.47239:1.20746:40.5:44.333:0.4767:0:1.1 +7 56749239 . T A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06023;SOR=Inf;LSEQ=TAAGAGTGAAAACTGTAGAC;RSEQ=GTGAATCTCACCCAGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:138,286:424,0:0:2,0:27.1:1:30.8:1:1:0:48.6:83.8:1:0:0.7 0/1:275:3:1,2:97,175:272,3:0.0109:2,2:30.7:1:28.7:1:1:1.10818:48.3:6:0.0111:0:1.3 +7 56749338 . C T 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.235;SOR=0.54272;LSEQ=TATTATTCCAAATTTTAAAT;RSEQ=CACAGAACTCATTTTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:66:51:2,49:2,13:15,51:0.7727:2,1:20.9:1:31.2:1:0.21984:3.67351:34.3:102:0.7727:0:1.4 1/0:34:22:0,22:2,10:12,22:0.6471:2,1:20.5:1:29:1:0.11765:0:35.5:44:0.6667:0:1.5 +7 56749362 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.87252;LSEQ=AGAACTCATTTTATTTGCAA;RSEQ=ATTTAACATTCACACTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:23:1,22:0,6:6,23:0.7931:0,1:21.1:1:33:1:1:0:28.7:46:0.7931:0:2 1/0:13:10:0,10:0,3:3,10:0.7692:0,0:23.6:1:31.9:1:1:0:29.4:20:0.7692:0:2.1 +7 56749612 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGTGGACAGTGTATGCCTC;RSEQ=TATCTCAATTAACTGATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:26:1:32:0:1:0:41.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 56873755 . T C 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39303;SOR=0.25106;LSEQ=AATGAGACGCAGAAGTACCA;RSEQ=GACCTGGCCTTCCAGGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:1,5:4,18:22,6:0.2143:2,2:13.7:1:30.2:1:1:1.10702:21.5:12:0.2143:0:1.2 0/1:16:1:0,1:7,8:15,1:0.0625:2,0:5:0:29:0:1:0:22:2:0.0625:0:1 +7 56873822 . T C 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38675;SOR=2.17129;LSEQ=AAGAAGTCCAGCTCAGAGGC;RSEQ=AAGCCCACAAACCAGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:0,3:24,33:57,3:0.05:2,0:33.3:1:31:1:0.2678:0:29.7:6:0.0508:0:1.3 0/1:29:3:1,2:10,16:26,3:0.1034:2,2:16.7:1:31:1:1:1.24064:42:6:0.1071:0:1 +7 56877516 . G A 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GAGAGGCAGGAGCTGACCCC;RSEQ=GAGGGGCCCTCGTTGACGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44:1:31.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:28:1:31:0:1:0:60:4:1:0:0 +7 57227889 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6044;SOR=0.42404;LSEQ=GCAATAGCAATAGAAACTCT;RSEQ=CATATTGTGGGTCCAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:37.3:1:30:0:1:0:59:6:0.3333:0:1 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:34:0:24:0:1:0:49:2:0.1667:0:1 +7 57228051 . C T 227 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGGTTGTGAACACAATAAA;RSEQ=GTCTTTGCATGAAAAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:163:163:117,46:0,0:0,163:1:0,2:27.1:1:31:1:1:0:46.8:326:1:0:1.1 1/0:186:99:61,38:57,30:87,99:0.5323:2,2:21.4:1:29.6:1:0.64794:1.18253:42.8:198:0.538:0:1.2 +7 57228283 . G T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28118;SOR=0;LSEQ=CCAAATTGTAAATCCACAGA;RSEQ=CTCATTTTATTTGCAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:4:0,4:1,23:24,4:0.1429:1,0:22.5:1:30.3:1:1:0:42:8:0.1481:0:1.3 0/0:17:0:0,0:0,17:17,0:0:1,0:30.1:1:31.1:1:1:0:58:16:1:0:0.2 +7 57536431 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50499;SOR=0;LSEQ=ATGATTATTTTTGAGTGGGT;RSEQ=AAGTTCACAGTCTACAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:64,17:81,2:0.0241:2,2:19.5:1:30:1:0.38877:3.68736:54.5:4:0.0241:0:1 0/0:64:0:0,0:39,25:64,0:0:2,0:21.5:1:28.3:1:1:0:59.3:128:1:0:0 +7 57536496 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51113;SOR=0;LSEQ=CAACATTTTGGTCATTTTCT;RSEQ=TGAGCAAATTTTGGAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:65,65:130,2:0.0152:2,2:25:1:29:1:1:1:60:4:0.0153:0:1 0/0:95:0:0,0:49,46:95,0:0:2,0:25.7:1:30.9:1:1:0:60:190:1:0:0.1 +7 57536632 . C T 73 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37458;SOR=0.30037;LSEQ=CCCTGATTTTTAGTGTCTTC;RSEQ=GTTACATTGCCATCAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:0,5:0,13:13,5:0.2778:1,0:18.4:1:31.6:1:1:0:53.2:10:0.2941:0:1 0/1:10:1:0,1:0,9:9,1:0.1:0,0:8:0:31:0:1:0:60:2:0.1:0:1 +7 57659196 . T G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTGTTTTTTATATACTG;RSEQ=TTTTACTTTATATAGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:12:1:33.5:1:1:0:21:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 57659464 . T C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12968;SOR=Inf;LSEQ=ACATGATTGTTTATTGGCGT;RSEQ=GATCTTACAGTCTGGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:190,33:223,0:0:2,0:25.2:1:30.5:1:1:0:36:222:1:0:0.1 0/1:126:2:1,1:85,39:124,2:0.0159:2,2:6:1:28:1:0.53587:2.16474:22.5:4:0.0163:0:1 +7 57669868 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17865;SOR=Inf;LSEQ=CAGAAGATATTTTTGAGTTT;RSEQ=CCATATTTTGAAACTTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:15,69:84,0:0:2,0:17.8:1:30.6:1:1:0:25.7:83:1:0:0.1 0/1:62:2:1,1:13,47:60,2:0.0323:2,2:22:1:29:1:0.40349:3.52:21.5:4:0.0323:0:1 +7 57669908 . TA CG 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.52;SOR=0;LSEQ=ATAAAAGGAATCATGCCTTA;RSEQ=TATTCTGACTTGCTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:14,2:0.125:1,0:46.5:1:30:0:1:0:27:4:0.125:0:2 0/0:9:0:0,0:1,8:9,0:0:2,0:39.9:1:27.3:1:1:0:39.4:18:1:0:0 +7 61968901 . T G 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.93312;LSEQ=ATGTGTGCGTTCAACTCACA;RSEQ=AGTTTAACCTTTCTTTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:1:1,0:35,32:67,1:0.0147:2,0:6:0:35:0:1:0:21:2:0.0147:0:2 0/1:71:2:1,1:31,38:69,2:0.0282:2,2:9:1:27.5:1:1:1.22:26.5:4:0.0282:0:2 +7 61968903 . G C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23106;SOR=0;LSEQ=GTGTGCGTTCAACTCACATA;RSEQ=TTTAACCTTTCTTTTCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:36,31:67,2:0.029:2,2:29:1:32:1:1:1.15877:20:4:0.029:0:2.5 0/0:74:0:0,0:34,40:74,0:0:2,0:20.2:1:31.2:1:1:0:28.5:148:1:0:0.4 +7 61968926 . C G 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.81673;LSEQ=TAACCTTTCTTTTCATAGAG;RSEQ=AGTTTGGAAACACTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:2,0:51,51:102,2:0.0192:2,0:20.5:1:33.5:1:0.49533:0:29:4:0.0196:0:2 0/1:127:2:1,1:59,66:125,2:0.0157:2,2:33.5:1:30:1:1:1.12:29:4:0.0163:0:1.5 +7 61968946 . T G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08131;SOR=0;LSEQ=CAGTTTGGAAACACTCTGTT;RSEQ=GTAAAGTCTGCAAGTGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:3:1,2:65,66:131,3:0.0224:2,2:22.3:1:31.3:1:1:1.96012:22:6:0.0231:0:1.7 0/0:174:0:0,0:88,86:174,0:0:2,0:27.4:1:29.9:1:1:0:33.4:348:1:0:0.4 +7 61968951 . A C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19149;SOR=0;LSEQ=TGGAAACACTCTGTTTGTAA;RSEQ=GTCTGCAAGTGGATATATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:71,66:137,2:0.0144:2,2:29:1:33:1:1:1.07517:40.5:4:0.0146:0:1.5 0/0:178:0:0,0:87,90:177,0:0:2,0:27.8:1:29.9:1:1:0:33.3:354:0.9944:0:0.4 +7 61968962 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20051;SOR=0;LSEQ=TGTTTGTAAAGTCTGCAAGT;RSEQ=GATATATGGACCGCATTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:79,76:155,2:0.0127:2,2:27:1:32:1:1:1.03923:22.5:4:0.0131:0:2 0/0:193:0:0,0:95,98:193,0:0:2,0:26.9:1:30.7:1:1:0:32.6:63.333:1:0:0.4 +7 61968966 . A C 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.09173;SOR=0.15538;LSEQ=TGTAAAGTCTGCAAGTGGAT;RSEQ=TATGGACCGCATTGAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:5:2,3:76,74:150,5:0.0323:2,2:22.2:1:34:1:0.68133:1.53629:24:10:0.0329:0:1.6 0/0:195:1:1,0:95,99:194,1:0.0051:2,0:4:0:31:0:0.49231:0:29:2:0.0052:0:1 +7 61968968 . A T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.13288;SOR=Inf;LSEQ=TAAAGTCTGCAAGTGGATAT;RSEQ=TGGACCGCATTGAGGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:78,75:153,0:0:2,0:25.6:1:29.8:1:1:0:32.5:152:1:0:0.4 0/1:193:4:2,2:93,96:189,4:0.0207:2,2:14.8:1:31.5:1:1:1.03:22:8:0.0208:0:1.3 +7 61968975 . G A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07735;SOR=0;LSEQ=TGCAAGTGGATATATGGACC;RSEQ=CATTGAGGCCTTCGTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:2,1:74,71:145,3:0.0203:2,2:27:1:31.3:1:1:1.91:26.7:6:0.021:0:1.3 0/0:198:0:0,0:100,97:197,0:0:2,0:25.2:1:30.2:1:1:0:32.9:64.667:0.9949:0:0.4 +7 61968976 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18508;SOR=0;LSEQ=GCAAGTGGATATATGGACCG;RSEQ=ATTGAGGCCTTCGTTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:76,72:148,2:0.0133:2,2:22:1:30:0:1:1.0552:26.5:4:0.0136:0:1 0/0:198:0:0,0:99,97:196,0:0:2,0:25.3:1:31.3:1:1:0:33:64.333:0.9897:0:0.4 +7 61968983 . G A 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.74026;LSEQ=GATATATGGACCGCATTGAG;RSEQ=CCTTCGTTGGAAACGGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:2,0:71,71:142,2:0.0139:2,0:28:1:32:0:0.4966:0:28.5:4:0.0144:0:2 0/1:194:2:1,1:101,91:192,2:0.0103:2,2:35.5:1:30:1:1:1.10929:53:4:0.0103:0:1.5 +7 61968989 . G A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.73521;LSEQ=TGGACCGCATTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:2,0:66,64:130,2:0.0152:2,0:19.5:1:32:0:0.49665:0:25:4:0.0153:0:2 0/1:179:2:2,0:94,82:176,2:0.0112:2,0:12.5:1:31:0:0.50029:0:28:4:0.0112:0:1 +7 61968997 . C T 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57068;SOR=0.34769;LSEQ=ATTGAGGCCTTCGTTGGAAA;RSEQ=GGGATTTCTTCATTTCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:56,59:115,2:0.0171:2,2:28.5:1:32.5:1:1:1.05:26:4:0.0174:0:1 0/0:167:1:0,1:88,74:162,1:0.006:2,0:50:0:28:0:0.46012:0:23:2:0.006:0:3 +7 61968999 . G A 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57201;SOR=0.35226;LSEQ=TGAGGCCTTCGTTGGAAACG;RSEQ=GATTTCTTCATTTCATGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:55,58:113,2:0.0174:2,2:36:1:32.5:1:1:1.05:23:4:0.0175:0:2 0/0:162:1:0,1:86,75:161,1:0.0062:2,0:48:0:30:0:0.46914:0:23:2:0.0063:0:3 +7 61969009 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50805;SOR=Inf;LSEQ=GTTGGAAACGGGATTTCTTC;RSEQ=TTTCATGCTAGACAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:50,56:106,0:0:2,0:28:1:30.8:1:1:0:33.1:52:1:0:0.5 0/1:141:2:1,1:73,66:139,2:0.0142:2,2:28:1:28:1:1:1.10527:52:4:0.0142:0:3.5 +7 61969012 . TC GA 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50551;SOR=Inf;LSEQ=GGAAACGGGATTTCTTCATT;RSEQ=ATGCTAGACAGAAGAATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:49,54:103,0:0:2,0:27.4:1:30.5:1:1:0:33.3:50.5:1:0:0.5 0/1:132:2:1,1:69,61:130,2:0.0152:2,2:29.5:1:29.3:1:1:1.13009:26.5:4:0.0152:0:1 +7 61969013 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25954;SOR=Inf;LSEQ=GAAACGGGATTTCTTCATTT;RSEQ=ATGCTAGACAGAAGAATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:48,51:99,0:0:2,0:28:1:32.1:1:1:0:33.4:98:0.9899:0:0.5 0/1:130:3:1,2:67,58:125,3:0.0231:2,2:28.3:1:27:1:0.59962:2.29567:47:6:0.0234:0:1.7 +7 61969014 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.50414;SOR=Inf;LSEQ=AAACGGGATTTCTTCATTTC;RSEQ=TGCTAGACAGAAGAATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:50,53:103,0:0:2,0:26.4:1:30.6:1:1:0:33.1:206:1:0:0.4 0/1:129:2:1,1:67,60:127,2:0.0155:2,2:26:0:33:1:1:1.11571:38:4:0.0156:0:1.5 +7 61969016 . G A 62 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46408;SOR=2.06354;LSEQ=ACGGGATTTCTTCATTTCAT;RSEQ=CTAGACAGAAGAATTCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:47,53:100,2:0.0194:2,2:30:1:28:1:1:1.13:50:4:0.0198:0:1.5 0/1:127:5:2,3:63,58:121,5:0.0394:2,2:17.8:1:27:1:0.6727:1.62305:44.6:10:0.0394:0:2.2 +7 61969018 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20548;SOR=0;LSEQ=GGGATTTCTTCATTTCATGC;RSEQ=AGACAGAAGAATTCTCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:46,51:97,2:0.02:2,2:19:1:30.5:1:1:1.11:59:4:0.0208:0:1.5 0/0:120:0:0,0:62,57:119,0:0:2,0:27.5:1:28.9:1:1:0:31.7:238:0.9917:0:0.6 +7 61969032 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50565;SOR=Inf;LSEQ=TCATGCTAGACAGAAGAATT;RSEQ=TCAGTAACTTCTTTGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:38,39:77,0:0:2,0:24.4:1:32.4:1:1:0:28.2:24.667:1:0:0.5 0/1:100:2:1,1:49,49:98,2:0.02:2,2:28:1:29.5:1:1:1:52:4:0.02:0:3.5 +7 61969037 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50375;SOR=Inf;LSEQ=CTAGACAGAAGAATTCTCAG;RSEQ=AACTTCTTTGTGCTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:36,36:72,0:0:2,0:22.7:1:28.8:1:1:0:26.8:71:1:0:0.5 0/1:91:2:1,1:42,47:89,2:0.022:2,2:40.5:1:31:1:1:1.12:47:4:0.022:0:1 +7 61969049 . G A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50291;SOR=Inf;LSEQ=ATTCTCAGTAACTTCTTTGT;RSEQ=CTGTGTGTATTCAACTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:29,28:57,0:0:2,0:20.4:1:31.5:1:1:0:26.6:27.5:1:0:0.5 0/1:72:2:1,1:35,35:70,2:0.0278:2,2:44:0:29:1:1:1:37:4:0.0282:0:1.5 +7 61969087 . A G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47255;SOR=0.53076;LSEQ=ACAGAGTGGAACGTCCCTTT;RSEQ=CACAGAGCAGATTTGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:4,3:2,2:4,7:0.5833:2,2:13.1:1:29.4:1:1:1.30:27.7:6:0.5455:0:1.9 0/1:19:8:2,6:5,6:11,8:0.4211:2,2:16.4:1:32:1:0.63325:2.38223:33:16:0.4211:0:1.9 +7 61969269 . T C 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68752;SOR=1.62461;LSEQ=CCTTTCTTTTCTTAGAGCAG;RSEQ=TTAGAAACACTCTGCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:0,2:18,9:27,2:0.069:2,0:27:1:35:0:0.13547:0:22:4:0.069:0:1 0/1:37:4:1,3:16,17:33,4:0.1081:2,2:9.5:1:30.3:1:0.60875:2.75122:20.5:8:0.1081:0:3.8 +7 61969272 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5073;SOR=Inf;LSEQ=TTCTTTTCTTAGAGCAGTTT;RSEQ=GAAACACTCTGCTTGTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:21,12:33,0:0:2,0:15.9:1:30.3:1:1:0:24.8:66:1:0:1 0/1:46:2:1,1:20,24:44,2:0.0435:2,2:16:0:32.5:1:1:1.20:21:4:0.0435:0:2.5 +7 61969281 . C A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50073;SOR=Inf;LSEQ=TAGAGCAGTTTAGAAACACT;RSEQ=TGCTTGTTATGTCTGCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:27,20:47,0:0:2,0:13.9:1:32.6:1:1:0:28.1:94:1:0:1.2 0/1:58:2:1,1:27,29:56,2:0.0345:2,2:25:0:28:1:1:1.07:21:4:0.0345:0:2.5 +7 61969291 . T C 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.34762;SOR=0.29666;LSEQ=TAGAAACACTCTGCTTGTTA;RSEQ=GTCTGCAAGTGGATATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:3:2,1:29,29:58,3:0.0476:2,2:16.7:1:31.3:1:1:1.98:30.7:6:0.0476:0:2.3 0/1:69:1:1,0:32,34:66,1:0.0145:2,0:27:0:33:0:0.49254:0:25:2:0.0145:0:2 +7 61969302 . G T 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.6893;SOR=1.69438;LSEQ=TGCTTGTTATGTCTGCAAGT;RSEQ=GATATTTGGACCTCTTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:2,0:39,29:68,2:0.0286:2,0:19.5:1:33:0:0.50766:0:26.5:4:0.029:0:3.5 0/1:84:4:1,3:40,40:80,4:0.0476:2,2:26:1:30:1:0.61624:2.96426:20.5:8:0.0482:0:3.8 +7 61969309 . TG CA 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50707;SOR=Inf;LSEQ=TATGTCTGCAAGTGGATATT;RSEQ=GACCTCTTTGAGGGCTTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:41,32:73,0:0:2,0:25.6:1:31.2:1:1:0:31.6:146:1:0:2 0/1:97:2:1,1:50,44:94,2:0.0206:2,2:11.5:1:29.5:1:1:1.13485:25:4:0.0206:0:3.5 +7 61969312 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51066;SOR=Inf;LSEQ=GTCTGCAAGTGGATATTTGG;RSEQ=CCTCTTTGAGGGCTTCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:41,33:74,0:0:2,0:28:1:30.4:1:1:0:31.8:148:1:0:2.1 0/1:103:2:1,1:52,48:100,2:0.0194:2,2:14.5:1:30:1:1:1.08246:41:4:0.0198:0:3.5 +7 61969323 . GG AC 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50684;SOR=Inf;LSEQ=GATATTTGGACCTCTTTGAG;RSEQ=CTTCGTTGCAAACGGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:51,38:89,0:0:2,0:30.8:1:31.9:1:1:0:32:88:1:0:2.1 0/1:117:2:2,0:59,55:114,2:0.0171:2,0:27.5:1:31.5:1:0.497:0:24:4:0.0179:0:4 +7 61969324 . G C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19489;SOR=0.32289;LSEQ=ATATTTGGACCTCTTTGAGG;RSEQ=CTTCGTTGCAAACGGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:93:91:51,40:1,0:1,91:0.9785:0,2:29.9:1:31.9:1:1:0:31.9:90:0.989:0:2.1 1/1:125:117:59,58:0,0:0,117:0.936:0,2:27.2:1:30.5:1:1:0:32.3:38:0.9744:0:2.3 +7 61969333 . C G 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51012;SOR=Inf;LSEQ=CCTCTTTGAGGGCTTCGTTG;RSEQ=AAACGGGGTTTCTTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:59,49:108,0:0:2,0:29.1:1:32.3:1:1:0:32.6:107:0.9907:0:2 0/1:149:2:1,1:74,73:147,2:0.0134:2,2:8:0:29.5:1:1:1.01361:44:4:0.0136:0:2.5 +7 61969353 . C A 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.00923;LSEQ=CAAACGGGGTTTCTTCCTTT;RSEQ=ATGCTAGACTAAGAAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:21:13,8:59,50:109,21:0.1615:2,2:29.2:1:28.3:1:0.63349:1.37:24.8:20:0.155:0:3 0/1:172:28:13,15:78,66:144,28:0.1628:2,2:29.3:1:29.3:1:0.53637:1.36115:24.3:56:0.1677:0:3.3 +7 61969355 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50804;SOR=Inf;LSEQ=AACGGGGTTTCTTCCTTTCA;RSEQ=GCTAGACTAAGAAGAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:72,58:130,0:0:2,0:27.3:1:30.8:1:1:0:31.7:129:1:0:1.9 0/1:172:2:1,1:89,79:168,2:0.0116:2,2:25.5:1:31:0:1:1.12579:60:4:0.0119:0:3 +7 61969357 . C G 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.51563;LSEQ=CGGGGTTTCTTCCTTTCATG;RSEQ=TAGACTAAGAAGAGTTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:1:1,0:71,58:129,1:0.0077:2,0:15:0:25:0:1:0:36:2:0.0078:0:3 0/1:172:2:1,1:89,80:169,2:0.0116:2,2:23:1:31:1:1:1.1118:28:4:0.012:0:2.5 +7 61969369 . G T 28 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.42858;LSEQ=CTTTCATGCTAGACTAAGAA;RSEQ=AGTTCTCAGGAACTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:1,0:57,50:107,1:0.0092:2,0:25:0:33:0:1:0:33:2:0.0092:0:3 0/1:153:2:1,1:80,71:151,2:0.0131:2,2:29:0:28.5:1:1:1.12588:36:4:0.0134:0:3.5 +7 61969370 . A T 44 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.08132;LSEQ=TTTCATGCTAGACTAAGAAG;RSEQ=GTTCTCAGGAACTTTTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:56,50:106,2:0.0185:2,2:33:1:32:0:1:1.11882:35:4:0.0187:0:3 0/1:150:3:1,2:79,67:146,3:0.02:2,2:41.7:1:28:1:0.59643:2.345:35:6:0.0204:0:4.7 +7 61969372 . T A 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14211;SOR=Inf;LSEQ=TCATGCTAGACTAAGAAGAG;RSEQ=TCTCAGGAACTTTTTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:54,50:104,0:0:2,0:29.7:1:30.4:1:1:0:32.5:103:1:0:2 0/1:146:4:3,1:76,66:142,4:0.0274:2,2:12:1:23:1:0.62496:2.59:28.8:3:0.0211:0:4 +7 61969374 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50994;SOR=Inf;LSEQ=ATGCTAGACTAAGAAGAGTT;RSEQ=TCAGGAACTTTTTTGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:55,49:104,0:0:2,0:29.3:1:33:1:1:0:32.5:208:1:0:2 0/1:142:2:1,1:75,65:140,2:0.0141:2,2:22:0:32:1:1:1.15268:22:4:0.0144:0:3.5 +7 61969376 . C G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17948;SOR=0;LSEQ=GCTAGACTAAGAAGAGTTCT;RSEQ=AGGAACTTTTTTGTGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:52,45:97,2:0.0202:2,2:43.5:1:33:1:1:1.15386:23:4:0.0202:0:3.5 0/0:134:0:0,0:72,62:134,0:0:2,0:27.9:1:31.5:1:1:0:34:268:1:0:2.1 +7 61969379 . G T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26578;SOR=0;LSEQ=AGACTAAGAAGAGTTCTCAG;RSEQ=AACTTTTTTGTGTTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:95:95:51,44:0,0:0,95:1:0,2:29.7:1:29.6:1:1:0:31.9:94:1:0:2 1/1:131:128:68,60:0,0:0,128:0.9771:0,2:27.1:1:28.7:1:1:0:34:127:0.9769:0:2.1 +7 61969399 . T C 33 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.48466;LSEQ=GAACTTTTTTGTGTTGTGTG;RSEQ=ATTCAACTCACAGAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:1:1,0:35,29:64,1:0.0154:2,0:22:0:29:0:1:0:26:2:0.0156:0:4 0/1:88:2:1,1:47,39:86,2:0.0227:2,2:22:0:33:0:1:1.20256:23:4:0.023:0:3.5 +7 61969416 . T G 32 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60174;SOR=2.25992;LSEQ=GTGTATTCAACTCACAGAGT;RSEQ=GAACCTTGCTTTAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:1,0:26,23:49,1:0.02:2,0:5:0:27:0:1:0:26:2:0.0204:0:4 0/1:45:2:1,1:25,18:43,2:0.0444:2,2:5:0:32.5:1:1:1.3786:23:4:0.0455:0:3.5 +7 61969478 . T A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03206;SOR=0;LSEQ=GTGGCATTTTCAGGTGGAGA;RSEQ=TTCAAGCGATTTGAGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:5,7:12,3:0.2:2,2:39.3:1:25:1:0.56923:2.61:23.7:2:0.1429:0:1 0/0:30:0:0,0:16,14:30,0:0:2,0:38.2:1:29.2:1:1:0:21.1:29:1:0:0.4 +7 61969484 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12121;SOR=0;LSEQ=TTTTCAGGTGGAGATTTCAA;RSEQ=CGATTTGAGGACAATTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:6,8:14,2:0.125:2,2:29:0:32.5:1:1:1.31:26.5:4:0.1333:0:2 0/0:29:0:0,0:16,13:29,0:0:2,0:42.7:1:31.9:1:1:0:21:58:1:0:0.4 +7 61969487 . A T 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5457;SOR=0.27439;LSEQ=TCAGGTGGAGATTTCAAGCG;RSEQ=TTTGAGGACAATTGCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:16,2:0.1111:2,2:26:0:32:0:1:1:26.5:4:0.1176:0:2 0/1:31:1:0,1:17,13:30,1:0.0323:2,0:47:0:28:0:0.45161:0:22:2:0.0323:0:1 +7 61969501 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54978;SOR=Inf;LSEQ=CAAGCGATTTGAGGACAATT;RSEQ=CAGAAAAGGAAATATCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:26,0:0:2,0:18.2:1:31.8:1:1:0:22.8:25:1:0:0.6 0/1:52:2:1,1:32,17:49,2:0.0385:2,2:29.5:1:30:1:1:1.85775:21.5:4:0.0385:0:1 +7 61969515 . A T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.05271;SOR=0;LSEQ=ACAATTGCAGAAAAGGAAAT;RSEQ=TCTTCGTATAATAACCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:3:1,2:31,12:43,3:0.0652:2,2:17.3:1:32.3:1:0.21581:4.95729:21:6:0.0667:0:1.3 0/0:75:0:0,0:47,28:75,0:0:2,0:17:1:28.5:1:1:0:24.3:74:1:0:0.4 +7 61969518 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51556;SOR=Inf;LSEQ=ATTGCAGAAAAGGAAATATC;RSEQ=TCGTATAATAACCAGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:33,18:51,0:0:2,0:14.1:1:31.6:1:1:0:24.2:50:1:0:0.3 0/1:76:2:1,1:46,28:74,2:0.0263:2,2:11.5:1:28:1:1:1.63167:25:4:0.0263:0:1.5 +7 61969526 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51303;SOR=Inf;LSEQ=AAAGGAAATATCTTCGTATA;RSEQ=TAACCAGACAGAATCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:33,18:51,0:0:2,0:18.9:1:31:1:1:0:24.2:50:1:0:0.3 0/1:74:2:1,1:46,26:72,2:0.027:2,2:19:1:33.5:1:1:1.75484:24.5:4:0.027:0:1 +7 61969560 . G C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49939;SOR=Inf;LSEQ=TCATTCTCAGAAAGTGCTTT;RSEQ=TGATGTGTGCGTTCAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:29,12:41,0:0:2,0:42:1:32.9:1:1:0:24.8:82:1:0:0.2 0/1:50:2:1,1:32,16:48,2:0.04:2,2:42:0:31.5:1:1:1.97043:43:4:0.04:0:1.5 +7 61969568 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49838;SOR=Inf;LSEQ=AGAAAGTGCTTTGTGATGTG;RSEQ=GCGTTCAACTCACAGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:29,12:41,0:0:2,0:35.8:1:30.4:1:1:0:24.8:82:1:0:0.2 0/1:49:2:1,1:31,16:47,2:0.0408:2,2:21.5:1:29:1:1:1.90979:26:4:0.0408:0:1 +7 61969575 . A C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.20024;SOR=0;LSEQ=GCTTTGTGATGTGTGCGTTC;RSEQ=ACTCACAGAGTTTAACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:28,11:39,2:0.0488:2,2:38:0:33.5:1:0.50488:2.48023:22.5:4:0.0488:0:1 0/0:50:0:0,0:32,18:50,0:0:2,0:23.9:1:29.3:1:1:0:26.2:100:1:0:0.4 +7 61970349 . T C 52 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.74999;LSEQ=TATGGACCTGTTTGAGGCCT;RSEQ=CGTTGGAAACGGGATTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:9,1:10,3:0.2308:2,2:43.3:1:33:1:0.42308:3.87298:28:6:0.2308:0:1.3 0/1:11:2:1,1:3,3:6,2:0.1818:2,2:2:1:29.5:1:1:1:28:4:0.1818:0:2 +7 61970351 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=TGGACCTGTTTGAGGCCTTC;RSEQ=TTGGAAACGGGATTTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:15,2:17,2:0.1:2,2:21:1:29.5:1:0.29825:6.32456:23:4:0.1:0:3 0/0:19:0:0,0:10,8:18,0:0:2,0:16.5:1:29.3:1:1:0:26.1:36:0.9474:0:0.9 +7 61970372 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49333;SOR=Inf;LSEQ=TTGGAAACGGGATTTCTTCA;RSEQ=TGAATGCTAGACGGAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:25,12:37,0:0:2,0:24.8:1:30.9:1:1:0:24.4:36:1:0:0.6 0/1:38:2:1,1:23,13:36,2:0.0526:2,2:25:1:33.5:1:1:1.74146:28:4:0.0526:0:2 +7 61970383 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49333;SOR=Inf;LSEQ=ATTTCTTCATTGAATGCTAG;RSEQ=CGGAAGAATTCTCAGTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:25,12:37,0:0:2,0:29.8:1:29.9:1:1:0:24.4:74:1:0:0.6 0/1:38:2:1,1:23,13:36,2:0.0526:2,2:30.5:1:29.5:1:1:1.74146:27.5:4:0.0556:0:1 +7 61970385 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49315;SOR=Inf;LSEQ=TTCTTCATTGAATGCTAGAC;RSEQ=GAAGAATTCTCAGTAAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:25,12:37,0:0:2,0:30.6:1:30.5:1:1:0:24.4:74:1:0:0.6 0/1:37:2:1,1:23,12:35,2:0.0541:2,2:18:1:25.5:1:1:1.88115:29.5:4:0.0541:0:2.5 +7 61970390 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23973;SOR=Inf;LSEQ=CATTGAATGCTAGACGGAAG;RSEQ=ATTCTCAGTAAATTCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:25,12:37,0:0:2,0:32.6:1:29.6:1:1:0:24.4:17.5:1:0:0.6 0/1:36:2:1,1:22,12:34,2:0.0556:2,2:22.5:1:32:0:1:1.8009:21.5:4:0.0571:0:1.5 +7 61970392 . T G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49315;SOR=0;LSEQ=TTGAATGCTAGACGGAAGAA;RSEQ=TCTCAGTAAATTCTTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:24,11:35,2:0.0541:2,2:32.5:1:31.5:1:1:2.13205:23:4:0.0541:0:3 0/0:36:0:0,0:23,13:36,0:0:2,0:35.6:1:30:1:1:0:23.8:35:1:0:0.7 +7 61970413 . T G 32 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.59513;SOR=0.42766;LSEQ=TCTCAGTAAATTCTTTGTGT;RSEQ=GTGTGCATTCAACTCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:17,10:27,2:0.069:2,2:47:0:32.5:1:1:1.66781:22:4:0.069:0:1 0/1:33:1:0,1:22,10:32,1:0.0303:2,0:2:0:31:0:0.33333:0:21:2:0.0313:0:1 +7 61970428 . C G 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.6153;SOR=2.74112;LSEQ=TGTGTTGTGTGCATTCAACT;RSEQ=ACAGAGTGGAACGTCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:1:0,1:16,10:26,1:0.037:2,0:21:0:34:0:0.40741:0:22:2:0.0385:0:4 0/1:31:3:2,1:19,9:28,3:0.0968:2,2:24.3:1:29:1:1:1.0537:21.7:6:0.0968:0:1.7 +7 61970435 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49499;SOR=Inf;LSEQ=TGTGCATTCAACTCACAGAG;RSEQ=GGAACGTCCCTTTAGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:26,0:0:2,0:19.2:1:29.9:1:1:0:23.9:52:1:0:0.4 0/1:31:2:1,1:20,9:29,2:0.0645:2,2:15:1:31.5:1:1:2.16029:22.5:4:0.0645:0:2 +7 63230653 . G A 89 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0203;SOR=0.11634;LSEQ=TGCTAGCCCCTGGCTTGTGG;RSEQ=CTTGGCCTCTGAGCTGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:9:5,4:30,31:61,9:0.1286:2,2:34.8:1:28.1:1:1:1.29:39.1:3.5:0.1045:0:1 0/1:60:1:0,1:33,26:59,1:0.0167:2,0:2:0:29:0:0.45:0:21:2:0.0175:0:1 +7 63230769 . G A 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06487;SOR=2.99398;LSEQ=CCCAGGGTGTACCACCGCTC;RSEQ=CTCAGGATCTGGCAGACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:11,3:10,9:19,14:0.4242:2,2:37.5:1:29.6:1:0.16036:3.18:24.4:13:0.4194:0:1.6 1/0:26:18:9,9:5,3:8,18:0.6923:2,2:33.9:1:28.7:1:0.68284:1.6343:28.2:36:0.6923:0:1.3 +7 63230786 . C A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.83201;SOR=0.8931;LSEQ=CTCGCTCAGGATCTGGCAGA;RSEQ=GGTCCGGTTGTCCTGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:17:10,7:20,21:41,17:0.2881:2,2:17.4:1:30.1:1:0.57026:1.49:25.6:34:0.2931:0:1.4 0/1:49:13:8,5:18,18:36,13:0.2653:2,2:14.4:1:29.8:1:0.53219:1.58:25.1:26:0.2653:0:1.7 +7 63230820 . C T 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01215;SOR=Inf;LSEQ=TGGTTGGGGTGACCCTGGTG;RSEQ=GCCCTGCCAGGGCCTGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:31,44:75,0:0:2,0:27:1:29.9:1:1:0:29.1:17.75:1:0:0.4 0/1:55:5:3,2:25,25:50,5:0.0909:2,2:35.2:1:30:1:1:1.49:29.2:10:0.0926:0:1.4 +7 63317423 . C CA 32 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACAAGAATGAAACTCTGCCT;RSEQ=AAAAAAAAAAAAAAATTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28.5:1:32:0:1:0:58:4:1:0:0 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 63317573 . G T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49417;SOR=0;LSEQ=CTGCCAGGCTCAGTGGAGGA;RSEQ=GCAGATGACAACAGGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:19,14:33,2:0.0571:2,2:48:0:31.5:1:1:1.34517:38:4:0.0571:0:3 0/0:31:0:0,0:17,14:31,0:0:2,0:30.1:1:30.5:1:1:0:52.7:30:1:0:0.7 +7 63317590 . GT CG 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61258;SOR=1.31733;LSEQ=GGAGGCAGATGACAACAGGG;RSEQ=CAGCATGGGTGGCGACTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:5,6:19,13:32,11:0.2558:2,2:31.5:1:32:1:0.49468:1.73067:50.8:22:0.2558:0:1.2 0/1:32:10:6,4:11,11:22,10:0.3125:2,2:30.5:1:29.1:1:0.71195:1.48:49.3:9:0.3:0.0313:1.2 +7 63318062 . A T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAATCCCAGCACTTTGGG;RSEQ=GGCCGAGGTGGGCAGATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10:1:31:0:1:0:60:4:1:0:2 +7 63398593 . GT G 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.18136;SOR=Inf;LSEQ=AAGCAGTGAGCCATTCATGA;RSEQ=TTTTAGAGCACAGCTACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:37,205:242,0:0:2,0:25.2:1:30.7:1:1:0:59.8:120:1:0:0.1 0/1:180:2:1,1:34,144:178,2:0.0111:2,2:6.5:1:27:1:0.35196:4.19:60:4:0.0112:0.0056:0.5 +7 63398616 . G A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13601;SOR=0;LSEQ=TTTAGAGCACAGCTACACTG;RSEQ=CATAGACGTCCAACTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:4:3,1:34,145:179,4:0.0219:2,2:26:1:30.3:1:0.02655:12.55:60:8:0.0222:0:1 0/0:140:0:0,0:30,110:140,0:0:2,0:22.4:1:30.8:1:1:0:59.7:45.667:1:0:0.2 +7 63398887 . C CAATAT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=45;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGCCATGTCAATTAGCTGGA;RSEQ=AATATAATATAATATAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:0,7:7,2:0.2222:0,2:29:1:29.4:1:0.22222:0:56.5:4:0.2222:0:0 0/0:4:0:0,0:1,3:4,0:0:2,0:19:1:32:1:1:0:60:8:1:0:0 +7 63733693 . C T 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGGAGAGTTAATATTAA;RSEQ=GGATAATTATTAAATGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:35.5:1:31.5:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 63734030 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23313;SOR=Inf;LSEQ=TGGAGATTATGGCAGATTTA;RSEQ=ATTAAAACAATTACTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:38,74:112,0:0:2,0:28.2:1:32.3:1:1:0:59.9:36.333:0.9909:0:0.1 0/1:106:2:1,1:44,60:104,2:0.0189:2,2:18:1:29.5:1:1:1.36:60:4:0.0192:0:1 +7 63734057 . C A 31 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49983;SOR=0;LSEQ=ACAATTACTCAGTTATTTTT;RSEQ=ATGCAAAGATGTTTATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:2:1,1:25,55:80,2:0.0244:2,2:7:0:31.5:1:0.53628:2.18:60:4:0.0247:0:2.5 0/0:70:0:0,0:24,46:70,0:0:2,0:21:1:31.4:1:1:0:59.1:140:1:0:0 +7 63734095 . CAT C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08099;SOR=3.87888;LSEQ=GTGTTCACAGAGTGACCAAT;RSEQ=GTGACAGGTGGCAACACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:0,3:0,34:34,3:0.0811:1,0:21:1:31.5:1:1:0:58:6:0.0811:0.027:0 0/1:27:7:0,7:4,16:20,7:0.2593:2,0:34:1:32.1:1:0.5453:0:52.1:14:0.2593:0:0 +7 64721312 . GA G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.68928;SOR=1.74976;LSEQ=CACAGCAAGACTCTGTCTCA;RSEQ=AAAAAAAAAAAGAACCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:9:9,0:18,0:18,9:0.3103:1,0:19.1:1:33.9:1:1:0:60:18:0.3103:0.1034:0.4 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:22.3:1:32.8:1:1:0:60:8:0.4444:0.1111:0.5 +7 64721546 . A G 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.83186;LSEQ=CCAGGCCCCTTTTCTCCCCA;RSEQ=CTAGGAGCTCCCCAGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:189:77,112:186,258:444,189:0.2981:2,2:23.4:1:32.4:1:0.86014:1.04856:60:36.8:0.3007:0:1.1 1/0:443:242:109,133:89,112:201,242:0.5463:2,2:24.8:1:30.8:1:0.9236:1.03:60:25.889:0.5431:0:1.2 +7 64721622 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11878;SOR=Inf;LSEQ=TGCTATAGCCAGAGTATTCA;RSEQ=GATGCCAACCCTAAGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:25,168:193,0:0:2,0:23:1:31.7:1:1:0:60:192:1:0:0.2 0/1:102:2:1,1:22,78:100,2:0.0196:2,2:16.5:1:28.5:1:0.40186:3.49:60:4:0.0196:0:1.5 +7 64721626 . G A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10614;SOR=Inf;LSEQ=ATAGCCAGAGTATTCAGGAT;RSEQ=CCAACCCTAAGGTCCCTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:22,157:179,0:0:2,0:22.6:1:32.5:1:1:0:60:178:1:0:0.2 0/1:87:2:1,1:15,70:85,2:0.023:2,2:7.5:1:25.5:1:0.33574:4.55:60:4:0.023:0:2.5 +7 65969262 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACGTGAGCTCCAGTGGGGT;RSEQ=CACTCCAGCCGGGACAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:42:1:31:1:1:0:60:4:1:0:1 +7 65970002 . T TA 59 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=0.02769;SOR=6.29841;LSEQ=AAACCATTTGTTAAAAATAT;RSEQ=AAAAAAAAAAAAAAATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:3,0:27,0:27,3:0.0968:1,0:10.3:1:30.6:1:1:0:60:6:0.0968:0.0645:0.3 0/1:12:5:4,1:6,0:6,5:0.4167:0,2:19.6:1:25.8:1:0.45455:0:59:4:0.3636:0.0833:1.2 +7 65970113 . T C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17846;SOR=Inf;LSEQ=GGTTTGTCCCGGCCCTTGTC;RSEQ=CCGTCCCGTCTCCCTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:169,60:229,0:0:2,0:18.9:1:31:1:1:0:59.6:56.25:1:0:0.1 0/1:168:2:1,1:122,44:166,2:0.0119:2,2:25:0:30:1:0.46514:2.75296:60:4:0.012:0:1.5 +7 65970295 . G A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGTCCACTAACATCTTCA;RSEQ=GATGAACTCCCGCGCCGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:725:0:0,0:381,344:725,0:0:2,0:25.5:1:32:1:1:0:58.5:71.5:1:0:0.2 0/1:579:32:16,16:283,264:547,32:0.0553:2,2:27.8:1:29.2:1:0.85789:1.07181:54.9:31:0.0544:0:1.1 +7 65970528 . A C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=7.48138;LSEQ=GGACTTGGTCGTATTCACTG;RSEQ=GGGCGACGAGAAACGGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:664:23:9,14:264,376:640,23:0.0346:2,2:19.5:1:29.7:1:1:1.09208:57.9:22:0.034:0:1 0/1:538:114:57,57:198,224:422,114:0.2119:2,2:22.5:1:30.2:1:0.59776:1.13:56.5:113:0.2128:0:1.1 +7 65970570 . T G 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0011;SOR=Inf;LSEQ=ACGTCAGGTTCTCAAAGCAG;RSEQ=GGATCCACTTCCTCTGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:533:0:0,0:240,293:533,0:0:2,0:25.6:1:30.2:1:1:0:59.8:87.833:1:0:0.1 0/1:475:9:2,7:204,262:466,9:0.0189:2,2:27.6:1:30:1:0.3108:2.72008:60:18:0.0191:0:1 +7 65970698 . A G 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCCTGCTGGGTGGGCAGGT;RSEQ=GCTCGAGGTGGCGATGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:489:0:0,0:278,211:489,0:0:2,0:26.3:1:29.8:1:1:0:55.7:96.8:1:0:0.1 0/1:428:42:25,17:223,161:384,42:0.0981:2,2:28:1:31.2:1:1:1.06:57:84:0.1002:0:1.2 +7 65970787 . T A 165 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCCTGCGGTCGTAGCACTCG;RSEQ=GGATGCCGGGGTCGTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:40:23,17:426,356:782,40:0.0487:2,2:22.6:1:31.1:1:0.74709:1.13:58.7:39:0.048:0:1.2 0/0:716:0:0,0:384,332:716,0:0:2,0:25.7:1:29.2:1:1:0:59.5:118.333:1:0:0.2 +7 65971009 . T G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=14.51688;LSEQ=AGCCCCTTTTGTCCTCCTCC;RSEQ=AGTACCCGGCGCCATGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:841:43:23,20:375,423:798,43:0.0511:2,2:27.3:1:30.4:1:0.43587:1.30:53.4:20.5:0.0498:0:1.1 0/1:619:272:133,139:164,182:346,272:0.4394:2,2:24:1:30:1:0.74583:1.06:54.5:89.667:0.4461:0:1.2 +7 65971238 . G C 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.03065;SOR=Inf;LSEQ=GCCACGGCCGCCACCCACCG;RSEQ=CCCCCGGCCCGACTTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:458:0:0,0:109,347:456,0:0:2,0:24.9:1:31.6:1:1:0:58:23:0.9954:0:0.2 0/1:331:4:2,2:93,231:324,4:0.0121:2,2:10.8:1:29.3:1:0.58244:2.48:37.5:8:0.0125:0:1.3 +7 65971260 . A G 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.26181;LSEQ=CCCCGGCCCGACTTTGGCCG;RSEQ=AGCCGCCTCGGTCGCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:14:1,13:26,214:240,14:0.0551:2,1:9.9:1:32.2:1:1:1.57702:59.4:28:0.0556:0:1.1 0/1:160:67:10,57:19,74:93,67:0.4188:2,2:16.9:1:30.9:1:0.41203:1.4601:59.7:134:0.4241:0:1.3 +7 65971276 . C G 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.11884;SOR=Inf;LSEQ=GCCGAAGCCGCCTCGGTCGC;RSEQ=GCCCGCCTCGGCCCTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:7,127:134,0:0:2,0:14.6:1:30.3:1:1:0:60:25.8:1:0:0.2 0/1:71:2:1,1:7,62:69,2:0.0282:2,2:5.5:1:27:1:0.21408:8.35:60:4:0.0294:0:3 +7 66224040 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.5;SOR=Inf;LSEQ=ATTTGTGCAATGTATGTGTA;RSEQ=AGTGTCATGCACATTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:8,2:10,0:0:2,0:14.2:1:30.3:1:1:0:43.8:20:1:0:0 0/1:15:2:1,1:8,5:13,2:0.1333:2,2:27.5:1:27.5:1:1:1.54914:38.5:4:0.1333:0:1 +7 66762461 . T A 76 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1;LSEQ=AAAAAAAAATGGACCCATGC;RSEQ=ATAAGCTTTTATATTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:14.8:1:33:0:1:0:22:10:0.5:0:2.6 1/0:2:1:0,1:0,1:1,1:0.5:0,0:20:0:32:0:1:0:22:2:0.5:0:4 +7 66764265 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2188;SOR=0;LSEQ=TGTGGCTTAAAACTCTCCCA;RSEQ=ACTTACCAATATTGGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:159,39:198,2:0.01:2,2:39.5:1:32:1:0.3608:4.03828:23:4:0.0101:0:1.5 0/0:227:0:0,0:167,60:227,0:0:2,0:38.8:1:29.1:1:1:0:38.4:55.75:1:0:0.1 +7 66764392 . T C 58 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12024;SOR=Inf;LSEQ=CTTCCGATCGATAGGTTTGA;RSEQ=GGCCTTAGCAGGTTCTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:28,40:68,0:0:2,0:8.1:1:30.9:1:1:0:25.6:136:1:0:0 0/1:72:4:2,2:38,30:68,4:0.0556:2,2:7.8:1:29:1:1:1.26247:25:8:0.0556:0:1 +7 66767267 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21022;SOR=Inf;LSEQ=GGGGCCTCCACGCCTCGCCA;RSEQ=GCCCCTCGGCCATGTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:56,6:62,0:0:2,0:24.7:1:31.6:1:1:0:59.3:30:1:0:0.1 0/1:53:2:1,1:43,8:51,2:0.0377:2,2:16:1:27.5:1:0.3135:5.12631:60:4:0.0385:0:1 +7 66767335 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49875;SOR=0;LSEQ=GGTTCTCAAGGAGGACGCGC;RSEQ=AGAAGGGAGACCGCGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:135,61:196,2:0.0101:2,2:16.5:1:27.5:1:0.5293:2.20335:60:4:0.0102:0:2 0/0:195:0:0,0:123,72:195,0:0:2,0:23.8:1:29:1:1:0:60:64:1:0:0.2 +7 66767460 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07271;SOR=Inf;LSEQ=ACAGGCGCCCCGCCTCCTGG;RSEQ=CTCCCATTGGCTGCTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:56,145:201,0:0:2,0:24.7:1:31.7:1:1:0:58.1:99.5:1:0:0.2 0/1:145:3:2,1:37,105:142,3:0.0207:2,2:26.7:1:27.7:1:0.1762:5.59:54.7:6:0.021:0:1 +7 66767476 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53253;SOR=0;LSEQ=CTGGGCTCCCATTGGCTGCT;RSEQ=TTGACGTTGTGCTCCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:27,120:147,2:0.0134:2,2:28.5:1:31.5:1:0.34156:4.38:39:4:0.0137:0:1 0/0:87:0:0,0:18,69:87,0:0:2,0:20.6:1:29.3:1:1:0:59.1:86:1:0:0.1 +7 66767579 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03676;SOR=Inf;LSEQ=GTCGAGTCCGTGACGTCAAA;RSEQ=AGCATGGGCCAATCAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:3,19:22,0:0:2,0:26:1:31.7:1:1:0:57.3:21:1:0:0.5 0/1:12:3:0,3:1,8:9,3:0.25:2,0:11:1:32:0:1:0:46:6:0.3:0:2.3 +7 66767611 . T G 39 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=13.000;MSILEN=1;SSF=0.08333;SOR=9.27984;LSEQ=ATCAGAGCACACCGGACTGC;RSEQ=TTTTTTTTTTTTCCCGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:1,2:1,10:11,3:0.2143:2,2:18:1:32:1:0.3956:4.28:40.7:6:0.2143:0:1 1/0:4:3:1,2:0,1:1,3:0.75:0,2:8.7:1:24.7:1:1:0:41.3:2:0.6667:0:2.7 +7 66767624 . C T 30 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49091;SOR=3.05504;LSEQ=GGACTGCTTTTTTTTTTTTT;RSEQ=CCGAACGACCGCAGCAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:1,5:6,2:0.2222:2,0:30.5:1:30.5:1:1:0:59.5:4:0.2222:0:2 1/0:2:1:0,1:0,1:1,1:0.5:0,0:27:0:31:0:1:0:60:2:0.5:0:4 +7 67073834 . T TAAAACAAAAC 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=33;MSI=8.000;MSILEN=5;SSF=0.44173;SOR=1.86975;LSEQ=TACAGAGTGAGACTCTGTCT;RSEQ=AAAACAAAACAAAACAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:7:7,0:20,0:20,7:0.2593:1,0:17.9:1:31.8:1:1:0:49.1:14:0.2593:0.1481:0 0/1:10:4:4,0:6,0:6,4:0.4:0,0:32.8:1:29.9:1:1:0:48:8:0.4:0.1:0.3 +7 67073876 . C CA 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAAAACAAACAAACAAA;RSEQ=AAAAAAACCCACCATGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:2,0:70,10:80,2:0.0241:2,0:31.5:1:31:1:1:0:60:4:0.0244:0:0.5 0/0:39:0:0,0:36,3:39,0:0:2,0:24.3:1:31.5:1:1:0:58.8:38:1:0:0.2 +7 67073935 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21629;SOR=Inf;LSEQ=AAAATCTGTTTTGGACCTTC;RSEQ=AATCAGGATATCAGAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:107,50:157,0:0:2,0:25.6:1:31.2:1:1:0:60:77.5:1:0:0.6 0/1:137:2:1,1:87,48:135,2:0.0146:2,2:41:1:30.5:1:1:1.80409:60:4:0.0148:0:1 +7 67073968 . G A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.35663;LSEQ=AGAAGAAAATGTCCCTTGTG;RSEQ=CATATGAAGGCATAGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:199:117:71,46:49,33:82,117:0.5879:2,2:24.2:1:30:1:1:1.04:60:57.5:0.5897:0:1.6 0/1:202:68:46,22:71,63:134,68:0.3366:2,2:25.3:1:28.3:1:0.05103:1.85:60:136:0.3383:0:1.8 +7 67074004 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.11927;SOR=0;LSEQ=CACAGAGCGGTAGCCAGCCA;RSEQ=CCAGCAAGGGGAGGGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:2,1:131,121:252,3:0.0118:2,2:32:1:29.3:1:1:1.84:60:6:0.0121:0:2.3 0/0:262:0:0,0:132,130:262,0:0:2,0:25.2:1:31.1:1:1:0:59.9:42.667:1:0:0.8 +7 67074017 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.44318;LSEQ=CCAGCCAGCCAGCAAGGGGA;RSEQ=GGTTTTACACCAAGAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:279:162:83,79:59,58:117,162:0.5806:2,2:25.7:1:30.8:1:0.90402:1.03:60:53:0.5846:0:1.6 0/1:279:106:50,56:88,85:173,106:0.3799:2,2:26:1:29.4:1:0.62188:1.15891:59.8:105:0.3846:0:1.6 +7 67074055 . A G 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10197;SOR=Inf;LSEQ=AAAGCCACTCCTGCAGAAAA;RSEQ=GTGATGAGTAGAGGGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:106,162:268,0:0:2,0:26.7:1:31.2:1:1:0:59.9:66:1:0:0.6 0/1:236:3:2,1:99,134:233,3:0.0127:2,2:20.7:1:26.3:1:0.57764:2.70:60:2:0.0087:0:2 +7 67074069 . G A 23 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.59905;SOR=2.31882;LSEQ=AGAAAAAGTGATGAGTAGAG;RSEQ=GCATTTCTCAGACTGCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:1:0,1:77,153:230,1:0.0043:2,0:32:0:19:0:1:0:60:0:0:0:2 0/1:200:2:1,1:78,119:197,2:0.01:2,2:10:1:23.5:1:1:1.52:60:4:0.0109:0:1.5 +7 67074094 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51327;SOR=0;LSEQ=TTCTCAGACTGCTTTGGGCA;RSEQ=AAGCAGTTTTCTTAGCAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:1,1:44,120:164,2:0.012:2,2:28.5:1:29:1:0.46988:2.71:60:4:0.0123:0:1.5 0/0:117:0:0,0:36,81:117,0:0:2,0:25.2:1:30.6:1:1:0:60:234:1:0:0.3 +7 67074170 . A G 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.95102;LSEQ=GAGCCCAGAGGTCAGAAAAG;RSEQ=GGTGAGATGATTCTGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:0,12:0,19:19,12:0.3871:1,0:23.8:1:32.6:1:1:0:60:24:0.4:0:1 0/1:16:6:0,6:0,10:10,6:0.375:0,0:22.8:1:30.8:1:1:0:60:12:0.4:0:1 +7 68105734 . A C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16471;SOR=0;LSEQ=AACATAAAAACTCCCAGAAA;RSEQ=CTAGAAATAGCCTTTCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:14,5:19,2:0.0952:2,2:18:1:30:1:0.5:2.64575:60:4:0.0952:0:1 0/0:30:0:0,0:17,13:30,0:0:2,0:24.9:1:28.1:1:1:0:60:29:1:0:0.1 +7 68105743 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51429;SOR=Inf;LSEQ=ACTCCCAGAAAACTAGAAAT;RSEQ=GCCTTTCGGCCAGAACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,6:21,0:0:2,0:26.2:1:29:1:1:0:60:42:1:0:0.1 0/1:34:2:1,1:17,15:32,2:0.0588:2,2:31:1:30.5:1:1:1.12916:60:4:0.0588:0:1 +7 68105811 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18363;SOR=Inf;LSEQ=AAAGCAAAGGGAAAGAGGAG;RSEQ=AGCACCCGATATATGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:16,22:38,0:0:2,0:23.3:1:30.7:1:1:0:59.7:76:1:0:0.2 0/1:29:2:1,1:14,13:27,2:0.069:2,2:33:1:32.5:1:1:1.07415:60:4:0.069:0:1 +7 68105921 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13178;SOR=0;LSEQ=GTAGACATCAAGGGAATGGG;RSEQ=ACTGTTCAAAAAAGAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:27,2:0.069:2,2:28:1:29:1:1:1.07415:60:4:0.069:0:1 0/0:50:0:0,0:28,22:50,0:0:2,0:17:1:27.4:1:1:0:57.4:15.667:1:0:0.2 +7 69180637 . G T 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12422;SOR=Inf;LSEQ=GTCAAAATGGAGAGATGAAG;RSEQ=ATTGGTGTTGGGTAATGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,26:45,0:0:2,0:23.9:1:31.4:1:1:0:60:44:1:0:0.2 0/1:25:2:1,1:9,14:23,2:0.08:2,2:7:0:30:1:1:1.53:60:4:0.08:0:1 +7 69180656 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50529;SOR=0;LSEQ=GGATTGGTGTTGGGTAATGA;RSEQ=AGCAAGGGATGGTCATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:11,13:24,2:0.0769:2,2:24.5:1:28:1:1:1.17:60:4:0.0769:0:1 0/0:18:0:0,0:6,12:18,0:0:2,0:20.5:1:29.8:1:1:0:60:36:1:0:0 +7 69180681 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47895;SOR=0;LSEQ=AGGGATGGTCATAGAACTCA;RSEQ=AGATGATAATGTGACCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:1,8:9,2:0.1818:2,2:20.5:1:30.5:1:0.34545:6.00:60:4:0.1818:0:1 0/0:9:0:0,0:1,8:9,0:0:2,0:27.2:1:29.2:1:1:0:60:18:1:0:0 +7 70231200 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49614;SOR=Inf;LSEQ=CCGCCCTACCTGCGGACCGA;RSEQ=TTCCATCAGCACCAGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:27,27:54,0:0:2,0:25.8:1:32.4:1:1:0:60:108:1:0:0.2 0/1:58:2:1,1:30,26:56,2:0.0345:2,2:11.5:1:28.5:1:1:1.15099:60:4:0.0351:0:4.5 +7 70231291 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13564;SOR=0;LSEQ=CCCACGCCATCCCACCCACC;RSEQ=CCATCATGCCGACGCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:3,13:16,2:0.1111:2,2:25:1:28.5:1:0.40523:3.89:60:4:0.1111:0:1.5 0/0:30:0:0,0:11,19:30,0:0:2,0:20.5:1:29.3:1:1:0:60:14:1:0:0.3 +7 70859491 . C T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01122;SOR=1.50163;LSEQ=TCTGCTCCACTTTATGTGTT;RSEQ=TGACAGTTTCCCATTGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:337:186:100,86:73,78:151,186:0.5519:2,2:25.7:1:30.6:1:0.32674:1.24:60:61:0.5512:0:1.1 1/0:325:211:103,108:57,57:114,211:0.6492:2,2:24.7:1:29.7:1:0.90752:1.04842:60:210:0.6502:0:1.1 +7 70859603 . A G 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00172;SOR=Inf;LSEQ=TCCTGGGTCTTTGTAGCTCC;RSEQ=TTGGTCCAATGATGAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:27,102:129,0:0:2,0:20.1:1:30.6:1:1:0:59.7:42:1:0:0.1 0/1:90:7:2,5:26,57:83,7:0.0778:2,2:28:1:29.3:1:1:1.13871:60:14:0.0787:0:1 +7 70859670 . C T 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02797;SOR=0;LSEQ=GTGACCAGGATGGAGGAATT;RSEQ=GGGTGCACAGAGGTATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:1,5:0,33:33,6:0.1538:1,2:19.7:1:32.3:1:0.15385:0:54:12:0.1538:0:1 0/0:33:0:0,0:0,33:33,0:0:1,0:24.1:1:29.6:1:1:0:60:66:1:0:0.1 +7 71296782 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTACTCGGGAAGCTGAGT;RSEQ=AGAAGAATCGCATGAGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:28.5:1:1:0:60:4:1:0:1 +7 71297418 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22833;SOR=0;LSEQ=TTGCTTGTGCTTAGCAAATG;RSEQ=ATGAAGTGTGGATTTACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:141,57:198,2:0.01:2,2:9:1:28:1:0.49693:2.46096:60:4:0.0102:0:1 0/0:218:0:0,0:155,63:218,0:0:2,0:23.6:1:28.4:1:1:0:60:42.6:1:0:0.1 +7 71297516 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.48167;SOR=0.89926;LSEQ=TTCCCAGATGCCAAGGTGAC;RSEQ=GCTGAAAACCCTTCAATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:170:79,91:125,141:266,170:0.389:2,2:24.7:1:30.5:1:0.92196:1.02114:60:340:0.3926:0:1.1 0/1:423:154:74,80:119,150:269,154:0.3641:2,2:26.9:1:29.6:1:0.47831:1.17:59.9:76:0.3645:0:1.1 +7 71679909 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTCACCGTCTCCCATCAC;RSEQ=CCCAGATAGGACTATCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:25:1:29.5:1:1:0:37:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 71681409 . C A 50 d5;MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTATGTCTTTAAAAAAAAA;RSEQ=ATTAAAGATAAATAAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:5:1:31.7:1:1:0:60:6:0.75:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:35:0:30:0:1:0:60:2:1:0:1 +7 71681489 . T C 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTGGAGAAGCCATAATTCTG;RSEQ=GTATCATAGGGTGCATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:7,4:1,0:1,11:0.9167:0,2:17.7:1:30.7:1:1:0:60:22:0.9167:0:1.4 1/1:11:11:8,3:0,0:0,11:1:0,2:18.7:1:31:1:1:0:60:22:1:0:1 +7 71681620 . T G 72 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.79176;LSEQ=CCTGCCTTCTCACTCCTGAG;RSEQ=TCTAGACATAGAGAACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:3,2:0.4:2,0:25.5:1:31.5:1:1:0:60:4:0.4:0:1 1/0:9:5:1,4:2,2:4,5:0.5556:2,2:27.8:1:31.4:1:0.52381:3.38757:60:10:0.5556:0:1 +7 71682465 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTCTATAGCAACCAGTT;RSEQ=CTCTTCAAAGAGCAAAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:30:1:1:0:60:4:1:0:1 +7 73260381 . TTC T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAACGCTGACGTATGCTGCC;RSEQ=TCTCTCTCTGTTTCGGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:19,11:30,2:0.0625:2,2:28:1:31:1:1:1.69662:40:4:0.0625:0:0 0/0:12:0:0,0:8,4:12,0:0:2,0:20.9:1:28.4:1:1:0:53.8:24:1:0:0.4 +7 73260415 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07949;SOR=Inf;LSEQ=TTCGGCTACCTAAGAGGGAA;RSEQ=GGCCCCCTGTCCTACGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:22,20:42,0:0:2,0:26:1:32:1:1:0:47.8:41:1:0:0.1 0/1:17:2:1,1:10,5:15,2:0.1176:2,2:41:0:28:1:1:1.91491:41:4:0.1176:0:1.5 +7 73260509 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52688;SOR=Inf;LSEQ=CCCCCTTGTCTCCTATGCAA;RSEQ=AAATATCAGCACTTCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:11,0:0:2,0:22.7:1:27.9:1:1:0:48.7:22:1:0:0 0/1:20:2:1,1:7,11:18,2:0.1:2,2:22:1:28:1:1:1.54:47:4:0.1053:0:1.5 +7 74307015 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49927;SOR=Inf;LSEQ=CGCGCCCTCTTTGAGAACCA;RSEQ=GGCTTCCAACCTCCCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:48,97:145,0:0:2,0:25.1:1:30.4:1:1:0:38.8:71.5:1:0:0.1 0/1:158:2:1,1:56,100:156,2:0.0127:2,2:41.5:1:30.5:1:1:1.78:45:4:0.0128:0:1 +7 74307022 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=TCTTTGAGAACCACGGCTTC;RSEQ=AACCTCCCTGGAAATGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:39,104:143,0:0:2,0:23.4:1:31.9:1:1:0:37.1:34.75:1:0:0.1 0/1:152:2:1,1:46,104:150,2:0.0132:2,2:31:1:29.5:1:0.52422:2.25:27:4:0.0132:0:1 +7 74310274 . C T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55643;SOR=Inf;LSEQ=CAAACCTATTGATCGGAAGT;RSEQ=AGTCCATCAGATTTGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:38,33:71,0:0:2,0:14.2:1:32:1:1:0:31.7:142:1:0:0.1 0/1:167:3:1,2:103,61:164,3:0.018:2,2:7:1:26.7:1:0.55739:3.35164:60:6:0.0181:0:1 +7 74310385 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11461;SOR=0;LSEQ=TAATATTGGTAAGTTTGGGA;RSEQ=AGTTTTAAGCCACAAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:43,42:85,2:0.023:2,2:16.5:1:26.5:1:1:1.02354:29:4:0.023:0:1 0/0:169:0:0,0:73,94:167,0:0:2,0:14.6:1:30.8:1:1:0:26:54.667:0.988:0:0.1 +7 75140392 . G T 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CGTGATCAAACACCAGTCGA;RSEQ=TCCCAACCTTCACCGACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:31.5:1:31:1:1:0:25:4:0.5:0:1 0/0:5:0:0,0:2,3:5,0:0:2,0:18.4:1:31.6:1:1:0:54.6:10:1:0:0.4 +7 76669302 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.18325;SOR=Inf;LSEQ=AGGCCATCAAACCTATTGAT;RSEQ=GGAAGTCAGTCCATCAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:112,53:165,0:0:2,0:14:1:31.3:1:1:0:32:81.5:1:0:0.1 0/1:124:2:1,1:95,27:122,2:0.0161:2,2:14:1:28:1:0.40205:3.4731:35:4:0.0167:0:1 +7 76669333 . A C 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12535;SOR=0.78996;LSEQ=CCATCAGATTTGCTCTGGGC;RSEQ=GGTGGTACTGAGTCTAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:143:74,69:247,184:431,143:0.2224:2,2:13.8:1:30.1:1:0.28501:1.25119:24.9:34.75:0.2196:0:1.1 0/1:521:96:50,46:202,151:353,96:0.1843:2,2:12.8:1:29.5:1:0.41706:1.23015:25.6:95:0.1848:0:1.1 +7 76669341 . C T 159 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=49.05857;LSEQ=TTTGCTCTGGGCAGGTGGTA;RSEQ=TGAGTCTAAGCACTGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:759:1:0,1:417,341:758,1:0.0013:2,0:1:0:25:0:0.45059:0:60:2:0.0013:0:1 0/1:673:41:24,17:346,286:632,41:0.0609:2,2:26.1:1:29.7:1:0.74648:1.17:42.6:82:0.0614:0:1.1 +7 77857327 . A C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09804;SOR=Inf;LSEQ=ACATGATCTCTGTTGCAACT;RSEQ=CTCAACTCTGCCCTCACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:23,0:0:2,0:23:1:28.2:1:1:0:60:22:1:0:0 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:46.5:1:30.5:1:1:1.87:60:4:0.1818:0:1 +7 78021432 . C T 125 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=0;LSEQ=GATACGATCCTTGCCTCAAA;RSEQ=ACTTTACCATCTACTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:15,1:0,0:0,16:1:0,1:23.3:1:31.4:1:1:0:60:32:1:0:1.3 1/0:5:3:3,0:2,0:2,3:0.6:0,0:38.7:1:31:1:1:0:60:6:0.6:0:1.3 +7 78021500 . A G 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00469;SOR=Inf;LSEQ=GAAATGGATCTGTAAGGGGT;RSEQ=TTTATGCATGAAGGTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:68,5:73,0:0:2,0:24:1:28.9:1:1:0:60:72:1:0:0.2 0/1:40:5:5,0:34,1:35,5:0.125:1,0:27.6:1:32.6:1:1:0:60:10:0.125:0:1.2 +7 78021636 . A T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00068;SOR=0.5572;LSEQ=TGAAGAAGGCAAAAAATAGA;RSEQ=GTGGGGGCTGTTAGGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:113:57,56:287,241:528,113:0.1763:2,2:28.2:1:30.7:1:0.46811:1.16969:60:112:0.1767:0:1.1 0/1:554:59:26,33:258,237:495,59:0.1065:2,2:29.3:1:29.7:1:0.2714:1.38088:60:118:0.1081:0:1.1 +7 78319485 . T C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13122;SOR=0.14271;LSEQ=GTTTTTATTTTCCTATCTTT;RSEQ=AATTCTTGACAAAATTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:8,0:1,0:1,8:0.8889:0,0:24:1:33.4:1:1:0:60:16:0.8889:0:1 1/0:8:4:4,0:4,0:4,4:0.5:0,0:9.5:1:30.8:1:1:0:60:8:0.5:0:2 +7 78319656 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.35096;SOR=3.32753;LSEQ=GCATATGAGTTTCCATAATA;RSEQ=CATGTATGTTTCACAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:0,1:176,93:269,1:0.0037:2,0:1:0:25:0:0.34815:0:60:2:0.0037:0:3 0/1:245:3:1,2:144,98:242,3:0.0122:2,2:23:1:26:1:0.56879:2.92578:60:6:0.0125:0:2.3 +7 78319710 . C A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.03517;SOR=Inf;LSEQ=TTTGCTAAATTCCCATTCCT;RSEQ=TCTGACCGCTGCTCCCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:192,204:396,0:0:2,0:27.3:1:32.6:1:1:0:59.9:197:1:0:1.5 0/1:304:4:3,1:144,156:300,4:0.0132:2,2:12.5:1:26.8:1:0.35674:3.24:60:8:0.0134:0:1.5 +7 78319728 . G A 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17582;LSEQ=CTCTCTGACCGCTGCTCCCT;RSEQ=CTTAACTGTCATCATAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:345:289:118,171:25,30:55,289:0.8377:2,2:26.7:1:29.2:1:0.55249:1.20695:60:71.25:0.8407:0:2.1 0/1:259:123:54,69:56,80:136,123:0.4749:2,2:25.7:1:27.7:1:0.70631:1.12:60:29.75:0.4722:0:2.1 +7 78319731 . T C 270 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCTGACCGCTGCTCCCTGCT;RSEQ=AACTGTCATCATAGCATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:340:340:140,200:0,0:0,340:1:0,2:26.2:1:32.2:1:1:0:60:55.667:1:0:1.9 1/0:249:173:74,99:31,45:76,173:0.6948:2,2:26.3:1:30.8:1:0.78252:1.08:60:85.5:0.6951:0:1.8 +7 78319761 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17232;SOR=Inf;LSEQ=CATAGCATTAAGAAGCAAAA;RSEQ=TATTTATAAAATTTGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:71,165:236,0:0:2,0:22.7:1:31.1:1:1:0:60:472:1:0:1.5 0/1:168:2:1,1:57,109:166,2:0.0119:2,2:8.5:1:27.5:1:1:1.90:60:4:0.0121:0:1 +7 78319797 . T C 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06577;SOR=Inf;LSEQ=AAGAACTGTAGACATTAGCT;RSEQ=GAGAATGTGAGCCACTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:24,106:130,0:0:2,0:24.9:1:30.8:1:1:0:60:260:1:0:0.8 0/1:89:3:1,2:21,65:86,3:0.0337:2,2:18:1:21.7:1:1:1.54:60:2:0.0227:0:2.3 +7 78319926 . G A 105 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTGTTGTATAAGAGAGA;RSEQ=CACACAAAAGATACTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:19.2:1:30.5:1:1:0:60:22:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:46:0:29:0:1:0:60:2:1:0:1 +7 78867410 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24903;SOR=0.8323;LSEQ=ACAAATCTAAGCATTCCATT;RSEQ=GATTCTACTGGGAAATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:412:227:108,119:95,89:184,227:0.551:2,2:25.5:1:30.9:1:0.42876:1.17566:60:226:0.5526:0:1.1 1/0:289:146:75,71:70,71:141,146:0.5052:2,2:26.8:1:29.2:1:0.81371:1.07:60:35.5:0.4982:0:1.1 +7 78902550 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15182;SOR=Inf;LSEQ=AATCACCCTTAAGATGGTAG;RSEQ=CCAAAAAAAAATAGTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:103,9:112,0:0:2,0:26:1:31:1:1:0:60:27:1:0:0.2 0/1:72:2:1,1:61,9:70,2:0.0278:2,2:25.5:1:27:1:0.26017:6.48246:60:4:0.0278:0:1 +7 78902552 . C CA 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.24087;SOR=0.68731;LSEQ=TCACCCTTAAGATGGTAGGC;RSEQ=AAAAAAAAATAGTTTTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:62:56,6:56,10:66,62:0.4844:2,2:25.4:1:30.1:1:0.42768:1.66:59.9:61:0.4959:0.0781:0.1 0/1:74:29:26,3:35,8:43,29:0.3919:2,2:25.9:1:29.6:1:0.50721:1.96:60:58:0.3919:0.0135:0.2 +7 78902615 . G T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.31301;SOR=4.23257;LSEQ=CACTTAGCCAATTAGCCACA;RSEQ=AAAATTAGTACTGAATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:1:0,1:213,124:337,1:0.0029:2,0:1:0:24:0:0.36982:0:60:2:0.003:0:2 0/1:242:3:1,2:148,90:238,3:0.0124:2,2:16:1:26:1:0.55972:3.27219:60:6:0.0128:0:1.7 +7 78902684 . G A 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77825;SOR=0.95873;LSEQ=CTTAGTATGAGGCTCCCCAT;RSEQ=TTCCAGGAAACAATTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:461:255:105,150:99,107:206,255:0.5531:2,2:27.1:1:29.9:1:0.15729:1.32094:60:84:0.5538:0:1.1 1/0:363:197:89,108:78,86:164,197:0.5427:2,2:24.3:1:28.5:1:0.67254:1.10031:60:48.25:0.5406:0:1.1 +7 78924617 . G T 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATTTTAAGACCAGAGTTCA;RSEQ=ATAGTGAAGGAATAGACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:305:0:0,0:181,123:304,0:0:2,0:26:1:32.5:1:1:0:59.8:100.333:0.9967:0:0.3 0/1:240:16:10,6:132,92:224,16:0.0667:2,2:20.8:1:29.4:1:1:1.16:60:32:0.0675:0:1.4 +7 78924689 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0018;SOR=0.59596;LSEQ=AAAATCAAGACAAAAAGTGA;RSEQ=TTCAGTATAAAATAATCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:322:173:69,104:67,82:149,173:0.5373:2,2:26.5:1:30.6:1:0.36767:1.23072:60:172:0.5375:0:1.2 0/1:274:112:42,70:77,83:160,112:0.4088:2,2:27.5:1:29.6:1:0.10626:1.54367:60:111:0.4081:0:1.1 +7 78924696 . A G 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAAAAAGTGACTTCAGT;RSEQ=TAAAATAATCAGTGCTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:125,181:306,0:0:2,0:25.4:1:30:1:1:0:60:101:0.9967:0:0.7 0/1:259:29:14,15:97,133:230,29:0.112:2,2:28:1:31.3:1:0.55534:1.28:60:58:0.1124:0:1.2 +7 78924711 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0965;SOR=Inf;LSEQ=TCAGTATAAAATAATCAGTG;RSEQ=TATCACCTGCAGTATATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:96,164:260,0:0:2,0:24.5:1:33:1:1:0:60:259:0.9923:0:0.6 0/1:223:3:1,2:87,132:219,3:0.0135:2,2:10:1:26.3:1:1:1.3166:60:6:0.0135:0:1.7 +7 78924870 . G T 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCAGGCACGGTCGAGTCAA;RSEQ=GGAAAATGGTTAATATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:24.3:1:28.6:1:1:0:60:7:1:0:1.5 1/1:7:7:1,6:0,0:0,7:1:0,2:19.6:1:30.3:1:1:0:60:14:1:0:1.1 +7 79764514 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51515;SOR=0;LSEQ=CGCCGAGGACAAGGCGGCGG;RSEQ=GGAGCGGAGTAAGATGATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:30:1:31.5:1:1:1.36624:60:4:0.1429:0:1 0/0:8:0:0,0:5,3:8,0:0:2,0:15.3:1:28.3:1:1:0:60:16:1:0:0 +7 80802042 . GA G 42 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.11242;SOR=Inf;LSEQ=AAAAAAGAAACTGGTTCTGG;RSEQ=AAACCAGCCATAACTTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:84,65:149,0:0:2,0:15.1:1:29.8:1:1:0:41.9:36.25:1:0:0.7 0/1:140:3:0,3:69,68:137,3:0.0214:2,0:32:0:27:0:0.24476:0:60:6:0.0214:0:1 +7 80802077 . C G 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00079;SOR=Inf;LSEQ=CTTAGGGGTTCTTCTTTCAC;RSEQ=CAATCCCATTGGAATTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:163,150:313,0:0:2,0:28.4:1:31.1:1:1:0:41.8:43.714:1:0:0.7 0/1:263:9:6,3:134,119:253,9:0.0342:2,2:14.1:1:29.1:1:0.50973:1.77:33.3:18:0.0347:0:2 +7 80802110 . A C 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.94109;SOR=1.01787;LSEQ=AATTCTGCTTTGCTATAGAA;RSEQ=CATGCTCAAACCAAGGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:403:251:120,131:70,80:150,251:0.6228:2,2:28.7:1:31.9:1:0.83694:1.05:34.4:82.667:0.6247:0:1.1 1/0:378:237:119,118:64,77:141,237:0.627:2,2:27.8:1:30.8:1:0.39528:1.21:36.1:236:0.626:0:1.1 +7 80802406 . C T 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATGAAACCTATGAATTC;RSEQ=TTGTATCATATATATTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:33:1:31.3:1:1:0:50.8:8:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 81061460 . T C 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCTCTTCCCCCCTTCGCT;RSEQ=GGCACTTCTCCTTCCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:5,5:10,6:0.375:2,2:20.7:1:32.3:1:1:1:54.7:12:0.4:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:41:0:32:0:1:0:60:2:1:0:0 +7 81061523 . C T 61 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=2.56905;LSEQ=TTCCTTGTTACCTTCCGCCA;RSEQ=GATTGTAAGTTTCCTGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:4,0:7,4:11,4:0.2667:2,0:35.3:1:30.5:1:0.51648:0:41.8:8:0.2667:0:1.8 1/0:2:1:1,0:1,0:1,1:0.5:0,0:48:0:30:0:1:0:32:2:0.5:0:1 +7 81061668 . A G 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00035;SOR=Inf;LSEQ=TATTCTTGTAGATCCTATGT;RSEQ=CCACCTGCAACAGTGGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:156,112:268,0:0:2,0:28.1:1:28.5:1:1:0:60:43.667:0.9924:0:0.3 0/1:162:8:4,4:97,57:154,8:0.0494:2,2:35.4:1:31.1:1:0.47624:1.69586:60:16:0.0497:0:1 +7 81061732 . G A 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14572;SOR=1.39037;LSEQ=TTAACCTATAAGTATGGCCT;RSEQ=AGCTCCACTCAAAGATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:72:26,46:43,69:112,72:0.3913:2,2:20.2:1:29.1:1:0.87611:1.10198:60:23:0.3855:0:1.2 0/1:144:68:28,40:31,45:76,68:0.4722:2,2:26.4:1:28.2:1:1:1.02:60:33:0.4748:0:1.1 +7 81061754 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19905;SOR=Inf;LSEQ=GCTCCACTCAAAGATTTTCA;RSEQ=ACCTGAAACTGTGGCAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:26,99:125,0:0:2,0:21.3:1:32:1:1:0:60:250:0.9921:0:0.4 0/1:102:2:1,1:29,71:100,2:0.0196:2,2:16:1:25.5:1:0.50379:2.42:60:4:0.0198:0:1 +7 81061893 . C G 77 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.71643;LSEQ=GGGATGCTCAGAGCATGGTT;RSEQ=ACAGGGAACAGCTGAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:1,6:7,5:0.4167:2,2:30.2:1:33.2:1:1:1.45:47.6:10:0.4167:0:1.2 0/1:3:1:1,0:0,2:2,1:0.3333:0,0:1:0:30:0:0.33333:0:60:2:0.5:0:1 +7 81062013 . C A 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.71617;SOR=0.63912;LSEQ=GGGCAGGATTCTCCTTCAGG;RSEQ=ATTCAATCAACTGTCATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:19:14,5:5,1:6,19:0.76:2,2:24.1:1:31:1:1:1.74814:60:38:0.76:0:1.8 1/0:15:10:9,1:4,1:5,10:0.6667:2,2:20.5:1:29:1:1:2.12:60:20:0.6667:0:1.8 +7 81062046 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.49648;SOR=0;LSEQ=GTCATCCCACCTGAGCAAAA;RSEQ=CAGCAGCAGAAACAGCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:25,11:36,2:0.0526:2,2:36:1:29.5:1:0.5377:2.2191:60:4:0.0526:0:2.5 0/0:32:0:0,0:19,13:32,0:0:2,0:24.5:1:30.1:1:1:0:60:64:1:0:1.1 +7 81062065 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36727;SOR=1.59344;LSEQ=AGCAGCAGCAGAAACAGCAG;RSEQ=AGCAGGACCACATCTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:26:14,12:14,5:19,26:0.5652:2,2:25.2:1:31.9:1:0.22239:2.35358:60:52:0.5909:0:1.6 1/0:37:25:15,10:5,7:12,25:0.6757:2,2:29.6:1:30.2:1:0.48211:2.06:60:50:0.6757:0:1.4 +7 81076550 . A G 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.38462;SOR=0;LSEQ=ATTTAATCAAACATTTTAAT;RSEQ=CTGTGAAAATTCTTAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:26.6:1:33.3:1:1:0:60:16:0.6667:0:1.8 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:29:0:1:0:60:2:1:0:0 +7 81076607 . C T 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02667;SOR=0;LSEQ=AAAACAAACTCAAAAATATA;RSEQ=GTGCCCTATGAACATAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:9,0:9,0:9,9:0.5:0,0:17.6:1:30.3:1:1:0:60:18:0.5:0:1.7 0/0:7:0:0,0:7,0:7,0:0:0,0:28.4:1:32.4:1:1:0:60:14:1:0:0 +7 81076682 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54801;SOR=0;LSEQ=AAAAATTGCTTTTGGATTTT;RSEQ=CTTCTTTTTTCCTGTACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:57,0:57,2:0.0339:1,0:33:1:30:0:1:0:60:4:0.0345:0:1 0/0:30:0:0,0:30,0:30,0:0:1,0:24.2:1:31.8:1:1:0:60:60:1:0:0.3 +7 81076719 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52446;SOR=0;LSEQ=CATCAAAAAAATCATGCAGT;RSEQ=CCCTTCTAATAATAAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:101,22:123,2:0.016:2,2:25.5:1:28.5:1:0.33535:4.51219:60:4:0.0164:0:2 0/0:78:0:0,0:65,13:78,0:0:2,0:21.3:1:31.4:1:1:0:60:156:1:0:0.5 +7 81076743 . A C 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16623;SOR=1.3706;LSEQ=TTCTAATAATAAATATAAAC;RSEQ=TTTTAACTATTTTTGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:76:57,19:100,39:139,76:0.3519:2,2:22.4:1:32.1:1:0.74812:1.17:60:152:0.3585:0:1.3 0/1:164:70:49,21:71,23:94,70:0.4268:2,2:21.5:1:30.4:1:0.47808:1.32068:60:140:0.4321:0:1.3 +7 81076832 . G A 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69721;SOR=0.94341;LSEQ=GAAACTGACAGCAGAACTAC;RSEQ=TGCAATGTCCCTGATAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:503:220:116,104:144,138:282,220:0.4374:2,2:25.2:1:31:1:0.71972:1.07:59.8:219:0.4415:0:1.2 0/1:468:198:98,100:137,132:269,198:0.4231:2,2:26.9:1:29.2:1:0.77931:1.05891:60:197:0.4264:0:1.2 +7 81076924 . G A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50985;SOR=0;LSEQ=CTACTCCCTGTGAGGGATTC;RSEQ=TATTTACCTTCATCTGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:30,151:181,2:0.0109:2,2:6.5:1:29.5:1:0.31087:4.97:60:4:0.0112:0:1.5 0/0:135:0:0,0:35,100:135,0:0:2,0:21.6:1:30.5:1:1:0:60:270:1:0:0.5 +7 81076933 . T A 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01582;LSEQ=GTGAGGGATTCGTATTTACC;RSEQ=TCATCTGCTATGTGATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:65:8,57:10,79:89,65:0.4221:2,2:22.3:1:31.2:1:1:1.11:60:130:0.4248:0:1.1 0/1:108:46:9,37:11,51:62,46:0.4259:2,2:18.2:1:29.5:1:0.80798:1.13:60:45:0.4286:0:1.1 +7 81076943 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.51807;SOR=0;LSEQ=CGTATTTACCTTCATCTGCT;RSEQ=TGTGATGGTGGTGGGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:11,112:123,2:0.016:2,2:23.5:1:31.5:1:0.18348:9.79:60:4:0.0161:0:2 0/0:83:0:0,0:10,73:83,0:0:2,0:20.3:1:29.8:1:1:0:60:166:1:0:0.4 +7 81331847 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16017;SOR=Inf;LSEQ=TCCACATTCTCTGAAATCTT;RSEQ=ATGTAAAAGACAGTTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:223,55:278,0:0:2,0:23.4:1:32.2:1:1:0:60:138:1:0:0 0/1:186:2:1,1:133,50:183,2:0.0108:2,2:17.5:1:27.5:1:0.47644:2.64368:60:4:0.0108:0:1 +7 81332000 . C T 180 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=50.60787;LSEQ=GATTTGGAATGGCACATCCA;RSEQ=GACCAGGAACAATGACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1349:2:0,2:687,657:1344,2:0.0015:2,0:1:0:26:0:0.23952:0:60:4:0.0015:0:1 0/1:1028:72:35,37:504,452:956,72:0.07:2,2:23.1:1:29.3:1:0.54159:1.17857:60:71:0.0697:0:1.1 +7 81332114 . T TA 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.07583;SOR=Inf;LSEQ=AACAAAGTATTATTAGGAAT;RSEQ=AAAAAAAAGCTCATTAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:46,296:342,0:0:2,0:24.2:1:28.6:1:1:0:59.9:84.5:1:0:0.1 0/1:252:3:1,2:48,201:249,3:0.0119:2,2:28.7:1:27.7:1:0.47877:2.09:60:6:0.012:0:0 +7 81335460 . C T 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.13333;LSEQ=CACAGAGAGACCCAAACGCA;RSEQ=GCATATATACATATATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:49:48,1:30,1:31,49:0.6125:1,1:25.3:1:30.9:1:1:1.59:60:48:0.6076:0:1.1 0/1:35:6:6,0:27,1:28,6:0.1714:1,0:14.2:1:31.5:1:1:0:60:12:0.1765:0:1 +7 81336265 . C T 82 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAAAGAAGTAGTGAGGA;RSEQ=TGAAAAAAGCCTATTGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:2,0:2,6:0.75:0,2:25.3:1:31.8:1:1:0:52.3:12:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 81336535 . C A 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14226;LSEQ=AAAATGAATACATATTATAA;RSEQ=CTTAAGAGCAAAGTGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:110:93,17:248,61:309,110:0.2619:2,2:25.7:1:30.6:1:0.39232:1.34:60:220:0.2625:0:1 0/1:292:14:11,3:217,60:277,14:0.0479:2,2:18.4:1:29.9:1:1:1.01:60:28:0.0486:0:1 +7 81336744 . C T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.28224;SOR=0;LSEQ=AGAGTGACTGCCAATTAATG;RSEQ=AAAGCCTGTGGCTCCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:0,3:20,219:239,3:0.0124:2,0:22.7:1:23.3:1:1:0:60:2:0.0084:0:1 0/0:157:0:0,0:15,142:157,0:0:2,0:24.3:1:31.6:1:1:0:60:77.5:1:0:0.1 +7 81338269 . T A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTTGAGAAAAGGGTATAC;RSEQ=AAAAAAAGAACTTTAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 81339005 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTCTAGAATTTAAAATT;RSEQ=CCATTTTTCATTTGATTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:34:0:1:0:52:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 81339304 . A C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01641;SOR=4.52957;LSEQ=AATTATAGTCCAGAGCTTAC;RSEQ=GTCTGGCAAGCAGATGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:84:57:56,1:27,0:27,57:0.6786:1,1:25.7:1:31.5:1:1:0:60:56:0.6829:0:1.1 1/1:32:29:29,0:3,0:3,29:0.9063:0,1:21.7:1:31.2:1:1:0:60:58:0.9063:0:1.1 +7 81339357 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5487;SOR=0;LSEQ=TTACTGCCTCACCCAGGTGC;RSEQ=CTGTGGAGGGTACAACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:186,1:187,2:0.0106:1,0:25:1:32:1:1:0:60:4:0.0108:0:1 0/0:98:0:0,0:97,1:98,0:0:1,0:23.8:1:29.5:1:1:0:60:23.5:1:0:0.3 +7 81340916 . C A 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00216;SOR=0;LSEQ=AACCAAATATATATTAAAAT;RSEQ=CAAGTATCAATGAATTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:12:1,11:16,163:179,12:0.0628:2,2:21.3:1:30.3:1:1:1.07934:60:24:0.0638:0:1 0/0:127:0:0,0:17,110:127,0:0:2,0:22:1:30.6:1:1:0:60:126:1:0:0.1 +7 81340934 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51924;SOR=0;LSEQ=ATCCAAGTATCAATGAATTC;RSEQ=GTAATTTACTAAAATTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:2,118:120,2:0.0164:1,2:21.5:1:29.5:1:0.04877:48.38:60:4:0.0164:0:2 0/0:80:0:0,0:6,74:80,0:0:2,0:22.8:1:30.6:1:1:0:60:160:1:0:0.1 +7 81346292 . A G 33 v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAATGCTTTCGGAATCCCA;RSEQ=TGGAAATCTTCTGAGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:14,0:14,2:0.125:1,0:7:1:33:1:1:0:60:4:0.125:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 81346393 . CTG C 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.31283;SOR=0;LSEQ=AGAGAGACCATGTGGTGTGT;RSEQ=TGTGTGTGTTGTGTACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:4:4,0:84,1:85,4:0.0449:1,0:23.8:1:32.3:1:1:0:60:8:0.046:0.0112:0.3 0/0:39:0:0,0:38,1:39,0:0:1,0:23.4:1:30.5:1:1:0:60:38:1:0:0.1 +7 81346685 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.00983;LSEQ=GTTCCCAGAAGATATGACTG;RSEQ=GGAAACAACAGGCCTTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:688:456:129,327:68,158:226,456:0.6628:2,2:25.4:1:30.4:1:0.65393:1.09082:60:455:0.6642:0:1.1 1/1:449:414:137,277:11,24:35,414:0.922:2,2:24.4:1:29.7:1:1:1.08:60:58.143:0.9208:0:1.1 +7 81346925 . G A 93 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCATAATTGGCATATTAG;RSEQ=TTTTGTGATTTTGCCTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:0,2:2,8:0.8:0,0:26.5:1:31:1:1:0:57:16:0.8:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 81350208 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.4298;LSEQ=AGTCCAATGAATATCAAGGC;RSEQ=GATAAAACAAAAAGGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:402:246:33,213:19,137:156,246:0.6119:2,2:22.2:1:31.2:1:0.76233:1.12:60:245:0.6171:0:1.7 1/1:288:252:40,212:5,31:36,252:0.875:2,2:23.2:1:30.2:1:1:1.17:60:62:0.8732:0:1.7 +7 81350223 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=3.81294;LSEQ=AAGGCAGATAAAACAAAAAG;RSEQ=TTTTTTACAAGTATATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:160:7,153:4,105:109,160:0.5948:1,1:25.4:1:31.7:1:1:1.20:60:159:0.6069:0:2.1 1/1:205:174:11,163:2,28:30,174:0.8488:2,2:22.5:1:30.5:1:1:1.05815:60:348:0.8488:0:2 +7 81350445 . C T 50 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTGGTGGGCGCCTGTAGT;RSEQ=CCAGCTACTCGAGAGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:13.7:1:32:0:1:0:31:6:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:19:1:30:0:1:0:27.5:4:1:0:1 +7 81355066 . G A 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1401;SOR=2.64421;LSEQ=ATAAACATAAGAAAAATCCA;RSEQ=CTTCAAACTTGGTGATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:61:59,2:25,0:25,61:0.7093:1,1:22.8:1:30.1:1:1:0:60:60:0.7059:0:1.1 1/1:30:26:26,0:4,0:4,26:0.8667:0,1:22.5:1:30.6:1:1:0:60:52:0.8667:0:1.1 +7 81355069 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACATAAGAAAAATCCAGCT;RSEQ=CAAACTTGGTGATTTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:88,2:90,2:0.0217:1,2:17.5:1:30.5:1:0.0645:36.12514:60:4:0.0227:0:2 0/0:34:0:0,0:34,0:34,0:0:1,0:20.3:1:30.6:1:1:0:60:68:1:0:0.9 +7 81355449 . T A 92 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00015;SOR=Inf;LSEQ=TTTATAAATAGAGTTCTAAC;RSEQ=TTTTGGACTCAGAATAGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:0,96:96,0:0:1,0:26:1:30.4:1:1:0:60:192:1:0:0.1 0/1:52:8:0,8:1,43:44,8:0.1538:1,0:21.4:1:30.9:1:1:0:60:16:0.1569:0:1 +7 81358266 . C G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACACATGGCATTGTGT;RSEQ=TGTGCCTGTCTGCAAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:40:1:33:0:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 81358712 . G A 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.94223;LSEQ=TCTGGATCTGAACCACCTAG;RSEQ=GTCCTTAATGAAATGCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:10,0:10,0:10,10:0.5:0,0:26.9:1:28.4:1:1:0:57.8:9:0.4737:0:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:6.5:1:30:0:1:0:60:4:0.6667:0:1 +7 81359051 . C T 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=37.08638;LSEQ=TCCTTGACCTTGGATGCATT;RSEQ=AGTTGTTTCCAAAGGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1382:2:1,1:575,803:1378,2:0.0014:2,2:25:1:20.5:1:1:1.40:60:1:7e-04:0:2 0/1:1058:54:19,35:452,550:1002,54:0.051:2,2:26.3:1:28.1:1:0.16245:1.51329:60:53:0.0506:0:1.1 +7 81359116 . CA C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=2.13395;LSEQ=CTATTGGCAAAAAACAACAA;RSEQ=AAAAAAAACTTATATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:219:21,198:56,187:243,219:0.474:2,2:26.1:1:32.4:1:1e-04:2.81742:59.9:218:0.4781:0.039:0.2 1/0:351:231:39,192:39,78:117,231:0.6581:2,2:26.4:1:31.4:1:0.00067:2.45462:59.9:230:0.659:0.0285:0.2 +7 81359189 . A AT 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.44619;SOR=2.024;LSEQ=ATTGGCATTTGTATTAGCAG;RSEQ=TTTTTTTTTCTGTTACTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:4:0,4:0,128:128,4:0.0303:1,0:29.5:1:30.4:1:1:0:60:8:0.0305:0.0076:0 0/1:67:4:0,4:1,62:63,4:0.0597:1,0:15:1:29.6:1:1:0:60:8:0.0615:0.0299:0.3 +7 81372047 . A G 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11215;SOR=3.72316;LSEQ=ATTGTAAATTCAGAAAAGCT;RSEQ=GGTAAGGGCCAGCATGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:29:29,0:20,0:20,29:0.5918:1,1:25.2:1:32.9:1:1:0:60:28:0.5833:0:1.2 1/1:13:11:10,1:2,0:2,11:0.8462:0,2:20:1:33.1:1:1:0:60:22:0.8462:0:1 +7 81372114 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.08744;SOR=Inf;LSEQ=ACAGATCGAAACAGAATGCA;RSEQ=GCTGGGTACAAAGACAGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:154,2:156,0:0:1,0:22.5:1:33.1:1:1:0:60:38:1:0:0.6 0/1:66:2:2,0:60,4:64,2:0.0303:2,0:26.5:1:32.5:1:1:0:60:4:0.0308:0:2 +7 81372156 . A G 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.39494;LSEQ=AGAGGTAGGGATCAGCTATA;RSEQ=AGATTAGAGACATCTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:189:181,8:120,5:125,189:0.6:1,1:23.4:1:33.2:1:1:1.06058:60:93.5:0.6013:0:1.1 1/1:170:154:143,11:15,1:16,154:0.9059:1,2:21.9:1:31.7:1:1:1.15289:59.9:76:0.9048:0:1.1 +7 81372452 . A G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01682;SOR=2.4971;LSEQ=CATAAGTAAAAATGTTTTCT;RSEQ=TGGATGTGTGTATTTGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:146:93:27,66:18,35:53,93:0.637:2,2:22.5:1:32.8:1:0.57856:1.25513:59.5:92:0.6389:0:1.1 1/1:54:44:7,37:2,8:10,44:0.8148:2,2:20:1:32:1:0.66673:1.31422:60:88:0.8148:0:1 +7 81372893 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12159;SOR=Inf;LSEQ=GGTTGTCTACACCTAGCTGG;RSEQ=GAAAGAGGACGTTTTCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:1,111:112,0:0:1,0:26.3:1:31.4:1:1:0:59.7:27:1:0:0.2 0/1:61:2:1,1:0,59:59,2:0.0328:1,2:13:1:29:1:0.03279:0:60:4:0.0333:0:1 +7 81374247 . G C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13409;SOR=Inf;LSEQ=ATATAAAGAGAATTTCCACA;RSEQ=CAGTGTGTCATAGAGTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:198,40:238,0:0:2,0:23.5:1:33:1:1:0:60:118:1:0:0.1 0/1:138:2:1,1:112,24:136,2:0.0145:2,2:17.5:1:27:1:0.33058:4.59277:60:4:0.0147:0:1 +7 81374500 . G C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCAAAAACACCACTGTT;RSEQ=CATTTAAAGAACAGCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:240:240:41,199:0,0:0,240:1:0,2:22.5:1:31.2:1:1:0:60:47:1:0:1.1 1/1:168:168:30,138:0,0:0,168:1:0,2:21.9:1:30.1:1:1:0:60:55:1:0:1.1 +7 81374551 . A T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29775;SOR=0;LSEQ=AGATTTTTAAAAAATCCTAC;RSEQ=CATCATTCTAACTTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:4:0,4:1,85:86,4:0.0444:1,0:27:1:29.5:1:1:0:60:8:0.0449:0:1.5 0/0:48:0:0,0:1,47:48,0:0:1,0:22.3:1:29.7:1:1:0:60:96:1:0:0.9 +7 81375051 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCAGGTTTACATTCCT;RSEQ=TCTGGCTTAGGATAGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 81381326 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.07585;LSEQ=TATTTGTAGTTGCATTTGCA;RSEQ=GAACAACATATTTGTTATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:125:125,0:96,3:99,125:0.558:1,1:26.5:1:32.3:1:0.08486:0:59.7:250:0.558:0:1.1 1/1:119:103:100,3:16,0:16,103:0.8655:1,1:24.1:1:30.7:1:1:0:60:206:0.8655:0:1 +7 81381621 . C CT 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.59331;SOR=1.3718;LSEQ=TACAGTATAAGAGCATGCAA;RSEQ=TTTTTTTTGCCTATTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:464:7:2,5:74,381:455,7:0.0151:2,2:32.6:1:30.7:1:0.32407:2.06:60:14:0.0152:0:0 0/1:340:7:1,6:62,270:332,7:0.0206:2,2:17.1:1:29.4:1:1:1.37659:60:14:0.0208:0.0029:0 +7 81381731 . T C 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02209;SOR=3.93406;LSEQ=ACCTTAAAATTCTGTCATTT;RSEQ=CATCTGTCCTTAAAACGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:30:0,30:0,24:24,30:0.5556:1,1:20.7:1:31.7:1:1:0:58.6:60:0.5556:0:1 1/1:24:20:0,20:1,3:4,20:0.8333:2,1:21.9:1:31.4:1:0.16667:0:60:40:0.8333:0:1 +7 81386418 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1635;SOR=Inf;LSEQ=TGGCTAAGTTATTTTAGGAT;RSEQ=TAGAATTATTCTGAAGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:224,36:260,0:0:2,0:22.5:1:32.5:1:1:0:60:259:1:0:0 0/1:177:2:1,1:153,22:175,2:0.0113:2,2:21:1:29:1:0.24364:6.82324:60:4:0.0114:0.0056:0 +7 81387856 . GT G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06383;SOR=Inf;LSEQ=TAAAAATAGTCAAGATACTA;RSEQ=TTCAACTGTCTTAATGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:105,0:105,0:0:1,0:22.7:1:30.4:1:1:0:60:104:1:0:0 0/1:36:2:1,1:34,0:34,2:0.0556:1,2:44.5:1:32:1:0.05556:0:60:4:0.0571:0:0 +7 81388001 . C A 172 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCAATATTTAGGGAGAAGT;RSEQ=AGTTACCTTTGTTTTCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1085:58:41,17:600,425:1025,58:0.0535:2,2:22.3:1:29.4:1:0.07451:1.71:60:116:0.0538:0:1 0/0:847:0:0,0:501,344:845,0:0:2,0:47:0:12:0:1:0:60:0:0:0:7 +7 82274286 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19255;SOR=Inf;LSEQ=AATGCCTTTCAAACTCTATA;RSEQ=CAAACTCTGGAGTTGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:22,17:39,0:0:2,0:30.4:1:30.3:1:1:0:47.6:12:1:0:0.3 0/1:31:2:2,0:17,12:29,2:0.0645:2,0:13.5:1:30.5:1:0.50968:0:50.5:4:0.0645:0:1 +7 82948338 . C T 97 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.51811;LSEQ=TGTGAGGAAAAACATTATTC;RSEQ=AACTTCATGCTCACTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:7,1:8,0:8,8:0.5:0,2:27.4:1:32.4:1:1:0:60:16:0.5333:0:2 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:22:0:33:0:1:0:60:2:0.3333:0:2 +7 82948362 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTCATGCTCACTTTTTTTAA;RSEQ=CCTTTTTTTTGCACTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:9,1:9,0:9,10:0.5:0,2:28:1:31.4:1:1:0:60:20:0.5:0:2 1/0:6:3:3,0:3,0:3,3:0.5:0,0:23.3:1:31.3:1:1:0:60:6:0.5:0:2 +7 82948434 . T G 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00567;SOR=0.15666;LSEQ=TGCAACTCCACAGAATTGAG;RSEQ=ACTCTGTCTGTGTAAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:25:24,1:9,0:9,25:0.7353:0,1:27:1:31.8:1:1:0:60:50:0.7353:0:1.3 0/1:17:5:4,1:12,0:12,5:0.2941:0,2:25.2:1:29.6:1:0.29412:0:60:10:0.2941:0:1.4 +7 82948537 . C T 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38049;LSEQ=TCCCTGCTCTCTTCTTGTCA;RSEQ=TCAGGCAAAGAATTTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:244:137:102,35:77,30:107,137:0.5615:2,2:27.3:1:30.5:1:0.6648:1.13:60:67.5:0.5649:0:1.9 0/1:214:70:51,19:97,47:144,70:0.3271:2,2:25.8:1:30.3:1:0.43527:1.30:59.8:34:0.3269:0:1.9 +7 82948594 . T C 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.35849;LSEQ=GATTTACAAACTTTTGCCAA;RSEQ=GGAAGAAAATAATGAGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:455:260:136,124:110,85:195,260:0.5714:2,2:26.2:1:30.5:1:0.39394:1.1795:59.9:25:0.5643:0:2.2 0/1:458:148:80,68:169,141:310,148:0.3231:2,2:25.4:1:29.8:1:1:1.01876:60:73:0.3259:0:2.2 +7 82948627 . G T 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.36742;LSEQ=TGAGGTTGCTTGGAGGTAGA;RSEQ=AAGAGGTGGGATTTATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:480:269:118,151:95,115:210,269:0.5604:2,2:26.7:1:28.9:1:0.7816:1.05697:59.9:28.889:0.5591:0:1.9 0/1:480:153:69,84:149,177:326,153:0.3188:2,2:28.2:1:28.2:1:0.92186:1.02476:60:29.6:0.3136:0:1.9 +7 82948727 . C CTGTT 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=6.000;MSILEN=4;SSF=0.00128;SOR=0.24799;LSEQ=AGACTATGTCTGTTTTTTCC;RSEQ=TGTTTGTTTGTTTGTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:35:0,35:0,58:58,35:0.3723:1,1:30.5:1:30.3:1:1:0:59.7:70:0.3804:0.0319:0.2 0/1:55:7:0,7:2,46:48,7:0.1273:1,0:30.9:1:31.1:1:1:0:59.3:14:0.1296:0.0182:0.4 +7 82948848 . G A 47 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TAAAGTAACTGAAATTGTAA;RSEQ=CAGGTAGACTGAGACAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:25:1:30:1:1:0:60:6:0.75:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:10:0:33:0:1:0:60:2:1:0:0 +7 82949154 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCAATTTAATATTTG;RSEQ=TATTTTTCAAAATCTTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:31.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 82949179 . G C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCAAAATCTTCAAGGATA;RSEQ=ATCATCTCTGGAAAAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:33:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 82956889 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.46966;LSEQ=AATAATGCCTCCTGTGATTG;RSEQ=CTGGCTTGTGGTAGAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:587:380:207,173:112,95:207,380:0.6474:2,2:26.4:1:29.7:1:0.93117:1.01:59.9:41.222:0.6475:0:1.1 0/1:538:249:133,116:154,135:289,249:0.4628:2,2:27:1:28.4:1:1:1.01:60:123.5:0.4643:0:1.1 +7 83192801 . ACAG A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.16944;SOR=Inf;LSEQ=AGGTGGTCTCTGGACCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,10:24,0:0:2,0:22:1:32.5:1:1:0:60:48:0.96:0:0 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:43:0:30:0:1:1.26772:60:4:0.1111:0:0.5 +7 83542173 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=2.1803;LSEQ=ATGTCTTTCAGAGATGACAT;RSEQ=TCTCCCATTTGTCTTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:594:90:37,53:256,246:502,90:0.1515:2,2:26:1:29.6:1:0.08727:1.48965:60:44:0.1512:0:1.1 0/1:403:113:59,54:142,147:289,113:0.2804:2,2:25.7:1:28.8:1:0.6573:1.13:60:226:0.2839:0:1.2 +7 83542230 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06135;SOR=Inf;LSEQ=TATTTCTGTAAGCAGAATGG;RSEQ=CTTTTCTGTTTCCTTATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:390:0:0,0:138,252:390,0:0:2,0:23.5:1:31.5:1:1:0:59.9:54.714:1:0:0.2 0/1:255:3:2,1:98,154:252,3:0.0118:2,2:32:1:26.7:1:0.563:3.13:60:6:0.0119:0:1 +7 83542648 . C A 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTCACTTAGGTTAATGA;RSEQ=CTTCAGTTCCATCCATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:28:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:30:1:1:0:60:4:1:0:1.5 +7 84354805 . T C 25 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATTGAACAACCTGCTCC;RSEQ=GAATGACTCCTGGGTAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:25:1:1:0:40:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 85244212 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51652;SOR=0;LSEQ=GAGCAGTGGAAAGTTCCAGG;RSEQ=AGCCAGTCCCTGTGACCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:21,2:0.087:2,2:19.5:1:28:1:1:1.09544:60:4:0.0909:0:1 0/0:14:0:0,0:7,7:14,0:0:2,0:28.1:1:31.7:1:1:0:60:28:1:0:0.2 +7 85244362 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACACAGGAGTGCAGTTTG;RSEQ=CCCCATTTCCCCACTGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:12.5:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 85607920 . A G 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00151;SOR=Inf;LSEQ=AAGGGTGAATAGGAAGTCAA;RSEQ=TTAGTAAATTAAGTATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:29,0:0:1,0:26.5:1:30.5:1:1:0:60:58:1:0:0 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:17:1:33:0:1:0:60:10:0.3846:0:1 +7 85608016 . TTGTC T 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AAAAACTAAGCTAAAGGATA;RSEQ=TATTATCTTTGTAATATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:115,21:136,0:0:2,0:21.2:1:31:1:1:0:59.8:272:1:0:0.3 0/1:102:18:13,5:70,14:84,18:0.1765:2,2:27.4:1:28.5:1:0.31845:1.90917:60:17:0.1683:0.0098:1 +7 85608081 . A T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.00701;LSEQ=TGATTCACATATATGAAATG;RSEQ=GGAATTAAATGAGCAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:150:88,62:140,100:240,150:0.3846:2,2:27.7:1:30.2:1:1:1.01:59.9:149:0.387:0:1.7 1/0:343:224:125,99:66,53:119,224:0.6531:2,2:27.3:1:29.1:1:1:1.01:59.9:73.667:0.6558:0:1.8 +7 85608107 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.07899;LSEQ=TAAATGAGCAAAAAATTAAT;RSEQ=GTTTTTCAGGGGTCATGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:98:52,46:173,165:338,98:0.2248:2,2:26.6:1:30.3:1:0.81854:1.08:60:97:0.2261:0:2.2 1/0:378:205:102,103:83,90:173,205:0.5423:2,2:26.2:1:28.6:1:0.75732:1.07:60:410:0.5467:0:2 +7 85608162 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01908;SOR=1.62513;LSEQ=GTTATATTATGAGGTTTCTC;RSEQ=AAATAGTGCTGTCTTGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:65:21,44:68,142:210,65:0.2364:2,2:24.7:1:30.5:1:1:1.00334:60:130:0.2372:0:1.9 0/1:212:71:27,44:43,98:141,71:0.3349:2,2:22.9:1:30:1:0.28252:1.40:60:142:0.3381:0:2 +7 85608189 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1768;SOR=Inf;LSEQ=TGCTGTCTTGGGTAGAAAGA;RSEQ=GTCCCCAAAGGACAATCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:41,143:184,0:0:2,0:23.6:1:31.6:1:1:0:60:60.333:1:0:0.3 0/1:134:2:1,1:32,100:132,2:0.0149:2,2:46.5:1:30.5:1:0.43328:3.09:60:4:0.015:0:1 +7 86544591 . C T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08155;SOR=Inf;LSEQ=TTCAAATTTTTTATCTTTTT;RSEQ=CTTCAGAGATTCTGATAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:350:0:0,0:248,102:350,0:0:2,0:23.5:1:31.6:1:1:0:60:57.333:1:0:0.3 0/1:269:3:0,3:185,81:266,3:0.0112:2,0:8:1:21.3:1:0.0297:0:60:2:0.0076:0:2.7 +7 86544667 . G T 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49086;LSEQ=ATACTTGCAAGTTCCAGGGT;RSEQ=ACTTTATCCAAGTGCATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:617:384:176,208:108,123:231,384:0.6224:2,2:25.5:1:29.8:1:0.86743:1.03765:60:191:0.6221:0:1.1 0/1:472:211:96,115:115,146:261,211:0.447:2,2:24.4:1:28.2:1:0.78042:1.06:60:69.333:0.4454:0:1.2 +7 87600830 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24696;SOR=Inf;LSEQ=CAATATTATTCTGTAATACC;RSEQ=GAAGTACCTGTTTAATAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:95,29:124,0:0:2,0:22.5:1:31.6:1:1:0:60:123:1:0:0.1 0/1:123:2:1,1:92,28:120,2:0.0163:2,2:40.5:1:30:1:0.4204:3.24605:60:4:0.0165:0:1 +7 87600844 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24341;SOR=0;LSEQ=AATACCTGAAGTACCTGTTT;RSEQ=ATAGTTTTTAAAATCACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:123,43:166,2:0.0119:2,2:24.5:1:28:1:0.45637:2.83924:60:4:0.012:0:1.5 0/0:172:0:0,0:122,50:172,0:0:2,0:23.6:1:27.7:1:1:0:60:42:1:0:0.3 +7 87600926 . G C 272 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10667;LSEQ=ATTACGTTTTTCCAGTATCT;RSEQ=TGAGGGGTATTACTACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:362:317:156,161:20,24:44,317:0.8757:2,2:26.7:1:32.8:1:0.74794:1.16:60:104.667:0.8771:0:2 0/1:327:140:65,75:98,89:187,140:0.4281:2,2:28.2:1:31.1:1:0.31504:1.26958:60:139:0.429:0:2 +7 87600931 . G A 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.10601;LSEQ=GTTTTTCCAGTATCTGTGAG;RSEQ=GGTATTACTACTTTTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:359:313:151,162:22,23:45,313:0.8719:2,2:26.5:1:31:1:1:1.02613:60:77.25:0.8754:0:2 0/1:330:138:62,76:98,94:192,138:0.4182:2,2:27.9:1:29.1:1:0.31507:1.27701:60:137:0.419:0:2 +7 91077127 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15455;SOR=Inf;LSEQ=GGCGAGTAATAGCAAGATGG;RSEQ=TGCCAAGAGACCTAGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:15,12:27,0:0:2,0:25.1:1:33.3:1:1:0:33.3:54:1:0:0.1 0/1:18:2:1,1:10,6:16,2:0.1111:2,2:19:1:27.5:1:1:1.61828:24.5:4:0.1111:0:1 +7 91177925 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATATATATATTTATGGTGC;RSEQ=TGTGTGTGTGTGTAATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:28.5:1:1:0:60:4:1:0:3 +7 91179796 . C T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.74445;LSEQ=ACACTTTCAGTGTAATAGAC;RSEQ=TCTGCACCCAGTTGAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:1,2:146,84:230,3:0.0128:2,2:26:1:28.7:1:0.55656:3.45685:60:6:0.013:0:1 0/0:209:2:1,1:134,73:207,2:0.0096:2,2:7.5:1:16:1:1:1.83003:60:0:0:0:2 +7 91179891 . A G 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00145;SOR=0.57225;LSEQ=TACTTCTCTGAAGTATGCAC;RSEQ=AGTACAAAATGACATATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:313:212:99,113:45,56:101,212:0.6773:2,2:23.9:1:31.1:1:0.80842:1.09:60:105:0.6752:0:1.1 1/0:264:144:67,77:52,68:120,144:0.5455:2,2:20.8:1:29.3:1:0.62124:1.14:60:71:0.5441:0:1.1 +7 91179983 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50325;SOR=0;LSEQ=TAATGCTATTTAGAATGTTT;RSEQ=TATTAGCATATTTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:32,87:119,2:0.0165:2,2:24:1:30:1:0.47273:2.69:60:4:0.0168:0:1.5 0/0:98:0:0,0:22,76:98,0:0:2,0:24:1:31.4:1:1:0:60:97:1:0:0.3 +7 91180001 . C T 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.51134;SOR=0;LSEQ=TTGTATTAGCATATTTTTTC;RSEQ=TTTCTTGCTCCTATTAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:19,72:91,2:0.0215:2,2:6.5:1:31.5:1:0.38569:3.72:60:4:0.0217:0:1 0/0:66:0:0,0:12,54:66,0:0:2,0:22.1:1:31.8:1:1:0:60:132:1:0:0.2 +7 91180056 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19115;SOR=0.40365;LSEQ=GTAAAAACTAGGTTTTGGCC;RSEQ=CTGGCATCCATTCATCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:35:26:1,25:0,9:9,26:0.7429:0,1:31.5:1:31.8:1:1:0:60:52:0.7429:0:1 1/0:15:8:0,8:0,7:7,8:0.5333:0,0:19.8:1:29:1:1:0:60:7:0.5:0:1.3 +7 91180083 . T C 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30855;SOR=0;LSEQ=TCCATTCATCCTACTTCCTT;RSEQ=ACTAATTCTCCTTTCTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:0,8:1,20:21,8:0.2759:1,0:23.9:1:33:1:1:0:60:16:0.2759:0:1 0/0:5:0:0,0:0,5:5,0:0:0,0:30:1:27:1:1:0:60:10:1:0:0.4 +7 92242414 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCATCTCCTTTATTATCTT;RSEQ=CTCTAGAAAACAATGTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:27.5:1:32:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 92244368 . C T 32 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.27837;SOR=0;LSEQ=GCCTCCAGATAGCAATCCTC;RSEQ=ACAGCTCTGTAGGGCTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:1,2:115,14:129,3:0.0227:2,2:7.7:1:20.3:1:0.03865:15.74956:60:2:0.0156:0:1 0/0:87:0:0,0:77,10:87,0:0:2,0:23.5:1:30.1:1:1:0:60:28:1:0:0.3 +7 92244422 . C T 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=13.80828;LSEQ=AAGCCACCAAGGGTGTTCTC;RSEQ=GCAGGATCAGCTTAAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:8:5,3:250,94:344,8:0.0227:2,2:21.3:1:31.6:1:0.68943:1.59343:60:16:0.0231:0:1 0/1:316:77:50,27:169,70:239,77:0.2437:2,2:23.6:1:29.1:1:0.39409:1.30255:60:18.25:0.2362:0:1.2 +7 92244630 . TATACA T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0;SOR=21.22915;LSEQ=AGAAAAAAATAATTGGTTGA;RSEQ=ATACATCAATGTAAATAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:1,2:42,197:239,3:0.0124:2,2:28:1:33:0:0.44545:2.33:60:6:0.0129:0:0.3 0/1:194:41:7,34:30,123:153,41:0.2113:2,2:25.5:1:29.8:1:0.82515:1.18365:59.9:40:0.2083:0.0155:0.2 +7 92244650 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.50525;SOR=0;LSEQ=TATACAATACATCAATGTAA;RSEQ=TAATGTACTTACAGAGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:13,146:159,2:0.0124:2,2:14:1:31:1:0.16685:10.86:60:4:0.0125:0:1 0/0:127:0:0,0:13,114:127,0:0:2,0:23.2:1:30.1:1:1:0:60:62.5:1:0:0.1 +7 92247112 . C T 62 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACATATGTCAAAGTGAAT;RSEQ=GAGAGGCTTCTAAACCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:29.8:1:31:1:1:0:55.3:8:0.4444:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 92247333 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=10.33933;LSEQ=CCACCACCCAGTCTGGGTAG;RSEQ=GCAGGTGTCTCACTGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:12:10,2:347,90:437,12:0.0267:2,2:17.2:1:31.8:1:1:1.30:60:24:0.0271:0:1.1 0/1:330:73:56,17:198,59:257,73:0.2212:2,2:21:1:30.6:1:1:1.01872:60:146:0.2253:0:1.1 +7 92247539 . A G 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGCTACAAAAGAACCACAC;RSEQ=TGGACATAAGCATTAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:695:0:0,0:199,496:695,0:0:2,0:24.6:1:30.8:1:1:0:59.9:52.462:1:0:0.1 0/1:558:57:16,41:161,338:499,57:0.1022:2,2:26.1:1:30.4:1:0.55255:1.22022:60:27.5:0.1009:0:1.1 +7 92252191 . AC A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CTGCATAAAACGGCACTTCT;RSEQ=CATGTCTCCACTCACCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:2,0:56,1:57,2:0.0333:1,0:30:1:29.5:1:1:0:60:4:0.0339:0:0.5 0/0:45:0:0,0:43,2:45,0:0:1,0:22.6:1:31.5:1:1:0:60:44:1:0:0.2 +7 92252203 . C G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20574;LSEQ=GCACTTCTACCATGTCTCCA;RSEQ=TCACCACACAAATAGTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:5,0:63,1:64,5:0.0725:1,0:14.4:1:30.6:1:1:0:60:10:0.0725:0:1 0/1:58:5:5,0:51,2:53,5:0.0862:1,0:20.6:1:28:1:1:0:60:4:0.0702:0:1.4 +7 92252239 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18929;SOR=Inf;LSEQ=TAACACTGTCTGCAGCAGCT;RSEQ=CTTGAAGTAAGAAAGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:105,19:124,0:0:2,0:23.5:1:32:1:1:0:59.7:61:1:0:0.1 0/1:96:2:2,0:79,15:94,2:0.0208:2,0:25.5:1:28.5:1:1:0:60:4:0.0211:0:1 +7 92300587 . G A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00111;SOR=Inf;LSEQ=ACTGTAAGCACTGAGAAGGC;RSEQ=GTTTCAGGACAGGCTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:31,0:0:1,0:24.9:1:30.2:1:1:0:59.3:30:1:0:0.1 0/1:22:7:7,0:14,1:15,7:0.3182:1,0:15:1:31.1:1:1:0:60:14:0.3182:0:1 +7 92300798 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04711;SOR=Inf;LSEQ=CCAGAGATCCACGGGGGTGG;RSEQ=GTAGCTGGACTGGAGCAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:237,213:450,0:0:2,0:26.4:1:30.8:1:1:0:60:63.286:1:0:0.2 0/1:394:4:2,2:196,193:389,4:0.0102:2,2:29.8:1:29.3:1:1:1.01551:60:8:0.0104:0:1 +7 92300858 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04725;SOR=Inf;LSEQ=CAGCGTGACGACCTGCAATG;RSEQ=CAAGCGGATCCAAGTGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:124,204:328,0:0:2,0:26.4:1:31.5:1:1:0:60:40:1:0:0.1 0/1:288:4:3,1:99,185:284,4:0.0139:2,2:20.8:1:28.3:1:0.1289:5.57:59.5:8:0.0141:0:1 +7 92300880 . G A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.318;SOR=4.04386;LSEQ=AAGCGGATCCAAGTGTTACT;RSEQ=AGAAGGTGGCTGTTGGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:1,0:79,189:268,1:0.0037:2,0:1:0:24:0:0.2974:0:60:2:0.0038:0:1 0/1:202:3:2,1:58,141:199,3:0.0149:2,2:29.7:1:26:1:0.21099:4.82:60:6:0.015:0:1 +7 92354913 . A T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0814;SOR=Inf;LSEQ=AAATAGGAAAAATAAGTTTA;RSEQ=TAAAAGGACAGCACTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:293,93:386,0:0:2,0:23.3:1:30.5:1:1:0:60:54.143:0.9974:0:0.1 0/1:297:3:1,2:205,89:294,3:0.0101:2,2:11.3:1:21.7:1:0.22327:4.58014:60:2:0.0068:0:2.3 +7 92355225 . C T 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=Inf;LSEQ=GGCATGCGGCAGGCATTTGA;RSEQ=AGGTATTGGCTGAATGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:2,33:35,0:0:2,0:24.8:1:32.4:1:1:0:60:34:1:0:0.1 0/1:20:7:0,7:0,13:13,7:0.35:1,0:16.6:1:28.9:1:1:0:60:14:0.35:0:1 +7 92404120 . G A 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00326;SOR=Inf;LSEQ=TTTGGTTTCTCTGTCTGTTC;RSEQ=TGACACTGTGCACACATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:847:0:0,0:340,507:847,0:0:2,0:25.3:1:31.3:1:1:0:60:76:1:0:0.1 0/1:533:6:5,1:200,327:527,6:0.0113:2,2:13.8:1:25.3:1:0.03353:8.14:60:5:0.0094:0:1.3 +7 92404179 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10527;SOR=Inf;LSEQ=CAAAGAGGTTAAGTAGGTGG;RSEQ=AATAAGCAAAGAAGTAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:73,282:355,0:0:2,0:23.6:1:32.4:1:1:0:59.8:58.167:1:0:0.1 0/1:171:2:1,1:29,140:169,2:0.0117:2,2:8:1:29:1:0.32095:4.76:60:4:0.0119:0:1 +7 92404285 . A G 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17683;SOR=0;LSEQ=TCTTGTGATCATATGTAAAG;RSEQ=TATCAAATGAGATCTGATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:0,6:0,45:45,6:0.1154:1,0:19.8:1:32.2:1:1:0:58.7:12:0.1176:0:1 0/0:20:0:0,0:0,20:20,0:0:1,0:21.3:1:30.7:1:1:0:60:19:1:0:0 +7 92462641 . G A 43 v3;q25;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24194;SOR=2.80876;LSEQ=AGGCCGTCCTTCTCCATGCC;RSEQ=CCTGGACGCCGCCCGCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:452:2:1,1:80,367:447,2:0.0044:2,2:9.5:1:29:1:0.32859:4.57:60:4:0.0045:0:1 0/1:324:4:4,0:74,246:320,4:0.0123:2,0:8.3:1:21.8:1:0.00316:0:60:3:0.0095:0:1.8 +7 92462690 . T C 32 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56215;SOR=3.06964;LSEQ=GGGGCGGGCGGGGGGTGCGC;RSEQ=CAACTAGCTGGCGGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:1:0,1:2,57:59,1:0.0167:1,0:3:0:19:0:1:0:60:0:0:0:1 0/1:40:2:1,1:1,37:38,2:0.05:1,2:7:1:32:0:0.09872:26.51:60:4:0.0513:0:1 +7 92462938 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12;SOR=0;LSEQ=CCTCTTCCCTCCTCGAAGCG;RSEQ=AGTCCTCAACACAGACACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:2,5:7,2:0.2222:2,2:33.5:1:27.5:1:1:2.24:60:4:0.2222:0:1 0/0:16:0:0,0:7,9:16,0:0:2,0:27.3:1:28.9:1:1:0:60:32:1:0:0 +7 95912679 . CA C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49206;SOR=0;LSEQ=TCACCAAAATGGGATGAACA;RSEQ=AAGGGAAAGAGGAGAGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:14,2:0.125:2,2:15:1:30.5:1:1:1.30929:60:4:0.125:0:0 0/0:12:0:0,0:8,4:12,0:0:2,0:21.6:1:27:1:1:0:60:5:1:0:0.2 +7 95912778 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49315;SOR=0;LSEQ=TATGCAAATCTATAAGAAAG;RSEQ=TGATATTGTAGACATTAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:23,12:35,2:0.0541:2,2:17.5:1:28.5:1:1:1.88115:40:4:0.0556:0:1 0/0:36:0:0,0:20,16:36,0:0:2,0:27.1:1:31:1:1:0:57.3:72:1:0:0.2 +7 95912847 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22169;SOR=Inf;LSEQ=TTACAAGTGTTACCATGGCA;RSEQ=AAGTAGAGGAGTCTACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:29,30:59,0:0:2,0:30.7:1:30.3:1:1:0:59.9:58:1:0:0.1 0/1:53:2:1,1:29,22:51,2:0.0377:2,2:44.5:1:30.5:1:1:1.31123:60:4:0.0377:0:1 +7 95913083 . T C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAACTCACGGGAAGGAGC;RSEQ=TGCATTGCTGGAAGCTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1:0,2:24.2:1:33:1:1:0:60:12:1:0:1.8 1/1:3:3:0,3:0,0:0,3:1:0,0:16.7:1:33:1:1:0:60:6:1:0:1 +7 96635355 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50101;SOR=0;LSEQ=TCGTCCAAATCCGCCTTCAT;RSEQ=GAGTTCGGGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:9,15:24,2:0.0769:2,2:8.5:1:28:1:1:1.63:56.5:4:0.087:0:1.5 0/0:19:0:0,0:12,7:19,0:0:2,0:27.4:1:28.1:1:1:0:56.8:5.333:1:0:0.3 +7 96635388 . ACAG A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.49057;SOR=Inf;LSEQ=CAGCAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:7,20:27,0:0:2,0:28.1:1:32:1:1:0:59.2:26:1:0:0.4 0/1:27:2:1,1:10,14:24,2:0.0741:2,2:29.5:1:30:1:1:1.38:57.5:4:0.0769:0:0 +7 96635543 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGCGGCAGCGGCCGGCT;RSEQ=GCACCACCACCACCACCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:15.5:1:28.5:1:1:1.22474:60:4:0.1818:0:1.5 0/0:4:0:0,0:2,2:4,0:0:2,0:19.3:1:29:1:1:0:60:8:1:0:0.3 +7 96636627 . C A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCCGCTCCGCCCGGACAG;RSEQ=TGCCGCCTTGCTGCGCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 97096756 . AT A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATAAGGAAAACCATCACT;RSEQ=TTTTTTTTTTTAAGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:35:1:33:0:1:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 97097087 . A G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00249;SOR=2.01396;LSEQ=CTTTACAGTTAAAAAAGGAG;RSEQ=GTAGGTTATCTGTTAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:33:16,17:174,162:336,33:0.0894:2,2:25.8:1:30.7:1:0.71999:1.14079:60:66:0.0904:0:1.1 0/1:357:59:31,28:137,160:297,59:0.1653:2,2:24.7:1:30.6:1:0.39389:1.29:60:118:0.1667:0:1.1 +7 97097173 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.13927;SOR=Inf;LSEQ=TCATGAGGTTAACCAGGAAT;RSEQ=AAAACACCCAAAGCAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:37,115:152,0:0:2,0:24.3:1:31.9:1:1:0:60:49.667:1:0:0.1 0/1:91:2:1,1:24,65:89,2:0.022:2,2:21.5:1:27:1:0.47619:2.67:60:4:0.022:0:1 +7 97793130 . GC G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.5046;SOR=0;LSEQ=CATAACCCAAGGCAGGACCT;RSEQ=CCCCTGGCCGCAATACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:103,53:156,2:0.0127:2,2:27:1:31:1:1:1.93471:60:4:0.013:0:0 0/0:126:0:0,0:84,42:126,0:0:2,0:21.8:1:30.4:1:1:0:60:62:1:0:0.3 +7 97793182 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1085;SOR=Inf;LSEQ=GCACAGAGGGCAGCGGTCTG;RSEQ=GCTCTGTAAAAAGCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:137,123:260,0:0:2,0:27.5:1:30.5:1:1:0:60:17.571:1:0:0.4 0/1:239:3:1,2:130,106:236,3:0.0126:2,2:18.3:1:26.3:1:0.5907:2.44383:60:6:0.0128:0:1.7 +7 97793209 . G T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.92256;SOR=0.96985;LSEQ=TAAAAAGCTGCTGTGGCCAC;RSEQ=GTGAAGGACCGGCTATCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:77:36,41:83,86:169,77:0.313:2,2:26.5:1:30:1:0.78386:1.09874:60:18.25:0.3067:0:1.2 0/1:248:76:38,38:87,85:172,76:0.3065:2,2:26.7:1:30.1:1:1:1.02344:60:75:0.3099:0:1.2 +7 97793227 . G A 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.05541;SOR=0;LSEQ=ACGGTGAAGGACCGGCTATC;RSEQ=CTGCCTGTCTTAGCAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:4:3,1:87,114:201,4:0.0194:2,2:17.3:1:28.5:1:0.32159:3.91:60:8:0.0198:0:1.5 0/0:217:0:0,0:100,117:217,0:0:2,0:25.3:1:30.3:1:1:0:60:107.5:1:0:0.4 +7 97793237 . T G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22765;SOR=0;LSEQ=ACCGGCTATCGCTGCCTGTC;RSEQ=TAGCAGGTCAAGAGCGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:72,109:181,2:0.0109:2,2:33.5:1:31:1:1:1.51:60:4:0.0111:0:2.5 0/0:200:0:0,0:88,111:199,0:0:2,0:24.7:1:29.8:1:1:0:60:398:0.995:0:0.4 +7 97826105 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53387;SOR=0;LSEQ=AGGTACAGAGATCAAATACC;RSEQ=GACATGCTTAATGGACGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:2,0:85,20:105,2:0.0185:2,0:24:1:31.5:1:1:0:60:4:0.0187:0:1 0/0:62:0:0,0:50,12:62,0:0:2,0:22.2:1:29.6:1:1:0:60:124:1:0:0 +7 97826123 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.57136;SOR=2.85359;LSEQ=CCAGACATGCTTAATGGACG;RSEQ=GAGGCTTTGACAAGGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:1:0,1:110,39:149,1:0.0067:2,0:1:0:26:0:0.26667:0:60:2:0.0067:0:1 0/1:106:2:1,1:74,30:104,2:0.0189:2,2:12.5:1:27.5:1:0.50135:2.44291:60:4:0.019:0:1.5 +7 97826220 . G A 37 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07556;SOR=Inf;LSEQ=TTTCTGATGATCTGAAATTC;RSEQ=TTTGCTTATGCGTCTCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:180,175:355,0:0:2,0:24.1:1:30.9:1:1:0:60:117.333:1:0:0.4 0/1:261:3:2,1:138,119:257,3:0.0115:2,2:7:1:23.7:1:1:1.72:60:6:0.0116:0:1 +7 97826232 . G A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21104;SOR=1.23996;LSEQ=TGAAATTCGTTTGCTTATGC;RSEQ=TCTCATGCAGCATGCCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:129:65,64:102,120:222,129:0.3675:2,2:26:1:30.7:1:0.43943:1.19:60:128:0.3668:0:1.1 0/1:265:111:62,49:76,78:154,111:0.4189:2,2:27:1:29.2:1:0.32021:1.30:60:26.75:0.4131:0:1.1 +7 97826289 . G T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25504;SOR=0;LSEQ=CGTTCAGGCCGAGGACTGAG;RSEQ=GTTTCCTCCCACTCCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:88,165:253,3:0.0117:2,2:33.7:1:31:1:1:1.06641:60:6:0.012:0:2 0/0:212:0:0,0:86,126:212,0:0:2,0:25.2:1:30.3:1:1:0:60:105:1:0:0.6 +7 97826331 . T G 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73544;SOR=0.64762;LSEQ=CTTTTTTAATGAGCTGGTTT;RSEQ=GAAGTTGTGTAGTTTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:6:2,4:29,99:128,6:0.0448:2,2:28.8:1:30.8:1:0.62193:1.70:60:12:0.0451:0:1.2 0/1:102:3:0,3:24,75:99,3:0.0294:2,0:25.7:1:30.3:1:1:0:60:6:0.0297:0:1 +7 97826340 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2521;SOR=0.70233;LSEQ=TGAGCTGGTTTTGAAGTTGT;RSEQ=TAGTTTTTAAGCAGTTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:111:57:13,44:10,44:54,57:0.5135:2,2:20.5:1:30.4:1:0.64371:1.30:60:114:0.5229:0:1.1 0/1:87:37:6,31:9,41:50,37:0.4253:2,2:22:1:29.9:1:1:1.13251:60:74:0.4458:0:1.1 +7 97826359 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50484;SOR=0;LSEQ=TGTAGTTTTTAAGCAGTTGA;RSEQ=GTATCTTGGCTCCAAACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:7,64:71,2:0.0274:2,2:26.5:1:29.5:1:0.20852:8.62:60:4:0.0278:0:1.5 0/0:56:0:0,0:6,49:55,0:0:2,0:23.4:1:30.2:1:1:0:60:54:1:0:0.6 +7 99926442 . G T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.56653;SOR=2.9552;LSEQ=ACCAATATTCTTGAAAACCA;RSEQ=GATTAATTTACTGTACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:0,1:71,5:76,1:0.013:2,0:1:0:28:0:0.07792:0:60:2:0.013:0:1 0/1:53:2:1,1:42,9:51,2:0.0377:2,2:7.5:1:27.5:1:0.3447:4.4796:45:4:0.0385:0:1 +7 99927870 . G A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49849;SOR=0;LSEQ=GTTTCAACCTGAGGTAGGTC;RSEQ=GCAAACTCTTGAATCTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:1,1:3,69:72,2:0.027:1,2:13:0:33:1:0.10589:20.06:22:4:0.027:0:1 0/0:65:0:0,0:5,60:65,0:0:2,0:16.1:1:28:1:1:0:22.5:130:1:0:0.1 +7 99928384 . CT C 35 MSI12;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TAGCATTTTCTTTCTTTCCT;RSEQ=TTTTTTTTTTTTCCTTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:32:1:35.5:1:1:0:20:4:0.3333:0:0 0/0:9:0:0,0:1,7:8,0:0:2,0:32.5:1:28.8:1:1:0:26.3:16:0.8889:0:1.1 +7 99933398 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21164;SOR=Inf;LSEQ=ATGTTCCCCCCATTTCCAGG;RSEQ=AGGTTGGACGCCGTGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:100,24:124,0:0:2,0:22:1:31.8:1:1:0:52.7:123:1:0:0.1 0/1:107:2:1,1:88,17:105,2:0.0187:2,2:19.5:1:28:0:0.30947:5.05927:57:4:0.019:0:1.5 +7 100401825 . T G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGAGATGGGGTTTTGCTAT;RSEQ=TTGGCCAGGCTGCTCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:31.5:1:1:0:60:4:1:0:1 +7 100403213 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50695;SOR=0;LSEQ=CCTGGGGGAAGCGGGGCCGG;RSEQ=CATTCCGGTCTTTCTGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:38,25:63,2:0.0308:2,2:14.5:1:28.5:1:1:1.50993:60:4:0.0328:0:1 0/0:48:0:0,0:29,19:48,0:0:2,0:24.4:1:30.9:1:1:0:60:96:1:0:0.2 +7 100403250 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51256;SOR=0;LSEQ=CCAACAGTCCAGCATGAGCT;RSEQ=GTGGAGGGAGGTGGGACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:36,37:73,2:0.0267:2,2:27.5:1:28.5:1:1:1.03:60:4:0.027:0:1 0/0:52:0:0,0:30,22:52,0:0:2,0:28.9:1:30.8:1:1:0:60:104:1:0:0.2 +7 100403280 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.53512;SOR=0;LSEQ=GGTGGGACAGTCTGGGGGCG;RSEQ=GGGCAGCCGGTAGTCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:1,1:26,38:64,2:0.0303:2,2:45:1:31:1:1:1.45:60:4:0.0308:0:1 0/0:37:0:0,0:20,17:37,0:0:2,0:21.5:1:30.1:1:1:0:60:74:1:0:0.2 +7 100404135 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10989;SOR=Inf;LSEQ=CAGGCATCACTGGCGGAAGT;RSEQ=AACTTCCGGAAGGCAATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:25.7:1:30.9:1:1:0:60:18:1:0:0.1 0/1:5:2:1,1:1,2:3,2:0.4:2,2:29.5:1:27:1:1:1.73:60:4:0.4:0:1 +7 100405060 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22711;SOR=0;LSEQ=GGCCAAAGTCAGACACTTTG;RSEQ=AGACGAGGTTGCTGTTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:13,11:24,2:0.0769:2,2:32.5:1:29.5:1:1:1.17422:60:4:0.0769:0:1 0/0:28:0:0,0:16,12:28,0:0:2,0:26:1:31.2:1:1:0:60:27:1:0:0.2 +7 100405072 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49176;SOR=Inf;LSEQ=ACACTTTGCAGACGAGGTTG;RSEQ=TGTTGACTAGGATGTTGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:12,12:24,0:0:2,0:28.3:1:31.5:1:1:0:60:11:1:0:0.2 0/1:27:2:1,1:14,11:25,2:0.0741:2,2:10:0:30.5:1:1:1.2613:60:4:0.0769:0:1.5 +7 100411278 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTAGGGCAACCCACCATG;RSEQ=CCGATGAGATACTGTCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:31.5:1:1:0:60:4:1:0:1 +7 101978488 . GTA G 35 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATATATACATATATATGT;RSEQ=TATATATATATACACATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:36.5:1:35:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 103122556 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.08609;SOR=Inf;LSEQ=TTAATCACTTAAATTTGCTT;RSEQ=CAAATTGACTGAAATCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:166,49:215,0:0:2,0:23.4:1:32.5:1:1:0:60:430:1:0:0.1 0/1:171:3:2,1:130,38:168,3:0.0175:2,2:30:1:29:1:0.54243:1.70444:60:6:0.0176:0:2 +7 103122561 . T A 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTTAAATTTGCTTGCAAA;RSEQ=TGACTGAAATCAGCCAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:188,58:246,0:0:2,0:22.9:1:30.8:1:1:0:60:60.5:1:0:0.1 0/1:187:21:15,6:127,39:166,21:0.1123:2,2:21.3:1:29.5:1:0.59475:1.30063:60:20:0.1081:0:1.6 +7 103122645 . A G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.24253;LSEQ=CCTATCTACCGAGAAGATTC;RSEQ=CCTCTCCTTGCCAACCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:73:37,36:246,262:508,73:0.1256:2,2:26.3:1:31.8:1:0.80244:1.09:60:146:0.1265:0:1.1 0/1:503:160:80,80:163,177:340,160:0.3181:2,2:25.3:1:29.8:1:0.70166:1.09:59.8:79:0.3192:0:1.2 +7 103122715 . G A 46 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07808;SOR=Inf;LSEQ=TAAGCATTCCAGTTCTACAG;RSEQ=AACTAGATCATTAGAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:76,208:284,0:0:2,0:24.1:1:31.7:1:1:0:60:93.667:1:0:0.1 0/1:213:3:2,1:54,156:210,3:0.0141:2,2:5:1:29.3:1:0.16971:5.72:60:6:0.0144:0:1.7 +7 103122754 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51584;SOR=0;LSEQ=AAAGCAAGTCATCTCTCTGT;RSEQ=AGGGAACAGTCAACCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:0,2:12,111:123,2:0.016:2,0:40:1:30:0:1:0:60:4:0.0164:0:1 0/0:85:0:0,0:7,78:85,0:0:2,0:23.8:1:31.4:1:1:0:60:170:1:0:0.1 +7 103214940 . T C 269 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.25449;LSEQ=ATCAAAAACACTATTCTGCC;RSEQ=CTGTAAATTTTTATTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:517:407:137,270:42,66:108,407:0.7872:2,2:23.2:1:31.1:1:0.30916:1.25356:59.8:80.4:0.7898:0:1.1 0/1:388:188:71,117:76,123:199,188:0.4845:2,2:23.8:1:30.4:1:1:1.01816:60:93:0.4882:0:1.1 +7 103215120 . T A 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=1;SOR=1.47399;LSEQ=GGGGCAGTCAGTCTCAAATT;RSEQ=AAAAAAAATCCTTGAAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:12:0,12:0,5:5,12:0.6667:0,0:18.3:1:30.7:1:1:0:60:24:0.7059:0:1.2 1/0:4:3:0,3:0,1:1,3:0.75:0,0:14.3:1:32:0:1:0:60:6:0.75:0:1 +7 103275803 . T C 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.33086;LSEQ=ATATCTAGAATTTTATACCA;RSEQ=TTGAATTATGATTTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:224:115,109:64,57:121,224:0.6493:2,2:26.9:1:32.5:1:0.82177:1.06401:60:36.333:0.6488:0:1.1 0/1:311:118:63,55:106,87:193,118:0.3794:2,2:28.3:1:30.9:1:0.81525:1.06345:60:117:0.3799:0:1.1 +7 103275875 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0429;SOR=Inf;LSEQ=AATGCTTTCCAACATACCTG;RSEQ=GCTCATGATAGCTGAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:90,174:264,0:0:2,0:26:1:30.6:1:1:0:59.9:32:1:0:0.4 0/1:222:4:3,1:86,132:218,4:0.018:2,2:19.5:1:26.8:1:0.30462:4.57:60:8:0.0183:0:1 +7 103275910 . G T 39 pSTD;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2636;SOR=0;LSEQ=AGATATGAATAATGCTCCAG;RSEQ=AGTTTCCAAGTTATCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:3:1,2:23,116:139,3:0.021:2,2:25:0:24.7:1:0.42867:2.50:60:2:0.0144:0:1.3 0/0:106:0:0,0:19,87:106,0:0:2,0:23.8:1:31:1:1:0:60:212:1:0:0 +7 103275947 . A C 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.04013;SOR=0;LSEQ=CATTATCATAAGAATAATGC;RSEQ=ACAAAACTCCTTCACCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:0,7:0,53:53,7:0.1167:1,0:13.7:1:33.1:1:1:0:60:14:0.1273:0:1.1 0/0:39:0:0,0:3,36:39,0:0:2,0:23.9:1:31.1:1:1:0:60:78:1:0:0 +7 104414109 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02857;SOR=Inf;LSEQ=GCAGTCACACTGCAGTAGGG;RSEQ=AGGCCCCTGGCCCAGTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:29.8:1:29.7:1:1:0:60:5:1:0:0.2 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:9:1:29.5:1:1:0:60:4:1:0:1 +7 104414278 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49538;SOR=Inf;LSEQ=AGGGGAGAGGCCTGGGACAG;RSEQ=TGTTCCCTTGCAGCCCTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:15,28:43,0:0:2,0:25:1:30.7:1:1:0:60:86:1:0:0 0/1:47:2:1,1:19,26:45,2:0.0426:2,2:25:1:29.5:1:1:1.36:60:4:0.0435:0:1 +7 104414284 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49367;SOR=Inf;LSEQ=GAGGCCTGGGACAGATGTTC;RSEQ=CTTGCAGCCCTAAGGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:14,26:40,0:0:2,0:23.9:1:31.2:1:1:0:60:80:1:0:0.1 0/1:40:2:1,1:15,23:38,2:0.05:2,2:26.5:1:28.5:1:1:1.52:60:4:0.05:0:1 +7 104414291 . GC G 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.46573;SOR=0.51407;LSEQ=GGGACAGATGTTCCCTTGCA;RSEQ=CCTAAGGAGGAACCAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:7,21:28,5:0.1515:2,2:35.4:1:32:1:0.59705:1.95:60:10:0.1515:0:0 0/1:36:3:0,3:13,19:32,3:0.0833:2,0:33.3:1:31.3:1:0.27899:0:60:6:0.0857:0:0.3 +7 105280862 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGACTGTGGACAGCTTGTG;RSEQ=GGAGGTTACTTCTAAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:43:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 106507968 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17714;SOR=Inf;LSEQ=GGAAAGTGCCTTTCTTGTGA;RSEQ=AAATCCCTGTGTCCCTCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:0:0,0:178,80:258,0:0:2,0:23.2:1:32.2:1:1:0:60:257:1:0:0.1 0/1:188:2:1,1:122,64:186,2:0.0106:2,2:11:1:28:1:1:1.89933:60:4:0.0108:0:1.5 +7 106508385 . G T 40 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62411;SOR=2.86176;LSEQ=ACTGCCTGCGCTACTGGAAG;RSEQ=CCACGCACCGGAGCCCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:1:0,1:112,145:257,1:0.0039:2,0:1:0:29:0:1:0:60:2:0.004:0:1 0/1:273:3:1,2:143,127:270,3:0.011:2,2:7.7:1:25.3:1:0.60399:2.24549:60:6:0.0113:0:1.7 +7 106508397 . A G 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00022;SOR=Inf;LSEQ=ACTGGAAGGCCACGCACCGG;RSEQ=GCCCGGGCCAGATCCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:120,143:263,0:0:2,0:25.4:1:31.1:1:1:0:59.9:51.6:0.9961:0:0.1 0/1:277:13:4,9:135,129:264,13:0.0469:2,2:25.6:1:30.5:1:0.16842:2.3477:60:26:0.048:0:1.2 +7 106508462 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4987;SOR=0;LSEQ=GAGTCCCAAGCCTTCCAGCG;RSEQ=CAGCTCACGGCGCTGATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:87,103:190,2:0.0104:2,2:22:1:29.5:1:1:1.18:60:4:0.0106:0:1 0/0:190:0:0,0:81,109:190,0:0:2,0:25.7:1:30.8:1:1:0:60:46.5:1:0:0.3 +7 106508516 . C T 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.58577;LSEQ=GACGTCAGCAACGTGCACGA;RSEQ=GATGAGCTGGAGTTCACGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:128,58:186,2:0.0106:2,2:12.5:1:27:1:0.53032:2.19668:60:4:0.0108:0:1 0/0:160:1:0,1:96,63:159,1:0.0063:2,0:1:0:25:0:0.4:0:60:2:0.0063:0:1 +7 106508978 . A G 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.7337;LSEQ=GTGAGGAAGGAAGAGTGGCC;RSEQ=CTGGTGGATGACTGCACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:561:559:335,224:1,1:2,559:0.9964:2,2:24.8:1:30.8:1:1:1.49:60:92.167:0.9964:0:2 1/1:412:410:243,167:1,0:1,410:0.9951:0,2:24.8:1:29.9:1:1:0:59.9:81:0.9951:0:2.1 +7 106508987 . T C 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.49687;LSEQ=GAAGAGTGGCCACTGGTGGA;RSEQ=GACTGCACGGGAGTCACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:587:585:356,229:0,2:2,585:0.9966:0,2:25.6:1:31.4:1:0.15446:0:60:82.571:0.9966:0:2 1/1:439:438:262,176:0,0:0,438:0.9977:0,2:25.4:1:30.4:1:1:0:59.9:72:1:0:2 +7 106509082 . G A 142 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.30736;LSEQ=GTCCCTGTGGGACTGCGACC;RSEQ=CAAGTTCAGGGTCAAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:997:1:1,0:532,463:995,1:0.001:2,0:44:0:32:0:1:0:60:2:0.001:0:1 0/1:1015:30:18,12:536,445:981,30:0.0296:2,2:30.4:1:29.1:1:0.58308:1.25:60:29:0.0291:0:1.1 +7 106509331 . C A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=3.12485;LSEQ=CGGTAAAGCTCCAGCACTGT;RSEQ=CAGCAAGGCCTCTGCAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1013:65:41,24:497,451:948,65:0.0642:2,2:22.9:1:29.3:1:0.1226:1.55:59.9:130:0.0648:0:1.1 0/1:895:158:79,79:381,355:736,158:0.1765:2,2:26.1:1:28.3:1:0.72592:1.07314:60:316:0.1793:0:1 +7 106509933 . A G 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGATGAAAATGTAAGAGCC;RSEQ=TTGCAGTTCAGAAACTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1116:0:0,0:471,644:1115,0:0:2,0:23.8:1:31:1:1:0:59.9:184.833:0.9991:0:0.1 0/1:1006:47:20,27:439,519:958,47:0.0467:2,2:22.3:1:30.5:1:0.76462:1.14176:60:94:0.0472:0:1.1 +7 106510076 . A G 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.4574;SOR=1.17303;LSEQ=TATGCACAGGCACTCCATTC;RSEQ=GTTGTCATCAAATGCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:78:9,69:13,153:166,78:0.3197:2,2:23.1:1:30.2:1:0.34706:1.53:60:25:0.3138:0:1.1 0/1:166:59:9,50:20,87:107,59:0.3554:2,2:20.6:1:30:1:0.67199:1.2753:60:58:0.3537:0:1.1 +7 106512878 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21654;SOR=Inf;LSEQ=AGATTTTCATCTTTCTAGCC;RSEQ=TGAAGACCCAGTAAAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:129,6:135,0:0:1,0:22:1:29.9:1:1:0:60:44:1:0:0 0/1:118:2:2,0:107,9:116,2:0.0169:2,0:36.5:1:29.5:1:1:0:60:4:0.0169:0:1.5 +7 106513011 . C T 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19793;LSEQ=TTTGAACCATACCATGATAG;RSEQ=GCCCTTGCCAGATTTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:682:412:202,210:140,130:270,412:0.6041:2,2:28.8:1:30:1:0.48187:1.11939:59.9:67.667:0.6033:0:1.1 0/1:643:149:78,71:254,240:494,149:0.2317:2,2:27.7:1:29.4:1:0.85218:1.04:60:148:0.2316:0:1.2 +7 106519943 . T C 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50086;SOR=Inf;LSEQ=TATTCATTGTGTGTGGGGAA;RSEQ=ATGTGACTGCTTCCTTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:513:511:363,148:0,2:2,511:0.9961:0,2:23.8:1:32.1:1:0.08509:0:60:72:0.996:0:1.1 1/1:462:462:306,156:0,0:0,462:1:0,2:23.5:1:31.3:1:1:0:60:114.5:1:0:1.1 +7 106520111 . G T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02344;SOR=Inf;LSEQ=AAGACATGCTTATTTTACAG;RSEQ=TATGCTAATTTTAAGATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:441:0:0,0:116,324:440,0:0:2,0:26.3:1:32:1:1:0:60:87:0.9977:0:0.1 0/1:285:4:0,4:81,200:281,4:0.014:2,0:38.3:1:29.8:1:0.58041:0:60:8:0.0141:0:1 +7 106522307 . A AAAAAC 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCTACAAAACAAAAAC;RSEQ=AAAACAAAACAAAACAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:3:3,0:8,1:9,3:0.25:2,0:27:1:31.6:1:1:0:55:6:0.25:0.0833:0 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:28:0:1:0:60:2:1:0:0 +7 106522411 . T C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03613;SOR=Inf;LSEQ=AGAAACTTTAGAGTACCAGA;RSEQ=TGACCAATAAACGTACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:65,1:66,0:0:1,0:23.2:1:31.7:1:1:0:59.7:132:1:0:0 0/1:16:2:2,0:14,0:14,2:0.125:1,0:8.5:1:33:0:1:0:60:4:0.125:0:0.5 +7 106522520 . A AAT 69 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.24874;SOR=0.23016;LSEQ=GAAGAAAAATATATTAAGTT;RSEQ=ATATATATATAATATAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:6:4,2:342,73:415,6:0.0143:2,2:15.7:1:26.8:1:0.29075:2.33648:59.8:5:0.012:0.0071:1.7 0/0:302:1:1,0:226,75:301,1:0.0033:2,0:17:0:31.5:0:1:0:60:2:0.0033:0:0 +7 106522592 . A G 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATGGAGTCTATTTGGGAG;RSEQ=CTGAATCTTTGGATCTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1090:0:0,0:603,485:1088,0:0:2,0:27.2:1:29.8:1:1:0:59.9:44.333:1:0:0.1 0/1:901:41:21,20:479,380:859,41:0.0455:2,2:29.4:1:29.2:1:0.63042:1.20025:60:12.667:0.0427:0:1.2 +7 106522693 . G A 229 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01592;LSEQ=ATGAATAGACCTCTCAGCTC;RSEQ=TTTGAAAAGATTATAATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:176:46,130:128,330:458,176:0.2776:2,2:23.7:1:30.8:1:0.69156:1.09605:59.9:57.667:0.2755:0:1.1 0/0:495:3:1,2:167,323:490,3:0.0061:2,2:4:1:25.3:1:1:1.03399:60:2:0.0041:0:1 +7 106522738 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.18098;SOR=Inf;LSEQ=GTGTAGACATTTAATAACTG;RSEQ=AAAATCATAATCTTAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:20,240:260,0:0:2,0:23.3:1:31.2:1:1:0:59.9:85.667:1:0:0.2 0/1:193:2:1,1:23,168:191,2:0.0104:2,2:29.5:1:28.5:1:0.23381:7.17:60:4:0.0106:0:1 +7 106523440 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.07802;SOR=Inf;LSEQ=TCCTCTGGGCCAGGTACTGG;RSEQ=CCCCAATCTCCATCAGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:195,65:260,0:0:2,0:25.5:1:31.8:1:1:0:59.8:85.667:1:0:0.3 0/1:195:3:2,1:148,44:192,3:0.0154:2,2:36.7:1:28:0:0.54695:1.67676:60:6:0.0157:0:1.3 +7 106523446 . A G 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCCAGGTACTGGCCCCCA;RSEQ=TCTCCATCAGACTCTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:201,71:272,0:0:2,0:26.5:1:29.8:1:1:0:59.8:26.2:1:0:0.3 0/1:214:35:27,8:135,44:179,35:0.1636:2,2:26.8:1:31.6:1:1:1.10:60:70:0.1691:0:1.3 +7 106523620 . CT C 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.45122;SOR=0.39944;LSEQ=GAAGAAAAGGTGAGCTCATG;RSEQ=TTTTCCCAGTCTAATGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:432:5:2,3:157,270:427,5:0.0116:2,2:34.6:1:33.6:1:1:1.15:60:10:0.0119:0:0.2 0/0:430:2:1,1:166,259:425,2:0.0047:2,2:27:1:33.5:1:1:1.56:60:4:0.0047:0:0 +7 106523670 . G C 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.01876;SOR=2.45042;LSEQ=TTGTCATTTATATAGCAGTA;RSEQ=TGGCTTCAAGTTTTCAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:13:1,12:34,175:209,13:0.0586:2,1:30.3:1:33.1:1:0.69755:2.32468:60:26:0.061:0:1 0/1:166:22:5,17:33,111:144,22:0.1325:2,2:31.1:1:31.7:1:1:1.01075:60:44:0.135:0:1.1 +7 106523673 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.17181;SOR=Inf;LSEQ=TCATTTATATAGCAGTAGTG;RSEQ=CTTCAAGTTTTCAGAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:32,182:214,0:0:2,0:24.3:1:31.9:1:1:0:59.8:70.333:1:0:0.2 0/1:152:2:1,1:30,120:150,2:0.0132:2,2:12.5:1:25:0:0.36738:3.95:60:4:0.0135:0:1 +7 106524542 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17592;SOR=Inf;LSEQ=CTTTTTAGAAGTCATTTGTA;RSEQ=ATTCATGATGCTTTTTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:195,41:236,0:0:2,0:22.2:1:32.9:1:1:0:59.9:77.667:1:0:0.1 0/1:171:2:1,1:139,30:169,2:0.0117:2,2:20:1:27.5:1:0.33058:4.57438:60:4:0.0118:0:1 +7 106524644 . CTG C 177 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GTTTATTCCTGTGCAGGCTA;RSEQ=TGTGGCAACCTTTGTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:44:21,23:319,323:642,44:0.064:2,2:29.3:1:32.5:1:0.87659:1.08153:60:88:0.0651:0.0029:0.8 0/0:593:0:0,0:289,304:593,0:0:2,0:25.6:1:29.7:1:1:0:60:83.714:1:0:0.2 +7 106524689 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=2.34567;LSEQ=ATAGGCGACAGACACAATGA;RSEQ=AATATTATGATCACCGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:40:13,27:200,327:527,40:0.0705:2,2:24.7:1:29.3:1:0.61193:1.26977:60:80:0.0716:0:1 0/1:443:67:21,46:154,221:375,67:0.1512:2,2:25.5:1:27.6:1:0.13878:1.52498:60:21.333:0.1478:0:1.1 +7 106524745 . G T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17655;SOR=Inf;LSEQ=GTGCAGAATAAACTTTTATT;RSEQ=TGGTAAAATATATATAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:38,188:226,0:0:2,0:21.7:1:32.3:1:1:0:60:225:0.9956:0:0.1 0/1:165:2:1,1:36,127:163,2:0.0121:2,2:7.5:1:30.5:1:0.39926:3.49:60:4:0.0121:0:1 +7 106526802 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5641;SOR=3.08197;LSEQ=GATGGTTCCTGCAGCACTCC;RSEQ=CAGCCTTCACCTCTCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:1:1,0:15,129:144,1:0.0069:2,0:1:0:29:0:0.11034:0:60:2:0.007:0:1 0/1:95:2:0,2:9,84:93,2:0.0211:2,0:29.5:1:28:1:1:0:60:4:0.0213:0:1 +7 106546087 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GTGGCATTGGAGAATATTCT;RSEQ=GGTTTAAACAGACTAATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:21.7:1:30:1:1:0:60:6:0.4286:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:22.5:1:32:1:1:0:60:4:1:0:0 +7 107730490 . T A 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTACTAGATGTATGACTT;RSEQ=GAGTGACTTACCTAACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:3,0:14,0:14,3:0.1765:1,0:20.3:1:27.7:1:1:0:60:6:0.1765:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:15.8:1:30.8:1:1:0:60:8:1:0:0 +7 107730650 . G A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAACAGTAACAGCATAGCAA;RSEQ=CATACCATGAAATTTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:156,46:202,0:0:2,0:24.8:1:32.9:1:1:0:59.8:201:1:0:0 0/1:162:17:14,3:99,46:145,17:0.1049:2,2:23:1:29:1:0.27788:2.16:60:34:0.1056:0:1.1 +7 107730749 . C A 196 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCATACCCTCAGCAGAGAA;RSEQ=GAAAATTATTCACATTATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:0:0,0:264,276:540,0:0:2,0:26.5:1:31:1:1:0:60:89:0.9944:0:0.1 0/1:466:101:52,49:189,176:365,101:0.2167:2,2:24.3:1:29.5:1:1:1.01189:59.9:100:0.2169:0:1.1 +7 107730838 . C T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19008;LSEQ=TCATAGGTATTATTTTCTAA;RSEQ=TTGTTAAGAAAAATTCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:57:17,40:39,136:175,57:0.2446:2,2:19:1:30.9:1:0.28544:1.48:60:114:0.2468:0:1.1 0/1:173:10:2,8:37,126:163,10:0.0578:2,2:28:1:30.4:1:1:1.17355:60:20:0.0578:0:1.3 +7 107730846 . GA G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50482;SOR=0;LSEQ=ATTATTTTCTAACTTGTTAA;RSEQ=AAAATTCACCTGCCCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:35,146:181,2:0.0109:2,2:29.5:1:32:1:0.35561:4.13:60:4:0.011:0:0 0/0:146:0:0,0:26,120:146,0:0:2,0:23.9:1:30.1:1:1:0:60:72:1:0:0.2 +7 111819870 . A G 60 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.63089;SOR=0.32501;LSEQ=AAAATCAGAAATACACAGTG;RSEQ=AACACACACCTCAAAGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:4,0:18,1:19,4:0.1739:1,0:22:1:30.3:1:1:0:60:8:0.1739:0:1.8 0/1:16:1:1,0:15,0:15,1:0.0625:1,0:49:0:29:0:1:0:60:2:0.0625:0:2 +7 111819901 . T A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.79298;SOR=0.74197;LSEQ=TCAAAGGTATGATGAATATT;RSEQ=AACTGGGGCTCGTATCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:17:17,0:43,0:43,17:0.2787:1,1:19.3:1:29:1:1:0:60:34:0.2881:0:1.4 0/1:27:6:6,0:21,0:21,6:0.2222:1,0:14.2:1:27.7:1:1:0:60:12:0.2222:0:1.3 +7 111820090 . G A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.53628;LSEQ=ACTAAGTCCAAAAGTCTAAA;RSEQ=TAGAACATAAATGGAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:517:394:172,222:49,72:121,394:0.7621:2,2:23.8:1:30.6:1:0.5998:1.14:60:48.25:0.7583:0:1.1 1/0:470:297:132,165:73,99:172,297:0.6319:2,2:24.3:1:29.5:1:0.6999:1.08:60:48.5:0.6326:0:1.1 +7 111820157 . C CG 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.83181;SOR=0.94093;LSEQ=AATAGCTTCAAAGTCAACTA;RSEQ=GGTTTAGCTGTCAGTACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:76:22,54:61,154:215,76:0.2603:2,2:30.7:1:30.7:1:1:1.03:60:75:0.2622:0.024:0.4 0/1:193:48:16,32:43,102:145,48:0.2487:2,2:25.8:1:30:1:0.71809:1.18:59.9:96:0.25:0.0363:0.6 +7 111820439 . T C 32 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTCACTTCTGCAGACAAC;RSEQ=TTTACCCCGACAGGTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:29.5:1:32:1:1:0:60:4:0.5:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:19:0:33:0:1:0:60:2:1:0:1 +7 112160713 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18074;SOR=Inf;LSEQ=GCTGGTGCGAAGGATGAACT;RSEQ=CACATTGTTGAAGCAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:124,139:263,0:0:2,0:27.7:1:32.4:1:1:0:58.3:130.5:1:0:0.1 0/1:195:2:1,1:96,97:193,2:0.0103:2,2:20.5:1:29:1:1:1.01:24:4:0.0104:0:1.5 +7 112160813 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50405;SOR=0;LSEQ=AGGCAACAGTTTCCCTTGGG;RSEQ=GCTTTGAAATACCACTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:69,59:128,2:0.0154:2,2:23.5:1:31:0:1:1.16808:58.5:4:0.0157:0:1 0/0:104:0:0,0:53,51:104,0:0:2,0:21.9:1:30.1:1:1:0:59.6:33.667:1:0:0.1 +7 112160841 . T A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52252;SOR=0;LSEQ=AATACCACTACCTGTGGTCT;RSEQ=ACAATCGAAGTGTGGTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:111,75:186,2:0.0106:2,2:16:0:31.5:1:1:1.4768:38:4:0.0106:0:1 0/0:121:0:0,0:69,52:121,0:0:2,0:25.2:1:28.7:1:1:0:54.6:120:1:0:0.1 +7 112160911 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12792;SOR=Inf;LSEQ=GTAGCTGTGGAGGAAGATGC;RSEQ=GAATCAGAAGATGAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:94,126:220,0:0:2,0:25.5:1:31:1:1:0:49.8:440:1:0:0.3 0/1:123:2:1,1:52,69:121,2:0.0163:2,2:18:1:31.5:1:1:1.32:49.5:4:0.0163:0:1 +7 112160927 . G A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14079;SOR=0.53794;LSEQ=ATGCAGAATCAGAAGATGAG;RSEQ=TGGGGGACGTGAAACTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:27:8,19:53,100:153,27:0.15:2,2:26.2:1:30.7:1:0.66594:1.25718:48.1:54:0.1525:0:1.1 0/1:104:9:3,6:36,59:95,9:0.0865:2,2:17.7:1:30.1:1:1:1.21804:43.9:18:0.0874:0:1.1 +7 112161076 . C T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=ACGAGGAAACTGAAGAAAAA;RSEQ=TCCGGTGAAAAAATCTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:4,8:12,2:0.1429:2,2:6:0:32.5:1:1:1.90:41.5:4:0.1429:0:2.5 0/0:13:0:0,0:7,6:13,0:0:2,0:22.4:1:30.4:1:1:0:55.3:26:1:0:0.5 +7 112161080 . G A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.84527;LSEQ=GGAAACTGAAGAAAAACTCC;RSEQ=GTGAAAAAATCTATATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:4,6:3,4:7,10:0.5882:2,2:15.9:1:31.9:1:1:1.11721:56.3:20:0.5882:0:1.4 1/0:11:6:4,2:1,4:5,6:0.5455:2,2:31.5:1:30.3:1:0.24242:6.44:53.8:12:0.5455:0:1 +7 112161717 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=ATCTCTGGCAGTGGAGGGAG;RSEQ=CACTTTAAGAAAAGAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:28.3:1:30:1:1:0:60:12:1:0:0.3 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:26.5:1:29.5:1:1:1.41:60:4:0.2857:0:1 +7 112286315 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21429;SOR=Inf;LSEQ=AGTCTTTAAGGCTGCTGACC;RSEQ=TTGGATGGGGATTTTGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:23.6:1:32.2:1:1:0:45.8:22:1:0:0.1 0/1:10:2:1,1:6,2:8,2:0.2:2,2:48.5:1:30.5:1:1:2.64575:42:4:0.2:0:1.5 +7 112287067 . G T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCTTTCCCCTCCCAGGGA;RSEQ=CTGAGCGTGTTAGGCAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:35:1:33:1:1:0:60:4:1:0:1 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:33.5:1:31:1:1:1.41418:60:4:0.2857:0:2 +7 112287096 . G A 66 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAGGCAGTTGTGAGTCCC;RSEQ=GTGCTGGCTGTTGCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:30:1:1:0:60:4:1:0:1 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:24.8:1:28.8:1:1:1.41:47.6:10:0.7143:0:1.6 +7 112724525 . A G 53 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCCATAAGTCCAGGTAGA;RSEQ=CCATTTTTGACAGAGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:32.7:1:33.7:1:1:0:60:6:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:32:1:32.5:1:1:0:60:4:1:0:1 +7 112724644 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16844;SOR=Inf;LSEQ=CAAGGTCTTATCTTTCACTA;RSEQ=CAAAATGGAGATCAGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:19,9:28,0:0:2,0:16.9:1:32.1:1:1:0:60:13:1:0:0.1 0/1:20:2:1,1:12,6:18,2:0.1:2,2:31:1:28:1:1:1.92731:60:4:0.1:0:1 +7 112724654 . G T 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11389;SOR=Inf;LSEQ=TCTTTCACTAGCAAAATGGA;RSEQ=ATCAGGAGGTTGCCCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:21,13:34,0:0:2,0:20.5:1:33:1:1:0:60:68:1:0:0.1 0/1:33:3:1,2:17,13:30,3:0.0909:2,2:5.7:1:25.7:1:0.57936:2.54081:60:6:0.0909:0:1 +7 112724704 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49591;SOR=0;LSEQ=TATTATGAAACCCAAGGAAG;RSEQ=CAGTTTCAGAAAGGCTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:25,20:45,2:0.0426:2,2:11.5:1:31:1:1:1.24403:60:4:0.0444:0:1 0/0:42:0:0,0:20,22:42,0:0:2,0:28.4:1:29.1:1:1:0:60:84:1:0:0.2 +7 112724795 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06536;SOR=Inf;LSEQ=ATAGATGGATGGAGGATAAG;RSEQ=ATACAGCCTCAGTCAAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:0,13:13,0:0:1,0:27:1:32.5:1:1:0:60:26:1:0:0 0/1:5:2:0,2:0,3:3,2:0.4:0,0:18.5:1:28.5:1:1:0:60:4:0.4:0:1 +7 112726624 . CGCG C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.50549;SOR=Inf;LSEQ=TCCCCCAGTAACGCAGGGGC;RSEQ=GCGGCGGCGGCTGCGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:32.2:1:31.4:1:1:0:60:10:1:0:0.4 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:31:0:33:1:1:1.29098:60:4:0.2222:0:0 +7 112726660 . G C 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=GCGGTGGCGAGGGCGGCGGC;RSEQ=GGGCTGCTTCAGCCTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:30:1:31.5:1:1:0:60:4:0.6667:0:1 0/0:9:0:0,0:5,4:9,0:0:2,0:30.4:1:29.3:1:1:0:60:18:1:0:0.7 +7 114268637 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50427;SOR=0;LSEQ=TGACTCCCCAGGTGATCACC;RSEQ=CTCAGCAAATGCAGCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:44,47:91,2:0.0215:2,2:27.5:1:31:1:1:1.07:60:4:0.0222:0:1.5 0/0:73:0:0,0:38,35:73,0:0:2,0:23.2:1:29.1:1:1:0:60:35.5:1:0:0.1 +7 114268667 . C T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07463;SOR=Inf;LSEQ=TGCAGCAGATCCTTCAGCAA;RSEQ=AAGTCCTGTCTCCTCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:35,53:88,0:0:2,0:26:1:32.2:1:1:0:60:87:1:0:0.1 0/1:65:3:1,2:20,42:62,3:0.0462:2,2:16.7:1:21.7:1:1:1.05:60:2:0.0313:0:2 +7 114269859 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14901;SOR=Inf;LSEQ=AAGTCAAAATGGTTTATTCA;RSEQ=CAACAACTACAAGAGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:61,5:66,0:0:2,0:24.7:1:33.4:1:1:0:60:65:1:0:0.1 0/1:42:2:1,1:37,3:40,2:0.0476:2,2:20.5:1:31:0:0.18351:10.82458:60:4:0.05:0:1 +7 114269915 . TGCA T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.05698;SOR=Inf;LSEQ=GCAGTTACATCTTCAGCTTT;RSEQ=GCAGCAGCAGCAACAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:111,57:168,0:0:2,0:29.2:1:31.9:1:1:0:60:55:1:0:0.1 0/1:162:4:1,3:109,49:158,4:0.0247:2,2:33.5:1:30:1:0.09772:6.58912:60:8:0.0253:0.0062:0.3 +7 114269956 . C T 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24829;SOR=Inf;LSEQ=AGCAGCAGCAACAACAGCAG;RSEQ=AACAACAGCAGCAGCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:115,103:218,0:0:2,0:22.9:1:31.3:1:1:0:59.1:17.167:1:0:0.2 0/1:220:3:1,2:124,93:217,3:0.0136:2,2:11.7:1:20.7:1:0.57942:2.65491:57.3:2:0.0093:0:1.3 +7 114269970 . GCAA G 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=0.81414;LSEQ=CAGCAGCAACAACAGCAGCA;RSEQ=CAACAACAACAACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:3:0,3:102,99:201,3:0.0147:2,0:39.3:1:33.3:1:0.24631:0:60:6:0.0152:0:0 0/1:250:3:2,1:136,108:244,3:0.012:2,2:39:1:30:1:1:1.59:60:6:0.0128:0:0 +7 114269997 . ACAG A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.24064;SOR=2.50132;LSEQ=CAACAACAACAGCAGCAACA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:3:2,1:108,125:233,3:0.0127:2,2:15:1:31.7:1:0.5995:2.31:60:6:0.0133:0.0042:0.3 0/1:288:9:5,4:137,140:277,9:0.0313:2,2:24.4:1:32:1:0.74865:1.28:50.2:18:0.0326:0:0.2 +7 114270000 . G A 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.00306;SOR=0;LSEQ=CAACAACAGCAGCAACAACA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:7:4,3:99,118:217,7:0.031:2,2:34.1:1:28.1:1:0.70583:1.59:58.3:6:0.0279:0:1.4 0/0:287:0:0,0:132,138:270,0:0:2,0:24.8:1:30.9:1:1:0:58.4:26:0.9962:0:0.3 +7 114270001 . C A 63 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.23619;SOR=3.97374;LSEQ=AACAACAGCAGCAACAACAG;RSEQ=AGCAGCAGCAGCAACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:0,1:104,122:226,1:0.0044:2,0:31:0:13:0:1:0:60:0:0:0:6 0/1:290:5:3,2:138,145:283,5:0.0172:2,2:20.8:1:27.4:1:0.67894:1.57:60:4:0.0144:0:1.2 +7 114270015 . ACAG A 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.75212;SOR=0.7578;LSEQ=CAACAGCAGCAGCAGCAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:5:3,2:84,120:204,5:0.0237:2,2:30:1:32.8:1:0.65123:2.13:60:10:0.0242:0:0.2 0/1:277:5:2,3:123,149:272,5:0.0181:2,2:32.8:1:31.8:1:1:1.23731:56.8:10:0.0185:0:0.2 +7 114270025 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.18632;SOR=0;LSEQ=AGCAGCAGCAACAGCAGCAG;RSEQ=AGCAGCAACAGCATCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:80,118:198,2:0.01:2,2:27.5:1:30:0:1:1.47:59:4:0.0101:0:1.5 0/0:264:0:0,0:120,144:264,0:0:2,0:29.1:1:31.3:1:1:0:58.1:51.8:1:0.0076:0.3 +7 114270027 . G T 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.58252;SOR=0.38406;LSEQ=CAGCAGCAACAGCAGCAGCA;RSEQ=CAGCAACAGCATCCTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:79,118:197,2:0.0101:2,2:23.5:1:25.5:1:1:1.49:60:4:0.0101:0:2 0/0:258:1:1,0:112,142:254,1:0.0039:2,0:39:0:27:0:0.44314:0:60:2:0.004:0:1 +7 114270065 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50397;SOR=Inf;LSEQ=AAAGCAAGCGAAAGAGGTAG;RSEQ=ATCCGGTTATCTCATTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:42,98:140,0:0:2,0:21.6:1:31.1:1:1:0:60:22.333:1:0:0.6 0/1:173:2:1,1:59,112:171,2:0.0116:2,2:21:1:26.5:1:1:1.89:60:4:0.0118:0:1 +7 114270077 . T G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0.11935;LSEQ=AGAGGTAGGATCCGGTTATC;RSEQ=CATTGATACATAACAGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:47:11,36:12,43:55,47:0.4608:2,2:22.4:1:31.7:1:1:1.09:60:94:0.47:0:1.1 0/1:120:11:3,8:28,81:109,11:0.0917:2,2:15.6:1:30.3:1:1:1.08:60:22:0.0957:0:1 +7 114302159 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15797;SOR=Inf;LSEQ=TTAGCCTGCACAAGTGTTTT;RSEQ=TTCGAGTAGAAAATGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:97,69:166,0:0:2,0:26.4:1:32.3:1:1:0:60:165:1:0:0.1 0/1:110:2:1,1:54,54:108,2:0.0182:2,2:36:1:31.5:1:1:1:60:4:0.0183:0:1 +7 114302194 . T C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51369;SOR=0;LSEQ=GTTAAAGGAGCAGTATGGAC;RSEQ=GTGGATGAAGTAGAATACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:2:1,1:82,94:176,2:0.0112:2,2:30:0:31:1:1:1.15:60:4:0.0114:0:1 0/0:125:0:0,0:53,71:124,0:0:2,0:28.2:1:29.8:1:1:0:59.8:123:0.9919:0:0.1 +7 114302265 . T C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54914;SOR=0;LSEQ=TGTTTGTGATAGTTTTGTAA;RSEQ=CCTGTATCCTGCATCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:0,3:4,50:54,3:0.0526:2,0:24.7:1:33.3:1:1:0:60:6:0.0588:0:1 0/0:31:0:0,0:3,28:31,0:0:2,0:25.3:1:29.1:1:1:0:60:62:1:0:0 +7 114302267 . C A 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53109;SOR=0;LSEQ=TTTGTGATAGTTTTGTAATC;RSEQ=TGTATCCTGCATCCACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:2,50:52,2:0.037:1,2:6:1:27:1:0.10901:20.61:60:4:0.0377:0:1 0/0:31:0:0,0:3,28:31,0:0:2,0:23.9:1:31.7:1:1:0:60:62:1:0:0 +7 116187033 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21687;SOR=Inf;LSEQ=CCTTGTCTCTCCTAGTTTCT;RSEQ=GTGGTTTGCTGGCAATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:43,31:74,0:0:2,0:27.4:1:32.1:1:1:0:59.9:73:1:0:0.3 0/1:65:2:1,1:33,30:63,2:0.0308:2,2:20:1:29:1:1:1.09839:60:4:0.0308:0:1 +7 116187106 . G A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.08852;LSEQ=CTCTGCCTCCATCATTAATG;RSEQ=CCTTCTGCCTGAGTGTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:25:6,19:6,10:16,25:0.6098:2,2:28.3:1:29.8:1:0.48495:1.86941:60:50:0.6098:0:1 0/1:34:4:1,3:9,21:30,4:0.1176:2,2:20.5:1:29.5:1:1:1.27668:60:8:0.1176:0:1 +7 116339672 . C T 120 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0.05462;LSEQ=TGTCCTGACTGTGTGGTGAG;RSEQ=GCCCTGGGAGCCAAAGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:19:11,8:306,211:517,19:0.0354:2,2:24:1:28.3:1:1:1.05459:60:8.5:0.0323:0:1.4 0/0:500:1:0,1:279,220:499,1:0.002:2,0:1:0:24:0:0.442:0:60:2:0.002:0:1 +7 116340269 . C T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACGACTTCTTCAACAAGAT;RSEQ=GTCAACAAAAACAATGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:661:0:0,0:278,383:661,0:0:2,0:25.8:1:30.9:1:1:0:60:93.429:1:0:0.1 0/1:599:19:5,14:256,324:580,19:0.0317:2,2:21.3:1:27.4:1:0.15934:2.20961:60:8.5:0.0287:0:1 +7 116340401 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19728;SOR=Inf;LSEQ=ATTAGAAATAAGTATCAGTC;RSEQ=CAAAAAGAATATCCAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:6,106:112,0:0:2,0:24.7:1:30.4:1:1:0:60:36.333:1:0:0.1 0/1:90:2:1,1:10,78:88,2:0.0222:2,2:12.5:1:28:1:0.23071:7.48:60:4:0.0227:0:1 +7 116340531 . A AT 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08669;SOR=0;LSEQ=AATTATATCTTTAAAATGTA;RSEQ=ATGGTAACTAAAAGAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:0,9:0,6:6,9:0.6:0,0:21.1:1:29.3:1:1:0:58.3:18:0.6:0.2:0.4 0/0:4:0:0,0:0,4:4,0:0:0,0:20:1:31.5:1:1:0:60:8:1:0:0 +7 116340582 . A C 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=TTCAGATTTGCATGTTCGTG;RSEQ=CATTTCAGATTATATTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:27.4:1:31.7:1:1:0:60:14:0.875:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:33:0:32:0:1:0:60:2:1:0:0 +7 116371650 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.20771;SOR=Inf;LSEQ=CCTCCAGGCTCTGAAAATAC;RSEQ=CACTGAAAGGTTTCTTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:140,23:163,0:0:2,0:23.9:1:30.6:1:1:0:59.8:162:1:0:0.1 0/1:137:2:1,1:110,25:135,2:0.0146:2,2:16:1:29:1:0.34468:4.33413:60:4:0.0146:0:1 +7 116395257 . C T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAATTTGTGACCCTTTT;RSEQ=CCTTTAGTGAAAATTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:39:39:39,0:0,0:0,39:1:0,1:26.7:1:31.7:1:1:0:60:78:1:0:1 1/1:26:26:26,0:0,0:0,26:1:0,1:25.4:1:29.7:1:1:0:60:25:1:0:1 +7 116397478 . G GT 82 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.5885;SOR=1.37585;LSEQ=TGTCATGTATTAAACTTTGG;RSEQ=TTTTTTTTCCAGATTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:643:6:4,2:392,245:637,6:0.0093:2,2:33.2:1:28.3:1:1:1.25:60:12:0.0095:0:0.2 0/1:547:7:3,4:334,206:540,7:0.0128:2,2:31.1:1:29.3:1:0.43705:2.15867:60:14:0.013:0:0 +7 116397572 . A G 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04763;LSEQ=AATGGCCACGGGACAACACA;RSEQ=TACAGTACATTCTCCTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:336:176,160:339,333:672,336:0.3333:2,2:27.1:1:32.7:1:0.59302:1.08:60:111:0.3343:0:1.1 0/1:990:23:11,12:468,499:967,23:0.0232:2,2:23.8:1:31:1:1:1.02312:60:46:0.0235:0:1.2 +7 116397724 . C T 84 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07694;SOR=3.52839;LSEQ=ACAAGTATTTCGCCGAAATA;RSEQ=GGTCCTATGGCTGGTGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:961:3:1,2:539,417:956,3:0.0031:2,2:17:1:29.3:1:0.58388:2.58262:60:6:0.0032:0:1 0/1:823:9:5,4:470,344:814,9:0.0109:2,2:13.2:1:26.8:1:1:1.0929:60:8:0.0098:0:1.7 +7 116397904 . TTG T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.80119;SOR=1.15575;LSEQ=TAAAAATTAAGCAGATTGTT;RSEQ=TGTGTGTGTGTGGAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:7:0,7:127,315:442,7:0.0156:2,0:25:1:30.6:1:0.19894:0:60:14:0.0159:0.0022:0 0/1:445:8:2,6:119,315:434,8:0.018:2,2:34.6:1:29:1:1:1.13302:60:16:0.0181:0:0 +7 116398498 . A AT 94 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.28165;SOR=0.47734;LSEQ=AGCTAAAATTCACTTCCTTA;RSEQ=TTTTTTTTGTTCAGTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:10:4,6:390,186:576,10:0.0171:2,2:20:1:28.3:1:0.08735:3.13838:60:20:0.0174:0.0085:0.4 0/0:487:4:3,1:317,166:483,4:0.0082:2,2:16.3:1:29.1:1:1:1.57:60:8:0.0085:0.0041:0.3 +7 116399131 . G A 96 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36022;SOR=0.29661;LSEQ=GTTCAATCTGCCTTGTTTCC;RSEQ=TTAATTCTATCAGTCTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:7,1:6,3:9,8:0.4706:2,2:20:1:32:1:0.57647:3.26:60:16:0.5:0:1 0/1:5:1:1,0:2,2:4,1:0.2:2,0:18:0:31:0:1:0:60:2:0.2:0:1 +7 116399719 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50764;SOR=0;LSEQ=TGAAATTATCTAGAGTCTTG;RSEQ=GCTAACCATGTGGAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:0,2:8,161:169,2:0.0117:1,0:18.5:1:31.5:1:1:0:60:4:0.0118:0:1 0/0:130:0:0,0:16,114:130,0:0:2,0:22.4:1:30.6:1:1:0:60:260:1:0:0 +7 116400378 . G T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAGCTAACAAAGAAAGA;RSEQ=CATTAGAATATTTATGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:29:0:1:0:60:4:1:0:1 +7 116403052 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21992;SOR=Inf;LSEQ=TAAATTATAAAGTTGCTATG;RSEQ=ATGTTGCCAAGCTGTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:161,40:201,0:0:2,0:24.3:1:31.3:1:1:0:60:49.25:1:0:0.1 0/1:178:2:1,1:128,47:175,2:0.0112:2,2:20.5:1:27.5:1:0.46995:2.70539:60:4:0.0114:0:1 +7 116403127 . A G 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00058;SOR=0;LSEQ=TGTCAACATCGCTCTAATTC;RSEQ=GAGATAATCTGTTGTACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:12:9,3:252,184:436,12:0.0268:2,2:21.9:1:29.9:1:0.37431:2.19:60:24:0.0273:0:1.2 0/0:395:0:0,0:223,171:394,0:0:2,0:23.3:1:29.5:1:1:0:60:77.8:0.9974:0:0.1 +7 116409675 . CT C 203 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.91333;SOR=1.03991;LSEQ=AACTGTGAAGTGTTAACAAC;RSEQ=TTTTTTTTTTTTTTCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:76:71,5:91,20:111,76:0.3535:2,2:25.5:1:32.6:1:0.0284:3.10:59.3:75:0.3571:0.0279:1.1 0/1:160:58:47,11:68,14:82,58:0.3625:2,2:20.9:1:29.9:1:0.82471:1.13573:58.8:13.5:0.3506:0.125:0.9 +7 116409950 . T C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19291;LSEQ=GCTCATTTATGTGTGGGTTT;RSEQ=GGCTCATCAACTCAGCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:48:9,39:47,162:209,48:0.1868:2,2:24.2:1:30.4:1:0.69919:1.25609:59.6:96:0.1875:0:1 0/1:260:11:3,8:74,175:249,11:0.0423:2,2:29.5:1:29.5:1:1:1.12711:60:22:0.0425:0:1 +7 116409970 . C G 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2467;SOR=Inf;LSEQ=TGGCTCATCAACTCAGCCTG;RSEQ=ATTCCTAGTTGTTATTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:30,160:190,0:0:2,0:23:1:32.6:1:1:0:59.9:380:1:0:0.2 0/1:188:2:1,1:40,146:186,2:0.0106:2,2:7.5:1:28:1:0.38952:3.62:60:4:0.0106:0:1 +7 116411441 . T C 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00113;SOR=Inf;LSEQ=CCTGAAGGCAGTTATGCCAT;RSEQ=TGTAGAATGGTAATAACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:87,0:87,0:0:1,0:24.1:1:31.9:1:1:0:60:174:1:0:0.1 0/1:44:6:6,0:37,1:38,6:0.1364:1,0:20:1:30.8:1:1:0:60:12:0.1395:0:1 +7 116411824 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1137;SOR=Inf;LSEQ=GTAGTCCATAAAACCCATGA;RSEQ=TTCTGGGCACTGGGTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:0:0,0:145,84:229,0:0:2,0:26.9:1:33:1:1:0:60:56.25:1:0:0 0/1:117:2:0,2:73,42:115,2:0.0171:2,0:14:1:29.5:1:0.1394:0:60:4:0.0172:0:1 +7 116411832 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12521;SOR=Inf;LSEQ=TAAAACCCATGAGTTCTGGG;RSEQ=ACTGGGTCAAAGTCTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:154,77:231,0:0:2,0:26.9:1:32.4:1:1:0:60:56.75:1:0:0 0/1:127:2:1,1:88,37:125,2:0.0157:2,2:23:1:28.5:1:0.51056:2.36019:60:4:0.0159:0:1 +7 116411923 . C T 198 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02135;LSEQ=ATCTGGGCAGTGAATTAGTT;RSEQ=GCTACGATGCAAGAGTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:88:53,35:329,237:566,88:0.1346:2,2:27.7:1:30.8:1:0.72893:1.09:60:87:0.1345:0:1 0/0:606:2:0,2:348,256:604,2:0.0033:2,0:1:0:26.5:1:0.18085:0:60:4:0.0033:0:1 +7 116415226 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10323;SOR=Inf;LSEQ=CAGTAAGCATTTTATCTTTG;RSEQ=CCTTTGCAGATTAGGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:30,202:232,0:0:2,0:22.2:1:32:1:1:0:60:57:1:0:0.1 0/1:206:3:1,2:44,157:201,3:0.0146:2,2:28.3:1:28.3:1:0.52851:1.78:60:6:0.0149:0:2 +7 116416327 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTCAAACACCCCAGAG;RSEQ=GTAATCCTTTGTGTGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 116417606 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15907;SOR=Inf;LSEQ=TATAATAAAACGTTGATTTA;RSEQ=ACTTTCCCCTTGTGGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:12,144:156,0:0:2,0:22.7:1:32.7:1:1:0:60:312:1:0:0.1 0/1:104:2:1,1:17,85:102,2:0.0192:2,2:27:1:27.5:1:0.31759:4.89:60:4:0.0196:0:1 +7 116417848 . G C 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTATTGGAAGCATGTTG;RSEQ=CACCTACAGTAGTAATGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:1,2:3,2:0.4:2,0:45.5:1:31:1:1:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 116421967 . T C 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=0;SOR=0.07499;LSEQ=GATAATTTTTTATAAATAAA;RSEQ=ATTTCAGAATTCTAAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:166:156:138,18:10,0:10,156:0.9398:0,2:21.9:1:32.5:1:0.60293:0:60:155:0.9394:0:1.1 1/0:123:66:56,10:52,5:57,66:0.5366:2,2:20.9:1:31.2:1:0.40837:1.84807:60:65:0.5328:0:1.1 +7 116422185 . T A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11828;SOR=0;LSEQ=TCTCTGTGCCACAATCCAAA;RSEQ=TAAGTGACAAGGAGGAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:3:2,1:84,209:293,3:0.0101:2,2:18:1:28.3:1:0.20331:4.95:60:6:0.0104:0:1.3 0/0:307:0:0,0:88,217:305,0:0:2,0:23.7:1:29.2:1:1:0:60:37.125:0.9966:0:0.1 +7 116423161 . G A 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00642;SOR=0;LSEQ=TTTCCTCAGCCTGTTGAATT;RSEQ=GCAATGTCAATGTCAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:8,0:19,0:19,8:0.2963:1,0:24.3:1:29.4:1:1:0:59.6:16:0.2963:0:1 0/0:21:0:0,0:18,3:21,0:0:2,0:26:1:31.1:1:1:0:60:42:1:0:0 +7 116435768 . C T 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.62654;LSEQ=GGAGCCCCACCTTATCCTGA;RSEQ=GTAAACACCTTTGATATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:70:39,31:505,419:924,70:0.0704:2,2:22.7:1:31.1:1:0.90137:1.04:59.5:140:0.0708:0:1.1 0/1:910:445:230,215:237,227:464,445:0.489:2,2:24.4:1:29.6:1:0.89441:1.02:60:221.5:0.489:0:1.1 +7 116436022 . G A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=11.87259;LSEQ=CTGGTGTCCCGGATATCAGC;RSEQ=ATCTTCTCTACTTTCATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:89:48,41:443,475:918,89:0.0883:2,2:28.1:1:30.3:1:0.31936:1.26:60:28.667:0.0865:0:1.3 1/0:882:472:221,251:213,193:406,472:0.5351:2,2:25.7:1:29.7:1:0.1043:1.25311:59.9:156.333:0.5385:0:1.3 +7 116436097 . G A 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=9.05841;LSEQ=AACGTAAAATGTGTCGCTCC;RSEQ=TATCCTTCTCTGTTGTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:709:70:33,37:265,373:638,70:0.0987:2,2:23.1:1:30.9:1:0.37481:1.25:60:69:0.0984:0:1.4 0/1:684:341:146,195:142,199:341,341:0.4985:2,2:24.7:1:30:1:0.81611:1.05:60:340:0.5:0:1.4 +7 116436233 . G A 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55881;SOR=3.34827;LSEQ=TGTCCAATGGTTTTTTCACT;RSEQ=CCTGACCTTTAAAAGGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:1:1,0:37,163:200,1:0.005:2,0:1:0:23:0:0.18905:0:60:2:0.0051:0:1 0/1:121:2:1,1:23,96:119,2:0.0165:2,2:5:1:27.5:1:0.35868:4.11:60:4:0.0167:0:1.5 +7 116436249 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53945;SOR=0;LSEQ=CACTGCCTGACCTTTAAAAG;RSEQ=CCATCGATATTCTTTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:24,133:157,2:0.0126:2,2:11.5:1:29:1:0.29058:5.45:60:4:0.0127:0:1 0/0:88:0:0,0:15,73:88,0:0:2,0:22:1:31.3:1:1:0:60:176:1:0:0 +7 121088614 . A G 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCGTGGTGGTGCACGC;RSEQ=TGTAATCCCACTACTAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 121090859 . T G 281 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28942;LSEQ=GACAGCAAGAAAACCTTGGG;RSEQ=TACCCTAGATGGTGACTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:547:494:244,250:25,27:52,494:0.9031:2,2:25.9:1:31.5:1:0.88495:1.05:59.9:60.75:0.905:0:1.1 1/0:447:326:162,164:52,66:118,326:0.7293:2,2:27.7:1:31:1:0.33349:1.25:60:162:0.733:0:1.1 +7 123382152 . A C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.15087;SOR=0.62506;LSEQ=CAGAACTTGGTGAAAGAGAC;RSEQ=CTGTTCAAAAGGCCCAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:94:53:49,4:39,2:41,53:0.5638:1,2:25.3:1:31.6:1:0.6933:1.58427:59.9:106:0.5761:0:1 0/1:65:29:28,1:33,3:36,29:0.4462:2,1:19.4:1:30:1:0.62221:2.51:60:28:0.4444:0:1 +7 123382290 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00795;SOR=0.72148;LSEQ=TTTGCATCTTAAAAGCATGC;RSEQ=TAATTTTGGCATTCATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:579:303:166,137:143,133:276,303:0.5233:2,2:26.8:1:30.9:1:0.50494:1.13:60:49.5:0.522:0:1.1 0/1:525:232:124,108:148,145:293,232:0.4419:2,2:25:1:29.8:1:0.53847:1.12:60:231:0.4434:0:1.2 +7 123382412 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15076;SOR=Inf;LSEQ=CATAATTTCAGCATGTTGTC;RSEQ=AGTGCATTACAAAAAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:9,132:141,0:0:2,0:20.9:1:32.5:1:1:0:59.8:140:1:0:0.1 0/1:90:2:1,1:8,80:88,2:0.0222:2,2:35.5:1:30:1:0.19101:9.49:60:4:0.0227:0:1.5 +7 123382509 . C T 50 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.61419;LSEQ=TGAATCAGTCTCTAAAGTAA;RSEQ=CAAGTCAATTCACTATAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:0,3:0,20:20,3:0.1304:1,0:11:1:32:0:1:0:60:6:0.1304:0:1 0/1:12:1:0,1:0,11:11,1:0.0833:0,0:30:0:30:0:1:0:60:2:0.0909:0:1 +7 123522765 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08235;SOR=Inf;LSEQ=AGACTCAGACACAGACTGAA;RSEQ=TTATGCCATCAGCCCACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:8,0:0:2,0:17.9:1:33.1:1:1:0:60:16:1:0:0.1 0/1:9:4:2,2:5,0:5,4:0.4444:0,2:15:1:30.5:1:0.16667:0:60:8:0.4444:0:1 +7 124270259 . T C 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATTCTCAATTGAATTCCA;RSEQ=AATTCTGGATAAAAATAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:37.8:1:32:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 124270348 . G T 133 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.06274;SOR=0.10484;LSEQ=CATATTCTTATCACTTCCAG;RSEQ=TTTAATTACTTCAATAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:21:21,0:1,0:1,21:0.9545:0,1:18.2:1:30.3:1:1:0:59.9:42:0.9545:0:1.1 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:15.2:1:27.7:1:1:0:60:5:0.625:0:1.2 +7 124270427 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54201;SOR=0;LSEQ=TGCTAATTTAGAAAATAACT;RSEQ=ATTGAGCTTTTATCTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:88,3:91,2:0.0215:1,2:21:1:27.5:1:0.08462:25.54759:60:4:0.022:0:1 0/0:50:0:0,0:47,3:50,0:0:2,0:22.7:1:30.1:1:1:0:60:15.667:1:0:0.1 +7 124270508 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1266;SOR=Inf;LSEQ=TGAAAGAGTTGGTTGGCAGG;RSEQ=CTGAGTGACACCCAAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:167,95:262,0:0:2,0:26.5:1:31.6:1:1:0:60:86.333:1:0:0.4 0/1:297:4:1,3:182,110:292,4:0.0135:2,2:19.8:1:27.5:1:0.15725:4.93699:60:8:0.0136:0:1.3 +7 124270574 . A C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.31226;LSEQ=GAGTCTTCATGTAAAGAATT;RSEQ=ATTTATGGCTATTTTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:368:300:144,156:27,40:67,300:0.8152:2,2:25.6:1:32.2:1:0.28005:1.37:60:149:0.8209:0:1.1 1/0:449:260:126,134:94,94:188,260:0.5791:2,2:25.7:1:31:1:0.77437:1.06333:60:129:0.585:0:1.2 +7 124270654 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1061;SOR=Inf;LSEQ=TGTTTTAGTGCTTCTGGGAG;RSEQ=CATACTGCAAATTAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:58,150:208,0:0:2,0:22.3:1:31.8:1:1:0:60:40.6:1:0:0.5 0/1:188:3:1,2:57,127:184,3:0.016:2,2:27:1:30:1:1:1.11:60:6:0.0163:0:1 +7 124270668 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2242;SOR=Inf;LSEQ=TGGGAGGCATACTGCAAATT;RSEQ=AGATGACAGATGGGAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:33,121:154,0:0:2,0:22.3:1:30.2:1:1:0:60:76:1:0:0.3 0/1:139:2:1,1:32,105:137,2:0.0144:2,2:26.5:1:27.5:1:0.41977:3.25:60:4:0.0145:0:1.5 +7 124270732 . A G 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00054;SOR=0.13999;LSEQ=GAGAAGGTTGCCAAGAGCCC;RSEQ=TTAATTTTGTGTTTCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:41:0,41:0,8:8,41:0.8367:0,1:23.9:1:32.3:1:1:0:60:82:0.8367:0:1 0/1:22:9:0,9:0,13:13,9:0.4091:1,0:31:1:31.8:1:1:0:60:18:0.4091:0:1 +7 124271606 . G A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCAATGCATCATTAGCAC;RSEQ=ATACTTTTTAATACCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:31.5:1:1:0:60:4:1:0:1 +7 124954610 . C T 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.14899;LSEQ=ACCTTGCTATTACTTACCTT;RSEQ=CAGCCCTGTATTTTTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:0,3:3,12:15,3:0.1667:2,0:17.3:1:30:1:1:0:33.7:6:0.1667:0:1 0/1:16:3:1,2:3,10:13,3:0.1875:2,2:24:1:31:1:1:1.61:34:6:0.1875:0:1.7 +7 124954625 . T A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49206;SOR=Inf;LSEQ=ACCTTCCAGCCCTGTATTTT;RSEQ=AACTTCCTTGTCAAATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:1,11:12,0:0:2,0:25.1:1:29.9:1:1:0:51.1:24:1:0:0.1 0/1:16:2:1,1:4,10:14,2:0.125:2,2:6.5:1:28.5:1:1:2.35:28:4:0.125:0:1.5 +7 124954746 . A C 50 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGACCCCTGGACTGACCC;RSEQ=CTGGCCCTTTCACTGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:1,0:1,3:0.75:0,2:36.3:1:31.7:1:1:0:38.7:6:0.75:0:1.3 +7 125932788 . T A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.47895;SOR=Inf;LSEQ=ACACACCAGCGGTGGCAGTC;RSEQ=GCGGCCAGAGTGCTTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:29.3:1:30.8:1:1:0:58.2:18:1:0:0.2 0/1:11:2:1,1:2,7:9,2:0.1818:2,2:31:0:32:1:0.49091:3.06:55:4:0.1818:0:1.5 +7 127153538 . C T 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00223;SOR=0.05425;LSEQ=TAGCCCTGTTGTGCAAAGAA;RSEQ=AGTACCGCTGCTGCTGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:4,5:9,9:0.5:2,2:33:1:30:1:0.63719:2.37:60:18:0.5:0:1.2 0/1:21:1:0,1:11,9:20,1:0.0476:2,0:47:0:27:0:0.47619:0:60:2:0.0476:0:1 +7 127153540 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21764;SOR=0;LSEQ=GCCCTGTTGTGCAAAGAACA;RSEQ=TACCGCTGCTGCTGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:43.5:1:31:1:1:1.26772:60:4:0.1111:0:2 0/0:20:0:0,0:10,10:20,0:0:2,0:30.8:1:31.2:1:1:0:59:40:1:0:0.2 +7 127668967 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23333;SOR=Inf;LSEQ=CTGCTGCGGATGTTGCTGCT;RSEQ=GGATGTCTTCGTCCACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:13,10:23,0:0:2,0:26:1:31.8:1:1:0:60:46:1:0:0.2 0/1:22:2:1,1:7,12:19,2:0.0909:2,2:35.5:1:29:1:1:1.67:60:4:0.0952:0:1 +7 128298600 . T A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17119;SOR=0.29983;LSEQ=CCCAGGGTCAGCACTCCCTG;RSEQ=CCCACCTGGTGGACACTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:6,7:9,10:19,13:0.4063:2,2:33.9:1:30.5:1:1:1.04843:26.9:26:0.4194:0:1.5 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:32.5:1:28.5:1:1:1:31:4:0.1667:0:1 +7 128298668 . A T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25654;SOR=4.15166;LSEQ=CTTTGCTCTGGTTGGAGGCC;RSEQ=CTGAGTGACTGGCAGGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:1,0:36,19:55,1:0.0179:2,0:31:0:34:0:1:0:29:2:0.0185:0:1 0/1:28:2:0,2:19,7:26,2:0.0714:2,0:25.5:1:26.5:1:0.09524:0:28.5:4:0.0714:0:1 +7 128298741 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12613;SOR=Inf;LSEQ=AAGGGGACAGAGTACCAGGA;RSEQ=AACACAGCCACAGAGCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:37,22:59,0:0:2,0:29.4:1:32.3:1:1:0:28.8:58:1:0:0.2 0/1:33:2:1,1:18,13:31,2:0.0606:2,2:41:1:28:1:1:1.37079:28:4:0.0625:0:2 +7 128298749 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13025;SOR=Inf;LSEQ=AGAGTACCAGGAGAACACAG;RSEQ=CACAGAGCAAGGTTCCACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:33,21:54,0:0:2,0:23.9:1:30.8:1:1:0:27.1:17:1:0:0.2 0/1:31:2:1,1:16,13:29,2:0.0645:2,2:33:1:26:1:1:1.22249:28:4:0.0645:0:2 +7 128298920 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2502;SOR=0.31988;LSEQ=GCCAAGGCAGCTTGGACCCA;RSEQ=GGAAGTGGGGATGGAAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:0,7:1,11:12,7:0.35:2,0:39.1:1:31.6:1:1:0:29.1:14:0.3684:0:1 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:41:1:29.5:1:1:0:30.5:4:0.1429:0:1 +7 128431032 . TG T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.49126;SOR=Inf;LSEQ=AGTCAGCGCGGACTGCTAGG;RSEQ=GGGGCGCCGGCCGGGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:17,9:26,0:0:2,0:29.5:1:31.6:1:1:0:60:25:1:0:0.7 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:31.5:1:30:1:1:1.34838:60:4:0.0714:0:0.5 +7 128431054 . GA G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=GGGGCGCCGGCCGGGCGGGG;RSEQ=GGGAGGGAAGGAGGGGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:14,8:22,2:0.0833:2,2:47:0:32:1:1:1.70775:60:4:0.1053:0:0.5 0/0:23:0:0,0:12,11:23,0:0:2,0:24:1:28:1:1:0:60:10.5:1:0:0.4 +7 128519723 . G A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGGGTGATGTCGAGGCACAT;RSEQ=GGTGGACAGCACAGGATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:11:1:34:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:30:1:1:0:60:4:1:0:1 +7 128766553 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02972;SOR=2.00001;LSEQ=AGGCTAGAGGCGCCGCCGCC;RSEQ=CCGGCCCGCGGAGCCCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:34:24,10:45,9:54,34:0.3864:2,2:3.6:1:29.3:1:0.18839:2.0652:32.6:68:0.3908:0:1 1/0:77:43:33,10:21,13:34,43:0.5584:2,2:15.4:1:29.6:1:0.21074:2.02:29.1:86:0.5584:0:1.2 +7 128766731 . G A 45 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05064;SOR=0;LSEQ=ACGAGCAGCAGAAGCGGCTG;RSEQ=AAGCCTTTCTCACCCAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:4:3,1:194,169:363,4:0.0109:2,2:7.3:1:22.8:1:0.62704:2.61:30:3:0.0084:0:1.8 0/0:405:0:0,0:206,199:405,0:0:2,0:15.7:1:30:1:1:0:32.6:134:1:0:0.2 +7 128766757 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61475;SOR=2.11131;LSEQ=TTTCTCACCCAGAAAGCCAA;RSEQ=GTCGGCGAACTCAAAGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:1:0,1:98,104:202,1:0.0049:2,0:1:0:25:0:1:0:60:2:0.005:0:1 0/1:193:2:0,2:95,96:191,2:0.0104:2,0:25:1:29.5:1:0.49752:0:24.5:4:0.0105:0:1 +7 128766760 . C T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05889;SOR=Inf;LSEQ=CTCACCCAGAAAGCCAAGGT;RSEQ=GGCGAACTCAAAGACGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:94,95:189,0:0:2,0:30.9:1:31.1:1:1:0:39:62:1:0:0.2 0/1:185:4:1,3:89,92:181,4:0.0216:2,2:9.5:1:29:1:0.62145:2.88719:50.5:8:0.0217:0:1 +7 128766772 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24811;SOR=0;LSEQ=GCCAAGGTCGGCGAACTCAA;RSEQ=GACGATGACTTCGAAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:0,2:98,98:196,2:0.0101:2,0:16.5:1:31:1:0.49751:0:40:4:0.0102:0:1 0/0:199:0:0,0:98,101:199,0:0:2,0:29.3:1:30.2:1:1:0:40:48.75:1:0:0.2 +7 128766805 . C T 67 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06919;SOR=6.94067;LSEQ=GAAAGGACCTCAGAGCTGGA;RSEQ=GCGGGCAACGGCGGGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:1:0,1:213,225:438,1:0.0023:2,0:1:0:25:0:1:0:32:2:0.0023:0:1 0/1:449:7:0,7:219,222:441,7:0.0156:2,0:5.6:1:23.9:1:0.01506:0:31.3:6:0.0136:0:1 +7 128766971 . G A 146 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.03264;LSEQ=CGTACATCGTGGGCTTCTAC;RSEQ=GGGCCTTCTACTGTGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:592:26:11,15:302,263:565,26:0.0439:2,2:20.4:1:31.1:1:0.31684:1.56464:55:52:0.0448:0:1 0/0:669:1:1,0:335,333:668,1:0.0015:2,0:1:0:23:0:1:0:60:2:0.0015:0:1 +7 128767157 . C T 164 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATGCACCGAAATGTGAAG;RSEQ=CCTCCAACATCCTCGTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:0:0,0:390,336:726,0:0:2,0:28.4:1:31.7:1:1:0:51.8:71.6:1:0:0.1 0/1:789:52:25,27:360,377:737,52:0.0659:2,2:25.6:1:28.9:1:1:1.03127:54.1:25:0.0645:0:1.4 +7 128767216 . C T 54 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12444;SOR=Inf;LSEQ=CTGTGTGACTTCGGGGTGAG;RSEQ=GGCCAGCTCATCGACTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:0:0,0:178,205:383,0:0:2,0:12.6:1:30.1:1:1:0:36.1:53.714:0.9973:0:0.2 0/1:402:4:1,3:184,214:398,4:0.01:2,2:6.8:1:27.3:1:0.62791:2.57385:39.8:8:0.0101:0:1.5 +7 128767250 . G A 205 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTCCATGGCCAACTCCTTC;RSEQ=TGGGCACGCGCTCCTACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:104:43,61:201,238:439,104:0.1912:2,2:29.8:1:30.7:1:0.44391:1.19767:49.9:103:0.1911:0:1.1 0/0:499:0:0,0:228,268:496,0:0:2,0:30.3:1:30.4:1:1:0:48.8:164.333:0.994:0:0.2 +7 128767410 . A G 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1576;SOR=1.24425;LSEQ=GCTGGAGGCCATCTTTGGCC;RSEQ=GCCCGTGGTCGACAGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:612:485:219,266:51,73:124,485:0.7925:2,2:24.4:1:30.3:1:0.47846:1.18:34.6:47.5:0.793:0:1.3 1/1:558:461:217,244:45,51:96,461:0.8262:2,2:22.7:1:29.6:1:1:1.01:33.9:75.833:0.8273:0:1.3 +7 128767490 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00342;SOR=1.82923;LSEQ=CCGGGCGCCCCAACAGCGGT;RSEQ=ACGGGATGGACAGCCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:411:339:152,187:34,38:72,339:0.8248:2,2:25.1:1:31.9:1:0.79449:1.1005:59.1:29.818:0.8262:0:2.1 1/1:404:362:180,182:18,24:42,362:0.896:2,2:22.3:1:30.5:1:0.41961:1.32:59.5:59.333:0.8967:0:2.1 +7 128767506 . T G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00048;SOR=2.00445;LSEQ=CGGTTACGGGATGGACAGCC;RSEQ=GCCCGCCATGGCCATCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:399:317:155,162:45,35:80,317:0.7945:2,2:24.9:1:30.1:1:0.26142:1.34277:59.8:30.7:0.7974:0:2 1/1:394:349:176,173:22,21:43,349:0.8858:2,2:23.4:1:29.1:1:1:1.02969:60:86.25:0.8846:0:1.9 +7 128767796 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64271;SOR=2.1797;LSEQ=GGCCAGGCTCCCCGCGTCCC;RSEQ=CTGGTGACCTGCCCACCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:1:0,1:62,149:211,1:0.0047:2,0:34:0:27:0:1:0:29:2:0.0048:0:2 0/1:293:3:2,1:89,201:290,3:0.0102:2,2:15.7:1:27.3:1:0.22863:4.49:41:6:0.0104:0:1.3 +7 128767969 . A G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27341;SOR=Inf;LSEQ=GTCCCTGCCGGCGTGCCTCT;RSEQ=GGGACGGGCGACGCTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:0,15:1,3:4,15:0.7895:2,1:24.1:1:32.4:1:0.21053:0:45.5:30:0.7895:0:1 1/1:9:9:1,8:0,0:0,9:1:0,2:23.2:1:30.8:1:1:0:48.7:18:1:0:1 +7 128828953 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.49922;SOR=Inf;LSEQ=GGGGGGCTCCGAGGAGCAGG;RSEQ=GGGGGCGCCGGGGCTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:43,0:0:2,0:23.1:1:31.7:1:1:0:60:86:1:0:0.4 0/1:52:2:1,1:27,23:50,2:0.0385:2,2:26:1:30:1:1:1.17028:60:4:0.0392:0:1 +7 128828973 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.25552;SOR=Inf;LSEQ=CGGGGGCGCCGGGGCTTTTG;RSEQ=TGAGTTGGCGGGGTTGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:48,45:93,0:0:2,0:18.7:1:32.5:1:1:0:59.9:30:1:0:0.4 0/1:116:3:1,2:57,56:113,3:0.0259:2,2:16:1:27.3:1:1:2.0237:60:6:0.0261:0:1.3 +7 128828981 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51427;SOR=Inf;LSEQ=CCGGGGCTTTTGCTGAGTTG;RSEQ=CGGGGTTGGCCATGGCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:51,49:100,0:0:2,0:21.5:1:31.6:1:1:0:59.9:19:1:0:0.4 0/1:144:2:1,1:72,70:142,2:0.0139:2,2:6:1:27.5:1:1:1.02838:60:4:0.0139:0:1 +7 128829002 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50913;SOR=Inf;LSEQ=CGGGGTTGGCCATGGCCGCT;RSEQ=CCCGCCCAGCGCGGGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:56,56:112,0:0:2,0:25:1:32.4:1:1:0:59.9:55:1:0:0.4 0/1:151:2:1,1:74,75:149,2:0.0132:2,2:33:1:25:1:1:1.01:60:4:0.0136:0:1.5 +7 128829011 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=2;SSF=0.25968;SOR=Inf;LSEQ=CCATGGCCGCTGCCCGCCCA;RSEQ=CGCGGGGGCCGGAGCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:54,53:107,0:0:2,0:26.5:1:32.7:1:1:0:60:52.5:1:0:0.5 0/1:139:3:3,0:65,71:136,3:0.0216:2,0:11.3:1:22.7:1:0.11442:0:60:2:0.015:0:2 +7 128829014 . C A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.25863;SOR=Inf;LSEQ=TGGCCGCTGCCCGCCCAGCG;RSEQ=GGGGGCCGGAGCTCCCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:53,52:105,0:0:2,0:26.5:1:31.2:1:1:0:60:104:1:0:0.5 0/1:135:3:2,1:63,67:130,3:0.0222:2,2:9.7:1:22.3:1:0.6137:2.12:60:2:0.0153:0:1.3 +7 128829020 . C T 37 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3151;SOR=0.24336;LSEQ=CTGCCCGCCCAGCGCGGGGG;RSEQ=CGGAGCTCCCGCTCCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:3:1,2:50,48:98,3:0.0297:2,2:12:1:23.7:1:0.61746:2.06874:60:2:0.0202:0:1.3 0/0:136:1:0,1:67,68:135,1:0.0074:2,0:1:0:23:0:1:0:60:2:0.0075:0:1 +7 128829039 . GGCT G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.29435;SOR=0.44124;LSEQ=GCCGGAGCTCCCGCTCCTGG;RSEQ=GCTGCTGCTGCTGCTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:5:2,3:51,44:95,5:0.0495:2,2:37.4:1:28.4:1:0.66364:1.72906:60:4:0.0417:0:1 0/1:134:3:2,1:63,67:130,3:0.0224:2,2:9:1:30.3:1:0.6137:2.12:60:6:0.0224:0.0075:0.3 +7 128829052 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.51688;SOR=Inf;LSEQ=CTCCTGGGGCTGCTGCTGCT;RSEQ=CTGCTGCTGGGGGACCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:47,46:93,0:0:2,0:20.5:1:31.9:1:1:0:60:30:1:0:0.5 0/1:138:2:1,1:66,68:134,2:0.0145:2,2:16:1:27.5:1:1:1.03:60:4:0.015:0:1 +7 128829066 . A G 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00026;SOR=0;LSEQ=GCTGCTGCTGCTGCTGGGGG;RSEQ=CCCGGGCCGGGGGGCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:9:4,5:39,39:78,9:0.1034:2,2:21.7:1:33:1:1:1.2468:60:18:0.1084:0:1.3 0/0:125:0:0,0:61,64:125,0:0:2,0:21.1:1:27.5:1:1:0:60:14.625:1:0:0.4 +7 128829069 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0.7854;LSEQ=GCTGCTGCTGCTGGGGGACC;RSEQ=GGGCCGGGGGGCGGCCTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:0,2:44,46:90,2:0.0215:2,0:1:0:25:0:0.49546:0:60:4:0.0222:0:1 0/1:118:2:1,1:55,61:116,2:0.0169:2,2:38.5:1:30:1:1:1.11:60:4:0.0174:0:1 +7 128829098 . G A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.45109;LSEQ=GGGCGGCCTCGAGCGGGAAC;RSEQ=CGACCGGGCCTGGGCCTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:1,0:51,50:101,1:0.0098:2,0:1:0:29:0:1:0:60:2:0.0104:0:1 0/1:141:2:1,1:68,69:137,2:0.0142:2,2:12.5:1:30:1:1:1.01:60:4:0.0146:0:1 +7 128829105 . G T 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.64328;SOR=2.1521;LSEQ=CTCGAGCGGGAACGCGACCG;RSEQ=GCCTGGGCCTCGGAGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:1:0,1:49,51:100,1:0.0099:2,0:1:0:28:0:1:0:60:2:0.0102:0:1 0/1:142:3:0,3:70,69:139,3:0.0211:2,0:17.3:1:23.3:1:0.24483:0:60:2:0.0145:0:1.3 +7 128829150 . C T 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25606;SOR=Inf;LSEQ=GAGCGCGAGGAGGAGCGCGG;RSEQ=GGTGACTGGCCCTCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:151,48:199,0:0:2,0:16.6:1:32:1:1:0:60:65.333:1:0:0.2 0/1:244:3:1,2:169,72:241,3:0.0123:2,2:6:1:27.7:1:0.21911:4.66087:59.3:6:0.0124:0:1 +7 128829169 . G A 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.19352;SOR=0.22113;LSEQ=GCGGTGACTGGCCCTCCGCC;RSEQ=CCGCTGAGCCACTGCGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:4:4,0:244,72:316,4:0.0125:2,0:17:1:29:1:0.57826:0:60:8:0.0128:0:1 0/0:359:1:1,0:245,110:355,1:0.0028:2,0:39:0:32:0:1:0:60:2:0.0029:0:1 +7 128829172 . G T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.12741;SOR=Inf;LSEQ=GTGACTGGCCCTCCGCCGCC;RSEQ=CTGAGCCACTGCGGCCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:345:0:0,0:266,79:345,0:0:2,0:22.1:1:30.8:1:1:0:60:68:1:0:0.2 0/1:395:4:1,3:270,120:390,4:0.0101:2,2:21:1:26.3:1:0.09211:6.71435:60:8:0.0103:0:1 +7 128829694 . G C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGATTCAAGGAGGTGTT;RSEQ=AAGACCCTGGGGAAATTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:27.5:1:33:1:1:0:52:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 128843151 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19932;SOR=Inf;LSEQ=GCAGTGTGGCAAAGGCCTGG;RSEQ=GGACAGGGGTGAAGCTGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:196,34:230,0:0:2,0:24.8:1:29.8:1:1:0:59.8:27.75:1:0:0.5 0/1:186:2:1,1:145,38:183,2:0.0108:2,2:13:1:28.5:1:0.37808:3.77952:60:4:0.011:0:1 +7 128843169 . C T 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00176;SOR=1.68313;LSEQ=GGAGGACAGGGGTGAAGCTG;RSEQ=GTCTGTGGGTCAGAGTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:317:159:120,39:116,41:157,159:0.5016:2,2:22.3:1:29.6:1:0.79634:1.09:60:38.75:0.5032:0:1.1 1/0:283:178:132,46:75,29:104,178:0.629:2,2:22.4:1:29.1:1:0.78019:1.11:60:88:0.6286:0:1.1 +7 128843436 . T C 125 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.21989;LSEQ=CCTGAAGGCTGCACGGTGAG;RSEQ=GCTCTGTGAGACAAGGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:1:0,1:127,266:393,1:0.0025:2,0:30:0:9:0:1:0:60:0:0:0:6 0/1:355:23:8,15:121,209:330,23:0.0648:2,2:21.4:1:27.7:1:1:1.08529:60:6.667:0.0578:0:1.6 +7 128843490 . C T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50452;SOR=0;LSEQ=GGGCAGGACCGGGTATAGGG;RSEQ=AGGGTCCAGTGGGGAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:19,121:140,2:0.0141:2,2:7.5:1:28:1:0.26271:6.23:60:4:0.0143:0:1.5 0/0:113:0:0,0:21,92:113,0:0:2,0:24.3:1:31.4:1:1:0:60:226:1:0:0.1 +7 128843757 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTGGGAGTTAAGGCGCGAGC;RSEQ=TGTGAAACAGCTAGAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:28.5:1:32:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 128844853 . G A 48 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00664;SOR=Inf;LSEQ=AGACTGTCTAAAAAAAGAAA;RSEQ=AAAAAAAGAAAGAAAGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:30,0:0:1,0:20.9:1:34.2:1:1:0:57:60:1:0:0 0/1:8:3:3,0:4,1:5,3:0.375:2,0:5:1:30.3:1:1:0:60:6:0.375:0:2.3 +7 128844857 . A AAAAG 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00132;SOR=Inf;LSEQ=TGTCTAAAAAAAGAAAGAAA;RSEQ=AAAGAAAGAAAGAAGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:12,0:21,0:21,12:0.3636:1,0:23.4:1:32.4:1:1:0:60:24:0.3871:0.0606:0 1/1:9:9:8,1:0,0:0,9:1:0,2:20.4:1:29.8:1:1:0:60:18:1:0.4444:1.1 +7 128844953 . C A 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00118;SOR=Inf;LSEQ=CCTGGAAGTGTATCTCCAGC;RSEQ=ACCCTGCCATGCTACCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:139,5:144,0:0:1,0:22.6:1:31.4:1:1:0:59.7:71:1:0:0.4 0/1:92:7:6,1:81,4:85,7:0.0761:1,2:18.1:1:28.3:1:0.33299:3.3061:60:14:0.0769:0:1.1 +7 128845018 . C T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.19788;LSEQ=GTCCCTGAGCTGCCTTGACA;RSEQ=CGTCTTTTCCCATCCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:224:168,56:160,73:233,224:0.488:2,2:24:1:30.8:1:0.14608:1.37:59.9:43.8:0.4867:0:1.1 1/1:477:423:300,123:36,18:54,423:0.8868:2,2:25.3:1:29.4:1:0.52863:1.22:60:59.429:0.887:0:1.1 +7 128845223 . C T 196 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACATCGCGGCCTTCGGGGC;RSEQ=GTCACGGGCCTCTGCACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:81:27,54:98,250:348,81:0.1888:2,2:27.1:1:31:1:0.4153:1.27:60:80:0.1891:0:1.4 0/0:379:0:0,0:124,255:379,0:0:2,0:23.6:1:29.4:1:1:0:60:74.8:1:0:0.4 +7 128845275 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18799;SOR=Inf;LSEQ=TCAGCCGCGGGAGGGCAGGC;RSEQ=CGGGGGGCCCTCAGCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:52,142:194,0:0:2,0:24:1:31.1:1:1:0:60:47.5:1:0:0.9 0/1:149:2:1,1:38,109:147,2:0.0134:2,2:10:1:27:1:0.45629:2.84:60:4:0.0136:0:1.5 +7 128845277 . G C 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=5.88524;LSEQ=AGCCGCGGGAGGGCAGGCCC;RSEQ=GGGGGCCCTCAGCCTGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:99:30,69:26,73:99,99:0.4975:2,2:21.8:1:29.9:1:0.63616:1.22:60:32:0.4898:0:1.8 1/1:144:123:33,90:5,15:20,123:0.8542:2,2:20.5:1:29.5:1:1:1.10:60:122:0.8531:0:1.5 +7 128845299 . T C 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCCCTCAGCCTGGAACG;RSEQ=GGGAAGAGAGCCAGAGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:59,98:157,0:0:2,0:23.5:1:30.3:1:1:0:60:38.25:1:0:0.9 0/1:94:12:4,8:25,57:82,12:0.1277:2,2:21.7:1:29.8:1:1:1.14:60:24:0.129:0:1 +7 128845325 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=8.32248;LSEQ=GAGAGCCAGAGGGAAGGGGG;RSEQ=CAAAGAGGTCTTGGTGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:78:47,31:47,38:85,78:0.4785:2,2:22.5:1:30.5:1:0.53063:1.22:59.6:156:0.4845:0:1.6 1/1:87:77:35,42:4,6:10,77:0.8851:2,2:25:1:29.3:1:1:1.25:59.7:154:0.8953:0:1.6 +7 128845378 . G A 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00124;SOR=Inf;LSEQ=GGTCATGATCAGAAGGGTCT;RSEQ=GGGCTCAGTTAAGGGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:183,30:213,0:0:2,0:24.6:1:32.4:1:1:0:59.8:212:1:0:0.4 0/1:136:7:7,0:112,17:129,7:0.0515:2,0:14.3:1:29.3:1:0.59579:0:60:14:0.0519:0:1.3 +7 128845398 . T C 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.25711;SOR=0;LSEQ=GGGGCTCAGTTAAGGGTGTC;RSEQ=GTGTCAGCAGAATAACCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:241,41:282,3:0.0105:2,2:25:1:24.3:1:0.38129:2.92358:59.3:2:0.0071:0:3.7 0/0:230:0:0,0:192,38:230,0:0:2,0:20.8:1:30.5:1:1:0:60:75.667:1:0:0.2 +7 128845702 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.93065;LSEQ=TACCCCAAAGGGAGCAGGTG;RSEQ=GTGTAAAACCGAGATCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:145:84:11,73:7,54:61,84:0.5793:2,2:24.3:1:30.2:1:0.80513:1.16:60:83:0.5804:0:1.1 1/1:94:82:11,71:3,9:12,82:0.8723:2,2:21.5:1:29.6:1:0.37907:2.13042:60:164:0.8723:0:1.1 +7 128845907 . T C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=12.75957;LSEQ=AACCTCCAGACCTCAGCAGC;RSEQ=GAGGGTCTGGGCACAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:183:92:90,2:81,10:91,92:0.5027:2,1:20.5:1:31.3:1:0.01808:5.51:60:45:0.5:0:1.1 1/1:140:130:116,14:10,0:10,130:0.9286:0,2:22:1:30.3:1:0.59814:0:59.7:129:0.9281:0:1.1 +7 128846207 . G A 150 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=13.46952;LSEQ=GTGGCAATCCTTGCTGTGGC;RSEQ=CAGGTATAGTGACTGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:855:3:2,1:374,478:852,3:0.0035:2,2:16.3:1:21.7:1:0.58533:2.55:60:2:0.0024:0:1 0/1:816:37:17,20:346,433:779,37:0.0453:2,2:20.5:1:28.9:1:0.86708:1.06:59.5:74:0.0461:0:1.1 +7 128846223 . G A 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGCGCAGGTATAGTGACTG;RSEQ=TAGGAACGGGAGACCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:783:0:0,0:348,434:782,0:0:2,0:23.1:1:31.8:1:1:0:60:64.167:1:0:0.1 0/1:680:33:18,15:300,347:647,33:0.0485:2,2:18.7:1:29.1:1:0.37657:1.39:60:15.5:0.0463:0:1.1 +7 128846328 . G C 312 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.42413;LSEQ=GATGGGGACTCTGTGAGTGG;RSEQ=ATTTGTTTTGTGGGCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1056:498:249,249:289,268:557,498:0.4716:2,2:25.7:1:32.4:1:0.57882:1.07828:59.9:98.6:0.474:0:1.1 1/1:1186:1010:519,491:90,81:171,1010:0.8516:2,2:25.6:1:31.3:1:0.80414:1.05114:59.9:76.692:0.8543:0:1.2 +7 128846444 . G A 53 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38818;SOR=0.30963;LSEQ=CCGAGGTGAGTGAAGACCAG;RSEQ=CCAGGACCAGTTGGGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:4:3,1:88,309:397,4:0.01:2,2:7.8:1:26.8:1:0.038:10.45:60:8:0.0102:0:1.3 0/0:322:1:1,0:83,237:320,1:0.0031:2,0:1:0:25:0:0.26168:0:60:2:0.0031:0:1 +7 128846469 . A G 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0;SOR=5.31549;LSEQ=GACCAGTTGGGCAACAAAAT;RSEQ=TACTGGGCACTTGCTGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:120:16,104:13,110:123,120:0.4938:2,2:23.2:1:32.2:1:0.55642:1.30:59.9:59:0.4937:0:1.1 1/1:180:151:25,126:2,27:29,151:0.8389:2,2:23.3:1:31.7:1:0.25894:2.67:60:150:0.8427:0:1.1 +7 128846485 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51728;SOR=0;LSEQ=AAATATACTGGGCACTTGCT;RSEQ=CCAGTACTGGGAGCTGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:10,163:173,2:0.0114:2,2:22:1:26:1:0.1221:15.59:60:4:0.0116:0:2 0/0:118:0:0,0:10,108:118,0:0:2,0:25:1:31.8:1:1:0:60:58:1:0:0.9 +7 128846557 . C CAG 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.03467;SOR=3.90597;LSEQ=GCTCCTATAGGGCCTTCACA;RSEQ=AGTAGAAGGTGACCCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:16:0,16:1,31:32,16:0.3333:1,1:17.5:1:32.2:1:1:0:59.4:32:0.3404:0.125:0.6 1/0:15:10:0,10:0,5:5,10:0.6667:0,0:31.6:1:31.2:1:1:0:60:20:0.6667:0:0.2 +7 128846679 . GT G 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCCAGGGCTCACAGCTT;RSEQ=TTTTTTTGTTTGTTTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:36.4:1:32.2:1:1:0:55.2:10:0.5556:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 128846716 . A G 66 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTTTTTGAGACAGAGTCT;RSEQ=GCTCTGTTGCCCAGGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:18.3:1:33:0:1:0:54:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 128847732 . TC T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACAGAGTGAGACCCTGTC;RSEQ=CAAAGAAAACAAGACAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:46.5:1:32:1:1:0:55.5:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 128848301 . A AT 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCTCAAAAAAAAAATTAT;RSEQ=TGGATAGCGCTGTTCTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:10.5:1:30.2:1:1:0:60:4:0.3333:0.1667:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 128848756 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18336;SOR=Inf;LSEQ=CAACACTGCACCCTCCTGGG;RSEQ=CTATGCGACCGGCAGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:36,189:225,0:0:2,0:23.4:1:31.9:1:1:0:59.9:31.143:1:0:0.1 0/1:169:2:1,1:27,140:167,2:0.0118:2,2:18.5:1:26.5:1:0.30473:5.11:60:4:0.0122:0:1 +7 128849078 . C A 184 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=AGACTCTCTCCTCCCCACTG;RSEQ=TGCTGCGGGACTGGGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:70:50,20:351,183:534,70:0.1155:2,2:27.4:1:30.1:1:0.41956:1.30:60:69:0.1169:0:1.1 0/0:606:0:0,0:382,223:605,0:0:2,0:23.7:1:31:1:1:0:60:150.25:0.9983:0:0.1 +7 128849281 . C A 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.90819;LSEQ=GCAGTGCTGGGAGCTGGAGC;RSEQ=AAGGCCATAAAGACACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:4:3,1:97,264:361,4:0.0109:2,2:12.8:1:28.5:1:0.0643:8.11:60:8:0.0111:0:1 0/0:302:3:2,1:91,208:299,3:0.0099:2,2:17:1:27.3:1:0.22527:4.55:60:6:0.0105:0:1 +7 128850084 . T G 154 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.01786;LSEQ=TGAGCCCAGGAGTTGGAAGC;RSEQ=GCAGTGGGTTGTGATCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:39:39,0:36,0:36,39:0.52:1,1:26.4:1:29.3:1:1:0:59.4:12:0.5:0:1 0/1:54:1:1,0:53,0:53,1:0.0185:1,0:8:0:31:0:1:0:60:2:0.0185:0:1 +7 128850103 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21282;SOR=Inf;LSEQ=CTGCAGTGGGTTGTGATCAC;RSEQ=CCACCGCACTCTAGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:97,4:101,0:0:1,0:24.2:1:29.9:1:1:0:59.8:49.5:1:0:0.5 0/1:87:2:2,0:78,7:85,2:0.023:2,0:20:1:29.5:1:1:0:60:4:0.023:0:1 +7 128850167 . A G 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=AAAAAAGAGAGAGGAAAAGA;RSEQ=AGGAAAGCCTCACCTGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:276,110:386,0:0:2,0:24.1:1:30.3:1:1:0:59.9:47.25:1:0:0.2 0/1:427:11:5,6:284,132:416,11:0.0258:2,2:20.8:1:29.5:1:0.18709:2.57549:60:10:0.0236:0:1.3 +7 128850377 . G A 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44146;SOR=2.10251;LSEQ=CACGCTGCTCATCTGGAGGC;RSEQ=TACCTGGTGCAGGTGGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:2:1,1:105,257:362,2:0.0055:2,2:3:1:29:1:0.49818:2.44:60:4:0.0056:0:1 0/1:348:4:3,1:117,227:344,4:0.0115:2,2:19.8:1:29.8:1:0.12029:5.79:60:8:0.0117:0:1.3 +7 128850744 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49959;SOR=0;LSEQ=GAATGGCATCGCTGGCCCTT;RSEQ=CCAAGATTTGATGGGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:162,25:187,2:0.0106:2,2:27.5:1:27.5:1:0.25684:6.37375:60:4:0.0107:0:1 0/0:173:0:0,0:141,31:172,0:0:2,0:21.4:1:30.4:1:1:0:60:171:1:0:0.1 +7 128850798 . G T 77 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01052;SOR=0;LSEQ=GCTCCTTCCCTATCCCTTCT;RSEQ=CTCTCAGGTTGACTGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:6:3,3:309,183:492,6:0.012:2,2:9.5:1:29.8:1:0.67584:1.68659:60:12:0.0123:0:1 0/0:563:0:0,0:342,220:562,0:0:2,0:24.2:1:31.4:1:1:0:60:186.333:1:0:0.2 +7 128850875 . T C 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=ATGATTGCCAAGGCCTTCTC;RSEQ=AAGCGGCACGAGCTCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:0:0,0:314,331:645,0:0:2,0:23.9:1:29.8:1:1:0:60:70.667:0.9984:0:0.1 0/1:762:15:7,8:348,397:745,15:0.0197:2,2:22.7:1:30.6:1:1:1.0018:60:30:0.0199:0:1.1 +7 128850984 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62122;SOR=0.4908;LSEQ=ACCCCTCCTCTACCGGAGCC;RSEQ=CCTGGCCCCGCGCTGCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:39,156:195,2:0.0102:2,2:23.5:1:28.5:1:0.36569:3.96:60:4:0.0103:0:1 0/0:200:1:0,1:57,142:199,1:0.005:2,0:9:0:31:0:1:0:60:2:0.0051:0:1 +7 128850990 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.49868;SOR=0;LSEQ=CCTCTACCGGAGCCGCCTGG;RSEQ=CCCGCGCTGCCCATGTGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:31,151:182,2:0.0109:2,2:38.5:1:31:1:0.31837:4.81:60:4:0.0109:0:1 0/0:180:0:0,0:45,134:179,0:0:2,0:22.2:1:30.4:1:1:0:60:58.667:0.9944:0:0.1 +7 128851072 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14119;SOR=Inf;LSEQ=ACCGACTGTGAGGAGCAAGG;RSEQ=GCTCCCTCCATCGCTCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:2,47:49,0:0:1,0:22.7:1:30.9:1:1:0:59.7:98:1:0:0.1 0/1:30:2:0,2:1,27:28,2:0.0667:1,0:36:1:27:0:1:0:60:4:0.0667:0:1 +7 128851669 . T C 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.3374;SOR=3.56538;LSEQ=GCACAGAGGCTGGGGGCTTC;RSEQ=GGGACTGGAGTACAGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:0,1:79,214:293,1:0.0034:2,0:44:0:9:0:1:0:60:0:0:0:7 0/1:249:3:1,2:77,169:246,3:0.012:2,2:32:1:28.3:1:1:1.10:60:6:0.0123:0:1 +7 128851674 . C G 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00145;SOR=0;LSEQ=GAGGCTGGGGGCTTCTGGGA;RSEQ=TGGAGTACAGGGGCTGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:11:5,6:70,201:271,11:0.039:2,2:13.6:1:33.5:1:0.16847:2.38:60:22:0.0401:0:1 0/0:229:0:0,0:67,161:228,0:0:2,0:23.8:1:30.7:1:1:0:60:24.333:0.9955:0:0.1 +7 128851816 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02763;SOR=Inf;LSEQ=TCCCAGGGGAGCGGGGGTGG;RSEQ=ATGGACAGAGCCAGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:0:0,0:330,154:484,0:0:2,0:24.9:1:32:1:1:0:59.9:47.4:1:0:0.1 0/1:463:5:2,3:300,158:458,5:0.0108:2,2:17.2:1:26.4:1:0.34734:2.84118:60:10:0.0111:0:1.2 +7 128851980 . G A 179 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.25135;LSEQ=AGGAAGAAGGAGGTGTGCCC;RSEQ=CTGGCGCCGCCCCCTGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:893:3:2,1:460,425:885,3:0.0034:2,2:3:1:28.3:1:1:1.85:60:6:0.0034:0:1.3 0/1:842:78:45,33:396,365:761,78:0.0926:2,2:22.1:1:28.6:1:0.4048:1.26:59:38:0.0919:0:1.6 +7 128852381 . C T 155 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02664;LSEQ=AGCATGCTTCCCTAGGATCC;RSEQ=GTCTTCCAGAGAACCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:34:0,34:2,46:48,34:0.4146:1,1:24.3:1:30.6:1:0.50858:0:60:68:0.4198:0:1.1 0/1:55:1:0,1:2,52:54,1:0.0182:1,0:40:0:32:0:1:0:60:2:0.0185:0:1 +7 128852511 . G A 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26667;SOR=Inf;LSEQ=ACCCCAGGGACAGGGCCCTG;RSEQ=AGCTCAGGGTCCTTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:0,3:0,11:11,3:0.2143:0,0:22.7:1:31.3:1:1:0:55.7:6:0.2308:0:1.3 1/1:1:1:0,1:0,0:0,1:1:0,0:12:0:32:0:1:0:60:2:1:0:1 +7 131819962 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGGCTTTATTTGTAAAAAG;RSEQ=GTGAACAAATAACCTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:29.5:1:1:0:60:4:1:0:1.5 +7 131820939 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52767;SOR=0;LSEQ=GCGGCACTACCTCTGCCGGG;RSEQ=GAACCTTGCTTCCTTCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:10,13:23,2:0.08:2,2:32.5:1:30:1:1:1.29:60:4:0.08:0:1 0/0:14:0:0,0:6,8:14,0:0:2,0:24.5:1:29.8:1:1:0:60:28:1:0:0.1 +7 131936098 . G A 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16042;SOR=Inf;LSEQ=GCCCCTTCTGAACTGGGACC;RSEQ=GGAACCTACTGTTGTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:24,89:113,0:0:2,0:17.1:1:30.2:1:1:0:60:27.25:1:0:0.2 0/1:76:2:1,1:12,62:74,2:0.0263:2,2:5:1:29:1:0.31474:5.00:60:4:0.0267:0:1 +7 134249263 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19821;SOR=Inf;LSEQ=TGGGCGACATGGCTTCTCCC;RSEQ=TTTCTAGGTCCCATGAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:18,20:38,0:0:2,0:29.1:1:31.6:1:1:0:46.9:37:1:0:0 0/1:31:2:1,1:14,15:29,2:0.0645:2,2:26:0:31:0:1:1.07:54:4:0.0645:0:1.5 +7 134806700 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=CCCACGCCACCAGGGCCTAG;RSEQ=GTCCCAACCCCAGAGCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:8,3:11,0:0:2,0:32.6:1:31.8:1:1:0:60:22:1:0:0.1 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:12:1:27:1:1:1.13389:60:4:0.1176:0:1 +7 134807084 . T C 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTCATTGGGTGGGGCTT;RSEQ=CCTGCAGGAACTTCAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:18.5:1:30.5:1:1:0:34:4:0.6667:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:25:0:32:0:1:0:36:2:1:0:0 +7 134807552 . G A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGCAGCAGCCCTATAGAAAA;RSEQ=GGACCTGACCAATGAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:16.3:1:30.8:1:1:0:60:8:1:0:0.8 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:14.5:1:28.5:1:1:2.44949:60:4:0.3333:0:1.5 +7 135127927 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCACCATGGCGAAACCC;RSEQ=ATCTCTACCAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:31:1:1:0:60:4:1:0:1 +7 135127936 . CAA C 27 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=18.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCGAAACCCTATCTCTAC;RSEQ=AAAAAAAAAAAAAAAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:27.1:1:1:0:60:4:1:0.5:1 +7 135128789 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTAGCTACTCAGGAGGCC;RSEQ=AGGTAGGAGGATCACCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:34:1:32:1:1:0:49.5:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 135129053 . A G 68 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28003;SOR=0;LSEQ=CTGAAAGGACTTGAACAGAT;RSEQ=CTTGTGCACCAGTGTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:4,0:14,2:16,4:0.2:2,0:29.5:1:34:0:1:0:60:8:0.2:0:1 0/0:9:0:0,0:9,0:9,0:0:0,0:29:1:28.3:1:1:0:60:18:1:0:0 +7 135129250 . G A 148 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.79202;LSEQ=TTGCAGTGCCCAAGGAGGTC;RSEQ=AGCTCTGTTGCTGTGAACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:1:1,0:280,206:486,1:0.002:2,0:1:0:25:0:1:0:60:2:0.0021:0:1 0/1:554:33:18,15:301,219:520,33:0.0596:2,2:19.9:1:29.5:1:0.71963:1.14507:54.9:66:0.0603:0:1.2 +7 135129443 . G A 182 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=68.71809;LSEQ=TTGCTCCTGGGTCTGCTTCC;RSEQ=GCTGCTTGTTTGAATCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:883:1:1,0:470,411:881,1:0.0011:2,0:1:0:26:0:1:0:60:2:0.0011:0:1 0/1:1092:79:42,37:519,494:1013,79:0.0723:2,2:24.1:1:29:1:0.81541:1.08:50.1:38.5:0.0713:0:1.2 +7 135335678 . C T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20753;LSEQ=CCTCTATCCCTCCGCCTCCC;RSEQ=GACTACTGCTGCTGCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:16,1:17,2:0.1053:1,0:16.5:1:32.5:1:1:0:60:4:0.1053:0:1 0/1:16:2:1,1:14,0:14,2:0.125:1,2:19:0:31.5:1:0.125:0:59:4:0.125:0:1 +7 135335767 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22915;SOR=Inf;LSEQ=GAGAGTGACAAGCAACAACA;RSEQ=AGATTTCAATCTGCGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:81,23:104,0:0:2,0:24.3:1:32.6:1:1:0:59.7:103:1:0:0.2 0/1:96:2:1,1:61,33:94,2:0.0208:2,2:35:1:28.5:1:1:1.83604:60:4:0.0211:0:1.5 +7 135335822 . C T 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.10582;LSEQ=ATAATGCACTGGAATGAAAT;RSEQ=GTAGGGACCACATCAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:40:22,18:80,64:144,40:0.2174:2,2:30.2:1:30.2:1:1:1.02261:60:39:0.2167:0:1.2 0/1:176:5:2,3:89,82:171,5:0.0284:2,2:20:1:28.4:1:0.67364:1.62357:60:10:0.0289:0:1.2 +7 135335825 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49959;SOR=0;LSEQ=ATGCACTGGAATGAAATCGT;RSEQ=GGGACCACATCAAAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:105,85:190,2:0.0104:2,2:10:0:33.5:1:1:1.23392:60:4:0.0108:0:1.5 0/0:176:0:0,0:91,85:176,0:0:2,0:26.7:1:28.8:1:1:0:60:57.667:1:0:0.2 +7 135335842 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21902;SOR=Inf;LSEQ=CGTAGGGACCACATCAAAGG;RSEQ=AGCCTCCAGTTTGTGGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:95,92:187,0:0:2,0:26.7:1:31.9:1:1:0:60:45.75:1:0:0.4 0/1:165:2:1,1:83,80:163,2:0.0121:2,2:42:1:28.5:1:1:1.03728:60:4:0.0123:0:1 +7 135335861 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=GCAGCCTCCAGTTTGTGGGA;RSEQ=GCAGTCCCAACACTCCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:81,87:168,2:0.0118:2,2:37:1:30.5:1:1:1.07:60:4:0.0119:0:1 0/0:157:0:0,0:86,71:157,0:0:2,0:24.2:1:30.4:1:1:0:60:77.5:1:0:0.3 +7 135335862 . G A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00209;SOR=Inf;LSEQ=CAGCCTCCAGTTTGTGGGAC;RSEQ=CAGTCCCAACACTCCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:86,89:175,0:0:2,0:24.6:1:30.7:1:1:0:60:86.5:1:0:0.3 0/1:154:8:4,4:79,67:146,8:0.0519:2,2:37:1:29.1:1:1:1.17784:60:16:0.0533:0:1.1 +7 135335900 . T G 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00023;SOR=Inf;LSEQ=GGAGAGAAGGCCATAGAGTA;RSEQ=ATCCAGCATATGCGAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:83,93:176,0:0:2,0:22.8:1:29.7:1:1:0:60:28.333:1:0:0.1 0/1:159:11:6,5:81,67:148,11:0.0692:2,2:27.3:1:31:1:1:1.00742:60:22:0.0705:0:1.1 +7 135335907 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23224;SOR=Inf;LSEQ=AGGCCATAGAGTATATCCAG;RSEQ=ATATGCGAAGGGAAAAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:90,89:179,0:0:2,0:24.1:1:32.6:1:1:0:60:88.5:1:0:0.1 0/1:167:2:1,1:95,70:165,2:0.012:2,2:28.5:1:27.5:1:1:1.35461:60:4:0.0123:0:1 +7 135335913 . C T 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49873;SOR=0;LSEQ=TAGAGTATATCCAGCATATG;RSEQ=GAAGGGAAAAACCACACGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:93,85:178,2:0.0111:2,2:7.5:1:26:1:1:1.09357:60:4:0.0112:0:1.5 0/0:174:0:0,0:104,70:174,0:0:2,0:23.6:1:29.9:1:1:0:60:57:1:0:0.2 +7 135336211 . C A 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.60456;SOR=2.23017;LSEQ=TAAACACTGTCTCCATCATC;RSEQ=TCCTTTCCGTTTCCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:1:1,0:17,57:74,1:0.0133:2,0:1:0:29:0:0.24:0:60:2:0.0133:0:1 0/1:68:2:1,1:15,51:66,2:0.0294:2,2:6.5:1:28.5:1:0.41791:3.32:60:4:0.0308:0:1 +7 135336264 . T G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25996;SOR=0.31033;LSEQ=CTATTTTTCTCTTTCTCCCT;RSEQ=AAAAATTGTTTTTTAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:0,7:0,18:18,7:0.28:1,0:21.9:1:33.4:1:1:0:60:14:0.2917:0:1 0/1:19:2:0,2:1,16:17,2:0.1053:1,0:18:1:31.5:1:1:0:60:4:0.1111:0:2.5 +7 135681518 . T C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.62445;LSEQ=AAATCGTAAGATTGTTCTTA;RSEQ=GAGAAAATGTGATATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:31:19,12:65,87:152,31:0.1694:2,2:22.7:1:31.1:1:0.07516:2.11:60:62:0.1722:0:1.1 0/1:209:89:44,45:63,56:119,89:0.4258:2,2:26.8:1:30.2:1:0.67472:1.14979:60:178:0.4279:0:1.1 +7 135681586 . T A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24684;SOR=Inf;LSEQ=GGCACTGTATAGTAAAAATT;RSEQ=GGAACCACATATATGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:31,88:119,0:0:2,0:24:1:30.9:1:1:0:60:238:1:0:0.2 0/1:119:3:2,1:29,87:116,3:0.0252:2,2:15.7:1:26:1:0.16586:5.89:60:6:0.0254:0:1.7 +7 135878184 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGATTGGAGTGATGCGTCT;RSEQ=CAAGCCAAGGGACACCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:33.5:1:31:1:1:1.67325:60:4:0.1538:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:27.5:1:28:1:1:0:60:4:1:0:0 +7 136219193 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00162;SOR=0.12294;LSEQ=AAGTGCTTCGTTAAATGGGT;RSEQ=CTGCTCCCCGTGCCAACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:9,6:10,6:16,15:0.4839:2,2:24.9:1:30.7:1:1:1.10734:59.5:30:0.4839:0:1.3 0/1:30:3:2,1:14,13:27,3:0.1:2,2:31:1:31.7:1:1:1.82:58.7:6:0.1:0:1.3 +7 136219237 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48718;SOR=0;LSEQ=GGTGAGAACCTCCAACAGTG;RSEQ=CTGTCAGACAGCCTAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:9,9:18,2:0.1:2,2:28.5:1:29:1:1:1:60:4:0.1:0:1 0/0:20:0:0,0:8,12:20,0:0:2,0:16.5:1:30.6:1:1:0:59.2:19:1:0:0.3 +7 136220339 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAGAGGAGCAACGCCAAGAC;RSEQ=CATAATCATCAGATTTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:33:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 136299225 . CTTG C 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.27158;SOR=0.24974;LSEQ=GATGGGGGTTTTGTGGGGGC;RSEQ=TTGTTGTTGTTGTTGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:40:1:33:1:1:1.11803:52:4:0.1053:0:0.5 0/1:36:1:1,0:17,17:34,1:0.0278:2,0:42:0:31:0:1:0:60:2:0.0294:0:1 +7 136299244 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.14154;SOR=0;LSEQ=CCTTGTTGTTGTTGTTGTTG;RSEQ=TGATGCTGTTGTTATCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:16,2:0.1111:2,2:34:1:29:1:1:1:60:4:0.1111:0:1 0/0:29:0:0,0:15,14:29,0:0:2,0:22.1:1:29.1:1:1:0:55.4:58:1:0:0.6 +7 136299286 . C T 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04103;SOR=Inf;LSEQ=CTTTGTTTTTCTTTCAAACA;RSEQ=TCAGTCCCTCTTCTGTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:4,3:1,2:3,7:0.7:2,2:21.9:1:31.6:1:1:2.41:60:14:0.7:0:1 1/1:17:17:7,10:0,0:0,17:1:0,2:22.5:1:29.7:1:1:0:60:34:1:0:1.2 +7 136299366 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5328;SOR=Inf;LSEQ=ATCTGATTCGCTCCCATGCC;RSEQ=GGAAATGTCATTCAAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:17,0:0:2,0:33.9:1:31.7:1:1:0:56.5:34:1:0:0.1 0/1:31:2:1,1:12,17:29,2:0.0645:2,2:46:0:31:1:1:1.40:59:4:0.0645:0:1.5 +7 136299405 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52962;SOR=Inf;LSEQ=GGCTGGAGAGCAGCAAAAAT;RSEQ=GGTGCCTGCTCCTTCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:12.3:1:30.7:1:1:0:56:30:1:0:0.1 0/1:27:2:1,1:11,14:25,2:0.0741:2,2:13:0:32:1:1:1.26:20.5:4:0.0741:0:1 +7 136299515 . A G 84 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTTGGAGATTCTCACCC;RSEQ=GTTGGGTGGCATGGGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:39.5:1:31:1:1:0:60:4:1:0:1 1/1:7:7:2,5:0,0:0,7:1:0,2:28.7:1:30:1:1:0:60:14:1:0:1.3 +7 138883381 . A G 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTACGTGATAGGAACTCCC;RSEQ=GAATCTTACAGATTCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:11:0:15:0:1:0:60:0:0:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:9.5:1:29.5:1:1:0:60:4:1:0:1 +7 138883596 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23531;SOR=Inf;LSEQ=ATTACACAATCAGTTATATA;RSEQ=GGGATACACGTGGCCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:45,50:95,0:0:2,0:23.5:1:30.6:1:1:0:43.5:94:1:0:0.1 0/1:90:2:1,1:37,51:88,2:0.0222:2,2:13.5:1:29:1:1:1.37:27:4:0.0222:0:1.5 +7 138883637 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49553;SOR=Inf;LSEQ=ACAGTCCGTCATTGACTGCA;RSEQ=TAAGTCTGGTTTGGCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:11,39:50,0:0:2,0:26.1:1:33.5:1:1:0:58.3:100:1:0:0.1 0/1:53:2:1,1:15,36:51,2:0.0377:2,2:25:1:28.5:1:0.51669:2.36:47.5:4:0.0377:0:1 +7 139210235 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48;SOR=Inf;LSEQ=TGCGTCACCAAGGAGAAGAG;RSEQ=TGTAGCAGAGCTGTGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:10,2:12,0:0:2,0:21.1:1:31.7:1:1:0:60:24:1:0:0 0/1:13:2:1,1:10,1:11,2:0.1538:2,2:9:1:27:1:0.29487:7.41607:60:4:0.1667:0:1.5 +7 139210321 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50918;SOR=Inf;LSEQ=TGACGCTGTCTCCGGCTTTA;RSEQ=TGTTGGAGTGGCCCTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:33,0:0:2,0:26.1:1:32.6:1:1:0:60:66:1:0:0.1 0/1:47:2:1,1:21,24:45,2:0.0426:2,2:37:1:29:1:1:1.14:60:4:0.0426:0:1 +7 139338077 . A G 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.499;SOR=0;LSEQ=CTTTGATTTCTTCAGAGAGC;RSEQ=ACTACAGACAAAGAGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:117,67:184,2:0.0108:2,2:7.5:1:31.5:1:1:1.74069:60:4:0.011:0:1.5 0/0:176:0:0,0:121,55:176,0:0:2,0:22:1:29.7:1:1:0:60:352:1:0:0.6 +7 139338133 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.79711;LSEQ=GTAACTGGAAAATGCAGTGC;RSEQ=GAGGACTATCAACTGTTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:312:170:88,82:67,75:142,170:0.5449:2,2:27.5:1:30.2:1:0.42866:1.20:59.8:33:0.5464:0:1.1 1/1:350:287:140,147:32,31:63,287:0.82:2,2:29.4:1:29.8:1:0.78265:1.08361:60:286:0.8195:0:1.1 +7 139338197 . CT C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50118;SOR=0;LSEQ=TCTTATGGGACAAATCACAC;RSEQ=CCCACACCGCCATCTCGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:69,124:193,2:0.0103:2,2:17:1:30.6:1:1:1.79:60:4:0.0105:0.0051:0.5 0/0:169:0:0,0:54,115:169,0:0:2,0:23.1:1:28.9:1:1:0:60:83.5:1:0:0.6 +7 139338235 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50456;SOR=0;LSEQ=GTATGGTAAAACTCTGACCC;RSEQ=TGGACCTCGGGAAGGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:11,78:89,2:0.022:2,2:28.5:1:32:0:0.24762:6.83:60:4:0.0233:0:1.5 0/0:71:0:0,0:13,57:70,0:0:2,0:23.6:1:30.3:1:1:0:60:140:1:0:0.4 +7 139338270 . C G 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00312;SOR=12.79783;LSEQ=GAGGCCTCTGCCTCCTGTTA;RSEQ=AGACATGCCATTGAGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:32:0,32:0,15:15,32:0.6809:1,1:23:1:32.6:1:1:0:60:64:0.6809:0:1 1/1:29:28:2,26:0,1:1,28:0.9655:0,2:20.5:1:30.6:1:1:0:60:56:0.9655:0:1 +7 139435814 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2297;SOR=0;LSEQ=GGGTCTGGAAAGGCTGGAGT;RSEQ=AGCGTGGCAGGTCTTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:77,66:143,2:0.0138:2,2:12.5:1:29.5:1:1:1.16542:60:4:0.0139:0:1.5 0/0:157:0:0,0:80,77:157,0:0:2,0:24.5:1:30.6:1:1:0:60:156:1:0:0.2 +7 140111486 . A T 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.29868;LSEQ=AGATGGTCGTTCCCCAACCA;RSEQ=GGAGGATATCCAAGTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:3,1:4,3:0.4286:2,0:30.3:1:32.7:1:1:0:60:6:0.4286:0:2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:20:1:30.5:1:1:0:60:4:0.5:0:2 +7 140111509 . G C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.34694;SOR=0.32347;LSEQ=AGGATATCCAAGTCATCCAG;RSEQ=GAGCAACTGAAAGAATAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:29.2:1:33.4:1:1:0:60:10:0.625:0:1.6 0/1:9:3:3,0:6,0:6,3:0.3333:0,0:17:1:33:0:1:0:60:6:0.3333:0:1.7 +7 140111635 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20687;SOR=Inf;LSEQ=GGAGTTCCCATTACCTGTGG;RSEQ=AACCCCTGATTTGGACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:138,34:172,0:0:2,0:21.8:1:31.4:1:1:0:60:85:1:0:0.1 0/1:144:2:1,1:105,37:142,2:0.0139:2,2:11:1:29:1:0.4595:2.81355:60:4:0.0139:0:1 +7 140434294 . TA T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14175;SOR=0;LSEQ=AAGTGTTCTTTGGTTCACCT;RSEQ=AAAAAAAAGAGAGTATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:4:4,0:100,1:101,4:0.0381:1,0:19.8:1:31.5:1:1:0:37:8:0.0392:0:0 0/0:75:0:0,0:75,0:75,0:0:1,0:24.4:1:28:1:1:0:47:150:1:0:0.2 +7 140434572 . T TA 55 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09312;SOR=6.34063;LSEQ=GCTCAATAGAGGCGAGAATC;RSEQ=ACAAAAAAAAAAAGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:1:0,1:57,189:246,1:0.004:2,0:27:0:13:0:1:0:60:0:0:0:2 0/1:203:5:1,4:51,142:193,5:0.0246:2,2:39.6:1:23.7:1:1:1.43417:35:4:0.0256:0.0099:3.8 +7 140434574 . CA C 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.50995;SOR=0.66893;LSEQ=TCAATAGAGGCGAGAATCTA;RSEQ=AAAAAAAAAAGAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:14:4,10:45,161:206,14:0.0633:2,2:23.3:1:32.8:1:0.51928:1.43:57.3:28:0.0648:0:0.8 0/1:185:8:2,6:45,132:177,8:0.0432:2,2:22:1:31.6:1:1:1.02261:60:16:0.0437:0:1.1 +7 140434586 . G GA 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.8898;LSEQ=AGAATCTACAAAAAAAAAAA;RSEQ=AAAAAAAAAAGAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:4:0,4:20,97:117,4:0.029:2,0:24:1:32:1:1:0:44.8:8:0.0455:0:3.5 0/1:116:3:0,3:21,68:89,3:0.0259:2,0:14:1:27.4:1:1:0:47:6:0.0411:0.0086:2.3 +7 140434597 . G GA 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.02264;LSEQ=AAAAAAAAAGAAAAAAAAAA;RSEQ=AAAAAAAAAGAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:47:2,45:4,32:36,47:0.47:2,1:25.3:1:30.8:1:0.39556:2.77754:49.2:94:0.5402:0.04:2.2 0/1:82:39:1,38:5,21:26,39:0.4756:2,1:25.6:1:29.5:1:0.03385:8.7544:47.1:78:0.5652:0.0244:2.3 +7 140434607 . G A 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0.98346;LSEQ=AAAAAAAAAAGAAAAAAAAA;RSEQ=AAAAAAGAAAAAAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:5:3,2:1,58:59,5:0.0781:1,2:12.8:1:25.8:1:0.00094:66.80:50.8:4:0.0678:0:2.8 0/1:65:5:4,1:1,59:60,5:0.0769:1,2:9.4:1:29.4:1:4e-05:150.15:51.8:10:0.0862:0:3 +7 140434614 . G GA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.49558;SOR=0;LSEQ=AAAGAAAAAAAAAGAAAAAA;RSEQ=AAAAAAAAAGAAAGAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:0,2:2,50:52,2:0.0351:1,0:21.5:1:30.5:1:1:0:58:4:0.0385:0.0175:0.5 0/0:56:0:0,0:2,51:53,0:0:1,0:24.7:1:28.9:1:1:0:48.4:9.6:0.9796:0:2 +7 140434620 . A AAAAG 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.38806;SOR=0.57268;LSEQ=AAAAAAAGAAAAAAGAAAAA;RSEQ=AAAGAAAGAAAGAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:8:0,8:3,36:39,8:0.1633:2,0:32.5:1:32.2:1:1:0:43.4:16:0.1633:0:1.9 0/1:50:5:0,5:2,43:45,5:0.1:1,0:25.8:1:29:1:1:0:42.8:10:0.102:0.02:0.8 +7 140439319 . TG T 77 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATAAACAAAAGCTCTTTG;RSEQ=GGGGGGGGGGTCTTCGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:23.4:1:33.3:1:1:0:60:10:0.7143:0.1429:0.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 140439695 . G A 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33101;SOR=3.70031;LSEQ=GGCTTTTGGACAGTTACTCC;RSEQ=TACCTTACTGAGATCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:1:1,0:129,201:330,1:0.003:2,0:36:0:15:0:0.39275:0:28:0:0:0:1 0/1:270:3:1,2:110,157:267,3:0.0111:2,2:16:1:26.7:1:1:1.39959:37:6:0.0112:0:1 +7 140439756 . G GA 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=8.61494;LSEQ=ATAAAAATTATCTGGAGAGA;RSEQ=AAAAAAAAGGGAAATAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:5:4,1:139,319:458,5:0.0108:2,2:11.8:1:27:1:0.03348:9.13:45.4:10:0.0109:0.0065:0.6 0/1:418:36:9,27:134,246:380,36:0.0861:2,2:28.3:1:30:1:0.27144:1.63235:56.2:72:0.0867:0.0072:0.3 +7 140449071 . C G 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2744;LSEQ=CGGTAAAATAAACACCAAGA;RSEQ=GTGGTAAATATTTACCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:698:211:129,82:286,198:484,211:0.3023:2,2:25.9:1:32.2:1:0.67419:1.09:50.4:51.75:0.3:0:1.3 0/1:763:81:47,34:400,280:680,81:0.1062:2,2:25.4:1:30.9:1:0.90538:1.03341:50.5:162:0.107:0:1.4 +7 140449150 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.30625;LSEQ=ATCAATTCATACAGAACAAT;RSEQ=CCAAATGCATATACATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:88:44,44:188,261:449,88:0.1636:2,2:11.5:1:30.8:1:0.19531:1.39:32.5:87:0.1638:0:1.5 0/1:620:35:17,18:249,335:584,35:0.0565:2,2:10.3:1:30.2:1:0.48878:1.27:31:70:0.0572:0:1.7 +7 140453009 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50194;SOR=0;LSEQ=GTTGAGACCTTCAATGACTT;RSEQ=CTAGTAACTCAGCAGCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:166,32:198,2:0.01:2,2:19:1:32:1:0.30347:5.12379:60:4:0.0103:0:1 0/0:170:0:0,0:131,39:170,0:0:2,0:23.3:1:29.1:1:1:0:60:23.286:1:0:0.1 +7 140453136 . A T 194 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCACTCCATCGAGATTTC;RSEQ=CTGTAGCTAGACCAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:76:41,35:210,247:457,76:0.1426:2,2:26.8:1:31.1:1:0.21555:1.38:49.9:75:0.1415:0:1.1 0/0:639:0:0,0:303,336:639,0:0:2,0:25.8:1:29:1:1:0:58.6:62.9:1:0:0.1 +7 140453896 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49819;SOR=Inf;LSEQ=ACAGTATATCGAACTTAGCA;RSEQ=GAAAACTGTTTTTACATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:115,23:138,0:0:2,0:21.1:1:31:1:1:0:60:137:1:0:0.1 0/1:139:2:1,1:113,24:137,2:0.0144:2,2:14:1:28.5:1:0.32843:4.6336:60:4:0.0145:0:1 +7 140476936 . G A 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00076;SOR=Inf;LSEQ=TTAAATGTCGACAAACTTTA;RSEQ=CAATTCTTACAAAAGAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:31,195:226,0:0:2,0:27.6:1:32.2:1:1:0:59.8:36.667:1:0:0.1 0/1:189:9:3,6:33,147:180,9:0.0476:2,2:24.9:1:30.2:1:0.3761:2.22:60:18:0.0484:0:1 +7 140476958 . A G 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.57544;SOR=2.75081;LSEQ=AATTCTTACAAAAGAGAACC;RSEQ=AAGTAGTCTGTCGGTAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:1:0,1:8,148:156,1:0.0064:2,0:26:0:15:0:1:0:60:0:0:0:1 0/1:115:2:1,1:15,98:113,2:0.0174:2,2:16.5:1:27:1:0.25995:6.36:60:4:0.0183:0:2 +7 140476993 . CT C 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.86964;LSEQ=TAAAATGTTGTCAGAAAAAG;RSEQ=TTTTTTTTTTTAAAAAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:0,5:0,55:55,5:0.0833:1,0:34.4:1:32.4:1:1:0:60:10:0.0877:0:0 0/1:41:3:0,3:2,36:38,3:0.0732:2,0:29.3:1:32.7:1:1:0:60:6:0.0732:0:1 +7 140477006 . A T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.00932;SOR=Inf;LSEQ=GAAAAAGCTTTTTTTTTTTT;RSEQ=AAAAAGGCAACAAAAGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:0,51:51,0:0:1,0:21.9:1:30.4:1:1:0:59.4:50:1:0:0.3 0/1:35:5:0,5:1,28:29,5:0.1429:1,0:12.2:1:25.8:1:1:0:60:4:0.1176:0:1.4 +7 140477727 . T C 99 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=AAGCTAATAGTTGCTACCAC;RSEQ=GGGAACCAGGAGCTAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:233,44:277,0:0:2,0:24.5:1:31.8:1:1:0:59.9:68.25:1:0:0.1 0/1:223:10:8,2:167,46:213,10:0.0448:2,2:20.9:1:30.1:1:1:1.10:60:20:0.0455:0:1 +7 140477756 . C G 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GGAGCTAATAAAAATAACTT;RSEQ=TTTCTCTGGAAAAGAGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:0:0,0:340,129:469,0:0:2,0:23.6:1:32.3:1:1:0:59.9:57.625:1:0:0.1 0/1:460:17:12,5:297,146:443,17:0.037:2,2:22.9:1:31.7:1:1:1.18:60:34:0.0371:0:1.2 +7 140481964 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18896;SOR=Inf;LSEQ=GTGAGAACATGTGGTGTTTG;RSEQ=TTTTCTGTCCTTGTGATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:125,19:144,0:0:2,0:20.9:1:31.6:1:1:0:46.7:35:0.9929:0:0.1 0/1:112:2:1,1:94,16:110,2:0.0179:2,2:15.5:1:27.5:1:0.28169:5.72987:57.5:4:0.018:0:1 +7 140481972 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21658;SOR=Inf;LSEQ=ATGTGGTGTTTGGTTTTCTG;RSEQ=CCTTGTGATACTTTGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:142,24:166,0:0:2,0:23.2:1:30.4:1:1:0:49.9:54.333:1:0:0.1 0/1:145:2:1,1:119,24:143,2:0.0138:2,2:19:0:32.5:1:0.31609:4.87862:58.5:4:0.0139:0:1 +7 140482427 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06837;LSEQ=GAATGTGCAGGTTTGTTACA;RSEQ=ACGTATACATGTGCCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:537:170:85,85:171,196:367,170:0.3166:2,2:26.5:1:32.4:1:0.51568:1.15:44.5:340:0.3184:0:1.1 0/1:457:14:4,10:192,251:443,14:0.0306:2,2:24.5:1:30.6:1:0.41175:1.9098:44.1:28:0.0308:0:1.1 +7 140482430 . G A 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00895;SOR=Inf;LSEQ=TGTGCAGGTTTGTTACATAC;RSEQ=TATACATGTGCCATGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:272,276:548,0:0:2,0:26.4:1:31.4:1:1:0:45.5:136:0.9982:0:0.4 0/1:462:6:3,3:202,252:454,6:0.013:2,2:9.2:1:31:1:1:1.25:57.5:12:0.0131:0:1.3 +7 140482612 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04859;SOR=Inf;LSEQ=ACTGTTACTCTTCCAAAACT;RSEQ=CCTTTTACTAAATTATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:448:0:0,0:174,274:448,0:0:2,0:24.1:1:32.3:1:1:0:59.8:48.778:1:0:0.1 0/1:398:4:3,1:168,226:394,4:0.0101:2,2:12.5:1:26.5:1:0.3185:4.02:60:8:0.0101:0:1.3 +7 140483224 . G T 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TTTACTGGTGCAAAATCTAG;RSEQ=AGAAAAACAATCTCTCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:726:0:0,0:329,397:726,0:0:2,0:26.8:1:31.9:1:1:0:60:120:1:0:0.1 0/1:753:43:17,26:346,364:710,43:0.0571:2,2:24.6:1:28.3:1:0.27302:1.45306:60:42:0.0564:0:1.1 +7 140483231 . A T 168 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.29081;LSEQ=GTGCAAAATCTAGGAGAAAA;RSEQ=CAATCTCTCTAAAACAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:732:2:1,1:326,404:730,2:0.0027:2,2:1:0:23.5:1:1:1.24:60:1:0.0014:0:1.5 0/1:756:58:29,29:325,371:696,58:0.0767:2,2:26:1:28.7:1:0.68203:1.14:60:18.333:0.0735:0:1.2 +7 140483386 . T TA 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.79666;SOR=1.24671;LSEQ=CCTCAACAGCCAATCAATAT;RSEQ=AAAAAAAAGGAAATCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:7:4,3:355,290:645,7:0.0107:2,2:31:1:30:1:1:1.09:56:14:0.0108:0:1 0/1:601:8:5,3:315,277:592,8:0.0133:2,2:18:1:29:1:0.72963:1.46:60:16:0.0135:0.005:0.8 +7 140483400 . T C 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.35896;LSEQ=CAATATTAAAAAAAAGGAAA;RSEQ=CCCCAGATGGAAACATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:658:185:107,78:248,225:473,185:0.2812:2,2:28.1:1:32.2:1:0.22395:1.24:60:184:0.2857:0:2.1 0/1:634:78:42,36:296,257:553,78:0.123:2,2:26.6:1:30.5:1:1:1.01:60:38:0.1248:0:1.2 +7 140483403 . C T 237 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0.0039;LSEQ=TATTAAAAAAAAGGAAATCC;RSEQ=CAGATGGAAACATTTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:192:111,81:253,229:482,192:0.2849:2,2:26.7:1:31.3:1:0.2309:1.24:60:63:0.2872:0:2.1 0/0:646:1:0,1:337,307:644,1:0.0015:2,0:1:0:26:0:0.47752:0:60:2:0.0016:0:1 +7 140483605 . C T 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.09569;LSEQ=AAAGTTAATGTAAATAAAGC;RSEQ=GGGCATATTTCTCAAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:156:72,84:187,216:403,156:0.2791:2,2:24.7:1:31:1:1:1.01001:60:38:0.2764:0:1.1 0/1:533:19:8,11:242,270:512,19:0.0356:2,2:24.4:1:29.7:1:0.81584:1.23193:60:38:0.036:0:1.1 +7 140484450 . CT C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.20094;SOR=1.57337;LSEQ=GACATCTGTCCCAATTTTTA;RSEQ=TTTTTTTTTTTGAGATGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:17:3,14:85,211:296,17:0.0531:2,2:31:1:31.5:1:0.41432:1.87664:56.6:34:0.0572:0.0031:0.2 0/1:308:25:6,19:85,193:278,25:0.0812:2,2:22.5:1:30.8:1:0.64974:1.3932:56.3:50:0.0853:0.0097:0.2 +7 140484483 . CA TG 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21517;SOR=Inf;LSEQ=GAGATGGAGTCTTGCTCTGT;RSEQ=CCCAGGCTGGAGTACAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:25,90:115,0:0:2,0:23.2:1:30.9:1:1:0:50.7:10.5:1:0:0.5 0/1:100:2:1,1:14,84:98,2:0.02:2,2:8:1:27.8:1:0.27879:5.83:59:4:0.0204:0.01:0.5 +7 140484528 . T A 23 v3;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATCTCGGCTCACTGCAACC;RSEQ=CCGCCTCCTGGGTTCAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:0,2:4,39:43,2:0.0444:2,0:11:1:23.5:1:1:0:30:4:0.0476:0:2.5 0/0:22:0:0,0:0,22:22,0:0:1,0:12.8:1:26.8:1:1:0:29.5:6.333:1:0:0.3 +7 140484582 . T C 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCTCCCAAGTAGCTGGGA;RSEQ=TACAGGCATCCGCCATCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:12,32:44,2:0.0435:2,2:13:0:34.5:1:0.48986:2.60:52.5:4:0.0444:0:1.5 0/0:17:0:0,0:6,11:17,0:0:2,0:27.8:1:30.4:1:1:0:44.5:34:1:0:0.2 +7 140485297 . C T 160 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=53.97718;LSEQ=TAAAAATTTATGACAGACAG;RSEQ=ATACAGAAAGCTTGTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:0,1:284,250:534,1:0.0019:2,0:1:0:24:0:0.46916:0:60:2:0.0019:0:2 0/1:587:54:31,23:264,269:533,54:0.092:2,2:24.2:1:27.9:1:0.31786:1.37:60:53:0.0915:0:1.8 +7 140485335 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.41254;LSEQ=CAGTGAGTACGTGTGAGACG;RSEQ=ACATTCAAAGCATTCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:651:220:124,96:221,208:429,220:0.3379:2,2:24.8:1:32.2:1:0.24604:1.22:60:72.333:0.3391:0:1.1 0/1:719:125:70,55:308,286:594,125:0.1739:2,2:24.3:1:31.2:1:0.43108:1.18:60:124:0.1746:0:1.4 +7 140485690 . C T 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.48446;LSEQ=AAGAAGTCATGGGGAATAAA;RSEQ=AAGATGAATTGAAGCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:871:247:117,130:283,341:624,247:0.2836:2,2:25.4:1:29.5:1:0.59829:1.08:59.9:246:0.286:0:1.1 0/1:889:143:66,77:345,401:746,143:0.1609:2,2:25.3:1:28.5:1:1:1.00374:60:142:0.1608:0:1.2 +7 140485985 . G GA 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.17238;SOR=0.60117;LSEQ=GTTCATGAAATAACAAACAG;RSEQ=AAAAAAAAAGCTTGTGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:857:22:9,13:410,425:835,22:0.0257:2,2:26.3:1:30.1:1:0.52032:1.39293:60:21:0.0249:0.0058:0.5 0/1:834:13:7,6:387,426:813,13:0.0156:2,2:24.1:1:29:1:0.78196:1.28:60:26:0.0158:0.0036:0.1 +7 140486118 . C T 165 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGTTTATAACAATGTTTA;RSEQ=TCAATGTAAAATATTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:706:0:0,0:342,362:704,0:0:2,0:24.5:1:32.7:1:1:0:60:63:0.9971:0:0.1 0/1:691:51:24,27:317,321:638,51:0.0738:2,2:27.1:1:29.2:1:0.77195:1.11081:60:50:0.0737:0:1.1 +7 140486288 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.34746;LSEQ=CCTGGAAGAACACTTCAAGA;RSEQ=AGTCTCAAATATCACCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:196:90,106:203,254:457,196:0.3002:2,2:25:1:29.5:1:0.73208:1.06:60:64.333:0.2988:0:1.1 0/1:571:74:35,39:231,265:496,74:0.1296:2,2:22.9:1:27.8:1:1:1.03:60:36:0.1272:0:1.1 +7 140486513 . A G 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACATTTAAAACACTTCCAG;RSEQ=AAGTTGAAGGAAGTGGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:875:0:0,0:464,410:874,0:0:2,0:25.7:1:30.2:1:1:0:59.9:45:0.9988:0:0.1 0/1:860:38:23,15:433,385:818,38:0.0442:2,2:21:1:30.7:1:0.40782:1.36:60:76:0.0448:0:1.1 +7 140486743 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08283;LSEQ=TGTAGTCTACGGCCATACCA;RSEQ=CCTGAACGTGTCCGATCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1039:275:117,158:355,408:763,275:0.2647:2,2:25.3:1:31.9:1:0.25947:1.17482:59.6:136.5:0.2682:0:1.1 0/1:1348:39:19,20:635,670:1305,39:0.0289:2,2:24.5:1:30.9:1:1:1.00:57.4:38:0.0287:0:1.1 +7 140486825 . G A 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1276;SOR=Inf;LSEQ=TTAAGACTTCCTTTTGGCCG;RSEQ=GCGCGGTGGCTCACGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:100,217:317,0:0:2,0:24.4:1:31:1:1:0:56.4:34.222:1:0:0.2 0/1:366:4:3,1:105,256:361,4:0.0109:2,2:11.3:1:22.3:1:0.07949:7.27:60:3:0.0084:0:1 +7 140487202 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3896;LSEQ=TATTAGAGGTAAATGACAAA;RSEQ=ACTACAGAAAAACAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:781:266:142,124:262,250:512,266:0.3406:2,2:21.8:1:29.4:1:0.5966:1.09:59.9:65.5:0.3407:0:1.1 0/1:1069:179:88,91:417,470:887,179:0.1674:2,2:24.4:1:28.4:1:0.62296:1.09:59.9:21.375:0.164:0:1.2 +7 140487494 . C T 203 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00793;LSEQ=AATTATTTTATTAATTAAAA;RSEQ=AATACATCTTATAACTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:111:51,60:292,366:658,111:0.1442:2,2:24.9:1:29.9:1:0.75806:1.07:60:110:0.1444:0:1.2 0/0:751:1:0,1:348,401:749,1:0.0013:2,0:1:0:22:0:1:0:60:2:0.0013:0:1 +7 140487927 . G A 42 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04635;SOR=Inf;LSEQ=ACCCTGCACATCCTGCACAT;RSEQ=TACCCCTGAACTTTGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:165,263:428,0:0:2,0:21.9:1:32.2:1:1:0:60:84.6:1:0:0.1 0/1:372:4:4,0:149,219:368,4:0.0108:2,0:5:1:21:1:0.02795:0:58:3:0.0082:0:2 +7 140487982 . T TA 67 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.4966;SOR=1.75292;LSEQ=AAAATGGCTTCATCAATCCT;RSEQ=AAAAAAAATTATACTGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:3:1,2:238,163:401,3:0.0074:2,2:27.7:1:29.7:1:0.5698:2.91246:60:6:0.0076:0:0 0/1:386:5:2,3:201,180:381,5:0.013:2,2:27:1:29:1:0.67121:1.67276:60:10:0.0131:0:0.4 +7 140488156 . T G 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.11033;LSEQ=AAAAAGTTATAAATAATTAT;RSEQ=TCTCTATTATAGGCATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:172:84,88:196,196:392,172:0.305:2,2:25.5:1:32.2:1:0.85492:1.04756:60:56.333:0.3056:0:1.1 0/1:564:26:13,13:271,266:537,26:0.0461:2,2:21.2:1:30.9:1:1:1.01877:60:52:0.0468:0:1 +7 140488595 . G A 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50476;SOR=Inf;LSEQ=GACGGGGTTTCACCATGTTG;RSEQ=CCAGGCTGGTCTTGAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:41,11:52,0:0:2,0:11.3:1:31.5:1:1:0:31.8:104:1:0:0.1 0/1:68:2:1,1:47,19:66,2:0.0294:2,2:6:0:26:1:0.50483:2.43658:34:4:0.0299:0:1 +7 140488627 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50359;SOR=Inf;LSEQ=TTGAACTCCTGACCTCAGGT;RSEQ=ATCCGTCCACCTCAGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:69,83:152,0:0:2,0:18.6:1:31.3:1:1:0:51.5:304:1:0:0.1 0/1:186:2:2,0:102,82:184,2:0.0108:2,0:7.5:1:27.5:1:0.50433:0:60:4:0.0109:0:1.5 +7 140488645 . T C 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08853;SOR=0;LSEQ=GTGATCCGTCCACCTCAGCC;RSEQ=CCCAAAGTGCTGGGATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:2,1:103,174:277,3:0.0107:2,2:34.7:1:23.7:1:0.55834:3.36:51.7:2:0.0074:0:1 0/0:347:0:0,0:160,187:347,0:0:2,0:23.1:1:28.2:1:1:0:54:37.556:1:0:0.2 +7 140488655 . C T 61 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24003;SOR=3.89093;LSEQ=CACCTCAGCCTCCCAAAGTG;RSEQ=TGGGATTACATGCATAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:347:1:0,1:141,205:346,1:0.0029:2,0:1:0:27:0:1:0:60:2:0.0029:0:1 0/1:449:5:0,5:215,229:444,5:0.0111:2,0:7.4:1:26.4:1:0.06222:0:56:10:0.0112:0:1 +7 140488738 . C A 53 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06696;SOR=Inf;LSEQ=AGCTCTTTATGCGCCGGGTG;RSEQ=GGTGGCTCAAGCCTGTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:178,176:354,0:0:2,0:24.9:1:30.4:1:1:0:59.7:34.4:0.9971:0:0.2 0/1:429:5:4,1:207,216:423,5:0.0117:2,2:7.6:1:23.2:1:0.21014:4.16:60:4:0.0095:0:1.2 +7 140488743 . G A 50 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69289;SOR=1.69468;LSEQ=TTTATGCGCCGGGTGCGGTG;RSEQ=CTCAAGCCTGTAATACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:2:2,0:168,161:329,2:0.006:2,0:1:0:27:0:0.49886:0:60:4:0.0062:0:1 0/1:392:4:3,1:196,192:388,4:0.0102:2,2:5.8:1:25:1:0.62325:2.93:60:8:0.0105:0:1 +7 140488751 . C A 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69034;SOR=1.75373;LSEQ=CCGGGTGCGGTGGCTCAAGC;RSEQ=TGTAATACCAGCACTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:2:2,0:146,148:294,2:0.0068:2,0:1:0:28:1:0.49831:0:60:4:0.0069:0:1 0/1:339:4:3,1:159,176:335,4:0.0118:2,2:25.3:1:25:1:0.35198:3.31:60:3:0.009:0:1.5 +7 140488783 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23021;SOR=0;LSEQ=CACTTTGGGAGGCTGAGGCT;RSEQ=GTGGATCACGAGGTTAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:39,108:147,2:0.0134:2,2:11.5:1:30.5:1:0.46617:2.75:60:4:0.0135:0:1 0/0:161:0:0,0:33,128:161,0:0:2,0:23:1:30.2:1:1:0:57.5:160:1:0:0.1 +7 140489019 . C CA 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.21476;LSEQ=ACTCCATCACAGAAAAAAAA;RSEQ=AAAAAAAAAACTATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:153:119,34:269,60:329,153:0.2954:2,2:19.1:1:30:1:0.3241:1.28024:57:24.5:0.2922:0.1081:0.2 0/1:485:40:30,10:337,86:423,40:0.0825:2,2:24.4:1:29.2:1:0.53989:1.3054:58:39:0.0826:0.0021:0.1 +7 140489030 . CTA C 89 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.02126;SOR=8.74816;LSEQ=GAAAAAAAACAAAAAAAAAA;RSEQ=TATATATATTTAGCTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:654:1:1,0:490,163:653,1:0.0015:2,0:20:0:34:0:1:0:60:2:0.0016:0:0 0/1:680:9:4,5:469,200:669,9:0.0132:2,2:12.3:1:28.1:1:0.13851:2.92598:60:18:0.0136:0.0088:0.4 +7 140489173 . A G 194 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=GAGGGATTGAATGGCCCCAA;RSEQ=TATCTCTGAATAGTCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1275:62:27,35:508,705:1213,62:0.0486:2,2:25.6:1:32.6:1:0.79349:1.07:60:61:0.0485:0:1.1 0/0:1333:0:0,0:603,727:1330,0:0:2,0:26:1:29.8:1:1:0:60:82.125:0.9985:0:0.1 +7 140489562 . C T 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GATTTTGAGATGAAGTCTTG;RSEQ=TCTTGTCACCCAGGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:181,303:484,0:0:2,0:23.5:1:32.5:1:1:0:58.9:120:0.9979:0:0.1 0/1:504:57:25,32:165,279:444,57:0.1131:2,2:21.9:1:29.1:1:0.3844:1.32:55.4:114:0.1138:0:1.2 +7 140490074 . A C 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=CTTACAAGTTACTGCTAGTA;RSEQ=CAACATAAACTTAGATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:909:0:0,0:436,472:908,0:0:2,0:23.2:1:30.3:1:1:0:60:112.5:0.9989:0:0.1 0/1:943:40:21,19:461,441:902,40:0.0424:2,2:28.3:1:31.6:1:0.87333:1.06:60:80:0.0426:0:1.1 +7 140490207 . T C 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03966;SOR=1.39445;LSEQ=CAACTTTTTTCCCACTCTTT;RSEQ=GTAGTTCCTTCTCTTACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:931:73:28,45:394,463:857,73:0.0784:2,2:25.9:1:30.2:1:0.22269:1.36718:60:35.5:0.0773:0:1.1 0/1:971:103:50,53:384,483:867,103:0.1061:2,2:25.6:1:29.6:1:0.46333:1.19:60:102:0.1059:0:1.1 +7 140490382 . C T 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.41756;LSEQ=ATTCAAACCACTATGGAAGG;RSEQ=AAACACTACTAGCCCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:137:69,68:169,142:311,137:0.3058:2,2:23.3:1:28.9:1:0.4725:1.17247:60:136:0.3063:0:1.1 0/1:496:77:44,33:233,186:419,77:0.1552:2,2:26.1:1:28.8:1:0.90073:1.06:60:154:0.1565:0:1.1 +7 140490645 . G A 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25002;SOR=0;LSEQ=GGCTGGGTGCAGTGGCTCAC;RSEQ=CCTGTAATCCCAACACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:2,1:48,222:270,3:0.011:2,2:20.7:1:26:1:0.08729:9.14:42.7:2:0.0075:0:3.3 0/0:250:0:0,0:32,217:249,0:0:2,0:21.2:1:31.2:1:1:0:60:123.5:0.996:0:0.1 +7 140490928 . C A 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.48373;LSEQ=AAAACAAAACAAAAACAAAA;RSEQ=CCGAAAAACCAAAAAAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1626:513:297,216:651,457:1108,513:0.3155:2,2:25.5:1:30:1:0.7454:1.036:57.7:56:0.313:0:1.2 0/1:2145:391:215,176:970,778:1748,391:0.1823:2,2:25.7:1:28.9:1:0.86606:1.02062:57.1:64.167:0.1811:0:1.2 +7 140490938 . CA C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.10726;SOR=1.48534;LSEQ=AAAAACAAAACCCGAAAAAC;RSEQ=AAAAAAATTGTCCCTCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1916:27:15,12:1050,837:1887,27:0.0141:2,2:28.9:1:31.8:1:1:1.00358:58.2:54:0.0143:0.0016:0.5 0/1:2453:51:26,25:1267,1128:2395,51:0.0208:2,2:23.9:1:30.9:1:0.88746:1.07998:57.3:102:0.021:0.0037:0.4 +7 140491101 . A G 206 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAGTAAAGATGACATTTCA;RSEQ=TTGCCAAAATTGATAGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1163:0:0,0:527,635:1162,0:0:2,0:23.6:1:30.7:1:1:0:59.9:76.467:1:0:0.1 0/1:1286:98:41,57:549,637:1186,98:0.0762:2,2:21.3:1:31.2:1:0.40154:1.19802:60:196:0.0774:0:1 +7 140491258 . C T 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACTTAGGAAGAGCCAGCC;RSEQ=ATAAAGGAGACAGAGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:698:0:0,0:299,398:697,0:0:2,0:25.2:1:31.8:1:1:0:60:68.7:1:0:0.1 0/1:715:26:14,12:326,363:689,26:0.0364:2,2:25.7:1:28.9:1:0.55297:1.30:60:52:0.0365:0:1.1 +7 140491331 . T TCAATTTACATATGCTCTTTGAG 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTACATTTTCTCCCCTTT;RSEQ=CAATTTACATATGCTCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:783:0:0,0:376,406:782,0:0:2,0:25.2:1:30.6:1:1:0:59.9:110.714:1:0:0.1 0/1:832:19:10,9:404,409:813,19:0.0228:2,2:26.1:1:29.8:1:0.82103:1.12:58.1:38:0.0231:0.0108:0.1 +7 140491678 . G A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.30257;LSEQ=AAACAGTATAGTGGTTAAGT;RSEQ=TAAGAGAGAAAGGCCAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:341:176,165:345,314:659,341:0.341:2,2:23.4:1:29.7:1:0.84142:1.03004:60:55.833:0.3384:0:1.1 0/1:983:133:70,63:459,386:845,133:0.1353:2,2:20.3:1:28.7:1:0.77896:1.07012:60:132:0.1355:0:1.2 +7 140492039 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.06144;LSEQ=ATACTGTAAAAACCACATTA;RSEQ=TGACAGTCCTGCCTCTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:206:92,114:201,272:473,206:0.3034:2,2:25.8:1:32.9:1:0.61385:1.09:60:205:0.3046:0:1.1 0/1:615:16:5,11:271,328:599,16:0.026:2,2:26.3:1:32.3:1:0.31609:1.816:60:32:0.0264:0:1.1 +7 140492411 . T C 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTGTCCCTTCTCTGCTCAA;RSEQ=GTTCCTAGATCCAACCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1121:0:0,0:480,641:1121,0:0:2,0:25.6:1:30.7:1:1:0:60:123.556:1:0:0.1 0/1:1000:29:11,18:442,528:970,29:0.029:2,2:25.3:1:30.4:1:0.4543:1.36941:60:58:0.0293:0:1 +7 140493029 . A G 165 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTAAAAGGATGATAGTTTTC;RSEQ=AAGTAAAGATGAAGGTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1113:0:0,0:582,528:1110,0:0:2,0:24.4:1:30.8:1:1:0:60:110:0.9973:0:0.1 0/1:1083:49:24,25:515,518:1033,49:0.0452:2,2:28:1:29.5:1:1:1.03561:60:48:0.0447:0:1.1 +7 140493455 . T C 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.13292;SOR=Inf;LSEQ=TTTTCTTTTGAGACAGGGTC;RSEQ=CACTCTGTTGCTCAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:74,183:257,0:0:2,0:23.4:1:30.4:1:1:0:57.9:41.833:1:0:0.1 0/1:321:4:2,2:91,226:317,4:0.0125:2,2:26.5:1:31.3:1:0.58242:2.48:58:8:0.0127:0:1.3 +7 140494073 . G GT 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.09943;SOR=0.54708;LSEQ=AAAATAAAGATACATACTTG;RSEQ=TTTTTTTTTAGTTCTAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:804:24:15,9:446,333:779,24:0.0299:2,2:28.2:1:29.7:1:0.67905:1.24:60:23:0.029:0.0025:0.1 0/1:846:14:5,9:473,358:831,14:0.0165:2,2:34.7:1:29:1:0.17204:2.37579:60:28:0.0167:0:0.1 +7 140494413 . A C 206 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAGCAGTAATGACTTTTAA;RSEQ=AGTATTAATTTAAAAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:86:46,40:286,274:560,86:0.1329:2,2:25:1:32.2:1:0.72862:1.10:59.9:172:0.1342:0:1.1 0/0:763:0:0,0:378,384:762,0:0:2,0:23.7:1:29.7:1:1:0:60:761:0.9987:0:0.1 +7 140495349 . GA G 95 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.13259;SOR=0.34612;LSEQ=TTGTGAGACGTGAGGAATGG;RSEQ=AAAAAATATAGTAGGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:8:5,3:399,346:745,8:0.0106:2,2:21.6:1:31.9:1:0.73097:1.44:60:16:0.0107:0:0.1 0/0:815:3:1,2:423,386:809,3:0.0037:2,2:20.7:1:21.3:1:0.60862:2.18967:60:0.5:0.0012:0:1 +7 140495542 . C T 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.03073;SOR=Inf;LSEQ=TTATATTAATGAAATGAATC;RSEQ=ACTTAGAATTGATATGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:168,229:397,0:0:2,0:24.8:1:32.1:1:1:0:60:48.625:1:0:0.7 0/1:406:6:2,4:169,229:398,6:0.0148:2,2:21.5:1:28.7:1:1:1.47461:60:12:0.015:0:2.3 +7 140495573 . T C 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01837;LSEQ=GATATGCAAATAATAAAATA;RSEQ=TATGTACTAAAAAAAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:370:369:207,162:0,1:1,369:0.9973:0,2:23.1:1:32.6:1:0.44054:0:59.8:51.714:1:0:1.1 1/1:380:331:168,163:28,21:49,331:0.8711:2,2:22.2:1:31.3:1:0.44581:1.29277:60:65.2:0.8693:0:1.2 +7 140495581 . TA T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.1614;SOR=0.52271;LSEQ=AATAATAAAATATTATGTAC;RSEQ=AAAAAAAATTGGTATCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:17:13,4:206,160:366,17:0.0444:2,2:18:1:30.2:1:0.133:2.52:59.7:16:0.0428:0.0235:1 0/1:380:9:5,4:203,167:370,9:0.0237:2,2:20.4:1:29.5:1:1:1.03:60:18:0.0241:0.0079:1 +7 140495583 . A C 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.02884;SOR=Inf;LSEQ=TAATAAAATATTATGTACTA;RSEQ=AAAAAAATTGGTATCGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:383:0:0,0:220,163:383,0:0:2,0:22.9:1:30.6:1:1:0:59.8:62.833:1:0:1 0/1:373:5:3,2:203,165:368,5:0.0134:2,2:19:1:33:0:1:1.22:60:10:0.0136:0:2.6 +7 140495598 . C T 129 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACTAAAAAAAAATTGGTAT;RSEQ=GGCTCAATGAGAATTATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:406:0:0,0:245,160:405,0:0:2,0:24.3:1:31.1:1:1:0:59.8:66.5:1:0:0.8 0/1:410:19:9,10:225,166:391,19:0.0463:2,2:16.3:1:30.5:1:0.47787:1.50447:60:38:0.0467:0:1.7 +7 140496563 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07259;LSEQ=GTGATCATAATCTGATGTCA;RSEQ=TGAATATCTCAGCCATGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:227:85,142:222,278:500,227:0.3118:2,2:24.8:1:33:1:0.08883:1.33353:60:226:0.313:0:1.1 0/1:629:20:12,8:266,343:609,20:0.0318:2,2:24.6:1:31.2:1:0.17284:1.93:60:40:0.0319:0:1.1 +7 140496743 . A AT 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.11372;SOR=5.34421;LSEQ=TTACCTGGTATCCTGATTCA;RSEQ=TTTTTTTTCTGATTTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:1:1,0:301,215:516,1:0.0019:2,0:49:0:31:0:1:0:60:2:0.002:0:0 0/1:488:5:2,3:269,214:483,5:0.0102:2,2:24.4:1:29.8:1:0.65973:1.88303:60:10:0.0104:0:0 +7 140496901 . TC T 259 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGTCGGCAAACTGGCTTTC;RSEQ=CCAATGATACCTGTACCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:881:288:142,146:287,301:588,288:0.3269:2,2:26.6:1:31.8:1:0.94266:1.02:59.9:576:0.328:0.0375:0.1 0/0:847:0:0,0:415,431:846,0:0:2,0:25.1:1:30.5:1:1:0:60:119.857:0.9988:0:0.1 +7 140497586 . A T 239 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0;SOR=0.08833;LSEQ=GGACCTGCCATTAGAAAGGC;RSEQ=TCATGGTCTACAGAATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:205:103,102:209,219:428,205:0.3239:2,2:25.6:1:31.2:1:0.79889:1.06:59.9:40:0.319:0:1.1 0/1:543:22:14,8:278,242:520,22:0.0405:2,2:22.2:1:28.7:1:0.3894:1.52:60:21:0.0393:0:1.1 +7 140497677 . T TA 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.95545;LSEQ=AACATTTTGATTTGACCATC;RSEQ=AAAAAAAACACAGCTGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:11:8,3:389,340:729,11:0.0149:2,2:33.4:1:28:1:0.23685:2.33:60:10:0.014:0.0014:0.2 0/1:774:11:7,4:405,354:759,11:0.0142:2,2:32.3:1:28.5:1:0.55704:1.53:60:22:0.0146:0:0 +7 140498062 . C CT 106 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.36488;SOR=0.64458;LSEQ=GACAGAATGCTGTATGGGGA;RSEQ=TTTTTTTTTCTTTTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:773:11:7,4:356,393:749,11:0.0142:2,2:17.6:1:30.9:1:0.3676:1.93:59.2:22:0.0153:0:0 0/0:868:8:5,3:427,430:857,8:0.0092:2,2:14:1:26.5:1:0.50552:1.68:51.6:7:0.0085:0.0023:0.8 +7 140498071 . T C 120 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=15.08296;LSEQ=CTGTATGGGGACTTTTTTTT;RSEQ=CTTTTTTTTGAGACGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:574:1:0,1:278,291:569,1:0.0017:2,0:10:0:12:0:1:0:55:0:0:0:3 0/1:701:18:12,6:355,323:678,18:0.0257:2,2:9.7:1:28.9:1:0.33906:1.82:51.5:17:0.0249:0:1.1 +7 140498072 . C T 124 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTATGGGGACTTTTTTTTT;RSEQ=TTTTTTTTGAGACGGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:38:3,35:259,243:502,38:0.0677:2,2:8.7:1:23.8:1:0:12.39247:37.8:1.714:0.0521:0:2.7 0/0:685:0:0,0:268,258:526,0:0:2,0:11.9:1:28.4:1:1:0:57.9:6.306:0.7605:0:0.3 +7 140498381 . A T 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08262;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=AAGCATGTGCTTCCAGACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:7:2,5:199,131:330,7:0.0204:2,2:16.6:1:28.7:1:0.12313:3.78275:50.6:14:0.0216:0:1.3 0/1:408:9:2,7:231,167:398,9:0.0221:2,2:12.6:1:24.8:1:0.0416:4.82375:52.7:18:0.0234:0:1.3 +7 140498658 . T C 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACGCCTTTGCATTATTTTTA;RSEQ=TTTTTTGAGACAGAATCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:997:0:0,0:423,571:994,0:0:2,0:23.4:1:30.8:1:1:0:58.2:197.8:0.997:0:0.1 0/1:1215:42:15,27:490,677:1167,42:0.0346:2,2:21.3:1:31.5:1:0.5246:1.30253:56:84:0.0348:0:1.1 +7 140498800 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49558;SOR=Inf;LSEQ=GGATTACAGGTGTGTGCCAT;RSEQ=ATGCCCAGCTAATTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:23,31:54,0:0:2,0:30.1:1:31.6:1:1:0:38.2:26:1:0:0.6 0/1:56:2:2,0:25,29:54,2:0.0357:2,0:36:1:32.5:1:0.22792:0:39:4:0.0385:0:1 +7 140499107 . C T 279 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=1.74599;LSEQ=CCTCTCTCAGTTTTCACTAC;RSEQ=AACAACATCCTAGGTTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1550:564:259,305:461,522:983,564:0.3639:2,2:26.4:1:30:1:0.75073:1.03998:60:93:0.363:0:1.1 0/1:1771:885:415,470:415,466:881,885:0.4997:2,2:25.3:1:28.6:1:0.96198:1.00858:59.9:109.625:0.5014:0:1.1 +7 140500135 . C T 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=61.76857;LSEQ=AAGCGGTTCAAGTAGCATGT;RSEQ=GCCCAAGAGCAGAAGTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1504:1:1,0:793,709:1502,1:7e-04:2,0:50:0:30:0:1:0:60:2:7e-04:0:1 0/1:1671:66:35,31:787,817:1604,66:0.0395:2,2:25.1:1:29.5:1:0.53322:1.17:59.8:65:0.0394:0:1.2 +7 140500384 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11809;SOR=Inf;LSEQ=TGAGATCAAATTCCATTCTC;RSEQ=GAAACAACTGTTAAAATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:0,106:106,0:0:1,0:23.8:1:32.5:1:1:0:59.7:212:1:0:0.2 0/1:56:2:1,1:2,52:54,2:0.0357:1,2:25.5:1:28.5:1:0.10519:21.43:60:4:0.0357:0:1 +7 140501405 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22994;SOR=Inf;LSEQ=TTTCAAAAACTCACAAGAAA;RSEQ=CTTTCTAGAAACTGACGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:34,163:197,0:0:2,0:25.1:1:29.5:1:1:0:60:23.625:1:0:0.1 0/1:182:2:1,1:32,148:180,2:0.011:2,2:20.5:1:27:1:0.33058:4.57:60:4:0.0112:0:1 +7 140507735 . CA C 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.91318;LSEQ=TCTAAACATTTTTGACATTT;RSEQ=AAAAAAAATGTAAAGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:396:11:8,3:296,88:384,11:0.0278:2,2:24:1:32.5:1:0.72072:1.26058:48.9:22:0.0279:0.0025:0 0/1:354:9:7,2:239,103:342,9:0.0254:2,2:19:1:30.3:1:0.72997:1.51:49.4:18:0.0255:0.0085:0.1 +7 140507901 . C T 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCCTTTCTTGGTTATTACA;RSEQ=CTAAAAATATTCATATACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:27:6,21:71,239:310,27:0.0799:2,2:23.1:1:30.8:1:1:1.03966:60:54:0.0811:0:1.1 0/0:338:0:0,0:92,245:337,0:0:2,0:23:1:30.6:1:1:0:60:66.4:0.997:0:0.1 +7 140508842 . C A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25288;SOR=0;LSEQ=GAGGTAAAGGGAGCAAATTA;RSEQ=ATTTTTTCATATCATTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:3:2,1:31,200:231,3:0.0128:2,2:11:1:23:1:0.05293:12.66:60:2:0.0086:0:3.3 0/0:200:0:0,0:35,165:200,0:0:2,0:22.1:1:31.3:1:1:0:60:65.667:1:0:0 +7 140534267 . C T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45158;SOR=0.59054;LSEQ=ACTTTGCCACCAAATAATTA;RSEQ=ATATTTTTCATTCCTGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:16:15,1:45,2:47,16:0.254:1,1:20.8:1:30.8:1:1:1.48954:60:32:0.254:0:1.1 0/1:36:6:6,0:30,0:30,6:0.1667:1,0:24.8:1:31.2:1:1:0:60:12:0.1714:0:1 +7 140534563 . A C 175 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAAGATGTAACGGTATCC;RSEQ=TTGATGCAGAGCTAGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:673:0:0,0:360,313:673,0:0:2,0:26.3:1:30.8:1:1:0:57.5:133.6:1:0:0.1 0/1:694:50:23,27:325,319:644,50:0.072:2,2:23.9:1:31.1:1:0.56049:1.19568:43.9:100:0.0728:0:1.1 +7 140549900 . C T 66 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0071;SOR=Inf;LSEQ=AAATTACTAGATATGATACT;RSEQ=AAAAGCTTACCTCCAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:710:0:0,0:476,234:710,0:0:2,0:24.8:1:32.3:1:1:0:59.9:100.429:1:0:0.1 0/1:694:7:3,4:412,275:687,7:0.0101:2,2:18:1:23.7:1:0.44757:1.99556:58.4:6:0.0088:0:1.6 +7 140624311 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09231;SOR=Inf;LSEQ=CCTCTTTCCAAAATAAACAC;RSEQ=AGCCAGCCGCCGAGCCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:93,61:154,0:0:2,0:22.5:1:31.2:1:1:0:60:50.333:1:0:0.2 0/1:128:3:1,2:81,44:125,3:0.0234:2,2:11.3:1:26:1:0.29308:3.64239:60:6:0.0238:0:1 +7 140624380 . C T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.70425;SOR=1.51429;LSEQ=ACTCACCTCCTCCGGAATGG;RSEQ=AGGGTCCGCAGCCGAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:2:0,2:121,178:299,2:0.0066:2,0:1:0:24:0:0.51761:0:60:4:0.0068:0:1 0/1:400:4:2,2:189,206:395,4:0.01:2,2:12.5:1:27:1:1:1.09:60:8:0.0101:0:1 +7 140624431 . G T 59 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41025;SOR=3.36847;LSEQ=GGCGCCGGCGCCGGCCTCGG;RSEQ=CTCCATGTCCCCGTTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:1:0,1:139,143:282,1:0.0035:2,0:1:0:25:0:1:0:60:2:0.0035:0:1 0/1:423:5:1,4:197,221:418,5:0.0118:2,2:5:1:25.8:1:0.37716:3.55624:60:10:0.012:0:1 +7 140624459 . G A 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2409;SOR=3.87099;LSEQ=TCCCCGTTGAACAGAGCCTG;RSEQ=CCCGGCTCCGCGCCGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:322:1:1,0:167,154:321,1:0.0031:2,0:1:0:27:0:1:0:60:2:0.0032:0:1 0/1:419:5:4,1:202,211:413,5:0.0119:2,2:9.4:1:26.6:1:0.20993:4.17:60:10:0.0122:0:1.2 +7 140624460 . C T 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07326;SOR=Inf;LSEQ=CCCCGTTGAACAGAGCCTGG;RSEQ=CCGGCTCCGCGCCGCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:165,152:317,0:0:2,0:25.4:1:31.9:1:1:0:59.9:51.833:0.9968:0:0.2 0/1:418:5:2,3:202,211:413,5:0.012:2,2:22.2:1:29:1:1:1.43479:60:10:0.0122:0:1.4 +7 140624524 . C G 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24805;SOR=Inf;LSEQ=CTTATAACCGAGAGCCGGGG;RSEQ=CCGAGCGGCCGCTGTCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:72,116:188,0:0:2,0:23.7:1:30.4:1:1:0:60:16.091:0.9944:0:0.2 0/1:192:3:1,2:82,106:188,3:0.0156:2,2:14:1:25:1:1:1.54378:58.7:2:0.0109:0:3.7 +7 140624526 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24525;SOR=0;LSEQ=TATAACCGAGAGCCGGGGCC;RSEQ=GAGCGGCCGCTGTCGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:67,111:178,2:0.011:2,2:36.5:1:31.5:1:1:1.65:60:4:0.0116:0:1 0/0:185:0:0,0:80,105:185,0:0:2,0:23.2:1:28.6:1:1:0:59.9:25.429:1:0:0.3 +7 140624530 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49856;SOR=Inf;LSEQ=ACCGAGAGCCGGGGCCCGAG;RSEQ=GGCCGCTGTCGGGCGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:59,105:164,0:0:2,0:23.8:1:29.4:1:1:0:60:17.222:1:0:0.2 0/1:168:2:0,2:69,96:165,2:0.0119:2,0:14.5:1:27:1:0.51216:0:60:4:0.0122:0:1 +7 144115822 . G C 77 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0.23975;LSEQ=GAAACAAATTTGACAAGAAG;RSEQ=TTAAAAATACAGGGCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:2,0:2,5:0.7143:0,2:26.2:1:33.4:1:1:0:25:10:0.7143:0:1.6 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:21:0:33:0:1:0:22:2:0.3333:0:4 +7 144115885 . G A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50226;SOR=0.60245;LSEQ=GCCATGGGACCTAGAAATGG;RSEQ=AGAAGCCATGTTGCCCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:8,1:4,2:6,9:0.6:2,2:22.8:1:30.8:1:0.52527:3.62:25.7:18:0.6:0:1.4 0/1:17:8:4,4:4,5:9,8:0.4706:2,2:16.4:1:28:1:1:1.23:23.1:16:0.4706:0:1.6 +7 144662618 . TA T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12218;SOR=0;LSEQ=TAGCCTTTGCCTAATTCAAA;RSEQ=ATACCATATTCCCTGATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:1,2:168,92:260,3:0.0114:2,2:22.7:1:28.7:1:0.29117:3.63323:60:6:0.0116:0.0038:1.3 0/0:266:0:0,0:168,98:266,0:0:2,0:25.6:1:28.6:1:1:0:60:87.667:1:0:0.4 +7 144662674 . T G 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40812;SOR=1.13552;LSEQ=CCTCTGCTTTTAAGCAGGTG;RSEQ=TTATCCCATATAAAGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:135:75,60:102,109:211,135:0.389:2,2:26.8:1:31.4:1:0.22524:1.33:60:66.5:0.3935:0:1.1 0/1:386:162:78,84:115,109:224,162:0.4197:2,2:27.4:1:30.9:1:0.60614:1.13582:59.9:39.5:0.4158:0:1.1 +7 144662746 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11432;SOR=Inf;LSEQ=ATCGGTACACTTTTCTATGA;RSEQ=GATTTTGTGAATCTGGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:68,125:193,0:0:2,0:25.8:1:31.2:1:1:0:60:47.25:1:0:0.3 0/1:183:3:1,2:57,123:180,3:0.0164:2,2:22.3:1:31:1:1:1.08:60:6:0.0167:0:1.3 +7 144662974 . A C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAAGTGTGATATAAGAC;RSEQ=ACTACTATGGTGTCAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:33:1:32:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 144663029 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTGCATTTCATAAAGTTA;RSEQ=TTAAAGGGAACTTTAGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:18.5:1:32:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 144799690 . GCAA G 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.15821;SOR=0.30254;LSEQ=GACCCTATCTCAAAACAACA;RSEQ=CAACAACAACAACAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:7,4:4,3:7,11:0.5789:2,2:27.8:1:32.8:1:1:1.29:60:22:0.5789:0.0526:0.2 0/1:14:4:3,1:5,5:10,4:0.2857:2,2:43:1:32:1:0.58042:2.78:60:8:0.2857:0:0.5 +7 144799718 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.49956;SOR=Inf;LSEQ=AACAACAACAACAACAGCAA;RSEQ=AACAACAACAGCAACAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:19,11:30,0:0:2,0:27.1:1:31.1:1:1:0:58.1:14:1:0:0.2 0/1:38:2:1,1:23,13:36,2:0.0526:2,2:30:1:31:1:1:1.74146:60:4:0.0526:0:1 +7 148504716 . AG A 299 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0;SOR=2.60967;LSEQ=TAAGGCAGCTGTTTCAGAGG;RSEQ=GGGGGAGGAGGTAGCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1103:639:317,322:240,220:460,639:0.5793:2,2:28.4:1:32.6:1:0.42671:1.10801:58.8:318.5:0.5812:0.0553:0.2 1/0:1034:809:414,395:119,104:223,809:0.7824:2,2:27.2:1:31:1:0.59651:1.09162:58.6:160.8:0.7867:0.0851:0.2 +7 148504854 . A AGACTT 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.0458;SOR=1.47768;LSEQ=CACCCATCCAACATGTGCTG;RSEQ=GACTTAACACAACAAAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:243:134:8,126:16,90:106,134:0.5514:2,2:30.9:1:30.7:1:0.02871:2.78793:58.5:43.667:0.5696:0.0453:0.5 1/0:217:140:26,114:18,56:74,140:0.6452:2,2:27:1:29.3:1:0.3746:1.40695:59.2:139:0.6526:0.1336:0.4 +7 148505788 . T C 76 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAGATATGCATAGTATA;RSEQ=TGTCAAGTAAAACCATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:36.8:1:33:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 148505864 . G A 80 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGAAAACGCTCCACGAGT;RSEQ=AGCATGCAGCATGCGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:3,7:0.7:0,0:24.1:1:28.7:1:1:0:60:14:0.7:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 148506064 . A G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=2.84921;LSEQ=TGCTCATGGCAAAGTGACCC;RSEQ=TCAAAAGAAGCAAAGAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:186:117:106,11:66,3:69,117:0.629:1,2:24.9:1:30.4:1:0.25937:2.27404:60:116:0.6339:0:1.1 1/1:152:126:118,8:26,0:26,126:0.8289:1,2:24.2:1:29.8:1:0.35221:0:60:252:0.8289:0:1.1 +7 148506274 . G A 64 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01109;SOR=Inf;LSEQ=AGAGACACACTGGTGTCAGT;RSEQ=AGCATGAAGACGGGCCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:499:0:0,0:215,284:499,0:0:2,0:24:1:32.1:1:1:0:59.9:54.444:1:0:0.1 0/1:449:6:5,1:178,264:442,6:0.0134:2,2:14.3:1:24.8:1:0.04393:7.38:60:12:0.0135:0:1 +7 148506363 . T G 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAGTCCATCATCACAGGAC;RSEQ=GAAAAGGGAGTTCCAATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:622:0:0,0:346,276:622,0:0:2,0:26:1:31.2:1:1:0:59.8:61.2:1:0:0.1 0/1:567:35:21,14:305,227:532,35:0.0617:2,2:20.1:1:28.8:1:0.86048:1.12:59:34:0.0608:0:1.1 +7 148506754 . CA C 32 v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTACTGAGCAAAACATAG;RSEQ=AAAAAAAAAAAAAATCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:39:1:32.5:1:1:0:60:4:0.4:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 148507365 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24944;SOR=0;LSEQ=CCTCGTTTCTGAACACTCGG;RSEQ=CGGCAGAAGGCTGCCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:2,1:210,71:281,3:0.0106:2,2:29.3:1:30.7:1:1:1.47665:60:6:0.0106:0:1 0/0:266:0:0,0:194,72:266,0:0:2,0:26.2:1:30.8:1:1:0:59.9:52.2:1:0:0.1 +7 148507534 . C CT 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGACACAGGAGAAAATT;RSEQ=TTTTGGATAAAGGTGATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:88,200:288,0:0:2,0:24.7:1:32.6:1:1:0:60:40.143:1:0:0.1 0/1:265:17:6,11:71,177:248,17:0.0642:2,2:23.8:1:29.9:1:0.58493:1.36:60:34:0.0644:0.0075:0.2 +7 148507556 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1809;SOR=Inf;LSEQ=TTTGGATAAAGGTGATCAAG;RSEQ=CTGACAGAACACACAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:44,157:201,0:0:2,0:23.4:1:31.5:1:1:0:60:99.5:1:0:0.1 0/1:150:2:1,1:29,118:147,2:0.0133:2,2:19.5:1:28:1:0.36323:4.02:60:4:0.0137:0:1 +7 148508481 . A G 71 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCAACTCCTGAGCTCAAGC;RSEQ=ATCCACCTGCCTCGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:31.6:1:30.6:1:1:0:47.6:10:0.5556:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:42:0:31:0:1:0:60:2:1:0:2 +7 148508656 . CTAAAA C 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTTACCTAATAAAATCAAT;RSEQ=TAAAGTAAAGTTAGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:386:0:0,0:287,99:386,0:0:2,0:23.8:1:30.7:1:1:0:59.9:54.143:1:0:0.1 0/1:435:22:17,5:293,120:413,22:0.0506:2,2:22.7:1:30.9:1:0.63382:1.39:59.8:44:0.0515:0.0092:0.3 +7 148508821 . T C 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAGCAATAGATGCTAGAGAA;RSEQ=AAAACACAATCACATCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:476:0:0,0:153,322:475,0:0:2,0:25.1:1:29:1:1:0:60:78.167:0.9979:0:0.6 0/1:498:24:7,17:166,308:474,24:0.0482:2,2:23.3:1:30.8:1:0.66346:1.30823:60:23:0.0468:0:1.8 +7 148508833 . A G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=1.90915;LSEQ=CTAGAGAATAAAACACAATC;RSEQ=CATCATCAAAAAAGGAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:393:245:72,173:33,115:148,245:0.6234:2,2:25.1:1:31.4:1:0.12823:1.45:60:80.667:0.6205:0:1.1 1/0:383:291:86,205:26,65:91,291:0.7598:2,2:24.7:1:30.2:1:0.89575:1.05:60:40.571:0.7594:0:1.1 +7 148512455 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23317;SOR=Inf;LSEQ=ACTGGGGATTCATCAGTAGA;RSEQ=GTCCTCCATTCAAATTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:65,3:68,0:0:1,0:22.6:1:32.5:1:1:0:60:67:1:0:0 0/1:64:2:1,1:60,2:62,2:0.0313:1,2:8:1:28:1:0.09226:24.69852:60:4:0.0317:0:1 +7 148512722 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24696;SOR=0;LSEQ=TGCTTAACTGGATCTATCTG;RSEQ=GCCATGAATACAGGAATGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:10,111:121,2:0.0163:2,2:16.5:1:31:1:0.17153:10.63:60:4:0.0163:0:1 0/0:124:0:0,0:20,104:124,0:0:2,0:21.4:1:29.4:1:1:0:60:123:1:0:0.1 +7 148513943 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23799;SOR=0;LSEQ=CATTCTTATACTCATGCATA;RSEQ=CAGAAAAATGTCTTTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:15,154:169,2:0.0117:2,2:35:1:31:1:0.17888:9.97:60:4:0.0121:0:1 0/0:179:0:0,0:25,154:179,0:0:2,0:22.4:1:30.8:1:1:0:60:178:1:0:0.1 +7 148515269 . G GA 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.68755;SOR=0.55749;LSEQ=AAACTCATTTTGATGGAAGA;RSEQ=AAAAAAAAATACTATATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:4:0,4:7,139:146,4:0.0263:1,0:25.8:1:31.6:1:1:0:60:8:0.0274:0.0066:0 0/1:135:2:0,2:11,122:133,2:0.0148:2,0:18:1:32:0:1:0:60:4:0.0153:0:0.5 +7 148516878 . C T 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01207;SOR=Inf;LSEQ=GTCAATTAATGGATTATAAT;RSEQ=TTGCTAATATGTGGTTTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:44,0:0:1,0:18.4:1:32.9:1:1:0:60:88:1:0:0 0/1:43:6:0,6:1,36:37,6:0.1395:1,0:14.8:1:31:1:1:0:60:12:0.1395:0:1 +7 148523604 . C T 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2878;SOR=2.93235;LSEQ=AAACATCGCCTACAGAAAAG;RSEQ=GTATGAAAGGAGTGTAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:585:2:0,2:307,276:583,2:0.0034:2,0:1:0:27:1:0.2254:0:60:4:0.0034:0:1 0/1:602:6:2,4:314,281:595,6:0.01:2,2:18:1:26.7:1:0.43001:2.23199:60:12:0.01:0:1.2 +7 148523709 . G A 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01963;SOR=Inf;LSEQ=GCGCCTGGGAGCTGCTGTTC;RSEQ=GTGAGTTCTTTATATCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:0:0,0:170,306:476,0:0:2,0:25.4:1:30.3:1:1:0:59.9:46.6:0.9957:0:0.1 0/1:402:5:2,3:152,245:397,5:0.0124:2,2:15.4:1:28.4:1:1:1.07:60:10:0.0125:0:1.2 +7 148523777 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50309;SOR=0;LSEQ=TGAAACAAAAATCACTTTTT;RSEQ=GAAAACAGTTTCTAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:18,123:141,2:0.014:2,2:8.5:1:29.5:1:0.24889:6.68:60:4:0.014:0:1 0/0:117:0:0,0:20,97:117,0:0:2,0:21.9:1:29.5:1:1:0:60:116:1:0:0 +7 148524380 . G GA 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.2522;SOR=Inf;LSEQ=TAAACAGGAGAATATGAAAG;RSEQ=AAAAAAAGAATGGAAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:53,187:240,0:0:2,0:22.5:1:31.9:1:1:0:59.9:79:1:0:0.1 0/1:276:3:2,1:82,191:273,3:0.0109:2,2:16.7:1:25.7:1:0.22059:4.63:60:6:0.0109:0.0036:0.7 +7 148525760 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20832;SOR=Inf;LSEQ=AGAAAGAAGAAACTAAGCCC;RSEQ=ATTTCTACTCTTTCTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:158,26:184,0:0:2,0:21.8:1:31.9:1:1:0:60:91:1:0:0.1 0/1:155:2:2,0:135,18:153,2:0.0129:2,0:10.5:1:32:0:1:0:60:4:0.0129:0:1 +7 148525904 . C G 252 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=GTCTCCATCATCATCATCGT;RSEQ=ATCATCATTATATTGACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:922:0:0,0:465,457:922,0:0:2,0:26.5:1:31.9:1:1:0:59.8:60.467:1:0:0.1 0/1:1011:292:155,137:369,349:718,292:0.2888:2,2:24.6:1:30.8:1:0.67691:1.07:60:145:0.2883:0:1.1 +7 148526807 . G A 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTTTTTCCAAGAGAAGAA;RSEQ=CATATGGCTCACCTCTATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:0:0,0:397,249:646,0:0:2,0:26:1:32.9:1:1:0:59.9:70.778:1:0:0.1 0/1:613:38:22,16:337,237:574,38:0.062:2,2:28.2:1:29.1:1:1:1.0341:60:76:0.0629:0:1.1 +7 148527012 . C CT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.5003;SOR=0;LSEQ=TGAAATAACTAAAATACAAC;RSEQ=TTTTTTTCATGTGTACATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:5,101:106,2:0.0185:1,2:34.5:1:29.5:1:0.10852:18.53:60:4:0.0187:0:0 0/0:93:0:0,0:0,93:93,0:0:1,0:19.8:1:32.1:1:1:0:60:92:1:0:0.1 +7 148529918 . G C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49898;SOR=0;LSEQ=TAGCCATCATATTGTAAAGA;RSEQ=ATGCTGCCTACCCAAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:2,107:109,2:0.018:1,2:23.5:1:31:1:0.05356:43.88:60:4:0.0182:0:1 0/0:100:0:0,0:2,98:100,0:0:1,0:24:1:30.7:1:1:0:60:99:1:0:0.1 +7 148529946 . GA G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.19948;SOR=Inf;LSEQ=CTACCCAAATATTTAATTTT;RSEQ=AAAAAAAGTCCTTACCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:1,69:70,0:0:1,0:23.5:1:31.8:1:1:0:60:140:1:0:0 0/1:57:2:0,2:1,54:55,2:0.0351:1,0:40.5:1:32:1:1:0:60:4:0.0357:0:0 +7 148543525 . A G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0;SOR=2.43955;LSEQ=CCAATAGCATAAACCAAAAG;RSEQ=TGATGATAATTACTACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:329:196:144,52:99,33:132,196:0.5957:2,2:24.7:1:31.4:1:0.79805:1.08304:59.9:64.333:0.5938:0:1.1 1/0:345:270:193,77:52,23:75,270:0.7826:2,2:23.3:1:30.5:1:0.77382:1.11:60:134:0.7836:0:1.1 +7 148543693 . TA T 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.00171;SOR=1.67715;LSEQ=ATTGGAACTAAACATACTCT;RSEQ=AAAAAAAAAATGAAGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:302:158:39,119:42,91:133,158:0.5232:2,2:29:1:31.1:1:0.23729:1.40659:60:316:0.5267:0.0232:0.1 1/0:341:221:63,158:37,69:106,221:0.6481:2,2:27.9:1:29.7:1:0.25061:1.34355:60:109.5:0.646:0.0499:0.3 +7 148543753 . C T 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTTAGAAAATGTATAACA;RSEQ=CTGTAAAGCAGGTTAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:6,99:105,0:0:2,0:25.8:1:32:1:1:0:59.9:210:1:0:0.1 0/1:92:34:1,33:0,58:58,34:0.3696:1,1:24.4:1:28.4:1:0.36957:0:60:33:0.3626:0:1 +7 149018755 . G A 79 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26924;SOR=2.78045;LSEQ=CAGTGCTTACTTAGCTCACT;RSEQ=ACAGTGCTGCTGTTGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:18,2:0.1:2,2:15.5:1:31.5:1:1:1.23603:23:4:0.1:0:1 0/1:25:6:3,3:10,9:19,6:0.24:2,2:22:1:30.8:1:1:1.10643:27:12:0.24:0:1.3 +7 149031030 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24283;SOR=0;LSEQ=CTGCTGTCATTCTCTCCTGT;RSEQ=CGGCTGTTCTCTTGCGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:74,44:118,2:0.0167:2,2:20:1:28:1:1:1.67415:60:4:0.0167:0:1 0/0:123:0:0,0:77,46:123,0:0:2,0:21.4:1:30.3:1:1:0:59.8:19.5:1:0:0.1 +7 149031035 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23018;SOR=0;LSEQ=GTCATTCTCTCCTGTGCGGC;RSEQ=GTTCTCTTGCGCAGTGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:2:1,1:77,46:123,2:0.016:2,2:19.5:1:32:1:1:1.66666:60:4:0.016:0:1 0/0:135:0:0,0:83,52:135,0:0:2,0:22.5:1:29.6:1:1:0:59.8:270:1:0:0.1 +7 149031357 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50193;SOR=Inf;LSEQ=TTGAAAATGTCTGTACAGCC;RSEQ=ACGGTTTCCCTTGGGGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:62,58:120,0:0:2,0:22.8:1:30.5:1:1:0:30.2:59:1:0:0.3 0/1:143:2:1,1:83,58:141,2:0.014:2,2:15.5:1:27:1:1:1.42735:31:4:0.0142:0:1 +7 149031386 . C T 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05101;SOR=0.53947;LSEQ=CCTTGGGGGCTTTGAAATAA;RSEQ=ACCACCAGTGGTCTTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:32:17,15:57,71:128,32:0.2:2,2:25.6:1:30.1:1:0.43108:1.41:40.8:64:0.2025:0:1.1 0/1:177:21:10,11:84,72:156,21:0.1186:2,2:32.1:1:28.9:1:0.64596:1.28151:33.2:42:0.1193:0:1 +7 149031536 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24419;SOR=Inf;LSEQ=ATCTGGAAAGCAGTCTGCCC;RSEQ=TGGCGGTGGTAGCAAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:25,40:65,0:0:2,0:24.7:1:32.1:1:1:0:57:31.5:1:0:0.1 0/1:64:2:1,1:20,42:62,2:0.0313:2,2:22.5:1:30:1:1:2.07:60:4:0.0317:0:1 +7 149031681 . A G 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00026;SOR=Inf;LSEQ=CTCCAAGCCAAAAATGCACA;RSEQ=AAGTCAAATCAGAATGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:44,45:89,0:0:2,0:25.1:1:31.1:1:1:0:55.3:178:1:0:0.1 0/1:74:10:3,7:30,33:63,10:0.1351:2,2:27.1:1:31.2:1:0.49586:2.10038:54.5:20:0.1389:0:1.2 +7 149031692 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2051;SOR=Inf;LSEQ=AAATGCACAAAAGTCAAATC;RSEQ=GAATGGAAAAGACTCAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:43,47:90,0:0:2,0:24.9:1:30.8:1:1:0:55.3:44:1:0:0.1 0/1:75:2:1,1:33,40:73,2:0.0267:2,2:15:0:32:1:1:1.21:45.5:4:0.0267:0:2 +7 149031853 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19861;SOR=Inf;LSEQ=AAAAAGGTGGTTCTATTCCC;RSEQ=CAGTGGAAGCCAAGTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:23,0:0:2,0:27:1:30.1:1:1:0:25.5:46:1:0:0 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:32:1:30:1:1:1.12:25:4:0.1053:0:1 +7 149031988 . C CTCATT 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=3.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=ATTTATTAAAAAATTTTCAT;RSEQ=TCATTTCTGTAACAGTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:1,6:7,3:0.3:2,2:20.3:1:32.7:1:1:2.65:42:6:0.3:0.1:0.3 0/0:4:0:0,0:1,3:4,0:0:2,0:19.3:1:30.3:1:1:0:51.8:8:1:0:0.3 +7 150485659 . G C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTCTCCCTGTGTCCTCA;RSEQ=GTGGCCTTCCCTCTGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 150485701 . A G 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGCATTCTGATTGCCTCT;RSEQ=ATATGACATCAGACATATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:19.3:1:32.8:1:1:0:59.5:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 150485864 . G A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02652;SOR=0.24329;LSEQ=ACAAAAATTCAGCCTCTCAC;RSEQ=CCCACCACCTCCCACCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:16:16,0:19,0:19,16:0.4571:1,1:16.8:1:30.5:1:1:0:60:32:0.4848:0:1.1 0/1:24:4:4,0:20,0:20,4:0.1667:1,0:18.3:1:29.3:1:1:0:60:8:0.1739:0:1 +7 150486019 . C T 48 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11979;SOR=5.15453;LSEQ=CTGAATATCAACATCTGTGA;RSEQ=AACTAAAAGACAACCCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:445:1:0,1:257,187:444,1:0.0022:2,0:1:0:23:0:0.42247:0:60:2:0.0023:0:1 0/1:435:5:1,4:239,191:430,5:0.0115:2,2:5:1:21:1:0.17828:4.98924:60:4:0.0093:0:1.8 +7 150486083 . G A 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.09992;SOR=0.81317;LSEQ=TGGAGTCAGGGTGGTGAGTG;RSEQ=GCAAGTAACTCAGTCCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:242:111,131:116,139:255,242:0.4859:2,2:27.1:1:31:1:1:1.02:59.9:39.333:0.4807:0:1.1 0/1:596:259:116,143:160,177:337,259:0.4346:2,2:25.8:1:29.3:1:0.56196:1.11415:60:128.5:0.4349:0:1.1 +7 150486169 . G A 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24723;LSEQ=GCGTTCTCATGGCTGTTCAC;RSEQ=ACATGAGCAACGGCAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:63:13,50:10,82:92,63:0.4038:2,2:24.5:1:30.1:1:0.11002:2.12:60:30.5:0.3987:0:1 0/1:133:19:3,16:17,97:114,19:0.1429:2,2:27:1:30.3:1:1:1.07:60:38:0.1439:0:1.1 +7 150486191 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.15224;SOR=Inf;LSEQ=CATGAGCAACGGCAAGCTCA;RSEQ=GGTGCTCTGCCCCTGAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:6,112:118,0:0:2,0:25:1:31.6:1:1:0:60:117:1:0:0.4 0/1:76:2:1,1:3,71:74,2:0.0263:1,2:15:0:32:0:0.10316:20.64:60:4:0.0263:0:1.5 +7 150794726 . G C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTCAGGGAGCTTTTTAC;RSEQ=GGTGGCAGAAAGCAAAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 150904933 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49629;SOR=0;LSEQ=AGGGCACAGAAACAGTTCAC;RSEQ=CTTTATTTTTGTCAGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:2:1,1:33,19:52,2:0.037:2,2:22:1:30.5:1:1:1.71824:60:4:0.0377:0:1 0/0:49:0:0,0:31,17:48,0:0:2,0:19.2:1:30.2:1:1:0:60:96:0.9796:0:0.1 +7 151164348 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.45031;LSEQ=TTAGTGTGAAGCCGAACTCC;RSEQ=AGAGTATTTTACGGACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:578:341:86,255:55,181:236,341:0.59:2,2:22.5:1:30.9:1:0.6233:1.11:60:67.2:0.5905:0:1.1 0/1:514:202:55,147:87,225:312,202:0.393:2,2:21.6:1:29.5:1:0.91969:1.0334:60:201:0.3941:0:1.2 +7 151164378 . C T 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.32112;SOR=3.95086;LSEQ=TACGGACTGAGGAGGGCGTG;RSEQ=CGCCTGCCCTGCCCTCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:1:0,1:32,268:300,1:0.0033:2,0:35:0:32:0:1:0:60:2:0.0034:0:1 0/1:231:3:1,2:23,205:228,3:0.013:2,2:14:1:27:1:0.28152:4.41:60:6:0.0133:0:1.3 +7 151164470 . C A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCAGTAAGGCCACTGTC;RSEQ=ACCCCTCCTGACCCAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:0,57:57,2:0.0339:1,2:21.5:1:26.5:1:0.0339:0:60:4:0.0351:0:1 0/0:26:0:0,0:0,26:26,0:0:1,0:27.9:1:32.2:1:1:0:58.5:52:1:0:0 +7 151164622 . T TG 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCCCACCCCAGTGTCCTC;RSEQ=GACCTCAGGGTCCCTCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:18.3:1:33.7:1:1:0:60:6:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 151164844 . T C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=GCCCTCCCTATCTCCTGGCC;RSEQ=CTCCTCTCCTGCCCGTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:19.7:1:30.3:1:1:0:60:6:1:0:0.7 1/1:2:2:1,1:0,0:0,2:1:0,2:10:1:30.5:1:1:0:60:4:1:0:1 +7 151167575 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59918;SOR=2.31673;LSEQ=ACACAGGAGTGATCAAGACA;RSEQ=AGGTCAAATGCCAACTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:1:0,1:191,33:224,1:0.0044:2,0:1:0:23:0:0.15111:0:60:2:0.0045:0:1 0/1:195:2:1,1:156,37:193,2:0.0103:2,2:20.5:1:27:1:0.35258:4.17369:60:4:0.0104:0:1 +7 151168415 . CAAT C 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.00116;SOR=0.68933;LSEQ=AAATATTCTTGACATCAGAA;RSEQ=AATTAAAATGATACTTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:654:341:235,106:222,92:314,341:0.5214:2,2:25.3:1:32.3:1:0.67037:1.0883:60:682:0.523:0.0474:0.2 0/1:583:250:163,87:238,92:330,250:0.4288:2,2:23:1:31:1:0.0846:1.37996:59.9:249:0.4301:0.0961:0.2 +7 151168534 . G A 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.4872;LSEQ=ACATAATAGGTATTCTATTT;RSEQ=TAAGAAAAAAAAGACAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1183:650:342,308:263,263:526,650:0.5495:2,2:25.7:1:29.7:1:0.37933:1.11:59.9:80.25:0.5487:0:1.1 0/1:1162:433:216,217:352,373:725,433:0.3726:2,2:23.8:1:28.5:1:0.67103:1.05:59.9:85.6:0.3715:0:1.1 +7 151168756 . G A 201 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.02179;LSEQ=AGTTTTTAAATGTATGTTAT;RSEQ=TTGCCAGCTGGAAAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:93:19,74:92,322:414,93:0.1831:2,2:23.5:1:30.8:1:0.78221:1.11256:60:186:0.1849:0:1.2 0/0:413:2:1,1:98,312:410,2:0.0048:2,2:22:1:26:1:0.42329:3.17:60:4:0.0049:0:1 +7 151168830 . C T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10617;SOR=0.60368;LSEQ=AAAATGAACACAAAGAACTC;RSEQ=TGTTTTTTCCTAGCAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:137:74:0,74:2,61:63,74:0.5401:1,1:23:1:30.6:1:0.20964:0:59.6:73:0.5407:0:1.3 0/1:70:29:1,28:0,41:41,29:0.4143:1,1:23.4:1:29.8:1:0.41429:0:60:58:0.4203:0:1.1 +7 151174286 . C A 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04261;SOR=0.54773;LSEQ=CCAGCAATCCAGTTGCTCCA;RSEQ=GAGAAAATCACTAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:112:61:61,0:51,0:51,61:0.5446:1,1:24:1:30.9:1:1:0:60:122:0.5495:0:1.1 0/1:81:32:32,0:47,2:49,32:0.3951:1,1:22.6:1:30.4:1:0.51605:0:60:64:0.3951:0:1 +7 151174509 . GA G 103 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.34532;SOR=1.68724;LSEQ=TAGAATATTCATCCTGTGGG;RSEQ=AAAAAAATTATCTTTGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:892:7:3,4:333,552:885,7:0.0078:2,2:33.3:1:31.3:1:1:1.24:51:14:0.008:0:0 0/1:835:11:4,7:356,468:824,11:0.0132:2,2:28.4:1:29.9:1:0.76525:1.33075:50.9:22:0.0133:0.0024:0.3 +7 151175458 . G A 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGAATTACTGCCCTATG;RSEQ=TAAAGTTCTTTAAAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:20.7:1:30:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 151187851 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGATGGCAGGGGATGCAG;RSEQ=CATGGAAGGAAAAATCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:2,0:92,1:93,2:0.0208:1,0:29:0:34:0:1:0:60:4:0.0213:0:1 0/0:40:0:0,0:37,3:40,0:0:2,0:23:1:29.5:1:1:0:60:80:1:0:0.1 +7 151216510 . C T 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03062;SOR=Inf;LSEQ=GCTCCCAGGCGAGGCCCCGG;RSEQ=GGCGCGAGGAGGCCGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:208,82:290,0:0:2,0:17.7:1:31.9:1:1:0:59.9:71.5:1:0:0.2 0/1:301:6:2,4:200,94:294,6:0.0199:2,2:17.3:1:28:1:0.09151:4.23275:60:12:0.0203:0:1 +7 151216513 . C T 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.74736;SOR=0.76317;LSEQ=CCCAGGCGAGGCCCCGGCGG;RSEQ=GCGAGGAGGCCGCGCGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:5:2,3:220,88:308,5:0.016:2,2:17.6:1:28.4:1:0.14932:3.73178:60:10:0.0161:0:1.4 0/1:327:4:2,2:212,111:323,4:0.0122:2,2:12:1:27.3:1:0.61089:1.90594:57:8:0.0125:0:1.5 +7 151430709 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.08773;LSEQ=AAAAGTCATCTTTTTAGACC;RSEQ=TGTTAGTGAGTCTCCCGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:337:295:149,146:23,17:40,295:0.8754:2,2:26.2:1:30.1:1:0.50063:1.32459:60:41.143:0.8754:0:1.2 0/1:334:127:63,64:105,102:207,127:0.3802:2,2:25.6:1:29.5:1:0.91031:1.04564:60:62.5:0.3811:0:1.2 +7 151430890 . T C 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.12958;LSEQ=CTCCCAGGCTCAAGCGATCT;RSEQ=CCCACTTCAGCTTTCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:5:0,5:0,17:17,5:0.2273:1,0:36.4:1:31.2:1:1:0:60:10:0.2273:0:1 0/1:16:4:0,4:0,12:12,4:0.25:0,0:14.3:1:31.8:1:1:0:60:8:0.25:0:1 +7 151478602 . T C 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.6567;SOR=1.95517;LSEQ=TATGAAACTTATCATTGTCC;RSEQ=CTCTCACATGCGGGCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:4,8:1,3:4,12:0.75:2,2:21.1:1:32.1:1:1:1.46:60:24:0.75:0:1.8 1/1:14:12:4,8:1,1:2,12:0.8571:2,2:19.1:1:29.1:1:1:1.89743:60:24:0.8571:0:1.5 +7 151478613 . C T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19681;SOR=0.25669;LSEQ=TCATTGTCCTCTCTCACATG;RSEQ=GGGCCCCCCATAGTACCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:3,4:0,5:5,7:0.5833:0,2:19.4:1:29.9:1:0.20455:0:60:14:0.5833:0:2.1 0/1:8:2:0,2:1,5:6,2:0.25:2,0:16.5:1:30:1:1:0:60:4:0.25:0:3 +7 151828793 . T C 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=CTGGAACGCTGTTCCCACCA;RSEQ=GTTGGGTTACGTTGTAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:15:9,6:30,18:48,15:0.2381:2,2:25.1:1:30.6:1:1:1.10924:60:30:0.2459:0:1.1 0/0:54:0:0,0:27,27:54,0:0:2,0:24.2:1:28.8:1:1:0:60:108:1:0:0.1 +7 151828824 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22786;SOR=Inf;LSEQ=GTTGTAGGTTTGGCCGAAGT;RSEQ=AGCGTGGCGAGAGCAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:38,37:75,0:0:2,0:29.5:1:32.5:1:1:0:60:150:1:0:0.4 0/1:69:2:1,1:31,36:67,2:0.029:2,2:14.5:1:30.5:1:1:1.16:60:4:0.029:0:2 +7 151828951 . A AG 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCAGGGCTGGAGTGAGGG;RSEQ=GGGTAGTGGGAGGAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:19.5:1:29.7:1:1:0:60:12:1:0.1667:0 1/1:2:2:0,2:0,0:0,2:1:0,0:27.5:1:29:1:1:0:60:4:1:0:0 +7 151830436 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCAGGCTCAAGTGATCC;RSEQ=CCTGCCTCAGCCTCCCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:30.5:1:1:0:50:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 151830890 . G C 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CCACGTGACATGGGGCCAAA;RSEQ=GAGGATAGGAGAAGCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:19.3:1:25:1:1:0:60:2:1:0:1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:34.5:1:29:1:1:1:60:4:0.5:0:1 +7 151833641 . CA C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAACAAAACAAAAAACAAA;RSEQ=AAAAAAAAAGAAAAGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:14.5:1:31.8:1:1:0:60:4:0.1667:0.0833:0 0/0:2:0:0,0:2,0:2,0:0:0,0:27.5:1:30.5:1:1:0:60:4:1:0:0 +7 151833826 . A G 90 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01759;SOR=Inf;LSEQ=AAGTCATAAAACAGAAAACA;RSEQ=AAATCTCTTTCTGTCTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:118,11:129,0:0:2,0:20.6:1:30.8:1:1:0:60:63.5:1:0:0.1 0/1:157:7:7,0:130,20:150,7:0.0446:2,0:32.7:1:32.4:1:0.59648:0:60:14:0.0458:0:1 +7 151836188 . CT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49861;SOR=0;LSEQ=CGCCAGGCTGCCGTGAGAGC;RSEQ=TTCCCTTGGCTTCAGTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:121,32:153,2:0.0129:2,2:36:1:33.5:1:0.38157:3.739:60:4:0.0129:0:0 0/0:148:0:0,0:112,36:148,0:0:2,0:21.1:1:29.8:1:1:0:60:296:1:0:0.1 +7 151836228 . C T 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTCTCCACCAGCACTGGCC;RSEQ=CACAAGCAAAAGCACTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:161,89:250,0:0:2,0:24.6:1:30.8:1:1:0:60:61.5:1:0:0.1 0/1:260:17:10,7:153,90:243,17:0.0654:2,2:20.4:1:29.1:1:0.79742:1.18918:60:16:0.0635:0:1.3 +7 151836397 . T C 78 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00735;SOR=0;LSEQ=GTCGACCTGAAACTCCCCTC;RSEQ=GTGTTCCTATCCACACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:8:3,5:65,146:211,8:0.0364:2,2:24.9:1:26.1:1:0.70587:1.35:60:7:0.0324:0:1 0/0:215:0:0,0:60,154:214,0:0:2,0:21.6:1:29.4:1:1:0:60:41.8:0.9952:0:0.1 +7 151836659 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25257;SOR=0;LSEQ=TTTGTTTAAAGCTGAATGCA;RSEQ=CATGACAGATTTCATTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:1,2:189,8:197,3:0.015:1,2:8.7:1:28.3:1:0.0066:43.8613:60:6:0.0152:0:1 0/0:171:0:0,0:155,16:171,0:0:2,0:23.6:1:31.9:1:1:0:59.9:170:1:0:0.1 +7 151836878 . T TA 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.02228;SOR=2.38854;LSEQ=CAGCATACAGGCCCAGCCCC;RSEQ=AAAAAAAAGTGTGTACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:666:11:5,6:227,425:652,11:0.0165:2,2:29.6:1:29.1:1:0.52856:1.56:60:22:0.0168:0:0 0/1:596:23:13,10:228,343:571,23:0.0386:2,2:21.6:1:27.4:1:0.13111:1.95:60:46:0.0387:0.0084:0.3 +7 151836945 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23953;SOR=Inf;LSEQ=TTTTCTGTTTTTCATACAAA;RSEQ=GTTTCACCCTCGGGTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:12,168:180,0:0:2,0:23.3:1:31.3:1:1:0:59.9:44:0.9944:0:0.1 0/1:174:2:1,1:32,140:172,2:0.0115:2,2:14.5:1:28:1:0.34423:4.32:60:4:0.0116:0:1.5 +7 151841593 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19212;SOR=Inf;LSEQ=GGATTCCACTGGTCTGCTTT;RSEQ=CCTTTGGGGAAGCCAATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:16,0:16,0:0:1,0:26.4:1:32:1:1:0:57.6:32:1:0:0.1 0/1:13:2:1,1:11,0:11,2:0.1538:0,2:30.5:1:28:1:0.15385:0:60:4:0.1538:0:1 +7 151842217 . T C 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=3e-05;SOR=Inf;LSEQ=AGAAACCCTGGGCTGTACTA;RSEQ=GTGAAGTTAAAACAAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:461:0:0,0:306,155:461,0:0:2,0:24.5:1:30.8:1:1:0:60:75.833:1:0:0.1 0/1:423:14:10,4:274,135:409,14:0.0331:2,2:26.2:1:30.4:1:1:1.23:60:28:0.0336:0:1.2 +7 151842397 . C T 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.00021;SOR=Inf;LSEQ=GAAGCTGAAAAGAAGCAAAG;RSEQ=AGACACAAAGTCACCCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:113,289:402,0:0:2,0:24:1:32.2:1:1:0:59.9:56.429:0.9975:0:0.1 0/1:353:11:5,6:103,239:342,11:0.0312:2,2:24.2:1:27.3:1:0.3221:1.93:60:22:0.0318:0:1.2 +7 151843635 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50027;SOR=0;LSEQ=CATGTGTTCAAGTGGTCACA;RSEQ=TGAATCAGGAAAGCAATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:160,33:193,2:0.0103:2,2:18.5:1:32.5:1:0.31906:4.79162:60:4:0.0103:0:1 0/0:174:0:0,0:131,43:174,0:0:2,0:49:0:16:0:1:0:60:0:0:0:7 +7 151843648 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68989;LSEQ=GGTCACACTGAATCAGGAAA;RSEQ=CAATTCCAATCTCAAAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:1,2:180,63:243,3:0.0122:2,2:17:1:29:1:0.17143:5.6654:60:6:0.0123:0:1 0/0:237:2:0,2:170,65:235,2:0.0084:2,0:1:0:23.5:1:0.07906:0:60:4:0.0085:0:1 +7 151844858 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCAATGCAAATGACAGGC;RSEQ=ACCTTTATCTACAAATCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:9,1:10,2:0.1667:2,2:21:1:29.5:1:0.31818:6.70817:60:4:0.1667:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:32:1:31.5:1:1:0:60:4:1:0:0 +7 151846291 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20793;SOR=Inf;LSEQ=ATAATTCACAAGCCCGGAAA;RSEQ=CAATTCTTGTTAAGACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:27,143:170,0:0:2,0:23.8:1:32.4:1:1:0:59.9:84:1:0:0 0/1:143:2:1,1:19,122:141,2:0.014:2,2:18.5:1:28:1:0.26101:6.28:60:4:0.0141:0:1 +7 151847840 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13664;SOR=Inf;LSEQ=AAGGCTCCCTACACCCTCTC;RSEQ=TCCTCTGCCGGGTCAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:50,2:52,0:0:1,0:21.1:1:31.4:1:1:0:59.3:104:1:0:0 0/1:31:2:1,1:29,0:29,2:0.0645:1,2:18:1:27.5:1:0.06452:0:60:4:0.0667:0:1 +7 151847946 . G T 46 p8;q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05763;SOR=0;LSEQ=CCAGAACACAGAAGTCACTC;RSEQ=TTACACATTGTTATCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:4:0,4:201,77:278,4:0.0142:2,0:5.8:1:23:1:0.00645:0:60:3:0.0108:0:1 0/0:292:0:0,0:196,96:292,0:0:2,0:23.9:1:29.9:1:1:0:60:291:1:0:0.1 +7 151849692 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22409;SOR=Inf;LSEQ=GGACTATACGCCAGCATGTT;RSEQ=CCTGTCCGTTGTTAAAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:89,5:94,0:0:2,0:22.2:1:28.7:1:1:0:60:188:1:0:0.1 0/1:85:2:1,1:76,7:83,2:0.0235:2,2:27.5:1:30.5:1:0.18039:10.22258:60:4:0.0238:0:1 +7 151851197 . C T 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCAAAATATAAAGTGCCTGG;RSEQ=TCAGTTTTGATGTCATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:814:0:0,0:352,459:811,0:0:2,0:26.4:1:32.5:1:1:0:60:44.056:0.9962:0:0.1 0/1:748:35:17,18:320,392:712,35:0.0468:2,2:28.4:1:29.3:1:0.72933:1.16:60:70:0.0471:0:1.1 +7 151851275 . T A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06413;SOR=Inf;LSEQ=AGGAAAATAGTGTTAATGGA;RSEQ=TTTCAAAATCAAAATATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:0:0,0:217,210:427,0:0:2,0:24.5:1:30.9:1:1:0:60:105.75:1:0:0.1 0/1:286:3:2,1:122,161:283,3:0.0105:2,2:16.3:1:25.7:1:0.58086:2.63:60:2:0.0071:0:2.3 +7 151851663 . G C 73 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12013;SOR=3.90972;LSEQ=CTATACGATGAGCAGCAAAT;RSEQ=AATCAGCTCAGAGCCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:0,2:2,40:42,2:0.0444:1,0:33:1:33.5:1:1:0:60:4:0.0465:0:1 0/1:32:5:0,5:2,25:27,5:0.1563:2,0:22.4:1:31.8:1:1:0:60:10:0.1563:0:1 +7 151852951 . AG A 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.01603;SOR=Inf;LSEQ=ATACATTTATTTTTTTTAAA;RSEQ=AAGAAATAACTAAGAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:117,18:135,0:0:2,0:24.8:1:33.6:1:1:0:60:134:1:0:0.1 0/1:155:7:5,2:121,27:148,7:0.0452:2,2:29.9:1:30.1:1:0.61576:1.78472:60:14:0.0455:0.0065:0.6 +7 151853470 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50193;SOR=0;LSEQ=TTTAAATTATATGCTACTGA;RSEQ=CGAATATGCAATGACCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:32,117:149,2:0.0132:2,2:40.5:1:29.5:1:0.39046:3.62:60:4:0.0133:0:1 0/0:127:0:0,0:33,94:127,0:0:2,0:22.5:1:31.4:1:1:0:60:126:1:0:0.1 +7 151854778 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11064;SOR=Inf;LSEQ=AACTAAATACAAAAATAAGA;RSEQ=AAGCTCTATCAATTCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:241,59:300,0:0:2,0:22.2:1:32.5:1:1:0:59.9:600:1:0:0.1 0/1:278:3:1,2:209,66:275,3:0.0108:2,2:17.3:1:26.3:1:0.1492:6.28048:60:6:0.0109:0:2 +7 151855878 . G T 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59255;SOR=2.41933;LSEQ=CCAAAGTGCTGGGATTACAG;RSEQ=CATGAGCCACTGCCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:1:0,1:198,18:216,1:0.0046:2,0:1:0:25:0:0.08756:0:60:2:0.0047:0:1 0/1:181:2:1,1:168,11:179,2:0.011:2,2:23:1:24.5:1:0.12855:14.6648:55.5:4:0.0112:0:1 +7 151859061 . T TAGAAATG 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=2.000;MSILEN=7;SSF=0.01293;SOR=0;LSEQ=AAACATGGGTTCCAGAGAGG;RSEQ=AGAAATGACAAAATAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:10:10,0:62,1:63,10:0.1351:1,0:22.5:1:31.3:1:1:0:60:20:0.1389:0.0541:0 0/0:43:0:0,0:41,2:43,0:0:1,0:20.6:1:29.5:1:1:0:60:20.5:1:0:0 +7 151859129 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10479;SOR=Inf;LSEQ=AATAATGTGGAAATACAGTT;RSEQ=CTGGTACTAATCTGCTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:220,30:250,0:0:2,0:23.7:1:32.3:1:1:0:60:61.5:1:0:0.1 0/1:224:3:1,2:190,31:221,3:0.0134:2,2:11:1:26.3:1:0.05752:12.02486:60:6:0.0135:0:1 +7 151859670 . G T 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATATTGGGAGTGGATGGGCC;RSEQ=ACTGGTTCCACCGACTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:675:0:0,0:343,331:674,0:0:2,0:24.5:1:31.1:1:1:0:60:73.889:0.9985:0:0.1 0/1:620:31:14,17:306,282:588,31:0.05:2,2:19.1:1:28.7:1:0.46771:1.31704:60:30:0.0492:0:1.1 +7 151859683 . G A 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGGGCCGACTGGTTCCACC;RSEQ=ACTCTTGGTCGGCTTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:646:0:0,0:347,298:645,0:0:2,0:25.3:1:30.9:1:1:0:60:63.5:0.9984:0:0.1 0/1:637:46:26,20:315,276:591,46:0.0722:2,2:24:1:29.6:1:0.75951:1.14:60:92:0.073:0:1.1 +7 151866412 . GA G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.50441;SOR=0;LSEQ=AAAACTTTAAAAGAAAGAAA;RSEQ=AAAAAAGAAATGGAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:6,101:107,2:0.0183:2,2:34.5:1:31:1:0.12487:15.66:58.5:4:0.0183:0:3.5 0/0:86:0:0,0:9,77:86,0:0:2,0:23.3:1:29.9:1:1:0:60:172:1:0:0.1 +7 151868207 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51564;SOR=0;LSEQ=AATTGCGGTTTTTGCCACTG;RSEQ=CAAATGGCATATGGTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:106,1:107,2:0.0183:1,0:20.5:1:32:0:1:0:60:4:0.0189:0:1 0/0:74:0:0,0:74,0:74,0:0:1,0:23.2:1:30.9:1:1:0:60:73:1:0:0 +7 151871381 . T C 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.58956;SOR=2.46892;LSEQ=GTAATTAGTTCAACGTACAC;RSEQ=AAGAAGTAATTCAAATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:1:0,1:26,172:198,1:0.005:2,0:50:0:15:0:1:0:60:0:0:0:2 0/1:162:2:1,1:27,133:160,2:0.0123:2,2:11:1:28.5:1:0.31669:4.86:60:4:0.0126:0:1 +7 151873255 . G C 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TACCCATAGTAATATACGTT;RSEQ=AGACTCAAGAAAACTCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:476,244:720,0:0:2,0:26:1:32.3:1:1:0:60:64.455:1:0:0.1 0/1:583:21:15,6:336,225:561,21:0.036:2,2:20.2:1:31.3:1:0.36642:1.67:60:42:0.0367:0:1.4 +7 151873853 . C T 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.74854;LSEQ=GCAGGTAGTTGAGTGGATGC;RSEQ=TGAATGACATTTGCACTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1014:342:175,167:346,325:671,342:0.3373:2,2:24.2:1:31:1:0.94702:1.01593:60:84.5:0.3404:0:1.1 0/1:1032:486:251,235:260,285:545,486:0.4709:2,2:26.3:1:29.6:1:0.21258:1.17:59.9:43.182:0.4689:0:1.2 +7 151874060 . T C 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTTAGAATTTGGAGACAG;RSEQ=ACTTCCGTTTTTACCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1243:0:0,0:631,612:1243,0:0:2,0:25.5:1:29.1:1:1:0:60:112:1:0:0.1 0/1:1238:57:26,31:612,568:1180,57:0.046:2,2:22.6:1:31.3:1:0.41595:1.2844:60:56:0.0456:0:1.2 +7 151874147 . CT C 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.79846;SOR=0.93078;LSEQ=AGAGTTTTGTTTTCTTGTTC;RSEQ=TTTTTTTTGGTTCAACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:33:12,21:316,456:772,33:0.0408:2,2:27.3:1:32.8:1:0.71834:1.21243:60:66:0.0414:0.005:0.4 0/1:787:30:13,17:311,445:756,30:0.0381:2,2:28.6:1:30.5:1:0.8512:1.09:60:60:0.0385:0:0.1 +7 151874498 . C T 120 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00254;SOR=5.49858;LSEQ=TCCTCTAGACCATCAGAAGG;RSEQ=TGGGTGGTTATCTGTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:615:3:1,2:278,333:611,3:0.0049:2,2:23.3:1:25.3:1:1:1.66833:60:6:0.005:0:1.3 0/1:647:17:6,11:301,329:630,17:0.0263:2,2:29.9:1:29.6:1:0.33681:1.676:60:34:0.0266:0:1.2 +7 151874581 . G C 221 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTGAAAATTCACCACCTA;RSEQ=TGGATGGTTCAGAGTCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:114:60,54:282,254:536,114:0.1746:2,2:23.6:1:32.4:1:1:1.00:60:56:0.1742:0:1.1 0/0:670:0:0,0:357,312:669,0:0:2,0:24.8:1:31.5:1:1:0:60:166.25:0.9985:0:0.1 +7 151875047 . G A 193 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.02842;LSEQ=TGCTGAGGAGGCACAAGGAA;RSEQ=CGCTCTTGACTCGGCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:86:28,58:159,210:369,86:0.189:2,2:29:1:30.1:1:0.08826:1.56685:59.9:172:0.1982:0:1.2 0/0:457:3:0,3:191,262:453,3:0.0066:2,0:13:1:15.3:1:0.26815:0:43:0:0:0:6.3 +7 151875090 . C A 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25761;SOR=0;LSEQ=CATGACTACCTCCTGGAAAT;RSEQ=CAAATCTTTTAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:3:1,2:69,174:243,3:0.012:2,2:9.3:1:23:1:1:1.26:60:2:0.0102:0:1 0/0:200:0:0,0:75,124:199,0:0:2,0:9:0:12:0:1:0:60:0:0:0:6 +7 151875091 . C A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25758;SOR=0;LSEQ=ATGACTACCTCCTGGAAATC;RSEQ=AAATCTTTTAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:3:2,1:67,174:241,3:0.0122:2,2:16:1:22.7:1:0.19358:5.15:56.7:2:0.0102:0:3 0/0:196:0:0,0:74,121:195,0:0:2,0:29:0:17:0:1:0:29:0:0:0:3 +7 151876744 . TGGG T 68 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=15.000;MSILEN=1;SSF=0.35827;SOR=2.42293;LSEQ=TTTAAATTTGTTGAAGAGGT;RSEQ=GGGGGGGGGGGGTGGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:4:4,0:12,0:12,4:0.1667:0,0:20.8:1:34.3:1:1:0:52.3:8:0.1667:0:1.5 0/1:9:3:3,0:3,1:4,3:0.3333:2,0:12.7:1:33:0:1:0:56.7:6:0.3333:0:0 +7 151878923 . T C 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGCCCTAGGAGATGGTTTAG;RSEQ=AAAGTGATCACTGGTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:733:0:0,0:369,364:733,0:0:2,0:26.1:1:28.9:1:1:0:60:65.636:1:0:0.1 0/1:545:19:10,9:272,254:526,19:0.0349:2,2:29.2:1:31.4:1:1:1.04:60:38:0.0353:0:1.1 +7 151879433 . G A 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=67.88838;LSEQ=ATCTGAAGATGTAGACGTAG;RSEQ=GGTACTGGGTGGCTGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1169:1:1,0:561,606:1167,1:9e-04:2,0:1:0:25:0:0.48116:0:60:2:9e-04:0:1 0/1:1182:65:30,35:550,567:1117,65:0.055:2,2:27.9:1:29.7:1:0.70224:1.13157:59.7:31.5:0.0542:0:1.2 +7 151879937 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18206;SOR=Inf;LSEQ=ATTTTACTGAAAAGAGAAAC;RSEQ=AGTCTATCCTAAATCAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:173,1:174,0:0:1,0:25.7:1:31:1:1:0:59.9:173:1:0:0.1 0/1:130:2:2,0:127,1:128,2:0.0154:1,0:17.5:1:27:1:1:0:60:4:0.0157:0:1 +7 151882411 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTCCTTCCCCCCTAAAA;RSEQ=AGCTGATTTTCAATCTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:24.5:1:32.7:1:1:0:59.7:12:1:0:1.2 1/1:7:7:6,1:0,0:0,7:1:0,2:23.6:1:31.4:1:1:0:55:14:1:0:1.1 +7 151882672 . C A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00863;SOR=Inf;LSEQ=TGCTCTTTCTTGTGAGCTTG;RSEQ=TTTTCTCCACAATTTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:164,120:284,0:0:2,0:29.5:1:32.5:1:1:0:34.9:70:1:0:0.1 0/1:329:8:4,4:176,145:321,8:0.0243:2,2:32.5:1:30.5:1:1:1.21307:24.3:16:0.0245:0:1.4 +7 151884270 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03206;SOR=Inf;LSEQ=AATTAGTTAAGCTACCTTTC;RSEQ=ATTGCAGTTAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:114,8:122,0:0:2,0:22.8:1:32:1:1:0:59.8:121:1:0:0.5 0/1:91:4:4,0:80,7:87,4:0.044:2,0:20.5:1:31.8:1:1:0:57.5:8:0.0455:0:2.5 +7 151884272 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50745;SOR=0;LSEQ=TTAGTTAAGCTACCTTTCTA;RSEQ=TGCAGTTAAAAAAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:118,7:125,2:0.0157:2,2:27:1:30:1:0.12248:15.82823:60:4:0.016:0:1.5 0/0:96:0:0,0:87,9:96,0:0:2,0:20.8:1:29.5:1:1:0:59.9:47:1:0:0.4 +7 151884279 . TA T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.17093;SOR=0.64108;LSEQ=AGCTACCTTTCTATTGCAGT;RSEQ=AAAAAAAAAAAGGTATTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:34:34,0:110,9:119,34:0.2125:2,1:24.6:1:31:1:0.2084:0:59.2:33:0.2089:0.0313:0.6 0/1:129:19:17,2:87,18:105,19:0.1473:2,2:22.1:1:30.6:1:0.73576:1.75:60:38:0.1496:0.0388:0.1 +7 151884607 . C T 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00031;SOR=Inf;LSEQ=TTATGAACATAAAATAACTT;RSEQ=TTAATATATGTTCAAGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:0:0,0:62,219:281,0:0:2,0:22.4:1:32.9:1:1:0:60:139.5:1:0:0.1 0/1:230:10:3,7:44,175:219,10:0.0435:2,2:22.5:1:29:1:0.43241:1.70:60:20:0.0437:0:1 +7 151884963 . G T 37 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25177;SOR=0;LSEQ=AAAAATAATTCCGTTGGCAT;RSEQ=ATATTCACAAGTAACAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:3:1,2:25,167:192,3:0.0154:2,2:34.7:1:23.7:1:0.35059:3.31:60:2:0.0106:0:1.3 0/0:169:0:0,0:28,141:169,0:0:2,0:24.1:1:30.6:1:1:0:60:83.5:1:0:0.1 +7 151891018 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07871;SOR=Inf;LSEQ=TAAAGAATAGGGCAAAACTT;RSEQ=CTTGTGTGTGTATATGTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:132:0:0,0:123,9:132,0:0:2,0:20.9:1:32.5:1:1:0:60:131:1:0:0.1 0/1:100:3:2,1:87,10:97,3:0.03:2,2:23.7:1:23.3:1:0.29769:4.24719:60:2:0.0202:0:1 +7 151891255 . G A 211 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00685;LSEQ=GTAACAAGATTAAAAGACTA;RSEQ=TAGGGTCCTGGTATGGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:121:68,53:327,265:592,121:0.1685:2,2:26.6:1:30.5:1:0.92011:1.04:60:39.333:0.1676:0:1.1 0/0:723:1:1,0:391,328:719,1:0.0014:2,0:1:0:25:0:1:0:60:2:0.0014:0:1 +7 151891358 . TA T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.317;SOR=1.24276;LSEQ=GAATTGCTCCTAGAATAAAT;RSEQ=AAAAAAAAAAAGAAACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:49:11,38:131,234:365,49:0.1167:2,2:30.8:1:30.5:1:0.07738:1.93114:60:48:0.1171:0.0095:0.2 0/1:468:66:21,45:146,250:396,66:0.141:2,2:27.5:1:29.8:1:0.49:1.25083:59.9:65:0.1416:0.0128:0.2 +7 151896573 . G GGTTA 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.12306;SOR=Inf;LSEQ=AGATAAGCACATACAAAAAT;RSEQ=GTTAGAAAATTCTAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:40,137:177,0:0:2,0:24.8:1:31.8:1:1:0:60:176:1:0:0.1 0/1:183:4:2,2:46,133:179,4:0.0219:2,2:26.5:1:28.2:1:0.28161:2.87:60:8:0.0219:0:0 +7 151896582 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49842;SOR=0;LSEQ=CATACAAAAATGGTTAGAAA;RSEQ=TTCTAAAAAGACAATAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:31,125:156,2:0.0127:2,2:21.5:1:31.5:1:0.36507:3.98:60:4:0.013:0:1 0/0:156:0:0,0:40,116:156,0:0:2,0:23.4:1:29.5:1:1:0:60:77:1:0:0.1 +7 151899878 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.16069;SOR=Inf;LSEQ=TTTTATGGACCCCTGAAAGG;RSEQ=AAAAATGGCATTTATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:68,0:68,0:0:1,0:23:1:30.3:1:1:0:60:67:1:0:0 0/1:46:2:2,0:44,0:44,2:0.0435:1,0:23:1:30:1:1:0:60:4:0.0435:0:1 +7 151900186 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49901;SOR=0;LSEQ=ATTTATAAATATGTGACATT;RSEQ=AAAATTTCTAGACAAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:22,136:158,2:0.0124:2,0:15.5:1:34:0:1:0:60:4:0.0127:0:1 0/0:150:0:0,0:28,122:150,0:0:2,0:22.1:1:28.4:1:1:0:60:300:1:0:0.1 +7 151900951 . T A 30 d5;v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCTAGCCAGAACATAAGGAA;RSEQ=CCATGAAAAACAAAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:50:0:31:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:30:1:1:0:60:4:1:0:0 +7 151902156 . TA T 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.39394;SOR=1.57986;LSEQ=TCAAGACCAAAGGGTTACAT;RSEQ=AAAAAAAAATTTTTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:9:7,2:214,32:246,9:0.0353:2,2:23.3:1:30.2:1:0.34266:1.90483:59.1:18:0.036:0.0039:0.1 0/1:256:14:12,2:199,43:242,14:0.0547:2,2:22.4:1:28.9:1:1:1.30:57.5:28:0.0549:0.0234:0.4 +7 151902166 . A AT 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.44626;SOR=0.48656;LSEQ=AGGGTTACATTAAAAAAAAA;RSEQ=TTTTTTTTTAAGTCAGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:4:4,0:255,53:308,4:0.0126:2,0:25:1:28:1:1:0:45.5:3:0.0097:0:0.5 0/0:324:2:1,1:252,66:318,2:0.0062:2,2:12:1:27.5:1:0.37543:3.79709:53:4:0.0063:0.0031:0.5 +7 151919159 . GA G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.04672;LSEQ=TCTGAGGAAGGCACTGAAAC;RSEQ=AAAAAAAAAATCCAGGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:19:2,17:102,252:354,19:0.0505:2,2:22.1:1:31.6:1:0.11394:3.43182:31.8:38:0.0512:0.0027:0.2 0/1:379:20:4,16:126,231:357,20:0.0528:2,2:24:1:30.1:1:0.22697:2.17788:30:40:0.0535:0.0079:0.1 +7 151921255 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCTCCACAGTGTCTGCA;RSEQ=CAAACACACCTGAAATCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:30.5:1:1:0:55:4:1:0:1 +7 151927396 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61048;SOR=2.1587;LSEQ=CCTTATTTGATGAAATATCT;RSEQ=CAGTAGACACCTATAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:1:1,0:25,79:104,1:0.0095:2,0:1:0:27:0:0.24762:0:21:2:0.0095:0:1 0/1:98:2:1,1:38,58:96,2:0.0204:2,2:20.5:1:27:1:1:1.52:41:4:0.0204:0:1 +7 151927399 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2181;SOR=Inf;LSEQ=TATTTGATGAAATATCTGCA;RSEQ=TAGACACCTATAAAAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:25,76:101,0:0:2,0:33.3:1:33.3:1:1:0:22.3:202:1:0:0.1 0/1:89:2:1,1:32,55:87,2:0.0225:2,2:38.5:1:30:1:1:1.71:21:4:0.0227:0:1.5 +7 151932292 . G GTA 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGGTATCGTTTTCAAGGGT;RSEQ=TATATATATATATATATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:35:1:30.8:1:1:0:31.5:4:0.6667:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 151932761 . CAA C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=10.000;MSILEN=1;SSF=0.29029;SOR=0.58854;LSEQ=AGAAAACATAACCAGAGGCT;RSEQ=AAAAAAAAGCAAAGTAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:19:18,1:72,11:83,19:0.1712:2,1:8.1:1:31.5:1:0.45637:2.73:23.6:38:0.1727:0.1171:2.1 0/1:74:8:7,1:50,9:59,8:0.1081:2,2:6.6:1:30.3:1:1:1.26:22.9:16:0.1081:0.0811:2 +7 151932773 . C A 152 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.94848;LSEQ=CAGAGGCTCAAAAAAAAAAG;RSEQ=AAAGTAGGACAGTAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:29:27,2:96,14:110,29:0.2086:2,2:12.9:1:31.3:1:0.52315:1.96:22.6:28:0.2154:0:2.9 0/1:90:18:17,1:62,10:72,18:0.2:2,1:12.7:1:29.9:1:0.45225:2.72:21.8:36:0.2169:0:2.7 +7 151932774 . A G 49 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.28285;SOR=0;LSEQ=AGAGGCTCAAAAAAAAAAGC;RSEQ=AAGTAGGACAGTAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:1,2:125,14:139,3:0.0211:2,2:12:0:31:1:0.03356:17.11502:30.7:6:0.0213:0:2.3 0/0:91:0:0,0:79,12:91,0:0:2,0:24.6:1:29.5:1:1:0:30.4:29.333:1:0:0.6 +7 151932819 . T A 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.64919;SOR=0.84705;LSEQ=TTGACCTATTTATATGACTC;RSEQ=TAAGATCAAAATAACTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:29:27,2:196,25:221,29:0.116:2,2:39.3:1:30.4:1:0.75002:1.72:22.6:58:0.1198:0:2.9 0/1:200:20:18,2:156,24:180,20:0.1:2,2:38.5:1:29.4:1:1:1.38:22.3:40:0.1015:0:2.5 +7 151932824 . A T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25765;SOR=0;LSEQ=CTATTTATATGACTCTTAAG;RSEQ=TCAAAATAACTTGCTATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:217,24:241,3:0.0123:2,2:16.3:1:30:1:0.03071:17.63051:30.7:6:0.0128:0:2.3 0/0:195:0:0,0:169,26:195,0:0:2,0:28.1:1:28.3:1:1:0:24.4:47.75:1:0:0.3 +7 151932830 . A T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61649;SOR=0.7335;LSEQ=ATATGACTCTTAAGATCAAA;RSEQ=TAACTTGCTATGAGATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:10:9,1:202,24:226,10:0.0424:2,2:30.6:1:31.4:1:1:1.07:22.3:20:0.0431:0:4.2 0/1:191:6:6,0:159,26:185,6:0.0314:2,0:27.2:1:28:1:1:0:20.8:12:0.0316:0:4 +7 151932846 . T C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.61428;SOR=0.72349;LSEQ=CAAAATAACTTGCTATGAGA;RSEQ=TTTCATCATTAACTGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:10:9,1:179,20:199,10:0.0476:2,2:14.6:1:32.6:1:1:1.01:22.3:20:0.0498:0:4.2 0/1:172:6:6,0:142,23:165,6:0.0349:2,0:11.2:1:27.7:1:1:0:20.8:12:0.0353:0:4 +7 151932897 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23715;SOR=Inf;LSEQ=AAAATATACATGAAGCAAGC;RSEQ=TCACCCCAGGTAATACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:60,9:69,0:0:2,0:11:1:29.5:1:1:0:22.6:138:1:0:0 0/1:66:2:1,1:47,17:64,2:0.0303:2,2:18:0:31.5:1:0.47413:2.71525:53:4:0.0308:0:1.5 +7 151932967 . A T 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62638;SOR=0.40326;LSEQ=GCCTCGGCCACCTCGCCCCG;RSEQ=CAGTCCTGCACCTCGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:3:1,2:25,29:54,3:0.0526:2,2:13:1:29.7:1:1:1.70837:23.7:6:0.0526:0:1 0/1:46:1:0,1:23,22:45,1:0.0217:2,0:1:0:23:0:1:0:60:2:0.0222:0:1 +7 151933083 . GC G 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49878;SOR=0;LSEQ=AATAATTTTTAAATCCAAAT;RSEQ=CACTGAGATAAAACATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:36,157:193,2:0.0103:2,2:11:1:27.2:1:0.34428:4.32:60:4:0.0105:0.0051:0 0/0:190:0:0,0:41,147:188,0:0:2,0:22.2:1:30.2:1:1:0:30.4:61.667:0.9893:0:0.1 +7 151935868 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=GACCTTCTGAAATGTCTGGG;RSEQ=ACCAGGAAGGTGGGCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:19.4:1:32.6:1:1:0:26.9:20:1:0:0.3 0/1:10:2:1,1:4,4:8,2:0.2:2,2:32.5:1:27:1:1:1:48:4:0.2:0:1 +7 151944649 . T C 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=Inf;LSEQ=AATAGATGTTAGTTACTGTA;RSEQ=ACCCAAAACTATACTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:32:1:32:1:1:0:28:4:0.4:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:29.5:1:1:0:25:4:1:0:1 +7 151945007 . C T 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12202;SOR=2.89329;LSEQ=CTGTTTGGACCGAGGTCTAC;RSEQ=AGGAGAAAATTTTCTCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:5,3:5,5:10,8:0.4444:2,2:9.9:1:31.4:1:0.66406:1.62:21.6:16:0.4444:0:1.6 1/0:27:19:9,10:3,5:8,19:0.7037:2,2:14.8:1:29.4:1:0.69565:1.48:21.1:38:0.7308:0:1.4 +7 151945071 . G GT 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06669;SOR=1.52866;LSEQ=ATTTTTGGAGTGACTGAGAT;RSEQ=TAAGTTGTTGGCATGATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:39:14,25:81,98:179,39:0.1789:2,2:33.1:1:29.1:1:0.37314:1.47335:23.5:18.5:0.1737:0.0183:0.1 0/1:296:74:35,39:100,122:222,74:0.25:2,2:33.7:1:28.7:1:0.78806:1.09:23.5:17.5:0.2405:0.0068:0.2 +7 151945167 . G T 29 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTCTGAAGAAGGTGTTGG;RSEQ=GAGGAAGACACATCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:5.5:1:29:1:1:1:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 151945343 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49826;SOR=Inf;LSEQ=AAGTTCAGAATTTTCTTTCT;RSEQ=TTCCTTTTCTCCTTGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:58,62:120,0:0:2,0:24.8:1:32.5:1:1:0:21.7:240:1:0:0.1 0/1:126:2:1,1:66,58:124,2:0.0159:2,2:17:0:32:0:1:1.13676:24:4:0.016:0:1.5 +7 151945358 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=TTTCTGTTCCTTTTCTCCTT;RSEQ=TAGCCTTTCTATAACCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:67,66:133,0:0:2,0:35.7:1:32.3:1:1:0:22.5:65.5:1:0:0.1 0/1:146:2:1,1:80,64:144,2:0.0137:2,2:43.5:1:30:1:1:1.24807:23:4:0.0137:0:1.5 +7 151945672 . T A 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.45251;LSEQ=CTTCATTAGAAATCTGTTTT;RSEQ=CCAATTCAGTATTCACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:2:1,1:105,176:281,2:0.0071:2,2:13.5:1:24.5:1:1:1.67:33.5:4:0.0072:0:1 0/1:293:3:2,1:114,176:290,3:0.0102:2,2:18:1:26.3:1:0.56457:3.08:44:6:0.0103:0:1 +7 151946883 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.11895;SOR=Inf;LSEQ=CGTAATGTATATACATACAG;RSEQ=AATCGCAAAAATGTCTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:150,35:185,0:0:2,0:23.1:1:32.5:1:1:0:55.8:60.667:0.9945:0:0.1 0/1:181:3:2,1:141,37:178,3:0.0166:2,2:23.7:1:28.7:1:0.50905:1.89736:60:6:0.0166:0:1 +7 151946903 . G T 44 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.24901;SOR=0;LSEQ=CAATCGCAAAAATGTCTTTG;RSEQ=GATAAAGACATTATCTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:217,68:285,3:0.0104:2,2:7.7:1:28:1:0.14752:6.33055:60:6:0.0106:0:1 0/0:276:0:0,0:204,72:276,0:0:2,0:25:1:30.2:1:1:0:58.6:68:1:0:0.1 +7 151946985 . C G 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATAAGAAGACTATCTGTGT;RSEQ=AAGACTTTCTGAGGGATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:24:13,11:332,311:643,24:0.0359:2,2:26:1:31.5:1:0.83825:1.11:58.7:48:0.0361:0:1 0/0:795:0:0,0:413,382:795,0:0:2,0:25.9:1:30.8:1:1:0:59.8:131.5:1:0:0.1 +7 151948998 . TA T 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=9e-04;SOR=0;LSEQ=CATTACAAAAACAAAAAATT;RSEQ=AAAAAAAATCATTCTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:11:4,7:248,85:333,11:0.032:2,2:16.5:1:28.5:1:0.01006:5.07646:60:22:0.0324:0.0145:0.7 0/0:339:0:0,0:248,90:338,0:0:2,0:23:1:27.8:1:1:0:60:111.667:0.997:0:0.1 +7 151949068 . C G 143 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCTCACCTGGCTGTAAA;RSEQ=GATCCATCTCAGCTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:762:0:0,0:440,321:761,0:0:2,0:26.8:1:31.2:1:1:0:59.9:94.125:0.9987:0:0.1 0/1:747:25:11,14:392,329:721,25:0.0335:2,2:26.8:1:31:1:0.31624:1.51557:60:50:0.0338:0:1.1 +7 151949735 . T C 264 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTTGGTAACAATTGTCACA;RSEQ=ATCAGGCAATTGTGGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:829:308:129,179:206,314:520,308:0.3715:2,2:24.9:1:32:1:0.55796:1.10:60:101.667:0.372:0:1.1 0/0:835:0:0,0:354,478:832,0:0:2,0:24:1:28.2:1:1:0:60:137.667:0.9964:0:0.1 +7 151949832 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08374;SOR=Inf;LSEQ=GAAAAATAAAAACAAAAACA;RSEQ=TTTGTTATGCATTTGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:50,202:252,0:0:2,0:21.3:1:32.5:1:1:0:60:504:1:0:0.1 0/1:197:3:1,2:44,150:194,3:0.0152:2,2:12:1:24:1:0.54275:1.70:60:2:0.0104:0:3 +7 151949944 . C CT 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.53947;SOR=0;LSEQ=ACACTAATTTAGGGTACATG;RSEQ=TTTTTTTTTTTGAGATGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:0,3:0,23:23,3:0.1154:1,0:29.7:1:32:0:1:0:60:6:0.1154:0:0 0/0:14:0:0,0:0,14:14,0:0:1,0:20.2:1:31.6:1:1:0:59.2:13:1:0:0.1 +7 151961997 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.2029;SOR=Inf;LSEQ=AGTAATTTTTTTAAGTATGA;RSEQ=GAAGTCACTGAATGAATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:25,0:25,0:0:1,0:25.2:1:32:1:1:0:45.6:50:1:0:0 0/1:21:2:2,0:17,2:19,2:0.0952:2,0:20:0:33:0:1:0:41:4:0.0952:0:1 +7 151962176 . T A 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCAACCTGCACGTTTTAA;RSEQ=GGAGTAACCGCTATATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:32:0:1:0:47:4:1:0:1.5 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:31.5:1:1:0:41:4:1:0:1.5 +7 151970758 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12851;SOR=0;LSEQ=TTTCAGTAAATACATTGGTT;RSEQ=AAGTTTAAAAGTCTATCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:32,33:65,2:0.0299:2,2:22.5:1:30.5:1:1:1.03:21:4:0.0308:0:1.5 0/0:119:0:0,0:58,61:119,0:0:2,0:36.4:1:31.5:1:1:0:59.4:58.5:1:0:0.3 +7 151970806 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51209;SOR=Inf;LSEQ=TTACATCTTTCAGGAGCTTG;RSEQ=TCAATGTGTTCTGGACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:17,27:44,0:0:2,0:10.9:1:31.3:1:1:0:60:21:0.9767:0:0.2 0/1:65:2:1,1:22,39:61,2:0.0308:2,2:9.5:1:27.5:1:1:1.76:60:4:0.0308:0:1.5 +7 151983505 . AAT A 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.56568;LSEQ=AATCCTGAAAGCAGCCAGAG;RSEQ=ATCAAAACATTATTATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:0,1:2,6:8,1:0.1111:2,0:38:0:29:0:1:0:33:2:0.1111:0:0 0/1:12:2:0,2:2,8:10,2:0.1667:2,0:37:1:30:1:1:0:29.5:4:0.1667:0:0 +7 151983551 . A G 52 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28483;SOR=4.60474;LSEQ=GGAATAATGATACTACTGAC;RSEQ=CCACACCTGACTTCTCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:0,1:0,10:10,1:0.0909:0,0:10:0:34:0:1:0:30:2:0.0909:0:1 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:20:1:33.3:1:1:0:26.7:6:0.3333:0:1 +7 152006398 . AT A 31 d5;v3;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=21.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAATGGCTTACACAAATTA;RSEQ=TTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:31:1:1:0:42.5:4:1:0:1 +7 152011990 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52206;SOR=0;LSEQ=TTTAGTTTTGTGATCACACC;RSEQ=CTTTCATATACAATTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:10,0:10,3:0.2308:0,0:11:1:29.7:1:1:0:58:6:0.2308:0:1.3 0/0:5:0:0,0:5,0:5,0:0:0,0:23.2:1:29.8:1:1:0:60:10:1:0:0 +7 152012477 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49851;SOR=Inf;LSEQ=AAAAGTAGCTTTATTCAACT;RSEQ=CTTTAAGCGATAACTATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:17,141:158,0:0:2,0:22.3:1:32.2:1:1:0:60:38.5:1:0:0.1 0/1:162:2:1,1:21,139:160,2:0.0123:2,2:18.5:1:26:1:0.25389:6.49:60:4:0.0124:0:1 +7 152027452 . T C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01;SOR=Inf;LSEQ=GGTAATATTCTGTACTGGCC;RSEQ=GAGGTGACTAGAGTAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:22,0:22,0:0:1,0:16:1:31.9:1:1:0:58.9:44:1:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:29:1:26.5:1:1:0:60:4:0.6667:0:1 +7 152055618 . C A 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=CAAATGCTACATGCAGTGTA;RSEQ=AAACATATGCAAAGCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:530:0:0,0:397,133:530,0:0:2,0:22.7:1:32.3:1:1:0:59.9:264:1:0:0.1 0/1:509:13:10,3:359,136:495,13:0.0255:2,2:20.5:1:28.4:1:1:1.26:60:26:0.0259:0:1 +7 152055741 . T C 153 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=31.37065;LSEQ=GTCCTCATCTTCCACTGCAG;RSEQ=TTTCCCCCTACTTCGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:940:1:1,0:353,586:939,1:0.0011:2,0:27:0:26:0:0.3766:0:60:2:0.0011:0:1 0/1:958:31:10,21:347,577:924,31:0.0324:2,2:23:1:30.9:1:0.70635:1.26259:60:14.5:0.0309:0:1.3 +7 152055764 . C CA 66 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10799;SOR=0.25155;LSEQ=TCCCCCTACTTCGAGGTCTA;RSEQ=AGAAAAAAAAAAAAATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:598:8:1,7:162,415:577,8:0.0134:2,2:26:1:22.3:1:0.45378:2.72875:60:1.667:0.01:0.0017:2.8 0/0:589:2:0,2:172,396:568,2:0.0034:2,0:28:1:27:0:1:0:60:4:0.004:0:3 +7 152055780 . T A 73 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00081;SOR=Inf;LSEQ=TCTACAGAAAAAAAAAAAAA;RSEQ=AATAAGTACATAGAGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:0:0,0:81,346:427,0:0:2,0:23:1:28:1:1:0:59.5:17.565:1:0:0.5 0/1:421:10:8,2:96,313:409,10:0.0238:2,2:6.2:1:22.2:1:0.00033:12.94:56.5:1.5:0.0157:0:1.8 +7 152132473 . G T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGACTGAAAAGTAAAGTGT;RSEQ=CGGAGCCGGGCGCCGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:28:1:1:0:22:4:1:0:1 +7 152132689 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52584;SOR=Inf;LSEQ=CCGCCGCTGGCTCCCGGCCT;RSEQ=GCTCCCTCGCACTCAACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:43,29:72,0:0:2,0:10.9:1:30.9:1:1:0:21.8:35:1:0:0.5 0/1:117:2:1,1:66,47:113,2:0.0171:2,2:22:1:28:1:1:1.40002:21:4:0.0172:0:2 +7 152132690 . G T 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20853;LSEQ=CGCCGCTGGCTCCCGGCCTG;RSEQ=CTCCCTCGCACTCAACTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:46,29:75,1:0.0132:2,0:27:0:15:0:1:0:20:0:0:0:1 0/1:126:2:1,1:74,50:124,2:0.0159:2,2:6.5:1:28:1:1:1.47525:21:4:0.0161:0:1 +7 152132812 . C T 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGGCCGGGGCTCCAGGCTC;RSEQ=TCGGGGGGTGGTGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:779:0:0,0:372,407:779,0:0:2,0:24.9:1:31.7:1:1:0:53.5:42.278:1:0:0.2 0/1:1021:56:20,36:431,533:964,56:0.0548:2,2:22:1:29.5:1:0.21382:1.45501:45.7:55:0.0547:0:1.2 +7 152132933 . GGCC G 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=1.09505;LSEQ=TGGGGGGCTCCCGCCGCCGC;RSEQ=GCCGCCGCCGCCGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:0,2:15,96:111,2:0.0177:2,0:35.5:1:31.5:1:1:0:24:4:0.0182:0:0 0/1:155:3:0,3:37,115:152,3:0.0194:2,0:42:1:32:1:1:0:22.7:6:0.0195:0:0 +7 152132942 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0.16611;SOR=0;LSEQ=CCCGCCGCCGCGGCCGCCGC;RSEQ=GCCGCCGCTGCTGCTCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:8,82:90,2:0.0217:2,2:15.5:1:30:1:0.18705:9.72:29.5:4:0.023:0:1 0/0:133:0:0,0:26,106:132,0:0:2,0:24.8:1:28.7:1:1:0:44.1:25.4:1:0:0.1 +7 152132948 . C T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.19534;SOR=0;LSEQ=GCCGCGGCCGCCGCCGCCGC;RSEQ=GCTGCTGCTCGGGTTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:0,2:7,81:88,2:0.0222:2,0:20:0:29.5:1:1:0:29:4:0.0227:0:1.5 0/0:113:0:0,0:16,97:113,0:0:2,0:26.3:1:29.4:1:1:0:48.3:55.5:1:0:0.2 +7 152133893 . G T 25 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=AGCTGTGGACCCAGAGATCC;RSEQ=GGATCGGGATCGGGGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:35.3:1:31:1:1:0:60:8:1:0:0.3 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:18:1:25.5:1:0.33333:0:60:4:0.3333:0:1 +7 152345498 . GAA G 29 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=15.000;MSILEN=1;SSF=0.51648;SOR=3.98567;LSEQ=GAGTAAGACTGTTTCAAAAA;RSEQ=AAAAAAAAAAAAAGAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:6,0:6,2:0.1818:0,0:15:1:33.6:1:1:0:60:4:0.1818:0.0909:0 1/0:4:2:1,1:0,1:1,2:0.5:0,2:25.5:1:29.5:1:1:0:60:4:0.6667:0.25:0 +7 152346007 . C T 209 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0;SOR=16.67263;LSEQ=TCGTTGCAAAAAGAACCAGG;RSEQ=GATAGTCATTTACAAGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1285:9:0,9:629,645:1274,9:0.007:2,0:1.3:1:27.3:1:0.00385:0:60:18:0.0071:0:1 0/1:1425:150:79,71:627,648:1275,150:0.1053:2,2:25.5:1:29:1:0.43797:1.15:60:300:0.1066:0:1.1 +7 152346219 . CA C 121 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.70403;SOR=0.85934;LSEQ=GTGCTACTACTGCAGTACAC;RSEQ=AAAAAAATCTTCCCAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1304:14:5,9:664,626:1290,14:0.0107:2,2:28.2:1:31.9:1:0.28866:1.90833:58.7:28:0.0108:0.0015:0.1 0/0:1407:13:8,5:713,681:1394,13:0.0092:2,2:23.9:1:30.8:1:0.58083:1.53:60:26:0.0093:0.0014:0.2 +7 152357711 . G C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22694;SOR=Inf;LSEQ=AACTCTTGTGAGGAGTATGT;RSEQ=TATACATGTGAGCTTATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:182,12:194,0:0:2,0:25.3:1:32.7:1:1:0:60:193:1:0:0.1 0/1:177:2:1,1:160,15:175,2:0.0113:2,2:13.5:1:27:1:0.17309:10.36026:60:4:0.0115:0:1 +7 152357777 . A AT 173 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTTATTTATATAAAGGTTGT;RSEQ=TTTTTTACCATGCACAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:51:28,23:420,214:634,51:0.0745:2,2:26.9:1:30.5:1:0.12526:1.61102:60:102:0.0752:0.0117:0.2 0/0:782:0:0,0:483,294:777,0:0:2,0:25.4:1:28.4:1:1:0:60:76.7:0.9935:0:0.1 +7 152357922 . C A 47 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12806;SOR=Inf;LSEQ=TAAAAATATAAAATCCTAGA;RSEQ=ATCTATATTTATACCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:332:0:0,0:62,270:332,0:0:2,0:21.4:1:32.6:1:1:0:60:109.667:1:0:0.1 0/1:385:4:3,1:90,291:381,4:0.0104:2,2:6.8:1:23.5:1:0.04528:9.63:60:3:0.0079:0:1.8 +7 152357935 . A G 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09512;SOR=0;LSEQ=TCCTAGACATCTATATTTAT;RSEQ=CCATTTTCCGAAAGTCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:3:1,2:27,207:234,3:0.0127:2,2:26.3:1:30.7:1:0.31538:3.80:60:6:0.0127:0:1 0/0:281:0:0,0:56,224:280,0:0:2,0:19.9:1:29:1:1:0:60:139:1:0:0.1 +7 152357945 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23282;SOR=0;LSEQ=CTATATTTATACCATTTTCC;RSEQ=AAAGTCTGTAAGATTTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:13,158:171,2:0.0116:2,2:25.5:1:30:1:0.15573:11.75:60:4:0.0117:0:1 0/0:185:0:0,0:22,163:185,0:0:2,0:21.7:1:30.8:1:1:0:60:184:1:0:0.1 +7 152372816 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01282;SOR=Inf;LSEQ=GGGGTTTTTAGACCATAACT;RSEQ=TTGGGAGGAGAGACCTCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:10,1:11,0:0:2,0:24.3:1:33.2:1:1:0:60:22:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:29.5:1:32:1:1:0:60:4:1:0:1 +7 152372924 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8309;SOR=1.15371;LSEQ=CCCACCTCGGAGGACTCCAG;RSEQ=CTGCCCAGGGGCGGACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:34:34,0:25,0:25,34:0.5763:1,1:28:1:30.3:1:1:0:58.8:68:0.5763:0:1.1 1/0:36:22:21,1:14,0:14,22:0.6111:1,1:28.2:1:29:1:1:0:60:44:0.6111:0:1.1 +7 152372982 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50166;SOR=0;LSEQ=TGGCAGAGGGTGCCAGCATC;RSEQ=CGGGCGTCTAGGCCGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:135,3:138,2:0.0142:1,2:10:1:26:1:0.05653:39.09288:60:4:0.0146:0:1.5 0/0:119:0:0,0:116,3:119,0:0:1,0:22.4:1:29.8:1:1:0:60:118:1:0:0.2 +7 152373233 . A C 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCATTCACCAACTGCGCAG;RSEQ=CTCTACGGCCAGTCAAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:678:0:0,0:216,462:678,0:0:2,0:24.8:1:29.4:1:1:0:60:38.882:1:0:0.3 0/1:916:65:24,41:324,524:848,65:0.071:2,2:25:1:29.3:1:0.89507:1.05624:60:15.25:0.0682:0:1.2 +7 152373252 . C G 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=7e-05;SOR=1.74679;LSEQ=GACTCTACGGCCAGTCAAAC;RSEQ=CGCCCACCCGCGCGCGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:101:23,78:104,278:382,101:0.2091:2,2:24:1:30.9:1:0.44577:1.26806:60:32.667:0.2072:0:1.2 0/1:617:195:63,132:141,278:419,195:0.316:2,2:24.6:1:30:1:0.78281:1.06261:60:31.5:0.315:0:1.2 +7 152373367 . C T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03816;SOR=0;LSEQ=GTTCCTGTGACGTCAGACTT;RSEQ=CGCGTCCCCCGCGGCGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:4:0,4:2,28:30,4:0.1176:2,0:21.5:1:30:1:1:0:60:8:0.1212:0:1.3 0/0:41:0:0,0:0,41:41,0:0:1,0:15.4:1:30.5:1:1:0:60:40:1:0:0.1 +7 153621334 . T C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCCCGAGTAGCTGGGATTA;RSEQ=AGGCACATGTCACCACGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:33.5:1:1:0:26:4:1:0:1 +7 153622067 . T C 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCACCTACCTAGCTACAC;RSEQ=TGGTCTGGTTGTTGACATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:16:1:30:1:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 153622306 . G T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=3.7696;LSEQ=AGACCATCCGCATAGTAGAA;RSEQ=GTCCCCAAGATTCTGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:110:74,36:208,94:302,110:0.2657:2,2:24.9:1:30.6:1:0.81077:1.07629:60:35.667:0.2642:0:1.6 1/0:355:205:133,72:98,51:149,205:0.5775:2,2:22.7:1:29.7:1:0.91017:1.04015:60:204:0.5812:0:1.5 +7 153622382 . C G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.30846;LSEQ=TCTGATGAAGGGAGATCATC;RSEQ=CGCATGGTGGAGGGTCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:603:190:95,95:206,206:412,190:0.3151:2,2:27:1:30.3:1:1:1:60:26.143:0.3096:0:1.4 1/0:641:387:193,194:120,133:253,387:0.6037:2,2:25.5:1:30.1:1:0.57175:1.10:59.2:54.286:0.6061:0:1.5 +7 153622403 . A G 161 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=19.4912;LSEQ=CGCATGGTGGAGGGTCCCCG;RSEQ=GGTTCTGATGAAGAGAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:565:2:1,1:275,288:563,2:0.0035:2,2:8:1:21.5:1:1:1.05:60:1:0.0018:0:3 0/1:586:38:15,23:262,286:548,38:0.0648:2,2:26.3:1:30.7:1:0.40128:1.40385:59.7:76:0.066:0:1.2 +7 153622450 . G A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03439;SOR=1.45362;LSEQ=CATGGTTGAGGGTCCCTGCA;RSEQ=TTCTGATGAAGGGAGATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:75:34,41:180,229:409,75:0.1546:2,2:24.4:1:29.9:1:0.89949:1.05:60:36.5:0.1527:0:1.1 0/1:395:83:37,46:135,177:312,83:0.2101:2,2:27:1:29.7:1:0.90098:1.05:59.8:26.667:0.2067:0:1.2 +7 153622472 . C T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=4.40942;LSEQ=TCTGATGAAGGGAGATCATC;RSEQ=CGCATCGTGGAGGGTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:131:54,77:145,196:341,131:0.2775:2,2:26.3:1:30.4:1:0.83548:1.0548:58.5:25.2:0.2745:0:2.5 1/0:383:241:98,143:67,74:141,241:0.6292:2,2:22.5:1:28.4:1:0.20057:1.32016:59.3:25.778:0.6237:0:1.4 +7 153622478 . CG AA 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGGGAGATCATCCCGCAT;RSEQ=TGGAGGGTCCCTGAGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:41:17,24:185,241:426,41:0.0876:2,2:27.5:1:30.3:1:0.86985:1.08356:57.5:40:0.0897:0.0064:2.1 0/0:371:0:0,0:160,210:370,0:0:2,0:22.9:1:29.2:1:1:0:59.4:51.857:1:0:1 +7 153622479 . G A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.26005;LSEQ=AAGGGAGATCATCCCGCATC;RSEQ=TGGAGGGTCCCTGAGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:98:41,57:145,186:331,98:0.2099:2,2:24.2:1:30.4:1:0.81659:1.08356:58.7:31.667:0.2246:0:2.2 0/1:372:24:12,12:149,198:347,24:0.0645:2,2:21.9:1:29.2:1:0.52859:1.33:59.9:48:0.0652:0:2.5 +7 153622556 . A G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.29243;LSEQ=CGAGGTTCTGATGAAGGGAT;RSEQ=TCCTGCATGATCGAGGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:103:43,60:110,150:260,103:0.2837:2,2:24:1:31:1:1:1.0232:58.8:19.6:0.2808:0:1.7 0/1:328:34:18,16:137,157:294,34:0.1037:2,2:22.7:1:30.5:1:0.58687:1.29:55.7:16:0.0988:0:1.7 +7 153622591 . A G 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.41689;SOR=2.45402;LSEQ=GGGTCCCTGTGGTTCTGATG;RSEQ=GGGGAGATCATCCTGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:2:1,1:137,196:333,2:0.006:2,2:20:1:13.5:1:1:1.43:60:0:0:0:3.5 0/1:275:4:2,2:124,147:271,4:0.0145:2,2:23.3:1:30.8:1:1:1.18:51.5:8:0.0149:0:1 +7 153622662 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.14456;LSEQ=GACCACTCCATATGGTGGAG;RSEQ=GTCTCTGCAGTTCTGATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:78:32,46:68,85:153,78:0.3362:2,2:21.2:1:31.2:1:0.67454:1.1493:59.2:77:0.3438:0:1.8 0/1:206:14:9,5:92,100:192,14:0.068:2,2:31.1:1:29.2:1:0.27708:1.95:59.5:28:0.0697:0:1.9 +7 153622682 . T A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00352;SOR=2.64687;LSEQ=GGTCTCTGCAGTTCTGATAA;RSEQ=GGGAGATCATCCTGCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:215:180:77,103:16,19:35,180:0.8372:2,2:23.1:1:31.2:1:0.85243:1.12582:59:89:0.8357:0:1.4 1/1:205:191:93,98:9,5:14,191:0.9317:2,2:25.5:1:29.9:1:0.28334:1.89096:59.1:190:0.936:0:1.1 +7 153622714 . G T 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11836;SOR=Inf;LSEQ=CTGCATGGTAGAAGGTCCCT;RSEQ=AGGTTCTGATAAAGGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:105,121:226,0:0:2,0:25.8:1:32.5:1:1:0:59.2:112:1:0:0.8 0/1:219:3:1,2:104,112:216,3:0.0137:2,2:12:1:20:1:1:1.8521:60:2:0.0093:0:1.3 +7 153622715 . A T 44 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62341;SOR=0.33858;LSEQ=TGCATGGTAGAAGGTCCCTG;RSEQ=GGTTCTGATAAAGGGAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:3:1,2:104,120:224,3:0.0132:2,2:14.7:1:28:1:1:1.72931:58.3:6:0.0135:0:1.7 0/0:222:1:0,1:107,113:220,1:0.0045:2,0:1:0:28:0:1:0:60:2:0.0046:0:1 +7 153622749 . G T 103 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0;LSEQ=GGAGATCATCCCACATGGTG;RSEQ=AGGGTCCCTGAGGTTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:14:5,9:96,123:219,14:0.0601:2,2:22.8:1:27.2:1:0.59265:1.40288:58.9:6:0.0522:0:1.6 0/0:230:0:0,0:112,118:230,0:0:2,0:23.6:1:30.1:1:1:0:59.2:56.5:1:0:0.5 +7 153622819 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23365;SOR=Inf;LSEQ=TCCCCAAGGTTTGGATGAAC;RSEQ=GAGATCATCCCACATGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:23,78:101,0:0:2,0:24.7:1:30.7:1:1:0:60:49.5:1:0:0.2 0/1:95:2:1,1:29,64:93,2:0.0211:2,2:9:0:32:0:0.53415:2.19:60:4:0.0211:0:1.5 +7 153749753 . C T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.06993;SOR=Inf;LSEQ=TGGCGCGCGGGAGGAGCGGC;RSEQ=GCCGGCGCTGGGCTTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:1,2:3,3:6,3:0.3333:2,2:24.3:1:29.7:1:1:1.8525:26.3:6:0.375:0:1.3 1/1:4:4:2,2:0,0:0,4:1:0,2:42.8:1:30:1:1:0:28:8:1:0:1 +7 153749772 . TTGC T 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=1.29868;LSEQ=CCGCCGGCGCTGGGCTTGCC;RSEQ=TGCTGCTGCTGCTGCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:1,3:4,3:0.4286:2,2:31:1:28.3:1:1:1.41:26.3:6:0.4286:0:1.3 1/0:4:2:1,1:1,1:2,2:0.5:2,2:37:1:30:1:1:1:22:4:0.5:0:1 +7 153750177 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCTCGGGGGCGGGGGGCGG;RSEQ=GGCGGGTTCTCCGGGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:31.5:1:1:0:46:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 154594008 . G T 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00064;SOR=0;LSEQ=CCTCAAAGGCAATTTCAAAA;RSEQ=AAAATCCAAGAACATCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:12:8,4:91,49:140,12:0.0789:2,2:29.5:1:30.5:1:1:1.08:59.6:24:0.0795:0:1.2 0/0:126:0:0,0:69,57:126,0:0:2,0:27.5:1:30.7:1:1:0:57.9:252:1:0:0.4 +7 154594042 . TGATGGAATCAGGGTGGGGGCTGCGGGACCCCTGG T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=1;SOR=1.12821;LSEQ=ATCCGCACTAAGAGCAGCTC;RSEQ=GATGGAATCGGGGTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:8:3,5:99,79:178,8:0.043:2,2:19.9:1:30.1:1:0.47096:2.08039:25.9:16:0.043:0.043:1.3 0/1:145:7:4,3:70,67:137,7:0.0483:2,2:20.6:1:29.5:1:1:1.27:24.6:14:0.0486:0.0483:1.1 +7 154594052 . AGGGTGGGGGCTGCGGGACCCCTGGGATGGAATCG A 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=4.000;MSILEN=1;SSF=0.23182;SOR=0.7686;LSEQ=AGAGCAGCTCTGATGGAATC;RSEQ=GGGTGGGGGCTGCGGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:193:104:51,53:44,37:81,104:0.5389:2,2:20.6:1:32.3:1:0.55348:1.2344:54.8:208:0.5622:0.1865:0.7 0/1:148:70:40,30:31,39:70,70:0.473:2,2:18.6:1:30.6:1:0.17605:1.67:52.5:69:0.4929:0.25:0.7 +7 154594095 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50872;SOR=0;LSEQ=GGGATGGAATCGGGGTGGGG;RSEQ=CTGCGGGACTCCTGGGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:71,85:156,2:0.0127:2,2:25:1:29:1:1:1.20:57.5:4:0.0127:0:1.5 0/0:118:0:0,0:66,52:118,0:0:2,0:21.5:1:31.3:1:1:0:57.5:236:1:0:0.3 +7 154594099 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5874;SOR=2.50404;LSEQ=TGGAATCGGGGTGGGGGCTG;RSEQ=GGGACTCCTGGGATGGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:0,1:70,87:157,1:0.0063:2,0:23:0:29:0:1:0:29:2:0.0064:0:3 0/1:127:2:1,1:67,58:125,2:0.0157:2,2:27.5:1:27.5:1:1:1.15386:60:4:0.0157:0:1 +7 154594112 . A G 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09391;SOR=Inf;LSEQ=GGGGCTGCGGGACTCCTGGG;RSEQ=TGGAAATGGCGTCTCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:70,98:168,0:0:2,0:28.5:1:30.8:1:1:0:57.8:83:1:0:0.5 0/1:141:3:2,1:69,69:138,3:0.0213:2,2:23.3:1:24.3:1:1:1.99:60:2:0.0145:0:1.3 +7 154594127 . C T 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGGGATGGAAATGGCGTCT;RSEQ=TTGGAGGTTCAGGTGCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:35:12,23:46,80:126,35:0.216:2,2:26.1:1:29.6:1:0.84513:1.10146:57.5:16.5:0.2089:0:1.3 0/0:137:0:0,0:64,73:137,0:0:2,0:29.7:1:30.9:1:1:0:57.9:67.5:1:0:0.3 +7 154594141 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50079;SOR=0;LSEQ=GCGTCTCTTGGAGGTTCAGG;RSEQ=GCAATTTTTTCTCAGTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:2:1,1:49,98:147,2:0.0134:2,2:28:1:30.5:1:1:1.99:57.5:4:0.0136:0:1 0/0:129:0:0,0:58,71:129,0:0:2,0:30.6:1:28.7:1:1:0:58:63.5:1:0:0.3 +7 154594230 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01115;SOR=Inf;LSEQ=TCCTGCGGTCTTCATTCTAC;RSEQ=ATCCAAATTCTTTTGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:0,30:30,0:0:1,0:25.4:1:33:1:1:0:60:60:1:0:0 0/1:16:4:0,4:0,12:12,4:0.25:0,0:25.8:1:28.8:1:1:0:60:8:0.25:0:1 +7 154760119 . C T 28 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48897;SOR=Inf;LSEQ=TCTCCATTACTAACTCTCCA;RSEQ=TGCTGGATCATGTCCAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:14,6:20,0:0:2,0:26:1:32.5:1:1:0:60:40:1:0:0.1 0/1:22:2:1,1:12,8:20,2:0.0909:2,2:5:0:28:1:1:1.47192:60:4:0.0909:0:0 +7 154760182 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.4965;SOR=0;LSEQ=TGGTGGCTGCTGTTGCTGCT;RSEQ=CTGCTGCGGGGGCTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:34,2:0.0556:2,2:21:1:29:1:1:1.26:60:4:0.0571:0:1 0/0:30:0:0,0:12,18:30,0:0:2,0:24.6:1:30.8:1:1:0:60:14:1:0:0.1 +7 154760266 . TCTG T 32 v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=0.88734;LSEQ=TGGCGCTGTCTGACTTTGCA;RSEQ=CTGCTGCTGCTGCTGCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:7,14:21,2:0.08:2,2:36:0:32.5:1:1:1.94:60:4:0.087:0:0 0/1:14:1:0,1:5,7:12,1:0.0714:2,0:36:0:28:0:1:0:60:2:0.0769:0:0 +7 154760267 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52767;SOR=0;LSEQ=GGCGCTGTCTGACTTTGCAT;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:7,14:21,2:0.08:2,2:28:1:28.5:1:1:1.94:60:4:0.087:0:1 0/0:14:0:0,0:5,7:12,0:0:2,0:18.6:1:29.7:1:1:0:60:11:0.8462:0:0.3 +7 154760369 . A G 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.26354;SOR=0.33116;LSEQ=TGCTGCTGCTGGAGCTGGGC;RSEQ=AGCTGCTGCTGCTGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:7,4:5,2:7,11:0.6111:2,2:19.4:1:30.9:1:1:1.40086:57.8:22:0.6111:0:1 0/1:12:4:2,2:4,4:8,4:0.3333:2,2:25.5:1:29:1:1:1:60:8:0.3333:0:1 +7 154760495 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49198;SOR=Inf;LSEQ=TGTGGAGGATGCAACTGTTG;RSEQ=TGTGGAAACTGTAGCTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:15,0:0:2,0:17.2:1:32.1:1:1:0:60:30:1:0:0.2 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:7:0:31:1:1:1.40151:60:4:0.1053:0:1.5 +7 154760608 . TCTG T 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=1.04248;LSEQ=GGGGTAAGGTTGCTGAGAGA;RSEQ=CTGCTGCTGCTGCTGCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:16,2:0.1111:2,2:1.1:1:31.5:1:1:1.62:60:6:0.1175:0.1136:1.5 0/1:26:3:1,2:11,12:23,3:0.1154:2,2:35.3:1:31.7:1:1:1.79243:60:6:0.12:0:0 +7 154760666 . C T 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0419;SOR=Inf;LSEQ=TGGGGCTGAAGGTGTAAAAC;RSEQ=GGGTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:8,0:0:2,0:25.1:1:30.1:1:1:0:60:16:1:0:0.1 1/0:12:6:2,4:1,5:6,6:0.5:2,2:33.3:1:29:1:1:2.32:60:12:0.5:0:1.7 +7 154762322 . T G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAAATCCAGAAAAGAAGA;RSEQ=GGGACAATTCACCCCACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:33:0:1:0:60:4:1:0:1 +7 154798939 . G GA 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.23636;SOR=Inf;LSEQ=CTAGGAAAAATAAAAAATTA;RSEQ=AAAAAAAAAAGTAGATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:27,1:28,0:0:1,0:23.5:1:33.1:1:1:0:58.9:56:1:0:0.4 0/1:28:3:3,0:24,1:25,3:0.1071:1,0:14.7:1:29.6:1:1:0:60:6:0.1071:0.0357:0 +7 154799030 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.50601;SOR=0;LSEQ=TAGATTATTTCCAAATGGCT;RSEQ=TTTTTAAATGTATTTCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:120,61:181,2:0.0109:2,2:33:0:32.5:1:1:1.95946:60:4:0.011:0:1.5 0/0:143:0:0,0:93,50:143,0:0:2,0:24:1:30:1:1:0:60:286:1:0:0.8 +7 154799035 . T A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08109;SOR=0.67175;LSEQ=TATTTCCAAATGGCTTTTTT;RSEQ=AAATGTATTTCTATATTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:93:58,35:71,33:104,93:0.4721:2,2:24.8:1:29:1:0.45328:1.29659:60:92:0.4718:0:1.8 0/1:152:57:35,22:63,32:95,57:0.375:2,2:26.1:1:28.6:1:0.60079:1.23574:60:114:0.3775:0:1.6 +7 154799093 . T G 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03967;SOR=1.43525;LSEQ=TCATCTCTCCTGTTCAGCTA;RSEQ=CCATACATCCCTTAAAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:130:62,68:70,72:142,130:0.4745:2,2:25.7:1:32.5:1:0.8091:1.06605:60:64:0.4812:0:1.6 1/0:271:153:74,79:64,54:118,153:0.5646:2,2:27.6:1:31.3:1:0.39118:1.26415:60:152:0.5651:0:1.3 +7 155569538 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGTCACTGCCCACTCATT;RSEQ=CCACAGTTAGATACGGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 155571603 . A G 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01679;SOR=Inf;LSEQ=TCAGCGTGTGTGATGGCAGC;RSEQ=TGCTGTGCCGGCACATCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:9,12:21,0:0:2,0:26.5:1:30.9:1:1:0:60:42:1:0:0 0/1:29:7:4,3:10,12:22,7:0.2414:2,2:30.7:1:32:1:0.68166:1.57:60:14:0.2414:0:1.4 +7 155713471 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGGCTGGGAGGAGGGGCA;RSEQ=CTGTTCTCCGAGAAAAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 155714824 . T C 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCACCAGCGTCTCCCTGGC;RSEQ=CTGTGTGAAGCAGCCAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:35:24,11:0,0:0,35:1:0,2:24.5:1:31.3:1:1:0:60:34:1:0:1.1 1/1:26:26:15,11:0,0:0,26:1:0,2:24.2:1:30.4:1:1:0:60:52:1:0:1.1 +7 155714920 . C A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.12192;SOR=Inf;LSEQ=CGGGGGCCCTCCCTGGCCAG;RSEQ=TCAGCCCTCCTGCAGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:11,19:30,0:0:2,0:26.8:1:31:1:1:0:60:14:1:0:0.2 0/1:37:4:2,2:14,19:33,4:0.1081:2,2:35.3:1:24:1:1:1.35:60:3:0.0833:0:1 +7 155716465 . T A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACGGACATCGAGACCAA;RSEQ=CCCTGAGCTCCTCCTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:30:1:1:0:60:4:1:0:1.5 +7 155835193 . A G 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAACTGGGGGTCTCAGCA;RSEQ=TGCTGGGACTAGGGAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:7,2:0.2222:2,0:18:1:34.5:1:1:0:60:4:0.2222:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 155835521 . C T 116 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=29.50262;LSEQ=GGGATGGCCACTGGTCTCAC;RSEQ=GTAATTATTTGAGAAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:1:0,1:273,220:493,1:0.002:2,0:1:0:24:0:0.44737:0:60:2:0.0021:0:3 0/1:371:21:10,11:187,162:349,21:0.0566:2,2:22.5:1:26.5:1:0.65617:1.26892:58.6:4.25:0.0478:0:2.3 +7 155835541 . T TA 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.90421;LSEQ=CGTAATTATTTGAGAAGAAT;RSEQ=AATCCCCCCCCCCCAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:6:0,6:261,250:511,6:0.0115:2,0:22:1:24:1:0.01431:0:60:5:0.0102:0:2 0/1:383:4:0,4:199,178:377,4:0.0104:2,0:35:1:23.8:1:0.05117:0:57.5:3:0.0081:0:3.8 +7 155835544 . TC T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.04282;SOR=0.74467;LSEQ=AATTATTTGAGAAGAATTAA;RSEQ=CCCCCCCCCCAGGAAAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:557:196:97,99:162,172:334,196:0.3519:2,2:28.9:1:31.1:1:0.85736:1.04:59.7:38.2:0.3604:0.0251:0.3 0/1:403:116:58,58:134,137:271,116:0.2878:2,2:26.1:1:30.3:1:1:1.02:59.9:232:0.3118:0.1042:0.4 +7 155835549 . C A 125 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGAGAAGAATTAATCCCC;RSEQ=CCCCCCAGGAAAGCCTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:566:0:0,0:269,296:565,0:0:2,0:24.5:1:30.3:1:1:0:59.2:21.6:0.9982:0:1 0/1:362:21:11,10:163,175:338,21:0.058:2,2:26.1:1:28.6:1:0.82307:1.18:60:20:0.0573:0:2 +7 155835556 . A G 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.02848;LSEQ=AGAATTAATCCCCCCCCCCC;RSEQ=GGAAAGCCTTATCCAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:552:152:70,82:169,220:389,152:0.2754:2,2:24.3:1:28:1:0.63031:1.11:58.7:7.941:0.2789:0:2.1 0/1:372:162:78,84:89,110:199,162:0.4355:2,2:24.6:1:27.6:1:0.52617:1.15:59.4:11.462:0.4585:0:1.9 +7 155835626 . C G 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0234;SOR=0;LSEQ=GCTGAACAATGATATTTTGC;RSEQ=CAAAGCCTTCTTTCTGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:8:0,8:78,200:278,8:0.028:2,0:19.9:1:32.9:1:0.11248:0:59.4:16:0.0287:0:1.1 0/0:208:0:0,0:69,138:207,0:0:2,0:26.6:1:30.5:1:1:0:60:68:1:0:0.3 +7 155835631 . G T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01164;SOR=Inf;LSEQ=ACAATGATATTTTGCCCAAA;RSEQ=CCTTCTTTCTGTGAATTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:69,203:272,0:0:2,0:22.4:1:31.7:1:1:0:59.8:19.923:1:0:0.3 0/1:192:5:1,4:60,127:187,5:0.026:2,2:27.6:1:29.4:1:1:1.88428:60:10:0.0263:0:1.4 +7 155836562 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCATCGATCAACTCCATC;RSEQ=GTCCTTACACCCACCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 155973830 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=TTGCTCTGCACCAAGACATC;RSEQ=TCAAGCCTGCAGCCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:1,3:4,3:0.375:2,0:16:1:29:1:1:0:60:6:0.375:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:30.3:1:33.8:1:1:0:60:8:1:0:0 +7 156713290 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2458;SOR=Inf;LSEQ=GGGCAGGGTAAGGAGGGTGA;RSEQ=TCGTCCAAGTGATTGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:41,21:62,0:0:2,0:25.1:1:33.5:1:1:0:57:124:1:0:0.2 0/1:68:3:2,1:38,27:65,3:0.0441:2,2:31:1:30:1:1:1.41:57:6:0.0441:0:1 +7 157081587 . T C 31 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCTCCTGAGCCCCAGCTCC;RSEQ=GTGGGGGGATGTGAAGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:49:1:31.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:1:0:25:0:1:0:60:2:1:0:2 +7 157083569 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25237;SOR=Inf;LSEQ=GAGTCAGCGTTTCATGGGGA;RSEQ=AGAGATTCAGCTTGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:14,21:35,0:0:2,0:24.8:1:31.5:1:1:0:60:34:1:0:0.1 0/1:45:3:2,1:20,22:42,3:0.0667:2,2:35:1:24.3:1:0.60775:2.16:60:2:0.0465:0:1.3 +7 157083598 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49899;SOR=Inf;LSEQ=AGCTTGGGAAGATGGAAAGT;RSEQ=CTGCGGACGATGGAGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:9,15:24,0:0:2,0:29.3:1:30.1:1:1:0:60:48:1:0:0 0/1:31:2:1,1:10,19:29,2:0.0645:2,2:23.5:1:28:1:1:1.86:60:4:0.0645:0:1 +7 157745058 . G A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04396;SOR=0;LSEQ=CACGAAGGGAGACAGGCGAG;RSEQ=GTGGGACAGGCAAGGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:3,0:3,3:0.5:0,0:25:1:25.7:1:1:0:60:2:0.5:0:1.7 0/0:9:0:0,0:9,0:9,0:0:0,0:23.3:1:30.9:1:1:0:59.2:18:1:0:0.1 +7 157745070 . AAGGGTGGGTAGTGTGCATCCCTGAGACGGGGTGGGGGACACGGGGGGAGACAGGCG A 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00522;SOR=Inf;LSEQ=CAGGCGAGGGTGGGACAGGC;RSEQ=AGGGTGGGTAGTGTGCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:21:1:29.8:1:1:0:54.4:24:1:0:2.7 1/0:13:7:4,3:7,0:7,7:0.5385:0,2:19.4:1:28.4:1:0.19231:0:45.1:6:0.4615:0.3846:1.9 +7 157745089 . C G 124 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00014;SOR=0;LSEQ=CAAGGGTGGGTAGTGTGCAT;RSEQ=CCTGAGACGGGGTGGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:15:15,0:7,0:7,15:0.6818:0,1:19.1:1:31.8:1:1:0:55.5:14:0.6667:0:2.3 0/0:12:0:0,0:7,0:7,0:0:0,0:28.6:1:29.1:1:1:0:60:6:1:0:0.1 +7 157745114 . GGGGAGACAGGCGAGGGTGGGTAGTGTGCATGCCTGAGACGGGGTGGGGGACACA G 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.0123;SOR=Inf;LSEQ=AGACGGGGTGGGGGACACGG;RSEQ=GGGAGACAGGCGAGGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:35,3:38,0:0:2,0:22.6:1:29.7:1:1:0:58.4:11.667:1:0:1.4 0/1:29:5:3,2:18,4:22,5:0.1724:2,2:23:1:29.9:1:0.30312:2.85648:55:10:0.1852:0.0345:1.4 +7 157745168 . A GGG 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.49821;SOR=Inf;LSEQ=TGAGACGGGGTGGGGGACAC;RSEQ=GGGAGACAGGCGAGGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:67,49:116,0:0:2,0:25.6:1:30.6:1:1:0:60:11.889:1:0:0.6 0/1:122:2:1,1:73,43:116,2:0.0164:2,2:47.5:1:29.3:1:1:1.68965:24:4:0.0174:0:2.5 +7 157745220 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49836;SOR=Inf;LSEQ=TGACTCCGTGGTGGAACGTG;RSEQ=GTAGGTGATAGGCTGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:61,76:137,0:0:2,0:27.1:1:31.1:1:1:0:60:67.5:1:0:0.5 0/1:142:2:1,1:69,71:140,2:0.0141:2,2:24.5:1:31:1:1:1.03:60:4:0.0143:0:1 +7 157745232 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61701;SOR=2.08215;LSEQ=GGAACGTGGGTAGGTGATAG;RSEQ=CTGGCTCCCTGAGCAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:1:1,0:50,68:118,1:0.0084:2,0:1:0:26:0:0.42857:0:60:2:0.0088:0:1 0/1:115:2:1,1:50,63:113,2:0.0174:2,2:36.5:1:28:1:1:1.26:60:4:0.0179:0:1.5 +7 157745271 . T C 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.05629;LSEQ=CCTCCCCTGTGGTGCAGAGC;RSEQ=GTGGGTCTAGGGGTGAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:60:51:16,35:3,6:9,51:0.85:2,2:19.7:1:29.9:1:1:1.0921:60:50:0.8475:0:1 0/1:51:12:2,10:5,34:39,12:0.2353:2,2:22.2:1:29.5:1:0.66183:1.35:60:24:0.2353:0:1.3 +7 158387885 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCATGGTGGTGGAGGTGGA;RSEQ=CTGGTGATGATGGAGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:41:0:32:0:1:1.7321:60:4:0.4:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:4.5:1:29:1:1:0:60:4:1:0:2 +7 158387913 . G C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGATGGAGGTGGAGGTGTTA;RSEQ=TGGTGGTGACGCTGGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29:0:32:1:1:0:60:4:1:0:2 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:32:0:32:1:1:0:60:4:0.6667:0:2 +7 158387928 . G A 45 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.52923;SOR=Inf;LSEQ=TGTTAGTGGTGGTGACGCTG;RSEQ=TGGTGGTGGAGGTGGTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:5.1:1:30.9:1:1:0:37:18:1:0:1.2 0/1:17:3:2,1:6,8:14,3:0.1765:2,2:6:1:28.7:1:0.57647:2.52:33.3:6:0.1765:0:2.7 +7 158387936 . G A 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.57447;SOR=0.40906;LSEQ=GTGGTGACGCTGGTGGTGGT;RSEQ=GAGGTGGTGGTAGAGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:4,8:12,2:0.1429:2,2:6:0:28.5:1:1:1.90:60:4:0.1429:0:2 0/1:32:2:1,1:15,15:30,2:0.0625:2,2:9:0:30.5:1:1:1:60:4:0.0625:0:2 +7 158387945 . G A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19164;SOR=5.51539;LSEQ=CTGGTGGTGGTGGAGGTGGT;RSEQ=GTAGAGGTGGTGATGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:3,7:1,1:2,10:0.8333:2,2:18.2:1:29.1:1:1:2.16028:33.1:9:0.8182:0:1.3 1/1:30:29:14,15:1,0:1,29:0.9667:0,2:18.7:1:29.1:1:1:0:29.2:58:1:0:1.6 +7 158387955 . GTGA G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.07666;SOR=0;LSEQ=TGGAGGTGGTGGTAGAGGTG;RSEQ=TGGTGGTTATGGTGATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:10,2:0.1667:2,2:21:0:33.5:1:1:2.16:22:4:0.1818:0:0 0/0:30:0:0,0:15,15:30,0:0:2,0:21.2:1:27.8:1:1:0:29.5:14:1:0:1.6 +7 158387973 . A G 93 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26033;SOR=3.45496;LSEQ=TGGTGATGGTGGTTATGGTG;RSEQ=TGGTGGCGAAGTTGTAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:3,7:10,2:0.1667:2,2:7:0:34:0:1:2.16:31:4:0.1667:0:2 0/1:24:10:6,4:6,8:14,10:0.4167:2,2:5.1:1:28.2:1:0.68017:1.94:32.3:9:0.4286:0:2 +7 158387981 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGTTATGGTGATGGTGGC;RSEQ=AAGTTGTAACAGAGGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:11:1:29:1:1:0:60:4:0.6667:0:1 +7 158449534 . T C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTAGCACTTCCATGCTC;RSEQ=CCAATGCAGGAATAAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:31.5:1:1:0:60:4:1:0:1 +7 158450965 . A T 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.70738;SOR=0.92902;LSEQ=TGGTCTGCTGACATGAATTA;RSEQ=TAATTCAGCACAACAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:266:184:94,90:40,42:82,184:0.6917:2,2:23.6:1:30.5:1:0.79094:1.10:60:91:0.692:0:1.1 1/0:256:173:85,88:43,39:82,173:0.6758:2,2:23.9:1:29.9:1:0.68793:1.14088:59.6:346:0.6758:0:1.1 +7 158451054 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61243;SOR=2.13613;LSEQ=ATGGGGGGACAGCAGAGGCC;RSEQ=GCATAAAGGACATTAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:1:0,1:26,94:120,1:0.0083:2,0:2:0:17:0:1:0:60:0:0:0:2 0/1:114:2:1,1:33,78:111,2:0.0175:2,2:21:1:27:1:0.51312:2.34:60:4:0.018:0:1 +7 158451102 . T C 107 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02427;SOR=0;LSEQ=GGATCTTGCAGCGATCATCC;RSEQ=AAAAGCGAAAAAAGAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:9:0,9:2,49:51,9:0.15:1,0:18.8:1:33.8:1:1:0:60:18:0.1552:0:1.1 0/0:36:0:0,0:2,34:36,0:0:2,0:25.1:1:27.4:1:1:0:60:72:1:0:0.1 +7 158511431 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTAAGTGAAAGAAGCCAAT;RSEQ=TGAAAAGGCCGTATACTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:23.5:1:30:1:1:0:58:4:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 158512319 . T C 65 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTAAGTTAAAATATTCA;RSEQ=CTAGAGATGGACATGGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:7.5:1:32.5:1:1:0:60:8:1:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:13.7:1:32.3:1:1:0:60:6:1:0:1 +7 158512355 . AG A 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22474;LSEQ=GTAATGCACAACTAGAGTTC;RSEQ=CCACGCTTCCTTTCGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:35.5:1:34.5:1:1:0:60:8:0.8:0:1 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:31.4:1:32.3:1:1:0:60:10:0.8333:0.1667:0.6 +7 158512451 . T TGGC 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.06388;SOR=0;LSEQ=GGCTCCCGATGGATGTTCTC;RSEQ=GGCCTTTTAGAAAACGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:2,0:5,4:9,2:0.1818:2,0:28.5:1:33.2:1:0.49091:0:35.5:4:0.1818:0:0.5 0/0:31:0:0,0:18,12:30,0:0:2,0:27.7:1:29.9:1:1:0:44.9:60:1:0:0.6 +7 158512485 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACGTGGAGTTGTTCCTTTGG;RSEQ=CACGTATATGCGAGTCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:21,0:0:2,0:27:1:31:1:1:0:45.2:42:1:0:0.6 0/1:44:2:1,1:24,18:42,2:0.0455:2,2:8:0:30.5:1:1:1.32452:60:4:0.0488:0:1.5 +7 158512522 . A G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01127;SOR=4.48806;LSEQ=TATAAGAAAGGTGATACTGT;RSEQ=GACATCAAGGGAATAGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:5,8:5,7:12,13:0.52:2,2:27.2:1:32.1:1:1:1.13676:43.3:26:0.52:0:1.1 1/1:36:30:12,18:2,4:6,30:0.8333:2,2:26.9:1:30.7:1:1:1.32:46.9:60:0.8571:0:1.2 +7 158512748 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCCGCAGAGAAAGGTAC;RSEQ=TGCTTCAACTAAAGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:32.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +7 158512836 . T C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTGAGCTGCTGGAAGCTA;RSEQ=TCCCTGTGAATTCATGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:31:0:35:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:30.5:1:1:0:60:4:1:0:3 +7 158512856 . T C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTGTGAATTCATGACA;RSEQ=CATAGGTGTTCAAATAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:11:0:33:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:29.5:1:1:0:60:4:1:0:3 +7 158604837 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCACCCTGGAGAGGGCA;RSEQ=CCTGTGCCCACTCTGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39.5:1:28:1:1:0:60:4:1:0:1 +7 158628009 . A G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.04443;LSEQ=CCTTCTTACCCTGCCCCCTT;RSEQ=TCTTGTATGCAATAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:20:10,10:6,11:17,20:0.5405:2,2:22.2:1:31.5:1:0.50847:1.80:50.8:40:0.5556:0:1.1 0/1:42:2:1,1:16,24:40,2:0.0476:2,2:5:0:28.5:1:1:1.49:60:4:0.0476:0:0.5 +7 158628016 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49344;SOR=Inf;LSEQ=ACCCTGCCCCCTTATCTTGT;RSEQ=TGCAATAAATATCAGCGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:12,20:32,0:0:2,0:22.7:1:30.1:1:1:0:54.3:64:1:0:0.6 0/1:35:2:1,1:11,22:33,2:0.0571:2,2:12.5:1:29.5:1:1:1.96:57.5:4:0.0588:0:1 +7 158951489 . A AC 74 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCACTGCTGAGGCTGAAGG;RSEQ=CCACCTCCCACCGGGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:23.2:1:32.2:1:1:0:60:10:1:0.4:0 1/1:1:1:1,0:0,0:0,1:1:0,0:38:0:34:0:1:0:60:2:1:0:0 +7 158951622 . C T 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29551;SOR=3.86387;LSEQ=GGCCTCTCTCTGTCTCTCCA;RSEQ=GTGGGCTCTCTGTGTGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:10,9:19,2:0.0952:2,2:14:0:32.5:1:1:1.10554:60:4:0.0952:0:1.5 0/1:10:3:2,1:6,1:7,3:0.3:2,2:21.3:1:31.7:1:1:2.64575:60:6:0.3:0:1 +7 158951648 . G GC 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTGTGTGGCTGGGGCT;RSEQ=CCACGTGTGTGGAGTCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:26:13,13:0,0:0,26:1:0,2:29.9:1:31.6:1:1:0:60:52:1:0.0385:0.7 1/1:14:14:8,6:0,0:0,14:1:0,2:30.3:1:30.1:1:1:0:60:28:1:0.0714:1.1 +7 158951696 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCACATGGAGTGGCTTCC;RSEQ=GAAGGCAGGTGACATCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:6,13:0,0:0,19:1:0,2:29.3:1:30.6:1:1:0:60:38:1:0:1.1 1/1:14:14:6,8:0,0:0,14:1:0,2:27.4:1:30.8:1:1:0:60:28:1:0:1.2 +8 564840 . T A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGACTGATCTGAAAAAGCA;RSEQ=CCTTCGTGACAGGTGGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:35:1:30.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 564944 . G C 86 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TCTGGGAAATGCACTTATTA;RSEQ=GAGAGGGACAAACTGTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:28.2:1:33.5:1:1:0:60:12:1:0:2 1/0:2:1:1,0:1,0:1,1:0.5:0,0:26:0:27:0:1:0:60:2:0.5:0:2 +8 564957 . C G 81 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.41667;SOR=0.21822;LSEQ=CTTATTAGGAGAGGGACAAA;RSEQ=TGTGACTGAGCCACAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:31:1:31.5:1:1:0:60:5:0.8333:0:2 1/0:2:1:1,0:1,0:1,1:0.5:0,0:13:0:26:0:1:0:60:2:0.5:0:2 +8 565200 . G T 41 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06571;SOR=0;LSEQ=GTTCCTCTTGACCTGGAATT;RSEQ=TCCAAGTCAGCACCACAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:152,120:272,3:0.0109:2,2:6:1:26.3:1:0.58622:2.52493:60:6:0.0111:0:1 0/0:405:0:0,0:212,188:400,0:0:2,0:27.1:1:31.3:1:1:0:60:132.333:0.9876:0:0.6 +8 565219 . C G 105 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00702;SOR=Inf;LSEQ=TGTCCAAGTCAGCACCACAG;RSEQ=TGGTTAAGGCAGCCCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:150,144:294,0:0:2,0:26.3:1:32.5:1:1:0:60:72.5:1:0:0.2 0/1:430:10:5,5:216,204:420,10:0.0233:2,2:35.3:1:31.7:1:1:1.05871:60:20:0.0236:0:2.1 +8 565232 . C G 238 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCACAGCTGGTTAAGGCAG;RSEQ=CCCTCTCTCTTTCCTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:296:0:0,0:142,154:296,0:0:2,0:25:1:31.5:1:1:0:60:36:1:0:0.2 1/0:424:219:112,107:102,103:205,219:0.5165:2,2:26.7:1:30.7:1:0.84592:1.06:59.9:53.75:0.5193:0:1.2 +8 565280 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17694;SOR=0;LSEQ=TTGGCTTTAAGTCTGCTTAG;RSEQ=ACTCCTGGAAAATCAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:71,117:188,2:0.0105:2,2:19.5:1:28:1:1:1.64:60:4:0.0108:0:1 0/0:261:0:0,0:99,161:260,0:0:2,0:25.2:1:30.3:1:1:0:59.9:129:1:0:0.5 +8 565303 . G T 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01154;SOR=Inf;LSEQ=TCCTGGAAAATCAGGTTAAG;RSEQ=GAGATCAGTTGTGTTCATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:39,101:140,0:0:2,0:22.4:1:31.3:1:1:0:60:280:1:0:0.1 0/1:186:8:2,6:57,121:178,8:0.043:2,2:19.4:1:26.9:1:1:1.41076:60:7:0.0387:0:1.6 +8 566375 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTCGGCCAGGTGTGGGCGGC;RSEQ=GCCGTCCAGAGAGAAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:29:1:1:0:60:4:1:0:1.5 +8 566417 . C T 49 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACGTGTGTGAGGCTGAC;RSEQ=GAACCCCGCACACCCCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:13.3:1:31:1:1:0:43.7:6:1:0:2.7 +8 566429 . A C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCTGACCGAACCCCGCAC;RSEQ=CCCCATGCTCTCCTGGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:32:0:1:0:35.5:4:1:0:3 +8 566432 . C G 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGACCGAACCCCGCACACC;RSEQ=CATGCTCTCCTGGCTAAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:31.5:1:1:0:35.5:4:1:0:3 +8 2387881 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14289;SOR=0;LSEQ=ATTTAAATATCTGGCTCTAG;RSEQ=TGTTTTCACCATAATCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:52,17:69,2:0.0282:2,2:34.5:1:30:1:0.44547:3.00108:60:4:0.0282:0:1 0/0:116:0:0,0:85,31:116,0:0:2,0:21.8:1:28.7:1:1:0:60:115:1:0:0.1 +8 2387959 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14494;SOR=0;LSEQ=ACTCTCTCGTCCACGCTGGA;RSEQ=CCAAATAAATGCACTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:94,92:186,2:0.0106:2,2:9.5:1:30:1:1:1.02163:60:4:0.0109:0:1 0/0:305:0:0,0:151,152:303,0:0:2,0:26.8:1:31.5:1:1:0:60:100:0.9967:0:0.7 +8 2387976 . A G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.77916;SOR=0.94679;LSEQ=GGAGCCAAATAAATGCACTC;RSEQ=TCCTATTTGCTGAAGAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:190:112:49,63:40,37:77,112:0.5895:2,2:28.4:1:31.1:1:0.30063:1.3875:60:224:0.6022:0:1.6 1/0:302:174:80,94:62,63:125,174:0.5762:2,2:25.4:1:30.3:1:0.55871:1.15578:60:173:0.5786:0:1.1 +8 2387994 . T C 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=TCATCCTATTTGCTGAAGAG;RSEQ=GTGATTAATGCTCTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:49:20,29:57,70:127,49:0.2784:2,2:23.9:1:29.8:1:0.73494:1.1796:60:48:0.2775:0:2.1 0/0:278:0:0,0:123,155:278,0:0:2,0:24.1:1:29.1:1:1:0:60:277:1:0:0.7 +8 2388081 . A C 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58289;SOR=0.80381;LSEQ=TCAATGTCAGATTATTATGC;RSEQ=TGAGACCATAACTTCAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:23:4,19:3,26:29,23:0.4423:2,2:17.6:1:33.1:1:0.68559:1.80:60:46:0.4423:0:1.2 0/1:72:28:9,19:11,33:44,28:0.3889:2,2:26.3:1:30.8:1:0.59294:1.41:60:56:0.3889:0:1.3 +8 2388159 . G C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.68817;SOR=0.59617;LSEQ=GAGAGTGTCGTGTGTGTGTG;RSEQ=GTTGGTGTGTGCAAGTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:4,6:0.6:0,0:18.8:1:31.2:1:1:0:60:12:0.6667:0:2.2 0/1:15:7:0,7:0,8:8,7:0.4667:0,0:26.4:1:31:1:1:0:60:14:0.4667:0:2.1 +8 2388179 . G C 66 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.68659;LSEQ=GGTTGGTGTGTGCAAGTGTT;RSEQ=ACCTGCCAACACTGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:16.5:1:34:0:1:0:60:4:0.5:0:2.5 0/1:10:4:0,4:0,6:6,4:0.4:0,0:15.3:1:33:0:1:0:60:8:0.4:0:2.5 +8 3174523 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGAGGCAAGAGTGTGTGC;RSEQ=TGGATGAAGCATGCACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 3176240 . G A 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTTTGGGTGGTGGTCACA;RSEQ=GAGTTCCCTAGCTGGAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:31.5:1:27:1:1:0:51.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 3176263 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCCTAGCTGGAGTGTCA;RSEQ=GGTTCCTTCTGCAGGGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:8.5:1:28:1:1:0:51.5:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 3176512 . A T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.42365;LSEQ=TTATACAAAGGGAGACCCAG;RSEQ=AACACAACAACACAGATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:1:0,1:71,11:82,1:0.012:2,0:1:0:24:0:0.14458:0:60:2:0.0122:0:1 0/1:117:2:1,1:105,10:115,2:0.0171:2,2:8:1:28:1:0.17993:10.05896:60:4:0.0175:0:1 +8 3176527 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15845;SOR=0;LSEQ=CCCAGAAACACAACAACACA;RSEQ=ATTCAGCCATTCCTATGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:82,19:101,2:0.0194:2,2:25:1:29.5:1:0.35218:4.23209:60:4:0.0198:0:1 0/0:155:0:0,0:124,31:155,0:0:2,0:24.8:1:31.2:1:1:0:60:76.5:1:0:0.1 +8 3176558 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11833;SOR=0;LSEQ=TCCTATGGATCACTCCCTTA;RSEQ=ACAGAATGGAATTTGATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:2:1,1:101,48:149,2:0.0132:2,2:30.5:1:30:1:0.54517:2.09292:60:4:0.0132:0:1.5 0/0:287:0:0,0:185,102:287,0:0:2,0:23.9:1:31:1:1:0:60:56.4:1:0:0.3 +8 3176639 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20374;SOR=0.80758;LSEQ=GTCTTGCATCCAGATAATAA;RSEQ=TGAAGAAGTAACTTCCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:243:144:57,87:46,53:99,144:0.5926:2,2:28.2:1:30.6:1:0.29405:1.32316:59.9:47:0.5875:0:1.3 1/0:474:256:118,138:104,113:217,256:0.5401:2,2:24.6:1:29.5:1:0.71214:1.07618:59.8:84.333:0.5406:0:1.2 +8 3176670 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12227;SOR=0;LSEQ=ACTTCCTTGCTGAAAAGGCC;RSEQ=AGCTTTTAAAAAAAATCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:65,119:184,2:0.0108:2,2:40.5:1:32:1:1:1.82:60:4:0.0108:0:1 0/0:345:0:0,0:141,202:343,0:0:2,0:25.3:1:28.3:1:1:0:59.8:56.167:0.9941:0:0.7 +8 3176692 . A G 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.19724;LSEQ=GCTTTTAAAAAAAATCTAGG;RSEQ=ATAAATGGTCAAAAAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:32:11,21:29,66:95,32:0.252:2,2:23.4:1:31.3:1:0.66759:1.19:60:31:0.248:0:1.8 0/1:258:16:6,10:80,162:242,16:0.062:2,2:25.1:1:29.3:1:0.78588:1.21:60:15:0.0588:0:1.9 +8 3176717 . C G 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.32706;SOR=Inf;LSEQ=ATGGTCAAAAAAATGAAACT;RSEQ=ACATATTTCTGTTTTTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:20,57:77,0:0:2,0:20.6:1:32.5:1:1:0:60:154:1:0:0.6 0/1:175:5:1,4:42,128:170,5:0.0286:2,2:36:1:32.6:1:1:1.31058:60:10:0.0289:0:1.2 +8 3489660 . T C 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29901;SOR=Inf;LSEQ=AACATTTTCTTTAACATTCC;RSEQ=GCTAGAGAAAAGGGATTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:57,11:68,0:0:2,0:23.2:1:31.5:1:1:0:60:67:1:0:0.7 0/1:111:4:2,2:85,22:107,4:0.036:2,2:25.5:1:28:1:0.20358:3.80255:60:8:0.036:0:1 +8 3489668 . A C 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00066;SOR=Inf;LSEQ=CTTTAACATTCCTGCTAGAG;RSEQ=AAAGGGATTTATTTTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:69,18:87,0:0:2,0:20.7:1:29.5:1:1:0:60:20.75:1:0:0.7 0/1:142:15:12,3:90,37:127,15:0.1056:2,2:26.8:1:31.5:1:0.55717:1.64:60:30:0.1064:0:1.1 +8 3489674 . G A 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11627;LSEQ=CATTCCTGCTAGAGAAAAGG;RSEQ=ATTTATTTTAAAAAATTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:27:23,4:60,21:81,27:0.2477:2,2:20.4:1:30:1:0.29868:2.00:60:54:0.25:0:2 0/1:164:6:5,1:109,49:158,6:0.0366:2,2:22:1:29:1:0.66819:2.24:60:12:0.037:0:2 +8 3489677 . T C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.09784;LSEQ=TCCTGCTAGAGAAAAGGGAT;RSEQ=TATTTTAAAAAATTCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:30:25,5:60,21:81,30:0.2703:2,2:19.4:1:32.3:1:0.44943:1.74:60:60:0.2778:0:2 0/1:173:6:5,1:113,54:167,6:0.0347:2,2:25:1:31.3:1:0.66592:2.38:60:12:0.0349:0:2 +8 3489756 . G C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=7.3201;LSEQ=GAAAATGCAATCATTTCTAG;RSEQ=GCTGGGCTTTAACCATTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:18:10,8:101,104:205,18:0.0804:2,2:19.8:1:29.9:1:0.63257:1.29:60:36:0.0807:0:1.1 0/1:389:152:79,73:113,123:236,152:0.3907:2,2:25.6:1:30.3:1:0.46709:1.18:60:151:0.3984:0:1.1 +8 3489816 . T C 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15678;SOR=0;LSEQ=AGTGTTGGTTGGAGGCATTC;RSEQ=TCCATCTCATAGGTAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:60,105:165,2:0.012:2,2:6.5:1:32.5:1:1:1.74:60:4:0.012:0:1.5 0/0:254:0:0,0:98,156:254,0:0:2,0:24:1:29.8:1:1:0:59.9:126:1:0:0.4 +8 3489842 . C T 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0476;LSEQ=CTCATAGGTAAAGCCCCGTT;RSEQ=GCCTTCTTGGACCTTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:43:15,28:24,54:78,43:0.3554:2,2:24.6:1:29.2:1:0.68711:1.20:60:9.75:0.3362:0:1.3 0/1:158:4:0,4:54,100:154,4:0.0253:2,0:10.3:1:28.3:1:0.29986:0:60:8:0.026:0:1.5 +8 3489935 . G T 94 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00439;SOR=0.07133;LSEQ=AAAGACTACCCCTGGGATAT;RSEQ=TCCATGTTATAGGAGATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:14,9:0.3913:1,0:15.3:1:29.9:1:1:0:60:18:0.4091:0:1.3 0/1:24:1:0,1:2,21:23,1:0.0417:2,0:6:0:31:0:1:0:60:2:0.0417:0:2 +8 4166193 . C T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=ACAGTTTATAAGAGGCTTTA;RSEQ=GCAAATATCTGGGTGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:34.8:1:32.8:1:1:0:60:8:0.3636:0:1.5 0/0:3:0:0,0:3,0:3,0:0:0,0:16.3:1:33.3:1:1:0:60:6:1:0:0 +8 4166304 . A C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57595;SOR=0.62318;LSEQ=ATGACTAAAGATTATTTACA;RSEQ=AACTAATTCACAGATGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:43:40,3:6,0:6,43:0.8776:0,2:26.4:1:33.2:1:1:0:60:86:0.8776:0:2 1/1:49:40:33,7:7,2:9,40:0.8163:2,2:23.1:1:32.3:1:0.6631:1.34:60:80:0.8163:0:2 +8 4166317 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03474;SOR=0.32491;LSEQ=ATTTACAAAACTAATTCACA;RSEQ=ATGAGTTATTATGCTATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:67:62:53,9:5,0:5,62:0.9254:0,2:23.4:1:30.9:1:1:0:60:124:0.9254:0:1.7 1/1:80:64:46,18:13,3:16,64:0.8:2,2:20.7:1:29.4:1:0.54021:1.68536:60:63:0.7975:0:1.6 +8 4166426 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.0093;SOR=0.5478;LSEQ=ACATGGTTTAAAATACTCAG;RSEQ=AAATATCAAAGGTCCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:193:158:75,83:20,15:35,158:0.8187:2,2:27.5:1:31.6:1:0.35203:1.47256:60:38.5:0.8148:0:2.2 1/0:288:205:104,101:41,42:83,205:0.7118:2,2:25.8:1:30.3:1:0.89669:1.05:59.8:67.333:0.7113:0:2.2 +8 4166452 . C G 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00096;SOR=Inf;LSEQ=TCAAAGGTCCATTTATTTCT;RSEQ=CTTTTTTAAAGACTCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:85,106:191,0:0:2,0:25:1:31.7:1:1:0:60:190:1:0:2.1 0/1:266:13:7,6:114,139:253,13:0.0489:2,2:24:1:29.1:1:0.57813:1.42:60:5.5:0.0418:0:1 +8 4166465 . C A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14588;SOR=0.68435;LSEQ=TATTTCTCCTTTTTTAAAGA;RSEQ=TCTCAAATACTCCCTGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:164:133:55,78:15,16:31,133:0.811:2,2:26.2:1:30.9:1:0.54693:1.32719:60:132:0.8098:0:3 1/0:236:176:76,100:27,33:60,176:0.7458:2,2:25.5:1:29.8:1:0.88042:1.07622:59.7:175:0.7479:0:2.9 +8 4166475 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39057;SOR=0.79484;LSEQ=TTTTTAAAGACTCTCAAATA;RSEQ=TCCCTGTAACCTTCTGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:120:44,76:14,20:34,120:0.7792:2,2:26.2:1:30.4:1:0.69016:1.20757:60:59:0.7763:0:3.2 1/0:213:157:61,96:24,31:55,157:0.7371:2,2:24.6:1:29.3:1:0.63176:1.21725:59.7:38.25:0.7356:0:3 +8 4166496 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50343;SOR=Inf;LSEQ=TCCCTGTAACCTTCTGACAT;RSEQ=ATGTTGAACTAATTCCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:41,87:128,0:0:2,0:23.9:1:29.5:1:1:0:60:127:1:0:2.5 0/1:157:2:1,1:53,102:155,2:0.0127:2,2:18:1:27:1:1:1.92:60:4:0.0129:0:3.5 +8 4166516 . A T 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATGTTGAACTAATTCCTAA;RSEQ=ACTAGGTGAGAAAATGCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:16:4,12:17,62:79,16:0.1684:2,2:26.1:1:29.1:1:0.74778:1.21:60:32:0.1702:0:3.7 0/0:114:0:0,0:31,83:114,0:0:2,0:23.2:1:29.2:1:1:0:60:56:1:0:2.1 +8 4166522 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50376;SOR=0.76036;LSEQ=GAACTAATTCCTAAAACTAG;RSEQ=TGAGAAAATGCATAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:83:62:10,52:6,15:21,62:0.747:2,2:24.7:1:31.2:1:0.21811:2.05968:60:124:0.747:0:3.1 1/0:94:65:14,51:8,20:28,65:0.6915:2,2:26.4:1:29.2:1:0.59533:1.45105:60:64:0.6957:0:2.9 +8 4166565 . C T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.92948;LSEQ=TGATTATTGATGTCATTCTT;RSEQ=ACACCTATATTACTTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:28:0,28:0,11:11,28:0.7179:0,1:25.4:1:28.9:1:1:0:60:56:0.7179:0:2.5 1/0:37:26:1,25:0,11:11,26:0.7027:0,1:19.5:1:28.2:1:1:0:60:52:0.7027:0:2.5 +8 4166691 . G C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TTCAACAACTTTCTGAAGAT;RSEQ=TGTGGAGATTCTGAAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:36:0:34:0:1:0:60:2:1:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:34:1:31:1:1:0:60:4:1:0:3 +8 4166712 . C T 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGGAGATTCTGAAGGTTA;RSEQ=TTTCAATTCCTAGGGTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:4:0:27:0:1:0:60:2:0.5:0:5 1/1:2:2:0,2:0,0:0,2:1:0,0:23.5:1:30:0:1:0:60:4:1:0:3 +8 5498148 . CT C 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52381;SOR=3.38757;LSEQ=TGGGAGAACGGACTAACTCA;RSEQ=GGGATACAGAAATGTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:29.5:1:33:1:1:0:60:4:0.3333:0:0.5 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:12.5:1:33.5:1:1:0:60:4:0.6667:0:0 +8 5498230 . TTC T 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=12.000;MSILEN=2;SSF=0.05955;SOR=4.11024;LSEQ=CTTTCTCTCTCTCTTTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:4,0:16,0:16,4:0.1905:1,0:22.3:1:33:0:1:0:56:8:0.2:0:0.5 1/0:24:12:12,0:9,0:9,12:0.5:0,0:27.7:1:31.1:1:1:0:54.8:24:0.5455:0.0417:1.3 +8 5498260 . A G 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=8.12622;LSEQ=CTCTCTCTCTCTCTCTGTCT;RSEQ=TCTCTCTCTCTCATACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:4,0:22,2:24,4:0.1333:2,0:35:1:33.3:1:1:0:47.5:8:0.1538:0:1 1/0:48:27:25,2:20,0:20,27:0.5625:1,2:23.1:1:30.8:1:0.50046:0:56.7:26:0.5652:0:1.2 +8 5498335 . T C 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.0452;SOR=Inf;LSEQ=AAGTGCAATCTTCTTTCTCT;RSEQ=ATTAGGAATTCTAAATTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:131,50:181,0:0:2,0:24:1:30.1:1:1:0:60:59.333:1:0:0.7 0/1:271:7:7,0:177,87:264,7:0.0258:2,0:20.7:1:31.4:1:0.10067:0:60:14:0.026:0:2.9 +8 5498364 . G C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.7496;SOR=1.06348;LSEQ=TTCTAAATTACTTGGCATCG;RSEQ=TCTTACACCTTTACAAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:269:157:100,57:70,42:112,157:0.5836:2,2:25.7:1:32.4:1:0.89814:1.05:60:51.333:0.5811:0:1.6 1/0:411:246:144,102:96,69:165,246:0.5985:2,2:25.6:1:31:1:1:1.01:60:48.2:0.5951:0:2 +8 5498411 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.14416;LSEQ=AATCTCACTCCTTCTTGGCT;RSEQ=CCAGTTTCTCGATGGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:93:45,48:125,125:250,93:0.2711:2,2:26.2:1:31.5:1:0.80907:1.06644:60:45.5:0.2692:0:2.5 1/0:486:295:127,168:92,98:190,295:0.607:2,2:27:1:30.4:1:0.26272:1.24128:60:72.75:0.6088:0:2.4 +8 5498446 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.03145;LSEQ=GGCTCTGCTCTCTCCACCCC;RSEQ=GAGGCCTTACATACGGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:72:29,43:73,116:189,72:0.2759:2,2:26.1:1:31.1:1:0.88725:1.07:60:71:0.2763:0:2.5 1/0:353:214:74,140:50,88:138,214:0.6062:2,2:24.3:1:29.6:1:0.81931:1.07472:60:41.8:0.6023:0:2.6 +8 5498487 . C T 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.64143;LSEQ=CATATTCCTGAATGCCCACG;RSEQ=CTCACCTGACTCATTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:35:7,28:18,82:100,35:0.2593:2,2:19.8:1:29:1:0.80331:1.14:60:34:0.2556:0:2.2 1/0:137:85:20,65:10,42:52,85:0.6204:2,2:22.5:1:28.9:1:0.67163:1.29:60:170:0.6204:0:2.3 +8 5498584 . C A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.53202;SOR=0;LSEQ=GGACCGAGGCCCTGTGTGAC;RSEQ=CCAATAAGAGCAGTTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:0,17:17,3:0.15:1,0:36:1:29.3:1:1:0:60:6:0.15:0:1 0/0:10:0:0,0:0,10:10,0:0:0,0:24.6:1:31:1:1:0:60:20:1:0:0.2 +8 6327065 . A G 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.36252;SOR=0.27848;LSEQ=TATATGATTCTGATAGTACC;RSEQ=TATATATTTAGATGGGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:5,0:12,0:12,5:0.2941:0,0:22.2:1:32:0:1:0:60:10:0.3125:0:1 0/1:10:1:1,0:9,0:9,1:0.1:0,0:11:0:24:0:1:0:60:2:0.1:0:1 +8 6327147 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18227;SOR=0;LSEQ=GGTTATCTCCTTATTTTACT;RSEQ=ATTCTTAAGGAAAATTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:61,12:73,2:0.0267:2,2:14:1:32:1:0.31856:4.92389:60:4:0.027:0:1 0/0:100:0:0,0:82,18:100,0:0:2,0:23.5:1:30:1:1:0:60:200:1:0:0.1 +8 6327177 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16697;SOR=0;LSEQ=GAAAATTAATTTCACTGTTT;RSEQ=CCAAAGAACTGATAGCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:100,35:135,2:0.0145:2,2:10:1:30.5:1:0.45792:2.83123:60:4:0.0146:0:1.5 0/0:199:0:0,0:134,65:199,0:0:2,0:23.2:1:27.8:1:1:0:60:198:1:0:0.2 +8 6327194 . TA T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07131;SOR=0;LSEQ=TTTACCAAAGAACTGATAGC;RSEQ=AACCCAAAAGATTTCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:3:1,2:122,51:173,3:0.017:2,2:21.7:1:30:1:0.21599:4.73609:60:6:0.0172:0.0057:0.3 0/0:247:0:0,0:161,86:247,0:0:2,0:25.4:1:28.2:1:1:0:60:494:1:0:0.3 +8 6327274 . C G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.32412;LSEQ=AAACGGGTATATCTGTTTAA;RSEQ=TTGACCTATCTTTGGTCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:352:234:128,106:62,55:117,234:0.6648:2,2:26.2:1:32.7:1:0.82041:1.07:60:233:0.6638:0:1.1 1/1:494:406:226,180:43,42:85,406:0.8219:2,2:25.7:1:31.3:1:0.4039:1.23:60:134.333:0.8208:0:1.1 +8 6327350 . TTC T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.02582;SOR=0;LSEQ=TCATGCATTCAATACTCTTT;RSEQ=TCTCTCTCTCCCTGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:4:1,3:65,166:231,4:0.017:2,2:35.8:1:30.8:1:1:1.17392:60:8:0.0174:0:0.3 0/0:349:0:0,0:125,224:349,0:0:2,0:23.2:1:28.8:1:1:0:60:115.333:1:0:0.4 +8 6710087 . TC T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAGTCTCTGTTTGTTCT;RSEQ=CCCACTATTCTCAAATATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:8.5:1:32.3:1:1:0:60:4:1:0.5:0 1/1:2:2:2,0:0,0:0,2:1:0,0:23:1:29:1:1:0:60:4:1:0:0 +8 6710305 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1338;SOR=0;LSEQ=TTATCAGCTGCTAAGTCTTT;RSEQ=CACACAGCCTGTCAAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:80,50:130,2:0.0152:2,2:16:0:32.5:1:1:1.59405:60:4:0.0156:0:1.5 0/0:228:0:0,0:130,98:228,0:0:2,0:22:0:14:0:1:0:60:0:0:0:2 +8 6710324 . G T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.16234;SOR=Inf;LSEQ=TCCACACAGCCTGTCAAAGG;RSEQ=AGAAAGACATGTTTCTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:98,69:167,0:0:2,0:25.4:1:31.5:1:1:0:60:82.5:1:0:0.5 0/1:280:5:2,3:144,131:275,5:0.0179:2,2:20.6:1:26:1:0.67278:1.64592:60:10:0.0185:0:1.4 +8 6710326 . G T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30224;SOR=Inf;LSEQ=CACACAGCCTGTCAAAGGGA;RSEQ=AAAGACATGTTTCTAACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:100,73:173,0:0:2,0:25:1:32.5:1:1:0:60:85.5:1:0:0.5 0/1:285:4:1,3:144,137:281,4:0.014:2,2:17.3:1:26:1:0.36372:3.14173:60:8:0.0143:0:1.5 +8 6710357 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03007;SOR=1.4822;LSEQ=TTCTAACTGCCCGCATTCTG;RSEQ=TCTGCTGCATTTCTCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:197:101:53,48:49,47:96,101:0.5127:2,2:26.8:1:32.2:1:0.88703:1.06:60:32.667:0.5078:0:1.1 1/0:338:206:101,105:57,73:130,206:0.6095:2,2:26.8:1:31.7:1:0.37107:1.23:60:102:0.6108:0:1.3 +8 6710414 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19336;SOR=0;LSEQ=CTGGGCCCCATCCCAGGGAG;RSEQ=CAGAGAAGCTGGCTTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:46,82:128,2:0.0154:2,2:22:1:32:0:1:1.77:60:4:0.0157:0:2 0/0:165:0:0,0:57,108:165,0:0:2,0:23.4:1:30.4:1:1:0:60:164:1:0:0.7 +8 6710415 . C T 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGCCCCATCCCAGGGAGC;RSEQ=AGAGAAGCTGGCTTCTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:42,83:125,0:0:2,0:24.1:1:32:1:1:0:60:250:0.9921:0:0.5 0/1:162:22:9,13:48,92:140,22:0.1358:2,2:23.1:1:27.1:1:0.63237:1.32:60:44:0.1366:0:1.8 +8 6710502 . A C 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77459;SOR=0.82681;LSEQ=TGTTCCAGGAAACTTTCCCC;RSEQ=AGGGGAGACCACAAGTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:0,17:2,12:14,17:0.5484:2,1:24.1:1:32.3:1:0.1957:0:60:34:0.5667:0:1.1 1/0:18:9:0,9:1,8:9,9:0.5:2,0:28.2:1:33.8:1:1:0:60:18:0.5294:0:1 +8 7717592 . A G 29 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTTAAAGTCATCGTACGT;RSEQ=GCATTTGCAGATCTGACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:29.5:1:1:0:23:4:1:0:1.5 +8 10335775 . T C 42 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACCCTAATCCAGTGACC;RSEQ=AGCAGAAGTAATTCCTCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:14.7:1:27:1:1:0:60:2:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:15:1:32:0:1:0:60:4:1:0:1.5 +8 10335888 . AGGCTGCAGTGGTTGT A 34 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=1.133;MSILEN=1;SSF=0.18076;SOR=Inf;LSEQ=GCCTGGCTGCAGTGGTTGTC;RSEQ=GGCTGCAGTGGTTGTGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:24,1:25,0:0:1,0:25.4:1:31.6:1:1:0:60:7.333:1:0:0.3 0/1:19:2:2,0:16,1:17,2:0.1053:1,0:45.5:1:34:0:1:0:60:4:0.1111:0:0 +8 10336140 . A G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.64041;SOR=1.82405;LSEQ=TAAAAAGCTTAAAAGCTTTT;RSEQ=AAACAGCTCCCAGGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:3,8:0.7273:0,0:27.8:1:31.4:1:1:0:60:16:0.7273:0:1.1 1/1:12:10:0,10:0,2:2,10:0.8333:0,0:24.5:1:31.3:1:1:0:60:20:0.8333:0:1.1 +8 10470068 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGGCCGCCTTGCTCTGGGC;RSEQ=GCCCAGCCCTGCTCCATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:41:1:30.5:1:1:1:60:4:0.3333:0:1 +8 10470069 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCCGCCTTGCTCTGGGCC;RSEQ=CCCAGCCCTGCTCCATCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:17.5:1:27.5:1:1:1:60:4:0.3333:0:1 +8 10470758 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.21169;SOR=Inf;LSEQ=GCCAGGAGCAGGGCCCACCG;RSEQ=GGGGTTGCTAGGACCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:17,0:17,0:0:1,0:26.4:1:31.4:1:1:0:60:34:1:0:0.2 0/1:15:2:2,0:13,0:13,2:0.1333:1,0:32:1:33.5:1:1:0:60:4:0.1333:0:1.5 +8 10470801 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49653;SOR=Inf;LSEQ=TCTGGCAGCCGTGGCGTGCT;RSEQ=CCTGGCGGAGACCGCGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:27,2:29,0:0:2,0:21.6:1:33.2:1:1:0:60:58:1:0:0.1 0/1:35:2:1,1:30,3:33,2:0.0571:2,2:40:1:28:1:0.21849:8.80417:60:4:0.0571:0:1.5 +8 10470915 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.91986;SOR=1.03722;LSEQ=CTGTGAGCCATGGGGGCAGC;RSEQ=TCAGGATAAAGGAATAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:158:90:51,39:32,36:68,90:0.5696:2,2:26.5:1:30.8:1:0.26191:1.47:60:180:0.5696:0:2 1/0:280:162:83,79:65,53:118,162:0.5786:2,2:26.3:1:30.3:1:0.54618:1.16666:60:80:0.5861:0:2 +8 10470933 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.12782;SOR=0;LSEQ=GCATCAGGATAAAGGAATAA;RSEQ=ACAGTCACGAGCCTCCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:80,86:166,2:0.0119:2,2:15.5:1:30.5:1:1:1.07:60:4:0.0121:0:2.5 0/0:301:0:0,0:157,143:300,0:0:2,0:26.8:1:29.6:1:1:0:59.9:74:0.9966:0:1.6 +8 10470940 . AC GT 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1306;SOR=0;LSEQ=GATAAAGGAATAAAACAGTC;RSEQ=GAGCCTCCCACGACCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:79,87:166,2:0.0119:2,2:42.5:1:30.8:1:1:1.10:60:4:0.0121:0:1.5 0/0:296:0:0,0:148,148:296,0:0:2,0:26.6:1:29.4:1:1:0:59.9:48.333:1:0:1.7 +8 10470941 . C T 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13346;SOR=Inf;LSEQ=ATAAAGGAATAAAACAGTCA;RSEQ=GAGCCTCCCACGACCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:168:166:79,87:0,0:0,166:0.9881:0,2:27.4:1:30.6:1:1:0:60:82:1:0:1.6 1/1:291:291:145,146:0,0:0,291:1:0,2:26.9:1:29.5:1:1:0:59.9:57.2:1:0:1.7 +8 10470985 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30069;SOR=Inf;LSEQ=ACCACTGCCTCCAAAATGCA;RSEQ=GGTGACAGCTGTGCGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:36,65:101,0:0:2,0:22.9:1:31.2:1:1:0:60:202:1:0:1.2 0/1:183:4:2,2:68,111:179,4:0.0219:2,2:23.3:1:27.5:1:0.6375:1.63:60:8:0.0222:0:2 +8 10471002 . G A 91 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16987;SOR=5.10211;LSEQ=GCACGGTGACAGCTGTGCGC;RSEQ=GTGGCTCAGGCCTGTAATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:1:0,1:18,51:69,1:0.0143:2,0:29:0:34:0:1:0:60:2:0.0145:0:2 0/1:130:9:3,6:38,83:121,9:0.0692:2,2:16.6:1:28.9:1:1:1.09:60:18:0.0698:0:1.9 +8 10471109 . C A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAGTGAGACACCATCTCT;RSEQ=CAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1:0,0:5.2:1:30.7:1:1:0:60:22:1:0:1 1/1:5:5:0,5:0,0:0,5:1:0,0:5.4:1:29.8:1:1:0:60:10:1:0:1 +8 10584029 . A T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1827;SOR=0;LSEQ=TCAGAAGGAAGCCCGGGTCC;RSEQ=CGCGCTTGCACAGCCGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:36,17:53,2:0.0364:2,2:10.5:1:28.5:1:1:2.08642:60:4:0.0364:0:1 0/0:73:0:0,0:53,20:73,0:0:2,0:22:1:28.3:1:1:0:60:72:1:0:0 +8 10584048 . T C 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50779;SOR=Inf;LSEQ=CACGCGCTTGCACAGCCGCT;RSEQ=GGCCTGCTTCTTCCTGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:47,33:80,0:0:2,0:23:1:30:1:1:0:60:39:1:0:0.1 0/1:107:2:1,1:62,43:105,2:0.0187:2,2:5:0:30.5:1:1:1.4368:60:4:0.0187:0:1 +8 10584117 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17948;SOR=0;LSEQ=CATGTGCTGCAGGCGCAGCC;RSEQ=CTCCGCCTCGTCCACGTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:2,0:42,55:97,2:0.0202:2,0:22:1:27.5:1:0.19501:0:60:4:0.0204:0:1 0/0:134:0:0,0:57,77:134,0:0:2,0:25.7:1:30.4:1:1:0:60:66:1:0:0.2 +8 10584160 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4989;SOR=Inf;LSEQ=CTCTTCTGGGACAGCGTCAG;RSEQ=GCCTTCCACGACTTTCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:16,32:48,0:0:2,0:26.2:1:30.2:1:1:0:60:47:1:0:0.4 0/1:57:2:1,1:17,38:55,2:0.0351:2,2:10:0:31:0:0.53571:2.20:60:4:0.0351:0:1 +8 10584212 . C T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07363;SOR=0.28543;LSEQ=AGAGGAGGCCATGCTCAGTG;RSEQ=TGTGCCCCGCAGGCATCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:2,16:0,5:5,18:0.7826:0,2:21.2:1:30.6:1:1:0:60:36:0.8182:0:1.2 1/0:26:13:2,11:2,11:13,13:0.5:2,2:13.5:1:29.7:1:1:1:60:26:0.5:0:1.2 +8 10584288 . C T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACACCTCCCTTCCCCCTC;RSEQ=CAGCCACAGAGGACACGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:19.8:1:31:1:1:0:60:10:0.8333:0:2 1/1:5:5:0,5:0,0:0,5:1:0,0:29.8:1:26:1:1:0:60:4:1:0:1.6 +8 10634248 . T C 128 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02271;SOR=0.15384;LSEQ=GAGGAAGGGGAAGCAAGGGA;RSEQ=GGGATGGTGCTGCCCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:10,8:1,1:2,18:0.9:2,2:24.3:1:30.7:1:1:1.24:60:36:0.9:0:1 1/0:28:16:10,6:6,6:12,16:0.5714:2,2:24.1:1:30.9:1:0.70217:1.64:60:32:0.5926:0:1.4 +8 10634261 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50192;SOR=Inf;LSEQ=CAAGGGATGGGATGGTGCTG;RSEQ=CCAGACCTGTCACCAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:28,0:0:2,0:24:1:31.3:1:1:0:60:27:1:0:0.6 0/1:37:2:1,1:20,15:35,2:0.0541:2,2:43:0:30:1:1:1.32286:60:4:0.0556:0:2 +8 10634324 . C T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00087;SOR=Inf;LSEQ=ACGGCTGGAGACGCTGGAGA;RSEQ=GCAGAGCTTTGCCTTCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:23,0:0:2,0:21.1:1:31.5:1:1:0:60:46:1:0:0.4 0/1:37:13:6,7:11,13:24,13:0.3514:2,2:22.5:1:29.3:1:1:1.01:60:26:0.3514:0:1.4 +8 11096045 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.17179;SOR=0;LSEQ=GGAGGAAGGAAGGTGAGTAT;RSEQ=AGATATATTATCCAGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:113,20:133,2:0.0148:2,2:27:1:28:1:0.28789:5.53825:60:4:0.0148:0:2 0/0:190:0:0,0:151,39:190,0:0:2,0:23:1:31:1:1:0:60:46.5:1:0:0.6 +8 11096054 . T C 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49792;SOR=1.19344;LSEQ=AAGGTGAGTATGAGATATAT;RSEQ=ATCCAGGCAGTGTGTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:43:34,9:87,17:104,43:0.2925:2,2:27:1:32.7:1:0.48784:1.3518:60:86:0.2945:0:1 0/1:236:78:59,19:117,41:158,78:0.3305:2,2:25.5:1:30.9:1:0.87424:1.09:60:156:0.3333:0:1.2 +8 11096085 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.39801;LSEQ=TGTGTTCTTTTAAAAATTTC;RSEQ=TCCTAAGAACCAGAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:82:53,29:121,60:181,82:0.3118:2,2:24:1:30.7:1:0.77888:1.10304:60:40:0.3089:0:1.7 0/1:426:65:36,29:225,136:361,65:0.1526:2,2:26.7:1:29.3:1:0.33323:1.33177:60:130:0.1548:0:1.4 +8 11096119 . A G 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00842;SOR=0;LSEQ=AAAAAGATGGAAAAGCAAAA;RSEQ=GGCGAGGAGGGGTGGGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:5:2,3:209,172:381,5:0.0129:2,2:17.2:1:25.2:1:0.66225:1.81982:60:10:0.0132:0:2 0/0:616:0:0,0:317,298:615,0:0:2,0:26.3:1:29.8:1:1:0:60:152.75:1:0:0.7 +8 11096153 . G C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.49387;LSEQ=GGGATTCAAGAAGAAACTCA;RSEQ=TACATATGCTAATGTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:418:261:113,148:73,84:157,261:0.6244:2,2:26:1:32.6:1:0.54314:1.13787:59.9:86:0.6262:0:1.3 0/1:588:265:116,149:149,173:322,265:0.4507:2,2:23.6:1:31.4:1:0.56045:1.1061:60:264:0.4513:0:1.3 +8 11096235 . G T 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00234;SOR=0.22635;LSEQ=GTGAAGATATATTTCCAGCC;RSEQ=AAAAGAATAATTTTTAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:19:2,17:19,105:124,19:0.1319:2,2:24.5:1:30.1:1:0.73969:1.53394:60:38:0.1357:0:1.4 0/1:151:5:2,3:34,111:145,5:0.0331:2,2:28.2:1:28.4:1:0.59394:2.16:60:10:0.0331:0:1.4 +8 11096240 . G A 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25014;SOR=Inf;LSEQ=GATATATTTCCAGCCGAAAA;RSEQ=AATAATTTTTAAAACATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:16,112:128,0:0:2,0:24.4:1:32.4:1:1:0:59.6:41.667:1:0:0.4 0/1:146:3:1,2:32,111:143,3:0.0205:2,2:16.3:1:25:1:0.53917:1.73:60:2:0.0142:0:1.7 +8 11096295 . CA C 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=2.04723;LSEQ=GCACATGAAACCGTGTTGTC;RSEQ=AAAAAAAAACCCCAGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:1:0,1:0,29:29,1:0.0333:1,0:22:0:33:0:1:0:60:2:0.0333:0:0 0/1:30:2:0,2:0,28:28,2:0.0667:1,0:23:1:30.5:1:1:0:60:4:0.0667:0.0333:0.5 +8 11267777 . A G 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.66417;LSEQ=ACCTGAGTTAATATTAAGCT;RSEQ=AGAAATCCTTTTTAAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,1:7,2:0.2222:2,0:17:1:33.5:1:1:0:60:4:0.25:0:1 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:5:0:33:0:1:0:60:2:0.3333:0:1 +8 11268077 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=15.08621;LSEQ=TTTATATTATAAGGAACAGA;RSEQ=GGCCTTTTGTGATTGTAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:34:11,23:82,110:192,34:0.1504:2,2:26.9:1:30.1:1:0.34467:1.55571:60:33:0.1467:0:1.1 1/0:387:282:124,158:43,62:105,282:0.7287:2,2:24.3:1:30.3:1:0.64488:1.13:60:281:0.7337:0:1.1 +8 11268155 . T C 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=Inf;LSEQ=GAGATGGGCACCAGGAAGAC;RSEQ=GAAGAGGCAAACCGGAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:17,71:88,0:0:2,0:24.7:1:31:1:1:0:60:43:1:0:0.1 0/1:125:16:5,11:22,87:109,16:0.128:2,2:17:1:28.1:1:0.33526:1.79:60:15:0.122:0:1.7 +8 11268305 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=TGAAATCTGAAGTCTGGGGG;RSEQ=TTTTAATATATGAAAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:16.6:1:32.4:1:1:0:60:16:1:0:0.1 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:29.5:1:31:1:1:0:60:4:0.3333:0:1.5 +8 11268344 . G A 46 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=AATGATAGAAAGATGTAAGG;RSEQ=TTTCTTGCTTTTCAGTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:30:1:25.5:1:1:0:60:1:1:0:0 1/1:3:3:0,3:0,0:0,3:1:0,0:16:1:29.3:1:1:0:60:6:1:0:1.3 +8 11414237 . T C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCATGTCTCCAGAAGCCTT;RSEQ=CTGGGTGAGGCCAACGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:10,1:0,0:0,11:1:0,2:26.9:1:32.9:1:1:0:60:22:1:0:1 1/1:6:6:6,0:0,0:0,6:1:0,0:24.5:1:30.5:1:1:0:60:12:1:0:1 +8 11414294 . C A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4898;SOR=Inf;LSEQ=GAGCGGCTGGTCCGACTCTA;RSEQ=GCAGTGGTCACCAAGGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:25,0:0:2,0:29.6:1:31.3:1:1:0:60:50:1:0:0.3 0/1:25:2:1,1:11,12:23,2:0.08:2,2:30:0:32:1:1:1.09:60:4:0.0833:0:1 +8 11414440 . CA C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTGCGGTGGGTTCACCAGGC;RSEQ=GGGGGTCCTGCAGATCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:4,0:0:0,0:23.5:1:33.5:1:1:0:60:8:1:0:0.3 1/0:4:2:0,2:0,2:2,2:0.5:0,0:37.5:1:31.5:1:1:0:60:4:0.5:0:0 +8 11421358 . C A 47 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.4;SOR=0;LSEQ=GCGGGACGCTCAGGGCCCCC;RSEQ=ACCCACCGAGGACCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:35.3:1:29.7:1:1:0:60:6:1:0:2.3 1/0:2:1:1,0:1,0:1,1:0.5:0,0:12:0:31:0:1:0:60:2:0.5:0:2 +8 11421384 . C T 82 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.01515;SOR=0;LSEQ=CCGAGGACCCCAGCCCCTCA;RSEQ=CCCCGCTTGCGGTCTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1:0,2:19.3:1:32:1:1:0:60:12:1:0:1.7 0/1:5:1:1,0:4,0:4,1:0.2:0,0:38:0:31:0:1:0:60:2:0.2:0:2 +8 11421626 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49317;SOR=0;LSEQ=CTGCAGCCCTAGCCGGCCGC;RSEQ=CCCGCCTGCGCCCCGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:7,27:34,2:0.0556:2,2:19.5:1:27.5:1:0.4:3.67:60:4:0.0556:0:1 0/0:34:0:0,0:6,28:34,0:0:2,0:24.1:1:30.1:1:1:0:60:68:1:0:0.1 +8 11587064 . C CAA 98 v3;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.01284;SOR=10.9832;LSEQ=AACAGTGCGAGACTGTGTCT;RSEQ=AAAAAAAAAAAAAATGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:1:1,0:14,0:14,1:0.0526:1,0:10:0:32:0:1:0:60:2:0.0526:0:2 0/1:23:9:9,0:11,0:11,9:0.3913:0,0:28.4:1:31.1:1:1:0:56.3:18:0.3913:0:1.2 +8 11587138 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.51559;SOR=Inf;LSEQ=ACTGTGTAGTTCAGTAGTGT;RSEQ=TGTTCTGAGAAAGCCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:92,31:123,0:0:2,0:25.8:1:32.1:1:1:0:60:60.5:1:0:0.1 0/1:179:2:1,1:119,58:177,2:0.0112:2,2:23.5:1:28:1:0.55182:2.04285:60:4:0.0116:0:1.5 +8 11587234 . G T 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06882;LSEQ=CATGATGCAAAATTGTGTTC;RSEQ=CTGAAAAGCAGGGGTTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:56:25,31:46,64:110,56:0.3373:2,2:24:1:30.8:1:0.74273:1.12:60:27:0.3333:0:1.1 0/1:327:11:5,6:144,171:315,11:0.0336:2,2:24.7:1:28.7:1:1:1.01049:60:22:0.0342:0:1 +8 11587313 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17278;SOR=0;LSEQ=CCCATGGTGGTTGCTCAATT;RSEQ=TGAGTGAGTTTGGAGAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:22,64:86,2:0.0227:2,2:15.5:1:29.5:1:0.45664:2.87:60:4:0.0227:0:1 0/0:123:0:0,0:31,92:123,0:0:2,0:21.8:1:30.7:1:1:0:60:29.75:1:0:0.1 +8 11587396 . A G 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.10399;SOR=0.27514;LSEQ=TTGGTTTTTAAACCCAATAT;RSEQ=TAATTCCTGGATATTCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:0,10:0,12:12,10:0.4545:0,0:26.8:1:33.7:1:1:0:60:20:0.4545:0:1 0/1:22:4:0,4:0,18:18,4:0.1818:1,0:12.5:1:33.3:1:1:0:60:8:0.1818:0:1.3 +8 11587455 . G GAGA 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.46667;SOR=Inf;LSEQ=GTTGTTTCTATTGTTTTTGA;RSEQ=AGAAGGTCTTGCTCCATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:26.5:1:33.7:0:1:0:55:4:0.5:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:29.2:1:1:0:55:4:1:0:0 +8 11606312 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCCGAGGTGGTCTTCTC;RSEQ=TTCCAAGGAAAGGGCATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:24.3:1:31:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 11606451 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53558;SOR=Inf;LSEQ=TGTTTGACGACTTCTCAGAA;RSEQ=GCAGAGAGTGTGTCAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:23,0:23,0:0:1,0:23.3:1:33.7:1:1:0:60:46:1:0:0 0/1:42:2:1,1:36,4:40,2:0.0476:2,2:25:1:27.5:1:0.22648:8.16006:60:4:0.0488:0:1 +8 11606537 . C T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28085;SOR=Inf;LSEQ=TATCTGTGCAACGCCTGCGG;RSEQ=CTCTACCACAAGATGAACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:38,33:71,0:0:2,0:25.6:1:31.4:1:1:0:60:34.5:1:0:0.2 0/1:110:3:1,2:55,52:107,3:0.0273:2,2:31:1:22.3:1:0.61468:2.10148:60:2:0.0183:0:1.7 +8 11606567 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1259;SOR=0;LSEQ=AAGATGAACGGCATCAACCG;RSEQ=CCGCTCATCAAGCCTCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:2:1,1:22,26:48,2:0.04:2,2:17:1:28.5:1:1:1.18:60:4:0.0408:0:1 0/0:90:0:0,0:35,55:90,0:0:2,0:26.1:1:30.5:1:1:0:60:44:1:0:0.1 +8 11606591 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1293;SOR=0;LSEQ=CTCATCAAGCCTCAGCGCCG;RSEQ=CTGGTAAGCACGTGCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:13,22:35,2:0.0541:2,2:25.5:1:29:1:1:1.67:60:4:0.0588:0:1 0/0:65:0:0,0:19,46:65,0:0:2,0:22:1:30.7:1:1:0:60:64:1:0:0.1 +8 11607682 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.54902;SOR=Inf;LSEQ=ACCACCACCACCACGCTGTG;RSEQ=CGCCGCAATGCGGAGGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:30,16:46,0:0:2,0:30.3:1:31:1:1:0:60:45:1:0:0.1 0/1:90:2:1,1:49,39:88,2:0.0222:2,2:32.5:1:29.5:1:1:1.25319:60:4:0.0227:0:1 +8 12586219 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15262;SOR=0;LSEQ=GAATCTATGTTCTAGTCTTC;RSEQ=AAGTTCTCTTAGAATGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:109,78:187,2:0.0106:2,2:32:1:31.5:1:1:1.3949:60:4:0.0107:0:2 0/0:294:0:0,0:165,129:294,0:0:2,0:24.6:1:30.5:1:1:0:60:146:1:0:0.7 +8 12586261 . A G 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00112;SOR=1.777;LSEQ=CAGTTTCAGAGCAAGATACG;RSEQ=AAAAGGTAACTTGGAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:212:112:57,55:51,49:100,112:0.5283:2,2:24:1:31.6:1:1:1.00428:60:111:0.5311:0:1.1 1/0:383:255:120,135:63,63:126,255:0.6658:2,2:25.5:1:30.2:1:0.66299:1.12465:60:30.875:0.664:0:1.1 +8 12586264 . A C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.22017;LSEQ=TTTCAGAGCAAGATACGAAA;RSEQ=AGGTAACTTGGAGCACATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:60:35,25:75,80:155,60:0.2791:2,2:23.8:1:31.7:1:0.22442:1.49:60:59:0.277:0:1 0/1:383:30:15,15:171,182:353,30:0.0783:2,2:26.6:1:31:1:1:1.06:60:29:0.0763:0:1.3 +8 12586296 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05001;SOR=0;LSEQ=AGCACATTCTCATCACAGTG;RSEQ=TAAGGCTGTCTGATAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:3:1,2:78,102:180,3:0.0164:2,2:19:1:25.3:1:1:1.52601:60:2:0.011:0:1.3 0/0:312:0:0,0:139,172:311,0:0:2,0:25.8:1:30.7:1:1:0:59.9:61.2:1:0:0.8 +8 13443158 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50076;SOR=Inf;LSEQ=GGTTTGTTCCTTGTGAGGGC;RSEQ=GTGAGGGAGAATCTGTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:20,12:32,0:0:2,0:23.8:1:31.3:1:1:0:58.2:64:1:0:0.1 0/1:41:2:1,1:24,15:39,2:0.0488:2,2:18:1:29.5:1:1:1.58108:60:4:0.05:0:1 +8 13443286 . T C 60 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08492;SOR=0;LSEQ=TTCATATTTTATTCTACCCA;RSEQ=GCTCATATCCCTATCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:7.5:1:30:1:1:0:60:8:0.5:0:1 0/0:6:0:0,0:0,6:6,0:0:0,0:26.8:1:26.3:1:1:0:60:5:1:0:0.2 +8 13465795 . C A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=AAAGTCTTAAAGTCTTTGAT;RSEQ=TTTCTTATAAGTGCATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:6,1:7,0:0:2,0:31.3:1:32.6:1:1:0:44.3:14:1:0:0 0/1:8:3:2,1:3,2:5,3:0.375:2,2:26.7:1:30.3:1:1:1.29:42:6:0.375:0:2.3 +8 13465836 . T C 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22462;SOR=Inf;LSEQ=GAAAACGCTGATGTATGCCG;RSEQ=CTTCCCTCTCTGCTTCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:11,1:12,0:0:2,0:17.5:1:29.3:1:1:0:54.1:24:1:0:0 0/1:14:3:2,1:8,3:11,3:0.2143:2,2:32.3:1:29.3:1:1:1.30524:42:6:0.2143:0:2.3 +8 13466001 . C A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=Inf;LSEQ=CAGCCATTCTGGGCTACTAC;RSEQ=GGTCTCCGCGTCTTGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:31.4:1:30.2:1:1:0:53.2:10:1:0:0 0/1:12:3:0,3:0,9:9,3:0.25:0,0:16.7:1:31.7:1:1:0:42.3:6:0.25:0:2.7 +8 13745451 . A G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTGAATCTATTTATTATATG;RSEQ=ATTTGTAAGACGTCTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:11,0:12,0:12,11:0.4783:0,0:26.4:1:31.2:1:1:0:60:22:0.4783:0:2.7 0/1:23:11:11,0:12,0:12,11:0.4783:0,0:22.7:1:32:1:1:0:60:22:0.4783:0:3 +8 13745462 . C T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.97818;LSEQ=TATTATATGAATTTGTAAGA;RSEQ=GTCTCTTTTACTTAAATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:15:15,0:11,0:11,15:0.5769:0,1:22.9:1:31.1:1:1:0:60:30:0.5769:0:2.6 1/0:28:16:15,1:12,0:12,16:0.5714:0,1:23.6:1:30.9:1:1:0:60:32:0.5714:0:2.7 +8 13745472 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1157;LSEQ=ATTTGTAAGACGTCTCTTTT;RSEQ=CTTAAATACTACTTTCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:17:16,1:14,0:14,17:0.5484:1,1:22.8:1:32.4:1:1:0:60:34:0.5484:0:2.4 1/0:33:19:17,2:13,1:14,19:0.5758:1,2:25.9:1:31.8:1:1:1.51052:60:38:0.5758:0:2.5 +8 13745495 . G T 38 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.26653;SOR=Inf;LSEQ=TAAATACTACTTTCATAACT;RSEQ=AAATGTGCCATTTATTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:41,9:50,0:0:2,0:21.1:1:31.9:1:1:0:60:49:1:0:0.8 0/1:71:3:1,2:56,12:68,3:0.0423:2,2:6:1:24:1:0.09712:8.91114:60:6:0.0423:0:2 +8 13745588 . G A 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46699;SOR=1.17962;LSEQ=TATGGAGCTGTGTAATACTT;RSEQ=TATCTAAAAGCCAAAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:59:27,32:45,44:89,59:0.3986:2,2:28.1:1:29.6:1:0.61635:1.21054:60:58:0.3946:0:1.1 0/1:262:115:60,55:72,75:147,115:0.4389:2,2:29.1:1:28.8:1:0.62068:1.14:60:114:0.4402:0:1.2 +8 13745647 . AT A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52287;SOR=Inf;LSEQ=ATGACAGAAATAGAGCAGTA;RSEQ=TTCAAGAATTATGTTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:37,70:107,0:0:2,0:23.4:1:30.4:1:1:0:60:106:1:0:0.4 0/1:168:2:2,0:58,108:166,2:0.0119:2,0:7.5:1:26:1:0.12618:0:60:4:0.012:0.006:2 +8 13745701 . A G 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.82837;SOR=1.15517;LSEQ=AACAGTTGCTATGTCCTGAT;RSEQ=TAAATGAAGAGCCACGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:20:1,19:2,16:18,20:0.5263:2,1:27.8:1:30.9:1:0.59459:2.32256:60:9:0.5:0:1 1/0:48:27:4,23:2,19:21,27:0.5625:2,2:22.9:1:31:1:0.68299:1.64:60:54:0.5625:0:1 +8 14166427 . G C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24291;SOR=0;LSEQ=GAAATACATTTTCTTAATTT;RSEQ=AAATCCAGTAGACTAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:3,0:19,0:19,3:0.1364:1,0:38.3:1:32:1:1:0:60:6:0.1364:0:1 0/0:17:0:0,0:17,0:17,0:0:1,0:23.4:1:32.1:1:1:0:60:34:1:0:0 +8 14166528 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30117;SOR=Inf;LSEQ=CGGCCTCAGCCTCACTTTTA;RSEQ=CAGAAAATGAAACCGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:97,17:114,0:0:2,0:19.7:1:32:1:1:0:59.2:228:1:0:0.2 0/1:197:3:1,2:151,42:193,3:0.0152:2,2:15:1:26.3:1:0.12707:7.09502:60:6:0.0155:0:1 +8 14166550 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12453;SOR=0;LSEQ=AGAAAATGAAACCGGAAGCC;RSEQ=CCCCTACTCTTAATTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:143,42:185,2:0.0107:2,2:8:0:33:0:0.40797:3.37662:60:4:0.0107:0:1.5 0/0:342:0:0,0:233,109:342,0:0:2,0:23.4:1:29.8:1:1:0:58.1:84.5:1:0:0.2 +8 14166793 . T C 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.5207;SOR=Inf;LSEQ=CTAGTAATTTAATGCCTGGC;RSEQ=GTGACTACTCACTTTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:56,46:102,0:0:2,0:6.8:1:30.8:1:1:0:39:50:1:0:0.2 0/1:157:2:1,1:92,63:155,2:0.0127:2,2:7:0:31.5:1:1:1.45669:24:4:0.0128:0:1.5 +8 14166825 . G A 193 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CTTTTTAAGGATGGTATTGA;RSEQ=ACTATGTGGGAAGATGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:85:46,39:108,66:174,85:0.3282:2,2:17.4:1:30.2:1:0.22834:1.38554:38:84:0.3281:0:1.1 0/0:423:0:0,0:259,164:423,0:0:2,0:18.7:1:30.8:1:1:0:51.4:46:1:0:0.2 +8 14166895 . C T 159 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTGAACAGTCAGCAGAGA;RSEQ=GAAGTGACCTCGATCGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:729:0:0,0:368,361:729,0:0:2,0:25.8:1:31.2:1:1:0:35:103.143:1:0:0.2 0/1:1250:40:19,21:619,591:1210,40:0.032:2,2:26.4:1:29.9:1:0.74836:1.15749:28.9:80:0.0323:0:1.1 +8 14167023 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14337;SOR=Inf;LSEQ=AATTGTGATAAGAGAGCAGT;RSEQ=TGGACTACTGAATGTGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:71,181:252,0:0:2,0:24.1:1:32.1:1:1:0:58:125:1:0:0.1 0/1:349:4:2,2:93,251:344,4:0.0115:2,2:11.5:1:27.8:1:0.30059:2.69:57.3:8:0.0115:0:1 +8 14167065 . A C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24388;SOR=0;LSEQ=AAAGAAGCTGTTACACATAC;RSEQ=GGGACGGTATAACAAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:26,112:138,2:0.0142:2,2:12:1:32:1:0.34964:4.25:23:4:0.0143:0:2 0/0:144:0:0,0:25,119:144,0:0:2,0:24.1:1:30.5:1:1:0:55.9:143:1:0:0.3 +8 14167113 . C T 178 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACTTCATCCAAAGATAGTGA;RSEQ=TGGTTATCAGTCCCACGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:55:11,44:0,0:0,55:1:0,2:23.1:1:30.9:1:1:0:36.5:54:1:0:1.1 1/0:43:27:7,20:2,14:16,27:0.6279:2,2:19.1:1:30.3:1:0.4455:2.40:40:54:0.6279:0:1 +8 14167258 . T G 89 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGCTGAACCAAAGCCTCT;RSEQ=CAAAAAGCAGAGTGGACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:15.8:1:34.5:1:1:0:41.8:12:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 16703980 . A T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.46578;SOR=1.38783;LSEQ=GTTCCAAACAGGAAAAATGA;RSEQ=TGGGAAATTCCACCTACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:18:15,3:32,4:36,18:0.3333:2,2:23.4:1:31.7:1:0.67431:1.58542:60:36:0.3396:0:1.2 0/1:78:32:26,6:37,9:46,32:0.4103:2,2:24.3:1:29.3:1:1:1.05:60:31:0.4079:0:1.5 +8 16704010 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.14906;SOR=0;LSEQ=CCACCTACAGCTACTAGCGT;RSEQ=TGCCTGCTCAGTTCCCGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:57,22:79,2:0.0247:2,2:27.5:1:28.5:1:0.48981:2.5561:60:4:0.0247:0:1 0/0:128:0:0,0:93,35:128,0:0:2,0:24:1:31.2:1:1:0:60:127:1:0:0.9 +8 16704073 . C A 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01183;SOR=1.62822;LSEQ=TAAAGGGAGAGACATGGGGA;RSEQ=AGAGAATTAGGAGACAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:58:33,25:84,70:154,58:0.271:2,2:31.8:1:30.1:1:0.87701:1.10:60:28:0.2679:0:3 0/1:326:123:65,58:108,95:203,123:0.3773:2,2:26.4:1:29.7:1:1:1.01437:60:246:0.3808:0:2.9 +8 16704077 . G A 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02628;SOR=1.53334;LSEQ=GGGAGAGACATGGGGACAGA;RSEQ=AATTAGGAGACAGGCAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:61:33,28:83,71:154,61:0.2837:2,2:30.1:1:30.4:1:1:1.01:60:122:0.2877:0:3 0/1:328:124:64,60:109,95:204,124:0.378:2,2:26.6:1:29.6:1:0.81967:1.07542:60:123:0.3808:0:2.9 +8 16704099 . G C 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.05143;SOR=1.42546;LSEQ=ATTAGGAGACAGGCAATGGA;RSEQ=AGAATCAGAAGGTTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:70:33,37:76,81:157,70:0.3084:2,2:23.2:1:31.9:1:0.88643:1.05179:60:140:0.3084:0:2.6 0/1:355:138:66,72:102,114:216,138:0.3887:2,2:25.7:1:31.2:1:0.91362:1.02:60:137:0.3892:0:2.6 +8 17522020 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.2;SOR=Inf;LSEQ=GATGGAGAAGAGCAGCCTGC;RSEQ=TCCAGCTCTGCCTGCAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:8,0:0:2,0:22.4:1:30.8:1:1:0:60:7:1:0:0.1 0/1:7:2:0,2:2,3:5,2:0.2857:2,0:20.5:1:27:1:1:0:60:4:0.2857:0:1 +8 17945818 . A G 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02366;SOR=0.52941;LSEQ=TTACCTGTATTACTGCAAGT;RSEQ=GCTCAACCTAGTAAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:55:51,4:52,4:56,55:0.4955:2,2:21.8:1:32.6:1:1:1.01943:60:110:0.4955:0:1 0/1:123:42:39,3:75,5:80,42:0.3415:2,2:20.4:1:31.8:1:1:1.15246:60:84:0.3443:0:1.1 +8 17945990 . T G 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.02332;SOR=0.68454;LSEQ=CTGCTCATTTTGGATGCTTT;RSEQ=TTATTGGTTACTACTATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:80:23,57:105,185:290,80:0.2162:2,2:26.4:1:31.8:1:0.23422:1.40532:55.7:79:0.217:0:1.1 0/1:699:111:44,67:225,362:587,111:0.1588:2,2:25.4:1:30.5:1:0.83181:1.06:53.8:26.75:0.1571:0:1.2 +8 17946053 . AAC A 21 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.61241;SOR=0.5309;LSEQ=TTGTGTGTCTAACAGCCGTG;RSEQ=ACTCTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:0,2:6,75:81,2:0.0241:2,0:22:1:29:1:1:0:59.5:4:0.0247:0.012:3 0/1:155:2:0,2:17,136:153,2:0.0129:2,0:26.5:1:21:1:1:0:40:1:0.0066:0:2.5 +8 17946435 . G T 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16761;LSEQ=ATCTCCTGACCTCGTGATCC;RSEQ=TCCGCCGTCATCTCTTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:40:35,5:71,21:92,40:0.303:2,2:24.4:1:31.5:1:0.23467:2.06:55.7:80:0.3053:0:1.1 0/1:222:15:13,2:159,46:205,15:0.0676:2,2:26.6:1:30.5:1:0.53219:1.88:59.7:30:0.0676:0:1 +8 17946458 . C T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30255;SOR=Inf;LSEQ=CGCCGTCATCTCTTGAACTG;RSEQ=CATCTGTCAGCTAAGTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:157,58:215,0:0:2,0:24.2:1:32.2:1:1:0:58.8:214:1:0:0.3 0/1:358:4:1,3:238,116:354,4:0.0112:2,2:14.8:1:25.5:1:0.10904:6.1222:53.8:8:0.0113:0:1 +8 17946658 . G GA 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.28509;SOR=Inf;LSEQ=CATGAAGAATTCAGAATCTG;RSEQ=AAAAAAGGTCCATAATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:93,94:187,0:0:2,0:25.2:1:31.9:1:1:0:59.9:61.333:1:0:0.1 0/1:293:3:1,2:119,171:290,3:0.0102:2,2:20.7:1:28.6:1:1:1.3903:57.7:6:0.0105:0.0034:0 +8 17946946 . C T 168 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCTGTGTGTTTGTACTGCT;RSEQ=GGCTAAAACCAGTGGACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:0:0,0:221,173:394,0:0:2,0:30.4:1:30.9:1:1:0:45.2:64.667:0.9974:0:0.1 0/1:545:55:31,24:249,239:488,55:0.1009:2,2:27.7:1:29.1:1:0.47948:1.24:34.3:54:0.0998:0:1.1 +8 17947063 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00352;SOR=0.64004;LSEQ=AAAGTCCTTTTCGAGGTTTA;RSEQ=ATAAGGCATGTTCCAGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:118:47,71:115,145:260,118:0.3122:2,2:22.7:1:32.4:1:0.43483:1.19752:58.2:236:0.3155:0:1.1 0/1:520:117:47,70:168,235:403,117:0.225:2,2:22.1:1:31.3:1:0.83131:1.06463:58.2:234:0.2281:0:1.1 +8 17947211 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16115;SOR=0;LSEQ=TGTCATGATCTGATCTGAAT;RSEQ=ACGATGGAATTTGTAACAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:73,122:195,2:0.0102:2,2:40.5:1:30.5:1:1:1.67:45:4:0.0103:0:1 0/0:293:0:0,0:116,177:293,0:0:2,0:26.7:1:30.7:1:1:0:45.9:145.5:1:0:0.1 +8 17947318 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53347;SOR=Inf;LSEQ=ATTATAAAAACTAAAAAACT;RSEQ=ATAGCATGGAATATATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:47,57:104,0:0:2,0:24.2:1:31.6:1:1:0:57.8:25:1:0:0.2 0/1:179:2:0,2:92,85:177,2:0.0112:2,0:9.5:1:25.5:1:0.23483:0:32:4:0.0113:0:2 +8 17947327 . G C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53603;SOR=Inf;LSEQ=ACTAAAAAACTGATAGCATG;RSEQ=AATATATTTCTGAATGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:53,60:113,0:0:2,0:24.7:1:31.1:1:1:0:56.9:21.6:1:0:0.4 0/1:200:2:1,1:102,96:198,2:0.01:2,2:12:0:33.5:1:1:1.06221:60:4:0.0102:0:1.5 +8 17947391 . G A 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=4.67845;LSEQ=TCTATTTGGGAATCAGTAAT;RSEQ=CTATTCTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:8:4,4:27,33:60,8:0.1176:2,2:13.1:1:24.9:1:1:1.22:55.1:7:0.1167:0:1.5 0/1:153:59:34,25:41,52:93,59:0.3856:2,2:19.1:1:25.4:1:0.13407:1.72:46.9:13.75:0.4074:0:1.4 +8 17947397 . C TTTTT 55 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.18077;SOR=Inf;LSEQ=TGGGAATCAGTAATGCTATT;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:30,32:62,0:0:2,0:18.1:1:25.8:1:1:0:55.4:5.2:0.9811:0:0.8 0/1:146:6:0,6:67,68:135,6:0.0411:2,0:17.8:1:21.5:1:0.02909:0:36.7:5:0.04:0.0274:1.5 +8 17947440 . A G 135 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.01869;SOR=0;LSEQ=GAGTCTAGCTCTGTCACCCA;RSEQ=GTTGGAGTGAGGTGGCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:2,18:0,0:0,20:1:0,2:30.6:1:30.4:1:1:0:36.8:19:1:0:1.7 1/0:33:25:7,18:1,7:8,25:0.7576:2,2:24.4:1:29.2:1:0.64284:2.65:40.2:24:0.75:0:1.7 +8 17948372 . G T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AGATCTGCCTCCCCACAGTA;RSEQ=TAGATATGCCTGCCCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:31.5:1:1:0:60:4:1:0:1 +8 17996495 . A G 29 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGAGCATAAAATATTGC;RSEQ=TAGGTTTTAGCATGTCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:29:1:1:0:60:4:1:0:1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:25:0:30:0:1:0:60:2:0.5:0:1 +8 17996542 . C A 29 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24176;SOR=0.19209;LSEQ=CATTCCAATGTCTTCCTTTG;RSEQ=CTAACATTCAGAAGTAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:23.5:1:29:1:1:1.7321:60:4:0.4:0:1 0/1:10:1:1,0:8,1:9,1:0.1:2,0:24:0:30:0:1:0:60:2:0.1:0:1 +8 18040824 . A G 74 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=AATTTCAACATCAGTTGGGG;RSEQ=AGGGGACAAACATTCAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:35.6:1:32:1:1:0:60:10:1:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:22:0:31:0:1:0:60:2:0.5:0:1 +8 18100654 . C T 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60033;SOR=1.1822;LSEQ=AAAAGGGTCACATGTGTATG;RSEQ=CTGTAATATCTGTTTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:30:24,6:80,34:114,30:0.2083:2,2:23.7:1:29.8:1:0.36263:1.69:60:60:0.2113:0:1.1 0/1:198:47:30,17:103,45:148,47:0.2374:2,2:23.1:1:28.3:1:0.47599:1.29522:60:94:0.2423:0:1.1 +8 18100721 . T C 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.06727;SOR=0;LSEQ=ATTTCACTGTGAGTAGTAAG;RSEQ=ACAGTCATGGGGACTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:137,115:252,3:0.0117:2,2:29.3:1:26.3:1:0.59504:2.37471:60:2:0.0079:0:1.7 0/0:372:0:0,0:191,180:371,0:0:2,0:24.8:1:28.1:1:1:0:60:122.667:1:0:0.7 +8 18100755 . T G 251 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAAATTACTGTGTACAGTA;RSEQ=TAGGGCTCTTCAACGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:231:231:111,120:0,0:0,231:1:0,2:24.7:1:32.6:1:1:0:60:230:1:0:1.1 1/0:345:262:121,141:43,40:83,262:0.7594:2,2:24.5:1:31.3:1:0.38043:1.25186:60:51.4:0.7649:0:1.1 +8 18100778 . T A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06773;SOR=0;LSEQ=GGGCTCTTCAACGGAAAAGC;RSEQ=TCCAAGGCTGTCAGGACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:3:2,1:77,124:201,3:0.0147:2,2:11:1:30.3:1:0.56086:3.20:60:6:0.015:0:2 0/0:295:0:0,0:133,162:295,0:0:2,0:1:0:17:0:1:0:60:0:0:0:3 +8 18100789 . T A 34 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.279;SOR=Inf;LSEQ=CGGAAAAGCTTCCAAGGCTG;RSEQ=CAGGACACGATGCAAATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:69,123:192,0:0:2,0:23.8:1:29.8:1:1:0:60:95:1:0:0.8 0/1:289:3:2,1:119,167:286,3:0.0104:2,2:6.7:1:22:1:0.57366:2.80:57.7:2:0.007:0:3.3 +8 18100870 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49884;SOR=Inf;LSEQ=ATGGGCAACAGGGCCTCATC;RSEQ=CCTTTAAGGGCATTGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:13,60:73,0:0:2,0:20:1:32.4:1:1:0:59.7:146:1:0:0.2 0/1:83:2:1,1:10,70:80,2:0.0241:2,2:16.5:1:29:1:0.25173:6.72:60:4:0.0247:0:1 +8 18100881 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2312;SOR=0;LSEQ=GGCCTCATCGCCTTTAAGGG;RSEQ=ATTGAAATAAAACTTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:10,45:55,2:0.0351:2,2:35.5:1:27.5:1:0.3515:4.34:60:4:0.0351:0:1 0/0:61:0:0,0:9,52:61,0:0:2,0:18.6:1:30.6:1:1:0:60:19.333:1:0:0.1 +8 18100994 . G A 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22078;SOR=0;LSEQ=CTGTTTTTTTTCTTTCAGAA;RSEQ=GACACATGTGATTGTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:38:1:32.8:1:1:0:60:8:0.5:0:1.3 0/0:5:0:0,0:0,5:5,0:0:0,0:27:1:31.2:1:1:0:60:10:1:0:0 +8 18464688 . C A 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.17741;LSEQ=CTTTCTCTAATCTCACTCAA;RSEQ=TATAGGACCTTCAAAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:18.6:1:31.9:1:1:0:60:14:0.6364:0:1.1 1/1:5:4:4,0:1,0:1,4:0.8:0,0:35:1:31.5:1:1:0:60:8:0.8:0:1.3 +8 18464759 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.26488;SOR=Inf;LSEQ=AGGCACAGTCTCTGTGCCTG;RSEQ=CCCCTCAGGTGCTCCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:26,0:26,0:0:1,0:25.1:1:32.6:1:1:0:60:52:1:0:0.9 0/1:38:3:3,0:35,0:35,3:0.0789:1,0:12:1:29.3:1:1:0:60:6:0.0789:0:2.7 +8 18464798 . G A 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.99845;LSEQ=CTCCACATTTCTGCAGAATA;RSEQ=TTATCTAATATTACTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:49:40:35,5:8,1:9,40:0.8163:2,2:20.8:1:30.4:1:1:1.13985:60:80:0.8163:0:1 1/1:87:71:65,6:15,1:16,71:0.8161:1,2:21.8:1:29.3:1:1:1.37988:60:142:0.8161:0:1.1 +8 18464826 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.50799;SOR=Inf;LSEQ=ATATTACTAATAATTACAGA;RSEQ=GTAGTAATAGCACAGCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:102,25:127,0:0:2,0:20.2:1:30.9:1:1:0:59.7:126:1:0:0.4 0/1:168:2:1,1:123,43:166,2:0.0119:2,2:38.5:1:31:1:0.45637:2.83924:60:4:0.012:0:2.5 +8 18464842 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27589;SOR=Inf;LSEQ=CAGAAGTAGTAATAGCACAG;RSEQ=AAATGATTGCTGAACACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:0:0,0:130,45:175,0:0:2,0:24:1:32.6:1:1:0:59.8:174:1:0:0.4 0/1:258:3:1,2:166,89:255,3:0.0116:2,2:16.7:1:25.3:1:0.28467:3.71027:60:6:0.0117:0:1.3 +8 18464910 . G A 156 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=26.41869;LSEQ=ACCTGTATAAACAAAAGCCC;RSEQ=TAAGTCTATGAGGGATCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:1:1,0:192,169:361,1:0.0028:2,0:1:0:26:0:1:0:60:2:0.0028:0:1 0/1:527:36:16,20:242,248:490,36:0.0683:2,2:29.8:1:30.2:1:0.60752:1.2193:60:35:0.0672:0:1.1 +8 18464930 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01248;SOR=1.50359;LSEQ=GTAAGTCTATGAGGGATCCA;RSEQ=GGTTATAACCTCCATCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:81:36,45:123,136:259,81:0.2375:2,2:25.1:1:30.3:1:0.70225:1.13011:60:39.5:0.2358:0:1.1 0/1:492:157:77,80:160,173:333,157:0.3191:2,2:25.6:1:30:1:0.84696:1.04:60:314:0.3211:0:1.1 +8 18464950 . C T 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=CGGTTATAACCTCCATCTCA;RSEQ=AGATGTGGAACCTATGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:284:0:0,0:109,175:284,0:0:2,0:25.2:1:32.1:1:1:0:60:55.8:1:0:0.4 0/1:442:21:8,13:196,225:421,21:0.0475:2,2:23.6:1:28.8:1:0.50681:1.41446:60:42:0.0476:0:1 +8 18916823 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5182;SOR=1.65716;LSEQ=CCTTAGACCCCCTTTACCTG;RSEQ=GTAGGAAGATGTCCCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:6,0:6,8:0.5714:0,0:20.4:1:29.1:1:1:0:60:16:0.5714:0:1 1/0:42:29:29,0:12,1:13,29:0.6905:1,1:20.9:1:28.1:1:0.30952:0:60:28:0.6829:0:1 +8 18916911 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10795;SOR=0;LSEQ=AAAAGGAGAGCTCATGAGAA;RSEQ=CACAAGGAAAGCAGGGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:2:1,1:102,34:136,2:0.0145:2,2:43:0:31.5:1:0.4443:2.97127:60:4:0.0146:0:2.5 0/0:281:0:0,0:170,111:281,0:0:2,0:26.1:1:31.3:1:1:0:60:39.143:1:0:0.3 +8 18916918 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.10266;SOR=0;LSEQ=GAGCTCATGAGAAGCACAAG;RSEQ=AAAGCAGGGTACACCAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:103,36:139,2:0.0142:2,2:40.5:1:30:0:0.45735:2.83585:60:4:0.0145:0:2.5 0/0:298:0:0,0:177,121:298,0:0:2,0:26.3:1:30.4:1:1:0:60:73.5:1:0:0.3 +8 18916990 . A C 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.24799;LSEQ=GCAGCTGGTGCAGAACAAGA;RSEQ=ACTAGCCCCAGCAATCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:200:142:74,68:24,33:57,142:0.71:2,2:25.1:1:32.4:1:0.21361:1.49:60:141:0.7121:0:1.1 0/1:350:132:68,64:95,121:216,132:0.3771:2,2:22.8:1:31.4:1:0.18508:1.35:60:65:0.379:0:1.2 +8 18917036 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14632;SOR=0;LSEQ=AGAAAAGTCTAAGATTTAAG;RSEQ=CAGTATCAGGTGGGACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:63,104:167,2:0.0118:2,2:20:1:31.5:1:1:1.65:60:4:0.0121:0:2 0/0:272:0:0,0:104,168:272,0:0:2,0:29:0:15:0:1:0:60:0:0:0:1 +8 18917043 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2863;SOR=Inf;LSEQ=TCTAAGATTTAAGCCAGTAT;RSEQ=AGGTGGGACCAAAGTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:57,103:160,0:0:2,0:24.8:1:32.2:1:1:0:60:159:1:0:0.5 0/1:253:3:2,1:95,154:249,3:0.0119:2,2:19:1:25.7:1:0.56073:3.23:60:6:0.0119:0:1 +8 18917162 . A C 76 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.06846;SOR=0;LSEQ=GTTAGTCAAGAAATTTAAAA;RSEQ=ATTTCTACGTCTGTAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:0,21:21,5:0.1923:1,0:17.6:1:33:1:1:0:60:10:0.1923:0:1.2 0/0:18:0:0,0:0,18:18,0:0:1,0:20.4:1:30.7:1:1:0:60:36:1:0:0.2 +8 18917215 . A G 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAATCATTCCCACAAGA;RSEQ=AAAGAAGAAAGGTTAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:27.7:1:31.3:1:1:0:60:9:1:0:1.5 1/1:3:3:0,3:0,0:0,3:1:0,0:14.7:1:32:0:1:0:60:6:1:0:1 +8 19097201 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48949;SOR=0;LSEQ=GCCTTCTGTCTTCTGTATTT;RSEQ=TGTGTCCAAATTTCTATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:4,14:18,2:0.1:2,2:15:1:32.5:1:0.44737:3.24:60:4:0.1:0:1 0/0:17:0:0,0:4,13:17,0:0:2,0:24.2:1:30:1:1:0:60:16:1:0:0.1 +8 21417475 . C T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.67307;SOR=1.56399;LSEQ=GGACAGCACTTTCCAGATGA;RSEQ=CCCCATCTGTTCCTCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:2,3:7,1:8,5:0.3846:2,2:16.8:1:30.6:1:0.21678:8.36696:60:10:0.3846:0:1.4 1/0:8:4:3,1:3,1:4,4:0.5:2,2:24:1:29.8:1:1:1:60:8:0.5:0:1 +8 21417519 . CGAT C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=0.73782;SOR=0.69227;LSEQ=GATGATGATGAAGATGATGA;RSEQ=GATGATGATGATGATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:2,5:7,5:12,7:0.3684:2,2:34.1:1:31:1:0.34985:3.26886:60:14:0.3684:0:1 0/1:21:6:3,3:7,5:12,6:0.2857:2,2:32.2:1:31.5:1:1:1.3738:53.7:12:0.2857:0:0.3 +8 22248197 . C T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49708;SOR=Inf;LSEQ=ATTGCTGGAAGATGGTGGTT;RSEQ=CAGCTGAAAGGCTTTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:32,54:86,0:0:2,0:27.5:1:30.9:1:1:0:59.7:20.5:1:0:0.1 0/1:86:2:1,1:35,49:84,2:0.0233:2,2:7:0:31:1:1:1.39:60:4:0.0238:0:1.5 +8 22248226 . C CT 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.01836;LSEQ=AGGCTTTTTAAAATTTTTAA;RSEQ=TTTTTTTTTTTAACAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:4:0,4:18,37:55,4:0.0678:2,0:23.8:1:32:0:0.30274:0:60:8:0.0678:0:0 0/1:58:4:0,4:21,33:54,4:0.069:2,0:26:1:31:0:0.28576:0:60:8:0.0702:0:0 +8 22438859 . C G 86 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00152;SOR=0;LSEQ=TCCCTTCTCCAGCTGGGCCA;RSEQ=GGTCTGAGCATGCCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:5,1:9,2:11,6:0.3529:2,2:28:1:33.5:1:1:1.10:60:12:0.3529:0:1 0/0:28:0:0,0:14,13:27,0:0:2,0:14.9:1:29.3:1:1:0:60:54:0.9643:0:0.2 +8 22440434 . G C 30 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATGCCCACCCCCCCCCCC;RSEQ=CCCCCATCTCCCGCCTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:0,2:2,2:0.5:0,0:6.5:1:30:1:0.33333:0:60:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 22458349 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51954;SOR=0;LSEQ=CAGCCTTCAGGAATGCTGGG;RSEQ=GTGTTGGGGGTGGCCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:11,6:17,2:0.1053:2,2:13.5:1:29.5:1:1:1.77272:60:4:0.1053:0:1.5 0/0:11:0:0,0:6,5:11,0:0:2,0:16.9:1:29.9:1:1:0:60:22:1:0:0.2 +8 22458401 . C G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=Inf;LSEQ=GACTCTCCATGCAGATGGGG;RSEQ=TGGCGAGGGCCTGGCACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:21,0:0:2,0:21.8:1:32.7:1:1:0:60:42:1:0:0.4 0/1:15:2:1,1:5,8:13,2:0.1333:2,2:40.5:1:31:1:1:1.55:60:4:0.1429:0:2 +8 22994522 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGACTGCTGATTTGTAT;RSEQ=CAGGCAACCCATGTAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:30.5:1:1:0:52:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 22995745 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.543;SOR=Inf;LSEQ=CTGGAACCAGCAGCCTCCTC;RSEQ=TCTGACACCCTTCAGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:16,32:48,0:0:2,0:23.1:1:32.7:1:1:0:60:96:1:0:0.1 0/1:90:2:1,1:36,51:87,2:0.0222:2,2:44:1:29:1:1:1.41:60:4:0.0225:0:1 +8 23531306 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49936;SOR=Inf;LSEQ=TTGGAGATGGGTAATAAATG;RSEQ=TTCTGGATGACCAGGTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:178,8:186,0:0:1,0:22:1:32.6:1:1:0:60:185:1:0:0.1 0/1:200:2:1,1:189,9:198,2:0.01:1,2:5.5:1:27:1:0.09774:19.975:60:4:0.0101:0:1.5 +8 23531563 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.5119;SOR=Inf;LSEQ=AACTCCTCCCTTCCTGGTGG;RSEQ=CACCTCCAGGTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:4,104:108,0:0:1,0:23.6:1:32.4:1:1:0:60:53:1:0:0 0/1:151:2:0,2:12,135:147,2:0.0132:2,0:39.5:1:29.5:1:1:0:60:4:0.0133:0:1 +8 23535883 . C T 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0104;SOR=Inf;LSEQ=TGATGGTTGCGTATGTATTC;RSEQ=ATGGTATATATGCACATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:117,0:117,0:0:1,0:26.2:1:31.5:1:1:0:60:38:1:0:0 0/1:106:6:6,0:99,1:100,6:0.0566:1,0:26.8:1:32.7:1:1:0:60:12:0.0577:0:1.3 +8 23536098 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.35556;LSEQ=GCTGAGGCTTTTGATCACCA;RSEQ=AGGTTGCAATTGGTGTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:83:30,53:216,329:545,83:0.132:2,2:24.5:1:32.2:1:0.62947:1.15959:60:82:0.134:0:1.1 0/1:790:267:111,156:225,297:522,267:0.338:2,2:25.7:1:31.1:1:0.70402:1.06458:60:43.5:0.3381:0:1.1 +8 23538533 . A G 103 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10839;SOR=0.08049;LSEQ=TGACCTACAGTATGCACTGG;RSEQ=GGAATGACTTAGGTATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:1,9:0.9:0,0:27.9:1:32.7:1:1:0:60:18:0.9:0:1 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:45:0:30:0:1:0:60:2:0.3333:0:1 +8 23540036 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21074;SOR=0;LSEQ=GGAAGGTCCCTCTGCCTGTC;RSEQ=CCGCGGAGCCCCGCGTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:48,15:63,2:0.0308:2,2:19:1:32.5:1:0.43462:3.13049:60:4:0.0323:0:1 0/0:76:0:0,0:59,16:75,0:0:2,0:20.8:1:29.4:1:1:0:60:74:1:0:0.1 +8 23540054 . C T 21 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50115;SOR=Inf;LSEQ=TCGCCGCGGAGCCCCGCGTC;RSEQ=CTGCACCCCGAGCTCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:66,42:108,0:0:2,0:20:1:30.8:1:1:0:60:53:1:0:0.3 0/1:127:2:1,1:83,42:125,2:0.0157:2,2:19.5:1:21:1:1:1.96487:60:4:0.0161:0:1 +8 23540090 . C T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.30903;SOR=0.22693;LSEQ=TGGGGGTCCGCCTTGGGCTG;RSEQ=CCCCCTTCCCCGGCCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:3:1,2:108,80:188,3:0.0157:2,2:17.3:1:29:1:0.57778:2.68609:60:6:0.0161:0:1 0/0:278:1:0,1:172,105:277,1:0.0036:2,0:1:0:26:0:0.38129:0:60:2:0.0037:0:1 +8 23540338 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.13222;SOR=Inf;LSEQ=AGGACGTGAGCGGCTTGGAC;RSEQ=GGGTCGGCGGCGCGGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:97,145:242,0:0:2,0:25.4:1:30.4:1:1:0:60:79.667:1:0:0.3 0/1:300:4:2,2:119,177:296,4:0.0133:2,2:20.8:1:27.8:1:1:1.49:56.3:3:0.0102:0:1 +8 23540370 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.66274;LSEQ=GCGGCCCCCTCCGCTTTCGC;RSEQ=TCCCCGGGCCGCGGCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:1:1,0:56,108:164,1:0.0061:2,0:1:0:26:0:0.34545:0:60:2:0.0061:0:1 0/1:199:2:1,1:69,128:197,2:0.0101:2,2:23.5:1:28:1:1:1.85:60:4:0.0102:0:1 +8 23540375 . C G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25487;SOR=Inf;LSEQ=CCCCTCCGCTTTCGCCTCCC;RSEQ=GGGCCGCGGCTCCGGAACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:47,101:148,0:0:2,0:25.1:1:30:1:1:0:60:147:1:0:0.6 0/1:180:3:0,3:62,115:177,3:0.0167:2,0:16.7:1:32:0:0.55225:0:60:6:0.0173:0:1 +8 23540377 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50462;SOR=Inf;LSEQ=CCTCCGCTTTCGCCTCCCCG;RSEQ=GCCGCGGCTCCGGAACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:41,94:135,0:0:2,0:26.6:1:30.7:1:1:0:60:44:1:0:0.6 0/1:169:2:1,1:57,110:167,2:0.0118:2,2:27.5:1:29:1:1:1.92:60:4:0.0121:0:2 +8 23540382 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20574;SOR=0;LSEQ=GCTTTCGCCTCCCCGGGCCG;RSEQ=GGCTCCGGAACCCTGAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:39,88:127,2:0.0154:2,2:39:1:30.5:1:0.52568:2.24:60:4:0.0157:0:1.5 0/0:156:0:0,0:55,101:156,0:0:2,0:23.8:1:28.9:1:1:0:60:25:1:0:0.5 +8 23540408 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.49701;SOR=Inf;LSEQ=CGGAACCCTGAGCATCCCGG;RSEQ=GGCCCCGCCTTGGCCTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:14,64:78,0:0:2,0:23:1:30:1:1:0:60:25:1:0:1.1 0/1:81:2:1,1:20,59:79,2:0.0247:2,2:19.5:1:28:1:0.4537:2.90:60:4:0.025:0:2 +8 23540417 . C T 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00028;SOR=0;LSEQ=GAGCATCCCGGCGGCCCCGC;RSEQ=TTGGCCTGAATGCACCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:66:9,57:0,0:0,66:1:0,2:21.1:1:30.5:1:1:0:60:32:1:0:1.2 1/1:66:54:14,40:2,10:12,54:0.8182:2,2:23:1:29.1:1:0.715:1.74:60:108:0.8182:0:1.1 +8 23548231 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08867;SOR=Inf;LSEQ=TTGCTCATACCCATTCATGC;RSEQ=TCCTATCTCATACCTGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:20,0:20,0:0:1,0:26.4:1:32.8:1:1:0:60:40:1:0:0.2 0/1:9:2:1,1:7,0:7,2:0.2222:0,2:11.5:1:32:1:0.22222:0:60:4:0.2222:0:3 +8 23548345 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20801;SOR=Inf;LSEQ=CTCTCCCTGCAGGCCTTTCT;RSEQ=TAAGGCCAAGGCATGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:96,0:96,0:0:1,0:23.8:1:32.6:1:1:0:59.5:47:1:0:0.1 0/1:81:2:2,0:76,3:79,2:0.0247:1,0:17:1:32.5:1:1:0:60:4:0.0247:0:1 +8 23548490 . GC G 198 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAGTATTTTGCTAACAGT;RSEQ=CCTGGTCACCTTTCCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1061:0:0,0:606,453:1059,0:0:2,0:24.8:1:31.5:1:1:0:59.9:39.731:0.9981:0:0.2 0/1:1451:81:44,37:747,621:1368,81:0.0558:2,2:24.4:1:31.3:1:1:1.01152:59.9:162:0.0564:0.0048:0.3 +8 23548530 . T C 214 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCCTCCATGGCTGCCGGCT;RSEQ=CTGGAGAGCCCCAGGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1168:111:62,49:542,513:1055,111:0.095:2,2:24.8:1:31.5:1:0.42452:1.20:60:36:0.0938:0:1.1 0/0:1629:0:0,0:833,794:1627,0:0:2,0:25.4:1:29.1:1:1:0:59.9:59.259:0.9988:0:0.2 +8 23548749 . T C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42581;SOR=0;LSEQ=CTCTGCCACTCCCTGCCGCA;RSEQ=AGTGCCCACCATAAAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:89:89:2,87:0,0:0,89:1:0,1:25.5:1:32.3:1:1:0:59.5:28.667:1:0:1.2 1/1:66:65:3,62:0,1:1,65:0.9848:0,1:23.5:1:32:1:1:0:60:130:0.9848:0:1.1 +8 23548805 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.16156;SOR=Inf;LSEQ=CTCCTGGCGCCCCAACATGA;RSEQ=GCCTTCCCAGGTGGATGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:29,0:0:1,0:25:1:29.1:1:1:0:57.8:13.5:1:0:0.7 0/1:20:2:0,2:3,15:18,2:0.1:2,0:8.5:1:30:1:1:0:60:4:0.1:0:2 +8 23560366 . C A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12409;SOR=Inf;LSEQ=TGCGTGGACGTGAGCTGCAG;RSEQ=GCGCTGGCCAGGTGCTCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:90,152:242,0:0:2,0:26.5:1:30.5:1:1:0:59.5:79.667:1:0:0.1 0/1:256:4:2,2:106,146:252,4:0.0156:2,2:14.3:1:27.8:1:1:1.38:57.8:8:0.0159:0:1.3 +8 23560375 . C A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24843;SOR=Inf;LSEQ=GTGAGCTGCAGCGCGCTGGC;RSEQ=AGGTGCTCGCGCTCGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:80,143:223,0:0:2,0:24.4:1:31.6:1:1:0:59.6:54.75:1:0:0.1 0/1:228:3:2,1:88,137:225,3:0.0132:2,2:16.3:1:22:1:0.56359:3.10:47.7:2:0.009:0:2.3 +8 23560437 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50236;SOR=0;LSEQ=GAAGCGCCGCTCCAGGGCCA;RSEQ=CACCTGCGCCTGCGAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:5,62:67,2:0.029:2,2:40.5:1:30:1:0.16752:11.41:60:4:0.029:0:1 0/0:55:0:0,0:8,47:55,0:0:2,0:26:1:31.4:1:1:0:60:54:1:0:0.2 +8 23560449 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56964;SOR=2.84854;LSEQ=CAGGGCCAGCACCTGCGCCT;RSEQ=CGAAAAGAGCACGCGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:1:0,1:6,53:59,1:0.0167:2,0:26:0:27:0:1:0:60:2:0.0169:0:1 0/1:43:2:1,1:7,34:41,2:0.0465:2,2:42:1:27.5:1:0.34109:4.61:60:4:0.0465:0:1 +8 24533193 . C T 266 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00992;LSEQ=ATTTGCTTGAAAATAAATTA;RSEQ=GATTCACAACACAAAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:435:433:193,240:0,0:0,433:0.9954:0,2:24.6:1:30.4:1:1:0:60:85.6:1:0:1.1 1/0:600:409:205,204:86,105:191,409:0.6817:2,2:25.1:1:29.5:1:0.25532:1.23:60:408:0.6823:0:1.1 +8 25057387 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.23881;SOR=Inf;LSEQ=TGCTGAGCTTTGAACTTCCT;RSEQ=CAGAACAAAAGTAAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:14,20:34,0:0:2,0:21.5:1:29.9:1:1:0:60:33:1:0:0.1 0/1:33:2:1,1:14,17:31,2:0.0606:2,2:41.5:1:29.5:1:1:1.21:60:4:0.0606:0:1.5 +8 25057479 . AT A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.46249;LSEQ=GACTGCATGATTTGTTTTAG;RSEQ=TTGTTAATTTACATTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,1:1,9:0.9:0,0:21.6:1:31.7:1:1:0:60:18:0.9:0.4:0.1 1/1:10:8:0,8:0,2:2,8:0.8:0,0:37.1:1:29.5:1:1:0:60:16:0.8:0:0 +8 26148748 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAGAGCACGTAAACTGGA;RSEQ=TCCTAAGCCCGCCCCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:32:1:28.5:1:1:0:60:4:1:0:1 +8 28157847 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10714;SOR=Inf;LSEQ=GAACAAGATGAAGATGCTTA;RSEQ=AAGAAACAGTTCTCTCAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:1,0:4,1:5,1:0.1667:2,0:31:0:34:0:1:0:60:2:0.1667:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:30:1:1:0:33:4:1:0:1.5 +8 28157994 . C G 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=0.12258;LSEQ=TTAAAAAGAAGAGGTGGAAC;RSEQ=ATCCCAAAATGTCCCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:14:8,6:16,13:29,14:0.3256:2,2:25.7:1:30.9:1:1:1.08:49.6:28:0.3256:0:1.1 0/1:73:4:3,1:40,29:69,4:0.0548:2,2:25.5:1:29:1:0.63911:2.15:50.8:8:0.0548:0:1 +8 28158029 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5292;SOR=Inf;LSEQ=CTCACTCAGAAGAAAGATCA;RSEQ=GTAGCTCAAAAGAAGGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:27,24:51,0:0:2,0:30.7:1:32.8:1:1:0:52.7:50:1:0:0.4 0/1:86:2:1,1:42,42:84,2:0.0233:2,2:31:0:31.5:1:1:1:48:4:0.0235:0:1.5 +8 28158138 . A G 65 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.62785;SOR=0.41915;LSEQ=AGACAATAAACTTATGGACA;RSEQ=CAACTAAAAAAAAAGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:4:0,4:0,13:13,4:0.2353:1,0:21.5:1:32.8:1:1:0:46.5:8:0.2353:0:1 0/1:9:1:0,1:1,7:8,1:0.1111:2,0:23:0:33:0:1:0:38:2:0.1111:0:1 +8 29496672 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20681;SOR=0;LSEQ=AAAAATAGAACTTAATTGAA;RSEQ=GTGATTTTGAAAGAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:154,33:187,2:0.0106:2,2:23.5:1:32.5:1:0.32821:4.61246:60:4:0.0106:0:1 0/0:226:0:0,0:176,50:226,0:0:2,0:21.7:1:31.2:1:1:0:60:225:1:0:0.2 +8 29496762 . T G 288 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.70994;LSEQ=TGGGTCAGGCTGAGTTGGAC;RSEQ=CTTGGCAATTCTGAGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:637:454:228,226:91,90:181,454:0.7127:2,2:28:1:30.9:1:1:1.00224:59.9:89.8:0.7138:0:1.1 1/1:817:737:348,389:37,39:76,737:0.9021:2,2:27.3:1:30.3:1:0.81067:1.06038:60:80.889:0.9043:0:1.2 +8 29496868 . T C 130 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TGATGGTTAAGAACATAGTC;RSEQ=ATGGGGTCAGACATGCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:17:2,15:11,117:128,17:0.1172:2,2:16.1:1:31.9:1:0.65101:1.41:60:34:0.1172:0:1 0/0:129:0:0,0:13,116:129,0:0:2,0:23.1:1:28.1:1:1:0:60:258:1:0:0 +8 29497050 . TA T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTTGGCTCAGTCAGCAC;RSEQ=AAAAAATGGTGGCGATGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1:0,0:24.9:1:29.6:1:1:0:60:14:1:0.2857:0.1 1/1:2:2:0,2:0,0:0,2:1:0,0:38.5:1:31.5:1:1:0:60:4:1:0:0 +8 29885106 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21445;SOR=0;LSEQ=GGCTCACCCTCCGAAGGCAG;RSEQ=CTCGCCGAAGGCAGACGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:2,0:97,5:102,2:0.0192:1,0:17:1:32:0:1:0:60:4:0.0192:0:1.5 0/0:120:0:0,0:113,7:120,0:0:2,0:24.2:1:31.3:1:1:0:59.5:59:1:0:0.5 +8 29885149 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00116;SOR=0.56537;LSEQ=CGGACTTGGTCCTGCACAGC;RSEQ=GGCGCGGAGCAGCGCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:101:74,27:107,31:138,101:0.4226:2,2:23.6:1:30:1:0.45006:1.25813:53:49.5:0.4231:0:1.1 0/1:359:105:74,31:177,76:253,105:0.2925:2,2:22.8:1:29:1:1:1.02:53.5:51.5:0.2943:0:1.2 +8 29885245 . C A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00342;SOR=0.72547;LSEQ=CAAAATGCCCAAGAAGACGC;RSEQ=GACGCCCATCCAGCTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:631:213:102,111:214,204:418,213:0.3376:2,2:25.2:1:31.1:1:0.44939:1.14134:57.8:70:0.3382:0:1.2 0/1:1045:282:141,141:393,367:760,282:0.2699:2,2:24.9:1:29.6:1:0.62618:1.07076:57:55.4:0.2692:0:1.3 +8 29885635 . A G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06163;SOR=0.73743;LSEQ=GCTTCTGTGGTGCATTCTAC;RSEQ=GCGAGAGGCGAGATCAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:98:52,46:107,97:204,98:0.3245:2,2:26.9:1:30.2:1:1:1.02:58.4:48:0.3243:0:1.3 0/1:478:125:63,62:176,176:352,125:0.2615:2,2:23.1:1:29.2:1:1:1.02:57:40.667:0.2607:0:1.3 +8 29885706 . C T 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00319;SOR=0.58692;LSEQ=GGATCAAGTCCTGAAGAAAG;RSEQ=GGGAAGAATTCCTGAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:83:44,39:122,122:244,83:0.2538:2,2:25.6:1:30.3:1:0.70333:1.13:57.5:82:0.2531:0:1.3 0/1:487:81:36,45:198,208:406,81:0.1663:2,2:25.7:1:29.4:1:0.54287:1.18948:57.6:80:0.166:0:1.4 +8 29885884 . G A 185 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15271;SOR=1.33188;LSEQ=GGGTCAGTGGGCAGCTCATC;RSEQ=ACTCCATGGCCAACTCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:44:25,19:261,267:528,44:0.0768:2,2:26.5:1:30.7:1:0.43303:1.35:59.4:88:0.0786:0:1.8 0/1:802:80:44,36:379,343:722,80:0.0998:2,2:24.8:1:29.3:1:0.72385:1.11:59.3:39:0.0979:0:1.7 +8 29885928 . C G 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.43646;LSEQ=GGCCCAAGGTCCTACATGTC;RSEQ=CCAGAAAGATTCCAGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:208:104,104:158,178:336,208:0.381:2,2:25:1:30.7:1:0.53681:1.13:51.1:33.667:0.3819:0:1.3 0/1:775:164:81,83:258,288:546,164:0.2116:2,2:22.9:1:30.4:1:0.65635:1.09:49:163:0.2148:0:1.2 +8 29886141 . G C 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00061;SOR=0.58788;LSEQ=CCTCTTAGCTCATATGGAAT;RSEQ=GACAGCCGACCTCCCGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:110:48,62:160,182:342,110:0.2428:2,2:25.8:1:31.1:1:0.58402:1.13521:57:109:0.2433:0:1.9 0/1:637:101:48,53:254,279:533,101:0.1586:2,2:25.7:1:29.8:1:1:1.00522:55.9:32.667:0.1571:0:2 +8 29886157 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00015;SOR=0.55835;LSEQ=GAATGGACAGCCGACCTCCC;RSEQ=TGGCAATTTTTGAGTTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:114:51,63:160,174:334,114:0.2545:2,2:23.3:1:30.9:1:0.58796:1.13558:56.6:56:0.254:0:1.9 0/1:650:104:51,53:264,280:544,104:0.16:2,2:25.1:1:29.8:1:1:1.02:54.1:208:0.1622:0:2 +8 29886263 . TA T 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00049;SOR=0.62075;LSEQ=TTTTGTGAATAAATGCCTAA;RSEQ=AAAACCCCGTAGAGAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:358:209:99,110:67,82:149,209:0.5838:2,2:24:1:31.1:1:0.6685:1.10:53.6:103.5:0.5831:0.1145:0.2 0/1:591:275:142,133:155,161:316,275:0.4653:2,2:25.4:1:29.7:1:0.564:1.11:53.9:90.667:0.4658:0.0745:0.2 +8 29886372 . G A 55 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0271;SOR=0;LSEQ=GTTGGCTCTGCTCCACCATC;RSEQ=GGCTTAACCAGCCCAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:4:4,0:115,144:259,4:0.0152:2,0:5.8:1:27.5:1:0.04076:0:39:8:0.0154:0:1 0/0:383:0:0,0:159,224:383,0:0:2,0:21.2:1:29.3:1:1:0:42.2:46.875:1:0:0.4 +8 29886373 . G A 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.78686;SOR=1.06269;LSEQ=TTGGCTCTGCTCCACCATCG;RSEQ=GCTTAACCAGCCCAGCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:71:35,36:81,108:189,71:0.2731:2,2:15.9:1:30.6:1:0.40143:1.29:28.4:34.5:0.2727:0:1.1 0/1:368:105:48,57:105,158:263,105:0.2853:2,2:17.6:1:28.2:1:0.34905:1.27:28.8:20:0.2793:0:1.2 +8 29886452 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50001;SOR=Inf;LSEQ=CAAAGAGCAAGTCCCCTGCC;RSEQ=AGTGGTTTGCCATGTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:41,129:170,0:0:2,0:22.1:1:31.8:1:1:0:36.4:84:1:0:0.3 0/1:189:2:1,1:49,138:187,2:0.0106:2,2:12:1:27:1:0.46015:2.80:44:4:0.0107:0:1 +8 29886463 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.81044;LSEQ=TCCCCTGCCCAGTGGTTTGC;RSEQ=ATGTCACTTTTGGGCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:0,1:23,104:127,1:0.0078:2,0:22:0:11:0:1:0:29:0:0:0:1 0/1:142:2:1,1:31,109:140,2:0.0141:2,2:21:1:30:1:0.40116:3.48:28:4:0.0145:0:1 +8 30349808 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.52512;SOR=Inf;LSEQ=ATAAAGCACTTTCACACATG;RSEQ=ATGCATCCATTGTCTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:64,11:75,0:0:2,0:23.1:1:31.9:1:1:0:60:36.5:1:0:0.1 0/1:121:2:1,1:92,27:119,2:0.0165:2,2:24:1:26.5:1:0.41074:3.36408:60:4:0.0168:0:1 +8 30349837 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.52752;SOR=Inf;LSEQ=ATTGTCTCATTTTGCCTGAT;RSEQ=AGTGCATAATATGTATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:81,42:123,0:0:2,0:23.8:1:28.7:1:1:0:60:60.5:1:0:0.1 0/1:201:2:1,1:126,73:199,2:0.01:2,2:30.5:1:31:1:1:1.72103:60:4:0.0101:0:1 +8 30349914 . A G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29229;SOR=1.2352;LSEQ=AGATTAATGTGTAATTATGT;RSEQ=TAATTAGTCCTTTCTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:62:27,35:56,73:129,62:0.3246:2,2:27.1:1:31.2:1:1:1.01:60:14.5:0.3118:0:1.1 0/1:314:117:55,62:82,113:195,117:0.3726:2,2:26:1:31.1:1:0.41129:1.22:60:116:0.3742:0:1.1 +8 30349928 . C T 36 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.05647;SOR=0;LSEQ=TTATGTATAATTAGTCCTTT;RSEQ=TTTAAAGAGCTGACACCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:0,3:79,102:181,3:0.0163:2,0:8:1:23.3:1:0.26096:0:60:2:0.0111:0:2.7 0/0:294:0:0,0:125,169:294,0:0:2,0:25.3:1:30.6:1:1:0:60:97:1:0:0.5 +8 30349976 . T TA 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.03261;SOR=1.95636;LSEQ=ACACCAGTAACCCTTTGACT;RSEQ=AAAAAAAAAATACCCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:20:7,13:18,52:70,20:0.2062:2,2:33.4:1:30.5:1:0.4112:1.55:60:40:0.2083:0:0.2 0/1:160:54:19,35:35,68:103,54:0.3375:2,2:27.7:1:28.6:1:1:1.05:59.8:108:0.3439:0.025:0.3 +8 31397667 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.3021;SOR=0.2858;LSEQ=TTAGTGACCACGTGTGTTGA;RSEQ=GACAGGTAAATGTTTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:113,46:159,2:0.0124:2,2:31:1:29.5:1:0.49992:2.44099:60:4:0.0125:0:1 0/0:280:1:1,0:171,108:279,1:0.0036:2,0:4:0:29:0:1:0:60:2:0.0036:0:2 +8 31397748 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01085;LSEQ=GTTAATAATAATTAACACTA;RSEQ=GGAGGCAGCTGACAACTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:261:159:72,87:52,50:102,159:0.6092:2,2:24.5:1:31.1:1:0.37717:1.25555:59.9:158:0.61:0:1.1 1/0:340:208:93,115:63,69:132,208:0.6118:2,2:24.3:1:29.7:1:0.65524:1.12863:59.8:103:0.6113:0:1.1 +8 31398144 . T C 32 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTTTATTGTGAGGCACC;RSEQ=GTATGGTTTAGACTTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:33:1:32:0:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:25:0:1:0:60:2:1:0:2 +8 34731644 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54167;SOR=Inf;LSEQ=AAACTAAGATACAGCCTTTT;RSEQ=GCTGGAACCGCCATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:11,0:0:2,0:32.7:1:32.5:1:1:0:59.9:22:1:0:0.1 0/1:22:2:1,1:13,7:20,2:0.0909:2,2:13.5:1:29:1:1:1.80284:41:4:0.0909:0:1.5 +8 34731853 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.11178;SOR=0;LSEQ=GCCCCACAAGTGTTACCACG;RSEQ=CAAAACTGGAAGAGTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:58,52:110,2:0.0179:2,2:25:1:28.5:1:1:1.11429:59:4:0.0187:0:1 0/0:222:0:0,0:117,105:222,0:0:2,0:28.6:1:30.3:1:1:0:46:36:1:0:0.1 +8 34731913 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53476;SOR=Inf;LSEQ=GTTGTAAACAAACAAGTTAA;RSEQ=GGCAAGATTCTTGCCAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:21,26:47,0:0:2,0:17.4:1:31.8:1:1:0:33.4:94:1:0:0 0/1:83:2:1,1:31,50:81,2:0.0241:2,2:19:1:28:1:1:1.60:30:4:0.0244:0:1 +8 35982376 . TT C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.53635;SOR=Inf;LSEQ=GGTCTATCCGTTTTGTTAAT;RSEQ=TTTTCAGAAAACCTGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:26,21:47,0:0:2,0:22.1:1:30.1:1:1:0:59.2:94:1:0:0.2 0/1:84:2:1,1:49,32:81,2:0.0238:2,2:6:1:28.5:1:1:1.52314:60:4:0.0247:0.0119:0.5 +8 35982434 . A T 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.51158;LSEQ=TTGGAGGGTTTTTTGTGTTT;RSEQ=TATCTCCTTCAATTCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:1:0,1:27,21:48,1:0.02:2,0:40:0:15:0:0.44898:0:43:0:0:0:5 0/1:100:3:1,2:54,43:97,3:0.03:2,2:27.3:1:22.7:1:0.58673:2.48897:59:2:0.0206:0:3.3 +8 35982438 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54594;SOR=Inf;LSEQ=AGGGTTTTTTGTGTTTATAT;RSEQ=TCCTTCAATTCTTCTCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:47,0:0:2,0:26.2:1:32.2:1:1:0:58.1:46:1:0:0.4 0/1:90:2:1,1:48,40:88,2:0.0222:2,2:21.5:1:29.5:1:1:1.19756:35:4:0.0227:0:3.5 +8 35982446 . A G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29719;SOR=Inf;LSEQ=TTGTGTTTATATCTCCTTCA;RSEQ=TTCTTCTCTGATCTTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,18:39,0:0:2,0:23.4:1:30:1:1:0:58.6:38:1:0:0.4 0/1:75:4:2,2:37,32:69,4:0.0533:2,2:10:1:30:1:1:1.15394:47.5:8:0.0541:0:2.8 +8 35982447 . T C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54393;SOR=Inf;LSEQ=TGTGTTTATATCTCCTTCAA;RSEQ=TCTTCTCTGATCTTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:21,18:39,0:0:2,0:22.4:1:30.9:1:1:0:58.6:78:1:0:0.4 0/1:74:2:1,1:38,34:72,2:0.027:2,2:7:0:33:0:1:1.11596:60:4:0.0282:0:1 +8 35982451 . T G 60 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29315;SOR=Inf;LSEQ=TTTATATCTCCTTCAATTCT;RSEQ=CTCTGATCTTAATTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:21,13:34,0:0:2,0:21.3:1:30.3:1:1:0:58.4:68:1:0:0.5 0/1:61:4:2,2:33,24:57,4:0.0656:2,2:5:1:30.3:1:1:1.36771:47.5:8:0.0667:0:2.8 +8 36091703 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTTTACTTACAAAACA;RSEQ=AAATTCAGAGATACAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:27.5:1:1:0:60:4:1:0:1 +8 36092310 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20119;SOR=0;LSEQ=TTTCCTTTTTTCCCCTTTCT;RSEQ=TGCTGTCAAATCGACTATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:82,32:114,2:0.0172:2,2:23.5:1:32:1:0.48981:2.53872:60:4:0.0177:0:1 0/0:142:0:0,0:96,46:142,0:0:2,0:23.5:1:29.7:1:1:0:60:141:1:0:0.1 +8 36092421 . C T 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.94105;LSEQ=TACGCAGAACTCTCTCTGGG;RSEQ=GCCCAATGCTCCGTGATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:95:46,49:54,62:116,95:0.4481:2,2:23.4:1:30.1:1:0.88984:1.08:60:94:0.4541:0:1.2 1/1:263:218:105,113:24,21:45,218:0.8289:2,2:26.8:1:29.3:1:0.62366:1.22896:60:108:0.8276:0:1.2 +8 36092461 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17296;SOR=0;LSEQ=ACTGATCTGTGAAGCCAGAA;RSEQ=CCTCTCTGCTTTTGAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:2:1,1:60,93:153,2:0.0129:2,2:15.5:1:30.5:1:1:1.55:60:4:0.0133:0:1 0/0:217:0:0,0:91,126:217,0:0:2,0:24.1:1:28.6:1:1:0:60:107.5:1:0:0.7 +8 37136808 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47368;SOR=0;LSEQ=CACGAACCCATGCTACCGGG;RSEQ=CCTAGCGTCCCAACCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:1,7:8,2:0.2:2,2:5.5:1:29.5:1:0.37778:5.29:24:4:0.2:0:1.5 0/0:10:0:0,0:4,6:10,0:0:2,0:23.1:1:31:1:1:0:60:20:1:0:0 +8 37137291 . C T 41 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=Inf;LSEQ=AGGGGTGGCTACAGTATCTG;RSEQ=GGACCAGCAGACTTAGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:32:0:1:0:60:2:1:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:33.3:1:26:1:1:0:54.7:6:1:0:1.7 +8 37137809 . GA G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.08399;SOR=3.15455;LSEQ=GGAGATGGGAAAGAGTCAAT;RSEQ=AAAAAATGCTGAAAACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:2,4:8,10:18,6:0.25:2,2:23.7:1:33:1:1:1.56956:56.3:12:0.25:0:0.5 1/0:27:14:5,9:7,6:13,14:0.5185:2,2:20.5:1:31.1:1:0.44948:2.04175:47.7:28:0.5185:0.037:0.3 +8 37137887 . G C 73 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1451;SOR=6.57383;LSEQ=ACATCTCTCCATCAGGGGCA;RSEQ=AGAACTGGGTGGAGGATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:1,5:6,1:0.1429:2,0:20:0:28:0:1:0:47:2:0.1429:0:1 1/0:9:5:1,4:0,4:4,5:0.5556:0,2:34.6:1:31.6:1:1:0:51:10:0.5556:0:1.2 +8 38271057 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5008;SOR=Inf;LSEQ=TCCTGCCAGCAGGAAAGGGG;RSEQ=CAGGGACGGACAGGTGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:130,19:149,0:0:2,0:21.7:1:29.4:1:1:0:60:15.556:1:0:0.2 0/1:171:2:1,1:130,39:169,2:0.0117:2,2:12.5:1:32:0:0.41417:3.30401:60:4:0.0119:0:2 +8 38271106 . C T 54 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08297;SOR=Inf;LSEQ=GGGGCTGTGGGTGAGGGTTA;RSEQ=AGCTGACGGTGGAGTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:219,109:328,0:0:2,0:28:1:31.9:1:1:0:52.4:40:1:0:0.1 0/1:475:5:1,4:285,185:470,5:0.0105:2,2:23:1:23.4:1:0.0843:6.14006:48.4:4:0.0085:0:1 +8 38271215 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03444;SOR=0;LSEQ=AGGCAGGGCTCCTCGGGCAG;RSEQ=GGCTCATGAGAGAAGACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:4:1,3:151,181:332,4:0.0119:2,2:29.5:1:29.3:1:0.6296:2.49653:60:8:0.012:0:1.3 0/0:442:0:0,0:197,245:442,0:0:2,0:28.6:1:29.8:1:1:0:52.5:48.111:1:0:0.1 +8 38271547 . G A 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCATCATCATGTACCTGCG;RSEQ=CAGGACTGTAAGGTCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:549:0:0,0:205,342:547,0:0:2,0:22.5:1:31.9:1:1:0:60:90.167:0.9963:0:0.1 0/1:607:26:11,15:222,359:581,26:0.0428:2,2:25.6:1:27.7:1:0.68438:1.19:60:52:0.0436:0:1 +8 38271986 . A T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19398;SOR=Inf;LSEQ=TTTCTCTCTGGGGCAGAAAG;RSEQ=GGACTCCTCAGTCCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:173,36:209,0:0:2,0:24.5:1:31:1:1:0:60:208:1:0:0 0/1:165:2:1,1:131,31:162,2:0.0121:2,2:12.5:1:24.5:1:0.35313:4.1751:60:4:0.0123:0:1 +8 38272046 . A T 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.13584;SOR=4.98457;LSEQ=CTAGAAGCTCTCTATCCCAC;RSEQ=CCTCCCTGGCAATTGCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:456:1:0,1:284,171:455,1:0.0022:2,0:1:0:27:0:0.37719:0:60:2:0.0022:0:1 0/1:553:6:1,5:322,224:546,6:0.0108:2,2:14.8:1:25.5:1:0.0867:7.16356:60:12:0.0111:0:1 +8 38272417 . G A 50 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13615;SOR=0.28517;LSEQ=GCTGCCAGGTCTCGGTGTAT;RSEQ=CACTGAGGAAGGAGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:5:3,2:171,314:485,5:0.0102:2,2:21.8:1:21.6:1:0.3525:2.75:60:1.5:0.0063:0:1.4 0/0:683:2:2,0:246,435:681,2:0.0029:2,0:1:0:21.5:1:0.13151:0:60:4:0.003:0:1.5 +8 38272447 . G A 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13094;SOR=Inf;LSEQ=AGGAGGAAGGGAGAGCGGGA;RSEQ=GCGGGGAGGTGAGGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:313:0:0,0:78,235:313,0:0:2,0:22.5:1:31.4:1:1:0:59.9:155.5:1:0:0.1 0/1:380:4:3,1:94,282:376,4:0.0105:2,2:14:1:28:1:0.05284:8.94:60:8:0.0108:0:1 +8 38272475 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49895;SOR=0;LSEQ=GGTGAGGGAGCTGGAAGGCT;RSEQ=TGGGCGGCCGCCACCCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:26,164:190,2:0.0104:2,2:24:1:29:1:0.26211:6.21:60:4:0.0106:0:1 0/0:183:0:0,0:24,158:182,0:0:2,0:22.8:1:31.3:1:1:0:60:90:1:0:0.2 +8 38272485 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49831;SOR=Inf;LSEQ=CTGGAAGGCTCTGGGCGGCC;RSEQ=CCACCCATGCAACTAGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:14,133:147,0:0:2,0:25.8:1:32.1:1:1:0:59.8:72.5:1:0:0.1 0/1:148:2:1,1:12,134:146,2:0.0135:2,2:17.5:1:27:1:0.16851:10.77:60:4:0.014:0:1 +8 38272542 . C G 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TCTGCCACACTGCTCTGCCC;RSEQ=CCGAACCTTTGCTTTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:2,64:66,0:0:1,0:24.3:1:30.7:1:1:0:60:21:1:0:0.2 0/1:51:13:0,13:3,35:38,13:0.2549:2,1:24.9:1:30:1:0.56115:0:60:5.5:0.234:0:1.2 +8 38273261 . A T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50267;SOR=0;LSEQ=GAGAGCCTAAGACAACACAC;RSEQ=GGGCACACAGGGCCAGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:2,0:102,4:106,2:0.0185:1,0:17.5:1:31:1:1:0:60:4:0.0189:0:2.5 0/0:88:0:0,0:86,2:88,0:0:1,0:22:1:29.9:1:1:0:59.6:87:1:0:0.1 +8 38273278 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20924;SOR=Inf;LSEQ=CACAGGGCACACAGGGCCAG;RSEQ=GCTCAGTGCATCCACAACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:132,5:137,0:0:1,0:25.6:1:30.4:1:1:0:59.9:67.5:1:0:0.1 0/1:116:2:1,1:109,5:114,2:0.0172:1,2:15.5:1:27.5:1:0.1012:19.99168:60:4:0.0172:0:1 +8 38273613 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.21886;SOR=Inf;LSEQ=GAAGAGGCCATGGGGCCAGC;RSEQ=GCAGGTGAGCAGGTTTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:22,131:153,0:0:2,0:22:1:31.5:1:1:0:59.9:37.25:1:0:0.1 0/1:135:2:1,1:26,107:133,2:0.0148:2,2:27.5:1:29.5:1:0.36119:4.06:60:4:0.015:0:1.5 +8 38274799 . G T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09107;SOR=0;LSEQ=TCTTCTCCCCGCTGGGCAGG;RSEQ=AAAGCCAGTCTGGCCGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:3:1,2:205,67:272,3:0.0109:2,2:23:1:27.3:1:0.15624:6.06942:60:6:0.0111:0:1 0/0:335:0:0,0:235,100:335,0:0:2,0:23.6:1:30:1:1:0:60:29.455:1:0:0.1 +8 38275547 . G T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0945;SOR=0;LSEQ=GAGTGGCATAAGTTGGGGCT;RSEQ=GTGAAGTTCAAACCTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:3:0,3:63,196:259,3:0.0115:2,0:39:1:25:1:1:0:60:2:0.0078:0:1 0/0:312:0:0,0:78,233:311,0:0:2,0:25.3:1:30.4:1:1:0:60:50.833:0.9967:0:0.1 +8 38275607 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20902;SOR=Inf;LSEQ=TCTGTATTTCACCCAACTGC;RSEQ=AGCAGAAAGTGGAATGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:57,92:149,0:0:2,0:24.1:1:31.5:1:1:0:60:73.5:1:0:0.1 0/1:126:2:1,1:52,71:123,2:0.0159:2,2:37.5:1:29:1:1:1.36:60:4:0.016:0:1 +8 38275637 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61942;SOR=2.05572;LSEQ=TGGAATGAATGTTTCTGCAG;RSEQ=CATTTCATGAACCTTCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:0,1:81,54:135,1:0.0074:2,0:30:0:32:0:0.40441:0:60:2:0.0075:0:1 0/1:133:2:1,1:88,43:131,2:0.015:2,2:10.5:1:29:1:1:2.03464:60:4:0.0153:0:1 +8 38275661 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2442;SOR=Inf;LSEQ=TTCATGAACCTTCACCGCCC;RSEQ=GAAGGTGTTAGTATACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:124,71:195,0:0:2,0:21.6:1:31:1:1:0:60:64:1:0:0.1 0/1:191:2:1,1:131,58:189,2:0.0105:2,2:32.5:1:28.5:1:0.52351:2.24796:60:4:0.0106:0:1 +8 38275681 . C T 43 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.33664;SOR=0.27928;LSEQ=AGAAGGTGTTAGTATACACA;RSEQ=CTTCCACCACTAGAATAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:163,92:255,3:0.0116:2,2:6.3:1:27.7:1:0.30077:3.52532:60:6:0.0118:0:1 0/0:306:1:0,1:202,103:305,1:0.0033:2,0:1:0:22:0:0.33987:0:60:2:0.0033:0:1 +8 38275935 . G A 25 v3;p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.92985;LSEQ=CTAGAGCAAGGAGGGGGGAC;RSEQ=GGGTGACTCCTTCCCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:42,143:185,2:0.0107:2,2:6:1:23.5:1:0.40797:3.38:60:4:0.0107:0:1 0/1:201:2:0,2:45,154:199,2:0.01:2,0:5:1:25:1:1:0:60:1:0.0051:0:1 +8 38279065 . G A 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00243;SOR=0;LSEQ=CCAGATCCCGGGCATGCATT;RSEQ=CAATGGCCAGGGGGAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:13:13,0:29,0:29,13:0.3095:1,1:18.2:1:28.2:1:1:0:60:26:0.3095:0:1.2 0/0:23:0:0,0:22,1:23,0:0:1,0:24.3:1:32.6:1:1:0:60:46:1:0:0 +8 38279120 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50494;SOR=0;LSEQ=GGTGGGAGGCCTCCGTGCGC;RSEQ=TGCAAAACTAGGGAAGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:119,11:130,2:0.0152:2,2:11:1:27.5:1:0.17418:10.40114:60:4:0.0153:0:1 0/0:104:0:0,0:79,25:104,0:0:2,0:20.7:1:30.1:1:1:0:60:33.667:1:0:0.2 +8 38279133 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24165;SOR=Inf;LSEQ=CGTGCGCCTGCAAAACTAGG;RSEQ=AAGCTCTTCTCTGAGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:145,21:166,0:0:2,0:23.9:1:31.8:1:1:0:59.8:54.333:1:0:0.1 0/1:161:2:1,1:113,46:159,2:0.0124:2,2:19.5:1:27:1:0.49992:2.44099:60:4:0.0127:0:1.5 +8 38279138 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24789;SOR=Inf;LSEQ=GCCTGCAAAACTAGGGAAGC;RSEQ=CTTCTCTGAGCTGAGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:155,23:178,0:0:2,0:24.6:1:32.1:1:1:0:59.8:88:1:0:0.1 0/1:177:2:1,1:125,50:175,2:0.0113:2,2:18:0:32.5:1:0.49441:2.48526:60:4:0.0117:0:1.5 +8 38279177 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12592;SOR=Inf;LSEQ=ATTCAGCCCTCAAAGCTGGG;RSEQ=CAGGATGTGGCACCAGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:227,91:318,0:0:2,0:25.8:1:31.3:1:1:0:60:105:1:0:0.1 0/1:353:4:3,1:230,117:347,4:0.0113:2,2:11:1:26.8:1:1:1.52:60:8:0.0116:0:1.3 +8 38279518 . G A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01019;SOR=Inf;LSEQ=ACATGAGACCTCTAAGAGAC;RSEQ=CAGAGCAAGGGAAGGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:10,134:144,0:0:2,0:22.5:1:32.3:1:1:0:59.8:47:1:0:0.1 0/1:128:6:0,6:16,106:122,6:0.0469:2,0:34.2:1:27.5:1:1:0:60:5:0.04:0:1 +8 38281658 . G A 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=AAAGATCGTACGTAACTCAG;RSEQ=ACACAGGGCTAAGACTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:50,0:50,0:0:1,0:24.5:1:31:1:1:0:59.6:24:1:0:0 0/1:30:9:8,1:21,0:21,9:0.3:1,2:26.8:1:28:1:0.3:0:60:8:0.2759:0:1 +8 38281729 . A T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.58802;SOR=2.4912;LSEQ=CAATGAAAAGGCAGGGGTCC;RSEQ=AATGCCTTCCTTGTGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:1:0,1:122,18:140,1:0.0071:2,0:1:0:24:0:0.13475:0:60:2:0.0071:0:1 0/1:114:2:1,1:99,13:112,2:0.0175:2,2:24:1:27.5:1:0.23149:7.37604:60:4:0.018:0:1 +8 38281742 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23395;SOR=Inf;LSEQ=GGGGTCCAAATGCCTTCCTT;RSEQ=TGTAGCTGACCCCAAAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:148,34:182,0:0:2,0:22.4:1:32.3:1:1:0:60:59.667:1:0:0.1 0/1:171:2:1,1:137,32:169,2:0.0117:2,2:5.5:1:28.5:1:0.34964:4.23125:60:4:0.0117:0:1 +8 38283759 . C T 168 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGATGCTCCAGGTGGCATAA;RSEQ=GGACCTGAGGGGAAATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:45:13,32:165,272:437,45:0.093:2,2:25.9:1:30.6:1:0.26071:1.49203:60:90:0.0943:0:1 0/0:648:0:0,0:228,420:648,0:0:2,0:23.9:1:29.8:1:1:0:60:91.571:1:0:0.2 +8 38285614 . G A 48 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14192;SOR=Inf;LSEQ=TCCAATATGGAGCTACGGCT;RSEQ=CCCGGGGAAAGCCAAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:77,156:233,0:0:2,0:23.7:1:32.2:1:1:0:60:37.833:1:0:0.1 0/1:319:4:3,1:109,206:315,4:0.0125:2,2:6:1:24.3:1:0.1261:5.64:60:8:0.0128:0:1 +8 38285623 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17125;SOR=0;LSEQ=GAGCTACGGCTGCCCGGGGA;RSEQ=AGCCAAGAGAGACAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:66,133:199,2:0.01:2,2:22.5:1:34:1:1:2.01:60:4:0.0101:0:1 0/0:284:0:0,0:94,190:284,0:0:2,0:23.9:1:29.8:1:1:0:60:93.667:1:0:0.1 +8 38285645 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50276;SOR=Inf;LSEQ=GCCAAGAGAGACAGGCAGGG;RSEQ=GGAGAGGAGCAGCTGGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:55,97:152,0:0:2,0:24.8:1:30:1:1:0:60:49.667:1:0:0.1 0/1:184:2:1,1:48,134:182,2:0.0109:2,2:14:1:27.5:1:0.46276:2.77:60:4:0.0111:0:1.5 +8 38285913 . GTCA G 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.71181;SOR=1.17646;LSEQ=TCTTTCTCCTCTGAAGAGGA;RSEQ=TCATCATCATCATCATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:652:11:5,6:261,380:641,11:0.0169:2,2:25.8:1:32.1:1:0.76522:1.21:59.5:22:0.0172:0.0031:0.3 0/1:960:19:7,12:410,528:938,19:0.0198:2,2:26.3:1:31:1:0.64415:1.33078:60:18:0.0191:0.0042:0.2 +8 38285926 . T G 176 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=AAGAGGAGTCATCATCATCA;RSEQ=CATCATCCTCCGAGGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:611:0:0,0:231,377:608,0:0:2,0:24.4:1:30.1:1:1:0:60:34.765:0.9966:0:0.1 0/1:823:48:20,28:331,442:773,48:0.0583:2,2:25.7:1:31.6:1:1:1.04836:60:96:0.059:0:1.1 +8 38285934 . C A 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00267;SOR=0;LSEQ=TCATCATCATCATCATCATC;RSEQ=TCCGAGGAGGGGAGAGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:7:2,5:205,361:566,7:0.0122:2,2:32.7:1:28.3:1:1:1.41885:59.3:6:0.0106:0:1.6 0/0:760:0:0,0:310,448:758,0:0:2,0:22.6:1:30.7:1:1:0:59.9:74.8:1:0:0.2 +8 38286225 . G A 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCTATTTAACTTAATTCC;RSEQ=TCCTACATTCAAAGGCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:17:1:26:1:1:0:60:3:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 38287114 . A G 36 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.333;SOR=3.65274;LSEQ=GGGGCAGATCACGGAGGGGG;RSEQ=GGAGGTTCACCTTCCTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:1:1,0:214,18:232,1:0.0043:2,0:39:0:13:0:1:0:60:0:0:0:7 0/1:193:3:3,0:168,22:190,3:0.0155:2,0:31.3:1:23.3:1:1:0:53.3:2:0.0113:0:3.3 +8 38287486 . G A 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04578;SOR=0.1198;LSEQ=GCTGCAGCCACCACGGGGCC;RSEQ=GGAAGGGAAGCCAAGGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:6:4,2:102,202:304,6:0.0194:2,2:23:1:27.5:1:0.18583:3.94:60:5:0.0162:0:1.2 0/0:425:1:1,0:157,267:424,1:0.0024:2,0:1:0:24:0:0.37176:0:60:2:0.0024:0:1 +8 38297776 . G C 154 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTCCGGGGGCCCTCTGCAGA;RSEQ=GTTTTTTTATTACGTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:29:18,11:166,90:256,29:0.1007:2,2:25.8:1:31.8:1:0.83834:1.12668:59.2:58:0.1014:0:1 0/0:507:0:0,0:302,202:504,0:0:2,0:26.2:1:30.8:1:1:0:60:83:0.994:0:0.2 +8 38314796 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23814;SOR=0;LSEQ=CCCTGTTGACCACATCACCT;RSEQ=CAACCATATCACCTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:79,11:90,2:0.0217:2,2:27.5:1:29:1:0.2451:6.9194:60:4:0.022:0:1 0/0:96:0:0,0:77,19:96,0:0:2,0:20:1:31.2:1:1:0:60:47:1:0:0.1 +8 38314813 . C T 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05651;SOR=0;LSEQ=CCTGCAACCATATCACCTCC;RSEQ=TCCCAGCCCATCCTGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:4:3,1:99,25:124,4:0.031:2,2:27:1:27.3:1:1:1.31692:60:3:0.024:0:2.8 0/0:134:0:0,0:102,32:134,0:0:2,0:23.9:1:30.8:1:1:0:60:66:1:0:0.1 +8 38314814 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49913;SOR=Inf;LSEQ=CTGCAACCATATCACCTCCC;RSEQ=CCCAGCCCATCCTGTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:103,26:129,0:0:2,0:25.9:1:30.5:1:1:0:60:15.125:1:0:0.3 0/1:141:2:1,1:104,35:139,2:0.0142:2,2:31.5:1:31:1:0.44681:2.94382:60:4:0.0146:0:1.5 +8 38315105 . GA G 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0478;SOR=0;LSEQ=AGGGTCTAGGTAGGGGAGGG;RSEQ=AAGGAAAAACAGAAGGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:4:2,2:36,167:203,4:0.0193:2,2:13:1:31.1:1:0.15449:4.59:60:8:0.0194:0.0048:0.3 0/0:234:0:0,0:54,180:234,0:0:2,0:22.9:1:29:1:1:0:59.8:57.5:1:0:0.2 +8 38315123 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2279;SOR=0;LSEQ=GGGAAAGGAAAAACAGAAGG;RSEQ=AAAGTATGCCATGTGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:13,128:141,2:0.014:2,2:11.5:1:30:1:0.18684:9.52:60:4:0.0143:0:1 0/0:156:0:0,0:16,140:156,0:0:2,0:22.6:1:27.6:1:1:0:60:155:1:0:0.1 +8 38316852 . G C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=TCGCAAGTGAGTCAGTGCTG;RSEQ=CTGGCAGAAAAGCCCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:34.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 38736031 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20295;SOR=0;LSEQ=CTGAGAATGCATCTCTCTGA;RSEQ=GGATAGAAGGGACATTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:65,45:110,2:0.0179:2,2:15.5:1:30:1:1:1.43958:60:4:0.0182:0:1 0/0:136:0:0,0:79,57:136,0:0:2,0:26.6:1:30.8:1:1:0:60:67:1:0:0.4 +8 38736051 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20061;SOR=0;LSEQ=GGGATAGAAGGGACATTGAG;RSEQ=TGCAGGGACCTGCCAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:63,58:121,2:0.0163:2,2:22.5:1:29:1:1:1.08546:60:4:0.0164:0:1 0/0:151:0:0,0:79,72:151,0:0:2,0:24.7:1:31.3:1:1:0:60:302:1:0:0.5 +8 38736089 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49851;SOR=0;LSEQ=CTTCCCCGTGCCTCCTAGGC;RSEQ=TGGTTTGCTCCCAGGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:68,60:128,2:0.0154:2,2:16:0:32:0:1:1.13224:60:4:0.0155:0:1.5 0/0:122:0:0,0:18,26:44,0:0:2,0:31.7:1:30.5:1:1:0:60:88:0.3636:0:0.1 +8 38736105 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24493;SOR=Inf;LSEQ=AGGCGTGGTTTGCTCCCAGG;RSEQ=TGACTAGATGAGAACCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:57,67:124,0:0:2,0:25.1:1:32.3:1:1:0:60:30:1:0:0.1 0/1:122:2:1,1:46,74:120,2:0.0164:2,2:39.5:1:29:1:1:1.60:60:4:0.0168:0:1 +8 38858277 . CA TG 147 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.03388;LSEQ=ATTACAGGTGTGAACCACCA;RSEQ=CCTGGCCTTAAATCACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:28:27:26,1:0,0:0,27:0.9643:0,1:21.8:1:31:1:1:0:54.1:54:1:0.2143:0.8 0/1:47:22:20,2:24,1:25,22:0.4681:1,2:24:1:30.9:1:0.59297:2.35655:55.7:44:0.4681:0.0426:1 +8 38858278 . A G 106 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19385;SOR=3.25109;LSEQ=TTACAGGTGTGAACCACCAC;RSEQ=CCTGGCCTTAAATCACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:0,0:0,2:0.087:0,0:25.5:1:23:1:1:0:58.5:1:1:0:1.5 0/1:46:11:10,1:15,0:15,11:0.2391:1,2:19.9:1:30.8:1:0.42308:0:60:22:0.4231:0:1.1 +8 38858336 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53036;SOR=Inf;LSEQ=GAACCTTAGAAATTAACTTG;RSEQ=TCCGTTTTAAAATATGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:72,19:91,0:0:2,0:26.2:1:31.8:1:1:0:60:90:1:0:0.3 0/1:153:2:1,1:112,39:151,2:0.0131:2,2:28:1:28.5:1:0.4558:2.8483:60:4:0.0132:0:1 +8 38858353 . C T 27 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29702;SOR=0.28091;LSEQ=TTGGTCCGTTTTAAAATATG;RSEQ=AGTTCTGTTTGTATTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:85,37:122,2:0.0161:2,2:8.5:1:27.5:1:0.52072:2.28019:60:4:0.0164:0:1.5 0/0:219:1:0,1:146,72:218,1:0.0046:2,0:1:0:22:0:0.33333:0:60:2:0.0046:0:1 +8 38858431 . A T 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TACTGGAAGAAAAGAAAATG;RSEQ=TATCACCCCCAGACATGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:108,133:241,0:0:2,0:27.4:1:30.8:1:1:0:60:119.5:1:0:0.2 0/1:389:40:16,24:163,186:349,40:0.1028:2,2:26.6:1:28.8:1:0.50371:1.3136:60:39:0.1018:0:1.5 +8 38858484 . G A 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAACTCAAAGGGAATGGGAC;RSEQ=TTCCCTTTGATGAATTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:40,100:140,0:0:2,0:23.2:1:31.5:1:1:0:60:139:1:0:0.2 0/1:203:24:7,17:56,123:179,24:0.1182:2,2:18.9:1:29.5:1:1:1.10516:60:23:0.1156:0:1.8 +8 38858496 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16743;SOR=0;LSEQ=AATGGGACGTTCCCTTTGAT;RSEQ=AATTGTTCTTTTAATGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:20,80:100,2:0.0194:2,2:18.5:1:31.5:1:0.371:3.93:60:4:0.0198:0:1.5 0/0:148:0:0,0:42,105:147,0:0:2,0:24.8:1:30.8:1:1:0:60:146:1:0:0.2 +8 41790412 . C A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTGCATAGGAAGTCACAG;RSEQ=AGGAGAATGGCTATAAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:10:0:35:0:1:0:60:2:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:22:0:31:1:1:0:60:4:0.6667:0:1 +8 41790674 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGGGGTGGGGGTGGAGGCTG;RSEQ=TGGGGCTGAGGCTGCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:21:1:33.8:1:1:0:60:12:1:0:0 0/1:32:2:1,1:19,11:30,2:0.0625:2,2:18.5:1:27.5:1:1:1.69662:60:4:0.0645:0:1 +8 41790704 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GGCTGCGGCTGCTGTTGCGG;RSEQ=TGCTGCTGGGGTGGTGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:13,4:17,0:0:2,0:21:1:32.9:1:1:0:60:34:1:0:0 0/1:52:2:1,1:28,21:49,2:0.0385:2,2:31.5:1:28:1:1:1.32572:60:4:0.04:0:1 +8 41790787 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50376;SOR=Inf;LSEQ=CTGTGGAGGCGGTGGTGGCG;RSEQ=CTGCTGCTGCTGGTTACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:10,13:23,0:0:2,0:22.9:1:31.3:1:1:0:60:46:0.9583:0:0 0/1:33:2:1,1:13,17:30,2:0.0606:2,2:23:1:26:1:1:1.30:60:4:0.0606:0:1 +8 41790866 . G C 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19231;SOR=Inf;LSEQ=CTGCAGTTGGCAGCAGGCTG;RSEQ=ACGCTGCTCTGCTGCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:23.3:1:32.4:1:1:0:60:14:1:0:0.1 0/1:7:3:0,3:0,4:4,3:0.4286:0,0:37.7:1:33.7:1:1:0:60:6:0.4286:0:1 +8 42199219 . A AT 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=GCTGAACTGCAGTGGGAACA;RSEQ=TTTTTTTTTTCTGTCCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:4,0:4,0:0:0,0:23.8:1:29.3:1:1:0:43:8:1:0:0.5 0/1:8:2:2,0:6,0:6,2:0.25:0,0:20.5:1:32:0:1:0:29:4:0.25:0:1 +8 42199294 . T A 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGTTTGGTTTAGCTCTC;RSEQ=GCAGCCCCCTCCTGAGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:11,5:0,0:0,16:1:0,2:27.7:1:28.6:1:1:0:41.3:7:1:0:1.4 1/1:33:33:24,9:0,0:0,33:1:0,2:19.5:1:28.7:1:1:0:43.6:32:1:0:1.2 +8 42199367 . AT A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTCTTCTGAGCAAGGGAC;RSEQ=TTTGGGATGGTTCCACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:7,14:21,0:0:2,0:27:1:29.8:1:1:0:58.6:20:1:0:0.6 0/1:53:2:1,1:20,31:51,2:0.0377:2,2:7:1:27.3:1:1:1.54:44:4:0.0377:0.0189:1.5 +8 43092808 . T A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAATATGTAATTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:31:1:1:0:23:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 43092818 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGTACAGTATATAATAT;RSEQ=TAATTGGTGTAATTTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:31:1:1:0:23:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 43092824 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTATATAATATGTAATT;RSEQ=GTGTAATTTGATATTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:32:1:1:0:23:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 43092846 . T A 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAATTTGATATTTTATGT;RSEQ=CAGTATATAATATGTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:31:1:1:0:23:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 43092853 . A G 34 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGATATTTTATGTTCAGTAT;RSEQ=TAATATGTATTTGGTGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:34:0:1:0:23:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 43092867 . G A 61 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGTATATAATATGTATTTG;RSEQ=TGTACTTTTTGATATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:9:1:30.3:1:1:0:20.3:6:1:0:7.7 1/1:4:4:2,2:0,0:0,4:1:0,2:8.5:1:30.8:1:1:0:20:8:1:0:7.5 +8 43092876 . TTG C 95 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATATGTATTTGGTGTAC;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:15:1:31.2:1:1:0:20.3:6:1:0:6.7 1/1:9:9:4,5:0,0:0,9:1:0,2:7.6:1:30:1:1:0:20.9:18:1:0.5556:6.3 +8 43092882 . T G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGGTGTACTTTTTGATA;RSEQ=TTTATGTACAGTATATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:6.6:1:30.6:1:1:0:24.5:29:1:0:5.4 0/1:126:2:0,2:62,62:124,2:0.0159:2,0:8:0:32:1:0.49613:0:25.5:4:0.016:0:4 +8 43092883 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGGTGTACTTTTTGATAT;RSEQ=TTATGTACAGTATATAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:7.6:1:31.2:1:1:0:24.5:60:1:0:5.4 0/1:130:2:0,2:65,63:128,2:0.0154:2,0:9:0:31:1:0.49612:0:27:4:0.0154:0:6 +8 43092886 . A T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75616;SOR=0.8343;LSEQ=GGTGTACTTTTTGATATTTT;RSEQ=TGTACAGTATATAATATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:3,1:14,12:26,4:0.1333:2,2:11.5:1:32.3:1:0.61292:2.50:31.5:8:0.1333:0:5 0/1:132:15:6,9:58,57:115,15:0.1136:2,2:11.1:1:30.3:1:0.58507:1.52139:26.7:30:0.1136:0:5.9 +8 43092888 . G T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.35094;SOR=Inf;LSEQ=TGTACTTTTTGATATTTTAT;RSEQ=TACAGTATATAATATGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,12:29,0:0:2,0:12.8:1:33.2:1:1:0:24.6:58:0.9667:0:5.4 0/1:133:7:3,4:60,63:123,7:0.0526:2,2:10:0:31.1:1:1:1.26752:22.6:14:0.053:0:4.7 +8 43092890 . A G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01071;SOR=0.10065;LSEQ=TACTTTTTGATATTTTATGT;RSEQ=CAGTATATAATATGTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:2,2:15,11:26,4:0.1333:2,2:12.3:1:32.5:1:1:1.34941:25:8:0.1333:0:4 0/1:134:2:1,1:66,66:132,2:0.0149:2,2:12:0:31.5:1:1:1:27:4:0.0149:0:4 +8 43092891 . C G 69 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58562;SOR=Inf;LSEQ=ACTTTTTGATATTTTATGTA;RSEQ=AGTATATAATATGTATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:15.6:1:32.9:1:1:0:24.5:60:1:0:5.4 0/1:134:5:2,3:62,63:125,5:0.0373:2,2:17:0:30:1:1:1.47182:23.6:10:0.0373:0:5.2 +8 43092892 . A C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTTGATATTTTATGTAC;RSEQ=GTATATAATATGTATTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:16.6:1:30.7:1:1:0:24.5:14:1:0:5.4 0/1:134:2:1,1:65,65:130,2:0.0149:2,2:14:0:31:1:1:1:21:4:0.015:0:5.5 +8 43092894 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTTGATATTTTATGTACAG;RSEQ=ATATAATATGTATTTTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:18.6:1:29.9:1:1:0:24.5:60:1:0:5.4 0/1:134:2:2,0:65,67:132,2:0.0149:2,0:16:0:33:0:0.49624:0:20:4:0.015:0:7 +8 43092895 . A T 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59344;SOR=Inf;LSEQ=TTTGATATTTTATGTACAGT;RSEQ=TATAATATGTATTTTGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:19.6:1:30.3:1:1:0:24.5:60:1:0:5.4 0/1:134:6:3,3:64,64:128,6:0.0448:2,2:20.5:1:29:1:1:1:23.3:12:0.0451:0:5.3 +8 43092896 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTGATATTTTATGTACAGTA;RSEQ=ATAATATGTATTTTGGGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:20.6:1:30.6:1:1:0:24.5:60:1:0:5.4 0/1:134:2:1,1:66,66:132,2:0.0149:2,2:22.5:1:32:1:1:1:21:4:0.0149:0:6 +8 43092897 . ATA GCT 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03255;SOR=0;LSEQ=TGATATTTTATGTACAGTAT;RSEQ=ATATGTATTTTGGGTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:16,12:28,2:0.0667:2,2:21:0:32.5:1:1:1.32044:31:4:0.0667:0:5.5 0/0:134:0:0,0:67,67:134,0:0:2,0:19.7:1:29.3:1:1:0:23.8:268:1:0:5.2 +8 43092898 . T G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49693;SOR=0.64129;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATATGTATTTTGGGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:4:3,1:13,11:24,4:0.1333:2,2:23.5:1:34.8:1:0.61319:2.46:31.5:8:0.1429:0:5 0/1:134:12:5,7:58,56:114,12:0.0896:2,2:23.8:1:32.1:1:0.76289:1.44574:28:24:0.0902:0:6 +8 43092899 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATTTTATGTACAGTATAT;RSEQ=ATATGTATTTTGGGTACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:17,12:29,0:0:2,0:23:1:30.5:1:1:0:24:58:1:0:5.3 0/1:134:2:2,0:63,66:129,2:0.0149:2,0:19:1:29:1:0.24427:0:24:4:0.0153:0:5 +8 43092902 . A G 115 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07526;SOR=Inf;LSEQ=TTTTATGTACAGTATATAAT;RSEQ=TGTATTTTGGGTACTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:19,13:32,0:0:2,0:25.2:1:30.1:1:1:0:24.5:64:1:0:5.3 0/1:134:13:6,7:60,60:120,13:0.097:2,2:24:0:31.3:1:1:1.16532:24.1:26:0.0977:0:5 +8 43092903 . TG CA 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.69301;SOR=1.17988;LSEQ=TTTATGTACAGTATATAATA;RSEQ=TATTTTGGGTACTTTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:18:8,10:7,2:9,18:0.5625:2,2:28.3:1:32.3:1:0.21724:4.13986:21.9:36:0.5806:0:4.4 1/0:136:82:43,39:20,23:43,82:0.6029:2,2:25.9:1:31.2:1:0.57532:1.27:23.6:164:0.6074:0:4 +8 43092904 . G A 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66794;SOR=1.33818;LSEQ=TTATGTACAGTATATAATAT;RSEQ=TATTTTGGGTACTTTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:8:6,2:1,0:1,8:0.25:0,2:24.1:1:30.3:1:1:0:29.3:16:0.8889:0:5.1 0/1:136:42:20,22:1,1:2,42:0.3088:2,2:26.5:1:29.5:1:1:1.09762:24.5:84:0.9333:0:5.5 +8 43092906 . AT GC 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.31846;SOR=0.64032;LSEQ=ATGTACAGTATATAATATGT;RSEQ=TTTGGGTACTTTGATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:9,7:10,6:16,16:0.5:2,2:30.4:1:32.8:1:1:1.28579:22.1:32:0.5:0:4.1 0/1:136:53:27,26:39,41:80,53:0.3897:2,2:29.1:1:31.7:1:0.8603:1.09:21.8:106:0.3955:0:3.7 +8 43092907 . T C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.31381;SOR=0.6126;LSEQ=TGTACAGTATATAATATGTA;RSEQ=TTTGGGTACTTTGATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:8:5,3:0,0:0,8:0.25:0,2:27:1:33.4:1:1:0:24.6:16:0.5:0:2.9 0/1:136:23:13,10:6,5:11,23:0.1691:2,2:28.4:1:31:1:1:1.08:23.4:10.5:0.2692:0:4.1 +8 43092910 . T A 31 v3;pSTD;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGTATATAATATGTATTT;RSEQ=GGGTACTTTGATATTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:33,0:0:2,0:28.8:1:31.1:1:1:0:24.6:32:1:0:3.8 0/1:139:2:1,1:68,69:137,2:0.0144:2,2:8:0:31:1:1:1.01:25:4:0.0145:0:8 +8 43092911 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTATATAATATGTATTTT;RSEQ=GGTACTTTGATATTTTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:33,0:0:2,0:29:1:32.3:1:1:0:24.6:32:1:0:3.8 0/1:139:2:1,1:68,69:137,2:0.0144:2,2:25:0:32:1:1:1.01:25:4:0.0146:0:5 +8 43092914 . T C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATATAATATGTATTTTGGG;RSEQ=ACTTTGATATTTTATGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:33,0:0:2,0:27.3:1:28.5:1:1:0:24.6:10:1:0:3.8 0/1:139:3:2,1:67,69:136,3:0.0216:2,2:30.3:1:32.7:1:0.61955:2.05:21:6:0.0216:0:4.3 +8 43092921 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATGTATTTTGGGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:33,0:0:2,0:22:1:31.2:1:1:0:24.6:32:1:0:3.8 0/1:139:2:1,1:68,69:137,2:0.0144:2,2:23:0:33:0:1:1.01:21:4:0.0145:0:6 +8 43092927 . T A 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21199;SOR=Inf;LSEQ=TTTTGGGTACTTTGATATTT;RSEQ=ATGTACAGTATATAATAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:19,14:33,0:0:2,0:17.1:1:30.6:1:1:0:24.6:32:1:0:3.8 0/1:139:10:6,4:63,66:129,10:0.0719:2,2:17.8:1:29.6:1:0.53186:1.57:29:20:0.0719:0:3.1 +8 43092928 . A T 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55912;SOR=0.78684;LSEQ=TTTGGGTACTTTGATATTTT;RSEQ=TGTACAGTATATAATAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:15:7,8:12,6:18,15:0.4545:2,2:16.8:1:31.4:1:0.30411:2.22736:22:30:0.4688:0:4 0/1:139:55:28,27:40,43:83,55:0.3957:2,2:19.6:1:30.1:1:0.86214:1.11:21.7:110:0.3986:0:3.7 +8 43092929 . T A 41 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24934;SOR=0.34982;LSEQ=TTGGGTACTTTGATATTTTA;RSEQ=GTACAGTATATAATAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:18,13:31,2:0.0606:2,2:16:0:32.5:1:1:1.37079:27.5:4:0.0606:0:2 0/1:137:3:3,0:65,68:133,3:0.0219:2,0:6.3:1:26.3:1:0.24444:0:27:6:0.0219:0:5 +8 43092930 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGGTACTTTGATATTTTAT;RSEQ=TACAGTATATAATAAGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:18,14:32,0:0:2,0:14.9:1:33.1:1:1:0:24.6:64:1:0:3.8 0/1:134:2:1,1:65,66:131,2:0.0149:2,2:14:1:30.5:1:1:1.02:26.5:4:0.0149:0:5 +8 43092931 . T G 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21219;SOR=Inf;LSEQ=GGGTACTTTGATATTTTATG;RSEQ=ACAGTATATAATAAGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:18,14:32,0:0:2,0:14.1:1:29.8:1:1:0:24.6:64:1:0:3.8 0/1:132:10:5,5:58,63:121,10:0.0758:2,2:19.3:1:30.3:1:1:1.09:22.2:20:0.0763:0:5.2 +8 43092932 . A C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18077;SOR=0.24294;LSEQ=GGTACTTTGATATTTTATGT;RSEQ=CAGTATATAATAAGTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:16,13:29,2:0.0625:2,2:14.5:1:30.5:1:1:1.22249:31:4:0.0645:0:5.5 0/1:127:2:1,1:60,61:121,2:0.0157:2,2:9:0:32.5:1:1:1.02:21:4:0.0157:0:5 +8 43092934 . A C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTTTGATATTTTATGTAC;RSEQ=GTATATAATAAGTATTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:17,13:30,0:0:2,0:12.1:1:31.8:1:1:0:24.3:60:1:0:3.9 0/1:125:2:1,1:60,61:121,2:0.016:2,2:18.5:1:31.5:1:1:1.02:33.5:4:0.0161:0:4 +8 43092935 . G C 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35489;SOR=Inf;LSEQ=ACTTTGATATTTTATGTACA;RSEQ=TATATAATAAGTATTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:16,13:29,0:0:2,0:11.6:1:33.4:1:1:0:24.2:58:1:0:3.9 0/1:121:8:4,4:56,54:110,8:0.0661:2,2:13.6:1:29.4:1:1:1.03673:23.5:16:0.0667:0:5.9 +8 43092937 . A G 48 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTTGATATTTTATGTACAGT;RSEQ=TATAATAAGTATTTGGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,12:26,0:0:2,0:9.4:1:30.3:1:1:0:23:52:0.963:0:3.8 0/1:116:3:2,1:57,56:113,3:0.0259:2,2:8:0:30.7:1:1:1.95:20:6:0.0259:0:5 +8 43092940 . T G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.27109;SOR=0.58264;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATAAGTATTTGGTGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:14:7,7:7,3:10,14:0.5385:2,2:5.2:1:33.3:1:0.42122:2.25157:22:28:0.5385:0:4 0/1:109:44:24,20:27,27:54,44:0.4037:2,2:6.2:1:30.8:1:0.6885:1.20:21.9:88:0.4112:0:3.7 +8 43092944 . AAG CTA 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTATGTACAGTATATAAT;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,11:24,0:0:2,0:2.9:1:29.9:1:1:0:23.3:48:1:0:3.8 0/1:87:2:1,1:41,38:79,2:0.023:2,2:30.5:1:30.2:1:1:1.07791:25:4:0.0247:0:6 +8 43092945 . AGTATTTGGT CACAGTTTGG 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.55128;SOR=Inf;LSEQ=TTTATGTACAGTATATAATA;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,1:5,0:0:2,0:8.8:1:28.8:1:1:0:26:10:0.8333:0:5.4 0/1:21:3:2,1:2,0:2,3:0.1429:0,2:21.3:1:30.9:1:1:0:21.7:6:0.25:0.0476:5.7 +8 43092946 . G A 21 d5;v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0797;SOR=0.07842;LSEQ=TTATGTACAGTATATAATAA;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:19.5:1:30.5:1:1:0:27.5:4:1:0:7 0/1:18:2:1,1:0,0:0,2:0.1111:0,2:30.5:1:21.5:1:1:0:27:1:1:0:8 +8 43092949 . T G 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTACAGTATATAATAAGTA;RSEQ=TTGGTGTACTTTGATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:1,0:0:0,0:35:0:29:0:1:0:24:2:1:0:8 0/1:18:2:0,2:3,3:6,2:0.1111:2,0:27:1:33:0:0.46429:0:25:4:0.2222:0:6 +8 43092950 . T C 25 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACAGTATATAATAAGTAT;RSEQ=TGGTGTACTTTGATATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:1,0:0:0,0:34:0:30:0:1:0:24:2:1:0:8 0/1:18:2:2,0:1,6:7,2:0.1111:2,0:26:1:25.5:1:0.08333:0:25:4:0.2222:0:7 +8 43092952 . G T 49 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGTATATAATAAGTATTT;RSEQ=GTGTACTTTGATATTTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:1,0:0:0,0:32:0:31:0:1:0:24:2:1:0:8 0/1:18:3:0,3:4,2:6,3:0.1667:2,0:24.3:1:31.3:1:0.16667:0:24:6:0.3333:0:6.3 +8 43092953 . G A 40 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CAGTATATAATAAGTATTTG;RSEQ=TGTACTTTGATATTTTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,0:1,0:0:0,0:31:0:30:0:1:0:24:2:1:0:8 0/1:18:3:1,2:3,3:6,3:0.1667:2,2:24.7:1:25.7:1:1:1.8525:25.3:2:0.25:0:6.7 +8 43092954 . T G 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGTATATAATAAGTATTTGG;RSEQ=GTACTTTGATATTTTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:30:0:29:0:1:0:24:2:1:0:8 0/1:12:2:0,2:4,3:7,2:0.1667:2,0:25:1:32:0:0.44444:0:21:4:0.2222:0:6.5 +8 43092959 . T C 32 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATAATAAGTATTTGGTGTAC;RSEQ=TTGATATTTTATGTACAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:24.5:1:32:1:1:0:22:4:1:0:7.5 0/1:18:2:1,1:6,10:16,2:0.1111:2,2:15:1:32.5:1:1:1.62:26:4:0.1111:0:7.5 +8 43092962 . G C 49 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36842;SOR=0.22361;LSEQ=ATAAGTATTTGGTGTACTTT;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:1,1:0.5:0,0:23:0:30:0:1:0:24:2:0.5:0:8 0/1:18:3:1,2:6,9:15,3:0.1667:2,2:15.7:1:31.3:1:1:1.3127:25.3:6:0.1667:0:6.7 +8 43092963 . A G 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TAAGTATTTGGTGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:20.5:1:30:1:1:0:22:4:1:0:7.5 0/1:18:2:1,1:6,10:16,2:0.1111:2,2:13.5:1:32.5:1:1:1.62:22:4:0.1111:0:6 +8 43092978 . T A 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAACATGTATTTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:5.5:1:26.5:1:1:0:22:4:1:0:7.5 0/1:6:2:2,0:0,4:4,2:0.3333:0,0:14.5:1:28:1:0.06667:0:24:4:0.3333:0:6.5 +8 43093195 . AATGTATTTGGTGT TGTATGGTTTCTGA 70 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTATGTACAGTATATAA;RSEQ=ACTTTGATATTTTATGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:7:5:3,2:0,0:0,5:0.7143:0,2:16:1:30.4:1:1:0:32.4:10:0.7143:0.1429:4.8 +8 43093221 . T C 101 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGGTGTACTTTGATATTT;RSEQ=ATGCACAGTATATAATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:13:0:34:0:1:0:30:2:1:0:8 1/1:11:9:5,4:1,1:2,9:0.8182:2,2:13.1:1:32.1:1:1:1.22:31.8:18:0.8182:0:6.7 +8 43093225 . C T 90 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGTACTTTGATATTTTATG;RSEQ=ACAGTATATAATATGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:17:0:32:0:1:0:30:2:1:0:8 1/1:9:9:5,4:0,0:0,9:1:0,2:13.9:1:28.7:1:1:0:32:18:1:0:7.3 +8 43093227 . C G 87 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTACTTTGATATTTTATGCA;RSEQ=AGTATATAATATGTATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:19:0:35:0:1:0:30:2:1:0:8 1/0:9:7:4,3:1,1:2,7:0.7778:2,2:14.9:1:31.1:1:1:1.29:32.3:14:0.7778:0:7.4 +8 43093229 . G C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTTTGATATTTTATGCACA;RSEQ=TATATAATATGTATTTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:21:0:35:0:1:0:30:2:1:0:8 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:13.5:1:31.5:1:1:1.22474:31:4:0.1818:0:7 +8 43093234 . T A 124 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATATTTTATGCACAGTATA;RSEQ=AATATGTATTTGGTGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:26:0:32:0:1:0:30:2:1:0:8 1/1:20:17:9,8:0,0:0,17:0.85:0,2:7.8:1:30.5:1:1:0:33.7:34:0.85:0:7.4 +8 43093240 . G A 131 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTATGCACAGTATATAATAT;RSEQ=TATTTGGTGTACTTTGATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:32:0:30:0:1:0:30:2:1:0:8 1/1:24:24:12,12:0,0:0,24:1:0,2:11.1:1:28.7:1:1:0:32.7:23:1:0:7 +8 43093244 . T C 51 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCACAGTATATAATATGTAT;RSEQ=TGGTGTACTTTGATATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:36:0:33:0:1:0:30:2:1:0:8 0/1:29:3:2,1:11,15:26,3:0.1034:2,2:23.3:1:32.3:1:0.57307:2.63:30.3:6:0.1034:0:7 +8 43093246 . G C 45 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAGTATATAATATGTATTT;RSEQ=GTGTACTTTGATATTATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:38:0:34:0:1:0:30:2:1:0:8 0/1:30:3:1,2:12,15:27,3:0.1:2,2:16.7:1:29:1:1:1.57599:31.7:6:0.1:0:7.7 +8 43093248 . T G 146 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTATATAATATGTATTTGG;RSEQ=GTACTTTGATATTATATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:37:0:33:0:1:0:30:2:1:0:8 1/1:32:28:12,16:2,2:4,28:0.875:2,2:13.7:1:30.5:1:1:1.32125:32.7:56:0.875:0:6.4 +8 43093253 . T A 150 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATATGTATTTGGTGTAC;RSEQ=TTGATATTATATGTACAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:11.8:1:30.8:1:1:0:32.8:8:1:0:4.3 1/1:39:32:14,18:3,4:7,32:0.8205:2,2:15.7:1:30:1:1:1.04:33:64:0.8421:0:5.9 +8 43093256 . G T 31 d5;v3;pSTD;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATGTATTTGGTGTACTTT;RSEQ=ATATTATATGTACAGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:13.3:1:32.5:1:1:0:32.8:8:1:0:4.3 0/1:40:2:1,1:16,22:38,2:0.05:2,2:19:0:31:1:1:1.36:23:4:0.05:0:8 +8 43093266 . G T 30 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTGTACTTTGATATTATAT;RSEQ=TACAGTATATAATATATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:18.3:1:32.8:1:1:0:32.8:8:1:0:4.3 0/1:39:2:1,1:15,22:37,2:0.0513:2,2:34.5:1:30.5:1:1:1.45:33:4:0.0513:0:8 +8 43093269 . C G 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTACTTTGATATTATATGTA;RSEQ=AGTATATAATATATATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:19.8:1:32.8:1:1:0:32.8:8:1:0:4.3 0/1:39:2:1,1:15,21:36,2:0.0513:2,2:16.5:1:29:1:1:1.39:32:4:0.0513:0:1.5 +8 43093272 . T A 61 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CTTTGATATTATATGTACAG;RSEQ=ATATAATATATATTTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:21.3:1:29.8:1:1:0:32.8:8:1:0:4.3 0/1:39:4:2,2:14,21:35,4:0.1026:2,2:18.5:1:30.5:1:1:1.48:29.3:8:0.1026:0:6.3 +8 43093276 . T A 62 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GATATTATATGTACAGTATA;RSEQ=AATATATATTTGGTGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:23.3:1:30.5:1:1:0:32.8:8:1:0:4.3 0/1:39:4:2,2:14,21:35,4:0.1026:2,2:14.5:1:31.3:1:1:1.48:29.3:8:0.1026:0:6.3 +8 43093280 . A C 160 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTATATGTACAGTATATAAT;RSEQ=TATATTTGGTGTACTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:25.3:1:33:1:1:0:32.8:8:1:0:4.3 1/1:39:33:13,20:3,3:6,33:0.8462:2,2:25.5:1:31.8:1:0.67431:1.52111:32.6:66:0.8462:0:5.6 +8 43093289 . G A 153 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGTATATAATATATATTTG;RSEQ=TGTACTTTTTGATATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:23:0:32:1:1:0:33.7:6:1:0:3 1/1:34:34:13,21:0,0:0,34:1:0,2:17:1:30.2:1:1:0:32.2:68:1:0:5.6 +8 43093295 . TT ATTCATATTTTATGTACCCAAAATATA 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=Inf;LSEQ=ATAATATATATTTGGTGTAC;RSEQ=TTTGATATTTTATGTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:18:0:34:1:1:0:33.7:6:1:0:3 0/1:32:2:1,1:11,19:30,2:0.0625:2,2:33.5:1:28.4:1:1:1.70:30:4:0.0625:0.0625:4 +8 43093298 . TTG C 141 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATATATATTTGGTGTAC;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:17:0:32.8:1:1:0:33.7:6:1:0:2 1/1:31:25:9,16:2,2:4,25:0.8065:2,2:14.5:1:30.4:1:0.62208:1.74124:32.8:50:0.8065:0.1935:5.1 +8 43093475 . A T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATGTATTTGGTGTACTTTG;RSEQ=TATTTTATGTACAGTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:3:0:29:0:1:0:26:2:1:0:6 0/1:11:2:0,2:5,4:9,2:0.1818:2,0:9:1:27.5:1:0.45455:0:28.5:4:0.1818:0:7 +8 43093477 . A G 30 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTATTTGGTGTACTTTGAT;RSEQ=TTTTATGTACAGTATATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:31:0:1:0:26:2:1:0:6 0/1:16:2:1,1:6,7:13,2:0.125:2,2:16:1:30:1:1:1.15:32:4:0.125:0:7.5 +8 43093490 . T A 115 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTTTGATATTTTATGTACAG;RSEQ=ATATAGTATATATTTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:18:0:32:0:1:0:26:2:1:0:6 1/1:17:15:7,8:1,1:2,15:0.8824:2,2:21.6:1:29.6:1:1:1.13389:28:30:0.8824:0:6.2 +8 43093494 . T A 113 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AGTATATATTTGGTGTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:22:0:32:0:1:0:26:2:1:0:6 1/1:17:14:7,7:1,1:2,14:0.8235:2,2:24.9:1:29.8:1:1:1:27.8:28:0.875:0:6.1 +8 43093496 . G A 117 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTATGTACAGTATATA;RSEQ=TATATATTTGGTGTACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:24:0:32:0:1:0:26:2:1:0:6 1/1:17:15:7,8:0,1:1,15:0.8824:0,2:27.6:1:30.2:1:1:0:28:30:0.8824:0:6.1 +8 43093507 . G A 113 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGTATATAGTATATATTTG;RSEQ=TGTACTTTTTGATATTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:35:0:32:0:1:0:26:2:1:0:6 1/1:17:15:7,8:0,1:1,15:0.8824:0,2:33.9:1:29:1:1:0:28:14:0.875:0:6.1 +8 43093516 . TTG C 115 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTATATATTTGGTGTAC;RSEQ=ATATTTTATGTACAGTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:31:0:32.6:0:1:0:26:2:1:0:5 1/1:16:13:6,7:0,0:0,13:0.8125:0,2:29.3:1:31.2:1:1:0:28.5:26:0.8667:0:5.1 +8 43093801 . G T 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTATGGACAGTATATAATA;RSEQ=GTATTTTGTGTAGTTTGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:21.5:1:32:1:1:0:27:4:1:0:6 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 43093805 . T G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACAGTATATAATAGGTA;RSEQ=TTTGTGTAGTTTGATATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:25.5:1:34:1:1:0:27:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 43093812 . T A 49 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TATATAATAGGTATTTTGTG;RSEQ=AGTTTGATATTTTATGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:33:1:31:1:1:0:24.7:6:1:0:6 0/0:1:0:0,0:0,1:1,0:0:0,0:21:0:29:0:1:0:32:2:1:0:5 +8 43093814 . G C 53 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TATAATAGGTATTTTGTGTA;RSEQ=TTTGATATTTTATGTACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:31:1:33.7:1:1:0:24.7:6:1:0:6 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 43093825 . T C 54 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=TTTTGTGTAGTTTGATATTT;RSEQ=ATGTACAGTATAAAATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:20:1:34.3:1:1:0:24.7:6:1:0:6 0/0:1:0:0,0:0,1:1,0:0:0,0:8:0:30:0:1:0:32:2:1:0:5 +8 43093831 . C G 47 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=GTAGTTTGATATTTTATGTA;RSEQ=AGTATAAAATATGTATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:14:1:30:1:1:0:24.7:6:1:0:6 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:31:0:1:0:32:2:1:0:5 +8 43094017 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATATCAAAGTACACCAA;RSEQ=TGCATTTTATATACTGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:1:28:1:1:0:60:4:1:0:1 +8 43094675 . A G 83 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAATACATATTATATACT;RSEQ=TACATAATATATCAAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:0,6:1:0,2:12.3:1:32.2:1:1:0:21.2:12:1:0:6.2 +8 43094696 . A C 81 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACATAATATATCAAAGTAC;RSEQ=CAAAATATATATTATATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:0,6:1:0,2:28.5:1:31.7:1:1:0:21.2:12:1:0:6.2 +8 43094701 . A G 76 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATATATCAAAGTACACAAA;RSEQ=TATATATTATATGCTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:5:2,3:0,0:0,5:0.8333:0,2:22.6:1:33:1:1:0:20.8:10:0.8333:0:6 +8 43094705 . A G 84 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATCAAAGTACACAAAATAT;RSEQ=TATTATATGCTGTACATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:0,6:1:0,2:20.8:1:32.8:1:1:0:21.2:12:1:0:6.2 +8 43094714 . G A 77 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAAAATATATATTATAT;RSEQ=CTGTACATATAATATCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:2,4:0,0:0,6:1:0,2:11.8:1:29.8:1:1:0:21.2:12:1:0:6.2 +8 43094724 . T A 44 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATTATATGCTGTACATA;RSEQ=AATATCAAAGTATACATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:7.3:1:28.3:1:1:0:22.3:6:1:0:7 +8 43094771 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATACACTGTACTTAAAATA;RSEQ=CAAAGTACACAAAATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:16:1:29:1:1:1:20.5:4:0.5:0:7 +8 43094780 . A C 71 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACTTAAAATACCAAAGTAC;RSEQ=CAAAATATATATTATATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:15.6:1:30.6:1:1:0:21.8:10:1:0:5 +8 43094785 . A C 50 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAAATACCAAAGTACACAAA;RSEQ=TATATATTATATACTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:3:1,2:2,1:3,3:0.5:2,2:20.3:1:32:1:1:3.10575:23:6:0.5:0:3.3 +8 43094792 . T C 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGTACACAAAATATATA;RSEQ=TATATACTGTACATAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:1:30:1:1:1:20:4:0.3333:0:7.5 +8 43094814 . C G 31 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:45:1:31.5:1:1:0:20:4:0.6667:0:7.5 +8 43094817 . A G 31 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGTACATAAAATATCAA;RSEQ=GTACACCAAATACATATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:48:1:31.5:1:1:0:20:4:0.6667:0:7.5 +8 43094823 . C T 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:44.5:1:30.5:1:1:0:20:4:0.6667:0:7.5 +8 43094830 . C T 46 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:35:1:29.3:1:1:0:20:6:1:0:7.3 +8 43094840 . A C 32 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCAAATACATATTATAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:27.5:1:32.5:1:1:1.7321:20:4:0.5:0:7.5 +8 43094852 . A T 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATTATATACTGTACATAAA;RSEQ=TATCAAAGTACACCAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:21:0:29.5:1:1:1.7321:24:4:0.4:0:5.5 +8 43094866 . C A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:33.5:1:30:1:1:1:24:4:0.5:0:5.5 +8 43094871 . ACA GTG 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATCAAAGTACACCAAAT;RSEQ=TATTATATACTGTTCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:32.2:1:1:0:24:4:1:0:3.5 +8 43094969 . G C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATACATATTATATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:14:0:32.5:1:1:0:42:4:0.6667:0:6 +8 43094975 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:20:0:33:0:1:1.73:42:4:0.5:0:6 +8 43094978 . A C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TATTATATACTGTACATAAA;RSEQ=TATCAAAGTACACAAAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:8:0:31.5:1:1:1.73:29:4:0.4:0:5 +8 43094988 . A T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTACATAAAATATCAAAGT;RSEQ=CACAAAATACATATTATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:33:0:31:0:1:1.73:42:4:0.4:0:6 +8 43094990 . A C 50 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CAAAATACATATTATACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:2,3:0.6:2,2:24.3:1:32:1:1:1.7321:26.3:6:0.6:0:5 +8 43094995 . A C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATATCAAAGTACACAAA;RSEQ=TACATATTATACACTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:0,0:0,2:0.4:0,2:31:0:33:1:1:0:42:4:0.4:0:6 +8 43094998 . CA TG 51 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACAAAATA;RSEQ=TATTATACACTGTACATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:0,0:0,3:0.6:0,2:29.3:1:32.7:1:1:0:26.3:6:0.6:0:4 +8 43095083 . A T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTTACACGAAGTATATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:9:0:30.5:1:1:0:34:4:0.6667:0:5 +8 43095087 . A T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGAAGTATATATTATAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:13:0:30.5:1:1:0:34:4:0.6667:0:5 +8 43095114 . GA AG 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAAAATATCAAAGTACACC;RSEQ=ATATATATTATATACTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:19:0:32.5:1:1:1:37:4:0.5:0:7 +8 43095115 . A G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAAATATCAAAGTACACCG;RSEQ=ATATATATTATATACTGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,0:0,2:0.5:0,2:17:0:32:0:1:0:34:4:1:0:5 +8 43095125 . A C 65 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.2;SOR=Inf;LSEQ=AAGTACACCGAATATATATT;RSEQ=TATACTGAACATAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:9:0:30:0:1:0:20:2:1:0:8 1/1:4:4:2,2:0,0:0,4:1:0,2:17.8:1:32.5:1:1:0:35.5:8:1:0:6 +8 43095130 . C G 66 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=CACCGAATATATATTATATA;RSEQ=TGAACATAAAATATCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:14:0:34:0:1:0:20:2:1:0:8 1/1:4:4:2,2:0,0:0,4:1:0,2:12.8:1:33:1:1:0:35.5:8:1:0:6 +8 43095133 . A T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGAATATATATTATATACTG;RSEQ=ACATAAAATATCAAATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:17:0:32:0:1:0:20:2:1:0:8 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29.5:1:1:0:37:4:1:0:7 +8 43095144 . T A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TATATACTGAACATAAAATA;RSEQ=CAAATCACACATATTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:32:0:1:0:20:2:1:0:8 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:30:1:1:0:37:4:1:0:7 +8 43095163 . T G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.43243;SOR=3.24035;LSEQ=ATCAAATCACACATATTATA;RSEQ=ATTATATACTGTACATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:3,5:1,0:1,8:0.8889:0,2:5:0:33.8:1:0.44444:0:41.6:16:0.8889:0:6 1/1:28:27:13,14:1,0:1,27:0.9643:0,2:5:1:31.5:1:1:0:37.2:54:0.9643:0:6.6 +8 43095171 . A G 66 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56349;SOR=Inf;LSEQ=ACACATATTATATATTATAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:13.3:1:30:1:1:0:40.3:22:1:0:5.9 0/1:39:4:2,2:17,17:34,4:0.1026:2,2:13:0:33.3:1:1:1:32.8:8:0.1026:0:6 +8 43095175 . T C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATTATATATTATATACTG;RSEQ=ACATAAAATATCAAAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:16.5:1:29.7:1:1:0:40.3:22:1:0:5.9 0/1:48:2:1,1:23,23:46,2:0.0417:2,2:17:0:30.5:1:1:1:41:4:0.0417:0:7 +8 43095180 . A T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3056;SOR=0.35247;LSEQ=ATATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:4,5:1,1:2,9:0.8182:2,2:20.2:1:30.3:1:1:1.22474:43.7:18:0.8182:0:5.7 1/0:59:36:18,18:13,10:23,36:0.6102:2,2:18.1:1:29:1:0.78986:1.29422:36.8:72:0.6102:0:6.5 +8 43095186 . T C 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.88369;LSEQ=TATATACTGTACATAAAATA;RSEQ=CAAAGTACACCAAATACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:4,6:2,1:3,10:0.7692:2,2:26.4:1:32.4:1:0.55944:2.75172:42.3:20:0.7692:0:5.8 1/0:67:50:26,24:6,3:9,50:0.7463:2,2:20.1:1:31.3:1:0.48772:1.82755:36.6:49:0.7424:0:6 +8 43095190 . A T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02134;SOR=0;LSEQ=TACTGTACATAAAATATCAA;RSEQ=GTACACCAAATACATATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:7:0:32.5:1:1:1.18:33:4:0.1667:0:7 0/0:73:0:0,0:36,31:67,0:0:2,0:19.8:1:30.1:1:1:0:35.1:32.5:0.9155:0:5.6 +8 43095191 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02134;SOR=0;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACCAAATACATATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:33:0:32:1:1:1.18:38:4:0.1538:0:6.5 0/0:73:0:0,0:38,32:70,0:0:2,0:20.7:1:31.9:1:1:0:35.3:69:0.9718:0:5.7 +8 43095195 . A C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.64337;SOR=1.47226;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCAAATACATATTATATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:5,7:1,0:1,12:0.8571:0,2:28.4:1:31.8:1:0.46154:0:40.9:24:0.8571:0:6.1 1/1:79:71:36,35:3,1:4,71:0.8987:2,2:24.1:1:30.8:1:0.61592:2.87886:35.4:70:0.9091:0:5.7 +8 43095199 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAAATATCAAAGTACACCA;RSEQ=ATACATATTATATACTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:26.6:1:30.5:1:1:0:38.3:30:1:0:6.1 0/1:86:2:1,1:43,41:84,2:0.0233:2,2:22.5:1:29.5:1:1:1.04822:31:4:0.0235:0:6.5 +8 43095203 . C T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:6,8:0,0:0,14:1:0,2:26.9:1:29.4:1:1:0:39.6:28:1:0:6.1 1/1:86:85:43,42:0,0:0,85:0.9884:0,2:23.4:1:29.7:1:1:0:34.6:170:1:0:6 +8 43095206 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCAAAGTACACCAAATACAT;RSEQ=TTATATACTGTACATGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:14,0:0:2,0:25.6:1:29.9:1:1:0:39.6:28:1:0:6.1 0/1:91:2:1,1:46,43:89,2:0.022:2,2:29:0:33.5:1:1:1.06894:23:4:0.022:0:6.5 +8 43095208 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAAGTACACCAAATACATAT;RSEQ=ATATACTGTACATGAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:14,0:0:2,0:24.8:1:30.3:1:1:0:39.6:28:1:0:6.1 0/1:92:2:1,1:46,43:89,2:0.0217:2,2:17:1:32.5:1:1:1.06894:35.5:4:0.0225:0:6.5 +8 43095209 . A T 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.45969;SOR=0.36801;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTGTACATGAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:5,8:1,0:1,13:0.9286:0,2:25.4:1:30.5:1:0.42857:0:40.1:26:0.9286:0:6.1 1/1:92:76:39,37:9,6:15,76:0.8261:2,2:22.5:1:30:1:0.58353:1.41761:35:37:0.8222:0:6 +8 43095215 . T G 28 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACCAAATACATATTATATAC;RSEQ=GTACATGAAATATCAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:14,0:0:2,0:20.9:1:30.7:1:1:0:39.6:28:1:0:6.1 0/1:90:2:1,1:45,42:87,2:0.0222:2,2:22:1:28.5:1:1:1.07057:31.5:4:0.0222:0:7.5 +8 43095216 . G C 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.073;SOR=0.22058;LSEQ=CCAAATACATATTATATACT;RSEQ=TACATGAAATATCAAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:4,7:11,3:0.2143:2,2:22.3:1:33.3:1:0.53846:3.19:33:6:0.2143:0:6.7 0/1:90:5:3,2:44,41:85,5:0.0556:2,2:23.6:1:33:1:1:1.39:33.2:10:0.0556:0:6.8 +8 43095222 . G C 33 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:14,0:0:2,0:15.9:1:31.9:1:1:0:39.6:28:1:0:6.1 0/1:90:2:1,1:45,42:87,2:0.0222:2,2:17:1:33:0:1:1.07057:37:4:0.0222:0:8 +8 43095227 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TTATATACTGTACATGAAAT;RSEQ=TCAAAGTACACCAAATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:14,0:0:2,0:12.3:1:29.3:1:1:0:39.6:28:1:0:6.1 0/1:88:2:1,1:46,40:86,2:0.0227:2,2:8:0:32:1:1:1.14817:23:4:0.0227:0:3 +8 43095229 . C G 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATATACTGTACATGAAATAT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,7:13,0:0:2,0:11.2:1:30.8:1:1:0:40.3:26:0.9286:0:6.1 0/1:78:3:2,1:39,36:75,3:0.0385:2,2:17.7:1:33:1:1:1.83:25.7:6:0.0385:0:5.7 +8 43095230 . A G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATACTGTACATGAAATATC;RSEQ=AAGTACACCAAATACATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:14,0:0:2,0:9.9:1:28.5:1:1:0:39.6:13:1:0:6.1 0/1:77:4:2,2:39,34:73,4:0.0519:2,2:25.5:1:31.5:1:1:1.14501:28:8:0.0519:0:7 +8 43095235 . A T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.68968;LSEQ=TGTACATGAAATATCAAAGT;RSEQ=CACCAAATACATATTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:0,1:1,6:0.8571:0,2:12:1:30.3:1:1:0:37.5:12:0.8571:0:6.7 1/1:46:37:21,16:5,4:9,37:0.8043:2,2:16.4:1:30.1:1:1:1.05:33:74:0.8043:0:6.9 +8 43095238 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACATGAAATATCAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:9.3:1:32:1:1:0:37:12:1:0:6.7 0/1:34:3:2,1:18,13:31,3:0.0882:2,2:8.7:1:31.3:1:1:1.43:25.7:6:0.0882:0:5.7 +8 43095239 . C A 139 d5 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.56203;SOR=0;LSEQ=CATGAAATATCAAAGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:12.5:1:30:1:1:0:32.8:8:1:0:7 1/0:31:24:13,11:3,1:4,24:0.7742:2,2:16.4:1:30.5:1:0.61319:2.4611:33.2:48:0.7742:0:7.1 +8 43095242 . A C 152 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATATCAAAGTACACCAA;RSEQ=TACATATTATATACTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:34:1:1:0:32.5:4:1:0:7 1/1:31:26:14,12:4,1:5,26:0.8387:2,2:15.2:1:32.4:1:0.36787:3.30832:32.2:52:0.8387:0:7.1 +8 43095245 . C T 145 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:29.5:1:1:0:32.5:4:1:0:7 1/1:30:30:17,13:0,0:0,30:1:0,2:11:1:29.7:1:1:0:31.2:60:1:0:7 +8 43095262 . A C 48 d5;v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATACATATTATATACTGTAC;RSEQ=TAAAAAGCAACGTACACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:3:0:33:0:1:0:32:2:1:0:8 0/1:7:3:2,1:3,1:4,3:0.4286:2,2:6:0:30.3:1:1:1.41418:22:6:0.4286:0:6.7 +8 43095901 . T C 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.5404;SOR=Inf;LSEQ=AATACATATTATATACTGTA;RSEQ=ATAAAATATCAAAGTACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:15:0:29.7:1:1:0:28.2:12:1:0:5.8 0/1:19:4:2,2:8,6:14,4:0.2105:2,2:8.3:1:32.8:1:1:1.31198:25.5:8:0.2222:0:5 +8 43095910 . TC AG 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATATACTGTATATAAAATA;RSEQ=AAAGTACACAAAATATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:24:0:31.8:1:1:0:28.2:12:1:0:5.8 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:26:0:32:1:1:1.19087:22:4:0.0833:0:6 +8 43095911 . C G 113 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.66382;SOR=1.81079;LSEQ=ATATACTGTATATAAAATAT;RSEQ=AAAGTACACAAAATATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,1:2,2:0.3333:2,2:25:0:33:1:1:1:30.5:4:0.3333:0:6.5 0/1:25:12:5,7:8,3:11,12:0.48:2,2:21.1:1:31.7:1:0.21376:3.5128:27:24:0.5217:0:6.9 +8 43095919 . ACA CTG 33 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08788;SOR=0.09459;LSEQ=TATATAAAATATCAAAGTAC;RSEQ=AAATATGTATTGTATACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:35:0:33.2:1:1:1:23:4:0.3333:0:3 0/1:25:1:1,0:7,8:15,1:0.04:2,0:35:0:31:0:1:0:32:2:0.04:0:4 +8 43095920 . CA TC 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15098;SOR=0.20658;LSEQ=ATATAAAATATCAAAGTACA;RSEQ=AAATATGTATTGTATACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:0,0:0,4:0.6667:0,2:32.3:1:32.4:1:1:0:30.8:8:1:0:5.3 0/1:25:7:2,5:7,3:10,7:0.28:2,2:31.7:1:31.8:1:0.15343:5.18713:29.3:14:0.2917:0:5.6 +8 43095924 . A C 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.30226;SOR=Inf;LSEQ=AAAATATCAAAGTACACAAA;RSEQ=TATGTATTGTATACTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:24.3:1:31.4:1:1:0:26.9:16:1:0:5.3 0/1:25:5:3,2:8,8:16,5:0.2:2,2:24.4:1:33:1:1:1.47:26.4:10:0.2:0:2.8 +8 43095928 . G A 119 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07307;SOR=0;LSEQ=TATCAAAGTACACAAAATAT;RSEQ=TATTGTATACTGTACATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:22.3:1:30.3:1:1:0:26.9:16:1:0:5.3 1/0:25:16:8,8:6,3:9,16:0.64:2,2:26.2:1:29.9:1:0.67662:1.94529:26.5:32:0.64:0:5.3 +8 43095933 . G T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.0807;LSEQ=AAGTACACAAAATATGTATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:4,4:0.5:2,2:20.3:1:30:1:1:1:30.8:8:0.5:0:5.3 1/0:25:13:6,7:6,4:10,13:0.52:2,2:23.7:1:29.4:1:0.68017:1.70753:25.3:12:0.5:0:5.7 +8 43095935 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=GTACACAAAATATGTATTGT;RSEQ=TACTGTACATAAAATATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:18.8:1:30.3:1:1:0:26.9:16:1:0:5.3 0/1:25:2:1,1:13,10:23,2:0.08:2,2:18.5:1:28.5:1:1:1.28628:20:4:0.08:0:6.5 +8 43095937 . A T 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69515;SOR=1.48132;LSEQ=ACACAAAATATGTATTGTAT;RSEQ=CTGTACATAAAATATCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:2,2:2,2:4,4:0.5:2,2:16.3:1:30.3:1:1:1:30.8:8:0.5:0:5.3 1/0:25:15:7,8:7,3:10,15:0.6:2,2:22.1:1:30.3:1:0.41387:2.56224:26:30:0.6:0:5.7 +8 43095940 . G T 23 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAAAATATGTATTGTATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:16.3:1:31.1:1:1:0:26.9:7:1:0:5.3 0/1:26:2:1,1:13,11:24,2:0.0769:2,2:7.5:1:23.5:1:1:1.17422:31:4:0.0769:0:5 +8 43095945 . T A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTATTGTATACTGTACA;RSEQ=AAAATATCAAAGTACACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:13.8:1:30:1:1:0:26.9:16:1:0:5.3 0/1:27:2:1,1:14,11:25,2:0.0741:2,2:27:0:31:1:1:1.2613:29:4:0.0741:0:6 +8 43095949 . A C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TATTGTATACTGTACATAAA;RSEQ=TATCAAAGTACACCAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:11.8:1:30.8:1:1:0:26.9:16:1:0:5.3 0/1:26:2:1,1:13,9:22,2:0.0769:2,2:12:0:31.5:1:1:1.42202:21:4:0.0769:0:4 +8 43095953 . C G 27 v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.17928;SOR=0.19486;LSEQ=GTATACTGTACATAAAATAT;RSEQ=AAAGTACACCAAATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:2,2:0.4:2,2:31.5:1:34:0:1:1:23:4:0.4:0:7.5 0/1:19:2:2,0:9,7:16,2:0.1053:2,0:4:1:27.5:1:0.49673:0:27:4:0.1053:0:5.5 +8 43095956 . A G 34 pSTD;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03922;SOR=0;LSEQ=TACTGTACATAAAATATCAA;RSEQ=GTACACCAAATATATATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:32:0:34:1:1:1:23:4:0.5:0:7.5 0/0:14:0:0,0:8,6:14,0:0:2,0:10.5:1:29.6:1:1:0:27.4:28:1:0:4.6 +8 43095957 . G T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACCAAATATATATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:17:1:32.5:1:1:0:23:8:1:0:5.3 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:17.5:1:28.5:1:1:1.4491:30:4:0.1667:0:3.5 +8 43095961 . A C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.81844;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCAAATATATATTATTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:1:0:32:0:1:0:25:2:0.3333:0:4 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:21.5:1:29:1:1:1.41:30:4:0.2857:0:3.5 +8 43095962 . C T 32 pSTD;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02778;SOR=0;LSEQ=ACATAAAATATCAAAGTACA;RSEQ=CAAATATATATTATTTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:32.5:1:1:0:23:4:1:0:7.5 0/0:7:0:0,0:3,4:7,0:0:2,0:14.7:1:31.4:1:1:0:29.3:14:1:0:5.6 +8 43095963 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATATATATTATTTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:25:0:34:0:1:0:23:4:1:0:7.5 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:23.5:1:29:1:1:1.41:30:4:0.2857:0:3.5 +8 43095965 . A G 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAAAATATCAAAGTACACCA;RSEQ=ATATATATTATTTACTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:23:0:32.5:1:1:0:23:4:1:0:7.5 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:10.5:1:32.5:1:1:1.41:24:4:0.2857:0:6.5 +8 43095967 . T G 34 pSTD;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.02778;SOR=0;LSEQ=AAATATCAAAGTACACCAAA;RSEQ=ATATATTATTTACTGTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:34.5:1:1:0:23:4:1:0:7.5 0/0:7:0:0,0:3,4:7,0:0:2,0:12.6:1:29.9:1:1:0:29.3:14:1:0:5.6 +8 43095977 . T A 31 d5;v3;pSTD;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTACACCAAATATATATTAT;RSEQ=TACTGTACATAAAATATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:31.5:1:1:0:23:4:1:0:7.5 0/0:2:0:0,0:1,1:2,0:0:2,0:18:0:30:1:1:0:30:4:1:0:3.5 +8 43095979 . A T 32 d5;v3;pSTD;NM7.25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACACCAAATATATATTATTT;RSEQ=CTGTACATAAAATATCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:32.5:1:1:0:23:4:1:0:7.5 0/0:2:0:0,0:1,1:2,0:0:2,0:16:0:29:1:1:0:30:4:1:0:3.5 +8 43096094 . C T 25 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACCTAAGTACACCAAATA;RSEQ=ATATTATATACTCTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:8:0:33:0:1:0:20:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:25.5:1:1:0:21.5:4:1:0:6.5 +8 43096113 . A G 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACATATTATATACTCTACAT;RSEQ=AAATATCAAAGTACACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:30:0:1:0:20:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:29:1:1:0:21.5:4:1:0:6.5 +8 43096126 . A T 28 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=TCTACATAAAATATCAAAGT;RSEQ=CACAAAATACATATTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:40:0:32:0:1:0:20:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:44:0:28.5:1:1:0:21.5:4:1:0:6.5 +8 43096136 . C T 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACAAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:33:0:1:0:20:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:34:0:27.5:1:1:0:21.5:4:1:0:6 +8 43096414 . T G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATACTGTATGTAAAATAT;RSEQ=AAAGTACACCAAATACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:32.5:1:1:0:33.5:4:1:0:5.5 +8 43096423 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTAAAATATTAAAGTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:30.5:1:1:0:33.5:4:1:0:5.5 +8 43096430 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTAAAGTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:30.5:1:1:0:33.5:4:1:0:5.5 +8 43096436 . A T 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:32:0:1:0:33.5:4:1:0:5.5 +8 43096440 . A T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCAAATACATATTATAT;RSEQ=CTGTACATAAAATATCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:31:0:1:0:33.5:4:1:0:5.5 +8 43096562 . A T 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACACCAGATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:25:0:29.5:1:1:0:48:4:0.6667:0:3 +8 43096566 . AC CG 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACCAGATACATATTATAT;RSEQ=TGTACATAAAATATCAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:32:0:1:0:25:2:1:0:7 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:22:0:30:1:1:1.29:48:4:0.2222:0:2 +8 43096590 . A C 86 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.125;SOR=Inf;LSEQ=TACATAAAATATCAATGTAC;RSEQ=CAAAATACATATTATATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:3,4:0,0:0,7:1:0,2:27.4:1:30.7:1:1:0:29.1:14:1:0:6.3 +8 43096592 . A C 88 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=CATAAAATATCAATGTACAC;RSEQ=AAATACATATTATATACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:27:0:32:0:1:0:25:2:1:0:7 1/1:7:7:3,4:0,0:0,7:1:0,2:29.4:1:31.4:1:1:0:29.1:14:1:0:6.3 +8 43096598 . C T 82 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAATGTACACAAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:33:0:33:0:1:0:25:2:1:0:7 1/1:7:7:3,4:0,0:0,7:1:0,2:32:0:29.3:1:1:0:29.1:14:1:0:6.3 +8 43096604 . A T 83 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.125;SOR=Inf;LSEQ=ATGTACACAAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:29:0:1:0:25:2:1:0:7 1/1:7:7:3,4:0,0:0,7:1:0,2:26:0:29.9:1:1:0:29.1:14:1:0:6.3 +8 43096611 . G C 88 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=CAAAATACATATTATATACT;RSEQ=TACATAAAATATCAAAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:21:0:31:0:1:0:25:2:1:0:7 1/1:7:7:3,4:0,0:0,7:1:0,2:19:0:31.6:1:1:0:29.1:14:1:0:6.3 +8 43096617 . A G 88 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=ACATATTATATACTGTACAT;RSEQ=AAATATCAAAGTACACCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:15:0:28:0:1:0:25:2:1:0:7 1/1:7:7:3,4:0,0:0,7:1:0,2:13:0:31.4:1:1:0:29.1:14:1:0:6.3 +8 43096688 . A C 32 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAGTACACCAAATACATATT;RSEQ=TATACTGTGCATAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6:0:32.5:1:1:0:28.5:4:1:0:7 +8 43096716 . A C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCATAAAATATCAAAGTAC;RSEQ=CAAAGTACATATTATATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:0:31.5:1:1:0:28.5:4:1:0:7 +8 43096724 . CA TG 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACAAAGTA;RSEQ=TATTATATAGTGTACATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:31.3:1:1:0:28.5:4:1:0:6 +8 43096732 . AT GC 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTACACAAAGTACATATTAT;RSEQ=AGTGTACATAAAATATCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:31:1:1:0:28.5:4:1:0:5 +8 43096846 . A G 52 d5;v3;p8;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAAATATTAAACTACACCA;RSEQ=ATACATATTATATACTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:2,1:0,0:0,3:1:0,2:7.3:1:33:0:1:0:32.7:6:1:0:8 +8 43096850 . C T 60 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTAAACTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:3,1:0,0:0,4:1:0,2:9.3:1:30:1:1:0:30:8:1:0:8 +8 43096856 . A C 88 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACTACACCAAATACATATT;RSEQ=TATACTGTACATAAAATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:9:7:5,2:1,1:2,7:0.7778:2,2:10.7:1:31.4:1:1:2.24:28.3:14:0.7778:0:7.6 +8 43096861 . C G 92 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCAAATACATATTATATA;RSEQ=TGTACATAAAATATCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:12:7:5,2:3,2:5,7:0.5833:2,2:15.7:1:32.9:1:1:1.60:28.3:14:0.5833:0:7.6 +8 43096867 . A G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACATATTATATACTGTAC;RSEQ=TAAAATATCAAAGTACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:16:0:32.5:1:1:1.67325:27:4:0.1538:0:7 +8 43096875 . T A 95 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATATACTGTACATAAAATA;RSEQ=CAAAGTACACCAAATACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:26:10:5,5:9,6:15,10:0.3846:2,2:12.5:1:28.8:1:0.69683:1.47557:35.5:20:0.3846:0:7.9 +8 43096878 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACTGTACATAAAATATCA;RSEQ=AGTACACCAAATACACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:30:2:1,1:15,12:27,2:0.0667:2,2:27:0:33.5:1:1:1.24034:27:4:0.0667:0:7 +8 43096883 . CA AC 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACATAAAATATCAAAGTA;RSEQ=CCAAATACACATTATATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:31:2:1,1:17,12:29,2:0.0645:2,2:33:0:31:0:1:1.40053:27:4:0.0645:0:6 +8 43096884 . A C 119 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACATAAAATATCAAAGTAC;RSEQ=CCAAATACACATTATATACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:31:14:9,5:6,6:12,14:0.4516:2,2:12.6:1:31.5:1:0.69217:1.76:25.4:28:0.4828:0:7.8 +8 43096886 . C A 148 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATAAAATATCAAAGTACAC;RSEQ=AAATACACATTATATACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:31:28:16,12:1,1:2,28:0.9032:2,2:16.1:1:30.9:1:1:1.32:28.6:56:0.9333:0:7.6 +8 43096889 . A C 156 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATATCAAAGTACACCAA;RSEQ=TACACATTATATACTGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:3:0:29:0:1:0:26:2:1:0:6 1/1:32:29:16,13:1,1:2,29:0.9063:2,2:17:1:32.3:1:1:1.22:29.4:58:0.9355:0:7.7 +8 43096892 . C T 154 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATATCAAAGTACACCAAATA;RSEQ=ACATTATATACTGTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:4.5:1:29:1:1:0:26:4:1:0:5.5 1/1:41:37:21,16:1,1:2,37:0.9024:2,2:15.2:1:29.7:1:1:1.30:28.7:74:0.9024:0:7.1 +8 43096918 . C G 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATACTGTACATAAAATAT;RSEQ=AAACTACACCAAATACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:0,11:1:0,2:25.8:1:33.4:1:1:0:25.8:22:1:0:4.3 1/1:56:55:29,26:0,1:1,55:0.9821:0,2:23.9:1:31.3:1:0.48214:0:28.3:54:0.9818:0:6 +8 43096922 . C T 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTACATAAAATATCAAA;RSEQ=TACACCAAATACATATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:0,11:1:0,2:22:0:31.8:1:1:0:25.8:22:1:0:4.3 1/1:55:54:28,26:0,1:1,54:0.9818:0,2:20.7:1:30.4:1:0.49091:0:28:108:0.9818:0:6 +8 43096927 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.57884;SOR=0;LSEQ=ACATAAAATATCAAACTACA;RSEQ=CAAATACATATTATATACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:0,11:1:0,2:17:0:31.5:1:1:0:25.8:22:1:0:4.3 1/1:54:49:25,24:0,1:1,49:0.9074:0,2:16.2:1:29.3:1:1:0:27.9:48:0.9057:0:6.1 +8 43096934 . C T 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATCAAACTACACCAAATA;RSEQ=ATATTATATACTGTACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:0,11:1:0,2:10:0:30.4:1:1:0:25.8:22:1:0:4.3 1/1:52:52:25,27:0,0:0,52:1:0,2:10:1:29.1:1:1:0:28:104:1:0:5.8 +8 43096941 . TATACTGTACATAAAAAATCAAACTACACCAAATACATATT GGTACATAAAATATGAAAGCACCCAAACATTTATA 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33037;SOR=Inf;LSEQ=ACTACACCAAATACATATTA;RSEQ=ATAAACTGTACATAAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:11,0:0:2,0:3:0:30:1:1:0:25.8:22:1:0:4.3 0/1:44:6:1,5:21,17:38,6:0.1364:2,2:24.3:1:29.9:1:0.18528:5.95019:33.2:12:0.1364:0.1364:6.8 +8 43096944 . ACT TAG 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCAAATACATATTATAT;RSEQ=GTACATAAAAAATCAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:14:0:30.8:1:1:0:25:4:0.6667:0:6 +8 48101793 . T G 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGGGGCCTCTCCTTATTT;RSEQ=TGCATTGGTCTCTGTGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:31.5:1:1:0:60:4:1:0:1 +8 48649959 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22064;SOR=Inf;LSEQ=CCGGAGGCCGGCCAGGTCCC;RSEQ=CGTGAGCTGCTCCACGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:124,3:127,0:0:1,0:24.9:1:30.1:1:1:0:60:126:1:0:0.1 0/1:113:2:1,1:106,5:111,2:0.0177:1,2:13.5:1:31:0:0.10382:19.45094:60:4:0.0179:0:1 +8 48649975 . G C 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.24808;SOR=Inf;LSEQ=TCCCGCGTGAGCTGCTCCAC;RSEQ=CGCTGGTGCAGCTTCTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:145,19:164,0:0:2,0:23.6:1:29.9:1:1:0:60:163:1:0:0.1 0/1:171:3:2,1:139,29:168,3:0.0175:2,2:15:1:26.7:1:0.44149:2.38097:60:2:0.0119:0:1.7 +8 48649992 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25044;SOR=Inf;LSEQ=CACGCGCTGGTGCAGCTTCT;RSEQ=GTTCTCAGCCGACAGCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:173,57:230,0:0:2,0:23:1:31:1:1:0:60:37.333:0.9956:0:0.1 0/1:256:3:1,2:179,72:251,3:0.0117:2,2:21.7:1:24.3:1:0.20415:4.93611:60:2:0.0079:0:1.3 +8 48650123 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13077;SOR=Inf;LSEQ=ACTCGGGGCTGCCGCGGTCC;RSEQ=GGCCCCTCTTGCCGGCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:56,189:245,0:0:2,0:25.7:1:31.5:1:1:0:59.9:244:1:0:0.2 0/1:298:4:3,1:85,209:294,4:0.0134:2,2:8.5:1:27.8:1:0.07881:7.32:59:8:0.0138:0:1 +8 48650173 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5328;SOR=0;LSEQ=GCGGGGCCGGGCGCGGGGGT;RSEQ=TGCCTGGGGCTGCTGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:0,2:0,29:29,2:0.0645:1,0:12.5:1:32:0:1:0:60:4:0.0645:0:1.5 0/0:17:0:0,0:1,16:17,0:0:1,0:7.6:1:32.1:1:1:0:60:34:1:0:0.1 +8 48650427 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24226;SOR=Inf;LSEQ=CGCCTTGTGATTGCTGTTGA;RSEQ=GAGGTCGGCGAAGAGCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:82,32:114,0:0:2,0:21.6:1:30.4:1:1:0:60:113:1:0:0.1 0/1:111:2:1,1:81,28:109,2:0.018:2,2:14:1:30.5:1:0.45602:2.86004:60:4:0.018:0:1 +8 48650451 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24527;SOR=Inf;LSEQ=GTCGGCGAAGAGCTCGTCGT;RSEQ=GCACAGCTCCAGGGTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:102,84:186,0:0:2,0:22.1:1:31.3:1:1:0:60:61:1:0:0.2 0/1:183:2:1,1:106,75:181,2:0.0109:2,2:20:1:28.5:1:1:1.41059:60:4:0.0112:0:1 +8 48650452 . G T 40 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.36904;SOR=3.07324;LSEQ=TCGGCGAAGAGCTCGTCGTG;RSEQ=CACAGCTCCAGGGTGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:1:0,1:105,84:189,1:0.0053:2,0:1:0:27:0:0.44737:0:60:2:0.0053:0:1 0/1:187:3:1,2:108,76:184,3:0.016:2,2:5.3:1:25.3:1:0.57191:2.82625:60:6:0.0162:0:1 +8 48650457 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22474;SOR=0;LSEQ=GAAGAGCTCGTCGTGGCACA;RSEQ=CTCCAGGGTGGGCACGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:107,88:195,2:0.0102:2,2:25.5:1:30.5:1:1:1.21469:60:4:0.0102:0:1 0/0:218:0:0,0:125,93:218,0:0:2,0:25.1:1:30.9:1:1:0:60:71.667:1:0:0.2 +8 48650482 . G T 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12924;SOR=Inf;LSEQ=AGGGTGGGCACGGCGGCCAT;RSEQ=GAGTCGATGTAGGCGCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:113,135:248,0:0:2,0:28.8:1:31.8:1:1:0:60:496:1:0:0.2 0/1:295:4:2,2:142,149:291,4:0.0136:2,2:19.8:1:31.5:1:1:1.05:60:8:0.0137:0:1.5 +8 48650526 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49909;SOR=Inf;LSEQ=GATGGCGCTCTCGTCGTCGT;RSEQ=CATGGCGGGGGCGGCGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:63,117:180,0:0:2,0:24.1:1:29.3:1:1:0:60:89:1:0:0.3 0/1:191:2:1,1:68,121:189,2:0.0105:2,2:15:1:30.5:1:1:1.77:60:4:0.0106:0:1 +8 48650534 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.1021;SOR=Inf;LSEQ=TCTCGTCGTCGTACATGGCG;RSEQ=GGGCGGCGGCGCCTGGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:51,96:147,0:0:2,0:23.4:1:30.8:1:1:0:60:23.5:1:0:0.2 0/1:130:3:2,1:39,88:127,3:0.0231:2,2:11.3:1:29:1:0.23379:4.45:60:6:0.0233:0:1 +8 50562306 . G C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTGGGTTCGTGGTCTCA;RSEQ=TGGCCTCAGGAGTGAAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:33:0:1:0:44:4:1:0:1.5 +8 51786608 . G A 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00017;SOR=Inf;LSEQ=TTGGAAGATCCCACTCATGA;RSEQ=CCCATGCCTCCAGGGCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:15,21:36,0:0:2,0:28.4:1:32.9:1:1:0:60:72:1:0:0.1 0/1:44:13:7,6:14,17:31,13:0.2955:2,2:20.7:1:29.2:1:0.74375:1.41:55.9:26:0.2955:0:1.5 +8 51786658 . C A 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=CACAGAGCCAAGCGGATTCT;RSEQ=AACAGCCACTAAGCTAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:4,11:15,0:0:2,0:24.1:1:32.9:1:1:0:60:30:1:0:0 1/0:15:10:5,5:2,3:5,10:0.6667:2,2:15.3:1:28:1:1:1.46:60:20:0.6667:0:1.2 +8 53901153 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24599;SOR=Inf;LSEQ=ATTTGTCAAAGGCTCACTCA;RSEQ=TCAGAGCAAAAATAACTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:82,12:94,0:0:2,0:24:1:31.6:1:1:0:60:188:1:0:0 0/1:93:2:1,1:76,15:91,2:0.0215:2,2:11.5:1:29:1:0.31604:4.93807:60:4:0.0215:0:1 +8 53901222 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10057;SOR=0;LSEQ=GCCAGCCCTTAATCAGGTAA;RSEQ=CAGTCTCACATATACTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:1,2:169,115:284,3:0.0105:2,2:22.7:1:28.7:1:0.56893:2.92803:60:6:0.0105:0:1.3 0/0:329:0:0,0:190,138:328,0:0:2,0:27.7:1:31.2:1:1:0:60:81:0.9969:0:0.3 +8 53901248 . G T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04217;SOR=0;LSEQ=TCACATATACTTGGCTGACA;RSEQ=CACTGGGTATACATTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:4:1,3:173,150:323,4:0.0122:2,2:8:1:25:1:0.34353:3.44784:60:3:0.0092:0:1.3 0/0:394:0:0,0:210,184:394,0:0:2,0:25:1:31.1:1:1:0:60:77.8:1:0:0.4 +8 53901283 . G T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13216;SOR=Inf;LSEQ=TTGAATCTTCCACTTTGTGA;RSEQ=TAGTTCGTCTCCTATGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:141,148:289,0:0:2,0:24.5:1:32.5:1:1:0:60:95.333:1:0:0.7 0/1:357:4:3,1:164,189:353,4:0.0112:2,2:17.5:1:28.3:1:0.34367:3.45:60:3:0.0085:0:2 +8 53901286 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.47363;LSEQ=AATCTTCCACTTTGTGAGTA;RSEQ=TTCGTCTCCTATGGCTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:292:172:77,95:59,61:120,172:0.589:2,2:22.9:1:30.5:1:0.47634:1.19259:60:85:0.5923:0:1.1 0/1:344:139:62,77:95,110:205,139:0.4041:2,2:26.3:1:30:1:0.82548:1.07235:60:278:0.4076:0:1.2 +8 53901341 . G A 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.49046;LSEQ=TGAAAGAAAAATATCTCACA;RSEQ=TCTGCCAAAACTTGGAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:2,0:60,127:187,2:0.0106:2,0:1:0:25.5:1:0.10644:0:60:4:0.0107:0:1.5 0/1:191:3:2,1:62,126:188,3:0.0157:2,2:12.7:1:23.7:1:0.26042:4.03:49:2:0.0106:0:2.7 +8 53901365 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=GCCAAAACTTGGAATTGGTT;RSEQ=GCACAGAAATGCATGATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:38,104:142,2:0.0138:2,2:46:1:31:1:0.4697:2.71:60:4:0.0142:0:1 0/0:125:0:0,0:32,93:125,0:0:2,0:23.3:1:30.5:1:1:0:60:124:1:0:0.3 +8 53901381 . A C 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03992;SOR=Inf;LSEQ=GGTTGGCACAGAAATGCATG;RSEQ=TTAAAACATCAAAGTGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:18,89:107,0:0:2,0:22.1:1:31.4:1:1:0:60:214:1:0:0.2 0/1:88:4:0,4:17,67:84,4:0.0455:2,0:19.3:1:32:1:1:0:60:8:0.0455:0:1 +8 54049868 . T A 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00118;SOR=0.05468;LSEQ=TGTCTGATTTCAGAAGCCTT;RSEQ=TCCTGTAAATGCTGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:4,5:3,10:13,9:0.4091:2,2:16.9:1:28.8:1:0.37616:2.54:23.2:18:0.4091:0:1.9 0/1:29:1:0,1:12,16:28,1:0.0345:2,0:27:0:32:0:1:0:22:2:0.0345:0:3 +8 54049884 . G A 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05355;SOR=0.24775;LSEQ=CCTTTTCCTGTAAATGCTGG;RSEQ=TGGAGTCTTATACTATCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:14:4,10:0,5:5,14:0.7368:0,2:22.2:1:29.8:1:0.53044:0:31.5:28:0.7368:0:2.2 0/1:20:8:2,6:5,7:12,8:0.4:2,2:16.1:1:28.1:1:0.64241:2.06372:25.6:16:0.4:0:1.8 +8 54049893 . T C 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.39394;SOR=0;LSEQ=GTAAATGCTGGGTGGAGTCT;RSEQ=ATACTATCCCTGACTGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:4,16:0,0:0,20:1:0,2:24.3:1:31.9:1:1:0:35.1:40:1:0:1.9 1/1:13:12:3,9:0,1:1,12:0.9231:0,2:22.7:1:30.6:1:1:0:27.2:24:0.9231:0:1.6 +8 54445348 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06839;SOR=Inf;LSEQ=TCAGTCCAGCAGTTCGAGGC;RSEQ=GCACTGAGCCGCGATGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:39,0:39,0:0:1,0:27.8:1:31.8:1:1:0:60:78:1:0:0 0/1:28:3:3,0:25,0:25,3:0.1071:1,0:31.7:1:31.3:1:1:0:60:6:0.1111:0:1 +8 54445414 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22032;SOR=Inf;LSEQ=AGCAAGACTTTGTCTAATTA;RSEQ=AAGCAAAAACTGGCCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:100,68:168,0:0:2,0:21.8:1:29.9:1:1:0:60:32.6:0.9939:0:0.1 0/1:150:2:1,1:93,54:147,2:0.0133:2,2:21:1:29:1:1:1.71556:60:4:0.0135:0:1 +8 54445438 . G T 35 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10039;SOR=Inf;LSEQ=CAAAAACTGGCCTTTCAGCT;RSEQ=GAACCACCATCTTCCAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:0:0,0:132,111:243,0:0:2,0:26.4:1:31.4:1:1:0:58.8:59.75:1:0:0.2 0/1:212:3:0,3:116,93:209,3:0.0142:2,0:7.3:1:22.3:1:0.09126:0:32.7:2:0.0096:0:1.3 +8 54445482 . G A 126 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCAAAATGACGAACACAAA;RSEQ=GGAAAGAGGAGAGACACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:95,135:230,0:0:2,0:25.1:1:31.8:1:1:0:58.6:75.667:1:0:0.2 0/1:212:20:8,12:82,110:192,20:0.0943:2,2:20.7:1:29.2:1:1:1.11757:54.1:40:0.0976:0:1.3 +8 54445600 . T C 96 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03778;SOR=0;LSEQ=GAGAGGCCGAGGCAGGAGGA;RSEQ=TGCCTGAGCTCAGGAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:0,7:0,17:17,7:0.2917:1,0:33:1:34.3:1:1:0:56.1:14:0.2917:0:1 0/0:13:0:0,0:0,13:13,0:0:1,0:29.8:1:28.8:1:1:0:50:26:1:0:0.1 +8 54445817 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11667;SOR=Inf;LSEQ=GGGTGACAGAGTGAGACTCC;RSEQ=TCTCAAAAATACAAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:22,4:26,0:0:2,0:29.4:1:32.5:1:1:0:59.6:52:1:0:0.1 0/1:14:2:2,0:11,1:12,2:0.1429:2,0:12:1:30.5:1:1:0:46:4:0.1429:0:1 +8 54445839 . CA C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.13051;SOR=Inf;LSEQ=CTCAAAAATACAAACAACAA;RSEQ=AAAAAAAACATGGAGTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:33,5:38,0:0:2,0:22.1:1:31:1:1:0:59.9:76:1:0:0.1 0/1:22:2:2,0:19,1:20,2:0.0909:1,0:25.5:1:30:1:1:0:60:4:0.0909:0:0 +8 54445879 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21074;SOR=Inf;LSEQ=TTCCTTTGGCCATGTTTATG;RSEQ=AAATCTGTAAGAGAGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:60,16:76,0:0:2,0:22.9:1:32.6:1:1:0:58.9:152:1:0:0.1 0/1:65:2:1,1:55,8:63,2:0.0308:2,2:8.5:1:26.5:1:0.25962:6.54047:51:4:0.0317:0:1 +8 54445919 . G T 24 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0.83561;LSEQ=TATTATAGATATCAAGGGAA;RSEQ=GGGTACTGTTCAAAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:101,51:152,2:0.013:2,2:37.5:1:30:1:1:1.97101:39.5:4:0.0131:0:1 0/1:184:2:0,2:127,55:182,2:0.0109:2,0:1:0:24.5:1:0.0948:0:35:4:0.0109:0:2 +8 54446265 . T C 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTATGGATTCATGGCATAT;RSEQ=AACTGTTTAAATGAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:25:1:30.5:1:1:0:60:4:0.6667:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:12:0:33:0:1:0:60:2:1:0:1 +8 55364337 . C A 48 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0.58251;LSEQ=GTCTTTATTTTGTCCCTGCG;RSEQ=TTTCCATTAGGTTCTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,5:5,3:0.375:0,0:18.3:1:30.7:1:1:0:60:6:0.375:0:1 0/1:4:1:0,1:0,3:3,1:0.25:0,0:11:0:32:0:1:0:60:2:0.25:0:1 +8 55367444 . C T 55 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2671;SOR=2.76861;LSEQ=ATCTCTTGTGTTGAGAAAAG;RSEQ=AAGGCTTGCAGGAAGCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:389:2:0,2:278,108:386,2:0.0051:2,0:11.5:1:18:1:0.07985:0:60:1:0.0026:0:1 0/1:354:5:1,4:240,108:348,5:0.0141:2,2:7.8:1:23.8:1:0.03674:8.83132:60:10:0.0142:0:1.2 +8 55367460 . C T 71 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12322;SOR=0.19776;LSEQ=AAAGCAAGGCTTGCAGGAAG;RSEQ=CACTCCGGATGTTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:5:2,3:307,161:468,5:0.0106:2,2:31:1:30.8:1:0.34674:2.85341:60:10:0.0109:0:1.2 0/0:475:1:0,1:308,164:472,1:0.0021:2,0:1:0:23:0:0.34884:0:60:2:0.0021:0:1 +8 55370619 . C T 127 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGGCATCTCAGTGCCTCA;RSEQ=TCCCCACCCCCTCCCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:86,10:96,0:0:2,0:23.7:1:32.3:1:1:0:60:95:1:0:0.1 0/1:46:17:15,2:26,3:29,17:0.3696:2,2:26.8:1:31.1:1:1:1.15187:60:34:0.3696:0:1 +8 55370660 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.07658;SOR=Inf;LSEQ=TCGGGGGAGGCGGCGCGTCC;RSEQ=GCGGAGGGTTGAGGGGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:144,66:210,0:0:2,0:22.3:1:29.7:1:1:0:60:51.5:1:0:0.1 0/1:156:3:2,1:110,43:153,3:0.0192:2,2:22.7:1:30.7:1:1:1.27698:60:6:0.0194:0:1 +8 55370898 . G A 79 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07768;SOR=5.92646;LSEQ=CCGAGCCAAGGGCGAGTCCC;RSEQ=TATCCGGCGGCCGATGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:535:1:0,1:300,234:534,1:0.0019:2,0:19:0:33:0:0.43925:0:60:2:0.0019:0:1 0/1:637:7:4,3:334,294:628,7:0.011:2,2:15.4:1:28.3:1:1:1.17:60:14:0.0111:0:1.3 +8 55370946 . G A 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07338;SOR=6.25685;LSEQ=GGTGTGGGCTAAGGACGAGC;RSEQ=CAAGCGGCTGGCGCAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:605:1:1,0:300,304:604,1:0.0017:2,0:1:0:25:0:0.49752:0:60:2:0.0017:0:1 0/1:682:7:4,3:329,345:674,7:0.0103:2,2:23.4:1:29.9:1:0.71966:1.40:60:14:0.0104:0:1.3 +8 55371061 . C T 28 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.79325;LSEQ=GCTGGCGCGAATCGCTAGGC;RSEQ=GATTTCTTAAACCCCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:0,1:23,127:150,1:0.0066:2,0:18:0:33:0:1:0:60:2:0.0068:0:1 0/1:169:2:1,1:29,138:167,2:0.0118:2,2:7.5:1:28:1:0.32439:4.70:60:4:0.012:0:1.5 +8 55371080 . C CAG 167 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=79.87495;LSEQ=CCGATTTCTTAAACCCCAAA;RSEQ=TGTTCTTTGCGAGCCTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:1:0,1:10,97:107,1:0.0093:2,0:37:0:34.5:0:1:0:60:2:0.0093:0:0 0/1:102:44:6,38:11,47:58,44:0.4314:2,2:25.9:1:30.6:1:0.59491:1.47667:60:43:0.4257:0.098:0.1 +8 55371154 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01552;SOR=Inf;LSEQ=TTCTTAAGGCTCTGGGTTCC;RSEQ=TTCCCGCTTCCCGCCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:36,0:0:1,0:22.2:1:33.9:1:1:0:60:72:1:0:0.1 0/1:13:3:0,3:1,9:10,3:0.2308:2,0:23.3:1:31:1:1:0:60:6:0.2308:0:1 +8 55371472 . C A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.7914;SOR=0.75303;LSEQ=AAGGGCTCGGACTCAGGAGT;RSEQ=CCAGATCTCCCTCTTTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:12:12,0:26,1:27,12:0.3077:1,0:22.9:1:28.9:1:1:0:60:24:0.3077:0:2.6 0/1:32:8:8,0:24,0:24,8:0.25:1,0:23.1:1:28:1:1:0:60:16:0.2581:0:2.4 +8 55371474 . C A 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0628;SOR=0;LSEQ=GGGCTCGGACTCAGGAGTCC;RSEQ=AGATCTCCCTCTTTAACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:5:5,0:37,1:38,5:0.1163:1,0:20.2:1:30:1:1:0:60:10:0.1163:0:2 0/0:34:0:0,0:34,0:34,0:0:1,0:21.1:1:30.9:1:1:0:60:33:1:0:1.4 +8 55371478 . T C 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.08842;SOR=2.14031;LSEQ=TCGGACTCAGGAGTCCCAGA;RSEQ=CTCCCTCTTTAACTTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:20:20,0:23,1:24,20:0.4545:1,1:20.8:1:32.6:1:1:0:60:40:0.4545:0:2.4 1/0:42:27:27,0:15,0:15,27:0.6429:1,1:21.7:1:32.3:1:1:0:60:54:0.6429:0:2 +8 55371499 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11947;SOR=Inf;LSEQ=CTCCCTCTTTAACTTCACCC;RSEQ=GGTTGCGCAATTCAAAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:63,4:67,0:0:2,0:23:1:30.7:1:1:0:60:32.5:1:0:0.9 0/1:68:4:3,1:63,1:64,4:0.0588:1,2:16.5:1:30:1:0.11501:18.32472:60:8:0.0615:0:2.5 +8 55371538 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.12495;LSEQ=CTGAGGGGGGAGGTGCGTCC;RSEQ=GGTGGGGCCAGGTGGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:36:28,8:109,13:122,36:0.2264:2,2:24.6:1:28.7:1:0.09297:2.38011:60:17:0.2237:0:1.6 1/0:133:80:71,9:43,10:53,80:0.6015:2,2:27.3:1:29:1:0.31129:1.83:60:79:0.6077:0:1.4 +8 55371548 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20059;SOR=Inf;LSEQ=AGGTGCGTCCAGGTGGGGCC;RSEQ=GGTGGGGCCTGGAGCGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:188:0:0,0:151,37:188,0:0:2,0:23.9:1:30.2:1:1:0:60:25.857:1:0:0.4 0/1:153:2:1,1:125,26:151,2:0.0131:2,2:15:1:28:1:0.32276:4.7367:60:4:0.0133:0:1 +8 55371724 . G A 59 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01428;SOR=Inf;LSEQ=CACCCCAACTACAAGTACCG;RSEQ=CCGCGGCGGCGCAAGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:563:0:0,0:185,378:563,0:0:2,0:24.2:1:31.5:1:1:0:59.9:50.182:1:0:0.1 0/1:549:6:5,1:205,336:541,6:0.0109:2,2:7.7:1:23.2:1:0.03327:8.16:58.2:5:0.0094:0:1.2 +8 55371789 . C T 118 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00012;SOR=18.00242;LSEQ=CGGCTTCCTGCACGGCCTGG;RSEQ=TGAGCCGCAGGCGGCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:1:0,1:28,141:169,1:0.0059:2,0:11:0:32:0:1:0:60:2:0.006:0:2 0/1:155:15:2,13:38,102:140,15:0.0968:2,2:23.3:1:30.4:1:0.35674:2.41024:60:30:0.098:0:1 +8 55371820 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49708;SOR=0;LSEQ=GCGGCCGCGCTGGGCCCCGA;RSEQ=GGCGGCCGCGTGGCCATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:1,1:33,48:81,2:0.0241:2,2:5.5:1:29.5:1:1:1.45:60:4:0.0241:0:1.5 0/0:80:0:0,0:29,51:80,0:0:2,0:14.7:1:30.8:1:1:0:60:160:1:0:0.2 +8 55371888 . C T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11421;SOR=0;LSEQ=GGGCTTCCCCGCCGGCCCGC;RSEQ=GCTGCTGCCTCCGCACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:3:1,2:95,34:129,3:0.0227:2,2:25.3:1:29.3:1:0.18048:5.50151:60:6:0.0229:0:1 0/0:139:0:0,0:89,50:139,0:0:2,0:24.2:1:29.9:1:1:0:59.9:68.5:1:0:0.2 +8 55372088 . G A 55 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05011;SOR=0;LSEQ=ACGCGCAGGTCTCGGACTAC;RSEQ=CTGGCCCCCCGGAGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:4:4,0:126,193:319,4:0.0124:2,0:7.8:1:27.5:1:0.02552:0:60:8:0.0127:0:1 0/0:358:0:0,0:154,203:357,0:0:2,0:23.5:1:29.6:1:1:0:60:21.313:1:0:0.2 +8 55372109 . G A 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=0;LSEQ=CTGGCCCCCCGGAGCCTCCC;RSEQ=CCGGTCCCATGCACCCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:2,1:108,162:270,3:0.011:2,2:13.3:1:22:1:0.56697:2.99:60:2:0.0075:0:1 0/0:263:0:0,0:116,147:263,0:0:2,0:22.9:1:30.2:1:1:0:60:64.75:1:0:0.2 +8 55372224 . C T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38072;SOR=3.44808;LSEQ=CGCGATGGGCTCGCCCGGGG;RSEQ=GGGCGGCGGGCGCGGCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:1:0,1:184,155:339,1:0.0029:2,0:1:0:29:0:0.45882:0:60:2:0.0029:0:1 0/1:399:4:1,3:209,186:395,4:0.01:2,2:24.3:1:27.8:1:0.34876:3.3615:60:8:0.0103:0:1 +8 55372258 . ACACCAG A 88 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=4.000;MSILEN=6;SSF=0.01633;SOR=Inf;LSEQ=GGCTTCCAGATGCAGCCGCA;RSEQ=CACCAGCACCAGCACCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:291,208:499,0:0:2,0:26:1:32.4:1:1:0:59.8:165.333:0.998:0:0.2 0/1:559:7:4,3:293,257:550,7:0.0125:2,2:27.7:1:31.6:1:1:1.17:49.7:14:0.0128:0.0036:0.1 +8 55372516 . C G 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTCGGTGGTGTCCGACGC;RSEQ=AGCTCCGCGGTATATTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:717:0:0,0:270,447:717,0:0:2,0:24.1:1:31.9:1:1:0:60:101.429:1:0:0.2 0/1:804:68:28,40:308,426:734,68:0.0846:2,2:25.9:1:30:1:1:1.03283:60:136:0.0858:0:1.2 +8 55374911 . T TCTAA 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.01026;SOR=2.79078;LSEQ=AAATACTAGGTCTTATTCCT;RSEQ=CTATGTTTTTTTTTTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:11:10,1:140,6:146,11:0.0701:1,2:26:1:28.9:1:0.4048:2.31596:59.2:10:0.0658:0.0127:0.2 0/1:109:19:17,2:87,3:90,19:0.1743:1,2:22.5:1:28.5:1:0.20826:3.35975:54.2:18:0.1682:0.0642:1 +8 55374915 . TG ACTATGT 168 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=15.000;MSILEN=1;SSF=0;SOR=4.50566;LSEQ=AATACTAGGTCTTATTCCTT;RSEQ=TTTTTTTTTTTTTGGTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:20:20,0:127,6:133,20:0.125:1,1:33.6:1:31.7:1:1:0:56.9:40:0.1282:0:0.2 0/1:140:55:50,5:77,4:81,55:0.3929:1,2:19.5:1:29.2:1:0.48453:1.91549:56.9:54:0.3971:0.2143:0.7 +8 55374948 . A G 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGGTAGTTTTAAATTACCA;RSEQ=AACATTTGGTATCCTTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:26:20,6:236,75:311,26:0.0772:2,2:23.3:1:29.8:1:1:1.06:60:7.667:0.0699:0:1.1 0/0:330:0:0,0:251,79:330,0:0:2,0:18.6:1:29.2:1:1:0:59.2:81.5:1:0:0.3 +8 55379760 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49887;SOR=0;LSEQ=TCGGCGCGCGGGGCAGGCCT;RSEQ=GAGCGCCGTGAGCAGGCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:97,53:150,2:0.0132:2,2:42:1:30.5:1:1:1.82238:60:4:0.0135:0:1 0/0:142:0:0,0:89,53:142,0:0:2,0:25.1:1:30.8:1:1:0:60:141:1:0:0.2 +8 55379765 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22596;SOR=Inf;LSEQ=GCGCGGGGCAGGCCTGGAGC;RSEQ=CCGTGAGCAGGCCGGATGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:165:0:0,0:104,61:165,0:0:2,0:27.3:1:30.2:1:1:0:59.9:40.25:1:0:0.2 0/1:150:2:1,1:91,57:148,2:0.0133:2,2:36.5:1:28.5:1:1:1.59128:60:4:0.0135:0:2 +8 55379777 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2309;SOR=Inf;LSEQ=CCTGGAGCGCCGTGAGCAGG;RSEQ=CGGATGCGGGATACGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:108,72:180,0:0:2,0:28.6:1:31.4:1:1:0:60:21.5:1:0:0.2 0/1:167:2:1,1:96,69:165,2:0.012:2,2:24.5:1:27:1:1:1.38849:60:4:0.0122:0:2 +8 55379808 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20617;SOR=Inf;LSEQ=ATACGCCAGTGACTACCAGA;RSEQ=CCAGACCCGGAGCGCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:109,96:205,0:0:2,0:24.8:1:32.3:1:1:0:60:40:1:0:0.2 0/1:171:2:1,1:84,85:169,2:0.0117:2,2:17.5:1:28.5:1:1:1.01:60:4:0.0118:0:1.5 +8 55379824 . G A 98 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00661;SOR=6.69144;LSEQ=CAGAGCCAGACCCGGAGCGC;RSEQ=CTGCCGGCGGTGACGGCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:2,0:89,102:191,2:0.0104:2,0:1:0:28:1:0.22102:0:60:4:0.0109:0:1 0/1:152:10:4,6:64,78:142,10:0.0658:2,2:26.3:1:29.6:1:1:1.22911:60:20:0.0667:0:1.2 +8 55379825 . C A 28 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63687;LSEQ=AGAGCCAGACCCGGAGCGCG;RSEQ=TGCCGGCGGTGACGGCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:85,102:187,2:0.0106:2,2:5.5:1:28.5:1:1:1.20:60:4:0.0109:0:1.5 0/0:148:1:1,0:65,82:147,1:0.0068:2,0:1:0:24:0:0.44595:0:60:2:0.0069:0:2 +8 55379838 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18488;SOR=Inf;LSEQ=GAGCGCGCTGCCGGCGGTGA;RSEQ=GGCTAGGCTGGGCCCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:0:0,0:77,95:172,0:0:2,0:24.8:1:30.2:1:1:0:59.9:27.667:0.994:0:0.2 0/1:131:2:1,1:51,78:129,2:0.0153:2,2:26.5:1:29.5:1:1:1.52:60:4:0.0156:0:1 +8 55379851 . C A 36 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0.9421;LSEQ=GCGGTGACGGCTAGGCTGGG;RSEQ=CCCTGTCCTTGGGCCGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:3:2,1:63,91:154,3:0.0191:2,2:17.3:1:23.3:1:0.56996:2.87:60:2:0.0135:0:1 0/1:111:2:1,1:40,69:109,2:0.018:2,2:1.5:1:20:1:1:1.72:60:1:0.0095:0:1.5 +8 55379865 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13885;SOR=Inf;LSEQ=GCTGGGCCCCTGTCCTTGGG;RSEQ=CGAGTTGCCGAGCTCCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:54,95:149,0:0:2,0:26.2:1:30.9:1:1:0:60:28.8:1:0:0.1 0/1:89:2:1,1:29,58:87,2:0.0225:2,2:11.5:1:26.5:1:1:1.98:60:4:0.023:0:2 +8 55379903 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51218;SOR=0;LSEQ=TCGGGGACTTGAAGGTGAAG;RSEQ=GCGAGGCGCCGGCCGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:27,80:107,2:0.0183:2,2:13.5:1:29:1:0.44954:2.93:60:4:0.0192:0:1 0/0:77:0:0,0:24,53:77,0:0:2,0:24.3:1:29.7:1:1:0:59.4:37.5:1:0:0.3 +8 55379916 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.20554;SOR=Inf;LSEQ=GGTGAAGGGCGAGGCGCCGG;RSEQ=CGGGGCCGCGGGCCGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:21,64:85,0:0:2,0:22.8:1:30.2:1:1:0:60:9.625:1:0:0.2 0/1:71:2:1,1:21,48:69,2:0.0282:2,2:18:1:30.5:1:0.52676:2.26:60:4:0.0286:0:1 +8 56063806 . T C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00438;SOR=0.56834;LSEQ=AGAATTTATACTTTCATTTC;RSEQ=GGCCTGCCAAGCAAACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:95:41,54:50,60:110,95:0.4634:2,2:25.8:1:29.8:1:0.77906:1.09706:59.8:46.5:0.4581:0:1.8 0/1:228:75:35,40:63,88:151,75:0.3289:2,2:26.2:1:29.6:1:0.56876:1.22:60:150:0.3319:0:2 +8 56063814 . C A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.36113;SOR=0.8145;LSEQ=TACTTTCATTTCTGGCCTGC;RSEQ=AAGCAAACTTCACAGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:78:33,45:53,74:127,78:0.3805:2,2:25.9:1:30.4:1:1:1.02:59.8:156:0.3842:0:2 0/1:219:73:35,38:59,87:146,73:0.3333:2,2:27.1:1:29.5:1:0.3128:1.36:60:72:0.3349:0:2 +8 56063856 . T G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23799;SOR=Inf;LSEQ=ATCTGACCTTAACAATTATC;RSEQ=GATCTAACACTGACAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:57,101:158,0:0:2,0:24.5:1:30.9:1:1:0:60:78:1:0:0.6 0/1:151:2:1,1:47,102:149,2:0.0132:2,2:42.5:1:30.5:1:0.53616:2.16:60:4:0.0136:0:1 +8 56265933 . C G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53333;SOR=0;LSEQ=ACACACACACAGGGAGAATG;RSEQ=CCTGTGAAGAAGACAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:19,5:24,2:0.0769:2,2:14:1:30.5:1:0.41538:3.55868:60:4:0.08:0:1 0/0:14:0:0,0:12,2:14,0:0:2,0:21.4:1:30.1:1:1:0:60:28:1:0:0.1 +8 56265985 . CA C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49803;SOR=Inf;LSEQ=CTCTACAAGCTGAGGAATGC;RSEQ=AAGATTGCCAGCAAACCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:61,0:0:2,0:27.4:1:30.3:1:1:0:60:60:1:0:0.1 0/1:69:2:1,1:40,27:67,2:0.029:2,2:32:1:30:1:1:1.47282:60:4:0.029:0:0 +8 56266019 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51194;SOR=Inf;LSEQ=AAACCACCAGAAACTACTGA;RSEQ=GGGTGGCATGCAACAGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:21,27:48,0:0:2,0:28.3:1:31.2:1:1:0:60:23:1:0:0.1 0/1:69:2:1,1:33,34:67,2:0.029:2,2:46:0:32:1:1:1.03:60:4:0.0294:0:1.5 +8 56319983 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTATCCCACTTGAGAATTAC;RSEQ=GACTTAGAAGAGCTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:23,0:0:2,0:25.4:1:29.7:1:1:0:60:22:1:0:0 0/1:51:2:1,1:30,19:49,2:0.0392:2,2:35.5:1:29.5:1:1:1.56436:60:4:0.0392:0:1 +8 56319986 . CT C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCCACTTGAGAATTACGGA;RSEQ=TAGAAGAGCTGCAGTGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:25,0:0:2,0:26.3:1:29.7:1:1:0:60:11.5:1:0:0 0/1:56:2:1,1:32,22:54,2:0.0357:2,2:23.5:1:28.7:1:1:1.4446:60:4:0.0357:0.0179:0 +8 56320018 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5474;SOR=Inf;LSEQ=GCAGTGTCACCTACAGGGTC;RSEQ=CGCTGTCCACGCTGCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:19,18:37,0:0:2,0:26.2:1:32.4:1:1:0:60:74:1:0:0.2 0/1:72:2:1,1:35,35:70,2:0.0278:2,2:10:0:31:0:1:1:60:4:0.0278:0:1 +8 56320041 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53393;SOR=Inf;LSEQ=CTGTCCACGCTGCCTCCGCC;RSEQ=GAGTGATGAACCTGTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:17,18:35,0:0:2,0:25.9:1:31.9:1:1:0:60:70:1:0:0.2 0/1:62:2:1,1:25,35:60,2:0.0323:2,2:43.5:1:31:1:1:1.39:60:4:0.0323:0:1 +8 56320062 . G A 23 v3;p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12033;SOR=0;LSEQ=GAGTGATGAACCTGTCTGTT;RSEQ=CACATTCACGGGCCTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:11,13:24,2:0.0769:2,2:7.5:1:23.5:1:1:1.17:60:4:0.0769:0:2 0/0:48:0:0,0:19,29:48,0:0:2,0:22.2:1:31.4:1:1:0:60:96:1:0:0.2 +8 56320071 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14132;SOR=0;LSEQ=ACCTGTCTGTTGCACATTCA;RSEQ=GGGCCTGATGAACTGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:10,12:22,2:0.0833:2,2:40.5:1:31:1:1:1.19:60:4:0.0833:0:2 0/0:39:0:0,0:16,23:39,0:0:2,0:20.9:1:30:1:1:0:60:78:1:0:0.2 +8 56879449 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53324;SOR=Inf;LSEQ=TACATCATCACCGAGTACAT;RSEQ=GCCAAGGGTGAGTTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:24,0:0:2,0:33.8:1:32.2:1:1:0:60:48:1:0:0 0/1:43:2:1,1:17,24:41,2:0.0465:2,2:34.5:1:30:1:1:1.40:60:4:0.0476:0:1 +8 56879965 . C T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCACTGCAACCCCTGCCTC;RSEQ=CGGGTTCAAGCGATTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:30.5:1:1:0:38:4:1:0:2 +8 56880021 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCTGGGACTACAGGCAC;RSEQ=TGCCACCATGCCCAGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:27.5:1:1:0:38:4:1:0:2 +8 57013717 . G A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50803;SOR=Inf;LSEQ=TCCTTTCTCCCCATCTTTGG;RSEQ=CTTAATTTACCAGTAGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:37,35:72,0:0:2,0:30.9:1:32.3:1:1:0:53.1:144:1:0:0.1 0/1:97:2:1,1:54,41:95,2:0.0206:2,2:23:0:29:0:1:1.31328:32.5:4:0.0211:0:2 +8 57013846 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19918;SOR=Inf;LSEQ=GTTTTTCCTGTTTTTTGAAG;RSEQ=AGTCTTGTCCTTTTGATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:56,60:116,0:0:2,0:24.8:1:31.8:1:1:0:57.6:57:1:0:0.2 0/1:94:2:1,1:46,46:92,2:0.0213:2,2:14.5:1:27.5:1:1:1:33:4:0.0213:0:1.5 +8 57013974 . CTCA C 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=0.02741;SOR=Inf;LSEQ=GGTGCTTTCTCTTCAGTTCC;RSEQ=TCATCAAAATCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:40,19:59,0:0:2,0:25.4:1:31.1:1:1:0:59.4:58:1:0:0.1 0/1:42:4:3,1:24,14:38,4:0.0952:2,2:37.3:1:27.6:1:1:1.73:52.5:3:0.0732:0.0238:1.3 +8 57013992 . ATCATCT A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.03757;SOR=Inf;LSEQ=CCCTCATCATCAAAATCATC;RSEQ=TCATCATCATCATTATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:43,25:68,0:0:2,0:26.4:1:30:1:1:0:55.1:21.667:1:0:0.1 0/1:55:4:2,2:38,13:51,4:0.0727:2,2:31:1:28.5:1:0.2975:2.85655:41.8:8:0.0769:0.0182:0.3 +8 57014012 . TATC T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.49955;SOR=0;LSEQ=ATCATCTTCATCATCATCAT;RSEQ=ATCATCATCATCATCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:0,2:56,33:89,2:0.022:2,0:20.5:1:27:1:0.1453:0:31:4:0.0225:0:0 0/0:79:0:0,0:51,28:79,0:0:2,0:22.6:1:27.6:1:1:0:43.5:38.5:1:0:0.2 +8 57014031 . A T 46 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.67157;SOR=1.65383;LSEQ=TTATCATCATCATCATCATC;RSEQ=TCTTCATCAGCAGCAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:59,46:105,2:0.0187:2,2:34:0:31.5:1:1:1.27959:33:4:0.0187:0:1 0/1:98:3:2,1:59,36:95,3:0.0306:2,2:26.7:1:29.3:1:1:1.22:31.3:6:0.0309:0:1 +8 57014062 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.24029;SOR=Inf;LSEQ=CAGCAAGTTTTACTTTTTTC;RSEQ=GTGGAACCTTGCTACCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:52,39:91,0:0:2,0:30.4:1:31.1:1:1:0:37.9:90:1:0:0.1 0/1:88:2:1,1:47,39:86,2:0.0227:2,2:33.5:1:28.5:1:1:1.20256:40.5:4:0.0233:0:1 +8 57014152 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50562;SOR=Inf;LSEQ=CCTCTTCATCTTCTGACTCT;RSEQ=CATCTTCTACCACAGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:56,46:102,0:0:2,0:17:1:31.5:1:1:0:28.3:50:1:0:0.2 0/1:131:2:1,1:58,70:128,2:0.0153:2,2:16.5:1:26.5:1:1:1.21:24:4:0.0153:0:1 +8 57014164 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17939;SOR=0;LSEQ=CTGACTCTGCATCTTCTACC;RSEQ=CAGCTACTAAGTGCTGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:66,53:119,2:0.0165:2,2:28.5:1:30:1:1:1.243:30.5:4:0.0169:0:1 0/0:164:0:0,0:75,89:164,0:0:2,0:19.8:1:28.6:1:1:0:31.2:53.667:1:0:0.1 +8 57014350 . A G 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=CCTCTGCTTCAACAATGTGC;RSEQ=ATTCATCCTTTGCACCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:147,114:261,0:0:2,0:27.1:1:29.2:1:1:0:41.6:8.667:1:0:0.7 0/1:301:15:9,6:160,120:280,15:0.0498:2,2:23.6:1:30:1:1:1.12:47.9:14:0.0505:0:1.2 +8 57014659 . A G 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02347;SOR=Inf;LSEQ=AAAGTGCTGGGATTACAAGC;RSEQ=TGAGCCACCGCGCCCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:17,11:28,0:0:2,0:19.9:1:30.6:1:1:0:50:56:1:0:0.1 0/1:28:5:3,2:17,6:23,5:0.1786:2,2:26.4:1:28:1:0.60562:1.8428:53:10:0.1852:0:1.2 +8 57014752 . G A 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAAAGTGATAATCTTTGTT;RSEQ=GCCTTCAGTTCACAACCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:61,19:80,0:0:2,0:22.7:1:31.5:1:1:0:48:39:1:0:0.1 0/1:101:21:12,9:47,33:80,21:0.2079:2,2:27:1:28.4:1:1:1.06748:42.4:42:0.2121:0:1 +8 57014805 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50033;SOR=Inf;LSEQ=GGGCCTCAGGAGGCTCATGT;RSEQ=CATGTCCATCAAATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:76,51:127,0:0:2,0:24.3:1:31.4:1:1:0:58.6:62.5:1:0:0.1 0/1:146:2:1,1:82,60:142,2:0.0137:2,2:34:1:28.5:1:1:1.36364:60:4:0.0139:0:1 +8 57014840 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23503;SOR=0;LSEQ=CTTCCATCGGGTGGCAGCAC;RSEQ=CACTTAGGTGGCAGAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:80,86:166,2:0.0119:2,2:31:1:31.5:1:1:1.07:60:4:0.0122:0:1 0/0:178:0:0,0:92,85:177,0:0:2,0:28.8:1:30:1:1:0:58.9:43.25:0.9943:0:0.2 +8 59337107 . G T 57 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20743;SOR=0.23739;LSEQ=CTTTTTAGGGAGAGAGTGAA;RSEQ=TCCACATCTATTTTTGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:4:1,3:180,71:251,4:0.0157:2,2:11:1:28.8:1:0.07488:7.53692:60:8:0.0161:0:1 0/0:266:1:0,1:183,80:263,1:0.0038:2,0:1:0:26:0:0.30682:0:60:2:0.0038:0:1 +8 59337246 . CG C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.33368;SOR=0.8077;LSEQ=CGTGGAGTTGGAGTACAAGG;RSEQ=GGGGGGGGGGCTCTGATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:452:50:24,26:189,206:395,50:0.1106:2,2:30.3:1:32.2:1:1:1.01:52.6:100:0.1142:0.0066:0.5 0/1:504:46:19,27:227,222:449,46:0.0913:2,2:31.4:1:29.9:1:0.27886:1.45196:48.9:22:0.0913:0:0.3 +8 59337251 . G C 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.31562;SOR=0.85872;LSEQ=AGTTGGAGTACAAGGCGGGG;RSEQ=GGGGGGCTCTGATCTCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:134:63,71:156,167:323,134:0.2926:2,2:26.2:1:30.3:1:0.83738:1.05266:51.1:21.333:0.2916:0:1.2 0/1:519:136:65,71:184,198:382,136:0.262:2,2:25.8:1:29.5:1:1:1.01505:49.8:26.2:0.2604:0:1.1 +8 59337488 . CTCTCTGTTGATGTCAG C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0;SOR=4.42926;LSEQ=ATGTTGCAGTCAACACCTTT;RSEQ=TCAGAATATCAATCACAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:35:14,21:110,147:257,35:0.119:2,2:20.1:1:32.3:1:0.85599:1.12199:59.4:70:0.1232:0.0272:0.1 0/1:320:120:54,66:84,116:200,120:0.375:2,2:25.3:1:31.1:1:0.64158:1.13:58.9:240:0.3822:0.0563:0.1 +8 59337497 . G C 204 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TCAACACCTTTCTCTCTGTT;RSEQ=ATGTCAGTCAGAATATCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:83:38,45:70,105:175,83:0.2912:2,2:22.5:1:32.1:1:0.41859:1.27:59.2:82:0.3228:0:1.2 0/0:282:0:0,0:73,107:180,0:0:2,0:23.7:1:30.6:1:1:0:59.9:89:1:0:0.1 +8 59338272 . C A 61 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10955;SOR=5.49329;LSEQ=TCAGCAACATTTATACGAGT;RSEQ=GTGTTAAGGGGCTACGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:1:1,0:215,255:470,1:0.0021:2,0:1:0:23:0:0.4586:0:60:2:0.0022:0:1 0/1:433:5:4,1:203,223:426,5:0.0115:2,2:6.4:1:26.6:1:0.19948:4.38:60:10:0.0117:0:1 +8 59338663 . A C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00038;SOR=0.59216;LSEQ=CATCTCCATTCTTCTCTTTT;RSEQ=ATTGCCCGTGATGTTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:127:65,62:173,191:364,127:0.2587:2,2:25.7:1:32.2:1:0.53627:1.16:57.9:254:0.2629:0:1.1 0/1:631:108:39,69:253,269:522,108:0.1712:2,2:21:1:30.8:1:0.01991:1.66266:58.7:216:0.1725:0:1.1 +8 59338760 . T A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.45341;LSEQ=GTAATCACCAGTGTTCTGAA;RSEQ=CTTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:72,121:193,2:0.0103:2,2:15:1:27:1:1:1.68:40.5:4:0.0132:0:4 0/1:202:3:1,2:75,120:195,3:0.0149:2,2:14:1:18:1:1:1.24861:45.7:0.5:0.0066:0:4 +8 59339186 . A G 201 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGTCAGCTCCTCTTATCAAC;RSEQ=GTGGGTTTTCTGCCTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:109:63,46:234,218:452,109:0.194:2,2:26.4:1:29.8:1:0.28558:1.28:53.2:26.25:0.1909:0:1.2 0/0:592:0:0,0:313,277:590,0:0:2,0:25.8:1:29.6:1:1:0:57.1:72.75:1:0:0.2 +8 59339279 . T C 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=1.8559;LSEQ=CCGGCTCCGTGACAGACCCG;RSEQ=TCCTTGCTCAGGCTCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:503:387:175,212:45,68:113,387:0.7694:2,2:28:1:32.7:1:0.3334:1.25:54.7:95.75:0.7753:0:1.2 1/1:590:508:216,292:37,45:82,508:0.861:2,2:26.9:1:31.5:1:0.71859:1.11132:54.4:83.667:0.8625:0:1.1 +8 59339351 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50022;SOR=0;LSEQ=GCCCGCTCGGGACCAGATGC;RSEQ=GGGCGGAGCCAGCCGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:0,2:33,148:181,2:0.0109:2,0:26.5:1:32:0:1:0:60:4:0.0112:0:1 0/0:164:0:0,0:31,133:164,0:0:2,0:20.6:1:29.8:1:1:0:53:163:1:0:0.7 +8 59339364 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49868;SOR=0;LSEQ=CAGATGCGGGGCGGAGCCAG;RSEQ=CGACTGTGCACAGACCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:0,2:12,122:134,2:0.0147:2,0:18.5:1:29:1:1:0:59:4:0.0152:0:1 0/0:127:0:0,0:15,111:126,0:0:2,0:20.3:1:30.5:1:1:0:54.8:125:0.9921:0:0.6 +8 59339451 . AT A 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.68517;SOR=0.60918;LSEQ=GCTTGCTCCTCCTCCCTGTA;RSEQ=TTTTTTTTTCTCTGTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:4:0,4:1,28:29,4:0.1212:1,0:34.3:1:32.3:1:1:0:60:8:0.1212:0:0 0/1:26:2:0,2:1,23:24,2:0.0769:1,0:30.5:1:31:1:1:0:60:4:0.08:0:0 +8 59339914 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGCCTGTAGTCCCAACTGCT;RSEQ=GGGAGGCTGAAGTGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:49:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:29.5:1:1:0:60:4:1:0:2 +8 59339925 . A G 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAACTGCTCGGGAGGCTGA;RSEQ=GTGGCAGGATAGCTTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:38:0:32:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:30.5:1:1:0:60:4:1:0:2 +8 59790108 . G A 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50714;SOR=0;LSEQ=ATAACCCTCCAACCTTGCCT;RSEQ=CTGTTTGCACACATGGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:132,22:154,2:0.0127:2,2:32:0:29:1:0.27395:5.89033:60:4:0.0127:0:1 0/0:120:0:0,0:90,30:120,0:0:2,0:23:1:31.1:1:1:0:60:59:1:0:0 +8 59790110 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50629;SOR=0;LSEQ=AACCCTCCAACCTTGCCTGC;RSEQ=GTTTGCACACATGGTTAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:137,26:163,2:0.0121:2,2:9:0:32.5:1:0.30133:5.18969:60:4:0.0121:0:1 0/0:128:0:0,0:94,34:128,0:0:2,0:22.7:1:29.6:1:1:0:60:63:1:0:0 +8 59790210 . G C 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01832;SOR=0.65779;LSEQ=GGGATCTGAAAGAACATCCT;RSEQ=TAGGTTATATGCAGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:377:99:42,57:126,151:277,99:0.2626:2,2:24.5:1:32.3:1:0.63851:1.13208:60:98:0.2613:0:1 0/1:369:70:35,35:149,149:298,70:0.1897:2,2:27.2:1:31.3:1:1:1:60:69:0.188:0:1.1 +8 59790308 . A G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24306;SOR=0;LSEQ=GTCATCCAAAGCAAATATGC;RSEQ=GTCGTGCAGTGTACTAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:20,101:121,2:0.0161:2,2:17.5:1:28:0:0.31347:4.95:60:4:0.0161:0:1 0/0:127:0:0,0:28,99:127,0:0:2,0:22.1:1:30.2:1:1:0:60:254:1:0:0.1 +8 59790418 . A T 68 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=13.000;MSILEN=1;SSF=0.25654;SOR=0;LSEQ=TTGGAGAAAGCCTACATATT;RSEQ=AAAAAAAAAAAAGCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,6:6,5:0.3571:0,0:22.6:1:29.6:1:1:0:60:10:0.3571:0:1 0/0:5:0:0,0:0,2:2,0:0:0,0:11:1:26:1:1:0:60:4:0.4:0:0.5 +8 61207343 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTTTCATGTGCCTCCCATA;RSEQ=TCCTGGTTCCTCTTTGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:31:0:1:0:28:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:29.5:1:1:0:41:4:1:0:1 +8 61207493 . C T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.47619;SOR=0;LSEQ=GCTACCTAAAAGGGAAGGGC;RSEQ=CCCTGTCCTATGATCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:9,2:0.1818:2,2:6.5:1:30:1:1:1.87089:21.5:4:0.1818:0:1 0/0:10:0:0,0:8,2:10,0:0:2,0:12.3:1:31.1:1:1:0:21.1:20:1:0:0.2 +8 61207576 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.20854;SOR=Inf;LSEQ=TACCCTGACCCCCTTGTCTT;RSEQ=TATGCAATAAATAGCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:8,14:22,0:0:2,0:20.2:1:30.9:1:1:0:38.2:21:1:0:0.1 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:24:1:30.5:1:1:1.40:37:4:0.1111:0:1.5 +8 62114798 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61061;SOR=0.46291;LSEQ=TTTCTTTATCATGGCTAGCA;RSEQ=ATATTTAAGAATGTCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:132,13:145,2:0.0136:2,2:23.5:1:29.5:1:0.182:9.8215:54.5:4:0.0136:0:1 0/0:158:1:0,1:134,23:157,1:0.0063:2,0:1:0:20:0:0.1519:0:49:2:0.0063:0:2 +8 62114818 . G T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25203;SOR=Inf;LSEQ=GATATTTAAGAATGTCCCCT;RSEQ=GTGTGATTCCATCCTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:187,61:248,0:0:2,0:22.4:1:32.2:1:1:0:58.8:247:1:0:0.1 0/1:284:3:2,1:191,90:281,3:0.0106:2,2:14.3:1:30:1:1:1.06089:60:6:0.0106:0:1.3 +8 62114861 . G A 238 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=187.44912;LSEQ=TGTTCTCTGGAGCAGCATTC;RSEQ=TTTATCTTCGTCCGCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:2:1,1:276,203:479,2:0.0042:2,2:30.5:1:31:1:1:1.35871:60:4:0.0042:0:1 0/1:591:260:138,122:180,150:330,260:0.4399:2,2:27.1:1:29.7:1:0.73984:1.06075:54.4:520:0.4422:0:1.2 +8 62114982 . G T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62615;SOR=2.68239;LSEQ=TTTTTGGTTGTGAACTAAAG;RSEQ=CTGACAAAGATTGTCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:0,1:127,122:249,1:0.004:2,0:1:0:15:0:0.492:0:60:0:0:0:1 0/1:281:3:3,0:153,125:278,3:0.0107:2,0:25.7:1:27.3:1:0.25648:0:58:2:0.0073:0:1.3 +8 62115211 . G C 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0086;SOR=Inf;LSEQ=AACACCACCAGTAGTCTTAA;RSEQ=GTTGAAGTGTGGTTCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:43,38:81,0:0:2,0:28.9:1:32.4:1:1:0:27.1:162:1:0:0.1 0/1:53:5:3,2:29,19:48,5:0.0943:2,2:15.8:1:31.2:1:1:1.01722:21.4:10:0.0943:0:1.2 +8 62115359 . G A 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00341;SOR=Inf;LSEQ=GCCCTCGGAGGTAGTAGCAA;RSEQ=CTTCCACAGAAAAAAGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:44,68:112,0:0:2,0:25.3:1:32.9:1:1:0:43.7:224:1:0:0.1 0/1:118:9:4,5:54,55:109,9:0.0763:2,2:19.3:1:29.9:1:1:1.22515:43.2:18:0.0776:0:1.1 +8 62115395 . AGAT A 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=1.8466;LSEQ=GTAAAACTTGCTGCTGATGA;RSEQ=GATGATGATGATGAAGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:1:1,0:55,57:112,1:0.0088:2,0:43:0:35:0:0.49558:0:37:2:0.0088:0:1 0/1:123:2:1,1:60,61:121,2:0.0163:2,2:42.5:1:30.5:1:1:1.02:52:4:0.0165:0:0 +8 62115416 . AGAT A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.50397;SOR=Inf;LSEQ=GATGATGATGATGATGAAGA;RSEQ=GATGATGATGAAGATGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:48,47:95,0:0:2,0:26.5:1:33.5:1:1:0:43.1:190:1:0:0.1 0/1:119:2:1,1:59,58:117,2:0.0168:2,2:13.5:1:29:1:1:1.0171:28:4:0.0171:0:0 +8 62115431 . AGAT A 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=3e-05;SOR=0;LSEQ=GAAGAAGATGATGATGATGA;RSEQ=GATGATGATGATTTTAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:12:8,4:38,33:71,12:0.1463:2,2:33:1:32.8:1:0.53426:1.73:31.9:24:0.15:0.0244:0.2 0/0:105:0:0,0:50,55:105,0:0:2,0:22.9:1:30.7:1:1:0:40.4:34:1:0:0.2 +8 62115450 . A AATG 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=3;SSF=0.30205;SOR=0.68719;LSEQ=AAGATGATGATGATGATTTT;RSEQ=ATGAGGAAGCTGAAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:56:31,25:8,7:15,56:0.7778:2,2:26.5:1:31.4:1:1:1.08:36.1:112:0.7778:0.0694:0.1 1/0:102:72:36,36:14,16:30,72:0.7059:2,2:26.2:1:29.8:1:0.82959:1.14:34.3:144:0.72:0.098:0.2 +8 62115677 . G T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29066;SOR=Inf;LSEQ=AGCAAGTATAGAAAAAGGTG;RSEQ=TTCTCTTCCCAAAGTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:29,31:60,0:0:2,0:16.6:1:31.9:1:1:0:23.3:120:1:0:0.1 0/1:99:3:1,2:50,46:96,3:0.0303:2,2:6.7:1:26.3:1:0.60982:2.15746:22.3:6:0.0309:0:1 +8 62115713 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51966;SOR=Inf;LSEQ=GGAAGCCAAGTTCATCAATT;RSEQ=CGTGAAGAATTGCTTCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:36,47:83,0:0:2,0:37:1:29.6:1:1:0:22.6:166:1:0:0.1 0/1:127:2:1,1:59,66:125,2:0.0157:2,2:33.5:1:32:0:1:1.12:25.5:4:0.0157:0:1 +8 62136814 . T C 34 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55708;SOR=0.32284;LSEQ=AGGAAAGAGGCACTCTGGCC;RSEQ=TTTGGGTTTTCAGCATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:24:0:34:1:1:1.12:42.5:4:0.1053:0:1.5 0/1:28:1:1,0:16,11:27,1:0.0357:2,0:2:0:30:0:1:0:30:2:0.0385:0:1 +8 62136991 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATAGTCAGGCCTCTCTTCT;RSEQ=TAGGGCTGCTGCAGTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:26:1:32.6:1:1:0:44:10:1:0:0 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:22:1:27:1:1:1.87:49.5:4:0.2222:0:1 +8 62137199 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17787;SOR=Inf;LSEQ=CAACCCCTGTTGGGGGGTCT;RSEQ=ACCCCGTTGGGTGGCATAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:9,4:13,0:0:2,0:30.2:1:32.2:1:1:0:60:26:1:0:0.2 0/1:10:2:1,1:5,3:8,2:0.2:2,2:23.5:1:28.5:1:1:1.58108:60:4:0.2:0:1 +8 62137222 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16923;SOR=Inf;LSEQ=CCCGTTGGGTGGCATAGGGA;RSEQ=CAGGACCCATTTAACAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:15,0:0:2,0:30.8:1:32.7:1:1:0:60:30:1:0:0.1 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:31:0:31.5:1:1:1.22474:38:4:0.1818:0:1.5 +8 65193106 . C T 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=Inf;LSEQ=TCTGGTCACTTATGTTTTCA;RSEQ=TACTCAATCACTTCGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:421:0:0,0:220,201:421,0:0:2,0:26:1:32.6:1:1:0:60:139.333:1:0:0.2 0/1:423:26:10,16:215,182:397,26:0.0615:2,2:21.2:1:29.8:1:0.15533:1.88725:60:52:0.0618:0:1.1 +8 65193137 . T C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55491;SOR=0.87541;LSEQ=CTTCGCTTTTGTACGGATTG;RSEQ=TAGATAACTATGTCCAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:59:27,32:160,174:334,59:0.1501:2,2:27.2:1:32.6:1:0.77924:1.08957:60:118:0.1517:0:1.1 0/1:463:62:28,34:194,205:399,62:0.1339:2,2:26.3:1:31.4:1:0.68247:1.14878:60:61:0.1332:0:1.1 +8 65193242 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20516;SOR=Inf;LSEQ=TAGTAAGCAGCACCTTGAAG;RSEQ=TAGACACTGTGGCCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:20,105:125,0:0:2,0:22.6:1:32.6:1:1:0:60:250:1:0:0.1 0/1:104:2:1,1:17,85:102,2:0.0192:2,2:35:1:28:1:0.31759:4.89:60:4:0.0192:0:1 +8 65193342 . A G 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTCTCCTCAAAATTTGAAGA;RSEQ=GTAAGTATTTTGTGAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:4:0,4:0,17:17,4:0.1905:1,0:28:1:31.5:1:1:0:60:8:0.2:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:18:1:30.8:1:1:0:60:8:1:0:0 +8 65193545 . C CA 27 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=19.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTTTTAAAGATGGGTAA;RSEQ=AAAAAAAAAAAAAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:26.5:1:27.5:1:0.33333:0:60:4:0.6667:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 65193903 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAATGTATTCTTTCTTTTC;RSEQ=AAATGTTAAAGGACATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:30:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 66183802 . T C 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11559;SOR=Inf;LSEQ=AGAGGAGGTCACCTACAGTG;RSEQ=CCTGTTTGAGAGGCTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:148,111:259,0:0:2,0:27.2:1:29.9:1:1:0:60:128.5:1:0:0.5 0/1:247:3:2,1:138,106:244,3:0.0121:2,2:21.3:1:24.3:1:1:1.53:60:2:0.0083:0:1.7 +8 66183815 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11891;SOR=Inf;LSEQ=TACAGTGTCCTGTTTGAGAG;RSEQ=CTGGAGCCCACGGCTGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:155,121:276,0:0:2,0:27.8:1:31.6:1:1:0:60:54.2:1:0:0.6 0/1:269:3:2,1:141,125:266,3:0.0112:2,2:20.3:1:22.7:1:1:1.77:60:2:0.0076:0:3.3 +8 66183866 . G A 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATTTGGTATGTTTTGCCAGC;RSEQ=CAGCATTGCCTGCCCGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:255:255:116,139:0,0:0,255:1:0,2:24.7:1:29.7:1:1:0:60:50:1:0:1.1 1/1:246:204:93,111:20,21:41,204:0.8293:2,2:26:1:29.4:1:0.73391:1.13611:59.8:203:0.832:0:1.1 +8 66184044 . T C 122 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05037;SOR=0;LSEQ=TGTGCTCCCCAGAGCCTTTG;RSEQ=GTCCACATTTCAGAATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:0,17:0,0:0,17:1:0,1:30.4:1:29.9:1:1:0:60:34:1:0:1.1 1/0:11:8:0,8:1,2:3,8:0.7273:2,0:32.6:1:30.4:1:0.27273:0:57.6:16:0.7273:0:1 +8 66631972 . C T 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=8.70947;LSEQ=GAACTGACAAATATATCTAA;RSEQ=CTTTTCTGGTTATCCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:17:7,10:135,163:298,17:0.054:2,2:23.2:1:29.9:1:0.80635:1.18255:60:16:0.0516:0:1.1 0/1:421:140:67,73:137,144:281,140:0.3325:2,2:25.7:1:28.7:1:0.91764:1.03651:60:69:0.3325:0:1.1 +8 66632039 . T A 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.37184;SOR=3.94352;LSEQ=AAGCAAAAATACACTGCCCA;RSEQ=CTAAACTCTGAGGATACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:1:0,1:61,121:182,1:0.0055:2,0:2:0:29:0:1:0:60:2:0.0057:0:1 0/1:188:4:3,1:54,130:184,4:0.0213:2,2:10.5:1:28:1:0.08388:7.14:60:8:0.0219:0:1 +8 66632041 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=GCAAAAATACACTGCCCATC;RSEQ=AAACTCTGAGGATACTCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:57,117:174,0:0:2,0:23.9:1:29.3:1:1:0:60:86:1:0:0.1 0/1:178:2:1,1:51,125:176,2:0.0112:2,2:29.5:1:29.5:1:0.5001:2.44:60:4:0.0115:0:1 +8 66632048 . T C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22987;SOR=0;LSEQ=TACACTGCCCATCTAAACTC;RSEQ=GAGGATACTCGGGCATAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:2:1,1:44,112:156,2:0.0127:2,2:16:0:32:0:0.4898:2.53:60:4:0.0135:0:1 0/0:171:0:0,0:49,122:171,0:0:2,0:23.5:1:29.4:1:1:0:60:56:1:0:0.2 +8 66632081 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49677;SOR=Inf;LSEQ=GCATAGCCCAATTCGAGGCA;RSEQ=AGTTGCAGTGCAACAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:10,68:78,0:0:2,0:25.7:1:32.2:1:1:0:60:38:1:0:0.1 0/1:78:2:1,1:8,68:76,2:0.0256:2,2:15.5:1:30:0:0.21878:8.07:60:4:0.0256:0:1 +8 67249953 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24571;SOR=0;LSEQ=ATTTTAATCAATCTCCTGAA;RSEQ=CTTCCCCTAGGCCCAACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:3:2,1:14,11:25,3:0.1071:2,2:15.3:1:32.3:1:1:1.55:60:6:0.1111:0:1 0/0:22:0:0,0:12,10:22,0:0:2,0:27.5:1:31:1:1:0:60:44:1:0:0.1 +8 67251732 . G A 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGAAGAGCCAAGGTAG;RSEQ=GTTCTGTGTAATATGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:31:1:1:0:60:4:1:0:1.5 +8 68097716 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49959;SOR=Inf;LSEQ=TCCAATTAAAGTAACACTGG;RSEQ=AACTTTGAAAATGTACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:67,49:116,0:0:2,0:23.8:1:32.4:1:1:0:43.9:115:1:0:0.1 0/1:130:2:1,1:74,54:128,2:0.0154:2,2:28:1:28:1:1:1.36698:42:4:0.0155:0:1 +8 68097772 . C G 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06147;SOR=Inf;LSEQ=GGGCTTTGAAATAACATCAC;RSEQ=AGTGGTCTGTCGGTTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:96,83:179,0:0:2,0:25.3:1:31.6:1:1:0:57:88.5:1:0:0.1 0/1:191:5:3,2:100,86:186,5:0.0262:2,2:35.2:1:25:1:1:1.29:56:4:0.0214:0:1.2 +8 68097816 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.23545;SOR=0;LSEQ=CTTCAGGGCCAGTGCATATT;RSEQ=GTTGACAGCAATTAGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:83,88:171,2:0.0116:2,2:26.5:1:31:1:1:1.06:59.5:4:0.0119:0:1 0/0:183:0:0,0:92,91:183,0:0:2,0:25.4:1:28.8:1:1:0:57.7:90.5:1:0:0.1 +8 68097836 . T C 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50151;SOR=Inf;LSEQ=AGTTGACAGCAATTAGTAGC;RSEQ=GTGGAGGAAGATGCAGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:65,90:155,0:0:2,0:25.7:1:30.9:1:1:0:56.6:37.75:1:0:0.1 0/1:181:2:1,1:78,101:179,2:0.011:2,2:23.5:1:25.5:1:1:1.29:54:4:0.0113:0:1 +8 68097913 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.50611;SOR=Inf;LSEQ=TATCTGGAAAGCAGTCTACC;RSEQ=CTGGAGGTGGTAGCAAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:43,59:102,0:0:2,0:23.3:1:31.2:1:1:0:59.7:33:1:0:0.1 0/1:132:2:1,1:56,74:130,2:0.0152:2,2:6.5:1:27:1:1:1.32:42.5:4:0.0155:0:1 +8 68097955 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.22437;SOR=0;LSEQ=CAAAGAAAAAAGTAAAACTT;RSEQ=CTGCTGCTGAAGATGATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:63,57:120,2:0.0164:2,2:13:1:32.5:1:1:1.10435:60:4:0.0164:0:1 0/0:135:0:0,0:66,69:135,0:0:2,0:24.5:1:31.4:1:1:0:59.5:66.5:1:0:0.1 +8 68097975 . AGAT A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.49847;SOR=Inf;LSEQ=GCTGCTGCTGAAGATGATGA;RSEQ=GATGATGATGAGTTTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:74,57:131,0:0:2,0:26:1:32.8:1:1:0:59.3:42.667:1:0:0.2 0/1:138:2:1,1:67,69:136,2:0.0145:2,2:41.5:1:31:1:1:1.03:60:4:0.0147:0:0 +8 68098012 . G A 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5048;SOR=Inf;LSEQ=TTGATGATGAGGAAGCTGAA;RSEQ=AAAAAGCACCAGTGAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:73,46:119,0:0:2,0:26.2:1:32.9:1:1:0:55:118:1:0:0.1 0/1:150:2:1,1:85,63:148,2:0.0133:2,2:6:0:26.5:1:1:1.34646:60:4:0.0135:0:1 +8 68098042 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5053;SOR=Inf;LSEQ=CAGTGAAGAAATCTATACAA;RSEQ=ATACTCCAGCCAGAAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:84,51:135,0:0:2,0:21.4:1:32.8:1:1:0:55:134:1:0:0.1 0/1:171:2:1,1:108,61:169,2:0.0117:2,2:22.5:1:28:1:1:1.76418:60:4:0.012:0:1 +8 68098051 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50814;SOR=Inf;LSEQ=AATCTATACAAGATACTCCA;RSEQ=CCAGAAATGCATAAAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:89,47:136,0:0:2,0:23.2:1:33:1:1:0:55:135:1:0:0.1 0/1:180:2:1,1:117,61:178,2:0.0111:2,2:6.5:1:27:1:1:1.91068:56:4:0.0112:0:2 +8 68098207 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18422;SOR=0;LSEQ=CCTTTGCACTTAAAGCAAAA;RSEQ=TGCAAGCAAGTATAGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:21,72:93,2:0.0208:2,2:12.5:1:31:1:0.41142:3.37:53:4:0.0211:0:2 0/0:127:0:0,0:35,92:127,0:0:2,0:21.9:1:29.6:1:1:0:56.5:254:1:0:0.1 +8 69707655 . A C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01818;SOR=Inf;LSEQ=TGTTGAAAACTGGACATGTA;RSEQ=TATAACATAATGTGGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:22.5:1:30.6:1:1:0:60:16:1:0:0 1/0:4:3:3,0:1,0:1,3:0.75:0,0:23:1:32.7:1:1:0:60:6:0.75:0:1 +8 70250304 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16771;SOR=Inf;LSEQ=TCTGCAGAAAGTGAATCCAG;RSEQ=CTGCAGAGCTGAGGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:118,37:155,0:0:2,0:23.9:1:31.7:1:1:0:59.9:50.667:1:0:0 0/1:108:2:1,1:76,29:105,2:0.0185:2,2:29.5:1:27:1:0.48404:2.59354:41.5:4:0.0187:0:1 +8 70250326 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19713;SOR=Inf;LSEQ=TGCAGAGCTGAGGCTGCTCT;RSEQ=ATGCAGCAAAACTTGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:141,65:206,0:0:2,0:26:1:31.9:1:1:0:59.9:28.429:1:0:0.2 0/1:165:2:1,1:102,60:162,2:0.0121:2,2:19:1:30:1:1:1.69418:60:4:0.0125:0:1.5 +8 70250399 . C A 38 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.103;SOR=Inf;LSEQ=ACCCAAGAGGCCCTTCCCCA;RSEQ=TTGGACCACAGCCAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:145,161:306,0:0:2,0:25.3:1:32.4:1:1:0:60:101:1:0:0.5 0/1:271:3:2,1:129,139:268,3:0.0111:2,2:6.7:1:24.3:1:0.61145:2.15:60:6:0.0112:0:1.3 +8 70250407 . A G 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43973;SOR=0.86626;LSEQ=GGCCCTTCCCCACTTGGACC;RSEQ=CAGCCAGCAGTTTGCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:137:60,77:75,88:163,137:0.4567:2,2:26.2:1:31.3:1:0.7277:1.09342:60:274:0.4597:0:1.1 0/1:254:107:53,54:68,78:146,107:0.4213:2,2:27.9:1:30.5:1:0.70271:1.13:59.7:106:0.4257:0:1.2 +8 70250462 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22345;SOR=Inf;LSEQ=GCTGAAGGGACATCTGTGTC;RSEQ=ATGCAACCCACGTACAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:56,142:198,0:0:2,0:24.8:1:29.1:1:1:0:60:65:1:0:0.4 0/1:178:2:1,1:74,102:176,2:0.0112:2,2:9:1:29:1:1:1.38:60:4:0.0115:0:1.5 +8 70250559 . G A 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05839;SOR=0;LSEQ=GGGAGAGCTCAGTGGGAATC;RSEQ=ATGGAGAGGAGGACTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:0,5:2,24:26,5:0.1613:2,0:30:1:32:1:1:0:60:10:0.1613:0:1.2 0/0:25:0:0,0:0,25:25,0:0:1,0:21.8:1:31.4:1:1:0:60:50:1:0:0.3 +8 70250609 . G T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.65702;SOR=1.89033;LSEQ=CCAGAACCGGCTGACCATGT;RSEQ=CTGGCCACTCTCTGCCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:1,8:0,5:5,9:0.6429:0,2:28.6:1:29.8:1:1:0:58.4:18:0.6429:0:1.1 1/0:9:7:0,7:0,2:2,7:0.7778:0,0:23.1:1:28.7:1:1:0:60:14:0.7778:0:1.3 +8 72265404 . C T 28 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.58159;SOR=0.38276;LSEQ=GGTCACCTACGGGCCTTCTG;RSEQ=AGCTCCTGTCAGTGGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:62,44:106,2:0.0185:2,2:7.5:1:28:1:1:1.40451:60:4:0.0187:0:1.5 0/0:140:1:0,1:80,59:139,1:0.0071:2,0:1:0:23:0:0.42857:0:60:2:0.0072:0:1 +8 72265468 . C A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6268;SOR=2.57574;LSEQ=CCTGCCGGCGCAGGGACCTG;RSEQ=GGCAGTCTGGGTGACTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:1:1,0:42,64:106,1:0.0093:2,0:1:0:26:0:0.40187:0:60:2:0.0093:0:1 0/1:126:3:2,1:58,65:123,3:0.0238:2,2:18.3:1:28.3:1:0.60461:2.23:60:6:0.024:0:1.3 +8 72265495 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49645;SOR=0;LSEQ=CTGGGTGACTATATCCACAC;RSEQ=CAGTCTGTACTCTGCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:21,48:69,2:0.0282:2,2:30:1:30:1:0.52676:2.26:60:4:0.0282:0:1 0/0:70:0:0,0:21,49:70,0:0:2,0:20.6:1:30:1:1:0:60:34:1:0:0.1 +8 72265510 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09591;SOR=Inf;LSEQ=CACACCCAGTCTGTACTCTG;RSEQ=AGTAGGCATGCTTTACCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:10,35:45,0:0:2,0:22.9:1:32:1:1:0:60:44:1:0:0.1 0/1:39:3:1,2:5,31:36,3:0.0769:2,2:30.7:1:28.7:1:0.403:2.98:60:6:0.0789:0:1 +8 73306731 . T C 114 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01491;SOR=0;LSEQ=CAGTCAGGGATAGTACAAGA;RSEQ=GCTGCCTGGGATTTATAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:10,3:0,0:0,13:1:0,2:21.9:1:31:1:1:0:48.8:26:1:0:1.5 1/0:12:7:5,2:4,1:5,7:0.5833:2,2:15.4:1:31.6:1:1:1.53983:56:14:0.5833:0:1 +8 73307007 . A G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=GAGGACCCCTGGCCCAACCC;RSEQ=CTGGCCCTTTGACTGGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:11:1:33:1:1:0:21:4:0.5:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:35.5:1:31:1:1:0:37.5:4:1:0:0 +8 73408209 . CT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2182;SOR=0;LSEQ=CATCTCAGGGATGGGCCTGC;RSEQ=TAGTATTTCTGCCACATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:27,39:66,2:0.0294:2,2:45:1:33:1:1:1.44:60:4:0.0299:0:0 0/0:77:0:0,0:29,48:77,0:0:2,0:31.8:1:29.9:1:1:0:60:76:1:0:0.1 +8 73408246 . A C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49438;SOR=Inf;LSEQ=ATTCCATCATTGAGCAGCCC;RSEQ=TGGAAAGGATGGCCTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:16,29:45,0:0:2,0:21.8:1:30.3:1:1:0:60:44:1:0:0.1 0/1:45:2:0,2:14,29:43,2:0.0444:2,0:20:1:33:1:1:0:60:4:0.0444:0:1 +8 74502130 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.20913;SOR=0;LSEQ=GGATGACAAAGATGAGGATG;RSEQ=GGATGAGGAAGGAAGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:9,19:28,2:0.0667:2,2:35:1:30:1:1:2.05:60:4:0.0769:0:1 0/0:35:0:0,0:14,21:35,0:0:2,0:29.5:1:28.3:1:1:0:60:16.5:1:0:0.1 +8 74858994 . T A 25 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.69848;LSEQ=AAATACATGCATACTTTCGA;RSEQ=AGCACATGTGAAGGTATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:1:1,0:39,109:148,1:0.0067:2,0:1:0:26:0:0.26846:0:60:2:0.0068:0:1 0/1:176:2:1,1:45,129:174,2:0.0114:2,2:5:1:25.5:1:0.45552:2.85:55:4:0.0116:0:1 +8 74859123 . T G 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAATTCATATGTTGAAGTC;RSEQ=TAACCCCTTGTACCACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:1,52:53,0:0:1,0:23.9:1:30.7:1:1:0:59.5:52:1:0:0 1/0:21:11:0,11:0,10:10,11:0.5238:0,0:17.3:1:32.3:1:1:0:60:22:0.5238:0:1.1 +8 74859253 . G A 50 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=TGTTTGTTTGAGACAGAGTC;RSEQ=CGCTCTGTCACCCAGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:43:1:32:0:1:0:60:6:0.75:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:13:1:31:1:1:0:49.5:4:1:0:0.5 +8 74859292 . C G 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GAAGTGCAATGGCGGGATCT;RSEQ=AGCTCACTGCAACCTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:8.5:1:32.5:1:1:0:42.5:8:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:30.5:1:1:0:30.5:4:1:0:1 +8 74868238 . A T 46 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.03314;SOR=0;LSEQ=CATCAGATGATATCAATTTG;RSEQ=CATACATGGCATCAGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:352:4:0,4:171,177:348,4:0.0114:2,0:6:1:23.3:1:0.12347:0:56.3:3:0.0085:0:1 0/0:471:0:0,0:226,244:470,0:0:2,0:21.4:1:28.6:1:1:0:53.2:77.333:1:0:0.3 +8 74868305 . T C 223 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TCCATCTAAAGTAAAGTAAG;RSEQ=AGTGAAACAATTTTTGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:0:0,0:209,323:532,0:0:2,0:26.3:1:28.7:1:1:0:59:176.333:1:0:0.1 0/1:732:139:57,82:237,354:591,139:0.1899:2,2:26.3:1:31.4:1:0.84813:1.04:58.3:68.5:0.1908:0:1.1 +8 74868355 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24044;SOR=0;LSEQ=ACTAAAACTAAACAGGTTTG;RSEQ=CTGGGCGCAGTGGCTCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:0,2:27,161:188,2:0.0105:2,0:31.5:1:29.5:1:1:0:60:4:0.0108:0:1.5 0/0:198:0:0,0:30,167:197,0:0:2,0:21.1:1:31.2:1:1:0:59.9:64.667:0.9949:0:0.4 +8 74868359 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.61742;SOR=2.07953;LSEQ=AAACTAAACAGGTTTGGCTG;RSEQ=GCGCAGTGGCTCACGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:0,1:18,156:174,1:0.0057:2,0:12:0:15:0:1:0:60:0:0:0:7 0/1:169:2:1,1:21,146:167,2:0.0118:2,2:24:1:26.5:1:0.24408:6.82:60:4:0.0119:0:1 +8 74868374 . G A 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=37.68944;LSEQ=GGCTGGGCGCAGTGGCTCAC;RSEQ=CCTGTAATCCCAGCACTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:1:1,0:3,123:126,1:0.0079:1,0:1:0:26:0:0.0315:0:60:2:0.0079:0:1 0/1:112:26:0,26:2,84:86,26:0.2321:1,1:23.2:1:29.7:1:1:0:59.2:52:0.2321:0:1 +8 74868478 . T C 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.71398;SOR=1.59456;LSEQ=AAAAATACAAAAATTAGCTG;RSEQ=GTGTGGTGGCGCACACATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:13:0,13:0,14:14,13:0.4815:1,1:23.6:1:31.7:1:1:0:56.2:26:0.4815:0:1 1/0:10:6:0,6:0,4:4,6:0.6:0,0:23:1:28.8:1:1:0:55.8:12:0.6:0:1 +8 74872101 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.23672;SOR=Inf;LSEQ=ATTAATGTTGCAAGAGACAA;RSEQ=TTTTCATTCACTGTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:1,123:124,0:0:1,0:22.8:1:32.6:1:1:0:59.9:61:1:0:0.1 0/1:118:2:0,2:3,113:116,2:0.0169:1,0:14.5:1:24.5:1:1:0:60:4:0.0169:0:1 +8 74874810 . CA C 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.01172;LSEQ=TACTCTTTTAAAAAACAAAA;RSEQ=AAAAAAAAAACAAAACAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:14:13,1:32,1:33,14:0.2917:1,1:22.8:1:32.8:1:0.51156:2.40879:59.6:28:0.2979:0.0625:0.3 0/1:17:5:5,0:12,0:12,5:0.2941:0,0:25.2:1:33:1:1:0:60:10:0.2941:0:0 +8 74884451 . G A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACTTCCGCTGGGTCAGAGCC;RSEQ=CTTTCGGCGACGCGCGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:34:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:42:1:30:1:1:0:60:4:1:0:1 +8 74884999 . T C 169 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=33.11305;LSEQ=CACAGCAACGACTAGCGCAA;RSEQ=CGGCTGGCCTCATTTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1167:1:0,1:635,531:1166,1:9e-04:2,0:27:0:12:0:0.45587:0:60:0:0:0:1 0/1:1520:42:25,17:821,656:1477,42:0.0276:2,2:26.1:1:31.5:1:0.64025:1.17:60:84:0.028:0:1.2 +8 74885157 . A AC 305 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.04251;LSEQ=GAAAATCCAGGCGCCTGCCA;RSEQ=ACCGTTACTCAGTTTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:748:740:199,541:5,3:8,740:0.9893:2,2:24:1:32:1:0.03845:4.51995:59.9:147:0.9919:0.234:0.1 1/0:808:644:161,483:67,94:161,644:0.797:2,2:26.8:1:31.4:1:5e-05:2.13609:60:57.545:0.7952:0.0495:0.2 +8 74885209 . AC A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.09739;SOR=Inf;LSEQ=CATTCCACGCCCCGCTTCCC;RSEQ=CCCCCCGCGTTTCCTATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:12,218:230,0:0:2,0:24.6:1:31.2:1:1:0:60:27.75:1:0:0.1 0/1:197:3:1,2:7,187:194,3:0.0152:1,2:19.3:1:32.3:1:0.11752:12.83:53.3:6:0.0156:0:0 +8 74885277 . G A 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04005;SOR=0;LSEQ=GGCTGAAACAGCTAAATAAA;RSEQ=TTCACCTTCTACTGTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:6:0,6:1,43:44,6:0.12:1,0:15.8:1:31.5:1:1:0:60:12:0.1224:0:1 0/0:35:0:0,0:2,33:35,0:0:2,0:21.6:1:31.9:1:1:0:60:70:1:0:0 +8 74951823 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACAAGCGGGGCAGGGTAAGG;RSEQ=GGGTGGATCTTCTAAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:16,0:0:2,0:30.3:1:30.6:1:1:0:26:32:1:0:0.2 0/1:35:2:1,1:17,16:33,2:0.0571:2,2:31.5:1:30.5:1:1:1.06069:27:4:0.0571:0:1 +8 74951835 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.5461;SOR=Inf;LSEQ=GGGTAAGGAGGGTGGATCTT;RSEQ=TAAGTGATTGATAAGGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:16,0:0:2,0:36.8:1:32.1:1:1:0:26:32:1:0:0.2 0/1:32:2:1,1:14,16:30,2:0.0625:2,2:26.5:1:26.5:1:1:1.14:35:4:0.0625:0:1 +8 77617027 . A T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.18721;SOR=Inf;LSEQ=TGTCTATGATCTCCGACACA;RSEQ=GAGAGAGAAAGACTATCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:141,17:158,0:0:2,0:20.8:1:30.5:1:1:0:59.9:38.5:1:0:0.1 0/1:121:2:1,1:103,16:119,2:0.0165:2,2:6.5:1:29:1:0.26226:6.27554:60:4:0.0171:0:1 +8 77618304 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=AATATCAGCAGACCCTGGAG;RSEQ=CCCATATGAAGGAGAAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:102,27:129,0:0:2,0:27.1:1:31.2:1:1:0:59.8:42:1:0:0.1 0/1:108:2:1,1:67,39:106,2:0.0185:2,2:37.5:1:28:1:1:1.70887:60:4:0.0187:0:1 +8 77618681 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08335;SOR=Inf;LSEQ=AGGAACCTCCGAATTCATAT;RSEQ=ACCAGCGAAAAGCACATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:105,158:263,0:0:2,0:24.9:1:32:1:1:0:59.9:262:1:0:0.1 0/1:205:3:2,1:91,111:202,3:0.0146:2,2:24:1:24.3:1:0.59143:2.43:60:6:0.0149:0:1 +8 77618940 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCCTGCTTTTCTGCACT;RSEQ=TTGTTAGTTTCTAATCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:0,3:3,2:0.4:0,0:26.5:1:29:1:1:0:60:4:0.4:0:3.5 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:34:0:1:0:60:2:1:0:0 +8 77619945 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5172;SOR=0;LSEQ=TCACCTCTGACAGCCTGGAG;RSEQ=CCCTAAGTGTGCATGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:134,1:135,2:0.0146:1,2:46.5:1:30.5:1:0.02909:95.10689:60:4:0.0152:0:1 0/0:92:0:0,0:90,2:92,0:0:1,0:23.9:1:31.1:1:1:0:60:184:1:0:0.1 +8 77620114 . C A 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37319;SOR=3.94239;LSEQ=GCAGAAATATCAACTGGTGG;RSEQ=TCACATTAAAGAAGGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:1:1,0:68,248:316,1:0.0032:2,0:1:0:24:0:0.21767:0:60:2:0.0032:0:1 0/1:324:4:2,2:89,231:320,4:0.0123:2,2:21:1:29.3:1:0.3143:2.59:60:8:0.0126:0:1.3 +8 77764531 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15385;SOR=0;LSEQ=AACATCACGTTGGTCAAACT;RSEQ=AACTCCAGATACTACAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:14,0:14,2:0.125:1,0:47:1:31.5:1:1:0:60:4:0.125:0:1 0/0:24:0:0,0:22,2:24,0:0:2,0:23.4:1:31.6:1:1:0:60:48:1:0:0 +8 77764658 . T C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22483;SOR=Inf;LSEQ=ACAGCAGGCAAGCAAATTAT;RSEQ=GAAACAAGAGCAAAGTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:22,34:56,0:0:2,0:30.4:1:30.8:1:1:0:60:55:1:0:0.1 0/1:51:2:1,1:18,31:49,2:0.0392:2,2:23.5:1:26.5:1:1:1.70:60:4:0.0392:0:1.5 +8 77767089 . GA G 33 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=1.5344;LSEQ=ATTGCCCGCGAAGTCGGGCT;RSEQ=AAAAAAGGGTCGTGCAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:1:1,0:29,8:37,1:0.0263:2,0:24:0:34:0:1:0:60:2:0.0278:0:0 0/1:50:2:2,0:26,22:48,2:0.04:2,0:10.5:1:33.5:1:0.49714:0:60:4:0.04:0:0 +8 77767130 . C T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49712;SOR=Inf;LSEQ=CTGGTTCCAGAATACACGAG;RSEQ=GCGGGAGAGGAAAGGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:35,24:59,0:0:2,0:29.8:1:30.8:1:1:0:60:58:1:0:0.2 0/1:65:2:1,1:25,38:63,2:0.0308:2,2:20:0:27.5:1:1:1.51:60:4:0.0317:0:1 +8 77776848 . TA T 116 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.23529;SOR=0;LSEQ=AAAAATAAAAAATAAAAAAA;RSEQ=AAAAAAAAATAAGACTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:0,13:0,3:3,13:0.8125:0,1:30.6:1:31.5:1:1:0:60:26:0.8125:0:0 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:32:0:1:0:60:2:1:0:0 +8 81288634 . A G 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.475;SOR=Inf;LSEQ=GGTCACACATTTAAAAACTC;RSEQ=TTGAATTATACACTGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:4,0:3,0:3,4:0.5714:0,0:35.8:1:31.5:1:1:0:60:8:0.5714:0:1 1/1:3:3:3,0:0,0:0,3:1:0,0:22.3:1:29:1:1:0:60:6:1:0:1 +8 81288734 . A T 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48003;SOR=0.69561;LSEQ=TACCACAGGTGAGGCTGGAA;RSEQ=GGTGGGCAGGGACAGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:32:31,1:18,0:18,32:0.64:1,1:22.4:1:31:1:1:0:60:31:0.6327:0:1.1 1/0:29:16:15,1:12,1:13,16:0.5517:1,1:29.9:1:30.9:1:1:1.24:60:32:0.5714:0:1.1 +8 81288806 . T A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.20691;SOR=0;LSEQ=AAAGAGGCTGAACTTGGCTC;RSEQ=AAAAGCATTAGGGAGCTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:91,31:122,2:0.0161:2,2:13.5:1:27.5:1:0.45109:2.90529:60:4:0.0161:0:1.5 0/0:148:0:0,0:114,34:148,0:0:2,0:21.9:1:29.6:1:1:0:60:296:1:0:0.1 +8 81288812 . C A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2555;SOR=Inf;LSEQ=GCTGAACTTGGCTCTAAAAG;RSEQ=ATTAGGGAGCTATTGAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:100,40:140,0:0:2,0:22.3:1:31.7:1:1:0:60:139:1:0:0.2 0/1:172:3:2,1:121,48:169,3:0.0174:2,2:19.3:1:28:1:1:1.25868:60:6:0.0175:0:1 +8 81288925 . G T 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.87632;SOR=0.96444;LSEQ=TGCCTTTCCTAGTATTCATT;RSEQ=TTTTATGTCAACATCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:308:187:91,96:62,59:121,187:0.6071:2,2:27.3:1:30.8:1:0.72648:1.10821:59.9:374:0.6071:0:1.2 1/0:391:234:114,120:75,81:156,234:0.5985:2,2:25.7:1:29.5:1:0.91794:1.03:60:77:0.5969:0:1.1 +8 81289045 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22195;SOR=Inf;LSEQ=TTATCCCAAGAGATCTCTTT;RSEQ=ATTTCTTATGACCTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:10,77:87,0:0:2,0:24.7:1:28.1:1:1:0:60:42.5:1:0:0.1 0/1:78:2:1,1:7,69:76,2:0.0256:2,2:30:1:29.5:1:0.1958:9.29:60:4:0.026:0:1 +8 81289060 . T A 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50236;SOR=0;LSEQ=TCTTTTATTTCTTATGACCT;RSEQ=GTTTTATAGAAATCTGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:4,63:67,2:0.029:2,2:6.5:1:29.5:1:0.14066:14.19:60:4:0.0299:0:1 0/0:55:0:0,0:4,51:55,0:0:2,0:23.1:1:29.7:1:1:0:60:54:1:0:0.1 +8 81291019 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GGGATGCCAAGAACAGCTGT;RSEQ=GAAATGTGCTGATGACAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:21.5:1:30.5:1:1:0:60:4:1:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:20:0:31:1:1:0:60:4:0.6667:0:1.5 +8 83004063 . C G 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77227;LSEQ=ACTCTCTAGGCCAGCCAAAG;RSEQ=GTCAGCGGGTCAGTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:6,1:6,2:8,7:0.4667:2,2:24.3:1:28.3:1:1:1.91:36.6:6:0.4286:0:1 0/1:5:2:2,0:2,1:3,2:0.4:2,0:23.5:1:29.5:1:1:0:44:4:0.4:0:1 +8 83004264 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1125;SOR=Inf;LSEQ=AAAGGGGAGAAGCCATGTCG;RSEQ=CCAACTCCAGAGGTTGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:43,47:90,0:0:2,0:25.9:1:31.2:1:1:0:26.5:29:1:0:0.4 0/1:85:3:2,1:49,33:82,3:0.0353:2,2:37:1:29:1:1:1.34:27.3:6:0.0353:0:1.7 +8 83004303 . G C 152 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03212;SOR=0.45178;LSEQ=ATAAGAGTTTGAAAGGCATT;RSEQ=TCTGATTTCAGAAAACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:30:9,21:7,25:32,30:0.4762:2,2:25.1:1:31.1:1:0.56588:1.52:35:14:0.4667:0:1.2 0/1:69:20:11,9:19,30:49,20:0.2899:2,2:23.8:1:29.3:1:0.28648:1.91:33.4:19:0.2879:0:1.3 +8 83004383 . T C 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.41646;SOR=2.4409;LSEQ=GGTTAGTGTAAAAACAACAC;RSEQ=CTTCCCCTAAGAAGGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:0,2:2,13:15,2:0.1176:2,0:31.5:1:33:0:1:0:49.5:4:0.1176:0:1.5 0/1:20:5:0,5:2,13:15,5:0.25:2,0:23.6:1:31:1:1:0:45.4:10:0.25:0:1.4 +8 84050892 . T C 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23843;SOR=1.20008;LSEQ=AGATTTAACTACTTCCTCAT;RSEQ=TCCCAGAGCTTAAAGATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:432:265:127,138:76,90:166,265:0.6134:2,2:26.2:1:32.6:1:0.69231:1.09:60:264:0.6125:0:1.1 1/0:366:240:120,120:57,68:125,240:0.6557:2,2:25.3:1:30.6:1:0.44157:1.19:60:79:0.6565:0:1.1 +8 86484883 . T C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCAGAGCTTGGACACACA;RSEQ=AACTTCAGTTTCCTCAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:13:1:32:1:1:0:59:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 86485227 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49959;SOR=0;LSEQ=AATCAGCACCCAAATACTTA;RSEQ=GGATACTGCACTGTGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:124,66:190,2:0.0104:2,2:20.5:1:27:1:1:1.87229:60:4:0.0105:0:1 0/0:176:0:0,0:119,57:176,0:0:2,0:25.1:1:30.5:1:1:0:60:175:1:0:0.3 +8 86485232 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22206;SOR=Inf;LSEQ=GCACCCAAATACTTACGGAT;RSEQ=CTGCACTGTGAGGGGCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:143,73:216,0:0:2,0:24.9:1:28.6:1:1:0:59.8:215:1:0:0.3 0/1:193:2:1,1:125,66:191,2:0.0104:2,2:22.5:1:31:1:1:1.88733:60:4:0.0105:0:1.5 +8 86485245 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.102;SOR=Inf;LSEQ=TACGGATACTGCACTGTGAG;RSEQ=GGCTGTCACTAACCCTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:158,94:252,0:0:2,0:26.2:1:30.4:1:1:0:59.8:21.909:1:0:0.4 0/1:222:3:1,2:134,85:219,3:0.0135:2,2:13.7:1:28.3:1:0.56257:3.13633:60:6:0.0138:0:1.3 +8 86485306 . G C 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01214;SOR=1.53365;LSEQ=CTCATCGTGTTGCTCTGGGA;RSEQ=TTGAGCTCAGGCTACCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:285:150:66,84:67,67:134,150:0.5263:2,2:26.4:1:32.4:1:0.34155:1.27163:60:74:0.5267:0:1.1 1/0:303:191:91,100:56,56:112,191:0.6304:2,2:24.4:1:30.9:1:0.72187:1.09856:59.8:37.2:0.6284:0:1.2 +8 86485358 . T C 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGTGATCTGCTCACTCTC;RSEQ=GGCTTAAAATCACCCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:57,122:179,0:0:2,0:21:1:30.5:1:1:0:60:43.75:1:0:0.4 0/1:186:33:11,22:48,102:150,33:0.1774:2,2:24.2:1:29.5:1:1:1.06:60:32:0.1778:0:1.1 +8 87557789 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTAATTTCTAATACTCAA;RSEQ=AATTAATACTTATGATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:24.5:1:32.5:1:1:0:41.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 87558138 . A G 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00044;SOR=0.29593;LSEQ=TAAATTTCATATAGTTGTAG;RSEQ=AATTTAAAGAGGTAGATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:44:42,2:132,6:138,44:0.2418:1,1:25.3:1:31.9:1:1:1.04735:60:88:0.2431:0:1 0/1:128:11:11,0:112,5:117,11:0.0859:1,0:19.1:1:31.8:1:1:0:60:22:0.0859:0:1.2 +8 87558142 . T G 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.002;SOR=0.49765;LSEQ=TTTCATATAGTTGTAGAAAT;RSEQ=TAAAGAGGTAGATAGAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:194:115:107,8:74,5:79,115:0.5928:2,2:25.2:1:32.9:1:1:1.106:59.9:230:0.599:0:1 0/1:143:60:56,4:77,5:82,60:0.4196:2,2:25.3:1:31.9:1:1:1.09926:60:120:0.4225:0:1.1 +8 87558210 . G T 135 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACAGAGGAGAACAACTTGA;RSEQ=CCAAGCCCTAAAGATGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:0:0,0:343,257:600,0:0:2,0:27.2:1:32.3:1:1:0:59.9:53.545:1:0:0.4 0/1:599:25:14,11:332,242:574,25:0.0417:2,2:20.5:1:29.2:1:0.83979:1.07779:60:50:0.042:0:1.9 +8 87558283 . C A 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=0.64405;LSEQ=TTGGGGGAAGGAAATATAAA;RSEQ=AAGAGGAGGTGTTAGATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:576:318:124,194:110,145:255,318:0.5521:2,2:25.1:1:30.6:1:0.34704:1.18651:59.9:158:0.5544:0:1.1 0/1:721:319:147,172:173,228:401,319:0.4424:2,2:24.3:1:29.5:1:0.45071:1.13:60:105.333:0.442:0:1.2 +8 87558346 . C T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGAGAAGATCTTTGATG;RSEQ=ATATTTTACCATAGAGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:54,214:268,0:0:2,0:25.6:1:32.1:1:1:0:60:43.667:1:0:0.4 0/1:249:17:7,10:57,174:231,17:0.0683:2,2:23.6:1:28.5:1:0.1531:2.13:60:34:0.0694:0:1.6 +8 87558392 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=ATATATTTGTTTTATGATGT;RSEQ=ATTTTTTTTTCTTTTCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:5,100:105,0:0:1,0:25.9:1:28.8:1:1:0:59.9:104:1:0:0.1 0/1:88:2:1,1:7,79:86,2:0.0227:2,2:12:1:31.5:1:0.1745:10.62:60:4:0.0227:0:1.5 +8 87558393 . A AT 84 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.08188;SOR=4.43014;LSEQ=TATATTTGTTTTATGATGTT;RSEQ=TTTTTTTTTCTTTTCTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:0,2:5,96:101,2:0.0192:1,0:27:1:31:1:1:0:60:4:0.0192:0:0 0/1:87:7:0,7:8,72:80,7:0.0805:2,0:32.6:1:30.1:1:1:0:60:14:0.0805:0:0.1 +8 87558415 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1537;SOR=Inf;LSEQ=TTTTTTTTCTTTTCTTTGCA;RSEQ=CATATTTTCGTTCTTTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:0,69:69,0:0:1,0:23.4:1:33:1:1:0:59.9:33.5:1:0:0.1 0/1:45:2:1,1:1,42:43,2:0.0444:1,2:5:1:28:1:0.08788:30.05:60:4:0.0455:0:1 +8 87938650 . C T 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00699;SOR=Inf;LSEQ=AGTTGTAAGACCATCTGTAG;RSEQ=TTGATGGCCTTGATCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:8,0:0:2,0:20.5:1:32:1:1:0:55.3:16:1:0:0.1 1/0:8:6:3,3:1,1:2,6:0.75:2,2:35.8:1:28.2:1:1:1:46.3:12:0.75:0:1.3 +8 87938708 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11084;SOR=Inf;LSEQ=GGAGGTTAAAAATACAGGGC;RSEQ=TAAAGGCAAGTAATACCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:14,5:19,0:0:2,0:16.9:1:32.3:1:1:0:58:38:1:0:0.1 0/1:10:2:1,1:4,4:8,2:0.2:2,2:26:1:29.5:1:1:1:44.5:4:0.2:0:1.5 +8 87938783 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17582;SOR=Inf;LSEQ=ATGTCACCCAACTCCAGAGG;RSEQ=TGGTGTCAGAGTTTGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:19,26:45,0:0:2,0:27.9:1:29.7:1:1:0:54.6:44:1:0:0.1 0/1:33:2:1,1:17,14:31,2:0.0606:2,2:23:1:30.5:1:1:1.20712:42:4:0.0606:0:1.5 +8 87938824 . CT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.51152;SOR=Inf;LSEQ=CATTGTCTGATTTCAGAAGC;RSEQ=TTTCCTGTAAACACCAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:22.3:1:31.6:1:1:0:47.2:38:1:0:0.2 0/1:29:2:1,1:13,14:27,2:0.069:2,2:12.5:1:29.5:1:1:1.07:34.5:4:0.0714:0:0 +8 88515609 . T C 33 v3;MAF0.05;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTATATATATACTTAATTCC;RSEQ=GTAACAGGAAGAAGATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:7:1:33:0:1:0:60:4:0.3333:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:25:0:28:0:1:0:60:2:0.3333:0:1 +8 88515743 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4964;SOR=Inf;LSEQ=AGCATCAGATCTTGGGGAAA;RSEQ=GTTTTTATTCAAGGCTATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:43,27:70,0:0:2,0:26.8:1:32.4:1:1:0:59.6:140:1:0:0.1 0/1:70:2:1,1:48,20:68,2:0.0286:2,2:13.5:1:28:1:0.51304:2.36645:60:4:0.029:0:1 +8 88515744 . G T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.24468;SOR=0;LSEQ=GCATCAGATCTTGGGGAAAG;RSEQ=TTTTTATTCAAGGCTATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:3:1,2:42,26:68,3:0.0423:2,2:19.7:1:26.3:1:0.55762:3.17645:60:6:0.0423:0:1 0/0:70:0:0,0:49,21:70,0:0:2,0:21.9:1:31.1:1:1:0:60:140:1:0:0.2 +8 88515764 . GGTT G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.21146;SOR=0;LSEQ=GTTTTTATTCAAGGCTATGT;RSEQ=GTTGTTGTTGTTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:48,45:93,2:0.0211:2,2:41:1:33:1:1:1.06598:47:4:0.0215:0:0 0/0:111:0:0,0:63,48:111,0:0:2,0:24.1:1:30.6:1:1:0:58.3:54.5:1:0:0.2 +8 88515778 . TTGC T 31 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.58824;SOR=0.40246;LSEQ=CTATGTGGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGTTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:50,47:97,2:0.0202:2,2:49:0:31.5:1:1:1.0632:60:4:0.0202:0:0 0/0:122:1:1,0:64,57:121,1:0.0082:2,0:23:0:32:0:1:0:60:2:0.0083:0:0 +8 88515792 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50624;SOR=Inf;LSEQ=TTGTTGTTGCTGCTGCTGCT;RSEQ=TTGCTGCTGCTTTGCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:44,53:97,0:0:2,0:27.8:1:32.2:1:1:0:59.6:31.333:1:0:0.1 0/1:126:2:1,1:62,62:124,2:0.0159:2,2:32:1:27.5:1:1:1:60:4:0.016:0:1 +8 88515868 . G C 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.83585;LSEQ=AGGAAGACAGTAGTGTTAGA;RSEQ=AGTGAAAGAAAGAAAGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:2,4:1,19:20,6:0.2308:1,2:31.2:1:28.2:1:0.12308:8.40:60:5:0.2:0:1 0/1:35:7:0,7:5,23:28,7:0.2:2,0:20.3:1:31.3:1:0.5585:0:60:14:0.2:0:1 +8 90282757 . A T 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19335;SOR=4.52592;LSEQ=TTGTTACATCCAATAATATG;RSEQ=TACATGTTTTGAGATACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:0,1:147,97:244,1:0.0041:2,0:1:0:30:0:0.4:0:60:2:0.0041:0:1 0/1:219:4:4,0:133,82:215,4:0.0183:2,0:17.5:1:30:1:0.2995:0:60:8:0.0184:0:1 +8 90282811 . T A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57826;SOR=0.88853;LSEQ=AGATACTCCCTACTATCTTT;RSEQ=AACATTAAATTCCAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:81:42,39:100,114:214,81:0.2746:2,2:24.9:1:30:1:0.43721:1.23:60:162:0.2774:0:1.1 0/1:306:77:39,38:122,107:229,77:0.2516:2,2:27.4:1:28.6:1:0.69472:1.11057:60:37.5:0.2483:0:1.1 +8 90282866 . AT A 56 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.12346;SOR=0;LSEQ=TTTTTCTGGGTGTCATGGCC;RSEQ=TTTTAGCTGGCATTTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:4:3,1:83,141:224,4:0.0175:2,2:17.8:1:28.3:1:0.15189:5.06:60:8:0.0177:0.0088:0.5 0/0:222:0:0,0:94,128:222,0:0:2,0:25:1:29.5:1:1:0:60:110:1:0:0.2 +8 90947537 . C T 63 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=TTTAGTCTTTACCTTACGTA;RSEQ=ATTTAGAATTTTGAACTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:33:1:31.8:1:1:0:60:8:0.4:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:10:0:32:0:1:0:60:2:1:0:1 +8 90948042 . CA C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.54177;SOR=0;LSEQ=TGATGAAAATATGGTAAAAA;RSEQ=AAAAAAAAATCAACAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:3:0,3:1,26:27,3:0.1:1,0:31.7:1:34:1:1:0:60:6:0.1034:0:0 0/0:13:0:0,0:1,12:13,0:0:1,0:25.8:1:28.6:1:1:0:60:12:1:0:0.1 +8 90949097 . T C 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02586;SOR=0;LSEQ=GCTATAGCCAATAAACCCAA;RSEQ=TGAGAGGTGCTTAAGTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:10:10,0:31,0:31,10:0.2439:1,0:24.9:1:33.1:1:1:0:59.1:20:0.25:0:1.1 0/0:17:0:0,0:16,1:17,0:0:1,0:21.9:1:31.2:1:1:0:60:34:1:0:0 +8 90949166 . G C 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00256;SOR=Inf;LSEQ=ACTAGGTGTCTATGAGGACA;RSEQ=AAGAAACAAATTCTTAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:109,19:128,0:0:2,0:23.9:1:33.3:1:1:0:60:256:1:0:0.1 0/1:119:8:5,3:93,17:110,8:0.0672:2,2:12.1:1:31.6:1:0.13324:3.23805:60:16:0.0678:0:1 +8 90949174 . A T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.49786;LSEQ=TCTATGAGGACAGAAGAAAC;RSEQ=AATTCTTAATTTCTATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:123,32:155,2:0.0127:2,2:28:1:30.5:1:0.37727:3.80042:60:4:0.0127:0:1 0/0:157:1:0,1:121,35:156,1:0.0064:2,0:1:0:25:0:0.2293:0:60:2:0.0064:0:1 +8 90955170 . G C 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TACATTTAAGTGATATATTT;RSEQ=TAATATCCTCCACATTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:18.3:1:31.3:1:1:0:60:8:0.6667:0:1.5 0/0:2:0:0,0:2,0:2,0:0:0,0:9.5:1:33:0:1:0:60:4:1:0:0.5 +8 90955253 . T G 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13257;SOR=0;LSEQ=ATTAGGATGTAAACTGAATT;RSEQ=CTTAGGTCTCACCTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:7,0:11,0:11,7:0.3889:0,0:19.9:1:31.7:1:1:0:58.6:14:0.3889:0:3.1 0/0:7:0:0,0:7,0:7,0:0:0,0:15.7:1:31:1:1:0:60:14:1:0:1 +8 90955358 . C T 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06515;SOR=0.57798;LSEQ=TGCTCTGTAACTCAGGAATG;RSEQ=TCCTGAATGAATGACTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:61:60,1:85,0:85,61:0.4178:1,1:28.3:1:30.3:1:0.41781:0:60:60:0.4196:0:1 0/1:82:24:23,1:58,0:58,24:0.2927:1,1:27.5:1:28.8:1:0.29268:0:60:23:0.2875:0:1 +8 90955397 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15604;SOR=Inf;LSEQ=ATGTCACTTATTTTAATTTG;RSEQ=TTTTAAGAAGAATTTGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:266,38:304,0:0:2,0:22.7:1:31.5:1:1:0:60:59.8:1:0:0.2 0/1:199:2:1,1:160,36:196,2:0.0101:2,2:18.5:1:27.5:1:0.33959:4.39766:60:4:0.0102:0:1 +8 90955561 . T A 66 v3;p8;q25;Bias STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00219;SOR=Inf;LSEQ=TAGATCTGATCCTCCAATGA;RSEQ=GTGTGGAAGTTTTCCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:827:0:0,0:321,506:827,0:0:2,0:25:1:30.4:1:1:0:60:62.615:1:0:0.2 0/1:723:8:8,0:316,399:715,8:0.0111:2,0:6.6:1:22.3:1:0.00155:0:60:3:0.0084:0:1.3 +8 90955583 . A C 142 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGGAAGTTTTCCTGCTCC;RSEQ=GGATATGTGACCTATTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:708:0:0,0:237,471:708,0:0:2,0:25.9:1:31.3:1:1:0:59.9:40.647:1:0:0.3 0/1:554:26:10,16:209,319:528,26:0.0469:2,2:29.2:1:30.3:1:1:1.04819:60:52:0.0476:0:1.7 +8 90955624 . T A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.46362;LSEQ=AATAAAAGTAGTACAGTAAA;RSEQ=CATATTAACAAACAAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:158:42,116:55,168:223,158:0.4115:2,2:22.7:1:30.1:1:0.72068:1.11:60:157:0.4153:0:1.1 0/1:323:79:27,52:70,174:244,79:0.2446:2,2:23.2:1:29:1:0.39727:1.29:60:78:0.2461:0:1.4 +8 90955655 . T A 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=AACAAAAATGACCATTTTTT;RSEQ=AAAAAGATTAAAAAGCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:25,162:187,0:0:2,0:22.2:1:28.8:1:1:0:60:186:1:0:0.5 0/1:148:13:2,11:12,123:135,13:0.0878:2,2:27.1:1:30.2:1:0.35428:1.85:60:26:0.0878:0:2 +8 90958341 . C A 144 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAAACATTTCAAACACTGAC;RSEQ=TCTTGTGATACAGTTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:31:24,7:246,114:360,31:0.0791:2,2:26.3:1:29.2:1:0.41782:1.59:60:9.333:0.0727:0:1 0/0:346:0:0,0:236,110:346,0:0:2,0:24.3:1:30.5:1:1:0:60:114.333:1:0:0.2 +8 90958422 . T C 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32738;LSEQ=TAATCATCATTTATGCCAGA;RSEQ=GGATTTCTGGAAGTAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:264:144,120:241,197:438,264:0.375:2,2:26.4:1:31:1:0.93764:1.01944:59.9:131:0.3792:0:1.1 0/1:640:105:63,42:279,256:535,105:0.1641:2,2:26.1:1:30.5:1:0.16417:1.38:59.9:210:0.1667:0:1.1 +8 90958530 . T C 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.45201;LSEQ=AGTTTGTCATTGTTCTTAAA;RSEQ=GGGGTTAAGATGGATAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:169:55,114:78,174:252,169:0.4014:2,2:23.3:1:30.4:1:0.74912:1.08:60:41.25:0.4024:0:1.1 0/1:413:96:33,63:109,207:316,96:0.2324:2,2:25.1:1:29.7:1:1:1.00526:60:95:0.2363:0:1 +8 90959884 . A AAAT 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.27419;SOR=0;LSEQ=AATAAATAAACAAATAAATA;RSEQ=AATAATAATAATAATAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:3:3,0:72,0:72,3:0.04:1,0:24.7:1:27.4:1:1:0:49.3:2:0.027:0:2.7 0/0:50:0:0,0:50,0:50,0:0:1,0:21.8:1:30.4:1:1:0:60:100:1:0:0.1 +8 90959969 . T C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12526;SOR=Inf;LSEQ=TTAGGAAAGAGAAATAATCC;RSEQ=AAGAATGTAAAATCACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:216,54:270,0:0:2,0:24.4:1:31.3:1:1:0:59.9:269:1:0:0.1 0/1:296:4:2,2:231,61:292,4:0.0135:2,2:33.8:1:30.8:1:0.19984:3.7646:60:8:0.0137:0:1 +8 90965928 . T TA 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22639;SOR=0.40051;LSEQ=TCATCCCTTTCCCTTAGATT;RSEQ=AAAAAAAAAGAAGAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:8:2,6:69,236:305,8:0.0256:2,2:29.8:1:29.1:1:1:1.14:60:16:0.0261:0:0.1 0/1:289:3:2,1:89,197:286,3:0.0104:2,2:22.3:1:25.7:1:0.23417:4.40:60:6:0.0104:0.0035:0.3 +8 90967464 . CT C 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TTCTACAACAGTATAAAAAA;RSEQ=TTCATTTTTTTTTCAGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:317:0:0,0:248,69:317,0:0:2,0:23.2:1:31.8:1:1:0:60:62.4:1:0:0.1 0/1:275:15:12,3:190,70:260,15:0.0545:2,2:20.6:1:31:1:0.76586:1.47:60:30:0.0547:0.0109:0 +8 90967469 . A AT 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.86875;LSEQ=CAACAGTATAAAAAACTTTC;RSEQ=TTTTTTTTTCAGAGACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:345:8:6,2:254,80:334,8:0.0232:2,2:20.4:1:28.3:1:1:1.05816:60:7:0.0207:0.0029:0.1 0/1:297:6:3,3:210,80:290,6:0.0202:2,2:13:1:27.5:1:0.35458:2.61512:60:12:0.0205:0.0101:0.5 +8 90967711 . A G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.82755;SOR=1.02649;LSEQ=GACTCCTTTACAGTGGGTGC;RSEQ=TCTTGTGAAAGCATTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:281:122,159:178,228:406,281:0.409:2,2:25.1:1:31.4:1:0.93772:1.01745:59.9:69.25:0.4098:0:1.1 0/1:703:292:134,158:186,223:409,292:0.4154:2,2:26:1:30.1:1:0.93877:1.02:60:72:0.4162:0:1.2 +8 90967862 . G T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08891;SOR=0.53089;LSEQ=GAAACAAAGATCGTTAAATA;RSEQ=TTCTAACGTAATATAACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:38:1,37:0,67:67,38:0.3619:1,1:29.5:1:30.4:1:0.3619:0:60:76:0.3619:0:1.1 0/1:65:15:0,15:0,49:49,15:0.2308:1,1:17.1:1:30.2:1:1:0:60:30:0.2344:0:1.2 +8 90967869 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12357;SOR=Inf;LSEQ=AGATCGTTAAATAGTTCTAA;RSEQ=GTAATATAACCTTAGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:1,94:95,0:0:1,0:26.1:1:30.8:1:1:0:60:190:1:0:0.4 0/1:52:2:0,2:0,50:50,2:0.0385:1,0:8:1:30.5:1:1:0:60:4:0.0385:0:2 +8 90970862 . G T 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.58994;SOR=0.84378;LSEQ=TTCCATGCTTTCTCTCTCAA;RSEQ=AGACAACCTGATAAAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:55:53,2:97,3:100,55:0.3548:1,1:25.5:1:31.4:1:1:1.2185:60:54:0.3553:0:1.5 0/1:101:32:32,0:66,3:69,32:0.3168:1,1:24.5:1:31.1:1:0.54952:0:60:64:0.3168:0:1.4 +8 90970935 . G A 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.54597;LSEQ=AGAATAATAACAATAGTACG;RSEQ=TAATGAAGAAGCTTTACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:253:170,83:291,150:441,253:0.364:2,2:23.2:1:30.4:1:0.80226:1.06:60:83.333:0.3639:0:1.2 0/1:668:159:100,59:321,185:506,159:0.238:2,2:26.4:1:28.8:1:0.92498:1.02371:60:158:0.2394:0:1.2 +8 90976405 . C T 83 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.63559;LSEQ=CTAAATCTTGATCTTCAGAA;RSEQ=ATAAAGTTTATAATAACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:6,0:15,0:15,6:0.2857:1,0:12:1:32.2:1:1:0:60:12:0.3:0:1.2 0/1:5:1:1,0:4,0:4,1:0.2:0,0:3:0:28:0:1:0:60:2:0.2:0:2 +8 90976753 . T A 66 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00497;SOR=Inf;LSEQ=TGCCTATTAGAATAAAATAG;RSEQ=TTAAGTATGATAATATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:145,406:551,0:0:2,0:24.3:1:30.1:1:1:0:60:67.875:1:0:0.1 0/1:489:7:5,2:145,336:481,7:0.0143:2,2:5.4:1:23.7:1:0.031:5.77:60:6:0.0124:0:1 +8 90976799 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07852;SOR=Inf;LSEQ=AGCAACTTTTATTCAGATAA;RSEQ=GTCAAGATAAAGCAACCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:8,223:231,0:0:1,0:22:1:30.7:1:1:0:60:56.75:1:0:0.1 0/1:174:3:0,3:8,163:171,3:0.0172:1,0:12.7:1:31.7:1:1:0:60:6:0.0172:0:1 +8 90976818 . CT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50995;SOR=0;LSEQ=ATGTCAAGATAAAGCAACCT;RSEQ=TTTTTTTCCTCCCAAATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:0,2:0,147:147,2:0.0133:1,0:32.5:1:33.5:1:1:0:60:4:0.0137:0:0 0/0:110:0:0,0:2,108:110,0:0:1,0:21.9:1:30.1:1:1:0:59.7:109:1:0:0.1 +8 90976866 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54534;SOR=0;LSEQ=GTATAGACAGAATTTCAAAT;RSEQ=CAGAGTACTATAATAGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:0,2:0,69:69,2:0.0282:1,0:24.5:1:29:1:1:0:60:4:0.029:0:1 0/0:37:0:0,0:0,37:37,0:0:1,0:24.8:1:32.4:1:1:0:59.2:74:1:0:0.2 +8 90976906 . G A 61 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28366;SOR=0;LSEQ=ACTCGCTGGGGCACTGTTAC;RSEQ=TTGACAAGTCTACCATCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:0,4:0,28:28,4:0.125:1,0:6:1:30.8:1:1:0:60:8:0.125:0:1 0/0:17:0:0,0:0,17:17,0:0:1,0:20.8:1:31.1:1:1:0:60:16:1:0:0.3 +8 90982425 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06818;SOR=Inf;LSEQ=AGGCAGAAGTTGCAGTGAGC;RSEQ=GAGATCGTGCCACTGCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:24,0:24,0:0:1,0:24.7:1:30.8:1:1:0:39.5:23:1:0:0.2 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:12:1:32:0:1:0:31:4:0.2222:0:1 +8 90982477 . CA C 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=1.15094;LSEQ=ACAAGAGCAAGACTCCGTCT;RSEQ=AAAAAAAAAAATTCTTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:4:4,0:60,1:61,4:0.0597:1,0:32.8:1:33.5:1:1:0:44.3:8:0.0597:0:0 0/1:44:3:3,0:41,0:41,3:0.0682:1,0:30.3:1:31.3:1:1:0:57.7:6:0.0682:0:0 +8 90982556 . C T 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=6e-05;SOR=Inf;LSEQ=GTTAAACATAAAATCTCCTA;RSEQ=TTGCAGTTTTTTACTAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:0:0,0:224,62:286,0:0:2,0:23.6:1:32.1:1:1:0:60:34.75:1:0:0.1 0/1:303:15:13,2:217,71:288,15:0.0495:2,2:25.3:1:30.3:1:0.53523:2.12:60:30:0.0507:0:1.1 +8 90982803 . C T 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGCTAAAAATGGAAGGAAA;RSEQ=ATTTTTTAAAGTAAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:81,318:399,0:0:2,0:21.6:1:32.4:1:1:0:60:78.8:1:0:0.1 0/1:328:23:5,18:65,240:305,23:0.0701:2,2:23.3:1:28.5:1:1:1.03:60:46:0.0708:0:1 +8 90982814 . G A 102 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00169;SOR=13.75855;LSEQ=GGAAGGAAACATTTTTTAAA;RSEQ=TAAAATGTAGTAATTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:1:1,0:46,244:290,1:0.0034:2,0:1:0:25:0:0.16151:0:60:2:0.0035:0:1 0/1:242:11:2,9:45,186:231,11:0.0455:2,2:21.1:1:29.6:1:1:1.08833:60:22:0.0462:0:1 +8 90983251 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06604;SOR=Inf;LSEQ=TCACAGCCATGATCACTGGG;RSEQ=AGGTCTGGTGCCTGGGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:37,2:39,0:0:2,0:23.9:1:32.7:1:1:0:60:78:1:0:0.1 0/1:14:2:1,1:11,1:12,2:0.1429:2,2:27:0:31.5:1:0.27473:8.12278:60:4:0.1429:0:1.5 +8 90983317 . C G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00144;SOR=Inf;LSEQ=CAAAATCCCAAAATGAAATA;RSEQ=GTTAACAACTACTGATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:108,14:122,0:0:2,0:24.8:1:32.1:1:1:0:60:60:1:0:0.1 0/1:100:8:7,1:80,10:90,8:0.08:2,2:19.1:1:32.1:1:1:1.1412:60:16:0.0816:0:1.1 +8 90990479 . C G 265 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.49214;LSEQ=TGGAGGCTGCTTCTTGGACT;RSEQ=AACTGCTTTCAGGAATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:301:148,153:255,232:487,301:0.3815:2,2:26.9:1:32.2:1:0.41987:1.13608:60:74.25:0.3813:0:1.1 0/1:726:169:89,80:285,270:555,169:0.2328:2,2:25.7:1:30.8:1:0.79235:1.05:60:168:0.2337:0:1.2 +8 90992670 . G C 52 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTTAAGACTGAAAACACAAA;RSEQ=TATGCACTGTCATAACCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:24:1:33.3:1:1:0:60:6:0.75:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:21:0:33:0:1:0:60:2:1:0:0 +8 90992882 . TA T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.74517;LSEQ=TCTGATAGTTTTAAAGTAAT;RSEQ=AAAAAAAATCTGTGTATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:2,0:116,12:128,2:0.0154:2,0:32:1:28.5:1:1:0:60:4:0.0154:0:0 0/1:87:1:1,0:82,4:86,1:0.0115:1,0:34:0:33:0:1:0:60:2:0.0115:0:0 +8 90993138 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50997;SOR=0;LSEQ=TATTCTGTAAATGAGAATAA;RSEQ=TTAAATAAAGTCATAGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:27,141:168,2:0.0118:2,2:21:1:31.5:1:0.3031:5.15:60:4:0.012:0:1 0/0:125:0:0,0:21,104:125,0:0:2,0:23.5:1:31.6:1:1:0:60:250:1:0:0.1 +8 90993150 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16663;SOR=Inf;LSEQ=GAGAATAAGTTAAATAAAGT;RSEQ=ATAGTATCAGAGTTGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:14,123:137,0:0:2,0:22.3:1:32.6:1:1:0:59.8:67.5:1:0:0.1 0/1:95:2:0,2:12,81:93,2:0.0211:2,0:19.5:1:29:0:1:0:60:4:0.0217:0:1 +8 90993395 . C T 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2451;SOR=0;LSEQ=GAGGAATCGAAGAAATGTAA;RSEQ=TTCCCATGAAGTCCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:8,7:0.4667:0,0:23.1:1:32.1:1:1:0:55.7:14:0.4667:0:1 0/0:3:0:0,0:3,0:3,0:0:0,0:17:1:29.7:1:1:0:60:6:1:0:0 +8 90993883 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15704;SOR=0.27494;LSEQ=GCAGACAACAATTACTGCTT;RSEQ=GGTTGCCTTGAGAGGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:10:0,10:0,16:16,10:0.3846:1,0:21:1:31.5:1:1:0:60:20:0.3846:0:1.2 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:26:1:30.5:1:1:0:60:4:0.1429:0:1 +8 90995019 . C T 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.4883;LSEQ=ATCGACTGATCATTTTCAAT;RSEQ=AGAATGGCACAGTTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:802:315:148,167:222,265:487,315:0.3928:2,2:25.6:1:29.5:1:0.71721:1.06:60:314:0.394:0:1.1 0/1:721:173:87,86:258,290:548,173:0.2399:2,2:28.7:1:28.5:1:0.48554:1.14:59.8:346:0.242:0:1.1 +8 90995093 . AT A 59 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.71604;SOR=1.44157;LSEQ=GTATGGTTCTCCTGAGATAA;RSEQ=TTTTTTTTAAAAAAAGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:3:0,3:68,236:304,3:0.0098:2,0:23.3:1:29.9:1:1:0:60:6:0.0099:0.0033:0 0/1:285:4:1,3:75,206:281,4:0.014:2,2:26.5:1:29.8:1:1:1.0919:60:8:0.0142:0.0035:0.3 +8 90995102 . T A 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.11521;SOR=Inf;LSEQ=TCCTGAGATAAATTTTTTTT;RSEQ=AAAAAAAGATAAGTTGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:0:0,0:50,218:268,0:0:2,0:22.5:1:28.8:1:1:0:60:52.6:1:0:0.2 0/1:255:3:1,2:59,193:252,3:0.0118:2,2:13.3:1:28.3:1:0.55445:1.63:60:6:0.012:0:1.3 +8 90996258 . A G 30 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAAAAATCGACTTTTCCC;RSEQ=TTGTTCTGATGACATTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:15.5:1:30:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:11:0:31:0:1:0:60:2:1:0:1 +8 91433917 . T C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.01823;LSEQ=TGGTTCTGCTTTCCTCATTC;RSEQ=AACTCATTTCACTTGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:282:142,140:171,171:342,282:0.4519:2,2:26.4:1:31.4:1:0.93607:1.01:59.9:46:0.4495:0:1.8 1/0:581:363:174,189:114,104:218,363:0.6248:2,2:28:1:30.5:1:0.34594:1.19029:60:89.75:0.6233:0:1.7 +8 91433947 . C T 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06124;SOR=1.27021;LSEQ=CACTTGAGGTCGGGTTCTGA;RSEQ=GTTGTATCTTTGTCAATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:233:95,138:129,159:288,233:0.4472:2,2:25.8:1:30.4:1:0.37435:1.17817:60:57.25:0.4464:0:1.9 1/0:509:258:105,153:111,137:248,258:0.5069:2,2:24.3:1:29.2:1:0.36973:1.18021:59.9:35.857:0.5:0:1.9 +8 91434011 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18677;SOR=Inf;LSEQ=AAACATGTCATACTCAGCTG;RSEQ=ATTCAGCCAGAAAGACTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:45,158:203,0:0:2,0:23.5:1:31.8:1:1:0:60:100.5:1:0:0.6 0/1:155:2:1,1:33,120:153,2:0.0129:2,2:21:1:29.5:1:0.39171:3.60:60:4:0.0131:0:3 +8 91434018 . C T 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.38424;SOR=0.30305;LSEQ=TCATACTCAGCTGGATTCAG;RSEQ=CAGAAAGACTATGGGATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:4:2,2:31,142:173,4:0.0225:2,2:25.5:1:30.8:1:0.15846:4.53:60:8:0.0231:0:2.3 0/0:145:1:0,1:28,116:144,1:0.0069:2,0:34:0:25:0:1:0:60:2:0.0071:0:1 +8 91434037 . C A 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04339;SOR=0;LSEQ=GCCAGAAAGACTATGGGATC;RSEQ=CAGGAGTTTGTTCTAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:7:1,6:12,114:126,7:0.0526:2,2:24.1:1:30.3:1:0.5218:1.58:60:14:0.0538:0:2 0/0:90:0:0,0:6,84:90,0:0:2,0:22.3:1:30.7:1:1:0:60:180:1:0:0.6 +8 91434040 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47308;SOR=1.27482;LSEQ=AGAAAGACTATGGGATCCCA;RSEQ=GAGTTTGTTCTAGCATGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:50:4,46:6,66:72,50:0.4098:2,2:20.4:1:31.3:1:1:1.04508:60:49:0.4118:0:1.4 0/1:83:39:1,38:2,42:44,39:0.4699:1,1:22.9:1:31.4:1:1:1.79714:60:78:0.4756:0:1.2 +8 92236662 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13462;SOR=Inf;LSEQ=TGTTTTCTTTCAATAGTCAG;RSEQ=ACCCTCTTCTGTAGGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:16,9:25,0:0:2,0:23.9:1:30.1:1:1:0:55.1:24:1:0:0.2 0/1:15:2:1,1:11,2:13,2:0.1333:2,2:37.5:1:29.5:1:0.37143:4.69047:51:4:0.1333:0:1.5 +8 92236730 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07632;SOR=Inf;LSEQ=CCTTATTCATCTGATTTGCT;RSEQ=CCATGCCTGGAGATGTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:28,29:57,0:0:2,0:25.8:1:31.2:1:1:0:39.7:18:1:0:0.2 0/1:43:3:2,1:20,20:40,3:0.0698:2,2:26.3:1:30:1:1:1.97:41:6:0.0732:0:1.7 +8 92236869 . C T 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11077;SOR=Inf;LSEQ=TGTATAGGGTGTCTGACAAA;RSEQ=CCTGTTGGAAGGTCTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:17,0:0:2,0:21.6:1:31.6:1:1:0:57.9:16:1:0:0.2 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:5.5:1:25.5:1:1:1.29:60:4:0.2222:0:1.5 +8 92236962 . TG T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.51648;SOR=Inf;LSEQ=GTGGAGAGGGTGTGTTGTGC;RSEQ=GGGGGAAACCCACTTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:3,4:1,3:4,7:0.6364:2,2:30.7:1:31.6:1:1:2.09:60:14:0.6364:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:24.8:1:30.5:1:1:0:60:8:1:0.25:0.3 +8 92297537 . T TTCA 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=3.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=TCATGTGGCATTCACATGCC;RSEQ=TCATCACATGTGTTTTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:8:0:31:0:1:0:60:2:1:0:0 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:26:1:31.8:1:1:0:60:4:0.6667:0:0 +8 92833865 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18846;SOR=0;LSEQ=AGACCAGAAATAACTAAAAT;RSEQ=AGAGTAGAACTGAAGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:21,22:43,2:0.0444:2,2:10.5:1:31:1:1:1.05:60:4:0.0444:0:1 0/0:58:0:0,0:32,26:58,0:0:2,0:27.4:1:28:1:1:0:59.4:28:1:0:0.2 +8 93284530 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21587;SOR=0;LSEQ=CTCATGTATTGTTTTCTCCT;RSEQ=CCAAGGAGAGAAAAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:2,13:15,2:0.1176:2,2:14.5:1:28:1:0.33088:5.51:60:4:0.1176:0:1 0/0:19:0:0,0:4,15:19,0:0:2,0:19.8:1:30.5:1:1:0:60:38:1:0:0.1 +8 93406621 . G A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13737;SOR=Inf;LSEQ=AATACAGGGCCCAAAGGCGA;RSEQ=TAATGCAAGACGGCTGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:19,9:28,0:0:2,0:20.1:1:32.7:1:1:0:55:56:1:0:0.4 0/1:17:2:1,1:12,3:15,2:0.1176:2,2:15:0:28:1:0.42647:3.6058:60:4:0.1176:0:1 +8 93406768 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATCTCATACTATCCCTGA;RSEQ=TGGTTAGTGTAAAAACAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:3,15:18,2:0.1:2,2:28.5:1:30:1:0.36842:4.47:41.5:4:0.1053:0:1 0/0:7:0:0,0:0,7:7,0:0:0,0:25.3:1:33.4:1:1:0:48.9:14:1:0:0 +8 97963297 . A T 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATTGTTATAGAGTTAAAAC;RSEQ=GATGAAATAATGCTTCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:33:1:34:0:1:0:44.5:4:0.4:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 97963715 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.56623;SOR=3.03193;LSEQ=TCAGTTCAAACACCTGAATT;RSEQ=ATTTTCACCAATGCTACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:1:1,0:191,78:269,1:0.0037:2,0:15:0:11:0:1:0:60:0:0:0:4 0/1:179:2:1,1:119,58:177,2:0.0112:2,2:15:1:27:1:0.55182:2.04285:60:4:0.0115:0:1 +8 97963811 . T C 286 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61082;SOR=0.92122;LSEQ=TATAGCTTTTTCCCTTTTTG;RSEQ=AAGCTATTATTGAAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:646:480:248,232:79,85:164,480:0.743:2,2:24.9:1:32.2:1:0.46969:1.15:60:79:0.7418:0:1.1 1/0:392:285:143,142:51,56:107,285:0.727:2,2:25.7:1:31.3:1:0.73386:1.11:60:141.5:0.7256:0:1.2 +8 97964081 . G GT 62 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.51471;SOR=2.56905;LSEQ=AATCTTTCCTAGAGAGAATT;RSEQ=TTTTTTTTTTGAATGTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:0,10:10,4:0.2667:0,0:38.3:1:31:1:1:0:60:8:0.2667:0:0.8 1/0:2:1:0,1:0,1:1,1:0.5:0,0:47:0:30:0:1:0:60:2:0.5:0:7 +8 98179766 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12381;SOR=Inf;LSEQ=TAAGCTGAGGGAGTTACAGT;RSEQ=ATTCCCAGTGAGAGGCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:23,0:0:2,0:35.1:1:32.4:1:1:0:60:46:1:0:0.1 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:23:0:30.5:1:1:2.4495:60:4:0.1538:0:1.5 +8 98381926 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09756;SOR=Inf;LSEQ=TTAGGATGTCTGAACTTTCT;RSEQ=CTTTATGTTTTCAACTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:193,52:245,0:0:2,0:23.6:1:32.3:1:1:0:59.7:121.5:1:0:0.1 0/1:210:3:2,1:149,58:207,3:0.0143:2,2:14.7:1:28.7:1:1:1.2829:60:6:0.0146:0:1 +8 98381945 . C CT 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.9558;LSEQ=TGCTTTATGTTTTCAACTAT;RSEQ=TTTTTTTTTAATGGCATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:19:10,9:247,77:324,19:0.0548:2,2:17.6:1:30.4:1:0.02909:2.87625:60:38:0.0552:0.0202:0.7 0/1:305:16:10,6:191,98:289,16:0.0525:2,2:26.4:1:29.3:1:0.78995:1.16876:59.7:15:0.0502:0.0098:0.7 +8 98382025 . G A 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01222;SOR=1.34873;LSEQ=TTCTTAAACTCTGATGCTCT;RSEQ=GGGCTAAGAACAACAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:673:388:204,184:142,140:282,388:0.5765:2,2:24.4:1:29.8:1:0.58431:1.09:59.3:193:0.577:0:1.1 1/0:573:371:182,189:103,99:202,371:0.6475:2,2:26.1:1:28.6:1:0.66308:1.08027:59.2:73.2:0.6466:0:1.1 +8 98382120 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15756;SOR=Inf;LSEQ=GAATCGCTTTCCAGAAAGGC;RSEQ=GTTACTGGAAACAGCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:0:0,0:51,205:256,0:0:2,0:23:1:31.4:1:1:0:59.9:50.2:1:0:0.1 0/1:169:2:1,1:37,130:167,2:0.0118:2,2:18.5:1:32:0:0.40018:3.48:60:4:0.012:0:1 +8 98382175 . C CCTAT 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.68321;SOR=0.83124;LSEQ=AGGGCTGCTCAACAATGCCT;RSEQ=CTCCCCCAACACCCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:72:1,71:0,20:20,72:0.7742:1,1:24.8:1:30.7:1:1:0:59.7:71:0.7802:0.1935:0.1 1/0:50:37:1,36:0,13:13,37:0.74:1,1:27.2:1:29.7:1:1:0:59.4:74:0.74:0.1:0.2 +8 98382341 . C G 106 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAGGTCCTGCTACGTCCA;RSEQ=TGTTGTCTTAGATCTAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:1,10:0.9091:0,0:35.5:1:32:1:1:0:52.4:20:0.9091:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 98696815 . A G 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48837;SOR=0;LSEQ=TTGCAAAGCCTAACATATTT;RSEQ=CTATTTGATCCTTTGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:12,8:20,2:0.0909:2,2:10:0:31.5:1:1:1.47192:60:4:0.0909:0:1 0/0:22:0:0,0:11,11:22,0:0:2,0:30.5:1:26.8:1:1:0:60:10:1:0:0.1 +8 98924613 . C T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.50474;LSEQ=CCCTAACATAGGGCGTTAAG;RSEQ=TTAACGGAGTCAGCGAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:20,14:34,2:0.0556:2,2:10:1:28.5:1:1:1.41419:60:4:0.0556:0:1 0/1:35:1:1,0:18,16:34,1:0.0286:2,0:25:0:31:0:1:0:60:2:0.0286:0:1 +8 98924637 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20448;SOR=Inf;LSEQ=ACGGAGTCAGCGAGAGCAGC;RSEQ=GGAGCCGGGCATTGAAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:43,0:0:2,0:31.6:1:30.7:1:1:0:60:42:1:0:0.2 0/1:36:2:1,1:15,19:34,2:0.0556:2,2:13.5:1:31.5:1:1:1.26:60:4:0.0556:0:1 +8 98924642 . C G 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01598;SOR=Inf;LSEQ=GTCAGCGAGAGCAGCTGGAG;RSEQ=CGGGCATTGAAGCGCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:23,22:45,0:0:2,0:30.6:1:31.1:1:1:0:60:44:1:0:0.2 0/1:37:5:3,2:12,20:32,5:0.1351:2,2:30.6:1:26.6:1:0.37732:2.44:60:4:0.1111:0:1.6 +8 98924702 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53202;SOR=0;LSEQ=TTGGCTCAATAGTTTTCCTT;RSEQ=TGTGTAATATACTGTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:2,15:17,2:0.1053:2,0:33.5:1:33:1:1:0:60:4:0.1053:0:1 0/0:10:0:0,0:1,9:10,0:0:2,0:21.8:1:30.2:1:1:0:60:20:1:0:0.1 +8 99812821 . A G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGAAGGTGTGGAGGGAGA;RSEQ=GCGTGGGCAGGAACCAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:42:0:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 101822347 . C A 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=TGGCGACCACTTCCCCCACC;RSEQ=CCCACCCCGGTTCTCATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:18:1:32:0:1:0:60:4:1:0:1 0/0:3:0:0,0:1,2:3,0:0:2,0:44.3:1:29.7:1:1:0:60:6:1:0:1 +8 101822736 . ACAG A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=10.000;MSILEN=3;SSF=0.33218;SOR=1.96523;LSEQ=CCAGACCTTGTCTCAAAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:10,7:17,9:0.3333:2,2:20.3:1:32.4:1:0.68284:1.74571:59.9:18:0.3462:0.037:0.3 1/0:14:7:5,2:3,4:7,7:0.5:2,2:29.3:1:32.6:1:0.59207:3.04:58.9:14:0.5:0:0.1 +8 101981199 . T A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTAACACCAGTGCCTTGG;RSEQ=AGGCACCCGTACTTAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:30:1:1:0:57.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 101981658 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4697;SOR=Inf;LSEQ=ATAAATATCAGTGTGCCCAG;RSEQ=CATTCAGGGCCACTGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:5,0:0:2,0:26.4:1:32.6:1:1:0:52:10:1:0:0 0/1:7:2:1,1:1,4:5,2:0.2857:2,2:33.5:1:29.5:1:1:3.16:60:4:0.3333:0:1.5 +8 102983996 . C A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCCTTCTGTTGATGGCTGA;RSEQ=ATGGCTTAATAAAAGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:3,0:19,0:19,3:0.1364:1,0:18:1:31.3:1:1:0:60:6:0.1364:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:18:1:33.5:1:1:0:60:4:1:0:0 +8 102984091 . C T 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0194;SOR=2.77091;LSEQ=GCCCACCTAACCCCAGTTAT;RSEQ=CTCCCCTTTCCCTTCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:21:20,1:62,0:62,21:0.253:1,1:21.7:1:31.5:1:0.25301:0:60:42:0.253:0:1.1 0/1:37:18:17,1:17,1:18,18:0.4865:1,1:23.9:1:30.9:1:1:1:60:36:0.4865:0:1.1 +8 102984149 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12618;SOR=Inf;LSEQ=GAAATCTGGAAAAGACATGA;RSEQ=AAAATATGTAATGACTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:232,43:275,0:0:2,0:22.7:1:32.9:1:1:0:60:54:1:0:0.1 0/1:152:2:1,1:127,23:150,2:0.0132:2,2:25.5:1:28:1:0.29174:5.42681:60:4:0.0134:0:1 +8 102984279 . A G 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0508;SOR=1.33783;LSEQ=GTATTCTCACAAAACCTCTC;RSEQ=CAGGAATCCACGGATTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:600:408:166,242:76,116:192,408:0.68:2,2:24.5:1:31.2:1:0.85846:1.05:60:80.6:0.6796:0:1.5 1/0:369:273:113,160:38,56:94,273:0.7398:2,2:23.6:1:30.1:1:0.90372:1.04:60:90:0.7377:0:1.9 +8 102984312 . G A 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0;SOR=3.9214;LSEQ=GATTCACTAGAGGTATGTGA;RSEQ=GAGGAGGAGGATGTTGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:180:53,127:93,193:286,180:0.3846:2,2:25.2:1:31.7:1:0.53857:1.1543:60:89:0.3853:0:2.3 1/0:273:194:70,124:32,45:77,194:0.7106:2,2:26.4:1:29.9:1:0.40783:1.25858:60:63.667:0.7127:0:2.4 +8 102984352 . T A 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.97943;LSEQ=AGGATGAAAACTGACATGCA;RSEQ=ATTTAAACTTCTACCTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:108:23,85:44,135:179,108:0.3763:2,2:25.4:1:31.1:1:0.56668:1.20374:60:216:0.3803:0:2.3 1/0:150:106:28,78:17,27:44,106:0.7067:2,2:20.7:1:30:1:0.17099:1.74712:60:105:0.7047:0:2.5 +8 103647027 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48986;SOR=Inf;LSEQ=GCGTTTGTAGTTCACGGGAG;RSEQ=CAGCGTTGGTGGATGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:22,0:0:2,0:29.6:1:30.5:1:1:0:60:21:1:0:0.2 0/1:24:2:1,1:11,11:22,2:0.0833:2,2:25.5:1:30:1:1:1:60:4:0.087:0:1.5 +8 103647073 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GGAGGCTATGGTCAGATCAT;RSEQ=AAAATCTTCTGAATGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:9,10:19,0:0:2,0:22.7:1:32.1:1:1:0:60:38:1:0:0.1 0/1:13:2:1,1:3,8:11,2:0.1538:2,2:26.5:1:29:0:1:2.45:60:4:0.1538:0:1.5 +8 103648670 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAGCACAGGCCTTTGAGCA;RSEQ=GGATGGCAGCCAGGACTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 103805097 . T C 87 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ACACTTTTCTATAGAAGTCA;RSEQ=TGCAGATTGAATTGTGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:39.8:1:33.7:1:1:0:60:12:1:0:1.2 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:24.5:1:33.5:1:1:0:60:4:0.6667:0:1.5 +8 103805165 . T G 107 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00591;SOR=0;LSEQ=TAACCCTCAGGATCAGAATG;RSEQ=GACCTCTTTTGGAAATAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:6,5:0,0:0,11:1:0,2:24.1:1:31.2:1:1:0:60:22:1:0:1.1 0/1:13:6:3,3:4,3:7,6:0.4615:2,2:13.3:1:29.3:1:1:1.30401:60:5:0.4167:0:1.3 +8 103805792 . A G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTGCCTGCCAGTGCCCC;RSEQ=ACAGACATCCACAGAGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:47:1:30.5:1:1:0:60:4:1:0:1.5 +8 103858199 . G T 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56452;SOR=3.06333;LSEQ=TCTATGTCTTTTTGCTTAAA;RSEQ=TCGCAGTTTCCAAGAACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:0,1:115,22:137,1:0.0072:2,0:1:0:27:0:0.16667:0:60:2:0.0073:0:1 0/1:91:2:1,1:67,22:89,2:0.022:2,2:18:1:25.5:1:0.44371:3.00065:60:4:0.022:0:1 +8 103858308 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10694;SOR=0.76747;LSEQ=TATATATGTAGTATTTAGTA;RSEQ=TTAGTTGAAAACCTTTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:147:71,76:147,143:290,147:0.3364:2,2:22.3:1:30.4:1:0.68573:1.10012:60:72.5:0.3349:0:1.1 0/1:300:84:48,36:118,98:216,84:0.28:2,2:23.5:1:30:1:0.79601:1.11:60:168:0.2819:0:1.2 +8 103858488 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27768;SOR=2.25963;LSEQ=GTACTTATAAAAACATCAGG;RSEQ=CCACTGGATCAAGTCTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:0,29:29,7:0.1944:1,0:24.7:1:31.7:1:1:0:60:14:0.1944:0:1 0/1:14:5:1,4:0,9:9,5:0.3571:0,2:11.4:1:27.4:1:0.35714:0:60:10:0.3571:0:1 +8 104028894 . TC T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.53146;SOR=0;LSEQ=TGGTTGCTGGTATGATTCCA;RSEQ=CTGCACAGCTGTTCTCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:92,32:124,2:0.0159:2,2:14:1:29:1:0.45676:2.84645:60:4:0.016:0.0079:1.5 0/0:74:0:0,0:55,19:74,0:0:2,0:20.6:1:30.2:1:1:0:60:73:1:0:0.1 +8 104028971 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5061;SOR=0;LSEQ=CCTAAGTGCTTGCCGCCACC;RSEQ=ATGGAAGATTTGACGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:74,111:185,2:0.0107:2,2:41.5:1:29:1:1:1.50:60:4:0.0108:0:1 0/0:146:0:0,0:63,83:146,0:0:2,0:25.5:1:30.8:1:1:0:59.8:145:1:0:0.1 +8 104028978 . G T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50435;SOR=0;LSEQ=GCTTGCCGCCACCCATGGAA;RSEQ=ATTTGACGGACATGGACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:2:1,1:58,111:169,2:0.0116:2,2:8:1:25.5:1:1:1.91:60:4:0.0117:0:1 0/0:139:0:0,0:57,82:139,0:0:2,0:25.2:1:30.9:1:1:0:59.8:138:1:0:0.1 +8 104029480 . C G 91 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15152;SOR=0.10236;LSEQ=ATGATGATGAAGAGGAAGAA;RSEQ=ATTTTGATGAAGGGAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:3,4:1,0:1,7:0.875:0,2:26.6:1:32.6:1:1:0:60:14:0.875:0:1 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:41:0:28:0:1:0:60:2:0.3333:0:1 +8 104029679 . T G 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AAGGACCTAGTTTTGTAGAA;RSEQ=ATATTAAAAGCAAAAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:6,3:1,0:1,9:0.9:0,2:31:1:32.7:1:1:0:59.2:18:0.9:0:1.3 1/1:9:9:4,5:0,0:0,9:1:0,2:9.8:1:31:1:1:0:60:18:1:0:1.1 +8 104088015 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12204;SOR=Inf;LSEQ=TTACCTCCTACCGTTAGCTG;RSEQ=CCACCCTCTGCATTCAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:193,78:271,0:0:2,0:22.7:1:31.4:1:1:0:60:44.167:1:0:0.1 0/1:146:2:1,1:101,43:144,2:0.0137:2,2:9.5:1:30.5:1:0.51337:2.33348:60:4:0.0139:0:1 +8 104088053 . GC G 61 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.43344;SOR=2.27073;LSEQ=GCTTGTGAAGCATTCTGGAG;RSEQ=CCCCCCGCCCCATCCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:431:3:2,1:240,185:425,3:0.007:2,2:10:1:30.8:1:1:1.54:60:6:0.0071:0.0023:0.3 0/1:255:4:2,2:143,107:250,4:0.0157:2,2:33.5:1:30.5:1:1:1.33489:60:8:0.0158:0:1 +8 104088071 . C G 178 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGCCCCCCCGCCCCATCCT;RSEQ=CACTCCCGGCTCTTCCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:0:0,0:274,226:500,0:0:2,0:25.8:1:31.5:1:1:0:60:54.556:1:0:0.6 0/1:284:50:25,25:130,102:232,50:0.1761:2,2:24.4:1:31.6:1:0.43898:1.2734:59.5:49:0.1763:0:1.9 +8 104088119 . T C 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.40405;LSEQ=CACTGGCCATATTTCTTTCC;RSEQ=AGTCTGTTCTGACAGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:479:336:153,183:63,80:143,336:0.7015:2,2:26.2:1:32:1:0.84102:1.06:60:335:0.7053:0:1.2 0/1:263:128:58,70:64,71:135,128:0.4867:2,2:24:1:31:1:0.80476:1.08756:60:256:0.4904:0:1.4 +8 104088194 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54336;SOR=0;LSEQ=TCAGCTCACCCCAGTTCTGG;RSEQ=ACCAGAGGACTGGCAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:45,146:191,2:0.0104:2,2:15.5:1:28:1:0.42082:3.22:60:4:0.0106:0:1.5 0/0:104:0:0,0:27,77:104,0:0:2,0:24.8:1:30:1:1:0:60:33.667:1:0:0.2 +8 107805509 . T C 59 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10704;SOR=8.45724;LSEQ=ACCTCTGGAGTTGGGCGACA;RSEQ=GGCTTCTCCCCTTTCTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:1,9:10,2:0.1667:2,2:10.5:1:28.5:1:0.31818:6.71:23:4:0.1667:0:1 1/0:6:4:2,2:1,1:2,4:0.6667:2,2:16:1:29.5:1:1:1:22:8:0.6667:0:1 +8 109141918 . C A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGAAAGAAAGAAAGAAAG;RSEQ=AAAGGAAGAAAGAAAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46.5:1:31.5:1:1:0:33.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 109143183 . GA G 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.16747;SOR=0.21906;LSEQ=ACACTTATTTACCAAAAAAA;RSEQ=AAAAAAAAAAGCTTCAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:9,0:3,0:3,9:0.75:0,0:30.3:1:34:1:1:0:60:18:0.75:0.0833:0 0/1:8:3:2,1:4,0:4,3:0.375:0,2:17:1:32.7:1:0.42857:0:60:6:0.375:0.125:0 +8 109143310 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22832;SOR=Inf;LSEQ=AGACGCCCCCGAGTGAATGT;RSEQ=AGGGACCACCAGGGGACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:136,23:159,0:0:2,0:23:1:31.9:1:1:0:60:52:1:0:0.2 0/1:146:2:1,1:116,28:144,2:0.0137:2,2:20:1:27:1:0.3589:4.08831:60:4:0.014:0:1 +8 109143785 . C A 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14202;SOR=Inf;LSEQ=GCAGTACATCAGAGCATCTG;RSEQ=CACCTCCCCCGTGATGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:11,51:62,0:0:2,0:24.8:1:31:1:1:0:60:30:1:0:0.1 0/1:38:2:1,1:6,30:36,2:0.0526:2,2:6:0:26.5:1:0.33855:4.71:60:4:0.0526:0:1 +8 109143994 . T C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21737;SOR=Inf;LSEQ=TCTGCCTGCGCATCTGGTGC;RSEQ=CCCCACGCCCTCCTCTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:49,34:83,0:0:2,0:24.2:1:30.6:1:1:0:60:19.75:1:0:0.2 0/1:73:2:1,1:44,27:71,2:0.0274:2,2:7:1:29.5:1:1:1.61829:60:4:0.0274:0:1 +8 109144063 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49693;SOR=Inf;LSEQ=GAAATGGCTTGTCTTCTTTC;RSEQ=AGCCAAGTACACATGTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:31,51:82,0:0:2,0:25.3:1:30.8:1:1:0:60:81:1:0:0.2 0/1:82:2:1,1:35,45:80,2:0.0244:2,2:14.5:1:27.5:1:1:1.28:60:4:0.0244:0:1 +8 109144095 . CCCAGGGGACGC T 81 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01494;SOR=0;LSEQ=CATGTACAAACTTGTCTTTG;RSEQ=CCAGTCTCAAGGTCGTCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:2,5:10,36:46,7:0.1296:2,2:19.4:1:29:1:0.64996:1.43:60:14:0.1346:0.0556:0.6 0/0:45:0:0,0:13,32:45,0:0:2,0:21.4:1:31.6:1:1:0:60:90:1:0:0.2 +8 109235569 . G A 95 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.04545;SOR=0;LSEQ=AAACACAGGTAGGACACTAA;RSEQ=TAGACCTCCAGATGAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:0,9:1:0,0:31.6:1:30.1:1:1:0:60:18:1:0:1 0/1:3:1:1,0:2,0:2,1:0.3333:0,0:12:0:30:0:1:0:60:2:0.3333:0:1 +8 109235785 . G T 235 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAATTCAGATTATTTTTATT;RSEQ=AGAAAACAAAATACTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:237:237:153,84:0,0:0,237:1:0,2:25.3:1:29.8:1:1:0:60:58.25:1:0:1.5 0/1:294:91:60,31:128,75:203,91:0.3095:2,2:25.5:1:28.9:1:0.69421:1.13:60:182:0.3095:0:1.7 +8 109235849 . T C 178 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05985;SOR=1.59897;LSEQ=TTTCTACAAGTGGAGAGTAA;RSEQ=AGGGCATTGTATTACAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:28:14,14:176,168:344,28:0.0753:2,2:22.3:1:32.3:1:1:1.04751:60:56:0.0759:0:2.5 0/1:460:53:24,29:197,208:405,53:0.1152:2,2:26:1:31.2:1:0.66394:1.14409:60:106:0.1165:0:2.5 +8 109235858 . G C 276 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00237;LSEQ=GTGGAGAGTAATAGGGCATT;RSEQ=TATTACAAATGGATTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:365:363:177,186:0,0:0,363:0.9945:0,2:25.7:1:32.5:1:1:0:60:71.6:0.9972:0:1.6 0/1:426:127:61,66:140,159:299,127:0.2981:2,2:26.1:1:30.9:1:0.83266:1.05:60:62.5:0.2955:0:1.9 +8 109235929 . G A 235 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCTCATCTCCGATAGCCTAC;RSEQ=AACACTGCTCTATCTTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:192:192:44,148:0,0:0,192:1:0,2:26.6:1:31.1:1:1:0:60:95:1:0:1.5 0/1:162:46:12,34:36,80:116,46:0.284:2,2:27.2:1:29.4:1:0.57293:1.27313:59.8:45:0.2813:0:1.5 +8 109236119 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CTTTCATTTTAAGGACAAAC;RSEQ=TATACATGATCTCTAACGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:41.3:1:32:1:1:0:60:6:1:0:1 0/0:3:0:0,0:0,3:3,0:0:0,0:22:1:32.3:1:1:0:60:6:1:0:0 +8 109735675 . ATG A 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.31728;SOR=1.67466;LSEQ=GAAATCTATTTTTCGTGTGT;RSEQ=TGTGTGTGTGTGCATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:9:9,0:49,1:50,9:0.1525:1,0:21.9:1:30.5:1:1:0:60:18:0.1552:0.0339:0.1 0/1:43:10:9,1:32,1:33,10:0.2326:1,2:20.2:1:30.2:1:0.41528:3.42527:60:20:0.2381:0.0233:0.1 +8 109735688 . TGC CAT 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.17987;SOR=Inf;LSEQ=CGTGTGTATGTGTGTGTGTG;RSEQ=ATATATATATATATGAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:65,8:73,0:0:2,0:21.4:1:30.7:1:1:0:60:146:0.9865:0:0.2 0/1:55:2:2,0:47,6:53,2:0.0364:2,0:12.5:1:30:1:1:0:60:4:0.037:0.0182:0.5 +8 109735690 . CAT C 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.68929;LSEQ=TGTGTATGTGTGTGTGTGTG;RSEQ=ATATATATATATGAATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:4:4,0:67,9:76,4:0.0494:2,0:13:1:33.8:1:1:0:58.8:8:0.0506:0.0123:0.3 0/1:58:2:2,0:50,6:56,2:0.0345:2,0:26.5:1:33.5:1:1:0:60:4:0.0351:0:0 +8 109735723 . T C 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.134;LSEQ=ATGAATATGTTTCACTAAAA;RSEQ=AGGCAAGGCAGCAATCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:34:28,6:92,23:115,34:0.2282:2,2:21.6:1:33:1:1:1.17:59.9:68:0.2313:0:1 0/1:132:5:3,2:96,31:127,5:0.0379:2,2:25.6:1:31:1:0.59839:2.05154:58.8:10:0.0382:0:1 +8 109735830 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11215;SOR=1.36281;LSEQ=TCAACTATAAATGGCTTTCA;RSEQ=GGAAACAAGTCCAAATAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:64:30,34:178,178:356,64:0.1524:2,2:23.5:1:30.6:1:0.68504:1.13299:60:63:0.1518:0:1.1 0/1:381:75:40,35:158,148:306,75:0.1969:2,2:25.1:1:29.5:1:0.79819:1.07:60:74:0.1963:0:1.1 +8 110539105 . GGCA G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=6.000;MSILEN=3;SSF=0.49206;SOR=0;LSEQ=CAGAGTCTGTCTCTAGCAGT;RSEQ=GCAGCAGCAGCAGCAACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:18,2:0.1:2,2:33.5:1:33:1:1:1.23603:60:4:0.1:0:0 0/0:16:0:0,0:10,5:15,0:0:2,0:25.9:1:32:1:1:0:60:30:0.9375:0:0.3 +8 110595268 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50046;SOR=Inf;LSEQ=CTATGGTACTGGGTTATGCA;RSEQ=CCCTAGCAGACTAATATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:18,2:20,0:0:2,0:21.3:1:33.9:1:1:0:60:40:1:0:0.1 0/1:27:2:1,1:20,5:25,2:0.0741:2,2:22.5:1:30:1:0.40171:3.74166:60:4:0.08:0:1 +8 110595321 . CCAG C 65 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=1.50228;LSEQ=GATTACCATCATAACCACCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:36,22:58,2:0.0333:2,2:18.5:1:31:1:1:1.62241:60:4:0.0333:0:0 0/1:81:4:2,2:43,34:77,4:0.0494:2,2:32.5:1:32.8:1:1:1.26101:60:8:0.0506:0:0.5 +8 111298431 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19557;SOR=Inf;LSEQ=ACTTTCATTTCTTTATTTTA;RSEQ=TTTTGGTTTTAAAACTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:161,49:210,0:0:2,0:22.6:1:32.7:1:1:0:60:69:1:0:0.1 0/1:167:2:1,1:126,39:165,2:0.012:2,2:13:1:28.5:1:0.42277:3.20275:60:4:0.012:0:1 +8 111298543 . G A 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.96152;LSEQ=TGGTTTATTGACTCCACCGA;RSEQ=TGAAATAGTGTCTATGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:282:132,150:139,151:290,282:0.4921:2,2:25.5:1:30.6:1:0.80208:1.046:59.9:140:0.4912:0:1.1 1/0:592:388:180,208:100,104:204,388:0.6554:2,2:26.9:1:29.5:1:0.54577:1.11091:60:63.667:0.6552:0:1.1 +8 115984457 . T C 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TCGAGTGTTGATGGTTTTTA;RSEQ=AAAAGGTAGTGACGAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:30:1:34:0:1:0:60:6:0.75:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:39:1:32.8:1:1:0:60:8:1:0:0 +8 115984546 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.13986;SOR=Inf;LSEQ=GATGCTTTCGTGTTGTTGTT;RSEQ=TTATTGTTGTTGTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:21,20:41,0:0:2,0:26.4:1:32.3:1:1:0:60:82:1:0:0.1 0/1:25:2:1,1:12,11:23,2:0.08:2,2:40.5:1:29:1:1:1.0871:60:4:0.08:0:1.5 +8 115984574 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=0.17306;SOR=Inf;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGTTGCTGTTATTTTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:17,23:40,0:0:2,0:27.4:1:33:1:1:0:60:80:1:0:0.1 0/1:29:2:1,1:14,13:27,2:0.069:2,2:19:0:31:0:1:1.07415:27:4:0.069:0:1 +8 117352461 . G A 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06769;SOR=0;LSEQ=GCGCTCTTGGCATGGATAGG;RSEQ=CCCTCGGTGTTCACATCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:4,5:7,7:14,9:0.3913:2,2:34:1:30.1:1:1:1.23792:60:18:0.4091:0:1 0/0:8:0:0,0:3,5:8,0:0:2,0:22.3:1:31.1:1:1:0:60:16:1:0:0.3 +8 117860152 . T C 128 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06702;SOR=0.14596;LSEQ=CTGTGGCAATCAGTGAATTC;RSEQ=TGCTCGTTAGTTAACACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:15:1,14:0,19:19,15:0.4412:1,1:24.7:1:32.9:1:0.44118:0:60:30:0.4545:0:1.4 0/1:10:1:0,1:0,9:9,1:0.1:0,0:35:0:33:0:1:0:60:2:0.1:0:1 +8 117861000 . TA T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.43115;SOR=0.53286;LSEQ=AATTAAAACTTAAACTATAA;RSEQ=AAAAAAAAAAAGAAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:18:16,2:69,2:71,18:0.1957:1,2:24.2:1:30:1:0.1807:4.21741:58.1:17:0.1889:0.0435:0.7 0/1:35:4:4,0:28,3:31,4:0.1143:2,0:20.3:1:31.3:1:1:0:60:8:0.1212:0.0571:0 +8 117861112 . C CT 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.24445;SOR=0.74042;LSEQ=TTTCTGTTTCCAGCATCTAA;RSEQ=TTTTTTTTTTTCAGGGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:61:56,5:419,77:496,61:0.1087:2,2:29.7:1:32.3:1:0.17801:2.06:59.6:122:0.1117:0.0018:0.5 0/1:326:27:22,5:238,58:296,27:0.0828:2,2:29:1:30:1:1:1.07:59.1:54:0.0852:0:0.4 +8 117861516 . T C 127 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19868;SOR=0.1743;LSEQ=GCTGAAAGTATGCTTCTATA;RSEQ=TGCGCTATAAGGATGCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:0,14:0,14:14,14:0.5:1,1:21.4:1:33.6:1:1:0:60:28:0.5:0:1.1 0/1:7:1:0,1:1,5:6,1:0.1429:2,0:11:0:33:0:1:0:60:2:0.1667:0:1 +8 117862569 . T C 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGTCCACTGACCACAAGA;RSEQ=AGTAAAAGCAGCTACACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:17,2:0.1053:1,0:32:1:32:1:1:0:46:4:0.1111:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 117863365 . A AAAT 48 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=3.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTTGAATGTCTCACGGCAGC;RSEQ=AATAATAGGAGTGAGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:1,2:3,3:0.5:2,0:21.7:1:30.3:1:1:0:60:6:0.5:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 117864217 . A G 300 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.32659;LSEQ=GGCTCTGGGTCAATTTGTCC;RSEQ=GCTTTTCGCTTAACTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2456:929:473,456:764,760:1524,929:0.3783:2,2:25.6:1:30.5:1:0.70816:1.03:50.8:60.933:0.378:0:1.1 0/1:1762:292:145,147:761,705:1466,292:0.1657:2,2:27.1:1:29.7:1:0.52148:1.09426:49.6:145:0.1662:0:1.1 +8 117864369 . C G 210 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TATGAAGAGAAAACATAGGT;RSEQ=ATACAGTTTTGAACAGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:772:93:16,77:161,518:679,93:0.1205:2,2:25.9:1:32.2:1:0.18871:1.49508:60:45.5:0.1186:0:1.1 0/0:480:0:0,0:121,358:479,0:0:2,0:24.8:1:31.2:1:1:0:60:94.8:0.9979:0:0.2 +8 117864436 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.075;SOR=Inf;LSEQ=TACACTAAGACATACATAAT;RSEQ=CTTTCTTTAATGAAGAAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:18,214:232,0:0:2,0:23.9:1:32.4:1:1:0:59.8:37.667:1:0:0.1 0/1:88:2:0,2:0,86:86,2:0.0227:1,0:14:1:30:0:1:0:60:4:0.0227:0:1 +8 117866426 . CT C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.05908;SOR=0.6086;LSEQ=TGATTCAAAGGTTTTAGAAT;RSEQ=TTTTTTTTTAGATGCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:725:63:55,8:554,104:658,63:0.0869:2,2:20.1:1:31.7:1:0.58952:1.29:60:126:0.0873:0.0207:0.1 0/1:402:22:18,4:316,62:378,22:0.0547:2,2:25:1:30.5:1:0.77045:1.13228:60:44:0.0547:0.01:0.2 +8 117866817 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08039;SOR=Inf;LSEQ=CTTTTCTACACACAGACTCT;RSEQ=GCAGAGAAGTTAAACTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:4,255:259,0:0:1,0:24.5:1:32.3:1:1:0:60:63.75:1:0:0.1 0/1:103:2:0,2:1,100:101,2:0.0194:1,0:16.5:1:31:1:1:0:60:4:0.02:0:1 +8 117868278 . C CA 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0719;SOR=7.68354;LSEQ=TAGCAGATCAGTAGACAGGC;RSEQ=AAAAAAACAGAAAAAAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:1:1,0:198,6:204,1:0.0049:1,0:13:0:26:0:1:0:60:2:0.005:0:0 0/1:82:3:3,0:71,8:79,3:0.0366:2,0:13.7:1:29:1:1:0:60:6:0.037:0.0122:0.7 +8 117868529 . T A 78 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03408;SOR=0.14577;LSEQ=GGACTATCAGGCCCACCCAC;RSEQ=GTAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:907:10:7,3:300,581:881,10:0.011:2,2:6.3:1:23.7:1:0.0374:4.51:55.5:2.333:0.0092:0:1.7 0/0:617:1:0,1:227,380:607,1:0.0016:2,0:26:0:20:0:1:0:33:2:0.0019:0:6 +8 117868559 . C A 50 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.19156;LSEQ=AAAAAAAAAAAAAAAAGTCA;RSEQ=AAAAAGCTTTGGTATATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:5:5,0:9,357:366,5:0.0134:1,0:6.4:1:21.6:1:0:0:43:1.5:0.0082:0:3 0/1:251:4:4,0:2,244:246,4:0.0159:1,0:14.3:1:13:1:0:0:46.3:0:0:0:3.3 +8 117868703 . CA C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.06471;SOR=Inf;LSEQ=CAGACTTGAACCCAATTGGC;RSEQ=AAAAAATGGGGAGGGGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:29,34:63,0:0:2,0:28.8:1:30.6:1:1:0:59.6:62:1:0:0.2 0/1:22:2:2,0:11,9:20,2:0.0909:2,0:35:1:31:0:0.49351:0:60:4:0.0952:0:0 +8 117868714 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.06053;SOR=Inf;LSEQ=CCAATTGGCCAAAAAAATGG;RSEQ=GAGGGGTGCAAGATTAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:42,30:72,0:0:2,0:27.3:1:31.7:1:1:0:59.6:144:1:0:0.2 0/1:24:2:1,1:15,7:22,2:0.0833:2,2:34:1:27.5:1:1:2.07024:60:4:0.0833:0:1 +8 117869181 . T TA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTATAAAACACTTGGTATA;RSEQ=AAAAAAAAATTCTCATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:0,2:18,71:89,2:0.022:2,0:18:1:30:1:1:0:60:4:0.023:0:0 0/0:38:0:0,0:3,35:38,0:0:2,0:25:1:28.6:1:1:0:60:76:1:0:0 +8 117869241 . AT A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.0669;SOR=0.27924;LSEQ=ATTTATCTATTTTAAAAAAT;RSEQ=TTTACTTAACACAGCTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:47:24,23:7,4:11,47:0.8103:2,2:22.7:1:31.1:1:0.51805:1.66239:58.7:94:0.8103:0.1724:0.3 1/0:13:7:3,4:2,4:6,7:0.5385:2,2:20.4:1:31.1:1:1:1.45:60:14:0.5385:0.0769:0 +8 117869460 . A G 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=1.66935;LSEQ=TTCCAAAACTTTACAACTTA;RSEQ=TAAAGAAATTCTGTTTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1027:246:160,86:533,247:780,246:0.2395:2,2:25:1:33.1:1:0.34916:1.15969:60:245:0.2409:0:1.1 0/1:676:233:155,78:295,146:441,233:0.3447:2,2:22.4:1:31.4:1:0.93166:1.01677:60:466:0.3493:0:1.1 +8 117869851 . AAACTTT A 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATGTTAAAATATCTAGTTT;RSEQ=AATTCTTTAGCATCTGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:0,156:156,0:0:1,0:21.1:1:31.9:1:1:0:60:312:1:0:0 0/1:58:15:0,15:0,43:43,15:0.2586:1,1:22.7:1:29.9:1:1:0:57.5:30:0.2586:0.0517:0.1 +8 117870036 . TATA T 108 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACAGCTGAAACTTTCCCGT;RSEQ=ATGTGTTTCATCAAGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1:0,2:27.5:1:32.6:1:1:0:57.1:20:1:0.2:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 117870196 . A C 85 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGCCACGGCACTCCAGC;RSEQ=TGGATAACACAGCAGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:5,4:1,1:2,9:0.8182:2,2:27.6:1:27:1:1:1.22:57.7:3.5:0.7778:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 117870375 . A G 155 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17035;SOR=0.19298;LSEQ=GAAATCAATATATAGGTTCT;RSEQ=TGATTGCATATAGGGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:28:27,1:20,1:21,28:0.5714:1,1:21.4:1:32.4:1:1:1.34:60:56:0.5833:0:1.1 0/1:5:1:1,0:4,0:4,1:0.2:0,0:28:0:33:0:1:0:60:2:0.2:0:1 +8 117870446 . T A 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31433;SOR=0;LSEQ=AATAATGCTTAATCTACTGG;RSEQ=AGAAAGCCAAATTCTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:4:4,0:136,4:140,4:0.0278:1,0:26.5:1:30:1:1:0:60:8:0.0278:0:1 0/0:64:0:0,0:64,0:64,0:0:1,0:22.8:1:30:1:1:0:59.7:128:1:0:0 +8 117874055 . A AT 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01367;SOR=0;LSEQ=TATTGCAGACCAAGTCAACA;RSEQ=TTTTTTTTAAAAGAAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:896:9:5,4:634,253:887,9:0.01:2,2:19.2:1:29.8:1:0.2869:2.00308:59:18:0.0102:0.0045:0.4 0/0:596:0:0,0:400,195:595,0:0:2,0:24.1:1:29.2:1:1:0:59.9:58.5:0.9983:0:0.1 +8 117878493 . G GT 49 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=0.46429;SOR=0;LSEQ=TTTACAGCACTTCCACGTCG;RSEQ=TTTTTTTTTTTTTTGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,0:2,3:0.5:0,0:32.7:1:31:1:1:0:46.7:6:0.6:0.1667:2.7 0/0:2:0:0,0:1,0:1,0:0:0,0:15:0:13:0:1:0:60:0:0:0:0 +8 117878691 . C T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.88357;SOR=1.06806;LSEQ=TAGAGGTGATAAGGACTTCA;RSEQ=ATAATAAAGAAACATTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:54:54,0:151,2:153,54:0.2609:1,1:26.3:1:31.9:1:1:0:59.4:108:0.2609:0:1 0/1:84:23:22,1:59,2:61,23:0.2738:1,1:19.8:1:30.3:1:1:1.33596:59.2:46:0.2771:0:1 +8 117879010 . G GA 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03688;SOR=7.82448;LSEQ=CAGAAGAAAACCTAAGAGGG;RSEQ=AAAAAAAAGTTAATGTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:1:0,1:169,583:752,1:0.0013:2,0:16:0:33:0:1:0:60:2:0.0013:0:0 0/1:486:5:2,3:135,346:481,5:0.0103:2,2:8.6:1:28.9:1:0.62392:1.71:60:10:0.0105:0.0062:1.2 +8 117879369 . G C 50 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTATGAAGAAAGATACTCAG;RSEQ=CACAGATAAAAATCTGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:0,3:0,1:1,3:0.75:0,0:18.3:1:32:1:1:0:60:6:0.75:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:39:0:33:0:1:0:60:2:1:0:1 +8 120071761 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1605;SOR=Inf;LSEQ=AATGAACCATTAATGTGAGA;RSEQ=TGTATTTCTGGGCTTACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:87,8:95,0:0:2,0:23.4:1:30.2:1:1:0:60:46.5:1:0:0 0/1:64:2:1,1:52,9:61,2:0.0313:2,2:13:1:28:1:0.29442:5.5338:60:4:0.0313:0:1 +8 120071898 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=2.41248;LSEQ=GCTGATAAAACTGCAATTCT;RSEQ=ACCAACTGCCATGAGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:102:50,52:190,177:367,102:0.2175:2,2:25.8:1:29.4:1:0.65511:1.11612:59.9:101:0.2167:0:1.7 0/1:366:147:70,77:105,113:218,147:0.4016:2,2:28.8:1:28.8:1:1:1.02207:60:146:0.4056:0:1.7 +8 120071906 . G A 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03836;SOR=Inf;LSEQ=AACTGCAATTCTCACCAACT;RSEQ=CCATGAGGAGAGAGGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:0:0,0:230,248:478,0:0:2,0:25:1:32.1:1:1:0:59.9:78.667:1:0:0.5 0/1:381:4:2,2:176,201:377,4:0.0105:2,2:24.3:1:25.8:1:1:1.14:60:3:0.0079:0:3.3 +8 120071939 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=1.8884;LSEQ=AGGTGGAGTTTTTTCCATAC;RSEQ=TGAAGGCCTCATACTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:92:35,57:130,183:313,92:0.2272:2,2:26.6:1:31.4:1:0.62948:1.15649:60:184:0.23:0:1.8 0/1:308:110:39,71:85,113:198,110:0.3571:2,2:24.3:1:30.3:1:0.22598:1.36801:60:54:0.3541:0:2 +8 120072087 . C T 54 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15521;SOR=4.96976;LSEQ=TACTCAATCCATTCATGTAT;RSEQ=AAAATTGCAAATGTACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:0,2:0,26:26,2:0.0714:1,0:31:1:29:1:1:0:60:4:0.0714:0:1.5 0/1:14:4:0,4:0,10:10,4:0.2857:0,0:7.5:1:27.3:1:1:0:60:8:0.2857:0:2.3 +8 120072214 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCTGACTTCTTCACATAG;RSEQ=CATGGCTGAAACTTCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:0,6:6,2:0.25:0,0:28:1:33:0:1:0:60:4:0.25:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:22:0:31:0:1:0:60:2:1:0:0 +8 120428447 . G A 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00191;SOR=0.03302;LSEQ=GAGCCCTGGGTCCTGGCCTC;RSEQ=GAACTCCACCCAGCCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:6,2:1,0:1,8:0.8889:0,2:19.5:1:30.1:1:1:0:60:16:1:0:1.1 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:22.5:1:30:1:1:1.4491:60:4:0.1667:0:1 +8 120994394 . A G 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.50459;LSEQ=AGGGAGAGATTGGTTTCTAC;RSEQ=TATTTATTACTTTCACTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:306:83:42,41:100,122:222,83:0.2712:2,2:23.6:1:31.3:1:0.43943:1.25:60:166:0.2767:0:1.1 0/1:176:85:45,40:41,49:90,85:0.483:2,2:26.2:1:30.4:1:0.36574:1.34:60:170:0.4857:0:1.1 +8 121504119 . A G 305 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.3405;LSEQ=AGGAGAAGACTTAACCCCAA;RSEQ=AGGGCCATCCCTCCTGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:861:666:356,310:111,82:193,666:0.7735:2,2:27.7:1:32.6:1:0.32602:1.17852:59.9:54.5:0.7767:0:1.2 1/0:454:244:120,124:104,106:210,244:0.5374:2,2:26.1:1:30.8:1:1:1.01381:60:80.333:0.5367:0:1.1 +8 121504249 . TA T 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.29224;SOR=2.76766;LSEQ=GAGTACAGAAATGCTAAAAA;RSEQ=AAAAAAATTAAAAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:0,2:10,167:177,2:0.0111:2,0:22.5:1:33:0:1:0:60:4:0.0112:0:0 0/1:66:2:0,2:5,59:64,2:0.0303:2,0:19.5:1:32:0:1:0:60:4:0.0303:0:0 +8 121519850 . T TG 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58426;SOR=0.46721;LSEQ=GCTTAATCGGAATTATACTG;RSEQ=ATAAATATTGCCTTTAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:22:22,0:5,0:5,22:0.8148:0,1:27.9:1:33.3:1:1:0:60:44:0.8148:0.1481:0 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:15.8:1:30.8:1:1:0:60:8:0.6667:0.1667:0 +8 121520055 . CT TG 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.61328;SOR=1.87944;LSEQ=GAGTAATTTTTTTCCCATAA;RSEQ=TTGAAAGATTGATAACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:352:2:0,2:181,169:350,2:0.0057:2,0:2.1:1:27.2:1:0.23529:0:60:4:0.0041:0.0074:0 0/1:188:2:1,1:91,95:186,2:0.0106:2,2:24.5:1:29.8:1:1:1.04:60:4:0.0109:0:1 +8 121520056 . T G 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25557;LSEQ=AGTAATTTTTTTCCCATAAC;RSEQ=TTGAAAGATTGATAACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:355:295:154,141:33,27:60,295:0.831:2,2:26.6:1:31:1:0.77701:1.11869:59.9:97.333:0.8319:0:1.1 1/0:187:104:52,52:37,43:80,104:0.5561:2,2:25.2:1:29.8:1:0.65679:1.16:60:103:0.5659:0:1.1 +8 121520095 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09777;SOR=Inf;LSEQ=TTTGTTGTGGGAATCAAGAA;RSEQ=GTAAAGAAATATACATGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:149,195:344,0:0:2,0:26.2:1:31.1:1:1:0:60:67.8:1:0:0.7 0/1:157:2:1,1:60,95:155,2:0.0127:2,2:25.5:1:29.5:1:1:1.58:60:4:0.0128:0:1.5 +8 121520098 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09762;SOR=Inf;LSEQ=GTTGTGGGAATCAAGAAAGT;RSEQ=AAGAAATATACATGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:0:0,0:147,193:340,0:0:2,0:25.5:1:29.7:1:1:0:60:112.333:1:0:0.7 0/1:155:2:1,1:58,95:153,2:0.0129:2,2:16:0:33:1:1:1.63:60:4:0.0131:0:2.5 +8 121520223 . T TG 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.36194;SOR=0.42316;LSEQ=TATGTAAGTTGTACTCTTTT;RSEQ=ACAGAATGTCTTTCTAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:29:1,28:0,9:9,29:0.7632:0,1:25.6:1:32.2:1:1:0:60:58:0.7838:0.2105:0 1/0:7:4:0,4:0,3:3,4:0.5714:0,0:11.3:1:29.8:1:1:0:60:8:0.5714:0.2857:0.3 +8 121520238 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00605;SOR=Inf;LSEQ=CTTTTTACAGAATGTCTTTC;RSEQ=AGATGCATTGTAGGGGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:1,28:29,0:0:1,0:29.8:1:29.3:1:1:0:60:58:1:0:0.1 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:32:1:31.5:1:1:0:60:4:0.6667:0:1 +8 124660447 . A C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCATCTTTCAGTTTAGA;RSEQ=CATTGAGGCTCTGAGAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:31.5:1:1:0:60:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 124664130 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGTGACTGACCAGACTC;RSEQ=TCCCTGAGCTGACAGCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:28.5:1:1:0:60:4:1:0:2 +8 125184039 . A T 28 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACTAAGGTGCAGGGTAAA;RSEQ=GCCCCTGAGAGTAATAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:19.5:1:30.5:1:1:0:60:4:1:0:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:31:1:28.5:1:1:0:60:4:0.6667:0:3 +8 125184142 . A G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05257;SOR=0.09003;LSEQ=AATCCAGGAGTGGCCAACCC;RSEQ=GAGATTCATTCCTTGTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:12,5:1,0:1,17:0.9444:0,2:22.6:1:31.1:1:1:0:55.3:34:0.9444:0:1 1/0:7:4:3,1:2,1:3,4:0.5714:2,2:33.3:1:28.3:1:1:1.41:60:8:0.5714:0:1.3 +8 125184178 . C CCCCGT 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=6.000;MSILEN=5;SSF=0.53347;SOR=0.59903;LSEQ=TTTATGAGAAACATCTGAGT;RSEQ=CCCGTCCCGTCCCGTCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:19:10,9:7,2:9,19:0.6786:2,2:31.8:1:31:1:0.2495:3.02717:55.8:38:0.6786:0.1071:0.7 1/0:18:10:4,6:2,1:3,10:0.5556:2,2:20.2:1:31:1:0.55944:2.75172:55.2:20:0.5882:0.0556:0.4 +8 125184316 . C A 109 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23077;SOR=0;LSEQ=TGGAGGTCGTTAAGGGGAAG;RSEQ=TGTTAACTGAAAATGCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:23.8:1:33:1:1:0:60:20:1:0:1.3 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25:1:28.5:1:1:0:60:4:0.6667:0:1 +8 125313532 . A T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01893;SOR=Inf;LSEQ=TGATATAGGTCTGATGGACA;RSEQ=GATGTGTCATGTGGCAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:160,24:184,0:0:2,0:25.1:1:30.2:1:1:0:59.9:35.8:1:0:0.1 0/1:110:4:4,0:90,16:106,4:0.0364:2,0:24.8:1:30.5:1:1:0:60:8:0.0364:0:1.3 +8 125313560 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06711;SOR=Inf;LSEQ=CATGTGGCAACTTAAAAGTT;RSEQ=GCTCAACAGGGTCGGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:0:0,0:200,79:279,0:0:2,0:25.6:1:31.5:1:1:0:59.8:38.857:1:0:0.1 0/1:192:3:1,2:136,53:189,3:0.0156:2,2:19.7:1:27.7:1:0.19778:5.08135:60:6:0.0158:0:1 +8 125313780 . T C 318 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.37264;LSEQ=CAGTACAACTCCATGACCAG;RSEQ=TCGCAGACCTGCGAGAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:897:861:490,371:21,15:36,861:0.9599:2,2:26.4:1:32.7:1:1:1.05994:53.5:85.1:0.9616:0:1.1 1/1:525:472:262,210:28,20:48,472:0.899:2,2:25.8:1:31.3:1:0.7617:1.12187:52.5:156.333:0.9019:0:1.2 +8 125314015 . G A 94 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00214;SOR=13.04142;LSEQ=GCAGCCCGGTGCCCGCCACG;RSEQ=CCATTAACGACACACTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:1:1,0:119,272:391,1:0.0026:2,0:1:0:26:0:0.30612:0:60:2:0.0026:0:1 0/1:278:9:2,7:99,170:269,9:0.0324:2,2:19.9:1:29.8:1:0.49468:2.0336:60:18:0.033:0:1.4 +8 125873537 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAAGCAGGAAGGACTGGA;RSEQ=CAGATCCTTTCCTCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:33.5:1:1:0:49:4:1:0:1.5 +8 125874959 . T C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=4.42804;LSEQ=GAGGTAAAGTCTGTATTTAC;RSEQ=AATGGTTAGAGACATGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1033:162:71,91:409,461:870,162:0.1568:2,2:27.2:1:31.6:1:0.49284:1.13698:60:53:0.1557:0:1.1 0/1:582:263:119,144:146,173:319,263:0.4519:2,2:25.3:1:30.7:1:0.93343:1.0212:60:86.667:0.4514:0:1.1 +8 125875063 . G A 183 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AAGACCCAAATACTAGTAAT;RSEQ=AGATGCCAAAGTGAACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:60:11,49:39,190:229,60:0.2076:2,2:21:1:31.1:1:0.84836:1.09:60:120:0.2091:0:1.1 0/0:121:0:0,0:22,99:121,0:0:2,0:22.7:1:30.4:1:1:0:60:120:1:0:0 +8 125875306 . A C 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACATTTCTTCAAACTTT;RSEQ=TTGCTCAGAACGTCAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:26.3:1:32.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 126458554 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49949;SOR=0;LSEQ=CCAACCAGTTCCTGGGTGAG;RSEQ=CCGATGCTGCTGGCGTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:19,28:47,2:0.0408:2,2:29.5:1:29.5:1:1:1.46:60:4:0.0426:0:1.5 0/0:40:0:0,0:20,20:40,0:0:2,0:25:1:29.8:1:1:0:60:39:1:0:0.1 +8 128306327 . C A 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=ACCCAGAGTGACTTCCCATT;RSEQ=CTCATTGTCTCTTGCAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:35:1:29.5:1:1:0:60:4:0.6667:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:23.3:1:29.5:1:1:0:60:8:1:0:0 +8 128306459 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13725;SOR=Inf;LSEQ=TCACTGCTATTTGTGCAGTT;RSEQ=CCATGTGCCAGTGAATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:6,5:11,0:0:2,0:25.1:1:32.3:1:1:0:60:22:1:0:0.1 0/1:7:2:1,1:1,4:5,2:0.2857:2,2:36.5:1:27.5:1:1:3.16:60:4:0.2857:0:1 +8 128343601 . G GT 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTAGAGCAAGAACTTTTA;RSEQ=TTTTTTGAGAAAGGCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:4:4,0:22,1:23,4:0.1481:1,0:23.5:1:31:1:1:0:60:8:0.1481:0.037:0 0/0:2:0:0,0:2,0:2,0:0:0,0:25.5:1:33.5:1:1:0:60:4:1:0:0.5 +8 128343879 . G A 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.39688;LSEQ=CTAATTGTAAGTAATTCCAT;RSEQ=TATTTGTAGAATGCTTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:158:67,91:344,445:789,158:0.1667:2,2:26.4:1:30:1:0.79271:1.0499:60:316:0.1683:0:1.1 0/1:546:221:96,125:151,174:325,221:0.4048:2,2:25.5:1:28.7:1:0.53986:1.12971:60:109.5:0.4086:0:1.1 +8 128343948 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00917;SOR=0.6025;LSEQ=ACATGTACTATTATACAATA;RSEQ=GCAAAATAATTTTAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:338:211:41,170:33,94:127,211:0.6243:2,2:22.5:1:30.3:1:0.17536:1.45392:60:69.333:0.6209:0:1 1/0:164:82:19,63:15,65:80,82:0.5:2,2:25.1:1:29.9:1:0.56444:1.30:60:164:0.5031:0:1.1 +8 128343983 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGATATATTGACTATT;RSEQ=CACCCAAGACTTATATCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:18,149:167,2:0.0118:2,2:25:1:32:1:0.21281:8.08:60:4:0.012:0:2 0/0:77:0:0,0:6,71:77,0:0:2,0:25.4:1:28.7:1:1:0:60:76:1:0:0.6 +8 128747953 . G T 174 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGGGCGCGCAGTGCGTTCTC;RSEQ=GTGTGGAGGGCAGCTGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:43:40,3:237,46:283,43:0.1319:2,2:28:1:32.1:1:0.16671:2.58:59.1:42:0.1304:0:1 0/0:181:0:0,0:142,39:181,0:0:2,0:24.2:1:29.2:1:1:0:60:44.25:1:0:0.1 +8 128748494 . C G 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAACTCGCTGTAGTAATT;RSEQ=CAGCGAGAGGCAGAGGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:14,1:15,3:0.1667:1,2:42.3:1:34.3:1:0.05637:19.04025:55.3:6:0.1667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:32:0:1:0:43:2:1:0:0 +8 128748671 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAACCCTTGCCGCATCCAC;RSEQ=AAACTTTGCCCATAGCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:125,4:129,2:0.0153:1,2:25:1:28.5:1:0.07516:28.06607:60:4:0.0157:0:1 0/0:39:0:0,0:36,3:39,0:0:2,0:23.1:1:29.7:1:1:0:60:78:1:0:0.1 +8 128749165 . A C 32 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.59965;SOR=2.28617;LSEQ=GCTGACTCCCGGCCGGTCGG;RSEQ=CATTCCTGCTTTATTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:1:0,1:19,26:45,1:0.0217:2,0:47:0:13:0:1:0:60:0:0:0:2 0/1:41:2:1,1:18,21:39,2:0.0488:2,2:5:0:32:1:1:1.16:60:4:0.0488:0:0 +8 128750212 . C T 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=TTCCTCTGCCGCTGCGGGGC;RSEQ=GACTCCCGGGCTTTGCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:38.5:1:33.8:1:1:0:53:8:0.6667:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:34:0:27:0:1:0:33:2:1:0:0 +8 128750260 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGGGGGAGCGGGGGCTCGG;RSEQ=GGGCACCAAGCCGCTGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:2,0:10,0:10,2:0.1667:0,0:24.5:1:32:0:1:0:60:4:0.1667:0:1 0/0:5:0:0,0:5,0:5,0:0:0,0:20.2:1:32.6:1:1:0:56.8:10:1:0:0 +8 128750413 . C G 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.00044;SOR=0.3786;LSEQ=AGAGGTTCGGGACTGTGGCG;RSEQ=GCACTGCGCGCTGCGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:90:89,1:156,5:161,90:0.3586:1,1:23.7:1:31.5:1:0.42452:2.84:59.3:44:0.3592:0:1.1 0/1:109:19:19,0:87,3:90,19:0.1743:1,1:19.9:1:30.8:1:1:0:60:38:0.1792:0:1.1 +8 128750439 . G T 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11194;SOR=Inf;LSEQ=GCGCGCTGCGCCAGGTTTCC;RSEQ=CACCAAGACCCCTTTAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:333,21:354,0:0:2,0:24.4:1:30.1:1:1:0:59.7:49.571:0.9971:0:0.3 0/1:179:2:1,1:153,24:177,2:0.0112:2,2:13:0:27.5:1:0.2605:6.26659:60:4:0.0116:0:1 +8 128750604 . CCAG C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.87633;SOR=1.08282;LSEQ=GACGAGGAGGAGAACTTCTA;RSEQ=CAGCAGCAGCAGAGCGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1526:26:13,13:718,778:1496,26:0.017:2,2:26.8:1:31.8:1:0.84613:1.08:60:52:0.0172:0.0013:0.1 0/1:977:18:9,9:465,489:954,18:0.0184:2,2:30.9:1:32:1:1:1.05:60:36:0.0187:0:0.2 +8 128751016 . G A 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=58.52799;LSEQ=ACCCCGCCCGCGGCCACAGC;RSEQ=TCTGCTCCACCTCCAGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:882:1:1,0:469,412:881,1:0.0011:2,0:14:0:20:0:1:0:60:2:0.0012:0:1 0/1:465:29:18,11:220,216:436,29:0.0624:2,2:18.9:1:28.8:1:0.25365:1.60:60:28:0.0614:0:1.3 +8 128751201 . G A 197 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03363;LSEQ=TCCTCGACGGAGTCCTCCCC;RSEQ=CAGGGCAGCCCCGAGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:108:37,71:221,374:595,108:0.1534:2,2:26.9:1:29.3:1:0.58932:1.13367:60:53:0.153:0:1.1 0/0:496:3:3,0:185,308:493,3:0.006:2,0:13.7:1:21.7:1:0.05391:0:60:2:0.0041:0:1 +8 128751278 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12094;SOR=Inf;LSEQ=CGACTCTGGTAAGCGAAGCC;RSEQ=GCCCAGGCCTGTCAAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:0:0,0:31,209:240,0:0:2,0:23.5:1:30.1:1:1:0:60:47:0.9958:0:0.2 0/1:129:2:1,1:26,101:127,2:0.0155:2,2:30.5:1:30.5:1:0.37609:3.83:60:4:0.0159:0:1.5 +8 128751285 . G C 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0393;SOR=Inf;LSEQ=GGTAAGCGAAGCCCGCCCAG;RSEQ=CCTGTCAAAAGTGGGCGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:19,178:197,0:0:2,0:25.5:1:32.4:1:1:0:60:97.5:0.9949:0:0.1 0/1:103:3:1,2:18,81:99,3:0.0291:2,2:18.7:1:25.7:1:0.46487:2.23:58.7:2:0.0196:0:0.7 +8 128752552 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11911;SOR=Inf;LSEQ=AGAGACCTTTCTAACGTATT;RSEQ=ATGCCTTGTATTTGTACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:185:0:0,0:173,12:185,0:0:2,0:22.7:1:32.4:1:1:0:60:91.5:1:0:0.1 0/1:98:2:1,1:87,9:96,2:0.0204:2,2:13.5:1:30:1:0.19461:9.22316:60:4:0.0208:0:1 +8 128752745 . C A 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TCACCTTCTGCTGGAGGCCA;RSEQ=AGCAAACCTCCTCACAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:852:0:0,0:386,466:852,0:0:2,0:25.1:1:32.2:1:1:0:60:105.5:1:0:0.1 0/1:542:16:8,8:234,291:525,16:0.0295:2,2:21.6:1:29.2:1:0.7998:1.24:60:32:0.0297:0:1.1 +8 128753298 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09683;SOR=Inf;LSEQ=TGATCAAATGCAACCTCACA;RSEQ=CCTTGGCTGAGTCTTGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:0,82:82,0:0:1,0:24.8:1:29.2:1:1:0:60:26.333:1:0:0 0/1:38:2:0,2:2,34:36,2:0.0526:2,0:40:1:33.5:1:1:0:60:4:0.0556:0:1 +8 128755075 . A C 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTGATTATATAGGTAAATG;RSEQ=AGGATGCTATTGCTGTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:972:0:0,0:645,327:972,0:0:2,0:23.8:1:30.3:1:1:0:60:68.429:1:0:0.2 0/1:597:23:16,7:366,205:571,23:0.0385:2,2:23.2:1:31:1:0.66302:1.28:60:46:0.039:0:1.1 +8 128755087 . G A 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.91129;LSEQ=GGTAAATGAAGGATGCTATT;RSEQ=CTGTTCTAATTACCTCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1112:94:60,34:641,376:1017,94:0.0845:2,2:22.7:1:28.5:1:0.91149:1.04:59.7:93:0.0848:0:1.1 0/1:727:193:118,75:317,212:529,193:0.2655:2,2:24.8:1:28.3:1:0.79696:1.05:60:192:0.2659:0:1.1 +8 128755332 . A T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09863;SOR=Inf;LSEQ=CAAAGGGAGATGCAATCCAC;RSEQ=GAAGTATAGTAGTTCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:1,94:95,0:0:1,0:22.8:1:32.6:1:1:0:60:94:1:0:0.1 0/1:44:2:0,2:0,42:42,2:0.0455:1,0:11:1:30.5:1:1:0:60:4:0.0455:0:1 +8 129385621 . A G 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11002;SOR=4.68932;LSEQ=TTGGTGCTGGTGCTGCTGGT;RSEQ=CAGATTATGGTGCTGGTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:4,3:6,4:10,7:0.4118:2,2:23.7:1:33:1:1:1.11721:60:14:0.4375:0:1.3 1/0:9:7:5,2:1,1:2,7:0.7778:2,2:12.4:1:32.3:1:1:2.24:60:14:0.7778:0:1.1 +8 129385897 . G T 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.70756;SOR=1.4733;LSEQ=CTAGTGATGCAGGTGCTGGT;RSEQ=GTGCTGATGCTGCTGGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:3,2:13,13:26,5:0.1613:2,2:28.8:1:30:1:1:1.48:60:10:0.1613:0:1 0/1:18:4:2,2:6,8:14,4:0.2222:2,2:22.5:1:28.3:1:1:1.31:60:8:0.2222:0:1 +8 129386059 . T G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68879;SOR=1.82594;LSEQ=TTGCTGGTGCTGGTGCTGGT;RSEQ=CAGGCACTGGTGCTGCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:3,7:3,5:8,10:0.5556:2,2:33.6:1:31.7:1:1:1.3738:59.9:20:0.5556:0:1.8 1/0:10:7:3,4:1,2:3,7:0.7:2,2:27.4:1:32.1:1:1:1.44:60:14:0.7:0:1 +8 129386118 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GGTGCTGGCGCTGGTGCTAC;RSEQ=TGTGTTAGTACTGGTGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:4,5:9,0:0:2,0:16.6:1:31.1:1:1:0:59.9:18:1:0:1.1 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:10:1:31.5:1:1:1.29:60:4:0.2222:0:1 +8 130841905 . C A 57 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.40479;SOR=2.37144;LSEQ=CAGTTTAGCCAGAACCCCCA;RSEQ=CCTCATTATCTGCGCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:37.5:1:30:1:1:1.40:60:4:0.1111:0:1 0/1:18:4:2,2:7,7:14,4:0.2222:2,2:34.3:1:28.5:1:1:1:60:8:0.2222:0:1 +8 131098084 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06162;SOR=Inf;LSEQ=TCCACAGGACTATTTGTTTT;RSEQ=CTATCAAAAGCCTGCCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:142,51:193,0:0:2,0:24:1:32.1:1:1:0:60:95.5:1:0:0.2 0/1:127:3:0,3:87,37:124,3:0.0236:2,0:12:1:25.3:1:0.02964:0:60:6:0.024:0:1 +8 131098162 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.21441;SOR=0.82039;LSEQ=GCAGGACTTCAGTAATGTAA;RSEQ=GCTGGGGCTATTTTGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:157:75,82:140,140:280,157:0.3576:2,2:26.7:1:30.9:1:0.69045:1.09311:60:77.5:0.3555:0:1.2 0/1:319:100:54,46:104,114:218,100:0.3135:2,2:23.8:1:29.6:1:0.33442:1.29:60:32.333:0.3089:0:1.2 +8 131098227 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16496;SOR=Inf;LSEQ=GAAAAAGCCTGGGGTGGCCC;RSEQ=CCCAGCCTGGGCAGCGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:99,181:280,0:0:2,0:24.1:1:30.4:1:1:0:60:45.667:1:0:0.3 0/1:192:2:1,1:75,115:190,2:0.0104:2,2:30:0:32.5:1:1:1.53:60:4:0.0106:0:1 +8 131098238 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20429;SOR=Inf;LSEQ=GGGTGGCCCTCCCAGCCTGG;RSEQ=CAGCGCAGGAGCTGCATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:68,146:214,0:0:2,0:25.6:1:31.6:1:1:0:60:41.8:1:0:0.2 0/1:177:2:1,1:65,110:175,2:0.0113:2,2:21.5:1:27.5:1:1:1.69:60:4:0.0115:0:1.5 +8 131098264 . G T 29 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.51031;SOR=0;LSEQ=CAGGAGCTGCATACCAGGGT;RSEQ=CCATGCTGCAGATGGATAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:26,108:134,2:0.0147:2,2:8:0:29:1:0.35882:4.10:60:4:0.0149:0:1 0/0:99:0:0,0:21,76:97,0:0:2,0:21.3:1:31.3:1:1:0:60:194:0.9898:0:0.1 +8 131098341 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAACCATGCTAAGTTGATC;RSEQ=CCTTCTCCACACTTCAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:0,2:0,35:35,2:0.0541:1,0:26.5:1:28.5:1:1:0:60:4:0.0556:0:1 0/0:12:0:0,0:0,12:12,0:0:0,0:20.3:1:33:1:1:0:60:24:1:0:0 +8 131759339 . C T 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13043;SOR=0;LSEQ=AATAGTGAAAGTCTTAAAGT;RSEQ=TTTGATCTTTCTTACAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:10,1:11,8:0.4211:2,0:26.4:1:31.5:1:1:0:27.6:16:0.4211:0:1.5 0/0:5:0:0,0:4,1:5,0:0:2,0:14.2:1:29.8:1:1:0:23:10:1:0:0 +8 131759411 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12771;SOR=Inf;LSEQ=CCCTCTCTGCTTTGGCTACC;RSEQ=AGAAGGGAAGGGCCACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:59,39:98,0:0:2,0:23.5:1:30.1:1:1:0:48.7:48:1:0:0.4 0/1:55:2:1,1:31,22:53,2:0.0364:2,2:30.5:1:31:1:1:1.40015:56.5:4:0.0364:0:1.5 +8 131759413 . G T 137 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04867;SOR=0.4079;LSEQ=CTCTCTGCTTTGGCTACCTA;RSEQ=AAGGGAAGGGCCACCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:28:16,12:43,28:71,28:0.2828:2,2:23.6:1:28.7:1:0.82175:1.15013:41.6:27:0.2755:0:1.2 0/1:58:8:5,3:29,21:50,8:0.1379:2,2:16.4:1:28.1:1:1:1.20:37.3:16:0.1379:0:1 +8 131759529 . G A 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.03137;SOR=0.23334;LSEQ=TTTGCAATAAATGTCAGCGC;RSEQ=CCCAGCCATTCTGGGCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:23:6,17:0,13:13,23:0.6389:1,2:21.6:1:29.6:1:0.0679:0:49.1:22:0.6471:0:1 0/1:14:4:0,4:2,8:10,4:0.2857:2,0:14.3:1:27.3:1:1:0:36.3:8:0.2857:0:1 +8 131862420 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTTCAAGGTGGGTTTT;RSEQ=TGAAGATTTCCCCCTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:13:1:34:0:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 131862601 . C T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00429;SOR=0.14299;LSEQ=TCACTCTCGAGTTTACATCT;RSEQ=GAGTTTCAAACTCTCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:26:26,0:18,0:18,26:0.5909:1,1:28:1:30.6:1:1:0:60:25:0.5814:0:1.1 0/1:18:3:3,0:15,0:15,3:0.1667:1,0:15:1:30.3:1:1:0:60:6:0.1667:0:1 +8 131862736 . C G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=0.16633;LSEQ=CATCTTTAACTCCTGTCTCC;RSEQ=CTATCAACCTATTTATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:223:137,86:137,87:224,223:0.4967:2,2:25.5:1:31.1:1:1:1.01:60:110.5:0.4955:0:1.3 0/1:263:37:22,15:129,97:226,37:0.1407:2,2:25.5:1:30:1:0.85869:1.10:60:74:0.1407:0:1.3 +8 131862819 . T C 264 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38816;LSEQ=CTCTGTGTAGCCATTCATGT;RSEQ=CTACACTGGCAGCTCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:558:343:151,192:99,116:215,343:0.6147:2,2:22.9:1:31.4:1:0.66242:1.08502:60:56.167:0.6127:0:1.2 0/1:314:120:49,71:86,108:194,120:0.3822:2,2:24.4:1:30.5:1:0.55957:1.15329:60:240:0.3846:0:1.2 +8 131862896 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11565;SOR=Inf;LSEQ=TGTTAAAGGGTACCTTGATA;RSEQ=AAGTGGAGGGAAATTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:68,193:261,0:0:2,0:24.6:1:32.2:1:1:0:59.9:51.2:1:0:0.4 0/1:135:2:1,1:45,87:132,2:0.0148:2,2:6.5:1:26.5:1:1:1.92:60:4:0.015:0:1.5 +8 131907452 . G A 47 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATATTTAAAGTGCTATAC;RSEQ=TTTATTGGGTCTTGTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:18.7:1:30:1:1:0:60:6:0.4286:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 131907569 . C A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00683;SOR=0.11906;LSEQ=AGTTTTAGCAGGTTATCAGC;RSEQ=ATGGGAGTAACCGTGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:53:53,0:5,0:5,53:0.9138:0,1:23.6:1:30.8:1:1:0:59.7:106:0.9138:0:1.7 1/0:11:6:6,0:5,0:5,6:0.5455:0,0:26.5:1:28:1:1:0:60:12:0.5455:0:1 +8 131907638 . A C 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.17292;LSEQ=TATTTTTCATGTCTGTGGTT;RSEQ=TACATAAGCCTCAGTCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:226:201:183,18:25,0:25,201:0.8894:1,2:23:1:32.2:1:0.23257:0:60:66:0.8919:0:1.2 1/0:69:40:38,2:27,2:29,40:0.5797:2,2:23.9:1:31:1:1:1.40:60:39:0.5821:0:1 +8 131907776 . C G 292 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.21534;LSEQ=CATTCAATGTTCTCTGGAAG;RSEQ=CTTCAAATCCACTTGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:733:606:282,324:61,64:125,606:0.8267:2,2:26.4:1:31.6:1:0.69403:1.09494:60:49.5:0.8261:0:1.1 1/0:391:198:92,106:93,100:193,198:0.5064:2,2:26.9:1:31:1:0.76173:1.07133:59.8:65:0.5078:0:1.2 +8 132408439 . C A 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03022;SOR=Inf;LSEQ=GATAGAAATCAGGAGACATT;RSEQ=CTTTCAGGGCTGATTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:588:0:0,0:377,210:587,0:0:2,0:26.6:1:31.7:1:1:0:60:72.375:0.9983:0:0.1 0/1:267:3:1,2:162,102:264,3:0.0112:2,2:17:1:20:1:0.56226:3.16244:60:2:0.0077:0:3.3 +8 132408509 . A G 230 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=867.20366;LSEQ=TATTTGACTATAAAACCATC;RSEQ=TTTCCAACCATAGAACCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:821:1:0,1:392,428:820,1:0.0012:2,0:15:0:31:0:1:0:60:2:0.0012:0:1 1/0:388:200:97,103:93,94:187,200:0.5155:2,2:27.3:1:30.1:1:0.83911:1.05039:60:39:0.5145:0:1.1 +8 132506242 . ATAACCCCAGCTTCTGCCCCCACTATATCTACATTAATTAAT A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGAAAGCATAGGTGATTG;RSEQ=TAGTACAGATTCACTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:22.5:1:32.5:1:1:0:60:4:0.2857:0.2857:0 0/0:2:0:0,0:2,0:2,0:0:0,0:22:1:32:0:1:0:60:4:1:0:0 +8 132506286 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51471;SOR=0;LSEQ=ATATCTACATTAATTAATTA;RSEQ=TACAGATTCACTACTGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:9,2:0.1818:2,2:13:1:30:1:1:1.87089:60:4:0.1818:0:1.5 0/0:6:0:0,0:4,2:6,0:0:2,0:28.2:1:30.2:1:1:0:60:12:1:0:0 +8 132506457 . G C 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CATTGCTCTGGAGAGATGAT;RSEQ=AAGGTAGGGCAAGATAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:13.3:1:33:1:1:0:60:8:0.6667:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:37:1:32.5:1:1:0:60:4:1:0:0 +8 134015166 . T G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01771;SOR=5.88811;LSEQ=GCCATGGTAACACCTGTGGG;RSEQ=TATACCTTTTTGAACAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:34:18,16:23,11:34,34:0.5:2,2:28.6:1:31:1:0.32159:1.84152:57.6:33:0.5:0:1.1 1/1:14:12:6,6:1,1:2,12:0.8571:2,2:19.2:1:30.9:1:1:1:60:24:0.8571:0:1 +8 134015236 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTACAGATTCACATGTA;RSEQ=CTGGCCAAACGAACAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:57,28:85,2:0.023:2,2:28.5:1:31.5:1:1:2.01784:60:4:0.023:0:2 0/0:36:0:0,0:24,12:36,0:0:2,0:26.2:1:31.8:1:1:0:60:72:1:0:0.2 +8 134015264 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACGAACAACTCCATGTTTT;RSEQ=CAAAAGGCTTGGAGAACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:78,35:113,2:0.0174:2,0:16.5:1:27:1:1:0:60:4:0.0179:0:1.5 0/0:51:0:0,0:34,16:50,0:0:2,0:25.2:1:30.1:1:1:0:59.7:100:0.9804:0:0.1 +8 134015306 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54976;SOR=0;LSEQ=CAGGTACCTCTCCTCTTTCC;RSEQ=TTTGTGTTTGTCATTTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:117,80:197,2:0.01:2,2:8:1:30.5:1:1:1.45961:60:4:0.0102:0:1 0/0:103:0:0,0:64,39:103,0:0:2,0:23.4:1:30.3:1:1:0:57.7:102:1:0:0.1 +8 134015351 . AG A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11629;SOR=Inf;LSEQ=TACTGGAAGATGGTGGTTCC;RSEQ=CTGAAAGGCTTTTTGGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:85,115:200,0:0:2,0:26:1:32.7:1:1:0:57.6:400:1:0:0.1 0/1:104:2:1,1:47,55:102,2:0.0192:2,2:26.5:1:30:1:1:1.17:56:4:0.0192:0:0 +8 134015367 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10935;SOR=Inf;LSEQ=TTCCAGCTGAAAGGCTTTTT;RSEQ=GCAATTTTTAACAGCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:64,104:168,0:0:2,0:23.9:1:31.1:1:1:0:59.1:83:0.994:0:0.1 0/1:84:2:1,1:35,45:80,2:0.0238:2,2:41:1:31:1:1:1.28:60:4:0.0238:0:1 +8 134015382 . C A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.55228;SOR=0;LSEQ=TTTTTGGCAATTTTTAACAG;RSEQ=TGAAAATAAACCTTGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:3:2,1:43,88:131,3:0.0224:2,2:16.7:1:28:1:0.26091:4.05:56.3:6:0.0224:0:1 0/0:68:0:0,0:28,40:68,0:0:2,0:21.3:1:31:1:1:0:59.9:136:1:0:0.1 +8 134015507 . A G 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.57576;SOR=2.74155;LSEQ=AGAGTGAAGGAGGGAAGAAA;RSEQ=GAGAATTAAACACGATTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:0,4:0,4:4,4:0.5:0,0:20.5:1:31.8:1:1:0:60:8:0.5:0:1 1/0:4:3:0,3:0,1:1,3:0.75:0,0:17.7:1:32:0:1:0:60:6:0.75:0:1 +8 134042069 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4918;SOR=0;LSEQ=TTTCCTCTTTTCTGAAGGGT;RSEQ=CGGAGAGGTGAGTGGCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:20,9:29,2:0.0645:2,2:38:0:32:0:1:2.16029:60:4:0.0645:0:1.5 0/0:31:0:0,0:13,18:31,0:0:2,0:27.8:1:30:1:1:0:60:62:1:0:0.2 +8 134042158 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03153;SOR=Inf;LSEQ=TCCGAGGATTTGGCGGGGAC;RSEQ=CTCGGCGCGTGTCCCTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:10,20:30,0:0:2,0:21.5:1:30.8:1:1:0:60:29:1:0:0.3 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:35.5:1:31:0:1:1.41418:60:4:0.2857:0:1.5 +8 136801602 . C T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATCTCAGTGGTGTTCTCTG;RSEQ=ATTTCCTGAATTTGAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:1,1:0.5:0,0:35:0:32:0:1:0:42:2:0.5:0:2 1/1:2:2:2,0:0,0:0,2:1:0,0:20.5:1:31:0:1:0:39.5:4:1:0:2 +8 139766211 . G C 121 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06667;SOR=0;LSEQ=ATACTCCGTGGTGAAAACAG;RSEQ=AGAGGCTGCACAGTCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:0,14:1:0,1:21.9:1:32:1:1:0:59.9:13:1:0:1.6 0/0:1:0:0,0:1,0:1,0:0:0,0:15:0:32:0:1:0:60:2:1:0:0 +8 139766407 . G C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0996;SOR=Inf;LSEQ=AGTATAGACCTTCAATACTT;RSEQ=CCAATAATAGATCTGAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:201,81:282,0:0:2,0:23.3:1:32.4:1:1:0:60:281:0.9965:0:0.4 0/1:131:2:1,1:89,39:128,2:0.0153:2,2:11:0:32.5:1:0.52236:2.266:60:4:0.016:0:1 +8 139766478 . T C 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00682;SOR=0.66731;LSEQ=TTGGAACACACTGCATTCTC;RSEQ=GCATTATCTAGTTTAAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:602:395:212,183:104,103:207,395:0.6561:2,2:25:1:30.6:1:0.4402:1.15:59.8:130.667:0.6544:0:1.1 1/0:275:154:82,72:59,62:121,154:0.56:2,2:24:1:29.5:1:0.46875:1.20:59.9:50.333:0.5613:0:1.2 +8 139766508 . T TACA 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.14007;SOR=0.7914;LSEQ=AGTTTAAATCTCTCAACAGT;RSEQ=ACAATTGTGGGCAGCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:572:366:170,196:31,36:67,366:0.6399:2,2:26.7:1:30.7:1:1:1.01:59.7:365:0.6415:0.1241:0.8 1/0:255:149:74,75:29,40:69,149:0.5843:2,2:27.4:1:29.3:1:0.31069:1.36:59.9:298:0.5936:0.1059:0.9 +8 139766879 . A G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAACTCACATCATAAGAT;RSEQ=ATCACAAGGGCCCTTTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:22.7:1:31:1:1:0:35.3:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 141608898 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAATGGCACAAGACAATTG;RSEQ=ACAGCAGACCCACCTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:36.5:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 141609046 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATCTGCTCAATGACAGAAA;RSEQ=GCGACAACAGAGGCCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:30:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 141610497 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49929;SOR=Inf;LSEQ=GGTCTACAGATCCAAAACAC;RSEQ=GGCCGGGCGCGGTGGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:16,0:0:2,0:20.6:1:31.4:1:1:0:60:32:1:0:0.1 0/1:22:2:1,1:9,11:20,2:0.0909:2,2:33:1:30.5:1:1:1.21:55.5:4:0.0909:0:1 +8 141611030 . CA C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGAGTGAGGCTCCGTCT;RSEQ=AAAAAAAAAAACCCGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:32.5:1:1:0:60:4:1:0:1.5 +8 141611064 . A C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGAATTCGAATTGTGTCTA;RSEQ=ATCTGTCCACTTCACCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:32:1:1:0:60:4:1:0:1.5 +8 141611909 . C T 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATATTTTTTATTGCTTTT;RSEQ=TCCCCCCAAATATTTTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:44.5:1:31.5:1:1:0:60:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:33:0:27:0:1:0:60:2:1:0:1 +8 141840645 . G A 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.44834;SOR=1.87771;LSEQ=TCTGAAATATAAAAAGAAGC;RSEQ=TATTAACAAATAACACCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:8,0:38,0:38,8:0.1739:1,0:15:1:30.6:1:1:0:60:16:0.1739:0:1.3 0/1:14:4:4,0:10,0:10,4:0.2857:0,0:35:1:27.8:1:1:0:60:8:0.2857:0:1 +8 141840739 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=5.55787;LSEQ=ATCCTTCCATATATTATTTA;RSEQ=GAAGGAAACAAGTATAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:43:39,4:187,20:207,43:0.172:2,2:22.5:1:30.7:1:1:1.04:60:42:0.1694:0:1.1 1/0:80:43:40,3:34,2:36,43:0.5375:2,2:23.9:1:28.7:1:1:1.27113:60:9.75:0.52:0:1.1 +8 141840767 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08289;SOR=Inf;LSEQ=ACAAGTATAATAATGCTTTA;RSEQ=TTTACCAGTATATTCACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:439:0:0,0:320,119:439,0:0:2,0:23.2:1:30.4:1:1:0:60:86.8:1:0:0.1 0/1:178:2:1,1:127,49:176,2:0.0112:2,2:8:0:33.5:1:0.48403:2.57588:60:4:0.0114:0:1.5 +8 141840816 . T C 120 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACAAATCATTTTCTAGATA;RSEQ=GTACTGGAAACATGAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:834:0:0,0:459,375:834,0:0:2,0:27.9:1:30.7:1:1:0:60:74.818:1:0:0.2 0/1:371:15:9,6:197,159:356,15:0.0404:2,2:28.5:1:30.9:1:0.79581:1.21:60:30:0.0408:0:1.5 +8 141840881 . T C 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=6.26456;LSEQ=TGGTTTTTTCTTTTTTTACC;RSEQ=TTATTGTTGAAAACTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:645:90:38,52:216,337:553,90:0.1395:2,2:23:1:31.8:1:0.56367:1.14:60:44:0.1379:0:1.2 1/0:333:168:82,86:65,100:165,168:0.5045:2,2:24.3:1:30.2:1:0.0979:1.47:60:83:0.503:0:1.2 +8 141840944 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11775;SOR=Inf;LSEQ=TATAGTGTATTAAAAACTGT;RSEQ=CTTTTTCAGATATTTCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:357:0:0,0:99,257:356,0:0:2,0:24.4:1:31.6:1:1:0:59.8:117.667:1:0:0.1 0/1:187:2:1,1:60,124:184,2:0.0107:2,2:41.5:1:30.5:1:0.54955:2.06:60:4:0.0109:0:1 +8 142097729 . G A 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCAGGAAAGGGGGCGTGA;RSEQ=GTTGTGTGGCAGCAGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:32:0:1:0:60:4:1:0:2.5 +8 142098849 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09117;SOR=Inf;LSEQ=TTCTGGCAGCCACTGCACTT;RSEQ=CATTCAGAGTGGCAGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:78,11:89,0:0:2,0:28:1:32.4:1:1:0:60:43.5:1:0:0.2 0/1:39:2:1,1:32,5:37,2:0.0513:2,2:21:1:26.5:1:0.28745:5.93298:60:4:0.0526:0:1 +8 142098892 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=0.07763;SOR=Inf;LSEQ=GGTGCCTCGGGACCCCTCCC;RSEQ=TCCAAAGTAGCAGGAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:163,48:211,0:0:2,0:23.4:1:31.8:1:1:0:60:69.333:1:0:0.1 0/1:82:2:1,1:60,20:80,2:0.0244:2,2:27:0:31:1:0.44896:2.95195:60:4:0.025:0:1 +8 142098977 . A G 146 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=42.83048;LSEQ=AGGCCAGGCCCTGGGGAACC;RSEQ=GTTTGAGAAGCTCCTCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:2:1,1:252,257:509,2:0.0039:2,2:11:0:14.5:1:1:1.02:60:0:0:0:1 0/1:249:36:18,18:109,104:213,36:0.1446:2,2:21.8:1:28.4:1:1:1.0479:60:72:0.1463:0:1.3 +8 142099013 . G A 44 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.02713;SOR=Inf;LSEQ=CCTCTTCTGGGTACATGTGG;RSEQ=GTGGATGGGCTGGGAGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:0:0,0:183,263:446,0:0:2,0:26.9:1:31.1:1:1:0:59.9:62.714:0.9977:0:0.2 0/1:193:3:2,1:83,106:189,3:0.0155:2,2:5.7:1:28.3:1:0.58491:2.54:60:6:0.0158:0:2.3 +8 142099035 . G A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.19878;SOR=5.01682;LSEQ=TGGATGGGCTGGGAGGGTCT;RSEQ=CTCTGCGGCAGGGGGTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:1:1,0:115,235:350,1:0.0028:2,0:45:0:13:0:0.33048:0:60:0:0:0:1 0/1:141:2:1,1:52,87:139,2:0.0142:2,2:24:1:26.5:1:1:1.67:60:4:0.0143:0:1 +8 142099052 . G T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56214;SOR=0;LSEQ=TCTGCTCTGCGGCAGGGGGT;RSEQ=CATCCTTCTCTCTTGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:2,1:71,193:264,3:0.0112:2,2:18:1:24.7:1:0.18236:5.40:60:2:0.0078:0:1.3 0/0:105:0:0,0:34,70:104,0:0:2,0:23.9:1:30.9:1:1:0:60:33.667:1:0:0.2 +8 142591787 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52821;SOR=0;LSEQ=GGAGGCGGAGCAGGAGTCAG;RSEQ=GCTGAGGAGGGCACAGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:10,18:28,2:0.0667:2,2:31:1:32:0:1:1.76:60:4:0.0667:0:2.5 0/0:17:0:0,0:8,9:17,0:0:2,0:29.1:1:31.4:1:1:0:60:34:1:0:0.9 +8 142591816 . A G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCACAGGGGACATGCCTG;RSEQ=CTCCGTCTGGGTGCCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:7,12:0,0:0,19:1:0,2:20.3:1:30.8:1:1:0:60:8.5:1:0:1.3 1/1:12:12:5,7:0,0:0,12:1:0,2:20.8:1:31:1:1:0:60:24:1:0:1.2 +8 142592872 . C T 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACTGAGCAGCAGCGGGCTC;RSEQ=GCAGGGCCTCCAGGCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:22.8:1:31.5:1:1:0:60:8:1:0:2.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 142592961 . G T 57 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAGGCTGAGGGGCACAG;RSEQ=CTGGGGCAGGAATCTCGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:18.3:1:28.8:1:1:0:60:8:1:0:1.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 142593546 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGAGCATTTCTGAGGGA;RSEQ=CCGTGAGTGTCGGGAAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:30:1:1:0:60:4:1:0:1.5 +8 142938133 . G A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGGGAGGGGCAGACTGA;RSEQ=GACAAGAGGTGGGGGTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:1:33:1:1:1:60:4:0.3333:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:9:0:32.5:1:1:0:60:4:1:0:0 +8 142938272 . A T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGAGGGCCCTGGGGAGAA;RSEQ=GGGGCTGGGCTCTCAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29:1:29:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 142939269 . G A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.62671;LSEQ=TTGTTACCATCACCATCATC;RSEQ=CCATTCCCGTCATCATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:10.6:1:30.2:1:1:1.41418:60:10:0.7143:0:1 1/0:5:3:1,2:1,1:2,3:0.6:2,2:14.7:1:28.3:1:1:1.7321:60:6:0.6:0:1.3 +8 143164976 . G A 90 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGTGGGCTCTCCCAGGGTCA;RSEQ=TGTGGAATACAACAAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:2,5:3,3:6,7:0.5385:2,2:37.6:1:32.3:1:0.59207:2.32357:60:14:0.5385:0:1.1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 143283778 . C G 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCCCACCTCTGAGCGGGG;RSEQ=CCCTGTCCTGGTCTGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:29.5:1:33:0:1:1:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 143284867 . T G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGCACACTCACTGCCTC;RSEQ=GAGCGGCCCAGCCCCCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:32:0:1:0:41:4:1:0:1.5 +8 143285674 . C G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTTCTGGAAGCCTGGGGG;RSEQ=TGACTCCGGCACCAGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:17,12:29,2:0.0645:2,2:8:0:33.5:1:1:1.40053:60:4:0.0645:0:1 0/0:11:0:0,0:7,4:11,0:0:2,0:28.9:1:32.3:1:1:0:60:22:1:0:0.4 +8 143285754 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01579;SOR=Inf;LSEQ=ATTGATTCTCCTTTTCATGA;RSEQ=CGTGGCACCCACGATGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:5,12:17,0:0:2,0:24:1:29.3:1:1:0:60:16:1:0:0.6 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:22:1:27:1:1:0:60:4:0.6667:0:1 +8 143285765 . A G 90 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57842;LSEQ=TTTTCATGATCGTGGCACCC;RSEQ=CGATGGAAATGGCATCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:2,6:2,7:9,8:0.4706:2,2:16.8:1:30:1:1:1.16:60:16:0.4706:0:1 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:31:0:33:0:1:0:60:2:0.3333:0:1 +8 143285848 . A G 33 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGTGCGAGAATGCTTCAG;RSEQ=CAGAGGCATGCGGGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:26:1:33.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:5:0:31:0:1:0:60:2:1:0:1 +8 143287465 . A AAGGGGC 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=28;MSI=5.000;MSILEN=6;SSF=1;SOR=0;LSEQ=GAGCAGCCACGAGACAGCGG;RSEQ=AGGGGCAGGGGCAGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:0:32.1:1:1:0:60:4:1:0:0 +8 143349510 . A G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCTGCCCTCCCTGCGTGCC;RSEQ=CCTGCCATTCCATGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:20:10,10:1,0:1,20:0.9524:0,2:30.3:1:29.9:1:1:0:60:19:0.95:0:1.5 1/1:5:5:2,3:0,0:0,5:1:0,2:33.6:1:31.8:1:1:0:60:10:1:0:1.2 +8 143350750 . T C 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGTGAAGGTTGGGGCTCAGC;RSEQ=AGCACCAGAGTAGAGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:31:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:14.5:1:28:1:1:0:60:4:1:0:0 +8 143445733 . A G 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30769;SOR=0;LSEQ=TTTTTAAGATGCACAGAGAA;RSEQ=TACAGATATAGATGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:2,3:15,16:31,5:0.1389:2,2:25.2:1:34.6:1:1:1.39312:60:10:0.1389:0:1.4 0/0:16:0:0,0:6,10:16,0:0:2,0:25.8:1:28.3:1:1:0:60:15:1:0:0 +8 143486125 . G C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGGACCAATGCCTGTCTGA;RSEQ=AGCTGTCAGTCTGGACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:30.5:1:1:0:60:4:1:0:1.5 +8 143486688 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.28202;SOR=3.72692;LSEQ=AGCTCTGGGCTCCCTCCTTC;RSEQ=TCCAGAGAAGCAGGACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:1:0,1:193,133:326,1:0.003:2,0:1:0:27:0:0.40979:0:60:2:0.0031:0:2 0/1:177:2:1,1:97,77:174,2:0.0113:2,2:8.5:1:28:1:1:1.25807:60:4:0.0114:0:3.5 +8 143486698 . G A 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=5.20369;LSEQ=TCCCTCCTTCCTCCAGAGAA;RSEQ=CAGGACTCCCTGGGAAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:55:27,28:174,126:300,55:0.1541:2,2:27.6:1:30.1:1:0.23853:1.4306:60:54:0.1525:0:1.7 0/1:199:97:54,43:50,52:102,97:0.4874:2,2:22.7:1:29:1:0.3951:1.30:60:194:0.4924:0:1.9 +8 143486745 . T C 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00091;SOR=1.79017;LSEQ=CCCACCCCTTGGCCAACCAG;RSEQ=GAGACCAACAGGGTGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:194:92,102:94,105:199,194:0.4936:2,2:28.2:1:31.2:1:1:1.01:60:96:0.4948:0:1.3 1/0:217:138:63,75:31,46:77,138:0.6359:2,2:26.4:1:30.3:1:0.47577:1.25:60:137:0.6372:0:1.7 +8 143498097 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07433;SOR=Inf;LSEQ=TCCCCAGACCACCTGCATGG;RSEQ=CGGAGTCAGGTTCAGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:31,21:52,0:0:2,0:26.8:1:32.1:1:1:0:59.9:51:1:0:0.2 0/1:20:2:1,1:10,8:18,2:0.1:2,2:12:0:30.5:1:1:1.23603:60:4:0.1053:0:1.5 +8 143498115 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCGGAGTCAGGTTCAGCA;RSEQ=GGTCCCGGGCCACCTGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:28,26:54,2:0.0357:2,2:22:1:29:1:1:1.07547:58:4:0.0357:0:1 0/0:21:0:0,0:11,10:21,0:0:2,0:26.7:1:32.1:1:1:0:56.4:42:1:0:0.4 +8 143498175 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTCCCCGGCCACCTGCGT;RSEQ=ACCGGAGTCAGGTTCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:15,22:37,2:0.0513:2,2:30.5:1:31:1:1:1.45:31:4:0.0541:0:1.5 0/0:14:0:0,0:6,8:14,0:0:2,0:19.6:1:30.1:1:1:0:60:28:1:0:0.5 +8 143500243 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTTCCCCATGTCTTATGGA;RSEQ=GGGGAGACTGAGGCTGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 143714120 . C A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=GCAGTGGCCACTCTCTGGGG;RSEQ=CATGGCCCTGCAGGCGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:8,0:0:2,0:24.8:1:29.8:1:1:0:60:7:1:0:0 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:25.5:1:24.5:1:1:0:60:4:0.3333:0:1 +8 143714467 . A G 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGATGCAGGGGCTGTCTGA;RSEQ=TGGGTACAGGGCAAGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:0,2:2,2:0.4:0,2:5.5:1:30:1:1:0:60:4:0.5:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:40.5:1:29.5:1:1:0:60:4:1:0:0 +8 143716030 . G T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCTTCCAGAGGCCCTCT;RSEQ=GGATCCTCTGGCCCTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 143719962 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08304;SOR=Inf;LSEQ=GGTGAGTCGCTTCACAGGAA;RSEQ=CGTCCCCCGGTGGCCATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:0:0,0:172,305:477,0:0:2,0:22.1:1:31.9:1:1:0:60:42.364:0.9979:0:0.5 0/1:194:2:1,1:74,117:191,2:0.0103:2,2:17:1:27:1:1:1.58:60:4:0.0104:0:1 +8 143719983 . G C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.12867;LSEQ=CGTCCCCCGGTGGCCATGAC;RSEQ=CCAGTGGCCATGTGGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:297:209:51,158:20,67:87,209:0.7037:2,2:22.6:1:30.6:1:0.88161:1.08:60:51.25:0.6997:0:1.1 0/1:103:24:6,18:21,58:79,24:0.233:2,2:18.4:1:29.5:1:1:1.08536:60:11:0.2178:0:1.2 +8 143720876 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACAGGCAGATGGGTGGAC;RSEQ=GATGGACAGCCGGATGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 143855670 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGGCCCCAGGCTGCTCCCAA;RSEQ=CCCCAGCCTGTGCGCGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:30:0:1:0:60:2:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:28.5:1:29:1:1:0:60:4:1:0:1 +8 143855749 . A C 99 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTGTGGTTGGGGACCAGG;RSEQ=CTCGGGGGACCACCTGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:7,1:2,1:3,8:0.7273:2,2:24.5:1:33:1:0.49091:3.06:60:16:0.7273:0:2.1 1/1:1:1:0,1:0,0:0,1:1:0,0:26:0:33:0:1:0:60:2:1:0:2 +8 143855755 . G C 104 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGTTGGGGACCAGGACTCGG;RSEQ=GGACCACCTGCTCTGCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:8,1:4,2:6,9:0.6:2,2:26.9:1:33.1:1:0.52527:3.62:60:18:0.6:0:2 1/1:1:1:0,1:0,0:0,1:1:0,0:32:0:24:0:1:0:60:2:1:0:2 +8 143856488 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCATGGCTGAGGAGGTC;RSEQ=CAGGGAGTGTGGAGGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:28:1:30:1:1:1.67325:60:4:0.1538:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:39:0:25:0:1:0:60:2:1:0:0 +8 144226165 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07589;SOR=Inf;LSEQ=CTTGTGTACTTGGCTCAGCG;RSEQ=TGCCCGCACATGCCCACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:25,21:46,0:0:2,0:23.1:1:32.6:1:1:0:60:45:1:0:0.2 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:31:0:31:0:1:1.26772:60:4:0.1111:0:1 +8 144227057 . G C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTTCAATTAGCTGGACAA;RSEQ=GTGGCTCACATTTGTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:29.5:1:1:0:60:4:1:0:1 +8 144227433 . T G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGATTTATTCTGTGGGTG;RSEQ=GGGTGGTGTGCGATGAGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:29:1:1:0:60:4:1:0:2 +8 144227728 . A G 80 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGCCCCCTCCCCTTTCCA;RSEQ=CTGCGGAACCTGGAGCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:25:1:34.6:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144342581 . T C 28 v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACTCCGGTGAGGTCACCC;RSEQ=GGAGGGGAGTCCCAGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:0,2:2,1:3,2:0.4:2,0:6:1:28:1:0.4:0:60:4:0.4:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144342831 . G A 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=CCAGCCTCTCTTGGCCACCC;RSEQ=GACCAGCGGGCACCACCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:1:33.5:1:1:0:60:4:1:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:49:0:29:0:1:0:60:2:1:0:0 +8 144343973 . C G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54928;SOR=1.52695;LSEQ=GTCTCCAGCAGCCCCTGCCC;RSEQ=CACCCGCACCCCTGCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:20:8,12:7,7:14,20:0.5882:2,2:29.8:1:27.6:1:0.72824:1.48199:38.7:5.667:0.6071:0:1.7 1/0:16:11:5,6:3,2:5,11:0.6875:2,2:28:1:28:1:1:1.73457:42.6:10:0.7143:0:1.2 +8 144344011 . AGCCCCTGCCCGCACCCGCACCCCT A 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.28157;SOR=0;LSEQ=CTGCCACGCCTGTCTCCGGC;RSEQ=GCACCTGCCACGCCCGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:3:1,2:11,19:30,3:0.0909:2,2:19.7:1:24.3:1:1:1.15289:53.3:2:0.069:0.0909:1.3 0/0:20:0:0,0:8,12:20,0:0:2,0:22.5:1:30.1:1:1:0:39.8:19:1:0:1 +8 144344035 . TGCACCTGCCACGCCCGTCTCCGGCAGCACCTGCCACGCCCGTCTCCGGCA T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=52;MSI=2.000;MSILEN=3;SSF=0.08556;SOR=Inf;LSEQ=CCTGCCCGCACCCGCACCCC;RSEQ=GCACCTGCCACGCCCGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:5,13:18,0:0:2,0:23.1:1:31.9:1:1:0:38.4:36:1:0:1.2 0/1:16:3:1,2:6,7:13,3:0.1875:2,2:11:1:28.7:1:1:1.659:29:6:0.2:0.1875:1 +8 144344100 . C T 92 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10376;SOR=0;LSEQ=CCGGCAGCACCTGCCACGCC;RSEQ=GTCTCCGGCAGCACCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:5,4:3,5:8,9:0.5294:2,2:12.6:1:29.1:1:0.63719:1.99:40.1:3.5:0.5385:0:1.7 0/0:4:0:0,0:2,2:4,0:0:2,0:16.3:1:22.3:1:1:0:29.8:3:1:0:0.8 +8 144344194 . T C 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.63661;SOR=1.62233;LSEQ=CGTCTCCGGCAGCCCCTGCC;RSEQ=GCACCCGCACCCCTCACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,11:23,2:0.08:2,2:15:0:30:1:1:1.0871:25.5:4:0.087:0:2 0/1:16:2:1,1:9,5:14,2:0.125:2,2:12.5:1:28:1:1:1.73197:24:4:0.125:0:1.5 +8 144344213 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51923;SOR=0;LSEQ=CTGCACCCGCACCCCTCACG;RSEQ=CTGTCTCCGGCAGCCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:12,10:22,2:0.08:2,2:37:1:26:1:1:1.19087:60:4:0.087:0:3 0/0:15:0:0,0:8,7:15,0:0:2,0:27.5:1:30.1:1:1:0:58.6:30:1:0:0.6 +8 144344261 . G T 53 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.05268;SOR=Inf;LSEQ=CGCACCTCTGCACCTCCCAC;RSEQ=CCCCTCTCCGGCAGCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:23.7:1:25.8:1:1:0:60:4.5:1:0:0.1 0/1:15:5:2,3:4,6:10,5:0.3333:2,2:23.6:1:23.2:1:1:1:60:1.5:0.2308:0:1.2 +8 144344387 . A G 34 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGGCCACCGCTCAGCCAA;RSEQ=TGGATTCAGCGAGGGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:19:1:34.5:1:1:0:46:4:1:0:1.5 1/1:1:1:1,0:0,0:0,1:1:0,0:40:0:32:0:1:0:60:2:1:0:1 +8 144344456 . T C 49 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TGTTTCCTGGTGAGGCTGGA;RSEQ=GCCTGGCATGTCTGAACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:14.7:1:31.3:1:1:0:44:6:0.75:0:1.3 0/0:1:0:0,0:1,0:1,0:0:0,0:39:0:27:0:1:0:60:2:1:0:0 +8 144346229 . C T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCCCTTCTGCTGCCTCC;RSEQ=CTCCCTCCTTCCTGCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:36:0:33:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144350854 . A G 35 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTTTCTGGAAGACTCCCT;RSEQ=TGCCTTTCTCTGGGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:18.5:1:35:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144351029 . C CTGCTGCTGCTGCTGT 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.00896;SOR=0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGTTTGAGTCTTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:15:5,10:0,0:0,15:0.5769:0,2:24.5:1:30.7:1:1:0:48.3:30:0.5769:0.2692:0.7 0/0:7:0:0,0:2,0:2,0:0:0,0:3:0:27.5:1:1:0:51:4:0.2857:0:0 +8 144351109 . T G 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAACCTCCACCTCCTGA;RSEQ=TTCAAGCTGTTCTCCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:24.5:1:32.8:1:1:0:49.3:12:1:0:1.3 1/1:5:5:0,5:0,0:0,5:1:0,0:26.4:1:32.4:1:1:0:51.6:10:1:0:1 +8 144351632 . A G 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGTCAGTCTCTCATCACC;RSEQ=GGGACACCTGGAACCCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29.5:1:1:0:60:4:1:0:1 1/1:3:3:1,2:0,0:0,3:1:0,2:20:0:29.7:1:1:0:60:6:1:0:1 +8 144352953 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGCACCCCCCCAGGCC;RSEQ=GATGAGGTGTGACTTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144405960 . GCAC A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CACACACAGGCACACCACAC;RSEQ=AAGTGCACACACACCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:17.5:1:31.5:1:1:0:60:4:1:0.5:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144406043 . C A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGTGTGCACATGCACACAC;RSEQ=CCCCCCATCAGAATGAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:3,1:2,1:3,4:0.5714:2,2:22.3:1:31.8:1:1:1.41:57.8:8:0.5714:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:20:0:31:0:1:0:60:2:1:0:0 +8 144406627 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGGGACCTCCTGGGGAG;RSEQ=AAACACCCTGCCAAGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144579523 . C G 69 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.0013;SOR=47.98972;LSEQ=CACCGCCTTCCCAATCCCCC;RSEQ=CAACCCCGCCACCAGTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:8,7:15,1:0.0625:2,0:17:0:32:0:1:0:60:2:0.0625:0:1 1/1:6:5:2,3:0,1:1,5:0.8333:0,2:31.8:1:29.8:1:1:0:60:10:0.8333:0:1 +8 144595042 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACTGAGAGTGCTCAGTGGC;RSEQ=CGGGGAGGTACACGCAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144894702 . C CT 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGACCCTACCTACCTTGC;RSEQ=CCACAAGCCTGACCCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:32:1:32:1:1:0:60:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144896157 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACCCCACCCAGCCCCTG;RSEQ=CCAGGCTCCCCACCGTTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:34,2:0.0556:2,2:9:0:32:0:1:1:60:4:0.0556:0:1.5 0/0:13:0:0,0:7,6:13,0:0:2,0:22.1:1:27.4:1:1:0:60:3.333:1:0:0.4 +8 144905927 . T C 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GCTCCACCTCTGAGAGGACC;RSEQ=GCTCCCAAGGCTGGGCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:31:1:1:0:60:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:36:0:31:0:1:0:60:2:1:0:0 +8 144907814 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCATGCGCCGCCACACCT;RSEQ=GCTAATTTTTGTATTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144996408 . T G 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.23584;LSEQ=TGCTCCTCACGCAGCTGCTG;RSEQ=GCCTTGGCCACCTCGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:1,3:3,7:10,4:0.2857:2,2:31.3:1:30.3:1:1:1.2634:60:8:0.3077:0:1 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:38:1:29.5:1:1:2.45:60:4:0.3333:0:1 +8 144997656 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.02451;SOR=Inf;LSEQ=TGCTCCGCCTGTGCCCGCCG;RSEQ=GCCGCCTCTTGCTCGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:6,6:12,0:0:2,0:30.9:1:31.4:1:1:0:60:24:1:0:0 1/0:6:3:2,1:1,2:3,3:0.5:2,2:34.7:1:29.3:1:1:3.11:60:6:0.5:0:1 +8 144997927 . G A 49 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCTCCTTCTGCTGCACC;RSEQ=CGAAGGCGTGTGCCTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:0,2:2,3:0.6:0,2:7.7:1:31.3:1:1:0:60:6:0.6:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:34:0:33:0:1:0:60:2:1:0:0 +8 144998146 . C T 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACGCGCTCCTCAGCCTCA;RSEQ=GGCGCCGCCGCTCCTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,3:9,2:0.1818:2,2:32:1:30:1:1:1.87089:60:4:0.1818:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 144998266 . A G 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.42857;SOR=Inf;LSEQ=TGCGTCCCAGCTCCAGCTCC;RSEQ=GCTCCGCCTTGCCAGCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:30.5:1:32:1:1:0:60:8:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:46:0:31:1:1:1:60:4:0.6667:0:1.5 +8 144999065 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGGCCTGCTCCTCCGCCT;RSEQ=GCCGCGCCGCCGCGCCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:11,9:20,2:0.0909:2,2:15:1:29:0:1:1.21106:60:4:0.0909:0:1 0/0:8:0:0,0:4,4:8,0:0:2,0:33.4:1:29.6:1:1:0:60:16:1:0:0.3 +8 144999077 . G A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.15284;SOR=0;LSEQ=CTCCGCCTTGCCGCGCCGCC;RSEQ=CGCCTCGCGCTCCGCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:2,3:8,7:15,5:0.25:2,2:33.6:1:28.6:1:1:1.66859:60:10:0.25:0:1 0/0:9:0:0,0:5,4:9,0:0:2,0:29.6:1:29:1:1:0:60:8:1:0:0.2 +8 144999417 . C T 28 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGGGCCACCTGTACCTGCCG;RSEQ=GCTCGCTCCACCTCGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:35:1:31:1:1:0:60:4:1:0:0 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:46:0:28.5:1:1:1.41418:60:4:0.2857:0:1 +8 145002359 . A T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGTTGGGAGCCTCTGTAAC;RSEQ=CAAGGACACTCAGGACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:19:0:33:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 145002431 . C G 54 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACCCCAAGGCCCCGAGA;RSEQ=AGGACGAGCCCACTGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:2,1:1,1:2,3:0.6:2,2:40:1:34.3:1:1:1.73:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 145004255 . C T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.14154;SOR=Inf;LSEQ=CAGGTCAGGGCTACAGTCAG;RSEQ=GTCACCAGCGCCCCACCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:29,0:0:2,0:31.7:1:31.2:1:1:0:60:28:1:0:0.2 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:20:0:29.5:1:1:1.26772:60:4:0.1111:0:1.5 +8 145004345 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGCCTCCTGGTTGGGC;RSEQ=GGGGCACCAGGAAGCACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:0,11:11,2:0.1538:0,2:25.5:1:27:1:0.15385:0:60:4:0.1538:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:17.3:1:28.3:1:1:0:60:8:1:0:0.3 +8 145004546 . G A 47 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGTGGACCCCCGGCCTGC;RSEQ=CTCACCTCCACCTGCTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:27.7:1:30:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 145005450 . T C 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=ATCCTGCCTCATTCCCCCCT;RSEQ=GGCTGACCTCTACACCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:30.5:1:1:0:40.5:4:1:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:12:1:30.5:1:1:0:60:4:1:0:0 +8 145005688 . A AC 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTCCTGACACGCCCCTGCAC;RSEQ=CCCCCTCCCTCACCTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:24.5:1:33.5:1:1:1.73:60:4:0.4:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:30.5:1:1:0:60:4:1:0:0 +8 145005851 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCAGCGGGAGGGGGTCAC;RSEQ=CCAGGCTACCTGGGACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:8:0:32:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 145589672 . G T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=CTGCCTTCTCTCTCTGCTTC;RSEQ=GCTACCTAAGAGGGAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:43,17:60,0:0:2,0:23.6:1:30:1:1:0:30.7:59:0.9833:0:0.2 0/1:15:5:3,2:7,3:10,5:0.3333:2,2:29:1:30.6:1:1:1.50913:39:10:0.3333:0:1.2 +8 145736791 . C T 286 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGACAACCCCAGCTCTACC;RSEQ=GACATCCCCCAATGCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1275:575:381,194:442,253:695,575:0.451:2,2:24.5:1:31.2:1:0.34507:1.12:60:51.273:0.4498:0:1.1 0/0:472:0:0,0:291,181:472,0:0:2,0:23.2:1:29.6:1:1:0:59.9:66.429:1:0:0.2 +8 145737013 . G T 45 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00216;SOR=Inf;LSEQ=GAGCCTCCCAGGCCTCACCT;RSEQ=CCCCAGCCCCCAGCCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:868:0:0,0:442,425:867,0:0:2,0:24.7:1:32.2:1:1:0:59.9:44.632:1:0:0.4 0/1:240:4:0,4:124,111:235,4:0.0167:2,0:8.5:1:22.8:1:0.05215:0:60:3:0.0128:0:1.8 +8 145737040 . C T 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03799;SOR=0.73988;LSEQ=CCCCCAGCCCCAGCCTGCAG;RSEQ=GGGTGGGGCCTCCCAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:989:357:193,164:358,273:631,357:0.361:2,2:24.1:1:29.6:1:0.42433:1.11419:60:34.7:0.3596:0:1.1 0/1:302:89:54,35:129,84:213,89:0.2947:2,2:21.8:1:29:1:1:1.00:60:88:0.2983:0:1.2 +8 145737086 . C T 154 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=64.63158;LSEQ=ATGCCGTGGAAGATGCGGGC;RSEQ=ACAGCCCTGCTGGAGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1571:2:0,2:871,695:1566,2:0.0013:2,0:1:0:24.5:1:0.19744:0:60:4:0.0013:0:1 0/1:564:43:21,22:290,231:521,43:0.0762:2,2:20.6:1:28.5:1:0.42691:1.31454:59.9:86:0.0772:0:1.1 +8 145737123 . G A 173 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=37.41928;LSEQ=ACTTCTCCTCTGGCCTCAGG;RSEQ=ACAGGAACTGGCGGATGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1899:5:3,2:975,916:1891,5:0.0026:2,2:17.6:1:23.2:1:1:1.41:60:1.5:0.0016:0:2.2 0/1:711:64:35,29:325,321:646,64:0.09:2,2:21.8:1:28.9:1:0.51553:1.19:59.6:128:0.0905:0:1.3 +8 145737285 . TG CA 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GATGAGCTGCCTGGCCTTAC;RSEQ=CACTCACTCTGGCCTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2263:0:0,0:1199,1063:2262,0:0:2,0:24.7:1:30.8:1:1:0:59.9:112.1:1:0:0.5 0/1:785:94:52,42:360,328:688,94:0.1197:2,2:27.1:1:30.4:1:0.65978:1.13:60:188:0.1222:0.0025:1.1 +8 145737286 . G A 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.43019;LSEQ=ATGAGCTGCCTGGCCTTACT;RSEQ=CACTCACTCTGGCCTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2279:753:414,339:789,731:1520,753:0.3304:2,2:24.6:1:28.8:1:0.18049:1.13:59.9:74.3:0.331:0:1.2 0/1:794:139:74,65:289,273:562,139:0.1751:2,2:25.5:1:28.2:1:0.70587:1.08:60:278:0.2023:0:1.2 +8 145737514 . G A 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00379;SOR=1.44456;LSEQ=GATGGTCCCAGGCCCCGCCC;RSEQ=CCTCCTCCCAACCTGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1110:366:234,132:469,273:742,366:0.3297:2,2:23.3:1:30.3:1:0.84241:1.03:59.9:182:0.3336:0:1.1 0/1:349:145:90,55:124,80:204,145:0.4155:2,2:22.6:1:29:1:0.82436:1.06:60:144:0.4198:0:1.1 +8 145737636 . A G 353 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01201;SOR=0.1742;LSEQ=GTCCTTCTCCTCAGCGGTCA;RSEQ=GTCCCCCGGGCTGCGAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2097:2094:1007,1087:1,0:1,2094:0.9986:0,2:25.7:1:32:1:0.48115:0:60:66.548:0.9985:0:1.1 1/1:735:729:352,377:2,0:2,729:0.9918:0,2:24.9:1:30.4:1:0.23417:0:60:59.75:0.9931:0:1.2 +8 145737816 . C T 273 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00339;SOR=0.70208;LSEQ=ACTGCAGCTGGCAGAGAGCC;RSEQ=GCCGCACAGAGGCCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1252:443:216,227:420,387:807,443:0.3538:2,2:25.1:1:31.1:1:0.28712:1.14042:60:48.222:0.3531:0:1.1 0/1:443:123:64,59:159,159:318,123:0.2777:2,2:24.2:1:29.7:1:0.75035:1.08:60:122:0.2805:0:1.2 +8 145738410 . T TGGTGCA 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=4.000;MSILEN=6;SSF=0;SOR=Inf;LSEQ=TTCCTGCTCCGAGGGCGGCC;RSEQ=GGTGCAGGTGCAGGTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1671:0:0,0:706,963:1669,0:0:2,0:23.9:1:30.8:1:1:0:59.9:52.839:0.9994:0:0.5 0/1:630:41:17,24:262,325:587,41:0.0651:2,2:30.8:1:30.1:1:0.74691:1.13786:58:40:0.0651:0.0095:0.3 +8 145738441 . G A 279 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=CAGGTGCAGGCTGGGAACAC;RSEQ=CGCTGTACCAGCCTCTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1334:668:257,411:249,415:664,668:0.5007:2,2:24.8:1:29.8:1:0.73495:1.04:60:46.714:0.4992:0:1.2 0/0:487:0:0,0:196,291:487,0:0:2,0:23.5:1:29.9:1:1:0:59.8:36.462:1:0:0.2 +8 145738442 . C T 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00147;SOR=Inf;LSEQ=AGGTGCAGGCTGGGAACACG;RSEQ=GCTGTACCAGCCTCTTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1311:0:0,0:494,817:1311,0:0:2,0:25:1:30.6:1:1:0:59.9:49.423:1:0:0.7 0/1:490:5:2,3:194,291:485,5:0.0102:2,2:19.4:1:28.2:1:1:1:60:10:0.0105:0:1.2 +8 145738575 . GCA G 71 Bias STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.69018;SOR=0.48513;LSEQ=CACTGGGGGCTCGAGCACTG;RSEQ=GTGTGGGGGGGGGGGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:7:0,7:344,91:435,7:0.0156:2,0:29.1:1:25.4:1:2e-05:0:60:14:0.0171:0:3.7 0/0:131:1:0,1:94,28:122,1:0.0076:2,0:30:0:23:0:0.23577:0:60:2:0.0086:0:5 +8 145738581 . TGG T 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.00207;SOR=2.05468;LSEQ=GGGCTCGAGCACTGGCAGTG;RSEQ=GGGGGGGGGGTGCCAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:599:79:68,11:172,229:401,79:0.1319:2,2:24.4:1:31.3:1:0:8.20:59.5:25.333:0.141:0.0167:0.9 0/1:147:35:31,4:34,46:80,35:0.2381:2,2:29.4:1:31.3:1:0:10.28:60:70:0.2672:0.0204:1 +8 145738592 . GGT G 51 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.49358;SOR=1.62764;LSEQ=CTGGCAGTGTGGGGGGGGGG;RSEQ=GCCAACCTGGGGCTGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:9:9,0:341,276:617,9:0.0142:2,0:23.8:1:16.2:1:0.00568:0:60:0.286:0.0037:0:1.7 0/1:174:4:4,0:97,72:169,4:0.023:2,0:18.8:1:24.3:1:0.14183:0:58.5:3:0.0196:0:2.5 +8 145738604 . G A 94 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=34.43425;LSEQ=GGGGGGGGGGTGCCAACCTG;RSEQ=GGCTGCAGGAAGAGGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:672:1:1,0:368,302:670,1:0.0015:2,0:1:0:27:0:1:0:60:2:0.0015:0:1 0/1:204:10:6,4:111,83:194,10:0.049:2,2:29.9:1:28.4:1:1:1.12:60:9:0.0457:0:1.2 +8 145738622 . G A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01337;SOR=Inf;LSEQ=TGGGGCTGCAGGAAGAGGTG;RSEQ=CAGTGGGCAGGCTGCCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:768:0:0,0:421,343:764,0:0:2,0:24.4:1:30.6:1:1:0:59.3:11.949:0.9986:0:0.6 0/1:240:3:2,1:138,99:237,3:0.0125:2,2:26:1:23:1:1:1.43:60:2:0.0089:0:2.7 +8 145738767 . CG C 338 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.40363;SOR=0.70222;LSEQ=CCACCGTGGCCACCACCACC;RSEQ=GCAACTGGCCCTGCATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1690:1669:781,888:7,8:15,1669:0.9876:2,2:26.3:1:31.6:1:1:1.01:59.9:165.9:0.9881:0.1391:0.2 1/1:568:558:282,276:5,3:8,558:0.9824:2,2:26.6:1:30.7:1:0.72483:1.62982:59.9:278:0.9841:0.1074:0.3 +8 145738827 . C T 130 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=69.26195;LSEQ=CGTTCCCGGCTGCACATGCC;RSEQ=GCGTGGTAGGCCTCGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1076:1:0,1:431,644:1075,1:9e-04:2,0:31:0:14:0:1:0:60:0:0:0:1 0/1:346:21:6,15:118,207:325,21:0.0607:2,2:27.3:1:29.6:1:0.63964:1.42373:60:42:0.0616:0:1.3 +8 145738911 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.05044;SOR=Inf;LSEQ=GTGGGATGGGACCATGTGTG;RSEQ=CCAAGGTGGGTCCACGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:599:0:0,0:339,260:599,0:0:2,0:24.4:1:31.9:1:1:0:60:53.455:1:0:0.1 0/1:174:2:1,1:112,60:172,2:0.0115:2,2:23:1:26:1:1:1.85962:60:4:0.0118:0:1 +8 145739073 . G A 100 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=14.35813;LSEQ=TCGAGGTTTTGAAAACGTTT;RSEQ=CCTTGCAGCAGCGTCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1303:2:2,0:564,737:1301,2:0.0015:2,0:1:0:23.5:1:0.1885:0:60:4:0.0016:0:1 0/1:555:12:6,6:228,315:543,12:0.0216:2,2:26:1:27.9:1:0.57196:1.38:60:24:0.0218:0:1.3 +8 145739115 . CGTGGGCA C 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTGATGAGGAGCGGTTGG;RSEQ=GTGGGGAGTGAGGAGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:720:0:0,0:207,508:715,0:0:2,0:25.7:1:31.2:1:1:0:59.6:54:0.9929:0:0.2 0/1:257:23:8,15:66,168:234,23:0.0895:2,2:23.8:1:30.8:1:0.48025:1.36:58.7:46:0.0895:0.0156:0.5 +8 145739134 . G T 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCGTGGGCAGTGGGGAGTGA;RSEQ=GAGGGGTCGGCGTGTGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:0:0,0:110,440:550,0:0:2,0:23.6:1:31.4:1:1:0:58.8:67.75:0.9982:0:0.4 0/1:167:11:2,9:32,123:155,11:0.0659:2,2:18.5:1:30.7:1:1:1.16966:60:22:0.0671:0:1 +8 145739175 . C CGTGGGCG 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.55687;SOR=1.19622;LSEQ=GGGGAGTGAGGAGGGGTCGG;RSEQ=GTGGGGAGTGAGGAGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:94:74,20:14,190:204,94:0.2947:2,2:8.3:1:28.8:1:0:48.97:34.3:8.4:0.3182:0.2884:2.4 0/1:66:22:19,3:2,42:44,22:0.3333:1,2:7.5:1:28:1:0:110.86:35.6:6.333:0.3393:0.3182:3.5 +8 145739176 . GTGGGGAGTGAGGAGGGGTCGGCG C 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.00085;SOR=Inf;LSEQ=GGGAGTGAGGAGGGGTCGGC;RSEQ=TGGGCGGTGGGGAGTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:328:0:0,0:112,215:327,0:0:2,0:15.1:1:31.5:1:1:0:47.2:35.333:0.9969:0:1.7 0/1:69:4:2,2:23,42:65,4:0.058:2,2:24:1:26:1:0.617:1.81:27:3:0.0441:0.058:4.3 +8 145739182 . A G 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00459;SOR=Inf;LSEQ=GAGGAGGGGTCGGCGTGGGG;RSEQ=GTGAGGAGGGGTCGGCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:152,163:315,0:0:2,0:14.7:1:29.3:1:1:0:46.4:5.702:1:0:1.8 0/1:69:3:0,3:32,33:65,3:0.0435:2,0:19.3:1:21:1:0.24144:0:41.3:2:0.0317:0:3.3 +8 145739186 . A G 57 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.73007;SOR=1.21268;LSEQ=AGGGGTCGGCGTGGGGAGTG;RSEQ=GGAGGGGTCGGCGTGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:13:0,13:179,164:343,13:0.0361:2,1:13.4:1:15.5:1:9e-05:0:31.1:0.083:0.0032:0:4.1 0/1:69:3:1,2:37,28:65,3:0.0435:2,2:12:1:29.3:1:0.57918:2.60567:54.3:6:0.0484:0:4 +8 145739204 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.05529;SOR=12.15177;LSEQ=TGAGGAGGGGTCGGCGTGGG;RSEQ=GGTGGGGAGTGAGAAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:430:1:0,1:298,130:428,1:0.0023:2,0:22:0:15:0:0.30536:0:34:0:0:0:7 0/1:72:2:2,0:55,15:70,2:0.0278:2,0:29.5:1:27.5:1:1:0:46:4:0.0299:0:3 +8 145739205 . G A 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.91227;LSEQ=GAGGAGGGGTCGGCGTGGGC;RSEQ=GTGGGGAGTGAGAAGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:26:4,22:313,102:415,26:0.059:2,2:21.8:1:31.1:1:0:16.75175:44:7.667:0.0575:0:2.7 0/1:74:4:0,4:58,11:69,4:0.0541:2,0:6:1:31.3:1:0.00125:0:56.8:8:0.0556:0:1.3 +8 145739218 . A G 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00609;SOR=0.53856;LSEQ=CGTGGGCGGTGGGGAGTGAG;RSEQ=AGGGGTCGGCGTGGGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:506:329:225,104:1,0:1,329:0.6502:0,2:28.2:1:32:1:1:0:42.4:35.556:0.6612:0:2.5 1/0:98:49:39,10:0,1:1,49:0.5:0,2:30.1:1:30.4:1:0.22:0:41:23.5:0.5165:0:3.1 +8 145739244 . T A 112 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.84696;SOR=1.06068;LSEQ=TCGGCGTGGGCGGTGGGGAG;RSEQ=GAGGAGGGGTCGGCGTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:787:36:33,3:578,161:739,36:0.0457:2,2:21.8:1:21.8:1:0.05937:3.06:29.2:1.25:0.0287:0:4.3 0/1:186:9:9,0:125,48:173,9:0.0484:2,0:21:1:23.4:1:0.11477:0:28.8:3.5:0.0417:0:4.8 +8 145739289 . G T 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01191;SOR=13.25136;LSEQ=AGCAGCCAGGGCCCTGCAGG;RSEQ=TCCCCAGAGCACACACACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1269:1:0,1:824,444:1268,1:8e-04:2,0:1:0:25:0:0.35067:0:60:2:8e-04:0:1 0/1:386:4:1,3:231,151:382,4:0.0104:2,2:15.5:1:24.3:1:0.30595:4.57176:60:3:0.008:0:1.8 +8 145739817 . G A 181 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=99.6021;LSEQ=CCTCACCCCTAGGCCCATGA;RSEQ=GCCCCCACCTTCTGCAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2148:2:2,0:1157,986:2143,2:9e-04:2,0:1:0:27:1:0.50302:0:60:4:0.001:0:1 0/1:790:67:38,29:404,318:722,67:0.0848:2,2:26.8:1:30:1:1:1.03:60:21.333:0.0828:0:1.1 +8 145739924 . G A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00053;SOR=0.65795;LSEQ=AGACACCTGCAAATGCAGGA;RSEQ=CGACAGCCGTCATACGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1296:449:139,310:265,582:847,449:0.3465:2,2:23.9:1:29.8:1:0.94976:1.01547:59.9:148.667:0.3479:0:1.1 0/1:468:121:37,84:114,233:347,121:0.2585:2,2:23.8:1:28.8:1:0.73489:1.11049:60:59.5:0.2565:0:1.2 +8 145740238 . G A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00046;SOR=Inf;LSEQ=CCCAGGGGAGGGGGTGGTTA;RSEQ=GGGACAAGCAGCAGTTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:0:0,0:317,47:364,0:0:2,0:23.9:1:33.2:1:1:0:59.8:120.333:1:0:0.1 0/1:102:5:5,0:77,20:97,5:0.049:2,0:26.2:1:29:1:0.58002:0:60:10:0.0495:0:1.6 +8 145740375 . C T 151 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=52.78113;LSEQ=CCAACGTGAGGCAGGGGCTG;RSEQ=GCCGGCTGTAGAGCAGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1402:2:1,1:714,685:1399,2:0.0014:2,2:30:1:29.5:1:1:1.04232:60:4:0.0015:0:1 0/1:484:34:16,18:230,220:450,34:0.0702:2,2:31:1:29.7:1:0.72328:1.17574:60:68:0.0716:0:1.1 +8 145740443 . C A 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCACCTGTAGGCAGCACCAG;RSEQ=AGCGTGGAGATGCCTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1099:0:0,0:550,547:1097,0:0:2,0:25.1:1:32.3:1:1:0:60:90.417:0.9991:0:0.1 0/1:377:31:14,17:171,175:346,31:0.0822:2,2:18.7:1:29.3:1:0.70989:1.18599:60:62:0.0833:0:1.3 +8 145740956 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03134;SOR=Inf;LSEQ=AGGCAGTGCCCTTCCTCTGG;RSEQ=CTACTTTTTCCAAAGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:337:0:0,0:70,267:337,0:0:2,0:24.7:1:32.4:1:1:0:59.7:41.125:1:0:0.1 0/1:73:2:0,2:10,61:71,2:0.0274:2,0:19.5:1:31:0:1:0:60:4:0.0278:0:1 +8 145741073 . TA T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04485;SOR=Inf;LSEQ=AAGGCCTGTTGCTTGGAACA;RSEQ=AGTGTCCCCCAAAAGAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:616:0:0,0:517,98:615,0:0:2,0:22.9:1:28.7:1:1:0:60:75.875:1:0:0.4 0/1:166:2:1,1:135,29:164,2:0.012:2,2:13.5:1:30.5:1:0.32968:4.59387:55:4:0.012:0:2.5 +8 145741097 . C T 52 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05467;SOR=4.45353;LSEQ=TGTCCCCCAAAAGAGCACTG;RSEQ=GCCCTCTCCACAGTGTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:953:3:1,2:711,239:950,3:0.0031:2,2:6.3:1:23.3:1:0.15921:5.93608:60:2:0.0021:0:2.7 0/1:288:4:1,3:220,64:284,4:0.0139:2,2:23.5:1:26.3:1:0.04044:10.20353:60:8:0.014:0:2 +8 145741130 . C T 276 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03085;SOR=0.79231;LSEQ=GTGTTGGCCGGACCCACCCT;RSEQ=CAGGGCAGATGTCTCACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1555:562:367,195:679,312:991,562:0.3614:2,2:26.6:1:30.3:1:0.19585:1.15622:59.9:36.467:0.3601:0:1.1 0/1:533:165:104,61:242,126:368,165:0.3096:2,2:24.5:1:29.1:1:0.55683:1.12627:60:330:0.3102:0:1.2 +8 145741702 . C G 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=1.5889;LSEQ=TGTGCGGGGCTCTCCCAGGG;RSEQ=TCCTCGTTCCATCTCCGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1879:566:253,313:614,695:1309,566:0.3012:2,2:23.8:1:31.8:1:0.39131:1.09292:60:55.6:0.3005:0:1.4 0/1:642:261:133,128:182,199:381,261:0.4065:2,2:24.5:1:30.7:1:0.46956:1.14:59.9:64.25:0.4086:0:1.3 +8 145741765 . G A 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=0.66747;LSEQ=TGGGGGCTCCCCACACGGAT;RSEQ=CTGACTTCTTGGAAGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1800:552:295,257:645,599:1244,552:0.3067:2,2:24.4:1:28.9:1:0.53936:1.07:59.9:68:0.3067:0:1.5 0/1:645:147:78,69:253,245:498,147:0.2279:2,2:24.5:1:27.6:1:0.63997:1.09:60:72.5:0.2273:0:1.5 +8 145742005 . C T 72 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02602;SOR=4.18704;LSEQ=TGGAGCCGGCCTGGCCTTGG;RSEQ=TGGGGCTCAGGGAGCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1588:4:0,4:773,810:1583,4:0.0025:2,0:1:0:27.3:1:0.12503:0:60:8:0.0026:0:1 0/1:573:6:2,4:285,282:567,6:0.0105:2,2:26.3:1:28:1:0.45025:2.01887:60:12:0.0107:0:1 +8 145742138 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05024;SOR=Inf;LSEQ=GCCACGGTCTGCGGCCCAGG;RSEQ=CTGGTCCGGCCTGGGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:694:0:0,0:212,482:694,0:0:2,0:23.1:1:31.7:1:1:0:59.9:48.571:1:0:0.1 0/1:201:2:1,1:55,144:199,2:0.01:2,2:21:0:30.5:1:0.4806:2.60:60:4:0.0101:0:1.5 +8 145742172 . C G 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GGAGGGGAACAACAGAACAG;RSEQ=AGGAGGAACTCAGGCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:94,330:424,0:0:2,0:26.4:1:32.3:1:1:0:59.8:46.111:0.9952:0:0.1 0/1:118:7:1,6:24,87:111,7:0.0593:2,2:25.4:1:30.4:1:1:1.64896:60:14:0.0619:0:1 +8 145742514 . A G 338 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20057;LSEQ=GCGGCTCCGCCCTGGCGTAG;RSEQ=CTGTGGACTCTTGGTCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1654:1647:732,915:1,1:2,1647:0.9958:2,2:26.3:1:31.7:1:1:1.24982:59.9:48.909:0.9969:0:1.2 1/1:567:565:249,316:1,0:1,565:0.9965:0,2:24.4:1:30.8:1:0.4417:0:60:50.364:0.9982:0:1.2 +8 145742653 . T C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04215;SOR=Inf;LSEQ=CCAGCCACCCCTCCCGCACC;RSEQ=GGAGCGAGGCCCGGCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:0:0,0:65,235:300,0:0:2,0:23.3:1:30.5:1:1:0:60:22.077:1:0:0.5 0/1:78:2:1,1:22,54:76,2:0.0256:2,2:5:1:29.5:1:0.50549:2.42:60:4:0.0256:0:1 +8 145742716 . C A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.49819;LSEQ=CCAAGTTCTGTGCCCCACGG;RSEQ=GGCCTGGCCGCGACTCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:245:238:143,95:1,0:1,238:0.9714:0,2:22.7:1:29:1:1:0:59.9:7.815:0.9953:0:1.3 1/1:52:51:40,11:1,0:1,51:0.9808:0,2:21.1:1:28.1:1:1:0:60:16:1:0:1.1 +8 145742850 . T C 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=59.39408;LSEQ=TGCGGAGCCCGCCGCCGGCC;RSEQ=GGCCCGTGGTACGCTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1013:2:1,1:478,532:1010,2:0.002:2,2:8:1:21.5:1:1:1.11:60:1:0.001:0:1.5 0/1:370:39:20,19:158,172:330,39:0.1054:2,2:26.4:1:28.4:1:0.73641:1.15:59:18.5:0.1022:0:1.4 +8 145742879 . T C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1379;SOR=1.21609;LSEQ=GTACGCTTCAGAGTGCGGTA;RSEQ=TCCCGGTAGAGCGCTGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1039:306:121,185:292,440:732,306:0.2945:2,2:27.8:1:32.7:1:0.94461:1.01464:60:75.5:0.2952:0:1.2 0/1:389:131:60,71:107,150:257,131:0.3368:2,2:24.1:1:31.1:1:0.44943:1.18:60:42.667:0.3333:0:1.2 +8 145743000 . G A 67 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.003;SOR=Inf;LSEQ=GCTCACCGCGGGTCTCCTCC;RSEQ=GCGCCGCCTCCACGTCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1054:0:0,0:524,528:1052,0:0:2,0:26:1:30.3:1:1:0:60:51.6:0.9981:0:0.2 0/1:482:5:3,2:236,241:477,5:0.0104:2,2:24.8:1:29.2:1:0.68361:1.53:60:10:0.0105:0:1.2 +8 145743004 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00285;SOR=Inf;LSEQ=ACCGCGGGTCTCCTCCGGCG;RSEQ=CGCCTCCACGTCGTCCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1045:0:0,0:513,530:1043,0:0:2,0:26:1:31.6:1:1:0:60:51.15:0.998:0:0.2 0/1:471:5:1,4:230,236:466,5:0.0106:2,2:11:1:25.6:1:0.37279:3.8883:60:10:0.0107:0:1.4 +8 145743077 . G A 40 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.6343;SOR=1.60199;LSEQ=AGCCCCTCGGCCCCTGGGCA;RSEQ=CCCGCACCTGGCTCGGTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:359:3:3,0:143,213:356,3:0.0084:2,0:1:0:25.7:1:0.06644:0:60:6:0.0085:0:1 0/1:150:2:1,1:61,87:148,2:0.0133:2,2:34:1:28.5:1:1:1.42:60:4:0.0133:0:1 +8 145743081 . G A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18843;SOR=0;LSEQ=CCTCGGCCCCTGGGCAGCCC;RSEQ=CACCTGGCTCGGTCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:6:5,1:129,188:317,6:0.0186:2,2:9.7:1:27.8:1:0.08551:7.25:60:12:0.019:0:1.3 0/0:131:0:0,0:53,78:131,0:0:2,0:16.5:1:30.7:1:1:0:59.9:130:1:0:0.3 +8 145743087 . G A 37 pSTD;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63096;SOR=1.63261;LSEQ=CCCCTGGGCAGCCCGCACCT;RSEQ=GCTCGGTCGCCGCCCGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:3,0:109,173:282,3:0.0105:2,0:1:0:23.7:1:0.0597:0:60:6:0.0108:0:1 0/1:117:2:1,1:46,69:115,2:0.0171:2,2:10:0:24.5:1:1:1.49:60:4:0.0172:0:1.5 +8 145743096 . G A 44 pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61449;SOR=1.81633;LSEQ=AGCCCGCACCTGGCTCGGTC;RSEQ=CCGCCCGCGCTGCCGTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:3:2,1:86,127:213,3:0.0139:2,2:3.7:1:28:1:0.56817:2.94:60:6:0.014:0:1 0/1:80:2:1,1:33,45:78,2:0.025:2,2:31:0:30:1:1:1.36:60:4:0.0256:0:1 +8 145743121 . G A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.56283;SOR=0;LSEQ=CCGCGCTGCCGTCGGAACGC;RSEQ=CGCTCCCACGCCTGCAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:3:2,1:67,68:135,3:0.0214:2,2:12.7:1:25:1:1:2.02:60:2:0.0149:0:2 0/0:53:0:0,0:26,27:53,0:0:2,0:24.8:1:30.8:1:1:0:60:52:1:0:0.4 +8 145743128 . C A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.56002;SOR=0;LSEQ=GCCGTCGGAACGCGCGCTCC;RSEQ=ACGCCTGCAGCCGCTCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:3:3,0:71,68:139,3:0.0211:2,0:10.7:1:22.3:1:0.24603:0:60:2:0.0145:0:2 0/0:56:0:0,0:29,27:56,0:0:2,0:20.6:1:31.3:1:1:0:60:112:1:0:0.4 +8 145743136 . C A 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.13636;LSEQ=AACGCGCGCTCCCACGCCTG;RSEQ=AGCCGCTCCCGCACGTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:72,68:140,2:0.014:2,2:26.5:1:31:1:1:1.05842:60:4:0.0142:0:1.5 0/1:63:1:1,0:32,30:62,1:0.0159:2,0:1:0:24:0:1:0:60:2:0.0164:0:1 +8 145743160 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTCCCGCACGTCCCGCAG;RSEQ=CGCTCCATGGCGCGCGCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:64,66:130,2:0.0152:2,2:8:1:32:0:1:1.03:60:4:0.0155:0:1 0/0:49:0:0,0:24,25:49,0:0:2,0:19.6:1:31.2:1:1:0:59.6:98:1:0:0.3 +8 145743227 . C G 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52193;SOR=0;LSEQ=CCAGCGAATCTCCCGCGCAG;RSEQ=CGTCGCGGGGGCCGACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:19,23:42,2:0.0455:2,2:5.5:1:30:1:1:1.21:60:4:0.0455:0:1.5 0/0:27:0:0,0:12,14:26,0:0:2,0:18.5:1:30.8:1:1:0:60:52:0.963:0:0.3 +8 145743657 . C A 27 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCCCTGGTGGGAGACG;RSEQ=ATCCGACCTGGAGGAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:23:1:27.5:1:0.33333:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 145745182 . T C 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCCTGCCAGGCCCTGCCC;RSEQ=TGCTGCCACGCGAACTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:29.8:1:32.6:1:1:0:60:10:1:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 145892218 . A C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCTCCAGTTCTCACAGC;RSEQ=AAGCCCCAATACAGTGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:48,9:57,2:0.0339:2,2:25:1:31:1:0.31268:5.1122:60:4:0.0339:0:1 0/0:29:0:0,0:24,5:29,0:0:2,0:31.9:1:30.2:1:1:0:60:58:1:0:0.1 +8 146187396 . GT G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCAGGGATATTGGTCTGTA;RSEQ=TTTTTTTTTTTGTTTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:31:1:1:0:53.5:4:1:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 146260665 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCAAAGGATTTCTCAGTT;RSEQ=GCAATAAATAACAAAATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:15:1:31.5:1:1:1:22:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 146260670 . T G 34 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGATTTCTCAGTTCGCAA;RSEQ=AAATAACAAAATCTATCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:20:1:34.5:1:1:3.1622:22:4:0.2857:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +8 146261019 . T C 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58154;SOR=2.21075;LSEQ=CCTTGCCAAATTTGTTTCCT;RSEQ=CAGGATTGAGGCCATCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:1,6:5,11:16,7:0.3043:2,2:26.9:1:33:1:0.62139:2.6224:40.6:14:0.3043:0:1.9 1/0:4:2:0,2:1,1:2,2:0.5:2,0:21.5:1:30.5:1:1:0:39:4:0.5:0:1.5 +8 146261031 . C T 89 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.67697;LSEQ=TGTTTCCTTCAGGATTGAGG;RSEQ=CATCAAGCTACAGATGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:1,6:4,10:14,7:0.3333:2,2:20.1:1:32:0:0.62436:2.31002:45.1:14:0.3333:0:1.9 0/1:4:1:0,1:1,2:3,1:0.25:2,0:27:0:30:0:1:0:51:2:0.25:0:2 +8 146261151 . G A 32 v3;MAF0.05;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTAGAGAGTTCCCTTCTGA;RSEQ=GACACTACCACTGGAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:42:0:32.5:1:1:1.73:60:4:0.4:0:1.5 1/1:1:1:0,1:0,0:0,1:1:0,0:28:0:33:0:1:0:58:2:1:0:1 +8 146278052 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGCGGAGCCCGGCTTCC;RSEQ=GGCCCAGTTTCCAGCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:19,7:26,2:0.0714:2,2:30:1:32.5:1:0.49735:2.60494:60:4:0.0714:0:1 0/0:11:0:0,0:10,1:11,0:0:2,0:13.5:1:29.5:1:1:0:60:22:1:0:0.1 +8 146278107 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51097;SOR=0;LSEQ=TCTGTCTCTGCCCAGAGCAA;RSEQ=CTACGTGCAGTAACGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:27,23:50,2:0.0385:2,2:36:1:29.5:1:1:1.17028:60:4:0.0385:0:1 0/0:36:0:0,0:20,16:36,0:0:2,0:29.4:1:30.7:1:1:0:59.7:35:1:0:0.1 +8 146278188 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50089;SOR=0;LSEQ=CGAAAAAACAAAAGAATAAG;RSEQ=AGAAAACGCGGAACAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:18,2:0.1:2,2:21:1:27.5:1:1:1.54:60:4:0.1:0:1 0/0:14:0:0,0:2,12:14,0:0:2,0:20.7:1:30.3:1:1:0:60:28:1:0:0.1 +9 421860 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.1286;LSEQ=TTCTTCTTATATTCTAGTCT;RSEQ=TCAATCAAAGAGCGGGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:40:35,5:41,7:48,40:0.4545:2,2:28.2:1:33.1:1:1:1.19:60:80:0.4545:0:1 0/1:94:9:9,0:72,13:85,9:0.0957:2,0:23.8:1:32.8:1:0.35191:0:60:18:0.0978:0:1.1 +9 421980 . T A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2165;SOR=0.81925;LSEQ=CTTCTCAGTTGAGCTTGTTA;RSEQ=GAACTTCTGGTTATCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:153:75,78:85,83:168,153:0.4752:2,2:27:1:30.9:1:0.82343:1.06484:60:75.5:0.4719:0:1.1 0/1:357:152:71,81:94,111:205,152:0.4258:2,2:27.3:1:29.9:1:0.91466:1.03:60:151:0.4266:0:1.1 +9 422157 . T C 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66225;SOR=0.58813;LSEQ=TGAGTCACTCGGCAACTTTC;RSEQ=GCTACTTTTACCTAAAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:27:23:0,23:0,4:4,23:0.8519:0,1:27.8:1:31.1:1:1:0:60:46:0.8519:0:1 1/0:13:10:1,9:0,3:3,10:0.7692:0,2:26.9:1:29.9:1:1:0:56.1:20:0.7692:0:1 +9 1011564 . A AT 84 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TGCGCCATCACACCAGGCTA;RSEQ=TTTTTTTTTTTTGTATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:1,0:1,6:0.75:0,0:21.5:1:32.8:1:1:0:34.3:12:0.75:0:1.2 0/0:2:0:0,0:1,0:1,0:0:0,0:32:1:31:1:1:0:52:2:0.5:0:5 +9 1011653 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13356;SOR=0;LSEQ=GACCTCAAGTAATCTACCCG;RSEQ=CTCGGCCTCCCAAAGTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:22,3:25,2:0.0741:2,2:20:1:27:0:0.2792:6.49359:43:4:0.0769:0:1 0/0:46:0:0,0:41,5:46,0:0:2,0:23.8:1:31.5:1:1:0:57.9:92:1:0:0 +9 1011681 . A G 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14351;SOR=0;LSEQ=TCCCAAAGTACTGGGATTAC;RSEQ=GGCGTGAGCCACTGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:36,18:54,2:0.0357:2,2:23:0:32.5:1:1:1.97357:60:4:0.0364:0:1.5 0/0:91:0:0,0:68,23:91,0:0:2,0:21.7:1:29.4:1:1:0:59.2:90:1:0:0.1 +9 1011695 . G T 26 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17837;SOR=0;LSEQ=GATTACAGGCGTGAGCCACT;RSEQ=CAGCTGGCCTGGTTGGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:2:1,1:47,29:76,2:0.0256:2,2:6.5:1:26:0:1:1.61025:55.5:4:0.026:0:1 0/0:106:0:0,0:74,32:106,0:0:2,0:25.3:1:31.6:1:1:0:59.3:212:1:0:0.1 +9 1011710 . G C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.50566;SOR=Inf;LSEQ=CCACTGCAGCTGGCCTGGTT;RSEQ=GCCTTTTTTAAGATACCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:68,41:109,0:0:2,0:24.4:1:31.8:1:1:0:59.9:26.25:0.9906:0:0.2 0/1:141:2:1,1:86,51:137,2:0.0142:2,2:15:0:31.5:1:1:1.67959:60:4:0.0143:0:1.5 +9 1011738 . C T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20777;SOR=0;LSEQ=TTAAGATACCAACCTGTGTG;RSEQ=CATCCATGCCAGACATGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:2:1,1:87,74:161,2:0.0123:2,2:7:1:29:1:1:1.1745:60:4:0.0123:0:1 0/0:194:0:0,0:100,94:194,0:0:2,0:25.6:1:30.7:1:1:0:59.7:63.667:1:0:0.2 +9 1011775 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49837;SOR=Inf;LSEQ=GTAACAATTATGCCAAAAGG;RSEQ=ATCCAGCTAGCACGTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:71,81:152,0:0:2,0:28.9:1:31.7:1:1:0:60:49.667:0.9933:0:0.1 0/1:154:2:1,1:62,88:150,2:0.013:2,2:23:1:29.5:1:1:1.42:60:4:0.0131:0:1 +9 1011900 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.2381;SOR=0;LSEQ=GAACAATAGACATTTTTTTT;RSEQ=GTGGGGCCAAAAGGTACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:0,3:0,13:13,3:0.1875:1,0:31.3:1:31.3:1:1:0:60:6:0.1875:0:1 0/0:12:0:0,0:1,11:12,0:0:2,0:26.2:1:30:1:1:0:60:24:1:0:0.1 +9 2039699 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50508;SOR=0;LSEQ=AAATGCTGGCCCGAGGCCAG;RSEQ=CCCTCCCCGAAACGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:19,10:29,2:0.0645:2,2:30:1:31.5:1:1:1.85871:60:4:0.0667:0:1 0/0:22:0:0,0:18,4:22,0:0:2,0:19.7:1:30.9:1:1:0:60:21:1:0:0.2 +9 2039827 . G A 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCAGCAGCAACAGCAGCC;RSEQ=CAGCAGCAGCCGCCGCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:11,13:9,13:22,24:0.5217:2,2:22.8:1:31:1:0.77386:1.22:56.4:48:0.5333:0:1 0/0:33:0:0,0:15,18:33,0:0:2,0:22.9:1:30.5:1:1:0:52.4:32:1:0:0.3 +9 2039860 . A G 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.02087;SOR=Inf;LSEQ=CCGCAACCACAGACGCAGCA;RSEQ=CAACAGCAGCCGGCCCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:9,26:35,0:0:2,0:26.3:1:29.8:1:1:0:58.7:70:1:0:0.5 0/1:23:4:2,2:6,13:19,4:0.1739:2,2:38.8:1:32.8:1:0.58893:2.09:60:8:0.1739:0:1.3 +9 2039945 . G A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.005;SOR=0;LSEQ=ATAATGCCATGGTCCAACTC;RSEQ=GATAACAAAGACTGCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,1:1,4:0.8:0,0:12:1:31.8:1:1:0:60:8:0.8:0:1 0/0:9:0:0,0:1,8:9,0:0:2,0:24.1:1:30.1:1:1:0:60:18:1:0:0 +9 2047439 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14079;SOR=0;LSEQ=CATCAGCCCCATCCAGAAAC;RSEQ=GCAAGGCCTGGACCCCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:55,51:106,2:0.0185:2,2:31:0:31:0:1:1.07765:60:4:0.0187:0:1.5 0/0:179:0:0,0:92,87:179,0:0:2,0:28.3:1:29.5:1:1:0:60:178:1:0:0.2 +9 2047444 . G A 28 v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55889;SOR=0.30018;LSEQ=GCCCCATCCAGAAACCGCAA;RSEQ=GCCTGGACCCCGTGGAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:54,50:104,2:0.0189:2,2:37:0:28:1:1:1.07919:60:4:0.019:0:1 0/0:175:1:1,0:86,86:172,1:0.0057:2,0:1:0:24:0:1:0:60:2:0.0058:0:1 +9 2056861 . G GT 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00274;SOR=Inf;LSEQ=ACCAGGTTCTTAGACCCTGG;RSEQ=CTTTGCTCACCCTCACTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:11,24:35,0:0:2,0:22.3:1:31.8:1:1:0:60:70:1:0:0 0/1:40:9:2,7:12,19:31,9:0.225:2,2:27.7:1:29.6:1:0.45271:2.17012:60:18:0.225:0.025:0 +9 2086803 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22691;SOR=Inf;LSEQ=ATTTTCCCTTGCTTACTACA;RSEQ=GTCCGTCCTTCCTCTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:61,11:72,0:0:2,0:20.1:1:31.6:1:1:0:60:144:1:0:0.1 0/1:66:2:1,1:53,11:64,2:0.0303:2,2:29:1:29:1:0.33287:4.65641:60:4:0.0313:0:1 +9 2115851 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17849;SOR=0;LSEQ=GCCCAAGACCGAGCTCACCG;RSEQ=ATCGGGCAGCAGAACGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:2:1,1:45,23:68,2:0.0286:2,2:17:1:29:1:1:1.93656:60:4:0.0286:0:1 0/0:95:0:0,0:58,37:95,0:0:2,0:25.8:1:31.2:1:1:0:60:46.5:1:0:0.2 +9 2115881 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18019;SOR=0;LSEQ=CAGAACGAGGTCCGGGTACT;RSEQ=AGGCTCTGTACCGTGAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:1,1:42,31:73,2:0.0267:2,2:20.5:1:28.5:1:1:1.34927:60:4:0.0274:0:1 0/0:101:0:0,0:56,44:100,0:0:2,0:26.8:1:31.3:1:1:0:60:99:0.99:0:0.1 +9 2116002 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2321;SOR=Inf;LSEQ=AAAAGTCTTCAAGCCACGAG;RSEQ=GGAGGGCATTCCTGCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:15,49:64,0:0:2,0:23.5:1:31.2:1:1:0:60:128:1:0:0.1 0/1:60:2:1,1:18,40:58,2:0.0333:2,2:26:1:26.5:1:0.53672:2.19:60:4:0.0333:0:1 +9 2116037 . G A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02395;SOR=Inf;LSEQ=CAGGCCATCTTGGAGCATGA;RSEQ=GAGGAAAATGAGGTATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:1,30:31,0:0:1,0:26:1:31.7:1:1:0:60:62:1:0:0 0/1:30:5:0,5:3,22:25,5:0.1667:2,0:23:1:31.8:1:1:0:60:10:0.1667:0:1 +9 2875494 . A G 286 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=902.63089;LSEQ=GTTGGATGAAGGGGAGCCAA;RSEQ=GGCCAGGTTGGCTTGTAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1152:1:0,1:576,574:1150,1:9e-04:2,0:15:0:27:0:0.49957:0:60:2:9e-04:0:1 0/1:1362:602:312,290:362,398:760,602:0.442:2,2:24.2:1:31:1:0.1269:1.18:54.7:119.4:0.4435:0:1.1 +9 2876109 . C G 268 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=248.68541;LSEQ=ATGTCAGGGTGGTCAGGTCA;RSEQ=TCTGTTCCTTTCGCCTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1014:2:1,1:514,498:1012,2:0.002:2,2:22.5:1:30.5:1:1:1.0321:33:4:0.002:0:1 0/1:1146:378:186,192:397,370:767,378:0.3298:2,2:24.7:1:31.4:1:0.45073:1.10749:53.1:377:0.3313:0:1.1 +9 2876160 . T C 171 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATGTAAAACTTCCTTGAGC;RSEQ=GCAGGAAAAGCTGGTGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1021:0:0,0:559,462:1021,0:0:2,0:25:1:31.4:1:1:0:58.2:112.444:1:0:0.1 0/1:1122:56:28,28:561,503:1064,56:0.0499:2,2:24.7:1:29.6:1:0.78392:1.1152:42.9:55:0.0497:0:1.1 +9 2876417 . C G 254 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGCTTGGGGTGCTCCAAGA;RSEQ=TGCGGGCATGGTGCTGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:815:0:0,0:345,469:814,0:0:2,0:26:1:32.8:1:1:0:59.8:202.5:0.9988:0:0.1 0/1:937:288:128,160:285,364:649,288:0.3074:2,2:24.8:1:31.2:1:0.88682:1.02:52.9:56.6:0.305:0:1.2 +9 2876506 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60588;SOR=2.22265;LSEQ=AAACAGGGACCGCCTTCTCT;RSEQ=TGCTTTCTCCGTGTCTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:1:0,1:17,189:206,1:0.0048:2,0:44:0:13:0:1:0:60:0:0:0:1 0/1:187:2:1,1:26,159:185,2:0.0107:2,2:23.5:1:28.5:1:0.26859:6.02:60:4:0.0108:0:1 +9 2876508 . G T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10244;SOR=Inf;LSEQ=ACAGGGACCGCCTTCTCTGT;RSEQ=CTTTCTCCGTGTCTCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:17,182:199,0:0:2,0:24.5:1:32.2:1:1:0:60:38.8:1:0:0.2 0/1:176:3:0,3:24,149:173,3:0.017:2,0:17:1:26:1:1:0:60:2:0.0116:0:1.7 +9 3206158 . A G 205 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGTAAGAAATGGGGTAGGC;RSEQ=GTATTCATTTGTGATCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:451:0:0,0:246,205:451,0:0:2,0:26.7:1:31:1:1:0:60:55.375:1:0:0.1 0/1:506:124:64,60:202,180:382,124:0.2451:2,2:27.3:1:29.6:1:0.8364:1.05201:60:248:0.247:0:1.1 +9 3253549 . AT A 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.73425;SOR=1.13872;LSEQ=TCTGCCCAAGAAAGGCAGTG;RSEQ=TTTTTTTTTCTGCCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:188:167:127,40:16,1:17,167:0.8883:1,2:22.9:1:31.5:1:0.12553:5.01073:59.9:334:0.893:0.1809:0.8 1/1:171:154:117,37:11,4:15,154:0.9006:2,2:21.8:1:30.4:1:0.76063:1.15:60:308:0.9006:0.1871:0.8 +9 3253559 . TC T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.11733;SOR=Inf;LSEQ=AAAGGCAGTGATTTTTTTTT;RSEQ=TGCCTCCCAGGGAACCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:158,60:218,0:0:2,0:22.7:1:32.2:1:1:0:59.9:53.5:0.9907:0:0.9 0/1:212:3:1,2:148,60:208,3:0.0142:2,2:19.3:1:27:1:0.20705:4.89057:60:6:0.0144:0.0047:1.7 +9 3253564 . C T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.24868;SOR=0;LSEQ=CAGTGATTTTTTTTTTCTGC;RSEQ=TCCCAGGGAACCACAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:3:1,2:172,78:250,3:0.0119:2,2:16:1:22.7:1:0.23577:4.38156:60:2:0.008:0:3 0/0:245:0:0,0:164,81:245,0:0:2,0:21.2:1:30:1:1:0:60:34:1:0:0.8 +9 3253613 . G A 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0;SOR=0.01527;LSEQ=AGCCAGGTTAGGCAAGGAGA;RSEQ=AGCCCCCATTCAGAGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:471:470:249,221:0,0:0,470:0.9979:0,2:27.3:1:30.6:1:1:0:59.9:66.143:0.9978:0:1.1 1/1:473:415:219,196:29,28:57,415:0.8774:2,2:26.1:1:29.3:1:0.88765:1.08:60:58.286:0.8774:0:1.2 +9 3253649 . G A 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=32.92952;LSEQ=CAGAACCTCTTTGTAGCGCT;RSEQ=TATCAACTGCTATTATGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:432:1:1,0:180,251:431,1:0.0023:2,0:1:0:24:0:0.41898:0:60:2:0.0023:0:2 0/1:464:33:16,17:190,241:431,33:0.0711:2,2:22:1:28.9:1:0.71692:1.19:60:66:0.0717:0:1.2 +9 3776575 . A G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGTTAATGGAATTAAAGG;RSEQ=AGGAAAATTTCTGGGCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:0,10:1:0,2:19.3:1:31.6:1:1:0:60:20:1:0:1.5 1/1:9:9:9,0:0,0:0,9:1:0,0:27.8:1:31.4:1:1:0:60:18:1:0:1.2 +9 3776612 . C G 122 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00492;SOR=0.06465;LSEQ=TTTAGGGCTTTAGGGCAAGG;RSEQ=TCACTCACTCGCATTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:11,2:11,0:11,13:0.5417:0,2:27.7:1:33:1:0.48188:0:60:26:0.5417:0:1.4 0/1:15:1:1,0:14,0:14,1:0.0667:1,0:41:0:28:0:1:0:60:2:0.0667:0:2 +9 4099378 . G A 85 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01465;SOR=9.10194;LSEQ=AATCTTTGGCTTGCAGATGC;RSEQ=TCACTCCAATCCTTGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:0,2:6,11:17,2:0.1053:2,0:22:1:31:1:1:0:60:4:0.1053:0:1 1/0:13:7:2,5:1,5:6,7:0.5385:2,2:32:1:30.3:1:1:1.90:60:14:0.5385:0:1 +9 4099422 . C T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2451;SOR=0;LSEQ=TTCACTTGGAGTTGCCCCCC;RSEQ=GAGCCTCTGTCTTTGCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:1,3:1,7:8,4:0.3333:2,2:22.5:1:30.5:1:1:2.16:60:8:0.3333:0:1.3 0/0:6:0:0,0:2,4:6,0:0:2,0:12.2:1:29:1:1:0:60:12:1:0:0.8 +9 4110692 . C T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54747;SOR=2.71347;LSEQ=TTCCCTACTCAGGCTCTGGG;RSEQ=TAGCCAACCACAGATCCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:19:1:28.5:1:1:0:60:4:0.25:0:2.5 1/0:4:2:2,0:2,0:2,2:0.5:0,0:26:1:31.5:1:1:0:60:4:0.5:0:1.5 +9 4110798 . GA G 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.66534;LSEQ=GAAACTAATAAATCTACCTG;RSEQ=AAAAAAAATAAACATCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:2,0:51,6:57,2:0.0339:2,0:8.5:1:31.8:1:1:0:60:4:0.0345:0.0169:0 0/1:44:1:1,0:40,2:42,1:0.0227:1,0:34:0:33:0:1:0:60:2:0.0227:0:0 +9 4110947 . G A 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06368;LSEQ=ACACATTCAAATTCTATCTG;RSEQ=ACCCTAAAATGACAACACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:305:238:117,121:28,37:65,238:0.7803:2,2:28.9:1:30.4:1:0.40376:1.28:60:46.6:0.7819:0:1.1 0/1:479:88:46,42:190,201:391,88:0.1837:2,2:26.3:1:29.1:1:0.55672:1.16:60:87:0.1839:0:1.1 +9 4111006 . T A 39 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.90795;LSEQ=ATCAAGAAATATTCCAAAGG;RSEQ=CACAAAGGGTGTTTCTAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:58,129:187,2:0.0106:2,2:12:1:28.5:1:0.52803:2.21:60:4:0.0109:0:2 0/0:312:3:3,0:110,199:309,3:0.0096:2,0:1:0:25:1:0.0467:0:60:6:0.0096:0:1 +9 4111100 . A G 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02037;SOR=4.651;LSEQ=ACATTTTAGAATCTATATAC;RSEQ=AACAAATCTCCAAAGGTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:4:0,4:0,25:25,4:0.1379:1,0:25.8:1:32:1:1:0:60:8:0.1481:0:1 0/1:30:13:0,13:0,17:17,13:0.4333:1,1:24.8:1:30.3:1:1:0:60:12:0.4286:0:1.2 +9 4803726 . TA T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.22848;SOR=0.33272;LSEQ=TGGGGAGGCAGTGTGAAAGG;RSEQ=AAAAAAAAAAAGCTACTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:3,2:5,3:8,5:0.3846:2,2:21.4:1:30.2:1:1:1.10211:60:10:0.4167:0:0.2 0/1:18:3:2,1:9,1:10,3:0.1667:2,2:16:1:29.7:1:0.42308:3.87298:60:6:0.1667:0:1 +9 4804389 . G A 32 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCACTGCTGAGTGGGTGCC;RSEQ=GCACGGCTGCCTTTGCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:15:1:32.5:1:1:0:60:4:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:6:0:32:0:1:0:60:2:1:0:1 +9 4804708 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21336;SOR=Inf;LSEQ=AAAGCGGCCGGTGGCCGGTG;RSEQ=GCTGGTGGGGAGGACGATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:38,15:53,0:0:2,0:21.7:1:30.6:1:1:0:60:16.667:1:0:0.1 0/1:46:2:1,1:29,15:44,2:0.0435:2,2:36:1:28.5:1:1:1.90401:60:4:0.0435:0:1 +9 4804709 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.21776;SOR=Inf;LSEQ=AAGCGGCCGGTGGCCGGTGC;RSEQ=CTGGTGGGGAGGACGATCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:37,15:52,0:0:2,0:22.8:1:30.2:1:1:0:60:25:1:0:0.1 0/1:46:2:1,1:29,15:44,2:0.0435:2,2:21.5:1:31:0:1:1.90401:60:4:0.0435:0:1 +9 4804762 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50285;SOR=Inf;LSEQ=AGGACACGGTGGCGGCCACT;RSEQ=ACTCCTGCCGGAGCAGCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:32,31:63,0:0:2,0:27.8:1:30.8:1:1:0:60:14.75:1:0:0.1 0/1:79:2:1,1:35,42:77,2:0.0253:2,2:33.5:1:29:0:1:1.20:60:4:0.026:0:1 +9 4804901 . A G 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.03509;SOR=0;LSEQ=CAAGTCTGTCACCAGGTCAT;RSEQ=GGGTGGCTGGGAAGCACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:1,5:6,5:0.4545:2,0:37.4:1:32:1:1:0:60:10:0.4545:0:1.2 0/0:10:0:0,0:2,8:10,0:0:2,0:24:1:31.1:1:1:0:60:20:1:0:0.3 +9 4804950 . T C 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTTATGTGGAGAGCACCT;RSEQ=CAACTGCCGGACGGTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1:0,2:10.8:1:29.4:1:1:0:60:4:1:0:1.2 1/1:2:2:1,1:0,0:0,2:1:0,2:35:1:33:0:1:0:60:4:1:0:1 +9 4805110 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCGAAGCAGCAGGGGTAT;RSEQ=TCAAAGCCAATGAAGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:5,8:13,0:0:2,0:21.5:1:33:1:1:0:60:26:1:0:0.1 0/1:27:2:1,1:9,16:25,2:0.0741:2,2:34:1:28.5:1:1:1.74:60:4:0.0741:0:1 +9 5021924 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.79817;LSEQ=ATTACAGGTGTGAGACACTG;RSEQ=GCCCAGCCCATTTGTAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:1:0,1:136,27:163,1:0.0061:2,0:1:0:26:0:0.17073:0:60:2:0.0062:0:1 0/1:183:2:1,1:145,36:181,2:0.0109:2,2:22:1:28:1:0.36438:3.98665:60:4:0.011:0:1 +9 5042708 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGAGGGGTGCTGTGGG;RSEQ=CCATCTTGCCCAGGCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:28:1:1:0:60:4:1:0:1 +9 5050369 . G C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGTGGTGTGATCATAGCT;RSEQ=AAGAGATCCTCCTACCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:39.5:1:31.5:1:1:0:60:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 5050706 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.0947;LSEQ=TGGCGGCATGATTTTGTGCA;RSEQ=GGATGGATAAAAGTACCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:433:69:46,23:235,128:363,69:0.1594:2,2:29.2:1:30.6:1:0.78496:1.09:60:16.25:0.1529:0:1.1 0/1:531:151:87,64:215,165:380,151:0.2844:2,2:24.2:1:29.6:1:0.84651:1.04:60:150:0.2863:0:1.1 +9 5050860 . T A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.24862;SOR=Inf;LSEQ=CTTTTGCAAATCCTTACACA;RSEQ=AAGTGTGAGTAGAGATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:273:0:0,0:67,205:272,0:0:2,0:24.5:1:28.9:1:1:0:60:89.667:1:0:0.1 0/1:273:3:2,1:79,191:270,3:0.011:2,2:14.3:1:21.7:1:0.21092:4.80:60:2:0.0075:0:2 +9 5050864 . T C 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00643;SOR=Inf;LSEQ=TGCAAATCCTTACACATAAG;RSEQ=GTGAGTAGAGATTTTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:61,200:261,0:0:2,0:23.9:1:30:1:1:0:60:42.5:1:0:0.1 0/1:251:7:0,7:69,174:243,7:0.0279:2,0:13.6:1:29.1:1:0.19494:0:60:14:0.0282:0:1.1 +9 5050895 . A AT 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.50474;SOR=0;LSEQ=ATTTTATATAATTCGTATAT;RSEQ=TTTTCTGTGTTTACCCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:10,122:132,2:0.0149:2,2:37.5:1:31.5:1:0.15801:11.68:60:4:0.0149:0:0 0/0:106:0:0,0:13,93:106,0:0:2,0:23.2:1:30.3:1:1:0:60:212:1:0:0.1 +9 5050910 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.06623;SOR=Inf;LSEQ=TATATATTTTCTGTGTTTAC;RSEQ=CATGCCTTTTGATTTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:2,101:103,0:0:1,0:21.4:1:31.9:1:1:0:59.9:206:1:0:0.1 0/1:71:3:0,3:2,66:68,3:0.0423:1,0:26.7:1:29.7:1:1:0:60:6:0.0423:0:1 +9 5054548 . CT C 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.6082;SOR=2.19148;LSEQ=GTTTTGTTTTTCTGTATGTG;RSEQ=TTTTTATCCCTAGCTACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:1:1,0:146,32:178,1:0.0056:2,0:10:0:34:0:1:0:60:2:0.0056:0:0 0/1:165:2:1,1:134,29:163,2:0.0121:2,2:22.5:1:28.5:1:0.33149:4.55997:60:4:0.0122:0:0 +9 5055015 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.56921;LSEQ=GAAGTGGAAGTTTTTAATAG;RSEQ=GTGAACCTATCAAGGTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:38:0,38:0,1:1,38:0.95:0,1:23.4:1:30.3:1:1:0:59.1:37:0.9737:0:1 1/1:31:30:0,30:0,1:1,30:0.9677:0,1:21.9:1:29.9:1:1:0:60:60:0.9677:0:1 +9 5065149 . GT G 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.21917;SOR=Inf;LSEQ=AGAAAAAAATAATTTGACAA;RSEQ=TTTTTTTAAACAAAAGGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:0,71:71,0:0:1,0:22:1:30.9:1:1:0:60:70:1:0:0.1 0/1:63:2:0,2:1,60:61,2:0.0317:1,0:40:0:30:1:1:0:60:4:0.0328:0:0 +9 5066572 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.15116;SOR=Inf;LSEQ=AACATATAAAGTAGAGGAGA;RSEQ=AATTCTGACAGTTTTAGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:174,6:180,0:0:1,0:25:1:32.5:1:1:0:60:360:1:0:0.1 0/1:115:2:1,1:111,2:113,2:0.0174:1,2:20.5:1:29.5:1:0.05172:45.51972:60:4:0.0179:0:1 +9 5066795 . T A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0859;SOR=Inf;LSEQ=ACTTTTGCTGTCGAGGTTAG;RSEQ=ATGTCACACTTATTAGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:33,257:290,0:0:2,0:24.4:1:28.7:1:1:0:60:289:1:0:0 0/1:230:3:2,1:40,187:227,3:0.013:2,2:19:1:27.3:1:0.08661:9.21:60:6:0.0131:0:1 +9 5068944 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50357;SOR=0;LSEQ=ATTCTGTTGCTTGTTCTTGT;RSEQ=ATATCATTTTGTCAGAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:2,0:119,15:134,2:0.0147:2,0:11.5:1:30.5:1:1:0:60:4:0.0148:0:1 0/0:110:0:0,0:99,11:110,0:0:2,0:23.5:1:31.4:1:1:0:60:220:1:0:0 +9 5069836 . C T 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00104;SOR=Inf;LSEQ=GTTATTAAGCATTTCTTATA;RSEQ=GTAGAACACATTTCATTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:89,0:89,0:0:1,0:23.9:1:32.9:1:1:0:60:178:1:0:0.2 0/1:69:8:8,0:61,0:61,8:0.1159:1,0:21.9:1:31:1:1:0:60:16:0.1194:0:1.1 +9 5069837 . G A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=3.41919;LSEQ=TTATTAAGCATTTCTTATAC;RSEQ=TAGAACACATTTCATTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:20:20,0:73,0:73,20:0.2151:1,1:23.9:1:30.9:1:1:0:60:40:0.2174:0:1 0/1:70:34:34,0:36,0:36,34:0.4857:1,1:23.5:1:30.4:1:1:0:60:68:0.4857:0:1 +9 5070129 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51175;SOR=0;LSEQ=TTCTTGATTTACATTCATGT;RSEQ=ACATTGGAATTATTTTGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:8,123:131,2:0.015:2,2:17.5:1:28:1:0.13124:14.55:60:4:0.015:0:1.5 0/0:95:0:0,0:5,90:95,0:0:2,0:20.6:1:30.8:1:1:0:60:94:1:0:0 +9 5070227 . ATTATC A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.52696;SOR=0;LSEQ=GTTAGATGTTAGCAAAATTA;RSEQ=TTAATTATCCTAAGAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:0,3:0,14:14,3:0.1765:1,0:28.7:1:33:1:1:0:60:6:0.1765:0:0.3 0/0:8:0:0,0:0,8:8,0:0:0,0:23.3:1:30.9:1:1:0:60:16:1:0:0 +9 5072798 . T C 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28898;SOR=0;LSEQ=AGAATTACAGGGTTTGAAAA;RSEQ=TACCGGATTAAAAAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:0,4:0,19:19,4:0.1739:1,0:19.3:1:33.3:1:1:0:60:8:0.1739:0:1 0/0:10:0:0,0:2,8:10,0:0:2,0:25.6:1:30.3:1:1:0:60:20:1:0:0.4 +9 5072846 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00303;SOR=Inf;LSEQ=CTAATTATGTTTAGCATTAT;RSEQ=TTAGGAGTGTTATTACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:21.3:1:34:0:1:0:60:14:1:0:0.1 1/1:4:4:1,3:0,0:0,4:1:0,2:16.3:1:28.8:1:1:0:60:8:1:0:1 +9 5073681 . CT C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.98905;LSEQ=TCAAACAACAATTCTTTGTA;RSEQ=TTTTTTTTTCCTTAGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:11:7,4:176,57:233,11:0.0451:2,2:19.3:1:31.9:1:0.47439:1.75978:60:22:0.0451:0.0123:0.2 0/1:269:12:8,4:190,66:256,12:0.0446:2,2:19.5:1:30.4:1:0.51805:1.43729:60:24:0.0449:0.0149:0.2 +9 5073875 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50281;SOR=Inf;LSEQ=TTTCAGGATCACAGCTAGGT;RSEQ=TCAGTGTAAACTATAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:0,69:69,0:0:1,0:21.1:1:32.1:1:1:0:60:33.5:1:0:0 0/1:86:2:0,2:2,82:84,2:0.0233:1,0:41:1:31.5:1:1:0:60:4:0.0233:0:1 +9 5077508 . G T 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.37891;SOR=3.51161;LSEQ=CTAGATACATATCTGAAAAA;RSEQ=AATAAAAATTGTATAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:300:1:0,1:146,153:299,1:0.0033:2,0:1:0:27:0:1:0:60:2:0.0034:0:1 0/1:344:4:2,2:174,166:340,4:0.0116:2,2:22.3:1:29:1:1:1.04807:60:8:0.0117:0:1.3 +9 5077517 . T C 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03262;SOR=Inf;LSEQ=TATCTGAAAAAGAATAAAAA;RSEQ=TGTATAAATATATTATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:143,156:299,0:0:2,0:23.5:1:30.5:1:1:0:60:58.8:1:0:0.1 0/1:342:6:4,2:163,172:335,6:0.0175:2,2:12.5:1:30:1:0.44037:2.11:60:12:0.0176:0:1 +9 5077560 . G A 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10163;SOR=0;LSEQ=TTGAAGTTGCTAAACAGTTG;RSEQ=CATGGGCCATGCATTTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:2,1:113,158:271,3:0.0109:2,2:24.7:1:26:1:0.57402:2.79:60:2:0.0074:0:1.3 0/0:312:0:0,0:126,186:312,0:0:2,0:26.9:1:30.8:1:1:0:60:77:1:0:0.1 +9 5077615 . T C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-04;SOR=Inf;LSEQ=CTTTTTATCAAAAGATACTA;RSEQ=TTTATTTTATAAAACAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:46,95:141,0:0:2,0:24.6:1:30.7:1:1:0:59.9:140:1:0:0 0/1:150:13:5,8:37,100:137,13:0.0867:2,2:24.2:1:31.6:1:0.51793:1.68:60:26:0.0872:0:1 +9 5078117 . T C 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52632;SOR=0;LSEQ=TTCATCACAAGCATAGATTA;RSEQ=TGTGTTATTTAAAATGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:3,0:12,0:12,3:0.2:0,0:12.7:1:33.3:1:1:0:60:6:0.2:0:1 0/0:6:0:0,0:6,0:6,0:0:0,0:19.8:1:30.3:1:1:0:60:12:1:0:0.2 +9 5080382 . T A 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37533;SOR=0.26956;LSEQ=TGCTCTGGATTCTCAAAGAG;RSEQ=AAGTTTATATAGACTAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:4:3,1:139,227:366,4:0.0108:2,2:15.5:1:29:1:0.15977:4.88:60:8:0.0109:0:1 0/0:341:1:1,0:135,205:340,1:0.0029:2,0:1:0:23:0:0.39883:0:60:2:0.003:0:1 +9 5080448 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22904;SOR=Inf;LSEQ=ATATTTCTTTCACATGATTT;RSEQ=TATTTTTTAGCCCATCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:107,106:213,0:0:2,0:22.2:1:32.6:1:1:0:59.9:212:1:0:0.1 0/1:196:2:1,1:114,80:194,2:0.0102:2,2:10.5:1:24.5:1:1:1.42235:60:4:0.0103:0:1 +9 5080484 . G T 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10328;SOR=Inf;LSEQ=CTAATTTTAAAAAGAAGGTT;RSEQ=GTGTGGCATTACACAATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:210,100:310,0:0:2,0:22.5:1:32.3:1:1:0:59.9:620:1:0:0.1 0/1:275:3:0,3:181,90:271,3:0.0109:2,0:13:1:21:1:0.03827:0:60:2:0.0074:0:1 +9 5080718 . T C 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00401;SOR=Inf;LSEQ=GATCTTATTGATTTTCCAGC;RSEQ=TTCTATCTTTATTGTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:0:0,0:78,302:380,0:0:2,0:24.1:1:30.8:1:1:0:60:94:1:0:0.1 0/1:417:9:2,7:114,293:407,9:0.0216:2,2:12.3:1:30.8:1:1:1.36079:60:18:0.0218:0:1.3 +9 5081585 . A G 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00326;SOR=Inf;LSEQ=GATTAAAGGCTCCCATTAAT;RSEQ=TAATTGAAACTATTTGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:46,1:47,0:0:1,0:20.6:1:28.6:1:1:0:60:94:1:0:0.1 0/1:24:5:5,0:19,0:19,5:0.2083:1,0:26.6:1:31.2:1:1:0:60:10:0.2083:0:1.2 +9 5081678 . G T 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.60323;SOR=2.25877;LSEQ=GTATATCAGTTTAGTCCAGA;RSEQ=AATGTTATTTGCTAATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:1,0:178,37:215,1:0.0046:2,0:5:0:32:0:1:0:60:2:0.0048:0:1 0/1:192:2:1,1:158,32:190,2:0.0104:2,2:10:0:30.5:1:0.31495:4.87757:60:4:0.0105:0:1 +9 5081780 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.67275;LSEQ=AATATGAGGATAGGTGCCCT;RSEQ=GGGTTTTCTGGTGCCTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:124:69,55:294,274:568,124:0.1792:2,2:24.7:1:28.9:1:0.48738:1.17:60:23.8:0.1753:0:1.3 0/1:876:390:210,180:258,227:485,390:0.4452:2,2:25.3:1:28.7:1:0.89156:1.03:60:129:0.4464:0:1.1 +9 5081966 . TAG T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11802;SOR=Inf;LSEQ=AACATTTTAAGGAGTGCTTG;RSEQ=AAAAAAAAGGTTTGGTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:0,54:54,0:0:1,0:25.7:1:33.1:1:1:0:60:108:1:0:0.1 0/1:53:3:0,3:1,49:50,3:0.0566:1,0:8:1:27.7:1:1:0:60:6:0.0566:0.0377:0.7 +9 5090641 . G A 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACATTAGGAAATCATCTA;RSEQ=ACGTTTTCATAGATAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:0:0,0:110,118:228,0:0:2,0:22.6:1:32.5:1:1:0:60:44.6:1:0:0.1 0/1:156:48:20,28:60,47:107,48:0.3077:2,2:24.8:1:29:1:0.1184:1.78051:60:47:0.3052:0:1.1 +9 5090934 . A T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38372;SOR=0.75909;LSEQ=GAGTATATTTCAGTATGATA;RSEQ=ATGAAATTTTAGAGCACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:34:9,25:31,117:148,34:0.1868:2,2:20.2:1:27.9:1:0.49519:1.36:60:16:0.1818:0:1.1 0/1:155:23:7,16:31,100:131,23:0.1484:2,2:22.8:1:27.5:1:0.59996:1.41:60:46:0.1503:0:1 +9 5090966 . ATTG A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0.71235;SOR=0.86523;LSEQ=GAGCACAGACTTCAAACTTT;RSEQ=TTGTTATTTAATAGTTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:19:1,18:10,67:77,19:0.1979:2,1:33:1:31.2:1:0.68719:2.66505:60:38:0.1979:0.0104:1 0/1:91:16:3,13:13,63:76,16:0.1758:2,2:24.1:1:29.8:1:1:1.12:60:32:0.1758:0.033:0.7 +9 5091045 . C CT 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.51232;SOR=0;LSEQ=CTTTTAAGTCTTACATTTAA;RSEQ=TTTTTTTTTTTAGGTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:0,2:0,16:16,2:0.1111:1,0:36:1:32:0:1:0:60:4:0.1176:0:0 0/0:11:0:0,0:1,10:11,0:0:2,0:19.5:1:30.3:1:1:0:60:10:1:0:0.6 +9 5110427 . C G 32 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACAATTGGCATTAATCAG;RSEQ=CACATCTAGCATTCCTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:5.5:1:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 5110841 . TG T 48 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.69312;SOR=1.44487;LSEQ=GCCCGTTTGTTCGGGGAAGG;RSEQ=GGGGGGACGCTTCATGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:3:2,1:288,72:360,3:0.0083:2,2:31.7:1:30.7:1:0.49118:1.99552:60:6:0.0085:0.0028:0.3 0/1:252:3:2,1:196,52:248,3:0.0119:2,2:28:1:30.3:1:0.5107:1.87897:60:6:0.0122:0.004:0.7 +9 5110899 . T C 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0141;SOR=0.73828;LSEQ=TCCATGTCTGAGATGCCCGC;RSEQ=CTGGCCCCAAGAGAATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:875:181:104,77:408,286:694,181:0.2069:2,2:26.1:1:31.4:1:0.79948:1.05613:59.8:362:0.2127:0:1.1 0/1:892:144:89,55:427,321:748,144:0.1614:2,2:26.1:1:30.3:1:0.31168:1.22:58:71:0.1617:0:1.2 +9 5111224 . GC G 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=3.7382;LSEQ=CGGAGGCAAGAGCAGCTAGC;RSEQ=GGGCCTATTCCTCCTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:57:28,29:261,269:530,57:0.0969:2,2:23.7:1:30.5:1:1:1.0049:60:27.5:0.0948:0.0136:0.3 0/1:471:135:63,72:154,180:334,135:0.2866:2,2:24.9:1:30.2:1:0.91891:1.02:59.9:270:0.2916:0.0297:0.2 +9 5111358 . AC A 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.78648;SOR=1.04391;LSEQ=GAAGGGGACCTCCCGGTACT;RSEQ=CCCTCCTACGCCAGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:843:135:63,72:340,368:708,135:0.1601:2,2:23.7:1:31.2:1:0.77889:1.05586:60:270:0.1615:0.0403:0.1 0/1:759:126:73,53:314,316:630,126:0.166:2,2:26.4:1:31.3:1:0.11807:1.39:60:252:0.1673:0.0184:0.2 +9 5111380 . TGGCGGACAGA T 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CCCTCCTACGCCAGCAGCTC;RSEQ=GGCGGACAGCGGCCTGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:783:0:0,0:382,399:781,0:0:2,0:24.5:1:31.8:1:1:0:59.9:85.778:0.9974:0:0.1 0/1:740:65:30,35:360,313:673,65:0.0878:2,2:25.2:1:30.9:1:0.29824:1.34131:59.5:130:0.0892:0.0135:0.2 +9 5112054 . G T 200 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTATCACCCAGCTACGACG;RSEQ=GGGTCTCCACGGCCTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1190:0:0,0:577,613:1190,0:0:2,0:25.8:1:31.1:1:1:0:59.7:61.632:1:0:0.2 0/1:1073:118:57,61:466,489:955,118:0.11:2,2:25.1:1:29.1:1:0.92264:1.01982:59.9:117:0.1102:0:1.2 +9 5112171 . C A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07979;SOR=Inf;LSEQ=TGCACACGCTGCTACCCGGC;RSEQ=ACCGGGCGCTGGCCTTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:377:0:0,0:120,257:377,0:0:2,0:23:1:31.5:1:1:0:59.9:25.929:1:0:0.1 0/1:286:3:2,1:82,201:283,3:0.0105:2,2:18.3:1:25.7:1:0.20721:4.87:60:6:0.0106:0:1.7 +9 5112266 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.064;SOR=Inf;LSEQ=ACACCCTGAGGACGGCCCTG;RSEQ=GGGCAGCGCCAGCCTCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:184,134:318,0:0:2,0:26.1:1:31.2:1:1:0:59.8:44.429:1:0:0.3 0/1:213:3:1,2:113,97:210,3:0.0141:2,2:10.3:1:27:1:0.59845:2.32091:60:6:0.0143:0:1.3 +9 5112288 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=5e-05;SOR=2.20609;LSEQ=GGCAGCGCCAGCCTCATGCA;RSEQ=ATCCATGTTGCCCTCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:65:42,23:171,111:282,65:0.1873:2,2:26.7:1:30.3:1:0.57539:1.18:60:64:0.186:0:1.1 0/1:246:83:57,26:96,67:163,83:0.3374:2,2:24.8:1:30.1:1:0.16445:1.53:60:166:0.343:0:1.1 +9 5112447 . A G 204 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGACCACTCAAGAGGAGAAG;RSEQ=AGGAGCTGAAGGACCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1535:0:0,0:757,778:1535,0:0:2,0:26.4:1:30.5:1:1:0:60:62.958:1:0:0.2 0/1:1635:105:53,52:768,760:1528,105:0.0642:2,2:23.4:1:30.5:1:1:1.01:60:104:0.0644:0:1.2 +9 5112519 . G A 225 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGATGACCTTTTCCCCCCA;RSEQ=AGCAGAAGGCCGAGTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1180:0:0,0:612,568:1180,0:0:2,0:24.3:1:32.3:1:1:0:60:33.706:1:0:0.2 0/1:1226:213:114,99:506,504:1010,213:0.1737:2,2:24.9:1:29.2:1:0.36683:1.15:60:52.25:0.1747:0:1.1 +9 5112675 . C G 222 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTATCCTGCACCAGGCCGT;RSEQ=TCGGTCATCCTGAATTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1524:0:0,0:721,802:1523,0:0:2,0:24.2:1:32.4:1:1:0:59.1:79.158:0.9993:0:0.2 0/1:1719:139:74,65:770,808:1578,139:0.0809:2,2:23.5:1:31.2:1:0.33116:1.19:53.1:138:0.0811:0:1.2 +9 5112844 . G A 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.89322;LSEQ=CCCACAACCCCGCTGGGCAC;RSEQ=TGTGAAAGGTACGCCTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:132:54,78:156,288:444,132:0.2292:2,2:22.7:1:30.2:1:0.25725:1.28:58:32:0.2257:0:1.1 1/0:624:370:143,227:90,163:253,370:0.5929:2,2:23.9:1:29.9:1:0.44908:1.14:56.9:184:0.5984:0:1.1 +9 5112918 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23248;SOR=0;LSEQ=GGGCCCAGAACGCCCACTTG;RSEQ=GGCCCTGGGCTTCATCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:27,154:181,2:0.0109:2,2:33:1:29.5:1:0.28331:5.62:60:4:0.011:0:1.5 0/0:196:0:0,0:48,148:196,0:0:2,0:23:1:29.7:1:1:0:60:64.333:1:0:0.4 +9 5112921 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22619;SOR=0;LSEQ=CCCAGAACGCCCACTTGAGG;RSEQ=CCTGGGCTTCATCCACATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:2:1,1:20,149:169,2:0.0117:2,2:10.5:1:28:1:0.23117:7.29:60:4:0.0119:0:1 0/0:188:0:0,0:43,143:186,0:0:2,0:22.7:1:30.1:1:1:0:60:25.571:0.989:0:0.4 +9 5113087 . C G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.23646;SOR=3.00706;LSEQ=CCCCGGCTCACCCCTCACTG;RSEQ=CCTCGCTCCCCCTGCCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:0,7:0,11:11,7:0.3889:0,0:23.6:1:34:1:1:0:60:14:0.3889:0:1.1 1/0:9:6:2,4:0,3:3,6:0.6667:0,2:27.7:1:28.8:1:0.5:0:60:12:0.6667:0:1 +9 5122854 . AG A 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.01222;SOR=Inf;LSEQ=TTCACAGGTGCCAGGCAAAA;RSEQ=GCCCTTTTAATCATAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:29,0:29,0:0:1,0:22.2:1:34:1:1:0:59.1:58:1:0:0 0/1:16:4:4,0:12,0:12,4:0.25:0,0:36.8:1:31.5:1:1:0:60:8:0.2667:0:0.3 +9 5122910 . GT G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0.98996;LSEQ=GATAACTCTTTTCTCTACAT;RSEQ=TTTTTTTTTTAATTTATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:11:11,0:82,2:84,11:0.1158:1,0:23.2:1:32:1:1:0:60:22:0.1158:0.0316:0 0/1:61:7:7,0:52,2:54,7:0.1148:1,0:15.7:1:31.4:1:1:0:60:14:0.1148:0.0492:0.6 +9 5126281 . ATT A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.21404;SOR=0;LSEQ=CTGGAGGAAATTGAGAAAGA;RSEQ=TTGCTACAAATTAAATGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:138,37:175,2:0.0113:2,2:26.5:1:30.7:1:0.38424:3.6939:60:4:0.0114:0.0056:0 0/0:205:0:0,0:159,46:205,0:0:2,0:22.9:1:29.9:1:1:0:60:204:1:0:0.1 +9 5126453 . AT A 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.78156;SOR=0.77883;LSEQ=GATGCCCAGATGAGGTAACA;RSEQ=TTTTTTTTAATCCAGGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:7:4,3:100,207:307,7:0.0223:2,2:24.4:1:30.7:1:0.22542:2.75:60:14:0.0225:0.0032:0.1 0/1:344:6:2,4:122,215:337,6:0.0174:2,2:21.2:1:29.2:1:1:1.13449:60:12:0.0176:0.0058:0.5 +9 5126632 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.18696;SOR=Inf;LSEQ=ATTAATGTCTTCCACCAATT;RSEQ=AAAGATGGCCCTTAGTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:145,46:191,0:0:2,0:21.2:1:29.1:1:1:0:60:190:1:0:0 0/1:146:2:1,1:112,32:144,2:0.0137:2,2:29.5:1:29.5:1:0.40217:3.46178:60:4:0.0138:0:1 +9 5126742 . G T 179 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAATCAACGCCCCTCCTTTA;RSEQ=GGATCTAGCTCTTCGAGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:57:30,27:242,247:489,57:0.1044:2,2:30.3:1:30.8:1:0.67672:1.13:60:56:0.1047:0:1.2 0/0:670:0:0,0:355,315:670,0:0:2,0:26.1:1:30.6:1:1:0:60:50.538:1:0:0.2 +9 5126860 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49881;SOR=Inf;LSEQ=TTTATATTTCACATTGCTGT;RSEQ=GACTATTATTACATATATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:7,117:124,0:0:2,0:22.5:1:31.4:1:1:0:60:61:1:0:0 0/1:134:2:0,2:13,118:131,2:0.0149:2,0:15.5:1:31:0:1:0:60:4:0.0153:0:1 +9 5455732 . T G 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTCTCCTTGCTCTGAAAT;RSEQ=TTGTACAGGGCAGGTTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:30.3:1:32.8:1:1:0:60:8:0.6667:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 5456029 . G T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24809;SOR=Inf;LSEQ=ATTTCAGTTAGAACCACCAA;RSEQ=TCCCATATTGTCATATTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:153,41:194,0:0:2,0:24.3:1:32.8:1:1:0:60:96:1:0:0.1 0/1:196:3:2,1:151,42:193,3:0.0153:2,2:14.7:1:28:1:0.52639:1.79142:60:6:0.0153:0:1 +9 5456083 . G A 152 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=AGTGAAGCAGTCTTCTTTTC;RSEQ=TGTTTTCCATAATTAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:30:18,12:232,156:388,30:0.0716:2,2:24.7:1:31.1:1:1:1.01:60:60:0.0719:0:1.1 0/0:528:0:0,0:321,206:527,0:0:2,0:24.9:1:30:1:1:0:60:130.75:0.9981:0:0.1 +9 5456523 . T C 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTCAGTCTTGGTTGCTCTG;RSEQ=GACATGCCTTTCCTGATGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26:1:32:1:1:0:60:4:0.6667:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:35:0:32:0:1:0:60:2:1:0:0 +9 5456775 . C G 74 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGATGTCTACATGAAACCAA;RSEQ=TCTCCCTGGTTGTAAGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:15.4:1:32.2:1:1:0:60:10:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 5457032 . T G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11642;SOR=Inf;LSEQ=TGTGCCAATTTTGTAAATGT;RSEQ=TCGAGGAATTTTCCCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:122,31:153,0:0:2,0:23:1:30.7:1:1:0:59.6:152:1:0:0.1 0/1:147:3:1,2:112,32:144,3:0.0204:2,2:27.3:1:28.7:1:0.13376:6.87964:60:6:0.0204:0:2 +9 5457049 . T C 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00367;SOR=Inf;LSEQ=TGTTTCGAGGAATTTTCCCT;RSEQ=TTCTGAAGATTGTCCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:152,55:207,0:0:2,0:23.2:1:30.8:1:1:0:59.7:206:1:0:0.1 0/1:218:9:5,4:154,55:209,9:0.0413:2,2:19.1:1:30.6:1:0.2571:2.23055:60:18:0.0417:0:1.6 +9 5457364 . G T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13722;SOR=Inf;LSEQ=GCAGGATGCAGGGGTGTACC;RSEQ=CTGCATGATCAGCTATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:0:0,0:104,172:276,0:0:2,0:26.1:1:31.3:1:1:0:59.8:68:1:0:0.1 0/1:361:4:2,2:148,208:356,4:0.0111:2,2:13.5:1:28.5:1:1:1.40:60:8:0.0112:0:1 +9 5457443 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49876;SOR=0;LSEQ=AAGAATTATTATAGATGAGA;RSEQ=GCCTGATCTTTATTGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:33,115:148,2:0.0133:2,2:27:1:29:1:0.40313:3.45:60:4:0.0136:0:1 0/0:141:0:0,0:42,99:141,0:0:2,0:24.1:1:29.9:1:1:0:60:27.2:1:0:0.1 +9 5462746 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23579;SOR=Inf;LSEQ=TCTGAGAACCAGCCTGCATT;RSEQ=ATACTCTTTCTAATGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:95,21:116,0:0:2,0:22.8:1:32.2:1:1:0:59.9:115:1:0:0.1 0/1:110:2:1,1:88,20:108,2:0.0182:2,2:24.5:1:26.5:1:0.34679:4.31829:60:4:0.0187:0:1 +9 5462767 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10618;SOR=Inf;LSEQ=ATACTCTTTCTAATGTGGAC;RSEQ=GCATCAAGCTATGTACGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:135,54:189,0:0:2,0:22.9:1:30.9:1:1:0:60:378:1:0:0.1 0/1:171:3:2,1:121,46:167,3:0.0175:2,2:34:1:31:1:1:1.31299:60:6:0.018:0:1 +9 5462876 . C G 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=AAGAATTTTGGTTGTGGATC;RSEQ=AGTCACCTCTGAACATGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:437:0:0,0:261,175:436,0:0:2,0:25.5:1:31.6:1:1:0:59.9:71.667:0.9977:0:0.1 0/1:594:17:12,5:346,228:574,17:0.0286:2,2:27.8:1:28.6:1:0.45883:1.58:59.5:16:0.0274:0:1 +9 5463135 . T A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.24827;SOR=Inf;LSEQ=ATCCCAGGTAATATTCTGAA;RSEQ=GTGTCCATTAAAATATGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:47,155:202,0:0:2,0:25:1:30.7:1:1:0:60:201:1:0:0.1 0/1:207:3:2,1:50,154:204,3:0.0145:2,2:18.7:1:27.3:1:0.15624:6.09:60:6:0.0146:0:1 +9 5463243 . G A 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.0557;SOR=0.19286;LSEQ=GAATGAATGAATAACACTAT;RSEQ=TTTACAAAATATATCCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:16:0,16:0,20:20,16:0.4324:1,1:21.3:1:32.5:1:1:0:60:32:0.4324:0:1 0/1:16:2:0,2:0,14:14,2:0.125:1,0:20:1:31.5:1:1:0:60:4:0.125:0:1 +9 5465732 . G A 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15241;LSEQ=AGGCATTCCACTGTTCAACA;RSEQ=CAATTATATTGAAGCTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:59:0,59:1,33:34,59:0.6344:1,1:21.7:1:30.8:1:0.36559:0:60:118:0.6344:0:1 0/1:58:12:0,12:1,45:46,12:0.2069:1,0:18.8:1:28.6:1:1:0:60:24:0.2069:0:1 +9 5466739 . A G 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=26.22621;LSEQ=GGGATGTAGAGCTGTGCTAT;RSEQ=TGGAAATAAAAATGATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:274:1:1,0:177,96:273,1:0.0036:2,0:49:0:15:0:1:0:60:0:0:0:5 0/1:387:34:20,14:224,129:353,34:0.0879:2,2:24.7:1:30.9:1:0.58281:1.21486:60:33:0.0862:0:1.1 +9 5467801 . C T 109 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00512;SOR=10.26127;LSEQ=TTGTTACTTTTTCCCCAGAC;RSEQ=ACTTCCCATGAAATTAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:1:0,1:209,146:355,1:0.0028:2,0:1:0:22:0:0.41292:0:60:2:0.0029:0:1 0/1:462:13:8,5:265,184:449,13:0.0281:2,2:16.8:1:29.5:1:1:1.11:60:26:0.0284:0:1 +9 5467807 . C T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01772;SOR=0;LSEQ=CTTTTTCCCCAGACCACTTC;RSEQ=CATGAAATTAATATACTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:5:1,4:215,164:379,5:0.013:2,2:11.4:1:27.4:1:0.1727:5.22396:60:10:0.0132:0:1.2 0/0:475:0:0,0:275,200:475,0:0:2,0:25:1:30.1:1:1:0:60:117.75:1:0:0.2 +9 5467955 . G A 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.30199;SOR=1.28902;LSEQ=GTGACAAGAGGAAGGAATGG;RSEQ=CCCGTGGGATGCAGGCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:152:95:14,81:10,47:57,95:0.625:2,2:22.3:1:30.5:1:0.65244:1.22928:60:190:0.6333:0:1.1 1/0:189:129:28,101:8,52:60,129:0.6825:2,2:20.1:1:28.4:1:0.23248:1.80:60:258:0.6898:0:1 +9 5468257 . G C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACTCAATGCCTCAATTT;RSEQ=TTTTCTGCATGACTGAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:34:0:34.5:1:1:0:60:4:0.5:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 5670073 . G A 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49446;SOR=1.83738;LSEQ=TGAGGCACATCAGGTCTCCA;RSEQ=TTAGTATGGATACCTGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:0,5:0,16:16,5:0.2381:1,0:31.2:1:31.4:1:1:0:60:10:0.25:0:1 0/1:19:7:0,7:0,12:12,7:0.3684:0,0:24:1:29.7:1:1:0:60:14:0.3684:0:1 +9 5754903 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17625;SOR=0;LSEQ=GATTTTATGGTCCTTGCGTG;RSEQ=TATAACATAAATGACCGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:65,50:115,2:0.0171:2,2:43.5:1:33:1:1:1.29705:60:4:0.0172:0:1.5 0/0:161:0:0,0:90,71:161,0:0:2,0:27.5:1:29.1:1:1:0:60:160:1:0:0.2 +9 5754944 . C A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16075;SOR=0;LSEQ=AGAAGAGGTAAGTTTTTTCT;RSEQ=TCAGAAATAACAGATTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:61,66:127,2:0.0155:2,2:6.5:1:30:0:1:1.08:60:4:0.0155:0:2 0/0:192:0:0,0:91,101:192,0:0:2,0:24.3:1:30.9:1:1:0:60:384:1:0:0.3 +9 5754976 . T C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5005;SOR=Inf;LSEQ=AGATTTTTATATTTTAAAGC;RSEQ=ATTAAGCATGAATTAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:51,69:120,0:0:2,0:25.9:1:29.6:1:1:0:60:119:1:0:0.6 0/1:138:2:1,1:56,80:136,2:0.0145:2,2:6:0:33.5:1:1:1.42:60:4:0.0148:0:1.5 +9 5754988 . A T 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10221;SOR=1.60101;LSEQ=TTTAAAGCTATTAAGCATGA;RSEQ=TTAATTTTATATAGAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:37:15,22:29,39:68,37:0.3524:2,2:30.1:1:30.8:1:1:1.08969:60:74:0.3524:0:1.7 0/1:118:55:21,34:27,36:63,55:0.4661:2,2:26.1:1:29.3:1:0.70772:1.21228:60:110:0.4783:0:1.3 +9 5755022 . T A 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21045;SOR=0.62493;LSEQ=GAAAATAGTCGATTGAAAAC;RSEQ=GAACAAAACATTTTATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:24:6,18:16,32:48,24:0.3333:2,2:24.3:1:32.5:1:0.59072:1.49178:60:48:0.338:0:2 0/1:80:19:5,14:17,44:61,19:0.2375:2,2:20.1:1:30.6:1:1:1.08078:60:38:0.2375:0:1.8 +9 7549605 . C G 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.42857;SOR=0;LSEQ=TGTCCCCCACCATTCAAACA;RSEQ=ACGGGCTGTGGCAGACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:22.5:1:32:1:1:1:58:4:0.5:0:1 0/0:4:0:0,0:2,2:4,0:0:2,0:15.8:1:31.3:1:1:0:60:8:1:0:0 +9 7903859 . T A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTTCTACTGATTAAAAAAT;RSEQ=TTGAAGACCACTGAATTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:30.5:1:31.5:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 8317796 . A G 47 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.11239;SOR=Inf;LSEQ=AAGTTAAGAAGGACTTCTCA;RSEQ=GTGCCCTGTATGGCTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:239,73:312,0:0:2,0:24.3:1:30.4:1:1:0:60:103:1:0:0.1 0/1:292:3:2,1:215,73:288,3:0.0103:2,2:7:1:30:1:1:1.47047:60:6:0.0105:0:1 +9 8317999 . T TAGAAAAATAA 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=3.000;MSILEN=1;SSF=0.20451;SOR=0.49146;LSEQ=GGACCATGAGCATATTTTAA;RSEQ=AGAAAAATAAAAATCAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:10:1,9:35,158:193,10:0.0493:2,2:20:1:30.4:1:1:1.98815:60:20:0.0498:0.0148:0 0/1:242:6:1,5:51,185:236,6:0.0248:2,2:26.3:1:29.5:1:1:1.3767:60:12:0.0252:0.0083:0.2 +9 8319732 . G C 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24551;SOR=Inf;LSEQ=AGTTTGATGCTTTCCCCACA;RSEQ=TATTTTGTGTCTGGTGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:187,9:196,0:0:1,0:23.4:1:33.3:1:1:0:59.9:97:1:0:0.1 0/1:193:2:1,1:176,15:191,2:0.0104:2,2:7:1:31.5:1:0.15933:11.39325:60:4:0.0106:0:1 +9 8319806 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.22346;LSEQ=AAACGTAGGCTCTTGAGATG;RSEQ=GAAAAATGCAATGGATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:57:38,19:341,243:584,57:0.0889:2,2:22.5:1:29.9:1:0.25977:1.42:59.8:56:0.0889:0:1.2 0/1:689:165:96,69:299,225:524,165:0.2395:2,2:24:1:28.6:1:0.85685:1.05:60:54:0.2372:0:1.1 +9 8320065 . G A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56731;SOR=1.40676;LSEQ=TCTACCAGCTTCCACACTCC;RSEQ=TATCTCTTTATAGCCATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:8:0,8:3,91:94,8:0.0784:1,0:22.1:1:32.4:1:1:0:60:16:0.08:0:1.1 0/1:56:6:0,6:2,48:50,6:0.1071:1,0:13.8:1:29.5:1:1:0:60:12:0.1091:0:1 +9 8331207 . G T 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTGATAGCTATTCATGAG;RSEQ=TTTTCACAAACAGAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:2,0:6,0:6,2:0.25:0,0:37.5:1:32:0:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 8331406 . ATTATTTTCAC A 126 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=1.200;MSILEN=1;SSF=0.00572;SOR=0.08486;LSEQ=GGGCTAAACATTTTCCTCTG;RSEQ=TTATTTTCACTTTATGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:16:16,0:25,0:25,16:0.3902:1,1:27.6:1:31.7:1:1:0:59.8:32:0.3902:0.0976:0 0/1:20:1:1,0:19,0:19,1:0.05:1,0:41:0:33:0:1:0:60:2:0.05:0:0 +9 8331498 . A C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2498;SOR=Inf;LSEQ=CCAAGAATAAAATTTCAAAT;RSEQ=AGCAAACTTACTACAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:192,24:216,0:0:2,0:22.6:1:28.5:1:1:0:59.9:35:0.9953:0:0.1 0/1:237:3:3,0:198,36:234,3:0.0127:2,0:29.3:1:32.7:1:1:0:58.3:6:0.0127:0:1 +9 8331507 . T TA 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03258;SOR=Inf;LSEQ=AAATTTCAAATAAGCAAACT;RSEQ=ACTACAAAAAGTGTATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:221,39:260,0:0:2,0:22.7:1:30.9:1:1:0:59.9:129:1:0:0.1 0/1:298:6:6,0:232,60:292,6:0.0201:2,0:18.7:1:29.4:1:0.60416:0:59.2:12:0.0203:0.0101:0.5 +9 8331548 . C T 169 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01714;LSEQ=ACAATGAAGAAACACCACCA;RSEQ=TTATCACTGCTTTATTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:42:31,11:349,180:529,42:0.0736:2,2:21.6:1:31.4:1:0.3956:1.45:59.3:84:0.0739:0:1.1 0/0:738:1:0,1:456,281:737,1:0.0014:2,0:1:0:24:0:0.38211:0:60:2:0.0014:0:1 +9 8331574 . A AAACTTACCATTCTTGAACTGT 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.09084;LSEQ=ACTGCTTTATTCACAAATGG;RSEQ=AACTTACCTGCAATGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:284:174,110:239,177:416,284:0.3792:2,2:26.5:1:30.6:1:0.34776:1.17:59.5:568:0.3833:0.0948:0.2 0/1:1086:57:33,24:444,374:818,57:0.0525:2,2:31.7:1:29.7:1:0.68032:1.16:59.5:114:0.053:0:0.1 +9 8331761 . G A 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37426;SOR=3.78952;LSEQ=AGAAGGAAAGCCACATACCC;RSEQ=GCCGCAAAGGAAGACGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:1:1,0:68,249:317,1:0.0031:2,0:1:0:26:0:0.21698:0:60:2:0.0032:0:1 0/1:338:4:2,2:87,247:334,4:0.0118:2,2:21.3:1:29.8:1:0.28383:2.83:60:8:0.012:0:1 +9 8331841 . A G 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=TTCATTTCCCGAAAACAAAA;RSEQ=GGGTAGAAAAAGTTAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:0,2:1,81:82,2:0.0238:1,0:18.5:1:26.5:1:1:0:60:4:0.0241:0:1 0/0:75:0:0,0:0,75:75,0:0:1,0:24.1:1:31.2:1:1:0:60:150:1:0:0.2 +9 8331863 . T A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1578;SOR=Inf;LSEQ=GGTAGAAAAAGTTAGGAACA;RSEQ=GTTTAAATAGAAACTTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:1,65:66,0:0:1,0:27.2:1:30.4:1:1:0:59.7:65:1:0:0.2 0/1:44:2:0,2:0,42:42,2:0.0455:1,0:18.5:1:32:0:1:0:60:4:0.0455:0:1 +9 8331926 . TAAATCCTAAATTTATTTACTCTTG T 61 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.92081;LSEQ=TGTCCACACTCACATACCTT;RSEQ=AAATCCTAAATTTATTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:0,4:0,11:11,4:0.2667:0,0:30.3:1:30.5:1:1:0:60:8:0.2667:0:0.3 0/1:4:1:0,1:0,3:3,1:0.25:0,0:40:1:31.4:1:1:0:23:2:0.25:0.25:0 +9 8332033 . A G 80 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=0;LSEQ=TCCACATAGTTCCCCCATTA;RSEQ=CAAATGTTTCTGAGACCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:17.3:1:31.2:1:1:0:60:12:0.75:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:8:0:31.5:1:1:0:60:4:1:0:0 +9 8338690 . G T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06536;SOR=Inf;LSEQ=TGCATCCCCAAGGTTGAGCT;RSEQ=CCAGATGTTATGTTTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:26.6:1:32.8:1:1:0:58.1:26:1:0:0.1 0/1:5:2:2,0:3,0:3,2:0.4:0,0:27:1:32.5:1:1:0:60:4:0.4:0:1 +9 8338778 . T TA 130 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=33.56196;LSEQ=TTACTCTTACATATTAAACA;RSEQ=AAAAAAAAACGTTCTCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:2,0:72,0:72,2:0.027:1,0:22.5:1:27.5:1:1:0:60:4:0.0278:0:1.5 0/1:51:25:25,0:19,2:21,25:0.4902:2,1:26.8:1:28.1:1:0.2029:0:60:50:0.5:0.0196:0.2 +9 8338878 . A C 163 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAGAGAGGTATCTTAGACT;RSEQ=CTTTTCAGCTAATGGTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:434:0:0,0:307,127:434,0:0:2,0:23.3:1:28.6:1:1:0:59.9:107.5:1:0:0.1 0/1:458:43:29,14:277,135:412,43:0.0939:2,2:23.3:1:30.1:1:1:1.01:59.2:42:0.094:0:1.3 +9 8339203 . A T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATATGACTCATTTCCTCTT;RSEQ=GAAACCATGAGCTCCCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:0,29:29,0:0:1,0:22.9:1:30.9:1:1:0:58.9:28:1:0:0.2 1/0:12:9:1,8:0,3:3,9:0.75:0,2:19:1:27.6:1:1:0:60:8:0.7273:0:2 +9 8339233 . C G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=AGCTCCCTTCATAGGGAAAC;RSEQ=CTTTGGTTCAGTATTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:0,18:18,0:0:1,0:28.3:1:29.2:1:1:0:58.3:8:1:0:0.2 1/1:4:4:1,3:0,0:0,4:1:0,2:37:1:30:1:1:0:60:8:1:0:1.8 +9 8340155 . A C 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=ACTAGATCTTTCTTTAAAAC;RSEQ=CATAAATTTAAACACTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:31,1:32,0:0:1,0:23.8:1:30.4:1:1:0:60:31:1:0:0.1 1/0:20:14:14,0:5,1:6,14:0.7:2,1:15.4:1:29.1:1:0.3:0:60:13:0.6842:0:1.9 +9 8340168 . C A 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAAAACACATAAATTTAAA;RSEQ=ACTTGATGTGGCTTTACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:40,1:41,0:0:1,0:24.9:1:32.7:1:1:0:60:82:1:0:0.2 1/0:23:14:14,0:8,1:9,14:0.6087:2,1:23.3:1:30.7:1:0.3913:0:60:28:0.6364:0:1.9 +9 8340226 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11894;SOR=Inf;LSEQ=AATGATGGTCCGGATTATGT;RSEQ=CAGAGTGCACTGCATTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:92,1:93,0:0:1,0:22.9:1:32.1:1:1:0:60:30:1:0:0.1 0/1:91:3:3,0:86,2:88,3:0.033:1,0:20:1:31.7:1:1:0:60:6:0.0337:0:1 +9 8341018 . TA T 153 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTTGAATGGAGATGAAATT;RSEQ=TTCTGGTTATTAAACTAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:175,26:201,0:0:2,0:25.3:1:28.6:1:1:0:60:99.5:1:0:0.1 0/1:168:38:31,7:103,27:130,38:0.2262:2,2:27.7:1:29.3:1:0.82265:1.16:60:76:0.2262:0.0119:0.2 +9 8341280 . GA G 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.30079;SOR=0.74784;LSEQ=GGCTAGACGCTGTTGAATAG;RSEQ=AAAAAAAAAAAGGAAAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:37:10,27:59,148:207,37:0.1498:2,2:28.3:1:31.8:1:1:1.07604:60:74:0.1523:0.004:0.4 0/1:275:32:8,24:78,150:228,32:0.1164:2,2:28.4:1:31.1:1:0.42227:1.55749:59.8:64:0.1221:0:0.4 +9 8341445 . T C 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=Inf;LSEQ=TAATCACTCTCTATAGCCTA;RSEQ=TGGATTTCTATATATTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:18,8:26,0:0:2,0:21.9:1:29.8:1:1:0:59.3:12:1:0:0.3 1/1:4:4:3,1:0,0:0,4:1:0,2:25.3:1:31.3:1:1:0:55.3:8:1:0:2.5 +9 8375569 . G T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATAAATAGTAAAAAGGTT;RSEQ=TATCAGTCCAGCCCACAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:3,0:1,0:1,3:0.75:0,0:26.7:1:31:1:1:0:60:6:0.75:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 8375861 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49926;SOR=0;LSEQ=TTACTATTCCAGAATGTCAA;RSEQ=AAGTTGCAGAAACATCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:177,9:186,2:0.0106:1,2:12.5:1:30:1:0.10382:18.7021:60:4:0.0107:0:1 0/0:175:0:0,0:171,4:175,0:0:1,0:23.5:1:32:1:1:0:60:86.5:1:0:0.1 +9 8376049 . G A 67 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17927;SOR=3.3642;LSEQ=CCATGATCAGGCCAGGCGGT;RSEQ=AACTGGAATTGTCTCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:661:2:2,0:261,397:658,2:0.003:2,0:1:0:23.5:1:0.15843:0:60:4:0.0031:0:1 0/1:692:7:6,1:285,400:685,7:0.0101:2,2:9.7:1:23.9:1:0.04564:8.40:60:14:0.0102:0:1 +9 8376147 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.21483;SOR=Inf;LSEQ=CAAGCCTCAGGTGGTAATGA;RSEQ=GAATAACAGGGAAGAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:0:0,0:16,142:158,0:0:2,0:24.1:1:30.9:1:1:0:60:157:1:0:0.1 0/1:137:2:1,1:20,115:135,2:0.0146:2,2:27.5:1:29:1:0.28403:5.64:60:4:0.0152:0:1 +9 8376287 . A G 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.52206;SOR=0;LSEQ=ATATTTGCGCAGGAAGACAA;RSEQ=ATTCTTAGGTGAGAAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:4,6:10,3:0.2308:2,0:26:1:32:1:0.4965:0:60:6:0.2308:0:1 0/0:5:0:0,0:1,4:5,0:0:2,0:24.8:1:32.2:1:1:0:60:10:1:0:0 +9 8376477 . C T 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11733;SOR=0.52752;LSEQ=GCTGAGTGATAATGGAAGAT;RSEQ=TATTTCATTCTTCACTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:54:30:29,1:24,0:24,30:0.5556:1,1:25.6:1:31.9:1:1:0:60:60:0.566:0:1 0/1:48:19:19,0:29,0:29,19:0.3958:1,1:22.9:1:30.5:1:1:0:60:18:0.3913:0:1 +9 8376530 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49844;SOR=Inf;LSEQ=AGATTTAAGTAAAGCCTTAA;RSEQ=AGATTTCATTTCTCAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:142,19:161,0:0:2,0:24:1:32.9:1:1:0:59.8:52.667:1:0:0.2 0/1:161:2:1,1:138,21:159,2:0.0124:2,2:10:0:30.5:1:0.25536:6.44356:60:4:0.0126:0:1.5 +9 8376785 . G T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24265;SOR=Inf;LSEQ=TCAATTTCTCTATTAACTTT;RSEQ=CTTTGAGTTGCTGTTGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:9,111:120,0:0:2,0:24.8:1:32.7:1:1:0:60:119:1:0:0 0/1:117:2:1,1:12,103:115,2:0.0171:2,2:5:0:31:1:0.21073:8.29:60:4:0.0174:0:0.5 +9 8376899 . T C 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1032;SOR=0;LSEQ=AATTACTGCTCTGATGCCAA;RSEQ=ATAAACCACATTTTTCAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:0,7:7,8:0.5333:0,0:25.9:1:33.9:1:1:0:56.1:16:0.5333:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:11:1:28.8:1:1:0:60:8:1:0:0.3 +9 8388982 . CTT C 32 v3;MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=20.000;MSILEN=1;SSF=1;SOR=0.84709;LSEQ=GTCTATTCCTGTGAATATTC;RSEQ=TTTTTTTTTTTTTTTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:3,0:3,2:0.2857:0,0:36:1:32.5:1:1:0:52:4:0.2857:0:3.5 0/1:4:1:1,0:2,0:2,1:0.25:0,0:39:0:28:0:1:0:60:2:0.25:0:1 +9 8389364 . C G 312 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.00771;LSEQ=TAGGCATTTTGCTTCCTATA;RSEQ=CCATCTATGTAGTTGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:761:756:314,442:0,0:0,756:0.9934:0,2:24.9:1:32.7:1:1:0:60:93.5:0.9934:0:1.1 1/0:810:435:159,276:154,221:375,435:0.537:2,2:24.1:1:31.3:1:0.19348:1.2093:60:53.375:0.5364:0:1.1 +9 8389592 . A T 135 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04615;SOR=0;LSEQ=GAACCGTCATGTTAAAAAAA;RSEQ=GTATGCAAAAAAGTGTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:0,20:0,0:0,20:1:0,1:18.2:1:31.4:1:1:0:60:40:1:0:1.1 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:26.8:1:29:1:1:0:60:8:0.6667:0:1 +9 8404607 . G A 150 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=15.6692;LSEQ=GCGTATCTATTCTTTGGTTT;RSEQ=TTTACTTCCAAGTTTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:782:2:2,0:374,406:780,2:0.0026:2,0:1:0:27:1:0.23087:0:60:4:0.0026:0:1 0/1:983:38:18,20:456,488:944,38:0.0387:2,2:26.2:1:28.6:1:1:1.03822:60:76:0.039:0:1.2 +9 8404720 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49973;SOR=0;LSEQ=TGAAAACCACCAGATTATAG;RSEQ=CATTTATCACATGTAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:13,146:159,2:0.0124:2,0:32:1:32:0:1:0:60:4:0.0127:0:1 0/0:145:0:0,0:16,129:145,0:0:2,0:21.7:1:31.3:1:1:0:60:47.333:1:0:0.1 +9 8436531 . G T 33 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62352;SOR=3.01805;LSEQ=AAGTTAATTTTCAAGAATAT;RSEQ=GTCAAAAAAAGAGAAGAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:1:1,0:210,43:253,1:0.0039:2,0:47:0:30:0:1:0:60:2:0.004:0:1 0/1:254:3:0,3:195,56:251,3:0.0118:2,0:6.3:1:21:1:0.01204:0:60:2:0.008:0:1.7 +9 8436534 . C CA 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05814;SOR=0;LSEQ=TTAATTTTCAAGAATATGGT;RSEQ=AAAAAAAGAGAAGAGTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:4:2,2:215,43:258,4:0.0153:2,2:18:1:31.1:1:0.13775:4.95508:60:8:0.0154:0.0038:0.8 0/0:270:0:0,0:204,64:268,0:0:2,0:22.7:1:30.6:1:1:0:60:88.333:0.9962:0:0.3 +9 8436560 . A T 197 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGAGAAGAGTAACTCTTGA;RSEQ=ATTACTGTAAAGAATAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:415:0:0,0:286,129:415,0:0:2,0:24.8:1:30.4:1:1:0:60:206.5:1:0:0.1 0/1:447:112:74,38:219,116:335,112:0.2506:2,2:22.2:1:29:1:0.90918:1.03:60:224:0.2506:0:1.1 +9 8436703 . C G 231 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=541.07565;LSEQ=GCCATACCTATTGAAAAAAG;RSEQ=AAAGAAGAAACACATTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:419:1:0,1:118,299:417,1:0.0024:2,0:35:0:33:0:1:0:60:2:0.0024:0:1 1/0:341:193:56,137:48,97:145,193:0.566:2,2:22.5:1:30.5:1:0.47521:1.20991:60:192:0.5731:0:1.1 +9 8437015 . T G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14423;SOR=Inf;LSEQ=GCTTGATGTCAACTTCTGCT;RSEQ=TGAGTAATGACTTTTATGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:37,3:40,0:0:2,0:25:1:31:1:1:0:60:39:1:0:0.2 0/1:25:2:2,0:23,0:23,2:0.08:1,0:32:1:31.5:1:1:0:60:4:0.0833:0:1 +9 8437092 . T A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22152;SOR=0;LSEQ=AATTGTGTGGAATTAAATGG;RSEQ=GTAAAGTGAAATAAGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:2,0:167,12:179,2:0.011:2,0:21:1:26:1:1:0:60:4:0.0114:0:1 0/0:203:0:0,0:185,15:200,0:0:2,0:50:0:16:0:1:0:60:0:0:0:3 +9 8437288 . C CA 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.0242;LSEQ=ATAAAATAGAACAAATTCTT;RSEQ=AAAAAAAAATGAAATGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:6:1,5:24,160:184,6:0.0311:2,2:25.3:1:31.7:1:0.57628:1.33:60:12:0.0321:0:0 0/1:220:7:2,5:45,168:213,7:0.0318:2,2:23:1:27.6:1:0.64328:1.49:60:14:0.0327:0.0045:0.1 +9 8449502 . G C 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47368;SOR=Inf;LSEQ=AGTTCTTCCAAAATTTGAAG;RSEQ=ATACCCATATTTCTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:10,0:10,0:0:0,0:19.5:1:31.9:1:1:0:60:20:1:0:0.1 0/1:10:2:2,0:7,1:8,2:0.2:2,0:27.5:1:33.5:1:1:0:60:4:0.2222:0:1 +9 8449665 . A G 158 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACCTTCAACTCTTAATATCA;RSEQ=TTGAGCTGTACAACTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:244:0:0,0:213,31:244,0:0:2,0:24:1:30.3:1:1:0:60:33.857:1:0:0 0/1:249:31:25,6:176,42:218,31:0.1245:2,2:23.6:1:31.9:1:1:1.00569:60:62:0.126:0:1 +9 8449993 . C A 98 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.02019;SOR=0;LSEQ=ACCCAGTTCGGGTTGCTTTT;RSEQ=CCCCCTGGCCTAATTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:1,9:0,8:8,10:0.5556:0,2:21.3:1:29.6:1:1:0:60:20:0.5556:0:1.1 0/0:7:0:0,0:0,7:7,0:0:0,0:20.1:1:31.1:1:1:0:60:14:1:0:0 +9 8454073 . C A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTAGCTATTATTATTGCT;RSEQ=TTATTATTCAAGACTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28.5:1:28.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 8454265 . G T 105 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTATGAGACACCTCACAT;RSEQ=TCTGCTCTGTAAACACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1:0,0:19.9:1:30.6:1:1:0:58.6:10:1:0:1.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 8454413 . A G 215 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAATATTTATTTTCCCCAG;RSEQ=ATCATCTTAATGAAGTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:106:106:106,0:0,0:0,106:1:0,1:21.9:1:32:1:1:0:59.8:52:1:0:1 1/0:78:50:50,0:26,2:28,50:0.641:2,1:20.6:1:30.4:1:0.12587:0:60:49:0.6364:0:1 +9 8454491 . C T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.12409;SOR=Inf;LSEQ=GTATTATCTTTTGTGTGCAG;RSEQ=CCCGCCCTCCCCTCTTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:290,102:392,0:0:2,0:23.7:1:31.8:1:1:0:59.9:64.333:1:0:0.2 0/1:398:4:1,3:263,131:394,4:0.0101:2,2:18.8:1:26.8:1:0.11298:5.99441:60:8:0.0102:0:1.5 +9 8454495 . G A 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=TATCTTTTGTGTGCAGCCCC;RSEQ=CCCTCCCCTCTTCAACAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:307,121:428,0:0:2,0:23.1:1:30.3:1:1:0:59.9:70.333:1:0:0.2 0/1:444:17:11,6:277,147:424,17:0.0383:2,2:23.6:1:27.5:1:1:1.02779:60:34:0.0394:0:1.4 +9 8454566 . T C 237 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGAACATTAAAGGGGTTTGT;RSEQ=CTCTATTCCTCACCTGTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:819:0:0,0:394,424:818,0:0:2,0:26.9:1:30.5:1:1:0:60:61.923:0.9988:0:0.1 0/1:847:222:112,110:306,316:622,222:0.2621:2,2:25.5:1:30.5:1:0.7551:1.05:60:110:0.2619:0:1.2 +9 8460277 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.11281;SOR=Inf;LSEQ=TCTTACTGTAATGTAAACAC;RSEQ=TTTCCAAAAATAATTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:31,0:0:1,0:25.1:1:32.9:1:1:0:60:62:1:0:0 0/1:30:3:3,0:26,1:27,3:0.1:1,0:31.3:1:31:1:1:0:60:6:0.1:0:1 +9 8460591 . A G 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTGAGGAAAAGCAGAGTCT;RSEQ=TTTCAGTTATAAAATAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:312:0:0,0:78,234:312,0:0:2,0:24.8:1:30.6:1:1:0:60:77:1:0:0.1 0/1:399:42:12,30:123,233:356,42:0.1053:2,2:22.3:1:31.7:1:0.49414:1.31885:60:41:0.1035:0:1.1 +9 8470930 . AG A 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.00028;SOR=Inf;LSEQ=TCCTGAAAGGCCTCCAAGGG;RSEQ=GGGGGCGGAAATGCAGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:207,79:286,0:0:2,0:21.6:1:32.4:1:1:0:59.9:70.5:0.993:0:0.1 0/1:325:13:11,2:216,95:311,13:0.04:2,2:23.7:1:31:1:0.3579:2.41:60:26:0.041:0.0031:1.4 +9 8470932 . G T 55 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.37896;SOR=3.50745;LSEQ=CTGAAAGGCCTCCAAGGGAG;RSEQ=GGGGCGGAAATGCAGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:1,0:208,81:289,1:0.0034:2,0:17:0:32:0:1:0:60:2:0.0035:0:1 0/1:333:4:1,3:231,98:329,4:0.012:2,2:19.3:1:27.8:1:0.08495:7.02544:60:8:0.0121:0:1 +9 8470974 . G A 155 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATAACGAATAAAAGACAT;RSEQ=GCCAACAATGACACAGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:555:0:0,0:339,216:555,0:0:2,0:26.9:1:31.9:1:1:0:59.9:68.375:1:0:0.1 0/1:704:42:27,15:395,267:662,42:0.0597:2,2:22.6:1:28.8:1:0.62778:1.22:60:84:0.0606:0:1.4 +9 8471481 . A G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GATGTTTTTAAAAGGAGGAT;RSEQ=TAGATGAAAAATTTCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:31.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 8484039 . C T 144 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=30.70519;LSEQ=TTAAGCAGTATCTTCTTTTA;RSEQ=GACCTCTATAATTTTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:0,1:120,15:135,1:0.0074:2,0:1:0:26:0:0.11765:0:60:2:0.0074:0:1 0/1:134:25:22,3:98,11:109,25:0.1866:2,2:19.3:1:31.1:1:0.72491:1.21303:60:50:0.1866:0:1.1 +9 8484047 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49886;SOR=Inf;LSEQ=TATCTTCTTTTACGACCTCT;RSEQ=TAATTTTGAGATATAATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:138,23:161,0:0:2,0:22.5:1:28.8:1:1:0:60:160:1:0:0 0/1:170:2:2,0:141,27:168,2:0.0118:2,0:33.5:1:33.5:1:1:0:60:4:0.0118:0:2 +9 8484240 . T G 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=TGCAGTCTTTGCCGTGACCC;RSEQ=GTGCTGCAGCCCACCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:760:0:0,0:368,392:760,0:0:2,0:24.7:1:31.1:1:1:0:60:68.091:1:0:0.1 0/1:941:54:25,29:423,462:885,54:0.0574:2,2:25.6:1:29.9:1:0.88884:1.06203:60:108:0.058:0:1.2 +9 8484397 . T TA 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.85355;SOR=1.07879;LSEQ=ATCTAAAGAGATAAAACCAA;RSEQ=AAAAAAAAAATCTGGTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:15:3,12:66,218:284,15:0.0497:2,2:24.7:1:30.2:1:1:1.21026:60:14:0.0488:0.0066:0.1 0/1:281:15:4,11:72,191:263,15:0.0534:2,2:28.7:1:28.9:1:1:1.03648:60:30:0.0551:0.0036:0.1 +9 8485099 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49746;SOR=0;LSEQ=ACTGTCTCCCATGTGAAAGT;RSEQ=ACAAATGAAAATAGCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:44,1:45,2:0.0426:1,2:19.5:1:29:1:0.08418:31.46141:60:4:0.0426:0:1 0/0:40:0:0,0:40,0:40,0:0:1,0:20.8:1:30.3:1:1:0:60:80:1:0:0.1 +9 8485125 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10672;SOR=Inf;LSEQ=TGAAAATAGCAAGGACACGT;RSEQ=GCCAAAACAAAGTGGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:78,4:82,0:0:1,0:23.2:1:32.5:1:1:0:60:40:1:0:0.1 0/1:75:3:3,0:72,0:72,3:0.04:1,0:10.3:1:29:0:1:0:60:6:0.04:0:2 +9 8485128 . C A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.11821;SOR=Inf;LSEQ=AAATAGCAAGGACACGTGGC;RSEQ=AAAACAAAGTGGTCTGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:79,4:83,0:0:1,0:24.7:1:32:1:1:0:60:166:1:0:0.1 0/1:81:3:3,0:78,0:78,3:0.037:1,0:11.3:1:31:0:1:0:60:6:0.037:0:2 +9 8485201 . T C 208 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCTACTTTTATCTGTGAT;RSEQ=TCTTACAAATTAGAAAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:254,97:351,0:0:2,0:23.6:1:31:1:1:0:60:174.5:1:0:0.1 0/1:480:115:76,39:236,129:365,115:0.2396:2,2:23.7:1:30.5:1:0.82314:1.07:60:114:0.239:0:1.1 +9 8485380 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50001;SOR=Inf;LSEQ=TCTTAAAACAGATGACCTGT;RSEQ=CTTTCCACCATGGACCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:18,134:152,0:0:2,0:23.3:1:31.4:1:1:0:60:49.667:1:0:0.1 0/1:170:2:1,1:31,137:168,2:0.0118:2,2:26:1:27.5:1:0.34194:4.37:60:4:0.012:0:1 +9 8485435 . G C 82 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.0027;SOR=Inf;LSEQ=TGCTGTCTACTTTGATCAGA;RSEQ=AGAGAAGTATGATTTTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:3,62:65,0:0:1,0:26.4:1:32:1:1:0:59.6:31.5:1:0:0.1 0/1:52:7:0,7:2,43:45,7:0.1346:1,0:23.3:1:29.4:1:1:0:60:14:0.1346:0:1 +9 8485686 . T C 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGAATGGGCTGATCAGTTA;RSEQ=TATAGCTTCAAAATACTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:143,27:170,0:0:2,0:22.8:1:30.9:1:1:0:59.7:23.286:1:0:0.1 0/1:159:36:31,5:102,21:123,36:0.2264:2,2:21.9:1:31.4:1:0.80012:1.27:59:35:0.2229:0:1.2 +9 8485834 . G A 217 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=184.97228;LSEQ=CCCTTTGCTCGTATGAGCAC;RSEQ=TACTTTTACATCGTATGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:698:1:1,0:378,318:696,1:0.0014:2,0:45:0:13:0:1:0:60:0:0:0:2 0/1:738:155:82,73:322,260:582,155:0.21:2,2:21.8:1:29.9:1:0.64988:1.10239:60:310:0.2123:0:1.2 +9 8486420 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18045;SOR=Inf;LSEQ=TTTCAGTCATTGCCAAATGA;RSEQ=GGAGTTCCACTCTACTGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:0,44:44,0:0:1,0:25.7:1:31.4:1:1:0:60:43:1:0:0 0/1:33:2:1,1:0,31:31,2:0.0606:1,2:10:0:32:0:0.06061:0:60:4:0.0606:0:1.5 +9 8486482 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.12821;SOR=Inf;LSEQ=AAACAAAACAAAACAGGCAA;RSEQ=GTTTGACCTACATACCTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:0,17:17,0:0:1,0:21.7:1:28.9:1:1:0:60:4.667:1:0:0.1 0/1:10:2:0,2:0,8:8,2:0.2:0,0:15:1:31:0:1:0:60:4:0.2:0:1 +9 8492614 . CA C 50 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGACACACAGAAGGTGCT;RSEQ=AAAAAAAAAAAAAAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:3,0:2,0:2,3:0.5:0,0:12.7:1:31.9:1:1:0:60:6:0.6:0.3333:0.7 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 +9 8492703 . AT A 93 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.20173;SOR=2.61469;LSEQ=ACTATTTTTTTCCCTGATCT;RSEQ=TTTTTTTTTTTTACCCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:6:6,0:23,0:23,6:0.1875:1,0:19.8:1:31.9:1:1:0:60:12:0.1875:0.0313:0 0/1:21:8:8,0:9,0:9,8:0.381:0,0:26.1:1:31.2:1:1:0:60:16:0.381:0.0952:0 +9 8492902 . A T 165 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTTTGGGCTTGCTGCGAGC;RSEQ=CCATCTCCTTTGGTTGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:819:0:0,0:413,405:818,0:0:2,0:25.5:1:30:1:1:0:59.9:115.857:1:0:0.1 0/1:1007:51:24,27:475,481:956,51:0.0506:2,2:25.1:1:29.1:1:0.77456:1.11085:60:102:0.0508:0:1.2 +9 8499578 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50355;SOR=0;LSEQ=TCGAAAAACTAAAATAAGAG;RSEQ=AATTTCAGGATATGAACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:2,0:122,6:128,2:0.0154:1,0:20:1:26:0:1:0:60:4:0.0157:0:1 0/0:105:0:0,0:90,15:105,0:0:2,0:22.5:1:31.4:1:1:0:60:210:1:0:0.1 +9 8499906 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22788;SOR=Inf;LSEQ=ACCCTATCAGAGCATTTTCT;RSEQ=CATTTTCTTTACTTAGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:20,159:179,0:0:2,0:23.3:1:31.9:1:1:0:59.9:28.833:1:0:0.1 0/1:164:2:1,1:17,145:162,2:0.0122:2,2:12:1:26:1:0.20807:8.32:60:4:0.0125:0:1 +9 8499960 . T C 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00016;SOR=Inf;LSEQ=TGGGTAAACCCACTATGTTT;RSEQ=CTTTGAAGAATACAAACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:1,67:68,0:0:1,0:22.3:1:30.8:1:1:0:60:136:1:0:0 0/1:38:8:0,8:0,30:30,8:0.2105:1,0:18.3:1:30.6:1:1:0:60:16:0.2105:0:1 +9 8500029 . G A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTCTACCTTTTAAGAAAA;RSEQ=ATCAAAAAACATGACCGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:0,3:1,16:17,3:0.15:1,0:36.7:1:22.3:1:1:0:60:2:0.1111:0:4.3 0/0:6:0:0,0:0,6:6,0:0:0,0:31:0:10:0:1:0:38:0:0:0:7 +9 8501113 . G GA 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.46382;SOR=1.44977;LSEQ=GTGAAAGGACAGGAGTGGTT;RSEQ=AAAAAAAAAATGATAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:8:0,8:10,147:157,8:0.0476:2,0:25.1:1:30.9:1:1:0:60:16:0.0485:0:0.6 0/1:133:9:0,9:13,111:124,9:0.0677:2,0:32.4:1:30.8:1:0.59858:0:60:18:0.0703:0:0.7 +9 8504101 . G T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00914;SOR=Inf;LSEQ=ATCAAGTGATGAGACCAAAA;RSEQ=AAGTCACAGTTACACTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:38,1:39,0:0:1,0:27.6:1:33.6:1:1:0:60:38:1:0:0.2 0/1:19:4:4,0:15,0:15,4:0.2105:1,0:27:1:30:1:1:0:60:8:0.2105:0:1 +9 8504209 . C T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2487;SOR=0;LSEQ=GTGAAGGTGAAAGCTAGCAA;RSEQ=ATCTCCCCGAGGAAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:2,1:180,47:227,3:0.013:2,2:41.7:1:29.3:1:0.50623:1.90844:60:6:0.0133:0:1 0/0:220:0:0,0:168,52:220,0:0:2,0:23.8:1:31.3:1:1:0:60:440:1:0:0.1 +9 8504387 . G A 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01803;SOR=0;LSEQ=CAGCCTATATGATGTCCCTG;RSEQ=CTCAATGGTAATTCGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:5:4,1:153,287:440,5:0.0112:2,2:12.8:1:28.6:1:0.05459:7.47:60:10:0.0113:0:1 0/0:546:0:0,0:221,324:545,0:0:2,0:26:1:30.7:1:1:0:60:59.556:0.9981:0:0.1 +9 8517759 . C T 31 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24917;SOR=0;LSEQ=TCAAAAATTAAAATTCATAC;RSEQ=ATCTTTGTTCCTTCTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:3:2,1:221,29:250,3:0.0118:2,2:6.7:1:20:1:0.31632:3.77895:60:2:0.0081:0:2.3 0/0:239:0:0,0:207,32:239,0:0:2,0:23.2:1:29.8:1:1:0:60:33.143:1:0:0.1 +9 8518143 . T C 170 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=39.3784;LSEQ=TCCCTCGGGGCACTGGATGG;RSEQ=GCTTGCTCTGAGGTTTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:575:1:1,0:277,295:572,1:0.0017:2,0:36:0:13:0:0.48517:0:60:0:0:0:3 0/1:700:45:25,20:334,320:654,45:0.0643:2,2:24:1:31:1:0.64439:1.20:60:90:0.0654:0:1.1 +9 8518395 . G A 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00327;SOR=Inf;LSEQ=ATGCTTGTAGCTGTGCTCTC;RSEQ=GTCACTACAGGAGTTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:73,161:234,0:0:2,0:27.9:1:30.8:1:1:0:60:116:1:0:0.1 0/1:315:11:5,6:116,188:304,11:0.0349:2,2:20.2:1:29.5:1:0.75439:1.35:59.9:22:0.0353:0:1.5 +9 8521244 . C T 139 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCACTTGGCTTGAGTGTAC;RSEQ=CAGATCCTCAAAGCATAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:158,64:222,0:0:2,0:27.9:1:31.1:1:1:0:60:26.75:1:0:0.1 0/1:268:29:19,10:162,76:238,29:0.1082:2,2:21:1:28.7:1:0.83412:1.12139:60:28:0.1069:0:1.1 +9 8523421 . A G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00195;SOR=Inf;LSEQ=CCATTAACCAAAAGAAGAAC;RSEQ=CAATGCAGCTACATTCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:179,67:246,0:0:2,0:23.4:1:30:1:1:0:60:60.5:1:0:0.1 0/1:269:10:5,5:180,79:259,10:0.0372:2,2:24.3:1:29.8:1:0.29428:2.27078:60:20:0.0379:0:1.2 +9 8524875 . T C 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.6278;SOR=2.5965;LSEQ=GGACCCTGCGGCGTCTCAAC;RSEQ=CCCCCTGAGCCTGAATGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:1:1,0:187,67:254,1:0.0039:2,0:28:0:32:0:1:0:60:2:0.004:0:1 0/1:296:3:1,2:213,80:293,3:0.0101:2,2:23.7:1:24:1:0.1868:5.28955:60:2:0.0068:0:1.3 +9 8526505 . G GA 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.4033;SOR=1.49053;LSEQ=TCATAACCAAACAGTACAAA;RSEQ=AAAAAAAAAAAGTTGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:11:9,2:80,10:90,11:0.1068:2,2:32.4:1:30.2:1:0.61608:1.76581:60:22:0.11:0:0.1 0/1:99:15:12,3:70,12:82,15:0.1515:2,2:12.9:1:26.7:1:0.6973:1.45215:59.7:6.5:0.1368:0.0808:0.5 +9 8526566 . G T 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.127;SOR=Inf;LSEQ=AAACAGGACAAAGATGAGAG;RSEQ=GATGAAAGGACAGAAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:172,95:267,0:0:2,0:27.3:1:31.3:1:1:0:60:65.75:1:0:0.1 0/1:305:4:2,2:170,131:301,4:0.0131:2,2:38:1:29.3:1:1:1.29658:60:8:0.0135:0:1.3 +9 8526697 . G T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26326;SOR=Inf;LSEQ=GAAAGAAGAAGCATTAGTAC;RSEQ=AGAAGAAGGAGGCTAGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:64,154:218,0:0:2,0:26.2:1:31.5:1:1:0:60:71.667:1:0:0.1 0/1:289:3:2,1:105,179:284,3:0.0104:2,2:41.7:1:30.3:1:0.55788:3.39:60:6:0.0105:0:1 +9 8526718 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21778;SOR=0;LSEQ=AGAAGAAGGAGGCTAGGGCT;RSEQ=GGGAGAAGAATTAAATTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:2:1,1:37,132:169,2:0.0116:2,2:6.5:1:28:1:0.39608:3.53:60:4:0.0118:0:1 0/0:196:0:0,0:65,131:196,0:0:2,0:23.3:1:30.7:1:1:0:60:195:1:0:0.1 +9 8526744 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24151;SOR=0;LSEQ=AAGAATTAAATTAGATTTAC;RSEQ=GAATTAAATAAGGTCTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:13,86:99,2:0.0198:2,2:27.5:1:29.5:1:0.25921:6.41:60:4:0.0206:0:1 0/0:104:0:0,0:25,79:104,0:0:2,0:20.4:1:30.2:1:1:0:60:208:1:0:0.1 +9 8527273 . TTAA T 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.00022;SOR=Inf;LSEQ=AATGCATGCCATGCATTTTA;RSEQ=TAATAATAATAATATTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:114,33:147,0:0:2,0:24.1:1:30.9:1:1:0:60:294:1:0:0.1 0/1:161:13:7,6:107,41:148,13:0.0807:2,2:28.2:1:29.3:1:0.20322:2.22443:60:26:0.0818:0.0062:0.1 +9 8527408 . C A 22 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21204;SOR=Inf;LSEQ=ATAAAAATATTATTATATTC;RSEQ=TTATAATTTGGTACAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:62,153:215,0:0:2,0:23.8:1:32.5:1:1:0:60:430:1:0:0.1 0/1:184:2:1,1:54,127:181,2:0.0109:2,2:11:1:22:1:0.51192:2.34:60:4:0.011:0:2.5 +9 8528541 . TA T 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.02959;SOR=1.56983;LSEQ=AAATAAGGAGAGAGAAAAAT;RSEQ=AAAAAAAAAATTCTCTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:41:29,12:333,110:443,41:0.0847:2,2:24.3:1:30.6:1:0.57312:1.25208:60:82:0.0858:0.0207:0.1 0/1:591:75:51,24:352,156:508,75:0.1269:2,2:23.7:1:29.5:1:0.89355:1.06173:59.7:150:0.128:0.0305:0.3 +9 8528811 . T A 31 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24904;SOR=Inf;LSEQ=AAGGTGATAGAAACATTCAG;RSEQ=TAATAAGTCAGATGCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:0:0,0:61,228:289,0:0:2,0:20.7:1:30.2:1:1:0:60:95.333:1:0:0.1 0/1:301:3:3,0:80,218:298,3:0.01:2,0:7.3:1:20:1:0.02042:0:60:2:0.0068:0:2.3 +9 8632149 . C G 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTGTGTGTGTGTGTGT;RSEQ=TGTGTGTGTGTGTGTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:30.5:1:1:0:56:4:1:0:1.5 +9 8632223 . A G 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATTACTGCTGGCCTCCA;RSEQ=ATAAATAAGTTCTTGACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:27.5:1:1:0:60:4:1:0:1.5 +9 8632768 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGAAAGGGATTTGTCAG;RSEQ=CCAGTTATTTAGATCAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:34:1:28:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 8633210 . G T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25665;SOR=0;LSEQ=TCTTACAAACATTTAACTGA;RSEQ=TTTCCCATTTAAGCACCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:2,1:206,3:209,3:0.0142:1,2:22.7:1:25.3:1:0.0558:31.4017:60:2:0.0095:0:1 0/0:171:0:0,0:166,5:171,0:0:1,0:25:1:32.2:1:1:0:60:170:1:0:0 +9 10093976 . T G 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGAGTGGGCTAAAAAATCCC;RSEQ=ATAGGGTACTATGCTCACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:31.5:1:1:0:60:4:1:0:1 +9 10094898 . A T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=2.12224;LSEQ=TAATCGTGGACTACTTCAAA;RSEQ=GCAAGAATATTAGCATTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:547:55:30,25:213,279:492,55:0.1005:2,2:27.2:1:30.7:1:0.11756:1.57:60:110:0.102:0:1.1 0/1:589:113:53,60:227,249:476,113:0.1919:2,2:27.2:1:29.4:1:0.91676:1.03201:60:55.5:0.192:0:1.1 +9 10633805 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=TTTTTATTTTTTATTTATTT;RSEQ=TTGAGGGGGCATGAAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:6,0:6,0:0:0,0:23.2:1:30.5:1:1:0:60:12:1:0:0.2 1/0:4:2:2,0:2,0:2,2:0.5:0,0:9:1:32:0:1:0:60:4:0.5:0:1 +9 10633964 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50441;SOR=Inf;LSEQ=TCCTAGCCAATGGCTGAGCA;RSEQ=CAGGAAATACAAAGGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:38,34:72,0:0:2,0:29.9:1:32.7:1:1:0:60:71:1:0:0.1 0/1:92:2:1,1:46,44:90,2:0.0217:2,2:29.5:1:28:1:1:1.04497:60:4:0.0222:0:1 +9 10634079 . A G 102 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05366;SOR=0;LSEQ=ATCCTGTAACTATTTACTTG;RSEQ=GAGTATTAGACTCTTCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1:0,0:26:1:32.2:1:1:0:60:18:1:0:1 1/0:13:8:0,8:0,5:5,8:0.6154:0,0:24.1:1:30.5:1:1:0:60:16:0.6154:0:1 +9 12036108 . T G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTTCTATAGCTCCAGGCT;RSEQ=TGCTTTTCTGCTGCTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:0,8:1:0,2:15.5:1:30.3:1:1:0:60:16:1:0:1 1/1:12:12:5,7:0,0:0,12:1:0,2:28:1:32.1:1:1:0:60:24:1:0:1.1 +9 12036280 . G C 76 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACTCCAGCCAGAGGCTCAGA;RSEQ=ACAGAATTCGGATCTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:23.8:1:34:0:1:0:59.5:8:1:0:1 1/1:5:5:2,3:0,0:0,5:1:0,2:22.6:1:32.8:1:1:0:59.6:10:1:0:1 +9 12036394 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGAGGAATCTGGGCAGTC;RSEQ=AGACAAGTGGGTTTGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:17:9,8:0,0:0,17:1:0,2:32.8:1:31.6:1:1:0:56.8:16:1:0:1.8 1/1:12:12:6,6:0,0:0,12:1:0,2:33.5:1:30.7:1:1:0:51.3:24:1:0:1.6 +9 12036418 . G T 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.25064;LSEQ=CAAGTGGGTTTGCCCCCAGC;RSEQ=AAACACACCCTCTCAACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:5,5:3,6:9,10:0.5263:2,2:27.6:1:30:1:0.64992:1.93:56.7:20:0.5263:0:2.3 1/0:12:7:3,4:2,3:5,7:0.5833:2,2:17.6:1:28.9:1:1:1.11:49.4:14:0.5833:0:2 +9 12036736 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02564;SOR=0;LSEQ=ACTATTGAAAGAAAAACAAG;RSEQ=AGAAAGCAACAACAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:2,2:2,1:3,4:0.5714:2,2:15.8:1:29:1:1:1.81007:37.3:8:0.5714:0:1.8 0/0:8:0:0,0:4,4:8,0:0:2,0:24.5:1:31.5:1:1:0:46.8:16:1:0:1.1 +9 12036767 . CAAC T 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=23;MSI=8.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AACAACAACAGCATCATCAT;RSEQ=AACAACAACAACAACAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:3,3:0,0:0,6:1:0,2:19.7:1:28.9:1:1:0:36:12:1:0.5:1.2 1/1:7:7:3,4:0,0:0,7:1:0,2:37.4:1:30.6:1:1:0:49.4:14:1:0.1429:0.4 +9 12518558 . C CT 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.72996;SOR=1.10519;LSEQ=TCGTTTTCCTCTTTTACTGC;RSEQ=TTTTACCACACTTACTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:748:32:13,19:348,368:716,32:0.0428:2,2:27.6:1:31:1:0.47026:1.38151:60:64:0.0431:0.0053:0.1 0/1:1041:49:27,22:484,508:992,49:0.0471:2,2:28.4:1:30.3:1:0.46465:1.29:60:98:0.0475:0.0029:0.2 +9 12518586 . A T 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.40074;LSEQ=ACACTTACTGTTCATATTTT;RSEQ=TTTGTCCATTGAACTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:681:55:22,33:272,350:622,55:0.0808:2,2:29.1:1:30.8:1:0.67097:1.16545:60:110:0.0821:0:1.2 0/1:908:209:96,113:324,370:694,209:0.2302:2,2:24.8:1:29.7:1:0.87449:1.03072:60:103.5:0.2318:0:1.2 +9 12518676 . C A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00043;SOR=Inf;LSEQ=TGTTCCCATGTGCATTATTG;RSEQ=ATTATTTATCTTTCTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:47,173:220,0:0:2,0:22.1:1:32.2:1:1:0:60:109:1:0:0.1 0/1:229:12:3,9:41,176:217,12:0.0524:2,2:20.9:1:29.7:1:0.70489:1.43:60:24:0.0533:0:1.1 +9 12519087 . A G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGATATTAGGGTTGAAC;RSEQ=TGTAAATACCAACACTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27.5:1:34:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 12746316 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58698;SOR=0.4055;LSEQ=ATATCCTGAAGTATGTTTTC;RSEQ=AGTTTGTTTCCATTTTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:17,11:28,2:0.0667:2,2:45:1:30.5:1:1:1.52251:60:4:0.0667:0:2 0/1:36:1:0,1:21,14:35,1:0.0278:2,0:1:0:22:0:0.41667:0:60:2:0.0286:0:2 +9 12746337 . G A 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16176;LSEQ=AGTTTGTTTCCATTTTCCCC;RSEQ=TCTCCTTCTGGTACACCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:29:17,12:4,2:6,29:0.8286:2,2:28.4:1:30.9:1:1:1.39827:55.5:58:0.8286:0:1.2 1/1:53:45:24,21:5,3:8,45:0.8491:2,2:24.4:1:30.1:1:0.71525:1.44814:51.4:90:0.8491:0:1.2 +9 12746343 . T A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51277;SOR=Inf;LSEQ=TTTCCATTTTCCCCGTCTCC;RSEQ=TCTGGTACACCAATCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:20,16:36,0:0:2,0:28.4:1:31.4:1:1:0:56.4:72:1:0:0.9 0/1:53:2:1,1:28,23:51,2:0.0377:2,2:35:0:32:1:1:1.21285:52:4:0.0377:0:1 +9 12746401 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52715;SOR=Inf;LSEQ=TGAAGTCCCATATTTCTTGG;RSEQ=GGCTTTGTTCATTCCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:21:1:30.7:1:1:0:58.8:38:1:0:0.5 0/1:33:2:1,1:16,15:31,2:0.0606:2,2:16.5:1:27.5:1:1:1.06462:26:4:0.0606:0:2.5 +9 12746899 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5023;SOR=0;LSEQ=TTGTCTAGTTTTGGTCTTTG;RSEQ=GGCTGCTGACCCTTGGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:16,18:34,2:0.0556:2,2:37:1:31.5:1:1:1.12:49.5:4:0.0556:0:1 0/0:27:0:0,0:16,11:27,0:0:2,0:24.5:1:29.3:1:1:0:47.7:54:1:0:0.1 +9 13731155 . T C 241 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=5.23184;LSEQ=CTGGGCATTAACTGAAAAAA;RSEQ=CTCTGCATCTTGCTCACCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:101:59,42:73,47:120,101:0.457:2,2:26.3:1:31.7:1:0.78337:1.10516:59.9:100:0.4566:0:1.7 1/1:271:221:131,90:24,26:50,221:0.8155:2,2:26.3:1:31:1:0.15695:1.57:60:109.5:0.8172:0:1.7 +9 13731201 . C G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.25099;LSEQ=ATCATGGTCCCATCCTGGCC;RSEQ=TGTTTAAGCCCCAGGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:117:56,61:71,79:150,117:0.4382:2,2:25.8:1:30.5:1:1:1.02:59.9:38:0.4351:0:1.7 1/1:281:226:112,114:25,29:54,226:0.8043:2,2:25.5:1:29.9:1:0.76218:1.14:60:55.5:0.8043:0:1.7 +9 13731294 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49836;SOR=Inf;LSEQ=AGGATTCTCCAAAGCATCTC;RSEQ=ACTCATGTTTCTTGCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:25,79:104,0:0:2,0:23.7:1:32.2:1:1:0:60:103:1:0:0.2 0/1:112:2:1,1:28,81:109,2:0.0179:2,2:19.5:1:30.5:1:0.45602:2.86:60:4:0.018:0:1 +9 13731367 . G C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00274;SOR=6.07592;LSEQ=GCTCCCCACCCAGCTTCTAG;RSEQ=CCACCACTCTGACCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:0,12:1,20:21,12:0.3636:1,0:27.4:1:32.2:1:1:0:60:24:0.3636:0:2.3 1/0:23:18:0,18:0,5:5,18:0.7826:0,1:18.3:1:29.6:1:1:0:60:8:0.7619:0:1.6 +9 13731412 . G C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=1.66686;LSEQ=TAATATCCATTTCAATGCAG;RSEQ=TTTTTGGCTTGAGGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:6,7:0.5385:0,0:25.7:1:30.6:1:1:0:58.4:6:0.5:0:3.7 1/0:6:4:0,4:0,2:2,4:0.6667:0,0:31.3:1:33:1:1:0:60:8:0.6667:0:3.8 +9 13731416 . T A 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.06713;LSEQ=ATCCATTTCAATGCAGGTTT;RSEQ=TGGCTTGAGGTCTCTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:5,7:0.5833:0,0:24:1:30.1:1:1:0:58.4:14:0.5833:0:3.7 1/0:5:3:0,3:0,2:2,3:0.6:0,0:37:1:31.3:1:1:0:60:6:0.6:0:4.3 +9 13731425 . G C 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.68659;LSEQ=AATGCAGGTTTTTGGCTTGA;RSEQ=GTCTCTTTCCAAATTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:4,6:0.6:0,0:24.2:1:26.5:1:1:0:58.2:5:0.5556:0:3.7 1/0:4:2:0,2:0,1:1,2:0.5:0,0:27:1:28:1:1:0:60:4:0.5:0:4.5 +9 16181267 . G C 147 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=0.1071;LSEQ=TTTGGAGGGCAAGAGTTTCA;RSEQ=AAAGACACTAGAAAGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:23,0:26,0:26,23:0.4694:1,1:24.2:1:32.7:1:1:0:60:46:0.4694:0:1.1 0/1:59:5:5,0:54,0:54,5:0.0847:1,0:26.6:1:33.4:1:1:0:60:10:0.0877:0:1 +9 16181342 . ACTG A 46 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=4.000;MSILEN=3;SSF=1;SOR=0.75839;LSEQ=AGCAGATTATTGCTGCTACT;RSEQ=CTGCTGCTGTTGCTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:164,117:281,3:0.0105:2,2:25.7:1:33.3:1:1:1.43:60:6:0.0107:0:0.3 0/0:375:3:1,2:215,157:372,3:0.008:2,2:29.3:1:29.3:1:0.57655:2.73154:60:6:0.008:0.0027:0.3 +9 16181428 . G A 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.18744;LSEQ=TAACTGAAGAAGAACACGTT;RSEQ=CTGATGACTGTGAGACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:75:24,51:29,63:92,75:0.4491:2,2:23.3:1:29.6:1:1:1.02:60:150:0.4545:0:1.1 0/1:197:26:7,19:56,115:171,26:0.132:2,2:23.3:1:27.6:1:0.65526:1.31993:60:52:0.1333:0:1 +9 16181703 . A G 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATCATGTGCCGGTCACTGT;RSEQ=CTGAGTACTTCATAGGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28:1:33.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 16206644 . G T 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23751;SOR=Inf;LSEQ=ATGGAAATGATTTATTCGGA;RSEQ=AACCTTGTCAGTACTGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:60,11:71,0:0:2,0:23.3:1:33.3:1:1:0:60:142:1:0:0.1 0/1:68:2:1,1:59,7:66,2:0.0294:2,2:5.5:1:25:1:0.223:7.95036:60:4:0.0303:0:1 +9 16206695 . A G 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTATTTCATTATGGGCCATG;RSEQ=GTGGGCTAGACTACATTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:128,60:188,0:0:2,0:24.8:1:30.8:1:1:0:60:93:1:0:0.6 0/1:200:20:10,10:118,61:179,20:0.1:2,2:29:1:30.2:1:0.21752:1.92768:60:40:0.1026:0:1.6 +9 16206756 . T G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02047;LSEQ=CATTTCCACAACTGGTTATT;RSEQ=CAGTTGACAATTAACAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:108:53,55:73,75:148,108:0.4202:2,2:26.7:1:31.8:1:1:1.01002:59.9:26:0.416:0:2.2 0/1:344:5:3,2:174,164:338,5:0.0145:2,2:10.6:1:29.8:1:1:1.41:60:10:0.0148:0:2.2 +9 16206760 . T G 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.28516;LSEQ=TCCACAACTGGTTATTTCAG;RSEQ=TGACAATTAACAGGAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:110:54,56:73,74:147,110:0.4264:2,2:26:1:31.1:1:1:1.02294:59.9:26.5:0.4223:0:2.2 0/1:338:59:29,30:144,135:279,59:0.1746:2,2:25.9:1:30.5:1:0.77534:1.10313:60:28.5:0.1701:0:1.5 +9 16206766 . A G 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01221;SOR=Inf;LSEQ=ACTGGTTATTTCAGTTGACA;RSEQ=TTAACAGGAAATGATGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:120,131:251,0:0:2,0:26.2:1:30.3:1:1:0:60:40.833:1:0:1 0/1:337:9:3,6:166,162:328,9:0.0267:2,2:23:1:31.1:1:0.33636:2.04516:60:18:0.027:0:1.8 +9 16243162 . T A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACGGGTGTCTATAAAATT;RSEQ=TTTTTTTTATTACTCAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:4:1:28.5:1:1:0:60:4:1:0:2 1/1:2:2:2,0:0,0:0,2:1:0,0:26:1:27:1:1:0:60:4:1:0:1.5 +9 16243229 . G C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCTGAGTCCTACCAGATT;RSEQ=TTCTGCCCTCACACCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:0,10:1:0,2:25.8:1:32.8:1:1:0:60:20:1:0:1.2 1/1:5:5:4,1:0,0:0,5:1:0,2:28:1:30.2:1:1:0:60:10:1:0:1.2 +9 16243286 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48889;SOR=0;LSEQ=AGGCACGGCCCCCTCCACTG;RSEQ=CAGCCACTGTCTGGACGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:11,10:21,2:0.087:2,2:34.5:1:31:1:1:1.09544:60:4:0.087:0:1 0/0:23:0:0,0:12,11:23,0:0:2,0:32.3:1:31.5:1:1:0:60:46:1:0:0.4 +9 16243289 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=CACGGCCCCCTCCACTGCCA;RSEQ=CCACTGTCTGGACGCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:22,0:0:2,0:29.5:1:33.1:1:1:0:60:44:1:0:0.4 0/1:23:2:1,1:11,10:21,2:0.087:2,2:30.5:1:29:1:1:1.09544:60:4:0.087:0:1.5 +9 16243361 . A C 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00137;SOR=Inf;LSEQ=GACATCACAGCCCAGGCTCA;RSEQ=TTCAAAAGTGGCAGGACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:10,0:0:2,0:24.3:1:32.3:1:1:0:60:20:1:0:0.1 1/1:6:5:1,4:0,1:1,5:0.8333:0,2:21.2:1:32.4:1:1:0:60:10:0.8333:0:1 +9 16245046 . A C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACCAACCTAACAGCATTC;RSEQ=ACAGACAAAGAACAAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:28.5:1:1:0:60:4:1:0:2 +9 18994588 . C A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCGGCAGGGAAGTATGTT;RSEQ=AATGTTTTGAAGGTGCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:24:1:30:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 18994973 . T C 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.78441;SOR=1.29408;LSEQ=TGTGCAATGTTTAACTTTAT;RSEQ=AAATATGTCAAGGTTGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:17:17,0:9,0:9,17:0.6538:0,1:20.5:1:32.6:1:1:0:58:34:0.6538:0:1.1 1/0:38:27:27,0:11,0:11,27:0.7105:0,1:20.9:1:31.5:1:1:0:60:54:0.7105:0:1 +9 18995032 . T A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.03266;SOR=Inf;LSEQ=AAGAGACTGAGTTTTTCTTT;RSEQ=TGAAATGCACAAAATAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:86,5:91,0:0:2,0:24.1:1:31.5:1:1:0:60:182:1:0:0.2 0/1:109:6:6,0:96,7:103,6:0.055:2,0:18.2:1:27.3:1:1:0:60:12:0.055:0:1 +9 18995150 . C A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=1;SSF=0.0014;SOR=0.6731;LSEQ=TCTCCCTCCCTTTTCTCCCC;RSEQ=CAAAAATACCTTTGGGGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:465:245:117,128:110,110:220,245:0.5269:2,2:26.8:1:30:1:0.64321:1.0938:60:490:0.5269:0:1.1 0/1:621:266:127,139:171,184:355,266:0.4283:2,2:24.9:1:28.4:1:0.93543:1.01714:60:52.2:0.4293:0:1.1 +9 18995323 . C T 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.09801;LSEQ=GCTGGCATCAGCCAGTCTCA;RSEQ=TTGTGGGATAATTAATTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:14:1,13:1,21:22,14:0.3889:1,1:25.3:1:31.3:1:1:1.59:57.6:28:0.3889:0:1 0/1:17:7:0,7:0,10:10,7:0.4118:0,0:19:1:29.6:1:1:0:60:14:0.4118:0:1.1 +9 20776649 . CT C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50016;SOR=Inf;LSEQ=TTTTCATTTTTGCCTTCATA;RSEQ=TTTAAGTTCCATCCACTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:110,29:139,0:0:2,0:23.4:1:31.8:1:1:0:60:278:1:0:0.1 0/1:157:2:1,1:114,41:155,2:0.0127:2,2:38.5:1:30.5:1:0.46472:2.75921:60:4:0.0128:0:0 +9 20776658 . T A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50109;SOR=Inf;LSEQ=TTGCCTTCATACTTTTAAGT;RSEQ=CCATCCACTTAAAAATACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:118,37:155,0:0:2,0:25.1:1:30.9:1:1:0:60:76.5:1:0:0.1 0/1:179:2:1,1:128,49:177,2:0.0112:2,2:8.5:1:26:1:0.48177:2.59608:60:4:0.0112:0:2 +9 20776743 . A C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00243;SOR=1.90157;LSEQ=AGTAATAGCTTGTGTGAAAA;RSEQ=GGCTTTCCAATAATAGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:36:20,16:181,163:344,36:0.0942:2,2:25.5:1:31.1:1:0.86101:1.13:60:72:0.0945:0:1.1 0/1:478:79:42,37:209,189:398,79:0.1653:2,2:26.5:1:29.7:1:1:1.03:59.6:38.5:0.1628:0:1.2 +9 20776791 . T C 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13465;SOR=Inf;LSEQ=AGCAGTGCTTTTCTTTGTTG;RSEQ=TGATCGTTTTGGAATCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:112,190:302,0:0:2,0:26.1:1:30.4:1:1:0:60:150:1:0:0.2 0/1:384:4:2,2:158,221:379,4:0.0104:2,2:23.3:1:30.8:1:1:1.40:60:8:0.0104:0:1.3 +9 20777008 . A G 75 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCGACTGTATTTCAAAACA;RSEQ=TGAACACATATATTCCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:13.2:1:32.6:1:1:0:60:10:0.8333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 20781865 . G T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25396;SOR=Inf;LSEQ=GAAGAAGGTCCCTCTAGGCA;RSEQ=CAGTTGGCTCTAAACCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:101,30:131,0:0:2,0:22.2:1:32.7:1:1:0:60:130:1:0:0.1 0/1:158:3:1,2:121,34:155,3:0.019:2,2:7.3:1:26.7:1:0.13024:7.00189:60:6:0.0192:0:1 +9 20781866 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50378;SOR=Inf;LSEQ=AAGAAGGTCCCTCTAGGCAG;RSEQ=AGTTGGCTCTAAACCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:103,30:133,0:0:2,0:22.3:1:31.9:1:1:0:60:65.5:1:0:0.1 0/1:164:2:0,2:123,39:162,2:0.0122:2,0:14.5:1:26:1:0.06135:0:60:4:0.0123:0:1 +9 20781872 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59435;SOR=0.41864;LSEQ=GTCCCTCTAGGCAGCAGTTG;RSEQ=CTCTAAACCTTTTGGAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:112,38:150,2:0.013:2,2:12.5:1:29:1:0.44859:2.92209:60:4:0.0132:0:1.5 0/0:183:1:0,1:135,47:182,1:0.0055:2,0:1:0:24:0:0.2623:0:60:2:0.0056:0:1 +9 20781979 . C A 160 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=17.39909;LSEQ=AAAGTGTCGATGTGGGATTT;RSEQ=GGTCTTTACGGATAATCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:427:2:2,0:211,214:425,2:0.0047:2,0:1:0:23:0:0.24824:0:60:4:0.0047:0:1 0/1:673:51:24,27:312,306:618,51:0.0758:2,2:26.1:1:28.3:1:0.66438:1.14682:60:24.5:0.0749:0:1.1 +9 20782100 . T C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.41881;LSEQ=TGGACTATAAGAAGGGATAG;RSEQ=AGTCCTGTTGTGAAATAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:4:0,4:5,84:89,4:0.043:2,0:31.8:1:30.8:1:1:0:60:8:0.043:0:1 1/0:88:49:2,47:1,38:39,49:0.5568:1,1:25.7:1:32.2:1:1:1.61:60:98:0.5568:0:1.1 +9 20782260 . G A 75 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATTTTTTAAAATTATACT;RSEQ=TTAGTTAAGTACAGCATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:26.2:1:32.4:1:1:0:60:10:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:45:0:30:0:1:0:60:2:1:0:1 +9 21636636 . T TAC 26 v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=38;MSI=20.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGTGCCAGAAAGTAAAGAAT;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:25:1:26.4:1:1:1.73:60:4:0.5:0.2:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 21638439 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49891;SOR=Inf;LSEQ=GCCGGACCCTTCGTCATTAC;RSEQ=AGAAACTGACTGAGCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:144,30:174,0:0:2,0:23.2:1:31.1:1:1:0:60:23.857:1:0:0.1 0/1:183:2:1,1:145,36:181,2:0.0109:2,2:27.5:1:28:1:0.36438:3.98665:60:4:0.011:0:1 +9 21638592 . G A 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.88232;LSEQ=TGGTGGGTTTGTTTGAAGGT;RSEQ=CTAACGTGTGTGCCATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:299:151:78,73:85,63:148,151:0.505:2,2:22:1:29.3:1:0.35327:1.26172:60:302:0.5084:0:1 1/0:333:266:132,134:31,34:65,266:0.7988:2,2:25.3:1:28.1:1:0.78411:1.08:60:265:0.803:0:1.1 +9 21638732 . T G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.79787;SOR=0.78737;LSEQ=AGTGAAGGCAGATTTTATGG;RSEQ=ATTTTGTAATAAAGTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:10:2,8:1,72:73,10:0.1205:1,2:27.5:1:29.2:1:0.03706:16.76:59.4:9:0.1169:0:1.7 0/1:72:7:1,6:3,61:64,7:0.0972:1,2:20.6:1:29.1:1:0.34608:3.30:57.9:6:0.0909:0:2.1 +9 21968199 . C G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACTGATGATCTAAGTTTCC;RSEQ=GAGGTTTCTCAGAGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:231:231:115,116:0,0:0,231:1:0,2:27.5:1:27.8:1:1:0:60:6.966:1:0:1.4 1/1:621:503:244,259:61,52:113,503:0.81:2,2:25.1:1:27.4:1:0.29991:1.24474:59.9:7.825:0.7964:0:1.4 +9 21968225 . C T 41 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.15985;SOR=0.28112;LSEQ=TTCTCAGAGCCTCTCTGGTT;RSEQ=TTTCAATCGGGGATGTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:2,1:110,143:253,3:0.0117:2,2:8.3:1:26.3:1:0.58272:2.59:60:2:0.0085:0:1.7 0/0:603:2:2,0:275,326:601,2:0.0033:2,0:7:1:14.5:1:0.21061:0:60:0:0:0:4.5 +9 21968318 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09519;SOR=0;LSEQ=ACATCCCGCCCTCCTCTCTT;RSEQ=CCGTCCCTACCGGCATTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:23,73:96,2:0.02:2,2:24.5:1:29.5:1:0.43173:3.13:60:4:0.0211:0:1 0/0:223:0:0,0:54,169:223,0:0:2,0:24.5:1:30.9:1:1:0:60:36.167:1:0:0.2 +9 21968335 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTGCCGTCCCTACCGGCAT;RSEQ=GAAATACTTATGGATAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:14,56:70,0:0:2,0:28.2:1:30.7:1:1:0:60:69:0.9857:0:0.2 0/1:149:2:1,1:27,120:147,2:0.0134:2,2:12.5:1:31.5:1:0.34156:4.38:60:4:0.0139:0:1 +9 21968646 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23429;SOR=0.22774;LSEQ=GGCATCTTTTGCACCTGGTG;RSEQ=GGAGTGAGCCAGCCAGCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:2:1,1:90,26:116,2:0.0168:2,2:36.5:1:30:1:0.40678:3.41555:60:4:0.0169:0:1 0/0:259:1:0,1:187,71:258,1:0.0039:2,0:1:0:25:0:0.27799:0:60:2:0.0039:0:1 +9 21968658 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.09473;SOR=0;LSEQ=ACCTGGTGCGGAGTGAGCCA;RSEQ=CCAGCTTGCGATAACCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:2,0:101,38:139,2:0.0142:2,0:11:1:32.5:1:1:0:60:4:0.0145:0:1 0/0:316:0:0,0:216,100:316,0:0:2,0:25.1:1:31:1:1:0:60:34.111:1:0:0.1 +9 21968877 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GTTCGGTTCTCCCGAGGCAG;RSEQ=ATTTACACTTGAGAGTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:5,77:82,0:0:2,0:25.1:1:32:1:1:0:60:81:1:0:0.1 0/1:180:2:1,1:15,163:178,2:0.0111:2,2:19.5:1:27:1:0.17033:10.55:60:4:0.0111:0:1 +9 21970916 . C T 146 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=19.71604;LSEQ=CTCACCTGAGGGACCTTCCG;RSEQ=GGCATCTATGCGGGCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:484:1:0,1:251,231:482,1:0.0021:2,0:1:0:29:0:0.48033:0:60:2:0.0021:0:1 0/1:968:38:22,16:498,432:930,38:0.0393:2,2:28.4:1:27.9:1:0.62287:1.19:60:18:0.0377:0:1.1 +9 21971125 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09478;SOR=0;LSEQ=CGTCGTGCACGGGTCGGGTG;RSEQ=GAGTGGCGGGGTCGGCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:81,114:195,2:0.0101:2,2:23.5:1:30:1:1:1.40:32:4:0.0104:0:1 0/0:444:0:0,0:194,250:444,0:0:2,0:23.4:1:29.3:1:1:0:42.1:48.333:1:0:0.3 +9 21971145 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10104;SOR=0;LSEQ=AGAGTGGCGGGGTCGGCGCA;RSEQ=TTGGGCTCCGCGCCGTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:70,93:163,2:0.0121:2,2:5.5:1:28:1:1:1.33:60:4:0.0132:0:1.5 0/0:353:0:0,0:152,200:352,0:0:2,0:23.8:1:30:1:1:0:49.7:11.571:1:0:0.3 +9 21971227 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11446;SOR=0;LSEQ=CCTGCCAGAGAGAACAGAAT;RSEQ=GTCAGAGCCAGGGTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:31,58:89,2:0.022:2,2:24.5:1:30.5:1:1:1.86:28:4:0.0227:0:1.5 0/0:177:0:0,0:61,116:177,0:0:2,0:24.4:1:30.6:1:1:0:56.5:58:1:0:0.1 +9 21974218 . A G 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1;SOR=Inf;LSEQ=AATAATTTCGATCAAAATTT;RSEQ=TATTCGATATTTATTCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:3,0:3,0:0:0,0:28:1:28:1:1:0:60:6:1:0:0.3 1/1:2:2:2,0:0,0:0,2:1:0,0:18.5:1:33:0:1:0:60:4:1:0:1 +9 21974374 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51412;SOR=Inf;LSEQ=CCTTTTTATCCCAAACGTTC;RSEQ=TAAATTTTGTATCTGATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:108,0:108,0:0:1,0:22.7:1:30:1:1:0:60:26:1:0:0.1 0/1:155:2:2,0:152,1:153,2:0.0129:1,0:27.5:1:29.5:1:1:0:60:4:0.0131:0:1.5 +9 21974855 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54831;SOR=Inf;LSEQ=CCGCCGCCCGCTGCCTGCTC;RSEQ=CCCCCTCTCCGCAGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:47,56:103,0:0:2,0:23.9:1:30.2:1:1:0:60:16.167:1:0:0.1 0/1:198:2:1,1:83,113:196,2:0.0101:2,2:14.5:1:28.5:1:1:1.36:60:4:0.0105:0:1.5 +9 21975017 . C T 70 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00794;SOR=Inf;LSEQ=CTTTCCAGGCAAGGGGACGC;RSEQ=GTGAGCGAGTGCTCGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:0,4:4,0:0:0,0:21.8:1:32:0:1:0:60:8:1:0:0 1/1:5:5:0,5:0,0:0,5:1:0,0:24.2:1:30.2:1:1:0:60:10:1:0:1 +9 21993964 . T C 167 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAAGGGAGGTCCAGGTTCAA;RSEQ=GGTACTGCGAGAACCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:39:39,0:39,0:39,39:0.5:1,1:21.8:1:31.6:1:1:0:60:12:0.48:0:1.2 0/0:65:0:0,0:65,0:65,0:0:1,0:18.3:1:30.5:1:1:0:60:64:1:0:0.1 +9 21994030 . TCTC T 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.06386;SOR=Inf;LSEQ=GAAGCCTCCACCGGCGGTTA;RSEQ=CTCCTCCTCCTAGCCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:299:0:0,0:257,41:298,0:0:2,0:24.7:1:32.4:1:1:0:59.9:98.333:1:0:0.1 0/1:338:5:4,1:289,43:332,5:0.0148:2,2:27.2:1:29.7:1:0.50542:1.67713:60:10:0.0149:0.0059:0 +9 21994368 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24927;SOR=Inf;LSEQ=GGCCGAGCTCGGCAGCCGCT;RSEQ=CGCCGCCCTTTGGCACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:60,173:233,0:0:2,0:26.5:1:32:1:1:0:60:45.6:0.9956:0:0.1 0/1:250:3:2,1:63,184:247,3:0.012:2,2:10.7:1:23:1:0.16653:5.79:60:2:0.0082:0:3.7 +9 22003223 . C T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCATTGATAAGTTACTATTT;RSEQ=AATACAACCAGGTGGTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:31.5:1:32:1:1:0:60:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 22003367 . G A 41 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGTTTCCCTTAATATCA;RSEQ=GTTGTCATTAGGAAAGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:1,0:1,3:0.75:0,2:30.3:1:26:1:1:0:60:2:0.6667:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 22003749 . TG T 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.17879;SOR=1.79562;LSEQ=TTGGGTTTTTATAGGTGTGT;RSEQ=GGGGGGGTTATTCTCCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:8:3,5:191,311:502,8:0.0157:2,2:33.4:1:31.9:1:1:1.02353:60:16:0.0159:0:0.3 0/1:720:20:7,13:292,406:698,20:0.0278:2,2:30.9:1:31.4:1:0.64853:1.33515:60:40:0.0282:0.0014:0.2 +9 22003803 . C A 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.05232;SOR=0;LSEQ=AAAATAGTTTTCAAACAAAC;RSEQ=GTTTATATTTACTAGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:4:1,3:37,153:190,4:0.0206:2,2:23:1:31.8:1:0.58507:1.38:60:8:0.0211:0:1 0/0:210:0:0,0:42,168:210,0:0:2,0:23.3:1:29.5:1:1:0:60:209:1:0:0.1 +9 22003878 . C CT 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.21026;SOR=Inf;LSEQ=GAGATCATTGTGTATTTCTG;RSEQ=TTTTTTTTAAAAAAAGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:1,48:49,0:0:1,0:19.9:1:33.6:1:1:0:60:98:1:0:0.1 0/1:42:2:0,2:1,39:40,2:0.0476:1,0:34.5:1:26.5:1:1:0:60:4:0.0513:0:0 +9 22005882 . G A 39 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2483;SOR=Inf;LSEQ=ACAGGCTTGCAGGCTTACAG;RSEQ=CTTTCCGCCGCTCCCCGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:189:0:0,0:176,13:189,0:0:2,0:27.8:1:31.1:1:1:0:60:36.8:1:0:0.1 0/1:196:3:3,0:184,9:193,3:0.0153:1,0:29.7:1:24.7:1:1:0:60:2:0.0107:0:1.3 +9 22006266 . G A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24853;SOR=0;LSEQ=CCTGCCAGAGAGAGCAGAGT;RSEQ=GTCAGAGCCAGGGTGGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:3:1,2:56,196:252,3:0.0118:2,2:30:1:25.3:1:0.53346:1.75:51.7:2:0.008:0:1 0/0:254:0:0,0:71,183:254,0:0:2,0:24.3:1:30.5:1:1:0:56.5:253:1:0:0.2 +9 22006273 . G T 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAGAGAGCAGAGTGGTCAGA;RSEQ=CCAGGGTGGGGGCAGGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:49,183:232,0:0:2,0:28.4:1:32.6:1:1:0:59:76.333:1:0:0.1 0/1:220:25:6,19:54,141:195,25:0.1136:2,2:31.3:1:28.3:1:0.81426:1.21172:59:24:0.1111:0:1 +9 22006348 . C T 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05264;SOR=Inf;LSEQ=TTTAAAGAAACACCTAATTG;RSEQ=AAAGTTTTCACCCAGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:0,56:56,0:0:1,0:25.3:1:32.6:1:1:0:60:17.667:1:0:0.2 0/1:53:4:0,4:1,48:49,4:0.0755:1,0:24:1:28:1:1:0:60:8:0.0769:0:1.3 +9 22008026 . G T 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4958;SOR=0;LSEQ=AAAGTACAAAAGAGTTGTCC;RSEQ=AGATTGTAAAAGAAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:15,0:0,0:0,15:1:0,1:14.9:1:31.9:1:1:0:60:30:1:0:1.1 1/1:20:18:17,1:2,0:2,18:0.9:0,1:26.7:1:31.2:1:1:0:60:36:0.9:0:1.1 +9 22008143 . G T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2507;SOR=Inf;LSEQ=ATTATTTATGAAGATCCTTT;RSEQ=CCATTCAAAAAGGACCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:155,67:222,0:0:2,0:23.1:1:32.1:1:1:0:60:73:1:0:0.1 0/1:248:3:1,2:176,69:245,3:0.0121:2,2:9.7:1:24:1:0.19789:5.06257:60:2:0.0082:0:1.7 +9 22008380 . TA T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24321;SOR=0;LSEQ=CATATAGTAGCTTAGAAGTT;RSEQ=CATTGATTTTTTCCATGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:31,166:197,2:0.0101:2,2:23.5:1:30.5:1:0.29643:5.29:60:4:0.0101:0:0 0/0:204:0:0,0:39,165:204,0:0:2,0:24.1:1:28.8:1:1:0:60:203:1:0:0.1 +9 22008660 . C T 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.63273;SOR=2.41173;LSEQ=GGGTAAAAGCCTGTTTTACG;RSEQ=GTGGAATGCACACCTCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:0,1:146,69:215,1:0.0046:2,0:1:0:25:0:0.32407:0:60:2:0.0047:0:1 0/1:270:3:1,2:167,99:266,3:0.0111:2,2:28.3:1:23.7:1:0.55836:3.35797:60:2:0.0077:0:1.7 +9 22009031 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50259;SOR=Inf;LSEQ=GACACTCTTCCCTTCTTTCC;RSEQ=ACGCTGCTCCGGCGCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:6,77:83,0:0:2,0:21.4:1:32.8:1:1:0:60:166:1:0:0.1 0/1:102:2:1,1:10,90:100,2:0.0196:2,2:32.5:1:29:1:0.20501:8.63:60:4:0.02:0:1 +9 22011642 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTTATAATTATTTTTCA;RSEQ=TCTACACTGTGTTTTCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:30:1:31.5:1:1:0:54.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 22012051 . T C 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.10719;LSEQ=CTAGTAATAATATTTTTATA;RSEQ=TCTAGTTGGTGAAATTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:166:73,93:142,169:311,166:0.348:2,2:24:1:32.3:1:0.77219:1.07026:60:82:0.346:0:1.1 0/1:611:33:15,18:264,313:577,33:0.054:2,2:24.9:1:31.9:1:1:1.01212:60:66:0.0545:0:1.1 +9 22012135 . C A 35 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10971;SOR=0;LSEQ=CTTTTTCTTCAGCGAGGCAG;RSEQ=CGAGCTGCAGACACAGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:3,0:60,162:222,3:0.0133:2,0:6.3:1:22.7:1:0.0212:0:60:2:0.009:0:1.3 0/0:245:0:0,0:82,163:245,0:0:2,0:23.4:1:30:1:1:0:57:39.833:1:0:0.1 +9 22012151 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49964;SOR=Inf;LSEQ=GCAGCCGAGCTGCAGACACA;RSEQ=AGATGCAGATCTTTGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:30,131:161,0:0:2,0:23.1:1:32.2:1:1:0:53.7:79.5:1:0:0.1 0/1:177:2:1,1:41,133:174,2:0.0113:2,2:11:1:26.5:1:0.42136:3.22:60:4:0.0115:0:1 +9 22440462 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50464;SOR=Inf;LSEQ=TTTCCTACAGGAAAAGCTTC;RSEQ=CAAATCAGACAATGCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:42,24:66,0:0:2,0:30:1:30.4:1:1:0:56.1:21:1:0:0.2 0/1:85:2:1,1:52,31:83,2:0.0235:2,2:28:1:29:1:1:1.66673:53.5:4:0.0241:0:1 +9 22440494 . C T 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0.78009;LSEQ=ATGCCTTTCAAACTCTTATA;RSEQ=CAACCTCTGGATTTGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:36,38:74,2:0.0263:2,2:11:0:32:1:1:1.05:42.5:4:0.027:0:4.5 0/1:97:2:1,1:50,45:95,2:0.0206:2,2:11.5:1:29:1:1:1.1099:42:4:0.0206:0:4.5 +9 22440533 . T C 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=AACATGGCTTCTCCCCTTTC;RSEQ=AGGTCCTGTGGCAGCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:11,40:51,2:0.0377:2,2:19.5:1:32.5:1:0.40493:3.52:42.5:4:0.0385:0:4.5 0/1:53:2:1,1:20,31:51,2:0.0377:2,2:22:0:33:0:1:1.54:42:4:0.0385:0:4.5 +9 22440535 . G A 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.02063;LSEQ=CATGGCTTCTCCCCTTTCTA;RSEQ=GTCCTGTGGCAGCCATCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:11,38:49,2:0.0392:2,2:17.5:1:32:1:0.41882:3.35:42.5:4:0.0392:0:4.5 0/1:50:2:1,1:18,30:48,2:0.04:2,2:20:0:32:0:1:1.65:42:4:0.0408:0:4.5 +9 22440547 . G T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0471;LSEQ=CCTTTCTAGGTCCTGTGGCA;RSEQ=CCATCTTGCTGTTGCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:8,36:44,2:0.0435:2,2:5.5:1:29:0:0.35652:4.30:42.5:4:0.0435:0:4.5 0/1:44:2:1,1:13,29:42,2:0.0455:2,2:8:0:31:1:0.54017:2.19:42:4:0.0455:0:4.5 +9 23917489 . C A 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ACTCTTCCCCTAAGAAGGTG;RSEQ=AGAGTCCTCCTGTCTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:28.5:1:33:0:1:0:39.5:4:1:0:1.5 0/1:3:1:0,1:0,2:2,1:0.3333:0,0:38:0:27:0:1:0:36:2:0.3333:0:1 +9 24646774 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCTTCCAATCCATGGGTT;RSEQ=CACAGTCCCTTGGTAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:8,12:20,0:0:2,0:27.4:1:32.6:1:1:0:60:40:1:0:0.1 0/1:48:2:1,1:24,22:46,2:0.0417:2,2:42.5:1:27.5:1:1:1.08892:60:4:0.0417:0:1 +9 25247018 . C T 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04762;SOR=0;LSEQ=TAGGGGAAGAGTGTTGTTTT;RSEQ=ACACTAACCAGTCAGGGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:8:1:31.8:1:1:0:24.4:10:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:38.5:1:25:1:1:0:38:1:1:0:0.5 +9 25247125 . G A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57723;SOR=0.66698;LSEQ=TATACCAACCTCTGGAGTTG;RSEQ=GCAACATGGCTTTTCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:6,6:4,5:9,12:0.5714:2,2:26.4:1:29.9:1:1:1.24:26.9:11:0.55:0:1.1 0/1:32:15:7,8:10,7:17,15:0.4688:2,2:23:1:28.8:1:0.72348:1.6076:22.1:30:0.4688:0:1 +9 26077141 . G T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TTCAGTCAATTTGTCCACCT;RSEQ=ATACACCATTCAGTTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:42.3:1:33.3:1:1:0:60:6:1:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:10.5:1:28:1:1:1:60:4:0.5:0:1 +9 26077209 . T C 62 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TTGAAGGAGAAGAGGCACTC;RSEQ=GGCCTTTTGGGTTTTCCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:14:1:27:0:1:0:60:4:1:0:0 1/0:7:4:2,2:2,1:3,4:0.5714:2,2:10.5:1:31:1:1:1.81007:47:8:0.5714:0:1.5 +9 26077466 . G C 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0394;SOR=Inf;LSEQ=CTGATTTGCTCCCGTGCCTG;RSEQ=AAATGTTACTCAAGGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:17,25:42,0:0:2,0:27.8:1:31.8:1:1:0:55.9:84:1:0:0.1 0/1:59:7:4,3:24,27:51,7:0.1186:2,2:43.7:1:31.9:1:0.70141:1.49:60:14:0.1207:0:1.4 +9 26077627 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.1567;SOR=0;LSEQ=CTTACCCAGTTGGGTGGCAC;RSEQ=GGGAGCAGGACGCATTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:3,6:9,2:0.1818:2,2:43.5:1:31.5:1:1:1.87:57:4:0.1818:0:1 0/0:16:0:0,0:6,10:16,0:0:2,0:30.6:1:30.1:1:1:0:60:32:1:0:0.3 +9 26078320 . A G 97 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27273;SOR=0;LSEQ=GGAAAAAGCACAGTTTCCCC;RSEQ=GCTGGGTAGCGTGCTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:31.1:1:30.9:1:1:0:58.6:14:1:0:1.4 1/0:16:12:5,7:2,2:4,12:0.75:2,2:22.8:1:27.1:1:1:1.3705:50.7:11:0.7333:0:1.7 +9 26078375 . C T 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=CTCGGGGAATAGGGTTCTCC;RSEQ=TCCCTTTGTGTCTCGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:31:1:30:1:1:0:60:10:1:0:1.6 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:27.2:1:27.7:1:1:0:60:5:0.8333:0:2.2 +9 27687049 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.18367;SOR=0;LSEQ=AAGATCTGTAACTCAGGATG;RSEQ=TATTCCAGAACTTGAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:60,9:69,2:0.0282:2,2:21.5:1:33:0:0.26358:6.37705:60:4:0.0286:0:2 0/0:94:0:0,0:73,21:94,0:0:2,0:23.2:1:29.5:1:1:0:60:93:1:0:0 +9 27687125 . TA T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25658;SOR=Inf;LSEQ=CTTACATTATTTCAGATTTT;RSEQ=AAATGAGAAGAGGGAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:133,87:220,0:0:2,0:25.4:1:29.2:1:1:0:60:109:1:0:0.6 0/1:271:3:2,1:160,108:268,3:0.0111:2,2:16:1:28:1:1:1.35:55.7:6:0.0112:0.0074:2 +9 27687133 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09868;SOR=0;LSEQ=ATTTCAGATTTTTAAAATGA;RSEQ=AAGAGGGAAAATAGAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:2,1:149,99:248,3:0.012:2,2:18.7:1:30.7:1:1:1.33:60:6:0.0123:0:1.3 0/0:291:0:0,0:164,127:291,0:0:2,0:24.9:1:30.7:1:1:0:59.8:96:1:0:0.8 +9 27687159 . A G 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00152;SOR=1.68112;LSEQ=GGAAAATAGAGGATGAAACT;RSEQ=TTGGGACTGATGCTTTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:322:194:101,93:72,55:127,194:0.6025:2,2:25.1:1:32.3:1:0.42541:1.20469:60:96:0.6019:0:1.1 1/0:355:255:139,116:49,50:99,255:0.7183:2,2:25.5:1:31.2:1:0.40856:1.22:59.9:62.75:0.7213:0:1.2 +9 27687197 . A C 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00114;SOR=Inf;LSEQ=GGATTTTCCCATGCTTTCGT;RSEQ=TTTATGAAGCCAAGTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:137,164:301,0:0:2,0:26.6:1:29.7:1:1:0:59.9:74.25:1:0:0.6 0/1:345:11:5,6:148,186:334,11:0.0319:2,2:24.8:1:31.8:1:1:1.05:60:22:0.0321:0:2 +9 28385381 . A G 31 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGTTGAAAAGCAAATTCAC;RSEQ=TACAGGTTGATTTTATATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:34.5:1:31.5:1:1:0:60:4:0.4:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:25:0:1:0:60:2:1:0:2 +9 28385515 . C G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.05743;LSEQ=ATACTGTTATGCTTCATAAT;RSEQ=CTATTTTCTTCTTTCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:44:41,3:32,0:32,44:0.5789:1,2:23:1:32.4:1:0.25895:0:60:88:0.5789:0:1.2 1/0:54:32:29,3:21,1:22,32:0.5926:1,2:17.8:1:32.4:1:0.63771:2.14409:60:64:0.5926:0:1.2 +9 28385583 . G T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08915;SOR=0;LSEQ=AGAAGGTATATGCAGCTTAG;RSEQ=GAAAATTATGAAGCAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:141,75:216,3:0.0137:2,2:23.7:1:24.7:1:0.283:3.73614:60:2:0.0093:0:1.3 0/0:270:0:0,0:160,110:270,0:0:2,0:25.8:1:30.2:1:1:0:60:269:1:0:0.7 +9 28385612 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42646;SOR=1.14894;LSEQ=TGAAGCAGAAGGAAATGGAG;RSEQ=GAACAAAAGATAAATATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:124:65,59:92,67:159,124:0.4366:2,2:26.4:1:29.9:1:0.39943:1.2454:60:61:0.4342:0:1.5 0/1:363:171:96,75:99,92:191,171:0.4711:2,2:26.6:1:28.4:1:0.45999:1.19:59.9:84.5:0.4708:0:1.5 +9 28385636 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAAAGATAAATATTCAAAA;RSEQ=ATAAACTTGCCCTGGAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:146,161:307,0:0:2,0:25.8:1:32.3:1:1:0:60:306:1:0:0.7 0/1:405:26:13,13:191,188:379,26:0.0642:2,2:23.3:1:28.2:1:1:1.01592:60:52:0.0645:0:1.4 +9 28385672 . A C 226 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01578;SOR=1.48928;LSEQ=AAGTCTCAAATGTACTAAAT;RSEQ=CTCTATGAATTGTGTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:116:52,64:63,95:158,116:0.4234:2,2:23.9:1:31.6:1:0.45783:1.22:60:115:0.4212:0:1.8 1/0:356:186:83,103:75,95:170,186:0.5225:2,2:25.9:1:30.1:1:1:1.02:60:36.2:0.5216:0:1.7 +9 28385738 . C G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00532;SOR=0;LSEQ=GGAAAAATATATGTGCATGT;RSEQ=CTTCATTAGCATACCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:115:115:36,79:0,0:0,115:1:0,2:23:1:32.5:1:1:0:60:230:1:0:1.3 1/1:146:137:35,102:4,4:8,137:0.9384:2,2:24.3:1:31.2:1:0.21124:2.8889:60:67.5:0.9375:0:1.4 +9 28966193 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21752;SOR=0;LSEQ=TCATCCTGAGAAATTAAGAG;RSEQ=CTGAAAAAACTGGCTAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:92,21:113,2:0.0174:2,2:37.5:1:29.5:1:0.34737:4.30343:60:4:0.0179:0:1 0/0:131:0:0,0:100,31:131,0:0:2,0:23.4:1:30.3:1:1:0:60:42.667:1:0:1.3 +9 28966206 . G A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=5.14611;LSEQ=TTAAGAGGCTGAAAAAACTG;RSEQ=CTAATGTCTGAAAAGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:56:39,17:76,17:93,56:0.3758:2,2:26.1:1:30.5:1:0.10795:1.93963:60:112:0.3862:0:2 1/0:177:134:98,36:29,14:43,134:0.7571:2,2:22.5:1:28.6:1:0.55951:1.31:60:133:0.7557:0:1.9 +9 28966263 . G A 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0463;LSEQ=AAGAGAGGTTGAGAAGCAGG;RSEQ=TAAGAATCGAGGCCTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:346:343:192,151:1,2:3,343:0.9913:2,2:26.2:1:30.5:1:0.58579:2.54:60:170.5:0.9942:0:1.4 1/1:446:375:206,169:38,33:71,375:0.8408:2,2:27.2:1:29.1:1:0.8967:1.06:60:124:0.8416:0:1.9 +9 28966298 . T G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=3.96836;LSEQ=TCTTTACCTTTGAAGAACTA;RSEQ=GAACAAACGGTTAGAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:89:46,43:120,132:252,89:0.261:2,2:24.4:1:31.9:1:0.53881:1.18:59.3:88:0.2627:0:1.9 1/0:476:278:133,145:93,105:198,278:0.584:2,2:25.2:1:30.5:1:0.85292:1.04:59.9:91.667:0.5839:0:1.9 +9 28966306 . C T 179 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGAAGAACTATGAACAAA;RSEQ=GGTTAGAGAATCACACAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:320:0:0,0:152,168:320,0:0:2,0:25.1:1:30.8:1:1:0:59.8:63:1:0:1.1 0/1:467:68:32,36:182,216:398,68:0.1456:2,2:27.4:1:29.5:1:0.89549:1.05:59.7:33:0.1438:0:1.1 +9 28966324 . GTAA G 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=3.44325;LSEQ=AACGGTTAGAGAATCACACA;RSEQ=TAATTAGTAGCACTATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:68:29,39:80,116:196,68:0.2556:2,2:27.4:1:32.3:1:0.88643:1.08:60:136:0.2605:0.0263:1.3 1/0:378:205:77,128:68,104:172,205:0.5423:2,2:26:1:30.6:1:0.75004:1.08667:59.9:204:0.544:0.0688:1.4 +9 28966416 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18765;SOR=Inf;LSEQ=TTTATCTATTATAAACTGTA;RSEQ=GTCAACTTTGTCAGGTAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:2,68:70,0:0:1,0:21.1:1:29.9:1:1:0:60:140:1:0:0.3 0/1:54:2:1,1:4,48:52,2:0.037:2,2:27.5:1:27:1:0.1782:10.84:60:4:0.04:0:1.5 +9 28966455 . A G 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=12.98123;LSEQ=GCAGTGGATATTTTTTTTCC;RSEQ=GATAAAGCAAGGTTGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:17:0,17:0,23:23,17:0.425:1,1:28.9:1:32.8:1:1:0:58.1:34:0.425:0:1 1/1:22:20:2,18:0,2:2,20:0.9091:0,2:31.4:1:30.6:1:1:0:60:40:0.9091:0:1.2 +9 28966554 . C T 44 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=ATTATGTGAAATATGTAGTA;RSEQ=TATTACTCCTATCTTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:23.7:1:28:1:1:0:60:6:0.5:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:27:1:31:0:1:0:60:4:1:0:1.5 +9 28966575 . T A 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTACTCCTATCTTATGCA;RSEQ=GAACACACAAGTATATAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:30:1:31.5:1:1:0:44.5:4:0.5:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:13:0:31:0:1:0:60:2:1:0:1 +9 31112822 . T C 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.72246;LSEQ=TTTGCATTAATATTCTGCTA;RSEQ=AGATATTATACTTATGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:152:151:94,57:0,0:0,151:0.9934:0,2:25.3:1:32.1:1:1:0:60:150:1:0:1.8 1/1:220:218:140,78:1,1:2,218:0.9909:2,2:24:1:31.3:1:1:1.79:59.9:217:0.9909:0:1.4 +9 31112836 . A T 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.66475;LSEQ=CTGCTATAGATATTATACTT;RSEQ=TGTCCAAGGCAAAAATCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:102,70:172,2:0.0115:2,2:39:1:31:1:1:1.45389:60:4:0.0118:0:3 0/0:261:2:0,2:151,108:259,2:0.0077:2,0:1:0:25.5:1:0.17669:0:60:4:0.0077:0:1.5 +9 31112857 . A G 236 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0;LSEQ=TGTCCAAGGCAAAAATCATC;RSEQ=TAAAGATGCAATAAATGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:214:214:113,101:0,0:0,214:1:0,2:24.9:1:30.5:1:1:0:60:41.8:1:0:1.6 0/1:301:120:66,54:102,77:179,120:0.3987:2,2:27.1:1:30.3:1:0.81212:1.08353:60:240:0.4013:0:1.6 +9 31114520 . T G 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGCAATTTCACACCTTG;RSEQ=CATTTACCCAAATGAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46:0:32:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 32890348 . G A 68 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.00762;SOR=29.19004;LSEQ=AGTGTTGAAAGTGACGGTAG;RSEQ=AAAATTATAATGTCTTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:1:1,0:9,0:9,1:0.1:0,0:9:0:32:0:1:0:60:2:0.1:0:1 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:31:1:29.6:1:1:0:60:10:0.8333:0:1 +9 32890471 . A TTTT 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0;SOR=79.23707;LSEQ=GAGCATGGTGCTTGACAGTC;RSEQ=TACATTGGTACTCTCTAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:16:10,6:82,22:104,16:0.1333:2,2:20.3:1:30.6:1:0.2015:2.2191:60:32:0.1345:0.0417:1 1/1:82:76:55,21:10,0:10,76:0.9268:0,2:20.2:1:29.6:1:0.10996:0:59.9:152:0.9268:0.2683:1 +9 32890555 . G T 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=GGAATAATGTGCTATTCTTT;RSEQ=TACACTAAGATGGTGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:297:0:0,0:155,142:297,0:0:2,0:25.9:1:32.3:1:1:0:60:73.25:1:0:0.2 0/1:284:10:3,7:144,129:273,10:0.0352:2,2:25.3:1:28.1:1:0.20371:2.59623:60:9:0.0318:0:1 +9 32890588 . G A 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=17.40406;LSEQ=GTGCTACTAATCTTATATGC;RSEQ=TTTAGCCATATATAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:28:15,13:106,119:225,28:0.1107:2,2:30.8:1:30.8:1:0.55246:1.29:60:27:0.108:0:1.1 1/0:264:181:84,97:41,42:83,181:0.6856:2,2:25.2:1:29.9:1:0.69144:1.12675:59.9:362:0.6856:0:1.1 +9 32890699 . T G 94 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00088;SOR=Inf;LSEQ=CTAAATGGTAGCAAATTACT;RSEQ=CCTTGATGTGGTACAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:9,68:77,0:0:2,0:28.3:1:29.6:1:1:0:60:14.4:1:0:0.1 0/1:69:9:3,6:13,47:60,9:0.1304:2,2:21.2:1:29.8:1:0.42338:1.79:60:8:0.1212:0:1.2 +9 32890733 . C T 103 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=19.94672;LSEQ=CAGGAATATTCACTGCATAG;RSEQ=ACAGTTGAGGAAAAAGATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:0,2:0,39:39,2:0.0488:1,0:5:1:28.5:1:1:0:60:4:0.05:0:1 1/0:25:13:0,13:0,12:12,13:0.52:0,1:25:1:28:1:1:0:60:26:0.52:0:1.1 +9 32890815 . T C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.46429;SOR=Inf;LSEQ=TGACAGCCATCAGGAATCCA;RSEQ=TGATACAGTCTTTCCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:16.7:1:29:1:1:0:60:6:1:0:0 0/1:5:2:0,2:0,3:3,2:0.4:0,0:11.5:1:31.5:1:1:0:60:4:0.4:0:1.5 +9 33675364 . TA T 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.24899;SOR=0;LSEQ=ACACAATGTCCTATTGCCAT;RSEQ=AAAAAAAAGGTCCCTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:3:3,0:126,7:133,3:0.0221:2,0:36.3:1:32:1:1:0:24:6:0.0227:0:0 0/0:123:0:0,0:112,11:123,0:0:2,0:26.5:1:28:1:1:0:28.3:60.5:1:0:0.1 +9 33675427 . T TA 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.04895;SOR=Inf;LSEQ=TGGTGTTTTATCCCTCTTGA;RSEQ=AAAAAAAAATTCAGACTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:78,7:85,0:0:2,0:18.5:1:29:1:1:0:27.7:16:1:0:0.2 0/1:77:4:4,0:62,11:73,4:0.0519:2,0:27:1:24.8:1:1:0:24.3:8:0.0519:0:0.5 +9 33675629 . A C 204 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=104.72466;LSEQ=GAAGTACAGCTTCACCTTAA;RSEQ=ATTTGGAGAAAAGTATCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:1:1,0:305,409:714,1:0.0014:2,0:36:0:14:0:0.42797:0:43:0:0:0:2 0/1:719:92:43,49:261,366:627,92:0.128:2,2:31.9:1:31.4:1:0.36759:1.23:39.5:184:0.1303:0:1.1 +9 33675799 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49867;SOR=Inf;LSEQ=CTACTTTTTCTGAGGTTTCC;RSEQ=CTGGTCCTGGTATGAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:156:0:0,0:83,73:156,0:0:2,0:17.2:1:30.6:1:1:0:42.4:38:1:0:0 0/1:163:2:1,1:86,74:160,2:0.0123:2,2:25:0:32:0:1:1.16108:35:4:0.0125:0:1 +9 33676027 . C A 181 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACTGAGGATTGCAAGTTCCG;RSEQ=CACTGAACATTGGAATAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:0:0,0:182,205:387,0:0:2,0:26.1:1:31.5:1:1:0:48:47.375:1:0:0.1 0/1:355:86:42,44:125,144:269,86:0.2423:2,2:25.5:1:28.3:1:0.71148:1.10:46.2:85:0.2485:0:1.1 +9 33676094 . C G 121 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=TGCCACTGGTCTATAATCCA;RSEQ=ATGATTCTTTACCAGGTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:426:0:0,0:214,212:426,0:0:2,0:29:1:32.2:1:1:0:40.7:59.857:1:0:0.1 0/1:376:15:9,6:183,178:361,15:0.0399:2,2:11.1:1:31.1:1:0.60103:1.46:41.7:30:0.0404:0:1.1 +9 33676157 . C A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02564;SOR=Inf;LSEQ=CTGACTGGGAATAGTTACTC;RSEQ=CTTTTTGTCTCTGGTCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:375:0:0,0:184,191:375,0:0:2,0:26.9:1:31.1:1:1:0:48.4:40.667:1:0:0.1 0/1:349:5:3,2:170,174:344,5:0.0143:2,2:18.4:1:29.4:1:0.68301:1.53:50.4:10:0.0143:0:1 +9 33676618 . C T 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=0;LSEQ=CTTGATATCTCCTTTTGTTT;RSEQ=TGCTAACGATCTCTTTGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:10:5,5:75,103:178,10:0.0529:2,2:24.5:1:32:1:0.74598:1.37:41.4:20:0.0538:0:1 0/0:238:0:0,0:102,135:237,0:0:2,0:21:1:31:1:1:0:42.5:117.5:0.9958:0:0.1 +9 33676635 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.25645;LSEQ=TTTCTGCTAACGATCTCTTT;RSEQ=ATGATGGCTGTCCTGTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:1:1,0:53,52:105,1:0.0094:2,0:1:0:23:0:1:0:42:2:0.0095:0:1 0/1:169:2:1,1:71,96:167,2:0.0118:2,2:13:1:27.5:1:1:1.35:36.5:4:0.012:0:1 +9 33676691 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51881;SOR=Inf;LSEQ=GAAAAAGGAGGAGAGAGATG;RSEQ=CAGAAGCTGCTGGTGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:8,42:50,0:0:2,0:28.2:1:31:1:1:0:24.5:49:1:0:0.1 0/1:77:2:1,1:14,61:75,2:0.026:2,2:26.5:1:27.5:1:0.35373:4.24:23:4:0.0267:0:1 +9 33677007 . TGCC T 34 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=9.000;MSILEN=3;SSF=0.14286;SOR=0;LSEQ=CCGGCCCGGGTCCCTCCATG;RSEQ=GCCGCCGCCGCCGCCGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:25:1:34:0:0.33333:0:30.5:4:0.6667:0:0 0/0:4:0:0,0:2,2:4,0:0:2,0:14.5:1:30.5:1:1:0:46.5:8:1:0:1 +9 35207997 . G A 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTTAATTTTTGTATGTCAT;RSEQ=TGAGGTTTTTGGTTTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:85,2:87,0:0:1,0:26:1:32.6:1:1:0:60:174:1:0:0 0/1:94:23:22,1:69,2:71,23:0.2447:1,1:22.7:1:26.3:1:1:1.55992:60:10.5:0.2308:0:1.1 +9 35208096 . G A 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGATAACTGTCATTTTTAA;RSEQ=TCTGTGGATAAAAGAGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:436:0:0,0:250,186:436,0:0:2,0:26.9:1:32.7:1:1:0:60:217:1:0:0.6 0/1:505:23:13,10:267,214:481,23:0.0455:2,2:36:1:29.8:1:1:1.04:60:46:0.0461:0:1.7 +9 35208145 . T C 282 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24876;LSEQ=CCAACTTGTAAACTCCCCTT;RSEQ=CTGGAACGATACCTCTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:568:506:247,259:32,30:62,506:0.8908:2,2:25.4:1:31.5:1:0.68882:1.11827:59.9:41.167:0.8901:0:1.1 1/0:651:436:205,231:99,115:214,436:0.6697:2,2:25.5:1:30.4:1:0.86751:1.03:59.9:108:0.675:0:1.2 +9 36839398 . G T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCCCAGCTGCCTGCTAA;RSEQ=CTCCACGAGGACGGGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:38.5:1:26.5:1:1:0:60:4:1:0:2.5 +9 36840623 . G A 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00689;LSEQ=CGGGCGGCAGCGCTATAATA;RSEQ=TAGGGGGAGCCTGGAAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:611:610:225,385:0,0:0,610:0.9984:0,2:25.6:1:30.9:1:1:0:59.9:75.25:1:0:1.1 1/1:618:499:189,310:50,68:118,499:0.8074:2,2:25:1:29.5:1:0.4009:1.20566:60:98.8:0.8059:0:1.2 +9 36840665 . G T 35 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11149;SOR=Inf;LSEQ=GGGAGAGAGCACCGAGGTCA;RSEQ=ATCCGGGGTCCCCTTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:319:0:0,0:63,256:319,0:0:2,0:24.3:1:32.3:1:1:0:60:78.75:1:0:0.9 0/1:297:3:1,2:66,227:293,3:0.0101:2,2:7.3:1:22.7:1:0.53833:1.72:60:2:0.0069:0:3 +9 36840727 . C G 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05817;SOR=Inf;LSEQ=TTTCCTCCCCTCACTCAGTC;RSEQ=GGGCCACCATCCTCTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:1,97:98,0:0:1,0:22.4:1:30.2:1:1:0:60:97:1:0:0.1 0/1:63:3:0,3:3,57:60,3:0.0476:2,0:15.7:1:28.7:1:1:0:60:6:0.0492:0:1 +9 36841160 . A G 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTGAATTCATTTCCCTC;RSEQ=GGGAAGGCCCCTCCTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:27.5:1:29:1:1:0:60:4:0.6667:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:29:0:33:0:1:0:60:2:1:0:0 +9 36846990 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18423;SOR=Inf;LSEQ=ATCCAGTTCAGAAAAGGCCC;RSEQ=GGGTCCCAGCCAGCCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:46,205:251,0:0:2,0:22.3:1:30.4:1:1:0:59.9:82.667:0.996:0:0.1 0/1:190:2:1,1:38,149:187,2:0.0105:2,2:24.5:1:27.5:1:0.37099:3.88:60:4:0.0108:0:1 +9 36847139 . G A 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTCCCCTCCTTATCAGTG;RSEQ=GAGTGAATGGCAGACTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:0,14:0,0:0,14:1:0,1:22.4:1:32.3:1:1:0:60:13:1:0:1 1/1:3:3:0,3:0,0:0,3:1:0,0:25:1:26:1:1:0:60:2:1:0:2 +9 36880489 . A T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTGCATGGGAGAGTGGGCA;RSEQ=GGCTTCAGCAGGGCTAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:31:1:1:0:60:4:1:0:1.5 +9 36881866 . T C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00261;SOR=Inf;LSEQ=GCAGGCCCAGCTGCAGAGAG;RSEQ=GCAGACCTCTGCCTGATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:56,1:57,0:0:1,0:20.9:1:30.1:1:1:0:59.6:114:1:0:0.1 0/1:27:5:5,0:22,0:22,5:0.1852:1,0:17.2:1:31.6:1:1:0:60:10:0.1852:0:1.2 +9 36881930 . T TG 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.08261;SOR=0;LSEQ=TAGAGGTCACCCAGGCTGTT;RSEQ=GGGGGGGGATGTCCCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:5:4,1:158,20:178,5:0.0272:2,2:20:1:30.2:1:0.46026:1.96573:60:10:0.0279:0:0 0/0:126:0:0,0:103,23:126,0:0:2,0:23.6:1:29.7:1:1:0:59.8:62:1:0:0.1 +9 36881956 . C T 34 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.25703;SOR=0;LSEQ=GGGATGTCCCCCCACCGAAA;RSEQ=CCCGTCCGCTGCCTGCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:3:1,2:239,50:289,3:0.0103:2,2:7:1:21.7:1:0.08287:9.44801:60:2:0.007:0:3 0/0:236:0:0,0:179,57:236,0:0:2,0:22.9:1:31.1:1:1:0:59.9:235:1:0:0.1 +9 36881985 . G T 52 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02256;SOR=Inf;LSEQ=CTGCCTGCTGTGGAGACGCC;RSEQ=ACAGTGCAAACTCACCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:0:0,0:354,143:497,0:0:2,0:22.7:1:30:1:1:0:60:37.231:1:0:0.2 0/1:440:5:2,3:295,140:435,5:0.0114:2,2:7.8:1:22.8:1:0.33512:3.15159:60:4:0.0092:0:1.2 +9 36882141 . T C 127 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=20.37941;LSEQ=AAATCACAGGGTGAGCATCT;RSEQ=CGCGGCCAGCCGCTCATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:620:1:0,1:219,400:619,1:0.0016:2,0:43:0:30:0:1:0:60:2:0.0016:0:2 0/1:658:21:10,11:240,395:635,21:0.0319:2,2:26.2:1:29.1:1:0.36966:1.50:60:20:0.0309:0:1.4 +9 36882292 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.13569;SOR=Inf;LSEQ=CACACACACACACACACACA;RSEQ=TCATGCACACACATCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:0,42:42,0:0:1,0:24.5:1:33.2:1:1:0:58.7:20:1:0:0.5 0/1:25:2:1,1:2,21:23,2:0.08:2,2:37.5:1:31:1:0.23:8.78:60:4:0.08:0:1 +9 36922960 . T A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGATTCTGCCTGCCAACA;RSEQ=CAATCTGCAAGGAATCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:9.5:1:29:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 36923303 . ATC A 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.07586;SOR=0.34858;LSEQ=TCTTCCCACCACACACTCCT;RSEQ=TCTCTCTCTCTCCCTCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:12:8,4:253,77:330,12:0.0351:2,2:17.5:1:31.4:1:0.48848:1.6402:60:24:0.0352:0.0088:0.3 0/1:320:4:3,1:233,82:315,4:0.0125:2,2:24.5:1:30.5:1:1:1.06:60:8:0.0126:0.0031:0 +9 36923529 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23529;SOR=Inf;LSEQ=CACCAAGACTCCACAGTACC;RSEQ=TAGTCAAATGCCAACTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:23,158:181,0:0:2,0:22.7:1:30:1:1:0:60:35.2:1:0:0.1 0/1:171:2:1,1:22,147:169,2:0.0117:2,2:30:1:29.5:1:0.2516:6.56:60:4:0.0118:0:1 +9 36923608 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11507;SOR=Inf;LSEQ=TGTGCCAAGGCCCACAAGGG;RSEQ=CTCATGAACACTTCCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:0,38:38,0:0:1,0:25.8:1:32.7:1:1:0:60:76:1:0:0.1 0/1:38:4:1,3:1,33:34,4:0.1053:1,2:25.5:1:28.8:1:0.20199:9.67:60:8:0.1081:0:1 +9 36924719 . A AAAAG 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGAGCAAGACTCTGTCAAAA;RSEQ=AAAGAAAGAGGTGGAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:32:0:1:0:46:2:1:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:26.5:1:29:1:1:0:55:4:1:0.5:0 +9 36930460 . T G 92 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGAACTGCTGAGCTCAA;RSEQ=TGATCCACCCACCCCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1:0,0:28.7:1:33:1:1:0:41.6:14:1:0:1.9 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 36930536 . T G 68 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGGCCCTTAGTTCATTT;RSEQ=TATCTGCATCATTGATAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:4,0:1,0:1,4:0.8:0,0:22.5:1:34:0:1:0:50:8:0.8:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 36930973 . G C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05193;SOR=0.63028;LSEQ=TGGAGGAGAAAAGAAACACA;RSEQ=ACACGTGAGAAGGAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:50:17,33:148,334:482,50:0.0938:2,2:25.4:1:32.5:1:0.63237:1.16:60:49:0.094:0:1.1 0/1:539:33:12,21:177,329:506,33:0.0612:2,2:21.1:1:30.9:1:0.85288:1.06:60:66:0.0629:0:1.2 +9 36931239 . A G 64 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TGGGTGAGAGGTGTCTCCAG;RSEQ=GCCTGGCTCCAGCGACTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:0,4:0,0:0,4:0.8:0,0:14.5:1:32:1:1:0:60:8:0.8:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:32:0:1:0:60:2:1:0:1 +9 36966379 . A G 168 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09354;SOR=2.17299;LSEQ=AGACAAGCCCTCCCGACCTT;RSEQ=TAGGATGTAGCGACTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:64:37:36,1:26,1:27,37:0.5781:1,1:20.9:1:32.4:1:1:1.38:60:36:0.5714:0:1 1/0:40:30:26,4:10,0:10,30:0.75:0,2:26.2:1:32.2:1:0.55575:0:60:60:0.75:0:1.1 +9 36966501 . G A 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0022;SOR=Inf;LSEQ=TTCAGGAACCTGGCTGGGCC;RSEQ=GTGTGGCGGTGGCAGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:511:0:0,0:339,172:511,0:0:2,0:23.5:1:29.9:1:1:0:59.9:55.778:1:0:0.2 0/1:578:10:6,4:369,199:568,10:0.0173:2,2:28.8:1:28.9:1:0.74666:1.23569:60:20:0.0176:0:1 +9 37001471 . T A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACACAGCACCGCAGCCTAC;RSEQ=GAGTTAAAGACGTCTGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:48:0:30.5:1:1:1.7321:60:4:0.4:0:1 +9 37002439 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47826;SOR=Inf;LSEQ=GGGGAGGCCAGCAAGAATGC;RSEQ=ACAGTCTCACCCTGCTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:12,0:12,0:0:0,0:28.8:1:30.6:1:1:0:60:11:1:0:0.3 0/1:12:2:2,0:9,1:10,2:0.1667:2,0:34.5:1:31.5:1:1:0:60:4:0.1818:0:1 +9 37002556 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22064;SOR=Inf;LSEQ=TGCAGGTAAGGGGGGTGTTC;RSEQ=CGGGCACCTCTGCTGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:122,5:127,0:0:1,0:26.3:1:30:1:1:0:60:41.333:1:0:0.1 0/1:113:2:2,0:106,5:111,2:0.0177:1,0:24.5:1:28.5:1:1:0:60:4:0.018:0:1 +9 37002577 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49947;SOR=0;LSEQ=CGGGCACCTCTGCTGCCACC;RSEQ=GCGACCGAGCGCCGGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:157,33:190,2:0.0104:2,2:20:1:32.5:1:0.32357:4.70203:60:4:0.0105:0:1 0/0:177:0:0,0:146,31:177,0:0:2,0:23.9:1:29.7:1:1:0:60:58:1:0:0.1 +9 37002596 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10428;SOR=Inf;LSEQ=CCGCGACCGAGCGCCGGAAA;RSEQ=AGACCCCGTGGAGCGCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:218,80:298,0:0:2,0:22.1:1:31.8:1:1:0:60:73.5:1:0:0.1 0/1:266:3:2,1:195,68:263,3:0.0113:2,2:19:1:28.3:1:1:1.43173:60:6:0.0114:0:1 +9 37006208 . A AT 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTATAGACCCCCATTAGTGG;RSEQ=TTTTTTTTTGGCTTAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:38:1:30.5:1:1:0:60:4:1:0:0.5 1/0:4:2:2,0:2,0:2,2:0.5:0,0:23:1:32:0:1:0:60:4:0.5:0:0 +9 37006359 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16452;SOR=Inf;LSEQ=CAAAGAAGGCGCATTAGTAC;RSEQ=TGTGCTGAAGTGTTTTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:73,1:74,0:0:1,0:22.6:1:29.9:1:1:0:59.9:36:1:0:0.3 0/1:51:2:2,0:47,2:49,2:0.0392:1,0:10.5:1:31.5:1:1:0:60:4:0.0392:0:1 +9 37006455 . A T 56 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.06546;SOR=Inf;LSEQ=TAGATTTTTAAATTTTTTTT;RSEQ=AAAGTTCCTCTTACCTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:0:0,0:253,142:395,0:0:2,0:22.1:1:29.1:1:1:0:60:64.833:0.9949:0:0.1 0/1:463:5:1,4:287,171:458,5:0.0108:2,2:6.8:1:24.2:1:0.07011:6.68699:60:10:0.0109:0:1.6 +9 37006544 . G A 69 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12535;SOR=5.64556;LSEQ=TCCGGATGATCCTGTGGGCA;RSEQ=TTGAAAAACAAAATTGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:538:1:0,1:212,325:537,1:0.0019:2,0:42:0:16:0:1:0:60:0:0:0:1 0/1:576:6:5,1:236,333:569,6:0.0104:2,2:6.7:1:26.7:1:0.0873:7.03:60:12:0.0105:0:1.2 +9 37015450 . G A 90 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAATAATTTTGATATTAGTT;RSEQ=TATGTTGAAATAACAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:21.5:1:30.1:1:1:0:60:16:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 37020622 . A C 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54086;SOR=0.90976;LSEQ=ATCAAGGGAAGCCTCGAGCT;RSEQ=CTGCCTTTACCTGCCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:142:109,33:128,53:181,142:0.4396:2,2:25.8:1:31.9:1:0.25431:1.37:60:46.333:0.4344:0:1.1 0/1:377:157:112,45:148,71:219,157:0.4164:2,2:25.7:1:30.1:1:0.49717:1.19:60:38.25:0.4135:0:1.1 +9 37020950 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14413;SOR=Inf;LSEQ=GTCCAATCGTGCAAACTACA;RSEQ=GAAGTCCCCAGATTGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:0,58:58,0:0:1,0:18.9:1:29:1:1:0:60:13.5:1:0:0.2 0/1:36:2:0,2:0,34:34,2:0.0556:1,0:30.5:1:27:1:1:0:60:4:0.0556:0:1 +9 37033693 . A G 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AAATACATATACTGTAATGA;RSEQ=CACACTGAGTCCCTTATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:21.6:1:34:1:1:0:60:10:1:0:1.4 1/1:1:1:1,0:0,0:0,1:1:0,0:10:0:33:0:1:0:60:2:1:0:1 +9 37034081 . G C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50002;SOR=Inf;LSEQ=GGAAAAGTTTCCACTTTTTT;RSEQ=TGCCTTTTTTTTTCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:30,118:148,0:0:2,0:17.1:1:30.9:1:1:0:59.9:9.571:1:0:0.3 0/1:169:2:1,1:63,101:164,2:0.0118:2,2:22:0:31:1:1:1.60:60:4:0.0133:0:1.5 +9 37034085 . CT C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.23459;SOR=0;LSEQ=AAGTTTCCACTTTTTTGTGC;RSEQ=TTTTTTTTCTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:23,106:129,2:0.0152:2,2:14:0:31:1:0.334:4.53:60:4:0.0159:0:0 0/0:140:0:0,0:50,90:140,0:0:2,0:16.2:1:28.5:1:1:0:58.7:19:1:0:0.5 +9 37205328 . CA C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.48908;SOR=Inf;LSEQ=TAGCTTCACGTGTATGTGGC;RSEQ=AAAGAACAACTCTTTTCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:16,0:0:2,0:27.4:1:29.6:1:1:0:60:15:1:0:0.3 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:15:1:28.5:1:1:1.12:60:4:0.1111:0:0.5 +9 37206287 . T C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCGGCTTTCTCCCTCCCT;RSEQ=CCCCCTTCCCCCTCTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:17.5:1:29:1:1:0:60:4:0.6667:0:1.5 +9 37490422 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTTTTTAAACACCTGTCAC;RSEQ=CCATGAATTCATAGGGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:28.5:1:32:0:1:0:55.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 37490577 . C G 47 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54545;SOR=0.28445;LSEQ=TTCTAATCATCTTTCTTCAC;RSEQ=CGTTTCATGAAGCTTTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:1,3:0.75:0,2:7.7:1:29.3:1:1:0:36.7:6:0.75:0:2 0/1:7:3:2,1:3,1:4,3:0.4286:2,2:15:1:29.7:1:1:1.41418:60:6:0.4286:0:1 +9 37490620 . T A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.175;SOR=0;LSEQ=TCTTAGAGTGCTTAATGTGC;RSEQ=CAATACGCACACTAATTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:4,1:5,2:0.2857:2,2:41:0:31.5:1:1:3.1622:25:4:0.2857:0:2.5 0/0:9:0:0,0:6,3:9,0:0:2,0:30.3:1:29.4:1:1:0:60:18:1:0:0.3 +9 37490859 . G A 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0086;SOR=0.06436;LSEQ=GTCTAGAGAACATATATTGG;RSEQ=TGCCTCTCCTCTTTCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:24.6:1:30.4:1:1:0:54:10:0.7143:0:2.8 0/1:17:2:0,2:5,9:14,2:0.1176:2,0:28.5:1:32:0:1:0:41.5:4:0.125:0:2.5 +9 37490862 . C A 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01355;SOR=0.074;LSEQ=TAGAGAACATATATTGGGTG;RSEQ=CTCTCCTCTTTCCCTTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:26.4:1:29.4:1:1:0:54:10:0.7143:0:2.8 0/1:15:2:0,2:4,9:13,2:0.1333:2,0:28.5:1:31:0:1:0:41.5:4:0.1429:0:2.5 +9 37490930 . G T 78 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08788;SOR=0.08176;LSEQ=ATGGCAGTTCTGGCCGAAAG;RSEQ=GTTCTTTCTTAATTCTTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:2,4:0,1:1,6:0.8571:0,2:18.8:1:30.3:1:1:0:60:12:0.8571:0:2.3 0/1:4:1:0,1:1,2:3,1:0.25:2,0:4:0:29:0:1:0:60:2:0.25:0:3 +9 66456474 . CC TG 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGGCTCTGCTTTGCCCCG;RSEQ=CTGGCACTAGAGCCCCGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:33:0:1:0:24:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 66456478 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTGCTTTGCCCCGCCCT;RSEQ=GCACTAGAGCCCCGGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:32:1:1:0:24:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 66457019 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGACAGGAATTGCTCACTC;RSEQ=GAGAGCTTGGTTTTTGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:2,0:1,1:2,2:0.5:2,0:28.5:1:30:1:1:0:28:4:0.5:0:1 +9 66457063 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAGTCTGCGGATGCTCCCAG;RSEQ=TGAATAAAGCCCTTCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:17:0:35:0:1:0:23:2:1:0:7 0/1:5:2:1,1:2,1:3,2:0.4:2,2:29.5:1:29.5:1:1:1.7321:60:4:0.4:0:1 +9 66457076 . T C 30 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03571;SOR=0;LSEQ=CTCCCAGCTGAATAAAGCCC;RSEQ=TCCTTCTACAACTCGGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:30.5:1:1:0:36:4:1:0:7 0/0:6:0:0,0:4,2:6,0:0:2,0:22.5:1:30.3:1:1:0:33:12:1:0:0.5 +9 66457110 . C G 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=CGGTGTCTGAGGGGTTCTGT;RSEQ=TGCAGCTCCTCCTGCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:33:1:1:0:36:4:1:0:7 0/0:4:0:0,0:2,2:4,0:0:2,0:26:1:33.3:1:1:0:35.5:8:1:0:0.3 +9 66457112 . G A 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=GTGTCTGAGGGGTTCTGTCT;RSEQ=CAGCTCCTCCTGCTGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:29:1:1:0:36:4:1:0:7 0/0:4:0:0,0:2,2:4,0:0:2,0:26:1:33:1:1:0:35.5:8:1:0:0.3 +9 66457127 . GCA ATG 32 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.1;SOR=0;LSEQ=TGTCTGCAGCTCCTCCTGCT;RSEQ=GAAGGAGAGCAAGGGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:32:1:1:0:36:4:1:0:5 0/0:3:0:0,0:3,0:3,0:0:0,0:27.7:1:32:1:1:0:25.7:6:1:0:0.3 +9 66458014 . T C 44 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49091;SOR=Inf;LSEQ=GCTGCCTGGCGGTGCTGCAG;RSEQ=GGCGGATCTTCAGGAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:27.7:1:28.3:1:1:0:38.7:6:1:0:0.7 0/1:8:3:1,2:3,2:5,3:0.375:2,2:40:1:28.3:1:1:2.60168:22.7:6:0.4286:0:2.3 +9 66458028 . G T 41 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.52797;SOR=Inf;LSEQ=CTGCAGTGGCGGATCTTCAG;RSEQ=AGGAGGTCCTGGGCTTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:39.3:1:31.3:1:1:0:38.7:6:1:0:0.7 0/1:10:3:1,2:4,3:7,3:0.3:2,2:39:1:26:1:1:2.41422:22.7:6:0.3:0:2.3 +9 66458058 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGGCTTCGGCTGGGGCACG;RSEQ=GGGCGGTCAACGGGGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:29.3:1:32.3:1:1:0:38.7:6:1:0:0.7 0/1:10:2:1,1:3,5:8,2:0.2:2,2:17:1:27:1:1:1.58:35.5:4:0.2:0:1.5 +9 66458087 . C G 50 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AACGGGGAGCAGAGGCGGGG;RSEQ=GCAGTTGGGAAGCACGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:0,2:2,3:0.6:0,2:18.3:1:31.7:1:1:0:24.7:6:0.6:0:2 +9 66458329 . T C 50 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCATGACTCCAGGCGTCA;RSEQ=CGCCACCCCGGGGCCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:33.7:1:32:1:1:0:23:6:1:0:2.7 1/1:2:2:0,2:0,0:0,2:1:0,0:16.5:1:29:1:1:0:22:4:1:0:3 +9 66458331 . GC CT 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCATGACTCCAGGCGTCATC;RSEQ=CACCCCGGGGCCGCGGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:33:1:30.5:1:1:0:23:4:0.6667:0:2.5 1/1:2:2:0,2:0,0:0,2:1:0,0:19.5:1:28:1:1:0:22:4:1:0:2 +9 66835506 . G C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CAAATATCTTCCCATAAAAA;RSEQ=TTGACAGAAGCATTCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:18:0:34.5:1:1:0:22:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:30:1:1:0:57:4:1:0:1.5 +9 68412219 . C T 31 d5;v3;p8;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAAAGGAGAGCACCGACA;RSEQ=GATGCTGGTCTTCCACGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:31.5:1:1:0:20.5:4:1:0:7.5 +9 68412248 . G C 32 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTCCACGCATTCCTGGAA;RSEQ=TTTCTGGGGCCCCACAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:36:0:32.5:1:1:0:20.5:4:0.6667:0:7.5 +9 68412255 . G C 31 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCATTCCTGGAAGTTTCTG;RSEQ=GGCCCCACAGAGCTCGCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:43:0:31.5:1:1:0:20.5:4:0.6667:0:7.5 +9 68412270 . C T 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTCTGGGGCCCCACAGAGCT;RSEQ=GCGAAACAAACAGTCAACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:37.5:1:30:1:1:0:20.5:4:0.6667:0:7.5 +9 68412272 . C G 45 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGGGGCCCCACAGAGCTCG;RSEQ=GAAACAAACAGTCAACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:33.7:1:29:1:1:0:20.7:6:1:0:6.7 +9 68412283 . G C 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAGCTCGCGAAACAAACA;RSEQ=TCAACATGGTCACGCTTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:24.5:1:30:1:1:0:20.5:4:0.6667:0:7.5 +9 68412293 . T G 29 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACAAACAGTCAACATGG;RSEQ=CACGCTTTCGGGGGGCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:14.5:1:29:1:1:0:20.5:4:0.6667:0:7.5 +9 68412485 . A G 33 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTGGATGAAAAACAGACA;RSEQ=CTACCTGAGTCTCGGCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:33.5:1:1:0:42.5:4:1:0:5.5 +9 68412487 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGATGAAAAACAGACAAC;RSEQ=ACCTGAGTCTCGGCTCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32.5:1:1:0:42.5:4:1:0:5.5 +9 68412507 . G T 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCTGAGTCTCGGCTCATT;RSEQ=CTCTCTGGGGAATTCGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34.5:1:31:1:1:0:42.5:4:1:0:5.5 +9 68412517 . G A 46 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCGGCTCATTGCTCTCTGGG;RSEQ=AATTCGCTCATTCCTTCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:30:1:29.3:1:1:0:38:6:1:0:5.3 +9 68412534 . C T 47 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGGAATTCGCTCATTCCTT;RSEQ=GGAAACGGAATTGGTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:12:0:33:0:1:0:37:2:1:0:5 1/1:3:3:1,2:0,0:0,3:1:0,2:33.3:1:30:1:1:0:38:6:1:0:5.3 +9 68412584 . T C 29 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGAAGTAACCCAGGCTGG;RSEQ=GATCCAGAGGGCCGCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:29.5:1:1:0:36.5:4:1:0:3.5 1/0:2:1:0,1:1,0:1,1:0.5:0,0:30:0:31:0:1:0:29:2:0.5:0:5 +9 68412779 . A T 47 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATCCTTCCATCTGTTCT;RSEQ=CCCTCCCTCCCCTGGCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:11:1:30:1:1:0:25.3:6:1:0:5.3 1/1:1:1:0,1:0,0:0,1:1:0,0:31:0:30:0:1:0:21:2:1:0:4 +9 68412792 . T C 48 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25;SOR=0;LSEQ=CTGTTCTACCCTCCCTCCCC;RSEQ=GGCTTTTTCCTCCCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:24:1:30.7:1:1:0:25.3:6:1:0:5.3 0/0:1:0:0,0:0,1:1,0:0:0,0:18:0:31:0:1:0:21:2:1:0:4 +9 68412795 . C G 50 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTCTACCCTCCCTCCCCTGG;RSEQ=TTTTTCCTCCCTTTCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0,3:0.75:0,2:27:1:32:1:1:0:25.3:6:0.75:0:5.3 0/0:1:0:0,0:0,1:1,0:0:0,0:15:0:33:0:1:0:21:2:1:0:4 +9 68412801 . C T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCCTCCCCTGGCTTTTT;RSEQ=CTCCCTTTCTCCCTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:7:1:30.5:1:1:1.73:32:4:0.4:0:2.5 0/0:1:0:0,0:0,1:1,0:0:0,0:9:0:32:0:1:0:21:2:1:0:4 +9 68412809 . TCTCC T 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGCTTTTTCCTCCCTT;RSEQ=CTCCCTCCCTCTTTCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:2,1:3,3:0.5:2,2:40.3:1:33.3:1:1:3.10575:25.3:6:0.5:0:5.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68412820 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTCCCTTTCTCCCTCCCT;RSEQ=CCTCTTTCTCTCCCTTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:3,2:5,3:0.375:2,2:37.3:1:31:1:1:2.60168:25.3:6:0.375:0:5.3 0/0:2:0:0,0:1,1:2,0:0:2,0:10:0:32:0:1:0:60:4:1:0:1.5 +9 68412840 . G A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=CCCTCTTTCTCTCCCTTCCG;RSEQ=GGTCCCTCCTTCCACCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:6,2:0.25:2,2:17:0:33:1:1:1:32:4:0.25:0:2.5 0/0:6:0:0,0:3,3:6,0:0:2,0:21.2:1:30.7:1:1:0:38.8:12:1:0:3 +9 68412864 . G T 76 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.08788;SOR=12.23031;LSEQ=CCCTCCTTCCACCCATCCTT;RSEQ=CCTAGCTCCATCCTTCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,0:2,1:0.25:0,0:29:0:31:0:0.33333:0:46:2:0.3333:0:2 1/1:7:6:3,3:1,0:1,6:0.8571:0,2:34.3:1:29.5:1:1:0:38.8:12:0.8571:0:3 +9 68412896 . CT TC 58 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.44444;SOR=Inf;LSEQ=CCTTCCATCTCACTCTGTCT;RSEQ=GTTCCTGTCCTCATCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:16.5:1:27.5:1:1:0:47:4:1:0:1 1/0:7:4:2,2:2,1:3,4:0.5714:2,2:27.3:1:29.3:1:1:1.81007:28.3:8:0.5714:0:2.8 +9 68412969 . C G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGGTTTGCGCGAGGTCT;RSEQ=GGGTCTTTATTTAGTTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:29:1:29:1:1:1.73:40:4:0.4:0:2.5 +9 68412987 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGGGTCTTTATTTAGTTG;RSEQ=AAGGCGCTCTATGGTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:29:1:30.5:1:1:0:40:4:0.6667:0:2.5 +9 68413038 . G C 67 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGGGACACGGGTTGGCAA;RSEQ=TGATGGTGAGCGAAGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:13.8:1:33.8:1:1:0:48.5:8:1:0:2 1/1:3:3:1,2:0,0:0,3:1:0,2:27.7:1:31.3:1:1:0:32:6:1:0:3.7 +9 68413066 . T C 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCGAAGAGGCGGAGGAGT;RSEQ=GAGCCACAGAAAGGAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:1:0:33:1:1:0:60:4:1:0:2.5 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:31:1:1:0:22:4:1:0:4 +9 68413072 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGGCGGAGGAGTTGAGCC;RSEQ=CAGAAAGGAGAACTGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:1:31.5:1:1:0:22:4:1:0:4 +9 68413094 . A C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAAAGGAGAACTGGCCTGG;RSEQ=TTCTGCCCCGGCCCAGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:9:1:30.5:1:1:0:22:4:0.6667:0:4 +9 68413290 . G T 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCCGGGATGCTCAGGAAT;RSEQ=CTTTCTTTTCATTGTTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:39:1:32:1:1:0:39:4:0.6667:0:7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68413298 . T G 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCTCAGGAATGCTTTCTT;RSEQ=TCATTGTTGACAGCCCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:31:1:34:0:1:0:39:4:0.6667:0:7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68413304 . G C 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGAATGCTTTCTTTTCATT;RSEQ=TTGACAGCCCTACTCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:25:1:34.5:1:1:0:39:4:0.6667:0:7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68413316 . A C 33 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTTCATTGTTGACAGCCCT;RSEQ=CTCTGTGTGGAGTCTCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:13:1:33.5:1:1:0:39:4:0.6667:0:7 1/1:1:1:0,1:0,0:0,1:1:0,0:2:0:27:0:1:0:41:2:1:0:4 +9 68413363 . G C 50 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TGGAACTCAGGGATCCTAGG;RSEQ=AGGTCAGCTGGAAGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:1,1:0.5:0,0:38:0:33:0:1:0:20:2:0.5:0:4 1/1:3:3:1,2:0,0:0,3:1:0,2:32.3:1:32:1:1:0:30:6:1:0:4.7 +9 68413383 . A G 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4;SOR=Inf;LSEQ=GAGGTCAGCTGGAAGGGAAG;RSEQ=CACGCCTCTCCATACCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:42.5:1:30:1:1:0:40:4:1:0:2 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:37.5:1:31:1:1:0:24.5:4:0.6667:0:5 +9 68413396 . T C 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=AGGGAAGACACGCCTCTCCA;RSEQ=ACCAAGCCTGAGGTTCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:19.5:1:31.5:1:1:0:24.5:4:0.6667:0:3.5 0/0:3:0:0,0:1,2:3,0:0:2,0:31.3:1:28.3:1:1:0:30:6:1:0:4.7 +9 68413415 . T C 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATACCAAGCCTGAGGTTCAC;RSEQ=GCAAAAGAGAGGCCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:19.5:1:27.5:1:1:0:24.5:4:0.6667:0:3.5 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:28.5:1:1:0:24.5:4:1:0:5 +9 68413418 . A G 28 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CCAAGCCTGAGGTTCACTGC;RSEQ=AAAGAGAGGCCGCCGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:19.5:1:28.5:1:1:0:24.5:4:0.6667:0:3.5 0/0:2:0:0,0:1,1:2,0:0:2,0:22:1:28:1:1:0:24.5:4:1:0:5 +9 68413512 . T G 64 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGCCCTGTGTTCTTCCTG;RSEQ=CTGAGGAGTGGTTCCAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:3,1:0,0:0,4:1:0,2:38:1:32.3:1:1:0:24.8:8:1:0:2.5 +9 68413581 . G C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCCAGTGGCGCCGGATCTAG;RSEQ=AAAGGTTGTGCCTTTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:37:1:33.5:1:1:0:22:4:1:0:5 0/1:7:2:1,1:2,3:5,2:0.2857:2,2:36:1:31:1:1:1.41:39.5:4:0.2857:0:1 +9 68413585 . G T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.44721;LSEQ=GTGGCGCCGGATCTAGGAAA;RSEQ=GTTGTGCCTTTTGCTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:1,1:0.5:0,0:31:0:33:0:1:0:24:2:0.5:0:3 0/1:7:2:0,2:3,2:5,2:0.2857:2,0:36:1:31:0:0.42857:0:24:4:0.2857:0:1.5 +9 68413607 . C T 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.56923;SOR=0.26046;LSEQ=TTGTGCCTTTTGCTGAAACT;RSEQ=TGGGGTTGACAGGAGCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:3,2:5,3:0.375:2,2:9.7:1:32.3:1:1:2.60168:32:6:0.375:0:5.7 0/1:8:1:0,1:4,3:7,1:0.125:2,0:37:0:30:0:1:0:23:2:0.125:0:4 +9 68413612 . G A 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CCTTTTGCTGAAACTCTGGG;RSEQ=TTGACAGGAGCTCATCTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:1,2:3,2:5,3:0.375:2,2:11.3:1:33:1:1:2.60168:32:6:0.375:0:5.7 0/0:8:0:0,0:4,4:8,0:0:2,0:24.5:1:31.1:1:1:0:33.3:16:1:0:1.6 +9 68413638 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15441;SOR=0;LSEQ=AGGAGCTCATCTAACAGGCT;RSEQ=GAGGTGAGTGCAGACGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:39:0:31.5:1:1:1.41418:38:4:0.2857:0:5 0/0:10:0:0,0:5,5:10,0:0:2,0:15.3:1:30.9:1:1:0:32.4:20:1:0:1.7 +9 68413653 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=0;LSEQ=AGGCTGGAGGTGAGTGCAGA;RSEQ=GAGAGCCCCGGCTCCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:1,1:3,3:6,2:0.25:2,2:31:0:31:1:1:1:38:4:0.25:0:5 0/0:6:0:0,0:2,1:3,0:0:2,0:25.3:1:25.3:1:1:0:28.7:2:0.4:0:1.7 +9 68413664 . GC G 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=GAGTGCAGACGAGAGCCCCG;RSEQ=TCCTGGAGCGGTTGGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:19:0:31.5:1:1:1:38:4:0.3333:0:5 0/0:8:0:0,0:5,3:8,0:0:2,0:28.1:1:29.3:1:1:0:39.4:7:1:0:1.6 +9 68413675 . G T 30 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=AGAGCCCCGGCTCCTGGAGC;RSEQ=GTTGGGAGGTGCCCGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:10:0:30.5:1:1:1:38:4:0.3333:0:5 0/0:9:0:0,0:5,4:9,0:0:2,0:27.4:1:28.6:1:1:0:39.3:18:1:0:1.8 +9 68413706 . C T 86 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCGGTTGGCTGGCATCTG;RSEQ=GCTTGACGCGGAGGCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:31.5:1:1:0:60:4:1:0:1.5 1/1:9:8:3,5:1,0:1,8:0.8889:0,2:24.6:1:28.9:1:0.44444:0:35.5:16:0.8889:0:2 +9 68413740 . G C 50 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTCCGGGGTCACGAGCTC;RSEQ=GGAGGTGAAGGTGCCCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8:1:32.5:1:1:0:54:4:1:0:2.5 1/1:5:4:1,3:1,0:1,4:0.8:0,2:29.5:1:25:1:0.4:0:42.3:3:0.75:0:2.3 +9 68413916 . T C 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1;LSEQ=CCCAGCAGGCCGTCGCGCTG;RSEQ=GGGTTCTGGTCTTCCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:1,0:1,4:0.6667:0,2:19:1:31.8:1:1:0:59:8:0.8:0:4.8 1/0:3:2:0,2:0,0:0,2:0.6667:0,0:5:1:28:1:1:0:57.5:4:1:0:4.5 +9 68413918 . G C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.45455;SOR=0;LSEQ=CAGCAGGCCGTCGCGCTGTG;RSEQ=GTTCTGGTCTTCCTGTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:20.5:1:34:0:1:0:58:4:0.3333:0:5 0/0:5:0:0,0:0,4:4,0:0:0,0:15.8:1:29:1:1:0:44.3:8:0.8:0:4.5 +9 68413927 . C T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22807;SOR=0;LSEQ=GTCGCGCTGTGGGTTCTGGT;RSEQ=TTCCTGTCATTTGTTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:3:2,1:6,2:8,3:0.2727:2,2:22.7:1:32.3:1:1:1.44322:52.7:6:0.2727:0:4.3 0/0:8:0:0,0:2,6:8,0:0:2,0:13.9:1:30.6:1:1:0:50.1:16:1:0:5 +9 68413948 . T G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.40179;SOR=2.56643;LSEQ=TTCCTGTCATTTGTTGGGGT;RSEQ=CGGAGGCCACCAGGGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:6,3:1,3:4,9:0.6:2,2:30.4:1:30.6:1:0.26573:5.17:52.2:8:0.5714:0:4.7 1/1:10:8:2,6:0,2:2,8:0.8:0,2:23.5:1:32.5:1:1:0:46.9:16:0.8:0:5.3 +9 68413950 . G A 49 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61319;SOR=0.40632;LSEQ=CCTGTCATTTGTTGGGGTTC;RSEQ=GAGGCCACCAGGGAGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:7,6:13,3:0.1875:2,2:37.3:1:31:1:1:1.66:52.7:6:0.1875:0:4.3 0/1:12:1:0,1:3,8:11,1:0.0833:2,0:40:0:32:0:1:0:55:2:0.0909:0:6 +9 68413954 . G A 43 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.42528;LSEQ=TCATTTGTTGGGGTTCGGAG;RSEQ=CCACCAGGGAGTCTGAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:7,6:13,3:0.1875:2,2:29:1:30:1:1:1.66:56.7:6:0.2:0:6.7 0/1:12:3:1,2:2,7:9,3:0.25:2,2:28.3:1:27.7:1:1:1.66:58:6:0.25:0:7 +9 68413955 . C A 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.87108;LSEQ=CATTTGTTGGGGTTCGGAGG;RSEQ=CACCAGGGAGTCTGAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:1,2:8,5:13,3:0.1875:2,2:25:1:29:1:0.55:2.96927:60:6:0.1875:0:2.7 0/1:12:2:0,2:3,7:10,2:0.1667:2,0:40:1:26:0:1:0:60:4:0.1667:0:3 +9 68413956 . C T 43 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=1.28819;LSEQ=ATTTGTTGGGGTTCGGAGGC;RSEQ=ACCAGGGAGTCTGAGGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:7,6:13,3:0.1875:2,2:29.7:1:30.3:1:1:1.66:56.7:6:0.2:0:6.7 0/1:13:3:1,2:3,7:10,3:0.2308:2,2:30.3:1:27.3:1:1:1.15:58:6:0.2308:0:7 +9 68413958 . C G 34 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17931;SOR=Inf;LSEQ=TTGTTGGGGTTCGGAGGCCA;RSEQ=CAGGGAGTCTGAGGATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:9,8:17,0:0:2,0:26.6:1:31.5:1:1:0:54.2:34:1:0:3.5 0/1:13:2:0,2:4,7:11,2:0.1538:2,0:38:0:34:0:1:0:45:4:0.1538:0:5 +9 68413969 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50345;SOR=0;LSEQ=CGGAGGCCACCAGGGAGTCT;RSEQ=AGGATGGGAGAGCCCCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:20.5:1:28.5:1:1:1.26772:42.5:4:0.1111:0:4 0/0:12:0:0,0:4,8:12,0:0:2,0:32.8:1:31.1:1:1:0:53.9:24:1:0:4.4 +9 68413971 . G A 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15172;SOR=Inf;LSEQ=GAGGCCACCAGGGAGTCTGA;RSEQ=GATGGGAGAGCCCCAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:18,0:0:2,0:23.2:1:32:1:1:0:54.5:36:1:0:3.5 0/1:12:2:0,2:4,6:10,2:0.1667:2,0:25:0:33:0:0.51515:0:45:4:0.1667:0:5 +9 68413990 . TCGGAGGGAGGG CCGGAGGA 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42831;SOR=2.25359;LSEQ=AGGATGGGAGAGCCCCAGTT;RSEQ=GCCAGGACAGTGAACACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:2,4:1,2:3,6:0.4286:2,2:21:1:31.7:1:1:1:41.3:12:0.4615:0.2143:5.5 1/0:11:7:2,5:0,2:2,7:0.6364:0,2:18.6:1:30.7:1:1:0:54.9:14:0.6364:0.3636:4.3 +9 68413991 . CGGAG C 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0.36146;SOR=0.3518;LSEQ=GGATGGGAGAGCCCCAGTTT;RSEQ=GGAGGGGCCAGGACAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:2,2:1,2:3,4:0.4:2,2:32.3:1:33:1:1:1.81:60:8:0.5714:0:2.8 0/1:11:2:0,2:1,3:4,2:0.1818:2,0:24:1:32:0:1:0:60:4:0.3333:0:3 +9 68414008 . A G 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.1698;SOR=0.21947;LSEQ=TTTCGGAGGGAGGGGCCAGG;RSEQ=CAGTGAACACAAAGCCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:4,4:1,1:2,8:0.6667:2,2:25.4:1:32.4:1:1:1:48.3:16:0.6667:0:4.4 0/1:7:2:0,2:0,0:0,2:0.2857:0,0:12:1:33:0:1:0:60:4:0.3333:0:3 +9 68414012 . T C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52105;SOR=0;LSEQ=GGAGGGAGGGGCCAGGACAG;RSEQ=GAACACAAAGCCCCGCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:1,2:5,4:9,3:0.2308:2,2:21:1:32.7:1:1:2.31595:28.7:6:0.25:0:6.7 0/0:7:0:0,0:1,4:5,0:0:2,0:14.4:1:29.6:1:1:0:58.8:10:0.8333:0:5.4 +9 68414027 . G A 50 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21429;SOR=5.76413;LSEQ=GACAGTGAACACAAAGCCCC;RSEQ=CATGCTCGGGCAGGTTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:3,0:4,6:10,3:0.2308:2,0:18.7:1:32:0:0.19231:0:25.7:6:0.2308:0:6.3 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:18:1:29:1:0.33333:0:51.5:4:0.6667:0:6.5 +9 68414033 . T C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAACACAAAGCCCCGCATGC;RSEQ=CGGGCAGGTTGGGAGAGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:5,6:0,1:1,11:0.8462:0,2:23:1:31.5:1:1:0:43.9:22:0.8462:0:4.5 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:33:0:1:0:56.5:4:1:0:7.5 +9 68414040 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCCCCGCATGCTCGGGCA;RSEQ=GTTGGGAGAGTCCTTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:3:2,1:6,6:12,3:0.2:2,2:25.3:1:32.3:1:1:1.91:22.7:6:0.2:0:6.3 0/0:2:0:0,0:1,1:2,0:0:2,0:13.5:1:33:1:1:0:56.5:4:1:0:7.5 +9 68414063 . T C 105 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGGAGAGTCCTTCTGCCTG;RSEQ=GCAGCCTGGCTGGGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:7,4:0,0:0,11:0.8462:0,2:24.3:1:30.5:1:1:0:30.5:22:1:0:4.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68414094 . A G 101 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCTGGAGCAGGGGGATG;RSEQ=CCCTTGCTTCCTGGCTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:6,4:0,0:0,10:1:0,2:24.5:1:30.5:1:1:0:29.1:20:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68414103 . T G 95 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGGGGATGACCCTTGCT;RSEQ=CCTGGCTCACGAAAGCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:0,0:0,8:0.8889:0,2:27:1:31.9:1:1:0:29.5:16:0.8889:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68414170 . A C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGTGGGGTGCAGGAAGCG;RSEQ=CGTTCCCCACGCCCCGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:39.5:1:31:1:1:0:60:4:0.5:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68414172 . G T 59 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=TGTGGGGTGCAGGAAGCGAC;RSEQ=TTCCCCACGCCCCGGTGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:26.3:1:29.5:1:1:0:51.3:8:1:0:3.8 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:33:0:1:0:39:2:1:0:4 +9 68414199 . C T 65 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCCCGGTGTAGGTGAAC;RSEQ=CGATAGAGGAGGGAGGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:23.8:1:32.5:1:1:0:60:8:1:0:4.5 1/1:1:1:0,1:0,0:0,1:1:0,0:28:0:31:0:1:0:39:2:1:0:4 +9 68414203 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGGTGTAGGTGAACCCGA;RSEQ=AGAGGAGGGAGGAGGGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:12.5:1:32.5:1:1:2.45:60:4:0.4:0:7 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:30:0:1:0:39:2:1:0:4 +9 68414208 . G T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGGTGAACCCGATAGAG;RSEQ=AGGGAGGAGGGTGACACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:2:0,2:2,4:6,2:0.25:2,0:15:1:29:0:1:0:60:4:0.25:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68414231 . A G 63 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGGAGGGTGACACCCACC;RSEQ=GGGGTGCTAATTAGTAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:4:1,3:1,2:3,4:0.5714:2,2:32.5:1:31.8:1:1:1.41418:54.8:8:0.5714:0:4.5 1/1:1:1:0,1:0,0:0,1:1:0,0:25:0:32:0:1:0:39:2:1:0:4 +9 68414235 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGTGACACCCACCAGGG;RSEQ=TGCTAATTAGTAACCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:39:1:30:1:1:2.45:60:4:0.3333:0:7 0/0:1:0:0,0:0,1:1,0:0:0,0:21:0:33:0:1:0:39:2:1:0:4 +9 68414259 . C T 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTAGTAACCACAGTGGC;RSEQ=TCAAAGAACTCAAATGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:32.5:1:32.5:1:1:1.73:60:4:0.4:0:7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68414262 . A T 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGTAACCACAGTGGCCTC;RSEQ=AAGAACTCAAATGAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:29.5:1:31.5:1:1:2.45:60:4:0.3333:0:7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68414291 . A C 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATGAAAGGAAGACTTGCA;RSEQ=GTCTCTCACTTTAAGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:19.5:1:32:0:1:0:60:4:0.5:0:4 0/0:1:0:0,0:0,1:1,0:0:0,0:17:0:25:0:1:0:60:2:1:0:2 +9 68414626 . C A 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCTCAGAAAAAAAAAAAAAA;RSEQ=GATTCTTTTAAAAAGATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:42:0:33:0:1:0:21:2:1:0:7 1/1:2:2:1,1:0,0:0,2:1:0,2:21.5:1:28.5:1:1:0:24.5:4:1:0:4.5 +9 68414632 . T C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAAAAAAAAAACGATTC;RSEQ=TTTAAAAAGATTGTTGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:21:1:35:0:1:0:34:4:1:0:5.5 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:30:1:1:0:24.5:4:1:0:4.5 +9 68414641 . G T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAACGATTCTTTTAAAAA;RSEQ=ATTGTTGGTTGGCCAGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:35:1:30:0:1:0:21.5:4:0.6667:0:6.5 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 68414643 . T C 33 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACGATTCTTTTAAAAAGA;RSEQ=TGTTGGTTGGCCAGGCATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:35:1:33:1:1:0:21.5:4:0.6667:0:6.5 1/1:1:1:0,1:0,0:0,1:1:0,0:11:0:33:0:1:0:23:2:1:0:6 +9 68414649 . G C 53 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTCTTTTAAAAAGATTGTTG;RSEQ=TTGGCCAGGCATAGTGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:30.7:1:34:1:1:0:30:6:1:0:5.7 1/0:2:1:0,1:1,0:1,1:0.5:0,0:5:0:32:0:1:0:23:2:0.5:0:6 +9 68414671 . T C 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCAGGCATAGTGGCTCA;RSEQ=ACTTGTAATCCCTGCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:31:1:1:0:34.5:4:1:0:5 1/0:2:1:0,1:1,0:1,1:0.5:0,0:13:0:33:0:1:0:42:2:0.5:0:3 +9 68414674 . T C 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCATAGTGGCTCATAC;RSEQ=TGTAATCCCTGCACTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:31:1:1:0:34.5:4:1:0:5 1/0:2:1:0,1:1,0:1,1:0.5:0,0:16:0:33:0:1:0:42:2:0.5:0:3 +9 72744848 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19843;SOR=0;LSEQ=ATCTGCCCTATGCCTCTCTC;RSEQ=CATTTCTGGTGGTGTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:1,1:12,9:21,2:0.087:2,2:29.5:1:31:1:1:1.31655:60:4:0.087:0:1 0/0:28:0:0,0:19,9:28,0:0:2,0:19.9:1:29.9:1:1:0:59:13:1:0:0.2 +9 73641667 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51111;SOR=0;LSEQ=GGACTCCCCTGCACCCTAAG;RSEQ=GGCCACCACTGCCAGTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:8,12:20,2:0.0909:2,2:8:1:30:1:1:1.47:60:4:0.0909:0:1 0/0:14:0:0,0:1,13:14,0:0:1,0:18.7:1:29.9:1:1:0:60:28:1:0:0 +9 75046971 . T C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22872;SOR=Inf;LSEQ=CCAGTTTGAGAAATTTTTTT;RSEQ=CCTAAAGAAAATAGAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:54,12:66,0:0:2,0:26.2:1:30.6:1:1:0:60:65:1:0:0.2 0/1:61:2:1,1:51,8:59,2:0.0328:2,2:31:1:26.5:1:0.27541:6.06906:60:4:0.0328:0:1 +9 75047061 . C G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.42458;SOR=1.19093;LSEQ=ATATATTGCTTGCTGAGGAA;RSEQ=ACATTTAACTCAGAACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:105:55,50:58,51:109,105:0.4907:2,2:26.9:1:32.6:1:1:1.03372:60:104:0.4906:0:1.2 1/0:189:101:56,45:52,36:88,101:0.5344:2,2:22.7:1:30.2:1:0.65978:1.1598:60:49.5:0.5294:0:1 +9 75047282 . C T 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59207;SOR=0.32855;LSEQ=TTGGCTTACTGCAACCTCTG;RSEQ=CTCCTGGGTTCAGTTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:18.2:1:30:1:1:0:58:10:0.625:0:1 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:17:1:30:0:1:0:53.5:4:0.3333:0:1 +9 75154200 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGTGGTGGCATGTGCTTG;RSEQ=AGTCCCAGTTACTCGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:30:1:1:0:60:4:1:0:1 +9 75155834 . G A 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00049;SOR=0;LSEQ=GGATGTTGTGAAGCTTCAGT;RSEQ=AGTTAATACAGATATAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:14,1:14,0:14,15:0.5172:1,1:22.8:1:28.1:1:1:0:60:14:0.5:0:1 0/0:15:0:0,0:15,0:15,0:0:1,0:23.1:1:30.9:1:1:0:60:30:1:0:0.1 +9 75155897 . A G 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00241;SOR=Inf;LSEQ=TCCAATCATCAATACTACCC;RSEQ=GCTTTATTAAAACTTCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:85,1:86,0:0:1,0:26.9:1:30.6:1:1:0:60:85:1:0:0.2 0/1:66:7:7,0:59,0:59,7:0.1061:1,0:29.4:1:28.9:1:1:0:60:14:0.1077:0:1 +9 75156057 . C T 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.0024;SOR=1.49664;LSEQ=ATAATCTTTGATTTCTCTTG;RSEQ=CCACATGGATGGTTACCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:236:98,138:103,142:245,236:0.4896:2,2:25.1:1:29.9:1:0.92653:1.02138:60:235:0.4958:0:1.1 1/0:441:260:108,152:82,99:181,260:0.5896:2,2:25.6:1:28.7:1:0.43624:1.16532:60:259:0.5927:0:1.1 +9 75794689 . T A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.22209;LSEQ=GTGCCTTCTTACAATTATTA;RSEQ=CATTGCTTACTTTTTTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:48:20,28:171,223:394,48:0.1086:2,2:21.6:1:30.3:1:0.87808:1.07339:60:47:0.1085:0:1.1 0/1:397:135:57,78:121,141:262,135:0.3401:2,2:25.9:1:28.9:1:0.45837:1.17384:60:66.5:0.3419:0:1.1 +9 75794764 . G T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50747;SOR=0;LSEQ=CAACCCTAACTCAGAATTAG;RSEQ=CTATGTGATTCAAATCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:35,131:166,2:0.0119:2,2:7:0:32:0:0.38366:3.70:60:4:0.012:0:1 0/0:128:0:0,0:33,95:128,0:0:2,0:23.7:1:30.8:1:1:0:60:41.667:1:0:0.2 +9 75794996 . A T 70 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGAAACTTTCCTTTAACA;RSEQ=GATAATGCATTATGAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:20.4:1:30.4:1:1:0:56.2:10:0.8333:0:1.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 79105108 . A G 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24451;SOR=4.40909;LSEQ=ACTATCCCTGACTGGTTAGT;RSEQ=TAAAAGCAACACTCTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:0,2:5,5:10,2:0.1667:2,0:39:1:33:1:0.4697:0:27:4:0.1667:0:1 1/0:4:2:1,1:0,2:2,2:0.5:0,2:26:1:29.5:1:1:0:26:4:0.5:0:1 +9 79231007 . C A 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGTGTTTTTTTGAAATGAG;RSEQ=AAATAGCTCTTCGCTTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:21:1:31:1:1:0:60:6:0.6:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:30:0:1:0:60:2:1:0:1 +9 79231247 . G A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02655;SOR=Inf;LSEQ=AAAAGGTCCTTCCTGTTCCC;RSEQ=GAAATCTGTAGTAAGTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:241,96:337,0:0:2,0:23.3:1:30.4:1:1:0:59.9:111.333:0.997:0:0.2 0/1:319:5:2,3:199,114:313,5:0.0157:2,2:22.8:1:28.6:1:0.36131:2.61007:60:10:0.0158:0:1.8 +9 79231317 . T C 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=29.9614;LSEQ=TCACGGTGTTGGTTGACTTT;RSEQ=TCCCATAGATGAAGAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:476:1:0,1:231,242:473,1:0.0021:2,0:37:0:30:0:1:0:60:2:0.0021:0:1 0/1:471:28:13,15:221,222:443,28:0.0594:2,2:25.9:1:30.3:1:0.846:1.14831:60:27:0.0577:0:1.5 +9 79231339 . T G 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=3.30954;LSEQ=CCCATAGATGAAGAGAATAT;RSEQ=TACTAAACCAAAATTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:408:236:100,136:63,109:172,236:0.5784:2,2:23.7:1:32.2:1:0.26108:1.27:59.8:58:0.5743:0:1.9 1/1:405:332:139,193:31,42:73,332:0.8198:2,2:25.6:1:31:1:1:1.02479:60:109.667:0.8184:0:1.9 +9 79231357 . G A 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=8.82507;LSEQ=ATTTACTAAACCAAAATTTG;RSEQ=GGCACATCGTCTAAAAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:351:206:76,130:46,98:144,206:0.5869:2,2:25.5:1:31:1:0.36322:1.24:59.8:40.2:0.5843:0:2 1/1:353:327:132,195:14,12:26,327:0.9263:2,2:26.1:1:29.1:1:0.21553:1.72071:60:35.333:0.9244:0:2 +9 79231549 . C T 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0.77928;LSEQ=TAATTCATCCCTTCAGCTTT;RSEQ=GTTAACTCAAAAGCTAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:0,13:0,2:2,13:0.8667:0,1:18.5:1:29.5:1:1:0:60:12:0.8571:0:1 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:23.6:1:29:1:1:0:60:10:0.8333:0:1.2 +9 79634764 . T A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22319;SOR=Inf;LSEQ=GAACAGCCTGCGCCACAACC;RSEQ=CTCCTTCAACGACTGCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:14,10:24,0:0:2,0:27.6:1:31.2:1:1:0:60:48:1:0:0 0/1:22:2:1,1:13,7:20,2:0.0909:2,2:19:0:30.5:1:1:1.80284:38:4:0.0909:0:1.5 +9 79634815 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21647;SOR=Inf;LSEQ=GCGGAGGCCCGACCAGCCTG;RSEQ=CAAGGGTAGCTTCTGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:27,0:0:2,0:25.1:1:31:1:1:0:60:12.5:1:0:0.1 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:8:0:31:0:1:1.19087:44:4:0.087:0:1.5 +9 79635080 . CCCG C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.50529;SOR=0;LSEQ=CAGCCGCCGCCGCCGCCGCC;RSEQ=CCGCCGCCGCACATGGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:21.5:1:30:1:1:1.13389:60:4:0.1176:0:0 0/0:11:0:0,0:6,5:11,0:0:2,0:22.3:1:29.3:1:1:0:60:22:1:0:1 +9 80144099 . G A 28 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.96404;LSEQ=GTGAACCCCTTTCTGTCTTC;RSEQ=TCGCTGTAACCAGACCCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:0,1:8,9:17,1:0.0556:2,0:14:0:34:0:1:0:60:2:0.0588:0:1 0/1:19:2:1,1:7,10:17,2:0.1053:2,2:9.5:1:28.5:1:1:1.40:60:4:0.1111:0:1 +9 80336195 . A G 107 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01043;SOR=10.09389;LSEQ=GTCCCTCTTGTGTATCTTCA;RSEQ=TAGCCCACCAGGGAAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:1:1,0:104,23:127,1:0.0078:2,0:28:0:14:0:1:0:22:0:0:0:4 0/1:136:10:9,1:92,33:125,10:0.0735:2,2:13.6:1:32.5:1:0.45076:3.21:40.6:20:0.0735:0:1.2 +9 80336405 . G A 55 q25;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50623;SOR=1.97006;LSEQ=TCTTCAGAATGAATTCTCGG;RSEQ=CTGCCTGGGCATCTCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:551:3:3,0:201,346:547,3:0.0054:2,0:16.7:1:18:1:0.05055:0:42:0.5:0.0019:0:3.3 0/1:562:6:6,0:204,352:556,6:0.0107:2,0:9:1:21.5:1:0.0026:0:51:5:0.0091:0:1 +9 80343336 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21093;SOR=Inf;LSEQ=GGCTGCACAGGGCAAGGGCA;RSEQ=CAATGGTGCACTGTAGTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:78,5:83,0:0:2,0:22.9:1:33.4:1:1:0:60:166:1:0:0 0/1:71:2:2,0:67,2:69,2:0.0282:1,0:32:1:30:1:1:0:60:4:0.029:0:1.5 +9 80343349 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21211;SOR=Inf;LSEQ=AAGGGCAGCAATGGTGCACT;RSEQ=TAGTGCGTTAACTCCCACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:98,8:106,0:0:2,0:23.7:1:32.6:1:1:0:60:52:1:0:0.1 0/1:91:2:1,1:80,9:89,2:0.022:2,2:15.5:1:27:1:0.20879:8.48355:60:4:0.0225:0:1 +9 80343383 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4987;SOR=0;LSEQ=CCCACACTGGGGTTTGGAGA;RSEQ=AAAACCTATTCACAGCTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:2:1,1:146,44:190,2:0.0104:2,2:26:1:32.5:1:0.41476:3.29229:60:4:0.0106:0:1 0/0:192:0:0,0:141,51:192,0:0:2,0:21.6:1:31.1:1:1:0:59.8:95:1:0:0.1 +9 80343586 . G A 52 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.2193;SOR=4.63342;LSEQ=GCTTTCCTCCATTCGGTTCT;RSEQ=GAAAAAAAAAAAAAATCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:1:1,0:97,237:334,1:0.003:2,0:1:0:24:0:0.29254:0:30:2:0.0032:0:1 0/1:368:5:4,1:129,233:362,5:0.0136:2,2:5.6:1:22.4:1:0.05995:7.19:40.2:4:0.0119:0:1.6 +9 80409138 . C G 70 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.54771;LSEQ=TGTTATTTTCATTTTCAGAA;RSEQ=CTCTGCATAGTGTTAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:25.5:1:35.3:1:1:0:60:8:0.6667:0:1.3 1/0:2:1:1,0:1,0:1,1:0.5:0,0:33:0:34:0:1:0:60:2:0.5:0:1 +9 80409345 . A G 242 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00038;SOR=1.66337;LSEQ=TACTTGTATCAGATAATAAA;RSEQ=TGATAATCCATTGCCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:163:124,39:177,54:231,163:0.4127:2,2:24.7:1:32.7:1:0.90469:1.03085:59.8:39.75:0.4098:0:1.2 1/0:397:214:157,57:118,64:182,214:0.539:2,2:21.7:1:31.3:1:0.07978:1.49:59.8:106:0.5381:0:1.1 +9 80409358 . G T 60 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02892;SOR=0;LSEQ=TAATAAAATGATAATCCATT;RSEQ=CCTGTCTAAAGAACACTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:5:3,2:356,121:477,5:0.0104:2,2:23.8:1:26.2:1:0.60575:1.9584:60:4:0.0084:0:1.8 0/0:496:0:0,0:325,168:493,0:0:2,0:24.4:1:31:1:1:0:58.1:48.3:0.9938:0:0.5 +9 80412372 . G T 58 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20247;SOR=0.23183;LSEQ=ACATGATTCCAGTATTTATA;RSEQ=AGTTTACCAAATGTACTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:4:2,2:281,80:361,4:0.011:2,2:15.3:1:29.3:1:0.21903:3.4969:60:8:0.0111:0:1 0/0:391:1:0,1:285,105:390,1:0.0026:2,0:1:0:22:0:0.2711:0:60:2:0.0026:0:1 +9 80430741 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.22809;SOR=Inf;LSEQ=ATTACTTTCCAAATTTTCTT;RSEQ=GCTTTGCATATTACATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:16,153:169,0:0:2,0:22.3:1:30.7:1:1:0:59.7:83.5:1:0:0.2 0/1:155:2:1,1:18,135:153,2:0.0129:2,2:13:1:27:1:0.23083:7.33:60:4:0.0129:0:1 +9 80430802 . C A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01655;SOR=3.64577;LSEQ=CCTTCATATACTGGTCTTTA;RSEQ=ACTGGTTTACAATAAAGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:27:1,26:0,30:30,27:0.4737:1,1:24.6:1:31.9:1:0.47368:0:60:54:0.4737:0:1 1/0:26:20:0,20:0,6:6,20:0.7692:0,1:25.4:1:30.4:1:1:0:60:40:0.7692:0:1.2 +9 80537016 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49858;SOR=0;LSEQ=TCAAGAGGCTACTCGTGTTG;RSEQ=CACATTATTGTGAACACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:2:1,1:155,13:168,2:0.0118:2,2:21:1:30:1:0.15837:11.52661:60:4:0.0118:0:1 0/0:166:0:0,0:143,23:166,0:0:2,0:23.9:1:29.3:1:1:0:60:165:1:0:0.2 +9 80645940 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5004;SOR=0;LSEQ=GCCGGGGGGCGGGGGCGCCG;RSEQ=AGGCAGCTGCCCCGCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:101,14:115,2:0.0171:2,2:15.5:1:27.5:1:0.24094:7.00406:60:4:0.0175:0:1 0/0:101:0:0,0:84,17:101,0:0:2,0:11.8:1:29.2:1:1:0:60:100:1:0:0.2 +9 80646091 . T A 78 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00514;SOR=0;LSEQ=CCGCTCGATCTCGTCGTTGA;RSEQ=CCGCCGGGCTTCCTTGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:7:6,1:84,42:126,7:0.0526:2,2:7.6:1:28.1:1:0.42748:2.98:45.3:14:0.0538:0:1.1 0/0:146:0:0,0:87,58:145,0:0:2,0:8.7:1:28.2:1:1:0:34.8:71.5:1:0:0.1 +9 80646190 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.21763;SOR=0;LSEQ=CTGCAGCCCCGCCGGCACCC;RSEQ=CTGCTCACAGCGCGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:21,176:197,2:0.0101:2,2:40:1:29.5:1:0.20938:8.21:49:4:0.0102:0:1 0/0:227:0:0,0:49,177:226,0:0:2,0:33.7:1:30.1:1:1:0:46:24.111:1:0:0.2 +9 80646193 . G A 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21763;SOR=0;LSEQ=CAGCCCCGCCGGCACCCCCT;RSEQ=CTCACAGCGCGCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:21,176:197,2:0.0101:2,2:26:0:28:1:0.20938:8.21:32:4:0.0104:0:1 0/0:227:0:0,0:50,177:227,0:0:2,0:32.2:1:31.4:1:1:0:45.9:44.4:1:0:0.2 +9 80646504 . AGCC A 33 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GCGGCCCGCCTCGCCCCCCG;RSEQ=GCCGCCGCCGCCGCCGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:28.5:1:34.5:1:1:0:60:4:1:0:0.5 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:14:0:33.5:1:1:1:21.5:4:0.3333:0:0.5 +9 80795402 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51012;SOR=Inf;LSEQ=GTTTATAACAATGCCAACAG;RSEQ=ATGCTGGGGAACATTGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:66,31:97,0:0:2,0:32.8:1:32.7:1:1:0:32.2:194:1:0:0.4 0/1:133:2:1,1:77,54:131,2:0.015:2,2:34:1:30.5:1:1:1.42202:21:4:0.0153:0:1.5 +9 80795406 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50918;SOR=Inf;LSEQ=ATAACAATGCCAACAGCATG;RSEQ=TGGGGAACATTGTAGACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:67,32:99,0:0:2,0:33:1:32.7:1:1:0:31.8:98:1:0:0.4 0/1:134:2:1,1:74,58:132,2:0.0149:2,2:23:1:28.5:1:1:1.27351:45:4:0.0157:0:1 +9 80795416 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.16747;LSEQ=CAACAGCATGCTGGGGAACA;RSEQ=TGTAGACTCTTCCAGTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:31:20,11:48,27:75,31:0.2925:2,2:30.3:1:32.6:1:1:1.02:28:62:0.2952:0:1.1 0/1:140:9:5,4:65,66:131,9:0.0643:2,2:34.3:1:30.3:1:1:1.27:25.4:18:0.0652:0:1 +9 80795441 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50349;SOR=Inf;LSEQ=GACTCTTCCAGTTTAGCCAT;RSEQ=GTGACACTTGTGGGGCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:55,56:111,0:0:2,0:22.4:1:31.2:1:1:0:31.2:36:1:0:0.4 0/1:137:2:1,1:52,82:134,2:0.0146:2,2:32.5:1:29.5:1:1:1.57:28.5:4:0.015:0:1 +9 80795452 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20402;SOR=0;LSEQ=TTTAGCCATGGTGACACTTG;RSEQ=GGGGCATTCCTTTTTGAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:0,2:42,57:99,2:0.0198:2,0:29:1:32:0:0.50931:0:36:4:0.0202:0:1 0/0:122:0:0,0:41,80:121,0:0:2,0:21.8:1:28.6:1:1:0:30.6:39.333:0.9916:0:0.2 +9 80795495 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23412;SOR=0;LSEQ=ACCCATTCCCTTGATGTCAA;RSEQ=GATATCACCTTTCTCGTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:16,50:66,2:0.0294:2,2:20.5:1:30:1:0.4403:3.06:41.5:4:0.0299:0:1 0/0:72:0:0,0:14,58:72,0:0:2,0:21.3:1:30.2:1:1:0:45.4:144:1:0:0.2 +9 80801556 . G A 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CCCCACTCCTGCCCGCCAGA;RSEQ=AACAATACCCCTTTGACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:20.2:1:31.8:1:1:0:28.4:10:0.4167:0:1.6 0/0:2:0:0,0:2,0:2,0:0:0,0:17:1:32.5:1:1:0:27.5:4:1:0:0 +9 80801741 . G A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03243;SOR=Inf;LSEQ=CATGGATGCGCATGAAGTTC;RSEQ=TCATTTTGGCGAATTACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:166,143:309,0:0:2,0:29.5:1:31:1:1:0:57.1:76.25:1:0:0.2 0/1:351:6:3,3:180,165:345,6:0.0171:2,2:25.5:1:30.3:1:1:1.09063:51.3:12:0.0174:0:1.5 +9 80801786 . C A 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.20062;SOR=0.22965;LSEQ=TGGTGGTTCTGGCTGAAAGG;RSEQ=AAAAAAAACAAAAACATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:4:3,1:103,159:262,4:0.015:2,2:10.8:1:25:1:0.30466:4.61:56.3:3:0.0115:0:1 0/0:288:1:1,0:113,174:287,1:0.0035:2,0:1:0:23:0:0.39583:0:60:2:0.0036:0:1 +9 82832611 . C A 112 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=6e-05;SOR=15.94135;LSEQ=AGTTGTTCTTAGTATAGGTC;RSEQ=CTACTTGGTAAAGAGGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:2,0:41,0:41,2:0.0465:1,0:7:1:30.5:1:1:0:60:4:0.0476:0:1 0/1:29:13:12,1:15,0:15,13:0.4483:1,1:23.8:1:30.3:1:0.46429:0:60:26:0.4643:0:1.1 +9 82832653 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20801;SOR=Inf;LSEQ=CACAGCCAGAGCAAAGATTT;RSEQ=GACTAACTAAAGCTATTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:79,17:96,0:0:2,0:24.5:1:32.6:1:1:0:59.7:192:1:0:0.1 0/1:81:2:1,1:64,14:78,2:0.0247:2,2:21.5:1:29.5:1:0.34177:4.4508:60:4:0.025:0:1 +9 82832717 . T A 46 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12365;SOR=Inf;LSEQ=ACAGAATGCCTTTTCTCCAT;RSEQ=TCTTGGCAGAGACTGGTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:163,85:248,0:0:2,0:23.6:1:30.7:1:1:0:60:48.6:1:0:0.1 0/1:255:4:3,1:157,94:251,4:0.0157:2,2:28.3:1:23:1:1:1.79:60:3:0.0119:0:1.5 +9 82832769 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.9949;LSEQ=GTAGGGATATAAAAATGCTT;RSEQ=CCATTTCAACACAGTGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:20:12,8:174,177:351,20:0.0539:2,2:26.9:1:31.1:1:0.49141:1.52:60:40:0.0551:0:1 0/1:373:159:84,75:109,105:214,159:0.4263:2,2:25.9:1:30.2:1:0.75374:1.08:60:78.5:0.429:0:1.1 +9 82832848 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49857;SOR=Inf;LSEQ=ACAAATCACAGTGCTAATTA;RSEQ=AATTAAGCAAGTACGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:38,134:172,0:0:2,0:22.4:1:30.7:1:1:0:60:171:1:0:0.1 0/1:174:2:1,1:55,117:172,2:0.0115:2,2:15:1:29:1:0.54136:2.12:60:4:0.0116:0:1.5 +9 82929082 . T C 82 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=CCATAACTGACCCCCATTAT;RSEQ=CTTAATTTACTAATGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:17:1:32:1:1:0:60:12:1:0:2.2 1/0:5:3:3,0:2,0:2,3:0.6:0,0:41.7:1:31.7:1:1:0:60:6:0.6:0:1.3 +9 82929142 . A G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02479;SOR=0.1573;LSEQ=AGTCTCCCACTGCTGCTATC;RSEQ=TCTCTTTCTCTGCATATCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:16,1:3,1:4,17:0.8095:2,1:26.3:1:30.2:1:0.35238:4.76:60:34:0.8095:0:2.1 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:18.6:1:29.2:1:1:0:60:10:0.3846:0:2 +9 82929174 . C T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25599;SOR=0.45508;LSEQ=GCATATCCCTCTTCACCCAC;RSEQ=AGGGTTCTAACACTCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:38:32:23,9:3,3:6,32:0.8421:2,2:21.3:1:30.6:1:0.35666:2.49:60:64:0.8421:0:1.5 1/0:34:24:17,7:7,3:10,24:0.7059:2,2:23.7:1:29.7:1:1:1.04:60:48:0.7059:0:1.2 +9 82929206 . C T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.5098;SOR=Inf;LSEQ=ACTCTGGCCTTGGCTTCCAC;RSEQ=CTCTCACCTCACCTGTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:25,22:47,0:0:2,0:29.3:1:30.1:1:1:0:60:14.667:1:0:0.8 0/1:66:2:1,1:36,28:64,2:0.0303:2,2:15.5:1:23:1:1:1.28077:60:4:0.0313:0:1.5 +9 82929232 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50942;SOR=Inf;LSEQ=ACCTCACCTGTGCGCTGACA;RSEQ=CGGCATGAGGATATTCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:21,30:51,0:0:2,0:26.1:1:31.4:1:1:0:60:50:1:0:0.8 0/1:71:2:1,1:32,37:69,2:0.0282:2,2:37:1:28.5:1:1:1.15:60:4:0.0286:0:1 +9 82929301 . C G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=CCAACACTTCATGACAGGCA;RSEQ=CTTACCTACACAGCCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:3,12:0,0:0,15:1:0,2:21.9:1:33.3:1:1:0:60:30:1:0:1.1 1/1:21:19:3,16:0,2:2,19:0.9048:0,2:21.8:1:32.5:1:1:0:60:38:0.9048:0:1.1 +9 82929397 . T C 89 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCCTTGTCCTGCTAAGG;RSEQ=TTTGCCACTCTACACTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:26.8:1:34.5:1:1:0:60:12:1:0:1.2 1/1:1:1:0,1:0,0:0,1:1:0,0:19:0:33:0:1:0:60:2:1:0:1 +9 84386538 . A AT 63 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.65152;SOR=0.45024;LSEQ=GTTCTTGAGTTGCCTCCACT;RSEQ=TTTTTTTTTCTGTGTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:4:4,0:41,0:41,4:0.0889:1,0:15.3:1:31.7:1:1:0:60:8:0.0909:0.0444:0.5 0/1:24:1:1,0:23,0:23,1:0.0417:1,0:16:0:31:0:1:0:60:2:0.0417:0:0 +9 84386587 . G A 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02802;SOR=Inf;LSEQ=ATTGGCTAAATCATAGAAAA;RSEQ=CAAATTAAATTTGCAATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:86,9:95,0:0:2,0:23.9:1:32.5:1:1:0:60:22.75:1:0:0.1 0/1:93:5:5,0:76,12:88,5:0.0538:2,0:21.2:1:29.6:1:1:0:60:10:0.0556:0:1.6 +9 84386609 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49875;SOR=Inf;LSEQ=AAATTAAATTTGCAATCTAG;RSEQ=CAATTTCTGTAAACAAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:110,29:139,0:0:2,0:23.2:1:31.6:1:1:0:60:45.333:1:0:0.1 0/1:148:2:1,1:108,38:146,2:0.0135:2,2:13.5:1:26.5:1:0.45891:2.81839:60:4:0.0139:0:1 +9 84386667 . A G 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGGGGTTGTAGCTACGACA;RSEQ=CAGCTGCCTAGAATGAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:177,125:302,0:0:2,0:26.4:1:30:1:1:0:60:99.667:1:0:0.1 0/1:286:19:11,8:154,113:267,19:0.0664:2,2:19.4:1:30.8:1:1:1.01:60:38:0.0667:0:2.8 +9 84386700 . A T 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATGAAGTGGAATCTGTTTAG;RSEQ=GGGCTCATGTAAGAAGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:0:0,0:183,167:350,0:0:2,0:24.1:1:30.6:1:1:0:60:37.889:1:0:0.1 0/1:331:25:11,14:150,156:306,25:0.0755:2,2:26.7:1:29.4:1:0.68122:1.22303:59.8:50:0.0765:0:3 +9 84386712 . A G 233 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=508.94013;LSEQ=CTGTTTAGAGGGCTCATGTA;RSEQ=GAAGTGAGTCATACATTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:351:1:1,0:178,172:350,1:0.0028:2,0:35:0:31:0:1:0:60:2:0.0029:0:1 1/0:328:195:97,98:60,72:132,195:0.5945:2,2:26.2:1:30.7:1:0.49878:1.19:59.9:47.75:0.5895:0:1.4 +9 84386759 . C T 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34785;SOR=3.37811;LSEQ=TAAAGATGACCAGGAGGATA;RSEQ=AGACAGGGAAGGGGATATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:1:0,1:126,182:308,1:0.0032:2,0:31:0:30:0:1:0:60:2:0.0033:0:1 0/1:276:3:1,2:106,167:273,3:0.0109:2,2:17:1:28.7:1:1:1.26838:60:6:0.0109:0:1 +9 84386769 . A G 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=CAGGAGGATACAGACAGGGA;RSEQ=GGGGATATCACAGAACTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:285:0:0,0:108,176:284,0:0:2,0:26.3:1:31.1:1:1:0:60:93.667:1:0:0.1 0/1:236:13:4,9:86,137:223,13:0.0551:2,2:27.5:1:30.7:1:0.77088:1.41043:60:26:0.0553:0:2.2 +9 87285552 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52085;SOR=0;LSEQ=CTCGGCACGCCCGCAACAAG;RSEQ=ACCGAGGAGTTAAGAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:74,4:78,2:0.025:2,2:42.5:1:30:0:0.12184:16.65783:60:4:0.0253:0:2 0/0:51:0:0,0:49,2:51,0:0:1,0:28.4:1:31.5:1:1:0:60:50:1:0:0.5 +9 87285595 . C G 217 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2349;LSEQ=AAGCGCAGGGAAGGCCTCCC;RSEQ=GCACGGGTGGGGGAAAGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:185:145:131,14:35,5:40,145:0.7838:2,2:21.5:1:30.3:1:0.56596:1.33:60:71.5:0.7901:0:1.2 0/1:133:61:53,8:56,14:70,61:0.4586:2,2:19.4:1:29.1:1:0.35282:1.65:60:60:0.458:0:1.1 +9 87285607 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.17911;SOR=Inf;LSEQ=GGCCTCCCCGCACGGGTGGG;RSEQ=GAAAGCGGCCGGTGCAGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:193,37:230,0:0:2,0:23.3:1:31.1:1:1:0:60:56.5:1:0:0.7 0/1:170:2:1,1:134,33:167,2:0.0118:2,2:28:1:28:1:0.36285:4.01535:60:4:0.012:0:1 +9 87285616 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17875;SOR=Inf;LSEQ=GCACGGGTGGGGGAAAGCGG;RSEQ=CGGTGCAGCGCGGGGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:222,49:271,0:0:2,0:23.8:1:31.8:1:1:0:60:66.75:1:0:0.6 0/1:199:2:1,1:151,46:197,2:0.0101:2,2:15.5:1:27:1:0.41749:3.25822:60:4:0.0102:0:1 +9 87285915 . C T 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11041;LSEQ=CCTCCTTTTTCTCCTTGCCC;RSEQ=TAGGGCCCGAGCTGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:248:235:46,189:1,12:13,235:0.9476:1,2:22.4:1:30.3:1:0.472:2.91:60:32.571:0.9461:0:1.2 1/0:227:151:27,124:12,64:76,151:0.6652:2,2:22.3:1:29.2:1:0.85231:1.16:60:49.333:0.6607:0:1.2 +9 87285923 . C G 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60129;SOR=2.28575;LSEQ=TTCTCCTTGCCCCTAGGGCC;RSEQ=GAGCTGGCCAGGTGGGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:1:0,1:27,178:205,1:0.0049:2,0:26:0:15:0:1:0:60:0:0:0:4 0/1:181:2:1,1:22,157:179,2:0.011:2,2:11.5:1:29:1:0.23861:7.00:60:4:0.0114:0:1 +9 87285992 . G A 182 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=2e-05;SOR=0.06079;LSEQ=GGGGAGAAGTCAAAGACAAG;RSEQ=GATGCAGGACAGGGTCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:55:53:1,52:0,2:2,53:0.9636:0,1:21.4:1:31.9:1:1:0:60:52:0.963:0:1.6 1/0:41:25:0,25:0,16:16,25:0.6098:1,1:16.5:1:31.2:1:1:0:60:50:0.6098:0:1.9 +9 87314676 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTTTTATTTTTAAATTGT;RSEQ=TTTTTTCTTTTTTTTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:14.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 87315023 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.49941;SOR=0;LSEQ=CTTACACAGCTGGTAGGAGG;RSEQ=GACAGGCTTGCCTGGAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:110,49:159,2:0.0124:2,2:9:1:29:1:0.52601:2.23245:60:4:0.0127:0:1 0/0:147:0:0,0:99,48:147,0:0:2,0:24.2:1:30.1:1:1:0:60:48:1:0:0.2 +9 87315033 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.90724;LSEQ=TGGTAGGAGGGGACAGGCTT;RSEQ=CCTGGAAGTCTGGATTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:1:1,0:111,60:171,1:0.0058:2,0:20:0:27:0:1:0:60:2:0.006:0:1 0/1:181:2:1,1:119,60:179,2:0.011:2,2:40:1:29:1:1:1.97532:60:4:0.0114:0:1 +9 87315117 . T C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17067;LSEQ=CAGTTGCATGAGAAAAAGTA;RSEQ=TAAAATTCAGGGCTCTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:280:220:108,112:28,31:59,220:0.7857:2,2:25.8:1:32.8:1:0.88381:1.07:60:440:0.7885:0:1.1 0/1:315:121:65,56:97,97:194,121:0.3841:2,2:26:1:30.9:1:0.56294:1.16:60:120:0.3859:0:1.1 +9 87315204 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49876;SOR=Inf;LSEQ=GGTCTCTATTGAAAATGTTG;RSEQ=TGAAAAATCTTGCAAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:28,112:140,0:0:2,0:22.3:1:32:1:1:0:60:139:0.9929:0:0.2 0/1:150:2:1,1:45,103:148,2:0.0133:2,2:10:1:25:1:0.52072:2.27:60:4:0.0133:0:1.5 +9 87315206 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.22542;SOR=0;LSEQ=TCTCTATTGAAAATGTTGGT;RSEQ=AAAAATCTTGCAAAAATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:2:1,1:25,110:135,2:0.0146:2,2:34:1:30:1:0.34468:4.33:60:4:0.0146:0:1 0/0:151:0:0,0:44,107:151,0:0:2,0:22.3:1:30.8:1:1:0:60:302:1:0:0.1 +9 87315356 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCTTCCTGCACATTTATTA;RSEQ=GTGTGCCAGGCCCTGGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:0,7:7,2:0.2222:0,2:21.5:1:30.5:1:0.22222:0:60:4:0.25:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:29.5:1:30:0:1:0:60:4:1:0:0 +9 87316868 . A T 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.27793;SOR=0.43843;LSEQ=GAGAAATGAAACCCAGTGCA;RSEQ=GGGTTATTGACCATGAAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:21:21,0:9,0:9,21:0.7:0,1:23.5:1:31.8:1:1:0:60:42:0.7:0:1 1/0:10:5:5,0:5,0:5,5:0.5:0,0:29.6:1:30:1:1:0:60:10:0.5:0:1.2 +9 87317391 . C A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.2487;SOR=0;LSEQ=ATTTTATTCAATATTTCCCC;RSEQ=CTCTGTTTATTTTCCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:2,1:55,199:254,3:0.0117:2,2:24:1:22.7:1:0.12462:7.16:60:2:0.0079:0:1 0/0:249:0:0,0:72,177:249,0:0:2,0:23.6:1:30.3:1:1:0:60:61.25:1:0:0.1 +9 87317412 . TT CC 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22763;SOR=Inf;LSEQ=CTCTGTTTATTTTCCTTCTT;RSEQ=CCAACTTGAAACCTCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:177:0:0,0:23,154:177,0:0:2,0:23.5:1:30.5:1:1:0:60:176:1:0:0.2 0/1:162:2:1,1:32,128:160,2:0.0123:2,2:5.5:1:30:1:0.36692:3.95:60:4:0.0124:0.0062:0.5 +9 87322376 . A C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTCTTTAGTTTTAAGGCAT;RSEQ=TTTTTTCCCTACTGGGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:26:1:32:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 87322540 . T C 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.58856;LSEQ=GACATTAAAAATACACAATA;RSEQ=ATTTATGCTACCCCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:14:14,0:2,0:2,14:0.875:0,1:30.4:1:33.2:1:1:0:57.9:28:0.875:0:1 1/1:5:4:3,1:1,0:1,4:0.8:0,2:26.3:1:32.3:1:1:0:60:8:0.8:0:1 +9 87322719 . A T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12453;SOR=Inf;LSEQ=TACTGTGTTCCTAAAATGTA;RSEQ=CATTTTAAATTCATGTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:262,116:378,0:0:2,0:25.9:1:30.3:1:1:0:59.8:377:1:0:0.1 0/1:398:4:1,3:262,132:394,4:0.0101:2,2:10:1:25.5:1:0.11526:5.92666:60:8:0.0101:0:1.3 +9 87325451 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1908;SOR=Inf;LSEQ=TGGTATGACTTCCAAGCATT;RSEQ=CTGGCTAGAAAGAATTCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:122,5:127,0:0:1,0:26:1:32.1:1:1:0:60:20.167:1:0:0.1 0/1:99:2:1,1:84,13:97,2:0.0202:2,2:19:1:27:1:0.26407:6.26345:60:4:0.0204:0:1 +9 87325763 . G T 23 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19251;SOR=Inf;LSEQ=TTAATTATTCTCATTGCCTT;RSEQ=GTGCGGTAGTCTGGGAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:26,153:179,0:0:2,0:21.9:1:31.5:1:1:0:60:178:0.9889:0:0.1 0/1:142:2:1,1:16,123:139,2:0.0141:2,2:6:1:23.5:1:0.22736:7.49:60:4:0.0142:0:1 +9 87325994 . A G 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=1;SOR=0;LSEQ=GTTTTTCCATCTATCCATCC;RSEQ=TCCATTTATCCACCCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:0,4:0,0:0,4:1:0,0:19.3:1:31.5:1:1:0:60:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 87338267 . T A 93 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.01698;SOR=0.04234;LSEQ=GGCAATAATGCTTTAAGTAA;RSEQ=GTGCATAATTTATTTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:1,9:0.9:0,0:23.7:1:29.4:1:1:0:59.8:8:0.8889:0:1 0/1:5:1:1,0:3,1:4,1:0.2:2,0:31:0:31:0:1:0:60:2:0.2:0:1 +9 87339327 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.24844;SOR=Inf;LSEQ=AATGATCATGGACGTACCTA;RSEQ=GTTTGTTGCTGGGGCACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:210:0:0,0:31,178:209,0:0:2,0:24.4:1:30.3:1:1:0:60:40.8:1:0:0.1 0/1:217:3:1,2:40,174:214,3:0.0138:2,2:20.3:1:28.7:1:0.4682:2.17:60:6:0.0139:0:1 +9 87339329 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.23851;SOR=0;LSEQ=TGATCATGGACGTACCTACG;RSEQ=TTGTTGCTGGGGCACTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:28,169:197,2:0.01:2,2:8:1:34.5:1:0.27085:5.95:60:4:0.0103:0:1 0/0:209:0:0,0:39,170:209,0:0:2,0:23:1:29.3:1:1:0:60:208:1:0:0.1 +9 87342854 . G A 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0624;SOR=0;LSEQ=GATTTCTGCTCACTTCATGG;RSEQ=CTGGCCTGGAATTGACGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:5:3,2:143,286:429,5:0.0115:2,2:15:1:31.2:1:0.34049:2.99:60:10:0.012:0:1.2 0/0:407:0:0,0:156,251:407,0:0:2,0:25.1:1:30.7:1:1:0:60:57.143:1:0:0.1 +9 87356684 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51054;SOR=0;LSEQ=GTTTTGTTTACCTGTCCTGT;RSEQ=AAAGCAGTCTATTAAATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:170,14:184,2:0.0108:2,2:11:1:28:1:0.15519:11.76578:60:4:0.0112:0:1 0/0:136:0:0,0:132,4:136,0:0:1,0:23.6:1:31.5:1:1:0:60:135:1:0:0 +9 87359808 . G C 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5028;SOR=0;LSEQ=ATTTGTCTTGCTTCATTCTG;RSEQ=CTCTTACTGTGGCCCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:164,17:181,2:0.0109:2,2:6:1:31:1:0.18753:9.4038:60:4:0.0113:0:1 0/0:152:0:0,0:137,14:151,0:0:2,0:22.1:1:30.3:1:1:0:60:20.571:1:0:0.1 +9 87360021 . C A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12522;SOR=Inf;LSEQ=AATAGGTGTCTGAATTGGTT;RSEQ=TGAGCATTTTGGATGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:355:0:0,0:97,258:355,0:0:2,0:24.1:1:32.4:1:1:0:59.9:49.714:1:0:0.1 0/1:385:4:2,2:120,261:381,4:0.0104:2,2:11:1:26:1:0.59425:2.17:60:8:0.0105:0:1 +9 87360102 . GTTAACACCT ATTAA 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00257;SOR=Inf;LSEQ=TGTTCAGATATAAATAGGGT;RSEQ=AGGTTGGAAGAATTAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:0,94:94,0:0:1,0:24.6:1:32.6:1:1:0:59.4:93:1:0:0.4 0/1:73:7:2,5:1,64:65,7:0.0959:1,2:24.4:1:30.2:1:0.02347:22.91:60:14:0.0986:0:1.4 +9 87360106 . ACACCT A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00529;SOR=0.29205;LSEQ=CAGATATAAATAGGGTGTTA;RSEQ=AGGTTGGAAGAATTAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:85:76:0,76:0,9:9,76:0.8941:0,1:25.2:1:32.4:1:1:0:59.3:152:0.8941:0.1529:0.4 1/0:62:44:1,43:0,11:11,44:0.7097:0,1:20.4:1:30.7:1:1:0:59.7:88:0.8:0.1935:0.4 +9 87360153 . G A 158 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05862;SOR=0.12635;LSEQ=GGCTTAACAAAAGTGATAAA;RSEQ=GTGTTATATGGCCTTTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:29:0,29:0,1:1,29:0.9667:0,1:20.6:1:32.6:1:1:0:60:58:0.9667:0:1 1/0:18:14:2,12:0,4:4,14:0.7778:0,2:24.9:1:30.9:1:1:0:60:28:0.7778:0:1.6 +9 87475806 . GTTTATTTA G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=35;MSI=10.000;MSILEN=4;SSF=0.82563;SOR=0.84992;LSEQ=GCTTTCATCCCAAGTGGTTT;RSEQ=TTTATTTATTTATTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:18:18,0:36,0:36,18:0.2466:1,1:21.4:1:33.1:1:1:0:60:36:0.2535:0.0685:0.2 0/1:46:10:10,0:16,0:16,10:0.2174:1,0:22.6:1:32.9:1:1:0:60:20:0.2222:0.0435:0.2 +9 87482409 . T A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30975;SOR=4.3717;LSEQ=GCTGTATCAACCAGAGTGTT;RSEQ=ATCAGAGCCCCTGATAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:1,0:40,245:285,1:0.0035:2,0:1:0:23:0:0.14336:0:60:2:0.0035:0:1 0/1:198:3:2,1:24,171:195,3:0.0152:2,2:18:1:28:1:0.04591:13.90:60:6:0.0155:0:1 +9 87482418 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.173;SOR=Inf;LSEQ=ACCAGAGTGTTTATCAGAGC;RSEQ=CCTGATAGGGATGACTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:231:0:0,0:20,211:231,0:0:2,0:22.2:1:31.4:1:1:0:59.9:37.5:1:0:0.1 0/1:165:2:1,1:17,146:163,2:0.0121:2,2:21:1:28:1:0.20687:8.37:60:4:0.0125:0:1 +9 87549000 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50095;SOR=0;LSEQ=GGGCCTGGAAGCTCAGGTAC;RSEQ=GGCCACCAACTCTTCACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:142,31:173,2:0.0114:2,2:28:1:31.5:1:0.33314:4.52437:60:4:0.0116:0:1 0/0:152:0:0,0:122,30:152,0:0:2,0:21.7:1:29.3:1:1:0:60:151:1:0:0.1 +9 87549003 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49962;SOR=0;LSEQ=CCTGGAAGCTCAGGTACAGG;RSEQ=CACCAACTCTTCACCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:2:1,1:146,35:181,2:0.0109:2,2:22:1:28.5:1:0.35561:4.12715:60:4:0.0112:0:1 0/0:167:0:0,0:131,36:167,0:0:2,0:21.2:1:31.1:1:1:0:60:334:1:0:0.1 +9 87549007 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23893;SOR=Inf;LSEQ=GAAGCTCAGGTACAGGCCAC;RSEQ=AACTCTTCACCCGCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:153,41:194,0:0:2,0:24.7:1:31.1:1:1:0:60:31.333:1:0:0.1 0/1:186:2:1,1:141,43:184,2:0.0108:2,2:24:1:29:1:0.41813:3.25305:60:4:0.0109:0:1 +9 87549019 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11893;SOR=Inf;LSEQ=CAGGCCACCAACTCTTCACC;RSEQ=GCTGCCTTCACCTCCACATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:187,60:247,0:0:2,0:24.1:1:30.8:1:1:0:60:122.5:1:0:0.1 0/1:240:3:1,2:177,60:237,3:0.0125:2,2:16.3:1:29.3:1:0.16456:5.84669:60:6:0.0125:0:1 +9 87562375 . A C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AACCTTCCATGCCAGTGACC;RSEQ=CACCCAATATAGCATTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:31.5:1:1:0:57:4:1:0:2 +9 87563252 . T C 197 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=TCCTCAGTTATTAGCACAAA;RSEQ=GTTATTTCCTTAGGAACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:66:65,1:0,0:0,66:1:0,1:25.6:1:32.6:1:1:0:60:132:1:0:1.1 1/0:36:27:27,0:9,0:9,27:0.75:0,1:25:1:31.9:1:1:0:60:26:0.7429:0:1.2 +9 87563274 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10989;SOR=Inf;LSEQ=TTATTTCCTTAGGAACTAGG;RSEQ=TGTTTTCTCATCTTTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:116,6:122,0:0:1,0:20.1:1:32.2:1:1:0:60:23.4:1:0:0.6 0/1:61:2:2,0:56,3:59,2:0.0328:2,0:23.5:1:29.5:1:1:0:60:4:0.0333:0:1.5 +9 87563370 . T C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCTTCTCTTTTAACACCCA;RSEQ=CCCCAGACCCTGAAGGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:438:0:0,0:261,176:437,0:0:2,0:24.6:1:30:1:1:0:60:32.615:1:0:0.1 0/1:445:22:10,12:254,168:422,22:0.0494:2,2:27.3:1:30.2:1:0.18642:1.81172:60:21:0.0482:0:1.2 +9 87563460 . C A 136 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCTCCAGCATGAGCACAT;RSEQ=GTCAAGTTCTATGGCGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:559:0:0,0:256,303:559,0:0:2,0:25.3:1:30.8:1:1:0:59.9:61.111:1:0:0.1 0/1:563:26:13,13:263,274:537,26:0.0462:2,2:17:1:29:1:1:1.04:59.8:52:0.047:0:1.1 +9 87563562 . G A 230 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.28107;LSEQ=TTCCTCAGGTACAGTGAGGC;RSEQ=GGGAGGTGGGCTCCAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:375:167:55,112:83,123:206,167:0.4453:2,2:24.1:1:31.2:1:0.1613:1.37295:60:166:0.4486:0:1.1 0/1:359:66:26,40:126,167:293,66:0.1838:2,2:22.9:1:29.6:1:0.67947:1.16028:59.7:32:0.1813:0:1.1 +9 87563984 . G T 28 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCCAGACTGTGGAATGAACA;RSEQ=TAAGGAAGGGAAGCAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:0,3:3,0:0:0,0:44.7:1:27:1:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:28:1:1:0:60:4:1:0:1 +9 87570089 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13188;SOR=Inf;LSEQ=CTTTTAGCACCAGCAGCTAC;RSEQ=GGGTGGGGGTGAGGAGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:58,6:64,0:0:2,0:23.6:1:30.8:1:1:0:59.9:63:1:0:0 0/1:37:2:1,1:32,3:35,2:0.0541:2,2:13.5:1:29:1:0.20721:9.38084:60:4:0.0556:0:1.5 +9 87570143 . C T 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00982;SOR=9.70304;LSEQ=GGAGGGGCAGGGGCAAAGGG;RSEQ=CCCTGGAGTGAAAATGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:1:1,0:103,24:127,1:0.0078:2,0:2:0:29:0:1:0:60:2:0.0079:0:1 0/1:126:9:5,4:83,34:117,9:0.0714:2,2:28.4:1:26.3:1:0.45133:1.94164:60:8:0.065:0:1 +9 87570173 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2367;SOR=Inf;LSEQ=GAAAATGCTGAGGCCCCCAG;RSEQ=TTCATTCTCCATGTCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:143,57:200,0:0:2,0:24.5:1:32.6:1:1:0:60:49:1:0:0.2 0/1:190:2:1,1:124,63:187,2:0.0105:2,2:16.5:1:27:1:1:1.96074:60:4:0.0108:0:2 +9 87570204 . C T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04012;SOR=Inf;LSEQ=ATGTCCTTCCCCAGGGCACA;RSEQ=GGCCCTGATGCCGTGCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:0:0,0:190,97:287,0:0:2,0:26.4:1:31.7:1:1:0:60:94.667:1:0:0.2 0/1:234:4:2,2:156,74:230,4:0.0171:2,2:19.3:1:28.8:1:0.59739:2.10083:60:8:0.0172:0:1 +9 87570478 . C A 203 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.02727;LSEQ=CCCAGGGACCTCTTTCCCTG;RSEQ=GGGACCCCTGCTGTATTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:84:28,56:167,367:534,84:0.1357:2,2:26.2:1:31.8:1:0.70615:1.10:60:168:0.1375:0:1.1 0/0:705:3:2,1:273,427:700,3:0.0043:2,2:32.3:1:27.3:1:0.56417:3.12:60:6:0.0043:0:1.3 +9 87570601 . G A 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0337;SOR=Inf;LSEQ=AGTCCAAGCTCAAGGTGTGA;RSEQ=TGGGATTGGTTCCTCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:0,62:62,0:0:1,0:24.8:1:32.9:1:1:0:59.6:61:1:0:0.2 0/1:48:4:0,4:1,43:44,4:0.0833:1,0:26.8:1:31:1:1:0:60:8:0.0833:0:1 +9 87636058 . G A 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=CTGAGAAAACAAAACCAAGA;RSEQ=TGGGCTTCTTTTGTAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:87,4:91,0:0:1,0:27.5:1:32.7:1:1:0:60:29.333:1:0:0.1 0/1:76:10:10,0:57,8:65,10:0.1316:2,0:26:1:31.1:1:0.58735:0:60:20:0.1351:0:1 +9 87636107 . C T 31 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25127;SOR=Inf;LSEQ=CTGCTGTTTTTTTGCACTGA;RSEQ=ATTTCTTCGATGTGCATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:156,43:199,0:0:2,0:22.6:1:32.4:1:1:0:60:98.5:1:0:0.1 0/1:226:3:1,2:163,60:223,3:0.0133:2,2:25:1:20:1:0.18328:5.38512:60:2:0.009:0:2 +9 87636619 . T TC 91 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=10.000;MSILEN=1;SSF=0.41176;SOR=Inf;LSEQ=TTTTTAAATTTTCTTTTTCT;RSEQ=TTTTTTTTCGTCTTCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:10,6:0.375:0,0:39.8:1:35.3:1:1:0:60:12:0.375:0:0.2 1/1:1:1:0,1:0,0:0,1:1:0,0:36:0:34:0:1:0:60:2:1:0:0 +9 88763628 . G A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GAAACAAATTTGACAAGGAG;RSEQ=TTAAAAATACAGGGCCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:27.5:1:32.5:1:1:0:21.3:8:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:41:1:29:1:1:0:30:4:1:0:1 +9 91100046 . A G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18018;SOR=0;LSEQ=ATACCAACAGCATGTGGGTA;RSEQ=CATTATAGACTGCTCCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:9,5:14,2:0.125:2,2:32:1:34:1:1:1.73197:60:4:0.125:0:1 0/0:21:0:0,0:12,9:21,0:0:2,0:28.8:1:30:1:1:0:59.5:42:1:0:0.1 +9 92494768 . A G 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCGCTGTGAGGGTCAGGGA;RSEQ=GGCCTCTGGATTCACCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:3,0:3,2:0.4:0,0:12:1:35:0:1:0:60:4:0.4:0:1 0/0:2:0:0,0:2,0:2,0:0:0,0:9:1:31:0:1:0:60:4:1:0:0.5 +9 92494807 . C T 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86755;LSEQ=GAAATGGCTCGTTAAAGCAG;RSEQ=GTGGACCCCTTCCACCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:3,7:0.7:0,0:23.4:1:29.4:1:1:0:60:14:0.7:0:1 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:33.5:1:30:1:1:0:60:4:0.6667:0:1 +9 92494972 . T C 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49822;SOR=Inf;LSEQ=AGGCTTGTAGCATTTACAGT;RSEQ=ACAAAAGCAAACACTTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:87,38:125,0:0:2,0:25.2:1:30.1:1:1:0:60:124:1:0:0.1 0/1:130:2:1,1:91,37:128,2:0.0154:2,2:25:0:29.5:1:0.50078:2.44019:60:4:0.0159:0:1 +9 92495076 . C T 210 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.42463;LSEQ=ACAGATGAGTCATATGTAGG;RSEQ=ACTCGGTGTCAGCTGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:212:155:68,87:30,26:56,155:0.7311:2,2:24.1:1:28.9:1:0.27382:1.47347:60:154:0.7404:0:2.1 1/0:254:136:61,75:57,61:118,136:0.5354:2,2:24.1:1:27.9:1:0.61513:1.14825:60:272:0.5354:0:2.1 +9 92495109 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.3771;LSEQ=CTGCAGAGAGGCCGCAGTCC;RSEQ=ACTGTGTGCTTGGGTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:161:117:45,72:18,26:44,117:0.7267:2,2:24.4:1:29.2:1:0.85664:1.10698:60:57.5:0.7278:0:2.6 1/0:204:102:41,61:44,58:102,102:0.5:2,2:26.2:1:27.9:1:0.77648:1.12801:60:101:0.4975:0:2.8 +9 92495123 . G C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=9e-05;SOR=0.40628;LSEQ=CAGTCCCACTGTGTGCTTGG;RSEQ=TGTCTTGAGCTGGCAGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:105:32,73:13,30:43,105:0.7095:2,2:25.1:1:32.5:1:1:1.01:60:51.5:0.7153:0:2.6 0/1:187:93:32,61:40,54:94,93:0.4973:2,2:24.8:1:30.8:1:0.2936:1.4094:60:45.5:0.4973:0:2.8 +9 92495136 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5029;SOR=Inf;LSEQ=TGCTTGGGTGTCTTGAGCTG;RSEQ=CAGGGCCGGACCTCGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:34,92:126,0:0:2,0:26.6:1:31.6:1:1:0:60:30.5:1:0:1.7 0/1:153:2:1,1:50,101:151,2:0.0131:2,2:23:1:30.5:1:1:2.01:60:4:0.0132:0:3 +9 92495150 . C T 112 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=GAGCTGGCAGGGCCGGACCT;RSEQ=GGCTTTGAACCCTGGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:29,83:112,0:0:2,0:26.5:1:30.3:1:1:0:60:224:1:0:1.5 0/1:124:16:5,11:31,77:108,16:0.129:2,2:23.3:1:28.2:1:0.77739:1.13:60:7:0.1157:0:3.1 +9 92496042 . C A 25 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCTCAGGTTATTCACCTG;RSEQ=CTGGGCCTCCCAAAGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:25:1:1:0:59.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 92802411 . A T 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22375;SOR=0;LSEQ=TGGGGTTCCTGGCTAAACTG;RSEQ=CTTAGCAGGTTTCTTGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:18,20:38,2:0.05:2,2:26.5:1:25:1:1:1.11:60:4:0.0526:0:1 0/0:44:0:0,0:19,25:44,0:0:2,0:28.9:1:28.2:1:1:0:60:43:1:0:0.1 +9 92803759 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGGTTTACTGTGAAGAC;RSEQ=GCAAGGACAAAGCTTCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:31.5:1:1:0:60:4:1:0:1 +9 93606103 . G A 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=8e-05;SOR=0.34809;LSEQ=AAACGTTCCCTGCCACGTGG;RSEQ=GTCCTCACCAAAGTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:164:83:81,2:77,4:81,83:0.5061:1,1:25.6:1:30.9:1:0.4401:2.09:59.9:82:0.5125:0:1.2 0/1:103:27:25,2:69,7:76,27:0.2621:2,2:22.1:1:28.5:1:1:1.27:60:54:0.2647:0:1.1 +9 93606151 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08096;SOR=Inf;LSEQ=CTTGCCCAGGTGGACACCTG;RSEQ=GCAGGTGTGTGCCCTCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:291,71:362,0:0:2,0:24.6:1:31.7:1:1:0:59.9:59.333:1:0:0.3 0/1:277:3:1,2:206,68:274,3:0.0108:2,2:12.7:1:24.3:1:0.15829:6.01014:60:6:0.0109:0:1 +9 93606309 . G A 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.96223;LSEQ=GGGCTTTATTTGCTGCGCCA;RSEQ=AGCCGCAACTACCTGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:851:55:29,26:373,420:793,55:0.0646:2,2:22.5:1:29.6:1:0.48545:1.26:60:26.5:0.063:0:1.1 0/1:818:209:100,109:291,318:609,209:0.2555:2,2:24.3:1:29.6:1:1:1.00:60:103.5:0.2559:0:1.2 +9 93606505 . C T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00306;SOR=Inf;LSEQ=TCCTCAAGAAGCCCTTCAAC;RSEQ=GGCCCCAAGGGGTGCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:693:0:0,0:311,382:693,0:0:2,0:26.8:1:30.6:1:1:0:59.9:137.6:1:0:0.1 0/1:656:8:5,3:294,352:646,8:0.0122:2,2:16.9:1:29.3:1:0.47957:1.99:60:7:0.0108:0:1.3 +9 93606676 . A G 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=4.98523;LSEQ=TTCCTGGCTACATGCAACAC;RSEQ=TGTGCCTATGTGCCCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:11:1,10:2,72:74,11:0.1294:1,2:29.1:1:32.6:1:0.34369:3.52:60:22:0.1294:0:1.3 0/1:63:27:1,26:1,34:35,27:0.4286:1,1:22.6:1:30.7:1:1:1.30:60:26:0.4262:0:1.1 +9 93607520 . G A 43 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03529;SOR=14.21149;LSEQ=GAGCCACCGTGCCCGGCCAT;RSEQ=TTATTTTTATTTATACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:16,1:17,1:0.0556:1,0:16:0:30:0:1:0:60:2:0.0556:0:1 1/0:6:3:3,0:3,0:3,3:0.5:0,0:17:1:27.3:1:1:0:60:6:0.5:0:1 +9 93607623 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53295;SOR=0;LSEQ=AAGTTTTGATCCTGTTTTAC;RSEQ=ATGCCAGGACTCGAGATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:2,0:88,2:90,2:0.0217:1,0:25.5:1:31:1:1:0:60:4:0.0222:0:3 0/0:53:0:0,0:49,4:53,0:0:2,0:22.6:1:30.8:1:1:0:60:52:1:0:0.1 +9 93607642 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.60322;LSEQ=CCATGCCAGGACTCGAGATA;RSEQ=ATTGGAAATGCCTTCTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:118,6:124,2:0.0159:1,2:37:1:29:1:0.10844:18.27967:60:4:0.0161:0:1 0/0:104:1:1,0:84,19:103,1:0.0096:2,0:14:0:32:0:1:0:60:2:0.0096:0:1 +9 93607915 . G A 178 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCTCACCTCCTGCCACCAG;RSEQ=CCTGTGTGGACAATTGGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:63:19,44:126,242:368,63:0.1462:2,2:25.5:1:29.9:1:0.56667:1.2052:60:62:0.1473:0:1.1 0/0:346:0:0,0:112,233:345,0:0:2,0:23.1:1:30.7:1:1:0:60:56.5:1:0:0.1 +9 93608130 . G A 95 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.47712;SOR=0;LSEQ=CGAGGGATGTAATATTTAAA;RSEQ=AAAATGTGATTCAGCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:8,8:0.5:0,0:18.8:1:31.9:1:1:0:55.1:16:0.5333:0:1.3 0/0:2:0:0,0:0,2:2,0:0:0,0:22.5:1:32.5:1:1:0:60:4:1:0:0 +9 93624407 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=0;LSEQ=AGAGAGCGGCTGCTGACCAT;RSEQ=CAGGCCAGGGTGCTTCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:137,30:167,2:0.0118:2,2:13:0:33.5:1:0.33411:4.50879:60:4:0.012:0:1.5 0/0:164:0:0,0:125,39:164,0:0:2,0:23.9:1:29.5:1:1:0:60:53.667:1:0:0.1 +9 93624419 . G T 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.35267;SOR=0.30299;LSEQ=CTGACCATTCAGGCCAGGGT;RSEQ=CTTCCTCCCAGGGTCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:3:2,1:161,52:213,3:0.0138:2,2:12:1:30.3:1:0.57222:1.54462:60:6:0.014:0:1 0/0:237:1:0,1:163,73:236,1:0.0042:2,0:1:0:24:0:0.31224:0:60:2:0.0043:0:1 +9 93624755 . T C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00108;SOR=0;LSEQ=TGTGGTCCCCAGGCCAGCAG;RSEQ=AGCTCTGGAGCTCATGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:66:0,66:0,0:0,66:1:0,1:25.5:1:33:1:1:0:60:65:1:0:1.1 1/1:43:36:1,35:0,6:6,36:0.8372:0,1:22.7:1:32.3:1:1:0:60:72:0.8372:0:1 +9 93626609 . C T 102 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51471;SOR=0.38925;LSEQ=ATAAACAAAGGACACAGATA;RSEQ=GGTATGAGGCCCACAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:11:11,0:4,0:4,11:0.7333:0,0:26.2:1:29.7:1:1:0:57.2:10:0.7143:0:1.1 1/0:2:1:1,0:1,0:1,1:0.5:0,0:27:0:32:0:1:0:60:2:0.5:0:1 +9 93627226 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17579;SOR=Inf;LSEQ=CAGAAAGCGTGCTCACTTCT;RSEQ=AAGCAGCAGCACATCCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:224,26:250,0:0:2,0:25.3:1:32.4:1:1:0:59.9:82.333:1:0:0.1 0/1:181:2:1,1:150,29:179,2:0.011:2,2:24:1:30:1:0.30479:5.10254:60:4:0.011:0:1 +9 93627484 . C T 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09144;SOR=0.63759;LSEQ=AGGCATTGATATTTTGATTG;RSEQ=GCTTCAAAACATACTCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:80:3,77:0,50:50,80:0.6154:1,1:24.5:1:30.4:1:0.28444:0:59.9:79:0.6124:0:1.1 1/0:111:56:4,52:0,54:54,56:0.5045:1,2:26.8:1:29.9:1:0.1184:0:60:55:0.5189:0:1.1 +9 93629347 . G A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0145;LSEQ=GCAAATTTAAGTAGCATGTC;RSEQ=TGGAAGGGATCCTGTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:304:303:208,95:0,0:0,303:0.9967:0,2:24.4:1:30.4:1:1:0:60:49.5:0.9966:0:1.1 1/1:317:258:192,66:40,17:57,258:0.8139:2,2:22.1:1:28.9:1:0.50987:1.24:60:35.857:0.8149:0:1.1 +9 93629530 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24899;SOR=Inf;LSEQ=AACTAAGTGGTAGGACCAAC;RSEQ=CGCACTCAGCTCCCGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:269:0:0,0:74,195:269,0:0:2,0:23.1:1:31.1:1:1:0:60:37.429:1:0:0.2 0/1:281:3:1,2:78,200:278,3:0.0107:2,2:19:1:28.7:1:1:1.28:60:6:0.0109:0:1.3 +9 93629630 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.00011;SOR=0.11439;LSEQ=TTGCCCTTGCTCACACCTGC;RSEQ=GTTCCTGGGCAGCCGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:25:1,24:1,17:18,25:0.5814:1,1:21.3:1:29.8:1:1:1.40026:60:24:0.5854:0:1.1 0/1:30:4:0,4:0,26:26,4:0.1333:1,0:18:1:26.8:1:1:0:60:8:0.1379:0:1 +9 93629789 . C G 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATAGCTAATTATCATGTC;RSEQ=GAAAATCTTTTCAAAGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:41.3:1:30.7:1:1:0:60:6:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:49:0:32:0:1:0:60:2:1:0:1 +9 93636257 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02747;SOR=0.20026;LSEQ=ACCCTCTGAACACCTCACAG;RSEQ=GTCCCTTGAGTTGTAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:17:17,0:12,0:12,17:0.5862:0,1:28.4:1:32.6:1:1:0:60:34:0.5862:0:1.9 0/1:14:3:3,0:11,0:11,3:0.2143:0,0:40.3:1:31.3:1:1:0:60:6:0.2143:0:2.3 +9 93636270 . G C 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00538;SOR=0.13018;LSEQ=CTCACAGAGTCCCTTGAGTT;RSEQ=TAGCAGCACAAGCTTGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:19:19,0:11,0:11,19:0.6333:0,1:32.7:1:32.8:1:1:0:60:38:0.6333:0:1.8 0/1:17:3:3,0:14,0:14,3:0.1765:1,0:40.7:1:30.3:1:1:0:60:6:0.1765:0:2.3 +9 93636357 . G A 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00738;SOR=Inf;LSEQ=TATTTTCTTCCCTGTTTTTC;RSEQ=TAATTCTTTCCTTTGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:179,3:182,0:0:1,0:25.4:1:30.5:1:1:0:60:90:0.9945:0:0.3 0/1:147:6:6,0:139,2:141,6:0.0408:1,0:29.5:1:30.7:1:1:0:60:12:0.0414:0:1 +9 93636424 . C T 69 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07056;SOR=6.62596;LSEQ=GGAAAATAAAAATAATTATG;RSEQ=AGATCAACTTAACAGTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:652:1:0,1:442,208:650,1:0.0015:2,0:1:0:25:0:0.32104:0:60:2:0.0016:0:2 0/1:694:7:2,5:429,258:687,7:0.0101:2,2:17.9:1:24.7:1:0.11124:4.14829:60:14:0.0102:0:1 +9 93636431 . A G 271 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08114;LSEQ=AAAAATAATTATGCAGATCA;RSEQ=CTTAACAGTTTTGTGGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:731:315:207,108:275,140:415,315:0.4309:2,2:24.3:1:32.7:1:0.87502:1.02482:60:77.75:0.4302:0:1.1 0/1:796:46:25,21:453,294:747,46:0.0578:2,2:27.8:1:31.3:1:0.43872:1.29384:59.8:92:0.0582:0:1.3 +9 93636664 . G A 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-04;SOR=0.30037;LSEQ=GGTTCACGAATCCACACCAC;RSEQ=TCCGTGATTGCAATACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:100:50:2,48:3,47:50,50:0.5:2,1:22.4:1:30.5:1:1:1.52546:60:24:0.4948:0:1.2 0/1:74:17:0,17:1,56:57,17:0.2297:1,1:24.5:1:30.2:1:1:0:60:34:0.2297:0:1.6 +9 93636671 . A G 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00171;SOR=Inf;LSEQ=GAATCCACACCACGTCCGTG;RSEQ=TTGCAATACAGCCACAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:5,81:86,0:0:2,0:23.6:1:31.4:1:1:0:59.6:85:1:0:0.6 0/1:61:7:0,7:1,53:54,7:0.1148:1,0:21.6:1:31.1:1:1:0:60:14:0.1167:0:2.3 +9 93636875 . A G 86 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00162;SOR=Inf;LSEQ=TACTCTGAGTTCATATTCCC;RSEQ=TGAAGATCATGTTCTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:162:0:0,0:137,25:162,0:0:2,0:22.7:1:30:1:1:0:59.7:22.143:1:0:0.1 0/1:135:8:7,1:113,14:127,8:0.0593:2,2:14.8:1:28.8:1:1:1.15176:60:16:0.0606:0:1 +9 93636923 . C T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.04673;SOR=0;LSEQ=TCCTGGTGTGGGGTCCAGCC;RSEQ=CAGGTCGTATGTTTCTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:4:2,2:216,123:339,4:0.0117:2,2:13.3:1:26:1:0.62435:1.75298:60:3:0.009:0:2.3 0/0:393:0:0,0:254,139:393,0:0:2,0:25.3:1:30.2:1:1:0:60:130:1:0:0.1 +9 93637015 . C T 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15317;LSEQ=GAGAGCCCCTACGCGGACCC;RSEQ=GAGGAGATCAGGCCCAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:299:161,138:184,120:304,299:0.495:2,2:24:1:31:1:0.10049:1.31367:59.9:41.714:0.4924:0:1.1 0/1:744:97:52,45:368,277:645,97:0.1304:2,2:23.4:1:29.4:1:0.58297:1.14946:60:31.333:0.1286:0:1.1 +9 93637282 . G T 111 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00185;SOR=0.06592;LSEQ=GGTACTATTATAATGAAAGC;RSEQ=TCCATTACCTTTAATGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:0,15:0,17:17,15:0.4688:1,1:20.1:1:28.6:1:1:0:60:6.5:0.4483:0:1.3 0/1:19:1:0,1:0,18:18,1:0.0526:1,0:15:0:31:0:1:0:60:2:0.0526:0:1 +9 93637525 . AT A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTGTCTCTACAAAAAAA;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:20:1:32.3:1:1:0:39.5:4:0.6667:0.3333:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 93639489 . A G 43 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACAGGCTTGCACTGTCAC;RSEQ=CCTGGGTGATTTTTTTTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:29:1:27.7:1:1:0:46.7:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 93639590 . A G 84 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTCAACCTCCCAAAGT;RSEQ=TGGGGATTGTCAGCATGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1:0,0:32.5:1:32.5:1:1:0:60:12:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 93639640 . T C 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50549;SOR=0;LSEQ=CAGCCCCCACCATTCTTTTT;RSEQ=AGTAATGGAGTATTACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:21:1:32.4:1:1:0:60:10:0.4167:0:2 0/0:3:0:0,0:3,0:3,0:0:0,0:27:1:32.3:1:1:0:60:6:1:0:0 +9 93639679 . G A 119 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02041;SOR=0.08518;LSEQ=TCATTGTCTATAAAATAAGG;RSEQ=AATATAGGTTGGAAGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:14,0:10,0:10,14:0.5833:0,1:23.5:1:31.4:1:1:0:60:28:0.6087:0:1.2 0/1:10:1:1,0:9,0:9,1:0.1:0,0:33:0:15:0:1:0:60:0:0:0:1 +9 93639789 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25238;SOR=Inf;LSEQ=AGGGGGATTATGCTTCACAG;RSEQ=ATAAGATTATCTAAAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:133,35:168,0:0:2,0:23.5:1:31.5:1:1:0:60:55:1:0:1.3 0/1:196:3:1,2:150,43:193,3:0.0153:2,2:16:1:25.3:1:0.13245:6.88667:60:6:0.0155:0:2 +9 93639793 . A T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13175;SOR=Inf;LSEQ=GGATTATGCTTCACAGGATA;RSEQ=GATTATCTAAAAGTGAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:140,44:184,0:0:2,0:23.4:1:30.6:1:1:0:60:91:1:0:1.4 0/1:228:4:2,2:166,58:224,4:0.0175:2,2:13.8:1:25:1:0.2833:2.84642:60:3:0.0136:0:3 +9 93639803 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.58219;SOR=2.61203;LSEQ=TCACAGGATAAGATTATCTA;RSEQ=AAGTGAGGCATTTTGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:229:227:160,67:0,0:0,227:0.9913:0,2:23.9:1:32.7:1:1:0:60:55.75:0.9911:0:1.4 1/1:298:297:207,90:1,0:1,297:0.9966:0,2:21.4:1:31.1:1:1:0:60:98:1:0:1.3 +9 93639846 . C G 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14773;LSEQ=TCTTGTGTGTTATGATTTCT;RSEQ=TTGCAGAGTTGTGAAAACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:209:114,95:137,85:222,209:0.4849:2,2:26.5:1:32.1:1:0.14324:1.34219:59.9:103.5:0.4894:0:1.5 0/1:558:68:33,35:281,209:490,68:0.1219:2,2:27.8:1:31.7:1:0.19247:1.42504:60:136:0.123:0:1.6 +9 93639849 . G A 175 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGTGTGTTATGATTTCTCTT;RSEQ=CAGAGTTGTGAAAACCGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:0:0,0:254,188:442,0:0:2,0:26.2:1:32:1:1:0:59.9:72.667:0.9977:0:1 0/1:567:76:44,32:272,218:490,76:0.134:2,2:26.6:1:28.1:1:0.71168:1.10:60:75:0.1335:0:1.6 +9 93639973 . G C 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.15733;LSEQ=GACAACCCGTACATCGTGCG;RSEQ=ATGATCGGGATATGCGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:550:281:142,139:140,125:265,281:0.5109:2,2:26.4:1:31.9:1:0.60797:1.09615:60:45.833:0.5121:0:1.8 0/1:518:73:32,41:222,222:444,73:0.1409:2,2:18.6:1:30.7:1:0.37698:1.28063:60:72:0.1404:0:1.8 +9 93640009 . G A 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17755;LSEQ=GAGGCCGAGTCCTGGATGCT;RSEQ=GTTATGGAGATGGCAGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:598:306:140,166:144,148:292,306:0.5117:2,2:24.8:1:30.3:1:0.41293:1.15339:60:152:0.5144:0:1.8 0/1:600:94:46,48:251,254:505,94:0.1567:2,2:23.7:1:28.7:1:0.91096:1.03111:60:93:0.1563:0:1.7 +9 93640072 . G A 56 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20351;SOR=0.23303;LSEQ=CAGCAGAACAGGTATTGTCA;RSEQ=GTGCCCCCACACATCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:4:3,1:134,241:375,4:0.0106:2,2:16.3:1:28.3:1:0.13649:5.37:60:8:0.0106:0:1 0/0:404:1:1,0:162,241:403,1:0.0025:2,0:1:0:24:0:0.40347:0:60:2:0.0025:0:1 +9 93640120 . C T 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.14137;LSEQ=CCTAAGGGACAGGGCCCACC;RSEQ=CTGGATGGGCCGAGCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:159:86:14,72:13,60:73,86:0.5409:2,2:28:1:30.4:1:0.8345:1.11352:60:27.667:0.539:0:1.8 0/1:155:22:3,19:27,106:133,22:0.1419:2,2:21.4:1:28.8:1:0.57189:1.60879:60:21:0.1409:0:1.7 +9 93640131 . C T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12512;LSEQ=GGGCCCACCCCTGGATGGGC;RSEQ=GAGCAGCCTGATTTCCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:135:71:7,64:10,54:64,71:0.5259:2,2:28.9:1:31.1:1:0.43675:1.68649:60:70:0.5224:0:2 0/1:124:15:2,13:19,90:109,15:0.121:2,2:22.7:1:30.5:1:1:1.36898:60:30:0.121:0:2 +9 93640226 . T C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01193;SOR=0.12599;LSEQ=GACAGAGGGACAGGGAGACA;RSEQ=AGTCTTTGGATTCAGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:21:0,21:0,10:10,21:0.6774:0,1:23.2:1:30.5:1:1:0:58.9:6:0.6429:0:1.5 0/1:10:2:0,2:0,8:8,2:0.2:0,0:30:1:33.5:1:1:0:60:4:0.2:0:1.5 +9 93640294 . T C 84 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0.53451;LSEQ=CATTTGACAGTTTTGTCTTT;RSEQ=TTTTCTTCCTGTAGTCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,3:3,6:0.6667:0,0:6.8:1:32.7:1:1:0:60:12:0.6667:0:1.8 1/0:2:1:0,1:0,1:1,1:0.5:0,0:5:0:32:0:1:0:60:2:0.5:0:2 +9 93640832 . G A 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTTGCAATTCCAAGCAT;RSEQ=CCAGGAAACTCAATCCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:4,0:5,0:5,4:0.4444:0,0:30.3:1:29.8:1:1:0:55.3:8:0.4444:0:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:19:0:33:0:1:0:60:2:1:0:0 +9 93640872 . C A 100 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.61462;SOR=0.319;LSEQ=TGAACACCAGGAGAATATGG;RSEQ=ATTGAGTCCTGAAGAGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:9,0:11,0:11,9:0.45:0,0:22.8:1:31.6:1:1:0:57.9:18:0.45:0:2.2 0/1:5:1:1,0:4,0:4,1:0.2:0,0:16:0:30:0:1:0:60:2:0.2:0:2 +9 93640895 . G A 115 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00387;SOR=0.07411;LSEQ=TGAGTCCTGAAGAGCTATAT;RSEQ=CTAACAAAGTTATTTGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:15,0:17,0:17,15:0.4688:1,1:21.5:1:29.5:1:1:0:60:30:0.4688:0:1.6 0/1:17:1:1,0:16,0:16,1:0.0588:1,0:39:0:30:0:1:0:60:2:0.0588:0:2 +9 93641175 . C T 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13136;LSEQ=TTGCTAGTTACCCAACATTA;RSEQ=GCCAAGATCAGTGATTTCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:637:327:148,179:143,163:306,327:0.5133:2,2:24.6:1:30.7:1:0.74971:1.06094:59.7:162.5:0.5151:0:1.6 0/1:683:83:41,42:273,327:600,83:0.1215:2,2:26.7:1:29.5:1:0.55728:1.17:60:40.5:0.1202:0:1.3 +9 93641193 . C T 157 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TACGCCAAGATCAGTGATTT;RSEQ=GGACTTTCCAAAGCACTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:610:38:14,24:252,319:571,38:0.0623:2,2:20.6:1:30.1:1:0.40394:1.35357:60:37:0.0615:0:1.1 0/0:617:0:0,0:270,346:616,0:0:2,0:24.7:1:29.5:1:1:0:60:40.067:0.9983:0:0.3 +9 93641199 . T C 252 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.08109;LSEQ=AAGATCAGTGATTTCGGACT;RSEQ=TCCAAAGCACTGCGTGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:221:92,129:165,199:364,221:0.3778:2,2:24.7:1:32.4:1:0.39154:1.16231:59.9:72.667:0.3759:0:2 0/1:598:28:11,17:241,328:569,28:0.0468:2,2:21:1:30.7:1:0.84575:1.13526:60:56:0.0469:0:1.9 +9 93641282 . G A 204 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.16645;LSEQ=AGCAGCAGGTGGTAAAAAAT;RSEQ=CAAGATAAATGTACGTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:110:13,97:19,94:113,110:0.4933:2,2:24.3:1:30.2:1:0.34131:1.50541:60:109:0.4955:0:1.3 0/1:180:25:5,20:25,130:155,25:0.1389:2,2:21.7:1:29.2:1:0.57431:1.30:60:50:0.1397:0:1.2 +9 93641296 . C T 140 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAAAATGCAAGATAAATGTA;RSEQ=GTTTTCTTTATTTTATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:13,158:171,0:0:2,0:22.7:1:30.5:1:1:0:60:170:1:0:0.5 0/1:134:29:2,27:13,92:105,29:0.2164:2,2:19.8:1:28.9:1:0.52271:1.89974:60:28:0.2121:0:1 +9 93649829 . A C 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06776;SOR=Inf;LSEQ=TCCCAAGTAGCTGGAATTAC;RSEQ=GGCACCCGCCACCACACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:13,0:13,0:0:1,0:18.5:1:30.3:1:1:0:41.1:26:1:0:0 0/1:10:3:3,0:7,0:7,3:0.3:0,0:22:1:29.3:1:1:0:38.7:6:0.3:0:1 +9 93649968 . A T 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1276;SOR=0;LSEQ=GTGCTGGGATTACAGGCATG;RSEQ=ACCAATGTGCCCGGCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:4:1,3:251,58:309,4:0.0128:2,2:18.3:1:24.3:1:0.02445:12.83552:59.3:8:0.0132:0:1 0/0:271:0:0,0:207,64:271,0:0:2,0:20.2:1:28.5:1:1:0:59.8:89.333:1:0:0.3 +9 93650015 . T A 208 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=92.41128;LSEQ=TTCTTAATGGAATTTCTCCC;RSEQ=CTGCTTTGCTTTTAGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:716:2:0,2:433,279:712,2:0.0028:2,0:44.5:1:17.5:1:0.15455:0:60:1:0.0014:0:1 0/1:699:144:84,60:330,225:555,144:0.206:2,2:25.6:1:29.1:1:0.84918:1.04752:60:71:0.2085:0:1.2 +9 93650231 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.16955;SOR=Inf;LSEQ=TAGAACAGATAAGCACCAGA;RSEQ=TGTCTTTACAACAACCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:0:0,0:18,187:205,0:0:2,0:23.2:1:30.4:1:1:0:60:101.5:1:0:0.1 0/1:144:2:1,1:15,127:142,2:0.0139:2,2:35:1:31.5:1:0.21057:8.23:60:4:0.0142:0:1 +9 93650245 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51614;SOR=0;LSEQ=ACCAGATTGTCTTTACAACA;RSEQ=CCTGAAAATCCTAATCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:2:1,1:6,139:145,2:0.0136:1,2:23:1:31:1:0.09328:21.52:60:4:0.014:0:1 0/0:100:0:0,0:10,90:100,0:0:2,0:23:1:29.4:1:1:0:60:200:1:0:0.1 +9 93650322 . G A 109 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00965;SOR=0;LSEQ=CCCTCAGTCTATTCCAAACT;RSEQ=AGAATGAAATATCTGATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:13:0,13:3,18:21,13:0.3824:2,1:20.3:1:29.6:1:0.27005:0:60:12:0.3636:0:1 0/0:14:0:0,0:0,14:14,0:0:1,0:29.7:1:30.3:1:1:0:60:28:1:0:0.2 +9 93650755 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25348;SOR=Inf;LSEQ=TTGTTTTGTTTGACTAACAC;RSEQ=TTTAAAAAAAAAAAAGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:164,54:218,0:0:2,0:20.5:1:30.8:1:1:0:59.6:20.8:1:0:0.5 0/1:257:3:1,2:185,69:254,3:0.0117:2,2:16.7:1:30:1:0.18574:5.32096:60:6:0.0119:0:1 +9 93650758 . TA T 146 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.88901;SOR=0.92726;LSEQ=TTTTGTTTGACTAACACCTT;RSEQ=AAAAAAAAAAAGCTTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:28:17,11:147,49:196,28:0.1167:2,2:21.1:1:31:1:0.11604:1.93486:59.8:56:0.1212:0.0208:0.1 0/1:275:30:21,9:167,66:233,30:0.1091:2,2:30.6:1:29.8:1:0.83235:1.08407:59.1:60:0.1128:0:0.4 +9 93650759 . A T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=0.58867;SOR=1.58883;LSEQ=TTTGTTTGACTAACACCTTT;RSEQ=AAAAAAAAAAAGCTTATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:5:3,2:147,49:196,5:0.0208:2,2:10.4:1:29.4:1:0.60264:1.99219:60:10:0.0216:0:1 0/1:275:9:5,4:167,66:233,9:0.0327:2,2:8.4:1:27.9:1:0.28642:2.01773:60:18:0.0338:0:1 +9 93650771 . G T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1276;SOR=Inf;LSEQ=ACACCTTTAAAAAAAAAAAA;RSEQ=CTTATGCATATCTTGCATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:302:0:0,0:201,99:300,0:0:2,0:21.9:1:31.4:1:1:0:59.9:15.667:1:0:0.4 0/1:348:4:1,3:225,119:344,4:0.0115:2,2:15:1:24.8:1:0.12572:5.64316:60:8:0.0121:0:1 +9 93650950 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50087;SOR=0;LSEQ=GTGATGTATTCAGATGCTCT;RSEQ=GAAACAGGTGAAATGGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:190:2:1,1:35,153:188,2:0.0105:2,2:19:1:27:1:0.34386:4.32:60:4:0.0105:0:1 0/0:166:0:0,0:39,127:166,0:0:2,0:25.5:1:30.5:1:1:0:60:165:1:0:0 +9 93650976 . TA T 49 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.78882;LSEQ=AGGTGAAATGGTTGGGCGTC;RSEQ=AAAAAAAGGATAAAGTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:1,2:6,98:104,3:0.028:2,2:21:1:31.3:1:0.18533:7.81:60:6:0.0286:0:0 0/1:90:2:0,2:15,73:88,2:0.0222:2,0:39.5:1:33:0:1:0:60:4:0.0222:0:0 +9 93657740 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21253;SOR=Inf;LSEQ=CACTGGTACTCAGCCTGCAG;RSEQ=GGCCCTGCTTGTGATCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:160,37:197,0:0:2,0:22.7:1:30.4:1:1:0:60:48.25:1:0:1 0/1:169:2:1,1:131,36:167,2:0.0118:2,2:24:1:29.5:1:0.39096:3.60271:60:4:0.0119:0:1 +9 93657745 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22271;SOR=Inf;LSEQ=GTACTCAGCCTGCAGAGGCC;RSEQ=TGCTTGTGATCAGCAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:174,47:221,0:0:2,0:22.3:1:31.8:1:1:0:60:442:1:0:1 0/1:198:2:1,1:146,50:196,2:0.0101:2,2:8.5:1:28.5:1:0.44978:2.90126:60:4:0.0102:0:2.5 +9 93657761 . A T 255 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGCCCTGCTTGTGATCAGCA;RSEQ=TTTTTCACAAGCACATTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:296:296:214,82:0,0:0,296:1:0,2:23.3:1:31.1:1:1:0:60:295:1:0:1.1 1/0:293:189:133,56:73,31:104,189:0.6451:2,2:22.7:1:30:1:1:1.01:60:378:0.6517:0:1.1 +9 93657832 . G A 82 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01331;SOR=8.85028;LSEQ=TGGAAAACAGGCCCGGATTC;RSEQ=CAGCAGTGGAACTGCGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:616:1:1,0:311,303:614,1:0.0016:2,0:1:0:29:0:1:0:60:2:0.0016:0:3 0/1:704:10:6,4:369,323:692,10:0.0142:2,2:23.7:1:24.9:1:0.75794:1.31:60:4:0.0116:0:1.6 +9 93657958 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49861;SOR=Inf;LSEQ=TGTATCCAGAGGAATTGATT;RSEQ=TCAGCCACCTCCCTCTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:20,128:148,0:0:2,0:21.7:1:32.4:1:1:0:60:147:1:0:0.1 0/1:155:2:1,1:28,125:153,2:0.0129:2,2:17:1:28.5:1:0.34018:4.40:60:4:0.0131:0:1 +9 93659079 . C A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCACTTTAGGAGGCCGAGG;RSEQ=GGGTGGATCACTTGAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:31:1:1:0:45:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 94661354 . C T 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57328;SOR=0.35629;LSEQ=CGTGTGTCAGGACAAACAGC;RSEQ=GCCAAGAGCTGCCTGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:80,40:120,2:0.0164:2,2:8.5:1:30:1:1:1.98783:60:4:0.0167:0:1 0/0:170:1:0,1:100,69:169,1:0.0059:2,0:1:0:25:0:0.41176:0:60:2:0.0061:0:1 +9 94661448 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.26342;SOR=Inf;LSEQ=AAACACATGGACCGGAAAGG;RSEQ=CCCCCAGGGGGTGCGGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:51,88:139,0:0:2,0:23.6:1:31.6:1:1:0:60:138:1:0:0 0/1:186:3:2,1:75,108:183,3:0.0161:2,2:19.3:1:25.7:1:0.5705:2.86:60:6:0.0164:0:1 +9 94661537 . G A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05066;SOR=Inf;LSEQ=GCAAATAGGTGGCATTATCT;RSEQ=CTGGGAGCCTCTGCAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:0,19:19,0:0:1,0:19.7:1:32.2:1:1:0:60:18:1:0:0.2 0/1:22:5:0,5:0,17:17,5:0.2273:1,0:11.2:1:30.6:1:1:0:60:10:0.2273:0:1 +9 94768173 . A T 112 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=16.000;MSILEN=1;SSF=0.02505;SOR=0.12484;LSEQ=CCATCTCAAAAAAAAAAAAA;RSEQ=AATAATAATAATAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:10,1:7,0:7,11:0.6111:0,2:11.2:1:32.4:1:1:0:60:22:0.6111:0:1 0/1:13:2:2,0:10,0:10,2:0.1538:0,0:35:1:28.5:1:1:0:49.5:4:0.1538:0:1 +9 94768176 . T A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.27899;SOR=0;LSEQ=TCTCAAAAAAAAAAAAAAAA;RSEQ=AATAATAATAAATAAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:3,0:18,1:19,3:0.1364:1,0:8:1:32.7:1:1:0:60:6:0.1364:0:1 0/0:13:0:0,0:13,0:13,0:0:1,0:20:0:12:0:1:0:60:0:0:0:5 +9 94768377 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1213;SOR=Inf;LSEQ=AGGGAAAGGGGAGAGGCACC;RSEQ=GATATGTGTTCTCTAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:73,130:203,0:0:2,0:23.5:1:30.1:1:1:0:58.3:66.667:1:0:0.1 0/1:200:3:1,2:72,124:196,3:0.015:2,2:24:1:27:1:1:1.16047:45.3:6:0.0152:0:1 +9 94768388 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50116;SOR=0;LSEQ=AGAGGCACCCGATATGTGTT;RSEQ=TCTAGGCCTTTTGGAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:2:0,2:54,109:163,2:0.012:2,0:14.5:1:28:1:1:0:60:4:0.0123:0:1 0/0:143:0:0,0:52,91:143,0:0:2,0:20.5:1:30.8:1:1:0:57.2:286:1:0:0.1 +9 94768402 . GA G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.17287;SOR=Inf;LSEQ=TGTGTTCTCTAGGCCTTTTG;RSEQ=AAACATGGAGTTGTTCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:41,96:137,0:0:2,0:23.5:1:30.5:1:1:0:59:44.667:1:0:0.1 0/1:98:2:1,1:27,69:96,2:0.0204:2,2:24.5:1:28:1:0.4919:2.53:48.5:4:0.0206:0.0102:0 +9 94768542 . A G 156 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAACTGGAAGAGTCTACAAT;RSEQ=TTACCCAGCATGCTCTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:20,40:60,0:0:2,0:27.8:1:29.3:1:1:0:60:19:1:0:0.2 1/0:61:35:16,19:11,15:26,35:0.5738:2,2:28.6:1:30.6:1:1:1.15:54.1:34:0.5763:0:1.1 +9 95232038 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16944;SOR=0;LSEQ=CAGAGTCAGCGAGGCAGGAG;RSEQ=TGTGCTGAGGGGAGGCGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:6,10:16,2:0.1111:2,2:28.5:1:28.5:1:1:1.62:60:4:0.1111:0:1 0/0:25:0:0,0:12,13:25,0:0:2,0:26.9:1:31.1:1:1:0:60:11.5:1:0:0.3 +9 95439427 . A G 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.0515;SOR=0;LSEQ=GAGCTTAATGTGCTCAATAC;RSEQ=CACGTTAATTCTCTTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:4,2:6,1:7,6:0.4615:2,2:28.2:1:31.8:1:0.55944:2.75172:44.5:12:0.4615:0:1.3 0/0:7:0:0,0:6,1:7,0:0:2,0:25.1:1:30.7:1:1:0:59.4:14:1:0:0.1 +9 95439439 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48308;SOR=0;LSEQ=CTCAATACACACGTTAATTC;RSEQ=CTTGGCAAGAATCTTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:10,2:12,2:0.1429:2,2:32.5:1:31.5:1:0.3956:4.28175:48:4:0.1429:0:2 0/0:12:0:0,0:10,2:12,0:0:2,0:20.7:1:31.2:1:1:0:59.7:24:1:0:0.1 +9 95439555 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54902;SOR=Inf;LSEQ=CATTCCTTTTTGAACAGTAC;RSEQ=TATTCTTTTGATGTCTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:23,0:0:2,0:25:1:32.1:1:1:0:59.8:46:1:0:0 0/1:46:2:1,1:24,20:44,2:0.0435:2,2:18:1:28:1:1:1.19523:60:4:0.0435:0:1.5 +9 95439677 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50343;SOR=Inf;LSEQ=GGGCCCCTCTTCTCTTCCCT;RSEQ=TGTGTTCATCATTTTGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:85,43:128,0:0:2,0:25:1:31:1:1:0:59:127:1:0:0.2 0/1:157:2:1,1:96,59:155,2:0.0127:2,2:28.5:1:29.5:1:1:1.62182:60:4:0.0131:0:1 +9 95439693 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17968;SOR=0;LSEQ=CCCTTTGTGTTCATCATTTT;RSEQ=GCAAATTACTGGAAGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:75,53:128,2:0.0154:2,2:34.5:1:32:0:1:1.41122:60:4:0.0155:0:1 0/0:176:0:0,0:93,83:176,0:0:2,0:29.3:1:30.7:1:1:0:59.6:175:1:0:0.2 +9 95439721 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16835;SOR=0;LSEQ=ACTGGAAGATGGCGCTTCCA;RSEQ=CCAAAAGGCAGAACTTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:2:1,1:53,61:114,2:0.0172:2,2:16.5:1:29.5:1:1:1.15:60:4:0.0172:0:1 0/0:166:0:0,0:74,92:166,0:0:2,0:26.7:1:30:1:1:0:59.6:17.444:1:0:0.2 +9 95439722 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16662;SOR=0;LSEQ=CTGGAAGATGGCGCTTCCAG;RSEQ=CAAAAGGCAGAACTTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:2,0:51,62:113,2:0.0174:2,0:15.5:1:30:1:0.21022:0:49:4:0.0175:0:1 0/0:166:0:0,0:73,93:166,0:0:2,0:26.2:1:30:1:1:0:59.6:82:1:0:0.2 +9 95439768 . T A 25 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86183;LSEQ=GATGGCATTAATCCCACCTA;RSEQ=GAGGACAGAGCCCTTATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:1,0:11,47:58,1:0.0169:2,0:1:0:26:0:0.20339:0:60:2:0.0182:0:1 0/1:64:2:1,1:5,57:62,2:0.0313:2,2:9:1:25:1:0.18006:10.50:42.5:4:0.0345:0:4.5 +9 95439897 . G A 49 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAACCTCTGCCTTGCAG;RSEQ=TTCAAGTGATTCTCCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:0,3:0,3:3,3:0.5:0,0:20.3:1:31.3:1:1:0:60:6:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 95625972 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATAGTGTCATATACTGAAG;RSEQ=AGAGATTGATGAATGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41.5:1:32:1:1:0:60:4:1:0:1 +9 95626730 . A C 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=10.000;MSILEN=1;SSF=1;SOR=1.87936;LSEQ=GACATAGAGAACAACAACAA;RSEQ=AAAAAAAGGTGTATAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:1:0,1:0,4:4,1:0.2:0,0:15:0:34:0:1:0:60:2:0.2:0:1 0/1:6:2:1,1:0,4:4,2:0.3333:0,2:10.5:1:29.5:1:0.33333:0:60:4:0.3333:0:1 +9 97401653 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49499;SOR=0;LSEQ=CAGGTGCGGGGCTGCAGGTG;RSEQ=GGGCGGCAAGAGAGGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:29,2:0.0645:2,2:11:1:26.5:1:1:1.22249:60:4:0.0645:0:1 0/0:26:0:0,0:12,14:26,0:0:2,0:21.5:1:28:1:1:0:60:12:1:0:0.1 +9 97401786 . G A 33 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTCCGCAGCGCTCGTG;RSEQ=TGCAACTGGGCCAGGCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:31.5:1:33:0:1:0:60:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 97408513 . G A 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGGCAGTTCCAAAGAC;RSEQ=GATGACAGCTGAGCACCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:33:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 97409370 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49231;SOR=Inf;LSEQ=ACAAAATAGCATGAGAAAGC;RSEQ=GAAGTGAGTGTGTAACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:26.9:1:30.7:1:1:0:60:22:1:0:0.3 0/1:15:2:1,1:7,6:13,2:0.1333:2,2:33:1:28.5:1:1:1.1547:60:4:0.1333:0:1 +9 97409419 . G T 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.23636;SOR=Inf;LSEQ=AGTGGAGCGTGTTAGTGAGA;RSEQ=AGGAGTCAGCGTGCCCCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:28,0:0:2,0:17:1:32.6:1:1:0:60:27:1:0:0.3 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:6.5:1:26.5:1:1:1.0801:60:4:0.0741:0:1.5 +9 97409437 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.19831;SOR=0;LSEQ=GAGAGGAGTCAGCGTGCCCC;RSEQ=AGAGCCGGTGGGCGAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:18:0:32.5:1:1:1.0801:60:4:0.0769:0:1.5 0/0:33:0:0,0:17,16:33,0:0:2,0:19.9:1:30.4:1:1:0:59.1:66:1:0:0.4 +9 97409450 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.23469;SOR=Inf;LSEQ=GTGCCCCGAGAGCCGGTGGG;RSEQ=GAGGCCACGGAGGGAGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:25,0:0:2,0:25.8:1:31.3:1:1:0:60:50:1:0:0.4 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:40.5:1:30:1:1:1.19087:60:4:0.087:0:1 +9 97409454 . G C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48936;SOR=0;LSEQ=CCCGAGAGCCGGTGGGCGAG;RSEQ=CCACGGAGGGAGGGCGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:11,11:22,2:0.0833:2,2:26:1:30.5:1:1:1:60:4:0.0909:0:1 0/0:24:0:0,0:13,11:24,0:0:2,0:31.5:1:31.6:1:1:0:60:48:1:0:0.4 +9 97863896 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50875;SOR=0;LSEQ=CAGCCCAGCGAGGGCACTTA;RSEQ=TCCACAAATGCGTGGCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:2,0:126,0:126,2:0.0156:1,0:35.5:1:33:0:1:0:60:4:0.0159:0:1 0/0:95:0:0,0:91,4:95,0:0:1,0:23.6:1:31.4:1:1:0:60:46.5:1:0:0.1 +9 97869591 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.07824;SOR=Inf;LSEQ=AGGGGAGAGGTTAGGAAGAG;RSEQ=CAGGACAGACATACTTCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:0:0,0:94,286:380,0:0:2,0:24:1:32.2:1:1:0:59.9:62.333:1:0:0.1 0/1:285:3:2,1:83,199:282,3:0.0105:2,2:8.3:1:25.3:1:0.2129:4.77:60:6:0.0105:0:1 +9 97869692 . A G 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19294;SOR=2.3392;LSEQ=GGGAGCTAGGCAGCGGCCGA;RSEQ=TTTACACTCGATTTCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:0,6:1,44:45,6:0.1176:1,0:24:1:32.2:1:1:0:60:12:0.1176:0:1 0/1:25:6:0,6:0,19:19,6:0.24:1,0:26.3:1:31.8:1:1:0:60:12:0.25:0:1.2 +9 97873339 . G A 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00142;SOR=5.18714;LSEQ=GATGGAAGCAAGCCCTGGCC;RSEQ=GGCTGCTGGGGAGCGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:6:6,0:71,0:71,6:0.0779:1,0:25.5:1:30.5:1:1:0:60:12:0.0789:0:1 0/1:52:16:14,2:34,2:36,16:0.3077:2,2:31:1:29.2:1:0.57802:2.38266:60:32:0.3137:0:1.3 +9 97873432 . G T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.07495;SOR=Inf;LSEQ=GCCTCTGCAGGGCACGCCTT;RSEQ=GAGGACGCGACCCTGGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:0:0,0:272,97:369,0:0:2,0:22.9:1:31.8:1:1:0:60:51.714:1:0:0.3 0/1:270:3:1,2:183,84:267,3:0.0111:2,2:9:1:27.3:1:0.23885:4.33088:60:6:0.0112:0:1 +9 97873435 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.02423;SOR=1.60704;LSEQ=TCTGCAGGGCACGCCTTGGA;RSEQ=GACGCGACCCTGGGGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:56:41,15:244,92:336,56:0.1425:2,2:21.8:1:31.1:1:1:1.03:60:112:0.1458:0:1.1 0/1:294:62:47,15:152,80:232,62:0.2109:2,2:23.4:1:29.8:1:0.12998:1.65:59.9:61:0.2096:0:1.1 +9 97873553 . G A 103 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00161;SOR=12.40077;LSEQ=GTCTCGTCTCTGGCCACCTC;RSEQ=GTGGGGACAGGAGAACGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:882:1:0,1:420,461:881,1:0.0011:2,0:22:0:34:0:1:0:60:2:0.0011:0:1 0/1:864:12:8,4:399,453:852,12:0.0139:2,2:27.3:1:29:1:0.24472:2.27:59.6:24:0.0141:0:1.1 +9 97873698 . C T 59 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=1;SOR=1.11934;LSEQ=TCTCTGCAAGCTCCTCTCAG;RSEQ=CCCCCAGAGCCCACCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:5:4,1:234,217:451,5:0.0109:2,2:18.8:1:25.8:1:0.37467:3.70:60:4:0.009:0:1.6 0/1:327:4:1,3:172,151:323,4:0.0122:2,2:9.8:1:22.3:1:0.34602:3.40535:60:1:0.0063:0:2.5 +9 97873931 . G A 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11925;SOR=0.19342;LSEQ=CCGCAGGACCTGGAACAGAG;RSEQ=CAGAACACATGGCAGTTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:5:4,1:122,327:449,5:0.011:2,2:8.6:1:27:1:0.02244:10.66:60:4:0.009:0:1.2 0/0:466:1:1,0:148,317:465,1:0.0021:2,0:1:0:23:0:0.31974:0:60:2:0.0022:0:1 +9 97873957 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00083;SOR=1.98982;LSEQ=CACATGGCAGTTGACAACCT;RSEQ=AATTCTTCTTCCTTTGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:48:10,38:30,200:230,48:0.1727:2,2:25.2:1:32.3:1:0.17629:1.75:60:96:0.1758:0:1.1 0/1:269:79:14,65:33,157:190,79:0.2937:2,2:23.2:1:31.1:1:1:1.02:60:78:0.2932:0:1.1 +9 97873995 . G A 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04585;SOR=Inf;LSEQ=GTTTTTAAAGCAACTTTAAC;RSEQ=TTTGCCAACGGTTGGCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:3,116:119,0:0:1,0:23.9:1:32.5:1:1:0:60:238:1:0:0.2 0/1:104:4:0,4:4,96:100,4:0.0385:1,0:23:1:31.5:1:1:0:60:8:0.0385:0:2 +9 97879887 . A AAAATAAT 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.04817;SOR=0.09834;LSEQ=AAGTCACCTTCTGGGACTTA;RSEQ=AAATTTATGCTCTTGATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:16:0,16:0,2:2,16:0.8889:0,1:25:1:31:1:1:0:60:32:0.8889:0.2778:0.1 0/1:5:2:0,2:0,3:3,2:0.4:0,0:31:1:31.3:0:1:0:60:4:0.4:0:0 +9 97887335 . G T 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2174;SOR=4.86443;LSEQ=CAACAGCGTCTTATTCTCTG;RSEQ=GATGAATGAGTAATATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:384:1:1,0:266,116:382,1:0.0026:2,0:48:0:14:0:1:0:60:0:0:0:3 0/1:398:5:2,3:270,123:393,5:0.0126:2,2:17:1:27:1:0.33174:3.28168:60:10:0.0128:0:1 +9 97888730 . C T 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CCCCATGATACAGCCAGAGA;RSEQ=TACCACAACATTTTCTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:323:0:0,0:263,60:323,0:0:2,0:24.2:1:32.5:1:1:0:60:63.6:1:0:0.1 0/1:337:17:13,4:248,71:319,17:0.0504:2,2:22:1:29.3:1:1:1.07453:60:16:0.048:0:1.1 +9 97888955 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1735;SOR=Inf;LSEQ=AAAGGAGTTACTGGGAACTG;RSEQ=TGATGTCCAGAAAACTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:10,170:180,0:0:2,0:25.2:1:33:1:1:0:59.8:44:1:0:0.1 0/1:129:2:0,2:8,119:127,2:0.0155:2,0:25:1:29.5:1:1:0:60:4:0.0156:0:1 +9 97897840 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=3;SSF=0.23487;SOR=0;LSEQ=ATGGCTCACTGAAAAAAGAA;RSEQ=ATTAAAAAAAGTTCAAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:7,94:101,2:0.0194:2,2:14.5:1:27:1:0.15001:12.63:60:4:0.0194:0:4.5 0/0:109:0:0,0:11,98:109,0:0:2,0:24:1:30.7:1:1:0:60:108:1:0:0.1 +9 97931108 . G A 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCATGTGCCACCGCACCTG;RSEQ=CCTAAATTGTGTACTGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:26.5:1:1:0:60:4:1:0:1 +9 97933252 . T C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00025;SOR=2.94321;LSEQ=AATAATCTTTCTATATAAAA;RSEQ=ACAACCATAACTGAACATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:20:17,3:115,16:131,20:0.1325:2,2:21.7:1:31.6:1:0.71948:1.26625:60:40:0.1333:0:1.2 0/1:148:46:34,12:84,18:102,46:0.3108:2,2:20.5:1:30.8:1:0.27179:1.64113:60:45:0.3061:0:1.1 +9 97933268 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24823;SOR=Inf;LSEQ=AAAATACAACCATAACTGAA;RSEQ=ATCCATTTCCTATGAATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:197:0:0,0:160,37:197,0:0:2,0:22.4:1:32.4:1:1:0:60:196:1:0:0.2 0/1:202:3:1,2:148,51:199,3:0.0149:2,2:11.3:1:25:1:0.16902:5.74266:60:6:0.0151:0:2.3 +9 98002436 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGAGTGAGCAGCAGAGGC;RSEQ=GCGCAGCACCAAGATCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:26.5:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 98009492 . CGCGTGT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=12.000;MSILEN=2;SSF=0.03968;SOR=Inf;LSEQ=GATCTGCATGGGTGCGTGCA;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:21,1:22,0:0:1,0:32.4:1:28.6:1:1:0:60:21:1:0:0.1 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:12:1:29:1:1:0:60:4:0.3333:0.1667:1 +9 98009494 . CGT C 98 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=12.000;MSILEN=2;SSF=0.41053;SOR=0.33626;LSEQ=TCTGCATGGGTGCGTGCACG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:8,0:19,1:20,8:0.2759:1,0:22.8:1:32.9:1:1:0:57:16:0.2759:0.1034:0.6 0/1:9:1:1,0:7,0:7,1:0.1111:0,0:42:0:32:0:1:0:60:2:0.125:0:0 +9 98009613 . TA T 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.03616;SOR=0.45594;LSEQ=CATTTGATAAGTTGTTCCAT;RSEQ=AAAAAAAAAAACTAGGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:25:23,2:139,5:144,25:0.1471:1,2:24.8:1:30.9:1:0.27664:2.40097:59:50:0.1497:0.0353:0.6 0/1:165:12:12,0:138,12:150,12:0.0727:2,0:28.2:1:31.4:1:0.60247:0:60:24:0.0736:0.0061:0.1 +9 98009794 . G C 156 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATCTTTCAATGACTGTATTA;RSEQ=AATCCTGTGAAAGAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:28:11,17:215,361:576,28:0.0461:2,2:26.2:1:32.5:1:0.84344:1.09:60:56:0.0467:0:1.1 0/0:603:0:0,0:221,380:601,0:0:2,0:23.7:1:30.5:1:1:0:60:199.333:0.9967:0:0.1 +9 98011320 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24099;SOR=Inf;LSEQ=CTTCAGTCAATACCACAAGT;RSEQ=CCGATTCTGGGTGGCATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:119,7:126,0:0:2,0:25.1:1:32:1:1:0:59.7:62:1:0:0.1 0/1:122:2:1,1:110,10:120,2:0.0164:2,2:15:1:26.5:1:0.17288:10.53577:60:4:0.0165:0:1.5 +9 98011608 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.12146;SOR=Inf;LSEQ=AAAGGTGATGTCCCTTCACA;RSEQ=CAGCCTGTCCAGCACTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:58,207:265,0:0:2,0:25.5:1:32.4:1:1:0:59.9:87.333:1:0:0.1 0/1:261:3:2,1:74,184:258,3:0.0115:2,2:20.3:1:28.7:1:0.20399:4.94:60:6:0.0115:0:1 +9 98209594 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0;SOR=4.7486;LSEQ=CGTCTCTGCGCGGTCTGTAG;RSEQ=GGGGTGGCCACAAGCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:27:15,12:160,139:299,27:0.0828:2,2:23.7:1:30.6:1:1:1.09:60:54:0.0849:0:1 0/1:336:101:62,39:119,116:235,101:0.3006:2,2:24.1:1:29.2:1:0.07452:1.55:60:49.5:0.3037:0:1.1 +9 98209693 . G A 176 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=52.48254;LSEQ=CCAGGTGGGGCTGCTGTCTC;RSEQ=GGTTCGAGGGTGGGTGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:593:1:1,0:292,300:592,1:0.0017:2,0:1:0:28:0:0.4941:0:60:2:0.0017:0:1 0/1:699:57:28,29:312,328:640,57:0.0815:2,2:26.9:1:30.3:1:1:1.02:60:114:0.0827:0:1.3 +9 98209764 . G T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24886;SOR=0;LSEQ=TGAGGGTGGGTTAGAAGGGT;RSEQ=GTATCCCAGGCTGGGCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:299:3:2,1:83,212:295,3:0.01:2,2:30.3:1:31.3:1:0.19678:5.08:60:6:0.0102:0:1 0/0:291:0:0,0:91,200:291,0:0:2,0:20.7:1:30.1:1:1:0:60:40.571:1:0:0.2 +9 98209777 . G A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.25038;SOR=0;LSEQ=GAAGGGTGGTATCCCAGGCT;RSEQ=GGCATGGTCCCCGCAGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:3:2,1:43,166:209,3:0.0142:2,2:20:1:21.3:1:0.11466:7.62:60:2:0.0096:0:1 0/0:190:0:0,0:50,140:190,0:0:2,0:20.7:1:30.5:1:1:0:60:62.333:1:0:0.1 +9 98209907 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13937;SOR=Inf;LSEQ=TCTAATAACCTCCAGGACCT;RSEQ=GCGGAGGAGCGTGTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:0,26:26,0:0:1,0:19.8:1:32:1:1:0:60:52:1:0:0.1 0/1:16:2:1,1:2,12:14,2:0.125:2,2:9.5:1:27:1:0.35:5.10:60:4:0.125:0:1.5 +9 98211012 . G GA 49 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=15.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGACATGCACCTTAAGAG;RSEQ=AAAAAAAAAAAAAAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:5,0:5,3:0.375:0,0:18:1:31.3:1:1:0:59:6:0.375:0.125:2.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 98211572 . T A 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGTGGCTCAGGGGAGGGTG;RSEQ=GGGCAGGCGGTTCAAGCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:648:0:0,0:270,378:648,0:0:2,0:25.2:1:30:1:1:0:60:63.8:1:0:0.2 0/1:661:34:15,19:288,339:627,34:0.0514:2,2:22.3:1:29.3:1:0.86177:1.07601:60:68:0.0518:0:1.2 +9 98211643 . C A 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24872;SOR=0;LSEQ=ATGTTAAAAGTGTTCTTGTC;RSEQ=ATTTACCTGCTGGCCACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:3:2,1:84,204:288,3:0.0103:2,2:8:1:28.3:1:0.20951:4.83:60:6:0.0105:0:1 0/0:288:0:0,0:100,188:288,0:0:2,0:23.5:1:30.6:1:1:0:60:56.6:1:0:0.1 +9 98212282 . C T 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49865;SOR=Inf;LSEQ=GGGTGGATCGCGCCACCCTC;RSEQ=GTGTGCCCGACACAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:21,159:180,0:0:2,0:22.7:1:29.7:1:1:0:60:35:1:0:0.1 0/1:183:2:1,1:26,155:181,2:0.0109:2,2:7.5:1:30:1:0.274:5.87:60:4:0.0112:0:1 +9 98215421 . A AT 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCACCTGAGCTAATAACAAT;RSEQ=TTTTTTTTTTTGAGACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:36.5:1:30.5:1:1:0:52.5:4:0.5:0:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 98215631 . T C 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02579;SOR=Inf;LSEQ=CCATCTTGGCCAGGCTGGTC;RSEQ=TGAACTCCTTGACCTTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:71,0:71,0:0:1,0:26.4:1:32.1:1:1:0:55.1:70:1:0:0.2 0/1:49:4:4,0:45,0:45,4:0.0816:1,0:47:1:29.8:1:1:0:58.5:8:0.0833:0:1 +9 98215968 . C G 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03215;SOR=Inf;LSEQ=TGGTAAATGCTCAGCTCTGT;RSEQ=CTAAATGTTACAAGCTCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:16,129:145,0:0:2,0:22.1:1:31.8:1:1:0:60:71.5:1:0:0.1 0/1:108:4:0,4:20,84:104,4:0.037:2,0:14.5:1:29.5:1:1:0:60:8:0.0374:0:1 +9 98218474 . G GC 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13222;SOR=0.66452;LSEQ=CTGCCACGCACAGGGAGAAT;RSEQ=CAAGGTTCCCACTTGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:64:54,10:68,10:78,64:0.4476:2,2:23.8:1:32:1:0.6377:1.25719:60:128:0.4539:0.0839:0 0/1:123:43:37,6:71,9:80,43:0.3496:2,2:22.5:1:30.8:1:0.77397:1.27662:59.7:42:0.3471:0.0813:0.3 +9 98218744 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49832;SOR=Inf;LSEQ=GCGGGCAGGTCACCCTCTGG;RSEQ=GCTGCCCACAAGGGAGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:23,126:149,0:0:2,0:24.8:1:31.3:1:1:0:60:148:1:0:0.1 0/1:149:2:1,1:36,111:147,2:0.0134:2,2:30:1:30:1:0.43624:3.05:60:4:0.0139:0:1 +9 98220237 . A T 34 p8;q25;Bias STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24841;SOR=0;LSEQ=AAACAAAACTTCCCGGCTGC;RSEQ=GAAAGAGCTATGCTGAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:3:0,3:179,44:223,3:0.0133:2,0:7:1:21.7:1:0.00854:0:60:2:0.0089:0:1 0/0:221:0:0,0:170,51:221,0:0:2,0:22.1:1:29.4:1:1:0:59.9:72.667:1:0:0.2 +9 98220322 . A C 170 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGGCCGTCCAGGGGTTCAG;RSEQ=AGGAAGACAGCGCACACGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:631:0:0,0:387,243:630,0:0:2,0:24.7:1:30.3:1:1:0:59.9:47.462:0.9984:0:0.1 0/1:624:45:23,22:339,240:579,45:0.0721:2,2:23.2:1:31:1:0.3497:1.3504:60:44:0.0715:0:1.4 +9 98220556 . G A 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06208;SOR=Inf;LSEQ=AAAGGGAACTGGGCATACTC;RSEQ=ATGGGCTCTGCTGCCGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:0:0,0:154,257:411,0:0:2,0:24.3:1:30.8:1:1:0:59.9:67.5:0.9975:0:0.1 0/1:431:5:3,2:158,268:426,5:0.0116:2,2:10:1:27.8:1:0.36699:2.54:60:10:0.0118:0:1 +9 98220603 . G T 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.67298;SOR=0.60595;LSEQ=GAGAAGGGCACAGGTTAGGA;RSEQ=CAGCCCAGGGTAGAAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:3:1,2:41,156:197,3:0.015:2,2:18.3:1:30.3:1:0.50894:1.90:60:6:0.015:0:1 0/0:219:2:1,1:52,165:217,2:0.0091:2,2:19.5:1:29:1:0.42629:3.15:60:4:0.0095:0:1.5 +9 98221780 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17325;SOR=Inf;LSEQ=ATTGTTCTGTTTACACTTCT;RSEQ=AACCCTGGGTAGCGTCAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:157,12:169,0:0:2,0:22.4:1:32.7:1:1:0:59.8:83.5:1:0:0.2 0/1:121:2:1,1:108,11:119,2:0.0165:2,2:24.5:1:26.5:1:0.18926:9.44362:60:4:0.0168:0:1 +9 98221861 . T C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06814;SOR=0.78992;LSEQ=CCTCTGTAAGTTCCCAGACC;RSEQ=CCCGATAAAACGCTACTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:200:125,75:191,117:308,200:0.3937:2,2:25.8:1:30.9:1:0.92566:1.02:60:49:0.392:0:1.2 0/1:590:200:124,76:230,160:390,200:0.339:2,2:24.5:1:30:1:0.53442:1.13:59.9:99:0.3402:0:1.2 +9 98222104 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24713;SOR=Inf;LSEQ=CAGAGGCCTTTGAGAATGGG;RSEQ=TTGGGGGTAAACACACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:131:0:0,0:26,105:131,0:0:2,0:22.9:1:31.9:1:1:0:59.8:42.667:1:0:0.1 0/1:130:2:1,1:34,94:128,2:0.0154:2,2:32:1:28:1:0.4675:2.74:60:4:0.0156:0:1 +9 98224087 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61734;SOR=2.08049;LSEQ=TCAAGCAGCCTCCACCAGGG;RSEQ=AGCGGCCCCGCAGCCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:173:1:0,1:142,30:172,1:0.0058:2,0:1:0:25:0:0.17919:0:60:2:0.0058:0:1 0/1:167:2:1,1:143,22:165,2:0.012:2,2:13:1:26.5:1:0.2572:6.37932:60:4:0.012:0:1 +9 98224090 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24385;SOR=Inf;LSEQ=AGCAGCCTCCACCAGGGCAG;RSEQ=GGCCCCGCAGCCCTGGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:184:0:0,0:151,33:184,0:0:2,0:21.9:1:32:1:1:0:60:368:1:0:0.1 0/1:180:2:1,1:152,26:178,2:0.0111:2,2:11:1:27:1:0.27821:5.75576:60:4:0.0114:0:1.5 +9 98224360 . C G 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.8638;SOR=0.89353;LSEQ=AGCGGGGTGGGCTGAGGAGA;RSEQ=TGAGCAGGGCAGGGGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:28:1,27:2,48:50,28:0.359:1,1:20.9:1:31.1:1:1:1.12335:60:13:0.3421:0:1 0/1:72:24:3,21:1,47:48,24:0.3333:1,2:25.8:1:31.2:1:0.10476:6.52:60:48:0.3333:0:1 +9 98229297 . G A 169 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08891;SOR=0.62264;LSEQ=AGTCCATGAAACACGTCAGT;RSEQ=TTACATTCTAATCTAACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:59:58,1:92,5:97,59:0.3782:2,1:23.2:1:28.8:1:0.40967:3.13:60:58:0.3742:0:1.4 0/1:113:31:29,2:78,4:82,31:0.2743:1,2:19.8:1:28.2:1:0.66522:1.3411:60:62:0.2743:0:1.3 +9 98229389 . C G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.002;SOR=0.69957;LSEQ=AAGGACGAGAGCCTCCCACG;RSEQ=CGTCTTACCCTGAAGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:265:176,89:260,154:414,265:0.3886:2,2:23.2:1:31.5:1:0.36697:1.17:59.9:131.5:0.3885:0:1.2 0/1:663:204:122,82:276,183:459,204:0.3077:2,2:23.2:1:30.2:1:1:1.01369:60:28.143:0.3017:0:1.2 +9 98229707 . C T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24963;SOR=Inf;LSEQ=AAAAAGGAAGATCACCACTA;RSEQ=CTGGAACAGAAGAGGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:0:0,0:60,205:265,0:0:2,0:24.8:1:31.6:1:1:0:60:65.25:1:0:0.1 0/1:285:3:1,2:87,195:282,3:0.0105:2,2:37:1:30.3:1:1:1.12:60:6:0.0107:0:1.3 +9 98229745 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21989;SOR=Inf;LSEQ=CAAGGTCAGACCCCAGGGAG;RSEQ=ACCACTGACTCTTCCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:18,123:141,0:0:2,0:24.4:1:31.8:1:1:0:59.8:19.143:1:0:0.1 0/1:125:2:1,1:26,97:123,2:0.016:2,2:14:1:26.5:1:0.38671:3.68:60:4:0.0161:0:1 +9 98229754 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22006;SOR=Inf;LSEQ=ACCCCAGGGAGCACCACTGA;RSEQ=TCTTCCTGGACAAAGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:11,105:116,0:0:2,0:24.4:1:33.2:1:1:0:59.7:57:1:0:0.1 0/1:103:2:1,1:17,84:101,2:0.0194:2,2:18:1:28:1:0.32039:4.83:60:4:0.0196:0:1 +9 98230924 . AT A 120 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.57455;SOR=0.69721;LSEQ=ATGTATCATACTTAAACGAA;RSEQ=TTTTTTTTTTTTAAGGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:13,1:16,0:16,14:0.4375:1,1:24.4:1:31.6:1:0.46667:0:60:28:0.4375:0:0.5 0/1:20:7:7,0:11,0:11,7:0.35:0,0:24:1:30.4:1:1:0:60:14:0.35:0:0.3 +9 98230982 . G T 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18307;SOR=Inf;LSEQ=CAATCTGATGAACTCCAAAG;RSEQ=TTCTGTTATTTTTTTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:92,25:117,0:0:2,0:21.7:1:31.2:1:1:0:60:22.4:1:0:0.1 0/1:88:2:1,1:63,23:86,2:0.0227:2,2:5.5:1:25.5:1:0.47335:2.70266:60:4:0.0235:0:1.5 +9 98231008 . A G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07271;SOR=Inf;LSEQ=TTATTTTTTTGAAGACAGGA;RSEQ=GAGCCTTAAGTTGTGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:201:0:0,0:146,55:201,0:0:2,0:24.3:1:30.7:1:1:0:60:49.25:1:0:0.1 0/1:145:3:2,1:94,48:142,3:0.0207:2,2:20.7:1:31:1:1:1.02:60:6:0.0208:0:1 +9 98231043 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25102;SOR=0;LSEQ=GGCAGATTACCTTGGCTTTT;RSEQ=GTTTCAAGAGGAAAGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:2,1:183,92:275,3:0.0108:2,2:21:1:30.3:1:1:1.01:60:6:0.0109:0:1 0/0:248:0:0,0:154,94:248,0:0:2,0:24.6:1:31.1:1:1:0:60:81.667:1:0:0.2 +9 98231419 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.22046;SOR=Inf;LSEQ=CTGAGGTTCAACCTGAATCA;RSEQ=TCTGCTGACGCAGGGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:55,167:222,0:0:2,0:25.7:1:32.7:1:1:0:60:54.5:1:0:0.2 0/1:197:2:1,1:57,138:195,2:0.0102:2,2:18:1:28.5:1:0.50321:2.41:60:4:0.0104:0:1 +9 98231424 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19817;SOR=Inf;LSEQ=GTTCAACCTGAATCACTCTG;RSEQ=TGACGCAGGGGCTGAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:0:0,0:46,168:214,0:0:2,0:24.3:1:32.9:1:1:0:60:106:1:0:0.1 0/1:173:2:1,1:46,125:171,2:0.0116:2,2:36.5:1:29:0:0.47069:2.70:60:4:0.0116:0:1.5 +9 98231908 . G A 80 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.63781;SOR=0.39178;LSEQ=ACTGTTCAGCTGCGGCAGGG;RSEQ=AGAAGGAAGCCCAGGGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:6,0:15,1:16,6:0.2727:1,0:26.3:1:31:1:1:0:60:12:0.2727:0:1 0/1:8:1:1,0:7,0:7,1:0.125:0,0:24:0:24:0:1:0:60:2:0.125:0:1 +9 98232223 . G GA 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.1261;SOR=0;LSEQ=ACTACCGCTGCCTGGGAGCA;RSEQ=AAAAAAAATTCAGAGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:399:4:0,4:143,252:395,4:0.01:2,0:18.5:1:24:1:0.30152:0:60:3:0.0076:0.0025:0.8 0/0:359:0:0,0:132,227:359,0:0:2,0:26.1:1:30.6:1:1:0:60:88.75:1:0:0.1 +9 98232255 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09331;SOR=Inf;LSEQ=AGAGGTCACCAACATGCCTC;RSEQ=GCCCAATCAGAGGACTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:253:0:0,0:46,207:253,0:0:2,0:24.4:1:30.5:1:1:0:60:125.5:1:0:0.1 0/1:211:3:2,1:49,159:208,3:0.0142:2,2:13:1:29.7:1:0.14566:6.42:60:6:0.0142:0:1 +9 98238244 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19133;SOR=Inf;LSEQ=ACTGAAGTGCCTTAGCAGAG;RSEQ=CCGCAGACATGGGATGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:167,33:200,0:0:2,0:25:1:29.7:1:1:0:60:24:1:0:0.1 0/1:156:2:1,1:127,27:154,2:0.0128:2,2:26:1:30.5:1:0.32771:4.63712:60:4:0.0128:0:1 +9 98238358 . G A 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.29996;LSEQ=GCGGGAATTGGGATTAACGC;RSEQ=GCCATGAAGAAGGCTGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:616:250:130,120:174,192:366,250:0.4058:2,2:26:1:31:1:0.28699:1.20:60:49:0.4036:0:1.2 0/1:771:131:73,58:335,304:639,131:0.1699:2,2:27.8:1:29.7:1:0.50278:1.14:60:262:0.1708:0:1.2 +9 98238379 . A G 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCATGAAGAAGGCTGTGAC;RSEQ=TTGCTGATGGACGTGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:627:0:0,0:296,331:627,0:0:2,0:26.1:1:30.6:1:1:0:60:47.231:1:0:0.5 0/1:791:27:14,13:377,387:764,27:0.0341:2,2:18.2:1:28.3:1:0.84652:1.11:60:12.5:0.0323:0:1.2 +9 98238466 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.26451;SOR=Inf;LSEQ=GAATAAAAAAACACAGCGCT;RSEQ=AGAGCTGCACTGGACATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:195:0:0,0:43,152:195,0:0:2,0:24.3:1:31.9:1:1:0:60:194:1:0:0.1 0/1:262:3:2,1:61,198:259,3:0.0115:2,2:18.3:1:26:1:0.14456:6.43:60:6:0.0118:0:1 +9 98238473 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2602;SOR=Inf;LSEQ=AAAACACAGCGCTGAGAGCT;RSEQ=CACTGGACATGGTCCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:32,140:172,0:0:2,0:24.1:1:32.1:1:1:0:60:42:1:0:0.1 0/1:222:3:1,2:39,180:219,3:0.0135:2,2:18:1:30.3:1:0.45064:2.30:60:6:0.014:0:1 +9 98239147 . A G 161 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAATGGCAAAACCTACAGC;RSEQ=AAAACAGAGGATGGTGGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:455:0:0,0:168,287:455,0:0:2,0:25.8:1:30.5:1:1:0:60:74.833:1:0:0.3 0/1:420:49:19,30:134,236:370,49:0.1167:2,2:24.1:1:28.8:1:0.75343:1.12:60:11.25:0.1095:0:1.1 +9 98239190 . G C 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09662;SOR=0.69372;LSEQ=GACATGCGAGATGCAATTCA;RSEQ=ATGATTCTAAAGCTAGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:95:18,77:19,100:119,95:0.4419:2,2:22.2:1:32.4:1:0.58942:1.23:59.9:94:0.4476:0:1.2 0/1:175:62:15,47:22,90:112,62:0.3543:2,2:22.9:1:30.6:1:0.56238:1.30:60:30:0.3529:0:1.2 +9 98239200 . AAGCTAGTTA GCTAGTT 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18483;SOR=Inf;LSEQ=ATGCAATTCAGATGATTCTA;RSEQ=GGACTCTGCCACCAGCACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:24,157:181,0:0:2,0:23.1:1:31.2:1:1:0:59.9:362:1:0:0.6 0/1:137:2:1,1:23,112:135,2:0.0146:2,2:9.5:1:26.6:1:0.32074:4.79:60:4:0.0146:0.0073:0 +9 98239730 . G A 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00256;SOR=Inf;LSEQ=AAAGGCTGCAAGACCCTTCC;RSEQ=GTGAGAAGGACACACAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:195,23:218,0:0:2,0:22.1:1:30.1:1:1:0:60:108:1:0:0.1 0/1:165:7:5,2:137,21:158,7:0.0424:2,2:21.9:1:27.3:1:0.25246:2.58911:60:6:0.0366:0:1 +9 98240028 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.19808;SOR=Inf;LSEQ=CAGAACAAAAGCCGAACATT;RSEQ=GAATGTGTTGTGATTCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:25,124:149,0:0:2,0:26.9:1:32:1:1:0:59.9:298:1:0:0.1 0/1:120:2:1,1:20,98:118,2:0.0167:2,2:30:1:28:1:0.32059:4.81:60:4:0.0168:0:1 +9 98240120 . G A 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.75306;SOR=0.73123;LSEQ=AACAAAACTTTACATCAAGG;RSEQ=CGTCACATAAAATGACAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:11:3,8:9,19:28,11:0.2821:2,2:26.1:1:31:1:1:1.25576:60:22:0.2821:0:1 0/1:18:4:2,2:2,12:14,4:0.2222:2,2:25.8:1:29.3:1:0.19706:5.26:60:8:0.2222:0:1 +9 98240230 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24013;SOR=Inf;LSEQ=CGCTCTCTCTGTCCTGGATG;RSEQ=ACATCGATGTTAAGAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:61,3:64,0:0:1,0:26.2:1:32.2:1:1:0:60:31:1:0:0.1 0/1:62:2:1,1:55,5:60,2:0.0323:2,2:14.5:1:26.5:1:0.18562:10.1325:60:4:0.0339:0:1.5 +9 98240535 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15287;SOR=Inf;LSEQ=CCACAAGCCTCGACAGCACA;RSEQ=ATCTCAGGTGACACAGCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:19,150:169,0:0:2,0:24:1:32.4:1:1:0:60:55.333:1:0:0.1 0/1:109:2:1,1:12,95:107,2:0.0183:2,2:23.5:1:28:1:0.22528:7.65:60:4:0.0185:0:1 +9 98240879 . C A 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGGCCACTTTTAAAAGGTCA;RSEQ=ATGCAGCTCAGTAGAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:21.5:1:29.5:1:1:2.44949:60:4:0.3333:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 98241185 . G T 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19952;SOR=Inf;LSEQ=TCCCAGAATTGCAATGTTTT;RSEQ=AAAATAAAGCGAATGGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:162,17:179,0:0:2,0:23.2:1:32.4:1:1:0:60:88.5:1:0:0 0/1:145:2:1,1:129,14:143,2:0.0138:2,2:7.5:1:25:0:0.19684:8.93663:60:4:0.0138:0:1 +9 98242112 . A G 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.40691;SOR=0.65508;LSEQ=GTCTGCTACTATTTCTTAAT;RSEQ=TTCTATGACGCCACCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:29:29,0:40,1:41,29:0.4143:1,1:17.1:1:32.5:1:1:0:60:58:0.4203:0:1.2 0/1:38:12:12,0:26,0:26,12:0.3158:1,0:22.8:1:32.8:1:1:0:60:24:0.3158:0:1 +9 98242151 . A G 28 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18319;SOR=Inf;LSEQ=CTAGCGAGGATAACGGTTTA;RSEQ=GTATTAATACAAATACACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:143,2:145,0:0:1,0:21.2:1:30.5:1:1:0:59.7:47.333:1:0:0.2 0/1:109:2:1,1:102,5:107,2:0.0183:1,2:5:0:28:1:0.10754:18.70551:60:4:0.0185:0:0.5 +9 98242177 . T C 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=AATACAAATACACTTGCCGA;RSEQ=GTCAGGAGGGAAGTGGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:194,27:221,0:0:2,0:23.8:1:31.3:1:1:0:59.8:109.5:1:0:0.1 0/1:215:13:10,3:165,37:202,13:0.0605:2,2:20:1:31.5:1:0.7127:1.33588:60:26:0.0613:0:1 +9 98242443 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22987;SOR=Inf;LSEQ=ATGCCTTGTTAAAATCCAGT;RSEQ=CATTAAGGGCTTGTGTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:20,113:133,0:0:2,0:24.6:1:32.1:1:1:0:59.9:43.333:1:0:0.1 0/1:123:2:1,1:14,106:120,2:0.0163:2,2:25:1:24.5:1:0.23168:7.35:60:4:0.0168:0:1 +9 98242593 . TA T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.19393;SOR=Inf;LSEQ=TGAAATGTTAAAAATGAAAA;RSEQ=ATAAAGTGAACGATGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:204,33:237,0:0:2,0:23.5:1:29:1:1:0:60:236:1:0:0.1 0/1:187:2:1,1:154,31:185,2:0.0107:2,2:12:1:28.6:1:0.31373:4.90546:60:4:0.0109:0.0053:0 +9 98242625 . G T 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.04777;SOR=Inf;LSEQ=CGATGAATGGACACAAAAAA;RSEQ=TGTTTTGCTCTCCACCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:422:0:0,0:308,114:422,0:0:2,0:24.6:1:32.9:1:1:0:60:69.333:1:0:0.1 0/1:372:4:1,3:266,102:368,4:0.0108:2,2:14.8:1:27:1:0.06984:7.77362:59:8:0.0109:0:1 +9 98242925 . A G 192 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.30407;LSEQ=GAGCCTTCTAAACGCATCGT;RSEQ=AAGTAACACGGCTGCGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:63:5,58:11,93:104,63:0.3772:2,2:26.9:1:32.2:1:0.7871:1.36954:60:62:0.3735:0:1.3 0/1:187:29:4,25:28,130:158,29:0.1551:2,2:21.3:1:30.3:1:0.79032:1.34413:60:58:0.1551:0:1.4 +9 98242984 . G A 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55297;SOR=0.74059;LSEQ=AGGTTCCTGGCAATGCTGCA;RSEQ=TTCTGGGACTCTGGCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:30:0,30:0,32:32,30:0.4839:1,1:25.7:1:31.3:1:1:0:60:29:0.4754:0:1.6 0/1:44:18:0,18:1,25:26,18:0.4091:1,1:26.8:1:30.9:1:1:0:60:36:0.4186:0:1.4 +9 98244096 . CA C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCCCCCGACTATTCACT;RSEQ=AAAAATGCACATGGAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:2,0:76,1:77,2:0.0253:1,0:35.5:1:34:0:1:0:60:4:0.0253:0:0 0/0:30:0:0,0:29,1:30,0:0:1,0:25:1:29.8:1:1:0:60:60:1:0:0 +9 98244157 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.20047;SOR=Inf;LSEQ=CAAAACTGAAATGGAACAAA;RSEQ=AATGATAAGCAACATTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:196,18:214,0:0:2,0:23.5:1:32.5:1:1:0:60:428:1:0:0 0/1:174:2:2,0:150,22:172,2:0.0115:2,0:17:1:29.5:1:1:0:60:4:0.0115:0:1 +9 98244563 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.22023;SOR=Inf;LSEQ=AATTCGAAATGATAGAACAT;RSEQ=AAAAAGAACTGCAATTTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:5,103:108,0:0:1,0:23.4:1:28.5:1:1:0:60:216:1:0:0.1 0/1:96:2:1,1:16,78:94,2:0.0208:2,2:10.5:1:28:1:0.32434:4.76:60:4:0.0213:0:0.5 +9 98244575 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21928;SOR=Inf;LSEQ=TAGAACATATAAAAAGAACT;RSEQ=CAATTTCGATCACTTTTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:1,87:88,0:0:1,0:24.2:1:32.3:1:1:0:60:43:1:0:0.1 0/1:78:2:1,1:9,67:76,2:0.0256:2,2:23:1:27:1:0.24143:7.11:60:4:0.0278:0:1 +9 98247897 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21732;SOR=Inf;LSEQ=TCATTTACTAAAATAACGGG;RSEQ=CCTAAACCAGCAGCCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:130,16:146,0:0:2,0:24.2:1:31.1:1:1:0:59.9:28.2:1:0:0.1 0/1:128:2:1,1:106,20:126,2:0.0156:2,2:14:0:30.5:1:0.30229:5.19673:60:4:0.0164:0:1 +9 98268595 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5314;SOR=0;LSEQ=GGCAGGGGGTTTCGCCGGCC;RSEQ=CAGCCAGGCTCTAGGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:2,0:157,2:159,2:0.0124:1,0:38.5:1:32.5:1:1:0:60:4:0.0126:0:1 0/0:95:0:0,0:95,0:95,0:0:1,0:26.5:1:29.4:1:1:0:60:46.5:1:0:0.2 +9 98268765 . G A 268 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.13443;LSEQ=GCGAAGGCCCCAAATATGAG;RSEQ=AGGCCCACAACCAAGAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1156:474:219,255:326,355:681,474:0.41:2,2:25.4:1:30.2:1:0.59007:1.06919:60:35.462:0.4101:0:1.1 0/1:1429:122:59,63:641,661:1302,122:0.0854:2,2:24.3:1:28.2:1:0.9246:1.03547:59.7:23.4:0.0855:0:1.2 +9 98268923 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24816;SOR=0;LSEQ=GGAGTGAGCGCCGGGGAGTC;RSEQ=CGGCCCGCGCGCCCACGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:3:1,2:5,114:119,3:0.0246:1,2:34.7:1:30:1:0.14151:10.80:60:6:0.025:0:1 0/0:112:0:0,0:14,98:112,0:0:2,0:22.6:1:31.2:1:1:0:60:27:1:0:0.2 +9 98270316 . TGTGA T 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0.00877;SOR=Inf;LSEQ=TGCTGCTTTTCCTGGAGAGG;RSEQ=GTGAGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:133,1:134,0:0:1,0:25.9:1:33.1:1:1:0:59.9:133:1:0:0.2 0/1:114:6:6,0:105,3:108,6:0.0526:1,0:30.3:1:30.7:1:1:0:60:12:0.0536:0.0088:0.2 +9 98270320 . AGTGAGTGT A 193 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=8.000;MSILEN=2;SSF=0.01283;SOR=0.50131;LSEQ=GCTTTTCCTGGAGAGGTGTG;RSEQ=GTGTGTGTGTGTGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:60:59,1:86,1:87,60:0.4082:1,1:25.3:1:32.8:1:1:1.45378:59.3:59:0.4041:0.0816:0.3 0/1:117:30:30,0:82,3:85,30:0.2564:1,1:25.6:1:32.3:1:0.56623:0:59.8:60:0.2632:0.0342:0.2 +9 98270369 . T G 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.21362;SOR=4.09413;LSEQ=GAGGAAGAGAGTGTGTGTGT;RSEQ=TGTGTGTGGCGGGGGCGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:365:1:1,0:276,88:364,1:0.0027:2,0:46:0:32:0:1:0:60:2:0.0028:0:6 0/1:359:4:3,1:258,97:355,4:0.0111:2,2:10.5:1:25.5:1:1:1.13:54:3:0.0085:0:2.3 +9 98270385 . C T 73 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34495;SOR=2.17357;LSEQ=GTGTTTGTGTGTGGCGGGGG;RSEQ=GATCCCAAAGAGTTAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:3:0,3:321,147:468,3:0.0064:2,0:1:0:27:1:0.03186:0:60:6:0.0066:0:1 0/1:509:7:2,5:316,185:501,7:0.0138:2,2:5.3:1:26.3:1:0.10859:4.25778:60:14:0.0143:0:1.3 +9 98270568 . G A 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62472;SOR=2.78024;LSEQ=CCTCCCGCCTCCAGCCGGCC;RSEQ=TCCCGGGGCACCGATACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:1:1,0:60,173:233,1:0.0043:2,0:1:0:22:0:0.26068:0:60:2:0.0043:0:1 0/1:255:3:2,1:82,170:252,3:0.0118:2,2:25.7:1:29:1:0.25315:4.12:60:6:0.0122:0:1.3 +9 98270569 . T A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.24889;SOR=Inf;LSEQ=CTCCCGCCTCCAGCCGGCCG;RSEQ=CCCGGGGCACCGATACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:59,171:230,0:0:2,0:20.2:1:30.5:1:1:0:60:56.5:1:0:0.3 0/1:242:3:1,2:80,159:239,3:0.0124:2,2:17.3:1:20.3:1:1:1.00626:53.3:2:0.0087:0:4.3 +9 98270588 . C T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21607;SOR=0;LSEQ=GTCCCGGGGCACCGATACAG;RSEQ=CGCTGCCGCCGCCGCCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:45,89:134,2:0.0147:2,2:5:0:32:0:1:1.97:60:4:0.015:0:1 0/0:156:0:0,0:61,95:156,0:0:2,0:20.9:1:31.1:1:1:0:59.7:77:1:0:0.4 +9 98270592 . TGCC T 64 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.69226;SOR=1.66845;LSEQ=CGGGGCACCGATACAGCCGC;RSEQ=GCCGCCGCCGCGGTCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:42,65:107,2:0.0183:2,2:39.5:1:32:1:1:1.54:60:4:0.0183:0:0 0/1:132:4:2,2:52,75:127,4:0.0303:2,2:38.3:1:32:1:1:1.44:60:8:0.0317:0:0.3 +9 98270596 . G A 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.12423;SOR=Inf;LSEQ=GCACCGATACAGCCGCTGCC;RSEQ=CCGCCGCCGCGGTCCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:44,58:102,0:0:2,0:22.6:1:30.9:1:1:0:59.9:50:1:0:0.4 0/1:115:4:3,1:49,62:111,4:0.0348:2,2:21.8:1:26.5:1:0.32671:3.75:60:8:0.0357:0:1 +9 98278644 . C A 30 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GGCGCTCGGGGCTCGCTCCT;RSEQ=CGTCCGCCGCGCGGGGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40:0:30.5:1:1:0:60:4:1:0:1.5 0/0:2:0:0,0:1,1:2,0:0:2,0:31:0:32.5:1:1:0:60:4:1:0:0.5 +9 98278729 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25207;SOR=Inf;LSEQ=AGGCGAGGTGGCGTCGGCGG;RSEQ=CGCCGCGCTGGCTGCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:164,56:220,0:0:2,0:21.2:1:32.3:1:1:0:60:43:1:0:0.2 0/1:253:3:2,1:173,77:250,3:0.0119:2,2:11:1:28.7:1:1:1.12284:60:6:0.012:0:1 +9 98278828 . C CT 120 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.00797;SOR=0.24101;LSEQ=CTTGGATTTCACATCAATTC;RSEQ=TTTTTTTTCCCTGGCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:830:14:11,3:570,241:811,14:0.0169:2,2:19.1:1:31.7:1:0.76825:1.55:59.6:28:0.0173:0.0048:0.7 0/0:972:4:3,1:607,356:963,4:0.0041:2,2:21:1:27:1:1:1.76:60:3:0.0031:0:0.3 +9 98278958 . TTTC T 133 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.1079;SOR=0.53461;LSEQ=GTCTTTTTCTTCTCCTCCGT;RSEQ=TTCTTCTTCTTCTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1260:20:6,14:519,718:1237,20:0.0159:2,2:33.5:1:30.8:1:0.363:1.68596:57.3:40:0.0161:8e-04:0.6 0/0:1404:12:5,7:590,798:1388,12:0.0085:2,2:34.9:1:29.3:1:1:1.03507:59.2:24:0.0087:0:0.3 +9 98278972 . T C 194 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=3;SSF=0;SOR=14.60691;LSEQ=CTCCGTTTTCTTCTTCTTCT;RSEQ=CTCCTCCTCCTCCGTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1074:6:2,4:426,642:1068,6:0.0056:2,2:22:1:32:1:1:1.32676:60:12:0.0057:0:1 0/1:1173:89:35,54:464,619:1083,89:0.0759:2,2:22.8:1:30.1:1:0.57761:1.15637:60:88:0.0766:0:1.1 +9 98278975 . C T 116 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=3;SSF=0.00992;SOR=0.20977;LSEQ=CGTTTTCTTCTTCTTCTTCT;RSEQ=CTCCTCCTCCGTCTTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1044:13:6,7:406,624:1030,13:0.0125:2,2:26.9:1:31.5:1:0.7765:1.32:55.8:26:0.0126:0:1 0/0:1138:3:1,2:480,653:1133,3:0.0026:2,2:31.3:1:28.3:1:1:1.46966:56.7:6:0.0027:0:1 +9 98279102 . T A 111 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00025;SOR=Inf;LSEQ=GTTTCTATTAAGCAGTTCCA;RSEQ=GGCCCTCGGCGTGGGTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:450:0:0,0:150,300:450,0:0:2,0:23.6:1:30.4:1:1:0:60:39.909:1:0:0.1 0/1:485:13:4,9:170,301:471,13:0.0268:2,2:17.5:1:30:1:0.77813:1.27018:60:26:0.0274:0:1.4 +9 98279188 . T A 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=7e-04;SOR=0.24497;LSEQ=AAAACTTTACCCCTTTACAA;RSEQ=AAACTCAAGGAAAGCAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:29:1,28:0,59:59,29:0.3295:1,1:22.2:1:30:1:0.32955:0:58.1:13.5:0.3176:0:1.3 0/1:75:8:0,8:1,66:67,8:0.1067:1,0:19.3:1:28:1:1:0:60:7:0.0946:0:1 +9 98851044 . C CGAT 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.46074;SOR=0.46187;LSEQ=TGATGAGATGACAATGATAA;RSEQ=GATGATGATGATATGATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:6,4:2,2:4,10:0.7143:2,2:25.4:1:30.1:1:1:1.46:59.6:9:0.6923:0.1429:1.2 1/0:17:9:5,4:5,3:8,9:0.5294:2,2:16.1:1:28.1:1:1:1.31092:59.4:18:0.5294:0.2353:0.9 +9 98851075 . C G 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0114;SOR=0.15632;LSEQ=ATATGATGACAATGAGATTT;RSEQ=ATGATAATGATGATGACGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:9,8:1,2:3,17:0.85:2,2:26.1:1:30.4:1:1:2.16:59.8:16:0.8421:0:1.1 0/1:24:11:5,6:7,6:13,11:0.4583:2,2:26.3:1:31.1:1:1:1.3804:59.5:22:0.4583:0:1.2 +9 98852303 . A G 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTTGCTGGTGCCAGCTAC;RSEQ=GATGCCCTTGCCGAAGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:11:1:30.7:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 98981273 . C A 86 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01446;SOR=13.14064;LSEQ=GTTAGATTTTAACCCAAACA;RSEQ=TGTCCCTTCTAATGTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:9,2:11,1:0.0833:2,0:2:0:31:0:1:0:60:2:0.0833:0:1 1/0:14:8:4,4:3,3:6,8:0.5714:2,2:24.4:1:28.9:1:1:1:60:7:0.5385:0:1.3 +9 98981308 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5328;SOR=0;LSEQ=TTCTCCGCTGCCGCCCAGTG;RSEQ=AGCTCCCAACGCTGACCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:29,2:0.0645:2,2:25.5:1:30.5:1:1:1.22249:60:4:0.0645:0:1 0/0:17:0:0,0:9,8:17,0:0:2,0:32.2:1:31.8:1:1:0:60:34:1:0:0.6 +9 98981387 . C T 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12782;SOR=8.54954;LSEQ=ACTCCCGCGCTCCACCGAGC;RSEQ=GGAGGGCAGCCCAGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:0,1:5,10:15,1:0.0625:2,0:19:0:32:0:1:0:60:2:0.0625:0:1 0/1:5:2:1,1:1,2:3,2:0.4:2,2:10.5:1:27:1:1:1.73:60:4:0.4:0:1 +9 100615914 . A G 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGAGTCCAGTCCCGGTC;RSEQ=CGAGGCCACCGCCGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:36:0:30:0:1:0:60:2:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:29:1:1:0:60:4:1:0:1.5 +9 100616396 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GCTCATCGCCATGGCCATCG;RSEQ=GCACGCGCCCGAGCGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:8,0:0:0,0:19.1:1:33.6:1:1:0:60:16:1:0:0 0/1:17:2:1,1:15,0:15,2:0.1176:1,2:24:0:31:1:0.11765:0:60:4:0.1176:0:1.5 +9 100616453 . G A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50456;SOR=Inf;LSEQ=CTACAAGTTCATCACCGAGC;RSEQ=CTTCCCCTTCTACCGCGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:37,7:44,0:0:2,0:25.1:1:30.5:1:1:0:60:88:1:0:0 0/1:58:2:1,1:38,18:56,2:0.0345:2,2:5.5:1:26.5:1:1:2.08172:60:4:0.0351:0:1.5 +9 100616468 . G C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19636;SOR=0;LSEQ=CGAGCGCTTCCCCTTCTACC;RSEQ=CGACAACCCCAAAAAGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:43,12:55,2:0.0351:2,2:23:0:33:0:0.40727:3.48238:60:4:0.0357:0:1 0/0:71:0:0,0:43,28:71,0:0:2,0:23.7:1:29.3:1:1:0:60:34.5:1:0:0.3 +9 100616583 . T C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18555;SOR=1.85488;LSEQ=AAGGGCAACTACTGGGCGCT;RSEQ=GACCCCAACGCGGAGGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:30:7,23:2,14:16,30:0.6522:2,2:21.4:1:30.4:1:0.46277:2.10:60:60:0.6522:0:1.1 1/0:54:42:11,31:3,9:12,42:0.7778:2,2:19.5:1:29.3:1:1:1.06:60:84:0.7778:0:1.1 +9 100968490 . A G 103 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02769;SOR=5.60529;LSEQ=CCTCGTGATCTGCCTGCCTC;RSEQ=GCCTCCCAAAGTGCTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:2:2,0:20,1:21,2:0.087:1,0:20:1:32:0:1:0:34.5:4:0.087:0:1 0/1:31:11:7,4:14,6:20,11:0.3548:2,2:12.1:1:30:1:1:1.32078:42.5:22:0.3667:0:1.5 +9 100968566 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.22025;LSEQ=GTAACTTTCTGTTTTAAGCA;RSEQ=TAAATATTTACATGAATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:0,1:74,41:115,1:0.0085:2,0:1:0:26:0:0.36207:0:60:2:0.0088:0:1 0/1:192:2:1,1:110,80:190,2:0.0104:2,2:26.5:1:29.5:1:1:1.37266:60:4:0.0105:0:1 +9 100968598 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-04;SOR=0.45259;LSEQ=ATGAATACCAATTATCTGCA;RSEQ=TTGCATATCAAATTTAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:175:112:63,49:34,28:62,112:0.64:2,2:25.5:1:32.4:1:0.87459:1.06:60:111:0.6453:0:1.1 0/1:238:106:59,47:72,60:132,106:0.4454:2,2:26.4:1:31.3:1:0.89618:1.05:60:212:0.4454:0:1.1 +9 100968820 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.46154;SOR=Inf;LSEQ=TCTGCCCCTTCAGCACAGGT;RSEQ=GAACTCCAAAAGCAGGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:0,7:7,0:0:0,0:24:1:31.4:1:1:0:60:14:1:0:0 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:42:1:29:1:1:0:60:4:0.2857:0:1 +9 101866715 . C A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCTCAGGATCTGGGTCTGA;RSEQ=GCTGGGATCTGAGGACTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:33:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 101867396 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50529;SOR=Inf;LSEQ=GCCGGAGCGAGGCCGCCGCG;RSEQ=CGGCTAGGGAGGTGGGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:11,0:0:2,0:19.3:1:32.2:1:1:0:60:22:1:0:0.2 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:38.5:1:28:1:1:1.13389:60:4:0.1176:0:1 +9 101867411 . G T 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.29153;SOR=Inf;LSEQ=CCGCGGCGGCTAGGGAGGTG;RSEQ=GGCGAGGCGAGGTTTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:22,0:0:2,0:17.1:1:30.9:1:1:0:60:44:1:0:0.2 0/1:38:3:1,2:18,17:35,3:0.0789:2,2:7.7:1:27.3:1:1:2.0774:60:6:0.0789:0:1 +9 101867454 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.52697;SOR=Inf;LSEQ=TGAGGCAGCGGCGCGGCCGG;RSEQ=CCGGGCCGGGCCACAGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:24,23:47,0:0:2,0:25.6:1:31.4:1:1:0:60:22.5:1:0:0.3 0/1:78:2:1,1:36,39:75,2:0.0256:2,2:32:1:27.5:1:1:1.08:60:4:0.0278:0:1 +9 101867464 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=0.28088;SOR=Inf;LSEQ=GCGCGGCCGGGCCGGGCCGG;RSEQ=CCACAGGCGGTGGCGGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:34,35:69,0:0:2,0:19.9:1:31.3:1:1:0:59.3:22:1:0:0.4 0/1:107:3:1,2:51,52:103,3:0.028:2,2:31.7:1:26.7:1:1:1.94956:60:6:0.0286:0:1 +9 101867506 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53389;SOR=Inf;LSEQ=CCATGGAGGCGGCGGTCGCT;RSEQ=CTCCGCGTCCCCGGCTGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:39,40:79,0:0:2,0:26.4:1:32.2:1:1:0:60:18.75:1:0:0.5 0/1:137:2:1,1:67,68:135,2:0.0146:2,2:14.5:1:28.5:1:1:1.01:60:4:0.0149:0:1.5 +9 101891409 . G A 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12168;SOR=Inf;LSEQ=TGTATAAAATTTTTTTCCTA;RSEQ=ATACTACAAGAAAAACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:30,196:226,0:0:2,0:24:1:32.2:1:1:0:59.9:55.5:1:0:0.1 0/1:223:3:3,0:48,172:220,3:0.0135:2,0:9.7:1:21.7:1:0.01142:0:60:2:0.0091:0:2.3 +9 101900151 . G T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01628;SOR=Inf;LSEQ=TTACCTTTAGGTTTACCATT;RSEQ=CTTGTTCAGAGAACAATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:486:0:0,0:360,126:486,0:0:2,0:24.4:1:32.5:1:1:0:60:80:1:0:0.1 0/1:542:7:2,5:382,153:535,7:0.0129:2,2:12.3:1:25.3:1:0.02462:6.21706:60:14:0.0132:0:1 +9 101904795 . G T 52 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.04733;SOR=0;LSEQ=AAATGGTCTGCAGCCCAACC;RSEQ=AAATGTTAATTCTGTTTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:4:1,3:272,118:390,4:0.0102:2,2:8:1:26.3:1:0.08809:6.87794:60:8:0.0102:0:1 0/0:449:0:0,0:302,147:449,0:0:2,0:23.9:1:29.3:1:1:0:60:111.25:1:0:0.1 +9 101905005 . T A 42 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.30723;SOR=0.22088;LSEQ=GGTAATTCTATAAGCAGTTC;RSEQ=ATTATTTAAGCTTTAAATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:2,1:43,189:232,3:0.0128:2,2:13:1:27:1:0.09473:8.67:60:6:0.0128:0:1 0/0:352:1:1,0:93,257:350,1:0.0028:2,0:1:0:23:0:0.26781:0:60:2:0.0029:0:1 +9 101907193 . T A 33 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.10262;SOR=Inf;LSEQ=ATACTTTTGAACAACTATAT;RSEQ=TAATATCTTCTGAAATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:48,186:234,0:0:2,0:24.6:1:30.7:1:1:0:60:57.5:1:0:0.1 0/1:207:3:1,2:57,147:204,3:0.0145:2,2:19:1:21.3:1:1:1.29:60:2:0.0099:0:1.7 +9 101907243 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06785;SOR=Inf;LSEQ=TTCTCTTTCATATATACATA;RSEQ=CATTGCTGAAACTCAGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:2,88:90,0:0:1,0:22.1:1:30.5:1:1:0:60:180:1:0:0.1 0/1:63:3:0,3:2,58:60,3:0.0476:1,0:17:1:32:0:1:0:60:6:0.0517:0:1.3 +9 101908756 . AT A 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0.93049;LSEQ=TTTCAAAGTTCTTTTTGCAA;RSEQ=TTTTTTTAGGTACATGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:701:9:3,6:370,321:691,9:0.0128:2,2:36.3:1:31.6:1:0.31713:2.30263:58.6:18:0.0129:0:0.9 0/1:920:11:6,5:500,409:909,11:0.012:2,2:28.8:1:29.6:1:1:1.01873:60:22:0.012:0.0011:0.2 +9 101908915 . G A 192 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=88.84178;LSEQ=AATTGCTCTCCTCTCCCCCA;RSEQ=TAGTTTGTCATGAGCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:473:1:1,0:155,317:472,1:0.0021:2,0:1:0:25:0:0.32981:0:60:2:0.0022:0:1 0/1:586:93:33,60:177,315:492,93:0.1587:2,2:25.2:1:29.5:1:1:1.02161:60:45.5:0.1583:0:1.1 +9 101910151 . ACTTTT A 119 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=GCTACTTTTCTTTAAGGAAA;RSEQ=CTTTAAGAATTTTCTTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:0,118:118,0:0:1,0:23.3:1:33:1:1:0:59.9:15.857:1:0:0.2 0/1:110:13:0,13:1,95:96,13:0.1182:1,1:28.6:1:32.3:1:1:0:57.5:26:0.1193:0.0091:0 +9 101911436 . A AT 137 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.15346;SOR=0.58767;LSEQ=GGAAAATGGTGCATGCATTA;RSEQ=TTTTTTTTTTTATATTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:20:18,2:137,28:165,20:0.1075:2,2:21.7:1:31.9:1:0.53824:1.83:60:40:0.1087:0.0161:0.4 0/1:212:14:13,1:157,40:197,14:0.066:2,1:24.3:1:30.4:1:0.31321:3.30:60:28:0.068:0.0189:0.1 +9 101911656 . A G 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGTTTTAATTTGGGAGGTCA;RSEQ=TTGTTCTACCTCACTGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:17,133:150,0:0:2,0:24.1:1:31.6:1:1:0:60:149:1:0:0 0/1:180:40:4,36:18,122:140,40:0.2222:2,2:22.3:1:31.4:1:0.7874:1.32587:60:39:0.2203:0:1.1 +9 102136067 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23662;SOR=0;LSEQ=TATTTCAACCCAATTCTCCT;RSEQ=CCTCCCAACCCAGGTGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:101,32:133,2:0.0148:2,2:17:1:27.5:1:0.43051:3.12354:60:4:0.0154:0:1 0/0:142:0:0,0:104,38:142,0:0:2,0:22.9:1:30.6:1:1:0:60:27.4:1:0:0.1 +9 102136177 . T G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=5.35264;LSEQ=CCACTCCCCACAAATTCAAT;RSEQ=TTCCCCCTCTTCCTAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:129:50,79:67,94:161,129:0.4448:2,2:25:1:31.5:1:0.63223:1.12571:60:42:0.4452:0:1.2 1/1:334:271:111,160:30,32:62,271:0.8114:2,2:25.5:1:31.6:1:0.31958:1.35009:60:134.5:0.8127:0:1.1 +9 102136212 . CG C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=AGAAGCACAGGCCCTGGGGT;RSEQ=GGGGGTCCTGGCTGTGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:44,127:171,0:0:2,0:23:1:30.3:1:1:0:60:33.2:1:0:0.7 0/1:177:2:1,1:43,131:174,2:0.0113:2,2:10:1:28:1:0.43857:3.02:60:4:0.0114:0:1 +9 102136227 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49955;SOR=0;LSEQ=GGGGTCGGGGGGTCCTGGCT;RSEQ=TGCCCAGTATGCAGGGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:0,2:27,105:132,2:0.0149:2,0:24.5:1:27:1:1:0:60:4:0.0153:0:2.5 0/0:120:0:0,0:27,93:120,0:0:2,0:22.4:1:31.4:1:1:0:60:240:1:0:0.8 +9 102136291 . A G 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAAGCCGCTACTTGCCAC;RSEQ=GTTGGAAACCCACTGCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:41:41:0,41:0,0:0,41:1:0,1:23.1:1:31:1:1:0:59:19.5:1:0:1.2 1/1:21:21:0,21:0,0:0,21:1:0,1:20.1:1:29.8:1:1:0:60:20:1:0:1 +9 102159548 . G A 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31202;SOR=0.45489;LSEQ=AGGGCTGCAAGCCCTGGAGA;RSEQ=CAACATTAAGGTGATGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:11:10,1:10,1:11,11:0.5:2,2:18.5:1:30.8:1:1:1:60:22:0.5:0:1 0/1:13:4:4,0:8,1:9,4:0.3077:2,0:27:1:28:1:1:0:60:8:0.3077:0:1 +9 102159610 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07797;SOR=Inf;LSEQ=TGTGAATTCCAAGCCATCCT;RSEQ=TTACCTTCACTTTGGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:37,26:63,0:0:2,0:26:1:32.5:1:1:0:60:62:1:0:0.3 0/1:48:3:2,1:26,19:45,3:0.0625:2,2:21.7:1:28.7:1:1:1.45:60:6:0.0625:0:1 +9 102159777 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTTTGCCATTTCAGTGCA;RSEQ=GCAGCCAGACTTCCAGTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:18.5:1:29.5:1:1:0:60:4:0.3333:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:39.5:1:29.5:1:1:0:60:4:1:0:0 +9 102160116 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTTATCATTGTTCAGCTCC;RSEQ=ACTTATGAGTGAGAACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:1:27.5:1:1:0:34:4:1:0:1.5 +9 102585044 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.50909;SOR=Inf;LSEQ=CTCTCGGCGGCGGCGGCGGC;RSEQ=GCGGCAGCGGCAGCGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:7,11:18,0:0:2,0:30.3:1:30.3:1:1:0:60:17:1:0:0.1 0/1:27:2:1,1:15,10:25,2:0.0741:2,2:39:1:27.5:1:1:1.47706:60:4:0.0741:0:1 +9 106905519 . G T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAACTCTTAATCTGGAGTCA;RSEQ=CGTTTCCCTCAGGTGCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:9,12:21,0:0:2,0:23.9:1:32.1:1:1:0:60:42:1:0:0 0/1:54:2:1,1:23,29:52,2:0.037:2,2:44:0:28.5:1:1:1.26:60:4:0.0377:0:1.5 +9 107040713 . C T 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=4.52329;LSEQ=AATTTTTGGCACACCTTTTA;RSEQ=GATCACCCTCTCTTAAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:73:29,44:243,250:493,73:0.1287:2,2:25.2:1:31:1:0.13381:1.47375:60:146:0.1292:0:1.1 0/1:646:259:126,133:185,201:386,259:0.4009:2,2:28.4:1:29.6:1:0.87255:1.03:60:258:0.4038:0:1.2 +9 107040779 . AT A 68 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.45021;SOR=2.51424;LSEQ=AGATGCCTTTATTAGATGCC;RSEQ=TTTTTTTTCTTTTAGATAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:2:0,2:85,195:280,2:0.0071:2,0:30:1:31:0:1:0:60:4:0.0071:0:0 0/1:283:5:1,4:85,193:278,5:0.0177:2,2:27.4:1:29.6:1:1:1.75855:60:10:0.0179:0.0035:0.4 +9 107040789 . C T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0296;SOR=Inf;LSEQ=ATTAGATGCCATTTTTTTTT;RSEQ=TTTTAGATAACTCTGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:235:0:0,0:58,177:235,0:0:2,0:21.6:1:32.7:1:1:0:60:77.333:1:0:0.2 0/1:232:5:4,1:56,171:227,5:0.0216:2,2:10.2:1:21.2:1:0.01666:12.06:59.2:1.5:0.0132:0:2 +9 107068085 . G C 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00444;SOR=0.03977;LSEQ=GCAAAAGCCCTACAGAAGAG;RSEQ=GACTGGACTATTGAAAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:1,6:0.8571:0,2:25.2:1:28.7:1:1:0:60:5:0.8333:0:1.2 0/1:13:2:2,0:8,3:11,2:0.1538:2,0:34.5:1:29.5:1:1:0:60:4:0.1538:0:1.5 +9 107068102 . G GA 46 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=2.11388;LSEQ=GAGGGACTGGACTATTGAAA;RSEQ=AAAAAAAAAACAAGTGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:1:1,0:6,2:8,1:0.1111:2,0:15:0:32:0:1:0:60:2:0.1111:0:0 0/1:14:3:2,1:9,2:11,3:0.2143:2,2:24:1:29.3:1:1:2.10574:60:6:0.2143:0:1 +9 107068143 . A G 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.50166;SOR=Inf;LSEQ=GTGACAACAGCATCAACAAA;RSEQ=ACAACAAAAAGGCCCCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:10,8:18,0:0:2,0:23.6:1:29.8:1:1:0:60:36:1:0:0.3 0/1:25:2:1,1:13,10:23,2:0.08:2,2:7.5:1:29:1:1:1.28628:60:4:0.0833:0:1.5 +9 109484504 . A G 149 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATAAAAATGAGAATTACAGT;RSEQ=AAATTCAGCTTGTCTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:24:24,0:16,0:16,24:0.6:1,1:23.1:1:32.7:1:1:0:60:48:0.6:0:1 0/0:24:0:0,0:23,1:24,0:0:1,0:22.1:1:28.3:1:1:0:60:48:1:0:0 +9 109485116 . C T 212 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGATGATACAAATGAATA;RSEQ=GTTAGTGCTGTGTGCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:0:0,0:271,272:543,0:0:2,0:23.8:1:31.3:1:1:0:59.7:89.5:1:0:0.1 0/1:460:136:67,69:151,171:322,136:0.2957:2,2:22.9:1:30:1:0.68254:1.10:51.4:135:0.2961:0:1.1 +9 109485333 . G A 167 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCATCAGGGTTTTGGGTTT;RSEQ=TTTTGAATATTTTTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:9,172:181,0:0:1,0:22.8:1:32.6:1:1:0:46.7:89.5:1:0:0 0/1:132:46:3,43:4,82:86,46:0.3485:1,2:21.4:1:30.3:1:0.69414:1.43:41.9:92:0.3594:0:1.1 +9 110246982 . G GT 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.82797;SOR=1.12468;LSEQ=ATTTATGGTAAAACTAAATA;RSEQ=TTTTTTTTTAATAAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:322:9:6,3:228,85:313,9:0.028:2,2:21.9:1:29.9:1:0.70909:1.33988:58.3:18:0.0281:0:0.9 0/1:383:12:9,3:262,106:368,12:0.0313:2,2:29.5:1:28.5:1:1:1.21:60:24:0.0314:0.0026:0.3 +9 110246994 . TA T 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.36226;SOR=0.48263;LSEQ=ACTAAATAGTTTTTTTTTAA;RSEQ=AAAAAAGGTATTTTAATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:7:3,4:281,130:411,7:0.0167:2,2:28.3:1:31.4:1:0.21763:2.87395:60:14:0.017:0.0024:0.4 0/0:491:4:2,2:324,163:487,4:0.0081:2,2:16.8:1:26.3:1:0.60538:1.98479:60:8:0.0082:0.0041:0.5 +9 110247041 . C T 91 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07697;SOR=4.07253;LSEQ=ATAAAGTTGGCTTTTTTGTG;RSEQ=GTGCTTCTTACATGCCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:804:2:0,2:425,377:802,2:0.0025:2,0:1:0:26:0:0.2219:0:60:4:0.0025:0:1 0/1:994:10:4,6:524,459:983,10:0.0101:2,2:24.4:1:27.4:1:0.5285:1.71148:60:20:0.0102:0:1.2 +9 110247965 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19198;SOR=0;LSEQ=CTCCTTCCCTCATCGGGAAG;RSEQ=CAGTGTGAAAAGTAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:88,15:103,2:0.019:2,2:34:1:29.5:1:0.28278:5.71261:60:4:0.019:0:1 0/0:134:0:0,0:102,32:134,0:0:2,0:21.2:1:28.1:1:1:0:60:66:1:0:0.1 +9 110248129 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08701;SOR=Inf;LSEQ=GGCGGTGCCCCGTGTGTTTA;RSEQ=GGTAGTGCCTGGTCAGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:392:0:0,0:187,205:392,0:0:2,0:23.9:1:30.7:1:1:0:60:64.333:1:0:0.2 0/1:563:6:3,3:262,295:557,6:0.0107:2,2:18.2:1:29.7:1:1:1.13:60:12:0.0108:0:1.2 +9 110248177 . C T 72 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08744;SOR=0.14122;LSEQ=GGGCGAATTTCCATCCACAG;RSEQ=CGTCCCAGTCACAGTGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:5:2,3:124,216:340,5:0.0145:2,2:22.2:1:31.2:1:1:1.16:60:10:0.0147:0:1.2 0/0:485:1:0,1:195,289:484,1:0.0021:2,0:1:0:25:0:1:0:60:2:0.0021:0:1 +9 110248222 . G GA 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.08069;SOR=0.49802;LSEQ=TCTCACCTGTAAAGGTAAAA;RSEQ=AAAAAAAAAATTGACGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:17:2,15:34,127:161,17:0.095:2,2:24.5:1:31.8:1:0.53017:2.00139:58.8:34:0.0983:0.0112:0.4 0/1:242:12:4,8:66,162:228,12:0.0496:2,2:22.3:1:27.9:1:0.74983:1.23:59.6:24:0.0517:0.0083:0.5 +9 110248233 . T A 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07965;SOR=Inf;LSEQ=AAGGTAAAAGAAAAAAAAAA;RSEQ=TGACGCTATTGCTATATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:0:0,0:20,116:136,0:0:2,0:24.5:1:30.8:1:1:0:60:272:1:0:0.1 0/1:196:5:1,4:48,143:191,5:0.0255:2,2:15.2:1:28.8:1:1:1.34076:59:10:0.0259:0:1.4 +9 110249505 . C T 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=2.76844;LSEQ=GAAGGTGGGGTGAGCATCAT;RSEQ=CCGTGTGTCCCGAAGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1279:170:83,87:529,578:1107,170:0.1329:2,2:25.3:1:30.8:1:0.80525:1.04:60:169:0.1343:0:1.1 0/1:1510:450:211,239:513,545:1058,450:0.298:2,2:23.6:1:29.3:1:0.57381:1.06612:59.6:149:0.2988:0:1.1 +9 110249840 . G A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12435;SOR=Inf;LSEQ=GCACGAAGAGACCGCCTCCT;RSEQ=CTTGATCTTGGGGCACGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:131,163:294,0:0:2,0:24.8:1:32.3:1:1:0:60:146:1:0:0.1 0/1:311:4:3,1:136,170:306,4:0.0129:2,2:16.3:1:24.3:1:0.32904:3.73:60:8:0.0132:0:1 +9 110249872 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25081;SOR=Inf;LSEQ=GGCACGTGCGCGGCGGCCCG;RSEQ=CGTTGTAGGGCGCCACCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:108,143:251,0:0:2,0:25.5:1:31.5:1:1:0:60:61.75:0.996:0:0.1 0/1:281:3:1,2:121,157:278,3:0.0107:2,2:12:1:28.3:1:1:1.53912:60:6:0.0108:0:1.7 +9 110249994 . G T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25008;SOR=0;LSEQ=GACGCCTTCAGCACGAACTT;RSEQ=CCCATCAGCCCGCCACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:1,2:126,113:239,3:0.0124:2,2:19.7:1:30:1:0.60559:2.22294:60:6:0.0125:0:1 0/0:220:0:0,0:135,84:219,0:0:2,0:24.5:1:31.5:1:1:0:60:53.75:1:0:0.2 +9 110250003 . C T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20546;SOR=4.2525;LSEQ=AGCACGAACTTGCCCATCAG;RSEQ=CCGCCACCTGGCGGCTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:243:1:1,0:133,108:241,1:0.0041:2,0:20:0:25:0:1:0:60:2:0.0042:0:1 0/1:231:4:2,2:141,86:227,4:0.0173:2,2:29.5:1:29.8:1:0.63669:1.63582:60:8:0.0177:0:1 +9 110250554 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.1713;SOR=Inf;LSEQ=CTCCTCCCGCCAGCGCTGCG;RSEQ=GGACAGGGCGGGAGAGACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:97:0:0,0:9,88:97,0:0:2,0:22.7:1:31.8:1:1:0:60:194:1:0:0.1 0/1:69:2:1,1:6,61:67,2:0.029:2,2:38:1:29.5:1:0.19395:9.49:60:4:0.0294:0:1 +9 110251860 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAACTGGTCGGCGGCGCA;RSEQ=GGCGCGGACTCCGGTGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:33:1:1:0:60:4:1:0:1.5 +9 112787105 . GTT G 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GCCAGTGTCTTGGGTTTTTT;RSEQ=TTTTTTTTTTAACAGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:31:1:31:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:31.5:1:1:0:60:4:1:0:0 +9 112787369 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20798;SOR=0;LSEQ=TGCTTAATGTGCTCAATATG;RSEQ=ACATTAATTCTCTTGGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:2,0:50,3:53,2:0.0364:2,0:22.5:1:32:0:1:0:28:4:0.0385:0:1 0/0:65:0:0,0:60,5:65,0:0:2,0:25.4:1:32.2:1:1:0:26.9:64:1:0:0.1 +9 112787398 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49888;SOR=Inf;LSEQ=TCTCTTGGCAAGAATCTTGC;RSEQ=CTTAACTTGTTTGTTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:60,8:68,0:0:2,0:29.2:1:31.1:1:1:0:26.6:67:0.971:0:0.4 0/1:80:2:1,1:64,14:78,2:0.025:2,2:19.5:1:27.5:1:0.34177:4.4508:20:4:0.0253:0:1.5 +9 112787483 . CA C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53202;SOR=Inf;LSEQ=CCATGGTAACACTTGTGGGG;RSEQ=TTCCTTTTTGAACAGTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:6.6:1:29.4:1:1:0:20.3:20:1:0:0.7 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:9.5:1:29.5:1:1:1.12:21:4:0.1053:0:0.5 +9 112787668 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52068;SOR=Inf;LSEQ=TTACTGGAAGATGGAGGTTC;RSEQ=GCCCGAAAGGCTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:38,66:104,0:0:2,0:24.3:1:27.4:1:1:0:42.2:5.5:1:0:0.6 0/1:160:2:1,1:81,77:158,2:0.0125:2,2:36.5:1:30.5:1:1:1.05164:47:4:0.0134:0:1 +9 112787669 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.52441;SOR=Inf;LSEQ=TACTGGAAGATGGAGGTTCC;RSEQ=CCCGAAAGGCTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:38,61:99,0:0:2,0:24.2:1:27.6:1:1:0:42.4:4.5:1:0:0.6 0/1:161:2:1,1:81,76:157,2:0.0124:2,2:43.5:1:28.5:1:1:1.0654:51.5:4:0.0139:0:2 +9 113137239 . G GT 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.53184;SOR=1.55268;LSEQ=AATGGTAGACTGGATAAAGT;RSEQ=TTTTTTTTTTCATTTTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:10,0:9,0:9,10:0.4762:0,0:28.1:1:30.2:1:1:0:60:20:0.4762:0.0476:0 1/0:17:10:10,0:7,0:7,10:0.5882:0,0:19.3:1:30.6:1:1:0:60:20:0.5882:0.1765:0 +9 113137380 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50022;SOR=Inf;LSEQ=GTGTAATGTCTTCTCTATGC;RSEQ=CTGCAAAATGAAGCAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:135:0:0,0:78,57:135,0:0:2,0:24.7:1:30.9:1:1:0:60:26:1:0:0.6 0/1:153:2:1,1:89,62:151,2:0.0131:2,2:22.5:1:28:1:1:1.432:60:4:0.0133:0:1 +9 113137400 . A T 191 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73642;SOR=1.08418;LSEQ=TCTGCAAAATGAAGCAGATG;RSEQ=CATAAAGAAGACAGATAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:151:90:50,40:30,31:61,90:0.596:2,2:27.5:1:30:1:0.50723:1.29:60:89:0.5933:0:1.1 1/0:182:112:64,48:40,30:70,112:0.6154:2,2:25.4:1:28.1:1:1:1:60:36.333:0.6124:0:1.1 +9 113560061 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11442;SOR=0;LSEQ=CTTATTTACTTTCTCAAATA;RSEQ=TATACATTTAGTCATTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:1,2:140,91:231,3:0.0128:2,2:21.7:1:28.7:1:0.5646:3.06194:60:6:0.0129:0:2 0/0:248:0:0,0:144,104:248,0:0:2,0:25.3:1:30.9:1:1:0:60:34.429:1:0:0.8 +9 113560071 . A C 189 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64743;SOR=0.91195;LSEQ=TTCTCAAATAGTATACATTT;RSEQ=GTCATTAAACAAACATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:88:52,36:96,77:173,88:0.3359:2,2:25.1:1:30.7:1:0.59952:1.16:60:87:0.3346:0:1.7 0/1:282:89:42,47:111,81:192,89:0.3156:2,2:24.7:1:29.3:1:0.12212:1.53111:60:88:0.3154:0:2 +9 113560119 . A G 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=2.18783;LSEQ=TATTTTCAAGATTATCAAGC;RSEQ=ATTCCTGTTTCAACTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:147:65,82:55,70:125,147:0.5404:2,2:26.5:1:30.9:1:1:1.01:59.9:48:0.5373:0:2 1/0:304:219:96,123:43,42:85,219:0.7204:2,2:26.9:1:30:1:0.30681:1.31056:60:72:0.7248:0:1.9 +9 113560161 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AAAATGTTGACTCTGTATTC;RSEQ=TATACAGTTTATAACATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:193:193:62,131:0,0:0,193:1:0,2:25.5:1:31:1:1:0:60:192:1:0:1.5 1/1:207:168:62,106:16,23:39,168:0.8116:2,2:23.9:1:29.7:1:0.71435:1.18832:60:83:0.8098:0:1.8 +9 113560217 . C A 27 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23676;SOR=Inf;LSEQ=ATTCAAACAGAAACTATGTA;RSEQ=AGTTTTCCAATTTAACCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:8,59:67,0:0:2,0:19.7:1:33.2:1:1:0:60:134:1:0:0.9 0/1:64:2:1,1:9,53:62,2:0.0313:2,2:6:0:27.5:1:0.29018:5.64:60:4:0.0317:0:2 +9 114910765 . G A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTGTGAGCCAACAGCCG;RSEQ=GTGCCAGCCCCCAGATTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:30.5:1:1:0:60:4:1:0:1.5 +9 114912617 . A C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03362;SOR=0.73682;LSEQ=TCCTTTTAGAGCTGATCTAC;RSEQ=CAGTTAGCTTTTTTTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:369:164:90,74:109,96:205,164:0.4444:2,2:27.8:1:31.1:1:0.75367:1.07:60:81:0.4438:0:1.1 0/1:472:175:90,85:153,143:296,175:0.3708:2,2:25.3:1:30.2:1:1:1.01047:60:86.5:0.3704:0:1.1 +9 114912625 . C CT 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.03743;SOR=0;LSEQ=GAGCTGATCTACACAGTTAG;RSEQ=TTTTTTTGGGAGAAAAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:4:1,3:199,177:376,4:0.0105:2,2:16.3:1:28.8:1:0.34865:3.36293:60:8:0.0106:0.0053:1 0/0:482:0:0,0:245,237:482,0:0:2,0:26.5:1:31.2:1:1:0:60:79.333:1:0:0.5 +9 114912713 . GT G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.05633;SOR=Inf;LSEQ=CCAGTGGGCCCCTCATATCC;RSEQ=TTAATGGCCTCTCACAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:48,141:189,0:0:2,0:24.9:1:29.5:1:1:0:60:22.625:1:0:0.1 0/1:182:4:1,3:48,130:178,4:0.022:2,2:27.8:1:31.2:1:1:1.10708:60:8:0.0223:0.0055:0 +9 114912752 . A C 141 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGCACTCAATTCTTATTCA;RSEQ=CCAAAAGTACCCTCCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:4,81:85,0:0:1,0:23.1:1:30.3:1:1:0:60:41.5:1:0:0.1 0/1:77:23:0,23:6,48:54,23:0.2987:2,1:24.7:1:31.3:1:0.17047:0:60:46:0.2987:0:1.1 +9 116790592 . A C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATCAGGCCCCTCTGCCTC;RSEQ=CCCCCAGCCCCGGCATGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25.5:1:33.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 116791055 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50431;SOR=0;LSEQ=ACCGGATGATCCAGACACGG;RSEQ=CTCTGAGTGTTCACATCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:2:1,1:101,30:131,2:0.015:2,2:37.5:1:31.5:1:0.41319:3.32823:60:4:0.0156:0:1 0/0:106:0:0,0:79,25:104,0:0:2,0:23.8:1:30.5:1:1:0:60:33.667:0.9806:0:0.1 +9 116791095 . C T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24872;SOR=0;LSEQ=GAGGTCTCCCCATCTCCACG;RSEQ=TTCGTGGCAGCGAAGACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:3:1,2:178,80:258,3:0.0115:2,2:17:1:25.3:1:0.23317:4.42174:60:6:0.0118:0:2 0/0:253:0:0,0:161,92:253,0:0:2,0:23.6:1:31.2:1:1:0:60:506:1:0:0.5 +9 116791143 . G T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.0508;SOR=Inf;LSEQ=CAGTCGGGGAAAAAAGCTCC;RSEQ=GCCTCCGTGGTCCGATGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:442:0:0,0:250,190:440,0:0:2,0:25.3:1:30.2:1:1:0:60:47.889:0.9977:0:0.9 0/1:401:4:1,3:213,183:396,4:0.01:2,2:15.8:1:28.8:1:0.34172:3.48169:56:8:0.0102:0:2 +9 116791161 . T C 267 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.34495;LSEQ=CCGGCCTCCGTGGTCCGATG;RSEQ=GCCACCCTCTTACACCGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:468:398:216,182:36,34:70,398:0.8504:2,2:27.3:1:31:1:0.69753:1.12:60:65.333:0.8503:0:1.1 1/0:432:286:146,140:78,67:145,286:0.662:2,2:24.3:1:30.3:1:0.61103:1.11605:59.9:142:0.6636:0:1.2 +9 117485190 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCACTGCACGTCTGCAAG;RSEQ=TCACTGGATGAAAACGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:14,0:0:2,0:23.6:1:32.8:1:1:0:60:28:1:0:0 0/1:39:2:1,1:21,15:36,2:0.0513:2,2:13.5:1:27.5:1:1:1.38742:60:4:0.0513:0:1 +9 117485255 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.56614;SOR=Inf;LSEQ=GTGCTTGGGTACAGTTCCTC;RSEQ=AAATGCCTCTTGCTAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:9,9:18,0:0:2,0:21.3:1:31.1:1:1:0:60:17:1:0:0 0/1:55:4:2,2:22,29:51,4:0.0727:2,2:24.8:1:29.5:1:1:1.31:60:8:0.0727:0:1.3 +9 118486252 . G T 29 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TTACGGAGCTCCCATGGGGA;RSEQ=GGGCAACCAGCATCACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:30:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:29:0:1:0:60:4:1:0:1.5 +9 118486817 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50529;SOR=Inf;LSEQ=CCCAACTGGGTGAGACCCTC;RSEQ=AACAGGGGATGTCAGACACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:8,10:18,0:0:2,0:24.1:1:31.3:1:1:0:42.3:36:1:0:0.1 0/1:26:2:1,1:11,13:24,2:0.0769:2,2:37.5:1:31:1:1:1.17:40.5:4:0.08:0:1 +9 118486836 . C T 68 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02866;SOR=Inf;LSEQ=CCAACAGGGGATGTCAGACA;RSEQ=CCTATACAGGAGCGATCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:16,0:0:2,0:16.5:1:31.4:1:1:0:42:32:1:0:0.1 0/1:23:7:3,4:7,9:16,7:0.3043:2,2:15.9:1:24.4:1:1:1.03541:42.7:2.5:0.2381:0:2 +9 118486938 . G C 52 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=0;LSEQ=TTTGCTGTCCTCCAGCCTCC;RSEQ=TGAGTGACATCTCCAGGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:29:1:33.3:1:1:0:53:6:1:0:1 0/1:5:1:1,0:2,2:4,1:0.2:2,0:37:0:31:0:1:0:60:2:0.2:0:1 +9 119904284 . G C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGGTGAGGTTGGACAGA;RSEQ=CAGAGAAGACAGCGTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:18:1:31:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 119905188 . C G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20458;SOR=0.35481;LSEQ=TTCTTCTTCAGTTTGAGCTA;RSEQ=CTGCTGTCTGATGCCAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:18:17,1:23,0:23,18:0.439:1,1:21.8:1:33.3:1:0.43902:0:60:36:0.439:0:1.1 0/1:14:3:3,0:10,1:11,3:0.2143:2,0:31:1:33:1:1:0:60:6:0.2143:0:1 +9 119905254 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5177;SOR=0;LSEQ=TCTTTGAAGGGGCTTCATCA;RSEQ=ACTAGACAAAGAAGGCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:2:1,1:105,18:123,2:0.0159:2,2:14:1:28.5:1:0.28194:5.70477:60:4:0.0161:0:1 0/0:84:0:0,0:67,17:84,0:0:2,0:21.8:1:31.3:1:1:0:60:83:1:0:0.2 +9 119905342 . G T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.37487;SOR=3.74928;LSEQ=GCTTATCAGGTTAGACAGAT;RSEQ=TGTCTGCAGAGTAAGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:354:1:0,1:197,156:353,1:0.0028:2,0:1:0:27:0:0.4435:0:60:2:0.0028:0:2 0/1:380:4:2,2:212,164:376,4:0.0105:2,2:29.5:1:27.3:1:1:1.29179:60:8:0.0106:0:1.8 +9 119905369 . G C 227 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.26139;SOR=0.84725;LSEQ=CAGAGTAAGTCAGACCTAGA;RSEQ=GGCTTGTTCTGGTATTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:161:77,84:135,145:280,161:0.3643:2,2:24.8:1:31:1:1:1.01564:60:160:0.3628:0:1.2 0/1:456:149:78,71:158,148:306,149:0.3268:2,2:26.2:1:30.3:1:0.92053:1.03:60:73.5:0.3245:0:1.2 +9 119905437 . C T 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00071;SOR=Inf;LSEQ=ATAGGGAAAAGGTATGATTG;RSEQ=TAAGGTAAAAAGACAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:117,184:301,0:0:2,0:25.4:1:32.7:1:1:0:60:74.25:1:0:0.3 0/1:287:10:2,8:99,177:276,10:0.0348:2,2:30.2:1:30.5:1:0.50257:2.23184:60:20:0.0352:0:1 +9 119905583 . T C 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15556;SOR=6.88885;LSEQ=TCCAGACATGGGGTCCCTTC;RSEQ=TCAAGCCTGGGATGAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:1:0,1:1,18:19,1:0.05:1,0:30:0:35:0:1:0:60:2:0.05:0:1 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:38:1:31:1:1:0:60:4:0.3333:0:1 +9 119965718 . AT A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.49351;SOR=Inf;LSEQ=TGCTCTTTTGGGTTTTTAGC;RSEQ=TTTTTCATTGATTATTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:9,0:0:2,0:24.4:1:29.7:1:1:0:60:18:1:0:0 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:24.5:1:31.5:1:1:1.67325:53:4:0.1538:0:0 +9 119965809 . TTTG T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=7.000;MSILEN=3;SSF=0.52159;SOR=Inf;LSEQ=ATGGGGTTTTTGTGGGGGCC;RSEQ=TTGTTGTTGTTGTTGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:7,9:16,0:0:2,0:25.8:1:29.9:1:1:0:53.5:15:1:0:0.1 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:42.5:1:30.5:1:1:1.0801:60:4:0.08:0:0 +9 119966410 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48387;SOR=0;LSEQ=TACACCTGAACAGGCACTGT;RSEQ=GCCGCCTACTGCCATTGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:7,7:14,2:0.125:2,2:35.5:1:29.5:1:1:1:60:4:0.125:0:1 0/0:16:0:0,0:6,10:16,0:0:2,0:25.5:1:30.7:1:1:0:60:32:1:0:0.1 +9 119966491 . A G 51 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCCTCCCTGGCTCCACA;RSEQ=AAATTTTTGTGTATTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:18.3:1:32.3:1:1:0:60:6:1:0:1 1/1:1:1:0,1:0,0:0,1:1:0,0:27:0:32:0:1:0:60:2:1:0:1 +9 122204648 . A AG 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.6662;SOR=0.77632;LSEQ=GAAGTCAAAATTCAAATCTC;RSEQ=CAGGCTGACTCCAAAGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:30:30,0:19,0:19,30:0.6122:1,1:25.6:1:32.4:1:1:0:60:29:0.6042:0.0816:0.1 1/0:40:22:22,0:18,0:18,22:0.55:1,1:21.3:1:31.2:1:1:0:59.5:44:0.55:0.175:0.1 +9 122204709 . A T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.59814;SOR=0.4293;LSEQ=CTTCCTCTGCTGCATCCCAC;RSEQ=CTGCTCCCCATCCACAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:107,30:137,2:0.0144:2,2:19:1:29:1:0.39756:3.52481:60:4:0.0145:0:1 0/0:161:1:0,1:115,45:160,1:0.0062:2,0:1:0:23:0:0.28571:0:60:2:0.0064:0:1 +9 122204804 . A C 248 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00323;SOR=1.55358;LSEQ=AAGACAGGATGTGTTCTGCC;RSEQ=AGTGGCACCTTAAACGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:375:211:101,110:82,80:162,211:0.5627:2,2:27.6:1:31.7:1:0.60327:1.11601:60:104.5:0.5618:0:1.1 1/0:408:272:142,130:56,80:136,272:0.6667:2,2:25.4:1:30.7:1:0.03643:1.56:60:67:0.6634:0:1.1 +9 122204884 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23764;SOR=Inf;LSEQ=GTTCCTGCCTCTGCCCCAGT;RSEQ=TAAGAAGGGGGCAGGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:42,132:174,0:0:2,0:24.3:1:33.1:1:1:0:60:348:1:0:0.3 0/1:166:2:1,1:48,116:164,2:0.012:2,2:33.5:1:28:1:0.50449:2.40:60:4:0.0123:0:1 +9 122204917 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2314;SOR=Inf;LSEQ=AGGCAGATACTGAGGCCCTG;RSEQ=CTTTATTTCTGTGTCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:11,78:89,0:0:2,0:24.6:1:30.1:1:1:0:60:43.5:1:0:0.1 0/1:83:2:1,1:9,72:81,2:0.0241:2,2:29:1:31.5:1:0.22774:7.64:60:4:0.025:0:1 +9 122623982 . A C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2029;SOR=0;LSEQ=TTACAGGGCCCTAGCAAACC;RSEQ=ATACACTGGATAACCTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:24:1:31:1:1:1.11:48:4:0.1:0:1 0/0:25:0:0,0:12,13:25,0:0:2,0:29.8:1:29.6:1:1:0:48.4:50:1:0:0.5 +9 122623999 . T C 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12921;SOR=2.8153;LSEQ=ACCAATACACTGGATAACCT;RSEQ=GAGCAATATATTAAACTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:3,6:6,8:14,9:0.3913:2,2:25.1:1:30.7:1:1:1.47391:42:18:0.3913:0:1.1 1/0:20:13:6,7:3,4:7,13:0.65:2,2:24.6:1:29.5:1:1:1.14:49.3:26:0.65:0:1 +9 124037184 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52087;SOR=Inf;LSEQ=TGGATTTTACAAGGAAGTGC;RSEQ=CAGGTAGGCCTAGGAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:13,9:22,0:0:2,0:32.3:1:30.4:1:1:0:60:44:1:0:0.2 0/1:36:2:1,1:18,16:34,2:0.0556:2,2:41.5:1:31.5:1:1:1.12132:60:4:0.0556:0:1.5 +9 125532953 . G A 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.53112;SOR=0;LSEQ=GATGGGAAATAACCAAGATC;RSEQ=GGGGGAACTGAAGGAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:25:12,13:0,0:0,25:1:0,2:23.7:1:30.4:1:1:0:60:24:1:0:1.1 1/1:44:42:25,17:1,1:2,42:0.9545:2,2:25.4:1:28.9:1:1:1.46:60:41:0.9535:0:1.2 +9 125767432 . G T 35 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33171;SOR=0.27137;LSEQ=GGAACTTCTTTTTGTCCTTT;RSEQ=AATATGTTTCAGTAAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:3:2,1:228,45:273,3:0.0109:2,2:5.3:1:22.3:1:0.42256:2.52213:57.7:2:0.0074:0:3 0/0:337:1:0,1:262,74:336,1:0.003:2,0:1:0:21:0:0.22255:0:60:2:0.003:0:1 +9 125767540 . C G 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=4.00454;LSEQ=ATAGTTAGGTTCATTTGTTT;RSEQ=CATTTATTTTAGCTTAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:734:49:20,29:308,371:679,49:0.0668:2,2:26:1:30.3:1:0.55617:1.20347:60:6:0.0633:0:1.3 0/1:965:215:106,109:319,426:745,215:0.2228:2,2:26.7:1:29.9:1:0.10172:1.30:59.9:10.316:0.2168:0:1.3 +9 125767567 . AT A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0;SOR=0.50153;LSEQ=TTTTAGCTTAGGGGCTTGGG;RSEQ=TTTTTTTTTTCCTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:538:348:116,232:77,105:182,348:0.6468:2,2:28.7:1:30.9:1:0.04606:1.46553:60:57:0.6502:0.0167:0.4 0/1:679:325:104,221:137,187:324,325:0.4786:2,2:29.9:1:30.2:1:0.00736:1.55571:59.9:107.333:0.4828:0:0.3 +9 125767578 . T C 157 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14167;SOR=1.46027;LSEQ=GGGCTTGGGATTTTTTTTTT;RSEQ=CCTTTTTTTTTTGAATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:26:12,14:133,280:413,26:0.0569:2,2:18.5:1:28.3:1:0.19553:1.80:59.5:5.5:0.0499:0:2.4 0/1:568:46:19,27:154,347:501,46:0.081:2,2:16.6:1:28.5:1:0.18409:1.58:59:14.333:0.0776:0:2 +9 125767580 . C T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=0.55848;SOR=1.20906;LSEQ=GCTTGGGATTTTTTTTTTTC;RSEQ=TTTTTTTTTTGAATATATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:20:7,13:130,280:410,20:0.0458:2,2:25.2:1:28.2:1:0.80718:1.16:59.4:4:0.0394:0:2.9 0/1:529:29:11,18:149,342:491,29:0.0548:2,2:24.2:1:29.1:1:0.4105:1.40:58.5:28:0.0556:0:2.7 +9 125767591 . G T 58 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51641;SOR=1.73025;LSEQ=TTTTTTTTCCTTTTTTTTTT;RSEQ=AATATATAAAATACTTATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:364:3:3,0:89,268:357,3:0.0082:2,0:12.3:1:18.7:1:0.01629:0:60:2:0.0061:0:2 0/1:423:6:3,3:107,307:414,6:0.0142:2,2:11.7:1:22.7:1:0.18733:2.86:59.2:2:0.0104:0:3.8 +9 126974713 . AT A 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.66086;SOR=0.53979;LSEQ=TCCGGCTTTCTTTTCTAATC;RSEQ=TTTTTTTGTTGCTCCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:2,1:139,51:190,3:0.0155:2,2:40:1:31.3:1:1:1.36042:60:6:0.0155:0:1.3 0/0:237:2:2,0:179,56:235,2:0.0084:2,0:48.5:1:33:0:1:0:60:4:0.0085:0:1.5 +9 126974738 . C T 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.12145;LSEQ=TTTTGTTGCTCCTTTTCTCC;RSEQ=TTTGACATAACAAACCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:272:240:158,82:23,9:32,240:0.8824:2,2:26.4:1:31.3:1:0.55508:1.32497:60:119:0.8848:0:1.1 0/1:351:167:114,53:119,63:182,167:0.4758:2,2:25.3:1:30:1:0.57214:1.14:60:166:0.477:0:2.1 +9 126974767 . G T 208 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACAAACCAGTTTGTTTTCC;RSEQ=ATCTGATTGTTCTCAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:202,146:348,0:0:2,0:26.8:1:30.7:1:1:0:60:68.6:1:0:0.7 0/1:484:160:93,67:179,144:323,160:0.3306:2,2:26.4:1:28.5:1:0.62623:1.12:60:31:0.3263:0:2.5 +9 126974804 . C G 226 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGAATGTCCTTTCCTTCTC;RSEQ=GTTACTCTCGGTTTAATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:396:0:0,0:181,215:396,0:0:2,0:25.9:1:30.6:1:1:0:60:98:1:0:0.4 0/1:530:207:98,109:151,172:323,207:0.3906:2,2:27.1:1:29.4:1:0.92901:1.02:60:102.5:0.3905:0:2 +9 126974902 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23182;SOR=0;LSEQ=CCCACAAACGCTGTCCTGTG;RSEQ=GTCCCCTTCCTCATCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:17,105:122,2:0.0161:2,2:15:1:30:1:0.27026:6.03:60:4:0.0168:0:1 0/0:133:0:0,0:25,108:133,0:0:2,0:21.9:1:29.9:1:1:0:60:65.5:1:0:0.2 +9 126975022 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.06536;SOR=Inf;LSEQ=TGAGACCTTCTCCCATGTGT;RSEQ=TGTCCTGTGATTGTGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:1,12:13,0:0:1,0:19.8:1:31.5:1:1:0:58:12:1:0:0.5 0/1:5:2:0,2:0,3:3,2:0.4:0,0:40.5:1:29.5:1:1:0:60:4:0.4:0:1 +9 127180842 . T TA 29 d5;v3;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=18.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CAACAGAGAAAGACTCTGTC;RSEQ=AAAAAAAAAAAAAAAAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:9.5:1:29.5:1:1:0:60:4:0.6667:0.3333:1.5 0/0:3:0:0,0:1,0:1,0:0:0,0:26:1:29.5:1:1:0:60:2:0.3333:0:5 +9 127181726 . C T 27 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCTGGGAGGCGGAGGTTG;RSEQ=AGTGAGCTGAGATCACACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:0:27.5:1:1:0:33.5:4:1:0:1 +9 127911821 . TA T 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.83137;SOR=1.11064;LSEQ=AATTTAGATAATTTAAAATT;RSEQ=AAAAAAAAAAGGCAAGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:13:13,0:127,2:129,13:0.0909:1,1:20.5:1:31:1:1:0:60:26:0.0922:0.035:0.2 0/1:110:11:10,1:97,2:99,11:0.1:1,2:24.5:1:30.4:1:0.27324:4.73152:60:22:0.1:0.0364:0.2 +9 127912316 . G A 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.041;SOR=1.86749;LSEQ=AGGCATCAAGATTATAGAAC;RSEQ=CACTCTATAATTATCTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:33:0,33:2,51:53,33:0.3837:1,1:21.2:1:30.1:1:0.52148:0:60:32:0.3902:0:1.1 1/0:104:56:3,53:1,47:48,56:0.5385:1,2:23:1:29.8:1:0.62221:2.64:60:112:0.5437:0:1 +9 127915872 . A G 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGGGGACTGATAGCCCAGGT;RSEQ=TCCACATCTTCAGGATCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1230:0:0,0:662,567:1229,0:0:2,0:24.4:1:29.5:1:1:0:60:135.556:0.9992:0:0.1 0/1:1509:59:31,28:783,664:1447,59:0.0391:2,2:25.3:1:31.4:1:0.89415:1.06503:60:58:0.0387:0:1.2 +9 127916095 . A C 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=CTCATCAGTGAATACTAAAG;RSEQ=TATCAATATAATTGAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:440:0:0,0:221,218:439,0:0:2,0:24.4:1:31:1:1:0:59.9:145.333:1:0:0.1 0/1:432:43:23,20:183,206:389,43:0.0995:2,2:24:1:31.7:1:0.42715:1.29:60:86:0.1005:0:1 +9 127916233 . A G 157 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGGTACAGTATCTCCAGGC;RSEQ=TTAGCATTTCCATATTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1062:0:0,0:499,562:1061,0:0:2,0:24.9:1:30.7:1:1:0:60:131.625:0.9991:0:0.2 0/1:1245:37:19,18:585,622:1207,37:0.0297:2,2:20.5:1:30.2:1:0.74172:1.12:60:74:0.0299:0:1.2 +9 127916457 . G A 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.79012;SOR=1.323;LSEQ=GTGACTAACTACATACAGTT;RSEQ=TATGTCCCTTAACCATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:16:0,16:0,18:18,16:0.4706:1,1:23.7:1:31.1:1:1:0:60:32:0.4706:0:1.1 1/0:24:13:0,13:0,11:11,13:0.5417:0,1:19.8:1:29.4:1:1:0:60:26:0.5417:0:1.1 +9 127920158 . A C 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTGTATTTTTAGAAGAGA;RSEQ=GGGGTTTCACCATATTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:11:1:32:1:1:0:41:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 127920934 . A AT 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTGAAAAAAAAAACCACC;RSEQ=TTTTTTTTTCTTTTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:0,2:0,12:12,2:0.1429:0,0:7.5:1:30.5:1:1:0:53:4:0.1429:0.0714:1.5 0/0:2:0:0,0:0,2:2,0:0:0,0:13.5:1:30:1:1:0:60:4:1:0:0 +9 127923013 . TG CT 182 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.01057;SOR=0.49482;LSEQ=ATACACATCTTTTAATATAC;RSEQ=AAATAGGGACTGTCACATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:53:51,2:62,0:62,53:0.4609:1,1:21.1:1:31.9:1:0.21022:0:58.3:106:0.469:0.0609:0.9 0/1:118:35:35,0:79,3:82,35:0.2966:1,1:19.5:1:30.8:1:0.55317:0:59.2:70:0.2966:0.0678:0.9 +9 127923255 . G A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24876;SOR=Inf;LSEQ=AAAGCAACAAAACTGAGAGT;RSEQ=AAATGTGTAAAGAAGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:0:0,0:47,245:292,0:0:2,0:25.4:1:32.4:1:1:0:60:291:1:0:0.1 0/1:297:3:1,2:70,224:294,3:0.0101:2,2:19.3:1:23:1:0.56079:1.60:59.3:2:0.0069:0:2.7 +9 127933739 . TAC T 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCAAACACACACACACATA;RSEQ=ACACACACACACACACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:21:1:29.5:1:1:0:52.5:4:0.2857:0.1429:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 127951072 . C CAATAAT 184 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=11.000;MSILEN=3;SSF=0.01894;SOR=0.5483;LSEQ=GACTCTATCTCAGTTAAAAA;RSEQ=AATAATAATAATAATAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:59:57,2:104,9:113,59:0.3207:2,1:23.8:1:31.3:1:0.33481:2.46:59.8:118:0.3207:0.087:0 0/1:151:31:26,5:101,5:106,31:0.2053:1,2:20.2:1:29.4:1:0.04674:3.83542:60:62:0.2053:0.0662:0.4 +9 127951429 . G C 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09621;SOR=Inf;LSEQ=CCGCCAGTACCAAACCACTC;RSEQ=GGCCCACCGCCTTCCCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:2,37:39,0:0:2,0:19.3:1:31:1:1:0:59.4:38:1:0:0.1 0/1:34:3:0,3:0,31:31,3:0.0882:1,0:16:1:29.3:1:1:0:60:6:0.0882:0:1 +9 127951582 . GC CT 91 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.65753;LSEQ=GGCACTGCCGCGGGGGCTCG;RSEQ=TCCGACTGCGGGAGACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:4,3:6,3:9,7:0.4375:2,2:26.7:1:32.6:1:1:1.46198:55.4:14:0.4375:0:1 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:20:0:32.5:0:1:0:60:2:0.3333:0:1 +9 127951863 . G A 262 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00408;SOR=1.30287;LSEQ=GGCGGGGGTCCTGGAGAAAG;RSEQ=AAGGGCCGGCCGGCGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:885:410:223,187:258,215:473,410:0.4633:2,2:26.3:1:30.4:1:1:1.00627:59.9:67.333:0.4649:0:1.1 1/0:1056:559:318,241:262,233:495,559:0.5294:2,2:24.6:1:28.8:1:0.21476:1.17:59.8:45.583:0.5285:0:1.2 +9 127952023 . AGCG A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.0625;SOR=1.78306;LSEQ=GAATAACAAGCCGCGGCAAC;RSEQ=GCGGCGGCGGCTGTAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:17:7,10:232,395:627,17:0.0264:2,2:32.5:1:32.2:1:0.80072:1.19:60:34:0.0267:0:0.1 0/1:737:34:11,23:275,425:700,34:0.0461:2,2:29.4:1:31.8:1:0.47492:1.3524:59.9:68:0.0466:0.0027:0.2 +9 127952210 . G T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=CGACTGCAGGCCCCAAGAGA;RSEQ=CCCGCTTCGGTCCACCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:5,8:0.6154:0,0:27.1:1:29.5:1:1:0:60:16:0.6154:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:2:0:32:0:1:0:60:2:1:0:0 +9 127952430 . A ACTCT 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=4.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TTTTTCCAACCCTTTTAAGC;RSEQ=CTCTCCAGAATATCTTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:35:1:32.1:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 128736041 . T C 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00162;SOR=4.70464;LSEQ=GAGGTGCCGGCTGGAGTAGG;RSEQ=CTCTGCATCGGGGCTGTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:24:10,14:11,12:23,24:0.5106:2,2:26.3:1:32.3:1:0.77248:1.27651:60:48:0.5333:0:1.2 1/1:42:35:16,19:3,4:7,35:0.8333:2,2:24.1:1:29.5:1:1:1.12:60:34:0.8293:0:1.1 +9 128736150 . C T 79 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10909;SOR=Inf;LSEQ=GAAACACACACGCATCACCC;RSEQ=AGCTGCTTGAGAGTGTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:0,2:2,2:0.5:0,0:45.5:1:30:0:1:0:60:4:0.5:0:2 1/1:7:7:1,6:0,0:0,7:1:0,2:22.6:1:28.3:1:1:0:60:14:1:0:1.9 +9 128736180 . G A 80 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGTGTGCAATCTGAATGC;RSEQ=TCTCAGTTTTTTGGTTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:23:1:33:0:1:0:60:4:1:0:2 1/1:6:6:1,5:0,0:0,6:1:0,2:29.3:1:31:1:1:0:60:12:1:0:2 +9 129467722 . G T 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGTCAGGCCACGAGGTGGC;RSEQ=ATCCGGAGTCAGTCAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:27:0:30.5:1:1:0:60:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 129467746 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=0;LSEQ=CGGAGTCAGTCAGGTGTAGC;RSEQ=CACGTGGCCGGCGGAGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:33:1:30.3:1:1:0:60:6:1:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:16.5:1:29:1:1:0:60:4:1:0:0.5 +9 129469433 . G A 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02551;SOR=0.38864;LSEQ=TTTTTGATGTAAGATACGCA;RSEQ=TGGACAACATATATCATCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:66:53:38,15:11,2:13,53:0.803:2,2:23:1:30.6:1:0.48761:2.14869:59.8:106:0.803:0:1.2 1/0:54:33:22,11:15,6:21,33:0.6111:2,2:22.2:1:29.2:1:0.77174:1.24489:60:66:0.6111:0:1.2 +9 129469523 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.19828;SOR=Inf;LSEQ=CTGGTGTGGGGTCTCCTCTG;RSEQ=TCCCCCTCACACACAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:53,56:109,0:0:2,0:22.5:1:31.4:1:1:0:59.9:218:1:0:0.8 0/1:88:2:1,1:44,42:86,2:0.0227:2,2:20:1:28.5:1:1:1.04708:60:4:0.023:0:2 +9 129469533 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.50029;SOR=0;LSEQ=GTCTCCTCTGGTCCCCCTCA;RSEQ=ACACAGAGAGCAGGGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:39,55:94,2:0.0208:2,2:37:1:29:1:1:1.41:60:4:0.0213:0:2.5 0/0:82:0:0,0:37,45:82,0:0:2,0:24:1:31.6:1:1:0:59.9:164:1:0:0.5 +9 129469539 . G C 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.21927;LSEQ=TCTGGTCCCCCTCACACACA;RSEQ=AGAGCAGGGACAGCTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:93:72:31,41:8,12:20,72:0.7742:2,2:24.8:1:32.4:1:1:1.13:60:71:0.7802:0:1.1 0/1:82:35:14,21:21,26:47,35:0.4268:2,2:25:1:31.5:1:0.82174:1.2087:60:70:0.4268:0:1.1 +9 129470630 . T C 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCAGCCAGCAGGTTGGTT;RSEQ=AGACATGACAAGAAGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:34:0:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 131041700 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49661;SOR=Inf;LSEQ=TGCATACAAAACAAGGGGGG;RSEQ=AGGGTAAGGAAGGTGAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,12:26,0:0:2,0:18.4:1:32.2:1:1:0:55.3:52:0.963:0:0.2 0/1:33:2:1,1:20,11:31,2:0.0606:2,2:5:0:31.5:1:1:1.78367:60:4:0.0645:0:1 +9 131041752 . A G 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03615;SOR=Inf;LSEQ=GATAAGATCAAGCAAGTCAC;RSEQ=TGATCGTGGGCCAGTGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:18,24:42,0:0:2,0:27.8:1:30.5:1:1:0:53.3:41:1:0:0.2 0/1:34:4:2,2:13,17:30,4:0.1176:2,2:32.5:1:31.8:1:1:1.30:37.5:8:0.1176:0:1.3 +9 131482467 . T C 30 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGCCCTAAGTGAGCGCC;RSEQ=GTCCTATTGCCCAGCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:30.5:1:1:0:60:4:1:0:1 1/1:1:1:1,0:0,0:0,1:1:0,0:4:0:31:0:1:0:60:2:1:0:1 +9 133710740 . G GC 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.44135;LSEQ=CGGCTGGCGGGGCCGGGGGC;RSEQ=CCGGGGGGGCGCGCGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:3,1:0,0:0,4:0.6667:0,2:9.5:1:32.6:1:1:0:56.3:8:0.6667:0.5:1.8 1/0:4:3:2,1:0,0:0,3:0.75:0,2:5.1:1:27.7:1:1:0:60:8:0.7444:0.7333:0.3 +9 133710760 . G T 28 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.34927;LSEQ=GCCGGGGGGGCGCGCGGGCC;RSEQ=AGCCGGGCCTGAGCCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:0,1:63,12:75,1:0.0132:2,0:1:0:23:0:0.17105:0:60:2:0.0135:0:2 0/1:113:2:1,1:87,24:111,2:0.0177:2,2:6:0:28.5:1:0.39507:3.57182:60:4:0.0179:0:2.5 +9 133710768 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.4678;LSEQ=GGCGCGCGGGCCGAGCCGGG;RSEQ=CTGAGCCGGGCCCGCGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:1:0,1:118,26:144,1:0.0069:2,0:1:0:26:0:0.18621:0:60:2:0.0071:0:2 0/1:198:2:1,1:147,49:196,2:0.0101:2,2:10.5:1:26.5:1:0.44224:2.97992:60:4:0.0104:0:2 +9 133710774 . C T 55 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.7055;SOR=1.74094;LSEQ=CGGGCCGAGCCGGGCCTGAG;RSEQ=CGGGCCCGCGGACCGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:2:1,1:139,36:175,2:0.0113:2,2:17.5:1:29:1:0.37532:3.82225:60:4:0.0116:0:2 0/1:256:5:1,4:190,61:251,5:0.0195:2,2:5:1:24:1:0.01562:12.31215:60:10:0.0198:0:2 +9 133710785 . G T 32 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07611;SOR=0;LSEQ=GGGCCTGAGCCGGGCCCGCG;RSEQ=ACCGAGCTGGGAGAGGGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:1,2:205,71:276,3:0.0108:2,2:15.3:1:20.3:1:0.16856:5.73062:60:2:0.0073:0:2.3 0/0:378:0:0,0:274,104:378,0:0:2,0:18.7:1:30.8:1:1:0:59.8:125:1:0:1.2 +9 133710804 . T C 295 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=1;SOR=1.39205;LSEQ=GGACCGAGCTGGGAGAGGGG;RSEQ=TCCGGCCCCCGACGTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:480:479:335,144:0,1:1,479:0.9979:0,2:23.8:1:32.5:1:0.30208:0:59.8:33.214:0.9979:0:1.3 1/1:668:667:438,229:0,1:1,667:0.9985:0,2:23.2:1:31.5:1:0.34431:0:59.5:54.583:0.9985:0:1.2 +9 133710819 . T TC 290 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02483;SOR=0.25986;LSEQ=AGGGGTTCCGGCCCCCGACG;RSEQ=GCTGGCGCGGGAAAATGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:722:719:481,238:0,0:0,719:0.9958:0,2:23.8:1:31.2:1:1:0:59.7:58.917:1:0.2147:0.9 1/1:822:809:515,294:6,7:13,809:0.9842:2,2:27.7:1:30.1:1:0.24656:2.04:59.6:43.944:0.9838:0.0243:1.1 +9 133711028 . C CT 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.63813;SOR=0.44074;LSEQ=GCGCCCTCCCCGGGTCTTGT;RSEQ=TTTTTTTTCTTTCTTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:3:0,3:12,215:227,3:0.013:2,0:11.3:1:32:1:1:0:60:6:0.0133:0.0043:0.3 0/0:173:1:0,1:6,165:171,1:0.0058:1,0:45:0:27:0:1:0:60:2:0.0058:0:0 +9 133711045 . CCTCTT C 195 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=4.000;MSILEN=5;SSF=0;SOR=3.64422;LSEQ=TGTCTTTTTTTTCTTTCTTC;RSEQ=CTCTTCTCTTCTCTTCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:43:0,43:5,112:117,43:0.2688:1,1:33.4:1:34.1:1:0.32509:0:60:86:0.2688:0.0063:0.2 1/0:122:70:3,67:1,50:51,70:0.5738:1,1:32.5:1:31.9:1:0.63755:2.23:59.8:140:0.5785:0.0082:0.3 +9 133711062 . T A 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=5;SSF=0.03638;SOR=Inf;LSEQ=TTCCCTCTTCTCTTCTCTTC;RSEQ=CTTCAGTTCTCTTATATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:0,116:116,0:0:1,0:26.8:1:30.4:1:1:0:60:37.667:1:0:0.1 0/1:93:4:1,3:3,86:89,4:0.043:1,2:10.3:1:23.5:1:0.16375:9.00:57.5:3:0.033:0:2.8 +9 133711138 . T TTTTCTC 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.04544;SOR=4.4858;LSEQ=CTCTTCTCTTGTCTCTCTCT;RSEQ=TTTCTCTCTCTCTGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:0,7:0,11:11,7:0.3889:0,0:27:1:32.6:1:1:0:58.6:14:0.3889:0.0556:0.4 1/0:16:12:2,10:0,4:4,12:0.75:0,2:23.4:1:28.9:1:1:0:58.3:11:0.7333:0.25:0.6 +9 133711140 . TTCTC T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=5.000;MSILEN=2;SSF=0.05743;SOR=0;LSEQ=CTTCTCTTGTCTCTCTCTTT;RSEQ=TCTCTCTGTCTCTTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:14,5:0.2632:1,0:25.2:1:30.7:1:1:0:60:10:0.2778:0.1053:0 0/0:14:0:0,0:2,12:14,0:0:2,0:26.9:1:28.5:1:1:0:58.6:13:1:0:0.5 +9 133729466 . C T 62 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12799;SOR=5.39755;LSEQ=TCCAGAAGCCCTTCAGCGGC;RSEQ=AGTAGCATCTGACTTTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:518:1:0,1:358,159:517,1:0.0019:2,0:1:0:24:0:0.30888:0:60:2:0.0019:0:1 0/1:580:6:1,5:376,196:572,6:0.0103:2,2:8.8:1:24.3:1:0.02111:9.55725:60:12:0.0105:0:1 +9 133730139 . A T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24808;SOR=Inf;LSEQ=AGAATCAATGAAAAAGAACG;RSEQ=AGCTGGTTTCCAAAGCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:0:0,0:159,34:193,0:0:2,0:23.8:1:30.5:1:1:0:60:95.5:1:0:0.1 0/1:195:3:1,2:143,49:192,3:0.0154:2,2:10.7:1:26:1:0.16799:5.7726:60:6:0.0155:0:1 +9 133730543 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1977;SOR=Inf;LSEQ=CAGGGGAACCAGAGGTCCTG;RSEQ=TGTCGGATTGATAAATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:18,145:163,0:0:2,0:22.6:1:33.6:1:1:0:59.8:326:1:0:0 0/1:131:2:0,2:26,102:128,2:0.0153:2,0:18:1:31.5:1:1:0:60:4:0.0154:0:1 +9 133730792 . TA T 24 d5;v3;q25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTACAATAAGATTCTTCCTT;RSEQ=AAAAAAATATTTTATAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:21:1:24:0:1:0:60:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 133732029 . G T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCCCAGAGGCAAGCACT;RSEQ=GTACTAGTTCCTTCTAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:31.5:1:1:0:60:4:1:0:1.5 +9 133738320 . G A 145 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=26.43392;LSEQ=AAGTGGGAGATGGAACGCAC;RSEQ=GACATCACCATGAAGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:546:1:1,0:231,314:545,1:0.0018:2,0:1:0:26:0:0.42491:0:60:2:0.0019:0:1 0/1:626:29:13,16:257,340:597,29:0.0463:2,2:16.9:1:30:1:0.85027:1.07:60:58:0.0472:0:1.1 +9 133738401 . G T 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04361;SOR=0;LSEQ=TGGAAGAAATACAGCCTGAC;RSEQ=GTGGCCGTGAAGACCTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:4:2,2:91,180:271,4:0.0145:2,2:16.3:1:32.3:1:0.60577:1.97:60:8:0.0148:0:1 0/0:325:0:0,0:120,205:325,0:0:2,0:24.6:1:29.7:1:1:0:60:53.167:1:0:0.2 +9 133747414 . C T 82 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14265;SOR=4.00829;LSEQ=TCACAAAACGCAGCCCAGGA;RSEQ=GAGTATGCGCTGAAGCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:2:1,1:118,11:129,2:0.0153:2,2:24:1:20:1:0.17546:10.31408:60:1:0.0079:0:4.5 0/1:102:6:6,0:81,15:96,6:0.0588:2,0:19:1:31.8:1:0.58839:0:60:12:0.06:0:2 +9 133747425 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=AGCCCAGGACGAGTATGCGC;RSEQ=GAAGCTCCATTTTGCATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:131,20:151,2:0.0131:2,2:16.5:1:32.5:1:0.25645:6.4165:60:4:0.0132:0:1 0/0:136:0:0,0:108,28:136,0:0:2,0:21.8:1:29.9:1:1:0:60:33:1:0:0.3 +9 133747457 . C T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-05;SOR=Inf;LSEQ=TTGCATTAACTAGTCAAGTA;RSEQ=TTACCCACTGAAAAGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:179,91:270,0:0:2,0:24.4:1:32.1:1:1:0:60:37.571:1:0:0.1 0/1:284:15:10,5:190,79:269,15:0.0528:2,2:27.2:1:29.8:1:0.77398:1.2017:60:30:0.0536:0:1.6 +9 133747640 . G A 44 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.62741;SOR=2.61561;LSEQ=TGAAGAGAGGGTCTCGCGCC;RSEQ=CACCCCCAGGGTGACACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:256:1:1,0:64,191:255,1:0.0039:2,0:1:0:26:0:0.25391:0:60:2:0.004:0:1 0/1:295:3:2,1:83,208:291,3:0.0102:2,2:10.3:1:28.3:1:0.20154:4.98:60:6:0.0103:0:1 +9 133747734 . C T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00273;SOR=0.229;LSEQ=GTGCTCTGCCGACGTTCAGC;RSEQ=GCGGGTAAAATGAGGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:39:22:1,21:0,17:17,22:0.5641:1,1:28.6:1:29:1:1:0:60:10:0.5405:0:1.3 0/1:40:9:1,8:0,30:30,9:0.225:1,2:23.2:1:30.7:1:0.23077:0:60:18:0.2308:0:1.3 +9 133748083 . A G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.06083;SOR=0.24164;LSEQ=AGCCTGGCCATGTCCCTCCC;RSEQ=CACGAGCACAGTCTCAGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:11:11,0:18,1:19,11:0.3667:1,0:25.3:1:30.4:1:1:0:59.5:22:0.3667:0:1 0/1:25:3:2,1:22,0:22,3:0.12:1,2:26.3:1:30:1:0.12:0:60:6:0.12:0:1 +9 133748150 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24308;SOR=0;LSEQ=TTGGGCCCAGGACTGAGGAG;RSEQ=AGAGTCAGAATCCTTCAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:85,2:87,2:0.0225:1,2:24.5:1:27.5:1:0.06665:34.90295:60:4:0.0227:0:1 0/0:91:0:0,0:85,6:91,0:0:2,0:23.3:1:31.5:1:1:0:60:90:1:0:0.1 +9 133748468 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60004;SOR=2.30107;LSEQ=GCGCCATGGAGTCACAGGGC;RSEQ=TGGAGCCGGGCAGCCTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:1:1,0:31,119:150,1:0.0066:2,0:1:0:28:0:0.21192:0:60:2:0.0066:0:1 0/1:132:2:0,2:27,103:130,2:0.0152:2,0:25:1:29.5:1:1:0:60:4:0.0154:0:1 +9 133748475 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21201;SOR=Inf;LSEQ=GGAGTCACAGGGCGTGGAGC;RSEQ=GGGCAGCCTTTTACAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:21,112:133,0:0:2,0:21.9:1:30.2:1:1:0:60:266:1:0:0.1 0/1:114:2:1,1:18,94:112,2:0.0175:2,2:14:1:26.5:1:0.30678:5.11:60:4:0.0177:0:1 +9 133750539 . G GT 73 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00249;SOR=Inf;LSEQ=TCTTTTCTTCCTTTCTTTTT;RSEQ=TTTTTTTGAGACGGAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:0,159:159,0:0:1,0:20.8:1:32.7:1:1:0:56:158:1:0:0.3 0/1:146:8:0,8:1,137:138,8:0.0548:1,0:25.9:1:24.6:1:1:0:46.9:3:0.0423:0.0068:0.4 +9 133750550 . A G 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03607;LSEQ=TTTCTTTTTGTTTTTTTGAG;RSEQ=CGGAGTCTCACTCTGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:39:0,39:0,79:79,39:0.3277:1,1:20.3:1:32.6:1:1:0:53.2:78:0.3362:0:1.1 0/1:117:2:0,2:0,115:115,2:0.0171:1,0:36.5:1:30:1:1:0:54.5:4:0.0179:0:1 +9 133750552 . G A 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01384;SOR=Inf;LSEQ=TCTTTTTGTTTTTTTGAGAC;RSEQ=GAGTCTCACTCTGTCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:0,115:115,0:0:1,0:22.2:1:31.4:1:1:0:52.4:56.5:1:0:0.4 0/1:113:6:0,6:0,107:107,6:0.0531:1,0:15.5:1:31.3:1:1:0:49.7:12:0.0545:0:1.2 +9 133750687 . C G 67 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10256;SOR=9.47099;LSEQ=TATAGGCACCCGCCACCACA;RSEQ=CCAGCTAATTTTTGGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:16:0:12:0:1:0:56:0:0:0:5 1/0:6:4:2,2:0,2:2,4:0.6667:0,2:10:0:33.5:1:0.46667:0:50:8:0.6667:0:2 +9 133750838 . TT C 34 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGCACAGCCACCCTTTT;RSEQ=TTTTTTTTTTAACTGTGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:16.5:1:34:1:1:0:42:4:0.6667:0.3333:0.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 133753901 . G A 81 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4229;SOR=0.57312;LSEQ=GCTGCTAGAGAAGGACTACC;RSEQ=CATGGAGCGCCCAGAAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:801:9:7,2:333,458:791,9:0.0112:2,2:8.3:1:25.7:1:0.04162:4.80:60:8:0.0102:0:1 0/0:773:5:4,1:332,435:767,5:0.0065:2,2:5.8:1:25.2:1:0.17307:5.23:60:10:0.0065:0:1.2 +9 133754032 . A G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.21313;LSEQ=TGTGCAGGAGTGTGTACACA;RSEQ=AGTTGAAAGTTTTTCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:70:9,61:6,69:75,70:0.4828:2,2:23.8:1:32:1:0.41756:1.69:59.6:69:0.4825:0:1.2 0/1:103:17:4,13:15,71:86,17:0.165:2,2:20.6:1:29.5:1:0.51201:1.45:60:16:0.16:0:1.2 +9 133754099 . C A 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.07063;LSEQ=GCAGCTAATGTAGCCATTTG;RSEQ=TACCTATTGACCTTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:28:0,28:0,22:22,28:0.56:1,1:26.9:1:32.6:1:1:0:59:56:0.5714:0:1.6 0/1:25:2:0,2:1,22:23,2:0.08:1,0:10.5:1:30:1:1:0:60:4:0.08:0:2 +9 133754220 . T C 110 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACAGATTCCTGGGCCCTGC;RSEQ=TTCACAGACATTCTGCTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:0,12:0,1:1,12:0.9231:0,0:28.8:1:30.8:1:1:0:58.2:11:0.9167:0:1.4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 133754261 . AT A 48 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=20.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAGCTAAGCTCATGAGGTG;RSEQ=TTTTTTTTTTTTTTTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:0,3:0,3:3,3:0.375:0,0:35.3:1:30.7:1:1:0:54:6:0.375:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 133754326 . G A 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTACAATGGC;RSEQ=CAATGTTGGCTCACTTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:10.5:1:28:1:1:0:39.5:4:0.6667:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 133755282 . T G 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.05681;LSEQ=CATCTAACGTCTTTTCAAAT;RSEQ=CTTAATGTCTATAACAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:25:24,1:17,0:17,25:0.5952:1,1:23.7:1:33.1:1:1:0:60:50:0.5952:0:1.2 0/1:27:2:2,0:22,3:25,2:0.0741:2,0:6:1:28.5:1:1:0:60:4:0.0741:0:1 +9 133755293 . A G 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05571;SOR=Inf;LSEQ=TTTTCAAATTCTTAATGTCT;RSEQ=TAACAGGACATGATGACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:54,1:55,0:0:1,0:20.6:1:28.9:1:1:0:60:54:1:0:0.6 0/1:35:3:2,1:30,2:32,3:0.0857:2,2:29.7:1:26.3:1:0.24217:6.73144:60:2:0.0588:0:1.7 +9 133755528 . A G 285 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.21317;LSEQ=TTTGAAACAATGTTCCAGGA;RSEQ=TCCAGTATCTCAGACGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:849:427:181,246:168,254:422,427:0.5029:2,2:24.7:1:32.7:1:0.4855:1.11:59.9:84.4:0.5072:0:1.2 0/1:801:142:61,81:283,376:659,142:0.1773:2,2:22.8:1:31.1:1:1:1.00:60:34.5:0.1765:0:1.2 +9 133755573 . G T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02272;SOR=Inf;LSEQ=CCCATCCCGGGGTACCTGCA;RSEQ=TGGGGTGAAAGGGCAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:0:0,0:132,270:402,0:0:2,0:24.7:1:32.2:1:1:0:60:79.4:0.9975:0:0.5 0/1:359:5:2,3:116,238:354,5:0.0139:2,2:33.8:1:26.8:1:0.66524:1.37:60:4:0.0112:0:1.2 +9 133755636 . A C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06277;SOR=Inf;LSEQ=TCGGTTCACTTCCTGGTGAA;RSEQ=GTTCACAGACCAGCCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:13,128:141,0:0:2,0:24.1:1:32:1:1:0:60:46:1:0:0.1 0/1:94:3:0,3:3,88:91,3:0.0319:1,0:27.3:1:31.3:1:1:0:60:6:0.0333:0:1 +9 133755748 . C A 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53855;SOR=0;LSEQ=AGAAATGCTAAGGGCTGTTT;RSEQ=TCCGGTATCCACGTGCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:69,25:94,2:0.0208:2,2:23:1:25.5:1:0.47039:2.72594:60:4:0.0213:0:2 0/0:53:0:0,0:46,7:53,0:0:2,0:19.9:1:30.9:1:1:0:60:52:1:0:0.5 +9 133755754 . T C 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0712;LSEQ=GCTAAGGGCTGTTTCTCCGG;RSEQ=ATCCACGTGCCTTTTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:94:85:66,19:8,1:9,85:0.9043:2,2:25.2:1:32.6:1:0.67855:2.2866:60:170:0.914:0:1.1 0/1:58:23:19,4:32,3:35,23:0.3966:2,2:19.4:1:31.7:1:0.41844:2.21314:60:46:0.3966:0:1 +9 133758838 . C T 64 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGTTGCAGTGAGCTGAGAT;RSEQ=GTGCCACTGCACTCCAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:4,0:0,0:0,4:1:0,0:23.3:1:32.3:1:1:0:37.8:8:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 133759201 . TTTTG T 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0.10992;SOR=Inf;LSEQ=GGGATGACCTTTGACAATTT;RSEQ=TTTGTTTGTTTGTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:87,0:87,0:0:1,0:22.5:1:31.4:1:1:0:59.2:28:1:0:0.2 0/1:81:3:3,0:77,1:78,3:0.037:1,0:20.3:1:30.3:1:1:0:60:6:0.037:0.0123:0.3 +9 133759283 . C T 56 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18022;SOR=4.9255;LSEQ=AGCAGTGGCACTCTGCCTCC;RSEQ=GGGTTCAAGCGATTCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:397:1:1,0:334,62:396,1:0.0025:2,0:45:0:34:0:1:0:60:2:0.0026:0:1 0/1:325:4:2,2:253,68:321,4:0.0123:2,2:16.5:1:28:1:0.20399:3.70123:60:8:0.0124:0:1 +9 133759489 . CAAG C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=0.00343;SOR=1.71798;LSEQ=AACTTGTTCAGCGCCTTGAT;RSEQ=AAGAAGAAGAAGACAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1286:51:22,29:637,597:1234,51:0.0397:2,2:27.7:1:32.3:1:0.25484:1.40612:59.9:102:0.04:0.0016:0.1 0/1:1147:76:38,38:527,544:1071,76:0.0663:2,2:27.7:1:31.4:1:0.90607:1.03:59.9:152:0.0668:0.0026:0.3 +9 133759745 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18056;SOR=Inf;LSEQ=CTCCCCACCTGTGGAAGAAG;RSEQ=CCAGCACGCTGACCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:86,184:270,0:0:2,0:26:1:29.9:1:1:0:59.9:23.545:1:0:0.1 0/1:200:2:1,1:83,115:198,2:0.01:2,2:37.5:1:31.5:1:1:1.38:60:4:0.0103:0:1.5 +9 133759957 . G T 176 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0172;LSEQ=GGGCACAAAAGTGAGAAGCC;RSEQ=GCTCTGCCTCGGAAGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:922:54:23,31:422,444:866,54:0.0586:2,2:27.7:1:30.6:1:0.40281:1.2807:60:53:0.0584:0:1.3 0/0:937:1:0,1:472,463:935,1:0.0011:2,0:1:0:31:0:0.49573:0:37:2:0.0011:0:1 +9 133760029 . C G 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19913;LSEQ=GGCACAGTAACGCCTCCCCC;RSEQ=AGGCTGGTGAAAAAGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:657:311:141,170:154,191:345,311:0.4734:2,2:24.7:1:31.4:1:0.87531:1.03:60:310:0.4747:0:1.1 0/1:666:101:41,60:241,323:564,101:0.1517:2,2:25.6:1:30:1:0.74337:1.09172:60:202:0.1535:0:1.2 +9 133760038 . GA G 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.00746;SOR=Inf;LSEQ=ACGCCTCCCCCCAGGCTGGT;RSEQ=AAAAGAATGAGGAAGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:618:0:0,0:282,333:615,0:0:2,0:24:1:30.5:1:1:0:60:86.857:0.9984:0:0.6 0/1:613:7:3,4:260,346:606,7:0.0114:2,2:27:1:31.3:1:1:1.00192:58:14:0.0116:0:0.4 +9 133760617 . C T 139 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=27.22302;LSEQ=ACCCCCATCAGCCCAGCCCC;RSEQ=GTTCCCTCCACGTTGCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1244:1:0,1:604,637:1241,1:8e-04:2,0:1:0:15:0:1:0:60:0:0:0:2 0/1:1119:24:13,11:530,562:1092,24:0.0214:2,2:22.2:1:30.4:1:0.68129:1.25:60:48:0.0217:0:1.4 +9 133761001 . A G 296 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.2514;LSEQ=GCGACAGCAGGCAGTGGTCC;RSEQ=GCGGCCACTCAGGACTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1009:839:380,459:78,91:169,839:0.8315:2,2:25.6:1:30.5:1:0.8657:1.03532:60:82.9:0.8307:0:1.1 1/0:990:548:255,293:201,240:441,548:0.5535:2,2:24.2:1:29.8:1:0.7975:1.04:59.9:181.667:0.5567:0:1.2 +9 133761115 . G A 42 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17025;SOR=5.36744;LSEQ=GCCCGTCGGAGCTGCCTGCA;RSEQ=CACATGCGGGCTCGCCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:289:1:1,0:42,246:288,1:0.0035:2,0:1:0:25:0:0.14879:0:60:2:0.0035:0:1 0/1:218:4:3,1:40,174:214,4:0.0183:2,2:19.5:1:21.3:1:0.02494:12.84:60:3:0.014:0:1.3 +9 133761139 . G A 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00039;SOR=Inf;LSEQ=ATGCGGGCTCGCCCATACCC;RSEQ=TGACAGTGGCTGACAAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:5,158:163,0:0:1,0:24.3:1:32.4:1:1:0:60:162:0.9939:0:0.1 0/1:122:9:1,8:5,108:113,9:0.0738:1,2:9.9:1:30.1:1:0.37494:2.67:60:18:0.0744:0:1 +9 133762433 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGGCCGGAGCCCAGATAC;RSEQ=GGGGCTGTGACTCTGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:14:1:32:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 133762590 . G A 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTGCCAGCAGCCTCGCACA;RSEQ=GCCCTAGCTTTACGCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28:1:30:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 133797274 . T C 158 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.29755;SOR=1.6903;LSEQ=CTTGAAGACAGGTTTAGAGA;RSEQ=GTGTCTGTCTTTGGGGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:60:33:21,12:17,10:27,33:0.55:2,2:26.5:1:31.4:1:1:1.03:60:66:0.55:0:1.1 1/0:40:27:18,9:8,5:13,27:0.675:2,2:26.1:1:29.8:1:1:1.24:60:26:0.7027:0:1.1 +9 133797332 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51641;SOR=Inf;LSEQ=CGCACGCTGACTCCTAACAT;RSEQ=GCAGGCTCTGCCTTGCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:28,35:63,0:0:2,0:26.1:1:30.1:1:1:0:60:30.5:1:0:0.3 0/1:94:2:1,1:45,47:92,2:0.0213:2,2:47:1:31:0:1:1.04:60:4:0.022:0:1 +9 133887735 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCAGCCTCAGTTTCCTTA;RSEQ=CTGTACCGTACGGATAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:15,0:0:2,0:19.8:1:31.7:1:1:0:60:30:1:0:0 0/1:35:2:1,1:18,15:33,2:0.0571:2,2:28.5:1:27:1:1:1.19373:60:4:0.0571:0:1 +9 133887746 . C T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54498;SOR=Inf;LSEQ=GTTTCCTTACCTGTACCGTA;RSEQ=GGATAAGAGTCGCCACTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:11,7:18,0:0:2,0:20.6:1:32.2:1:1:0:60:36:1:0:0 0/1:40:3:1,2:17,20:37,3:0.075:2,2:25.7:1:29.3:1:1:1.67842:60:6:0.075:0:1 +9 133887901 . C T 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TGCTCGTCCCGGCCGCCCTG;RSEQ=CTCCTCAAAGACATCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:38:1:32:0:1:0:60:4:0.6667:0:1.5 0/0:3:0:0,0:1,2:3,0:0:2,0:13.3:1:29.3:1:1:0:60:6:1:0:0 +9 135771515 . A G 159 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02251;LSEQ=CCTCCGTCCCATTTCCACAC;RSEQ=TGAACTTGCACTCAGACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:39:39,0:50,0:50,39:0.4382:1,1:24:1:30.2:1:1:0:60:78:0.4382:0:1.1 0/1:59:1:1,0:54,4:58,1:0.0169:2,0:11:0:31:0:1:0:60:2:0.0169:0:1 +9 135771524 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51716;SOR=0;LSEQ=CATTTCCACACATGAACTTG;RSEQ=ACTCAGACCCTGGAAACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:98,2:100,2:0.0196:1,2:13:1:28:1:0.05824:40.17587:60:4:0.0202:0:1 0/0:68:0:0,0:65,3:68,0:0:1,0:24.3:1:31.7:1:1:0:60:67:1:0:0.1 +9 135771987 . CGCT C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.000;MSILEN=3;SSF=0.77889;SOR=0.82019;LSEQ=TTTCTCTGGGGTAGAAAGCT;RSEQ=GCTGCTGCTGCTGCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:7:2,5:97,198:295,7:0.0232:2,2:39:1:32.1:1:1:1.22392:60:14:0.0236:0:0 0/1:262:5:1,4:96,160:256,5:0.0191:2,2:34.8:1:32:1:0.65396:2.3931:60:10:0.0195:0:0 +9 135772053 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49893;SOR=0;LSEQ=GCCCCGGGCGCTGCTGGGCC;RSEQ=GGGGGTCTTGGTCTCACCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:82,117:199,2:0.01:2,2:19.5:1:29:1:1:1.42:60:4:0.0103:0:1 0/0:193:0:0,0:86,106:192,0:0:2,0:49:0:9:0:1:0:60:0:0:0:2 +9 135772144 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49983;SOR=Inf;LSEQ=TCATTACAACAGTCAAGCCT;RSEQ=TAAGAAAGCCGGGGAGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:154:0:0,0:45,108:153,0:0:2,0:26.4:1:32.5:1:1:0:59.9:75.5:1:0:0.2 0/1:171:2:1,1:68,101:169,2:0.0117:2,2:29.5:1:30:1:1:1.48:60:4:0.0118:0:1 +9 135772530 . C T 59 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21936;SOR=4.64317;LSEQ=AGTCCTTATGCTGGAATTGG;RSEQ=AGCTTAGTCCCAAGGTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:1:1,0:290,96:386,1:0.0026:2,0:46:0:30:0:1:0:60:2:0.0027:0:1 0/1:420:5:2,3:298,117:415,5:0.0119:2,2:22.8:1:25.8:1:0.14342:3.80628:60:10:0.012:0:1.2 +9 135772717 . G A 207 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=67.29488;LSEQ=GCCTCATACCTGCTCTCTGC;RSEQ=GCCTGCAGCTGTCCTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:925:2:2,0:403,520:923,2:0.0022:2,0:1:0:25.5:1:0.19144:0:60:4:0.0022:0:1 0/1:973:124:51,73:368,481:849,124:0.1274:2,2:25:1:29.8:1:0.69803:1.09497:60:123:0.1288:0:1.1 +9 135772977 . G A 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTAGCTCTTTCCGATAGGC;RSEQ=GCTTTCATCATTTCTACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:472:0:0,0:150,321:471,0:0:2,0:23.1:1:29.8:1:1:0:59.3:15.821:1:0:0.6 0/1:512:35:11,24:173,303:476,35:0.0684:2,2:22.8:1:29.5:1:0.71558:1.24518:58.3:34:0.0714:0:1.4 +9 135773114 . C T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04153;SOR=0.24121;LSEQ=GCATTTTAGTATACTGATAA;RSEQ=AGAAATATAAACTAGTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:14:1,13:1,21:22,14:0.3889:1,1:20.1:1:28.6:1:1:1.59:60:28:0.4:0:1.8 0/1:23:3:0,3:1,19:20,3:0.1304:1,0:40.3:1:28:1:1:0:60:6:0.1304:0:1 +9 135773164 . C T 88 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13116;SOR=0;LSEQ=AAGTAAGCTGGTAGTATTAT;RSEQ=CTAGTAACCCTTCCTTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:0,8:0,9:9,8:0.4706:0,0:26.5:1:29.6:1:1:0:60:16:0.4706:0:2.4 0/0:4:0:0,0:0,4:4,0:0:0,0:25.5:1:31:1:1:0:60:8:1:0:0 +9 135776034 . C T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21389;SOR=1.28188;LSEQ=AAGCCATTCTCTATGCCATG;RSEQ=GGGAGACATACTGTCTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:91:76,15:125,24:149,91:0.3792:2,2:25:1:30.5:1:1:1.02786:60:182:0.3808:0:1.1 0/1:214:94:75,19:100,20:120,94:0.4393:2,2:24.2:1:29:1:0.59312:1.26524:59.7:93:0.4387:0:1 +9 135776341 . C A 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00163;SOR=0.24023;LSEQ=AATGTTAAGGCAAAATAAAC;RSEQ=AGTCCCATGGGTTCACAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:30:0,30:0,51:51,30:0.3659:1,1:21.3:1:31.5:1:1:0:60:60:0.375:0:1 0/1:58:7:0,7:2,49:51,7:0.1207:1,0:33.7:1:30.9:1:1:0:60:14:0.125:0:1 +9 135776845 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15472;SOR=Inf;LSEQ=AAATGTCAGGGACTATGGGG;RSEQ=CAGCAGAACCACTTCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:62,2:64,0:0:1,0:25.2:1:31.4:1:1:0:59.8:31:1:0:0 0/1:42:2:2,0:40,0:40,2:0.0476:1,0:26.5:1:29:1:1:0:60:4:0.0476:0:1 +9 135776925 . T C 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAACCTGTCTGAAGGAAGAA;RSEQ=GTTAGCAAATGGTGTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:218,34:252,0:0:2,0:23.6:1:31.7:1:1:0:59.8:125:1:0:0.1 0/1:303:30:23,7:209,63:272,30:0.099:2,2:27.3:1:31:1:1:1.00963:60:60:0.1007:0:1.3 +9 135777121 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.18907;LSEQ=GTGGACATGAAGTTTGAGGA;RSEQ=CACCAACAGGCCAGATCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:185:58,127:70,175:245,185:0.4302:2,2:25.3:1:32.6:1:0.59445:1.14:60:370:0.4322:0:1.1 0/1:441:55:16,39:102,284:386,55:0.1247:2,2:22.8:1:31.5:1:0.74483:1.14:60:110:0.125:0:1.1 +9 135777755 . G GA 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGTTTCCTTTTGGCTGCA;RSEQ=AAAAAAAAATGACTGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:17,0:17,2:0.1053:1,0:21.5:1:32:0:1:0:58:4:0.1111:0:0 0/0:4:0:0,0:3,1:4,0:0:2,0:29.5:1:32.3:1:1:0:60:8:1:0:0 +9 135778210 . C A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12291;SOR=0;LSEQ=AATGTCATCATTTTAGCTGT;RSEQ=TTCCAACACAGGCAATTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:3:2,1:47,217:264,3:0.0112:2,2:10:1:22.7:1:0.0876:9.12:60:2:0.0076:0:1.7 0/0:269:0:0,0:55,214:269,0:0:2,0:24.9:1:31.1:1:1:0:60:37.429:1:0:0.1 +9 135778867 . T C 104 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01637;SOR=0;LSEQ=CCCACGGTTTCTGAGAATTA;RSEQ=GAGGGAATTCCGAGGTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:8,1:19,0:19,9:0.3214:1,2:21.9:1:33.1:1:0.32143:0:60:18:0.3333:0:1 0/0:16:0:0,0:16,0:16,0:0:1,0:26.1:1:31.1:1:1:0:60:32:1:0:0.1 +9 135779251 . G A 32 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3579;SOR=3.2232;LSEQ=CAGAAATGCCTTTTACAGAT;RSEQ=GTTCAATCAAGCCCCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:268:1:1,0:41,224:265,1:0.0037:2,0:1:0:24:0:0.15789:0:60:2:0.0038:0:1 0/1:251:3:2,1:57,190:247,3:0.012:2,2:9:1:20.7:1:0.13965:6.60:60:2:0.0081:0:1.7 +9 135779530 . T C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.86239;LSEQ=TGTGTTCTCCCCCAGGAAGA;RSEQ=GCTTCACTCTGGTCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:5,2:7,5:12,7:0.3684:2,2:23.6:1:32.1:1:0.65617:1.73:60:14:0.4118:0:1.1 0/1:6:2:1,1:4,0:4,2:0.3333:0,2:9.5:1:31:0:0.33333:0:60:4:0.3333:0:1.5 +9 135780006 . TACACTGG T 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.70027;SOR=0.5747;LSEQ=AGAGAGTTAGAGGAGAAGCC;RSEQ=ACACAATGGGAGGCGGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:11:0,11:0,25:25,11:0.3056:1,0:23.9:1:31.5:1:1:0:60:22:0.3056:0:0 0/1:10:2:0,2:0,8:8,2:0.2:0,0:33:1:31:0:1:0:60:4:0.2:0:0 +9 135780288 . A G 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAGTAGGTAATTTACCT;RSEQ=AGCCTATCATACCAAATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20:1:31.7:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 135781563 . G A 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.14267;LSEQ=AAACAAAAGAAATGGCAGTC;RSEQ=GTATTCCACCTGGGAAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1548:554:258,296:478,516:994,554:0.3579:2,2:24.6:1:31.1:1:0.59557:1.06273:59.7:78.143:0.3585:0:1.1 0/1:1861:137:63,74:810,914:1724,137:0.0736:2,2:21.8:1:30.2:1:0.85904:1.04094:60:274:0.0745:0:1.2 +9 135781709 . G C 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0;SOR=0.10096;LSEQ=TTGGGAGGCTGAGGAGGGAG;RSEQ=ATCACTTGAGCCCAGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:79:0,79:1,100:101,79:0.4365:1,1:25.4:1:32.3:1:1:0:57.4:78:0.4382:0:1 0/1:111:8:0,8:2,100:102,8:0.0721:1,0:27.4:1:33.1:1:1:0:57.8:16:0.0727:0:1 +9 135781735 . C G 124 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGAGCCCAGGAGTTAGAGA;RSEQ=CAGCCTGGACAACATAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:1,122:123,0:0:1,0:26.3:1:31.7:1:1:0:58.2:122:1:0:0.5 0/1:66:14:0,14:0,52:52,14:0.2121:1,1:24.4:1:32.6:1:1:0:54.4:28:0.2188:0:1 +9 135782026 . C A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.0757;LSEQ=ACCTCAAGAGAAGAAAAATC;RSEQ=AGCAAGCCTGTGAGCAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:94:84,10:113,22:135,94:0.4069:2,2:21.5:1:30.7:1:0.25038:1.63:60:93:0.4097:0:1.1 0/1:224:11:9,2:183,30:213,11:0.0491:2,2:11.5:1:28.5:1:0.65986:1.35353:60:22:0.0505:0:1.8 +9 135782221 . T C 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08256;LSEQ=CCTTTGCTGCCAGGTGGCTC;RSEQ=TCTGAAGAGAAACAAAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:238:83,155:94,187:281,238:0.4577:2,2:23:1:32.4:1:0.78058:1.07:60:118:0.4574:0:1.1 0/1:477:31:9,22:146,300:446,31:0.065:2,2:20.7:1:30.8:1:0.84309:1.18924:60:30:0.0637:0:1.1 +9 135782396 . A G 119 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.07054;SOR=0;LSEQ=ACTGAAATATTAAAAATAAT;RSEQ=TAACTAAAAGTACCAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:4,10:7,12:19,14:0.4242:2,2:21.6:1:31.4:1:0.71934:1.44185:59.6:13:0.4063:0:1.1 0/0:6:0:0,0:1,5:6,0:0:2,0:30.3:1:30.7:1:1:0:60:12:1:0:0.2 +9 135782479 . G A 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18827;SOR=0.31678;LSEQ=AAAGAGATATAGTCAAGTCA;RSEQ=AATACAGGTACTTCACTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:9,6:12,5:17,15:0.4688:2,2:17.9:1:30.2:1:0.71195:1.57637:60:14:0.4516:0:1.1 0/1:14:3:3,0:9,2:11,3:0.2143:2,0:27.3:1:28.7:1:1:0:60:6:0.2143:0:1 +9 135782869 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25474;SOR=0;LSEQ=GCAGTGATTCTCAAATTGTT;RSEQ=GGATGTTTTCTTTTCTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:3:1,2:1,92:93,3:0.0313:1,2:13.3:1:24:1:0.06184:37.75:49:2:0.0213:0:2.7 0/0:77:0:0,0:1,76:77,0:0:1,0:22:1:31:1:1:0:57.9:154:1:0:0.1 +9 135782947 . G GC 66 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.30769;SOR=0.22947;LSEQ=AGTGCAATGGCACAATCTCG;RSEQ=CTCACTGCAACCTCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:4:0,4:0,5:5,4:0.4444:0,0:18.8:1:33.3:1:1:0:34.3:8:0.4444:0:0 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:18:0:26:0:1:0:29:2:0.1429:0:0 +9 135785688 . CA C 34 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=22.000;MSILEN=1;SSF=1;SOR=1.60599;LSEQ=ACAGAGCAAGACCCTGTCTC;RSEQ=AAAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:3,0:3,3:0.375:0,0:9.7:1:31.7:1:1:0:56.3:6:0.375:0.25:1.7 1/0:6:3:3,0:2,0:2,3:0.5:0,0:14.3:1:21.9:1:1:0:41.7:6:0.1964:0.4643:1 +9 135785789 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56071;SOR=3.20204;LSEQ=TTGGAACCACCCAGGGGTCG;RSEQ=CAGATCACACCTTGAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:1:0,1:104,12:116,1:0.0085:2,0:1:0:26:0:0.11111:0:60:2:0.0088:0:1 0/1:74:2:1,1:64,8:72,2:0.027:2,2:14.5:1:26.5:1:0.22991:7.60108:60:4:0.0282:0:1 +9 135785790 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14852;SOR=Inf;LSEQ=TGGAACCACCCAGGGGTCGG;RSEQ=AGATCACACCTTGAGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:109,13:122,0:0:2,0:21.1:1:31.8:1:1:0:60:29.5:1:0:0 0/1:77:2:1,1:66,9:75,2:0.026:2,2:21:1:27:1:0.24436:7.00947:60:4:0.026:0:1 +9 135786112 . T C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.12723;LSEQ=GGCAGAACATATATGAACAC;RSEQ=GAGCCCAACTATTAGAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:195:58,137:98,228:326,195:0.3743:2,2:23:1:30.1:1:1:1.01525:60:96.5:0.3755:0:1.1 0/1:425:30:11,19:146,249:395,30:0.0706:2,2:23.4:1:29.6:1:1:1.01275:60:60:0.0711:0:1.1 +9 135786139 . A AT 78 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.1468;SOR=3.89066;LSEQ=AACTATTAGAAAAACTGCCG;RSEQ=TTTTTTTTCAGCCTATAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:2:0,2:60,237:297,2:0.0066:2,0:21:1:29.5:1:1:0:60:4:0.0069:0.0033:0.5 0/1:236:6:2,4:56,174:230,6:0.0254:2,2:16.7:1:30.5:1:0.63741:1.55:60:12:0.0256:0.0042:0 +9 135786557 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15385;SOR=Inf;LSEQ=GAATGCTAAGTCATCCACGA;RSEQ=GTTTATATCCATGGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:27,200:227,0:0:2,0:25.6:1:31.9:1:1:0:59.9:226:1:0:0.1 0/1:147:2:1,1:17,128:145,2:0.0136:2,2:20:1:28.5:1:0.23064:7.35:60:4:0.0137:0:1 +9 135786727 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25384;SOR=Inf;LSEQ=TATCATGGATCCTTAAAAGT;RSEQ=ACTCCTGAAATGAGCAGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:247:0:0,0:191,56:247,0:0:2,0:25:1:32.3:1:1:0:59.9:34.286:1:0:0.1 0/1:292:3:1,2:221,67:288,3:0.0103:2,2:12:1:25.3:1:0.14102:6.54235:60:6:0.0104:0:1 +9 135786904 . A G 246 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.16848;LSEQ=TCTGAGGTAGCTGCCCTGGC;RSEQ=TATTTAACAACATCAGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:652:235:97,138:181,234:415,235:0.3604:2,2:25.9:1:31.3:1:0.62062:1.10029:59.9:77.333:0.3608:0:1.2 0/1:739:64:25,39:292,381:673,64:0.0866:2,2:24:1:30.8:1:0.59749:1.1953:60:128:0.0876:0:1.2 +9 135786975 . C A 47 p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.52563;SOR=0.56827;LSEQ=CCTAAAATGGAAGAGAAGAA;RSEQ=ACAGGGGGTTAGTGTGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:6:1,5:88,199:287,6:0.0205:2,2:14:1:18.5:1:0.6713:2.20606:43.7:0.5:0.0071:0:5.7 0/1:341:4:3,1:117,220:337,4:0.0117:2,2:6.3:1:22.3:1:0.12697:5.61:56.8:3:0.0091:0:2.3 +9 135787591 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20834;SOR=Inf;LSEQ=GAACTAAGTCTTACTCCAGA;RSEQ=AAGAAAATCAACAAAGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:198,36:234,0:0:2,0:24.4:1:30.3:1:1:0:60:38:1:0:0.1 0/1:197:2:1,1:159,36:195,2:0.0102:2,2:17.5:1:29:1:0.34114:4.37026:60:4:0.0103:0:1 +9 135796608 . A C 157 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.03184;LSEQ=TTTAAACTCACACAAATTTT;RSEQ=GCTGTATGAGTGCTTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:28:28,0:40,1:41,28:0.4058:1,1:26.3:1:32.8:1:1:0:60:56:0.4058:0:1 0/1:48:1:1,0:46,1:47,1:0.0208:1,0:9:0:32:0:1:0:60:2:0.0208:0:1 +9 135798707 . C T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08084;SOR=0;LSEQ=AAAGCATTCACCTCACAGGG;RSEQ=CCAACAGGTATATGAGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:3:1,2:177,64:241,3:0.0123:2,2:14:1:25.7:1:0.17879:5.48499:60:2:0.0084:0:1.3 0/0:319:0:0,0:204,115:319,0:0:2,0:24:1:30.5:1:1:0:59.9:34.444:1:0:0.1 +9 135798868 . G A 53 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.20675;LSEQ=CCTGTTGTGAGGACAACGAC;RSEQ=TCAGTGTCCATCTGCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:3:3,0:106,200:306,3:0.0097:2,0:1:0:27.3:1:0.04311:0:60:6:0.0099:0:1 0/1:342:4:3,1:126,212:338,4:0.0117:2,2:13.3:1:26.5:1:0.15257:5.02:60:8:0.0118:0:1 +9 135798898 . A T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12669;SOR=Inf;LSEQ=ATCTGCAGGAGAAAAGGTCA;RSEQ=ACAGGAAACGTCTGTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:181:0:0,0:39,142:181,0:0:2,0:23.3:1:30.4:1:1:0:60:24.857:1:0:0.1 0/1:208:4:2,2:62,142:204,4:0.0192:2,2:27.8:1:28.8:1:0.58831:2.28:60:8:0.0192:0:1.3 +9 135800897 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.1958;SOR=Inf;LSEQ=TAAAAGTTAAAATCTAGCTT;RSEQ=CTTGCTTTAAGTTGCCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:175,31:206,0:0:2,0:20.5:1:31.8:1:1:0:59.8:50.5:1:0:0.1 0/1:164:2:1,1:131,31:162,2:0.0122:2,2:11.5:1:28.5:1:0.35313:4.1751:60:4:0.0123:0:1 +9 135800911 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10362;SOR=Inf;LSEQ=TAGCTTCCTTGCTTTAAGTT;RSEQ=CCTAAAATTTCAGAAACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:199,46:245,0:0:2,0:25.4:1:32.1:1:1:0:59.9:34:1:0:0.1 0/1:218:3:1,2:156,59:215,3:0.0138:2,2:17.3:1:25.7:1:0.18984:5.24073:60:6:0.0139:0:1 +9 135802549 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24845;SOR=0;LSEQ=ACAGAAGCTGTTGTACTCAT;RSEQ=AAGAACATATGAAATGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:3:1,2:171,45:216,3:0.0137:2,2:23.7:1:29:1:0.11707:7.50481:60:6:0.014:0:1 0/0:212:0:0,0:162,50:212,0:0:2,0:21.1:1:31.1:1:1:0:60:105:1:0:0.1 +9 135804327 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49917;SOR=Inf;LSEQ=TTCTGAAGGTTCTTCATTGG;RSEQ=GCCACTACCAAACTGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:0:0,0:27,151:178,0:0:2,0:24:1:30.5:1:1:0:60:24.429:1:0:0.1 0/1:190:2:1,1:34,154:188,2:0.0105:2,2:13.5:1:26.5:1:0.33528:4.48:60:4:0.0108:0:1 +9 136205738 . T C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.41667;SOR=0;LSEQ=TCCTGTTTTAGATTTTAAGA;RSEQ=TCCAAAATAACAACCAAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:0,14:1:0,1:24.3:1:32.4:1:1:0:60:28:1:0:1.7 1/1:10:9:9,0:1,0:1,9:0.9:0,0:28:1:30.7:1:1:0:60:18:0.9:0:1.7 +9 136205775 . T C 167 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AATGCAACACACAATAAAAA;RSEQ=AGGCATAAAAGCCTTTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:34:34:22,12:0,0:0,34:1:0,2:22.2:1:33:1:1:0:52.2:68:1:0:1.4 1/0:27:14:7,7:7,6:13,14:0.5185:2,2:24.6:1:30.7:1:1:1.16002:51.5:28:0.5185:0:1.5 +9 136206057 . CAAGT C 114 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.00164;SOR=0;LSEQ=GCTGTTGGCACTGTTGTAAA;RSEQ=AAGGGCAAGATTCTTGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:5,7:5,4:9,12:0.5714:2,2:19.9:1:31.9:1:0.66992:1.70337:52.3:24:0.6:0.0952:0.1 0/0:11:0:0,0:5,6:11,0:0:2,0:17.5:1:29.5:1:1:0:60:22:1:0:0 +9 136546924 . A G 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=Inf;LSEQ=CGGTGCGCGGCGTGTTTCCC;RSEQ=GCAGCTGGGCCTCCTTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:21:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:28:1:1:0:60:4:1:0:1.5 +9 136548625 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCTGGAGCTGGAGTCGGG;RSEQ=CATCTGAAGGCCGTGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:2,0:14,0:14,2:0.125:1,0:27.5:1:30:1:1:0:60:4:0.125:0:1.5 0/0:3:0:0,0:3,0:3,0:0:0,0:24.7:1:32.7:1:1:0:60:6:1:0:0.3 +9 136548767 . C T 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00271;SOR=Inf;LSEQ=TGCTTCCTGCCCCTGTGCAG;RSEQ=CTCTGGAGAGGGGAGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:62,50:112,0:0:2,0:24.8:1:31.6:1:1:0:60:111:1:0:0.2 0/1:106:8:4,4:57,41:98,8:0.0755:2,2:21.6:1:29.9:1:0.72008:1.38584:60:16:0.0769:0:2.6 +9 136548777 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49842;SOR=Inf;LSEQ=CCCTGTGCAGCCTCTGGAGA;RSEQ=GGGAGGTGAGAGCAGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:65,60:125,0:0:2,0:26.3:1:31.9:1:1:0:60:124:1:0:0.2 0/1:132:2:1,1:75,55:130,2:0.0152:2,2:35:0:32:0:1:1.36037:60:4:0.0154:0:3.5 +9 136548790 . C T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49841;SOR=Inf;LSEQ=CTGGAGAGGGGAGGTGAGAG;RSEQ=AGAGCCGCTGGGATCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:73,74:147,0:0:2,0:26.8:1:31.8:1:1:0:60:72.5:1:0:0.2 0/1:151:2:1,1:84,65:149,2:0.0132:2,2:10.5:1:25:1:1:1.29008:60:4:0.0132:0:2 +9 136548799 . T C 199 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAGGTGAGAGCAGAGCCGC;RSEQ=GGGATCTCCCTAGTTTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:85,81:166,0:0:2,0:25.5:1:30.6:1:1:0:60:26.667:1:0:0.2 1/0:155:103:56,47:28,24:52,103:0.6645:2,2:28.6:1:29.9:1:1:1.02:59.9:206:0.6645:0:1.3 +9 136548809 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=GCAGAGCCGCTGGGATCTCC;RSEQ=TAGTTTCTGGCCGCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:84,85:169,0:0:2,0:26.2:1:32.1:1:1:0:60:41.25:1:0:0.2 0/1:174:2:1,1:92,80:172,2:0.0115:2,2:38:1:29.5:1:1:1.14907:60:4:0.0116:0:1 +9 136548873 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23501;SOR=Inf;LSEQ=TTATCTGCTAACAGAACCCA;RSEQ=ATTTGTCCCCCAGGACCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:43,67:110,0:0:2,0:22.3:1:32:1:1:0:60:54:1:0:0.2 0/1:104:2:1,1:37,65:102,2:0.0192:2,2:12:1:29.5:1:1:1.75:60:4:0.0196:0:1 +9 136548879 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49902;SOR=0;LSEQ=GCTAACAGAACCCAGATTTG;RSEQ=CCCCCAGGACCTCCAGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:2:1,1:41,61:102,2:0.0192:2,2:40.5:1:33:1:1:1.48:60:4:0.0194:0:1.5 0/0:93:0:0,0:30,63:93,0:0:2,0:25.9:1:28.6:1:1:0:60:92:1:0:0.3 +9 136548920 . T A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.19234;SOR=Inf;LSEQ=TCTGCAGGCCAGGACCTCGC;RSEQ=CCTCCCCAACCTTCCTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:7,41:48,0:0:2,0:25.1:1:30.4:1:1:0:60:96:1:0:0.1 0/1:38:2:1,1:5,31:36,2:0.0526:2,2:17.5:1:24.5:1:0.29445:5.75:60:4:0.0526:0:1 +9 136549171 . G A 24 d5;v3;pSTD;q25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGGCGACATCTCCTCCA;RSEQ=CATGAGCGCTGGAGGGCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:24.5:1:1:0:60:4:1:0:1.5 +9 136901221 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50653;SOR=Inf;LSEQ=TCCAGTTCCCGCAAAGTGGT;RSEQ=GGTTTCAGAGTCTCAAAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:50,22:72,0:0:2,0:24.2:1:31.9:1:1:0:60:35:1:0:0.1 0/1:95:2:1,1:60,33:93,2:0.0211:2,2:17:1:27:1:1:1.80601:60:4:0.0215:0:1 +9 136901317 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.55172;SOR=Inf;LSEQ=ATGTGCACTACCCGGCCCAG;RSEQ=TTCTCCCCGGGCAGCCGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:13,38:51,0:0:2,0:26.6:1:33.1:1:1:0:60:50:1:0:0.2 0/1:108:3:2,1:41,64:105,3:0.0278:2,2:24:1:27:1:0.5619:3.09:60:6:0.0278:0:1 +9 136913123 . C G 27 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.86195;LSEQ=CCCTGCTCCCCGACAGCCCC;RSEQ=ACTCAGCCGGCACAAGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:21:1:31.5:1:1:0:60:4:0.3333:0:1 1/0:4:2:2,0:2,0:2,2:0.5:0,0:46:1:27.5:1:1:0:60:4:0.5:0:1 +9 136913355 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00553;SOR=0.35294;LSEQ=AGGATGCTGTCGCAGTAGCG;RSEQ=AGGTGCTCCGACAGCTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:96:24,72:3,8:11,96:0.8972:2,2:23:1:32.1:1:1:1.12372:60:47:0.8952:0:1.1 1/0:122:92:26,66:7,23:30,92:0.7541:2,2:22.2:1:30.6:1:0.64532:1.29:60:22:0.7521:0:1.1 +9 136913369 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1.78216;LSEQ=GTAGCGTAGGTGCTCCGACA;RSEQ=CTTGCCCTTCTTGCCTGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:1:1,0:12,64:76,1:0.013:2,0:1:0:26:0:0.16883:0:60:2:0.013:0:2 0/1:87:2:1,1:18,67:85,2:0.023:2,2:24:1:28:1:0.39107:3.65:60:4:0.0238:0:2.5 +9 136917487 . C A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25378;SOR=0;LSEQ=GTCCTGCATACATTCGCTTG;RSEQ=ACTCCAATAATAATTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:3:2,1:26,19:45,3:0.0625:2,2:12:1:30.3:1:1:1.45:60:6:0.0638:0:1 0/0:37:0:0,0:15,22:37,0:0:2,0:23:1:30.6:1:1:0:60:36:1:0:0.1 +9 136918260 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGACTTCCTGAGGCAC;RSEQ=GGCTGTCCCCAGCTTAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:14.5:1:29.5:1:1:0:60:4:0.6667:0:1 +9 138041494 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AAGAAATAAAGACACAAGAC;RSEQ=AAGAGACAAAGAGAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:40.5:1:32.5:1:1:0:60:4:1:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:21:1:27.5:1:1:0:56:4:0.6667:0:1 +9 138041654 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.50571;LSEQ=TAAGTGATTGATAAGGTCAA;RSEQ=CAAGTCAAGTGATCATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:16,12:28,2:0.0667:2,2:22.5:1:28.5:1:1:1.32044:31.5:4:0.069:0:1 0/1:29:1:0,1:16,12:28,1:0.0345:2,0:43:0:30:0:0.44828:0:51:2:0.0345:0:1 +9 138263531 . A G 32 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.33333;SOR=0;LSEQ=CTGCAGCCGCCGTCAGCGTC;RSEQ=GCAGCCGCCCTTCTTCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:0:32:0:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:33:0:32:1:1:0:60:4:1:0:1.5 +9 138263555 . G T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=GCCGCCCTTCTTCGCCAGGT;RSEQ=TGCTGATTGCAAGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:15:0:34:0:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:29.5:1:1:0:60:4:1:0:1.5 +9 138265191 . A G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50435;SOR=0;LSEQ=CCAGTGCCTGGAATCCTGCA;RSEQ=CCTGGAGGCAGCCTTGCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:9,16:25,2:0.0741:2,2:29:0:34.5:1:1:1.74:60:4:0.0741:0:1.5 0/0:19:0:0,0:8,11:19,0:0:2,0:28.6:1:29.2:1:1:0:60:38:1:0:0.1 +9 138265212 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=CCTGGAGGCAGCCTTGCGAT;RSEQ=AGCTCTGCTGCAGGCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:3,9:12,2:0.1429:2,2:39.5:1:28:0:0.50549:2.74:60:4:0.1429:0:1 0/0:14:0:0,0:5,9:14,0:0:2,0:30.6:1:30.4:1:1:0:60:28:1:0:0.1 +9 138517853 . G C 78 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTCTTTGGAGGTTAAAG;RSEQ=CTCGTGAATGCTGATCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1:0,0:22:1:33.6:1:1:0:60:10:1:0:1.2 1/1:1:1:1,0:0,0:0,1:1:0,0:9:0:33:0:1:0:60:2:1:0:1 +9 138517935 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4915;SOR=0;LSEQ=CTGCCAGTAGCAAAGACGGC;RSEQ=AGGCCCACAGTGATATTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:14,10:24,2:0.0769:2,2:28:1:30:0:1:1.38168:60:4:0.0769:0:1.5 0/0:23:0:0,0:14,9:23,0:0:2,0:30.1:1:29.9:1:1:0:60:46:1:0:0.3 +9 138518010 . A G 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAGTCCCTTCCCATAGGAC;RSEQ=GGAGCGAGCCAGTCTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:0,9:0,0:0,9:0.9:0,0:24.8:1:32.4:1:1:0:60:18:1:0:1.1 1/1:7:7:1,6:0,0:0,7:1:0,2:25.6:1:30.9:1:1:0:60:14:1:0:1 +9 138570258 . G A 87 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02098;SOR=0;LSEQ=GTGGTCACAGCCATGGCTGT;RSEQ=GTTGCAGTGACCGTGGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1:0,2:26.9:1:31.3:1:1:0:60:14:1:0:1 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:43.5:1:30:1:1:2.45:60:4:0.3333:0:1 +9 138663730 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20408;SOR=Inf;LSEQ=GCCACCTCCGTACAGTGGCC;RSEQ=AGGCAGAGGCTGACCCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:38,16:54,0:0:2,0:23.7:1:31.9:1:1:0:60:108:1:0:0.4 0/1:45:2:1,1:28,15:43,2:0.0444:2,2:45.5:1:29.5:1:1:1.83945:60:4:0.0444:0:1.5 +9 138663773 . TG T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50803;SOR=0;LSEQ=GCACCCCAGCACGCCCACCC;RSEQ=GGGTGTTGTTACACGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:53,42:95,2:0.0206:2,2:35:1:31.5:1:1:1.25885:60:4:0.0208:0:0 0/0:72:0:0,0:33,39:72,0:0:2,0:23.4:1:30.1:1:1:0:60:71:1:0:0.6 +9 138663796 . G T 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.64209;SOR=1.19698;LSEQ=GGTGTTGTTACACGGTGGCT;RSEQ=CTGGGGCACCAGGTGGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:48:24,24:35,26:61,48:0.4404:2,2:25.3:1:30.5:1:0.56161:1.34245:60:96:0.4404:0:1.2 0/1:68:33:16,17:17,18:35,33:0.4853:2,2:27.4:1:29.4:1:1:1.00342:59.8:66:0.4853:0:1.2 +9 138829472 . A G 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCAAATGAGAGATTGTTT;RSEQ=AGGAGACACAAATACGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:0,10:1:0,2:21.8:1:33.4:1:1:0:60:20:1:0:1.2 1/1:4:4:4,0:0,0:0,4:1:0,0:17.5:1:32.8:1:1:0:60:8:1:0:1 +9 138829545 . G A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00814;SOR=4.97828;LSEQ=GCCACGGCGACGGCCACACC;RSEQ=GAGGGAGGGATGAGGTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:5,0:42,2:44,5:0.102:1,0:27.2:1:29.6:1:1:0:60:10:0.102:0:1.2 0/1:30:11:11,0:19,0:19,11:0.3667:1,0:19.4:1:29.2:1:1:0:60:22:0.3793:0:1.1 +9 138829610 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50136;SOR=0;LSEQ=AGCTGAATAGTAGATACATG;RSEQ=CTATTAGTTTTATTCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:106,32:138,2:0.0143:2,2:22.5:1:28.5:1:0.41716:3.27725:60:4:0.0147:0:1 0/0:119:0:0,0:94,25:119,0:0:2,0:23.5:1:30.1:1:1:0:60:38.667:1:0:0.2 +9 138829709 . C T 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00165;SOR=0.63219;LSEQ=ATTGCCATCGAAGACCCTGA;RSEQ=GAGTAGTAAGAGCAAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:389:206:103,103:94,89:183,206:0.5296:2,2:27.2:1:30.7:1:0.83913:1.05601:60:102:0.5285:0:1.2 0/1:397:165:82,83:112,120:232,165:0.4156:2,2:24.8:1:29.4:1:0.83866:1.06:60:164:0.4162:0:1.2 +9 138829775 . G T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21884;SOR=Inf;LSEQ=GTTCCTAAGCTGCTGGCGCA;RSEQ=TCTCCACCCCGCTGGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:219:0:0,0:63,156:219,0:0:2,0:25.7:1:32.6:1:1:0:60:108.5:1:0:0.4 0/1:193:2:1,1:59,132:191,2:0.0104:2,2:16:0:28:1:0.52623:2.23:60:4:0.0104:0:2 +9 138829787 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20613;SOR=Inf;LSEQ=CTGGCGCAGTCTCCACCCCG;RSEQ=TGGCCCTCGGAAAGCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:187:0:0,0:44,143:187,0:0:2,0:24.3:1:33.1:1:1:0:60:186:1:0:0.3 0/1:156:2:1,1:43,111:154,2:0.0128:2,2:39.5:1:27.5:1:0.48586:2.56:60:4:0.0132:0:1 +9 138980116 . C T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGGAACTGTACCACTGCCCA;RSEQ=ATCAGGCCCAGATGGAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:29.5:1:1:0:60:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 138981325 . AC A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCCTGAGCCTCCATGTC;RSEQ=CCCCCACAACCCCACCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:30:1:1:0:60:4:1:0:0 +9 138982093 . G T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10493;SOR=4.88092;LSEQ=TGGGGGCCCTGGCCAGAGGG;RSEQ=ATGCCTCAGGGGTCCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:5,2:7,6:0.4615:2,0:26.5:1:30.8:1:0.46154:0:60:12:0.4615:0:1 1/1:11:9:7,2:1,1:2,9:0.8182:2,2:17.8:1:28.4:1:0.49091:3.06:60:18:0.8182:0:1.1 +9 138982177 . CT C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.49429;SOR=0;LSEQ=GCAGGGCCAACGCTGACTCC;RSEQ=CCAAGACCGCCGCAGAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:19,15:34,2:0.0556:2,2:45.5:1:32.5:1:1:1.2583:60:4:0.0606:0:0 0/0:32:0:0,0:16,16:32,0:0:2,0:24.9:1:28.7:1:1:0:60:31:1:0:0.4 +9 138982193 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49508;SOR=0;LSEQ=CTCCCTCCAAGACCGCCGCA;RSEQ=AAGAACCAAGGAAGGCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:15,16:31,2:0.0606:2,2:32:1:31.5:1:1:1.06:60:4:0.0625:0:1 0/0:28:0:0,0:13,15:28,0:0:2,0:32.9:1:30.9:1:1:0:60:56:1:0:0.2 +9 139121812 . C T 31 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACAGTCTGGGCCCAGGC;RSEQ=AGGTGGTGCTGCTCTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7:0:31:1:1:0:59:4:1:0:1.5 +9 139141535 . T G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGGGTGCCTGGAGGCT;RSEQ=TGCTTCCCAGGAAAGTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:31.5:1:1:0:60:4:1:0:1.5 +9 139143513 . G A 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14376;SOR=Inf;LSEQ=CCCTTCCTGGCATAGGCGCT;RSEQ=CTCCGCCCCGTCCTCGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:27,0:0:2,0:28.7:1:31.4:1:1:0:60:26:1:0:0 0/1:17:2:1,1:8,7:15,2:0.1176:2,2:9.5:1:24:1:1:1.13389:60:4:0.1176:0:1 +9 139270366 . T A 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGCGCCGGCCACGCCCAGTC;RSEQ=GCTTGGTAAACCTGACCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:31.5:1:1:0:60:4:1:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:11:1:25.5:1:1:0:60:4:1:0:1 +9 139271664 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11475;SOR=0;LSEQ=AGCACACGTGTGTGTGGCGT;RSEQ=TGCGGCTCAGAGCCGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:12,7:19,2:0.0952:2,2:26:1:31.5:1:1:1.66897:60:4:0.0952:0:1 0/0:40:0:0,0:20,20:40,0:0:2,0:31:1:31.4:1:1:0:60:39:1:0:0.3 +9 139271747 . G A 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGGCAGCATCAGGATGGCC;RSEQ=GAGGCTCCTGCACGAGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:2,4:1,5:6,6:0.5:2,2:24.2:1:33:1:1:2.32:60:12:0.5:0:1.2 1/0:8:4:2,2:2,2:4,4:0.5:2,2:19.8:1:30.5:1:1:1:60:8:0.5:0:1 +9 139271850 . A G 79 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.28571;SOR=0;LSEQ=CGCAACTGGGCAGGCCAGGA;RSEQ=CCAGCTTCCTCCTCCTAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:20.6:1:34.4:1:1:0:60:10:1:0:1.6 1/0:2:1:0,1:0,1:1,1:0.5:0,0:6:0:34:0:1:0:60:2:0.5:0:1 +9 139271919 . C T 45 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ACTTCCACCAGCCCCCACCC;RSEQ=ACTGCTCCAGGCAGGCGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:10.7:1:29:1:1:0:60:6:0.75:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139390348 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53017;SOR=0;LSEQ=AAATAAAAAGGCAGTGTTTC;RSEQ=GTGTAAAATAAAAGTACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:45,0:45,2:0.0426:1,2:19.5:1:29.5:1:0.04255:0:60:4:0.0435:0:2.5 0/0:27:0:0,0:25,2:27,0:0:2,0:19.6:1:30.1:1:1:0:60:12.5:1:0:0.7 +9 139390378 . TA T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.52261;SOR=0;LSEQ=AAAAGTACATAAATAAATAC;RSEQ=AAAAAAATTAAAATCCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:2,0:86,1:87,2:0.0225:1,0:26.5:1:34:0:1:0:60:4:0.023:0:1 0/0:56:0:0,0:54,2:56,0:0:1,0:25.1:1:28.1:1:1:0:60:55:1:0:0.5 +9 139390397 . C T 221 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTAAAAAAAATTAAAATCCT;RSEQ=GTTCTTATTTTGTATAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:130:130:127,3:0,0:0,130:1:0,1:22:1:31.5:1:1:0:59.7:260:1:0:1.1 0/1:87:40:37,3:44,3:47,40:0.4598:2,2:23.5:1:30.4:1:1:1.18681:60:80:0.4598:0:1.1 +9 139390944 . TGTG T 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=5.000;MSILEN=3;SSF=1;SOR=0.99168;LSEQ=AGCTCACGCCAAGGTGCGGC;RSEQ=GTGGTGGTGGTGGCGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:664:14:7,7:320,330:650,14:0.0211:2,2:30.1:1:33:1:1:1.03:60:28:0.0213:0:0.6 0/1:526:11:8,3:253,262:515,11:0.0209:2,2:27.5:1:31.9:1:0.13919:2.76:59.5:22:0.0212:0.0019:0.2 +9 139391461 . T C 187 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGCCACGTTCAGGTGCCCGA;RSEQ=GCCCAGGTGGGTGTCGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:792:62:31,31:391,339:730,62:0.0783:2,2:22.2:1:31.5:1:0.59869:1.15318:59.9:61:0.0782:0:1.1 0/0:643:0:0,0:336,306:642,0:0:2,0:22.6:1:29.2:1:1:0:59.9:57.364:0.9984:0:0.2 +9 139391636 . G A 290 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00219;LSEQ=TCCAGCAGGCAGCCCTTGCC;RSEQ=TCCTGGGACTTCTTCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:661:660:310,350:0,0:0,660:0.9985:0,2:24.8:1:31:1:1:0:59.9:219:1:0:1.1 1/0:576:341:174,167:107,127:234,341:0.592:2,2:23.3:1:29.7:1:0.23465:1.24:59.9:169.5:0.5947:0:1.2 +9 139392025 . CG C 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.08391;SOR=6.13011;LSEQ=CTCCTCCTGGGGGATGAGGG;RSEQ=GGGGCCGGTGAGGGGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:543:1:0,1:133,409:542,1:0.0018:2,0:33:0:32:0:1:0:60:2:0.0019:0:1 0/1:357:4:1,3:93,260:353,4:0.0112:2,2:17.8:1:30.3:1:1:1.07287:60:8:0.0115:0.0028:0.3 +9 139392062 . C A 31 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.5572;SOR=3.48648;LSEQ=GGCCAGGCCAGGCGTGGGGA;RSEQ=CCTCCCCAAGGTTCCATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:1,0:23,255:278,1:0.0036:2,0:1:0:25:0:0.08602:0:60:2:0.0037:0:1 0/1:161:2:1,1:17,142:159,2:0.0124:2,2:16.5:1:31:0:0.21172:8.15:60:4:0.0128:0:1 +9 139392076 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10729;SOR=Inf;LSEQ=TGGGGACCCTCCCCAAGGTT;RSEQ=CATCACCAGAGGAAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:233:0:0,0:7,226:233,0:0:1,0:24.7:1:31.4:1:1:0:59.9:22.3:1:0:0.3 0/1:114:2:1,1:7,105:112,2:0.0175:2,2:20:1:30.5:1:0.136:14.10:60:4:0.0183:0:1 +9 139393067 . C T 118 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGCCAGGCTGTGTGCCC;RSEQ=GCCATGACTGCCGCCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:12,2:0,0:0,14:1:0,2:26.3:1:31.2:1:1:0:60:28:1:0:1.1 1/1:1:1:0,1:0,0:0,1:1:0,0:6:0:23:0:1:0:60:2:1:0:1 +9 139393162 . G A 177 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTGGAAGGGCTCCATAAAC;RSEQ=GGGGCTGAAGGAAGGCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:49,3:0,0:0,52:1:0,2:25.3:1:31.1:1:1:0:59.4:51:1:0:2 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:20.5:1:23.5:1:1:0:60:1:0.125:0:2.5 +9 139393175 . A G 196 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00678;LSEQ=CATAAACGGGGGCTGAAGGA;RSEQ=GGCAGGAGCACTAACGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:64:60,4:0,0:0,64:0.9846:0,2:24.7:1:32.8:1:1:0:59.5:15:0.9836:0:1.9 0/1:15:4:4,0:11,0:11,4:0.2667:0,0:20:1:27.5:1:1:0:60:3:0.2143:0:1.8 +9 139393307 . A G 245 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.17982;LSEQ=TGGCCCTCACTTCTCTGTGG;RSEQ=TTCAGCCCTCACGTCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:235:154,81:246,132:378,235:0.3827:2,2:25.3:1:31.2:1:0.93066:1.02:59.7:46:0.3853:0:1.1 0/1:549:55:37,18:305,188:493,55:0.1002:2,2:21.2:1:30.6:1:0.4664:1.27:60:54:0.1007:0:1.1 +9 139393520 . C T 70 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04204;SOR=4.77925;LSEQ=AGTCCCACCCGTCCCTGTGG;RSEQ=GGTCCCGCCCCACGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:590:2:2,0:313,275:588,2:0.0034:2,0:37.5:1:28:1:0.50145:0:60:4:0.0034:0:1 0/1:437:7:2,5:233,196:429,7:0.016:2,2:6.6:1:25:1:0.25626:2.96486:60:14:0.0163:0:1.1 +9 139393743 . T A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07508;SOR=Inf;LSEQ=GGAGAGGCTCAGGCGGGTGC;RSEQ=GGGCAGACGTACACCGATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:0:0,0:84,246:330,0:0:2,0:23.7:1:30.6:1:1:0:60:65:0.9939:0:0.2 0/1:244:3:3,0:81,160:241,3:0.0123:2,0:9:1:23.7:1:0.03984:0:60:6:0.0123:0:2.3 +9 139393790 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13174;SOR=Inf;LSEQ=CCCAGAACGAACGCCTGGAC;RSEQ=GGAAGCCCCACTGTCTTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:11,118:129,0:0:2,0:25.3:1:31:1:1:0:60:42:1:0:0 0/1:74:2:1,1:8,64:72,2:0.027:2,2:8.5:1:27:1:0.22991:7.60:60:4:0.0278:0:1.5 +9 139394573 . T G 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCACCGGCAAGCTGAGCCC;RSEQ=AGGTCTGCAGGCACCGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:1,0:1,1:0.5:0,0:12:0:25:0:1:0:60:2:0.5:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:31:1:1:0:60:4:1:0:1 +9 139394979 . G T 35 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.26673;SOR=0;LSEQ=CGGCCCTGAGGAGGGCAGGT;RSEQ=GGCACACAGGCAGCCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:3:1,2:201,70:271,3:0.0109:2,2:5.3:1:22.3:1:0.16985:5.69851:60:2:0.0075:0:1.7 0/0:200:0:0,0:135,64:199,0:0:2,0:23.9:1:30.7:1:1:0:60:48.75:0.9949:0:0.2 +9 139395161 . C T 92 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.03866;SOR=0.20854;LSEQ=GCAAGGCGGTCTCGCCCGTG;RSEQ=GGTCTGTCTGGTTGTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:954:10:2,8:449,495:944,10:0.0105:2,2:16.5:1:27.9:1:0.11276:3.62388:60:20:0.0106:0:1 0/0:908:2:0,2:445,461:906,2:0.0022:2,0:22.5:1:28:1:0.49965:0:60:4:0.0022:0:1 +9 139395259 . G A 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.25603;SOR=3.00018;LSEQ=CTGTTGCCCGTCTCCAGGCC;RSEQ=CCCCCGCTGCAGGAGGCGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:2:2,0:171,342:513,2:0.0039:2,0:1:0:26.5:1:0.11241:0:60:4:0.004:0:1 0/1:432:5:3,2:168,259:427,5:0.0116:2,2:24.4:1:28.6:1:0.38871:2.31:60:10:0.0117:0:1 +9 139395311 . G A 115 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=6e-05;SOR=20.12136;LSEQ=TGAAGCCATCTGCAGAGGCA;RSEQ=AGACGGGTGCTCAGTCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:1:1,0:56,193:249,1:0.004:2,0:1:0:28:0:0.228:0:60:2:0.0041:0:1 0/1:173:13:3,10:39,121:160,13:0.0751:2,2:29.2:1:31.2:1:1:1.07394:60:26:0.0751:0:1.1 +9 139395337 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18415;SOR=Inf;LSEQ=GGTGCTCAGTCTGGAGGGCC;RSEQ=GTCCCCAGCTGCAGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:15,132:147,0:0:2,0:22:1:30.7:1:1:0:59.8:28.4:1:0:0.1 0/1:111:2:1,1:18,91:109,2:0.018:2,2:14.5:1:28:1:0.31433:4.95:60:4:0.018:0:1 +9 139395473 . C T 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.66002;SOR=0.57652;LSEQ=TGAAGTCCGCCTGGGCTGCT;RSEQ=AGTGGACAGAGCCGAATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:0,8:0,9:9,8:0.4706:0,0:33.1:1:29.4:1:1:0:58.3:16:0.5:0:2.1 0/1:6:2:0,2:0,4:4,2:0.3333:0,0:16.5:1:25.5:1:1:0:60:4:0.3333:0:1 +9 139395891 . CA C 52 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGAGACTCCATCTCAAAAA;RSEQ=AAAAAAAAAGAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:3,0:4,0:4,3:0.4286:0,0:13.7:1:33.2:1:1:0:60:6:0.4286:0.1429:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139395901 . AG GAA 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=ATCTCAAAAACAAAAAAAAA;RSEQ=AAAAAAAAAAAGAAAAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:6,0:6,2:0.2222:0,0:39:1:31.3:1:1:0:40:4:0.2222:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139396113 . T A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.08135;LSEQ=CCAATTCTAAGTTTCCAGAG;RSEQ=ATCAACTGTACCCCAGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:90:83,7:98,10:108,90:0.4545:2,2:22.3:1:30:1:0.80211:1.21:59.8:29:0.4531:0:1.1 0/1:111:7:7,0:88,16:104,7:0.0631:2,0:24:1:27.7:1:0.59057:0:60:14:0.0631:0:1.3 +9 139396159 . G T 52 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02659;SOR=Inf;LSEQ=TTAGGGGAGAGAGGCAGGTG;RSEQ=GCCACGGGGCTAGGGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:485:0:0,0:338,147:485,0:0:2,0:26.4:1:31.2:1:1:0:60:59.625:1:0:0.3 0/1:330:4:1,3:215,111:326,4:0.0121:2,2:5.8:1:26.3:1:0.1208:5.7787:60:8:0.0125:0:1 +9 139396408 . A G 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0;SOR=0.08756;LSEQ=GCCTGTCAGGGCAGCCCGGC;RSEQ=GCAGGTGCCCGGGAGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:780:722:419,303:32,24:56,722:0.9256:2,2:24.2:1:30.3:1:0.88934:1.04:60:71.2:0.9271:0:1.1 1/0:643:335:185,150:165,142:307,335:0.521:2,2:22.3:1:29.4:1:0.75107:1.06:60:82.75:0.5221:0:1.2 +9 139396632 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13014;SOR=Inf;LSEQ=GCCTGGCGTGGGAGGTGGGC;RSEQ=CTGGGTCGGGAGGGGCAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:272:0:0,0:112,159:271,0:0:2,0:23.9:1:31.2:1:1:0:59.9:29.111:0.9962:0:0.1 0/1:154:2:1,1:57,95:152,2:0.013:2,2:27:1:27.5:1:1:1.66:60:4:0.0132:0:1 +9 139396690 . C T 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGCCAGGTCCCACCTCCCAC;RSEQ=GGGGACCCAGAAGCAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:366:0:0,0:206,160:366,0:0:2,0:25.2:1:30.4:1:1:0:59.9:35.6:1:0:0.1 0/1:257:81:49,32:101,75:176,81:0.3152:2,2:24.4:1:30.3:1:0.68404:1.14:60:162:0.3176:0:1.1 +9 139396772 . C T 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04977;SOR=7.46539;LSEQ=GCTCCCGCCGCTTCTTCTTG;RSEQ=TGGCCTCAGACACTTTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:639:1:1,0:350,288:638,1:0.0016:2,0:24:0:32:0:1:0:60:2:0.0016:0:1 0/1:518:6:2,4:272,240:512,6:0.0116:2,2:16.8:1:26.7:1:0.42753:2.2632:60:5:0.0098:0:1.2 +9 139396843 . C T 74 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.15015;SOR=3.69997;LSEQ=CGCCGGCGCTTGCGGGACAG;RSEQ=AGCACCCCGCAGCCCACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:644:2:1,1:270,371:641,2:0.0031:2,2:34.5:1:28:1:1:1.37:60:4:0.0031:0:1 0/1:526:6:2,4:236,283:519,6:0.0114:2,2:20.3:1:28.8:1:0.6939:1.66628:56.2:12:0.0116:0:1.5 +9 139396881 . C T 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09811;SOR=6.02258;LSEQ=GAAGAACAGAAGCACAAAGG;RSEQ=GGCCGCCGCCACGTACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:515:1:0,1:182,331:513,1:0.0019:2,0:1:0:30:0:1:0:60:2:0.002:0:1 0/1:431:5:1,4:179,247:426,5:0.0116:2,2:17:1:27:1:0.40585:2.89264:60:10:0.0117:0:1.4 +9 139396925 . G A 58 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16426;SOR=5.85134;LSEQ=GCAGCTGCGCCGGCGGGGGC;RSEQ=GCTCCACGGTCTCACCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:315:1:1,0:107,207:314,1:0.0032:2,0:1:0:25:0:0.34286:0:60:2:0.0032:0:1 0/1:218:4:2,2:73,141:214,4:0.0183:2,2:17.5:1:29:1:0.60902:1.93:60:8:0.0186:0:1 +9 139396959 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.55068;SOR=0;LSEQ=ACCTGCGGGCACGGGGGCCA;RSEQ=GGGCAGGTGCCCGGACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:38,139:177,2:0.0111:2,2:29.5:1:30.5:1:0.38924:3.62:60:4:0.0112:0:1 0/0:92:0:0,0:21,69:90,0:0:2,0:25.7:1:30.7:1:1:0:60:89:0.978:0:0.2 +9 139396983 . A G 160 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00365;SOR=0.2184;LSEQ=CAGGTGCCCGGACATCAGGC;RSEQ=GCGGCTACGCAGCAGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:32:3,29:19,59:78,32:0.2909:2,2:20.9:1:32.1:1:0.11376:3.08577:60:64:0.2963:0:1 0/1:49:4:0,4:7,38:45,4:0.0816:2,0:30.5:1:30.8:1:1:0:60:8:0.0816:0:1 +9 139397312 . C CT 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.43298;SOR=0.68579;LSEQ=ATCAATTCTTCTCTCTCTCT;RSEQ=TTTTTTTTTCTTTAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:16:14,2:248,77:325,16:0.0465:2,2:32.6:1:32.6:1:0.37934:2.17:60:32:0.0468:0:0 0/1:340:11:9,2:233,94:327,11:0.0324:2,2:19.3:1:30:1:0.73473:1.81:57.6:22:0.0328:0:0.3 +9 139397426 . G A 134 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=9.16509;LSEQ=ACTTTCCCGTGGCTGGACTC;RSEQ=TTCCCAGGTGGCTCCACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1063:3:2,1:549,509:1058,3:0.0028:2,2:5:1:24.7:1:1:1.85:59.3:2:0.0019:0:1 0/1:988:25:12,13:483,479:962,25:0.0253:2,2:20.4:1:29:1:0.84263:1.09227:60:50:0.0257:0:1 +9 139397551 . C T 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00155;SOR=Inf;LSEQ=CACCCGTGGGTAGCAACTGG;RSEQ=ACAAACAGCCAGCGTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:992:0:0,0:502,490:992,0:0:2,0:24.9:1:32:1:1:0:60:46.238:1:0:0.5 0/1:800:8:2,6:390,398:788,8:0.01:2,2:17.1:1:26.1:1:0.28703:2.93627:60:16:0.0102:0:1.3 +9 139397557 . C G 280 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.09588;LSEQ=TGGGTAGCAACTGGCACAAA;RSEQ=AGCCAGCGTGTCTGGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:417:209,208:300,288:588,417:0.4145:2,2:24.6:1:32.2:1:0.79803:1.03666:60:40.7:0.4136:0:1.1 0/1:819:52:26,26:376,390:766,52:0.0635:2,2:27.6:1:30.3:1:1:1.04:60:104:0.0644:0:1.1 +9 139397587 . G A 83 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0133;SOR=9.95215;LSEQ=GTCTGGGGCACGGGGGGATG;RSEQ=CACCCCCTGCAGGCAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:940:1:1,0:440,499:939,1:0.0011:2,0:1:0:26:0:0.46915:0:60:2:0.0011:0:1 0/1:762:8:4,4:362,391:753,8:0.0105:2,2:19:1:27.8:1:1:1.08:60:16:0.0107:0:1.1 +9 139397590 . CC A 147 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGGGGCACGGGGGGATGGCA;RSEQ=CCCTGCAGGCAGAGCCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:940:0:0,0:438,498:936,0:0:2,0:25.7:1:31.6:1:1:0:60:77:0.9968:0:0.4 0/1:756:29:15,14:344,381:725,29:0.0384:2,2:23.9:1:30.3:1:0.70685:1.19:59.8:58:0.0389:0.0106:0.4 +9 139397707 . G A 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0.56556;LSEQ=GCTCCCAGGAATGCGGCCAC;RSEQ=TCGGTGGCACTCTGGAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:602:316:142,174:131,155:286,316:0.5249:2,2:26:1:30.3:1:0.86986:1.03558:59.9:23.308:0.5188:0:1.1 0/1:463:178:84,94:133,152:285,178:0.3844:2,2:23.4:1:29.2:1:0.924:1.02:60:88:0.3834:0:1.2 +9 139399070 . G A 182 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TGAGGGGCAGGGAGGCCGTC;RSEQ=GGGAGGGCCCAGGAGAGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:236,100:336,0:0:2,0:24.2:1:30.3:1:1:0:60:111:0.994:0:0.2 0/1:256:78:49,29:114,62:176,78:0.3047:2,2:26.2:1:29.1:1:0.77811:1.08785:60:25:0.3:0:1.1 +9 139399641 . G A 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.07538;LSEQ=CTCCAGCCCACTGGCCAGCC;RSEQ=CGGGGGACGTCCCTGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:77:30,47:47,59:106,77:0.4208:2,2:22.5:1:31:1:0.54449:1.24651:60:154:0.4254:0:1.1 0/1:97:5:2,3:51,41:92,5:0.0515:2,2:37.2:1:30:1:0.65613:1.85383:60:10:0.0521:0:1 +9 139399711 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07612;SOR=Inf;LSEQ=GCCTCCGGGCCCAAGCCAGG;RSEQ=CACATCCAAGTTCAGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:253,109:362,0:0:2,0:23.5:1:31.9:1:1:0:60:50.714:1:0:0.1 0/1:268:3:1,2:184,81:265,3:0.0112:2,2:17:1:25:1:0.22742:4.51453:60:6:0.0115:0:1.3 +9 139399714 . C T 39 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.31844;SOR=4.03818;LSEQ=TCCGGGCCCAAGCCAGGCCA;RSEQ=ATCCAAGTTCAGGTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:1:1,0:262,117:379,1:0.0026:2,0:23:0:27:0:1:0:60:2:0.0026:0:2 0/1:284:3:1,2:189,92:281,3:0.0106:2,2:17:1:25:1:0.25534:4.08646:60:6:0.0109:0:1 +9 139400271 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12469;SOR=Inf;LSEQ=CCGGAGATGCATGTGCCGCC;RSEQ=TTGAGGCAGCGCAGGCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:89,249:338,0:0:2,0:25.4:1:31.6:1:1:0:60:55.333:1:0:0.1 0/1:185:2:1,1:56,127:183,2:0.0108:2,2:19:1:28:1:0.52244:2.26:60:4:0.0109:0:1 +9 139400406 . C T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.72821;SOR=0.77778;LSEQ=CCGCCACCTCACACCCAGCC;RSEQ=TCGGCCAGCAGTGCCACCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:47:31:0,31:0,15:15,31:0.6596:1,1:21.9:1:30.5:1:1:0:60:62:0.6739:0:1 1/0:10:6:1,5:0,4:4,6:0.6:0,2:20.8:1:30.3:1:1:0:60:12:0.6:0:1.2 +9 139400835 . TA T 105 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=14.000;MSILEN=1;SSF=0.10574;SOR=2.55178;LSEQ=CTAAAATCATTTATTGAAAC;RSEQ=AAAAAAAAAAAAAGACATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:9:9,0:48,4:52,9:0.1343:2,0:20.1:1:32.8:1:1:0:60:18:0.1385:0.0149:1.2 0/1:35:10:9,1:24,0:24,10:0.2857:1,2:18.1:1:31.7:1:0.29412:0:60:20:0.2941:0.0857:1.7 +9 139400887 . T C 45 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69611;SOR=1.43383;LSEQ=GAGGATGAAGGCCGGGAGGA;RSEQ=CACTGCCCGGTCTGCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:4:4,0:203,19:222,4:0.0177:2,0:17:1:22.8:1:1:0:54.8:3:0.0141:0:6.3 0/1:119:3:3,0:111,5:116,3:0.0252:1,0:27.3:1:12.7:1:1:0:60:0:0:0:5.7 +9 139400904 . C T 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.43783;SOR=0.85711;LSEQ=GGATCACTGCCCGGTCTGCG;RSEQ=CCCGAGGCCCCCACGTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:285:156:138,18:112,17:129,156:0.5474:2,2:28.5:1:30:1:0.71902:1.16:59.9:77:0.55:0:1.2 1/0:169:86:75,11:76,7:83,86:0.5089:2,2:21.9:1:28.7:1:0.45675:1.58804:60:27.667:0.5123:0:1.2 +9 139401456 . G A 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.2563;SOR=0;LSEQ=AGGTTTCGTCAGTGGCCCAA;RSEQ=CCCGCCACACCCCGGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:1,2:69,184:253,3:0.0116:2,2:33.3:1:29.3:1:1:1.33:60:6:0.0123:0:3 0/0:210:0:0,0:64,146:210,0:0:2,0:24.3:1:30.4:1:1:0:60:18.091:1:0:0.3 +9 139401467 . C A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20064;SOR=Inf;LSEQ=GTGGCCCAAGCCCGCCACAC;RSEQ=CCGGCCCTGCCGTGCCGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:220:0:0,0:53,167:220,0:0:2,0:22.6:1:30.9:1:1:0:59.9:30.429:1:0:0.7 0/1:179:2:2,0:48,128:176,2:0.0112:2,0:5:1:25:1:0.07776:0:60:4:0.0114:0:2.5 +9 139401504 . G A 213 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.06009;LSEQ=GCGTGTCCGTCCCGGAAGAC;RSEQ=AGCGCTCAGGTCTGGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:123:118:24,94:0,5:5,118:0.9593:0,2:24.1:1:31:1:0.58187:0:60:58:0.9587:0:1.5 1/0:67:39:8,31:3,25:28,39:0.5821:2,2:23.6:1:31.1:1:0.33662:2.13:60:78:0.5821:0:1.3 +9 139401565 . A G 157 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00024;SOR=0.06112;LSEQ=AGGTGTCAAGGGTGCCGTGG;RSEQ=GACGCCCTTCCCACTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:32:17,15:24,26:50,32:0.3902:2,2:18.6:1:31.5:1:0.82113:1.22:60:64:0.3902:0:1.7 0/1:27:1:0,1:15,11:26,1:0.037:2,0:40:0:33:0:0.44444:0:60:2:0.0385:0:1 +9 139401577 . C G 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39673;SOR=0.64314;LSEQ=TGCCGTGGAGACGCCCTTCC;RSEQ=ACTGGGACCCCCGCTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:45:23,22:23,12:35,45:0.5625:2,2:20.3:1:31:1:0.2551:1.81942:59.6:44:0.5641:0:1.5 0/1:31:14:10,4:10,7:17,14:0.4516:2,2:22.2:1:29.8:1:0.70738:1.72:60:28:0.4667:0:1.4 +9 139401646 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.06702;LSEQ=CTTGGCCTCACACAGGAAAA;RSEQ=GGGAGTTTCTGGCTGGTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:69:66,3:100,9:109,69:0.3876:2,1:24.7:1:32.5:1:0.37329:1.97:60:138:0.3876:0:1.1 0/1:99:4:4,0:89,6:95,4:0.0404:2,0:21.8:1:32.8:1:1:0:60:8:0.0408:0:1 +9 139401658 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.12367;SOR=Inf;LSEQ=CAGGAAAATGGGAGTTTCTG;RSEQ=CTGGTTCCTGGATGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:209,15:224,0:0:2,0:24.3:1:31.3:1:1:0:59.8:43.8:1:0:0.5 0/1:122:2:1,1:108,12:120,2:0.0164:2,2:25.5:1:30:1:0.20255:8.68875:60:4:0.0165:0:1 +9 139401686 . C T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05634;SOR=Inf;LSEQ=CTGGATGCCTCTGGCCGGTC;RSEQ=CGGGGTGCCTGCCCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:305,73:378,0:0:2,0:22.8:1:30.9:1:1:0:59.9:93.5:1:0:0.3 0/1:236:3:1,2:174,59:233,3:0.0127:2,2:9.7:1:23:1:0.1647:5.84413:60:2:0.0088:0:1.7 +9 139401725 . C T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0884;SOR=6.92471;LSEQ=CCTGCCCTGGCCATGGATGG;RSEQ=CAACACCAGCCCTCCGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:671:1:0,1:426,242:668,1:0.0015:2,0:25:0:26:0:0.36323:0:60:2:0.0015:0:1 0/1:488:5:1,4:290,193:483,5:0.0102:2,2:14.6:1:26.4:1:0.16314:5.98988:60:10:0.0104:0:1 +9 139401920 . G A 63 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23634;SOR=0.25154;LSEQ=GACAGAACGAGGGGCCCTTC;RSEQ=GCTCAGCCGGCGCCAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:5:3,2:98,290:388,5:0.0127:2,2:10.6:1:27.2:1:0.10967:4.42:60:4:0.0104:0:2.4 0/0:310:1:1,0:90,219:309,1:0.0032:2,0:1:0:24:0:0.29355:0:60:2:0.0033:0:1 +9 139401947 . TC T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14604;SOR=Inf;LSEQ=CCGGCGCCAGGATGCAGTGC;RSEQ=CCACACCCCACTGTGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:31,201:232,0:0:2,0:23.2:1:31.3:1:1:0:60:32.143:1:0:0.2 0/1:144:2:1,1:14,128:142,2:0.0139:2,2:8:1:29.5:1:0.19814:8.87:60:4:0.0141:0.0069:0 +9 139401969 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52707;SOR=0;LSEQ=CCACACCCCACTGTGAGGGC;RSEQ=GACAGGGCCACATGAGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:2:1,1:13,137:150,2:0.0132:2,2:25.5:1:32:0:0.17628:10.19:60:4:0.0134:0:1 0/0:93:0:0,0:5,88:93,0:0:2,0:22.4:1:29.6:1:1:0:60:92:1:0:0.1 +9 139402218 . CT C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.06452;SOR=Inf;LSEQ=TTCTCAGTATAGGTACCCTC;RSEQ=TCAGGCTTTCCACAGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:64,5:69,0:0:2,0:23.2:1:32.3:1:1:0:59.4:138:1:0:0 0/1:24:2:1,1:22,0:22,2:0.0833:1,2:12.5:1:26.4:1:0.08333:0:60:4:0.0833:0.0417:0 +9 139402663 . T C 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.1159;LSEQ=TGATGGGCTGGGACCCGAGC;RSEQ=GGGTGGGCACAGCAGGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:620:574:277,297:21,24:45,574:0.9258:2,2:25.5:1:30:1:0.8778:1.07:59.9:37.267:0.927:0:1.1 1/0:425:251:128,123:91,83:174,251:0.5906:2,2:25.1:1:29.3:1:0.84364:1.0534:59.9:40.833:0.5889:0:1.2 +9 139402880 . AT A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.12139;SOR=Inf;LSEQ=TGGGTGCCCGCGCCCCGGCC;RSEQ=TTCCCCGGTAGCTCAGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:62,198:260,0:0:2,0:21.6:1:30.5:1:1:0:60:85.667:1:0:0.6 0/1:256:3:2,1:73,180:253,3:0.0117:2,2:19.3:1:27.3:1:0.20619:4.90:60:6:0.012:0.0039:0.7 +9 139402908 . T C 206 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0.02313;LSEQ=GGTAGCTCAGAACGCACATC;RSEQ=GCCAAGGGGCCTACTCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:125:123:16,107:0,2:2,123:0.984:0,2:22.2:1:29.8:1:1:0:60:40:0.9836:0:1.3 1/0:142:83:16,67:12,47:59,83:0.5845:2,2:22.5:1:28.4:1:1:1.06864:60:40.5:0.5827:0:1.3 +9 139402959 . A G 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.0202;LSEQ=ACCCATTCTACAGAAGTGGA;RSEQ=ACTGCCGCCCCTGGACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:28:1,27:0,25:25,28:0.5283:1,1:24.9:1:31.4:1:1:0:60:13:0.5098:0:1.8 1/0:45:24:3,21:1,20:21,24:0.5333:1,2:23.1:1:31.3:1:0.61099:2.80:60:48:0.5333:0:1.8 +9 139403102 . T C 136 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=TTCCCCAATTCCTGAGCTCC;RSEQ=GCCCCGGCTCCAGAAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:15,5:0,0:0,20:1:0,2:18.2:1:31.6:1:1:0:58.3:40:1:0:1 1/0:2:1:0,1:1,0:1,1:0.5:0,0:1:0:29:0:1:0:60:2:0.5:0:1 +9 139403235 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54398;SOR=0;LSEQ=GACCCCGAGCCGACACAGTG;RSEQ=GACCTGGGGTGACCGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:137,18:155,2:0.0127:2,2:12.5:1:29:1:0.22807:7.43509:60:4:0.0131:0:2 0/0:84:0:0,0:76,8:84,0:0:2,0:23.5:1:30.4:1:1:0:60:27:1:0:0.7 +9 139403240 . T TG 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.90147;SOR=0.9455;LSEQ=CGAGCCGACACAGTGGGACC;RSEQ=GGGGTGACCGTTCCCACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:80:68,12:85,12:97,80:0.452:2,2:22.2:1:32:1:0.66281:1.24841:60:79:0.454:0.0791:1.1 0/1:105:46:38,8:49,10:59,46:0.4381:2,2:22.9:1:31.5:1:1:1.03129:60:92:0.46:0.0952:1.1 +9 139403268 . T C 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.11787;LSEQ=CCGTTCCCACCTCCCGCAGG;RSEQ=AGGCACCCACCCAGGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:264:240:189,51:17,7:24,240:0.9091:2,2:26:1:32.4:1:0.43681:1.52:59.9:119:0.9119:0:1.6 1/0:189:102:75,27:61,26:87,102:0.5397:2,2:23.7:1:31.2:1:0.62888:1.18:60:101:0.5372:0:1.3 +9 139403280 . C T 223 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0;SOR=0.14499;LSEQ=CCCGCAGGTAGGCACCCACC;RSEQ=AGGGCCCCTCCTTCGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:144:112,32:135,64:199,144:0.4186:2,2:25.5:1:31.2:1:0.05113:1.66:60:71:0.4226:0:1.9 0/1:244:23:16,7:146,75:221,23:0.0943:2,2:22.1:1:29.1:1:0.82001:1.17:60:22:0.0913:0:2 +9 139403554 . T C 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.07178;LSEQ=GTGGGCAGGCGGGGGCTGAG;RSEQ=GGAGGGCATTGGTGGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:382:360:68,292:4,16:20,360:0.9424:2,2:23.6:1:30.4:1:1:1.07334:60:179:0.9471:0:1.1 1/0:282:152:32,120:30,100:130,152:0.539:2,2:21.1:1:29.9:1:0.77321:1.12453:60:151:0.5393:0:1.1 +9 139403591 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.11925;SOR=Inf;LSEQ=TCCCCGCTCCAGCAGATTCT;RSEQ=CCTCGCCAGCACCTCCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:10,190:200,0:0:2,0:22.5:1:32.5:1:1:0:60:49:1:0:0.9 0/1:106:2:0,2:8,96:104,2:0.0189:2,0:16:1:26:1:1:0:60:4:0.0192:0:1.5 +9 139403661 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.08212;SOR=Inf;LSEQ=GACAGGCCCAGGGCAGCCTG;RSEQ=CTGACCCAGGGAGGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:1,55:56,0:0:1,0:26.2:1:32.7:1:1:0:59.6:55:1:0:0.1 0/1:23:2:1,1:1,20:21,2:0.087:1,2:29.5:1:27:1:0.16996:14.49:60:4:0.0952:0:1 +9 139404118 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17003;SOR=Inf;LSEQ=CGCCTGCATGGTGTGCCAGG;RSEQ=TGCCAGCTACTGCGTGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:152,24:176,0:0:2,0:26:1:32.8:1:1:0:60:352:1:0:0.1 0/1:124:2:1,1:101,21:122,2:0.0161:2,2:23.5:1:28.5:1:0.32455:4.7222:60:4:0.0161:0:1.5 +9 139404479 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11317;SOR=Inf;LSEQ=ACACCTGCGGGAGGGGGCCG;RSEQ=GAAGGCTGCATGGCTGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:29,187:216,0:0:2,0:23.9:1:30.9:1:1:0:60:42.2:1:0:0.1 0/1:110:2:1,1:12,95:107,2:0.0182:2,2:15:1:27.5:1:0.22528:7.65:60:4:0.0187:0:1 +9 139404895 . C T 110 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.06786;SOR=0.13788;LSEQ=GGGCTCTCGTGACTCTTCCG;RSEQ=GAAGTGCAGGGAGGAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:12,1:19,0:19,13:0.4063:1,1:28:1:29.8:1:0.40625:0:59.6:12:0.4:0:1 0/1:12:1:1,0:10,1:11,1:0.0833:2,0:4:0:27:0:1:0:60:2:0.0833:0:3 +9 139404988 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-04;SOR=Inf;LSEQ=ACACCTGACCCAACCCTCCC;RSEQ=GGCCACACTCCGGCCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:159:0:0,0:152,7:159,0:0:1,0:24.7:1:31.4:1:1:0:60:78.5:1:0:0.1 0/1:93:9:9,0:80,4:84,9:0.0968:1,0:19.9:1:31.2:1:1:0:60:18:0.0968:0:1.2 +9 139405093 . G A 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.08625;LSEQ=CTGGAGGAGGCCAGAGCCGC;RSEQ=GGGCTACTCACTGGGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:873:475:281,194:226,168:394,475:0.5441:2,2:27.3:1:30.9:1:0.62862:1.08:60:117.75:0.5483:0:1.1 0/1:719:67:39,28:361,290:651,67:0.0932:2,2:27.9:1:28.7:1:0.69997:1.12:60:15.75:0.0894:0:1.1 +9 139405261 . C T 243 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03005;SOR=1.3099;LSEQ=GACCTCACAGGTCTGCCCTG;RSEQ=GGGGCAGGAGGAGGCCGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:264:90,174:121,216:337,264:0.4393:2,2:25.7:1:30.3:1:0.6674:1.08287:59.9:65:0.4384:0:1.1 1/0:460:233:85,148:94,133:227,233:0.5065:2,2:25.2:1:28.9:1:0.29375:1.23004:60:28.125:0.5:0:1.1 +9 139405307 . A G 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26695;SOR=0;LSEQ=CCAGCGGCCCCTGGCCCTCC;RSEQ=GGCCCTTCCCAGGCTGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:55,226:281,3:0.0106:2,2:31:1:32.3:1:0.48392:2.05:60:6:0.0106:0:1.7 0/0:207:0:0,0:54,153:207,0:0:2,0:22.5:1:29.7:1:1:0:60:102.5:1:0:0.7 +9 139405361 . A G 218 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.01448;LSEQ=GCCTCTCCCGACCCAGGAGT;RSEQ=GGCTTCCGTGACCCCAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:114:113:12,101:0,0:0,113:0.9912:0,2:25.9:1:32:1:1:0:60:55.5:0.9911:0:1.1 1/0:65:40:2,38:2,23:25,40:0.6154:2,2:25.3:1:31.1:1:0.63518:1.63891:60:80:0.6154:0:1.2 +9 139405475 . C T 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=9e-05;SOR=Inf;LSEQ=TCCTGATTCCAGAACTTCTC;RSEQ=GACCAGGGCCTCCTCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:128,19:147,0:0:2,0:24.9:1:31.5:1:1:0:60:48:1:0:1 0/1:56:7:6,1:46,3:49,7:0.125:2,2:17:1:30.1:1:0.42314:2.49898:60:14:0.1273:0:1.7 +9 139405501 . A G 235 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00969;LSEQ=GGGCCTCCTCAGCACCCACC;RSEQ=GCTCCTCTTCAAAGACTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:225:224:202,22:0,0:0,224:0.9956:0,2:23:1:30.1:1:1:0:60:111:0.9955:0:1.1 1/0:91:62:57,5:29,0:29,62:0.6813:1,2:25.1:1:29.6:1:0.17337:0:60:61:0.6854:0:1.2 +9 139405530 . C T 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00167;SOR=Inf;LSEQ=TCAAAGACTCATCTAGCCTG;RSEQ=CTGGGAGCTGCCTGTGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:376:0:0,0:312,64:376,0:0:2,0:22.8:1:31.9:1:1:0:60:52.714:1:0:0.6 0/1:200:6:4,2:160,34:194,6:0.03:2,2:23.2:1:29:1:0.29495:2.3403:60:12:0.0308:0:1.3 +9 139406334 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTCTGGCAAAGGCTATGT;RSEQ=GGAACCACGTGCACAGCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:25:1:32.5:1:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139407359 . G GC 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTCACGGCTTCCCAGGCC;RSEQ=CCCCCACCCCTGGCCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:104,3:107,2:0.0183:1,2:16:1:34:0:0.07238:30.16298:60:4:0.0198:0:0 0/0:33:0:0,0:30,3:33,0:0:2,0:24.8:1:28.1:1:1:0:59.2:15.5:1:0:1.8 +9 139407438 . C T 41 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.19099;LSEQ=CGCCCCTCCCACATAGGCCC;RSEQ=GCCCCCTCCAGCACAGGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:333:3:0,3:240,90:330,3:0.009:2,0:9.7:1:26.3:1:0.02128:0:60:6:0.0092:0:2 0/1:280:3:1,2:191,86:277,3:0.0107:2,2:15:1:26:1:0.23337:4.41555:60:6:0.0109:0:1.3 +9 139407447 . C T 54 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25808;SOR=2.93964;LSEQ=CACATAGGCCCCGCCCCCTC;RSEQ=AGCACAGGCCCCACCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:2:0,2:247,130:377,2:0.0053:2,0:1:0:23:1:0.1207:0:60:4:0.0054:0:3 0/1:326:5:2,3:200,121:321,5:0.0153:2,2:6.8:1:23.6:1:0.37248:2.47215:60:4:0.0125:0:2.4 +9 139407452 . C T 236 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.12208;LSEQ=AGGCCCCGCCCCCTCCAGCA;RSEQ=AGGCCCCACCCACCCCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:432:373:243,130:32,23:55,373:0.8634:2,2:21.7:1:27.7:1:0.36601:1.34:59.8:6.936:0.8647:0:1.6 0/1:361:157:95,62:127,76:203,157:0.4349:2,2:21.5:1:27.6:1:0.74323:1.09032:59.8:11.077:0.4235:0:1.5 +9 139407610 . G A 66 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00593;SOR=Inf;LSEQ=GAGGGAAGGGGACAGCACTC;RSEQ=GCATGTCCAGCACTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:688:0:0,0:273,414:687,0:0:2,0:23.8:1:30.3:1:1:0:59.9:41.938:1:0:0.1 0/1:512:6:5,1:190,315:505,6:0.0117:2,2:5.3:1:25.8:1:0.03231:8.26:60:12:0.0118:0:1.2 +9 139407932 . A G 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=10.06165;LSEQ=CAAGGGTTGGATTCACACTC;RSEQ=TTGTTGTTGATGTCACAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1067:62:29,33:479,525:1004,62:0.0581:2,2:22.8:1:31.5:1:0.89668:1.0382:60:124:0.0592:0:1.1 0/1:1062:407:194,213:308,347:655,407:0.3832:2,2:26.5:1:30.4:1:0.84978:1.03:59.8:57.143:0.3817:0:1.2 +9 139408016 . G A 45 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.32228;SOR=3.92105;LSEQ=GGGGGACCACACTGCAGGTC;RSEQ=AGGGAGGCCCGAGCAGCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:369:1:1,0:73,295:368,1:0.0027:2,0:1:0:25:0:0.20054:0:60:2:0.0028:0:2 0/1:284:3:1,2:75,206:281,3:0.0106:2,2:11.7:1:29:1:1:1.37:60:6:0.0108:0:1.3 +9 139408756 . A G 123 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACCATGCAGCCCACAAGGAC;RSEQ=CGCAGCACACAGCTGCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:0,16:1:0,1:24.4:1:30.8:1:1:0:55.5:32:1:0:1.4 1/1:1:1:1,0:0,0:0,1:1:0,0:36:0:29:0:1:0:60:2:1:0:1 +9 139408840 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGAGGGGAGCTCCCTGCCA;RSEQ=CCAGCCCCGTCCGAGGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:58,0:58,2:0.0333:1,2:19:1:28.5:1:0.03333:0:60:4:0.0333:0:1.5 0/0:21:0:0,0:21,0:21,0:0:1,0:24:1:31.5:1:1:0:60:20:1:0:0.1 +9 139408892 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.00379;LSEQ=TCTCAAGCTCTGTGCAGGTG;RSEQ=CACCCTCCTGGCAGCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:150:139:124,15:11,0:11,139:0.9267:0,2:24.8:1:30.1:1:0.60315:0:60:45.333:0.9252:0:1.1 0/1:70:3:2,1:55,12:67,3:0.0429:2,2:16.7:1:28.7:1:0.46547:2.25824:60:6:0.0429:0:1 +9 139409648 . G A 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.15464;SOR=2.08261;LSEQ=CCCAGGTGGGCAGCACCAAA;RSEQ=CCCTCACCCAACCCCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:9:8,1:86,5:91,9:0.09:2,2:25.6:1:29.2:1:0.44083:2.12854:60:18:0.0918:0:1 0/1:70:12:9,3:48,10:58,12:0.1714:2,2:21:1:29.3:1:0.6834:1.58823:60:24:0.1739:0:1.1 +9 139409676 . G T 59 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07782;SOR=0;LSEQ=CCAACCCCTCAGCAGCCCCA;RSEQ=GGCAGAGTGGCTGACCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:5:3,2:134,29:163,5:0.0298:2,2:15:1:25.8:1:0.22975:3.05342:60:4:0.0247:0:2.4 0/0:120:0:0,0:92,28:120,0:0:2,0:23.9:1:31.2:1:1:0:60:119:1:0:0.2 +9 139409694 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16292;SOR=Inf;LSEQ=CAGGGCAGAGTGGCTGACCT;RSEQ=GACCTCTGAGCACAGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:246:0:0,0:177,68:245,0:0:2,0:22.8:1:30.4:1:1:0:59.8:60.25:1:0:0.2 0/1:167:2:1,1:118,47:165,2:0.012:2,2:30:1:28:1:0.49347:2.49486:60:4:0.012:0:1 +9 139409943 . C A 63 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0102;SOR=Inf;LSEQ=CTGGCCGGCCACCTGTGGTC;RSEQ=CCTTCAGGCAGAAGCAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:681:0:0,0:378,303:681,0:0:2,0:25.3:1:31:1:1:0:60:28.609:1:0:0.2 0/1:596:6:3,3:318,268:586,6:0.0101:2,2:33.3:1:24.7:1:1:1.18622:60:2:0.0069:0:1 +9 139410177 . T C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=9.73557;LSEQ=TCCCCGTGTACCCTGGACCG;RSEQ=GGGAGGGGCGGGCACAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:28:11,17:78,188:266,28:0.0946:2,2:21.6:1:30.5:1:0.28489:1.56:60:56:0.0976:0:1.1 1/0:174:88:24,64:18,68:86,88:0.5057:2,2:24.4:1:28.9:1:0.37762:1.41:60:21:0.5:0:1.1 +9 139410211 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54734;SOR=0;LSEQ=ACAGGAAGACTTAGGACTGG;RSEQ=GGCCCCCGGGACACCCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:2:1,1:50,122:172,2:0.0115:2,2:15.5:1:28.5:1:0.50149:2.43:60:4:0.0118:0:1 0/0:91:0:0,0:20,71:91,0:0:2,0:23.1:1:28.9:1:1:0:60:17.2:1:0:0.6 +9 139410218 . C G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.55269;SOR=0;LSEQ=GACTTAGGACTGGCGGCCCC;RSEQ=GGGACACCCATGACCAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:3:1,2:43,109:152,3:0.0194:2,2:12.7:1:31.3:1:1:1.27:60:6:0.0196:0:1 0/0:76:0:0,0:17,58:75,0:0:2,0:22.9:1:29.4:1:1:0:60:150:0.9868:0:0.6 +9 139410300 . TGGGGCTGA T 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=12.24971;LSEQ=CATTCCCACCTACTCAGGAT;RSEQ=GCTGTGCTCTCGGCCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:7:4,3:98,31:129,7:0.0515:2,2:17.1:1:31.5:1:0.36613:2.35337:60:14:0.0515:0.0147:0 0/1:67:27:26,1:34,6:40,27:0.403:2,1:23.9:1:31.3:1:0.22765:4.50:59.8:54:0.4091:0.0896:0.2 +9 139410424 . A G 275 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=426.25485;LSEQ=CCTCCCCGCTGGTGGGCGCC;RSEQ=GCCCGCACCTTCCGTGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:869:384:232,152:295,185:480,384:0.4419:2,2:24.2:1:29.8:1:0.77909:1.04471:59.9:37.4:0.441:0:1.1 1/1:679:677:390,287:0,0:0,677:0.9971:0,2:25.9:1:29.3:1:1:0:59.9:51.077:0.9985:0:1.2 +9 139410437 . C T 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGGCGCCAGCCCGCACCTTC;RSEQ=GTGCACACACAGGTGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1009:0:0,0:588,421:1009,0:0:2,0:24.7:1:30.5:1:1:0:59.9:111.111:1:0:0.5 0/1:787:20:9,11:423,343:766,20:0.0254:2,2:25:1:28.5:1:0.37379:1.50648:60:19:0.0245:0:1.8 +9 139410467 . G A 151 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=50.09952;LSEQ=CAGGTGTAAGTGTTGGGTCC;RSEQ=TCCAGGCACTTGGCACCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1262:1:1,0:656,604:1260,1:8e-04:2,0:1:0:26:0:1:0:60:2:8e-04:0:1 0/1:1045:40:21,19:517,488:1005,40:0.0383:2,2:23.2:1:28.5:1:1:1.04:60:39:0.0378:0:1.7 +9 139410589 . A G 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=6.09802;LSEQ=AGGGAGTCATGTGCAACAGC;RSEQ=CTATGGCCCTTCAGGGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:113:17,96:21,152:173,113:0.3951:2,2:22.2:1:32.1:1:0.4819:1.28:60:55.5:0.3964:0:1 1/1:170:136:18,118:4,30:34,136:0.8:2,2:21.3:1:30.8:1:1:1.14:60:44.333:0.8012:0:1.2 +9 139410595 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13603;SOR=Inf;LSEQ=TCATGTGCAACAGCACTATG;RSEQ=CCCTTCAGGGACCCCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:249:0:0,0:17,232:249,0:0:2,0:22.4:1:32.4:1:1:0:59.9:61.25:1:0:0.4 0/1:146:2:1,1:16,127:143,2:0.0137:2,2:31.5:1:27.5:1:0.22146:7.73:60:4:0.0142:0:2 +9 139410679 . T C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=8e-04;SOR=10.70733;LSEQ=TCAGCCTGAGCTCAGCCAGC;RSEQ=CCAGCTCTCCCTGCCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:4:0,4:0,64:64,4:0.0588:1,0:25.5:1:27.5:1:1:0:60:3:0.0476:0:1 0/1:17:7:0,7:0,10:10,7:0.4118:0,0:29.9:1:32.1:1:1:0:60:14:0.4118:0:1.1 +9 139411479 . G A 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00075;SOR=Inf;LSEQ=GGGCAGGGGACACAATCCAC;RSEQ=GCCAGGCCCCCCTCAGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:15,3:18,0:0:2,0:35.9:1:30.2:1:1:0:59.9:36:1:0:0.4 1/1:3:3:2,1:0,0:0,3:1:0,2:28.7:1:30.3:1:1:0:60:6:1:0:1.3 +9 139411619 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.02902;SOR=Inf;LSEQ=CCCTCACCCCTCAGGAGGCC;RSEQ=GGGTGCAGATGGCCCGGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:136,6:142,0:0:1,0:24.3:1:30.3:1:1:0:60:70:1:0:0.1 0/1:64:3:3,0:61,0:61,3:0.0469:1,0:42:1:25.7:1:1:0:60:2:0.0328:0:2.7 +9 139411622 . G A 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=21.74701;LSEQ=TCACCCCTCAGGAGGCCGGG;RSEQ=TGCAGATGGCCCGGGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:7:7,0:137,5:142,7:0.047:1,0:27.7:1:30:1:1:0:60:14:0.0476:0:1.1 1/0:67:35:35,0:32,0:32,35:0.5224:1,1:28.2:1:27.9:1:1:0:60:16.5:0.5156:0:1.3 +9 139411714 . T C 240 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=13.01073;LSEQ=CCGGGGGCAGGGGGCGGGGG;RSEQ=GGCCCTCACCCGTGGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:47:34,13:470,240:710,47:0.062:2,2:23.4:1:31.2:1:0.42856:1.34:60:22.5:0.0608:0:1.3 0/1:514:238:145,93:166,109:275,238:0.463:2,2:23.6:1:30.4:1:0.92792:1.02:60:118:0.4673:0:1.3 +9 139411880 . G A 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=14.4961;LSEQ=GGGGGGCACGCGCGGCCCCA;RSEQ=TGCCCCACTGGGCACAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:496:27:9,18:140,329:469,27:0.0544:2,2:22:1:29.3:1:0.67166:1.17:60:26:0.0535:0:1.1 0/1:373:170:52,118:62,140:202,170:0.4558:2,2:23.5:1:29.6:1:1:1.00493:60:84:0.4541:0:1.2 +9 139412073 . T C 167 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0.98966;LSEQ=GCCTCAGTTTCCCCATGCCC;RSEQ=GTGCAGGCTGTGGGCCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:44:34,10:42,13:55,44:0.4444:2,2:24.8:1:30.6:1:1:1.05:59.8:43:0.4574:0:1.2 0/1:43:19:16,3:23,1:24,19:0.4419:1,2:28.4:1:31.4:1:0.30596:4.17195:60:38:0.4419:0:1.1 +9 139412105 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCAGAAGGCATGGAGG;RSEQ=TGGGGAAAGCGGAAGCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:125,16:141,2:0.014:2,2:27:1:29.5:1:0.22437:7.60942:60:4:0.0145:0:1 0/0:67:0:0,0:62,5:67,0:0:2,0:26:1:31.4:1:1:0:60:66:1:0:0.3 +9 139412142 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18208;SOR=Inf;LSEQ=AACCCACAGATGTTCCCGGG;RSEQ=CTGCCCCTCCAAGGCTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:264:0:0,0:227,37:264,0:0:2,0:22.1:1:31.4:1:1:0:60:43:1:0:0.8 0/1:197:2:0,2:159,36:195,2:0.0102:2,0:14.5:1:24.5:1:0.03641:0:60:4:0.0102:0:1.5 +9 139412182 . G A 235 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CAGCCTCGACTCGGTTTCCC;RSEQ=CCCTGGCCCCGGCCGACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:228:163,65:218,106:324,228:0.4123:2,2:23.7:1:30.1:1:0.30514:1.22:60:56:0.4125:0:2 0/0:447:0:0,0:293,154:447,0:0:2,0:26.1:1:29.8:1:1:0:60:48.667:1:0:0.6 +9 139412197 . G A 254 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49606;SOR=0.92054;LSEQ=TTCCCGCCCTGGCCCCGGCC;RSEQ=ACGCACCGGGCATGCAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:328:216,112:234,144:378,328:0.4646:2,2:24.8:1:30.5:1:0.30763:1.19:60:163:0.4664:0:1.8 0/1:563:250:154,96:190,120:310,250:0.444:2,2:25.9:1:29.8:1:1:1.01:60:249:0.4462:0:1.2 +9 139412593 . C T 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73856;SOR=0.63348;LSEQ=CTGTGCTGGCACCTACCCAG;RSEQ=GAGCACTCATCCACGTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:6:2,4:319,166:485,6:0.0122:2,2:9.5:1:27.2:1:0.1888:3.83189:60:12:0.0123:0:1 0/0:386:3:2,1:241,141:382,3:0.0078:2,2:31.7:1:30:1:1:1.17:60:6:0.0079:0:1 +9 139412753 . G A 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01638;SOR=Inf;LSEQ=GGCACAGCAGACCTGGGCAG;RSEQ=CAGCGGCGGTCAGTGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:569:0:0,0:200,369:569,0:0:2,0:24.6:1:31.6:1:1:0:59.9:80.286:1:0:0.1 0/1:448:5:5,0:175,268:443,5:0.0112:2,0:13.8:1:21.2:1:0.01012:0:60:1.5:0.0068:0:2.2 +9 139412761 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03363;SOR=Inf;LSEQ=AGACCTGGGCAGGCAGCGGC;RSEQ=GTCAGTGGGCACGGCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:496:0:0,0:168,328:496,0:0:2,0:25.2:1:30.5:1:1:0:59.9:61:1:0:0.1 0/1:373:4:2,2:139,230:369,4:0.0107:2,2:20.8:1:27:1:0.63501:1.65:60:8:0.0109:0:1.3 +9 139412777 . C A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.065;SOR=Inf;LSEQ=CGGCGGTCAGTGGGCACGGC;RSEQ=CCTGGGCCAGGCATGGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:125,278:403,0:0:2,0:24.5:1:30.8:1:1:0:59.9:43.778:1:0:0.1 0/1:272:3:2,1:90,179:269,3:0.011:2,2:12.3:1:22.3:1:0.26501:3.96:60:2:0.0076:0:3 +9 139412853 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGAGGAGCTGCCCGCCGT;RSEQ=ACCCCGTCGGGCATCCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:2,0:24,110:134,2:0.0147:2,0:16.5:1:33:0:0.0354:0:60:4:0.0148:0:1 0/0:65:0:0,0:15,50:65,0:0:2,0:24.8:1:30.6:1:1:0:60:31.5:1:0:0.4 +9 139412884 . C T 149 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=17.94948;LSEQ=GCATCCCGTGACACTTGGGA;RSEQ=GTTCCGGGGGACTCACAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:6:5,1:46,64:110,6:0.0517:2,2:24:1:29.8:1:0.08537:6.85:60:5:0.0442:0:1 1/0:60:30:15,15:11,19:30,30:0.5:2,2:22.4:1:30.4:1:0.43482:1.71:60:60:0.5:0:1 +9 139413358 . C A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.55558;SOR=0;LSEQ=AAGACGCAGGGTGGCAATGC;RSEQ=GCCCCCTCCAGGAAGCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:3:1,2:14,235:249,3:0.0119:2,2:24.3:1:32.3:1:0.16878:8.23:60:6:0.012:0:1 0/0:140:0:0,0:11,129:140,0:0:2,0:7:0:19:0:1:0:60:0:0:0:2 +9 139413400 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGCTGACTCCTCCACCCA;RSEQ=CGCCAGCCTAAATCACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:2:1,1:4,115:119,2:0.0165:1,2:26:1:31.5:1:0.08127:25.83:60:4:0.0167:0:1 0/0:54:0:0,0:2,52:54,0:0:1,0:22.6:1:31.3:1:1:0:60:108:1:0:0.1 +9 139413539 . C T 85 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTAATTCCCGAACACAGGGC;RSEQ=TGTCTGTTCATCCAGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:1,6:7,7:0.4667:2,2:30.9:1:30.4:1:1:2.26:60:14:0.5833:0:1.1 0/0:1:0:0,0:0,1:1,0:0:0,0:19:0:33:0:1:0:60:2:1:0:0 +9 139413908 . C T 258 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.01126;LSEQ=TACGCGCCTGTCCACTCTGG;RSEQ=GGGCAGCGGCAGTTGTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:411:247,164:336,247:583,411:0.4131:2,2:25.9:1:29.8:1:0.47198:1.11:59.9:136:0.4142:0:1.1 0/0:766:6:2,4:437,323:760,6:0.0078:2,2:9.7:1:25.2:1:0.41032:2.7024:60:5:0.0066:0:1.3 +9 139414065 . G A 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTCCCTGAGGTCCAGTCCG;RSEQ=CTCCTGCCTGGACCCCCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:362:0:0,0:89,273:362,0:0:2,0:23:1:31.5:1:1:0:60:35.2:1:0:0.1 0/1:253:22:7,15:56,175:231,22:0.087:2,2:18.8:1:29.4:1:0.44349:1.46:60:44:0.0887:0:1.1 +9 139414099 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.12729;SOR=Inf;LSEQ=CCCCGACACACTGCTCTGGA;RSEQ=ACAAGAGCCTGGCCTCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:192:0:0,0:12,180:192,0:0:2,0:23.6:1:32.1:1:1:0:60:63:1:0:0.1 0/1:107:2:1,1:11,94:105,2:0.0187:2,2:22:1:27:1:0.21266:8.22:60:4:0.0189:0:1 +9 139415262 . G T 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCTGCACCCCGGCTCC;RSEQ=AGGCAGATGGGGCCCCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139417208 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTCCCCGCCATGGGCCCTC;RSEQ=CAGGGCTGCCCCTACACCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:2:2,0:69,1:70,2:0.0278:1,0:35.5:1:31.5:1:1:0:60:4:0.0278:0:1 0/0:35:0:0,0:33,2:35,0:0:2,0:27.2:1:29.6:1:1:0:60:70:1:0:0 +9 139417277 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13699;SOR=Inf;LSEQ=CAGCCGGGGAGGGGCTCGTG;RSEQ=ACCCCGGCCAGCGGGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:234,97:331,0:0:2,0:25.5:1:32:1:1:0:59.9:40.375:1:0:0.2 0/1:195:2:1,1:129,63:192,2:0.0103:2,2:18:1:27.5:1:0.55211:2.03947:60:4:0.0104:0:1 +9 139417309 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.02563;SOR=Inf;LSEQ=CGGGCAGCACTACCTGGCAG;RSEQ=CAGGCACACTCGTGGGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:539:0:0,0:360,177:537,0:0:2,0:25.6:1:31.3:1:1:0:59.9:34.8:0.9962:0:0.2 0/1:361:4:2,2:230,126:356,4:0.0111:2,2:18.8:1:28.8:1:0.61792:1.82206:60:8:0.0111:0:1.3 +9 139418124 . C T 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.65904;SOR=1.90999;LSEQ=GTTGCCTGGGCAGCTGGCGG;RSEQ=GGGCCTGGGTCTGCCCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:2:0,2:284,92:376,2:0.0053:2,0:1:0:26:0:0.06134:0:60:4:0.0054:0:1.5 0/1:298:3:1,2:212,82:294,3:0.0101:2,2:15.3:1:26:1:0.19383:5.13737:60:6:0.0103:0:1 +9 139418138 . C T 54 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.16712;SOR=5.61806;LSEQ=TGGCGGCGGGCCTGGGTCTG;RSEQ=CCACCCCTCAGGCTGTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:1:0,1:378,158:536,1:0.0019:2,0:1:0:26:0:0.29609:0:60:2:0.0019:0:1 0/1:385:4:2,2:256,124:380,4:0.0104:2,2:22.3:1:27.3:1:0.60033:2.06033:60:8:0.0105:0:1.3 +9 139418260 . A G 283 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06877;SOR=0.85896;LSEQ=CAGGGGTTGGTGAGGCAGGC;RSEQ=TTGTCCAGGGGTGTCAGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1325:584:297,287:376,364:740,584:0.4408:2,2:26.1:1:30.8:1:1:1.00:60:52.091:0.4408:0:1.2 0/1:1090:440:225,215:329,320:649,440:0.4037:2,2:24.2:1:30.2:1:0.90178:1.02:59.8:87:0.4024:0:1.2 +9 139418466 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.12586;SOR=Inf;LSEQ=GCCAGGGCAGTTAGTTCCCA;RSEQ=CTGCTTCCCCAGCGCCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:301:0:0,0:54,247:301,0:0:2,0:20.4:1:30.9:1:1:0:60:26.364:1:0:0.3 0/1:166:2:1,1:31,133:164,2:0.012:2,2:44.5:1:29:0:0.34932:4.24:60:4:0.0125:0:1.5 +9 139418642 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16484;SOR=Inf;LSEQ=AACTTTGGGAATGTACTGAA;RSEQ=GCCACTGAATGAGGCTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:1,7:8,0:0:2,0:28.6:1:30.1:1:1:0:59.8:16:1:0:0.4 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:32.5:1:30.5:1:1:2.45:41:4:0.3333:0:2 +9 139418661 . A G 47 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.88578;LSEQ=ATGCCACTGAATGAGGCTGA;RSEQ=GCAGGAGAATCACTTGAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:3:1,2:0,4:4,3:0.4286:0,2:14.7:1:31.3:1:0.42857:0:60:6:0.4286:0:1 1/0:5:3:1,2:1,1:2,3:0.6:2,2:37.3:1:30:1:1:1.7321:43.7:6:0.6:0:1.7 +9 139419951 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGCGGCCCGGGAAGGCAGC;RSEQ=GCCTCACGGCTCAGGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:29:1:1:0:60:4:1:0:1.5 +9 139420026 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGAACCGTCCCGCCTTCC;RSEQ=GAGCCCACCTGGGTGCGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:28.5:1:1:0:60:4:1:0:1 +9 139438653 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52594;SOR=0;LSEQ=GACCTGCACCCAGCCAAGGG;RSEQ=CATCGTCCGCCCCCTACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:13,153:166,2:0.0119:2,2:19:1:29.5:1:0.16018:11.38:60:4:0.012:0:1 0/0:104:0:0,0:11,93:104,0:0:2,0:18.9:1:31.5:1:1:0:60:103:1:0:0.1 +9 139440075 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2465;SOR=0;LSEQ=CTTTTCCCTCTCCATGCTGG;RSEQ=CTCCCCGCCGCCCGCTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:3:1,2:49,22:71,3:0.0405:2,2:11.7:1:27.3:1:0.24411:4.35573:60:6:0.0429:0:1 0/0:67:0:0,0:45,22:67,0:0:2,0:18:1:30.6:1:1:0:60:134:1:0:0.1 +9 139440112 . G A 43 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.35479;SOR=0.30603;LSEQ=CCCAGCCGTGGGGCGCGCGC;RSEQ=CCGGGCGCCGCCAAAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:3:1,2:92,80:172,3:0.017:2,2:23.7:1:27.3:1:0.60045:2.28938:60:2:0.0118:0:1.3 0/0:190:1:0,1:100,89:189,1:0.0053:2,0:38:0:31:0:0.47368:0:60:2:0.0054:0:1 +9 139440119 . G T 29 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59916;SOR=0.43155;LSEQ=GTGGGGCGCGCGCGCCGGGC;RSEQ=CCGCCAAAGTTTCCAAAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:106,93:199,2:0.01:2,2:5.5:1:29:1:1:1.13904:60:4:0.0101:0:1.5 0/0:232:1:0,1:121,110:231,1:0.0043:2,0:1:0:23:0:0.47845:0:60:2:0.0043:0:1 +9 139440142 . C T 53 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.37883;SOR=3.51687;LSEQ=GCCAAAGTTTCCAAAGGGCG;RSEQ=GGAAAGTGGGGGCTCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:311:1:0,1:154,156:310,1:0.0032:2,0:1:0:25:0:1:0:60:2:0.0033:0:1 0/1:356:4:1,3:179,172:351,4:0.0112:2,2:24:1:26.5:1:0.36593:3.11304:60:8:0.0116:0:1.3 +9 139440144 . G T 55 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.08437;LSEQ=CAAAGTTTCCAAAGGGCGCG;RSEQ=AAAGTGGGGGCTCGCGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:4:1,3:160,161:321,4:0.0123:2,2:9.8:1:19.5:1:0.62274:2.97242:60:1:0.0063:0:1 0/1:375:5:1,4:185,185:370,5:0.0133:2,2:12.2:1:23.8:1:0.37173:3.98686:60:10:0.0137:0:1 +9 139440203 . C T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0904;SOR=0;LSEQ=GCGGCGAGCGCGGGCAGCAG;RSEQ=GCCAGGCAGAGCAGGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:3:2,1:118,143:261,3:0.0114:2,2:37.3:1:24.7:1:0.59249:2.42:55.7:2:0.0077:0:2 0/0:323:0:0,0:146,176:322,0:0:2,0:26.3:1:30:1:1:0:59.9:52.667:0.9968:0:0.3 +9 139440261 . G T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20514;SOR=0;LSEQ=CTCCCCACCGGCTGCCCTCT;RSEQ=CGCCCGGGCGGCGGCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:8,17:25,2:0.0741:2,2:39.5:1:32:0:1:2.06:60:4:0.0833:0:1.5 0/0:32:0:0,0:11,21:32,0:0:2,0:6:0:14:0:1:0:60:0:0:0:1 +9 139561715 . G C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CTTACCCCAGCCTCTGCCCC;RSEQ=ACCCGAAGCCTGGCCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:30:1:1:0:60:4:1:0:1 +9 139562148 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTAGAATGTGTGCACCC;RSEQ=CCGCACGGTTCCTGCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:31:1:31:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139562460 . G C 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23636;SOR=5.73436;LSEQ=CACCAAGAGCTCTGGACAGC;RSEQ=TCACCCCCCCTGTGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:2,0:7,0:7,2:0.2222:0,0:37.5:1:31:1:1:0:60:4:0.2222:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:12:0:32.5:1:1:0:60:4:0.6667:0:1.5 +9 139562993 . C T 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=2e-05;SOR=1.73539;LSEQ=GGGACTCCTGGGCTGACCCC;RSEQ=TCTCCACCCCCGCAGCCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1097:122:69,53:543,431:974,122:0.1112:2,2:25.4:1:30.9:1:0.92305:1.03:60:121:0.1118:0:1.1 0/1:891:159:95,64:403,329:732,159:0.1785:2,2:25.8:1:29.3:1:0.2915:1.21:60:158:0.1795:0:1.1 +9 139563144 . C A 249 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.39257;LSEQ=CGGTGAGTGCCCCACCACAC;RSEQ=GAGCTCACCCAGCCCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:243:70,173:91,219:310,243:0.4394:2,2:25:1:31.5:1:0.92499:1.0269:59.9:80:0.4412:0:1.1 0/1:353:83:23,60:78,191:269,83:0.2351:2,2:25.1:1:30.2:1:0.89004:1.06515:60:166:0.2392:0:1.1 +9 139563893 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCACCGGAAGGCCCAGG;RSEQ=AGGGAAACGGCTGTGCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:2,0:101,0:101,2:0.0194:1,0:32:1:32:0:1:0:60:4:0.0198:0:1 0/0:44:0:0,0:43,1:44,0:0:1,0:22.3:1:31.2:1:1:0:60:21:1:0:0.1 +9 139564192 . G A 60 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1496;SOR=3.74359;LSEQ=AGGTGAGGGCTATGTCCCTC;RSEQ=GCGCCCGGTGTTAGGAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:694:2:2,0:267,425:692,2:0.0029:2,0:1:0:25.5:1:0.1499:0:60:4:0.0029:0:1 0/1:560:6:5,1:223,330:553,6:0.0107:2,2:14.3:1:23.5:1:0.04384:7.37:60:5:0.0091:0:1 +9 139564321 . G A 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03619;SOR=Inf;LSEQ=AGCAGCTGCCCCCACAGGGT;RSEQ=CTGGGGACCCAACTGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:435:0:0,0:239,196:435,0:0:2,0:25.8:1:32:1:1:0:59.9:47.333:1:0:0.1 0/1:338:4:2,2:193,141:334,4:0.0118:2,2:17.3:1:28.8:1:1:1.36748:60:8:0.0121:0:1.3 +9 139564474 . C G 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=4.4097;LSEQ=CCAGTCAGGTGAGGCTGGCT;RSEQ=TACCCTGGGGGGCCCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:27:12,15:180,215:395,27:0.064:2,2:22.9:1:32.3:1:1:1.04641:60:54:0.0651:0:1.3 0/1:319:74:32,42:109,136:245,74:0.232:2,2:22.8:1:31.6:1:0.89422:1.05178:60:148:0.2349:0:1.1 +9 139564668 . G A 260 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.29026;LSEQ=GCGGCTGTCCCCAGCGCTGC;RSEQ=TCAACACCGCCGGCAGTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:869:348:183,165:275,246:521,348:0.4005:2,2:26.2:1:30.9:1:1:1.00792:59.9:86:0.4009:0:1.1 0/1:764:124:61,63:327,312:639,124:0.1623:2,2:25.8:1:29.5:1:0.69582:1.08232:60:61:0.1631:0:1.2 +9 139564818 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.57023;SOR=2.90337;LSEQ=TGTGCCTGGCCTGGGGAGGC;RSEQ=GGCAGGCAGTGGACATTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:276:1:1,0:60,215:275,1:0.0036:2,0:1:0:26:0:0.22101:0:60:2:0.0036:0:1 0/1:191:2:1,1:47,142:189,2:0.0105:2,2:24.5:1:27:1:0.44045:3.00:60:4:0.0106:0:1 +9 139565150 . A G 126 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.69439;SOR=1.62423;LSEQ=TCCACGGCACCGCATCGAAA;RSEQ=CGCCGCTGAGACCTCAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:14:14,0:20,3:23,14:0.3784:2,1:21.3:1:33.1:1:0.27477:0:60:28:0.3889:0:1 1/0:8:4:3,1:4,0:4,4:0.5:0,2:12:1:30.8:1:1:0:60:8:0.5:0:1 +9 139565285 . C T 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14671;SOR=1.48981;LSEQ=CGCCAGGCAGGCAGCGGGGG;RSEQ=GGCAGAGGCCTGGGCCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:38:35,3:211,23:234,38:0.1392:2,2:27.6:1:30.4:1:1:1.27:60:76:0.1423:0:1.1 0/1:175:34:31,3:127,12:139,34:0.1943:2,2:26.7:1:29.6:1:1:1.02405:60:68:0.1965:0:1.1 +9 139565474 . ATTGG A 79 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01908;SOR=0.18774;LSEQ=CCTGCTGGAGGAGGTGAGGC;RSEQ=TGGGGGGGGGGGGGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:10:6,4:484,410:894,10:0.0109:2,2:14.8:1:23.9:1:0.76123:1.27:56.8:2.333:0.0089:0.0065:1.7 0/0:969:2:1,1:481,469:950,2:0.0021:2,2:45:1:29:1:1:1.02556:46:4:0.0023:0:3.5 +9 139565475 . TTGG T 131 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0;SOR=0.08861;LSEQ=CTGCTGGAGGAGGTGAGGCA;RSEQ=TGGGGGGGGGGGGGGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:31:5,26:437,376:813,31:0.0349:2,2:31.2:1:26.6:1:3e-05:6.03204:46.7:5.2:0.0377:0:3.6 0/0:941:3:1,2:443,463:906,3:0.0032:2,2:38.3:1:23.3:1:1:1.91229:51.7:2:0.0026:0:3.3 +9 139565606 . G A 44 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1926;SOR=4.54619;LSEQ=GGGGTAGGCAGGCAGTCCAG;RSEQ=GTGGACCTGCTGGAGGAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:395:1:1,0:177,216:393,1:0.0025:2,0:1:0:25:0:0.45178:0:60:2:0.0027:0:1 0/1:350:4:3,1:157,189:346,4:0.0114:2,2:17:1:22.3:1:0.33547:3.60:42:3:0.0091:0:1.5 +9 139565644 . G A 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12337;SOR=1.90336;LSEQ=GGTGAGGCGTCGGGGGGGCA;RSEQ=GCAGTCCAGGGTGGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:11:6,5:104,115:219,11:0.0478:2,2:34.7:1:25.5:1:0.76122:1.33:25.8:1.75:0.0338:0:1.6 0/1:206:18:8,10:87,100:187,18:0.0874:2,2:36.4:1:27.7:1:1:1.08702:23.5:5:0.0769:0:1.8 +9 139565683 . G A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=7.000;MSILEN=1;SSF=0;SOR=0.08003;LSEQ=GCTGGAGGAGGTGAGGCGTC;RSEQ=GGGGGGCAGGCAGTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:148:115:69,46:14,15:29,115:0.777:2,2:22.7:1:29.6:1:0.29577:1.60:29:10.5:0.814:0:1.7 0/1:125:27:18,9:50,48:98,27:0.216:2,2:21.5:1:28:1:0.19156:1.91:33.5:5.75:0.1983:0:1.7 +9 139565692 . G A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00465;SOR=4.17135;LSEQ=GGTGAGGCGTCGGGGGGGCA;RSEQ=GCAGTCCAGGGTGGACCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:5:3,2:90,79:169,5:0.0287:2,2:24.6:1:24.4:1:1:1.31:21.8:1.5:0.0183:0:2 0/1:136:15:9,6:67,54:121,15:0.1103:2,2:23.7:1:25.9:1:0.78934:1.21:23:6.5:0.1016:0:1.4 +9 139565694 . C T 44 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.63585;SOR=0.43197;LSEQ=TGAGGCGTCGGGGGGGCAGG;RSEQ=AGTCCAGGGTGGACCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:1,2:98,83:181,3:0.0163:2,2:6.3:1:28.3:1:0.5963:2.35071:33.3:6:0.0181:0:2 0/0:141:1:0,1:76,63:139,1:0.0071:2,0:1:0:22:0:0.45714:0:33:2:0.0079:0:1 +9 139565711 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06704;SOR=Inf;LSEQ=AGGCAGTCCAGGGTGGACCT;RSEQ=CTGGAGGAGATGAGGCGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:111,95:206,0:0:2,0:21.7:1:30.4:1:1:0:33.4:8.81:1:0:1.6 0/1:144:3:2,1:70,71:141,3:0.0208:2,2:17.7:1:22.3:1:1:2.02:35.3:2:0.0153:0:2.3 +9 139565721 . A G 62 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53633;SOR=1.71046;LSEQ=GGGTGGACCTGCTGGAGGAG;RSEQ=TGAGGCGTCGGGGGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:5:1,4:109,96:205,5:0.0236:2,2:18.4:1:20.6:1:0.1939:4.51336:25.4:0.667:0.0123:0:4.6 0/1:151:6:1,5:73,68:141,6:0.0397:2,2:12.2:1:24:1:0.11607:5.31537:28.2:2:0.0317:0:4 +9 139565730 . C CG 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=7.99591;LSEQ=TGCTGGAGGAGATGAGGCGT;RSEQ=GGGGGGGGAGGCAGGCAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:5:4,1:116,102:218,5:0.0217:2,2:36:1:27.4:1:0.37671:3.50:27.4:10:0.0263:0:1.2 0/1:165:25:14,11:70,63:133,25:0.1515:2,2:27.1:1:29.8:1:0.82906:1.14:37:50:0.1748:0:1 +9 139565735 . GGGGA G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=7.000;MSILEN=1;SSF=0.03995;SOR=3.05342;LSEQ=GAGGAGATGAGGCGTCGGGG;RSEQ=GGCAGGCAGTCCAGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:5:2,3:130,125:255,5:0.0192:2,2:12.8:1:29:1:0.6803:1.55735:37.8:10:0.0202:0.0077:1.4 0/1:195:11:8,3:96,88:184,11:0.0564:2,2:9.5:1:28.9:1:0.22489:2.43:35.6:22:0.0588:0.0462:2 +9 139565737 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.000;MSILEN=1;SSF=0.17369;SOR=Inf;LSEQ=GGAGATGAGGCGTCGGGGGG;RSEQ=GAGGCAGGCAGTCCAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:261:0:0,0:132,126:258,0:0:2,0:26.6:1:30.4:1:1:0:40:24.8:1:0:1.6 0/1:187:2:1,1:96,87:183,2:0.0107:2,2:10.5:1:28.5:1:1:1.10286:30.5:4:0.0115:0:2.5 +9 139565738 . G T 51 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.45875;SOR=1.87117;LSEQ=GAGATGAGGCGTCGGGGGGG;RSEQ=AGGCAGGCAGTCCAGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:3:1,2:133,123:256,3:0.0114:2,2:6.7:1:17.3:1:0.61083:2.15639:45:0.5:0.0041:0:2 0/1:189:4:3,1:96,86:182,4:0.0212:2,2:8.3:1:25.8:1:0.6241:2.67:46.5:3:0.0169:0:3 +9 139565739 . A G 81 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14218;SOR=2.22014;LSEQ=AGATGAGGCGTCGGGGGGGG;RSEQ=GGCAGGCAGTCCAGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:7:4,3:131,123:254,7:0.0263:2,2:11.3:1:22.4:1:1:1.25:39.1:1.333:0.0185:0:3.3 0/1:194:11:4,7:97,83:180,11:0.0567:2,2:9.6:1:23.5:1:0.35392:2.03763:47.7:1.75:0.044:0:2.5 +9 139565778 . A G 255 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GACCTGCTGGAGGAGGTGAG;RSEQ=CGTCGGCAGGGGGCAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:289:289:123,166:0,0:0,289:1:0,2:27.3:1:31.2:1:1:0:46.3:23.083:1:0:1.5 1/1:229:196:83,113:16,17:33,196:0.8559:2,2:29.1:1:30.3:1:0.57071:1.27995:47.7:31.667:0.852:0:1.5 +9 139565780 . G A 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.25955;SOR=0;LSEQ=CCTGCTGGAGGAGGTGAGAC;RSEQ=TCGGCAGGGGGCAGGTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:1,2:119,165:284,3:0.0105:2,2:34.7:1:32:1:1:1.44065:53.3:6:0.0109:0:4.3 0/0:225:0:0,0:97,127:224,0:0:2,0:28.6:1:29.7:1:1:0:49.2:43.8:1:0:1.4 +9 139565815 . C A 23 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.33855;LSEQ=GTCTTCACAACAGCAGAGGC;RSEQ=CAGGCCCGGGTACAGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:215:2:2,0:64,148:212,2:0.0093:2,0:1:0:26:1:0.09412:0:46:4:0.01:0:2 0/1:161:2:1,1:59,100:159,2:0.0124:2,2:28.5:1:23:1:1:1.69:60:4:0.0133:0:2 +9 139565820 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50736;SOR=0;LSEQ=CACAACAGCAGAGGCCCAGG;RSEQ=CCGGGTACAGGCTCCGTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:192:2:1,1:53,137:190,2:0.0104:2,2:13.5:1:31:1:0.48446:2.57:56.5:4:0.0108:0:2 0/0:147:0:0,0:52,95:147,0:0:2,0:23.7:1:29.2:1:1:0:57.4:15.333:1:0:1.1 +9 139565987 . A AC 94 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.27273;SOR=0;LSEQ=GCAGCTGGACACTGACCAGG;RSEQ=CCCCCCAGGGCCGGAGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:1,1:2,8:0.8:2,0:29.6:1:31.6:1:0.2:0:60:16:0.8:0.1:0 0/0:1:0:0,0:0,1:1,0:0:0,0:28:0:31:0:1:0:60:2:1:0:0 +9 139566232 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAAGCTTTTCTGCCACGG;RSEQ=AGCCCCCTCTAGTGGACACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:31,0:31,2:0.0606:1,2:17:0:31:1:0.06061:0:60:4:0.0606:0:1.5 0/0:12:0:0,0:12,0:12,0:0:0,0:31.7:1:31.9:1:1:0:60:24:1:0:0.3 +9 139566288 . G A 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=0.12047;LSEQ=GAGGCGGGGGCTGGAGGCTT;RSEQ=TGGAGCCCTTCCCAGGGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:96:50:47,3:43,3:46,50:0.5208:2,2:23.8:1:29:1:1:1.09:59.5:100:0.5208:0:1.1 0/1:35:4:4,0:26,5:31,4:0.1143:2,0:24.3:1:25.5:1:1:0:60:8:0.1176:0:1 +9 139566362 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11818;SOR=Inf;LSEQ=GGCCGGCCCAGGGTCACTGC;RSEQ=CTTCTGCACCCACAGAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:335:0:0,0:237,97:334,0:0:2,0:25.6:1:31.2:1:1:0:59.9:46.714:1:0:0.2 0/1:176:2:1,1:114,60:174,2:0.0114:2,2:16:1:31:0:1:1.89268:60:4:0.0114:0:1 +9 139566421 . A G 62 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17447;SOR=5.1655;LSEQ=ACTGCACAGCCTGGCCTCGC;RSEQ=GGCACTGGAGCATGGGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:1:1,0:285,191:476,1:0.0021:2,0:39:0:28:0:1:0:60:2:0.0021:0:1 0/1:372:4:2,2:223,144:367,4:0.0108:2,2:36.5:1:31:1:0.64787:1.54668:60:8:0.0109:0:1.3 +9 139566548 . C A 103 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.00163;SOR=8.08183;LSEQ=CAGCTGGGGTCCTGTGAGTG;RSEQ=CCCCACCCTCCAGAGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:787:2:1,1:378,407:785,2:0.0025:2,2:27.5:1:13.5:1:1:1.08:60:0:0:0:5 0/1:594:12:5,7:285,297:582,12:0.0202:2,2:22.5:1:28.9:1:0.77287:1.34277:60:24:0.0207:0:1 +9 139566748 . G A 157 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=24.63013;LSEQ=AAGACTCGTGACTGCCCAGC;RSEQ=CCCCAGGCTGGACTGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1091:2:2,0:513,573:1086,2:0.0018:2,0:23:1:19.5:1:0.22383:0:60:1:9e-04:0:2 0/1:1039:45:20,25:478,514:992,45:0.0433:2,2:25.4:1:28.7:1:0.65018:1.16228:60:21.5:0.0425:0:1.2 +9 139566823 . A G 258 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.44748;LSEQ=AACATGCTGGGGGTCCAGAA;RSEQ=CCACCTCGGGGTGACTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:452:282:71,211:39,128:167,282:0.6239:2,2:23.9:1:32.4:1:0.73369:1.10:60:55.4:0.6211:0:1.2 1/1:370:315:87,228:15,40:55,315:0.8514:2,2:23.6:1:31.1:1:1:1.02:60:314:0.8533:0:1.1 +9 139566889 . G A 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.01965;LSEQ=TCTTCCTCCTCCCCTTCCTC;RSEQ=GGAGGCTCCCCAGACCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:8:0,8:1,123:124,8:0.0606:1,0:27.9:1:32.5:1:1:0:60:16:0.0625:0:1.8 0/1:81:5:0,5:0,76:76,5:0.0617:1,0:14.4:1:32.2:1:1:0:60:10:0.0633:0:1.6 +9 139566996 . G A 115 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01299;SOR=0;LSEQ=GGCATCCCAAGGCCAGGTGG;RSEQ=CCCTCAGCTGAGGGAAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:16:0,16:0,3:3,16:0.8421:0,1:22.2:1:28.9:1:1:0:57.6:7:0.875:0:1.1 0/0:3:0:0,0:0,3:3,0:0:0,0:6:1:31.3:1:1:0:60:6:1:0:0 +9 139587610 . CA C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1918;SOR=Inf;LSEQ=CTGACTCCGTAGAACAAAAT;RSEQ=AATGGAAACACATCAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:15,19:34,0:0:2,0:27.3:1:30.5:1:1:0:59.5:68:1:0:0.8 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:18.5:1:31:1:1:1.0801:60:4:0.0741:0.037:1.5 +9 139587632 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGGAAACACATCAGCTAC;RSEQ=ACAGGAAATAACCTCTCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:9,15:0,0:0,24:1:0,2:24.6:1:31.3:1:1:0:60:48:1:0:1.1 1/1:16:16:8,8:0,0:0,16:1:0,2:25.6:1:29.2:1:1:0:60:32:1:0:1.1 +9 139588349 . A C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TTGCCTCTGGGTAAGAGGTG;RSEQ=GGGTTAAGGTCCAGCAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29:1:33:1:1:0:60:4:1:0:0.5 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:9:0:32.5:1:1:0:60:4:0.6667:0:1.5 +9 139637087 . T C 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACTTGCGGGGCCCCTGTGC;RSEQ=GGAGGCTGCAGTGGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:29:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139637329 . C G 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04429;SOR=0;LSEQ=AGCACCAGCACCAGCACCAG;RSEQ=GCCAGCACCAGCAGCCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:4:2,2:28,28:56,4:0.0667:2,2:26.8:1:32.5:1:1:1:60:8:0.0667:0:1 0/0:69:0:0,0:30,39:69,0:0:2,0:29.6:1:30.2:1:1:0:60:138:1:0:0.2 +9 139637341 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.4962;SOR=Inf;LSEQ=AGCACCAGCGCCAGCACCAG;RSEQ=AGCCCCTGCCTCATCTTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:29,31:60,0:0:2,0:29:1:32.3:1:1:0:60:59:1:0:0.4 0/1:63:2:1,1:24,37:61,2:0.0317:2,2:23.5:1:29.5:1:1:1.53:60:4:0.0323:0:1 +9 139637383 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.49508;SOR=Inf;LSEQ=CTCCTCCCTCAGCCGCCAAG;RSEQ=CCAGTGTTTAAACCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:7,21:28,0:0:2,0:18.2:1:30.5:1:1:0:60:27:1:0:0.3 0/1:33:2:1,1:9,22:31,2:0.0606:2,2:9:1:26.5:1:0.52083:2.37:60:4:0.0606:0:1 +9 139792926 . T C 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63287;SOR=1.91506;LSEQ=CTGTGGGTTGGTTGTGTGGA;RSEQ=GCCAGCTGTGTGGTCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:27.4:1:33.4:1:1:0:55.2:10:0.5:0:2 1/0:6:4:4,0:1,1:2,4:0.6667:2,0:33.5:1:30:1:0.33333:0:60:8:0.6667:0:1 +9 139793211 . AC A 108 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.52476;SOR=1.37315;LSEQ=TCATGGCTGCAGCTAGCGTG;RSEQ=CCCCCCTGGCTCCCTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1110:9:3,6:629,469:1098,9:0.0081:2,2:27.3:1:29.6:1:0.18377:2.67994:60:8:0.0073:0.0027:0.4 0/1:1171:13:7,6:625,530:1155,13:0.0111:2,2:18.2:1:29.4:1:1:1.01077:60:26:0.0112:0.0026:0.3 +9 139793425 . C T 49 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.1009;SOR=Inf;LSEQ=GGAGGGGCAGGCAGGCTAGG;RSEQ=TGGTTTTAGAGCCACGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:318:0:0,0:52,265:317,0:0:2,0:21.8:1:32.8:1:1:0:60:44.286:0.9968:0:0.1 0/1:278:3:1,2:60,215:275,3:0.0108:2,2:5:1:31:1:0.52585:1.79:60:6:0.0109:0:1 +9 139793845 . C A 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.07952;SOR=2.70742;LSEQ=GTTCAGGCGTGCCTTCCTCA;RSEQ=AAACGGAGTGATAAAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:20,3:24,2:26,23:0.4694:2,2:27:1:31.3:1:0.65504:1.7785:60:46:0.4694:0:1.1 1/0:24:17:17,0:7,0:7,17:0.7083:0,1:27.2:1:30.3:1:1:0:60:34:0.7083:0:1.1 +9 139794209 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24128;SOR=0;LSEQ=GGGTGGGGCTGGGCACAGTG;RSEQ=CTCACACCTGTAATCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:0,2:15,165:180,2:0.011:2,0:32:1:31.5:1:1:0:60:4:0.0112:0:1 0/0:188:0:0,0:22,166:188,0:0:2,0:23.6:1:31.3:1:1:0:59.1:46:1:0:0.1 +9 139794225 . C A 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22525;SOR=Inf;LSEQ=AGTGGCTCACACCTGTAATC;RSEQ=CAGCACTTTGGGAGGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:3,147:150,0:0:1,0:26.5:1:31.6:1:1:0:58.3:49:1:0:0.1 0/1:136:2:1,1:2,132:134,2:0.0147:1,2:6:0:31.5:1:0.04379:54.08:27:4:0.0149:0:1 +9 139794331 . C T 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01759;LSEQ=TACAAAAAGCAAAAAACTTA;RSEQ=CAGGGGCCGGGCTCAGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:0,11:0,7:7,11:0.6111:0,0:19.9:1:31.1:1:1:0:45.8:22:0.6111:0:1 1/0:13:8:0,8:1,4:5,8:0.6154:2,0:14.1:1:30:1:0.38462:0:45.3:16:0.6154:0:1 +9 139794565 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCGGAGGTTGCAGTGA;RSEQ=CCAAGATCGCATGCCACTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:27.3:1:31.7:1:1:0:60:6:1:0:1.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139794638 . T A 62 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41667;SOR=Inf;LSEQ=CTTTAAAAAAAAAAAAAGAA;RSEQ=AAAGGGCCGCCAGAAGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:6:1:31.3:1:1:0:60:8:0.4:0:1.3 1/1:1:1:1,0:0,0:0,1:1:0,0:29:0:32:0:1:0:34:2:1:0:8 +9 139802949 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGGGAGGCTGAGGCGGG;RSEQ=GGATCACGAGGTCCGGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:0,3:0,6:6,3:0.3333:0,0:23:1:31:1:1:0:43.7:6:0.3333:0:1 0/0:1:0:0,0:0,1:1,0:0:0,0:41:0:30:0:1:0:50:2:1:0:0 +9 139803958 . G A 44 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTGACCATAGCACATCT;RSEQ=GGGTGCCAAGCCCTCCGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:3,0:2,0:2,3:0.6:0,0:26:1:28.3:1:1:0:60:6:0.6:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139804274 . G A 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01493;SOR=1.61884;LSEQ=GGGTGACCACGTGCTCCTGC;RSEQ=GCCCCTCGGCGCTGCCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:114:112,2:114,4:118,114:0.4914:1,1:24.8:1:30.9:1:0.68368:1.96:59.8:113:0.4978:0:1.5 1/0:195:119:116,3:71,5:76,119:0.6103:2,1:23.5:1:29.3:1:0.26576:2.71:60:238:0.6166:0:1.6 +9 139804346 . C T 261 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=1.79873;LSEQ=CTGGCATTGGCGTCCACCCT;RSEQ=ACACTCCTGATCCCTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:949:452:259,193:296,201:497,452:0.4763:2,2:25.2:1:29.6:1:0.50968:1.09726:60:112:0.4751:0:1.2 1/0:928:576:329,247:196,155:351,576:0.6207:2,2:24.9:1:28.5:1:0.73278:1.05:59.9:71:0.6208:0:1.3 +9 139804679 . T C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.28466;SOR=2.59793;LSEQ=TCCTCATCCTCCAGTGTACA;RSEQ=AGCTGCTTACTTTTCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:0,13:0,11:11,13:0.5:0,1:26.2:1:33.3:1:1:0:57.5:26:0.52:0:1 1/0:11:8:0,8:0,3:3,8:0.7273:0,0:28.6:1:32.4:1:1:0:60:16:0.7273:0:1.1 +9 139810595 . C T 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTTACGTTTTGCTTCATGT;RSEQ=GTGTCTGTGTCATCCTGTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:35.5:1:30.5:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:0,1:1,0:0:0,0:32:0:31:0:1:0:60:2:1:0:0 +9 139810652 . G A 65 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGTGGGCGTTTGATTCT;RSEQ=GGTTTTGAACCCAGGCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:32.4:1:28.4:1:1:0:60:10:0.5556:0:1.2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139811482 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTGAGCCCTCCGCCACCA;RSEQ=CAGGCACTCGGGCCCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:32:0:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139811585 . A G 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCCGTCACTGCCCTGTCCAC;RSEQ=TCATCCTCATCTCTCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:24.7:1:31.3:1:1:0:60:6:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139814584 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51435;SOR=0;LSEQ=ATCCCTATCTATGACCCTGG;RSEQ=CTGTCTCCTCAGCTCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:150,2:152,2:0.013:1,2:19.5:1:28:1:0.03871:61.4348:60:4:0.0132:0:1 0/0:107:0:0,0:102,5:107,0:0:1,0:23.5:1:31.6:1:1:0:59.7:106:1:0:0.2 +9 139814629 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09624;SOR=Inf;LSEQ=CCACGTCTTGGTGGCCGTCC;RSEQ=CGGGTGGGAGCCGAATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:261,70:331,0:0:2,0:22.3:1:31.1:1:1:0:60:109.333:1:0:0.1 0/1:281:3:1,2:216,62:278,3:0.0107:2,2:13.7:1:27.7:1:0.13096:6.90484:60:6:0.0108:0:1 +9 139814631 . G T 38 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33089;SOR=3.70376;LSEQ=ACGTCTTGGTGGCCGTCCCC;RSEQ=GGTGGGAGCCGAATGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:356:1:1,0:277,78:355,1:0.0028:2,0:44:0:31:0:1:0:60:2:0.0029:0:1 0/1:290:3:2,1:221,66:287,3:0.0103:2,2:12.3:1:24.3:1:0.54672:1.67088:60:2:0.0069:0:1.3 +9 139815053 . G A 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=6.89848;LSEQ=AGCAGGTTCTAGCAGGTCCT;RSEQ=GAGCTTTAGAGCCCGGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:46:2,44:27,241:268,46:0.1465:2,1:21.9:1:32.3:1:0.27894:2.45941:60:45:0.1461:0:1.1 1/0:267:145:27,118:10,112:122,145:0.5431:2,2:21:1:30:1:0.01989:2.55:60:144:0.5455:0:1.1 +9 139815159 . GG AA 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.07809;SOR=Inf;LSEQ=CTGAGTCCTGTCATCTAAGG;RSEQ=CCCAAACCCTGGAAGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:6,52:58,0:0:2,0:27.7:1:32.2:1:1:0:59.4:57:1:0:1.1 0/1:23:2:0,2:3,18:21,2:0.087:2,0:41.5:1:31.5:1:1:0:60:4:0.087:0:1 +9 139815160 . G A 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08006;SOR=0;LSEQ=TGAGTCCTGTCATCTAAGGG;RSEQ=CCCAAACCCTGGAAGGTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:57:5,52:0,0:0,57:1:0,2:27.7:1:30.2:1:1:0:59.4:56:1:0:1.1 1/1:23:21:3,18:0,0:0,21:0.913:0,2:23.8:1:29.4:1:1:0:60:20:1:0:1.1 +9 139815354 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55155;SOR=0;LSEQ=GGGGTTGGGTTCTTGTGTGC;RSEQ=GGGAGTGGACATGAGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:102,7:109,2:0.018:2,2:25:1:29:1:0.13956:13.69699:60:4:0.018:0:1 0/0:56:0:0,0:54,2:56,0:0:1,0:20.4:1:29.6:1:1:0:59.8:112:1:0:0.2 +9 139815417 . G A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00069;SOR=Inf;LSEQ=GCACTGTCCTGCTGGAGATC;RSEQ=GTGGGTGTGGGAGGCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:0:0,0:270,20:290,0:0:2,0:24.2:1:30.4:1:1:0:59.8:95.667:1:0:0.2 0/1:199:8:8,0:178,13:191,8:0.0402:2,0:19.1:1:29:1:1:0:60:16:0.0402:0:1 +9 139815960 . A G 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01515;SOR=0;LSEQ=AGCCTGGTCCTCTGGCACAC;RSEQ=GCCCTAAAGCAGACATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1:0,0:23.1:1:30.7:1:1:0:56.3:20:1:0:1.4 0/0:2:0:0,0:1,1:2,0:0:2,0:3:0:24:1:1:0:60:1:1:0:2 +9 139817331 . A C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATGGGCCTGGGGGCACG;RSEQ=GGTGGAGAGGACTAGGACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:31:1:1:0:57:4:1:0:1 +9 139818169 . CTT C 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.00013;SOR=3.69665;LSEQ=ATAGTTTGAGGGAAAAAAAA;RSEQ=TTCTTTGCACCCCAGAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:53:53,0:61,1:62,53:0.4569:1,1:24.6:1:32.6:1:1:0:59.9:106:0.469:0.1034:0.1 1/0:62:47:47,0:15,0:15,47:0.7581:1,1:24.4:1:31.5:1:1:0:60:94:0.7705:0.2097:0.1 +9 139818263 . G T 61 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09815;SOR=6.02083;LSEQ=AAGAGCCCTGCCCCGCCCTT;RSEQ=CTGAGTGTCAGCTCACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:557:1:1,0:401,155:556,1:0.0018:2,0:37:0:32:0:1:0:60:2:0.0019:0:1 0/1:466:5:2,3:319,141:460,5:0.0107:2,2:19.4:1:26.6:1:0.17499:3.38337:60:10:0.0109:0:1 +9 139818485 . G A 56 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06176;SOR=Inf;LSEQ=CTGCAGGCTTCGCTAGGGCC;RSEQ=CACCTGGGAGTCCCTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:100,303:403,0:0:2,0:25.7:1:32:1:1:0:60:200.5:1:0:0.1 0/1:409:5:4,1:122,282:404,5:0.0122:2,2:7:1:24.4:1:0.03306:9.19:60:4:0.0098:0:1.2 +9 139818543 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50147;SOR=0;LSEQ=TGCAGGGTTGTGCGGGACAA;RSEQ=GTGGCTTGGGCTCGCTGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:6,138:144,2:0.0137:1,2:36:1:30.5:1:0.09391:21.37:60:4:0.014:0:1 0/0:124:0:0,0:8,116:124,0:0:2,0:23.8:1:30.8:1:1:0:60:123:1:0:0.1 +9 139818848 . C CA 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAGTGAGAACCCATGTCTA;RSEQ=AAAAAAAATAGAAAAATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:30:1:33:0:1:0:54:4:0.6667:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +9 139819984 . C T 132 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCTGTGGCAGGAGCAAGGC;RSEQ=GCCCACCACGTGGTCTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:90,1:91,0:0:1,0:27.8:1:31.5:1:1:0:59.8:90:1:0:0.3 0/1:39:19:19,0:20,0:20,19:0.4872:1,1:26.1:1:31.2:1:1:0:60:38:0.4872:0:1.1 +9 139820048 . G A 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.004;SOR=0.54305;LSEQ=TCCTGGGATGGCCTCCTGCT;RSEQ=GTGGCCCTGCCAGTGTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:203:99:92,7:97,6:103,99:0.4877:2,2:23.1:1:28.2:1:0.78003:1.22881:60:48.5:0.485:0:1.2 0/1:188:64:60,4:116,8:124,64:0.3404:2,2:19.2:1:28.2:1:1:1.03:60:63:0.3387:0:1.1 +9 139820363 . A G 211 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=134.38502;LSEQ=CAGGGCTCTAACTGCCCCCT;RSEQ=CTGGTGTCTGGGGGTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1026:1:0,1:433,592:1025,1:0.001:2,0:49:0:17:0:1:0:60:0:0:0:4 0/1:922:107:43,64:352,461:813,107:0.1161:2,2:23.1:1:31.3:1:0.60372:1.13629:60:214:0.1172:0:1.1 +9 139820421 . G A 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.87426;LSEQ=GCTCACGGAGGGGCCACCAC;RSEQ=CTGGGCCAGGGTCTCACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:45:4,41:40,282:322,45:0.1226:2,2:25.1:1:29.9:1:0.62842:1.45256:59.4:44:0.1232:0:1 1/0:282:148:24,124:23,111:134,148:0.5248:2,2:22.9:1:29:1:0.87369:1.07029:60:73:0.5252:0:1 +9 139820621 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGTCTTCGGGTGCTTCC;RSEQ=AGCACAAGCTGCCCTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:20:1:27:1:1:0:60:4:0.2222:0:1 0/0:2:0:0,0:0,2:2,0:0:0,0:12.5:1:31.5:1:1:0:60:4:1:0:0 +GL000199.1 34115 . A T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTGCTCCATGAAAGGCAATA;RSEQ=TCAACTCCGTGACTTGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:28:1:1:0:60:4:1:0:1 +GL000199.1 34440 . C T 57 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAAGAGTGTTTCAAACCTG;RSEQ=TCTATGAAAGGGAATGTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:34:0:32:0:1:0:29:2:1:0:8 1/1:5:4:1,3:1,0:1,4:0.8:0,2:17:0:28.5:1:0.4:0:32.5:8:0.8:0:5 +GL000199.1 34444 . A G 61 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTTTCAAACCTGCTCT;RSEQ=TGAAAGGGAATGTTCAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:38:0:34:0:1:0:29:2:1:0:8 1/1:5:4:1,3:1,0:1,4:0.8:0,2:21:0:30.8:1:0.4:0:32.5:8:0.8:0:5 +GL000199.1 34455 . T C 60 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCTGCTCTATGAAAGGGAA;RSEQ=GTTCAATTCTGTGACTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:42:0:32:0:1:0:29:2:1:0:8 1/1:5:4:1,3:1,0:1,4:0.8:0,2:30.8:1:30:1:0.4:0:32.5:8:0.8:0:5 +GL000199.1 34460 . A C 62 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCTATGAAAGGGAATGTTC;RSEQ=ATTCTGTGACTTGAATGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:37:0:33:0:1:0:29:2:1:0:8 1/1:5:4:1,3:1,0:1,4:0.8:0,2:28.5:1:31:1:0.4:0:32.5:8:0.8:0:5 +GL000199.1 57101 . G C 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAATGCAAACATCACAGA;RSEQ=AAGTTTCTGAGAATGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:30:1:1:0:24.5:4:1:0:8 +GL000199.1 57118 . T A 29 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAGAAGTTTCTGAGAATGC;RSEQ=TCTGTCTTGATTTTATATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:29.5:1:1:0:24.5:4:1:0:8 +GL000199.1 57129 . T G 31 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGAGAATGCTTCTGTCTTGA;RSEQ=TTTATATGAAGATATTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:31.5:1:1:0:24.5:4:1:0:8 +GL000199.1 57133 . A C 31 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATGCTTCTGTCTTGATTTT;RSEQ=TATGAAGATATTCCCGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:31.5:1:1:0:24.5:4:1:0:8 +GL000199.1 57138 . A C 32 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTCTTGATTTTATATG;RSEQ=AGATATTCCCGTTTCCAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:32:1:1:0:24.5:4:1:0:8 +GL000199.1 57142 . T A 30 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTGATTTTATATGAAGA;RSEQ=ATTCCCGTTTCCAACGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:30.5:1:1:0:24.5:4:1:0:8 +GL000199.1 57245 . A G 29 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCAAACAAAGGTTCAACT;RSEQ=TGTTAGTTGAGGACACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:29.5:1:1:0:20.5:4:1:0:6 +GL000199.1 57250 . A C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAAAGGTTCAACTATGTT;RSEQ=GTTGAGGACACACATCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:29:1:1:0:20.5:4:1:0:6 +GL000199.1 57254 . G T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGTTCAACTATGTTAGTT;RSEQ=AGGACACACATCGCAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:28:1:1:0:20.5:4:1:0:6 +GL000199.1 57267 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTAGTTGAGGACACACATC;RSEQ=CAAATAAGTTTCTGAGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:29.5:1:30:1:1:0:20.5:4:1:0:6 +GL000199.1 57269 . A C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGTTGAGGACACACATCGC;RSEQ=AATAAGTTTCTGAGAATCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:31.5:1:1:0:20.5:4:1:0:6 +GL000199.1 57308 . G C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCTGTCTAGTTTTTATTT;RSEQ=AAGATATTTCCTTTCTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:33:0:1:0:20.5:4:1:0:6 +GL000199.1 72891 . A T 59 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=AAACTGCTCTGTCAAAAGGA;RSEQ=GGTTCAACTCTGTTACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:12.5:1:30:1:1:0:24:4:0.6667:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:19:1:29.8:1:1:0:21.3:8:1:0:6.3 +GL000199.1 72900 . T A 59 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGTCAAAAGGAAGGTTCAAC;RSEQ=CTGTTACTTGAGTACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:21.5:1:29.5:1:1:0:24:4:0.6667:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:23.5:1:29.5:1:1:0:21.3:8:1:0:6.3 +GL000199.1 72908 . T A 59 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GGAAGGTTCAACTCTGTTAC;RSEQ=TGAGTACACACATCACAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:29.5:1:30.5:1:1:0:24:4:0.6667:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:27.5:1:29.8:1:1:0:21.3:8:1:0:6.3 +GL000199.1 72921 . T A 60 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTGTTACTTGAGTACACACA;RSEQ=CACAAGGAAGTTTCTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:42.5:1:29.5:1:1:0:24:4:0.6667:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:34:1:30:1:1:0:21.3:8:1:0:6.3 +GL000199.1 72927 . G A 60 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGAGTACACACATCACAA;RSEQ=GAAGTTTCTGAGAATGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:45:1:31.3:1:1:0:25.7:6:1:0:7 1/1:4:4:3,1:0,0:0,4:1:0,2:37:1:30:1:1:0:21.3:8:1:0:6.3 +GL000199.1 72949 . G T 47 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTTTCTGAGAATGCTTCT;RSEQ=TCTGGTTTTTATGAGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:26:1:30.7:1:1:0:25.7:6:1:0:7 1/1:3:3:2,1:0,0:0,3:1:0,2:32:1:29.7:1:1:0:21.7:6:1:0:6.3 +GL000204.1 56386 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.09804;SOR=Inf;LSEQ=CCGCCACAGCCACCACCACC;RSEQ=CCACCGCCACCGCCACTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:14,9:23,0:0:2,0:25.2:1:32:1:1:0:60:46:1:0:0.3 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:27:0:30.5:1:1:1.22474:60:4:0.1818:0:1.5 +GL000204.1 56431 . T C 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00513;SOR=Inf;LSEQ=CCACGCAGCGCGCGGGACTC;RSEQ=CTGGCGTCTCCATGGAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:12,11:23,0:0:2,0:22.3:1:30.5:1:1:0:60:22:1:0:0.2 0/1:10:4:2,2:3,3:6,4:0.4:2,2:33.5:1:31.8:1:1:1:60:8:0.4:0:1.5 +GL000204.1 56622 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GTCAGCCCCGGCCGCGCTCA;RSEQ=CAGCCCGCCTCCCACTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41.5:1:28.5:1:1:0:60:4:1:0:1.5 +GL000212.1 628 . G A 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAATTATTGGCCCATTCT;RSEQ=TTCTTTCCCGCATTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:34.5:1:33:0:1:0:22:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000212.1 40671 . T C 52 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGCCCTATCGCCATGGTGA;RSEQ=GGGATTAGGGATCTCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:0,3:1:0,0:17:1:33:0:1:0:25.7:6:1:0:7.7 +GL000212.1 40674 . G A 45 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTATCGCCATGGTGATGG;RSEQ=ATTAGGGATCTCCTGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:3,0:0,0:0,3:1:0,0:20:1:29:0:1:0:25.7:6:1:0:7.7 +GL000212.1 40682 . A G 74 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCATGGTGATGGGATTAGGG;RSEQ=TCTCCTGCCCTTGGTCCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:4,1:0,0:0,5:1:0,2:18.8:1:32.2:1:1:0:28.6:10:1:0:7.8 +GL000212.1 40691 . C T 75 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGATTAGGGATCTCCTGC;RSEQ=CTTGGTCCTAAGTGCCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:4,1:0,0:0,5:1:0,2:18.8:1:32.4:1:1:0:28.6:10:1:0:7.8 +GL000212.1 40695 . G C 75 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAGGGATCTCCTGCCCTT;RSEQ=GTCCTAAGTGCCACTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:4,1:0,0:0,5:1:0,2:18:1:32.6:1:1:0:28.6:10:1:0:7.8 +GL000212.1 40699 . C G 32 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATCTCCTGCCCTTGGTC;RSEQ=TAAGTGCCACTGTCTGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:7:2:2,0:2,3:5,2:0.2857:2,0:12:0:32:0:0.42857:0:21:4:0.2857:0:8 +GL000212.1 40704 . TG GA 89 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCTGCCCTTGGTCCTAAG;RSEQ=CCACTGTCTGTGATGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:4,3:0,0:0,7:1:0,2:14.3:1:32:1:1:0:30.1:14:1:0:6.9 +GL000212.1 40709 . C G 34 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCCCTTGGTCCTAAGTGCCA;RSEQ=TGTCTGTGATGAGTTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:5:0:34:0:1:0:51:2:1:0:8 0/1:7:2:0,2:4,1:5,2:0.2857:2,0:14:0:34:0:0.14286:0:34:4:0.2857:0:7 +GL000212.1 40718 . A C 78 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTAAGTGCCACTGTCTGTG;RSEQ=TGAGTTTTTCAAAGGTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11:1:34:0:1:0:35.5:4:1:0:8 1/1:5:5:2,3:0,0:0,5:1:0,2:17.6:1:33.6:1:1:0:31:10:1:0:7 +GL000212.1 40721 . A T 71 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTGCCACTGTCTGTGATG;RSEQ=GTTTTTCAAAGGTCAGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14:1:32.5:1:1:0:35.5:4:1:0:8 1/1:5:5:2,3:0,0:0,5:1:0,2:18.2:1:31:1:1:0:31:10:1:0:7 +GL000212.1 40724 . T C 66 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=TGCCACTGTCTGTGATGAGT;RSEQ=TTTCAAAGGTCAGAGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:17:1:32.5:1:1:0:35.5:4:1:0:8 1/1:5:4:1,3:1,0:1,4:0.8:0,2:20.5:1:33:0:0.4:0:33.5:8:0.8:0:7 +GL000212.1 40739 . GC AG 79 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=TGAGTTTTTCAAAGGTCAGA;RSEQ=AGATTGAACCTTTGTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:8:6:2,4:0,0:0,6:0.75:0,2:12.3:1:30.8:1:1:0:34.2:12:0.75:0:6.5 +GL000212.1 40744 . T G 34 d5;v3;MAF0.05;NM7.25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=0;LSEQ=TTTTCAAAGGTCAGAGCAGA;RSEQ=TGAACCTTTGTGGTTTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:34.5:1:1:0:35.5:4:1:0:7.5 0/1:8:1:1,0:3,4:7,1:0.125:2,0:32:0:33:0:1:0:21:2:0.125:0:7 +GL000212.1 40757 . G T 61 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=GAGCAGATTGAACCTTTGTG;RSEQ=TTTCATTTTCCCTGATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:42.5:1:33.5:1:1:0:35.5:4:1:0:7.5 1/0:6:4:2,2:2,0:2,4:0.6667:0,2:27.5:1:30.5:1:0.46667:0:34.3:8:0.6667:0:6.8 +GL000212.1 40761 . C T 78 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTGAACCTTTGTGGTTT;RSEQ=ATTTTCCCTGATTTTGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:40.5:1:31.5:1:1:0:35.5:4:1:0:7.5 1/1:6:6:4,2:0,0:0,6:1:0,2:24.8:1:30.2:1:1:0:29.7:12:1:0:6 +GL000212.1 40772 . AT TG 62 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.44444;SOR=Inf;LSEQ=TTGTGGTTTCATTTTCCCTG;RSEQ=TTTGATTTTTCTTATGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29.5:1:33:1:1:0:35.5:4:1:0:7.5 1/0:7:4:2,2:1,1:2,4:0.5714:2,2:12:0:31.4:1:1:1:32.5:8:0.6667:0:6 +GL000212.1 40773 . T G 30 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=TGTGGTTTCATTTTCCCTGA;RSEQ=TTTGATTTTTCTTATGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:35:0:1:0:35.5:4:1:0:7.5 0/1:7:2:2,0:0,0:0,2:0.2857:0,0:23.5:1:30:1:1:0:26:4:0.6667:0:7 +GL000212.1 40778 . A C 67 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.54545;SOR=4.34109;LSEQ=TTTCATTTTCCCTGATTTTG;RSEQ=TTTTTCTTATGGGGAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:1,2:2,1:3,3:0.5:2,2:4:0:32.3:1:1:3.10575:39.3:6:0.5:0:7.3 1/1:6:5:3,2:1,0:1,5:0.8333:0,2:9:1:29:1:1:0:32.2:4:0.8:0:6.2 +GL000212.1 40786 . T C 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTGATTTTGATTTTTCT;RSEQ=ATGGGGAACCTGTGTTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:11.9:1:33.1:1:1:0:34:14:1:0:7.4 1/1:9:9:3,6:0,0:0,9:1:0,2:10.7:1:31.2:1:1:0:28.2:18:1:0:7.2 +GL000212.1 40801 . T G 62 v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5453;SOR=Inf;LSEQ=TTTCTTATGGGGAACCTGTG;RSEQ=TGCTGCATTCAAGGTATGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:7,0:0:2,0:19.7:1:30.4:1:1:0:30.1:14:1:0:7.3 0/1:21:4:1,3:8,9:17,4:0.1905:2,2:19.3:1:31.3:1:0.60301:2.55208:21.3:8:0.1905:0:7.3 +GL000212.1 40808 . A T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGAACCTGTGTTGCTGC;RSEQ=TTCAAGGTATGTTCATACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1:0,2:25.4:1:31:1:1:0:30.3:14:1:0:7.3 1/1:23:22:9,13:1,0:1,22:0.9565:0,2:18.6:1:29.5:1:0.43478:0:28.6:44:0.9565:0:6.5 +GL000212.1 40811 . C G 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43182;SOR=3.27323;LSEQ=GGAACCTGTGTTGCTGCATT;RSEQ=AAGGTATGTTCATACTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:3,4:1,0:1,7:0.875:0,2:28.4:1:32.4:1:1:0:30.3:14:0.875:0:7.3 1/1:25:24:12,12:0,1:1,24:0.96:0,2:19.3:1:30.9:1:1:0:28.5:48:0.96:0:6.2 +GL000212.1 40819 . G A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2;SOR=Inf;LSEQ=TGTTGCTGCATTCAAGGTAT;RSEQ=TTCATACTGGCCTGTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:1,0:1,8:0.8889:0,2:31.1:1:29.9:1:1:0:29.5:16:0.8889:0:7 1/1:36:36:16,20:0,0:0,36:1:0,2:19.9:1:28.8:1:1:0:26.9:72:1:0:5.7 +GL000212.1 40833 . G T 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3515;SOR=4.338;LSEQ=AGGTATGTTCATACTGGCCT;RSEQ=TCAAATGCGAACTCTTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:4,6:1,0:1,10:0.9091:0,2:28.3:1:30.6:1:0.45455:0:29:20:0.9091:0:6.5 1/1:46:45:22,23:0,0:0,45:0.9783:0,2:24.6:1:29.6:1:1:0:25.5:90:0.9783:0:5.3 +GL000212.1 40842 . G C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35714;SOR=4.24264;LSEQ=CATACTGGCCTGTCAAATGC;RSEQ=AACTCTTCAAATTACTAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:4,6:1,0:1,10:0.9091:0,2:28.3:1:31.6:1:0.45455:0:29:20:0.9091:0:6.5 1/1:45:44:22,22:0,0:0,44:0.9778:0,2:29.4:1:31.4:1:1:0:25.7:88:0.9778:0:5.3 +GL000212.1 40844 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTGGCCTGTCAAATGCGA;RSEQ=CTCTTCAAATTACTAGTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:5,6:11,0:0:2,0:28.8:1:29.9:1:1:0:28.5:22:1:0:6.2 0/1:45:2:1,1:21,22:43,2:0.0444:2,2:21:1:33:0:1:1.05:21.5:4:0.0455:0:4.5 +GL000212.1 40865 . T G 157 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00601;SOR=9.35695;LSEQ=CTCTTCAAATTACTAGTTAA;RSEQ=GCTTTCAAAATATGTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:4,3:7,2:0.2222:2,0:21.5:1:33:0:0.44444:0:35.5:4:0.2222:0:7 1/0:42:31:16,15:4,5:9,31:0.7381:2,2:36.1:1:31.7:1:1:1.32:23.3:62:0.7381:0:5.1 +GL000212.1 40875 . A G 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00211;SOR=0.05956;LSEQ=TACTAGTTAATGCTTTCAAA;RSEQ=TATGTTATTTAAAAAATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:3,5:0.625:2,2:39.4:1:33.6:1:1:2.60:24.6:10:0.625:0:5 0/1:37:3:0,3:19,15:34,3:0.0811:2,0:23.7:1:33.3:1:0.10502:0:21.7:6:0.0857:0:6.3 +GL000212.1 40880 . T G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTAATGCTTTCAAAATATG;RSEQ=TATTTAAAAAATTATCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:3,4:7,0:0:2,0:28.7:1:31.3:1:1:0:24.4:14:1:0:5.4 0/1:35:3:2,1:16,15:31,3:0.0857:2,2:34.7:1:32.7:1:1:1.84:24:6:0.0857:0:4.3 +GL000212.1 40886 . A C 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.00276;SOR=0.0403;LSEQ=GCTTTCAAAATATGTTATTT;RSEQ=AAAAATTATCCTCTGTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:2,2:1,1:2,4:0.6667:2,2:33:1:33:1:1:1:24.8:8:0.6667:0:5.5 0/1:32:2:0,2:17,12:29,2:0.0625:2,0:19.5:1:32.5:1:0.1957:0:22:4:0.0625:0:5.5 +GL000212.1 160695 . G T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.7233;LSEQ=CATATCCTAGGAGGCCTGGA;RSEQ=TACCCATAATACTGTGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:158:1:0,1:98,59:157,1:0.0063:2,0:1:0:28:0:0.37975:0:60:2:0.0065:0:1 0/1:276:3:1,2:165,108:273,3:0.0109:2,2:14.3:1:21:1:0.56538:3.04303:26.3:2:0.0074:0:1 +GL000212.1 160769 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14908;SOR=0;LSEQ=GGGAAATTTTTAAACCCAGG;RSEQ=AGCTTCCTGGCAGTGCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:159:2:1,1:85,71:156,2:0.0126:2,2:12:0:32.5:1:1:1.19581:22:4:0.0126:0:1.5 0/0:252:0:0,0:125,127:252,0:0:2,0:26.3:1:31.2:1:1:0:29.7:62:1:0:0.1 +GL000212.1 163616 . G A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12706;SOR=0;LSEQ=AGCGGAGACCTCGAGGTGCA;RSEQ=GACTGTCGGGGTGAGGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:1,1:50,41:91,2:0.0215:2,2:19.5:1:33:1:1:1.21689:53:4:0.0217:0:1.5 0/0:167:0:0,0:89,78:167,0:0:2,0:18.8:1:30.6:1:1:0:29:166:1:0:0.1 +GL000212.1 163713 . C A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCTTCCTTCATGTATATTTT;RSEQ=TCTAATCTAAATGTCAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1:0,2:34.4:1:30.4:1:1:0:36.7:20:1:0:1.8 1/1:18:18:2,16:0,0:0,18:1:0,2:32.5:1:28.4:1:1:0:21.6:36:1:0:1.9 +GL000212.1 163775 . T C 156 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTATTTTGAACTTAAGAGT;RSEQ=ATATAAATAGGTCAAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:19:1,18:0,0:0,19:1:0,1:17.3:1:32.4:1:1:0:31.5:38:1:0:1.4 1/1:37:37:6,31:0,0:0,37:1:0,2:18.6:1:30.1:1:1:0:23.1:36:1:0:1.5 +GL000212.1 163817 . CT C 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTTACTGTTCTACTTTG;RSEQ=TTTTTTTTGAGCCTCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:0,12:12,0:0:0,0:29.2:1:31.8:1:1:0:24.4:24:1:0:0.9 0/1:39:3:1,2:9,27:36,3:0.0769:2,2:36.7:1:32.7:1:1:1.48:22.3:6:0.0769:0:0.7 +GL000220.1 6904 . C T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=GGTGCGATGCTCTGGAAACC;RSEQ=CCCGCGGGTGTGTATGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:25:1:33.7:1:1:0:60:6:1:0:1.3 1/1:2:2:1,1:0,0:0,2:1:0,2:10:0:30.5:1:1:0:60:4:1:0:1.5 +GL000220.1 6908 . G A 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=CGATGCTCTGGAAACCCCCC;RSEQ=CGGGTGTGTATGTGAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:16.5:1:32:1:1:0:60:4:0.6667:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:6:0:33:1:1:0:60:4:1:0:1.5 +GL000220.1 6910 . G T 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=ATGCTCTGGAAACCCCCCGC;RSEQ=GGTGTGTATGTGAGAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:14.5:1:31:0:1:0:60:4:0.6667:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:4:0:30:1:1:0:60:4:1:0:1.5 +GL000220.1 7456 . G A 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CGCCCCCAAGCCCAACGCAT;RSEQ=CTGGGATTGTAGTCAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:8.3:1:33.3:1:1:0:60:6:1:0:0.7 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:42.5:1:27:1:1:0:60:4:0.6667:0:2 +GL000220.1 7476 . A G 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGGGATTGTAGTCAGGTA;RSEQ=TCCTGGGACCAACTGACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:25:0:34:0:1:0:60:2:1:0:1 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:32:1:30.5:1:1:0:60:4:0.6667:0:2 +GL000220.1 7604 . T G 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=GCCCGGTGGCTGCTGGGATT;RSEQ=TAGTCTGCAGGCCGGGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:44:0:34:0:1:0:60:2:0.3333:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:30.5:1:1:0:60:4:1:0:1.5 +GL000220.1 8064 . G A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51417;SOR=Inf;LSEQ=GGGGAGCCTATCTGTTCCCA;RSEQ=ACTTCTGCGTGCGAGGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:10,12:1,1:2,22:0.9167:2,2:31.5:1:31:1:1:1.19087:60:44:0.9167:0:1.5 1/1:15:15:8,7:0,0:0,15:1:0,2:30.4:1:29.5:1:1:0:60:30:1:0:1.6 +GL000220.1 8087 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4926;SOR=0;LSEQ=TTCTGCGTGCGAGGAGACAG;RSEQ=GTGGCCAGGGCAGGTGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:2:1,1:9,13:22,2:0.0833:2,2:15.5:1:32.5:1:1:1.42:60:4:0.0833:0:2 0/0:20:0:0,0:10,10:20,0:0:2,0:27.6:1:30.5:1:1:0:60:40:1:0:1.6 +GL000220.1 8122 . G A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.1197;LSEQ=TGGTCTCACTTGTAATTGTG;RSEQ=CACAGTCTCCCCACGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:2,6:2,2:4,8:0.6667:2,2:20.8:1:29.8:1:0.54747:2.71347:60:16:0.6667:0:2.3 1/0:13:9:4,5:2,2:4,9:0.6923:2,2:27.9:1:27.9:1:1:1.22862:60:18:0.75:0:2.4 +GL000220.1 8143 . G C 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.37423;SOR=2.76313;LSEQ=CACAGTCTCCCCACGTGCCA;RSEQ=TTGTACGACTATTTGTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:2,5:7,2:0.2222:2,0:27.5:1:35:0:1:0:60:4:0.2222:0:3.5 0/1:11:5:2,3:3,3:6,5:0.4545:2,2:24.8:1:30.6:1:1:1.44544:60:10:0.4545:0:3.4 +GL000220.1 8160 . G C 68 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54545;SOR=2.97405;LSEQ=CCAGTTGTACGACTATTTGT;RSEQ=CCTGAAGTTTGATTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:36:0:33:0:1:0:60:2:0.3333:0:4 1/0:8:5:2,3:1,2:3,5:0.625:2,2:24.4:1:29.4:1:1:1.29:60:10:0.625:0:3.4 +GL000220.1 8193 . A G 63 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCTCTCTGACAAGACAGA;RSEQ=CCCGGGAGCCTCCAACAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:9.3:1:30.7:1:1:0:60:6:1:0:2.7 1/1:4:4:1,3:0,0:0,4:1:0,2:26:1:31.5:1:1:0:60:8:1:0:3.5 +GL000220.1 8227 . C T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAGCCTGCCCAGCGTTGC;RSEQ=GTAACGCTTGCTCTCGGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:47:0:29:0:1:0:60:2:1:0:3 0/1:5:2:1,1:1,2:3,2:0.4:2,2:33:0:31.5:1:1:1.73:60:4:0.4:0:2.5 +GL000220.1 8232 . C A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTGCCCAGCGTTGCCGTAA;RSEQ=GCTTGCTCTCGGGGAGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:49:0:30:0:1:0:60:2:1:0:3 1/0:4:2:0,2:1,1:2,2:0.5:2,0:26:1:30:0:1:0:60:4:0.5:0:3.5 +GL000220.1 8240 . C T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCGTTGCCGTAACGCTTGCT;RSEQ=TCGGGGAGCTGGGCGCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:41:0:31:0:1:0:60:2:1:0:3 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:46:0:31:1:1:0:60:4:0.6667:0:2.5 +GL000220.1 9608 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGAGTCACTGGGACCGCAG;RSEQ=CTTGCACCACCATGCCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:46.5:1:32:1:1:0:60:4:1:0:1 +GL000220.1 9666 . T C 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGTAGAGACAGGGTTTCAC;RSEQ=ATGTTGCCCAAACTGGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:33.5:1:1:0:29:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000220.1 9676 . A C 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGTTTCACTATGTTGCCC;RSEQ=AACTGGCATGTCTGCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:33.5:1:1:0:29:4:1:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000220.1 10143 . A T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGAGATCAGGTCATGGTG;RSEQ=TTATAGAGAAAGGTAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:17.5:1:31.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000220.1 118144 . GC G 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.6233;LSEQ=CCTGTCCCCGCCGGCGGGCC;RSEQ=CCCCCCCCTCCACGCGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:2,4:3,7:10,6:0.375:2,2:27.2:1:30.2:1:1:1.16:44:5:0.3333:0:1.5 1/0:4:2:0,2:1,1:2,2:0.5:2,0:19:0:32.5:1:1:0:42:4:0.5:0:0.5 +GL000220.1 118253 . C T 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08722;SOR=5.51999;LSEQ=CCTGGGAAACGGGGCGCGGC;RSEQ=GGAGAGGCGGCCGCCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:3,1:10,2:12,4:0.25:2,2:18:1:30:1:1:1.60994:41.8:8:0.25:0:1.5 1/0:9:6:4,2:3,0:3,6:0.6667:0,2:31.8:1:30:1:0.5:0:24.7:12:0.6667:0:2.2 +GL000220.1 118257 . G A 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGAAACGGGGCGCGGCCGGA;RSEQ=AGGCGGCCGCCCCCTCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:12,2:0,0:0,14:1:0,2:35.4:1:31.2:1:1:0:24:28:1:0:1.2 1/1:9:9:7,2:0,0:0,9:1:0,2:29.7:1:28.7:1:1:0:25.2:18:1:0:1.8 +GL000220.1 118387 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51921;SOR=Inf;LSEQ=GCTCCCTCGCTGCGATCTAT;RSEQ=GAAAGTCAGCCCTCGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:6,17:23,0:0:2,0:34.7:1:31.5:1:1:0:40.7:46:1:0:0.5 0/1:37:2:1,1:14,21:35,2:0.0541:2,2:49.5:1:29:0:1:1.48:49.5:4:0.0571:0:1.5 +GL000220.1 118436 . C T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=11.000;MSILEN=2;SSF=0.26829;SOR=0;LSEQ=TCCGCGCGCGCGCGCGCGCG;RSEQ=GCGTGCGGGGGGCCCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:6,10:0,0:0,16:1:0,2:20.6:1:31.2:1:1:0:57:32:1:0:1.4 1/1:25:22:8,14:1,1:2,22:0.88:2,2:16.8:1:27.7:1:1:1.70775:54.5:6.333:0.8636:0:1.5 +GL000220.1 118442 . C CG 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.5122;SOR=Inf;LSEQ=CGCGCGCGCGCGCGCGCGTG;RSEQ=GGGGGGCCCGGCGGGGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:8,8:16,0:0:2,0:18.8:1:31.8:1:1:0:58.4:32:1:0:1.3 0/1:25:2:1,1:8,15:23,2:0.08:2,2:16:0:32:0:1:1.83:51:4:0.0833:0:0.5 +GL000220.1 118515 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16083;SOR=0;LSEQ=TTCCTCCCTCCCGGCCTCTC;RSEQ=CGCCGACCGCGGGCGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:20,16:36,2:0.0526:2,2:21:0:32.5:1:1:1.24262:60:4:0.0541:0:1.5 0/0:56:0:0,0:32,24:56,0:0:2,0:26.9:1:30.1:1:1:0:55.7:27:1:0:0.7 +GL000220.1 118541 . GGT G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.28337;SOR=1.7144;LSEQ=ACCGCGGGCGTGGTGGTGGG;RSEQ=GTGGGGGGGAGGGCGCGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:15:10,5:12,11:23,15:0.3947:2,2:20:1:32.5:1:0.50608:1.80:58.8:30:0.4054:0:0.1 1/0:51:27:15,12:17,8:25,27:0.5294:2,2:24:1:31.2:1:0.40392:1.68258:58.1:54:0.5294:0.0392:0.4 +GL000220.1 118545 . T G 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.23203;SOR=0.53369;LSEQ=CGGGCGTGGTGGTGGGGGTG;RSEQ=GGGGGGGAGGGCGCGCGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:14:7,7:10,5:15,14:0.4:2,2:19.1:1:31.6:1:0.46214:1.95183:58.1:28:0.4118:0:1.6 0/1:46:12:7,5:16,13:29,12:0.2609:2,2:15:1:29.7:1:1:1.13:57.8:24:0.2927:0:1.4 +GL000220.1 118552 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18072;SOR=0;LSEQ=GGTGGTGGGGGTGTGGGGGG;RSEQ=AGGGCGCGCGACCCCGGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:34,2:0.0556:2,2:30.5:1:30.5:1:1:1:60:4:0.0606:0:2 0/0:48:0:0,0:27,20:47,0:0:2,0:19.6:1:29.1:1:1:0:58.9:10.75:1:0:0.7 +GL000220.1 118597 . G A 50 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.10902;SOR=0;LSEQ=GCCCCGCTTCTTCGGTTCCC;RSEQ=CCTCCTCCCCGTTCACCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:3:1,2:18,23:41,3:0.0682:2,2:26:0:32:0:1:1.54994:37.3:6:0.0714:0:1.7 0/0:47:0:0,0:22,25:47,0:0:2,0:25:1:29.1:1:1:0:58.7:14.667:1:0:0.5 +GL000220.1 118607 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22599;SOR=Inf;LSEQ=TTCGGTTCCCGCCTCCTCCC;RSEQ=GTTCACCGCCGGGGCGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:21,26:47,0:0:2,0:23.6:1:30.4:1:1:0:58.6:46:0.9787:0:0.3 0/1:44:2:1,1:19,23:42,2:0.0455:2,2:21:1:26.5:1:1:1.21:60:4:0.0476:0:1.5 +GL000220.1 118655 . G A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50906;SOR=0;LSEQ=CCGGGCCGGGACGGGGTCCG;RSEQ=GGAGCGTGGTTTGGGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:15,18:33,2:0.0571:2,2:13:0:33:1:1:1.19:51:4:0.0571:0:1.5 0/0:24:0:0,0:9,15:24,0:0:2,0:18.1:1:30.3:1:1:0:60:23:1:0:0.3 +GL000220.1 118796 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53427;SOR=Inf;LSEQ=TCGCGCGTCCTTCCTCCTCG;RSEQ=TCCTCCGCACGGGTCGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:20,18:38,0:0:2,0:26.5:1:32.9:1:1:0:47:76:0.9744:0:0.7 0/1:69:2:1,1:34,33:67,2:0.029:2,2:5.5:1:27:1:1:1.02986:23:4:0.0317:0:1.5 +GL000220.1 118807 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16514;SOR=0;LSEQ=TCCTCCTCGCTCCTCCGCAC;RSEQ=GGTCGACCAGCAGACCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:2:1,1:22,21:43,2:0.0444:2,2:36:1:30.5:1:1:1.04655:60:4:0.0455:0:1 0/0:65:0:0,0:33,32:65,0:0:2,0:23.8:1:29.4:1:1:0:53.8:64:1:0:0.6 +GL000220.1 118825 . C CGGGTGGT 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=2.000;MSILEN=3;SSF=0.08564;SOR=0;LSEQ=ACGGGTCGACCAGCAGACCG;RSEQ=GGGTGGTGGGCGGCGGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:3:2,1:18,21:39,3:0.0714:2,2:33.3:1:32.5:1:0.59756:2.29:37.3:6:0.0732:0:0.3 0/0:52:0:0,0:25,27:52,0:0:2,0:22.3:1:29.1:1:1:0:52.4:25:1:0:0.8 +GL000220.1 118829 . TGGTGGGC T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.04227;SOR=0;LSEQ=GTCGACCAGCAGACCGCGGG;RSEQ=GGCGGGCGGCGAGGCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:4:2,2:18,21:39,4:0.093:2,2:34.5:1:31.8:1:1:1.16:37.5:8:0.093:0:0 0/0:50:0:0,0:24,26:50,0:0:2,0:21.2:1:30.6:1:1:0:51.8:49:1:0:0.9 +GL000220.1 118832 . T C 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12945;SOR=0.50086;LSEQ=GACCAGCAGACCGCGGGTGG;RSEQ=GGGCGGCGGGCGGCGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:20:9,11:9,9:18,20:0.4762:2,2:25:1:31.6:1:1:1.21576:38.8:40:0.5405:0:1.6 0/1:45:14:6,8:15,16:31,14:0.3111:2,2:26.1:1:30.8:1:0.75883:1.24382:38:28:0.3256:0:1.6 +GL000220.1 118861 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17972;SOR=0;LSEQ=GGCGGCGAGGCCCCACGGGG;RSEQ=GTCCCCGCACCCGGCCGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:11,14:25,2:0.0741:2,2:42.5:1:31.5:1:1:1.26:53:4:0.0769:0:2 0/0:36:0:0,0:17,19:36,0:0:2,0:19.4:1:30.8:1:1:0:45.9:35:1:0:1.2 +GL000220.1 118878 . G T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20186;SOR=0.29441;LSEQ=GGGCGTCCCCGCACCCGGCC;RSEQ=ACCTCCGCTCGCGACCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:4:1,3:8,10:18,4:0.1739:2,2:12.5:1:30:1:0.61613:2.31239:47.5:8:0.1739:0:2.5 0/1:35:2:1,1:16,17:33,2:0.0571:2,2:24.5:1:30:1:1:1.06:35.5:4:0.0571:0:3 +GL000220.1 118882 . T G 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.14428;SOR=Inf;LSEQ=GTCCCCGCACCCGGCCGACC;RSEQ=CCGCTCGCGACCTCTCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:11,12:23,0:0:2,0:19:1:30.3:1:1:0:35.8:22:1:0:1.6 0/1:35:4:2,2:15,16:31,4:0.1143:2,2:15:1:29.8:1:1:1.06:24.5:8:0.1143:0:2.3 +GL000220.1 118890 . C T 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.40775;SOR=1.6337;LSEQ=ACCCGGCCGACCTCCGCTCG;RSEQ=GACCTCTCCTCGGTCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:10:5,5:5,6:11,10:0.4762:2,2:18.4:1:29.3:1:1:1.19:35.7:9:0.45:0:2 1/0:30:18:9,9:6,6:12,18:0.6:2,2:19.2:1:29.4:1:1:1:43.2:36:0.6:0:2.1 +GL000220.1 118908 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18928;SOR=0;LSEQ=CGCGACCTCTCCTCGGTCGG;RSEQ=CCTCCGGGGTCGACCGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:16,11:27,2:0.069:2,2:38.5:1:31.5:1:1:1.43545:32.5:4:0.0741:0:2 0/0:37:0:0,0:20,17:37,0:0:2,0:22.5:1:30.5:1:1:0:40.3:36:1:0:1.8 +GL000220.1 118944 . G A 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.11777;LSEQ=GCCTGCCGCCCGCGGGCGTG;RSEQ=GACTCAGCCGGCGTCTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:42:25,17:3,2:5,42:0.8936:2,2:24.7:1:30.7:1:1:1.01957:40.6:84:0.913:0:2 1/1:52:47:24,23:2,2:4,47:0.9038:2,2:27.1:1:29.1:1:1:1.04:39.4:94:0.9038:0:2.2 +GL000220.1 118959 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24312;SOR=Inf;LSEQ=GCGTGGGACTCAGCCGGCGT;RSEQ=TCGCCGTGTCCCGGGTCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:31,24:55,0:0:2,0:24.7:1:32.5:1:1:0:41.8:110:1:0:1.8 0/1:54:2:1,1:26,26:52,2:0.037:2,2:13:1:27.5:1:1:1:26:4:0.037:0:3 +GL000220.1 118979 . A C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCGCCGTGTCCCGGGTCGA;RSEQ=CGGCGGGCCTTCTCCACCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:57:32,25:0,0:0,57:1:0,2:26.3:1:30.8:1:1:0:43.2:56:1:0:1.7 1/1:55:55:30,25:0,0:0,55:1:0,2:24.4:1:30.6:1:1:0:41.7:110:1:0:1.9 +GL000220.1 119071 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.54098;SOR=Inf;LSEQ=CTCGGTCGGCACCTCCGGGG;RSEQ=CGACCAGCTGCCGCCCGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:7,14:21,0:0:2,0:15.8:1:28:1:1:0:43.3:9.5:1:0:0.8 0/1:40:2:1,1:18,19:37,2:0.05:2,2:33.5:1:27.5:1:1:1.05:44:4:0.0513:0:1.5 +GL000220.1 119111 . C T 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.7226;SOR=0.63268;LSEQ=AGCTCCGGACTTAGCCGGCG;RSEQ=CTGCACGTGTCCCGGGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:3,3:3,9:12,6:0.3333:2,2:15.7:1:29.3:1:0.34405:2.81:29.8:12:0.3333:0:1.2 0/1:21:5:3,2:6,10:16,5:0.2381:2,2:6.8:1:27.8:1:0.61079:2.39:28:10:0.25:0:1.4 +GL000220.1 119130 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48949;SOR=Inf;LSEQ=GCCTGCACGTGTCCCGGGTC;RSEQ=ACCAGCAGGCGGCCGCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:7,10:17,0:0:2,0:25.4:1:31.1:1:1:0:28.8:34:1:0:1.1 0/1:20:2:1,1:10,8:18,2:0.1:2,2:19:1:29.5:1:1:1.23603:23.5:4:0.1:0:1 +GL000220.1 119152 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48936;SOR=Inf;LSEQ=CCAGCAGGCGGCCGCCGGAC;RSEQ=CTGCGGCGCACCGACGCGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,10:23,0:0:2,0:28.3:1:31.4:1:1:0:36.9:46:0.9583:0:1 0/1:24:2:1,1:12,10:22,2:0.0833:2,2:31:1:29:1:1:1.19087:36.5:4:0.087:0:1.5 +GL000220.1 119172 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49123;SOR=0;LSEQ=GCTGCGGCGCACCGACGCGA;RSEQ=GGCGCTGATTCCCGTTCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:16,11:27,2:0.069:2,2:40.5:1:31.5:1:1:1.43545:36:4:0.069:0:1.5 0/0:29:0:0,0:15,14:29,0:0:2,0:23.1:1:30.9:1:1:0:37.7:58:1:0:0.8 +GL000220.1 119175 . C T 31 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60455;SOR=2.20882;LSEQ=GCGGCGCACCGACGCGAGGG;RSEQ=GCTGATTCCCGTTCACGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:1,0:16,12:28,1:0.0345:2,0:47:0:29:0:1:0:23:2:0.0345:0:2 0/1:27:2:1,1:13,12:25,2:0.0741:2,2:31:0:31.5:1:1:1.0801:49:4:0.0741:0:1.5 +GL000220.1 119177 . CT TC 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59764;SOR=2.29847;LSEQ=GGCGCACCGACGCGAGGGCG;RSEQ=GATTCCCGTTCACGCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:1:0,1:17,11:28,1:0.0345:2,0:25:0:32:0:0.41379:0:21:2:0.0345:0:2 0/1:26:2:0,2:14,10:24,2:0.0769:2,0:22.5:1:29:1:0.20308:0:22:4:0.0769:0.0385:1.5 +GL000220.1 119178 . T C 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02525;SOR=0;LSEQ=GCGCACCGACGCGAGGGCGC;RSEQ=GATTCCCGTTCACGCGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:4,2:13,9:22,6:0.2069:2,2:30:1:32:1:1:1.37:29.8:12:0.2143:0:1.2 0/0:25:0:0,0:14,10:24,0:0:2,0:28.6:1:29.5:1:1:0:41.1:23:1:0:0.8 +GL000220.1 119190 . A G 69 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.43201;SOR=2.37412;LSEQ=GAGGGCGCTGATTCCCGTTC;RSEQ=CGCGCCCGCGACCTCCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:15,11:26,2:0.0714:2,2:12:1:31.5:1:1:1.34838:21.5:4:0.0714:0:2.5 0/1:32:5:4,1:15,12:27,5:0.1563:2,2:9.4:1:30:1:0.62467:3.10:26.6:10:0.1667:0:2.2 +GL000220.1 119223 . C G 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.60801;SOR=0.52865;LSEQ=CTCCACCGGCCTCGGCCCGC;RSEQ=GTGGAGCTGGGACCACGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:2,0:8,5:13,2:0.1333:2,0:36.5:1:30:1:0.52381:0:25.5:4:0.1333:0:2 0/1:27:2:2,0:15,10:25,2:0.0741:2,0:42.5:1:30.5:1:0.51567:0:23:4:0.0741:0:2.5 +GL000220.1 119255 . C T 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67517;SOR=0.54777;LSEQ=ACCACGCGGAACTCCCTCTC;RSEQ=CACATTTTTTTCAGCCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:3,2:3,3:6,5:0.4545:2,2:17.2:1:31.6:1:1:1.45:21.2:10:0.4545:0:1.6 0/1:13:4:3,1:5,4:9,4:0.3077:2,2:31.3:1:28:1:1:2.25:29:8:0.3077:0:2.5 +GL000220.1 119256 . C T 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.68427;SOR=0.60896;LSEQ=CCACGCGGAACTCCCTCTCC;RSEQ=ACATTTTTTTCAGCCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:3,3:3,2:5,6:0.5455:2,2:14.2:1:31:1:1:1.44544:28.2:12:0.5455:0:1 0/1:12:5:2,3:5,1:6,5:0.4167:2,2:8.6:1:29:1:0.24242:6.06919:31.8:10:0.4545:0:1 +GL000220.1 119333 . A C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20421;SOR=0.42972;LSEQ=ACTGCTGCCGTCAGCCAGTA;RSEQ=TGCTTCCTCCTTTTTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:6:6,0:44,24:68,6:0.0811:2,0:31.3:1:33.3:1:0.16824:0:45:12:0.0896:0:1.7 0/1:110:4:3,1:80,26:106,4:0.0364:2,2:38.5:1:31.8:1:1:1.0254:43.8:8:0.0385:0:2 +GL000220.1 119356 . A T 40 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64847;SOR=2.06061;LSEQ=CTTCCTCCTTTTTTGCTTTT;RSEQ=GGTTTTGTCTTGCCTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:1:0,1:56,24:80,1:0.012:2,0:29:0:13:0:0.30864:0:21:0:0:0:2 0/1:122:3:2,1:91,28:119,3:0.0246:2,2:30.7:1:25.7:1:0.56047:1.61779:25.7:2:0.0185:0:2.7 +GL000220.1 119403 . TTC T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.18919;SOR=0;LSEQ=TTTTTTCTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:2:1,1:28,18:46,2:0.0408:2,2:17.5:1:29:1:1:1.54082:36:4:0.0417:0:2 0/0:63:0:0,0:38,25:63,0:0:2,0:17.5:1:27.5:1:1:0:38.4:30.5:1:0:1.6 +GL000220.1 119407 . TTC T 58 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.74945;SOR=0.78283;LSEQ=TTCTTTCTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:3,2:30,18:48,5:0.0909:2,2:17.4:1:30.2:1:1:1.10888:43.6:10:0.0926:0:1.4 0/1:69:5:5,0:31,30:61,5:0.0725:2,0:14.6:1:25.2:1:0.05813:0:49.2:10:0.0758:0.029:0.8 +GL000220.1 119411 . TTC T 87 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=4;SSF=0.03749;SOR=7.52162;LSEQ=TTCTTTCTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:1:1,0:30,19:49,1:0.0167:2,0:45:0:33:0:1:0:23:2:0.0182:0:2 0/1:70:8:4,4:31,28:59,8:0.1143:2,2:28.6:1:29:1:1:1.10546:35.1:16:0.1194:0.0143:1.9 +GL000220.1 119415 . TTC T 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=7.000;MSILEN=4;SSF=0.10947;SOR=0.55746;LSEQ=TTCTTTCTTTCTTTCTTTCT;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:24:17,7:22,18:40,24:0.338:2,2:10.4:1:29.3:1:0.29119:1.97:26.5:23:0.3594:0.2394:2 0/1:86:19:10,9:32,32:64,19:0.2209:2,2:11.1:1:28.9:1:1:1.11:24:38:0.2405:0.1279:2.1 +GL000220.1 119452 . T C 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.28992;SOR=Inf;LSEQ=TCTTTCTTTCTCGCTCTCGC;RSEQ=CTCTCGCTCTCTCCCTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:63,45:108,0:0:2,0:27.3:1:30.4:1:1:0:39.1:14.429:1:0:1.3 0/1:177:3:1,2:81,91:172,3:0.0169:2,2:9:1:22.3:1:1:1.7746:32.3:2:0.0118:0:3 +GL000220.1 119454 . TCTCG T 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=0.82632;LSEQ=TTTCTTTCTCGCTCTCGCTC;RSEQ=CTCTCTCCCTCGCTCGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:3:1,2:38,30:68,3:0.0268:2,2:27.7:1:30:1:0.58513:2.50085:21.7:6:0.0278:0:3 0/1:180:4:2,2:56,64:120,4:0.0222:2,2:28:1:30.7:1:1:1.14:23.3:8:0.0229:0.0111:1.8 +GL000220.1 119458 . GCTCT C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.44348;SOR=0.81349;LSEQ=TTCTTTCTCGCTCTCGCTCT;RSEQ=CTCCCTCGCTCGTTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:40:26,14:38,30:68,40:0.3571:2,2:27.1:1:32:1:0.4194:1.46:26.8:80:0.3704:0.0179:1.1 0/1:180:56:24,32:56,64:120,56:0.3111:2,2:26.2:1:31.2:1:0.7454:1.16565:25.7:55:0.3143:0.0278:1.5 +GL000220.1 119477 . TTCTTTCTCTTTCTCTTTCTCTCTCTC T 178 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=16.000;MSILEN=2;SSF=0.62414;SOR=0.86437;LSEQ=CGCTCTCTCCCTCGCTCGTT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:43:26,17:44,36:80,43:0.3468:2,2:27.7:1:30.9:1:0.57377:1.25:26.2:9.75:0.3223:0.3468:4.2 0/1:194:61:29,32:57,71:128,61:0.3144:2,2:24.9:1:30.1:1:0.75554:1.13:25.4:14.25:0.3:0.3093:4 +GL000220.1 119482 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=6;SSF=0.52478;SOR=Inf;LSEQ=TCTCCCTCGCTCGTTTTCTT;RSEQ=CTCTTTCTCTTTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:45,39:84,0:0:2,0:13.7:1:31.6:1:1:0:48.3:168:1:0:1.5 0/1:193:2:1,1:59,77:136,2:0.0104:2,2:11:0:33:0:1:1.30:60:4:0.0146:0:2 +GL000220.1 119486 . T C 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.52087;SOR=Inf;LSEQ=CCTCGCTCGTTTTCTTTCTC;RSEQ=TTCTCTTTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:44,38:82,0:0:2,0:12.3:1:31.9:1:1:0:49:81:1:0:1.5 0/1:183:2:1,1:53,75:128,2:0.0109:2,2:7:0:32.5:1:1:1.41:60:4:0.0157:0:2 +GL000220.1 119490 . TCTTTCTCTCTCT GCTCTTGCCCTCTCG 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.52798;SOR=Inf;LSEQ=GCTCGTTTTCTTTCTCTTTC;RSEQ=CTCTCTCTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:44,37:81,0:0:2,0:26.4:1:30.2:1:1:0:49.4:19.25:1:0:0.5 0/1:137:2:0,2:54,73:127,2:0.0146:2,0:30:1:32:1:0.50945:0:28:4:0.0159:0:6 +GL000220.1 119493 . TTCTCTC T 132 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=16.000;MSILEN=2;SSF=0.01024;SOR=0.38767;LSEQ=CGTTTTCTTTCTCTTTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:22:13,9:18,18:36,22:0.2418:2,2:26.3:1:29.8:1:0.59185:1.44:47.4:44:0.2529:0.1209:0.8 0/1:146:16:6,10:28,34:62,16:0.1096:2,2:22.6:1:27.7:1:0.77825:1.36705:50.2:7:0.1077:0.0479:1.1 +GL000220.1 119529 . CTCTCGCTCTCGCCCTCTCTCTCTCTCTCTTTCTCTCTG C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=5.000;MSILEN=2;SSF=0.50904;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTGT;RSEQ=TCTCTCTCTGTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:56,45:101,0:0:2,0:23.7:1:30.9:1:1:0:44.1:32.667:0.9899:0:0.9 0/1:139:2:2,0:64,73:137,2:0.0144:2,0:14.5:1:31.8:1:0.22365:0:24.5:4:0.015:0.0144:2 +GL000220.1 119533 . C T 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=6;SSF=0.02031;SOR=Inf;LSEQ=CTCTCTCTCTCTCTGTCTCT;RSEQ=GCTCTCGCCCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:58,47:105,0:0:2,0:23.4:1:30.1:1:1:0:44.1:20:1:0:0.8 0/1:138:7:2,5:60,69:129,7:0.0507:2,2:21.3:1:29.7:1:0.45405:2.16224:44.9:14:0.0522:0:1.1 +GL000220.1 119567 . G C 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.21268;SOR=0.52317;LSEQ=CTCTCTCTCTCTTTCTCTCT;RSEQ=TCTCTCTCTGTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:10:3,7:38,32:70,10:0.125:2,2:9.7:1:32.9:1:0.18787:2.73655:34.2:20:0.1695:0:3.1 0/1:101:7:4,3:44,47:91,7:0.0693:2,2:11.3:1:31.1:1:0.71208:1.42:26.6:14:0.0854:0:4 +GL000220.1 119577 . G C 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=12;MSI=1.000;MSILEN=1;SSF=0.19746;SOR=0.59188;LSEQ=CTTTCTCTCTGTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:21:9,12:28,24:52,21:0.2838:2,2:11.9:1:29.1:1:0.44595:1.54609:41.7:4.25:0.2982:0:2.4 0/1:95:18:12,6:29,32:61,18:0.1895:2,2:10.8:1:31.3:1:0.1862:2.19:37:36:0.2093:0:2.6 +GL000220.1 119591 . CTCTCTC GTCGCTCTCGCCCTCTCGCTCTCTCTCTGTCTCTGTCTGTG 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.53709;SOR=1.6715;LSEQ=CTCTCTGTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTCCCTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:4:0,4:32,36:68,4:0.0548:2,0:17:1:30.1:1:0.12379:0:35.3:8:0.0597:0.0548:2.5 0/1:79:7:4,3:41,31:72,7:0.0886:2,2:12.3:1:30.1:1:1:1.01:35.6:8:0.0852:0.0824:4 +GL000220.1 119610 . C T 89 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00031;SOR=0;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CTCCCCCTCCCTCCCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:12:7,5:22,36:58,12:0.16:2,2:7.6:1:25:1:0.21465:2.26:52.1:2:0.125:0:1.7 0/0:72:0:0,0:29,35:64,0:0:2,0:20.3:1:28.9:1:1:0:49.6:15:1:0:2.1 +GL000220.1 119612 . TCC T 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.21271;SOR=0.48808;LSEQ=TCTCTCTCTCTCTCTCTCCC;RSEQ=CCCTCCCTCCCTCTCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:12:3,9:27,43:70,12:0.1481:2,2:10.7:1:27.5:1:0.52095:1.87021:50.4:5:0.1266:0.0988:3.7 0/1:77:6:1,5:37,34:71,6:0.0779:2,2:14.3:1:28.8:1:0.20025:5.33814:38.2:12:0.0789:0.039:3.3 +GL000220.1 119614 . C CCT 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00088;SOR=4.66307;LSEQ=TCTCTCTCTCTCTCTCCCTC;RSEQ=CCCTCCCTCCCTCTCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:6:1,5:24,39:63,6:0.0789:2,2:18.2:1:30.7:1:0.40617:3.0353:43.8:12:0.0896:0:4.7 0/1:80:23:13,10:27,27:54,23:0.2875:2,2:13.7:1:28.6:1:0.62762:1.30:43.6:10.5:0.2917:0.1125:4.4 +GL000220.1 119626 . T TCTCTCCCC 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=5.000;MSILEN=1;SSF=0.06288;SOR=Inf;LSEQ=TCTCCCTCCCCCTCCCTCCC;RSEQ=CTCTCCCCTTCCTTGGTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:43,59:102,0:0:2,0:22.7:1:29:1:1:0:54.4:9.2:0.9892:0:1.8 0/1:120:5:3,2:56,59:115,5:0.0417:2,2:18.2:1:25.8:1:0.67688:1.57:45.4:4:0.0354:0.025:2.6 +GL000220.1 119628 . T C 179 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.00892;SOR=2.12272;LSEQ=TCCCTCCCCCTCCCTCCCTC;RSEQ=CTCCCCTTCCTTGGTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:29:12,17:31,44:75,29:0.2788:2,2:18.2:1:31.5:1:1:1.00:53.7:58:0.299:0:3.8 0/1:124:56:26,30:34,34:68,56:0.4516:2,2:19.2:1:30.9:1:0.72106:1.15251:49.7:112:0.4746:0:3.6 +GL000220.1 119656 . C A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.17648;SOR=0;LSEQ=TCCTTGGTGCCTTCTCGGCT;RSEQ=TTGACACTTAGCCGCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:2:1,1:49,76:125,2:0.0156:2,2:45:1:26.5:1:1:1.55:56.5:4:0.0167:0:6 0/0:176:0:0,0:79,97:176,0:0:2,0:27.4:1:29.9:1:1:0:55.5:12.538:1:0:2 +GL000220.1 119661 . C G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0864;SOR=1.48992;LSEQ=GGTGCCTTCTCGGCTCTTGA;RSEQ=ACTTAGCCGCTGTCTCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:65:27,38:26,43:69,65:0.4851:2,2:29:1:31.9:1:0.72459:1.17:56.2:20.667:0.4733:0:2.9 1/0:178:104:47,57:32,40:72,104:0.5843:2,2:27.4:1:30.3:1:1:1.03:53.4:19.8:0.5723:0:2.9 +GL000220.1 119665 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51095;SOR=Inf;LSEQ=CCTTCTCGGCTCTTGACACT;RSEQ=AGCCGCTGTCTCGCCGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:57,79:136,0:0:2,0:27:1:29.1:1:1:0:57.5:44.333:1:0:1.7 0/1:187:2:1,1:79,103:182,2:0.0107:2,2:36:0:32.5:1:1:1.30:60:4:0.0114:0:3.5 +GL000220.1 119680 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17014;SOR=0;LSEQ=ACACTTAGCCGCTGTCTCGC;RSEQ=GTGTCCCGGGTCGACCGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:1,1:60,74:134,2:0.0147:2,2:29:1:30.5:1:1:1.23:60:4:0.015:0:1 0/0:193:0:0,0:86,107:193,0:0:2,0:26:1:28.7:1:1:0:58:23.125:1:0:1.7 +GL000220.1 119683 . GT AC 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.09978;LSEQ=CTTAGCCGCTGTCTCGCCGT;RSEQ=CCCGGGTCGACCGGCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:9:4,5:59,69:128,9:0.0657:2,2:29.2:1:29.8:1:1:1.06835:57.8:18:0.0682:0:2.3 0/1:195:14:5,9:80,100:180,14:0.0718:2,2:24.6:1:30.3:1:0.58728:1.43736:55.5:28:0.0791:0:2.7 +GL000220.1 119684 . T C 187 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.00604;LSEQ=TTAGCCGCTGTCTCGCCGTG;RSEQ=CCCGGGTCGACCGGCGGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:57:26,31:33,38:71,57:0.4161:2,2:27.2:1:31.8:1:1:1.03516:56.8:56:0.4516:0:2.4 0/1:194:81:39,42:41,58:99,81:0.4175:2,2:25.1:1:29.5:1:0.37109:1.31:56.9:15.2:0.4551:0:2.6 +GL000220.1 119688 . G C 15 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.72846;LSEQ=CCGCTGTCTCGCCGTGTCCC;RSEQ=GGTCGACCGGCGGGCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:2:1,1:66,73:139,2:0.0142:2,2:28.5:1:29:1:1:1.11:57.5:4:0.0145:0:1 0/1:193:2:2,0:83,107:190,2:0.0104:2,0:12.5:1:15:0:0.1947:0:60:0:0:0:2.5 +GL000220.1 119705 . T C 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.09034;SOR=0;LSEQ=CCCGGGTCGACCGGCGGGCC;RSEQ=TCTCCACCGAGCGGCGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:3:2,1:60,77:137,3:0.0213:2,2:39.7:1:32.3:1:0.58402:2.55:59.3:6:0.0216:0:2.7 0/0:172:0:0,0:75,97:172,0:0:2,0:24:1:29.2:1:1:0:58.9:23.571:1:0:1.2 +GL000220.1 119716 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20931;SOR=0;LSEQ=CGGCGGGCCTTCTCCACCGA;RSEQ=CGGCGTGTAAGAGTGCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:2:1,1:56,69:125,2:0.0157:2,2:19:0:32.5:1:1:1.23:60:4:0.0164:0:3 0/0:150:0:0,0:62,87:149,0:0:2,0:25.7:1:31.1:1:1:0:57.9:48.667:0.9932:0:0.9 +GL000220.1 119726 . A G 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.3348;SOR=0.2771;LSEQ=TCTCCACCGAGCGGCGTGTA;RSEQ=GAGTGCCCGTCGGGACGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:3:1,2:51,69:120,3:0.0244:2,2:27.7:1:32.7:1:1:1.47375:34.3:6:0.0254:0:1 0/0:146:1:1,0:56,89:145,1:0.0068:2,0:2:0:33:0:0.39041:0:29:2:0.0072:0:2 +GL000220.1 119734 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1958;SOR=0;LSEQ=GAGCGGCGTGTAAGAGTGCC;RSEQ=GTCGGGACGAGCCGGACCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:52,60:112,2:0.0175:2,2:34.5:1:31:1:1:1.15:52:4:0.0179:0:1 0/0:143:0:0,0:59,84:143,0:0:2,0:23.5:1:28.4:1:1:0:53.5:14.889:1:0:0.8 +GL000220.1 119753 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.25734;SOR=Inf;LSEQ=CCGTCGGGACGAGCCGGACC;RSEQ=GCCGCGTCCCCGTCTCGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:43,57:100,0:0:2,0:26.3:1:29.9:1:1:0:50.6:32.333:1:0:0.7 0/1:127:3:2,1:51,73:124,3:0.0236:2,2:17.3:1:26.7:1:0.57059:2.84:55.3:6:0.0246:0:2 +GL000220.1 119756 . C T 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50495;SOR=Inf;LSEQ=TCGGGACGAGCCGGACCCGC;RSEQ=GCGTCCCCGTCTCGGTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:41,54:95,0:0:2,0:26.8:1:30.2:1:1:0:50.1:190:1:0:0.7 0/1:121:2:1,1:48,71:119,2:0.0165:2,2:14:0:28:1:1:1.47:60:4:0.0171:0:2 +GL000220.1 119764 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19012;SOR=0;LSEQ=AGCCGGACCCGCCGCGTCCC;RSEQ=GTCTCGGTCGGCACCTCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:34,48:82,2:0.0238:2,2:23.5:1:30.5:1:1:1.41:35.5:4:0.0238:0:1.5 0/0:108:0:0,0:45,63:108,0:0:2,0:26.6:1:28.7:1:1:0:48.2:26:1:0:0.6 +GL000220.1 119775 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50016;SOR=Inf;LSEQ=CCGCGTCCCCGTCTCGGTCG;RSEQ=CACCTCCGGGGTCGACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:31,43:74,0:0:2,0:25:1:31.4:1:1:0:47.6:36:1:0:0.5 0/1:87:2:1,1:36,49:85,2:0.023:2,2:19.5:1:27:1:1:1.36:52:4:0.0244:0:1 +GL000220.1 119822 . T C 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.61881;SOR=0.73786;LSEQ=CCGCGAGCTCCGGACTTAGC;RSEQ=GGCGTCTGCACGTGTCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:12:3,9:7,7:14,12:0.4615:2,2:11.3:1:30.5:1:0.24752:2.87254:29.9:24:0.4615:0:1.3 0/1:44:17:7,10:11,16:27,17:0.3864:2,2:8.1:1:28.2:1:1:1.02:31.8:16:0.381:0:1.4 +GL000220.1 119851 . G A 48 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.11087;LSEQ=CACGTGTCCCGGGTCGACCA;RSEQ=CAGGCGGCCGCCGGACGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:13,10:23,2:0.08:2,2:19.5:1:29.5:1:1:1.28628:54.5:4:0.087:0:1 0/1:34:3:1,2:14,17:31,3:0.0882:2,2:24.7:1:30.3:1:1:1.62392:28.7:6:0.0882:0:1.3 +GL000220.1 119880 . T C 104 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11343;SOR=3.86554;LSEQ=CGCCGGACGCTGCGGCGCAC;RSEQ=GACGCGAGGGCGTCGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:15,10:25,2:0.0741:2,2:40.5:1:31.5:1:1:1.47706:26:4:0.0833:0:1.5 0/1:46:11:7,4:14,20:34,11:0.2391:2,2:28.2:1:30.2:1:0.29888:2.45:28.3:22:0.25:0:1.1 +GL000220.1 119911 . C T 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=0;LSEQ=CGTCGATTCCGGTTCACGCG;RSEQ=CGGCGACCTCCACCGGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:8:5,3:13,9:22,8:0.2667:2,2:16.1:1:27.5:1:1:1.15:40.4:7:0.25:0:2.1 0/0:55:0:0,0:29,24:53,0:0:2,0:26.1:1:30:1:1:0:46.9:16.667:0.9615:0:0.5 +GL000220.1 119967 . T C 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.02891;SOR=0;LSEQ=TGGGACCACGCGGAACTCCC;RSEQ=CTCCTACATTTTTTTCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:4:2,2:16,11:27,4:0.129:2,2:35.8:1:31.8:1:1:1.43671:21:8:0.129:0:1.5 0/0:42:0:0,0:23,19:42,0:0:2,0:27.2:1:28.9:1:1:0:46.3:41:1:0:0.3 +GL000220.1 119970 . C T 91 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00818;SOR=0.07621;LSEQ=GACCACGCGGAACTCCCTCT;RSEQ=CTACATTTTTTTCAGCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:8:5,3:13,10:23,8:0.2581:2,2:35.8:1:30.5:1:1:1.27:34.9:16:0.2581:0:1.5 0/1:40:1:0,1:21,17:38,1:0.025:2,0:4:0:27:0:0.46154:0:60:2:0.0256:0:1 +GL000220.1 120003 . G C 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21347;SOR=0;LSEQ=CAGCCCCACTGCGAGTTTGC;RSEQ=TCCGCGGGACTTTTAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:2:1,1:19,13:32,2:0.0588:2,2:31:0:32.5:1:1:1.44493:20:4:0.0588:0:2 0/0:39:0:0,0:21,18:39,0:0:2,0:14.6:1:29.4:1:1:0:35:78:1:0:0 +GL000220.1 120111 . CTT C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.000;MSILEN=4;SSF=0.49845;SOR=Inf;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TCTTTCTTTCTTTCTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:31,40:71,0:0:2,0:21.6:1:31:1:1:0:43.1:70:1:0:0.6 0/1:83:2:1,1:41,39:80,2:0.0241:2,2:8:1:28.7:1:1:1.05066:54:4:0.0244:0.012:0 +GL000220.1 120137 . T C 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=8.000;MSILEN=4;SSF=0;SOR=Inf;LSEQ=TTCTTTCTTTCTTTCTTTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:12,17:29,0:0:2,0:21.4:1:28.8:1:1:0:46.2:8.667:1:0:0.7 0/1:53:19:7,12:13,17:30,19:0.3585:2,2:14.6:1:31:1:0.76882:1.30372:47.4:18:0.4:0:2.5 +GL000220.1 120161 . G C 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.6993;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCCCCTCCCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:0,1:33,42:75,1:0.0132:2,0:1:0:31:0:1:0:21:2:0.0145:0:3 0/1:90:2:0,2:44,44:88,2:0.0222:2,0:16.5:1:32.5:1:0.49463:0:29:4:0.0247:0:3.5 +GL000220.1 120210 . TGCTGCCTCTGCCTCCACGGTTCAAGCAAA AAG 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.703;SOR=0.60597;LSEQ=TGCCTTCTCGGCTCGCTGCT;RSEQ=CAGCAAGTTTTCTATTTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:4:3,1:35,48:83,4:0.046:2,2:13.8:1:29.8:1:0.31406:4.05:44.5:8:0.0488:0.0345:0.8 0/1:106:3:1,2:45,55:100,3:0.0283:2,2:31.3:1:31.4:1:1:1.62887:56.3:6:0.03:0.0094:0 +GL000220.1 120211 . G A 27 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=3;SSF=0.50799;SOR=Inf;LSEQ=CTTCTCGGCTCGCTGCTGCT;RSEQ=CTGCCTCTGCCTCCACGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:33,45:78,0:0:2,0:25.6:1:31.8:1:1:0:59.2:14.6:1:0:0.2 0/1:106:2:1,1:47,55:102,2:0.0189:2,2:22:0:27.5:1:1:1.17:60:4:0.0206:0:1 +GL000220.1 120319 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.65579;LSEQ=GAACTCCCGACCTAGTGATC;RSEQ=GCCCGCCTCGGCCTCCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:0,2:9,20:29,2:0.0625:2,0:37:0:28.5:1:1:0:60:4:0.0667:0:1 0/1:48:2:1,1:17,29:46,2:0.0417:2,2:44:0:30.5:1:1:1.69:60:4:0.0426:0:1.5 +GL000220.1 120481 . ACACACACACACC A 47 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=19.000;MSILEN=2;SSF=0.22222;SOR=Inf;LSEQ=ACACACACACACACACACAC;RSEQ=CCCCGTAGTGATAAAACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:4,7:11,0:0:2,0:27.9:1:31.5:1:1:0:45.9:10:1:0:0.7 0/1:14:3:1,2:5,7:12,3:0.2143:2,2:15.7:1:29.7:1:1:1.39581:44.3:6:0.2308:0.1429:1.3 +GL000220.1 120483 . ACACACACACC A 59 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=20.000;MSILEN=2;SSF=0.04215;SOR=0;LSEQ=ACACACACACACACACACAC;RSEQ=CCCCGTAGTGATAAAACTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:2,2:3,6:9,4:0.2857:2,2:24.3:1:29.5:1:1:1.89:54.8:8:0.3333:0.1429:0.5 0/0:15:0:0,0:6,8:14,0:0:2,0:16.5:1:27.7:1:1:0:49.2:3.667:1:0:1.1 +GL000220.1 120724 . A T 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50834;SOR=Inf;LSEQ=CTCTGCGCTCTGGTGACCTC;RSEQ=GCCTCCCAAATAGCTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:17,11:28,0:0:2,0:26.1:1:30:1:1:0:60:27:1:0:0.1 0/1:40:2:1,1:21,17:38,2:0.05:2,2:7:0:29.5:1:1:1.22874:58:4:0.05:0:1 +GL000220.1 120725 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51153;SOR=Inf;LSEQ=TCTGCGCTCTGGTGACCTCA;RSEQ=CCTCCCAAATAGCTGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:16,11:27,0:0:2,0:26.9:1:32.4:1:1:0:60:54:1:0:0.1 0/1:40:2:1,1:20,18:38,2:0.05:2,2:40:1:28:1:1:1.10818:60:4:0.05:0:1 +GL000220.1 120822 . CTGCGG C 56 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.05282;SOR=Inf;LSEQ=TCCACTCCAGCTTACGTGGG;RSEQ=TGGGGTGGGGTGGGGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:32:0:0,0:17,13:30,0:0:2,0:21.7:1:29.2:1:1:0:57.3:6.5:0.963:0:0.6 0/1:32:5:4,1:17,6:23,5:0.1563:2,2:6.2:1:24.2:1:1:1.40:58.2:1.5:0.1:0.125:2.4 +GL000220.1 120825 . CGGTGGGGTGG C 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=7.000;MSILEN=5;SSF=0.47412;SOR=2.12828;LSEQ=ACTCCAGCTTACGTGGGCTG;RSEQ=GGTGGGGTGGGGTGGGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:1,2:15,10:25,3:0.0968:2,2:38:1:32.3:1:0.56044:2.88294:54:6:0.1:0:2.7 0/1:32:6:5,1:17,6:23,6:0.1875:2,2:27.8:1:31.3:1:1:1.73:53.5:12:0.1935:0.0313:0.7 +GL000220.1 120836 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=0.4918;SOR=Inf;LSEQ=CGTGGGCTGCGGTGGGGTGG;RSEQ=GTGGGGTGGGGTGGGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:19.4:1:30.3:1:1:0:57.7:29:1:0:1.1 0/1:31:2:1,1:23,6:29,2:0.0645:2,2:19.5:1:29.5:1:0.40645:3.62563:60:4:0.0645:0:2 +GL000220.1 120848 . T G 33 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=0.82429;LSEQ=TGGGGTGGGGTGGGGTGGGG;RSEQ=GGGGTGGGGTGGGGTGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:0,3:17,6:23,3:0.1154:2,0:14.3:1:26:1:0.03231:0:60:6:0.1364:0:4 0/1:31:3:1,2:21,7:28,3:0.0968:2,2:17.7:1:21.3:1:0.19488:5.59497:60:2:0.0741:0:3.3 +GL000220.1 120865 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50101;SOR=Inf;LSEQ=GGGTGGGGTGGGGTGGGGTG;RSEQ=AGAGAAAACGATTGATTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:31,0:0:2,0:21.7:1:32:1:1:0:58.2:30:1:0:0.9 0/1:40:2:1,1:20,18:38,2:0.05:2,2:34.5:1:28:1:1:1.10818:60:4:0.0526:0:1.5 +GL000220.1 120903 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50361;SOR=Inf;LSEQ=GCGATCTCAATTGCCTTTTA;RSEQ=CTTCATTCATACCCTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:23,20:43,0:0:2,0:23.1:1:32.3:1:1:0:60:42:1:0:0.5 0/1:56:2:0,2:25,29:54,2:0.0357:2,0:8:1:29:1:0.49675:0:60:4:0.0364:0:1 +GL000220.1 120929 . C T 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.58176;SOR=1.40916;LSEQ=TTCATACCCTGTTATTTGCT;RSEQ=GTTTATTCTCATGGGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:6:4,2:30,23:53,6:0.1017:2,2:24.8:1:27.2:1:1:1.52:60:5:0.0862:0:1.3 0/1:58:8:3,5:23,27:50,8:0.1379:2,2:28.5:1:29.1:1:0.71953:1.41133:60:16:0.1379:0:1.4 +GL000220.1 120952 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50032;SOR=0;LSEQ=TTATTCTCATGGGTTCTTCT;RSEQ=TGTCATTGTCACGTTCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:32,28:60,2:0.0323:2,2:32:0:32.5:1:1:1.14039:60:4:0.0328:0:1.5 0/0:51:0:0,0:22,29:51,0:0:2,0:25.8:1:31.5:1:1:0:60:102:1:0:0.4 +GL000220.1 121026 . TTCCTTCCC T 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=4;SSF=0.00303;SOR=4.92987;LSEQ=TTCCTTCCTTCCTTCCTTCC;RSEQ=TCCTTCCTTCCTTCCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:3,2:22,25:47,5:0.0962:2,2:48.2:1:31:1:0.66236:1.69:45.2:10:0.1:0:0.6 0/1:46:16:8,8:12,14:26,16:0.3478:2,2:27.8:1:30.2:1:1:1.16:46.4:32:0.4:0.1739:0.9 +GL000220.1 121057 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22284;SOR=Inf;LSEQ=CTTCCTTCCTTCCTTCCCTC;RSEQ=CTTACTGGCAGGGTCTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:26,26:52,0:0:2,0:27.8:1:29.3:1:1:0:51.7:9.4:1:0:0.6 0/1:47:2:1,1:24,21:45,2:0.0426:2,2:35:1:27.5:1:1:1.1396:60:4:0.0426:0:2 +GL000220.1 121287 . TATCTAT AGTATCTATGTATGTAC 74 v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=24.000;MSILEN=2;SSF=0.06172;SOR=Inf;LSEQ=TGTGTGTGTGTGTGTGTGTG;RSEQ=GTATGTATGTATGTATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:28.8:1:31.2:1:1:0:50.9:26:1:0:0.4 0/1:21:6:3,3:5,9:14,6:0.2857:2,2:16:1:28.9:1:0.64241:1.75:52.3:12:0.2857:0.2381:0.5 +GL000220.1 121293 . T TGTATGTAC 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=1;SOR=0.82366;LSEQ=TGTGTGTGTGTGTGTATCTA;RSEQ=GTATGTATGTATGTATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:4,7:2,1:3,11:0.7857:2,2:31.5:1:29.2:1:0.53846:3.18702:53.9:22:0.7857:0.0714:0.3 1/0:16:12:4,8:1,1:2,12:0.75:2,2:23.8:1:29:1:1:1.89743:53.3:24:0.8571:0.125:0.8 +GL000220.1 121297 . T TGTAC 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.05561;SOR=0;LSEQ=TGTGTGTGTGTATCTATGTA;RSEQ=GTATGTATGTATGTGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:3:2,1:4,7:11,3:0.2143:2,2:41:1:24.7:1:0.53846:3.19:43:2:0.1538:0:0.7 0/0:21:0:0,0:7,13:20,0:0:2,0:21:1:29:1:1:0:53.7:40:0.9524:0:0.7 +GL000220.1 121453 . TTGCCTGCCTGCC T 73 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=37;MSI=12.000;MSILEN=4;SSF=0.05323;SOR=0;LSEQ=GCGCCTGGCTCCTTCTACAT;RSEQ=TGCCTGCCTGCCTGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:2,3:8,7:15,5:0.2174:2,2:25:1:31.6:1:1:1.66859:49.6:10:0.2273:0.0435:0.4 0/0:19:0:0,0:8,8:16,0:0:2,0:25.3:1:29.9:1:1:0:55.7:32:0.8421:0:0.6 +GL000220.1 121738 . T C 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24891;SOR=Inf;LSEQ=TTTGTCGTGGGTCGGTTCTT;RSEQ=CCGTTTTTAATACGGGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,13:23,0:0:2,0:25.3:1:30.8:1:1:0:60:46:1:0:0.1 0/1:30:3:2,1:14,13:27,3:0.1:2,2:43:1:32:1:1:1.82:60:6:0.1:0:2.3 +GL000220.1 121776 . C T 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07985;SOR=Inf;LSEQ=ACTGCGAACGAAGAAAATTT;RSEQ=CAGACGCATCTCACCGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:26.7:1:31.1:1:1:0:60:30:1:0:0.1 0/1:32:7:4,3:13,12:25,7:0.2188:2,2:15.3:1:30.3:1:1:1.22:60:14:0.2258:0:1.7 +GL000220.1 121989 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.17273;SOR=0;LSEQ=CGGCTAATTTTTCTATTTTT;RSEQ=CTACAGATGGGGTTTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:1,1:12,4:16,2:0.1053:2,2:23.5:1:31:0:0.4902:2.79285:60:4:0.1176:0:1 0/0:26:0:0,0:15,11:26,0:0:2,0:24:1:28.3:1:1:0:54.2:52:1:0:0.3 +GL000220.1 121990 . C G 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68228;SOR=1.90571;LSEQ=GGCTAATTTTTCTATTTTTA;RSEQ=TACAGATGGGGTTTCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:2:2,0:11,6:17,2:0.1053:2,0:42.5:1:33.5:1:1:0:48:4:0.1111:0:1 0/1:27:5:4,1:12,10:22,5:0.1852:2,2:27.4:1:31:1:0.61848:3.20:39.6:10:0.1852:0:1.4 +GL000220.1 122041 . G C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06157;SOR=0;LSEQ=CTGGTCTTCAACTTCCGACC;RSEQ=TTGGAGAATCTTAACTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:8,8:16,2:0.1111:2,2:23:1:29.5:1:1:1:60:4:0.1111:0:1 0/0:53:0:0,0:28,25:53,0:0:2,0:25.1:1:30.2:1:1:0:56.6:106:1:0:0.3 +GL000220.1 122079 . C CT 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.15543;SOR=0;LSEQ=TCTTGGTGGTGGTTGTTTTC;RSEQ=TTTTTCTTTTTTTTCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:17,16:33,2:0.0571:2,2:19:1:28.8:1:1:1.06069:60:4:0.0571:0.0286:0 0/0:53:0:0,0:27,26:53,0:0:2,0:26.3:1:30.3:1:1:0:59.7:52:1:0:0.5 +GL000220.1 122085 . C CT 48 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.64542;SOR=2.56443;LSEQ=TGGTGGTTGTTTTCCTTTTT;RSEQ=TTTTTTTTCTTTTCTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:15,16:31,1:0.0294:2,0:35:0:28:0:1:0:56:2:0.0303:0:4 0/1:55:4:1,3:26,25:51,4:0.0727:2,2:31:1:24:1:0.61098:3.06075:60:3:0.0556:0:1 +GL000220.1 122089 . TTTTTC T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.17469;SOR=0;LSEQ=GGTTGTTTTCCTTTTTCTTT;RSEQ=TTTTCTTTTCTTTCCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:17,21:38,2:0.05:2,2:28.5:1:29:1:1:1.23:60:4:0.05:0:1 0/0:55:0:0,0:26,29:55,0:0:2,0:23.5:1:29.5:1:1:0:58.8:110:1:0:0.5 +GL000220.1 122116 . T TC 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.66696;SOR=0.60049;LSEQ=TTTCTTTTCTTTCCTTCTCC;RSEQ=CCCCCCCCACCCCCCCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:0,3:15,18:33,3:0.0811:2,0:34:1:33:1:0.25:0:60:6:0.1:0:0 0/1:40:2:0,2:15,21:36,2:0.05:2,0:8:1:27.7:1:0.50925:0:33:4:0.0571:0.025:1 +GL000220.1 122141 . G C 38 MAF0.05;p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.62935;SOR=0.44567;LSEQ=CCCCACCCCCCCTTGTCGTC;RSEQ=TCCTCCTCCTCCTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:1,2:3,18:21,3:0.125:2,2:6.3:1:24.3:1:0.43676:2.83:55:2:0.0909:0:3.7 0/1:17:1:0,1:1,15:16,1:0.0588:1,0:25:0:31:0:1:0:23:2:0.0625:0:2 +GL000220.1 122382 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24324;SOR=0;LSEQ=GGTGTGAACGTTTCTCTTGC;RSEQ=GTCTCCCGGGGTGTACCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:30,23:53,2:0.0364:2,2:31.5:1:30.5:1:1:1.29798:60:4:0.037:0:1.5 0/0:56:0:0,0:29,26:55,0:0:2,0:26.8:1:29.4:1:1:0:59.1:110:0.9821:0:0.1 +GL000220.1 122448 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49946;SOR=Inf;LSEQ=GCTGAGTGGGTTTTCGGTGC;RSEQ=GAAACCTCCCGAGGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:52:0:0,0:30,22:52,0:0:2,0:25.9:1:29.8:1:1:0:57:51:1:0:0.1 0/1:62:2:1,1:30,30:60,2:0.0323:2,2:23.5:1:28:1:1:1:43.5:4:0.0323:0:1.5 +GL000220.1 122511 . C G 54 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24447;SOR=0;LSEQ=CTTCTCCCCCAGCCGAGGCT;RSEQ=CCACCGCCGCCCTGGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:3:2,1:34,28:62,3:0.0462:2,2:10.7:1:34.3:1:1:1.63:60:6:0.0462:0:1.3 0/0:62:0:0,0:28,34:62,0:0:2,0:27.1:1:30.4:1:1:0:54.7:124:1:0:0.2 +GL000220.1 122550 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0.77498;LSEQ=TTTCCATAGGAGAGGTATGG;RSEQ=AGAGGACTGACACGCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:41,41:82,2:0.0238:2,2:24:1:29:1:1:1:60:4:0.0241:0:1 0/1:54:1:0,1:26,27:53,1:0.0185:2,0:1:0:22:0:1:0:60:2:0.0189:0:1 +GL000220.1 122573 . A G 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0657;SOR=0.41778;LSEQ=AGGACTGACACGCCTTCCAG;RSEQ=TCTATATCCTGCCGGACGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:25:13,12:28,33:61,25:0.2907:2,2:24.4:1:31:1:0.64127:1.27:59.6:24:0.2892:0:1.2 0/1:55:8:4,4:24,23:47,8:0.1455:2,2:19:1:30.9:1:1:1.04269:60:16:0.1538:0:1 +GL000220.1 122625 . C T 117 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00023;SOR=8.02965;LSEQ=GTGCCCCACCGGCTACCTGC;RSEQ=ACCTTCCAGGGAGCTCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:1,2:44,42:86,3:0.0337:2,2:33.3:1:29:1:0.61643:2.07845:60:6:0.0337:0:1 0/1:77:17:9,8:33,27:60,17:0.2208:2,2:25.6:1:28.8:1:1:1.08525:60:16:0.2133:0:1.4 +GL000220.1 122661 . A AC 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.5005;SOR=0;LSEQ=CTGAGGCGGATGCGACCCCC;RSEQ=CCCCCCCGTCACGTCCCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:50,39:89,2:0.022:2,2:24.5:1:33:0:1:1.27851:60:4:0.0244:0:0 0/0:77:0:0,0:42,35:77,0:0:2,0:22.9:1:26.8:1:1:0:60:6:1:0:0.4 +GL000220.1 122711 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2451;SOR=Inf;LSEQ=CGGCTGGCCTTTGCCGGGCG;RSEQ=CCCCAGGGGAACCGCGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:37,40:77,0:0:2,0:23.8:1:28.9:1:1:0:52.4:24.667:1:0:0.2 0/1:76:2:1,1:38,36:74,2:0.0263:2,2:32:0:33:0:1:1.05483:60:4:0.0286:0:1.5 +GL000220.1 122817 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49658;SOR=Inf;LSEQ=ACTGGACCACCCCGGACCGT;RSEQ=CTGTTCTTGGGGGTGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:19,21:40,0:0:2,0:33.6:1:32.5:1:1:0:34.4:80:1:0:0.1 0/1:46:2:1,1:22,22:44,2:0.0435:2,2:24:0:30.5:1:1:1:26:4:0.0435:0:1.5 +GL000220.1 123139 . G GTCTCTCTCTCTCTC 86 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=23.000;MSILEN=2;SSF=0.001;SOR=0;LSEQ=GGGTCCTCGTGGTGGGATTG;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:4,4:9,7:16,8:0.2963:2,2:13.5:1:28.8:1:1:1.27224:50.8:7:0.28:0.2593:0.4 0/0:32:0:0,0:10,11:21,0:0:2,0:24.5:1:28:1:1:0:54.5:6:0.6207:0:0.6 +GL000220.1 123172 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CACGCGCACGCGCGCACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,12:25,0:0:2,0:20.4:1:30.5:1:1:0:58:11.5:1:0:0.5 0/1:40:2:1,1:20,18:38,2:0.05:2,2:10:1:27.5:1:1:1.10818:52.5:4:0.0513:0:3.5 +GL000220.1 123174 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50766;SOR=Inf;LSEQ=TCTCTCTCTCTCTCTCTCGC;RSEQ=CGCGCACGCGCGCACACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:14,15:29,0:0:2,0:18:1:29.9:1:1:0:58.2:28:1:0:0.4 0/1:41:2:1,1:19,19:38,2:0.0488:2,2:8:1:28:1:1:1:52.5:4:0.0556:0:3.5 +GL000220.1 123186 . GCA G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.49907;SOR=Inf;LSEQ=TCTCTCGCACGCGCACGCGC;RSEQ=CACACACACACAATTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:33,0:0:2,0:20:1:30.9:1:1:0:58.3:10:1:0:0.5 0/1:41:2:1,1:19,20:39,2:0.0488:2,2:16.5:1:30:1:1:1.05:60:4:0.0541:0:0.5 +GL000220.1 123188 . A ACG 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.50054;SOR=Inf;LSEQ=TCTCGCACGCGCACGCGCGC;RSEQ=CACACACACACAATTTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:33,0:0:2,0:20.4:1:30.3:1:1:0:58.3:32:1:0:0.5 0/1:42:2:1,1:19,19:38,2:0.0476:2,2:28.5:1:27:1:1:1:60:4:0.05:0:0.5 +GL000220.1 123214 . G C 87 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.03968;SOR=0.11403;LSEQ=ACACACAATTTCCATATCTA;RSEQ=TTCACAGAGCACACTCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:3,3:13,15:28,6:0.1765:2,2:30.2:1:34:1:1:1.15:59.2:12:0.1818:0:1 0/1:43:1:0,1:20,22:42,1:0.0233:2,0:43:0:34:0:1:0:60:2:0.0238:0:1 +GL000220.1 123219 . C G 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.61807;SOR=2.71516;LSEQ=CAATTTCCATATCTAGTTCA;RSEQ=AGAGCACACTCACTTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:16,17:33,1:0.0294:2,0:21:0:34:0:1:0:60:2:0.0303:0:2 0/1:39:3:3,0:16,20:36,3:0.0769:2,0:11.3:1:23.7:1:0.10603:0:47.3:2:0.0526:0:2.3 +GL000220.1 123233 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49864;SOR=Inf;LSEQ=AGTTCACAGAGCACACTCAC;RSEQ=TCCCCTTTTCACAGTACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:37,0:0:2,0:27:1:31.3:1:1:0:59.7:74:1:0:0.5 0/1:45:2:1,1:19,24:43,2:0.0444:2,2:21:0:33:1:1:1.26:49:4:0.0455:0:1.5 +GL000220.1 123239 . T C 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.25551;LSEQ=CAGAGCACACTCACTTCCCC;RSEQ=TTTCACAGTACGCAGGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:1,2:15,19:34,3:0.0811:2,2:26:1:33.3:1:1:1.56027:60:6:0.0811:0:1.3 0/1:40:4:2,2:18,18:36,4:0.1:2,2:12.8:1:29.8:1:1:1:42.5:8:0.1:0:2.3 +GL000220.1 123261 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.22247;SOR=Inf;LSEQ=TTCACAGTACGCAGGCTGAG;RSEQ=AAAACCCGCCCCACCCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:42:0:0,0:20,22:42,0:0:2,0:24.8:1:28.5:1:1:0:58.2:20:1:0:0.5 0/1:38:2:1,1:16,20:36,2:0.0526:2,2:30:1:28:1:1:1.24:54:4:0.0526:0:1 +GL000220.1 123277 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24;SOR=Inf;LSEQ=TGAGTAAAACCCGCCCCACC;RSEQ=TCCACCCGTTGGCTGACGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:17,21:38,0:0:2,0:26.6:1:32:1:1:0:57:37:1:0:0.5 0/1:37:2:1,1:16,19:35,2:0.0541:2,2:33:0:31.5:1:1:1.18:42:4:0.0556:0:2.5 +GL000220.1 123315 . G T 72 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0.82269;LSEQ=GAAACCCCTTCTCTACAATT;RSEQ=ATGAAAAAGATGATCTGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:4,3:9,13:22,7:0.2414:2,2:22.1:1:25.7:1:0.6665:1.88:49.1:6:0.2143:0:1.4 0/1:29:6:2,4:12,11:23,6:0.2069:2,2:23:1:29.2:1:0.65134:2.12461:44.7:12:0.2069:0:1.2 +GL000220.1 123380 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54872;SOR=Inf;LSEQ=ACTCCGGCACTTTGGGAGGC;RSEQ=GAGGCGGGTGGATCGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:11,11:22,0:0:2,0:20.5:1:29.5:1:1:0:58.1:21:1:0:0.8 0/1:44:2:1,1:21,21:42,2:0.0455:2,2:31.5:1:28.5:1:1:1:60:4:0.0455:0:1 +GL000220.1 123444 . G A 76 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49613;SOR=1.80804;LSEQ=GGCCGACGTGGCGAAACCCC;RSEQ=TCTCTCTGAAAAATAGAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:4:3,1:14,14:28,4:0.125:2,2:26.3:1:28.8:1:0.60289:2.91:60:8:0.129:0:1 0/1:29:6:3,3:15,8:23,6:0.2069:2,2:15.5:1:29.5:1:0.6457:1.83303:60:12:0.2069:0:1.2 +GL000220.1 123455 . A C 85 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.05853;SOR=7.28173;LSEQ=CGAAACCCCGTCTCTCTGAA;RSEQ=AATAGAACGATTAGCCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:19,14:33,1:0.0294:2,0:18:0:34:0:0.44118:0:60:2:0.0313:0:1 0/1:38:7:5,2:17,14:31,7:0.1842:2,2:11.3:1:30.4:1:0.67541:2.02:60:14:0.2:0:1 +GL000220.1 123504 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51386;SOR=Inf;LSEQ=GTGGGCTTGGAATCACGACC;RSEQ=CTCGGGAGACTGGGGCGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:23,14:37,0:0:2,0:22.2:1:31.5:1:1:0:59:74:1:0:0.4 0/1:55:2:1,1:31,21:52,2:0.0364:2,2:30.5:1:27.5:1:1:1.46529:60:4:0.0364:0:1 +GL000220.1 123520 . C A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16433;SOR=0;LSEQ=GACCGCTCGGGAGACTGGGG;RSEQ=GGGCGACTTGTTCCAACCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:23,13:36,2:0.0526:2,2:14:1:33:1:1:1.74146:60:4:0.0526:0:1 0/0:55:0:0,0:29,26:55,0:0:2,0:25.2:1:30.3:1:1:0:60:110:1:0:0.3 +GL000220.1 123569 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50022;SOR=Inf;LSEQ=AGGTTGCGATGAGCTGAGAT;RSEQ=GTGCCGTGGCGATGCGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:22,21:43,0:0:2,0:26.4:1:30.5:1:1:0:60:42:1:0:0.3 0/1:53:2:1,1:23,27:50,2:0.0377:2,2:39:1:29:1:1:1.17:60:4:0.0377:0:1 +GL000220.1 123612 . C G 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.07066;LSEQ=ATGACGGAGCGAGACCCCGT;RSEQ=TCGAGAGAATCATGATGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:6:2,4:21,24:45,6:0.1176:2,2:37.2:1:28.5:1:0.67785:1.7315:60:5:0.1042:0:1.3 0/1:48:6:2,4:18,24:42,6:0.125:2,2:22.3:1:31.7:1:1:1.48776:60:12:0.1304:0:1 +GL000220.1 123725 . T G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10753;SOR=Inf;LSEQ=ATCACTTGAGGCCCCACAGG;RSEQ=CGAGGCTTCGGTCGGCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:43,0:0:2,0:25.1:1:30:1:1:0:59.1:42:1:0:0.1 0/1:40:3:2,1:21,16:37,3:0.075:2,2:32.3:1:31:1:1:1.51:44.3:6:0.0769:0:1.3 +GL000220.1 123806 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24622;SOR=Inf;LSEQ=CCCCTTCCCCGTTTGCTTTT;RSEQ=TTTTCTTCCCTTCTCTTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:49,40:89,0:0:2,0:24.2:1:32.6:1:1:0:58.8:178:1:0:0.1 0/1:93:3:1,2:45,45:90,3:0.0323:2,2:8.3:1:32:0:1:1.98567:38:6:0.0326:0:3 +GL000220.1 123809 . T G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49753;SOR=Inf;LSEQ=CTTCCCCGTTTGCTTTTCTT;RSEQ=TCTTCCCTTCTCTTTTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:50,41:91,0:0:2,0:24.1:1:30.6:1:1:0:58.6:182:1:0:0.1 0/1:95:2:1,1:47,46:93,2:0.0211:2,2:13:0:33.5:1:1:1.02151:29:4:0.0215:0:4.5 +GL000220.1 123816 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49825;SOR=Inf;LSEQ=GTTTGCTTTTCTTTTCTTCC;RSEQ=TTCTCTTTTCTTCTTTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:48,43:91,0:0:2,0:24.6:1:32.3:1:1:0:58.6:182:1:0:0.1 0/1:99:2:1,1:49,48:97,2:0.0202:2,2:40:1:29.5:1:1:1.02062:60:4:0.0202:0:1 +GL000220.1 123835 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50486;SOR=Inf;LSEQ=CCTTCTCTTTTCTTCTTTTT;RSEQ=CTTCTCTTTTCTTTCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:37,41:78,0:0:2,0:27.6:1:32.6:1:1:0:58.2:156:1:0:0.1 0/1:100:2:1,1:50,48:98,2:0.02:2,2:24.5:1:30.5:1:1:1.04125:29:4:0.0204:0:4.5 +GL000220.1 123842 . T TTTTC 120 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=35;MSI=9.000;MSILEN=4;SSF=0.00613;SOR=0.23777;LSEQ=TTTTCTTCTTTTTGCTTCTC;RSEQ=TTTCTTTCTTTCTTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:14:7,7:20,27:47,14:0.2029:2,2:26.9:1:31.6:1:0.76127:1.34:57.3:28:0.2059:0.058:0.5 0/1:106:6:3,3:36,32:68,6:0.0566:2,2:31.8:1:30.3:1:1:1.12321:60:12:0.0566:0:0 +GL000220.1 123893 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23676;SOR=Inf;LSEQ=TCTTTTTCTTTTTCTCTCTT;RSEQ=CCCTCTTTCTTTCCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:30,37:67,0:0:2,0:23.8:1:31.4:1:1:0:56.6:32.5:1:0:0.3 0/1:64:2:1,1:29,33:62,2:0.0313:2,2:40.5:1:30:0:1:1.14:60:4:0.0333:0:1 +GL000220.1 123919 . CTTTCTTCT C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=1;SSF=0.08163;SOR=0;LSEQ=TTTCTTTCCTGCCTTCCTGC;RSEQ=TTTCTTCTTTCCTCCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:3:1,2:24,33:57,3:0.05:2,2:29.3:1:31.2:1:1:1.44582:33.3:6:0.05:0.0167:0 0/0:77:0:0,0:35,42:77,0:0:2,0:23.3:1:29.7:1:1:0:55:76:1:0:0.3 +GL000220.1 123938 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49993;SOR=Inf;LSEQ=CCTTTCTTCTTTTCTTCTTT;RSEQ=CTCCCTTCCTCCCTTCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:56:0:0,0:21,35:56,0:0:2,0:19.6:1:31.2:1:1:0:57.7:55:1:0:0.3 0/1:67:2:1,1:28,37:65,2:0.0299:2,2:8.5:1:27:1:1:1.32:60:4:0.0303:0:1.5 +GL000220.1 123943 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.50398;SOR=Inf;LSEQ=CTTCTTTTCTTCTTTCCTCC;RSEQ=TTCCTCCCTTCCTTCTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:21,30:51,0:0:2,0:20.5:1:31.4:1:1:0:57.5:24.5:1:0:0.3 0/1:66:2:1,1:27,36:63,2:0.0303:2,2:27:0:30.5:1:1:1.33:55.5:4:0.0313:0:1 +GL000220.1 124003 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49352;SOR=Inf;LSEQ=AGTGCTGGGATGACTGGCGG;RSEQ=AGGCACCATGCCTGCTTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:11,24:35,0:0:2,0:24.7:1:32.2:1:1:0:57.5:34:0.9714:0:0.2 0/1:38:2:1,1:14,22:36,2:0.0526:2,2:8.5:1:30:1:1:1.55:36:4:0.0541:0:1.5 +GL000220.1 124249 . T TG 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49649;SOR=Inf;LSEQ=GTGCCCACACCGTTTTTAAT;RSEQ=GTTTTTTTTTCCCCCGAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:18,13:31,0:0:2,0:25.8:1:31.1:1:1:0:60:62:1:0:0.1 0/1:37:2:1,1:18,17:35,2:0.0541:2,2:34.5:1:31.5:1:1:1.05721:60:4:0.0556:0:0 +GL000220.1 124250 . G GT 42 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.62671;SOR=2.40481;LSEQ=TGCCCACACCGTTTTTAATT;RSEQ=TTTTTTTTTCCCCCGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:1:0,1:17,12:29,1:0.0323:2,0:31:0:32:0:0.43333:0:60:2:0.0323:0:0 0/1:40:3:2,1:19,18:37,3:0.075:2,2:23.7:1:27:1:1:1.87:60:6:0.0769:0:0.7 +GL000220.1 124381 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.48949;SOR=0;LSEQ=CATCGGCCTCCTGAGTAGCC;RSEQ=GGATTGCGGGCATGCGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:18,2:0.1:2,2:30:1:32.5:1:1:1.54:55:4:0.1:0:1 0/0:17:0:0,0:7,10:17,0:0:2,0:23.2:1:29.8:1:1:0:58.5:34:1:0:0 +GL000220.1 124599 . C A 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.29551;SOR=Inf;LSEQ=CTCATCATTTCTTTGCAACC;RSEQ=TCCTGCCCGGCGTCTCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:20,13:33,0:0:2,0:23.5:1:32.7:1:1:0:57.8:66:1:0:0.2 0/1:57:3:2,1:31,23:54,3:0.0526:2,2:7.3:1:26.7:1:1:1.47:50.7:6:0.0536:0:1.3 +GL000220.1 124609 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTGCAACCCTCCTGCCCG;RSEQ=CGTCTCAAAGTGCTGGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:20,9:29,0:0:2,0:27.3:1:31.9:1:1:0:57.6:58:1:0:0.2 0/1:59:2:1,1:34,23:57,2:0.0339:2,2:21.5:1:26.5:1:1:1.46823:53:4:0.037:0:1 +GL000220.1 124621 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTGCCCGGCGTCTCAAAGT;RSEQ=CTGGCGTGACGGGCGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:23,10:33,0:0:2,0:25.5:1:31.5:1:1:0:57.8:15.5:1:0:0.2 0/1:67:2:1,1:34,31:65,2:0.0299:2,2:13.5:1:28:1:1:1.09526:60:4:0.0308:0:1.5 +GL000220.1 124623 . T C 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1839;LSEQ=TGCCCGGCGTCTCAAAGTGC;RSEQ=GGCGTGACGGGCGTGAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:3:3,0:21,10:31,3:0.0882:2,0:24.3:1:30.3:1:0.53877:0:53:6:0.0909:0:1 0/1:68:7:4,3:31,30:61,7:0.1029:2,2:29.9:1:29.9:1:1:1.29:60:14:0.1045:0:1.4 +GL000220.1 124637 . TG CA 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52412;SOR=Inf;LSEQ=AAGTGCTGGCGTGACGGGCG;RSEQ=AGCCACTGCGCCTGGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:28,17:45,0:0:2,0:21.2:1:29.3:1:1:0:57.8:90:1:0:0.4 0/1:73:2:1,1:38,33:71,2:0.0274:2,2:22.5:1:32.3:1:1:1.14928:38:4:0.0278:0:2.5 +GL000220.1 124648 . G A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27725;SOR=Inf;LSEQ=TGACGGGCGTGAGCCACTGC;RSEQ=CCTGGACTCCGGGGAATGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:51,0:0:2,0:21.3:1:30.2:1:1:0:57.7:102:1:0:0.5 0/1:78:3:2,1:38,37:75,3:0.0385:2,2:13.7:1:28.7:1:1:1.93:45.3:6:0.039:0:2 +GL000220.1 124658 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15573;SOR=0;LSEQ=GAGCCACTGCGCCTGGACTC;RSEQ=GGGGAATGACTCACGACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:23,25:48,2:0.0385:2,2:34.5:1:29.5:1:1:1.09:60:4:0.0417:0:1 0/0:79:0:0,0:42,37:79,0:0:2,0:23.4:1:29.9:1:1:0:56.2:78:1:0:0.6 +GL000220.1 124668 . C T 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.73012;SOR=1.57484;LSEQ=GCCTGGACTCCGGGGAATGA;RSEQ=TCACGACCACCATCGCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:3:1,2:24,25:49,3:0.0577:2,2:21.3:1:29:1:1:1.8969:40:6:0.0577:0:1 0/1:68:6:4,2:31,31:62,6:0.0882:2,2:35.3:1:29.3:1:0.67375:1.98:55.7:12:0.0882:0:2.2 +GL000220.1 124694 . C CCTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT 108 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=4e-05;SOR=0;LSEQ=ACCACCATCGCTCTACTGAT;RSEQ=CTTTCTTTCTTTCTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:13:4,9:13,15:28,13:0.2453:2,2:14.1:1:29.2:1:0.49861:1.91893:32.7:26:0.2653:0.2453:0.6 0/0:55:0:0,0:16,16:32,0:0:2,0:24.8:1:30.7:1:1:0:57:64:0.5926:0:0.3 +GL000220.1 124732 . TTTC ATTTA 44 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=1.31271;LSEQ=TTTCTTTCTTTCTTTCTTTC;RSEQ=TTGATGAATTATCTTATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:13,23:36,2:0.0526:2,2:26:1:31.6:1:1:1.74:60:4:0.0541:0:4 0/1:44:3:1,2:17,24:41,3:0.0682:2,2:20.7:1:28:1:1:1.40587:60:6:0.0698:0.0227:2.7 +GL000220.1 124792 . T TGGGCG 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=4.000;MSILEN=1;SSF=0.57255;SOR=0.67997;LSEQ=TTTCAGACGGAGTCTCGCTC;RSEQ=GGGCGGGGCGAGGCGAGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:4,5:13,6:19,9:0.3214:2,2:25.6:1:31.5:1:0.4087:2.60758:60:18:0.3333:0.0714:0.9 0/1:33:8:4,4:11,14:25,8:0.2424:2,2:28.8:1:31:1:1:1.26:60:16:0.2424:0.0303:0.6 +GL000220.1 124874 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50766;SOR=Inf;LSEQ=AAAGCCCCATTCGTATGCAC;RSEQ=GAGCCTTATTCCCTTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:29,0:0:2,0:27.6:1:31.8:1:1:0:60:58:1:0:0 0/1:41:2:1,1:20,19:39,2:0.0488:2,2:30.5:1:28:1:1:1.05134:60:4:0.05:0:1 +GL000220.1 124875 . G C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50766;SOR=Inf;LSEQ=AAGCCCCATTCGTATGCACA;RSEQ=AGCCTTATTCCCTTCCTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:29,0:0:2,0:27.5:1:33.6:1:1:0:60:58:1:0:0 0/1:41:2:1,1:20,19:39,2:0.0488:2,2:29:0:33.5:1:1:1.05134:60:4:0.0488:0:1.5 +GL000220.1 124959 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.16953;SOR=0;LSEQ=GGAAGCTTTGACAGGCGCAA;RSEQ=CCCACCCAGAGGCTGGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:1,1:18,26:44,2:0.0435:2,2:33:0:32.5:1:1:1.43:45:4:0.0435:0:1 0/0:65:0:0,0:36,29:65,0:0:2,0:24.6:1:30.5:1:1:0:55.6:64:1:0:0.2 +GL000220.1 124986 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51158;SOR=Inf;LSEQ=CAGAGGCTGGCTGCGGCTGA;RSEQ=GATTAGGGGGTGTGTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:19,27:46,0:0:2,0:22.6:1:32.4:1:1:0:57.6:92:1:0:0.2 0/1:66:2:1,1:34,30:64,2:0.0303:2,2:10:1:29:1:1:1.13118:60:4:0.0313:0:1 +GL000220.1 125098 . C G 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02061;SOR=0.09924;LSEQ=CTGAGATCCCCCGCCTCCAC;RSEQ=GCCTTGCAGGCTCACCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:2,3:20,14:34,5:0.1282:2,2:22.6:1:32:1:0.63624:2.10061:60:10:0.1351:0:1.2 0/1:71:1:0,1:33,37:70,1:0.0141:2,0:14:0:32:0:1:0:60:2:0.0143:0:1 +GL000220.1 125113 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51784;SOR=Inf;LSEQ=TCCACCGCCTTGCAGGCTCA;RSEQ=CTCTTACTTTCATTTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:24,19:43,0:0:2,0:22.5:1:30.6:1:1:0:60:13.333:1:0:0.4 0/1:66:2:1,1:28,36:64,2:0.0303:2,2:36.5:1:29.5:1:1:1.28:60:4:0.0313:0:1.5 +GL000220.1 125157 . G C 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.16855;LSEQ=CTTGCGTTTGAGGAGGGGGT;RSEQ=CGGGAATGAGGGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:3:3,0:15,21:36,3:0.0769:2,0:26.3:1:26:1:0.08929:0:47:2:0.0556:0:1.7 0/1:45:4:2,2:19,22:41,4:0.0889:2,2:21.3:1:31.5:1:1:1.15:58:8:0.093:0:1 +GL000220.1 125243 . TCAC T 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.6404;SOR=0.46657;LSEQ=GATTTAGTGTCATGCCTCTT;RSEQ=CACCACCACCACCACCGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:1,2:9,11:20,3:0.1304:2,2:43.3:1:33:1:1:1.60281:34.7:6:0.1304:0:1.3 0/1:31:2:1,1:13,16:29,2:0.0645:2,2:44:0:31:1:1:1.22:46:4:0.0645:0:1 +GL000220.1 125277 . G A 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63843;SOR=0.48503;LSEQ=ACCACCGAAGATGACAGCAA;RSEQ=GATCGGCTAAATACCGCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:3:1,2:7,8:15,3:0.1667:2,2:15:1:33.3:1:1:1.69794:34.7:6:0.1765:0:1.3 0/1:23:2:1,1:9,12:21,2:0.087:2,2:14:0:28.5:1:1:1.32:46:4:0.087:0:1 +GL000220.1 125517 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23585;SOR=Inf;LSEQ=ACAAGTTTACCTATGTCACA;RSEQ=TCTTGCACATGTATGCTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:12,15:27,0:0:2,0:19.4:1:29.9:1:1:0:52.6:26:1:0:0.3 0/1:26:2:1,1:16,7:23,2:0.0769:2,2:14.5:1:29:1:1:2.20393:43:4:0.0769:0:2 +GL000220.1 125555 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.14843;SOR=Inf;LSEQ=TGAACGACAAATAAAAGTTA;RSEQ=GGGGGAGAAGAGAGGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:33,38:71,0:0:2,0:24.7:1:31.9:1:1:0:53.6:70:1:0:0.3 0/1:45:2:1,1:27,16:43,2:0.0444:2,2:31:0:30:1:1:1.66708:25:4:0.0455:0:1.5 +GL000220.1 125564 . AGAGAG GAGGA 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.56782;SOR=2.91649;LSEQ=AAATAAAAGTTAGGGGGGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:1:1,0:36,39:75,1:0.0132:2,0:40:0:33.6:0:0.48684:0:29:2:0.0137:0:0 0/1:53:2:1,1:29,20:49,2:0.0377:2,2:47:0:32.4:1:1:1.43922:42.5:4:0.0426:0:0.5 +GL000220.1 125592 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.51089;SOR=0;LSEQ=GAGAGAGAGAGAGAGAGAGA;RSEQ=AGAGAGAGACAGAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:2:1,1:38,39:77,2:0.0253:2,2:35:1:28:1:1:1.03:60:4:0.029:0:1 0/0:56:0:0,0:25,25:50,0:0:2,0:26:1:28.7:1:1:0:54.4:6.143:0.9149:0:0.5 +GL000220.1 125691 . C G 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TGGCCTTTTGGGAGAACGTT;RSEQ=AGCGACAATGCAGTATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:3:2,1:7,7:14,3:0.1765:2,2:25.7:1:32.3:1:1:1.92:32.3:6:0.1765:0:1 0/1:17:3:1,2:6,8:14,3:0.1765:2,2:23:1:30.3:1:1:1.46561:35.7:6:0.1765:0:1 +GL000220.1 126180 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.05217;SOR=0;LSEQ=TCCGTCCCCCCACCTCCCCG;RSEQ=GCACATAATAACTAACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:5,2:7,3:0.3:2,2:11.3:1:30:1:0.5:4.17095:51.7:6:0.3:0:1.3 0/0:15:0:0,0:6,9:15,0:0:2,0:27.8:1:29.7:1:1:0:46.9:30:1:0:0.2 +GL000220.1 126188 . A ATAACTAAC 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=5.000;MSILEN=4;SSF=0.58602;SOR=0.462;LSEQ=CCCACCTCCCCGCGCACATA;RSEQ=TAACTAACTAACAAACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:6,2:8,2:0.1818:2,2:24:0:32.4:1:1:2.64575:47.5:4:0.1818:0:1.5 0/1:22:2:1,1:10,10:20,2:0.0909:2,2:15:1:31:1:1:1:57:4:0.0606:0.1212:0.5 +GL000220.1 126229 . A C 50 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.03238;SOR=0;LSEQ=TAACTAACTAAACTAACTAA;RSEQ=TAAATAAAATCTCTACACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:3:2,1:7,6:13,3:0.1875:2,2:29.3:1:32:1:1:1.66:31:6:0.1875:0:3 0/0:32:0:0,0:19,13:32,0:0:2,0:21.2:1:29.7:1:1:0:48.4:31:1:0:0.2 +GL000220.1 126233 . A C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.13564;SOR=0;LSEQ=TAACTAAACTAACTAAATAA;RSEQ=TAAAATCTCTACACGTCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:9,7:16,2:0.1111:2,2:39.5:1:33:1:1:1.26772:33.5:4:0.1111:0:4 0/0:30:0:0,0:18,12:30,0:0:2,0:22.3:1:30:1:1:0:49.9:60:1:0:0.3 +GL000220.1 126254 . TC CA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19192;SOR=0;LSEQ=TAAAATCTCTACACGTCACC;RSEQ=TAAGTGTGTGTTCCCGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:10,8:18,2:0.1:2,2:17.5:1:30.5:1:1:1.23603:33.5:4:0.1:0:3 0/0:25:0:0,0:16,9:25,0:0:2,0:25.5:1:30.2:1:1:0:50:50:1:0:0.2 +GL000220.1 126307 . G A 55 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.12451;SOR=0;LSEQ=AAGAAATGGCACTGTACACT;RSEQ=AACGCAGTGGCTCACGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:4:3,1:6,5:11,4:0.2667:2,2:20.8:1:27.5:1:0.6044:2.36:31.8:8:0.2667:0:1 0/0:10:0:0,0:7,3:10,0:0:2,0:14.2:1:30.2:1:1:0:43.1:20:1:0:0.2 +GL000220.1 126582 . CACAT C 69 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=40;MSI=11.000;MSILEN=4;SSF=0.10446;SOR=0;LSEQ=TACGTACATAAATAAATACA;RSEQ=ACATACATACATACATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:4:2,2:5,4:9,4:0.3077:2,2:29:1:34.5:1:1:1.22862:21.3:8:0.3077:0:0 0/0:10:0:0,0:8,2:10,0:0:2,0:20.3:1:28.5:1:1:0:32.3:9:1:0:0.4 +GL000220.1 126627 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.17235;SOR=Inf;LSEQ=ACATACATACATACATACAT;RSEQ=CATGCATACAGATATACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:19,0:0:2,0:29.8:1:31.7:1:1:0:30.6:38:1:0:0.6 0/1:14:2:1,1:9,3:12,2:0.1429:2,2:35:0:30:0:0.50549:2.73861:21:4:0.1429:0:1.5 +GL000220.1 126839 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15862;SOR=Inf;LSEQ=TGTCTCTCTCTCTCCCTCTC;RSEQ=GCCTGTCTCACTGTGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:50,55:105,0:0:2,0:24.6:1:31:1:1:0:52.4:34:1:0:0.3 0/1:70:2:1,1:33,35:68,2:0.0286:2,2:18.5:1:27:1:1:1.06:48:4:0.029:0:1 +GL000220.1 126880 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50598;SOR=0;LSEQ=CTTCTGTCTTACTCTCTTTC;RSEQ=CTCCCCGTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:57,54:111,2:0.0177:2,2:42:1:31.5:1:1:1.05507:60:4:0.0179:0:1 0/0:87:0:0,0:45,42:87,0:0:2,0:24.2:1:29.1:1:1:0:56.2:86:1:0:0.4 +GL000220.1 126883 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19973;SOR=Inf;LSEQ=CTGTCTTACTCTCTTTCTCT;RSEQ=CCCGTCTGTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:56,56:112,0:0:2,0:24.8:1:32.1:1:1:0:55.8:224:1:0:0.5 0/1:91:2:1,1:46,42:88,2:0.022:2,2:9.5:1:30.5:1:1:1.09413:48.5:4:0.0222:0:2 +GL000220.1 126886 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59052;SOR=2.44372;LSEQ=TCTTACTCTCTTTCTCTCCC;RSEQ=GTCTGTCTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:1,0:55,53:108,1:0.0092:2,0:50:0:32:0:1:0:60:2:0.0093:0:1 0/1:90:2:1,1:45,43:88,2:0.0222:2,2:12.5:1:29.5:1:1:1.046:48.5:4:0.0227:0:2 +GL000220.1 126919 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.67534;SOR=1.25162;LSEQ=CTCTCTCTCTCCCTCCCTGT;RSEQ=TGTTTCTCTCTCTCCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:12:7,5:48,39:87,12:0.1212:2,2:26.6:1:31.3:1:1:1.14:54.5:11:0.117:0:1.9 0/1:95:14:9,5:40,41:81,14:0.1474:2,2:30.4:1:29.3:1:0.38988:1.83:56.4:6:0.1304:0:2.4 +GL000220.1 126923 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=3.000;MSILEN=1;SSF=0.52855;SOR=1.426;LSEQ=CTCTCTCCCTCCCTGTTTGT;RSEQ=TCTCTCTCTCCCTCCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:11:5,6:49,39:88,11:0.1111:2,2:24.5:1:32.6:1:0.54033:1.50137:58.5:22:0.1134:0:1.8 0/1:99:15:9,6:42,42:84,15:0.1515:2,2:27.8:1:29.9:1:0.5794:1.49:56.7:14:0.1474:0:2.3 +GL000220.1 126937 . C A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50706;SOR=Inf;LSEQ=GTTTGTTTCTCTCTCTCCCT;RSEQ=CCTGTCTGTTTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:46,38:84,0:0:2,0:24.2:1:31.3:1:1:0:58.9:83:1:0:0.6 0/1:111:2:1,1:56,53:109,2:0.018:2,2:10.5:1:25.5:1:1:1.0561:53.5:4:0.018:0:1 +GL000220.1 126947 . TTC T 74 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.00461;SOR=0;LSEQ=CTCTCTCCCTCCCTGTCTGT;RSEQ=TCTCTCTCTCTTTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:6:2,4:41,32:73,6:0.0759:2,2:23.8:1:28.8:1:0.40329:2.53243:54.5:12:0.0759:0.0127:2 0/0:111:0:0,0:57,54:111,0:0:2,0:22.1:1:28.8:1:1:0:54.8:36:1:0:0.5 +GL000220.1 126952 . T TCGGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCC 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.51792;SOR=Inf;LSEQ=TCCCTCCCTGTCTGTTTCTC;RSEQ=CTCTCTCTTTCTGTCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:44,33:77,0:0:2,0:24.2:1:31.1:1:1:0:57.6:154:1:0:0.5 0/1:116:2:0,2:58,54:112,2:0.0172:2,0:24.5:1:28.2:1:0.23909:0:25:4:0.0175:0.0172:0.5 +GL000220.1 126968 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.51314;SOR=Inf;LSEQ=TCTCTCTCTCTCTTTCTGTC;RSEQ=GTTTCTGTCTCTCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:43,36:79,0:0:2,0:23.2:1:31.5:1:1:0:58.2:78:1:0:0.4 0/1:113:2:1,1:57,54:111,2:0.0177:2,2:40.5:1:29:1:1:1.05507:60:4:0.0179:0:1 +GL000220.1 126973 . CTG C 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=5.000;MSILEN=2;SSF=0.27504;SOR=Inf;LSEQ=CTCTCTCTTTCTGTCTGTTT;RSEQ=TCTCTCTCTGTCTGTCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:42,36:78,0:0:2,0:24.2:1:31.6:1:1:0:58.1:77:1:0:0.4 0/1:116:3:1,2:61,51:112,3:0.0259:2,2:32:1:28.9:1:0.59408:2.37448:58.3:6:0.0268:0.0086:0.7 +GL000220.1 126975 . G GTCTC 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=6.000;MSILEN=2;SSF=0.51518;SOR=Inf;LSEQ=CTCTCTTTCTGTCTGTTTCT;RSEQ=TCTCTCTCTGTCTGTCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:42,37:79,0:0:2,0:23.5:1:32.8:1:1:0:58.1:158:1:0:0.3 0/1:117:2:2,0:61,51:112,2:0.0171:2,0:49.5:1:29.8:1:0.50116:0:51:4:0.018:0:0 +GL000220.1 127030 . C T 77 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.14475;SOR=5.11698;LSEQ=TCTCTTTCTCTGTCTGTCTG;RSEQ=CTCTCTCTTTCTTTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:1:0,1:51,46:97,1:0.0102:2,0:3:0:27:0:0.47959:0:40:2:0.0106:0:7 0/1:139:7:3,4:62,70:132,7:0.0504:2,2:19.7:1:27.7:1:1:1.17955:51.7:14:0.0526:0:2 +GL000220.1 127035 . CTCTT C 124 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.12095;SOR=2.24082;LSEQ=TTCTCTGTCTGTCTGCCTCT;RSEQ=TCTTTTTCTGTGTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:6:2,4:51,46:97,6:0.0588:2,2:9.5:1:31.8:1:0.42801:2.20076:36:12:0.0612:0.0392:3.7 0/1:138:17:8,9:57,64:121,17:0.1232:2,2:30:1:30.5:1:1:1.00194:46.2:34:0.125:0.0072:1.4 +GL000220.1 127051 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.24986;SOR=Inf;LSEQ=CTCTCTCTTTCTTTTTCTGT;RSEQ=TCTCTCTGTCGGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:56,54:110,0:0:2,0:22.5:1:31.6:1:1:0:56.1:54:1:0:0.5 0/1:125:3:1,2:60,62:122,3:0.024:2,2:31:1:29.3:1:1:1.92566:47.7:6:0.024:0:1 +GL000220.1 127063 . GTC G 90 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.08238;SOR=6.23436;LSEQ=TTTTCTGTGTCTCTCTGTCG;RSEQ=TCTCTCTCTCTGTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:1:0,1:50,52:102,1:0.0094:2,0:10:0:34:0:1:0:41:2:0.0099:0:0 0/1:142:8:5,3:65,69:134,8:0.0563:2,2:35.8:1:30.2:1:0.49045:1.76:60:16:0.0576:0.007:0.1 +GL000220.1 127074 . T C 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.26834;SOR=Inf;LSEQ=TCTCTGTCGGTCTCTCTCTC;RSEQ=CTGTCTGTCTGTCTGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:49,52:101,0:0:2,0:26.2:1:30.5:1:1:0:51.4:24.25:1:0:0.5 0/1:142:3:1,2:71,68:139,3:0.0211:2,2:35.7:1:22.7:1:0.61702:2.07779:48.3:2:0.0149:0:1.7 +GL000220.1 127077 . G C 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=4;SSF=0.8085;SOR=1.17776;LSEQ=CTGTCGGTCTCTCTCTCTCT;RSEQ=TCTGTCTGTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:7:3,4:45,48:93,7:0.07:2,2:38.9:1:28.4:1:1:1.24723:30.1:2.5:0.0538:0:4.1 0/1:135:11:4,7:64,60:124,11:0.0815:2,2:20.1:1:29.6:1:0.36529:1.85818:45.1:10:0.0769:0:2.3 +GL000220.1 127081 . G CTCTTTC 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.73839;SOR=1.44817;LSEQ=TCGGTCTCTCTCTCTCTGTC;RSEQ=TCTGTCTGTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:3:2,1:42,50:92,3:0.0306:2,2:45.3:1:32.3:1:0.5947:2.36:23.7:6:0.0323:0:3 0/1:137:6:3,3:64,62:126,6:0.0438:2,2:17.2:1:29.9:1:1:1.03202:48:12:0.0458:0.0292:2 +GL000220.1 127128 . C T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.51214;SOR=Inf;LSEQ=TGTGCCTATCTTCTGTCTTA;RSEQ=TCTCTTTCTCTGCCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:52,44:96,0:0:2,0:22.7:1:32.8:1:1:0:45.6:95:1:0:0.4 0/1:135:2:1,1:71,62:133,2:0.0148:2,2:6.5:1:27.5:1:1:1.14401:60:4:0.0152:0:1 +GL000220.1 127134 . T C 55 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.25522;LSEQ=TATCTTCTGTCTTACTCTCT;RSEQ=TCTCTGCCTGTCTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:3:0,3:53,45:98,3:0.0297:2,0:10.7:1:15:1:0.10379:0:54.3:0:0:0:2 0/1:135:5:1,4:69,61:130,5:0.037:2,2:10.8:1:23.8:1:0.19543:4.48036:42.8:1.5:0.0236:0:3.4 +GL000220.1 127141 . CCTGT C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=3.000;MSILEN=4;SSF=0.26376;SOR=Inf;LSEQ=TGTCTTACTCTCTTTCTCTG;RSEQ=CTGTCTGTCTCTCCCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:52,46:98,0:0:2,0:24.3:1:31.7:1:1:0:46.5:23.5:0.9895:0:0.4 0/1:134:3:1,2:70,62:132,3:0.0224:2,2:19:1:30.7:1:0.60339:2.24487:48.7:6:0.0229:0.0149:1 +GL000220.1 127164 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.50975;SOR=Inf;LSEQ=GTCTGTCTGTCTCTCCCTCC;RSEQ=TTTCTGTTTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:55,47:102,0:0:2,0:27.6:1:31.5:1:1:0:50.7:33:1:0:0.4 0/1:139:2:1,1:70,66:136,2:0.0144:2,2:39:0:31.5:1:1:1.06018:48.5:4:0.0147:0:1.5 +GL000220.1 127221 . C T 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.69818;SOR=0.8632;LSEQ=TCTCCCTGTCTGTTTCTCTC;RSEQ=GTCTCTCTCTCTTTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:13:6,7:46,49:95,13:0.1204:2,2:10.7:1:29.7:1:1:1.0943:47.7:12:0.1188:0:1.5 0/1:161:17:10,7:72,72:144,17:0.1056:2,2:24.1:1:28.4:1:0.61038:1.43:40.6:7.5:0.0987:0:1.5 +GL000220.1 127222 . GTC G 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.15472;SOR=Inf;LSEQ=CTCCCTGTCTGTTTCTCTCC;RSEQ=TCTCTCTCTTTCTGTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:52,55:107,0:0:2,0:24.1:1:29:1:1:0:57.3:34.667:1:0:0.4 0/1:163:4:2,2:79,78:157,4:0.0245:2,2:25.5:1:29.8:1:1:1.01274:60:8:0.025:0:0 +GL000220.1 127232 . C A 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=1;SOR=1.34856;LSEQ=GTTTCTCTCCGTCTCTCTCT;RSEQ=TTTCTGTCTGTTTCTCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:1,0:55,53:108,1:0.0092:2,0:11:0:24:0:1:0:59:2:0.0093:0:2 0/1:162:2:1,1:74,86:160,2:0.0123:2,2:26:0:30:1:1:1.16:60:4:0.0127:0:1 +GL000220.1 127244 . T C 56 v3;p8;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.38736;SOR=3.21486;LSEQ=CTCTCTCTCTTTCTGTCTGT;RSEQ=TCTCACTGTCTCTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:1:1,0:59,62:121,1:0.0082:2,0:3:0:15:0:0.4918:0:60:0:0:0:1 0/1:154:4:2,2:71,79:150,4:0.026:2,2:5:0:28:1:1:1.11:52.8:3:0.0204:0:0.5 +GL000220.1 127266 . ATC A 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.23421;SOR=2.59553;LSEQ=CTCACTGTCTCTCTCTGTCC;RSEQ=TCTCTCTCTCTCTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:3:2,1:52,58:110,3:0.0261:2,2:31.7:1:31.7:1:0.60538:2.22:60:6:0.0283:0:0 0/1:138:9:4,5:64,63:127,9:0.0652:2,2:30.4:1:29.8:1:1:1.26762:56.8:18:0.0677:0:0.7 +GL000220.1 127280 . C G 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.49953;SOR=Inf;LSEQ=CTGTCCATCTCTCTCTCTCT;RSEQ=TGTCTGTCTCTTTCGTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:60,62:122,0:0:2,0:26.1:1:32.8:1:1:0:54.6:244:1:0:0.6 0/1:136:2:2,0:68,65:133,2:0.0147:2,0:7.5:1:27:1:0.49696:0:47.5:4:0.0148:0:3 +GL000220.1 127312 . G C 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0;SOR=0;LSEQ=TTCGTTCTCTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:32:11,21:23,28:51,32:0.2857:2,2:18.1:1:33.2:1:0.36747:1.55971:47.8:64:0.2936:0:1.8 0/0:100:0:0,0:29,36:65,0:0:2,0:23:1:30.2:1:1:0:57.6:64:0.7033:0:0.6 +GL000220.1 127316 . CTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTGTCTCTCACTCTCTGTGTGTATCT C 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.1012;SOR=Inf;LSEQ=TTCTCTCTGTCTGTCTGTCT;RSEQ=TCTGTCTTACTCTCCTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:50,58:108,0:0:2,0:20.9:1:30.5:1:1:0:51:26:1:0:0.9 0/1:97:3:1,2:39,52:91,3:0.0309:2,2:68:1:28.6:1:1:1.49379:60:6:0.0323:0.0309:0.7 +GL000220.1 127366 . G C 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49829;SOR=Inf;LSEQ=CTGTCTCTCACTCTCTGTGT;RSEQ=TATCTTCTGTCTTACTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:45,51:96,0:0:2,0:26.1:1:31.8:1:1:0:50.8:23:1:0:0.9 0/1:104:2:1,1:44,55:99,2:0.0192:2,2:6.5:1:27.5:1:1:1.25:50.5:4:0.0206:0:2 +GL000220.1 127368 . A G 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49831;SOR=Inf;LSEQ=GTCTCTCACTCTCTGTGTGT;RSEQ=TCTTCTGTCTTACTCTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:43,52:95,0:0:2,0:25.6:1:29:1:1:0:51.2:14.833:1:0:0.8 0/1:106:2:1,1:44,56:100,2:0.0189:2,2:6.5:1:30:1:1:1.27:50.5:4:0.0206:0:2 +GL000220.1 127378 . T C 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20117;SOR=0.55487;LSEQ=CTCTGTGTGTATCTTCTGTC;RSEQ=TACTCTCCTTCTCTGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:15:9,6:36,42:78,15:0.1613:2,2:20.2:1:31.5:1:0.40274:1.74:41.1:14:0.1573:0:1.5 0/1:104:10:4,6:42,52:94,10:0.0962:2,2:22.9:1:30.8:1:1:1.20933:47.8:20:0.0971:0:1.9 +GL000220.1 127386 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24377;SOR=0;LSEQ=GTATCTTCTGTCTTACTCTC;RSEQ=TTCTCTGCCTGTCCGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:45,50:95,2:0.0202:2,2:34:1:31:1:1:1.11:60:4:0.0215:0:1 0/0:101:0:0,0:45,56:101,0:0:2,0:24.7:1:30.2:1:1:0:54.1:15.833:1:0:0.6 +GL000220.1 127389 . CTCTGCCTGTCCGTCTG C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=4;SSF=0.23633;SOR=Inf;LSEQ=TCTTCTGTCTTACTCTCCTT;RSEQ=TCTGTCTGTCTGTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:49,53:102,0:0:2,0:23.7:1:31:1:1:0:54.4:204:1:0:0.7 0/1:97:2:1,1:45,50:95,2:0.0206:2,2:20.5:1:27.7:1:1:1.11:32:4:0.0208:0.0206:0 +GL000220.1 127394 . CCTGTCCGTCTGTCTGT C 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=5.000;MSILEN=4;SSF=0.13267;SOR=0.46693;LSEQ=TGTCTTACTCTCCTTCTCTG;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:17:11,6:40,46:86,17:0.165:2,2:23.4:1:32.7:1:0.19413:2.09:43.9:34:0.1683:0.0485:1.4 0/1:95:8:3,5:41,42:83,8:0.0842:2,2:26.8:1:29.6:1:0.71509:1.61844:48.4:7:0.0795:0:1.9 +GL000220.1 127400 . CGTCT C 29 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=6.000;MSILEN=4;SSF=0.61923;SOR=0.48643;LSEQ=ACTCTCCTTCTCTGCCTGTC;RSEQ=GTCTGTCTGTCTGTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:39,43:82,2:0.0206:2,2:7:1:29:1:1:1.10:60:4:0.0253:0.0103:0.5 0/1:99:1:1,0:42,45:87,1:0.0101:2,0:40:0:30:0:0.48864:0:56:2:0.0118:0:0 +GL000220.1 127439 . GTC G 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.41108;SOR=0.39574;LSEQ=CTGTCTCTCTCTCCCTTTCT;RSEQ=TCTCTCTCTCTCTGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:4:1,3:51,41:92,4:0.0412:2,2:29.3:1:31:1:0.32967:3.68378:60:8:0.0421:0:0 0/1:120:2:2,0:60,58:118,2:0.0167:2,0:25:1:30.1:1:0.49636:0:60:4:0.0171:0.0083:0 +GL000220.1 127457 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=1;SSF=0.25003;SOR=Inf;LSEQ=CTGTCTCTCTCTCTCTCTGT;RSEQ=CCTCTCTCTTTCTGTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:57,47:104,0:0:2,0:23.2:1:30.7:1:1:0:57.1:16.333:1:0:0.4 0/1:119:3:1,2:64,52:116,3:0.0252:2,2:28.7:1:27.7:1:0.5898:2.44333:55.7:6:0.0268:0:1.3 +GL000220.1 127478 . CCT C 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.77161;SOR=1.28807;LSEQ=CCTCTCTCTTTCTGTCTGTT;RSEQ=CTCTCTCTCTCTGTCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:5:4,1:51,53:104,5:0.0455:2,2:38.4:1:32.6:1:0.36337:4.11:55.8:10:0.0476:0:0.4 0/1:121:7:4,3:59,55:114,7:0.0579:2,2:34.7:1:30.1:1:1:1.24:60:14:0.0593:0:0.9 +GL000220.1 127531 . T C 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.62243;SOR=0.34962;LSEQ=CTGTCTGCCTCTCTCTTTCT;RSEQ=TCTCTTTCTGTGTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:3:1,2:56,61:117,3:0.025:2,2:20.7:1:33:1:1:1.82715:34.3:6:0.0254:0:1.7 0/0:113:1:1,0:52,59:111,1:0.0088:2,0:38:0:27:0:0.47321:0:59:2:0.0089:0:1 +GL000220.1 127601 . T C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.60682;SOR=2.20586;LSEQ=ACTCTCTTTCTCTGCCTGCC;RSEQ=GCCTGTCTGTCTGTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:1,0:56,58:114,1:0.0087:2,0:6:0:34:0:0.49565:0:59:2:0.0089:0:2 0/1:105:2:1,1:49,53:102,2:0.019:2,2:20.5:1:29.5:1:1:1.08:22:4:0.0194:0:2.5 +GL000220.1 127603 . C T 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.05979;SOR=3.16832;LSEQ=TCTCTTTCTCTGCCTGCCTG;RSEQ=CTGTCTGTCTGTCTGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:4:1,3:55,55:110,4:0.0351:2,2:15.8:1:30.5:1:0.61851:2.97374:25.5:8:0.036:0:1.5 0/1:106:11:5,6:46,48:94,11:0.1038:2,2:29.6:1:30.1:1:1:1.14847:30.7:22:0.1058:0:1.4 +GL000220.1 127607 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=4;SSF=0.10123;SOR=Inf;LSEQ=TTTCTCTGCCTGCCTGCCTG;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:60,58:118,0:0:2,0:23.1:1:29.9:1:1:0:47.4:236:1:0:0.4 0/1:104:3:1,2:48,51:99,3:0.0288:2,2:21.3:1:30.7:1:1:1.87116:28.7:6:0.0294:0:1.3 +GL000220.1 127628 . G C 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24631;SOR=Inf;LSEQ=CTGTCTGTCTGTCTCTCTCT;RSEQ=TCTCTCTCCCTGCCTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:52,50:102,0:0:2,0:26.9:1:31.7:1:1:0:49.6:24.5:1:0:0.4 0/1:101:2:1,1:51,48:99,2:0.0198:2,2:5.5:1:28:1:1:1.06189:59:4:0.0206:0:2 +GL000220.1 127630 . C T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.24377;SOR=Inf;LSEQ=GTCTGTCTGTCTCTCTCTGT;RSEQ=TCTCTCCCTGCCTTTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:51,50:101,0:0:2,0:27.1:1:32.6:1:1:0:49.9:100:1:0:0.4 0/1:99:2:1,1:50,47:97,2:0.0202:2,2:7.5:1:28:1:1:1.0632:59:4:0.0208:0:2 +GL000220.1 127633 . T C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.18194;SOR=0.56616;LSEQ=TGTCTGTCTCTCTCTGTCTC;RSEQ=CTCCCTGCCTTTCTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:21:11,10:41,40:81,21:0.2039:2,2:30:1:31.6:1:1:1.07:54.9:42:0.21:0:1.1 0/1:95:12:5,7:45,38:83,12:0.1263:2,2:24.6:1:27.8:1:0.53993:1.64905:49.4:5:0.1075:0:1.6 +GL000220.1 127650 . TTC T 41 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=1;SOR=0.6606;LSEQ=CTCTCTCCCTGCCTTTCTGT;RSEQ=TCTCTCTCTCTCCCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:0,3:43,44:87,3:0.0333:2,0:9:1:26.3:1:0.24307:0:30.3:2:0.0225:0.0222:1.3 0/1:90:2:2,0:50,38:88,2:0.0222:2,0:24:1:32.5:1:0.50662:0:37:4:0.0222:0:0 +GL000220.1 127665 . C T 47 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11695;SOR=Inf;LSEQ=TCTGTTTCTCTCTCTCTCTC;RSEQ=CTCTCTCTCTCCCTCTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:31,39:70,0:0:2,0:27.5:1:31:1:1:0:51.7:34:1:0:0.4 0/1:68:3:0,3:39,26:65,3:0.0441:2,0:7.7:1:29.7:1:0.07291:0:38:6:0.0441:0:2 +GL000220.1 127667 . T C 48 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.11683;SOR=Inf;LSEQ=TGTTTCTCTCTCTCTCTCCC;RSEQ=CTCTCTCTCCCTCTCTCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:31,38:69,0:0:2,0:26.8:1:31.1:1:1:0:51.6:138:1:0:0.4 0/1:67:3:0,3:38,26:64,3:0.0448:2,0:5.7:1:30.7:1:0.07628:0:38:6:0.0462:0:2 +GL000220.1 127687 . T C 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.23411;SOR=0;LSEQ=TCTCTCTCTCCCTCTCTCGC;RSEQ=CTCTCTGTCTTTCTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:2:1,1:23,28:51,2:0.0377:2,2:5.5:1:32.5:1:1:1.21:51:4:0.0385:0:1 0/0:56:0:0,0:33,23:56,0:0:2,0:25.7:1:29.3:1:1:0:43.8:55:1:0:0.4 +GL000220.1 127738 . C CTGTCTGTCTGTCTGTCTG 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=6.000;MSILEN=4;SSF=0.27334;SOR=Inf;LSEQ=CTCTGTCTCTCTCTGTCCGT;RSEQ=TCTGTCTTTTTCTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:25,26:51,0:0:2,0:29.8:1:33:1:1:0:36.8:50:1:0:0.1 0/1:76:3:2,1:42,31:73,3:0.0395:2,2:27.3:1:25.1:1:1:1.47:46:2:0.027:0.0395:1.3 +GL000220.1 127790 . G CTCTCTCTGTC 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.20622;SOR=0;LSEQ=TTCTGTCTGTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTCTCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:54,41:95,2:0.0206:2,2:23.5:1:33.7:1:1:1.31328:36.5:4:0.0217:0.0103:2 0/0:116:0:0,0:62,54:116,0:0:2,0:23.2:1:30.1:1:1:0:49.6:28:1:0.0172:0.2 +GL000220.1 127808 . G C 66 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04336;SOR=0;LSEQ=CTGTCTCTCTCTCTCTCTCT;RSEQ=CTTGTCTCTCTCACTGTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:4:2,2:53,35:88,4:0.043:2,2:15.8:1:33:1:1:1.50725:27.5:8:0.0444:0:1.5 0/0:109:0:0,0:55,53:108,0:0:2,0:24.9:1:30.9:1:1:0:55.1:17:1:0:0.2 +GL000220.1 127843 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22993;SOR=Inf;LSEQ=TGTGTCTGTCCTCTGTCTTA;RSEQ=TCTCCTTCTCTGCCTGTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:57,51:108,0:0:2,0:24.9:1:32.3:1:1:0:53.6:35:1:0:0.3 0/1:100:2:1,1:44,53:97,2:0.02:2,2:26:1:30.5:1:1:1.20:44:4:0.0217:0:2.5 +GL000220.1 127848 . C T 48 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3558;SOR=3.25079;LSEQ=CTGTCCTCTGTCTTACTCTC;RSEQ=TTCTCTGCCTGTCCGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:1:1,0:55,55:110,1:0.009:2,0:11:0:34:0:1:0:43:2:0.0095:0:1 0/1:104:3:1,2:46,54:100,3:0.0288:2,2:23.7:1:30.3:1:1:1.69527:44.3:6:0.0309:0:2.7 +GL000220.1 127868 . T C 33 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.19534;SOR=Inf;LSEQ=CTTCTCTGCCTGTCCGTCTG;RSEQ=CTGTCTGTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:58,55:113,0:0:2,0:26.6:1:29.7:1:1:0:54.9:55.5:1:0:0.3 0/1:90:2:1,1:41,46:87,2:0.0222:2,2:5:0:33:0:1:1.12:25.5:4:0.0227:0:0.5 +GL000220.1 127871 . G A 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.42918;SOR=0.6099;LSEQ=CTCTGCCTGTCCGTCTGTCT;RSEQ=TCTGTCTCTCTCTCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:10:6,4:50,51:101,10:0.0901:2,2:24:1:29:1:0.74218:1.52:39:20:0.0943:0:1.4 0/1:88:5:2,3:39,43:82,5:0.0568:2,2:30.8:1:26.4:1:1:1.35572:46.6:4:0.0476:0:1.2 +GL000220.1 127875 . GTC G 48 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.6549;SOR=1.96302;LSEQ=GCCTGTCCGTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCCCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:2,0:55,53:108,2:0.018:2,0:31:1:34:0:0.49608:0:52.5:4:0.0182:0:0.5 0/1:86:3:2,1:38,44:82,3:0.0349:2,2:17.3:1:30.7:1:0.59907:2.29:60:6:0.0366:0:0 +GL000220.1 127891 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.5057;SOR=0;LSEQ=GTCTGTCTCTCTCTCTCTCC;RSEQ=TCCCTTTCTGTTTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:55,57:112,2:0.0174:2,2:35:1:28:1:1:1.04:59.5:4:0.0179:0:1 0/0:89:0:0,0:42,46:88,0:0:2,0:22.5:1:30.5:1:1:0:54.4:176:1:0:0.4 +GL000220.1 127895 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50879;SOR=0;LSEQ=GTCTCTCTCTCTCTCCCTCC;RSEQ=TTTCTGTTTCTCTCTCGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:54,58:112,2:0.0174:2,2:14.5:1:29.5:1:1:1.07:59.5:4:0.0179:0:1 0/0:85:0:0,0:42,41:83,0:0:2,0:23.9:1:30.8:1:1:0:53.8:82:1:0:0.4 +GL000220.1 127910 . T G 60 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.40712;SOR=2.63776;LSEQ=CCTCCCTTTCTGTTTCTCTC;RSEQ=CGCTCTCTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:47,60:107,2:0.0179:2,2:6.5:1:21:1:1:1.27:21:1:0.0093:0:2 0/1:87:4:3,1:40,42:82,4:0.046:2,2:6:1:30.3:1:0.61602:3.11:23.3:8:0.0471:0:2 +GL000220.1 127912 . G GCT 150 MSI12;MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=28;MSI=15.000;MSILEN=2;SSF=0.00039;SOR=0.18675;LSEQ=TCCCTTTCTGTTTCTCTCTC;RSEQ=CTCTCTCTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:28:12,16:24,32:56,28:0.2545:2,2:23.5:1:31.3:1:1:1:48.1:56:0.2642:0.0818:0.6 0/1:84:5:5,0:20,26:46,5:0.0595:2,0:36:1:30.6:1:0.02262:0:56:10:0.0617:0:0.8 +GL000220.1 127941 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09543;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=CCTGTTTCTCTTTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:48,50:98,0:0:2,0:23.8:1:30.8:1:1:0:47.1:8.8:0.9888:0:0.5 0/1:86:3:2,1:42,38:80,3:0.0349:2,2:24.7:1:23.3:1:1:1.80:52.7:2:0.0282:0:1.7 +GL000220.1 127944 . T C 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49976;SOR=0;LSEQ=TCTCTCTCTCTCTCTCTGCC;RSEQ=GTTTCTCTTTCTCTCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:48,49:97,2:0.0202:2,2:30:1:28.5:1:1:1.02:49.5:4:0.0217:0:1 0/0:86:0:0,0:45,41:86,0:0:2,0:25.8:1:29.7:1:1:0:44.9:172:1:0:0.4 +GL000220.1 127960 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.24615;SOR=0;LSEQ=TGCCTGTTTCTCTTTCTCTC;RSEQ=CTGTCTGTCTCTGTCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:49,46:95,2:0.0206:2,2:26.5:1:29.5:1:1:1.06456:60:4:0.022:0:1.5 0/0:98:0:0,0:51,47:98,0:0:2,0:23.8:1:29.1:1:1:0:44.4:97:1:0:0.4 +GL000220.1 127977 . T C 29 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.85578;LSEQ=CTCTCTGTCTGTCTCTGTCT;RSEQ=TCTCTGTCTGTCTCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:1:0,1:45,49:94,1:0.0105:2,0:1:0:32:0:1:0:60:2:0.0112:0:1 0/1:103:2:1,1:49,52:101,2:0.0194:2,2:7.5:1:29.5:1:1:1.06:48:4:0.0208:0:2 +GL000220.1 127985 . C T 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0.9512;LSEQ=CTGTCTCTGTCTTTCTCTGT;RSEQ=TGTCTCTTTCTCTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:44,53:97,2:0.0202:2,2:20:1:20:1:1:1.20:49:1:0.0103:0:2.5 0/1:104:2:0,2:48,54:102,2:0.0192:2,0:7:1:27.5:1:0.49813:0:60:4:0.0198:0:1 +GL000220.1 127987 . G T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.000;MSILEN=4;SSF=1;SOR=2.01329;LSEQ=GTCTCTGTCTTTCTCTGTCT;RSEQ=TCTCTTTCTCTGTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:0,1:46,55:101,1:0.0098:2,0:15:0:23:0:1:0:60:2:0.0102:0:2 0/1:102:2:1,1:45,53:98,2:0.0196:2,2:12.5:1:28:1:1:1.18:60:4:0.02:0:2 +GL000220.1 127993 . T C 33 v3;p8;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.61089;SOR=0.46427;LSEQ=GTCTTTCTCTGTCTGTCTCT;RSEQ=TCTCTGTCTGTCTGTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:46,52:98,2:0.0198:2,2:5:0:33:0:1:1.13:41.5:4:0.0204:0:2 0/0:108:1:1,0:52,55:107,1:0.0093:2,0:16:0:32:0:0.49074:0:24:2:0.0095:0:4 +GL000220.1 128026 . C T 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16568;SOR=0.42132;LSEQ=TGTCTCCTTCTCTCTGTCTC;RSEQ=GTCTCTGTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:9:6,3:47,55:102,9:0.0811:2,2:20.7:1:30.3:1:0.30587:2.32:44:8:0.0748:0:1.7 0/1:112:4:3,1:51,57:108,4:0.0357:2,2:24.8:1:27.3:1:0.35086:3.32:46:3:0.0273:0:1.8 +GL000220.1 128033 . GTC G 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.34917;SOR=0.29838;LSEQ=TTCTCTCTGTCTCCGTCTCT;RSEQ=TCTCTCTCTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:3:2,1:52,54:106,3:0.0275:2,2:18:1:32.8:1:0.61802:2.06:57.7:6:0.0291:0.0092:0 0/0:120:1:1,0:60,59:119,1:0.0083:2,0:11:0:33:0:1:0:60:2:0.0083:0:0 +GL000220.1 128047 . GTC G 75 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=1.22527;LSEQ=GTCTCTGTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTGCCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:4:3,1:51,53:104,4:0.037:2,2:44.8:1:32.5:1:0.61789:3.09:60:8:0.0381:0:0 0/1:111:5:3,2:53,53:106,5:0.045:2,2:32.6:1:32.6:1:1:1.49:47.8:10:0.045:0:0.6 +GL000220.1 128059 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.23266;SOR=0;LSEQ=CTCTCTCTGTCTCTCTCTCT;RSEQ=TGCCTGTCTCACTGTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:49,52:101,2:0.0194:2,2:42.5:1:30:0:1:1.06:53:4:0.02:0:1.5 0/0:110:0:0,0:54,55:109,0:0:2,0:23.9:1:30.9:1:1:0:54.8:108:0.9908:0:0.3 +GL000220.1 128063 . CTGTCTCACTG C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.000;MSILEN=2;SSF=0.49947;SOR=Inf;LSEQ=CTCTGTCTCTCTCTCTCTGC;RSEQ=TGTCTGTCTTCTGTCTTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:50,54:104,0:0:2,0:24.1:1:31:1:1:0:55.9:33.667:1:0:0.4 0/1:117:2:1,1:54,60:114,2:0.0171:2,2:9:1:28:1:1:1.11:41.5:4:0.0175:0.0171:1 +GL000220.1 128065 . GTCTCACTGTGTCTGTCTTCTGTCTTAT G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.50037;SOR=Inf;LSEQ=CTGTCTCTCTCTCTCTGCCT;RSEQ=TCTCTTTCTCTGTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:49,53:102,0:0:2,0:24.4:1:29.9:1:1:0:55.2:50:1:0:0.4 0/1:118:2:1,1:55,59:114,2:0.0169:2,2:36:1:28.6:1:1:1.07:60:4:0.0174:0.0169:0 +GL000220.1 128110 . C G 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=4;SSF=0.83825;SOR=0.92269;LSEQ=TATTCTCTTTCTCTGTCTGT;RSEQ=TGTCTCTCTCTCTCCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:12:8,4:40,36:76,12:0.1364:2,2:21.2:1:32.6:1:0.53474:1.79:48.7:24:0.1364:0:1.8 0/1:118:15:9,6:59,44:103,15:0.1271:2,2:26.5:1:31.7:1:1:1.12:50.7:30:0.1282:0:1.9 +GL000220.1 128112 . GTC G 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.17047;SOR=0;LSEQ=TTCTCTTTCTCTGTCTGTCT;RSEQ=TCTCTCTCTCCCTTCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:2,0:46,39:85,2:0.023:2,0:26.5:1:34:0:0.4996:0:60:4:0.0233:0:0.5 0/0:123:0:0,0:70,53:123,0:0:2,0:25:1:28.7:1:1:0:52.6:246:1:0:0.5 +GL000220.1 128138 . TTCTC T 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=10.000;MSILEN=2;SSF=0.39678;SOR=0.76798;LSEQ=CTCTCTCCCTTCCTGTCTCT;RSEQ=TCTCTCTCTCTCTCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:88:54:31,23:15,15:30,54:0.6136:2,2:27:1:31.3:1:0.64783:1.34:56.5:108:0.6279:0.0909:0.3 1/0:122:67:37,30:16,21:37,67:0.5492:2,2:25.2:1:29.7:1:0.30652:1.61:54:134:0.5583:0.1148:0.4 +GL000220.1 128154 . CTCTCTTTCTG T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.57471;SOR=0.65968;LSEQ=TGTCTCTTTCTCTCTCTCTC;RSEQ=TCTGTTTCTCTCTGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:7:3,4:44,33:77,7:0.0814:2,2:34.9:1:31.8:1:0.69402:1.76544:45.1:14:0.0854:0:1.4 0/1:127:7:4,3:62,54:116,7:0.0551:2,2:24.3:1:32.1:1:1:1.16:43:14:0.0569:0:0.9 +GL000220.1 128164 . G C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.14639;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTTTCT;RSEQ=TCTGTTTCTCTCTGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:44,33:77,0:0:2,0:24.4:1:31.8:1:1:0:54:37.5:0.9868:0:0.2 0/1:113:4:2,2:57,49:106,4:0.0354:2,2:13.5:1:30.3:1:1:1.16166:44:8:0.0364:0:4 +GL000220.1 128187 . CGTCTTTCTCTGTCTGCCTCTCTCTT TCTCTCTGTCTGCCTC 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01668;SOR=Inf;LSEQ=TGTTTCTCTCTGCCTGTCTC;RSEQ=TCTTTTTCTGCGTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:51,45:96,0:0:2,0:23:1:29.9:1:1:0:51.5:31:1:0:0.4 0/1:115:7:4,3:53,54:107,7:0.0609:2,2:8.7:1:30:1:1:1.35:30.3:14:0.0636:0.0609:0.9 +GL000220.1 128188 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.000;MSILEN=1;SSF=0.50066;SOR=Inf;LSEQ=GTTTCTCTCTGCCTGTCTCC;RSEQ=TCTTTCTCTGTCTGCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:50,43:93,0:0:2,0:23.8:1:30:1:1:0:52:30:1:0:0.3 0/1:109:2:1,1:54,53:107,2:0.0183:2,2:14:1:31.5:1:1:1.0187:51.5:4:0.0185:0:1 +GL000220.1 128194 . C CTCTG 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=3.000;MSILEN=4;SSF=0.51809;SOR=1.66894;LSEQ=CTCTGCCTGTCTCCGTCTTT;RSEQ=TCTGTCTGCCTCTCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:3:2,1:45,42:87,3:0.0333:2,2:13.7:1:30.7:1:1:1.85:46.7:6:0.0333:0.0111:1.3 0/1:110:6:4,2:51,53:104,6:0.0545:2,2:5.8:1:28.9:1:0.67865:2.07:43.8:12:0.0556:0.0455:1.7 +GL000220.1 128203 . CCTCTCTCTT TCTGCCTC 79 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00935;SOR=0;LSEQ=TCTCCGTCTTTCTCTGTCTG;RSEQ=TCTTTTTCTGCGTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:6:2,4:49,40:89,6:0.0632:2,2:14.2:1:30.6:1:0.41065:2.42736:31.2:12:0.0667:0.0421:0.8 0/0:109:0:0,0:52,53:105,0:0:2,0:24.1:1:30.7:1:1:0:51.9:25.25:0.9806:0:0.3 +GL000220.1 128216 . T A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.50822;SOR=Inf;LSEQ=CTGTCTGCCTCTCTCTTTCT;RSEQ=TTTCTGCGTCTCTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:43,45:88,0:0:2,0:27:1:30.6:1:1:0:49.3:87:1:0:0.3 0/1:118:2:1,1:54,62:116,2:0.0169:2,2:8:0:30.5:1:1:1.15:51:4:0.0169:0:1 +GL000220.1 128232 . GTC G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.83761;SOR=1.13654;LSEQ=TTCTTTTTCTGCGTCTCTCT;RSEQ=TCTCTCTCTCTGTGCCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:11:7,4:44,42:86,11:0.1134:2,2:24.8:1:31.6:1:0.53061:1.66:31.8:22:0.1158:0.0103:0.5 0/1:126:16:6,10:54,57:111,16:0.127:2,2:20.5:1:28.9:1:0.43609:1.57336:27.7:15:0.122:0.0238:0.8 +GL000220.1 128282 . CCTGT C 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=0.03747;SOR=0;LSEQ=TTACTCTGTTTCTCTGCCTG;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:4:1,3:56,47:103,4:0.0377:2,2:22:1:30.8:1:0.33766:3.53488:36.8:8:0.0381:0.0189:1.3 0/0:133:0:0,0:66,66:132,0:0:2,0:24:1:30.2:1:1:0:52.6:21:1:0:0.3 +GL000220.1 128293 . GTCTGTC G 32 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=7.000;MSILEN=2;SSF=1;SOR=0.86561;LSEQ=CTCTGCCTGCCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:2:1,1:59,50:109,2:0.018:2,2:39.5:1:31.5:1:1:1.17823:45.5:4:0.0182:0:0 0/1:128:2:1,1:61,63:124,2:0.0156:2,2:44:0:32.5:1:1:1.03:60:4:0.0161:0:0.5 +GL000220.1 128297 . GTC G 102 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.81556;SOR=0.83685;LSEQ=GCCTGCCTGTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:10:5,5:51,44:95,10:0.0935:2,2:29.3:1:32.7:1:1:1.15746:51.8:20:0.0952:0:0.1 0/1:126:10:6,4:55,58:113,10:0.0794:2,2:28.5:1:30.9:1:0.52954:1.58:55.3:20:0.082:0:0.3 +GL000220.1 128305 . C CTT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.21549;SOR=0;LSEQ=GTCTGTCTGTCTGTCTCTCT;RSEQ=TCTCTCTGTCTCTCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:60,52:112,2:0.0175:2,2:10.5:1:29.8:1:1:1.15239:30:4:0.0177:0.0088:1 0/0:131:0:0,0:60,70:130,0:0:2,0:23.9:1:30.8:1:1:0:53.6:42.333:0.9922:0:0.3 +GL000220.1 128351 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=8;SSF=0.4977;SOR=Inf;LSEQ=CTGTTTCTCTCTGTCTCTCT;RSEQ=TCCATCTCTGTCTTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:57,49:106,0:0:2,0:28.8:1:32.3:1:1:0:55.4:52:1:0:0.2 0/1:108:2:1,1:50,54:104,2:0.0185:2,2:29.5:1:29.5:1:1:1.08:53.5:4:0.0189:0:1 +GL000220.1 128374 . C T 87 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=1.000;MSILEN=1;SSF=0.33278;SOR=0.4302;LSEQ=CATCTCTGTCTTTCTCTGTC;RSEQ=GTCTCTCTCTTTCTCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:7:3,4:50,51:101,7:0.0648:2,2:11.9:1:31:1:1:1.30397:35.3:14:0.0667:0:2.3 0/1:104:3:1,2:49,52:101,3:0.0288:2,2:4:1:26.3:1:1:1.8736:42.3:6:0.0291:0:2.3 +GL000220.1 128389 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=1;SSF=0.49751;SOR=Inf;LSEQ=CTGTCCGTCTCTCTCTTTCT;RSEQ=CCTGTCTCTGTCTCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:48,52:100,0:0:2,0:24.3:1:31.8:1:1:0:57.8:200:1:0:0.3 0/1:101:2:1,1:48,51:99,2:0.0198:2,2:15.5:1:26.5:1:1:1.06:60:4:0.0198:0:1.5 +GL000220.1 128412 . CCT C 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.35601;SOR=0.49691;LSEQ=TGTCTCTGTCTCTGCCTCTG;RSEQ=CTCTCTCTCTCTGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:7:4,3:43,48:91,7:0.0714:2,2:29.6:1:30.4:1:0.7071:1.48:57.1:6:0.0625:0:0.1 0/1:109:4:2,2:54,51:105,4:0.0367:2,2:31.3:1:29:1:1:1.0583:55:8:0.0367:0:0 +GL000220.1 128425 . C G 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.26454;SOR=0.3598;LSEQ=GCCTCTGCCTCTCTCTCTCT;RSEQ=TGTCTCTCTCTTTCTATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:5:1,4:47,45:92,5:0.0505:2,2:30.6:1:31:1:0.36191:4.12423:38:10:0.0526:0:3.2 0/1:107:2:2,0:52,53:105,2:0.0187:2,0:39:1:33.5:1:0.49533:0:32:4:0.019:0:3.5 +GL000220.1 128427 . G C 73 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49424;SOR=0.57265;LSEQ=CTCTGCCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTTTCTATCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:5:1,4:50,47:97,5:0.0481:2,2:31:1:31.8:1:0.36244:4.2027:38:10:0.05:0:3.2 0/1:107:3:3,0:52,52:104,3:0.028:2,0:26.7:1:31.3:1:0.24352:0:31.3:6:0.0294:0:3 +GL000220.1 128467 . A G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.96378;LSEQ=TTCTCTCTGTCTCTCTGTCC;RSEQ=TCTCTGTCTTTCTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:10:2,8:53,53:106,10:0.0862:2,2:28.3:1:32.6:1:0.09884:3.9579:37.5:20:0.0885:0:2.1 0/1:120:10:4,6:64,45:109,10:0.0833:2,2:26:1:28.3:1:0.32302:2.11956:35.4:9:0.0804:0:2 +GL000220.1 128495 . CTT C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.49813;SOR=0;LSEQ=CTTTCTCTGTCTGTCTCTCT;RSEQ=TCTCCCTGTCTCTGTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:59,62:121,2:0.0163:2,2:31.5:1:31.5:1:1:1.05:27:4:0.0164:0:0 0/0:118:0:0,0:64,54:118,0:0:2,0:25.4:1:29.6:1:1:0:54.2:58:1:0:0.4 +GL000220.1 128497 . T C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16859;SOR=0.40144;LSEQ=TTCTCTGTCTGTCTCTCTCT;RSEQ=TCTCCCTGTCTCTGTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:10:6,4:52,59:111,10:0.0813:2,2:14.1:1:34.1:1:0.51761:1.69:54.8:20:0.084:0:1.2 0/1:117:4:2,2:62,51:113,4:0.0342:2,2:37:1:30.8:1:1:1.21364:48.5:8:0.0351:0:1 +GL000220.1 128500 . TC T 97 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.80215;SOR=1.24397;LSEQ=TCTGTCTGTCTCTCTCTTTC;RSEQ=CCTGTCTCTGTCTCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:8:2,6:58,56:114,8:0.0656:2,2:23.6:1:32.1:1:0.273:3.0805:38.5:16:0.0667:0:1.4 0/1:112:9:3,6:57,45:102,9:0.0804:2,2:37.1:1:30.8:1:0.29688:2.51241:34.4:18:0.0818:0:1.4 +GL000220.1 128551 . CTG C 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.62171;SOR=2.9593;LSEQ=CTCTCTGTCTGTCTCTCTCA;RSEQ=TGTGTGTGTCTCTGTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:1,0:50,58:108,1:0.0092:2,0:40:0:30:0:0.46789:0:59:2:0.0095:0:0 0/1:112:3:2,1:49,58:107,3:0.0268:2,2:29.3:1:33:1:0.59568:2.35:35:6:0.0286:0:0.7 +GL000220.1 128606 . TCTCACTGTGT ACC 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.49828;SOR=Inf;LSEQ=TCTCTCTCTCTGTCTGTCTC;RSEQ=GTGTCTGTCTTCTGTCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:43,0:0:2,0:27.9:1:30.4:1:1:0:45.8:20.5:1:0:0.4 0/1:51:2:0,2:19,30:49,2:0.0392:2,0:16.5:1:30.3:1:0.52314:0:49:4:0.0392:0.0196:1.5 +GL000220.1 128676 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=0.49233;SOR=Inf;LSEQ=GTCTGTCTGTCTGTCTCTCC;RSEQ=TCTCTCTCCCTCCCTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:15,15:30,0:0:2,0:21.1:1:32.5:1:1:0:25.2:60:1:0:0.1 0/1:32:2:1,1:15,15:30,2:0.0625:2,2:8:0:32:1:1:1:28:4:0.0667:0:1 +GL000220.1 128802 . GTC G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=4.000;MSILEN=2;SSF=0.21256;SOR=Inf;LSEQ=TTCTTTTTCTCTGTCTCTCT;RSEQ=TCTCTCTGTGCCTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:25,20:45,0:0:2,0:21.8:1:30.6:1:1:0:38.3:44:1:0:0.1 0/1:39:2:1,1:19,18:37,2:0.0513:2,2:28.5:1:29:1:1:1.05412:24:4:0.0513:0:0 +GL000220.1 128855 . TTCTCTGGCTGACTGCCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGCCTGTCTCCGTCCCTCCCTCCCTGTCTGTCTGTTTCTC T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=4.000;MSILEN=2;SSF=0.49793;SOR=Inf;LSEQ=TATCTTCTGTCTTACTCTCT;RSEQ=TCTCTGTCCATTTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:41,43:84,0:0:2,0:25:1:30.5:1:1:0:47.4:168:1:0:0.3 0/1:91:2:1,1:45,44:89,2:0.022:2,2:31.5:1:28.5:1:1:1.02248:42:4:0.0222:0.022:0 +GL000220.1 128917 . G A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.59218;SOR=2.41646;LSEQ=CTCTCTCTCTGCCTGTCTCC;RSEQ=TCCCTCCCTCCCTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:1,0:55,53:108,1:0.0092:2,0:1:0:28:0:1:0:60:2:0.0099:0:1 0/1:91:2:1,1:42,44:86,2:0.022:2,2:39:1:28.5:1:1:1.05:54:4:0.026:0:1 +GL000220.1 128921 . C A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.21994;SOR=Inf;LSEQ=CTCTCTGCCTGTCTCCGTCC;RSEQ=TCCCTCCCTGTCTGTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:54,53:107,0:0:2,0:24.8:1:32.4:1:1:0:50.9:214:1:0:0.3 0/1:95:2:1,1:43,48:91,2:0.0211:2,2:22:0:28.5:1:1:1.11:29:4:0.0217:0:2.5 +GL000220.1 128940 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.22627;SOR=Inf;LSEQ=CCTCCCTCCCTGTCTGTCTG;RSEQ=TTCTCTCTCTGTCCATTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:60,63:123,0:0:2,0:25.1:1:29.6:1:1:0:52.9:40:0.9917:0:0.3 0/1:113:2:1,1:53,56:109,2:0.0177:2,2:34:0:33:1:1:1.06:49:4:0.0183:0:1.5 +GL000220.1 128957 . TTCTG T 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.02951;SOR=0;LSEQ=CTGTTTCTCTCTCTGTCCAT;RSEQ=TCTGTCTCTTTCTCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:6:4,2:58,57:115,6:0.0492:2,2:18.3:1:32.5:1:0.6801:1.95:47.8:12:0.0504:0:0 0/0:117:0:0,0:60,57:117,0:0:2,0:25.7:1:29.2:1:1:0:51.6:38:1:0:0.7 +GL000220.1 128996 . T C 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.11001;SOR=Inf;LSEQ=TTTCTCTCTCTTTCTTTCTC;RSEQ=CTGTCTCTCTCTGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:56,44:100,0:0:2,0:24.8:1:31:1:1:0:51.4:32.333:1:0:0.3 0/1:93:3:1,2:54,36:90,3:0.0323:2,2:24.7:1:31.3:1:0.56514:2.96436:44.7:6:0.0341:0:1 +GL000220.1 129009 . G C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0.07927;SOR=2.62149;LSEQ=CTTTCTCTCTGTCTCTCTCT;RSEQ=TCTCTCTCTGTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:6:2,4:52,34:86,6:0.0645:2,2:20.8:1:27.5:1:0.22624:3.02121:40.2:2:0.0494:0:2.2 0/1:78:12:6,6:41,24:65,12:0.1538:2,2:18.3:1:30.8:1:0.52162:1.69599:48.8:24:0.1622:0:1.8 +GL000220.1 129017 . C G 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.59843;SOR=2.31689;LSEQ=CTGTCTCTCTCTGTCTCTCT;RSEQ=TGTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:1,0:46,39:85,1:0.0116:2,0:8:0:34:0:1:0:35:2:0.0122:0:3 0/1:75:2:2,0:44,28:72,2:0.0267:2,0:23:1:32.5:1:0.52314:0:37.5:4:0.0278:0:5 +GL000220.1 129019 . G C 93 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.0032;SOR=0;LSEQ=GTCTCTCTCTGTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:9:3,6:42,28:70,9:0.1098:2,2:16.3:1:29.6:1:0.16274:2.95782:42.8:3.5:0.0986:0:2 0/0:77:0:0,0:37,22:59,0:0:2,0:21.3:1:29.6:1:1:0:47:10.8:0.9818:0:0.4 +GL000220.1 129072 . TCTCTCACTGTGTCGGTCTTCTGTCTTACTCTCTTTCTCTGCCTGCCTCTCTG T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=4;SSF=0.11446;SOR=Inf;LSEQ=TCTCTCTCTCTCTGCCTTTC;RSEQ=TCTGTCTGTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:46,43:89,0:0:2,0:24:1:32.8:1:1:0:48.2:88:1:0:0.5 0/1:85:3:1,2:39,43:82,3:0.0353:2,2:8.3:1:27.4:1:1:1.80178:41:6:0.0357:0.0353:1 +GL000220.1 129090 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2307;SOR=Inf;LSEQ=TCTCTCTCACTGTGTCGGTC;RSEQ=TCTGTCTTACTCTCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:48,51:99,0:0:2,0:24.3:1:30.3:1:1:0:49.4:23.75:1:0:0.5 0/1:92:2:1,1:43,46:89,2:0.0217:2,2:31:1:30.5:1:1:1.07:33.5:4:0.023:0:1 +GL000220.1 129120 . C CTCTGTCTG 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=6.000;MSILEN=4;SSF=0.2494;SOR=Inf;LSEQ=CTCTCTTTCTCTGCCTGCCT;RSEQ=TCTGTCTGTCTGTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:44,50:94,0:0:2,0:26.9:1:32.4:1:1:0:51.5:93:1:0:0.2 0/1:107:3:1,2:52,49:101,3:0.028:2,2:20:1:31.3:1:0.61408:2.10762:21.7:6:0.0286:0.0187:0.7 +GL000220.1 129150 . A ACGTC 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21578;SOR=0;LSEQ=CTGTCTGTCTCTCTCCCTCC;RSEQ=TGTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:48,51:99,2:0.0196:2,2:29.5:1:32.1:1:1:1.06:20:4:0.0213:0:1.5 0/0:117:0:0,0:64,53:117,0:0:2,0:24:1:28.4:1:1:0:46.6:18.5:1:0:0.4 +GL000220.1 129180 . G C 103 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02017;SOR=5.46713;LSEQ=CTCTCTCTCTCTCACTCACT;RSEQ=TCTCTCCGTCTCTCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:52,59:111,2:0.0174:2,2:18:0:35:1:1:1.13:20:4:0.0177:0:1.5 0/1:124:11:6,5:61,52:113,11:0.0887:2,2:15.1:1:30:1:1:1.02:39.3:10:0.087:0:2.5 +GL000220.1 129184 . C G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49826;SOR=Inf;LSEQ=CTCTCTCTCACTCACTGTCT;RSEQ=TCCGTCTCTCTCTCTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:57,63:120,0:0:2,0:23.4:1:32.9:1:1:0:55.5:119:1:0:0.2 0/1:126:2:1,1:66,58:124,2:0.0159:2,2:35:0:33.5:1:1:1.13676:31:4:0.0168:0:1.5 +GL000220.1 129187 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=1.000;MSILEN=1;SSF=0.23537;SOR=Inf;LSEQ=TCTCTCACTCACTGTCTCTC;RSEQ=GTCTCTCTCTCTTTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:64,66:130,0:0:2,0:22.1:1:30.3:1:1:0:55.7:31.5:1:0:0.2 0/1:123:2:1,1:65,56:121,2:0.0163:2,2:11.5:1:27:1:1:1.1593:51:4:0.0179:0:1.5 +GL000220.1 129228 . TTCTGTGTG T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=0.50023;SOR=Inf;LSEQ=GTTTCTCTCTGTCTCTGTCT;RSEQ=TCTGTCTGTCTCTCTCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:134:0:0,0:67,67:134,0:0:2,0:27.1:1:30.7:1:1:0:58:133:1:0:0.3 0/1:152:2:1,1:71,79:150,2:0.0132:2,2:20.5:1:27.5:1:1:1.11:57.5:4:0.0136:0.0066:1.5 +GL000220.1 129230 . CTGTG C 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.20102;SOR=1.86065;LSEQ=TTCTCTCTGTCTCTGTCTTT;RSEQ=TGTCTGTCTGTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:8:4,4:63,61:124,8:0.0606:2,2:33.3:1:32.2:1:1:1.03254:54.3:16:0.0611:0.0076:1.4 0/1:149:16:7,9:63,69:132,16:0.1074:2,2:31.1:1:30.4:1:0.79741:1.17265:44.9:15:0.1049:0:1.9 +GL000220.1 129234 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=2;SSF=0.49929;SOR=Inf;LSEQ=CTCTGTCTCTGTCTTTCTGT;RSEQ=TGTCTGTCTGTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:65,61:126,0:0:2,0:26.3:1:32.3:1:1:0:58.6:125:1:0:0.3 0/1:146:2:1,1:60,67:127,2:0.0137:2,2:35:1:30.5:1:1:1.12:43.5:4:0.0157:0:3.5 +GL000220.1 129240 . GTCTGTC G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=5.000;MSILEN=2;SSF=0.50193;SOR=Inf;LSEQ=CTCTGTCTTTCTGTGTGTCT;RSEQ=TCTCTCTCTATTTGTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:63,64:127,0:0:2,0:27.5:1:30.4:1:1:0:58.6:254:1:0:0.4 0/1:151:2:1,1:71,78:149,2:0.0132:2,2:35:1:30.5:1:1:1.10:43.5:4:0.0135:0:3.5 +GL000220.1 129256 . A G 135 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05151;SOR=2.32626;LSEQ=GTCTGTCTGTCTCTCTCTCT;RSEQ=TTTGTCTTTCTCCCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:9:4,5:56,62:118,9:0.0703:2,2:32.3:1:32.7:1:1:1.12796:50.7:18:0.0756:0:1.8 0/1:140:21:10,11:54,63:117,21:0.15:2,2:26.5:1:30.9:1:1:1.06:44.7:42:0.1667:0:2 +GL000220.1 129313 . C T 164 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08547;SOR=0.53764;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CTGTCTGTCTGTTTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:39:15,24:7,17:24,39:0.5132:2,2:27.3:1:31.2:1:0.58818:1.51:47:38:0.6333:0:1.5 0/1:61:22:7,15:6,13:19,22:0.3607:2,2:21.6:1:28.7:1:1:1.01:50.5:21:0.5385:0:1.4 +GL000220.1 129329 . T A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=1;SOR=1.03812;LSEQ=TCTCCCTGTCTGTCTGTTTC;RSEQ=CTCTATCTCTCGCTGTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:8:4,4:20,34:54,8:0.129:2,2:32.9:1:29.5:1:0.69953:1.68:32.5:16:0.129:0:1.8 0/1:45:6:3,3:13,26:39,6:0.1333:2,2:19.2:1:25.7:1:0.65008:1.97:30.8:5:0.1163:0:2.8 +GL000220.1 129667 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.50274;SOR=Inf;LSEQ=GTCCTAAGGGTCGATTTAGT;RSEQ=TCATGCCTCTTTCACCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:13,18:31,0:0:2,0:22:1:33:1:1:0:53.6:62:1:0:0.2 0/1:41:2:1,1:19,20:39,2:0.0488:2,2:42.5:1:29:1:1:1.05:60:4:0.0488:0:1 +GL000220.1 129728 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51954;SOR=Inf;LSEQ=GATCGGCTAAATACCGCGTG;RSEQ=TCTCATCTAGAAGTGGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:4,7:11,0:0:2,0:16.7:1:30.2:1:1:0:54.9:22:1:0:0.1 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:9.5:1:31.5:1:1:1.11803:46.5:4:0.1053:0:1 +GL000220.1 129989 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.16757;SOR=0;LSEQ=CGACAAATAAAAGTTCGGGG;RSEQ=GGAGAAGAGAGGAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:18,11:29,2:0.0645:2,2:9.5:1:30:1:1:1.60957:60:4:0.0667:0:1.5 0/0:44:0:0,0:30,14:44,0:0:2,0:23.3:1:30:1:1:0:54.7:21:1:0:0.6 +GL000220.1 130027 . GGGGGGA TGGG 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=6.000;MSILEN=1;SSF=0.05474;SOR=0;LSEQ=GAGAGAGAGACGGGGAGAGA;RSEQ=GAGGGGGGGGGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:11,6:17,3:0.15:2,2:16.7:1:25.6:1:0.53684:3.42394:32.7:6:0.1875:0.1:1.3 0/0:31:0:0,0:24,7:31,0:0:2,0:21.4:1:31.1:1:1:0:54.4:62:1:0:1 +GL000220.1 130035 . AG A 33 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.195;LSEQ=GACGGGGAGAGAGGGGGGAG;RSEQ=GGGGGGGGAGAGAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:1:1,0:11,4:15,1:0.0625:2,0:46:0:29:0:1:0:52:2:0.0667:0:0 0/1:27:2:2,0:19,6:25,2:0.0741:2,0:30:1:33:0:1:0:54.5:4:0.0769:0:0 +GL000220.1 130043 . G A 45 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=1;SOR=1.86306;LSEQ=GAGAGGGGGGAGAGGGGGGG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:9,1:10,1:0.0769:2,0:39:0:16:0:0.18182:0:23:0:0:0:3 0/1:22:3:2,1:15,2:17,3:0.1364:2,2:24:1:29:1:0.40351:3.42835:57:6:0.15:0:1.7 +GL000220.1 130045 . A G 40 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=23.000;MSILEN=2;SSF=0.13382;SOR=0.16792;LSEQ=GAGGGGGGAGAGGGGGGGGG;RSEQ=GAGAGAGAGAGAGAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:2,1:8,2:10,3:0.2308:2,2:21.7:1:25.7:1:1:1.88511:50.3:2:0.25:0:3 0/1:22:1:0,1:13,2:15,1:0.0455:2,0:12:0:32:0:0.1875:0:40:2:0.0625:0:4 +GL000220.1 130109 . C A 56 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.05544;SOR=0;LSEQ=AGAAAGAGAAGTAAAACCAA;RSEQ=CACCACCTCCTTGACCTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:3,2:19,20:39,5:0.1136:2,2:38.4:1:24.4:1:1:1.56:32.8:1.5:0.0789:0:2.8 0/0:44:0:0,0:24,20:44,0:0:2,0:27:1:29.4:1:1:0:46.7:7.8:1:0:0.7 +GL000220.1 130131 . CA C 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24064;SOR=0;LSEQ=ACCACCTCCTTGACCTGAGT;RSEQ=GGGGGTTTCTGGCCTTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:3:1,2:20,14:34,3:0.0811:2,2:31:1:31.3:1:0.56757:2.7768:32.7:6:0.0882:0:2.7 0/0:34:0:0,0:19,15:34,0:0:2,0:23.9:1:28.7:1:1:0:47.4:16:1:0:0.6 +GL000220.1 130669 . T TA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=4;SSF=0.20168;SOR=0;LSEQ=CCGCGCACATAATAACTAAC;RSEQ=AACTAACTAACTAACTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:1,1:8,6:14,2:0.125:2,2:9.5:1:30.2:1:1:1.30929:60:4:0.125:0.0625:0 0/0:19:0:0,0:11,8:19,0:0:2,0:23.5:1:29.2:1:1:0:55.3:38:1:0:0.3 +GL000220.1 131027 . A C 33 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATAAATACGTACATAAATA;RSEQ=ATACACACATACATACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:12:0:32:0:1:0:25:2:1:0:0 0/1:6:2:2,0:2,2:4,2:0.3333:2,0:28:1:33.5:1:0.46667:0:44:4:0.3333:0:1.5 +GL000220.1 131033 . C T 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=TACGTACATAAATAAATACA;RSEQ=ACATACATACATACATACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:18:0:34:0:1:0:25:2:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:11:0:30.5:1:1:2.44949:26:4:0.3333:0:1 +GL000220.1 131211 . C CTCTG 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=27;MSI=7.000;MSILEN=4;SSF=1;SOR=0.90109;LSEQ=CTTTCTCTCTGTGTCTCTTT;RSEQ=TCTGTCTGTCTGTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:10:5,5:19,15:34,10:0.2273:2,2:26.7:1:33.4:1:1:1.25983:50.8:20:0.2273:0.0455:0.4 0/1:43:9:3,6:15,19:34,9:0.2093:2,2:20.3:1:30:1:0.7117:1.56264:53.4:18:0.2093:0.0465:0.7 +GL000220.1 131247 . C T 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23273;SOR=Inf;LSEQ=GTCTGTCTGTCTCTTTCTTT;RSEQ=TTTCTGTCTCTGTCTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:45,36:81,0:0:2,0:23.2:1:33.2:1:1:0:52.6:162:1:0:0.2 0/1:76:2:1,1:33,41:74,2:0.0263:2,2:5:0:32:1:1:1.24:35:4:0.0267:0:0.5 +GL000220.1 131280 . TCTCTGCCTGTCTCACTGTGTCTGTCT CCTGTCTGTTTCTCTCTCTCTCTCTCTCTCTGTCTCCCTCTCTTGCTCTC 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.12068;SOR=Inf;LSEQ=TCTTTGTCCCTCTCTCTCCC;RSEQ=TCTATCTTACTCTCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:52,34:86,0:0:2,0:24.7:1:32.4:1:1:0:54.4:172:1:0:0.2 0/1:87:4:2,2:41,42:83,4:0.046:2,2:23.5:1:28.6:1:1:1.02:54.3:8:0.046:0.046:0.3 +GL000220.1 131285 . G A 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.60925;SOR=2.1718;LSEQ=GTCCCTCTCTCTCCCTCTCT;RSEQ=CCTGTCTCACTGTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:1:1,0:47,37:84,1:0.0118:2,0:1:0:26:0:1:0:60:2:0.0119:0:1 0/1:79:2:2,0:39,38:77,2:0.0253:2,0:25.5:1:26.5:1:0.49432:0:60:4:0.026:0:1 +GL000220.1 131310 . A G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.76763;SOR=0.74165;LSEQ=TCTCACTGTGTCTGTCTTCT;RSEQ=TCTTACTCTCTTTCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:7:3,4:44,41:85,7:0.0761:2,2:14.1:1:31:1:0.71109:1.42534:32.4:14:0.0761:0:2.3 0/1:87:5:3,2:43,38:81,5:0.0575:2,2:10.4:1:30.4:1:1:1.32:31.4:10:0.0581:0:2.2 +GL000220.1 131327 . TC T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.21842;SOR=0;LSEQ=TCTATCTTACTCTCTTTCTC;RSEQ=CCCGTCTGTCTCTCTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:45,43:88,2:0.0222:2,2:21.5:1:32:1:1:1.046:60:4:0.0222:0:0 0/0:102:0:0,0:52,49:101,0:0:2,0:23.6:1:30.2:1:1:0:52.4:49.5:1:0:0.4 +GL000220.1 131331 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50156;SOR=Inf;LSEQ=TCTTACTCTCTTTCTCTCCC;RSEQ=GTCTGTCTCTCTCTCACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:45,46:91,0:0:2,0:25.5:1:30.3:1:1:0:54.7:182:1:0:0.3 0/1:109:2:1,1:56,50:106,2:0.0183:2,2:22.5:1:28:1:1:1.11882:47.5:4:0.0187:0:1 +GL000220.1 131332 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50199;SOR=Inf;LSEQ=CTTACTCTCTTTCTCTCCCC;RSEQ=TCTGTCTCTCTCTCACTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:45,46:91,0:0:2,0:25.5:1:30.9:1:1:0:54.7:182:1:0:0.3 0/1:110:2:1,1:57,51:108,2:0.0182:2,2:9.5:1:28:1:1:1.11651:59:4:0.0185:0:1 +GL000220.1 131347 . A T 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.77567;SOR=0.75002;LSEQ=TCCCCGTCTGTCTCTCTCTC;RSEQ=CTCCCTCCCTGTCTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:7:3,4:45,45:90,7:0.0722:2,2:41.1:1:30.7:1:1:1.3294:32.4:14:0.0753:0:2.3 0/1:109:6:3,3:53,50:103,6:0.055:2,2:38.2:1:30.5:1:1:1.05946:24.2:12:0.0577:0:2.3 +GL000220.1 131364 . TTC T 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.4734;SOR=1.33992;LSEQ=CTCACTCCCTCCCTGTCTGT;RSEQ=TCTCTCTCTCTCTTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:16:8,8:38,42:80,16:0.1649:2,2:29.3:1:30.9:1:1:1.10:36.1:32:0.1667:0:1.1 0/1:105:22:11,11:42,42:84,22:0.2095:2,2:27.4:1:29.7:1:1:1:36.1:44:0.2115:0.0476:1.3 +GL000220.1 131386 . CTGTT C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49902;SOR=Inf;LSEQ=CTCTCTCTCTCTCTTTCTGT;RSEQ=TCTGTCTCTCTCTGTCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:46,45:91,0:0:2,0:26.5:1:31.4:1:1:0:55.7:182:1:0:0.2 0/1:103:2:1,1:51,50:101,2:0.0194:2,2:25.5:1:30:1:1:1.01981:30:4:0.0196:0:2.5 +GL000220.1 131388 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2181;SOR=0;LSEQ=CTCTCTCTCTCTTTCTGTCT;RSEQ=TTTCTGTCTCTCTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:44,43:87,2:0.0225:2,2:25.5:1:30:1:1:1.023:60:4:0.0225:0:1 0/0:101:0:0,0:50,48:98,0:0:2,0:25.6:1:31.6:1:1:0:53.8:97:0.9898:0:0.3 +GL000220.1 131395 . TCTCTCTCTGTCTGC T 54 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=2.000;MSILEN=1;SSF=0.6876;SOR=1.75508;LSEQ=TCTCTTTCTGTCTGTTTCTG;RSEQ=CTCTCTCTTTCTCTATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:2:1,1:41,47:88,2:0.0222:2,2:20:1:30:1:1:1.14:33:4:0.0222:0.0111:1.5 0/1:104:4:2,2:48,52:100,4:0.0385:2,2:4.7:1:27.3:1:1:1.08:31.3:4:0.0356:0.0331:2.5 +GL000220.1 131398 . C T 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=2;SSF=1;SOR=1.86764;LSEQ=CTTTCTGTCTGTTTCTGTCT;RSEQ=TCTCTGTCTGCCTCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:90:1:0,1:42,46:88,1:0.0111:2,0:1:0:25:0:1:0:60:2:0.0114:0:2 0/1:97:2:1,1:47,48:95,2:0.0206:2,2:18.5:1:28.5:1:1:1.02:30:4:0.0208:0:2.5 +GL000220.1 131399 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=2;SSF=0.49786;SOR=Inf;LSEQ=TTTCTGTCTGTTTCTGTCTC;RSEQ=CTCTGTCTGCCTCTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:44,47:91,0:0:2,0:24.4:1:30.7:1:1:0:55.1:90:1:0:0.3 0/1:98:2:1,1:48,48:96,2:0.0204:2,2:10.5:1:27:1:1:1:42:4:0.0211:0:1.5 +GL000220.1 131401 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=2;SSF=0.49874;SOR=Inf;LSEQ=TCTGTCTGTTTCTGTCTCTC;RSEQ=CTGTCTGCCTCTCTCTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:44,48:92,0:0:2,0:24:1:30.9:1:1:0:55.7:184:1:0:0.2 0/1:103:2:1,1:50,51:101,2:0.0194:2,2:31.5:1:30:1:1:1.02:31:4:0.02:0:1.5 +GL000220.1 131450 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=0.49721;SOR=0;LSEQ=CTCTTTCTCTGTCTGTCTGC;RSEQ=CCTCTCTTTCTTTTTCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:44,41:85,2:0.023:2,2:18.5:1:30.5:1:1:1.07227:21:4:0.023:0:1.5 0/0:84:0:0,0:43,41:84,0:0:2,0:25.2:1:30.4:1:1:0:52.5:41:1:0:0.3 +GL000220.1 131478 . G C 39 p8;q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.62142;SOR=0.3522;LSEQ=TTCTTTTTCTGTGTCTCTCT;RSEQ=TCTGTCTCTCTCTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:3:1,2:41,42:83,3:0.0349:2,2:7.7:1:24.7:1:1:1.9378:23.7:2:0.0244:0:4.7 0/1:80:1:1,0:40,39:79,1:0.0125:2,0:10:0:33:0:1:0:21:2:0.013:0:3 +GL000220.1 131482 . GTC G 61 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0.77098;LSEQ=TTTTCTGTGTCTCTCTGTCT;RSEQ=TCTCTCTCTCTCTGTGCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:4:1,3:37,40:77,4:0.0488:2,2:5.3:1:30.7:1:0.61844:2.74346:42.5:8:0.0494:0.0366:0.8 0/1:79:3:1,2:42,34:76,3:0.038:2,2:25.3:1:31:1:0.58892:2.44296:43:6:0.039:0:0.3 +GL000220.1 131497 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.23573;SOR=Inf;LSEQ=TGTCTGTCTCTCTCTCTCTC;RSEQ=GTGCCTATCTTCTGTCTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:39,41:80,0:0:2,0:19.4:1:30.6:1:1:0:45.7:79:1:0:0.4 0/1:76:2:1,1:38,35:73,2:0.0263:2,2:27.5:1:29:1:1:1.08451:39.5:4:0.0267:0:1 +GL000220.1 131537 . G GTTTCTCTCTCTCTCTCTTTCTGTCTGTT 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.08617;SOR=Inf;LSEQ=CTCTCTTTCTCTGCCTGTCT;RSEQ=TCTGTCTCTCTCTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:91:0:0,0:46,44:90,0:0:2,0:28.3:1:32:1:1:0:50.6:21.5:1:0:0.5 0/1:73:3:1,2:35,34:69,3:0.0411:2,2:14:1:27.5:1:1:2.03895:58.3:6:0.0435:0.0411:0.3 +GL000220.1 131545 . C CTCTCCCTGTCTCTCTTTCTCTATATCTGTCTTTCTCTCTCTG 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=2;SSF=0.11104;SOR=Inf;LSEQ=CTCTGCCTGTCTGTCTGTCT;RSEQ=TCTCTGTCTCTCCCTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:46,46:92,0:0:2,0:29.3:1:32.8:1:1:0:51.6:29.667:1:0:0.5 0/1:88:3:2,1:41,42:83,3:0.0341:2,2:20:1:28.1:1:1:2.03:60:6:0.0349:0.0341:0.3 +GL000220.1 131565 . T C 39 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.32677;SOR=3.77711;LSEQ=CTCTCTGTCTCTCCCTCCCT;RSEQ=TCTGCTTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:1:0,1:57,57:114,1:0.0087:2,0:49:0:29:0:1:0:60:2:0.0092:0:4 0/1:93:3:1,2:46,42:88,3:0.0323:2,2:30.7:1:24.7:1:0.60848:2.17225:55.3:2:0.0244:0:1.7 +GL000220.1 131594 . C T 62 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.69196;SOR=0.59929;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CCCCTCCCTGTCTGTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:4:1,3:61,55:116,4:0.0333:2,2:18.3:1:31.3:1:0.35245:3.29655:42:8:0.0339:0:2 0/1:99:2:1,1:48,46:94,2:0.0202:2,2:12.5:1:29:1:1:1.04303:52:4:0.0211:0:1 +GL000220.1 131614 . CT C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.23118;SOR=Inf;LSEQ=CCCCCTCCCTGTCTGTTTCT;RSEQ=CTGTCTCCCTCTCTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:59,56:115,0:0:2,0:23.1:1:30.6:1:1:0:56.7:22:1:0:0.4 0/1:107:2:1,1:56,48:104,2:0.0187:2,2:13.5:1:30:1:1:1.16496:60:4:0.0189:0:0.5 +GL000220.1 131616 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49838;SOR=0;LSEQ=CCCTCCCTGTCTGTTTCTCT;RSEQ=TGTCTCCCTCTCTTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:2:1,1:56,56:112,2:0.0175:2,2:21.5:1:29.5:1:1:1:33.5:4:0.018:0:1 0/0:106:0:0,0:56,49:105,0:0:2,0:23.7:1:31.1:1:1:0:57.9:104:1:0:0.3 +GL000220.1 131654 . CTCTG C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.21952;SOR=2.05139;LSEQ=GTCTGTTTCTCACTGTCTCT;RSEQ=TCTGTCTGTTTCATTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:6:2,4:56,50:106,6:0.0531:2,2:33.5:1:34:1:0.42632:2.22434:60:12:0.0541:0:0 0/1:116:12:5,7:56,48:104,12:0.1034:2,2:26.2:1:31.1:1:0.54531:1.62641:57.6:24:0.1043:0:0.1 +GL000220.1 131665 . T A 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=4;SSF=0.23399;SOR=0;LSEQ=ACTGTCTCTCTCTGTCTGTC;RSEQ=GTTTCATTCTCTCTGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:57,53:110,2:0.0179:2,2:5:0:33:1:1:1.07475:60:4:0.0183:0:1 0/0:119:0:0,0:65,54:119,0:0:2,0:24.4:1:30:1:1:0:57.7:238:1:0:0.3 +GL000220.1 131681 . T C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=6;SSF=0.49859;SOR=Inf;LSEQ=TGTCTGTTTCATTCTCTCTG;RSEQ=CTCTGTCTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:0:0,0:60,51:111,0:0:2,0:24.7:1:29.9:1:1:0:59.3:54.5:0.9909:0:0.2 0/1:121:2:1,1:62,57:119,2:0.0165:2,2:5.5:1:29:1:1:1.08695:51:4:0.0165:0:1.5 +GL000220.1 131686 . GTCTCTGTC G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=7.000;MSILEN=2;SSF=0.24661;SOR=Inf;LSEQ=GTTTCATTCTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:0:0,0:59,52:111,0:0:2,0:25.1:1:29.6:1:1:0:58.7:36:1:0:0.2 0/1:110:2:1,1:56,52:108,2:0.0182:2,2:43.5:1:31.5:1:1:1.07617:60:4:0.0182:0:0 +GL000220.1 131692 . GTC G 122 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.38516;SOR=0.6568;LSEQ=TTCTCTCTGTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:14:10,4:54,47:101,14:0.1197:2,2:30.5:1:32.1:1:0.25816:2.16:60:28:0.1207:0.0171:0.4 0/1:110:9:5,4:51,48:99,9:0.0818:2,2:30.2:1:32.4:1:1:1.17:57.1:18:0.0841:0:0 +GL000220.1 131700 . C CACTGTGTCTGTCTCTCTCTTTCCT 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.23166;SOR=Inf;LSEQ=GTCTCTGTCTCTGTCTCTCT;RSEQ=TCTCTCTGTCTCTCCCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:67,50:117,0:0:2,0:25.3:1:32.3:1:1:0:57.8:116:0.9915:0:0.2 0/1:110:2:1,1:54,53:107,2:0.0182:2,2:19.5:1:27.2:1:1:1.0187:45.5:4:0.0187:0.0182:0.5 +GL000220.1 131773 . GTC G 70 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.21994;SOR=4.45272;LSEQ=GCCTGTCCGTCTGTCTGTCT;RSEQ=TCTCTCTCTCCCTGTCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:112:1:0,1:55,56:111,1:0.0089:2,0:39:0:28:0:1:0:60:2:0.0091:0:1 0/1:129:5:2,3:59,63:122,5:0.0388:2,2:17.6:1:30.4:1:1:1.40105:59:10:0.0394:0:0.2 +GL000220.1 131841 . G C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.06145;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTGTCTTTCTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:56,58:114,0:0:2,0:27.3:1:30.4:1:1:0:57.2:7.769:1:0:0.4 0/1:127:5:2,3:59,62:121,5:0.0394:2,2:15.4:1:31.6:1:1:1.42344:45.8:10:0.0413:0:2.4 +GL000220.1 131847 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=6;SSF=0.49794;SOR=Inf;LSEQ=CTCTCTCTCTCTCTGTCTCT;RSEQ=TCTTTCTCTGTCTGTCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:61,60:121,0:0:2,0:25.8:1:31.5:1:1:0:56.1:16.286:1:0:0.4 0/1:122:2:1,1:57,60:117,2:0.0164:2,2:12:1:29:1:1:1.05:43:4:0.0169:0:3.5 +GL000220.1 131851 . T G 39 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.24699;SOR=Inf;LSEQ=CTCTCTCTCTGTCTCTGTCT;RSEQ=TCTCTGTCTGTCCCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:59,62:121,0:0:2,0:25.5:1:29.1:1:1:0:55.5:9.083:1:0:0.3 0/1:124:3:2,1:57,62:119,3:0.0242:2,2:6.3:1:25:1:0.60972:2.16:48.7:2:0.0171:0:2.7 +GL000220.1 131877 . G C 30 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49977;SOR=Inf;LSEQ=GTCTGTCCCTTTCTCTGTCT;RSEQ=TCTGCCTCTCTCTTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:64,56:120,0:0:2,0:24.5:1:31.3:1:1:0:49.9:14:1:0:0.4 0/1:135:2:1,1:67,65:132,2:0.0148:2,2:5:0:30:1:1:1.03054:40:4:0.0149:0:0 +GL000220.1 131882 . C T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=1;SSF=0.24757;SOR=Inf;LSEQ=TCCCTTTCTCTGTCTGTCTG;RSEQ=CTCTCTCTTTCTCTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:65,56:121,0:0:2,0:24:1:30.2:1:1:0:48.1:9.083:1:0:0.4 0/1:128:3:3,0:64,61:125,3:0.0234:2,0:14.3:1:22:1:0.24576:0:49:2:0.0169:0:2 +GL000220.1 131893 . C T 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.21619;SOR=0;LSEQ=GTCTGTCTGCCTCTCTCTTT;RSEQ=TCTTTCTGTGTCTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:57,51:108,2:0.0182:2,2:6:0:33:0:1:1.11651:20:4:0.0185:0:2.5 0/0:126:0:0,0:66,60:126,0:0:2,0:23.8:1:30.8:1:1:0:43.7:41:1:0:0.3 +GL000220.1 131939 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50226;SOR=Inf;LSEQ=CTCTGTGCCTATCTTCTGTC;RSEQ=TACTCTCTTTCTCTGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:48,52:100,0:0:2,0:24.1:1:31:1:1:0:36.8:99:1:0:0.3 0/1:121:2:1,1:56,61:117,2:0.0165:2,2:42.5:1:31.5:1:1:1.09:28:4:0.0165:0:1 +GL000220.1 131962 . A G 79 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.31713;SOR=0.44587;LSEQ=CTCTCTTTCTCTGCCTGTCT;RSEQ=TCTGTCTGTCTCTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:6:2,4:52,60:112,6:0.0508:2,2:7.3:1:30.8:1:0.68638:1.72557:22.8:12:0.0522:0:1.3 0/1:129:3:1,2:62,63:125,3:0.0233:2,2:6.3:1:29.3:1:1:1.95824:23.3:6:0.0242:0:1 +GL000220.1 131966 . GTCTGTCTCTC G 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=4.000;MSILEN=2;SSF=0.83637;SOR=0.90724;LSEQ=CTTTCTCTGCCTGTCTATCT;RSEQ=TCTGTCTCTCTCCCTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:13:6,7:50,62:112,13:0.104:2,2:22:1:31.2:1:1:1.06:42.7:26:0.1057:0.04:0.2 0/1:126:12:4,8:58,56:114,12:0.0952:2,2:31.3:1:32.7:1:0.36422:2.05982:45.8:24:0.0976:0.0159:0.4 +GL000220.1 131969 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.23048;SOR=0;LSEQ=TCTCTGCCTGTCTATCTGTC;RSEQ=GTCTCTCTCTGTCTCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:45,58:103,2:0.0174:2,2:33:1:30:1:1:1.29:28:4:0.019:0:1 0/0:124:0:0,0:59,55:114,0:0:2,0:24.7:1:29.6:1:1:0:35.6:27.5:1:0:0.3 +GL000220.1 132003 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=7;MSI=6.000;MSILEN=2;SSF=0.2246;SOR=Inf;LSEQ=TCTCTCCCTGCCTTTCTGTT;RSEQ=CTCTCTCTCTCCCTCTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:48,68:116,0:0:2,0:29.2:1:30.7:1:1:0:35.9:115:1:0:0.2 0/1:105:2:1,1:47,56:103,2:0.019:2,2:18:0:32.5:1:1:1.19:22:4:0.0192:0:1.5 +GL000220.1 132056 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.20337;SOR=Inf;LSEQ=TTCTCTCTTTCTCTCTGTTT;RSEQ=TCTGTCTCTCTCTGTCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:31,39:70,0:0:2,0:17.3:1:31.7:1:1:0:31.7:34:1:0:0.2 0/1:58:2:2,0:27,29:56,2:0.0345:2,0:20.5:1:26:1:0.49123:0:27:4:0.0345:0:1 +GL000220.1 132074 . G A 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26699;SOR=2.73017;LSEQ=TTCTCTGTCTCTCTCTGTCC;RSEQ=TCTCTGTCTTTTTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:0,2:30,36:66,2:0.0294:2,0:24:1:31.5:1:0.49956:0:26:4:0.0294:0:1 0/1:65:5:4,1:29,30:59,5:0.0769:2,2:23.4:1:26.2:1:0.35597:4.06:24.6:4:0.0645:0:1.8 +GL000220.1 132081 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4985;SOR=Inf;LSEQ=TCTCTCTCTGTCCGTCTCTG;RSEQ=CTTTTTCTGTCTGTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:28,36:64,0:0:2,0:25.9:1:30.5:1:1:0:43.7:128:1:0:0.2 0/1:73:2:1,1:35,36:71,2:0.0274:2,2:10.5:1:32:1:1:1.03:40:4:0.0274:0:1 +GL000220.1 132084 . TTTTCTGTCTGTCTGTCTCTCTCTTTC A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49847;SOR=Inf;LSEQ=CTCTCTGTCCGTCTCTGTCT;RSEQ=TTTCTGTCGTCTGTCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:27,40:67,0:0:2,0:26.1:1:30.8:1:1:0:43.8:134:1:0:0.2 0/1:76:2:1,1:37,37:74,2:0.0263:2,2:9.5:1:27.9:1:1:1:45:4:0.0274:0.0263:0 +GL000220.1 132098 . G C 29 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=4;SSF=1;SOR=1.53961;LSEQ=CTGTCTTTTTCTGTCTGTCT;RSEQ=TCTCTCTCTTTCTTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:1:0,1:32,39:71,1:0.0139:2,0:6:0:16:0:1:0:54:0:0:0:4 0/1:94:2:1,1:47,42:89,2:0.0213:2,2:7.5:1:29.5:1:1:1.11766:44:4:0.0217:0:4.5 +GL000220.1 132108 . T C 60 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=1.48335;LSEQ=CTGTCTGTCTGTCTCTCTCT;RSEQ=TCTTTCTGTCGTCTGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:0,2:38,43:81,2:0.0241:2,0:31:1:15.5:1:0.4975:0:57:0:0:0:2.5 0/1:113:4:2,2:55,52:107,4:0.0354:2,2:13.8:1:30:1:1:1.05718:45:8:0.0367:0:3.3 +GL000220.1 132112 . T C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.13861;SOR=Inf;LSEQ=CTGTCTGTCTCTCTCTTTCT;RSEQ=TCTGTCGTCTGTCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:43,47:90,0:0:2,0:24.2:1:30.9:1:1:0:49.4:44:1:0:0.2 0/1:122:4:2,2:59,59:118,4:0.0328:2,2:17.8:1:30:1:1:1:45:8:0.0345:0:3.3 +GL000220.1 132119 . GTCTGTC G 116 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=4.000;MSILEN=6;SSF=0.01383;SOR=5.69652;LSEQ=TCTCTCTCTTTCTTTCTGTC;RSEQ=TCTGTCTCTGTCTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:2,0:45,45:90,2:0.0217:2,0:15.5:1:32:0:0.49474:0:60:4:0.0225:0:0 0/1:115:13:5,8:50,52:102,13:0.113:2,2:24.7:1:31.6:1:0.56291:1.53278:48.3:26:0.115:0.0174:0.7 +GL000220.1 132162 . C A 21 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.70751;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=TTGTCTCTCTCACTGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:2:1,1:46,43:89,2:0.022:2,2:16.5:1:27.5:1:1:1.06894:52.5:4:0.0235:0:1 0/1:128:2:1,1:62,63:125,2:0.0156:2,2:23:1:21.5:1:1:1.02:33:1:0.0083:0:1.5 +GL000220.1 132169 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.51377;SOR=Inf;LSEQ=CTCTCTCTCTCTCCTTGTCT;RSEQ=TCTCACTGTGTCTGTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:48,44:92,0:0:2,0:27.8:1:31.9:1:1:0:55.9:29.667:1:0:0.3 0/1:132:2:1,1:64,65:129,2:0.0152:2,2:38:1:27:1:1:1.02:60:4:0.0154:0:1 +GL000220.1 132201 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25013;SOR=Inf;LSEQ=CTGTCTTCTGTCTTACTCTC;RSEQ=TTCTCTGCCTGTCCATCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:53,48:101,0:0:2,0:23.4:1:31.2:1:1:0:56.6:19.2:1:0:0.2 0/1:116:3:0,3:55,57:112,3:0.0259:2,0:14.7:1:28.3:1:0.24485:0:55:6:0.0273:0:2 +GL000220.1 132215 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1.79885;LSEQ=ACTCTCCTTCTCTGCCTGTC;RSEQ=ATCTGTCTGTCTGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:1:0,1:50,50:100,1:0.0098:2,0:41:0:11:0:1:0:39:0:0:0:7 0/1:114:2:1,1:55,56:111,2:0.0175:2,2:10.5:1:27.5:1:1:1.02:53:4:0.0182:0:1.5 +GL000220.1 132216 . ATCTG A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=3.000;MSILEN=4;SSF=0.73518;SOR=0.66332;LSEQ=CTCTCCTTCTCTGCCTGTCC;RSEQ=TCTGTCTGTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:5:3,2:46,50:96,5:0.0495:2,2:18.6:1:30.8:1:0.67188:1.62:36.8:10:0.0505:0:1.4 0/1:120:4:3,1:56,58:114,4:0.0333:2,2:27:1:31.5:1:0.61851:3.08:41:8:0.0336:0.0083:1.3 +GL000220.1 132248 . A C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.82939;SOR=1.13035;LSEQ=GTCTCTCTCTCTCTCTCCCT;RSEQ=CCTTTCTGTTTCTCTCTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:10:4,6:50,57:107,10:0.0855:2,2:31.8:1:30.1:1:0.75079:1.31274:41.5:9:0.0811:0:1.3 0/1:136:13:7,6:66,56:122,13:0.0956:2,2:23.5:1:29.3:1:1:1.01013:46.8:12:0.0938:0:1.7 +GL000220.1 132262 . CTCTCGCTAG GTCT 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.50309;SOR=Inf;LSEQ=CTCCCTACCTTTCTGTTTCT;RSEQ=CTCTCTCTCTCTCTGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:56,61:117,0:0:2,0:24.7:1:32.7:1:1:0:57.4:116:1:0:0.2 0/1:143:2:1,1:75,66:141,2:0.014:2,2:36:0:31.6:1:1:1.13534:39:4:0.0142:0:3.5 +GL000220.1 132271 . GCT G 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.2355;SOR=2.48728;LSEQ=TTTCTGTTTCTCTCTCGCTA;RSEQ=CTCTCTCTCTCTGCCTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:3:2,1:52,51:103,3:0.028:2,2:32.3:1:34.7:1:1:1.95:58:6:0.0291:0:0.3 0/1:134:9:4,5:68,57:125,9:0.0672:2,2:21.2:1:31.7:1:0.73244:1.48675:59.2:18:0.0687:0.0299:0.1 +GL000220.1 132322 . C G 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.25381;SOR=Inf;LSEQ=CTCTCTCTGTCTTTCTCTGT;RSEQ=TGTCTCTTTCTCTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:102:0:0,0:51,51:102,0:0:2,0:23.4:1:32.1:1:1:0:54.2:19.4:1:0:0.3 0/1:124:3:2,1:60,61:121,3:0.0242:2,2:14.3:1:24.3:1:1:2.02:52:2:0.0164:0:1 +GL000220.1 132323 . T C 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.000;MSILEN=4;SSF=0.50287;SOR=Inf;LSEQ=TCTCTCTGTCTTTCTCTGTC;RSEQ=GTCTCTTTCTCTGTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:53,50:103,0:0:2,0:23.1:1:31:1:1:0:54.2:24.75:1:0:0.3 0/1:126:2:1,1:62,62:124,2:0.0159:2,2:8:1:27.5:1:1:1:60:4:0.0159:0:1.5 +GL000220.1 132326 . CTCTTTCTCTG C 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=4;SSF=0.03948;SOR=Inf;LSEQ=CTCTGTCTTTCTCTGTCTGT;RSEQ=TCTGTCTGTCTCTTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:53,45:98,0:0:2,0:24.1:1:30.6:1:1:0:53.9:15.333:1:0:0.2 0/1:132:6:3,3:65,61:126,6:0.0455:2,2:11.3:1:29.8:1:1:1.06503:46.7:12:0.0462:0.0455:1 +GL000220.1 132352 . CTCTCTG C 85 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=3.000;MSILEN=6;SSF=0.05474;SOR=0.14388;LSEQ=CTCTGTCTGTCTGTCTCTTT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:6:1,5:58,44:102,6:0.0556:2,2:16:1:33.2:1:0.08965:6.48853:49.2:12:0.0571:0.037:0.7 0/0:120:1:0,1:57,62:119,1:0.0083:2,0:14:0:33:0:1:0:60:2:0.0084:0:0 +GL000220.1 132362 . C G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=6;SSF=0.49809;SOR=Inf;LSEQ=CTGTCTCTTTCTCTCTGTCT;RSEQ=TGTCTCTGTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:55,52:107,0:0:2,0:23.1:1:32.3:1:1:0:53.7:214:1:0:0.3 0/1:113:2:1,1:52,59:111,2:0.0177:2,2:16.5:1:30:1:1:1.13:42:4:0.018:0:2 +GL000220.1 132405 . A T 16 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TCTCTCTCTCTGCCTCTCTC;RSEQ=CTGTGTCTGTCTTCTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:2:1,1:44,62:106,2:0.0185:2,2:12.5:1:26.5:1:1:1.40:50.5:4:0.02:0:2 0/1:108:2:1,1:47,59:106,2:0.0185:2,2:20:1:16:1:1:1.25:53.5:0:0:0:1.5 +GL000220.1 132414 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.49875;SOR=Inf;LSEQ=CTGCCTCTCTCACTGTGTCT;RSEQ=TCTTCTGTCTTATTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:44,56:100,0:0:2,0:25.8:1:31.1:1:1:0:54.5:13.286:1:0:0.4 0/1:110:2:1,1:48,60:108,2:0.0182:2,2:16:0:31.5:1:1:1.25:58:4:0.0194:0:1.5 +GL000220.1 132461 . T C 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.10262;SOR=2.32348;LSEQ=CTGTCTCTCTCTCTCTCTCC;RSEQ=TTCCTGTCTGTTTTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:6:3,3:34,52:86,6:0.0652:2,2:15.8:1:30.7:1:0.68146:1.52:30:12:0.0659:0:2.2 0/1:100:14:7,7:42,44:86,14:0.14:2,2:24.6:1:29.4:1:1:1.05:44.9:13:0.1313:0:2.2 +GL000220.1 132467 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.23862;SOR=0;LSEQ=CTCTCTCTCTCTCCTTTCCT;RSEQ=TCTGTTTTTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:2:1,1:39,55:94,2:0.0208:2,2:45:1:29:1:1:1.41:60:4:0.0217:0:4 0/0:100:0:0,0:51,49:100,0:0:2,0:21.5:1:31:1:1:0:56.7:49:1:0:0.8 +GL000220.1 132473 . T G 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00044;SOR=6.02787;LSEQ=CTCTCTCCTTTCCTGTCTGT;RSEQ=TTTCTCTCTCTCTCTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:4:2,2:36,49:85,4:0.0435:2,2:41.3:1:29:1:1:1.36:60:3:0.0341:0:1.5 0/1:97:21:11,10:40,36:76,21:0.2165:2,2:19.6:1:31:1:1:1.01:57.8:20:0.2128:0:1.6 +GL000220.1 132475 . T C 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=15;MSI=5.000;MSILEN=1;SSF=0.00525;SOR=0;LSEQ=CTCTCCTTTCCTGTCTGTTT;RSEQ=TCTCTCTCTCTCTCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:7:2,5:35,44:79,7:0.0787:2,2:26:1:29.4:1:0.69361:1.97375:50.3:2.5:0.0588:0:2.3 0/0:96:0:0,0:45,41:86,0:0:2,0:22.8:1:29.6:1:1:0:58.5:85:0.977:0:0.6 +GL000220.1 132495 . C A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09207;SOR=3.33623;LSEQ=TTCTCTCTCTCTCTCTCTTT;RSEQ=TGCCTGTTTCTCTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:2,1:37,48:85,3:0.0337:2,2:22.7:1:28.3:1:0.58205:2.57:43:6:0.0349:0:1.7 0/1:105:11:6,5:49,44:93,11:0.1048:2,2:20.6:1:28.7:1:1:1.08:40.4:22:0.1078:0:1.9 +GL000220.1 132507 . CTCTG C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.49935;SOR=Inf;LSEQ=CTCTCTTTCTGCCTGTTTCT;RSEQ=TCTGTCTCTGTCTTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:42,47:89,0:0:2,0:22.7:1:30.9:1:1:0:55.6:43.5:0.9886:0:0.5 0/1:102:2:1,1:52,46:98,2:0.0196:2,2:30:1:32:1:1:1.12905:57.5:4:0.0196:0:0.5 +GL000220.1 132539 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50684;SOR=Inf;LSEQ=CTGTCTTTCTCTGTCTGTCT;RSEQ=CCTCTCTCTTTCTTTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:51,38:89,0:0:2,0:25:1:32.1:1:1:0:52.3:88:1:0:0.2 0/1:117:2:1,1:64,51:115,2:0.0171:2,2:12:1:28:1:1:1.25244:43:4:0.0185:0:1 +GL000220.1 132552 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.49931;SOR=Inf;LSEQ=TCTGTCTGCCTCTCTCTTTC;RSEQ=TTTTCTGCGTCTCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:52,41:93,0:0:2,0:24.7:1:31.1:1:1:0:52.6:92:1:0:0.3 0/1:105:2:1,1:58,45:103,2:0.019:2,2:24:1:28.5:1:1:1.28574:59:4:0.019:0:1.5 +GL000220.1 132567 . C G 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.50822;SOR=Inf;LSEQ=CTTTCTTTTTCTGCGTCTCT;RSEQ=TGTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:88:0:0,0:52,36:88,0:0:2,0:27.3:1:32.3:1:1:0:52.2:43:1:0:0.4 0/1:118:2:0,2:64,49:113,2:0.0169:2,0:5.5:1:29.5:1:0.19451:0:60:4:0.0175:0:2 +GL000220.1 132590 . T A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.21032;SOR=0;LSEQ=TCTCTCTCTCTCTCTCTCTG;RSEQ=TCCTATCTTCTGTCTTACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:57,44:101,2:0.0194:2,2:20.5:1:28.5:1:1:1.29216:54.5:4:0.0202:0:1 0/0:121:0:0,0:68,53:121,0:0:2,0:22.4:1:28.5:1:1:0:54.9:59.5:1:0:0.5 +GL000220.1 132591 . T A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25082;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTGT;RSEQ=CCTATCTTCTGTCTTACTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:62,45:107,0:0:2,0:24:1:28.6:1:1:0:54.5:8.727:1:0:0.7 0/1:124:3:2,1:68,50:118,3:0.0242:2,2:17.7:1:24:1:1:1.47:56:6:0.0256:0:1 +GL000220.1 132608 . C T 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10484;SOR=0;LSEQ=TGTTCCTATCTTCTGTCTTA;RSEQ=TCTGTTTCCTTGCCTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:3:2,1:65,49:114,3:0.0256:2,2:44:1:25.7:1:1:1.50:60:2:0.0177:0:1.7 0/0:130:0:0,0:69,61:130,0:0:2,0:40:0:16:0:1:0:60:0:0:0:1 +GL000220.1 132633 . T C 98 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.31256;SOR=0.54058;LSEQ=TTTCCTTGCCTGCCTGCCTG;RSEQ=CTGTGTGTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:10:8,2:54,50:104,10:0.0877:2,2:29:1:29.6:1:0.10745:3.67:41.1:9:0.0804:0:3.7 0/1:142:7:4,3:72,63:135,7:0.0493:2,2:34.4:1:32.1:1:1:1.17:35.7:14:0.0496:0:5.1 +GL000220.1 132638 . G C 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.00146;SOR=Inf;LSEQ=TTGCCTGCCTGCCTGTCTGT;RSEQ=TGTCTGTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:51,49:100,0:0:2,0:25.4:1:32.2:1:1:0:57.5:24:1:0:0.5 0/1:139:11:6,5:69,59:128,11:0.0791:2,2:29.6:1:31.5:1:1:1.03:35.5:22:0.0809:0:4.6 +GL000220.1 132644 . GTCTC G 152 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=15.000;MSILEN=2;SSF=1;SOR=0.97368;LSEQ=GCCTGCCTGTCTGTGTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:25:13,12:32,27:59,25:0.2252:2,2:20.3:1:29.3:1:1:1.09284:54.6:7.333:0.2:0.1171:1.3 0/1:136:30:17,13:38,35:73,30:0.2206:2,2:29.9:1:31:1:0.8282:1.20:58.5:29:0.2148:0.0441:0.6 +GL000220.1 132683 . T C 113 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.17811;SOR=0.52817;LSEQ=TCTCTCTCTCTCCCTCCCTT;RSEQ=CTCTTTCTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:13:6,7:50,45:95,13:0.1204:2,2:20.2:1:30.8:1:0.77072:1.29317:30.9:12:0.1132:0:3.4 0/1:119:8:5,3:60,50:110,8:0.0672:2,2:20.6:1:25.1:1:0.72898:1.39:30.8:1.667:0.0442:0:4.4 +GL000220.1 132690 . CTCTG C 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=1;SOR=1.72848;LSEQ=CTCTCCCTCCCTTTCTCTTT;RSEQ=TCTCTCTCTCTCTTTCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:111:1:0,1:58,51:109,1:0.009:2,0:49:0:35:0:0.47273:0:31:2:0.0093:0:5 0/1:129:2:2,0:66,60:126,2:0.0155:2,0:16:1:29.5:1:0.49803:0:27:4:0.0157:0:3.5 +GL000220.1 132694 . GTC G 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.68482;SOR=1.87329;LSEQ=CCCTCCCTTTCTCTTTCTCT;RSEQ=TCTCTCTCTCTTTCTGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:2,0:54,54:108,2:0.0182:2,0:16.5:1:34:0:0.49558:0:38.5:4:0.0183:0:0 0/1:119:4:1,3:58,57:115,4:0.0336:2,2:18.3:1:30.3:1:0.61862:3.02655:52:8:0.0339:0.0084:0.5 +GL000220.1 132713 . G T 153 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.01374;SOR=2.09953;LSEQ=TGTCTCTCTCTCTCTTTCTG;RSEQ=GTGTTTCTCTCTGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:23:11,12:43,46:89,23:0.2054:2,2:26:1:28.5:1:1:1.01959:44.6:10.5:0.2019:0:2 0/1:122:43:22,21:38,41:79,43:0.3525:2,2:23.4:1:28.3:1:0.85004:1.13:48.2:42:0.3621:0:1.6 +GL000220.1 132782 . G C 30 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=1.65733;LSEQ=CTCTCTTTCTCTCTGTCTCT;RSEQ=TCTCTGCCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:1:0,1:48,50:98,1:0.0101:2,0:29:0:14:0:1:0:42:0:0:0:1 0/1:120:2:0,2:54,64:118,2:0.0167:2,0:6:1:30:1:0.50084:0:22.5:4:0.0182:0:2.5 +GL000220.1 133051 . T G 95 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.5876;SOR=0.65845;LSEQ=CTCTCTGTGTCTGTCTCTCT;RSEQ=TCTGTGCCTATCTTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:9:4,5:37,28:65,9:0.1216:2,2:14.2:1:30:1:0.50058:1.64044:39.1:8:0.1143:0:1.8 0/1:72:6:4,2:33,33:66,6:0.0833:2,2:13:1:31.2:1:0.67451:1.98:34.5:12:0.087:0:2 +GL000220.1 133087 . G T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.99303;LSEQ=TGTCTTACTCTCTTTCTCTG;RSEQ=CTGTCTGCCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:0,2:79,63:142,2:0.0139:2,0:15:1:18.5:1:0.20202:0:29:1:0.0072:0:2 0/1:145:2:1,1:76,67:143,2:0.0138:2,2:20:1:26.5:1:1:1.13334:46.5:4:0.0143:0:1 +GL000220.1 133088 . C T 45 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=GTCTTACTCTCTTTCTCTGG;RSEQ=TGTCTGCCTGTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:3:1,2:80,64:144,3:0.0204:2,2:19.3:1:24.7:1:0.58771:2.48473:37:2:0.014:0:3.7 0/1:147:3:1,2:77,67:144,3:0.0204:2,2:29.3:1:28.7:1:0.6005:2.28588:37.3:6:0.0205:0:1.7 +GL000220.1 133091 . T A 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=1;LSEQ=TTACTCTCTTTCTCTGGCTG;RSEQ=CTGCCTGTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:4:1,3:82,66:148,4:0.0263:2,2:31.5:1:30.5:1:0.32988:3.69708:27.3:8:0.0265:0:1.5 0/1:152:4:3,1:76,70:146,4:0.0263:2,2:31.5:1:29.8:1:0.6221:2.75:31:8:0.0265:0:1.5 +GL000220.1 133098 . GTC G 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.96038;LSEQ=CTTTCTCTGGCTGTCTGCCT;RSEQ=TCTCTCTCTCTGCCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:8:4,4:76,70:146,8:0.0523:2,2:27.1:1:32.5:1:1:1.08512:44.3:16:0.0523:0.0065:0.3 0/1:159:8:4,4:78,73:151,8:0.0503:2,2:36:1:32.1:1:1:1.06802:48.6:16:0.0506:0:0.3 +GL000220.1 133113 . C T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=1.01945;LSEQ=TGCCTGTCTCTCTCTCTCTG;RSEQ=CTGTCTCCGTCCCTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:24:14,10:68,70:138,24:0.1481:2,2:41.6:1:31.1:1:0.50861:1.44:25.5:48:0.1538:0:2.7 0/1:166:25:13,12:66,73:139,25:0.1506:2,2:40.5:1:29.4:1:0.82834:1.20:29.8:50:0.1543:0:2.8 +GL000220.1 133122 . G GTCCC 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=4.000;MSILEN=4;SSF=0.01067;SOR=0.36628;LSEQ=CTCTCTCTCTGCCTGTCTCC;RSEQ=TCCCTCCCTCCCTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:24:11,13:74,67:141,24:0.1446:2,2:24.3:1:29:1:0.65981:1.30317:56.8:11:0.1358:0.0361:0.6 0/1:172:10:2,8:81,81:162,10:0.0581:2,2:24.6:1:30.4:1:0.10125:3.9721:51.9:20:0.0606:0.0116:0.8 +GL000220.1 133129 . C T 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.8795;SOR=0.95217;LSEQ=TCTGCCTGTCTCCGTCCCTC;RSEQ=CTCCCTGTCTGTCTGTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:25:14,11:72,67:139,25:0.1524:2,2:26.3:1:30.6:1:0.82849:1.18:26.9:11.5:0.1438:0:2.7 0/1:171:25:13,12:68,77:145,25:0.1462:2,2:27.3:1:28.7:1:0.66978:1.23:29.8:11.5:0.1386:0:2.8 +GL000220.1 133157 . T C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=1.0717;LSEQ=TCTGTCTGTTTCTCTCTCTG;RSEQ=CTCTGTCTCTCTGTCCATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:7:3,4:67,68:135,7:0.049:2,2:9:1:28.6:1:1:1.31121:25.3:6:0.0429:0:4.4 0/1:153:8:4,4:71,72:143,8:0.0523:2,2:5.5:1:30:1:1:1.01:28.6:16:0.0544:0:3.5 +GL000220.1 133196 . TTC T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.000;MSILEN=2;SSF=0.1059;SOR=0;LSEQ=CTCTGTCTGTCTCTTTCTCT;RSEQ=TCTCTCTCTGTCTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:3:1,2:69,60:129,3:0.0226:2,2:26.7:1:30:1:0.60036:2.28592:59:6:0.0233:0:0 0/0:147:0:0,0:73,74:147,0:0:2,0:22.9:1:29.5:1:1:0:51.4:48:1:0:0.3 +GL000220.1 133202 . C CTCTCTG 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.50011;SOR=Inf;LSEQ=CTGTCTCTTTCTCTTTCTCT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:69,57:126,0:0:2,0:23.7:1:32.3:1:1:0:53.5:41:1:0:0.2 0/1:145:2:1,1:74,68:142,2:0.0138:2,2:18.5:1:29.5:1:1:1.08758:48:4:0.0141:0.0069:0.5 +GL000220.1 133214 . GTC G 119 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.3711;SOR=1.55578;LSEQ=CTTTCTCTCTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:8:3,5:69,49:118,8:0.064:2,2:19.4:1:31:1:0.28659:2.3309:52.5:16:0.064:0.024:0.6 0/1:135:13:7,6:67,55:122,13:0.0963:2,2:30.3:1:32.3:1:1:1.04384:37.8:26:0.0977:0:0.2 +GL000220.1 133216 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=7.000;MSILEN=2;SSF=0.2493;SOR=Inf;LSEQ=TTCTCTCTCTCTGTCTCTGT;RSEQ=TCTCTCTCTCTCTGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:68,48:116,0:0:2,0:23.6:1:31.5:1:1:0:50.7:18.333:1:0:0.3 0/1:136:3:2,1:65,55:120,3:0.0221:2,2:19.3:1:26:1:1:1.69:43:2:0.0167:0:0.7 +GL000220.1 133242 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.22998;SOR=0;LSEQ=CTCTCTCTGCCTGTCTCTCT;RSEQ=ACTGTGTCTGTCTTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:2:1,1:59,51:110,2:0.0179:2,2:33:1:27.5:1:1:1.15535:46.5:4:0.0179:0:1 0/0:121:0:0,0:63,56:119,0:0:2,0:22.9:1:30.6:1:1:0:44.9:58.5:1:0:0.2 +GL000220.1 133281 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24045;SOR=Inf;LSEQ=CTTACTCTCTTTCTCTGCCT;RSEQ=CCTCTCTGTCTGTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:62,56:118,0:0:2,0:25.5:1:31.6:1:1:0:46.9:18.667:1:0:0.3 0/1:115:2:1,1:62,51:113,2:0.0174:2,2:48:1:28.5:1:1:1.21361:60:4:0.018:0:1 +GL000220.1 133285 . C G 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=1;SOR=0.84908;LSEQ=CTCTCTTTCTCTGCCTGCCT;RSEQ=TCTGTCTGTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:118:6:2,4:60,52:112,6:0.0508:2,2:24.8:1:33.7:1:0.42113:2.29178:38.2:12:0.0508:0:1.8 0/1:115:5:2,3:60,50:110,5:0.0435:2,2:16.6:1:31.6:1:0.66043:1.79081:39.4:10:0.0435:0:1.2 +GL000220.1 133312 . T C 46 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68324;SOR=0.65578;LSEQ=TGTCTGTCTCTCTCCCTCCA;RSEQ=GTCTCTCTCTCTCTCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:3:1,2:57,51:108,3:0.027:2,2:6:1:29.3:1:0.60504:2.21962:41.7:6:0.028:0:2.7 0/1:112:2:0,2:54,56:110,2:0.0179:2,0:13:1:18:1:0.49614:0:36.5:1:0.0091:0:2.5 +GL000220.1 133397 . G A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07403;SOR=Inf;LSEQ=GTCTGTCTCTCTCCCTCCAT;RSEQ=TCTCTCTCTCTCTCTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,11:25,0:0:2,0:11.7:1:32.2:1:1:0:22.5:50:0.9259:0:0.1 0/1:41:6:3,3:13,19:32,6:0.1463:2,2:20.5:1:28.5:1:0.68203:1.45:26.5:12:0.1579:0:2.2 +GL000220.1 133431 . G ATC 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.03251;SOR=Inf;LSEQ=CTCTCACTCACTCTCTCTCC;RSEQ=TCTCTCTCTCTCTTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:21,14:35,0:0:2,0:26.6:1:29.3:1:1:0:21.8:10.667:1:0:0.2 0/1:45:6:3,3:20,19:39,6:0.1333:2,2:41.8:1:28.9:1:1:1.05146:26.5:12:0.1429:0:2.2 +GL000220.1 133485 . G GTC 32 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.21775;SOR=0;LSEQ=GTCTGTCTCTCTCCCTCCAT;RSEQ=TCTCTCTCTCTCCCTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:21,16:37,2:0.0513:2,2:6:1:32.5:1:1:1.30327:43.5:4:0.0541:0.0256:0.5 0/0:44:0:0,0:22,19:41,0:0:2,0:17.6:1:30.9:1:1:0:28:19.5:1:0:0.3 +GL000220.1 133519 . G GTC 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=1;SOR=0.95781;LSEQ=CTCTCACTCACTCTCTCTCC;RSEQ=TCTCTCTCTCTCTTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:9:3,6:22,23:45,9:0.1667:2,2:20.8:1:31.3:1:0.48022:1.89072:44.1:18:0.2:0.0556:0.4 0/1:56:9:4,5:25,20:45,9:0.1607:2,2:25:1:26.7:1:0.71751:1.54951:46.8:8:0.16:0:0.4 +GL000220.1 133532 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50557;SOR=Inf;LSEQ=TCTCTCCGTCTCTCTCTCTC;RSEQ=TTCTGTCTGTTTCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:27,34:61,0:0:2,0:30.5:1:31.1:1:1:0:44.4:29.5:1:0:0.5 0/1:80:2:1,1:40,37:77,2:0.025:2,2:22:0:32.5:1:1:1.07999:38.5:4:0.0256:0:1.5 +GL000220.1 133549 . G C 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=4;SSF=0.51788;SOR=1.8256;LSEQ=CTCTTTCTGTCTGTTTCTCT;RSEQ=TCTGTCTGTCTGTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:3:1,2:33,38:71,3:0.0395:2,2:20.7:1:26:1:1:1.72444:34:2:0.0313:0:1.3 0/1:100:7:2,5:48,46:94,7:0.07:2,2:20.4:1:25.3:1:0.43638:2.5853:34.1:2:0.0524:0:1.4 +GL000220.1 133565 . GTCTG CTC 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.000;MSILEN=4;SSF=0.07539;SOR=0;LSEQ=CTCTGTCTGTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:3:1,2:35,40:75,3:0.0375:2,2:11.3:1:24.6:1:1:1.73798:48.7:2:0.0263:0.025:2 0/0:108:0:0,0:53,52:105,0:0:2,0:24.7:1:29.7:1:1:0:43.9:104:1:0:0.5 +GL000220.1 133605 . G C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50962;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TTTGTCTTTCTCCCTCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:35,36:71,0:0:2,0:24.8:1:31.1:1:1:0:56:9.143:1:0:0.6 0/1:103:2:2,0:37,54:91,2:0.0194:2,0:14:1:28:1:0.17321:0:41:4:0.0225:0:2.5 +GL000220.1 133613 . T A 84 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.00031;SOR=0;LSEQ=CTCTCTCTCTCTGTTTGTCT;RSEQ=TCTCCCTCCCTGTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:9:4,5:35,35:70,9:0.1111:2,2:20.3:1:26.6:1:1:1.24648:55.9:8:0.1111:0:1 0/0:112:0:0,0:48,63:111,0:0:2,0:24.2:1:29.2:1:1:0:51.4:26.75:1:0:0.4 +GL000220.1 133622 . CCTGT C 32 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.000;MSILEN=4;SSF=1;SOR=1.46288;LSEQ=TCTGTTTGTCTTTCTCCCTC;RSEQ=CTGTCTGTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:1,0:43,42:85,1:0.0116:2,0:43:0:30:0:1:0:60:2:0.0122:0:1 0/1:118:2:1,1:50,65:115,2:0.0169:2,2:28.5:1:32.5:1:1:1.30:60:4:0.0172:0:0 +GL000220.1 133645 . CTCTCTG C 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=2;SSF=0.16426;SOR=2.05308;LSEQ=GTCTGTCTGTCTGTCTCTCT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:6:3,3:40,40:80,6:0.0674:2,2:32.7:1:33.7:1:1:1:56:12:0.0706:0:0.3 0/1:108:14:8,6:40,53:93,14:0.1296:2,2:37.6:1:31.6:1:0.39283:1.76:42.7:28:0.1296:0:0.6 +GL000220.1 133647 . CTCTG C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=7.000;MSILEN=2;SSF=0.20918;SOR=0;LSEQ=CTGTCTGTCTGTCTCTCTCT;RSEQ=TCTCTGTCTCTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:40,39:79,2:0.0225:2,2:33.5:1:34.5:1:1:1.02533:59.5:4:0.025:0:0 0/0:105:0:0,0:40,51:91,0:0:2,0:23.2:1:29.5:1:1:0:55:90:1:0:0.3 +GL000220.1 133704 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.244;SOR=0;LSEQ=TGTCTGTTTCTCTCTATCTC;RSEQ=CGCTGTCCATCTCTGTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:30,30:60,2:0.0323:2,2:29.5:1:32:1:1:1:41.5:4:0.0328:0:1 0/0:63:0:0,0:31,32:63,0:0:2,0:27.2:1:28.9:1:1:0:43.3:62:1:0:0.1 +GL000220.1 134012 . T G 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.43105;SOR=2.36454;LSEQ=TCGACTTCAACATAAACTGT;RSEQ=AAGGCCGGACGCAACACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:2,0:8,16:24,2:0.0769:2,0:25:1:32:1:0.13846:0:57.5:4:0.08:0:1 0/1:30:5:2,3:12,13:25,5:0.1667:2,2:26:1:31:1:1:1.36981:54:10:0.1724:0:1.4 +GL000220.1 134021 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50502;SOR=Inf;LSEQ=ACATAAACTGTTAAGGCCGG;RSEQ=CGCAACACGGCGAAACCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:10,16:26,0:0:2,0:32.2:1:29.5:1:1:0:55.6:25:1:0:0.1 0/1:36:2:1,1:15,19:34,2:0.0556:2,2:15.5:1:29.5:1:1:1.26:55.5:4:0.0571:0:1 +GL000220.1 134075 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50992;SOR=Inf;LSEQ=TACAAAGCTGAGTCGGGAGC;RSEQ=GTGGGGCAGGCCCCTGTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:11,15:26,0:0:2,0:23.6:1:30.8:1:1:0:58.9:52:1:0:0.2 0/1:38:2:1,1:18,18:36,2:0.0526:2,2:41.5:1:27:1:1:1:60:4:0.0526:0:1 +GL000220.1 134098 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.52425;SOR=Inf;LSEQ=GGGGCAGGCCCCTGTAATGC;RSEQ=AGCTCCTCGGGAGGCTGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:9,13:22,0:0:2,0:28.4:1:31.6:1:1:0:56.9:44:1:0:0.3 0/1:37:2:1,1:17,18:35,2:0.0541:2,2:23.5:1:28:1:1:1.06:60:4:0.0556:0:2 +GL000220.1 134139 . G A 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.3136;SOR=0.25045;LSEQ=CGGGAGAATCGCTTGAACCA;RSEQ=GGAAGCGGAGGCTGCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:3:1,2:6,13:19,3:0.1364:2,2:27.3:1:31.3:1:1:1.08:56:6:0.1429:0:2 0/1:27:1:0,1:12,14:26,1:0.037:2,0:2:0:31:0:1:0:60:2:0.0385:0:2 +GL000220.1 134143 . A G 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08034;SOR=0;LSEQ=AGAATCGCTTGAACCAGGGA;RSEQ=GCGGAGGCTGCAGGGAGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:3:1,2:5,12:17,3:0.15:2,2:26:1:31.3:1:1:1.19:56:6:0.1579:0:2 0/0:25:0:0,0:11,14:25,0:0:2,0:23.1:1:30:1:1:0:57.8:50:1:0:0.3 +GL000220.1 134439 . C A 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50752;SOR=Inf;LSEQ=TCCCTCGTTGCCTAGGGAAC;RSEQ=TCGCCTAGGGAACCTCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:20,16:36,0:0:2,0:22:1:31.7:1:1:0:50.4:72:1:0:0.1 0/1:50:2:1,1:25,23:48,2:0.04:2,2:23:0:28.5:1:1:1.08513:46:4:0.04:0:1.5 +GL000220.1 134473 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49949;SOR=Inf;LSEQ=CTCCGCCCTGGCGGGGGCCC;RSEQ=ATTGTTCTTTGATCGGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:19,21:40,0:0:2,0:25.2:1:30:1:1:0:57.7:39:1:0:0.1 0/1:49:2:1,1:21,26:47,2:0.0408:2,2:13.5:1:29:1:1:1.23:57:4:0.0408:0:1 +GL000220.1 134633 . T TC 23 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.64054;SOR=0.62623;LSEQ=GTGAGTCGGTTAGGTGGGTT;RSEQ=CCCCCAAACCGCCCCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:14,13:27,2:0.0667:2,2:31:1:30.5:1:1:1.07415:52.5:4:0.0714:0:2.5 0/1:47:2:2,0:26,19:45,2:0.0426:2,0:25:0:23.5:1:0.50786:0:46.5:1:0.0256:0:1 +GL000220.1 134643 . CG AC 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04011;SOR=0;LSEQ=TAGGTGGGTTTCCCCCAAAC;RSEQ=CCCCCCCCCCCCCGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:3:2,1:12,11:23,3:0.1154:2,2:9.3:1:32.2:1:1:1.79:55:6:0.15:0:1.7 0/0:48:0:0,0:28,17:45,0:0:2,0:18.6:1:26.5:1:1:0:50:6.5:0.975:0:1.2 +GL000220.1 134763 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51482;SOR=Inf;LSEQ=GATCTCATTCTTGCCAGGCT;RSEQ=ACATTTGCATCGGTGGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:31,0:0:2,0:22.6:1:32.1:1:1:0:34.3:62:1:0:0.2 0/1:47:2:1,1:24,21:45,2:0.0426:2,2:20:0:31:1:1:1.1396:37:4:0.0426:0:1.5 +GL000220.1 134793 . C T 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09026;SOR=0.26778;LSEQ=TCGGTGGGCGTCAGGCCTCA;RSEQ=TCGGGGGCCACCGTTTTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:7:3,4:24,28:52,7:0.1186:2,2:22.1:1:29.6:1:1:1.14029:32:14:0.1186:0:2.4 0/1:87:3:2,1:43,41:84,3:0.0345:2,2:30.7:1:32:0:1:1.89:23.7:6:0.0349:0:2.7 +GL000220.1 134796 . G A 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.28664;SOR=0.42796;LSEQ=GTGGGCGTCAGGCCTCACTC;RSEQ=GGGGCCACCGTTTTTGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:5:2,3:26,35:61,5:0.0758:2,2:27.4:1:30.6:1:1:1.11244:33.4:10:0.0781:0:3 0/1:89:3:2,1:44,42:86,3:0.0337:2,2:33.7:1:32:1:1:1.90:23.7:6:0.0337:0:2.7 +GL000220.1 134800 . G T 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14087;SOR=0.2886;LSEQ=GCGTCAGGCCTCACTCGGGG;RSEQ=CCACCGTTTTTGAAGATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:5:2,3:26,36:62,5:0.0735:2,2:30.8:1:29.8:1:1:1.08207:33.4:10:0.0781:0:3 0/1:90:2:1,1:45,43:88,2:0.0222:2,2:38:1:31.5:1:1:1.046:24:4:0.0222:0:3 +GL000220.1 134831 . TC T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.50242;SOR=Inf;LSEQ=TGAAGATGGGGGCGGCACGG;RSEQ=CCACTTCCCCGGAGGCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:38,47:85,0:0:2,0:25.9:1:31.4:1:1:0:46.6:84:1:0:0.4 0/1:104:2:1,1:53,49:102,2:0.0192:2,2:21.5:1:26.5:1:1:1.0808:30.5:4:0.0194:0.0096:0.5 +GL000220.1 134851 . C G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50388;SOR=Inf;LSEQ=TCCCACTTCCCCGGAGGCAG;RSEQ=TTGGGCCGATGGCATAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:35,41:76,0:0:2,0:26.8:1:33.3:1:1:0:52.3:152:1:0:0.4 0/1:96:2:1,1:46,47:93,2:0.0208:2,2:38:0:32.5:1:1:1.02:40:4:0.0215:0:1 +GL000220.1 134868 . GC G 55 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.66153;SOR=0.55626;LSEQ=CAGCTTGGGCCGATGGCATA;RSEQ=CCCTTGACCCGCGTGGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:3:2,1:32,42:74,3:0.039:2,2:30.3:1:35:1:0.58029:2.59:28.3:6:0.0395:0:0.7 0/1:91:2:0,2:44,45:89,2:0.022:2,0:16:1:26:0:0.49499:0:46:4:0.0227:0:0 +GL000220.1 134919 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.22004;SOR=0;LSEQ=TCTGCAGTTGTGAGGCTTTT;RSEQ=CCCCCGCTGCTTCCCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:34,28:62,2:0.0308:2,2:22:0:32.5:1:1:1.21058:46:4:0.0317:0:1.5 0/0:73:0:0,0:29,43:72,0:0:2,0:26.1:1:31:1:1:0:58.9:144:0.9863:0:0.2 +GL000220.1 134999 . T C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16391;SOR=Inf;LSEQ=TCGGTCACCTTTTATCACGA;RSEQ=GTTTTAGTTTCTCCGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:25,36:61,0:0:2,0:20.2:1:30.6:1:1:0:56.8:60:1:0:0.3 0/1:42:2:1,1:17,23:40,2:0.0476:2,2:33:0:30:1:1:1.34:23:4:0.0476:0:1.5 +GL000220.1 135180 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=TTTGTTGGCTTGTTTTGTTT;RSEQ=GTTCTGTTTTGTTTTGTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:21,0:0:2,0:22.8:1:30.9:1:1:0:59.5:20:1:0:0.3 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:17:0:32:1:1:1.36624:20:4:0.1429:0:3.5 +GL000220.1 135183 . TC AT 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15294;SOR=Inf;LSEQ=GTTGGCTTGTTTTGTTTCGT;RSEQ=TGTTTTGTTTTGTTCGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:10,11:21,0:0:2,0:23.8:1:30.2:1:1:0:59.5:20:1:0:0.3 0/1:14:2:1,1:8,4:12,2:0.1429:2,2:13:0:31.5:0:1:1.89743:20:4:0.1429:0:2.5 +GL000220.1 135224 . T C 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.23585;SOR=0;LSEQ=TTTTCCTTTCTCGTATGTCT;RSEQ=TCTTTTCAGGTGAAGTAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:1,1:15,9:24,2:0.0769:2,2:19:0:30:1:1:1.63293:60:4:0.0833:0:1.5 0/0:27:0:0,0:13,14:27,0:0:2,0:26:1:29.5:1:1:0:60:26:1:0:0.3 +GL000220.1 135265 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.48889;SOR=Inf;LSEQ=ATCCCCAGTTTTCAGGAAGA;RSEQ=GTCTATTTTCCCCAAGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:10,12:22,0:0:2,0:29.7:1:30.7:1:1:0:60:44:1:0:0.3 0/1:23:2:1,1:11,10:21,2:0.087:2,2:5.5:1:28:1:1:1.09544:60:4:0.0952:0:1 +GL000220.1 135295 . C T 47 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62567;SOR=0.43796;LSEQ=CCCCAAGACACGTTAGCTGC;RSEQ=GTTTTTTCCTGTTGTGAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:3:1,2:8,10:18,3:0.1429:2,2:36.3:1:29.7:1:1:1.56568:60:6:0.1429:0:1 0/1:15:1:1,0:8,6:14,1:0.0667:2,0:48:0:33:0:1:0:60:2:0.0714:0:1 +GL000220.1 135366 . T C 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95327;LSEQ=GAGAGCCGGTTGATGTTTAC;RSEQ=ATCCTTCATCATGACATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:2,3:12,8:20,5:0.2:2,2:16.6:1:31.2:1:0.62319:2.17635:52.6:10:0.2083:0:1.4 0/1:26:5:3,2:11,10:21,5:0.1923:2,2:18.8:1:30.8:1:1:1.35:60:10:0.1923:0:1.2 +GL000220.1 135436 . G GCTTTTGTTATTGTTGCAGCTACTTTTGTTGCTCCTC 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=6.000;MSILEN=3;SSF=0.50485;SOR=Inf;LSEQ=CTGCTGCTCTTGTTGCTGTT;RSEQ=TTGTTGTTGTTGTTGTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:25,18:43,0:0:2,0:27.7:1:32.9:1:1:0:58.1:86:1:0:0.2 0/1:57:2:1,1:29,26:55,2:0.0351:2,2:43.5:1:27.1:1:1:1.11325:60:4:0.037:0.0351:0 +GL000220.1 135438 . T C 68 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.23655;SOR=0.29627;LSEQ=GCTGCTCTTGTTGCTGTTGT;RSEQ=GTTGTTGTTGTTGTCGTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:1,4:24,17:41,5:0.1087:2,2:15.6:1:29.4:1:0.16276:5.4499:52.6:10:0.1111:0:1.6 0/1:58:2:0,2:30,26:56,2:0.0345:2,0:21:1:31:0:0.22868:0:60:4:0.0351:0:1.5 +GL000220.1 135480 . T C 50 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=3;SSF=0.63925;SOR=2.18944;LSEQ=GCTGTTGTCGTTGTCGTTGT;RSEQ=GTTGTCGTTGTCGTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:1:0,1:24,23:47,1:0.0208:2,0:44:0:28:0:1:0:60:2:0.0208:0:2 0/1:67:3:2,1:35,29:64,3:0.0448:2,2:25.3:1:31.7:1:1:1.65:60:6:0.0455:0:1 +GL000220.1 135510 . C T 31 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49895;SOR=Inf;LSEQ=GTCGTTGTTTTCAAAGTATA;RSEQ=CCCGGCCACCGTTTATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:23,24:47,0:0:2,0:23.9:1:32.3:1:1:0:60:94:1:0:0.1 0/1:56:2:1,1:27,27:54,2:0.0357:2,2:7:0:31:1:1:1:60:4:0.037:0:1 +GL000220.1 135621 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49664;SOR=0;LSEQ=GTCTGTCTCTGTCTCTCTCT;RSEQ=TCTCTGTCTGTCTTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:2:0,2:39,34:73,2:0.0267:2,0:8.5:1:29.5:1:0.22703:0:49.5:4:0.0278:0:3.5 0/0:74:0:0,0:41,33:74,0:0:2,0:26.4:1:29:1:1:0:57.6:23.667:1:0:0.3 +GL000220.1 135654 . G C 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21076;SOR=5.19678;LSEQ=TTCTCTCTCTCTCTCTCTCT;RSEQ=TGTCTCTCTCTCTCTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:0,1:47,40:87,1:0.0112:2,0:36:0:14:0:0.46591:0:39:0:0:0:5 0/1:89:5:3,2:45,39:84,5:0.0562:2,2:9.8:1:30:1:1:1.30:47.4:10:0.0575:0:2 +GL000220.1 135656 . GTC G 52 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.66818;LSEQ=CTCTCTCTCTCTCTCTCTGT;RSEQ=TCTCTCTCTCTGCCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:3:1,2:46,40:86,3:0.0337:2,2:37:1:33:1:0.60021:2.27913:60:6:0.0341:0:0 0/1:88:2:1,1:46,40:86,2:0.0227:2,2:29:1:34:0:1:1.14817:60:4:0.0233:0:0.5 +GL000220.1 135693 . CCT C 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=12.000;MSILEN=2;SSF=0.30948;SOR=1.36569;LSEQ=TGTCTGTTTCTCTCTCTCTG;RSEQ=CTCTCTCTCTCTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:39:23,16:21,21:42,39:0.3482:2,2:26.1:1:32.2:1:0.50486:1.43:47.5:78:0.3679:0.0625:0.3 0/1:90:38:21,17:14,13:27,38:0.4222:2,2:30.3:1:30.8:1:0.80602:1.14:50.3:76:0.4318:0.0444:0.4 +GL000220.1 135722 . GTCTC G 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=4.000;MSILEN=2;SSF=0.49782;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTGCCT;RSEQ=TCTCACTGTGTCTGTCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:58,48:106,0:0:2,0:27.2:1:30.1:1:1:0:49.6:212:0.9907:0:0.2 0/1:112:2:1,1:55,55:110,2:0.0179:2,2:6.5:1:31:1:1:1:55:4:0.0179:0.0089:1 +GL000220.1 135747 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49844;SOR=Inf;LSEQ=TCTCACTGTGTCTGTCTTCT;RSEQ=TCTTACTCCCTTTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:63,48:111,0:0:2,0:24.8:1:31.5:1:1:0:50.7:36:0.9908:0:0.3 0/1:121:2:1,1:60,57:117,2:0.0165:2,2:17:1:29:1:1:1.0522:28:4:0.0169:0:2.5 +GL000220.1 135756 . C T 50 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.37772;SOR=3.47218;LSEQ=GTCTGTCTTCTGTCTTACTC;RSEQ=CTTTCTCTGTCTGTCTGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:1:1,0:60,49:109,1:0.0091:2,0:9:0:17:0:1:0:41:0:0:0:3 0/1:129:4:2,2:66,59:125,4:0.031:2,2:6.8:1:25.3:1:1:1.11767:44:3:0.0238:0:2 +GL000220.1 135799 . GT CC 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.50731;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCTCCCT;RSEQ=CTGTATGTTTCTCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:59,55:114,0:0:2,0:23.9:1:32:1:1:0:58.6:27.5:0.991:0:0.3 0/1:151:2:1,1:72,74:146,2:0.0132:2,2:15:0:29:1:1:1.03:53:4:0.014:0:2 +GL000220.1 135801 . CTGTA C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50307;SOR=Inf;LSEQ=CTCTCTCTCTCTCTCCCTGT;RSEQ=TGTTTCTCTCTGTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:66,57:123,0:0:2,0:23:1:30.9:1:1:0:58.7:40:1:0:0.3 0/1:150:2:1,1:72,75:147,2:0.0133:2,2:28:0:33.5:1:1:1.04:24:4:0.0134:0:1.5 +GL000220.1 135805 . A C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50426;SOR=Inf;LSEQ=CTCTCTCTCTCCCTGTCTGT;RSEQ=TGTTTCTCTCTGTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:66,55:121,0:0:2,0:24.1:1:29:1:1:0:58.8:19.167:1:0:0.3 0/1:151:2:1,1:68,78:146,2:0.0132:2,2:20:0:30:1:1:1.15:53:4:0.0138:0:2 +GL000220.1 135823 . G GTC 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.50442;SOR=Inf;LSEQ=GTATGTTTCTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTTTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:67,51:118,0:0:2,0:26.5:1:31.6:1:1:0:59.4:18.667:0.9912:0:0.3 0/1:149:2:1,1:75,72:147,2:0.0134:2,2:24.5:1:29:1:1:1.04139:60:4:0.014:0.0067:1 +GL000220.1 135829 . C CTCTCTCTTTCTGTTTCTCTCTCTCCG 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=2;SSF=0.01108;SOR=Inf;LSEQ=TTCTCTCTGTCTCTGTCTCT;RSEQ=TCTCTCTTTCTGTTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:66,51:117,0:0:2,0:26.9:1:32.5:1:1:0:59.4:57.5:1:0:0.3 0/1:154:8:3,5:71,73:144,8:0.0519:2,2:20.9:1:28.3:1:0.7199:1.61595:60:16:0.0526:0.039:0.1 +GL000220.1 135832 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=2;SSF=0.50822;SOR=Inf;LSEQ=TCTCTGTCTCTGTCTCTCTC;RSEQ=CTCTTTCTGTTTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:64,51:115,0:0:2,0:27.2:1:31.1:1:1:0:59.4:56.5:1:0:0.3 0/1:153:2:1,1:74,77:151,2:0.0131:2,2:11.5:1:29.5:1:1:1.04:60:4:0.0134:0:2.5 +GL000220.1 135843 . T A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.58728;SOR=0.39929;LSEQ=GTCTCTCTCTCTCTTTCTGT;RSEQ=TCTCTCTCTCCGTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:2:1,1:61,52:113,2:0.0174:2,2:10.5:1:28:1:1:1.17144:60:4:0.0183:0:1.5 0/0:143:1:1,0:66,72:138,1:0.007:2,0:1:0:23:0:0.48201:0:60:2:0.0072:0:3 +GL000220.1 135854 . C T 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.25452;SOR=Inf;LSEQ=TCTTTCTGTTTCTCTCTCTC;RSEQ=GTCTCTGTCTTTCTCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:67,57:124,0:0:2,0:22.4:1:30:1:1:0:59.7:23.8:1:0:0.3 0/1:151:3:2,1:71,77:148,3:0.0199:2,2:20:1:31:1:0.61026:2.16:43.3:6:0.0201:0:3 +GL000220.1 135872 . A ACTGT 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.39917;SOR=0.69094;LSEQ=TCCGTCTCTGTCTTTCTCTG;RSEQ=CTGTCTCTCTCTTTCCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:13:7,6:54,52:106,13:0.1092:2,2:19.7:1:30.5:1:1:1.12:60:26:0.1171:0.042:0.2 0/1:141:11:5,6:68,62:130,11:0.078:2,2:20.3:1:30.1:1:0.75868:1.31356:55.5:22:0.0797:0.0284:0.6 +GL000220.1 135874 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=1.000;MSILEN=1;SSF=0.50147;SOR=Inf;LSEQ=CGTCTCTGTCTTTCTCTGAC;RSEQ=GTCTCTCTCTTTCCTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:59,57:116,0:0:2,0:23.9:1:30.8:1:1:0:59.9:37.667:1:0:0.2 0/1:137:2:1,1:69,66:135,2:0.0146:2,2:19:1:28:1:1:1.04513:60:4:0.0147:0:1 +GL000220.1 135887 . CCTTCTC TTCTGTCTG 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.50825;SOR=Inf;LSEQ=CTCTGACTGTCTCTCTCTTT;RSEQ=TCTGTCTCTCTCTGCCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:56,52:108,0:0:2,0:26.1:1:32.3:1:1:0:59.8:107:1:0:0.2 0/1:144:2:1,1:69,73:142,2:0.0139:2,2:25.5:1:29.3:1:1:1.06:54:4:0.0141:0:3.5 +GL000220.1 135893 . CTCTGTCTC GTCGTCTG 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25666;SOR=Inf;LSEQ=CTGTCTCTCTCTTTCCTTCT;RSEQ=TCTCTGCCTGTCTCTCTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:55,59:114,0:0:2,0:25.6:1:32:1:1:0:59.9:21.8:1:0:0.2 0/1:143:3:2,1:69,69:138,3:0.021:2,2:12:1:26.5:1:1:1.99:60:6:0.0216:0.014:0.7 +GL000220.1 135908 . CCTGT C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50578;SOR=Inf;LSEQ=CTTCTCTCTGTCTCTCTCTG;RSEQ=CTCTCTCACTCTGTCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:54,59:113,0:0:2,0:26.2:1:32.2:1:1:0:60:36.667:1:0:0.2 0/1:145:2:1,1:69,74:143,2:0.0138:2,2:9:1:29.1:1:1:1.07:60:4:0.0142:0.0069:0 +GL000220.1 135937 . ACT A 64 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.38318;SOR=3.30889;LSEQ=CTCACTCTGTCTTCTGTCTT;RSEQ=CTCTCTCTCTGCCTGCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:1:0,1:51,57:108,1:0.0092:2,0:46:0:36:0:1:0:60:2:0.0093:0:0 0/1:134:4:1,3:63,67:130,4:0.0299:2,2:19:1:32.4:1:0.62084:2.80131:58.8:8:0.031:0.0149:0.3 +GL000220.1 135960 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=0.50363;SOR=Inf;LSEQ=CTCTCTCTCTGCCTGCCTGT;RSEQ=TCTCTCACTCTCTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:44,59:103,0:0:2,0:22.5:1:32.4:1:1:0:59.7:33.333:0.9901:0:0.2 0/1:129:2:1,1:60,67:127,2:0.0155:2,2:16:1:30.5:1:1:1.12:60:4:0.0159:0:2 +GL000220.1 135967 . ACT A 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.50397;SOR=Inf;LSEQ=TCTGCCTGCCTGTCTCTCTC;RSEQ=CTCTCTCTCTGTGTGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:43,55:98,0:0:2,0:23.2:1:32.8:1:1:0:58.6:48:0.9796:0:0.3 0/1:125:2:0,2:57,66:123,2:0.016:2,0:21:1:33.5:1:0.49987:0:60:4:0.0161:0:0 +GL000220.1 135976 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=2;SSF=0.49974;SOR=Inf;LSEQ=CTGTCTCTCTCACTCTCTCT;RSEQ=TCTGTGTGTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:50,54:104,0:0:2,0:21.5:1:32.9:1:1:0:57.4:103:1:0:0.3 0/1:118:2:1,1:52,62:114,2:0.0169:2,2:21.5:1:31.5:1:1:1.19:45.5:4:0.0171:0:1 +GL000220.1 135980 . G C 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=0.06212;SOR=Inf;LSEQ=CTCTCTCACTCTCTCTCTCT;RSEQ=TGTGTCTCTCTCTCTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:49,52:101,0:0:2,0:21.9:1:32.3:1:1:0:57.2:49.5:0.99:0:0.2 0/1:120:5:1,4:55,60:115,5:0.0417:2,2:28:1:28.8:1:0.37009:3.63207:47:4:0.0345:0:2.4 +GL000220.1 135982 . G C 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.49971;SOR=Inf;LSEQ=CTCTCACTCTCTCTCTCTGT;RSEQ=TGTCTCTCTCTCTCTTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:51,53:104,0:0:2,0:21.6:1:32.6:1:1:0:57:208:0.9905:0:0.3 0/1:120:2:1,1:56,61:117,2:0.0167:2,2:6.5:1:30:1:1:1.09:60:4:0.0169:0:1.5 +GL000220.1 135984 . GTC G 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=0.84489;LSEQ=CTCACTCTCTCTCTCTGTGT;RSEQ=TCTCTCTCTCTTTCTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:2:1,1:48,54:102,2:0.019:2,2:14:0:34:0:1:1.12:40:4:0.0192:0:0.5 0/1:124:2:1,1:59,63:122,2:0.0161:2,2:21:1:30.7:1:1:1.07:60:4:0.0163:0.0081:0 +GL000220.1 135998 . T TTCTG 115 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02594;SOR=0.30159;LSEQ=CTGTGTGTCTCTCTCTCTCT;RSEQ=TCTGTTTCTCTCTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:13:6,7:39,45:84,13:0.1327:2,2:21.4:1:31.3:1:1:1.011:49.7:26:0.1327:0.0408:0.5 0/1:114:5:3,2:46,60:106,5:0.0439:2,2:39:1:30.7:1:0.65298:1.94:44.4:10:0.0446:0:1.2 +GL000220.1 136020 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=8;SSF=0.49874;SOR=Inf;LSEQ=CTGTTTCTCTCTGTCTCTCT;RSEQ=TCCGTCTCTGTCTTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:49,47:96,0:0:2,0:25.5:1:32.3:1:1:0:56:47:1:0:0.2 0/1:106:2:1,1:48,56:104,2:0.0189:2,2:39.5:1:29.5:1:1:1.16:46.5:4:0.019:0:1 +GL000220.1 136036 . CTCTG C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.000;MSILEN=4;SSF=0.49754;SOR=Inf;LSEQ=CTCTGTCCGTCTCTGTCTTT;RSEQ=TCTGTCTCTTTGTCTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:50,49:99,0:0:2,0:23.8:1:31.3:1:1:0:56.3:98:1:0:0.3 0/1:101:2:0,2:48,50:98,2:0.0198:2,0:29:1:30.5:1:0.49576:0:60:4:0.02:0:0 +GL000220.1 136039 . T C 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=9;MSI=2.000;MSILEN=4;SSF=0.04958;SOR=0.26283;LSEQ=TGTCCGTCTCTGTCTTTCTC;RSEQ=GTCTGTCTCTTTGTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:11:7,4:44,47:91,11:0.1078:2,2:29.7:1:30.8:1:0.52507:1.86:55:22:0.1078:0:1.2 0/1:98:3:1,2:45,48:93,3:0.0306:2,2:19.3:1:28.7:1:1:1.86323:47.7:6:0.0316:0:1.7 +GL000220.1 136042 . C T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=0.23917;SOR=0;LSEQ=CCGTCTCTGTCTTTCTCTGT;RSEQ=TGTCTCTTTGTCTGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:2:1,1:50,49:99,2:0.0198:2,2:6.5:1:30:1:1:1.02021:60:4:0.02:0:1.5 0/0:105:0:0,0:49,56:105,0:0:2,0:23:1:30.4:1:1:0:54.1:51.5:1:0:0.3 +GL000220.1 136103 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49821;SOR=Inf;LSEQ=TCTCTGTCTCTCTCACTGTG;RSEQ=CTGTCTTCTGTCTTAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:62,54:116,0:0:2,0:24.4:1:29.8:1:1:0:57.7:57:1:0:0.4 0/1:122:2:1,1:60,60:120,2:0.0164:2,2:10.5:1:29:1:1:1:60:4:0.0164:0:2.5 +GL000220.1 136106 . G A 26 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=1.87747;LSEQ=CTGTCTCTCTCACTGTGTCT;RSEQ=TCTTCTGTCTTAGTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:1:1,0:62,50:112,1:0.0088:2,0:1:0:25:0:1:0:60:2:0.0097:0:1 0/1:121:2:1,1:58,61:119,2:0.0165:2,2:7.5:1:26.5:1:1:1.05:60:4:0.0172:0:2.5 +GL000220.1 136166 . C T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.34754;SOR=3.37624;LSEQ=TCTGTCTCTCTCTCTCTCTC;RSEQ=CCCTGTCTGTTTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:1:0,1:45,58:103,1:0.0096:2,0:10:0:25:0:1:0:60:2:0.0103:0:1 0/1:94:3:2,1:50,40:90,3:0.0319:2,2:13.7:1:27.7:1:1:1.59:46.7:6:0.0333:0:2 +GL000220.1 136168 . CCTGTCTGTT TGCCTTTCTGTA 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.23109;SOR=Inf;LSEQ=TGTCTCTCTCTCTCTCTCCC;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:44,57:101,0:0:2,0:23.9:1:31.2:1:1:0:57.7:202:1:0:0.5 0/1:94:2:1,1:52,39:91,2:0.0213:2,2:6.5:1:24.5:1:1:1.32915:50.5:4:0.0213:0.0106:1.5 +GL000220.1 136257 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=3.000;MSILEN=2;SSF=0.21164;SOR=0;LSEQ=CTCTCTCTCTCTCTCTGTGT;RSEQ=TCTGTCTTCTGTCTTACTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:35,47:82,2:0.0238:2,2:42:0:32:1:1:1.34:60:4:0.0244:0:1 0/0:98:0:0,0:54,44:98,0:0:2,0:27.3:1:31.2:1:1:0:54.3:48:1:0:0.4 +GL000220.1 136294 . GTCTGTCTGTCTCTC G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=4.000;MSILEN=2;SSF=0.51927;SOR=Inf;LSEQ=CTGTCTTTCTCTGCCTGTCT;RSEQ=TCTGTCTGTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:41,42:83,0:0:2,0:23.6:1:30:1:1:0:55.9:82:1:0:0.3 0/1:128:2:2,0:69,57:126,2:0.0156:2,0:11.5:1:31.5:1:0.50209:0:60:4:0.0157:0.0078:1 +GL000220.1 136313 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.52807;SOR=Inf;LSEQ=TGTCTGTCTGTCTCTCTCTG;RSEQ=CTGTCTCTCTCTCTCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:41,37:78,0:0:2,0:24.6:1:29.8:1:1:0:55.6:38:1:0:0.3 0/1:129:2:1,1:65,60:125,2:0.0155:2,2:28.5:1:29:1:1:1.08263:55:4:0.0157:0:2.5 +GL000220.1 136316 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.52899;SOR=Inf;LSEQ=CTGTCTGTCTCTCTCTGTCT;RSEQ=TCTCTCTCTCTCTCTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:39,39:78,0:0:2,0:24.2:1:30.9:1:1:0:55.7:10.143:1:0:0.3 0/1:130:2:1,1:67,61:128,2:0.0154:2,2:28.5:1:29.5:1:1:1.09757:55:4:0.0161:0:2.5 +GL000220.1 136320 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.5268;SOR=Inf;LSEQ=CTGTCTCTCTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCCCCCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:38,39:77,0:0:2,0:23.9:1:32.3:1:1:0:55.7:24.667:1:0:0.3 0/1:126:2:1,1:63,61:124,2:0.0159:2,2:34.5:1:29.5:1:1:1.03253:53:4:0.0164:0:1.5 +GL000220.1 136324 . CTCTCTCTCCCCCCGTCGGCTGTTTCTCTGTCTCTGTCTGTGTCTCTCTTTCTGTCTGTTTCTC G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.53312;SOR=Inf;LSEQ=CTCTCTCTGTCTGTCTCTCT;RSEQ=TCTGTCTGTCTTTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:35,38:73,0:0:2,0:24.3:1:32.8:1:1:0:55.6:72:1:0:0.3 0/1:126:2:1,1:62,60:122,2:0.0159:2,2:17.5:1:28.1:1:1:1.03307:60:4:0.0159:0.0159:0 +GL000220.1 136326 . CTCTCT C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=2;SSF=0.53113;SOR=Inf;LSEQ=CTCTCTGTCTGTCTCTCTCT;RSEQ=CCCCCCGTCGGCTGTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:36,37:73,0:0:2,0:23.8:1:30.5:1:1:0:55.6:23.333:1:0:0.4 0/1:124:2:1,1:61,57:118,2:0.0161:2,2:16:1:32:1:1:1.06954:35.5:4:0.0167:0.0161:0 +GL000220.1 136330 . CT C 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.00477;SOR=Inf;LSEQ=CTGTCTGTCTCTCTCTCTCT;RSEQ=CCCCCCGTCGGCTGTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:31,34:65,0:0:2,0:23.2:1:30.6:1:1:0:56.2:64:0.9275:0:0.2 0/1:129:12:7,5:53,54:107,12:0.093:2,2:13.3:1:30:1:0.76227:1.42:54.8:24:0.1:0.0775:0.8 +GL000220.1 136333 . C CT 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.15915;SOR=Inf;LSEQ=TCTGTCTCTCTCTCTCTCTC;RSEQ=CCCCGTCGGCTGTTTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:35,38:73,0:0:2,0:22.5:1:30.9:1:1:0:56.4:35.5:1:0:0.3 0/1:122:5:2,3:56,51:107,5:0.041:2,2:35.2:1:25.7:1:0.67086:1.63978:57.4:1.5:0.028:0.0164:2.2 +GL000220.1 136337 . C CT 186 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.27874;SOR=0.67968;LSEQ=TCTCTCTCTCTCTCTCCCCC;RSEQ=GTCGGCTGTTTCTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:72:50:26,24:3,7:10,50:0.6944:2,2:28:1:31.1:1:0.30218:2.49:57.9:100:0.7143:0:0.2 1/0:122:74:37,37:6,7:13,74:0.6066:2,2:28.7:1:30.1:1:1:1.16:57.1:148:0.6667:0:0.3 +GL000220.1 136340 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.54014;SOR=Inf;LSEQ=CTCTCTCTCTCTCCCCCCGT;RSEQ=GGCTGTTTCTCTGTCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:34,34:68,0:0:2,0:25:1:30.3:1:1:0:58.4:67:1:0:0.5 0/1:124:2:1,1:63,56:119,2:0.0161:2,2:9:0:31:1:1:1.1239:45:4:0.0177:0:1.5 +GL000220.1 136362 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16256;SOR=0;LSEQ=GCTGTTTCTCTGTCTCTGTC;RSEQ=GTGTCTCTCTTTCTGTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:2:1,1:43,44:87,2:0.0225:2,2:37.5:1:31.5:1:1:1.02:60:4:0.023:0:1.5 0/0:131:0:0,0:67,62:129,0:0:2,0:22.8:1:29.3:1:1:0:58.7:42:1:0:0.5 +GL000220.1 136383 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51121;SOR=Inf;LSEQ=GTGTCTCTCTTTCTGTCTGT;RSEQ=TCTCTCTGTCTGTCTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:44,45:89,0:0:2,0:25.7:1:30.2:1:1:0:59.2:28.667:1:0:0.4 0/1:124:2:1,1:59,59:118,2:0.0161:2,2:27.5:1:30.5:1:1:1:48.5:4:0.0169:0:1 +GL000220.1 136403 . C T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=2;SSF=0.51104;SOR=Inf;LSEQ=TTCTCTCTGTCTGTCTTTCT;RSEQ=TCTCTGTCTCTTTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:84:0:0,0:42,42:84,0:0:2,0:24.8:1:33.1:1:1:0:59.4:168:1:0:0.4 0/1:117:2:1,1:56,58:114,2:0.0171:2,2:8:0:31.5:1:1:1.04:36:4:0.0174:0:2.5 +GL000220.1 136453 . GTC G 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=1;SOR=1.73116;LSEQ=CTGTCTCTGTCTCTCTCTCT;RSEQ=TCTCTCTCTCTGTGGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:1:0,1:28,27:55,1:0.0179:2,0:40:0:26:0:1:0:60:2:0.0179:0:0 0/1:98:3:2,1:49,46:95,3:0.0306:2,2:33:1:29.7:1:1:1.87:56.7:6:0.0309:0:0.7 +GL000220.1 136467 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51817;SOR=Inf;LSEQ=CTCTCTGTCTCTCTCTCTCT;RSEQ=TGGGGGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:26,25:51,0:0:2,0:25.8:1:31.7:1:1:0:58:50:1:0:0.6 0/1:78:2:0,2:45,31:76,2:0.0256:2,0:20:1:32:1:0.17582:0:32:4:0.0274:0:3 +GL000220.1 136472 . G T 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.73581;SOR=1.42025;LSEQ=TGTCTCTCTCTCTCTGTGGG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:3:1,2:24,23:47,3:0.06:2,2:26.3:1:26.7:1:1:2.0574:53.3:6:0.06:0:2.7 0/1:72:6:4,2:35,27:62,6:0.0833:2,2:29.3:1:25.8:1:1:1.53:50.5:5:0.0746:0:1.8 +GL000220.1 136491 . GTGTATG A 126 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=21.000;MSILEN=2;SSF=0.16259;SOR=0.54579;LSEQ=GGGGTGTGTGTGTGTGTGTG;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:20:9,11:11,13:24,20:0.4167:2,2:21:1:29.3:1:1:1.03341:57.2:19:0.4419:0.1875:0.3 0/1:68:19:12,7:22,21:43,19:0.2794:2,2:24.7:1:27.1:1:0.42009:1.62:49.8:18:0.2903:0.1176:0.7 +GL000220.1 136574 . GTC G 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.65425;SOR=1.27244;LSEQ=GTCTGTCTGCCTGTCTGTTT;RSEQ=TCTCTCTCTCTGCCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:10:5,5:47,39:86,10:0.1042:2,2:28.7:1:32.7:1:1:1.20277:56.7:20:0.1042:0.0104:0.1 0/1:93:12:7,5:42,40:82,12:0.129:2,2:22.5:1:31.1:1:0.76149:1.33:54.3:24:0.1304:0.043:0.2 +GL000220.1 136576 . C G 34 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=6.000;MSILEN=2;SSF=0.49736;SOR=0;LSEQ=CTGTCTGCCTGTCTGTTTGT;RSEQ=TCTCTCTCTCTGCCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:2:1,1:45,38:83,2:0.0213:2,2:18:0:34:0:1:1.18184:36:4:0.0241:0:1.5 0/0:92:0:0,0:43,40:83,0:0:2,0:25.1:1:31.2:1:1:0:57:40.5:1:0:0.4 +GL000220.1 136637 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=6;SSF=0.49763;SOR=Inf;LSEQ=TCTCTCTTTCTGTTTCTCTC;RSEQ=GTCTCTGTCCATCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:56,44:100,0:0:2,0:25.8:1:31:1:1:0:57.8:99:1:0:0.2 0/1:103:2:1,1:54,47:101,2:0.0194:2,2:35:0:32:1:1:1.14738:60:4:0.0196:0:1.5 +GL000220.1 136650 . CTCTGTCTTTCTCCGTCTGTCTCTTTA C 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.000;MSILEN=2;SSF=0.25082;SOR=Inf;LSEQ=TTCTCTCTGTCTCTGTCCAT;RSEQ=TCTGTCTCTCTCCGTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:44,42:86,0:0:2,0:25.3:1:30.4:1:1:0:57.5:42:1:0:0.2 0/1:101:3:0,3:52,46:98,3:0.0297:2,0:8:1:26.9:1:0.11056:0:34:6:0.03:0.0297:1.7 +GL000220.1 136658 . TTCTCCGTCTGTCTCTTTATCTGTCTC T 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=4.000;MSILEN=2;SSF=0.51399;SOR=0.62732;LSEQ=GTCTCTGTCCATCTCTGTCT;RSEQ=TCTCCGTCTGTCTCTTTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:5:2,3:39,40:79,5:0.0595:2,2:21.6:1:27.7:1:1:1.45597:46:10:0.0625:0.0595:1.2 0/1:105:4:1,3:48,51:99,4:0.0381:2,2:16.5:1:28:1:0.61937:2.7979:32.5:8:0.0396:0.0286:0.8 +GL000220.1 136680 . G A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.17977;SOR=0;LSEQ=CTCCGTCTGTCTCTTTATCT;RSEQ=TCTCTCTCCGTCTGTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:2,0:40,35:75,2:0.025:2,0:25.5:1:26.5:1:0.49761:0:44.5:4:0.0263:0:1 0/0:108:0:0,0:49,55:104,0:0:2,0:23:1:31.1:1:1:0:56.8:103:0.9717:0:0.2 +GL000220.1 136706 . GTC G 67 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.03033;SOR=0;LSEQ=CTCCGTCTGTCTCTTTATCT;RSEQ=TCTCTCTCTCTTTCTGTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:4:3,1:31,41:72,4:0.0526:2,2:31:1:33.5:1:0.31928:3.90:60:8:0.0541:0:0.3 0/0:104:0:0,0:53,51:104,0:0:2,0:25.1:1:28.7:1:1:0:58.8:103:1:0:0.2 +GL000220.1 136736 . C T 85 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=2;SSF=1;SOR=1.12532;LSEQ=CTCTTTCTGTCTTTCTCTCT;RSEQ=TGTGTATCGTTGTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:5:2,3:32,42:74,5:0.0633:2,2:21:1:27.6:1:1:1.14093:50.4:4:0.0533:0:1.4 0/1:99:7:4,3:45,46:91,7:0.0707:2,2:33.7:1:30.3:1:1:1.36:44.4:14:0.0722:0:1.3 +GL000220.1 136737 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.20338;SOR=0;LSEQ=TCTTTCTGTCTTTCTCTCTC;RSEQ=GTGTATCGTTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:2:1,1:33,46:79,2:0.0247:2,2:23:1:29:1:1:1.39:60:4:0.0247:0:1 0/0:98:0:0,0:49,49:98,0:0:2,0:22.9:1:29.9:1:1:0:57.3:196:1:0:0.4 +GL000220.1 136782 . GTC G 138 MSI12;MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=13.000;MSILEN=2;SSF=0.71887;SOR=0.87607;LSEQ=GTCTCTGTCTCTGTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:19:7,12:14,22:36,19:0.2879:2,2:34.8:1:32.7:1:1:1.08917:60:38:0.2879:0.0152:0.1 0/1:88:23:10,13:22,16:38,23:0.2614:2,2:29.1:1:30.6:1:0.30242:1.77034:57.4:46:0.2674:0.0341:0.6 +GL000220.1 136821 . C T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.16019;SOR=Inf;LSEQ=TCTCTCTCTGTCTGTCTGTC;RSEQ=GTCTGTCTGTCTCGGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:21,24:45,0:0:2,0:21.9:1:30:1:1:0:58.9:44:1:0:0.2 0/1:82:5:2,3:33,44:77,5:0.061:2,2:10.8:1:27.8:1:1:1.12337:39.2:10:0.0641:0:3 +GL000220.1 136825 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=4;SSF=0.54356;SOR=Inf;LSEQ=TCTCTGTCTGTCTGTCCGTC;RSEQ=GTCTGTCTCGGTCTCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:21,23:44,0:0:2,0:22.1:1:31.6:1:1:0:58.9:88:1:0:0.2 0/1:83:2:1,1:35,46:81,2:0.0241:2,2:43.5:1:30.5:1:1:1.31:60:4:0.025:0:1.5 +GL000220.1 136875 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51482;SOR=Inf;LSEQ=TCCCGCCCTCTCTTTTTTTG;RSEQ=AAAAGAAGCTCAAGTACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:14,17:31,0:0:2,0:25:1:32.3:1:1:0:60:62:1:0:0.2 0/1:47:2:1,1:18,27:45,2:0.0426:2,2:15:1:30:1:1:1.49:60:4:0.0426:0:1 +GL000220.1 136901 . T G 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10182;LSEQ=AAGCTCAAGTACATCTAATC;RSEQ=AATCCCTTACCAAGGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:1,5:11,13:24,6:0.2:2,2:8.7:1:29.8:1:0.35753:4.05493:52:5:0.1724:0:1 0/1:37:8:2,6:14,15:29,8:0.2162:2,2:17.1:1:31.5:1:0.42271:2.72671:57.8:16:0.2162:0:1.1 +GL000220.1 137170 . C T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12963;SOR=0.34871;LSEQ=TGTGACCGAGCCCTGTCCGT;RSEQ=CTGTCTCAAATATGTACGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:9:4,5:8,13:21,9:0.3:2,2:24.2:1:29.9:1:1:1.29:46.3:18:0.3214:0:1.1 0/1:39:5:2,3:18,16:34,5:0.1282:2,2:30.6:1:28.8:1:0.66142:1.66507:44:10:0.1316:0:1 +GL000220.1 137224 . G A 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48988;SOR=Inf;LSEQ=CCATTTCCACAACTACCCAC;RSEQ=GCCCCTTGTGGAACCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:18,0:0:2,0:25.8:1:30.4:1:1:0:54.7:17:1:0:0.4 0/1:21:2:1,1:8,11:19,2:0.0952:2,2:25:0:32:0:1:1.35:37.5:4:0.0952:0:1.5 +GL000220.1 137458 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22284;SOR=0;LSEQ=CACCGAGGTCAAATGGATAC;RSEQ=TCTGCATTGGCCCGAGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:26,19:45,2:0.0426:2,2:26.5:1:31:1:1:1.35916:60:4:0.0435:0:2.5 0/0:52:0:0,0:31,21:52,0:0:2,0:23.7:1:30.4:1:1:0:56.1:51:1:0:0.3 +GL000220.1 137494 . G A 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12274;SOR=Inf;LSEQ=GGCCTCCGAAGTACATCACC;RSEQ=TCACCAACCGTCACCGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:33,31:64,0:0:2,0:23.8:1:30:1:1:0:58.2:11.8:1:0:0.4 0/1:73:4:2,2:34,35:69,4:0.0548:2,2:20.8:1:27:1:1:1.03:52:3:0.0423:0:1.8 +GL000220.1 137543 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18787;SOR=0;LSEQ=TGAGCCTGCCCAAGGCCCCG;RSEQ=CTCCGGGGAGACTCTTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:2:1,1:33,29:62,2:0.0313:2,2:36.5:1:30.5:1:1:1.13563:29:4:0.0333:0:3.5 0/0:83:0:0,0:39,43:82,0:0:2,0:25.2:1:30.5:1:1:0:56.1:26.333:0.9875:0:0.3 +GL000220.1 137666 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50024;SOR=Inf;LSEQ=TAGGTCAGAGAGGGGACCAG;RSEQ=AGGGGAGACGTCCCGACAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:95:0:0,0:51,44:95,0:0:2,0:22.4:1:31.3:1:1:0:58.7:190:1:0:0.2 0/1:110:2:1,1:55,53:108,2:0.0182:2,2:37.5:1:28.5:1:1:1.0374:57:4:0.0183:0:1 +GL000220.1 137690 . C T 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.06261;LSEQ=GGAGACGTCCCGACAGGCGA;RSEQ=GAGTTCCCAAGGCTCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:6:3,3:51,50:101,6:0.0561:2,2:19.5:1:30.3:1:1:1.01981:53.3:12:0.0571:0:2.2 0/1:111:33:17,16:42,36:78,33:0.2973:2,2:17.4:1:30.1:1:0.83815:1.09711:50:66:0.3028:0:1.5 +GL000220.1 137741 . G A 83 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01283;SOR=0;LSEQ=CGCCCCACGCCCCACGTCCC;RSEQ=GGCACCCGCGGGACACCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:6:3,3:55,54:109,6:0.0522:2,2:21:1:32.3:1:1:1.01836:60:12:0.0561:0:1.2 0/0:120:0:0,0:60,60:120,0:0:2,0:23.3:1:28.2:1:1:0:59.2:16.143:1:0:0.7 +GL000220.1 137748 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49998;SOR=Inf;LSEQ=CGCCCCACGTCCCGGGCACC;RSEQ=GCGGGACACCGCCGCTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:57,49:106,0:0:2,0:26.7:1:30.4:1:1:0:59.8:105:1:0:0.6 0/1:121:2:1,1:59,60:119,2:0.0165:2,2:20.5:1:31.5:1:1:1.02:60:4:0.0171:0:1 +GL000220.1 137762 . G C 145 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.6398;SOR=1.16416;LSEQ=GGCACCCGCGGGACACCGCC;RSEQ=CTTTATCCCCTCCTCTGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:23:13,10:46,39:85,23:0.213:2,2:25.3:1:29.8:1:1:1.10:58.9:22:0.2056:0:2 0/1:121:29:15,14:44,47:91,29:0.2397:2,2:23.2:1:29.9:1:0.83237:1.14:58.1:58:0.2458:0:1.5 +GL000220.1 137766 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2379;SOR=0;LSEQ=CCCGCGGGACACCGCCGCTT;RSEQ=ATCCCCTCCTCTGTCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:57,51:108,2:0.0182:2,2:37:1:31.5:1:1:1.11651:60:4:0.0182:0:2 0/0:115:0:0,0:55,60:115,0:0:2,0:25.5:1:27.9:1:1:0:59.2:37.333:1:0:0.6 +GL000220.1 137786 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24395;SOR=0;LSEQ=TATCCCCTCCTCTGTCCACA;RSEQ=CCGGCCCCACCCCACCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:1,1:46,53:99,2:0.0196:2,2:15:1:28:1:1:1.15:60:4:0.0202:0:1.5 0/0:104:0:0,0:46,57:103,0:0:2,0:25.2:1:30.8:1:1:0:59.5:33.333:0.9901:0:0.3 +GL000220.1 137788 . C T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49756;SOR=0;LSEQ=TCCCCTCCTCTGTCCACAGC;RSEQ=GGCCCCACCCCACCACGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:1,1:47,54:101,2:0.0194:2,2:27.5:1:33:1:1:1.15:58:4:0.0202:0:1.5 0/0:102:0:0,0:45,57:102,0:0:2,0:25:1:29.3:1:1:0:60:101:1:0:0.4 +GL000220.1 137843 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20152;SOR=Inf;LSEQ=CTGGAGGTTCCAAAACCACA;RSEQ=GGTGTGACTAGAGCCTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:89:0:0,0:41,47:88,0:0:2,0:27.8:1:30.9:1:1:0:59.6:43:1:0:0.4 0/1:73:2:1,1:34,37:71,2:0.0274:2,2:25:0:32:1:1:1.09:57.5:4:0.0278:0:1 +GL000220.1 137868 . G A 22 v3;pSTD;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.20325;SOR=Inf;LSEQ=TGACTAGAGCCTGACGGAGC;RSEQ=AGAGCCCATTTCACGAGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:81:0:0,0:39,42:81,0:0:2,0:22.7:1:30.5:1:1:0:59.5:162:1:0:0.5 0/1:67:2:1,1:36,29:65,2:0.0299:2,2:10:0:22.5:1:1:1.23734:60:4:0.0303:0:2 +GL000220.1 137901 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.50178;SOR=Inf;LSEQ=ACGAGGTGGGAGGGGTGGGG;RSEQ=TGGGGTGGGTTGGGGGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:28,25:53,0:0:2,0:23.5:1:29.9:1:1:0:58.8:12.25:1:0:0.8 0/1:66:2:0,2:33,31:64,2:0.0303:2,0:21:1:32:0:0.49231:0:60:4:0.0333:0:1 +GL000220.1 137902 . T G 71 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.78493;SOR=1.2565;LSEQ=CGAGGTGGGAGGGGTGGGGG;RSEQ=GGGGTGGGTTGGGGGTTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:6:0,6:28,19:47,6:0.1132:2,0:15.5:1:16.8:1:0.00771:0:56.2:1:0.0638:0:3.5 0/1:65:9:0,9:32,24:56,9:0.1385:2,0:10.6:1:22.6:1:0.00208:0:51.2:3.5:0.1207:0:2.2 +GL000220.1 137912 . T TG 24 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=1;SOR=1.56766;LSEQ=GGGGTGGGGGTGGGGTGGGT;RSEQ=GGGGGTTGTGGGGTCTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:1:0,1:26,19:45,1:0.0204:2,0:21:0:9:0:0.43478:0:60:0:0:0:3 0/1:63:2:0,2:30,28:58,2:0.0317:2,0:19:1:24:1:0.49153:0:41.5:4:0.0408:0:2 +GL000220.1 137933 . C A 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.39698;SOR=3.6465;LSEQ=GGGGGTTGTGGGGTCTGTGG;RSEQ=GAGCCCGATTCTCCCTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:1:1,0:17,25:42,1:0.0233:2,0:1:0:25:0:0.4186:0:60:2:0.0238:0:1 0/1:62:5:3,2:22,34:56,5:0.0806:2,2:26.4:1:29.2:1:0.39241:2.29:54.4:10:0.0847:0:2.2 +GL000220.1 137987 . T C 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.24958;SOR=2.8726;LSEQ=TAGAAATGAATATCGCTTCT;RSEQ=GGGCGGAGGGGCTTCCTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:3:1,2:22,20:42,3:0.0667:2,2:23:1:23.3:1:0.60775:2.16282:60:2:0.0476:0:1.7 0/1:29:5:3,2:8,16:24,5:0.1724:2,2:15.2:1:30.2:1:0.33864:2.88:60:10:0.1724:0:1.2 +GL000220.1 138028 . T A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCATCACCGCTTGCGGGAC;RSEQ=ACCTCTCAAACCCTCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:24,30:54,2:0.0357:2,2:30:1:31:1:1:1.24:55.5:4:0.0364:0:1 0/0:25:0:0,0:11,14:25,0:0:2,0:22.4:1:29.4:1:1:0:56.6:50:1:0:0.4 +GL000220.1 138752 . A T 31 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13725;SOR=0;LSEQ=GATACACATTTAAAAAAATA;RSEQ=CAACACAAGGATCAACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:1,1:1,4:5,2:0.2857:2,2:27.5:1:31:1:1:3.16:49.5:4:0.2857:0:1 0/0:11:0:0,0:6,5:11,0:0:2,0:27.1:1:29.8:1:1:0:60:22:1:0:0.4 +GL000220.1 138786 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AACCAGACTTGGGAAAAAAT;RSEQ=GAAAACCACACAAGTCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:1,5:6,0:0:2,0:23.5:1:30.2:1:1:0:60:12:1:0:0.2 0/1:10:2:1,1:4,4:8,2:0.2:2,2:11:1:30.5:1:1:1:60:4:0.2:0:1 +GL000220.1 139010 . G T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=AAGTGTTTCAGTAATATAAT;RSEQ=CTTCAGATTTAGAAGCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:18:1:29.7:1:1:0:60:6:1:0:0 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:41.5:1:29:1:1:2.44949:59.5:4:0.3333:0:1 +GL000220.1 139128 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49351;SOR=Inf;LSEQ=TGACTTCAGAATCATACTTT;RSEQ=TCTTGATATTTACTTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:6,3:9,0:0:2,0:28.4:1:33.6:1:1:0:60:18:1:0:0.2 0/1:13:2:1,1:5,6:11,2:0.1538:2,2:40:0:30.5:1:1:1.18:60:4:0.1538:0:1.5 +GL000220.1 139156 . AT A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.22414;SOR=0;LSEQ=ATTTACTTATGTATGTATTT;RSEQ=TTTTTTTAATTTATTTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:20.5:1:31:1:1:1.36624:60:4:0.1538:0:0.5 0/0:15:0:0,0:7,8:15,0:0:2,0:17.6:1:30.7:1:1:0:60:30:1:0:0.3 +GL000220.1 139403 . G A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATCTCTTGACCTCGTGACCC;RSEQ=CCCGCCTCGGCCTCCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:15.5:1:29.3:1:1:0:45:8:1:0:0.3 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:24.5:1:29:1:1:1.12:46:4:0.1111:0:1 +GL000220.1 139635 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50877;SOR=Inf;LSEQ=ATACACGAGTACAAAAGAGT;RSEQ=AAACAGAGAGACTGCTAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:25.1:1:27:1:1:0:53.6:6:1:0:0.1 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:25:1:29:1:1:1.45:48.5:4:0.1667:0:1 +GL000220.1 139749 . T G 78 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.80856;LSEQ=GTTTCCATGTATTTTTCTAT;RSEQ=ATCCAATAAGTGAACTATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:3,3:6,5:0.4545:2,2:24.2:1:33.8:1:0.54545:3.52:60:10:0.4545:0:1 0/1:10:4:2,2:2,4:6,4:0.4:2,2:22.5:1:31.3:1:1:1.86:60:8:0.4:0:1 +GL000220.1 139949 . C CGAT 47 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.000;MSILEN=3;SSF=0.58204;SOR=0.31051;LSEQ=TATAAGGATCTGGTATTCTA;RSEQ=GATCATGAGTTCACTTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:2,1:3,4:7,3:0.3:2,2:34.7:1:30.2:1:1:2.41:60:6:0.3:0:0 0/1:9:1:0,1:4,4:8,1:0.1111:2,0:30:0:32:0:1:0:60:2:0.1111:0:0 +GL000220.1 140156 . C T 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CATTAGCACTTACCATGCCT;RSEQ=ACAATGTCTAGGATTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:31.4:1:29.6:1:1:0:59.4:10:1:0:1.2 1/1:9:9:5,4:0,0:0,9:1:0,2:30.7:1:29.7:1:1:0:58.2:18:1:0:1.4 +GL000220.1 140190 . A G 59 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.54545;SOR=3.51553;LSEQ=TTGACCCTGATAGCATTTCG;RSEQ=AAACAAGCTAATGCTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:3,1:0.25:2,0:6:0:34:0:1:0:60:2:0.25:0:2 1/0:7:4:2,2:1,2:3,4:0.5714:2,2:24.3:1:29.8:1:1:1.81:60:8:0.5714:0:2 +GL000220.1 140243 . A C 34 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13333;SOR=Inf;LSEQ=GAAGACAAGCTCACGCCCTA;RSEQ=TGCGCTATAGGCATAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:4,2:6,0:0:2,0:17.2:1:31.7:1:1:0:60:12:1:0:0 1/0:4:2:1,1:0,2:2,2:0.5:0,2:13:0:34:0:1:0:60:4:0.5:0:2.5 +GL000220.1 140251 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14286;SOR=Inf;LSEQ=GCTCACGCCCTAATGCGCTA;RSEQ=AGGCATAAGCATCATTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:5,4:9,0:0:2,0:15:1:30.7:1:1:0:60:18:1:0:0.1 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:21:0:32:1:1:2.45:60:4:0.3333:0:2.5 +GL000220.1 140679 . T G 53 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.5671;SOR=0.3704;LSEQ=CCTTTCACGAAGAAGGCTCA;RSEQ=CAAGCCTTCCGCTGCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:5:3:1,2:1,1:2,3:0.6:2,2:8.3:1:33.7:1:1:1.7321:54.3:6:0.6:0:1.3 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:38.5:1:31:1:1:1:33.5:4:0.3333:0:1 +GL000220.1 140745 . C T 100 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=AGGCGCGATTGCGGCTATTT;RSEQ=CCCTTCTGAAATGACGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:5,5:0,0:0,10:1:0,2:16.6:1:30.4:1:1:0:44.8:9:1:0:1.3 1/0:6:4:2,2:1,1:2,4:0.6667:2,2:26:1:29.8:1:1:1:51.3:8:0.6667:0:1.8 +GL000220.1 140759 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11029;SOR=Inf;LSEQ=CTATTTCCCCTTCTGAAATG;RSEQ=CGGAAGAGTCCAATTTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:7,4:11,0:0:2,0:16.9:1:31.1:1:1:0:46.2:22:1:0:1.1 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:44.5:1:31.5:1:1:1:60:4:0.3333:0:2.5 +GL000220.1 140832 . T C 62 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61945;SOR=2.96757;LSEQ=TATTGCTCCTTTATTAGTTT;RSEQ=ACTTTTGGTTCTTCTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:1:1,0:5,5:10,1:0.0909:2,0:43:0:34:0:1:0:53:2:0.0909:0:2 0/1:17:4:2,2:8,5:13,4:0.2353:2,2:22:1:31.3:1:1:1.55528:50.8:8:0.2353:0:1 +GL000220.1 140869 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08523;SOR=0;LSEQ=TTTGGGATTTTAGGTGGAAA;RSEQ=TTCATTTTTAATTTTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:1,1:4,4:8,2:0.2:2,2:20:1:30:1:1:1:56.5:4:0.2:0:1.5 0/0:23:0:0,0:13,10:23,0:0:2,0:26.7:1:32:1:1:0:57.7:46:1:0:0.2 +GL000220.1 140934 . T G 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.25134;SOR=Inf;LSEQ=ACTAGTCAAGAGTCGTGAAT;RSEQ=TCTTCGAGGCGGTGCATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,7:14,0:0:2,0:24.9:1:30.1:1:1:0:60:13:1:0:0.1 0/1:20:3:1,2:10,7:17,3:0.15:2,2:27:1:31:1:0.56579:2.70974:60:6:0.1579:0:1.7 +GL000220.1 140964 . C T 30 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.0812;LSEQ=CGGTGCATTTGGGGGAGATG;RSEQ=CATAGTGGGGCTCAATACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:1,0:8,5:13,1:0.0714:2,0:18:0:32:0:1:0:60:2:0.0769:0:1 0/1:26:2:1,1:13,11:24,2:0.0769:2,2:25:0:30.5:1:1:1.17422:57:4:0.08:0:1.5 +GL000220.1 140975 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54017;SOR=Inf;LSEQ=GGGGAGATGCCATAGTGGGG;RSEQ=TCAATACCTGAGGTGTTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:9,6:15,0:0:2,0:29.1:1:32.7:1:1:0:60:30:1:0:0.1 0/1:29:2:1,1:16,11:27,2:0.069:2,2:28:1:30:0:1:1.43545:60:4:0.08:0:2 +GL000220.1 141112 . T C 51 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.67393;SOR=0.64629;LSEQ=CCGATTCTGGCAACAGGCTT;RSEQ=TTTGAAGGGGCTCCGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:3:2,1:8,8:16,3:0.1579:2,2:23.7:1:31.7:1:1:1.93:60:6:0.1579:0:1 0/1:28:3:1,2:10,15:25,3:0.1071:2,2:16.3:1:32.7:1:1:1.32008:60:6:0.1071:0:1 +GL000220.1 141114 . T C 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.36716;SOR=1.90379;LSEQ=GATTCTGGCAACAGGCTTTT;RSEQ=TGAAGGGGCTCCGGTGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:4,4:5,5:10,8:0.4444:2,2:16.5:1:31.8:1:1:1:60:16:0.4444:0:1.6 1/0:28:17:7,10:4,7:11,17:0.6071:2,2:30.2:1:31.6:1:1:1.22:60:34:0.6071:0:1.6 +GL000220.1 141143 . A G 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09144;SOR=0.27138;LSEQ=CTCCGGTGGATGGCACGTCA;RSEQ=TGACAGACGGTGTCTCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:5,4:1,4:5,9:0.6429:2,2:23.7:1:31.3:1:0.3007:4.45:60:18:0.6429:0:1.9 0/1:25:8:4,4:7,10:17,8:0.32:2,2:22.9:1:31.6:1:1:1.41:60:16:0.32:0:2.3 +GL000220.1 141152 . G T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.19386;LSEQ=ATGGCACGTCAATGACAGAC;RSEQ=GTGTCTCATACCAGTGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:1:0,1:6,6:12,1:0.0769:2,0:1:0:30:0:1:0:60:2:0.0769:0:1 0/1:22:2:1,1:10,10:20,2:0.0909:2,2:19.5:1:31.5:1:1:1:60:4:0.0909:0:2.5 +GL000220.1 141228 . G A 114 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTAATGGCAAAATGCCAAC;RSEQ=CTTGGGGTTAATGGACTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:6,9:0,0:0,15:1:0,2:17.9:1:29.4:1:1:0:45:30:1:0:1.7 1/1:11:11:5,6:0,0:0,11:1:0,2:30.2:1:29.9:1:1:0:47.2:22:1:0:1.4 +GL000220.1 141281 . T G 46 v3 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.63159;LSEQ=TCCTAATAAACTTCGACCAG;RSEQ=TTTTGGTTTATGTTGAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:16.5:1:30.5:1:1:1.45:28.5:4:0.1667:0:1.5 0/1:12:3:2,1:5,4:9,3:0.25:2,2:1.7:1:29.3:1:1:1.54:46.7:6:0.25:0:1.7 +GL000220.1 141440 . C G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51515;SOR=Inf;LSEQ=TAAATTCCATCCGTTTCATT;RSEQ=GACGGTGTCCTGGGGTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:5,3:8,0:0:2,0:21.9:1:31.8:1:1:0:58.5:16:1:0:0.3 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:30:1:31:1:1:1.36624:60:4:0.1429:0:1.5 +GL000220.1 141518 . T C 83 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.75898;LSEQ=AGGACGAGGTCCAAGTGTTG;RSEQ=GGCGCAACACTTGGACAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:3,3:6,3:9,6:0.4:2,2:28.7:1:32.2:1:0.62238:1.90694:60:12:0.4:0:1.2 0/1:9:3:0,3:3,3:6,3:0.3333:2,0:31:1:29.7:1:0.46429:0:60:6:0.3333:0:1.3 +GL000220.1 142014 . C CGGTA 74 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=2.000;MSILEN=4;SSF=1;SOR=0.97892;LSEQ=CTGCGGGGGAAACCGCATCT;RSEQ=GGTAGGCATAGTGGTTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:4,2:26,20:46,6:0.1154:2,2:23.3:1:30.9:1:1:1.53:55.3:12:0.1154:0.0385:0 0/1:53:6:3,3:30,17:47,6:0.1132:2,2:20.8:1:28.7:1:0.66134:1.74497:50.7:12:0.1132:0.0377:0.5 +GL000220.1 142091 . G C 52 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62121;SOR=0.36773;LSEQ=ACCGCCATCCTCGAGGCTCA;RSEQ=GCCCACTTTCTGCAGTGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:3:2,1:32,26:58,3:0.0492:2,2:29.3:1:33:1:1:1.61:39.3:6:0.0517:0:2 0/1:54:1:1,0:31,22:53,1:0.0185:2,0:21:0:33:0:1:0:24:2:0.0204:0:2 +GL000220.1 142111 . A T 60 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48124;SOR=0.55016;LSEQ=GGCCCACTTTCTGCAGTGCC;RSEQ=CAGGCACCCCCCCCCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:2,3:24,15:39,5:0.1087:2,2:25:1:26:1:0.38592:2.35103:44.2:4:0.1053:0:2 0/1:48:3:2,1:25,18:43,3:0.0625:2,2:20.3:1:27:1:1:1.43:38.7:2:0.0488:0:3.3 +GL000220.1 142155 . C T 81 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.3422;SOR=0.46612;LSEQ=CGGCTCCGGCCCGGCCAGCC;RSEQ=CGGCTCATTTAAAGGCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:3,4:20,27:47,7:0.1296:2,2:27.7:1:29:1:1:1.01:58.6:6:0.1176:0:1.6 0/1:62:4:2,2:25,33:58,4:0.0645:2,2:11.8:1:30.5:1:1:1.31:55.3:8:0.0678:0:1 +GL000220.1 142201 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.5133;SOR=Inf;LSEQ=CGTTACCGGGGGATGGGGGA;RSEQ=TCCGAGACAGAATGACTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:24,29:53,0:0:2,0:23.7:1:32.3:1:1:0:59.4:25.5:1:0:0.5 0/1:77:2:1,1:35,39:74,2:0.026:2,2:16:0:30:1:1:1.11:44:4:0.0274:0:1.5 +GL000220.1 142271 . G C 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGTGATCCATTGCAAAC;RSEQ=GAGAGTCACCTCGTGTTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:28,19:0,0:0,47:1:0,2:28.7:1:30.6:1:1:0:60:46:1:0:1.1 1/1:66:66:32,34:0,0:0,66:1:0,2:21.7:1:29.4:1:1:0:60:65:1:0:1.3 +GL000220.1 142378 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50625;SOR=0;LSEQ=TCTTCCTTCTGATTCGGTCT;RSEQ=CACAGTGGGGCCTAGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:2:1,1:40,35:75,2:0.026:2,2:30:0:31:1:1:1.14087:33:4:0.0267:0:1.5 0/0:58:0:0,0:27,31:58,0:0:2,0:26.9:1:31.1:1:1:0:56.7:57:1:0:0.3 +GL000220.1 142392 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49845;SOR=0;LSEQ=CGGTCTGCACAGTGGGGCCT;RSEQ=GGGCTGGAGCTCTCTCCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:43,38:81,2:0.0238:2,2:20:1:30:1:1:1.12989:50.5:4:0.025:0:2 0/0:75:0:0,0:36,39:75,0:0:2,0:21.3:1:28.2:1:1:0:54.5:24:1:0:0.3 +GL000220.1 142413 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.4992;SOR=0;LSEQ=GGGCTGGAGCTCTCTCCGTG;RSEQ=GGACCGCTGACTCCCTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:48,37:85,2:0.023:2,2:12.5:1:29.5:1:1:1.29337:60:4:0.0238:0:1 0/0:76:0:0,0:41,35:76,0:0:2,0:22.8:1:30.1:1:1:0:54.3:75:1:0:0.3 +GL000220.1 142419 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18519;SOR=Inf;LSEQ=GAGCTCTCTCCGTGCGGACC;RSEQ=CTGACTCCCTCTACCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:53,38:91,0:0:2,0:24.9:1:30.7:1:1:0:56.8:44.5:0.9889:0:0.3 0/1:70:2:1,1:36,30:66,2:0.0286:2,2:18.5:1:32:0:1:1.19677:23:4:0.029:0:1.5 +GL000220.1 142483 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22289;SOR=Inf;LSEQ=GCCGGGCCTTGGCAGATTCT;RSEQ=GCCCTTCCTGGCCCTTCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:35,36:71,0:0:2,0:25.7:1:30.8:1:1:0:59.4:22.667:1:0:0.1 0/1:64:2:1,1:33,29:62,2:0.0313:2,2:19.5:1:30:1:1:1.13563:60:4:0.0317:0:1.5 +GL000220.1 142627 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49568;SOR=Inf;LSEQ=CCACAGGAGCTCGGGACACA;RSEQ=GTGCTTTCGGGAGAGAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:13,25:38,0:0:2,0:27.2:1:31.4:1:1:0:59.1:76:1:0:0.2 0/1:43:2:1,1:19,22:41,2:0.0465:2,2:41.5:1:30:1:1:1.15:60:4:0.0465:0:1 +GL000220.1 142636 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4965;SOR=Inf;LSEQ=CTCGGGACACACGTGCTTTC;RSEQ=GGAGAGAATGCTGAGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:13,23:36,0:0:2,0:27.8:1:31.6:1:1:0:59.4:72:1:0:0.1 0/1:42:2:1,1:18,22:40,2:0.0476:2,2:11:0:32:0:1:1.22:60:4:0.0476:0:1.5 +GL000220.1 142900 . ACAGG A 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=27;MSI=7.000;MSILEN=4;SSF=0.1748;SOR=0.37091;LSEQ=AGACAGAATGAGGCCCTGCC;RSEQ=CAGGCAGGCAGGCAGGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:2,5:3,3:6,7:0.5385:2,2:30.3:1:30.9:1:0.59207:2.32357:50.3:14:0.5385:0.0769:0.6 0/1:27:8:5,3:8,11:19,8:0.2963:2,2:25.6:1:31.3:1:0.41971:2.22:44.6:16:0.2963:0:0.3 +GL000220.1 143001 . AT A 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.40039;SOR=0.40877;LSEQ=CAGAATACAGCACTTAATTA;RSEQ=TTTTTTTTTTCCCTTCGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:4:2,2:10,6:16,4:0.2:2,2:26:1:32.3:1:1:1.6233:59.5:8:0.2:0:0.8 0/1:22:2:1,1:10,10:20,2:0.0909:2,2:11:0:32.5:1:1:1:60:4:0.0909:0:0.5 +GL000220.1 143067 . C T 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23256;SOR=0;LSEQ=CTGGAGTGCAGTGGCACCAT;RSEQ=TCGGCTCACCGCAACCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:8,11:19,2:0.0952:2,2:7.5:1:30.5:1:1:1.35:52.5:4:0.1:0:1.5 0/0:22:0:0,0:10,12:22,0:0:2,0:22.4:1:29:1:1:0:53.3:10:1:0:0.5 +GL000220.1 143111 . C T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06054;SOR=Inf;LSEQ=CCCGCGTTCAAGCGATTCTC;RSEQ=TGCCTCAGCCTCCTGAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:17,0:0:2,0:28.7:1:32.4:1:1:0:49.8:34:1:0:0.5 0/1:23:5:2,3:9,9:18,5:0.2174:2,2:8.6:1:31:1:1:1.47392:38.4:10:0.2174:0:1.4 +GL000220.1 143162 . G A 120 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.7298;SOR=0.70895;LSEQ=AGGGAGGAGCCACCACACCC;RSEQ=GCTGATTTTGTATTGTTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:18:7,11:1,3:4,18:0.8182:2,2:23.6:1:28.1:1:1:1.86:38.3:5:0.7895:0:1.3 1/0:25:19:9,10:5,1:6,19:0.76:2,2:24:1:28.3:1:0.18043:5.21274:38.5:8.5:0.7727:0:1.4 +GL000220.1 143164 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.22067;SOR=0;LSEQ=GGAGGAGCCACCACACCCGG;RSEQ=TGATTTTGTATTGTTAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:7,11:18,2:0.1:2,2:36.5:1:31:1:1:1.54:43.5:4:0.1:0:2 0/0:22:0:0,0:12,10:22,0:0:2,0:23.4:1:30.5:1:1:0:40.9:21:1:0:1.2 +GL000220.1 143376 . C CATTT 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=7.000;MSILEN=4;SSF=1;SOR=1.44805;LSEQ=TTAATCTATTTATTTATTTA;RSEQ=ATTTATTTATTTATTTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:1:1,0:5,6:11,1:0.0833:2,0:45:0:29:0:1:0:50:2:0.0833:0:0 0/1:17:2:1,1:6,8:14,2:0.1176:2,2:40:0:31:1:1:1.31:60:4:0.125:0:0 +GL000220.1 143398 . T C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=4;SSF=0.48276;SOR=0;LSEQ=TTTATTTATTTATTTATTTA;RSEQ=TTACTTATTTATTTATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:14.5:1:33.5:1:1:1.15:33.5:4:0.1333:0:1 0/0:15:0:0,0:8,7:15,0:0:2,0:20.3:1:30.1:1:1:0:59.6:30:1:0:0.1 +GL000220.1 144015 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50769;SOR=Inf;LSEQ=GGCCTCACGGACTCTGAGCC;RSEQ=AGGAGTCCCCTGGTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:19.7:1:30.2:1:1:0:59.3:20:1:0:0.3 0/1:16:2:1,1:6,8:14,2:0.125:2,2:41:1:28:1:1:1.31:51.5:4:0.125:0:1 +GL000220.1 144120 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.51111;SOR=Inf;LSEQ=ACAGAAATACACGGATTCAC;RSEQ=CAAAACACAGAAAGCAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,4:13,0:0:2,0:22.2:1:29:1:1:0:60:12:1:0:0.5 0/1:22:2:1,1:13,7:20,2:0.0909:2,2:11:0:30.5:1:1:1.80284:60:4:0.0909:0:1.5 +GL000220.1 144134 . G C 51 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63994;SOR=0.65149;LSEQ=ATTCACCCAAAACACAGAAA;RSEQ=CAGTCTTTTAGAAATGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:2:1,1:7,2:9,2:0.1818:2,2:9.5:1:28.5:1:0.49091:3.05504:60:4:0.1818:0:2 0/1:24:3:1,2:13,8:21,3:0.125:2,2:18.7:1:32.3:1:0.5504:3.08979:60:6:0.125:0:1 +GL000220.1 144208 . G A 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18857;SOR=0;LSEQ=GTTTGGACCTTGACTGAGAG;RSEQ=ATTCCCAGTCGGTCTCTCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:2:1,1:13,7:20,2:0.0909:2,2:6:0:33:1:1:1.80284:58.5:4:0.0909:0:1.5 0/0:28:0:0,0:14,14:28,0:0:2,0:28.6:1:31:1:1:0:60:56:1:0:0.2 +GL000220.1 144421 . A G 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.56537;SOR=1.50415;LSEQ=GGGCTGACACGCTCACTGGC;RSEQ=GGCGTCGGGCATCACCTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:2,3:22,28:50,5:0.0909:2,2:26.4:1:31.6:1:1:1.17509:49.8:10:0.0909:0:1.2 0/1:61:8:4,4:21,31:52,8:0.1311:2,2:23.1:1:30.5:1:0.70818:1.47:53.4:16:0.1356:0:1 +GL000220.1 144510 . G T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21187;SOR=Inf;LSEQ=AGGCCGCCTGCGCACAGCCT;RSEQ=GGGCAACTGTGTCTTCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:24,27:51,0:0:2,0:23.7:1:31.8:1:1:0:58:50:1:0:0.7 0/1:44:2:1,1:18,24:42,2:0.0455:2,2:34:0:32:0:1:1.32:60:4:0.0465:0:1.5 +GL000220.1 144597 . T C 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05563;SOR=0;LSEQ=GAAATCGCCACTTTGACGAC;RSEQ=GGGTCTGATTGACCTTTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:15,18:0,0:0,33:1:0,2:28.6:1:30.6:1:1:0:59.9:32:1:0:1.7 1/1:37:32:16,16:2,3:5,32:0.8649:2,2:30.2:1:29.8:1:1:1.48:59.9:64:0.8649:0:1.8 +GL000220.1 144635 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.2427;SOR=Inf;LSEQ=GATCAGGCAAAAACGAACAA;RSEQ=CAGATAAATCAATAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:13,16:29,0:0:2,0:22:1:30.6:1:1:0:60:58:1:0:1.5 0/1:34:3:2,1:14,17:31,3:0.0882:2,2:22.7:1:31.7:1:0.59091:2.37:60:6:0.0882:0:2 +GL000220.1 144645 . C A 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACGAACAAACAGATAAAT;RSEQ=AATAAAATAACACAAAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:31:31:16,15:0,0:0,31:1:0,2:21.5:1:29.7:1:1:0:60:62:1:0:1.5 1/1:35:35:16,19:0,0:0,35:1:0,2:20.9:1:29:1:1:0:59.5:70:1:0:1.6 +GL000220.1 144739 . T A 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49206;SOR=Inf;LSEQ=TACGATAGGATGCGATAGGA;RSEQ=ACGATAGGATACAATACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:16,0:0:2,0:23.8:1:29.8:1:1:0:60:32:1:0:0.5 0/1:20:2:1,1:10,8:18,2:0.1:2,2:5:0:32:0:1:1.23603:51:4:0.1053:0:0.5 +GL000220.1 144761 . C G 65 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.35;SOR=0.30711;LSEQ=CGATAGGATACAATACAATA;RSEQ=GATACGATACAATACAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:0,4:3,4:7,4:0.3636:2,0:21:1:32.5:1:0.23636:0:60:8:0.3636:0:1 0/1:14:2:2,0:6,5:11,2:0.1429:2,0:34:1:29:1:0.48718:0:58.5:4:0.1429:0:1 +GL000220.1 144792 . A G 46 v3;p8;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=5;SSF=0.50893;SOR=Inf;LSEQ=AATACAATACAATACAATAC;RSEQ=ATACAATACAATACAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:5,0:0:2,0:21.2:1:32.4:1:1:0:49.6:10:1:0:0.4 0/1:11:3:2,1:7,1:8,3:0.2727:2,2:5:1:29.3:1:0.49091:3.05504:25.3:6:0.3:0:1.7 +GL000220.1 144797 . A G 50 v3;p8;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=18.000;MSILEN=5;SSF=0.52206;SOR=Inf;LSEQ=AATACAATACAATACAATAC;RSEQ=ATACAATACAATACAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:1,4:5,0:0:2,0:16.2:1:31.8:1:1:0:49.6:10:1:0:0.4 0/1:13:3:2,1:7,3:10,3:0.2308:2,2:7.7:1:31.7:1:1:1.15267:28.3:6:0.2308:0:2 +GL000220.1 144861 . C G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.51613;SOR=Inf;LSEQ=CAATACAATACAATACAATA;RSEQ=GCCGGGCGCGGTGGCTCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:12,0:0:2,0:25.3:1:30.7:1:1:0:54:24:1:0:0.4 0/1:20:2:0,2:8,10:18,2:0.1:2,0:41.5:1:32.5:1:0.49474:0:60:4:0.1:0:1.5 +GL000220.1 145162 . A AATAC 74 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=31;MSI=8.000;MSILEN=4;SSF=0.68;SOR=0.49443;LSEQ=CAAAAATAAATACATAAATA;RSEQ=ATACATACATACATACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:2,4:6,7:13,6:0.2727:2,2:30.2:1:28.8:1:1:1.66686:60:12:0.3529:0.0455:0.3 0/1:13:2:1,1:2,9:11,2:0.1538:2,2:22:1:30:1:0.42308:3.87:60:4:0.1538:0.0769:0.5 +GL000220.1 145237 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47826;SOR=0;LSEQ=AAATAAATAAATGGGCCCTG;RSEQ=GCGGTGGCTCAAGCCTGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:11.5:1:29:0:1:1:50:4:0.1667:0:2.5 0/0:12:0:0,0:6,6:12,0:0:2,0:33.6:1:31.7:1:1:0:60:24:1:0:0.4 +GL000220.1 145257 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5;SOR=Inf;LSEQ=CGCGGTGGCTCAAGCCTGTC;RSEQ=TCCCCTCACTTTGGGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:23.6:1:30.1:1:1:0:58:20:1:0:0.7 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:23:1:32.5:1:1:1.15:60:4:0.1333:0:1.5 +GL000220.1 145368 . T C 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.27126;SOR=0;LSEQ=ACACAACATTAGCCGGGCGC;RSEQ=GTGCTGTGCTGTACTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:3:1,2:10,11:21,3:0.125:2,2:18.7:1:30.7:1:1:1.77484:60:6:0.125:0:1.3 0/0:15:0:0,0:8,7:15,0:0:2,0:30.9:1:30.4:1:1:0:60:30:1:0:0.2 +GL000220.1 145381 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50639;SOR=0;LSEQ=CGGGCGCTGTGCTGTGCTGT;RSEQ=CTGTCTGTAATCCCAGCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:11,12:23,2:0.08:2,2:29.5:1:29:0:1:1.09:59.5:4:0.08:0:1.5 0/0:17:0:0,0:9,8:17,0:0:2,0:25.8:1:28.2:1:1:0:59.2:34:1:0:0.2 +GL000220.1 145421 . C T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.85124;LSEQ=CTCGGGAGGCCGAGCTGAGG;RSEQ=AGGAGAATCGCTTGAACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:0,2:5,6:11,2:0.1538:2,0:20:1:26.5:1:0.48718:0:41:4:0.1538:0:1.5 0/1:15:2:2,0:7,6:13,2:0.1333:2,0:20:1:31:0:0.48571:0:36.5:4:0.1333:0:1.5 +GL000220.1 145454 . T G 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25889;SOR=Inf;LSEQ=TGAACCTGGGAGGCGGAGGT;RSEQ=GCAGTGAGCCGAGATCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:3,6:9,0:0:2,0:26:1:27.9:1:1:0:37.8:8:1:0:0.2 0/1:15:4:2,2:6,5:11,4:0.2667:2,2:27.5:1:31:1:1:1.18545:36.8:8:0.2667:0:1.5 +GL000220.1 146096 . TTC T 28 d5;v3;MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=22.000;MSILEN=3;SSF=0.52381;SOR=0.2952;LSEQ=TCTTCTTCTTCTTCTTCTTC;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:18:1:28.4:1:1:1:48:4:0.5:0.25:0 0/1:5:1:1,0:2,2:4,1:0.2:2,0:20:0:32:0:1:0:29:2:0.2:0:0 +GL000220.1 146097 . TC T 30 d5;v3;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=22.000;MSILEN=3;SSF=0.46429;SOR=Inf;LSEQ=CTTCTTCTTCTTCTTCTTCT;RSEQ=TTTTTTTTTTGAGACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,1:2,0:0:2,0:21:0:34.5:1:1:0:25.5:4:1:0:0 0/1:5:2:1,1:1,0:1,2:0.4:0,2:44:1:30:1:1:0:39:4:0.5:0:0 +GL000220.1 146098 . CTT C 34 d5;v3;pSTD;MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=23.000;MSILEN=3;SSF=0.16667;SOR=0;LSEQ=TTCTTCTTCTTCTTCTTCTT;RSEQ=TTTTTTTTGAGACAGAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:22:0:34.5:1:1:1:25.5:4:0.5:0:0 0/0:5:0:0,0:3,2:5,0:0:2,0:31.2:1:29.6:1:1:0:39.6:10:1:0:0.2 +GL000224.1 3528 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.45455;SOR=Inf;LSEQ=GATGAAAGGAAGGAGAAAAC;RSEQ=CCGGTGTTACTAAAACCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:35.7:1:29.7:1:1:0:22.3:12:1:0:1.2 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:26.5:1:29.5:1:1:1:25:4:0.4:0:1.5 +GL000224.1 3577 . C T 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5;SOR=0;LSEQ=GGTTTCCCCCTGTGGGTAAG;RSEQ=CTACAATGTGGATGAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:5:0:32:0:1:1:23:4:0.3333:0:1.5 0/0:3:0:0,0:1,2:3,0:0:2,0:4:0:31.7:1:1:0:24.3:6:1:0:1 +GL000225.1 42673 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTGGGCCTTTATATGAGCC;RSEQ=GTGGCTGGTAGTCCGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:20.5:1:29:1:1:0:56.5:4:1:0:3 +GL000225.1 42712 . C T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTCCTGGCTGCACCTG;RSEQ=GGCAGTGCACAGGCCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:17:0:32:0:1:0:60:2:1:0:4 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:31:0:1:0:56.5:4:1:0:3 +GL000225.1 43001 . T A 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCCAGGGTCCAGATTTGG;RSEQ=TTCAGAATGAGAGGTCACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:31.5:1:1:0:21.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 43014 . G T 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATTTGGTTTCAGAATGAGA;RSEQ=GTCACGCCAGCTGAGGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:30.5:1:1:0:21.5:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 43298 . TG CA 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAAGCAGCCTATGCAACG;RSEQ=GCCCCCGGCCTTTGTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:33.5:1:1:0:35:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 43309 . C G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATGCAACGTGGCCCCCGGC;RSEQ=TTTGTCACCCTGCTCCCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:18:0:33:1:1:0:35:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 43311 . T G 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAACGTGGCCCCCGGCCT;RSEQ=TGTCACCCTGCTCCCTCGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:0:34:0:1:0:35:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 43318 . C T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCCCCCGGCCTTTGTCAC;RSEQ=CTGCTCCCTCGTGGGTCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:0:33:1:1:0:35:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 43326 . C T 31 d5;v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGCCTTTGTCACCCTGCTCC;RSEQ=TCGTGGGTCGCCTTCACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:35:0:34:1:1:0:35:4:1:0:6 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:31.5:1:1:0:60:4:1:0:3 +GL000225.1 43333 . G C 34 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTCACCCTGCTCCCTCGTGG;RSEQ=TCGCCTTCACCCACACTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:0:34.5:1:1:0:35:4:1:0:6 0/0:2:0:0,0:1,1:2,0:0:2,0:12:0:32.5:1:1:0:60:4:1:0:3 +GL000225.1 43356 . G A 30 d5;v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCCTTCACCCACACTGGCAC;RSEQ=TGGGGGACGGGGCTTCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:6:0:30.5:1:1:0:35:4:0.6667:0:6 0/0:2:0:0,0:1,1:2,0:0:2,0:35:0:32.5:1:1:0:60:4:1:0:3 +GL000225.1 43362 . G A 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCCACACTGGCACGTGGGG;RSEQ=ACGGGGCTTCCCGCACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:29:0:33:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:41:0:30.5:1:1:0:60:4:1:0:3 +GL000225.1 43364 . C T 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CCACACTGGCACGTGGGGGA;RSEQ=GGGGCTTCCCGCACCCCACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:31:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43:0:31:1:1:0:60:4:1:0:3 +GL000225.1 43395 . G A 30 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.4;SOR=0;LSEQ=GCACCCCACGTTCCCTGCGC;RSEQ=CCTGTGGCTCTCCCACAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:13.5:1:30.5:1:1:0:39.5:4:0.6667:0:5.5 0/0:2:0:0,0:1,1:2,0:0:2,0:15.5:1:29:1:1:0:60:4:1:0:3 +GL000225.1 43412 . AG A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCGCCTGTGGCTCTCCCAC;RSEQ=GGGGCTTTCGTGAGGCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:31.5:1:32.5:1:1:0:39.5:4:0.6667:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 43450 . G A 29 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGGAGCGAGGGCCGTCCCC;RSEQ=TGCTCCAGCGCAGCCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:33.5:1:29:1:1:0:39.5:4:0.6667:0:5.5 0/0:1:0:0,0:1,0:1,0:0:0,0:2:0:27:0:1:0:60:2:1:0:3 +GL000225.1 43460 . G C 29 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=GGCCGTCCCCGTGCTCCAGC;RSEQ=CAGCCAGGCCGGGCTGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:23.5:1:29:1:1:0:39.5:4:0.6667:0:5.5 1/1:1:1:1,0:0,0:0,1:1:0,0:12:0:32:0:1:0:60:2:1:0:3 +GL000225.1 43471 . G A 28 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTCCAGCGCAGCCAGGCC;RSEQ=GGCTGGCAGATGGGATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:12.5:1:28:1:1:0:39.5:4:0.6667:0:5.5 1/1:1:1:1,0:0,0:0,1:1:0,0:23:0:29:0:1:0:60:2:1:0:3 +GL000225.1 43532 . C T 26 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGATATTGCCTACGAGGCCC;RSEQ=GGCTACTCCAGAAGGGGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:24:1:31:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:33:1:26:1:1:0:60:4:1:0:2.5 +GL000225.1 43622 . GC AG 32 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.46667;SOR=0;LSEQ=GGAGGACTGGGACCCACAGC;RSEQ=GACAGCCTGCCGGGCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:43.5:1:32:1:1:0:60:4:0.5:0:2 0/0:2:0:0,0:1,1:2,0:0:2,0:14.5:1:27.5:1:1:0:60:4:1:0:3 +GL000225.1 43634 . C T 43 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=CCCACAGCGCGACAGCCTGC;RSEQ=GGGCCCTTGCACGTTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:27.3:1:30.3:1:1:0:52:6:1:0:3.7 1/1:3:3:2,1:0,0:0,3:1:0,2:10:1:27.3:1:1:0:60:6:1:0:3.3 +GL000225.1 43685 . G A 44 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTGAAGCAGGGCCACAGG;RSEQ=CCAAGGTGTGCCTGCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:34.7:1:28:1:1:0:60:6:1:0:3.7 +GL000225.1 43701 . A G 48 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCAAGGTGTGCCTGC;RSEQ=CCACCCGTGTCCCAGGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:29.3:1:30.3:1:1:0:60:6:1:0:3.7 +GL000225.1 43707 . C T 46 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGGTGTGCCTGCACCACC;RSEQ=GTGTCCCAGGGGAGCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:25:1:29.3:1:1:0:60:6:1:0:3.7 +GL000225.1 43827 . G C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCCCCGGAGGACTCCGC;RSEQ=TGGCAGGTGCAGATGCACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:29:1:1:0:43.5:4:1:0:4.5 +GL000225.1 43853 . T C 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGCAGATGCACGGCATCC;RSEQ=GGCGCCCTCCCAGGATCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:27.5:1:1:0:43.5:4:1:0:4.5 +GL000225.1 43859 . C A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGCACGGCATCCTGGCGC;RSEQ=CTCCCAGGATCTCCAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:27.5:1:1:0:43.5:4:1:0:4.5 +GL000225.1 43869 . T G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATCCTGGCGCCCTCCCAGGA;RSEQ=CTCCAGGAGCCGGAACGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:31:1:1:0:43.5:4:1:0:4.5 +GL000225.1 44349 . G A 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTTGCGGGCAGCTGCCTGG;RSEQ=CTGTGGGAGCAGCCCGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:9:0:31.5:1:1:0:57:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 44364 . C T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGGGCTGTGGGAGCAGCC;RSEQ=GGGCAGAGCTCTCATGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:24:0:33.5:1:1:0:57:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 44474 . C A 44 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGCTGGGTGGAGACCCA;RSEQ=GTCCCTCAAAACACTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:0,0:0,3:0.6:0,2:25:1:28.3:1:1:0:32.7:6:0.6:0:7.7 +GL000225.1 44480 . T G 71 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGTGGAGACCCACGTCCC;RSEQ=CAAAACACTGGGACCGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:25.6:1:30.6:1:1:0:36:10:1:0:6.2 +GL000225.1 44487 . A C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGACCCACGTCCCTCAAAAC;RSEQ=CTGGGACCGTGCAGCATCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:16:0:31.5:1:1:1.73:41:4:0.4:0:4 +GL000225.1 44489 . T C 46 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCACGTCCCTCAAAACAC;RSEQ=GGGACCGTGCAGCATCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:2,3:0.6:2,2:30.3:1:29.3:1:1:1.7321:32.7:6:0.6:0:7.7 +GL000225.1 44494 . C G 50 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTCCCTCAAAACACTGGGA;RSEQ=CGTGCAGCATCCGGGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:5:3:1,2:1,1:2,3:0.6:2,2:32:1:31.7:1:1:1.7321:32.7:6:0.6:0:7.7 +GL000225.1 44496 . G A 70 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTCAAAACACTGGGACC;RSEQ=TGCAGCATCCGGGCCTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:22.4:1:30.2:1:1:0:36:10:1:0:6.2 +GL000225.1 44503 . A G 50 d5;v3;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACTGGGACCGTGCAGC;RSEQ=TCCGGGCCTGACACCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:35:1:32:1:1:0:32.7:6:1:0:7.7 +GL000225.1 44517 . C A 62 d5;v3;NM7.25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=TGCAGCATCCGGGCCTGACA;RSEQ=CCCTCCGGCGGCTCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:8.5:1:30.5:1:1:0:24.5:4:1:0:5.5 1/0:6:4:1,3:2,0:2,4:0.6667:0,2:21.5:1:31.3:1:0.4:0:29.5:8:0.6667:0:7.3 +GL000225.1 44546 . A T 31 d5;v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=CGGCTCGCCTCCTCTGTGCC;RSEQ=CCACGCCACCGTCGCCGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:31:1:1:0:24.5:4:1:0:5.5 0/1:7:2:1,1:2,2:4,2:0.2857:2,2:39:0:31.5:1:1:1:22:4:0.2857:0:6.5 +GL000225.1 44548 . CA TG 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=Inf;LSEQ=GCTCGCCTCCTCTGTGCCAC;RSEQ=CGCCACCGTCGCCGGCCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:39.5:1:31:1:1:0:24.5:4:1:0:5.5 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:22:0:32.8:1:1:1.41418:29:4:0.2857:0:2 +GL000225.1 44551 . G A 48 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.41418;LSEQ=CGCCTCCTCTGTGCCACCAC;RSEQ=CCACCGTCGCCGGCCCGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,1:1,1:0.5:0,0:42:0:31:0:1:0:22:2:0.5:0:6 1/0:5:3:2,1:1,1:2,3:0.6:2,2:30.7:1:30.7:1:1:1.73:27.3:6:0.6:0:3.7 +GL000225.1 44562 . C T 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=1.8525;LSEQ=TGCCACCACGCCACCGTCGC;RSEQ=GGCCCGCCCGTGCCCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:1,0:2,1:3,1:0.25:2,0:43:0:31:0:1:0:22:2:0.25:0:6 0/1:5:2:2,0:1,2:3,2:0.4:2,0:46:0:30.5:1:0.4:0:25.5:4:0.4:0:7 +GL000225.1 45812 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGTAGGCAAAGTCCATA;RSEQ=AAGGCTTACAACACCTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36.5:1:33.5:1:1:0:22:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 46492 . G T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CTCCCTGTAGACAAATCCCA;RSEQ=AAAATTGTTACATTACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:23:0:34:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:1:28:1:1:0:48:4:1:0:1.5 +GL000225.1 50853 . T G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGTGGTATATCACCTGG;RSEQ=TGATCATTGCAGGGATATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:43.5:1:31:1:1:0:22.5:4:1:0:3.5 +GL000225.1 50869 . T A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGTTGATCATTGCAGGGA;RSEQ=ATGTCACAAAGCACCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:38:1:31:1:1:0:22.5:4:0.6667:0:3.5 +GL000225.1 50878 . A C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGCAGGGATATGTCACA;RSEQ=AGCACCCTGTGGGCAGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:9:0:33.5:1:1:1.7321:21:4:0.4:0:4 +GL000225.1 50891 . G T 65 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTCACAAAGCACCCTGTGG;RSEQ=CAGATCCTAGAGAAGAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:3,2:0,0:0,5:1:0,2:20:1:28:1:1:0:22:4:1:0:4 +GL000225.1 50906 . G T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGTGGGCAGATCCTAGAGAA;RSEQ=AGTTATATCACCTGGGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:37:0:30:1:1:1:21:4:0.5:0:4 +GL000225.1 50912 . T A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGATCCTAGAGAAGAGTTA;RSEQ=ATCACCTGGGTGATCAGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:0,1:1,2:0.5:0,2:40:0:30.5:1:1:0:21:4:0.5:0:4 +GL000225.1 51218 . A T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGCAGAGATATGTCAAA;RSEQ=TGCCCCTGTAGGCAGAGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:28.5:1:1:0:40.5:4:1:0:1 +GL000225.1 52049 . T C 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCATGCTCACTGTTTGCTCC;RSEQ=GGAGCTCTGCGGGCACCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:28.5:1:1:0:30.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 52217 . G A 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGGCATCTTCTCTCTGGG;RSEQ=TCTCACTCTGGTCTCCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:3,1:4,2:0.3333:2,0:32:1:30:0:1:0:21.5:4:0.3333:0:6.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 52265 . CAT GGC 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACGAGAGCCACAAGCCTG;RSEQ=GTGTGAGACTGTCCCGGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:19:1:33.3:0:1:0:28.5:4:0.6667:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 52617 . G A 28 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACGCCCTGGGACCCTTCCAG;RSEQ=GCGGGGCAGGCTGTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:26:0:28.5:1:1:0:39:4:0.5:0:4.5 +GL000225.1 52619 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGGGACCCTTCCAGGG;RSEQ=GGGGCAGGCTGTCCCAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,0:1,2:0.5:0,2:24.5:1:29.5:1:1:0:33.5:4:0.6667:0:4 +GL000225.1 52625 . A G 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACCCTTCCAGGGCGGGGC;RSEQ=GGCTGTCCCAGGGCTCACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,0:1,2:0.5:0,2:25.5:1:27.5:1:1:0:39:4:0.6667:0:4.5 +GL000225.1 52629 . T A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCCAGGGCGGGGCAGGC;RSEQ=GTCCCAGGGCTCACCGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:2,0:2,2:0.5:0,2:21.5:1:27:1:1:0:39:4:0.5:0:4.5 +GL000225.1 52644 . C T 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCTGTCCCAGGGCTCAC;RSEQ=GCCATTCATGAAGGGGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:6.5:1:28.5:1:1:0:39:4:0.6667:0:4.5 +GL000225.1 52943 . A G 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTGCGAGCTTGCTTTGAGC;RSEQ=GAACCCGTACCCGGGCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12.5:1:27.5:1:1:0:28:4:1:0:5 +GL000225.1 63067 . A G 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCACGTCAGCAGGTGTGC;RSEQ=CAATAAGCGCAGGTCTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:33:1:1:0:54:4:1:0:2.5 +GL000225.1 63096 . G C 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAGGTCTAGCCAGGAGTCC;RSEQ=GCAAAGAGAGCTAGAGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:25.5:1:31:1:1:0:21.5:4:0.6667:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:30:1:1:0:54:4:1:0:2.5 +GL000225.1 63127 . A G 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGAGGTCTGCGTTCCGCC;RSEQ=CCAGGCCCTCCATGGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:24:0:33:1:1:0:21.5:4:0.6667:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63342 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGTATGGGTTGGTCAGGCG;RSEQ=GGGTGGGGTGGTAGAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:30.5:1:32.5:1:1:1:42.5:4:0.5:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63355 . A G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAGGCGGGGGTGGGGTGGT;RSEQ=GAAAAGCATGAGAGCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:1,3:0.75:0,2:42:1:32.7:1:1:0:42.7:6:0.75:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63360 . A G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGGGTGGGGTGGTAGAAA;RSEQ=GCATGAGAGCTCTGCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,0:0,3:0.75:0,2:43.7:1:32.7:1:1:0:42.7:6:0.75:0:3.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63398 . G A 29 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TGGCTGCTCCCACTGCCCAG;RSEQ=CGGCTGCCCACAAACCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:13:1:29:1:1:2.45:35.5:4:0.3333:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63416 . G C 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGGCGGCTGCCCACAAACCC;RSEQ=CGCATGCGCAGTAGGCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:0,2:1,3:4,2:0.3333:2,0:25.5:1:32.5:1:1:0:33:4:0.3333:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63418 . G A 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCGGCTGCCCACAAACCCGC;RSEQ=CATGCGCAGTAGGCGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:0,3:3,2:0.3333:0,2:24:1:32.5:1:0.4:0:26:4:0.4:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63426 . A T 40 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACAAACCCGCGCATGCGC;RSEQ=GTAGGCGTCCCATCTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:28.7:1:25.7:1:1:0:26.3:2:0.6667:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63433 . G T 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGCGCATGCGCAGTAGGC;RSEQ=TCCCATCTGCTGGTACCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:35.7:1:30.7:1:1:0:26.3:6:0.75:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63439 . T C 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGCGCAGTAGGCGTCCCA;RSEQ=CTGCTGGTACCTGGGCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:36.8:1:32.5:1:1:0:27.8:8:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63494 . A C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GATGCCCAGGAAAGAATGGC;RSEQ=GTTCTCCACTGTGTGGAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:9:1:31:1:1:0:25.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63624 . A T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGGTGTTCCCCGCGAAA;RSEQ=AGAGGCCACCGCCCTGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:31.5:1:30:1:1:0:24:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63641 . C T 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAAAGAGGCCACCGCCCTG;RSEQ=CCCGACCCGACACCGTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:19:0:31.5:1:1:0:24:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63649 . C T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCACCGCCCTGCCCCGACC;RSEQ=GACACCGTCCCAACCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:11:0:33:1:1:0:24:4:0.6667:0:3.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63706 . T G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGAGCCTGGTATTCTTGC;RSEQ=CACTGAGGGGGGTGCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:29:1:29.5:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63814 . G C 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGCAGAAACTCCGGGCTCA;RSEQ=CAGGAGCTTATCCAGTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33:0:33.5:1:1:0:56.5:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 63917 . T C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTGCATCTGCCAGTGCCA;RSEQ=GCAGAGGCCTCTGGGTGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37:1:28:1:1:0:60:4:1:0:6.5 +GL000225.1 63920 . A G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TGCATCTGCCAGTGCCATGC;RSEQ=GAGGCCTCTGGGTGCGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:40:1:28.5:1:1:0:60:4:1:0:6.5 +GL000225.1 63937 . C T 27 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGCAGAGGCCTCTGGGTGCG;RSEQ=GGGCTGGCAAGGTGGAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:13:0:35:0:1:0:60:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:42.5:1:27.5:1:1:0:60:4:1:0:6.5 +GL000225.1 63946 . A G 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTGGGTGCGCGGGCTGGC;RSEQ=AGGTGGAGCTGCCCCGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:22:0:32:0:1:0:60:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:29:1:1:0:60:4:1:0:6.5 +GL000225.1 63948 . G C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGGTGCGCGGGCTGGCAA;RSEQ=GTGGAGCTGCCCCGCCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:24:0:34:0:1:0:60:2:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:29.5:1:1:0:60:4:1:0:6.5 +GL000225.1 64027 . T C 62 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CCAGCCCCACCACGGACTCC;RSEQ=CTGGGACGCGGGTTGCGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:14.3:1:31.3:1:1:0:39.3:8:1:0:4.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 64036 . C T 44 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGGACTCCTCTGGGACG;RSEQ=GGGTTGCGCAAACACACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:1,0:1,3:0.75:0,2:23.3:1:28:1:1:0:42.3:6:0.75:0:4.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 64070 . T C 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACCTTGGCCCTGTTGCCC;RSEQ=GCTTGAGCAGGCCCAGGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:41.3:1:30.5:1:1:0:39.3:8:1:0:4.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 64098 . A G 51 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CAGGCCCAGGATGTCCCACC;RSEQ=CTCAAGGGCCTGGCAGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,0:0,3:0.75:0,2:22.3:1:32.7:1:1:0:37.7:6:1:0:4.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 64100 . T G 66 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCCAGGATGTCCCACCAC;RSEQ=CAAGGGCCTGGCAGGCCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:19.8:1:33.3:1:1:0:35.8:8:1:0:4.8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 64237 . A G 31 d5;v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCGTATGCAAAATCCCCAC;RSEQ=TCCTGGGGCAGGTTGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:24.5:1:31:1:1:0:60:4:1:0:3 1/1:1:1:0,1:0,0:0,1:1:0,0:33:0:34:0:1:0:60:2:1:0:2 +GL000225.1 64496 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCCTGCCAGCCTGTCCCGG;RSEQ=TGCCTGGCCCTGAGATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:31:1:1:0:31:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 64520 . AG CC 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGGCCCTGAGATTCTGAAA;RSEQ=ATTTCTGAATTCTGGACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:30.5:1:1:0:31:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 64532 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTGAAAAGATTTCTGAAT;RSEQ=CTGGACTCCGGGAAGCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:30:1:1:0:31:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 64650 . T C 30 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGATCCAGTGACGGCGGTC;RSEQ=GCTTTCGCCTGCCTTCTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:30.5:1:1:0:29:4:1:0:8 +GL000225.1 64653 . T C 32 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCAGTGACGGCGGTCTGC;RSEQ=TTCGCCTGCCTTCTTGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:32.5:1:1:0:29:4:1:0:8 +GL000225.1 64656 . C T 31 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGTGACGGCGGTCTGCTTT;RSEQ=GCCTGCCTTCTTGCGGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:31.5:1:1:0:29:4:1:0:8 +GL000225.1 64662 . C T 31 d5;v3;pSTD;NM7.25 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGCGGTCTGCTTTCGCCTG;RSEQ=CTTCTTGCGGGCCGCGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:31:1:1:0:29:4:1:0:8 +GL000225.1 64676 . GC AT 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCTGCCTTCTTGCGGGCC;RSEQ=GTCTCCCGGGCCAGGGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:32:1:1:0:29:4:1:0:7 +GL000225.1 64682 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTTCTTGCGGGCCGCGTCT;RSEQ=CCGGGCCAGGGCCCAGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:31:1:1:0:29:4:1:0:7 +GL000225.1 64979 . T C 49 d5 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAATTTCACGGACGGACA;RSEQ=GGGCAGAGAGAGGCCGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:15:1:31:1:1:0:22:6:1:0:2 1/1:1:1:1,0:0,0:0,1:1:0,0:3:0:31:0:1:0:22:2:1:0:2 +GL000225.1 64997 . T C 45 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATGGGCAGAGAGAGGCCGG;RSEQ=GGGCTCCCGTGCACCTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:21:1:29:1:1:0:22:6:1:0:2 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:32:1:1:0:22:4:1:0:1.5 +GL000225.1 65091 . A G 33 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=0;LSEQ=AGCGGCTCTTATAAAGGCCC;RSEQ=CAGGCAGGCAGGCTCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:16:0:33:1:1:1:20:4:0.5:0:5.5 0/0:3:0:0,0:2,1:3,0:0:2,0:16:1:28.7:1:1:0:34.3:6:1:0:5 +GL000225.1 65096 . C A 32 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.42857;SOR=0;LSEQ=CTCTTATAAAGGCCCACAGG;RSEQ=AGGCAGGCTCCACCACTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:21:0:32.5:1:1:1:20:4:0.5:0:5.5 0/0:3:0:0,0:2,1:3,0:0:2,0:17.7:1:31:1:1:0:34.3:6:1:0:5 +GL000225.1 65104 . C T 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=AAGGCCCACAGGCAGGCAGG;RSEQ=TCCACCACTTCATGAATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:19.5:1:33.8:1:1:0:24.3:8:1:0:5.8 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:26:0:31.5:1:1:0:38:4:0.6667:0:4.5 +GL000225.1 65110 . CA AC 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.14286;SOR=Inf;LSEQ=CACAGGCAGGCAGGCTCCAC;RSEQ=CTTCATGAATGGCGGTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:3,1:4,0:0:2,0:25.5:1:34:1:1:0:24.3:8:1:0:5.8 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:23.5:1:31.8:1:1:0:38:4:0.6667:0:3.5 +GL000225.1 65125 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCACCACTTCATGAATGGC;RSEQ=GTGAGCCCTGGGACAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:42.5:1:32:1:1:1.7321:20:4:0.4:0:5.5 0/0:2:0:0,0:1,1:2,0:0:2,0:9.5:1:30.5:1:1:0:38:4:1:0:3.5 +GL000225.1 65127 . T G 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.04762;SOR=Inf;LSEQ=CACCACTTCATGAATGGCGG;RSEQ=GAGCCCTGGGACAGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:30.6:1:30.8:1:1:0:24:10:1:0:5.8 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:30:1:1:0:38:4:1:0:3.5 +GL000225.1 65132 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCATGAATGGCGGTGAGC;RSEQ=CTGGGACAGCCTGCCCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:35.5:1:30.5:1:1:1.7321:20:4:0.4:0:5.5 0/0:2:0:0,0:1,1:2,0:0:2,0:2.5:1:29.5:1:1:0:38:4:1:0:3.5 +GL000225.1 65248 . C A 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGGGACAGAGGCACGAA;RSEQ=AGGAAGGGGGCGAGGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:29:0:33:0:1:0:60:2:1:0:4 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:30:1:1:0:39:4:1:0:1.5 +GL000225.1 65485 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGTGGGTGTTGCTGTTG;RSEQ=CTGGAAAGTCTCACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:30.5:1:1:0:53.5:4:1:0:3.5 +GL000225.1 65510 . C G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAGTCTCACACACACAGGC;RSEQ=TGTGGCTCTCGTTCGTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:29.5:1:1:0:53.5:4:1:0:3.5 +GL000225.1 65522 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAGGCCTGTGGCTCTCG;RSEQ=TCGTTTCCACGTAGGAGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:30.5:1:1:0:53.5:4:1:0:3.5 +GL000225.1 65627 . A C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGGCAAAATGGGGAGTCTGC;RSEQ=GTGTGGCCGGTTTGGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:14:0:34:0:1:0:26:2:1:0:2 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:41:1:30.5:1:1:0:51:4:0.6667:0:1.5 +GL000225.1 72073 . A T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCGTTTCTAGGAAATTT;RSEQ=GCGCCTGCTGCAGAAACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:17.7:1:31.3:1:1:0:60:6:1:0:4.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72075 . C A 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCGTTTCTAGGAAATTTAG;RSEQ=GCCTGCTGCAGAAACTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:19.7:1:31.3:1:1:0:60:6:1:0:4.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72104 . A G 54 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAAACTCCAGGCTCGCCA;RSEQ=GAGCTCATCCAGCAGCAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:34.3:1:34.3:1:1:0:60:6:1:0:4.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72110 . C T 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAGGCTCGCCAAGAGCT;RSEQ=ATCCAGCAGCAAGCCGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:1,3:0.75:0,2:32.3:1:32:1:1:0:60:6:0.75:0:4.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72151 . A G 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTGCAGACGAGCGCCCC;RSEQ=GCTCCTGTAGCGCCTGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:23:1:30.3:1:1:0:52.7:6:1:0:3.7 1/1:1:1:1,0:0,0:0,1:1:0,0:21:0:31:0:1:0:60:2:1:0:2 +GL000225.1 72315 . C G 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCGCACCACGGACTCCA;RSEQ=TGGGACGTGGGTGGTGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35.5:1:31.5:1:1:0:48.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72323 . T C 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACGGACTCCACTGGGACG;RSEQ=GGGTGGTGCAAGCACACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:25.3:1:31:1:1:0:52.3:6:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72330 . T C 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=CTCCACTGGGACGTGGGTGG;RSEQ=GCAAGCACACCTTGACCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:27.7:1:32:1:1:0:52.3:6:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72365 . C T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTGTGGCCCCGCTTGAA;RSEQ=GGGACCAGGCTGTTCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:25:1:31.3:1:1:0:52.3:6:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72384 . C T 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACGGGACCAGGCTGTTCCTC;RSEQ=GCGCAGGGCCCGGCAGGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:24:1:33:1:1:0:54:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72417 . C T 28 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAGGCCGTCGTGCTGTGGG;RSEQ=CCCGATCCTCCCGGCTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:11.5:1:28:1:1:0:48.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72582 . A G 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTGCTGGGCTGGAGCAC;RSEQ=GGGACCGCCCTCGCTCCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:29:1:1:0:55:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72638 . CG TA 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGTGGGAGAGCACCAGGTG;RSEQ=CAGGGCACATGGGTTGCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:45:0:30:1:1:0:33:4:0.6667:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72657 . G A 50 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCGCAGGGCACATGGGTTGC;RSEQ=GGAAGCCCCGTTCCCCACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:23.7:1:31.7:1:1:0:38.7:6:1:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72677 . A C 33 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGAAGCCCCGTTCCCCACG;RSEQ=GCCAGTGTGGGCGAAGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:7:0:33:1:1:0:33:4:0.6667:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 72828 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATCTGAATCCTGGACTCC;RSEQ=GGGGGACCCTCCAGCTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:29:1:1:0:50.5:4:1:0:2.5 +GL000225.1 72962 . C A 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCTGCCTTCTTGTGGGCC;RSEQ=CGTCTCCCGGGCCAGGGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:30.5:1:1:0:23:4:1:0:5 +GL000225.1 72975 . C G 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=GTGGGCCCCGTCTCCCGGGC;RSEQ=AGGGCCAAGATTCCCGCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:0:30:1:1:0:23:4:1:0:5 +GL000225.1 72995 . T C 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGGCCAAGATTCCCGCTG;RSEQ=TGCTGCCTCAGCTGGAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:30:1:1:0:23:4:1:0:5 +GL000225.1 72997 . G T 27 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GGGCCAAGATTCCCGCTGTT;RSEQ=CTGCCTCAGCTGGAGTGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:0:27.5:1:1:0:23:4:1:0:5 +GL000225.1 73011 . A C 27 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTGTTGCTGCCTCAGCTGG;RSEQ=GTGACCTCTCATTCTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:27.5:1:1:0:23:4:1:0:5 +GL000225.1 73259 . C T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGGTCAGAATTTCACGGA;RSEQ=GGACACGGGCAGAGAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:31:0:1:0:42:4:1:0:5.5 +GL000225.1 73281 . GC AG 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACGGGCAGAGAGAAGCC;RSEQ=CGTGCTCCGTGCACCTCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:30.8:1:1:0:42:4:1:0:4.5 +GL000225.1 73291 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGAGAAGCCGCCGTGCTCC;RSEQ=TGCACCTCAGCCGGCCTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:29:1:1:0:42:4:1:0:4.5 +GL000225.1 73314 . T C 29 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CACCTCAGCCGGCCTGTGCA;RSEQ=TGCGGCAGGAGCAGCCAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:29:1:1:0:42:4:1:0:4.5 +GL000225.1 73939 . T G 29 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACTGGGAAGGAGAGCGAA;RSEQ=GCACCATGCTGGTCTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:29.5:1:1:0:21:4:1:0:3.5 +GL000225.1 73965 . C A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=ATGCTGGTCTTCCACCCTTC;RSEQ=CTGCATGTTTCCGGGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:16:1:29.5:1:1:0:20:4:1:0:3 1/0:4:2:1,1:1,1:2,2:0.5:2,2:31.5:1:30:1:1:1:21:4:0.5:0:3.5 +GL000225.1 73972 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTTCCACCCTTCCCTGCAT;RSEQ=TTTCCGGGTGCCCGCAGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:23:1:30:1:1:0:20:4:1:0:3 0/1:5:2:1,1:1,2:3,2:0.4:2,2:35:0:31:1:1:1.73:21:4:0.4:0:3.5 +GL000225.1 73979 . G T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=CCCTTCCCTGCATGTTTCCG;RSEQ=GTGCCCGCAGAGCTCCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,1:1,1:0.5:0,0:31:0:28:0:1:0:20:2:0.5:0:2 0/1:5:2:1,1:1,2:3,2:0.4:2,2:39:1:29:1:1:1.73:31:4:0.4:0:5 +GL000225.1 73987 . C T 28 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCATGTTTCCGGGTGCCCG;RSEQ=AGAGCTCCGGGAGCAAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:38:1:32:1:1:0:20:4:1:0:3 0/1:5:2:1,1:1,2:3,2:0.4:2,2:47:1:28.5:1:1:1.73:31:4:0.4:0:5 +GL000225.1 74006 . A C 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GCAGAGCTCCGGGAGCAAAC;RSEQ=GTCAGCATGACACATCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:30:1:34:0:1:0:20:4:1:0:3 0/1:5:2:1,1:1,2:3,2:0.4:2,2:33.5:1:31:1:1:1.73:31:4:0.4:0:5 +GL000225.1 74008 . T A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=AGAGCTCCGGGAGCAAACAG;RSEQ=CAGCATGACACATCTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:28:1:32:0:1:0:20:4:1:0:3 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:31.5:1:30.5:1:1:0:31:4:0.6667:0:5 +GL000225.1 75403 . A C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAATGATCACCCAGGTG;RSEQ=CATACCAGTTGTCAAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:33:0:1:0:51.5:4:1:0:2 +GL000225.1 75458 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCGATGTATCTCTGCAAC;RSEQ=ACCACCTAGGTAATGTAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:29:1:1:0:51.5:4:1:0:2 +GL000225.1 76885 . C T 29 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGATTTATGACATATCTCTG;RSEQ=GCTGATCACCCAGGTGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:29.5:1:1:0:21:4:1:0:2 +GL000225.1 78160 . A G 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGGCACAGAGAGAACTGAG;RSEQ=CCTCCCTTGCACGTCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:18.5:1:29:1:1:0:51:4:1:0:4 +GL000225.1 78186 . CT TG 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGCACGTCAGCCAGGGTG;RSEQ=CAATGAGCGCAGGTCTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:45.5:1:30.5:1:1:0:51:4:1:0:3 +GL000225.1 78195 . C A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGCCAGGGTGCTCAATGAG;RSEQ=GCAGGTCTAGCCAGGAGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:29.5:1:1:0:51:4:1:0:3 +GL000225.1 78410 . G A 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTCCACCCAGCCCAGGGG;RSEQ=GGATGCATTTTCCTGGGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:30:1:1:0:58:4:1:0:3.5 +GL000225.1 78414 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCACCCAGCCCAGGGGGGGA;RSEQ=GCATTTTCCTGGGCTGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:31:1:1:0:58:4:1:0:3.5 +GL000225.1 78466 . T A 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGGGGGTGATCAGGCGGGG;RSEQ=GGGGTGGTGGAAAGGCATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:40:0:30:0:1:0:60:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:27:1:1:0:58:4:1:0:3.5 +GL000225.1 78690 . T G 33 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AGGCCGGTCAGCCTGGTGGA;RSEQ=GGGGCGGGGGGAAGACACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:26.5:1:32:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25:0:33:0:1:0:33:4:1:0:5 +GL000225.1 78695 . CG C 33 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGTCAGCCTGGTGGATGGGG;RSEQ=GGGGGAAGACACGTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:20.5:1:33:0:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:31:0:33:0:1:0:33:4:1:0:5 +GL000225.1 78706 . C A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGATGGGGCGGGGGGAAGA;RSEQ=ACGTCCCTCCATAGCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:10.5:1:34.5:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:28:0:31:1:1:0:33:4:1:0:5 +GL000225.1 78710 . T C 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TGGGGCGGGGGGAAGACACG;RSEQ=CCCTCCATAGCCAGCCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:6.5:1:31:1:1:0:60:4:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:31.5:1:1:0:33:4:1:0:5 +GL000225.1 78720 . G A 29 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GGAAGACACGTCCCTCCATA;RSEQ=CCAGCCAGGTGTTCCCCGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:32:0:1:0:60:2:1:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:29.5:1:1:0:33:4:1:0:5 +GL000225.1 78725 . C A 28 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACGTCCCTCCATAGCCAG;RSEQ=CAGGTGTTCCCCGGGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9:0:28.5:1:1:0:33:4:1:0:5 +GL000225.1 78957 . G A 47 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14286;SOR=Inf;LSEQ=AGCTCATCCAGCAGCAGGCC;RSEQ=GAGGGGAGTGCAGAAGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:16:1:30.7:1:1:0:46.7:6:1:0:2.7 1/0:4:3:1,2:1,0:1,3:0.75:0,2:29:1:29.7:1:1:0:22.3:6:0.75:0:4.3 +GL000225.1 78972 . A T 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.81007;LSEQ=AGGCCGGAGGGGAGTGCAGA;RSEQ=GAGCGCCCCGGCTCCTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:1,0:1,1:2,1:0.3333:2,0:37:0:33:0:1:0:20:2:0.3333:0:7 1/0:4:2:1,1:0,0:0,2:0.5:0,2:45.5:1:32.5:1:1:0:21.5:4:0.5:0:6 +GL000225.1 78976 . C T 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CGGAGGGGAGTGCAGAAGAG;RSEQ=GCCCCGGCTCCTGGAGCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:25.7:1:33.3:1:1:0:46.7:6:1:0:2.7 1/0:4:2:1,1:1,0:1,2:0.5:0,2:48.5:1:29:1:1:0:23:4:0.6667:0:3 +GL000225.1 79089 . C T 32 d5;v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAGCTGCCCCGGCTTGGTG;RSEQ=TCCCACGGCTCCCCTGCGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:25:1:32:0:0.33333:0:28:4:0.6667:0:5 1/1:1:1:0,1:0,0:0,1:1:0,0:5:0:28:0:1:0:41:2:1:0:6 +GL000225.1 79097 . G C 35 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCGGCTTGGTGCTCCCACG;RSEQ=CTCCCCTGCGACCTGGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:25:1:35:0:1:0:28:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 79145 . C A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGCCCCACCATGGACTCC;RSEQ=CTGGGACGCGGGTGGTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:38:1:29.5:1:1:0:35.5:4:0.6667:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 79170 . T A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACGCGGGTGGTGCAAGCAC;RSEQ=CCTTGGCCCTGTGGCCCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:16.5:1:29:1:1:0:35.5:4:0.6667:0:4 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 80116 . G A 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGGCAGAGAGAGGCCGGC;RSEQ=GGCACCCGTGCAACTCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:14:1:29.5:1:1:0:51.5:4:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 80129 . A C 30 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCGGCGGGCACCCGTGCA;RSEQ=CTCAGCTGGCCTGTGCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:18:1:30.5:1:1:0:22.5:4:0.4:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 80150 . T A 31 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCAGCTGGCCTGTGCACTG;RSEQ=GGCAGGTGCAGCCAGGAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:21.5:1:31.5:1:1:1.7321:20:4:0.4:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 80176 . C A 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAGCCAGGAGGCCTGCA;RSEQ=GGACAGCCAGCCAGCGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:32:0:33:1:1:1:20:4:0.5:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 80288 . CC TG 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ACCACGGAAGGATCCCAGGG;RSEQ=TCGAGTCCTGTGGCAGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29:1:24.5:1:1:0:60:1:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:32:0:1:0:21:4:1:0:6.5 +GL000225.1 80292 . G A 31 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CGGAAGGATCCCAGGGCCTC;RSEQ=AGTCCTGTGGCAGGGGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29:1:25:1:1:0:60:1:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:31.5:1:1:0:21:4:1:0:6.5 +GL000225.1 80295 . T G 33 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=AAGGATCCCAGGGCCTCGAG;RSEQ=CCTGTGGCAGGGGTGTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:29:1:30:1:1:0:60:4:1:0:0.5 1/1:2:2:1,1:0,0:0,2:1:0,2:19:0:33:1:1:0:21:4:1:0:6.5 +GL000225.1 80300 . T C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1;SOR=Inf;LSEQ=TCCCAGGGCCTCGAGTCCTG;RSEQ=GGCAGGGGTGTGGTGGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:20.7:1:30.3:1:1:0:60:6:1:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:24:0:32.5:1:1:0:21:4:1:0:6.5 +GL000225.1 80343 . CC TG 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=2.000;MSILEN=1;SSF=0.06667;SOR=Inf;LSEQ=GTGGGAGGGCGTGGTGATGG;RSEQ=GTGGTGGGGCCGGAGACACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,2:3,0:0:2,0:25:1:30.7:1:1:0:60:6:0.75:0:0.3 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:29:1:1:0:21:4:1:0:5.5 +GL000225.1 80444 . A C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTGCTCCAGGAATCCCG;RSEQ=GGGAACTGGAAGCCACTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:31.5:1:1:0:59.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 80500 . C A 32 d5;v3;p8;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCAGCAGGGAGAAACCGG;RSEQ=CTGCGAGGGTGGAGGGGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:7:0:32:0:1:0:60:4:0.6667:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 88948 . C T 30 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTGGTGGAAAGGCATGAGAG;RSEQ=TCTGCCTGGGCTGTTCCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:24:0:30:1:1:0:34:4:0.6667:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 89002 . G T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCCGCCTACCCGCACGTGC;RSEQ=CAGTAGGCGGCCCACTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:1:0:30:0:1:0:60:2:1:0:3 1/1:2:2:1,1:0,0:0,2:1:0,2:28.5:1:31:1:1:0:60:4:1:0:1.5 +GL000225.1 89522 . T G 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCAGGAGCACGGGCTGGC;RSEQ=AGGTGGATCTGCCCCGGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:28.5:1:1:0:56:4:1:0:4 +GL000225.1 89538 . G A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGCTAGGTGGATCTGCCCC;RSEQ=GCTTGTGGTTCCCACGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:19.5:1:28:1:1:0:56:4:1:0:4 +GL000225.1 89772 . C T 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTGAGGGTGGGAGAGTGC;RSEQ=GCTTCTGGAAGAGCCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:28.5:1:1:0:43:4:1:0:4.5 +GL000225.1 89792 . CA TG 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTCTGGAAGAGCCGGGG;RSEQ=GCGTAGGCAAAATCCCTGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:46.5:1:30.8:1:1:0:43:4:1:0:3.5 +GL000225.1 89810 . T C 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCAGCGTAGGCAAAATCCC;RSEQ=GCGTGCCAGGGCAGGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:34:0:31.5:1:1:0:43:4:1:0:3.5 +GL000225.1 89966 . T C 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AGGAAGCCCCATTCCCCAAG;RSEQ=GCCGGTGTTGGCGATGGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:31.5:1:31:1:1:0:60:4:1:0:4.5 0/0:2:0:0,0:1,1:2,0:0:2,0:14:1:28.5:1:1:0:60:4:1:0:0 +GL000225.1 89979 . G T 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.33333;SOR=0;LSEQ=CCCCAAGTGCCGGTGTTGGC;RSEQ=ATGGCGACCCACGAGGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:44.5:1:31:1:1:0:60:4:1:0:4.5 0/0:1:0:0,0:0,1:1,0:0:0,0:11:0:33:0:1:0:60:2:1:0:0 +GL000225.1 90022 . G A 32 d5;v3;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAGACACCCGCCAGGGACC;RSEQ=CGATACACCGGCCGCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8:0:32:0:1:0:60:4:1:0:4.5 1/1:1:1:1,0:0,0:0,1:1:0,0:14:0:31:0:1:0:54:2:1:0:8 +GL000225.1 90025 . A T 31 d5;v3;p8;pSTD STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACACCCGCCAGGGACCGCG;RSEQ=TACACCGGCCGCCTGCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:31.5:1:1:0:60:4:1:0:4.5 1/1:1:1:1,0:0,0:0,1:1:0,0:17:0:31:0:1:0:54:2:1:0:8 +GL000225.1 90070 . G T 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACCCTGCCAGCCTTCCCC;RSEQ=GGTGCCTGGCTCTTTGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:43:0:34:0:1:0:41:2:1:0:6 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:28:1:1:0:42:4:1:0:5.5 +GL000225.1 90080 . C T 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AGCCTTCCCCGGGTGCCTGG;RSEQ=TCTTTGATTCTGAAACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:48:0:32:0:1:0:41:2:1:0:6 1/1:2:2:1,1:0,0:0,2:1:0,2:27:1:28:1:1:0:42:4:1:0:5.5 +GL000225.1 90276 . TTCC T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCGGTCCAGGGCCGAGA;RSEQ=CACTGGTGCTCCCTCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:12:0:31.5:1:1:0:24:4:1:0:1.5 +GL000225.1 90499 . G A 27 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCGCAGGGAGGGTGCCGTCC;RSEQ=AAGGTGTCGGGAGGGTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:27:1:1:0:60:4:1:0:2.5 +GL000225.1 90519 . C T 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GAAGGTGTCGGGAGGGTCAT;RSEQ=GCGGGGAGCCCCGTCCGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:29:1:1:0:60:4:1:0:2.5 +GL000225.1 91248 . A G 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAGAGCAAAGGCACCATGCC;RSEQ=GTCTTCCACCCTTCCCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:43:0:32:0:1:0:26:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:27.5:1:31.5:1:1:0:46:4:1:0:3.5 +GL000225.1 91250 . T C 32 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=GAGCAAAGGCACCATGCCAG;RSEQ=CTTCCACCCTTCCCTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:45:0:32:0:1:0:26:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25.5:1:32.5:1:1:0:46:4:1:0:3.5 +GL000225.1 91259 . C T 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=CACCATGCCAGTCTTCCACC;RSEQ=TTCCCTGCATGTTTCCGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:1,0:1,0:0:0,0:47:0:33:0:1:0:26:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:16.5:1:31:0:1:0:46:4:1:0:3.5 +GL000225.1 91441 . T G 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=GTCTAGACTCTGCCTATGGG;RSEQ=GCATTGTGAGATATCTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:8.5:1:31.5:1:1:0:52.5:4:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:33:0:32:0:1:0:60:2:1:0:0 +GL000225.1 92344 . C G 34 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTGTGACATATCTCTGCA;RSEQ=TGATCTCCCAGGTACTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:20:1:34.5:1:1:0:39.5:4:1:0:8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 92358 . A G 34 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTGCACTGATCTCCCAGGT;RSEQ=CTGTAACTTTAGTCTAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:34:0:1:0:39.5:4:1:0:8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 92360 . T C 32 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCACTGATCTCCCAGGTAC;RSEQ=GTAACTTTAGTCTAGGTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:32:0:1:0:39.5:4:1:0:8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 92370 . G T 31 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCAGGTACTGTAACTTTA;RSEQ=TCTAGGTTCTGGCTACACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:31.5:1:1:0:39.5:4:1:0:8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 92380 . T C 31 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAACTTTAGTCTAGGTTC;RSEQ=GGCTACACGGCATTGTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:45:1:31:1:1:0:39.5:4:1:0:8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 92386 . C A 30 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTAGTCTAGGTTCTGGCTA;RSEQ=ACGGCATTGTGACATATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:39:1:30.5:1:1:0:39.5:4:0.6667:0:8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 92389 . G A 30 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTCTAGGTTCTGGCTACAC;RSEQ=GCATTGTGACATATCTCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:36:1:30.5:1:1:0:39.5:4:0.6667:0:8 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 92419 . C T 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATATCTCTGCACTGATCAC;RSEQ=CAGGTGATATATCTCTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:20.5:1:30:1:1:1:35:4:0.5:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 92435 . T C 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCACCCAGGTGATATATCTC;RSEQ=CTTCTAGGATCTGCCTACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:31.5:1:1:0:35:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000225.1 131687 . G T 25 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGATGTATCACTTTTATAA;RSEQ=CACTGCCTACAGGGAATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:4:0:27:0:1:0:20:2:1:0:5 1/0:3:2:0,2:0,1:1,2:0.6667:0,0:7:1:25.5:1:1:0:22:4:0.6667:0:3 +GL000225.1 131721 . A T 33 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06593;SOR=0;LSEQ=GAATTTTGACAAATCTCTGC;RSEQ=CTGATCACCTAGGTGATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:1,1:2,2:0.5:2,2:32:1:33:1:1:1:20:4:0.5:0:4 0/0:10:0:0,0:2,8:10,0:0:2,0:27.6:1:27.5:1:1:0:26.8:20:1:0:3.4 +GL000225.1 131736 . G T 24 d5;v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGCACTGATCACCTAGGT;RSEQ=ATGTAACTCTTGTCTACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:39.5:1:32.5:1:1:0:21.8:8:1:0:4 0/1:10:2:0,2:2,6:8,2:0.2:2,0:41:1:24.5:1:1:0:20.5:4:0.2:0:4.5 +GL000225.1 131760 . C T 98 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACTCTTGTCTACCCTCTG;RSEQ=CCAAGGGGGCATTGTGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:34.5:1:30:1:1:0:21.8:8:1:0:4 1/1:10:10:2,8:0,0:0,10:1:0,2:31.9:1:29.6:1:1:0:26.8:20:1:0:3.4 +GL000225.1 131765 . G C 104 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTGTCTACCCTCTGCCCAA;RSEQ=GGGGCATTGTGAAATATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:29.5:1:31:1:1:0:21.8:8:1:0:4 1/1:10:10:2,8:0,0:0,10:1:0,2:26.9:1:31.6:1:1:0:26.8:20:1:0:3.4 +GL000225.1 133741 . G T 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAGGCTCCACCTACAGGGG;RSEQ=TATTGTGACGTATCTCTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:33:0:31:1:1:0:20:4:0.6667:0:1 +GL000225.1 133779 . G C 29 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCACTGATCACCCAGGTGAT;RSEQ=TAACATTTATCTAGGCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,1:2,2:0.5:2,2:5:0:29:1:1:1:20:4:0.5:0:1 +GL000226.1 150 . T C 60 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGAAACGTCTTTGTGATGT;RSEQ=TGCATTCAACTCATAGAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:6:4:2,2:1,1:2,4:0.6667:2,2:13:1:30.3:1:1:1:24.5:8:0.6667:0:2.8 +GL000226.1 152 . G A 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAACGTCTTTGTGATGTTT;RSEQ=CATTCAACTCATAGAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:16.5:1:27.5:1:1:1:46:4:0.3333:0:1.5 +GL000226.1 216 . T C 75 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=TTGAAGCACTCTTTTTGTAG;RSEQ=ACGTGCAAGTGGATATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:16:0:35:0:1:0:47.5:4:1:0:3 1/1:5:5:3,2:0,0:0,5:1:0,2:31.6:1:32.6:1:1:0:32.8:10:1:0:5.4 +GL000226.1 218 . C T 72 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGCACTCTTTTTGTAGTA;RSEQ=GTGCAAGTGGATATTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14:0:33:1:1:0:47.5:4:1:0:3 1/1:5:5:3,2:0,0:0,5:1:0,2:30:1:31.4:1:1:0:32.8:10:1:0:5.4 +GL000226.1 230 . T C 75 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGTAGTACGTGCAAGTGGA;RSEQ=ATTTGGAGTCCTCTGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:2:0:33.5:1:1:0:47.5:4:1:0:3 1/1:5:5:3,2:0,0:0,5:1:0,2:18:1:32.4:1:1:0:32.8:10:1:0:5.4 +GL000226.1 239 . TC CG 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGCAAGTGGATATTTGGAG;RSEQ=CTCTGAGGCCTAAGGTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:28.8:1:1:0:33:4:1:0:7 +GL000226.1 249 . C T 27 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATATTTGGAGTCCTCTGAGG;RSEQ=CTAAGGTGAAAAAGCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:12.5:1:27:1:1:0:33:4:1:0:7 +GL000226.1 253 . A C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGGAGTCCTCTGAGGCCTA;RSEQ=GGTGAAAAAGCAAATATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:8.5:1:29.5:1:1:0:33:4:1:0:7 +GL000226.1 256 . T G 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTCCTCTGAGGCCTAAGG;RSEQ=GAAAAAGCAAATATCTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:5.5:1:28.5:1:1:0:33:4:1:0:7 +GL000228.1 117248 . A G 31 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCAGTTCAGGGATATGTG;RSEQ=AAACGCCCCTGTAGGCAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:36:1:31.5:1:1:0:32:4:1:0:7.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000228.1 117272 . A G 31 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCCCCTGTAGGCAGAGCTT;RSEQ=GACAAGAGTTACATCACCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:31:1:1:0:32:4:1:0:7.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000228.1 117279 . A G 31 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTAGGCAGAGCTTAGACAAG;RSEQ=GTTACATCACCTAGTTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:32:1:31:1:1:0:32:4:1:0:7.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000228.1 117286 . T C 30 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGCTTAGACAAGAGTTACA;RSEQ=CACCTAGTTGATCAGTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:30.5:1:1:0:32:4:1:0:7.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000228.1 117296 . G T 28 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGAGTTACATCACCTAGTT;RSEQ=ATCAGTGCAGAGATATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:15:1:28.5:1:1:0:32:4:1:0:7.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000229.1 6068 . G C 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.42857;SOR=Inf;LSEQ=CTGTCTGTTTCTCTCTCTTT;RSEQ=TCTCTCTCTCTTTCTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:19.3:1:34:0:1:0:49.3:6:1:0:1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:13:1:30:1:1:1:33.5:4:0.5:0:3 +GL000229.1 7922 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48817;SOR=0;LSEQ=TACTAGACTTCAGAACATCT;RSEQ=ATGTTCTAGAAATCCGTAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:10,5:15,2:0.1176:2,0:25:1:34:0:1:0:20.5:4:0.1176:0:2 0/0:14:0:0,0:12,2:14,0:0:2,0:26.3:1:29.9:1:1:0:29.1:28:1:0:0.8 +GL000229.1 7935 . T C 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.06467;LSEQ=AACATCTTATGTTCTAGAAA;RSEQ=CCGTAAGCGATTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:12,4:16,2:0.1111:2,2:25.5:1:31:1:0.4902:2.79285:32.5:4:0.1111:0:2 0/1:17:2:1,1:11,4:15,2:0.1176:2,2:28.5:1:29:1:0.51471:2.56905:27:4:0.1176:0:1.5 +GL000229.1 7938 . G A 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.6026;SOR=2.21548;LSEQ=ATCTTATGTTCTAGAAATCC;RSEQ=TAAGCGATTGCTGCTGCTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:1:1,0:12,5:17,1:0.0556:2,0:30:0:27:0:1:0:29:2:0.0556:0:1 0/1:17:2:2,0:10,5:15,2:0.1176:2,0:33.5:1:31.5:1:1:0:29:4:0.1176:0:1.5 +GL000229.1 7982 . T C 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00134;SOR=0.04027;LSEQ=TGCTGCTGCTGCTGCTCTTG;RSEQ=TGCTGTTGTTGTTGTTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:5,4:1,0:1,9:0.9:0,2:16.4:1:31.7:1:1:0:38.7:8:0.8889:0:1.3 0/1:17:4:3,1:7,6:13,4:0.2353:2,2:5:1:28.3:1:0.60294:2.44:29.8:8:0.2353:0:1.5 +GL000229.1 8117 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCTCTGTCTCTCTTTCTC;RSEQ=GTCTTCTCTCTGTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:2,5:7,2:0.2222:2,0:46:1:30:0:1:0:24:4:0.2222:0:5 0/0:2:0:0,0:0,2:2,0:0:0,0:19.5:1:31.5:1:1:0:60:4:1:0:0 +GL000229.1 8276 . GTC G 33 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=10.000;MSILEN=2;SSF=0.33333;SOR=0;LSEQ=CTCTCTCTCTCTGCCTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:23:0:33.5:1:1:0:31.5:4:1:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:28:0:31:0:1:0:25:2:1:0:7 +GL000229.1 8294 . CTCCCTG GTC 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=9.000;MSILEN=2;SSF=0.33333;SOR=Inf;LSEQ=CTGTCTCTCTCTCTCTCTCT;RSEQ=TCTGTCTCTTTCTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:30:0:33:1:1:0:31.5:4:1:0:0 1/1:2:2:2,0:0,0:0,2:1:0,0:28.5:1:30.6:1:1:0:38:4:1:0.5:6 +GL000229.1 8316 . C G 50 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.19643;SOR=Inf;LSEQ=CCCTGTCTGTCTCTTTCTCT;RSEQ=TGTCTCTCTCTTTCTGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:15.5:1:32.5:1:1:1.7321:24.5:4:0.4:0:2 1/1:3:3:2,1:0,0:0,3:1:0,2:22.3:1:32:1:1:0:40:6:1:0:5.3 +GL000229.1 8318 . G C 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=8;MSI=1.000;MSILEN=1;SSF=0.19643;SOR=Inf;LSEQ=CTGTCTGTCTCTTTCTCTCT;RSEQ=TCTCTCTCTTTCTGTTTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:2,1:3,2:0.4:2,2:17.5:1:33.5:1:1:1.7321:24.5:4:0.4:0:2 1/1:3:3:2,1:0,0:0,3:1:0,2:23:1:31:1:1:0:40:6:1:0:5.3 +GL000229.1 8373 . T A 46 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=4;SSF=0.16667;SOR=Inf;LSEQ=TCTTTCTCTGTCTGTCTCTC;RSEQ=GTCTGTCTCTCTCTCTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:27:1:31.3:1:1:0:52.8:8:1:0:0.8 1/0:5:3:1,2:1,1:2,3:0.6:2,2:29.7:1:29.3:1:1:1.7321:45.7:6:0.6:0:4.3 +GL000229.1 8378 . G GTCTC 64 d5;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=8.000;MSILEN=2;SSF=0.16667;SOR=0;LSEQ=CTCTGTCTGTCTCTCTGTCT;RSEQ=TCTCTCTCTCTCTGTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:27:1:32.1:1:1:0:52.8:8:1:0:0.8 0/1:5:2:1,1:1,2:3,2:0.4:2,2:24:0:32.3:1:1:1.73:53:4:0.4:0:0.5 +GL000229.1 8384 . CTC TTCTT 45 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.16667;SOR=Inf;LSEQ=CTGTCTCTCTGTCTGTCTCT;RSEQ=TCTCTGTCTCTCTGTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:27:1:33.3:1:1:0:52.8:8:1:0:0.8 1/0:5:3:1,2:1,1:2,3:0.6:2,2:19.3:1:28.8:1:1:1.7321:45.7:6:0.6:0.2:4.3 +GL000229.1 8417 . T A 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCTGTCTCTGTGTCTCTCTC;RSEQ=CTCTGCCTGTCTCTCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:18:1:31:1:1:0:50.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000229.1 8758 . GTC G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.04762;SOR=Inf;LSEQ=CTTTCTCTGCCTGTCTGTCT;RSEQ=TCTCTCTCTCTCCTTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:23.8:1:30:1:1:0:60:10:1:0:0 1/1:2:2:0,2:0,0:0,2:1:0,0:22:1:28.5:1:1:0:44:4:1:0:1.5 +GL000229.1 8794 . T C 49 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.03333;SOR=Inf;LSEQ=TTGTCTGTTTCTCTCTCTCT;RSEQ=TGTCTCTGTTTCTCTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:1:1,0:3,3:6,1:0.1429:2,0:37:0:33:0:1:0:28:2:0.1429:0:3 1/1:3:3:1,2:0,0:0,3:1:0,2:26.7:1:31:1:1:0:44.3:6:1:0:1.3 +GL000229.1 8858 . ATCTG CTGTCTA 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=1;SOR=0;LSEQ=CTCTCTCTGTCTCTTTCTCT;RSEQ=TCTCTCTCCTTCTTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,1:2,2:0.4:2,2:22:1:30.5:1:1:1:37.5:4:0.5:0.2:2.5 0/0:1:0:0,0:1,0:1,0:0:0,0:6:0:32:0:1:0:45:2:1:0:1 +GL000229.1 8954 . G A 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCTCTTTCTCTGACTGTCT;RSEQ=CCTGTCTGCCTGTCTGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:24:1:29:0:1:0:29:4:0.6667:0:5.5 +GL000229.1 8959 . T C 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=8;SSF=1;SOR=0;LSEQ=TTTCTCTGACTGTCTGCCTG;RSEQ=CTGCCTGTCTGTCTCTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:29:1:32.5:1:1:0:29:4:0.6667:0:5.5 +GL000229.1 8963 . C T 45 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=TCTGACTGTCTGCCTGTCTG;RSEQ=CTGTCTGTCTCTCTCTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:3:0:32:1:1:0:60:4:1:0:0.5 1/0:4:3:2,1:1,0:1,3:0.75:0,2:22.7:1:28.7:1:1:0:35:6:0.75:0:4.7 +GL000229.1 8982 . C A 68 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=2.31595;LSEQ=GCCTGTCTGTCTCTCTCTGT;RSEQ=TGTCTCTCTCTCTTTCTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:19:0:33:0:1:0:47:2:0.3333:0:2 1/0:9:5:4,1:2,2:4,5:0.5556:2,2:22:1:29.4:1:0.52381:3.39:31:10:0.5556:0:3.6 +GL000229.1 8995 . T C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTCTGTCTGTCTCTCTCTC;RSEQ=TTCTGTCTCTGTCTCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:34:1:32.7:1:1:0:55.7:6:1:0:1 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:17:0:32.5:1:1:2.23609:41:4:0.2222:0:1 +GL000229.1 9006 . GTC G 74 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.000;MSILEN=2;SSF=1;SOR=2.31595;LSEQ=CTCTCTCTCTTTCTGTCTCT;RSEQ=TCTCTTTCTGTTTCTCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:44:0:34:0:1:0:47:2:0.3333:0:2 1/0:9:5:4,1:2,2:4,5:0.5556:2,2:29.2:1:32.2:1:0.52381:3.39:31:10:0.5556:0:3.6 +GL000229.1 9024 . C T 71 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=1;SOR=2.31595;LSEQ=CTGTCTCTCTTTCTGTTTCT;RSEQ=TCTGTCTCTGTCCATCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:42:0:32:0:1:0:47:2:0.3333:0:2 1/0:9:5:4,1:2,2:4,5:0.5556:2,2:28:1:31:1:0.52381:3.39:31:10:0.5556:0:3.6 +GL000229.1 9912 . G A 29 d5;v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=TCGTCGGCTAAAGTACAAAG;RSEQ=GATGGCGACTTCCACCCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:25.5:1:30:1:1:0:44:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:29.5:1:1:0:40.5:4:1:0:4.5 +GL000229.1 9938 . C T 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CGACTTCCACCCACAAGGTC;RSEQ=CCACTGAACTGTGAAGATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:18.3:1:31:1:1:0:36.3:6:1:0:1.7 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:26:0:32:1:1:0:40.5:4:0.6667:0:4.5 +GL000229.1 9950 . T C 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.4;SOR=Inf;LSEQ=ACAAGGTCCCCACTGAACTG;RSEQ=GAAGATGTGGAGCGTAGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:22.3:1:30.7:1:1:0:36.3:6:1:0:1.7 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:14:0:32.5:1:1:0:40.5:4:0.6667:0:4.5 +GL000229.1 9959 . G A 30 d5;v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=Inf;LSEQ=CCACTGAACTGTGAAGATGT;RSEQ=GAGCGTAGGTCAGAGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:37:1:32.5:1:1:0:24.5:4:1:0:1.5 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:5:0:30.5:1:1:0:40.5:4:0.6667:0:4.5 +GL000231.1 24460 . C T 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTGATTGGATTTTTCCTG;RSEQ=CTACAGACAGGAATGAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:2,0:2,1:3,2:0.4:2,0:32.5:1:32:0:1:0:20.5:4:0.4:0:2.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +GL000231.1 24498 . T A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=TCTGCTGTTTTCTTTTTTAA;RSEQ=CCCGAGGGGACTGAGCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:1,2:3,5:0.625:2,0:27.2:1:31:1:0.10714:0:22.4:10:0.625:0:3.6 0/0:3:0:0,0:2,1:3,0:0:2,0:3:1:27.3:1:1:0:60:6:1:0:0 +GL000231.1 24537 . GA TC 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49091;SOR=0;LSEQ=GAGGGCCTCGAGCGCGGCCA;RSEQ=CTCCCCAAACCCCCAACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:3:3,0:3,2:5,3:0.375:2,0:37:1:30:1:0.46429:0:26.3:6:0.375:0:4.7 0/0:4:0:0,0:3,1:4,0:0:2,0:39:1:31:1:1:0:58.8:8:1:0:0 +GL000231.1 24543 . C T 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.22857;SOR=0;LSEQ=CTCGAGCGCGGCCAGACTCC;RSEQ=CAAACCCCCAACTGGTGATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:4,2:6,3:0.3333:2,0:35.3:1:30:1:0.5:0:26.3:6:0.3333:0:4.7 0/0:6:0:0,0:5,1:6,0:0:2,0:31.8:1:32.2:1:1:0:58.2:12:1:0:0 +GL000231.1 24545 . A C 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22857;SOR=0;LSEQ=CGAGCGCGGCCAGACTCCCC;RSEQ=AACCCCCAACTGGTGATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:4,2:6,3:0.3333:2,0:34.7:1:29.3:1:0.5:0:26.3:6:0.3333:0:4.7 0/0:6:0:0,0:5,1:6,0:0:2,0:33.5:1:28.2:1:1:0:58.2:5:1:0:0 +GL000231.1 24551 . C A 42 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2125;SOR=0;LSEQ=CGGCCAGACTCCCCAAACCC;RSEQ=CAACTGGTGATTGTGGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:3:3,0:4,2:6,3:0.3333:2,0:32.7:1:27:1:0.5:0:26.3:6:0.3333:0:4.7 0/0:7:0:0,0:5,2:7,0:0:2,0:29.6:1:31.7:1:1:0:58.4:14:1:0:0 +GL000231.1 24613 . TTGC T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.49091;SOR=0;LSEQ=CAGCTTCTGTTCTGTTGTTG;RSEQ=TGCTGCTGCTGCTGGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:2,0:16,7:23,2:0.0714:2,0:33:1:33:0:1:0:36:4:0.0769:0:0 0/0:27:0:0,0:13,13:26,0:0:2,0:24.5:1:29.3:1:1:0:51:52:0.963:0:0.1 +GL000231.1 24616 . CTGC T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=1;SOR=0.50613;LSEQ=AGCTTCTGTTCTGTTGTTGT;RSEQ=TGCTGCTGCTGGTGCTGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:2:1,1:16,7:23,2:0.0714:2,2:43:1:31.3:1:1:2.20393:32.5:4:0.0769:0:1 0/1:27:1:0,1:13,13:26,1:0.037:2,0:41:0:27.5:0:1:0:35:2:0.037:0:2 +GL000231.1 24628 . C G 33 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=0.50591;LSEQ=TGTTGTTGCTGCTGCTGCTG;RSEQ=TGGTGCTGTCGTCATTGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:17,10:27,2:0.069:2,2:47:1:33:1:1:1.66781:32.5:4:0.0741:0:2 0/1:28:1:0,1:13,14:27,1:0.0357:2,0:49:0:30:0:1:0:35:2:0.0357:0:3 +GL000231.1 24664 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49789;SOR=0;LSEQ=TGTTTTGGTATTTTACAGAC;RSEQ=CAGGGGGTGTATGTGCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:13,10:23,2:0.08:2,2:24.5:1:30:1:1:1.28628:59:4:0.08:0:1 0/0:19:0:0,0:8,11:19,0:0:2,0:22.7:1:30.2:1:1:0:43.5:38:1:0:0.2 +GL000231.1 24665 . CAG C 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.01269;SOR=Inf;LSEQ=GTTTTGGTATTTTACAGACT;RSEQ=GGGGTGTATGTGCTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:25,0:0:2,0:26:1:29.7:1:1:0:38.7:24:1:0:0.2 0/1:20:5:2,3:6,9:15,5:0.25:2,2:17.8:1:31:1:1:1:54:10:0.25:0.05:1.2 +MT 73 . A G 155 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0749;SOR=2.8424;LSEQ=GGTATTTTCGTCTGGGGGGT;RSEQ=TGCACGCGATAGCATTGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:30:14,16:8,10:18,30:0.625:2,2:27.1:1:31.7:1:1:1.09:49.3:29:0.617:0:1.3 1/1:29:24:8,16:2,3:5,24:0.8276:2,2:29.1:1:32:1:1:1.31975:48.9:48:0.8276:0:1.2 +MT 75 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52427;SOR=0;LSEQ=TATTTTCGTCTGGGGGGTAT;RSEQ=CACGCGATAGCATTGCGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:21,25:46,2:0.0417:2,2:30:1:30.5:1:1:1.19:60:4:0.0417:0:1 0/0:29:0:0,0:10,19:29,0:0:2,0:28:1:32:1:1:0:50.8:58:1:0:1 +MT 150 . C T 95 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:37,22:59,0:0:2,0:21.5:1:31.8:1:1:0:58:118:1:0:1.6 0/1:19:9:5,4:4,6:10,9:0.4737:2,2:29.3:1:30.1:1:0.65628:1.81:60:18:0.4737:0:3.1 +MT 152 . T C 163 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=5e-05;SOR=0.06779;LSEQ=CTTTGATTCCTGCCTCATCC;RSEQ=ATTATTTATCGCACCTACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:36:18,18:15,5:20,36:0.6429:2,2:21.8:1:31.6:1:0.09199:2.94184:57.6:72:0.6429:0:2.6 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:38.5:1:30.5:1:1:1.12:60:4:0.1053:0:1.5 +MT 178 . A G 162 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=TTATCGCACCTACGTTCAAT;RSEQ=TTACAGGCGAACATACTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:33:19,14:20,9:29,33:0.5323:2,2:23.7:1:32.3:1:0.43363:1.62437:60:66:0.5323:0:2.8 0/0:19:0:0,0:10,9:19,0:0:2,0:22.8:1:29.2:1:1:0:60:38:1:0:1.9 +MT 185 . G A 85 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.57479;LSEQ=ACCTACGTTCAATATTACAG;RSEQ=CGAACATACTTACTAAAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:7:5,2:35,25:60,7:0.1045:2,2:27.4:1:30.3:1:0.69262:1.77:60:14:0.1061:0:1.7 0/1:16:1:0,1:9,6:15,1:0.0625:2,0:44:0:27:0:0.4375:0:60:2:0.0625:0:1 +MT 189 . A G 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00014;SOR=Inf;LSEQ=ACGTTCAATATTACAGGCGA;RSEQ=CATACTTACTAAAGTGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:41,27:68,0:0:2,0:24.8:1:30:1:1:0:60:136:1:0:1.8 0/1:16:5:3,2:5,6:11,5:0.3125:2,2:32:1:32.6:1:1:1.73:60:10:0.3125:0:5.2 +MT 194 . CT TC 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=CAATATTACAGGCGAACATA;RSEQ=TACTAAAGTGTGTTAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:40,29:69,0:0:2,0:25.2:1:31.9:1:1:0:60:138:1:0:1.7 0/1:18:7:5,2:5,6:11,7:0.3889:2,2:23:1:31.1:1:0.36652:2.82:60:14:0.3889:0.1111:3.9 +MT 195 . T C 162 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.00528;SOR=0.13608;LSEQ=AATATTACAGGCGAACATAC;RSEQ=TACTAAAGTGTGTTAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:68:34:18,16:21,13:34,34:0.5:2,2:25.9:1:32:1:0.62425:1.42821:60:68:0.5:0:2.7 0/1:17:2:1,1:4,6:10,2:0.1176:2,2:12:1:31:1:1:1.45:60:4:0.1667:0:3 +MT 204 . T C 89 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1e-05;SOR=Inf;LSEQ=GGCGAACATACTTACTAAAG;RSEQ=GTGTTAATTAATTAATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:33,30:63,0:0:2,0:29:1:29.8:1:1:0:60:126:1:0:1.6 0/1:18:7:4,3:5,6:11,7:0.3889:2,2:21.1:1:31.9:1:1:1.56:60:14:0.3889:0:4 +MT 207 . G A 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=2;SSF=4e-05;SOR=Inf;LSEQ=GAACATACTTACTAAAGTGT;RSEQ=TTAATTAATTAATGCTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:33,30:63,0:0:2,0:29.4:1:31.9:1:1:0:60:126:1:0:1.6 0/1:17:6:4,2:5,6:11,6:0.3529:2,2:25.3:1:29.7:1:0.61991:2.28:60:12:0.3529:0:4 +MT 225 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5666;SOR=0;LSEQ=GTGTTAATTAATTAATGCTT;RSEQ=TAGGACATAATAATAACAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:3:1,2:33,36:69,3:0.0417:2,2:15.7:1:28.7:1:1:1.81855:60:6:0.0423:0:2.7 0/0:25:0:0,0:14,11:25,0:0:2,0:16.7:1:31.5:1:1:0:59.7:50:1:0:2.3 +MT 228 . G A 87 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.47856;SOR=1.65545;LSEQ=TTAATTAATTAATGCTTGTA;RSEQ=GACATAATAATAACAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:7:3,4:32,35:67,7:0.0946:2,2:22.7:1:31.3:1:1:1.21581:60:14:0.0946:0:2.7 0/1:27:4:2,2:13,10:23,4:0.1481:2,2:10.8:1:30.8:1:1:1.28731:60:8:0.1481:0:2.8 +MT 247 . G A 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00782;SOR=Inf;LSEQ=AGGACATAATAATAACAATT;RSEQ=AATGTCTGCACAGCCACTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:32,40:72,0:0:2,0:23.4:1:32.4:1:1:0:59.7:144:1:0:1.8 0/1:32:4:2,2:17,11:28,4:0.125:2,2:16.5:1:30.5:1:1:1.52399:58:8:0.125:0:3.3 +MT 263 . A G 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52111;SOR=Inf;LSEQ=AATTGAATGTCTGCACAGCC;RSEQ=CTTTCCACACAGACATCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:65:63:28,35:1,0:1,63:0.9692:0,2:24.3:1:30.7:1:0.45313:0:59.2:14.75:0.9833:0:2 1/1:41:41:23,18:0,0:0,41:1:0,2:25.2:1:30.5:1:1:0:59.4:82:1:0:2.6 +MT 295 . C T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29162;SOR=1.773;LSEQ=GACATCATAACAAAAAATTT;RSEQ=CACCAAACCCCCCCTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:8:5,3:19,27:46,8:0.1481:2,2:28.5:1:32:1:0.44291:2.33:59.1:16:0.1633:0:3.8 0/1:38:9:5,4:14,14:28,9:0.2368:2,2:30.9:1:29:1:1:1.24:58.3:18:0.2368:0:3.1 +MT 302 . A AC 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.75737;SOR=1.34843;LSEQ=TAACAAAAAATTTCCACCAA;RSEQ=CCCCCCCTCCCCCGCTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:3,3:20,25:45,6:0.1154:2,2:22.8:1:32.5:1:1:1.24:58.8:12:0.125:0.0192:3.3 0/1:40:6:6,0:13,20:33,6:0.15:2,0:31.2:1:29.8:1:0.00832:0:53.8:12:0.1538:0:4.7 +MT 310 . T C 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=1;SOR=0.91509;LSEQ=AATTTCCACCAAACCCCCCC;RSEQ=CCCCCGCTTCTGGCCACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:16:14,2:1,2:3,16:0.3721:2,2:12.2:1:27.6:1:0.09701:11.19:53.9:7:0.56:0:2.7 0/1:37:13:13,0:2,1:3,13:0.3514:2,1:19.5:1:21.5:1:0.1875:0:54.6:2.25:0.36:0:4.4 +MT 340 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06496;SOR=Inf;LSEQ=CTGGCCACAGCACTTAAACA;RSEQ=ATCTCTGCCAAACCCCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:26,32:58,0:0:2,0:20.4:1:31.3:1:1:0:59.7:13.5:1:0:0.8 0/1:40:3:2,1:15,22:37,3:0.075:2,2:14.7:1:24:1:0.56468:2.85:60:2:0.0571:0:3 +MT 357 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15495;SOR=Inf;LSEQ=ACACATCTCTGCCAAACCCC;RSEQ=AAAACAAAGAACCCTAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:31,35:66,0:0:2,0:25:1:30.7:1:1:0:59.9:32:1:0:0.5 0/1:44:2:1,1:17,24:41,2:0.0455:2,2:12.5:1:32:1:1:1.40:41:4:0.0488:0:1.5 +MT 434 . C G 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.000;MSILEN=1;SSF=0.50695;SOR=0;LSEQ=TATGCACTTTTAACAGTCAC;RSEQ=CCCCAACTAACACATTATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:2:1,1:31,32:63,2:0.0308:2,2:13:1:27.5:1:1:1.03:60:4:0.0313:0:3 0/0:48:0:0,0:22,26:48,0:0:2,0:24:1:30:1:1:0:60:47:1:0:0.5 +MT 462 . C T 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.56581;SOR=1.48078;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:7:2,5:28,27:55,7:0.1129:2,2:30.6:1:30:1:0.42674:2.5548:60:14:0.1167:0:2.7 0/1:44:7:3,4:20,17:37,7:0.1591:2,2:34.7:1:30.1:1:0.69267:1.55258:60:14:0.1591:0:1.9 +MT 477 . T C 151 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CCCTCCCACTCCCATACTAC;RSEQ=AATCTCATCAATACAACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:26:13,13:16,16:32,26:0.4483:2,2:21.4:1:32.2:1:1:1:59.3:52:0.4643:0:1.3 0/0:49:0:0,0:24,25:49,0:0:2,0:23.3:1:28.4:1:1:0:60:23.5:1:0:0.6 +MT 488 . AT GC 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4989;SOR=0;LSEQ=CCATACTACTAATCTCATCA;RSEQ=ACAACCCCCGCCCATCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:2:1,1:28,27:55,2:0.0351:2,2:13:1:30.1:1:1:1.03639:60:4:0.0364:0.0175:1.5 0/0:48:0:0,0:24,24:48,0:0:2,0:23.1:1:29.3:1:1:0:60:47:1:0:0.7 +MT 489 . T C 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.42318;SOR=1.60786;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:7:3,4:25,23:48,7:0.125:2,2:25.3:1:33:1:0.70487:1.43953:60:14:0.1321:0:2.9 0/1:48:9:5,4:19,20:39,9:0.1875:2,2:11.6:1:31.3:1:1:1.31:60:18:0.1915:0:1.8 +MT 491 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50222;SOR=0;LSEQ=TACTACTAATCTCATCAATA;RSEQ=AACCCCCGCCCATCCTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:2:1,1:27,27:54,2:0.0357:2,2:26.5:1:29.5:1:1:1:60:4:0.0364:0:3.5 0/0:44:0:0,0:22,22:44,0:0:2,0:24.9:1:31.3:1:1:0:60:43:1:0:0.7 +MT 497 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.20495;SOR=Inf;LSEQ=TAATCTCATCAATACAACCC;RSEQ=CGCCCATCCTACCCAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:27,28:55,0:0:2,0:24.5:1:30.7:1:1:0:60:54:1:0:0.9 0/1:46:2:1,1:22,22:44,2:0.0435:2,2:34:1:30:0:1:1:60:4:0.0455:0:1 +MT 508 . A G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00073;SOR=Inf;LSEQ=ATACAACCCCCGCCCATCCT;RSEQ=CCCAGCACACACACACCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:25,29:54,0:0:2,0:25.8:1:28.6:1:1:0:60:26:1:0:0.7 0/1:48:9:5,4:16,23:39,9:0.1875:2,2:27.3:1:30.6:1:0.47716:1.77:59.8:8:0.1778:0:1.1 +MT 513 . G GCA 123 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0;SOR=30.93227;LSEQ=ACCCCCGCCCATCCTACCCA;RSEQ=CACACACACACCGCTGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:25,33:58,1:0.0169:2,0:41:0:32:0:1:0:60:2:0.0175:0:4 0/1:48:17:7,10:14,17:31,17:0.3542:2,2:26.5:1:30.3:1:1:1.1725:59.9:34:0.3542:0.0833:0.6 +MT 525 . C T 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.57047;SOR=2.82863;LSEQ=CCTACCCAGCACACACACAC;RSEQ=GCTGCTAACCCCATACCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:1:0,1:25,35:60,1:0.0164:2,0:1:0:27:0:1:0:45:2:0.0167:0:1 0/1:44:2:1,1:18,23:41,2:0.0455:2,2:27:0:32:1:1:1.27:60:4:0.0465:0:1.5 +MT 533 . A G 105 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0047;SOR=0;LSEQ=GCACACACACACCGCTGCTA;RSEQ=CCCCATACCCCGAACCAACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:9:4,5:20,27:47,9:0.1607:2,2:26.2:1:33.2:1:1:1.08:45.2:18:0.1607:0:1.9 0/0:43:0:0,0:19,24:43,0:0:2,0:28.3:1:29.4:1:1:0:60:86:1:0:0.5 +MT 709 . G A 82 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.10463;LSEQ=TTACACATGCAAGCATCCCC;RSEQ=TTCCAGTGAGTTCACCCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:3,3:3,2:5,6:0.5455:2,2:18.8:1:31.8:1:1:1.44544:36.8:12:0.5455:0:2.8 1/0:7:4:1,3:0,1:1,4:0.5714:0,2:20.3:1:29.3:1:1:0:35.8:8:0.5714:0:2 +MT 750 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAATCACCACGATCAAAAGG;RSEQ=ACAAGCATCAAGCACGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:18:10,8:0,0:0,18:1:0,2:30.2:1:32:1:1:0:33.1:36:1:0:1.7 1/1:12:12:4,8:0,0:0,12:1:0,2:34.1:1:30.4:1:1:0:29.4:24:1:0:1.8 +MT 769 . G A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03684;SOR=Inf;LSEQ=GAACAAGCATCAAGCACGCA;RSEQ=CAATGCAGCTCAAAACGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:13,13:26,0:0:2,0:23.7:1:32.2:1:1:0:35:25:1:0:1.1 0/1:14:3:1,2:5,6:11,3:0.2143:2,2:38:1:29.7:1:1:1.60839:25.3:6:0.2143:0:3 +MT 1355 . G A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGCCCATGAGGTGGCAA;RSEQ=AAATGGGCTACATTTTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:11,14:25,2:0.0741:2,2:29.5:1:32.5:1:1:1.26:25:4:0.0769:0:1 0/0:4:0:0,0:0,4:4,0:0:0,0:33.8:1:30.3:1:1:0:38.3:8:1:0:0 +MT 1438 . A G 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGTGGATTTAGCAGTAAACT;RSEQ=AGAGTAGAGTGCTTAGTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:10,3:0,0:0,13:1:0,2:25.7:1:31.5:1:1:0:35.2:26:1:0:1.2 1/1:5:5:3,2:0,0:0,5:1:0,2:34.8:1:26.6:1:1:0:28.2:4:1:0:1.8 +MT 1719 . G A 49 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.08098;SOR=Inf;LSEQ=CTTACTACCAGACAACCTTA;RSEQ=CCAAACCATTTACCCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:10,7:17,0:0:2,0:25.4:1:32.8:1:1:0:48.5:34:1:0:0 0/1:14:3:2,1:6,5:11,3:0.2143:2,2:34:1:31.3:1:1:1.61:48:6:0.2143:0:1 +MT 1811 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07143;SOR=Inf;LSEQ=GGGAAAGATGAAAAATTATA;RSEQ=CCAAGCATAATATAGCAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:5,9:14,0:0:2,0:19.4:1:30.4:1:1:0:35.3:28:0.9333:0:0.1 0/1:6:2:1,1:3,1:4,2:0.3333:2,2:36.5:1:31.5:1:1:2.44949:54:4:0.3333:0:1 +MT 1836 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.12121;SOR=Inf;LSEQ=GCATAATATAGCAAGGACTA;RSEQ=CCCCTATACCTTCTGCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:6,8:14,0:0:2,0:16.1:1:30.9:1:1:0:36:28:1:0:0.1 0/1:8:2:1,1:3,3:6,2:0.25:2,2:15.5:1:29.5:1:1:1:43.5:4:0.25:0:1 +MT 1990 . G A 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16667;SOR=0;LSEQ=GAAGATTTATAGGTAGAGGC;RSEQ=ACAAACCTACCGAGCCTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:17.6:1:30.8:1:1:1.41:30.8:10:0.7143:0:1.2 0/0:3:0:0,0:1,2:3,0:0:2,0:8.7:1:29:1:1:0:42:6:1:0:0 +MT 2294 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.17235;SOR=Inf;LSEQ=ATCTATCACCCTATAGAAGA;RSEQ=CTAATGTTAGTATAAGTAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:19,0:0:2,0:20.3:1:29.9:1:1:0:51:38:1:0:0.3 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:19.5:1:33:0:1:1.36624:44.5:4:0.1429:0:1 +MT 2706 . A G 133 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15794;SOR=3.60062;LSEQ=GCCCGTGAAGAGGCGGGCAT;RSEQ=ACACAGCAAGACGAGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:17:8,9:4,5:9,17:0.6538:2,2:27.5:1:32.6:1:1:1.11:50.8:34:0.6538:0:1.1 1/1:16:14:6,8:1,1:2,14:0.875:2,2:20.3:1:30.8:1:1:1.30929:49.9:28:0.875:0:1.2 +MT 2836 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15726;SOR=Inf;LSEQ=GGCGACCTCGGAGCAGAACC;RSEQ=AACCTCCGAGCAGTACATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:8,11:19,0:0:2,0:32:1:31.8:1:1:0:60:38:1:0:0.1 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:33.5:1:30.5:1:1:2.4495:60:4:0.1667:0:1 +MT 3010 . G A 51 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.58204;SOR=0.27695;LSEQ=ATGTTGGATCAGGACATCCC;RSEQ=ATGGTGCAGCCGCTATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:3:1,2:3,4:7,3:0.3:2,2:26.3:1:32.7:1:1:1.44135:33:6:0.3:0:1 0/1:10:1:1,0:5,4:9,1:0.1:2,0:39:0:26:0:1:0:39:2:0.1:0:1 +MT 3106 . CN C 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCAGGTCGGTTTCTATCTA;RSEQ=TTCAAATTCCTCCCTGTACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:11,10:0,0:0,21:1:0,2:19.8:1:31.6:1:1:0:57.3:42:1:0.1905:0.1 1/1:14:14:6,8:0,0:0,14:1:0,2:21.9:1:32:1:1:0:60:28:1:0.2143:0.4 +MT 3480 . A G 51 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11674;SOR=5.98438;LSEQ=GCCATAAAACTCTTCACCAA;RSEQ=GAGCCCCTAAAACCCGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:1:0,1:50,37:87,1:0.0114:2,0:31:0:14:0:0.43182:0:60:0:0:0:1 0/1:46:3:3,0:19,24:43,3:0.0652:2,0:12.7:1:32.7:1:0.10145:0:60:6:0.0652:0:1 +MT 3505 . A G 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCTAAAACCCGCCACATCT;RSEQ=CCATCACCCTCTACATCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:100:0:0,0:53,47:100,0:0:2,0:26.5:1:29:1:1:0:59.5:99:1:0:0.2 0/1:56:12:6,6:19,23:42,12:0.2143:2,2:20.8:1:31.6:1:1:1.21:55.3:24:0.2143:0:1.2 +MT 3512 . C T 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.55135;SOR=0;LSEQ=ACCCGCCACATCTACCATCA;RSEQ=CCTCTACATCACCGCCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:3:1,2:54,47:101,3:0.0288:2,2:28:1:25:1:0.60042:2.28004:59.7:2:0.0198:0:1.7 0/0:53:0:0,0:25,28:53,0:0:2,0:22.5:1:31.3:1:1:0:58.1:106:1:0:0.6 +MT 3528 . C T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCACCCTCTACATCACCGC;RSEQ=CCGACCTTAGCTCTCACCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:2:1,1:54,57:111,2:0.0177:2,2:20:1:32.5:1:1:1.06:60:4:0.018:0:1 0/0:54:0:0,0:26,28:54,0:0:2,0:22.7:1:30.4:1:1:0:58.1:53:1:0:0.6 +MT 3594 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.09611;SOR=Inf;LSEQ=CCCATACCCAACCCCCTGGT;RSEQ=AACCTCAACCTAGGCCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:36,42:78,0:0:2,0:23.2:1:31.9:1:1:0:60:18.5:1:0:0.3 0/1:36:2:1,1:13,21:34,2:0.0556:2,2:17.5:1:30.5:1:1:1.59:43:4:0.0556:0:1.5 +MT 3643 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGCCACCTCTAGCCTAGCC;RSEQ=TTTACTCAATCCTCTGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:34,26:60,2:0.0323:2,2:21:1:30:1:1:1.30197:60:4:0.0323:0:1 0/0:27:0:0,0:13,14:27,0:0:2,0:24.7:1:30.7:1:1:0:60:54:1:0:0.1 +MT 3812 . A G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCACCCTTATCACAACAC;RSEQ=AGAACACCTCTGATTACTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:2:1,1:24,16:40,2:0.0476:2,2:33:0:33:1:1:1.48518:27:4:0.0488:0:1 0/0:18:0:0,0:11,7:18,0:0:2,0:22.5:1:29:1:1:0:44.3:36:1:0:0.1 +MT 3915 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTCGACCTTGCCGAAGG;RSEQ=GAGTCCGAACTAGTCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:19,27:46,2:0.0417:2,2:33.5:1:30:1:1:1.41:41.5:4:0.0417:0:1 0/0:7:0:0,0:2,5:7,0:0:2,0:26.4:1:30:1:1:0:50.3:14:1:0:0 +MT 4917 . A G 141 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCAAATCTCTCCCTCACTA;RSEQ=ACGTAAGCCTTCTCCTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:20:9,11:11,15:26,20:0.4348:2,2:26:1:32.8:1:1:1.11:28.3:40:0.4348:0:1.1 0/0:43:0:0,0:22,21:43,0:0:2,0:18.3:1:29.3:1:1:0:48.1:42:1:0:0.2 +MT 5279 . C T 27 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.48571;SOR=4.4496;LSEQ=TGGGCCATTATCGAAGAATT;RSEQ=ACAAAAAACAATAGCCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4:1:0,1:2,1:3,1:0.25:2,0:1:0:23:0:1:0:60:2:0.25:0:1 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:6:1:27:1:1:0:60:4:0.6667:0:1 +MT 5429 . A G 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.10436;SOR=Inf;LSEQ=AAATGACAGTTTGAACATAC;RSEQ=AAACCCACCCCATTCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:29,37:66,0:0:2,0:22.6:1:30.6:1:1:0:50.2:132:1:0:0.2 0/1:32:2:1,1:12,18:30,2:0.0625:2,2:34:0:31.5:1:1:1.48:23:4:0.0667:0:2 +MT 5460 . G A 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=CATTCCTCCCCACACTCATC;RSEQ=CCCTTACCACGCTACTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:26,34:60,0:0:2,0:27.4:1:31.4:1:1:0:45.4:120:1:0:0.2 0/1:23:6:2,4:6,11:17,6:0.2609:2,2:31:1:28.5:1:1:1.08684:23.5:12:0.2609:0:1 +MT 6291 . C T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50502;SOR=0;LSEQ=GAACAGGTTGAACAGTCTAC;RSEQ=CTCCCTTAGCAGGGAACTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:17,17:34,2:0.0556:2,2:47:0:31.5:1:1:1:22:4:0.0556:0:1 0/0:26:0:0,0:16,10:26,0:0:2,0:30.9:1:29:1:1:0:43.9:25:1:0:0.1 +MT 6371 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.11515;SOR=Inf;LSEQ=TTACACCTAGCAGGTGTCTC;RSEQ=TCTATCTTAGGGGCCATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:16,20:36,0:0:2,0:24.6:1:32:1:1:0:47.5:35:1:0:0.2 0/1:19:2:2,0:4,13:17,2:0.1053:2,0:30.5:1:30.5:1:0.08772:0:41:4:0.1053:0:1 +MT 6518 . C T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.02049;SOR=Inf;LSEQ=CTCCCAGTCCTAGCTGCTGG;RSEQ=ATCACTATACTACTAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:29,26:55,0:0:2,0:26.4:1:32.8:1:1:0:41.3:110:1:0:0.1 0/1:35:4:1,3:16,15:31,4:0.1143:2,2:14.5:1:27.8:1:0.6026:3.10187:47.8:8:0.1176:0:1 +MT 7867 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.08359;SOR=Inf;LSEQ=GACGAGGTCAACGATCCCTC;RSEQ=CTTACCATCAAATCAATTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:14,13:27,0:0:2,0:28.2:1:31.6:1:1:0:38.4:54:1:0:0.1 0/1:22:3:1,2:10,9:19,3:0.1364:2,2:11.7:1:28:1:1:2.1446:35.3:6:0.1364:0:1.3 +MT 8170 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11628;SOR=Inf;LSEQ=CCGGGGGTATACTACGGTCA;RSEQ=TGCTCTGAAATCTGTGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:28:0:0,0:16,12:28,0:0:2,0:20.6:1:30.8:1:1:0:30.6:56:1:0:0.1 0/1:15:2:1,1:4,9:13,2:0.1333:2,2:26:0:33.5:1:1:2.12:33:4:0.1333:0:1.5 +MT 8229 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATCGTCCTAGAATTAATTC;RSEQ=CCTAAAAATCTTTGAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:11,5:16,2:0.1111:2,2:44.5:1:31:1:1:2.09766:22:4:0.1111:0:1 0/0:6:0:0,0:1,5:6,0:0:2,0:23.3:1:30.8:1:1:0:38:12:1:0:0.3 +MT 8251 . G A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01961;SOR=Inf;LSEQ=CTAAAAATCTTTGAAATAGG;RSEQ=CCCGTATTTACCCTATAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:15,0:0:2,0:16.6:1:30.8:1:1:0:24.9:14:1:0:0.3 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:16.5:1:26.5:1:0.33333:0:24:4:0.6667:0:1 +MT 8697 . G A 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0018;SOR=0;LSEQ=AAACTAACCTCAAAACAAAT;RSEQ=ATAACCATACACAACACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:6,8:9,10:19,14:0.4242:2,2:30.4:1:29.8:1:1:1.19338:29.4:28:0.4242:0:1.2 0/0:17:0:0,0:10,7:17,0:0:2,0:24.2:1:30.8:1:1:0:43.2:16:1:0:0.3 +MT 9540 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09627;SOR=Inf;LSEQ=GCCTAGCCCCTACCCCCCAA;RSEQ=TAGGAGGGCACTGGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:24,26:50,0:0:2,0:27:1:30.4:1:1:0:35.7:24:1:0:0.1 0/1:23:2:1,1:11,9:20,2:0.087:2,2:21:1:29.5:1:1:1.21106:22:4:0.0909:0:1 +MT 9891 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19048;SOR=Inf;LSEQ=AACTAATATTTCACTTTACA;RSEQ=CCAAACATCACTTTGGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:9,11:20,0:0:2,0:24:1:30.4:1:1:0:60:40:1:0:0.5 0/1:16:2:1,1:7,7:14,2:0.125:2,2:30.5:1:31:1:1:1:60:4:0.1333:0:2 +MT 9899 . T C 90 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00414;SOR=0;LSEQ=TTTCACTTTACATCCAAACA;RSEQ=CACTTTGGCTTCGAAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:7,7:14,8:0.3636:2,2:27.9:1:30.1:1:0.67492:1.62835:60:7:0.3333:0:1 0/0:19:0:0,0:9,10:19,0:0:2,0:24.7:1:29.3:1:1:0:60:38:1:0:0.3 +MT 10250 . A T 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0.84324;LSEQ=GTAGCTATTACCTTCTTATT;RSEQ=TTTGATCTAGAAATTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:0,2:17,20:37,2:0.0513:2,0:9:1:25:0:0.49528:0:60:4:0.0541:0:1 0/1:23:1:0,1:11,11:22,1:0.0435:2,0:1:0:23:0:1:0:60:2:0.0435:0:1 +MT 10463 . T C 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00766;SOR=0;LSEQ=TTAAATTATGATAATCATAT;RSEQ=TACCAAATGCCCCTCATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:6,1:7,8:0.5333:2,2:27.9:1:33.4:1:0.11888:8.40708:33.9:16:0.5333:0:1.3 0/0:10:0:0,0:5,5:10,0:0:2,0:17.3:1:27.3:1:1:0:48.9:20:1:0:0.1 +MT 10537 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.48988;SOR=0;LSEQ=TCTAGGAATACTAGTATATC;RSEQ=CTCACACCTCATATCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:2:1,1:11,8:19,2:0.0952:2,2:14.5:1:28.5:1:1:1.35399:60:4:0.0952:0:1 0/0:18:0:0,0:6,12:18,0:0:2,0:24.1:1:31.2:1:1:0:55.7:36:1:0:0.2 +MT 10550 . A G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.23077;SOR=Inf;LSEQ=GTATATCGCTCACACCTCAT;RSEQ=TCCTCCCTACTATGCCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:20:0:0,0:11,9:20,0:0:2,0:27.2:1:28.4:1:1:0:54.4:19:1:0:0.2 0/1:20:3:1,2:7,10:17,3:0.15:2,2:21:1:30.7:1:1:1.37728:47:6:0.1579:0:1 +MT 10601 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21041;SOR=0;LSEQ=CTATCGCTGTTCATTATAGC;RSEQ=ACTCTCATAACCCTCAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:1,1:11,7:18,2:0.1:2,2:30.5:1:31:1:1:1.53525:25:4:0.1:0:1 0/0:23:0:0,0:13,10:23,0:0:2,0:22.8:1:29.2:1:1:0:56.3:46:1:0:0.3 +MT 10688 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12057;SOR=Inf;LSEQ=GCCGCCTGCGAAGCAGCGGT;RSEQ=GGCCTAGCCCTACTAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:16,15:31,0:0:2,0:27.8:1:32.1:1:1:0:60:62:1:0:0 0/1:17:2:1,1:7,8:15,2:0.1176:2,2:38.5:1:29.5:1:1:1.13:50:4:0.1176:0:1.5 +MT 10866 . T G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.09898;SOR=Inf;LSEQ=CCACAGCCTAATTATTAGCA;RSEQ=CATCCCTCTACTATTTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,23:49,0:0:2,0:22.9:1:31:1:1:0:53.8:98:1:0:0.2 0/1:23:2:1,1:11,10:21,2:0.087:2,2:28.5:1:30:1:1:1.09544:54:4:0.087:0:1 +MT 10876 . A G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10798;SOR=Inf;LSEQ=ATTATTAGCATCATCCCTCT;RSEQ=CTATTTTTTAACCAAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:26,22:48,0:0:2,0:22.5:1:28.7:1:1:0:55.1:96:1:0:0.2 0/1:24:2:1,1:11,11:22,2:0.0833:2,2:47:1:32:1:1:1:46:4:0.0833:0:1 +MT 11192 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCAGCCAGAACGCCTGAAC;RSEQ=CAGGCACATACTTCCTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:2:1,1:19,20:39,2:0.0488:2,2:23.5:1:29.5:1:1:1.05:41.5:4:0.05:0:1 0/0:14:0:0,0:8,6:14,0:0:2,0:17.7:1:29.6:1:1:0:55.9:28:1:0:0.3 +MT 11195 . G A 31 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAGAACGCCTGAACGCA;RSEQ=GCACATACTTCCTATTCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:16,21:37,2:0.0513:2,2:5.5:1:31:1:1:1.30:41.5:4:0.0513:0:2 0/0:13:0:0,0:8,5:13,0:0:2,0:18.6:1:30.3:1:1:0:55.5:26:1:0:0.3 +MT 11238 . TA T 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCTAGTAGGCTCCCTTCCCC;RSEQ=CTCATCGCACTAATTTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:16,21:37,2:0.0513:2,2:15:0:31.5:1:1:1.30:58.5:4:0.0513:0:3 0/0:10:0:0,0:6,4:10,0:0:2,0:26.8:1:27.6:1:1:0:52.8:20:1:0:0.6 +MT 11251 . A G 154 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10504;SOR=0.30913;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:31:13,18:6,9:15,31:0.6739:2,2:29:1:31.2:1:1:1.08:49.4:30:0.6818:0:1.4 0/1:13:5:3,2:5,3:8,5:0.3846:2,2:22.8:1:31.6:1:1:1.10211:45.6:10:0.3846:0:1.4 +MT 11294 . C A 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.56923;SOR=0;LSEQ=GCTCACTAAACATTCTACTA;RSEQ=TCACTCTCACTGCCCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:3:2,1:20,26:46,3:0.0612:2,2:29.3:1:26:1:0.58087:2.55:56.3:2:0.0417:0:3 0/0:16:0:0,0:8,7:15,0:0:2,0:24.2:1:31.2:1:1:0:59.1:30:0.9375:0:0.3 +MT 11467 . A G 68 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00238;SOR=Inf;LSEQ=GTACTTGCCGCAGTACTCTT;RSEQ=AAACTAGGCGGCTATGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:35:0:0,0:18,17:35,0:0:2,0:21.4:1:30:1:1:0:33.5:70:1:0:0.1 0/1:17:5:3,2:6,6:12,5:0.2941:2,2:18:1:29.6:1:1:1.46:24.2:10:0.2941:0:1 +MT 11719 . G A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14736;SOR=3.23275;LSEQ=ATTCTCATAATCGCCCACGG;RSEQ=CTTACATCCTCATTACTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:12:7,5:11,8:19,12:0.375:2,2:14:1:28.9:1:1:1.02:25.4:24:0.375:0:1.2 1/0:9:6:5,1:1,2:3,6:0.6667:2,2:17.7:1:28.7:1:0.22619:7.11:23.5:12:0.6667:0:1 +MT 11812 . A G 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03878;SOR=Inf;LSEQ=TCTCAAGGACTTCAAACTCT;RSEQ=CTCCCACTAATAGCTTTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:20,21:41,0:0:2,0:24:1:28.3:1:1:0:55.5:82:1:0:0.3 0/1:22:3:1,2:8,11:19,3:0.1364:2,2:28:1:31.7:1:1:1.43071:43:6:0.1429:0:1 +MT 11947 . A G 66 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0049;SOR=Inf;LSEQ=AATATCACTCTCCTACTTAC;RSEQ=GGACTCAACATACTAGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:20,14:34,0:0:2,0:24.1:1:30:1:1:0:58.9:16:1:0:0 0/1:20:5:2,3:9,6:15,5:0.25:2,2:13.4:1:28.6:1:0.61687:2.1583:48.6:10:0.2632:0:1 +MT 12372 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.0119;SOR=Inf;LSEQ=ACTATAACCACCCTAACCCT;RSEQ=ACTTCCCTAATTCCCCCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:25,29:54,0:0:2,0:25.7:1:31.8:1:1:0:57.7:26:1:0:0.2 0/1:17:3:2,1:7,7:14,3:0.1765:2,2:35:1:27.7:1:1:1.92:48.7:6:0.2:0:1.3 +MT 12414 . T C 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTACCACCCTCGTTAACCC;RSEQ=AACAAAAAAAACTCATACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:55:0:0,0:30,24:54,0:0:2,0:20.6:1:29.9:1:1:0:60:26:0.9811:0:0.1 1/0:20:10:5,5:6,4:10,10:0.5:2,2:22:1:30.7:1:1:1.46966:60:20:0.5:0:1.3 +MT 12479 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.53112;SOR=0;LSEQ=ATCCACCTTTATTATCAGTC;RSEQ=CTTCCCCACAACAATATTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:21,21:42,2:0.0455:2,2:21.5:1:30.5:1:1:1:60:4:0.0455:0:1 0/0:25:0:0,0:15,10:25,0:0:2,0:23.1:1:28.9:1:1:0:57.2:24:1:0:0.4 +MT 12612 . A G 53 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.58292;LSEQ=TCCATAATATTCATCCCTGT;RSEQ=GCATTGTTCGTTACATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:4:2,2:15,15:30,4:0.1176:2,2:20.3:1:26.8:1:1:1:60:3:0.0909:0:1 0/1:14:1:0,1:5,8:13,1:0.0714:2,0:25:0:26:0:1:0:60:2:0.0714:0:1 +MT 12621 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08067;SOR=Inf;LSEQ=TTCATCCCTGTAGCATTGTT;RSEQ=GTTACATGGTCCATCATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:16,17:33,0:0:2,0:23.7:1:31.6:1:1:0:60:66:0.9706:0:0.9 0/1:14:2:1,1:5,7:12,2:0.1429:2,2:36:1:26.5:1:1:1.37:48.5:4:0.1429:0:4.5 +MT 12633 . C A 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GCATTGTTCGTTACATGGTC;RSEQ=ATCATAGAATTCTCACTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:24:12,12:4,5:9,24:0.7273:2,2:20.9:1:30.7:1:1:1.24:60:48:0.7273:0:1.1 0/0:14:0:0,0:7,7:14,0:0:2,0:25.9:1:30.4:1:1:0:58.4:13:1:0:0.9 +MT 12687 . C A 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCCAAACATTAATCAGTT;RSEQ=TTCAAATATCTACTCATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:15,15:30,2:0.0625:2,2:43:0:30:1:1:1:60:4:0.0625:0:1.5 0/0:13:0:0,0:6,7:13,0:0:2,0:17.1:1:29.9:1:1:0:60:12:1:0:0.5 +MT 12705 . C T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01552;SOR=Inf;LSEQ=TTCTTCAAATATCTACTCAT;RSEQ=TTCCTAATTACCATACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:19,17:36,0:0:2,0:21.9:1:33.1:1:1:0:60:72:1:0:0.4 0/1:13:3:2,1:6,4:10,3:0.2308:2,2:12.7:1:28.3:1:1:1.30:60:6:0.2308:0:1.3 +MT 12766 . T C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15;SOR=Inf;LSEQ=TATTCCAACTGTTCATCGGC;RSEQ=GAGAGGGCGTAGGAATTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:34,0:0:2,0:23:1:31.1:1:1:0:60:68:1:0:0.1 0/1:22:2:1,1:13,7:20,2:0.0909:2,2:43:1:26.5:1:1:1.80284:60:4:0.0909:0:1.5 +MT 13020 . T C 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09611;SOR=Inf;LSEQ=GGCAAATCAGCCCAATTAGG;RSEQ=CTCCACCCCTGACTCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:37,42:79,0:0:2,0:23.6:1:30:1:1:0:58.5:78:1:0:0.1 0/1:36:2:1,1:20,14:34,2:0.0556:2,2:21:0:32.5:1:1:1.41419:60:4:0.0571:0:1 +MT 13105 . A G 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08264;SOR=Inf;LSEQ=GCACTATAGTTGTAGCAGGA;RSEQ=TCTTCTTACTCATCCGCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:57:0:0,0:25,32:57,0:0:2,0:23.4:1:30.8:1:1:0:56.6:114:1:0:0.2 0/1:45:3:1,2:20,22:42,3:0.0667:2,2:44:1:30.7:1:1:1.79505:22.3:6:0.0667:0:1 +MT 13209 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05388;SOR=Inf;LSEQ=ACTCTGTTCGCAGCAGTCTG;RSEQ=GCCCTTACACAAAATGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:20,18:38,0:0:2,0:26.5:1:31.4:1:1:0:29.3:76:1:0:0.1 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:20.5:1:28.5:1:1:1.45:25:4:0.1667:0:1 +MT 13506 . C T 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14194;SOR=Inf;LSEQ=CCTTTCCTCACAGGTTTCTA;RSEQ=TCCAAAGACCACATCATCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:10,9:19,0:0:2,0:25.6:1:32.7:1:1:0:35.8:38:1:0:0.1 0/1:12:2:1,1:4,6:10,2:0.1667:2,2:33:0:32:1:1:1.45:26:4:0.1667:0:1.5 +MT 13650 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09653;SOR=Inf;LSEQ=ACAGGTCAACCTCGCTTCCC;RSEQ=ACCCTTACTAACATTAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:34,27:61,0:0:2,0:23.1:1:31.3:1:1:0:49.5:29.5:1:0:0.2 0/1:28:2:1,1:13,13:26,2:0.0714:2,2:35.5:1:28.5:1:1:1:31:4:0.0714:0:1.5 +MT 13708 . G A 90 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.43374;SOR=0.33719;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:8:3,5:27,21:48,8:0.1429:2,2:19.1:1:30:1:0.45074:2.11375:60:16:0.1509:0:1.5 0/1:19:1:1,0:10,8:18,1:0.0526:2,0:23:0:23:0:1:0:60:2:0.0526:0:1 +MT 13734 . T C 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00542;SOR=Inf;LSEQ=GGAAGCCTATTCGCAGGATT;RSEQ=CTCATTACTAACAACATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:33,30:63,0:0:2,0:24.6:1:30.4:1:1:0:60:62:1:0:0.3 0/1:25:4:2,2:10,11:21,4:0.16:2,2:24.5:1:31:1:1:1.10:60:8:0.1667:0:1.3 +MT 13759 . G A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10298;SOR=Inf;LSEQ=TTACTAACAACATTTCCCCC;RSEQ=CATCCCCCTTCCAAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:37,36:73,0:0:2,0:24.8:1:30.6:1:1:0:60:35.5:1:0:0.2 0/1:35:2:1,1:15,18:33,2:0.0571:2,2:14:0:30.5:1:1:1.19:60:4:0.0588:0:1.5 +MT 13789 . T C 56 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00793;SOR=Inf;LSEQ=TCCAAACAACAATCCCCCTC;RSEQ=ACCTAAAACTCACAGCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:74:0:0,0:35,39:74,0:0:2,0:25.8:1:29:1:1:0:59.6:17.5:1:0:0.2 0/1:33:4:2,2:13,16:29,4:0.1212:2,2:25.8:1:28.3:1:1:1.22:60:3:0.0968:0:1 +MT 13934 . C T 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=2;SSF=6e-05;SOR=Inf;LSEQ=CGGATTCTACCCTAGCATCA;RSEQ=ACACCGCACAATCCCCTATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:25,25:50,0:0:2,0:24.3:1:32:1:1:0:60:49:1:0:0.1 0/1:35:10:5,5:12,13:25,10:0.2857:2,2:26.1:1:29.3:1:1:1.08:60:20:0.2857:0:1 +MT 14139 . A G 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00303;SOR=Inf;LSEQ=CTCATCCTAACCCTACTCCT;RSEQ=ATCACATAACCTATTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:28,31:59,0:0:2,0:28:1:30.1:1:1:0:38.8:118:1:0:0.1 0/1:29:5:3,2:13,11:24,5:0.1724:2,2:26.4:1:30.2:1:1:1.26:43.4:10:0.1724:0:1 +MT 14258 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11102;SOR=Inf;LSEQ=ACAAAGCCCCCGCACCAATA;RSEQ=GATCCTCCCGAATCAACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:17,16:33,0:0:2,0:18.2:1:31.9:1:1:0:49.1:32:1:0:0.2 0/1:17:2:1,1:7,8:15,2:0.1176:2,2:45.5:1:30:1:1:1.13:25.5:4:0.125:0:1 +MT 14306 . C T 31 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53567;SOR=0;LSEQ=CTCCTTCATAAATTATTCAG;RSEQ=TTCCTACACTATTAAAGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:33,33:66,2:0.0294:2,2:7:0:31:1:1:1:22:4:0.0303:0:1.5 0/0:38:0:0,0:20,18:38,0:0:2,0:22.6:1:31.3:1:1:0:50.7:76:1:0:0.1 +MT 14362 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.29849;SOR=3.56924;LSEQ=CCATCATACTCTTTCACCCA;RSEQ=AGCACCAATCCTACCTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:1:0,1:51,48:99,1:0.01:2,0:1:0:24:0:0.49:0:60:2:0.0101:0:1 0/1:57:2:1,1:27,28:55,2:0.0351:2,2:27.5:1:26.5:1:1:1.04:37:4:0.0351:0:1 +MT 14470 . T C 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00482;SOR=Inf;LSEQ=ATAGCCATCGCTGTAGTATA;RSEQ=CCAAAGACAACCATCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:24,36:60,0:0:2,0:30.8:1:31:1:1:0:45.2:120:1:0:0.1 0/1:23:4:2,2:7,12:19,4:0.1739:2,2:26.3:1:32:1:1:1.67:56.5:8:0.1739:0:1 +MT 14560 . G A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01033;SOR=Inf;LSEQ=TTCAGAATAATAACACACCC;RSEQ=ACCACACCGCTAACAATCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:20,28:48,0:0:2,0:28.7:1:32:1:1:0:49:96:1:0:0.1 0/1:24:4:2,2:12,8:20,4:0.1667:2,2:37.5:1:29.3:1:1:1.47432:36.8:8:0.1667:0:1.8 +MT 14766 . C T 141 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00736;SOR=5.86456;LSEQ=AATGACCCCAATACGCAAAA;RSEQ=TAACCCCCTAATAAAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:26:15,11:12,6:18,26:0.5909:2,2:27:1:30.8:1:0.75371:1.45399:40.5:25:0.5814:0:1.3 1/1:29:26:12,14:1,2:3,26:0.8966:2,2:23.2:1:30.2:1:1:1.68:40.2:52:0.8966:0:1.5 +MT 14769 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15449;SOR=Inf;LSEQ=GACCCCAATACGCAAAACTA;RSEQ=CCCCCTAATAAAATTAATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:27,17:44,0:0:2,0:25.3:1:28.9:1:1:0:46.5:13.667:1:0:0.9 0/1:29:2:1,1:12,15:27,2:0.069:2,2:17:0:32.5:1:1:1.24:48:4:0.069:0:2.5 +MT 14798 . T C 86 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.73766;LSEQ=TAAAATTAATTAACCACTCA;RSEQ=TCATCGACCTCCCCACCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:6:2,4:27,23:50,6:0.1071:2,2:24.7:1:33.3:1:0.41406:2.31289:49:12:0.1111:0:1.8 0/1:37:3:2,1:15,19:34,3:0.0811:2,2:33.7:1:32.7:1:0.5843:2.47:51:6:0.0833:0:1.7 +MT 14803 . C T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55692;SOR=3.27187;LSEQ=TTAATTAACCACTCATTCAT;RSEQ=GACCTCCCCACCCCATCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:1:0,1:30,28:58,1:0.0169:2,0:1:0:25:0:0.49153:0:60:2:0.0169:0:1 0/1:37:2:1,1:17,18:35,2:0.0541:2,2:29.5:1:30.5:1:1:1.06:36:4:0.0541:0:2.5 +MT 14887 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52193;SOR=0;LSEQ=CTGATCCTCCAAATCACCAC;RSEQ=GGACTATTCCTAGCCATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:20,21:41,2:0.0455:2,2:37.5:1:31.5:1:1:1.05:24:4:0.0455:0:2.5 0/0:27:0:0,0:12,15:27,0:0:2,0:22.2:1:29.9:1:1:0:46:54:1:0:0.1 +MT 14905 . G A 128 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-04;SOR=0.0767;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:21:11,10:8,13:21,21:0.5:2,2:27.4:1:29.3:1:0.5359:1.76:32.5:42:0.5:0:1.3 0/1:29:2:1,1:12,15:27,2:0.069:2,2:2.5:1:24.5:1:1:1.24:42.5:4:0.069:0:1 +MT 15324 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12367;SOR=Inf;LSEQ=CTTCATTATTGCAGCCCTAG;RSEQ=AACACTCCACCTCCTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:23,24:47,0:0:2,0:21.6:1:32:1:1:0:57.5:22.5:1:0:1.1 0/1:26:2:1,1:11,13:24,2:0.0769:2,2:29:1:26.5:1:1:1.17:56.5:4:0.0769:0:2 +MT 15326 . A G 176 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=TCATTATTGCAGCCCTAGCA;RSEQ=CACTCCACCTCCTATTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:47:47:22,25:0,0:0,47:1:0,2:21.4:1:31.8:1:1:0:57.5:14.667:1:0:1.1 1/1:27:27:11,16:0,0:0,27:1:0,2:30.2:1:31.3:1:1:0:56.3:26:1:0:1.1 +MT 15452 . C A 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48948;SOR=0.5377;LSEQ=CCCTCGGCTTACTTCTCTTC;RSEQ=TTCTCTCCTTAATGACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:22:11,11:9,5:14,22:0.6111:2,2:19.4:1:31.1:1:0.50067:1.77077:60:44:0.6111:0:1.1 0/1:11:5:3,2:2,4:6,5:0.4545:2,2:34.6:1:28.2:1:0.5671:2.70:60:4:0.4:0:1.2 +MT 15607 . A G 123 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=6e-04;SOR=0.0527;LSEQ=CTCCGATCCGTCCCTAACAA;RSEQ=CTAGGAGGCGTCCTTGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:15:6,9:6,9:15,15:0.5:2,2:22:1:31.5:1:1:1:60:30:0.5357:0:1.1 0/1:21:1:0,1:11,9:20,1:0.0476:2,0:26:0:34:0:0.47619:0:60:2:0.0476:0:1 +MT 15627 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52087;SOR=0;LSEQ=ACTAGGAGGCGTCCTTGCCC;RSEQ=ATTACTATCCATCCTCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:2:1,1:15,19:34,2:0.0556:2,2:35.5:1:31:1:1:1.26:60:4:0.0571:0:1 0/0:22:0:0,0:11,11:22,0:0:2,0:25:1:28.8:1:1:0:60:44:1:0:0.1 +MT 15698 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1918;SOR=Inf;LSEQ=AACAACAAAGCATAATATTT;RSEQ=GCCCACTAAGCCAATCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:34:0:0,0:17,17:34,0:0:2,0:24.8:1:30.4:1:1:0:60:33:1:0:0.1 0/1:27:2:1,1:10,15:25,2:0.0741:2,2:30.5:1:28:1:1:1.48:60:4:0.0741:0:1.5 +MT 15884 . G C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16173;SOR=Inf;LSEQ=AAAACAAAATACTCAAATGG;RSEQ=CCTGTCCTTGTAGTATAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:10,16:26,0:0:2,0:23.5:1:31.5:1:1:0:60:52:1:0:0.1 0/1:18:2:1,1:6,10:16,2:0.1111:2,2:25.5:1:31:1:1:1.62:60:4:0.1111:0:1.5 +MT 15928 . G A 99 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49357;SOR=0.55327;LSEQ=TACACCAGTCTTGTAAACCG;RSEQ=AGATGAAAACCTTTTTCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:8,10:18,9:0.3333:2,2:26.8:1:31.3:1:1:1:60:18:0.3333:0:1.1 0/1:14:3:1,2:6,5:11,3:0.2143:2,2:28:1:29.3:1:1:2.2554:60:6:0.2143:0:1 +MT 16019 . C T 72 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.14485;SOR=0;LSEQ=AGATTCTAATTTAAACTATT;RSEQ=TCTGTTCTTTCATGGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:2,3:16,13:29,5:0.1471:2,2:28:1:31.2:1:0.64809:1.813:60:10:0.1563:0:1.8 0/0:22:0:0,0:13,9:22,0:0:2,0:21.4:1:30.2:1:1:0:60:21:1:0:0.3 +MT 16069 . C T 74 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22689;SOR=0.23018;LSEQ=GTACCACCCAAGTATTGACT;RSEQ=ACCCATCAACAACCGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:6:2,4:13,14:27,6:0.1818:2,2:23.3:1:29:1:0.66478:1.82342:60:12:0.1818:0:1.8 0/1:21:1:0,1:9,11:20,1:0.0476:2,0:21:0:29:0:1:0:60:2:0.0476:0:1 +MT 16086 . T C 81 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00311;SOR=Inf;LSEQ=ACTCACCCATCAACAACCGC;RSEQ=ATGTATTTCGTACATTACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:33,0:0:2,0:22.9:1:30.1:1:1:0:60:66:1:0:0.5 0/1:23:6:2,4:8,9:17,6:0.2609:2,2:26.7:1:31.7:1:0.66002:1.73456:60:12:0.2609:0:1.2 +MT 16110 . G T 33 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49675;SOR=0;LSEQ=TATTTCGTACATTACTGCCA;RSEQ=CCACCATGAATATTGTACGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:2:1,1:16,13:29,2:0.0645:2,2:6:0:33:1:1:1.22249:42:4:0.0645:0:1.5 0/0:25:0:0,0:13,12:25,0:0:2,0:19.5:1:31:1:1:0:60:11.5:1:0:0.9 +MT 16126 . T C 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0027;SOR=0.15883;LSEQ=GCCAGCCACCATGAATATTG;RSEQ=ACGGTACCATAAATACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:8,8:10,6:16,16:0.5:2,2:18.8:1:32.9:1:0.72239:1.63996:60:32:0.5:0:2.9 0/1:30:4:2,2:13,13:26,4:0.1333:2,2:15.5:1:33:1:1:1:60:8:0.1333:0:1.5 +MT 16129 . G C 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01438;SOR=Inf;LSEQ=AGCCACCATGAATATTGTAC;RSEQ=GTACCATAAATACTTGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:21,15:36,0:0:2,0:19.8:1:31.1:1:1:0:59:72:1:0:1.6 0/1:29:5:3,2:12,12:24,5:0.1724:2,2:31.6:1:30.2:1:1:1.48:60:10:0.1724:0:1.6 +MT 16163 . A G 146 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTGACCACCTGTAGTACATA;RSEQ=AAACCCAATCCACATCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:21:12,9:17,9:26,21:0.4468:2,2:29:1:33.3:1:0.76341:1.40609:60:42:0.4468:0:3.4 0/0:43:0:0,0:24,19:43,0:0:2,0:26.5:1:30.1:1:1:0:60:86:1:0:1.1 +MT 16179 . CA C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.09047;SOR=Inf;LSEQ=CATAAAAACCCAATCCACAT;RSEQ=AAACCCCCTCCCCATGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:33,21:54,0:0:2,0:24.4:1:31:1:1:0:60:108:1:0:1.7 0/1:45:3:1,2:20,22:42,3:0.0667:2,2:25:1:29.7:1:1:1.79505:60:6:0.0714:0:3.7 +MT 16186 . C T 142 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ACCCAATCCACATCAAAACC;RSEQ=CCTCCCCATGCTTACAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:25:14,11:21,12:33,25:0.431:2,2:24.4:1:30.6:1:0.59697:1.36738:60:24:0.4211:0:3.2 0/0:40:0:0,0:19,20:39,0:0:2,0:25.6:1:30.3:1:1:0:59.8:38:1:0:1.4 +MT 16189 . T C 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.20402;SOR=0.55646;LSEQ=CAATCCACATCAAAACCCCC;RSEQ=CCCCATGCTTACAAGCAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:24:13,11:22,13:35,24:0.4068:2,2:25.2:1:31.6:1:0.59334:1.42313:60:48:0.4068:0:3.2 0/1:40:11:5,6:14,14:28,11:0.275:2,2:27.6:1:26.9:1:1:1.1944:60:4.5:0.25:0:2.8 +MT 16190 . C A 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51609;SOR=0;LSEQ=AATCCACATCAAAACCCCCT;RSEQ=CCCATGCTTACAAGCAAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:2:1,1:36,24:60,2:0.0323:2,2:32:0:28:1:1:1.48993:60:4:0.0323:0:1.5 0/0:41:0:0,0:19,22:41,0:0:2,0:24.6:1:30.1:1:1:0:59.8:40:1:0:1.5 +MT 16192 . C T 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=TCCACATCAAAACCCCCTCC;RSEQ=CATGCTTACAAGCAAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:37,25:62,0:0:2,0:22.5:1:31.9:1:1:0:60:124:1:0:1.5 0/1:41:11:6,5:13,17:30,11:0.2683:2,2:15.9:1:30:1:0.7254:1.55:59.4:22:0.275:0:1.7 +MT 16223 . C T 102 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGCAAGTACAGCAATCAACC;RSEQ=TCAACTATCACACATCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:34,32:66,0:0:2,0:25.2:1:31.8:1:1:0:60:132:1:0:1.1 0/1:27:13:6,7:7,7:14,13:0.4815:2,2:24:1:27.7:1:1:1.16002:59.5:12:0.48:0:3.2 +MT 16224 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07491;SOR=Inf;LSEQ=GCAAGTACAGCAATCAACCC;RSEQ=CAACTATCACACATCAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:34,31:65,0:0:2,0:25.7:1:30.6:1:1:0:60:130:1:0:1.2 0/1:25:2:0,2:11,12:23,2:0.08:2,0:19:1:32:0:0.48667:0:60:4:0.0833:0:1 +MT 16234 . C T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.55198;SOR=0;LSEQ=CAATCAACCCTCAACTATCA;RSEQ=ACATCAACTGCAACTCCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:3:1,2:36,35:71,3:0.0405:2,2:35.7:1:28:1:1:2.03784:60:6:0.0405:0:1 0/0:32:0:0,0:15,16:31,0:0:2,0:18.4:1:30.7:1:1:0:60:14.5:0.9667:0:1.5 +MT 16248 . C T 79 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.00042;SOR=Inf;LSEQ=CTATCACACATCAACTGCAA;RSEQ=TCCAAAGCCACCCCTCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:34,39:73,0:0:2,0:24.7:1:32.6:1:1:0:59.5:72:1:0:1.2 0/1:30:6:2,4:11,13:24,6:0.2:2,2:22.3:1:30.7:1:0.67247:1.66358:60:12:0.2:0:3.2 +MT 16263 . T C 164 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCAACTCCAAAGCCACCCC;RSEQ=CACCCACTAGGATACCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:37:17,20:15,18:33,37:0.5286:2,2:27.7:1:31.6:1:1:1.02:60:74:0.5286:0:1.6 0/0:30:0:0,0:15,15:30,0:0:2,0:22.3:1:29.9:1:1:0:60:60:1:0:1.5 +MT 16264 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.08614;SOR=Inf;LSEQ=GCAACTCCAAAGCCACCCCT;RSEQ=ACCCACTAGGATACCAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:32,39:71,0:0:2,0:26.3:1:32.5:1:1:0:59.5:142:1:0:1.2 0/1:30:2:1,1:14,14:28,2:0.0667:2,2:32.5:1:27.5:1:1:1:60:4:0.0667:0:4 +MT 16270 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07435;SOR=Inf;LSEQ=CCAAAGCCACCCCTCACCCA;RSEQ=TAGGATACCAACAAACCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:32,36:68,0:0:2,0:26.4:1:33.2:1:1:0:59.5:136:1:0:1.3 0/1:26:2:1,1:15,9:24,2:0.0769:2,2:38.5:1:29:1:1:1.63293:60:4:0.0769:0:4 +MT 16278 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07491;SOR=Inf;LSEQ=ACCCCTCACCCACTAGGATA;RSEQ=CAACAAACCTACCCACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:29,36:65,0:0:2,0:25.3:1:31.9:1:1:0:60:130:1:0:1.2 0/1:25:2:1,1:14,9:23,2:0.08:2,2:46.5:1:29:1:1:1.52748:60:4:0.08:0:4 +MT 16292 . C T 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGATACCAACAAACCTACC;RSEQ=ACCCTTAACAGTACATAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:26,34:60,0:0:2,0:23.5:1:32.2:1:1:0:60:120:1:0:1.4 0/1:28:11:6,5:11,6:17,11:0.3929:2,2:24:1:29.1:1:0.70114:1.50442:60:22:0.3929:0:1.7 +MT 16294 . C T 143 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GATACCAACAAACCTACCCA;RSEQ=CCTTAACAGTACATAGTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:26:13,13:12,21:33,26:0.4407:2,2:21.8:1:30.5:1:0.4264:1.73:60:25:0.431:0:1 0/0:29:0:0,0:17,12:29,0:0:2,0:23.9:1:30.8:1:1:0:60:58:1:0:1.2 +MT 16311 . T C 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00157;SOR=Inf;LSEQ=CCACCCTTAACAGTACATAG;RSEQ=ACATAAAGCCATTTACCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:23,30:53,0:0:2,0:22.8:1:29.5:1:1:0:60:106:1:0:1.4 0/1:30:6:4,2:12,12:24,6:0.2:2,2:19.8:1:32.2:1:0.6567:1.96:60:12:0.2069:0:2 +MT 16316 . A G 155 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTAACAGTACATAGTACAT;RSEQ=AAGCCATTTACCGTACATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:29:12,17:10,13:23,29:0.5577:2,2:20.2:1:32:1:1:1.08794:60:28:0.549:0:1.9 0/0:31:0:0,0:16,15:31,0:0:2,0:21.5:1:27.3:1:1:0:59.8:14.5:1:0:1.1 +MT 16325 . T C 85 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=7e-04;SOR=Inf;LSEQ=ACATAGTACATAAAGCCATT;RSEQ=ACCGTACATAGCACATTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:24,25:49,0:0:2,0:22.8:1:29.6:1:1:0:60:48:1:0:1.3 0/1:30:7:3,4:13,10:23,7:0.2333:2,2:27.3:1:30.3:1:0.67458:1.70145:60:14:0.2333:0:1.9 +MT 16343 . A G 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06869;SOR=Inf;LSEQ=TTTACCGTACATAGCACATT;RSEQ=CAGTCAAATCCCTTCTCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:26,23:49,0:0:2,0:24.3:1:29.1:1:1:0:60:48:1:0:1 0/1:35:3:1,2:18,14:32,3:0.0857:2,2:20.7:1:26:1:0.58197:2.50361:58:2:0.0588:0:1.7 +MT 16362 . T C 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00681;SOR=Inf;LSEQ=TACAGTCAAATCCCTTCTCG;RSEQ=CCCCATGGATGACCCCCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:53:0:0,0:27,25:52,0:0:2,0:25.1:1:29.6:1:1:0:59.3:16.333:1:0:0.8 0/1:33:5:3,2:14,14:28,5:0.1515:2,2:11:1:31:1:1:1.48:60:10:0.1563:0:1.2 +MT 16365 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.51628;SOR=0;LSEQ=AGTCAAATCCCTTCTCGTCC;RSEQ=CATGGATGACCCCCCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:27,23:50,2:0.0385:2,2:14.5:1:31:1:1:1.17028:60:4:0.0385:0:3 0/0:34:0:0,0:17,17:34,0:0:2,0:22:1:28.5:1:1:0:60:7.5:1:0:0.6 +MT 16390 . G A 137 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00012;SOR=0.05048;LSEQ=GATGACCCCCCTCAGATAGG;RSEQ=GTCCCTTGACCACCATCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:10,12:20,18:38,22:0.3667:2,2:20.4:1:30.8:1:0.78917:1.32692:60:21:0.3621:0:1.5 0/1:36:1:0,1:19,16:35,1:0.0278:2,0:13:0:32:0:0.47222:0:60:2:0.0286:0:2 +MT 16456 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.07279;SOR=Inf;LSEQ=GTGCTACTCTCCTCGCTCCG;RSEQ=GCCCATAACACTTGGGGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:33,36:69,0:0:2,0:21.9:1:30.9:1:1:0:59.4:22:1:0:0.6 0/1:26:2:2,0:10,14:24,2:0.0769:2,0:11.5:1:27.5:1:0.20308:0:60:4:0.0769:0:1.5 +MT 16519 . T C 174 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0028;SOR=0.0488;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:45:44:22,22:0,1:1,44:0.9778:0,2:25.8:1:31.9:1:1:0:58.6:88:0.9778:0:1.2 1/0:15:10:6,4:3,2:5,10:0.6667:2,2:28.9:1:31.2:1:1:1:55.7:20:0.6667:0:1.5 +MT 16524 . A G 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01475;SOR=Inf;LSEQ=GTTCCTACTTCAGGGTCATA;RSEQ=AGCCTAAATAGCCCACACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:21,22:43,0:0:2,0:25.7:1:30.6:1:1:0:58.5:86:1:0:1.1 0/1:15:3:2,1:7,5:12,3:0.2:2,2:45:1:32.3:1:1:1.40:60:6:0.2:0:2 +X 450736 . C CTG 63 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GGCCAGCAGCAGGACGCTGA;RSEQ=TGCGTGAGTGATGCAGCCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:1,3:0,0:0,4:1:0,2:28.5:1:31.8:1:1:0:60:8:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 450894 . TAA T 90 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=12.000;MSILEN=1;SSF=0.33333;SOR=0;LSEQ=AAATATGATTTAGGCAATGT;RSEQ=AAAAAAAAAACAAAACCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:0,8:1:0,2:28.3:1:30:1:1:0:58.8:16:1:0.25:0.4 1/0:4:3:3,0:0,0:0,3:0.75:0,0:10.7:1:30.6:1:1:0:60:6:0.75:0.25:0 +X 451056 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55506;SOR=Inf;LSEQ=GTGGGTGTCTCCACGCCTTC;RSEQ=GTGCAAACTGTGTGTATTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:55,28:83,0:0:2,0:24.9:1:31:1:1:0:60:166:1:0:0.1 0/1:187:3:1,2:122,62:184,3:0.016:2,2:8.3:1:25.3:1:0.27007:3.90454:60:6:0.0163:0:1 +X 451096 . C T 184 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=Inf;LSEQ=GACAGATGAATGGTTTGTCT;RSEQ=TGGGATGATACTTTTCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:96,67:163,0:0:2,0:24.6:1:32.4:1:1:0:60:80.5:1:0:0.2 0/1:339:70:40,30:146,123:269,70:0.2065:2,2:25.1:1:30.1:1:0.68809:1.12:60:140:0.2102:0:1.3 +X 451139 . T C 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13256;SOR=0;LSEQ=TGCAGCCTGCAGATAACATC;RSEQ=AACGAGGGGAGAAGGATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:89,95:184,2:0.0108:2,2:39:0:31.5:1:1:1.07:60:4:0.011:0:1 0/0:324:0:0,0:145,178:323,0:0:2,0:29.5:1:28.2:1:1:0:59.4:25.917:0.9968:0:0.9 +X 451142 . C T 202 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=3.79262;LSEQ=AGCCTGCAGATAACATCTAA;RSEQ=GAGGGGAGAAGGATTATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:27:14,13:73,81:154,27:0.1492:2,2:27:1:30.4:1:0.68246:1.19:59.7:26:0.1503:0:1.3 0/1:315:126:53,73:89,98:187,126:0.4:2,2:30.4:1:29:1:0.35597:1.24996:59.2:24.2:0.4074:0:1.3 +X 451164 . G C 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01483;SOR=Inf;LSEQ=AGGGGAGAAGGATTATGTGA;RSEQ=CAGTGGTGGCTGAGGTCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:65,84:149,0:0:2,0:26.3:1:32.3:1:1:0:59.5:28.8:1:0:0.6 0/1:241:9:5,4:95,137:232,9:0.0373:2,2:17.1:1:31:1:0.49525:1.80:60:18:0.0393:0:2.1 +X 451175 . T A 46 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30089;SOR=Inf;LSEQ=ATTATGTGAGCAGTGGTGGC;RSEQ=GAGGTCTCTCTCTCTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:49,72:121,0:0:2,0:22:1:30.4:1:1:0:59.3:14.125:1:0:0.6 0/1:206:4:3,1:76,123:199,4:0.0194:2,2:6.3:1:23:1:0.30122:4.82:56.3:3:0.0165:0:2 +X 1314656 . T C 62 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.6004;SOR=0.39896;LSEQ=CATATTGGCCAGGCTGGTCT;RSEQ=GAACTCGTGACCTCGTGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:6,0:6,4:0.4:0,0:31.5:1:31:1:1:0:38:8:0.4:0:1.5 0/1:5:1:1,0:4,0:4,1:0.2:0,0:3:0:30:0:1:0:60:2:0.25:0:1 +X 1314694 . G C 25 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGCCTGCCTTGGTCTCC;RSEQ=CAAGTGCTGGGATGACAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:14,0:14,2:0.1176:1,0:16.5:1:25:1:1:0:27:4:0.1176:0:2 0/0:7:0:0,0:7,0:7,0:0:0,0:32.1:1:30.3:1:1:0:58.6:14:1:0:0.3 +X 1314764 . T G 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62353;SOR=1.37723;LSEQ=TTTCTTATAATCCACCATCA;RSEQ=AAGAGTGGGCATTGTATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:23:23,0:14,0:14,23:0.6216:1,1:19:1:33.7:1:1:0:59.3:46:0.6216:0:1.3 1/0:36:25:25,0:11,0:11,25:0.6944:0,1:19:1:31.2:1:1:0:60:24:0.6857:0:1 +X 1314857 . GG AT 194 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.1438;LSEQ=TCACAGACATTGTGCAAGCA;RSEQ=TCCCTCCACCCACGGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:79:58,21:126,50:176,79:0.3062:2,2:24.1:1:30.8:1:0.88004:1.10:60:158:0.3123:0.0349:1 0/1:353:21:15,6:220,112:332,21:0.0595:2,2:26.3:1:29.8:1:0.81223:1.27:60:42:0.06:0.0085:1.1 +X 1314858 . G T 49 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0296;SOR=0;LSEQ=CACAGACATTGTGCAAGCAG;RSEQ=TCCCTCCACCCACGGGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:4:2,2:126,51:177,4:0.0159:2,2:9.3:1:24.8:1:0.58169:2.45661:60:3:0.017:0:2 0/0:352:0:0,0:219,114:333,0:0:2,0:24.6:1:30.6:1:1:0:60:65.6:1:0:0.2 +X 1314931 . C T 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGACAGAAGGAGGAGAGACA;RSEQ=CATCAGAAGGATGGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:469:0:0,0:237,232:469,0:0:2,0:24.4:1:31.5:1:1:0:60:45.9:1:0:0.2 0/1:705:28:13,15:352,325:677,28:0.0397:2,2:26:1:28.8:1:0.57019:1.2493:60:27:0.0386:0:1.3 +X 1315104 . G C 156 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.06184;SOR=0.51182;LSEQ=TTACATCTCATCCCTAACCA;RSEQ=TCTCCCTCATTTTTTGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:25:0,25:1,50:51,25:0.3289:1,1:24.4:1:33.8:1:1:0:60:50:0.3289:0:1.1 0/1:120:24:0,24:10,86:96,24:0.2:2,1:19.4:1:30.5:1:0.20875:0:60:11:0.188:0:1.1 +X 1315114 . T C 84 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=6.000;MSILEN=1;SSF=0.03709;SOR=Inf;LSEQ=TCCCTAACCAGTCTCCCTCA;RSEQ=TTTTTGGTGTTCGTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:73:0:0,0:0,73:73,0:0:1,0:21.8:1:30.8:1:1:0:59.7:146:1:0:0.3 0/1:96:6:0,6:2,88:90,6:0.0625:1,0:23.8:1:32.7:1:1:0:60:12:0.0645:0:1 +X 1315127 . G GT 65 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.22439;SOR=4.21448;LSEQ=TCCCTCATTTTTTGGTGTTC;RSEQ=TTTTTTTTTCTTGGTTCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:1:0,1:0,57:57,1:0.0172:1,0:46:0:29:0:1:0:60:2:0.0175:0:0 0/1:72:5:0,5:2,64:66,5:0.0694:1,0:39.2:1:28.2:1:1:0:60:10:0.0704:0:0.6 +X 1317404 . T C 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15078;SOR=0.8204;LSEQ=AAGGCTATGGGACACTGCCG;RSEQ=GTAACAAGCATTACCCCGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:127:84,43:163,102:265,127:0.3223:2,2:25.3:1:31.4:1:0.43407:1.22:60:126:0.3239:0:1.1 0/1:734:206:119,87:311,217:528,206:0.2807:2,2:23.8:1:30.2:1:0.80272:1.04769:59.8:205:0.2828:0:1.2 +X 1317589 . AACATAC A 101 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00491;SOR=Inf;LSEQ=TTTCCTGTTTGGACTGGAGA;RSEQ=ACATACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:83,175:258,0:0:2,0:20.4:1:29.5:1:1:0:57.2:85:1:0:0.4 0/1:439:12:1,11:165,261:426,12:0.0273:2,2:28.1:1:28.3:1:0.03521:6.93466:51.7:24:0.0277:0.0046:1 +X 1317688 . G C 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.29332;SOR=Inf;LSEQ=CTGTCCAGAGTTTTCCTTCC;RSEQ=GAGGGTTCACAGTCTCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:36,0:0:1,0:25.1:1:31.8:1:1:0:58.6:72:1:0:0.2 0/1:61:4:0,4:1,56:57,4:0.0656:1,0:25.8:1:30.3:1:1:0:60:8:0.0678:0:1 +X 1321079 . G C 108 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.08938;SOR=0.15638;LSEQ=ATTGGTTCTCTTTCTCTGGA;RSEQ=ACCCCTCAGAGACACAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:10,0:2,0:2,10:0.8333:0,0:23.4:1:32.8:1:1:0:60:20:0.8333:0:1 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:29.6:1:32.4:1:1:0:60:10:0.4545:0:1 +X 1321215 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.55295;SOR=Inf;LSEQ=TGAAACAGCGAATCCCACAG;RSEQ=CCGCACCTGGGGGACGCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:74,12:86,0:0:2,0:25.2:1:32:1:1:0:60:85:1:0:0.1 0/1:171:2:2,0:140,29:169,2:0.0117:2,0:32.5:1:31.5:1:1:0:60:4:0.012:0:1 +X 1321222 . C T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.55345;SOR=Inf;LSEQ=GCGAATCCCACAGCCCGCAC;RSEQ=TGGGGGACGCTCAGCCACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:85,16:101,0:0:2,0:24.2:1:30.7:1:1:0:60:49.5:1:0:0.1 0/1:207:3:2,1:165,39:204,3:0.0145:2,2:23.3:1:25.3:1:0.47674:2.1061:60:2:0.01:0:2.3 +X 1321243 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10108;SOR=0;LSEQ=TGGGGGACGCTCAGCCACCA;RSEQ=CGCCCTGAGTCGCGGCCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:2:1,1:108,35:143,2:0.0138:2,2:24.5:1:30.5:1:0.43621:3.0565:60:4:0.0139:0:1 0/0:310:0:0,0:226,83:309,0:0:2,0:23.8:1:29.2:1:1:0:60:27.091:1:0:0.3 +X 1321433 . G A 60 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.26375;SOR=3.66502;LSEQ=GAAGAAATAACGGAAGCGAC;RSEQ=TCCCTCCTCTCTGAGCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:228:1:1,0:65,162:227,1:0.0044:2,0:1:0:25:0:0.28947:0:60:2:0.0045:0:1 0/1:377:6:5,1:121,250:371,6:0.0159:2,2:8.5:1:23.5:1:0.01729:10.26:60:5:0.0135:0:1 +X 1321517 . G GT 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00027;SOR=Inf;LSEQ=CCTCCCCTTAATACCTTATG;RSEQ=GTCTCGGGGTTCACCCGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:1,62:63,0:0:1,0:21.1:1:30.7:1:1:0:60:20:1:0:0.1 0/1:63:12:0,12:3,48:51,12:0.1905:2,0:21.8:1:29.9:1:1:0:60:24:0.1967:0.0476:0.1 +X 1324241 . G T 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTGAAGGTAAGGAGATGAAG;RSEQ=GGTACTGAAAAGTGTGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:24.5:1:30.5:1:1:0:60:4:1:0:1.5 +X 1325301 . G T 114 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00011;SOR=0.053;LSEQ=AAGGAAGTACTGAAAAGCAT;RSEQ=GTGAGCTGGCTTTACAATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:12:10,2:167,91:258,12:0.0444:2,2:20:1:31.8:1:0.22848:2.72:60:24:0.0446:0:1.1 0/0:408:1:0,1:257,150:407,1:0.0025:2,0:1:0:24:0:0.3701:0:60:2:0.0025:0:1 +X 1325426 . C T 220 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TGCTCTGCGTCTAGGAGGCA;RSEQ=CCCGAAGTGTGACCTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:147:65,82:143,160:303,147:0.3267:2,2:25.8:1:30.6:1:0.61436:1.1272:60:294:0.3296:0:1.1 0/0:697:0:0,0:311,386:697,0:0:2,0:26.3:1:30.5:1:1:0:60:48.786:1:0:0.2 +X 1325519 . G T 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58284;SOR=0.38573;LSEQ=TTTAAAACGATGACCATTCA;RSEQ=CAACAAAACAAAAAAGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:15,125:140,2:0.0141:2,2:28.5:1:32.5:1:0.21337:8.10:60:4:0.0142:0:1 0/0:183:1:0,1:48,134:182,1:0.0055:2,0:31:0:30:0:1:0:60:2:0.0056:0:1 +X 1327620 . G A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14313;SOR=0;LSEQ=CTTTACACTTTTGTTCTCAA;RSEQ=CATTCCCAATCGCTGACGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:89,16:105,2:0.0187:2,2:41.5:1:31:1:0.29378:5.42674:60:4:0.0189:0:1 0/0:175:0:0,0:143,32:175,0:0:2,0:22:1:31.4:1:1:0:60:86.5:1:0:0.1 +X 1327635 . G T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.29627;SOR=Inf;LSEQ=CTCAAGCATTCCCAATCGCT;RSEQ=ACGGCTCAGAAGAGCGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:117,26:143,0:0:2,0:25.2:1:32.5:1:1:0:60:46.667:1:0:0 0/1:240:3:2,1:187,50:237,3:0.0125:2,2:12:1:23:1:0.51328:1.86425:60:2:0.0086:0:1 +X 1327655 . T A 110 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00086;SOR=Inf;LSEQ=GACGGCTCAGAAGAGCGATT;RSEQ=TGAGCCCCCTGGGCGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:161,51:212,0:0:2,0:23.3:1:30.9:1:1:0:60:105:1:0:0 0/1:346:16:10,6:232,98:330,16:0.0462:2,2:26.4:1:27.5:1:0.57792:1.41889:60:15:0.044:0:1.3 +X 1327837 . G A 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02384;SOR=Inf;LSEQ=CGCATGAAGTTCACGGTGAG;RSEQ=CAACTCTATTTTTTTATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:33,180:213,0:0:2,0:24.3:1:32.3:1:1:0:60:105.5:1:0:0.1 0/1:311:8:1,7:76,226:302,8:0.0257:2,2:21.5:1:29.3:1:0.68445:2.34893:59.4:16:0.026:0:1.3 +X 1327868 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.51258;SOR=Inf;LSEQ=TTTTTATTTTTTTAAATTTA;RSEQ=TTTTCTTTTTGAGACAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:6,104:110,0:0:2,0:20.7:1:31.2:1:1:0:58.7:220:1:0:0 0/1:155:2:1,1:26,127:153,2:0.0129:2,2:26.5:1:29.5:1:0.31898:4.81:59.5:4:0.013:0:1 +X 1331145 . G A 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=0;LSEQ=AATCAATCAATCAATAGATA;RSEQ=ACACACACACGCACACATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:0,1:1,2:0.6667:0,0:15.5:1:31.5:1:0.33333:0:55.5:4:0.6667:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 1331182 . C T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATACAGTTCCTAGTTCTGGC;RSEQ=ACCGAAAGCTCATATAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:39:1:31.5:1:1:0:55.5:4:1:0:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 1331279 . A G 73 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54118;SOR=0.62768;LSEQ=TGTTTTGTCCCAGCTACTTG;RSEQ=GAAGCTGAGGCAGGAGAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:7:7,0:23,1:24,7:0.2258:1,0:28.6:1:26.1:1:1:0:50.9:2.5:0.1852:0:2 0/1:39:6:6,0:32,1:33,6:0.1538:1,0:24.5:1:23.2:1:1:0:41.8:1:0.0909:0:2.3 +X 1331309 . C CAG 84 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02308;SOR=0.14355;LSEQ=GCAGGAGAATTGCTTGAACC;RSEQ=GGAAAAAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:7,0:21,0:21,7:0.2333:1,0:26.1:1:30.2:1:1:0:40.6:14:0.2414:0:0.3 0/1:49:2:2,0:46,1:47,2:0.0408:1,0:23.5:1:32.5:1:1:0:29:4:0.0444:0:0 +X 1331337 . G A 71 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13088;SOR=3.27741;LSEQ=AAAAAAAAAAAAAAAGAAAA;RSEQ=AAGAAAGAAACCTCCATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:2,0:90,7:97,2:0.02:2,0:9.5:1:30.5:1:1:0:53:4:0.026:0:4 0/1:143:9:9,0:121,12:133,9:0.0629:2,0:14.1:1:22.7:1:1:0:45.7:2:0.0545:0:3.6 +X 1331495 . G C 245 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=258.09447;LSEQ=CAGCCTCCCAGCAGAAAGAC;RSEQ=GCAGCTCCCCACAGCAGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:477:1:0,1:218,257:475,1:0.0021:2,0:36:0:28:0:1:0:60:2:0.0021:0:1 0/1:939:329:157,172:271,335:606,329:0.3504:2,2:25.5:1:29.4:1:0.40958:1.13:60:108.667:0.3517:0:1.2 +X 1331616 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49874;SOR=Inf;LSEQ=GCAGAGGTCACCATCGATTT;RSEQ=AAAAAGTCAGAAAGGAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:4,92:96,0:0:1,0:24.7:1:28.7:1:1:0:60:95:1:0:0.1 0/1:106:2:1,1:6,98:104,2:0.0189:2,2:25:1:27:1:0.1283:15.20:60:4:0.0189:0:1 +X 3085317 . G A 80 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.1752;LSEQ=GACCTCCCGTGGACTTTTCA;RSEQ=GCAGCCCCCACGGTGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:5,1:22,1:23,6:0.2069:1,2:25.3:1:31:1:0.37685:4.10691:60:12:0.2069:0:1 0/1:17:4:4,0:13,0:13,4:0.2353:1,0:28:1:30.5:1:1:0:60:8:0.2353:0:1 +X 3085398 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49975;SOR=Inf;LSEQ=TCAGTGCAAGGGCTGGGGAA;RSEQ=GAGGGCTATTATTTGCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:87,35:122,0:0:2,0:23.7:1:32.8:1:1:0:60:121:1:0:0.2 0/1:137:2:1,1:87,48:135,2:0.0146:2,2:14:1:29:1:1:1.80409:56:4:0.0147:0:2 +X 3085419 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.23616;SOR=0;LSEQ=GAGGGCTATTATTTGCACAT;RSEQ=GGGAGGCATGAGCATCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:2:1,1:103,60:163,2:0.0121:2,2:17:0:32.5:1:1:1.7107:60:4:0.0122:0:2 0/0:174:0:0,0:97,77:174,0:0:2,0:24.4:1:30.7:1:1:0:59.8:86:1:0:0.3 +X 3085464 . C T 172 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21276;SOR=0.74332;LSEQ=GTTTCGCTGCAGAGAATCTA;RSEQ=ATGTACCAGAGATGAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:61:28,33:71,76:147,61:0.2933:2,2:28.5:1:29.1:1:0.76298:1.10052:59.6:29.5:0.2878:0:1.2 0/1:191:45:21,24:70,76:146,45:0.2356:2,2:30.9:1:28:1:1:1.05237:59.8:44:0.2328:0:1.2 +X 3573359 . A C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50885;SOR=Inf;LSEQ=GAGCCCCGTGGTGCTGGAGA;RSEQ=GCGCCCCCGGTTGCGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:11,32:43,0:0:2,0:24.5:1:32:1:1:0:57.3:86:1:0:0.1 0/1:60:2:1,1:19,39:58,2:0.0333:2,2:37:1:29.5:1:1:2.03:25.5:4:0.0339:0:1 +X 5699290 . G C 198 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0;SOR=0;LSEQ=ATACTCTCTCCTCTCCTGAA;RSEQ=AGAATGAATGGCCAGGCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:75:75:61,14:0,0:0,75:1:0,2:19.8:1:31.9:1:1:0:60:150:1:0:1.1 1/0:61:31:24,7:25,5:30,31:0.5082:2,2:24:1:31.1:1:0.74904:1.44935:60:62:0.5082:0:1.1 +X 5699307 . C T 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61414;SOR=0.47326;LSEQ=GAAGAGAATGAATGGCCAGG;RSEQ=ATCTTCAGGAAGGGGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:59,23:82,2:0.0238:2,2:24.5:1:28.5:1:0.49225:2.53241:60:4:0.0238:0:1.5 0/1:88:1:0,1:64,23:87,1:0.0114:2,0:1:0:22:0:0.27273:0:60:2:0.0115:0:1 +X 5699379 . G T 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07872;SOR=0;LSEQ=GCGTCTACAGCAAGCAGCAT;RSEQ=AAGGTGGATTCTCACGCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:1,2:97,84:181,3:0.0163:2,2:28.3:1:29.3:1:0.5998:2.29932:60:6:0.0164:0:2 0/0:244:0:0,0:125,119:244,0:0:2,0:26.5:1:30.5:1:1:0:60:80.333:1:0:0.6 +X 5699394 . C T 236 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCATGAAGGTGGATTCTCA;RSEQ=GCATTTTAACCCAAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:199:199:102,97:0,0:0,199:1:0,2:25:1:31:1:1:0:59.8:198:1:0:1.2 1/0:253:147:79,68:52,54:106,147:0.581:2,2:24.3:1:29.9:1:0.52405:1.21:60:146:0.5794:0:1.1 +X 5699496 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24039;SOR=Inf;LSEQ=CAAGGCAACACAGCCCTTGG;RSEQ=CCGCCTGCTTGGCTCTAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:92:0:0,0:24,67:91,0:0:2,0:25.1:1:32:1:1:0:60:90:0.989:0:0.1 0/1:89:2:1,1:24,63:87,2:0.0225:2,2:35.5:1:27.5:1:0.48519:2.59:60:4:0.0227:0:1 +X 5699512 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49652;SOR=0;LSEQ=TTGGGCCGCCTGCTTGGCTC;RSEQ=AATTACAACCTTGATGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:2:1,1:12,55:67,2:0.029:2,2:13:1:31:1:0.34356:4.44:60:4:0.029:0:1 0/0:66:0:0,0:13,53:66,0:0:2,0:23.8:1:28.1:1:1:0:60:132:1:0:0.2 +X 8703231 . T C 150 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.17462;SOR=0.42297;LSEQ=TTTTTTGTTTTGTTTTGTTT;RSEQ=CATTCTGCCCATGTATGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:36:26:26,0:10,0:10,26:0.7222:0,1:22.8:1:32.1:1:1:0:60:12:0.7059:0:1.1 1/0:25:13:13,0:12,0:12,13:0.52:0,1:23.8:1:31.2:1:1:0:60:26:0.52:0:1.2 +X 8703411 . G A 231 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.29661;LSEQ=GATAAAGGGGTAGGACCCTC;RSEQ=GGTGCAGCTAGTAAGACGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:281:182:84,98:45,54:99,182:0.6477:2,2:20.6:1:30.9:1:1:1.03:26.5:181:0.6464:0:1.1 0/1:298:105:48,57:95,98:193,105:0.3523:2,2:22.7:1:29.8:1:0.62761:1.1506:28.7:210:0.3571:0:1.1 +X 8703727 . C CT 32 v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TATTGGTTTTTCTTTTCTTT;RSEQ=TTTTTTTTTTTCCTGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,3:3,2:0.2857:0,0:32:1:32:0:1:0:60:4:0.3333:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 11316961 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15333;SOR=0;LSEQ=ATGCAGCCCCAGCCACCTGT;RSEQ=CACCCCATGCAGCCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:1,1:25,34:59,2:0.0328:2,2:28.5:1:28:1:1:1.35:33.5:4:0.0339:0:2 0/0:94:0:0,0:46,48:94,0:0:2,0:22.9:1:30.4:1:1:0:41.2:22.5:1:0:0.1 +X 11316968 . A C 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14714;SOR=0;LSEQ=CCCAGCCACCTGTGCACCCC;RSEQ=TGCAGCCCCTGCCGCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:2:1,1:23,34:57,2:0.0339:2,2:28.5:1:26.5:1:1:1.47:33.5:4:0.0364:0:2 0/0:94:0:0,0:43,51:94,0:0:2,0:22.3:1:28.4:1:1:0:43.2:30.333:1:0:0.1 +X 11503157 . C CA 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACAAACAAACAACAACAA;RSEQ=AAAAAAAAAACATATCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32:0:31.5:1:1:0:52:4:1:0:0 +X 13078706 . TA T 44 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.27069;SOR=Inf;LSEQ=CTTAAGAATCTTCTAGTACT;RSEQ=AAAAAAGTAGGCCATTGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:127:0:0,0:87,40:127,0:0:2,0:22.7:1:28.6:1:1:0:60:126:1:0:0.2 0/1:181:3:2,1:117,61:178,3:0.0166:2,2:15.3:1:27.9:1:1:1.04:60:6:0.0168:0.011:0.7 +X 13078775 . G A 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=2.76634;LSEQ=TGGAGAAGTAGAGATGATGA;RSEQ=AAGTGAAAAAGGCTTTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:70:35,35:84,97:181,70:0.2789:2,2:30.6:1:30.4:1:0.67298:1.15:60:69:0.2782:0:1.1 1/0:288:149:76,73:69,70:139,149:0.5174:2,2:26.9:1:29.3:1:0.90616:1.06:60:148:0.5211:0:1.1 +X 14852765 . G C 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.11359;LSEQ=TACAGAACTAGGTCCCTTTG;RSEQ=TGTTTTAGGAGTTTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:48:41:34,7:6,1:7,41:0.8542:2,2:29.8:1:32.3:1:1:1.23013:31.4:82:0.8542:0:1 0/1:86:34:28,6:39,13:52,34:0.3953:2,2:27.3:1:30.7:1:0.59586:1.55:30.9:33:0.3929:0:1 +X 14852912 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.4978;SOR=0;LSEQ=AGATTTCTTCACTGGTGCTT;RSEQ=TTCTTCAGTTTCCTCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:2:1,1:23,70:93,2:0.0211:2,2:14.5:1:31.5:1:0.44345:3.00:46.5:4:0.0211:0:1 0/0:89:0:0,0:28,61:89,0:0:2,0:21:1:30:1:1:0:40.6:43.5:1:0:0.3 +X 14852936 . A G 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.0088;SOR=3.01772;LSEQ=TTCAGTTTCCTCATCATCAA;RSEQ=ATCATCATCATCATCATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:12:3,9:31,41:72,12:0.1412:2,2:20.4:1:32.8:1:0.34453:2.24774:52.6:24:0.1412:0:1.1 0/1:63:21:9,12:17,24:41,21:0.3333:2,2:18.4:1:30.6:1:1:1.06:50.8:42:0.3387:0:1.1 +X 14853120 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49836;SOR=0;LSEQ=TGCTGTCCACTAATATGCAC;RSEQ=GGCCCTGAATCACACTTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:65,68:133,2:0.0148:2,2:37:1:30:1:1:1.05:34.5:4:0.015:0:1 0/0:129:0:0,0:66,63:129,0:0:2,0:31.3:1:30:1:1:0:45.6:258:1:0:0.1 +X 14853439 . T C 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15516;SOR=Inf;LSEQ=TGTCCATGTCCATCGAATCT;RSEQ=CCATCAGGTGGCTACATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:19,31:50,0:0:2,0:21.5:1:29.9:1:1:0:45.3:15.667:1:0:0.1 0/1:33:2:1,1:12,19:31,2:0.0606:2,2:7:1:29:1:1:1.56:60:4:0.0606:0:1 +X 15172106 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50301;SOR=Inf;LSEQ=TGTCTGGTATCCTCATCTGC;RSEQ=ATAAAACATGCAGAGCTAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:93,31:124,0:0:2,0:25.7:1:31.5:1:1:0:60:61:1:0:0.3 0/1:151:2:1,1:93,56:149,2:0.0132:2,2:34.5:1:28:1:1:1.65484:60:4:0.0133:0:1 +X 15172121 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20086;SOR=0;LSEQ=TCTGCCATAAAACATGCAGA;RSEQ=CTAGTGTTTAATTAAAGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:2:1,1:113,39:152,2:0.013:2,2:33:1:28:1:0.45327:2.87362:60:4:0.0131:0:1 0/0:189:0:0,0:116,73:189,0:0:2,0:27.6:1:31.5:1:1:0:60:188:1:0:0.3 +X 15172127 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.18868;SOR=0;LSEQ=ATAAAACATGCAGAGCTAGT;RSEQ=TTTAATTAAAGCTTGATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:0,2:113,46:159,2:0.0124:2,0:20.5:1:30.5:1:0.08758:0:60:4:0.0127:0:1 0/0:209:0:0,0:128,81:209,0:0:2,0:27.7:1:31.5:1:1:0:60:68.667:1:0:0.4 +X 15172189 . A G 221 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.92736;SOR=1.02558;LSEQ=GATCTACATGGTTCTGTTGA;RSEQ=GAGTAGACATTCCTGAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:234:132:64,68:52,49:101,132:0.5641:2,2:27.8:1:32.1:1:0.69257:1.12697:60:264:0.5641:0:1.1 1/0:256:146:74,72:55,54:109,146:0.5703:2,2:26.2:1:30.8:1:1:1.01:60:145:0.5754:0:1.1 +X 15808477 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18796;SOR=Inf;LSEQ=GCAGGGTTCTGGAAGACGAG;RSEQ=CGCCGAAGGGTACCTCCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:130,0:130,0:0:1,0:24.2:1:33.1:1:1:0:59.7:260:1:0:0 0/1:100:2:2,0:98,0:98,2:0.02:1,0:32:1:31.5:1:1:0:60:4:0.0202:0:1 +X 15808562 . G T 55 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27289;SOR=2.6852;LSEQ=CGCCTGCGCGTGCCCGTCTC;RSEQ=ACTCTTAGGCCCGCCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:474:2:0,2:321,151:472,2:0.0042:2,0:1.5:1:24.5:1:0.10373:0:60:4:0.0043:0:1 0/1:444:5:1,4:273,166:439,5:0.0113:2,2:7.8:1:23.8:1:0.07339:6.55172:60:10:0.0115:0:1 +X 15808586 . C T 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0154;SOR=Inf;LSEQ=CTTAGGCCCGCCCTTTCCTG;RSEQ=CAGACCTGGAGGGGCGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:644:0:0,0:366,278:644,0:0:2,0:25:1:31.7:1:1:0:59.7:106.333:1:0:0.1 0/1:656:7:1,6:355,294:649,7:0.0107:2,2:14.6:1:25.4:1:0.05164:7.22648:51.6:14:0.0109:0:1 +X 15808795 . T C 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CATTCCTTCCTGGTGCGCGC;RSEQ=CTGGTGCCCTCCCCGGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:193:148:12,136:5,40:45,148:0.7668:2,2:26.3:1:31.2:1:0.55193:1.41392:60:36:0.7701:0:1.1 1/1:153:153:3,150:0,0:0,153:1:0,1:22.7:1:30.7:1:1:0:60:152:1:0:1.1 +X 15808816 . G A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5249;SOR=0;LSEQ=CTGGTGCCCTCCCCGGACTT;RSEQ=CACGGGCGGCTGTGGCTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:11,144:155,2:0.0127:2,2:29:1:30.5:1:0.14748:12.58:60:4:0.0131:0:1 0/0:98:0:0,0:2,96:98,0:0:1,0:25.1:1:31.5:1:1:0:60:48:1:0:1 +X 15808933 . A G 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51628;SOR=0;LSEQ=CTGTTCTGTAATTAAAATAC;RSEQ=GGAAGCAAGGTTTCTCTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:2,0:110,28:138,2:0.0143:2,0:6:1:30:1:1:0:60:4:0.0147:0:1 0/0:95:0:0,0:85,10:95,0:0:2,0:22.6:1:30:1:1:0:60:94:1:0:0.2 +X 15817963 . A G 204 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGACCAAGGATTTGCAGC;RSEQ=CTCAGTTTAATAAAACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:212:0:0,0:182,30:212,0:0:2,0:24.2:1:30.2:1:1:0:60:69.667:1:0:0.1 1/0:163:123:110,13:34,2:36,123:0.7546:2,2:24.7:1:29.5:1:0.52345:2.00166:60:122:0.7578:0:1 +X 15818114 . AT A 241 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CACTTAAAGTGAATGAAGTT;RSEQ=TTTATTGGAATATTATCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:399:0:0,0:125,272:397,0:0:2,0:23.8:1:30.5:1:1:0:59.5:55.714:0.9949:0:0.1 1/0:430:262:85,177:59,109:168,262:0.6093:2,2:24.2:1:30.1:1:0.60107:1.12683:59.7:524:0.6121:0.0721:0.1 +X 15818304 . TC T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCTAATTTATAATTTTTTT;RSEQ=TTTCTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:0,2:0,7:7,2:0.2222:0,0:15:1:29:1:1:0:32:4:0.2222:0.1111:2 0/0:3:0:0,0:0,3:3,0:0:0,0:16.3:1:33.3:1:1:0:60:6:1:0:0 +X 15821745 . CGT C 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.05119;SOR=Inf;LSEQ=AAAATGTGTCATTTTGCTCT;RSEQ=GTGTGTGTGTATTTGTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:160,6:166,0:0:1,0:25.3:1:29.9:1:1:0:60:54.333:1:0:0.1 0/1:153:4:4,0:138,11:149,4:0.0261:2,0:22:1:28.8:1:1:0:60:8:0.0267:0.0065:0 +X 15821979 . T A 39 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.34419;SOR=3.43991;LSEQ=CTTCACCATAATAACTCTCA;RSEQ=GAAGAGTTGCCTATCTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:1:1,0:63,230:293,1:0.0034:2,0:1:0:25:0:0.21769:0:60:2:0.0034:0:1 0/1:258:3:3,0:61,194:255,3:0.0116:2,0:11:1:24.7:1:0.01473:0:60:6:0.0117:0:1 +X 15822013 . C T 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCTTGGGAGGTTGGAGTGAG;RSEQ=TGAGATCACGCCATTGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:137:0:0,0:16,121:137,0:0:2,0:26.2:1:32.9:1:1:0:57.7:33.25:1:0:0.2 1/0:104:65:4,61:1,38:39,65:0.625:1,2:21.1:1:28.7:1:0.64804:2.47:57:20.667:0.6263:0:2 +X 15822022 . C T 159 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=170.3426;LSEQ=GTTGGAGTGAGCTGAGATCA;RSEQ=GCCATTGCACTCCAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:1:1,0:12,112:124,1:0.008:2,0:32:0:29:0:0.104:0:59:2:0.0081:0:1 1/0:82:48:4,44:1,32:33,48:0.5854:1,2:24.2:1:28.5:1:0.64357:2.88:56.2:11:0.5789:0:2.3 +X 15822066 . C CA 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.29831;SOR=4.94299;LSEQ=GCAAGAGCGGAACTCCATCT;RSEQ=AAAAAGAAAAAAAAAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:1:0,1:27,54:81,1:0.0116:2,0:34:0:28:0:1:0:60:2:0.0143:0:1 0/1:54:3:0,3:20,31:51,3:0.0556:2,0:26.3:1:27.3:1:0.28721:0:42.3:6:0.0667:0:4 +X 15822072 . GA G 100 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0.98496;LSEQ=GCGGAACTCCATCTCAAAAA;RSEQ=AAAAAAAAAAAGAGTTGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:9:5,4:36,41:77,9:0.1034:2,2:22:1:31.8:1:0.73094:1.42:57.9:18:0.1034:0.046:1.2 0/1:49:5:3,2:18,25:43,5:0.102:2,2:28:1:30.6:1:0.64127:2.05:46.8:10:0.102:0:2.4 +X 15822104 . TA T 118 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.02012;SOR=0.12641;LSEQ=AGAGTTGCCTATCTTGAACT;RSEQ=AAAAAAAAAAACAAAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:13:9,4:61,21:82,13:0.1354:2,2:29.7:1:32:1:0.73854:1.28741:60:26:0.1368:0.0208:1 0/1:52:1:0,1:40,7:47,1:0.0192:2,0:23:0:32:0:0.16667:0:60:2:0.0213:0:0 +X 15822154 . G T 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.25402;SOR=0;LSEQ=TCAGTTTGCCAGTGTTTTAA;RSEQ=TTTTTCATCTATGTGCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:3:2,1:154,35:189,3:0.0155:2,2:10.7:1:26.3:1:0.46557:2.18887:60:2:0.012:0:2 0/0:161:0:0,0:129,31:160,0:0:2,0:22.2:1:30.6:1:1:0:59.8:11.308:1:0:0.3 +X 15822390 . G GT 139 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.02799;SOR=0.45208;LSEQ=GTAGGCATGTCAGAGTTTGG;RSEQ=TTTTTTTTTTCTCTTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:26:9,17:50,170:220,26:0.1048:2,2:27.1:1:29.7:1:0.22297:1.80:60:25:0.102:0:0.7 0/1:239:12:0,12:53,173:226,12:0.0502:2,0:32.9:1:28.3:1:0.07341:0:59.9:11:0.047:0.0042:0.8 +X 15822401 . C T 71 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.03141;SOR=0;LSEQ=AGAGTTTGGGTTTTTTTTTT;RSEQ=TCTTTTTCTTGTCATTTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:6:2,4:36,162:198,6:0.0294:2,2:6:1:27.8:1:0.3105:2.24:60:5:0.0255:0:1.8 0/0:183:0:0,0:29,153:182,0:0:2,0:21.3:1:31.3:1:1:0:60:29.333:1:0:0.2 +X 15822422 . TG T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49792;SOR=0;LSEQ=TCTTTTTCTTGTCATTTCAT;RSEQ=TTTGTTTGGAAAGAATCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:1,1:6,101:107,2:0.0183:2,2:24.5:1:30:1:0.12487:15.66:60:4:0.0187:0.0092:0.5 0/0:104:0:0,0:3,101:104,0:0:1,0:20.8:1:31.8:1:1:0:60:103:1:0:0.2 +X 15826162 . CA C 122 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GACAGAGTGAGACCCTGTCT;RSEQ=AAAAAAAAAGAGAAAAGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:39:0:0,0:38,1:39,0:0:1,0:20.6:1:30.7:1:1:0:55.5:38:1:0:0.1 1/0:29:15:15,0:14,0:14,15:0.5172:1,1:29.1:1:31.4:1:1:0:52.4:30:0.5172:0:0 +X 15826556 . T C 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TACAACAACAACAAACTTTA;RSEQ=TGATGAACAAATACAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:0,62:62,0:0:1,0:24.7:1:30.5:1:1:0:60:124:1:0:0 1/0:42:21:0,21:0,21:21,21:0.5:1,1:30.6:1:31.3:1:1:0:60:20:0.4878:0:1 +X 15827504 . C T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.26715;SOR=0;LSEQ=AATGCTGACGTTTTTGAGTT;RSEQ=CCCTTTTGGGAGAGGCGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:3:1,2:24,229:253,3:0.0117:2,2:12:1:30.7:1:0.26623:4.72:60:6:0.0118:0:1 0/0:186:0:0,0:23,163:186,0:0:2,0:22.2:1:30.7:1:1:0:60:185:1:0:0.6 +X 15827524 . T G 194 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCCCTTTTGGGAGAGGCGCA;RSEQ=GTTTCCATTTCAAATGTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:6,170:176,0:0:1,0:23.6:1:30.9:1:1:0:60:57.667:1:0:0.1 1/0:115:79:0,79:1,35:36,79:0.687:1,1:24.2:1:30.9:1:0.31304:0:60:78:0.6842:0:1.3 +X 15827563 . C T 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGTCATCAGACATCTGCTGC;RSEQ=TTCTTGCTGCTGCTCTCGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:1,84:85,0:0:1,0:22.5:1:33.4:1:1:0:60:84:1:0:0.1 1/0:50:32:0,32:0,18:18,32:0.64:1,1:22.8:1:30.1:1:1:0:60:64:0.64:0:1.8 +X 15836644 . A G 117 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=5e-05;SOR=Inf;LSEQ=AATGTTAGCCTGGACAAACA;RSEQ=CATTTGATGAATGGCTGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:282:0:0,0:222,60:282,0:0:2,0:23.8:1:29.8:1:1:0:60:93:1:0:0.1 0/1:280:14:11,3:206,60:266,14:0.05:2,2:21.9:1:30.8:1:1:1.07:60:28:0.0507:0:2 +X 15836648 . T G 241 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTAGCCTGGACAAACAACAT;RSEQ=TGATGAATGGCTGGTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:309:0:0,0:236,73:309,0:0:2,0:23.1:1:30.4:1:1:0:60:60.8:1:0:0.1 1/0:304:198:154,44:78,28:106,198:0.6513:2,2:23.2:1:31.6:1:0.47926:1.26:60:197:0.6502:0:1.2 +X 15838366 . C T 268 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=375.28079;LSEQ=GCAGCCCTTTCTCTGTTTAA;RSEQ=GGACGATGGTATGCAGGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:784:4:1,3:406,373:779,4:0.0051:2,2:27.5:1:29.3:1:0.35538:3.26093:48.3:8:0.0051:0:1 1/0:834:550:278,272:146,137:283,550:0.6595:2,2:22.3:1:29.5:1:0.82629:1.04266:49.3:136.5:0.6594:0:1.1 +X 15840686 . G A 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTAGAGCACGTTTGAAATC;RSEQ=TGGGAACCAAATTATGACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:38:0:0,0:38,0:38,0:0:1,0:22.5:1:30.7:1:1:0:60:76:1:0:0.1 1/0:31:22:22,0:8,0:8,22:0.7097:0,1:20.8:1:30.2:1:1:0:60:44:0.7333:0:1.1 +X 15841422 . G A 47 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.3718;SOR=0.32906;LSEQ=ATTATGGTTGCTACATACTC;RSEQ=GATAGAAGGCTATGAACGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:3:2,1:51,219:270,3:0.011:2,2:21:1:29.7:1:0.09738:8.49:60:6:0.0112:0:1 0/0:275:1:1,0:66,208:274,1:0.0036:2,0:1:0:23:0:0.24364:0:60:2:0.0037:0:1 +X 15841443 . G T 26 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.24633;SOR=Inf;LSEQ=GATAGAAGGCTATGAACGCA;RSEQ=ATGGGTTCGCAAGTCTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:0,171:171,0:0:1,0:30.1:1:32.1:1:1:0:60:27.5:1:0:0.1 0/1:169:2:1,1:11,156:167,2:0.0118:2,2:6:0:26.5:1:0.13736:13.62:60:4:0.012:0:1.5 +X 17952872 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23658;SOR=Inf;LSEQ=TGTTTTCACTGTGCCAGAAG;RSEQ=TTAAAGAAGTCTGGTTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:85:0:0,0:36,49:85,0:0:2,0:26:1:30:1:1:0:60:27.333:1:0:0.2 0/1:81:2:1,1:33,46:79,2:0.0247:2,2:8.5:1:28:1:1:1.39:60:4:0.0247:0:1 +X 17952885 . G A 21 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.21961;SOR=Inf;LSEQ=CCAGAAGATTAAAGAAGTCT;RSEQ=GTTTTCATGCCTCCTTTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:72:0:0,0:29,43:72,0:0:2,0:25.2:1:30.9:1:1:0:60:71:1:0:0.2 0/1:64:2:1,1:27,35:62,2:0.0313:2,2:14:1:21:1:1:1.29:60:4:0.0313:0:1.5 +X 20146514 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.22197;SOR=Inf;LSEQ=TATATAAGGGAGACTTTCAC;RSEQ=TCCTTAGGCTATGTGAGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:31,111:142,0:0:2,0:21.4:1:32.8:1:1:0:60:141:1:0:0.1 0/1:127:2:1,1:21,103:124,2:0.0157:2,2:29.5:1:28.5:1:0.31987:4.82:60:4:0.016:0:1 +X 20148516 . C T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05835;SOR=Inf;LSEQ=ATTATTTAATTCAGACAATT;RSEQ=TCAAAATACAACCTTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:73,2:75,0:0:1,0:27.2:1:32.4:1:1:0:59.3:74:1:0:0.2 0/1:74:4:4,0:68,2:70,4:0.0541:1,0:27.3:1:31.3:1:1:0:60:8:0.0563:0:1 +X 20148543 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.49857;SOR=Inf;LSEQ=TACAACCTTATTTAAGTGTC;RSEQ=CATGTTCTTAAAATTAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:142:0:0,0:128,14:142,0:0:2,0:21.4:1:31.4:1:1:0:59.8:141:1:0:0.1 0/1:149:2:1,1:134,12:146,2:0.0134:2,2:20:1:29:1:0.16851:10.76875:60:4:0.0138:0:1 +X 20154346 . C G 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACCTTTATAAACACGTGTG;RSEQ=GTGCACACACACACACACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:46:0:30.5:1:1:0:60:4:1:0:1 +X 20156750 . T TA 91 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.10838;SOR=3.86435;LSEQ=ACCTCCTTTACCTGATGGTT;RSEQ=AAAAAAAAGAAAAGGAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:447:2:1,1:128,316:444,2:0.0045:2,2:7:1:29.5:1:0.49528:2.46:27.5:4:0.0045:0.0022:0.5 0/1:468:8:1,7:138,319:457,8:0.0171:2,2:29.8:1:30.5:1:0.44545:3.02261:49.1:16:0.0171:0.0021:0 +X 20159636 . C T 43 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.2781;SOR=0;LSEQ=CCAGCCGCGGGCAGGCAGGG;RSEQ=GGGAAGGAAAAAGGGTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:3:1,2:199,25:224,3:0.0132:2,2:9.7:1:27.7:1:0.03801:15.53977:60:6:0.0136:0:1.3 0/0:152:0:0,0:138,14:152,0:0:2,0:25.3:1:30.8:1:1:0:60:49.667:1:0:0.1 +X 21705268 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.54802;SOR=0;LSEQ=AAAGGGAAGGGCCCCCTGTC;RSEQ=CATGATCACGTGAGTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:20,18:38,2:0.05:2,2:31.5:1:30:1:1:1.10818:53.5:4:0.05:0:1 0/0:20:0:0,0:11,9:20,0:0:2,0:27.5:1:30.6:1:1:0:53.6:40:1:0:0.1 +X 22516092 . T A 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.09091;SOR=Inf;LSEQ=TTGATCTGTGGCTCCAGGAA;RSEQ=GTTATTCTGAAATATCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:8,0:0:0,0:20:1:32.4:1:1:0:58.3:16:1:0:0 1/0:4:2:2,0:2,0:2,2:0.5:0,0:7:1:31:0:1:0:60:4:0.5:0:1 +X 22516183 . G A 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.00088;SOR=0;LSEQ=ATCACATATTGCTGATCTTT;RSEQ=CTTCTACTGAGCACTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:12,0:35,0:35,12:0.2553:1,0:27.4:1:28:1:1:0:60:11:0.2444:0:1 0/0:35:0:0,0:35,0:35,0:0:1,0:22.1:1:31.6:1:1:0:60:70:1:0:0.1 +X 22516304 . A T 53 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.04559;SOR=Inf;LSEQ=TGAGGTTGGAAAGAGTAATA;RSEQ=AGGGAGACAGTTTTTATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:344:0:0,0:185,158:343,0:0:2,0:25.9:1:30.8:1:1:0:60:342:1:0:0.1 0/1:297:4:1,3:146,147:293,4:0.0135:2,2:24.3:1:26.5:1:0.62253:2.96979:60:8:0.0136:0:1.3 +X 22516340 . G A 208 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=368.82897;LSEQ=ATAATACACATGCCTATCTT;RSEQ=CCAGAATTGCTGGTGGGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:340:1:0,1:162,177:339,1:0.0029:2,0:18:0:32:0:1:0:60:2:0.003:0:1 1/0:281:147:67,80:55,78:133,147:0.5231:2,2:28.3:1:28.9:1:0.54638:1.19:60:294:0.5269:0:1.1 +X 22516401 . A G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50621;SOR=0;LSEQ=ATCACCCAACATACTCTGGT;RSEQ=CTTATGAGGTTCCAGTTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:2:1,1:46,98:144,2:0.0137:2,2:34:1:33:1:0.54171:2.12:60:4:0.0138:0:1 0/0:113:0:0,0:32,81:113,0:0:2,0:20.6:1:28.5:1:1:0:60:112:1:0:0.4 +X 23465760 . C T 70 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.58042;SOR=3.65648;LSEQ=GAAAATAATTCCTGGAAATA;RSEQ=ATAAAGATGAAAATAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:3,0:3,5:0.5556:0,0:17.8:1:30.4:1:1:0:60:10:0.625:0:1 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:31.8:1:30.4:1:1:0:60:10:0.8333:0:1 +X 24197670 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51572;SOR=0;LSEQ=GATTCTATACATGTGTCTGA;RSEQ=GTTGGACATGTTGGACATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:16,15:31,2:0.0606:2,2:23.5:1:30:1:1:1.06462:54.5:4:0.0625:0:1 0/0:21:0:0,0:11,10:21,0:0:2,0:24.2:1:28.5:1:1:0:60:20:1:0:0.1 +X 25314412 . GT G 32 d5;v3;MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGTCTGGCTAATTTTGTAGG;RSEQ=TTTTTTTTTTTTTTTTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:2,0:1,0:1,2:0.6667:0,0:14:1:32.1:1:1:0:54.5:4:0.6667:0.3333:3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 25314578 . A T 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.05877;SOR=0;LSEQ=CTTTCTTTTTTTTTTTTTTT;RSEQ=AATTTTGAATTTTGCTGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:3:3,0:32,1:33,3:0.0833:1,0:18:1:22.3:1:1:0:47.7:2:0.0571:0:1.3 0/0:55:0:0,0:49,6:55,0:0:2,0:24.2:1:26.4:1:1:0:59.4:26.5:1:0:0.9 +X 25314722 . T C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=5e-04;SOR=0.55192;LSEQ=TTAAGTGTATCTTAGCAGAC;RSEQ=TGGCTACTGTTCCACTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:122:54,68:65,72:137,122:0.471:2,2:27.1:1:32.5:1:0.61966:1.13627:60:121:0.4745:0:1.1 0/1:331:109:56,53:98,123:221,109:0.3293:2,2:24.9:1:30.4:1:0.24239:1.32:60:53.5:0.3272:0:1.1 +X 25314763 . A G 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03097;SOR=0;LSEQ=TTGAGTTATGAAGCATGTAC;RSEQ=GCTAGCAAGGTTTCTGTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:4:2,2:62,114:176,4:0.0222:2,2:17.5:1:30.5:1:0.61649:1.83:60:8:0.0227:0:1 0/0:247:0:0,0:92,155:247,0:0:2,0:26.2:1:29.8:1:1:0:60:60.75:1:0:0.4 +X 25314812 . C T 100 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.00286;SOR=Inf;LSEQ=GGGAGTAACAGTATCTACTA;RSEQ=TGACCACTCCCTCTTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:9,68:77,0:0:2,0:22.8:1:33.1:1:1:0:59.9:154:0.9872:0:0.2 0/1:108:11:3,8:19,78:97,11:0.1019:2,2:17.5:1:29.1:1:0.69208:1.53:60:22:0.1019:0:1.5 +X 25648085 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.21121;SOR=Inf;LSEQ=CGATCTCTTGAGTTAAATTT;RSEQ=TATTTCTTGAAGAGAAGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:117:0:0,0:86,31:117,0:0:2,0:25.9:1:32.6:1:1:0:60:234:1:0:0.2 0/1:100:2:1,1:69,29:98,2:0.02:2,2:23:1:27:1:0.51212:2.35623:60:4:0.02:0:1 +X 25648094 . G C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22416;SOR=Inf;LSEQ=GAGTTAAATTTCTATTTCTT;RSEQ=AAGAGAAGTGACTACAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:124:0:0,0:88,36:124,0:0:2,0:27:1:32.3:1:1:0:60:123:1:0:0.3 0/1:112:2:1,1:73,37:110,2:0.0179:2,2:8.5:1:29:1:1:1.96019:60:4:0.0179:0:2 +X 25648134 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22828;SOR=Inf;LSEQ=AACTCATTTGAGGATGACTG;RSEQ=AAAGAAAGATATCAAAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:109,85:194,0:0:2,0:22.2:1:31.4:1:1:0:60:63.667:1:0:0.6 0/1:178:2:1,1:93,82:175,2:0.0112:2,2:20:1:27.5:1:1:1.13334:60:4:0.0113:0:2.5 +X 25648137 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.49918;SOR=0;LSEQ=TCATTTGAGGATGACTGGAA;RSEQ=GAAAGATATCAAAGCTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:108,87:195,2:0.0102:2,2:19.5:1:27.5:1:1:1.24:60:4:0.0102:0:2 0/0:185:0:0,0:97,88:185,0:0:2,0:22.2:1:29.1:1:1:0:60:45.25:1:0:0.7 +X 25648140 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21984;SOR=Inf;LSEQ=TTTGAGGATGACTGGAAAGA;RSEQ=AGATATCAAAGCTCTATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:116,92:208,0:0:2,0:22.3:1:30.2:1:1:0:60:51:0.9951:0:0.7 0/1:185:2:1,1:96,87:183,2:0.0108:2,2:20.5:1:29:1:1:1.10286:60:4:0.011:0:1.5 +X 25648157 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01859;SOR=1.57264;LSEQ=AGAAAGATATCAAAGCTCTA;RSEQ=TTAGAATCTATTTGATGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:108:52,56:70,64:134,108:0.4463:2,2:25:1:32.1:1:0.6051:1.17708:60:53:0.4492:0:1.6 1/0:211:118:60,58:46,47:93,118:0.5592:2,2:22.9:1:30.8:1:0.89009:1.06:60:58:0.555:0:1.5 +X 25648222 . T C 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.45939;SOR=1.17338;LSEQ=TTGAGTTTCCGTATCCATAA;RSEQ=TGGTTTTAAGTAAACTCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:80:30,50:41,67:108,80:0.4255:2,2:22.3:1:33:1:1:1.0198:60:160:0.4278:0:1.8 0/1:172:80:33,47:38,54:92,80:0.4651:2,2:27.4:1:31.4:1:1:1.00223:60:79:0.4647:0:1.5 +X 26064958 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19501;SOR=0;LSEQ=CTGAAACAAGACAACGCCTT;RSEQ=CAAACTCTTATACCAACCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:2:1,1:26,16:42,2:0.0455:2,2:40.5:1:31.5:1:1:1.60645:60:4:0.0455:0:1 0/0:55:0:0,0:31,24:55,0:0:2,0:34:1:29.3:1:1:0:44.9:110:1:0:0.1 +X 26065100 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48188;SOR=0;LSEQ=TGTTACCTCCAGGATTGATG;RSEQ=CATGAAGCTACAGATGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:2,9:11,2:0.1538:2,2:27:1:29:1:0.42308:3.87:52:4:0.1538:0:1 0/0:11:0:0,0:2,9:11,0:0:2,0:10.5:1:28.5:1:1:0:53.7:10:1:0:0.4 +X 26693427 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49947;SOR=0;LSEQ=CTACAATTCTTATGGATCAC;RSEQ=TATAAACATGAGGTCAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:2:1,1:76,39:115,2:0.0171:2,2:17:1:30.5:1:1:1.93689:60:4:0.0174:0:1 0/0:104:0:0,0:67,37:104,0:0:2,0:22.9:1:30.4:1:1:0:60:208:1:0:0.4 +X 26693438 . A G 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49836;SOR=Inf;LSEQ=ATGGATCACCTATAAACATG;RSEQ=GGTCAAGTTGAGAAACTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:78,51:129,0:0:2,0:26.6:1:30.4:1:1:0:60:63.5:1:0:0.5 0/1:135:2:1,1:84,49:133,2:0.0148:2,2:17.5:1:26:1:1:1.70705:60:4:0.0148:0:1.5 +X 26693462 . T A 65 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0625;SOR=Inf;LSEQ=CAAGTTGAGAAACTCCTTTT;RSEQ=AAGATAACTCAGTATGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:96,75:171,0:0:2,0:25.5:1:29.5:1:1:0:60:33.2:1:0:0.7 0/1:190:5:4,1:109,76:185,5:0.0263:2,2:23.2:1:28.4:1:0.6499:2.78:60:10:0.0266:0:1.4 +X 26693505 . G A 232 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.00621;LSEQ=AATAGTTTGATTACAAAAAG;RSEQ=ATGATGTCCAAATAATTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:200:199:103,96:0,0:0,199:0.995:0,2:25.3:1:30.4:1:1:0:60:65.333:0.9949:0:1.1 1/0:256:141:73,68:60,54:114,141:0.5508:2,2:26:1:29:1:0.90038:1.03488:60:46:0.5498:0:1.1 +X 28677096 . T TTATC 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.62979;SOR=2.27265;LSEQ=TTTGACCCCATGGAAAAAAA;RSEQ=TAACGTTCAGAACTACCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:26:23,3:2,0:2,26:0.8966:0,2:26.8:1:29.4:1:1:0:32:25:0.9259:0.3448:0.6 1/1:21:20:16,4:1,0:1,20:0.9524:0,2:20.9:1:29:1:1:0:29.1:40:0.9524:0.4286:0.3 +X 28677132 . C CT 107 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.18667;SOR=0.45924;LSEQ=CCAGTAACAGGAAGAAGAGA;RSEQ=TTTTTTTTTTTATTGAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:10:10,0:66,19:85,10:0.1042:2,0:15.3:1:32.5:1:0.2034:0:28.9:20:0.1099:0.0417:0.5 0/1:99:5:4,1:72,21:93,5:0.0505:2,2:25:1:30.6:1:1:1.16:26.8:10:0.0505:0:0.6 +X 28677134 . T C 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=0.49853;SOR=Inf;LSEQ=AGTAACAGGAAGAAGAGACT;RSEQ=TTTTTTTTTATTGAGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:80,21:101,0:0:2,0:18.2:1:31.1:1:1:0:33.8:100:1:0:0.5 0/1:110:2:1,1:82,25:107,2:0.0182:2,2:29:0:33:1:0.42185:3.23584:31:4:0.0183:0:1 +X 28677144 . A G 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50122;SOR=Inf;LSEQ=AGAAGAGACTTTTTTTTTTT;RSEQ=TTGAGAATGAAATGTTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:123:0:0,0:85,35:120,0:0:2,0:22.4:1:27.1:1:1:0:31.4:8.231:0.9907:0:0.3 0/1:144:2:0,2:98,43:141,2:0.0139:2,0:7:1:30.5:1:0.09751:0:41:4:0.0154:0:2 +X 28677223 . T A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.09536;SOR=0;LSEQ=GCCTGCTAGCTTGATGTCTT;RSEQ=TGGCATAATTGTTACACGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:3:2,1:154,130:284,3:0.0105:2,2:13:1:29.7:1:1:1.69:27.3:6:0.0106:0:1 0/0:340:0:0,0:175,165:340,0:0:2,0:29.1:1:29.6:1:1:0:28.7:339:1:0:0.1 +X 28677326 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4996;SOR=Inf;LSEQ=TCCTGCAAAGCACCGATAGC;RSEQ=GCACTCTGGAAGCGCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:34,105:139,0:0:2,0:28.3:1:31:1:1:0:41.5:138:1:0:0.1 0/1:154:2:1,1:58,94:152,2:0.013:2,2:18:1:29.5:1:1:1.62:60:4:0.013:0:2 +X 28677353 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.18961;SOR=0;LSEQ=TGGAAGCGCAGATCTGTTTT;RSEQ=AAGTCCTGAGCAATTTCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:2:1,1:25,73:98,2:0.02:2,2:23:1:31:1:0.45434:2.88:52:4:0.02:0:1 0/0:129:0:0,0:50,79:129,0:0:2,0:26.6:1:29:1:1:0:49:128:1:0:0.1 +X 28677529 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49637;SOR=Inf;LSEQ=AGCGGCTTTTGTAGCCAGTT;RSEQ=CTTCCCGGGTGTTTTACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:36,27:63,0:0:2,0:20.8:1:32.6:1:1:0:59.6:126:1:0:0.1 0/1:66:2:0,2:30,34:64,2:0.0303:2,0:18:1:27.5:1:0.4965:0:60:4:0.0303:0:1 +X 28677536 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.49706;SOR=Inf;LSEQ=TTTGTAGCCAGTTGCTTCCC;RSEQ=GGTGTTTTACCACCAGTCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:68:0:0,0:38,30:68,0:0:2,0:22:1:30.8:1:1:0:59.6:136:1:0:0.1 0/1:73:2:1,1:33,38:71,2:0.0274:2,2:20.5:1:28.5:1:1:1.15:60:4:0.0278:0:1 +X 32172371 . C T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53846;SOR=3.18702;LSEQ=AAAGGTAAAATTTAGAAGTG;RSEQ=AAAGGTATCTTTATCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:8:1:1,0:7,0:7,1:0.125:0,0:27:0:32:0:1:0:60:2:0.125:0:1 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:23.5:1:31.5:1:1:0:60:4:0.3333:0:1 +X 32172584 . A C 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.00019;SOR=0.46548;LSEQ=TCAAATAACTTGTTACAAAG;RSEQ=AATTTTCATCCTAAAACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:87:38,49:53,55:108,87:0.4462:2,2:25.9:1:32.1:1:0.47344:1.24119:60:86:0.4456:0:1.1 0/1:246:67:30,37:79,100:179,67:0.2724:2,2:21.9:1:31.2:1:1:1.03:60:66:0.2716:0:1.1 +X 32223980 . T C 116 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=1.12559;LSEQ=GTCCTTTATCATCATCTGCC;RSEQ=TCTCTCCCACCTAAGTGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:12:10,2:14,2:16,12:0.4286:2,2:25.8:1:32.6:1:1:1.38301:60:24:0.4286:0:1.1 0/1:24:11:9,2:9,4:13,11:0.4583:2,2:33.2:1:30:1:0.6494:1.94:60:22:0.4583:0:1 +X 32224078 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20363;SOR=Inf;LSEQ=TTTGGTTGTGAACTAAAGGC;RSEQ=GACAAAGATGATCACTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:45,31:76,0:0:2,0:26.3:1:31:1:1:0:56.8:75:1:0:0.1 0/1:63:2:2,0:34,27:61,2:0.0317:2,0:33:1:32:0:0.5023:0:26.5:4:0.0328:0:1 +X 32224251 . T C 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50165;SOR=0;LSEQ=GGCAGCTTTGAAAATGTCTG;RSEQ=ACAGCCCATGGTTTCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:2:1,1:26,39:65,2:0.0299:2,2:9:0:33.5:1:1:1.49:60:4:0.0303:0:1 0/0:54:0:0,0:30,24:54,0:0:2,0:20.3:1:28.4:1:1:0:58.8:108:1:0:0.1 +X 32224322 . G C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50156;SOR=Inf;LSEQ=TACGGTTGAAGTGTGGTTCA;RSEQ=GGCCAGTGCATGTGAGTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:24,24:48,0:0:2,0:28.1:1:32.6:1:1:0:59.2:96:1:0:0 0/1:60:2:2,0:34,24:58,2:0.0333:2,0:41.5:1:32:1:0.51186:0:54.5:4:0.0339:0:1 +X 32224384 . C T 72 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02806;SOR=Inf;LSEQ=GAAGATACAGAGTCAGAAGA;RSEQ=GAACAGGAGGAGGATGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:54:0:0,0:39,15:54,0:0:2,0:24.1:1:31.6:1:1:0:47.7:53:1:0:0.5 0/1:59:6:3,3:30,23:53,6:0.1017:2,2:19.5:1:28.2:1:1:1.29842:60:12:0.1017:0:1.2 +X 32224435 . T C 180 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.18412;LSEQ=ATATCTGGAAAGCGATCTGC;RSEQ=CCTGGAGGTGGTAGCAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:72:59:38,21:9,4:13,59:0.8194:2,2:16.8:1:30.6:1:1:1.23975:30.3:58:0.8169:0:1 0/1:73:33:20,13:21,19:40,33:0.4521:2,2:19:1:30.1:1:0.63597:1.39:30.2:66:0.4648:0:1 +X 32224450 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50143;SOR=Inf;LSEQ=TCTGCTCCTGGAGGTGGTAG;RSEQ=AAGGTTCCACAGAAAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:47,31:78,0:0:2,0:21.7:1:32.4:1:1:0:34.2:156:1:0:0.8 0/1:94:2:1,1:48,44:92,2:0.0213:2,2:5.5:1:27.5:1:1:1.08989:38:4:0.0215:0:1.5 +X 32224452 . A G 97 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.00946;SOR=Inf;LSEQ=TGCTCCTGGAGGTGGTAGCA;RSEQ=GGTTCCACAGAAAAAAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:47,33:80,0:0:2,0:21.7:1:30.7:1:1:0:34.8:79:1:0:0.8 0/1:101:8:5,3:48,45:93,8:0.0792:2,2:21:1:32.5:1:0.71806:1.56:48.4:16:0.0792:0:1 +X 32224482 . C T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20239;SOR=0;LSEQ=GAAAAAAGTAAAACTTGCTG;RSEQ=TGATGAAGATGATGATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:0,2:54,41:95,2:0.0206:2,0:20:1:26.5:1:0.19394:0:35:4:0.0208:0:5 0/0:118:0:0,0:63,55:118,0:0:2,0:27.3:1:31.5:1:1:0:43.4:117:1:0:0.4 +X 32224499 . TT GA 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.2044;SOR=0;LSEQ=CTGCTGATGAAGATGATGAT;RSEQ=TGATGATGATGATGATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:2:0,2:57,43:100,2:0.0196:2,0:38:1:26:1:0.1922:0:35:4:0.0206:0:4 0/0:123:0:0,0:67,56:123,0:0:2,0:28.3:1:30.3:1:1:0:42:246:1:0:0.3 +X 32224525 . T A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.50099;SOR=Inf;LSEQ=GATGATGATGATTTTGATGA;RSEQ=GAGGAAACTGAAGAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:77:0:0,0:42,35:77,0:0:2,0:26.7:1:30.4:1:1:0:44:37.5:1:0:0.4 0/1:92:2:2,0:47,42:89,2:0.0217:2,0:34.5:1:31.5:1:0.49744:0:60:4:0.022:0:1 +X 32224532 . A G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.19195;SOR=0;LSEQ=ATGATTTTGATGATGAGGAA;RSEQ=CTGAAGAAAAAGCGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:2:0,2:36,28:64,2:0.0303:2,0:31:1:32.5:1:0.2028:0:35:4:0.0303:0:4 0/0:84:0:0,0:44,40:84,0:0:2,0:25.1:1:29.5:1:1:0:45.5:168:1:0:0.2 +X 32224545 . C T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23228;SOR=0;LSEQ=TGAGGAAACTGAAGAAAAAG;RSEQ=GCCAGTGAAGAAATCTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:2:0,2:36,36:72,2:0.027:2,0:18:1:31:1:0.49352:0:35:4:0.0278:0:4 0/0:79:0:0,0:41,38:79,0:0:2,0:17.8:1:29.5:1:1:0:43.8:78:1:0:0.2 +X 32224567 . A G 28 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.21426;SOR=Inf;LSEQ=CCAGTGAAGAAATCTATATG;RSEQ=GATACTCCAGCCAAAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:33,43:76,0:0:2,0:17.7:1:30.7:1:1:0:42.5:75:1:0:0.1 0/1:66:2:1,1:31,33:64,2:0.0303:2,2:14:0:28.5:1:1:1.06:37:4:0.0303:0:1 +X 32224583 . AA T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21871;SOR=Inf;LSEQ=TATGAGATACTCCAGCCAAA;RSEQ=TGCACAAAAGTCAAATCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:70:0:0,0:29,41:70,0:0:2,0:27.4:1:30.6:1:1:0:44.3:140:1:0:0.1 0/1:62:2:1,1:26,34:60,2:0.0323:2,2:49:0:31:1:1:1.30:27.5:4:0.0323:0:0 +X 34405705 . T C 94 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04718;SOR=6.10722;LSEQ=TAGAGTCTCTACCCAAGAGC;RSEQ=CCTTGAGCAACTGAGAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:4:4,0:10,0:10,4:0.2857:0,0:33:1:32.8:1:1:0:60:8:0.3077:0:1 1/0:11:8:8,0:3,0:3,8:0.7273:0,0:17.9:1:31.4:1:1:0:60:16:0.7273:0:1.1 +X 34405933 . C T 49 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13825;SOR=Inf;LSEQ=GTCGGCCAACACCCTGCGAG;RSEQ=TGTGTTCAAGAAGTATGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:103,174:277,0:0:2,0:25.8:1:32.1:1:1:0:60:26.7:1:0:0.1 0/1:366:4:2,2:142,218:360,4:0.0109:2,2:28.8:1:24.8:1:0.64963:1.53:60:3:0.0084:0:1 +X 39769863 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18477;SOR=0;LSEQ=GGCCCAGGCAGGGCTCGAAC;RSEQ=CTGACTCCAGCCCCTTCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:2:1,1:21,25:46,2:0.0417:2,2:29.5:1:29:1:1:1.19:60:4:0.0426:0:1 0/0:63:0:0,0:35,28:63,0:0:2,0:27.5:1:30.2:1:1:0:60:126:1:0:0.4 +X 39769887 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49939;SOR=Inf;LSEQ=ACTCCAGCCCCTTCCCACCT;RSEQ=GAGGGAGGCCCGGCTTGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:16,25:41,0:0:2,0:27.4:1:30.3:1:1:0:60:82:1:0:0.2 0/1:50:2:1,1:24,24:48,2:0.04:2,2:16.5:1:30.5:1:1:1:60:4:0.0417:0:1 +X 39911657 . C A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=2e-05;SOR=0.45145;LSEQ=GTAGCCAGTTTCGTGGCCTA;RSEQ=AAAACAGAAAGGAAAATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:93:34,59:82,149:231,93:0.287:2,2:25:1:30.8:1:0.89832:1.05:60:92:0.2857:0:1 0/1:397:61:22,39:128,208:336,61:0.1537:2,2:25.4:1:31:1:0.88598:1.0907:59.3:122:0.1548:0:1.2 +X 39913076 . T C 118 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCATCTGCTCAAAGCGCATT;RSEQ=CTAACTCCTGTCACCTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:214:0:0,0:177,36:213,0:0:2,0:23.5:1:30.8:1:1:0:60:70:0.9953:0:0.1 0/1:183:16:11,5:136,31:167,16:0.0874:2,2:21.8:1:29.5:1:0.31876:1.98538:60:32:0.0874:0:1.1 +X 39913655 . C T 146 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAAAATGATGGCAGAGCCA;RSEQ=GTGGCATTTTTTCCTATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:7,144:151,0:0:1,0:22.4:1:30.3:1:1:0:60:150:1:0:0.1 0/1:139:29:2,27:7,103:110,29:0.2086:2,2:19.3:1:30.1:1:1:1.09:60:58:0.2117:0:1.1 +X 39914540 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21086;SOR=Inf;LSEQ=TTTCAGCCTTTGTGATTTCT;RSEQ=CCTAGTCAAATTCCAATCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:149,20:169,0:0:2,0:25.1:1:32.5:1:1:0:60:168:1:0:0 0/1:144:2:1,1:124,18:142,2:0.0139:2,2:21:1:28:1:0.24728:6.73343:60:4:0.0141:0:1 +X 39916715 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07646;SOR=Inf;LSEQ=CGGGCTGTGGATGTCTTGGT;RSEQ=AGGGGGAAACACATGTGCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:0,51:51,0:0:1,0:23:1:32.4:1:1:0:59.7:50:1:0:0.1 0/1:20:2:0,2:0,18:18,2:0.1:1,0:28:1:32:0:1:0:60:4:0.1:0:1 +X 39920974 . C T 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCTGCCTACTCCCCCTACA;RSEQ=GGCCACCCTTCCACCCGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:27:0:31:1:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 39920989 . C G 34 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTACACGGCCACCCTTCCAC;RSEQ=CGAAACAGTACAAGCAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:12:0:34:0:1:0:60:4:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 39921336 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11549;SOR=Inf;LSEQ=CCCTCCCCTCGCCCACCACA;RSEQ=TCCGCAGGCCCCGCCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:171,32:203,0:0:2,0:23.3:1:32.3:1:1:0:60:24.375:1:0:0.1 0/1:105:2:1,1:84,19:103,2:0.019:2,2:25.5:1:28:1:0.34615:4.33469:60:4:0.0194:0:1 +X 39921348 . C T 47 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.13965;SOR=5.29513;LSEQ=CCACCACAGTCCGCAGGCCC;RSEQ=GCCCCCCAGCCTGCAGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:258:1:0,1:196,61:257,1:0.0039:2,0:1:0:15:0:0.24031:0:60:0:0:0:1 0/1:148:3:2,1:111,34:145,3:0.0203:2,2:24.3:1:29.7:1:0.55773:1.62631:60:6:0.0204:0:1.3 +X 39921349 . GC G 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.55715;SOR=3.48576;LSEQ=CACCACAGTCCGCAGGCCCC;RSEQ=CCCCCAGCCTGCAGCCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:265:1:1,0:200,64:264,1:0.0038:2,0:35:0:34:0:1:0:60:2:0.0038:0:0 0/1:153:2:1,1:116,35:151,2:0.0131:2,2:20:1:29.5:1:0.41641:3.28196:60:4:0.0134:0:0 +X 39921707 . C A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57582;SOR=2.74898;LSEQ=CCTTCTAACAGCCGCTGCTT;RSEQ=CCCTCCTCCTCCCCACGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:1:1,0:41,172:213,1:0.0046:2,0:1:0:24:0:0.19626:0:60:2:0.0049:0:1 0/1:158:2:1,1:35,120:155,2:0.0127:2,2:26.5:1:27:1:0.40715:3.39:60:4:0.0127:0:1 +X 39921860 . C A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=GCTGCCACCCAGAAGACATG;RSEQ=TCCTCTAGGACAGGGGAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:93,15:108,0:0:2,0:24.2:1:32.3:1:1:0:60:53:1:0:0.1 0/1:62:11:8,3:42,9:51,11:0.1774:2,2:19.7:1:26.5:1:0.43214:1.73243:60:4.5:0.15:0:1 +X 39921867 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.53607;SOR=0;LSEQ=CCCAGAAGACATGCTCCTCT;RSEQ=GGACAGGGGAGTGACGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:2,0:105,14:119,2:0.0164:2,0:22:1:31:1:1:0:60:4:0.0167:0:1 0/0:69:0:0,0:60,9:69,0:0:2,0:21.1:1:28.4:1:1:0:60:68:1:0:0.2 +X 39922359 . A G 199 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25931;SOR=1.21914;LSEQ=GGTGACGGGGTGGCGGGCGG;RSEQ=TGGGAGACGGGAGAAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:100:39,61:83,140:223,100:0.3086:2,2:24.9:1:30.1:1:0.80433:1.08:60:15.667:0.2984:0:1.4 0/1:278:98:34,64:73,106:179,98:0.3525:2,2:24.1:1:29.7:1:0.36686:1.29513:59.9:15.333:0.3433:0:1.4 +X 39922384 . G T 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50191;SOR=0;LSEQ=AGACGGGAGAAGAAGCGGGC;RSEQ=TTACACAGTTGTAGCCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:2:1,1:54,145:199,2:0.01:2,2:24.5:1:33:1:0.47338:2.67:60:4:0.0101:0:2 0/0:171:0:0,0:50,121:171,0:0:2,0:21.8:1:30.1:1:1:0:60:84.5:1:0:0.5 +X 39923462 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0941;SOR=Inf;LSEQ=CCGCTCCACTGCTGCGCCCC;RSEQ=ACGGCTTCCCCTCACCGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:82,4:86,0:0:1,0:23.7:1:31.7:1:1:0:59.6:85:1:0:0.2 0/1:39:2:2,0:36,1:37,2:0.0513:1,0:42.5:1:29.5:1:1:0:60:4:0.0541:0:1 +X 39923499 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16349;SOR=Inf;LSEQ=GACTCTGTCTACGGGGGCAG;RSEQ=GCGCCGCACATCCACATCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:151:0:0,0:142,9:151,0:0:2,0:23.7:1:32.3:1:1:0:60:49.333:1:0:0.1 0/1:103:2:1,1:93,8:101,2:0.0194:2,2:12.5:1:27:1:0.1679:11.01924:60:4:0.0206:0:1 +X 39923713 . G A 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TCCACCCGGAGGGTGGGGCT;RSEQ=TGAGGCATGTCCGAGGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:754:0:0,0:403,351:754,0:0:2,0:24.8:1:32.4:1:1:0:59.9:106.714:1:0:0.1 0/1:764:25:15,10:394,344:738,25:0.0327:2,2:21.5:1:28.9:1:0.54769:1.31:60:50:0.0329:0:1.2 +X 39923898 . C A 38 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09401;SOR=Inf;LSEQ=TTAATGAAGCCCGAAGGTCG;RSEQ=CATGAGAAGGCAGGATCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:331:0:0,0:75,256:331,0:0:2,0:21.7:1:31:1:1:0:60:35.778:1:0:0.2 0/1:277:3:2,1:54,220:274,3:0.0108:2,2:6:1:24.3:1:0.10504:8.06:60:6:0.0111:0:1 +X 39930099 . C G 99 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00533;SOR=0;LSEQ=TCTTTCACAGACGCCTCGTT;RSEQ=CTGGTTGCCACCATTCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:9:9,0:139,3:142,9:0.0596:1,0:21.7:1:31.3:1:1:0:60:8:0.0544:0:1.1 0/0:119:0:0,0:119,0:119,0:0:1,0:22.6:1:30.4:1:1:0:59.7:22.8:1:0:0.1 +X 39931158 . C CT 46 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTTTAAGCAACCTTTTTT;RSEQ=TTTTTTTTTTCCTTTCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:3:0,3:3,25:28,3:0.0968:2,0:16.3:1:29.3:1:1:0:60:6:0.0968:0.0323:0.3 0/0:8:0:0,0:1,7:8,0:0:2,0:20.5:1:32.8:1:1:0:60:16:1:0:0.9 +X 39931492 . A G 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.26646;SOR=0;LSEQ=TTCAAATTACCACAAGCTTC;RSEQ=TTCACCAAATCTGCCTGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:3:2,1:118,4:122,3:0.024:1,2:15:1:22.3:1:0.11616:13.79441:60:2:0.0163:0:2.3 0/0:90:0:0,0:88,2:90,0:0:1,0:21.6:1:29.9:1:1:0:60:180:1:0:0 +X 39932907 . T C 176 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=85.43527;LSEQ=GATGCGGAGGCTGGGCGGCC;RSEQ=GCACTCGACACTGACCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:610:1:0,1:301,308:609,1:0.0016:2,0:49:0:27:0:1:0:60:2:0.0017:0:1 0/1:519:64:34,30:225,229:454,64:0.1233:2,2:24.6:1:29.4:1:0.689:1.15:60:31:0.1213:0:1.1 +X 39933339 . A G 277 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=2e-05;SOR=1.64351;LSEQ=AACAGAGGAGGTGAGCTGCC;RSEQ=TCTTTTCTGTCTTGAACCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:795:539:251,288:118,138:256,539:0.678:2,2:26.5:1:31.1:1:0.93937:1.02:59.9:88.833:0.6773:0:1.1 1/0:754:585:299,286:78,89:167,585:0.7759:2,2:23.2:1:30.2:1:0.33508:1.19:60:116:0.7744:0:1.2 +X 39933358 . G A 88 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.11031;SOR=0.2662;LSEQ=CATCTTTTCTGTCTTGAACC;RSEQ=CTGTCTTCCGGGCATGCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:757:8:3,5:341,408:749,8:0.0106:2,2:18.8:1:29.6:1:0.7342:1.39238:60:16:0.0107:0:1.8 0/0:706:2:1,1:340,364:704,2:0.0028:2,2:37.5:1:29:1:1:1.07:60:4:0.0029:0:2 +X 39934488 . C T 98 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=ACTCCTTCAAGGCAGCAGCA;RSEQ=CCAAAGACACTGCCAACTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:15,98:113,0:0:2,0:24.3:1:31.5:1:1:0:60:55.5:1:0:0.1 0/1:65:11:5,6:8,46:54,11:0.1692:2,2:16.4:1:28.5:1:0.03481:4.64:60:22:0.1719:0:1.2 +X 39935599 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17307;SOR=Inf;LSEQ=ACTCAGCCCTGCTCTGAACT;RSEQ=CCACCCCTCCCCCATTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:102,11:113,0:0:2,0:24.9:1:32.6:1:1:0:59.8:112:1:0:0.2 0/1:81:2:1,1:66,13:79,2:0.0247:2,2:17.5:1:27.5:1:0.31759:4.92929:60:4:0.025:0:1 +X 39936970 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0.78834;LSEQ=TTAAAACTGTAAATCAAGAG;RSEQ=GGCCTACTAGGCGGGAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:2:1,1:85,0:85,2:0.023:1,2:12.5:1:29:1:0.02299:0:60:4:0.0235:0:1.5 0/1:55:1:1,0:53,1:54,1:0.0182:1,0:5:0:28:0:1:0:60:2:0.0185:0:2 +X 39937038 . G T 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.26194;SOR=0;LSEQ=CGGTGGCTGTGAGAAGTTGA;RSEQ=GGGGGCTTCAGCATGGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:1,2:208,72:280,3:0.0106:2,2:25.7:1:24.7:1:0.16838:5.73432:60:2:0.0072:0:1.3 0/0:217:0:0,0:156,59:215,0:0:2,0:22.3:1:30.8:1:1:0:59.9:70.667:0.9953:0:0.1 +X 39937053 . G T 34 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.08385;SOR=Inf;LSEQ=GTTGAGGGGGGCTTCAGCAT;RSEQ=GGCGTGGGCTCCACTCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:379:0:0,0:259,120:379,0:0:2,0:22.7:1:31.6:1:1:0:60:74.8:1:0:0.1 0/1:296:3:1,2:190,102:292,3:0.0101:2,2:12.3:1:21.7:1:0.28454:3.70796:60:2:0.0069:0:2.3 +X 39945625 . A T 151 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTCACAAATCTTAAAAACTC;RSEQ=GCCATAAACAGCTGAGGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:254:0:0,0:138,116:254,0:0:2,0:24.3:1:30.9:1:1:0:59.9:253:1:0:0.2 0/1:247:33:18,15:104,110:214,33:0.1336:2,2:26.8:1:30:1:0.57757:1.27:60:66:0.1347:0:1.2 +X 39945696 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.21268;SOR=Inf;LSEQ=AACACGGTGACACTCACGGC;RSEQ=CCGTGGGCCTTCTCCCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:56,114:170,0:0:2,0:24.2:1:31:1:1:0:60:84:1:0:0.1 0/1:146:2:2,0:55,89:144,2:0.0137:2,0:15.5:1:29:1:0.15078:0:60:4:0.0141:0:1.5 +X 40594768 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49495;SOR=Inf;LSEQ=GAGCGGGCAGAGTCGCCACC;RSEQ=CCTACCGCCGGGCCGCCTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:14,11:25,0:0:2,0:29.2:1:31.3:1:1:0:60:50:1:0:0.2 0/1:30:2:1,1:19,9:28,2:0.0667:2,2:15.5:1:29:1:1:2.05485:60:4:0.0667:0:1.5 +X 41031175 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49451;SOR=Inf;LSEQ=TAAATATGCCACCCCTTAGA;RSEQ=ATGGAGCAAGAGTACTTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:20,23:43,0:0:2,0:29.7:1:32.5:1:1:0:59.1:86:1:0:0.1 0/1:45:2:1,1:19,24:43,2:0.0444:2,2:23:1:27.5:1:1:1.26:60:4:0.0444:0:1 +X 44732755 . AG A 91 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.05904;SOR=Inf;LSEQ=TCACTGCGGGCCCCGGTCCG;RSEQ=GGGGGGTGTCGGCGTTGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:155,102:257,0:0:2,0:25.2:1:31.9:1:1:0:60:84.667:1:0:0.2 0/1:533:8:4,4:323,201:524,8:0.015:2,2:19.8:1:30.4:1:0.49214:1.60542:60:16:0.0152:0.0038:0.3 +X 44732959 . G A 25 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63212;SOR=0.59553;LSEQ=GCGCTCGGCGGACTGGACAG;RSEQ=TACGGGCCGCCGTCACTCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:64,121:185,2:0.0107:2,2:45.5:1:30.5:1:1:1.88:60:4:0.0109:0:2 0/0:313:2:2,0:115,196:311,2:0.0064:2,0:1:0:25.5:1:0.13898:0:60:4:0.0064:0:1 +X 44732963 . G A 55 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.41401;SOR=3.13439;LSEQ=TCGGCGGACTGGACAGGTAC;RSEQ=GGCCGCCGTCACTCGCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:175:1:0,1:56,118:174,1:0.0057:2,0:9:0:34:0:1:0:60:2:0.0058:0:1 0/1:282:5:3,2:98,179:277,5:0.0177:2,2:24.6:1:23.8:1:0.35312:2.73:60:1.5:0.0109:0:1 +X 44732995 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.17577;SOR=0;LSEQ=CTCGCCCGGTCGGCTCCGGA;RSEQ=GGGCAGTAGCCGCTCTCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:36,91:127,2:0.0155:2,2:21:1:28.5:1:0.49297:2.51:60:4:0.0157:0:1 0/0:178:0:0,0:57,121:178,0:0:2,0:21.1:1:29.5:1:1:0:60:34.6:1:0:0.2 +X 44733054 . C T 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.15619;SOR=Inf;LSEQ=TGTCTCTGGCGGCGGCGGGG;RSEQ=GGGCACCTCGGTTTGGCGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:149:0:0,0:111,38:149,0:0:2,0:21.7:1:31.6:1:1:0:60:28.8:1:0:0.2 0/1:228:4:1,3:177,47:224,4:0.0175:2,2:9.5:1:26.3:1:0.03392:11.13495:60:8:0.0175:0:1.3 +X 44820500 . C T 41 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25618;SOR=Inf;LSEQ=TTTTAGGGCTTTATTTTTTG;RSEQ=TTACATATTTGTATTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:186,41:227,0:0:2,0:24.6:1:32.8:1:1:0:60:454:1:0:0.1 0/1:278:3:1,2:216,59:275,3:0.0108:2,2:6.3:1:26.3:1:0.12227:7.25206:60:6:0.0108:0:1 +X 44833826 . T C 152 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTACTGGGAGGTGGGTGTGG;RSEQ=GGGAATCTTGTTACCGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:105,23:128,0:0:2,0:25:1:30.1:1:1:0:60:127:1:0:0.1 0/1:172:28:25,3:122,22:144,28:0.1628:2,2:20.4:1:31.7:1:0.77015:1.50:60:27:0.1579:0:2.1 +X 44833829 . G A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18674;SOR=0;LSEQ=CTGGGAGGTGGGTGTGGTGG;RSEQ=AATCTTGTTACCGTGTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:2:1,1:111,25:136,2:0.0144:2,2:15:1:27.5:1:0.34243:4.37335:60:4:0.0148:0:1 0/0:182:0:0,0:152,30:182,0:0:2,0:24.6:1:30.9:1:1:0:60:364:1:0:0.8 +X 44833841 . C A 210 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=238.08263;LSEQ=TGTGGTGGGAATCTTGTTAC;RSEQ=GTGTTTGTTAAGTGTATTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:1:0,1:127,38:165,1:0.006:2,0:32:0:16:0:0.23494:0:60:0:0:0:2 1/0:228:135:111,24:72,21:93,135:0.5921:2,2:24.9:1:29.8:1:0.40005:1.35:60:44:0.5893:0:1.3 +X 44833842 . G A 32 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.17404;SOR=0;LSEQ=GTGGTGGGAATCTTGTTACC;RSEQ=TGTTTGTTAAGTGTATTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:2:1,1:128,38:166,2:0.0119:2,2:7:0:32.5:1:0.41146:3.33787:60:4:0.012:0:1.5 0/0:234:0:0,0:188,46:234,0:0:2,0:24.7:1:31.1:1:1:0:60:77:1:0:0.8 +X 44834045 . C CT 130 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAAAATTAATTGAGCTCTTG;RSEQ=TTTTTTTTGTTAATTACTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:31,139:170,0:0:2,0:22.1:1:32.1:1:1:0:60:20.25:0.9939:0:0.1 0/1:232:25:4,21:53,150:203,25:0.1078:2,2:25.3:1:28.2:1:0.33475:1.8506:60:50:0.1082:0.0043:0 +X 44870342 . TTG T 50 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.000;MSILEN=2;SSF=0.65582;SOR=0.49795;LSEQ=TTTTGTTTGTGCTTGATTTT;RSEQ=TGTGTGTGTGTAATAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:3:0,3:50,182:232,3:0.0128:2,0:23:1:31.6:1:1:0:59.3:6:0.0128:0.0043:2.3 0/0:313:2:1,1:84,227:311,2:0.0064:2,2:48:1:32.5:1:0.47002:2.69:60:4:0.0065:0:0 +X 44894091 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18713;SOR=0;LSEQ=ATGTATTTATTATTATTTTA;RSEQ=ACCTTACATACCTGAAAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:2:1,1:142,41:183,2:0.0108:2,2:13:1:28:1:0.40347:3.43386:60:4:0.0109:0:1 0/0:242:0:0,0:178,64:242,0:0:2,0:21.5:1:30.7:1:1:0:60:47.4:1:0:0.1 +X 44896821 . G T 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02771;SOR=0;LSEQ=AGACTGTGATAATGTTTGAT;RSEQ=CTTTGTTATTCTTACTTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:353:4:2,2:258,91:349,4:0.0113:2,2:24.3:1:30.8:1:0.2841:2.82525:60:8:0.0114:0:1.3 0/0:510:0:0,0:358,150:508,0:0:2,0:24.5:1:31.2:1:1:0:60:83.667:0.998:0:0.1 +X 44896832 . C G 237 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.0083;LSEQ=ATGTTTGATGCTTTGTTATT;RSEQ=TTACTTAATTTGCCCCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:160:105,55:176,88:264,160:0.3765:2,2:25.9:1:32.4:1:0.83288:1.04748:60:320:0.3791:0:1.7 0/0:606:3:2,1:396,206:602,3:0.005:2,2:26:1:28:1:1:1.04:60:2:0.0034:0:1.7 +X 44896888 . C T 231 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTGATTTTTTTGTCTTTCCT;RSEQ=ATCCTTTGCAGTTCAATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:233:106,127:207,232:439,233:0.3452:2,2:26.8:1:29.5:1:0.68555:1.06888:59.8:115.5:0.3468:0:1.5 0/0:1036:0:0,0:511,524:1035,0:0:2,0:25.6:1:31:1:1:0:60:128.375:0.999:0:0.2 +X 44897039 . TG T 116 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.00072;SOR=Inf;LSEQ=CAGATAATTTAATGGAGTTC;RSEQ=GGCGTTACTTCTTAGGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:1,58:59,0:0:1,0:21.7:1:31.2:1:1:0:60:58:1:0:0.1 0/1:83:13:0,13:1,69:70,13:0.1566:1,1:26.6:1:31.5:1:1:0:60:26:0.1585:0:0.1 +X 44911107 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21475;SOR=0;LSEQ=TCTTTATGTTTTTTCCATGT;RSEQ=GAGTGTGGCAAATATGTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:24,117:141,2:0.014:2,2:22:1:27.5:1:0.3201:4.80:60:4:0.014:0:1 0/0:165:0:0,0:28,136:164,0:0:2,0:25.2:1:29.7:1:1:0:60:163:1:0:0 +X 44913052 . T A 169 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTAAGTCATTTATGTAAAT;RSEQ=TTTTTAAATCATTTACTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:304:0:0,0:226,77:303,0:0:2,0:24.3:1:30.6:1:1:0:59.9:49.5:1:0:0.1 0/1:427:69:47,22:240,118:358,69:0.1616:2,2:22.8:1:27.8:1:0.88974:1.05:60:138:0.162:0:1.1 +X 44919285 . C T 23 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64565;SOR=0.63925;LSEQ=AGGCTCAGTTGTGTAACCTT;RSEQ=CACAAGGTAGTCTACAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:91,91:182,2:0.0109:2,2:11.5:1:26.5:1:1:1:22:4:0.0113:0:1.5 0/0:287:2:0,2:154,131:285,2:0.007:2,0:1:0:23:0:0.21388:0:25:4:0.007:0:1 +X 44919532 . G A 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.000;MSILEN=1;SSF=0.18816;SOR=Inf;LSEQ=CTTTTGATTTAATTGCAAAG;RSEQ=GAATCTAGATCAAAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:4,58:62,0:0:2,0:23.8:1:31.5:1:1:0:60:61:1:0:0 0/1:48:2:0,2:0,46:46,2:0.0417:1,0:18:1:32.5:1:1:0:60:4:0.0417:0:1 +X 44920068 . A G 131 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AGAAGTTTCAGCTGCCCTGA;RSEQ=ATTGTGCAGTTTGAACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:7,102:109,0:0:2,0:23.7:1:31.2:1:1:0:60:53.5:0.9907:0:0.1 0/1:146:20:3,17:11,115:126,20:0.137:2,2:18.3:1:30.4:1:0.40976:1.84:60:19:0.1329:0:1.1 +X 44920541 . A AT 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.52035;SOR=1.44356;LSEQ=ATTTAACCAAATATTCTTTA;RSEQ=TTTTTTTTTTAAATCGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:7:6,1:176,47:223,7:0.03:2,2:20.3:1:29.8:1:1:1.60:60:14:0.0311:0.0086:0 0/1:397:17:15,2:275,104:379,17:0.0428:2,2:23.8:1:30.2:1:0.26009:2.83:60:34:0.0433:0.0025:0.1 +X 44920542 . T A 39 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.000;MSILEN=1;SSF=0.049;SOR=0;LSEQ=TTTAACCAAATATTCTTTAA;RSEQ=TTTTTTTTTAAATCGATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:3:2,1:174,52:226,3:0.0129:2,2:11.3:1:25:1:0.54783:1.66883:60:2:0.0086:0:1.3 0/0:402:0:0,0:285,109:394,0:0:2,0:21.9:1:29.9:1:1:0:60:196:0.9825:0:0.1 +X 44922446 . T C 31 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07692;SOR=Inf;LSEQ=TTTTTTTTTGAAACCGACTT;RSEQ=TGCTTTTTCAAGGAAGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:9,0:0:2,0:23.2:1:29.3:1:1:0:58.4:8:1:0:0 1/0:4:2:2,0:2,0:2,2:0.5:0,0:6.5:1:31:1:1:0:60:4:0.5:0:1.5 +X 44922654 . GT G 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.30591;SOR=0.21569;LSEQ=CCAGCATTTACTTTTCCTTT;RSEQ=TTTTTTGACAGATGAGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:3:2,1:194,83:277,3:0.0107:2,2:37.7:1:31.3:1:1:1.16799:60:6:0.0108:0:0 0/0:430:1:0,1:278,151:429,1:0.0023:2,0:19:0:26:0:0.35349:0:60:2:0.0023:0:0 +X 44929077 . C A 180 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GCCTTCAGGAAACATATTGA;RSEQ=GGTGCCTGAAACAAGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:582:0:0,0:256,326:582,0:0:2,0:25.5:1:31.2:1:1:0:59.9:581:1:0:0.1 0/1:848:67:30,37:373,408:781,67:0.079:2,2:26.6:1:29.8:1:0.70274:1.12737:60:134:0.0795:0:1.1 +X 44929587 . T A 35 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.06015;SOR=0;LSEQ=ATACCCCAGCTCAGCAGAAG;RSEQ=TCTGAAGGCATGCAGGTTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:3:3,0:94,171:265,3:0.0112:2,0:8:1:22.3:1:0.04648:0:57.3:2:0.0075:0:3.3 0/0:416:0:0,0:153,262:415,0:0:2,0:38:0:14:0:1:0:60:0:0:0:2 +X 44929611 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16764;SOR=0;LSEQ=GAAGGCATGCAGGTTAGTGT;RSEQ=GGAAAGTTCATCAAAGTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:2:1,1:54,131:185,2:0.0107:2,2:49.5:1:27.5:1:0.50285:2.41:60:4:0.0109:0:1.5 0/0:269:0:0,0:76,193:269,0:0:2,0:25.3:1:30.5:1:1:0:60:66.25:1:0:0.1 +X 44929647 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51776;SOR=Inf;LSEQ=GTGAAAATGTTTGACTTACT;RSEQ=GCATGATCAGAATGCTGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:86:0:0,0:13,73:86,0:0:2,0:23.4:1:31.4:1:1:0:59.6:42:1:0:0.2 0/1:129:2:1,1:20,107:127,2:0.0155:2,2:12.5:1:27:1:0.30015:5.25:60:4:0.0157:0:1 +X 44935874 . A AT 30 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.19544;SOR=0;LSEQ=TAATTAGGACTTAATTCAGG;RSEQ=TTCTTTTTTTTTTTTTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:2:0,2:134,0:134,2:0.0147:1,0:29:1:30.5:1:0.00011:0:60:4:0.015:0:2 0/0:171:0:0,0:166,4:170,0:0:1,0:15:0:9:0:1:0:60:0:0:0:2 +X 44935920 . AT A 48 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08285;SOR=Inf;LSEQ=AAATAAATGTACAACTGATT;RSEQ=CCCTTTTTTTTTTTTTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:336:0:0,0:239,94:333,0:0:2,0:25:1:28.1:1:1:0:59.3:5.404:1:0:0.7 0/1:486:5:3,2:317,161:478,5:0.0103:2,2:26.4:1:21:1:1:1.31182:55.2:1.5:0.0073:0:1.4 +X 44935924 . CT C 239 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=0.06636;SOR=0.77287;LSEQ=AAATGTACAACTGATTATCC;RSEQ=TTTTTTTTTTTTCCAGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:368:193:131,62:73,26:99,193:0.5245:2,2:26.3:1:31.3:1:0.34646:1.32756:59.5:23.125:0.5271:0.0489:0.8 0/1:526:242:156,86:90,33:123,242:0.4601:2,2:30.3:1:30.3:1:0.09944:1.50184:59.8:59.5:0.4722:0:0.7 +X 44937801 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.15909;SOR=0;LSEQ=TGTCTCTTTGTTTTGCTATC;RSEQ=TTTAACTTTTCCAGCACTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:28,145:173,2:0.0114:2,2:17:1:34:1:0.30476:5.11:60:4:0.0115:0:1 0/0:263:0:0,0:62,200:262,0:0:2,0:21.4:1:29.3:1:1:0:60:261:1:0:0.1 +X 44937821 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08564;SOR=0;LSEQ=TTTTAACTTTTCCAGCACTG;RSEQ=CAGATACTTTTCTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:3:1,2:9,123:132,3:0.0222:2,2:12:1:24:1:0.2076:6.64:60:2:0.0154:0:1 0/0:170:0:0,0:14,156:170,0:0:2,0:21.1:1:30.7:1:1:0:60:23.286:1:0:0.1 +X 44937849 . C CT 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.21007;SOR=5.15032;LSEQ=TTTTCTTTTTTTTCTTTTTT;RSEQ=TTTTTTTTTCTTTTTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:1:0,1:5,75:80,1:0.0123:2,0:32:0:32:0:1:0:60:2:0.0125:0:0 0/1:82:5:0,5:0,77:77,5:0.061:1,0:33.2:1:30:1:1:0:60:10:0.0625:0.0122:0 +X 44938316 . TA T 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.21301;SOR=1.88227;LSEQ=AATGCTTTACCTTCTTCCTT;RSEQ=AAAAAAAAAAGCACTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:8:6,2:80,6:86,8:0.0825:2,2:28.5:1:31.3:1:0.13717:4.33231:57.5:16:0.0825:0:0.5 0/1:131:19:17,2:100,11:111,19:0.145:2,2:23.2:1:29.1:1:1:1.06897:60:18:0.1395:0.0534:0.3 +X 44938317 . A T 44 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=1;SSF=1;SOR=1.1128;LSEQ=ATGCTTTACCTTCTTCCTTT;RSEQ=AAAAAAAAAAGCACTTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:2,0:80,6:86,2:0.0206:2,0:13.5:1:31.5:1:1:0:60:4:0.0206:0:1 0/1:131:3:2,1:100,11:111,3:0.0229:2,2:3:1:28.3:1:0.28596:4.44573:60:4:0.0231:0:1.3 +X 44938331 . C T 36 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.65506;SOR=0.4984;LSEQ=TCCTTTAAAAAAAAAAAGCA;RSEQ=TTAAAATATTATCCCAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:3:1,2:121,20:141,3:0.0208:2,2:13:1:23:1:0.06099:11.75054:60:2:0.0155:0:1.7 0/1:191:2:1,1:153,36:189,2:0.0105:2,2:21:1:15.5:1:0.35073:4.20585:60:0:0:0:2 +X 44938563 . G A 190 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ACAATTGCTAAATATGCACA;RSEQ=TACCAGGCCTCCTCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:410:0:0,0:165,245:410,0:0:2,0:26.3:1:32.6:1:1:0:59.9:50.25:1:0:0.1 0/1:577:88:32,56:205,284:489,88:0.1525:2,2:25.1:1:29.5:1:0.34858:1.2627:55.3:176:0.1536:0:1.2 +X 44941741 . G T 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.27679;SOR=Inf;LSEQ=ATACTATTCAATCTAGATAT;RSEQ=AACTTTTTTTCAGTTGTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:125,25:150,0:0:2,0:23.3:1:32.6:1:1:0:59.7:74:1:0:0.1 0/1:223:3:1,2:164,56:220,3:0.0135:2,2:11.3:1:25.3:1:0.1665:5.80061:60:6:0.0136:0:1 +X 44942135 . A AT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=CTTCTGTTTCATTTATTGTC;RSEQ=TTTTTTTTAAGTTGACATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:105:0:0,0:2,103:105,0:0:1,0:25.6:1:31.2:1:1:0:59.6:51.5:1:0:0.1 0/1:88:2:0,2:4,82:86,2:0.0227:1,0:21.5:1:31:0:1:0:60:4:0.0238:0:0 +X 44942631 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51224;SOR=Inf;LSEQ=TTTTCTGATTGGAACACAAG;RSEQ=GTTTTGAAGAAATGGTAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:99,10:109,0:0:2,0:22.5:1:31.6:1:1:0:60:218:1:0:0 0/1:153:2:1,1:124,27:151,2:0.0131:2,2:9:1:28:1:0.33351:4.528:60:4:0.0133:0:1 +X 44942636 . TG T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.51184;SOR=Inf;LSEQ=TGATTGGAACACAAGGGTTT;RSEQ=AAGAAATGGTAAACTTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:107,15:122,0:0:2,0:23.3:1:32.2:1:1:0:60:39.667:1:0:0 0/1:170:2:0,2:137,31:168,2:0.0118:2,0:8.5:1:24:1:0.03676:0:60:4:0.012:0.0059:0.5 +X 44942641 . A T 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51188;SOR=Inf;LSEQ=GGAACACAAGGGTTTTGAAG;RSEQ=AATGGTAAACTTCCACAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:112,18:130,0:0:2,0:24.1:1:30.4:1:1:0:60:129:1:0:0 0/1:181:2:1,1:141,38:179,2:0.011:2,2:13.5:1:23.5:1:0.38545:3.67592:60:4:0.0115:0:1 +X 44945086 . A AT 49 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.31427;SOR=0.23882;LSEQ=ATTGCACCACTGGAGCTCCA;RSEQ=TTTTTTTTCTTTTCACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:3:3,0:210,70:280,3:0.0106:2,0:26:1:31:1:1:0:60:6:0.0109:0:0 0/0:394:1:1,0:279,114:393,1:0.0025:2,0:28:0:32:0:1:0:60:2:0.0026:0:0 +X 44945281 . C T 39 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26553;SOR=Inf;LSEQ=TAGAAAGCAGTAATTGTAAA;RSEQ=GACAACTTACCAAGCTGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:14,150:164,0:0:2,0:24.1:1:30.2:1:1:0:59.9:163:1:0:0.1 0/1:223:3:1,2:30,190:220,3:0.0135:2,2:22.7:1:25:1:0.36315:3.14:60:6:0.0136:0:1 +X 44949209 . T C 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.27049;SOR=Inf;LSEQ=TATGCTTTAAAAAAGTTAAT;RSEQ=TATAAAGGATTATATCCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:26,137:163,0:0:2,0:22.5:1:30.8:1:1:0:60:80.5:1:0:0.1 0/1:231:3:1,2:55,173:228,3:0.013:2,2:31:1:25.3:1:0.56703:1.57:60:2:0.0088:0:2.3 +X 44949284 . A T 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02718;SOR=Inf;LSEQ=TAAAAGTTGTAAGAAGAATG;RSEQ=CTCCTTGCATAGAATTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:45:0:0,0:1,44:45,0:0:1,0:23:1:30.8:1:1:0:60:90:1:0:0 0/1:49:6:1,5:1,42:43,6:0.1224:1,2:22:1:29.2:1:0.23214:7.76:60:12:0.1224:0:1 +X 44949951 . G GT 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.90021;SOR=1.04636;LSEQ=CTTTGGGTTGCTTTATAACT;RSEQ=TTTTTTTTTTTCCTAGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:30:23,7:186,52:238,30:0.1119:2,2:24.4:1:29.7:1:0.81795:1.08829:59.5:60:0.1186:0.0149:0.3 0/1:369:43:30,13:218,98:316,43:0.1165:2,2:28.8:1:29.8:1:1:1.04:60:86:0.1254:0:0.4 +X 44966570 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50181;SOR=Inf;LSEQ=CATTAGAATCAAGTCTCTTG;RSEQ=CATTATTTCTAGTTGGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:89,12:101,0:0:2,0:24.1:1:31.2:1:1:0:60:49.5:1:0:0.1 0/1:121:2:1,1:99,20:119,2:0.0165:2,2:15:1:24:1:0.31818:4.85513:60:4:0.0171:0:1 +X 44966795 . T C 205 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTGTGAAGTAAGTAATTGTT;RSEQ=TTATCCACAGTTGTTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:467:0:0,0:181,286:467,0:0:2,0:26.8:1:30.3:1:1:0:60:92.4:1:0:0.1 0/1:578:109:46,63:173,296:469,109:0.1886:2,2:24.7:1:30.3:1:0.32463:1.25:59.4:26.25:0.1845:0:1.1 +X 44966805 . GT G 200 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGTAATTGTTTTTATCCACA;RSEQ=TGTTTTATAAAGCCTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:403:0:0,0:140,262:402,0:0:2,0:25.5:1:30:1:1:0:60:66:0.9975:0:0.1 0/1:490:89:33,56:134,267:401,89:0.1816:2,2:25.2:1:30.9:1:0.53739:1.17:60:178:0.1835:0.0306:1 +X 44970742 . G A 56 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4046;SOR=2.91282;LSEQ=CTGGTTTTTGTAGCTATCTC;RSEQ=TAAGGCTGCTGGCTGAAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:1:1,0:47,150:197,1:0.0051:2,0:1:0:25:0:0.24242:0:60:2:0.0051:0:1 0/1:274:4:3,1:73,197:270,4:0.0146:2,2:6:1:28:1:0.06617:8.02:60:8:0.0149:0:1.3 +X 44970751 . C T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.20302;SOR=0;LSEQ=GTAGCTATCTCGTAAGGCTG;RSEQ=TGGCTGAAAACTGTGTCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:34,140:174,2:0.0114:2,2:28:0:32:0:0.35909:4.07:60:4:0.0115:0:1.5 0/0:214:0:0,0:50,164:214,0:0:2,0:23.9:1:31.4:1:1:0:60:70.333:1:0:0.1 +X 47004740 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.51493;SOR=Inf;LSEQ=GGGAGGGCAGCGCGCTTGGC;RSEQ=CTTCTCCCCTCCCCCCGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:100,7:107,0:0:2,0:25.9:1:30:1:1:0:60:106:1:0:0.1 0/1:155:2:1,1:142,11:153,2:0.0129:2,2:21.5:1:28:1:0.14931:12.40307:60:4:0.0131:0:1 +X 47004760 . C T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.56332;SOR=0.31836;LSEQ=GCTTCTCCCCTCCCCCCGAT;RSEQ=TGCCTCCAGTCTCGGACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:133,27:160,2:0.0123:2,2:10:1:29:1:0.31669:4.8554:60:4:0.0124:0:1.5 0/0:253:1:0,1:205,47:252,1:0.004:2,0:1:0:24:0:0.18972:0:60:2:0.004:0:1 +X 47004789 . G T 63 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.42293;SOR=2.91681;LSEQ=GTCTCGGACTTGGTTGTTGC;RSEQ=CGCTCCGGCTCCGGCTGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:279:1:0,1:177,100:277,1:0.0036:2,0:1:0:25:0:0.36331:0:60:2:0.0036:0:1 0/1:481:5:1,4:298,178:476,5:0.0104:2,2:5.4:1:27.2:1:0.07042:6.67128:60:10:0.0105:0:1 +X 47004966 . G T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61521;SOR=2.10527;LSEQ=GGCGCGAGGGCGGACTTCGG;RSEQ=TCGGGGGAGATGCGCGGAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:1:0,1:28,145:173,1:0.0057:2,0:40:0:12:0:1:0:60:0:0:0:1 0/1:166:2:1,1:24,140:164,2:0.012:2,2:37:1:29.5:1:0.2793:5.74:60:4:0.0121:0:1 +X 47007061 . C CCTGTGCT 64 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=2.000;MSILEN=2;SSF=0.2652;SOR=0;LSEQ=GCACCTGTTGTGAGCCAGGA;RSEQ=CTGTGCTAGGCTCTGATAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:0,4:0,14:14,4:0.2222:1,0:13.8:1:32:1:1:0:60:8:0.2222:0.1667:0 0/0:10:0:0,0:0,10:10,0:0:0,0:22:1:31:1:1:0:60:20:1:0:0.2 +X 47028893 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12725;SOR=Inf;LSEQ=CTCATCTGAGGAGCAGAGTG;RSEQ=GGAGGTGAGGAGGGGGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:288:0:0,0:98,190:288,0:0:2,0:22.9:1:30.5:1:1:0:60:95:1:0:0.1 0/1:330:4:1,3:116,209:325,4:0.0121:2,2:12.8:1:29.8:1:1:1.66271:60:8:0.0124:0:1 +X 47030378 . C T 50 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.14544;SOR=Inf;LSEQ=GCGGCCAGCTCCTAGGCCTG;RSEQ=CCAGACTGACTGCCCGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:164,78:242,0:0:2,0:26.2:1:31.9:1:1:0:60:59.5:1:0:0.2 0/1:341:4:1,3:208,129:337,4:0.0117:2,2:7.3:1:25.3:1:0.30283:4.81517:60:8:0.0119:0:1.3 +X 47030466 . AGGC A 151 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.02118;SOR=2.42328;LSEQ=CGGGCTCCGAGACTCAGCGT;RSEQ=GGCGGCGGCGGCACAGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:9:6,3:280,274:554,9:0.016:2,2:20.1:1:32.6:1:0.50479:1.95:60:18:0.0162:0.0036:0.4 0/1:818:31:22,9:428,358:786,31:0.0379:2,2:20.8:1:30.5:1:0.09624:2.04:60:62:0.0385:0.0086:0.3 +X 47030585 . TGAG T 114 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.00798;SOR=0.25248;LSEQ=GAGGAGGAGGAGGAGGAGGA;RSEQ=GAGGAGGAGGAGAAGGCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:14:5,9:181,220:401,14:0.0337:2,2:21.9:1:30.2:1:0.59012:1.47954:60:28:0.0347:0.0096:0.4 0/0:573:5:2,3:259,307:566,5:0.0087:2,2:32.2:1:31.2:1:1:1.26496:60:10:0.009:0:0.4 +X 47030674 . G A 57 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.13566;SOR=4.98601;LSEQ=TGACGTACGTGCCCCCCATG;RSEQ=CCCCGGGCAGGAGGCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:324:1:1,0:129,193:322,1:0.0031:2,0:1:0:28:0:0.40248:0:60:2:0.0032:0:1 0/1:394:6:5,1:167,221:388,6:0.0152:2,2:8.8:1:22.2:1:0.09016:6.59:60:5:0.0131:0:1 +X 47032418 . G T 46 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.36315;SOR=3.14931;LSEQ=CGAAAGAGGCGGAGGAGACT;RSEQ=TGTGCACATCACCGATGACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:138:1:1,0:123,14:137,1:0.0072:2,0:4:0:30:0:1:0:60:2:0.0075:0:1 0/1:133:3:2,1:108,22:130,3:0.0226:2,2:13:1:29.3:1:0.43695:2.43334:60:6:0.0227:0:1 +X 47032420 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.11451;SOR=Inf;LSEQ=AAAGAGGCGGAGGAGACTGT;RSEQ=TGCACATCACCGATGACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:143:0:0,0:126,17:143,0:0:2,0:21.4:1:32.2:1:1:0:60:70.5:1:0:0.2 0/1:136:3:2,1:110,23:133,3:0.0221:2,2:10.7:1:29:1:0.44415:2.37188:60:6:0.0221:0:1.3 +X 47032432 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23172;SOR=0;LSEQ=GAGACTGTGTGCACATCACC;RSEQ=ATGACCCCTCGGGATCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:143,30:173,2:0.0114:2,2:15.5:1:28.5:1:0.32374:4.70556:60:4:0.0119:0:1 0/0:188:0:0,0:146,42:188,0:0:2,0:21.7:1:29.3:1:1:0:60:93:1:0:0.2 +X 47032461 . G T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.0346;SOR=0;LSEQ=TCGGGATCCAGAGGCCTCCA;RSEQ=CCAGCCTCAGGTACCCAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:4:2,2:190,78:268,4:0.0147:2,2:10.8:1:29.3:1:0.58353:2.42689:60:8:0.0151:0:1.3 0/0:358:0:0,0:237,121:358,0:0:2,0:23.9:1:31.2:1:1:0:60:43.75:1:0:0.2 +X 47034511 . AC A 132 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=1.07454;LSEQ=GGTTGCTTTGCCGCACTTGA;RSEQ=CCCCCCCCAAACAAATACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:11:5,6:199,260:459,11:0.0233:2,2:27.7:1:31.4:1:1:1.09:58.2:22:0.0248:0:0.5 0/1:760:19:10,9:332,406:738,19:0.025:2,2:26.3:1:31.3:1:0.64179:1.36:60:18:0.0251:0.0026:0.4 +X 47034546 . C T 45 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.67928;SOR=0.61429;LSEQ=AATACTACTTTGTAATCGAG;RSEQ=GCTCCCCATCGCCTGATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:3:1,2:98,176:274,3:0.0108:2,2:12.7:1:23.7:1:1:1.11322:60:2:0.0078:0:1.7 0/0:451:3:2,1:146,299:445,3:0.0067:2,2:25.3:1:28.7:1:0.25479:4.08:60:6:0.007:0:3 +X 47035783 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50047;SOR=Inf;LSEQ=TCCGCTCTCCGACCTCCCTC;RSEQ=GTTCCCTGTCCCTCATCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:133:0:0,0:120,13:133,0:0:2,0:22.7:1:31.3:1:1:0:60:65.5:1:0:0.1 0/1:152:2:1,1:128,21:149,2:0.0132:2,2:17.5:1:28:1:0.27099:5.97834:60:4:0.0133:0:1 +X 47038395 . T G 34 v3;p8;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21804;SOR=0;LSEQ=GCCACCATTGCCTAGGGGCT;RSEQ=TCCTTCCTGGGGCACTGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:2:1,1:102,6:108,2:0.0182:2,2:7:0:34:0:0.12377:15.80921:60:4:0.0185:0:1 0/0:125:0:0,0:104,21:125,0:0:2,0:21.3:1:29.4:1:1:0:60:61.5:1:0:0.1 +X 47038449 . G T 57 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.13678;SOR=Inf;LSEQ=TCTCTTCATCCAAGTTTGGA;RSEQ=GGTGCAGTGGGAAATCCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:198,80:278,0:0:2,0:22.9:1:32.2:1:1:0:60:138:1:0:0.1 0/1:362:4:2,2:235,123:358,4:0.011:2,2:25.8:1:28.8:1:0.61088:1.90698:60:8:0.0113:0:1 +X 47038767 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.1679;SOR=0;LSEQ=AGGCTGGATCAGCAGACACT;RSEQ=CCACTGGGTGGCCGGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:85,94:179,2:0.011:2,2:32:1:31:1:1:1.11:60:4:0.011:0:1 0/0:260:0:0,0:120,140:260,0:0:2,0:23.1:1:30.8:1:1:0:60:31.5:1:0:0.2 +X 47038780 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.3007;SOR=Inf;LSEQ=AGACACTGCCACTGGGTGGC;RSEQ=GGGAGCTGAGCCAGGGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:67,79:146,0:0:2,0:25.5:1:30.7:1:1:0:60:145:1:0:0.1 0/1:251:3:1,2:112,136:248,3:0.012:2,2:16.3:1:28.7:1:1:1.64392:60:6:0.0121:0:1 +X 47039178 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24686;SOR=Inf;LSEQ=AGCGGCAGTTGCAAAGGCAC;RSEQ=GAGTGAGTGGGGGCAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:115,5:120,0:0:1,0:22.3:1:30:1:1:0:60:59:1:0:0.1 0/1:119:2:1,1:109,8:117,2:0.0168:2,2:8:1:29:1:0.14613:12.90462:60:4:0.0168:0:1 +X 47039188 . G T 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.49928;SOR=Inf;LSEQ=GCAAAGGCACGGAGTGAGTG;RSEQ=GGGCAGAGGAAAGGGAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:130,10:140,0:0:2,0:24:1:31.3:1:1:0:60:34:1:0:0.1 0/1:153:2:1,1:129,22:151,2:0.0131:2,2:10.5:1:25:1:0.2789:5.75698:60:4:0.0133:0:1 +X 47039479 . C A 35 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62984;SOR=2.50352;LSEQ=GGGCCGGGCAGCCAGGGTCC;RSEQ=GGCCCCCGGGGTGGAGACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:205:1:1,0:64,140:204,1:0.0049:2,0:1:0:25:0:0.31707:0:60:2:0.005:0:1 0/1:247:3:3,0:63,181:244,3:0.0121:2,0:8.7:1:22.7:1:0.01844:0:60:6:0.0123:0:2 +X 47039481 . G A 40 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2522;SOR=Inf;LSEQ=GCCGGGCAGCCAGGGTCCCG;RSEQ=CCCCCGGGGTGGAGACGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:64,134:198,0:0:2,0:22.5:1:31.7:1:1:0:60:48.5:1:0:0.1 0/1:229:3:2,1:60,166:226,3:0.0131:2,2:5.3:1:25.7:1:0.17901:5.48:60:6:0.0133:0:1.3 +X 47039558 . CG C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.21103;SOR=Inf;LSEQ=TGGAAATCGGGCAATGGAGC;RSEQ=GGGGCCTCCCCGGGCCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:183:0:0,0:133,50:183,0:0:2,0:23.8:1:30.3:1:1:0:60:60:1:0:0.1 0/1:156:2:2,0:115,39:154,2:0.0128:2,0:12.5:1:31.1:1:1:0:60:4:0.013:0.0064:0 +X 47039570 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21086;SOR=Inf;LSEQ=AATGGAGCCGGGGGCCTCCC;RSEQ=GGGCCTGACCCTTCTGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:222:0:0,0:156,66:222,0:0:2,0:22.7:1:30.9:1:1:0:60:110:1:0:0.1 0/1:189:2:2,0:136,51:187,2:0.0106:2,0:12:1:32:0:1:0:60:4:0.0107:0:1 +X 47039579 . C T 42 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.11017;SOR=Inf;LSEQ=GGGGGCCTCCCCGGGCCTGA;RSEQ=CCTTCTGTCCCTGCCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:176,64:240,0:0:2,0:23.5:1:31.8:1:1:0:60:39:1:0:0.1 0/1:222:3:1,2:164,55:219,3:0.0135:2,2:7.3:1:27:1:0.16265:5.90483:60:6:0.0136:0:1.3 +X 47039832 . A G 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCTCAGGGACATGGCCTCCA;RSEQ=TGAAGGCAGTCGCATCAGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:554:0:0,0:236,318:554,0:0:2,0:24.7:1:30.7:1:1:0:59.9:68.25:1:0:0.1 0/1:741:74:35,39:307,360:667,74:0.0999:2,2:22.9:1:31:1:0.90233:1.05:60:148:0.1007:0:1.1 +X 47039959 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.4973;SOR=Inf;LSEQ=AGACCTGGGCTTTCTCAACC;RSEQ=TCCTGCACCCTCTCTGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:90:0:0,0:8,82:90,0:0:2,0:22.4:1:33:1:1:0:60:180:1:0:0.1 0/1:92:2:1,1:10,80:90,2:0.0217:2,2:24.5:1:26:1:0.22599:7.68:60:4:0.0217:0:1 +X 47040531 . TG T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20535;SOR=Inf;LSEQ=AGAAATACTAGCCCCACGTG;RSEQ=GGACAGATGCTTCTAGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:89,19:108,0:0:2,0:21.4:1:31.7:1:1:0:57:35:1:0:0.8 0/1:90:2:1,1:68,19:87,2:0.0222:2,2:11.5:1:29:1:0.40092:3.51368:60:4:0.023:0.0111:0.5 +X 47040552 . G GT 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0.50154;LSEQ=GGGACAGATGCTTCTAGCAG;RSEQ=TTCCCCACCCCCCACCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:2:2,0:77,30:107,2:0.0183:2,0:24.5:1:29:1:1:0:49:4:0.0213:0:2.5 0/0:108:1:1,0:67,40:107,1:0.0093:2,0:20:0:27:0:1:0:60:2:0.0101:0:0 +X 47040634 . T C 233 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.3749;LSEQ=GCCTCCCAAGGTGGGGAGGG;RSEQ=ACCTGGGCCACCTCCGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:161:84,77:111,100:211,161:0.4328:2,2:25.6:1:31.8:1:1:1.01746:60:52.667:0.4293:0:1.1 0/1:486:108:63,45:207,170:377,108:0.2222:2,2:28.5:1:31:1:0.58317:1.15:59.9:26:0.2189:0:1.3 +X 47041002 . C T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07576;SOR=Inf;LSEQ=TCCTGGCATCTACCAACAAT;RSEQ=AGCCGAGGCGAGCAGTAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:348:0:0,0:167,181:348,0:0:2,0:23.8:1:31.8:1:1:0:60:48.714:1:0:0.1 0/1:470:5:1,4:222,243:465,5:0.0106:2,2:14.8:1:24.6:1:0.37561:3.64547:60:10:0.0108:0:1 +X 47041119 . C T 52 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.06923;SOR=Inf;LSEQ=GGCATGGGCAGACACTGAGC;RSEQ=CTGTTCTCCTGTCTGGCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:341:0:0,0:196,145:341,0:0:2,0:25.9:1:31.2:1:1:0:60:41.625:1:0:0.2 0/1:425:5:1,4:249,171:420,5:0.0118:2,2:11.4:1:22.8:1:0.16434:5.80245:60:4:0.0097:0:1.8 +X 47041731 . C T 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14705;SOR=Inf;LSEQ=AAGACAGCTCAACAGGTGAA;RSEQ=ACCAGGGTCCAGCAGTCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:280:0:0,0:93,186:279,0:0:2,0:25.1:1:32:1:1:0:60:38.857:1:0:0.2 0/1:399:4:2,2:155,240:395,4:0.01:2,2:21.8:1:30:1:0.6479:1.55:60:8:0.0101:0:1.3 +X 47041743 . G A 52 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15432;SOR=Inf;LSEQ=CAGGTGAACACCAGGGTCCA;RSEQ=CAGTCACTGGCTGGCTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:0:0,0:74,156:230,0:0:2,0:26.2:1:32.5:1:1:0:60:75.667:1:0:0.2 0/1:346:4:3,1:129,213:342,4:0.0116:2,2:8.8:1:26.3:1:0.15721:4.93:60:8:0.0119:0:1 +X 47041753 . G A 32 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.5742;SOR=0.35792;LSEQ=CCAGGGTCCAGCAGTCACTG;RSEQ=CTGGCTGTGTGGTGTCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:1,1:54,139:193,2:0.0102:2,2:22.5:1:32:0:0.48559:2.56:60:4:0.0104:0:1 0/0:274:1:0,1:89,184:273,1:0.0036:2,0:17:0:31:0:1:0:60:2:0.0037:0:1 +X 47044372 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.22039;SOR=Inf;LSEQ=CTGGCCCGTGTTTGAGGATG;RSEQ=AGGGCAGTGGGTCAGCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:0:0,0:126,26:152,0:0:2,0:23.7:1:32.1:1:1:0:60:75:1:0:0 0/1:135:2:1,1:109,24:133,2:0.0148:2,2:8.5:1:27:1:0.3372:4.47028:60:4:0.0149:0:1 +X 47044386 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.49884;SOR=Inf;LSEQ=AGGATGCAGGGCAGTGGGTC;RSEQ=GCAGATAGAGTTAGTAGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:140,54:194,0:0:2,0:22.8:1:30.1:1:1:0:60:37.8:1:0:0.1 0/1:200:2:1,1:138,60:198,2:0.01:2,2:11:1:28:1:0.51804:2.28935:60:4:0.0101:0:1 +X 47045549 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.08977;SOR=0;LSEQ=GCCCAAGAGGAGGAAGTACG;RSEQ=CGGCATATCCACAGCCTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:3:2,1:124,144:268,3:0.0111:2,2:30.7:1:30:1:0.59901:2.32:60:6:0.0113:0:1 0/0:333:0:0,0:145,188:333,0:0:2,0:19:0:16:0:1:0:60:0:0:0:1 +X 47045611 . C T 23 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=1;SOR=0.81156;LSEQ=AGGGGGTCTGGAGCCCGGGG;RSEQ=CGGGGCCGGCAGGCCGACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:2:1,1:94,95:189,2:0.0105:2,2:28.5:1:30.5:1:1:1.01:60:4:0.0106:0:1 0/0:235:2:0,2:113,120:233,2:0.0085:2,0:1:0:23.5:1:0.4986:0:60:4:0.0087:0:1 +X 47045615 . G T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.09652;SOR=0;LSEQ=GGTCTGGAGCCCGGGGCCGG;RSEQ=GCCGGCAGGCCGACCACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:3:1,2:110,88:198,3:0.0149:2,2:27:1:29:1:0.5879:2.48883:60:6:0.0152:0:1 0/0:236:0:0,0:116,120:236,0:0:2,0:23.2:1:29.8:1:1:0:60:46.2:1:0:0.2 +X 47045690 . C T 62 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47708;SOR=2.28513;LSEQ=CCTACTCGGGACGGGCTGGG;RSEQ=AGTGACAACATTGGCAGTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:2:0,2:185,150:335,2:0.0059:2,0:1:0:26.5:1:0.2027:0:54.5:4:0.006:0:1 0/1:448:6:2,4:248,194:442,6:0.0134:2,2:12.5:1:24.3:1:0.41265:2.55143:60:12:0.0136:0:1 +X 47045752 . G A 75 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.04463;SOR=Inf;LSEQ=GAAAGAGGGCAGCGGCCTGG;RSEQ=CCGCAAGAAGCAGGGCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:398:0:0,0:218,180:398,0:0:2,0:24:1:31.6:1:1:0:60:78.6:1:0:0.2 0/1:561:6:3,3:280,275:555,6:0.0107:2,2:23.7:1:29.3:1:1:1.01815:60:12:0.0108:0:1.3 +X 47046082 . C A 71 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00752;SOR=Inf;LSEQ=GTTGGATGGCTGGGACGGGG;RSEQ=CTTGCTCTTGTCGGCCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:58:0:0,0:0,58:58,0:0:1,0:23.8:1:31.7:1:1:0:60:57:1:0:0 0/1:37:5:0,5:1,31:32,5:0.1351:1,0:16.6:1:30.8:1:1:0:60:10:0.1389:0:1 +X 47424615 . C T 236 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=271.39922;LSEQ=GCCCTTACAGACAGCTGACC;RSEQ=GTGTCCCCTTGCTTTATACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:630:1:0,1:317,312:629,1:0.0016:2,0:1:0:31:0:0.49683:0:56:2:0.0016:0:1 0/1:825:248:136,112:308,268:576,248:0.3006:2,2:24.5:1:29.7:1:0.76067:1.06:59.9:61:0.2994:0:1.2 +X 47425058 . G A 90 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAAATAATCAATTTTTTT;RSEQ=TTATTAATTATAAATATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:25.1:1:32.3:1:1:0:60:14:0.875:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 47426008 . G T 61 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24894;SOR=4.43962;LSEQ=TCTCGGTTCTCTGATTCCTG;RSEQ=CAGTGATTTCACAGCCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:387:1:0,1:254,132:386,1:0.0026:2,0:7:0:14:0:0.34367:0:60:0:0:0:4 0/1:527:6:2,4:324,197:521,6:0.0114:2,2:7.5:1:23.7:1:0.20822:3.28169:60:5:0.0096:0:1.2 +X 47426848 . G T 46 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27714;SOR=Inf;LSEQ=TCAGGTGAGGTGGCATGTGT;RSEQ=CGTGGATGGGGGTGGCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:53,149:202,0:0:2,0:25.2:1:32.1:1:1:0:60:100:1:0:0.2 0/1:300:3:1,2:96,201:297,3:0.01:2,2:32:1:29.3:1:1:1.05:60:6:0.0101:0:1 +X 47426857 . G T 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.65288;SOR=0.6624;LSEQ=GTGGCATGTGTGCGTGGATG;RSEQ=GGGTGGCAGGCCCGGCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:43,137:180,2:0.011:2,2:24.5:1:29.5:1:0.42608:3.16:60:4:0.0111:0:1 0/0:274:2:1,1:87,185:272,2:0.0073:2,2:41.5:1:29:1:0.53999:2.12:60:4:0.0075:0:1 +X 47428044 . C A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18725;SOR=0;LSEQ=AGGAAGGTAAAGAACAGTGC;RSEQ=ACTCCTGATGCTCGGTAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:147,30:177,2:0.0112:2,2:23:1:29.5:1:0.31718:4.83676:60:4:0.0115:0:1 0/0:234:0:0,0:188,45:233,0:0:2,0:21.6:1:30.1:1:1:0:60:32.286:1:0:0.1 +X 47428570 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.21994;SOR=Inf;LSEQ=GGTGGCAGAGCTGTGGCCAG;RSEQ=CAGGGGGCTTTAATGGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:107:0:0,0:3,104:107,0:0:1,0:24.9:1:31.8:1:1:0:60:106:1:0:0.1 0/1:95:2:1,1:5,88:93,2:0.0211:2,2:42:1:29.5:1:0.12296:16.16:60:4:0.0213:0:1 +X 47428842 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49878;SOR=Inf;LSEQ=GGGCTCCTGGTCAGGATCAG;RSEQ=GGGATGAGTGGTATAGGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:146:0:0,0:138,8:146,0:0:2,0:25.9:1:30.2:1:1:0:60:28.2:1:0:0.1 0/1:155:2:1,1:137,16:153,2:0.0129:2,2:16.5:1:29.5:1:0.20796:8.33596:60:4:0.0132:0:1 +X 47428883 . C T 56 q25;Bias STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.95948;LSEQ=ACCAATGGGAACCTCCCAGG;RSEQ=AGGGTGAGAGGCATGGCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:4:0,4:219,98:317,4:0.0125:2,0:1:0:24.3:1:0.00979:0:60:8:0.0127:0:1 0/1:418:5:0,5:267,146:413,5:0.012:2,0:9.6:1:24.2:1:0.00589:0:60:10:0.0121:0:1 +X 47430163 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49888;SOR=Inf;LSEQ=ATCCTCTGGGCCTTGATACT;RSEQ=ACAGTACCCCAGCTCGCTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:142,2:144,0:0:1,0:25.4:1:32.6:1:1:0:60:47:1:0:0.8 0/1:154:2:1,1:151,1:152,2:0.013:1,2:25.5:1:27:1:0.02589:107.40534:60:4:0.0131:0:1 +X 47430165 . C T 213 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0.27802;LSEQ=CCTCTGGGCCTTGATACTGA;RSEQ=AGTACCCCAGCTCGCTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:149:117:114,3:32,0:32,117:0.7852:1,1:25:1:31.1:1:1:0:60:22.4:0.7887:0:1.1 1/0:165:83:83,0:79,3:82,83:0.503:1,1:22.2:1:30.4:1:0.12047:0:60:82:0.5:0:1.1 +X 47430209 . A T 51 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20565;SOR=0.23547;LSEQ=AACCTTCCAAGTCCCTCAAT;RSEQ=CAAAATTCCTTGGGCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:4:1,3:277,117:394,4:0.0101:2,2:7.3:1:25.5:1:0.08379:7.06371:60:3:0.0077:0:2.5 0/0:420:1:0,1:291,128:419,1:0.0024:2,0:1:0:23:0:0.30714:0:60:2:0.0024:0:1 +X 47430457 . A T 224 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.24786;LSEQ=CTTGGGTGGGTGACTCTGGG;RSEQ=TAGAGGAAGACTGAGATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:217:174:31,143:11,32:43,174:0.8018:2,2:23.4:1:30.1:1:0.28173:1.58203:60:86:0.8037:0:1.1 1/0:270:135:28,107:34,101:135,135:0.5:2,2:28.4:1:29.2:1:0.46957:1.28521:60:66.5:0.5038:0:1.1 +X 47430479 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.50327;SOR=Inf;LSEQ=AGAGGAAGACTGAGATGGAG;RSEQ=CAGATGTGAATATGAAAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:23,130:153,0:0:2,0:21.5:1:31.9:1:1:0:59.9:50:1:0:0.8 0/1:186:2:1,1:21,162:183,2:0.0108:2,2:12:1:27:1:0.22427:7.56:60:4:0.011:0:2 +X 47430509 . A AGTGT 138 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=18.000;MSILEN=2;SSF=0;SOR=0.06968;LSEQ=ATATGAAAGCTCAGAGGTAT;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:22:10,12:10,52:62,22:0.234:2,2:27.6:1:31.1:1:0.00889:4.24:59.4:44:0.2366:0.0319:0.5 0/1:97:2:1,1:12,81:93,2:0.0206:2,2:24.5:1:30.1:1:0.25622:6.53:60:4:0.0211:0.0103:0.5 +X 47430615 . TGTGTGTGT GGG 189 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=30;MSI=18.000;MSILEN=2;SSF=0.47647;SOR=0.83344;LSEQ=CATGAGGCTGGGACTGTTGG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:59:56,3:30,3:33,59:0.4069:2,2:25.7:1:32.2:1:0.663:1.85:58.8:118:0.4184:0.0828:0.1 0/1:154:56:47,9:51,10:61,56:0.3636:2,2:20.2:1:29.9:1:1:1.02:58.9:55:0.3691:0.1299:0.1 +X 47430621 . T G 106 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=2;SSF=0.1677;SOR=0.49273;LSEQ=GGGACTGTTGGGTGTGTGTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:13:9,4:40,5:45,13:0.2031:2,2:6.2:1:28.8:1:0.10249:3.4598:58.1:5.5:0.2075:0:2.4 0/1:90:10:6,4:65,14:79,10:0.1111:2,2:12.2:1:27.1:1:0.11205:3.04607:56.3:9:0.1047:0:2.7 +X 47430623 . T G 136 MSI12 STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=2;SSF=0.01652;SOR=0.40816;LSEQ=GACTGTTGGGTGTGTGTGTG;RSEQ=GTGTGTGTGTGTGTGTGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:23:17,6:37,4:41,23:0.3538:2,2:7.7:1:30.2:1:0.14822:3.19914:58.3:22:0.3607:0:2 0/1:99:18:14,4:63,18:81,18:0.1818:2,2:11.2:1:28.4:1:1:1:56.8:8:0.1684:0:2.4 +X 47430670 . TG T 228 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGCCATGAGGCTGGGGCTGT;RSEQ=GGATGCCCACAGGGCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:363:0:0,0:244,118:362,0:0:2,0:22.9:1:31.3:1:1:0:59.6:35.2:1:0:0.5 0/1:425:185:114,71:143,96:239,185:0.4353:2,2:26.1:1:30.4:1:0.76385:1.08:59.6:45.25:0.4415:0.0518:0.7 +X 47443791 . T A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.22581;SOR=Inf;LSEQ=GGGGTTCTTGCTAAACTGAC;RSEQ=TAGCAAGGCTCTCGGCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:10,6:16,0:0:2,0:22.2:1:31.6:1:1:0:59.3:32:1:0:0 0/1:16:3:2,1:10,3:13,3:0.1875:2,2:19:1:29.7:1:1:1.60994:44.3:6:0.1875:0:1.3 +X 48649423 . A G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24739;SOR=0;LSEQ=TGGAGTGGGAGGAGGGGGAA;RSEQ=GGAGGAAGAGGAGCAGGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:2:1,1:133,8:141,2:0.014:2,2:24.5:1:31:1:0.12233:15.72782:60:4:0.0144:0:4 0/0:144:0:0,0:130,13:143,0:0:2,0:26.1:1:29.1:1:1:0:59.9:19.429:1:0:1.9 +X 48649425 . GA AG 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.24384;SOR=0;LSEQ=GAGTGGGAGGAGGGGGAAAG;RSEQ=GGAAGAGGAGCAGGTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:130,8:138,2:0.0143:2,2:24.5:1:28.5:1:0.12487:15.37797:60:4:0.0146:0:3 0/0:143:0:0,0:129,14:143,0:0:2,0:26.8:1:30.6:1:1:0:59.9:34.75:1:0:1.9 +X 48649426 . A AG 234 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.11323;SOR=Inf;LSEQ=AGTGGGAGGAGGGGGAAAGG;RSEQ=GGAAGAGGAGCAGGTGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:180:177:154,23:1,0:1,177:0.9833:0,2:23.5:1:32.3:1:1:0:59.8:176:1:0.2667:2 1/1:191:191:160,31:0,0:0,191:1:0,2:21.8:1:30.9:1:1:0:59.9:62.667:1:0.2565:2 +X 48649449 . T G 256 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=1.13628;LSEQ=AAGAGGAGCAGGTGAAAGGA;RSEQ=GTGGGGTGGAAGGATTTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:272:271:206,65:0,1:1,271:0.9963:0,2:23.1:1:32.7:1:0.24265:0:59.9:134.5:0.9963:0:2.1 1/1:309:308:218,90:0,0:0,308:0.9968:0,2:22.4:1:31:1:1:0:60:307:1:0:2.1 +X 48649456 . T G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.77837;SOR=0.8129;LSEQ=GCAGGTGAAAGGATGTGGGG;RSEQ=GGAAGGATTTCTGTGTCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:310:305:216,89:0,1:1,305:0.9839:0,2:23:1:31.1:1:0.29412:0:60:75.25:0.9869:0:2 1/1:354:347:239,108:0,2:2,347:0.9802:0,2:23.2:1:30:1:0.09872:0:60:56.833:0.9855:0:2 +X 48652569 . T A 36 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.29512;SOR=Inf;LSEQ=TGGTGGCTCCGCTCAGCTCA;RSEQ=GAGGGCACAGAGCATGGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:110:0:0,0:16,94:110,0:0:2,0:26.2:1:30.7:1:1:0:60:109:1:0:0.1 0/1:184:3:2,1:49,132:181,3:0.0163:2,2:6.7:1:23.3:1:0.18641:5.33:60:2:0.0114:0:3.3 +X 48652595 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51699;SOR=Inf;LSEQ=CACAGAGCATGGCCTCCAGA;RSEQ=GAGGGGTGGTGTCCTTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:75:0:0,0:6,69:75,0:0:2,0:24.3:1:31.3:1:1:0:60:24:1:0:0.1 0/1:112:2:1,1:22,88:110,2:0.0179:2,2:17.5:1:27.5:1:0.37001:3.93:60:4:0.018:0:1 +X 48652792 . G A 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=AATGCCTGTGGCTCTCTGAT;RSEQ=ACAGTGCATGGCTGCAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:24:1:33:0:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 48687685 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.501;SOR=Inf;LSEQ=TGTGGTGGTGGGCGCCAGTG;RSEQ=CGTGGGCAAGAGTGCGCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:94:0:0,0:54,40:94,0:0:2,0:24.3:1:31.3:1:1:0:59.9:93:1:0:0.1 0/1:111:2:1,1:63,46:109,2:0.018:2,2:34.5:1:29:1:1:1.36561:60:4:0.0187:0:1.5 +X 48891721 . C T 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40863;SOR=3.61213;LSEQ=AGTGATGGCTGGTGTGGCCA;RSEQ=GCCTTGACTACTGTACACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:229:1:1,0:161,67:228,1:0.0044:2,0:5:0:27:0:1:0:60:2:0.0045:0:1 0/1:320:5:2,3:208,107:315,5:0.0156:2,2:19.6:1:28.6:1:0.34375:2.90535:60:10:0.016:0:1 +X 48892463 . G A 52 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24088;SOR=3.87208;LSEQ=ATTAGCACTGCTTTATGTCA;RSEQ=CCTAGTTTTTTTTTTTTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:343:1:1,0:122,220:342,1:0.0029:2,0:1:0:26:0:0.3586:0:60:2:0.0032:0:1 0/1:446:5:4,1:153,284:437,5:0.0112:2,2:9.4:1:22.4:1:0.05594:7.39:56:4:0.01:0:2.4 +X 48892482 . C T 52 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06576;SOR=Inf;LSEQ=AGCCTAGTTTTTTTTTTTTT;RSEQ=CTCTCCTTCACACTTTCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:283:0:0,0:84,197:281,0:0:2,0:21.6:1:30.9:1:1:0:59.3:20.615:1:0:0.8 0/1:334:5:3,2:102,226:328,5:0.015:2,2:9.2:1:22.6:1:0.18236:3.31:60:1.5:0.0094:0:2.2 +X 48892694 . A G 93 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAACAAAAAAAATTAGCC;RSEQ=AGCATGGTGGCCTGCACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:29.6:1:31.3:1:1:0:53.5:7:1:0:1 1/1:3:3:0,3:0,0:0,3:1:0,0:29:1:32.3:1:1:0:59.3:6:1:0:1 +X 48893174 . G A 43 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.29528;SOR=Inf;LSEQ=ATCTCCTGACCTTGTGATCT;RSEQ=CCCGCCTCAGCCTCCCAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:69,7:76,0:0:2,0:16.2:1:32.5:1:1:0:40:37:1:0:0 0/1:128:3:2,1:113,10:123,3:0.0234:2,2:6.3:1:27.3:1:0.24146:5.50668:43:6:0.0244:0:1 +X 48894095 . C T 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCCCAGCACTTTGGGAGGC;RSEQ=GAGGCAGGCAGATCACAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:2,0:5,0:5,2:0.2857:0,0:30:1:34:0:1:0:32.5:4:0.3333:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:44:0:33:0:1:0:39:2:1:0:0 +X 48894299 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50335;SOR=Inf;LSEQ=ATAGCACCATTGCGCTCCAG;RSEQ=CTGGGTGACAGAGCAAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:113:0:0,0:105,8:113,0:0:2,0:23.2:1:31.8:1:1:0:59.5:36.667:1:0:0.1 0/1:139:2:2,0:128,9:137,2:0.0144:2,0:17.5:1:28:0:1:0:60:4:0.0149:0:1 +X 48894787 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51237;SOR=Inf;LSEQ=AGCCAAGATCGCACCGCTGC;RSEQ=CTCCAGCCAGGGTGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:87:0:0,0:74,13:87,0:0:2,0:21.2:1:30.8:1:1:0:59.6:42.5:1:0:0.1 0/1:123:2:1,1:113,8:121,2:0.0163:2,2:25:1:29:1:0.14154:13.376:60:4:0.0164:0:1 +X 48894826 . G GA 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.93271;LSEQ=AGTGAGACTCTGTCTTAAAA;RSEQ=AAAAAAAAGGTAAAAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:3:3,0:145,57:202,3:0.0146:2,0:40.3:1:27:1:0.56178:0:60:2:0.0099:0:0 0/1:366:5:3,2:253,107:360,5:0.0137:2,2:22:1:28.7:1:0.63724:1.5742:59.8:10:0.014:0.0055:0 +X 48894950 . G A 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16261;SOR=Inf;LSEQ=AAGATGCTCATCTCGGCCGG;RSEQ=TGTGGTGGCTCACGCCTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:294:0:0,0:105,189:294,0:0:2,0:23.4:1:31.9:1:1:0:58.3:293:1:0:0.1 0/1:470:5:4,1:175,290:465,5:0.0106:2,2:9.8:1:26.2:1:0.07207:6.60:60:10:0.0107:0:1 +X 48894958 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0621;SOR=0;LSEQ=CATCTCGGCCGGGTGTGGTG;RSEQ=CTCACGCCTGTAATCCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:3:2,1:78,177:255,3:0.0116:2,2:17.7:1:29.7:1:0.22786:4.51:60:6:0.0119:0:1 0/0:392:0:0,0:135,257:392,0:0:2,0:22.3:1:30.7:1:1:0:58.3:48:1:0:0.1 +X 48894992 . G T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.198;SOR=0;LSEQ=TCCCAGTACTTTGGGAGGCC;RSEQ=AGGCAGGCAGATCACGAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:2:1,1:18,120:138,2:0.0143:2,2:11.5:1:28.5:1:0.25385:6.52:60:4:0.0144:0:1 0/0:174:0:0,0:29,143:172,0:0:2,0:20.2:1:30.1:1:1:0:56.4:171:0.9884:0:0.1 +X 48895250 . A T 64 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30228;SOR=0.46379;LSEQ=AAAAAAAAAAAAAGATTATC;RSEQ=TCTCTTGGTACTTCTCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:5:2,3:251,115:366,5:0.0134:2,2:9.8:1:27.8:1:0.332:3.26225:57.6:4:0.0141:0:1.4 0/0:641:4:0,4:387,250:637,4:0.0062:2,0:1:0:23.8:1:0.0243:0:60:8:0.0075:0:1 +X 48896013 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.22194;SOR=0;LSEQ=GAGAGGGGACAAGGCAGAAC;RSEQ=GGACTCAAAGGGGTGAATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:2:1,1:34,99:133,2:0.0148:2,2:20:1:29.5:1:0.45274:2.88:60:4:0.0153:0:1 0/0:151:0:0,0:40,111:151,0:0:2,0:21.6:1:29.8:1:1:0:59.8:302:1:0:0.1 +X 49070676 . G A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1836;SOR=Inf;LSEQ=ATAGTGAAGAGGCCAGTGAA;RSEQ=ACCATGTTGAGGATGTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:30,0:30,0:0:1,0:26.1:1:34.2:1:1:0:60:60:1:0:0.1 0/1:23:2:2,0:19,2:21,2:0.087:2,0:27:1:31:0:1:0:60:4:0.0952:0:1 +X 49070718 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49849;SOR=Inf;LSEQ=GCATAGTTGAAGGGAGCAGT;RSEQ=TGCTCATAGTGCTGCAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:53,12:65,0:0:2,0:21.1:1:32.2:1:1:0:60:130:1:0:0.2 0/1:74:2:1,1:60,12:72,2:0.027:2,2:28:1:27:1:0.32247:4.84379:60:4:0.0274:0:1 +X 49070759 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50811;SOR=Inf;LSEQ=AAAATCAGGTTGAGATGGAG;RSEQ=CTGAGGCAGAGATGCCGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:126:0:0,0:76,49:125,0:0:2,0:24.9:1:31.8:1:1:0:60:124:0.992:0:0.1 0/1:167:2:1,1:106,59:165,2:0.012:2,2:17.5:1:26.5:1:1:1.78986:60:4:0.012:0:1 +X 49070776 . G A 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.06865;SOR=0;LSEQ=GAGCCTGAGGCAGAGATGCC;RSEQ=CCACACCCAACCAAATATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:2,1:84,61:145,3:0.0203:2,2:37:1:31.3:1:1:1.45:60:6:0.0207:0:1 0/0:212:0:0,0:130,82:212,0:0:2,0:25.2:1:29.6:1:1:0:60:52:1:0:0.6 +X 49070813 . G A 204 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCCCTGGCCTGGGCTGAG;RSEQ=CGAGTCTGGGGACTTGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:87,84:171,0:0:2,0:25.9:1:31.5:1:1:0:59.9:56:1:0:0.1 1/0:265:137:68,69:66,62:128,137:0.517:2,2:26:1:28.8:1:0.80613:1.07986:60:274:0.5229:0:1.2 +X 49070891 . G A 27 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=1.27273;LSEQ=CCCATTATGGATACTGGAAA;RSEQ=TTTAGTTCTTGATTACTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:1:1,0:18,61:79,1:0.0125:2,0:1:0:26:0:0.2375:0:60:2:0.0125:0:1 0/1:126:2:1,1:34,90:124,2:0.0159:2,2:7.5:1:27:1:0.48:2.62:60:4:0.0163:0:3 +X 50350674 . T C 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TACTGGGGTGGCAGCTCCTC;RSEQ=TCCTCCTCCTCTGCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:0,8:1:0,2:26.5:1:30.3:1:1:0:60:16:1:0:1.4 1/1:7:7:7,0:0,0:0,7:1:0,0:20.7:1:28.7:1:1:0:57.9:6:1:0:1.4 +X 50350728 . T TTCC 144 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=8.000;MSILEN=3;SSF=0.4598;SOR=0.46345;LSEQ=TCTTCCTCTTCTTCTTCTTC;RSEQ=TCCTCCTCCTCCTCCTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:26:24:15,9:2,0:2,24:0.9231:0,2:20.7:1:30.6:1:0.52923:0:58.4:23:0.92:0.4231:0.3 1/1:39:33:16,17:5,1:6,33:0.8462:2,2:23:1:28.7:1:0.18974:5.11468:57.9:32:0.8421:0.3846:0.4 +X 50350742 . CCTCCTCCTGTTGCTTC GTTGCTTCTGCTGCTGCTGT 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0;MSILEN=0;SSF=0.51482;SOR=Inf;LSEQ=TTCTTCTTCCTCCTCCTCCT;RSEQ=TGCTGCTGCTGTTGCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:19,12:31,0:0:2,0:24.5:1:31.3:1:1:0:58.3:62:1:0:0.3 0/1:47:2:1,1:23,22:45,2:0.0426:2,2:38.5:1:32.1:1:1:1.04448:60:4:0.0435:0:6 +X 50350758 . C CTGCTGCTGCTGT 165 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=2.000;MSILEN=1;SSF=0.7496;SOR=0.70112;LSEQ=TCCTCCTCCTCCTGTTGCTT;RSEQ=TGCTGCTGCTGTTGCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:36:18,18:3,1:4,36:0.9:2,2:27.5:1:31.2:1:0.60707:2.92445:56.4:72:0.9:0.2:0.2 1/1:51:44:20,24:4,0:4,44:0.8627:0,2:29.1:1:30.4:1:0.10922:0:51.6:43:0.9348:0.1765:0.1 +X 50648296 . A AAAATAAAT 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=41;MSI=12.000;MSILEN=4;SSF=0.06061;SOR=0;LSEQ=AGCGAAACTTCGTCTCAAAT;RSEQ=AAATAAATAAATAAATAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:4,0:2,0:2,4:0.6667:0,0:14.8:1:31.2:1:1:0:53:8:0.6667:0.5:0 0/0:5:0:0,0:3,0:3,0:0:0,0:20.3:1:28.3:1:1:0:60:6:0.6:0:0 +X 50648447 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.50053;SOR=Inf;LSEQ=GTCTCTATACCATGGCTCGT;RSEQ=CAAGGTGGACTGCCCGCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:77,53:130,0:0:2,0:26.3:1:28.8:1:1:0:59.5:260:1:0:0.2 0/1:149:2:1,1:81,66:147,2:0.0134:2,2:30.5:1:31.5:1:1:1.22557:60:4:0.014:0:1.5 +X 50648608 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50673;SOR=Inf;LSEQ=GAAATTAGACATTATCAGAA;RSEQ=TCCACTGAACTTCTGATTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:48,23:71,0:0:2,0:32.2:1:33.4:1:1:0:30.8:142:1:0:0.1 0/1:94:2:1,1:65,27:92,2:0.0213:2,2:36.5:1:31:1:0.50927:2.38216:21:4:0.022:0:1 +X 50648628 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56819;SOR=0.34064;LSEQ=GTCCACTGAACTTCTGATTC;RSEQ=CAAACTTCCCTTCCAGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:2:1,1:57,25:82,2:0.0238:2,2:14.5:1:29:1:0.52582:2.25528:30:4:0.025:0:1 0/0:122:1:1,0:84,37:121,1:0.0082:2,0:14:0:27:0:1:0:60:2:0.0084:0:2 +X 50648864 . T A 39 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.62833;SOR=2.52713;LSEQ=TTTCAGAATACACCATGATG;RSEQ=GAAACATTTCATTCTCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:1:1,0:31,89:120,1:0.0083:2,0:1:0:26:0:0.26446:0:34:2:0.0093:0:1 0/1:145:3:2,1:44,95:139,3:0.0207:2,2:10.3:1:25:1:0.24517:4.27:51.3:6:0.0244:0:1 +X 50648874 . C A 58 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.06298;SOR=Inf;LSEQ=CACCATGATGTGAAACATTT;RSEQ=ATTCTCAAAAAAAAAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:22,78:100,0:0:2,0:17:1:30.3:1:1:0:56.3:9:1:0:0.2 0/1:117:5:0,5:31,80:111,5:0.0427:2,0:30.6:1:25:1:0.3223:0:50:1.5:0.0316:0:2.8 +X 50648931 . A AT 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=1.087;LSEQ=GGTAGTTCTGAACGTTAGAT;RSEQ=TTTTTTTTTCCATGGGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:2:1,1:5,32:37,2:0.0513:2,2:16:0:31.5:1:0.28745:5.93:24:4:0.0556:0:0 0/1:36:2:0,2:1,33:34,2:0.0556:1,0:13.5:1:31:1:1:0:47:4:0.0556:0.0278:0.5 +X 50920174 . T C 60 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.2;SOR=0;LSEQ=GCAGGTGTTCTCCCCATGTG;RSEQ=GGAGACGAGAGATCATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:3,1:0,0:0,4:1:0,2:31.3:1:30.3:1:1:0:37.8:8:1:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 +X 51231291 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19615;SOR=0;LSEQ=AGTTTTTGGTAGTGGTAGGG;RSEQ=TTGGAGGATGGAGGGATTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:2:1,1:11,5:16,2:0.1111:2,2:8.5:1:30:1:1:2.09766:60:4:0.1111:0:1 0/0:22:0:0,0:11,11:22,0:0:2,0:26.4:1:29.7:1:1:0:60:21:1:0:0.2 +X 52862090 . G A 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23682;SOR=0.34894;LSEQ=GAAACTGAAGTCTCTGGCAT;RSEQ=CATTTTCTCAGTCAGCCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:4:2,2:150,135:285,4:0.0138:2,2:20.5:1:30.5:1:1:1.1107:46.3:8:0.0139:0:2.3 0/0:411:2:1,1:210,199:409,2:0.0049:2,2:11:0:29.5:1:1:1.05516:60:4:0.0049:0:1 +X 52862973 . C T 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCAAAAAACCACTCAGTGCC;RSEQ=GACTGAAAAGTCCTCTTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:338:0:0,0:148,190:338,0:0:2,0:26.8:1:30.1:1:1:0:60:55.333:1:0:0.5 0/1:504:28:11,17:195,279:474,28:0.0556:2,2:31.5:1:30.1:1:1:1.08001:60:56:0.0562:0:1.3 +X 52863021 . T C 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.4441;SOR=Inf;LSEQ=ACCCTCCACTTGTCTGTGTA;RSEQ=CTTATACTTCCTGGATGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:143:142:29,113:0,0:0,142:0.993:0,2:22.1:1:31.2:1:1:0:60:70:0.9929:0:1 1/1:179:179:43,136:0,0:0,179:1:0,2:20.6:1:30.6:1:1:0:60:58.667:1:0:1.1 +X 53222043 . A AC 251 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.00056;SOR=0.59688;LSEQ=GGCGGGTAGCAGGGATGGCC;RSEQ=CCCCCCTACCCGCCCACCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:390:290:104,186:46,51:97,290:0.7436:2,2:27.2:1:31.1:1:0.05381:1.611:59.6:47.333:0.7474:0.0385:0.7 1/0:475:301:97,204:70,100:170,301:0.6337:2,2:26.6:1:30.5:1:0.05695:1.47088:59:49.167:0.633:0.0168:0.7 +X 53222050 . T C 98 PASS STATUS=AFDiff;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08377;SOR=1.90972;LSEQ=AGCAGGGATGGCCACCCCCC;RSEQ=ACCCGCCCACCCCCCAAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:11:3,8:103,201:304,11:0.0349:2,2:9:1:25.5:1:0.75618:1.36522:57.3:2.667:0.0294:0:1.9 0/1:371:24:13,11:108,239:347,24:0.0647:2,2:7.1:1:21.5:1:0.02485:2.61:55.8:1.4:0.0424:0:2.3 +X 53222448 . TCCG T 109 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.00476;SOR=10.88424;LSEQ=CTCCCCACCCCGATCCACCT;RSEQ=CCGCCGCCGCCTCTCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:478:1:0,1:183,291:474,1:0.0021:2,0:33:0:33:0:1:0:60:2:0.0021:0:0 0/1:582:13:8,5:249,320:569,13:0.0223:2,2:23.1:1:29.6:1:0.26106:2.05:58.8:26:0.0227:0.0034:0.4 +X 53222840 . C T 148 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TAGGAGGTTGCAGGAACAAG;RSEQ=GGCATTAGAGGCTGCCCTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:425:0:0,0:237,188:425,0:0:2,0:24:1:31.2:1:1:0:60:59.714:1:0:0.1 0/1:467:33:19,14:209,225:434,33:0.0707:2,2:24.1:1:29.4:1:0.36703:1.46:60:66:0.0717:0:1 +X 53223092 . C A 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.11083;SOR=0.18352;LSEQ=TGAAGAACCAGGCCCTATTC;RSEQ=TCCTCCGCCAACCCCAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:5:3,2:63,207:270,5:0.0182:2,2:8:1:26.6:1:0.09134:4.89:60:4:0.0149:0:1.8 0/0:296:1:1,0:68,227:295,1:0.0034:2,0:1:0:27:0:0.23311:0:60:2:0.0034:0:1 +X 53223093 . T C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.24995;SOR=Inf;LSEQ=GAAGAACCAGGCCCTATTCC;RSEQ=CCTCCGCCAACCCCAAACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:262:0:0,0:58,203:261,0:0:2,0:22.6:1:30.2:1:1:0:60:42.5:1:0:0.1 0/1:285:3:1,2:61,220:281,3:0.0105:2,2:30.7:1:29.7:1:0.52377:1.80:60:6:0.0109:0:1 +X 53223249 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49838;SOR=Inf;LSEQ=AAATTGGAGAACAAGGGGCA;RSEQ=GGCCGAGCCTAAACTGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:120,35:155,0:0:2,0:23.3:1:32.7:1:1:0:60:154:1:0:0.1 0/1:155:2:1,1:122,31:153,2:0.0129:2,2:26:1:30:1:0.37134:3.88935:60:4:0.0131:0:1 +X 53223485 . C T 59 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.13326;SOR=Inf;LSEQ=AGAGGCCAGAGCCTGCCTGG;RSEQ=GCGGCCTTGCCAGCTGATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:277:0:0,0:105,172:277,0:0:2,0:23.9:1:30.2:1:1:0:59.9:68.25:1:0:0.1 0/1:347:4:2,2:133,210:343,4:0.0115:2,2:28.8:1:29.5:1:0.644:1.58:60:8:0.0117:0:1 +X 53223548 . G A 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10411;SOR=0;LSEQ=GGCCTCGCCCTCGGGCAGCC;RSEQ=CACAGGCAGTCTCTGCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:3:1,2:99,82:181,3:0.0163:2,2:36:1:30.7:1:0.59291:2.40335:60:6:0.0165:0:1 0/0:206:0:0,0:116,90:206,0:0:2,0:23.6:1:30.2:1:1:0:59.8:67.667:1:0:0.2 +X 53224020 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12223;SOR=Inf;LSEQ=TCCCAAACCAGGAGAACTGA;RSEQ=GCTCAGGGGACAAGCGGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:203:0:0,0:132,70:202,0:0:2,0:25.7:1:32.4:1:1:0:60:66.333:0.995:0:0.1 0/1:201:3:2,1:136,62:198,3:0.0149:2,2:31:1:26.7:1:1:1.09626:60:2:0.0102:0:2 +X 53224036 . G T 48 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1171;SOR=0;LSEQ=CTGAGGCTCAGGGGACAAGC;RSEQ=GTCTGCTCATGGCCACCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:3:1,2:170,78:248,3:0.012:2,2:16.3:1:30.3:1:0.23905:4.33071:60:6:0.012:0:1 0/0:261:0:0,0:175,86:261,0:0:2,0:22.8:1:29.1:1:1:0:60:51.2:1:0:0.1 +X 53224366 . C T 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00839;SOR=0;LSEQ=ATGAGCCATCTCACAGAAGC;RSEQ=AGGGCAGGCGTTAAGAGACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:6:1,5:214,142:356,6:0.0166:2,2:14.8:1:27.2:1:0.04251:7.49592:60:12:0.0169:0:1.2 0/0:438:0:0,0:270,168:438,0:0:2,0:24.8:1:30.4:1:1:0:60:61.571:1:0:0.1 +X 53224479 . C T 70 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08711;SOR=0.29681;LSEQ=GCCTTCTCCCTCCAGGAGTG;RSEQ=GCTGTCAGTACCTGTAGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:595:6:3,3:325,264:589,6:0.0101:2,2:14.7:1:27.3:1:1:1.23062:60:5:0.0087:0:1.3 0/0:996:3:0,3:521,470:991,3:0.003:2,0:10:1:24:1:0.10739:0:60:2:0.002:0:1 +X 53225026 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49899;SOR=Inf;LSEQ=AACCCATCCCAGCAACCCAG;RSEQ=ACATCCCAGTGTATATGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:115,24:139,0:0:2,0:24:1:31.9:1:1:0:59.8:22.167:1:0:0.1 0/1:150:2:1,1:123,25:148,2:0.0133:2,2:14.5:1:26:1:0.31758:4.84411:60:4:0.0135:0:1 +X 53225058 . C T 52 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.37953;SOR=3.4802;LSEQ=TATATGCCATCTCTTCCCAG;RSEQ=TGGACTGAAGGCCTGGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:266:1:0,1:181,84:265,1:0.0038:2,0:1:0:29:0:0.31955:0:60:2:0.0038:0:1 0/1:308:4:1,3:214,90:304,4:0.013:2,2:15:1:26.3:1:0.08382:7.08283:60:8:0.0131:0:1 +X 53225501 . T C 86 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GCCTGCTAGCAATGCCTACA;RSEQ=ATACAACCTGTATTGTGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1:0,0:17.8:1:33.3:1:1:0:60:12:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 53225751 . A G 173 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05419;SOR=0;LSEQ=CAACAAAAGAGGGGAGAGTC;RSEQ=ATACAGTAACACAGGAGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:52:52:50,2:0,0:0,52:1:0,1:24.8:1:30.5:1:1:0:59.3:104:1:0:1 1/1:50:46:46,0:3,0:3,46:0.92:0,1:24.3:1:30.2:1:1:0:60:92:0.9388:0:1 +X 53225847 . G T 47 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.65304;SOR=2.73886;LSEQ=TTTGGAATAGGGCAGGGAAG;RSEQ=GAAGCAGCAGCTGGACCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:241:1:0,1:170,70:240,1:0.0041:2,0:46:0:14:0:0.29461:0:60:0:0:0:4 0/1:354:4:1,3:228,122:350,4:0.0113:2,2:23.8:1:23.5:1:0.12818:5.57856:60:3:0.0087:0:1 +X 53225904 . C T 76 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.53248;SOR=1.70725;LSEQ=GGTGGGCTTTCTCCTCCCAG;RSEQ=GTTCAGCAATGGTCAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:481:3:0,3:273,205:478,3:0.0062:2,0:2.3:1:23:1:0.0802:0:60:2:0.0042:0:1.3 0/1:660:7:1,6:349,302:651,7:0.0106:2,2:7.6:1:27.3:1:0.05496:6.91677:60:14:0.0107:0:1 +X 53226091 . G A 69 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30441;SOR=2.50056;LSEQ=TTCCACCTGCCGCTGGAGCT;RSEQ=CTGGGCCTCAGGCACCTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:500:2:0,2:226,272:498,2:0.004:2,0:20.5:1:32.5:1:0.50362:0:60:4:0.004:0:1 0/1:603:6:5,1:279,318:597,6:0.01:2,2:12:1:26.7:1:0.10484:5.68:59.2:12:0.0101:0:1.2 +X 53226311 . T C 211 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=0;LSEQ=ATGGAACCTTGTCCCACCTA;RSEQ=CTTCTTACCCTCCAAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:104:104:17,87:0,0:0,104:1:0,2:20.8:1:31.5:1:1:0:60:103:1:0:1 1/1:107:93:13,80:4,9:13,93:0.8692:2,2:21.5:1:30.5:1:0.21702:2.70233:60:186:0.8692:0:1.1 +X 53227343 . A G 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCAGGGATCAGGTCTATAC;RSEQ=TCTTTGTCCTGTTCTTACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:2,5:0,0:0,7:1:0,2:20.7:1:31.7:1:1:0:60:14:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:25:1:28.5:1:1:0:60:4:1:0:1 +X 53227592 . A G 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4986;SOR=0;LSEQ=TTCTGCCAAATGGTATTCAC;RSEQ=GTCTACCCCTTGCAGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:149,28:177,2:0.0112:2,2:25.5:1:29.5:1:0.29854:5.24651:60:4:0.0113:0:1 0/0:179:0:0,0:147,31:178,0:0:2,0:20:1:29.8:1:1:0:60:177:0.9944:0:0 +X 53228148 . C A 244 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.07725;LSEQ=CCCCACTTCCTCCAGAAAGG;RSEQ=CCATGCTCACCGCAGGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:320:318:165,153:0,0:0,318:0.9938:0,2:24.7:1:30:1:1:0:59.9:62.6:1:0:1.1 1/1:411:380:214,166:15,16:31,380:0.9246:2,2:22.4:1:28.5:1:0.45356:1.37:59.9:62.333:0.9235:0:1.2 +X 53230934 . C A 42 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.32088;SOR=0.25251;LSEQ=GCCCAGCAGGCAACTGTGGG;RSEQ=AGGTTCAAGGTTGAGTGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:260:3:3,0:122,135:257,3:0.0115:2,0:6.3:1:27:1:0.10973:0:60:6:0.0118:0:1 0/0:341:1:1,0:155,185:340,1:0.0029:2,0:1:0:25:0:0.45748:0:60:2:0.003:0:1 +X 53231196 . T C 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.18341;SOR=0;LSEQ=TGGCTGTTGAGATAGAGATT;RSEQ=TCCTGTATACAGACCTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:47,150:197,2:0.0101:2,2:33:1:32.5:1:0.42516:3.17:60:4:0.0101:0:1 0/0:265:0:0,0:66,198:264,0:0:2,0:22.1:1:29.5:1:1:0:60:43:0.9961:0:0.1 +X 53239607 . G T 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0461;SOR=Inf;LSEQ=GGTACTCACTGGCACACCAT;RSEQ=GGACATGAGGGTGTTGGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:454:0:0,0:279,175:454,0:0:2,0:25.9:1:31.6:1:1:0:59.9:40.273:1:0:0.1 0/1:677:7:2,5:384,286:670,7:0.0103:2,2:13.9:1:25.1:1:0.14596:3.35082:60:6:0.009:0:1 +X 53241443 . T C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTGACTTTAATATGCTATCC;RSEQ=GTGTTCTTCTGCCACCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:36.5:1:30:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 53243777 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.20059;SOR=0;LSEQ=CACAGAGACCCAAAACCTAA;RSEQ=ACTATGGCTGAGCTAAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:123,28:151,2:0.0131:2,2:22:1:27:1:0.34417:4.33397:60:4:0.0132:0:1 0/0:188:0:0,0:166,22:188,0:0:2,0:21.4:1:31.2:1:1:0:60:93:1:0:0.1 +X 53244906 . G T 48 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04948;SOR=0;LSEQ=GGTTAATGCGAACTGGTCCA;RSEQ=TGCCATGCAGGGGAATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:4:2,2:229,72:301,4:0.0131:2,2:10.5:1:24:1:0.24858:3.16571:60:3:0.0099:0:2.5 0/0:340:0:0,0:243,97:340,0:0:2,0:21.2:1:31:1:1:0:59.9:55.667:1:0:0.1 +X 53244924 . C T 73 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13069;SOR=5.22114;LSEQ=CAGTGCCATGCAGGGGAATG;RSEQ=TTATTGAAGGGACAAGAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:1:0,1:292,135:427,1:0.0023:2,0:1:0:26:0:0.31776:0:60:2:0.0023:0:1 0/1:496:6:2,4:321,169:490,6:0.0121:2,2:18.7:1:28.3:1:0.18977:3.78755:60:12:0.0122:0:1.3 +X 53246252 . C T 28 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50866;SOR=Inf;LSEQ=GGATAATGGAACAGGGAACA;RSEQ=AGCCTTAGCCAGAAGGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:148:0:0,0:126,22:148,0:0:2,0:22.5:1:32:1:1:0:59.9:296:1:0:0.1 0/1:197:2:1,1:158,37:195,2:0.0102:2,2:6:0:28.5:1:0.34937:4.22702:60:4:0.0103:0:1 +X 53246260 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18015;SOR=0;LSEQ=GAACAGGGAACACAGCCTTA;RSEQ=CCAGAAGGAAGGAGAGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:2:1,1:130,30:160,2:0.0123:2,2:25:1:30.5:1:0.34706:4.27924:60:4:0.0126:0:1.5 0/0:219:0:0,0:170,49:219,0:0:2,0:22.6:1:31.2:1:1:0:60:42.8:1:0:0.2 +X 53246268 . G T 47 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.14052;SOR=Inf;LSEQ=AACACAGCCTTAGCCAGAAG;RSEQ=AAGGAGAGGACTCCCTCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:144,47:191,0:0:2,0:23:1:31.1:1:1:0:59.9:94.5:1:0:0.1 0/1:259:4:1,3:192,63:255,4:0.0154:2,2:11.3:1:23.5:1:0.05215:9.04679:60:8:0.0157:0:1 +X 53246599 . C G 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00013;SOR=0;LSEQ=ACAGCCCCTGTTCCACTGGT;RSEQ=TTTAGCACTGACACCAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:13:0,13:3,31:34,13:0.2766:2,1:16.5:1:32.5:1:0.55023:0:60:26:0.2826:0:1 0/0:41:0:0,0:0,41:41,0:0:1,0:22.1:1:32.4:1:1:0:60:82:1:0:0 +X 53247209 . G A 31 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.59591;SOR=0.42287;LSEQ=TATTTATATGTGAGGGAGTA;RSEQ=GCCTGTAGAAAGGGCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:2:1,1:31,131:162,2:0.0122:2,2:5:1:31:1:0.35313:4.18:60:4:0.0123:0:1 0/0:193:1:1,0:42,150:192,1:0.0052:2,0:1:0:24:0:0.2228:0:60:2:0.0052:0:1 +X 53247366 . TA T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.23773;SOR=Inf;LSEQ=GTGCCCCTTCCATTGCAGCC;RSEQ=AAGATCTAATATCCAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:161,34:195,0:0:2,0:23.6:1:28.6:1:1:0:59.8:194:0.9949:0:0.1 0/1:187:2:1,1:151,34:185,2:0.0107:2,2:9.5:1:26:1:0.34012:4.39175:60:4:0.0108:0.0053:1 +X 53247651 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23834;SOR=Inf;LSEQ=TATCTTTGGGTCCAGTCTTA;RSEQ=GGGAGAACAGAGGAATACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:14,127:141,0:0:2,0:22.8:1:31.7:1:1:0:60:140:1:0:0.1 0/1:135:2:1,1:18,115:133,2:0.0148:2,2:10.5:1:28.5:1:0.26258:6.25:60:4:0.015:0:1.5 +X 53249916 . G T 43 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.10231;SOR=0;LSEQ=TCACAGAAGAGAGAATAAAG;RSEQ=CCTAGCTAGGTAAAGTACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:3:1,2:174,34:208,3:0.0142:2,2:7.7:1:27.7:1:0.07606:10.06025:60:6:0.0147:0:1 0/0:239:0:0,0:196,43:239,0:0:2,0:22.6:1:30.3:1:1:0:60:38.833:1:0:0.1 +X 53254122 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17987;SOR=0;LSEQ=GAGGCTTGGACCGCCCTTAA;RSEQ=GACTCATGGCGCCGCCGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:0,2:24,124:148,2:0.0133:2,0:12:1:26:1:1:0:60:4:0.0133:0:1 0/0:203:0:0,0:48,155:203,0:0:2,0:20.9:1:30.4:1:1:0:60:66.667:1:0:0.1 +X 54976727 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.23404;SOR=Inf;LSEQ=GAGCCATAGGTTAAACTCCC;RSEQ=CAGCTCCCTTACATGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:8,16:24,0:0:2,0:23.3:1:31.1:1:1:0:60:48:1:0:0 0/1:23:2:1,1:7,14:21,2:0.087:2,2:17.5:1:29:1:1:1.94:48:4:0.1053:0:1 +X 57960211 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.1489;SOR=0;LSEQ=TACTAAAGGGGAAGGGGAGG;RSEQ=CAAAAAATAAACTTGTGTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:2:1,1:30,15:45,2:0.0426:2,2:9:1:30:1:1:1.96856:60:4:0.0426:0:1 0/0:74:0:0,0:49,25:74,0:0:2,0:26.9:1:28.3:1:1:0:60:73:1:0:0.1 +X 57960284 . G C 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51113;SOR=Inf;LSEQ=GTTAGTAGCCACTGAGGTAC;RSEQ=CAATTCATTTCTGCAATTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:39,39:78,0:0:2,0:25:1:30.6:1:1:0:60:38:1:0:0.1 0/1:109:2:1,1:55,52:107,2:0.0183:2,2:14.5:1:26.5:1:1:1.05717:60:4:0.0185:0:1.5 +X 57960356 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51129;SOR=Inf;LSEQ=TAGACATCTTTTTCTCGGTT;RSEQ=ACGCCAGGTCTTGCAAGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:83:0:0,0:46,37:83,0:0:2,0:25.6:1:32.1:1:1:0:60:82:1:0:0.1 0/1:116:2:1,1:66,48:114,2:0.0172:2,2:33:1:27.5:1:1:1.37115:60:4:0.0174:0:2 +X 57960389 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52067;SOR=Inf;LSEQ=GCAAGTATCCCAAGGCCTTG;RSEQ=TTAGGATCACTACCGTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:57,48:105,0:0:2,0:25.5:1:32.6:1:1:0:60:104:0.9905:0:0.2 0/1:163:2:1,1:87,74:161,2:0.0123:2,2:24.5:1:30:0:1:1.1745:60:4:0.0124:0:2 +X 57960431 . G A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13618;SOR=0;LSEQ=CCTTAGAGCAGCTGGCCAAG;RSEQ=TGGGTACCTGGTCCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:2:1,1:41,54:95,2:0.0206:2,2:26:1:29.5:1:1:1.31:60:4:0.0208:0:1 0/0:165:0:0,0:74,91:165,0:0:2,0:25.7:1:30.5:1:1:0:59.9:54:1:0:0.1 +X 57960449 . A G 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.53114;SOR=Inf;LSEQ=AGGTGGGTACCTGGTCCCTC;RSEQ=GGGCCAAGAACTGAGAACGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:82:0:0,0:33,49:82,0:0:2,0:24.2:1:31.4:1:1:0:60:164:1:0:0.2 0/1:139:2:1,1:57,80:137,2:0.0144:2,2:26.5:1:27.5:1:1:1.40:60:4:0.0148:0:1.5 +X 57960605 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5068;SOR=Inf;LSEQ=CAATCCCCTCATCCTCCTCA;RSEQ=CTTCCGTTTCCCCTGGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:93:0:0,0:61,32:93,0:0:2,0:23.1:1:31:1:1:0:60:92:1:0:0.2 0/1:122:2:1,1:70,50:120,2:0.0164:2,2:36.5:1:27.5:1:1:1.39605:60:4:0.0165:0:2.5 +X 57960627 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.18164;SOR=0;LSEQ=TTCCGTTTCCCCTGGAGCAT;RSEQ=TCCCTCCAGAACCTCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:2:0,2:60,40:100,2:0.0194:2,0:14:1:29.5:1:0.16715:0:60:4:0.02:0:1 0/0:138:0:0,0:74,63:137,0:0:2,0:28.2:1:30.9:1:1:0:60:67.5:1:0:0.2 +X 57960679 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.5118;SOR=Inf;LSEQ=TCTGGAGCCTCTTCTTGGGA;RSEQ=CAGCTTTCTGGAGAAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:43,60:103,0:0:2,0:25.5:1:32.5:1:1:0:60:50.5:1:0:0.1 0/1:144:2:1,1:68,74:142,2:0.0139:2,2:9.5:1:27:1:1:1.09:60:4:0.0142:0:1.5 +X 57960680 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51282;SOR=Inf;LSEQ=CTGGAGCCTCTTCTTGGGAG;RSEQ=AGCTTTCTGGAGAAATATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:42,59:101,0:0:2,0:25.8:1:32.5:1:1:0:60:202:1:0:0.1 0/1:143:2:1,1:67,74:141,2:0.014:2,2:28:0:30.5:1:1:1.10:60:4:0.0143:0:1.5 +X 57960717 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20292;SOR=0;LSEQ=ATGGGCAGCGCAGTTGTGTT;RSEQ=TTGCTGGTGGATGGAGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:19,50:69,2:0.0282:2,2:40.5:1:30:1:0.48692:2.59:60:4:0.0282:0:1 0/0:86:0:0,0:29,57:86,0:0:2,0:25.3:1:31.1:1:1:0:60:42:1:0:0.2 +X 57961120 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.49901;SOR=Inf;LSEQ=CCAAGCTCTCGAGTGGCCCC;RSEQ=AGATTCCGTCTCATCCCCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:46:0:0,0:16,30:46,0:0:2,0:27.4:1:31:1:1:0:60:22:1:0:0.3 0/1:55:2:1,1:20,33:53,2:0.0364:2,2:34.5:1:28:1:1:1.63:60:4:0.0385:0:1 +X 58561396 . T G 33 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ATGCTTCCGTTTGGTTTTTA;RSEQ=ATGAAGTTATTTCCTTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:13.5:1:33:1:1:0:25:4:1:0:3.5 0/0:1:0:0,0:0,1:1,0:0:0,0:1:0:24:0:1:0:27:2:1:0:3 +X 58561419 . C A 49 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAGTTATTTCCTTTACTAC;RSEQ=GTAGGCCTCAAAGCAGTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:28.7:1:31:1:1:0:24.7:6:1:0:3.7 1/1:2:2:1,1:0,0:0,2:1:0,2:23.5:1:30.5:1:1:0:26:4:1:0:3 +X 58561423 . G C 33 d5;v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=TTATTTCCTTTACTACCGTA;RSEQ=GCCTCAAAGCAGTCCAAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:1,1:0,0:0,2:0.6667:0,2:25:0:33:1:1:0:25:4:1:0:3.5 0/0:2:0:0,0:1,1:2,0:0:2,0:27.5:1:32:1:1:0:26:4:1:0:3 +X 58561448 . T A 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAGCAGTCCAAATCTCCA;RSEQ=TTGCAGATTCTACAATAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15:0:32:0:1:0:26:4:1:0:3 +X 58561450 . T C 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCAGTCCAAATCTCCATT;RSEQ=GCAGATTCTACAATAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:13:0:32:1:1:0:26:4:1:0:3 +X 61720977 . C A 91 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATGTCCACTTGCAGATTCT;RSEQ=GAAAAAGAGTGTTTCATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:43:1:30.3:1:1:0:20.7:6:1:0:5 1/1:8:8:3,5:0,0:0,8:1:0,2:44.8:1:30.4:1:1:0:20.4:16:1:0:5.3 +X 61720987 . T G 94 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGCAGATTCTCGAAAAAGAG;RSEQ=GTTTCATAGCTGCTCTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:35:0:31.3:1:1:0:20.7:6:1:0:5 1/1:8:8:3,5:0,0:0,8:1:0,2:35.5:1:31.5:1:1:0:20.4:16:1:0:5.3 +X 61720994 . T G 95 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTCGAAAAAGAGTGTTTCA;RSEQ=AGCTGCTCTTTCAAAAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:28:0:32.3:1:1:0:20.7:6:1:0:5 1/1:8:8:3,5:0,0:0,8:1:0,2:28.5:1:31.9:1:1:0:20.4:16:1:0:5.3 +X 61721004 . T G 94 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAGTGTTTCATAGCTGCTCT;RSEQ=TCAAAAGGAAAGTTCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:18:0:30.7:1:1:0:20.7:6:1:0:5 1/1:8:8:3,5:0,0:0,8:1:0,2:18.5:1:31.5:1:1:0:20.4:16:1:0:5.3 +X 61721009 . A G 93 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTCATAGCTGCTCTTTCAA;RSEQ=AGGAAAGTTCAACTCTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:13:0:31:1:1:0:20.7:6:1:0:5 1/1:8:8:3,5:0,0:0,8:1:0,2:13.5:1:31:1:1:0:20.4:16:1:0:5.3 +X 63404910 . G T 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.08245;SOR=Inf;LSEQ=CTCCACCCACCACCTCCTTG;RSEQ=TTTCTCAATTTCTCTCCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:143,14:157,0:0:2,0:23.9:1:31.4:1:1:0:59.8:38.25:1:0:0.1 0/1:122:3:1,2:103,16:119,3:0.0246:2,2:11.3:1:22.7:1:0.05666:12.41384:60:2:0.0168:0:1.3 +X 63404927 . C A 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.09434;SOR=Inf;LSEQ=TTGGTTTCTCAATTTCTCTC;RSEQ=AAGGGCAATCCCAACAACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:171,42:213,0:0:2,0:23.5:1:31.2:1:1:0:59.9:41.6:1:0:0.1 0/1:179:3:2,1:136,40:176,3:0.0168:2,2:20.3:1:29:1:0.54408:1.69429:60:6:0.017:0:1 +X 63405225 . C G 30 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.15573;SOR=Inf;LSEQ=TGGGAGAGAAATAACTCTTA;RSEQ=ACCTGGGGTGATGATGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:2,77:79,0:0:1,0:24.9:1:32.5:1:1:0:59.6:78:1:0:0.1 0/1:52:2:0,2:1,49:50,2:0.0385:1,0:5:1:30.5:1:1:0:60:4:0.0385:0:1 +X 63409673 . A AC 65 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.000;MSILEN=1;SSF=0.4081;SOR=0.29074;LSEQ=GGTTTTCAAGTTAAACAACA;RSEQ=CCCCCACCCCCCCACCCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:5:5,0:176,56:232,5:0.0211:2,0:25.4:1:28:1:0.59441:0:54.8:4:0.0175:0:1.8 0/0:161:1:1,0:119,41:160,1:0.0062:2,0:14:0:30:0:1:0:50:2:0.0064:0:0 +X 63409681 . C A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.07186;SOR=Inf;LSEQ=AGTTAAACAACAACCCCCAC;RSEQ=CCCCCACCCTTCTGCCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:0:0,0:188,79:267,0:0:2,0:11.5:1:28.1:1:1:0:55.6:16.8:1:0:1.1 0/1:191:3:2,1:130,57:187,3:0.0157:2,2:11.7:1:24:1:1:1.13953:60:2:0.0114:0:2 +X 63409685 . C T 37 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0.31915;SOR=4.00839;LSEQ=AAACAACAACCCCCACCCCC;RSEQ=CACCCTTCTGCCCAACCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:281:1:0,1:193,87:280,1:0.0036:2,0:1:0:25:0:0.31317:0:60:2:0.0036:0:1 0/1:212:3:1,2:140,69:209,3:0.0142:2,2:20.3:1:23.7:1:0.26031:4.02897:60:2:0.0098:0:1 +X 63409699 . A C 63 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08558;SOR=0.42597;LSEQ=ACCCCCCCACCCTTCTGCCC;RSEQ=ACCCCTGATCCCCATTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:17:17,0:115,132:247,17:0.0644:2,1:16.1:1:15.5:1:1e-05:0:50.5:0.214:0.0127:0:4.9 0/1:211:6:6,0:92,113:205,6:0.0284:2,0:12.2:1:24.5:1:0.00923:0:47.3:2:0.0196:0:5.3 +X 63410110 . T C 186 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGGTGTGAGGGACGAGCTAG;RSEQ=TGAGGCCCAGATTCCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:781:0:0,0:378,402:780,0:0:2,0:24.7:1:30.1:1:1:0:59.9:194:0.9987:0:0.1 0/1:704:64:28,36:302,337:639,64:0.0909:2,2:25.7:1:31:1:0.60245:1.15195:58.9:31:0.0893:0:1.2 +X 63412291 . C G 201 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTACCTCTCCTGCTACTAC;RSEQ=TTCTCCCCTGTTTCTGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1212:0:0,0:600,611:1211,0:0:2,0:24.1:1:32.3:1:1:0:60:79.733:0.9992:0:0.1 0/1:954:98:49,49:427,429:856,98:0.1027:2,2:25:1:30.5:1:1:1.00:60:97:0.1025:0:1.2 +X 63412690 . A C 177 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TTTGGCTTGGGCATAGAGGG;RSEQ=AACTTCTCAGCCACAGCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:583:0:0,0:298,284:582,0:0:2,0:26.3:1:30.5:1:1:0:60:57.2:1:0:0.1 0/1:480:47:26,21:226,206:432,47:0.0979:2,2:26.7:1:32:1:0.75936:1.13:59.9:94:0.0983:0:1.3 +X 63415639 . A T 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07302;SOR=Inf;LSEQ=ACAGGTCCCTGGTTCCAAAA;RSEQ=GGTTGGGAACCGCTGCCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:298:0:0,0:220,78:298,0:0:2,0:23.9:1:30.3:1:1:0:59.9:48.667:1:0:0.2 0/1:215:3:0,3:156,56:212,3:0.014:2,0:14.7:1:23.3:1:0.0199:0:60:2:0.0094:0:1.3 +X 63415940 . C T 120 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.00136;SOR=0;LSEQ=TGCTTTCCAGAGCCTTGACG;RSEQ=CCCAGTTAGAAGACAGTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:16:0,16:1,63:64,16:0.2:1,1:27.7:1:30.1:1:1:0:60:15:0.1899:0:1.3 0/0:38:0:0,0:0,37:37,0:0:1,0:22.1:1:31.1:1:1:0:59:74:1:0:0.1 +X 63419338 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.10606;SOR=Inf;LSEQ=GTGGCCTAACCTCTCTGACA;RSEQ=TCAAATGCCTTATCTGTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:59:0:0,0:58,1:59,0:0:1,0:22.9:1:32.6:1:1:0:60:118:1:0:0.1 0/1:29:2:1,1:26,1:27,2:0.069:1,2:33:1:29.5:1:0.13547:18.72551:60:4:0.069:0:1 +X 63425821 . G A 166 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GGTGCGGAACCACTGGCTGG;RSEQ=GCTCCCCACTCCCGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:43:0,43:5,126:131,43:0.2457:1,1:25.6:1:30.7:1:0.33471:0:60:13.333:0.2395:0:1.2 0/0:149:0:0,0:5,142:147,0:0:1,0:23.7:1:30.6:1:1:0:60:146:0.9932:0:0.1 +X 65042284 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50723;SOR=Inf;LSEQ=TCCTGCGCCACACCCCAGCC;RSEQ=CCACGCTGCCTCCGCCTCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:65:0:0,0:38,27:65,0:0:2,0:27.7:1:31:1:1:0:60:64:1:0:0.2 0/1:87:2:1,1:45,40:85,2:0.023:2,2:21:1:27.5:1:1:1.12347:60:4:0.0244:0:1 +X 65042289 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50953;SOR=Inf;LSEQ=CGCCACACCCCAGCCGCCAC;RSEQ=CTGCCTCCGCCTCCGGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:36,27:63,0:0:2,0:29.6:1:30.9:1:1:0:60:30.5:1:0:0.2 0/1:87:2:1,1:44,41:85,2:0.023:2,2:27:0:31:0:1:1.07227:60:4:0.0238:0:1.5 +X 65042321 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.23946;SOR=Inf;LSEQ=TCCGGTGAGCTGACTTGTCT;RSEQ=CCAAGAGAACACTTATATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:60:0:0,0:28,32:60,0:0:2,0:23.4:1:30.8:1:1:0:59.5:14:1:0:0.2 0/1:58:2:1,1:22,34:56,2:0.0345:2,2:36:1:27:1:1:1.53:60:4:0.0357:0:1 +X 66764783 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.10218;SOR=Inf;LSEQ=GCAGGGCAGATCTTGTCCAC;RSEQ=GTGTGTCTTCTTCTGCACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:49,1:50,0:0:1,0:26.3:1:31.5:1:1:0:60:49:1:0:0.1 0/1:24:2:1,1:21,1:22,2:0.0833:1,2:42:0:31.5:1:0.16304:15.19615:60:4:0.087:0:1.5 +X 66764892 . G T 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.27411;SOR=0;LSEQ=CAGGTGGGCAGCTAGCTGCA;RSEQ=CGACTACCGCATCATCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:3:2,1:251,28:279,3:0.0106:2,2:23:1:32.3:1:0.27876:4.4421:60:6:0.0109:0:1 0/0:194:0:0,0:169,25:194,0:0:2,0:22.5:1:31.6:1:1:0:60:96:1:0:0.1 +X 66765158 . T A 88 p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.000;MSILEN=3;SSF=1;SOR=0.85126;LSEQ=CGGCGCCAGTTTGCTGCTGC;RSEQ=GCAGCAGCAGCAGCAGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:7:6,1:145,200:345,7:0.0198:2,2:4.4:1:31.6:1:0.0453:8.23:35.6:14:0.0201:0:2 0/1:237:4:4,0:91,141:232,4:0.0169:2,0:5.5:1:29.8:1:0.02527:0:30.5:8:0.0172:0:2 +X 66765242 . GGCA G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.42677;SOR=1.30304;LSEQ=GCAGCAAGAGACTAGCCCCA;RSEQ=GCAGCAGCAGCAGCAGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:591:20:15,5:322,244:566,20:0.0338:2,2:22.8:1:31.8:1:0.16574:2.27:57.8:19:0.0332:0.0102:0.5 0/1:481:21:13,8:252,206:458,21:0.0437:2,2:23.1:1:31.6:1:0.65535:1.33:59.4:42:0.0448:0.0083:0.4 +X 66765627 . G A 259 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=9e-05;SOR=0.66763;LSEQ=AGCAGCGGGAGAGCGAGGGA;RSEQ=GCCTCGGGGGCTCCCACTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:936:338:179,159:303,292:595,338:0.3611:2,2:24.1:1:30.9:1:0.5857:1.08:59.9:36.556:0.3568:0:1.1 0/1:836:229:111,118:318,289:607,229:0.2739:2,2:22.2:1:29.6:1:0.31456:1.16951:59.9:75.333:0.2729:0:1.2 +X 66766125 . G A 37 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.08367;SOR=Inf;LSEQ=GGACCGCCGCCCCCTCCGCC;RSEQ=CCTCCCCATCCCCACGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:310:0:0,0:140,170:310,0:0:2,0:25.4:1:30.9:1:1:0:59.9:50.667:1:0:0.2 0/1:242:3:1,2:107,132:239,3:0.0124:2,2:28.3:1:23.7:1:1:1.61811:60:2:0.0084:0:2.7 +X 66766220 . T C 41 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.32365;SOR=3.88343;LSEQ=GCAGTGCCGCTATGGGGACC;RSEQ=GGCGAGCCTGCATGGCGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:381:1:1,0:193,187:380,1:0.0026:2,0:12:0:12:0:1:0:60:0:0:0:1 0/1:296:3:1,2:150,143:293,3:0.0101:2,2:26.7:1:26:1:0.61621:2.09282:60:6:0.0103:0:1 +X 66766359 . C T 145 MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.000;MSILEN=3;SSF=0;SOR=0.08916;LSEQ=GGTGGTGGTGGGGGTGGTGG;RSEQ=GGCGGCGGCGGCGGCGGCGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:31:5,26:14,54:68,31:0.301:2,2:10.4:1:29.3:1:0.78454:1.34423:59.7:6.75:0.2903:0:1.5 0/1:82:3:1,2:25,48:73,3:0.0366:2,2:20:1:19.3:1:1:1.04111:60:0.5:0.0141:0:2 +X 66766638 . G A 65 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.0095;SOR=Inf;LSEQ=TCCAGAAATGTCGCCTTTCG;RSEQ=CCCAGGGCAGAGTCACTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:532:0:0,0:178,354:532,0:0:2,0:24.2:1:31.6:1:1:0:60:43.333:1:0:0.1 0/1:456:6:5,1:160,290:450,6:0.0132:2,2:5.5:1:25.5:1:0.02521:9.02:60:12:0.0133:0:1.5 +X 66766692 . G A 27 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5274;SOR=0;LSEQ=CTAGCGGCTCCTACCTGCGC;RSEQ=AACACTCAGATTGCCCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:1,1:7,166:173,2:0.0114:1,2:6.5:1:27.5:1:0.08959:22.25:60:4:0.0119:0:1 0/0:107:0:0,0:10,97:107,0:0:2,0:25.3:1:30.9:1:1:0:60:106:1:0:0.1 +X 66789057 . G T 101 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=1;SSF=0.00516;SOR=0;LSEQ=GTGGGGGATTTTGTGTGTGG;RSEQ=GGGGGGTTGGGGGTTGAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:0,15:1,23:24,15:0.3846:1,1:23.9:1:26.1:1:1:0:58.4:2.75:0.3235:0:1.4 0/0:14:0:0,0:2,12:14,0:0:2,0:17.6:1:29.5:1:1:0:51.7:28:1:0:2.1 +X 66863453 . T G 138 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTTGTTTGTACAGGCAAT;RSEQ=TAGGCAGTGAAGGTGGTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:20:2,18:0,0:0,20:1:0,2:29.4:1:32:1:1:0:58.7:40:1:0:1 1/1:2:2:0,2:0,0:0,2:1:0,0:17:1:34:0:1:0:60:4:1:0:1 +X 66906007 . T C 61 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.20704;SOR=0.23698;LSEQ=TCTTCCTCCTCCTTCCTCTC;RSEQ=CCCCCTTCTCCCTCATTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:4:1,3:68,208:276,4:0.0141:2,2:28.3:1:30.8:1:1:1.02:60:8:0.0145:0:1 0/0:296:1:1,0:93,201:294,1:0.0034:2,0:49:0:29:0:0.31864:0:60:2:0.0035:0:1 +X 66909171 . C G 111 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50476;SOR=Inf;LSEQ=AGTAGACTAGACAGATTATT;RSEQ=AGAGAGTGGAGGGCAGAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:11,0:8,0:8,11:0.5789:0,0:24.9:1:32.1:1:1:0:60:22:0.6111:0:1 1/1:2:2:2,0:0,0:0,2:1:0,0:44.5:1:27.5:1:1:0:60:4:1:0:1.5 +X 66909568 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0133;SOR=Inf;LSEQ=ACATATTGTTAATTGCTTGA;RSEQ=GAATTTAAATCCCTTGACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:104:0:0,0:3,101:104,0:0:1,0:24.6:1:30.4:1:1:0:60:103:1:0:0.1 0/1:55:4:0,4:3,48:51,4:0.0727:2,0:12.5:1:30.8:1:1:0:60:8:0.0727:0:1.5 +X 66914801 . T C 121 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27431;SOR=Inf;LSEQ=AGAAGTAATAGTGGTTACCA;RSEQ=TCATGTAGTTGTGAGTATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:13:0,13:0,7:7,13:0.65:0,1:22:1:32.7:1:1:0:60:26:0.65:0:1 1/1:5:5:1,4:0,0:0,5:1:0,2:10.6:1:32.2:1:1:0:60:10:1:0:1 +X 66931037 . A T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01587;SOR=Inf;LSEQ=AGAGTTTTCCTCTGCAAGCT;RSEQ=TGAAAAATTTGGGTTTAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:31,0:31,0:0:1,0:25.5:1:28:1:1:0:59.2:62:1:0:0 0/1:5:2:2,0:3,0:3,2:0.4:0,0:40.5:1:31:1:1:0:60:4:0.4:0:1 +X 66931567 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.15444;SOR=Inf;LSEQ=GTGGGAGCATGAGATAAGGG;RSEQ=GATCATATTTAGTGAACGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:0:0,0:40,194:234,0:0:2,0:21.7:1:31:1:1:0:60:45.8:1:0:0.1 0/1:152:2:1,1:27,123:150,2:0.0132:2,2:19.5:1:28:1:0.33548:4.49:60:4:0.0133:0:1 +X 66937278 . C T 56 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.72849;SOR=1.49886;LSEQ=TCAGACTTAGCTCAACCCGT;RSEQ=AGTACCCAGACTGACCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:380:3:0,3:268,109:377,3:0.0079:2,0:1:0:24:1:0.02512:0:60:6:0.0081:0:1 0/1:424:5:1,4:269,150:419,5:0.0118:2,2:8.8:1:24.4:1:0.06061:7.14079:60:10:0.012:0:1 +X 66937538 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.50699;SOR=0;LSEQ=TGGTTGGTGGTGATGGTGAT;RSEQ=GGGTGACAGTGAAGCTTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:2:1,1:24,170:194,2:0.0102:2,2:15:1:28:1:0.2394:6.96:60:4:0.0104:0:1 0/0:151:0:0,0:21,130:151,0:0:2,0:23.1:1:30.3:1:1:0:60:36.75:1:0:0.1 +X 66937707 . A G 114 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGAACCAATCCTAGTCAT;RSEQ=TTTCTGGTCTGCTTTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:0,6:6,11:0.6471:0,0:31.7:1:33.2:1:1:0:60:22:0.6875:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 66941517 . C A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09297;SOR=Inf;LSEQ=AAAACAAACAAACAGACAAA;RSEQ=AAACAAAAAAACCTTTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:106:0:0,0:104,2:106,0:0:1,0:23.7:1:31.9:1:1:0:59.9:52:1:0:0.5 0/1:47:2:1,1:42,2:44,2:0.0426:1,2:29:0:29:1:0.12754:17.3476:60:4:0.0426:0:1 +X 66941597 . T G 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12609;SOR=0;LSEQ=TTGGAAAACCTGGCGAGGGA;RSEQ=GGCAATCAGAGACATTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:484:484:355,129:0,0:0,484:1:0,2:23.4:1:32.2:1:1:0:60:79.667:1:0:1.1 1/1:267:265:210,55:1,0:1,265:0.9925:0,2:22.4:1:30.9:1:1:0:60:87.333:0.9924:0:1.1 +X 66942476 . A G 87 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.3124;SOR=0;LSEQ=ACTCCTTTCAGATCGGATCC;RSEQ=GCTATCCTTTCCCCTGAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:8,0:27,0:27,8:0.2286:1,0:29.3:1:29.3:1:1:0:60:16:0.2353:0:1.1 0/0:7:0:0,0:7,0:7,0:0:0,0:26:1:30.1:1:1:0:60:14:1:0:0 +X 66943154 . C CTCTGTG 79 MSI12 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=22.000;MSILEN=2;SSF=1;SOR=0;LSEQ=GTTCATGTGAGTTTGTCTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1:0,0:15.4:1:34.2:1:1:0:54.6:10:1:0.8:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 66943362 . A AACACACAC 135 MSI12 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=20;MSI=14.000;MSILEN=2;SSF=0.15806;SOR=2.40707;LSEQ=CTCTCTCGCTGTCTCTCTCT;RSEQ=ACACACACACACACACACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:17,1:3,0:3,18:0.4286:0,1:28.9:1:32.4:1:1:0:59.3:36:0.4286:0:0.2 1/0:17:11:11,0:0,0:0,11:0.6471:0,0:21:1:29.1:1:1:0:56.2:22:0.6471:0.2941:0.8 +X 66943769 . C A 106 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00215;SOR=0;LSEQ=AACTCTGCACTACTCCTCTG;RSEQ=AGTGCCTTGGGGAATTTCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:12:0,12:6,144:150,12:0.0741:1,0:24.2:1:29.6:1:1:0:60:11:0.0683:0:1.3 0/0:107:0:0,0:1,106:107,0:0:1,0:22.3:1:31.1:1:1:0:59.8:34.667:1:0:0.2 +X 69254637 . G A 177 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00223;SOR=0.19621;LSEQ=ACCTGTTTCCTCAATCATCA;RSEQ=ATGGGAGGCCCAAGGGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:62:56:49,7:5,1:6,56:0.9032:2,2:24.2:1:30.6:1:0.57987:1.39:60:55:0.9016:0:1.1 1/0:42:27:25,2:14,1:15,27:0.6429:1,2:23:1:28.2:1:1:1.11705:60:8:0.6154:0:1.2 +X 69254663 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22072;SOR=Inf;LSEQ=AGGCCCAAGGGGCACTGTGA;RSEQ=TCAGTGAGGGGAGTCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:80,21:101,0:0:2,0:23.6:1:30.5:1:1:0:59.8:100:1:0:0.7 0/1:90:2:1,1:72,16:88,2:0.0222:2,2:21.5:1:30.5:1:0.34382:4.39586:60:4:0.0222:0:1 +X 69254673 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0.22547;SOR=Inf;LSEQ=GGCACTGTGAATCAGTGAGG;RSEQ=GAGTCCAGGCCCAGGGGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:120:0:0,0:92,28:120,0:0:2,0:23.7:1:30.7:1:1:0:59.9:23:1:0:0.6 0/1:109:2:1,1:84,23:107,2:0.0183:2,2:20:1:24:1:0.39348:3.59616:60:4:0.0187:0:1 +X 69254701 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49887;SOR=0;LSEQ=GGCCCAGGGGAGGGGTGGTG;RSEQ=AAGCTGAATAAGCTTCTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:2:1,1:125,71:196,2:0.0101:2,2:8:1:28:1:1:1.75518:60:4:0.0103:0:2 0/0:191:0:0,0:120,71:191,0:0:2,0:24.1:1:30.9:1:1:0:60:94.5:1:0:0.3 +X 69254760 . C G 214 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.01604;SOR=0.64534;LSEQ=CAAGTTGTTACATGCCCTCT;RSEQ=TGGGGAATCAGTGACTTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:102:50,52:115,122:237,102:0.3009:2,2:25.4:1:32.2:1:1:1.02:60:204:0.3054:0:1.1 0/1:313:68:34,34:121,124:245,68:0.2173:2,2:24:1:30.9:1:1:1.02:60:136:0.2201:0:1.1 +X 69254912 . A G 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.07537;SOR=Inf;LSEQ=GCAGGGGTGGGCGGGGGAAC;RSEQ=GGGGCACGGTGAAGCTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:3,38:41,0:0:2,0:23.5:1:31.7:1:1:0:60:40:1:0:0.2 0/1:31:3:0,3:0,28:28,3:0.0968:1,0:14.3:1:24:1:1:0:60:2:0.069:0:1.7 +X 70338399 . A G 128 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.05812;SOR=0.09823;LSEQ=CCAGGCCCCACCTCCTCTGC;RSEQ=GTCGGTATTGTCCGATGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:18,1:5,0:5,19:0.7917:0,1:20.3:1:30.2:1:1:0:59.4:38:0.9048:0:1.3 0/1:4:1:1,0:3,0:3,1:0.25:0,0:4:0:29:0:1:0:60:2:0.25:0:1 +X 70338517 . C T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.07128;SOR=Inf;LSEQ=GCCGCCGTCCTCTCAACCAC;RSEQ=GCCCCCCTTTTCGGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:208,8:216,0:0:1,0:25.4:1:31:1:1:0:60:35:1:0:0.3 0/1:154:3:1,2:138,13:151,3:0.0195:2,2:15:1:28.7:1:0.02521:20.27672:54:6:0.02:0:1 +X 70338524 . C CT 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.000;MSILEN=1;SSF=0.18836;SOR=Inf;LSEQ=TCCTCTCAACCACCGCCCCC;RSEQ=TTTTCGGCTCCCTCTCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:238:0:0,0:225,12:237,0:0:2,0:25.3:1:31.2:1:1:0:60:78:1:0:0.3 0/1:183:2:2,0:155,26:181,2:0.0109:2,0:13.5:1:31:1:1:0:60:4:0.0112:0.0055:0.5 +X 70339385 . G C 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AGAATCTAAGAAGGAGCAAA;RSEQ=GCCCTGGGTTGGGAAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:75,123:198,0:0:2,0:23.2:1:31.9:1:1:0:60:98:1:0:0.1 0/1:201:22:7,15:50,127:177,22:0.1095:2,2:24:1:30.1:1:0.80323:1.18:60:44:0.1111:0:1.1 +X 70339498 . C T 263 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0.49003;LSEQ=GGCAGGACCACCTGTCTGCC;RSEQ=CTTCTTCCCACCCTGAGGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:476:321:213,108:92,62:154,321:0.6744:2,2:23.4:1:31.6:1:0.18376:1.33:60:159.5:0.6787:0:1.1 1/0:431:217:141,76:137,74:211,217:0.5035:2,2:22.7:1:29.1:1:1:1.00:60:42.4:0.5048:0:1.1 +X 70340322 . C G 60 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAGCTAGGAGCAGAAGGTT;RSEQ=TTTGAGTGGACAAAAGATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:4:2,2:0,1:1,4:0.8:0,2:29.5:1:30.3:1:1:0:60:8:0.8:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 70340738 . A G 198 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00608;SOR=0.4072;LSEQ=AAAGTGCTGGGATTACAGGC;RSEQ=TGAGCCACCGCACCCAGCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:111:87:71,16:21,3:24,87:0.7838:2,2:24:1:30.8:1:0.75994:1.57156:51:86:0.7818:0:1.1 1/0:79:47:41,6:29,3:32,47:0.5949:2,2:23.1:1:29.4:1:0.73199:1.40862:50.3:46:0.5974:0:1.1 +X 70340742 . G A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5097;SOR=0;LSEQ=TGCTGGGATTACAGGCATGA;RSEQ=CCACCGCACCCAGCCAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:2:1,1:100,21:121,2:0.0163:2,2:15:0:32:0:0.32694:4.67566:60:4:0.0163:0:3 0/0:90:0:0,0:75,15:90,0:0:2,0:22.9:1:31.3:1:1:0:53:29:1:0:0.6 +X 70341122 . T TACTTTATCTGCTTC 238 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.45143;LSEQ=GTTCTCTTCATCTTTTCATT;RSEQ=ACTTTATCTGCTTCATCTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:350:216:142,74:74,57:131,216:0.6171:2,2:22.1:1:30.8:1:0.08813:1.48:59.8:432:0.6225:0.2857:0.9 0/1:335:141:88,53:104,90:194,141:0.4209:2,2:19.6:1:30.1:1:0.11806:1.44:59.8:282:0.4234:0.2299:0.9 +X 70341169 . A C 274 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=0.44129;LSEQ=CCCCTCTTCCCTCCCCTGGT;RSEQ=CCCATAGGATGGAATGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:591:406:240,166:122,62:184,406:0.687:2,2:26.3:1:31.7:1:0.10121:1.36031:59.9:202:0.6882:0:1.2 0/1:549:270:153,117:155,122:277,270:0.4918:2,2:26.9:1:30.1:1:0.93131:1.03:59.9:37.571:0.4879:0:1.2 +X 70341973 . C T 45 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.11021;SOR=0;LSEQ=AACTTTGGATCTGGAATCTA;RSEQ=GGGTTGGGTCTTAGAATGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:3:2,1:191,52:243,3:0.0122:2,2:22:1:29:1:0.51872:1.83124:60:6:0.0123:0:1.3 0/0:266:0:0,0:197,69:266,0:0:2,0:22.7:1:30.5:1:1:0:60:265:1:0:0.2 +X 70342029 . T C 178 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0;SOR=55.54002;LSEQ=CCATGGTGAATGAGTTGGAC;RSEQ=TAGCTGTTTCTATCTGGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:570:1:0,1:357,212:569,1:0.0018:2,0:23:0:31:0:0.37368:0:60:2:0.0018:0:1 0/1:640:57:31,26:341,242:583,57:0.0891:2,2:27.7:1:30.6:1:0.57543:1.1815:60:114:0.0902:0:1.2 +X 70342820 . A G 219 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=8e-05;SOR=0.36905;LSEQ=AGGCATTGAAAGCAGAGCAT;RSEQ=TCTGCAGAAATGATCTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:156:106:39,67:16,34:50,106:0.6795:2,2:25.2:1:32.6:1:0.59456:1.24:59.8:105:0.6863:0:1.1 0/1:121:53:20,33:25,43:68,53:0.438:2,2:23.6:1:31.7:1:1:1.04:60:52:0.437:0:1.1 +X 70343621 . A G 237 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0.32754;LSEQ=CTGCCTAGACTCAGTTACCC;RSEQ=CCACTGTCATCAGAAAGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:244:176:25,151:8,60:68,176:0.7213:2,2:23.8:1:31.9:1:0.68187:1.24:60:175:0.7231:0:1.5 0/1:179:82:12,70:9,88:97,82:0.4581:2,2:21.9:1:31.3:1:0.35191:1.67:60:81:0.4602:0:1.6 +X 70343812 . T G 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGCATTTTCACTGCATAAA;RSEQ=CGCAACAAAGATGTTACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:2:1,1:23,10:33,2:0.0571:2,2:45.5:1:32.5:1:0.53613:2.24016:60:4:0.0588:0:1 0/0:11:0:0,0:8,3:11,0:0:2,0:21.9:1:31.3:1:1:0:60:22:1:0:0 +X 70344215 . GGCA G 85 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=3;SSF=0.09369;SOR=3.90622;LSEQ=CAGAGCACAAGGAGGCTGAA;RSEQ=GCAGCAGCAGCAAGCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:2:1,1:65,247:312,2:0.0064:2,2:17:1:31.5:1:0.37673:3.78:60:4:0.0064:0.0032:0 0/1:286:7:3,4:67,210:277,7:0.0245:2,2:25.6:1:30.3:1:0.36897:2.34:60:14:0.0249:0.007:0.3 +X 70344331 . G C 171 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.000;MSILEN=1;SSF=0.26036;SOR=0.59516;LSEQ=AGAGCCTCTTTTGCCTGGGG;RSEQ=AGGGGGGTAGTATTTTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:58:39:7,32:3,16:19,39:0.6724:2,2:24.5:1:32.4:1:1:1.16:59.9:38:0.6909:0:1.1 1/0:31:17:0,17:2,12:14,17:0.5484:2,1:22.9:1:30.6:1:0.1957:0:60:16:0.5517:0:1.1 +X 70344762 . TG T 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0.95403;LSEQ=CATTATGCCTGCTTTTGGCA;RSEQ=TTTTTTTGCCCCCTCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:8:3,5:101,75:176,8:0.0165:2,2:24.1:1:31.8:1:0.29734:2.23455:60:16:0.0168:0:0.1 0/1:508:8:5,3:143,119:262,8:0.0157:2,2:29:1:30.9:1:0.73281:1.39:60:16:0.0297:0:0.3 +X 70344763 . G T 252 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=1;SSF=0;SOR=0;LSEQ=ATTATGCCTGCTTTTGGCAT;RSEQ=TTTTTTTGCCCCCTCATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:485:293:161,132:101,75:176,293:0.6041:2,2:22.2:1:30.8:1:0.63188:1.10387:60:96.667:0.6105:0:1.1 0/0:508:0:0,0:143,119:262,0:0:2,0:23.3:1:31.8:1:1:0:60:261:0.9703:0:0.1 +X 70345593 . C T 122 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=23.82509;LSEQ=AGTAAGCCCCATACTGCCCT;RSEQ=CCTCCCTCTCCCTTCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:734:1:1,0:255,476:731,1:0.0014:2,0:10:0:33:0:0.34973:0:60:2:0.0014:0:2 0/1:698:22:7,15:271,402:673,22:0.0315:2,2:24.4:1:27.5:1:0.51103:1.44383:60:21:0.031:0:1.1 +X 70345683 . T G 206 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.00433;SOR=0.46759;LSEQ=GTGGTCCTCTAAACCTTTGC;RSEQ=TCACTGTCCCCTTCCCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:88:10,78:4,40:44,88:0.6667:2,2:24.4:1:32:1:0.77339:1.28:59.9:87:0.6692:0:1.1 0/1:114:55:3,52:7,52:59,55:0.4825:2,2:25.1:1:32:1:0.32445:2.31681:60:110:0.4911:0:1.2 +X 70345850 . C T 44 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.04704;SOR=Inf;LSEQ=CTAGTCAACTAGTTATCTTC;RSEQ=CTGTCTTGACTGGTCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:378:0:0,0:269,109:378,0:0:2,0:24.4:1:31:1:1:0:60:46.25:1:0:0.2 0/1:331:4:1,3:234,93:327,4:0.0121:2,2:10.8:1:22.3:1:0.07513:7.49606:60:3:0.0092:0:1 +X 70345867 . C T 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.02701;SOR=Inf;LSEQ=TTCCCTGTCTTGACTGGTCC;RSEQ=TTTCAACTGTCCCCTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:0:0,0:318,165:483,0:0:2,0:25:1:31.8:1:1:0:60:79.5:1:0:0.2 0/1:458:5:1,4:293,160:453,5:0.0109:2,2:15.8:1:24.6:1:0.05764:7.29371:60:4:0.0088:0:1 +X 70346022 . G A 76 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.03896;SOR=7.68559;LSEQ=CAGGTGTGGGCCTAAGCCCA;RSEQ=CCCCTTTCCCACATTCTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:680:1:1,0:295,384:679,1:0.0015:2,0:1:0:27:0:0.43529:0:60:2:0.0015:0:1 0/1:714:8:6,2:307,399:706,8:0.0112:2,2:9.8:1:25.4:1:0.14745:3.89:59.8:7:0.01:0:1.9 +X 70346404 . G T 28 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.59062;SOR=2.4475;LSEQ=GCGGCTACGGAGGGTCATAA;RSEQ=GACAGGCGTAGAGGCTCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:152:1:0,1:20,130:150,1:0.0066:2,0:15:0:13:0:1:0:60:0:0:0:1 0/1:125:2:1,1:18,105:123,2:0.016:2,2:17:0:28:1:0.28194:5.70:60:4:0.0163:0:1 +X 70347029 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20661;SOR=Inf;LSEQ=ACAAAGCTCTGGCGAATGCC;RSEQ=GTGGAAGTGGCCTGGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:88,149:237,0:0:2,0:24.2:1:30.6:1:1:0:59.9:58.25:1:0:0.1 0/1:198:2:1,1:68,128:196,2:0.0101:2,2:15:1:28:1:1:1.88:60:4:0.0102:0:1 +X 70347039 . G A 23 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19006;SOR=Inf;LSEQ=GGCGAATGCCGGTGGAAGTG;RSEQ=CCTGGGAAGAGCATGCACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:218:0:0,0:85,133:218,0:0:2,0:23.9:1:32:1:1:0:59.9:108:1:0:0.1 0/1:169:2:2,0:60,107:167,2:0.0118:2,0:10.5:1:23:1:0.13321:0:60:4:0.012:0:1 +X 70347614 . C T 123 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.00015;SOR=0;LSEQ=CAGTCTGTTTTGTCCCATCT;RSEQ=CCTTTTCTTGTCTCAAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:15:15,0:69,1:70,15:0.1765:1,1:27.5:1:31.5:1:1:0:60:30:0.1765:0:1.1 0/0:64:0:0,0:63,1:64,0:0:1,0:28:1:31:1:1:0:59.6:128:1:0:0.1 +X 70347654 . CT C 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.2497;SOR=Inf;LSEQ=CCTTCATCCCTCACTTTCTC;RSEQ=TTTTTTCTTTTCTCCCCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:182:0:0,0:161,20:181,0:0:2,0:23.2:1:32.2:1:1:0:59.8:362:1:0:0.2 0/1:200:3:2,1:170,27:197,3:0.015:2,2:10:1:29.9:1:0.36551:3.12244:60:6:0.0152:0.005:0.3 +X 70348317 . G C 150 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CTTGGGGTGGGGTTTTGCTA;RSEQ=TGGGGCAGTGACCAGGGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:528:0:0,0:224,304:528,0:0:2,0:23.1:1:32.2:1:1:0:59.9:51.8:1:0:0.5 0/1:558:27:10,17:228,303:531,27:0.0484:2,2:28.7:1:31.6:1:0.6907:1.27865:60:54:0.0492:0:1.2 +X 70348344 . G A 247 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.38072;LSEQ=AGTGACCAGGGCAGGGGGCT;RSEQ=GTTGTGATCCTCTGACCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:379:270:109,161:49,60:109,270:0.7124:2,2:21.9:1:30.6:1:0.42264:1.20566:59.8:269:0.7173:0:1.1 0/1:367:178:80,98:85,104:189,178:0.485:2,2:22.5:1:28.8:1:1:1.0012:60:88:0.4848:0:1.1 +X 70348874 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16651;SOR=Inf;LSEQ=TTCTCTCCCATGCCCCTGCC;RSEQ=TACACTTGCATGCATGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:153,16:169,0:0:2,0:25.9:1:30.6:1:1:0:60:168:1:0:0.2 0/1:117:2:1,1:103,12:115,2:0.0171:2,2:12:1:28.5:1:0.21073:8.28552:60:4:0.0177:0:1 +X 70349947 . A C 270 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.45607;LSEQ=AGCAATGACCTGCAAGACCC;RSEQ=GTGTTGAGTAGTGCCCAGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:702:474:226,248:104,122:226,474:0.6752:2,2:26.1:1:30.4:1:0.68649:1.07:59.9:66.714:0.6778:0:1.1 0/1:781:380:180,200:185,213:398,380:0.4866:2,2:26.2:1:29.8:1:0.82947:1.04:60:189:0.4884:0:1.1 +X 70350143 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.16664;SOR=Inf;LSEQ=ATAGGAACCTTGAGAAAAGG;RSEQ=GAGGGGCAGTTAAGTAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:108:0:0,0:7,101:108,0:0:2,0:24:1:32:1:1:0:60:35:1:0:0.1 0/1:75:2:1,1:6,67:73,2:0.0267:2,2:16.5:1:29.5:1:0.1791:10.42:60:4:0.027:0:1 +X 70351838 . C T 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CCGCCAGTGTTGTCCTTCTC;RSEQ=GTCATCTCCGATCTCTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:166,28:194,0:0:2,0:23.9:1:31.1:1:1:0:60:63.667:1:0:0.1 0/1:139:14:11,3:104,21:125,14:0.1007:2,2:17.1:1:29.8:1:0.7095:1.3475:60:28:0.1007:0:1.4 +X 70351847 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18554;SOR=Inf;LSEQ=TTGTCCTTCTCCGTCATCTC;RSEQ=GATCTCTCCTACCATCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:224:0:0,0:190,34:224,0:0:2,0:24.5:1:31:1:1:0:60:73.667:1:0:0.1 0/1:170:2:1,1:138,30:168,2:0.0118:2,2:11.5:1:28.5:1:0.33234:4.54158:60:4:0.0118:0:1.5 +X 70352417 . T C 287 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0.40293;LSEQ=GCTTAGGGAGTGGACCAAGA;RSEQ=TGAGGGGTAGAAAGGAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:641:445:150,295:67,127:194,445:0.6942:2,2:24:1:32.7:1:0.85611:1.03744:59.9:62.571:0.703:0:1.2 0/1:557:266:102,164:108,182:290,266:0.4776:2,2:24:1:31.4:1:0.7935:1.05:60:132:0.4862:0:1.1 +X 70352491 . G A 182 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GAGAAGCATCATAGGAAAGT;RSEQ=GAAAATCAGAGGATAAGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:53:12,41:15,108:123,53:0.3011:2,2:21.1:1:31.8:1:0.10886:2.10:60:106:0.3046:0:2.1 0/0:71:0:0,0:6,65:71,0:0:2,0:25.9:1:29.9:1:1:0:60:22.667:1:0:0.6 +X 70352516 . A G 203 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00673;SOR=0.39702;LSEQ=ATCAGAGGATAAGAGTGGGC;RSEQ=TGGCTGAGCAAGAGGCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:130:89:33,56:8,33:41,89:0.6846:2,2:20.2:1:31.5:1:0.06661:2.42:60:88:0.6822:0:1.5 0/1:52:24:3,21:7,21:28,24:0.4615:2,2:23.3:1:30.6:1:0.3087:2.29667:60:23:0.451:0:1 +X 70352617 . CCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT C 218 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=12.000;MSILEN=5;SSF=0.50679;SOR=1.17744;LSEQ=TTTCTCCTCTCCTCTTCTCT;RSEQ=CTCTTCTCTTCTCTTCTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:207:111:87,24:67,15:82,111:0.5362:2,2:16.5:1:32.1:1:0.5922:1.23086:49:54.5:0.5767:0.3092:0.7 1/0:137:79:54,25:46,2:48,79:0.5766:1,2:15.8:1:30.7:1:0.00012:10.49575:53:158:0.594:0.2774:0.5 +X 70352854 . G A 49 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17244;SOR=5.26842;LSEQ=GCAGGAGGTCAGGGAAGGAT;RSEQ=CACCTAAGGGGTTACTCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:526:1:1,0:179,346:525,1:0.0019:2,0:1:0:24:0:0.34221:0:60:2:0.0019:0:1 0/1:402:4:3,1:155,243:398,4:0.01:2,2:6.5:1:24.5:1:0.30452:4.69:60:8:0.0101:0:1 +X 70353062 . GGT G 60 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02505;SOR=Inf;LSEQ=CTCAAACTGCGGCTCAACCT;RSEQ=GAGAAGGCCAGCTGGGGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:494:0:0,0:207,287:494,0:0:2,0:25.1:1:31.5:1:1:0:60:37:1:0:0.1 0/1:455:5:4,1:178,272:450,5:0.011:2,2:14.4:1:26:1:0.08585:6.09:60:10:0.011:0.0066:0.6 +X 70353126 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16828;SOR=Inf;LSEQ=GAAATGCGGAGTGCAAAAGC;RSEQ=TCAGGTTGGGGAGAATGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:0:0,0:30,172:202,0:0:2,0:24.6:1:32.2:1:1:0:59.8:27.857:1:0:0.1 0/1:141:2:1,1:33,106:139,2:0.0142:2,2:5:1:27.5:1:0.42543:3.18:60:4:0.0144:0:1 +X 70354102 . C A 110 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.26316;SOR=1.77498;LSEQ=AAAAAAAAAAAAAAAAAAAA;RSEQ=TCAAGCATGAACTCAGGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:9,0:74,3:77,9:0.1023:1,0:13.8:1:31.3:1:1:0:60:18:0.12:0:1.4 0/1:83:14:12,2:62,5:67,14:0.1687:2,2:12.6:1:29.1:1:0.5982:2.04453:56.1:28:0.2:0:1.6 +X 70354111 . G T 31 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0.6335;LSEQ=AAAAAAAAAAACTCAAGCAT;RSEQ=AACTCAGGCGTCCCAACTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:2,0:153,12:165,2:0.0118:2,0:26.5:1:31.5:1:1:0:60:4:0.0145:0:2 0/0:133:1:0,1:116,15:131,1:0.0075:2,0:1:0:21:0:0.12121:0:60:2:0.0098:0:1 +X 70354133 . A T 32 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.35144;SOR=3.32011;LSEQ=ACTCAGGCGTCCCAACTCAG;RSEQ=TTGGAACTAAGCTTTCCTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:0,1:222,63:285,1:0.0035:2,0:1:0:14:0:0.22378:0:60:0:0:0:1 0/1:260:3:2,1:185,72:257,3:0.0115:2,2:24.3:1:20.3:1:1:1.28345:48.3:2:0.0084:0:3.7 +X 70354508 . T C 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.11112;SOR=Inf;LSEQ=TTGTGTCCTCTGCTGAGGCC;RSEQ=TTTTCTATCTTCACCTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:270:0:0,0:173,95:268,0:0:2,0:22:1:31.5:1:1:0:59.9:88.333:0.9925:0:0.1 0/1:251:3:2,1:176,72:248,3:0.012:2,2:19.3:1:30.3:1:1:1.22117:60:6:0.012:0:1 +X 70354651 . A G 199 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=48.93014;LSEQ=CTAGCATCTCGCAAGGTAGC;RSEQ=TGGAGGAAAACAAGCGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:730:2:2,0:351,376:727,2:0.0027:2,0:43.5:1:17:1:0.23413:0:60:1:0.0014:0:1.5 0/1:758:90:40,50:307,361:668,90:0.1187:2,2:24.9:1:30.7:1:0.82229:1.06296:60:89:0.1193:0:1.2 +X 70355258 . CTT C 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=3e-05;SOR=0.16051;LSEQ=CTGGGGTTTTGAGCAAATCA;RSEQ=AACTTTCCTTACATTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:47:0,47:0,11:11,47:0.7966:0,1:24.4:1:32.7:1:1:0:59.8:94:0.8103:0.1186:0.1 0/1:42:16:0,16:0,26:26,16:0.381:1,1:22.3:1:32.5:1:1:0:60:32:0.3902:0.0476:0.1 +X 70355882 . A T 91 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.29945;SOR=0.27545;LSEQ=CACACGCCCCCCGCCCCGTT;RSEQ=GTTCATCTCCTCTCCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:7,1:3,0:3,8:0.7273:0,2:29.9:1:30.4:1:1:0:60:16:0.7273:0:1.9 0/1:5:2:2,0:3,0:3,2:0.4:0,0:12:1:29:0:1:0:60:4:0.5:0:2 +X 70355942 . G C 143 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.56918;SOR=0.71118;LSEQ=GCCTCCACACCTCTCCCTGT;RSEQ=CCCCACCCTTCACTCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:23:23,0:9,0:9,23:0.697:0,1:28.5:1:31.8:1:1:0:60:46:0.7188:0:1.3 1/0:21:13:12,1:7,0:7,13:0.619:0,1:26.2:1:31.1:1:1:0:60:26:0.619:0:1.2 +X 70356039 . C T 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60357;SOR=2.25376;LSEQ=ACCATCTCTCCTGAATCTGC;RSEQ=TATGACTTTCTTTCTACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:202:1:1,0:189,12:201,1:0.005:2,0:5:0:20:0:1:0:60:2:0.005:0:1 0/1:180:2:1,1:164,14:178,2:0.0111:2,2:9.5:1:29.5:1:0.16015:11.3518:60:4:0.0112:0:1 +X 70356561 . G A 25 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.18506;SOR=Inf;LSEQ=TCTCACTTCATGACGCTCCG;RSEQ=TTTCTGGTTTGTGGGAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:85,166:251,0:0:2,0:26.5:1:31.6:1:1:0:59.9:49.2:1:0:0.3 0/1:190:2:2,0:55,133:188,2:0.0105:2,0:21.5:1:25.5:1:0.08889:0:60:4:0.0106:0:1 +X 70356642 . T C 250 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02251;SOR=0.64683;LSEQ=AAAATTAACCATATACGAAT;RSEQ=CAGCTCCTCTTTACCTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:298:210:174,36:70,17:87,210:0.7047:2,2:23.1:1:32.5:1:0.62068:1.17:59.8:209:0.7085:0:1.1 1/0:211:128:109,19:64,19:83,128:0.6066:2,2:22.4:1:30.8:1:0.14649:1.70:60:41.667:0.6039:0:1.3 +X 70356704 . C T 133 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATTCAGCTACAACCCACTCA;RSEQ=CCTCTTCCTCTGCCACTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:755:0:0,0:471,284:755,0:0:2,0:26.1:1:31.7:1:1:0:59.9:82.889:1:0:0.3 0/1:600:25:16,9:342,232:574,25:0.0417:2,2:29.4:1:28.8:1:0.83543:1.21:60:24:0.0405:0:1.4 +X 70356829 . A G 218 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=TTCTATAACACACCTTAACT;RSEQ=CAGGCAAGGCTCCATAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:975:129:57,72:390,454:844,129:0.1323:2,2:23.4:1:31.2:1:0.70487:1.08497:59.9:24.8:0.1288:0:1.1 0/0:922:0:0,0:447,474:921,0:0:2,0:24:1:28.1:1:1:0:59.9:130.571:1:0:0.2 +X 70360588 . GAGC G 130 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.39312;SOR=0.71407;LSEQ=GTTCAACAGCCATCCTACCT;RSEQ=AGCAGCAGCAGCAGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:732:20:10,10:297,413:710,20:0.0273:2,2:25.8:1:30.2:1:0.49702:1.39:60:40:0.0281:0.0068:0.5 0/1:763:15:8,7:335,408:743,15:0.0197:2,2:28:1:31.3:1:0.60471:1.39:60:30:0.0203:0.0026:0.3 +X 70360620 . G A 55 q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=0.5027;SOR=1.70068;LSEQ=CAGCAGCAACAGCAGCAACA;RSEQ=CAACAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:3:3,0:169,317:486,3:0.0061:2,0:1:0:25.3:1:0.04302:0:60:6:0.0064:0:1.3 0/1:482:5:4,1:177,299:476,5:0.0104:2,2:22.8:1:24:1:0.06904:6.73:60:4:0.0086:0:1.2 +X 70360623 . ACAG A 88 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.7893;SOR=0.77233;LSEQ=CAGCAACAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAACAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:8:4,4:154,299:453,8:0.0173:2,2:20.4:1:29.5:1:0.45453:1.94:52.3:16:0.0175:0.0065:0.3 0/1:447:6:1,5:153,286:439,6:0.0134:2,2:22.2:1:31.4:1:0.66931:2.66998:55.7:12:0.0137:0.0022:0 +X 70360647 . ACAG A 109 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.34347;SOR=1.66023;LSEQ=CAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:7:1,6:55,216:271,7:0.0247:2,2:30.4:1:30.7:1:1:1.52571:58.9:14:0.0252:0:0.6 0/1:272:11:3,8:60,201:261,11:0.0404:2,2:31.2:1:31.6:1:0.72056:1.26:58.1:22:0.0409:0.0037:0.5 +X 70360666 . C T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=0.23965;SOR=0;LSEQ=AACAGCAGCAGCAGCAGCAG;RSEQ=AGTACCACATCCGGCAGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:0,2:14,160:174,2:0.0114:2,0:8.5:1:27.5:1:1:0:60:4:0.0118:0:1.5 0/0:183:0:0,0:28,155:183,0:0:2,0:24.7:1:31.4:1:1:0:59.3:44.75:1:0:0.1 +X 70360679 . GGCA G 104 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=6.000;MSILEN=3;SSF=0.60242;SOR=0.71226;LSEQ=GCAGCAGCAGTACCACATCC;RSEQ=GCAGCAGCAGCAGCAGATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:9:0,9:11,132:143,9:0.0592:2,0:36.3:1:32.9:1:1:0:60:18:0.0621:0:0 0/1:140:6:1,5:16,118:134,6:0.0429:2,2:33.5:1:31.2:1:0.54706:1.47:60:12:0.0441:0:0 +X 70361077 . TAGC T 48 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.000;MSILEN=3;SSF=0.68424;SOR=0.65553;LSEQ=AAGTATCTTTTGTGTTCTTA;RSEQ=AGCAGCAGCAACAGCAACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:3:2,1:232,47:279,3:0.0105:2,2:24.3:1:30.7:1:0.42991:2.45769:57:6:0.0109:0.0035:0.3 0/0:289:2:1,1:225,63:288,2:0.0069:2,2:6:1:26.5:1:0.39327:3.55104:54:6:0.0061:0.0078:1 +X 70361097 . ACAG A 125 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.000;MSILEN=3;SSF=0.01861;SOR=0.32693;LSEQ=TAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:17:9,8:271,111:382,17:0.0425:2,2:24.1:1:30.7:1:0.172:2.1655:51.9:16:0.0415:0.0075:0.5 0/1:420:6:3,3:274,140:414,6:0.0143:2,2:29.7:1:31.5:1:0.41386:1.95385:56:12:0.0145:0:0.3 +X 70361100 . G A 76 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.21104;SOR=0.39802;LSEQ=CAGCAGCAGCAACAGCAACA;RSEQ=CAGCAGCAGCAGCAGCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:7:6,1:269,114:383,7:0.0173:2,2:14.6:1:27.4:1:0.67888:2.54:57.6:6:0.0163:0:2 0/0:432:3:1,2:278,145:423,3:0.0069:2,2:20:1:22.7:1:0.27455:3.82126:59.3:2:0.0049:0:1 +X 70361127 . ACAG A 83 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.57733;SOR=1.41951;LSEQ=CAGCAGCAGCAGCAACAGCA;RSEQ=CAGCAGCAGCAACAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:647:5:4,1:394,244:638,5:0.0077:2,2:32.8:1:31.6:1:0.65435:2.47:60:10:0.0078:0:0 0/1:640:7:3,4:355,275:630,7:0.0109:2,2:27.3:1:29.8:1:0.705:1.7197:60:14:0.0111:0.0031:0 +X 70361273 . C T 138 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.01847;LSEQ=ACAGCTGCCCAGGTTGGGCA;RSEQ=GCAGCCAGTGAACTGGGTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:497:1:0,1:153,342:495,1:0.002:2,0:27:0:32:0:1:0:60:2:0.002:0:1 0/1:373:24:7,17:102,247:349,24:0.0643:2,2:18.5:1:30.1:1:1:1.00288:60:48:0.0652:0:1.3 +X 70361608 . T C 161 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.68551;SOR=0.79689;LSEQ=GTTGCAGTGAGCCAAGATCA;RSEQ=GCCACTGCACTCCAGCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:33:33,0:19,0:19,33:0.6346:1,1:24.3:1:32:1:1:0:30.4:66:0.6346:0:1 1/0:50:29:29,0:21,0:21,29:0.58:1,1:18.4:1:31.2:1:1:0:32.6:58:0.5918:0:1.3 +X 70361619 . T C 57 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02876;SOR=Inf;LSEQ=CCAAGATCATGCCACTGCAC;RSEQ=CCAGCCTGGGGGACAGAGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:66:0:0,0:64,2:66,0:0:1,0:18.8:1:31.7:1:1:0:37.8:32:1:0:0.8 0/1:72:6:4,2:64,2:66,6:0.0833:1,2:17:1:22.2:1:0.03257:14.57743:36:2:0.0571:0:2.7 +X 70361651 . C CA 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.02928;SOR=0.62744;LSEQ=GACAGAGCGAGACTCCATCT;RSEQ=AAAAAAAAAAACGGATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:91:69,22:55,25:80,91:0.4764:2,2:25.8:1:30.9:1:0.30954:1.42:55.1:90:0.4813:0.0052:0.4 0/1:190:69:48,21:73,30:103,69:0.3632:2,2:25.7:1:29.6:1:0.86624:1.06419:54.2:68:0.3656:0.0263:0.6 +X 70361967 . G A 278 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.38128;LSEQ=ATACCTGAACAGCTTTCCTC;RSEQ=TGCATACCCACACCCCTGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:797:565:334,231:131,96:227,565:0.7089:2,2:23.6:1:30.5:1:0.74972:1.06:60:69.625:0.7096:0:1.1 0/1:561:270:160,110:177,114:291,270:0.4813:2,2:26.1:1:29.6:1:0.73044:1.0673:60:134:0.4846:0:1.1 +X 70362490 . G A 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CCAGGCTGGAGTGCAGTGGC;RSEQ=CGATCTCGGCTCACTGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:14:1:32:0:1:0:31.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 70510544 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.54667;SOR=Inf;LSEQ=AACCATACTCCAAGAAAGCA;RSEQ=CATCAACATCACCACCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:17,0:0:2,0:25.4:1:29.4:1:1:0:52.8:7.5:1:0:0.2 0/1:34:2:1,1:16,16:32,2:0.0588:2,2:39.5:1:30.5:1:1:1:37.5:4:0.0588:0:2.5 +X 70715155 . C G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGTAAGACCATCTGTAG;RSEQ=TTGATGGCCTCGATCCTAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:5,0:5,0:0:0,0:27.4:1:33:1:1:0:22.2:10:1:0:0 0/1:11:2:1,1:7,2:9,2:0.1818:2,2:25.5:1:29:1:0.49091:3.05504:29:4:0.1818:0:1 +X 71788795 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20087;SOR=0;LSEQ=GACCCAGCGTATGCCAGAAG;RSEQ=TAGAAACAGAAGCCAGCAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:2:1,1:114,51:165,2:0.012:2,2:21.5:1:29:1:0.52709:2.22342:60:4:0.012:0:1 0/0:205:0:0,0:121,84:205,0:0:2,0:25.7:1:30.9:1:1:0:60:50.25:1:0:0.2 +X 71788870 . T C 145 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAGGCTGGAGTAATAAACA;RSEQ=ATTCTGTTCTTCCACTGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:252:0:0,0:118,133:251,0:0:2,0:27:1:29.3:1:1:0:60:40.833:0.9959:0:0.1 0/1:260:23:10,13:114,123:237,23:0.0885:2,2:22.3:1:32.2:1:0.8275:1.20402:60:46:0.0895:0:1.1 +X 72744762 . C CT 75 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.01167;SOR=0;LSEQ=CCTTTTGCTTCCTCTCAGCC;RSEQ=TTTTTTTTAGTCTGATGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:6:3,3:107,35:142,6:0.0405:2,2:24.7:1:29.3:1:0.17621:3.02932:56.7:12:0.0414:0.0068:0.5 0/0:160:0:0,0:118,40:158,0:0:2,0:23.7:1:30.4:1:1:0:60:51.667:0.9936:0:0.2 +X 72744860 . C T 61 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12395;SOR=Inf;LSEQ=ATTTGACAAAACATAGCATG;RSEQ=GACTTCAATGGTACGTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:291:0:0,0:134,156:290,0:0:2,0:25.3:1:30.5:1:1:0:59.9:40.429:0.9965:0:0.1 0/1:301:4:2,2:129,167:296,4:0.0133:2,2:20.5:1:30.8:1:1:1.29:51.8:8:0.0135:0:1.3 +X 72744866 . C A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.2487;SOR=0;LSEQ=CAAAACATAGCATGCGACTT;RSEQ=AATGGTACGTTCTTCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:3:1,2:133,152:285,3:0.0104:2,2:22.3:1:30:1:1:1.74674:60:6:0.0106:0:1 0/0:287:0:0,0:124,163:287,0:0:2,0:25:1:30.5:1:1:0:59.7:70.75:1:0:0.2 +X 72745551 . C A 39 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08715;SOR=0;LSEQ=TGCATTACTTCATCCAAATC;RSEQ=GTAAGAGGTTGTTTTTGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:3:2,1:110,114:224,3:0.0132:2,2:29.3:1:24.7:1:0.61839:2.07:60:2:0.009:0:3.3 0/0:285:0:0,0:141,144:285,0:0:2,0:24.3:1:29.6:1:1:0:59.9:56:1:0:0.1 +X 72745734 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.49869;SOR=Inf;LSEQ=TGTTCAGGGGAGATCTTCAG;RSEQ=TTTCCTGATGACTCAATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:76,92:168,0:0:2,0:20.7:1:29.7:1:1:0:46.4:167:1:0:0.1 0/1:174:2:1,1:80,92:172,2:0.0115:2,2:24:1:32.5:1:1:1.15:45.5:4:0.0115:0:1 +X 72745947 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.50106;SOR=Inf;LSEQ=CCCGGGGTGAGGCTGCCGCT;RSEQ=CTGCCCCCGGAGCCGCAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:147:0:0,0:56,91:147,0:0:2,0:22.3:1:31.8:1:1:0:60:146:1:0:0.7 0/1:170:2:1,1:63,105:168,2:0.0118:2,2:24.5:1:28.5:1:1:1.66:60:4:0.0121:0:1.5 +X 72745977 . T G 215 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.00027;SOR=0;LSEQ=GAGCCGCAGCCGCCGCTCAG;RSEQ=CTCGGAGCTGCCATTGTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:115:115:33,82:0,0:0,115:1:0,2:26.4:1:31.5:1:1:0:60:56.5:1:0:1.1 1/1:134:121:41,80:4,8:12,121:0.903:2,2:26.5:1:31.2:1:1:1.02:59.9:120:0.9091:0:1.1 +X 73434855 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50567;SOR=Inf;LSEQ=GAAAAGTGCCAGTGGAAGGA;RSEQ=AAAGTTATGGCTTTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:139:0:0,0:86,53:139,0:0:2,0:23.8:1:32.5:1:1:0:60:45.333:1:0:0.1 0/1:177:2:1,1:107,68:175,2:0.0113:2,2:39.5:1:28.5:1:1:1.56932:60:4:0.0114:0:1 +X 73434946 . GT TG 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.20871;SOR=0;LSEQ=AATATGAGCACAAGGATTGG;RSEQ=TTACTTTCAAATCAGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:92,105:197,2:0.0101:2,2:40.5:1:32.5:1:1:1.14:60:4:0.0102:0:2 0/0:236:0:0,0:103,131:234,0:0:2,0:25.6:1:30.8:1:1:0:60:468:0.9957:0:0.5 +X 73434947 . T G 197 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19831;SOR=0.76822;LSEQ=ATATGAGCACAAGGATTGGG;RSEQ=TTACTTTCAAATCAGCTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:82:40,42:54,63:117,82:0.408:2,2:25.9:1:31.6:1:0.77356:1.11:60:40:0.4082:0:1.1 0/1:237:82:34,48:70,84:154,82:0.346:2,2:24.4:1:31:1:0.58403:1.17566:60:81:0.3476:0:1.1 +X 73434975 . C A 33 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11035;SOR=0;LSEQ=CAAATCAGCTGACTACTCTC;RSEQ=TTCTATGAAGCTGGGTCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:3:3,0:67,96:163,3:0.0181:2,0:8.3:1:21:1:0.07312:0:60:2:0.0125:0:1.7 0/0:179:0:0,0:73,106:179,0:0:2,0:23.2:1:31:1:1:0:60:178:1:0:0.4 +X 73516031 . C CTT 31 d5;v3;pSTD;MSI12 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=16.000;MSILEN=1;SSF=0.33333;SOR=Inf;LSEQ=ATATAATGTTTTAACATTAA;RSEQ=TTTTTTTTTTTTTTGAGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:30:0:31.8:1:1:0:26:4:1:0:1.5 +X 73516050 . C T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTTTTTTTTTTTTTGAGA;RSEQ=AGTCTTGCTCTGTGGCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:44:0:31:0:1:0:38:2:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:22.5:1:29:0:1:0:26:4:1:0:1.5 +X 73516287 . A G 111 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13043;SOR=0;LSEQ=GCCCGCCTCGGCCTCCCAAA;RSEQ=TGCTGGGATTACAGGTGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1:0,0:19.5:1:34.1:1:1:0:55.3:16:1:0:1 1/0:16:11:11,0:5,0:5,11:0.6875:0,0:27.6:1:32.1:1:1:0:52.9:22:0.6875:0:1.3 +X 73516407 . G T 38 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08057;SOR=0;LSEQ=TGAATATTCATCAGCAAACA;RSEQ=ATTTAGTTCTGTTTCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:3:1,2:41,49:90,3:0.0323:2,2:25.7:1:24:1:1:1.6646:60:2:0.0222:0:1.3 0/0:121:0:0,0:57,64:121,0:0:2,0:27.4:1:30.2:1:1:0:60:120:1:0:0.5 +X 73516451 . T A 170 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.00074;SOR=0;LSEQ=AACTTCTACTTCTACCTTCA;RSEQ=CTCAGGCAAGGAGCTTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:63:63:23,40:0,0:0,63:1:0,2:23.9:1:28.5:1:1:0:60:20:1:0:1.1 1/1:70:59:19,40:1,9:10,59:0.8429:2,2:24.9:1:28.7:1:0.26076:4.21:60:58:0.8406:0:1.1 +X 74604188 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50622;SOR=Inf;LSEQ=GTAATTCGCCAAAATGACGA;RSEQ=CACAAAGGGAAAGAGGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:26,36:62,0:0:2,0:22.2:1:30.5:1:1:0:46.5:124:1:0:0 0/1:82:2:1,1:33,47:80,2:0.0244:2,2:32:0:33:0:1:1.42:41.5:4:0.0244:0:1 +X 74802478 . A G 127 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.0214;SOR=0.34049;LSEQ=GGCATTTATCCCAGATAAAT;RSEQ=AAAACATATGATAAGATGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:14:10,4:36,25:61,14:0.1867:2,2:23.6:1:33.6:1:0.54557:1.72:60:28:0.1892:0:1.1 0/1:111:8:5,3:74,29:103,8:0.0721:2,2:18.3:1:31.4:1:0.68774:1.52474:60:16:0.0727:0:1.6 +X 74802536 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52032;SOR=Inf;LSEQ=GTGGTGGCAGTGCGGAGCCC;RSEQ=GTGAGGCTCTATTCAACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:115:0:0,0:62,53:115,0:0:2,0:28.4:1:30.8:1:1:0:59.9:114:1:0:0.2 0/1:176:2:1,1:89,84:173,2:0.0114:2,2:38.5:1:29.5:1:1:1.0592:60:4:0.0114:0:2 +X 74802567 . C A 93 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.01205;SOR=Inf;LSEQ=ATTCAACGGGGACGTGGAGC;RSEQ=TGAAGCCGGCGCTGGCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:51,52:103,0:0:2,0:22.6:1:32:1:1:0:59.9:102:1:0:0.1 0/1:151:9:3,6:65,76:141,9:0.0596:2,2:14.4:1:29.4:1:0.5123:1.70464:60:18:0.0604:0:1.6 +X 74802569 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.51534;SOR=Inf;LSEQ=TCAACGGGGACGTGGAGCCT;RSEQ=AAGCCGGCGCTGGCGCCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:103:0:0,0:50,53:103,0:0:2,0:22.1:1:32.1:1:1:0:59.5:206:1:0:0.1 0/1:150:2:1,1:66,82:148,2:0.0133:2,2:15:1:28:1:1:1.24:60:4:0.0135:0:2 +X 74802910 . C A 40 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.07913;SOR=0;LSEQ=CACTCCAACAAAGAGAACAA;RSEQ=AGTTATTGGAATGTCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:3:2,1:118,126:244,3:0.0121:2,2:31.3:1:25.7:1:0.61303:2.13:34.7:2:0.0082:0:1 0/0:327:0:0,0:148,179:327,0:0:2,0:26.6:1:31.1:1:1:0:57.8:64.4:1:0:0.1 +X 74803004 . C A 39 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34289;SOR=0.289;LSEQ=TTCTTCCTCTTTTAGCCTTT;RSEQ=AGTTTTTCTCTTTCAGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:3:2,1:77,95:172,3:0.0171:2,2:20.3:1:24.7:1:0.58969:2.46:38.3:2:0.0116:0:3.3 0/0:200:1:1,0:81,118:199,1:0.005:2,0:1:0:22:0:0.41:0:26:2:0.0051:0:1 +X 74803054 . C T 31 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.59802;SOR=0.42884;LSEQ=CTTTATCTCTTTCAGTTTTC;RSEQ=GAAATCCCATAGATGTGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:2:1,1:93,55:148,2:0.0133:2,2:6:1:31.5:1:1:1.68465:51:4:0.0135:0:1 0/0:174:1:0,1:97,76:173,1:0.0057:2,0:1:0:23:0:0.44253:0:60:2:0.0058:0:1 +X 74803062 . C A 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25212;SOR=Inf;LSEQ=CTTTCAGTTTTCCGAAATCC;RSEQ=ATAGATGTGACATGGAGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:101,65:166,0:0:2,0:22.8:1:31.4:1:1:0:59.3:54.333:0.9939:0:0.1 0/1:194:3:2,1:110,81:191,3:0.0155:2,2:36.7:1:29.7:1:1:1.47:60:6:0.0155:0:1 +X 74803172 . G A 47 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.1028;SOR=0;LSEQ=AAGGTGTGGAGTTACAGTCG;RSEQ=AGACAGTCTAAAGAAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:3:2,1:168,127:295,3:0.0101:2,2:32.3:1:30:1:1:1.51:43.3:6:0.0102:0:1.7 0/0:337:0:0,0:175,161:336,0:0:2,0:27.2:1:30.4:1:1:0:46:111:0.997:0:0.1 +X 74803507 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=5.000;MSILEN=1;SSF=0.22884;SOR=Inf;LSEQ=ATGACCATCTTGATTTGTTG;RSEQ=TTTTCTCCAAGTTCTTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:199:0:0,0:98,101:199,0:0:2,0:25.1:1:30.3:1:1:0:59.9:198:1:0:0.1 0/1:183:2:1,1:83,98:181,2:0.0109:2,2:20:1:27:1:1:1.18:60:4:0.011:0:2 +X 74803555 . T A 144 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CAATACCCCAGGAAGAGGCC;RSEQ=CCTTAGCAGAGACTGCCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:242:0:0,0:120,122:242,0:0:2,0:25.3:1:31:1:1:0:59.9:120:1:0:0.1 0/1:227:28:14,14:106,93:199,28:0.1233:2,2:23.5:1:30:1:0.84054:1.13913:58.7:56:0.1239:0:1.3 +X 74803679 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.62828;SOR=2.57323;LSEQ=TCCAATTCCACAGCCCTTCC;RSEQ=ACCAGCAGATGAAGATCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:1,0:114,130:244,1:0.0041:2,0:1:0:27:0:0.46939:0:60:2:0.0041:0:1 0/1:287:3:2,1:148,136:284,3:0.0105:2,2:8.3:1:27.7:1:1:1.83:60:6:0.0105:0:1 +X 74803832 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49914;SOR=0;LSEQ=AGGCTCAACCACAGGTTTGT;RSEQ=TGCCACACCCCCTGCCTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:90,77:167,2:0.0118:2,2:46:1:30:1:1:1.16775:60:4:0.0119:0:1 0/0:157:0:0,0:81,76:157,0:0:2,0:21.6:1:30.6:1:1:0:60:77.5:1:0:0.1 +X 74803836 . C G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22669;SOR=Inf;LSEQ=TCAACCACAGGTTTGTCTGC;RSEQ=ACACCCCCTGCCTGGGTCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:93,77:170,0:0:2,0:25.5:1:31.9:1:1:0:58.9:84:1:0:0.2 0/1:155:2:1,1:82,71:153,2:0.0129:2,2:35:1:31.5:1:1:1.15385:60:4:0.0131:0:1 +X 74803877 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23893;SOR=0;LSEQ=TCACTAACGTGAAAGCCTTA;RSEQ=AGAAATCTCCAGGACTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:2:1,1:116,68:184,2:0.0108:2,2:32:1:31.5:1:1:1.70068:60:4:0.0108:0:1 0/0:194:0:0,0:116,78:194,0:0:2,0:23.3:1:31.4:1:1:0:58.5:193:1:0:0.1 +X 74803898 . T C 180 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGAAATCTCCAGGACTTCAG;RSEQ=GAGAAAGGAAGTCATCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:54:36,18:110,61:171,54:0.24:2,2:27.5:1:31.4:1:0.87032:1.11:45.9:53:0.2366:0:1.1 0/0:254:0:0,0:159,95:254,0:0:2,0:26.1:1:29.1:1:1:0:58.3:83.667:1:0:0.1 +X 74804297 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.50108;SOR=0;LSEQ=GATCAAACTTATAGATATTG;RSEQ=ACAACAGACTGCACAGGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:2:1,1:79,119:198,2:0.01:2,2:10.5:1:31:1:1:1.50:60:4:0.0101:0:1 0/0:174:0:0,0:65,109:174,0:0:2,0:25.2:1:31.7:1:1:0:60:348:1:0:0.1 +X 74804791 . C T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.36157;SOR=3.17186;LSEQ=AGCTGCTGACCCGCTCATTG;RSEQ=CAAAAATTCACCACAGTGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:287:1:1,0:146,140:286,1:0.0035:2,0:33:0:12:0:1:0:60:0:0:0:2 0/1:273:3:1,2:141,127:268,3:0.011:2,2:29.7:1:27.3:1:0.60633:2.21415:60:6:0.011:0:1 +X 74804896 . G A 106 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=8e-05;SOR=Inf;LSEQ=CTCCAAAAACACCCATCCAG;RSEQ=CAGGGGGATATGGTGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:349:0:0,0:141,208:349,0:0:2,0:26.6:1:31.7:1:1:0:58.4:42.625:1:0:0.1 0/1:332:13:3,10:140,179:319,13:0.0392:2,2:28.1:1:28.8:1:0.16273:2.60031:42.6:26:0.0398:0:1.2 +X 76297518 . C G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=1;SOR=0;LSEQ=GCCAGTCCCAGTGCTGGCTG;RSEQ=TGCCCCTCCCCCAAGGAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:1,1:2,2:0.5:2,0:18.5:1:32:1:1:0:60:4:0.5:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 76297592 . C A 26 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCTGGTCACAGGCTAGGGT;RSEQ=CCTCCCCACAGGAGTTTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:29.7:1:32:1:1:0:60:6:1:0:0.3 0/1:9:2:1,1:5,2:7,2:0.2222:2,2:25.5:1:26.5:1:1:2.23609:60:4:0.2222:0:1 +X 76297682 . C T 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.63089;SOR=0.59928;LSEQ=ACACAGATTGGGACAATAGG;RSEQ=CACGGGACACTAAACCATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:22:13,9:1,1:2,22:0.9167:2,2:26.1:1:29:1:1:1.42:60:44:0.9167:0:1.1 1/1:15:13:7,6:1,1:2,13:0.8667:2,2:15.5:1:28.8:1:1:1.15:60:26:0.8667:0:1.3 +X 76775992 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=AACTCTGGCAAAAATTCCTA;RSEQ=GTAGATGTCCAGAATATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:2,0:4,0:4,2:0.3333:0,0:31.5:1:30:1:1:0:60:4:0.3333:0:1 0/0:4:0:0,0:4,0:4,0:0:0,0:16.8:1:30.8:1:1:0:60:8:1:0:0 +X 76776740 . G A 29 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.57178;SOR=2.81939;LSEQ=AATTGCTGGGTTACGGTTTG;RSEQ=CATTATCCATCCATTTTACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:1:1,0:85,3:88,1:0.0112:1,0:48:0:29:0:1:0:60:2:0.0114:0:1 0/1:64:2:2,0:62,0:62,2:0.0313:1,0:22:1:29.5:1:1:0:60:4:0.0313:0:1 +X 76777682 . C T 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24868;SOR=Inf;LSEQ=GCATAGGGAACCCTCAACAA;RSEQ=AAGGCACTTGAAATTGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:278:0:0,0:225,53:278,0:0:2,0:23.4:1:32.4:1:1:0:60:277:1:0:0.1 0/1:281:3:2,1:209,69:278,3:0.0107:2,2:29.7:1:30:1:1:1.51204:60:6:0.0108:0:1.3 +X 76777926 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23643;SOR=Inf;LSEQ=TAAAACTTGAAATTCTACAT;RSEQ=ACCTACTGGTTTAGAAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:140:0:0,0:14,126:140,0:0:2,0:21.7:1:32.7:1:1:0:59.9:139:1:0:0 0/1:133:2:1,1:14,117:131,2:0.015:2,2:11:1:30:1:0.2136:8.11:60:4:0.0156:0:1 +X 76778062 . CT C 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.48529;SOR=0;LSEQ=CTTTAACCCCTAAAGGTGTA;RSEQ=TTTTTTTTCTGATAATTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:2:0,2:0,8:8,2:0.2:0,0:26:1:33:1:1:0:60:4:0.2:0:0 0/0:7:0:0,0:1,6:7,0:0:2,0:16.3:1:29.6:1:1:0:60:14:1:0:0 +X 76812822 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49811;SOR=Inf;LSEQ=TTTTATTATCCTTGAAAAAT;RSEQ=CTGAAATATAGCCTTAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:121,9:130,0:0:2,0:22.8:1:31.1:1:1:0:60:64:1:0:0.1 0/1:132:2:1,1:123,7:130,2:0.0152:2,2:17:1:30.5:1:0.11797:16.50291:60:4:0.0152:0:1 +X 76812834 . C A 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.000;MSILEN=1;SSF=0.50066;SOR=Inf;LSEQ=TGAAAAATTCTGAAATATAG;RSEQ=CTTAATCAGATGACTAAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:134,23:157,0:0:2,0:22.7:1:32.2:1:1:0:60:77.5:1:0:0.1 0/1:179:2:1,1:150,26:176,2:0.0112:2,2:12:1:26.5:1:0.28109:5.68028:60:4:0.0114:0:1 +X 76813413 . C A 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGGAGGAGGACAGCAGG;RSEQ=AGATACCAGAGTAAACAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:0,7:7,2:0.2222:0,2:26:0:30.5:1:0.22222:0:53.5:4:0.2857:0:2 0/0:1:0:0,0:0,1:1,0:0:0,0:35:0:33:0:1:0:60:2:1:0:0 +X 76814070 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22718;SOR=Inf;LSEQ=CCTCTCTGTAATACACATAT;RSEQ=TTCCATATCTCTAAAATATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:0:0,0:168,28:196,0:0:2,0:22.4:1:32.4:1:1:0:60:97:1:0:0.1 0/1:179:2:1,1:149,28:177,2:0.0112:2,2:5:1:28:1:0.29854:5.24651:60:4:0.0113:0:1 +X 76814401 . GT G 82 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.03494;SOR=0;LSEQ=ATATGACTTTTTGATACTTA;RSEQ=TTTTTTTTAACTATCAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:6:0,6:4,67:71,6:0.0779:2,0:24.7:1:32:1:1:0:60:12:0.08:0.026:0.2 0/0:60:0:0,0:2,58:60,0:0:1,0:26.2:1:29.8:1:1:0:60:120:1:0:0 +X 76829870 . T A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1352;SOR=Inf;LSEQ=AGGAATTTGATATATCGCTC;RSEQ=GCTTACTGGTAAGAACAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:259:0:0,0:45,214:259,0:0:2,0:23.8:1:30.4:1:1:0:60:50.8:1:0:0.1 0/1:332:4:3,1:78,250:328,4:0.012:2,2:10.5:1:27.5:1:0.04643:9.53:60:8:0.0123:0:1 +X 76845212 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22167;SOR=0;LSEQ=ATGATAGAGTTGTGAGACTG;RSEQ=GTAGTTTTGTTTCTTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:165,15:180,2:0.011:2,2:28.5:1:31:1:0.16854:10.6831:60:4:0.0111:0:1 0/0:204:0:0,0:184,20:204,0:0:2,0:22.6:1:30.3:1:1:0:60:101:1:0:0.1 +X 76845263 . A T 63 v3;p8;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.14079;SOR=4.80668;LSEQ=TTGTATGGTATGTTTAAATC;RSEQ=GTATTTTTAAAATTACGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:471:1:0,1:289,181:470,1:0.0021:2,0:1:0:29:0:0.38641:0:60:2:0.0021:0:1 0/1:592:6:1,5:359,227:586,6:0.0101:2,2:7.8:1:24.7:1:0.03661:7.88064:60:12:0.0103:0:1 +X 76848940 . C T 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAATAAGTTCAAGTTGCAA;RSEQ=AGGTAGAAGCAGAAATTTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:4:4,0:7,0:7,4:0.3636:0,0:28.5:1:32.8:1:1:0:60:8:0.3636:0:1 0/0:1:0:0,0:1,0:1,0:0:0,0:17:0:33:0:1:0:60:2:1:0:2 +X 76849126 . A T 33 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.33842;SOR=3.54549;LSEQ=TAAGCAATAAAAACATAATC;RSEQ=AAAGGTTAATTTATATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:290:1:0,1:209,80:289,1:0.0034:2,0:2:0:26:0:0.27931:0:60:2:0.0035:0:1 0/1:247:3:1,2:170,74:244,3:0.0121:2,2:15.3:1:21.3:1:0.22476:4.5628:60:2:0.0082:0:1.3 +X 76855053 . AAAAC A 101 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=5.000;MSILEN=4;SSF=0.33287;SOR=1.73136;LSEQ=TCCCTTTTTTCTTCTTTCTA;RSEQ=AAACAAACAAACAAACAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:6:1,5:204,309:513,6:0.0115:2,2:30.7:1:32.8:1:0.41065:3.29479:60:12:0.0117:0:0 0/1:555:11:6,5:244,299:543,11:0.0198:2,2:27.3:1:29.2:1:0.55529:1.47:60:22:0.0202:0.0036:0.4 +X 76855295 . G GA 140 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.76894;SOR=0.9007;LSEQ=TTCATCAAAATAACCCTAGA;RSEQ=AAAAAAAAATGACCACTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:25:8,17:169,339:508,25:0.0466:2,2:27.6:1:30.3:1:1:1.05926:60:50:0.0473:0.0019:0 0/1:545:23:6,17:202,318:520,23:0.0422:2,2:27.2:1:28.5:1:0.27556:1.79799:60:22:0.0411:0.0037:0.6 +X 76874208 . GA G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.23734;SOR=Inf;LSEQ=ATTATTAAACTTTAAGCTCA;RSEQ=AAATATGTTGGGATTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:151,19:170,0:0:2,0:22.3:1:30.5:1:1:0:60:340:1:0:0.1 0/1:162:2:1,1:137,23:160,2:0.0123:2,2:19:1:28.5:1:0.27513:5.85239:60:4:0.0126:0.0062:0.5 +X 76875758 . T C 123 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AACCTATGTAGATCATGGTC;RSEQ=AGGACTATACTAGAATAAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:118:0:0,0:115,3:118,0:0:1,0:24.6:1:32.2:1:1:0:60:236:1:0:0.1 0/1:88:16:16,0:69,3:72,16:0.1818:1,1:19.6:1:30.9:1:1:0:60:32:0.1818:0:1.1 +X 76876036 . T A 41 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.12023;SOR=0;LSEQ=GAAAAATAACACAATTAATA;RSEQ=ATAATAAAACTGAAAATGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:3:2,1:55,173:228,3:0.013:2,2:10:0:26:1:0.15138:6.23:60:2:0.0089:0:1.3 0/0:236:0:0,0:67,169:236,0:0:2,0:24.1:1:27.8:1:1:0:60:46.2:1:0:0.1 +X 76888654 . T A 162 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAATATAAACACATTTTTTA;RSEQ=TCAACTTGCTTCTTTATGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:342:0:0,0:237,105:342,0:0:2,0:23:1:30.9:1:1:0:60:113:1:0:0.1 0/1:390:44:37,7:243,102:345,44:0.1128:2,2:21.8:1:29.8:1:0.07355:2.21:60:43:0.1105:0:1.2 +X 76891446 . A G 194 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=34.06702;LSEQ=AATTTGATAACCATATTTCT;RSEQ=TGAACCTGCACTAAAGGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:771:2:2,0:420,349:769,2:0.0026:2,0:28.5:1:25:1:0.50384:0:60:1:0.0013:0:1 0/1:896:73:40,33:444,379:823,73:0.0815:2,2:27.8:1:31.4:1:0.90321:1.03:60:72:0.0816:0:1.2 +X 76907781 . TTCC T 131 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.000;MSILEN=3;SSF=0.7486;SOR=0.86426;LSEQ=TTTTCATCTTCCTCCTCCTC;RSEQ=TCCTCCTCCTCCTCTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:19:5,14:160,344:504,19:0.0362:2,2:24.1:1:30.5:1:0.80259:1.30174:60:38:0.0368:0.0095:0.2 0/1:700:22:9,13:246,428:674,22:0.0314:2,2:31.2:1:29.5:1:0.65979:1.20:59.6:21:0.0305:0.0014:0.1 +X 76918804 . A G 80 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01456;SOR=Inf;LSEQ=CCTCAGCTTCCCAAAGTGCT;RSEQ=GGATTACAGGCATAAGCCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:412:0:0,0:323,88:411,0:0:2,0:23.4:1:28.6:1:1:0:59.8:44.667:0.9975:0:0.1 0/1:405:6:3,3:297,99:396,6:0.0148:2,2:7:1:31.2:1:0.1739:2.99011:60:12:0.0149:0:1.7 +X 76919127 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.5001;SOR=0;LSEQ=TATTTTGCCTGTTGACAACT;RSEQ=CTGCAACTTATGAAAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:2:1,1:1,73:74,2:0.0263:1,2:18:1:27:0:0.05228:51.98:60:4:0.0263:0:1 0/0:64:0:0,0:1,63:64,0:0:1,0:24.3:1:30:1:1:0:59.4:128:1:0:0 +X 76919991 . T C 134 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00012;SOR=5.69963;LSEQ=CTCAAGTGATCCACCTGCTT;RSEQ=GGCCTCCCAAAGTCCTGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:11:11,0:67,0:67,11:0.141:1,0:24.3:1:32.4:1:1:0:46.1:22:0.141:0:1 0/1:41:20:20,0:21,0:21,20:0.4878:1,1:22.1:1:31.2:1:1:0:55.9:40:0.4878:0:1.1 +X 76931638 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.11513;SOR=Inf;LSEQ=ACTCCTGGTTTTTACAACCT;RSEQ=CTTGCTGTTCCGTTGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:137,34:171,0:0:2,0:23.4:1:32.1:1:1:0:60:56:1:0:0.1 0/1:163:3:1,2:125,35:160,3:0.0184:2,2:16.3:1:26.7:1:0.1294:7.02983:60:6:0.0185:0:1 +X 76931656 . G T 44 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.12211;SOR=0;LSEQ=CTGCTTGCTGTTCCGTTGCT;RSEQ=CTGTTTGTGCCCATGCCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:3:1,2:191,63:254,3:0.0117:2,2:14.7:1:28.3:1:0.15845:6.01097:60:6:0.0117:0:1 0/0:260:0:0,0:170,87:257,0:0:2,0:21.4:1:30.9:1:1:0:60:63.25:0.9883:0:0.1 +X 76931666 . C T 43 p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.3573;SOR=0.30938;LSEQ=TTCCGTTGCTGCTGTTTGTG;RSEQ=CCATGCCTAGGGTGTGTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:3:1,2:202,88:290,3:0.0102:2,2:5.3:1:27.7:1:0.22424:4.56413:60:6:0.0103:0:1 0/0:314:1:1,0:193,119:312,1:0.0032:2,0:24:0:31:0:1:0:60:2:0.0033:0:1 +X 76931741 . GTCA G 109 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.04225;SOR=3.56565;LSEQ=CTATTCTCAGGATCATTGTC;RSEQ=TCATCATCATCCACTGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:670:3:3,0:357,310:667,3:0.0045:2,0:20:1:30.3:1:0.25306:0:60:6:0.0046:0.0015:0.3 0/1:823:13:7,6:415,394:809,13:0.0158:2,2:27.8:1:29.5:1:1:1.11:60:26:0.016:0.0024:0.2 +X 76937963 . G C 228 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=5.75158;LSEQ=TTCCAAAGAAGTAAAACTCT;RSEQ=CTCTTTCCCAGAAAGCTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:42:18,24:175,159:334,42:0.1117:2,2:24.6:1:31.1:1:0.25622:1.466:60:41:0.1105:0:1.1 0/1:445:187:92,95:146,111:257,187:0.4202:2,2:24.4:1:30.3:1:0.12346:1.35724:60:92.5:0.4195:0:1.1 +X 76939830 . A G 192 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GATGTATGTTCATATACTTT;RSEQ=TTACTCTTTTCACTGTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:702:61:29,32:326,315:641,61:0.0869:2,2:25:1:32.4:1:0.68821:1.14176:59.7:60:0.0866:0:1.1 0/0:896:0:0,0:452,444:896,0:0:2,0:24.1:1:28.5:1:1:0:60:111:1:0:0.1 +X 76940534 . A G 232 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.000;MSILEN=1;SSF=0;SOR=5.75145;LSEQ=AGGAAGGGGAAATTTAATTC;RSEQ=AAATTGATAACATTCATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:49:15,34:107,259:366,49:0.1181:2,2:25:1:31.7:1:0.86793:1.07:60:98:0.1192:0:1.1 0/1:473:206:65,141:97,170:267,206:0.4355:2,2:25.4:1:30.2:1:0.28437:1.23718:60:412:0.4355:0:1.1 +X 76940627 . AT A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.20512;SOR=Inf;LSEQ=GGACACTGGTGTGGGCAAAG;RSEQ=TTATTGAGCATATTACACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:61:0:0,0:0,61:61,0:0:1,0:28.1:1:30.5:1:1:0:59.2:29.5:1:0:0.2 0/1:51:2:0,2:0,49:49,2:0.0392:1,0:15.5:1:30.5:1:1:0:60:4:0.0392:0.0196:1 +X 76944240 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21497;SOR=0;LSEQ=CATCTTTCTTCAAGACTGTG;RSEQ=CCTCAAAGGCCTGGTATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:2,0:162,29:191,2:0.0103:2,0:30.5:1:32:0:1:0:60:4:0.0109:0:1 0/0:225:0:0,0:182,43:225,0:0:2,0:23.6:1:30:1:1:0:60:15.071:1:0:0.1 +X 76949226 . G T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50791;SOR=Inf;LSEQ=TAAACAAAAGGCAGAAAAGT;RSEQ=GAGGTATTTTTAGTAAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:145:0:0,0:136,9:145,0:0:2,0:26.4:1:32.7:1:1:0:60:290:1:0:0 0/1:191:2:1,1:160,29:189,2:0.0105:2,2:14.5:1:29:1:0.29016:5.44152:60:4:0.0106:0:1 +X 76952289 . C G 118 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.30133;SOR=0.51605;LSEQ=GTTGAGATTGAGCAGTGGGT;RSEQ=TCAACAAGGAAGCACATCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:12:0,12:1,73:74,12:0.1395:1,0:26.8:1:33.1:1:1:0:60:24:0.1412:0:1.1 0/1:65:5:0,5:1,59:60,5:0.0769:1,0:29.2:1:31:1:1:0:60:10:0.0769:0:1 +X 76953957 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.23734;SOR=Inf;LSEQ=TGAAGTATAATGACAACTGG;RSEQ=TATCAGTAGCCTTCGACACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:163,27:190,0:0:2,0:22.3:1:31.4:1:1:0:59.9:94:1:0:0.1 0/1:181:2:1,1:153,26:179,2:0.011:2,2:21:1:27.5:1:0.2768:5.7935:60:4:0.0111:0:1 +X 76972553 . T TA 96 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.81103;SOR=0.8806;LSEQ=AATGGTTACCTCCATAAGTG;RSEQ=AAAAAAAAAATAGAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:8:5,3:139,42:181,8:0.0423:2,2:22.3:1:28.6:1:0.39807:1.97749:60:16:0.0432:0.0106:0.1 0/1:267:10:8,2:187,70:257,10:0.0375:2,2:32.8:1:29:1:1:1.50:59.5:20:0.0382:0:0.4 +X 77041336 . G T 24 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.50359;SOR=Inf;LSEQ=CGAAACCCTTCTCACCTAAA;RSEQ=AGAAAACGATGCCTCTTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:58,5:63,0:0:2,0:23.4:1:33.4:1:1:0:60:62:1:0:0.2 0/1:80:2:1,1:75,2:77,2:0.025:1,2:22.5:1:24:1:0.07498:30.84276:60:4:0.0263:0:1 +X 77041377 . A G 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.22125;SOR=0;LSEQ=GCTAAGCAACACACAGGCCT;RSEQ=ACCCACCAAGCGAACGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:135,58:193,2:0.0103:2,2:7.5:1:29.5:1:0.51467:2.31633:60:4:0.0103:0:1.5 0/0:219:0:0,0:153,66:219,0:0:2,0:21.2:1:27.7:1:1:0:60:108.5:1:0:0.1 +X 85302305 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49667;SOR=Inf;LSEQ=TCAAATGGCGATAAGCACTG;RSEQ=GGGTCCCAGCCCCTCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:15,11:26,0:0:2,0:28:1:30.3:1:1:0:60:12:1:0:0.2 0/1:32:2:1,1:14,16:30,2:0.0625:2,2:24.5:1:27.5:1:1:1.14:60:4:0.0625:0:1 +X 85302315 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.19831;SOR=0;LSEQ=ATAAGCACTGCGGGTCCCAG;RSEQ=CCCTCCCTGTAACTGCCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:2:1,1:14,11:25,2:0.0741:2,2:19.5:1:28.5:1:1:1.2613:60:4:0.0769:0:1 0/0:33:0:0,0:16,17:33,0:0:2,0:34.2:1:30.6:1:1:0:60:66:1:0:0.2 +X 86830845 . C T 200 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00352;SOR=1.80337;LSEQ=GCAAATCTTGGATTTCACTT;RSEQ=CATTTAACTAAAAATGAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:54:23,31:64,76:140,54:0.2784:2,2:27.1:1:30.1:1:0.74874:1.13427:60:53:0.2804:0:2 0/1:285:117:54,63:85,82:167,117:0.4105:2,2:26.5:1:29.2:1:0.47016:1.20853:59.9:116:0.4128:0:1.9 +X 86830854 . TA T 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.16756;SOR=0;LSEQ=GGATTTCACTTCCATTTAAC;RSEQ=AAAATGAGGGGCTAAAAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:2:1,1:84,103:187,2:0.0106:2,2:36:1:32:1:1:1.22:60:4:0.0107:0:0 0/0:272:0:0,0:127,145:272,0:0:2,0:26.2:1:28.6:1:1:0:60:67:1:0:0.9 +X 86830863 . G A 201 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00111;SOR=1.94015;LSEQ=TTCCATTTAACTAAAAATGA;RSEQ=GGGCTAAAAAGCAAATAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:52:21,31:67,78:145,52:0.264:2,2:21.8:1:31.1:1:0.51765:1.26649:60:51:0.2656:0:2 0/1:263:108:49,59:69,86:155,108:0.4106:2,2:27.2:1:29.8:1:0.90039:1.04:59.9:107:0.41:0:2 +X 86831002 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.1707;SOR=0;LSEQ=GTGTTGGTTTGAAAATTTGG;RSEQ=AAATACTGTGATAACATAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:2:0,2:0,14:14,2:0.125:1,0:42.5:1:30:0:1:0:60:4:0.125:0:1 0/0:22:0:0,0:0,22:22,0:0:1,0:25:1:30.9:1:1:0:60:44:1:0:0.2 +X 87956989 . C A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.22222;SOR=0;LSEQ=TTCGATTTTCAGCACTTTCT;RSEQ=ATTGATTCCTTCTCATCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:1,1:7,4:11,2:0.1538:2,2:17:0:31.5:1:1:1.67325:57.5:4:0.1667:0:1.5 0/0:14:0:0,0:7,7:14,0:0:2,0:21.4:1:30.4:1:1:0:58.6:28:1:0:0.2 +X 87957056 . G T 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.23256;SOR=Inf;LSEQ=AGGCTGCTGACTCTTGGATG;RSEQ=GGTTTTTGTGGGGGCCTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:10,12:22,0:0:2,0:29.4:1:31.7:1:1:0:59.8:44:1:0:0.2 0/1:21:2:1,1:9,10:19,2:0.0952:2,2:20:0:29:1:1:1.11:38:4:0.0952:0:1 +X 87957083 . T A 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12644;SOR=Inf;LSEQ=TGTGGGGGCCTTTTTTGTCG;RSEQ=TGTTGCTTTCTGCTTGTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:7,12:19,0:0:2,0:20.2:1:30.1:1:1:0:57.1:38:1:0:0.1 0/1:11:2:1,1:4,5:9,2:0.1818:2,2:5.5:1:25.5:1:1:1.22:53:4:0.1818:0:1.5 +X 90689704 . G A 92 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=2;SSF=0.71525;SOR=1.47899;LSEQ=CTCCGTTGGACTGTCCTGCG;RSEQ=AGAGAAACCCCAGCCCATCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:4,2:5,2:7,6:0.4615:2,2:18.8:1:30.5:1:1:1.22862:60:12:0.4615:0:1.2 1/0:16:9:7,2:5,2:7,9:0.5625:2,2:19.7:1:29.1:1:1:1.37:60:18:0.5625:0:1 +X 91136946 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49842;SOR=Inf;LSEQ=CATTACTCGTCTGAATAGAA;RSEQ=CAGGAAAGTGGAAAATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:125:0:0,0:54,71:125,0:0:2,0:26.6:1:29.8:1:1:0:23.6:61.5:1:0:0.1 0/1:132:2:1,1:57,73:130,2:0.0152:2,2:32:1:27:1:1:1.28:22:4:0.0154:0:1 +X 92181907 . T C 33 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAACACAAAAAAAGGAGAAA;RSEQ=CATTTTAAGTTAATTTATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:16:0:33:0:1:1:24:4:0.3333:0:1.5 +X 93324980 . A G 253 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.72393;SOR=0.92955;LSEQ=CTTTGTTTCAATTTATTTTA;RSEQ=CCCATGAACACCTTTTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:307:215:95,120:42,49:91,215:0.7003:2,2:25.1:1:32.7:1:0.80182:1.08242:60:214:0.7133:0:1.1 1/0:295:202:95,107:36,56:92,202:0.6847:2,2:26.8:1:31.5:1:0.25474:1.38:60:404:0.6894:0:1.1 +X 93325029 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49859;SOR=Inf;LSEQ=TTTCTCTTTATGTCTGATTG;RSEQ=TATGGCAAAATCCAGGATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:58,114:172,0:0:2,0:24:1:32.1:1:1:0:60:344:1:0:0.6 0/1:175:2:1,1:59,114:173,2:0.0114:2,2:29:1:28:1:1:1.92:60:4:0.0116:0:1.5 +X 93325074 . G A 78 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01314;SOR=Inf;LSEQ=ATAAGCTATGCATTCAAGAC;RSEQ=CCAGGTCCTTGAAACCATAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:64:0:0,0:12,52:64,0:0:2,0:22:1:32:1:1:0:60:128:1:0:0.1 0/1:63:6:2,4:10,47:57,6:0.0952:2,2:25:1:30.3:1:0.32007:2.31:60:12:0.0984:0:1.2 +X 93325079 . G T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4958;SOR=0;LSEQ=CTATGCATTCAAGACGCCAG;RSEQ=TCCTTGAAACCATACATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:2:1,1:10,48:58,2:0.0333:2,2:6.5:1:28.5:1:0.33559:4.62:60:4:0.0333:0:1.5 0/0:59:0:0,0:11,48:59,0:0:2,0:24:1:31.6:1:1:0:60:118:1:0:0.2 +X 93434358 . GT G 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.49908;SOR=0;LSEQ=CCTGAAGTGGCTTAGGAAAT;RSEQ=TTTTTTAACCTGTCAATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:116,70:186,2:0.0106:2,2:24.5:1:28.4:1:1:1.65244:60:4:0.0107:0.0053:0 0/0:177:0:0,0:105,72:177,0:0:2,0:23.2:1:29:1:1:0:60:176:1:0:0.3 +X 93434435 . G A 222 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1e-05;SOR=0.46176;LSEQ=TCAATAAACTTATTTTCTTC;RSEQ=TTGGGGACCTGTTATGGAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:153:79,74:45,52:97,153:0.612:2,2:24.7:1:30.7:1:0.43853:1.23:60:152:0.6154:0:1.1 0/1:285:120:59,61:84,79:163,120:0.4211:2,2:22.7:1:29.7:1:0.7193:1.09897:60:39:0.4179:0:1.3 +X 93434463 . C G 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00181;SOR=Inf;LSEQ=CCTGTTATGGAAAAGCAATT;RSEQ=CACTGCAGAAATTAATTAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:227:0:0,0:103,124:227,0:0:2,0:25.8:1:31.4:1:1:0:60:55.75:1:0:0.6 0/1:237:10:5,5:106,120:226,10:0.0422:2,2:17.3:1:29.1:1:1:1.13:60:20:0.0427:0:1.8 +X 93434491 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.50003;SOR=Inf;LSEQ=GAAATTAATTAGCTGACAGA;RSEQ=AAATCTTCCCATACAAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:167:0:0,0:63,104:167,0:0:2,0:27.8:1:32.6:1:1:0:60:82.5:1:0:0.5 0/1:186:2:1,1:70,114:184,2:0.0108:2,2:21.5:1:28:0:1:1.62:60:4:0.0108:0:2.5 +X 93434496 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49886;SOR=Inf;LSEQ=TAATTAGCTGACAGAGAAAT;RSEQ=TTCCCATACAAATGAATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:61,100:161,0:0:2,0:26.8:1:32.6:1:1:0:60:52.667:1:0:0.5 0/1:170:2:1,1:62,106:168,2:0.0118:2,2:27:1:29:1:1:1.70:60:4:0.0121:0:1 +X 97019100 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49868;SOR=Inf;LSEQ=CCACTTATCAGCAAAACCCT;RSEQ=GGCAACTGAGCTGGGGCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:128:0:0,0:96,32:128,0:0:2,0:24.8:1:31.5:1:1:0:60:31:1:0:0.1 0/1:137:2:1,1:92,43:135,2:0.0146:2,2:27:1:27:1:0.54079:2.12659:60:4:0.0147:0:1.5 +X 97019115 . G A 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24843;SOR=Inf;LSEQ=ACCCTGGGCAACTGAGCTGG;RSEQ=GCAGAATCAGCAGCTGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:164:0:0,0:109,54:163,0:0:2,0:23.8:1:30.9:1:1:0:60:53.333:0.9938:0:0.2 0/1:174:3:1,2:113,58:171,3:0.0172:2,2:17:1:24.3:1:0.27349:3.86388:60:2:0.0117:0:1.3 +X 97019120 . A T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24517;SOR=0;LSEQ=GGGCAACTGAGCTGGGGCAG;RSEQ=ATCAGCAGCTGAAACTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:2:1,1:117,60:177,2:0.0112:2,2:21:1:30.5:1:1:1.94226:60:4:0.0112:0:1.5 0/0:182:0:0,0:115,67:182,0:0:2,0:24.8:1:28.6:1:1:0:60:181:1:0:0.3 +X 97019123 . C A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2453;SOR=0;LSEQ=CAACTGAGCTGGGGCAGAAT;RSEQ=AGCAGCTGAAACTTTCATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:118,64:182,2:0.0109:2,2:14.5:1:30:0:1:1.83732:60:4:0.0109:0:1.5 0/0:187:0:0,0:119,68:187,0:0:2,0:25:1:30.2:1:1:0:60:61.333:1:0:0.3 +X 97019199 . G A 39 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.67118;SOR=1.67962;LSEQ=TTAACTTTTTCCATCCTCAT;RSEQ=CGTCATTGCTAAGGGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:327:2:2,0:163,162:325,2:0.0061:2,0:22.5:1:27.5:1:0.49851:0:60:4:0.0062:0:1.5 0/1:293:3:2,1:148,142:290,3:0.0102:2,2:9.3:1:25:1:1:1.91:60:6:0.0105:0:1.7 +X 97019201 . G A 229 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=2.19151;LSEQ=AACTTTTTCCATCCTCATGC;RSEQ=TCATTGCTAAGGGATTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:324:179:91,88:70,74:144,179:0.5525:2,2:27.5:1:30.8:1:0.73738:1.09:60:178:0.5528:0:1.1 1/0:293:214:109,105:40,39:79,214:0.7304:2,2:26.2:1:29.7:1:1:1.01:60:70.333:0.7301:0:1.1 +X 97019268 . C A 28 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.57575;SOR=2.75204;LSEQ=TCCACCCTGGTAATCAGTGC;RSEQ=TTACATACAATGGTAGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:1:1,0:79,150:229,1:0.0043:2,0:5:0:14:0:0.34783:0:60:0:0:0:1 0/1:168:2:1,1:57,109:166,2:0.0119:2,2:23:1:28.5:1:1:1.90:60:4:0.012:0:1 +X 97019326 . G A 174 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50795;SOR=0.70448;LSEQ=CTTTTCAAGAAAGGTGACTG;RSEQ=TAAGAATTTCTCAGGGACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:61:47:5,42:1,13:14,47:0.7705:1,2:24.9:1:31.5:1:1:1.54:60:46:0.7667:0:1.1 1/0:47:33:5,28:2,12:14,33:0.7021:2,2:21.6:1:30:1:1:1.07:60:32:0.6957:0:1.1 +X 97157710 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49826;SOR=Inf;LSEQ=GGATATGGCAATCCTTGCTT;RSEQ=TTGACAAGGATCCTTTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:15,3:18,0:0:2,0:22.5:1:32.9:1:1:0:60:36:1:0:0.1 0/1:24:2:1,1:18,4:22,2:0.0833:2,2:18:1:30:1:0.38043:4.13522:60:4:0.0833:0:1 +X 97157753 . T C 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12957;SOR=0;LSEQ=CTGAACTTTAGTCAGGCTCC;RSEQ=GAAACTTCTTCTAGGCCTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:1,1:18,12:30,2:0.0625:2,2:36.5:1:30:1:1:1.48061:60:4:0.0625:0:1 0/0:56:0:0,0:30,26:56,0:0:2,0:25:1:29.3:1:1:0:58:55:1:0:0.1 +X 100056870 . G A 44 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21183;SOR=4.1266;LSEQ=ACAAACTTATTAGTAATAAT;RSEQ=ATGGTAGTATCTTTGATGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:404:1:1,0:178,225:403,1:0.0025:2,0:1:0:26:0:0.44307:0:55:2:0.0025:0:1 0/1:394:4:2,2:185,205:390,4:0.0102:2,2:11.5:1:22.3:1:1:1.11:52:3:0.0077:0:2 +X 100057572 . C T 229 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=AGCTATGCCTCCACCACCAC;RSEQ=TCAGGGAGTTAAGTGAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:176:95,81:262,221:483,176:0.2671:2,2:27:1:30.7:1:1:1.0108:52.7:87:0.2681:0:1.1 0/0:766:0:0,0:395,370:765,0:0:2,0:24.7:1:30.4:1:1:0:57.2:28.423:1:0:0.2 +X 100594828 . G T 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.22321;SOR=0;LSEQ=CTATTTGATATGCCAGTGTT;RSEQ=TGTGGGAAGTATAATTCTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:2:1,1:102,38:140,2:0.0141:2,2:29.5:1:26:1:0.47528:2.66253:57.5:4:0.0142:0:6 0/0:158:0:0,0:120,38:158,0:0:2,0:21:1:30.8:1:1:0:60:51.667:1:0:0.1 +X 100594834 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50074;SOR=Inf;LSEQ=GATATGCCAGTGTTGTGTGG;RSEQ=AAGTATAATTCTTTTTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:112,51:163,0:0:2,0:20.3:1:30.7:1:1:0:60:31.6:1:0:0.2 0/1:186:2:1,1:132,52:184,2:0.0108:2,2:14:0:30:1:0.4898:2.52391:60:4:0.0109:0:1 +X 100594872 . G T 51 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13218;SOR=Inf;LSEQ=TAAAAAAGAGCTTCCTTTTG;RSEQ=CCGGAACTGCCATCTTTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:307:0:0,0:176,130:306,0:0:2,0:28.2:1:31.1:1:1:0:59:33:1:0:0.2 0/1:379:4:1,3:211,164:375,4:0.0106:2,2:12.5:1:25.8:1:0.32462:3.84681:53.8:8:0.0108:0:1 +X 100595660 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.000;MSILEN=1;SSF=0.50634;SOR=Inf;LSEQ=TGTGTCTACACTGTTAACCA;RSEQ=CATGCTGTTGGCATTGTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:50:0:0,0:23,27:50,0:0:2,0:31.1:1:32.8:1:1:0:60:49:1:0:0 0/1:67:2:1,1:27,38:65,2:0.0299:2,2:14:1:29.5:1:1:1.40:57:4:0.0299:0:1 +X 100604681 . C T 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01681;SOR=Inf;LSEQ=AATTTCAGGCACAATAATTT;RSEQ=TTGGCCTTTGCTCAGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:26,0:26,0:0:1,0:23.3:1:32.2:1:1:0:60:25:1:0:0.2 0/1:10:3:3,0:7,0:7,3:0.3:0,0:15.3:1:31.7:1:1:0:60:6:0.3:0:1 +X 100604757 . T G 181 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.000;MSILEN=1;SSF=0.12934;SOR=0.58919;LSEQ=AGATGTAGAGAGGGGCCTTT;RSEQ=TGTATTGAGTGGGAGCACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:46:46,0:32,2:34,46:0.575:2,1:26:1:32.9:1:0.17753:0:59.3:92:0.575:0:1 0/1:61:27:27,0:34,0:34,27:0.4426:1,1:20.1:1:32.8:1:1:0:60:54:0.4426:0:1 +X 100608120 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18309;SOR=Inf;LSEQ=CAGTCTTTGGTGGCTGAATG;RSEQ=CCAGCTAAATGGGCAAGTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:240:0:0,0:195,44:239,0:0:2,0:26.8:1:30.8:1:1:0:59.9:16.071:1:0:0.3 0/1:180:2:1,1:129,49:178,2:0.0111:2,2:15.5:1:28:1:0.47952:2.61628:60:4:0.0113:0:1.5 +X 100608191 . G A 215 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=250.71601;LSEQ=AAAGCACTTACCTCATGCCA;RSEQ=CAACTGTACATGATGGTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:490:1:1,0:281,208:489,1:0.002:2,0:1:0:29:0:1:0:60:2:0.0021:0:1 0/1:471:160:87,73:175,135:310,160:0.3397:2,2:25.5:1:29.5:1:0.69562:1.0875:60:79:0.3383:0:1.2 +X 100609517 . G GA 70 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.0291;SOR=0;LSEQ=GGCAGAAAACGCTAGAATGA;RSEQ=AAAAAAAAGAAAAGGAGAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:5:4,1:158,13:171,5:0.0284:2,2:21.2:1:30.5:1:0.34258:3.00912:60:10:0.0286:0.017:0.4 0/0:179:0:0,0:161,18:179,0:0:2,0:20.8:1:31.5:1:1:0:60:88.5:1:0:0.8 +X 100609547 . G A 235 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=7.53694;LSEQ=AAAAGGAGAGGATTAAAACT;RSEQ=TAACACCTACCCATGTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:171:130,41:133,46:179,171:0.4886:2,2:22.6:1:29:1:0.71277:1.10:60:56:0.4855:0:1.1 1/1:370:325:238,87:32,12:44,325:0.8784:2,2:22:1:28.2:1:1:1.03:60:161.5:0.8801:0:1.1 +X 100611131 . C T 76 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.01679;SOR=Inf;LSEQ=GCAGCTGCTGAGTCTGGAAG;RSEQ=GGTGGCGCATCTCCCTCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:596:0:0,0:259,337:596,0:0:2,0:23.7:1:30.8:1:1:0:60:48.667:1:0:0.1 0/1:680:7:2,5:310,359:669,7:0.0103:2,2:21:1:27.4:1:0.46043:2.15643:60:14:0.0104:0:1 +X 100611283 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49875;SOR=Inf;LSEQ=GAAAGGCAAGGAACTAGTCT;RSEQ=CTCCTTTTGGCTCTGCATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:200:0:0,0:52,148:200,0:0:2,0:23.2:1:30.2:1:1:0:60:49:1:0:0.2 0/1:200:2:1,1:53,145:198,2:0.01:2,2:15:1:32:0:0.46809:2.72:60:4:0.0104:0:1 +X 100611285 . T C 172 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AAGGCAAGGAACTAGTCTTC;RSEQ=CCTTTTGGCTCTGCATAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:191:0:0,0:50,141:191,0:0:2,0:23.4:1:30.3:1:1:0:60:30.833:1:0:0.2 0/1:192:59:14,45:38,93:131,59:0.3073:2,2:20.7:1:29.4:1:0.48684:1.31152:60:28.5:0.3032:0:1.2 +X 100611299 . C A 34 q25 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.62245;SOR=0.33684;LSEQ=GTCTTCTCCTTTTGGCTCTG;RSEQ=ATAATAGCAATAAAGGGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:3:2,1:35,106:141,3:0.0207:2,2:15.7:1:22:1:0.16217:5.96:60:2:0.0142:0:2 0/0:142:1:1,0:36,105:141,1:0.007:2,0:1:0:24:0:0.26056:0:60:2:0.0072:0:1 +X 100612389 . C T 25 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49871;SOR=Inf;LSEQ=TGTCTTGAGCGTCCTTGAGG;RSEQ=AGCTGCTGCAGAACAGTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:194:0:0,0:177,17:194,0:0:2,0:24.2:1:32.4:1:1:0:59.9:37.8:1:0:0.1 0/1:195:2:1,1:169,23:192,2:0.0103:2,2:5.5:1:25.5:1:0.23268:7.21356:60:4:0.0104:0:1 +X 100613489 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=5;SSF=0.49844;SOR=Inf;LSEQ=AACAGAACCCAGGAAGTGAA;RSEQ=TGAGATGAGTTTTGAGTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:80,79:159,0:0:2,0:22:1:32.6:1:1:0:60:38.75:1:0:0.1 0/1:161:2:1,1:78,81:159,2:0.0124:2,2:14.5:1:28.5:1:1:1.04:60:4:0.0126:0:1 +X 100613537 . G T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2516;SOR=Inf;LSEQ=GAGGAAGTGGGACGGGCACA;RSEQ=CATCAAGGAGCTATTAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:223:0:0,0:156,67:223,0:0:2,0:24.5:1:32.8:1:1:0:59.9:73.333:1:0:0.1 0/1:254:3:1,2:153,96:249,3:0.0118:2,2:23:1:26.7:1:0.56193:3.17253:60:6:0.0122:0:1 +X 100613750 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.24301;SOR=Inf;LSEQ=ACACCTGCATCCCACCTGCC;RSEQ=AAACTTGAGAGAGAAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:38,160:198,0:0:2,0:23:1:31.6:1:1:0:60:27.286:1:0:0.1 0/1:193:2:1,1:43,148:191,2:0.0104:2,2:40.5:1:29.5:1:0.4049:3.41:60:4:0.0104:0:1 +X 100614139 . CA C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.50093;SOR=0;LSEQ=CCGTCTCAGAAAAACAAAAA;RSEQ=AAAAAAATGGTGTAATTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:2:2,0:89,2:91,2:0.0215:1,0:29.5:1:31.5:1:1:0:60:4:0.022:0:0 0/0:78:0:0,0:78,0:78,0:0:1,0:24.7:1:29.8:1:1:0:60:156:1:0:0.1 +X 100614867 . GTA G 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.54972;SOR=0;LSEQ=TGTTGAAAGTAGAAAAAAGT;RSEQ=TATATATATATACACACTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:3:3,0:17,3:20,3:0.1304:2,0:16.3:1:32.4:1:1:0:60:6:0.1304:0.087:0 0/0:8:0:0,0:8,0:8,0:0:0,0:21.6:1:30:1:1:0:60:16:1:0:0 +X 100614965 . TTA T 73 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.000;MSILEN=2;SSF=0.22742;SOR=0.24059;LSEQ=CATATATACACTTGTGTGTG;RSEQ=TATATATATATAAATATATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:5:5,0:87,5:92,5:0.0515:2,0:30.6:1:31.5:1:1:0:60:10:0.0515:0.0103:0 0/1:78:1:1,0:73,3:76,1:0.0128:1,0:20:0:32:0:1:0:60:2:0.013:0:0 +X 100614997 . T TATAA 60 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=4.000;MSILEN=4;SSF=0.42006;SOR=2.36735;LSEQ=ATAAATATATATAAAATATA;RSEQ=ATAAATAAATAAATATATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:2:1,1:148,30:178,2:0.0111:2,2:12.5:1:31.9:1:0.31558:4.86957:52.5:8:0.002:0.01:2.5 0/1:154:4:3,1:114,36:150,4:0.026:2,2:11:1:30.4:1:1:1.05519:58.8:8:0.026:0.013:1.8 +X 100615009 . AAT A 123 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.69162;SOR=0.79844;LSEQ=AAAATATATATAAATAAATA;RSEQ=ATATATATATATAGAGAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:16:13,3:166,65:231,16:0.0648:2,2:26.5:1:30.8:1:0.56741:1.69:59.7:32:0.0648:0.004:0.1 0/1:210:11:7,4:141,59:200,11:0.0524:2,2:10.9:1:28.4:1:0.73632:1.36352:59.5:22:0.0526:0.0333:0.5 +X 100615023 . TAG T 90 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=7.000;MSILEN=2;SSF=0.47323;SOR=1.45453;LSEQ=TAAATAAATATATATATATA;RSEQ=AGAGAGAGAGTTCCTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:7:6,1:226,98:324,7:0.021:2,2:34.4:1:32.9:1:0.67892:2.60:60:14:0.0211:0:0 0/1:330:10:4,6:213,106:319,10:0.0303:2,2:22.3:1:27.1:1:0.09531:3.00315:59:9:0.0274:0.0091:0.9 +X 100615025 . G T 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.24155;SOR=1.2239;LSEQ=AATAAATATATATATATATA;RSEQ=AGAGAGAGAGTTCCTCCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:94:68,26:163,76:239,94:0.2765:2,2:20.3:1:30:1:0.51031:1.22:59.3:93:0.2827:0:1.1 0/1:342:109:75,34:146,80:226,109:0.3187:2,2:18.2:1:29.1:1:0.46315:1.21:59.5:218:0.3313:0:1.2 +X 100615027 . G T 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=2;SSF=0.21362;SOR=0.24425;LSEQ=TAAATATATATATATATAGA;RSEQ=AGAGAGAGTTCCTCCTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:4:3,1:245,110:355,4:0.0111:2,2:11:1:25.8:1:1:1.35:49.5:3:0.0084:0:2 0/0:365:1:1,0:236,128:364,1:0.0027:2,0:7:0:24:0:1:0:60:2:0.0028:0:2 +X 100615217 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.1799;SOR=Inf;LSEQ=TTCATATGCCCACGTCCCTG;RSEQ=GCTCAGAACAAATCTCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:260:0:0,0:53,207:260,0:0:2,0:22.6:1:31.6:1:1:0:60:129:1:0:0.1 0/1:192:2:1,1:36,154:190,2:0.0104:2,2:35:1:29:1:0.34909:4.23:60:4:0.0105:0:1 +X 100615478 . C T 212 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.22721;LSEQ=TCTGATGAGGATGCTGATCA;RSEQ=GGGAATTATGCCGCAGCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:198:113:98,15:81,4:85,113:0.5707:1,2:22.8:1:31.1:1:0.05174:3.08399:60:55.5:0.5692:0:1 0/1:173:40:36,4:110,23:133,40:0.2312:2,2:21.6:1:30.5:1:0.32776:1.88:60:39:0.2281:0:1.1 +X 100615505 . G T 174 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=0.0189;LSEQ=TATGCCGCAGCACTTTTTGC;RSEQ=TGTAGGGAGTGGGCAGGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:44:37,7:209,55:264,44:0.1429:2,2:25.5:1:32:1:0.54558:1.39:60:88:0.1443:0:1 0/0:320:1:0,1:224,95:319,1:0.0031:2,0:1:0:27:0:0.3:0:60:2:0.0031:0:1 +X 100615777 . T A 31 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.34332;SOR=3.4552;LSEQ=AGAAAAGGTAGGAGGGTTTG;RSEQ=CAAGATACCAAGCACTCTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:293:1:1,0:66,226:292,1:0.0034:2,0:1:0:25:0:0.22867:0:60:2:0.0034:0:1 0/1:256:3:3,0:78,175:253,3:0.0117:2,0:8.7:1:20:1:0.03087:0:60:2:0.0079:0:1 +X 100615793 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2144;SOR=Inf;LSEQ=TTTGTCAAGATACCAAGCAC;RSEQ=CTTCTCTTCTCTCCCAACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:207:0:0,0:33,174:207,0:0:2,0:24.2:1:30.3:1:1:0:60:40.4:1:0:0.1 0/1:179:2:1,1:40,136:176,2:0.0112:2,2:16:1:29.5:1:0.40862:3.37:60:4:0.0114:0:1 +X 100616989 . C T 103 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=3e-05;SOR=Inf;LSEQ=ACATGGTTGCTGAGAGCCTT;RSEQ=TATCTTTCCATCGAGGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:63:0:0,0:63,0:63,0:0:1,0:22.9:1:32.2:1:1:0:59.8:62:1:0:0 0/1:45:11:10,1:34,0:34,11:0.2444:1,2:25.3:1:29.8:1:0.24444:0:60:22:0.25:0:1.2 +X 100617372 . T C 166 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=7e-05;SOR=5.64174;LSEQ=GCATGCCAGGTCACATAGCT;RSEQ=GGAGAGCAGATTACCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:43:12,31:12,31:43,43:0.5:2,2:27.8:1:30.7:1:1:1:59.5:86:0.5:0:1 1/1:47:40:8,32:3,4:7,40:0.8511:2,2:23.6:1:29.5:1:0.32963:2.91644:60:80:0.8511:0:1.1 +X 100617706 . A T 149 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGAAAGAAGAGAGAGATCAC;RSEQ=TCTGACATGGAGGAGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:99,254:353,0:0:2,0:23.4:1:30.9:1:1:0:60:49.429:1:0:0.2 0/1:376:35:8,27:105,236:341,35:0.0931:2,2:23.9:1:29.2:1:0.43901:1.50008:60:34:0.0914:0:1.1 +X 100624728 . TTTCTTTG T 63 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAAATACAAACTTTCCTTTG;RSEQ=TTATTTGTCTTTCTTTCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:4:4,0:4,0:4,4:0.5:0,0:40.3:1:31.5:1:1:0:44:8:0.5714:0:0 0/0:1:0:0,0:1,0:1,0:0:0,0:14:0:32:0:1:0:60:2:1:0:0 +X 100624842 . A AT 48 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.05427;SOR=Inf;LSEQ=TCTTTTCTCCCCTTCTATCC;RSEQ=TTTTTTTCTTCTTTTCTCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:41:0:0,0:39,2:41,0:0:1,0:15.9:1:29.6:1:1:0:59.9:19.5:1:0:0.2 0/1:26:3:3,0:23,0:23,3:0.1154:1,0:10:1:30.7:1:1:0:60:6:0.1154:0.0769:0 +X 100624920 . C T 28 v3;p8 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.60357;SOR=0.44391;LSEQ=TCCTTCTTTCCTTTTCCTCC;RSEQ=GTCTATCTCCTCTTCCTTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:2:1,1:141,14:155,2:0.0127:2,2:5.5:1:28:1:0.18251:9.76438:60:4:0.013:0:1 0/0:176:1:0,1:149,26:175,1:0.0057:2,0:1:0:24:0:0.15341:0:60:2:0.0058:0:1 +X 100624939 . C T 62 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.13095;SOR=Inf;LSEQ=CCGTCTATCTCCTCTTCCTT;RSEQ=CTTTCCTTCTTTCTTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:216:0:0,0:170,45:215,0:0:2,0:22.8:1:31.6:1:1:0:60:106.5:0.9953:0:0.1 0/1:264:4:2,2:201,59:260,4:0.0152:2,2:8.5:1:31:1:0.22923:3.3868:60:8:0.0154:0:2 +X 100624945 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25566;SOR=Inf;LSEQ=ATCTCCTCTTCCTTCCTTTC;RSEQ=TTCTTTCTTTGGAAACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:178,59:237,0:0:2,0:22.8:1:31.1:1:1:0:60:46.4:1:0:0.1 0/1:288:3:2,1:207,78:285,3:0.0104:2,2:14.3:1:24.3:1:1:1.32554:60:2:0.0071:0:1.7 +X 100626506 . C T 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50218;SOR=0;LSEQ=CTTGGTTCAGCATCCTTGTC;RSEQ=ACCTCAACTTCTATTCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:2:1,1:143,16:159,2:0.0124:2,2:11.5:1:28:0:0.20062:8.70277:60:4:0.0127:0:1 0/0:135:0:0,0:124,11:135,0:0:2,0:23.9:1:29.5:1:1:0:60:44:1:0:0.1 +X 100626751 . A G 47 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.25053;SOR=Inf;LSEQ=GCTCTTTTCTGAATTTCCTT;RSEQ=GGTACTAGAAGCCTTTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:166:0:0,0:27,139:166,0:0:2,0:23.1:1:31.7:1:1:0:60:54.333:1:0:0.1 0/1:187:3:1,2:46,138:184,3:0.016:2,2:15.7:1:30:1:1:1.50:60:6:0.016:0:1 +X 100626764 . C A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.60556;SOR=0.44953;LSEQ=TTTCCTTAGGTACTAGAAGC;RSEQ=TTTTGCTGTGGCTTCAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:19,111:130,2:0.0152:2,2:9:1:29.5:1:0.28105:5.72:60:4:0.0153:0:1 0/0:146:1:1,0:28,117:145,1:0.0068:2,0:1:0:24:0:0.19863:0:60:2:0.0069:0:1 +X 100626864 . C T 106 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.06531;SOR=0.28375;LSEQ=ACATATCCAATACGACCCAA;RSEQ=ACATACCCAGTCAAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:0,14:0,10:10,14:0.5833:0,1:33:1:28:1:1:0:60:13:0.5652:0:1.1 0/1:18:5:0,5:0,13:13,5:0.2778:1,0:22.8:1:27.2:1:1:0:60:10:0.2778:0:1.2 +X 100627125 . G T 31 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCAAGCTTTTTCTAATATAA;RSEQ=GATGAAACTTAGAACTATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:19.5:1:31:1:1:0:60:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 100629354 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12367;SOR=Inf;LSEQ=GAGATGTTCTGAATATGAAG;RSEQ=AAAGAAGCTAAGATTCTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:47,0:47,0:0:1,0:26.3:1:31.4:1:1:0:58.9:94:1:0:0 0/1:26:2:2,0:24,0:24,2:0.0769:1,0:32:1:27.5:1:1:0:60:4:0.08:0:1 +X 100629673 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19116;SOR=Inf;LSEQ=AAAGATTAAGAGGGATTAAG;RSEQ=AACCAGATGATTAGATTTTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:186:0:0,0:15,171:186,0:0:2,0:23.1:1:32.7:1:1:0:59.7:185:1:0:0.1 0/1:145:2:1,1:15,128:143,2:0.0138:2,2:12.5:1:26:1:0.2092:8.29:60:4:0.0139:0:1 +X 100629748 . G GA 65 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=0.28975;SOR=0;LSEQ=GGACCTGTCATGTGGGGGAA;RSEQ=AAAAAAAAATCCTTCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:4:0,4:4,39:43,4:0.0851:2,0:27.5:1:32.8:1:1:0:50:8:0.087:0:0 0/0:27:0:0,0:0,27:27,0:0:1,0:19.1:1:30.7:1:1:0:60:54:1:0:0.1 +X 100630054 . T A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.51143;SOR=0;LSEQ=CCTCCTCCTACCAACGAAAA;RSEQ=TTACCTCTTCCCCAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:2:1,1:170,27:197,2:0.0101:2,2:32:1:32:1:0.26222:6.20101:60:4:0.0101:0:1 0/0:144:0:0,0:122,22:144,0:0:2,0:22.3:1:30:1:1:0:60:143:1:0:0.1 +X 100630321 . C A 32 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.25242;SOR=Inf;LSEQ=TGCTGTTGATAATGAAAGTT;RSEQ=CTGAGGACCCAGGACATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:255:0:0,0:55,200:255,0:0:2,0:25.5:1:31.5:1:1:0:60:84:1:0:0.1 0/1:294:3:3,0:87,204:291,3:0.0102:2,0:5.3:1:20.3:1:0.02802:0:60:2:0.0069:0:1.7 +X 100630329 . C G 138 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATAATGAAAGTTCCTGAGGA;RSEQ=CCAGGACATTAATCCTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:226:0:0,0:42,184:226,0:0:2,0:25.9:1:31.4:1:1:0:60:55.5:1:0:0.1 0/1:250:21:5,16:58,171:229,21:0.084:2,2:22.4:1:31.5:1:1:1.08503:60:42:0.0864:0:1.1 +X 100630500 . G A 84 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=1;LSEQ=ATGCACACTGAATTGGGGGG;RSEQ=GATTGGTTCGATGTTGTGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:0,6:0,6:6,6:0.5:0,0:25.8:1:32.5:1:1:0:60:12:0.5:0:1 1/0:2:1:0,1:0,1:1,1:0.5:0,0:16:0:32:0:1:0:60:2:0.5:0:1 +X 100645467 . T C 239 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=82.94161;LSEQ=GCCTATTAGATTACTGTACC;RSEQ=CTCCCCCGGAACAGTGCCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:600:4:2,2:331,264:595,4:0.0067:2,2:20.5:1:31.3:1:1:1.2533:60:8:0.0068:0:1 0/1:661:237:129,108:221,202:423,237:0.3585:2,2:25.8:1:30.4:1:0.62595:1.09:60:117.5:0.3615:0:1.1 +X 101870343 . AAGTGGGTGGCTCTTAAAAGTGACTTTGAGTTGGGTAGAATTATTGCTGAGGAAGCTTTATGCTTTCTGTCTACGAATGTGGCATGTAAGCTCGATGTTCTTGAGCATGATAGTCACTCAG A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.21187;SOR=Inf;LSEQ=CATAATTATGTTTTCAGATA;RSEQ=AGTGGATGGCGCACAGATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:51:0:0,0:51,0:51,0:0:1,0:22.1:1:30.5:1:1:0:60:50:1:0:0.1 0/1:44:2:1,1:41,1:42,2:0.0455:1,2:17:1:27.6:1:0.08985:29.33286:60:4:0.0455:0.0455:0 +X 101870511 . G A 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.05043;SOR=Inf;LSEQ=CAAAGAGCCCCACCAGGTAG;RSEQ=CCTCTCACACTTCCTGCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:428:0:0,0:213,213:426,0:0:2,0:24.2:1:31.5:1:1:0:59.9:52.25:0.9952:0:0.1 0/1:387:4:2,2:178,205:383,4:0.0103:2,2:20.8:1:27.5:1:1:1.15:60:8:0.0105:0:1 +X 101870739 . AT A 51 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=0.53295;LSEQ=CGGGCTACCTTGGTGGCCAG;RSEQ=TTTTTTTTTGTTTGTTTTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:3:0,3:1,77:78,3:0.037:1,0:29:1:32.7:1:1:0:60:6:0.038:0:0 0/1:50:1:0,1:1,48:49,1:0.02:1,0:16:0:32:0:1:0:60:2:0.0208:0:0 +X 101870747 . TTTG T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=11.000;MSILEN=1;SSF=0.5052;SOR=0;LSEQ=CTTGGTGGCCAGATTTTTTT;RSEQ=TTTGTTTTATAATTTTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:2:0,2:1,58:59,2:0.0328:1,0:19.5:1:29.7:1:1:0:54:4:0.0333:0.0164:0.5 0/0:46:0:0,0:1,45:46,0:0:1,0:22.7:1:29:1:1:0:58.4:45:1:0:0.4 +X 102721317 . G A 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03116;SOR=Inf;LSEQ=AGATGTGGAAGTGATCAGGT;RSEQ=CAACTCGAATTTTTCATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:67:0:0,0:37,30:67,0:0:2,0:25.8:1:31.8:1:1:0:60:66:1:0:0.1 0/1:79:6:5,1:48,25:73,6:0.0759:2,2:24.8:1:27.3:1:0.65762:2.58:60:12:0.0759:0:1 +X 102721326 . A T 87 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.00728;SOR=Inf;LSEQ=AGTGATCAGGTGCAACTCGA;RSEQ=TTTTTCATACAAGCAAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:42,36:78,0:0:2,0:27.6:1:29.9:1:1:0:60:18.5:1:0:0.1 0/1:88:8:6,2:50,30:80,8:0.0909:2,2:27.4:1:29.3:1:0.70524:1.79:60:16:0.092:0:1 +X 102721361 . GGGT G 80 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.03879;SOR=Inf;LSEQ=AAAGCCCGAGTCAGCGTGAG;RSEQ=GGTGGTGGTGGGGCAGGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:99:0:0,0:45,54:99,0:0:2,0:27.6:1:31.5:1:1:0:60:98:1:0:0.1 0/1:132:6:3,3:60,65:125,6:0.0455:2,2:24:1:31.3:1:1:1.08:59.2:12:0.0455:0:0.5 +X 102721388 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52257;SOR=Inf;LSEQ=GGTGGTGGGGCAGGGAGAGA;RSEQ=TGCCATTGCTTGGAGTTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:27,42:69,0:0:2,0:25.8:1:32.9:1:1:0:60:138:1:0:0.1 0/1:109:2:1,1:42,65:107,2:0.0183:2,2:47.5:1:29.5:1:1:1.54:60:4:0.0183:0:1.5 +X 102721403 . GT G 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.13889;SOR=0;LSEQ=AGAGACTGCCATTGCTTGGA;RSEQ=TACTTAGGACACAGTCAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:17,32:49,2:0.0392:2,2:29:1:33.5:1:1:1.86:60:4:0.0392:0:0 0/0:85:0:0,0:27,58:85,0:0:2,0:26.1:1:29:1:1:0:60:170:1:0:0.2 +X 105425922 . C T 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.11494;SOR=0;LSEQ=GCAAGATGGCTGTCACGGGA;RSEQ=CTAGAAAGGGGAGAAGCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:2:0,2:13,5:18,2:0.1:2,0:5:1:28:1:0.11053:0:22.5:4:0.1:0:1 0/0:38:0:0,0:22,16:38,0:0:2,0:21.2:1:30.6:1:1:0:26.6:76:1:0:0.2 +X 106444086 . T C 83 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00423;SOR=Inf;LSEQ=GTCAAATGCAAAAGACAGCC;RSEQ=CAAAGGTACGCCCATATTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:33,0:0:1,0:28.2:1:32.6:1:1:0:60:66:1:0:0.1 0/1:31:7:7,0:24,0:24,7:0.2258:1,0:23.6:1:29.7:1:1:0:60:14:0.2333:0:1 +X 106444141 . C CA 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.49781;SOR=Inf;LSEQ=AAAACTCTGGAAAAGTAGAG;RSEQ=AAAAAAACCCTCAAAAAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:76:0:0,0:59,17:76,0:0:2,0:23.3:1:32.2:1:1:0:60:37:1:0:0.2 0/1:83:2:1,1:67,14:81,2:0.0241:2,2:9.5:1:26.3:1:0.33059:4.65785:60:4:0.0244:0.012:0 +X 106444209 . G A 174 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=AATCATAAAAACCTTTTACA;RSEQ=ACATGCAAGTAAGAAAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:0:0,0:111,100:211,0:0:2,0:25.8:1:32.6:1:1:0:60:69.333:1:0:0.1 0/1:238:67:34,33:86,85:171,67:0.2815:2,2:29.3:1:28.7:1:1:1.02:60:32.5:0.2766:0:1.1 +X 106515857 . G A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24877;SOR=Inf;LSEQ=ATTTCTACGACTATGACGGC;RSEQ=GGGAGGATTTCTACCGCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:275:0:0,0:127,148:275,0:0:2,0:25:1:30.9:1:1:0:59.9:274:1:0:0.2 0/1:282:3:2,1:130,148:278,3:0.0106:2,2:14:1:27:1:0.60219:2.27:60:6:0.0107:0:1 +X 106515879 . C A 32 v3;q25 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=1;SOR=1.48594;LSEQ=GGAGGATTTCTACCGCTCCA;RSEQ=GACGCCCAGCGAGGACATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:234:2:2,0:116,116:232,2:0.0085:2,0:1:0:29:0:0.49789:0:60:4:0.0087:0:1 0/1:237:3:3,0:100,133:233,3:0.0127:2,0:9:1:20.7:1:0.08176:0:60:2:0.0085:0:1 +X 106515914 . T G 114 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=2e-05;SOR=Inf;LSEQ=ACATCTGGAAGAAATTCGAG;RSEQ=TGGTGCCGCCGCCCTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:79,94:173,0:0:2,0:25.2:1:30:1:1:0:59.7:56.667:1:0:0.1 0/1:144:13:6,7:57,74:131,13:0.0903:2,2:22.6:1:30.9:1:1:1.11:56.8:26:0.0909:0:1.2 +X 106515938 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.19084;SOR=Inf;LSEQ=TGCCGCCGCCCTGGGACTTG;RSEQ=GTCCCGCAGCCGGGAACCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:0:0,0:57,79:136,0:0:2,0:22.9:1:31:1:1:0:59.8:67:1:0:0.1 0/1:106:2:1,1:41,63:104,2:0.0189:2,2:19.5:1:27.5:1:1:1.53:60:4:0.0192:0:1 +X 106515940 . T A 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.50739;SOR=0;LSEQ=CCGCCGCCCTGGGACTTGGG;RSEQ=CCCGCAGCCGGGAACCCAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:2:1,1:56,74:130,2:0.0152:2,2:23:1:29:1:1:1.32:55.5:4:0.0155:0:1 0/0:100:0:0,0:38,61:99,0:0:2,0:23.8:1:28.5:1:1:0:59.6:98:1:0:0.2 +X 106516025 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50027;SOR=0;LSEQ=GGGACGAGACGGAATCCCAG;RSEQ=ACTACTGGAAAGCTTGGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:2:1,1:62,58:120,2:0.0164:2,2:21:1:30:0:1:1.06835:60:4:0.0167:0:1 0/0:106:0:0,0:62,44:106,0:0:2,0:22:1:30:1:1:0:60:105:1:0:0.2 +X 106516056 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49844;SOR=Inf;LSEQ=AGCTTGGGACGCGAACTACG;RSEQ=CTCCCTCATCCGCCGTGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:161:0:0,0:77,84:161,0:0:2,0:26.6:1:31.5:1:1:0:59.8:79.5:1:0:0.2 0/1:161:2:1,1:86,73:159,2:0.0124:2,2:31:1:27:1:1:1.17688:60:4:0.0127:0:1 +X 106516061 . C A 29 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49877;SOR=Inf;LSEQ=GGGACGCGAACTACGCCTCC;RSEQ=TCATCCGCCGTGACTGCATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:160:0:0,0:75,85:160,0:0:2,0:27.5:1:32.3:1:1:0:59.8:79:1:0:0.2 0/1:168:2:1,1:86,80:166,2:0.0119:2,2:31:0:29:1:1:1.07451:60:4:0.012:0:1.5 +X 106516102 . G A 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.62444;SOR=2.72762;LSEQ=TGGAGCGGCTTCTCCACCCA;RSEQ=GAGCCGCTGGAGAGAGCGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:136:1:1,0:51,84:135,1:0.0074:2,0:1:0:25:0:0.38235:0:60:2:0.0076:0:1 0/1:151:3:2,1:64,84:148,3:0.0199:2,2:10.3:1:27.7:1:0.5811:2.61:52.3:6:0.02:0:1.3 +X 106516106 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49846;SOR=Inf;LSEQ=GCGGCTTCTCCACCCAGGAG;RSEQ=CGCTGGAGAGAGCGGTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:46,83:129,0:0:2,0:26.9:1:31.8:1:1:0:60:128:1:0:0.2 0/1:136:2:1,1:57,77:134,2:0.0147:2,2:45:1:29:1:1:1.35:60:4:0.0147:0:1 +X 106516125 . G C 108 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00164;SOR=Inf;LSEQ=GCCGCTGGAGAGAGCGGTGA;RSEQ=TGACCTGCTTGCCGTTGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:98:0:0,0:30,67:97,0:0:2,0:24.3:1:32.5:1:1:0:60:96:0.9897:0:0.1 0/1:105:10:2,8:38,57:95,10:0.0952:2,2:24.7:1:32.7:1:0.3115:2.6449:60:20:0.0962:0:1 +X 106516195 . C A 32 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.57376;SOR=2.70412;LSEQ=GCCACCCCCGACTACACTCC;RSEQ=GAGCTCGAAGCCGGCAACCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:1:0,1:10,23:33,1:0.0294:2,0:47:0:19:0:1:0:60:0:0:0:1 0/1:26:2:1,1:10,14:24,2:0.0769:2,2:10:0:32:0:1:1.38:60:4:0.0769:0:1.5 +X 106516319 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.17457;SOR=Inf;LSEQ=AAGAAATCGACGTGACAGTA;RSEQ=AGAAGAGGCAGTCTTTGAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:62:0:0,0:45,17:62,0:0:2,0:22:1:30.9:1:1:0:60:61:1:0:0.1 0/1:45:2:1,1:32,11:43,2:0.0444:2,2:23:1:27.5:1:0.46667:2.82843:60:4:0.0444:0:1 +X 106516387 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20052;SOR=Inf;LSEQ=CGTGCAGACCTTCTGGATCC;RSEQ=CGCATGAATCTCTTCCACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:119:0:0,0:76,43:119,0:0:2,0:25.4:1:30.8:1:1:0:60:58.5:1:0:0.1 0/1:97:2:1,1:58,37:95,2:0.0206:2,2:23:1:29:1:1:1.56003:60:4:0.0206:0:1 +X 106516395 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20278;SOR=Inf;LSEQ=CCTTCTGGATCCCCGCATGA;RSEQ=TCTCTTCCACATCTCCATCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:130:0:0,0:80,50:130,0:0:2,0:24.4:1:30.6:1:1:0:60:260:1:0:0.1 0/1:107:2:1,1:62,43:105,2:0.0187:2,2:31.5:1:28.5:1:1:1.4368:60:4:0.0187:0:1.5 +X 106516409 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.49968;SOR=0;LSEQ=GCATGAATCTCTTCCACATC;RSEQ=CCATCCACCAGCAACAGCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:144:2:1,1:78,64:142,2:0.0139:2,2:16.5:1:31.5:1:1:1.21706:60:4:0.0144:0:1 0/0:129:0:0,0:69,60:129,0:0:2,0:24.7:1:28.7:1:1:0:59.4:31.25:1:0:0.1 +X 106516443 . CT C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.20271;SOR=Inf;LSEQ=ACAGCACAACTATGCTGCCC;RSEQ=TTTCCTCCAGAAAGCTGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:174:0:0,0:84,90:174,0:0:2,0:26.8:1:31:1:1:0:59.7:86:1:0:0.2 0/1:143:2:1,1:60,81:141,2:0.014:2,2:34:1:30.5:1:1:1.35:60:4:0.0141:0:0 +X 106516447 . T C 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.20793;SOR=Inf;LSEQ=CACAACTATGCTGCCCCTTT;RSEQ=CCTCCAGAAAGCTGCTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:170:0:0,0:80,90:170,0:0:2,0:27.6:1:30.3:1:1:0:59.7:84:1:0:0.2 0/1:143:2:1,1:60,81:141,2:0.014:2,2:39.5:1:31.5:1:1:1.35:60:4:0.0143:0:1 +X 106516475 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16031;SOR=Inf;LSEQ=AAAGCTGCTTCCAAGAAGGG;RSEQ=CTCCAAAGAGGATGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:70,85:155,0:0:2,0:25.6:1:32:1:1:0:59.7:154:1:0:0.1 0/1:104:2:1,1:39,63:102,2:0.0192:2,2:39:0:30:0:1:1.61:60:4:0.0192:0:1 +X 106516721 . G A 29 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=1.04369;LSEQ=CCCTGAGGGACGAGGTACCC;RSEQ=CCCTGGCCAGCTGCTCTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:2:1,1:29,42:71,2:0.0274:2,2:20.5:1:29.5:1:1:1.44:60:4:0.029:0:1 0/1:35:1:1,0:13,21:34,1:0.0286:2,0:1:0:25:0:0.4:0:60:2:0.0286:0:1 +X 106516786 . T A 96 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=Inf;LSEQ=AAGGCCACGGAATACTTACA;RSEQ=GAACTGGCGGAAGCCGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:7,23:30,0:0:2,0:23.3:1:30.5:1:1:0:60:29:1:0:0.1 1/0:19:10:4,6:4,5:9,10:0.5263:2,2:29.9:1:28.9:1:1:1.18851:60:20:0.5263:0:1.1 +X 106516931 . CT C 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.46667;SOR=Inf;LSEQ=CTTAAAAAGACACAAGTTTT;RSEQ=TTTTGATCTCCCTCTCCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:1,7:8,0:0:2,0:30.6:1:30:1:1:0:60:16:1:0:0.4 0/1:8:2:1,1:2,4:6,2:0.25:2,2:28:0:30:1:1:1.83:60:4:0.25:0:0 +X 106518947 . C A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.49806;SOR=Inf;LSEQ=ACTGATGTTTCACCTGAATA;RSEQ=CTTGTATTTTATAAGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:69:0:0,0:20,49:69,0:0:2,0:26.8:1:31.1:1:1:0:60:33.5:1:0:0.1 0/1:77:2:1,1:26,49:75,2:0.026:2,2:6:1:27:1:1:1.87:60:4:0.0263:0:1 +X 106519338 . G GA 59 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.68604;SOR=0.6008;LSEQ=TGTTAACTCTTTCTGTACAA;RSEQ=AAAAAAAAAACCTCTTGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:4:2,2:25,11:36,4:0.0976:2,2:30.5:1:29.6:1:0.58393:2.22215:56.5:8:0.1:0.0244:1 0/1:33:2:2,0:19,12:31,2:0.0606:2,0:25.5:1:30.5:1:0.52273:0:60:4:0.0645:0.0303:0 +X 106846417 . CCAG C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.21616;SOR=0;LSEQ=TCCACAGCCCGTAACCTTAA;RSEQ=CAGCAGCAGCAACAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:2:1,1:21,14:35,2:0.0541:2,2:36:1:31.5:1:1:1.4832:60:4:0.0571:0:0 0/0:42:0:0,0:24,18:42,0:0:2,0:25.5:1:30.4:1:1:0:56.4:20:1:0:0.2 +X 106846441 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=3;SSF=0.49619;SOR=Inf;LSEQ=CAGCAGCAGCAACAACAACA;RSEQ=CAGCAGCAGCAACAACAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:47:0:0,0:23,23:46,0:0:2,0:28.6:1:31.5:1:1:0:58.5:14.333:1:0:0.3 0/1:52:2:1,1:28,22:50,2:0.0385:2,2:22:1:27:1:1:1.26678:43:4:0.0408:0:1.5 +X 106846480 . G A 28 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=3;SSF=1;SOR=0.49205;LSEQ=CAGCAGCAGCAACAACAACA;RSEQ=CAGCAGCAGCAGCAGCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:2:1,1:17,23:40,2:0.0465:2,2:25.5:1:28.5:1:1:1.34:60:4:0.05:0:1 0/1:43:1:1,0:20,21:41,1:0.0233:2,0:45:0:23:0:1:0:60:2:0.0263:0:6 +X 108880224 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51566;SOR=Inf;LSEQ=GGGAACTAAATTTATTCCAG;RSEQ=CAGTTAAAGATTCAGAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:18,19:37,0:0:2,0:27.2:1:28.8:1:1:0:60:36:1:0:0.3 0/1:56:2:1,1:26,28:54,2:0.0357:2,2:34:1:29.5:1:1:1.08:60:4:0.0357:0:1 +X 108880251 . C A 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18365;SOR=0;LSEQ=AAGATTCAGAATGTGTTATT;RSEQ=CTCCCAGAACAATGACACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:2:1,1:13,23:36,2:0.0526:2,2:10.5:1:26:1:1:1.74:60:4:0.0541:0:1 0/0:50:0:0,0:21,29:50,0:0:2,0:24.5:1:30:1:1:0:60:100:1:0:0.3 +X 108880269 . C A 32 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.18045;SOR=0;LSEQ=TTCCTCCCAGAACAATGACA;RSEQ=CGAGGACATAATTTTTCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:2:1,1:8,23:31,2:0.0606:2,2:21:1:32:0:0.47727:2.77:60:4:0.0645:0:1 0/0:44:0:0,0:15,29:44,0:0:2,0:26.6:1:30.6:1:1:0:60:88:1:0:0.3 +X 108880333 . CT C 69 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.18438;SOR=0.26276;LSEQ=CTGAACCATTTATGTGCCGT;RSEQ=TTTTTTTTTTTACAGAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:4:0,4:1,7:8,4:0.3333:2,0:32.3:1:34.8:1:1:0:60:8:0.3333:0:0 0/1:18:2:0,2:3,13:16,2:0.1111:2,0:20:1:33.5:1:1:0:60:4:0.1176:0:0 +X 109590175 . G T 29 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.48148;SOR=0;LSEQ=GGCCGATTCGTGGGTCGGTG;RSEQ=GTCGTGGGCCGTGGGTCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:1,1:0,12:12,2:0.1429:0,2:7.5:1:29:1:0.14286:0:60:4:0.1429:0:1 0/0:13:0:0,0:4,9:13,0:0:2,0:19.2:1:29.8:1:1:0:57.9:26:1:0:0 +X 110437571 . G A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50226;SOR=0;LSEQ=TGGGTAGTCATGGAATACTT;RSEQ=GCTGGTGGCTCTCTGACTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:2:1,1:15,13:28,2:0.0667:2,2:26.5:1:28.5:1:1:1.14834:60:4:0.069:0:1 0/0:22:0:0,0:12,10:22,0:0:2,0:26:1:29.5:1:1:0:60:21:1:0:0.1 +X 111353206 . C A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.47059;SOR=Inf;LSEQ=GCAAGACCATCTGTAGCTTA;RSEQ=TGGCCTTGATCCTGGAGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:7,1:8,0:0:2,0:28.1:1:33.1:1:1:0:60:16:1:0:0.3 0/1:9:2:1,1:4,3:7,2:0.2222:2,2:9:1:30:1:1:1.29098:60:4:0.2222:0:1 +X 112058737 . T C 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATAAGAAGCAGAGGATGGC;RSEQ=GAGCCCGAGGCATAGCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:5,1:6,0:0:2,0:18.3:1:32.3:1:1:0:60:12:1:0:0.2 0/1:13:2:1,1:8,3:11,2:0.1538:2,2:22:0:31.5:1:1:2.4495:60:4:0.1538:0:1.5 +X 112058796 . C T 29 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=3;SSF=1;SOR=0.93845;LSEQ=TGCTGTGGCTGCTGCTGCTG;RSEQ=TGTTGTTGGTGGTGATGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:2:0,2:21,9:30,2:0.0625:2,0:8.5:1:19.5:1:0.11089:0:60:1:0.0345:0:2 0/1:34:2:1,1:18,14:32,2:0.0588:2,2:22.5:1:29.5:1:1:1.27615:60:4:0.0588:0:1.5 +X 112058838 . TTGC T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.000;MSILEN=3;SSF=0.49474;SOR=0;LSEQ=TGATGGTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGACTCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:1,1:21,17:38,2:0.05:2,2:30:1:30.5:1:1:1.22874:60:4:0.0541:0:0 0/0:36:0:0,0:19,17:36,0:0:2,0:26.9:1:29:1:1:0:60:35:1:0:0.2 +X 114303670 . C A 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.49484;SOR=Inf;LSEQ=GCAGCAGCCACCATCTCAAC;RSEQ=GTCCCTCAAGGGCCAAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:37:0:0,0:19,18:37,0:0:2,0:22.6:1:30.4:1:1:0:60:74:1:0:0.1 0/1:41:2:1,1:18,21:39,2:0.0488:2,2:9.5:1:31.5:1:1:1.16:60:4:0.05:0:1 +X 114303720 . G T 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.14423;SOR=Inf;LSEQ=CGCAACCCTCCCAGGGGCAG;RSEQ=GTCTGCCGTCCAGGCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:40:0:0,0:27,13:40,0:0:2,0:23.2:1:31.2:1:1:0:60:80:1:0:0.1 0/1:25:2:1,1:14,9:23,2:0.08:2,2:6.5:1:27:1:1:1.52748:60:4:0.0833:0:2 +X 114303816 . T C 33 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.50284;SOR=0;LSEQ=CAGGCACCAGATCGTGCACG;RSEQ=CCAGGAGGACTTGGAGACCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:2,0:79,25:104,2:0.0189:2,0:7:1:33:1:1:0:60:4:0.019:0:1 0/0:86:0:0,0:61,24:85,0:0:2,0:23.6:1:28.4:1:1:0:60:27.333:1:0:0.3 +X 114304092 . A G 41 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24907;SOR=0;LSEQ=TAGTCTGGCCCAGCTGCTAC;RSEQ=CCCACAGCTCAACATCTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:3:1,2:105,133:238,3:0.0124:2,2:47.3:1:26:1:1:1.57608:60:2:0.0086:0:1.3 0/0:228:0:0,0:112,116:228,0:0:2,0:27:1:29.1:1:1:0:59.9:56:1:0:0.1 +X 114304447 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.5028;SOR=Inf;LSEQ=TAAAGGGTCATCTCCAAACC;RSEQ=TTTTAGATGTTTTTTATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:116:0:0,0:43,72:115,0:0:2,0:25:1:30.3:1:1:0:60:37.333:0.9912:0:0.1 0/1:141:2:1,1:49,90:139,2:0.0142:2,2:34:1:30.5:1:1:1.83:60:4:0.0143:0:1.5 +X 115503918 . T C 220 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0.19679;LSEQ=CAGTCCCATTCCAGTGATAA;RSEQ=CTGAGCTTCCATTTGAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:125:60,65:61,72:133,125:0.4845:2,2:23.5:1:31.7:1:0.80303:1.09:60:250:0.4864:0:1.1 0/1:257:40:16,24:97,119:216,40:0.1556:2,2:22.9:1:31.3:1:0.60659:1.22174:60:80:0.1569:0:1.2 +X 115503945 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.24371;SOR=0;LSEQ=TTCCATTTGAAGTTTTCAAA;RSEQ=GGCTTTAATATAAATCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:2:1,1:70,104:174,2:0.0114:2,2:27.5:1:30.5:1:1:1.48:60:4:0.0114:0:2.5 0/0:180:0:0,0:70,110:180,0:0:2,0:22.9:1:30.8:1:1:0:60:89:1:0:0.3 +X 115761425 . C CT 30 d5;v3;pSTD;MSI12 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTGTTCATTCCTTTTCATT;RSEQ=TTTTTTTTTTTTCTATTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:30:1:1:0:40:4:1:0:0 +X 115761903 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.20085;SOR=Inf;LSEQ=AGGCTGCAGACCCTTGGATG;RSEQ=GGTTTTTGTGGGGGCCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:13,11:24,0:0:2,0:33:1:31.1:1:1:0:59.6:48:1:0:0.3 0/1:20:2:1,1:10,8:18,2:0.1:2,2:19.5:1:28:1:1:1.23603:60:4:0.1:0:1 +X 115761919 . C CTTG 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=18;MSI=7.000;MSILEN=3;SSF=0.18937;SOR=Inf;LSEQ=GATGGGGTTTTTGTGGGGGC;RSEQ=TTGTTGTTGTTGTTGTTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:24:0:0,0:11,13:24,0:0:2,0:31.2:1:31.2:1:1:0:59.6:23:1:0:0.3 0/1:19:2:1,1:9,8:17,2:0.1053:2,2:47:1:31:1:1:1.11803:60:4:0.1053:0:0 +X 118708829 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52427;SOR=Inf;LSEQ=GCCGGGAGCGGGCGCCAGTG;RSEQ=CGGCCTAGGGGGACCCCTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:22,7:29,0:0:2,0:21.8:1:30.6:1:1:0:60:13.5:1:0:0.2 0/1:48:2:1,1:35,11:46,2:0.0417:2,2:17.5:1:27.5:1:0.44149:3.08979:60:4:0.0455:0:1.5 +X 118708841 . G T 45 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.05221;SOR=0;LSEQ=CGCCAGTGCCGGCCTAGGGG;RSEQ=ACCCCTGTCTGTCTTCCCGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:3:1,2:30,8:38,3:0.0732:2,2:5:1:29:1:0.14212:7.02909:60:6:0.0769:0:1.3 0/0:67:0:0,0:47,20:67,0:0:2,0:23.2:1:30.2:1:1:0:60:21.333:1:0:0.4 +X 118708898 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.51718;SOR=Inf;LSEQ=CTCCAGCCGGAGTCAGCGGG;RSEQ=CTCCGTCCGAGAACAACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:114:0:0,0:65,48:113,0:0:2,0:26.2:1:31.6:1:1:0:59.9:112:0.9912:0:0.2 0/1:169:2:1,1:94,73:167,2:0.0118:2,2:44.5:1:29:1:1:1.28572:60:4:0.012:0:1 +X 118708909 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17511;SOR=0;LSEQ=GTCAGCGGGGCTCCGTCCGA;RSEQ=AACAACATAATGGTGTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:2:1,1:58,47:105,2:0.0187:2,2:37.5:1:29.5:1:1:1.2316:60:4:0.0187:0:1 0/0:148:0:0,0:79,69:148,0:0:2,0:28.2:1:30.6:1:1:0:59.9:296:1:0:0.2 +X 118708927 . G T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17861;SOR=0;LSEQ=GAGAACAACATAATGGTGTG;RSEQ=AACGCGGTCATTTTCGGGTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:2:1,1:48,42:90,2:0.0217:2,2:14.5:1:27.5:1:1:1.14119:60:4:0.0222:0:1 0/0:125:0:0,0:62,63:125,0:0:2,0:27.2:1:29.2:1:1:0:60:30.25:1:0:0.1 +X 121137409 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.48538;SOR=Inf;LSEQ=TTTTTGTTGATGTTGTTATT;RSEQ=TTGCTTTTTGCTTGTTTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:6,2:8,0:0:2,0:23:1:32.4:1:1:0:60:16:1:0:0 0/1:11:2:1,1:6,3:9,2:0.1818:2,2:15.5:1:27:1:1:1.87089:60:4:0.1818:0:1.5 +X 121138010 . C A 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18182;SOR=0;LSEQ=GGTGTGTTGGGCTGTGGGGA;RSEQ=AAGTCTTGGGACGAAGCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:32:0:32:0:1:1.73:39.5:4:0.4:0:2 0/0:6:0:0,0:2,4:6,0:0:2,0:31:1:31.5:1:1:0:49.3:12:1:0:0.7 +X 121138020 . G A 66 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0.43179;LSEQ=GCTGTGGGGACAAGTCTTGG;RSEQ=ACGAAGCCTTCCATCCTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:2,3:1,0:1,5:0.8333:0,2:19.2:1:28.8:1:1:0:39.6:4:0.8:0:1.6 1/0:6:4:1,3:1,1:2,4:0.6667:2,2:27.8:1:29.8:1:1:2.44949:49.8:8:0.6667:0:1 +X 122035670 . C T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=3;SSF=0.04448;SOR=0;LSEQ=AACTGTTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:4:2,2:6,6:12,4:0.25:2,2:31:1:29:1:1:1:51.5:8:0.25:0:1.3 0/0:17:0:0,0:7,10:17,0:0:2,0:33.4:1:32.5:1:1:0:60:34:1:0:0.2 +X 122648346 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.20185;SOR=Inf;LSEQ=TCCTACAAAGCGGACTGCCC;RSEQ=CAAACCGACCAGTGGTAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:171:0:0,0:91,80:171,0:0:2,0:27:1:31:1:1:0:44.7:33.2:1:0:0.1 0/1:140:2:1,1:76,62:138,2:0.0143:2,2:29:1:28.5:1:1:1.22401:46.5:4:0.0146:0:1.5 +X 122696472 . CA C 35 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.5263;SOR=0;LSEQ=ATGTCCATGAAGGAGGTGGA;RSEQ=AGCAGATGCTGAGCCTGCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:2:1,1:35,15:50,2:0.0385:2,2:17.5:1:35:0:0.52489:2.29131:60:4:0.0385:0:2.5 0/0:31:0:0,0:24,7:31,0:0:2,0:23.6:1:28.8:1:1:0:60:62:1:0:0.2 +X 122696563 . C T 202 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CGGCCGTGTGCGACATCTCG;RSEQ=CCCACGGCCTGAAGATAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:107:107:55,52:0,0:0,107:1:0,2:29.6:1:30.1:1:1:0:60:106:1:0:1.1 0/1:117:32:18,14:43,42:85,32:0.2735:2,2:27.6:1:28.8:1:0.67937:1.25:60:64:0.2807:0:1 +X 122696575 . A G 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.23439;SOR=Inf;LSEQ=ACATCTCGCCCCACGGCCTG;RSEQ=AGATAGCCGCAACTTTCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:122:0:0,0:61,61:122,0:0:2,0:26.1:1:30.8:1:1:0:60:121:1:0:0.9 0/1:115:2:1,1:57,56:113,2:0.0174:2,2:37.5:1:31:1:1:1.0177:60:4:0.0175:0:1.5 +X 123019821 . G A 137 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=TATCTTGAAAATAGTGCCAC;RSEQ=CAGTCTACAAATTCTGGTAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:401:0:0,0:199,202:401,0:0:2,0:24.7:1:31.2:1:1:0:59.9:65.833:1:0:0.1 0/1:337:26:13,13:164,147:311,26:0.0772:2,2:19.3:1:29.3:1:0.83983:1.11528:60:52:0.0778:0:1 +X 123022371 . C A 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.19028;SOR=Inf;LSEQ=GTTTTAAGCTGTGAGATTTT;RSEQ=ATGTTTTTTAGATGTGCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:232:0:0,0:212,20:232,0:0:2,0:23.8:1:32.4:1:1:0:59.9:115:1:0:0.1 0/1:180:2:1,1:166,11:177,2:0.0111:2,2:44:0:30:0:0.12994:14.48902:60:4:0.0112:0:1.5 +X 123022775 . C CT 57 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTATAACATTCAGATTATCC;RSEQ=TTTTTTTTTTTGAGACGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:4:0,4:0,14:14,4:0.2222:1,0:24:1:28.8:1:1:0:50:8:0.2353:0.0556:0.5 0/0:2:0:0,0:0,2:2,0:0:0,0:25.5:1:33.5:1:1:0:60:4:1:0:0 +X 123022854 . T C 30 v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCTTGGCTCACTGCAACCTC;RSEQ=GCCTCCCAGGTTCAAGTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7:2:0,2:0,5:5,2:0.2857:0,0:6:1:30:1:1:0:41:4:0.2857:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123024901 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04983;SOR=Inf;LSEQ=TTAGCATAGGTAGCATAACA;RSEQ=AGGGAACTTTTTTAACCTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:33,0:33,0:0:1,0:22.8:1:33.9:1:1:0:60:66:1:0:0 0/1:10:2:2,0:8,0:8,2:0.2:0,0:27:1:28.5:1:1:0:60:4:0.2:0:1 +X 123034227 . A G 148 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02901;SOR=2.48988;LSEQ=TGCTTTGCTGGTTTGTTTTT;RSEQ=TTCTTTCGCTTGCTCCTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:24:24,0:41,0:41,24:0.3692:1,1:27.5:1:32.8:1:1:0:60:48:0.375:0:1 1/0:42:25:24,1:16,1:17,25:0.5952:1,1:23.4:1:32:1:1:1.49:60:50:0.5952:0:1 +X 123034247 . A AT 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.000;MSILEN=1;SSF=0.16418;SOR=Inf;LSEQ=ATTCTTTCGCTTGCTCCTTA;RSEQ=TTTTTTCATTTTAACTATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:80:0:0,0:80,0:80,0:0:1,0:25:1:30.5:1:1:0:60:79:1:0:0.3 0/1:55:2:1,1:49,4:53,2:0.0364:2,2:27:1:28.5:1:0.17508:11.06826:60:4:0.0377:0:0.5 +X 123034284 . G T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.22607;SOR=Inf;LSEQ=ATATTTTGCTATTGAGTTGT;RSEQ=ATAATGAAAATAATTGTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:139,16:155,0:0:2,0:24.2:1:32.3:1:1:0:59.8:76.5:1:0:0.2 0/1:141:2:1,1:108,31:139,2:0.0142:2,2:17:1:26.5:1:0.40365:3.44472:60:4:0.0143:0:1 +X 123034497 . G T 58 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.12402;SOR=0;LSEQ=GCAGATCTAGTGAATGCTCA;RSEQ=AAAGACAGTATGCAAGATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:4:2,2:137,235:372,4:0.0106:2,2:28.5:1:29:1:0.62846:1.71:52:8:0.0108:0:1.3 0/0:372:0:0,0:150,221:371,0:0:2,0:27.4:1:30.9:1:1:0:48.9:122.667:1:0:0.5 +X 123034511 . A C 225 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.48681;SOR=1.12193;LSEQ=TGCTCAGAAAGACAGTATGC;RSEQ=AGATGAGTCAAGTCAGACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:138:42,96:88,142:230,138:0.375:2,2:25.4:1:31.7:1:0.14363:1.41516:39.9:137:0.3753:0:1.1 0/1:338:136:50,86:83,118:201,136:0.4024:2,2:25.9:1:31.3:1:0.42803:1.20914:35.7:272:0.4084:0:1.1 +X 123034551 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.18729;SOR=Inf;LSEQ=TCATTACAGAAAGGTATGCA;RSEQ=TGCTGTTTTTAAAAAGCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:251:0:0,0:77,174:251,0:0:2,0:23.4:1:30.7:1:1:0:57:61.75:1:0:0.4 0/1:192:2:1,1:65,125:190,2:0.0104:2,2:30:1:30.5:1:1:1.92:60:4:0.0104:0:1 +X 123034598 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18019;SOR=Inf;LSEQ=CCAGATGTGGTGGCTCATAC;RSEQ=TGTAATCCCAGCACTTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:101:0:0,0:20,81:101,0:0:2,0:24.3:1:33.1:1:1:0:60:202:1:0:0.1 0/1:75:2:1,1:12,61:73,2:0.0267:2,2:27.5:1:28.5:1:0.31856:4.92:56:4:0.0267:0:1.5 +X 123040729 . C T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1402;SOR=Inf;LSEQ=TGAGTCATCCTCATATCTCC;RSEQ=GGCACTTGTTGGGTGCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:71:0:0,0:69,2:71,0:0:1,0:25.8:1:31.5:1:1:0:60:142:1:0:0 0/1:43:2:2,0:41,0:41,2:0.0465:1,0:18:1:32:0:1:0:60:4:0.0476:0:1 +X 123156220 . CA C 65 MAF0.05;MSI12 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.000;MSILEN=1;SSF=1;SOR=1.4491;LSEQ=GACAGAGTGAGACTGTGTCT;RSEQ=AAAAAAAAAAAAAAAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:10:4:4,0:5,0:5,4:0.4:0,0:27:1:32.5:1:1:0:55:8:0.4:0.1:0.5 1/0:2:1:1,0:1,0:1,1:0.5:0,0:41:0:33:0:1:0:22:2:0.5:0:2 +X 123159372 . G C 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AAGTAGGAAATGGAACCAAC;RSEQ=ATTACATGGAACACCACAGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:32:1:30.5:1:1:0:48:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123159474 . T C 34 v3 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.1888;LSEQ=AAAATGTTTAGGTATTTGTA;RSEQ=TTTAGATTATTATTTTTGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:2:2,0:11,1:12,2:0.1429:2,0:23.5:1:34:0:1:0:60:4:0.1538:0:2 0/1:6:1:1,0:5,0:5,1:0.1667:0,0:1:0:30:0:1:0:60:2:0.2:0:2 +X 123159533 . A G 100 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.10123;SOR=0;LSEQ=TGTGTTTGGTAACGTGCTAT;RSEQ=GTATGATGTTTTGGGGAAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:8,0:57,1:58,8:0.1212:1,0:28.6:1:33.4:1:1:0:60:16:0.1231:0:1.4 0/0:29:0:0,0:29,0:29,0:0:1,0:28.8:1:28.1:1:1:0:60:58:1:0:0.1 +X 123159810 . TCA T 77 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.000;MSILEN=2;SSF=0.21746;SOR=0.20444;LSEQ=TTATTTTGTTTCCTAAGATC;RSEQ=CACACACACAGATTTAAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:5:1,4:151,293:444,5:0.0111:2,2:34:1:33.4:1:0.66645:2.05856:60:10:0.0112:0:0.6 0/0:437:1:0,1:148,288:436,1:0.0023:2,0:33:0:28:0:1:0:60:2:0.0023:0:0 +X 123159901 . C A 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.52081;SOR=0;LSEQ=GAGCTGATTGGTATGGTAAG;RSEQ=CTTCTGAGTAAATGTGGTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:2:0,2:0,81:81,2:0.0241:1,0:28.5:1:27.5:1:1:0:60:4:0.0247:0:1 0/0:53:0:0,0:1,52:53,0:0:1,0:22.6:1:30.8:1:1:0:60:106:1:0:0 +X 123159978 . AAATAATAAT A 45 MSI12 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=34;MSI=14.000;MSILEN=3;SSF=0.52105;SOR=0;LSEQ=TTACACTGCTGTAAAGTTGC;RSEQ=AATAATAATAATAATAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:3:0,3:0,10:10,3:0.2308:0,0:38:1:29:1:1:0:60:6:0.2308:0:0 0/0:7:0:0,0:0,7:7,0:0:0,0:14.7:1:30.4:1:1:0:59.3:14:1:0:0 +X 123165385 . G T 29 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=4;SSF=1;SOR=0;LSEQ=ATGCCTGGCTAGTGTTTTTT;RSEQ=TTTGTTTGTTTGTTTGTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:22.5:1:29.5:1:1:0:55.5:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123176358 . G T 55 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.12675;SOR=Inf;LSEQ=TTAGTGTTAGAGACTTACTT;RSEQ=GAAGTTTTCTTTATTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:225:0:0,0:184,41:225,0:0:2,0:23.6:1:32.3:1:1:0:60:450:1:0:0.1 0/1:257:4:2,2:192,61:253,4:0.0156:2,2:11.5:1:27.8:1:0.25266:3.13039:60:8:0.0157:0:1.5 +X 123176582 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.16239;SOR=Inf;LSEQ=TATTAAATTGTAAGCATTAG;RSEQ=CTGGGCATGGTGGCTCATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:31,149:180,0:0:2,0:21.9:1:31.9:1:1:0:59.4:89:1:0:0.1 0/1:122:2:1,1:15,105:120,2:0.0164:2,2:7.5:1:27:1:0.24604:6.81:54.5:4:0.0165:0:1 +X 123179265 . GA G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.1765;SOR=Inf;LSEQ=TATTGTCTTAGATTTGAGAT;RSEQ=AAAAGATTCTCATTTAAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:0:0,0:51,193:244,0:0:2,0:24.6:1:30.9:1:1:0:60:80.333:1:0:0.1 0/1:178:2:1,1:45,131:176,2:0.0112:2,2:35:1:32:1:0.45115:2.89:60:4:0.0114:0:0.5 +X 123181404 . A G 26 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.5235;SOR=0;LSEQ=ATTGTGTGACCAACTTGGTC;RSEQ=CCATTAATTAGGATATAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:2:1,1:18,148:166,2:0.0118:2,2:31:1:26.5:1:0.214:8.03:60:4:0.0121:0:1 0/0:107:0:0,0:13,94:107,0:0:2,0:24:1:29:1:1:0:60:214:1:0:0.1 +X 123181551 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02222;SOR=Inf;LSEQ=TTCTTATTTTCAACCTGCGT;RSEQ=GACTAGTATTAAGAGTGGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:0,8:8,0:0:0,0:29.1:1:27.9:1:1:0:60:7:1:0:0.8 1/1:2:2:0,2:0,0:0,2:1:0,0:10.5:1:27.5:1:1:0:60:4:1:0:1 +X 123182770 . C CT 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.24721;SOR=0;LSEQ=CAAAATACTGGGGAATTCTG;RSEQ=TTTTTTTGTGCTTGTAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:2:1,1:118,14:132,2:0.0149:2,2:22:1:29.5:1:0.2121:8.17647:60:4:0.0152:0.0075:0.5 0/0:135:0:0,0:112,23:135,0:0:2,0:24.9:1:31.5:1:1:0:60:66.5:1:0:0.1 +X 123182980 . C A 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24964;SOR=0;LSEQ=ATTATGTAATTTCTACTCAG;RSEQ=AAGTTTGCATATTTCGTGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:3:3,0:83,193:276,3:0.0108:2,0:14:1:21.7:1:0.02858:0:60:2:0.0072:0:1.7 0/0:259:0:0,0:67,192:259,0:0:2,0:24.2:1:31.2:1:1:0:60:63.75:1:0:0.1 +X 123184000 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0965;SOR=Inf;LSEQ=TAAGTTTTGTGGTATATTGG;RSEQ=ACTAATTATGCATCGTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:321:0:0,0:253,67:320,0:0:2,0:24.3:1:32.2:1:1:0:60:79:1:0:0.2 0/1:273:3:1,2:206,64:270,3:0.011:2,2:10.3:1:27:1:0.14603:6.38196:60:6:0.0112:0:1 +X 123184027 . C T 174 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0;SOR=0.0195;LSEQ=TATGCATCGTTTTTCCTTCC;RSEQ=CCATTCAGTGATGCGATAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:51:33,18:337,165:502,51:0.0922:2,2:20.4:1:30.8:1:0.75562:1.11382:60:50:0.0921:0:1.1 0/0:507:1:0,1:308,196:504,1:0.002:2,0:1:0:22:0:0.3901:0:60:2:0.002:0:1 +X 123184219 . C A 40 p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.2502;SOR=0;LSEQ=GCGTGGCTGTCTGCACCTCT;RSEQ=ATTCATGAGTTATCTCCCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:3:2,1:47,216:263,3:0.0113:2,2:5:1:25.7:1:0.08822:9.08:60:6:0.0113:0:1 0/0:242:0:0,0:53,189:242,0:0:2,0:21.7:1:31.3:1:1:0:60:120:1:0:0.1 +X 123184284 . T A 110 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.00697;SOR=0;LSEQ=TGGAAGCCTCCCCTTTATTC;RSEQ=TTTCTATCTTCTCTGTAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:11:1,10:2,72:74,11:0.1294:1,2:24.8:1:31.8:1:0.34369:3.52:60:22:0.131:0:1 0/0:50:0:0,0:1,49:50,0:0:1,0:23.4:1:29.2:1:1:0:60:49:1:0:0 +X 123185446 . C CT 32 v3;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=1.08838;LSEQ=ATGGAAATTCTTTTTTTTTT;RSEQ=TTTTTTTTTTCTGAGACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:2:0,2:0,24:24,2:0.0769:1,0:18.5:1:32:0:1:0:60:4:0.0833:0:0 0/1:12:1:0,1:0,10:10,1:0.0833:0,0:28:0:31:0:1:0:60:2:0.0833:0:0 +X 123189846 . G GT 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.11397;SOR=2.36067;LSEQ=AATTAAATAAGCTTGATTTG;RSEQ=TTTTTTTTTTCCTTTAACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:53:53,0:15,0:15,53:0.6625:1,1:26.6:1:30.6:1:1:0:59.4:106:0.6709:0.0125:0.3 1/1:34:28:28,0:1,0:1,28:0.8235:0,1:22.8:1:30.3:1:1:0:59.1:56:0.8235:0.0588:0.6 +X 123190746 . CT C 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTGCTTATGCTATAATTAGG;RSEQ=TTTTTTTTTTTGAGACAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:23:1:28:1:1:0:60:4:1:0.5:0.5 +X 123191922 . A G 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00141;SOR=0;LSEQ=AAAAATATTCCTTGTAGCAC;RSEQ=GTAAATTGTGAATAGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:15:0,15:0,109:109,15:0.121:1,1:21.8:1:30.1:1:1:0:60:14:0.1176:0:1 0/0:67:0:0,0:1,66:67,0:0:1,0:24.6:1:31:1:1:0:60:134:1:0:0.1 +X 123191949 . ACCCACTCC A 63 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.000;MSILEN=1;SSF=0.00785;SOR=Inf;LSEQ=TGTGAATAGAATGGAGAGCC;RSEQ=CCCACTCCCCCAATTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:79:0:0,0:0,79:79,0:0:1,0:28.6:1:30.9:1:1:0:58.9:12.167:1:0:0.5 0/1:35:4:0,4:1,30:31,4:0.1143:1,0:32.5:1:31.5:1:1:0:60:8:0.1212:0:0 +X 123191970 . AT A 51 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.54916;SOR=0;LSEQ=CCCACTCCCCCACTCCCCCA;RSEQ=TTTTTTTTTTAAATATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:3:0,3:0,50:50,3:0.0566:1,0:18.7:1:32.7:1:1:0:60:6:0.06:0:0.3 0/0:23:0:0,0:1,22:23,0:0:1,0:16.7:1:30.2:1:1:0:58.6:46:1:0:0.2 +X 123191982 . A T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTCCCCCAATTTTTTTTTTT;RSEQ=AATATGCTTTCTACTTTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:2:0,2:0,38:38,2:0.05:1,0:17:1:29.5:1:1:0:60:4:0.0526:0:2.5 0/0:16:0:0,0:1,15:16,0:0:1,0:15.6:1:30.4:1:1:0:56.2:32:1:0:0.3 +X 123195035 . A C 175 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00028;SOR=2.509;LSEQ=TTTGAGTTAAGGCTAGTATG;RSEQ=TAATTGTCTAAGACCACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:29:22,7:186,58:244,29:0.1062:2,2:25.1:1:31.7:1:1:1.0203:60:28:0.1045:0:1.1 0/1:213:49:37,12:120,43:163,49:0.23:2,2:19.8:1:31.3:1:0.85439:1.10:60:98:0.2311:0:1.1 +X 123195339 . C A 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.04478;SOR=Inf;LSEQ=GTTTTCATATAAATATTATG;RSEQ=TATGTAAAAAGATGTAATTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:49:0:0,0:7,42:49,0:0:2,0:24.4:1:32.9:1:1:0:59.2:48:1:0:0.2 0/1:28:3:1,2:0,25:25,3:0.1071:1,2:17:1:27:1:0.10714:0:60:6:0.1071:0:1 +X 123196540 . AT A 33 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCCCTATAGGACTATCCAA;RSEQ=TTTTTTTTGTTATTTCAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:2:2,0:15,0:15,2:0.1176:1,0:11.5:1:33.5:1:1:0:60:4:0.125:0:0 0/0:8:0:0,0:8,0:8,0:0:0,0:26.8:1:31.8:1:1:0:60:16:1:0:0 +X 123196884 . G GT 67 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.14151;SOR=3.41769;LSEQ=ATAGTGTTACTAAGAAATGA;RSEQ=TTTTTTTTCCCTAAATGCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:488:2:0,2:184,301:485,2:0.0041:2,0:42.5:1:31:1:0.52889:0:60:4:0.0041:0:0 0/1:360:5:1,4:140,214:354,5:0.0139:2,2:30:1:29.2:1:0.65215:2.61083:60:10:0.014:0:0 +X 123197072 . T TA 89 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=0.81254;SOR=1.20508;LSEQ=AAAGGTAAGATTATTTTGTG;RSEQ=AAAAAAAACCTTTAAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:602:9:3,6:210,381:591,9:0.015:2,2:34.2:1:30.1:1:1:1.1022:60:18:0.0152:0.0017:0.2 0/1:501:9:3,6:183,309:492,9:0.018:2,2:32.3:1:28.3:1:1:1.18411:60:18:0.0181:0.002:0.2 +X 123197557 . T C 183 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.09525;SOR=0.29493;LSEQ=GTGTATTTATTTATCATGAT;RSEQ=AGAAAAGCACCTTAAAATGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:58:52:51,1:6,0:6,52:0.8966:0,1:27.5:1:32.2:1:1:0:60:51:0.8947:0:1 1/0:14:10:10,0:4,0:4,10:0.7143:0,0:30.7:1:31.9:1:1:0:60:20:0.7143:0:1.1 +X 123199712 . A T 54 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.04379;SOR=Inf;LSEQ=TTGATGGTTCTTAATGTATA;RSEQ=TTAATATTTATAGGGTGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:443:0:0,0:262,181:443,0:0:2,0:24.7:1:30.3:1:1:0:59.9:54.375:1:0:0.1 0/1:375:4:1,3:230,141:371,4:0.0107:2,2:14.3:1:27.3:1:0.16002:4.87313:60:8:0.0107:0:1 +X 123199726 . G T 64 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.01923;SOR=Inf;LSEQ=TGTATAATTAATATTTATAG;RSEQ=GTGAAGAACCTGATGAAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:0:0,0:299,238:537,0:0:2,0:23.7:1:31.1:1:1:0:60:75.714:1:0:0.1 0/1:448:5:2,3:258,185:443,5:0.0112:2,2:28:1:27.6:1:0.65388:2.08842:60:10:0.0113:0:1 +X 123199914 . GTTTACTGCA G 53 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=1.222;MSILEN=1;SSF=0.55433;SOR=0;LSEQ=CGTTGTGGGGGCATTTTAAA;RSEQ=TTTACTGCATTCTGTTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:3:3,0:79,66:145,3:0.0203:2,0:26:1:33.7:1:0.25372:0:60:6:0.0204:0:0 0/0:82:0:0,0:36,46:82,0:0:2,0:23:1:29.4:1:1:0:60:81:1:0:0.1 +X 123199991 . TA T 30 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.58665;SOR=2.52327;LSEQ=CTTAGCTTTTTAATAAAACT;RSEQ=ATTTTTTTTTTTTTTTTTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:245:1:0,1:202,30:232,1:0.0041:2,0:15:0:10:0:0.13305:0:53:0:0:0:4 0/1:195:2:2,0:156,31:187,2:0.0103:2,0:27.5:1:30.5:1:1:0:42.5:4:0.0122:0:6.5 +X 123200482 . ATTG A 74 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=5.000;MSILEN=1;SSF=0.00128;SOR=Inf;LSEQ=GGTATGATTTTTAATTAAAA;RSEQ=TTGTTCACATTTGAAGGTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:36:0:0,0:0,36:36,0:0:1,0:22.2:1:30.7:1:1:0:59:35:1:0:0.1 0/1:15:5:0,5:0,10:10,5:0.3333:0,0:24:1:32.2:1:1:0:60:10:0.3333:0:0 +X 123200860 . G A 44 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAAACATTGTACTTGTAGT;RSEQ=CTGGATATTACCTTAAATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:22:1:28:1:1:0:60:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123202318 . C CTATA 113 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.000;MSILEN=2;SSF=0.00108;SOR=0;LSEQ=CAGAAGTAGAGTTAATAAAG;RSEQ=TATGAGATAATGTTTTACAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:14:13,1:98,0:98,14:0.125:1,1:28.2:1:29.8:1:0.125:0:60:28:0.1308:0.0268:0 0/0:69:0:0,0:68,1:69,0:0:1,0:21.6:1:32.2:1:1:0:59.8:138:1:0:0.1 +X 123204992 . T A 32 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.09278;SOR=Inf;LSEQ=TTTCCTCTTTTTTTTTTTTT;RSEQ=AAATAGGCCTTCACTATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:353:0:0,0:269,78:347,0:0:2,0:22.8:1:28.8:1:1:0:59.6:15.524:0.9849:0:0.6 0/1:293:3:2,1:203,86:289,3:0.0102:2,2:25:1:20.3:1:1:1.17952:60:2:0.0072:0:1 +X 123204993 . A T 63 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.000;MSILEN=1;SSF=0.4683;SOR=0.48969;LSEQ=TTCCTCTTTTTTTTTTTTTT;RSEQ=AATAGGCCTTCACTATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:5:2,3:275,77:352,5:0.0136:2,2:19.2:1:27.4:1:0.07668:5.32398:58:10:0.0145:0:1.6 0/0:298:2:1,1:209,86:295,2:0.0067:2,2:29:1:27:1:0.50075:2.42202:60:4:0.0071:0:1.5 +X 123210120 . T TA 48 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=0.7694;LSEQ=GCATGTTTCATAGTGAGAAT;RSEQ=AAAAAAAATACATGGTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:3:3,0:221,57:278,3:0.0107:2,0:14.3:1:30.5:1:1:0:60:6:0.0109:0.0071:0.3 0/0:243:2:1,1:190,51:241,2:0.0082:2,2:23:1:28:1:0.38289:3.69945:60:4:0.0084:0:0 +X 123210377 . G A 44 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=0.08062;SOR=Inf;LSEQ=AATGCAACGCTAGTTTTTAT;RSEQ=CATGGCTGCCATTGAATTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:213:0:0,0:40,173:213,0:0:2,0:24.2:1:32.2:1:1:0:59.9:105.5:1:0:0.1 0/1:163:3:2,1:36,124:160,3:0.0184:2,2:7.3:1:28:1:0.13592:6.78:60:6:0.0186:0:1 +X 123211740 . T C 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=0.15237;SOR=Inf;LSEQ=ACGTGTTTACATGACTAACC;RSEQ=AAAATTTGTCTTATTGTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:221:0:0,0:204,17:221,0:0:2,0:23.8:1:32.2:1:1:0:59.9:220:1:0:0 0/1:142:2:1,1:120,20:140,2:0.0141:2,2:31.5:1:32:1:0.2748:5.87978:60:4:0.0142:0:1 +X 123214947 . T TC 34 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAATTTGCTGGGGTTTTTTT;RSEQ=CCCCTTTATATTTTTATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:33:1:34:0:1:0:60:4:1:0:0 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123217056 . T TTG 84 MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=17;MSI=9.000;MSILEN=2;SSF=1;SOR=0.46372;LSEQ=TAAGTGGCGTGTGTGTGTGT;RSEQ=TGTGTGTGTGTGTGTGTATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:7,0:7,6:0.4286:0,0:32.8:1:32.6:1:1:0:54.7:12:0.4286:0.0714:0 0/1:4:1:1,0:3,0:3,1:0.25:0,0:22:0:32.5:0:1:0:60:2:0.25:0:0 +X 123217226 . G A 35 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.0765;SOR=Inf;LSEQ=TTATTGACTTTTTTATTATA;RSEQ=TCCCTCAAATATTTATTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:263:0:0,0:226,37:263,0:0:2,0:24.1:1:33.1:1:1:0:60:86.667:1:0:0.1 0/1:195:3:2,1:155,37:192,3:0.0154:2,2:16:1:22.3:1:0.48005:2.08501:60:2:0.0104:0:1 +X 123217527 . A G 117 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.03469;SOR=0;LSEQ=ATTAATACACAAAAAAGTTT;RSEQ=TACTTCAGCAACTTTATAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:12:0,12:1,75:76,12:0.1364:1,0:22.6:1:32.8:1:1:0:60:24:0.1463:0:1.1 0/0:31:0:0,0:0,31:31,0:0:1,0:23.3:1:30.6:1:1:0:60:62:1:0:0 +X 123220306 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.13573;SOR=Inf;LSEQ=TGTAAGGCTGAGTTTGAGTA;RSEQ=TGAAGTAATATGCCTATGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:150:0:0,0:145,5:150,0:0:1,0:24.2:1:33.4:1:1:0:60:74:1:0:0.1 0/1:88:2:1,1:80,6:86,2:0.0227:2,2:19:1:28.5:1:0.15361:12.42128:60:4:0.023:0:1 +X 123224615 . G A 74 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0.00296;SOR=Inf;LSEQ=CAAACACCTCTTGATTATAA;RSEQ=TAAGTACATTTGATCATTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:894:0:0,0:393,501:894,0:0:2,0:24.7:1:32.7:1:1:0:59.9:177.8:1:0:0.1 0/1:692:7:5,2:308,377:685,7:0.0101:2,2:7.4:1:26.6:1:0.2538:3.06:60:14:0.0102:0:1 +X 123227822 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.63297;SOR=0.41656;LSEQ=CTGCTGCCTAGATATTAATA;RSEQ=TCACGACATTAGTTCAGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:3:1,2:197,40:237,3:0.0125:2,2:23:1:28.7:1:0.07997:9.70673:60:6:0.0126:0:1 0/0:191:1:1,0:150,40:190,1:0.0052:2,0:5:0:30:0:1:0:60:2:0.0053:0:1 +X 123229169 . T A 134 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GGATATTTTCAGTTACTATC;RSEQ=GGTTTGTAGATATAGCTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:219,87:306,0:0:2,0:23.5:1:31.5:1:1:0:60:75.5:1:0:0.1 0/1:263:24:16,8:176,63:239,24:0.0913:2,2:23.9:1:29.3:1:0.47403:1.39494:60:48:0.092:0:1 +X 123234405 . C CCT 74 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=7.000;MSILEN=2;SSF=0.52599;SOR=1.79033;LSEQ=CTTTTAACGAGATTTTCTCC;RSEQ=CTCTCTCTCTCTCATTAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:545:4:2,2:350,189:539,4:0.0073:2,2:21:1:29.4:1:0.61574:1.84969:60:8:0.0075:0.0018:0 0/1:459:6:4,2:290,163:453,6:0.0131:2,2:17.7:1:28.8:1:1:1.12:60:12:0.0134:0.0065:1.3 +X 123414449 . A T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.49536;SOR=Inf;LSEQ=ATCTTTTTAATTGTGAACTA;RSEQ=AGGCCGACAAAGATGATCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:48:0:0,0:30,18:48,0:0:2,0:29.5:1:30.4:1:1:0:32.4:47:1:0:0.1 0/1:51:2:1,1:30,19:49,2:0.0392:2,2:36.5:1:28.5:1:1:1.56436:22:4:0.0392:0:1 +X 123414650 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.20801;SOR=Inf;LSEQ=GTAAATGGTTTCCACTGGGG;RSEQ=CTTTGAAATAACACCACCAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:60,36:96,0:0:2,0:26.3:1:32:1:1:0:52.5:95:1:0:0.1 0/1:81:2:1,1:46,33:79,2:0.0247:2,2:26.5:1:30.5:1:1:1.38811:54:4:0.0247:0:1 +X 123414651 . C A 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.21639;SOR=Inf;LSEQ=TAAATGGTTTCCACTGGGGG;RSEQ=TTTGAAATAACACCACCACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:96:0:0,0:60,36:96,0:0:2,0:26.5:1:32.8:1:1:0:52.5:47:1:0:0.1 0/1:84:2:1,1:47,35:82,2:0.0238:2,2:6.5:1:28:1:1:1.33807:26:4:0.0238:0:1 +X 123414690 . T A 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50261;SOR=0;LSEQ=CTGGTCTTATGGTTGAACTG;RSEQ=GGTTCAGGGCCAGTGCATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:2:1,1:67,61:128,2:0.0154:2,2:35.5:1:30.5:1:1:1.09757:33:4:0.0156:0:1.5 0/0:107:0:0,0:59,48:107,0:0:2,0:29.4:1:29.1:1:1:0:37.6:106:1:0:0.1 +X 123414692 . G T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.50314;SOR=0;LSEQ=GGTCTTATGGTTGAACTGTG;RSEQ=TTCAGGGCCAGTGCATATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:2:1,1:67,60:127,2:0.0155:2,2:21.5:1:29.5:1:1:1.11571:44.5:4:0.0155:0:1.5 0/0:105:0:0,0:57,48:105,0:0:2,0:30.1:1:31.1:1:1:0:37.2:210:1:0:0.1 +X 123480610 . G A 66 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.10266;SOR=5.78331;LSEQ=ACAGCGAGAGCGTGCCAGGC;RSEQ=TGTACTGCCTATGTGTGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:483:1:1,0:213,268:481,1:0.0021:2,0:1:0:27:0:0.44398:0:60:2:0.0021:0:1 0/1:421:5:3,2:175,240:415,5:0.0119:2,2:16.8:1:28.6:1:0.6544:2.05:60:10:0.0121:0:1.2 +X 123480687 . G A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=3;SSF=0.16581;SOR=Inf;LSEQ=GTGGGCGGTGGGCAACAGCA;RSEQ=CTGGGGCCAGGGTGGAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:206:0:0,0:55,150:205,0:0:2,0:25.5:1:32.4:1:1:0:59.9:50.25:0.995:0:0.2 0/1:142:2:1,1:33,107:140,2:0.0141:2,2:29:1:28:1:0.42283:3.21:60:4:0.0146:0:1 +X 123480720 . G T 28 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.53769;SOR=0;LSEQ=TGGAGGCCGAGGCAGGCAGG;RSEQ=GCGCCGGCGTTAGCAGCTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:2:1,1:9,109:118,2:0.0167:2,2:9:0:28.5:1:0.16036:11.54:60:4:0.0167:0:1 0/0:67:0:0,0:4,63:67,0:0:2,0:22:1:31:1:1:0:60:134:1:0:0.1 +X 123488238 . G C 159 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13329;SOR=1.97042;LSEQ=TCTCTCAGTGGACAGTTCTA;RSEQ=CTCCATGTCCAAGCAGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:31:0,31:0,40:40,31:0.4306:1,1:27.1:1:32.1:1:1:0:58.7:62:0.4493:0:1.1 1/0:30:18:0,18:0,12:12,18:0.6:0,1:18.6:1:28.9:1:1:0:60:17:0.6296:0:1.1 +X 123499949 . T TAGAA 101 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTAGTGACTATGTGAAATCT;RSEQ=AGCATATCAAAAGTAGGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:0,2:2,9:0.8182:0,0:30.6:1:31.9:1:1:0:57.4:18:0.8182:0:0.6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123499991 . T G 96 PASS STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATAATTAAATGAACAATTAT;RSEQ=TACCAAATGATACCAATATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1:0,0:19.4:1:32.1:1:1:0:58.8:16:1:0:1.3 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123500066 . C A 52 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCTTATTTTCTAAGAGACTA;RSEQ=AATATACTTGGGAAGTTATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:15.3:1:33:0:1:0:56.7:6:1:0:2 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123500274 . A T 49 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCCTTATGCACAAGGCTCA;RSEQ=TTTGAAAAGTAAATAAGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:39:1:31:1:1:0:60:6:1:0:2.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 123503943 . C A 107 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GTTACACAAATGTTACTTCT;RSEQ=TTAGCATCCCTAGCACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:155:0:0,0:142,13:155,0:0:2,0:23.6:1:32.1:1:1:0:59.8:37.75:1:0:0.1 0/1:130:15:12,3:101,14:115,15:0.1154:2,2:26.9:1:27.5:1:0.4154:1.7939:60:30:0.1172:0:1 +X 123504227 . C A 30 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.52268;SOR=0;LSEQ=GCTCAGAGTTATGAGTCAAC;RSEQ=TGTTCATAACCATATAATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:2:2,0:23,172:195,2:0.0102:2,0:5:1:30.5:1:0.01554:0:60:4:0.0103:0:1 0/0:126:0:0,0:19,107:126,0:0:2,0:21.2:1:31.3:1:1:0:60:252:1:0:0.1 +X 123505272 . C A 46 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.93983;LSEQ=AACACCTTGTACTTTATTTT;RSEQ=TATAATTTAAATATATGCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:3:2,1:100,165:265,3:0.0112:2,2:15:1:29.3:1:0.55966:3.28:60:6:0.0113:0:1 0/1:190:2:2,0:67,121:188,2:0.0105:2,0:1:0:22.5:1:0.13066:0:60:4:0.0107:0:1 +X 123505439 . GA G 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.000;MSILEN=1;SSF=0.10784;SOR=10.41485;LSEQ=AGCTTTGAAACGAGGATTGG;RSEQ=AAAAGTAATTCCGTAGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:1:0,1:0,13:13,1:0.0714:1,0:43:0:31:0:1:0:60:2:0.0714:0:0 1/0:4:2:0,2:0,2:2,2:0.5:0,0:12:1:31.5:1:1:0:60:4:0.5:0.25:0.5 +X 125161355 . C T 49 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.2;SOR=0;LSEQ=CAGAGACTGTGGCCAGCCCT;RSEQ=CCCCTAGGGGCTCAGATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:3:2,1:1,2:3,3:0.5:2,2:20:1:31:1:1:3.11:59:6:0.6:0:1.3 0/0:4:0:0,0:0,4:4,0:0:0,0:14.8:1:31:1:1:0:60:8:1:0:0.3 +X 125161775 . A G 32 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTAAGCAGATTCCAGCTGA;RSEQ=AGGCTGTAAGATTCTGGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:38:1:32.5:1:1:0:58:4:1:0:1.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 125318839 . A T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.30508;SOR=4.59413;LSEQ=ATAAATACAAAGGGGATTTT;RSEQ=AAATAAATCTTTAAGCCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:178:1:0,1:136,41:177,1:0.0056:2,0:1:0:23:0:0.23596:0:60:2:0.0058:0:1 0/1:118:3:1,2:87,28:115,3:0.0254:2,2:25.3:1:27.7:1:0.15863:6.09544:60:6:0.0259:0:1.3 +X 125318842 . A T 34 q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=4;SSF=0.27886;SOR=0;LSEQ=AATACAAAGGGGATTTTAAA;RSEQ=TAAATCTTTAAGCCAGAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:3:1,2:139,47:186,3:0.0159:2,2:16:1:22:1:0.16531:5.84701:60:2:0.0106:0:3 0/0:125:0:0,0:91,34:125,0:0:2,0:23.1:1:29.5:1:1:0:60:124:1:0:0.1 +X 125318941 . A G 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.02466;SOR=0.63294;LSEQ=CAAGAAATAGGTAATAAGAA;RSEQ=GACTGAAAAAATTACCTTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:90:40,50:155,191:346,90:0.2059:2,2:25.1:1:31.6:1:1:1.01437:60:89:0.2046:0:1.1 0/1:298:42:19,23:126,129:255,42:0.1409:2,2:26.8:1:30.6:1:0.73937:1.18171:60:41:0.1385:0:1.1 +X 125499259 . T A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.23426;SOR=Inf;LSEQ=CTTATTAGATGCCAAGATAT;RSEQ=GATTATTACTGGTTCTTTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:121:0:0,0:78,43:121,0:0:2,0:24.8:1:30.4:1:1:0:60:120:1:0:0.3 0/1:114:2:1,1:72,40:112,2:0.0175:2,2:41.5:1:29:1:1:1.79012:60:4:0.0177:0:1.5 +X 125499267 . A T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.24317;SOR=Inf;LSEQ=ATGCCAAGATATTGATTATT;RSEQ=CTGGTTCTTTAAGGTAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:129:0:0,0:77,51:128,0:0:2,0:25.7:1:28.3:1:1:0:60:41.667:1:0:0.2 0/1:126:2:1,1:73,51:124,2:0.0159:2,2:10:0:30.5:1:1:1.42719:60:4:0.016:0:2 +X 125499312 . A G 28 v3;p8 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.24278;SOR=0;LSEQ=TGTAAATTAAATATGCTAAT;RSEQ=AAAGTGGCACCATTACATAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:1,1:78,73:151,2:0.0131:2,2:5:1:28.5:1:1:1.068:60:4:0.0131:0:1 0/0:157:0:0,0:72,85:157,0:0:2,0:24.6:1:29:1:1:0:60:156:1:0:0.6 +X 125499336 . A C 196 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.67905;LSEQ=GTGGCACCATTACATATATT;RSEQ=ATGATAACCAGTCATACATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:52:28,24:35,60:95,52:0.3537:2,2:25:1:31.4:1:0.05593:1.99:60:51:0.3566:0:1.1 1/0:124:83:38,45:18,23:41,83:0.6694:2,2:28.1:1:30.9:1:1:1.08:60:82:0.6667:0:1.1 +X 125499396 . T C 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.54573;SOR=0;LSEQ=TTTGAATTCAAAGCATAAGC;RSEQ=GAAGAATAATTCATAGATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:2:1,1:21,65:86,2:0.0227:2,2:12.5:1:29.5:1:0.43966:3.05:60:4:0.023:0:1 0/0:46:0:0,0:14,32:46,0:0:2,0:21.4:1:28.3:1:1:0:60:22:1:0:0.4 +X 127677424 . A G 31 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGTGTTGGGCTTGGGGGAC;RSEQ=AGTTTTGGAACCAAGCCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:39:0:31.5:1:1:0:60:4:1:0:1.5 +X 131623188 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.14125;SOR=Inf;LSEQ=GGTATAAAATGTCAAGTCTA;RSEQ=AGACACGCGCACGCTGACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:44:0:0,0:26,18:44,0:0:2,0:20.7:1:31.9:1:1:0:60:88:1:0:0.1 0/1:27:2:1,1:17,8:25,2:0.0741:2,2:26:1:27.5:1:1:2.0616:60:4:0.0741:0:1 +X 132127787 . C A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08593;SOR=Inf;LSEQ=AATCAAGGCAAAAATAATTA;RSEQ=GTGGAAGCTCTAAATTGCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:314:0:0,0:185,127:312,0:0:2,0:27:1:31.1:1:1:0:60:155:0.9936:0:0.2 0/1:249:3:2,1:144,101:245,3:0.012:2,2:24.7:1:27.7:1:1:1.40:60:6:0.0122:0:1 +X 132127845 . C T 207 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=2.87935;LSEQ=GAAACATTCTTCTCCCTGAG;RSEQ=TCTAATATCAAAAAACATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:100:48,52:123,128:251,100:0.2849:2,2:26.1:1:29.8:1:0.90609:1.04091:60:49:0.2816:0:1.2 1/0:288:154:70,84:61,73:134,154:0.5347:2,2:23.1:1:28.6:1:1:1.00273:59.9:50.333:0.5336:0:1.1 +X 132127908 . G A 33 p8;q25 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.25864;SOR=0;LSEQ=TTTTGGGAAGTTCTGTGTTT;RSEQ=ACTATGAAGCCAGATTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:3:2,1:58,120:178,3:0.0166:2,2:5.3:1:21:1:0.25555:4.10:51:2:0.0113:0:2.3 0/0:142:0:0,0:46,96:142,0:0:2,0:21.7:1:30.7:1:1:0:60:141:1:0:0.5 +X 132127915 . A G 32 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17782;SOR=Inf;LSEQ=AAGTTCTGTGTTTGACTATG;RSEQ=AGCCAGATTCCTAGACCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:168:0:0,0:48,120:168,0:0:2,0:22.3:1:30.3:1:1:0:59.8:55:1:0:0.2 0/1:123:2:1,1:35,86:121,2:0.0163:2,2:5:0:32.5:1:0.5014:2.44:60:4:0.0163:0:1.5 +X 132127924 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17318;SOR=Inf;LSEQ=GTTTGACTATGAAGCCAGAT;RSEQ=CCTAGACCCATCTATTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:141:0:0,0:35,105:140,0:0:2,0:23.3:1:29.8:1:1:0:60:45.667:1:0:0.2 0/1:101:2:1,1:27,72:99,2:0.0198:2,2:32.5:1:28:1:0.4796:2.64:60:4:0.0198:0:1 +X 132467696 . A C 190 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAAGAGTAGCAGTGCTTTC;RSEQ=AACTAAATCGGAGACCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:257:0:0,0:148,109:257,0:0:2,0:26.2:1:30.7:1:1:0:60:127.5:1:0:0.1 0/1:189:74:45,29:62,53:115,74:0.3915:2,2:25.6:1:30.7:1:0.3706:1.32:60:36:0.385:0:2 +X 132467723 . T A 187 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=ATCGGAGACCACTGGCATAA;RSEQ=CTGGAAGAAACACTGCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:250:0:0,0:126,124:250,0:0:2,0:29:1:30.6:1:1:0:60:124:1:0:0.1 0/1:219:89:48,41:67,63:130,89:0.4064:2,2:27.1:1:29:1:0.78347:1.10:60:88:0.4055:0:1.8 +X 132467759 . G T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.1974;SOR=Inf;LSEQ=CATTTGCAGGAAGGCCAGAA;RSEQ=GCCTCATGTCTTTCTCCGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:217:0:0,0:79,137:216,0:0:2,0:23.1:1:31.8:1:1:0:60:215:0.9954:0:0.1 0/1:174:2:1,1:71,101:172,2:0.0115:2,2:21:1:31.5:1:1:1.42:60:4:0.0115:0:1 +X 132467761 . C T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19529;SOR=Inf;LSEQ=TTTGCAGGAAGGCCAGAAGG;RSEQ=CTCATGTCTTTCTCCGTACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:76,133:209,0:0:2,0:23.3:1:31.1:1:1:0:60:40.8:1:0:0.1 0/1:166:2:1,1:66,98:164,2:0.012:2,2:21.5:1:30.5:1:1:1.48:60:4:0.0123:0:1 +X 133300745 . T C 86 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.07092;SOR=5.03608;LSEQ=TGAAGCCGATGGAGCGGAGT;RSEQ=GCAGCACCTGGTGGCCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:2:2,0:43,1:44,2:0.0435:1,0:34.5:1:32.5:1:1:0:60:4:0.0455:0:1 0/1:37:7:7,0:30,0:30,7:0.1892:1,0:24.9:1:30.7:1:1:0:54.4:14:0.1892:0:1.6 +X 133300776 . G T 28 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.20833;SOR=Inf;LSEQ=GTGGCCGCCGAACAGCAGAA;RSEQ=GCGCAGTTTACTGCACAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:78:0:0,0:77,1:78,0:0:1,0:21.7:1:33.6:1:1:0:54.9:77:1:0:0.1 0/1:66:2:1,1:63,1:64,2:0.0303:1,2:5:1:28:1:0.06014:44.90018:36:4:0.0308:0:1 +X 133301028 . G A 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=1.49575;LSEQ=CAGACTTAAGGGCCAGTGGG;RSEQ=GAAGGCTGTCAACCCATTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:267:2:2,0:61,204:265,2:0.0075:2,0:1:0:26.5:1:0.055:0:34:4:0.0076:0:1 0/1:179:2:1,1:41,136:177,2:0.0112:2,2:10.5:1:27.5:1:0.41523:3.29:31.5:4:0.0116:0:1 +X 133301064 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.53304;SOR=0;LSEQ=ATTGTCAGATCAGCATCAGG;RSEQ=TGTTATCAAGTCTGTTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:2:0,2:5,145:150,2:0.0131:1,0:12:1:31.5:1:1:0:48:4:0.0147:0:1 0/0:89:0:0,0:3,86:89,0:0:1,0:24.9:1:30.5:1:1:0:46.9:8.889:1:0:0.2 +X 133741142 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.18837;SOR=Inf;LSEQ=ATAAAAAAGACAGATGATCA;RSEQ=TTTTGGCCAGAACCACCATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:118,90:208,0:0:2,0:25.6:1:32.5:1:1:0:60:103:1:0:0.1 0/1:160:2:1,1:94,64:158,2:0.0125:2,2:24.5:1:28.5:1:1:1.46511:60:4:0.0127:0:1.5 +X 133741194 . A AG 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.50888;SOR=0;LSEQ=TGCCAAAATAATGAACACAA;RSEQ=GGGAAAGAGAAGAGGCACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:2:1,1:72,120:192,2:0.0103:2,2:18:1:30.5:1:1:1.66:60:4:0.0104:0:0 0/0:146:0:0,0:54,92:146,0:0:2,0:23.3:1:29.1:1:1:0:60:28.2:1:0:0.2 +X 136523405 . G T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.57553;SOR=2.7555;LSEQ=GGGACAGGACCAAGAACTAG;RSEQ=GGCTCAGACATTTACAACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:211:1:1,0:143,67:210,1:0.0047:2,0:6:0:12:0:1:0:60:0:0:0:2 0/1:154:2:1,1:100,52:152,2:0.013:2,2:13:1:27.5:1:1:1.91442:37:4:0.0133:0:1 +X 136523442 . C T 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.09151;SOR=Inf;LSEQ=ACTGCAGGCATTTTCTCTTC;RSEQ=TCTTCTTCACGGGAGGTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:306:0:0,0:176,130:306,0:0:2,0:27.9:1:32:1:1:0:57.9:50:1:0:0.1 0/1:252:3:1,2:137,110:247,3:0.0119:2,2:12.7:1:27.3:1:0.58852:2.482:51.7:6:0.012:0:1 +X 136523931 . C G 154 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=GAAATGCGTTGGTTGTGTAA;RSEQ=TGATCAGTAGGCAAGTTTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:457:0:0,0:195,262:457,0:0:2,0:25.5:1:32.8:1:1:0:37.5:227.5:1:0:0.1 0/1:376:31:13,18:143,202:345,31:0.0824:2,2:23.9:1:31.2:1:1:1.02:34.7:62:0.0838:0:1.1 +X 136524003 . G A 61 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.08356;SOR=0;LSEQ=TGATGGCCTGCATCTGGGCC;RSEQ=CTCGCTGGGCCGCAGCTGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:5:3,2:76,210:286,5:0.0172:2,2:22:1:26.6:1:0.12559:4.12:35.6:10:0.0175:0:1 0/0:199:0:0,0:65,134:199,0:0:2,0:28:1:30.3:1:1:0:38.7:48.75:1:0:0.3 +X 138188496 . G A 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.46667;SOR=0;LSEQ=ACCCAAGGCCATCCAGCTGG;RSEQ=CAGCCACAGAGTTGGCGTTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:0,2:1,1:2,2:0.5:2,0:12.5:1:31:1:1:0:60:4:0.5:0:1 0/0:2:0:0,0:1,1:2,0:0:2,0:22:0:33.5:1:1:0:60:4:1:0:0.5 +X 138992339 . G T 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.19519;SOR=0;LSEQ=ATGATTTGAACTCATGTTAA;RSEQ=AGAGGGTGTCAAATTGAGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:2:1,1:14,13:27,2:0.069:2,2:11.5:1:31.5:1:1:1.07415:32.5:4:0.069:0:1 0/0:36:0:0,0:20,16:36,0:0:2,0:27.8:1:30.8:1:1:0:40.4:72:1:0:0.1 +X 139479299 . C T 31 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.17787;SOR=Inf;LSEQ=AAGCTGAGCAGTGACGAGAC;RSEQ=AGCAACCCTCACCTCTCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:109:0:0,0:81,28:109,0:0:2,0:27:1:31.9:1:1:0:60:218:1:0:0.1 0/1:80:2:1,1:60,18:78,2:0.025:2,2:33.5:1:31:1:0.42089:3.27133:60:4:0.026:0:1.5 +X 139479364 . G T 45 PASS STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.64302;SOR=0.46083;LSEQ=TAGAAAGTGGTACAATCACT;RSEQ=AACACCCTGATATACCTACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:3:1,2:157,78:235,3:0.0126:2,2:10:1:28.7:1:0.26207:4.00021:60:6:0.0127:0:1 0/0:172:1:0,1:111,60:171,1:0.0058:2,0:1:0:21:0:0.35465:0:60:2:0.0058:0:1 +X 139479523 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=0.49894;SOR=0;LSEQ=TTGGAGTTCAATTTAATTAG;RSEQ=ACAGTAAAGAAGAAGATCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:2:1,1:78,107:185,2:0.0106:2,2:36:1:31.5:1:1:1.37:58.5:4:0.0108:0:1 0/0:179:0:0,0:76,103:179,0:0:2,0:25:1:31.8:1:1:0:60:358:1:0:0.1 +X 139479534 . A G 33 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=3;SSF=0.24649;SOR=Inf;LSEQ=TTTAATTAGCACAGTAAAGA;RSEQ=GAAGATCCATTACTGTTTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:179:0:0,0:80,99:179,0:0:2,0:26.6:1:31.6:1:1:0:59.7:358:1:0:0.1 0/1:177:2:1,1:81,94:175,2:0.0113:2,2:23.5:1:33:1:1:1.16:60:4:0.0114:0:2 +X 139479551 . T C 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.4987;SOR=0;LSEQ=AGAAGAAGATCCATTACTGT;RSEQ=TGCAACTGTAGGAAGCAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:2:1,1:81,99:180,2:0.011:2,2:23.5:1:31.5:1:1:1.22:59:4:0.011:0:1.5 0/0:177:0:0,0:89,88:177,0:0:2,0:25.3:1:29.9:1:1:0:60:354:1:0:0.1 +X 139479570 . C T 30 v3;pSTD STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.61728;SOR=2.08171;LSEQ=TTTGCAACTGTAGGAAGCAA;RSEQ=AGAGTTACCTTGTATGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:196:1:0,1:92,103:195,1:0.0051:2,0:1:0:23:0:1:0:60:2:0.0052:0:1 0/1:189:2:1,1:91,96:187,2:0.0106:2,2:16:0:30.5:1:1:1.05:60:4:0.0107:0:2 +X 139479605 . A G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.22345;SOR=Inf;LSEQ=TGAATGTCATTGACAAGGAG;RSEQ=AATTCGGTTGTTGCAATCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:198:0:0,0:87,111:198,0:0:2,0:26:1:30.7:1:1:0:59.8:197:1:0:0.1 0/1:178:2:1,1:81,95:176,2:0.0112:2,2:49.5:1:28.5:1:1:1.17:60:4:0.0114:0:2 +X 139479663 . G C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21119;SOR=Inf;LSEQ=GACGAAACTTTTACACTTGT;RSEQ=CATGGACCTATGATAGCAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:157:0:0,0:67,90:157,0:0:2,0:26.1:1:32.3:1:1:0:59.8:77.5:1:0:0.1 0/1:134:2:1,1:52,80:132,2:0.0149:2,2:43.5:1:30.5:1:1:1.53:60:4:0.0152:0:1 +X 139479797 . C T 140 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=0;LSEQ=CTTAGAGATCCAAATCTACT;RSEQ=CTATCAGTAAGTAAAGATCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:25:15,10:64,59:123,25:0.1689:2,2:24.6:1:30.3:1:0.51541:1.38:60:24:0.1678:0:1 0/0:98:0:0,0:56,42:98,0:0:2,0:24.7:1:30.3:1:1:0:60:97:1:0:0.2 +X 139479802 . C T 77 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00286;SOR=Inf;LSEQ=AGATCCAAATCTACTCCTAT;RSEQ=AGTAAGTAAAGATCATGCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:83,70:153,0:0:2,0:22.4:1:32:1:1:0:60:75.5:1:0:0.3 0/1:95:6:5,1:51,38:89,6:0.0632:2,2:21.8:1:29.8:1:0.39536:3.68:60:12:0.0638:0:1 +X 139479898 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.21702;SOR=Inf;LSEQ=ACAGAGTTGAAGTTCTAAGC;RSEQ=CTGGTTGTGATCTTTTGCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:176:0:0,0:84,92:176,0:0:2,0:24.1:1:30.8:1:1:0:59.8:175:1:0:0.1 0/1:154:2:1,1:73,78:151,2:0.013:2,2:35.5:1:29:1:1:1.07:60:4:0.0132:0:1 +X 139479907 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50288;SOR=0;LSEQ=AAGTTCTAAGCGCTGGTTGT;RSEQ=ATCTTTTGCGTGAAAAAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:2:1,1:83,96:179,2:0.011:2,2:37.5:1:30.5:1:1:1.16:60:4:0.0112:0:1 0/0:150:0:0,0:71,79:150,0:0:2,0:24.9:1:30.7:1:1:0:59.7:149:1:0:0.1 +X 139479930 . G T 30 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50439;SOR=0;LSEQ=CTTTTGCGTGAAAAAATAAT;RSEQ=TCCTGTGGTATGGATCACTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:2:1,1:77,105:182,2:0.0109:2,2:12:1:30.5:1:1:1.36:60:4:0.0109:0:1 0/0:148:0:0,0:70,78:148,0:0:2,0:25.7:1:31.5:1:1:0:59.7:73:1:0:0.1 +X 139480142 . G A 31 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGATACTTTCTAAGTCTTGT;RSEQ=AAAATGCAGTTGTGTTGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:2:1,1:42,36:78,2:0.025:2,2:17:0:31.5:1:1:1.16441:60:4:0.0253:0:1 0/0:36:0:0,0:19,17:36,0:0:2,0:23.8:1:31:1:1:0:60:72:1:0:0.1 +X 139586707 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15982;SOR=Inf;LSEQ=AGCAGTTTCCAGTCGGCGCC;RSEQ=AAGCGCTTGCTGATCTCAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:271:0:0,0:173,97:270,0:0:2,0:25.5:1:31:1:1:0:60:44:0.9962:0:0.1 0/1:181:2:1,1:107,72:179,2:0.011:2,2:31:1:28.5:1:1:1.48274:60:4:0.0113:0:1 +X 139586766 . G A 62 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=3;SSF=0.14078;SOR=0;LSEQ=CTCCAGGGCCATTTTGCGCC;RSEQ=CTGCCCGCGGGACCATACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:4:2,2:160,192:352,4:0.0112:2,2:19:1:31.3:1:1:1.20:52.3:8:0.0116:0:1 0/0:263:0:0,0:121,142:263,0:0:2,0:27.2:1:30.2:1:1:0:59.8:42.833:1:0:0.2 +X 139586803 . C T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.15898;SOR=Inf;LSEQ=ACCATGAAGGCGTTCATGGG;RSEQ=CGTTTCACACGGTCCTGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:236:0:0,0:73,163:236,0:0:2,0:24:1:31.3:1:1:0:59.6:58:1:0:0.1 0/1:157:2:1,1:56,99:155,2:0.0127:2,2:23.5:1:29:0:1:1.76:60:4:0.0131:0:1 +X 139586813 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.15142;SOR=Inf;LSEQ=CGTTCATGGGCCGTTTCACA;RSEQ=GGTCCTGGTCTGTACCCCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:208:0:0,0:48,160:208,0:0:2,0:23.4:1:30.3:1:1:0:59.8:103:1:0:0.1 0/1:133:2:1,1:42,89:131,2:0.015:2,2:29:1:28:1:0.54375:2.11:60:4:0.0153:0:1 +X 140462166 . C T 33 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATAGAAATCCTCAGAAC;RSEQ=CTCTACCCCAAATCAACAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:15:0:33.5:1:1:0:32:4:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 140462644 . A T 27 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.49804;SOR=0;LSEQ=TAAGACAAGAAATTTCTAAG;RSEQ=TCACAACAGAATTGAAGGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:2:1,1:43,26:69,2:0.0282:2,2:38:1:27.5:1:1:1.64163:60:4:0.029:0:1.5 0/0:63:0:0,0:44,19:63,0:0:2,0:19.7:1:28:1:1:0:60:20:1:0:0.1 +X 140462686 . C CA 216 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.00432;SOR=0.44883;LSEQ=TAGAGACACAAAAATCCCTC;RSEQ=AAAAAAATCAATCCAGGAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:163:134:73,61:17,12:29,134:0.8221:2,2:29.8:1:30.6:1:0.83719:1.18257:58.5:32.5:0.828:0.0491:0.4 1/0:135:91:47,44:27,17:44,91:0.6741:2,2:31.7:1:29.8:1:0.35698:1.48249:60:182:0.6741:0.0222:0.2 +X 140462705 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.19417;SOR=Inf;LSEQ=CCAAAAAAATCAATCCAGGA;RSEQ=CCGTTTTTTTTTTAAATGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:172:0:0,0:85,86:171,0:0:2,0:27.3:1:32:1:1:0:58.8:20.375:1:0:0.3 0/1:136:2:1,1:66,68:134,2:0.0147:2,2:33.5:1:28:1:1:1.03:60:4:0.0149:0:1 +X 140462708 . G GT 112 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=0.26752;SOR=0.55743;LSEQ=AAAAAATCAATCCAGGAGCC;RSEQ=TTTTTTTTTTAAATGAACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:15:8,7:74,79:153,15:0.0882:2,2:35.5:1:28.7:1:0.79049:1.22:60:14:0.0848:0:0.5 0/1:137:7:4,3:63,67:130,7:0.0511:2,2:36.9:1:30.3:1:0.71441:1.41:60:14:0.0511:0:0.6 +X 140462745 . G A 30 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.50223;SOR=0;LSEQ=ACAAAATTGATGGCTAGTTA;RSEQ=ACTAATAAAGAAGAAAAGAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:2:1,1:39,58:97,2:0.0202:2,2:10:0:30:0:1:1.48:60:4:0.0204:0:1.5 0/0:81:0:0,0:31,50:81,0:0:2,0:18.8:1:29.9:1:1:0:59.9:19.25:1:0:0.3 +X 140462941 . T G 31 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGGCGTAGTGGCGGGCGCC;RSEQ=GTAGTCCCAGCTACTCGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:6.5:1:31:1:1:0:52.5:4:1:0:1.5 +X 140519098 . C T 31 d5;v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCTTTATATAACAGCAGCC;RSEQ=CTGCACCGCCACTCCCAGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:2,0:2,0:2,2:0.5:0,0:10.5:1:31.5:1:1:0:60:4:0.5:0:1.5 0/0:1:0:0,0:1,0:1,0:0:0,0:1:0:31:0:1:0:60:2:1:0:0 +X 140519337 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.21245;SOR=Inf;LSEQ=AGCATGATGAGCTATCAGTA;RSEQ=CTGGCTTCTATGTACACATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:169:0:0,0:105,64:169,0:0:2,0:25.4:1:32.4:1:1:0:60:55.333:1:0:0.5 0/1:145:2:1,1:85,58:143,2:0.0138:2,2:25:1:30.5:1:1:1.46153:60:4:0.014:0:1 +X 140519367 . G A 208 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0;SOR=0.25473;LSEQ=ATGTACACATAATCTACCTC;RSEQ=TTTCATGATACAATCTTCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:197:125:61,64:38,34:72,125:0.6345:2,2:23.4:1:29.9:1:0.65777:1.17166:60:40.667:0.6289:0:1.1 0/1:157:48:23,25:61,48:109,48:0.3057:2,2:27.9:1:29:1:0.38808:1.37846:60:47:0.3013:0:1.1 +X 141806035 . C G 77 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.71586;SOR=1.46501;LSEQ=CGCCTTTCAAACTCTTATAC;RSEQ=AACCTCTGGAGTTGGGCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:4,2:8,8:16,6:0.2727:2,2:31.2:1:29.8:1:0.64617:1.94:37.2:12:0.2857:0:1 0/1:14:5:2,3:4,5:9,5:0.3571:2,2:22.8:1:29.2:1:1:1.18452:37.2:10:0.3571:0:1 +X 141806066 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48387;SOR=Inf;LSEQ=GTTGGGCAACATGGCTTCTC;RSEQ=CCTTTCTGTGTCCTGTGGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:5,10:15,0:0:2,0:32.3:1:31.2:1:1:0:35.7:30:1:0:0.3 0/1:16:2:1,1:6,8:14,2:0.125:2,2:27:1:28:1:1:1.31:44.5:4:0.1333:0:1 +X 141806238 . T G 53 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTCCTCTGCCATGGCTCCA;RSEQ=CTGGTCCCTCCATTCGGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:25.3:1:33.7:1:1:0:43.3:6:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +X 142682796 . C G 105 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=1.21404;LSEQ=AATTTCAGGTGAACTTGCCT;RSEQ=TCAAAATAAATCAGACCCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:9,0:10,1:11,9:0.45:2,0:18.3:1:33.3:1:1:0:55.2:18:0.45:0:1.7 1/0:10:5:5,0:4,1:5,5:0.5:2,0:33.6:1:32:1:1:0:46.6:10:0.5:0:1.2 +X 142682875 . C T 209 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1e-05;SOR=0;LSEQ=AAGCAGTTAACACCACTTCC;RSEQ=GAAAGGCATACAAAAATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:87:87:84,3:0,0:0,87:1:0,1:23.7:1:32.5:1:1:0:60:174:1:0:1.7 1/1:68:55:51,4:13,0:13,55:0.8088:1,2:24.4:1:31:1:1:0:60:110:0.8088:0:1.8 +X 142682931 . T C 257 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=0;LSEQ=GATTCCTCCCAGCATACTAC;RSEQ=CAACAGCAGCTTATAAAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:316:316:233,83:0,0:0,316:1:0,2:25.1:1:31:1:1:0:59.7:44.143:1:0:1.3 1/0:240:191:139,52:33,16:49,191:0.7958:2,2:24.8:1:30:1:0.47934:1.29:59.7:62.667:0.7932:0:1.3 +X 145042055 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.17487;SOR=Inf;LSEQ=ACTATTATCCTTAGAGACAA;RSEQ=TCAAAATAATATAACTTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:144:0:0,0:93,51:144,0:0:2,0:23.8:1:30.7:1:1:0:60:71:1:0:0.2 0/1:104:2:1,1:65,37:102,2:0.0192:2,2:12:1:27.5:1:1:1.74668:60:4:0.0198:0:2.5 +X 145042082 . G T 43 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30904;SOR=4.37774;LSEQ=TAATATAACTTAAAATAAAT;RSEQ=GAAGCCAACAATTTAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:193:1:0,1:113,79:192,1:0.0052:2,0:1:0:15:0:0.41451:0:60:0:0:0:1 0/1:134:3:1,2:77,54:131,3:0.0224:2,2:27.3:1:27.7:1:0.57109:2.82958:60:6:0.0231:0:1 +X 145042095 . T A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.16435;SOR=Inf;LSEQ=AATAAATGGAAGCCAACAAT;RSEQ=TAGAAATGCATGCAAAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:209:0:0,0:119,90:209,0:0:2,0:26.6:1:30.6:1:1:0:60:208:1:0:0.3 0/1:143:2:1,1:76,65:141,2:0.014:2,2:40.5:1:27.5:1:1:1.16795:60:4:0.0143:0:2 +X 145042104 . C T 188 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=0;SOR=9.49077;LSEQ=AAGCCAACAATTTAGAAATG;RSEQ=ATGCAAAAAAGACATAGGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:49:29,20:83,79:162,49:0.2311:2,2:27.2:1:29.6:1:0.41427:1.38:60:98:0.2356:0:1.1 1/0:155:115:59,56:19,21:40,115:0.7419:2,2:26.3:1:27.6:1:0.7163:1.16:60:114:0.755:0:1.2 +X 145042124 . TA T 71 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=0.0686;SOR=0;LSEQ=CATGCAAAAAAGACATAGGT;RSEQ=AAAAAAATAGTTTCTATGTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:5:2,3:87,101:188,5:0.0259:2,2:21.2:1:31:1:1:1.29039:60:10:0.0265:0:0.4 0/0:154:0:0,0:70,84:154,0:0:2,0:25.8:1:28.1:1:1:0:60:50.333:1:0:0.8 +X 145042128 . A G 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.000;MSILEN=1;SSF=0.19391;SOR=Inf;LSEQ=CAAAAAAGACATAGGTTAAA;RSEQ=AAAATAGTTTCTATGTAGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:190:0:0,0:86,104:190,0:0:2,0:26.7:1:30.7:1:1:0:60:189:1:0:0.3 0/1:150:2:1,1:64,84:148,2:0.0133:2,2:22.5:1:29:1:1:1.31:60:4:0.0134:0:2 +X 145701240 . C T 26 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.56741;SOR=2.99304;LSEQ=AGCTGCCACTCCATCCTCTG;RSEQ=ACGGCGTTCAGGGCCGCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:286:1:0,1:131,154:285,1:0.0035:2,0:1:0:24:0:1:0:44:2:0.0035:0:1 0/1:192:2:1,1:81,109:190,2:0.0104:2,2:8:1:26.5:1:1:1.34:46.5:4:0.0106:0:1 +X 145701530 . T G 214 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0;SOR=306.46598;LSEQ=GGATACGATCAGCTTCTCCC;RSEQ=CTCGATGCTGTGCTGTAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:868:1:0,1:437,430:867,1:0.0012:2,0:30:0:34:0:0.49654:0:38:2:0.0012:0:1 0/1:489:128:62,66:169,192:361,128:0.2618:2,2:35.5:1:30.6:1:0.75836:1.07:42.5:63:0.2625:0:1.7 +X 145701553 . A T 192 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0;SOR=Inf;LSEQ=CGATGCTGTGCTGTAGACGC;RSEQ=GCTTTCCCCGGACGGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:891:0:0,0:451,440:891,0:0:2,0:25.3:1:31.1:1:1:0:43.5:58.4:1:0:0.1 0/1:488:93:42,51:193,202:395,93:0.1906:2,2:24.5:1:29.4:1:0.56484:1.15983:41.7:30:0.1867:0:1.2 +X 145701579 . C T 202 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=347.26447;LSEQ=CCCCGGACGGCCTCCTGCTG;RSEQ=CTGAACAGCTCCTTCAGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:860:1:0,1:462,396:858,1:0.0012:2,0:1:0:22:0:0.46217:0:60:2:0.0012:0:1 0/1:513:148:74,74:177,188:365,148:0.2885:2,2:16.9:1:28.1:1:0.77074:1.06:43.5:48.333:0.2923:0:1.5 +X 145701679 . G A 42 v3;p8 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.35469;SOR=2.71687;LSEQ=CGTCCAGGAGGTAGGAGCCC;RSEQ=TGTAGGTGACGTACTGGGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:537:2:2,0:230,305:535,2:0.0037:2,0:1:0:24:1:0.18619:0:48.5:4:0.0038:0:2 0/1:298:3:3,0:143,152:295,3:0.0101:2,0:6.7:1:26.7:1:0.11636:0:44.7:6:0.0101:0:1 +X 145961889 . G C 205 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0;SOR=3.02391;LSEQ=TTCTCAGCTTCAATGTCAGT;RSEQ=GCTCAGAGGATGTCTCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:99:48,51:100,140:240,99:0.292:2,2:27.4:1:31.2:1:0.27901:1.32:60:198:0.2982:0:1.1 1/0:225:125:61,64:49,51:100,125:0.5556:2,2:27.1:1:29.5:1:1:1.008:60:124:0.5586:0:1.2 +X 147332664 . G T 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.15793;SOR=Inf;LSEQ=TTTCAAATATAAATGTGTAC;RSEQ=TATGCAGTTACAGACGTGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:163:0:0,0:74,89:163,0:0:2,0:25.3:1:31.1:1:1:0:60:162:1:0:0.5 0/1:108:2:1,1:50,56:106,2:0.0185:2,2:11:0:31.5:1:1:1.12:60:4:0.0185:0:1.5 +X 147332680 . G A 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.01279;SOR=0.50911;LSEQ=GTACGTATGCAGTTACAGAC;RSEQ=TGACTGTAAATATGAAATGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:140:71:29,42:31,38:69,71:0.5071:2,2:25:1:31:1:0.73288:1.18008:60:142:0.5145:0:1.1 0/1:102:35:13,22:32,35:67,35:0.3431:2,2:31.8:1:30:1:0.40129:1.54064:60:70:0.3431:0:1 +X 147582812 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12821;SOR=Inf;LSEQ=AGCCACCTCTGGCCCCGGCC;RSEQ=CGCTGACTCCTAGGTCGGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:3,5:8,0:0:2,0:18.9:1:32.5:1:1:0:60:16:1:0:0.3 0/1:5:2:1,1:1,2:3,2:0.4:2,2:23:0:31:0:1:1.73:60:4:0.4:0:1.5 +X 149924637 . C T 27 v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.6269;SOR=1.72633;LSEQ=TCTTCTTATAAACTACTTTA;RSEQ=CTGCAGATATGGGGGTTGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:2:0,2:123,50:173,2:0.0114:2,0:1:0:26:0:0.08709:0:60:4:0.0117:0:1 0/1:102:2:1,1:71,29:100,2:0.0196:2,2:21.5:1:27.5:1:0.50379:2.42403:60:4:0.0196:0:1 +X 149924638 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.13655;SOR=Inf;LSEQ=CTTCTTATAAACTACTTTAC;RSEQ=TGCAGATATGGGGGTTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:180:0:0,0:127,53:180,0:0:2,0:23.5:1:31.3:1:1:0:60:29:1:0:0.2 0/1:106:2:1,1:74,30:104,2:0.0189:2,2:20:1:28.5:1:0.50135:2.44291:60:4:0.0192:0:1 +X 149924662 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.16251;SOR=Inf;LSEQ=AGATATGGGGGTTGGGGTGG;RSEQ=AGCCCTTTTCCCTGTTTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:248:0:0,0:163,85:248,0:0:2,0:27.2:1:31.7:1:1:0:60:23.8:1:0:0.2 0/1:168:2:1,1:104,61:165,2:0.0119:2,2:12:1:27:1:1:1.69915:60:4:0.012:0:1 +X 149924692 . G A 43 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.0707;SOR=Inf;LSEQ=CCCTGTTTCCACGTAGAGGT;RSEQ=GTAGAAAGGCGTGTGGAAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:339:0:0,0:189,149:338,0:0:2,0:25:1:31.7:1:1:0:60:168:0.997:0:0.3 0/1:240:3:2,1:138,99:237,3:0.0125:2,2:19.3:1:27.7:1:1:1.43:60:6:0.0126:0:1 +X 149924738 . C T 190 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.31066;SOR=0.80542;LSEQ=CAGGGCTACAGTGTATAGAC;RSEQ=CTGTTAGTCCAGCAGTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:329:74:36,38:124,131:255,74:0.2249:2,2:27:1:30.6:1:1:1.00:60:73:0.2288:0:1 0/1:264:50:22,28:104,108:212,50:0.1894:2,2:25.3:1:28.2:1:0.53378:1.22464:60:24:0.1846:0:1.2 +X 149924781 . A G 33 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.18338;SOR=Inf;LSEQ=GCAGGTGCTTGAATCACAGA;RSEQ=CAGGTGCCCCTTTGAAGAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:237:0:0,0:87,149:236,0:0:2,0:23.7:1:29.6:1:1:0:60:117:1:0:0.3 0/1:178:2:1,1:63,113:176,2:0.0112:2,2:36:0:33:1:1:1.79:60:4:0.0114:0:1.5 +X 155208866 . T C 99 PASS STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.00699;SOR=0;LSEQ=CTGGGCCACTCAACATGGGT;RSEQ=TCCTTCTTCCTGATGTTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:5,3:0,0:0,8:1:0,2:40.9:1:33.3:1:1:0:60:16:1:0:1.3 0/1:7:2:1,1:3,2:5,2:0.2857:2,2:20:1:29:1:1:1.41418:60:4:0.2857:0:1 +X 155209025 . G T 26 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCTACTTTGATTCTCTAG;RSEQ=AACTTCAGTTGTTTCTTGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:0,2:2,0:0:0,0:14:1:31:1:1:0:60:4:1:0:0 0/1:5:2:1,1:1,2:3,2:0.4:2,2:22:1:26:1:1:1.73:60:4:0.4:0:1 +Y 7194144 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGATTTGAAGCCGGAGAACA;RSEQ=CCTGCTGGATAGGGATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:12,10:22,0:0:2,0:28.1:1:29.9:1:1:0:54.4:21:1:0:0.3 0/1:104:2:1,1:46,56:102,2:0.0192:2,2:46:1:28.5:1:1:1.22:46:4:0.0194:0:1 +Y 13457407 . G T 30 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CATTCCATTCCACTCGAATT;RSEQ=TTTCCATTCCTTTCGATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:26:0:30.5:1:1:0:20.5:4:1:0:4 +Y 13457418 . TTTCGAT AG 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=13;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ACTCGAATTGTTTCCATTCC;RSEQ=TCCATTCCATTTCATTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:32.5:1:32.5:1:1:0:20.5:4:1:0:3 +Y 13457446 . C A 28 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=5;SSF=1;SOR=0;LSEQ=CCATTCCATTTCATTCCATT;RSEQ=CATTCCATTCCATTGCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:9.5:1:28.5:1:1:0:20.5:4:1:0:4 +Y 13458422 . A C 33 d5;v3;p8;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTCCCTTCC;RSEQ=TTCCATTCCACTCGGAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5:0:33:1:1:0:23:4:1:0:2.5 +Y 13458451 . C A 30 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CACTCGGAATGATTCCATTC;RSEQ=ATTCCATTCCATTCCATTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:16:0:34:0:1:0:26:2:1:0:1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:17.5:1:30.5:1:1:1:23:4:0.5:0:2.5 +Y 13458455 . C A 30 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=CGGAATGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:12:0:33:0:1:0:26:2:1:0:1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:15:0:30.5:1:1:1:22:4:0.5:0:1 +Y 13458460 . C G 31 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.000;MSILEN=5;SSF=1;SOR=Inf;LSEQ=TGATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:1:0:0,0:0,1:1,0:0:0,0:7:0:33:0:1:0:26:2:1:0:1 1/0:4:2:1,1:1,1:2,2:0.5:2,2:8.5:1:31:1:1:1:23:4:0.5:0:2.5 +Y 13458692 . A T 26 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCACTCCACTCC;RSEQ=CTCCACTCCACTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:18.5:1:26:1:1:0:22:4:0.6667:0:3 +Y 13459268 . TT CA 28 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=8.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=CCATTCCATTCCATTCCATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:28.2:1:1:0:23.5:4:1:0.5:5.5 +Y 13459288 . T C 30 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.000;MSILEN=5;SSF=1;SOR=0;LSEQ=TTCCATTCCATTCCATTCCA;RSEQ=TCCACTCCACTGCACTCCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:30:1:1:0:23.5:4:1:0:5.5 +Y 13459327 . A T 28 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATTCCATTCCATTGCATTCC;RSEQ=TTCCATTCCATTCCATTCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:11:0:28.5:1:1:0:23.5:4:1:0:5.5 +Y 13488013 . T C 33 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGGGCTCCCCGCGATGGCC;RSEQ=TCCCGACAACTTCGGACAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:29.5:1:33:1:1:0:29.5:4:1:0:4.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488353 . A T 61 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCTCCGAGCCTTTGAGAAGG;RSEQ=TCGCTTTCCAGGCATCGCCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:13.3:1:30.8:1:1:0:25.5:8:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488370 . G A 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGATCGCTTTCCAGGCATC;RSEQ=CCGCCAGGGAAGAGGTGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:30.3:1:30.3:1:1:0:25.5:8:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488377 . G A 65 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTTCCAGGCATCGCCGCCA;RSEQ=GGAAGAGGTGGCCAGAGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:37.3:1:32.5:1:1:0:25.5:8:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488410 . A T 60 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CAGAGAGACGGGCCTCCCAG;RSEQ=GTCCAGGATTCAGATCTGAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:15.3:1:30:1:1:0:25.5:8:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488505 . G A 30 d5;v3;NM7.25 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGGCGGCCTGTGCAAAGCG;RSEQ=CCCCAGGCGGGTGTCACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30.5:1:30:1:1:0:27.5:4:1:0:7.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488510 . AGG TAT 30 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGCCTGTGCAAAGCGGCCCC;RSEQ=CGGGTGTCACCCTGCTCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:37.5:1:30.8:1:1:0:27.5:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488527 . C T 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCAGGCGGGTGTCACCCTG;RSEQ=TCCCTCGTGGGTCGCCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:35:0:31.5:1:1:0:27.5:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488541 . G A 32 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCCTGCTCCCTCGTGGGTC;RSEQ=CCTTCGCCCACACCGGCGCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:21:0:32:0:1:0:27.5:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488868 . C A 31 pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.09091;SOR=0;LSEQ=GCGCGGTGGGACAGCCTGGG;RSEQ=CCGCTCAAGCGGGGCCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:2:1,1:0,2:2,2:0.5:0,2:17:0:31.5:1:1:0:24.5:4:0.5:0:3 0/0:8:0:0,0:3,5:8,0:0:2,0:11:1:30.4:1:1:0:22.1:16:1:0:2.5 +Y 13488871 . G T 29 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.47253;SOR=Inf;LSEQ=CGGTGGGACAGCCTGGGCCC;RSEQ=CTCAAGCGGGGCCACAGGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:13.5:1:33.2:1:1:0:23.2:12:1:0:3.8 0/1:8:2:1,1:2,3:5,2:0.25:2,2:7.5:1:29:1:1:1.41:22:4:0.25:0:2 +Y 13488874 . C G 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.16484;SOR=0;LSEQ=TGGGACAGCCTGGGCCCGCT;RSEQ=AAGCGGGGCCACAGGGCCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:1,3:4,2:0.3333:2,2:23:0:33:1:1:2.45:24.5:4:0.3333:0:3 0/0:8:0:0,0:3,5:8,0:0:2,0:17:1:31.4:1:1:0:22.1:16:1:0:2.5 +Y 13488879 . G T 31 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=1.60839;LSEQ=CAGCCTGGGCCCGCTCAAGC;RSEQ=GGGCCACAGGGCCAAGGTGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:1:0,1:2,3:5,1:0.1667:2,0:27:0:32:0:1:0:22:2:0.1667:0:7 0/1:8:2:1,1:2,4:6,2:0.25:2,2:35:0:31:0:1:1.83:22:4:0.25:0:3.5 +Y 13488891 . C A 64 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.27739;SOR=0.19316;LSEQ=GCTCAAGCGGGGCCACAGGG;RSEQ=CAAGGTGTGCTTGCGCCACC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:6:4:1,3:1,1:2,4:0.6667:2,2:30:1:32:0:1:2.44949:22.5:8:0.6667:0:4.3 0/1:8:2:1,1:2,4:6,2:0.25:2,2:23.5:1:29:1:1:1.83:22:4:0.25:0:3.5 +Y 13488897 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.47253;SOR=Inf;LSEQ=GCGGGGCCACAGGGCCAAGG;RSEQ=GTGCTTGCGCCACCCGCGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:2,4:6,0:0:2,0:23.8:1:31.2:1:1:0:23.2:12:1:0:3.8 0/1:8:2:1,1:2,4:6,2:0.25:2,2:17.5:1:30.5:1:1:1.83:22:4:0.25:0:3.5 +Y 13488914 . C G 32 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.49091;SOR=Inf;LSEQ=AGGTGTGCTTGCGCCACCCG;RSEQ=GTCCCAGGGGAGTCCGTGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:1,3:4,0:0:2,0:30.8:1:32.3:1:1:0:22.5:8:1:0:4.3 0/1:7:2:1,1:1,3:4,2:0.2857:2,2:9:0:32.5:1:1:2.45:22:4:0.2857:0:2 +Y 13488924 . G T 47 d5 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.4;SOR=0;LSEQ=GCGCCACCCGCGTCCCAGGG;RSEQ=AGTCCGTGTTGGGGCTGGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:1,2:0,1:1,3:0.75:0,2:25.7:1:29.7:1:1:0:22:6:0.75:0:4.7 0/0:2:0:0,0:0,2:2,0:0:0,0:4:1:32:0:1:0:22.5:4:1:0:3.5 +Y 13488938 . G A 48 d5 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=6;SSF=1;SOR=0;LSEQ=CCAGGGGAGTCCGTGTTGGG;RSEQ=CTGGGGCAGGGGTTCCCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:11.7:1:30.3:1:1:0:22:6:1:0:4.7 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13488946 . A C 30 d5;v3;p8 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCCGTGTTGGGGCTGGGGC;RSEQ=GGGGTTCCCAGGGCCCAGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:5.5:1:30:1:1:0:22:4:1:0:5.5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13489680 . C A 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=CCTGGGCTGGGTGGAGACCC;RSEQ=CGTCCCATGAAACACCGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:1,1:0.5:0,0:43:0:12:0:1:0:23:0:0:0:7 0/1:5:2:1,1:2,1:3,2:0.4:2,2:26.5:1:31:0:1:1.7321:24.5:4:0.4:0:4 +Y 13489682 . G T 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0.70712;LSEQ=TGGGCTGGGTGGAGACCCCC;RSEQ=TCCCATGAAACACCGTGCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:1,0:1,1:0.5:0,0:45:0:28:0:1:0:23:2:0.5:0:7 0/1:5:2:1,1:2,1:3,2:0.4:2,2:28.5:1:31.5:1:1:1.7321:24.5:4:0.5:0:4 +Y 13489688 . T C 50 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=2.44949;LSEQ=GGGTGGAGACCCCCGTCCCA;RSEQ=GAAACACCGTGCCCGCACAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,0:0,1:0.5:0,0:28:0:34:0:1:0:42:2:1:0:7 1/0:4:3:1,2:1,0:1,3:0.75:0,2:33.7:1:32:0:1:0:30.3:6:0.75:0:5 +Y 13489698 . T G 50 d5;v3 STATUS=LikelyLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCCGTCCCATGAAACACCG;RSEQ=GCCCGCACAGCGTCCAGGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:34:1:33:1:1:0:32.5:4:1:0:6.5 1/0:4:3:1,2:1,0:1,3:0.75:0,2:34:1:31.7:1:1:0:30.3:6:0.75:0:5 +Y 13489724 . C T 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.48571;SOR=0.22474;LSEQ=CACAGCGTCCAGGCCTGACA;RSEQ=CCCTCTGGCCGCTCGCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:4:3:2,1:0,1:1,3:0.75:0,2:24.3:1:30.3:1:1:0:42.7:6:0.75:0:4.3 0/1:3:1:0,1:1,1:2,1:0.3333:2,0:33:0:31:0:1:0:42:2:0.3333:0:7 +Y 13489734 . C G 48 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGGCCTGACACCCCTCTGGC;RSEQ=GCTCGCCTCCTCTGCGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:27.3:1:30.7:1:1:0:42.7:6:1:0:4.3 1/1:1:1:0,1:0,0:0,1:1:0,0:23:0:32:0:1:0:42:2:1:0:7 +Y 13489739 . G A 47 d5;MAF0.05 STATUS=LikelySomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGACACCCCTCTGGCCGCTC;RSEQ=CCTCCTCTGCGCCTCCGCGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:22.3:1:30:1:1:0:42.7:6:1:0:4.3 1/1:1:1:0,1:0,0:0,1:1:0,0:18:0:31:0:1:0:42:2:1:0:7 +Y 13574411 . C A 29 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTGAACTCCGTGGTTTGAA;RSEQ=ATGAAAGAAATGTACCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:6.8:1:28.3:1:1:0:50.3:3:1:0:0.3 0/1:59:2:1,1:29,28:57,2:0.0339:2,2:20.5:1:29.5:1:1:1.03511:60:4:0.0357:0:1.5 +Y 13574414 . G A 26 d5;v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GAACTCCGTGGTTTGAACAT;RSEQ=AAAGAAATGTACCTTCTTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:8.5:1:33:1:1:0:40.5:4:1:0:0 0/1:56:2:1,1:27,27:54,2:0.0357:2,2:16.5:1:26.5:1:1:1:22:4:0.0364:0:1.5 +Y 13801082 . T A 87 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGGAATGGAATTGAATGGAG;RSEQ=CGAATGGAATAGAATCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:17.3:1:32:0:1:0:21:6:1:0:6 1/1:9:9:5,4:0,0:0,9:1:0,2:14.9:1:27.6:1:1:0:21.7:18:1:0:5.3 +Y 13801084 . G T 91 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATTGAATGGAGTC;RSEQ=AATGGAATAGAATCAAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:19.3:1:31:1:1:0:21:6:1:0:6 1/1:9:9:5,4:0,0:0,9:1:0,2:16.9:1:28.9:1:1:0:21.7:18:1:0:5.3 +Y 13801126 . A C 91 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=ATGGCATCGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:37.3:1:34.7:1:1:0:21:6:1:0:6 1/1:9:9:5,4:0,0:0,9:1:0,2:40.2:1:28.9:1:1:0:21.7:8:1:0:5.3 +Y 13801128 . G C 89 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGCATCGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:35.3:1:32.3:1:1:0:21:6:1:0:6 1/1:9:9:5,4:0,0:0,9:1:0,2:38.2:1:28.2:1:1:0:21.7:8:1:0:5.3 +Y 13801138 . G GTGCTC 71 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=12.000;MSILEN=5;SSF=1;SOR=1;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:3:2:0,2:0,0:0,2:0.6667:0,0:22.5:1:33:0:1:0:20:4:0.6667:0:6 1/0:9:6:4,2:0,0:0,6:0.6667:0,2:27:1:27.6:1:1:0:21.2:12:0.6667:0:5.3 +Y 13801153 . G C 78 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATGGAATGGAATGGAAT;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:5.3:1:28.7:1:1:0:21:6:1:0:6 1/1:9:8:4,4:1,0:1,8:0.8889:0,2:8.3:1:26:1:1:0:21.4:7:0.875:0:5.5 +Y 13833050 . AC TG 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAAATGTAATGGACTTGAA;RSEQ=GAATGGACTGAAATAGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:43:0:33:0:1:0:21:2:1:0:6 1/1:2:2:2,0:0,0:0,2:1:0,0:32.5:1:30.8:1:1:0:24:4:1:0:5 +Y 13833059 . C A 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGACTTGAAACGAATGGA;RSEQ=TGAAATAGAATAGACTCAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:37:0:33:0:1:0:21:2:1:0:6 1/1:2:2:2,0:0,0:0,2:1:0,0:32.5:1:29:1:1:0:24:4:1:0:5 +Y 13833061 . G C 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGACTTGAAACGAATGGACT;RSEQ=AAATAGAATAGACTCAAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:35:0:35:0:1:0:21:2:1:0:6 1/1:2:2:2,0:0,0:0,2:1:0,0:32.5:1:29.5:1:1:0:24:4:1:0:5 +Y 13833063 . A T 29 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAAACGAATGGACTGA;RSEQ=ATAGAATAGACTCAAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:33:0:30:0:1:0:21:2:1:0:6 1/1:2:2:2,0:0,0:0,2:1:0,0:32.5:1:29.5:1:1:0:24:4:1:0:5 +Y 13833091 . T C 28 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGACTCAAAAGCAATGGTCT;RSEQ=GAATGGCATTTATTCGAATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:5:0:32:0:1:0:21:2:1:0:6 1/1:2:2:2,0:0,0:0,2:1:0,0:5:0:28.5:1:1:0:24:4:1:0:5 +Y 13833349 . A G 33 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTGGAATGGAATCGAATGGA;RSEQ=TGAACTGGAATGGAATGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:25.5:1:34:0:1:0:21:4:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:33.5:1:1:0:21:4:1:0:6 +Y 13833354 . C A 31 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGGAATCGAATGGAATGAA;RSEQ=TGGAATGGAATGGACACTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:25.5:1:33:0:1:0:21:4:1:0:5 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:31.5:1:1:0:21:4:1:0:6 +Y 13842718 . G C 66 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATCAACCCGAGTG;RSEQ=AATGGAATGGAGTGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:36.5:1:33.3:1:1:0:21.3:8:1:0:2.3 +Y 13842726 . T G 32 d5;v3;pSTD STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAACCCGAGTGGAATGGAA;RSEQ=GGAGTGGAATGGAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:2:1,1:1,0:1,2:0.5:0,2:47:0:32:1:1:0:21:4:0.5:0:2 +Y 13851242 . A G 32 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAGACGAATGGAATGGAATC;RSEQ=AATGGAATGCAATCCAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:15.5:1:32:0:1:0:24:4:1:0:1.5 +Y 13851603 . T A 30 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATTAGAATAGACTGGAATGG;RSEQ=ATTGAATGGAATCGAATGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:11:0:32:0:1:0:20:2:1:0:8 1/1:2:2:1,1:0,0:0,2:1:0,2:7.5:1:30:0:1:0:21.5:4:1:0:8 +Y 13851606 . T G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGAATAGACTGGAATGGTAT;RSEQ=GAATGGAATCGAATGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:14:0:34:0:1:0:20:2:1:0:8 1/1:2:2:1,1:0,0:0,2:1:0,2:10.5:1:32.5:1:1:0:21.5:4:1:0:8 +Y 13851610 . T G 32 d5;v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAGACTGGAATGGTATTGAA;RSEQ=GGAATCGAATGGAATGGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:18:0:35:0:1:0:20:2:1:0:8 1/0:3:2:1,1:0,1:1,2:0.6667:0,2:14.5:1:32.5:1:1:0:21.5:4:0.6667:0:8 +Y 13851616 . C G 65 d5 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATGGTATTGAATGGAAT;RSEQ=GAATGGAATGGAATTGACCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:10:1:33.3:1:1:0:23.3:6:1:0:6.3 1/1:5:4:3,1:0,0:0,4:0.8:0,2:12.3:1:32.5:1:1:0:26.5:8:0.8:0:7 +Y 13851634 . C A 103 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCGAATGGAATGGAATTGA;RSEQ=CCAAATGTAATAGACTTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:3,6:0,0:0,9:1:0,2:15.9:1:30.8:1:1:0:24.6:18:1:0:4.8 1/1:13:12:6,6:0,0:0,12:0.9231:0,2:17.8:1:28.8:1:1:0:25.5:24:0.9231:0:5.2 +Y 13851646 . A G 129 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGAATTGACCCAAATGTAAT;RSEQ=GACTTGAAAGGAATGGAATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:4,6:0,0:0,10:1:0,2:24.1:1:32.4:1:1:0:24.6:20:1:0:4.7 1/1:19:19:8,11:0,0:0,19:1:0,2:21.5:1:30.4:1:1:0:27.1:38:1:0:4.5 +Y 13851655 . A T 136 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.30556;SOR=Inf;LSEQ=CCAAATGTAATAGACTTGAA;RSEQ=GGAATGGAATCAAATAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:3,7:0,0:0,10:0.9091:0,2:29.9:1:31.3:1:1:0:25.5:20:1:0:4.5 1/1:25:25:11,14:0,0:0,25:1:0,2:21.6:1:29.5:1:1:0:28.5:50:1:0:4 +Y 13851668 . A T 142 PASS STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTTGAAAGGAATGGAATCA;RSEQ=ATAGAATGGACTCAAAAGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:4,8:0,0:0,12:1:0,2:24.2:1:29.8:1:1:0:26.2:24:1:0:4.1 1/1:30:30:14,16:0,0:0,30:1:0,2:21.6:1:29.1:1:1:0:28.4:60:1:0:3.7 +Y 13851695 . A T 60 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCAAAAGCAATGGTC;RSEQ=CAAATGGAATTTATTTGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:7:1:30:1:1:0:24.8:8:1:0:4.3 +Y 13851697 . A G 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACTCAAAAGCAATGGTCAC;RSEQ=AATGGAATTTATTTGAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:1,1:1,0:1,2:0.6667:0,2:9.5:1:31:1:1:0:22.5:4:0.6667:0:4.5 +Y 13851701 . G T 30 d5;v3;p8 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CAAAAGCAATGGTCACAAAT;RSEQ=GAATTTATTTGAATAGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:2:2:1,1:0,0:0,2:1:0,2:5.5:1:30.5:1:1:0:22.5:4:1:0:4.5 +Y 13866464 . G A 29 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GGAATCGAACTGAATGGAAT;RSEQ=GAATGGAAAAGAATGGACGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:10:0:29.5:1:1:0:39.5:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13866490 . C G 31 d5;v3;pSTD STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAAAAGAATGGACGTCAATG;RSEQ=AATGGAGTCGAATGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:36:0:31:1:1:0:39.5:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13866504 . G A 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCAATGCAATGGAGTCGAAT;RSEQ=GAATGGAACCGAATGCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:38.5:1:26.5:1:1:0:39.5:4:1:0:6 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13866520 . CA GT 26 d5;v3 STATUS=SampleSpecific;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAATGGAATGGAACCGAATG;RSEQ=ATGGAATTGAAGGGAATTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:2,0:0,0:0,2:1:0,0:21.5:1:26:1:1:0:39.5:4:1:0:5 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +Y 13866978 . T C 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGAATGGACTGGAATGGAA;RSEQ=GGACTCGAATGGAATGGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:19:1:31.5:1:0.33333:0:22:4:0.6667:0:7 +Y 13867041 . T A 31 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=AATGGACTGCAGAGGAATGG;RSEQ=CTCGAATGGAATGGAAACGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:3:2:0,2:1,0:1,2:0.6667:0,0:14.5:1:31:0:0.33333:0:22:4:0.6667:0:7 +Y 13869133 . T A 60 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTGGAGTGGAATGGAC;RSEQ=CGAATGGAATGGAAAAGAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:2,2:0,0:0,4:1:0,2:30:1:30:1:1:0:21.8:8:1:0:5.5 +Y 13869148 . AA GC 49 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGGACTCGAATGGAATGGAA;RSEQ=GAATGGAATGGAATGGAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:0,0:0,3:0.75:0,2:45.3:1:31.2:1:1:0:21.7:6:0.75:0:5 +Y 13869170 . G A 47 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/0:4:3:1,2:1,0:1,3:0.75:0,2:33.7:1:30:1:1:0:21.7:6:0.75:0:5 +Y 13869190 . G A 45 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=10.000;MSILEN=5;SSF=1;SOR=0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:13.7:1:28.7:1:1:0:21.7:6:1:0:5 +Y 15372143 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAACAAAACAACTATCAGTA;RSEQ=AAACAGTTACTCACCTCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:26:0:0,0:19,7:26,0:0:2,0:20.5:1:31.2:1:1:0:60:25:1:0:0.3 0/1:174:2:1,1:106,66:172,2:0.0115:2,2:34:1:28.5:1:1:1.60147:60:4:0.0115:0:1 +Y 15372253 . G A 44 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAGCTTCTCTCAATGTCT;RSEQ=ATATTGCTTCAGAATTTTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:3,10:13,0:0:2,0:21.5:1:32.8:1:1:0:60:26:1:0:0.1 0/1:121:4:2,2:36,81:117,4:0.0331:2,2:5:1:22.3:1:0.58902:2.23:60:3:0.0254:0:1 +Y 15409551 . C A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGAATGGCTACCAATACCCC;RSEQ=AAAGAGAAACTGCAGCAGTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:27:0:0,0:20,7:27,0:0:2,0:20:1:29.4:1:1:0:60:12.5:1:0:0 0/1:162:2:1,1:112,47:159,2:0.0123:2,2:19.5:1:27.5:1:0.5087:2.36855:60:4:0.0126:0:1 +Y 15414854 . T G 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTTAACAGAGCAGAAGT;RSEQ=GTTATTTTCTTGGTGACCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:16,0:0:2,0:25.3:1:31.4:1:1:0:60:32:1:0:0.2 0/1:132:2:1,1:39,91:130,2:0.0152:2,2:26:1:32.5:1:0.51585:2.32:60:4:0.0152:0:2 +Y 15414856 . T A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGTTAACAGAGCAGAAGTTG;RSEQ=TATTTTCTTGGTGACCTGAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:16,0:0:2,0:24.1:1:29.5:1:1:0:60:15:1:0:0.2 0/1:123:2:1,1:34,87:121,2:0.0163:2,2:24:1:30.5:1:0.4898:2.54:60:4:0.0163:0:2 +Y 15435442 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAAAAACTTACTCTCAAT;RSEQ=ATTCCTGGAAGGAGGAAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:11,2:13,0:0:2,0:24.2:1:33.4:1:1:0:60:26:1:0:0 0/1:85:2:1,1:67,16:83,2:0.0235:2,2:16.5:1:27:1:0.3619:4.09268:60:4:0.0238:0:1.5 +Y 15435453 . G T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTCTCAATGATTCCTGGAA;RSEQ=GAGGAAGCCTGGTATTGTGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:13,3:16,0:0:2,0:25.6:1:33.5:1:1:0:60:32:1:0:0 0/1:112:2:1,1:86,24:110,2:0.0179:2,2:22:1:28.5:1:0.39817:3.53106:57.5:4:0.0179:0:1 +Y 15435495 . A T 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATTTGGCAATTGTAGTATG;RSEQ=GATCTATTGCTTTCACAACG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:29:0:0,0:18,11:29,0:0:2,0:26.1:1:30.6:1:1:0:60:28:1:0:0 0/1:200:2:1,1:126,72:198,2:0.01:2,2:29:1:29:1:1:1.74477:39.5:4:0.0101:0:1 +Y 15436447 . TA T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTATAAAAGTTTAAAGATAG;RSEQ=AAATATATATTCAATCTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:7,0:0:2,0:18.1:1:28.1:1:1:0:60:14:1:0:0 0/1:87:2:1,1:68,17:85,2:0.023:2,2:12:1:26:1:0.37289:3.91578:57:4:0.023:0.0115:0.5 +Y 15436494 . T C 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCTTACCTAATTTAAGAGC;RSEQ=CCAGCAAGGCCACGTATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:9,3:12,0:0:2,0:33.6:1:32.8:1:1:0:54.2:24:1:0:0 0/1:186:2:1,1:124,60:184,2:0.0108:2,2:27:1:28.5:1:0.54955:2.05796:58.5:4:0.0111:0:1 +Y 15436505 . C A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTAAGAGCTCCAGCAAGGC;RSEQ=ACGTATTACTGTAACAGGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:8,5:13,0:0:2,0:31.5:1:32:1:1:0:48.8:26:1:0:0 0/1:192:2:1,1:119,70:189,2:0.0104:2,2:47:0:31:1:1:1.69499:60:4:0.0107:0:1.5 +Y 15438169 . T C 34 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.01656;SOR=0;LSEQ=GTATGGTGAAGTTGGTGGTC;RSEQ=TGGAGGTGGACATTTATCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:2:1,1:27,26:53,2:0.0364:2,2:30:1:34:1:1:1.03776:33:4:0.0364:0:1.5 0/0:369:0:0,0:170,199:369,0:0:2,0:24.9:1:29.5:1:1:0:59.1:45.125:1:0:0.1 +Y 15447831 . A T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGGATTGTCTGCAATTAATA;RSEQ=ATTTGGTGAATCTCCATGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:25.5:1:31.6:1:1:0:60:20:1:0:0.1 0/1:102:2:1,1:45,55:100,2:0.0196:2,2:29.5:1:27:1:1:1.22:60:4:0.0198:0:1 +Y 15447876 . T C 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTGGAAACAGCATCTGCTA;RSEQ=CAACTGATGAACATGATTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:7,0:0:2,0:23.3:1:31.9:1:1:0:60:14:1:0:0 0/1:75:2:1,1:38,35:73,2:0.0267:2,2:35.5:1:30:1:1:1.08451:60:4:0.027:0:1 +Y 15470363 . C A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCTTTGTTGGACTAGATGTT;RSEQ=TTTTCTTCTTGGCAGGACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:16,17:33,0:0:2,0:23.6:1:33.2:1:1:0:58:66:1:0:0.1 0/1:180:2:1,1:109,69:178,2:0.0111:2,2:43:1:28.5:1:1:1.57551:56:4:0.0111:0:1 +Y 15470913 . G GA 96 v3 STATUS=Germline;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.65969;SOR=0.74011;LSEQ=AAACTTGATTACTGAAGAGT;RSEQ=AAAAAAAAAAACCCTTAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:2:2,0:9,2:11,2:0.1538:2,0:15:1:32.1:1:1:0:32:4:0.1538:0.0769:0 0/1:93:11:8,3:65,16:81,11:0.1183:2,2:30.2:1:27.9:1:0.69116:1.51582:50.6:22:0.125:0.0215:0.2 +Y 15470934 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAAAAAAAAAACCCTTAAAG;RSEQ=TGGGCACCTACAGAACATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:10,2:12,0:0:2,0:28.9:1:32.8:1:1:0:44.9:24:1:0:0.6 0/1:85:2:1,1:63,20:83,2:0.0235:2,2:23.5:1:27.5:1:0.43529:3.09864:43:4:0.0256:0:1 +Y 15471059 . G T 32 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=0.01926;SOR=0;LSEQ=CAATACTAGGAAGTAATTTA;RSEQ=TTTTATTCTGTAGACTACTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:2:1,1:13,10:23,2:0.08:2,2:16:0:32.5:1:1:1.28628:60:4:0.08:0:1.5 0/0:152:0:0,0:63,88:151,0:0:2,0:32.2:1:31.8:1:1:0:45.3:150:0.9934:0:0.1 +Y 15471192 . TA T 32 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCCTCAGGGTTATAGGTATT;RSEQ=AAAAAAAATTCTAAATTTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:1,9:10,0:0:2,0:25.7:1:31.6:1:1:0:53.2:20:1:0:0 0/1:83:2:0,2:9,72:81,2:0.0241:2,0:23.5:1:32.5:1:1:0:49:4:0.0241:0:0 +Y 15471841 . G A 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGCCTGTAAAGCATCCATAG;RSEQ=CTGATTTTGCTGCTGATACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:30:0:0,0:16,14:30,0:0:2,0:24.1:1:30.8:1:1:0:60:29:1:0:0.1 0/1:224:3:2,1:99,122:221,3:0.0134:2,2:18.7:1:26:1:0.58998:2.45:60:6:0.0137:0:1 +Y 15471877 . A G 29 v3;p8;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATACAACACACTGGAAAGAA;RSEQ=AAGAATGCTGTCAAAAACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:5,11:16,0:0:2,0:28.8:1:31.6:1:1:0:60:32:1:0:0.1 0/1:146:2:1,1:51,93:144,2:0.0137:2,2:6:0:29:1:1:1.82:60:4:0.0137:0:1 +Y 15478164 . C T 41 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACCTTCCAAGAAAATACCA;RSEQ=GATTGGCCAGAATTAGGATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:10,5:15,0:0:2,0:26.1:1:31.7:1:1:0:60:30:1:0:0.1 0/1:159:3:1,2:93,61:154,3:0.0189:2,2:13.7:1:26.3:1:0.56477:3.02729:60:6:0.0194:0:1.3 +Y 15478170 . G A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CCAAGAAAATACCACGATTG;RSEQ=CCAGAATTAGGATCTGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:13,6:19,0:0:2,0:22.7:1:30.2:1:1:0:60:18:1:0:0.2 0/1:183:2:1,1:105,76:181,2:0.0109:2,2:35.5:1:29:1:1:1.37908:55:4:0.0116:0:1.5 +Y 15478226 . C A 28 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.00502;SOR=0;LSEQ=ATACTGAATAGCATAGCTTT;RSEQ=CTTTGTGGCTTTGTCTCCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:7,6:13,2:0.1333:2,2:28:1:28.5:1:1:1.1547:60:4:0.1538:0:1 0/0:190:0:0,0:75,113:188,0:0:2,0:26.9:1:30.2:1:1:0:58.5:30.333:1:0:0.3 +Y 15478270 . C T 38 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATCCATATTATGATGCATC;RSEQ=AACCTATAATTAAGAAGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:1,8:9,0:0:2,0:13.6:1:29.6:1:1:0:60:8:1:0:0.1 0/1:78:3:2,1:17,58:75,3:0.0385:2,2:13:1:24.3:1:0.14535:6.61:60:2:0.0263:0:2 +Y 15522866 . C A 26 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TATGTGGGAAAAATCTCAAC;RSEQ=ACCTACCTTTAAACTAGACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:7,3:10,0:0:2,0:21.7:1:32.1:1:1:0:60:20:1:0:0.1 0/1:117:2:1,1:84,31:115,2:0.0171:2,2:7.5:1:26:1:0.47392:2.68283:43:4:0.0171:0:1 +Y 15522952 . C A 33 v3;pSTD STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.00538;SOR=0;LSEQ=TTTCCTTGGCTCGACAAAAG;RSEQ=TGGGGTCAACATAAAGGACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:2:1,1:6,7:13,2:0.1333:2,2:19:0:33:1:1:1.15:26:4:0.1429:0:1.5 0/0:183:0:0,0:79,104:183,0:0:2,0:27.8:1:31.1:1:1:0:58.5:35.6:1:0:0.1 +Y 15581983 . G A 128 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.19161;SOR=Inf;LSEQ=TAAGTCAAGCAAGAAATTTA;RSEQ=AAAGAGAATAACAATACCTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:8,0:8,0:0:0,0:23:1:33.5:1:1:0:60:16:1:0:0 0/1:79:19:15,4:45,15:60,19:0.2405:2,2:28.6:1:30.3:1:1:1.25:60:38:0.2468:0:1.1 +Y 15582103 . G A 31 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GATTAAAGATTCGTAGCAGC;RSEQ=AACAGCCTAGAAATAAAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:19:0:0,0:6,13:19,0:0:2,0:25.3:1:30.8:1:1:0:60:38:1:0:0 0/1:156:2:1,1:54,100:154,2:0.0128:2,2:16:0:31.5:1:1:1.84:60:4:0.0129:0:1.5 +Y 15591133 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTTGCGTCTGGTTGCTTTTA;RSEQ=CTTGCCTAGTAGGGTCTTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:8,6:14,0:0:2,0:19.8:1:32.6:1:1:0:60:28:1:0:0.1 0/1:114:2:1,1:69,43:112,2:0.0175:2,2:42:1:29:1:1:1.59771:60:4:0.0179:0:1 +Y 15591445 . T G 70 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CGACTGTCAGGCTAACAGAC;RSEQ=CCTCTTCACTCTCGCGGCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:7,0:0:2,0:15.7:1:30:1:1:0:60:14:1:0:0.1 0/1:52:5:4,1:35,12:47,5:0.0962:2,2:18.2:1:30.2:1:1:1.36:60:10:0.098:0:1 +Y 15591537 . G C 73 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTAGTGAGCGACACTGCGCA;RSEQ=GATTTCATGGAAACAACAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:2,5:7,0:0:2,0:26.3:1:31.7:1:1:0:60:14:1:0:0 0/1:91:5:1,4:37,49:86,5:0.0549:2,2:42.8:1:31.6:1:0.3959:2.98877:60:10:0.0549:0:1.2 +Y 15860530 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAAATTCCGATCATGGGG;RSEQ=TCAAGGAGACTTGGAGAAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:6,4:10,0:0:2,0:22.7:1:32.1:1:1:0:60:20:1:0:0 0/1:113:2:1,1:69,42:111,2:0.0177:2,2:22:1:27:1:1:1.6353:60:4:0.018:0:1 +Y 15860590 . C A 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACTAGCTGCACCTGAGGGTC;RSEQ=TACCCCTTTATCCATCATTT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:15:0:0,0:7,8:15,0:0:2,0:30.4:1:32.3:1:1:0:58.5:30:1:0:0 0/1:151:2:1,1:70,79:149,2:0.0132:2,2:20:1:29:1:1:1.13:44.5:4:0.0137:0:1 +Y 15860645 . G A 40 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=4;SSF=1;SOR=Inf;LSEQ=TAGTGTTTTCCTCCCCTGTG;RSEQ=CTGGCTTTCATGAACTTAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:25.7:1:32.3:1:1:0:57.6:20:1:0:0.1 0/1:101:3:2,1:32,66:98,3:0.0297:2,2:13.7:1:25.7:1:0.26145:4.06:40.3:6:0.03:0:1 +Y 19370898 . T C 29 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTCTGTTCTTGGATCTCTT;RSEQ=GGTTTGTTTGTATTCAGGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:6,12:18,0:0:2,0:26.7:1:31.2:1:1:0:60:36:1:0:0.1 0/1:154:2:1,1:67,84:151,2:0.013:2,2:41:1:29.5:1:1:1.25:60:4:0.0132:0:2 +Y 19370916 . G A 113 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.36486;SOR=Inf;LSEQ=TTTGGTTTGTTTGTATTCAG;RSEQ=GAAGAGATCCATTAGAGATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:6,7:13,0:0:2,0:25.6:1:31.8:1:1:0:60:26:1:0:0.1 0/1:138:15:8,7:57,66:123,15:0.1087:2,2:27.6:1:29.1:1:0.78513:1.32:58.8:30:0.1103:0:1.5 +Y 21636121 . G T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTTGTTACTTCCCTCTAGG;RSEQ=CCAGGTATCTAATGAATAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:16:0:0,0:4,12:16,0:0:2,0:19.5:1:32.3:1:1:0:60:32:1:0:0.1 0/1:89:2:1,1:30,57:87,2:0.0225:2,2:12:0:30.5:1:1:1.89:60:4:0.023:0:1 +Y 21868363 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTCTGTCCAGGTCTGGAGG;RSEQ=TGTCCAGCCTGCAGCAGCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:22:0:0,0:15,7:22,0:0:2,0:25.6:1:32.6:1:1:0:56.6:44:1:0:0.1 0/1:189:2:1,1:111,76:187,2:0.0106:2,2:28.5:1:28.5:1:1:1.4575:60:4:0.0106:0:1.5 +Y 21868539 . T A 24 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTCCAGGTCTGGGCGGAAGG;RSEQ=GGTGCGGTGAAAGGTGCAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:2,7:9,0:0:2,0:27.6:1:30.2:1:1:0:60:18:1:0:0 0/1:82:2:1,1:22,58:80,2:0.0244:2,2:7:1:24.5:1:0.48479:2.60:60:4:0.025:0:1 +Y 21868553 . G T 45 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGAAGGTGGTGCGGTGAAAG;RSEQ=TGCAGGGACAGACTGGGTTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:2,6:8,0:0:2,0:31:1:32.3:1:1:0:60:16:1:0:0 0/1:61:3:1,2:15,43:58,3:0.0492:2,2:17.7:1:28.7:1:1:1.42:60:6:0.0492:0:1 +Y 21868666 . C T 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=AGCCAACAGCCTACCCAAAC;RSEQ=ACACCTGTCTTACCAGAGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:9,5:14,0:0:2,0:19.5:1:31.1:1:1:0:60:28:1:0:0 0/1:106:2:1,1:67,36:103,2:0.0189:2,2:14.5:1:28.5:1:1:1.84951:60:4:0.0194:0:1 +Y 21868785 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AATGGGTAACAATAATTGAG;RSEQ=TGATGAACCAGGTCCTATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:5,9:14,0:0:2,0:16.8:1:31.6:1:1:0:60:28:1:0:0.1 0/1:62:2:1,1:16,43:59,2:0.0323:2,2:9.5:1:26.5:1:0.48306:2.64:60:4:0.0328:0:1.5 +Y 21869246 . A G 32 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGAGACACTGAAGGGCCTC;RSEQ=CCCTCAGGCAGCCGCACGGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:5,2:7,0:0:2,0:29.4:1:30:1:1:0:60:14:1:0:0 0/1:39:2:1,1:22,15:37,2:0.0513:2,2:30:0:32.5:1:1:1.45198:60:4:0.0526:0:1.5 +Y 21869593 . C G 31 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01395;SOR=0;LSEQ=GCGACGCAGCTGCAGGATAC;RSEQ=CTCCTTCTCCTTCTGTTCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:2:1,1:20,29:49,2:0.0392:2,2:45:1:31.5:1:1:1.44:49.5:4:0.0417:0:1 0/0:377:0:0,0:161,216:377,0:0:2,0:26.2:1:30:1:1:0:55.4:74.4:1:0:0.1 +Y 21869679 . G A 27 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TAGGTCAGCAGTCCACCCTC;RSEQ=CCCTTGTCTGGCATCCTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:4,10:14,0:0:2,0:21.1:1:31.6:1:1:0:60:28:1:0:0 0/1:66:2:1,1:14,50:64,2:0.0303:2,2:7.5:1:27:1:0.40559:3.48:60:4:0.0303:0:1 +Y 21869784 . A T 36 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTTTTCAGAGAGAAACCCAG;RSEQ=ACCCATCTTTTCCCCATCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:18:0:0,0:17,1:18,0:0:1,0:32.8:1:31.4:1:1:0:60:36:1:0:0.1 0/1:149:3:1,2:97,49:146,3:0.0201:2,2:6.3:1:23:1:0.26982:3.91997:60:2:0.0138:0:1 +Y 21870257 . C T 29 v3 STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.01329;SOR=0;LSEQ=GCCCCACAGGCAGGTCCCGG;RSEQ=CCACAGCCACCAGGCCCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:2:1,1:32,34:66,2:0.0294:2,2:33.5:1:29.5:1:1:1.06:60:4:0.0294:0:1 0/0:518:0:0,0:252,266:518,0:0:2,0:27.2:1:30.6:1:1:0:59.9:56.556:1:0:0.2 +Y 21870329 . C A 36 v3;p8;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TCTGGAATAGGGGAAAGAAA;RSEQ=TTTATTTAAATTATGTCAAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:33:0:0,0:5,28:33,0:0:2,0:24:1:33.1:1:1:0:60:32:1:0:0.2 0/1:205:3:2,1:56,146:202,3:0.0146:2,2:5.7:1:23.3:1:0.19354:5.17:60:2:0.01:0:1.3 +Y 21870904 . AT A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TGGTGGATGCTTCTGCCTAA;RSEQ=TTTTTTTGAAAAAGAGAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:23:0:0,0:9,14:23,0:0:2,0:25.9:1:29.6:1:1:0:60:22:1:0:0.2 0/1:155:2:0,2:48,105:153,2:0.0129:2,0:34:1:28.5:1:1:0:60:4:0.013:0:0 +Y 21871569 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CTGCTGAAGCTGATGGGCTT;RSEQ=AGGCACCTCTACACCCAGCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:3,2:5,0:0:2,0:21.2:1:32.6:1:1:0:60:10:1:0:0 0/1:64:2:1,1:41,21:62,2:0.0313:2,2:23:1:27:1:1:1.93068:60:4:0.0313:0:2 +Y 21877385 . C T 26 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTGCCCTTAGCTCTTCAAAG;RSEQ=CTGGAGAGTGTAAGTTGCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:3,7:10,0:0:2,0:27.4:1:32:1:1:0:60:20:1:0:0 0/1:79:2:1,1:35,42:77,2:0.0253:2,2:42.5:1:26:0:1:1.20:60:4:0.027:0:1 +Y 21877588 . G A 50 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AGCCCGAATCTTCAGTTTAT;RSEQ=CAGCATGGTGGGGAGCTCAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:43:0:0,0:16,27:43,0:0:2,0:27:1:31.9:1:1:0:60:42:1:0:0.1 0/1:314:4:3,1:130,180:310,4:0.0127:2,2:9:1:25:1:0.3148:4.14:60:8:0.0129:0:1 +Y 21877709 . C T 42 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CACAGTGTTCCCATGCTCAC;RSEQ=GGAGGTACTGTCGGCTACTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:12:0:0,0:7,5:12,0:0:2,0:26.8:1:30:1:1:0:60:24:1:0:0 0/1:119:3:1,2:67,49:116,3:0.0252:2,2:16.7:1:26.7:1:0.57571:2.71177:60:6:0.0252:0:1 +Y 21877822 . G A 36 v3;q25 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GACAAGAAGCACGTGGTCTT;RSEQ=CACTTGATGCACTGGCGTTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:31:0:0,0:17,14:31,0:0:2,0:27.6:1:32.1:1:1:0:59.7:30:1:0:0.2 0/1:239:3:1,2:110,126:236,3:0.0126:2,2:38.7:1:23.3:1:1:1.74213:53.3:2:0.0084:0:1 +Y 21877909 . C G 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=Inf;LSEQ=CCCTGGGGGTGTTCAACCCA;RSEQ=ATATACTGTAAAGACTAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:3,8:11,0:0:2,0:22.9:1:29.4:1:1:0:60:10:1:0:0.2 0/1:94:2:1,1:28,64:92,2:0.0213:2,2:11.5:1:28.5:1:0.52414:2.26:60:4:0.0213:0:1 +Y 21878194 . G A 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGGCCTTTCGTAGACGTC;RSEQ=CTCCTCCTGAACCATAATGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:7:0:0,0:4,3:7,0:0:2,0:19:1:31.1:1:1:0:60:14:1:0:0 0/1:37:2:1,1:22,13:35,2:0.0541:2,2:41:1:30:1:1:1.66733:60:4:0.0556:0:1 +Y 21878285 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGGCAGCCATCTTGCAGAT;RSEQ=AGCTCCTCGTGGGAGAAGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:8:0:0,0:4,4:8,0:0:2,0:24.9:1:32.1:1:1:0:60:16:1:0:0.3 0/1:75:2:1,1:40,33:73,2:0.0267:2,2:18:1:30.5:1:1:1.20899:60:4:0.0274:0:1 +Y 21878324 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ACACAATAGCGCCGGAGCCG;RSEQ=CGGTAGTGTTCAATGCACTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:2,3:5,0:0:2,0:27.4:1:32.6:1:1:0:60:10:1:0:0.4 0/1:78:2:1,1:32,44:76,2:0.0256:2,2:28.5:1:27.5:1:1:1.37:60:4:0.026:0:1 +Y 21878469 . C T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCTACCTGCAGGCCCACTG;RSEQ=ATGCTCACTCACCCAGTCAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:9:0:0,0:7,2:9,0:0:2,0:25.1:1:30.8:1:1:0:60:8:1:0:0 0/1:82:2:1,1:53,27:80,2:0.0244:2,2:35:1:27.5:1:1:1.94576:60:4:0.0247:0:1 +Y 21878550 . C T 30 v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GTTAAAACCACTGTGGTAAG;RSEQ=ACGAGGAAAAGTGATGACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:14:0:0,0:7,6:13,0:0:2,0:25.8:1:31.4:1:1:0:60:12:1:0:0.2 0/1:149:2:1,1:70,77:147,2:0.0134:2,2:8:0:30:1:1:1.10:60:4:0.0138:0:1.5 +Y 21882771 . G T 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TACTTACTGGCACACCATGG;RSEQ=ACATCAAAGTGTTGGGATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:11:0:0,0:10,1:11,0:0:2,0:29.5:1:31.6:1:1:0:60:22:1:0:0 0/1:128:2:1,1:89,37:126,2:0.0156:2,2:16.5:1:27.5:1:0.50726:2.38686:60:4:0.0157:0:1 +Y 21882786 . G A 27 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CATGGGACATCAAAGTGTTG;RSEQ=GATTCATGAGAGTGACAAGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:13:0:0,0:10,3:13,0:0:2,0:27.6:1:29.8:1:1:0:60:12:1:0:0 0/1:157:2:1,1:102,53:155,2:0.0127:2,2:32:1:27.5:1:1:1.91602:60:4:0.013:0:1 +Y 21882929 . G T 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=TTCGGCTCACCCCTGCTCAC;RSEQ=TAGACAGAAGACACGTCAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:10:0:0,0:5,5:10,0:0:2,0:23.5:1:31.5:1:1:0:60:20:1:0:0 0/1:89:2:1,1:36,51:87,2:0.0225:2,2:31.5:1:30.5:1:1:1.41:60:4:0.0227:0:1 +Y 21883019 . T A 28 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATTGGGGTCATGCTCACCAA;RSEQ=GCAGATAGTTAATAGAGTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:21:0:0,0:13,8:21,0:0:2,0:23.9:1:30:1:1:0:60:42:1:0:0 0/1:155:2:1,1:87,66:153,2:0.0129:2,2:33:1:28.5:1:1:1.31579:60:4:0.0131:0:1 +Y 21883247 . G A 29 PASS STATUS=StrongSomatic;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02646;SOR=0;LSEQ=TAGGGAGTAGGATACGATGA;RSEQ=GAGAGGCAAACTGAGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5:2:1,1:1,2:3,2:0.4:2,2:22.5:1:29.5:1:1:1.73:60:4:0.4:0:1.5 0/0:23:0:0,0:3,20:23,0:0:2,0:22.7:1:30.8:1:1:0:60:46:1:0:0 +Y 22744451 . C CT 28 d5;v3;pSTD STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=ATGTGGACCAAGATCTCAAC;RSEQ=TTTTTTTTTATCTCCTCTCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:41:1:33.5:1:1:0:60:4:1:0:0 0/1:93:2:1,1:69,22:91,2:0.0215:2,2:23:0:28.5:1:0.43548:3.08929:60:4:0.0215:0:0 +Y 22744561 . A G 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=AAGAGGTTATGCCATATCAG;RSEQ=GGGAAATTGAGAAAAAAGGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:17:0:0,0:8,9:17,0:0:2,0:27:1:30.9:1:1:0:60:34:1:0:0.1 0/1:189:2:1,1:79,108:187,2:0.0106:2,2:16.5:1:30:1:1:1.36:60:4:0.0106:0:1.5 +Y 22746399 . CG C 29 d5;v3 STATUS=Deletion;SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACATTATATTGGTTGGTCTA;RSEQ=GGACTATCAGGTAAAAATAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:5:2:1,1:2,1:3,2:0.4:2,2:13:1:29:1:1:1.7321:60:4:0.4:0:0 +Y 22930752 . C A 46 v3;p8 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=GGGAATTCCACACCTGGTGA;RSEQ=TCATGATGCTCGAACCATTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:25:0:0,0:13,12:25,0:0:2,0:23.2:1:32.3:1:1:0:60:50:1:0:0 0/1:164:3:2,1:81,80:161,3:0.0183:2,2:5.7:1:29.3:1:1:1.97:54:6:0.0184:0:1 +Y 22930880 . G GT 30 v3 STATUS=StrongLOH;SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.000;MSILEN=1;SSF=1;SOR=Inf;LSEQ=CAGGTAAGGTTTTTTTTGTT;RSEQ=TTTTTTTTTTCCCTTGTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:5:0:0,0:0,5:5,0:0:0,0:14.6:1:34:0:1:0:60:10:1:0:0 0/1:30:2:0,2:2,26:28,2:0.0667:2,0:22:1:30:1:1:0:60:4:0.069:0:0.5 diff --git a/data/sample_output/PoolTumor2-T_bc52_VarDict_1.4.6_STDfilter.txt b/data/sample_output/PoolTumor2-T_bc52_VarDict_1.4.6_STDfilter.txt index 650d3ed..91cd7be 100644 --- a/data/sample_output/PoolTumor2-T_bc52_VarDict_1.4.6_STDfilter.txt +++ b/data/sample_output/PoolTumor2-T_bc52_VarDict_1.4.6_STDfilter.txt @@ -2,7 +2,6 @@ PoolTumor2-T 1 4955833 A T . PoolTumor2-T 1 9780743 TG T . PoolTumor2-T 1 9781880 A G . PoolTumor2-T 1 11181985 G A . -PoolTumor2-T 1 11227864 C T . PoolTumor2-T 1 11291380 G A . PoolTumor2-T 1 11303131 C T . PoolTumor2-T 1 14192818 G T . @@ -10,34 +9,9 @@ PoolTumor2-T 1 16245610 GT G . PoolTumor2-T 1 16258302 A G . PoolTumor2-T 1 16262650 G A . PoolTumor2-T 1 16971804 A T . -PoolTumor2-T 1 16972489 C A . -PoolTumor2-T 1 16972496 G A . PoolTumor2-T 1 16972790 GAAT AA . -PoolTumor2-T 1 16972793 T A . -PoolTumor2-T 1 16973028 A C . -PoolTumor2-T 1 16973259 G C . -PoolTumor2-T 1 16973855 G A . -PoolTumor2-T 1 16973957 G T . -PoolTumor2-T 1 16974458 G C . PoolTumor2-T 1 16974817 C G . -PoolTumor2-T 1 16974868 G T . -PoolTumor2-T 1 16974955 A G . -PoolTumor2-T 1 16975201 CT C . PoolTumor2-T 1 16975228 C T . -PoolTumor2-T 1 16975429 T C . -PoolTumor2-T 1 16975489 C G . -PoolTumor2-T 1 16975642 C T . -PoolTumor2-T 1 16975689 G C . -PoolTumor2-T 1 16975951 A G . -PoolTumor2-T 1 16976345 T C . -PoolTumor2-T 1 17083778 C T . -PoolTumor2-T 1 17083816 G A . -PoolTumor2-T 1 17083918 C T . -PoolTumor2-T 1 17085227 G C . -PoolTumor2-T 1 17085254 GA G . -PoolTumor2-T 1 17085532 T C . -PoolTumor2-T 1 17085790 C T . -PoolTumor2-T 1 17086541 T C . PoolTumor2-T 1 17087395 G A . PoolTumor2-T 1 17345073 G GC . PoolTumor2-T 1 17380195 TC T . @@ -55,18 +29,15 @@ PoolTumor2-T 1 29644328 C T . PoolTumor2-T 1 34805896 G A . PoolTumor2-T 1 36824305 C T . PoolTumor2-T 1 36941539 G GT . -PoolTumor2-T 1 40799145 A G . PoolTumor2-T 1 45798981 C A . PoolTumor2-T 1 45805566 G C . PoolTumor2-T 1 46509146 G A . -PoolTumor2-T 1 46532925 C CATATATAT . PoolTumor2-T 1 46740500 A G . PoolTumor2-T 1 51436157 G T . PoolTumor2-T 1 51439777 C T . PoolTumor2-T 1 51441409 A G . PoolTumor2-T 1 58158647 C G . PoolTumor2-T 1 59250675 C G . -PoolTumor2-T 1 63226758 G A . PoolTumor2-T 1 65312100 TG T . PoolTumor2-T 1 65332766 T C . PoolTumor2-T 1 65349304 G A . @@ -93,35 +64,16 @@ PoolTumor2-T 1 120429402 A G . PoolTumor2-T 1 120468134 C T . PoolTumor2-T 1 120468487 T C . PoolTumor2-T 1 120469388 ACACT A . -PoolTumor2-T 1 120612040 TCCG T . -PoolTumor2-T 1 121484092 G A . -PoolTumor2-T 1 121484526 C G . -PoolTumor2-T 1 121484565 T G . +PoolTumor2-T 1 120611715 A G . PoolTumor2-T 1 121484636 T G . -PoolTumor2-T 1 121484728 TC T . -PoolTumor2-T 1 121484749 A G . PoolTumor2-T 1 121484973 C T . PoolTumor2-T 1 121485011 T A . -PoolTumor2-T 1 121485042 GT TGA . -PoolTumor2-T 1 121485236 T C . -PoolTumor2-T 1 121485361 A T . -PoolTumor2-T 1 121485390 C T . -PoolTumor2-T 1 144693358 G A . -PoolTumor2-T 1 145273701 C T . -PoolTumor2-T 1 145273705 C T . -PoolTumor2-T 1 148873205 A T . -PoolTumor2-T 1 148876318 G A . -PoolTumor2-T 1 148882036 T C . -PoolTumor2-T 1 148888291 G A . -PoolTumor2-T 1 148889639 G A . -PoolTumor2-T 1 148889774 G A . -PoolTumor2-T 1 148889823 G A . -PoolTumor2-T 1 148891116 T C . -PoolTumor2-T 1 148891287 A G . +PoolTumor2-T 1 121485204 C A . PoolTumor2-T 1 149857797 T C . PoolTumor2-T 1 150552042 G A . PoolTumor2-T 1 152330829 G T . PoolTumor2-T 1 152331013 G A . +PoolTumor2-T 1 154842199 G GGCTGCTGCT . PoolTumor2-T 1 156785653 C G . PoolTumor2-T 1 156838809 TC T . PoolTumor2-T 1 156848778 C T . @@ -132,6 +84,7 @@ PoolTumor2-T 1 157599882 C A . PoolTumor2-T 1 162736690 C T . PoolTumor2-T 1 162737241 A G . PoolTumor2-T 1 162740121 G A . +PoolTumor2-T 1 162750208 C T . PoolTumor2-T 1 162830985 CCCTCCCTA C . PoolTumor2-T 1 165044147 G A . PoolTumor2-T 1 168652905 G C . @@ -143,6 +96,7 @@ PoolTumor2-T 1 176050676 A T . PoolTumor2-T 1 176085412 C G . PoolTumor2-T 1 176103954 C T . PoolTumor2-T 1 176175885 C A . +PoolTumor2-T 1 177294353 G A . PoolTumor2-T 1 181819068 G A . PoolTumor2-T 1 181819202 C T . PoolTumor2-T 1 184327323 T G . @@ -156,48 +110,39 @@ PoolTumor2-T 1 193202953 G A . PoolTumor2-T 1 193203035 C T . PoolTumor2-T 1 193203268 C T . PoolTumor2-T 1 193203305 TCACACACACACACA T . -PoolTumor2-T 1 193203368 T G . PoolTumor2-T 1 193203397 T TTATAATATATATAATTTATTATATATATATTATA . PoolTumor2-T 1 198167287 T C . PoolTumor2-T 1 202188932 A G . PoolTumor2-T 1 203224985 G T . -PoolTumor2-T 1 204316213 G A . PoolTumor2-T 1 204495610 G T . PoolTumor2-T 1 204511602 C A . PoolTumor2-T 1 206648147 T G . PoolTumor2-T 1 206650065 A G . PoolTumor2-T 1 206669136 C A . PoolTumor2-T 1 206944952 T G . +PoolTumor2-T 1 219991332 A ATGG . PoolTumor2-T 1 221053574 A C . -PoolTumor2-T 1 222642304 A G . -PoolTumor2-T 1 224135537 A G . -PoolTumor2-T 1 224135680 G T . +PoolTumor2-T 1 224137928 T C . PoolTumor2-T 1 226253926 T C . PoolTumor2-T 1 226254036 T C . -PoolTumor2-T 1 226551178 A G . -PoolTumor2-T 1 226553467 C CA . PoolTumor2-T 1 226554736 G C . PoolTumor2-T 1 226554951 T C . PoolTumor2-T 1 226567172 A C . PoolTumor2-T 1 226595403 A AGGGCCC . -PoolTumor2-T 1 228613442 G A . -PoolTumor2-T 1 228613471 T C . PoolTumor2-T 1 228617397 G A . PoolTumor2-T 1 229106423 C CTG . PoolTumor2-T 1 229223719 G C . PoolTumor2-T 1 230355441 G A . PoolTumor2-T 1 230355471 G A . PoolTumor2-T 1 230724588 G GGTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA . +PoolTumor2-T 1 241663893 T TTGAG . PoolTumor2-T 1 241669668 C T . -PoolTumor2-T 1 242508644 G A . -PoolTumor2-T 1 242508928 C A . PoolTumor2-T 1 243809488 C T . PoolTumor2-T 1 247555079 A G . PoolTumor2-T 1 248567502 T TGTGTGTGGCAGAGGCCGCTATTACATGTAC . PoolTumor2-T 10 3280619 T C . PoolTumor2-T 10 8100647 C T . PoolTumor2-T 10 8106274 C T . -PoolTumor2-T 10 8111168 C T . PoolTumor2-T 10 8111850 GA G . PoolTumor2-T 10 8116079 C T . PoolTumor2-T 10 9959556 C T . @@ -205,34 +150,8 @@ PoolTumor2-T 10 10923431 T A . PoolTumor2-T 10 15009109 T C . PoolTumor2-T 10 19229864 GC AT . PoolTumor2-T 10 20007127 A C . -PoolTumor2-T 10 29188207 C A . PoolTumor2-T 10 36853842 G A . PoolTumor2-T 10 36853858 G C . -PoolTumor2-T 10 38539283 G T . -PoolTumor2-T 10 38743615 G A . -PoolTumor2-T 10 38744432 C T . -PoolTumor2-T 10 39012451 AT A . -PoolTumor2-T 10 42360771 G C . -PoolTumor2-T 10 42364715 T A . -PoolTumor2-T 10 42364735 T G . -PoolTumor2-T 10 42380300 A ATTCCGGAAGATTCCATTCCATTGTATTCCG . -PoolTumor2-T 10 42380308 A C . -PoolTumor2-T 10 42385248 T C . -PoolTumor2-T 10 42385258 T A . -PoolTumor2-T 10 42387303 C A . -PoolTumor2-T 10 42396882 AA TC . -PoolTumor2-T 10 42398682 AGAGA GAGC . -PoolTumor2-T 10 42399298 C G . -PoolTumor2-T 10 42399313 CC GT . -PoolTumor2-T 10 42528052 C G . -PoolTumor2-T 10 42528063 T G . -PoolTumor2-T 10 42528076 T C . -PoolTumor2-T 10 42529468 C G . -PoolTumor2-T 10 42596918 A T . -PoolTumor2-T 10 42599622 C A . -PoolTumor2-T 10 42599688 A T . -PoolTumor2-T 10 42599799 T A . -PoolTumor2-T 10 42600080 CGAATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG TGA . PoolTumor2-T 10 43596179 G A . PoolTumor2-T 10 43596241 C T . PoolTumor2-T 10 43600210 AGCACAGTCAT A . @@ -253,27 +172,31 @@ PoolTumor2-T 10 70406518 A T . PoolTumor2-T 10 70406864 C T . PoolTumor2-T 10 70412132 AAG A . PoolTumor2-T 10 70451383 A T . +PoolTumor2-T 10 74677784 GTCA G . PoolTumor2-T 10 86331960 A G . PoolTumor2-T 10 88866085 TCA T . PoolTumor2-T 10 89692844 C T . PoolTumor2-T 10 89717709 AGCCGT A . -PoolTumor2-T 10 89720881 T A . +PoolTumor2-T 10 99804144 G GCAGCAAAA . PoolTumor2-T 10 99804159 A G . +PoolTumor2-T 10 99804161 A G . PoolTumor2-T 10 99804170 AG GA . -PoolTumor2-T 10 99804180 G GCAGTAGCAACAGAAATAGCAGTAATAGCAGCAGCAGCAGTAGCAGCAATAATTA . +PoolTumor2-T 10 99804171 G A . +PoolTumor2-T 10 99804173 G A . PoolTumor2-T 10 99804184 C T . +PoolTumor2-T 10 99804192 G A . +PoolTumor2-T 10 99804194 AAT GACAAC . +PoolTumor2-T 10 99804205 C T . +PoolTumor2-T 10 99804211 CAGCAAT C . +PoolTumor2-T 10 99804215 A G . +PoolTumor2-T 10 99804216 A ACAG . +PoolTumor2-T 10 99804224 G A . PoolTumor2-T 10 99804243 GCAACAA G . -PoolTumor2-T 10 99804244 C CAACAACAACAGCAGCAGCAACAGCAGTCACAATTAACAACAGCAACAATAGCAGCAGTAAA . -PoolTumor2-T 10 99804264 A G . -PoolTumor2-T 10 99804273 A GTAAAAACAG . -PoolTumor2-T 10 99804285 AC GCAATAATTATAACAGCAGCAACAACAGCAACGTCAGAAAAAGCAGCAACAGCAATAGCAACAAAAGCATCAGCAACAGCAATAGCATCACAATT . -PoolTumor2-T 10 99804306 A GCAACAACAGAAATCACAGTAACAACAGTAGCAG . -PoolTumor2-T 10 99804318 ACAACAATAGCAACAACAGTAGTGG A . +PoolTumor2-T 10 99804253 C T . PoolTumor2-T 10 104378688 CGT C . PoolTumor2-T 10 110550348 A C . PoolTumor2-T 10 114911035 AAG A . PoolTumor2-T 10 114912534 C T . -PoolTumor2-T 10 114919606 C T . PoolTumor2-T 10 114919608 T C . PoolTumor2-T 10 114920089 A G . PoolTumor2-T 10 123240645 C T . @@ -284,11 +207,13 @@ PoolTumor2-T 10 123242589 G A . PoolTumor2-T 10 123274653 A G . PoolTumor2-T 10 123279795 C T . PoolTumor2-T 10 123488416 A G . +PoolTumor2-T 10 124403674 G T . +PoolTumor2-T 10 124403681 C T . +PoolTumor2-T 10 124403689 T C . PoolTumor2-T 10 134913291 C T . PoolTumor2-T 11 2156741 T G . PoolTumor2-T 11 8246137 C T . PoolTumor2-T 11 8248574 G T . -PoolTumor2-T 11 17457720 CA TG . PoolTumor2-T 11 17746976 G T . PoolTumor2-T 11 20246743 C A . PoolTumor2-T 11 20575654 G C . @@ -301,7 +226,6 @@ PoolTumor2-T 11 32437699 T C . PoolTumor2-T 11 32437841 A C . PoolTumor2-T 11 32439001 T C . PoolTumor2-T 11 32450244 CG C . -PoolTumor2-T 11 32452001 GGA G . PoolTumor2-T 11 35242653 C T . PoolTumor2-T 11 39894274 C T . PoolTumor2-T 11 42138434 C T . @@ -319,16 +243,11 @@ PoolTumor2-T 11 85963619 C T . PoolTumor2-T 11 85963632 T C . PoolTumor2-T 11 85980945 G T . PoolTumor2-T 11 86333429 TA T . -PoolTumor2-T 11 86807222 GT AG . -PoolTumor2-T 11 86807229 A AA . -PoolTumor2-T 11 86807230 TC AT . -PoolTumor2-T 11 86807231 C CC . +PoolTumor2-T 11 86807219 A AA . PoolTumor2-T 11 88359287 AT GG . PoolTumor2-T 11 94153641 C G . PoolTumor2-T 11 94203801 C A . PoolTumor2-T 11 94770943 G T . -PoolTumor2-T 11 94771621 GA G . -PoolTumor2-T 11 95825356 TTGC T . PoolTumor2-T 11 99322049 T C . PoolTumor2-T 11 100913165 G A . PoolTumor2-T 11 100999043 G T . @@ -349,15 +268,12 @@ PoolTumor2-T 11 108206868 TA T . PoolTumor2-T 11 108224757 A T . PoolTumor2-T 11 108224791 CACACAA C . PoolTumor2-T 11 108225473 G A . -PoolTumor2-T 11 117226715 G GAGCAGCAGC . PoolTumor2-T 11 118342819 T G . PoolTumor2-T 11 118370615 C G . PoolTumor2-T 11 118372452 C G . PoolTumor2-T 11 119077003 C T . PoolTumor2-T 11 119145274 A G . -PoolTumor2-T 11 121232871 G A . -PoolTumor2-T 11 121232886 G A . -PoolTumor2-T 11 121232936 TA GG . +PoolTumor2-T 11 121232811 A G . PoolTumor2-T 11 121779664 T C . PoolTumor2-T 11 123606029 A C . PoolTumor2-T 11 132534934 G A . @@ -376,13 +292,14 @@ PoolTumor2-T 12 1038742 A G . PoolTumor2-T 12 1038766 C G . PoolTumor2-T 12 1038854 C T . PoolTumor2-T 12 1040143 TA T . -PoolTumor2-T 12 9085320 T G . +PoolTumor2-T 12 9848439 T TTGCTGC . +PoolTumor2-T 12 9848467 T A . PoolTumor2-T 12 9848470 A T . +PoolTumor2-T 12 9848648 A G . PoolTumor2-T 12 12006544 G A . PoolTumor2-T 12 12007893 C G . PoolTumor2-T 12 12009741 A G . PoolTumor2-T 12 12010056 G A . -PoolTumor2-T 12 12011340 T A . PoolTumor2-T 12 12013626 T TC . PoolTumor2-T 12 12016089 C T . PoolTumor2-T 12 12018392 C T . @@ -420,7 +337,6 @@ PoolTumor2-T 12 46208438 A G . PoolTumor2-T 12 46254505 C G . PoolTumor2-T 12 46287550 A G . PoolTumor2-T 12 49421368 G A . -PoolTumor2-T 12 49426908 C T . PoolTumor2-T 12 49428717 G A . PoolTumor2-T 12 49431654 C T . PoolTumor2-T 12 49436248 G A . @@ -430,7 +346,6 @@ PoolTumor2-T 12 49441376 AT A . PoolTumor2-T 12 50413034 C A . PoolTumor2-T 12 50484405 C T . PoolTumor2-T 12 52906415 C A . -PoolTumor2-T 12 52906434 G A . PoolTumor2-T 12 52906545 C T . PoolTumor2-T 12 52921297 C A . PoolTumor2-T 12 53030489 C T . @@ -468,21 +383,19 @@ PoolTumor2-T 12 120541570 G A . PoolTumor2-T 12 120541597 G A . PoolTumor2-T 12 120554466 G A . PoolTumor2-T 12 121435778 C T . -PoolTumor2-T 12 124887058 G GGCTGCTGCTGCT . -PoolTumor2-T 12 128101958 C T . PoolTumor2-T 12 131945101 C T . PoolTumor2-T 12 131945403 A G . PoolTumor2-T 12 132547162 G A . PoolTumor2-T 12 133208752 T A . PoolTumor2-T 12 133211059 T C . PoolTumor2-T 12 133226249 G T . +PoolTumor2-T 12 133240781 CACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT C . PoolTumor2-T 12 133243788 T A . PoolTumor2-T 12 133244668 CA C . PoolTumor2-T 12 133257837 C A . PoolTumor2-T 13 21004758 T C . PoolTumor2-T 13 21554217 A T . PoolTumor2-T 13 21563715 C T . -PoolTumor2-T 13 27793546 G A . PoolTumor2-T 13 28601389 TAC T . PoolTumor2-T 13 28608709 G A . PoolTumor2-T 13 28611186 G C . @@ -515,10 +428,6 @@ PoolTumor2-T 13 43550043 CA C . PoolTumor2-T 13 43550243 A G . PoolTumor2-T 13 43550270 T A . PoolTumor2-T 13 48939018 C T . -PoolTumor2-T 13 49026852 C T . -PoolTumor2-T 13 49034073 C CT . -PoolTumor2-T 13 49034085 CTT TC . -PoolTumor2-T 13 49034104 TCTC T . PoolTumor2-T 13 49037825 G T . PoolTumor2-T 13 49047529 G C . PoolTumor2-T 13 49051848 G A . @@ -526,9 +435,7 @@ PoolTumor2-T 13 67591561 CA TG . PoolTumor2-T 13 68406205 T A . PoolTumor2-T 13 71158400 G A . PoolTumor2-T 13 72248871 T TAATAGAGTGCTCCATTCAAGTTTGAAAACTA . -PoolTumor2-T 13 72249649 T A . PoolTumor2-T 13 103508378 C T . -PoolTumor2-T 13 103513578 G A . PoolTumor2-T 13 104378382 A G . PoolTumor2-T 13 106826430 G T . PoolTumor2-T 13 110414685 A G . @@ -539,20 +446,6 @@ PoolTumor2-T 13 110435914 G A . PoolTumor2-T 13 110436790 ACCG A . PoolTumor2-T 13 111588868 C T . PoolTumor2-T 13 111590803 T A . -PoolTumor2-T 13 112722133 C T . -PoolTumor2-T 14 19487496 C A . -PoolTumor2-T 14 19487907 A C . -PoolTumor2-T 14 19487914 T C . -PoolTumor2-T 14 19488825 G A . -PoolTumor2-T 14 19492018 C CGT . -PoolTumor2-T 14 19890157 GGCC G . -PoolTumor2-T 14 20084718 A G . -PoolTumor2-T 14 20084805 G C . -PoolTumor2-T 14 20085200 A G . -PoolTumor2-T 14 20085423 G A . -PoolTumor2-T 14 20085849 G C . -PoolTumor2-T 14 20086143 A T . -PoolTumor2-T 14 20086572 G A . PoolTumor2-T 14 20893115 T A . PoolTumor2-T 14 20969716 C T . PoolTumor2-T 14 21336860 A AT . @@ -567,12 +460,11 @@ PoolTumor2-T 14 33960172 TGCA T . PoolTumor2-T 14 34771783 G T . PoolTumor2-T 14 35871430 T TTTAAAAAAGAGTAAGCTA . PoolTumor2-T 14 35872920 G T . -PoolTumor2-T 14 36417343 G A . -PoolTumor2-T 14 36417741 T C . PoolTumor2-T 14 36983065 A C . PoolTumor2-T 14 36983623 A G . PoolTumor2-T 14 36986190 A AC . PoolTumor2-T 14 36986272 T TTA . +PoolTumor2-T 14 36986304 AAAA GGGGGG . PoolTumor2-T 14 36988175 G A . PoolTumor2-T 14 36989638 A C . PoolTumor2-T 14 36989645 TCCCC T . @@ -582,7 +474,6 @@ PoolTumor2-T 14 38061106 T A . PoolTumor2-T 14 38882673 T A . PoolTumor2-T 14 38910644 G C . PoolTumor2-T 14 38910766 TAG T . -PoolTumor2-T 14 49557672 C A . PoolTumor2-T 14 52640760 ACTA T . PoolTumor2-T 14 57141401 G A . PoolTumor2-T 14 61799782 G T . @@ -609,7 +500,6 @@ PoolTumor2-T 14 87813214 G A . PoolTumor2-T 14 87813312 A C . PoolTumor2-T 14 88360375 C T . PoolTumor2-T 14 88360384 T A . -PoolTumor2-T 14 92134141 T C . PoolTumor2-T 14 95556644 A C . PoolTumor2-T 14 95560444 G A . PoolTumor2-T 14 95562999 C A . @@ -629,15 +519,8 @@ PoolTumor2-T 14 105241607 G A . PoolTumor2-T 14 105242374 G A . PoolTumor2-T 14 105242826 C T . PoolTumor2-T 15 20489987 A G . -PoolTumor2-T 15 20490611 T C . -PoolTumor2-T 15 21134146 G T . -PoolTumor2-T 15 21137279 G T . -PoolTumor2-T 15 22140237 G A . -PoolTumor2-T 15 22146341 T G . -PoolTumor2-T 15 22147856 AT A . -PoolTumor2-T 15 22148122 G T . +PoolTumor2-T 15 20495202 A AG . PoolTumor2-T 15 33027179 T A . -PoolTumor2-T 15 35384455 TAA T . PoolTumor2-T 15 35385071 C T . PoolTumor2-T 15 35385596 T C . PoolTumor2-T 15 38457041 G A . @@ -692,16 +575,10 @@ PoolTumor2-T 16 396234 G A . PoolTumor2-T 16 1987179 C T . PoolTumor2-T 16 2105055 A G . PoolTumor2-T 16 2110795 G A . -PoolTumor2-T 16 2127944 G T . PoolTumor2-T 16 2132583 G A . PoolTumor2-T 16 2134852 G A . PoolTumor2-T 16 2136455 C T . -PoolTumor2-T 16 2215618 GCA CTG . -PoolTumor2-T 16 2215645 G T . -PoolTumor2-T 16 2215648 T C . PoolTumor2-T 16 2215659 CT GC . -PoolTumor2-T 16 2215686 T G . -PoolTumor2-T 16 2215689 C T . PoolTumor2-T 16 2226763 C G . PoolTumor2-T 16 3777496 C A . PoolTumor2-T 16 3786594 C G . @@ -709,40 +586,25 @@ PoolTumor2-T 16 3794705 T G . PoolTumor2-T 16 3807171 G A . PoolTumor2-T 16 3807946 C T . PoolTumor2-T 16 3860554 C T . -PoolTumor2-T 16 3929235 GCACACACACA G . PoolTumor2-T 16 8382667 T A . PoolTumor2-T 16 9944017 G A . PoolTumor2-T 16 10273656 C T . PoolTumor2-T 16 10273821 C T . PoolTumor2-T 16 11345660 AAAG A . -PoolTumor2-T 16 11346956 AAAAG A . PoolTumor2-T 16 11349302 C T . PoolTumor2-T 16 11352930 G A . PoolTumor2-T 16 14028861 C T . PoolTumor2-T 16 14041760 C A . PoolTumor2-T 16 14042077 A G . -PoolTumor2-T 16 16100728 C CGGTGGCGGTGGCGGTGGCGGTGGT . PoolTumor2-T 16 17380507 T TATCATCATCATCCTC . +PoolTumor2-T 16 24788422 AGCAGCCACAGCC A . PoolTumor2-T 16 27356584 T G . PoolTumor2-T 16 30129936 C T . -PoolTumor2-T 16 32369286 C T . -PoolTumor2-T 16 32369738 CC AA . -PoolTumor2-T 16 32374889 C T . -PoolTumor2-T 16 33365663 A G . PoolTumor2-T 16 33371341 CG C . PoolTumor2-T 16 33373312 G T . PoolTumor2-T 16 33948696 G C . PoolTumor2-T 16 33948711 T C . -PoolTumor2-T 16 33948789 CA TG . -PoolTumor2-T 16 33957556 T A . -PoolTumor2-T 16 33957584 C A . -PoolTumor2-T 16 33957977 ACT A . -PoolTumor2-T 16 46395394 A T . -PoolTumor2-T 16 46403662 C G . -PoolTumor2-T 16 46403773 G C . PoolTumor2-T 16 52085593 A G . -PoolTumor2-T 16 55329374 C CCTCTCTGTCTCTCTGT . -PoolTumor2-T 16 55329381 G GTCTCTCTGTCTCTCTGTC . PoolTumor2-T 16 56863229 T C . PoolTumor2-T 16 56866054 A AT . PoolTumor2-T 16 56866196 T C . @@ -755,6 +617,7 @@ PoolTumor2-T 16 58032026 G A . PoolTumor2-T 16 58960831 G A . PoolTumor2-T 16 59584343 G A . PoolTumor2-T 16 59584360 C T . +PoolTumor2-T 16 67450281 T TGGCTCC . PoolTumor2-T 16 67645883 TGCAGTTACA T . PoolTumor2-T 16 68862182 A G . PoolTumor2-T 16 68867456 C T . @@ -763,6 +626,7 @@ PoolTumor2-T 16 72828383 C T . PoolTumor2-T 16 72830539 C G . PoolTumor2-T 16 72832377 G A . PoolTumor2-T 16 72924122 T C . +PoolTumor2-T 16 72991696 TGCC T . PoolTumor2-T 16 72991715 A G . PoolTumor2-T 16 72993622 C T . PoolTumor2-T 16 72993706 G A . @@ -795,15 +659,14 @@ PoolTumor2-T 16 85490399 T C . PoolTumor2-T 16 86601049 C T . PoolTumor2-T 16 89337526 G A . PoolTumor2-T 16 89350597 C G . -PoolTumor2-T 16 89356882 CGGGGGAGGCTCAGGGCTCCAATG C . +PoolTumor2-T 16 89356864 T G . +PoolTumor2-T 16 89809061 CA C . PoolTumor2-T 16 89839915 G A . PoolTumor2-T 16 89877720 C T . -PoolTumor2-T 17 1760942 C G . PoolTumor2-T 17 3568401 G A . PoolTumor2-T 17 4540268 G C . PoolTumor2-T 17 7577407 A C . PoolTumor2-T 17 7577427 G A . -PoolTumor2-T 17 7577709 C T . PoolTumor2-T 17 7578461 C A . PoolTumor2-T 17 7580500 C T . PoolTumor2-T 17 7976917 A T . @@ -811,23 +674,15 @@ PoolTumor2-T 17 7979468 C T . PoolTumor2-T 17 7983681 G A . PoolTumor2-T 17 7984157 A C . PoolTumor2-T 17 7984552 G A . -PoolTumor2-T 17 7990555 G C . PoolTumor2-T 17 12043531 A AG . PoolTumor2-T 17 15977132 T C . PoolTumor2-T 17 15983458 G A . +PoolTumor2-T 17 16041777 C T . +PoolTumor2-T 17 16041792 A G . PoolTumor2-T 17 16049563 C A . PoolTumor2-T 17 16049641 TA T . -PoolTumor2-T 17 16068215 A G . -PoolTumor2-T 17 16068420 G T . -PoolTumor2-T 17 16097430 C T . PoolTumor2-T 17 17125595 A G . -PoolTumor2-T 17 21535940 G A . -PoolTumor2-T 17 21535981 A G . PoolTumor2-T 17 21544599 A G . -PoolTumor2-T 17 22253299 T TATTTGGACCTCTCTGAGGATTTCGTTGGAAACGGGATA . -PoolTumor2-T 17 22259989 T A . -PoolTumor2-T 17 22261386 A T . -PoolTumor2-T 17 29096004 C G . PoolTumor2-T 17 29482701 C T . PoolTumor2-T 17 29533685 CTTTTGAACAAAAATA C . PoolTumor2-T 17 29553719 GT G . @@ -844,7 +699,6 @@ PoolTumor2-T 17 37657481 AT A . PoolTumor2-T 17 37687968 A G . PoolTumor2-T 17 37866797 G T . PoolTumor2-T 17 37871848 G A . -PoolTumor2-T 17 37880725 T C . PoolTumor2-T 17 37880997 G GTGT . PoolTumor2-T 17 38497450 G A . PoolTumor2-T 17 38497833 G A . @@ -853,7 +707,6 @@ PoolTumor2-T 17 38512197 T C . PoolTumor2-T 17 38512457 C G . PoolTumor2-T 17 38512461 G T . PoolTumor2-T 17 39874283 T A . -PoolTumor2-T 17 40452429 C A . PoolTumor2-T 17 40458193 TTG T . PoolTumor2-T 17 40458742 CT C . PoolTumor2-T 17 40467934 C T . @@ -887,8 +740,9 @@ PoolTumor2-T 17 72843378 C T . PoolTumor2-T 17 72843411 GC G . PoolTumor2-T 17 72904115 G A . PoolTumor2-T 17 77280452 A G . -PoolTumor2-T 17 77386058 GGGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA G . -PoolTumor2-T 17 77386084 CAGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT C . +PoolTumor2-T 17 77386106 T G . +PoolTumor2-T 17 77386109 A G . +PoolTumor2-T 17 77386118 T C . PoolTumor2-T 17 78765080 A C . PoolTumor2-T 17 78796361 T A . PoolTumor2-T 17 78796907 C G . @@ -900,20 +754,11 @@ PoolTumor2-T 17 78919466 G T . PoolTumor2-T 17 78922952 C G . PoolTumor2-T 17 78923126 T G . PoolTumor2-T 17 78934088 G A . -PoolTumor2-T 17 80759544 G A . -PoolTumor2-T 18 112258 G A . -PoolTumor2-T 18 756282 T TG . +PoolTumor2-T 17 79996915 T C . PoolTumor2-T 18 4131501 C G . PoolTumor2-T 18 8413657 G A . PoolTumor2-T 18 12912750 C T . PoolTumor2-T 18 12912821 G C . -PoolTumor2-T 18 18511155 T C . -PoolTumor2-T 18 18517177 G A . -PoolTumor2-T 18 18519858 C G . -PoolTumor2-T 18 18519863 A T . -PoolTumor2-T 18 18519891 T G . -PoolTumor2-T 18 18520246 A G . -PoolTumor2-T 18 18520315 T G . PoolTumor2-T 18 23784839 A G . PoolTumor2-T 18 28787355 T A . PoolTumor2-T 18 28787634 G T . @@ -923,10 +768,12 @@ PoolTumor2-T 18 39537688 G C . PoolTumor2-T 18 39593388 CT C . PoolTumor2-T 18 46996404 A G . PoolTumor2-T 18 48190817 G A . +PoolTumor2-T 18 48584855 A TTT . PoolTumor2-T 18 55466751 G GTA . PoolTumor2-T 18 56378529 C T . PoolTumor2-T 18 56412894 A T . PoolTumor2-T 18 60910366 G A . +PoolTumor2-T 18 66534393 CCCC ACCCT . PoolTumor2-T 18 69372730 A G . PoolTumor2-T 19 1221161 C T . PoolTumor2-T 19 1221991 G A . @@ -935,7 +782,6 @@ PoolTumor2-T 19 1622115 C T . PoolTumor2-T 19 2194896 T C . PoolTumor2-T 19 2207386 G C . PoolTumor2-T 19 2211220 G T . -PoolTumor2-T 19 2213298 G T . PoolTumor2-T 19 2214242 G A . PoolTumor2-T 19 2217203 G A . PoolTumor2-T 19 3110361 C T . @@ -954,10 +800,12 @@ PoolTumor2-T 19 5208257 A T . PoolTumor2-T 19 5208514 TG T . PoolTumor2-T 19 5212482 G A . PoolTumor2-T 19 5212586 G T . +PoolTumor2-T 19 5212680 C T . PoolTumor2-T 19 5214116 A G . PoolTumor2-T 19 5214904 C T . PoolTumor2-T 19 5214986 G A . PoolTumor2-T 19 5215474 G A . +PoolTumor2-T 19 5218213 T TA . PoolTumor2-T 19 5218684 G A . PoolTumor2-T 19 5220134 C T . PoolTumor2-T 19 5222088 C G . @@ -977,6 +825,7 @@ PoolTumor2-T 19 7172526 C A . PoolTumor2-T 19 7184238 G A . PoolTumor2-T 19 7184243 C G . PoolTumor2-T 19 7184490 G A . +PoolTumor2-T 19 7184651 GGA G . PoolTumor2-T 19 7805951 A T . PoolTumor2-T 19 7815587 G C . PoolTumor2-T 19 7815690 G T . @@ -986,7 +835,6 @@ PoolTumor2-T 19 10287635 A T . PoolTumor2-T 19 10292608 C A . PoolTumor2-T 19 10292901 C T . PoolTumor2-T 19 10305434 C T . -PoolTumor2-T 19 10597746 T A . PoolTumor2-T 19 10600615 C CT . PoolTumor2-T 19 10600654 G A . PoolTumor2-T 19 10610017 G C . @@ -1004,7 +852,6 @@ PoolTumor2-T 19 15271135 T G . PoolTumor2-T 19 15273576 GTGTGTGTT G . PoolTumor2-T 19 15288062 G GGA . PoolTumor2-T 19 15288072 A T . -PoolTumor2-T 19 15289366 T G . PoolTumor2-T 19 15290491 G A . PoolTumor2-T 19 15290648 C T . PoolTumor2-T 19 15291576 C G . @@ -1015,6 +862,7 @@ PoolTumor2-T 19 15299048 G A . PoolTumor2-T 19 15308287 G C . PoolTumor2-T 19 15308545 G A . PoolTumor2-T 19 15311604 GC G . +PoolTumor2-T 19 15366010 A AG . PoolTumor2-T 19 15366663 G A . PoolTumor2-T 19 15890625 CG GA . PoolTumor2-T 19 15890725 G T . @@ -1026,14 +874,10 @@ PoolTumor2-T 19 18279861 C T . PoolTumor2-T 19 18280096 G A . PoolTumor2-T 19 19256768 TG T . PoolTumor2-T 19 19260105 T C . -PoolTumor2-T 19 27732195 G T . -PoolTumor2-T 19 27736207 G C . -PoolTumor2-T 19 28778494 A G . PoolTumor2-T 19 30311555 CCCCT TC . PoolTumor2-T 19 30312874 C T . PoolTumor2-T 19 30313622 G T . PoolTumor2-T 19 33792520 G A . -PoolTumor2-T 19 33792731 G GGCGGGT . PoolTumor2-T 19 33792751 C T . PoolTumor2-T 19 33905969 G A . PoolTumor2-T 19 34080443 CC TT . @@ -1064,17 +908,15 @@ PoolTumor2-T 19 50920581 T C . PoolTumor2-T 19 52693297 C CT . PoolTumor2-T 19 52714917 G A . PoolTumor2-T 19 53081735 C T . +PoolTumor2-T 2 6636119 T A . PoolTumor2-T 2 6636414 G A . PoolTumor2-T 2 6636735 G A . +PoolTumor2-T 2 7541706 TA T . PoolTumor2-T 2 7541718 C G . PoolTumor2-T 2 14528089 C T . PoolTumor2-T 2 16085519 C T . PoolTumor2-T 2 16086469 C T . PoolTumor2-T 2 17675655 TTTTCA T . -PoolTumor2-T 2 21324997 C A . -PoolTumor2-T 2 21325009 G A . -PoolTumor2-T 2 21325028 A T . -PoolTumor2-T 2 21325039 T C . PoolTumor2-T 2 25466810 C T . PoolTumor2-T 2 25469945 C T . PoolTumor2-T 2 25471169 GC G . @@ -1088,7 +930,6 @@ PoolTumor2-T 2 29445798 T C . PoolTumor2-T 2 29449423 G A . PoolTumor2-T 2 29451354 A G . PoolTumor2-T 2 29451557 GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G . -PoolTumor2-T 2 29451670 AGGGGA G . PoolTumor2-T 2 29451675 A AGGGCG . PoolTumor2-T 2 29451986 C T . PoolTumor2-T 2 29454901 G GCAAGTTGGTAAAACC . @@ -1102,6 +943,7 @@ PoolTumor2-T 2 30433204 T G . PoolTumor2-T 2 43081218 CGT C . PoolTumor2-T 2 43952068 G A . PoolTumor2-T 2 44311676 C A . +PoolTumor2-T 2 44561591 C CA . PoolTumor2-T 2 46128526 C A . PoolTumor2-T 2 47602178 A T . PoolTumor2-T 2 47613870 T C . @@ -1121,6 +963,7 @@ PoolTumor2-T 2 48028465 C T . PoolTumor2-T 2 48030629 G T . PoolTumor2-T 2 48032572 C T . PoolTumor2-T 2 48033272 ATTTTTGTTTTAATTCCT A . +PoolTumor2-T 2 48033546 C CT . PoolTumor2-T 2 48033549 CTC TCTG . PoolTumor2-T 2 48033846 CAGTAAA C . PoolTumor2-T 2 51288710 A C . @@ -1143,23 +986,8 @@ PoolTumor2-T 2 81425558 C T . PoolTumor2-T 2 81425585 C T . PoolTumor2-T 2 81426909 C T . PoolTumor2-T 2 81427308 G A . -PoolTumor2-T 2 91884263 C G . -PoolTumor2-T 2 91886661 A AT . -PoolTumor2-T 2 91886670 T A . -PoolTumor2-T 2 91888488 T C . -PoolTumor2-T 2 91894045 T C . -PoolTumor2-T 2 91894266 A G . -PoolTumor2-T 2 91894464 A G . -PoolTumor2-T 2 91899415 A G . -PoolTumor2-T 2 91899419 A C . -PoolTumor2-T 2 91899421 A G . -PoolTumor2-T 2 91902433 G A . -PoolTumor2-T 2 91902876 CAT C . -PoolTumor2-T 2 92145660 T A . -PoolTumor2-T 2 92151474 T C . -PoolTumor2-T 2 92315446 A C . -PoolTumor2-T 2 92319253 T A . -PoolTumor2-T 2 92319260 G A . +PoolTumor2-T 2 91884897 T A . +PoolTumor2-T 2 91884911 A T . PoolTumor2-T 2 95849653 T C . PoolTumor2-T 2 99160361 G C . PoolTumor2-T 2 99168953 T C . @@ -1175,18 +1003,13 @@ PoolTumor2-T 2 113688949 C T . PoolTumor2-T 2 113978894 G A . PoolTumor2-T 2 113979364 G A . PoolTumor2-T 2 113981691 T A . -PoolTumor2-T 2 113993631 G A . PoolTumor2-T 2 121735983 C T . PoolTumor2-T 2 125301742 C T . PoolTumor2-T 2 128014913 C T . PoolTumor2-T 2 128036701 G T . PoolTumor2-T 2 128038005 C A . -PoolTumor2-T 2 128044048 G T . -PoolTumor2-T 2 131947825 T C . -PoolTumor2-T 2 131947893 C G . -PoolTumor2-T 2 131949242 C A . +PoolTumor2-T 2 131947526 AT A . PoolTumor2-T 2 131950767 A G . -PoolTumor2-T 2 131955336 G A . PoolTumor2-T 2 133919631 G A . PoolTumor2-T 2 139308127 G A . PoolTumor2-T 2 158617379 A G . @@ -1197,10 +1020,10 @@ PoolTumor2-T 2 158636341 A G . PoolTumor2-T 2 158637137 A G . PoolTumor2-T 2 158637445 A C . PoolTumor2-T 2 158655838 G C . +PoolTumor2-T 2 178883104 A ACTTGACTTTAACTTGGCACG . PoolTumor2-T 2 180265135 C T . PoolTumor2-T 2 180265174 G A . PoolTumor2-T 2 183484981 T C . -PoolTumor2-T 2 184373044 C T . PoolTumor2-T 2 187558960 G A . PoolTumor2-T 2 189541807 C G . PoolTumor2-T 2 190708712 G A . @@ -1214,7 +1037,8 @@ PoolTumor2-T 2 204637705 TTCATCATCATCA T . PoolTumor2-T 2 209102117 A ACT . PoolTumor2-T 2 209103969 G GA . PoolTumor2-T 2 212251910 G A . -PoolTumor2-T 2 212292969 T AAATAAAATA . +PoolTumor2-T 2 212292936 T TTAAAATAAAA . +PoolTumor2-T 2 212292968 AT A . PoolTumor2-T 2 212295468 GTA G . PoolTumor2-T 2 212295492 GATATAT ATATATC . PoolTumor2-T 2 212426588 C T . @@ -1226,7 +1050,6 @@ PoolTumor2-T 2 212589774 A G . PoolTumor2-T 2 212698775 T A . PoolTumor2-T 2 212812057 G A . PoolTumor2-T 2 213402964 A AC . -PoolTumor2-T 2 220439102 G T . PoolTumor2-T 2 225069340 C A . PoolTumor2-T 2 226701540 A C . PoolTumor2-T 2 237242244 T C . @@ -1237,7 +1060,7 @@ PoolTumor2-T 20 11361032 G A . PoolTumor2-T 20 16142333 A C . PoolTumor2-T 20 22563356 G T . PoolTumor2-T 20 25733062 T G . -PoolTumor2-T 20 26094706 G GA . +PoolTumor2-T 20 26084383 GT G . PoolTumor2-T 20 30296422 C T . PoolTumor2-T 20 30296428 T C . PoolTumor2-T 20 30296664 G C . @@ -1252,7 +1075,6 @@ PoolTumor2-T 20 39743905 G A . PoolTumor2-T 20 39751809 C T . PoolTumor2-T 20 40709305 G A . PoolTumor2-T 20 40710486 C T . -PoolTumor2-T 20 40714097 G C . PoolTumor2-T 20 40714218 G A . PoolTumor2-T 20 40714305 T C . PoolTumor2-T 20 40714307 G A . @@ -1273,8 +1095,9 @@ PoolTumor2-T 20 46256424 C T . PoolTumor2-T 20 46271008 G A . PoolTumor2-T 20 46275917 A C . PoolTumor2-T 20 46277834 A T . -PoolTumor2-T 20 48450866 C CTG . -PoolTumor2-T 20 48450987 C TACTG . +PoolTumor2-T 20 48450891 ATATATATATACTGTG A . +PoolTumor2-T 20 48450944 ATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG A . +PoolTumor2-T 20 48450987 C CTG . PoolTumor2-T 20 52777119 G A . PoolTumor2-T 20 54945145 C T . PoolTumor2-T 20 55178239 C G . @@ -1283,42 +1106,14 @@ PoolTumor2-T 20 59632034 C T . PoolTumor2-T 20 59928237 T C . PoolTumor2-T 20 61041333 C T . PoolTumor2-T 20 62173029 A G . -PoolTumor2-T 21 11013029 TAA T . -PoolTumor2-T 21 11013622 A AT . -PoolTumor2-T 21 11020831 T C . -PoolTumor2-T 21 11020869 G A . -PoolTumor2-T 21 11021018 TAA T . PoolTumor2-T 21 11021107 A T . PoolTumor2-T 21 11021189 G A . -PoolTumor2-T 21 11021330 CA TG . -PoolTumor2-T 21 11021519 T G . -PoolTumor2-T 21 11026527 C CAAAGAGGAAGGTAAGA . -PoolTumor2-T 21 11026550 A G . -PoolTumor2-T 21 11026647 C A . -PoolTumor2-T 21 11026766 C T . -PoolTumor2-T 21 11026786 C T . -PoolTumor2-T 21 11026875 A T . -PoolTumor2-T 21 11026964 A G . -PoolTumor2-T 21 11026966 G A . -PoolTumor2-T 21 11027038 C A . -PoolTumor2-T 21 11027052 T C . PoolTumor2-T 21 11029526 A G . -PoolTumor2-T 21 11029536 T C . -PoolTumor2-T 21 11029675 A C . -PoolTumor2-T 21 11029842 G T . -PoolTumor2-T 21 11038551 G A . -PoolTumor2-T 21 11038994 C T . -PoolTumor2-T 21 11039600 C T . -PoolTumor2-T 21 11040864 C T . PoolTumor2-T 21 11047650 C T . PoolTumor2-T 21 11047979 CA TG . -PoolTumor2-T 21 11049651 T C . -PoolTumor2-T 21 11049870 A G . +PoolTumor2-T 21 11049346 C T . PoolTumor2-T 21 11057701 C A . PoolTumor2-T 21 11057983 G A . -PoolTumor2-T 21 11058081 C A . -PoolTumor2-T 21 11058248 G A . -PoolTumor2-T 21 15377688 T C . PoolTumor2-T 21 21056234 C T . PoolTumor2-T 21 27340191 C T . PoolTumor2-T 21 28978250 G A . @@ -1341,20 +1136,17 @@ PoolTumor2-T 21 42850911 C T . PoolTumor2-T 21 42860532 G A . PoolTumor2-T 21 42866296 TG CA . PoolTumor2-T 21 42867003 A T . -PoolTumor2-T 21 42868997 A C . PoolTumor2-T 21 42872398 C T . PoolTumor2-T 21 42878126 A C . PoolTumor2-T 21 42878780 T G . PoolTumor2-T 21 43124132 T C . PoolTumor2-T 21 43124280 CAT TGC . PoolTumor2-T 21 44524290 A C . +PoolTumor2-T 21 45649498 C T . PoolTumor2-T 21 45649748 C T . PoolTumor2-T 21 45651275 G A . -PoolTumor2-T 22 16349345 C A . -PoolTumor2-T 22 16350086 C T . -PoolTumor2-T 22 16352062 G T . -PoolTumor2-T 22 17055619 G A . PoolTumor2-T 22 17519579 A G . +PoolTumor2-T 22 20918896 TGCA T . PoolTumor2-T 22 21135741 G A . PoolTumor2-T 22 21272198 G A . PoolTumor2-T 22 21272752 C T . @@ -1366,8 +1158,6 @@ PoolTumor2-T 22 24159437 G T . PoolTumor2-T 22 24176232 C T . PoolTumor2-T 22 24176677 GCAACAGGTCATGTTCAATTTCTT G . PoolTumor2-T 22 24176959 CA C . -PoolTumor2-T 22 24656818 A T . -PoolTumor2-T 22 24656822 G C . PoolTumor2-T 22 26388019 G T . PoolTumor2-T 22 29090363 G A . PoolTumor2-T 22 29093239 A G . @@ -1384,10 +1174,8 @@ PoolTumor2-T 22 41562785 A G . PoolTumor2-T 22 41568804 TAGAG T . PoolTumor2-T 22 41574383 A C . PoolTumor2-T 22 47217677 C T . -PoolTumor2-T 3 2576521 T C . PoolTumor2-T 3 10191219 C G . PoolTumor2-T 3 14387169 A AG . -PoolTumor2-T 3 17822644 A G . PoolTumor2-T 3 25482579 C T . PoolTumor2-T 3 25502851 G A . PoolTumor2-T 3 25569630 G T . @@ -1398,6 +1186,8 @@ PoolTumor2-T 3 32670533 G C . PoolTumor2-T 3 37034946 G A . PoolTumor2-T 3 37050254 T C . PoolTumor2-T 3 37061720 G C . +PoolTumor2-T 3 37067097 A T . +PoolTumor2-T 3 37067099 A T . PoolTumor2-T 3 37092173 GTTC G . PoolTumor2-T 3 41266226 A G . PoolTumor2-T 3 41275350 C T . @@ -1405,14 +1195,7 @@ PoolTumor2-T 3 41443220 C A . PoolTumor2-T 3 47061453 C T . PoolTumor2-T 3 47098278 A G . PoolTumor2-T 3 48515221 G A . -PoolTumor2-T 3 49724236 C A . -PoolTumor2-T 3 49724260 C G . PoolTumor2-T 3 49725284 CT C . -PoolTumor2-T 3 49725685 G A . -PoolTumor2-T 3 49725728 C T . -PoolTumor2-T 3 49725734 A G . -PoolTumor2-T 3 49725737 G A . -PoolTumor2-T 3 49725743 T C . PoolTumor2-T 3 49934678 C T . PoolTumor2-T 3 52436441 C A . PoolTumor2-T 3 52584477 C T . @@ -1425,12 +1208,10 @@ PoolTumor2-T 3 52695835 T C . PoolTumor2-T 3 55487222 A T . PoolTumor2-T 3 55487515 C T . PoolTumor2-T 3 69986144 A G . -PoolTumor2-T 3 70005281 A G . PoolTumor2-T 3 70005712 T C . PoolTumor2-T 3 70014447 T C . PoolTumor2-T 3 70348641 A C . PoolTumor2-T 3 71019797 A T . -PoolTumor2-T 3 71049945 A AAAAATAAAAT . PoolTumor2-T 3 71096086 C T . PoolTumor2-T 3 71103136 T C . PoolTumor2-T 3 71246918 C T . @@ -1460,7 +1241,6 @@ PoolTumor2-T 3 134851577 A T . PoolTumor2-T 3 134884695 G C . PoolTumor2-T 3 134885042 A C . PoolTumor2-T 3 134911143 A AAAAACAAACTCACATATATTCTGAAATTCCACTT . -PoolTumor2-T 3 134960472 T C . PoolTumor2-T 3 134967265 G A . PoolTumor2-T 3 135644964 C T . PoolTumor2-T 3 137443260 G A . @@ -1480,15 +1260,12 @@ PoolTumor2-T 3 142241690 C CA . PoolTumor2-T 3 142266439 C T . PoolTumor2-T 3 142278101 T C . PoolTumor2-T 3 142297576 G A . -PoolTumor2-T 3 145542355 G T . PoolTumor2-T 3 166229248 C T . PoolTumor2-T 3 168576884 T C . PoolTumor2-T 3 178511531 C A . PoolTumor2-T 3 178921158 G A . PoolTumor2-T 3 178927345 T C . PoolTumor2-T 3 178927645 C T . -PoolTumor2-T 3 178936227 T G . -PoolTumor2-T 3 178937877 A G . PoolTumor2-T 3 184298663 G A . PoolTumor2-T 3 185155807 G A . PoolTumor2-T 3 185183491 C T . @@ -1505,42 +1282,12 @@ PoolTumor2-T 3 189586470 C T . PoolTumor2-T 3 189590871 G A . PoolTumor2-T 3 189597951 G A . 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PoolTumor2-T 3 195412960 T C . -PoolTumor2-T 3 195692349 T A . -PoolTumor2-T 3 195692516 C T . -PoolTumor2-T 3 195692570 G A . -PoolTumor2-T 3 195694127 C T . -PoolTumor2-T 3 195694256 G GA . -PoolTumor2-T 3 195697927 A G . -PoolTumor2-T 3 195700978 A C . -PoolTumor2-T 3 195701306 T C . -PoolTumor2-T 3 195702877 A G . -PoolTumor2-T 3 195704217 A T . -PoolTumor2-T 3 195708767 C T . -PoolTumor2-T 3 195710978 C G . -PoolTumor2-T 3 195711785 C T . -PoolTumor2-T 3 195712899 A C . -PoolTumor2-T 3 195713494 C G . -PoolTumor2-T 3 197346530 C G . -PoolTumor2-T 3 197348570 C G . -PoolTumor2-T 3 197349123 C T . +PoolTumor2-T 3 195692069 A G . +PoolTumor2-T 3 195701198 CA C . PoolTumor2-T 4 1795701 G T . PoolTumor2-T 4 1795719 G A . PoolTumor2-T 4 1795762 G A . @@ -1552,22 +1299,10 @@ PoolTumor2-T 4 6927471 T G . PoolTumor2-T 4 8043703 G A . PoolTumor2-T 4 28400060 A G . PoolTumor2-T 4 28400468 C T . -PoolTumor2-T 4 35861432 C T . PoolTumor2-T 4 37822923 G A . PoolTumor2-T 4 41747691 C G . PoolTumor2-T 4 41748217 G A . PoolTumor2-T 4 46726267 C T . -PoolTumor2-T 4 46726491 G T . -PoolTumor2-T 4 49110443 C G . -PoolTumor2-T 4 49111815 TTCCATTCCTTTCAAC G . -PoolTumor2-T 4 49121015 ATTCCATTCCATTCCT A . -PoolTumor2-T 4 49123023 C T . -PoolTumor2-T 4 49149291 T TTCCATTCCATTGCATTCCATTCCCTCGTGTTGATTCCATTCTTTCCATTCCATTCAAGTTGAA . -PoolTumor2-T 4 49155270 G C . -PoolTumor2-T 4 49156547 T C . -PoolTumor2-T 4 49637270 T TGGAATGGAATCATCC . -PoolTumor2-T 4 49644677 A T . -PoolTumor2-T 4 49659659 A ATGTAATGGAATTTAG . PoolTumor2-T 4 54245372 T A . PoolTumor2-T 4 55129831 C T . PoolTumor2-T 4 55161516 CA TG . @@ -1585,7 +1320,6 @@ PoolTumor2-T 4 66218527 A T . PoolTumor2-T 4 66218677 C T . PoolTumor2-T 4 66270345 G A . PoolTumor2-T 4 66286376 G A . -PoolTumor2-T 4 66286633 C T . PoolTumor2-T 4 69761131 T C . PoolTumor2-T 4 78271554 C G . PoolTumor2-T 4 87163541 G T . @@ -1628,19 +1362,17 @@ PoolTumor2-T 4 187557113 C G . PoolTumor2-T 4 187558187 CA C . PoolTumor2-T 4 187584530 G A . PoolTumor2-T 4 187628352 A T . -PoolTumor2-T 4 189192088 G C . PoolTumor2-T 4 190093234 C T . +PoolTumor2-T 5 223890 G C . PoolTumor2-T 5 223909 GATTTAA G . PoolTumor2-T 5 223958 T C . -PoolTumor2-T 5 224196 A T . -PoolTumor2-T 5 224207 C T . -PoolTumor2-T 5 224211 C T . PoolTumor2-T 5 225267 C A . -PoolTumor2-T 5 228071 A C . -PoolTumor2-T 5 231337 A C . +PoolTumor2-T 5 228279 T C . +PoolTumor2-T 5 230778 T C . +PoolTumor2-T 5 233325 G A . +PoolTumor2-T 5 233362 T G . +PoolTumor2-T 5 236932 T A . PoolTumor2-T 5 240664 A C . -PoolTumor2-T 5 420898 C T . -PoolTumor2-T 5 420915 GCCACGCAGCCACCCAC G . PoolTumor2-T 5 1255297 C A . PoolTumor2-T 5 1260195 T C . PoolTumor2-T 5 1264152 A G . @@ -1649,7 +1381,6 @@ PoolTumor2-T 5 1272414 G A . PoolTumor2-T 5 1279964 G C . PoolTumor2-T 5 1280190 G A . PoolTumor2-T 5 1280830 G C . -PoolTumor2-T 5 1284554 TCTGGCGACCTCACCCCGGACCGGCACCATCCGGACTCCATACATCCAGCTCACCGAGGGC T . PoolTumor2-T 5 1293389 C G . PoolTumor2-T 5 1295250 G A . PoolTumor2-T 5 1576000 C G . @@ -1685,7 +1416,6 @@ PoolTumor2-T 5 38958167 A G . PoolTumor2-T 5 38962656 T C . PoolTumor2-T 5 38972335 T C . PoolTumor2-T 5 38990820 G C . -PoolTumor2-T 5 38990930 TATATGAGATATATG T . PoolTumor2-T 5 38997170 G A . PoolTumor2-T 5 39002519 C T . PoolTumor2-T 5 39021493 G A . @@ -1696,7 +1426,6 @@ PoolTumor2-T 5 56168571 G A . PoolTumor2-T 5 56183637 G C . PoolTumor2-T 5 56183743 T G . PoolTumor2-T 5 56184610 C T . -PoolTumor2-T 5 56188977 G A . PoolTumor2-T 5 57752811 CA C . PoolTumor2-T 5 57754489 ACT A . PoolTumor2-T 5 62835420 G A . @@ -1727,7 +1456,6 @@ PoolTumor2-T 5 149434518 C A . PoolTumor2-T 5 149436598 A T . PoolTumor2-T 5 149460627 G A . PoolTumor2-T 5 149495050 T C . -PoolTumor2-T 5 149497672 C T . PoolTumor2-T 5 149498064 C G . PoolTumor2-T 5 149502838 G C . PoolTumor2-T 5 154505054 CAGA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG . @@ -1746,14 +1474,13 @@ PoolTumor2-T 5 176636882 C T . PoolTumor2-T 5 176637149 G A . PoolTumor2-T 5 176637240 G T . PoolTumor2-T 5 176637576 T C . -PoolTumor2-T 5 178012712 A T . -PoolTumor2-T 5 178012715 GC AT . -PoolTumor2-T 5 178012719 T TG . PoolTumor2-T 5 178996554 G A . PoolTumor2-T 5 180056434 G A . PoolTumor2-T 5 180058008 C A . +PoolTumor2-T 5 180058451 T C . PoolTumor2-T 5 180525845 T G . PoolTumor2-T 5 180525899 C G . +PoolTumor2-T 5 180527792 C CGCGGAGCTCCCGCCCGGGCG . PoolTumor2-T 6 6728616 G A . PoolTumor2-T 6 7516674 A ATATATACATATATATATATATATATG . PoolTumor2-T 6 8909371 T C . @@ -1763,9 +1490,7 @@ PoolTumor2-T 6 23515364 G A . PoolTumor2-T 6 25261662 A T . PoolTumor2-T 6 25606672 C T . PoolTumor2-T 6 26031720 C G . -PoolTumor2-T 6 26200050 C G . PoolTumor2-T 6 26322501 G A . -PoolTumor2-T 6 27114488 G C . PoolTumor2-T 6 27840221 C A . PoolTumor2-T 6 29230520 A C . PoolTumor2-T 6 29236588 A G . @@ -1777,11 +1502,7 @@ PoolTumor2-T 6 29760730 AC A . PoolTumor2-T 6 29760765 C A . PoolTumor2-T 6 29760799 T C . PoolTumor2-T 6 29760856 C T . -PoolTumor2-T 6 29768908 T G . -PoolTumor2-T 6 29768948 CAGATGTCCCATCCAT AGGTTTCCCGTCCTA . PoolTumor2-T 6 29769246 G A . -PoolTumor2-T 6 29770158 C G . -PoolTumor2-T 6 29795253 C A . PoolTumor2-T 6 29795566 C T . PoolTumor2-T 6 29795913 A T . PoolTumor2-T 6 29796106 G T . @@ -1790,110 +1511,57 @@ PoolTumor2-T 6 29796265 G T . PoolTumor2-T 6 29796675 G T . PoolTumor2-T 6 29797155 G C . PoolTumor2-T 6 29797211 C T . -PoolTumor2-T 6 29855296 C T . -PoolTumor2-T 6 29855325 C A . -PoolTumor2-T 6 29855328 C G . PoolTumor2-T 6 29855571 GGGGCCCT G . -PoolTumor2-T 6 29855999 G A . PoolTumor2-T 6 29856198 C T . PoolTumor2-T 6 29856655 G C . -PoolTumor2-T 6 29857971 TG AC . -PoolTumor2-T 6 29864379 G A . -PoolTumor2-T 6 29864413 T G . -PoolTumor2-T 6 29864421 C T . PoolTumor2-T 6 29893922 A T . PoolTumor2-T 6 29895837 CC GCA . PoolTumor2-T 6 29896636 C T . PoolTumor2-T 6 29896850 TCC GATCT . PoolTumor2-T 6 29896852 C T . PoolTumor2-T 6 29897036 G T . -PoolTumor2-T 6 29902073 GA AG . -PoolTumor2-T 6 29902078 C CG . -PoolTumor2-T 6 29910444 AAGCAAGGGGCCCTCCT GAGCGGGCTGCCCGCCC . -PoolTumor2-T 6 29910516 G A . -PoolTumor2-T 6 29910519 A C . +PoolTumor2-T 6 29902040 A G . +PoolTumor2-T 6 29910507 CA TG . PoolTumor2-T 6 29910856 G A . -PoolTumor2-T 6 29911857 G T . -PoolTumor2-T 6 29911879 T G . -PoolTumor2-T 6 29911895 T A . -PoolTumor2-T 6 29911912 A G . -PoolTumor2-T 6 29911921 C T . -PoolTumor2-T 6 29912395 T TGG . -PoolTumor2-T 6 29912918 G A . -PoolTumor2-T 6 29912923 C A . -PoolTumor2-T 6 29912927 G T . +PoolTumor2-T 6 29911272 T A . +PoolTumor2-T 6 29911329 G A . +PoolTumor2-T 6 29912149 G C . +PoolTumor2-T 6 29912345 A T . +PoolTumor2-T 6 29912652 CAGA C . PoolTumor2-T 6 29913483 T C . -PoolTumor2-T 6 29913518 C A . -PoolTumor2-T 6 29913526 A G . PoolTumor2-T 6 29917801 G A . -PoolTumor2-T 6 29925209 C T . -PoolTumor2-T 6 29925217 A TC . -PoolTumor2-T 6 29925228 T A . -PoolTumor2-T 6 29925235 A T . PoolTumor2-T 6 29925438 C T . PoolTumor2-T 6 29974083 CG C . PoolTumor2-T 6 29975766 G C . PoolTumor2-T 6 29975775 A C . -PoolTumor2-T 6 29976971 C A . -PoolTumor2-T 6 29976978 CT AA . -PoolTumor2-T 6 29976982 G A . -PoolTumor2-T 6 29977004 G A . -PoolTumor2-T 6 29977047 G T . -PoolTumor2-T 6 29977101 CC TG . -PoolTumor2-T 6 29977402 AAAGGCATCTGAATGTGTCTGTGTCCCTATAGGCATAATGTGAGGTGGTGGG A . -PoolTumor2-T 6 30228918 TA GG . -PoolTumor2-T 6 30228932 G A . -PoolTumor2-T 6 30228974 C T . -PoolTumor2-T 6 30228992 G A . -PoolTumor2-T 6 30458875 AG GA . -PoolTumor2-T 6 30458879 A G . -PoolTumor2-T 6 30458907 C T . -PoolTumor2-T 6 30458915 G T . PoolTumor2-T 6 30459165 C T . PoolTumor2-T 6 30670292 C T . PoolTumor2-T 6 30672326 T C . PoolTumor2-T 6 30954245 T C . PoolTumor2-T 6 31053516 G C . PoolTumor2-T 6 31053521 A G . -PoolTumor2-T 6 31237955 TAAGAGATGTGACCCCCCATT GAAGACACATCACCCCTCATC . -PoolTumor2-T 6 31238027 C A . -PoolTumor2-T 6 31238068 C T . -PoolTumor2-T 6 31238267 C T . +PoolTumor2-T 6 31237802 A G . PoolTumor2-T 6 31238492 C A . PoolTumor2-T 6 31238524 G A . +PoolTumor2-T 6 31238801 C G . PoolTumor2-T 6 31238815 A G . PoolTumor2-T 6 31239171 GC AGT . -PoolTumor2-T 6 31239172 C T . PoolTumor2-T 6 31239279 T C . PoolTumor2-T 6 31239602 G A . -PoolTumor2-T 6 31239607 G A . PoolTumor2-T 6 31239616 CG AT . PoolTumor2-T 6 31239621 TC AA . PoolTumor2-T 6 31239630 C T . PoolTumor2-T 6 31239727 C A . PoolTumor2-T 6 31322204 C CCT . PoolTumor2-T 6 31322205 A CTC . -PoolTumor2-T 6 31322767 G A . -PoolTumor2-T 6 31322920 C T . PoolTumor2-T 6 31323020 T C . -PoolTumor2-T 6 31323025 G GGCCCTGACCCTCCAAGCCTCA . -PoolTumor2-T 6 31323041 AAGGG TAGGGCTCCAGGA . PoolTumor2-T 6 31323414 G A . PoolTumor2-T 6 31324143 GT TA . -PoolTumor2-T 6 31324176 C G . -PoolTumor2-T 6 31324184 C G . -PoolTumor2-T 6 31324200 GCTCTGGAGG CGTCTGCCAA . -PoolTumor2-T 6 31324295 C A . -PoolTumor2-T 6 31324719 C T . PoolTumor2-T 6 31324941 C T . PoolTumor2-T 6 31325159 GC AA . PoolTumor2-T 6 31325164 C T . -PoolTumor2-T 6 31325201 C A . PoolTumor2-T 6 31345484 G A . PoolTumor2-T 6 31349819 C A . -PoolTumor2-T 6 31456099 T G . -PoolTumor2-T 6 31456104 G A . -PoolTumor2-T 6 31456108 G A . PoolTumor2-T 6 32169795 TTCC T . PoolTumor2-T 6 32182243 G GAT . PoolTumor2-T 6 32185246 T G . @@ -1904,7 +1572,7 @@ PoolTumor2-T 6 32190028 A G . PoolTumor2-T 6 32190484 G A . PoolTumor2-T 6 32877176 C T . PoolTumor2-T 6 33290827 A T . -PoolTumor2-T 6 36648084 C CGTGTGTGT . +PoolTumor2-T 6 36648084 C CGTGT . PoolTumor2-T 6 36650547 G A . PoolTumor2-T 6 42701641 G A . PoolTumor2-T 6 43738977 C T . @@ -1912,18 +1580,15 @@ PoolTumor2-T 6 43746352 CT C . PoolTumor2-T 6 43748328 C G . PoolTumor2-T 6 46910123 C T . PoolTumor2-T 6 46910144 G A . +PoolTumor2-T 6 54635613 G C . PoolTumor2-T 6 54873784 A G . PoolTumor2-T 6 54873908 G A . PoolTumor2-T 6 54874135 A G . -PoolTumor2-T 6 58776318 AC GT . PoolTumor2-T 6 58777300 T G . PoolTumor2-T 6 58777419 T C . -PoolTumor2-T 6 58777508 T G . -PoolTumor2-T 6 58777960 T C . PoolTumor2-T 6 58778828 T A . PoolTumor2-T 6 58779032 T G . PoolTumor2-T 6 80564836 C T . -PoolTumor2-T 6 82852407 AAAATAAATAAAT A . PoolTumor2-T 6 89795551 G C . PoolTumor2-T 6 90009220 G A . PoolTumor2-T 6 93968294 A ACTGT . @@ -1979,18 +1644,9 @@ PoolTumor2-T 6 157150230 A G . PoolTumor2-T 6 157511319 G A . PoolTumor2-T 6 157527280 TCTC T . PoolTumor2-T 6 159215375 G T . -PoolTumor2-T 6 160639744 C TAATAATAGAAACAGCAACATAGCAGTAGCAGCAACAACAGCAGCAGCAACAGCAATGTCAGCAACAGGT . -PoolTumor2-T 6 160639753 CAACAATAACAAAAGCAACAGAAACAGT C . -PoolTumor2-T 6 160639965 GTAGCAGT ATAGC . -PoolTumor2-T 6 160639980 G A . -PoolTumor2-T 6 160639986 A ACAGCAGCAGCAGCAGCAGCAGCAATCATTACCATAGTAGCAACAACAGTAGCAGCAACTAACAATGGAAGCATCGGCAACAACAATAGCAAGAGCATCACAGTCAACAACAGCAACAGCAGCAACAATAGCCACAGCAACAGCAACAGCAGCAGTAGCAACAGAAATCACAGTAATAACAGTAG . -PoolTumor2-T 6 160640080 T TAGCAGCCACAGCATCAGTAGCAGCAGCAGCAACAAGAGCAACAATAACAAAAGCAACAATAGCAAC . -PoolTumor2-T 6 160640085 G GCAGCAACAGCAATAGCAACAGTAGCAGCATCAGCAACAATAACAGCAAGTAAAAACAGCAACAGCAGCAGCAACAACAACAGTAGCAGCAGCAGCAACAACAGCAACAATAACAAAAGCAACGATAGCAACAGTATCAGCAA . -PoolTumor2-T 6 160640124 ATAACAGCAACAGAAGCAATAACAGC GCAATAGTATCACAATTAACAACAGCAACAATAGCCACAGCAACAGCAACAGCAGCAGTAGCAACAGCAATAGCAGTAATAGCAGCAGCAGCAGTAGCAGCAATAATTACAACAATAGCAGCAAT . -PoolTumor2-T 6 160640134 CAGAAGCAATAACAGCAGCAGCAACAACAGCAGTACGAACACCAGCAGTAA TAATAACAGCAACAACAACAGCAACAGCAGCAACAACAGCAACAATAACAAAAGCAACGATAGCAACAGTATCAGCAACAG . -PoolTumor2-T 6 160640163 G A . -PoolTumor2-T 6 160640193 G T . -PoolTumor2-T 6 160640212 C T . +PoolTumor2-T 6 160639986 A G . +PoolTumor2-T 6 160640146 C G . +PoolTumor2-T 6 160640164 CAGTACGAACACCAGCAGT C . PoolTumor2-T 6 161771035 CGTGT C . PoolTumor2-T 6 161771037 T C . PoolTumor2-T 6 161771039 T C . @@ -2005,12 +1661,13 @@ PoolTumor2-T 7 60033 C T . PoolTumor2-T 7 60055 G T . PoolTumor2-T 7 2166580 C T . PoolTumor2-T 7 2951934 C T . +PoolTumor2-T 7 2952796 G A . +PoolTumor2-T 7 2952799 GAAA AGGGGAG . PoolTumor2-T 7 2952802 A AGAGGGAAGAGAAGAGGGGAG . PoolTumor2-T 7 2952915 G A . PoolTumor2-T 7 2961909 A C . PoolTumor2-T 7 2962036 C T . PoolTumor2-T 7 2962201 A C . -PoolTumor2-T 7 2963521 G T . PoolTumor2-T 7 2963744 T C . PoolTumor2-T 7 2968289 T C . PoolTumor2-T 7 2968548 G A . @@ -2031,8 +1688,6 @@ PoolTumor2-T 7 6431523 C CT . PoolTumor2-T 7 6438388 C T . PoolTumor2-T 7 6441229 T TC . PoolTumor2-T 7 6441993 C G . -PoolTumor2-T 7 6442156 C A . -PoolTumor2-T 7 6776825 AGA G . PoolTumor2-T 7 11297507 T G . PoolTumor2-T 7 12462931 G GCC . PoolTumor2-T 7 13935307 C T . @@ -2041,56 +1696,37 @@ PoolTumor2-T 7 14025528 C A . PoolTumor2-T 7 14026421 C T . PoolTumor2-T 7 14028575 C T . PoolTumor2-T 7 32159902 G A . +PoolTumor2-T 7 34959604 C T . PoolTumor2-T 7 36858427 G T . PoolTumor2-T 7 36859286 A G . PoolTumor2-T 7 39836727 G T . PoolTumor2-T 7 41729758 CA AG . PoolTumor2-T 7 41730289 G C . PoolTumor2-T 7 41739141 G C . -PoolTumor2-T 7 43288295 TTCCTCC T . +PoolTumor2-T 7 41740079 G T . PoolTumor2-T 7 43299616 T C . PoolTumor2-T 7 45551574 A T . -PoolTumor2-T 7 45856989 T TAGG . -PoolTumor2-T 7 45857101 C T . -PoolTumor2-T 7 45857415 G A . -PoolTumor2-T 7 45858363 G C . +PoolTumor2-T 7 47092258 G GC . PoolTumor2-T 7 47092291 G T . PoolTumor2-T 7 47802771 C T . PoolTumor2-T 7 50444040 G A . PoolTumor2-T 7 50455179 C A . PoolTumor2-T 7 50739151 G A . -PoolTumor2-T 7 51451784 C T . PoolTumor2-T 7 53854866 G A . PoolTumor2-T 7 55210733 G C . PoolTumor2-T 7 55219290 T C . PoolTumor2-T 7 55219307 C G . PoolTumor2-T 7 55222593 A C . PoolTumor2-T 7 55228160 T G . -PoolTumor2-T 7 55805756 G C . PoolTumor2-T 7 55807008 G A . PoolTumor2-T 7 56430693 C A . PoolTumor2-T 7 56430843 C T . -PoolTumor2-T 7 56431383 C T . -PoolTumor2-T 7 56431756 G A . -PoolTumor2-T 7 56439453 T C . -PoolTumor2-T 7 56873374 C T . -PoolTumor2-T 7 56873424 G A . -PoolTumor2-T 7 56874006 C G . -PoolTumor2-T 7 56874457 C T . +PoolTumor2-T 7 56432708 T C . +PoolTumor2-T 7 56432714 C A . PoolTumor2-T 7 61968966 A C . -PoolTumor2-T 7 61968975 G A . -PoolTumor2-T 7 61969240 A C . -PoolTumor2-T 7 61969422 T C . -PoolTumor2-T 7 61969454 T C . -PoolTumor2-T 7 61970454 G C . PoolTumor2-T 7 63230653 G A . PoolTumor2-T 7 65970787 T A . -PoolTumor2-T 7 66761667 A T . PoolTumor2-T 7 70859670 C T . -PoolTumor2-T 7 74306708 G GA . -PoolTumor2-T 7 74312339 CG TA . -PoolTumor2-T 7 74712316 C T . -PoolTumor2-T 7 76641232 G A . PoolTumor2-T 7 81061460 T C . PoolTumor2-T 7 81076550 A G . PoolTumor2-T 7 81076607 C T . @@ -2101,7 +1737,6 @@ PoolTumor2-T 7 81346925 G A . PoolTumor2-T 7 81388001 C A . PoolTumor2-T 7 91180083 T C . PoolTumor2-T 7 92404285 A G . -PoolTumor2-T 7 101977547 A G . PoolTumor2-T 7 103275947 A C . PoolTumor2-T 7 106522693 G A . PoolTumor2-T 7 106524644 CTG C . @@ -2116,8 +1751,6 @@ PoolTumor2-T 7 116403127 A G . PoolTumor2-T 7 116411923 C T . PoolTumor2-T 7 116423161 G A . PoolTumor2-T 7 127153538 C T . -PoolTumor2-T 7 128296052 T G . -PoolTumor2-T 7 128298370 C G . PoolTumor2-T 7 128766971 G A . PoolTumor2-T 7 128767250 G A . PoolTumor2-T 7 128829066 A G . @@ -2129,7 +1762,6 @@ PoolTumor2-T 7 128850798 G T . PoolTumor2-T 7 128851674 C G . PoolTumor2-T 7 128852381 C T . PoolTumor2-T 7 135335822 C T . -PoolTumor2-T 7 140434607 G A . PoolTumor2-T 7 140439319 TG T . PoolTumor2-T 7 140453136 A T . PoolTumor2-T 7 140482427 T C . @@ -2144,6 +1776,7 @@ PoolTumor2-T 7 140494413 A C . PoolTumor2-T 7 140496563 T C . PoolTumor2-T 7 140496901 TC T . PoolTumor2-T 7 140497586 A T . +PoolTumor2-T 7 140498072 C T . PoolTumor2-T 7 140507901 C T . PoolTumor2-T 7 148505788 T C . PoolTumor2-T 7 148505864 G A . @@ -2154,19 +1787,9 @@ PoolTumor2-T 7 151859061 T TAGAAATG . PoolTumor2-T 7 151874581 G C . PoolTumor2-T 7 151875047 G A . PoolTumor2-T 7 151891255 G A . -PoolTumor2-T 7 151932694 C CAAAGAGGAAGGTAAGA . -PoolTumor2-T 7 151932748 A G . -PoolTumor2-T 7 151935768 G T . -PoolTumor2-T 7 151944908 C A . -PoolTumor2-T 7 151945252 C T . -PoolTumor2-T 7 151945313 A G . PoolTumor2-T 7 151946985 C G . PoolTumor2-T 7 151948998 TA T . PoolTumor2-T 7 151949735 T C . -PoolTumor2-T 7 151962294 G A . -PoolTumor2-T 7 151962296 T C . -PoolTumor2-T 7 151971015 G A . -PoolTumor2-T 7 151971078 TAAAC T . PoolTumor2-T 7 152357777 A AT . PoolTumor2-T 7 153622478 CG AA . PoolTumor2-T 7 153622749 G T . @@ -2185,6 +1808,7 @@ PoolTumor2-T 8 4166516 A T . PoolTumor2-T 8 11096119 A G . PoolTumor2-T 8 11587234 G T . PoolTumor2-T 8 14166825 G A . +PoolTumor2-T 8 14167258 T G . PoolTumor2-T 8 18917162 A C . PoolTumor2-T 8 22438859 C G . PoolTumor2-T 8 23548530 T C . @@ -2195,9 +1819,6 @@ PoolTumor2-T 8 38283759 C T . PoolTumor2-T 8 38285934 C A . PoolTumor2-T 8 38287486 G A . PoolTumor2-T 8 38297776 G C . -PoolTumor2-T 8 43092933 C G . -PoolTumor2-T 8 43092940 T G . -PoolTumor2-T 8 43094789 A ATATTATATACTGTACATAAAATATCAAAGTACCCCAAGGTATATATTCAATACTGTACAAAAAATATCAAAGTACCCAAAGCATG . PoolTumor2-T 8 54049868 T A . PoolTumor2-T 8 54445600 T C . PoolTumor2-T 8 55367460 C T . @@ -2220,6 +1841,7 @@ PoolTumor2-T 8 109144095 CCCAGGGGACGC T . PoolTumor2-T 8 109735723 T C . PoolTumor2-T 8 117352461 G A . PoolTumor2-T 8 117864369 C G . +PoolTumor2-T 8 117868529 T A . PoolTumor2-T 8 117870036 TATA T . PoolTumor2-T 8 117870196 A C . PoolTumor2-T 8 117874055 A AT . @@ -2227,28 +1849,27 @@ PoolTumor2-T 8 120428447 G A . PoolTumor2-T 8 125875063 G A . PoolTumor2-T 8 128747953 G T . PoolTumor2-T 8 128751201 G A . +PoolTumor2-T 8 131759339 C T . PoolTumor2-T 8 139766211 G C . PoolTumor2-T 8 143164976 G A . PoolTumor2-T 8 143445733 A G . PoolTumor2-T 8 144227728 A G . -PoolTumor2-T 8 144343986 TGCACCTGCCACGCCTGTCTCCGGCAGCCCCTGCCCGCACCCGCACCCCTGCACCTGCCACGCCCGTCTCCGGCAGCACCTGCCACGCCCGTCTCCGGCA T . PoolTumor2-T 8 144344100 C T . PoolTumor2-T 8 144351029 C CTGCTGCTGCTGCTGT . PoolTumor2-T 8 144999077 G A . PoolTumor2-T 8 145736791 C T . PoolTumor2-T 8 145738441 G A . -PoolTumor2-T 8 145739175 C G . PoolTumor2-T 8 145743081 G A . PoolTumor2-T 8 145745182 T C . PoolTumor2-T 9 1011564 A AT . PoolTumor2-T 9 2039827 G A . PoolTumor2-T 9 3776612 C G . PoolTumor2-T 9 4804901 A G . -PoolTumor2-T 9 5072798 T C . PoolTumor2-T 9 5126742 G T . PoolTumor2-T 9 5456083 G A . PoolTumor2-T 9 5456775 C G . PoolTumor2-T 9 5467807 C T . +PoolTumor2-T 9 8331406 ATTATTTTCAC A . PoolTumor2-T 9 8331548 C T . PoolTumor2-T 9 8331574 A AAACTTACCATTCTTGAACTGT . PoolTumor2-T 9 8332033 A G . @@ -2261,15 +1882,16 @@ PoolTumor2-T 9 16206756 T G . PoolTumor2-T 9 20777008 A G . PoolTumor2-T 9 21993964 T C . PoolTumor2-T 9 22012051 T C . +PoolTumor2-T 9 25247018 C T . PoolTumor2-T 9 33676618 C T . PoolTumor2-T 9 36881930 T TG . PoolTumor2-T 9 36930460 T G . PoolTumor2-T 9 37015450 G A . -PoolTumor2-T 9 66458606 G A . -PoolTumor2-T 9 66833834 TG CT . -PoolTumor2-T 9 68413168 G T . -PoolTumor2-T 9 68414161 CAGGAAGCGACGTTCCCCACGCCCCGGTGTAGGTGAACCCG TGGGAAGCGCAATTCCCGGGCGAACTCA . -PoolTumor2-T 9 68414170 A C . +PoolTumor2-T 9 37490859 G A . +PoolTumor2-T 9 37490862 C A . +PoolTumor2-T 9 68414063 T C . +PoolTumor2-T 9 68414094 A G . +PoolTumor2-T 9 68414103 T G . PoolTumor2-T 9 75155834 G A . PoolTumor2-T 9 75794996 A T . PoolTumor2-T 9 80409358 G T . @@ -2288,11 +1910,9 @@ PoolTumor2-T 9 93640895 G A . PoolTumor2-T 9 93641193 C T . PoolTumor2-T 9 93641199 T C . PoolTumor2-T 9 93650322 G A . -PoolTumor2-T 9 94768176 T A . PoolTumor2-T 9 95439427 A G . PoolTumor2-T 9 97873931 G A . PoolTumor2-T 9 98009794 G C . -PoolTumor2-T 9 98278972 TCTC T . PoolTumor2-T 9 107068085 G C . PoolTumor2-T 9 109484504 A G . PoolTumor2-T 9 110248177 C T . @@ -2325,81 +1945,43 @@ PoolTumor2-T 9 139409676 G T . PoolTumor2-T 9 139412182 G A . PoolTumor2-T 9 139413539 C T . PoolTumor2-T 9 139413908 C T . +PoolTumor2-T 9 139565474 ATTGG A . PoolTumor2-T 9 139565475 TTGG T . PoolTumor2-T 9 139565987 A AC . PoolTumor2-T 9 139566996 G A . -PoolTumor2-T 9 139794638 T A . PoolTumor2-T 9 139810652 G A . PoolTumor2-T 9 139815960 A G . -PoolTumor2-T GL000199.1 72929 A C . -PoolTumor2-T GL000212.1 246 A G . -PoolTumor2-T GL000212.1 40744 T G . -PoolTumor2-T GL000212.1 40827 T G . PoolTumor2-T GL000212.1 40875 A G . -PoolTumor2-T GL000212.1 40886 A C . -PoolTumor2-T GL000212.1 163535 T A . -PoolTumor2-T GL000212.1 163555 T C . -PoolTumor2-T GL000212.1 163574 T C . -PoolTumor2-T GL000212.1 163644 G A . -PoolTumor2-T GL000212.1 175100 A T . PoolTumor2-T GL000220.1 119178 T C . -PoolTumor2-T GL000220.1 119477 TTCTTTCTCTTTCTCTTTCTCTCTCTC T . -PoolTumor2-T GL000220.1 119479 CTTTCTCTTTCTCTTTCTCTCTC ATCTCTCTCTCGCTCTTGCCCTCTCGCTCTCTCCCTCGCTCGTTT . -PoolTumor2-T GL000220.1 119493 T C . -PoolTumor2-T GL000220.1 119595 CTC GTCGCTCTCGCCCTCTCGCTCTCTCTCTGTCTCTGTCTGTG . PoolTumor2-T GL000220.1 119610 C T . PoolTumor2-T GL000220.1 119911 C T . -PoolTumor2-T GL000220.1 119967 T C . -PoolTumor2-T GL000220.1 120161 G C . +PoolTumor2-T GL000220.1 119970 C T . PoolTumor2-T GL000220.1 121453 TTGCCTGCCTGCC T . +PoolTumor2-T GL000220.1 123139 G GTCTCTCTCTCTCTC . PoolTumor2-T GL000220.1 123214 G C . +PoolTumor2-T GL000220.1 124694 C CCTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT . PoolTumor2-T GL000220.1 125098 C G . -PoolTumor2-T GL000220.1 126307 G A . +PoolTumor2-T GL000220.1 126947 TTC T . PoolTumor2-T GL000220.1 127312 G C . -PoolTumor2-T GL000220.1 127757 T TCTGC . -PoolTumor2-T GL000220.1 127790 G CTCTCTCTGTC . -PoolTumor2-T GL000220.1 128282 CCTGT C . -PoolTumor2-T GL000220.1 128928 C CCTGTCTCCTCTCTCTCTCA . +PoolTumor2-T GL000220.1 128203 CCTCTCTCTT TCTGCCTC . PoolTumor2-T GL000220.1 128957 TTCTG T . PoolTumor2-T GL000220.1 129019 G C . -PoolTumor2-T GL000220.1 130027 GGGGGGA TGGG . PoolTumor2-T GL000220.1 130109 C A . PoolTumor2-T GL000220.1 132352 CTCTCTG C . PoolTumor2-T GL000220.1 132475 T C . -PoolTumor2-T GL000220.1 133311 A ACGTC . -PoolTumor2-T GL000220.1 133431 G A . -PoolTumor2-T GL000220.1 133549 G C . PoolTumor2-T GL000220.1 133613 T A . PoolTumor2-T GL000220.1 137741 G A . -PoolTumor2-T GL000220.1 146098 CTT C . -PoolTumor2-T GL000224.1 4495 G T . -PoolTumor2-T GL000225.1 44342 T C . -PoolTumor2-T GL000225.1 44344 C A . -PoolTumor2-T GL000225.1 44549 A G . -PoolTumor2-T GL000225.1 65091 A G . -PoolTumor2-T GL000225.1 78924 C T . -PoolTumor2-T GL000225.1 91008 T A . -PoolTumor2-T GL000225.1 131540 T A . -PoolTumor2-T GL000225.1 131568 T G . -PoolTumor2-T GL000229.1 7982 T C . -PoolTumor2-T GL000229.1 8042 C G . -PoolTumor2-T GL000231.1 24616 C T . +PoolTumor2-T GL000231.1 24498 T A . PoolTumor2-T MT 152 T C . PoolTumor2-T MT 178 A G . PoolTumor2-T MT 477 T C . PoolTumor2-T MT 533 A G . -PoolTumor2-T MT 1888 G A . PoolTumor2-T MT 1990 G A . PoolTumor2-T MT 4917 A G . -PoolTumor2-T MT 5007 G A . -PoolTumor2-T MT 7051 T C . PoolTumor2-T MT 8697 G A . -PoolTumor2-T MT 9150 A G . PoolTumor2-T MT 9899 T C . PoolTumor2-T MT 10463 T C . -PoolTumor2-T MT 10601 T C . PoolTumor2-T MT 12633 C A . -PoolTumor2-T MT 13368 G A . PoolTumor2-T MT 14905 G A . PoolTumor2-T MT 15607 A G . PoolTumor2-T MT 16019 C T . @@ -2410,19 +1992,17 @@ PoolTumor2-T MT 16294 C T . PoolTumor2-T MT 16316 A G . PoolTumor2-T MT 16390 G A . PoolTumor2-T X 1314857 GG AT . -PoolTumor2-T X 1317599 T C . PoolTumor2-T X 1325301 G T . PoolTumor2-T X 1325426 C T . +PoolTumor2-T X 1331309 C CAG . PoolTumor2-T X 15822104 TA T . PoolTumor2-T X 15822401 C T . PoolTumor2-T X 22516183 G A . -PoolTumor2-T X 39911835 G T . PoolTumor2-T X 39930099 C G . PoolTumor2-T X 44896832 C G . PoolTumor2-T X 44896888 C T . PoolTumor2-T X 47425058 G A . PoolTumor2-T X 47430509 A AGTGT . -PoolTumor2-T X 50648296 A AAAATAAAT . PoolTumor2-T X 53223092 C A . PoolTumor2-T X 53224366 C T . PoolTumor2-T X 53225501 T C . @@ -2433,7 +2013,7 @@ PoolTumor2-T X 66766359 C T . PoolTumor2-T X 66789057 G T . PoolTumor2-T X 66937707 A G . PoolTumor2-T X 66942476 A G . -PoolTumor2-T X 66943154 C CTCTGTGTGTGTG . +PoolTumor2-T X 66943154 C CTCTGTG . PoolTumor2-T X 66943769 C A . PoolTumor2-T X 70344763 G T . PoolTumor2-T X 70347614 C T . @@ -2446,11 +2026,6 @@ PoolTumor2-T X 76939830 A G . PoolTumor2-T X 100057572 C T . PoolTumor2-T X 100609517 G GA . PoolTumor2-T X 100615505 G T . -PoolTumor2-T X 106846430 C CAACAACAACAGCAGCAGCAGCAACAACAACAGCAGCAGCAACAACAACAGCAGACAATAACAAAAGCAACGATAGCAACAGTATCAGCAACAGCAACAGCATCAGCAACAACAGCAACAATAGCAGCAGTAAA . -PoolTumor2-T X 106846447 G GCAGCAACAACAACAGCAGACAATAACAAAAGCAACGATAGCAACAGTAT . -PoolTumor2-T X 122035670 C T . -PoolTumor2-T X 122035688 C T . -PoolTumor2-T X 123041111 G C . PoolTumor2-T X 123159533 A G . PoolTumor2-T X 123184027 C T . PoolTumor2-T X 123184284 T A . @@ -2462,14 +2037,3 @@ PoolTumor2-T X 123499991 T G . PoolTumor2-T X 136524003 G A . PoolTumor2-T X 139479797 C T . PoolTumor2-T X 145042124 TA T . -PoolTumor2-T Y 13489086 G A . -PoolTumor2-T Y 13573061 A G . -PoolTumor2-T Y 13573216 G A . -PoolTumor2-T Y 13573240 C T . -PoolTumor2-T Y 13801134 G GAATGTGCTCGAATGGAATGGAATCGTATGGATTGATATCA . -PoolTumor2-T Y 13801161 AT TTGATATCAAGTGGAAA . -PoolTumor2-T Y 13842723 G C . -PoolTumor2-T Y 13842730 G A . -PoolTumor2-T Y 13868369 T TCGAATGGAATGGAATGGAATGGAACGGAACTACGGAATAGAATGGAATGGAATTAACC . -PoolTumor2-T Y 13868375 G A . -PoolTumor2-T Y 13869847 T A . diff --git a/data/sample_output/PoolTumor2-T_bc52_VarDict_1.4.6_STDfilter.vcf b/data/sample_output/PoolTumor2-T_bc52_VarDict_1.4.6_STDfilter.vcf index 614ebcd..9348087 100644 --- a/data/sample_output/PoolTumor2-T_bc52_VarDict_1.4.6_STDfilter.vcf +++ b/data/sample_output/PoolTumor2-T_bc52_VarDict_1.4.6_STDfilter.vcf @@ -10,13 +10,14 @@ ##INFO= ##INFO= ##INFO= -##INFO= -##INFO= +##INFO= +##INFO= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= -##FORMAT= +##FORMAT= +##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= @@ -31,2499 +32,2063 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##FILTER= +##FILTER= ##FILTER= -##FILTER= +##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= 0.05, thus not somatic"> -##FILTER= -##FILTER= +##FILTER= +##FILTER= ##FILTER= ##FILTER= 0.05"> ##FILTER= ##FILTER= 0.01/5**vd2"> ##FILTER= -##FILTER= -##FILTER== 4, thus likely false positive"> +##FILTER= +##FILTER== 7.25, thus likely false positive"> ##FILTER= ##FILTER= -##FILTER= +##FILTER= ##FILTER==14)"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PoolTumor2-T PoolNormal-N -1 4955833 . A T 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAGCGGCAGATAAAAAAAC;RSEQ=GACAAACCGGAGAGCACGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:18:9,9:90,91:0.0905:2,2:26.8:1.0:29.8:1.0:1.0:1.01:60.0:36.0:0.0914:0.0:1.2 0/0:278:0:0,0:147,131:0.0:2,0:27.0:1.0:30.1:1.0:1.0:0.0:60.0:68.5:1.0:0.0:0.5 -1 9780743 . TG T 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.03061;SOR=0.0;LSEQ=AGTGGGGTGGGGGTGTGGGG;RSEQ=GGGGGCATGGAGCCGGCGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:5:3,2:226,256:0.0102:2,2:30.2:1.0:30.8:1.0:0.66973:1.7:60.0:10.0:0.0105:0.0:0.2 0/0:490:0:0,0:225,258:0.0:2,0:22.9:1.0:30.0:1.0:1.0:0.0:59.9:39.25:0.9874:0.0:0.8 -1 9781880 . A G 49 q23 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.02779;SOR=0.0;LSEQ=TCATCCTGGAGGCCTACTGC;RSEQ=GGGGCAGCACCCACCACATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:5:2,3:228,253:0.0103:2,2:33.4:1.0:21.2:1.0:1.0:1.35095:60.0:1.5:0.0063:0.0:2.0 0/0:507:0:0,0:212,294:0.0:2,0:23.6:1.0:30.1:1.0:1.0:0.0:60.0:55.222:0.998:0.0:0.2 -1 11181985 . G A 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ATGAGAAAAGCAGCGCTACG;RSEQ=AGATTCCCTGCCACGGAAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:40:30,10:156,47:0.1646:2,2:22.5:1.0:30.0:1.0:0.83885:1.10591:60.0:39.0:0.1632:0.0:1.1 0/0:211:0:0,0:162,49:0.0:2,0:23.1:1.0:30.9:1.0:1.0:0.0:60.0:51.75:1.0:0.0:0.2 -1 11227864 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGCTGGGTGTGGTGGCTCA;RSEQ=GCCTGTAATCCCAGCACTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:20.0:1.0:31.0:1.0:1.0:0.0:53.4:10.0:0.5556:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 11291380 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01273;SOR=0.09558;LSEQ=TCTGCGTGTACCCTGGTTCT;RSEQ=CTCAGTCTTCAGAAAATTCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:690:8:6,2:387,295:0.0116:2,2:15.6:1.0:26.1:1.0:0.47678:2.28:60.0:16.0:0.0117:0.0:1.0 0/0:894:1:1,0:457,436:0.0011:2,0:1.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 -1 11303131 . C T 60 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.06251;SOR=0.0;LSEQ=GAGCGTCCTTCCTCTCCAAC;RSEQ=AAATGGAGTGGAAGGTGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:5:1,4:204,64:0.0183:2,2:11.4:1.0:26.0:1.0:0.01456:12.60622:60.0:10.0:0.0187:0.0:1.0 0/0:250:0:0,0:185,65:0.0:2,0:23.4:1.0:30.0:1.0:1.0:0.0:60.0:40.667:1.0:0.0:0.1 -1 14192818 . G T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.00554;SOR=0.0;LSEQ=CTGTTCATGGCTAATTCTTG;RSEQ=GTGGCTTCCATCACAGCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:0,8:1,32:0.1951:1,0:11.1:1.0:31.4:1.0:1.0:0.0:60.0:16.0:0.1951:0.0:1.0 0/0:38:0:0,0:2,35:0.0:2,0:25.9:1.0:30.0:1.0:1.0:0.0:60.0:17.5:1.0:0.0:0.1 -1 16245610 . GT G 189 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.0;SOR=0.06745;LSEQ=TGTTTTTTAAGACTTGAAGG;RSEQ=TTTTTTTTTGCATATGCCTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:60:5,55:16,96:0.3488:2,2:30.1:1.0:32.0:1.0:0.33178:1.82738:60.0:120.0:0.3529:0.0:0.0 0/1:202:7:0,7:37,158:0.0347:2,0:26.6:1.0:31.6:1.0:0.35364:0.0:60.0:14.0:0.0354:0.0:0.0 -1 16258302 . A G 259 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04699;LSEQ=GGAAAAACTCAAGCGGTCCA;RSEQ=TTCTCCTCGGGGAGAAGCAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:623:273:126,147:159,189:0.4382:2,2:23.1:1.0:32.1:1.0:0.93542:1.02:60.0:135.5:0.4399:0.0:1.1 0/1:765:27:15,12:353,385:0.0353:2,2:22.5:1.0:31.1:1.0:0.44122:1.36:60.0:54.0:0.0357:0.0:1.0 -1 16262650 . G A 62 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02748;SOR=0.0;LSEQ=AGCGGGGAGCTGTTTCAAGA;RSEQ=TACCGGTACGGCGACATCCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:5:4,1:186,272:0.0108:2,2:6.8:1.0:26.8:1.0:0.16424:5.83:60.0:10.0:0.011:0.0:1.0 0/0:485:0:0,0:222,263:0.0:2,0:24.3:1.0:30.9:1.0:1.0:0.0:60.0:59.625:1.0:0.0:0.2 -1 16971804 . A T 95 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.15963;SOR=0.0;LSEQ=CTGGCAGCTGTCACTTTCAC;RSEQ=ATGCCCTTGGGCTGACTAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:8,0:18,1:0.2963:1,0:30.4:1.0:31.8:1.0:1.0:0.0:49.6:16.0:0.2963:0.0:1.1 0/0:9:0:0,0:7,2:0.0:2,0:24.9:1.0:29.6:1.0:1.0:0.0:54.2:18.0:1.0:0.0:0.3 -1 16972489 . C A 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01099;SOR=0.0;LSEQ=TTGTGCAGGTGAGAGCCCAG;RSEQ=TTTGGAGTCTGAATGCCTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:1,1:0.8182:2,0:28.4:1.0:28.8:1.0:0.18182:0.0:31.6:8.0:1.0:0.0:2.2 0/0:4:0:0,0:2,2:0.0:2,0:9.0:1.0:30.8:1.0:1.0:0.0:44.0:8.0:1.0:0.0:0.0 -1 16972496 . G A 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.25824;SOR=0.0;LSEQ=GGTGAGAGCCCAGCTTTGGA;RSEQ=TCTGAATGCCTAGCCAGGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:1,5:0.4545:2,0:39.4:1.0:29.0:1.0:1.0:0.0:30.2:10.0:0.4545:0.0:2.6 0/0:3:0:0,0:2,1:0.0:2,0:12.7:1.0:30.0:1.0:1.0:0.0:50.0:6.0:1.0:0.0:0.0 -1 16972790 . GAAT AA 129 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTTGTAGCTTTGATCCCCT;RSEQ=GAACAAACTGTGGACATGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:19:18,1:294,39:0.0534:2,1:27.1:1.0:30.4:1.0:0.70861:2.38:52.1:38.0:0.0543:0.0028:0.1 0/0:357:0:0,0:287,69:0.0:2,0:23.1:1.0:31.3:1.0:1.0:0.0:53.6:43.5:0.9971:0.0:0.1 -1 16972793 . T A 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02719;SOR=0.0;LSEQ=TGTAGCTTTGATCCCCTGAA;RSEQ=GAACAAACTGTGGACATGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:5:5,0:316,53:0.0134:2,0:9.6:1.0:27.2:1.0:1.0:0.0:55.2:4.0:0.011:0.0:1.4 0/0:393:0:0,0:311,82:0.0:2,0:22.3:1.0:29.5:1.0:1.0:0.0:54.3:48.125:1.0:0.0:0.1 -1 16973028 . A C 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCGGTGAGTGGCCACTGGGC;RSEQ=TAGATAAGACTGGGGGCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1659:106:49,57:785,766:0.0639:2,2:27.9:1.0:31.8:1.0:0.4222:1.19199:39.6:105.0:0.0642:0.0:1.2 0/0:1855:0:0,0:899,955:0.0:2,0:26.0:0.0:14.0:0.0:1.0:0.0:40.0:0.0:0.0:0.0:2.0 -1 16973259 . G C 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00099;SOR=0.0;LSEQ=AGGGGACCTCAGCCCAAGTT;RSEQ=ATCTTCTGTCTCTTGCTCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:809:11:4,7:244,552:0.0136:2,2:26.9:1.0:31.4:1.0:0.74465:1.29:29.4:22.0:0.0138:0.0:1.2 0/0:760:0:0,0:263,497:0.0:2,0:23.0:1.0:31.1:1.0:1.0:0.0:37.9:83.444:1.0:0.0:0.2 -1 16973855 . G A 202 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.1445;LSEQ=GCCCTGGGGGCCGGGCTAGG;RSEQ=AAGGTCCAGGACTCCAGGGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1442:116:74,42:839,484:0.0804:2,2:20.5:1.0:29.5:1.0:1.0:1.02:32.7:37.667:0.0798:0.0:1.1 0/1:1042:13:9,4:671,358:0.0125:2,2:27.0:1.0:28.8:1.0:1.0:1.2:32.7:26.0:0.0128:0.0:1.1 -1 16973957 . G T 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACGCCCCATTACCGCCCCCA;RSEQ=GTTCCTCGACCAAGGTCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2906:168:58,110:1191,1547:0.0578:2,2:27.8:1.0:30.0:1.0:0.02444:1.45992:37.8:55.0:0.0576:0.0:1.9 0/0:2748:0:0,0:1321,1426:0.0:2,0:28.5:1.0:30.6:1.0:1.0:0.0:37.8:69.436:0.9996:0.0:0.6 -1 16974458 . G C 207 InIns SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACGCGTGCAAGTGAGGTGGG;RSEQ=GGGCGGGCGTTGGGACGTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3438:128:31,97:1617,1687:0.0372:2,2:5.4:1.0:29.7:1.0:0.0:2.99849:40.6:41.667:0.0373:0.0:1.6 0/0:3403:0:0,0:1549,1729:0.0:2,0:24.8:1.0:30.0:1.0:1.0:0.0:56.3:44.528:0.9994:0.0:0.3 -1 16974817 . C G 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.05318;LSEQ=GCTACCACGGCGCGGGGGAG;RSEQ=AGTACCGCGGCACGGTCAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:987:309:154,155:245,430:0.3131:2,2:24.6:1.0:30.9:1.0:7e-05:1.74:47.8:43.143:0.3149:0.0:1.7 0/1:1100:26:14,12:525,545:0.0236:2,2:26.8:1.0:30.3:1.0:0.6939:1.21:46.4:25.0:0.0232:0.0:1.6 -1 16974868 . G T 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.17855;LSEQ=AGGGTGTCCAGTGCCAGCGC;RSEQ=GGTCCGCTGAGACGCCGCAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:959:51:10,41:472,436:0.0532:2,2:20.1:1.0:31.1:1.0:0.0:4.43287:28.2:102.0:0.0539:0.0:1.6 0/0:1411:14:0,14:727,668:0.0099:2,1:21.5:1.0:30.6:1.0:4e-05:0.0:33.3:28.0:0.0101:0.0:1.6 -1 16974955 . A G 136 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00014;SOR=0.16038;LSEQ=CCCTGGGGCGGCATGCTTTG;RSEQ=TGTCTGGGACCAGAGCCTGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:938:21:10,11:589,328:0.0224:2,2:20.9:1.0:31.0:1.0:0.16607:1.97384:27.5:9.5:0.0208:0.0:2.4 0/0:1094:4:2,2:630,459:0.0037:2,2:21.5:1.0:31.8:1.0:1.0:1.37213:24.0:8.0:0.0037:0.0:2.8 -1 16975201 . CT C 251 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCATGACCCTGCCTCAGCC;RSEQ=CACCACCAAAGGCTGGCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5584:255:131,124:1464,1584:0.0457:2,2:27.1:1.0:31.4:1.0:0.32794:1.14:43.3:254.0:0.0463:0.0061:0.8 0/0:5426:0:0,0:1751,1793:0.0:2,0:25.8:1.0:29.6:1.0:1.0:0.0:48.9:69.88:0.6532:0.0:0.7 -1 16975228 . C T 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01693;LSEQ=CCAAAGGCTGGCTCCCTTAA;RSEQ=CGCAGTGAACTTTGTCTTTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4642:179:89,90:2048,2408:0.0386:2,2:22.3:1.0:30.2:1.0:0.35889:1.16:58.0:58.667:0.0383:0.0:1.1 0/0:4421:3:1,2:2106,2309:0.0007:2,2:29.3:1.0:26.3:1.0:1.0:1.82392:44.3:6.0:0.0007:0.0:1.7 -1 16975429 . T C 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.17518;LSEQ=TGGATCGGCTGGATCAGCGT;RSEQ=GTTCCAAGCTGCGCGTGGCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1214:41:12,29:514,659:0.0338:2,2:25.1:1.0:28.9:1.0:0.07741:1.88398:26.6:12.667:0.0319:0.0:1.5 0/0:1644:10:0,10:737,897:0.0061:2,0:22.8:1.0:31.4:1.0:0.00287:0.0:25.4:20.0:0.0062:0.0:1.1 -1 16975489 . C G 260 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.06995;LSEQ=CACCCTGGACAGTCAGCTTG;RSEQ=GGAATTGGTGAGGCACAACT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:855:345:173,172:211,298:0.4035:2,2:27.9:1.0:30.9:1.0:0.01412:1.42:32.4:85.25:0.404:0.0:2.0 0/1:687:31:15,16:255,401:0.0451:2,2:18.0:1.0:30.6:1.0:0.34719:1.47:32.8:62.0:0.0457:0.0:1.8 -1 16975642 . C T 241 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.1752;LSEQ=ATCTGTCCCAGGAGTCTGTT;RSEQ=CCTGTCCTAATTCCCCACTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2762:265:157,108:1604,892:0.0959:2,2:31.9:1.0:30.0:1.0:0.10722:1.23687:30.9:52.0:0.0958:0.0:1.8 0/1:2466:45:37,8:1498,923:0.0182:2,2:19.7:1.0:29.4:1.0:0.00482:2.85:27.7:44.0:0.0181:0.0:1.4 -1 16975689 . G C 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.16701;LSEQ=GCAGGGCCAGCATTTCTGCG;RSEQ=GGGGTCTCTAGTGAAGGAGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3209:287:176,111:1513,1408:0.0894:2,2:20.5:1.0:31.3:1.0:0.00235:1.48:29.1:286.0:0.09:0.0:1.8 0/1:2913:47:47,0:1443,1422:0.0161:2,1:28.3:1.0:32.3:1.0:0.0:0.0:25.3:46.0:0.016:0.0:1.5 -1 16975951 . A G 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03292;LSEQ=ACATGGAGAGCCAGGCCTAC;RSEQ=GCGGGTCCCAGTAGCCAAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1076:373:200,173:331,371:0.3467:2,2:26.5:1.0:29.9:1.0:0.04702:1.3:38.8:123.333:0.3484:0.0:1.4 0/1:1283:22:16,6:684,573:0.0171:2,2:27.0:1.0:28.9:1.0:0.12872:2.23:39.8:21.0:0.0167:0.0:1.5 -1 16976345 . T C 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06716;LSEQ=CTAAATGTGGCCTTGCTGAA;RSEQ=GTCATCTCCAACCAGGAGTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1158:64:30,34:568,525:0.0553:2,2:25.4:1.0:31.8:1.0:0.44281:1.22594:27.0:128.0:0.0559:0.0:1.2 0/0:1790:7:2,5:917,866:0.0039:2,2:24.6:1.0:27.0:1.0:0.27608:2.64589:28.9:6.0:0.0034:0.0:1.6 -1 17083778 . C T 297 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.10033;LSEQ=TCCACAAACACAGAGACACG;RSEQ=GTGAAGACGGCTGGCCAGCG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2341:1050:521,529:480,808:0.4485:2,2:27.0:1.0:29.6:1.0:0.0:1.66:33.9:130.25:0.4509:0.0:1.9 0/1:1008:76:19,57:354,577:0.0754:2,2:22.7:1.0:30.6:1.0:0.0259:1.83952:33.3:152.0:0.0767:0.0:1.9 -1 17083816 . G A 290 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.1254;LSEQ=GCGCGACCTTGTGCATACTC;RSEQ=GTTGGGGATTCTAATTCCTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2187:784:319,465:692,711:0.3585:2,2:27.2:1.0:30.2:1.0:0.00012:1.41848:33.3:34.636:0.3557:0.0:3.0 0/1:932:61:33,28:406,465:0.0655:2,2:22.6:1.0:30.7:1.0:0.28926:1.35:28.0:122.0:0.0659:0.0:3.2 -1 17083918 . C T 207 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.11342;LSEQ=AGGAGAACTGATGAGGGCCC;RSEQ=GGGCCACAGCAATGACTAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1159:108:28,80:424,627:0.0932:2,2:29.6:1.0:30.7:1.0:0.00358:1.93107:29.2:216.0:0.0943:0.0:1.5 0/1:782:9:6,3:338,433:0.0115:2,2:17.3:1.0:29.6:1.0:0.19318:2.56:29.0:18.0:0.0117:0.0:1.1 -1 17085227 . G C 227 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.14641;LSEQ=CTGAAAGACAAAGTTCACTG;RSEQ=GGTTAAGGGAGCCAGCCTTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1102:153:105,48:474,471:0.1388:2,2:27.8:1.0:31.4:1.0:2e-05:2.17:44.5:75.5:0.1389:0.0:2.1 0/1:1085:25:18,7:532,525:0.023:2,2:24.2:1.0:31.6:1.0:0.04162:2.54:46.8:50.0:0.0233:0.0:3.2 -1 17085254 . GA G 136 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=GGGAGCCAGCCTTTGGTGGT;RSEQ=GGGCTGAGGTAAGGTCATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1198:19:14,5:376,365:0.0159:2,2:19.4:1.0:32.2:1.0:0.06202:2.71:33.9:38.0:0.0162:0.0025:1.7 0/0:1016:0:0,0:392,376:0.0:2,0:19.6:1.0:29.5:1.0:1.0:0.0:51.7:75.8:0.7542:0.0:0.4 -1 17085532 . T C 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCGCCCCAGGGTTAGGGCCC;RSEQ=GGCGGGGCCGGGAGCACCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2107:153:92,61:987,966:0.0726:2,2:22.1:1.0:30.2:1.0:0.02338:1.48:41.3:50.0:0.0719:0.0:1.9 0/0:1618:0:0,0:791,827:0.0:2,0:22.5:1.0:30.2:1.0:1.0:0.0:41.5:63.72:1.0:0.0:0.8 -1 17085790 . C T 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03702;LSEQ=GCCGCACGTCGTCTGTACAA;RSEQ=GCCGGATCTGGTAGCAAAAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2646:123:53,70:1070,1452:0.0465:2,2:22.2:1.0:30.2:1.0:0.92565:1.03:40.8:40.0:0.0458:0.0:1.6 0/0:2221:4:0,4:1022,1192:0.0018:2,0:1.0:0.0:24.3:1.0:0.12928:0.0:57.5:8.0:0.0018:0.0:1.8 -1 17086541 . T C 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00212;SOR=0.03491;LSEQ=CGTGAAGAAGACCCTGGTAC;RSEQ=CTGGCTTATCTGGCCCCGCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:1,2:0.625:2,2:8.0:1.0:29.4:1.0:1.0:1.8258:25.4:10.0:0.625:0.0:1.4 0/1:22:1:0,1:10,11:0.0455:2,0:3.0:0.0:28.0:0.0:1.0:0.0:25.0:2.0:0.0455:0.0:1.0 -1 17087395 . G A 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.16586;LSEQ=AGAAGAAGGCACAGGGTAAC;RSEQ=CCACGGCCCAGGCTCCCCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4046:45:27,18:2005,1992:0.0111:2,2:22.4:1.0:28.8:1.0:0.23039:1.49:50.8:44.0:0.0111:0.0:2.2 0/0:3223:6:4,2:1626,1588:0.0019:2,2:22.5:1.0:27.5:1.0:0.68735:1.95:49.7:5.0:0.0016:0.0:2.7 -1 17345073 . G GC 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGAACAAGCTGCAGGCCCT;RSEQ=CTGATGTCAGTTCCACGGCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:0.5455:0,0:20.7:1.0:30.6:1.0:1.0:0.0:60.0:12.0:0.5455:0.2727:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 17380195 . TC T 92 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.13116;SOR=0.0;LSEQ=TCAAGTCCCCTTTCTGAACG;RSEQ=CCCCCCCCCCGCACCCTTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:8,0:9,0:0.4706:0,0:34.3:1.0:30.8:1.0:1.0:0.0:60.0:16.0:0.5:0.0:0.6 0/0:4:0:0,0:4,0:0.0:0,0:15.5:1.0:29.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:3.5 -1 17380653 . C A 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11654;LSEQ=ACCAAGTGGGAGGCGGCTTC;RSEQ=GGTTTCCCGGGTGGGCGGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:45:0,45:0,57:0.4412:1,1:23.6:1.0:32.2:1.0:1.0:0.0:60.0:90.0:0.4455:0.0:1.0 0/1:60:5:1,4:2,53:0.0833:1,2:28.4:1.0:31.4:1.0:0.23334:6.24:60.0:10.0:0.0862:0.0:1.0 -1 23111036 . C T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00216;SOR=0.0;LSEQ=CCACGTGGAGATGAAGTTTT;RSEQ=GGTGCGTGACTGCAGCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1.0:0,2:24.7:1.0:29.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:5:0:0,0:2,3:0.0:2,0:17.8:1.0:31.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 -1 23880912 . G A 224 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01501;LSEQ=TGCCACTGACTGACCCCTAA;RSEQ=AGGAGAACTAATCAGAGAAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:253:181:164,17:61,10:0.7154:2,2:23.4:1.0:29.9:1.0:0.36446:1.58:60.0:35.2:0.7126:0.0:1.2 0/1:334:12:8,4:279,43:0.0359:2,2:18.5:1.0:29.5:1.0:0.07251:3.22799:60.0:24.0:0.0366:0.0:1.3 -1 23881005 . G A 296 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00735;LSEQ=GTGGGGAAGGACTTCGAGAG;RSEQ=GCAGAGGCTTCCCGGAGGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1198:904:507,397:165,128:0.7546:2,2:25.4:1.0:30.2:1.0:1.0:1.00938:60.0:44.2:0.7543:0.0:1.2 0/1:1542:34:16,18:788,718:0.022:2,2:25.4:1.0:29.8:1.0:0.60431:1.23451:60.0:68.0:0.0224:0.0:1.2 -1 23885230 . C G 127 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.00269;SOR=0.06591;LSEQ=GCCACTGCGGGAGGGCAGGG;RSEQ=CCAGGCGCATTTAAGGCTTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:19:19,0:13,0:0.5938:1,1:26.3:1.0:30.1:1.0:1.0:0.0:60.0:18.0:0.6207:0.0:1.1 0/1:12:1:1,0:11,0:0.0833:0,0:47.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0833:0.0:1.0 -1 23886338 . G GC 72 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTAGCCCAACACTGGTTCGA;RSEQ=CCACAGCTCCTCCGAGGTCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,1:0.8333:0,2:33.4:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 27023140 . TGGC T 81 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.0;MSILEN=3.0;SSF=0.03138;SOR=0.17547;LSEQ=GGGGCCGAGAGCAATGGGGG;RSEQ=GGCGGCGGCGGAGCCGGCAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:7:3,4:93,125:0.0311:2,2:19.1:1.0:29.1:1.0:1.0:1.01:60.0:6.0:0.0271:0.0133:0.6 0/0:358:2:1,1:169,182:0.0056:2,2:15.0:1.0:32.0:0.0:1.0:1.08:60.0:4.0:0.0056:0.0:0.0 -1 27106967 . G A 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.10057;SOR=0.16986;LSEQ=AGTGCAGAAGGGCAGTATCG;RSEQ=CAACCTCCTGGGCTTCCTAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:5:2,3:230,233:0.0107:2,2:19.8:1.0:29.4:1.0:1.0:1.47945:60.0:10.0:0.0109:0.0:1.2 0/0:547:1:1,0:268,278:0.0018:2,0:1.0:0.0:24.0:0.0:0.49177:0.0:60.0:2.0:0.0018:0.0:1.0 -1 27533368 . G T 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02011;LSEQ=CGGCTGTTCTCTTGAGCAGC;RSEQ=TTCATTTATCTCCGTCTGCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:31:17,14:135,83:0.1245:2,2:26.1:1.0:29.7:1.0:0.55535:1.33784:60.0:30.0:0.1215:0.0:1.1 0/0:352:1:0,1:203,148:0.0028:2,0:1.0:0.0:27.0:0.0:0.4233:0.0:60.0:2.0:0.0029:0.0:1.0 -1 28637962 . AT A 92 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=13.0;MSILEN=1.0;SSF=0.12821;SOR=0.0;LSEQ=AAAAAAAATTAAAAAAAAAA;RSEQ=AATAATAATAATAATATGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:0,0:0.7273:0,0:13.4:1.0:30.7:1.0:1.0:0.0:60.0:16.0:0.7273:0.2727:0.1 0/0:2:0:0,0:2,0:0.0:0,0:12.0:1.0:24.0:1.0:1.0:0.0:60.0:1.0:1.0:0.0:0.0 -1 29644328 . C T 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00048;SOR=0.0;LSEQ=GCCCTGTTGCCCCGGAACCG;RSEQ=GACAAGAACCGCAGCATGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:6,4:7,3:0.5:2,2:26.0:1.0:30.1:1.0:1.0:1.52135:60.0:20.0:0.5:0.0:1.2 0/0:18:0:0,0:11,7:0.0:2,0:25.2:1.0:30.6:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.1 -1 34805896 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04805;SOR=0.0;LSEQ=CCTGGGAACCAGTGAATCCT;RSEQ=CCTCCACCCCATGTCTGACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:24.2:1.0:27.8:1.0:1.0:0.0:60.0:12.0:0.4286:0.0:1.7 0/0:9:0:0,0:9,0:0.0:0,0:21.3:1.0:32.1:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 -1 36824305 . C T 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTGGCATGACAGGCCCTGTT;RSEQ=CTGAGGCACCCTCACCCCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:695:105:57,48:344,246:0.1511:2,2:25.8:1.0:29.4:1.0:0.45457:1.17729:60.0:210.0:0.1537:0.0:2.1 0/0:691:0:0,0:409,281:0.0:2,0:25.9:1.0:30.8:1.0:1.0:0.0:60.0:68.0:1.0:0.0:0.4 -1 36941539 . G GT 104 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03612;SOR=0.0;LSEQ=AGTGTGTGCCTTTCCGCGGT;RSEQ=TAAGTGCTCTCACTGTAGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:0,12:1,3:0.75:2,0:19.0:1.0:29.2:1.0:0.25:0.0:60.0:24.0:0.75:0.3125:0.2 0/0:3:0:0,0:1,2:0.0:2,0:42.0:1.0:31.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -1 40799145 . A G 88 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02705;SOR=0.16171;LSEQ=TCTTATAGATTCGCATATAC;RSEQ=TGGCCAAAGGAACAACTCCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:7:2,5:7,32:0.1522:2,2:28.3:1.0:31.6:1.0:0.6091:1.8:38.7:14.0:0.1591:0.0:1.9 0/1:72:2:1,1:18,52:0.0278:2,2:10.0:1.0:30.5:1.0:0.46088:2.84:43.5:4.0:0.029:0.0:1.5 -1 45798981 . C A 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02835;LSEQ=ATATGCCCGCCTGTCCAGGT;RSEQ=CATCTCATCTTCTGCCTGTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:32:21,11:439,410:0.0363:2,2:21.5:1.0:28.8:1.0:0.14947:1.78:60.0:64.0:0.0369:0.0:1.3 0/0:938:1:1,0:486,451:0.0011:2,0:1.0:0.0:21.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 -1 45805566 . G C 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=7.0;SSF=1.0;SOR=0.0;LSEQ=ACCCAGCCACCCCACTACCC;RSEQ=CTACCCGCGGCCCACGCTGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:17.6:1.0:31.0:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 46509146 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01087;SOR=0.0;LSEQ=GCTTAGTATGTCAGTGCAGC;RSEQ=GCATGGCTGAGTCCTAGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:0.4545:0,0:31.2:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.4545:0.0:1.0 0/0:13:0:0,0:12,1:0.0:1,0:23.5:1.0:30.4:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.2 -1 46532925 . C CATATATAT 74 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=25;MSI=16.0;MSILEN=2.0;SSF=0.30246;SOR=0.0;LSEQ=CATGTTATTCTGTGTGTGAA;RSEQ=ATATATATATATATATATAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:0,6:0,13:0.2143:1,0:26.7:1.0:28.8:1.0:1.0:0.0:59.2:12.0:0.2222:0.0:0.5 0/0:9:0:0,0:0,8:0.0:0,0:16.8:1.0:30.1:1.0:1.0:0.0:60.0:7.0:0.875:0.0:0.0 -1 46740500 . A G 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00728;SOR=0.0;LSEQ=TCTGCCTCTAGCAGTAGCCA;RSEQ=GCTATGGGCCCAGAAGTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:8:0,8:0,79:0.092:1,0:32.8:1.0:32.3:1.0:1.0:0.0:60.0:16.0:0.093:0.0:1.0 0/0:77:0:0,0:0,77:0.0:1,0:23.5:1.0:32.0:1.0:1.0:0.0:60.0:154.0:1.0:0.0:0.0 -1 51436157 . G T 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=GCACAAAATGGATTTGGAAG;RSEQ=ACTGCGCTGCAGGTTGGTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:14:5,9:170,265:0.0312:2,2:22.3:1.0:29.2:1.0:1.0:1.15439:60.0:28.0:0.0314:0.0:1.0 0/0:530:0:0,0:210,320:0.0:2,0:26.6:1.0:30.8:1.0:1.0:0.0:60.0:105.0:1.0:0.0:0.2 -1 51439777 . C T 189 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11593;LSEQ=CACTTGGCTGCCAAAGAAGG;RSEQ=CACCTCCGGGTGGTGGAGTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:80:32,48:167,202:0.1782:2,2:22.0:1.0:29.9:1.0:0.45661:1.23951:60.0:79.0:0.1779:0.0:1.1 0/1:572:14:9,5:237,320:0.0245:2,2:33.3:1.0:27.6:1.0:0.16968:2.43:60.0:13.0:0.0232:0.0:1.2 -1 51441409 . A G 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03054;SOR=0.0;LSEQ=TTTTCAATAATTTATTTTCC;RSEQ=TGATAGTATAAAAGAATATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:5:2,3:100,222:0.0153:2,2:34.6:1.0:31.6:1.0:0.64904:1.48:60.0:10.0:0.0154:0.0:1.0 0/0:328:0:0,0:129,199:0.0:2,0:24.5:1.0:29.7:1.0:1.0:0.0:60.0:108.333:1.0:0.0:0.1 -1 58158647 . C G 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00516;SOR=0.0;LSEQ=CCCCTTTCTAGGTCCCATAA;RSEQ=AGCCATCTTGCTATTACTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:2,6:8,13:0.2759:2,2:24.8:1.0:31.5:1.0:0.6749:1.80915:60.0:16.0:0.2759:0.0:1.1 0/0:25:0:0,0:11,13:0.0:2,0:19.1:1.0:30.5:1.0:1.0:0.0:60.0:48.0:0.96:0.0:0.3 -1 59250675 . C G 256 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10775;LSEQ=TAACAGGGTCCAGATGGGAA;RSEQ=AAGCGTGTAGGCGATCCGAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1545:274:158,116:676,593:0.1773:2,2:28.3:1.0:31.7:1.0:0.20412:1.19:60.0:273.0:0.1795:0.0:1.1 0/1:1631:37:22,15:844,747:0.0227:2,2:25.7:1.0:31.3:1.0:0.5066:1.3:60.0:36.0:0.0224:0.0:1.2 -1 63226758 . G A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04545;SOR=0.0;LSEQ=GAGGCCATCAAGCTACAGAT;RSEQ=GTCTTACAAATGGAACCCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:4,5:0,1:0.9:0,2:34.1:1.0:30.7:1.0:1.0:0.0:52.9:18.0:0.9:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:7.5:1.0:30.5:1.0:1.0:0.0:53.5:4.0:1.0:0.0:0.5 -1 65312100 . TG T 66 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.54404;SOR=0.0;LSEQ=CTAGCACAGTGTAGGGTTCT;RSEQ=GCCAGCGTTGACAAGAAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:5,0:14,1:0.25:1,0:26.0:1.0:28.6:1.0:1.0:0.0:60.0:4.0:0.2:0.1:0.2 0/0:5:0:0,0:5,0:0.0:0,0:29.4:1.0:33.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -1 65332766 . T C 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATGCGTGGACACGCTGCTG;RSEQ=CACAAATGGTCTTGTTGTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:25:10,15:271,336:0.0394:2,2:21.6:1.0:30.9:1.0:0.68672:1.20946:60.0:24.0:0.0385:0.0:1.0 0/0:658:0:0,0:317,341:0.0:2,0:24.1:1.0:29.2:1.0:1.0:0.0:60.0:218.333:1.0:0.0:0.1 -1 65349304 . G A 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00228;SOR=0.0;LSEQ=CCCTGCCCCTTCCCTTCCTG;RSEQ=AAACCAAACATGTCAGATCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:11:1,10:1,35:0.234:1,2:29.2:1.0:31.1:1.0:0.41721:3.38:60.0:22.0:0.2444:0.0:1.3 0/0:32:0:0,0:0,32:0.0:1,0:25.6:1.0:31.2:1.0:1.0:0.0:60.0:15.0:1.0:0.0:0.1 -1 65351748 . C T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01358;SOR=0.0;LSEQ=CAAGGGAAGTTTAACTTTTA;RSEQ=TCTGTACCTCCTATACTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:7,0:47,0:0.1296:1,0:21.0:1.0:31.4:1.0:1.0:0.0:60.0:14.0:0.1321:0.0:1.0 0/0:48:0:0,0:47,1:0.0:1,0:24.5:1.0:31.5:1.0:1.0:0.0:60.0:47.0:1.0:0.0:0.0 -1 69777307 . A G 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01767;SOR=0.0;LSEQ=ATTGATTCTTTCTCGTCATG;RSEQ=GTTTGTCTACTTTCAGTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:8,6:0.2632:2,2:28.2:1.0:30.4:1.0:0.62848:1.92739:60.0:10.0:0.2632:0.0:1.4 0/0:21:0:0,0:12,9:0.0:2,0:20.8:1.0:29.7:1.0:1.0:0.0:59.0:42.0:1.0:0.0:0.0 -1 72058827 . G A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03794;SOR=0.0;LSEQ=TTAGTAGATTTGGGGGAGGT;RSEQ=AGGTTGCATGTCAGCTGTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:6:0,6:1,43:0.12:1,0:20.0:1.0:31.0:1.0:1.0:0.0:60.0:12.0:0.1224:0.0:2.0 0/0:36:0:0,0:2,34:0.0:2,0:23.9:1.0:31.4:1.0:1.0:0.0:60.0:35.0:1.0:0.0:0.6 -1 78414402 . GT G 80 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.00605;SOR=0.0;LSEQ=CATCCATATATTTAACAAAG;RSEQ=TTTTTTCCCCCACACAATGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:6:3,3:252,206:0.0129:2,2:29.7:1.0:31.3:1.0:1.0:1.22276:60.0:12.0:0.0131:0.0:0.2 0/0:621:0:0,0:347,274:0.0:2,0:27.1:1.0:28.6:1.0:1.0:0.0:60.0:35.529:1.0:0.0:0.2 -1 78432659 . T A 125 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTAGTTAGAAAAAAAAAAA;RSEQ=TTTTTTTTTGGTTGAAAGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:18:6,12:128,145:0.0594:2,2:13.7:1.0:30.0:1.0:0.33222:1.76219:60.0:36.0:0.0606:0.0:1.1 0/0:362:0:0,0:138,159:0.0:2,0:22.5:1.0:29.4:1.0:1.0:0.0:59.9:48.5:0.8244:0.0:0.3 -1 84971819 . G A 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.0087;SOR=0.0;LSEQ=TCGTGGGTCGGTGGGTCGTG;RSEQ=GCCGTGGGTCGGCGGGGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:1,5:6,13:0.24:2,2:24.0:1.0:28.7:1.0:0.63715:2.23947:60.0:5.0:0.2083:0.0:2.0 0/0:27:0:0,0:5,22:0.0:2,0:19.1:1.0:29.3:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.2 -1 85733704 . TA T 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.06218;SOR=0.0;LSEQ=GATGTAAATGAAAAAGTAAC;RSEQ=AAAAAATGGAGTCACTGTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:5:2,3:100,338:0.0113:2,2:35.6:1.0:30.4:1.0:0.32539:2.25:60.0:10.0:0.0115:0.0:0.0 0/0:421:0:0,0:97,324:0.0:2,0:22.0:1.0:29.0:1.0:1.0:0.0:60.0:59.143:1.0:0.0:0.1 -1 85739751 . T C 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.2719;SOR=0.0;LSEQ=ATGCTCTTCCCTCAGTTCTG;RSEQ=CAAATCTTTCAGGAATCAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:7,0:10,1:0.3889:2,0:22.4:1.0:31.9:1.0:1.0:0.0:60.0:14.0:0.3889:0.0:1.3 0/0:5:0:0,0:5,0:0.0:0,0:26.0:1.0:30.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -1 85739778 . A G 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01124;SOR=0.0;LSEQ=TTTCAGGAATCAGTTTAAAT;RSEQ=TAACCTCTCCTGACCATCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:10,1:23,0:0.3235:1,2:22.6:1.0:32.8:1.0:0.32353:0.0:60.0:22.0:0.3235:0.0:1.7 0/0:15:0:0,0:15,0:0.0:1,0:18.9:1.0:28.5:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 -1 85739861 . A G 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=4e-05;SOR=0.13736;LSEQ=ATTCCTTCATAGTAATTGCA;RSEQ=TAATGAAAACAAAATTTATT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:31:31,0:77,0:0.287:1,1:23.2:1.0:32.3:1.0:1.0:0.0:60.0:62.0:0.2897:0.0:1.2 0/1:77:4:4,0:73,0:0.0519:1,0:19.0:1.0:30.0:1.0:1.0:0.0:60.0:8.0:0.0526:0.0:1.0 -1 85741968 . G C 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGCCCGCCCTGGGCACAGCT;RSEQ=CGTTACTCACGTCCTTCTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1483:70:39,31:713,695:0.0472:2,2:26.2:1.0:31.5:1.0:0.46286:1.23:60.0:140.0:0.0483:0.0:1.6 0/0:1927:0:0,0:969,954:0.0:2,0:24.9:1.0:31.4:1.0:1.0:0.0:60.0:67.679:0.9984:0.0:0.8 -1 85742157 . G C 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.00185;SOR=0.0;LSEQ=GAGGAGGCGGAGCGGGTCGG;RSEQ=AGAAAGACGGCCGCCCCTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:10:0,10:14,223:0.04:2,0:27.9:1.0:30.9:1.0:1.0:0.0:60.0:9.0:0.0375:0.0:1.1 0/0:236:0:0,0:13,223:0.0:2,0:24.1:1.0:31.4:1.0:1.0:0.0:60.0:77.667:1.0:0.0:0.2 -1 90228304 . TCT GAAAAACGTAA 77 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.06061;SOR=0.0;LSEQ=CATTTCAGACCTGGGACTGG;RSEQ=GAAACTGTATAATGGAATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:1,5:0,2:0.75:0,2:18.7:1.0:29.9:1.0:1.0:0.0:59.2:12.0:0.75:0.375:1.3 0/0:3:0:0,0:1,2:0.0:2,0:13.0:1.0:30.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 -1 101971074 . T C 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTATACTGACCACTGGAGT;RSEQ=GGGCGACATGGCTTCTCCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:13:3,10:26,23:0.2097:2,2:27.9:1.0:30.5:1.0:0.06704:3.69123:60.0:26.0:0.2167:0.0:1.0 0/0:87:0:0,0:40,47:0.0:2,0:29.6:1.0:29.8:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.4 -1 117753543 . G A 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGCCGCTGCCTTCCTTGGT;RSEQ=ACTCACAACCAGCTCCCGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:48:9,39:98,256:0.1194:2,2:25.4:1.0:30.3:1.0:0.22493:1.65696:60.0:96.0:0.1224:0.0:1.0 0/0:337:0:0,0:108,229:0.0:2,0:22.4:1.0:30.6:1.0:1.0:0.0:60.0:47.143:1.0:0.0:0.1 -1 118156191 . T A 169 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.16973;LSEQ=CTGTGTGTTGGCTTCTCACT;RSEQ=CTTAGTGGGAAGTGAGAATT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:53:12,41:52,257:0.1464:2,2:22.5:1.0:29.6:1.0:0.33012:1.44:60.0:106.0:0.1489:0.0:1.1 0/1:248:7:0,7:50,191:0.0282:2,0:15.4:1.0:30.1:1.0:0.35031:0.0:60.0:14.0:0.0287:0.0:1.3 -1 118161094 . GTC G 226 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.11934;LSEQ=AGGCATTCTAAAGGAAAAGA;RSEQ=TCTCTTCCTCTGTTCATCCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:686:130:73,57:316,240:0.1895:2,2:28.9:1.0:32.2:1.0:0.92181:1.02805:60.0:260.0:0.1917:0.0131:0.2 0/1:664:18:9,9:350,295:0.0271:2,2:20.6:1.0:30.8:1.0:0.81224:1.18613:60.0:36.0:0.0274:0.0075:0.3 -1 118166096 . C T 225 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.14709;LSEQ=GACTGTTCCAATAATCCCAT;RSEQ=TCTGAGCACTTCCACCCCAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1143:189:86,103:455,499:0.1654:2,2:25.0:1.0:29.8:1.0:0.63246:1.09197:60.0:36.8:0.1636:0.0:1.1 0/1:1025:29:17,12:497,497:0.0283:2,2:24.4:1.0:29.9:1.0:0.45188:1.42:60.0:58.0:0.0286:0.0:1.1 -1 118166750 . A G 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00016;SOR=0.0;LSEQ=GCCTCCTTCTAGATGTAGGC;RSEQ=TTTGGCTTTTAAAGGGGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:20:1,19:0,32:0.3846:1,1:25.7:1.0:30.1:1.0:0.38462:0.0:60.0:9.0:0.3913:0.0:1.4 0/0:24:0:0,0:1,23:0.0:1,0:29.3:1.0:30.0:1.0:1.0:0.0:60.0:48.0:1.0:0.0:0.2 -1 120429402 . A G 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07847;SOR=0.0;LSEQ=CTCTCTTCTAGTTAGAGGGT;RSEQ=GAATTGGAAATTAAGAATTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:5:5,0:70,3:0.0641:1,0:27.0:1.0:33.0:1.0:1.0:0.0:60.0:10.0:0.0641:0.0:1.0 0/0:54:0:0,0:51,3:0.0:2,0:26.4:1.0:28.1:1.0:1.0:0.0:60.0:108.0:1.0:0.0:0.0 -1 120468134 . C T 224 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCCTCATCACAGACGCCATC;RSEQ=CGAGCTTTGTCGGCACAATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:969:176:80,96:352,440:0.1816:2,2:22.2:1.0:30.1:1.0:0.86691:1.04:60.0:34.2:0.1806:0.0:1.1 0/0:804:0:0,0:358,446:0.0:2,0:24.8:1.0:30.2:1.0:1.0:0.0:60.0:72.091:1.0:0.0:0.2 -1 120468487 . T C 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGTAGGAAAACAGTCATAT;RSEQ=GGAAGTTTGAGGTTTCTAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:32:3,29:14,95:0.227:2,2:26.6:1.0:29.1:1.0:0.7627:1.42131:60.0:31.0:0.223:0.0:1.2 0/0:154:0:0,0:34,119:0.0:2,0:22.0:1.0:29.8:1.0:1.0:0.0:60.0:152.0:0.9935:0.0:0.1 -1 120469388 . ACACT A 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.15209;SOR=0.0;LSEQ=AATCTGAGCATAGAAAGAAA;RSEQ=CACTGCATCTCAACATGATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:0,20:0.2:1,0:20.6:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.2:0.0:0.2 0/0:12:0:0,0:0,12:0.0:0,0:28.0:1.0:32.7:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.2 -1 120612040 . TCCG T 108 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.0;MSILEN=3.0;SSF=0.00626;SOR=0.09428;LSEQ=TCTTCTCGGTCGCCTCCTCC;RSEQ=CCGCCGCCGCCGCCGCCTGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:11:5,6:160,250:0.0227:2,2:38.5:1.0:31.4:1.0:0.75767:1.3:58.0:22.0:0.0266:0.0021:0.4 0/0:458:1:0,1:143,230:0.0022:2,0:32.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.0025:0.0:0.0 -1 121484092 . G A 70 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00278;SOR=0.08162;LSEQ=ATTCTCAGTAACTTCCTTGT;RSEQ=TTGTGTGTATTCAACTCACA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:3,2:17,14:0.1389:2,2:37.6:1.0:30.2:1.0:1.0:1.23:48.8:10.0:0.1389:0.0:1.6 0/1:157:2:1,1:95,60:0.0127:2,2:33.0:0.0:28.5:1.0:1.0:1.57849:49.0:4.0:0.0128:0.0:1.0 -1 121484526 . C G 78 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00075;SOR=0.0;LSEQ=TTGCAAGTGGAGATTTCAAG;RSEQ=GCTTTGGGGCCAAAGGCAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:6:2,4:60,56:0.0492:2,2:20.0:1.0:30.5:1.0:0.43555:2.12991:50.2:12.0:0.0492:0.0:4.0 0/0:277:0:0,0:144,131:0.0:2,0:24.2:1.0:30.7:1.0:1.0:0.0:51.9:90.667:0.9963:0.0:2.8 -1 121484565 . T G 81 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0137;SOR=0.19194;LSEQ=GAAAAGGAAATATCTTCGTA;RSEQ=AAAAACTAGACAGAATCATT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:7:5,2:75,69:0.0461:2,2:16.0:1.0:29.1:1.0:0.44805:2.29:45.3:6.0:0.04:0.0:4.1 0/0:328:3:1,2:173,152:0.0091:2,2:18.0:1.0:30.3:1.0:0.60226:2.27078:56.0:6.0:0.0092:0.0:3.7 -1 121484636 . T G 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=5.0;SSF=0.01274;SOR=0.14575;LSEQ=AACTCTCAGAGTTTAACTTT;RSEQ=CTTTTCATTCAGCAGTTTGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:6:3,3:97,93:0.0306:2,2:26.2:1.0:31.8:1.0:1.0:1.0428:57.2:12.0:0.0311:0.0:2.5 0/0:438:2:1,1:215,219:0.0046:2,2:24.0:1.0:31.5:1.0:1.0:1.02:60.0:4.0:0.0046:0.0:4.0 -1 121484728 . TC T 81 NM4 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.00096;SOR=0.0;LSEQ=CTTCTTTGGAAACGGTTTTT;RSEQ=TCATGTAAGGCTAGACAGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:6:4,2:0,0:0.0594:0,2:30.3:1.0:31.7:1.0:1.0:0.0:37.3:12.0:0.0612:0.0:5.2 0/0:215:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 121484749 . A G 98 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00014;SOR=0.07804;LSEQ=CTCATGTAAGGCTAGACAGA;RSEQ=GAATTCCCAGTAACTTCCTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:10:5,5:55,57:0.082:2,2:27.7:1.0:29.8:1.0:1.0:1.04:39.7:9.0:0.0744:0.0:5.6 0/0:291:2:1,1:152,137:0.0069:2,2:18.0:0.0:33.0:1.0:1.0:1.10909:51.0:4.0:0.0069:0.0:2.0 -1 121484973 . C T 95 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCTGTTCATAGAGCAGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:8:5,3:54,50:0.069:2,2:24.1:1.0:31.8:1.0:0.71972:1.54:55.5:16.0:0.069:0.0:5.0 0/0:338:0:0,0:161,173:0.0:2,0:36.0:0.0:17.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:4.0 -1 121485011 . T A 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00361;SOR=0.11496;LSEQ=GTTAGGAAACGCTCTGTTTG;RSEQ=AAAGTCTGTAAGTGGATATT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:123:7:3,4:59,57:0.0569:2,2:15.1:1.0:31.3:1.0:0.71733:1.37652:60.0:14.0:0.0569:0.0:3.9 0/0:292:2:2,0:132,158:0.0068:2,0:25.0:1.0:26.0:1.0:0.20974:0.0:60.0:4.0:0.0069:0.0:4.0 -1 121485042 . GT TGA 68 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.00242;SOR=0.0;LSEQ=AGTGGATATTCTGACATCTT;RSEQ=GGCCTTCGTTGGAAACGGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:5:5,0:63,61:0.0376:2,0:11.2:1.0:29.4:1.0:0.05949:0.0:34.2:10.0:0.0382:0.0301:3.2 0/0:306:0:0,0:144,145:0.0:2,0:24.1:1.0:31.5:1.0:1.0:0.0:56.6:288.0:0.9505:0.0:3.3 -1 121485236 . T C 82 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00392;SOR=0.1569;LSEQ=CAATGGTAGAAAAGGAAATA;RSEQ=CTTCGTATAGAAACAAGACA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:586:8:4,4:292,282:0.0137:2,2:28.0:1.0:27.6:1.0:1.0:1.03541:52.9:3.0:0.0103:0.0:6.1 0/0:1386:3:1,2:671,702:0.0022:2,2:16.3:1.0:32.7:1.0:1.0:1.91081:54.7:6.0:0.0022:0.0:5.0 -1 121485361 . A T 105 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00049;SOR=0.16187;LSEQ=CTCTGTTTGTAAAGTCTGCA;RSEQ=GTGGATATTCAGACCTCCTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:452:11:3,8:150,289:0.0243:2,2:21.1:1.0:30.4:1.0:0.75642:1.38314:53.1:22.0:0.0246:0.0:4.2 0/0:1245:5:2,3:478,759:0.004:2,2:30.0:1.0:30.4:1.0:1.0:1.06:47.8:10.0:0.0041:0.0:4.2 -1 121485390 . C T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0117;SOR=0.17197;LSEQ=TCAGACCTCCTTGAGGCCTT;RSEQ=GTTGGAAACGGGATTTCTTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:6:3,3:71,181:0.023:2,2:35.2:1.0:29.7:1.0:0.35817:2.54:49.0:12.0:0.0233:0.0:3.3 0/0:746:3:1,2:251,486:0.004:2,2:19.0:1.0:29.3:1.0:1.0:1.03288:50.3:6.0:0.0041:0.0:2.7 -1 144693358 . G A 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00076;SOR=0.0;LSEQ=AGCGTATCACAATGCTGCTC;RSEQ=GACTATGTTCAGACACTAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:14:9,5:14,6:0.4118:2,2:30.4:1.0:30.2:1.0:1.0:1.28632:29.1:28.0:0.4118:0.0:1.3 0/0:20:0:0,0:12,8:0.0:2,0:25.7:1.0:29.8:1.0:1.0:0.0:29.3:40.0:1.0:0.0:0.1 -1 145273701 . C T 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.34843;SOR=0.0;LSEQ=GTCAGGGCCAGGTGCGGTGG;RSEQ=GCACGCTTGCAATCCCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:9:1,8:3,62:0.1216:1,2:19.4:1.0:28.4:1.0:0.41159:2.54:36.1:18.0:0.1216:0.0:1.3 0/0:12:0:0,0:1,11:0.0:2,0:14.8:1.0:30.5:1.0:1.0:0.0:58.0:24.0:1.0:0.0:0.5 -1 145273705 . C T 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.58149;SOR=0.0;LSEQ=GGGCCAGGTGCGGTGGCGCA;RSEQ=GCTTGCAATCCCAGCATTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:6:1,5:1,57:0.0938:1,2:24.5:1.0:30.8:1.0:0.18006:10.5:43.8:12.0:0.0952:0.0:1.0 0/0:12:0:0,0:1,11:0.0:2,0:11.5:1.0:30.1:1.0:1.0:0.0:58.0:24.0:1.0:0.0:0.5 -1 148873205 . A T 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00721;SOR=0.0;LSEQ=TGATGTCTCTGTAGCAGCAA;RSEQ=CATTTAAGTTATTTGTTATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:15:14,1:131,5:0.0993:1,1:26.6:1.0:31.7:1.0:0.47218:1.86161:33.8:30.0:0.1:0.0:1.0 0/0:59:0:0,0:54,5:0.0:2,0:25.2:1.0:29.6:1.0:1.0:0.0:30.7:13.75:1.0:0.0:0.3 -1 148876318 . G A 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.33286;SOR=0.0;LSEQ=GTCTGGATTTCCAGGAAAGC;RSEQ=GAGACCTCGAGGTGCAGGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:5:0,5:215,212:0.0115:2,0:28.6:1.0:31.6:1.0:0.06107:0.0:23.8:10.0:0.0117:0.0:3.4 0/0:201:0:0,0:79,122:0.0:2,0:24.9:1.0:30.3:1.0:1.0:0.0:37.2:200.0:1.0:0.0:0.2 -1 148882036 . T C 243 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTTTTCTAGCAGTGACAAAT;RSEQ=CACTTTGAATCAGGTTTGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3080:237:117,120:1373,1468:0.0769:2,2:27.6:1.0:30.9:1.0:0.78685:1.04:38.7:58.25:0.0765:0.0:1.2 0/0:1873:0:0,0:906,967:0.0:2,0:25.9:1.0:29.4:1.0:1.0:0.0:40.9:116.063:1.0:0.0:0.2 -1 148888291 . G A 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.07411;LSEQ=TGTAGCAAAAAAAAAAAAAG;RSEQ=AAAATAGCTTTTCCTTAATC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:333:48:15,33:78,204:0.1441:2,2:21.8:1.0:26.9:1.0:0.60591:1.19:40.2:5.0:0.1429:0.0:1.8 0/1:244:3:3,0:85,156:0.0123:2,0:9.7:1.0:15.3:1.0:0.04589:0.0:44.7:0.0:0.0:0.0:1.7 -1 148889639 . G A 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGAAGTGGAAAATGTAGCA;RSEQ=ACATTGGTTTTGATTGTAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:4061:53:27,26:2134,1867:0.0131:2,2:29.5:1.0:30.1:1.0:0.78235:1.10065:39.3:52.0:0.0129:0.0:1.5 0/0:2385:0:0,0:1231,1153:0.0:2,0:27.1:1.0:31.1:1.0:1.0:0.0:41.6:87.296:0.9996:0.0:0.3 -1 148889774 . G A 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=5.0;SSF=5e-05;SOR=0.0;LSEQ=ATAACCAATGAATTAGCTTA;RSEQ=CTCTACTCTATTTTGTCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:30:1,29:15,684:0.0411:1,1:22.1:1.0:30.1:1.0:0.49315:1.57:29.2:60.0:0.0416:0.0:1.3 0/0:309:0:0,0:9,300:0.0:1,0:24.2:1.0:32.2:1.0:1.0:0.0:28.4:60.8:1.0:0.0:0.5 -1 148889823 . G A 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.19925;SOR=0.0;LSEQ=TACTTTGACAAGTATTTTAT;RSEQ=AAAAATATTATTGTTGGTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:7:0,7:3,270:0.025:1,0:30.3:1.0:31.1:1.0:1.0:0.0:34.4:14.0:0.0255:0.0:2.0 0/0:94:0:0,0:3,91:0.0:1,0:22.2:1.0:31.6:1.0:1.0:0.0:30.0:188.0:1.0:0.0:0.3 -1 148891116 . T C 76 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTCCTGCCTCAGCCTCACG;RSEQ=ACAGCTGGGATTACAGGTGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1.0:0,2:19.2:1.0:33.0:1.0:1.0:0.0:34.8:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 148891287 . A G 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAGGCATGAGCCCCCACAAC;RSEQ=GGCCCAGGAAGACCATTTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:29.0:1.0:30.6:1.0:1.0:0.0:31.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 149857797 . T C 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCGAGCGAGCGAGCGCCAGG;RSEQ=CCCGGCAGGGACTCACTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:23:14,9:38,25:0.2674:2,2:22.4:1.0:30.6:1.0:1.0:1.02:55.0:22.0:0.2588:0.0:1.1 0/0:57:0:0,0:35,22:0.0:2,0:27.0:1.0:29.1:1.0:1.0:0.0:56.2:114.0:1.0:0.0:0.1 -1 150552042 . G A 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.08189;LSEQ=CCGCCTGGCTGAGAAAACTG;RSEQ=GGAAGACCCCGACTCCTTAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:571:337:106,231:75,157:0.5902:2,2:22.1:1.0:30.4:1.0:0.85487:1.041:60.0:32.7:0.586:0.0:1.2 0/1:532:56:15,41:157,317:0.1053:2,2:20.4:1.0:30.2:1.0:0.36905:1.35298:60.0:55.0:0.1048:0.0:1.2 -1 152330829 . G T 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTAGATGGAATAAAATGCT;RSEQ=GCATTTTATTTTTGATTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:79:56,23:134,43:0.3086:2,2:21.9:1.0:30.0:1.0:0.44125:1.2786:60.0:158.0:0.3123:0.0:1.1 0/0:145:0:0,0:105,40:0.0:2,0:21.2:1.0:31.2:1.0:1.0:0.0:60.0:144.0:1.0:0.0:0.1 -1 152331013 . G A 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0001;SOR=0.06305;LSEQ=AAAGTCTGAGAGTCTATGAG;RSEQ=TAGGAGTGCATAGGTGGAAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:26:7,19:46,140:0.1226:2,2:22.5:1.0:30.3:1.0:0.81109:1.12:60.0:52.0:0.125:0.0:1.1 0/0:115:1:1,0:28,86:0.0087:2,0:1.0:0.0:25.0:0.0:0.25217:0.0:60.0:2.0:0.0087:0.0:1.0 -1 156785653 . C G 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ACTCCTCATTTTCGTTCTCT;RSEQ=TCTCTGTGCCCCAGCCCGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1266:43:17,26:547,672:0.034:2,2:28.6:1.0:32.4:1.0:0.53505:1.24471:60.0:42.0:0.0335:0.0:1.9 0/0:988:0:0,0:463,524:0.0:2,0:25.7:1.0:31.4:1.0:1.0:0.0:60.0:108.667:0.999:0.0:0.7 -1 156838809 . TC T 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCGTACATCACTTTTCTCTC;RSEQ=CCTTCCTTCCTTCCTTCCTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:1,5:0,0:0.8571:0,2:29.5:1.0:29.4:1.0:1.0:0.0:52.7:12.0:1.0:0.1429:0.5 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 156848778 . C T 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.004;SOR=0.0;LSEQ=ACCCCTCTGGACAGCTGCCT;RSEQ=TACTGTTCTCTCAATCCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:20:20,0:92,1:0.177:1,1:25.5:1.0:29.5:1.0:1.0:0.0:59.8:19.0:0.1712:0.0:3.1 0/0:38:0:0,0:37,1:0.0:1,0:26.5:1.0:30.8:1.0:1.0:0.0:60.0:37.0:1.0:0.0:1.6 -1 156849047 . G T 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=ACCTGGCGGGTCTGCATTTT;RSEQ=TGCACCGGGACCTGGCCACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1255:27:14,13:656,570:0.0215:2,2:21.8:1.0:29.6:1.0:1.0:1.06859:60.0:26.0:0.021:0.0:1.4 0/0:678:0:0,0:369,308:0.0:2,0:23.4:1.0:31.3:1.0:1.0:0.0:60.0:60.545:0.9985:0.0:0.4 -1 156849505 . G A 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTGACTCCCTGGTTCAAGC;RSEQ=ATTCTCCTGCTTCAGCCTCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:4,1:8,6:0.2632:2,2:12.4:1.0:29.4:1.0:0.60268:2.84:57.4:10.0:0.2632:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 156849658 . C T 107 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.11847;SOR=0.0;LSEQ=TGATTGCCCACCTCGGCCTC;RSEQ=CAAAGTGCTGGGATTACAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:11:10,1:90,0:0.1089:1,2:30.0:1.0:31.1:1.0:0.10891:0.0:60.0:22.0:0.1146:0.0:1.1 0/0:26:0:0,0:25,1:0.0:1,0:28.5:1.0:30.0:1.0:1.0:0.0:59.3:52.0:1.0:0.0:0.2 -1 157599882 . C A 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAGCAGAACTGGAGCTGGA;RSEQ=TTCTGATCTCTCTAGAGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:32:18,14:115,87:0.1368:2,2:26.6:1.0:30.9:1.0:1.0:1.02799:60.0:64.0:0.1379:0.0:3.0 0/0:204:0:0,0:114,87:0.0:2,0:26.6:1.0:31.2:1.0:1.0:0.0:60.0:99.5:0.9851:0.0:0.9 -1 162736690 . C T 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATTAGCCGGGCGTAGTGG;RSEQ=GCATGCCTGTAATCCCAGCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:2,0:0.8:0,0:28.1:1.0:29.5:1.0:1.0:0.0:55.4:16.0:0.8:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 162737241 . A G 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00223;SOR=0.0;LSEQ=GTAAAAGGCAAATTGCAAAC;RSEQ=TTTATTAATGGTTGGAATTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:18:0,18:7,148:0.104:1,1:25.9:1.0:29.1:1.0:1.0:0.0:60.0:8.0:0.0982:0.0:1.2 0/0:71:0:0,0:3,68:0.0:1,0:20.3:1.0:30.1:1.0:1.0:0.0:60.0:142.0:1.0:0.0:0.0 -1 162740121 . G A 231 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.14744;LSEQ=AGGATGCTGGATGATGAAAT;RSEQ=ACAGTCAGCCTTTCCCTGCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1057:262:179,83:477,317:0.2479:2,2:24.5:1.0:28.8:1.0:0.01871:1.43:60.0:130.0:0.2488:0.0:1.1 0/1:756:35:21,14:420,301:0.0463:2,2:27.5:1.0:28.1:1.0:0.86293:1.07:60.0:34.0:0.0452:0.0:1.2 -1 162830985 . CCCTCCCTA C 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACTTGAAAGCTCTCTTCGT;RSEQ=CCTCCCCTGGTCAGGAATGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:3,0:0.6667:0,0:25.5:1.0:32.0:1.0:1.0:0.0:60.0:12.0:0.6667:0.1111:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 165044147 . G A 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTGTTTGTTTATTTTTTGG;RSEQ=AATAGCGCAAATGTTCTACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:62:11,51:8,38:0.5741:2,2:22.3:1.0:30.6:1.0:1.0:1.02:60.0:124.0:0.5741:0.0:1.1 0/0:75:0:0,0:18,57:0.0:2,0:25.0:1.0:30.8:1.0:1.0:0.0:60.0:74.0:1.0:0.0:0.2 -1 168652905 . G C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00445;SOR=0.0;LSEQ=TGTATAGGGTGTCTGACAAC;RSEQ=CCTGTTGGAGGGTCTCACCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:5,3:5,5:0.4444:2,2:24.1:1.0:28.6:1.0:0.66406:1.62:60.0:7.0:0.4118:0.0:1.5 0/0:14:0:0,0:9,5:0.0:2,0:12.5:1.0:29.1:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.4 -1 171207335 . C T 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00279;SOR=0.0;LSEQ=GATATCTCCAGGCACAGGAG;RSEQ=GAATCAGATGAATAAGACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:5,4:4,2:0.6:2,2:22.7:1.0:28.3:1.0:1.0:1.5508:60.0:18.0:0.6:0.0:1.7 0/0:10:0:0,0:4,6:0.0:2,0:32.0:1.0:31.0:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.7 -1 173485336 . C T 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTTGTCCCTTGGTCTTTGG;RSEQ=TCATTTCTATTTGAATTCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:19:7,12:7,4:0.6333:2,2:23.4:1.0:29.8:1.0:0.25677:2.88672:60.0:38.0:0.6333:0.0:1.1 0/0:27:0:0,0:14,13:0.0:2,0:27.9:1.0:31.6:1.0:1.0:0.0:60.0:54.0:1.0:0.0:0.1 -1 175869807 . C G 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06479;SOR=0.0;LSEQ=ACATTGTGCAACTCAGTGAG;RSEQ=CCTCACACATTGAACACATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:0.4118:0,0:22.1:1.0:29.4:1.0:1.0:0.0:60.0:6.0:0.375:0.0:1.3 0/0:7:0:0,0:0,7:0.0:0,0:19.9:1.0:31.4:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.1 -1 175958637 . T A 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00047;SOR=0.0;LSEQ=TAAAACAAAACAAAATTAGA;RSEQ=AAATGTAGTAAATGCAGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:17:4,13:85,372:0.0359:2,2:19.3:1.0:28.4:1.0:0.5385:1.35:60.0:7.5:0.0325:0.0:1.3 0/0:293:0:0,0:59,233:0.0:2,0:23.1:1.0:28.0:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 -1 176050676 . A T 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCAATAATTCCTTGGAAAAA;RSEQ=AATAATAACAATAATAATAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:17.3:1.0:29.2:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 176085412 . C G 75 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCATAGGGCCAGCTACTTGA;RSEQ=AGGCTGAGGTAGGAGAATTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:13.2:1.0:32.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 176103954 . C T 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.57425;SOR=0.0;LSEQ=TAACATTATAGTATTCTACT;RSEQ=GCTAACTCTTCCTGGCATGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:8:8,0:38,1:0.1702:1,0:25.5:1.0:30.3:1.0:1.0:0.0:60.0:16.0:0.1778:0.0:1.0 0/0:6:0:0,0:6,0:0.0:0,0:22.3:1.0:32.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -1 176175885 . C A 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00227;SOR=0.0;LSEQ=TGGACACCGCCCCGCCGCCG;RSEQ=TACCCGATACGGCGGGCGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:13:5,8:49,176:0.0546:2,2:24.8:1.0:31.1:1.0:0.17753:2.24:60.0:26.0:0.0563:0.0:1.3 0/0:153:0:0,0:51,102:0.0:2,0:20.3:1.0:32.3:1.0:1.0:0.0:60.0:152.0:1.0:0.0:0.3 -1 181819068 . G A 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.28871;SOR=0.0;LSEQ=ACATTTCCAGGCATGGAAGC;RSEQ=AATCAGATGAATAGGGCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:3,3:6,8:0.3:2,2:33.7:1.0:30.5:1.0:1.0:1.31:60.0:12.0:0.3:0.0:1.0 0/0:5:0:0,0:3,2:0.0:2,0:17.0:1.0:33.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.6 -1 181819202 . C T 129 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=5e-05;SOR=0.0;LSEQ=AAAAATAACAACAAAACGGG;RSEQ=CCCCACAAAAACCCCATCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:22:11,11:42,38:0.2157:2,2:27.7:1.0:29.0:1.0:1.0:1.10418:60.0:44.0:0.2178:0.0:2.6 0/0:55:0:0,0:27,28:0.0:2,0:27.9:1.0:30.0:1.0:1.0:0.0:59.7:54.0:1.0:0.0:1.6 -1 184327323 . T G 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAAGAAAAAGTAAGAATATA;RSEQ=TCTTCTTAATAACCTTCACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:76:28,48:71,145:0.2603:2,2:25.8:1.0:31.0:1.0:0.57385:1.19:60.0:24.333:0.2544:0.0:1.1 0/0:150:0:0,0:48,101:0.0:2,0:22.5:1.0:29.4:1.0:1.0:0.0:60.0:48.667:0.9932:0.0:0.3 -1 185520654 . C G 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00031;SOR=0.0;LSEQ=TGTGAAGTTTCTGCAACAGT;RSEQ=CTATGGTCTTTCACCTTCGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:614:23:6,17:173,417:0.0375:2,2:22.9:1.0:29.9:1.0:0.81969:1.17515:60.0:10.5:0.0347:0.0:1.0 0/0:281:0:0,0:89,192:0.0:2,0:23.2:1.0:30.8:1.0:1.0:0.0:60.0:139.5:1.0:0.0:0.4 -1 193091490 . G T 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00011;SOR=0.0;LSEQ=GGCATGGCTGTGGCCCAGGG;RSEQ=TGGCAGGGCAGAGTTGGGCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:767:21:6,15:224,521:0.0274:2,2:22.0:1.0:29.8:1.0:1.0:1.07476:60.0:42.0:0.0276:0.0:1.2 0/0:422:0:0,0:132,290:0.0:2,0:22.8:1.0:30.5:1.0:1.0:0.0:60.0:104.5:1.0:0.0:0.1 -1 193104712 . G A 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCAGAAGCAAAGAAACCAC;RSEQ=AATTGAGGTAAAGAAACTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:815:134:45,89:268,413:0.1644:2,2:28.6:1.0:30.1:1.0:0.24362:1.28301:60.0:66.0:0.1632:0.0:1.1 0/0:525:0:0,0:219,306:0.0:2,0:26.5:1.0:30.1:1.0:1.0:0.0:60.0:74.0:1.0:0.0:0.1 -1 193105216 . A G 74 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTTTCCGTGTTGGCCAGGCT;RSEQ=CAGAATTCTTTCTTTATGAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:32.8:1.0:32.0:1.0:1.0:0.0:58.2:10.0:1.0:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 193173335 . GTGTATATATA G 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=4.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ACACACACACATATATATAC;RSEQ=TGTATATATATGTATATATA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:30.6:1.0:29.2:1.0:1.0:0.0:55.2:10.0:0.625:0.125:2.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 193173356 . TG CA 74 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTATATATATGTATATATA;RSEQ=TATATATACACGTATATATA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:35.4:1.0:32.2:1.0:1.0:0.0:55.2:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 193202953 . G A 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=AACACTTTTATTGAATTTAA;RSEQ=TGTCCTTTAACAAAATATTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1.0:0,2:14.6:1.0:30.3:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 193203035 . C T 104 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.26154;SOR=0.0;LSEQ=AATTACCTTATTTCTTTAAC;RSEQ=GGGAGTAAAAGTTGAGTATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:9,1:13,0:0.4348:1,2:28.5:1.0:31.5:1.0:0.43478:0.0:60.0:20.0:0.4348:0.0:1.2 0/0:3:0:0,0:3,0:0.0:0,0:23.3:1.0:30.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 -1 193203268 . C T 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=6e-05;SOR=0.0;LSEQ=CTTAAACTTATGCCTCAAGA;RSEQ=TGGTAGGATAATTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:22:7,15:224,325:0.0383:2,2:18.1:1.0:30.4:1.0:0.50837:1.47596:59.8:44.0:0.0411:0.0:1.0 0/0:326:0:0,0:131,194:0.0:2,0:23.4:1.0:30.0:1.0:1.0:0.0:59.5:13.773:1.0:0.0:0.5 -1 193203305 . TCACACACACACACA T 191 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=23.0;MSILEN=2.0;SSF=0.0;SOR=0.13326;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CACACACACACACACACACA;STATUS=AFDiff GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:262:83:9,74:53,54:0.3168:2,2:28.0:1.0:30.1:1.0:0.0:7.98056:57.3:19.75:0.3251:0.1527:0.7 0/1:138:8:0,8:36,74:0.058:2,0:33.1:1.0:30.4:1.0:0.10418:0.0:56.9:16.0:0.0606:0.0072:0.8 -1 193203368 . T G 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.18006;SOR=0.0;LSEQ=CACATATATATATTTAAAAT;RSEQ=TATATATTTATTTATATATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:0,6:1,75:0.0732:1,0:11.8:1.0:32.8:1.0:1.0:0.0:54.8:12.0:0.0759:0.0:2.0 0/0:33:0:0,0:0,33:0.0:1,0:27.5:1.0:30.3:1.0:1.0:0.0:57.8:66.0:1.0:0.0:0.8 -1 193203397 . T TTATAATATATATAATTTATTATATATATATTATA 111 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=4.0;MSILEN=2.0;SSF=0.00059;SOR=0.0;LSEQ=TATTTATATATATAATTTAA;RSEQ=TATAATATATATAATATACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:14:1,13:0,16:0.4667:1,1:20.4:1.0:29.4:1.0:0.46667:0.0:57.1:28.0:0.5185:0.3333:0.5 0/0:18:0:0,0:0,18:0.0:1,0:16.9:1.0:30.5:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.4 -1 198167287 . T C 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01067;SOR=0.0;LSEQ=GTGGGGGGATATGGATTTGG;RSEQ=CCTGGCTGGCCGGCATTGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:2,10:9,16:0.3243:2,2:21.9:1.0:30.3:1.0:0.27934:2.74057:60.0:11.0:0.3235:0.0:1.0 0/0:17:0:0,0:7,10:0.0:2,0:23.8:1.0:29.5:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.1 -1 202188932 . A G 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTCATTCTATACTAATAATT;RSEQ=TAATTCAGTTAGATGAGTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:1,3:0.5556:2,0:28.8:1.0:31.6:1.0:0.44444:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:44.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -1 203224985 . G T 60 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0614;SOR=0.0;LSEQ=ACCAGTTATCTTTAATAACG;RSEQ=CCAGTTTAGGGGCTGCTACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:3,2:36,28:0.0725:2,2:21.8:1.0:26.0:1.0:1.0:1.16:60.0:4.0:0.0597:0.0:1.0 0/0:59:0:0,0:26,33:0.0:2,0:27.3:1.0:31.0:1.0:1.0:0.0:59.9:118.0:1.0:0.0:0.1 -1 204316213 . G A 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.0;MSILEN=1.0;SSF=0.00014;SOR=0.0;LSEQ=TAGACTCTTCCAGTTTTGCC;RSEQ=TGGTAACGCGTGTGGGGCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:25:11,14:92,123:0.1042:2,2:23.8:1.0:30.0:1.0:1.0:1.05:45.4:24.0:0.1004:0.0:1.1 0/0:104:0:0,0:45,59:0.0:2,0:26.6:1.0:30.4:1.0:1.0:0.0:59.6:103.0:1.0:0.0:0.1 -1 204495610 . G T 86 LongAT SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00176;SOR=0.0;LSEQ=TTTTTGTTTTTTTTTTTTTT;RSEQ=AGATGGAGTCTCCCTCTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:10:5,5:33,158:0.0495:2,2:6.2:1.0:26.1:1.0:0.02287:4.74:60.0:4.0:0.0457:0.0:1.4 0/0:195:0:0,0:39,150:0.0:2,0:19.0:1.0:29.1:1.0:1.0:0.0:58.4:8.45:0.9826:0.0:1.1 -1 204511602 . C A 80 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CCATTTAGAAATTCTTTTAG;RSEQ=ACAAGGTCATTGTTCAGATG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:9.0:1.0:31.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 206648147 . T G 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11969;LSEQ=GCTCCAGGCTGAGCCACTTC;RSEQ=TCCTGGTGGGTGGGGAGGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:119:89,30:214,73:0.2924:2,2:24.8:1.0:30.3:1.0:1.0:1.01:60.0:118.0:0.2935:0.0:1.1 0/1:234:11:8,3:157,66:0.047:2,2:27.8:1.0:29.8:1.0:1.0:1.12:60.0:10.0:0.0439:0.0:1.2 -1 206650065 . A G 256 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTGCTTCGAAAGCCCCAGCA;RSEQ=AAAGCGTTCGGGGTGACTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1088:277:161,116:447,364:0.2546:2,2:25.7:1.0:31.6:1.0:0.40086:1.13:60.0:91.333:0.2537:0.0:1.1 0/0:817:0:0,0:422,395:0.0:2,0:25.1:1.0:29.7:1.0:1.0:0.0:60.0:101.125:1.0:0.0:0.2 -1 206669136 . C A 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATCCATTTAAACTCCTTTC;RSEQ=CCTCCTAAACCTTGGCTACA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:24.4:1.0:30.4:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 206944952 . T G 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.18394;SOR=0.0;LSEQ=TCACTTAAATCAGGTCCTCC;RSEQ=CCTCAGAGTCAAGTTATTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:8:0,8:1,31:0.2:1,0:27.9:1.0:33.4:1.0:1.0:0.0:60.0:16.0:0.2051:0.0:1.3 0/0:10:0:0,0:1,9:0.0:2,0:22.2:1.0:29.8:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 -1 221053574 . A C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.03088;SOR=0.0;LSEQ=TACCACCACCATCACCCGCA;RSEQ=CAACAACAGCAGCAGCAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:5,1:54,46:0.0566:2,2:25.2:1.0:33.0:1.0:0.22369:4.21:60.0:12.0:0.0577:0.0:1.0 0/0:93:0:0,0:57,36:0.0:2,0:24.2:1.0:29.4:1.0:1.0:0.0:60.0:186.0:1.0:0.0:0.3 -1 222642304 . A G 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.57406;SOR=0.0;LSEQ=GAGCGGAGCATATCAGAGAC;RSEQ=GGCACTGCCACTGCCCCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:5:1,4:22,23:0.1:2,2:14.0:1.0:31.2:1.0:0.35734:3.73625:34.2:10.0:0.102:0.0:1.0 0/0:13:0:0,0:7,6:0.0:2,0:25.1:1.0:29.5:1.0:1.0:0.0:36.0:12.0:1.0:0.0:0.2 -1 224135537 . A G 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.50893;SOR=0.0;LSEQ=GAGTGTCCACCAGGTGGGAC;RSEQ=GGGAGCGTTGACCCTGGGCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:4,1:3,5:0.3846:2,2:11.6:1.0:30.0:1.0:0.26573:5.7:33.2:10.0:0.4167:0.0:1.4 0/0:3:0:0,0:2,1:0.0:2,0:6.3:1.0:28.0:1.0:1.0:0.0:28.7:6.0:1.0:0.0:0.3 -1 224135680 . G T 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00358;SOR=0.07228;LSEQ=GCCCTGGGCCCCTCAGGGGA;RSEQ=TCCCTGCTGGACAGTGACAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:13:11,2:15,3:0.4194:2,2:29.6:1.0:29.2:1.0:1.0:1.1:37.9:12.0:0.4:0.0:1.4 0/1:21:1:0,1:17,3:0.0476:2,0:33.0:0.0:27.0:0.0:0.19048:0.0:40.0:2.0:0.0476:0.0:1.0 -1 226253926 . T C 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CTTCAGGTCCTGAAGAAACA;RSEQ=ATAGGTAGAGAGAGCTTAAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:18.6:1.0:32.8:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 226254036 . T C 59 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAGGATTGGATTGGCAAGAT;RSEQ=GGGGGAACGGTGCTTAAAGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:23.8:1.0:25.8:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 226551178 . A G 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCAGACCCCTGGCCTTTTAC;RSEQ=TGACCTTGTGCTTTTGGTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:1,4:2,10:0.2941:2,2:28.6:1.0:32.4:1.0:1.0:1.23:60.0:10.0:0.3333:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:43.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -1 226553467 . C CA 70 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.55991;SOR=0.0;LSEQ=GATAGAGTGAGACTCCATGT;RSEQ=AAAAAAAAAAACAAAAAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:23,1:0.1667:1,0:17.8:1.0:30.2:1.0:1.0:0.0:56.0:10.0:0.1724:0.0667:2.0 0/0:7:0:0,0:7,0:0.0:0,0:19.9:1.0:29.6:1.0:1.0:0.0:57.4:6.0:1.0:0.0:2.0 -1 226554736 . G C 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCACCAGAGAAAAATGAAC;RSEQ=CAAGCATTGTGTTTTTATTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:21.4:1.0:30.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 226554951 . T C 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCAAGCTGAGGTGCTGGCT;RSEQ=GGAAGGCTGCCTTGCAAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:6:6,0:29,0:0.1714:1,0:23.7:1.0:30.3:1.0:1.0:0.0:60.0:12.0:0.1765:0.0:1.0 0/0:4:0:0,0:4,0:0.0:0,0:25.0:1.0:28.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -1 226567172 . A C 178 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.14824;LSEQ=GTGAGGACAAAGGCACGACC;RSEQ=CACTGCCCCAGGTATGCTGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:58:47,11:138,48:0.2367:2,2:22.3:1.0:30.4:1.0:0.37984:1.48:60.0:18.333:0.2301:0.0:1.0 0/1:137:6:6,0:111,19:0.0438:2,0:28.5:1.0:30.8:1.0:0.59491:0.0:60.0:12.0:0.0451:0.0:1.0 -1 226595403 . A AGGGCCC 100 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=3.0;MSILEN=1.0;SSF=0.14987;SOR=0.0;LSEQ=AGGCCCCAAGTGCCGCTCCG;RSEQ=GGGCCCGGGCCCGCTCGCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:8,1:17,0:0.3462:1,2:15.0:1.0:31.7:1.0:0.34615:0.0:60.0:18.0:0.3462:0.0769:0.0 0/0:6:0:0,0:6,0:0.0:0,0:8.3:1.0:30.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -1 228613442 . G A 72 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGTTTCACTCTTGTTGCCCA;RSEQ=GCTGGAGTGCAATAGCGTGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:22.0:1.0:28.0:1.0:1.0:0.0:43.8:5.0:1.0:0.0:1.7 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 228613471 . T C 82 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCAATAGCGTGATCTCTGCT;RSEQ=ACTGCAACCTCCACCTCCCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:21.8:1.0:31.8:1.0:1.0:0.0:41.2:12.0:1.0:0.0:1.7 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 228617397 . G A 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGAGATTTCCTCTGCAAACT;RSEQ=AAGAGAATGTGAGATACAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:46:45,1:301,8:0.1296:1,1:20.8:1.0:28.5:1.0:1.0:1.2:60.0:92.0:0.1311:0.0:1.2 0/0:120:0:0,0:119,1:0.0:1,0:23.6:1.0:31.8:1.0:1.0:0.0:60.0:39.0:1.0:0.0:0.3 -1 229106423 . C CTG 138 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.00297;SOR=0.1238;LSEQ=CAGCTGGTGAAGTAAGTACT;RSEQ=TGGATGGTGGCGACTCTGGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:20:9,11:14,15:0.4082:2,2:27.1:1.0:32.1:1.0:1.0:1.13768:59.8:40.0:0.4082:0.0408:0.2 0/1:26:2:1,1:15,8:0.0769:2,2:26.0:0.0:31.5:1.0:1.0:1.82581:60.0:4.0:0.0769:0.0:0.5 -1 229223719 . G C 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.36364;SOR=0.0;LSEQ=GGGGTTTCAAGAAAGGCTCA;RSEQ=AGTCAGCCTCACTTCAGGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,1:0.7:2,0:39.7:1.0:32.9:1.0:0.3:0.0:60.0:14.0:0.7:0.0:1.0 0/0:1:0:0,0:1,0:0.0:0,0:24.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -1 230355441 . G A 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTCTTGAGACTTCTGACGT;RSEQ=GATGCATTCCAGATGTGGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:114:56,58:154,162:0.2651:2,2:26.5:1.0:29.4:1.0:1.0:1.02:60.0:56.0:0.2623:0.0:2.1 0/0:304:0:0,0:143,161:0.0:2,0:25.8:1.0:30.3:1.0:1.0:0.0:60.0:75.0:1.0:0.0:0.4 -1 230355471 . G A 62 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07843;SOR=0.0;LSEQ=CAGATGTGGGGGCATTCTTT;RSEQ=CAAAGTGCTTGTGGCTGTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:5:3,2:162,221:0.0129:2,2:24.2:1.0:27.0:1.0:0.65449:2.04:60.0:10.0:0.0129:0.0:1.8 0/0:279:0:0,0:120,159:0.0:2,0:26.2:1.0:31.3:1.0:1.0:0.0:60.0:68.75:1.0:0.0:0.3 -1 230724588 . G GGTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA 167 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=37;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=AGTAGGTAGGTGTGTGGATA;RSEQ=GTAGGTGTGCAGGTAAGTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:49:12,37:33,30:0.4261:2,2:23.3:1.0:29.9:1.0:0.00355:3.35363:59.8:98.0:0.4414:0.3391:0.1 0/0:58:0:0,0:19,28:0.0:2,0:18.1:1.0:30.3:1.0:1.0:0.0:59.4:22.5:0.9574:0.0:0.7 -1 241669668 . C T 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTTTATAGAACCATAAGGTA;RSEQ=GACAATGCCACTGATAACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:0,5:1,21:0.1852:1,0:18.4:1.0:30.2:1.0:1.0:0.0:60.0:10.0:0.1852:0.0:2.2 0/0:3:0:0,0:0,3:0.0:0,0:18.7:1.0:29.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 -1 242508644 . G A 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTTCCTAATTTCAAAGTCC;RSEQ=TGGTTGTTAACTGCGTTAGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:1.0:0,0:18.8:1.0:30.2:1.0:1.0:0.0:40.1:20.0:1.0:0.0:2.5 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -1 242508928 . C A 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00018;SOR=0.0;LSEQ=CCTCTGTTGGCAGAATATGA;RSEQ=TTTCAGAAGGATTCTGTCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:17:8,9:172,223:0.0413:2,2:19.9:1.0:30.0:1.0:0.80679:1.15:40.5:34.0:0.0415:0.0:1.1 0/0:286:0:0,0:146,140:0.0:2,0:24.0:1.0:31.3:1.0:1.0:0.0:35.5:285.0:1.0:0.0:0.1 -1 243809488 . C T 109 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.06046;SOR=0.0;LSEQ=CATACACTCTCACCATCACC;RSEQ=CAAAGTGAAAATAATCCTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:12:1,11:0,53:0.1846:1,2:25.9:1.0:30.6:1.0:0.18462:0.0:60.0:24.0:0.1905:0.0:1.3 0/0:18:0:0,0:0,18:0.0:1,0:24.8:1.0:30.3:1.0:1.0:0.0:60.0:17.0:1.0:0.0:0.1 -1 247555079 . A G 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00059;SOR=0.0;LSEQ=CCTTATAAAATCCAGCTTTA;RSEQ=CAAGAATCCTGCTAAGTCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:15:6,9:9,24:0.3125:2,2:23.9:1.0:32.3:1.0:0.50411:1.76:60.0:30.0:0.3125:0.0:1.1 0/0:28:0:0,0:9,19:0.0:2,0:21.4:1.0:29.1:1.0:1.0:0.0:60.0:56.0:1.0:0.0:0.1 -1 248567502 . T TGTGTGTGGCAGAGGCCGCTATTACATGTAC 77 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=8.0;MSILEN=2.0;SSF=0.28327;SOR=0.0;LSEQ=TGCTATTACATATACGTGTG;RSEQ=GTGTGTGTGTATAAAATGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:3,4:3,3:0.35:2,2:26.4:1.0:27.6:1.0:1.0:1.30401:60.0:6.0:0.5:0.35:1.3 0/0:4:0:0,0:2,2:0.0:2,0:8.3:1.0:30.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:1.8 -10 3280619 . T C 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01242;SOR=0.0;LSEQ=GTGCTAGTCTGGAAGTGGAG;RSEQ=CTGGAGCTTAGATTAGAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:4,2:237,213:0.0131:2,2:18.3:1.0:32.0:1.0:0.68851:1.8:60.0:12.0:0.0135:0.0:1.2 0/0:490:0:0,0:252,238:0.0:2,0:23.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 -10 8100647 . C T 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02231;LSEQ=TCCCGTGGCAGCATGACCGC;RSEQ=CTGGGTGGAGCCTCCTCGTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:950:39:19,20:446,465:0.0411:2,2:27.3:1.0:30.3:1.0:1.0:1.00961:60.0:38.0:0.0409:0.0:1.1 0/0:1050:1:0,1:529,519:0.001:2,0:1.0:0.0:25.0:0.0:0.49571:0.0:60.0:2.0:0.001:0.0:1.0 -10 8106274 . C T 113 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=17.0;MSILEN=1.0;SSF=0.00021;SOR=0.0;LSEQ=TTCTTTCTTTTCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTTTTCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:0,13:0,0:0.8667:0,1:17.4:1.0:30.8:1.0:1.0:0.0:58.4:26.0:1.0:0.0:3.7 0/0:7:0:0,0:0,2:0.0:0,0:14.5:1.0:22.0:1.0:1.0:0.0:51.5:1.0:1.0:0.0:3.5 -10 8111168 . C T 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAAGACTGCCAGGGAGGAGG;RSEQ=CCCGGCTTCCTGCTCCTACC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:21.8:1.0:30.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -10 8111850 . GA G 78 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.03333;SOR=0.0;LSEQ=GGGCCTGTGTGGTTTATAAG;RSEQ=AAAAAAAAAAATCTTCCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,0:0.8571:0,0:31.3:1.0:30.5:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:0.7 0/0:3:0:0,0:1,2:0.0:2,0:24.0:1.0:29.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:1.7 -10 8116079 . C T 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GCAGTATCATGAAGCCTAAA;RSEQ=GCGATGGATATATGTTTTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:40:0,40:0,19:0.678:1,1:17.7:1.0:30.3:1.0:1.0:0.0:60.0:19.0:0.6667:0.0:1.1 0/0:29:0:0,0:3,26:0.0:2,0:23.0:1.0:29.0:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.2 -10 9959556 . C T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.0;MSILEN=1.0;SSF=0.02718;SOR=0.0;LSEQ=ATGTTTTAAATATATCCTGT;RSEQ=TAAAATAGAAATCAAAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:6,1:13,1:0.3333:1,2:15.1:1.0:31.4:1.0:1.0:2.08171:60.0:14.0:0.35:0.0:1.0 0/0:14:0:0,0:13,0:0.0:1,0:19.5:1.0:32.1:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.0 -10 10923431 . T A 246 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00918;LSEQ=GCTGTTAGTAAAATATGAGA;RSEQ=ACTTCAAACTTAATGCCTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:349:327:180,147:11,11:0.937:2,2:25.0:1.0:29.5:1.0:0.66439:1.22:60.0:35.333:0.9353:0.0:1.1 0/1:445:53:27,26:192,200:0.1191:2,2:29.5:1.0:29.4:1.0:0.8838:1.08:60.0:52.0:0.119:0.0:1.3 -10 15009109 . T C 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00879;SOR=0.0;LSEQ=TGGGAGAAGAGGTGGTCGTT;RSEQ=AGCTGGGCACATTCAGAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:11:11,0:1,0:0.9167:0,0:27.5:1.0:31.7:1.0:1.0:0.0:60.0:22.0:0.9167:0.0:2.3 0/0:3:0:0,0:2,1:0.0:2,0:39.3:1.0:28.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -10 19229864 . GC AT 70 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01243;SOR=0.0;LSEQ=AGACCAATAATGCTGTTTCT;RSEQ=ATCATCTTCCAACTTTACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:5:2,3:102,137:0.0205:2,2:6.4:1.0:30.2:1.0:1.0:1.11632:60.0:10.0:0.0207:0.0123:0.8 0/0:340:0:0,0:152,188:0.0:2,0:24.4:1.0:31.6:1.0:1.0:0.0:60.0:67.0:1.0:0.0:0.3 -10 20007127 . A C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=3.0;MSILEN=3.0;SSF=0.01806;SOR=0.0;LSEQ=AAGGAAAAAGAAGACGAAGA;RSEQ=GAAGAGGAAGAAGAAGAAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:5,3:3,2:0.6154:2,2:11.5:1.0:30.8:1.0:1.0:1.1:60.0:16.0:0.6154:0.0:1.0 0/0:6:0:0,0:3,3:0.0:2,0:25.8:1.0:28.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -10 29188207 . C A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01496;SOR=0.0;LSEQ=ACAACAATGCCAACAGCATG;RSEQ=TGGGTAACATTGTAGACTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:7:3,4:123,97:0.0308:2,2:30.4:1.0:29.4:1.0:0.70282:1.68675:41.3:14.0:0.0313:0.0:1.0 0/0:221:0:0,0:113,108:0.0:2,0:31.0:1.0:31.0:1.0:1.0:0.0:41.2:43.2:1.0:0.0:0.1 -10 36853842 . G A 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ATGGAAGTTGTAGCTGAAAC;RSEQ=TGTCCTCTGAGAGAGGCTGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1.0:0,1:24.3:1.0:30.3:1.0:1.0:0.0:60.0:26.0:1.0:0.0:2.5 0/1:16:2:2,0:14,0:0.125:1,0:7.5:1.0:32.0:0.0:1.0:0.0:60.0:4.0:0.125:0.0:2.0 -10 36853858 . G C 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAACGTGTCCTCTGAGAGAG;RSEQ=CTGGCGCTCTCTCCGCCCGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:24,0:0,0:1.0:0,1:21.0:1.0:32.2:1.0:1.0:0.0:60.0:48.0:1.0:0.0:2.4 0/1:22:3:3,0:19,0:0.1364:1,0:10.7:1.0:33.7:1.0:1.0:0.0:60.0:6.0:0.15:0.0:2.3 -10 38539283 . G T 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.00015;SOR=0.0;LSEQ=TGCACAGGATGAGGAGGTAG;RSEQ=GTTGCTGCATTACCTTATAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:16:15,1:19,0:0.4571:1,1:20.8:1.0:30.8:1.0:0.45714:0.0:49.3:32.0:0.4571:0.0:1.2 0/0:20:0:0,0:19,1:0.0:1,0:15.3:1.0:30.0:1.0:1.0:0.0:52.7:19.0:1.0:0.0:0.0 -10 38743615 . G A 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=AGCTCCATACTGAGTAGAAG;RSEQ=CTTTGGGCCAGAGTATGATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:14:8,6:29,27:0.2:2,2:27.5:1.0:30.1:1.0:0.77241:1.24:43.6:28.0:0.2:0.0:1.1 0/0:78:0:0,0:39,39:0.0:2,0:28.6:1.0:30.5:1.0:1.0:0.0:46.0:18.5:1.0:0.0:0.1 -10 38744432 . C T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.04396;SOR=0.0;LSEQ=CCCCAAAATGTGTGGGGTTG;RSEQ=GGGCCCTGGGCTTTCAGGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:0,4:0.6:0,2:15.3:1.0:30.2:1.0:0.07619:0.0:50.5:12.0:0.6:0.0:1.0 0/0:5:0:0,0:2,3:0.0:2,0:23.6:1.0:31.8:1.0:1.0:0.0:49.0:10.0:1.0:0.0:1.0 -10 39012451 . AT A 132 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTTTATAGTTTGTATTTTA;RSEQ=TATGGGAATAATTGCTTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:19:3,16:2,20:0.4634:2,2:27.9:1.0:31.2:1.0:0.6486:1.85:48.3:38.0:0.475:0.0488:0.6 0/0:52:0:0,0:10,42:0.0:2,0:26.7:1.0:30.0:1.0:1.0:0.0:55.0:51.0:1.0:0.0:0.2 -10 42360771 . G C 92 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CGGGTTGATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCAATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:7,1:15,17:0.1951:2,2:16.8:1.0:30.9:1.0:0.05375:7.58:41.0:16.0:0.2051:0.0:5.5 0/0:115:0:0,0:45,54:0.0:2,0:7.0:1.0:15.0:1.0:1.0:0.0:24.0:0.0:0.0:0.0086:6.0 -10 42364715 . T A 78 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTCCTTTCCATTCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:0,1:0.8571:0,2:12.3:1.0:30.5:1.0:0.42857:0.0:37.3:12.0:1.0:0.0:7.2 0/0:29:0:0,0:4,3:0.0:2,0:7.3:1.0:29.4:1.0:1.0:0.0:46.9:14.0:0.7:0.0:5.4 -10 42364735 . T G 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0212;SOR=0.13551;LSEQ=TTTCCATTCCTTTCCATTCA;RSEQ=TTCCATTCCATTCCATTCCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:1,1:0.2778:2,2:7.6:1.0:30.2:1.0:1.0:1.41418:42.4:10.0:0.625:0.0556:3.8 0/1:42:2:0,2:3,3:0.0476:2,0:19.5:1.0:31.0:1.0:0.46429:0.0:25.5:4.0:0.1667:0.0:5.0 -10 42380300 . A ATTCCGGAAGATTCCATTCCATTGTATTCCG 101 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.0;MSILEN=5.0;SSF=1e-05;SOR=0.0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCATTACATTCCACTCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:10:4,6:27,25:0.1563:2,2:15.2:1.0:30.7:1.0:0.73149:1.60748:47.6:20.0:0.1639:0.1563:2.3 0/0:123:0:0,0:51,71:0.0:2,0:9.7:1.0:29.3:1.0:1.0:0.0:39.4:60.0:0.9917:0.0081:3.0 -10 42380308 . A C 105 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.02559;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCACTCGGATTGATTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:5,5:4,3:0.4348:2,2:15.2:1.0:31.8:1.0:1.0:1.31092:32.0:20.0:0.4545:0.0:4.5 0/1:55:1:1,0:8,10:0.0182:2,0:4.0:1.0:26.0:1.0:0.47368:0.0:40.0:2.0:0.0435:0.0182:2.0 -10 42385248 . T C 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00747;SOR=0.166;LSEQ=GGTCTCGAATGGAATCATTA;RSEQ=CAAATGGAATCGAATGGAAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:7:4,3:65,81:0.0455:2,2:23.1:1.0:32.0:1.0:0.70161:1.66:44.7:14.0:0.0464:0.0:3.7 0/0:384:3:1,2:169,209:0.0078:2,2:24.3:1.0:29.7:1.0:1.0:1.61527:34.0:6.0:0.008:0.0:3.3 -10 42385258 . T A 67 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.02446;SOR=0.16024;LSEQ=GGAATCATTATCAAATGGAA;RSEQ=CGAATGGAATCACCGAATAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:5:2,3:59,77:0.0355:2,2:9.4:1.0:29.0:1.0:1.0:1.14821:52.6:10.0:0.0362:0.0:4.2 0/0:343:2:2,0:149,190:0.0058:2,0:1.0:0.0:24.5:1.0:0.19536:0.0:60.0:4.0:0.006:0.0:3.0 -10 42387303 . C A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00203;SOR=0.0;LSEQ=AATCTAATGGAATCATTGAA;RSEQ=AGAATTGAATGGAATCGTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:3,2:26,28:0.0847:2,2:22.0:1.0:30.8:1.0:0.67075:1.6:40.0:10.0:0.0862:0.0:2.6 0/0:140:0:0,0:83,57:0.0:2,0:25.9:1.0:31.0:1.0:1.0:0.0:37.1:45.667:1.0:0.0:3.1 -10 42396882 . AA TC 80 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00086;SOR=0.0;LSEQ=TCGAATGGAATCATCATCCA;RSEQ=GGAAGCTAATGGAATCAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:3,3:19,23:0.125:2,2:39.2:1.0:31.0:1.0:1.0:1.21:33.3:12.0:0.1277:0.0:5.3 0/0:102:0:0,0:48,52:0.0:2,0:29.7:1.0:28.5:1.0:1.0:0.0:38.1:24.0:0.9897:0.0:4.3 -10 42398682 . AGAGA GAGC 79 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.01216;SOR=0.15851;LSEQ=AATTTGCAAGTGGAGATTTC;RSEQ=TTTGAGACCAATGGTAGAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:2,4:7,2:0.2143:2,2:19.8:1.0:30.8:1.0:0.13566:5.99855:31.0:12.0:0.2143:0.0357:4.8 0/1:74:3:0,3:25,35:0.0405:2,0:26.7:1.0:33.2:1.0:0.27035:0.0:40.0:6.0:0.0417:0.0:5.3 -10 42399298 . C G 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=TTCAACTCACAGAGTTGAAC;RSEQ=TTCCTTTAGACAGACCAGAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:1.0:0,2:25.4:1.0:31.0:1.0:1.0:0.0:39.7:18.0:1.0:0.0:7.8 0/1:19:3:3,0:9,5:0.1579:2,0:16.3:1.0:29.7:1.0:0.51471:0.0:36.3:6.0:0.1765:0.0:6.7 -10 42399313 . CC GT 97 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=7e-05;SOR=0.0;LSEQ=TGAACCTTCCTTTAGACAGA;RSEQ=AGATTTGAAACACTCTTTTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:7,2:0,0:1.0:0,2:36.4:1.0:30.8:1.0:1.0:0.0:39.7:18.0:1.0:0.1111:6.9 0/1:17:3:2,1:0,0:0.1765:0,2:34.0:1.0:31.8:1.0:1.0:0.0:44.3:6.0:0.1875:0.0:4.3 -10 42528052 . C G 105 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00049;SOR=0.13319;LSEQ=AATCCCGTTTCCAACGAAGG;RSEQ=CTCAAAGAGGTCCAAATATC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:10:5,5:33,37:0.125:2,2:24.6:1.0:31.9:1.0:1.0:1.12:33.9:20.0:0.1266:0.0:5.2 0/1:216:4:2,2:106,106:0.0185:2,2:15.0:1.0:30.3:1.0:1.0:1.0:25.5:8.0:0.0188:0.0:3.8 -10 42528063 . T G 98 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00023;SOR=0.07743;LSEQ=CAACGAAGGCCTCAAAGAGG;RSEQ=CCAAATATCCACTTGCAGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:9:4,5:33,37:0.1139:2,2:16.4:1.0:31.0:1.0:1.0:1.11333:33.2:18.0:0.1154:0.0:5.1 0/0:205:2:1,1:95,105:0.0098:2,2:11.5:1.0:30.5:1.0:1.0:1.1:25.0:4.0:0.01:0.0:4.0 -10 42528076 . T C 82 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00148;SOR=0.05433;LSEQ=AAAGAGGTCCAAATATCCAC;RSEQ=TGCAGACTTTACAAACAGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:6:2,4:19,33:0.1:2,2:14.5:1.0:31.8:1.0:1.0:1.1488:31.2:12.0:0.1017:0.0:5.2 0/0:169:1:0,1:71,94:0.0059:2,0:5.0:0.0:33.0:0.0:1.0:0.0:25.0:2.0:0.006:0.0:4.0 -10 42529468 . C G 83 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02681;SOR=0.17792;LSEQ=ACAAACAGAGTGTTTCCAAA;RSEQ=TGCTCTATGAAAAGAAAGGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:6:3,3:43,45:0.0638:2,2:19.5:1.0:32.2:1.0:1.0:1.05:56.2:12.0:0.0652:0.0:5.5 0/1:168:2:1,1:68,97:0.0119:2,2:28.0:1.0:32.5:1.0:1.0:1.42:40.5:4.0:0.012:0.0:7.5 -10 42596918 . A T 89 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00211;SOR=0.0;LSEQ=GGAATCATCTTCAAATGGAA;RSEQ=GGAATGGAATCATCGCATAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:7:7,0:44,30:0.0864:2,0:24.9:1.0:32.0:1.0:0.04259:0.0:27.4:14.0:0.0875:0.0:5.4 0/0:110:0:0,0:39,56:0.0:2,0:22.1:1.0:30.4:1.0:1.0:0.0:42.9:190.0:1.0:0.0:3.9 -10 42599622 . C A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.00375;SOR=0.0;LSEQ=CAGATGGAAACGAATGGAAT;RSEQ=ATCATCGAATGGAAATGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:5:2,3:72,46:0.04:2,2:32.6:1.0:30.6:1.0:0.38625:2.33106:45.8:10.0:0.0403:0.0:3.8 0/0:253:0:0,0:144,106:0.0:2,0:27.6:1.0:31.0:1.0:1.0:0.0:48.1:49.0:0.9959:0.0:3.6 -10 42599688 . A T 74 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01826;SOR=0.09872;LSEQ=TGGAATCATCATCAAATGGA;RSEQ=TCGAATGGAATCATCATCAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:5:3,2:46,48:0.0505:2,2:22.4:1.0:32.2:1.0:0.67773:1.56:44.4:10.0:0.0521:0.0:5.6 0/0:193:1:1,0:84,107:0.0052:2,0:36.0:0.0:31.0:0.0:0.44271:0.0:52.0:2.0:0.0052:0.0:5.0 -10 42599799 . T A 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.05519;SOR=0.18838;LSEQ=AATGGTCTCGAATGGAATCA;RSEQ=CTTCAAATGGAATGGAATGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:3,3:38,60:0.0566:2,2:33.7:1.0:31.0:1.0:0.6781:1.57:38.3:12.0:0.0571:0.0:3.5 0/1:180:2:1,1:74,99:0.0111:2,2:29.0:1.0:28.5:1.0:1.0:1.34:43.5:4.0:0.0112:0.0:2.5 -10 42600080 . CGAATGGAATCGTCATCGAATGGAATCGAATGGAATCATCAAATGGGATCAG TGA 176 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAATCATCATCGGATGGAAA;RSEQ=ATGGAATCATCATCAAATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:57:52:21,31:1,3:0.9123:2,2:22.7:1.0:30.9:1.0:1.0:2.01:28.2:104.0:0.9123:0.2456:3.9 0/0:32:0:0,0:6,6:0.0:2,0:20.6:1.0:29.8:1.0:1.0:0.0:36.0:24.0:0.375:0.0:3.1 -10 43596179 . G A 261 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02162;LSEQ=TCAGTGTCCGCAGTAAGGGA;RSEQ=CCGCCCCAACACCCACCCCG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:544:491:176,315:18,34:0.9026:2,2:26.9:1.0:29.2:1.0:1.0:1.06:60.0:34.071:0.9034:0.0:1.3 0/1:482:80:34,46:160,242:0.166:2,2:24.0:1.0:28.6:1.0:0.70838:1.12:60.0:79.0:0.1667:0.0:1.3 -10 43596241 . C T 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAGCCGCCCTTATCACAGC;RSEQ=GCTGACACTGAAGCTTGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:87:7,80:9,79:0.4943:2,2:25.8:1.0:29.1:1.0:0.79406:1.30003:60.0:16.4:0.4881:0.0:1.9 0/0:137:0:0,0:17,120:0.0:2,0:22.0:1.0:29.2:1.0:1.0:0.0:59.8:33.25:1.0:0.0:0.5 -10 43600210 . AGCACAGTCAT A 140 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00014;SOR=0.0;LSEQ=CTGCAAACTGCAAACTCGTA;RSEQ=CGCTGCAAACTGCAAACTCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:22:21,1:19,1:0.5238:1,1:21.7:1.0:31.5:1.0:1.0:1.1:58.9:44.0:0.5238:0.0952:0.3 0/0:16:0:0,0:14,2:0.0:2,0:20.9:1.0:32.5:1.0:1.0:0.0:60.0:32.0:1.0:0.0:0.2 -10 43604148 . A C 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTATGCACAGACACCACACA;RSEQ=ATGCATACTACACACTTACA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,0:0.7:0,0:27.6:1.0:32.7:1.0:1.0:0.0:60.0:14.0:0.7778:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -10 43604950 . A G 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCAAAAATGCAAGAGCAAT;RSEQ=CTGGGTAAATCTGCATATGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:19.1:1.0:31.9:1.0:1.0:0.0:60.0:14.0:0.875:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -10 43607471 . T G 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00041;SOR=0.0;LSEQ=GGGCAGCTCAGCTGGTGCTG;RSEQ=TCCCTGTCCTTGGGCACTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:14:11,3:111,4:0.1085:1,2:27.8:1.0:31.1:1.0:0.02778:7.35353:60.0:28.0:0.1085:0.0:1.1 0/0:94:0:0,0:85,9:0.0:2,0:21.1:1.0:29.6:1.0:1.0:0.0:60.0:188.0:1.0:0.0:0.2 -10 43610119 . G A 310 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02017;LSEQ=CGGTCAGCTACTCCTCTTCC;RSEQ=GTGCCCGCCGGCCCTCGCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1334:1223:611,612:56,53:0.9168:2,2:24.2:1.0:30.3:1.0:0.84166:1.05831:60.0:32.972:0.9173:0.0:1.1 0/1:1009:183:97,86:450,373:0.1814:2,2:23.9:1.0:30.2:1.0:0.68262:1.06954:60.0:60.0:0.1816:0.0:1.2 -10 43615382 . C T 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00346;LSEQ=GTCACACCCTGACTCCACCA;RSEQ=GCCCCTGCCATGCCACACCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:81:77:57,20:3,1:0.9506:2,2:28.3:1.0:30.3:1.0:1.0:1.05196:60.0:14.4:0.9474:0.0:1.2 0/1:37:2:1,1:24,11:0.0541:2,2:34.5:1.0:31.0:1.0:1.0:2.13205:60.0:4.0:0.0556:0.0:1.5 -10 43618751 . G A 66 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGTGGCCTGCATTCTCACC;RSEQ=CTTTAAGTGTGAGAATCTTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:13.2:1.0:28.6:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:2.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -10 43620134 . C T 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.09804;SOR=0.0;LSEQ=GACCTGAGCACAGTGGCCCA;RSEQ=GGGCTGGGATCCTGCAACAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:11,1:4,0:0.75:0,2:36.1:1.0:32.4:1.0:1.0:0.0:60.0:24.0:0.75:0.0:1.1 0/0:2:0:0,0:2,0:0.0:0,0:32.5:1.0:29.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -10 52388952 . G A 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATAAAAGGTACAGTATTTGC;RSEQ=TATAACCTCCCCATATCCTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1.0:0,0:21.4:1.0:30.6:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -10 52389659 . G A 220 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.09488;LSEQ=TCTGAATCACCTGCCTCAGA;RSEQ=CTGCAGCAAAGTTTCTGCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:173:83,90:66,76:0.5492:2,2:22.9:1.0:29.7:1.0:0.82113:1.06:60.0:56.667:0.5502:0.0:1.1 0/1:281:29:15,14:124,127:0.1032:2,2:19.4:1.0:29.7:1.0:0.84665:1.1:60.0:58.0:0.1074:0.0:1.2 -10 54611395 . A G 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.04762;SOR=0.0;LSEQ=AGCCACAGCCAGTGCTGGTC;RSEQ=CCCCTCACCTCAGGAGTTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1.0:0,2:24.8:1.0:28.2:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.2 0/0:2:0:0,0:2,0:0.0:0,0:27.0:1.0:27.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -10 70404938 . G T 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.06191;SOR=0.0;LSEQ=TGAGTTGTGATCATCTCAAG;RSEQ=GGAGAAGTAACGTTTTAGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:5:0,5:246,199:0.0111:2,0:7.2:1.0:27.6:1.0:0.01863:0.0:60.0:10.0:0.0113:0.0:1.0 0/0:438:0:0,0:216,221:0.0:2,0:24.5:1.0:30.3:1.0:1.0:0.0:60.0:47.556:0.9977:0.0:0.1 -10 70405237 . G A 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.09363;LSEQ=TCAAAGTCAGAGAAGGATGA;RSEQ=GAATCAGAGCAGAGAACAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:331:181:94,87:80,70:0.5468:2,2:23.7:1.0:30.6:1.0:0.82557:1.05755:60.0:362.0:0.5485:0.0:1.0 0/1:435:44:19,25:203,188:0.1011:2,2:23.3:1.0:30.4:1.0:0.34007:1.41962:60.0:88.0:0.1021:0.0:1.2 -10 70406345 . C T 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00878;SOR=0.0;LSEQ=AAGCTTATAATTCTCAGGTA;RSEQ=AGTTAACGGTGAATGCCAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:6:2,4:278,262:0.011:2,2:21.8:1.0:28.3:1.0:0.43961:2.1193:60.0:12.0:0.0111:0.0:1.2 0/0:653:0:0,0:324,329:0.0:2,0:1.0:0.0:13.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -10 70406518 . A T 249 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00445;LSEQ=CCTGGTATCTCTCATGAAAC;RSEQ=CCCTTACCGGAGTCAGCACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:663:305:172,133:190,168:0.46:2,2:24.5:1.0:30.2:1.0:0.43392:1.14:60.0:37.125:0.4555:0.0:1.1 0/0:797:3:0,3:411,381:0.0038:2,0:1.0:0.0:24.0:1.0:0.11224:0.0:60.0:6.0:0.0038:0.0:1.0 -10 70406864 . C T 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.05677;LSEQ=TTTTGTGTGATATTTTTTCC;RSEQ=CATTCTTATTCTAACTAAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:28:0,28:0,21:0.5714:1,1:21.9:1.0:30.3:1.0:1.0:0.0:60.0:56.0:0.5714:0.0:1.1 0/1:44:3:0,3:0,41:0.0682:1,0:28.7:1.0:28.3:1.0:1.0:0.0:60.0:6.0:0.0682:0.0:1.3 -10 70412132 . AAG A 172 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.05586;LSEQ=TTTAACAAGAGTAAATTACG;RSEQ=AGTGTCTAATTTTTGAACTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:48:48,0:32,0:0.6:1,1:21.9:1.0:30.9:1.0:1.0:0.0:60.0:96.0:0.6076:0.1875:0.0 0/1:66:5:5,0:61,0:0.0758:1,0:25.0:1.0:29.6:1.0:1.0:0.0:60.0:10.0:0.0769:0.0:0.2 -10 70451383 . A T 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTGAGGCTAAAGAAGCTAAG;RSEQ=ATAAGAAAATGAAGGCCTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:131:61,70:435,407:0.1345:2,2:24.6:1.0:28.3:1.0:0.30183:1.22623:60.0:31.75:0.1333:0.0:1.1 0/0:1342:0:0,0:648,694:0.0:2,0:25.2:1.0:29.1:1.0:1.0:0.0:60.0:69.632:1.0:0.0:0.1 -10 86331960 . A G 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00776;SOR=0.10947;LSEQ=GGGTCCTTTTCCACACTGGG;RSEQ=AAAGTTTGTTCTTTTGCTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:4,5:0.4375:2,2:26.1:1.0:33.0:1.0:1.0:1.06235:60.0:14.0:0.4375:0.0:2.1 0/1:27:2:0,2:12,13:0.0741:2,0:26.5:1.0:26.5:1.0:0.48718:0.0:60.0:4.0:0.0769:0.0:3.0 -10 88866085 . TCA T 135 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGGAATAATTGTTAGACAAC;RSEQ=CAGTGTCTGCCATATTTGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:18:11,7:69,45:0.1364:2,2:29.6:1.0:32.5:1.0:1.0:1.02:60.0:36.0:0.1385:0.0:0.3 0/0:233:0:0,0:127,105:0.0:2,0:25.6:1.0:31.0:1.0:1.0:0.0:60.0:76.333:0.9957:0.0:0.3 -10 89692844 . C T 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTTTTGTGAAGATCTTGAC;RSEQ=AATGGCTAAGTGAAGATGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:224:117,107:158,157:0.4148:2,2:22.3:1.0:29.4:1.0:0.66249:1.09:50.6:73.667:0.4139:0.0:1.1 0/0:619:0:0,0:313,304:0.0:2,0:22.3:1.0:30.5:1.0:1.0:0.0:50.3:204.667:0.9984:0.0:0.1 -10 89717709 . AGCCGT A 237 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATGTACTTTGAGTTCCCTC;RSEQ=TACCTGTGTGTGGTGATATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:524:215:93,122:137,172:0.4103:2,2:25.8:1.0:30.7:1.0:0.85804:1.04482:59.7:430.0:0.4167:0.0687:0.0 0/0:722:0:0,0:343,378:0.0:2,0:25.8:1.0:31.9:1.0:1.0:0.0:59.7:179.25:0.9986:0.0:0.2 -10 89720881 . T A 55 Bias SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00921;SOR=0.0;LSEQ=TCTCCAAATTTTAAGGTCAG;RSEQ=TAAATTAAACATTTTGTGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:5:5,0:194,298:0.0101:2,0:8.8:1.0:24.0:1.0:0.00998:0.0:43.8:4.0:0.0081:0.0:2.2 0/0:769:0:0,0:314,455:0.0:2,0:23.9:1.0:29.5:1.0:1.0:0.0:58.8:108.857:1.0:0.0:0.2 -10 99804159 . A G 224 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGCAGCGACAGCAGCA;RSEQ=CAACAGCAGCAGCGACAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:228:136:61,75:44,19:0.5965:2,2:25.4:1.0:31.7:1.0:0.00129:2.83216:56.1:21.667:0.628:0.0:4.0 0/0:369:0:0,0:104,97:0.0:2,0:20.7:1.0:29.6:1.0:1.0:0.0:55.9:200.0:0.9091:0.0:1.2 -10 99804170 . AG GA 93 NM4;Bias SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.01632;SOR=0.1527;LSEQ=ACAGCAGCAACAACAGCAGC;RSEQ=CGACAGCAGCAACAACAGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:8:0,8:123,82:0.0354:2,0:36.0:0.0:31.0:1.0:0.00084:0.0:37.0:16.0:0.0386:0.0:7.0 0/0:360:2:0,2:169,169:0.0056:2,0:36.0:0.0:30.8:1.0:0.49854:0.0:44.0:4.0:0.006:0.0:7.0 -10 99804180 . G GCAGTAGCAACAGAAATAGCAGTAATAGCAGCAGCAGCAGTAGCAGCAATAATTA 132 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CAACAGCAGCAGCGACAGCA;RSEQ=CAACAACAGCAGCAATAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:20:15,5:196,145:0.0552:2,2:28.1:1.0:30.6:1.0:0.16186:2.21:39.9:40.0:0.058:0.0552:3.7 0/0:502:0:0,0:259,242:0.0:2,0:17.6:1.0:31.4:1.0:1.0:0.0:46.8:49.1:1.0:0.0:2.3 -10 99804184 . C T 90 NM4;Bias SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00483;SOR=0.1329;LSEQ=AGCAGCAGCGACAGCAGCAA;RSEQ=AACAGCAGCAATAGCAGCAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:10:0,10:219,149:0.0265:2,0:28.5:1.0:27.2:1.0:0.00015:0.0:40.6:9.0:0.0247:0.0:7.0 0/0:557:2:0,2:285,270:0.0036:2,0:37.5:1.0:28.0:1.0:0.23802:0.0:44.0:4.0:0.0036:0.0:7.0 -10 99804243 . GCAACAA G 172 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.11302;LSEQ=CGACAACAGCAATAGCAGCA;RSEQ=CAACAGCAGCAGCAACAGCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:47:20,27:30,40:0.1577:2,2:15.9:1.0:31.0:1.0:1.0:1.01239:56.8:46.0:0.1637:0.0738:3.4 0/1:387:8:3,5:123,129:0.0207:2,2:27.0:1.0:27.8:1.0:0.72334:1.58637:56.3:7.0:0.0197:0.0:5.3 -10 99804244 . C CAACAACAACAGCAGCAGCAACAGCAGTCACAATTAACAACAGCAACAATAGCAGCAGTAAA 78 NM4 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=26;MSI=5.0;MSILEN=1.0;SSF=0.00659;SOR=0.0;LSEQ=GACAACAGCAATAGCAGCAG;RSEQ=AACAACAACAGCAGCAGCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:298:6:2,4:30,40:0.0201:2,2:14.7:1.0:30.3:1.0:1.0:1.49229:38.3:12.0:0.0214:0.0201:4.8 0/0:387:0:0,0:123,129:0.0:2,0:22.4:1.0:31.5:1.0:1.0:0.0:50.3:49.4:0.6958:0.0181:2.3 -10 99804264 . A G 142 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAACAACAACAGCAGCAGCA;RSEQ=CAGCAGCAACAACAGCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:432:20:9,11:183,222:0.0463:2,2:20.5:1.0:33.0:1.0:1.0:1.00749:34.7:40.0:0.0473:0.0:6.3 0/0:514:0:0,0:198,264:0.0:2,0:22.4:1.0:29.5:1.0:1.0:0.0:53.3:230.0:1.0:0.0:3.0 -10 99804273 . A GTAAAAACAG 82 NM4;Bias SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.02601;SOR=0.19402;LSEQ=AACAGCAGCAGCAACAGCAG;RSEQ=CAACAGCAGCAACAACAACA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:8:8,0:192,248:0.0178:2,0:32.0:1.0:27.6:1.0:0.00146:0.0:34.8:16.0:0.0185:0.0067:6.3 0/0:571:2:2,0:231,298:0.0035:2,0:44.0:0.0:27.5:1.0:0.19208:0.0:33.5:4.0:0.0039:0.0:7.0 -10 99804285 . AC GCAATAATTATAACAGCAGCAACAACAGCAACGTCAGAAAAAGCAGCAACAGCAATAGCAACAAAAGCATCAGCAACAGCAATAGCATCACAATT 152 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGCAACAACAGCAGCA;RSEQ=AACAACAGCAACAGCAGCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:33:12,21:176,187:0.0755:2,2:45.4:1.0:30.2:1.0:0.20549:1.64502:27.2:66.0:0.0776:0.0755:0.0 0/0:521:0:0,0:201,236:0.0:2,0:22.2:1.0:29.4:1.0:1.0:0.0:54.3:38.727:0.9201:0.0:2.2 -10 99804306 . A GCAACAACAGAAATCACAGTAACAACAGTAGCAG 67 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.02027;SOR=0.0;LSEQ=CAACAACAGCAACAGCAGCA;RSEQ=CAGCAGCAGCAACAACAATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:5:3,2:154,205:0.0136:2,2:21.6:1.0:29.2:1.0:0.65558:1.99:33.2:10.0:0.0139:0.0136:4.2 0/0:431:0:0,0:177,221:0.0:2,0:24.0:1.0:29.5:1.0:1.0:0.0:56.9:43.222:0.9873:0.0023:1.9 -10 99804318 . ACAACAATAGCAACAACAGTAGTGG A 127 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGCAACAGCAGCAGCA;RSEQ=CAATAACAGCAGCAAAACAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:21:5,16:139,190:0.0592:2,2:17.6:1.0:29.0:1.0:0.11251:2.33588:42.1:42.0:0.0625:0.0592:1.9 0/0:376:0:0,0:152,197:0.0:2,0:22.7:1.0:31.1:1.0:1.0:0.0:57.7:42.625:1.0:0.0:1.4 -10 104378688 . CGT C 170 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=46;MSI=24.0;MSILEN=2.0;SSF=0.0;SOR=0.12002;LSEQ=TCCCAAGTGTCCTCAGGTAG;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:39:35,4:88,1:0.2241:1,2:22.8:1.0:32.3:1.0:0.02985:9.85932:59.0:38.0:0.2275:0.0517:0.6 0/1:180:6:6,0:112,4:0.0333:1,0:27.7:1.0:33.7:1.0:1.0:0.0:60.0:12.0:0.0347:0.0:0.3 -10 110550348 . A C 97 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0079;SOR=0.07215;LSEQ=TAGTCCCAGGAAAAGTCAGC;RSEQ=AGGTCATCTGTGAGTTCTTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:8,1:0.5:2,2:16.8:1.0:30.9:1.0:0.57647:3.70691:60.0:18.0:0.5294:0.0:1.0 0/1:16:1:1,0:13,2:0.0625:2,0:7.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0625:0.0:1.0 -10 114911035 . AAG A 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.0;MSILEN=2.0;SSF=0.08151;SOR=0.0;LSEQ=GGGCTCTTCACTCCCTTACA;RSEQ=AGAGAGAGAGTGCACAGTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:5:0,5:2,127:0.0373:1,0:30.0:1.0:32.8:1.0:1.0:0.0:60.0:10.0:0.0388:0.0:0.4 0/0:92:0:0,0:1,91:0.0:1,0:24.4:1.0:31.0:1.0:1.0:0.0:60.0:91.0:1.0:0.0:0.4 -10 114912534 . C T 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.44444;SOR=0.0;LSEQ=ACCCAAAGGACCTTATGTTC;RSEQ=GGATTAGGTTCCGCAGGCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:22.6:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.625:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:3.5:1.0:26.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -10 114919606 . C T 68 q23;NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00741;SOR=0.0;LSEQ=TCTTCCCCCCCCCCCCCCCT;RSEQ=TTTCTCTCTCTCTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:8:8,0:147,46:0.0392:2,0:24.0:1.0:22.8:1.0:0.20225:0.0:55.4:1.667:0.0407:0.0:4.5 0/0:194:0:0,0:132,57:0.0:2,0:31.0:0.0:17.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:6.0 -10 114919608 . T C 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00089;SOR=0.0;LSEQ=TTCCCCCCCCCCCCCCCTCT;RSEQ=TCTCTCTCTCTCTCTCTCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:11:7,4:144,46:0.0524:2,2:20.0:1.0:28.5:1.0:0.47139:1.78297:58.2:4.5:0.052:0.0:3.3 0/0:198:0:0,0:126,62:0.0:2,0:10.9:1.0:27.1:1.0:1.0:0.0:59.3:6.833:1.0:0.0:1.0 -10 114920089 . A G 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07368;SOR=0.0;LSEQ=CCTAGGTAGAAGCAAATGAC;RSEQ=TCACCTTCTCCCCTCCTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:9,2:3,3:0.6471:2,2:25.8:1.0:29.9:1.0:0.28006:4.07:60.0:22.0:0.6471:0.0:1.2 0/0:3:0:0,0:1,2:0.0:2,0:34.7:1.0:31.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.7 -10 123240645 . C T 258 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.08516;LSEQ=AAAGCTGAAAATATTTACTC;RSEQ=CTGGCCCTTTACAGAAAGCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:796:365:168,197:190,240:0.4585:2,2:24.9:1.0:30.4:1.0:0.6171:1.08:60.0:72.0:0.4609:0.0:1.9 0/1:938:63:31,32:402,472:0.0672:2,2:24.3:1.0:29.4:1.0:0.69505:1.14:60.0:14.75:0.0638:0.0:1.9 -10 123241323 . G A 262 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04495;LSEQ=CATTAAAATAGAACTTTAGT;RSEQ=CTTTTCCCGGTTTCTTTCTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:930:484:184,300:236,209:0.5204:2,2:26.9:1.0:29.4:1.0:1e-05:1.83986:59.9:241.0:0.5285:0.0:3.4 0/1:1637:76:38,38:778,781:0.0464:2,2:27.0:1.0:28.0:1.0:1.0:1.0:59.6:37.0:0.048:0.0:3.2 -10 123241354 . AT TA 233 MSI6 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.0;SOR=0.02795;LSEQ=TTTCTTTCTTTTTTATTTTT;RSEQ=TTTTTTTTTTTTTGAGACGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:425:250:71,179:18,22:0.5882:2,2:23.6:1.0:29.3:1.0:0.04234:2.05714:59.6:249.0:0.8527:0.0:3.8 0/1:968:37:9,28:264,377:0.0382:2,2:29.9:1.0:28.2:1.0:0.05659:2.17631:58.9:74.0:0.0541:0.0:3.6 -10 123241361 . T A 237 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.0;SOR=0.02566;LSEQ=CTTTTTTATTTTTATTTTTT;RSEQ=TTTTTTTGAGACGGAGTCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:392:244:68,176:96,52:0.6224:2,2:20.8:1.0:30.0:1.0:0.0:4.75697:59.6:121.0:0.6237:0.0:3.8 0/1:867:35:11,24:374,458:0.0404:2,2:25.0:1.0:29.0:1.0:0.1218:1.78053:59.0:70.0:0.0405:0.0:3.7 -10 123242589 . G A 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0667;LSEQ=CCAAAATGCTGGGATTACAG;RSEQ=CGAGAGCATAAATATTTTAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:154:105,49:138,59:0.4387:2,2:23.8:1.0:29.9:1.0:0.72768:1.09125:60.0:153.0:0.4422:0.0:1.1 0/1:405:20:11,9:258,127:0.0494:2,2:22.9:1.0:28.1:1.0:0.33139:1.65996:60.0:40.0:0.05:0.0:1.1 -10 123274653 . A G 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTACCTGTCTCCGCAGGGGG;RSEQ=TACGTTTGGTCAGCTTGTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:37:23,14:341,160:0.0688:2,2:25.9:1.0:31.8:1.0:0.46971:1.29658:60.0:74.0:0.0703:0.0:1.1 0/0:674:0:0,0:410,263:0.0:2,0:24.0:1.0:28.5:1.0:1.0:0.0:60.0:28.261:0.9985:0.0:0.2 -10 123279795 . C T 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01553;LSEQ=CATGCCAGAAAAGCCTCAAG;RSEQ=CTGCTGGCTGACACCTTTGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:23:0,23:0,2:0.92:0,1:21.5:1.0:29.3:1.0:1.0:0.0:60.0:10.5:0.913:0.0:1.9 0/1:16:2:0,2:0,14:0.125:1,0:11.0:1.0:27.0:1.0:1.0:0.0:60.0:4.0:0.1333:0.0:2.0 -10 123488416 . A G 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=8e-05;SOR=0.0;LSEQ=AGCACGCTGCCTCCTTCTTA;RSEQ=CCAAGCTGGCCACTGTGTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:4,6:4,5:0.5263:2,2:30.3:1.0:30.2:1.0:1.0:1.18851:60.0:9.0:0.5:0.0:2.4 0/0:22:0:0,0:12,10:0.0:2,0:26.0:1.0:27.6:1.0:1.0:0.0:60.0:21.0:1.0:0.0:1.0 -10 134913291 . C T 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04556;SOR=0.0;LSEQ=ACAGCCCAGTACAGTCACCT;RSEQ=CAGGGCCCAGACACAGCCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:3,4:0.5333:2,2:19.0:1.0:26.9:1.0:1.0:1.23147:60.0:7.0:0.5:0.0:1.0 0/0:6:0:0,0:3,3:0.0:2,0:17.8:1.0:31.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.2 -11 2156741 . T G 225 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACCAGCATCGACTTCCCCA;RSEQ=TGGGATTCCCATTGGTGTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1041:131:56,75:420,490:0.1258:2,2:24.2:1.0:32.0:1.0:0.51171:1.14781:60.0:130.0:0.127:0.0:1.1 0/0:1037:0:0,0:485,552:0.0:2,0:24.9:1.0:29.4:1.0:1.0:0.0:60.0:44.087:1.0:0.0:0.2 -11 8246137 . C T 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.02427;SOR=0.0;LSEQ=CAGGCGGGCAGATGGACAGA;RSEQ=GGGCCTGGAGGCCAGGCGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:5:1,4:295,194:0.0101:2,2:9.0:1.0:28.4:1.0:0.16276:6.06174:60.0:10.0:0.0102:0.0:1.2 0/0:543:0:0,0:315,227:0.0:2,0:23.7:1.0:30.1:1.0:1.0:0.0:60.0:179.667:0.9981:0.0:0.3 -11 8248574 . G T 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGGTGATACACGTTGTCCC;RSEQ=GGCCCGCATCACCATCTCGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:884:74:38,36:408,402:0.0837:2,2:26.6:1.0:30.9:1.0:0.90375:1.04:60.0:148.0:0.0845:0.0:1.2 0/0:1008:0:0,0:508,496:0.0:2,0:24.8:1.0:29.6:1.0:1.0:0.0:60.0:76.231:0.997:0.0:0.2 -11 17457720 . CA TG 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.06539;SOR=0.15968;LSEQ=CCAACATGTCTCAGCAAGAG;RSEQ=CAGCCATCTTGGGTTCTGGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:6:0,6:84,149:0.025:2,0:14.3:1.0:30.8:1.0:0.09323:0.0:24.3:12.0:0.0253:0.0:2.7 0/0:246:1:0,1:98,147:0.0041:2,0:17.0:0.0:29.0:0.0:1.0:0.0:25.0:2.0:0.0042:0.0:6.0 -11 17746976 . G T 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01879;LSEQ=CAAGAGGGAAGGGAACAGCT;RSEQ=GAGACTGGATCACACCATCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1194:50:27,23:634,510:0.0419:2,2:23.4:1.0:30.0:1.0:0.88498:1.05889:60.0:100.0:0.0426:0.0:1.2 0/0:1220:1:0,1:651,568:0.0008:2,0:1.0:0.0:24.0:0.0:0.46639:0.0:60.0:2.0:0.0008:0.0:1.0 -11 20246743 . C A 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.06372;SOR=0.0;LSEQ=AGATTGATACTAGTGGGAAC;RSEQ=CCTTGGAGATTACTTAGATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:0,10:0,13:0.4348:1,0:22.7:1.0:31.6:1.0:1.0:0.0:60.0:20.0:0.4348:0.0:1.0 0/0:7:0:0,0:1,6:0.0:2,0:20.4:1.0:31.6:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.0 -11 20575654 . G C 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01919;LSEQ=GTGCTAGGTGTGGGGTTAGA;RSEQ=TGGGGAGCAAGATGGAGATG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:33:32,1:48,3:0.3929:2,1:30.2:1.0:30.5:1.0:1.0:1.99:60.0:10.0:0.3704:0.0:1.1 0/1:83:1:1,0:72,10:0.012:2,0:16.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.012:0.0:1.0 -11 21635295 . T G 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAATCAGCGGTAATGGGAGC;RSEQ=GCTAGACAGGAGGGAAGACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:94:47,47:88,102:0.3298:2,2:27.1:1.0:30.5:1.0:0.61402:1.16:60.0:188.0:0.3333:0.0:2.3 0/0:305:0:0,0:142,163:0.0:2,0:25.0:1.0:29.9:1.0:1.0:0.0:60.0:60.0:1.0:0.0:0.8 -11 23122852 . A C 77 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGATTCTCAGCAATAAATA;RSEQ=TTTTCCCAAATGTTTGCATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:27.6:1.0:33.4:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:29.0:0.0:18.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -11 25022172 . T C 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.02526;SOR=0.09713;LSEQ=CTTAGAAAGGGGAGAAGCCA;RSEQ=GTTGCCCAACTCCAGAGGTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:5,3:12,9:0.2759:2,2:33.3:1.0:31.6:1.0:1.0:1.24:60.0:16.0:0.2759:0.0:1.9 0/1:29:1:1,0:15,13:0.0345:2,0:31.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0345:0.0:2.0 -11 30098849 . G T 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0033;SOR=0.0;LSEQ=AGACTAAAAATTGTGTAAAT;RSEQ=TAGACAGCATATACCTCTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:0.5:0,0:22.6:1.0:31.0:1.0:1.0:0.0:60.0:16.0:0.5:0.0:1.0 0/0:13:0:0,0:0,13:0.0:1,0:22.2:1.0:32.5:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.4 -11 30254268 . T G 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.45455;SOR=0.0;LSEQ=GAAATAGTTTCCATGGTGCT;RSEQ=TCTTTTTTCTCTGCAGCACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:27.6:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:2:0:0,0:2,0:0.0:0,0:8.0:1.0:31.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -11 32437699 . T C 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCAAGTTAAGACTGAAAGC;RSEQ=TTGACTGATCTAACAGGAAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:12.0:1.0:30.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 32437841 . A C 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0001;SOR=0.0;LSEQ=TCCAGGGGCATGTTGATGAG;RSEQ=AATGCTACTCCCTCCATTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:14,0:19,0:0.4242:1,1:17.6:1.0:31.6:1.0:1.0:0.0:60.0:13.0:0.4063:0.0:1.1 0/0:25:0:0,0:25,0:0.0:1,0:26.9:1.0:29.2:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.2 -11 32439001 . T C 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGAGGAAAGCGTTCTAATG;RSEQ=CACAGAGAGCTTTGCCCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:41:40,1:67,0:0.3796:1,1:27.2:1.0:31.8:1.0:0.37963:0.0:60.0:19.5:0.3679:0.0:1.0 0/0:85:0:0,0:85,0:0.0:1,0:24.4:1.0:30.1:1.0:1.0:0.0:60.0:170.0:1.0:0.0:0.1 -11 32450244 . CG C 169 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGTCTGAACCAGCCACGGG;RSEQ=GGGGGGGTGTGCGCTGAACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:40:3,37:8,47:0.4211:2,2:26.5:1.0:31.9:1.0:0.34719:2.08397:60.0:80.0:0.4255:0.0105:0.1 0/0:67:0:0,0:8,59:0.0:2,0:17.3:1.0:29.6:1.0:1.0:0.0:60.0:32.5:1.0:0.0:0.3 -11 32452001 . GGA G 206 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=34;MSI=18.0;MSILEN=2.0;SSF=0.0;SOR=0.10004;LSEQ=AGAGAGAGAGAGAGAGGGAG;RSEQ=GAGAGAGAGAGAGAGAGAGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:115:77,38:90,21:0.2987:2,2:20.8:1.0:30.2:1.0:0.02262:2.10802:59.4:13.375:0.294:0.0935:0.7 0/1:417:17:12,5:173,57:0.0408:2,2:16.1:1.0:30.1:1.0:0.77199:1.26337:60.0:34.0:0.0421:0.0192:0.3 -11 35242653 . C T 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04608;SOR=0.0;LSEQ=TATACCAAAATGTGATTACA;RSEQ=CTTACACGGTGTTTAGCAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:7,0:0.4615:0,0:26.5:1.0:31.2:1.0:1.0:0.0:60.0:12.0:0.4615:0.0:2.2 0/0:9:0:0,0:9,0:0.0:0,0:17.4:1.0:31.1:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.9 -11 39894274 . C T 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCTGTTATTTCACTAACCC;RSEQ=CTCTACTCACAAAAATTTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:49:37,12:67,25:0.3475:2,2:24.2:1.0:30.8:1.0:0.84148:1.15:60.0:98.0:0.3475:0.0:1.1 0/0:166:0:0,0:118,47:0.0:2,0:25.2:1.0:30.3:1.0:1.0:0.0:60.0:330.0:1.0:0.0:0.1 -11 42138434 . C T 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01073;LSEQ=AACATATGTACAATCCTGTG;RSEQ=CTTTAGTACCCTTTTGATTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:55:34,21:34,20:0.5046:2,2:23.7:1.0:29.5:1.0:1.0:1.04956:60.0:110.0:0.514:0.0:1.0 0/1:94:1:0,1:59,34:0.0106:2,0:1.0:0.0:22.0:0.0:0.37234:0.0:60.0:2.0:0.0108:0.0:2.0 -11 44368605 . T C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.10294;SOR=0.0;LSEQ=TTTGTTGGCTGGCTTTGCCT;RSEQ=CGGGAGGTGTGAGCCTCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:0.5385:0,0:32.1:1.0:31.3:1.0:1.0:0.0:60.0:14.0:0.5385:0.0:1.0 0/0:4:0:0,0:0,4:0.0:0,0:20.5:1.0:29.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -11 62098295 . T A 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00223;SOR=0.05206;LSEQ=GGAATTGTGGGTGTATACAT;RSEQ=TATCTGTAAAAGATGTGGTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:9,0:10,0:0.4737:0,0:15.1:1.0:28.9:1.0:1.0:0.0:60.0:18.0:0.4737:0.0:1.3 0/1:24:1:1,0:23,0:0.0417:1,0:41.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0417:0.0:1.0 -11 64571710 . C T 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01644;SOR=0.0;LSEQ=GGTTTGGGTAGAGGTGAGGC;RSEQ=TGTCCCCTTTGGGCTGGGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:7:6,1:365,43:0.0169:2,2:19.7:1.0:28.7:1.0:0.54643:1.41338:60.0:6.0:0.0147:0.0:1.0 0/0:367:0:0,0:329,38:0.0:2,0:23.3:1.0:30.4:1.0:1.0:0.0:60.0:72.4:1.0:0.0:0.1 -11 64575505 . C T 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04041;LSEQ=ACAGGGCGAGGTGGACATCC;RSEQ=GGAGACCCAGGGCCTGGCAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:862:94:44,50:311,456:0.109:2,2:23.5:1.0:30.2:1.0:0.26743:1.29:60.0:30.333:0.1067:0.0:1.1 0/0:1017:5:1,4:474,535:0.0049:2,2:8.6:1.0:30.2:1.0:0.37875:3.53998:60.0:10.0:0.005:0.0:1.0 -11 68132731 . A G 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.10714;SOR=0.0;LSEQ=CATAGGAGCTTGGTGGGAGG;RSEQ=AGCAGATGGGGAGATGTCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:28.4:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:31.0:1.0:31.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -11 69069783 . T C 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCGTGTCCTCGTCTGTAG;RSEQ=CGGGCTGTCGGCAGGCACCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:23.8:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:19.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 -11 69515423 . G A 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTGCCTTTATCATTCTAAG;RSEQ=CCTTCTGGTCTGCAGCAGTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1.0:0,0:32.4:1.0:27.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 81185242 . G T 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=6e-05;SOR=0.0;LSEQ=CTTTCCTTTTCTCCTTCCAT;RSEQ=TTTCCTTTACTAAAAATTAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:11:6,5:92,47:0.0728:2,2:27.9:1.0:30.1:1.0:0.51475:1.62566:60.0:22.0:0.0743:0.0:1.1 0/0:208:0:0,0:134,74:0.0:2,0:22.9:1.0:31.3:1.0:1.0:0.0:60.0:416.0:1.0:0.0:0.2 -11 81185452 . TC T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.05466;SOR=0.0;LSEQ=CTCAAACATCCCAAAAGTCA;RSEQ=TTTGAAAGAGATCTCACTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:0,5:1,30:0.1389:1,0:34.6:1.0:30.8:1.0:1.0:0.0:60.0:10.0:0.1389:0.0:0.0 0/0:33:0:0,0:1,32:0.0:1,0:28.3:1.0:32.2:1.0:1.0:0.0:60.0:66.0:1.0:0.0:0.0 -11 85961166 . C T 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.2605;SOR=0.0;LSEQ=AATATAAAATATCTACAAAC;RSEQ=TTCTAACCTGTAGCTGGATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:7,1:0.3846:2,0:20.8:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.3846:0.0:1.0 0/0:4:0:0,0:4,0:0.0:0,0:38.3:1.0:31.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -11 85963619 . C T 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGTATTTATCATTCAAATAG;RSEQ=GTAAGAACTGGCTGTGATTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:0.6:0,2:30.3:1.0:28.8:1.0:1.0:0.0:60.0:12.0:0.6:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 85963632 . T C 60 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CAAATAGCGTAAGAACTGGC;RSEQ=GTGATTTTTTTAAAATTAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:0.625:0,2:31.8:1.0:26.0:1.0:1.0:0.0:60.0:10.0:0.625:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 85980945 . G T 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06833;SOR=0.0;LSEQ=TTATGTAACTATCTATGGTA;RSEQ=GAGGTTTTGGTCATTTCCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:5:5,0:62,1:0.0735:1,0:18.2:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.0746:0.0:2.0 0/0:52:0:0,0:52,0:0.0:1,0:23.8:1.0:32.6:1.0:1.0:0.0:60.0:104.0:1.0:0.0:1.0 -11 86333429 . TA T 190 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.0;SOR=0.12304;LSEQ=CAGGGATTGTGGGAGGGCAT;RSEQ=AAAAAAAAAAAGTTGTTTGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:81:31,50:106,101:0.2691:2,2:28.8:1.0:30.0:1.0:0.05037:1.68963:59.8:80.0:0.2667:0.0:0.3 0/1:324:14:7,7:150,156:0.0432:2,2:28.7:1.0:29.4:1.0:1.0:1.04:60.0:28.0:0.0438:0.0:0.4 -11 86807222 . GT AG 164 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACTTGGAAAACTAGCAAAA;RSEQ=TTTTTATCCGTTAAACTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:38:25,13:202,202:0.0854:2,2:21.1:1.0:31.3:1.0:0.08851:1.92:59.6:76.0:0.0862:0.0:2.5 0/0:535:0:0,0:269,257:0.0:2,0:25.0:1.0:31.2:1.0:1.0:0.0:60.0:130.5:0.9739:0.0:0.5 -11 86807229 . A AA 68 pSTD SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02064;SOR=0.0;LSEQ=AAAACTAGCAAAAGTTTTTT;RSEQ=TCCGTTAAACTCTTCTACAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:5:3,2:222,226:0.011:2,2:18.0:0.0:29.6:1.0:0.68404:1.53:60.0:10.0:0.0111:0.0:2.4 0/0:529:0:0,0:264,265:0.0:2,0:24.2:1.0:29.0:1.0:1.0:0.0:60.0:263.5:1.0:0.0:0.5 -11 86807230 . TC AT 95 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00087;SOR=0.0;LSEQ=AAACTAGCAAAAGTTTTTTA;RSEQ=CGTTAAACTCTTCTACAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:9:6,3:214,223:0.0201:2,2:18.7:1.0:30.0:1.0:0.33292:2.08:59.4:18.0:0.0203:0.0:2.6 0/0:526:0:0,0:261,264:0.0:2,0:24.2:1.0:29.2:1.0:1.0:0.0:60.0:130.25:0.9981:0.0:0.5 -11 86807231 . C CC 70 NM4 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.02064;SOR=0.0;LSEQ=AACTAGCAAAAGTTTTTTAT;RSEQ=CGTTAAACTCTTCTACAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:447:5:3,2:212,226:0.0112:2,2:17.4:1.0:30.4:1.0:0.67734:1.6:59.0:10.0:0.0114:0.0:4.4 0/0:522:0:0,0:257,263:0.0:2,0:24.4:1.0:30.6:1.0:1.0:0.0:60.0:64.0:0.9961:0.0:0.5 -11 88359287 . AT GG 85 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATTGAGAGCAGCCTTTACA;RSEQ=TTACACCAAATATAGAGAGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:23.8:1.0:32.9:1.0:1.0:0.0:60.0:12.0:1.0:0.3333:0.7 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 94153641 . C G 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGTAAGCCAGAAAAATAATT;RSEQ=AAGTCATTTTATATTTGGTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:24.6:1.0:29.2:1.0:1.0:0.0:60.0:4.0:0.6667:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 94203801 . C A 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04473;LSEQ=CCCTTTAATACGCAGCAAAC;RSEQ=AACATGTCTGAAGTGGAGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:37:15,22:145,252:0.0851:2,2:27.9:1.0:30.3:1.0:0.72199:1.18:60.0:36.0:0.0845:0.0:1.1 0/0:484:2:2,0:197,285:0.0041:2,0:1.0:0.0:25.0:0.0:0.16855:0.0:60.0:4.0:0.0041:0.0:1.0 -11 94770943 . G T 148 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCGCCTTCGTCCGCTTTCAC;RSEQ=ACCGGAGCGACGCGCAAGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:39:8,31:152,361:0.0705:2,2:24.5:1.0:28.1:1.0:0.27408:1.63027:52.9:38.0:0.0704:0.0:1.1 0/0:435:0:0,0:170,265:0.0:2,0:25.1:1.0:30.2:1.0:1.0:0.0:59.9:86.0:1.0:0.0:0.2 -11 94771621 . GA G 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.06846;SOR=0.0;LSEQ=AAGGACAAGTGCCCTCCTAG;RSEQ=AAATGATCATCAGCTAACGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:5:2,3:54,259:0.0157:2,2:8.0:1.0:29.2:1.0:0.21371:3.18:51.8:10.0:0.0158:0.0126:0.2 0/0:257:0:0,0:51,206:0.0:2,0:22.5:1.0:29.6:1.0:1.0:0.0:45.6:256.0:1.0:0.0:0.1 -11 95825356 . TTGC T 85 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.0;MSILEN=3.0;SSF=0.03557;SOR=0.13645;LSEQ=TGTTGCTGTTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGTTGCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:7:2,5:118,142:0.0262:2,2:27.1:1.0:30.6:1.0:0.46394:2.07213:50.9:14.0:0.0266:0.0037:0.6 0/0:274:1:1,0:130,143:0.0036:2,0:19.0:0.0:32.0:0.0:0.4781:0.0:60.0:2.0:0.0037:0.0:0.0 -11 99322049 . T C 84 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GATGACCCCATGTTACATTA;RSEQ=ACAAAAGTTATGAGATGAAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:16.0:1.0:32.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 100913165 . G A 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TACATGCTTCTTAAATACTT;RSEQ=GTTTGACTTAGTTTACAGCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:17.6:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 100999043 . G T 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01022;LSEQ=GCCCCCGGCGGGACAGCCGC;RSEQ=GCTCCTCCTCCAGCCGCCGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1554:112:56,56:768,671:0.0721:2,2:23.7:1.0:30.6:1.0:0.49345:1.14446:60.0:55.0:0.0716:0.0:1.1 0/0:1262:1:0,1:657,603:0.0008:2,0:1.0:0.0:26.0:0.0:0.47898:0.0:60.0:2.0:0.0008:0.0:1.0 -11 100999194 . G T 205 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGGGCCCCGGACCAGTGA;RSEQ=GGCTCTCAGAGGCCGGGAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1513:120:60,60:702,689:0.0793:2,2:27.6:1.0:29.8:1.0:0.92456:1.01886:60.0:16.143:0.0765:0.0:1.3 0/0:1236:0:0,0:607,628:0.0:2,0:23.2:1.0:30.6:1.0:1.0:0.0:60.0:55.136:0.9992:0.0:0.3 -11 102057068 . C A 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00188;SOR=0.07796;LSEQ=GAATCAGATTTTTAGGGCTC;RSEQ=TCAGGTTGGGGTGGGGGAAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:0,13:0,6:0.6842:0,1:23.6:1.0:32.2:1.0:1.0:0.0:60.0:26.0:0.7222:0.0:1.2 0/1:15:2:0,2:1,12:0.1333:1,0:7.0:1.0:29.5:1.0:1.0:0.0:60.0:4.0:0.1333:0.0:1.0 -11 102077200 . G A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.11111;SOR=0.0;LSEQ=TTATTAATAACTTACGTGGC;RSEQ=GGATACACCAATATGACATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1.0:0,0:19.9:1.0:29.6:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.1 0/0:1:0:0,0:0,1:0.0:0,0:44.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -11 102098001 . G C 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.2;SOR=0.0;LSEQ=GAGCTGCCAGCTTCAATTAG;RSEQ=ATTAACTTGTCTATTTCACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:0.6154:0,0:25.0:1.0:33.5:1.0:1.0:0.0:60.0:16.0:0.6154:0.0:1.0 0/0:2:0:0,0:2,0:0.0:0,0:21.5:1.0:32.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -11 102098343 . G A 54 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07045;SOR=0.0;LSEQ=TTTATTCCTCTTAGTAACCT;RSEQ=ACTTAACAGTGGGATATGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:5:4,1:143,341:0.0102:2,2:11.2:1.0:23.4:1.0:0.03031:9.49:60.0:4.0:0.0083:0.0:1.8 0/0:387:0:0,0:127,260:0.0:2,0:23.0:1.0:30.8:1.0:1.0:0.0:60.0:76.4:1.0:0.0:0.3 -11 102206417 . T C 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.44444;SOR=0.0;LSEQ=AAGACAGGGTATTGCTATGT;RSEQ=GCCCAGTCTGGTCTCTGACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:34.8:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.625:0.0:1.0 0/0:2:0:0,0:2,0:0.0:0,0:29.0:1.0:31.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -11 108115594 . C T 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.05224;LSEQ=AGACTTTGGCTGTCAACTTT;RSEQ=GAATTCGAGTGTGTGAATTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:857:18:11,7:411,428:0.021:2,2:25.4:1.0:30.1:1.0:0.34787:1.64:60.0:17.0:0.02:0.0:1.0 0/0:894:1:0,1:444,448:0.0011:2,0:1.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 -11 108124299 . G A 96 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGAATTTGCCTTTGAGATT;RSEQ=TAACTTGTATTTTTTCTCTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1.0:0,0:23.6:1.0:27.0:1.0:1.0:0.0:60.0:11.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 108127288 . T C 115 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGTTCTGGGGTACATGATG;RSEQ=AGAGCATGCAGGTTTGTTAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:1.0:0,1:18.5:1.0:31.1:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 108143456 . C G 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTTTTCCCGTAGGCTGATC;RSEQ=TTATTCAAAATGGGCCATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1030:305:172,133:394,328:0.2961:2,2:25.3:1.0:30.9:1.0:0.63091:1.08:60.0:100.667:0.2964:0.0:1.1 0/0:925:0:0,0:500,423:0.0:2,0:8.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -11 108160632 . C T 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGACAAAGACTCACTCTGTC;RSEQ=GCCCAGGCTGGGTGCAGTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:30:0,30:1,25:0.5357:1,1:24.4:1.0:30.7:1.0:0.46429:0.0:60.0:60.0:0.5455:0.0:1.1 0/0:46:0:0,0:0,46:0.0:1,0:9.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 -11 108188342 . TTATATA T 105 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=19.0;MSILEN=2.0;SSF=0.03136;SOR=0.0;LSEQ=TGAATATAACAGGAGTTGTT;RSEQ=TATATATATATATATATATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:13:0,13:0,36:0.2097:1,1:37.8:1.0:28.6:1.0:1.0:0.0:58.2:26.0:0.2167:0.0161:1.5 0/0:20:0:0,0:0,13:0.0:1,0:15.3:1.0:26.6:1.0:1.0:0.0:58.6:12.0:0.6316:0.0:0.7 -11 108188462 . T A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.06061;SOR=0.0;LSEQ=TATATATATATAAAAAAATA;RSEQ=ATAGTAGATGTTGCAAGCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:24.2:1.0:31.2:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.5 0/0:3:0:0,0:0,3:0.0:0,0:19.0:1.0:29.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -11 108206868 . TA T 74 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.0;MSILEN=1.0;SSF=0.27249;SOR=0.0;LSEQ=ACCCCATCTTGACAAAAAGT;RSEQ=AAAAAAAAAAAAAAGCCAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:21.7:1.0:29.0:1.0:1.0:0.0:60.0:12.0:0.3333:0.0556:0.5 0/0:5:0:0,0:1,4:0.0:2,0:20.8:1.0:28.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 -11 108224757 . A T 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00047;SOR=0.0;LSEQ=GTTTGAGTCCAGCCTAGGCA;RSEQ=TACAGCAAGACCCTGTATCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:1,12:0,12:0.52:0,1:20.6:1.0:31.3:1.0:1.0:0.0:60.0:26.0:0.52:0.0:2.0 0/0:15:0:0,0:0,15:0.0:1,0:14.5:1.0:30.9:1.0:1.0:0.0:58.7:30.0:1.0:0.0:1.1 -11 108224791 . CACACAA C 92 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=21.0;MSILEN=2.0;SSF=0.00033;SOR=0.0;LSEQ=TGTATCTAAAAAAATACACA;RSEQ=ACACACACACACACACACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:8:1,7:0,0:1.0:0,2:18.5:1.0:30.9:1.0:1.0:0.0:55.4:16.0:1.0:0.75:1.6 0/0:6:0:0,0:0,6:0.0:0,0:28.0:1.0:30.5:1.0:1.0:0.0:56.7:12.0:1.0:0.0:1.5 -11 108225473 . G A 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00025;SOR=0.0;LSEQ=ACTACACATGAGAGTATACA;RSEQ=ATAAAGATACGTTGACAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:13:9,4:218,58:0.0447:2,2:18.7:1.0:30.0:1.0:0.48654:1.66714:60.0:26.0:0.045:0.0:2.1 0/0:266:0:0,0:192,73:0.0:2,0:22.0:1.0:31.5:1.0:1.0:0.0:60.0:87.333:1.0:0.0:0.8 -11 117226715 . G GAGCAGCAGC 87 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=10.0;MSILEN=3.0;SSF=0.00087;SOR=0.04884;LSEQ=TTGTCTGGGCCTGACTTGGA;RSEQ=AGCAGCAGCAGCAGCAGCAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:4,3:13,5:0.28:2,2:29.4:1.0:31.3:1.0:0.63956:1.89552:60.0:14.0:0.28:0.0:0.0 0/1:56:1:1,0:23,30:0.0179:2,0:42.0:0.0:33.2:0.0:0.44444:0.0:50.0:2.0:0.0182:0.0:1.0 -11 118342819 . T G 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=ACAGAAAGGATAAAGACCCC;RSEQ=TCGGGTCTCCTCATTAATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:18:10,8:431,438:0.0202:2,2:25.1:1.0:31.3:1.0:0.64252:1.27:60.0:36.0:0.0206:0.0:1.0 0/0:710:0:0,0:347,361:0.0:2,0:23.9:1.0:30.1:1.0:1.0:0.0:60.0:63.364:0.9986:0.0:0.2 -11 118370615 . C G 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=ACTGTGAAGATAAGCTCTTT;RSEQ=CTATTGGATATCAGTAAGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:15:8,7:208,288:0.0293:2,2:28.2:1.0:32.1:1.0:0.43201:1.58:60.0:30.0:0.0299:0.0:1.1 0/0:530:0:0,0:229,301:0.0:2,0:24.9:1.0:30.7:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.1 -11 118372452 . C G 220 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCATCACCAGACCGACCT;RSEQ=CTCATTCACAAACCTCTGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1401:119:69,50:677,600:0.0849:2,2:25.4:1.0:32.0:1.0:0.33682:1.22:60.0:118.0:0.0856:0.0:1.1 0/0:1404:0:0,0:737,664:0.0:2,0:24.8:1.0:30.9:1.0:1.0:0.0:60.0:86.563:0.9978:0.0:0.2 -11 119077003 . C T 71 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=CCCTCCGCCCGGATAGCCGG;RSEQ=GGCGGCGGCGGCGGCGGCGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:2,1:0.6667:2,2:29.3:1.0:27.8:1.0:1.0:2.24:60.0:5.0:0.625:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -11 119145274 . A G 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=TTTCAGTTTGTTGTTGTTCA;RSEQ=CCCCACTACTGTTAATTAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:11,2:6,0:0.6842:0,2:29.2:1.0:29.3:1.0:1.0:0.0:60.0:5.5:0.6471:0.0:1.8 0/0:2:0:0,0:2,0:0.0:0,0:15.5:1.0:30.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -11 121232871 . G A 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06761;LSEQ=ATTAGGCCGAAGCTGTAGAT;RSEQ=TCAGCCATGATGTAGGGCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:57:11,46:30,34:0.4672:2,2:12.2:1.0:30.5:1.0:0.00194:3.64883:33.0:114.0:0.4672:0.0:2.1 0/1:414:23:3,20:162,229:0.0556:2,2:11.2:1.0:29.6:1.0:0.00741:4.70241:32.3:46.0:0.0562:0.0:2.2 -11 121232886 . G A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.04336;LSEQ=TAGATGTCAGCCATGATGTA;RSEQ=GGCTGGAAGTGGTTTTTGTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:17:10,7:21,28:0.2576:2,2:22.1:1.0:27.8:1.0:0.27605:1.89:29.5:4.667:0.2258:0.0:2.7 0/1:342:5:1,4:145,191:0.0146:2,2:21.0:1.0:31.4:1.0:0.39715:3.02814:25.8:10.0:0.0147:0.0:2.8 -11 121232936 . TA GG 130 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.09204;LSEQ=GTCCAGCACTTCTGGAGCCA;RSEQ=TAGCGTTTGGTGCCCACCCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:18:18,0:28,23:0.2609:2,1:22.2:1.0:31.2:1.0:0.00026:0.0:31.1:36.0:0.2647:0.1014:1.1 0/1:257:8:7,1:119,130:0.0311:2,2:11.6:1.0:29.6:1.0:0.03322:7.6:32.0:16.0:0.0315:0.0195:1.1 -11 121779664 . T C 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.00588;SOR=0.0;LSEQ=GGCTTTATGCATTTATCTCT;RSEQ=GGTTCCAGGCACAGCTTTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,1:0.9286:0,1:17.0:1.0:30.9:1.0:1.0:0.0:60.0:26.0:0.9286:0.0:1.4 0/0:3:0:0,0:0,3:0.0:0,0:32.3:1.0:26.3:1.0:1.0:0.0:60.0:2.0:1.0:0.0:0.7 -11 123606029 . A C 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08544;LSEQ=ATCCTACAACGTATGCATTG;RSEQ=CAGAAGAGTTCCTGCTCTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:84:18,66:27,71:0.4615:2,2:24.4:1.0:31.9:1.0:0.39072:1.39182:60.0:168.0:0.4641:0.0:1.0 0/1:177:12:3,9:42,123:0.0678:2,2:19.1:1.0:31.7:1.0:1.0:1.02426:60.0:24.0:0.0686:0.0:1.2 -11 132534934 . G A 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07302;SOR=0.0;LSEQ=ACAGTGCCACACTAACACCA;RSEQ=CTGGAGGGGAGATGTCACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:5:4,1:71,202:0.018:2,2:17.0:1.0:27.8:1.0:0.01978:11.27:60.0:10.0:0.0184:0.0:1.2 0/0:211:0:0,0:72,139:0.0:2,0:22.4:1.0:31.6:1.0:1.0:0.0:60.0:104.5:1.0:0.0:0.5 -12 401969 . C A 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTTCTGTGCTGCGCACACAG;RSEQ=ATTCTCATCATCAGACTCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1679:41:19,22:796,839:0.0244:2,2:27.0:1.0:28.5:1.0:0.87459:1.09847:60.0:9.25:0.0222:0.0:1.2 0/0:1130:0:0,0:552,577:0.0:2,0:24.8:1.0:31.6:1.0:1.0:0.0:60.0:111.9:0.9991:0.0:0.1 -12 406427 . G C 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TTTAACTTATTTTATGACAA;RSEQ=GCCCAAAATGGAGGCTTTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:29:2,27:17,232:0.1043:2,2:24.0:1.0:30.1:1.0:1.0:1.01:60.0:58.0:0.1058:0.0:1.1 0/0:135:0:0,0:16,119:0.0:2,0:25.0:1.0:30.0:1.0:1.0:0.0:60.0:44.0:1.0:0.0:0.1 -12 416764 . C A 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTTCATCTGTGGCTAGAGC;RSEQ=TGCCGCGCTCTATCTTGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1194:85:45,40:608,500:0.0712:2,2:25.2:1.0:30.2:1.0:0.7359:1.08082:60.0:41.5:0.0709:0.0:1.1 0/0:807:0:0,0:428,379:0.0:2,0:24.2:1.0:30.8:1.0:1.0:0.0:60.0:114.286:1.0:0.0:0.2 -12 427077 . G A 77 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.53924;SOR=0.0;LSEQ=GGGAGAGAGGAGAATCTCCC;RSEQ=GTTTCCTTCAGGCCCTGGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:6,0:14,0:0.3:1,0:19.7:1.0:30.0:1.0:1.0:0.0:60.0:12.0:0.3:0.0:2.0 0/0:3:0:0,0:3,0:0.0:0,0:19.7:1.0:29.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -12 459805 . C A 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCTCTTCTTCTGGCAGAAT;RSEQ=TTTCTCCGCCCATCCTTCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1658:25:15,10:872,759:0.0151:2,2:23.6:1.0:29.4:1.0:0.551:1.31:60.0:50.0:0.0152:0.0:1.1 0/0:1088:0:0,0:575,512:0.0:2,0:25.5:1.0:31.3:1.0:1.0:0.0:60.0:82.615:1.0:0.0:0.2 -12 461807 . A G 75 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CATGCCTAGGGATGCCTAAC;RSEQ=TTCTTGGCATACCCAGTGGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:36.2:1.0:29.3:1.0:1.0:0.0:60.0:5.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 465673 . C G 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATCTGAAGTTTCTTCAGTT;RSEQ=CGTGTTTCTACTCACATCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1196:98:38,60:437,661:0.0819:2,2:27.0:1.0:32.2:1.0:0.91432:1.04384:60.0:196.0:0.0832:0.0:1.2 0/0:932:0:0,0:384,547:0.0:2,0:25.2:1.0:30.6:1.0:1.0:0.0:60.0:83.636:0.9989:0.0:0.1 -12 1022352 . A G 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00036;SOR=0.05979;LSEQ=TCTGTCCAGAGCCTCTCCCT;RSEQ=CTAGAGTGATGGACAAGCTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:25:25,0:44,0:0.3623:1,1:23.1:1.0:33.4:1.0:1.0:0.0:60.0:50.0:0.3623:0.0:1.0 0/1:31:1:1,0:30,0:0.0323:1,0:21.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0323:0.0:1.0 -12 1034943 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGATGAGTATGAAAAGATTA;RSEQ=GGCGCCATTCACAAAACCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:22.0:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:23.5:1.0:31.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -12 1036562 . AG A 145 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00068;SOR=0.0;LSEQ=GCTACAGGGGCACGGGCAGA;RSEQ=GCTGGGTGAGAATCCATCGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:22:0,22:0,52:0.2973:1,1:22.9:1.0:32.6:1.0:1.0:0.0:60.0:44.0:0.2973:0.0676:0.2 0/0:26:0:0,0:0,26:0.0:1,0:20.9:1.0:29.6:1.0:1.0:0.0:60.0:25.0:1.0:0.0:0.3 -12 1038602 . AT CA 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=AAACAACTTATTAACAAAAC;RSEQ=ATTTTTGTTTTCATCAATGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:0,0:0.8333:0,0:20.6:1.0:30.7:1.0:1.0:0.0:60.0:10.0:1.0:0.1667:0.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 1038742 . A G 103 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.47826;SOR=0.0;LSEQ=CCAAAAAATACATCCTTTGC;RSEQ=ACAATTTTTATATATGGTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:11,0:10,0:0.5238:0,0:21.7:1.0:30.0:1.0:1.0:0.0:60.0:22.0:0.5238:0.0:1.1 0/0:2:0:0,0:2,0:0.0:0,0:39.0:1.0:29.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -12 1038766 . C G 115 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.53613;SOR=0.0;LSEQ=ATTTTTATATATGGTGAAAA;RSEQ=TTTTAGGTGTCAGCTTGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:12,0:21,0:0.3636:1,0:19.6:1.0:32.1:1.0:1.0:0.0:60.0:24.0:0.3636:0.0:1.2 0/0:3:0:0,0:3,0:0.0:0,0:27.3:1.0:30.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -12 1038854 . C T 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.00168;SOR=0.0;LSEQ=AGAGTATTTGAATTCCACCA;RSEQ=TCTAGGGAACGCTGGCTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:25:25,0:140,2:0.1497:1,1:24.8:1.0:31.1:1.0:1.0:0.0:60.0:50.0:0.1515:0.0:1.1 0/0:51:0:0,0:48,3:0.0:2,0:22.0:1.0:31.6:1.0:1.0:0.0:60.0:102.0:1.0:0.0:0.1 -12 1040143 . TA T 90 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.0;MSILEN=1.0;SSF=0.52273;SOR=0.0;LSEQ=CAAGACCCTGTCTTTAAAAA;RSEQ=AAAAAAAAAAAAGATGATGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:7,0:10,0:0.3684:0,0:27.0:1.0:32.3:1.0:1.0:0.0:60.0:14.0:0.3684:0.0526:0.0 0/0:3:0:0,0:3,0:0.0:0,0:11.7:1.0:29.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -12 9085320 . T G 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACACAGCTACACACCTCCAG;RSEQ=TGGCGCAGCAGCAGCAGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:25:13,12:109,106:0.1042:2,2:27.9:1.0:31.0:1.0:1.0:1.05:33.2:50.0:0.1055:0.0:1.0 0/0:284:0:0,0:147,137:0.0:2,0:31.5:1.0:28.2:1.0:1.0:0.0:35.8:39.571:1.0:0.0:0.1 -12 9848470 . A T 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTGATGATGATGATGATGA;RSEQ=GATGATGATGATGATGATGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:76:49,27:97,52:0.3378:2,2:27.8:1.0:30.7:1.0:1.0:1.02776:57.8:37.0:0.3426:0.0:2.2 0/0:223:0:0,0:128,75:0.0:2,0:23.4:1.0:30.0:1.0:1.0:0.0:59.9:49.75:0.99:0.0:0.9 -12 12006544 . G A 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01033;LSEQ=CTGAGGTTTAGACAAATCCA;RSEQ=GAAGTTTAATTGTTAACTTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:170:83,87:421,407:0.17:2,2:21.5:1.0:30.6:1.0:0.67391:1.08415:60.0:41.5:0.169:0.0:1.1 0/0:949:2:2,0:477,469:0.0021:2,0:16.5:1.0:28.0:1.0:0.49953:0.0:60.0:4.0:0.0021:0.0:1.0 -12 12007893 . C G 319 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04363;LSEQ=ATTTAATTTAGGCCCTGGAC;RSEQ=TAGTTCCAGAATAGGTGTTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1515:1234:489,745:116,161:0.8145:2,2:26.7:1.0:31.1:1.0:0.49802:1.09762:60.0:175.286:0.8169:0.0:1.1 0/1:1638:263:115,148:613,757:0.1606:2,2:23.8:1.0:30.4:1.0:0.78668:1.04213:60.0:64.75:0.1604:0.0:1.2 -12 12009741 . A G 253 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATATGTTAACATACAGAAAG;RSEQ=TCTGGTTCTGAAAAAAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1524:267:132,135:648,604:0.1752:2,2:26.2:1.0:31.4:1.0:0.50073:1.09716:60.0:43.5:0.1764:0.0:1.1 0/0:1382:0:0,0:699,683:0.0:2,0:24.9:1.0:29.1:1.0:1.0:0.0:60.0:52.154:1.0:0.0:0.1 -12 12010056 . G A 313 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0802;LSEQ=CCTTGTGATTTCACCTCGTC;RSEQ=TGGCCACAAACTTAACCAGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1886:1210:599,611:333,340:0.6416:2,2:24.4:1.0:30.6:1.0:1.0:1.0:60.0:92.077:0.6429:0.0:1.1 0/1:1626:204:107,97:701,721:0.1255:2,2:24.7:1.0:29.9:1.0:0.41096:1.13:60.0:101.0:0.1252:0.0:1.1 -12 12011340 . T A 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTTAAATATATATATATAT;RSEQ=TTTTTTTAATTGTCATTTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1197:181:90,91:502,509:0.1512:2,2:22.4:1.0:29.2:1.0:1.0:1.0:59.9:44.25:0.15:0.0:1.1 0/0:951:0:0,0:237,215:0.0:2,0:21.1:1.0:29.7:1.0:1.0:0.0:59.9:112.0:0.9978:0.0:0.2 -12 12013626 . T TC 255 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.00809;LSEQ=CTGGCTGTTATTTGGTTGTT;RSEQ=CCCCCCCTCTGTTTGTGTAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1779:296:149,147:772,707:0.1664:2,2:28.3:1.0:31.1:1.0:0.56688:1.07722:60.0:48.333:0.1659:0.0157:1.0 0/0:1862:3:3,0:925,931:0.0016:2,0:42.3:1.0:31.3:1.0:0.12419:0.0:60.0:6.0:0.0016:0.0:0.3 -12 12016089 . C T 220 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00641;LSEQ=TGGAAACTTATCGGTCAAAA;RSEQ=TTTCACTAAAGGCAGTTTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1860:138:66,72:822,898:0.0742:2,2:25.1:1.0:31.0:1.0:1.0:1.0:60.0:276.0:0.0749:0.0:1.3 0/0:1949:1:0,1:934,1011:0.0005:2,0:1.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0005:0.0:2.0 -12 12018392 . C T 239 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01438;LSEQ=TATACATTGCAGATGGTTAA;RSEQ=GTATCTCTTAAGTTTTTTTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1441:242:120,122:576,623:0.1679:2,2:23.4:1.0:30.3:1.0:0.67273:1.06:60.0:79.667:0.1683:0.0:1.1 0/0:1384:4:0,4:634,746:0.0029:2,0:1.0:0.0:25.3:1.0:0.12973:0.0:60.0:8.0:0.0029:0.0:1.0 -12 12018911 . T C 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTATTCTACTCTGTTTTTT;RSEQ=CTATATTCTCCTTCTTGGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1760:90:45,45:888,782:0.0511:2,2:22.9:1.0:31.4:1.0:0.58862:1.13547:59.8:180.0:0.0516:0.0:1.1 0/0:1566:0:0,0:804,761:0.0:2,0:23.1:1.0:29.3:1.0:1.0:0.0:60.0:119.385:0.9994:0.0:0.1 -12 12022533 . C T 268 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACATGATCCGCCGCCTCTC;RSEQ=CCGGCTGAGAGAGCTCAGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1239:474:201,273:334,430:0.3826:2,2:23.7:1.0:30.2:1.0:0.67962:1.05496:60.0:58.25:0.3835:0.0:1.2 0/0:1148:0:0,0:526,620:0.0:2,0:23.8:1.0:30.2:1.0:1.0:0.0:60.0:70.625:0.9982:0.0:0.2 -12 12027431 . TATGTGTA CGTGTG 68 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.07537;SOR=0.0;LSEQ=TATGTGCGTGTGTACACACA;RSEQ=TGTGCGTGTGTACACACATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:3,0:0.625:0,2:23.4:1.0:29.6:1.0:1.0:0.0:46.2:10.0:0.625:0.125:3.0 0/0:5:0:0,0:5,0:0.0:0,0:1.0:0.0:28.0:1.0:1.0:0.0:42.6:10.0:1.0:0.0:2.0 -12 12027664 . GTA G 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.0;MSILEN=2.0;SSF=0.16133;SOR=0.0;LSEQ=GTATATGTGTATATATATGT;RSEQ=TATATATATGAAATTTTTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:5:3,2:158,83:0.0203:2,2:28.6:1.0:32.0:1.0:1.0:1.26778:59.0:10.0:0.0204:0.0:0.2 0/0:154:0:0,0:97,57:0.0:2,0:24.9:1.0:28.9:1.0:1.0:0.0:59.8:76.0:1.0:0.0:0.2 -12 12029765 . A G 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGTTGGGTCATTAATCCT;RSEQ=CAGCAGGCAAGACACAGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:78:45,33:251,203:0.1463:2,2:21.7:1.0:31.8:1.0:0.7131:1.1:60.0:156.0:0.1477:0.0:1.8 0/0:431:0:0,0:232,199:0.0:2,0:22.8:1.0:28.3:1.0:1.0:0.0:60.0:70.833:1.0:0.0:0.8 -12 12030834 . TC T 94 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.00758;SOR=0.0;LSEQ=TTAATTGCTACGTGTCACTG;RSEQ=CCCCCCTGCCTCACTGCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:8:3,5:167,210:0.0208:2,2:30.6:1.0:31.5:1.0:1.0:1.32445:60.0:16.0:0.0212:0.0:0.1 0/0:373:0:0,0:168,203:0.0:2,0:23.6:1.0:30.7:1.0:1.0:0.0:60.0:52.0:0.9945:0.0:0.2 -12 12031265 . G A 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGAGTGGAAAATAATAGAA;RSEQ=GGGCTTGAGGAGACTGGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:61:35,26:187,134:0.1597:2,2:27.9:1.0:29.7:1.0:0.88862:1.0366:60.0:19.333:0.1538:0.0:1.1 0/0:396:0:0,0:214,182:0.0:2,0:24.6:1.0:30.7:1.0:1.0:0.0:60.0:78.2:1.0:0.0:0.2 -12 12308074 . G A 110 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00288;SOR=0.066;LSEQ=TGGGAGGCGGATGTTGCAGT;RSEQ=AGCCAAGATCACGCCACTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:14,0:14,0:0.5:1,1:19.1:1.0:28.9:1.0:1.0:0.0:60.0:28.0:0.5:0.0:2.1 0/1:17:1:1,0:16,0:0.0588:1,0:13.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0588:0.0:2.0 -12 12308087 . G A 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00064;SOR=0.08927;LSEQ=TTGCAGTGAGCCAAGATCAC;RSEQ=CCACTTTACTCCAGCCTGGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:17:17,0:16,0:0.5152:1,1:25.5:1.0:30.5:1.0:1.0:0.0:60.0:34.0:0.5152:0.0:1.8 0/1:24:2:2,0:22,0:0.0833:1,0:17.0:1.0:31.5:1.0:1.0:0.0:60.0:4.0:0.0833:0.0:2.0 -12 12767856 . A G 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=GGCTGGAGTGCAGTGGCACG;RSEQ=TCTCAGCTCACTGCAATCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1.0:0,2:32.0:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:41.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -12 12873211 . A T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.02984;SOR=0.0;LSEQ=TTTGATCTGGCCCTGTTCTG;RSEQ=CATGCAATGAGGCATTTGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:6:1,5:1,65:0.0833:1,2:23.2:1.0:30.3:1.0:0.1608:11.96:60.0:12.0:0.0833:0.0:1.7 0/0:63:0:0,0:4,59:0.0:2,0:23.0:1.0:29.6:1.0:1.0:0.0:60.0:62.0:1.0:0.0:0.4 -12 16753747 . G A 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGGTCCTTGATCTTTCGGTT;RSEQ=CAGCCAGCACAACCTTTCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:25:7,18:17,113:0.1613:2,2:22.4:1.0:29.2:1.0:0.07212:2.57:60.0:50.0:0.1678:0.0:1.0 0/0:112:0:0,0:22,89:0.0:2,0:23.1:1.0:32.0:1.0:1.0:0.0:60.0:222.0:1.0:0.0:0.1 -12 18467122 . T C 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AATACATGTTTATTTAAATA;RSEQ=ATTCATTGAAACATGATGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:67:1,66:0,37:0.6442:1,1:23.4:1.0:32.7:1.0:1.0:0.0:60.0:134.0:0.6442:0.0:1.0 0/0:51:0:0,0:0,51:0.0:1,0:20.8:1.0:28.9:1.0:1.0:0.0:60.0:102.0:1.0:0.0:0.2 -12 18473881 . T G 280 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03952;LSEQ=ACTCAATAAATATTAATATA;RSEQ=TCTGCTGTCTACAGCATGAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:659:444:289,155:136,79:0.6737:2,2:24.4:1.0:31.9:1.0:0.66471:1.08:60.0:110.0:0.6728:0.0:1.1 0/1:452:34:22,12:264,154:0.0752:2,2:25.0:1.0:31.4:1.0:1.0:1.07:60.0:68.0:0.0754:0.0:1.1 -12 18524061 . T G 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATTATAAGAACATTTTCAT;RSEQ=AAAATATCAGTACAATTGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:24:17,7:262,85:0.0647:2,2:26.5:1.0:31.9:1.0:0.62703:1.26836:60.0:48.0:0.0652:0.0:1.0 0/0:303:0:0,0:217,86:0.0:2,0:24.1:1.0:29.1:1.0:1.0:0.0:60.0:74.75:1.0:0.0:0.1 -12 18690977 . A G 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00011;SOR=0.0;LSEQ=GAAGGAAATTTATCTATTAC;RSEQ=GTAGAGAAAAAAAAAAGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:13:13,0:41,0:0.2407:1,1:24.9:1.0:28.5:1.0:1.0:0.0:60.0:12.0:0.2264:0.0:1.3 0/0:52:0:0,0:52,0:0.0:1,0:18.8:1.0:30.3:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.1 -12 18715728 . T G 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCCATAAGCCCTGCCAAA;RSEQ=CTACTTCACAGACTTTTCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:532:45:21,24:238,248:0.0846:2,2:27.7:1.0:31.9:1.0:0.87635:1.09657:60.0:90.0:0.0854:0.0:1.0 0/0:946:0:0,0:469,476:0.0:2,0:25.0:1.0:29.0:1.0:1.0:0.0:60.0:71.692:0.9989:0.0:0.1 -12 18719938 . G T 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.00853;SOR=0.0;LSEQ=CAGATCACAGAAGATTCAGA;RSEQ=ATCTAAATCATTACATGGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:5:2,3:203,270:0.0104:2,2:14.8:1.0:27.4:1.0:1.0:1.12746:60.0:10.0:0.0106:0.0:1.0 0/0:760:0:0,0:337,420:0.0:2,0:26.4:1.0:31.1:1.0:1.0:0.0:60.0:74.7:0.9973:0.0:0.2 -12 21600952 . CG TA 88 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=CATGCGTACTTTTGATAGCA;RSEQ=TGTGAAGGTATCTCTCTAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:9:6,3:21,16:0.1837:2,2:29.4:1.0:27.8:1.0:0.71598:1.51:57.8:8.0:0.2051:0.0:1.8 0/0:93:0:0,0:48,43:0.0:2,0:25.9:1.0:29.0:1.0:1.0:0.0:59.9:7.273:1.0:0.0:1.4 -12 23618113 . G A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02778;SOR=0.0;LSEQ=AAGAAAAACAAGCAGAAAGT;RSEQ=ACAACAACAGCATCAACAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1.0:0,2:26.3:1.0:29.3:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:2:0:0,0:1,1:0.0:2,0:25.0:1.0:21.0:1.0:1.0:0.0:60.0:1.0:1.0:0.0:1.5 -12 25368084 . T C 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAAACTTTTCCCTTAAAAA;RSEQ=AAAGGTAAATATCAGTTTCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1.0:0,0:28.6:1.0:33.3:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.7 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 25378224 . ATATATATATATATATATATATATA T 78 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=22;MSI=24.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TTTGTTGCCCTGTTCTTTAT;RSEQ=TATATATATATATATATATA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:0,0:0.6667:0,0:17.7:1.0:30.4:1.0:1.0:0.0:60.0:12.0:0.6667:0.6667:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 25398285 . C A 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=GGCACTCTTGCCTACGCCAC;RSEQ=AGCTCCAACTACCACAAGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:114:49,65:386,494:0.1146:2,2:25.4:1.0:29.9:1.0:0.92017:1.03649:60.0:37.0:0.1129:0.0:1.1 0/0:666:0:0,0:289,377:0.0:2,0:24.7:1.0:30.8:1.0:1.0:0.0:60.0:221.0:1.0:0.0:0.1 -12 27578740 . G A 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00256;SOR=0.0;LSEQ=TCTAGAGAGTCAACCATCAT;RSEQ=AATTATAAGGTTCTATTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:13,0:12,0:0.52:0,1:30.8:1.0:28.8:1.0:1.0:0.0:60.0:26.0:0.52:0.0:1.0 0/0:11:0:0,0:11,0:0.0:0,0:17.6:1.0:31.3:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.1 -12 30848675 . C T 98 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.17222;SOR=0.0;LSEQ=CAGCCTCCTCTTCCGCGACC;RSEQ=CTGGATTACCTCACACCCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:6,3:14,13:0.25:2,2:18.8:1.0:31.0:1.0:0.70027:1.83:60.0:18.0:0.25:0.0:1.7 0/0:10:0:0,0:5,5:0.0:2,0:20.7:1.0:30.3:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 -12 31932814 . A C 118 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01992;SOR=0.10853;LSEQ=ATCCCCTCGGAGGGTTTTAC;RSEQ=AACATTTACAATTTTCTTCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:14,0:19,0:0.4242:1,1:12.4:1.0:31.1:1.0:1.0:0.0:60.0:28.0:0.4242:0.0:1.0 0/1:14:1:1,0:12,1:0.0714:1,0:6.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0769:0.0:1.0 -12 32411481 . C T 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0419;SOR=0.0;LSEQ=GGGGACCACTACCACCAAGA;RSEQ=GCAGAGACCAGTAATGGCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:5,1:0.5714:2,0:24.8:1.0:31.8:1.0:0.42857:0.0:60.0:16.0:0.5714:0.0:2.3 0/0:6:0:0,0:6,0:0.0:0,0:27.3:1.0:31.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.3 -12 38601111 . A T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.01692;SOR=0.0;LSEQ=TACAAGAAATGTAAAAAAAC;RSEQ=CATTAAAATCAACCCCAAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:0,7:0,28:0.2:1,0:33.3:1.0:26.7:1.0:1.0:0.0:60.0:6.0:0.1765:0.0:1.1 0/0:26:0:0,0:2,24:0.0:2,0:24.9:1.0:29.8:1.0:1.0:0.0:59.4:52.0:1.0:0.0:0.0 -12 43130905 . G A 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.25359;SOR=0.0;LSEQ=GTTTTCTGGCATGAAACATA;RSEQ=TTTTATTTGTTTTCAGACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:8,0:10,0:0.4444:0,0:32.4:1.0:30.3:1.0:1.0:0.0:60.0:16.0:0.4444:0.0:1.0 0/0:4:0:0,0:4,0:0.0:0,0:10.3:1.0:33.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -12 43131208 . T C 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0116;LSEQ=TAGATCGGGTATGTATTCTT;RSEQ=TGGAGTTATCAAATATAGCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:24:4,20:0,10:0.7059:0,2:22.1:1.0:31.4:1.0:0.29576:0.0:60.0:23.0:0.697:0.0:1.2 0/1:40:1:0,1:3,36:0.025:2,0:19.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.025:0.0:2.0 -12 46208438 . A G 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0063;SOR=0.0;LSEQ=CAAAACTCCATCTCAAAAAA;RSEQ=TAATAAACTTCCCTCCTCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:0.8462:0,0:28.4:1.0:32.5:1.0:1.0:0.0:60.0:22.0:0.8462:0.0:1.1 0/0:4:0:0,0:4,0:0.0:0,0:10.3:1.0:30.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -12 46254505 . C G 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=GAAATGTATAACAACATAAT;RSEQ=AAATTTATAAGACTATACTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:11:11,0:98,10:0.0924:2,0:29.1:1.0:32.5:1.0:0.59561:0.0:60.0:22.0:0.0932:0.0:1.1 0/0:177:0:0,0:157,19:0.0:2,0:21.8:1.0:30.8:1.0:1.0:0.0:60.0:24.143:1.0:0.0:0.1 -12 46287550 . A G 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGTGAATTTAGTTTATTTT;RSEQ=TTTTTACATATAAGTTAATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:13:3,10:25,88:0.1032:2,2:29.5:1.0:29.1:1.0:1.0:1.06:60.0:5.5:0.0894:0.0:1.2 0/0:210:0:0,0:61,149:0.0:2,0:22.5:1.0:29.1:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.1 -12 49421368 . G A 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.04448;SOR=0.0;LSEQ=TCAGCCTTTCGAGTAGCTGG;RSEQ=ATTACAGGCACGCACCATCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:13,3:9,3:0.5714:2,2:30.5:1.0:30.4:1.0:1.0:1.43:60.0:32.0:0.5714:0.0:1.1 0/0:5:0:0,0:4,1:0.0:2,0:28.0:1.0:32.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -12 49426908 . C T 92 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=3.0;SSF=0.00936;SOR=0.0;LSEQ=TGCTGTTGGTGCTGTTGTTG;RSEQ=TGCTGCTGCTGCTGGGCTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:761:8:5,3:345,388:0.0105:2,2:17.1:1.0:30.8:1.0:0.48618:1.87:60.0:16.0:0.011:0.0:1.3 0/0:638:0:0,0:303,313:0.0:2,0:25.3:1.0:31.5:1.0:1.0:0.0:60.0:50.333:0.9983:0.0:0.2 -12 49428717 . G A 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01971;LSEQ=TCTGCAGCAAATTTGTCCAG;RSEQ=TCTGGAGAGGGGAGAACCAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:748:57:23,34:229,462:0.0762:2,2:28.5:1.0:29.5:1.0:0.30744:1.36:60.0:13.25:0.0723:0.0:1.3 0/0:617:1:1,0:239,377:0.0016:2,0:1.0:0.0:24.0:0.0:0.38898:0.0:60.0:2.0:0.0017:0.0:1.0 -12 49431654 . C T 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01494;LSEQ=CCATCCGGGTATCCCGGCTG;RSEQ=CCATCATGCTCTGTCCTGGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:914:148:81,67:411,355:0.1619:2,2:24.8:1.0:29.6:1.0:0.85721:1.04:60.0:36.0:0.1609:0.0:1.2 0/0:696:2:0,2:370,323:0.0029:2,0:1.0:0.0:23.5:1.0:0.21832:0.0:60.0:4.0:0.0029:0.0:1.0 -12 49436248 . G A 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGAATGGGGAGGAGCAGGG;RSEQ=AAGTGCTGCAGGAGTCCGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:46:41,5:226,54:0.1411:2,2:23.7:1.0:29.6:1.0:0.21623:1.96:60.0:22.0:0.1406:0.0:1.1 0/0:240:0:0,0:198,42:0.0:2,0:22.3:1.0:31.0:1.0:1.0:0.0:60.0:79.0:1.0:0.0:0.1 -12 49438490 . C A 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACTCCCAGAGTCACGCTCC;RSEQ=CCTACTCTGCCGCTCCCTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:612:181:127,54:281,149:0.2958:2,2:25.7:1.0:29.5:1.0:0.26034:1.25:60.0:44.25:0.294:0.0:1.1 0/0:556:0:0,0:359,196:0.0:2,0:23.3:1.0:29.9:1.0:1.0:0.0:60.0:38.643:0.9982:0.0:0.2 -12 49439376 . A G 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGCAAAGCTTGCAATGTGCC;RSEQ=AGCTTGTGCCACTGCACTCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:31.2:1.0:30.6:1.0:1.0:0.0:52.2:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 49441376 . AT A 99 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACACTCAGCTAATTTTTGTT;RSEQ=TTTTTAGAAGAGACGGGGTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:0.9:0,0:22.0:1.0:31.4:1.0:1.0:0.0:60.0:18.0:0.9:0.3:0.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 50413034 . C A 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01599;SOR=0.1107;LSEQ=TTCCTCCAGTCCTTCCCCTA;RSEQ=TGCTTCAGGCAGTTGCCACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:8:0,8:19,129:0.0513:2,0:24.0:1.0:32.0:1.0:0.59685:0.0:60.0:16.0:0.0513:0.0:2.1 0/0:169:1:1,0:29,139:0.0059:2,0:1.0:0.0:25.0:0.0:0.17751:0.0:60.0:2.0:0.0059:0.0:2.0 -12 50484405 . C T 186 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTGGGAGGCAGTGCTGTGC;RSEQ=GGAGCTGCCTTGTGCCGATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:72:15,57:56,206:0.2149:2,2:26.2:1.0:30.2:1.0:1.0:1.03291:60.0:35.0:0.2121:0.0:1.2 0/0:352:0:0,0:112,239:0.0:2,0:21.3:1.0:29.1:1.0:1.0:0.0:60.0:57.5:0.9971:0.0:0.1 -12 52906415 . C A 112 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00024;SOR=0.0165;LSEQ=TTACTCTCCAGCCTGGGCAA;RSEQ=AATAGCAAAACTCTGTAGGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:12,0:1,0:0.9231:0,0:22.6:1.0:31.3:1.0:1.0:0.0:55.4:24.0:0.9231:0.0:2.4 0/1:9:1:1,0:8,0:0.1111:0,0:18.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.125:0.0:2.0 -12 52906434 . G A 77 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.0;MSILEN=1.0;SSF=0.02121;SOR=0.0;LSEQ=ACAATAGCAAAACTCTGTAG;RSEQ=AAAAAAAAAAAAAACAAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:15,0:0.2857:1,2:10.5:1.0:30.0:1.0:0.07143:0.0:54.2:12.0:0.3529:0.0:3.8 0/0:19:0:0,0:15,2:0.0:2,0:16.5:1.0:28.7:1.0:1.0:0.0:56.5:4.667:0.875:0.0:1.2 -12 52906545 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.16033;SOR=0.0;LSEQ=ACCGCTGCCGCTGCCTATGC;RSEQ=TCTGTTACCAGAAAAGATCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:5:1,4:53,70:0.0388:2,2:31.0:1.0:30.8:1.0:0.39615:3.00602:60.0:10.0:0.0394:0.0:1.0 0/0:75:0:0,0:30,45:0.0:2,0:24.3:1.0:31.2:1.0:1.0:0.0:60.0:150.0:1.0:0.0:1.2 -12 52921297 . C A 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATAACATCTTCCAGCAGCC;RSEQ=CAAGAGAGAGGGACCCCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:34:12,22:156,219:0.0831:2,2:29.7:1.0:30.0:1.0:0.58576:1.3051:60.0:68.0:0.0848:0.0:1.2 0/0:272:0:0,0:121,151:0.0:2,0:26.6:1.0:30.2:1.0:1.0:0.0:60.0:67.0:1.0:0.0:1.8 -12 53030489 . C T 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CACGGGTATCATGTATTGCC;RSEQ=GATTATTGTGTTTCACAACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:18:7,11:35,54:0.1682:2,2:27.6:1.0:29.5:1.0:1.0:1.01835:60.0:17.0:0.1635:0.0:1.0 0/0:92:0:0,0:39,53:0.0:2,0:26.6:1.0:29.4:1.0:1.0:0.0:60.0:91.0:1.0:0.0:0.3 -12 53130533 . G A 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCACTGCGGTGGGGTCCTC;RSEQ=GGATGCAGGGGCCATCAAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:0,5:1,33:0.1282:1,0:34.2:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.1282:0.0:1.0 0/0:7:0:0,0:0,7:0.0:0,0:19.6:1.0:31.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.9 -12 55427158 . A C 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.05131;SOR=0.0;LSEQ=AGTGATTGAGTAAAAGCTAA;RSEQ=AGATGAGGCAAAAATCGACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:7:7,0:95,3:0.0667:1,0:24.4:1.0:31.0:1.0:1.0:0.0:60.0:14.0:0.068:0.0:1.0 0/0:58:0:0,0:55,3:0.0:2,0:21.6:1.0:29.8:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 -12 56474480 . A G 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.22222;SOR=0.0;LSEQ=TGCAGGGAGGGGAGCAGGGA;RSEQ=CTTCATTCTGTAAACAGGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:23.9:1.0:30.4:1.0:1.0:0.0:60.0:6.0:0.8571:0.0:1.3 0/0:1:0:0,0:1,0:0.0:0,0:8.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -12 56478002 . A C 79 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGATGAGGAAGGGGCCCT;RSEQ=CTGGTATGAGGCACTTTGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:15.7:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 56489613 . T C 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGTACTTAGCTTACTTTTG;RSEQ=TTTTTCTTTTCTTTTTTTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:97:33,64:120,211:0.2266:2,2:24.2:1.0:32.1:1.0:0.71918:1.10276:60.0:96.0:0.2264:0.0:1.1 0/0:444:0:0,0:156,288:0.0:2,0:25.6:1.0:29.6:1.0:1.0:0.0:60.0:73.0:1.0:0.0:0.2 -12 57860293 . T C 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01506;SOR=0.0;LSEQ=CCATAAACAAATATTAAAAA;RSEQ=AATGTTTGTGTGACTGTGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:10:0,10:3,144:0.0637:1,0:14.1:1.0:32.3:1.0:1.0:0.0:60.0:20.0:0.0645:0.0:1.0 0/0:97:0:0,0:4,93:0.0:1,0:22.1:1.0:28.3:1.0:1.0:0.0:60.0:47.5:1.0:0.0:0.1 -12 57860826 . T C 109 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AACAGCCCGTTCCCCCAAGA;RSEQ=GACCCCATCTTGGGACAGCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:13,0:3,0:0.8125:0,1:30.9:1.0:29.7:1.0:1.0:0.0:60.0:12.0:0.8:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 57865284 . C T 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01996;LSEQ=GCAGGGAAGATGCCCCCGCC;RSEQ=AGGAACCTTCCTACCAGAGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1567:93:45,48:760,713:0.0593:2,2:24.1:1.0:29.8:1.0:0.59328:1.13689:60.0:92.0:0.0595:0.0:1.1 0/0:1592:2:0,2:816,773:0.0013:2,0:1.0:0.0:23.0:1.0:0.23712:0.0:60.0:4.0:0.0013:0.0:1.5 -12 58144359 . G T 188 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCCCTGGTCTCAAAAAAAAA;RSEQ=AATGGGCAAGGTATGGATGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:91:74,17:135,28:0.3583:2,2:22.8:1.0:28.9:1.0:0.86409:1.10717:60.0:12.0:0.3443:0.0:1.1 0/0:198:0:0,0:151,46:0.0:2,0:20.7:1.0:31.3:1.0:1.0:0.0:60.0:196.0:1.0:0.0:0.1 -12 61873046 . G A 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CCACAACTAATATAAGTCAC;RSEQ=TCTTCACATAGTAAATATCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:18:9,9:165,159:0.0525:2,2:21.3:1.0:30.6:1.0:1.0:1.03764:60.0:36.0:0.0529:0.0:2.7 0/0:332:0:0,0:183,149:0.0:2,0:27.3:1.0:29.8:1.0:1.0:0.0:60.0:109.667:1.0:0.0:1.5 -12 62290651 . C G 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.07004;SOR=0.0;LSEQ=ATGATGTTTCCTTTCTTTTG;RSEQ=CTGCCATCAAGCTATTTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:5:2,3:86,122:0.0235:2,2:18.4:1.0:30.8:1.0:1.0:1.05711:60.0:10.0:0.0236:0.0:3.6 0/0:167:0:0,0:70,97:0.0:2,0:26.7:1.0:31.2:1.0:1.0:0.0:60.0:82.5:1.0:0.0:1.2 -12 62290742 . T C 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00021;SOR=0.08292;LSEQ=TAGATAATATCTTATCTCTA;RSEQ=TGAGGGTCCAGATGATCTCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:20:3,17:0,20:0.5:1,2:22.3:1.0:32.1:1.0:0.23077:0.0:60.0:40.0:0.5:0.0:1.3 0/1:27:2:0,2:4,21:0.0741:2,0:16.5:1.0:33.5:1.0:1.0:0.0:60.0:4.0:0.0741:0.0:1.0 -12 63295001 . T C 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0053;SOR=0.09094;LSEQ=CTGATACCATATGTTCCCAG;RSEQ=GGGCAACAGCCAATCACTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:24:1,23:1,44:0.3478:1,1:26.9:1.0:30.5:1.0:1.0:1.89:60.0:48.0:0.3478:0.0:1.0 0/1:22:1:0,1:1,20:0.0455:1,0:3.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0455:0.0:1.0 -12 66943230 . T A 57 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06305;SOR=0.0;LSEQ=TACTACTATTGAAAAAAATA;RSEQ=TATTGCTCATACTACAGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:5:4,1:91,200:0.0169:2,2:6.0:1.0:24.6:1.0:0.03813:8.72:60.0:4.0:0.0137:0.0:1.8 0/0:267:0:0,0:87,180:0.0:2,0:24.4:1.0:29.7:1.0:1.0:0.0:60.0:88.0:1.0:0.0:0.3 -12 69202867 . G C 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00482;SOR=0.0;LSEQ=CTTTTTCTCTGCTGATCCAG;RSEQ=TAAGCACCGACTTGCTTGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:13:13,0:119,2:0.097:1,1:27.7:1.0:30.6:1.0:1.0:0.0:60.0:12.0:0.0916:0.0:1.0 0/0:75:0:0,0:73,2:0.0:1,0:21.9:1.0:31.7:1.0:1.0:0.0:60.0:150.0:1.0:0.0:0.1 -12 69203524 . T A 76 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTGTGCGTACCCACATATA;RSEQ=TTACATTTGAATTTAAATCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:23.3:1.0:29.5:1.0:1.0:0.0:60.0:5.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 72825422 . GT G 97 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.0;MSILEN=1.0;SSF=0.04952;SOR=0.1084;LSEQ=GCCAATAACAGGAAGAAGAG;RSEQ=TTTTTTTTTTTTGAGAATGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:5,4:6,5:0.45:2,2:14.9:1.0:30.9:1.0:1.0:1.04:60.0:18.0:0.45:0.25:0.1 0/1:13:1:0,1:7,5:0.0769:2,0:34.0:0.0:30.0:0.0:0.46154:0.0:60.0:2.0:0.0769:0.0:4.0 -12 77054235 . G T 180 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02143;LSEQ=ACCCCATATATGTTCTCTAG;RSEQ=CCTTTTAGAAAACATGGAGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:105:60:28,32:23,22:0.5714:2,2:26.1:1.0:30.5:1.0:0.69622:1.19277:54.7:120.0:0.5769:0.0:1.1 0/1:110:3:2,1:49,58:0.0273:2,2:28.3:1.0:30.3:1.0:0.59568:2.35:57.7:6.0:0.0275:0.0:1.0 -12 78288910 . GA G 83 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.02947;SOR=0.0;LSEQ=AAAGGACAGGAGTGTTTCTT;RSEQ=AAAAAAAAATTCTCACAGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:6:2,4:9,66:0.0741:2,2:19.2:1.0:32.3:1.0:0.18577:3.58:60.0:12.0:0.075:0.0123:0.2 0/0:73:0:0,0:15,58:0.0:2,0:24.2:1.0:30.0:1.0:1.0:0.0:60.0:146.0:1.0:0.0:0.2 -12 82298589 . G GC 118 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CCCAGCGTTTACAGGAAAAG;RSEQ=CTTGTGAAATCAGACAACGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:13:7,6:28,10:0.2549:2,2:24.4:1.0:31.9:1.0:0.29846:2.35547:60.0:26.0:0.2549:0.0588:0.8 0/0:62:0:0,0:37,24:0.0:2,0:19.6:1.0:31.2:1.0:1.0:0.0:60.0:122.0:0.9839:0.0:0.2 -12 87756834 . G A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00028;SOR=0.0;LSEQ=CACCTGCTCCTTCTTCTGGG;RSEQ=ACTTCTGACCTCTAGGGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,2:0.6667:2,2:28.0:1.0:29.7:1.0:1.0:1.85:60.0:12.0:0.6667:0.0:1.2 0/0:18:0:0,0:7,11:0.0:2,0:18.2:1.0:30.3:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.2 -12 91238015 . G A 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAAAAAAATACATCATAAG;RSEQ=ATATGAGCTAACTGTTGGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:18:5,13:9,44:0.2535:2,2:20.1:1.0:29.6:1.0:0.32418:1.86:60.0:36.0:0.2535:0.0:1.1 0/0:88:0:0,0:26,62:0.0:2,0:24.4:1.0:31.1:1.0:1.0:0.0:60.0:176.0:1.0:0.0:0.1 -12 97487829 . TTG GT 116 MSI6 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=AGGGATACGTGTTTTTTTTT;RSEQ=TTTTTTTTTTGTAACTTTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:17:8,9:203,282:0.0333:2,2:8.2:1.0:28.5:1.0:0.80357:1.23:60.0:34.0:0.0336:0.0294:0.2 0/0:505:0:0,0:206,287:0.0:2,0:21.3:1.0:29.3:1.0:1.0:0.0:59.0:69.429:0.9838:0.0:1.0 -12 97487836 . T TG 199 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.0;MSILEN=1.0;SSF=0.0;SOR=0.10149;LSEQ=CGTGTTTTTTTTTTTGTTTT;RSEQ=TTTTTGTAACTTTAACTTTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:129:39,90:152,200:0.2665:2,2:22.0:1.0:28.4:1.0:0.0115:1.75183:58.7:3.778:0.2262:0.0455:1.3 0/1:479:17:6,11:188,274:0.0355:2,2:24.3:1.0:32.5:1.0:0.80317:1.25732:60.0:34.0:0.0358:0.0063:0.3 -12 108602855 . C G 180 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.05095;LSEQ=AGGTTTTGTCCTTCCTACTC;RSEQ=CAGAGCCAGAGCAAGCAATG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:69:62,7:20,3:0.75:2,2:26.0:1.0:29.6:1.0:0.70662:1.32:60.0:68.0:0.764:0.0:1.1 0/1:77:10:10,0:50,17:0.1299:2,0:30.6:1.0:30.5:1.0:0.10568:0.0:60.0:20.0:0.1316:0.0:1.0 -12 115109672 . C A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02338;LSEQ=GGACGCGCTGCGGGACCTGT;RSEQ=CGGCTTGGCTTCCAAGCCGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:37:21,16:400,362:0.0463:2,2:23.2:1.0:27.1:1.0:0.73647:1.19:60.0:17.5:0.0446:0.0:1.2 0/0:885:1:1,0:463,421:0.0011:2,0:1.0:0.0:21.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 -12 115110038 . C T 60 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.06263;SOR=0.0;LSEQ=GGAGGCTGCCGCAGAGGAGG;RSEQ=GGCCGCCGCTGCGGCCATGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:5:2,3:219,248:0.0106:2,2:15.0:1.0:26.2:1.0:1.0:1.32382:60.0:4.0:0.0087:0.0:1.4 0/0:439:0:0,0:218,220:0.0:2,0:24.3:1.0:29.9:1.0:1.0:0.0:60.0:61.571:0.9977:0.0:0.2 -12 115110078 . C T 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00016;SOR=0.0;LSEQ=TACGTGTAGGGGTAAGGGAA;RSEQ=AGGCTTCCGAAAGGGGACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:14:7,7:156,241:0.0341:2,2:20.3:1.0:30.3:1.0:0.42078:1.54:60.0:28.0:0.0347:0.0:1.2 0/0:357:0:0,0:141,216:0.0:2,0:26.3:1.0:30.9:1.0:1.0:0.0:60.0:38.667:1.0:0.0:0.2 -12 115117337 . G A 215 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTGGTATGCAGTCACAGC;RSEQ=ATGAATTCAGTTTCGGGGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:152:89,63:407,344:0.1683:2,2:25.2:1.0:29.7:1.0:0.37148:1.19:60.0:304.0:0.1698:0.0:1.1 0/0:1097:0:0,0:586,510:0.0:2,0:26.0:1.0:30.2:1.0:1.0:0.0:60.0:77.286:0.9991:0.0:0.2 -12 115118589 . G A 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATGCTTAGGGAGAAGCAAA;RSEQ=GAGAAGTCTGGGCTGAAACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:35:26,9:152,38:0.1556:2,2:25.7:1.0:30.7:1.0:0.49752:1.38248:60.0:70.0:0.157:0.0:1.0 0/0:203:0:0,0:158,45:0.0:2,0:24.3:1.0:31.8:1.0:1.0:0.0:60.0:100.5:1.0:0.0:0.1 -12 120541570 . G A 221 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01217;LSEQ=ACCATGACCAGGCACCGGTC;RSEQ=CTCAACTGTGTCCACAGGTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:184:141,43:455,198:0.2196:2,2:22.3:1.0:29.5:1.0:0.07962:1.43:60.0:25.286:0.2153:0.0:2.0 0/0:587:2:1,1:402,181:0.0034:2,2:17.0:1.0:32.0:0.0:0.5258:2.21767:60.0:4.0:0.0035:0.0:1.0 -12 120541597 . G A 236 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00703;LSEQ=TGTGTCCACAGGTCAGTGGC;RSEQ=CGGGTTGGGTGGGAGTGGGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1232:276:178,98:578,374:0.224:2,2:25.4:1.0:29.2:1.0:0.26181:1.18:60.0:22.0:0.2198:0.0:1.7 0/0:989:2:2,0:595,389:0.002:2,0:11.0:1.0:23.5:1.0:0.52177:0.0:60.0:1.0:0.001:0.0:1.5 -12 120554466 . G A 238 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00243;LSEQ=CCGGGCCATGGCGGGCGGGG;RSEQ=CGGTGCGCGCGGGCGGGCGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:291:170,121:224,169:0.423:2,2:27.1:1.0:29.2:1.0:0.75437:1.06:60.0:35.375:0.4268:0.0:1.2 0/0:560:1:1,0:299,257:0.0018:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0018:0.0:1.0 -12 121435778 . C T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03945;SOR=0.0;LSEQ=ATGAATTTCTAAAATCTATT;RSEQ=AGATTTTAGAAAGGTAATCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:0,7:0,53:0.1167:1,0:20.1:1.0:27.0:1.0:1.0:0.0:60.0:6.0:0.1053:0.0:1.6 0/0:41:0:0,0:0,41:0.0:1,0:21.9:1.0:32.7:1.0:1.0:0.0:60.0:82.0:1.0:0.0:0.1 -12 124887058 . G GGCTGCTGCTGCT 112 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=37;MSI=16.0;MSILEN=3.0;SSF=0.00094;SOR=0.0;LSEQ=CCTGGCTGCTGCGGGGCATG;RSEQ=GCTGCTGCTGCTGCTGCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:6,6:11,7:0.3243:2,2:25.2:1.0:31.3:1.0:0.71062:1.54757:56.1:24.0:0.3243:0.1081:1.0 0/0:25:0:0,0:6,3:0.0:2,0:39.3:1.0:27.8:1.0:1.0:0.0:60.0:8.0:0.3333:0.0:0.2 -12 128101958 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.07622;SOR=0.13343;LSEQ=ATCTTGCTATTACTCACCTT;RSEQ=GGGCCCTGTATTTTTAACCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:2,3:3,15:0.2174:2,2:24.8:1.0:30.6:1.0:0.29068:3.13:54.6:10.0:0.2174:0.0:1.0 0/1:29:1:0,1:6,22:0.0345:2,0:12.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0345:0.0:1.0 -12 131945101 . C T 60 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.02628;SOR=0.0;LSEQ=AGCGAACCTAAGTGTGGGTG;RSEQ=ACAGAGTGTCACCATATTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:5:2,3:203,149:0.014:2,2:20.0:1.0:26.0:1.0:0.6544:2.03951:60.0:4.0:0.0113:0.0:1.2 0/0:380:0:0,0:214,166:0.0:2,0:23.5:1.0:31.5:1.0:1.0:0.0:60.0:94.0:1.0:0.0:0.8 -12 131945403 . A G 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATAATGACAGGCAAAGAAA;RSEQ=TAAACCCTATAAATTTGTAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:22.7:1.0:31.5:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 132547162 . G A 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.00345;SOR=0.06658;LSEQ=CAGCAGCAGCAACAGACGAC;RSEQ=ACGACCTCTCAGGTGCAAGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:5,4:7,9:0.36:2,2:27.6:1.0:30.3:1.0:0.68817:1.58:58.3:18.0:0.36:0.0:1.3 0/1:29:1:0,1:11,17:0.0345:2,0:9.0:0.0:31.0:0.0:1.0:0.0:55.0:2.0:0.0345:0.0:3.0 -12 133208752 . T A 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.077;SOR=0.0;LSEQ=ATTCATTAACATCCTTACCA;RSEQ=GCACAGGTATGTCGGTGTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:5:5,0:41,1:0.1064:1,0:23.0:1.0:30.2:1.0:1.0:0.0:60.0:10.0:0.1087:0.0:1.0 0/0:32:0:0,0:31,1:0.0:1,0:20.0:1.0:30.9:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.4 -12 133211059 . T C 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCCTCCAACCTGGGTCCA;RSEQ=CTGCCCCGTTTGACCAGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:31:0,31:0,61:0.337:1,1:23.9:1.0:31.4:1.0:1.0:0.0:60.0:30.0:0.3333:0.0:1.5 0/0:71:0:0,0:1,70:0.0:1,0:22.2:1.0:29.5:1.0:1.0:0.0:60.0:142.0:1.0:0.0:0.4 -12 133226249 . G T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03696;SOR=0.1392;LSEQ=CAGAGACAGACAGTATCACA;RSEQ=CTGTGTGCCTTACCTGGCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:7:1,6:378,239:0.0112:2,2:11.3:1.0:26.7:1.0:0.01651:9.45822:60.0:14.0:0.0116:0.0:1.1 0/0:635:1:0,1:402,232:0.0016:2,0:1.0:0.0:24.0:0.0:0.36693:0.0:60.0:2.0:0.0016:0.0:1.0 -12 133243788 . T A 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAAACAATAGGCGAAGGCAG;RSEQ=TGGGTTCGTAAAACTTGATG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:13.3:1.0:28.7:1.0:1.0:0.0:60.0:14.0:0.7778:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -12 133244668 . CA C 71 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.23077;SOR=0.0;LSEQ=GACAGAGTGAGACCTCATTT;RSEQ=AAAAAAAAAAGAAAGAAATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:3,0:0.5:0,0:28.0:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:0.0 0/0:3:0:0,0:3,0:0.0:0,0:16.7:1.0:31.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 -12 133257837 . C A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02541;LSEQ=CCGTTCCAGGCGCTTGAGTG;RSEQ=CGAAACTGAGGAAGTGGCGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:28:10,18:203,251:0.0579:2,2:22.7:1.0:29.5:1.0:0.43438:1.45467:60.0:56.0:0.0587:0.0:1.0 0/0:643:1:1,0:283,358:0.0016:2,0:1.0:0.0:22.0:0.0:0.44237:0.0:60.0:2.0:0.0016:0.0:1.0 -13 21004758 . T C 129 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGCTCTTGCAATGGAGAGT;RSEQ=CTTTGTGTACACCTCCCACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:18:8,10:147,156:0.0561:2,2:24.4:1.0:31.0:1.0:0.81122:1.17729:60.0:36.0:0.057:0.0:1.7 0/0:359:0:0,0:168,191:0.0:2,0:26.1:1.0:29.0:1.0:1.0:0.0:60.0:58.833:1.0:0.0:1.1 -13 21554217 . A T 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATTGTTAGCAAATAGTTACT;RSEQ=GCCAGAATTTTATGTTCTTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:22.6:1.0:27.6:1.0:1.0:0.0:60.0:4.0:0.6667:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 21563715 . C T 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGAAGACTGCGTCCACATCC;RSEQ=GAGGTGCGTCCCTGCCCCCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:0.5833:0,0:19.1:1.0:25.9:1.0:1.0:0.0:60.0:2.5:0.5:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 27793546 . G A 83 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCAAATGAGCTCAATTAACA;RSEQ=CTTCTACCAAGGACCCCTGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1.0:0,0:19.7:1.0:29.7:1.0:1.0:0.0:56.7:14.0:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 28601389 . TAC T 201 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAAATTGGTCCTGAAATAGT;RSEQ=AGTTTCAATTATAGGCATAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:93:23,70:64,148:0.3049:2,2:25.6:1.0:30.8:1.0:0.40864:1.31494:59.9:186.0:0.3079:0.0525:0.1 0/0:398:0:0,0:132,266:0.0:2,0:24.9:1.0:28.8:1.0:1.0:0.0:60.0:78.6:1.0:0.0:0.1 -13 28608709 . G A 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02924;SOR=0.0;LSEQ=CCCACAGACAATCAGGCAAT;RSEQ=TCCCTGTAAAGGATACATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:0,11:0,13:0.4583:1,0:22.4:1.0:30.5:1.0:1.0:0.0:60.0:22.0:0.4583:0.0:1.0 0/0:8:0:0,0:0,8:0.0:0,0:20.6:1.0:31.8:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.3 -13 28611186 . G C 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02753;LSEQ=CCAGTAGATATGAGAGTAAA;RSEQ=TTTCAAAACACTTCAGCGTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:20:20,0:25,0:0.4444:1,1:23.9:1.0:31.8:1.0:1.0:0.0:60.0:19.0:0.4318:0.0:2.0 0/1:48:1:1,0:47,0:0.0208:1,0:19.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0208:0.0:3.0 -13 28611219 . TGT GC 153 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGCGTACAAAAACAGTTT;RSEQ=AGTAGCCCTTCTAAGCCATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:31:31,0:33,0:0.4306:1,1:26.8:1.0:30.9:1.0:1.0:0.0:60.0:30.0:0.4478:0.0972:0.8 0/0:80:0:0,0:41,1:0.0:1,0:25.3:1.0:28.1:1.0:1.0:0.0:60.0:20.0:0.5195:0.0:0.2 -13 28636446 . G A 83 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGTACGGACTGTCATGGCGT;RSEQ=TGTCCCCCTACCTCTGCAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1.0:0,0:19.4:1.0:29.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 28644610 . A C 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAAAACAGCTAAAGGTATA;RSEQ=TTTTAATGTTACTTTACCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:39:24,15:234,125:0.098:2,2:24.8:1.0:31.9:1.0:0.72449:1.16952:60.0:38.0:0.0964:0.0:1.1 0/0:513:0:0,0:311,201:0.0:2,0:25.1:1.0:29.6:1.0:1.0:0.0:60.0:127.0:0.998:0.0:0.1 -13 28885593 . TTCTTTCTTTCTTTCTC T 127 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=4.0;SSF=2e-05;SOR=0.0;LSEQ=GGTGGTGATCAACATAATCT;RSEQ=TCTTTCTTTCTTTCTCTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:17:17,0:43,0:0.2833:1,1:29.5:1.0:31.3:1.0:1.0:0.0:58.5:34.0:0.2833:0.0167:0.8 0/0:46:0:0,0:46,0:0.0:1,0:23.2:1.0:31.1:1.0:1.0:0.0:60.0:92.0:1.0:0.0:0.5 -13 28964198 . C T 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00028;SOR=0.14334;LSEQ=AGTTTCAGGTCCTCTCCTTC;RSEQ=GTCGGCATTTTTTCCAAGTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:18:6,12:179,295:0.0366:2,2:28.1:1.0:30.4:1.0:0.8076:1.21306:60.0:36.0:0.0369:0.0:1.2 0/0:555:3:1,2:238,314:0.0054:2,2:22.7:1.0:26.3:1.0:1.0:1.51483:60.0:6.0:0.0055:0.0:1.0 -13 28971220 . G A 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02893;LSEQ=AGCCATCTGCAAAAGAAAAG;RSEQ=AAACTTTAGCTAGCAACAGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:76:17,59:43,162:0.2705:2,2:24.0:1.0:30.3:1.0:0.86998:1.09:60.0:152.0:0.2714:0.0:1.1 0/1:284:3:3,0:78,202:0.0106:2,0:1.0:0.0:24.3:1.0:0.02283:0.0:60.0:6.0:0.0107:0.0:1.0 -13 29069039 . G A 93 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02556;SOR=0.17709;LSEQ=TCCCCGCGGCCAACGACCCG;RSEQ=CCGCCAGAGTCCGTCCTCTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:9:3,6:18,73:0.09:2,2:15.8:1.0:29.6:1.0:0.39198:2.01:60.0:18.0:0.0909:0.0:1.1 0/1:117:2:1,1:30,85:0.0171:2,2:7.5:1.0:26.5:1.0:0.46139:2.8:60.0:4.0:0.0175:0.0:1.0 -13 32747212 . C G 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0632;LSEQ=GTGTAATACCAAGTGGTATA;RSEQ=ATGAAAGGAGTTGTGTTTTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:50:9,41:18,56:0.4032:2,2:23.9:1.0:31.5:1.0:0.50735:1.45988:60.0:100.0:0.4032:0.0:1.0 0/1:148:6:2,4:34,108:0.0405:2,2:20.3:1.0:31.5:1.0:0.63336:1.58:60.0:12.0:0.0411:0.0:1.0 -13 32893791 . A G 74 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AACTAAACTATATTTCTGCA;RSEQ=GCTATCACAGAGGACAGAGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1.0:0,2:22.2:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 32899388 . A C 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0674;LSEQ=TACATATATTTGTTCTATAA;RSEQ=GATGAATCTGATTTTTATGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:49:3,46:3,51:0.4757:2,2:25.1:1.0:29.9:1.0:1.0:1.11:60.0:98.0:0.4757:0.0:1.2 0/1:158:9:1,8:12,137:0.057:2,2:21.6:1.0:30.4:1.0:0.54796:1.42:60.0:18.0:0.057:0.0:1.0 -13 32900149 . T C 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08443;LSEQ=TAGTATTCCAACAATTTATA;RSEQ=GAATGAGAATCTTCTTTTAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:138:64:53,11:61,11:0.4638:2,2:21.7:1.0:31.7:1.0:0.81817:1.14975:60.0:63.0:0.4667:0.0:1.1 0/1:163:11:10,1:122,30:0.0675:2,2:18.4:1.0:30.8:1.0:0.69192:2.45:60.0:22.0:0.0692:0.0:1.0 -13 32900933 . T A 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02754;SOR=0.0;LSEQ=GGAATAAATACAAATACATT;RSEQ=AGTGGTAGTCCAGTGGTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:1,12:0,12:0.52:0,1:28.0:1.0:30.3:1.0:1.0:0.0:60.0:26.0:0.52:0.0:1.0 0/0:6:0:0,0:0,6:0.0:0,0:31.2:1.0:28.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -13 32906480 . A C 257 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.08861;LSEQ=ACATTGGAAAGTCAATGCCA;RSEQ=ATGTCCTAGAAGATGAAGTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:274:134,140:202,195:0.4083:2,2:24.6:1.0:31.8:1.0:0.63787:1.08215:60.0:90.333:0.4081:0.0:1.1 0/1:730:42:18,24:334,353:0.0575:2,2:25.2:1.0:31.5:1.0:0.52625:1.26117:60.0:84.0:0.0583:0.0:1.1 -13 32906980 . A G 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.10951;LSEQ=ATTTCTAGCCTACCAAAATC;RSEQ=GAGAAGCCATTAAATGAGGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:118:59,59:109,83:0.3806:2,2:25.0:1.0:30.5:1.0:0.29076:1.31208:60.0:117.0:0.3824:0.0:1.1 0/1:350:22:12,10:172,156:0.0629:2,2:23.3:1.0:29.0:1.0:1.0:1.09:60.0:44.0:0.063:0.0:1.1 -13 32910351 . G T 224 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10368;LSEQ=CTTAGTGAAAAATATTTAGT;RSEQ=AATGTGATTGATGGTACTTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:381:182:151,31:174,25:0.4777:2,2:23.3:1.0:29.9:1.0:0.24759:1.42752:60.0:90.0:0.4787:0.0:1.1 0/1:440:38:27,11:306,96:0.0864:2,2:22.0:1.0:28.8:1.0:0.55259:1.2978:60.0:76.0:0.087:0.0:1.1 -13 32910721 . T C 300 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0999;LSEQ=GCATGTCACCCAGTACAACA;RSEQ=TCAAAAGTGGAATACAGTGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1600:676:341,335:463,460:0.4225:2,2:26.9:1.0:32.0:1.0:0.91942:1.01:60.0:83.5:0.4241:0.0:1.1 0/1:1866:127:65,62:843,895:0.0681:2,2:24.8:1.0:31.1:1.0:0.58195:1.11:60.0:41.333:0.0673:0.0:1.1 -13 32911463 . A G 294 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08802;LSEQ=AAAAAAATAATGATTACATG;RSEQ=ACAAATGGGCAGGACTCTTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1557:692:356,336:472,391:0.4444:2,2:23.4:1.0:31.2:1.0:0.21971:1.13924:60.0:75.889:0.445:0.0:1.1 0/1:1780:117:62,55:859,801:0.0657:2,2:21.5:1.0:30.7:1.0:0.84834:1.05:60.0:116.0:0.0661:0.0:1.2 -13 32912885 . G A 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.08569;LSEQ=ATAACTTTTCCTTAAATTCT;RSEQ=AATTACATTCTGACATAAGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1573:21:10,11:763,788:0.0134:2,2:21.0:1.0:28.5:1.0:1.0:1.06509:60.0:20.0:0.0128:0.0:1.1 0/0:1728:2:1,1:855,869:0.0012:2,2:16.0:1.0:27.0:1.0:1.0:1.02:60.0:4.0:0.0012:0.0:1.0 -13 32929478 . C T 281 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06881;LSEQ=GCCTTTCAGTTAGATATTTC;RSEQ=GTTGTTAAATAATGTCCTGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1177:589:229,360:238,348:0.5004:2,2:26.8:1.0:30.6:1.0:0.55157:1.07507:60.0:146.25:0.5004:0.0:1.2 0/1:1444:93:38,55:582,766:0.0644:2,2:27.4:1.0:29.8:1.0:0.7455:1.09966:60.0:45.5:0.0634:0.0:1.2 -13 32930673 . C T 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00967;LSEQ=CAGTCTGTATCTTGCAAAAA;RSEQ=ATCCACTCTGCCTCGAATCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:133:64,69:206,235:0.2317:2,2:26.3:1.0:29.5:1.0:0.84295:1.06:60.0:132.0:0.2316:0.0:1.1 0/0:690:2:1,1:332,356:0.0029:2,2:15.0:0.0:24.0:1.0:1.0:1.07:60.0:4.0:0.0029:0.0:1.5 -13 32968793 . T C 134 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAATTCATCTAACACATCTA;RSEQ=AATAACATTCTTTTCTTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:18:13,5:137,28:0.0984:2,2:22.9:1.0:32.3:1.0:0.32836:1.87439:60.0:36.0:0.0994:0.0:1.1 0/0:205:0:0,0:166,39:0.0:2,0:23.0:1.0:29.1:1.0:1.0:0.0:60.0:101.5:1.0:0.0:0.2 -13 41032432 . G C 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCACTGGGACAGTCGCCCAG;RSEQ=GGACACGAGACATATACAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:56:31,25:61,52:0.3294:2,2:31.9:1.0:30.8:1.0:1.0:1.06:60.0:55.0:0.3293:0.0:2.0 0/0:191:0:0,0:101,89:0.0:2,0:27.3:1.0:29.9:1.0:1.0:0.0:60.0:46.5:0.9947:0.0:0.4 -13 41161770 . G A 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.12884;SOR=0.0;LSEQ=TCCATCTATACCTAAAGCAC;RSEQ=GCTCAAGTGCTTGGAGAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:10,1:14,0:0.44:1,2:23.6:1.0:29.7:1.0:0.44:0.0:60.0:22.0:0.44:0.0:1.6 0/0:5:0:0,0:5,0:0.0:0,0:25.8:1.0:31.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -13 41161979 . C G 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGTGTTCACAGTAGCCTCT;RSEQ=CCCACCTTTTAAAAGGGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1029:68:48,20:647,313:0.0661:2,2:26.9:1.0:31.8:1.0:0.68778:1.16:60.0:67.0:0.0654:0.0:1.1 0/0:1138:0:0,0:712,426:0.0:2,0:25.4:1.0:30.6:1.0:1.0:0.0:60.0:102.455:1.0:0.0:0.2 -13 43549921 . AAC A 99 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.0;MSILEN=2.0;SSF=0.01652;SOR=0.17541;LSEQ=ATGATGTATTTCTTCACTTA;RSEQ=ACACACACACACATAAGTAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:10:6,4:168,76:0.0394:2,2:16.3:1.0:30.0:1.0:0.51213:1.47132:59.5:20.0:0.0397:0.0157:0.2 0/0:281:2:0,2:183,90:0.0071:2,0:23.0:1.0:32.0:0.0:0.11111:0.0:60.0:4.0:0.0071:0.0:0.0 -13 43550043 . CA C 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.10611;SOR=0.1776;LSEQ=ACTCACCATCTTTAAGAGGC;RSEQ=AAAACCAATGATGGGACCAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:5:2,3:112,191:0.0162:2,2:30.0:1.0:32.5:1.0:1.0:1.14:60.0:10.0:0.0164:0.0032:0.8 0/0:343:1:0,1:125,217:0.0029:2,0:50.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0029:0.0:0.0 -13 43550243 . A G 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.26316;SOR=0.0;LSEQ=ACTGTTTCACAGACACTGGC;RSEQ=GAAGACATGAAATTCCTGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:0,7:0,9:0.4375:0,0:29.3:1.0:31.1:1.0:1.0:0.0:60.0:14.0:0.4375:0.0:2.0 0/0:3:0:0,0:1,2:0.0:2,0:18.0:1.0:31.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -13 43550270 . T A 102 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATGAAATTCCTGGATCAGAG;RSEQ=CAAAGACTTTATTACTGATG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1.0:0,0:26.2:1.0:31.0:1.0:1.0:0.0:60.0:20.0:1.0:0.0:1.9 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 48939018 . C T 51 q23 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01465;SOR=0.0;LSEQ=TAATGATCATGTTGTAACTT;RSEQ=ATCTTTTTCAGGTGAAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:5:1,4:217,150:0.0134:2,2:5.0:1.0:22.0:1.0:0.16451:5.76167:60.0:4.0:0.011:0.0:1.8 0/0:491:0:0,0:280,211:0.0:2,0:24.2:1.0:31.3:1.0:1.0:0.0:60.0:162.667:1.0:0.0:0.1 -13 49026852 . C T 72 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCTTTCTCTCCACTTTCTT;RSEQ=GTTTTTTTTCTGTCTTTCCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:29.6:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 49034073 . C CT 122 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=15.0;MSILEN=4.0;SSF=0.0001;SOR=0.0;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TTTCTTTCTTTCTTTTTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:15:0,15:0,49:0.2344:1,1:16.7:1.0:31.3:1.0:1.0:0.0:56.3:30.0:0.25:0.0625:0.8 0/0:53:0:0,0:0,52:0.0:1,0:14.4:1.0:31.4:1.0:1.0:0.0:52.5:16.333:1.0:0.0:0.4 -13 49034085 . CTT TC 99 MSI6 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=15.0;MSILEN=4.0;SSF=0.00213;SOR=0.0;LSEQ=CTTTCTTTCTTTCTTTCTTT;RSEQ=TTTCTTTCTTTCTTTCTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:0,9:0,10:0.2727:0,0:12.6:1.0:31.4:1.0:1.0:0.0:53.9:18.0:0.5:0.0606:0.6 0/0:31:0:0,0:0,23:0.0:1,0:8.4:1.0:32.5:1.0:1.0:0.0:50.6:46.0:1.0:0.0:0.3 -13 49034104 . TCTC T 86 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.11371;SOR=0.0;LSEQ=TCTTTTTCTTTCTTTCTTTC;RSEQ=TTTCTTTCTTTTTTTTGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,0:0.4667:0,0:17.1:1.0:30.9:1.0:1.0:0.0:37.7:14.0:0.5:0.3333:0.7 0/0:5:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 49037825 . G T 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02587;LSEQ=TTTTTTAAGAACAAAACCAT;RSEQ=TAATAAAATTCTGACTACTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:34:25,9:199,58:0.1168:2,2:20.8:1.0:29.6:1.0:0.66496:1.23426:60.0:33.0:0.1158:0.0:1.0 0/0:294:1:1,0:216,77:0.0034:2,0:27.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0034:0.0:1.0 -13 49047529 . G C 233 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTGGTGAATCATTCGGGGT;RSEQ=AGTATTTTCTTTCTATGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:390:159:63,96:89,140:0.4077:2,2:27.4:1.0:31.9:1.0:0.91595:1.03:60.0:158.0:0.4083:0.0:1.1 0/0:508:0:0,0:217,290:0.0:2,0:25.9:1.0:31.0:1.0:1.0:0.0:60.0:100.4:0.998:0.0:0.1 -13 49051848 . G A 78 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAGCAGAACTACAAAGAGGA;RSEQ=CTATTTGGGAGTGTTAGATA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:25.3:1.0:30.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 67591561 . CA TG 161 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGGCATTGATATTCCCTAA;RSEQ=GTTTAAAATACCCCTGTTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:35:35,0:69,1:0.3333:1,1:23.3:1.0:31.5:1.0:1.0:0.0:60.0:70.0:0.3333:0.0381:1.4 0/0:64:0:0,0:63,1:0.0:1,0:25.8:1.0:31.3:1.0:1.0:0.0:60.0:128.0:1.0:0.0:0.2 -13 68406205 . T A 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=1.0;SSF=0.00044;SOR=0.0;LSEQ=TTAGGAGTTCTTTCCCGTTT;RSEQ=TTGTAGGATTTTTGTTCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:10:8,2:37,16:0.1587:2,2:28.5:1.0:27.7:1.0:0.71026:1.72:60.0:20.0:0.1724:0.0:1.0 0/0:68:0:0,0:49,19:0.0:2,0:23.0:1.0:29.7:1.0:1.0:0.0:60.0:33.0:1.0:0.0:0.2 -13 71158400 . G A 61 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01614;SOR=0.0;LSEQ=CAGACCACCGTGTTCAGTTT;RSEQ=TATTTTCGATTGAGAATGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:5:3,2:119,200:0.0154:2,2:11.6:1.0:26.4:1.0:0.36892:2.51:55.4:10.0:0.0157:0.0:1.0 0/0:413:0:0,0:151,262:0.0:2,0:23.4:1.0:30.8:1.0:1.0:0.0:60.0:102.25:1.0:0.0:0.2 -13 72248871 . T TAATAGAGTGCTCCATTCAAGTTTGAAAACTA 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTACGGCAGGCACAGGAAAC;RSEQ=AATAAATTGCATGATGAAGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1.0:0,0:41.3:1.0:29.4:1.0:1.0:0.0:60.0:14.0:1.0:1.0:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 72249649 . T A 126 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTCATTCTCAAAAAAAAAA;RSEQ=TTTTTTTTTTCTCTTCTTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:19:3,16:21,45:0.0709:2,2:16.7:1.0:29.8:1.0:0.24944:2.46533:57.0:38.0:0.0722:0.0:1.1 0/0:262:0:0,0:25,31:0.0:2,0:13.1:1.0:28.9:1.0:1.0:0.0:51.0:55.0:0.2148:0.0:0.2 -13 103508378 . C T 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01711;LSEQ=TCCTTAAAAATCATAGATAT;RSEQ=GTAAAAGTATGTTTGACTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:46:30,16:158,109:0.1465:2,2:25.8:1.0:30.0:1.0:0.51555:1.29:60.0:92.0:0.1494:0.0:1.1 0/0:343:1:1,0:206,136:0.0029:2,0:16.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0029:0.0:1.0 -13 103513578 . G A 67 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=CGAACTCCTGACCTCCGGTG;RSEQ=TCCACCCATCTCGGCCTCCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:22.2:1.0:29.2:1.0:1.0:0.0:42.8:10.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 104378382 . A G 129 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00174;SOR=0.03601;LSEQ=TAGGTAGTGTCCACATGCAG;RSEQ=TATTGATATAATGTATATTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:0,3:0.85:0,1:22.1:1.0:31.8:1.0:1.0:0.0:60.0:34.0:0.85:0.0:1.3 0/1:7:1:0,1:0,6:0.1429:0,0:33.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.1429:0.0:2.0 -13 106826430 . G T 180 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.09836;LSEQ=ACAATTGTGGGTTGTTTCAC;RSEQ=TTTCAGTGAAAGGAGAGAAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:62:21,41:84,130:0.2246:2,2:27.6:1.0:30.3:1.0:0.4621:1.26049:60.0:124.0:0.2271:0.0:1.5 0/1:326:9:4,5:123,194:0.0276:2,2:32.2:1.0:29.9:1.0:0.74007:1.26:60.0:18.0:0.0278:0.0:1.2 -13 110414685 . A G 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.12362;LSEQ=GGGTGGACCCTTTCTTTTAA;RSEQ=TTATGAAATGTTAGACCCTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:58:3,55:3,80:0.4113:1,2:22.9:1.0:31.2:1.0:0.69:1.45:60.0:28.0:0.4058:0.0:1.1 0/1:114:9:2,7:10,95:0.0789:2,2:18.3:1.0:32.2:1.0:0.24065:2.68:60.0:18.0:0.0804:0.0:1.1 -13 110419404 . C T 245 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00966;LSEQ=CACCAGAGGACCCAGATCTG;RSEQ=GAAATGCTTTGGTCAGGGAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:324:311:279,32:12,1:0.9599:1,2:23.7:1.0:29.7:1.0:1.0:1.37514:60.0:33.556:0.9587:0.0:1.1 0/1:275:51:43,8:191,33:0.1855:2,2:23.4:1.0:28.3:1.0:0.82978:1.07653:60.0:16.0:0.1791:0.0:1.2 -13 110428702 . A G 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0119;SOR=0.0;LSEQ=GACAGAGTTTCCAAGGCTTC;RSEQ=CCTTTACCCATTCAAGTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:27.0:1.0:27.0:1.0:1.0:0.0:60.0:5.0:1.0:0.0:2.2 0/0:3:0:0,0:2,1:0.0:2,0:35.3:1.0:28.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 -13 110428923 . G A 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01497;LSEQ=ATAACACACAGAAGCATCTT;RSEQ=CATTATTTGCACCTACAGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:170:155,15:49,12:0.7359:2,2:25.6:1.0:28.7:1.0:0.03485:2.52:59.9:84.0:0.7336:0.0:1.1 0/1:177:7:7,0:151,19:0.0395:2,0:26.7:1.0:29.4:1.0:1.0:0.0:60.0:14.0:0.0407:0.0:1.1 -13 110435914 . G A 220 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.00738;LSEQ=TCCTCCAGGATGCGCCCCAC;RSEQ=GGGGAGCTCATGAGCACGTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:170:104,66:33,20:0.7589:2,2:26.9:1.0:29.7:1.0:1.0:1.04691:60.0:20.25:0.7535:0.0:1.2 0/1:179:4:3,1:97,78:0.0223:2,2:20.0:1.0:28.5:1.0:0.63124:2.4:60.0:3.0:0.0172:0.0:1.0 -13 110436790 . ACCG A 100 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.0;MSILEN=3.0;SSF=0.02451;SOR=0.12788;LSEQ=GTCATGTACCCGTAGAACTC;RSEQ=CCGCCGCCGCCGTCTCGGGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:9:4,5:367,461:0.0107:2,2:20.4:1.0:31.7:1.0:1.0:1.0:60.0:18.0:0.0109:0.0036:0.3 0/0:722:1:1,0:336,379:0.0014:2,0:25.0:0.0:26.0:0.0:0.47067:0.0:60.0:2.0:0.0014:0.0:0.0 -13 111588868 . C T 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTTACAGACCGAATGAAAA;RSEQ=ATCCAGGAGAAAGAGTTTAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:8,0:2,0:0.8:0,0:25.1:1.0:30.9:1.0:1.0:0.0:60.0:16.0:0.8:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -13 111590803 . T A 57 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02885;SOR=0.0;LSEQ=TCGTTAAAGGAACCAACTCC;RSEQ=ATTACAAGCTGAAGTTGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:3,2:205,288:0.01:2,2:9.0:1.0:24.8:1.0:0.6538:2.1:59.0:4.0:0.0081:0.0:1.0 0/0:512:0:0,0:224,286:0.0:2,0:24.7:1.0:29.0:1.0:1.0:0.0:59.9:71.857:1.0:0.0:0.1 -13 112722133 . C T 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06299;SOR=0.0;LSEQ=CCAGGACCGGGTCAAACGGC;RSEQ=CATGAACGCCTTCATGGTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:351:5:1,4:257,88:0.0142:2,2:12.8:1.0:27.8:1.0:0.01811:11.58614:54.8:10.0:0.0147:0.0:1.2 0/0:319:0:0,0:216,103:0.0:2,0:24.2:1.0:30.2:1.0:1.0:0.0:58.8:78.75:1.0:0.0:0.2 -14 19487496 . C A 91 InIns SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=0.00658;SOR=0.0;LSEQ=TCTGAAGTCATACCCCCCCA;RSEQ=ACACACACCTTCAGTCATGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:10:4,6:100,205:0.0317:2,2:25.5:1.0:27.6:1.0:0.73483:1.37:29.7:9.0:0.029:0.0:1.1 0/0:222:0:0,0:69,153:0.0:2,0:27.4:1.0:30.6:1.0:1.0:0.0:28.5:110.0:1.0:0.0:0.1 -14 19487907 . A C 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.08932;SOR=0.0;LSEQ=CTCTTTTGAGAACTCACCTA;RSEQ=ATTTCATCTCTCGGCAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:6:6,0:68,17:0.0659:2,0:30.2:1.0:33.7:1.0:0.58916:0.0:24.7:12.0:0.0667:0.0:1.2 0/0:50:0:0,0:31,19:0.0:2,0:24.1:1.0:28.6:1.0:1.0:0.0:28.0:49.0:1.0:0.0:0.0 -14 19487914 . T C 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.00846;SOR=0.0;LSEQ=GAGAACTCACCTAAATTTCA;RSEQ=CTCTCGGCAAAATGAGAGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:12:12,0:69,17:0.1212:2,0:22.8:1.0:32.6:1.0:0.11916:0.0:26.3:24.0:0.1212:0.0:1.2 0/0:52:0:0,0:32,20:0.0:2,0:23.4:1.0:29.0:1.0:1.0:0.0:27.9:104.0:1.0:0.0:0.0 -14 19488825 . G A 95 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06138;SOR=0.0;LSEQ=GAAAGGTGAAAAATAAAAAA;RSEQ=AGCACACTTTACCTGTCCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:9:9,0:120,0:0.0698:1,0:22.3:1.0:30.2:1.0:1.0:0.0:24.2:18.0:0.0709:0.0:2.0 0/0:52:0:0,0:52,0:0.0:1,0:17.7:1.0:31.8:1.0:1.0:0.0:36.1:25.0:1.0:0.0:0.3 -14 19492018 . C CGT 139 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=34;MSI=18.0;MSILEN=2.0;SSF=0.00013;SOR=0.057;LSEQ=CCCAACAATGCAATAAACTG;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:28:2,26:11,32:0.3373:2,2:35.0:1.0:29.1:1.0:0.06325:4.38835:24.0:56.0:0.359:0.0:0.5 0/1:36:1:0,1:6,19:0.0278:2,0:48.0:0.0:27.5:0.0:1.0:0.0:21.0:2.0:0.0323:0.0:0.0 -14 19890157 . GGCC G 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACCCCCAGCCGGGCAGCAGC;RSEQ=GCCAAGCATGGCAAGGAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:3,4:6,8:0.3333:2,2:30.7:1.0:31.9:1.0:1.0:1.0:54.3:14.0:0.35:0.0:0.4 0/0:1:0:0,0:1,0:0.0:0,0:13.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -14 20084718 . A G 119 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.53668;SOR=0.0;LSEQ=TCAGATTATTTAAATTAGGT;RSEQ=CTCACAGTTTTTAAAAATTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:3,9:8,14:0.3529:2,2:20.8:1.0:33.2:1.0:0.70493:1.68798:38.8:24.0:0.3529:0.0:1.0 0/0:3:0:0,0:0,3:0.0:0,0:24.0:1.0:32.0:0.0:1.0:0.0:40.0:6.0:1.0:0.0:0.0 -14 20084805 . G C 104 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.55575;SOR=0.0;LSEQ=GCTTCTAGGAACTCTGATGT;RSEQ=TATGTGTGCCTGAGGGTATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:10:10,0:22,3:0.2857:2,0:20.5:1.0:31.4:1.0:0.54163:0.0:40.0:20.0:0.303:0.0:1.9 0/0:4:0:0,0:4,0:0.0:0,0:25.8:1.0:32.5:1.0:1.0:0.0:40.0:8.0:1.0:0.0:0.0 -14 20085200 . A G 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.32771;SOR=0.0;LSEQ=AAAACCTCTTACACATTGAT;RSEQ=TTGATAGTAATTGATAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:5:1,4:45,160:0.0238:2,2:37.2:1.0:29.0:1.0:1.0:1.12439:43.0:4.0:0.0193:0.0:1.4 0/0:92:0:0,0:18,74:0.0:2,0:23.6:1.0:29.9:1.0:1.0:0.0:43.9:91.0:1.0:0.0:0.4 -14 20085423 . G A 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01009;LSEQ=CTCTATGTCTGTATAGGTAC;RSEQ=TTTGTGTGCTTGGGAATATG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:724:139:94,45:378,207:0.192:2,2:25.2:1.0:30.6:1.0:0.55273:1.14:31.2:278.0:0.1928:0.0:1.2 0/0:419:1:1,0:276,142:0.0024:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0024:0.0:1.0 -14 20085849 . G C 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=ATCCGCCCGCCTCGGCCTCC;RSEQ=AAAGTGCTGGGTAAATCTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:2,0:0.7143:0,2:27.4:1.0:30.2:1.0:1.0:0.0:51.4:10.0:0.7143:0.0:1.2 0/0:2:0:0,0:1,1:0.0:2,0:11.0:1.0:27.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -14 20086143 . A T 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.32454;SOR=0.0;LSEQ=CTGGCTTTTACATCTATGAT;RSEQ=GCAGTATCTCTTTTATAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:5:4,1:88,9:0.049:2,2:30.0:1.0:29.8:1.0:0.40958:2.41542:25.0:10.0:0.05:0.0:2.0 0/0:37:0:0,0:33,4:0.0:2,0:20.4:1.0:28.5:1.0:1.0:0.0:27.3:74.0:1.0:0.0:0.1 -14 20086572 . G A 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.24451;SOR=0.0;LSEQ=GACTTTCAGGAAAAATAAAT;RSEQ=TGCGAGAGCGGTATGTTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:0,5:0,7:0.4167:0,0:32.4:1.0:29.8:1.0:1.0:0.0:24.8:10.0:0.4167:0.0:1.0 0/0:4:0:0,0:0,4:0.0:0,0:15.5:1.0:32.0:1.0:1.0:0.0:41.0:8.0:1.0:0.0:0.5 -14 20893115 . T A 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TAGGCACAGGAGACAAGTGA;RSEQ=ACCTAGAGTCCCACACACTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:28:18,10:239,117:0.0729:2,2:23.1:1.0:29.8:1.0:0.8352:1.13447:60.0:56.0:0.0737:0.0:1.2 0/0:213:0:0,0:143,70:0.0:2,0:25.1:1.0:28.6:1.0:1.0:0.0:60.0:41.6:1.0:0.0:0.1 -14 20969716 . C T 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATATTCCATGGTACATGTAC;RSEQ=ATGGTTTGCTTAATGCATCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,1:0.7143:2,0:18.8:1.0:32.6:1.0:0.28571:0.0:60.0:10.0:0.8333:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 21336860 . A AT 76 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=CATGCCTGGCTTATTTTTGT;RSEQ=TTTTTAGTACAGACGGGGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:25.8:1.0:32.8:1.0:1.0:0.0:58.6:10.0:1.0:0.0:0.0 0/0:1:0:0,0:1,0:0.0:0,0:2.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -14 22395405 . A T 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.33085;SOR=0.0;LSEQ=AAATTATCTTTTATATATTC;RSEQ=TTTTTACTGATATTCCCAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:7:0,7:0,36:0.1628:1,0:18.0:1.0:31.0:1.0:1.0:0.0:60.0:14.0:0.1628:0.0:1.6 0/0:9:0:0,0:0,9:0.0:0,0:26.9:1.0:31.4:1.0:1.0:0.0:60.0:18.0:1.0:0.0:1.6 -14 22395437 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATTCCCAGTACAAACAAATG;RSEQ=TATTTAAAAATCATCTTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:0.2083:1,0:28.6:1.0:30.8:1.0:1.0:0.0:60.0:10.0:0.2083:0.0:1.8 0/0:4:0:0,0:0,4:0.0:0,0:17.0:1.0:32.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:1.0 -14 22592304 . G A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00068;SOR=0.056;LSEQ=CTGGTGGCAAGTGAGGAGGA;RSEQ=GGTAGCATTCACCTAGAGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:4,10:6,12:0.4375:2,2:17.9:1.0:29.9:1.0:1.0:1.24135:60.0:28.0:0.4375:0.0:1.0 0/1:25:1:1,0:10,14:0.04:2,0:9.0:0.0:32.0:0.0:0.44:0.0:60.0:2.0:0.04:0.0:1.0 -14 23587046 . A C 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01173;SOR=0.10491;LSEQ=AGGGGCCTGGAGGGGAAGGC;RSEQ=CGGAGAGACGGAGAGGTGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:19:0,19:1,58:0.2436:1,1:20.2:1.0:31.0:1.0:1.0:0.0:60.0:18.0:0.2368:0.0:1.2 0/1:31:1:0,1:3,27:0.0323:2,0:8.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0323:0.0:1.0 -14 23652305 . A C 279 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.06062;LSEQ=TATTCCTACTCCGCATTCAC;RSEQ=CTTTCTGGTCACTCGCGTTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1331:520:255,265:408,403:0.3907:2,2:26.9:1.0:31.0:1.0:0.6536:1.05204:60.0:36.143:0.3941:0.0:1.2 0/1:1177:44:21,23:576,557:0.0374:2,2:20.5:1.0:27.6:1.0:0.7593:1.13248:59.2:5.286:0.0329:0.0:2.0 -14 23764770 . C G 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=7e-05;SOR=0.0;LSEQ=GCTTCCTGTCATTGGTAGTT;RSEQ=TGAATGTTAGATATTTTTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:20:2,18:3,69:0.2174:1,2:31.3:1.0:33.0:1.0:0.29708:2.52:59.8:40.0:0.2198:0.0:1.2 0/0:53:0:0,0:6,47:0.0:2,0:24.6:1.0:31.4:1.0:1.0:0.0:59.8:16.667:1.0:0.0:0.4 -14 25438196 . T C 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAGAACCAGGCCATCTGTAC;RSEQ=TTGAGAAATTCTAGAGGGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:40:24,16:253,179:0.0847:2,2:31.8:1.0:31.2:1.0:1.0:1.06:60.0:80.0:0.0862:0.0:1.6 0/0:264:0:0,0:146,118:0.0:2,0:25.3:1.0:30.1:1.0:1.0:0.0:60.0:51.8:1.0:0.0:0.5 -14 33960172 . TGCA T 75 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.0;MSILEN=3.0;SSF=0.15749;SOR=0.0;LSEQ=GCAAAAATACAATTTTTCAC;RSEQ=GCAGCAGCAGCAGCAGCAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:5:3,2:29,17:0.098:2,2:31.4:1.0:32.6:1.0:1.0:1.13435:60.0:10.0:0.098:0.0:0.0 0/0:27:0:0,0:17,10:0.0:2,0:28.0:1.0:31.9:1.0:1.0:0.0:60.0:54.0:1.0:0.0:0.1 -14 34771783 . G T 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCTCTCAGTCTGGTTTCCTG;RSEQ=GACGCTTGTCACCACTGGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:5,3:2,1:0.7273:2,2:26.4:1.0:30.4:1.0:1.0:1.18052:60.0:16.0:0.7273:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 35871430 . T TTTAAAAAAGAGTAAGCTA 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.60107;SOR=0.0;LSEQ=GTTTGCCTTTAATGCTTCTC;RSEQ=TTAAAAAAAGAGGGGGGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:7:6,1:113,328:0.0156:2,2:7.9:1.0:27.9:1.0:0.00175:17.3:57.6:6.0:0.0138:0.0134:3.1 0/0:71:0:0,0:20,51:0.0:2,0:18.0:1.0:30.7:1.0:1.0:0.0:59.7:70.0:1.0:0.0:0.8 -14 35872920 . G T 230 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01114;LSEQ=TGCAGGTTGTTCTGGAAGTT;RSEQ=AGGAAGGCCAGGTCTCCCTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5601:257:124,133:2686,2655:0.0459:2,2:24.3:1.0:28.8:1.0:0.52397:1.08507:60.0:84.667:0.0457:0.0:1.2 0/0:1871:1:0,1:969,901:0.0005:2,0:1.0:0.0:23.0:0.0:0.4821:0.0:60.0:2.0:0.0005:0.0:1.0 -14 36417343 . G A 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACAGGCCGGAGGACACGGAG;RSEQ=GTAATCACAGGCCGGAGGAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:3,2:1,2:0.5556:2,2:11.2:1.0:32.0:1.0:1.0:2.6:38.6:10.0:0.5556:0.0:3.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 36417741 . T C 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGAAATCACAGGCCGGAGGA;RSEQ=ATGGAGGGTAATCACAGGCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:1,1:0.7143:2,2:17.6:1.0:32.0:1.0:1.0:1.41:46.8:10.0:0.7143:0.0:2.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 36983065 . A C 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGGGGCCAGGGTGGGGAGC;RSEQ=GCTTTGGGATGCTAAACATC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1.0:0,2:25.6:1.0:30.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 36983623 . A G 138 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGCGGATGGAGCCAGCGT;RSEQ=ATTGATGGCAAGAAAGAGGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:23,1:0,0:1.0:0,1:25.3:1.0:30.3:1.0:1.0:0.0:60.0:11.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 36986190 . A AC 177 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.04286;SOR=0.0;LSEQ=TTGAATCACCAAAAAAAGAC;RSEQ=CCCCAAAGCTGTTTTATGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:44:39,5:10,0:0.8148:0,2:23.2:1.0:32.5:1.0:0.57075:0.0:60.0:88.0:0.8148:0.1111:0.4 0/0:2:0:0,0:2,0:0.0:0,0:31.0:1.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -14 36986272 . T TTA 143 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.0;MSILEN=1.0;SSF=0.61856;SOR=0.0;LSEQ=TGTTTTTCATTTTCTTTTTT;RSEQ=AAAAAAAAAAACCCACAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:29:29,0:234,7:0.1062:1,1:19.4:1.0:29.5:1.0:1.0:0.0:60.0:58.0:0.1094:0.0256:0.7 0/0:12:0:0,0:12,0:0.0:0,0:28.3:1.0:30.5:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.7 -14 36988175 . G A 309 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCCCGCGGCCCCGCAGTGG;RSEQ=GCGGCCTCACTTACTGGCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1727:1415:961,454:211,99:0.8193:2,2:23.8:1.0:29.6:1.0:1.0:1.00688:60.0:25.698:0.8161:0.0:1.3 0/0:235:0:0,0:143,92:0.0:2,0:24.1:1.0:29.6:1.0:1.0:0.0:60.0:38.167:1.0:0.0:0.3 -14 36989638 . A C 159 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCCGCTAACACGCCTCCCCC;RSEQ=AGGTCTTCCCCCCCCCCCCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:34:1,33:0,2:0.7907:0,1:19.0:1.0:31.4:1.0:1.0:0.0:60.0:33.0:0.8684:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 36989645 . TCCCC T 132 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=14.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACACGCCTCCCCCAAGGTCT;RSEQ=CCCCCCCCCCACCCCCGGCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:22:0,22:2,8:0.6471:2,1:27.5:1.0:29.7:1.0:0.09073:0.0:60.0:21.0:0.7778:0.1471:1.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 38055445 . C T 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGCAAGGGGGAGGAGTGCT;RSEQ=ACTCTCACCATGTGCTTTGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:0.9091:0,0:24.4:1.0:26.7:1.0:1.0:0.0:60.0:20.0:0.9091:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 38060768 . G A 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.05818;LSEQ=TTATGCTGCTGCTCCGAGGA;RSEQ=GACATGAGGTTGTTGATGGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7246:172:93,79:3576,3493:0.0237:2,2:25.2:1.0:30.7:1.0:0.3961:1.15:60.0:85.0:0.0238:0.0:1.1 0/0:2124:3:3,0:1070,1047:0.0014:2,0:1.0:0.0:26.7:1.0:0.24976:0.0:60.0:6.0:0.0014:0.0:1.0 -14 38061106 . T A 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00868;SOR=0.0;LSEQ=AGAGGCGCCAGAGGGGTCCT;RSEQ=GCGGCTCTCAGGGCCGCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:755:28:20,8:379,347:0.0371:2,2:22.0:1.0:29.7:1.0:0.05361:2.29:60.0:56.0:0.0376:0.0:1.3 0/0:155:0:0,0:81,74:0.0:2,0:19.5:1.0:29.8:1.0:1.0:0.0:60.0:50.667:1.0:0.0:0.1 -14 38882673 . T A 103 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.15441;SOR=0.0;LSEQ=AAAGACCTCATCCAAAGGTC;RSEQ=GCATCCTCAAAGACTGAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:7,3:2,3:0.6667:2,2:27.6:1.0:31.3:1.0:0.32867:3.2:60.0:20.0:0.6667:0.0:1.1 0/0:2:0:0,0:1,1:0.0:2,0:35.0:0.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 -14 38910644 . G C 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=TAAGAGTCTATGCCATAGGA;RSEQ=GTACCATGGGAGTTTTTTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:12.8:1.0:33.0:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:1:0:0,0:1,0:0.0:0,0:3.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -14 38910766 . TAG T 124 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.00572;SOR=0.0;LSEQ=CAGAGCCATCTTAAGGTTTA;RSEQ=AGTCTCAGTGAGCTCTCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:7,9:1,5:0.7273:2,2:21.6:1.0:31.1:1.0:0.35116:3.68:60.0:32.0:0.7273:0.1364:0.0 0/0:5:0:0,0:2,3:0.0:2,0:14.0:1.0:30.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -14 49557672 . C A 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.28871;SOR=0.0;LSEQ=CTCCATCAGCCAGAAATAGC;RSEQ=AGTCTCATTGGATCATGGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:25.8:1.0:30.0:1.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.2 0/0:6:0:0,0:0,6:0.0:0,0:24.5:1.0:32.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.3 -14 52640760 . ACTA T 108 MAF0.05;MSI6 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=42;MSI=15.0;MSILEN=3.0;SSF=0.01375;SOR=0.08954;LSEQ=CAGAGCTAGCCAAAATGCTT;RSEQ=CTACTACTACTACTACTACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:0,11:0,10:0.4231:0,0:22.7:1.0:31.4:1.0:1.0:0.0:60.0:22.0:0.44:0.1154:0.6 0/1:17:1:0,1:0,16:0.0588:1,0:44.0:0.0:32.8:0.0:1.0:0.0:60.0:2.0:0.0588:0.0:1.0 -14 57141401 . G A 102 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.31484;SOR=0.0;LSEQ=AGGAACAGGTGAAGGAAACA;RSEQ=CTTTCAGACACAAGTGAGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:11,0:32,0:0.2558:1,0:23.3:1.0:29.5:1.0:1.0:0.0:60.0:10.0:0.2439:0.0:1.1 0/0:6:0:0,0:5,1:0.0:2,0:27.5:1.0:32.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 -14 61799782 . G T 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.06899;SOR=0.0;LSEQ=TTTGGGAAGCGCACCCAAAA;RSEQ=TCATACGTGTATTAGCCTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:5:2,3:195,252:0.011:2,2:19.4:1.0:29.6:1.0:1.0:1.16032:60.0:10.0:0.0111:0.0:1.8 0/0:365:0:0,0:161,204:0.0:2,0:24.6:1.0:31.3:1.0:1.0:0.0:60.0:730.0:1.0:0.0:0.7 -14 61799788 . C T 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGCGCACCCAAAAGTCATA;RSEQ=GTGTATTAGCCTAATTCCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:58:20,38:159,224:0.1315:2,2:25.7:1.0:30.2:1.0:0.38945:1.34776:60.0:57.0:0.1323:0.0:1.1 0/0:353:0:0,0:155,198:0.0:2,0:24.7:1.0:30.0:1.0:1.0:0.0:60.0:87.25:1.0:0.0:0.7 -14 65544815 . G A 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCCAATCCAGGCAGTGAGG;RSEQ=AACCTGGCCTGCAGCAACTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:72:7,65:15,120:0.3462:2,2:23.4:1.0:29.5:1.0:0.81758:1.15993:60.0:144.0:0.3478:0.0:1.1 0/0:121:0:0,0:21,100:0.0:2,0:22.8:1.0:30.5:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.1 -14 65544917 . ATTTATTTT A 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=7.0;MSILEN=1.0;SSF=0.57728;SOR=0.0;LSEQ=ACTGTAGGCTTTATTTATTT;RSEQ=TTTATTTTTTTGAGACAGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:1,4:0,40:0.1111:1,2:27.8:1.0:32.4:1.0:0.11111:0.0:60.0:10.0:0.1111:0.0:0.0 0/0:13:0:0,0:0,13:0.0:1,0:22.2:1.0:30.7:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.2 -14 65568285 . C A 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GCAGATTGAAACCTCGGTTG;RSEQ=TCTTCCTGGAATAAGAGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:29:12,17:145,250:0.0684:2,2:21.0:1.0:29.6:1.0:0.69118:1.22:60.0:28.0:0.068:0.0:1.2 0/0:433:0:0,0:161,270:0.0:2,0:23.0:1.0:31.0:1.0:1.0:0.0:59.9:22.944:1.0:0.0:0.3 -14 65568563 . C T 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTCCTCCCTGCAGACCCAG;RSEQ=TCGGGCATCTAGGCACCCCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:0.625:2,2:13.6:1.0:29.8:1.0:1.0:2.60168:60.0:10.0:0.625:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 69061259 . C G 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGGCTCCAGAAATCCTCC;RSEQ=ACCTCAGCCTCCTGAGCAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:76:0,76:1,151:0.3333:1,1:26.0:1.0:31.9:1.0:1.0:0.0:60.0:152.0:0.3393:0.0:1.1 0/0:143:0:0,0:2,141:0.0:1,0:24.7:1.0:31.5:1.0:1.0:0.0:60.0:70.5:1.0:0.0:0.1 -14 69117298 . G A 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.08954;SOR=0.0;LSEQ=TAAAATCAGACCAGAACCTG;RSEQ=GGATGAGCCAAGAAATGTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:7:7,0:48,1:0.125:1,0:31.7:1.0:30.1:1.0:1.0:0.0:60.0:14.0:0.1273:0.0:1.0 0/0:28:0:0,0:28,0:0.0:1,0:24.5:1.0:31.0:1.0:1.0:0.0:60.0:27.0:1.0:0.0:0.4 -14 69117450 . T C 205 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGATGAATCCTCTCAAAA;RSEQ=AGGAAAAGCTAGGTTCCTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:734:89:60,29:412,233:0.1213:2,2:23.6:1.0:31.8:1.0:0.55645:1.17:60.0:88.0:0.1214:0.0:1.8 0/0:526:0:0,0:332,194:0.0:2,0:23.6:1.0:29.0:1.0:1.0:0.0:60.0:525.0:1.0:0.0:0.4 -14 70439776 . A G 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06213;SOR=0.0;LSEQ=TTCCCCAGAGGTGATTATTG;RSEQ=CCAAGGAGGAGAGAGCAGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:2,5:6,6:0.3684:2,2:22.4:1.0:31.0:1.0:0.63325:2.38223:60.0:14.0:0.3889:0.0:1.3 0/0:9:0:0,0:4,5:0.0:2,0:27.8:1.0:29.2:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 -14 77493815 . T C 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=6.0;SSF=0.02072;SOR=0.0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGTTGCGCGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:5:3,2:32,41:0.0641:2,2:19.2:1.0:32.8:1.0:0.65218:1.91:60.0:10.0:0.0641:0.0:2.0 0/0:89:0:0,0:38,51:0.0:2,0:20.0:1.0:29.5:1.0:1.0:0.0:51.2:88.0:1.0:0.0:2.2 -14 78150336 . C T 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01238;SOR=0.0;LSEQ=CCCTTTGTCTTCGTCATTTT;RSEQ=GCAAATTACTGGAAGATGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:11:7,4:3,2:0.6875:2,2:24.7:1.0:30.2:1.0:1.0:1.16:60.0:22.0:0.6875:0.0:1.2 0/0:6:0:0,0:3,3:0.0:2,0:31.3:1.0:30.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -14 80471852 . A G 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTTTCTACTCAAACATTCC;RSEQ=TGAACTCACTCCCCAGTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:55:27,28:184,164:0.1365:2,2:28.9:1.0:30.7:1.0:0.66375:1.16306:60.0:110.0:0.1389:0.0:1.5 0/0:333:0:0,0:168,165:0.0:2,0:25.9:1.0:29.5:1.0:1.0:0.0:60.0:46.571:1.0:0.0:0.7 -14 81557084 . G A 77 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ATAATTTTTTCCAATTAAAC;RSEQ=AGAAAATCACACACACACAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:24.7:1.0:30.0:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 81563195 . G A 134 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01278;SOR=0.0;LSEQ=AACATGGAAATGAGGTCAAG;RSEQ=AACTTGGCAGGGGCCCACTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:0,20:1,82:0.1942:1,1:19.8:1.0:31.2:1.0:1.0:0.0:60.0:40.0:0.198:0.0:1.1 0/0:25:0:0,0:0,25:0.0:1,0:26.2:1.0:31.7:1.0:1.0:0.0:60.0:50.0:1.0:0.0:0.0 -14 81563267 . G GGTGT 77 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=17.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GTTCCAAAGCTTTTCTCCCT;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:0,6:0,14:0.24:1,0:37.7:1.0:29.9:1.0:1.0:0.0:57.0:12.0:0.2609:0.04:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 81574429 . G A 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.33333;SOR=0.0;LSEQ=AAAAAATACAGTTGCCACTG;RSEQ=CCTGAAAAATAGGGAATTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:0.7273:0,0:18.6:1.0:27.1:1.0:1.0:0.0:60.0:3.0:0.6667:0.0:1.4 0/0:1:0:0,0:0,1:0.0:0,0:22.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -14 81575419 . T C 73 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCCCTTGGTTTTGCCTCAG;RSEQ=TTAGAATCTCATCATTGAGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:24.0:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -14 84782145 . C G 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05359;SOR=0.0;LSEQ=AGAGGGGTGGACATGACAAA;RSEQ=GGCTGCCTCACCTGCAGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:6,3:0.375:2,2:24.5:1.0:29.8:1.0:1.0:1.0:60.0:5.0:0.3333:0.0:1.2 0/0:11:0:0,0:6,5:0.0:2,0:19.0:1.0:30.1:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.1 -14 87813148 . T A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04453;SOR=0.0;LSEQ=TACAGAAAGCCCTAGGTCTC;RSEQ=GGTTTGGGGCTTTCCTAACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:7:1,6:13,106:0.0556:2,2:21.9:1.0:32.1:1.0:0.57092:1.36:60.0:14.0:0.0588:0.0:1.1 0/0:80:0:0,0:14,66:0.0:2,0:21.2:1.0:30.3:1.0:1.0:0.0:60.0:160.0:1.0:0.0:0.2 -14 87813214 . G A 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.08817;SOR=0.0;LSEQ=CTGCATAACCTACCAATTCA;RSEQ=GAATGCCTCTTTGGCATTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:7:0,7:0,37:0.1591:1,0:18.7:1.0:31.0:1.0:1.0:0.0:60.0:14.0:0.1591:0.0:1.6 0/0:20:0:0,0:0,20:0.0:1,0:20.7:1.0:29.8:1.0:1.0:0.0:60.0:19.0:1.0:0.0:0.1 -14 87813312 . A C 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=CTTGTAGTATCATCCATCCA;RSEQ=GTTCTTGCCATGGGCTCAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:15.0:1.0:29.4:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:12.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -14 88360375 . C T 108 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00019;SOR=0.0;LSEQ=GCTGACTCCCCCAAGTCTAC;RSEQ=GTGTTTTGTTCCTGGGTTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:3,9:10,12:0.3529:2,2:27.8:1.0:30.2:1.0:0.29195:2.43465:60.0:24.0:0.3529:0.0:2.0 0/0:30:0:0,0:13,17:0.0:2,0:30.3:1.0:29.6:1.0:1.0:0.0:60.0:60.0:1.0:0.0:0.1 -14 88360384 . T A 100 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=7e-05;SOR=0.0;LSEQ=CCCAAGTCTACCGTGTTTTG;RSEQ=TCCTGGGTTATCTTTGCTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:2,9:6,7:0.4583:2,2:24.2:1.0:29.1:1.0:0.2108:3.64266:60.0:22.0:0.4583:0.0:2.1 0/0:26:0:0,0:12,14:0.0:2,0:28.6:1.0:29.1:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.0 -14 92134141 . T C 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00018;SOR=0.07133;LSEQ=AGGCTTCTGAAATCAGACAA;RSEQ=GCCTTTCAAACTCTTATACC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:16:10,6:6,7:0.5517:2,2:22.2:1.0:31.4:1.0:0.46666:1.9:41.1:32.0:0.5517:0.0:1.7 0/1:26:2:1,1:16,8:0.0769:2,2:8.0:0.0:32.0:0.0:1.0:1.94371:33.0:4.0:0.0833:0.0:1.5 -14 95556644 . A C 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.15781;SOR=0.0;LSEQ=GCGCAAAAAACTAAAACTAC;RSEQ=ATTAGTTCCAAAATTTTATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:6,0:22,0:0.2143:1,0:31.3:1.0:32.0:1.0:1.0:0.0:60.0:12.0:0.2222:0.0:1.0 0/0:11:0:0,0:11,0:0.0:0,0:14.9:1.0:30.2:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.0 -14 95560444 . G A 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCATAAAGGTGCTTGGTTAT;RSEQ=AGGTAGTCCAAAATCGCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:26:9,17:168,268:0.0563:2,2:18.0:1.0:29.3:1.0:0.83618:1.18362:60.0:52.0:0.057:0.0:1.0 0/0:385:0:0,0:157,226:0.0:2,0:24.5:1.0:31.1:1.0:1.0:0.0:60.0:382.0:0.9948:0.0:0.1 -14 95562999 . C A 181 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=GCTCTCCTCCTCCTCATCCT;RSEQ=CTCCTCGTAATCCTCATCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1043:82:36,46:417,543:0.0786:2,2:25.2:1.0:28.5:1.0:1.0:1.02:60.0:164.0:0.0795:0.0:1.1 0/0:796:0:0,0:352,442:0.0:2,0:25.1:1.0:30.6:1.0:1.0:0.0:60.0:55.714:0.9987:0.0:0.2 -14 95566068 . TACACACACACAC T 203 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=20.0;MSILEN=2.0;SSF=0.0;SOR=0.08266;LSEQ=GAAAAGTAAATCCCTCCAGT;RSEQ=ACACACACACACACACACAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:109:88,21:51,0:0.3244:1,2:25.7:1.0:30.1:1.0:0.00024:0.0:59.1:108.0:0.3263:0.0595:1.3 0/1:184:7:6,1:41,0:0.038:1,2:26.9:1.0:30.6:1.0:0.14583:0.0:60.0:14.0:0.0391:0.0:1.0 -14 95569500 . C T 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.57302;SOR=0.0;LSEQ=TGTAAAGCAATACTCATCAA;RSEQ=TGCCAGGTAGTTCTGCCACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:5,0:35,0:0.125:1,0:28.0:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.125:0.0:1.0 0/0:8:0:0,0:8,0:0.0:0,0:22.6:1.0:31.0:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.1 -14 95578448 . CT C 94 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.02599;SOR=0.0;LSEQ=TCTATAAAGTCCTCTATATG;RSEQ=TTTTTTTTACAATGGTTGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:8:8,0:243,76:0.0244:2,0:21.5:1.0:31.6:1.0:0.20568:0.0:59.4:16.0:0.0246:0.0091:0.1 0/0:206:0:0,0:151,55:0.0:2,0:21.2:1.0:30.5:1.0:1.0:0.0:60.0:412.0:1.0:0.0:0.2 -14 95578675 . T C 210 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.09036;LSEQ=TGAAACCACTGCCCCAACAT;RSEQ=TTTAAAGTTCAATTTACCAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:96:8,88:12,113:0.4344:2,2:21.2:1.0:32.0:1.0:0.8163:1.16733:60.0:47.0:0.4332:0.0:1.1 0/1:93:6:1,5:18,69:0.0645:2,2:27.3:1.0:31.7:1.0:1.0:1.30087:60.0:12.0:0.0645:0.0:1.0 -14 95582395 . GAC G 78 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=16.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TACTGTACCGTGCCTACACA;RSEQ=ACACACACACACACACACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:1,5:4,11:0.2857:2,2:18.2:1.0:30.3:1.0:1.0:1.77078:60.0:12.0:0.2857:0.1429:1.2 0/0:2:0:0,0:0,1:0.0:0,0:9.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.5:0.0:0.0 -14 95583900 . C T 62 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0804;SOR=0.0;LSEQ=AAAAAGGGAGACCCTATGGG;RSEQ=ACTTTGTCTGTATATGTCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:5:2,3:230,48:0.0177:2,2:12.0:1.0:27.0:1.0:0.04236:7.11288:60.0:10.0:0.0179:0.0:1.0 0/0:199:0:0,0:150,49:0.0:2,0:23.5:1.0:31.8:1.0:1.0:0.0:60.0:65.333:1.0:0.0:0.1 -14 95591070 . G A 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATGTAGCATTTTCATGTGGG;RSEQ=TTTAACTGGGATTTCAGTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:33:1,32:1,46:0.4125:1,1:26.8:1.0:31.0:1.0:1.0:1.43:60.0:66.0:0.4177:0.0:1.3 0/0:48:0:0,0:3,45:0.0:2,0:22.4:1.0:31.1:1.0:1.0:0.0:60.0:96.0:1.0:0.0:0.1 -14 103707780 . G A 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01372;SOR=0.14574;LSEQ=TACATTGGTTCTTTAAAATG;RSEQ=CATCAGTGCCTTTTGGCCAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:11:8,3:22,11:0.25:2,2:28.4:1.0:31.0:1.0:1.0:1.32:60.0:22.0:0.25:0.0:1.1 0/1:44:2:1,1:25,17:0.0455:2,2:22.5:1.0:28.0:1.0:1.0:1.45743:60.0:4.0:0.0455:0.0:1.0 -14 104146611 . AT A 66 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGAATTTTTTAGCACATGG;RSEQ=TTTTTTTTTTTTTTTTGATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,8:0.3125:0,0:22.2:1.0:28.8:1.0:1.0:0.0:60.0:4.0:0.2857:0.0625:0.0 0/0:2:0:0,0:0,1:0.0:0,0:6.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.5:0.0:0.0 -14 104540796 . G T 66 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08474;SOR=0.0;LSEQ=GCATGTGGTCGTGTATATTT;RSEQ=CTTCCAGGCTATTTATTCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:5:2,3:277,155:0.0114:2,2:24.8:1.0:28.6:1.0:0.35706:2.67423:60.0:10.0:0.0116:0.0:1.2 0/0:297:0:0,0:179,118:0.0:2,0:25.8:1.0:31.6:1.0:1.0:0.0:60.0:73.25:1.0:0.0:0.3 -14 105238820 . G C 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAACAAGGCCACAGTGTCG;RSEQ=TACCGCCACCTGCCCAGGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:48:13,35:170,403:0.0772:2,2:23.4:1.0:32.1:1.0:0.86918:1.13548:60.0:96.0:0.0782:0.0:1.1 0/0:343:0:0,0:111,231:0.0:2,0:25.9:1.0:30.7:1.0:1.0:0.0:60.0:170.0:0.9971:0.0:0.2 -14 105241378 . C T 262 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07732;LSEQ=GTGAGCTGCCACCCCGCACC;RSEQ=TCATCTCCACCCTGCCCCAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1569:400:193,207:605,562:0.2549:2,2:23.3:1.0:30.4:1.0:0.22388:1.15449:60.0:49.0:0.2539:0.0:1.1 0/1:815:21:9,12:398,392:0.0258:2,2:22.4:1.0:28.8:1.0:0.51665:1.35323:60.0:42.0:0.0262:0.0:1.0 -14 105241607 . G A 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCCCAGCTGGTCGGCATGC;RSEQ=TGGGGTGGCATGAGGGGCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:128:26,102:64,273:0.2753:2,2:22.6:1.0:30.6:1.0:0.7929:1.09:60.0:41.667:0.2717:0.0:1.1 0/0:225:0:0,0:45,179:0.0:2,0:21.0:1.0:30.2:1.0:1.0:0.0:60.0:31.0:0.9954:0.0:0.2 -14 105242374 . G A 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.53924;SOR=0.0;LSEQ=AGGACTCTGTCCCCACAACC;RSEQ=GACTCCAACCCCCAGCAGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:0.2632:1,0:26.8:1.0:30.6:1.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.2 0/0:4:0:0,0:1,3:0.0:2,0:26.0:1.0:30.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.5 -14 105242826 . C T 108 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.05819;SOR=0.0;LSEQ=CCTCAGTTTCCCCACCCAAA;RSEQ=CCCACAGGCAGGACTGGGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:11:10,1:47,1:0.1864:1,2:30.3:1.0:31.3:1.0:0.34074:4.52871:60.0:22.0:0.1864:0.0:1.0 0/0:18:0:0,0:16,2:0.0:2,0:24.1:1.0:32.0:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.5 -15 20489987 . A G 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=5.0;SSF=1.0;SOR=0.0;LSEQ=AAAATTAAATGTCAAATAAC;RSEQ=TAACATAGGTAATTGTGTTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:3,2:0.5:2,0:24.8:1.0:31.8:1.0:0.16667:0.0:49.6:10.0:0.5:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 20490611 . T C 236 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.16369;LSEQ=GGGTGTGGGACAGTGCCTGC;RSEQ=AGCATAAAATACATGGGAAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:999:173:61,112:321,505:0.1732:2,2:27.5:1.0:31.8:1.0:0.39081:1.1669:53.3:172.0:0.1734:0.0:1.1 0/1:1268:42:13,29:497,729:0.0331:2,2:25.6:1.0:31.1:1.0:0.26294:1.52036:52.8:41.0:0.0327:0.0:1.3 -15 21134146 . G T 63 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.07156;SOR=0.0;LSEQ=TTGAACAAATATGTTCTGAA;RSEQ=GATTTGCTATGTGCCAGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:5:1,4:220,38:0.019:2,2:5.2:1.0:27.4:1.0:0.00254:22.70253:54.2:10.0:0.0193:0.0:1.4 0/0:203:0:0,0:156,47:0.0:2,0:23.0:1.0:31.4:1.0:1.0:0.0:43.1:202.0:1.0:0.0:0.3 -15 21137279 . G T 94 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.06332;SOR=0.0;LSEQ=TATCAGATATAGACAAAAGA;RSEQ=AAAGCATTCAAAGTACTTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:9:0,9:86,255:0.0257:2,0:6.6:1.0:29.8:1.0:0.11988:0.0:33.7:18.0:0.026:0.0:4.7 0/0:150:0:0,0:35,115:0.0:2,0:22.8:1.0:30.9:1.0:1.0:0.0:54.2:149.0:1.0:0.0:0.2 -15 22140237 . G A 181 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.15959;LSEQ=AAAAGCTGAAAATTTAGTTG;RSEQ=AAGGGGAATTTAAGATAGCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:67:54,13:165,50:0.2376:2,2:18.3:1.0:30.0:1.0:0.61497:1.26:32.1:66.0:0.2383:0.0:1.1 0/1:254:12:11,1:198,44:0.0472:2,2:27.0:1.0:29.3:1.0:0.69849:2.44:27.7:24.0:0.0478:0.0:1.1 -15 22146341 . T G 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.0;MSILEN=1.0;SSF=2e-05;SOR=0.09686;LSEQ=TTCTTTGTTTTCTTTTTTGT;RSEQ=TTTTTGTTTTTGTTTTGTTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:24:23,1:43,2:0.3478:1,1:27.3:1.0:33.3:1.0:1.0:1.07:49.5:48.0:0.3478:0.0:1.1 0/1:62:3:3,0:54,5:0.0484:2,0:20.3:1.0:34.0:0.0:1.0:0.0:37.0:6.0:0.0492:0.0:1.0 -15 22147856 . AT A 91 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.00199;SOR=0.0;LSEQ=GAAAAGAGAAACAGCAAACA;RSEQ=TTTTTTGAAGCCACACACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:8:3,5:187,364:0.0143:2,2:30.1:1.0:30.4:1.0:1.0:1.17:47.6:16.0:0.0144:0.0:0.1 0/0:653:0:0,0:244,408:0.0:2,0:26.6:1.0:29.8:1.0:1.0:0.0:45.2:129.4:0.9985:0.0:0.2 -15 22148122 . G T 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.15039;SOR=0.0;LSEQ=AGGCTTGCCACAGGCACAAA;RSEQ=CTTACGGAAATTTGAGGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:3,2:22,7:0.1471:2,2:25.8:1.0:31.6:1.0:0.59084:2.04473:38.0:10.0:0.1515:0.0:1.0 0/0:18:0:0,0:16,2:0.0:2,0:25.1:1.0:28.4:1.0:1.0:0.0:40.2:3.5:1.0:0.0:0.3 -15 33027179 . T A 77 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATCACACAGAAATGATAATA;RSEQ=CTTCATTTCAGGGTGTTCCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:30.2:1.0:29.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 35384455 . TAA T 80 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=14.0;MSILEN=1.0;SSF=0.13579;SOR=0.0;LSEQ=TTAACTTAGTTGCATGTCTG;RSEQ=AAAAAAAAAAAATATTCTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:2,0:0.3158:0,0:30.7:1.0:31.2:1.0:1.0:0.0:60.0:12.0:0.3158:0.0:0.0 0/0:8:0:0,0:2,0:0.0:0,0:19.0:1.0:22.0:1.0:1.0:0.0:60.0:1.0:0.1429:0.0:1.5 -15 35385071 . C T 249 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.07035;LSEQ=GCTGTGATTGACTTGAACAA;RSEQ=CGTTGGTTTAACGGACAGCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:287:147,140:199,218:0.4054:2,2:26.2:1.0:30.5:1.0:0.39882:1.15:59.7:94.667:0.4063:0.0:1.1 0/1:810:37:17,20:363,409:0.0457:2,2:26.7:1.0:28.9:1.0:1.0:1.04411:60.0:36.0:0.0448:0.0:1.1 -15 35385596 . T C 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01875;SOR=0.0;LSEQ=AAAGATTCTCCATAAATAGG;RSEQ=CGGGCGCGGTGCCTCACGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:10:0,10:0,21:0.3226:1,0:15.2:1.0:30.5:1.0:1.0:0.0:60.0:9.0:0.3103:0.0:1.0 0/0:15:0:0,0:0,15:0.0:1,0:20.2:1.0:28.1:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.4 -15 38457041 . G A 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.01832;SOR=0.0;LSEQ=AATTCCAGCATAAAAAAAGA;RSEQ=CACAAATCAGAAACACAGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:0,12:1,18:0.3871:1,0:24.3:1.0:29.6:1.0:1.0:0.0:60.0:11.0:0.3667:0.0:2.0 0/0:11:0:0,0:0,11:0.0:0,0:21.7:1.0:31.4:1.0:1.0:0.0:60.0:22.0:1.0:0.0:1.5 -15 40328575 . G C 283 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTTGTTGCTGCTGTTGTTG;RSEQ=TGCTGTTGCTGCTGCGGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:498:494:218,276:1,1:0.992:2,2:25.4:1.0:31.7:1.0:1.0:1.26544:59.9:40.167:0.9938:0.0:1.2 0/0:624:0:0,0:10,14:0.0:2,0:24.0:1.0:30.6:1.0:1.0:0.0:60.0:23.0:0.8846:0.0:0.1 -15 42004962 . G C 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.1;SOR=0.0;LSEQ=AGACCATACACTCTCTATAG;RSEQ=AGTTACTGAACTCTGCTGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1.0:0,0:21.8:1.0:32.1:1.0:1.0:0.0:60.0:18.0:1.0:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:41.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -15 42026363 . C T 70 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGATCTTCCCACCTCGGCCT;RSEQ=TCGGAATGCTGGGATTGCAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:28.6:1.0:30.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 42032655 . T C 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04348;SOR=0.0;LSEQ=TATTTTTTAATAACACTGAC;RSEQ=TGAAGGCAAGTTTTATAGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:3,19:0,0:1.0:0,2:25.3:1.0:31.7:1.0:1.0:0.0:60.0:44.0:1.0:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:29.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -15 42035713 . C A 70 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAAATACTAAAAAACATTA;RSEQ=AATGGAAGTGGTGGCTGAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:30.8:1.0:30.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 42046575 . A T 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.00081;SOR=0.0;LSEQ=ATAAGGGGAACAAACATTTG;RSEQ=AAAGTTTAGGTGTGCTTGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:13:11,2:235,17:0.0491:2,2:18.3:1.0:30.0:1.0:0.23672:2.50094:60.0:26.0:0.0504:0.0:2.2 0/0:214:0:0,0:194,20:0.0:2,0:23.0:1.0:29.2:1.0:1.0:0.0:60.0:213.0:1.0:0.0:0.7 -15 42049890 . A AC 177 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCACACCTTGGGAAAAAGAA;RSEQ=CTGGTTGTAATTTGGAATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:46:43,3:175,17:0.1925:2,2:26.4:1.0:32.2:1.0:0.77249:1.39:59.9:45.0:0.1915:0.0335:0.2 0/0:217:0:0,0:184,33:0.0:2,0:23.2:1.0:30.1:1.0:1.0:0.0:60.0:434.0:1.0:0.0:0.1 -15 50245089 . C CTTTTGT 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=5.0;MSILEN=1.0;SSF=0.07616;SOR=0.15721;LSEQ=GATGGGGTTTTTGTGGGGGC;RSEQ=TTTTGTTGTTGTTGTTGTTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:9:3,6:14,15:0.2368:2,2:27.7:1.0:31.6:1.0:0.47571:1.83674:60.0:18.0:0.2368:0.0526:0.2 0/1:22:1:1,0:10,11:0.0455:2,0:34.0:0.0:31.2:0.0:1.0:0.0:60.0:2.0:0.0476:0.0:0.0 -15 50245685 . C T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00521;SOR=0.0;LSEQ=ACCTGAAGAGGCCCTCTGGC;RSEQ=GCAGACTACCACAGCCAGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:2,4:10,8:0.25:2,2:22.8:1.0:30.3:1.0:0.64041:2.40592:60.0:12.0:0.25:0.0:1.2 0/0:30:0:0,0:14,16:0.0:2,0:31.0:1.0:29.7:1.0:1.0:0.0:60.0:60.0:1.0:0.0:0.6 -15 59502492 . TTGTACATTGAC T 200 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATTCAATAACAACTTCCAT;RSEQ=ATTTTACTCATATCCACATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:96:45,51:105,113:0.3057:2,2:27.2:1.0:30.4:1.0:0.90252:1.05295:59.8:192.0:0.3097:0.051:0.2 0/0:484:0:0,0:242,242:0.0:2,0:24.8:1.0:29.5:1.0:1.0:0.0:60.0:95.8:1.0:0.0:0.3 -15 66679684 . A G 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGCGCGTTACCCGGGTCCA;RSEQ=AATGCCCAAGAAGAAGCCGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1041:76:46,30:552,412:0.073:2,2:27.6:1.0:31.9:1.0:0.63068:1.14:60.0:75.0:0.0733:0.0:1.1 0/0:1240:0:0,0:664,575:0.0:2,0:24.4:1.0:29.6:1.0:1.0:0.0:60.0:60.95:0.9992:0.0:0.3 -15 66735925 . C CAG 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATCTGTGTGTCTTGAAAAA;RSEQ=GGGCCAGGCACAGTGGCTCG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1.0:0,0:27.4:1.0:31.3:1.0:1.0:0.0:60.0:16.0:1.0:0.25:0.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 66779698 . C T 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAAGAAAACACCCAGGTGGC;RSEQ=GGGTGCAGTGGTTCACGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:52:12,40:33,150:0.2203:2,2:21.4:1.0:29.9:1.0:0.42772:1.36:60.0:51.0:0.2237:0.0:1.2 0/0:248:0:0,0:57,190:0.0:2,0:21.6:1.0:29.5:1.0:1.0:0.0:60.0:122.5:0.9959:0.0:0.1 -15 66782048 . C T 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCTTACCTTGTCTTTCTT;RSEQ=CTTTAAGCTTAATAAAAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:110:60,50:288,246:0.1708:2,2:23.7:1.0:29.6:1.0:0.91678:1.02:60.0:35.667:0.1709:0.0:1.2 0/0:819:0:0,0:431,388:0.0:2,0:25.1:1.0:30.7:1.0:1.0:0.0:60.0:57.5:1.0:0.0:0.2 -15 67430733 . T C 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCTTGCCATCGCAGTGGAT;RSEQ=TGCGGAAGAGGGTTCCAGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1.0:0,0:17.3:1.0:32.3:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 67457480 . T TC 153 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTGCCAGGGGTCATCACCTC;RSEQ=CCCCGGCTCCCCATCCCCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:39:25,14:42,89:0.0975:2,2:10.6:1.0:29.1:1.0:0.00064:3.75:59.6:12.0:0.0916:0.07:1.3 0/0:217:0:0,0:82,135:0.0:2,0:21.0:1.0:29.3:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.7 -15 67457485 . G CC 245 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=AGGGGTCATCACCTCTCCCC;RSEQ=GCTCCCCATCCCCCCGAGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:400:230:74,156:42,89:0.575:2,2:28.3:1.0:31.3:1.0:1.0:1.01:60.0:229.0:0.5827:0.0375:1.1 0/0:217:0:0,0:82,135:0.0:2,0:21.0:1.0:29.3:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.7 -15 67458805 . G A 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTGGACGCCTCCCTGGAGG;RSEQ=GGTGGGGCTTAACCCTCACC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:0,0:0.875:0,0:29.6:1.0:28.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 67473790 . C T 241 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGCTGACACGGAGACACAT;RSEQ=GGTATGGGGTGGCTCCATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:259:95,164:137,236:0.4098:2,2:24.1:1.0:30.1:1.0:1.0:1.00214:59.9:63.75:0.414:0.0:1.3 0/0:589:0:0,0:239,347:0.0:2,0:24.0:1.0:29.9:1.0:1.0:0.0:59.9:64.111:0.9948:0.0:0.4 -15 67479678 . A AG 210 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGCCACTTCCATCCCCAC;RSEQ=GCCCTGTTTCTGTGTTTTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:787:99:66,33:418,265:0.1258:2,2:29.6:1.0:31.8:1.0:0.32028:1.27:60.0:98.0:0.1284:0.0038:0.1 0/0:708:0:0,0:419,288:0.0:2,0:25.1:1.0:30.1:1.0:1.0:0.0:60.0:77.556:0.9986:0.0:0.2 -15 88126117 . G T 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00403;LSEQ=AATGCTACCTCTGGGAATCG;RSEQ=ATCATTCAGGAAAAGACACC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:130:66,64:94,100:0.3976:2,2:25.9:1.0:28.7:1.0:0.73413:1.1:60.0:64.0:0.4:0.0:1.2 0/0:379:1:0,1:173,204:0.0026:2,0:44.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0027:0.0:1.0 -15 88472228 . G T 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.16588;SOR=0.0;LSEQ=TGTCCAAGAAGAAAGAAGGA;RSEQ=TGGGCAATTGAGAACATAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:6:6,0:35,0:0.1463:1,0:27.7:1.0:31.8:1.0:1.0:0.0:60.0:12.0:0.15:0.0:1.0 0/0:17:0:0,0:17,0:0.0:1,0:16.6:1.0:32.2:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.1 -15 88472655 . G T 225 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACAAGGATCATTGCATCTG;RSEQ=CCCATGGGCCCTGCAAGAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:195:52,143:91,208:0.3947:2,2:23.7:1.0:29.6:1.0:0.41699:1.20268:60.0:47.75:0.3979:0.0:1.1 0/0:375:0:0,0:112,262:0.0:2,0:24.1:1.0:31.4:1.0:1.0:0.0:60.0:40.556:0.9973:0.0:0.2 -15 88524788 . A G 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.03324;SOR=0.0;LSEQ=ATCTAGATCCTAAGAATCTC;RSEQ=CCCTGGCATTATAGAAATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:0.4:0,0:23.1:1.0:33.5:1.0:1.0:0.0:60.0:16.0:0.4:0.0:1.0 0/0:9:0:0,0:0,9:0.0:0,0:29.6:1.0:30.6:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 -15 88576408 . TATATATATATATATAT C 107 MSI6 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=24;MSI=20.0;MSILEN=2.0;SSF=0.01605;SOR=0.0;LSEQ=TTTACTTTTGGGGGGTGTGT;RSEQ=ATATATATATATATATATAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:11:0,11:0,8:0.4231:0,0:14.2:1.0:31.1:1.0:1.0:0.0:60.0:10.0:0.4348:0.3077:0.8 0/0:10:0:0,0:0,6:0.0:0,0:7.0:1.0:29.0:1.0:1.0:0.0:60.0:12.0:0.6:0.0:0.0 -15 88669163 . T C 72 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAACTAGGAGTCCCTTTAC;RSEQ=CACCCGTAATGAAAATAAAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:23.4:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 88726405 . G A 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.12797;SOR=0.0;LSEQ=GAAAGTGAACACACTTGGGT;RSEQ=TCAGGAGACTGACTCTCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:0.4286:0,0:23.2:1.0:26.5:1.0:1.0:0.0:60.0:12.0:0.4286:0.0:1.0 0/0:5:0:0,0:5,0:0.0:0,0:27.8:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -15 90631255 . G A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=GCTGGAACTGGGGATAAAGA;RSEQ=GCATTCTCTTCTGATAGGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:0,2:0.75:0,2:22.8:1.0:27.3:1.0:0.42857:0.0:60.0:5.0:0.7143:0.0:2.2 0/0:2:0:0,0:1,1:0.0:2,0:26.5:1.0:30.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.0 -15 90633416 . A G 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.36364;SOR=0.0;LSEQ=TGGCCTGGGAGATGGAAGAC;RSEQ=TGGATTCTGTTCTCAGCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:0.7:0,0:16.3:1.0:27.0:1.0:1.0:0.0:60.0:14.0:0.7:0.0:1.4 0/0:1:0:0,0:1,0:0.0:0,0:6.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -15 91292969 . G A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATCAATGATTGGGATGATAT;RSEQ=GATGACTTTGATACTTCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:26:15,11:238,254:0.0502:2,2:21.3:1.0:30.2:1.0:0.42263:1.45:60.0:52.0:0.051:0.0:1.2 0/0:541:0:0,0:275,264:0.0:2,0:25.0:1.0:30.8:1.0:1.0:0.0:60.0:133.75:0.9963:0.0:0.1 -15 91295363 . C T 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.28547;SOR=0.0;LSEQ=TTGCATTCTAAAGATGAAGT;RSEQ=CCATTATGATTAATTACATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:0,8:1,14:0.3478:1,0:26.8:1.0:30.3:1.0:1.0:0.0:59.4:16.0:0.3478:0.0:1.8 0/0:4:0:0,0:0,4:0.0:0,0:16.5:1.0:32.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -15 91352774 . A G 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGGGATCAGAGCCCTGGGT;RSEQ=CCAGTTCCAGATCTGCCACC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:0.7143:0,2:38.2:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 91792303 . C T 83 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=20.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CATACATCTACGTTTTCACA;RSEQ=ACACACACACACACACACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:3,4:5,4:0.35:2,2:23.3:1.0:29.9:1.0:1.0:1.61372:60.0:14.0:0.4375:0.0:1.1 0/0:2:0:0,0:1,0:0.0:0,0:28.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -15 92829452 . G A 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.08101;LSEQ=GAGTCAGAAGACGAAGAGGA;RSEQ=GAGGATGTGAGACTCTTAAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:94:42,52:58,70:0.4234:2,2:21.6:1.0:30.2:1.0:1.0:1.02574:59.3:30.333:0.4155:0.0:1.1 0/1:179:10:6,4:74,95:0.0559:2,2:15.6:1.0:30.2:1.0:0.34558:1.92:60.0:20.0:0.0565:0.0:1.0 -15 99434357 . G A 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.27776;SOR=0.0;LSEQ=GACTGAACTTTAAAGATATC;RSEQ=ACTCTCTGCAGGTCTAAGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:13,0:0.3158:1,0:15.8:1.0:28.3:1.0:1.0:0.0:60.0:5.0:0.2778:0.0:1.5 0/0:6:0:0,0:6,0:0.0:0,0:19.2:1.0:30.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -15 99460184 . G T 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GCCTTTCTCCCCACCAGGTA;RSEQ=TGTGTAAGTCAGCAGCTGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:35:2,33:8,111:0.2273:2,2:25.0:1.0:30.2:1.0:1.0:1.1879:60.0:34.0:0.2267:0.0:1.1 0/0:121:0:0,0:4,117:0.0:1,0:23.7:1.0:31.1:1.0:1.0:0.0:60.0:59.5:1.0:0.0:0.2 -15 99467930 . G A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00966;LSEQ=AAAAGTAAGGCTTGTGGAGG;RSEQ=AGAAGAAACGTGGTAAAACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:509:99:29,70:116,293:0.1945:2,2:25.2:1.0:29.9:1.0:0.90139:1.05:60.0:32.0:0.1924:0.0:1.1 0/0:431:1:1,0:144,286:0.0023:2,0:1.0:0.0:23.0:0.0:0.33643:0.0:60.0:2.0:0.0024:0.0:1.0 -15 99478966 . C T 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACCTGCCAAGCCAGGCCAG;RSEQ=GCCACTCCCTCCCCGAAGCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:21.4:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -15 99485931 . T A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.09023;SOR=0.0;LSEQ=GAATCAAATTGTAAATATAT;RSEQ=AAAAGTGGAGATTGCTTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:10,0:7,0:0.5882:0,0:24.5:1.0:28.4:1.0:1.0:0.0:60.0:20.0:0.5882:0.0:1.1 0/0:4:0:0,0:3,1:0.0:2,0:30.0:1.0:30.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -15 99861641 . T G 192 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGAGACTGGGGCTATTTAGC;RSEQ=TGTGGGCAGCTGGCGTTCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:77:35,42:155,203:0.177:2,2:25.4:1.0:30.7:1.0:0.80025:1.09:60.0:154.0:0.182:0.0:1.1 0/0:493:0:0,0:233,260:0.0:2,0:26.3:1.0:30.1:1.0:1.0:0.0:60.0:81.167:1.0:0.0:0.6 -15 99945673 . C G 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00041;SOR=0.0;LSEQ=GAGAAGGCCCAGGAATCTGA;RSEQ=TAAAGTTTGGTCAAGCAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:4,5:1,0:0.9:0,2:17.1:1.0:30.7:1.0:1.0:0.0:60.0:18.0:0.9:0.0:1.2 0/0:8:0:0,0:3,5:0.0:2,0:26.3:1.0:30.8:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.1 -16 337871 . T C 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAGCAGGGACCTCGGCTGCC;RSEQ=CACTTGGGCTGGGCCCTCCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:0.3333:0,0:31.0:1.0:31.5:1.0:1.0:0.0:60.0:12.0:0.3333:0.0:1.5 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 339415 . G T 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.12714;LSEQ=CCACATACTCGTGCGGGGAG;RSEQ=GGGCACCCCAGCCCTCACAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:667:214:148,66:312,138:0.3208:2,2:25.1:1.0:29.4:1.0:1.0:1.00821:60.0:34.667:0.318:0.0:1.1 0/1:495:28:14,14:294,173:0.0566:2,2:22.4:1.0:28.9:1.0:0.22776:1.69745:60.0:27.0:0.0556:0.0:1.1 -16 339727 . C T 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCAGGGGTGAGCAGCACCC;RSEQ=ATTCAAACACCTGGGGCCCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:30:1,29:0,63:0.3226:1,1:21.8:1.0:27.9:1.0:0.32258:0.0:60.0:14.0:0.3146:0.0:1.7 0/0:43:0:0,0:0,43:0.0:1,0:20.1:1.0:31.9:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.3 -16 347184 . A G 240 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07861;LSEQ=CTGGCGCTCTTCCCCGACTC;RSEQ=GCCTTCTTGGCATTTCTTTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:244:96,148:265,407:0.2661:2,2:25.7:1.0:30.3:1.0:1.0:1.00378:60.0:243.0:0.2703:0.0:1.1 0/1:831:23:9,14:347,459:0.0277:2,2:24.5:1.0:29.2:1.0:0.83193:1.17575:60.0:46.0:0.0281:0.0:1.2 -16 347326 . G A 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGCATCTGTAAGGCTCCC;RSEQ=TGGTGCAGCCGCCGCCCGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:36:0,36:2,72:0.3273:1,1:21.3:1.0:30.3:1.0:1.0:0.0:60.0:17.0:0.3178:0.0:1.2 0/0:43:0:0,0:1,42:0.0:1,0:17.8:1.0:31.0:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.2 -16 360149 . G A 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01556;SOR=0.0;LSEQ=CCAATAGAGCTCCTGGCCCC;RSEQ=ACCGCCGGTCAGCAGGCAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:10:1,9:23,187:0.0455:2,2:18.4:1.0:30.1:1.0:1.0:1.10648:60.0:20.0:0.0457:0.0:1.0 0/0:129:0:0,0:17,112:0.0:2,0:23.2:1.0:30.6:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.1 -16 396234 . G A 148 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCTTCTGAGGGAGTCTTCC;RSEQ=GGGGGAGCAGCGTCTCTGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:795:32:17,15:451,310:0.0403:2,2:26.1:1.0:29.7:1.0:0.58265:1.28326:60.0:31.0:0.0393:0.0:1.9 0/0:707:0:0,0:391,316:0.0:2,0:23.6:1.0:29.6:1.0:1.0:0.0:60.0:234.667:1.0:0.0:0.6 -16 1987179 . C T 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00675;SOR=0.0;LSEQ=ATCCACTCCCACATGCTCCC;RSEQ=GGATTTCTGTGGGTATAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:8:1,7:1,31:0.2:1,2:24.9:1.0:28.8:1.0:0.3641:4.21:60.0:7.0:0.1795:0.0:1.3 0/0:33:0:0,0:3,30:0.0:2,0:20.4:1.0:29.8:1.0:1.0:0.0:60.0:66.0:1.0:0.0:0.1 -16 2105055 . A G 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCACACGTCTCCTCCGAGCC;RSEQ=CTCTCTGCTGGGGGTGGGGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:3,0:0.625:0,2:33.8:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 2110795 . G A 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00592;LSEQ=TCTGCTGAACATCATCGAAC;RSEQ=GCTCCTTCAGCAGCTCCAGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:905:173:71,102:331,401:0.1912:2,2:26.3:1.0:30.6:1.0:0.34964:1.18561:60.0:85.5:0.1924:0.0:1.1 0/0:717:1:1,0:319,397:0.0014:2,0:37.0:0.0:25.0:0.0:0.4463:0.0:60.0:2.0:0.0014:0.0:1.0 -16 2127944 . G T 62 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.48718;SOR=0.0;LSEQ=CGCATCCCCAGGCCCCCTCG;RSEQ=GGTGCCGCTCCGAGAGAGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:1,4:0,6:0.4545:0,2:22.6:1.0:27.0:1.0:0.45455:0.0:60.0:4.0:0.4:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:28.5:1.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -16 2132583 . G A 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGTGCTCGTCGCCTCATCC;RSEQ=CCCACCCCCATGGTCCGTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:252:94:16,78:20,137:0.373:2,2:25.6:1.0:30.1:1.0:0.35798:1.4:60.0:188.0:0.3775:0.0:1.1 0/0:152:0:0,0:29,122:0.0:2,0:20.7:1.0:30.8:1.0:1.0:0.0:60.0:24.167:1.0:0.0:0.1 -16 2134852 . G A 205 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTGGAACCCCTGGGAGGGC;RSEQ=GTGGAGTGGGAGATGGCCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:113:100,13:194,35:0.3304:2,2:23.6:1.0:30.2:1.0:0.40937:1.39:60.0:36.667:0.3323:0.0:1.1 0/0:170:0:0,0:140,29:0.0:2,0:22.1:1.0:30.2:1.0:1.0:0.0:60.0:338.0:1.0:0.0:0.2 -16 2136455 . C T 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATCCAGTCCTGCTACCCCA;RSEQ=GCCCTGGGGCATGGCCCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:38:4,34:28,158:0.1696:2,2:25.6:1.0:29.7:1.0:0.61401:1.50378:60.0:76.0:0.1704:0.0:1.1 0/0:118:0:0,0:14,104:0.0:2,0:23.3:1.0:29.4:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.1 -16 2215618 . GCA CTG 94 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.57669;SOR=0.0;LSEQ=GCGTGTGAGTGCTGTGTGGC;RSEQ=GCCTGGTCGCATGGTTAAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:8:6,2:32,8:0.1667:2,2:25.5:1.0:31.6:1.0:0.66555:1.32491:59.4:16.0:0.1818:0.0:6.0 0/0:7:0:0,0:5,2:0.0:2,0:19.9:1.0:25.1:1.0:1.0:0.0:45.0:6.0:1.0:0.0:0.4 -16 2215645 . G T 117 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0599;SOR=0.0;LSEQ=GGTCGCATGGTTAAGCGTGT;RSEQ=AGTGCTGCGTGGCCTGGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:14:12,2:45,5:0.2188:2,2:28.4:1.0:30.8:1.0:0.64188:1.48968:55.5:28.0:0.2222:0.0:5.2 0/0:15:0:0,0:12,3:0.0:2,0:21.8:1.0:31.6:1.0:1.0:0.0:53.9:30.0:1.0:0.0:0.5 -16 2215648 . T C 125 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06324;SOR=0.0;LSEQ=CGCATGGTTAAGCGTGTGAG;RSEQ=GCTGCGTGGCCTGGCCTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:16:14,2:48,5:0.2319:2,2:25.8:1.0:31.3:1.0:0.65954:1.36474:56.1:15.0:0.2239:0.0:4.9 0/0:15:0:0,0:12,3:0.0:2,0:23.6:1.0:30.1:1.0:1.0:0.0:53.9:30.0:1.0:0.0:0.5 -16 2215659 . CT GC 133 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=5.0;SSF=0.02062;SOR=0.0;LSEQ=GCGTGTGAGTGCTGCGTGGC;RSEQ=GGCCTGGTCGCATGGTTAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:20:18,2:56,6:0.2381:2,2:20.5:1.0:31.0:1.0:1.0:1.03658:57.6:40.0:0.2532:0.0119:3.0 0/0:19:0:0,0:16,3:0.0:2,0:25.8:1.0:31.3:1.0:1.0:0.0:58.0:38.0:1.0:0.0:0.3 -16 2215686 . T G 107 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0641;SOR=0.0;LSEQ=GGTCGCATGGTTAAGCGTGT;RSEQ=AGCGCTGCGTGGCGCGGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:10:10,0:114,7:0.0763:2,0:24.8:1.0:32.3:1.0:1.0:0.0:56.4:20.0:0.082:0.0:2.1 0/0:51:0:0,0:47,4:0.0:2,0:22.1:1.0:28.7:1.0:1.0:0.0:60.0:7.5:1.0:0.0:0.2 -16 2215689 . C T 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.03541;SOR=0.0;LSEQ=CGCATGGTTAAGCGTGTTAG;RSEQ=GCTGCGTGGCGCGGCCTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:11:11,0:114,7:0.0827:2,0:25.6:1.0:29.7:1.0:1.0:0.0:54.9:22.0:0.0948:0.0:2.6 0/0:54:0:0,0:50,4:0.0:2,0:22.5:1.0:30.1:1.0:1.0:0.0:60.0:6.714:1.0:0.0:0.2 -16 2226763 . C G 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.18678;SOR=0.0;LSEQ=TCTACTCGGCACTGTCCTTG;RSEQ=TGCCCAGCCCCTCTCTGGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:7:0,7:0,58:0.1077:1,0:29.7:1.0:32.4:1.0:1.0:0.0:60.0:14.0:0.1077:0.0:1.0 0/0:21:0:0,0:0,21:0.0:1,0:19.1:1.0:32.2:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.1 -16 3777496 . C A 62 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.2605;SOR=0.0;LSEQ=GGAAAAAAAAGAACCCCCCC;RSEQ=ACCCCCCCGCCAAAAAAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:20.4:1.0:26.8:1.0:1.0:0.0:60.0:4.0:0.4444:0.0:2.6 0/0:4:0:0,0:4,0:0.0:0,0:10.8:1.0:30.5:1.0:1.0:0.0:55.0:8.0:1.0:0.0:0.8 -16 3786594 . C G 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAATGCAAGAAAAAGGCACA;RSEQ=AAATATCCTCCCCTCAGTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:51:40,11:331,70:0.1123:2,2:26.9:1.0:30.9:1.0:0.44353:1.29955:60.0:50.0:0.1124:0.0:1.1 0/0:367:0:0,0:286,81:0.0:2,0:23.6:1.0:31.0:1.0:1.0:0.0:60.0:72.4:1.0:0.0:0.1 -16 3794705 . T G 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00073;SOR=0.0;LSEQ=ACATTCTTGCATTCTTACCC;RSEQ=CATGACTGGCCTGGCTCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:14:13,1:53,0:0.209:1,1:19.6:1.0:30.1:1.0:0.20896:0.0:60.0:28.0:0.209:0.0:1.0 0/0:43:0:0,0:41,2:0.0:1,0:17.5:1.0:31.8:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.1 -16 3807171 . G A 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGCGTGAGCCACCACACCC;RSEQ=GCCTGAAATTGGGCCACTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:17:17,0:28,0:0.3778:1,1:29.3:1.0:30.1:1.0:1.0:0.0:58.8:34.0:0.3778:0.0:1.1 0/0:63:0:0,0:58,4:0.0:2,0:24.0:1.0:29.2:1.0:1.0:0.0:60.0:61.0:1.0:0.0:0.0 -16 3807946 . C T 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0197;LSEQ=AGGCATTGTTGAACATGAGC;RSEQ=AGACGTCGTCCACGTACTGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:40:16,24:247,285:0.0699:2,2:25.2:1.0:29.5:1.0:0.51146:1.29941:60.0:80.0:0.0708:0.0:1.2 0/0:678:1:0,1:329,348:0.0015:2,0:2.0:0.0:22.0:0.0:1.0:0.0:60.0:2.0:0.0015:0.0:1.0 -16 3860554 . C T 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAATGGTAAAAATCCACAGA;RSEQ=CACAGCACCCACCGGAGAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:130:93,37:181,67:0.3439:2,2:23.0:1.0:30.8:1.0:0.80872:1.07458:60.0:260.0:0.3476:0.0:1.1 0/0:322:0:0,0:222,100:0.0:2,0:1.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -16 3929235 . GCACACACACA G 75 d7;MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=14.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GACTAAAAACACACACGCGC;RSEQ=CACACACACACACACACAAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1.0:0,2:29.6:1.0:32.4:1.0:1.0:0.0:54.6:10.0:1.0:0.2:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 8382667 . T A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.0;MSILEN=1.0;SSF=0.02375;SOR=0.0;LSEQ=AGTTTTATGTGCCTGCTCCA;RSEQ=AAAAAAAAGAAATGCGCTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:0.4:0,0:11.5:1.0:31.5:1.0:1.0:0.0:60.0:12.0:0.4:0.0:2.0 0/0:11:0:0,0:11,0:0.0:0,0:22.9:1.0:30.9:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.2 -16 9944017 . G A 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.54887;SOR=0.0;LSEQ=GGCAGTTCTCCATCCCAGCC;RSEQ=CCCTCATCCCCAGAGGAATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:0,5:0,13:0.2778:1,0:17.2:1.0:29.4:1.0:1.0:0.0:60.0:10.0:0.2778:0.0:1.0 0/0:3:0:0,0:0,3:0.0:0,0:27.3:1.0:32.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:1.0 -16 10273656 . C T 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.25824;SOR=0.0;LSEQ=GTGTACACCATTTTCAGAAA;RSEQ=AAGGCAAAAGGCATTTCCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:0.4545:0,0:10.8:1.0:28.2:1.0:1.0:0.0:60.0:4.0:0.4:0.0:1.8 0/0:3:0:0,0:2,1:0.0:2,0:11.3:1.0:32.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 -16 10273821 . C T 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CCATGCAGCTGGTGGCTTCC;RSEQ=AGGTCCTGGCAGGGCATCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:20:16,4:254,63:0.0593:2,2:23.5:1.0:30.6:1.0:1.0:1.00791:60.0:19.0:0.0571:0.0:1.2 0/0:269:0:0,0:191,78:0.0:2,0:23.9:1.0:30.5:1.0:1.0:0.0:60.0:88.667:1.0:0.0:0.2 -16 11345660 . AAAG A 72 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.0;MSILEN=1.0;SSF=0.29976;SOR=0.0;LSEQ=AGACTCTGTCTTAAAAAAAA;RSEQ=AAGAAGAAACCTGTCTTGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:5:5,0:25,0:0.1667:1,0:15.2:1.0:31.1:1.0:1.0:0.0:59.0:10.0:0.1667:0.1:0.2 0/0:11:0:0,0:10,1:0.0:2,0:25.4:1.0:29.4:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.5 -16 11346956 . AAAAG A 72 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.48718;SOR=0.0;LSEQ=AGGGGTGTGGCAAAAAAAAA;RSEQ=AAAAGAAAAGAAAAGAAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:2,0:0.4545:0,2:9.4:1.0:31.1:1.0:1.0:0.0:60.0:10.0:0.7143:0.1818:0.0 0/0:2:0:0,0:1,0:0.0:0,0:1.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -16 11349302 . C T 63 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.09061;SOR=0.15141;LSEQ=CTCTGCTGCTGTGGAGACTG;RSEQ=ATTGTCGGCTGCCACCTGGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:5:2,3:232,169:0.0123:2,2:21.0:1.0:27.4:1.0:0.65431:2.05549:60.0:10.0:0.0126:0.0:1.0 0/0:533:1:0,1:299,233:0.0019:2,0:1.0:0.0:24.0:0.0:0.43902:0.0:60.0:2.0:0.0019:0.0:2.0 -16 11352930 . G A 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0004;SOR=0.12796;LSEQ=GCAAGTGACCTGTCCTCTTG;RSEQ=GACCTGATTTGCCCCAACTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:21:0,21:0,45:0.3182:1,1:28.6:1.0:31.9:1.0:1.0:0.0:60.0:42.0:0.3387:0.0:2.0 0/1:54:3:0,3:5,46:0.0556:2,0:18.7:1.0:33.0:0.0:1.0:0.0:60.0:6.0:0.0556:0.0:2.0 -16 14028861 . C T 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.03594;SOR=0.0;LSEQ=ATTTGATCAATACCTAAGAC;RSEQ=CTTTTTAAATAGTTTGTAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:7:7,0:32,0:0.1795:1,0:30.4:1.0:31.9:1.0:1.0:0.0:60.0:14.0:0.1795:0.0:1.6 0/0:28:0:0,0:28,0:0.0:1,0:22.3:1.0:30.8:1.0:1.0:0.0:60.0:56.0:1.0:0.0:0.0 -16 14041760 . C A 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTAGCAAGCCTTTCTCTCT;RSEQ=ACTTCCCGAGGTGCCTTGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:19:9,10:290,350:0.0288:2,2:28.8:1.0:28.9:1.0:1.0:1.09:60.0:38.0:0.0288:0.0:1.1 0/0:751:0:0,0:357,392:0.0:2,0:24.6:1.0:31.0:1.0:1.0:0.0:60.0:123.833:0.9973:0.0:0.1 -16 14042077 . A G 186 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCACGTTAAGAACATCGCAG;RSEQ=ATTAGCAGCCCTGTCACAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:61:26,35:269,323:0.0934:2,2:26.2:1.0:31.4:1.0:0.688:1.12089:60.0:122.0:0.0953:0.0:1.2 0/0:727:0:0,0:358,369:0.0:2,0:24.8:1.0:29.2:1.0:1.0:0.0:60.0:102.857:1.0:0.0:0.2 -16 16100728 . C CGGTGGCGGTGGCGGTGGCGGTGGT 111 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.0;MSILEN=6.0;SSF=2e-05;SOR=0.0;LSEQ=GGCGGTGGCGGTGGCGGTGG;RSEQ=GGTGGCGGTGATGGTGGTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:5,7:6,4:0.5455:2,2:17.5:1.0:31.0:1.0:0.66992:2.02883:58.8:24.0:0.5455:0.3636:0.7 0/0:24:0:0,0:5,16:0.0:2,0:16.4:1.0:29.2:1.0:1.0:0.0:60.0:42.0:0.875:0.0:1.4 -16 17380507 . T TATCATCATCATCCTC 103 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=39;MSI=2.6;MSILEN=1.0;SSF=0.00453;SOR=0.0;LSEQ=CAACAATCCCCATGGATAGG;RSEQ=ATCATCATCATCCTCATCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:6,5:7,3:0.5238:2,2:21.9:1.0:30.0:1.0:0.65944:1.88324:60.0:22.0:0.5238:0.2381:0.1 0/0:11:0:0,0:7,4:0.0:2,0:30.5:1.0:29.5:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.1 -16 27356584 . T G 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTGTTTCCACCCCTGAACT;RSEQ=AAGTGCCCAGGAAGGCGTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:56:43,13:70,40:0.3373:2,2:24.1:1.0:31.6:1.0:0.11282:1.88:60.0:27.0:0.3293:0.0:1.3 0/0:150:0:0,0:100,50:0.0:2,0:23.6:1.0:28.7:1.0:1.0:0.0:60.0:49.0:1.0:0.0:0.3 -16 30129936 . C T 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00817;LSEQ=AGGAAAACAGGCTCTGAAGG;RSEQ=GAGGCTGCACACCTCCTCCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:91:7,84:14,150:0.3569:2,2:22.5:1.0:30.1:1.0:1.0:1.11953:60.0:90.0:0.3571:0.0:1.1 0/0:223:1:0,1:30,192:0.0045:2,0:21.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0045:0.0:1.0 -16 32369286 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.00361;SOR=0.0;LSEQ=AATAGAGTCTTTTGAAATTG;RSEQ=CTTGCAGGTGACCTTTTGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:15.4:1.0:30.8:1.0:1.0:0.0:50.0:10.0:0.625:0.0:1.0 0/0:12:0:0,0:11,1:0.0:2,0:24.3:1.0:31.7:1.0:1.0:0.0:45.5:11.0:1.0:0.0:0.1 -16 32369738 . CC AA 70 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.02267;SOR=0.0;LSEQ=ATGTCCTTCCAAGAATCATC;RSEQ=CTTGATGAAGCTCCCACAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:0,5:5,45:0.0909:2,0:17.8:1.0:30.3:1.0:1.0:0.0:51.4:10.0:0.0943:0.0182:0.8 0/0:60:0:0,0:8,52:0.0:2,0:23.7:1.0:31.4:1.0:1.0:0.0:49.6:120.0:1.0:0.0:0.3 -16 32374889 . C T 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATGTCTCTCAGGCAGCAGGG;RSEQ=TTCCCATGTATTTTATGCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:13:9,4:195,85:0.0444:2,2:20.3:1.0:30.2:1.0:1.0:1.01954:41.4:26.0:0.0453:0.0:1.1 0/0:569:0:0,0:377,192:0.0:2,0:24.4:1.0:31.7:1.0:1.0:0.0:42.0:141.25:1.0:0.0:0.1 -16 33365663 . A G 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.01093;SOR=0.0;LSEQ=TTATCAAAGTTCCTCAATGT;RSEQ=CTTCCAGTAAAGTGGGGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:5:0,5:11,78:0.0532:2,0:11.8:1.0:33.4:1.0:1.0:0.0:24.8:10.0:0.0532:0.0:3.8 0/0:135:0:0,0:17,118:0.0:2,0:22.5:1.0:29.3:1.0:1.0:0.0:36.7:66.5:1.0:0.0:0.4 -16 33371341 . CG C 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.51471;SOR=0.0;LSEQ=GCAGGAGGATCACTTGAACC;RSEQ=GGGGGCAGAGGTTGCAGTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:0.4:0,0:29.5:1.0:31.8:1.0:1.0:0.0:57.2:12.0:0.4:0.0:0.0 0/0:3:0:0,0:1,1:0.0:2,0:7.5:1.0:28.5:1.0:1.0:0.0:54.0:4.0:0.6667:0.0:0.5 -16 33373312 . G T 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGTCCAACACAAACAA;RSEQ=AACTTCAGGAGCCAAGCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:641:28:15,13:370,243:0.0437:2,2:22.2:1.0:29.2:1.0:0.55483:1.31901:59.6:56.0:0.0444:0.0:1.2 0/0:1267:0:0,0:708,559:0.0:2,0:24.6:1.0:31.2:1.0:1.0:0.0:59.3:65.684:1.0:0.0:0.3 -16 33948696 . G C 142 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTGTTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGTTGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:23:11,12:21,22:0.2421:2,2:33.7:1.0:31.5:1.0:1.0:1.0407:53.6:10.5:0.3333:0.0:3.6 0/0:111:0:0,0:25,28:0.0:2,0:25.5:1.0:31.1:1.0:1.0:0.0:59.7:106.0:1.0:0.0:0.2 -16 33948711 . T C 147 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTTGGTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGGTGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:24:12,12:32,35:0.2581:2,2:35.3:1.0:32.1:1.0:1.0:1.09:54.2:23.0:0.2584:0.0:4.0 0/0:111:0:0,0:34,37:0.0:2,0:28.5:1.0:30.0:1.0:1.0:0.0:55.9:142.0:1.0:0.0:0.7 -16 33948789 . CA TG 85 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05408;SOR=0.13256;LSEQ=TATGTGCTTGTTTGTTAGAT;RSEQ=GCATACTACTGCTTCCGGAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:7:3,4:3,13:0.3043:2,2:13.6:1.0:30.5:1.0:0.31849:3.07:54.1:14.0:0.3043:0.0:5.0 0/1:19:1:0,1:4,14:0.0526:2,0:15.0:0.0:32.0:0.0:1.0:0.0:50.0:2.0:0.0526:0.0:5.0 -16 33957556 . T A 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=3.0;SSF=0.15554;SOR=0.0;LSEQ=GCTCTTGTTGCTGTTGTTGT;RSEQ=GTTGTTTTCAAAGCACACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:3,2:15,14:0.1471:2,2:32.0:1.0:29.8:1.0:1.0:1.39:45.0:10.0:0.1471:0.0:3.4 0/0:17:0:0,0:10,7:0.0:2,0:31.4:1.0:30.1:1.0:1.0:0.0:48.0:34.0:1.0:0.0:2.1 -16 33957584 . C A 74 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.14179;SOR=0.0;LSEQ=TCAAAGCACACCTCGGCCAC;RSEQ=GTTTATGGGATCAAAAGCGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:1,4:12,12:0.1724:2,2:19.0:1.0:32.2:1.0:0.34319:3.82896:43.6:10.0:0.1852:0.0:4.0 0/0:19:0:0,0:9,10:0.0:2,0:22.1:1.0:29.7:1.0:1.0:0.0:45.8:38.0:1.0:0.0:2.3 -16 33957977 . ACT A 77 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.0;MSILEN=2.0;SSF=0.04762;SOR=0.0;LSEQ=CTGTGTCTGTCTTCTGTCTT;RSEQ=CTCTTTCTCTGCCGGTCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:1,0:0.8333:0,2:28.2:1.0:33.4:1.0:1.0:0.0:58.8:10.0:0.8333:0.0:2.8 0/0:3:0:0,0:2,1:0.0:2,0:15.0:1.0:27.7:1.0:1.0:0.0:34.0:6.0:1.0:0.0:1.7 -16 46395394 . A T 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0029;SOR=0.0;LSEQ=TTCAATTCTATGATGATTAC;RSEQ=TTGGATTCCATTCGTTGATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:3,3:6,7:0.3158:2,2:21.0:1.0:31.7:1.0:1.0:1.16:55.7:12.0:0.3158:0.0:1.3 0/0:27:0:0,0:13,14:0.0:2,0:29.0:1.0:30.0:1.0:1.0:0.0:42.8:54.0:1.0:0.0:0.4 -16 46403662 . C G 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=5.0;SSF=0.00182;SOR=0.12139;LSEQ=ATTCGATGATGATTCCATTC;RSEQ=AGTCCATATGATCATTCCAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:9,9:0.3333:2,2:25.4:1.0:31.3:1.0:1.0:1.23971:46.9:18.0:0.3333:0.0:2.2 0/1:54:3:2,1:31,19:0.0556:2,2:35.0:1.0:31.7:1.0:1.0:1.22:46.7:6.0:0.0566:0.0:1.7 -16 46403773 . G C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00037;SOR=0.03257;LSEQ=TCCATTCGAGTCCATTCGAT;RSEQ=ATTCCATTCGAGTCCATTTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:1,1:0.7143:2,2:20.0:1.0:32.6:1.0:1.0:3.1622:57.6:10.0:0.7143:0.0:3.0 0/1:46:3:0,3:13,30:0.0652:2,0:27.3:1.0:32.0:1.0:0.54783:0.0:53.3:6.0:0.0667:0.0:2.7 -16 52085593 . A G 244 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.04722;LSEQ=CTCCTTTTTCTATGGGGAGA;RSEQ=AATTAATATCCAGGCAGTGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:272:213:99,114:25,34:0.7831:2,2:25.3:1.0:31.6:1.0:0.65816:1.18:60.0:105.5:0.7815:0.0:1.1 0/1:311:45:23,22:125,141:0.1447:2,2:27.5:1.0:31.6:1.0:0.63148:1.18:60.0:90.0:0.1456:0.0:1.0 -16 55329374 . C CCTCTCTGTCTCTCTGT 83 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=3.0;MSILEN=8.0;SSF=0.00769;SOR=0.0;LSEQ=AATTAATACCACAATCTCAA;RSEQ=CTCTCTGTCTCTCTCTCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:6,0:14,0:0.2857:1,0:21.8:1.0:32.3:1.0:1.0:0.0:59.0:12.0:0.2857:0.1429:0.2 0/0:23:0:0,0:22,1:0.0:1,0:23.9:1.0:31.8:1.0:1.0:0.0:56.6:46.0:1.0:0.0:0.5 -16 55329381 . G GTCTCTCTGTCTCTCTGTC 110 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=16.0;MSILEN=2.0;SSF=0.00287;SOR=0.07002;LSEQ=ACCACAATCTCAACCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:11,0:17,0:0.3548:1,0:16.0:1.0:32.0:1.0:1.0:0.0:55.5:22.0:0.3548:0.2581:0.8 0/1:28:1:1,0:11,0:0.0357:0,0:39.0:0.0:32.9:0.0:1.0:0.0:40.0:2.0:0.0385:0.0:0.0 -16 56863229 . T C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07975;SOR=0.0;LSEQ=CAGCTCCGGGTGGAGAAGAG;RSEQ=GCATGGAGAAGATGTCATTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:7:0,7:0,25:0.2188:1,0:22.7:1.0:31.3:1.0:1.0:0.0:60.0:14.0:0.2188:0.0:1.0 0/0:17:0:0,0:0,17:0.0:1,0:17.7:1.0:30.1:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.3 -16 56866054 . A AT 172 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.02565;LSEQ=GTTCCTCGTCTCCTGTCCCC;RSEQ=TTTTTTGTTGTGTAATTCCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:49:20,29:88,87:0.2188:2,2:28.3:1.0:30.7:1.0:0.26107:1.46415:60.0:48.0:0.2192:0.0268:0.1 0/0:141:1:0,1:71,69:0.0071:2,0:12.0:0.0:31.0:0.0:0.49645:0.0:60.0:2.0:0.0072:0.0:0.0 -16 56866196 . T C 237 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.11893;LSEQ=ACCAATGCATGTGTTTCTCT;RSEQ=GGGGATTTAGTTGAACCAAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1123:221:130,91:526,376:0.1968:2,2:24.8:1.0:30.5:1.0:0.93934:1.02:60.0:220.0:0.1984:0.0:1.2 0/1:1202:34:24,10:675,493:0.0283:2,2:23.6:1.0:29.7:1.0:0.15959:1.75:60.0:33.0:0.0277:0.0:1.1 -16 56866801 . G T 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCTTGAGTGACTTAACAGG;RSEQ=TAAAGGAGATAAACACTCTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:8,1:1,0:0.9:0,2:19.4:1.0:28.9:1.0:1.0:0.0:60.0:18.0:0.9:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 56871762 . T C 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.00044;SOR=0.0;LSEQ=ACAGCTTTCCAAAGTGGTTC;RSEQ=ACTAACTCACCATGCCACCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:15:0,15:2,70:0.1724:1,1:26.3:1.0:32.0:1.0:1.0:0.0:60.0:30.0:0.1744:0.0:1.0 0/0:56:0:0,0:0,56:0.0:1,0:23.1:1.0:28.8:1.0:1.0:0.0:60.0:112.0:1.0:0.0:0.0 -16 56872824 . G A 214 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.15683;LSEQ=CGGATTACACAGAAATTCCT;RSEQ=ATACACTCTTACTACCCCCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:169:106,63:383,184:0.2296:2,2:25.3:1.0:29.0:1.0:0.26558:1.23674:60.0:338.0:0.2312:0.0:1.1 0/1:807:36:24,12:485,285:0.0446:2,2:19.6:1.0:28.7:1.0:0.72609:1.18:60.0:72.0:0.0454:0.0:1.1 -16 56873613 . T TA 172 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.103;LSEQ=ACAGCTTTAAGAATTCTAGT;RSEQ=ACAGTAACTATCCAGACTGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:49:1,48:8,183:0.2042:1,1:23.0:1.0:30.7:1.0:0.69047:2.09308:60.0:98.0:0.2059:0.0458:0.0 0/1:195:5:1,4:10,180:0.0256:2,2:13.4:1.0:28.3:1.0:0.2543:4.44:59.0:10.0:0.0259:0.0051:0.2 -16 56873789 . T C 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ACAGGTTTCTGGTTGATCTG;RSEQ=GAAGTCTGGTTTAATTCTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:0.4667:0,0:23.6:1.0:29.4:1.0:1.0:0.0:60.0:14.0:0.4667:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:33.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -16 58032026 . G A 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01686;SOR=0.0;LSEQ=TGCAGGAGGATGCCATAGAC;RSEQ=GCACAGCCCAGGGGGTTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:5,1:7,2:0.4:2,2:32.3:1.0:29.0:1.0:1.0:1.4:60.0:5.0:0.3571:0.0:1.2 0/0:14:0:0,0:10,4:0.0:2,0:22.9:1.0:30.1:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 -16 58960831 . G A 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATACAGTAATTGACCAAGG;RSEQ=TACCAACTATTGTGCTTTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:24:24,0:39,1:0.375:1,1:21.5:1.0:30.0:1.0:1.0:0.0:60.0:48.0:0.375:0.0:1.2 0/0:45:0:0,0:44,1:0.0:1,0:22.5:1.0:31.4:1.0:1.0:0.0:60.0:90.0:1.0:0.0:0.0 -16 59584343 . G A 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.10373;LSEQ=TTACAAGGAAATGCACAGAT;RSEQ=AGCCTAGGTGAAGATTCGAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:31:15,16:18,18:0.4627:2,2:26.0:1.0:29.4:1.0:1.0:1.06563:60.0:62.0:0.4627:0.0:1.9 0/1:99:8:4,4:42,49:0.0808:2,2:24.4:1.0:29.8:1.0:1.0:1.16:60.0:16.0:0.0808:0.0:1.8 -16 59584360 . C T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0833;LSEQ=GATGAGCCTAGGTGAAGATT;RSEQ=GATCTAAGGTTTTGACTGAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:25:10,15:13,18:0.4464:2,2:22.3:1.0:29.8:1.0:1.0:1.08178:60.0:24.0:0.4364:0.0:2.0 0/1:81:5:2,3:30,46:0.0617:2,2:32.4:1.0:30.0:1.0:1.0:1.02:60.0:10.0:0.0625:0.0:2.0 -16 67645883 . TGCAGTTACA T 209 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGACATTCCAGTGTGAGCTT;RSEQ=CGTGTCCACGGCGTTCAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:111:66,45:227,170:0.2185:2,2:27.9:1.0:30.9:1.0:0.74457:1.1:60.0:110.0:0.2187:0.0197:0.1 0/0:723:0:0,0:406,317:0.0:2,0:25.0:1.0:31.8:1.0:1.0:0.0:60.0:102.286:1.0:0.0:0.1 -16 68862182 . A G 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAACGTTTATTACTATGATG;RSEQ=AGAAGGAGGCGGAGAAGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:18:8,10:177,284:0.0375:2,2:31.1:1.0:31.2:1.0:0.62772:1.28:60.0:36.0:0.0384:0.0:1.0 0/0:623:0:0,0:281,342:0.0:2,0:24.6:1.0:29.1:1.0:1.0:0.0:60.0:50.917:1.0:0.0:0.2 -16 68867456 . C T 137 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.15792;LSEQ=GCTGGGAAATGCAGAAATCA;RSEQ=GTTGCTGGTGGTTTTTCAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:23:4,19:16,76:0.2:2,2:20.0:1.0:30.5:1.0:1.0:1.0:60.0:46.0:0.2018:0.0:1.1 0/1:159:6:1,5:29,124:0.0377:2,2:22.2:1.0:31.3:1.0:1.0:1.16826:60.0:12.0:0.0387:0.0:1.2 -16 72822296 . G A 253 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.15831;LSEQ=GTGGGGTCCGAAGTCAACGC;RSEQ=GCCTGCAGGGCCTGCAGCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1801:337:185,152:776,685:0.1871:2,2:24.5:1.0:30.2:1.0:0.58573:1.07:60.0:36.444:0.1848:0.0:1.1 0/1:2134:75:39,36:1078,978:0.0351:2,2:25.5:1.0:30.3:1.0:1.0:1.01746:60.0:150.0:0.0355:0.0:1.2 -16 72828383 . C T 243 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01438;LSEQ=TCTTGGCTTCATGCCAGTGA;RSEQ=GGGACCGGATATGAGCCTCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1364:270:134,136:530,562:0.1979:2,2:23.7:1.0:30.1:1.0:0.78573:1.04:60.0:37.571:0.1954:0.0:1.1 0/0:1416:5:2,3:720,690:0.0035:2,2:19.2:1.0:29.0:1.0:0.68089:1.56472:60.0:10.0:0.0036:0.0:1.0 -16 72830539 . C G 256 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.16928;LSEQ=TGTTTGGCAAACCTCTCGAG;RSEQ=TGTTTGAAAGGAAAGTAATT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1825:283:140,143:747,791:0.1551:2,2:24.2:1.0:31.5:1.0:0.79601:1.04:60.0:55.6:0.1544:0.0:1.2 0/1:1992:60:28,32:939,989:0.0301:2,2:30.2:1.0:31.1:1.0:0.79409:1.085:60.0:120.0:0.0307:0.0:1.2 -16 72832377 . G A 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04335;LSEQ=CAGGCTACACTGATTACAGC;RSEQ=GTACTTGTACACATGGCGAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1542:64:29,35:726,752:0.0415:2,2:27.5:1.0:30.9:1.0:0.61015:1.16505:60.0:128.0:0.042:0.0:1.1 0/0:1602:3:3,0:804,792:0.0019:2,0:1.0:0.0:28.3:1.0:0.2496:0.0:60.0:6.0:0.0019:0.0:1.0 -16 72924122 . T C 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATATGGGGGTGGTTCCCCCA;RSEQ=GCTGTTCTTGTGATACTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:0.3333:0,0:24.8:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.3571:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:9.5:1.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -16 72991715 . A G 252 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGCCGCCGCCGCCGCAGCC;RSEQ=CCGCCGCCGCCGCCGCCCCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:851:291:152,139:268,283:0.342:2,2:22.3:1.0:30.8:1.0:0.34629:1.15:60.0:96.0:0.3466:0.0:1.6 0/0:813:0:0,0:83,79:0.0:2,0:22.9:1.0:29.0:1.0:1.0:0.0:60.0:39.5:0.9814:0.0:0.2 -16 72993622 . C T 231 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.14549;LSEQ=CTCAGGCTCTCCACAATGTA;RSEQ=GCGGAGCCGTCCGGCTGGTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1276:196:88,108:492,587:0.1536:2,2:24.4:1.0:30.4:1.0:0.87633:1.02863:60.0:97.0:0.1545:0.0:1.3 0/1:1439:37:16,21:684,713:0.0257:2,2:19.5:1.0:29.3:1.0:0.51035:1.25891:60.0:36.0:0.0254:0.0:1.3 -16 72993706 . G A 225 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.1476;LSEQ=CCCTCCTCACCGGTGTCGCT;RSEQ=GCGCTCTCCTCTCTCAGGGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:193:92,101:586,551:0.1449:2,2:22.8:1.0:29.7:1.0:0.35019:1.16742:60.0:63.333:0.1454:0.0:1.3 0/1:1517:37:17,20:716,764:0.0244:2,2:22.1:1.0:29.0:1.0:0.86815:1.10247:60.0:74.0:0.0248:0.0:1.3 -16 79167945 . A G 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01786;SOR=0.0;LSEQ=AGAGTTTGTTTCTTCCTGCT;RSEQ=TGGCCATAGAGGTTTGGTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:20.2:1.0:33.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:3:0:0,0:0,3:0.0:0,0:19.0:1.0:30.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -16 81887820 . C T 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.28327;SOR=0.0;LSEQ=GGGTGAGCGGAAACCCCAAA;RSEQ=TCTTCAGACTCCAGGGGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:12,1:0.35:1,0:30.1:1.0:30.1:1.0:1.0:0.0:60.0:14.0:0.35:0.0:1.1 0/0:4:0:0,0:4,0:0.0:0,0:29.0:1.0:30.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -16 81887903 . A G 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00101;SOR=0.11808;LSEQ=TCCATTTCCAGAAGGAGGGG;RSEQ=CACTGAGTCCAGACGCAGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:24:24,0:61,2:0.2759:1,1:29.5:1.0:29.9:1.0:1.0:0.0:60.0:11.0:0.2619:0.0:3.1 0/1:47:2:2,0:43,2:0.0426:1,0:16.5:1.0:32.5:1.0:1.0:0.0:60.0:4.0:0.0444:0.0:2.0 -16 81887977 . G C 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.05397;LSEQ=AGCCAGGCTGTGCCTGGGCT;RSEQ=CAGTTGTGTGGCTGCATCCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:107:96,11:141,17:0.4038:2,2:24.3:1.0:31.4:1.0:1.0:1.05:60.0:106.0:0.403:0.0:2.2 0/1:228:8:7,1:195,25:0.0351:2,2:24.1:1.0:31.4:1.0:1.0:1.1137:60.0:16.0:0.0356:0.0:2.0 -16 81888274 . C A 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.07242;LSEQ=CGCTAATAGCAGAATGCTCA;RSEQ=CCCTGCCTGCTCACTGATGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:105:10,95:21,138:0.3977:2,2:26.4:1.0:29.7:1.0:0.43685:1.4437:60.0:34.0:0.3969:0.0:2.0 0/1:264:12:1,11:39,213:0.0455:2,2:21.2:1.0:29.9:1.0:0.69968:2.00983:60.0:24.0:0.0462:0.0:1.9 -16 81891432 . C G 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCTTGGACACATGACTGAA;RSEQ=CTGTCTTAGGTTCAGTGGTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:0.6364:0,0:33.0:1.0:32.0:1.0:1.0:0.0:60.0:14.0:0.7:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 81891790 . C G 206 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06427;LSEQ=GCTTCTCCCATCTTCGTGAT;RSEQ=TGTATGGGGCAGGGCTTTGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:86:80,6:183,12:0.306:2,2:24.7:1.0:32.1:1.0:0.79503:1.14318:60.0:85.0:0.3069:0.0:1.2 0/1:255:7:7,0:225,23:0.0275:2,0:28.1:1.0:31.0:1.0:1.0:0.0:60.0:14.0:0.028:0.0:1.0 -16 81892498 . A T 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACTATCATCAGAAGGAATTG;RSEQ=CAATGTAAAGAAACCTGGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:10,1:0.3125:2,0:27.8:1.0:29.8:1.0:1.0:0.0:60.0:10.0:0.3125:0.0:1.0 0/0:1:0:0,0:1,0:0.0:0,0:47.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -16 81892913 . C T 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.10021;LSEQ=TGCGGATGCCATGTTGGGTC;RSEQ=TGGGGTTGAGGATGACAAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:37:0,37:0,91:0.2891:1,1:23.5:1.0:31.4:1.0:1.0:0.0:60.0:74.0:0.296:0.0:1.1 0/1:103:4:0,4:2,97:0.0388:1,0:26.8:1.0:29.8:1.0:1.0:0.0:60.0:8.0:0.0392:0.0:1.3 -16 81914851 . G GT 87 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.46667;SOR=0.0;LSEQ=TGAGATGTGACAGGTTAATA;RSEQ=TTTTTTTTTTTAATTACAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:0,8:0,5:0.5714:0,0:22.3:1.0:29.0:1.0:1.0:0.0:60.0:16.0:0.5714:0.0:0.1 0/0:2:0:0,0:0,2:0.0:0,0:18.0:1.0:31.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -16 81917099 . G T 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=6e-05;SOR=0.11666;LSEQ=GTCTTCATGGAACGATTGCA;RSEQ=TCTGCCAGATGCCAGAGACT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:26:0,26:2,65:0.2796:1,1:20.9:1.0:30.2:1.0:1.0:0.0:60.0:52.0:0.2889:0.0:1.2 0/1:70:3:0,3:2,65:0.0429:1,0:13.7:1.0:31.7:1.0:1.0:0.0:60.0:6.0:0.0441:0.0:1.0 -16 81941530 . CCTGGCTGGCTTGTCTCTGATTGG C 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.0;MSILEN=1.0;SSF=0.32451;SOR=0.0;LSEQ=TGATACTCTGGGTACCATGT;RSEQ=CTGGCTGCCCCAGGTGCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:0,6:3,43:0.1154:2,0:26.5:1.0:31.7:1.0:1.0:0.0:60.0:12.0:0.1176:0.0192:0.2 0/0:15:0:0,0:3,12:0.0:2,0:23.1:1.0:30.5:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.3 -16 81946328 . G A 253 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00465;LSEQ=GCCATCACCTTCAGGTGGGT;RSEQ=CGAGGGTGGGAGGCACATGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1286:441:182,259:367,476:0.3429:2,2:25.0:1.0:28.9:1.0:0.44073:1.09712:60.0:72.5:0.3444:0.0:1.2 0/0:1240:3:3,0:556,681:0.0024:2,0:1.0:0.0:24.0:1.0:0.09135:0.0:60.0:6.0:0.0025:0.0:1.0 -16 81955238 . A G 98 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCTTGCAGTGCAAATGCT;RSEQ=TCTCATATTCCCACCCTGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:0.5:0,0:24.3:1.0:32.9:1.0:1.0:0.0:60.0:16.0:0.5:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:10.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -16 81956810 . G C 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.53044;SOR=0.0;LSEQ=AGCCTAACCCTAACCCCAGC;RSEQ=CTAAACCCTAGCCCCAAACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:11,0:0.3125:0,0:20.6:1.0:29.4:1.0:1.0:0.0:60.0:10.0:0.3333:0.0:1.4 0/0:3:0:0,0:3,0:0.0:0,0:26.0:1.0:28.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 -16 81957227 . C T 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGAGTGGAGGCTGGGCTGCT;RSEQ=GGCAGGTGGGCTTGACTTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:133:44,89:224,392:0.1776:2,2:27.2:1.0:29.7:1.0:0.48721:1.1556:60.0:266.0:0.1807:0.0:1.1 0/0:775:0:0,0:284,491:0.0:2,0:24.8:1.0:29.7:1.0:1.0:0.0:60.0:63.583:1.0:0.0:0.2 -16 81957349 . G T 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00993;SOR=0.0;LSEQ=AGTCCCTTCTTAGGAAGGTG;RSEQ=CTTGGTGCATGCTCTATTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:13:0,13:1,85:0.1313:1,1:21.6:1.0:29.7:1.0:1.0:0.0:60.0:12.0:0.1224:0.0:1.5 0/0:43:0:0,0:1,42:0.0:1,0:25.5:1.0:32.4:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.9 -16 81961002 . T C 135 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.24;SOR=0.0;LSEQ=CGTGTTTTAATCAGGTTGTG;RSEQ=TGGGCTTGGAAGGATTTCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:1,18:0,5:0.7917:0,1:28.6:1.0:31.9:1.0:1.0:0.0:60.0:18.0:0.7826:0.0:2.9 0/0:1:0:0,0:0,1:0.0:0,0:14.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -16 81961020 . C G 129 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTTGGGCTTGGAAGGATTT;RSEQ=ATTATGCAGGAGAATTCCCG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:1,16:0,3:0.85:0,1:29.6:1.0:31.6:1.0:1.0:0.0:60.0:34.0:0.85:0.0:3.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 81961022 . T A 125 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGGGCTTGGAAGGATTTCA;RSEQ=TATGCAGGAGAATTCCCGCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:1,17:0,2:0.9:0,1:27.4:1.0:30.2:1.0:1.0:0.0:60.0:17.0:0.8947:0.0:3.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 81961873 . G T 123 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATAGTCTAGGATGTGTTT;RSEQ=GAAACCAGATCTGAGGAAGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:18:18,0:4,0:0.8182:0,1:28.3:1.0:29.7:1.0:1.0:0.0:60.0:17.0:0.8095:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 81962531 . T C 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.55202;SOR=0.0;LSEQ=GGATCCATCTGTGTTTCCCA;RSEQ=GCGTTGCGAAGGAAAGCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:8:0,8:0,17:0.32:1,0:18.8:1.0:31.3:1.0:1.0:0.0:60.0:16.0:0.32:0.0:1.5 0/0:4:0:0,0:0,4:0.0:0,0:37.5:1.0:30.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -16 81962574 . A C 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTCAGCCTGGCTGAAATGC;RSEQ=GCGTGGAGTTGGGAGTCTTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:0.6:0,0:45.3:1.0:30.8:1.0:1.0:0.0:60.0:12.0:0.6:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -16 81973841 . G C 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00118;SOR=0.0;LSEQ=GTGTAGCACACAGGTGGGAG;RSEQ=AAGTGGGTGACAGGGGAGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:18:0,18:0,26:0.4091:1,1:22.1:1.0:31.4:1.0:1.0:0.0:60.0:17.0:0.3953:0.0:1.2 0/0:17:0:0,0:1,16:0.0:1,0:19.7:1.0:31.5:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.6 -16 81990505 . G T 245 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTAGGTCAGCCCCTCCACCT;RSEQ=CAAAAACTTTTGGGGGGTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:960:316:114,202:238,404:0.3292:2,2:25.2:1.0:29.6:1.0:0.77604:1.04383:60.0:34.111:0.3269:0.0:1.1 0/0:1028:0:0,0:407,618:0.0:2,0:25.4:1.0:31.7:1.0:1.0:0.0:60.0:77.846:0.997:0.0:0.2 -16 85490399 . T C 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01947;SOR=0.0;LSEQ=GCTGTGGCGACTCAGGGTCC;RSEQ=GGCGGGGAGAACCTGCCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:8,10:0.3333:2,2:20.0:1.0:27.2:1.0:1.0:1.0:60.0:8.0:0.32:0.0:1.1 0/0:13:0:0,0:4,9:0.0:2,0:28.2:1.0:29.8:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.1 -16 86601049 . C T 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.23077;SOR=0.0;LSEQ=AGCTACGGCGGCATGGCCAG;RSEQ=CCCATGGGCGTCTATTCCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:0.4545:0,0:22.6:1.0:28.0:1.0:1.0:0.0:60.0:4.0:0.4:0.0:1.0 0/0:4:0:0,0:4,0:0.0:0,0:20.8:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -16 89337526 . G A 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00619;SOR=0.0;LSEQ=CTCCCTAAAATGCGCGTGGA;RSEQ=GCAGCTGGGCCTTTGTCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:19:0,19:1,17:0.5135:1,1:26.6:1.0:31.0:1.0:0.48649:0.0:60.0:18.0:0.5:0.0:1.2 0/0:9:0:0,0:0,9:0.0:0,0:20.3:1.0:28.6:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.8 -16 89350597 . C G 252 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTCTCTTTTGAAATTTTGT;RSEQ=CTCTTTTAAATCATTCTTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2079:231:128,103:956,889:0.1111:2,2:25.6:1.0:32.1:1.0:0.32813:1.16:59.7:114.5:0.1118:0.0:1.1 0/0:2294:0:0,0:1193,1099:0.0:2,0:24.7:1.0:30.9:1.0:1.0:0.0:59.9:133.824:0.9991:0.0:0.2 -16 89356882 . CGGGGGAGGCTCAGGGCTCCAATG C 169 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=60;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTGAGGCTCAGGGCTCCAG;RSEQ=GGGGGAGGCTCAGGGCTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:48:48,0:5,0:0.8889:0,1:21.7:1.0:30.4:1.0:1.0:0.0:57.4:47.0:0.9038:0.2222:1.0 0/0:24:0:0,0:19,4:0.0:2,0:22.0:1.0:27.4:1.0:1.0:0.0:47.8:22.0:1.0:0.0:2.2 -16 89839915 . G A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03173;SOR=0.0;LSEQ=AGCTGCTGTGTGTGGCAGAC;RSEQ=GAGGGACTGGGAGTCTCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:6:0,6:2,70:0.0759:1,0:33.0:1.0:31.8:1.0:1.0:0.0:60.0:12.0:0.0759:0.0:1.0 0/0:66:0:0,0:2,64:0.0:1,0:23.5:1.0:30.3:1.0:1.0:0.0:60.0:65.0:1.0:0.0:0.2 -16 89877720 . C T 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.50549;SOR=0.0;LSEQ=TTATACATTGGTATTTGTTA;RSEQ=GTTTCCCATGACACAAAAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:0,7:0.4167:0,2:19.4:1.0:31.2:1.0:0.41667:0.0:60.0:10.0:0.4167:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:10.0:1.0:31.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -17 1760942 . C G 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCACCCAAAGCCTCACCAAC;RSEQ=CACCCCCCACCCGGCCCGTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:25.8:1.0:29.5:1.0:1.0:0.0:55.2:12.0:0.8571:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 3568401 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00404;SOR=0.0;LSEQ=TGCTGTGGCTTCTGTAGGTG;RSEQ=GAAGCCCGTCTCACAGGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:8,0:16,0:0.3333:1,0:29.3:1.0:30.0:1.0:1.0:0.0:60.0:16.0:0.3478:0.0:1.1 0/0:22:0:0,0:22,0:0.0:1,0:24.4:1.0:31.1:1.0:1.0:0.0:60.0:44.0:1.0:0.0:0.1 -17 4540268 . G C 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=3e-05;SOR=0.0;LSEQ=CACTGCAAGGCCTTCGAATA;RSEQ=AGACTTGGCGCATTTCCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:13:7,6:87,83:0.0707:2,2:27.8:1.0:32.5:1.0:1.0:1.11:60.0:26.0:0.0718:0.0:2.0 0/0:218:0:0,0:105,113:0.0:2,0:26.1:1.0:31.0:1.0:1.0:0.0:59.6:35.333:1.0:0.0:0.5 -17 7577407 . A C 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03271;LSEQ=GTGGATGGGTAGTAGTATGG;RSEQ=AGAAATCGGTAAGAGGTGGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:122:71:57,14:47,4:0.582:2,2:22.3:1.0:32.4:1.0:0.07628:2.86327:60.0:70.0:0.5983:0.0:2.0 0/1:163:7:6,1:137,18:0.0429:2,2:22.7:1.0:31.3:1.0:0.58975:1.2665:60.0:14.0:0.0449:0.0:2.0 -17 7577427 . G A 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02986;LSEQ=AAGAAATCGGTAAGAGGTGG;RSEQ=CCCAGGGGTCAGAGGCAAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:155:94:78,16:54,7:0.6065:2,2:24.2:1.0:30.0:1.0:0.48837:1.57791:60.0:93.0:0.6078:0.0:1.8 0/1:230:10:8,2:179,38:0.0435:2,2:25.2:1.0:28.7:1.0:0.69041:1.1767:60.0:20.0:0.0452:0.0:1.7 -17 7577709 . C T 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00015;SOR=0.0;LSEQ=TTTTTTGAGATGGAATCTCG;RSEQ=TCTGTCGCCCAGGCTGGAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:11:1,10:0,31:0.2619:1,2:21.5:1.0:30.7:1.0:0.2619:0.0:48.8:22.0:0.2683:0.0:2.1 0/0:45:0:0,0:0,44:0.0:1,0:23.0:1.0:31.2:1.0:1.0:0.0:51.6:21.0:1.0:0.0:1.3 -17 7578461 . C A 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GTAGATGGCCATGGCGCGGA;RSEQ=GCGGGTGCCGGGCGGGGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:145:79,66:142,132:0.3461:2,2:20.9:1.0:30.4:1.0:0.60895:1.11:60.0:35.25:0.3431:0.0:1.2 0/0:625:0:0,0:342,281:0.0:2,0:23.5:1.0:29.9:1.0:1.0:0.0:60.0:61.3:0.9967:0.0:0.2 -17 7580500 . C T 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01571;LSEQ=CTTACTTCAGGTGATCGGCC;RSEQ=GCCTCAGCCTCCTAAAGTGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:64:64,0:30,0:0.6737:1,1:27.1:1.0:31.9:1.0:1.0:0.0:60.0:128.0:0.6809:0.0:1.0 0/1:98:3:3,0:94,1:0.0306:1,0:18.7:1.0:31.0:1.0:1.0:0.0:60.0:6.0:0.0319:0.0:1.3 -17 7976917 . A T 184 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTTTGAGGTTGGGGCATGG;RSEQ=CGAAATTTAGAAGGTCTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:87:58,29:145,44:0.3152:2,2:24.0:1.0:28.6:1.0:0.10561:1.64468:60.0:28.0:0.3111:0.0:1.2 0/0:261:0:0,0:193,67:0.0:2,0:23.2:1.0:28.1:1.0:1.0:0.0:60.0:22.636:1.0:0.0:0.1 -17 7979468 . C T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01276;SOR=0.0;LSEQ=CAGGTTGTCCACCCTAAGAG;RSEQ=CACCCACTGCTGTCCTGAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:6:3,3:348,209:0.0107:2,2:20.3:1.0:29.0:1.0:0.67712:1.66343:60.0:12.0:0.0108:0.0:1.7 0/0:599:0:0,0:381,218:0.0:2,0:25.1:1.0:31.2:1.0:1.0:0.0:60.0:58.9:1.0:0.0:0.7 -17 7983681 . G A 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGATGGGATTCCAGGAAGA;RSEQ=GCCTTCAGAGGGGCTGCCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:40:16,24:105,248:0.1018:2,2:21.6:1.0:29.9:1.0:0.20657:1.57:60.0:39.0:0.1008:0.0:1.1 0/0:360:0:0,0:117,243:0.0:2,0:23.6:1.0:30.5:1.0:1.0:0.0:60.0:89.0:1.0:0.0:0.2 -17 7984157 . A C 222 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.10576;LSEQ=CGGGGAGGAGGCAGGCGCCC;RSEQ=GGGGAAAACCATGGGCGGGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:157:91,66:301,224:0.2302:2,2:25.7:1.0:30.5:1.0:0.92682:1.03:60.0:156.0:0.2332:0.0:1.1 0/1:588:18:10,8:304,263:0.0306:2,2:21.0:1.0:27.7:1.0:1.0:1.08:60.0:8.0:0.0278:0.0:1.2 -17 7984552 . G A 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.07294;SOR=0.1595;LSEQ=AAGGGCTGACCCTTGCCCCT;RSEQ=CCCACTTCAGGAAGCAGGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:7:5,2:116,245:0.019:2,2:12.3:1.0:25.9:1.0:0.04118:5.25:60.0:14.0:0.0194:0.0:1.0 0/0:325:1:1,0:116,207:0.0031:2,0:1.0:0.0:23.0:0.0:0.36111:0.0:60.0:2.0:0.0032:0.0:1.0 -17 7990555 . G C 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GACACACACAGACACACACA;RSEQ=ACACACACACACACACACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:39:32,7:121,5:0.1931:1,2:18.5:1.0:31.0:1.0:0.00788:5.22407:58.1:38.0:0.2436:0.0:3.4 0/0:187:0:0,0:101,4:0.0:1,0:20.9:1.0:31.1:1.0:1.0:0.0:56.8:20.0:0.9901:0.0:1.4 -17 12043531 . A AG 74 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAAGAAAAAAATTAGTGAAA;RSEQ=TTTGTGTTTATTCTGCCTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:20.6:1.0:31.9:1.0:1.0:0.0:60.0:10.0:1.0:0.2:0.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 15977132 . T C 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATTAAGTCCCTTTCTGCA;RSEQ=GAAACTTACACAATAATGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:16.4:1.0:30.2:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.4 0/0:1:0:0,0:0,1:0.0:0,0:13.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -17 15983458 . G A 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAAACAGCCCCTACTTGGGA;RSEQ=AGTACTCAACTAAGAAGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:82:10,72:6,113:0.408:2,2:24.8:1.0:30.1:1.0:0.10896:2.6:60.0:81.0:0.4091:0.0:1.1 0/0:190:0:0,0:17,173:0.0:2,0:24.7:1.0:31.4:1.0:1.0:0.0:60.0:380.0:1.0:0.0:0.0 -17 16049563 . C A 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00578;SOR=0.09281;LSEQ=CTCCACTATTGTCCTATGAC;RSEQ=CTGCCAAATCCCCCTCTCCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:11:11,0:88,0:0.1111:1,0:17.9:1.0:30.8:1.0:1.0:0.0:55.5:22.0:0.1122:0.0:1.7 0/1:88:1:1,0:87,0:0.0114:1,0:39.0:0.0:31.0:0.0:1.0:0.0:49.0:2.0:0.0115:0.0:1.0 -17 16049641 . TA T 66 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.01291;SOR=0.0;LSEQ=TTTTTAAAAAAAAGAAACAA;RSEQ=AATATTTGAAGAAAAATATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:5:2,3:348,135:0.0102:2,2:20.2:1.0:28.8:1.0:0.13996:3.8541:60.0:10.0:0.0103:0.0041:0.6 0/0:674:0:0,0:469,205:0.0:2,0:23.4:1.0:28.2:1.0:1.0:0.0:60.0:167.5:1.0:0.0:0.5 -17 16068215 . A G 92 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.00588;SOR=0.0;LSEQ=TCCTTTTATGTAAAGTTTCA;RSEQ=AATATGGAAAACTCAAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:7:7,0:72,9:0.0795:2,0:21.9:1.0:33.0:1.0:1.0:0.0:33.3:14.0:0.0814:0.0:5.6 0/0:92:0:0,0:77,15:0.0:2,0:25.2:1.0:30.3:1.0:1.0:0.0:58.2:184.0:1.0:0.0:0.3 -17 16068420 . G T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.12101;LSEQ=CATTTTGATCATCTCCACAT;RSEQ=GTTGCCCCGAAATTGGAGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1135:31:14,17:531,572:0.0273:2,2:22.4:1.0:28.0:1.0:0.85589:1.12713:49.8:9.333:0.0251:0.0:2.5 0/0:1182:4:0,4:590,587:0.0034:2,0:1.0:0.0:24.8:1.0:0.12437:0.0:60.0:8.0:0.0034:0.0:1.8 -17 16097430 . C T 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.22222;SOR=0.0;LSEQ=GTCTTTATCTTGGCCCTCAC;RSEQ=CAAGACATGCCAAGTTATCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:1,0:0.875:0,0:18.1:1.0:32.6:1.0:1.0:0.0:44.9:14.0:0.875:0.0:1.1 0/0:1:0:0,0:0,1:0.0:0,0:49.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -17 17125595 . A G 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00179;SOR=0.0;LSEQ=CAGGAAGAAGTGAGTTCCAC;RSEQ=TCAATATGTTTTCAGCACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:1.0:0,1:23.3:1.0:29.9:1.0:1.0:0.0:59.5:26.0:1.0:0.0:1.1 0/0:3:0:0,0:3,0:0.0:0,0:19.3:1.0:31.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -17 21535940 . G A 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.09309;SOR=0.18467;LSEQ=TTTTTTCCCATCCTGTTTAG;RSEQ=TGGTTTCCTAGAAACATGAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:254:8:5,3:230,16:0.0315:2,2:30.3:1.0:30.6:1.0:0.01574:8.46617:36.9:16.0:0.0323:0.0:3.6 0/0:168:1:1,0:151,16:0.006:2,0:12.0:0.0:28.0:0.0:1.0:0.0:37.0:2.0:0.0061:0.0:5.0 -17 21535981 . A G 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08815;SOR=0.17297;LSEQ=TGTTTATTGGCATTGATCTC;RSEQ=CAGTCTGGTGAGGACTTCTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:8:6,2:281,77:0.019:2,2:25.3:1.0:28.5:1.0:0.68415:1.21577:38.0:7.0:0.0193:0.0:3.5 0/0:300:1:1,0:180,81:0.0033:2,0:41.0:0.0:26.0:0.0:1.0:0.0:37.0:2.0:0.0038:0.0:5.0 -17 21544599 . A G 224 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.09411;LSEQ=AAACTGAAAAAGAAACAAGT;RSEQ=AAAGTCTTTGCTTATAATAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:482:150:47,103:113,219:0.3112:2,2:27.5:1.0:31.1:1.0:0.60211:1.13048:59.9:36.5:0.3067:0.0:1.0 0/1:467:19:6,13:169,279:0.0407:2,2:27.1:1.0:31.2:1.0:0.6385:1.31168:60.0:38.0:0.0411:0.0:1.1 -17 22253299 . T TATTTGGACCTCTCTGAGGATTTCGTTGGAAACGGGATA 106 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=TTGTAGAAACTGCAAGTGGA;RSEQ=AACTGCACTTCTTTGAGGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:12:4,8:2,16:0.4:2,2:12.2:1.0:29.6:1.0:0.18438:3.81:30.8:24.0:0.4:0.4:3.6 0/0:35:0:0,0:9,25:0.0:2,0:11.8:1.0:28.4:1.0:1.0:0.0:32.3:68.0:0.9714:0.0:4.4 -17 22259989 . T A 68 d7;NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCCGTAAGAACTAGATAGA;RSEQ=GCATTCTCAGAAACTACTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1.0:0,2:11.4:1.0:29.4:1.0:1.0:0.0:40.4:10.0:1.0:0.0:6.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 22261386 . A T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.14286;SOR=0.0;LSEQ=TTGTGATGATTGAGTTTAAC;RSEQ=CACAGAGCTGAACATTCCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1.0:0,2:36.8:1.0:30.5:1.0:1.0:0.0:35.8:12.0:1.0:0.0:3.8 0/0:1:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 29096004 . C G 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00108;SOR=0.12164;LSEQ=AGCCACATGGTGAAGTCTTA;RSEQ=TCGTTGCTATTTAGAGTGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:572:13:4,9:230,328:0.0227:2,2:29.0:1.0:32.0:1.0:0.57377:1.57655:59.8:26.0:0.023:0.0:1.1 0/0:710:2:2,0:312,395:0.0028:2,0:12.0:1.0:21.5:1.0:0.19579:0.0:51.5:1.0:0.0014:0.0:4.0 -17 29482701 . C T 77 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATAGTGCTGGATAAAGAATT;RSEQ=TATTTTGTAGATAGAGATTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1.0:0,2:23.0:1.0:30.0:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 29533685 . CTTTTGAACAAAAATA C 97 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGTTTTTTTTCTCCTTAAAA;RSEQ=TTTTGATTAGCCTCTCACGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:1,8:0,0:1.0:0,2:20.1:1.0:30.8:1.0:1.0:0.0:57.9:18.0:1.0:0.5556:0.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 29553719 . GT G 72 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.02189;SOR=0.0;LSEQ=ACAGGTAAATGTGAATAGTG;RSEQ=TTTTTTTACTCAGTCTGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:5:2,3:69,232:0.0163:2,2:31.2:1.0:31.4:1.0:0.32906:2.23:60.0:10.0:0.0165:0.0:1.0 0/0:350:0:0,0:120,230:0.0:2,0:25.3:1.0:29.1:1.0:1.0:0.0:59.9:57.333:1.0:0.0:0.2 -17 29585907 . T C 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.17994;SOR=0.0;LSEQ=AGAAACACTACCTAAAATAA;RSEQ=TTATAGAATGAGGAATGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:8,0:33,5:0.1739:2,0:25.1:1.0:30.9:1.0:0.5692:0.0:60.0:16.0:0.1739:0.0:1.0 0/0:13:0:0,0:13,0:0.0:1,0:31.1:1.0:29.0:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -17 29587341 . G C 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTAATTCAAACATAAGTCT;RSEQ=GGTGTATCTGGTGTTGAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:69:44,25:235,100:0.1708:2,2:23.2:1.0:29.2:1.0:0.31797:1.33429:60.0:22.0:0.1654:0.0:1.2 0/0:442:0:0,0:278,164:0.0:2,0:24.6:1.0:30.5:1.0:1.0:0.0:60.0:43.2:1.0:0.0:0.1 -17 29663623 . TTT AAA 61 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.0;MSILEN=1.0;SSF=0.06466;SOR=0.0;LSEQ=TTGAGTCCCATGTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:5:3,2:295,130:0.011:2,2:26.4:1.0:26.7:1.0:0.64484:1.51126:57.0:10.0:0.0111:0.0:2.0 0/0:397:0:0,0:251,137:0.0:2,0:23.2:1.0:29.1:1.0:1.0:0.0:59.6:76.6:0.977:0.0:1.1 -17 29663625 . T A 198 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGTCCCATGTTTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:125:74,51:44,19:0.2671:2,2:19.5:1.0:28.5:1.0:0.20094:1.5921:60.0:40.667:0.5259:0.0:1.4 0/0:425:0:0,0:62,36:0.0:2,0:22.5:1.0:27.4:1.0:1.0:0.0:59.4:15.333:0.3046:0.0:0.5 -17 29665081 . C T 54 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.12177;SOR=0.1962;LSEQ=TCCATCCCTGCAACCAAGAG;RSEQ=TCTTGTTGTCTTTGGGTGTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:5:0,5:274,206:0.0103:2,0:9.2:1.0:23.6:1.0:0.01517:0.0:60.0:4.0:0.0084:0.0:2.0 0/0:491:1:0,1:260,229:0.002:2,0:1.0:0.0:24.0:0.0:0.46939:0.0:60.0:2.0:0.0021:0.0:1.0 -17 30315470 . C T 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTAGAAATTCAGAGAGTCT;RSEQ=CATCAGGAAAACAAGCCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:947:179:85,94:367,400:0.189:2,2:26.4:1.0:30.2:1.0:0.93402:1.01463:60.0:358.0:0.1912:0.0:1.1 0/0:1114:0:0,0:541,572:0.0:2,0:26.1:1.0:30.8:1.0:1.0:0.0:60.0:84.615:1.0:0.0:0.1 -17 33430327 . C A 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02964;LSEQ=TTCAGCTCTCGGGCCAGCTG;RSEQ=ATCATCAAGGCCAAGCCTGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:981:89:41,48:423,468:0.0907:2,2:26.6:1.0:29.6:1.0:0.82456:1.05812:60.0:21.25:0.0889:0.0:1.2 0/0:1018:3:3,0:442,572:0.0029:2,0:1.0:0.0:23.3:1.0:0.08346:0.0:60.0:6.0:0.003:0.0:1.3 -17 37618220 . C T 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00227;SOR=0.0;LSEQ=TGCCCTCCCCACCCCCTTCC;RSEQ=GGGGCGCTTTGGTGGGCGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:14:14,0:85,4:0.1359:1,1:21.7:1.0:31.9:1.0:1.0:0.0:60.0:28.0:0.1414:0.0:1.0 0/0:60:0:0,0:57,3:0.0:2,0:24.2:1.0:29.6:1.0:1.0:0.0:60.0:29.0:1.0:0.0:0.3 -17 37646947 . C T 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03021;LSEQ=AGACTCTCCAGAACCAAAGG;RSEQ=AATCACACCACCTCAGCAAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:878:32:17,15:363,483:0.0364:2,2:27.3:1.0:28.9:1.0:0.27831:1.51:60.0:64.0:0.0368:0.0:1.1 0/0:877:1:0,1:395,481:0.0011:2,0:1.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.0012:0.0:1.0 -17 37657481 . AT A 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.06438;SOR=0.0;LSEQ=TTTTTTTTTTCTTGCTTTTA;RSEQ=TTTTTTTCGTCTTTATGTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:5:3,2:330,155:0.0102:2,2:35.2:1.0:31.1:1.0:0.65747:1.41832:60.0:10.0:0.0104:0.002:0.0 0/0:432:0:0,0:270,160:0.0:2,0:25.8:1.0:29.4:1.0:1.0:0.0:59.8:85.0:0.9953:0.0:0.3 -17 37687968 . A G 76 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTAAAGTTTTGGGGTGGGGG;RSEQ=TTGTGTGTGGTTTCTTTCTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:38.2:1.0:32.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 37866797 . G T 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGTTTGTTTCTGTAAATGG;RSEQ=AGCATATGGGGAGCACTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:34:5,29:35,155:0.1504:2,2:24.6:1.0:27.4:1.0:0.80826:1.30817:60.0:33.0:0.15:0.0:1.0 0/0:149:0:0,0:27,122:0.0:2,0:20.8:1.0:30.9:1.0:1.0:0.0:60.0:148.0:1.0:0.0:0.2 -17 37871848 . G A 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCAGGGAGGAGTCCCTGTG;RSEQ=GAAGCTTTGGGCCTGAGGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:49:19,30:134,223:0.1207:2,2:26.1:1.0:30.3:1.0:0.87607:1.05:60.0:48.0:0.1206:0.0:1.0 0/0:229:0:0,0:64,165:0.0:2,0:24.1:1.0:30.1:1.0:1.0:0.0:60.0:31.714:1.0:0.0:0.2 -17 37880725 . T C 104 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.16219;SOR=0.0;LSEQ=ATTTCACCATGTTGGCCAGG;RSEQ=TGGTGTCAAACTCCTGACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:9,0:16,3:0.3214:2,0:23.1:1.0:32.9:1.0:0.53022:0.0:53.9:18.0:0.36:0.0:1.3 0/0:6:0:0,0:6,0:0.0:0,0:30.0:1.0:30.3:1.0:1.0:0.0:55.7:12.0:1.0:0.0:0.5 -17 37880997 . G GTGT 284 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGGAAGCATACGTGATGGCT;RSEQ=GTGTGGGCTCCCCATATGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1441:624:314,310:419,390:0.433:2,2:25.4:1.0:30.6:1.0:0.5943:1.06061:59.9:623.0:0.4357:0.0777:0.2 0/0:1127:0:0,0:581,544:0.0:2,0:26.2:1.0:30.8:1.0:1.0:0.0:60.0:79.357:0.9991:0.0:0.2 -17 38497450 . G A 95 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.20164;SOR=0.0;LSEQ=TAGTCCACTGGAAGGCACCA;RSEQ=CTCTTCCTTTTATCTCTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:9,0:78,1:0.1023:1,0:27.6:1.0:30.1:1.0:1.0:0.0:60.0:18.0:0.1023:0.0:1.1 0/0:21:0:0,0:20,1:0.0:1,0:24.5:1.0:32.0:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.1 -17 38497833 . G A 153 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02798;LSEQ=GCTGGCGGGCGAGCCCCGCG;RSEQ=GCGGGCTGGCGAGCGGGTGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:693:38:21,17:427,227:0.0548:2,2:28.3:1.0:29.3:1.0:0.22381:1.52185:60.0:11.667:0.0515:0.0:1.2 0/0:618:1:1,0:377,239:0.0016:2,0:1.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0016:0.0:1.0 -17 38497884 . G A 197 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00818;LSEQ=AGCGGTGGGTGGGTCACTCG;RSEQ=AGGTGAGGCGCCGCCAGGCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:109:55,54:356,275:0.1467:2,2:24.7:1.0:29.2:1.0:0.25284:1.27058:60.0:26.25:0.1446:0.0:1.1 0/0:713:1:1,0:371,341:0.0014:2,0:1.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.0014:0.0:1.0 -17 38512197 . T C 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08567;LSEQ=TTCCCACCTCGAGCCAGGCT;RSEQ=GCTGGGGCTGGGGGTGGGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:342:145:119,26:163,34:0.424:2,2:24.4:1.0:30.9:1.0:0.88643:1.04728:60.0:71.5:0.4218:0.0:1.1 0/1:220:13:11,2:165,42:0.0591:2,2:28.1:1.0:29.1:1.0:1.0:1.4:60.0:12.0:0.0553:0.0:1.5 -17 38512457 . C G 165 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCAGCTCCAACAGAAGCAG;RSEQ=CCGGCCACCCACTCCCCGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1140:41:15,26:488,608:0.036:2,2:24.3:1.0:30.9:1.0:0.34063:1.39083:60.0:19.5:0.0348:0.0:2.2 0/0:861:0:0,0:397,461:0.0:2,0:25.3:1.0:30.9:1.0:1.0:0.0:60.0:36.304:0.9964:0.0:0.3 -17 38512461 . G T 158 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03159;LSEQ=GCTCCAACAGAAGCAGCCCG;RSEQ=CCACCCACTCCCCGTGACCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1136:40:14,26:495,599:0.0352:2,2:25.8:1.0:29.7:1.0:0.25716:1.53414:60.0:39.0:0.0356:0.0:2.2 0/0:869:1:0,1:405,460:0.0012:2,0:6.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0012:0.0:1.0 -17 39874283 . T A 67 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.16667;SOR=0.0;LSEQ=GTCCTCGGCTGGGGCTCTGT;RSEQ=ATAAAAGACAGATTACAAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:24.8:1.0:29.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.6 0/0:1:0:0,0:1,0:0.0:0,0:27.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -17 40452429 . C A 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.01156;SOR=0.0;LSEQ=GCTCTTGTTTCTCCAGGGAG;RSEQ=CTGGTTCCTCAATCAGACTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:13:2,11:17,203:0.0558:2,2:22.8:1.0:29.2:1.0:0.28676:2.16:37.2:12.0:0.0538:0.0:1.2 0/0:106:0:0,0:8,98:0.0:2,0:21.1:1.0:31.2:1.0:1.0:0.0:39.7:34.333:1.0:0.0:0.1 -17 40458193 . TTG T 90 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.0;MSILEN=2.0;SSF=0.01309;SOR=0.0;LSEQ=TCTCTAGGTGTCTGTGTATC;RSEQ=TGTGTGTGTGAATATTTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:760:9:4,5:624,126:0.0118:2,2:19.7:1.0:28.6:1.0:0.00997:6.16815:60.0:8.0:0.0108:0.0026:0.2 0/0:522:0:0,0:430,92:0.0:2,0:21.7:1.0:29.6:1.0:1.0:0.0:60.0:64.25:1.0:0.0:0.1 -17 40458742 . CT C 88 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAGATGTGTTTGCTAATTTT;RSEQ=TTTTTTTTTTTAGAGACAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:7:0,7:0,29:0.1944:1,0:31.7:1.0:31.6:1.0:1.0:0.0:58.6:14.0:0.1944:0.0:0.4 0/0:3:0:0,0:0,3:0.0:0,0:11.3:1.0:31.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -17 40467934 . C T 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.03784;SOR=0.1384;LSEQ=CACTGCTATCCAATCTCCTG;RSEQ=CCCTTAAGGCCCAGGGATGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:12:0,12:15,343:0.0324:1,0:30.5:1.0:30.8:1.0:1.0:0.0:60.0:24.0:0.0335:0.0:1.0 0/0:217:1:0,1:12,204:0.0046:2,0:1.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0047:0.0:1.0 -17 40489660 . C T 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CCTCAGACTGTCTCTAACCA;RSEQ=ATTCTTTAGTCAACTCCAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:775:37:13,24:300,436:0.0477:2,2:24.6:1.0:29.5:1.0:0.60734:1.2699:60.0:74.0:0.0484:0.0:1.1 0/0:697:0:0,0:266,429:0.0:2,0:21.8:1.0:31.3:1.0:1.0:0.0:60.0:172.75:0.9971:0.0:0.1 -17 41231216 . C CA 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.0659;SOR=0.16069;LSEQ=AAAAACAAAACAAAACAAAA;RSEQ=AAAAAAAATGAAAGGCAGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:6:4,2:366,70:0.0135:2,2:21.2:1.0:30.3:1.0:0.25364:2.60676:60.0:12.0:0.0137:0.0068:0.0 0/0:455:1:1,0:349,103:0.0022:2,0:30.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0022:0.0:0.0 -17 41244880 . C G 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTTTGTTTCTTTAAGGACC;RSEQ=AGAGTGGGCAGAGAATGTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:56:33,23:278,270:0.0924:2,2:24.8:1.0:30.9:1.0:0.26355:1.39:60.0:112.0:0.0951:0.0:1.1 0/0:502:0:0,0:259,241:0.0:2,0:23.9:1.0:30.7:1.0:1.0:0.0:60.0:82.333:0.996:0.0:0.2 -17 41245586 . C CT 115 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.00106;SOR=0.07649;LSEQ=CTGACTGGCATTTGGTTGTA;RSEQ=TTTTTTTTCTTTATCTCTTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1021:14:4,10:427,577:0.0137:2,2:23.3:1.0:30.3:1.0:0.41605:1.84904:60.0:28.0:0.0139:0.0029:0.0 0/0:942:1:1,0:394,543:0.0011:2,0:28.0:0.0:33.0:0.0:0.42111:0.0:60.0:2.0:0.0011:0.0:1.0 -17 41267608 . G C 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03751;SOR=0.0;LSEQ=ACTATATACTCTCTGAGAAA;RSEQ=AATGAAATGGAGTTGGATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:6:6,0:152,2:0.0373:1,0:18.5:1.0:32.0:1.0:1.0:0.0:60.0:12.0:0.0387:0.0:1.0 0/0:124:0:0,0:121,3:0.0:1,0:25.1:1.0:31.8:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 -17 43344458 . C A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCGGGGCCACAACCGACTCA;RSEQ=CTTCTCACTGTCATCCGACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:578:28:19,9:368,182:0.0484:2,2:24.8:1.0:29.4:1.0:1.0:1.04:60.0:56.0:0.0492:0.0:1.2 0/0:498:0:0,0:324,173:0.0:2,0:22.7:1.0:31.0:1.0:1.0:0.0:60.0:123.25:0.998:0.0:0.1 -17 43347610 . C T 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01996;LSEQ=GCGCTGCCTCTGGGTCCAGG;RSEQ=GTGGCACTGTCGCAATCTCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:109:109,0:17,0:0.8583:1,1:26.5:1.0:30.0:1.0:1.0:0.0:60.0:108.0:0.864:0.0:1.1 0/1:48:5:5,0:42,1:0.1042:1,0:27.6:1.0:29.6:1.0:1.0:0.0:60.0:10.0:0.1042:0.0:1.2 -17 43348887 . G A 101 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CATGCCCAGCTAATTTTTAT;RSEQ=TTTTTGTAGAGATGGGGTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1.0:0,0:25.4:1.0:32.1:1.0:1.0:0.0:58.3:18.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 43350514 . G A 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACTGTGCTTCCAGCCAACC;RSEQ=TGCTCAGAGGCGCAGGAGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:17.8:1.0:30.2:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 43352049 . C T 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=2.0;SSF=0.0;SOR=0.00891;LSEQ=CAGCACCCTAGTGCTCCACA;RSEQ=ACAGAGGCTGCTGCTGTTTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:267:14,253:1,28:0.899:1,2:24.4:1.0:28.2:1.0:1.0:1.55:60.0:52.4:0.8973:0.0:1.1 0/1:125:9:0,9:7,109:0.072:2,0:15.3:1.0:26.7:1.0:1.0:0.0:60.0:8.0:0.0656:0.0:1.1 -17 46801231 . G C 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01686;SOR=0.0;LSEQ=GAAATTATTTCGGGCCTGGA;RSEQ=CCCGCGTAGACGCGACCCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:10:0,10:3,191:0.049:1,0:28.6:1.0:29.7:1.0:1.0:0.0:60.0:9.0:0.0446:0.0:1.0 0/0:109:0:0,0:3,106:0.0:1,0:26.1:1.0:32.2:1.0:1.0:0.0:60.0:35.333:1.0:0.0:0.0 -17 47685477 . AATAC A 112 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02254;SOR=0.0;LSEQ=AACAATAAGTAACTAATTAT;RSEQ=ATAAAGGAAAATAAGAAACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:0,12:0,22:0.3529:1,0:26.4:1.0:31.4:1.0:1.0:0.0:60.0:24.0:0.375:0.0294:0.0 0/0:11:0:0,0:0,11:0.0:0,0:21.8:1.0:31.0:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.0 -17 51931075 . C T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01373;SOR=0.0;LSEQ=ATCATCAGCATCATCAACAA;RSEQ=GACAACAACAACAACAAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:3,2:4,2:0.4545:2,2:35.4:1.0:30.0:1.0:1.0:1.29868:60.0:10.0:0.4545:0.0:1.6 0/0:12:0:0,0:6,6:0.0:2,0:10.6:1.0:29.8:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.6 -17 56440474 . G A 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.00013;SOR=0.0;LSEQ=GTAGGTGAGGCCCAAAGACG;RSEQ=GGGAAAACTTGCCCAGAGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:27:27,0:132,4:0.1656:1,1:19.3:1.0:30.4:1.0:1.0:0.0:60.0:26.0:0.1625:0.0:2.7 0/0:61:0:0,0:60,1:0.0:1,0:26.8:1.0:31.6:1.0:1.0:0.0:60.0:122.0:1.0:0.0:0.3 -17 56440642 . C T 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.03396;LSEQ=TCTAGTGTGCTTACCCAGGC;RSEQ=GGGGGCTCCTTCAGCTCAAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1697:78:43,35:857,762:0.046:2,2:24.0:1.0:29.5:1.0:0.72884:1.09:60.0:12.0:0.0434:0.0:1.1 0/0:1225:2:0,2:649,572:0.0016:2,0:1.0:0.0:29.5:1.0:0.22007:0.0:60.0:4.0:0.0017:0.0:1.0 -17 58678009 . T A 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00606;LSEQ=GCCCGAGAGGCTCGCGACCC;RSEQ=CTCCCGGACGCCGGGGCCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:853:145:79,66:375,329:0.17:2,2:23.2:1.0:30.2:1.0:0.85499:1.05:60.0:144.0:0.1735:0.0:1.1 0/0:808:1:1,0:440,366:0.0012:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0013:0.0:1.0 -17 59761706 . A G 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCTAATGTTTCCTAGCCCA;RSEQ=GTTATAATGCTGTCTGGTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:25.8:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:32.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -17 59924512 . C T 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02021;LSEQ=CAGTGGAGAGTTGAGTTTTA;RSEQ=AGTCTTTCCTGAATCAACTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1268:56:26,30:617,593:0.0442:2,2:21.6:1.0:28.9:1.0:0.58491:1.20037:60.0:112.0:0.0446:0.0:1.1 0/0:1073:1:0,1:521,551:0.0009:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0009:0.0:1.0 -17 59926645 . C T 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGTAATTTAAAAAAAACAG;RSEQ=ATAAATAACTTACAGGTAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:138:32,106:47,147:0.4157:2,2:20.4:1.0:28.6:1.0:0.89618:1.05894:60.0:276.0:0.4169:0.0:1.1 0/0:210:0:0,0:54,156:0.0:2,0:23.0:1.0:31.5:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.1 -17 59926837 . A AT 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.5;SOR=0.0;LSEQ=AATAGGAAAAGTCCAATTTG;RSEQ=TTTTTTAAATCGCCTTATGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:0,6:0,8:0.4286:0,0:34.3:1.0:30.3:1.0:1.0:0.0:60.0:12.0:0.4286:0.0:0.2 0/0:2:0:0,0:0,2:0.0:0,0:26.0:1.0:30.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -17 61878535 . G A 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00699;SOR=0.0;LSEQ=TCTGCCTGCCTCAGCCTCCT;RSEQ=GGTAACTGGGATTACAGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:3,5:0,1:0.8889:0,2:38.1:1.0:29.0:1.0:1.0:0.0:60.0:7.0:0.875:0.0:1.4 0/0:4:0:0,0:1,3:0.0:2,0:25.5:1.0:30.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -17 62008760 . G A 242 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCAGCTGCTGGGTGGGAG;RSEQ=AAGTGGGCGGGGCCAGTCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:290:113,177:282,396:0.299:2,2:26.7:1.0:29.7:1.0:0.47553:1.11532:60.0:47.333:0.298:0.0:1.2 0/0:713:0:0,0:294,419:0.0:2,0:25.1:1.0:30.5:1.0:1.0:0.0:60.0:46.533:1.0:0.0:0.2 -17 63313715 . A T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAATCATTACATCAGCTCTG;RSEQ=GTGGCAGGTTCTTTGATTGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,0:0.7143:0,0:32.4:1.0:30.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 63532779 . T TA 86 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.06011;SOR=0.0;LSEQ=ATTCTGCTCAGAGAGAGAGT;RSEQ=AAAAAAAAAACTACCATAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:9:2,7:40,47:0.0938:2,2:34.1:1.0:27.2:1.0:0.29081:2.94815:60.0:8.0:0.087:0.0:1.0 0/0:38:0:0,0:7,31:0.0:2,0:25.0:1.0:27.7:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.9 -17 64938402 . GG TT 103 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0033;SOR=0.0;LSEQ=CTCCTGTGACCATTATTTCA;RSEQ=AAACAAACTCCTTTAAACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:11:1,10:58,124:0.057:2,2:18.7:1.0:29.9:1.0:0.17751:4.65062:60.0:22.0:0.0576:0.0052:0.9 0/0:137:0:0,0:43,94:0.0:2,0:24.2:1.0:30.4:1.0:1.0:0.0:60.0:44.667:1.0:0.0:0.3 -17 70120111 . G A 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00271;SOR=0.0;LSEQ=GCGCCCCCACAGCAGCCGGC;RSEQ=GCACCCCCGCAGCAGCCACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:20:18,2:173,13:0.0971:2,2:22.1:1.0:31.0:1.0:0.64418:1.47542:60.0:40.0:0.0995:0.0:1.1 0/0:74:0:0,0:66,8:0.0:2,0:20.4:1.0:30.5:1.0:1.0:0.0:60.0:148.0:1.0:0.0:0.1 -17 72843378 . C T 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.50549;SOR=0.0;LSEQ=CCAGACTCGACTGTCCAGGG;RSEQ=CTGCCCACTCACGGCCTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:6,0:0.4167:0,0:17.6:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.4545:0.0:2.0 0/0:2:0:0,0:1,1:0.0:2,0:38.5:1.0:31.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.0 -17 72843411 . GC G 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.28327;SOR=0.0;LSEQ=GGCCTGTCCCCACCCTCAGT;RSEQ=CCCCCCCCACCCCCAGCAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:13,0:0.35:1,0:36.4:1.0:33.4:1.0:1.0:0.0:60.0:14.0:0.3684:0.0:1.4 0/0:4:0:0,0:3,1:0.0:2,0:19.0:1.0:32.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.8 -17 72904115 . G A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.05818;SOR=0.0;LSEQ=AGCCTTTTCCTGTAAACGCC;RSEQ=GGTGGCATCTCTTACTATCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:3,5:5,4:0.4706:2,2:30.4:1.0:31.4:1.0:0.63719:1.99353:60.0:16.0:0.4706:0.0:1.0 0/0:6:0:0,0:2,4:0.0:2,0:23.0:1.0:26.5:1.0:1.0:0.0:60.0:5.0:1.0:0.0:0.2 -17 77280452 . A G 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTTTCTTCAATGTTTTGTT;RSEQ=TTCCAAATCCACAACCCAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:37:1,36:1,24:0.5968:1,1:28.1:1.0:32.7:1.0:1.0:1.48993:60.0:74.0:0.5968:0.0:1.0 0/0:27:0:0,0:1,26:0.0:1,0:24.0:1.0:30.8:1.0:1.0:0.0:60.0:54.0:1.0:0.0:0.4 -17 77386058 . GGGTCTCCGCAGCCTCCAGGTCTCCGCAGCCTCCA G 97 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.18268;SOR=0.0;LSEQ=TCCAGGTCTCTGTAGCCTCC;RSEQ=GGTCTCCGCAGCCTCCAGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:10:4,6:33,5:0.2083:2,2:14.0:1.0:29.2:1.0:0.00507:9.23383:52.1:20.0:0.2174:0.125:1.2 0/0:11:0:0,0:10,1:0.0:2,0:33.5:1.0:30.0:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.9 -17 77386084 . CAGCCTCCAGGTCTCCGCAGCCTCCAGGTCTCCGT C 188 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=21;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCGCAGCCTCCAGGTCTCCG;RSEQ=AGCCTCCAGGTCTCCGCAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:76:62:35,27:7,2:0.8158:2,2:24.9:1.0:31.6:1.0:0.29285:2.66588:57.4:61.0:0.8592:0.1711:0.5 0/0:30:0:0,0:20,10:0.0:2,0:17.8:1.0:28.8:1.0:1.0:0.0:58.7:29.0:1.0:0.0:1.3 -17 78765080 . A C 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00097;SOR=0.0996;LSEQ=GCCTTGACAGAATGGCAATG;RSEQ=GATTTTCTTTACAAATCTAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:19:19,0:22,0:0.4634:1,1:21.6:1.0:32.4:1.0:1.0:0.0:60.0:38.0:0.4872:0.0:1.1 0/1:26:2:2,0:22,2:0.0769:2,0:9.5:1.0:33.0:1.0:1.0:0.0:60.0:4.0:0.0769:0.0:1.0 -17 78796361 . T A 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GACCGGTGCACAGCCCTTAC;RSEQ=GCGCACCGGCGGCTTATCTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:30.0:1.0:30.0:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 78796907 . C G 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAAAGCTCTTCAGACAGGA;RSEQ=TTGCTGGTGGCTAGTCTGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:37:22,15:386,304:0.0507:2,2:25.6:1.0:31.8:1.0:0.73574:1.15:60.0:74.0:0.0513:0.0:1.1 0/0:620:0:0,0:336,283:0.0:2,0:25.3:1.0:31.1:1.0:1.0:0.0:60.0:87.429:1.0:0.0:0.2 -17 78829114 . G C 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.15855;SOR=0.0;LSEQ=CTAAAAGCATGAACTTGTAA;RSEQ=GAAAGGAGCACCAGCTCTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:5:5,0:86,1:0.0543:1,0:29.0:1.0:33.0:1.0:1.0:0.0:60.0:10.0:0.0556:0.0:1.0 0/0:53:0:0,0:52,1:0.0:1,0:24.5:1.0:32.0:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.1 -17 78857631 . C T 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03127;LSEQ=ATCTGCCTGGAGCAGCTCAA;RSEQ=GACCCGCACCCCTTGCTGCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:862:40:17,23:397,425:0.0464:2,2:27.5:1.0:30.2:1.0:0.51938:1.26346:60.0:39.0:0.046:0.0:1.1 0/0:659:1:0,1:342,316:0.0015:2,0:1.0:0.0:23.0:0.0:0.48103:0.0:60.0:2.0:0.0015:0.0:1.0 -17 78882329 . G A 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.125;SOR=0.0;LSEQ=GTGGTCATGCCCTCCGATCC;RSEQ=CTGAGGCATTTCAAGGAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1.0:0,0:31.4:1.0:30.3:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.1 0/0:1:0:0,0:1,0:0.0:0,0:49.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -17 78897732 . CT TA 114 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00735;SOR=0.0;LSEQ=TGCACTCTTTAGGAGCACTG;RSEQ=GGGTGTGTCCCGGTTCTCCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:1.0:0,1:26.0:1.0:29.3:1.0:1.0:0.0:60.0:30.0:1.0:0.0:1.4 0/0:2:0:0,0:1,1:0.0:2,0:9.0:0.0:34.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 -17 78919466 . G T 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTGTGTGTTTCTTTTGACA;RSEQ=GCATTACGAGATTGGACGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1178:37:21,16:631,510:0.0314:2,2:29.2:1.0:30.2:1.0:1.0:1.06:60.0:74.0:0.0321:0.0:1.4 0/0:965:0:0,0:521,443:0.0:2,0:26.6:1.0:30.5:1.0:1.0:0.0:60.0:42.818:1.0:0.0:0.2 -17 78922952 . C G 104 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGAGGAAGGGCAGCCCCGG;RSEQ=TCCCAGGGCAGCCAAACCTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1.0:0,0:21.5:1.0:30.3:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -17 78923126 . T G 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.11713;LSEQ=CCACGGGTAGTGAGTCAGGC;RSEQ=GGCCGCCCAGGGTCACTGCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:54:53,1:92,0:0.3699:1,1:22.1:1.0:29.6:1.0:0.36986:0.0:60.0:26.0:0.3611:0.0:1.1 0/1:47:3:3,0:43,1:0.0638:1,0:21.0:1.0:32.0:0.0:1.0:0.0:60.0:6.0:0.0652:0.0:1.0 -17 78934088 . G A 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGTGTCACTGCCATTTGGTT;RSEQ=GGTCCAGGTTTCTCAGTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:68:2,66:6,88:0.4198:2,1:24.3:1.0:31.8:1.0:0.46971:2.23975:60.0:136.0:0.4198:0.0:1.1 0/0:89:0:0,0:5,84:0.0:2,0:23.9:1.0:30.5:1.0:1.0:0.0:60.0:178.0:1.0:0.0:0.1 -17 80759544 . G A 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00041;SOR=0.0;LSEQ=GCGTGTGCGTTGTGTGGGTC;RSEQ=GAGTCAGCGTGGCAGGAGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:202:12:4,8:117,72:0.0594:2,2:9.4:1.0:28.7:1.0:0.06777:3.23042:45.8:5.0:0.0568:0.0:3.4 0/0:201:0:0,0:111,90:0.0:2,0:25.7:1.0:27.7:1.0:1.0:0.0:59.1:15.75:1.0:0.0:1.2 -18 112258 . G A 78 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02721;SOR=0.0;LSEQ=GGAAAGAATGGCAGTTCTCC;RSEQ=CTGTGTGGAGTCTCTCACCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:3,3:5,5:0.3158:2,2:23.2:1.0:30.2:1.0:1.0:1.0:40.0:12.0:0.3158:0.0:4.8 0/0:14:0:0,0:7,5:0.0:2,0:32.6:1.0:30.4:1.0:1.0:0.0:30.8:24.0:0.8571:0.0:4.5 -18 756282 . T TG 74 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TATGTTCCCGGTGCCTACAG;RSEQ=GGGGGGGGGCTCAATAACTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1.0:0,2:22.6:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.2:0.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -18 4131501 . C G 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=CTTTTCTAGAACAAAAGCAG;RSEQ=CACAGACAATACATAAGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:20.8:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:2:0:0,0:2,0:0.0:0,0:24.0:1.0:30.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -18 8413657 . G A 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=GTCTAACAGGAGCGTGAGAA;RSEQ=AGGTGTTGAAGTGTTTCATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:39:21,18:266,342:0.0603:2,2:20.4:1.0:29.9:1.0:0.24612:1.5:60.0:38.0:0.0598:0.0:1.1 0/0:486:0:0,0:215,271:0.0:2,0:23.1:1.0:31.2:1.0:1.0:0.0:60.0:120.5:1.0:0.0:0.1 -18 12912750 . C T 86 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01884;SOR=0.0;LSEQ=TGTTGGATCAGGAACTGTGT;RSEQ=TGCTCTTAAGTGCTTGTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:7:7,0:95,2:0.0673:1,0:25.6:1.0:30.9:1.0:1.0:0.0:60.0:14.0:0.0686:0.0:1.4 0/0:81:0:0,0:80,1:0.0:1,0:24.0:1.0:31.5:1.0:1.0:0.0:60.0:80.0:1.0:0.0:0.0 -18 12912821 . G C 139 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTCTTTTCAGTTGGGTGTT;RSEQ=AGTGGTTTTCCAGATCACGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:22:18,4:308,90:0.0524:2,2:22.7:1.0:31.2:1.0:0.79529:1.31:60.0:44.0:0.0531:0.0:1.3 0/0:399:0:0,0:293,105:0.0:2,0:22.4:1.0:31.0:1.0:1.0:0.0:60.0:78.6:0.9975:0.0:0.1 -18 18511155 . T C 69 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.10714;SOR=0.0;LSEQ=TTGTGATATCTGCATTCAAG;RSEQ=CACACAGTTCAACATTCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:0,1:0.8333:0,2:11.4:1.0:29.8:1.0:0.33333:0.0:46.2:10.0:0.8333:0.0:6.4 0/0:2:0:0,0:0,2:0.0:0,0:43.5:1.0:31.0:0.0:1.0:0.0:33.5:4.0:1.0:0.0:7.0 -18 18517177 . G A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.00047;SOR=0.11835;LSEQ=TGGAAGTGGACATTTGGAGC;RSEQ=CTTTGACGCCTTTGGTGAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:6,3:10,7:0.3462:2,2:26.6:1.0:30.8:1.0:1.0:1.38:50.8:18.0:0.3462:0.0:3.9 0/1:87:5:4,1:40,42:0.0575:2,2:42.0:1.0:30.4:1.0:0.36038:4.14:54.6:10.0:0.0581:0.0:4.4 -18 18519858 . C G 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00398;SOR=0.06714;LSEQ=TTAGTTGAGGACACACATCA;RSEQ=AAACAAGTTTCTGAGAATGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:4,4:2,1:0.7273:2,2:31.6:1.0:32.3:1.0:1.0:1.87936:41.1:16.0:0.7273:0.0:4.6 0/1:15:2:1,1:7,6:0.1333:2,2:29.0:0.0:33.5:1.0:1.0:1.1547:25.0:4.0:0.1333:0.0:5.0 -18 18519863 . A T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00411;SOR=0.07079;LSEQ=TGAGGACACACATCACAAAC;RSEQ=AGTTTCTGAGAATGCTTCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:4,4:0,1:0.6667:0,2:32.6:1.0:30.3:1.0:1.0:0.0:41.1:16.0:0.6667:0.0:4.6 0/1:18:2:1,1:2,4:0.1111:2,2:34.0:0.0:30.5:1.0:1.0:1.83:25.0:4.0:0.1111:0.0:5.0 -18 18519891 . T G 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.00096;SOR=0.05448;LSEQ=GAGAATGCTTCTGTCTAGTT;RSEQ=TTGTGGGAAGATATTTCCTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:2,4:2,3:0.5455:2,2:19.0:1.0:31.8:1.0:1.0:1.29868:35.2:12.0:0.5455:0.0:5.2 0/1:36:2:1,1:16,18:0.0556:2,2:8.5:1.0:29.5:1.0:1.0:1.12:25.0:4.0:0.0556:0.0:5.0 -18 18520246 . A G 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00652;SOR=0.07685;LSEQ=TGTAGTTTTTATGGGAAGAT;RSEQ=TTTCCTTTTCCACCATAGGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:5,2:7,10:0.2917:2,2:6.7:1.0:33.3:1.0:0.37071:3.38:51.6:14.0:0.2917:0.0:3.7 0/1:34:1:0,1:14,19:0.0294:2,0:7.0:0.0:25.0:0.0:1.0:0.0:22.0:2.0:0.0294:0.0:4.0 -18 18520315 . T G 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00207;SOR=0.06026;LSEQ=GATACTACAGAAAGAGTGTT;RSEQ=CAAACCTGCTCTATGAAAGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:7:2,5:9,12:0.2414:2,2:21.0:1.0:33.0:1.0:0.66834:1.83476:49.1:14.0:0.2414:0.0:3.6 0/1:55:1:0,1:23,30:0.0182:2,0:18.0:0.0:34.0:0.0:1.0:0.0:22.0:2.0:0.0182:0.0:4.0 -18 23784839 . A G 108 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00205;SOR=0.04814;LSEQ=CACGCCTCCACCCCATGGGA;RSEQ=ATTCGATGGACATGGACATA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:8,2:5,1:0.625:2,2:22.4:1.0:32.8:1.0:1.0:1.23302:60.0:20.0:0.625:0.0:1.0 0/1:15:1:1,0:9,5:0.0667:2,0:15.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0667:0.0:1.0 -18 28787355 . T A 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.00307;SOR=0.11065;LSEQ=TCATTTTATAAATTCTTTCC;RSEQ=AATTACCTCAAATCACAAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:14:14,0:21,0:0.4:1,1:28.0:1.0:29.6:1.0:1.0:0.0:60.0:13.0:0.3939:0.0:1.1 0/1:30:2:2,0:26,2:0.0667:2,0:28.5:1.0:28.5:1.0:1.0:0.0:60.0:4.0:0.0667:0.0:1.0 -18 28787634 . G T 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00016;SOR=0.0;LSEQ=ATAATAACTTCCATTTATTG;RSEQ=TCTAGAAATCACTGTGTGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:11:2,9:9,37:0.193:2,2:24.7:1.0:29.9:1.0:1.0:1.09289:60.0:22.0:0.193:0.0:1.1 0/0:63:0:0,0:14,49:0.0:2,0:13.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 -18 34883082 . T G 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.10526;SOR=0.0;LSEQ=GTACCATTGTTCTCAGCACT;RSEQ=CCTTTGGCTCATTTGAACCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:0,17:0,1:0.9444:0,1:21.6:1.0:32.2:1.0:1.0:0.0:60.0:34.0:0.9444:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:19.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -18 35069156 . C T 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01767;SOR=0.0;LSEQ=ATCCGATGCAGCGGCTGACA;RSEQ=GCCAGCATGGCAGATTAGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:8,2:0.375:2,0:20.3:1.0:31.8:1.0:0.5:0.0:60.0:12.0:0.375:0.0:1.0 0/0:16:0:0,0:12,4:0.0:2,0:28.1:1.0:30.3:1.0:1.0:0.0:60.0:32.0:1.0:0.0:0.2 -18 39537688 . G C 245 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAGCCTTTGGCCTTGCCAGT;RSEQ=AGAACATCCTACAAAGCATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:220:90,130:117,163:0.44:2,2:24.5:1.0:31.6:1.0:0.85534:1.03675:60.0:72.333:0.4393:0.0:1.1 0/0:622:0:0,0:268,354:0.0:2,0:25.4:1.0:30.9:1.0:1.0:0.0:60.0:61.2:1.0:0.0:0.1 -18 39593388 . CT C 85 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.00858;SOR=0.0;LSEQ=CTTTTCCTAATATTACTTTA;RSEQ=TTTTTTTGTTTTCCAGGATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:6:5,1:171,42:0.0274:2,2:30.8:1.0:33.2:1.0:1.0:1.23:60.0:12.0:0.0274:0.0:0.0 0/0:262:0:0,0:202,60:0.0:2,0:24.1:1.0:30.7:1.0:1.0:0.0:60.0:261.0:1.0:0.0:0.1 -18 46996404 . A G 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00281;SOR=0.0;LSEQ=GGGTCCCTACCTTCCTCCAT;RSEQ=CCCACCACCTGCCCCTGGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:0.6:0,2:21.7:1.0:32.8:1.0:1.0:0.0:60.0:12.0:0.6:0.0:1.3 0/0:12:0:0,0:3,9:0.0:2,0:21.8:1.0:28.2:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.8 -18 48190817 . G A 181 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.10694;LSEQ=ATCAGCACAGAGGACCTCGT;RSEQ=CTCAAGATTGGGGATTTCGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:80:22,58:26,59:0.4848:2,2:18.6:1.0:28.7:1.0:0.73266:1.16073:60.0:25.667:0.4753:0.0:1.2 0/1:209:19:8,11:56,134:0.0909:2,2:17.5:1.0:28.8:1.0:0.29807:1.74:60.0:38.0:0.0927:0.0:1.2 -18 55466751 . G GTA 94 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0054;SOR=0.0;LSEQ=CAGGAGTTTGAGACTAGCCT;RSEQ=GCCAACATGGTGAAACCCGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:0,9:0,14:0.375:1,0:25.8:1.0:29.7:1.0:1.0:0.0:60.0:18.0:0.375:0.0417:0.4 0/0:18:0:0,0:0,18:0.0:1,0:26.2:1.0:30.9:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.2 -18 56378529 . C T 74 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTAAGAAAGATAGGTGGCTA;RSEQ=GTGATCATGGATATTTGTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:14.5:1.0:28.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -18 56412894 . A T 47 q23 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01393;SOR=0.0;LSEQ=AGTCCCTAATTTTTTTTTTT;RSEQ=CAGGATCTAGATATTGATCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:3,2:341,151:0.01:2,2:10.6:1.0:20.4:1.0:0.64578:1.5042:60.0:1.5:0.0062:0.0:1.8 0/0:670:0:0,0:459,211:0.0:2,0:23.4:1.0:27.6:1.0:1.0:0.0:60.0:36.222:1.0:0.0:0.1 -18 60910366 . G A 70 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCAGTGATAGACTGGATAAA;RSEQ=AAAATTTGGTACATATACAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:22.8:1.0:30.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -18 69372730 . A G 84 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=TGGCATTTAAAAAAATTATT;RSEQ=TCTATGCCTAGTTTCCTTTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:25.7:1.0:32.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 1221161 . C T 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.09565;LSEQ=TAGAGCTGGGGCTCCTAGGG;RSEQ=GTCAACCACCTTGACTGACC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:605:207:133,74:257,141:0.3421:2,2:24.4:1.0:29.7:1.0:1.0:1.01411:60.0:68.0:0.3406:0.0:1.1 0/1:613:29:18,11:346,238:0.0473:2,2:23.2:1.0:29.1:1.0:0.84781:1.13:60.0:28.0:0.0462:0.0:1.1 -19 1221991 . G A 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02271;SOR=0.19111;LSEQ=AAGAGGTTCTCCATCCGGCA;RSEQ=ATCCGGCAGCACAGGTGAGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:909:11:6,5:365,532:0.0121:2,2:17.9:1.0:30.3:1.0:0.3711:1.75:60.0:22.0:0.0123:0.0:1.3 0/0:857:2:1,1:366,489:0.0023:2,2:9.0:1.0:19.0:1.0:1.0:1.34:60.0:1.0:0.0012:0.0:3.5 -19 1611856 . G A 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01696;LSEQ=TTCAGGTTCCGCTCTGGAGG;RSEQ=AGGGGGGAGAGCTCTGTGGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:49:17,32:390,561:0.049:2,2:24.9:1.0:29.6:1.0:0.45654:1.30824:60.0:23.5:0.0482:0.0:1.2 0/0:1147:1:1,0:490,656:0.0009:2,0:1.0:0.0:23.0:0.0:0.42807:0.0:60.0:2.0:0.0009:0.0:3.0 -19 1622115 . C T 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCCACTGCTGCCCACCGGGC;RSEQ=GCTACCGGGCGGGAGGGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1122:33:14,19:523,566:0.0294:2,2:23.5:1.0:30.6:1.0:0.59752:1.25379:60.0:32.0:0.029:0.0:1.1 0/0:950:0:0,0:466,482:0.0:2,0:24.9:1.0:29.9:1.0:1.0:0.0:60.0:93.8:0.9989:0.0:0.5 -19 2194896 . T C 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03571;SOR=0.0;LSEQ=GGACAGGCTGGGTTCTGGGC;RSEQ=GGCTGCGGCATCCTTGGGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1.0:0,2:20.5:1.0:29.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.3 0/0:2:0:0,0:1,1:0.0:2,0:1.0:0.0:30.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 -19 2207386 . G C 113 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.15565;SOR=0.0;LSEQ=GGTTGGAGGGGCCCAGGCCA;RSEQ=GTGGTGTTGAATGGTGCACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:12:12,0:23,0:0.3429:1,0:24.3:1.0:31.7:1.0:1.0:0.0:60.0:24.0:0.3429:0.0:1.4 0/0:6:0:0,0:6,0:0.0:0,0:18.5:1.0:33.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 -19 2211220 . G T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGAAGCTTCTAGGTGAGCCC;RSEQ=TGTGAGGCGTCCGGCGAAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:24:7,17:182,344:0.0434:2,2:21.7:1.0:30.3:1.0:0.6653:1.28434:60.0:48.0:0.0442:0.0:1.1 0/0:535:0:0,0:195,340:0.0:2,0:22.5:1.0:30.2:1.0:1.0:0.0:60.0:88.167:1.0:0.0:0.2 -19 2213298 . G T 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCCTGGCTGAGTCCAGGTG;RSEQ=GGTGGCAGGTGCAGTCCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,1:0.2:1,0:20.8:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.2083:0.0:1.0 0/0:2:0:0,0:2,0:0.0:0,0:4.0:1.0:30.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -19 2214242 . G A 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCGAGGTGTGGGGTCATGC;RSEQ=AGCATCCCACCATCGTGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:5,1:7,5:0.3333:2,2:20.8:1.0:27.7:1.0:0.60003:3.34:60.0:5.0:0.3125:0.0:2.0 0/0:1:0:0,0:1,0:0.0:0,0:9.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -19 2217203 . G A 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.04334;SOR=0.0;LSEQ=TTGGGGCACGGTGAGGTACT;RSEQ=GGGCTGACCTGGAGTAGGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:7:1,6:1,51:0.1186:1,2:24.9:1.0:30.6:1.0:0.22501:7.95:60.0:14.0:0.1207:0.0:1.0 0/0:35:0:0,0:2,33:0.0:2,0:18.3:1.0:30.8:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.2 -19 3110361 . C T 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07767;LSEQ=CGGGCGCCTGGGGAGGGGAG;RSEQ=GCCTGGGCAGCTGTGGGCTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:86:19,67:43,164:0.2935:2,2:25.6:1.0:29.8:1.0:0.87532:1.08:60.0:85.0:0.2951:0.0:2.1 0/1:321:10:2,8:82,228:0.0312:2,2:21.9:1.0:29.3:1.0:1.0:1.43705:60.0:20.0:0.0321:0.0:2.0 -19 3110585 . A G 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.14286;SOR=0.0;LSEQ=CCAAGTAGCTGTGGGCGCCC;RSEQ=CATCCTGTGGGTGGGGAAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1.0:0,2:39.7:1.0:32.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.2 0/0:1:0:0,0:0,1:0.0:0,0:14.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -19 3114864 . C T 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.1508;LSEQ=CTGGTGGCTTTCCGTCCTCC;RSEQ=GCTGGTTTGGGTGCTGTGTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:47:40,7:117,19:0.2554:2,2:23.2:1.0:31.3:1.0:1.0:1.07718:60.0:94.0:0.2626:0.0:1.1 0/1:143:7:5,2:117,19:0.049:2,2:19.7:1.0:31.0:1.0:0.27337:2.44297:60.0:14.0:0.0493:0.0:1.0 -19 3118851 . G T 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00014;SOR=0.0;LSEQ=GGCAGGAGGGGCTTGGGTGG;RSEQ=AGCCGTCCTGGGATTGCAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:20:18,2:208,19:0.081:2,2:27.9:1.0:29.2:1.0:0.68184:1.21534:60.0:40.0:0.0823:0.0:1.3 0/0:143:0:0,0:125,18:0.0:2,0:20.9:1.0:31.0:1.0:1.0:0.0:60.0:142.0:1.0:0.0:0.2 -19 3121609 . T C 69 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GCCCCCACACCGCAGCCCCC;RSEQ=GTGGCTGTCCTTCCAACCCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:30.2:1.0:29.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 4094775 . G A 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.0;MSILEN=1.0;SSF=0.44444;SOR=0.0;LSEQ=GGTGGGTCAGAAGCCTGGAC;RSEQ=CAACCCCAGCTAACTGTCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:0.625:0,2:22.0:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.625:0.0:1.2 0/0:1:0:0,0:0,1:0.0:0,0:47.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -19 4102132 . A C 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02098;SOR=0.0;LSEQ=GGGACCAGTGTGGCAAACAG;RSEQ=GGATACTAAGAGTGAAGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:22.6:1.0:29.3:1.0:1.0:0.0:60.0:6.0:0.75:0.0:2.0 0/0:4:0:0,0:4,0:0.0:0,0:25.5:1.0:28.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -19 4102449 . G A 260 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03883;LSEQ=ACCTGGTCCAGGGAGCCGCC;RSEQ=TCCTAGAGGGCACACAAGGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:641:399:171,228:109,132:0.6225:2,2:26.0:1.0:30.2:1.0:0.56588:1.10084:59.9:56.0:0.6252:0.0:1.1 0/1:700:42:17,25:288,370:0.06:2,2:29.7:1.0:28.9:1.0:0.74941:1.14444:60.0:20.0:0.0581:0.0:1.2 -19 5174304 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0069;SOR=0.0;LSEQ=TTTGCTGAATAAAGCAGTGT;RSEQ=GGATTTGTGGTTCCCGAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:9:0,9:0,22:0.2903:1,0:28.3:1.0:28.7:1.0:1.0:0.0:60.0:8.0:0.2667:0.0:1.7 0/0:22:0:0,0:2,20:0.0:2,0:19.5:1.0:28.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.1 -19 5206724 . C A 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTCCAGGCCTCAGGAGGTC;RSEQ=GCCCGGGAGGGGCAGAGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:101:77,24:180,36:0.3186:2,2:24.0:1.0:30.2:1.0:0.1656:1.55619:60.0:202.0:0.3248:0.0:1.7 0/0:303:0:0,0:233,70:0.0:2,0:24.0:1.0:29.5:1.0:1.0:0.0:60.0:49.5:1.0:0.0:0.7 -19 5207183 . T C 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TTGGCTCCCTGCAACCTCTG;RSEQ=CTCCTGGGTTCAAGTGATTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1.0:0,0:26.8:1.0:31.6:1.0:1.0:0.0:59.6:18.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 5208216 . G A 238 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0703;LSEQ=GGCCTCAGTTTCCCCAGCAG;RSEQ=GCCAAAAGCTGGGACACTCG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:487:249:151,98:139,95:0.5113:2,2:24.8:1.0:30.0:1.0:0.85257:1.05:60.0:40.5:0.5127:0.0:2.0 0/1:483:33:21,12:284,164:0.0683:2,2:23.2:1.0:28.4:1.0:1.0:1.01:60.0:66.0:0.0689:0.0:1.8 -19 5208257 . A T 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01618;LSEQ=AGGGAGCTCACCTGCAGTGG;RSEQ=CAGAGATGGGGCCGTCCTGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:798:54:33,21:396,348:0.0677:2,2:25.8:1.0:29.6:1.0:0.32256:1.38:60.0:108.0:0.0691:0.0:1.1 0/0:854:1:0,1:459,394:0.0012:2,0:1.0:0.0:26.0:0.0:0.46253:0.0:60.0:2.0:0.0012:0.0:1.0 -19 5208514 . TG T 171 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.1036;LSEQ=TTGTTTGTTTGTTTTTGAGA;RSEQ=GAGTTTCACTCTTGTCGCCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:44:0,44:1,53:0.449:1,1:26.8:1.0:31.4:1.0:1.0:0.0:60.0:88.0:0.4536:0.0816:0.2 0/1:65:5:1,4:0,60:0.0769:1,2:28.4:1.0:31.6:1.0:0.07692:0.0:60.0:10.0:0.0769:0.0154:0.2 -19 5212482 . G A 260 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03134;LSEQ=AACTGGAACTGGCGGACCTC;RSEQ=CGTTTCTCACTGGAGCCATT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:720:419:194,225:145,156:0.5819:2,2:25.9:1.0:29.9:1.0:0.64995:1.0779:60.0:82.8:0.5823:0.0:1.2 0/1:767:32:16,16:343,392:0.0417:2,2:25.3:1.0:29.5:1.0:0.72149:1.14:60.0:64.0:0.0422:0.0:1.2 -19 5212586 . G T 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.05642;LSEQ=CCCAAGTGGCCGGGTGTGGT;RSEQ=GCTCATGCCTGTTATCCCAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:161:85:4,81:5,71:0.528:2,1:22.1:1.0:30.4:1.0:0.73618:1.4229:59.2:170.0:0.5313:0.0:1.1 0/1:119:7:1,6:8,104:0.0588:2,2:18.9:1.0:31.1:1.0:0.43193:2.15:58.4:14.0:0.0603:0.0:1.4 -19 5214116 . A G 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.11111;SOR=0.0;LSEQ=GGGCATGAGTAAAGGCAAGA;RSEQ=GAAATCAGGCTCATTGCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:23.9:1.0:33.0:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.8 0/0:1:0:0,0:0,1:0.0:0,0:10.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -19 5214904 . C T 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00035;SOR=0.0;LSEQ=CAGTTTCTCCCCCTCAGCGC;RSEQ=ATCACCATTTGGGGCCAGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:20:1,19:1,19:0.5:1,1:18.6:1.0:28.6:1.0:1.0:1.0:60.0:40.0:0.5128:0.0:1.1 0/0:15:0:0,0:0,15:0.0:1,0:27.3:1.0:32.1:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.2 -19 5214986 . G A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.03251;SOR=0.0;LSEQ=GAGCAGCATCCCTGGCCTCC;RSEQ=CCCACTCCACGCCAGCAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:5,4:1,4:0.6429:2,2:30.2:1.0:29.9:1.0:0.3007:4.45:60.0:18.0:0.75:0.0:1.1 0/0:5:0:0,0:1,4:0.0:2,0:26.0:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.4 -19 5215474 . G A 243 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07874;LSEQ=GGGTAGGTGCCTGTGAGGCC;RSEQ=AGGTGATGAGGGTGGGAGGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:555:285:142,143:138,132:0.5135:2,2:24.4:1.0:29.8:1.0:0.79905:1.05269:60.0:34.625:0.5111:0.0:1.1 0/1:627:48:28,20:313,265:0.0766:2,2:25.9:1.0:30.5:1.0:0.65182:1.18:60.0:47.0:0.0768:0.0:1.1 -19 5218684 . G A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CCAGGACCAAGTACAGCTAC;RSEQ=TGTACAAGCTGTGGGGGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:88:60,28:132,67:0.3056:2,2:28.3:1.0:30.7:1.0:0.78714:1.09:60.0:176.0:0.3088:0.0:1.0 0/0:194:0:0,0:137,57:0.0:2,0:22.5:1.0:29.6:1.0:1.0:0.0:60.0:193.0:1.0:0.0:0.1 -19 5220134 . C T 56 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01908;SOR=0.0;LSEQ=GACGCGAGTGCCGCAGGCTG;RSEQ=GCCTCTGTAGCCGTGAGATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:5:2,3:146,174:0.0154:2,2:19.6:1.0:24.4:1.0:1.0:1.25774:60.0:4.0:0.0125:0.0:1.0 0/0:390:0:0,0:177,213:0.0:2,0:24.8:1.0:30.4:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.1 -19 5222088 . C G 225 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAAGCCCTGCTGAACTACAA;RSEQ=CCCTGACCCTGCCTGCCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:247:128:108,20:99,19:0.5182:2,2:21.9:1.0:32.2:1.0:1.0:1.04:60.0:127.0:0.5184:0.0:1.7 0/0:216:0:0,0:182,34:0.0:2,0:22.7:1.0:30.8:1.0:1.0:0.0:60.0:107.0:1.0:0.0:0.7 -19 5225558 . G C 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=0.00055;SOR=0.0;LSEQ=AAAGGAGGAGGCAGGGGCGG;RSEQ=GGGGGCCAAGCTGGGCCCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:21:21,0:25,1:0.4468:1,1:27.3:1.0:32.5:1.0:1.0:0.0:60.0:42.0:0.4468:0.0:1.0 0/0:16:0:0,0:15,1:0.0:1,0:19.4:1.0:30.7:1.0:1.0:0.0:60.0:15.0:1.0:0.0:0.3 -19 5229728 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00199;SOR=0.0;LSEQ=AGGGGAGGGGAGGGGCGGGC;RSEQ=GAGCCGTTACCAGGGCGCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:5,2:8,7:0.3182:2,2:22.7:1.0:29.1:1.0:0.64783:2.11:60.0:14.0:0.3684:0.0:1.1 0/0:27:0:0,0:15,12:0.0:2,0:14.2:1.0:28.5:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.4 -19 5238944 . C T 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.06426;SOR=0.0;LSEQ=ACCTACTGGACTGCAGCGTG;RSEQ=GCTGCCGCACCACGGGGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:5:3,2:356,94:0.011:2,2:31.0:1.0:29.4:1.0:0.28501:2.51844:60.0:10.0:0.0112:0.0:1.2 0/0:401:0:0,0:278,122:0.0:2,0:24.0:1.0:30.9:1.0:1.0:0.0:60.0:39.0:1.0:0.0:0.1 -19 5240392 . C T 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.06494;LSEQ=GTCGGGGAGCGTCCACCCCA;RSEQ=AAAGGGGGCCCCACCTGCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:115:32,83:37,132:0.4049:2,2:25.3:1.0:28.6:1.0:0.26262:1.37:60.0:56.5:0.4036:0.0:1.1 0/1:261:11:3,8:70,180:0.0421:2,2:21.3:1.0:26.9:1.0:1.0:1.03686:60.0:22.0:0.0423:0.0:1.2 -19 7116778 . TG T 98 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.11111;SOR=0.0;LSEQ=TTCCATCTGCTGGGGGCGGG;RSEQ=GGGGGAACGAAAAAACACAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:32.5:1.0:32.8:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.1 0/0:1:0:0,0:1,0:0.0:0,0:38.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -19 7116843 . G A 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.24451;SOR=0.0;LSEQ=GCCCCAAAGGAGCAGCAACT;RSEQ=TGGAAACCCCTTGCCCTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:17.8:1.0:29.0:1.0:1.0:0.0:60.0:10.0:0.4167:0.0:1.0 0/0:5:0:0,0:5,0:0.0:0,0:14.2:1.0:33.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -19 7119651 . G A 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ATTTAGACACACACACACAC;RSEQ=CGCGCGCGCAAACACACACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:18:3,15:33,171:0.0811:2,2:20.9:1.0:29.7:1.0:1.0:1.04:59.2:36.0:0.0833:0.0:2.2 0/0:247:0:0,0:40,156:0.0:2,0:23.1:1.0:30.7:1.0:1.0:0.0:60.0:27.0:1.0:0.0:0.1 -19 7123031 . G A 223 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.06548;LSEQ=AGCAACCAGGGTTCTTGGAG;RSEQ=AGGGTCCGTGATTCGACTCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:179:52,127:119,211:0.3503:2,2:25.5:1.0:29.8:1.0:0.11669:1.37655:60.0:43.75:0.3507:0.0:1.1 0/1:529:18:5,13:196,315:0.034:2,2:21.8:1.0:29.6:1.0:0.46269:1.6164:60.0:36.0:0.0342:0.0:1.3 -19 7132343 . G A 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCTCCTGGGAGGAAGAGA;RSEQ=GAGGAGAAGGAGGGTGGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:82:21,61:31,126:0.3431:2,2:24.4:1.0:30.4:1.0:0.32377:1.4:60.0:40.0:0.3433:0.0:1.1 0/0:241:0:0,0:56,185:0.0:2,0:24.2:1.0:30.5:1.0:1.0:0.0:60.0:59.25:1.0:0.0:0.2 -19 7162789 . T C 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCGATGAGCCAAGGTCGCG;RSEQ=CATTGCACTCCAGCCTGGGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:11.7:1.0:31.5:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 7162968 . C T 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.10488;SOR=0.17588;LSEQ=CAGGAAGAGATAGCTGCTTC;RSEQ=CTAGAGGTGAAGCAAAGTGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:5:5,0:144,18:0.0299:2,0:31.2:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.0299:0.0:1.0 0/0:186:1:0,1:153,32:0.0054:2,0:1.0:0.0:24.0:0.0:0.17742:0.0:60.0:2.0:0.0056:0.0:1.0 -19 7168240 . C G 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.03778;SOR=0.0;LSEQ=ATTCCCTTAAGGGTCTCCTC;RSEQ=CCATGTGCCTGGCTGAGTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:0,9:0,18:0.3333:1,0:27.4:1.0:33.4:1.0:1.0:0.0:60.0:18.0:0.3462:0.0:1.0 0/0:11:0:0,0:0,11:0.0:0,0:26.5:1.0:32.0:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.3 -19 7172526 . C A 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTCCATGGTGAGAAGATAA;RSEQ=CCTCAGGCTGCAAATGACTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:26:0,26:0,40:0.3939:1,1:27.0:1.0:31.0:1.0:1.0:0.0:60.0:52.0:0.4:0.0:1.1 0/0:68:0:0,0:3,65:0.0:1,0:23.5:1.0:31.4:1.0:1.0:0.0:60.0:67.0:1.0:0.0:0.1 -19 7184238 . G A 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06618;LSEQ=AGCCAATTAACCCTGGGTTT;RSEQ=CACACAGTTTTAACAAGCGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:164:85:75,10:67,12:0.5183:2,2:23.6:1.0:28.6:1.0:0.64761:1.34:60.0:170.0:0.5247:0.0:2.2 0/1:182:12:9,3:145,23:0.0659:2,2:19.5:1.0:28.0:1.0:0.38522:2.09072:60.0:24.0:0.0674:0.0:2.0 -19 7184243 . C G 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.04718;LSEQ=ATTAACCCTGGGTTTGCACA;RSEQ=AGTTTTAACAAGCGGCATCG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:90:77,13:76,18:0.4891:2,2:24.6:1.0:32.3:1.0:0.43521:1.4:60.0:180.0:0.4891:0.0:2.1 0/1:210:9:6,3:165,36:0.0429:2,2:20.4:1.0:31.1:1.0:0.37274:2.28049:60.0:18.0:0.0429:0.0:2.3 -19 7184490 . G A 225 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.00535;LSEQ=GTCCTGGAAGTGGTAGTACG;RSEQ=GGGCGGGCAGGTCTCCACAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:174:65,109:122,191:0.3566:2,2:25.0:1.0:30.3:1.0:0.77081:1.07094:60.0:57.0:0.3563:0.0:1.1 0/0:679:2:2,0:290,387:0.0029:2,0:1.0:0.0:25.5:1.0:0.18458:0.0:60.0:4.0:0.003:0.0:1.0 -19 7805951 . A T 302 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00512;LSEQ=CATGTTTACAGTGTTTGGAA;RSEQ=GGAGCAGTGCAGGAGGGATG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1026:965:502,463:36,24:0.9405:2,2:24.9:1.0:30.5:1.0:0.28647:1.38303:60.0:73.231:0.9407:0.0:1.1 0/1:1239:92:50,42:582,565:0.0743:2,2:22.5:1.0:30.3:1.0:0.51757:1.16:60.0:91.0:0.0742:0.0:1.2 -19 7815587 . G C 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.07265;LSEQ=AAAATGATGAACGCAAAGGG;RSEQ=AAGAGGAGAGGCACCCAATA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:65:38:13,25:12,15:0.5846:2,2:21.7:1.0:32.6:1.0:0.44632:1.5281:59.9:76.0:0.5938:0.0:1.3 0/1:77:7:3,4:32,38:0.0909:2,2:26.3:1.0:32.7:1.0:1.0:1.12112:60.0:14.0:0.0909:0.0:1.1 -19 7815690 . G T 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=GTAAGAAAGGTGATATTGTA;RSEQ=ACATCAAGGGAATGGGTACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:15:11,4:30,14:0.2542:2,2:28.5:1.0:31.0:1.0:1.0:1.28:60.0:30.0:0.2632:0.0:1.0 0/0:56:0:0,0:39,17:0.0:2,0:21.8:1.0:31.3:1.0:1.0:0.0:59.6:27.0:1.0:0.0:0.3 -19 10260400 . T C 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01473;SOR=0.0;LSEQ=CAGATATGTGACCAAGTCTA;RSEQ=GCAGGAGCACTCGTCCTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:7:2,5:43,105:0.0452:2,2:25.0:1.0:30.9:1.0:1.0:1.02367:60.0:14.0:0.0467:0.0:1.0 0/0:148:0:0,0:60,88:0.0:2,0:23.8:1.0:29.9:1.0:1.0:0.0:60.0:73.0:1.0:0.0:0.1 -19 10278953 . T G 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTATTTTACCAAGATACTTA;RSEQ=GTTAGCAATTCAGTTTCACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:93:64,29:228,150:0.1975:2,2:26.5:1.0:32.0:1.0:0.15254:1.45:60.0:186.0:0.2009:0.0:1.1 0/0:585:0:0,0:357,227:0.0:2,0:22.6:1.0:29.4:1.0:1.0:0.0:60.0:63.889:1.0:0.0:0.1 -19 10287635 . A T 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=2.0;SSF=0.44444;SOR=0.0;LSEQ=CTAGAAATATACTAAACTAT;RSEQ=TATGGACAAAGTAATCCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:18.2:1.0:29.2:1.0:1.0:0.0:60.0:10.0:0.625:0.0:1.0 0/0:2:0:0,0:1,1:0.0:2,0:8.5:1.0:30.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -19 10292608 . C A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00478;SOR=0.0;LSEQ=TCCAAATTATCTTTGAAACT;RSEQ=CATGGGAAAAAATGCAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:7:7,0:68,4:0.0886:2,0:25.9:1.0:27.9:1.0:1.0:0.0:60.0:14.0:0.0886:0.0:1.0 0/0:87:0:0,0:79,8:0.0:2,0:23.1:1.0:30.6:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.1 -19 10292901 . C T 86 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06512;SOR=0.15027;LSEQ=TAAGCTGGCTTTTGTCTCCC;RSEQ=GCAAGAGTCTAGAGTGTCCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:7:0,7:1,33:0.1707:1,0:23.4:1.0:30.9:1.0:1.0:0.0:60.0:14.0:0.175:0.0:1.0 0/1:34:1:0,1:1,32:0.0294:1,0:50.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0294:0.0:1.0 -19 10305434 . C T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00435;SOR=0.0;LSEQ=CCGGCCACCCCGAGGGGAAG;RSEQ=GACCCCCCACCCAGCGCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:7:1,6:325,151:0.0144:2,2:8.0:1.0:27.1:1.0:0.00563:12.84973:60.0:14.0:0.0147:0.0:1.1 0/0:566:0:0,0:371,195:0.0:2,0:23.1:1.0:30.1:1.0:1.0:0.0:60.0:25.952:1.0:0.0:0.4 -19 10597746 . T A 73 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAAAAAAAAAATGGCCAGGC;RSEQ=TGGTAGCTCACGCCTATAAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:16.8:1.0:31.6:1.0:1.0:0.0:52.0:10.0:1.0:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 10600615 . C CT 78 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.03983;SOR=0.0;LSEQ=GCCAGATACTCTTTTTTTTC;RSEQ=TTTTTTTTTTCCCCCTTAAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:0,6:1,60:0.0896:1,0:21.3:1.0:30.5:1.0:1.0:0.0:60.0:12.0:0.0909:0.0:0.3 0/0:48:0:0,0:1,47:0.0:1,0:17.0:0.0:12.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -19 10600654 . G A 90 MAF0.05;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0536;SOR=0.12276;LSEQ=AAGAGACAGGTTCATCCGGC;RSEQ=CGATGGCTCATGCCTGTAAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:0,8:0,15:0.3478:1,0:19.1:1.0:30.0:1.0:1.0:0.0:57.9:16.0:0.3478:0.0:1.1 0/1:17:1:0,1:0,16:0.0588:1,0:44.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0667:0.0:1.0 -19 10610017 . G C 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07154;LSEQ=GGAGACAGTGATGAGCACTC;RSEQ=TCCATCCCTGGTCCTTCTCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:120:81,39:118,46:0.4225:2,2:22.1:1.0:30.3:1.0:0.43381:1.23417:60.0:23.0:0.4152:0.0:1.1 0/1:323:16:10,6:211,96:0.0495:2,2:20.6:1.0:30.4:1.0:0.59035:1.31762:60.0:32.0:0.0497:0.0:1.2 -19 11096829 . C T 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.06263;SOR=0.0;LSEQ=GTAAAAATCACAGACATATG;RSEQ=TGCCGAGTGACCAGTGGGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:1,4:341,152:0.01:2,2:15.6:1.0:27.8:1.0:0.03534:8.93213:60.0:10.0:0.0102:0.0:1.2 0/0:464:0:0,0:301,163:0.0:2,0:24.7:1.0:31.8:1.0:1.0:0.0:60.0:76.333:1.0:0.0:0.2 -19 11098455 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00664;SOR=0.0;LSEQ=TCCCACCCGCCGCCTCGCCC;RSEQ=TGATGCCACCGCAGACCCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:7:4,3:305,332:0.0109:2,2:17.6:1.0:25.6:1.0:0.71549:1.45:60.0:2.5:0.0079:0.0:1.7 0/0:671:0:0,0:315,353:0.0:2,0:1.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -19 11130431 . G A 210 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00549;LSEQ=GGCCGAGTGCTCACACGTGG;RSEQ=TCACGCTGCCCGTCTCCTCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:410:115:30,85:82,213:0.2805:2,2:24.1:1.0:30.7:1.0:0.8054:1.09056:60.0:114.0:0.2808:0.0:1.1 0/0:470:1:1,0:143,326:0.0021:2,0:1.0:0.0:24.0:0.0:0.30638:0.0:60.0:2.0:0.0022:0.0:1.0 -19 11138292 . A G 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00107;SOR=0.0;LSEQ=GCTTATTTCAGTTGGGGGAA;RSEQ=TGGCTTTGCTGAAGCTTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:19:19,0:24,0:0.4419:1,1:22.1:1.0:33.1:1.0:1.0:0.0:60.0:38.0:0.4524:0.0:1.1 0/0:15:0:0,0:13,2:0.0:2,0:19.5:1.0:29.2:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.4 -19 11144287 . AT A 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.07859;SOR=0.0;LSEQ=TTTACCTTTTTTGCACTCTT;RSEQ=TTTTTTTGCATCCCTTTGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:5:4,1:64,74:0.035:2,2:31.0:1.0:32.0:1.0:0.19117:4.58:60.0:10.0:0.0355:0.0:0.0 0/0:101:0:0,0:47,54:0.0:2,0:20.9:1.0:30.1:1.0:1.0:0.0:60.0:100.0:1.0:0.0:0.2 -19 11169305 . T C 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.07935;LSEQ=GCTGGGCCTCAGTCATGCAG;RSEQ=TCCCATGCCTAGTGAGCCAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:30:26,4:37,11:0.3846:2,2:26.9:1.0:32.3:1.0:0.38274:1.92:60.0:60.0:0.3846:0.0:1.4 0/1:43:2:2,0:36,4:0.0465:2,0:21.5:1.0:27.0:1.0:1.0:0.0:60.0:4.0:0.0476:0.0:1.0 -19 11172439 . C T 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.02795;SOR=0.12147;LSEQ=GGGTGGCCAACGCACACTCT;RSEQ=TCCTCCTGTCCCCTCTCCAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:7:3,4:373,241:0.0113:2,2:21.6:1.0:28.3:1.0:0.4427:2.06117:60.0:14.0:0.0114:0.0:1.1 0/0:724:1:0,1:423,300:0.0014:2,0:1.0:0.0:25.0:0.0:0.41575:0.0:60.0:2.0:0.0014:0.0:1.0 -19 13051554 . G T 261 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00312;LSEQ=TCGGTTTCCTTCTCCCTTCT;RSEQ=CAGGGTGAGTGGAAGCCCCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1333:418:204,214:448,467:0.3136:2,2:23.5:1.0:30.0:1.0:1.0:1.00634:60.0:51.25:0.3123:0.0:1.1 0/0:1401:2:0,2:733,660:0.0014:2,0:1.0:0.0:27.5:1.0:0.22502:0.0:60.0:4.0:0.0014:0.0:1.0 -19 14627140 . C T 263 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00127;LSEQ=ACGAAAGCTCCACAACAGCG;RSEQ=CCTGGTCAGTCCTGTTCACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1567:464:243,221:588,513:0.2961:2,2:23.0:1.0:29.8:1.0:0.73938:1.04242:60.0:153.667:0.2986:0.0:1.2 0/0:1895:1:1,0:978,915:0.0005:2,0:2.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.0005:0.0:1.0 -19 14629336 . G A 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00404;SOR=0.0;LSEQ=ATCGCCGCCGCCCTTTCAGC;RSEQ=ACACGCGACATCCGGGGCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:0,11:0,23:0.3235:1,0:11.5:1.0:31.1:1.0:1.0:0.0:60.0:22.0:0.3333:0.0:2.0 0/0:20:0:0,0:0,20:0.0:1,0:14.2:1.0:31.8:1.0:1.0:0.0:60.0:40.0:1.0:0.0:1.5 -19 15271135 . T G 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTAAAAAAAAAAAGAAAAA;RSEQ=AAAAATAATAATAATTCATT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:23.5:1.0:29.5:1.0:1.0:0.0:59.5:5.0:0.8333:0.0:1.5 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 15273576 . GTGTGTGTT G 116 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=13.0;MSILEN=2.0;SSF=0.05882;SOR=0.0;LSEQ=GAAGCACTTTGTGTCTGTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:0,13:0,10:0.5:0,1:19.9:1.0:31.5:1.0:1.0:0.0:58.5:26.0:0.5909:0.2692:1.7 0/0:6:0:0,0:0,6:0.0:0,0:12.8:1.0:27.5:1.0:1.0:0.0:60.0:5.0:1.0:0.0:1.5 -19 15288062 . G GGA 107 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=15.0;MSILEN=1.0;SSF=0.21429;SOR=0.0;LSEQ=AGAGCAAGACTCCATCTCGG;RSEQ=AAAAAAAAAAAAAAGTAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:11:11,0:7,0:0.5789:0,0:18.8:1.0:31.0:1.0:1.0:0.0:60.0:22.0:0.5789:0.2632:1.2 0/0:2:0:0,0:2,0:0.0:0,0:20.0:1.0:31.0:0.0:1.0:0.0:57.0:4.0:1.0:0.0:4.5 -19 15288072 . A T 109 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.0;MSILEN=1.0;SSF=0.05854;SOR=0.0;LSEQ=TCCATCTCGGGAAAAAAAAA;RSEQ=AAAAGTAATTATTGGATGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:12:12,0:13,0:0.48:1,0:21.6:1.0:30.6:1.0:1.0:0.0:60.0:11.0:0.4583:0.0:1.2 0/0:6:0:0,0:6,0:0.0:0,0:11.3:1.0:30.0:1.0:1.0:0.0:59.0:12.0:1.0:0.0:1.5 -19 15289366 . T G 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.50893;SOR=0.0;LSEQ=CCACTACGCCCGGCTAATTT;RSEQ=TATATTTTTAGTAGAGACGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:23.6:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.3846:0.0:1.0 0/0:3:0:0,0:3,0:0.0:0,0:23.0:1.0:30.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -19 15290491 . G A 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.01606;SOR=0.0;LSEQ=TCACCTGAGATCAGGAGTTC;RSEQ=AGACCAGCCTGGCCAACATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:13:2,11:3,13:0.4483:2,2:20.9:1.0:29.5:1.0:1.0:1.25893:57.2:12.0:0.4286:0.0:2.2 0/0:10:0:0,0:0,10:0.0:0,0:24.3:1.0:31.0:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.8 -19 15290648 . C T 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.28323;SOR=0.0;LSEQ=AGGTTGCAGTGAGCTGAGAT;RSEQ=GCGCCACTGCACTCGTCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:7,1:15,1:0.3333:1,2:30.1:1.0:31.3:1.0:1.0:2.07024:60.0:16.0:0.3333:0.0:1.0 0/0:5:0:0,0:4,1:0.0:2,0:11.6:1.0:30.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -19 15291576 . C G 256 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGGGGACAAAGGCAATAGG;RSEQ=CCCAGTCTGGACGCAGCGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:284:139,145:286,282:0.3326:2,2:25.7:1.0:31.5:1.0:0.71668:1.05786:60.0:46.333:0.3337:0.0:1.1 0/0:808:0:0,0:416,388:0.0:2,0:23.8:1.0:31.1:1.0:1.0:0.0:60.0:66.0:0.9975:0.0:0.2 -19 15291675 . TG T 82 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.03648;SOR=0.0;LSEQ=TCAGAGTCAGTACTGTGGGG;RSEQ=GGGGGTAGTCTGGGAGAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:6:2,4:159,253:0.0143:2,2:36.8:1.0:32.0:1.0:1.0:1.25623:55.8:12.0:0.0146:0.0:1.3 0/0:335:0:0,0:116,216:0.0:2,0:22.4:1.0:30.1:1.0:1.0:0.0:60.0:40.5:0.9908:0.0:0.2 -19 15291699 . T C 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GGGTAGTCTGGGAGAAACTG;RSEQ=GCCCCGACTTGGCTTCTCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:108:55,53:108,152:0.2935:2,2:18.7:1.0:30.8:1.0:0.10749:1.46:60.0:107.0:0.2972:0.0:1.1 0/0:251:0:0,0:106,144:0.0:2,0:22.4:1.0:29.9:1.0:1.0:0.0:60.0:249.0:1.0:0.0:0.1 -19 15296513 . C T 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=5.0;SSF=0.0;SOR=0.0;LSEQ=GGGGAGTACACAAGCAATCT;RSEQ=ATCTCAGAACAAAGTCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:153:48,105:101,245:0.306:2,2:24.8:1.0:28.2:1.0:0.67151:1.11:60.0:37.25:0.3028:0.0:1.1 0/0:434:0:0,0:135,298:0.0:2,0:23.3:1.0:31.0:1.0:1.0:0.0:60.0:85.6:1.0:0.0:0.1 -19 15299048 . G A 237 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCTCCTGAGGTCCTCACCC;RSEQ=AGGGGCAGGTGCAGCTGAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:254:151,103:320,205:0.3261:2,2:23.9:1.0:29.7:1.0:0.69652:1.06468:60.0:62.5:0.3255:0.0:1.1 0/0:718:0:0,0:403,315:0.0:2,0:24.4:1.0:29.8:1.0:1.0:0.0:60.0:78.778:1.0:0.0:0.2 -19 15308287 . G C 230 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCCACACACAGGGCCCACT;RSEQ=GTGGCTCTGAGCCAGGCACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:759:230:134,96:299,226:0.303:2,2:26.1:1.0:29.4:1.0:0.74977:1.05:60.0:16.692:0.3091:0.0:1.5 0/0:700:0:0,0:394,306:0.0:2,0:24.4:1.0:29.0:1.0:1.0:0.0:60.0:10.864:1.0:0.0:0.5 -19 15308545 . G A 119 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.0001;SOR=0.0489;LSEQ=CCCCCATCCACAGTTCCCAC;RSEQ=CCCCCCCCCCCCCCGCCCCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:28:0,28:1,21:0.4667:1,1:19.3:1.0:24.9:1.0:0.44:0.0:60.0:2.5:0.5405:0.0:1.9 0/1:25:1:0,1:0,23:0.04:1,0:42.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0455:0.0:1.0 -19 15311604 . GC G 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.06948;SOR=0.0;LSEQ=GTCCCGGCCCCTCACCTGCA;RSEQ=CCCCGGCCCCGCTAGCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:5:2,3:86,139:0.0217:2,2:30.0:1.0:32.6:1.0:1.0:1.08:60.0:10.0:0.0221:0.0:0.0 0/0:182:0:0,0:66,116:0.0:2,0:26.8:1.0:31.1:1.0:1.0:0.0:60.0:90.0:1.0:0.0:0.2 -19 15366663 . G A 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01284;SOR=0.0;LSEQ=ATCCTCCCCAACCAAACATG;RSEQ=TGAGCTCCGAAGGCTCATCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:18:16,2:27,4:0.3673:2,2:26.4:1.0:29.7:1.0:1.0:1.18:60.0:17.0:0.3542:0.0:1.2 0/0:13:0:0,0:11,2:0.0:2,0:25.6:1.0:30.8:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.0 -19 15890625 . CG GA 194 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01285;LSEQ=ATAGGTCCAGGCCAGGAAGC;RSEQ=GCCAGGAGCCGGGAGGCCCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:80:24,56:0,1:0.6107:0,2:21.8:1.0:30.7:1.0:1.0:0.0:60.0:160.0:0.6299:0.0763:1.0 0/1:103:2:1,1:10,19:0.0194:2,2:17.0:1.0:26.3:1.0:1.0:1.86:60.0:4.0:0.0198:0.0097:0.5 -19 15890725 . G T 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00255;SOR=0.0;LSEQ=AGGCTCAGCTGCGGCATCCT;RSEQ=CAGGGCAGACAGGATGGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:0,10:0,6:0.625:0,0:17.3:1.0:29.8:1.0:1.0:0.0:60.0:20.0:0.625:0.0:1.0 0/0:10:0:0,0:0,10:0.0:0,0:26.3:1.0:31.3:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.6 -19 17953950 . G C 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTTGAGACTGAGGCCCACG;RSEQ=GGAGGCGCCCACTCACCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:35:11,24:203,317:0.0631:2,2:24.0:1.0:30.0:1.0:0.47356:1.39638:60.0:34.0:0.0622:0.0:1.1 0/0:586:0:0,0:252,333:0.0:2,0:29.0:0.0:12.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 -19 18266882 . C T 57 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.02956;SOR=0.0;LSEQ=CCGGCCTCAACGAGCGCACA;RSEQ=GGCAGCGAGGTGACTTCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:5:1,4:186,258:0.0111:2,2:9.6:1.0:24.8:1.0:0.4069:2.87788:60.0:4.0:0.009:0.0:1.0 0/0:458:0:0,0:204,254:0.0:2,0:25.4:1.0:30.0:1.0:1.0:0.0:60.0:75.333:1.0:0.0:0.3 -19 18271576 . C T 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=8e-05;SOR=0.0;LSEQ=TGACCAGGCCACTGCATGTG;RSEQ=TGTGCCCTCTCCCAGTTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:17:12,5:37,13:0.2537:2,2:32.5:1.0:30.9:1.0:0.76166:1.1828:60.0:34.0:0.2615:0.0:1.0 0/0:45:0:0,0:37,8:0.0:2,0:21.3:1.0:32.1:1.0:1.0:0.0:60.0:90.0:1.0:0.0:0.2 -19 18277820 . C G 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0028;SOR=0.0;LSEQ=GCCAGACATGGTGGTGCACA;RSEQ=CTGTGGTCCCAGCTACTCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:11:10,1:90,0:0.1089:1,2:23.3:1.0:32.9:1.0:0.10891:0.0:60.0:22.0:0.11:0.0:1.1 0/0:73:0:0,0:72,1:0.0:1,0:26.6:1.0:31.3:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 -19 18279861 . C T 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00696;SOR=0.10003;LSEQ=GGAAAGCTTGGCGGGGAGGC;RSEQ=AGCCTTCCGACTCCCCCTCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:11:6,5:221,105:0.0325:2,2:19.3:1.0:28.0:1.0:0.34764:1.75087:60.0:22.0:0.0327:0.0:1.2 0/0:299:1:0,1:192,106:0.0033:2,0:1.0:0.0:24.0:0.0:0.35786:0.0:60.0:2.0:0.0034:0.0:1.0 -19 18280096 . G A 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.05158;LSEQ=GCCCCGGCCCGCCGCCTGCC;RSEQ=CCCGCTGAGCACCGAGGACC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:23:7,16:14,35:0.3194:2,2:19.3:1.0:29.5:1.0:1.0:1.09:60.0:22.0:0.3099:0.0:1.5 0/1:86:2:0,2:30,54:0.0233:2,0:11.0:1.0:31.5:1.0:0.54036:0.0:60.0:4.0:0.0238:0.0:1.0 -19 19256768 . TG T 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.06176;SOR=0.0;LSEQ=CGCTCAGACTTGATGCTGAC;RSEQ=GGGGGGTCGGCGGGGAGGCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:5:2,3:156,247:0.0122:2,2:30.6:1.0:31.8:1.0:1.0:1.06:60.0:10.0:0.0123:0.0:0.0 0/0:404:0:0,0:180,224:0.0:2,0:23.6:1.0:30.7:1.0:1.0:0.0:60.0:201.0:1.0:0.0:0.3 -19 19260105 . T C 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTACTTCAGCAGCACACGG;RSEQ=CCATGTCCGTGCTGGCATAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:24:9,15:333,321:0.0353:2,2:27.2:1.0:31.8:1.0:0.21768:1.72759:60.0:48.0:0.036:0.0:1.1 0/0:642:0:0,0:332,310:0.0:2,0:23.2:1.0:28.8:1.0:1.0:0.0:60.0:52.5:1.0:0.0:0.2 -19 27732195 . G T 71 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00307;SOR=0.0;LSEQ=GGAGATTTCAGCCGCTTTGA;RSEQ=GTCAGTGGTAGAAAAGGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:5:2,3:20,26:0.0962:2,2:32.8:1.0:31.0:1.0:1.0:1.15064:38.2:10.0:0.0962:0.0:5.4 0/0:109:0:0,0:51,51:0.0:2,0:22.6:1.0:30.8:1.0:1.0:0.0:44.6:101.0:0.9352:0.0:4.3 -19 27736207 . G C 78 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01786;SOR=0.0;LSEQ=GAACCTTCCTTTAGACAGAG;RSEQ=AGATTTAAAACACTCTTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1.0:0,2:15.8:1.0:33.6:1.0:1.0:0.0:35.2:10.0:1.0:0.0:6.6 0/0:3:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 28778494 . A G 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=3.0;SSF=0.00296;SOR=0.0;LSEQ=TCATCGTCATCATCATCATC;RSEQ=TCATCGTCAACATCATCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:7,8:2,2:0.7895:2,2:23.0:1.0:29.9:1.0:1.0:1.13484:60.0:30.0:0.8333:0.0:3.7 0/0:5:0:0,0:1,1:0.0:2,0:11.5:1.0:27.0:1.0:1.0:0.0:60.0:4.0:0.4:0.0:0.0 -19 30311555 . CCCCT TC 115 MSI6 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=12.0;MSILEN=1.0;SSF=0.0002;SOR=0.0;LSEQ=ATTACAAGTTTTTTTTTTTT;RSEQ=CCCTCAAGTAAAACTTACTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:17:15,2:188,30:0.0714:2,2:18.5:1.0:28.3:1.0:1.0:1.2:59.1:16.0:0.0727:0.0336:1.2 0/0:153:0:0,0:127,24:0.0:2,0:21.8:1.0:29.3:1.0:1.0:0.0:59.6:12.727:0.9929:0.0:0.4 -19 30312874 . C T 245 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00495;LSEQ=GAACTTCTTTTCTCAATCAT;RSEQ=GGTCTCTTTTCTCTCTGTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:297:187,110:299,193:0.3764:2,2:24.5:1.0:29.9:1.0:0.54666:1.1:60.0:58.4:0.3763:0.0:1.1 0/0:673:2:0,2:407,264:0.003:2,0:1.0:0.0:25.5:1.0:0.15586:0.0:60.0:4.0:0.003:0.0:1.0 -19 30313622 . G T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01107;SOR=0.0;LSEQ=GCACTTTGGGAGGCCGAGGT;RSEQ=GGCCGATCACTTGAGGCCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:0,9:1,78:0.1023:1,0:26.7:1.0:29.9:1.0:1.0:0.0:60.0:18.0:0.1059:0.0:1.2 0/0:60:0:0,0:0,60:0.0:1,0:27.7:1.0:30.6:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.6 -19 33792520 . G A 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.04963;SOR=0.13997;LSEQ=GCCTTGCCCGCGCCGCTGCC;RSEQ=CCACTCGCGCGGAGGTCGGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:793:9:6,3:240,544:0.0113:2,2:17.1:1.0:30.0:1.0:0.02911:4.52:60.0:18.0:0.0116:0.0:1.3 0/0:624:1:1,0:215,408:0.0016:2,0:1.0:0.0:25.0:0.0:0.34615:0.0:60.0:2.0:0.0016:0.0:1.0 -19 33792731 . G GGCGGGT 148 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=21;MSI=4.0;MSILEN=6.0;SSF=0.0;SOR=0.0;LSEQ=GGGCGGCCAGGTGCGCGGGC;RSEQ=GCGGGTGCGGGTGCGGGTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:28:16,12:134,142:0.0918:2,2:15.7:1.0:30.9:1.0:0.4315:1.41:59.3:56.0:0.093:0.0492:0.3 0/0:253:0:0,0:121,132:0.0:2,0:14.0:1.0:29.9:1.0:1.0:0.0:59.6:83.333:1.0:0.0:0.3 -19 33792751 . C T 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=6.0;SSF=0.08048;SOR=0.0;LSEQ=GGCGGGTGCGGGTGCGGGTG;RSEQ=GAGGGCGGCGGCGGCGGCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:279:5:2,3:149,122:0.0179:2,2:6.0:1.0:28.0:1.0:0.66126:1.82793:60.0:10.0:0.0182:0.0:1.2 0/0:196:0:0,0:106,88:0.0:2,0:13.2:1.0:30.2:1.0:1.0:0.0:59.8:31.333:0.9895:0.0:0.3 -19 33905969 . G A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00832;SOR=0.0;LSEQ=CCACATGGCAAGCCCTGTGC;RSEQ=CCAGGCCAGACAGGCAGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:8,1:24,2:0.2571:2,2:27.4:1.0:30.8:1.0:1.0:1.48133:60.0:18.0:0.2571:0.0:1.1 0/0:23:0:0,0:19,4:0.0:2,0:25.0:1.0:28.3:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.6 -19 34080443 . CC TT 161 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTGACACTTGTGAGGCATT;RSEQ=TTTTTGAACAGTGCCCATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:39:14,25:26,39:0.3679:2,2:27.5:1.0:30.5:1.0:0.8353:1.18849:59.5:78.0:0.3786:0.0:1.3 0/0:81:0:0,0:39,42:0.0:2,0:20.4:1.0:30.6:1.0:1.0:0.0:59.7:80.0:1.0:0.0:0.3 -19 39538680 . G A 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGATTTGAGGGTGCCCACAG;RSEQ=ATTTGCTGAAGAATTGGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:21:6,15:18,93:0.1591:2,2:22.3:1.0:30.0:1.0:0.21631:2.05:60.0:42.0:0.1603:0.0:2.1 0/0:108:0:0,0:28,80:0.0:2,0:23.2:1.0:30.9:1.0:1.0:0.0:60.0:216.0:1.0:0.0:0.7 -19 40739513 . A G 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00202;SOR=0.0;LSEQ=TTGTGTGGATTAAAACCTGA;RSEQ=TCTCCAACCGCCCAACAGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:29.1:1.0:31.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:4:0:0,0:3,1:0.0:2,0:27.5:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -19 41173904 . TTGC T 85 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.0;MSILEN=3.0;SSF=0.04835;SOR=0.0;LSEQ=TGCTGCTGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:7:2,5:50,52:0.0642:2,2:28.9:1.0:30.3:1.0:0.44118:2.38569:60.0:14.0:0.0667:0.0:0.0 0/0:63:0:0,0:28,35:0.0:2,0:25.3:1.0:29.7:1.0:1.0:0.0:58.7:62.0:1.0:0.0:0.9 -19 41727143 . G C 222 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTCCCAGCCTGGCTATGTTG;RSEQ=GCTGGAGGGTGAGCTCTGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:845:154:63,91:276,415:0.1822:2,2:26.8:1.0:30.6:1.0:0.8559:1.04:60.0:153.0:0.1841:0.0:1.1 0/0:749:0:0,0:313,432:0.0:2,0:25.1:1.0:30.0:1.0:1.0:0.0:60.0:42.824:0.9945:0.0:0.2 -19 41727197 . C T 192 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGGGTCAGAGGACATGTGG;RSEQ=GCTCATAGGTTGTGGGAAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:87:16,71:46,240:0.2332:2,2:22.7:1.0:29.9:1.0:0.62336:1.18:59.9:86.0:0.2356:0.0:1.1 0/0:274:0:0,0:65,209:0.0:2,0:23.3:1.0:29.4:1.0:1.0:0.0:60.0:29.444:1.0:0.0:0.1 -19 41727231 . GGGTCAA G 164 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGAAGTCAGGAATCCTGAG;RSEQ=GGTCAAAGGGTGCTGGAGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:39:3,36:6,142:0.2074:1,2:27.4:1.0:31.1:1.0:0.39773:1.96:60.0:38.0:0.2077:0.0266:0.9 0/0:119:0:0,0:8,111:0.0:2,0:21.1:1.0:29.9:1.0:1.0:0.0:60.0:58.5:1.0:0.0:0.1 -19 41748982 . G A 66 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.07602;SOR=0.0;LSEQ=GAGAGGCTGGAGGCAGGGAG;RSEQ=CCAGTGAGGAGGCTGGTGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:5:3,2:74,305:0.013:2,2:16.0:1.0:28.6:1.0:0.05711:6.14:60.0:10.0:0.0133:0.0:1.0 0/0:283:0:0,0:58,225:0.0:2,0:22.4:1.0:31.7:1.0:1.0:0.0:60.0:93.333:1.0:0.0:0.1 -19 41749397 . C T 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00042;SOR=0.0;LSEQ=GTAGCTGCCCAAGGCATGCT;RSEQ=AGCAAATGTTAGCACAGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:17:17,0:219,5:0.0705:1,1:25.9:1.0:30.9:1.0:1.0:0.0:60.0:34.0:0.0723:0.0:1.1 0/0:146:0:0,0:141,5:0.0:1,0:26.8:1.0:31.6:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 -19 41749511 . TC T 115 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.00022;SOR=0.0;LSEQ=CTGCCCTCACCTACTCCCCC;RSEQ=CCCCCCAGAGAAGTGTTTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1347:14:9,5:706,626:0.0104:2,2:20.6:1.0:30.4:1.0:0.43436:1.6:60.0:28.0:0.0106:0.0015:0.1 0/0:1118:0:0,0:594,523:0.0:2,0:24.6:1.0:30.6:1.0:1.0:0.0:60.0:43.68:1.0:0.0:0.2 -19 41759474 . C T 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGCATCAAGGACTCTGTTGA;RSEQ=CTCTCCTCCCACCTGCCTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:55:38,17:410,181:0.0851:2,2:21.6:1.0:30.3:1.0:1.0:1.01336:60.0:26.5:0.0837:0.0:1.1 0/0:516:0:0,0:328,188:0.0:2,0:23.2:1.0:30.9:1.0:1.0:0.0:60.0:128.0:1.0:0.0:0.2 -19 41763269 . A T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.16004;SOR=0.0;LSEQ=AAAGTATTATGTTTCTATGA;RSEQ=TACTTGTGATGCTCCCAGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:5:5,0:152,1:0.0316:1,0:26.2:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.0318:0.0:1.0 0/0:102:0:0,0:100,2:0.0:1,0:19.2:1.0:30.5:1.0:1.0:0.0:60.0:101.0:1.0:0.0:0.2 -19 42382729 . C G 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAGGGCCAGAGTACAAAGTG;RSEQ=GTATGCGGGAGGGGGACAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:1.0:0,0:17.4:1.0:32.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 42382745 . A G 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGTGCGTATGCGGGAGGGGG;RSEQ=CAAGAGATGGCGCTGCAGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:26.2:1.0:27.8:1.0:1.0:0.0:60.0:4.0:0.5:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -19 42790821 . G C 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00124;SOR=0.0;LSEQ=GGTGTTGGGGGTGGGGGGTA;RSEQ=ACAAAAGGGGTGGGGCTACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:13:13,0:310,10:0.0388:1,1:17.5:1.0:31.3:1.0:1.0:0.0:60.0:26.0:0.0405:0.0:1.0 0/0:226:0:0,0:213,12:0.0:2,0:17.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:8.0 -19 42791015 . C A 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04928;LSEQ=GCCAGCCTGACCCCTCCGTG;RSEQ=AGCCGAGCGAGGCCCAGCAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1164:55:24,31:474,635:0.0473:2,2:23.6:1.0:29.9:1.0:0.89003:1.04:60.0:54.0:0.0469:0.0:1.1 0/0:821:2:2,0:345,472:0.0024:2,0:1.0:0.0:25.0:0.0:0.17921:0.0:60.0:4.0:0.0024:0.0:1.0 -19 42795554 . T C 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCAACGGCAAAGTCCTGGC;RSEQ=GCCACTGCACCCACTCCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:198:109,89:583,550:0.1486:2,2:25.9:1.0:29.8:1.0:0.35613:1.16:60.0:32.0:0.1468:0.0:1.1 0/0:1079:0:0,0:549,528:0.0:2,0:23.0:0.0:9.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:7.0 -19 42797603 . C T 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.04102;SOR=0.0;LSEQ=CTCCTCTCCCATCTGAGGCC;RSEQ=CTGTCTTGGCCTTCCTGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:15:7,8:56,37:0.1389:2,2:28.2:1.0:31.1:1.0:0.40085:1.72069:60.0:30.0:0.1429:0.0:1.2 0/0:30:0:0,0:23,7:0.0:2,0:23.9:1.0:30.6:1.0:1.0:0.0:60.0:60.0:1.0:0.0:0.0 -19 45856260 . G A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGGGGTGGGTGGTTCCCC;RSEQ=CGGGAGCAGACAGCAGAGCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:27:19,8:249,94:0.073:2,2:22.3:1.0:29.8:1.0:0.82419:1.115:60.0:54.0:0.074:0.0:1.3 0/0:276:0:0,0:196,80:0.0:2,0:23.6:1.0:29.9:1.0:1.0:0.0:60.0:68.0:1.0:0.0:0.2 -19 45868647 . G A 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01084;SOR=0.0;LSEQ=CACTTTGTGAGGCTGAGGTG;RSEQ=GCAGATCACGAGGTCAGGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:0,10:0,4:0.7143:0,0:27.2:1.0:31.2:1.0:1.0:0.0:54.4:20.0:0.7143:0.0:2.0 0/0:6:0:0,0:0,6:0.0:0,0:20.3:1.0:30.5:1.0:1.0:0.0:58.0:12.0:1.0:0.0:0.3 -19 46376217 . C A 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06619;SOR=0.0;LSEQ=GAACAGACACCAGCACCTCC;RSEQ=AAACTGGACGTGGGGTTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:2,3:10,19:0.1471:2,2:24.8:1.0:30.0:1.0:1.0:1.26:60.0:10.0:0.1471:0.0:1.0 0/0:25:0:0,0:11,14:0.0:2,0:25.7:1.0:28.7:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.1 -19 50906507 . C T 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCACGCCCCACACCATTT;RSEQ=CCGGGGTCCCCGCCAGCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:719:63:20,43:275,381:0.0876:2,2:24.1:1.0:29.6:1.0:0.1401:1.55092:60.0:62.0:0.0879:0.0:1.1 0/0:692:0:0,0:272,419:0.0:2,0:21.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:7.0 -19 50910196 . A G 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.02128;LSEQ=CTTCTCCTGCTCCACCTCCC;RSEQ=CCCCCAACCCCTGGTCCCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:792:81:60,21:469,240:0.1023:2,2:26.8:1.0:27.9:1.0:0.17081:1.46:60.0:12.5:0.1015:0.0:1.1 0/0:829:2:1,1:513,307:0.0024:2,2:25.5:1.0:11.5:1.0:1.0:1.66985:60.0:0.0:0.0:0.0:4.0 -19 50912821 . G C 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACAGACCCCCTCCGGCGCCA;RSEQ=GTCCTGGATGGACGGCAGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1184:136:68,68:545,502:0.1149:2,2:25.0:1.0:31.0:1.0:0.71535:1.08558:60.0:135.0:0.1152:0.0:1.1 0/0:1116:0:0,0:544,567:0.0:2,0:23.5:1.0:30.8:1.0:1.0:0.0:60.0:68.438:0.9955:0.0:0.2 -19 50920581 . T C 53 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.064;SOR=0.0;LSEQ=CCCTTCCCAGCTCCCAGGCC;RSEQ=GTGGGTTGTGGACCCAACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:5:3,2:127,287:0.0119:2,2:13.6:1.0:23.2:1.0:0.17567:3.38:60.0:1.5:0.0074:0.0:1.6 0/0:373:0:0,0:142,227:0.0:2,0:24.4:1.0:29.7:1.0:1.0:0.0:60.0:40.0:0.989:0.0:0.2 -19 52693297 . C CT 173 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTCCCAGCATTGCCCCCCC;RSEQ=ACGTTTCAGCACAGCGCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:55:39,16:98,41:0.2821:2,2:24.4:1.0:30.0:1.0:1.0:1.02:60.0:110.0:0.288:0.0564:0.3 0/0:166:0:0,0:128,38:0.0:2,0:22.8:1.0:29.6:1.0:1.0:0.0:59.5:32.2:1.0:0.0:0.4 -19 52714917 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.0;MSILEN=1.0;SSF=0.06636;SOR=0.0;LSEQ=GAGAGTTGGTCTCTGGACAC;RSEQ=GCCACGTGTCAGTTTACCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:0.375:0,0:15.3:1.0:31.7:1.0:1.0:0.0:60.0:12.0:0.375:0.0:2.3 0/0:8:0:0,0:0,8:0.0:0,0:23.5:1.0:29.4:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.0 -19 53081735 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01409;SOR=0.0;LSEQ=TTTGGGGCCACTACCTGTCT;RSEQ=CGCGTCTTGATGGTAGTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:1,5:1,4:0.5455:2,2:27.8:1.0:29.8:1.0:1.0:1.22474:60.0:12.0:0.5455:0.0:1.0 0/0:9:0:0,0:3,6:0.0:2,0:24.1:1.0:31.3:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.1 -2 6636414 . G A 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATGGGACACGCTGACGGTT;RSEQ=ATTCCAAACGTGGTCTTGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:982:54:22,32:447,481:0.055:2,2:25.3:1.0:29.4:1.0:0.32763:1.35131:60.0:108.0:0.0558:0.0:2.0 0/0:706:0:0,0:349,356:0.0:2,0:24.8:1.0:31.3:1.0:1.0:0.0:59.9:77.333:0.9986:0.0:0.6 -2 6636735 . G A 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=CCACAGGACGTCCATGAGCC;RSEQ=GATCGTCTGCATGGTCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:20:10,10:306,322:0.0308:2,2:31.2:1.0:30.4:1.0:1.0:1.05:60.0:19.0:0.0299:0.0:2.1 0/0:443:0:0,0:217,226:0.0:2,0:26.5:1.0:29.6:1.0:1.0:0.0:60.0:62.286:1.0:0.0:1.0 -2 7541718 . C G 181 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGATTCATAAAAAAAAAAG;RSEQ=AAAATGTTCTCTCTTTTCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:59:49,10:104,29:0.3026:2,2:24.4:1.0:30.8:1.0:0.56038:1.36:60.0:28.5:0.3167:0.0:2.9 0/0:193:0:0,0:146,46:0.0:2,0:23.3:1.0:31.1:1.0:1.0:0.0:60.0:23.0:1.0:0.0:1.3 -2 14528089 . C T 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TCATCCTCCTTTCTCTTTCC;RSEQ=TCTCTTTCTCTCATCTCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:42:13,29:119,250:0.1019:2,2:24.9:1.0:29.6:1.0:1.0:1.0617:60.0:20.0:0.1003:0.0:1.2 0/0:308:0:0,0:106,201:0.0:2,0:23.7:1.0:31.1:1.0:1.0:0.0:59.9:152.5:0.9967:0.0:0.6 -2 16085519 . C T 94 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.10683;SOR=0.0;LSEQ=AGCAGTCTGCCAGGGTCTGC;RSEQ=GGAAGAGACAGATAAGCATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:8:8,0:83,1:0.087:1,0:19.0:1.0:31.5:1.0:1.0:0.0:60.0:16.0:0.0879:0.0:1.1 0/0:34:0:0,0:34,0:0.0:1,0:22.4:1.0:30.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.2 -2 16086469 . C T 73 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACAGCGCTAAACGTTGGTGA;RSEQ=GGTTGGGAGCCTCTGGGGCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:30.8:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 17675655 . TTTTCA T 80 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.03383;SOR=0.0;LSEQ=GGCCAGTGATGATGACCATT;RSEQ=TGCCTGACACCCTATTCTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:6:4,2:97,44:0.0405:2,2:32.5:1.0:31.2:1.0:1.0:1.10153:60.0:12.0:0.0408:0.0:0.0 0/0:122:0:0,0:73,49:0.0:2,0:22.4:1.0:29.6:1.0:1.0:0.0:59.4:121.0:1.0:0.0:0.6 -2 21324997 . C A 71 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.02735;SOR=0.0;LSEQ=GGAGAAGCCATGTTGCCCAA;RSEQ=TCCAGAGGTTGGTATAAGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:5:3,2:26,27:0.0862:2,2:22.8:1.0:30.8:1.0:1.0:1.55:23.0:10.0:0.0862:0.0:5.0 0/0:59:0:0,0:25,34:0.0:2,0:30.2:1.0:30.5:1.0:1.0:0.0:51.7:28.5:1.0:0.0:0.3 -2 21325009 . G A 77 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.02743;SOR=0.0;LSEQ=TTGCCCAACTCCAGAGGTTG;RSEQ=TATAAGAGTTTGAAAGGTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:6:3,3:22,29:0.1053:2,2:31.0:1.0:29.8:1.0:1.0:1.31:23.0:12.0:0.1053:0.0:5.0 0/0:54:0:0,0:22,32:0.0:2,0:28.8:1.0:30.3:1.0:1.0:0.0:50.9:26.0:1.0:0.0:0.3 -2 21325028 . A T 77 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.02717;SOR=0.0;LSEQ=GGTATAAGAGTTTGAAAGGT;RSEQ=TTGTCTGATTTCAGAAGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:6:3,3:19,28:0.1132:2,2:36.2:1.0:29.8:1.0:0.6834:1.46:23.0:12.0:0.1132:0.0:5.0 0/0:50:0:0,0:20,30:0.0:2,0:19.1:1.0:28.4:1.0:1.0:0.0:52.4:49.0:1.0:0.0:0.3 -2 21325039 . T C 80 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03015;SOR=0.0;LSEQ=TTGAAAGGTATTGTCTGATT;RSEQ=CAGAAGCCTTTTCCTGTAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:6:3,3:15,21:0.1429:2,2:34.2:1.0:31.2:1.0:1.0:1.39:23.0:12.0:0.1429:0.0:5.0 0/0:34:0:0,0:11,23:0.0:2,0:19.9:1.0:28.8:1.0:1.0:0.0:55.7:68.0:1.0:0.0:0.1 -2 25466810 . C T 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02818;LSEQ=GACAGCACCCGGATGGGCTT;RSEQ=CTCTTCTCAGCTGGGACAGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1076:40:18,22:479,556:0.0372:2,2:26.1:1.0:29.9:1.0:1.0:1.05292:60.0:80.0:0.0384:0.0:1.2 0/0:921:1:0,1:425,492:0.0011:2,0:1.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 -2 25469945 . C T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02597;SOR=0.13163;LSEQ=GGACCTCGTAGATGGCTTTG;RSEQ=GGTACATGGGCTGCTTGTTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:9:2,7:467,396:0.0103:2,2:11.0:1.0:28.4:1.0:0.08922:4.12164:60.0:18.0:0.0105:0.0:1.2 0/0:731:1:1,0:391,336:0.0014:2,0:47.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0014:0.0:2.0 -2 25471169 . GC G 216 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.1406;LSEQ=CTTGACCTCTCCAGGAATTA;RSEQ=AAGGCCACCTGACACTCAAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:118:18,100:33,208:0.3278:2,2:20.1:1.0:31.4:1.0:0.74801:1.13:60.0:117.0:0.3296:0.0694:0.2 0/1:250:16:4,12:40,194:0.064:2,2:18.4:1.0:30.8:1.0:0.4938:1.61:60.0:32.0:0.0643:0.012:0.4 -2 25972936 . C T 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTCTCAGATTCCTGTTCAG;RSEQ=AGAGGTGACTGGCTTCTGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:991:73:34,39:467,448:0.0737:2,2:22.3:1.0:28.6:1.0:0.46872:1.19549:60.0:72.0:0.0735:0.0:1.1 0/0:785:0:0,0:374,409:0.0:2,0:24.1:1.0:31.8:1.0:1.0:0.0:60.0:77.3:0.9974:0.0:0.1 -2 27014885 . G A 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01523;SOR=0.0;LSEQ=TAAAACAGACAAAAATCCCT;RSEQ=CTCTGTGGAGGGTAGGCACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:10:10,0:163,3:0.0568:1,0:30.8:1.0:27.8:1.0:1.0:0.0:60.0:20.0:0.0575:0.0:1.6 0/0:108:0:0,0:107,1:0.0:1,0:20.5:1.0:31.5:1.0:1.0:0.0:60.0:35.0:1.0:0.0:0.2 -2 29415792 . G A 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGCAGAGCACACACAATTT;RSEQ=AAAGAAGCATAAGGAAGTAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1.0:0,0:26.0:1.0:26.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 29429741 . C CTT 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.28571;SOR=0.0;LSEQ=GTGGCTGTTAATGTGTGGTC;RSEQ=CAGCCAGCAATGGCAGCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:28.8:1.0:30.6:1.0:1.0:0.0:60.0:10.0:0.8333:0.1667:0.4 0/0:1:0:0,0:1,0:0.0:0,0:21.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -2 29429948 . C T 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02378;LSEQ=TTTCCCTCCCTACTAACACA;RSEQ=GGGCTCCCGGCTTAGAGTAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:57:48,9:267,37:0.1579:2,2:24.1:1.0:30.5:1.0:0.51498:1.35182:60.0:56.0:0.1569:0.0:1.1 0/0:226:1:1,0:180,45:0.0044:2,0:2.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0045:0.0:1.0 -2 29437182 . T C 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04396;SOR=0.0;LSEQ=GTATTTGTACATTTGAAGTC;RSEQ=TCCCAGGTAATATGATGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:1,8:0,3:0.75:0,2:21.8:1.0:32.1:1.0:1.0:0.0:60.0:18.0:0.75:0.0:1.3 0/0:3:0:0,0:0,3:0.0:0,0:14.0:1.0:32.0:0.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -2 29445798 . T C 106 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGCTTTTCCCCGGGGGAGG;RSEQ=TCATGCTCCTTGGGGAGAGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:6,6:0,0:1.0:0,2:25.1:1.0:29.8:1.0:1.0:0.0:60.0:11.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 29449423 . G A 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCACATGCACAGCTGCTGCT;RSEQ=TAAGGAAACCTAGGAGAGGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:9,0:5,0:0.6429:0,0:21.3:1.0:25.4:1.0:1.0:0.0:57.6:8.0:0.6154:0.0:1.9 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 29451354 . A G 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCAGGAAGCTGGTGGGCTG;RSEQ=GGTAGGGAGCAGGAGTAAGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1.0:0,2:16.4:1.0:31.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 29451557 . GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G 77 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.0;MSILEN=1.0;SSF=0.33914;SOR=0.0;LSEQ=GCTGTCGCTGAGGAAGCCTG;RSEQ=AGGCAGGTCGAGAGGGAGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:6:6,0:64,0:0.0857:1,0:28.8:1.0:30.0:1.0:1.0:0.0:60.0:12.0:0.0896:0.0857:0.5 0/0:18:0:0,0:18,0:0.0:1,0:26.3:1.0:29.4:1.0:1.0:0.0:60.0:17.0:1.0:0.0:0.4 -2 29451670 . AGGGGA G 97 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=4;MSI=4.0;MSILEN=1.0;SSF=0.03551;SOR=0.0;LSEQ=TGGGCAGGCCAGGGGAGGGC;RSEQ=GGGCAGGGCAGGGAGGTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:10:6,4:440,101:0.0181:2,2:5.7:1.0:29.4:1.0:0.10292:2.8969:60.0:20.0:0.0185:0.0163:0.1 0/0:264:0:0,0:206,57:0.0:2,0:22.6:1.0:29.3:1.0:1.0:0.0:60.0:31.875:1.0:0.0:0.2 -2 29451675 . A AGGGCG 146 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=AGGCCAGGGGAGGGCAGGGG;RSEQ=GGGCAGGGCAGGGAGGTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:590:25:23,2:430,128:0.0424:2,2:27.0:1.0:31.6:1.0:0.0884:3.42:60.0:50.0:0.0441:0.0051:0.1 0/0:300:0:0,0:218,81:0.0:2,0:22.3:1.0:28.6:1.0:1.0:0.0:60.0:32.222:1.0:0.0:0.1 -2 29451986 . C T 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00037;SOR=0.0;LSEQ=GCTGGCAAGGTTCAATTAGC;RSEQ=ATGCTGGCCAGAGAAGCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:19:2,17:45,302:0.0519:2,2:24.5:1.0:28.5:1.0:1.0:1.2658:60.0:38.0:0.0528:0.0:1.1 0/0:189:0:0,0:29,160:0.0:2,0:21.0:1.0:31.3:1.0:1.0:0.0:60.0:62.0:1.0:0.0:0.2 -2 29454901 . G GCAAGTTGGTAAAACC 103 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGGGGAGGCTCTAACAATT;RSEQ=CAGGGAGGGCCAGCTGGCTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:11,0:6,1:0.6111:2,0:17.2:1.0:29.8:1.0:0.38889:0.0:58.2:22.0:0.6471:0.3889:0.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 29456384 . T C 261 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGTCATGAGGCTCTGACAT;RSEQ=GCAGATGCACAGGAACCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1305:371:240,131:602,332:0.2843:2,2:24.9:1.0:30.6:1.0:0.94895:1.01:60.0:184.5:0.2856:0.0:1.1 0/0:813:0:0,0:437,297:0.0:2,0:37.0:0.0:17.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 -2 29456865 . T TG 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=9.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGAAGGATAGGGAGTTTTT;RSEQ=TTTGTTTGTTTTTGTTTTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:0.4545:0,0:29.2:1.0:30.6:1.0:1.0:0.0:60.0:10.0:0.4545:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 29456882 . T C 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTTTTTTGTTTGTTTTTGTT;RSEQ=TTTTCACAGAGAGTGGGGCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:32.6:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 29519851 . C A 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02259;LSEQ=CATCCTGCCTTGCTCCTTCC;RSEQ=GGTTTTGTTCTCCACTAGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1148:51:22,29:524,573:0.0444:2,2:25.6:1.0:30.2:1.0:0.56769:1.20526:60.0:50.0:0.0438:0.0:1.1 0/0:954:1:1,0:439,512:0.001:2,0:1.0:0.0:26.0:0.0:0.46218:0.0:60.0:2.0:0.0011:0.0:1.0 -2 29940332 . A G 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00842;SOR=0.0;LSEQ=GAAAGACTTCTTTTGCATAT;RSEQ=GGGAGCTGAGGGAATGCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:12:12,0:83,1:0.125:1,0:27.6:1.0:31.3:1.0:1.0:0.0:60.0:11.0:0.1209:0.0:1.2 0/0:52:0:0,0:51,1:0.0:1,0:18.7:1.0:29.1:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.1 -2 29940820 . C T 107 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAGGATCTCTGGGAGATGAA;RSEQ=TAGAAGCCAGGGCACTTAAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:0,12:0,1:0.9231:0,0:26.9:1.0:30.0:1.0:1.0:0.0:60.0:24.0:0.9231:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 30433204 . T G 73 LongAT SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.12131;SOR=0.0;LSEQ=TTATGATGGGGAACATTTCA;RSEQ=TCTCAAAAAAAAAAAAAATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:7,4:0.3125:2,2:40.8:1.0:31.8:1.0:1.0:1.15538:60.0:10.0:0.3333:0.0:1.6 0/0:10:0:0,0:6,4:0.0:2,0:24.1:1.0:29.1:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.1 -2 43081218 . CGT C 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.0;MSILEN=2.0;SSF=0.15097;SOR=0.0;LSEQ=TGTGTGTTTACATGTGTCTG;RSEQ=GTGTGTGTGTTGTGCCTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:3,2:20,15:0.125:2,2:37.0:1.0:30.6:1.0:1.0:1.12:60.0:10.0:0.125:0.0:0.2 0/0:22:0:0,0:13,9:0.0:2,0:32.1:1.0:29.9:1.0:1.0:0.0:60.0:44.0:1.0:0.0:0.1 -2 43952068 . G A 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0017;SOR=0.0;LSEQ=TTCTTGTTCTCAAGGACAAG;RSEQ=AGATCTGGGTCATGGACACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:10:1,9:1,51:0.1613:1,2:18.2:1.0:29.7:1.0:0.29878:5.43:60.0:20.0:0.1639:0.0:1.0 0/0:53:0:0,0:2,51:0.0:1,0:20.4:1.0:31.2:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.1 -2 44311676 . C A 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.26749;SOR=0.0;LSEQ=ATTCTCTGCTTGGCCAAACT;RSEQ=TAGTCAGCCTTCTGAACTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:8,2:0.375:2,2:22.5:1.0:29.0:1.0:0.6044:1.91107:60.0:12.0:0.375:0.0:1.0 0/0:4:0:0,0:2,2:0.0:2,0:19.8:1.0:31.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -2 46128526 . C A 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GTAAGGTATTAGCCTGTTCA;RSEQ=ATATTTCTCATGTAATATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:40:10,30:115,256:0.0973:2,2:24.2:1.0:30.6:1.0:0.47553:1.34673:60.0:80.0:0.098:0.0:1.0 0/0:240:0:0,0:79,160:0.0:2,0:24.8:1.0:31.5:1.0:1.0:0.0:60.0:78.667:1.0:0.0:0.3 -2 47602178 . A T 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00252;SOR=0.10309;LSEQ=TGTCCAGAGAACAGAGGGTC;RSEQ=ATATTAGAAAAGGTGTTCCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:19:19,0:15,0:0.5588:1,1:25.5:1.0:31.9:1.0:1.0:0.0:60.0:38.0:0.5588:0.0:1.0 0/1:18:2:2,0:16,0:0.1111:1,0:10.5:1.0:33.0:0.0:1.0:0.0:60.0:4.0:0.1111:0.0:1.0 -2 47613870 . T C 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.05745;LSEQ=TTTGTTAGTTTAACATCATA;RSEQ=ATTTGTAATAGTGAAACCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:33:3,30:1,38:0.4583:1,2:22.5:1.0:32.5:1.0:0.32655:3.73:60.0:66.0:0.4648:0.0:1.2 0/1:44:2:0,2:1,41:0.0455:1,0:27.0:1.0:34.0:0.0:1.0:0.0:60.0:4.0:0.0455:0.0:1.0 -2 47630213 . T C 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.06602;LSEQ=AACGCAGCCCTGGAAGCTGA;RSEQ=TGGGTGTGGTCGCCGTGGCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:53:51,2:70,4:0.4141:2,1:24.2:1.0:31.8:1.0:1.0:1.45:60.0:52.0:0.4228:0.0:1.1 0/1:68:3:2,1:61,3:0.0441:1,2:25.0:1.0:30.3:1.0:0.17105:9.36402:60.0:6.0:0.0448:0.0:1.0 -2 47630314 . G T 161 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGCATTTTCTTCAACCAGGA;RSEQ=GTGAGGAGGTTTCGACATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:40:20,20:302,266:0.0658:2,2:25.3:1.0:30.4:1.0:0.74462:1.1351:60.0:39.0:0.0653:0.0:1.2 0/0:492:0:0,0:274,218:0.0:2,0:26.4:1.0:30.7:1.0:1.0:0.0:60.0:43.727:1.0:0.0:0.2 -2 47630371 . C T 74 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03863;SOR=0.0;LSEQ=GACGCTGCAGTTGGAGAGCG;RSEQ=GGCCGAGGTCGGCTTCGTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:6:2,4:262,307:0.0104:2,2:26.3:1.0:28.7:1.0:0.69216:1.70532:60.0:12.0:0.0106:0.0:1.0 0/0:444:0:0,0:210,233:0.0:2,0:24.7:1.0:30.2:1.0:1.0:0.0:60.0:109.75:0.9977:0.0:0.2 -2 47637065 . C T 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGTTGCAGTGAGTTGAGAT;RSEQ=GCACCATTGCACTCTAGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:13,0:0.3158:1,0:30.7:1.0:31.3:1.0:1.0:0.0:60.0:12.0:0.3158:0.0:1.0 0/0:2:0:0,0:2,0:0.0:0,0:12.0:1.0:32.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 -2 47693788 . A T 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10365;LSEQ=TACTTTTTCTTTTCTTCTTG;RSEQ=TTATCAAGGCTTGGACCCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:210:150,60:248,97:0.3784:2,2:21.0:1.0:29.4:1.0:0.9228:1.02265:60.0:51.5:0.378:0.0:1.2 0/1:422:25:19,6:276,121:0.0592:2,2:19.0:1.0:29.7:1.0:0.65389:1.39:60.0:50.0:0.0601:0.0:1.1 -2 47703241 . A G 108 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTCTTTCTAGGCCACAGTCA;RSEQ=ATTACAGGTATATTTGTCAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:12,0:4,0:0.75:0,0:29.2:1.0:30.3:1.0:1.0:0.0:60.0:11.0:0.7333:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 47703290 . G A 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGATGAAAGGCCCAGTATC;RSEQ=GTTTGTCTGAAGATATATAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:7,0:9,0:0.4375:0,0:21.7:1.0:31.3:1.0:1.0:0.0:60.0:14.0:0.4375:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 47704027 . G C 86 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGGAATGGTCCTTCTTGCC;RSEQ=TTTATCCAACTTCTTTCTAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1.0:0,0:17.4:1.0:30.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:2.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 47888014 . A G 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03158;LSEQ=CTTCAAAGAATGTATCTCTC;RSEQ=TCCTGTAGAGATATTAAATG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:100:55,45:14,9:0.8065:2,2:26.7:1.0:30.4:1.0:0.64867:1.27026:60.0:99.0:0.8049:0.0:1.1 0/1:114:13:6,7:53,48:0.114:2,2:26.2:1.0:30.8:1.0:0.77178:1.28533:60.0:26.0:0.1161:0.0:1.1 -2 47905398 . C A 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00473;LSEQ=CATTTCCTAGGCCTGAAATT;RSEQ=ATTGCTTGTGTACCCAGAAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:170:79,91:308,330:0.2104:2,2:26.3:1.0:29.0:1.0:0.72978:1.07498:60.0:55.667:0.2093:0.0:1.1 0/0:795:1:1,0:394,400:0.0013:2,0:1.0:0.0:25.0:0.0:0.49686:0.0:60.0:2.0:0.0013:0.0:2.0 -2 48010214 . C T 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.54404;SOR=0.0;LSEQ=GGGGCCTGGCGCGCACCGCC;RSEQ=GCGCACGGCGAGGCGCCTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:0.2632:1,0:21.8:1.0:33.0:0.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.0 0/0:5:0:0,0:5,0:0.0:0,0:18.0:1.0:31.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 -2 48025764 . C T 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.13647;LSEQ=TGGCAGGTAGGCACAACTTA;RSEQ=GTAACAGATAAGAGTGAAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:122:86,36:231,102:0.2681:2,2:23.6:1.0:30.5:1.0:0.90841:1.05:60.0:121.0:0.2695:0.0:1.3 0/1:526:25:17,8:321,180:0.0475:2,2:21.5:1.0:29.1:1.0:0.83162:1.19:60.0:24.0:0.046:0.0:1.4 -2 48028465 . C T 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.14877;SOR=0.0;LSEQ=AATTTAAGTTACTTGAAACT;RSEQ=GCTTTTATCTTAGTAGCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:0,21:0.1923:1,0:23.4:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.1923:0.0:1.0 0/0:13:0:0,0:0,13:0.0:1,0:28.6:1.0:29.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -2 48030629 . G T 180 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTCGCCCAGTAATTCTGTT;RSEQ=CCGGAAGATACCCCCCCCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:73:30,43:599,691:0.0536:2,2:24.7:1.0:29.1:1.0:0.4:1.2423:60.0:23.333:0.0524:0.0:1.1 0/0:1439:0:0,0:678,760:0.0:2,0:25.4:1.0:31.4:1.0:1.0:0.0:60.0:48.586:1.0:0.0:0.2 -2 48032572 . C T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.02696;SOR=0.0;LSEQ=GGTGATCTGCTTGCCTCGGC;RSEQ=TCCCAAAGTGCTGGGATTAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:5,1:11,3:0.3:2,2:22.0:1.0:28.7:1.0:1.0:1.34:56.7:5.0:0.2632:0.0:2.0 0/0:15:0:0,0:14,1:0.0:1,0:22.7:1.0:30.9:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.8 -2 48033272 . ATTTTTGTTTTAATTCCT A 176 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.04894;LSEQ=TGTTGCTTTTCTGTCCTAGC;RSEQ=TTTTTGTTTTAATTCCTTTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:186:52:46,6:119,14:0.2796:2,2:24.0:1.0:31.0:1.0:0.79802:1.10806:60.0:51.0:0.2757:0.0538:0.1 0/1:162:3:3,0:135,24:0.0185:2,0:34.3:1.0:32.0:0.0:1.0:0.0:60.0:6.0:0.0186:0.0:0.0 -2 48033549 . CTC TCTG 196 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.06211;LSEQ=TCGGTTTTTTGAGAGGGCAC;RSEQ=TTGCTAGCACATGTATCGCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:79:35,44:78,128:0.2743:2,2:24.4:1.0:31.1:1.0:0.34521:1.3:60.0:78.0:0.2766:0.066:1.0 0/1:175:4:1,3:73,98:0.0229:2,2:17.0:1.0:32.1:1.0:0.6387:2.22541:60.0:8.0:0.0237:0.0057:1.0 -2 48033846 . CAGTAAA C 215 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GACCTTAAGTTTCAAAGAAA;RSEQ=AGGGGAAGGGATGATGCACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:107:42,65:67,128:0.3531:2,2:24.7:1.0:32.0:1.0:0.45254:1.23:59.7:52.5:0.3559:0.0462:0.3 0/0:206:0:0,0:84,122:0.0:2,0:25.1:1.0:30.5:1.0:1.0:0.0:60.0:40.2:1.0:0.0:0.3 -2 51288710 . A C 282 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10605;LSEQ=GCAAAGTTGCGGGGTACAAG;RSEQ=TTGATACTCAAAAATCAGTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1202:485:153,332:222,494:0.4035:2,2:25.5:1.0:31.7:1.0:0.84924:1.03:60.0:47.5:0.4022:0.0:1.1 0/1:957:64:22,42:315,578:0.0669:2,2:24.2:1.0:31.5:1.0:1.0:1.04038:60.0:63.0:0.0669:0.0:1.2 -2 54660484 . G A 148 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.03505;LSEQ=GTATGATGTTAGGGATCTGC;RSEQ=TGTTCATAGGCTTCACTGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:31:22,9:242,95:0.0842:2,2:26.1:1.0:30.0:1.0:1.0:1.04199:60.0:30.0:0.0843:0.0:1.3 0/0:312:1:1,0:194,117:0.0032:2,0:36.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0033:0.0:1.0 -2 61108926 . C G 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGACTGACTGCGGCCGCCT;RSEQ=CGGCCAGGACGCTGGGAGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:122:71,51:134,68:0.3742:2,2:24.7:1.0:31.3:1.0:0.1544:1.41391:60.0:60.0:0.3715:0.0:1.1 0/0:381:0:0,0:231,150:0.0:2,0:23.4:1.0:30.4:1.0:1.0:0.0:60.0:33.636:1.0:0.0:0.3 -2 61710320 . T A 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0396;SOR=0.0;LSEQ=AAGTATTCTGAATCTAACCC;RSEQ=GTTCTCCCTTTTTTTTGGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:6:0,6:1,86:0.0645:1,0:26.7:1.0:32.5:1.0:1.0:0.0:60.0:12.0:0.0659:0.0:1.0 0/0:68:0:0,0:0,68:0.0:1,0:24.0:1.0:30.1:1.0:1.0:0.0:60.0:136.0:1.0:0.0:0.1 -2 61713110 . GA G 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.06482;SOR=0.0;LSEQ=TCAGCGACCTGTTGGGGAGG;RSEQ=AAAAAAAGTTATGTTTTAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:365:5:1,4:67,293:0.0137:2,2:25.6:1.0:30.5:1.0:1.0:1.09:60.0:10.0:0.0139:0.0027:0.6 0/0:316:0:0,0:89,227:0.0:2,0:22.2:1.0:29.5:1.0:1.0:0.0:60.0:157.0:1.0:0.0:0.1 -2 61760814 . C T 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAATGCAAACTATGGAATAT;RSEQ=TTTTTTAAAGGTGATAATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:27:23,4:172,8:0.1304:1,2:22.3:1.0:30.1:1.0:0.05474:3.70438:60.0:54.0:0.1311:0.0:1.0 0/0:150:0:0,0:138,12:0.0:2,0:22.7:1.0:31.6:1.0:1.0:0.0:60.0:149.0:1.0:0.0:0.1 -2 66352599 . G A 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.04341;LSEQ=CAAAGCTGGAATTTGTTTGT;RSEQ=TGGTTCCTCCACAGCTGTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:55:55,0:19,0:0.7432:1,1:26.2:1.0:28.8:1.0:1.0:0.0:60.0:110.0:0.7432:0.0:1.0 0/1:37:4:4,0:33,0:0.1081:1,0:19.5:1.0:28.5:1.0:1.0:0.0:60.0:8.0:0.1081:0.0:1.0 -2 67049381 . T C 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCAAGCCACATGACACAG;RSEQ=GGGTGCCTTCAGCTGCTCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:71:46,25:199,165:0.1632:2,2:27.0:1.0:31.0:1.0:0.11917:1.52:60.0:70.0:0.162:0.0:1.1 0/0:278:0:0,0:156,122:0.0:2,0:23.8:1.0:29.3:1.0:1.0:0.0:60.0:45.333:1.0:0.0:0.1 -2 67977367 . G GT 117 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.00028;SOR=0.0802;LSEQ=ATCAAGGAGTCAATAGGGTT;RSEQ=TTTTTTTTTTTCCTAGGGCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:16:13,3:15,4:0.4103:2,2:22.6:1.0:29.3:1.0:1.0:1.15:60.0:32.0:0.4324:0.1538:0.6 0/1:39:2:2,0:27,10:0.0513:2,0:12.0:1.0:32.0:0.0:1.0:0.0:60.0:4.0:0.0526:0.0:0.0 -2 75660834 . G T 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.002;SOR=0.0;LSEQ=TGCTTTGTTAAATGGGTCCT;RSEQ=CTCCCCGTGCCACCCAACTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:5,4:5,8:0.4091:2,2:19.6:1.0:30.3:1.0:0.66563:1.94:56.2:18.0:0.4091:0.0:1.0 0/0:18:0:0,0:9,9:0.0:2,0:24.7:1.0:31.3:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.6 -2 79228890 . G A 63 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00699;SOR=0.0;LSEQ=TATTGGATGCCATCCACATG;RSEQ=CAAATGAGTAGGCTAAACGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,1:0.7143:2,2:22.4:1.0:27.2:1.0:1.0:3.16:60.0:4.0:0.6667:0.0:3.2 0/0:8:0:0,0:5,3:0.0:2,0:22.6:1.0:31.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.0 -2 79228925 . T A 89 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00191;SOR=0.03262;LSEQ=AAACGGAAGGTAGCACAGAA;RSEQ=TGTCTCTGTCCTCAACAATG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:6,3:1,1:0.8182:2,2:23.8:1.0:28.3:1.0:1.0:1.87:60.0:8.0:0.8:0.0:2.6 0/1:10:1:1,0:4,5:0.1:2,0:18.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.1:0.0:2.0 -2 79423062 . TTTTG T 106 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.03318;SOR=0.1254;LSEQ=GTAGGGGGATGAACTCAGTT;RSEQ=TTTGTTTGTTTTATGAGATG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:12:4,8:17,79:0.1101:2,2:25.3:1.0:29.7:1.0:0.2432:2.3:60.0:24.0:0.1121:0.0092:0.0 0/1:66:1:0,1:14,51:0.0152:2,0:48.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0152:0.0:0.0 -2 79524994 . C T 228 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAATTCTGAGGCAGATTATC;RSEQ=ACACTCATTGGAAACAAATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:209:125,84:104,65:0.5529:2,2:27.7:1.0:29.7:1.0:0.75173:1.07498:60.0:103.5:0.5535:0.0:1.1 0/0:315:0:0,0:172,143:0.0:2,0:25.9:1.0:30.8:1.0:1.0:0.0:60.0:314.0:1.0:0.0:0.5 -2 79524996 . C T 69 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.03483;SOR=0.0;LSEQ=ATTCTGAGGCAGATTATCCA;RSEQ=ACTCATTGGAAACAAATAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:6:3,3:226,154:0.0155:2,2:38.2:1.0:26.8:1.0:0.69065:1.46601:60.0:5.0:0.0131:0.0:2.0 0/0:319:0:0,0:174,145:0.0:2,0:26.0:1.0:31.3:1.0:1.0:0.0:60.0:158.5:1.0:0.0:0.5 -2 81424759 . C T 233 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.01707;LSEQ=CTCATCTTCACAGAGTCGTC;RSEQ=TTTTCTTTTTCTGCACTGTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1862:204:107,97:826,832:0.1096:2,2:26.9:1.0:30.4:1.0:0.50459:1.11:60.0:39.8:0.1086:0.0:1.2 0/0:1432:3:0,3:725,704:0.0021:2,0:1.0:0.0:26.0:1.0:0.12009:0.0:60.0:6.0:0.0021:0.0:1.0 -2 81425558 . C T 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00018;SOR=0.11201;LSEQ=ACTTCTCAAGGACTTCCTCT;RSEQ=CTTGGAATATTCTTTATCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2041:24:16,8:1008,1007:0.0118:2,2:21.5:1.0:29.6:1.0:0.14927:2.0:60.0:48.0:0.012:0.0:1.1 0/0:1503:2:0,2:764,735:0.0013:2,0:1.0:0.0:24.0:0.0:0.24092:0.0:60.0:4.0:0.0013:0.0:1.0 -2 81425585 . C T 277 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.11149;LSEQ=ATATTCTTTATCTGACTTCT;RSEQ=TTTGTGTTTGCTGTTAGCCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1956:595:302,293:676,677:0.3042:2,2:24.5:1.0:30.1:1.0:0.76795:1.03:60.0:73.375:0.3048:0.0:1.1 0/1:1464:68:39,29:713,682:0.0464:2,2:22.6:1.0:29.4:1.0:0.32346:1.29:60.0:67.0:0.0463:0.0:1.1 -2 81426909 . C T 271 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.00317;LSEQ=CTGATTTTTATTAAAATATT;RSEQ=ATCAAAAGCAGAATCTTCCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2349:619:333,286:869,859:0.2635:2,2:24.2:1.0:29.3:1.0:0.14632:1.15:59.7:205.333:0.2646:0.0:1.1 0/0:1777:2:0,2:895,877:0.0011:2,0:1.0:0.0:23.5:1.0:0.24537:0.0:57.5:4.0:0.0011:0.0:1.0 -2 81427308 . G A 259 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTTTTTTAAAGTGGTCTC;RSEQ=ATCAAGCTATAACACTTTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1283:379:181,198:462,441:0.2954:2,2:24.0:1.0:30.3:1.0:0.27119:1.14589:60.0:188.5:0.2959:0.0:1.1 0/0:963:0:0,0:472,490:0.0:2,0:25.0:1.0:30.3:1.0:1.0:0.0:60.0:67.714:0.9989:0.0:0.1 -2 91884263 . C G 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.54612;SOR=0.0;LSEQ=TATGGTGCTCCTTGAGATTT;RSEQ=TGTAAGGTAGGTCTGTTCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:7:7,0:16,2:0.28:2,0:32.4:1.0:31.9:1.0:1.0:0.0:29.1:14.0:0.2917:0.0:1.4 0/0:4:0:0,0:3,1:0.0:2,0:26.8:1.0:30.0:1.0:1.0:0.0:39.3:8.0:1.0:0.0:0.0 -2 91886661 . A AT 79 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.03776;SOR=0.0;LSEQ=TAAAAAGACCATATTTGTAC;RSEQ=TTTTTTTTTAAAAATGGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:6:0,6:41,221:0.0224:2,0:22.7:1.0:30.8:1.0:0.59498:0.0:34.3:12.0:0.0231:0.0037:0.2 0/0:208:0:0,0:45,161:0.0:2,0:23.5:1.0:29.2:1.0:1.0:0.0:34.3:33.333:0.995:0.0:0.1 -2 91886670 . T A 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATATTTGTACATTTTTTTT;RSEQ=AAAAATGGAATATACTGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:52:5,47:34,161:0.2105:2,2:19.7:1.0:30.4:1.0:0.20321:1.98034:33.1:104.0:0.2122:0.0:1.1 0/0:188:0:0,0:37,149:0.0:2,0:23.7:1.0:28.0:1.0:1.0:0.0:35.2:92.0:0.9892:0.0:0.1 -2 91888488 . T C 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCATCACACAGCAGGAGTCT;RSEQ=CCTGGGTCAGTTGCCTTCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:3395:88:42,46:1441,1865:0.0259:2,2:28.2:1.0:30.8:1.0:0.44786:1.18:28.8:43.0:0.0257:0.0:1.1 0/0:2553:0:0,0:1146,1405:0.0:2,0:15.0:0.0:10.0:0.0:1.0:0.0:40.0:0.0:0.0:0.0:2.0 -2 91894045 . T C 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00365;SOR=0.0;LSEQ=TCTTAACTAATATAGCTCTA;RSEQ=AGCTAAATATTGGATCACTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:11:8,3:379,121:0.0215:2,2:20.8:1.0:32.5:1.0:0.73281:1.17416:25.7:22.0:0.0219:0.0:1.0 0/0:360:0:0,0:291,69:0.0:2,0:22.6:1.0:29.8:1.0:1.0:0.0:25.5:119.0:1.0:0.0:0.2 -2 91894266 . A G 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00341;SOR=0.0;LSEQ=TAAAAAGCAAAATACACAAA;RSEQ=TACGAAGTTATATTTTTCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:527:11:0,11:32,483:0.0209:2,0:30.5:1.0:32.0:1.0:1.0:0.0:26.0:22.0:0.0214:0.0:1.3 0/0:388:0:0,0:16,372:0.0:1,0:22.7:1.0:29.9:1.0:1.0:0.0:26.8:28.846:1.0:0.0:0.5 -2 91894464 . A G 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.17461;SOR=0.0;LSEQ=AGAATTCCTTTAGACCAAGA;RSEQ=GTAATGAGAAAATATAATAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:6:0,6:3,52:0.0984:2,0:8.3:1.0:31.8:1.0:1.0:0.0:27.0:12.0:0.1017:0.0:1.0 0/0:25:0:0,0:2,23:0.0:2,0:10.7:1.0:30.0:1.0:1.0:0.0:34.0:50.0:1.0:0.0:0.4 -2 91899415 . A G 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAAATATTTGCTAGTAGTTA;RSEQ=CAAATATATTTGTAATACAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:2,2:0.6:2,2:34.7:1.0:33.0:1.0:1.0:1.86:33.3:12.0:0.6:0.0:3.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 91899419 . A C 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TATTTGCTAGTAGTTAACAA;RSEQ=TATATTTGTAATACACATAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:2,2:0.6:2,2:38.7:1.0:33.2:1.0:1.0:1.86:33.3:12.0:0.6:0.0:3.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 91899421 . A G 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TTTGCTAGTAGTTAACAAAT;RSEQ=TATTTGTAATACACATATAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:4,2:2,2:0.6:2,2:39.7:1.0:32.7:1.0:1.0:1.86:33.3:12.0:0.6:0.0:3.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 91902433 . G A 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.30406;SOR=0.0;LSEQ=GACTTCTCCCTCATAAAACC;RSEQ=GTAGTAATCACAACAAAAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:5,0:16,2:0.2174:2,0:27.2:1.0:31.6:1.0:1.0:0.0:26.4:10.0:0.2174:0.0:1.6 0/0:7:0:0,0:6,1:0.0:2,0:22.4:1.0:31.1:1.0:1.0:0.0:41.1:14.0:1.0:0.0:0.3 -2 91902876 . CAT C 137 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.00012;SOR=0.0;LSEQ=ACAGCAAAAACAAATGCAAA;RSEQ=ATGGAAATTTAGGACAAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:21:2,19:2,24:0.4375:2,2:25.1:1.0:31.2:1.0:1.0:1.26:32.7:20.0:0.4348:0.0208:0.4 0/0:21:0:0,0:4,17:0.0:2,0:26.0:1.0:29.7:1.0:1.0:0.0:36.1:42.0:1.0:0.0:0.0 -2 92145660 . T A 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00727;SOR=0.0;LSEQ=TTTAATCTAATTGTTTTAGA;RSEQ=GTATGGGGGGTATCTTGGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:8:0,8:8,90:0.0755:2,0:28.9:1.0:29.3:1.0:1.0:0.0:50.6:7.0:0.0667:0.0:1.5 0/0:96:0:0,0:11,85:0.0:2,0:22.3:1.0:29.0:1.0:1.0:0.0:46.1:12.714:1.0:0.0:0.5 -2 92151474 . T C 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.011;SOR=0.0;LSEQ=TACCCCCACTTTACTGGAAG;RSEQ=ACATTGAGGAACTTTGATAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:9:8,1:85,17:0.0811:2,2:25.7:1.0:31.0:1.0:1.0:1.59:41.8:8.0:0.0727:0.0:3.1 0/0:81:0:0,0:61,20:0.0:2,0:28.8:1.0:28.7:1.0:1.0:0.0:41.0:80.0:1.0:0.0:1.2 -2 92315446 . A C 154 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGGAAATATCTTCCCATAA;RSEQ=AACAAGACAGAAGCATTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:29:9,20:2,2:0.8788:2,2:17.1:1.0:31.8:1.0:0.58602:2.16451:35.3:58.0:0.9063:0.0:6.1 0/0:82:0:0,0:3,8:0.0:2,0:18.4:1.0:30.1:1.0:1.0:0.0:32.8:22.0:1.0:0.0:2.8 -2 92319253 . T A 66 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03097;SOR=0.0;LSEQ=ACAGAGTTGAACATTTCTTT;RSEQ=GAGAGAGCAGTTTTGAAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:0.625:2,2:14.8:1.0:28.8:1.0:1.0:2.6:20.6:10.0:0.625:0.0:6.0 0/0:6:0:0,0:3,3:0.0:2,0:23.0:1.0:29.5:1.0:1.0:0.0:29.0:12.0:1.0:0.0:2.8 -2 92319260 . G A 69 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03097;SOR=0.0;LSEQ=TGAACATTTCTTTTGAGAGA;RSEQ=CAGTTTTGAAACACTCTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:0.625:2,2:21.8:1.0:30.0:1.0:1.0:2.6:20.6:10.0:0.625:0.0:6.0 0/0:6:0:0,0:2,3:0.0:2,0:24.2:1.0:30.8:1.0:1.0:0.0:30.8:10.0:1.0:0.0:2.6 -2 95849653 . T C 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCTGGGATTACAGACGTAAG;RSEQ=CACCGTGCCCGGCCTATATT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:1,10:0,0:1.0:0,2:22.0:1.0:29.1:1.0:1.0:0.0:51.5:10.0:1.0:0.0:1.5 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 99160361 . G C 174 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTGTGTGAGCTGGAGGAGCT;RSEQ=GGAGAGCTGTCCCCTTGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:55:34,21:485,361:0.061:2,2:25.7:1.0:30.1:1.0:0.57452:1.2:60.0:54.0:0.0609:0.0:1.2 0/0:785:0:0,0:440,339:0.0:2,0:24.8:1.0:30.5:1.0:1.0:0.0:60.0:40.0:0.9922:0.0:0.2 -2 99168953 . T C 115 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TACGATCATTTGGGTGATTA;RSEQ=GGGATATGATTGTTCAATAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:1.0:0,0:22.4:1.0:32.3:1.0:1.0:0.0:60.0:24.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 99185423 . C G 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGGCATGCATTGTGCACCT;RSEQ=CTGGTAGGACTTGGGGGAAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:1.0:0,2:21.1:1.0:31.6:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 99193007 . A G 83 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CCTACCTTCCAGGGAGACCT;RSEQ=GAGACCTGGCCCAGGACTGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1.0:0,2:26.8:1.0:32.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 106021437 . C T 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCGTCGGATACAGTTTCCA;RSEQ=TGTGGCTTTGATACCTCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:47:33,14:186,111:0.1366:2,2:26.8:1.0:30.3:1.0:0.33351:1.41:60.0:22.5:0.1331:0.0:1.1 0/0:312:0:0,0:187,125:0.0:2,0:24.5:1.0:31.4:1.0:1.0:0.0:60.0:61.4:1.0:0.0:0.4 -2 106021465 . ACT A 141 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TTGATACCTCTTTAAGAAAG;RSEQ=CTGTTTGGTACATTAATGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:22:12,10:231,176:0.0513:2,2:21.7:1.0:31.7:1.0:0.82947:1.09352:60.0:44.0:0.0516:0.0093:1.0 0/0:411:0:0,0:231,177:0.0:2,0:25.5:1.0:31.4:1.0:1.0:0.0:60.0:101.0:0.9975:0.0:0.6 -2 108622946 . G A 77 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCGGTCTCCCAAAGTGCTGG;RSEQ=ATTATAGGTGTGAGCTACTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:1.0:0,2:17.2:1.0:29.8:1.0:1.0:0.0:55.3:12.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 111885565 . C T 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCATCTGAACCATTTATTT;RSEQ=TAAGTGTACTGTTCAGTAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:47:27,20:108,82:0.1983:2,2:26.4:1.0:30.4:1.0:1.0:1.02:60.0:94.0:0.2009:0.0:1.1 0/0:218:0:0,0:133,85:0.0:2,0:24.9:1.0:30.8:1.0:1.0:0.0:60.0:26.25:1.0:0.0:0.1 -2 111901935 . GGT G 88 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.0;MSILEN=2.0;SSF=0.14474;SOR=0.18843;LSEQ=GAGAAATAGACCTGGAGGGA;RSEQ=GTGTGTGTGTGTTGTTGGTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:7:5,2:166,14:0.0374:2,2:25.4:1.0:31.4:1.0:0.11203:4.67441:60.0:14.0:0.0378:0.0053:0.1 0/0:138:1:1,0:121,14:0.0072:2,0:20.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.0075:0.0:0.0 -2 111911182 . ATCC A 142 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.00037;SOR=0.0;LSEQ=GCTGTCTTCACAAGGGAATT;RSEQ=TCTCTTGGCAAGCGAGTGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:23:23,0:32,2:0.4035:2,1:27.0:1.0:31.6:1.0:0.51003:0.0:60.0:46.0:0.4107:0.0175:0.0 0/0:20:0:0,0:19,1:0.0:1,0:26.3:1.0:30.1:1.0:1.0:0.0:60.0:40.0:1.0:0.0:0.4 -2 113688949 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.04516;SOR=0.0;LSEQ=GGCCATGAAAAGTCCACCTG;RSEQ=AGTAGTGGTAGGAGGAACAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:6:2,4:308,183:0.0121:2,2:22.0:1.0:27.7:1.0:0.20443:3.35761:60.0:12.0:0.0122:0.0:1.7 0/0:350:0:0,0:218,132:0.0:2,0:24.4:1.0:31.3:1.0:1.0:0.0:60.0:69.0:1.0:0.0:0.6 -2 113978894 . G A 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00428;LSEQ=AATGTCCACCCAGCCTTTCA;RSEQ=AAACTCACCTACGATTGGGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:568:190:102,88:187,189:0.3345:2,2:24.5:1.0:30.2:1.0:0.42302:1.17:60.0:189.0:0.3351:0.0:1.1 0/0:467:1:1,0:230,236:0.0021:2,0:1.0:0.0:26.0:0.0:0.49465:0.0:60.0:2.0:0.0022:0.0:1.0 -2 113979364 . G A 185 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.12278;LSEQ=GCATTTATACAGGAAGAAGA;RSEQ=AGATGAAGAGGAGCAGCCTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:70:34,36:209,198:0.1468:2,2:24.6:1.0:30.3:1.0:0.69911:1.11739:60.0:140.0:0.1471:0.0:1.1 0/1:436:9:5,4:233,194:0.0206:2,2:15.0:1.0:28.7:1.0:1.0:1.04:60.0:18.0:0.0207:0.0:1.1 -2 113981691 . T A 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.06931;LSEQ=ATGGATGATGAAAGGATAGA;RSEQ=GGAAAGACAGATTAAAGGAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:27:14,13:328,332:0.0393:2,2:30.6:1.0:31.1:1.0:0.84699:1.09:60.0:54.0:0.0398:0.0:1.0 0/0:708:2:1,1:381,325:0.0028:2,2:24.5:1.0:15.5:1.0:1.0:1.17204:60.0:0.0:0.0:0.0:1.0 -2 113993631 . G A 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06589;SOR=0.0;LSEQ=TGAGGCCCGGCCTAGGACCG;RSEQ=AGGCGCGACCCCTCGGCCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:2,3:56,53:0.0439:2,2:33.6:1.0:30.2:1.0:0.67631:1.57857:49.8:10.0:0.0439:0.0:1.2 0/0:93:0:0,0:50,43:0.0:2,0:26.2:1.0:30.3:1.0:1.0:0.0:51.2:45.5:1.0:0.0:0.4 -2 121735983 . C T 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGCCTCTGGCCCTGCTTAC;RSEQ=CTCTTCTGGGCATGTCCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:19:13,6:187,96:0.0629:2,2:23.5:1.0:29.4:1.0:1.0:1.11:60.0:18.0:0.061:0.0:1.2 0/0:268:0:0,0:177,91:0.0:2,0:22.2:1.0:30.0:1.0:1.0:0.0:60.0:133.0:1.0:0.0:0.2 -2 125301742 . C T 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.36364;SOR=0.0;LSEQ=AAGTTAAACTAACCATCTAA;RSEQ=AGGTCTTAAGGGATCATCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:1,6:0,3:0.7:0,2:17.7:1.0:27.4:1.0:1.0:0.0:60.0:6.0:0.6667:0.0:1.6 0/0:1:0:0,0:0,1:0.0:0,0:33.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -2 128014913 . C T 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.42857;SOR=0.0;LSEQ=TCAGAACGGTAACATAAATA;RSEQ=ACCTTAAATATTAACATTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:0.6154:0,0:27.5:1.0:27.6:1.0:1.0:0.0:60.0:7.0:0.5833:0.0:1.3 0/0:1:0:0,0:1,0:0.0:0,0:40.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -2 128036701 . G T 66 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.06576;SOR=0.0;LSEQ=CCACCTTCTGCACTCTCAAT;RSEQ=GGGAAGAGAAACTGGCCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:5:3,2:295,93:0.0127:2,2:9.6:1.0:28.8:1.0:0.59829:2.11004:60.0:10.0:0.0128:0.0:1.0 0/0:334:0:0,0:232,102:0.0:2,0:23.2:1.0:30.9:1.0:1.0:0.0:60.0:54.667:1.0:0.0:0.1 -2 128038005 . C A 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGCCCTTTCCCAGACGCCCC;RSEQ=AGCCCAGGCCCAGCTACCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:25:19,6:325,168:0.0483:2,2:21.2:1.0:29.4:1.0:0.38715:1.64:59.7:11.5:0.0451:0.0:1.3 0/0:512:0:0,0:327,184:0.0:2,0:25.5:1.0:30.1:1.0:1.0:0.0:60.0:38.308:0.998:0.0:0.3 -2 128044048 . G T 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAGAGAACTGCTTGAACCTG;RSEQ=GAGGTGGAAGTTGTGGTGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:28.2:1.0:29.8:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.2 0/0:1:0:0,0:1,0:0.0:0,0:28.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -2 131947825 . T C 86 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07824;SOR=0.0;LSEQ=GGGAAATCTGAGGAGAGACA;RSEQ=AGAGAAAAACAAACATGTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:5,1:22,2:0.2:2,2:13.7:1.0:33.3:1.0:0.50148:2.13203:42.7:12.0:0.2:0.0:2.8 0/0:16:0:0,0:12,4:0.0:2,0:20.1:1.0:30.1:1.0:1.0:0.0:60.0:32.0:1.0:0.0:0.0 -2 131947893 . C G 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01074;SOR=0.0;LSEQ=TACCAGTAACCAGATATCTA;RSEQ=TCTATTTCTGTACTTCATTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:8:6,2:76,4:0.0909:2,2:22.1:1.0:30.0:1.0:0.09062:6.09674:43.5:16.0:0.0952:0.0:2.9 0/0:66:0:0,0:59,7:0.0:2,0:24.0:1.0:31.2:1.0:1.0:0.0:60.0:132.0:1.0:0.0:0.1 -2 131949242 . C A 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCCAAGGGCACAAAGGAAG;RSEQ=CAGTCATGTTGATCCATGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:25:11,14:130,182:0.0742:2,2:23.2:1.0:29.1:1.0:0.83573:1.1:51.3:24.0:0.0732:0.0:1.4 0/0:283:0:0,0:106,177:0.0:2,0:23.5:1.0:31.1:1.0:1.0:0.0:52.1:46.167:1.0:0.0:0.3 -2 131950767 . A G 221 InIns SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGACAAAAGGCAACTTTACA;RSEQ=ACTTACCTGGCCATCTTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:131:89,42:194,89:0.3164:2,2:24.9:1.0:31.5:1.0:0.90992:1.02861:51.3:64.5:0.3162:0.0:1.0 0/0:367:0:0,0:241,126:0.0:2,0:23.0:1.0:29.6:1.0:1.0:0.0:59.9:121.333:1.0:0.0:0.1 -2 131955336 . G A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03937;SOR=0.12751;LSEQ=TTTCAGTTATGATCAGAAAG;RSEQ=ATCAGTAAGTGCTCTTGAGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:9:9,0:40,4:0.1698:2,0:29.9:1.0:29.7:1.0:1.0:0.0:55.7:18.0:0.1698:0.0:1.0 0/1:40:1:1,0:39,0:0.025:1,0:38.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.025:0.0:1.0 -2 133919631 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01806;SOR=0.0;LSEQ=ATTTGCACTTACTCATTCTT;RSEQ=GCCTTTTCTGTGCCCTCTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:0.6154:0,0:27.0:1.0:30.0:1.0:1.0:0.0:60.0:7.0:0.5833:0.0:1.5 0/0:6:0:0,0:1,5:0.0:2,0:30.5:1.0:28.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.5 -2 139308127 . G A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0094;SOR=0.0;LSEQ=CGAGAGGAAATGGGTGAAGT;RSEQ=TTAAAAAGTTCAACATTTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:5,4:4,4:0.5294:2,2:22.9:1.0:29.4:1.0:1.0:1.23:60.0:18.0:0.5294:0.0:1.0 0/0:9:0:0,0:5,4:0.0:2,0:29.6:1.0:31.8:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 -2 158617379 . A G 250 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTAAGACAATATTATATTAG;RSEQ=TTAGATACCTACCATTGCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1398:266:163,103:685,445:0.1903:2,2:25.3:1.0:31.1:1.0:0.88905:1.03:60.0:52.2:0.1901:0.0:1.1 0/0:1334:0:0,0:792,540:0.0:2,0:24.2:1.0:29.1:1.0:1.0:0.0:60.0:110.0:0.9985:0.0:0.1 -2 158622572 . C A 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00712;LSEQ=AGACCACTAGCTATGGACAG;RSEQ=ACTATTCGAAGGCAGCTAAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1925:157:72,85:849,918:0.0816:2,2:26.0:1.0:30.0:1.0:0.61774:1.09175:60.0:77.5:0.0817:0.0:1.2 0/0:1582:1:1,0:757,819:0.0006:2,0:1.0:0.0:24.0:0.0:0.48066:0.0:60.0:2.0:0.0006:0.0:1.0 -2 158634289 . G A 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCAAAAGGTGCCTTTTTAAA;RSEQ=GAGCACTTTTATGGCTAAAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:26.5:1.0:30.4:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 158636320 . C T 66 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAAAACTACAGGGTTTGTG;RSEQ=GAAATCTCATCCTGCTTCAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:25.8:1.0:28.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 158636341 . A G 72 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAAATCTCATCCTGCTTCAA;RSEQ=TTTCAGTGATAGGGTCACTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:21.6:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 158637137 . A G 290 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAAGGAGAGAAAGGAAGGGG;RSEQ=AAAAAAAAAAAAAGAGGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1177:772:299,473:73,141:0.6559:2,2:20.8:1.0:30.3:1.0:0.23239:1.22:60.0:21.706:0.6554:0.0:1.4 0/0:1220:0:0,0:118,171:0.0:2,0:25.9:1.0:28.0:1.0:1.0:0.0:59.9:14.211:0.5556:0.0:0.7 -2 158637445 . A C 112 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTTCAGCGTGATTGGCTCT;RSEQ=AGATCCCAATTACTGCATCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1.0:0,0:29.2:1.0:32.6:1.0:1.0:0.0:60.0:22.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 158655838 . G C 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=CCAAATATTTATTATAAAAA;RSEQ=AGTGTTTTAAGTTTGATAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:20:20,0:230,11:0.0766:1,1:26.2:1.0:33.0:1.0:1.0:0.0:58.8:40.0:0.0797:0.0:1.4 0/0:182:0:0,0:174,8:0.0:1,0:22.7:1.0:31.8:1.0:1.0:0.0:59.5:44.5:1.0:0.0:0.4 -2 180265135 . C T 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00986;LSEQ=TACAATTTCCAAGTGCGTTC;RSEQ=GAAAACTCCTGGGGGCTTGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:84:47,37:287,198:0.1476:2,2:24.6:1.0:30.5:1.0:0.63155:1.14082:60.0:168.0:0.1495:0.0:1.9 0/0:588:1:0,1:349,238:0.0017:2,0:1.0:0.0:25.0:0.0:0.40646:0.0:60.0:2.0:0.0017:0.0:2.0 -2 180265174 . G A 210 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01123;LSEQ=GCTTTAGCCCGTCTGTCACC;RSEQ=CCTCCTTCCTTGCCTTCTCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:776:133:66,67:350,293:0.1714:2,2:23.9:1.0:29.9:1.0:0.33986:1.21233:59.9:132.0:0.1719:0.0:1.8 0/0:865:2:1,1:446,416:0.0023:2,2:35.5:1.0:30.5:1.0:1.0:1.072:60.0:4.0:0.0023:0.0:2.5 -2 183484981 . T C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0634;SOR=0.0;LSEQ=CAACTATTAACACATTTCTA;RSEQ=ATTAATATGAATTTCAGTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:6,0:17,0:0.2609:1,0:27.5:1.0:33.0:1.0:1.0:0.0:60.0:12.0:0.2727:0.0:1.0 0/0:15:0:0,0:15,0:0.0:1,0:17.1:1.0:30.7:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.0 -2 184373044 . C T 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=8e-05;SOR=0.0;LSEQ=CAGAAGCCTTTTCCTGTAAA;RSEQ=GCCAGGTGGCAGTCGTACTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:5,9:0.3636:2,2:24.6:1.0:30.6:1.0:1.0:1.08:54.1:16.0:0.3636:0.0:1.0 0/0:41:0:0,0:17,24:0.0:2,0:24.2:1.0:30.2:1.0:1.0:0.0:55.3:82.0:1.0:0.0:0.2 -2 187558960 . G A 66 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.20455;SOR=0.0;LSEQ=CTCGGCCTGGCCGTGGTGCT;RSEQ=CTGAAAGCGCGGCTGGTCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:3,1:0.5556:2,0:34.6:1.0:28.8:1.0:0.44444:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:3:0:0,0:3,0:0.0:0,0:43.0:1.0:32.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -2 189541807 . C G 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00039;SOR=0.0;LSEQ=CATAAAACATTCAAAATTAT;RSEQ=TTGATTATTTGCTTTATTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:13:0,13:2,34:0.2653:2,1:24.8:1.0:32.7:1.0:1.0:0.0:60.0:26.0:0.2708:0.0:1.2 0/0:39:0:0,0:0,39:0.0:1,0:22.1:1.0:32.3:1.0:1.0:0.0:60.0:38.0:1.0:0.0:0.0 -2 190708712 . G A 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTTATTTGGCAGAAAAGCA;RSEQ=AGTATCAGATCACAAGATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:171:99,72:475,353:0.171:2,2:27.5:1.0:29.9:1.0:0.93241:1.02:60.0:56.0:0.169:0.0:1.1 0/0:838:0:0,0:453,384:0.0:2,0:26.1:1.0:31.4:1.0:1.0:0.0:60.0:103.625:0.9988:0.0:0.1 -2 190718940 . A C 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTATTTTCATAATTTCCCCT;RSEQ=ACATTTGTTAATTTGTATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:71:49,22:109,55:0.3021:2,2:24.5:1.0:31.6:1.0:0.76324:1.12:60.0:142.0:0.3034:0.0:1.0 0/0:228:0:0,0:160,68:0.0:2,0:23.3:1.0:28.4:1.0:1.0:0.0:60.0:113.0:1.0:0.0:0.1 -2 196860410 . G T 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.09245;LSEQ=ACTAGGGAGAGAAGATAAAG;RSEQ=GTGGTGGTGCTGGGCAGATG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:34:2,32:1,36:0.4789:1,2:25.4:1.0:30.5:1.0:0.60381:2.23:60.0:33.0:0.4714:0.0:1.1 0/1:39:3:0,3:1,35:0.0769:1,0:26.3:1.0:28.0:1.0:1.0:0.0:60.0:6.0:0.0769:0.0:1.3 -2 198257008 . C G 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGAAGTAGCTGTGCATTAAA;RSEQ=ACAAAATAAACAATAAAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:110:80,30:120,54:0.3873:2,2:25.2:1.0:31.7:1.0:0.59362:1.2:60.0:220.0:0.3873:0.0:1.2 0/0:247:0:0,0:164,83:0.0:2,0:24.4:1.0:31.3:1.0:1.0:0.0:60.0:494.0:1.0:0.0:0.1 -2 198265952 . CA C 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.14086;SOR=0.0;LSEQ=TAAGTATTAATCCTCGAATC;RSEQ=AAATCAAAATGGAAGTTAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:5,0:17,7:0.1724:2,0:34.2:1.0:32.2:1.0:0.29649:0.0:60.0:10.0:0.1724:0.0:0.0 0/0:18:0:0,0:17,1:0.0:1,0:22.2:1.0:31.1:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.2 -2 198266602 . G A 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=ACCCAATAGCCTTCAAGAAA;RSEQ=CAGCCAAACCCTATTTTTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:38:18,20:201,279:0.0731:2,2:22.4:1.0:30.3:1.0:0.60933:1.25:60.0:76.0:0.0738:0.0:1.1 0/0:506:0:0,0:230,275:0.0:2,0:24.1:1.0:31.9:1.0:1.0:0.0:60.0:100.0:1.0:0.0:0.1 -2 202149589 . G C 206 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.15456;LSEQ=ATTTTGAGATCAAGCCCCAC;RSEQ=ATGACTGCACAGTAGAGCAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:91:39,52:264,265:0.1463:2,2:25.8:1.0:31.8:1.0:0.25623:1.32769:60.0:182.0:0.1472:0.0:1.1 0/1:776:20:11,9:389,365:0.0258:2,2:21.2:1.0:30.8:1.0:0.82353:1.15:60.0:40.0:0.026:0.0:1.1 -2 204637705 . TTCATCATCATCA T 177 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=11.0;MSILEN=3.0;SSF=0.0;SOR=0.06525;LSEQ=TCATCAAAATCATTATCATT;RSEQ=TCATCATCATCATCATCATC;STATUS=AFDiff GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:104:56:31,25:9,11:0.5385:2,2:26.6:1.0:30.5:1.0:0.44756:1.51:59.3:112.0:0.5385:0.125:0.2 0/1:86:6:5,1:7,8:0.0698:2,2:25.8:1.0:30.8:1.0:0.1778:5.28:55.0:12.0:0.0698:0.0233:0.3 -2 209102117 . A ACT 104 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CTAGGCAACCGGCAGTAGAG;RSEQ=CAGCCATACATACTCAGTTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:1.0:0,2:24.1:1.0:31.4:1.0:1.0:0.0:60.0:20.0:1.0:0.2:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 209103969 . G GA 97 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.00398;SOR=0.0;LSEQ=AAATGGAAGCTAAAAGAGGG;RSEQ=AAAAAAAACACAACACTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:9:3,6:99,238:0.0259:2,2:28.4:1.0:30.8:1.0:0.7264:1.2:60.0:18.0:0.0264:0.0:0.2 0/0:317:0:0,0:107,210:0.0:2,0:23.8:1.0:30.7:1.0:1.0:0.0:60.0:104.667:1.0:0.0:0.1 -2 212251910 . G A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.15394;LSEQ=AACATATGTGGAGAGAAGGC;RSEQ=TTGTTAGAAATAGTTTAAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:55:13,42:29,132:0.2546:2,2:21.7:1.0:30.9:1.0:0.42992:1.41:60.0:110.0:0.2558:0.0:1.1 0/1:221:11:2,9:53,157:0.0498:2,2:19.0:1.0:30.7:1.0:0.73544:1.51644:60.0:22.0:0.0505:0.0:1.1 -2 212292969 . T AAATAAAATA 82 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.07824;SOR=0.0;LSEQ=AAATAAAATAAAATAAAATA;RSEQ=TTTTTTTTCATTGAGAAAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:7:7,0:23,0:0.2258:1,0:25.4:1.0:29.4:1.0:1.0:0.0:60.0:14.0:0.2258:0.0645:1.3 0/0:16:0:0,0:15,0:0.0:1,0:19.9:1.0:27.8:1.0:1.0:0.0:60.0:14.0:0.9333:0.0:0.6 -2 212295468 . GTA G 118 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.0;MSILEN=2.0;SSF=0.00585;SOR=0.0;LSEQ=ACGGAAGCTGGTAATATATG;RSEQ=TATATATATGTGTGTGTATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:13,0:13,0:0.5:1,1:26.8:1.0:32.0:1.0:1.0:0.0:60.0:26.0:0.5:0.0769:0.0 0/0:10:0:0,0:10,0:0.0:0,0:23.0:1.0:30.0:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 -2 212295492 . GATATAT ATATATC 139 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=2e-05;SOR=0.0;LSEQ=ATATATATGTGTGTGTATAT;RSEQ=ATATACACACACATATATAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:24:24,0:19,0:0.5581:1,1:23.5:1.0:30.4:1.0:1.0:0.0:60.0:48.0:0.5714:0.186:0.1 0/0:17:0:0,0:17,0:0.0:1,0:23.6:1.0:32.4:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.2 -2 212426588 . C T 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01853;LSEQ=TCCAGGTTAGGAAATATTAA;RSEQ=CTAAAAATGTAATTTCCATA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:41:31,10:272,146:0.0893:2,2:25.6:1.0:30.4:1.0:0.22631:1.66:60.0:40.0:0.0877:0.0:1.0 0/0:553:1:0,1:351,200:0.0018:2,0:1.0:0.0:25.0:0.0:0.36413:0.0:60.0:2.0:0.0018:0.0:1.0 -2 212522450 . C T 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00299;LSEQ=TAACTAGGAAAGGATTTGAG;RSEQ=GACAAAATGGAAACATGGTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:143:94,49:154,81:0.3773:2,2:24.3:1.0:29.5:1.0:1.0:1.01:60.0:46.667:0.3794:0.0:1.1 0/0:556:1:0,1:324,230:0.0018:2,0:1.0:0.0:25.0:0.0:0.41622:0.0:60.0:2.0:0.0018:0.0:1.0 -2 212522651 . A G 232 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGAGCCTTGGAGGAAGAAC;RSEQ=TGGGAAGCAAGCACACCAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:187:99,88:225,242:0.2859:2,2:26.4:1.0:30.8:1.0:0.29917:1.21:60.0:92.5:0.2864:0.0:1.1 0/0:808:0:0,0:391,415:0.0:2,0:26.4:1.0:29.9:1.0:1.0:0.0:60.0:200.5:0.9975:0.0:0.1 -2 212544080 . T C 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00814;SOR=0.0;LSEQ=TACCCACAACTTCTTCTATA;RSEQ=TGCAGAGTCCTAGTAGCTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:1,7:0.4667:2,0:26.6:1.0:33.6:1.0:1.0:0.0:60.0:14.0:0.4667:0.0:1.0 0/0:12:0:0,0:1,11:0.0:2,0:31.3:1.0:30.7:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.3 -2 212578523 . C T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03082;SOR=0.0;LSEQ=ACAACTCTTTGTTTAAATAT;RSEQ=TCAACCTGAAATTGTATTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:0,6:0,22:0.2143:1,0:21.5:1.0:30.3:1.0:1.0:0.0:60.0:12.0:0.2222:0.0:1.0 0/0:21:0:0,0:1,20:0.0:1,0:21.2:1.0:32.8:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.0 -2 212589774 . A G 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAGGAAAGGAGAGCAGGAT;RSEQ=ATAAAAGAGAGAAATCACAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:21:17,4:194,76:0.0722:2,2:30.2:1.0:32.7:1.0:0.45452:1.66:60.0:42.0:0.0724:0.0:1.1 0/0:346:0:0,0:243,103:0.0:2,0:24.0:1.0:28.2:1.0:1.0:0.0:60.0:85.5:1.0:0.0:0.1 -2 212698775 . T A 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0616;LSEQ=TAATTTTATGTCTATGAAAC;RSEQ=GACAATATGTCATCCTTCCG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:129:46,83:45,74:0.5202:2,2:25.8:1.0:30.4:1.0:0.79226:1.09683:60.0:42.0:0.5207:0.0:1.7 0/1:241:15:7,8:82,144:0.0622:2,2:20.6:1.0:29.9:1.0:0.42147:1.53:60.0:30.0:0.0622:0.0:1.3 -2 212812057 . G A 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00015;SOR=0.0;LSEQ=TGATATTTAAATGCCTTAGA;RSEQ=TGTTCCTCAATGTAACAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:17:17,0:117,1:0.1259:1,1:22.2:1.0:29.7:1.0:1.0:0.0:60.0:16.0:0.1203:0.0:1.0 0/0:88:0:0,0:84,4:0.0:1,0:25.2:1.0:32.3:1.0:1.0:0.0:60.0:176.0:1.0:0.0:0.4 -2 213402964 . A AC 104 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01457;SOR=0.0;LSEQ=AGGAGAGAAAAGAGGGACTC;RSEQ=GAGTGATTTTTCACGATAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:9,0:15,0:0.375:1,0:18.8:1.0:32.9:1.0:1.0:0.0:60.0:18.0:0.375:0.0833:0.0 0/0:13:0:0,0:11,2:0.0:2,0:24.8:1.0:31.1:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.1 -2 220439102 . G T 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCATTGAAGTCTAATACAAA;RSEQ=TCTTAGTGCTGGTGAAGTGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:28.8:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -2 225069340 . C A 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTCAAAGGATTTTTCAGTT;RSEQ=CATTTTTCTTATAGGAAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:19:8,11:97,102:0.0872:2,2:23.3:1.0:29.3:1.0:0.63691:1.306:60.0:38.0:0.0884:0.0:1.1 0/0:224:0:0,0:116,108:0.0:2,0:26.7:1.0:30.8:1.0:1.0:0.0:60.0:55.0:1.0:0.0:0.4 -2 226701540 . A C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.0;MSILEN=1.0;SSF=0.00773;SOR=0.0;LSEQ=ACAAAAAAAAACTGTAAAAC;RSEQ=AAAAGGTCATTATGTCATAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:6:0,6:0,27:0.1818:1,0:30.0:1.0:33.7:1.0:1.0:0.0:60.0:12.0:0.1818:0.0:1.0 0/0:38:0:0,0:0,38:0.0:1,0:25.0:1.0:30.9:1.0:1.0:0.0:60.0:76.0:1.0:0.0:0.1 -2 237242244 . T C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03571;SOR=0.0;LSEQ=GGGTTTCATGCTTGCGGACT;RSEQ=GGTTCTGGGCACGCATGAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:21.7:1.0:29.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:38.0:1.0:31.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -20 61098 . C T 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06342;SOR=0.0;LSEQ=CTGCCAAGCACAGACAACCA;RSEQ=TGGGCCCCAGGGGAGCTGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:2,4:5,6:0.3529:2,2:20.7:1.0:31.7:1.0:1.0:1.6177:60.0:12.0:0.3529:0.0:1.3 0/0:9:0:0,0:5,4:0.0:2,0:25.3:1.0:31.3:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.2 -20 1421974 . T C 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACAGGGTTGCTGGGCATGA;RSEQ=TGTTAACAAGATCAAACAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:37:14,23:63,124:0.1652:2,2:26.5:1.0:32.4:1.0:0.70539:1.2:60.0:74.0:0.1682:0.0:1.9 0/0:152:0:0,0:57,95:0.0:2,0:23.6:1.0:29.0:1.0:1.0:0.0:60.0:29.4:1.0:0.0:0.7 -20 9624587 . C T 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.0;MSILEN=1.0;SSF=0.00168;SOR=0.0;LSEQ=ACATCTAAAGCCAAAGTTCC;RSEQ=TTTCATGGGCTGCAATTTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:33,0:0,0:1.0:0,1:26.1:1.0:31.1:1.0:1.0:0.0:60.0:32.0:1.0:0.0:1.2 0/0:2:0:0,0:2,0:0.0:0,0:18.0:1.0:31.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -20 11361032 . G A 56 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGCAAATCAGATTAATAG;RSEQ=GCCTGAACTGAACCCCCAGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:0.8333:0,2:24.6:1.0:24.4:1.0:1.0:0.0:60.0:1.5:0.75:0.0:2.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -20 16142333 . A C 253 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08435;LSEQ=ATTTTCCTACAGACGACAAC;RSEQ=TCTGAGCAACAGAATAGGCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:465:279:139,140:94,92:0.6:2,2:25.7:1.0:31.2:1.0:0.92465:1.02904:60.0:54.8:0.5996:0.0:1.1 0/1:366:41:17,24:160,165:0.112:2,2:22.4:1.0:30.2:1.0:0.40816:1.36781:60.0:82.0:0.1142:0.0:1.2 -20 22563356 . G T 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03064;SOR=0.0;LSEQ=GGCTCTGCTGGATGGCCATG;RSEQ=TGATGAGCGAGATGTACGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:730:9:3,6:251,470:0.0123:2,2:12.9:1.0:25.8:1.0:1.0:1.06799:60.0:3.5:0.0098:0.0:2.1 0/0:425:0:0,0:187,238:0.0:2,0:26.5:1.0:31.0:1.0:1.0:0.0:60.0:211.5:1.0:0.0:0.2 -20 25733062 . T G 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.31676;SOR=0.0;LSEQ=CTTTAACCATACCCAAAGTC;RSEQ=ATTTTTATTTCTTGACAGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:6,0:32,1:0.1538:1,0:13.8:1.0:26.2:1.0:1.0:0.0:60.0:5.0:0.1316:0.0:1.0 0/0:11:0:0,0:10,1:0.0:2,0:30.2:1.0:31.5:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.0 -20 26094706 . G GA 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.05244;SOR=0.0;LSEQ=AAAACATCTAAACAGGATGG;RSEQ=AAAAAAATAGAATTAATAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:7:0,7:9,260:0.0254:1,0:20.6:1.0:31.3:1.0:1.0:0.0:40.4:14.0:0.0256:0.0036:3.0 0/0:156:0:0,0:13,142:0.0:2,0:22.7:1.0:30.9:1.0:1.0:0.0:46.7:76.5:0.9935:0.0:1.7 -20 30296422 . C T 211 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCCAAACTGACCCCTCCC;RSEQ=CCAGCTGAGCCCAGCTGTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:118:97,21:188,32:0.3471:2,2:23.9:1.0:30.7:1.0:0.43676:1.27095:60.0:117.0:0.3514:0.0:1.1 0/0:248:0:0,0:200,48:0.0:2,0:22.7:1.0:30.3:1.0:1.0:0.0:60.0:247.0:1.0:0.0:0.1 -20 30296428 . T C 189 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACTGACCCCTCCCCCCAGC;RSEQ=GAGCCCAGCTGTCAACGGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:78:63,15:251,57:0.2021:2,2:22.8:1.0:30.2:1.0:0.87164:1.04833:60.0:25.0:0.1979:0.0:1.2 0/0:267:0:0,0:210,57:0.0:2,0:23.5:1.0:30.3:1.0:1.0:0.0:60.0:52.4:1.0:0.0:0.1 -20 30296664 . G C 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05439;SOR=0.0;LSEQ=CTGGCATTGTCACTGCAGGT;RSEQ=GCAGGAGACAGGTGATGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:8:1,7:16,199:0.0359:2,2:22.6:1.0:29.3:1.0:0.47532:1.77:60.0:16.0:0.0369:0.0:1.0 0/0:121:0:0,0:9,112:0.0:2,0:22.2:1.0:30.6:1.0:1.0:0.0:60.0:242.0:1.0:0.0:0.1 -20 30309960 . C G 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAAACTGACTCCAGCTGTAT;RSEQ=CTTTCTGGGAAAGCTTGTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:29:7,22:232,409:0.0433:2,2:26.9:1.0:32.7:1.0:0.23537:1.78134:60.0:58.0:0.0438:0.0:1.1 0/0:574:0:0,0:238,336:0.0:2,0:24.9:1.0:30.6:1.0:1.0:0.0:60.0:70.75:1.0:0.0:0.1 -20 31016119 . C T 232 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.01056;LSEQ=GGACTAACCTTTATTTTCCT;RSEQ=TCTTCCAGTATCTCTTGATG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1683:206:109,97:720,757:0.1224:2,2:24.4:1.0:30.2:1.0:0.26565:1.18:60.0:205.0:0.1228:0.0:1.1 0/0:1361:2:1,1:708,651:0.0015:2,2:3.5:1.0:27.0:1.0:1.0:1.08748:60.0:4.0:0.0015:0.0:1.0 -20 31019299 . C T 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03243;LSEQ=GACAGACAGGTGCACATGGG;RSEQ=AGCCTCCCCTTTGCCTCTCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:900:82:29,53:332,486:0.0911:2,2:27.8:1.0:28.9:1.0:0.40859:1.24817:60.0:164.0:0.0927:0.0:1.1 0/0:618:2:1,1:253,362:0.0032:2,2:37.0:1.0:28.0:1.0:1.0:1.43:60.0:4.0:0.0033:0.0:1.0 -20 36030658 . C T 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.28003;SOR=0.0;LSEQ=GTGCCCTGTGCTCCCTACTC;RSEQ=CGCAGAGCACTGCTCCTGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:5,4:14,2:0.36:2,2:26.2:1.0:29.4:1.0:0.14245:5.16859:60.0:8.0:0.381:0.0:1.3 0/0:4:0:0,0:3,1:0.0:2,0:32.0:1.0:30.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -20 36970823 . C A 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.0;MSILEN=1.0;SSF=0.22078;SOR=0.0;LSEQ=CAAGATCCCTGGGGGACTTG;RSEQ=CTGCACGTCTTTGTTTCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:0.5:0,0:15.6:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.0 0/0:4:0:0,0:3,1:0.0:2,0:26.0:1.0:32.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -20 36971052 . G A 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.04162;SOR=0.0;LSEQ=CAGAAGAAATGCTCAGTGTT;RSEQ=CTAATTGTGTCCAACAGGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:6:3,3:337,174:0.0116:2,2:25.0:1.0:28.5:1.0:0.41667:1.93419:60.0:12.0:0.0118:0.0:1.0 0/0:382:0:0,0:228,153:0.0:2,0:25.1:1.0:31.6:1.0:1.0:0.0:60.0:75.2:0.9973:0.0:0.3 -20 39704995 . G A 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTTTTGTTTACCTTTGAAA;RSEQ=CAGATATCTTAATTGCATAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:29:3,26:26,130:0.1568:2,2:22.3:1.0:29.9:1.0:0.57872:1.7289:60.0:58.0:0.1593:0.0:1.0 0/0:161:0:0,0:28,133:0.0:2,0:22.4:1.0:31.8:1.0:1.0:0.0:60.0:79.5:1.0:0.0:0.1 -20 39743905 . G A 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00012;SOR=0.0;LSEQ=TCTCGGTGACGGATGTATGC;RSEQ=TGTTCCTTGTGCCTTTTTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:24:22,2:153,8:0.1297:1,2:22.3:1.0:30.4:1.0:0.62107:1.73244:60.0:48.0:0.1311:0.0:1.2 0/0:82:0:0,0:78,4:0.0:1,0:25.1:1.0:29.9:1.0:1.0:0.0:60.0:81.0:1.0:0.0:0.4 -20 39751809 . C T 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.02777;LSEQ=TTGCTGAGTCACCCTAATCC;RSEQ=CCCCTTATTTCTCCTTTGTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:971:52:32,20:546,373:0.0536:2,2:25.6:1.0:30.3:1.0:0.8847:1.09:60.0:104.0:0.054:0.0:1.1 0/0:638:1:0,1:386,251:0.0016:2,0:1.0:0.0:23.0:0.0:0.39498:0.0:60.0:2.0:0.0016:0.0:1.0 -20 40709305 . G A 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.57299;SOR=0.0;LSEQ=TGGCTGGTTAGGTTGAAAAG;RSEQ=AAGCCTGGGCCTTTTGGAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:5,0:40,0:0.1111:1,0:22.4:1.0:29.2:1.0:1.0:0.0:60.0:10.0:0.1163:0.0:1.0 0/0:12:0:0,0:12,0:0.0:0,0:23.9:1.0:31.3:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.1 -20 40710486 . C T 57 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.1631;SOR=0.0;LSEQ=AGGTCAAGGGAACTAGTCAG;RSEQ=CCTGGCTGTTGGAGAACAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:5:2,3:335,146:0.0103:2,2:11.6:1.0:24.6:1.0:0.17081:3.43182:60.0:4.0:0.0084:0.0:1.0 0/0:293:0:0,0:192,101:0.0:2,0:25.2:1.0:31.1:1.0:1.0:0.0:60.0:57.6:1.0:0.0:0.1 -20 40714097 . G C 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TACAGAGACACAGTGGGGAA;RSEQ=AGCTAATGTCTAAGAAGTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:6,0:0.4545:0,2:23.0:1.0:30.6:1.0:0.45455:0.0:60.0:10.0:0.4545:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -20 40714218 . G A 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.18296;SOR=0.0;LSEQ=TCATTGCTGAGTCTGGAGCC;RSEQ=GAATCAGCACAGGCATCACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:6:6,0:73,1:0.075:1,0:31.2:1.0:30.7:1.0:1.0:0.0:60.0:12.0:0.0779:0.0:1.0 0/0:31:0:0,0:30,1:0.0:1,0:19.8:1.0:29.4:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 -20 40714305 . T C 189 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGGCTCAGCGGGATCCTCTC;RSEQ=CGGCAGCCTCCATCTGTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:66:56,10:254,62:0.1728:2,2:25.0:1.0:31.4:1.0:0.48988:1.37:60.0:132.0:0.1769:0.0:2.1 0/0:205:0:0,0:149,56:0.0:2,0:23.6:1.0:30.0:1.0:1.0:0.0:60.0:40.0:1.0:0.0:0.1 -20 40714307 . G A 208 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCAGCGGGATCCTCTCTC;RSEQ=GCAGCCTCCATCTGTCTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:121:97,24:220,64:0.298:2,2:25.3:1.0:30.2:1.0:0.59987:1.18:60.0:59.5:0.3013:0.0:1.7 0/0:224:0:0,0:159,65:0.0:2,0:22.6:1.0:29.5:1.0:1.0:0.0:60.0:55.0:1.0:0.0:0.1 -20 40730515 . C T 77 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTAGACTTGCCATGGTGACA;RSEQ=GGGAGCCACCTTACGCTTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:0.5455:0,0:28.8:1.0:30.0:1.0:1.0:0.0:60.0:12.0:0.5455:0.0:1.0 0/0:1:0:0,0:1,0:0.0:0,0:2.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -20 40738926 . G A 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTCTCGAACTCCTGACCTC;RSEQ=TGATCTGCCCGCCTCGGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:53:41,12:297,90:0.1199:2,2:23.3:1.0:29.9:1.0:1.0:1.04:60.0:52.0:0.1201:0.0:1.1 0/0:241:0:0,0:179,61:0.0:2,0:23.6:1.0:29.8:1.0:1.0:0.0:60.0:119.0:0.9958:0.0:0.1 -20 40746918 . C T 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.00068;SOR=0.0;LSEQ=AATAGGAGTGATGACACCTC;RSEQ=CTTGTAGGTTGCCGTGAGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:25:25,0:93,2:0.2066:1,1:27.1:1.0:30.6:1.0:1.0:0.0:60.0:11.5:0.2035:0.0:1.2 0/0:41:0:0,0:41,0:0.0:1,0:20.8:1.0:30.2:1.0:1.0:0.0:60.0:40.0:1.0:0.0:0.0 -20 40748532 . C A 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGCCCTTTCCCCTGGGACC;RSEQ=CTGAAGCCTCTCTGAGGCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:27:20,7:368,185:0.0465:2,2:19.0:1.0:29.6:1.0:0.53145:1.44:60.0:54.0:0.0469:0.0:1.1 0/0:369:0:0,0:240,129:0.0:2,0:23.6:1.0:30.0:1.0:1.0:0.0:60.0:91.25:1.0:0.0:0.1 -20 40748802 . C A 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.31714;SOR=0.0;LSEQ=GTGTAGTAAGTCACTAAATG;RSEQ=TAGCTATTTTTATAGTTACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:5:0,5:0,57:0.0806:1,0:25.6:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.0806:0.0:1.0 0/0:23:0:0,0:0,23:0.0:1,0:22.0:1.0:32.0:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.1 -20 40944069 . A G 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.15152;SOR=0.0;LSEQ=TCTCTTTACTTTAATACAGG;RSEQ=GTGTGCAAAGGTTTTATGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:0.7:0,0:34.0:1.0:32.4:1.0:1.0:0.0:60.0:14.0:0.7:0.0:1.4 0/0:2:0:0,0:2,0:0.0:0,0:24.0:1.0:22.5:1.0:1.0:0.0:60.0:1.0:1.0:0.0:1.0 -20 40944812 . C T 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACGTTGTAGAACTTTACCTC;RSEQ=ACTTAGCTGTCTCAGAGCCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:0.4118:0,0:25.7:1.0:28.1:1.0:1.0:0.0:60.0:14.0:0.4118:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -20 40979469 . A T 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=9e-05;SOR=0.0;LSEQ=TAAAGACACAGCATGGATAG;RSEQ=GGGAGGACGTTTAGGAAAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:0,20:2,81:0.1942:1,1:23.4:1.0:30.6:1.0:1.0:0.0:60.0:40.0:0.198:0.0:1.5 0/0:57:0:0,0:1,56:0.0:1,0:22.2:1.0:31.2:1.0:1.0:0.0:60.0:56.0:1.0:0.0:0.3 -20 40980486 . G C 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACGTGTACTATTTAATGCAA;RSEQ=CCTGTGGGAAAATTATTTAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:0.6364:0,0:38.3:1.0:32.6:1.0:1.0:0.0:60.0:14.0:0.6364:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -20 40980495 . A C 102 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATTTAATGCAAGCCTGTGGG;RSEQ=AAATTATTTAGTGGCTTGCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:10,0:4,0:0.7143:0,0:25.4:1.0:30.9:1.0:1.0:0.0:60.0:9.0:0.6923:0.0:1.7 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -20 40980987 . G A 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.09729;LSEQ=CACTCAGGAAGCTGGATGGA;RSEQ=CTCCTTTAGAGGAACCTTAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:181:98:3,95:7,75:0.5414:2,1:25.3:1.0:29.5:1.0:0.18932:2.93825:60.0:18.6:0.5345:0.0:1.1 0/1:88:9:0,9:7,72:0.1023:2,0:19.8:1.0:29.4:1.0:1.0:0.0:60.0:18.0:0.1023:0.0:1.0 -20 41101067 . A T 186 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTCGTACTGCTGCTGGTTG;RSEQ=ACACATACTGGTACTGCACG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1064:90:43,47:456,517:0.0846:2,2:24.3:1.0:28.7:1.0:0.91228:1.04:60.0:89.0:0.0848:0.0:1.1 0/0:685:0:0,0:327,358:0.0:2,0:25.9:1.0:29.4:1.0:1.0:0.0:60.0:61.273:1.0:0.0:0.2 -20 41759593 . G A 62 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06856;SOR=0.0;LSEQ=CAACTGGTGCAGAGACAGCT;RSEQ=GCTAAGCATCTAAATACAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:366:5:4,1:133,228:0.0137:2,2:5.0:1.0:27.0:1.0:0.06741:6.82:60.0:10.0:0.0137:0.0:1.2 0/0:296:0:0,0:115,181:0.0:2,0:24.1:1.0:30.3:1.0:1.0:0.0:59.9:97.667:1.0:0.0:0.8 -20 46256424 . C T 266 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00225;LSEQ=TAAACGCCAGTCCTGAAATG;RSEQ=GCCAGAGATATGAAACAATG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1971:476:212,264:659,833:0.2415:2,2:24.4:1.0:30.0:1.0:0.91561:1.02:60.0:157.667:0.2429:0.0:1.1 0/0:1402:1:0,1:664,734:0.0007:2,0:1.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0007:0.0:1.0 -20 46271008 . G A 239 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02359;LSEQ=GTTGGGCCACCTTCCAACCT;RSEQ=GAAGGCCAGAGTGACGAAAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2367:286:145,141:1063,1015:0.1208:2,2:25.2:1.0:29.3:1.0:0.89972:1.0184:60.0:56.2:0.1209:0.0:1.1 0/0:1548:5:4,1:790,751:0.0032:2,2:11.8:1.0:25.0:1.0:0.37511:3.8:60.0:10.0:0.0033:0.0:1.0 -20 46275917 . A C 215 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGACAGACATACCCAGCAC;RSEQ=GGGGCCTCCAATGCAAGGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2348:145:71,74:1092,1108:0.0618:2,2:24.3:1.0:30.0:1.0:0.93171:1.0272:60.0:28.0:0.0602:0.0:1.2 0/0:1521:0:0,0:777,743:0.0:2,0:24.0:1.0:30.4:1.0:1.0:0.0:60.0:107.571:0.9993:0.0:0.1 -20 46277834 . A T 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01107;LSEQ=GGTGATGAGGCCTATGATGC;RSEQ=GCCCCAGGTGAGCTCCCAGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1671:114:50,64:744,811:0.0682:2,2:27.4:1.0:30.6:1.0:0.43787:1.17414:60.0:113.0:0.0685:0.0:1.2 0/0:1236:1:0,1:576,658:0.0008:2,0:1.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0008:0.0:1.0 -20 48450866 . C CTG 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=3.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=AGTGTGTATATATATATATA;RSEQ=TGTGTATATATATATATACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:4,3:0.3846:2,0:30.0:1.0:32.7:1.0:0.20455:0.0:52.8:10.0:0.4167:0.0769:0.0 0/0:1:0:0,0:0,1:0.0:0,0:17.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -20 48450987 . C TACTG 98 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.04482;SOR=0.0;LSEQ=ACTGTATATATATATATATA;RSEQ=TGTATATATATATACTGTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:10:9,1:25,0:0.2778:1,2:11.5:1.0:29.8:1.0:0.28571:0.0:58.0:20.0:0.2857:0.1944:1.0 0/0:13:0:0,0:13,0:0.0:1,0:26.3:1.0:27.1:1.0:1.0:0.0:59.8:12.0:1.0:0.0:0.8 -20 52777119 . G A 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTCAGAGGACTGGCAGCCTC;RSEQ=GCTGCAAATAAACTGTAGAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:23.0:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -20 54945145 . C T 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCAGTCAATGGTAAAATAAA;RSEQ=TTCAGTAGCATGTTCCTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:110:88,22:320,69:0.22:2,2:24.4:1.0:30.7:1.0:0.57824:1.15904:60.0:54.0:0.2204:0.0:1.1 0/0:257:0:0,0:204,53:0.0:2,0:21.4:1.0:31.4:1.0:1.0:0.0:60.0:127.5:1.0:0.0:0.1 -20 55178239 . C G 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=4e-05;SOR=0.06653;LSEQ=ACCCACCACTCACCTGCCTT;RSEQ=CCCACTTCCAGGCAGCCACC;STATUS=AFDiff GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:26:0,26:0,20:0.5652:1,1:29.3:1.0:31.8:1.0:1.0:0.0:60.0:52.0:0.5778:0.0:1.2 0/1:26:2:0,2:0,24:0.0769:1,0:10.5:1.0:24.0:1.0:1.0:0.0:60.0:1.0:0.0417:0.0:3.0 -20 57428287 . C G 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGTGCTCCATCTTACGGAG;RSEQ=CCCAAACTTATTTTGAGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1037:78:58,20:701,258:0.0752:2,2:27.7:1.0:31.1:1.0:0.89458:1.07:60.0:25.0:0.0737:0.0:1.1 0/0:572:0:0,0:358,212:0.0:2,0:25.5:1.0:31.2:1.0:1.0:0.0:60.0:80.429:0.9982:0.0:0.2 -20 59632034 . C T 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.02876;SOR=0.0;LSEQ=TCAGGATTTGAAGTTTCACG;RSEQ=CCAGCAGCAGCCCAGCCTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:7,3:8,4:0.4545:2,2:26.7:1.0:30.2:1.0:1.0:1.16:60.0:20.0:0.4545:0.0:1.1 0/0:8:0:0,0:5,3:0.0:2,0:24.6:1.0:33.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.3 -20 59928237 . T C 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.41667;SOR=0.0;LSEQ=GTTTCCACCTGTGGAAAGCA;RSEQ=ATACATGATGAATGTGCTAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:1,6:0,4:0.6364:0,2:16.6:1.0:32.6:1.0:1.0:0.0:60.0:14.0:0.6364:0.0:1.3 0/0:1:0:0,0:0,1:0.0:0,0:19.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -20 61041333 . C T 132 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00042;SOR=0.02774;LSEQ=CCCGGGGGTGGTGCCGCAGT;RSEQ=GGCCGGCCGGGACATGTGTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:19,0:3,0:0.8636:0,1:25.1:1.0:31.2:1.0:1.0:0.0:60.0:38.0:0.8636:0.0:1.1 0/1:8:1:1,0:7,0:0.125:0,0:33.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.125:0.0:1.0 -20 62173029 . A G 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGCCAACGGCCGGTGAGGCC;RSEQ=GCGTCCACCCACGTCACCTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:1,1:0.7143:2,0:28.6:1.0:30.8:1.0:0.28571:0.0:60.0:10.0:0.7143:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -21 11013029 . TAA T 92 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00264;SOR=0.0;LSEQ=GTAATTCTTTTCAGAAAAGG;RSEQ=AGTGTATTTACATACTTATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:7:0,7:21,121:0.047:2,0:27.9:1.0:32.9:1.0:0.59379:0.0:43.0:14.0:0.0483:0.0:0.0 0/0:195:0:0,0:27,167:0.0:2,0:21.7:1.0:29.8:1.0:1.0:0.0:44.1:26.714:1.0:0.0:0.6 -21 11013622 . A AT 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.08527;SOR=0.0;LSEQ=TAAAAAGACCATATTTGTAC;RSEQ=TTTTTTTTTAAAAATGGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:6:1,5:45,186:0.0253:2,2:32.7:1.0:27.3:1.0:1.0:1.20876:25.5:5.0:0.0216:0.0:0.3 0/0:158:0:0,0:36,122:0.0:2,0:26.1:1.0:29.7:1.0:1.0:0.0:26.3:51.667:1.0:0.0:0.1 -21 11020831 . T C 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00258;SOR=0.17658;LSEQ=ACCTTAATACTGACACAGTA;RSEQ=GGATGGTAACACTGACCACA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:14:12,2:190,100:0.0459:2,2:18.9:1.0:31.3:1.0:0.15233:3.15:25.4:28.0:0.0462:0.0:3.0 0/0:357:3:3,0:234,120:0.0084:2,0:15.3:1.0:32.7:1.0:0.55371:0.0:24.7:6.0:0.0085:0.0:3.0 -21 11020869 . G A 160 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.1358;LSEQ=ACACTGAGAACAGGCAAGTA;RSEQ=TCTTCCTTCTGCTCCTTGGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:40:36,4:232,207:0.0833:2,2:24.8:1.0:30.2:1.0:0.0:8.0:25.9:39.0:0.0826:0.0:2.2 0/1:575:7:7,0:309,259:0.0122:2,0:21.4:1.0:30.6:1.0:0.01829:0.0:26.6:14.0:0.0123:0.0:2.1 -21 11021018 . TAA T 207 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.18097;LSEQ=AACTAATATAGCTCTATAGC;RSEQ=ATATTGGATCACTTCTGTGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:928:106:89,17:711,111:0.1142:2,2:23.3:1.0:30.9:1.0:0.45648:1.22322:39.8:212.0:0.1156:0.0269:1.1 0/1:790:18:15,3:649,122:0.0228:2,2:20.7:1.0:30.6:1.0:1.0:1.06386:46.3:36.0:0.0231:0.0089:1.0 -21 11021107 . A T 223 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0051;LSEQ=ACAGTAAATTGTCAAGTTCA;RSEQ=ACCTGATTCAAAGTGAACTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2805:179:106,73:1527,1099:0.0638:2,2:25.8:1.0:29.9:1.0:0.81449:1.05:50.5:358.0:0.0647:0.0:1.2 0/0:2864:1:0,1:1592,1270:0.0003:2,0:1.0:0.0:26.0:0.0:0.44394:0.0:60.0:2.0:0.0004:0.0:1.0 -21 11021189 . G A 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.05512;LSEQ=TTTCTTCATCATCCTTATTT;RSEQ=ATGAAATATCTGCAGTAGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2772:88:33,55:1013,1671:0.0317:2,2:24.8:1.0:29.0:1.0:1.0:1.01037:56.4:28.333:0.031:0.0:1.2 0/0:2772:5:5,0:1131,1634:0.0018:2,0:1.0:0.0:20.6:1.0:0.01154:0.0:60.0:4.0:0.0015:0.0:1.6 -21 11021330 . CA TG 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.08436;SOR=0.16443;LSEQ=TTTGCTAAGGTCTAGAATAA;RSEQ=ATTCCAAATATTAATGCTAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:8:0,8:13,177:0.0404:2,0:18.8:1.0:31.3:1.0:1.0:0.0:36.3:16.0:0.041:0.0101:1.1 0/0:146:1:0,1:9,136:0.0068:2,0:25.0:0.0:32.5:0.0:1.0:0.0:40.0:2.0:0.0069:0.0:1.0 -21 11021519 . T G 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=4.0;SSF=0.11371;SOR=0.0;LSEQ=CTATAAATGATAATATTATA;RSEQ=GTATGTACACACACAAATCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:2,6:0.3846:2,0:34.0:1.0:31.6:1.0:0.48718:0.0:37.4:10.0:0.4167:0.0:2.0 0/0:7:0:0,0:2,5:0.0:2,0:23.0:1.0:29.0:1.0:1.0:0.0:53.1:14.0:1.0:0.0:0.1 -21 11026527 . C CAAAGAGGAAGGTAAGA 146 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=4.0;MSILEN=1.0;SSF=6e-05;SOR=0.11456;LSEQ=GGCATAGAAAGATAAGGAGT;RSEQ=AAAGAGGAAGGTAAGAAAAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:28:24,4:48,9:0.3294:2,2:19.5:1.0:30.5:1.0:1.0:1.12:41.4:27.0:0.3253:0.1882:1.3 0/1:57:3:3,0:45,9:0.0526:2,0:11.3:1.0:30.3:1.0:1.0:0.0:32.3:6.0:0.0536:0.0526:1.3 -21 11026550 . A G 146 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00043;SOR=0.15065;LSEQ=AGAGGAAGGTAAGAAAAGAG;RSEQ=AAGGATGAGAAAGTAAATAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:26:21,5:105,17:0.1757:2,2:22.1:1.0:31.2:1.0:0.54416:1.46642:36.7:52.0:0.1793:0.0:1.8 0/1:97:3:3,0:77,17:0.0309:2,0:15.3:1.0:31.3:1.0:1.0:0.0:36.7:6.0:0.0316:0.0:2.0 -21 11026647 . C A 61 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.06148;SOR=0.0;LSEQ=GACCTATTTATATGACTCAT;RSEQ=AAAATAACTTGCTATGAGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:5:5,0:233,46:0.0176:2,0:10.0:1.0:26.4:1.0:1.0:0.0:49.4:10.0:0.0177:0.0:1.6 0/0:277:0:0,0:213,57:0.0:2,0:20.3:1.0:30.6:1.0:1.0:0.0:49.7:53.0:1.0:0.0:0.2 -21 11026766 . C T 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.13335;LSEQ=TTCCACTTTTCAGCTTTGAC;RSEQ=TGCCTCGGCCACCTCGCCCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1019:31:7,24:575,413:0.0304:2,2:23.2:1.0:30.9:1.0:0.00013:4.76652:28.7:62.0:0.0306:0.0:2.4 0/0:1201:5:1,4:705,489:0.0042:2,2:15.8:1.0:30.6:1.0:0.16581:5.75947:28.2:10.0:0.0042:0.0:2.0 -21 11026786 . C T 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00021;SOR=0.16531;LSEQ=CTGCCTCGGCCACCTCGCCC;RSEQ=GACAGTCCTGCACCTCGAGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1174:19:7,12:602,553:0.0162:2,2:16.5:1.0:31.2:1.0:0.24748:1.86519:28.6:38.0:0.0165:0.0:2.6 0/0:1476:4:2,2:778,694:0.0027:2,2:12.3:1.0:27.0:1.0:1.0:1.12095:40.3:3.0:0.0021:0.0:2.8 -21 11026875 . A T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01475;SOR=0.10725;LSEQ=GGAAAAGTCAACATTCTGTG;RSEQ=CAGCCCAAAATAATTTTTAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:8:6,2:175,472:0.0122:2,2:28.6:1.0:30.0:1.0:0.00695:8.06:33.4:16.0:0.0123:0.0:1.5 0/0:756:1:1,0:229,526:0.0013:2,0:28.0:0.0:32.0:0.0:0.30423:0.0:40.0:2.0:0.0013:0.0:1.0 -21 11026964 . A G 92 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00811;SOR=0.09717;LSEQ=CTTCTTTAGATAAGTATTAA;RSEQ=AGACCTGGCTTATTATTTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:9:0,9:10,123:0.0634:2,0:20.6:1.0:29.3:1.0:1.0:0.0:25.2:18.0:0.0647:0.0:4.3 0/0:154:1:0,1:26,127:0.0065:2,0:35.0:0.0:33.0:0.0:1.0:0.0:24.0:2.0:0.0066:0.0:3.0 -21 11026966 . G A 84 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00791;SOR=0.09635;LSEQ=TCTTTAGATAAGTATTAAAA;RSEQ=ACCTGGCTTATTATTTTTAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:9:0,9:10,121:0.0643:2,0:22.6:1.0:26.8:1.0:1.0:0.0:25.2:8.0:0.058:0.0:4.3 0/0:153:1:0,1:26,126:0.0065:2,0:37.0:0.0:32.0:0.0:1.0:0.0:24.0:2.0:0.0066:0.0:3.0 -21 11027038 . C A 110 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00268;SOR=0.07929;LSEQ=TAAATATAAAATGCTTACAA;RSEQ=CTTAGAATCATACTTTAGGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:12:0,12:3,39:0.2222:2,0:23.1:1.0:30.8:1.0:1.0:0.0:30.7:24.0:0.2222:0.0:3.8 0/1:46:1:0,1:9,36:0.0217:2,0:29.0:0.0:32.0:0.0:1.0:0.0:40.0:2.0:0.0217:0.0:3.0 -21 11027052 . T C 104 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.01463;SOR=0.09156;LSEQ=TTACAACCTTAGAATCATAC;RSEQ=TTAGGCCTGTCACTGTGAAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:9:0,9:3,30:0.2143:2,0:15.9:1.0:33.0:1.0:1.0:0.0:34.3:18.0:0.2143:0.0:3.7 0/1:42:1:0,1:7,34:0.0238:2,0:43.0:0.0:34.0:0.0:1.0:0.0:40.0:2.0:0.0238:0.0:3.0 -21 11029526 . A G 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00192;SOR=0.0;LSEQ=ATCTAGAAAAGAAAGATTTA;RSEQ=TTCTTAACATCCAGTAGGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:10:8,2:250,30:0.0345:2,2:14.6:1.0:32.5:1.0:0.30406:2.07653:57.4:20.0:0.0351:0.0:1.0 0/0:269:0:0,0:230,37:0.0:2,0:24.5:1.0:29.8:1.0:1.0:0.0:50.1:52.4:0.9924:0.0:1.6 -21 11029536 . T C 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.12351;SOR=0.17042;LSEQ=GAAAGATTTAATTCTTAACA;RSEQ=CCAGTAGGGCAAAACAAATC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:356:6:6,0:298,52:0.0169:2,0:27.8:1.0:31.7:1.0:0.59834:0.0:36.0:12.0:0.0171:0.0:2.2 0/0:344:1:1,0:282,61:0.0029:2,0:43.0:0.0:33.0:0.0:1.0:0.0:25.0:2.0:0.0029:0.0:2.0 -21 11029675 . A C 220 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08487;LSEQ=ACCTCCTGAAATGTCTGGGG;RSEQ=CCACGAGGGTGGGCTCACTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1248:133:58,75:527,586:0.1066:2,2:26.9:1.0:31.3:1.0:0.46228:1.16277:40.8:43.333:0.1054:0.0:3.3 0/1:1398:14:7,7:625,756:0.01:2,2:28.6:1.0:31.0:1.0:0.79102:1.21:39.5:28.0:0.0102:0.0:3.1 -21 11029842 . G T 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00432;SOR=0.0;LSEQ=ATGGAAATTTAGGACAAATT;RSEQ=CTTCAAGGAAGGCAAAATAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:12:1,11:33,182:0.0529:2,2:26.8:1.0:30.1:1.0:1.0:1.98964:54.5:24.0:0.0533:0.0:1.0 0/0:142:0:0,0:29,113:0.0:2,0:23.5:1.0:31.9:1.0:1.0:0.0:51.3:70.0:1.0:0.0:0.3 -21 11038551 . G A 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00218;SOR=0.0;LSEQ=CCCTTCAAATTTAATAAATG;RSEQ=CATTCTTCATTAACAGCATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:14:11,3:55,9:0.1795:2,2:34.6:1.0:29.5:1.0:0.44292:1.65453:51.7:28.0:0.1842:0.0:1.3 0/0:41:0:0,0:36,5:0.0:2,0:33.9:1.0:31.0:1.0:1.0:0.0:38.8:19.5:1.0:0.0:0.5 -21 11038994 . C T 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATAACTTTATAGATTTGCCT;RSEQ=CTTGGTATGAAACATCTTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1727:76:50,26:916,732:0.044:2,2:22.2:1.0:30.4:1.0:0.09746:1.54:43.8:152.0:0.0447:0.0:2.4 0/0:1629:0:0,0:886,740:0.0:2,0:22.8:1.0:30.6:1.0:1.0:0.0:41.8:57.071:0.9981:0.0:0.4 -21 11039600 . C T 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.17084;SOR=0.0;LSEQ=TGAATGAAAGCCAAAGTACA;RSEQ=AAGGATTTATGGATTAGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:6:1,5:4,39:0.1224:2,2:14.0:1.0:29.0:1.0:0.4952:1.92:41.2:12.0:0.125:0.0:1.2 0/0:20:0:0,0:4,16:0.0:2,0:23.4:1.0:31.8:1.0:1.0:0.0:46.0:40.0:1.0:0.0:0.8 -21 11040864 . C T 61 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.07462;SOR=0.0;LSEQ=AAAAACAAAGTCAAAAGACA;RSEQ=ATAATACAGCCTGGATAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:5:1,4:0,65:0.0714:1,2:21.0:1.0:26.4:1.0:0.07143:0.0:53.0:10.0:0.0725:0.0:3.2 0/0:50:0:0,0:3,47:0.0:2,0:22.8:1.0:32.4:1.0:1.0:0.0:57.4:100.0:1.0:0.0:0.9 -21 11047650 . C T 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00115;SOR=0.0;LSEQ=TTTAAACTTATGTTTTGCAA;RSEQ=ATAAGTAATCATGAAAATCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1001:11:2,9:89,901:0.011:2,2:26.3:1.0:28.2:1.0:0.26377:2.25:60.0:22.0:0.0111:0.0:1.0 0/0:885:0:0,0:106,778:0.0:2,0:23.0:1.0:31.7:1.0:1.0:0.0:59.7:109.5:0.9989:0.0:0.2 -21 11047979 . CA TG 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=TTGAAAAGACTGTCATATAA;RSEQ=TAAAGAGGATCAAATTTGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:0.7143:0,2:24.8:1.0:31.7:1.0:1.0:0.0:60.0:10.0:0.7143:0.1429:1.8 0/0:1:0:0,0:1,0:0.0:0,0:42.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:3.0 -21 11049651 . T C 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.09753;LSEQ=ACAGTAAAACAATGAAATTG;RSEQ=TGTATAAGAATTTAAATTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:28:13,15:89,236:0.0791:2,2:26.4:1.0:31.0:1.0:0.04835:2.29:48.4:27.0:0.0778:0.0:1.3 0/0:362:3:1,2:108,251:0.0083:2,2:24.7:1.0:31.0:1.0:1.0:1.16:56.3:6.0:0.0083:0.0:1.0 -21 11049870 . A G 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.50549;SOR=0.0;LSEQ=GGCTATATCTACTTAAGACC;RSEQ=TAAGCAGGTCTTCTTTAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:2,5:0.4167:2,2:23.4:1.0:30.6:1.0:1.0:1.53983:40.6:10.0:0.4167:0.0:1.2 0/0:2:0:0,0:1,1:0.0:2,0:29.0:0.0:31.5:1.0:1.0:0.0:50.0:4.0:1.0:0.0:0.0 -21 11057701 . C A 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCACACCTATCAGGGATACA;RSEQ=AATTTCCAAGAATTTCAGAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:2,1:0.5556:2,2:9.4:1.0:30.2:1.0:1.0:1.83:53.0:10.0:0.5556:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -21 11057983 . G A 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.02288;SOR=0.0;LSEQ=TTTTTGGATTTAATTTCAAT;RSEQ=AAACCGTTGATAACATTTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:8:8,0:108,9:0.064:2,0:30.9:1.0:28.1:1.0:1.0:0.0:39.4:16.0:0.0645:0.0:3.0 0/0:83:0:0,0:62,20:0.0:2,0:21.2:1.0:31.2:1.0:1.0:0.0:53.4:40.0:0.9877:0.0:2.4 -21 11058081 . C A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03227;SOR=0.13;LSEQ=TTTTAATACAAGTAGAATAA;RSEQ=ACTCAGGGAATTTACAACAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:7:3,4:98,25:0.0538:2,2:15.0:1.0:29.1:1.0:0.04361:5.13853:30.7:14.0:0.0556:0.0:3.9 0/0:137:1:1,0:99,37:0.0073:2,0:4.0:0.0:27.0:0.0:1.0:0.0:24.0:2.0:0.0074:0.0:4.0 -21 11058248 . G A 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.12745;LSEQ=GTCGGCTCCTGCAGCACAAG;RSEQ=ATAATGATACATCTGGGTAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:30:13,17:222,245:0.0602:2,2:17.4:1.0:29.6:1.0:0.70883:1.18453:35.4:29.0:0.0591:0.0:1.9 0/0:618:5:3,2:315,297:0.0081:2,2:6.6:1.0:29.2:1.0:1.0:1.41:40.4:10.0:0.0082:0.0:2.0 -21 15377688 . T C 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0069;SOR=0.0;LSEQ=TAACTCTATAGTATTTAGTA;RSEQ=ATTGTAAAACTTATACTTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:10:0,10:0,90:0.1:1,0:30.3:1.0:32.6:1.0:1.0:0.0:40.2:20.0:0.1:0.0:1.1 0/0:64:0:0,0:0,64:0.0:1,0:22.2:1.0:28.1:1.0:1.0:0.0:45.3:63.0:1.0:0.0:0.1 -21 21056234 . C T 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01658;SOR=0.11888;LSEQ=AACGAAGCACTTTGGCTGTC;RSEQ=TTTGGTGGCGGGGCTGTGCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:3,6:0.4375:2,2:23.9:1.0:31.1:1.0:1.0:1.46:60.0:14.0:0.4375:0.0:1.6 0/1:25:2:1,1:9,14:0.08:2,2:5.5:1.0:30.0:1.0:1.0:1.53:60.0:4.0:0.08:0.0:1.5 -21 27340191 . C T 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.12012;SOR=0.19381;LSEQ=GTATTTAATCTGGTAGCTTG;RSEQ=AGGCCTCCAAAGGTGGTAGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:5:3,2:133,32:0.0292:2,2:19.2:1.0:29.0:1.0:0.26147:2.74974:60.0:10.0:0.0298:0.0:1.0 0/0:173:1:1,0:136,36:0.0058:2,0:15.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0058:0.0:1.0 -21 28978250 . G A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.03036;SOR=0.0;LSEQ=GAGCTGTCCCTTTTTGGAGG;RSEQ=GGTGTGCTACGTTGGGGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:6,8:0.3636:2,2:27.3:1.0:31.6:1.0:1.0:1.23744:60.0:16.0:0.3636:0.0:1.0 0/0:12:0:0,0:4,8:0.0:2,0:25.0:1.0:30.4:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.0 -21 31384240 . C T 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00166;SOR=0.16797;LSEQ=GCCTTTTGACCCAAAAAGAC;RSEQ=GCATAGCCTCCAATTTGAAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:19:8,11:187,141:0.0548:2,2:32.2:1.0:31.5:1.0:0.23816:1.82035:60.0:38.0:0.0556:0.0:1.5 0/0:312:3:1,2:170,139:0.0096:2,2:29.0:1.0:28.7:1.0:0.5912:2.43919:60.0:6.0:0.0098:0.0:1.3 -21 36164388 . G C 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00713;SOR=0.0;LSEQ=AGGCCCGCGCGCCCGGAGGC;RSEQ=AAGGCGGCGGCCCGCGGGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:9,0:23,0:0.2727:1,0:7.0:1.0:31.8:1.0:1.0:0.0:60.0:18.0:0.3:0.0:1.0 0/0:24:0:0,0:21,3:0.0:2,0:9.5:1.0:27.9:1.0:1.0:0.0:60.0:11.0:1.0:0.0:1.0 -21 36971853 . G A 119 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.04101;SOR=0.12689;LSEQ=CCCTGATCCTCGGTCAGAGC;RSEQ=AGCGCTTAGGTTCCCGCTGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:15,0:24,0:0.3846:1,1:20.2:1.0:30.7:1.0:1.0:0.0:60.0:30.0:0.3846:0.0:1.1 0/1:14:1:1,0:13,0:0.0714:1,0:33.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.0714:0.0:2.0 -21 37954734 . T A 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.06193;SOR=0.0;LSEQ=TATCTCCAACAAACCAGCTG;RSEQ=CAGGAAATGGTCTCAAATCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:5:3,2:188,274:0.0107:2,2:32.4:1.0:27.6:1.0:0.40344:2.18:60.0:10.0:0.011:0.0:1.6 0/0:455:0:0,0:209,246:0.0:2,0:26.5:1.0:28.8:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.9 -21 39755976 . T A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.13002;SOR=0.0;LSEQ=TCACCAGGCCTGTCCGTCCA;RSEQ=CCCTCAGCTGCAGGGGTGCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:0,7:0,11:0.3889:0,0:33.1:1.0:29.4:1.0:1.0:0.0:60.0:14.0:0.4118:0.0:1.0 0/0:6:0:0,0:1,5:0.0:2,0:33.8:1.0:28.2:1.0:1.0:0.0:60.0:5.0:1.0:0.0:0.0 -21 39764016 . A T 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CATGGCCAAGATTCAGGAAA;RSEQ=CACCGATTATTTAATGTGTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:3,4:6,1:0.5:2,2:30.0:1.0:29.3:1.0:0.26573:6.78852:60.0:14.0:0.5385:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -21 39764588 . G A 63 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=TTGTCTGAAAACTTCCATTG;RSEQ=CAGATTCTCCCAGAGCTTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:12.8:1.0:27.4:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.2 0/0:1:0:0,0:0,1:0.0:0,0:20.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -21 39794880 . T G 69 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAACAATAATCTCCAAGAAG;RSEQ=GGCAATTCCTCCCTAGAAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:24.0:1.0:29.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -21 39795279 . A T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCTCCCTGAGGCTCAGCCT;RSEQ=GCCTTGGGGAAGTTGCGATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:35:27,8:361,93:0.0716:2,2:21.6:1.0:30.9:1.0:0.67112:1.14977:60.0:70.0:0.0725:0.0:1.1 0/0:359:0:0,0:275,84:0.0:2,0:22.5:1.0:28.5:1.0:1.0:0.0:60.0:118.667:1.0:0.0:0.1 -21 42842591 . C T 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.06703;LSEQ=TCACCTTTCTCCTCGGTGGC;RSEQ=CCCCACCCGGAAATCCAGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:990:33:19,14:530,424:0.0333:2,2:25.9:1.0:29.9:1.0:0.86033:1.09:60.0:32.0:0.0331:0.0:1.2 0/0:868:2:1,1:475,391:0.0023:2,2:22.0:1.0:28.0:1.0:1.0:1.21456:60.0:4.0:0.0023:0.0:1.0 -21 42842949 . T C 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATTACATATCTCCAGGTGA;RSEQ=CAAGACGGGAAAGACACACA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:1.0:0,2:23.1:1.0:28.6:1.0:1.0:0.0:60.0:7.0:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -21 42847036 . A G 75 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAGTGAGGGGATGAGGGAGT;RSEQ=ATTCAGAGGGTGAAGGGGTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1.0:0,2:26.0:1.0:32.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -21 42848187 . C T 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCAGGGCTCACTAACGCCA;RSEQ=CCCCCTTTGCTTTCTGGAGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:1.0:0,2:22.3:1.0:30.4:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -21 42848747 . C T 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.56914;SOR=0.0;LSEQ=AGACACTGAGCCAAGGTACG;RSEQ=GGCTCACATCCCCACAGTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:5:0,5:2,28:0.1429:2,0:36.8:1.0:29.2:1.0:1.0:0.0:60.0:10.0:0.1471:0.0:1.2 0/0:7:0:0,0:0,7:0.0:0,0:15.3:1.0:30.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.7 -21 42848835 . T C 95 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=AGGACGGTTGTGAGGGTAAG;RSEQ=ATACAATAATGCTAGTTTTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:1.0:0,2:15.3:1.0:31.9:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -21 42850911 . C T 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02206;SOR=0.0;LSEQ=TAGCAGAGAAACCTCAGCCA;RSEQ=TTCCTATGAATAAACCAAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:14,0:1,0:0.9333:0,1:21.4:1.0:31.9:1.0:1.0:0.0:60.0:28.0:0.9333:0.0:2.1 0/0:2:0:0,0:2,0:0.0:0,0:21.5:1.0:33.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 -21 42860532 . G A 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05303;SOR=0.0;LSEQ=CCGTGGCATTACTGTAGCTC;RSEQ=CTGCAGCCTCCAACTCCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:8:0,8:4,124:0.0588:1,0:23.5:1.0:30.3:1.0:1.0:0.0:60.0:16.0:0.0593:0.0:1.8 0/0:77:0:0,0:6,70:0.0:2,0:25.8:1.0:31.9:1.0:1.0:0.0:60.0:75.0:0.9868:0.0:0.9 -21 42866296 . TG CA 123 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=6e-05;SOR=0.0;LSEQ=ATCCTACTTGAGGTGCACAC;RSEQ=TCCCGGATGGGGATTTGGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:16:13,3:331,192:0.0296:2,2:23.3:1.0:30.8:1.0:0.18884:2.51:60.0:32.0:0.0303:0.0074:0.9 0/0:453:0:0,0:230,172:0.0:2,0:25.4:1.0:30.4:1.0:1.0:0.0:60.0:200.0:0.8909:0.0:0.2 -21 42867003 . A T 216 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.0;MSILEN=1.0;SSF=0.0;SOR=0.00544;LSEQ=AGACTATGTCTCAAAAAAAA;RSEQ=AAAAAAAGTAATAGAAAAGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:142:109,33:238,79:0.3094:2,2:18.7:1.0:30.3:1.0:0.72586:1.1:59.9:141.0:0.3092:0.0:1.0 0/0:413:1:0,1:293,119:0.0024:2,0:1.0:0.0:22.0:0.0:0.29056:0.0:60.0:2.0:0.0024:0.0:1.0 -21 42868997 . A C 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08152;LSEQ=AGGCTGGTCTCGAACTCCCA;RSEQ=CCTCAGGTGATCTGCCTGCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:151:95:91,4:53,3:0.6291:2,1:26.5:1.0:32.3:1.0:0.71068:1.29:60.0:94.0:0.6351:0.0:1.5 0/1:108:13:13,0:95,0:0.1204:1,1:22.1:1.0:31.5:1.0:1.0:0.0:60.0:26.0:0.1238:0.0:1.5 -21 42872398 . C T 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01191;LSEQ=TTCAGTACACCATCGCTTTC;RSEQ=TGTGTCCTAAGCAGAACTGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1052:93:45,48:452,507:0.0884:2,2:22.7:1.0:30.6:1.0:0.82859:1.05:60.0:186.0:0.089:0.0:1.1 0/0:868:1:0,1:410,456:0.0012:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0012:0.0:1.0 -21 42878126 . A C 273 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07524;LSEQ=CCTGAGGCTCCAGCAACAGC;RSEQ=CAAGCTTGTTGTTAGAAGGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:804:491:251,240:167,146:0.6107:2,2:25.5:1.0:30.6:1.0:0.56278:1.09358:60.0:39.917:0.6102:0.0:1.1 0/1:655:69:44,25:304,280:0.1053:2,2:24.9:1.0:29.8:1.0:0.07416:1.62:60.0:33.5:0.1039:0.0:1.1 -21 42878780 . T G 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTCGCGGCTGGGAGCTCCG;RSEQ=GAGGTCAGGCATTGCCTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:661:52:19,33:237,370:0.0787:2,2:26.6:1.0:31.5:1.0:0.76862:1.11237:60.0:104.0:0.0801:0.0:1.2 0/0:528:0:0,0:219,309:0.0:2,0:23.8:1.0:29.2:1.0:1.0:0.0:60.0:51.8:1.0:0.0:0.2 -21 43124132 . T C 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=GGGAGTGGGGGGAGCCAAGG;RSEQ=CCGGGAGACGGAGGCTCACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:22:18,4:35,16:0.3014:2,2:28.6:1.0:31.5:1.0:0.39124:2.04:60.0:44.0:0.3099:0.0:2.5 0/0:45:0:0,0:26,19:0.0:2,0:19.6:1.0:29.2:1.0:1.0:0.0:60.0:90.0:1.0:0.0:1.7 -21 43124280 . CAT TGC 110 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.02756;SOR=0.0;LSEQ=CCCAACTCCCCCCACCCCAC;RSEQ=GCCCCCGCCCAGCCTGGCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:11:0,11:2,31:0.2292:2,0:17.2:1.0:32.0:1.0:1.0:0.0:60.0:22.0:0.2391:0.0625:1.4 0/0:18:0:0,0:2,16:0.0:2,0:22.1:1.0:31.3:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.7 -21 44524290 . A C 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0001;SOR=0.08199;LSEQ=GCCTCACTATTATTTAAATA;RSEQ=AAGAACACACTTATGAACAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:22,0:37,1:0.3667:1,1:22.2:1.0:31.9:1.0:1.0:0.0:60.0:44.0:0.3667:0.0:1.1 0/1:45:2:2,0:42,1:0.0444:1,0:10.0:1.0:29.0:1.0:1.0:0.0:60.0:4.0:0.0444:0.0:1.0 -21 45649748 . C T 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTGCACACCAGGATGCCATC;RSEQ=CATGCCAAGGGGAGGCTGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:88:43,45:334,377:0.11:2,2:24.4:1.0:30.2:1.0:0.82104:1.08:60.0:43.0:0.1101:0.0:1.9 0/0:770:0:0,0:363,407:0.0:2,0:23.1:1.0:30.1:1.0:1.0:0.0:60.0:50.333:1.0:0.0:0.5 -21 45651275 . G A 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02521;LSEQ=CACGTGGCCGCGTTTTTCTC;RSEQ=CCGGTACTGACTGGATTCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1141:151:71,80:455,532:0.1323:2,2:25.1:1.0:29.3:1.0:0.86108:1.04:60.0:36.75:0.1311:0.0:1.2 0/0:1044:4:3,1:523,516:0.0038:2,2:8.8:1.0:27.3:1.0:0.62434:2.96:60.0:8.0:0.0039:0.0:1.0 -22 16349345 . C A 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=GGGTTTTATACATAAAATTA;RSEQ=CCAAGTTGCAAATATATGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:943:19:16,3:702,221:0.0201:2,2:19.8:1.0:29.9:1.0:0.58768:1.68:45.5:18.0:0.0196:0.0:1.3 0/0:699:0:0,0:522,176:0.0:2,0:23.9:1.0:30.6:1.0:1.0:0.0:44.9:76.556:1.0:0.0:0.2 -22 16350086 . C T 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00104;SOR=0.0;LSEQ=TGTAGAGTCTAAGATAAGTA;RSEQ=CTTTCCTGTGAGGTTAGTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:17:16,1:192,8:0.0783:1,1:25.1:1.0:30.8:1.0:0.52703:1.49672:35.8:16.0:0.0755:0.0:1.1 0/0:109:0:0,0:102,7:0.0:2,0:22.1:1.0:31.2:1.0:1.0:0.0:42.0:35.333:1.0:0.0:0.2 -22 16352062 . G T 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01958;SOR=0.0;LSEQ=TTGTGTTTAGGCTGTTGAAA;RSEQ=CTTCACAAGACCATTGTTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:10:5,5:245,218:0.0211:2,2:29.7:1.0:31.3:1.0:1.0:1.12357:26.3:20.0:0.0213:0.0:2.0 0/0:239:0:0,0:112,127:0.0:2,0:27.6:1.0:32.1:1.0:1.0:0.0:26.3:118.5:1.0:0.0:0.4 -22 17055619 . G A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00143;SOR=0.0;LSEQ=TATACAGATCATGGTCCTTG;RSEQ=AATCAAGCAGATTAGGATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:13:1,12:0,50:0.2063:1,1:20.6:1.0:30.8:1.0:0.20635:0.0:48.8:26.0:0.2063:0.0:1.2 0/0:40:0:0,0:2,38:0.0:2,0:28.8:1.0:31.4:1.0:1.0:0.0:46.5:80.0:1.0:0.0:0.4 -22 17519579 . A G 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.05947;LSEQ=GCCTGAGTACCTAAGATGCA;RSEQ=TTATATGAACTCTACTCTGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:54:25,29:63,59:0.3068:2,2:24.6:1.0:32.6:1.0:0.62412:1.23713:60.0:108.0:0.3086:0.0:1.0 0/1:157:4:2,2:75,78:0.0255:2,2:19.5:1.0:31.3:1.0:1.0:1.04:60.0:8.0:0.0256:0.0:1.3 -22 21135741 . G A 62 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.11222;SOR=0.18531;LSEQ=GCTCCCGTGGTTTTATAGCA;RSEQ=CCCAGGCGAAGGAAGGAGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:5:4,1:222,208:0.0114:2,2:6.2:1.0:26.8:1.0:0.37404:3.74:60.0:10.0:0.0117:0.0:1.0 0/0:468:1:1,0:211,256:0.0021:2,0:1.0:0.0:25.0:0.0:0.45299:0.0:60.0:2.0:0.0022:0.0:1.0 -22 21272198 . G A 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.13296;SOR=0.1959;LSEQ=GGACAGCCGCCGCCCCTACC;RSEQ=CCGCAGAGTCCCCGGTCCAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:459:6:4,2:289,164:0.0131:2,2:33.3:1.0:28.8:1.0:1.0:1.13:60.0:12.0:0.0132:0.0:1.3 0/0:387:1:1,0:228,158:0.0026:2,0:3.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0026:0.0:1.0 -22 21272752 . C T 66 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.26632;SOR=0.0;LSEQ=CCTCTCACGAGGCTGTTTCT;RSEQ=AATGTGAAGAGGATGCGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:0.3333:0,0:25.2:1.0:28.6:1.0:1.0:0.0:60.0:10.0:0.3333:0.0:2.2 0/0:5:0:0,0:1,4:0.0:2,0:16.8:1.0:31.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.4 -22 21288518 . G A 59 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06543;SOR=0.0;LSEQ=CCTGTGCTTATGACAAGACT;RSEQ=CCTTGGCATTAGAGGTAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:5:4,1:122,260:0.0129:2,2:6.8:1.0:25.6:1.0:0.04053:8.48:60.0:10.0:0.0131:0.0:1.0 0/0:331:0:0,0:124,207:0.0:2,0:42.0:0.0:13.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:6.0 -22 21304408 . A G 109 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACAAGTGGAGAGAAGTTGAC;RSEQ=TGGAAAGGGTCTTCCTTCTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:1.0:0,0:19.9:1.0:31.7:1.0:1.0:0.0:60.0:22.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -22 22127490 . C T 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.28989;SOR=0.0;LSEQ=ACCGCAAACAAAAACACTGG;RSEQ=ACTACTTAATGAAGCGTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:0,5:1,11:0.2941:2,0:30.0:1.0:28.4:1.0:1.0:0.0:60.0:10.0:0.3125:0.0:1.2 0/0:5:0:0,0:0,5:0.0:0,0:26.2:1.0:33.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 -22 24134394 . T C 79 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGCGATGCTCTGCCATCTG;RSEQ=CGTGGGTGTGTCGCCATAAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:23.8:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -22 24159437 . G T 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCAGGCTGAGTGCTCCAGGG;RSEQ=GGCCTAGTAACCCAATAAGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1.0:0,0:28.1:1.0:30.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -22 24176232 . C T 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCACATCCTGCCTCTGTTCC;RSEQ=ACCCCTACACTTGGCTGCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:25:19,6:265,46:0.0744:2,2:19.7:1.0:30.8:1.0:0.2471:1.81534:60.0:50.0:0.0753:0.0:1.0 0/0:226:0:0,0:181,45:0.0:2,0:22.0:1.0:30.3:1.0:1.0:0.0:60.0:112.0:1.0:0.0:0.2 -22 24176677 . GCAACAGGTCATGTTCAATTTCTT G 228 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.14596;LSEQ=TAACAGTTTTTAAATAAAAG;RSEQ=CAACAGGTCATGTTCAATTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:601:140:55,85:205,255:0.2329:2,2:32.1:1.0:32.0:1.0:0.28514:1.24198:59.9:280.0:0.2365:0.0266:0.1 0/1:637:27:14,13:276,333:0.0424:2,2:28.9:1.0:31.2:1.0:0.55669:1.3:60.0:54.0:0.0431:0.0126:0.1 -22 24176959 . CA C 77 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGTAGCTGTGAGGCTCAGGG;RSEQ=AGAGGCTCTCTGCCTTTCAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:1,0:0.8333:0,0:16.0:1.0:33.3:1.0:0.16667:0.0:60.0:10.0:0.8333:0.1667:2.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -22 24656818 . A T 111 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01789;SOR=0.12076;LSEQ=AGCAGCGTGGGGCCAAAGAC;RSEQ=GTGGCGAGGTTGTGCAGGGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:12:7,5:45,73:0.0923:2,2:30.4:1.0:31.0:1.0:0.22021:2.26:31.2:24.0:0.0923:0.0:3.2 0/1:83:1:1,0:34,47:0.012:2,0:17.0:0.0:33.0:0.0:0.42683:0.0:23.0:2.0:0.0128:0.0:2.0 -22 24656822 . G C 114 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01737;SOR=0.11857;LSEQ=GCGTGGGGCCAAAGACAGTG;RSEQ=CGAGGTTGTGCAGGGACATC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:12:7,5:42,71:0.096:2,2:29.8:1.0:31.8:1.0:0.21401:2.35:31.2:24.0:0.0976:0.0:3.2 0/1:81:1:1,0:32,48:0.0123:2,0:13.0:0.0:34.0:0.0:0.40741:0.0:23.0:2.0:0.0127:0.0:2.0 -22 26388019 . G T 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02006;SOR=0.0;LSEQ=AGATGGGCTGAGTATCCACT;RSEQ=TGCGTGGTGGTGCAGATTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:7,1:52,6:0.1212:2,2:25.8:1.0:30.8:1.0:1.0:1.23383:60.0:16.0:0.1231:0.0:1.1 0/0:46:0:0,0:39,7:0.0:2,0:20.1:1.0:31.6:1.0:1.0:0.0:60.0:92.0:1.0:0.0:0.0 -22 29090363 . G A 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACTGCCTGTTCCCTCTCTT;RSEQ=TTGCTAGACTCAAGGTCGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:0.5556:0,0:16.8:1.0:30.4:1.0:1.0:0.0:52.6:10.0:0.5556:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:10.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -22 29093239 . A G 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=TAATAAACAACTCTTCACAC;RSEQ=GCAGAAATGTAAGGTGTCAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1.0:0,0:19.0:1.0:31.3:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -22 29120915 . T A 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGGACAAATTTTCCTCCTA;RSEQ=GAGAGAGTGGAAAAAAAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:34:28,6:185,62:0.121:2,2:23.4:1.0:30.0:1.0:0.39982:1.56:59.6:68.0:0.1241:0.0:1.1 0/0:271:0:0,0:193,78:0.0:2,0:5.0:0.0:17.0:0.0:1.0:0.0:35.0:0.0:0.0:0.0:5.0 -22 29682881 . CT C 75 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.56028;SOR=0.0;LSEQ=CAAGCCTCTTTCTAAAAAAG;RSEQ=TTTTTTTTTTTCTCTTCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,0:0.2:1,0:24.2:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.2:0.04:0.0 0/0:7:0:0,0:6,1:0.0:2,0:31.4:1.0:30.6:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.3 -22 29689837 . A G 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAAGTTTTGTGATTGCAGAC;RSEQ=TGAGCCACTGTGCCTGGCCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:5,2:0,0:1.0:0,2:23.1:1.0:30.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.9 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -22 29689868 . G A 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCCTGGCCTGTCTCTATTT;RSEQ=TTATTTTATTTTACTTTGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:1.0:0,2:17.9:1.0:29.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:2.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -22 29691910 . C T 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAAAGTCTGACTACCCCTA;RSEQ=GAGGTGGCTGTGCTCAGTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:60:36,24:194,160:0.1446:2,2:30.0:1.0:30.9:1.0:0.48495:1.24:60.0:120.0:0.1456:0.0:1.1 0/0:364:0:0,0:193,169:0.0:2,0:24.2:1.0:30.0:1.0:1.0:0.0:60.0:71.4:0.9944:0.0:0.2 -22 30053939 . C A 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.54941;SOR=0.0;LSEQ=GAAACTAAGGCCAAGAAACT;RSEQ=CGTGATGAGTCTGTTCTCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:5,0:15,1:0.2381:1,0:14.0:1.0:28.4:1.0:1.0:0.0:60.0:10.0:0.2381:0.0:1.6 0/0:4:0:0,0:4,0:0.0:0,0:24.8:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -22 37903975 . G A 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.23077;SOR=0.0;LSEQ=GCAGGTACTGAGGGTGGCAC;RSEQ=GGGCGGGGTCAGACCACAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:0.4545:2,2:10.2:1.0:30.6:1.0:1.0:1.3:60.0:10.0:0.4545:0.0:1.0 0/0:4:0:0,0:1,3:0.0:2,0:20.5:1.0:30.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -22 41525892 . A G 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAATATGTTTTCTTCTCTTT;RSEQ=GTGGCACACTGTGCATCTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:510:28:17,11:314,168:0.0549:2,2:23.9:1.0:31.9:1.0:0.68519:1.20891:60.0:56.0:0.0559:0.0:1.1 0/0:484:0:0,0:298,184:0.0:2,0:24.6:1.0:28.6:1.0:1.0:0.0:60.0:42.818:0.9958:0.0:0.1 -22 41542838 . T A 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGTAAATAGTGAAAAAAA;RSEQ=TTTTTTATTTTAAAAGAATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:30:5,25:53,229:0.0955:2,2:20.5:1.0:30.1:1.0:1.0:1.15668:60.0:29.0:0.0932:0.0:1.2 0/0:351:0:0,0:94,256:0.0:2,0:22.8:1.0:29.9:1.0:1.0:0.0:60.0:115.667:0.9971:0.0:0.1 -22 41562785 . A G 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.00029;SOR=0.0;LSEQ=TAATAGAGTAAAAATAAAAT;RSEQ=ATTCTATAATCTCCTTATAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:10:0,10:1,31:0.2381:1,0:26.0:1.0:32.5:1.0:1.0:0.0:60.0:20.0:0.2381:0.0:1.2 0/0:47:0:0,0:0,47:0.0:1,0:23.9:1.0:29.6:1.0:1.0:0.0:60.0:22.5:1.0:0.0:0.1 -22 41568804 . TAGAG T 132 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=2.0;SSF=0.00063;SOR=0.0;LSEQ=TTGGACAAGAAATATTGGCT;RSEQ=AGGTTATTAGGGTTCTGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:18:0,18:0,29:0.383:1,1:24.5:1.0:31.8:1.0:1.0:0.0:60.0:36.0:0.3913:0.0851:0.1 0/0:21:0:0,0:0,21:0.0:1,0:19.1:1.0:32.0:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.0 -22 41574383 . A C 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=AGTTGGCTACCCACCACAGC;RSEQ=GCAGCAGCGGATGCAGCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:96:46,50:403,487:0.0974:2,2:24.1:1.0:30.7:1.0:0.66658:1.11:60.0:192.0:0.0986:0.0:1.1 0/0:1042:0:0,0:470,571:0.0:2,0:25.7:1.0:30.3:1.0:1.0:0.0:60.0:68.4:0.999:0.0:0.2 -22 47217677 . C T 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCCGAATTTACATGTTGGC;RSEQ=CGTCTTGCTAGGTTGGGGAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1.0:0,2:20.0:1.0:30.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 2576521 . T C 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTATGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTATTGTTGCTGCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:18:7,11:2,2:0.7826:2,2:31.9:1.0:32.8:1.0:1.0:1.53863:52.6:36.0:0.8182:0.0:1.1 0/0:21:0:0,0:10,11:0.0:2,0:26.3:1.0:29.5:1.0:1.0:0.0:53.7:42.0:1.0:0.0:0.5 -3 10191219 . C G 95 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ATTGCCAGTGTCGCTTCATC;RSEQ=ACATTCAGTTAGTTAAAGCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:9,0:2,0:0.8182:0,0:18.8:1.0:30.0:1.0:1.0:0.0:60.0:18.0:0.8182:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 14387169 . A AG 114 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0007;SOR=0.0;LSEQ=GACTTTTCCTGATGCCCTTT;RSEQ=GTAGCCGAGCTGGCTCCAAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:1.0:0,0:27.1:1.0:31.8:1.0:1.0:0.0:60.0:24.0:1.0:0.0833:1.3 0/1:6:1:0,1:1,4:0.1667:2,0:36.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.1667:0.0:0.0 -3 17822644 . A G 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.25;SOR=0.0;LSEQ=GAGACCTAGACCTCCTCACT;RSEQ=CTGAGAAAGGAGGACTTTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:33.8:1.0:33.0:1.0:1.0:0.0:54.5:12.0:0.8571:0.0:1.0 0/0:1:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 25482579 . C T 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.00016;SOR=0.07069;LSEQ=AGGAAGAAGAAATTTTTTTT;RSEQ=GGGGGGGTGGGTGGGAATGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:16:15,1:11,0:0.5333:0,1:30.6:1.0:28.1:1.0:1.0:0.0:58.8:7.0:0.5385:0.0:1.1 0/1:28:2:1,1:23,1:0.0714:1,2:23.0:1.0:28.0:1.0:0.15077:16.61257:60.0:4.0:0.08:0.0:2.5 -3 25502851 . G A 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.07228;SOR=0.0;LSEQ=AGGTGAGTATTCACACTTCT;RSEQ=TGCCTGATGAACTCTCATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:2,3:15,29:0.102:2,2:20.0:1.0:27.6:1.0:1.0:1.28:60.0:10.0:0.102:0.0:1.0 0/0:35:0:0,0:13,22:0.0:2,0:26.4:1.0:31.3:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.2 -3 25569630 . G T 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=4.0;SSF=0.0;SOR=0.0;LSEQ=TTGAGGAAGGAAGACAGACA;RSEQ=ACTTGAAGCCAAGCCTCGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:56:18,38:32,60:0.3784:2,2:24.4:1.0:29.5:1.0:0.85806:1.12503:60.0:112.0:0.3784:0.0:1.7 0/0:233:0:0,0:95,138:0.0:2,0:23.3:1.0:31.1:1.0:1.0:0.0:60.0:76.667:1.0:0.0:0.3 -3 29047705 . C A 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=2e-05;SOR=0.0;LSEQ=ATAAGAAAATATTTAAGACT;RSEQ=TAAGAAACAAGATTAAAGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:12:4,8:57,74:0.0839:2,2:29.8:1.0:31.3:1.0:0.55719:1.53605:60.0:24.0:0.0857:0.0:2.3 0/0:203:0:0,0:87,116:0.0:2,0:25.9:1.0:31.5:1.0:1.0:0.0:60.0:66.667:1.0:0.0:0.4 -3 30692219 . T C 72 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGTTTCTCAAAGTGCGGCC;RSEQ=CTTGAGCAGCCAGCATCAGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:14.2:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 30713834 . G A 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02023;LSEQ=TCAAGAGCTCCAATATCCTC;RSEQ=TGAAGAACGACCTAACCTGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:727:37:23,14:363,327:0.0509:2,2:22.5:1.0:30.1:1.0:0.3111:1.48:60.0:36.0:0.0504:0.0:1.1 0/0:925:1:1,0:494,429:0.0011:2,0:1.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 -3 32670533 . G C 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=4e-05;SOR=0.06423;LSEQ=AGGCCAAGGCAGGTGGATTG;RSEQ=TTGAGTCCAGGCGTTTGAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:0,16:0,9:0.64:0,1:26.2:1.0:33.4:1.0:1.0:0.0:60.0:32.0:0.64:0.0:1.4 0/1:31:3:0,3:1,27:0.0968:1,0:19.3:1.0:33.3:1.0:1.0:0.0:60.0:6.0:0.1:0.0:1.0 -3 37034946 . G A 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03755;LSEQ=GGATGGCGTAAGCTACAGCT;RSEQ=AAGGAAGAACGTGAGCACGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:55:54,1:44,4:0.534:2,1:23.3:1.0:27.1:1.0:0.18155:4.84:60.0:17.333:0.5253:0.0:1.1 0/1:123:5:5,0:110,8:0.0407:2,0:19.4:1.0:27.4:1.0:1.0:0.0:60.0:10.0:0.041:0.0:1.4 -3 37050254 . T C 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.049;LSEQ=TGCCAGGACATCTTGGGTTT;RSEQ=ATTTTCAAGTACTTCTATGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:67:59,8:98,22:0.3583:2,2:23.0:1.0:31.4:1.0:0.30266:1.65:60.0:66.0:0.3568:0.0:1.1 0/1:189:5:5,0:144,40:0.0265:2,0:23.2:1.0:30.8:1.0:0.586:0.0:60.0:10.0:0.0266:0.0:1.0 -3 37061720 . G C 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11316;LSEQ=CATCTGGCCTCAAATCTTCT;RSEQ=GCCACCACATACACCATATG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:56:45,11:99,12:0.3353:2,2:22.7:1.0:30.5:1.0:0.15316:2.00761:60.0:55.0:0.3333:0.0:1.1 0/1:149:8:6,2:119,22:0.0537:2,2:28.5:1.0:30.4:1.0:0.61546:1.79459:60.0:16.0:0.0552:0.0:1.0 -3 37092173 . GTTC G 231 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.11637;LSEQ=ATTTATGCACTGTGGGATGT;RSEQ=TTCTTTCTCTGTATTCCGAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:149:47,102:97,194:0.3379:2,2:25.0:1.0:32.0:1.0:0.74797:1.08487:59.9:298.0:0.3394:0.0363:0.1 0/1:447:25:8,17:145,277:0.0559:2,2:24.2:1.0:31.5:1.0:1.0:1.11212:60.0:50.0:0.0566:0.0045:0.1 -3 41266226 . A G 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGGATTTTCTCAGTCCTTC;RSEQ=CTCAAGAACAAGTAGCTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:34:14,20:221,319:0.0591:2,2:25.7:1.0:30.8:1.0:1.0:1.01:60.0:68.0:0.0598:0.0:1.1 0/0:639:0:0,0:294,344:0.0:2,0:26.7:1.0:29.4:1.0:1.0:0.0:60.0:158.5:1.0:0.0:0.2 -3 41275350 . C T 223 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ACCCACCATCCCACTGGCCT;RSEQ=TGATAAAGGTAAATTGTCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:168:56,112:74,130:0.4492:2,2:26.2:1.0:30.3:1.0:0.58579:1.13806:60.0:167.0:0.4514:0.0:1.1 0/0:425:0:0,0:178,246:0.0:2,0:24.7:1.0:30.9:1.0:1.0:0.0:60.0:37.545:0.9976:0.0:0.1 -3 41443220 . C A 129 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCCACTCAATACTTCCACC;RSEQ=CAATTTCTCAATTTCAGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:20:10,10:168,174:0.0552:2,2:19.9:1.0:30.0:1.0:1.0:1.04:60.0:40.0:0.056:0.0:1.2 0/0:451:0:0,0:234,217:0.0:2,0:25.7:1.0:30.4:1.0:1.0:0.0:60.0:149.333:1.0:0.0:0.3 -3 47061453 . C T 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGATTCTTGGTATTAGAATC;RSEQ=GTTTAGAGGCCCTGACTCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:31:0,31:0,37:0.4559:1,1:23.4:1.0:29.5:1.0:1.0:0.0:60.0:30.0:0.4688:0.0:1.1 0/0:65:0:0,0:1,64:0.0:1,0:20.6:1.0:28.9:1.0:1.0:0.0:60.0:15.25:1.0:0.0:0.3 -3 47098278 . A G 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACATCCCATGAACAGACCAT;RSEQ=AAGCAGAAAAGAAAAGTTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:70:53,17:166,49:0.2456:2,2:23.4:1.0:32.1:1.0:0.87054:1.08631:60.0:140.0:0.2491:0.0:1.1 0/0:308:0:0,0:203,103:0.0:2,0:13.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 -3 48515221 . G A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=GGCTCACACCTGCAATCCCA;RSEQ=CACTTTGGGAGGCCGAGGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:0,9:1,8:0.5:2,0:33.2:1.0:30.8:1.0:1.0:0.0:60.0:18.0:0.5:0.0:1.0 0/0:29:0:0,0:1,28:0.0:1,0:18.8:1.0:32.2:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.0 -3 49724236 . C A 130 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CCAGACCTTGGTCGAGGAAC;RSEQ=TGGGGGCGGTAATGGGGCGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:20:5,15:434,435:0.0225:2,2:27.1:1.0:30.3:1.0:0.03946:2.98985:30.1:19.0:0.0217:0.0:3.8 0/0:684:0:0,0:334,349:0.0:2,0:29.3:1.0:30.4:1.0:1.0:0.0:46.6:39.176:1.0:0.0:0.2 -3 49724260 . C G 194 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGCGGTAATGGGGCGTGAA;RSEQ=AAGACCCTGGGACTCTGGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:834:69:12,57:344,421:0.0827:2,2:12.3:1.0:31.8:1.0:1e-05:3.87562:32.3:68.0:0.083:0.0:3.5 0/0:662:0:0,0:285,376:0.0:2,0:24.1:1.0:31.2:1.0:1.0:0.0:50.8:93.429:0.9985:0.0:0.2 -3 49725284 . CT C 195 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATGTAGCAGGTGCTGTAG;RSEQ=CTGTGCCCCGGAGCACTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1060:70:26,44:476,510:0.066:2,2:28.8:1.0:31.9:1.0:0.08278:1.57881:54.1:140.0:0.0669:0.0038:0.2 0/0:1084:0:0,0:523,560:0.0:2,0:24.9:1.0:29.7:1.0:1.0:0.0:54.9:62.706:1.0:0.0:0.1 -3 49725685 . G A 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCATCACATTACCCAGCCA;RSEQ=GGGCCCTGGCTAGGCATTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:7,0:5,1:0.5385:2,0:28.0:1.0:31.3:1.0:0.46154:0.0:40.9:14.0:0.5385:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:15.0:0.0:24.0:0.0:1.0:0.0:50.0:2.0:1.0:0.0:0.0 -3 49725728 . C T 76 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCAAATCTGGGCTCTCAC;RSEQ=TGCACAAAGGCATATGCTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:17,3:0.2:2,0:35.8:1.0:33.0:1.0:1.0:0.0:33.4:10.0:0.2:0.0:4.0 0/0:3:0:0,0:2,1:0.0:2,0:23.3:1.0:30.7:1.0:1.0:0.0:56.7:6.0:1.0:0.0:0.0 -3 49725734 . A G 73 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATCTGGGCTCTCACCTGCAC;RSEQ=AAGGCATATGCTAGGTTAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:5,0:18,4:0.1852:2,0:39.2:1.0:31.8:1.0:0.56125:0.0:33.4:10.0:0.1852:0.0:4.0 0/0:3:0:0,0:2,1:0.0:2,0:25.3:1.0:31.3:1.0:1.0:0.0:56.7:6.0:1.0:0.0:0.0 -3 49725737 . G A 73 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGGCTCTCACCTGCACAAA;RSEQ=GCATATGCTAGGTTAGAGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:5,0:18,5:0.1786:2,0:39.8:1.0:31.8:1.0:0.5495:0.0:33.4:10.0:0.1786:0.0:4.0 0/0:3:0:0,0:2,1:0.0:2,0:26.3:1.0:32.7:1.0:1.0:0.0:56.7:6.0:1.0:0.0:0.0 -3 49725743 . T C 86 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCACCTGCACAAAGGCATA;RSEQ=GCTAGGTTAGAGGGGTAGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:6:5,1:20,4:0.2:2,2:39.7:1.0:33.3:1.0:1.0:1.0:32.0:12.0:0.2:0.0:3.7 0/0:4:0:0,0:3,1:0.0:2,0:22.3:1.0:31.5:1.0:1.0:0.0:57.5:8.0:1.0:0.0:0.0 -3 49934678 . C T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00702;SOR=0.0;LSEQ=GGTCCCCACCTGGATAGAAC;RSEQ=CTGCGGCCTCCCATGCCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:7:1,6:352,167:0.0133:2,2:11.6:1.0:27.3:1.0:0.00605:12.59002:60.0:14.0:0.0136:0.0:1.0 0/0:539:0:0,0:366,172:0.0:2,0:23.3:1.0:30.0:1.0:1.0:0.0:60.0:88.667:0.9981:0.0:0.2 -3 52436441 . C A 231 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAGGTTGGCCAGCATGCCTG;RSEQ=GAAGAGGTAGAGACCCTTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:188:73,115:87,163:0.4282:2,2:24.8:1.0:30.6:1.0:0.42287:1.19:60.0:61.667:0.4263:0.0:1.1 0/0:333:0:0,0:116,217:0.0:2,0:21.9:1.0:30.2:1.0:1.0:0.0:60.0:110.0:1.0:0.0:0.1 -3 52584477 . C T 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01454;SOR=0.10646;LSEQ=TTGCTAATGCTGTTGGACTC;RSEQ=GCACTGAGTCCTTCAATGTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:703:8:2,6:399,296:0.0114:2,2:7.5:1.0:28.6:1.0:0.08048:4.03628:60.0:16.0:0.0115:0.0:1.0 0/0:818:1:0,1:457,359:0.0012:2,0:1.0:0.0:25.0:0.0:0.44064:0.0:60.0:2.0:0.0012:0.0:2.0 -3 52597664 . G A 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00055;SOR=0.0;LSEQ=GAGTTTAAATGTGTATTTAT;RSEQ=AAATTACTTGTACTTAGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:3,13:1,8:0.64:2,2:22.6:1.0:29.7:1.0:1.0:1.8:60.0:32.0:0.64:0.0:1.0 0/0:10:0:0,0:0,10:0.0:0,0:16.7:1.0:31.8:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.0 -3 52620628 . GT G 81 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.00518;SOR=0.0;LSEQ=TAATTTTCTTAAAAGATTTG;RSEQ=TTTGGCAGAATACCGTGATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:516:6:2,4:195,310:0.0116:2,2:24.2:1.0:31.7:1.0:1.0:1.25749:60.0:12.0:0.0121:0.0:0.2 0/0:721:0:0,0:308,410:0.0:2,0:25.7:1.0:29.0:1.0:1.0:0.0:60.0:28.917:1.0:0.0:0.2 -3 52663084 . T A 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGAAATTGCTAGAATTTTC;RSEQ=GTCATGAAAATTATGAAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:15:2,13:24,118:0.0955:2,2:22.4:1.0:31.4:1.0:1.0:1.31985:60.0:30.0:0.0962:0.0:1.3 0/0:215:0:0,0:51,164:0.0:2,0:22.2:1.0:30.2:1.0:1.0:0.0:60.0:430.0:1.0:0.0:0.1 -3 52676079 . G A 51 q23;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06168;SOR=0.0;LSEQ=TTACTACAAAAAAAAAAAAA;RSEQ=CAATTAGACAGGGAAGGATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:5:3,2:64,237:0.0162:2,2:13.8:1.0:22.2:1.0:0.07189:5.51:60.0:1.5:0.0117:0.0:2.0 0/0:298:0:0,0:68,229:0.0:2,0:7.0:0.0:11.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 -3 52685397 . A G 75 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATAAACAACAGGTTACCCC;RSEQ=TCTACCCTGATGTGATTATT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:28.0:1.0:29.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 52695835 . T C 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.02098;SOR=0.0;LSEQ=CAACACTGCCTTTCCTTACA;RSEQ=GATGTCTCAATGTAGCAATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:22.3:1.0:31.6:1.0:1.0:0.0:60.0:14.0:0.7778:0.0:1.0 0/0:4:0:0,0:3,1:0.0:2,0:5.0:1.0:28.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -3 55487222 . A T 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0041;SOR=0.08718;LSEQ=CAATGGTCTCTTGCTCTTGC;RSEQ=GCCCCAGGTCAGAAATCTAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:10:6,4:156,62:0.0439:2,2:29.5:1.0:29.6:1.0:0.48052:1.67328:60.0:20.0:0.0441:0.0:1.0 0/0:252:1:0,1:170,81:0.004:2,0:1.0:0.0:23.0:0.0:0.3254:0.0:60.0:2.0:0.004:0.0:1.0 -3 55487515 . C T 131 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.00818;LSEQ=GTGCTATGATTCCAAACTGC;RSEQ=AAACTGCTGAGCAATCCTAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:28:0,28:0,1:0.9655:0,1:24.5:1.0:27.3:1.0:1.0:0.0:60.0:27.0:0.9643:0.0:1.3 0/1:8:1:0,1:0,7:0.125:0,0:39.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.125:0.0:1.0 -3 69986144 . A G 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.2125;SOR=0.0;LSEQ=TGTGTGGCTAAACTATCTTC;RSEQ=TCAGCTCCTGTTCATTGCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:0.5385:0,0:20.6:1.0:31.7:1.0:1.0:0.0:60.0:14.0:0.5833:0.0:1.7 0/0:3:0:0,0:0,3:0.0:0,0:14.7:1.0:28.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:2.7 -3 70005281 . A G 72 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=AGAATTTGGGCTTTCACCAG;RSEQ=TATTGTTGGATGTCCTCGCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:27.2:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 70005712 . T C 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TCGCGTGTTAATCTGCATCA;RSEQ=ATATTTTTCGTACCTGAATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:24:8,16:136,275:0.055:2,2:24.7:1.0:31.5:1.0:1.0:1.01:60.0:23.0:0.0536:0.0:1.4 0/0:449:0:0,0:162,287:0.0:2,0:6.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 -3 70014447 . T C 308 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01916;LSEQ=AAACTGCTTCCTTTCTTGAT;RSEQ=CGTAGATTTAATAACTTACC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1159:992:376,616:63,101:0.8559:2,2:25.1:1.0:31.0:1.0:0.93086:1.0219:60.0:75.308:0.8565:0.0:1.1 0/1:1374:140:61,79:511,723:0.1019:2,2:25.3:1.0:30.7:1.0:0.65143:1.09:60.0:280.0:0.1025:0.0:1.1 -3 70348641 . A C 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01136;SOR=0.0;LSEQ=CCCCTAGAGACATATTAAAA;RSEQ=TTCCCATTGAATCCAGAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,1:0.7:2,0:22.6:1.0:32.1:1.0:0.3:0.0:60.0:14.0:0.7778:0.0:1.3 0/0:6:0:0,0:6,0:0.0:0,0:36.5:1.0:29.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 -3 71019797 . A T 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00899;LSEQ=TTTAACGGAATTAAAATTTA;RSEQ=TATCTAATTAGAGCAAGGCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:56:50,6:89,13:0.3544:2,2:23.7:1.0:30.9:1.0:0.80225:1.22:60.0:112.0:0.3544:0.0:1.5 0/0:206:1:0,1:175,30:0.0049:2,0:1.0:0.0:26.0:0.0:0.15049:0.0:60.0:2.0:0.0049:0.0:1.0 -3 71049945 . A AAAAATAAAAT 125 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=53;MSI=12.0;MSILEN=5.0;SSF=5e-05;SOR=0.0;LSEQ=TGAACCTGCCCAAAGAGGTA;RSEQ=AAAATAAAATAAAATAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:16:16,0:2,0:0.6957:0,1:12.1:1.0:31.3:1.0:1.0:0.0:57.9:32.0:0.6957:0.4348:0.0 0/0:13:0:0,0:5,0:0.0:0,0:22.4:1.0:30.4:1.0:1.0:0.0:60.0:10.0:0.3846:0.0:0.0 -3 71096086 . C T 59 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.09442;SOR=0.15965;LSEQ=TATGCCTTCTGTAAAATCAA;RSEQ=GCATACCTTGAGCAAGAGGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:5:2,3:240,151:0.0126:2,2:28.8:1.0:25.8:1.0:0.38132:2.3787:60.0:1.5:0.0077:0.0:1.2 0/0:493:1:0,1:276,216:0.002:2,0:1.0:0.0:28.0:0.0:0.44016:0.0:60.0:2.0:0.002:0.0:1.0 -3 71103136 . T C 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.02424;SOR=0.0;LSEQ=GTAAAATCTTGCAGTACTGA;RSEQ=GGGGGTTCCAGGCAGCCTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:14.7:1.0:30.1:1.0:1.0:0.0:60.0:14.0:0.875:0.0:1.0 0/0:3:0:0,0:0,3:0.0:0,0:14.3:1.0:31.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -3 71246918 . C T 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATGTATTTATTTCAACTCT;RSEQ=CTTACTCATCTACTCTTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:15,1:16,0:0.5:1,1:26.1:1.0:30.6:1.0:1.0:0.0:60.0:32.0:0.5:0.0:1.1 0/0:35:0:0,0:34,1:0.0:1,0:20.1:1.0:29.9:1.0:1.0:0.0:60.0:16.5:1.0:0.0:0.3 -3 71247014 . A T 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00056;SOR=0.0;LSEQ=CGTTTAATTTTTATTTTTGC;RSEQ=TGAAAGCAGTGGGAACCATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:9:7,2:178,35:0.0405:2,2:24.2:1.0:31.7:1.0:0.64735:1.45033:60.0:18.0:0.0411:0.0:1.0 0/0:283:0:0,0:199,84:0.0:2,0:22.5:1.0:29.3:1.0:1.0:0.0:60.0:39.429:1.0:0.0:0.1 -3 71247304 . A G 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.1111;LSEQ=TAAGTGTAAAATTCAGCAGT;RSEQ=AAATTCGCACCCACCACCTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:118:81,37:131,64:0.3758:2,2:22.8:1.0:31.8:1.0:0.80437:1.07:60.0:38.333:0.3746:0.0:1.1 0/1:384:24:14,10:243,117:0.0625:2,2:26.0:1.0:31.2:1.0:0.37478:1.48195:60.0:48.0:0.0628:0.0:1.1 -3 71247572 . A T 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.07771;LSEQ=AGGATTTCCAAGATGGGGGG;RSEQ=GGGAGGGGGGGAGAAAAAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:250:132:72,60:11,11:0.528:2,2:14.7:1.0:27.1:1.0:0.81808:1.2:59.8:8.429:0.5673:0.0:1.3 0/1:314:25:15,10:124,61:0.0796:2,2:13.5:1.0:26.1:1.0:0.50462:1.35311:60.0:7.333:0.0833:0.0:1.2 -3 72323080 . G A 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGGAACTCCAGAACTTCCC;RSEQ=AGCACCTTGTCTGGTGGTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:21:15,6:117,40:0.118:2,2:22.9:1.0:29.7:1.0:0.79248:1.16891:60.0:20.0:0.113:0.0:1.4 0/0:242:0:0,0:177,65:0.0:2,0:26.3:1.0:29.3:1.0:1.0:0.0:60.0:25.889:1.0:0.0:0.1 -3 72323287 . A G 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.08131;LSEQ=ACTTCGGGTTTCCCCAAGAC;RSEQ=CTCAGGGTTCCCCAGGGCAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:68:9,59:11,85:0.4146:2,2:25.0:1.0:31.4:1.0:0.81032:1.18:60.0:33.0:0.4074:0.0:1.1 0/1:148:8:0,8:15,125:0.0541:2,0:34.3:1.0:32.8:1.0:1.0:0.0:60.0:16.0:0.0541:0.0:1.0 -3 72455797 . A C 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00207;SOR=0.0;LSEQ=AACAAAGGTATTTTAAATAG;RSEQ=TCCCCCGAGGAGATTCTAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:11,0:10,0:0.5238:0,0:24.3:1.0:32.8:1.0:1.0:0.0:60.0:22.0:0.5238:0.0:1.0 0/0:12:0:0,0:12,0:0.0:0,0:14.7:1.0:28.4:1.0:1.0:0.0:60.0:11.0:1.0:0.0:0.1 -3 75164938 . A T 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATGCCCCATAATTTGAATA;RSEQ=ATAATCAAGAAAATGAGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:44:8,36:16,35:0.4632:2,2:24.0:1.0:28.3:1.0:0.16173:2.04174:60.0:43.0:0.4574:0.0:1.1 0/0:137:0:0,0:41,96:0.0:2,0:22.1:1.0:29.8:1.0:1.0:0.0:60.0:274.0:1.0:0.0:0.1 -3 87348307 . A ATTTG 89 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.0;MSILEN=4.0;SSF=0.00466;SOR=0.0;LSEQ=GAACGTAGCTATGTATGTTC;RSEQ=TTTGTGTATTGTCTATGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:33.7:1.0:31.8:1.0:1.0:0.0:60.0:14.0:0.875:0.0:0.1 0/0:5:0:0,0:0,5:0.0:0,0:10.4:1.0:30.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.6 -3 89156692 . A G 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.0;MSILEN=1.0;SSF=0.00736;SOR=0.0;LSEQ=ATCCCGCTCTGCTTCAGCGC;RSEQ=CGCTGAAGACGGCACTAGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:9,1:17,0:0.3704:1,2:33.2:1.0:31.0:1.0:0.37037:0.0:60.0:20.0:0.3704:0.0:1.3 0/0:15:0:0,0:15,0:0.0:1,0:27.2:1.0:30.4:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 -3 89905902 . C G 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTATAGGTGAGGTGAAAAT;RSEQ=CAGTGGTTGAGATTCTAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:36:0,36:0,63:0.3636:1,1:29.0:1.0:31.8:1.0:1.0:0.0:60.0:17.0:0.3542:0.0:1.2 0/0:86:0:0,0:3,83:0.0:1,0:23.2:1.0:31.7:1.0:1.0:0.0:60.0:172.0:1.0:0.0:0.2 -3 94429115 . A G 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=ATTCTTAGTGGGGAACAACA;RSEQ=CCACGGAAATTAGAACTAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:54:33,21:387,267:0.0763:2,2:27.7:1.0:32.5:1.0:0.8856:1.08:60.0:108.0:0.077:0.0:1.1 0/0:662:0:0,0:376,285:0.0:2,0:26.2:1.0:29.3:1.0:1.0:0.0:60.0:164.25:1.0:0.0:0.5 -3 106824274 . G A 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.05966;LSEQ=GGCACTCCGTGGTACAGCCA;RSEQ=GTCCACAAGTGGTATTGCCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:92:52,40:78,67:0.3882:2,2:23.9:1.0:30.7:1.0:0.69034:1.12:60.0:184.0:0.3898:0.0:1.8 0/1:248:9:5,4:127,112:0.0363:2,2:24.0:1.0:30.3:1.0:1.0:1.1:60.0:18.0:0.0364:0.0:1.7 -3 106824304 . C T 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0924;LSEQ=TGGTATTGCCAGACCATTCT;RSEQ=TCCATATTCCCTTGTCCAAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:106:62,44:80,83:0.3941:2,2:23.1:1.0:30.2:1.0:0.13607:1.46:60.0:212.0:0.3985:0.0:1.7 0/1:248:14:10,4:121,111:0.0565:2,2:20.2:1.0:28.9:1.0:0.18018:2.29:60.0:13.0:0.0533:0.0:1.6 -3 106825018 . A AT 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.06153;SOR=0.0;LSEQ=CGCGCCCGGCCTTTATATCT;RSEQ=TTTTTGGTTTTGTTTTCTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:5:1,4:233,73:0.0161:2,2:12.8:1.0:28.2:1.0:0.01433:12.64045:60.0:10.0:0.0164:0.0096:0.6 0/0:306:0:0,0:221,85:0.0:2,0:21.2:1.0:28.4:1.0:1.0:0.0:60.0:152.0:1.0:0.0:0.3 -3 106825024 . G C 230 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08663;LSEQ=CGGCCTTTATATCTATTTTT;RSEQ=GTTTTGTTTTCTTGCCTTCG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:345:177:131,46:124,42:0.513:2,2:21.6:1.0:30.8:1.0:0.90213:1.03662:59.9:87.5:0.5147:0.0:1.3 0/1:336:28:20,8:218,90:0.0833:2,2:25.7:1.0:30.8:1.0:1.0:1.03:60.0:56.0:0.0843:0.0:1.3 -3 106825180 . A T 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=ACTCTGCTTTCTATTTCAGC;RSEQ=GCATTTGTACAAGTCGTGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:38:21,17:373,347:0.0501:2,2:21.0:1.0:31.0:1.0:0.74047:1.15:59.4:76.0:0.0505:0.0:1.2 0/0:724:0:0,0:329,395:0.0:2,0:25.8:1.0:30.4:1.0:1.0:0.0:59.6:102.429:1.0:0.0:0.2 -3 117078556 . C G 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.00027;SOR=0.0;LSEQ=AAAAAGGCCTCCACAAAAAA;RSEQ=CCATCCAAGGGTCAGCAGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:9:5,4:19,17:0.2:2,2:22.6:1.0:32.1:1.0:1.0:1.12:60.0:18.0:0.2045:0.0:1.1 0/0:61:0:0,0:31,30:0.0:2,0:26.4:1.0:31.0:1.0:1.0:0.0:60.0:60.0:1.0:0.0:0.3 -3 117078561 . C T 129 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGCCTCCACAAAAAACCCAT;RSEQ=CAAGGGTCAGCAGCCTCAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:21:10,11:13,10:0.4565:2,2:26.3:1.0:29.5:1.0:0.76304:1.41833:60.0:20.0:0.4651:0.0:1.2 0/0:61:0:0,0:30,31:0.0:2,0:25.3:1.0:30.7:1.0:1.0:0.0:60.0:29.5:1.0:0.0:0.3 -3 117863221 . C A 85 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.03518;SOR=0.08879;LSEQ=ATTTCTGCTGGTTTGTTTTT;RSEQ=TTTCAATAGTCAGGTCCCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:3,5:0.4667:2,2:29.6:1.0:30.3:1.0:1.0:1.46001:60.0:14.0:0.4667:0.0:2.1 0/1:15:1:0,1:6,8:0.0667:2,0:19.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0667:0.0:2.0 -3 118845663 . T C 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02424;SOR=0.0;LSEQ=AAAGAAAAACAAGCAGAAAG;RSEQ=GACAACAACAGCATCAACAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:2,5:1,0:0.875:0,2:24.4:1.0:31.4:1.0:0.375:0.0:60.0:14.0:0.875:0.0:1.0 0/0:3:0:0,0:1,2:0.0:2,0:11.0:1.0:31.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 -3 128199913 . G T 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00484;LSEQ=TGGGGGTGGCCGAAGGAGAG;RSEQ=CTGGAGGAGGGGTGGATGGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:895:223:129,94:374,296:0.2492:2,2:24.5:1.0:29.4:1.0:0.64019:1.09:60.0:43.6:0.2489:0.0:1.2 0/0:622:1:0,1:327,294:0.0016:2,0:1.0:0.0:23.0:0.0:0.47428:0.0:60.0:2.0:0.0016:0.0:1.0 -3 134670080 . A C 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00097;SOR=0.0;LSEQ=CTTAGATGTGTTCATTTCTC;RSEQ=AGTCAATCTGCTGGACTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:20:19,1:88,1:0.1835:1,1:25.1:1.0:31.0:1.0:0.33469:4.5399:60.0:19.0:0.1776:0.0:1.1 0/0:45:0:0,0:44,0:0.0:1,0:20.9:1.0:30.2:1.0:1.0:0.0:60.0:43.0:0.9773:0.0:0.1 -3 134851577 . A T 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGTCCCATCAGGTCCCCGCA;RSEQ=TGTTATCTCCATCGTCAATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:841:95:56,39:412,334:0.113:2,2:25.4:1.0:30.3:1.0:0.51246:1.16:60.0:46.5:0.1122:0.0:1.2 0/0:707:0:0,0:388,319:0.0:2,0:24.7:1.0:29.7:1.0:1.0:0.0:60.0:87.375:1.0:0.0:0.2 -3 134884695 . G C 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=ACTTACAACTCTGACACATA;RSEQ=AAACTATCCTCTACATATAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:25:24,1:93,3:0.2066:1,1:22.4:1.0:32.1:1.0:1.0:1.28874:60.0:50.0:0.2083:0.0:1.1 0/0:67:0:0,0:65,2:0.0:1,0:23.1:1.0:31.8:1.0:1.0:0.0:60.0:32.5:1.0:0.0:0.2 -3 134885042 . A C 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACAATCATCACTCCATCTC;RSEQ=ATCCAAGAGCAGCCTAGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:40:0,40:0,91:0.3053:1,1:22.4:1.0:32.3:1.0:1.0:0.0:60.0:80.0:0.315:0.0:1.1 0/0:58:0:0,0:1,57:0.0:1,0:21.2:1.0:30.7:1.0:1.0:0.0:60.0:57.0:1.0:0.0:0.1 -3 134911143 . A AAAAACAAACTCACATATATTCTGAAATTCCACTT 109 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGAAAAATTAAGTGTGGGG;RSEQ=AAAACAAACTCACATATATT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:12,0:2,0:0.8571:0,0:18.8:1.0:30.6:1.0:1.0:0.0:57.5:24.0:0.8571:0.6429:0.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 134960472 . T C 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTCTACCCTGCTTCTAAGTG;RSEQ=TCAGGTTCTGTGTTTTCCTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:15.0:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.625:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 134967265 . G A 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0907;LSEQ=CAGAAGGACCGGAACAGCCG;RSEQ=CCCCGGTTTGCGGAGATTGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:918:33:19,14:463,421:0.0359:2,2:25.7:1.0:30.0:1.0:0.59805:1.23:60.0:66.0:0.037:0.0:1.1 0/0:891:3:2,1:456,432:0.0034:2,2:23.0:1.0:29.0:1.0:1.0:1.89:60.0:6.0:0.0034:0.0:1.0 -3 135644964 . C T 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAATCCAGGGAAGGCTACTG;RSEQ=GGAAATCAAGAAAATGTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:32:8,24:52,121:0.1561:2,2:23.0:1.0:30.2:1.0:0.67456:1.28769:60.0:31.0:0.1535:0.0:1.2 0/0:193:0:0,0:60,133:0.0:2,0:23.0:1.0:30.2:1.0:1.0:0.0:60.0:95.5:1.0:0.0:0.1 -3 137443260 . G A 64 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.01149;SOR=0.0;LSEQ=GCTGATGAAGATGATGATAT;RSEQ=ATGATGCAGATGATGATGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:2,3:18,22:0.1111:2,2:29.6:1.0:27.6:1.0:1.0:1.22176:60.0:4.0:0.093:0.0:1.0 0/0:62:0:0,0:29,33:0.0:2,0:25.0:1.0:31.0:1.0:1.0:0.0:60.0:19.667:1.0:0.0:0.3 -3 137483362 . G T 66 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTTGGGTCCCAGCCCCTGGT;RSEQ=CCTGAAGCCCCCCGGCCGAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:18.0:1.0:28.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 138374293 . C T 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01849;LSEQ=CACTTTAGTAGTCCAGCTTT;RSEQ=CCTGAGCGCCTCATCAAATT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:891:50:20,30:406,433:0.0561:2,2:24.2:1.0:29.7:1.0:0.30782:1.40593:60.0:100.0:0.0573:0.0:1.0 0/0:912:1:0,1:424,486:0.0011:2,0:1.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 -3 138383144 . A C 94 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGTGGGGCTGTGAGTAGACT;RSEQ=ATGTTCACAGTACTTAGAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:1,2:0.7:2,0:23.3:1.0:33.6:1.0:0.3:0.0:60.0:14.0:0.7:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 138423181 . CAT C 161 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ACACTCACAGACTGTTCTTG;RSEQ=ATGAGTTACGGTCTTCTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:34:28,6:159,30:0.1525:2,2:24.8:1.0:31.7:1.0:0.80141:1.13502:59.4:33.0:0.1493:0.0269:0.3 0/0:204:0:0,0:153,51:0.0:2,0:22.7:1.0:30.0:1.0:1.0:0.0:60.0:101.0:1.0:0.0:0.1 -3 138661770 . CACAA C 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.29151;SOR=0.0;LSEQ=AATTTTCACGCTAGACAAAG;RSEQ=ACAGACATGCACACAGCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:4,1:18,2:0.2:2,2:17.4:1.0:30.4:1.0:0.50435:2.16466:60.0:10.0:0.2:0.04:0.2 0/0:10:0:0,0:10,0:0.0:0,0:13.0:1.0:29.8:1.0:1.0:0.0:60.0:9.0:1.0:0.0:0.0 -3 138662227 . G GGGGGGGGGGGGT 86 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.0;MSILEN=1.0;SSF=0.0092;SOR=0.0;LSEQ=GGCCAGGCCCCGAGATAGAC;RSEQ=GGGGGGGGGCAGTGAGGGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:11:0,11:1,101:0.094:1,0:42.0:1.0:25.0:1.0:1.0:0.0:59.3:22.0:0.1019:0.0855:0.1 0/0:62:0:0,0:0,60:0.0:1,0:19.5:1.0:29.7:1.0:1.0:0.0:59.9:59.0:0.9672:0.0:0.5 -3 138663179 . A G 254 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=TAGAAAATTTGGTCCCCCAA;RSEQ=CAACAAGCTACAGTACAACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:791:243:149,94:314,232:0.3072:2,2:28.4:1.0:32.1:1.0:0.34749:1.17:60.0:120.5:0.3082:0.0:1.1 0/0:789:0:0,0:427,361:0.0:2,0:26.5:1.0:29.4:1.0:1.0:0.0:60.0:97.5:1.0:0.0:0.2 -3 142188172 . C A 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATATAAAAAGGTAAAAGACC;RSEQ=TTTTACCTTTGACACAGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:47:29,18:214,101:0.1298:2,2:22.0:1.0:29.9:1.0:0.40842:1.31405:60.0:46.0:0.1281:0.0:1.2 0/0:353:0:0,0:219,133:0.0:2,0:25.0:1.0:30.6:1.0:1.0:0.0:60.0:175.0:0.9972:0.0:0.1 -3 142188373 . C A 52 q23;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06186;SOR=0.0;LSEQ=GATAACCTTGTTTATTTTAC;RSEQ=CAAATCATTCCTCATTTGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:5:3,2:187,284:0.0105:2,2:20.0:1.0:22.4:1.0:0.39246:2.27:60.0:1.5:0.0065:0.0:2.0 0/0:470:0:0,0:188,282:0.0:2,0:26.9:1.0:30.3:1.0:1.0:0.0:60.0:66.143:1.0:0.0:0.1 -3 142215149 . T C 175 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=29.0;MSILEN=2.0;SSF=0.0;SOR=0.09743;LSEQ=TATATATATATATATATATA;RSEQ=ATATATATATATATATATAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:46:35,11:128,30:0.2244:2,2:23.4:1.0:31.7:1.0:0.53082:1.33893:56.8:45.0:0.225:0.0:2.5 0/1:110:3:3,0:80,23:0.0273:2,0:19.3:1.0:32.7:1.0:1.0:0.0:53.3:6.0:0.0283:0.0:4.0 -3 142218675 . T A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01047;SOR=0.0;LSEQ=ATTGAATTTGCATTATATTG;RSEQ=ATTTTGTTCTTAGATATAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:8:0,8:1,72:0.0988:1,0:11.3:1.0:29.5:1.0:1.0:0.0:60.0:7.0:0.0921:0.0:1.3 0/0:61:0:0,0:3,58:0.0:1,0:24.3:1.0:28.5:1.0:1.0:0.0:60.0:122.0:1.0:0.0:0.1 -3 142234589 . C A 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.33333;SOR=0.0;LSEQ=CCTCAGATCCTTCCAACTCT;RSEQ=TTCTTATATAAGAAAAACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:0,8:0,3:0.7273:0,0:25.3:1.0:30.9:1.0:1.0:0.0:60.0:16.0:0.7273:0.0:1.9 0/0:1:0:0,0:0,1:0.0:0,0:1.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -3 142241690 . C CA 66 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03087;SOR=0.0;LSEQ=TCTTCTACTCCAGTCTCAAT;RSEQ=AGAAAAAAAAAAAAGAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:6:1,5:170,360:0.0112:2,2:26.8:1.0:25.8:1.0:0.66982:2.35799:60.0:5.0:0.01:0.0056:1.7 0/0:526:0:0,0:185,340:0.0:2,0:22.6:1.0:29.8:1.0:1.0:0.0:60.0:17.75:0.998:0.0:0.3 -3 142266439 . C T 148 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCCTTTTCAAAATAAAAATA;RSEQ=CAACTTAAAATTTAAACAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:30:30,0:23,0:0.566:1,1:25.9:1.0:30.2:1.0:1.0:0.0:60.0:9.0:0.54:0.0:1.0 0/0:29:0:0,0:28,1:0.0:1,0:18.8:1.0:31.3:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.2 -3 142278101 . T C 235 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTTGTACTCACCTTGCATA;RSEQ=AAATCAAAGCATCATAAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:164:100,64:271,211:0.2539:2,2:26.7:1.0:32.0:1.0:0.31497:1.22:60.0:53.667:0.2543:0.0:1.1 0/0:656:0:0,0:375,281:0.0:2,0:25.6:1.0:28.8:1.0:1.0:0.0:60.0:130.2:1.0:0.0:0.1 -3 142297576 . G A 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06932;SOR=0.16506;LSEQ=GCGAGGCACTAGTCAACCAC;RSEQ=CCAACGCGGGTTCCCGGCGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:6:4,2:187,355:0.0109:2,2:14.5:1.0:28.8:1.0:0.18992:3.79:60.0:12.0:0.0112:0.0:1.0 0/0:549:1:1,0:222,326:0.0018:2,0:1.0:0.0:25.0:0.0:0.40619:0.0:60.0:2.0:0.0018:0.0:1.0 -3 145542355 . G T 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=2.0;MSILEN=1.0;SSF=0.00037;SOR=0.0;LSEQ=GACTCTTCCAGTTTTGCCAT;RSEQ=GTAACACTTGTGGGGCATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:17:8,9:57,74:0.1149:2,2:25.7:1.0:30.3:1.0:0.8004:1.15:37.0:34.0:0.1172:0.0:1.0 0/0:87:0:0,0:42,45:0.0:2,0:25.4:1.0:31.7:1.0:1.0:0.0:35.3:174.0:1.0:0.0:0.1 -3 166229248 . C T 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00226;SOR=0.0;LSEQ=AAAGGCCCCCACAAAAGCCC;RSEQ=ATCCAAGGGTCAGCAACCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:6,6:10,12:0.3529:2,2:29.5:1.0:29.5:1.0:1.0:1.19:60.0:24.0:0.3529:0.0:1.3 0/0:19:0:0,0:9,10:0.0:2,0:25.3:1.0:30.5:1.0:1.0:0.0:59.2:38.0:1.0:0.0:0.2 -3 168576884 . T C 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03165;SOR=0.0;LSEQ=TAAAAGGCCTAGAGAACACG;RSEQ=ATCAAGTGCCTCTCCTCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:4,5:6,8:0.3913:2,2:21.4:1.0:32.3:1.0:1.0:1.06:60.0:18.0:0.3913:0.0:1.2 0/0:10:0:0,0:1,9:0.0:2,0:18.7:1.0:28.7:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.1 -3 178511531 . C A 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=GGCATGGGGCTATCAGGGAT;RSEQ=CAAGCCAGCTACCTCATCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:17:7,10:155,153:0.0523:2,2:23.4:1.0:29.1:1.0:0.61962:1.44561:60.0:16.0:0.0502:0.0:1.1 0/0:283:0:0,0:144,139:0.0:2,0:24.2:1.0:30.9:1.0:1.0:0.0:60.0:140.5:1.0:0.0:0.1 -3 178921158 . G A 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.17022;SOR=0.0;LSEQ=GATTGATCTTGTGCTTCAAC;RSEQ=TAAATCCTAAATGTTAGTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:6,0:33,0:0.1538:1,0:15.0:1.0:29.7:1.0:1.0:0.0:60.0:12.0:0.1579:0.0:1.2 0/0:15:0:0,0:12,3:0.0:2,0:21.6:1.0:30.3:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.0 -3 178927345 . T C 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00597;SOR=0.09725;LSEQ=ATATACTTTGATGAAGACTT;RSEQ=TCTTGATGTATTATTTTTGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:14:11,3:273,87:0.0374:2,2:22.0:1.0:31.4:1.0:1.0:1.17:60.0:28.0:0.0376:0.0:1.0 0/0:266:1:1,0:196,69:0.0038:2,0:16.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0038:0.0:1.0 -3 178927645 . C T 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00032;SOR=0.08317;LSEQ=AATGTATCATGGAAGAATAC;RSEQ=TTGGGAGAGCTTCAGGAATT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:25:4,21:4,14:0.5814:2,2:24.8:1.0:30.0:1.0:0.70102:1.4856:60.0:24.0:0.5714:0.0:1.0 0/1:20:2:0,2:1,17:0.1:1,0:15.5:1.0:31.0:1.0:1.0:0.0:60.0:4.0:0.1:0.0:1.0 -3 178936227 . T G 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.17281;SOR=0.0;LSEQ=ACCATACCTATTGGAATAAA;RSEQ=AAAGCAGAATTTACATGATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:5:0,5:2,82:0.0562:1,0:36.8:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.0562:0.0:1.0 0/0:43:0:0,0:2,41:0.0:1,0:23.5:1.0:28.5:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.1 -3 178937877 . A G 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08908;SOR=0.0;LSEQ=TCCCATTAAATTCTTAAGGT;RSEQ=CATATTACTTGCTTTCTTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:6:3,3:30,136:0.0349:2,2:20.8:1.0:29.3:1.0:0.08553:4.48:30.2:12.0:0.0349:0.0:1.0 0/0:99:0:0,0:23,76:0.0:2,0:21.1:1.0:29.4:1.0:1.0:0.0:34.6:198.0:1.0:0.0:0.0 -3 184298663 . G A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.14055;SOR=0.0;LSEQ=TACTGGGACATGAGCAACCA;RSEQ=GATGTGAGTGAGGCTACGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:6,9:0.2857:2,2:21.3:1.0:29.7:1.0:0.36146:2.84:60.0:12.0:0.2857:0.0:1.0 0/0:9:0:0,0:5,4:0.0:2,0:27.1:1.0:30.4:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.1 -3 185155807 . G A 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CAAAACAAAGTTGGCCGGGC;RSEQ=CAGTGGCTCATGTCTGTAAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:22.0:1.0:30.6:1.0:1.0:0.0:59.0:10.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 185183491 . C T 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01122;LSEQ=CATCAAGCGGACTTTTTTCT;RSEQ=CCGAAGTTGGTTGGCTGGGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:129:85,44:192,99:0.3071:2,2:26.8:1.0:30.1:1.0:1.0:1.00391:60.0:128.0:0.3107:0.0:1.2 0/0:406:2:0,2:254,150:0.0049:2,0:1.0:0.0:25.5:1.0:0.13959:0.0:60.0:4.0:0.0051:0.0:1.0 -3 185183656 . G A 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00406;LSEQ=AGAAGGAGCTCATTAAGTAT;RSEQ=TATCCAGACTAGTGTCTGTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:162:55,107:133,199:0.3279:2,2:25.9:1.0:29.6:1.0:0.20056:1.29954:60.0:39.5:0.3251:0.0:1.1 0/0:508:1:1,0:198,309:0.002:2,0:1.0:0.0:23.0:0.0:0.39173:0.0:60.0:2.0:0.002:0.0:1.0 -3 186504406 . A C 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTGACCCTTGAAGGAATCA;RSEQ=ACAGTTTTATATTAATGTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1326:91:44,47:546,687:0.0686:2,2:28.3:1.0:32.5:1.0:0.51223:1.18:59.8:90.0:0.0686:0.0:1.1 0/0:1489:0:0,0:691,795:0.0:2,0:25.3:1.0:29.9:1.0:1.0:0.0:59.8:122.833:0.9986:0.0:0.2 -3 187440126 . G C 67 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08579;SOR=0.0;LSEQ=CACCCCCAACCCCCAGCTAT;RSEQ=ATTTGCACTAGTGGATGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:6:6,0:62,0:0.0882:1,0:18.8:1.0:26.2:1.0:1.0:0.0:60.0:2.0:0.0784:0.0:1.3 0/0:38:0:0,0:36,2:0.0:2,0:20.5:1.0:27.9:1.0:1.0:0.0:60.0:3.222:1.0:0.0:1.0 -3 187451349 . C A 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CATGAGGACCGTTTTATGGG;RSEQ=TCTAAACTGCTCACGGCTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:962:29:14,15:461,470:0.0301:2,2:25.1:1.0:30.3:1.0:1.0:1.05088:60.0:28.0:0.0297:0.0:1.1 0/0:857:0:0,0:445,412:0.0:2,0:25.3:1.0:31.6:1.0:1.0:0.0:60.0:49.412:1.0:0.0:0.2 -3 189349501 . G A 180 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01506;LSEQ=TATTATTTTGGACTTTCTGT;RSEQ=GACTTAAAGTGGTCTGTGGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:54:0,54:0,56:0.4909:1,1:26.0:1.0:31.3:1.0:1.0:0.0:60.0:108.0:0.5094:0.0:1.0 0/1:71:1:0,1:0,70:0.0141:1,0:2.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0143:0.0:1.0 -3 189525713 . G A 80 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AACAACCTCAAAATGGAATA;RSEQ=CAGGCAGTATTTATTTAAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:24.0:1.0:31.0:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -3 189584420 . C T 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.03103;LSEQ=ATGCAATTTCATTTTATTTT;RSEQ=TTTATTTTTAAGGTAAAGAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:34:29,5:180,29:0.1399:2,2:23.1:1.0:30.2:1.0:1.0:1.06986:60.0:68.0:0.1405:0.0:1.1 0/0:200:1:0,1:158,41:0.005:2,0:1.0:0.0:23.0:0.0:0.21:0.0:60.0:2.0:0.005:0.0:1.0 -3 189585692 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00821;SOR=0.0;LSEQ=TTGTGTTGGAGGGATGAACC;RSEQ=CCGTCCAATTTTAATCATTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:8:6,2:331,450:0.0101:2,2:7.0:1.0:27.3:1.0:0.07908:4.07:60.0:7.0:0.009:0.0:1.3 0/0:714:0:0,0:323,390:0.0:2,0:25.3:1.0:30.3:1.0:1.0:0.0:60.0:49.929:1.0:0.0:0.1 -3 189586466 . G A 136 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATAGCATCAGAAAGCAGCAA;RSEQ=TTTCGGACAGTACAAAGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:25:13,12:238,263:0.0475:2,2:22.9:1.0:29.4:1.0:0.68653:1.2:60.0:24.0:0.0462:0.0:1.1 0/0:493:0:0,0:253,239:0.0:2,0:25.1:1.0:31.3:1.0:1.0:0.0:60.0:97.4:0.998:0.0:0.2 -3 189586470 . C T 215 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATCAGAAAGCAGCAAGTTT;RSEQ=GGACAGTACAAAGAACGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:150:69,81:179,191:0.2885:2,2:27.0:1.0:29.8:1.0:0.62954:1.09996:60.0:49.0:0.2899:0.0:1.1 0/0:485:0:0,0:245,239:0.0:2,0:25.8:1.0:30.2:1.0:1.0:0.0:60.0:59.5:0.9979:0.0:0.2 -3 189590871 . G A 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTGATTGATGAGCAATGTG;RSEQ=AACATAATGGGAGATAGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:57:6,51:8,145:0.2714:2,2:20.7:1.0:30.4:1.0:0.21256:2.12:60.0:114.0:0.2754:0.0:1.1 0/0:134:0:0,0:14,119:0.0:2,0:23.2:1.0:31.1:1.0:1.0:0.0:60.0:43.333:1.0:0.0:0.5 -3 189597951 . G A 241 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00871;LSEQ=ACATTCCAAGCCCCCAAACC;RSEQ=ATCAGTGTACCCATAGAGCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1067:267:111,156:332,464:0.2502:2,2:26.7:1.0:29.9:1.0:1.0:1.00559:60.0:32.375:0.2486:0.0:1.2 0/0:1037:3:3,0:441,593:0.0029:2,0:1.0:0.0:25.3:1.0:0.07819:0.0:60.0:6.0:0.003:0.0:1.0 -3 189598095 . G A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01133;SOR=0.0;LSEQ=TGAAGACACTTTGGCTCAGA;RSEQ=ACCCAACTGCTCAAAGGCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:14:1,13:2,85:0.1386:1,1:24.0:1.0:29.7:1.0:0.36397:3.21:60.0:13.0:0.1383:0.0:1.5 0/0:38:0:0,0:1,37:0.0:1,0:23.6:1.0:31.1:1.0:1.0:0.0:60.0:37.0:1.0:0.0:0.1 -3 195388761 . G C 111 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.06212;SOR=0.0;LSEQ=AATGATTTTTTTGGCTTGGG;RSEQ=GTAAGGATCTATACCAGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:11:11,0:61,6:0.141:2,0:18.5:1.0:32.1:1.0:0.5864:0.0:24.8:22.0:0.1486:0.0:1.1 0/0:27:0:0,0:24,3:0.0:2,0:24.6:1.0:29.7:1.0:1.0:0.0:25.0:26.0:1.0:0.0:0.1 -3 195390357 . C T 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00458;LSEQ=TGTCAGGCCTGGCTGCTCCT;RSEQ=TGCTGAGGTCAGCCCTCACT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:37:36:33,3:1,0:0.973:0,2:26.7:1.0:30.9:1.0:1.0:0.0:29.3:35.0:0.9722:0.0:1.1 0/1:33:4:4,0:27,2:0.1212:2,0:20.8:1.0:31.5:1.0:1.0:0.0:32.5:8.0:0.1212:0.0:1.0 -3 195392753 . T C 107 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.19847;SOR=0.0;LSEQ=CTCTAGCACACCTGCCTTGT;RSEQ=GGTACTGCTGGGCGTGGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:11:10,1:59,2:0.1528:1,2:15.3:1.0:31.2:1.0:0.39655:2.89012:27.0:22.0:0.1528:0.0:2.1 0/0:14:0:0,0:13,1:0.0:1,0:20.4:1.0:31.1:1.0:1.0:0.0:29.0:28.0:1.0:0.0:0.6 -3 195395129 . AAAAT A 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=5.0;MSILEN=4.0;SSF=0.29014;SOR=0.0;LSEQ=CAAGAGTTAGACCCTATCTC;RSEQ=AAATAAATAAATAAATAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:5,1:14,1:0.2609:1,2:18.2:1.0:30.2:1.0:0.5:2.64575:36.2:12.0:0.2609:0.087:0.2 0/0:7:0:0,0:6,1:0.0:2,0:21.0:1.0:29.4:1.0:1.0:0.0:57.7:14.0:1.0:0.0:0.7 -3 195395399 . G A 249 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.12799;LSEQ=TGTTTCCATAGGCTACGGGC;RSEQ=CACCTACTTGAGCTGCACGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1467:317:211,106:692,453:0.2161:2,2:27.9:1.0:30.0:1.0:0.05014:1.3:27.7:78.25:0.2178:0.0:2.2 0/1:1439:49:38,11:795,594:0.0341:2,2:25.4:1.0:28.9:1.0:0.00478:2.58:27.8:15.333:0.0327:0.0:2.2 -3 195395402 . C A 249 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.12973;LSEQ=TTCCATAGGCTACGGGCGCA;RSEQ=CTACTTGAGCTGCACGTCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1489:309:205,104:704,475:0.2075:2,2:28.9:1.0:30.2:1.0:0.03593:1.33:27.7:102.0:0.2092:0.0:2.2 0/1:1462:48:38,10:794,619:0.0328:2,2:25.2:1.0:28.9:1.0:0.0016:2.96:27.2:15.0:0.0313:0.0:2.2 -3 195397933 . T TA 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.05157;SOR=0.0;LSEQ=CTCCCCCAAAAAATATCTTG;RSEQ=AAAAAAAAGTAATGCATTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:7:6,1:335,43:0.0182:2,2:20.3:1.0:28.3:1.0:0.57542:1.29748:30.0:14.0:0.0182:0.0052:0.7 0/0:222:0:0,0:182,24:0.0:2,0:24.4:1.0:29.6:1.0:1.0:0.0:35.2:205.0:0.9276:0.0:0.5 -3 195398365 . T G 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=4.0;SSF=0.10229;SOR=0.0;LSEQ=TTTGAAAATTTTAGCCAGTT;RSEQ=CTTTCTCAAATCTGTGGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:1,5:0,6:0.5:0,2:17.8:1.0:29.2:1.0:1.0:0.0:37.7:5.0:0.4545:0.0:1.0 0/0:5:0:0,0:1,4:0.0:2,0:22.2:1.0:26.2:1.0:1.0:0.0:31.0:4.0:1.0:0.0:0.4 -3 195399318 . A G 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.01551;SOR=0.0;LSEQ=TCAGGTCTGCTGCCGTTGCC;RSEQ=TTCTCTGCCTTATGTGATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:10:9,1:115,93:0.0459:2,2:25.7:1.0:29.2:1.0:0.0459:7.23:37.4:9.0:0.0421:0.0:1.0 0/0:132:0:0,0:70,62:0.0:2,0:26.8:1.0:28.4:1.0:1.0:0.0:33.3:65.0:1.0:0.0:0.1 -3 195400728 . A G 168 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.17316;LSEQ=GCCAGGATCAGATTGTGCCC;RSEQ=GCCTGTACGCCTGTGGGGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1182:50:35,15:585,547:0.0423:2,2:20.5:1.0:29.9:1.0:0.01332:2.18:39.6:100.0:0.043:0.0:2.6 0/0:791:6:5,1:401,383:0.0076:2,2:23.8:1.0:30.5:1.0:0.21806:4.77:33.3:12.0:0.0077:0.0:2.5 -3 195400816 . GGTCAGG TTGGTCGGA 186 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=GCTGTTGGACCTGGTTGTCT;RSEQ=CATGTGCCCTGAGCATCGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:70:59,11:317,448:0.0799:2,2:22.3:1.0:30.5:1.0:0.0:7.56:40.6:140.0:0.0821:0.0251:3.4 0/0:627:0:0,0:270,324:0.0:2,0:26.6:1.0:31.0:1.0:1.0:0.0:46.0:36.125:0.9507:0.0:0.2 -3 195404506 . A G 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.08883;LSEQ=TCCAGGCTCCTTGAGCGGCT;RSEQ=TGCTACATTTTTGTGTGTAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:17:14,3:27,0:0.3864:1,2:13.2:1.0:32.5:1.0:0.05134:0.0:29.2:34.0:0.3864:0.0:1.3 0/1:58:3:3,0:55,0:0.0517:1,0:13.7:1.0:32.0:1.0:1.0:0.0:27.0:6.0:0.0517:0.0:1.3 -3 195407868 . T G 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.52941;SOR=0.0;LSEQ=ATATGTATATAATAGAAACA;RSEQ=TTATTCAGAAGCTTTAGTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:6,4:0.375:2,0:18.7:1.0:30.8:1.0:0.23352:0.0:27.0:12.0:0.375:0.0:1.3 0/0:2:0:0,0:2,0:0.0:0,0:31.0:1.0:30.0:1.0:1.0:0.0:27.0:4.0:1.0:0.0:1.0 -3 195410875 . A T 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACAGATTTGAGGCACCGCTG;RSEQ=AAAAGGCACTCTGACAGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:222:53:1,52:8,160:0.2387:1,1:23.0:1.0:28.7:1.0:0.69034:2.59152:54.8:52.0:0.2364:0.0:1.1 0/0:80:0:0,0:8,72:0.0:2,0:20.3:1.0:30.1:1.0:1.0:0.0:57.1:79.0:1.0:0.0:0.4 -3 195410967 . T C 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.04661;SOR=0.0;LSEQ=GCCTTAAGGAAGGGTTGCTC;RSEQ=GTGGTGTGGGCCAGATGGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:12:0,12:1,22:0.3429:1,0:17.3:1.0:29.5:1.0:1.0:0.0:40.4:24.0:0.3429:0.0:2.0 0/0:9:0:0,0:1,8:0.0:2,0:22.4:1.0:30.1:1.0:1.0:0.0:51.9:18.0:1.0:0.0:0.1 -3 195412788 . T C 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00569;SOR=0.0;LSEQ=CCTACTGATGAGACAAGATG;RSEQ=GGTGATGACAGAATCAGCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:380:13:8,5:133,234:0.0342:2,2:28.8:1.0:30.5:1.0:0.08057:2.81:30.9:12.0:0.0319:0.0:1.6 0/0:212:0:0,0:74,136:0.0:2,0:24.2:1.0:29.3:1.0:1.0:0.0:54.8:29.0:0.9951:0.0:0.2 -3 195412863 . C T 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06498;SOR=0.0;LSEQ=ATGTCATAACTGTCTTTATA;RSEQ=GCTTCTGCACTCTGGGGAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:10:4,6:9,106:0.08:2,2:21.3:1.0:27.9:1.0:0.01068:7.62:46.4:20.0:0.0826:0.0:2.1 0/0:44:0:0,0:6,38:0.0:2,0:21.6:1.0:30.2:1.0:1.0:0.0:40.3:88.0:1.0:0.0:0.7 -3 195412960 . T C 99 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.18928;SOR=0.0;LSEQ=TTTGTCCCTTGCTTCATTCT;RSEQ=GTGACAAGATAAAACTGGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:10:0,10:3,34:0.2128:2,0:27.4:1.0:30.1:1.0:1.0:0.0:46.3:20.0:0.2128:0.0:2.2 0/0:9:0:0,0:3,6:0.0:2,0:27.3:1.0:28.2:1.0:1.0:0.0:56.2:18.0:1.0:0.0:1.2 -3 195692349 . T A 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00938;LSEQ=GGGTGTGCTTCCTCCAGTGC;RSEQ=CCTCAAAGGGCTTCTTCTGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2864:171:154,17:1471,1222:0.0597:2,2:23.0:1.0:30.9:1.0:0.0:7.52:35.1:56.0:0.06:0.0:1.7 0/0:1677:1:1,0:915,758:0.0006:2,0:1.0:0.0:27.0:0.0:1.0:0.0:51.0:2.0:0.0006:0.0:1.0 -3 195692516 . C T 204 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.10109;LSEQ=AGAGACAGATGCCCTAGAAC;RSEQ=CATTCCATTTCCACTTCAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:116:9,107:29,367:0.2266:2,2:22.9:1.0:29.8:1.0:0.84206:1.06:41.4:28.0:0.2222:0.0:1.6 0/1:209:6:0,6:16,187:0.0287:2,0:14.2:1.0:29.2:1.0:1.0:0.0:30.2:12.0:0.0294:0.0:2.2 -3 195692570 . G A 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCATCAACACGTTCAGAAC;RSEQ=CACAGAGGCCACATGGCTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:51:5,46:18,151:0.2257:2,2:24.9:1.0:30.2:1.0:1.0:1.09624:44.0:102.0:0.2318:0.0:1.6 0/0:72:0:0,0:4,66:0.0:2,0:23.7:1.0:32.4:1.0:1.0:0.0:55.5:69.0:0.9718:0.0:0.1 -3 195694127 . C T 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.07297;SOR=0.0;LSEQ=GGCTGCACTTCTAACCTTGG;RSEQ=CTTCTAACAGCAAAGCACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:13:3,10:14,5:0.4063:2,2:16.5:1.0:26.8:1.0:0.01045:8.57696:29.6:12.0:0.3871:0.0:1.0 0/0:7:0:0,0:2,5:0.0:2,0:20.7:1.0:30.9:1.0:1.0:0.0:29.7:14.0:1.0:0.0:0.1 -3 195694256 . G GA 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGATCAAAGTTACCAGAGG;RSEQ=AAAAAGGCATTTTTTGGATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:6:0,6:0,55:0.0984:1,0:31.0:1.0:31.3:1.0:1.0:0.0:28.2:12.0:0.0984:0.0164:2.7 0/0:6:0:0,0:0,6:0.0:0,0:21.2:1.0:32.3:1.0:1.0:0.0:29.2:12.0:1.0:0.0:0.7 -3 195697927 . A G 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=CTTGGAAGTGGGAGCTGAAC;RSEQ=GTGAGTACACATGGACACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:12,1:1,0:0.9286:0,1:24.9:1.0:28.2:1.0:1.0:0.0:49.2:26.0:1.0:0.0:1.2 0/0:1:0:0,0:0,1:0.0:0,0:14.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -3 195700978 . A C 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.45455;SOR=0.0;LSEQ=CTGTTCTATAAAAACAGCAG;RSEQ=AATGATGCTAAACAGTTAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:6,0:4,0:0.6:0,0:21.8:1.0:32.7:1.0:1.0:0.0:47.5:12.0:0.6:0.0:1.0 0/0:2:0:0,0:2,0:0.0:0,0:32.0:1.0:31.0:0.0:1.0:0.0:45.0:4.0:1.0:0.0:0.0 -3 195701306 . T C 253 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06717;LSEQ=CGATGCTCAGGGCACATGCC;RSEQ=GACCAGACAACCAGGTCCAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2178:328:215,113:1120,730:0.1506:2,2:29.4:1.0:30.3:1.0:0.09669:1.24:36.9:64.6:0.1497:0.0:2.9 0/1:1105:13:12,1:629,463:0.0118:2,1:24.5:1.0:30.2:1.0:0.01048:8.82:37.9:12.0:0.011:0.0:4.0 -3 195702877 . A G 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCAACATGTTTTGATACTG;RSEQ=GGAAAATTTCCCCTCATGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:119:6,113:21,404:0.2188:1,2:26.2:1.0:30.7:1.0:1.0:1.02:43.2:22.8:0.2163:0.0:1.6 0/0:234:0:0,0:17,217:0.0:2,0:23.7:1.0:31.3:1.0:1.0:0.0:41.4:233.0:1.0:0.0:0.2 -3 195704217 . A T 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=ATATTTTTTGGGGGAGAGAC;RSEQ=AAAAAGATATGCAGAAGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:27:1,26:5,102:0.2015:1,1:21.3:1.0:28.7:1.0:1.0:1.27235:32.7:54.0:0.203:0.0:1.1 0/0:62:0:0,0:0,62:0.0:1,0:18.3:1.0:30.4:1.0:1.0:0.0:36.5:124.0:1.0:0.0:0.0 -3 195708767 . C T 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACAGTTTCCTCATCTAAAAT;RSEQ=GGGAGAGGTACGCTGTGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:5,0:21,1:0.1852:1,0:23.6:1.0:31.8:1.0:1.0:0.0:43.8:10.0:0.1852:0.0:2.6 0/0:1:0:0,0:1,0:0.0:0,0:3.0:0.0:29.0:0.0:1.0:0.0:38.0:2.0:1.0:0.0:0.0 -3 195710978 . C G 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00038;SOR=0.0;LSEQ=TCAGGTGGACGGGGGGCGGC;RSEQ=TTACCCTCCCGTATAAGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:19:13,6:490,150:0.0288:2,2:21.0:1.0:27.7:1.0:0.41505:1.50666:35.1:18.0:0.0277:0.0:2.3 0/0:346:0:0,0:273,71:0.0:2,0:24.0:1.0:30.0:1.0:1.0:0.0:51.4:56.333:0.9941:0.0:1.1 -3 195711785 . C T 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.01444;SOR=0.0;LSEQ=CAGATTCCAGATCACAACCC;RSEQ=TCCCAGACTCACCCAGTGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:17:0,17:3,136:0.1083:1,1:15.0:1.0:30.6:1.0:1.0:0.0:35.4:34.0:0.109:0.0:1.2 0/0:50:0:0,0:6,44:0.0:2,0:15.7:1.0:31.1:1.0:1.0:0.0:40.5:24.0:1.0:0.0:0.3 -3 195712899 . A C 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=GGTCTATTCCATGGGATCAG;RSEQ=CTGAGGACCACAACTCTACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:32.0:1.0:32.0:1.0:1.0:0.0:25.0:10.0:0.7143:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:33.0:0.0:31.0:0.0:1.0:0.0:25.0:2.0:1.0:0.0:0.0 -3 195713494 . C G 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CACTGGAGACACAGAAGACA;RSEQ=AGATCCAGAGGGTTAGTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:755:102:51,51:325,324:0.1351:2,2:21.5:1.0:30.4:1.0:1.0:1.00308:25.7:101.0:0.1348:0.0:1.1 0/0:394:0:0,0:199,195:0.0:2,0:22.5:1.0:30.1:1.0:1.0:0.0:27.0:130.333:1.0:0.0:0.3 -3 197346530 . C G 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=5e-05;SOR=0.0;LSEQ=ACTGCTATTCTACAATGCCT;RSEQ=TATTTTCCTTAAAATAAAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:20:20,0:122,4:0.137:1,1:20.3:1.0:32.8:1.0:1.0:0.0:58.9:40.0:0.1379:0.0:1.2 0/0:91:0:0,0:83,7:0.0:2,0:22.2:1.0:31.5:1.0:1.0:0.0:58.2:180.0:0.989:0.0:0.3 -3 197348570 . C G 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGGTGGACGGAGGGCGGC;RSEQ=TTACCCTCCCATATGAGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:77:42,35:288,90:0.1692:2,2:24.9:1.0:29.9:1.0:0.00023:2.66029:43.1:37.5:0.1678:0.0:2.3 0/0:334:0:0,0:227,104:0.0:2,0:23.7:1.0:30.5:1.0:1.0:0.0:55.2:109.333:0.9909:0.0:0.6 -3 197349123 . C T 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATCCTGGTCCCCCAGCCAGT;RSEQ=GGAGCCCTTCACGGTGTCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:55:13,42:72,154:0.1957:2,2:25.8:1.0:30.5:1.0:0.25621:1.50838:33.5:110.0:0.1971:0.0:1.1 0/0:161:0:0,0:49,112:0.0:2,0:24.8:1.0:29.5:1.0:1.0:0.0:31.9:31.2:1.0:0.0:0.3 -4 1795701 . G T 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.077;SOR=0.0;LSEQ=CCCTCGCGCTCTGCGTGGCC;RSEQ=TGGCCATCGTGGCCGGCGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:5:2,3:257,111:0.0134:2,2:21.8:1.0:28.2:1.0:0.16919:3.45983:60.0:10.0:0.0139:0.0:1.0 0/0:272:0:0,0:180,92:0.0:2,0:23.8:1.0:29.9:1.0:1.0:0.0:60.0:53.4:1.0:0.0:0.2 -4 1795719 . G A 78 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.04255;SOR=0.0;LSEQ=CCGTGGCCATCGTGGCCGGC;RSEQ=CCTCCTCGGAGTCCTTGGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:6:3,3:336,157:0.012:2,2:20.5:1.0:30.2:1.0:0.39093:2.13659:60.0:12.0:0.0124:0.0:1.2 0/0:364:0:0,0:231,131:0.0:2,0:27.7:1.0:29.9:1.0:1.0:0.0:60.0:50.714:0.9972:0.0:0.2 -4 1795762 . G A 175 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01973;LSEQ=GGAGCAGCGCGTCGTGGGGC;RSEQ=AGCGGCAGGTAAGAAGGGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:65:37,28:394,281:0.0878:2,2:27.0:1.0:29.1:1.0:0.89537:1.06098:60.0:20.667:0.0854:0.0:1.2 0/0:528:1:1,0:277,250:0.0019:2,0:1.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.002:0.0:1.0 -4 1806937 . C T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00113;SOR=0.0;LSEQ=GGTGACACTCTTCGTCCTTA;RSEQ=GAGCAGGCTGTAGGGGGAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:22:19,3:77,9:0.2018:2,2:23.0:1.0:31.1:1.0:0.70669:1.34686:60.0:21.0:0.2:0.0:1.4 0/0:37:0:0,0:30,7:0.0:2,0:19.3:1.0:31.0:1.0:1.0:0.0:60.0:17.5:1.0:0.0:0.3 -4 1807244 . GCGC G 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.09954;SOR=0.17836;LSEQ=GGTGCAGAGCAGGGCTGGGG;RSEQ=CGCCGCCGCCTGACACAGGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:745:9:4,5:377,358:0.0121:2,2:23.1:1.0:31.8:1.0:0.74712:1.31585:60.0:18.0:0.0123:0.0027:0.1 0/0:460:1:1,0:249,208:0.0022:2,0:14.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.0022:0.0:0.0 -4 1809127 . CGTGT C 122 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=9.0;MSILEN=2.0;SSF=0.00708;SOR=0.0;LSEQ=GGTCTGTGTGTGTGTGTGTG;RSEQ=GTGTGTGTGTGTGTGCACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:14:1,13:1,20:0.2857:1,1:32.4:1.0:32.1:1.0:1.0:1.52:60.0:28.0:0.2917:0.0612:0.0 0/0:19:0:0,0:0,12:0.0:0,0:12.4:1.0:30.6:1.0:1.0:0.0:60.0:11.0:0.6111:0.0:1.3 -4 6113451 . C G 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=CCCGTGCTTTAATTAGACTG;RSEQ=CAGCACCCAACCAGGCACTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:18:14,4:111,43:0.1047:2,2:22.2:1.0:31.2:1.0:0.78233:1.35:60.0:36.0:0.1078:0.0:1.0 0/0:128:0:0,0:85,42:0.0:2,0:24.3:1.0:31.6:1.0:1.0:0.0:60.0:254.0:1.0:0.0:0.1 -4 6927471 . T G 72 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GATCTTGTCACTATCCCTTC;RSEQ=GAGGCTGTAGCCATATCGCG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:29.0:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -4 8043703 . G A 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=TGCAGGTTCCAACAACAACA;RSEQ=CAGCAACAACAGCAACAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:48:25,23:25,12:0.5581:2,2:27.3:1.0:29.5:1.0:0.18513:1.90197:60.0:47.0:0.5663:0.0:2.2 0/0:135:0:0,0:7,7:0.0:2,0:28.4:1.0:32.1:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 -4 28400060 . A G 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=AATACATGCTTCTGTTTCTC;RSEQ=AGTGTGAAAAATCTGTTTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:13.6:1.0:30.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.4 0/0:1:0:0,0:1,0:0.0:0,0:40.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -4 28400468 . C T 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCACCTTGAGCATGCATAGC;RSEQ=TTGTCCTCATCATCCTTAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:33:7,26:20,123:0.1875:2,2:22.8:1.0:31.1:1.0:0.2934:1.65:60.0:66.0:0.1886:0.0:1.1 0/0:139:0:0,0:30,109:0.0:2,0:21.7:1.0:31.7:1.0:1.0:0.0:60.0:278.0:1.0:0.0:0.2 -4 35861432 . C T 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=4e-05;SOR=0.0;LSEQ=AGAAGCCATGTCACCCAACT;RSEQ=TAGAGGTTGGTATAAGAGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:10:6,4:16,13:0.2564:2,2:33.4:1.0:30.3:1.0:1.0:1.21:58.2:20.0:0.2703:0.0:1.2 0/0:60:0:0,0:32,28:0.0:2,0:31.5:1.0:31.0:1.0:1.0:0.0:60.0:59.0:1.0:0.0:0.2 -4 37822923 . G A 64 q23;MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=12.0;MSILEN=1.0;SSF=0.00047;SOR=0.0;LSEQ=ATGATCAATAAAAAAAAAAA;RSEQ=AAAAAAAAAAAAGATTTAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:8:2,6:36,9:0.125:2,2:13.3:1.0:21.4:1.0:0.00425:11.2728:57.5:1.667:0.119:0.0:1.3 0/0:97:0:0,0:51,31:0.0:2,0:12.0:0.0:10.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -4 41747691 . C G 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06291;SOR=0.0;LSEQ=CTTTATTCTTAGCGCGATTA;RSEQ=TTTAGGCCCTCAATGAAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:13,2:0.25:2,2:8.2:1.0:31.8:1.0:1.0:1.58265:60.0:10.0:0.25:0.0:1.2 0/0:14:0:0,0:13,1:0.0:1,0:19.7:1.0:29.6:1.0:1.0:0.0:60.0:13.0:1.0:0.0:0.0 -4 41748217 . G A 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03018;LSEQ=TCAGTGCTCTTGGCCTCTTT;RSEQ=CTCTCGTCGTCCCTGGAAGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1221:118:60,58:606,497:0.0966:2,2:25.4:1.0:28.6:1.0:0.43672:1.17851:60.0:38.333:0.0961:0.0:1.1 0/0:1555:5:5,0:844,704:0.0032:2,0:1.0:0.0:24.6:1.0:0.06756:0.0:60.0:10.0:0.0033:0.0:1.0 -4 46726267 . C T 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03019;LSEQ=CCAGCTGTATCCCATAAGCC;RSEQ=AGATTCACCGGTTTTCCATC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:639:99:47,52:255,285:0.1549:2,2:27.4:1.0:29.5:1.0:1.0:1.01:53.3:98.0:0.1551:0.0:1.1 0/0:728:4:2,2:357,366:0.0055:2,2:5.0:1.0:24.3:1.0:1.0:1.03:52.3:3.0:0.0042:0.0:1.3 -4 46726491 . G T 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.00487;SOR=0.0;LSEQ=TAGGAAGCGGCGGGCTCGGG;RSEQ=CGCGGCGGACGGGCGCGCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:10:1,9:5,38:0.1887:2,2:10.8:1.0:28.7:1.0:1.0:1.18059:47.5:9.0:0.1765:0.0:1.0 0/0:36:0:0,0:3,33:0.0:2,0:7.5:1.0:32.1:1.0:1.0:0.0:49.5:72.0:1.0:0.0:0.3 -4 49110443 . C G 75 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=5.0;SSF=0.07552;SOR=0.13317;LSEQ=CCATACCATTCCATTCCATT;RSEQ=CACTCGGGTTGATTCCATTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:3,2:6,4:0.3333:2,2:21.4:1.0:32.6:1.0:1.0:1.0:47.6:10.0:0.3333:0.0:4.4 0/1:17:1:0,1:5,8:0.0588:2,0:32.0:0.0:32.0:0.0:1.0:0.0:30.0:2.0:0.0625:0.0:7.0 -4 49111815 . TTCCATTCCTTTCAAC G 70 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00192;SOR=0.0;LSEQ=TTCCATTCCACTCCATTCCA;RSEQ=TCCTTTCCATTCCATTCCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:0,2:0.5556:0,2:10.8:1.0:30.5:1.0:1.0:0.0:47.8:10.0:0.625:0.5556:4.4 0/0:17:0:0,0:5,7:0.0:2,0:7.8:1.0:28.5:1.0:1.0:0.0:36.7:24.0:1.0:0.0:4.3 -4 49121015 . ATTCCATTCCATTCCT A 78 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=5.0;SSF=0.00326;SOR=0.0;LSEQ=ATTCCATTCCATTCCATTCC;RSEQ=TTCCACTCGGGTTGATTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:3,3:10,11:0.2222:2,2:27.5:1.0:30.2:1.0:1.0:1.1:34.2:12.0:0.2308:0.1852:3.8 0/0:39:0:0,0:15,23:0.0:2,0:24.4:1.0:29.3:1.0:1.0:0.0:36.2:18.0:1.0:0.0:4.9 -4 49123023 . C T 76 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.04075;SOR=0.11459;LSEQ=ATTCCATTCAATTCCACTCG;RSEQ=ATTCAATCTATTCCATTCCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:3,3:6,5:0.3529:2,2:25.7:1.0:29.5:1.0:1.0:1.18716:60.0:12.0:0.3529:0.0:6.0 0/1:18:1:0,1:6,10:0.0556:2,0:18.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0588:0.0:4.0 -4 49149291 . T TTCCATTCCATTGCATTCCATTCCCTCGTGTTGATTCCATTCTTTCCATTCCATTCAAGTTGAA 68 NM4 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=23;MSI=2.0;MSILEN=1.0;SSF=0.002;SOR=0.0;LSEQ=CTAGGGTTGATCCCATACCA;RSEQ=TCCATTCCATTGCATTCCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:2,0:0.8333:0,2:17.6:1.0:29.7:1.0:1.0:0.0:28.2:10.0:0.8333:0.8333:4.2 0/0:9:0:0,0:7,2:0.0:2,0:2.6:1.0:31.8:1.0:1.0:0.0:32.7:18.0:1.0:0.0:5.3 -4 49155270 . G C 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:5,4:2,2:0.4737:2,2:27.4:1.0:31.0:1.0:1.0:1.23:38.2:18.0:0.4737:0.0:3.3 0/0:58:0:0,0:5,6:0.0:2,0:22.0:1.0:32.8:1.0:1.0:0.0:47.8:22.0:0.3667:0.0:3.1 -4 49156547 . T C 71 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00034;SOR=0.0;LSEQ=CCATTCCATTCCATTCCATT;RSEQ=CATTCCATTCCATTCCATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:1,2:0.4545:2,2:17.2:1.0:30.6:1.0:1.0:1.29:36.0:10.0:0.4545:0.0:4.0 0/0:35:0:0,0:7,11:0.0:2,0:17.2:1.0:26.9:1.0:1.0:0.0:47.2:8.0:0.8:0.0:4.3 -4 49637270 . T TGGAATGGAATCATCC 85 NM4 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=TGGAATGGAATGGAATGCAA;RSEQ=GGAATGGAATGGTATGGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:2,5:4,0:0.5833:0,2:10.6:1.0:30.3:1.0:0.06061:0.0:26.9:14.0:0.5833:0.5833:4.1 0/0:30:0:0,0:17,13:0.0:2,0:11.5:1.0:29.7:1.0:1.0:0.0:32.0:60.0:1.0:0.0:3.3 -4 49644677 . A T 83 NM4;MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=5.0;SSF=0.00488;SOR=0.07038;LSEQ=AATGGAATGGAATGGAATGG;RSEQ=ATGGAATAGAATGGAATGGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:4,3:8,7:0.3182:2,2:28.3:1.0:29.7:1.0:1.0:1.16:33.1:14.0:0.3182:0.0:4.3 0/1:33:1:0,1:16,16:0.0303:2,0:30.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0323:0.0:5.0 -4 49659659 . A ATGTAATGGAATTTAG 81 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=ATGGAATGTAATGGAGTGGA;RSEQ=TGGATTGGATTGGAGTGGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:3,4:2,5:0.5:2,2:11.9:1.0:29.1:1.0:1.0:1.79:58.7:14.0:0.5385:0.5:3.4 0/0:49:0:0,0:21,28:0.0:2,0:13.7:1.0:30.2:1.0:1.0:0.0:50.0:98.0:1.0:0.0204:4.4 -4 54245372 . T A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0147;SOR=0.0;LSEQ=TTGTTTGCTTATTTATTTAT;RSEQ=TGTTTATTTTACTTGGTAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:5:2,3:202,222:0.0117:2,2:23.0:1.0:31.2:1.0:1.0:1.36389:60.0:10.0:0.0118:0.0:1.0 0/0:566:0:0,0:285,280:0.0:2,0:23.1:1.0:29.7:1.0:1.0:0.0:60.0:79.714:0.9982:0.0:0.1 -4 55129831 . C T 238 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CTTCATTCTTTTTTAAACCA;RSEQ=AGACCCAGATGTAGCCTTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:258:172,86:240,130:0.4102:2,2:24.3:1.0:29.8:1.0:0.6699:1.08:60.0:257.0:0.4105:0.0:1.1 0/0:686:0:0,0:412,274:0.0:2,0:24.8:1.0:31.2:1.0:1.0:0.0:60.0:227.667:1.0:0.0:0.1 -4 55161516 . CA TG 73 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03112;SOR=0.0;LSEQ=AAAACCACTTTATTGCAATG;RSEQ=GAGGTTGAGAGGAGGACTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:6:2,4:31,174:0.0284:2,2:18.7:1.0:28.3:1.0:0.23736:2.79:60.0:12.0:0.0288:0.0047:0.8 0/0:192:0:0,0:32,160:0.0:2,0:21.2:1.0:30.0:1.0:1.0:0.0:60.0:95.0:1.0:0.0:1.1 -4 55955737 . A AT 211 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.0;SOR=0.09951;LSEQ=TCCTCATCACCTATGTATCT;RSEQ=TTTTTTTTTTCAAAGCTTCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:223:118:54,64:33,65:0.5291:2,2:27.5:1.0:30.8:1.0:0.09427:1.66:60.0:117.0:0.5318:0.0628:0.2 0/1:120:12:4,8:45,60:0.1:2,2:25.6:1.0:30.0:1.0:0.7588:1.49497:60.0:24.0:0.1008:0.0:0.8 -4 55962165 . AC TT 104 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.05878;SOR=0.0;LSEQ=CTTCTCTGGACATCTGTTAC;RSEQ=AAGTAACAAACTGTATCATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:12:10,2:10,2:0.5:2,2:18.8:1.0:29.2:1.0:1.0:1.0:60.0:24.0:0.5:0.0417:1.1 0/0:5:0:0,0:5,0:0.0:0,0:22.4:1.0:30.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 -4 55965031 . AT A 117 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00017;SOR=0.0;LSEQ=TTATACTTTTTGTTTGTAAG;RSEQ=GACAAATTTTAGCACTAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:13:2,11:5,94:0.1161:2,2:24.0:1.0:31.8:1.0:0.18698:3.36:60.0:26.0:0.1161:0.0268:0.2 0/0:110:0:0,0:9,101:0.0:2,0:23.8:1.0:30.1:1.0:1.0:0.0:60.0:220.0:1.0:0.0:0.2 -4 55979609 . G A 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02748;LSEQ=CTTCATCTCACTCCCAGACT;RSEQ=GGTTTTTAGGTCTCGGTTTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:780:57:26,31:298,425:0.0731:2,2:24.9:1.0:29.7:1.0:0.57708:1.2:60.0:114.0:0.0736:0.0:1.1 0/0:926:2:2,0:400,524:0.0022:2,0:1.0:0.0:24.5:1.0:0.1882:0.0:60.0:4.0:0.0022:0.0:1.0 -4 55985209 . C G 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.46154;SOR=0.0;LSEQ=AACATGGTAAAACCCTGTCT;RSEQ=TACTAAAAATACAAAAATGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:0,6:0,5:0.5455:0,0:32.8:1.0:32.7:1.0:1.0:0.0:60.0:12.0:0.5455:0.0:1.8 0/0:2:0:0,0:0,2:0.0:0,0:16.5:1.0:33.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.0 -4 55991731 . T C 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.22222;SOR=0.0;LSEQ=GGAAACGCAGCGACCACACA;RSEQ=TGACCGCTCTCCCGGGGTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:1,6:0,0:0.875:0,2:25.3:1.0:32.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.6 0/0:1:0:0,0:0,1:0.0:0,0:5.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -4 65604620 . C T 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01192;LSEQ=TTTACAAGAACCTTTAATAT;RSEQ=AATACAATAATGCCATGAGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:59:27,32:51,66:0.3352:2,2:25.0:1.0:28.5:1.0:0.87252:1.09:59.9:118.0:0.343:0.0:2.7 0/0:169:1:0,1:79,89:0.0059:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.006:0.0:1.0 -4 65604632 . G GA 63 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.12123;SOR=0.16637;LSEQ=TTTAATATCAATACAATAAT;RSEQ=CCATGAGCTAGACTTCTACA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:6:4,2:14,21:0.0357:2,2:26.0:1.0:24.7:1.0:0.37729:2.92:60.0:2.0:0.0241:0.006:2.8 0/0:164:1:1,0:49,54:0.0061:2,0:10.0:0.0:29.0:0.0:0.48077:0.0:60.0:2.0:0.0061:0.0:2.0 -4 66189753 . C CT 189 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.14857;LSEQ=CACTGTTTTCCCTTTTCCCC;RSEQ=TTTTTTTGTTAAAATAAATC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:64:57,7:185,38:0.2078:2,2:28.5:1.0:31.6:1.0:0.32898:1.67:60.0:128.0:0.2254:0.0:0.1 0/1:294:11:11,0:225,55:0.0374:2,0:25.6:1.0:30.8:1.0:0.13281:0.0:60.0:22.0:0.0375:0.0068:0.5 -4 66216523 . C T 69 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCAATTTTCCATAGTGTAGA;RSEQ=GTAACAGTTTTTAAATAGCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1.0:0,2:21.8:1.0:30.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -4 66218527 . A T 105 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.17194;SOR=0.0;LSEQ=TTTTTTTTTCAAATTAAGAC;RSEQ=TACTTAAATAAAACTTTAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:10:10,0:28,0:0.2632:1,0:29.6:1.0:31.8:1.0:1.0:0.0:60.0:20.0:0.2632:0.0:1.1 0/0:9:0:0,0:9,0:0.0:0,0:25.4:1.0:29.8:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 -4 66218677 . C T 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGTGGCCCAAATTCAACTT;RSEQ=AACATCACAGCATCATCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:28:21,7:306,93:0.0656:2,2:23.0:1.0:29.4:1.0:0.81929:1.09654:60.0:56.0:0.0671:0.0:1.9 0/0:364:0:0,0:273,91:0.0:2,0:24.7:1.0:30.8:1.0:1.0:0.0:59.9:59.667:1.0:0.0:0.6 -4 66270345 . G A 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.17595;SOR=0.0;LSEQ=CCTAATATCCTTTCTTAAAA;RSEQ=TGTGTAATTGAAAAGTCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:7:0,7:0,36:0.1628:1,0:24.9:1.0:31.4:1.0:1.0:0.0:60.0:14.0:0.1667:0.0:1.0 0/0:14:0:0,0:0,14:0.0:1,0:19.1:1.0:32.6:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 -4 66286376 . G A 95 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05177;SOR=0.15512;LSEQ=TATATTGGCATTTTGAGAAC;RSEQ=TAGCAATATAAAAAAAATCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:9:0,9:1,89:0.0909:1,0:21.8:1.0:30.1:1.0:1.0:0.0:60.0:18.0:0.0928:0.0:1.7 0/1:66:1:0,1:1,64:0.0152:1,0:23.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0154:0.0:1.0 -4 66286633 . C T 67 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATGAGCTCTATATGACATAT;RSEQ=CCATTATGCTAATAGATACA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1.0:0,2:21.8:1.0:29.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -4 69761131 . T C 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05249;SOR=0.0;LSEQ=AAAATGTCACATTTGTAGTT;RSEQ=CCATTTTCTTGTCTCTATAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:3,10:0.2778:2,2:18.0:1.0:31.6:1.0:0.58275:2.12:60.0:10.0:0.2778:0.0:1.2 0/0:14:0:0,0:7,7:0.0:2,0:14.3:1.0:29.5:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 -4 78271554 . C G 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00014;SOR=0.0;LSEQ=TCCCTTTCATCTTCATTTCT;RSEQ=TTAGCAAATTCAGGGCATAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:11:9,2:145,93:0.0438:2,2:24.3:1.0:32.6:1.0:0.21349:2.88:60.0:22.0:0.0442:0.0:1.0 0/0:306:0:0,0:178,126:0.0:2,0:23.5:1.0:31.4:1.0:1.0:0.0:60.0:151.0:0.9934:0.0:0.5 -4 87163541 . G T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.02707;SOR=0.0;LSEQ=TTTGTCCCTTGATGGAGAGG;RSEQ=TGTGCTTTGCTGAGGGAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:2,4:17,16:0.1538:2,2:13.7:1.0:28.2:1.0:0.66142:2.08513:60.0:5.0:0.1316:0.0:2.0 0/0:34:0:0,0:16,18:0.0:2,0:27.9:1.0:30.7:1.0:1.0:0.0:60.0:68.0:1.0:0.0:0.2 -4 99808693 . T C 102 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTTAATGAATGTCCCGTCCC;RSEQ=CTACCAACTGACAAAGCCCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:3,6:0,0:1.0:0,2:24.3:1.0:32.2:1.0:1.0:0.0:60.0:18.0:1.0:0.0:2.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -4 120324304 . C T 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00245;SOR=0.0;LSEQ=GGAGGAGGGGGTGATGATGT;RSEQ=ATTGCTGATGACGGCTTTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:8:8,0:52,31:0.0879:2,0:13.8:1.0:30.9:1.0:0.04739:0.0:52.5:16.0:0.0879:0.0:1.1 0/0:98:0:0,0:53,45:0.0:2,0:22.1:1.0:30.8:1.0:1.0:0.0:49.1:31.667:1.0:0.0:0.2 -4 124344819 . G A 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10929;LSEQ=TCTTCAACCAAAGGCTGCTA;RSEQ=GATTGTTTCTGTAATCTCCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:168:85:11,74:14,69:0.506:2,2:24.0:1.0:30.8:1.0:0.52078:1.36242:60.0:84.0:0.503:0.0:1.1 0/1:160:16:3,13:38,106:0.1:2,2:25.9:1.0:30.4:1.0:0.76332:1.54956:60.0:32.0:0.1006:0.0:1.1 -4 136777565 . CT C 143 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTCATCCCTCTTTACAATT;RSEQ=TTTCCTTGGGTATCTAAATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:24:20,4:55,7:0.2791:2,2:25.4:1.0:31.4:1.0:0.49141:1.56259:60.0:48.0:0.2791:0.0465:0.0 0/0:102:0:0,0:86,16:0.0:2,0:25.8:1.0:30.8:1.0:1.0:0.0:60.0:101.0:1.0:0.0:0.0 -4 143043397 . G A 193 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11451;LSEQ=TCTAGCATTCCAATTTCATC;RSEQ=CCTAAACAATAGAAAAGGCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:93:28,65:119,219:0.2158:2,2:26.8:1.0:29.6:1.0:0.38907:1.26075:60.0:45.5:0.2156:0.0:1.2 0/1:492:15:7,8:172,304:0.0305:2,2:15.5:1.0:28.4:1.0:0.42299:1.54:60.0:30.0:0.031:0.0:1.3 -4 143043464 . C T 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.12966;LSEQ=AAATGTCACTAGCTACTATG;RSEQ=CTCCCTGCTGGAATTTGTTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:35:1,34:12,98:0.2414:2,1:26.4:1.0:30.3:1.0:0.18949:4.13508:60.0:70.0:0.2448:0.0:1.4 0/1:127:5:0,5:17,104:0.0394:2,0:22.6:1.0:29.4:1.0:1.0:0.0:60.0:10.0:0.04:0.0:1.8 -4 143066973 . G GA 61 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.10249;SOR=0.17267;LSEQ=TTTACTCAGTAAATGATTGG;RSEQ=AAAAAAAATTATTTCTTACC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:5:4,1:311,145:0.0108:2,2:14.6:1.0:26.3:1.0:1.0:1.86:60.0:4.0:0.0088:0.0022:0.2 0/0:530:1:1,0:352,177:0.0019:2,0:39.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0019:0.0:0.0 -4 143095139 . C T 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.05699;SOR=0.0;LSEQ=TATGTAAGGTGACGAAAATG;RSEQ=TTTTTAAAACTAGGTAATCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:0.3529:0,0:19.5:1.0:30.7:1.0:1.0:0.0:60.0:12.0:0.375:0.0:1.0 0/0:10:0:0,0:0,10:0.0:0,0:26.4:1.0:33.2:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 -4 143158979 . A C 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.03099;LSEQ=AAAATTTTTAAATGGTATAA;RSEQ=ATAATTAATATGAGAGAAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:98:77,21:98,22:0.4495:2,2:20.8:1.0:31.5:1.0:0.61003:1.21378:60.0:48.0:0.4486:0.0:1.1 0/1:204:5:3,2:152,46:0.0245:2,2:30.2:1.0:30.8:1.0:0.33834:2.19283:60.0:10.0:0.0249:0.0:1.0 -4 143326714 . T G 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.33333;SOR=0.0;LSEQ=TTGCAGTTCATGCAAGTCTT;RSEQ=ACTGGTCTGAGATCCCAGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:24.3:1.0:31.8:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.3 0/0:1:0:0,0:0,1:0.0:0,0:19.0:0.0:12.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:0.0 -4 147770229 . T G 168 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTGCTGCCCTCAGTATGCC;RSEQ=GAGTCAGCAGTCTCACCCTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:28,26:0,0:1.0:0,2:26.5:1.0:29.2:1.0:1.0:0.0:60.0:17.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -4 153245521 . C G 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00093;SOR=0.0;LSEQ=GGATTGATGTATCAAGAGAT;RSEQ=CACTCACCACATGGATACCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:11:4,7:190,351:0.0198:2,2:30.8:1.0:31.7:1.0:1.0:1.06:60.0:22.0:0.0203:0.0:1.1 0/0:550:0:0,0:214,334:0.0:2,0:24.8:1.0:30.9:1.0:1.0:0.0:60.0:77.286:0.9963:0.0:0.1 -4 153253991 . TA T 88 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.03581;SOR=0.0;LSEQ=TAATTCTGCACTCTGATTTC;RSEQ=AAATTATGAAAGGCAGTAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:7:0,7:0,29:0.1892:1,0:28.6:1.0:31.7:1.0:1.0:0.0:60.0:14.0:0.1892:0.0:0.0 0/0:24:0:0,0:0,24:0.0:1,0:21.9:1.0:31.1:1.0:1.0:0.0:60.0:48.0:1.0:0.0:0.1 -4 153270964 . A G 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.27778;SOR=0.0;LSEQ=TTTAAATTTTTGTTCACAAG;RSEQ=TAATTTCTGCTTGTGTCCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:0.3571:0,0:28.6:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.3571:0.0:1.0 0/0:4:0:0,0:4,0:0.0:0,0:27.8:1.0:30.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -4 166144830 . A G 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CTTTTGAGAAACGGAGCATC;RSEQ=TGCTAAGATTAATGATGTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:391:26:8,18:160,205:0.0665:2,2:28.3:1.0:31.4:1.0:0.22295:1.75369:60.0:52.0:0.0668:0.0:1.4 0/0:500:0:0,0:216,284:0.0:2,0:25.9:1.0:29.6:1.0:1.0:0.0:59.2:99.0:1.0:0.0:0.3 -4 168210641 . C A 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.01282;SOR=0.0;LSEQ=GGCTTTTGTGGGGACTTTTT;RSEQ=TTTTTGTTGTTGTTGATGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:5,2:2,2:0.6364:2,2:25.4:1.0:27.0:1.0:0.57576:2.29:60.0:14.0:0.6364:0.0:1.0 0/0:7:0:0,0:5,2:0.0:2,0:7.7:1.0:29.1:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -4 171735386 . C T 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.27982;SOR=0.0;LSEQ=AAACTCTTGGATTTTATAGC;RSEQ=TAGGCAATTTGAAGTCAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:0.2632:1,0:21.4:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.0 0/0:8:0:0,0:8,0:0.0:0,0:28.1:1.0:28.3:1.0:1.0:0.0:60.0:7.0:1.0:0.0:0.0 -4 175047618 . G A 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.11129;LSEQ=CACCAGGGCCTGATAGAACC;RSEQ=TAAAAATGAGTTTTGCAGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:97:48,49:72,88:0.3774:2,2:24.1:1.0:30.4:1.0:0.52027:1.2:60.0:96.0:0.381:0.0:1.1 0/1:270:17:9,8:119,134:0.063:2,2:26.4:1.0:30.4:1.0:0.80278:1.27:60.0:34.0:0.063:0.0:1.2 -4 182443933 . G C 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGTAAATGGAGAACAACTG;RSEQ=ATCTGGATCCTGGTCAAACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:40:23,17:149,123:0.1282:2,2:30.6:1.0:32.4:1.0:0.86509:1.12:60.0:80.0:0.1286:0.0:1.1 0/0:501:0:0,0:278,222:0.0:2,0:24.4:1.0:30.6:1.0:1.0:0.0:60.0:61.5:0.998:0.0:0.1 -4 182444093 . T A 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATTTCCAGAAAGAAGAGAA;RSEQ=GGCAAAGTATGAGAAGGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:37:13,24:125,198:0.1025:2,2:26.5:1.0:31.1:1.0:0.72423:1.16499:60.0:74.0:0.1048:0.0:1.0 0/0:710:0:0,0:305,405:0.0:2,0:24.5:1.0:29.6:1.0:1.0:0.0:59.9:100.429:1.0:0.0:0.4 -4 182444132 . G T 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGAGATAAAGGAGATGGGTA;RSEQ=GATGCATAGGGAACTCAATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:95:32,63:51,112:0.3668:2,2:26.2:1.0:30.8:1.0:0.78241:1.11:60.0:94.0:0.3701:0.0:1.1 0/0:463:0:0,0:157,305:0.0:2,0:12.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 -4 183806854 . G T 56 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02106;SOR=0.0;LSEQ=GAATGCCCATTTAAAACCTG;RSEQ=ACCAAATGGCATGTTTAAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:5:2,3:182,155:0.0146:2,2:21.8:1.0:24.4:1.0:0.6654:1.75837:60.0:4.0:0.0119:0.0:1.4 0/0:397:0:0,0:228,169:0.0:2,0:26.0:1.0:30.7:1.0:1.0:0.0:60.0:65.167:1.0:0.0:0.4 -4 187509875 . G A 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGGCTGACACGTCAGA;RSEQ=CAGGAGGCGGTGGAGGCGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:56:32,24:206,150:0.1353:2,2:27.4:1.0:29.5:1.0:1.0:1.02994:60.0:55.0:0.1361:0.0:1.4 0/0:611:0:0,0:320,289:0.0:2,0:26.4:1.0:31.6:1.0:1.0:0.0:60.0:120.8:0.9967:0.0:0.2 -4 187525910 . A T 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.27761;SOR=0.0;LSEQ=GTGAGGAGGAGGGAAAGGAG;RSEQ=AGGGGTGTAGCGAAAAGGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,11:0.3125:0,0:23.6:1.0:29.6:1.0:1.0:0.0:60.0:10.0:0.3125:0.0:1.8 0/0:5:0:0,0:0,5:0.0:0,0:25.8:1.0:30.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.4 -4 187527089 . T C 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=AAATGCTCATCTTTTAATAC;RSEQ=GATAGCGACTTCTTGAATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:13:13,0:35,2:0.26:2,1:30.6:1.0:31.8:1.0:1.0:0.0:60.0:26.0:0.26:0.0:1.4 0/0:60:0:0,0:58,2:0.0:1,0:23.8:1.0:31.2:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.2 -4 187530731 . T C 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.01373;SOR=0.0;LSEQ=CAGGCGCCCGCCACCACGCC;RSEQ=GGCTAATTTTTTTTTGTATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:8,3:2,4:0.6471:2,2:12.5:1.0:29.8:1.0:0.16176:4.77:47.8:22.0:0.6471:0.0:1.6 0/0:6:0:0,0:4,2:0.0:2,0:25.8:1.0:29.2:1.0:1.0:0.0:58.5:5.0:1.0:0.0:0.2 -4 187531022 . A G 215 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00449;LSEQ=TGTAGGTGTCTTGGCTGAAC;RSEQ=CAGGGGTATTATCGTTGATA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:591:133:77,56:242,216:0.225:2,2:24.6:1.0:30.6:1.0:0.32396:1.23:60.0:43.333:0.2238:0.0:1.1 0/0:769:1:1,0:400,367:0.0013:2,0:18.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.0013:0.0:1.0 -4 187534689 . G T 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00606;SOR=0.0;LSEQ=AGGTCTCCAACCCTGCCAGG;RSEQ=GCTAGCTCTTTAAGTCCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1.0:0,0:18.6:1.0:31.0:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:3:0:0,0:0,3:0.0:0,0:17.3:1.0:30.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -4 187535063 . T C 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.03333;SOR=0.0;LSEQ=AAGCTTGAGTTATATTTTAA;RSEQ=TTCTGAGGGTTGTTTTTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:0.8571:0,0:26.3:1.0:30.5:1.0:1.0:0.0:60.0:5.0:0.8333:0.0:1.2 0/0:3:0:0,0:3,0:0.0:0,0:28.0:1.0:31.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -4 187535765 . T C 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.375;SOR=0.0;LSEQ=TACAAAATGCTATTATATGT;RSEQ=ATTAAGCTGATTTCATATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:0.7143:0,0:24.6:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:8.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -4 187540042 . G A 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATCCTTAGCCATTAAACG;RSEQ=ACTGAGATCACTTTCTCCGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:708:74:36,38:314,320:0.1045:2,2:27.1:1.0:29.9:1.0:0.90283:1.03572:60.0:36.0:0.1043:0.0:1.1 0/0:917:0:0,0:475,442:0.0:2,0:26.0:0.0:13.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:4.0 -4 187541598 . C G 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=TGTCACTTCTACAACCACAT;RSEQ=AAACGCCTCCTGCTGCTCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:14:5,9:208,273:0.0283:2,2:24.6:1.0:29.7:1.0:0.78543:1.37058:60.0:13.0:0.0269:0.0:1.1 0/0:555:0:0,0:267,288:0.0:2,0:23.8:1.0:31.2:1.0:1.0:0.0:60.0:68.375:1.0:0.0:0.1 -4 187542755 . T C 240 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00369;LSEQ=ATGTAAACTTCGGAGAGGCG;RSEQ=TGTCAGCAATTGTGACAAAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:790:180:90,90:290,318:0.2278:2,2:26.0:1.0:32.1:1.0:0.61095:1.1:60.0:59.0:0.2272:0.0:1.1 0/0:920:1:0,1:443,476:0.0011:2,0:17.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 -4 187542922 . A G 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAATCATAAAAGAATTTCC;RSEQ=ATATTTCCTGGAAGGAGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:42:16,26:112,214:0.1141:2,2:23.7:1.0:30.1:1.0:0.73094:1.18:60.0:41.0:0.1139:0.0:1.1 0/0:402:0:0,0:147,255:0.0:2,0:24.5:1.0:29.5:1.0:1.0:0.0:60.0:99.5:1.0:0.0:0.2 -4 187542986 . G C 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CACAAGGGGCAGTAGTAGTA;RSEQ=TAGTTAGAGAAACAGAAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:36:2,34:9,84:0.2791:2,2:27.8:1.0:32.4:1.0:0.72667:1.81396:60.0:72.0:0.2835:0.0:1.1 0/0:119:0:0,0:15,104:0.0:2,0:22.3:1.0:31.5:1.0:1.0:0.0:60.0:118.0:1.0:0.0:0.1 -4 187557113 . C G 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=GACTTGTGCCCAAAACTCAT;RSEQ=AAACCGTATGCAGGTTCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:18:12,6:161,31:0.0857:2,2:20.6:1.0:30.8:1.0:0.09839:2.58191:60.0:36.0:0.0865:0.0:2.0 0/0:193:0:0,0:151,42:0.0:2,0:22.8:1.0:30.9:1.0:1.0:0.0:60.0:63.333:1.0:0.0:0.1 -4 187558187 . CA C 120 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00051;SOR=0.07257;LSEQ=CATTTTGCAGGGCACGATGA;RSEQ=ACATACACAGCAGATCTTCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:14:1,13:0,9:0.6087:0,1:25.6:1.0:31.7:1.0:1.0:0.0:60.0:28.0:0.6087:0.0435:0.4 0/1:21:2:0,2:0,19:0.0952:1,0:34.0:1.0:28.0:1.0:1.0:0.0:60.0:4.0:0.0952:0.0:0.0 -4 187584530 . G A 181 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01327;LSEQ=TGAGCTTGTCATTAGAGCTC;RSEQ=AATCTGGATCAAATGCCTCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:650:66:37,29:347,237:0.1015:2,2:26.9:1.0:30.1:1.0:0.60007:1.14732:60.0:65.0:0.1009:0.0:1.1 0/0:669:1:1,0:376,290:0.0015:2,0:1.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0015:0.0:1.0 -4 187628352 . A T 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CCAGAGGGCGTGCGATGTTA;RSEQ=CAACACCCGTCACGCTGTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:320:96:55,41:124,100:0.3:2,2:24.5:1.0:30.0:1.0:0.80627:1.08:60.0:31.0:0.2962:0.0:1.7 0/0:412:0:0,0:217,194:0.0:2,0:23.0:1.0:29.8:1.0:1.0:0.0:60.0:204.5:1.0:0.0:0.6 -4 189192088 . G C 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.08394;SOR=0.14568;LSEQ=CAGCAGCAGCCCCACCAGCA;RSEQ=CAGCACCAGCACCAGCAGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:5:3,2:14,13:0.1563:2,2:9.4:1.0:28.2:1.0:1.0:1.38:52.4:4.0:0.1379:0.0:3.2 0/1:39:1:0,1:19,17:0.0256:2,0:47.0:0.0:29.0:0.0:0.48649:0.0:41.0:2.0:0.0313:0.0:6.0 -4 190093234 . C T 235 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01389;LSEQ=TAACGGGAGAAAAAATTCCC;RSEQ=GAAGCTGACACTCATCCAGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:323:206:98,108:58,59:0.6378:2,2:25.3:1.0:30.6:1.0:0.81686:1.08309:60.0:412.0:0.6398:0.0:1.1 0/1:464:11:5,6:214,236:0.0237:2,2:26.5:1.0:27.7:1.0:1.0:1.0879:59.7:4.5:0.0196:0.0:2.0 -5 223909 . GATTTAA G 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTTATGTATCTATAAACTA;RSEQ=ATTTAGATCAAGTAAAGCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:7:0,7:1,32:0.175:1,0:26.7:1.0:31.7:1.0:1.0:0.0:58.0:14.0:0.1795:0.025:1.6 0/0:4:0:0,0:0,4:0.0:0,0:11.3:1.0:29.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -5 223958 . T C 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATTAAAATAAAATGAACAG;RSEQ=GTCTGCTGTGATAGATGATA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:0,5:4,14:0.2174:2,0:17.4:1.0:28.2:1.0:0.53924:0.0:60.0:10.0:0.2174:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 224196 . A T 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.30773;SOR=0.0;LSEQ=CTTGGCACCTTCTCAGGCAT;RSEQ=AGCATAGGCACGGCCCTGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:8:6,2:20,3:0.25:2,2:26.6:1.0:30.6:1.0:0.58308:2.15834:56.3:16.0:0.2667:0.0:3.6 0/0:7:0:0,0:5,2:0.0:2,0:21.6:1.0:26.6:1.0:1.0:0.0:56.7:6.0:1.0:0.0:0.3 -5 224207 . C T 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.16449;SOR=0.0;LSEQ=CTCAGGCATAAGCATAGGCA;RSEQ=GGCCCTGAAGTAGAGTTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:7,2:21,3:0.2727:2,2:32.6:1.0:31.8:1.0:0.59705:1.95399:56.7:18.0:0.2813:0.0:3.6 0/0:8:0:0,0:6,2:0.0:2,0:28.8:1.0:31.4:1.0:1.0:0.0:57.1:16.0:1.0:0.0:0.3 -5 224211 . C T 96 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.16753;SOR=0.0;LSEQ=GGCATAAGCATAGGCACGGC;RSEQ=CTGAAGTAGAGTTGTGGTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:9:7,2:22,3:0.2647:2,2:34.8:1.0:30.3:1.0:0.59084:2.04473:56.7:8.0:0.2424:0.0:3.6 0/0:8:0:0,0:6,2:0.0:2,0:32.1:1.0:31.3:1.0:1.0:0.0:57.1:16.0:1.0:0.0:0.3 -5 225267 . C A 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.29839;SOR=0.0;LSEQ=GTAGCCTTTCACTCACTGCT;RSEQ=CAGTCAGCCCTTCCTGGAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:10:10,0:23,0:0.303:1,0:27.3:1.0:28.0:1.0:1.0:0.0:53.0:20.0:0.303:0.0:1.1 0/0:5:0:0,0:5,0:0.0:0,0:16.6:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -5 228071 . A C 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.56125;SOR=0.0;LSEQ=AGTAGGAAATGTGTCACCAA;RSEQ=ATAGGAGCTGTTGCTGCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:5,0:14,4:0.2174:2,0:27.6:1.0:33.8:1.0:0.53924:0.0:37.2:10.0:0.2174:0.0:2.0 0/0:4:0:0,0:3,1:0.0:2,0:23.5:1.0:31.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.5 -5 231337 . A C 97 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.56899;SOR=0.0;LSEQ=CACCGTCTTATGTATTTCTC;RSEQ=AGAGCGCTAAACCCTGCCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:0,29:0.2162:1,0:17.4:1.0:32.5:1.0:1.0:0.0:52.8:16.0:0.2222:0.0:3.9 0/0:4:0:0,0:0,4:0.0:0,0:24.0:1.0:30.0:1.0:1.0:0.0:56.5:8.0:1.0:0.0:0.0 -5 240664 . A C 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCACTGGTTTTGTTTTTTA;RSEQ=AAACTAGATCTAGGGGGATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:88:8,80:7,105:0.44:2,2:23.5:1.0:32.4:1.0:0.59012:1.5:58.0:176.0:0.4422:0.0:1.1 0/0:85:0:0,0:10,75:0.0:2,0:25.9:1.0:29.7:1.0:1.0:0.0:53.0:27.333:1.0:0.0:0.2 -5 420898 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ATTCCAGAAAGAGACACCTC;RSEQ=GCGCTGCACGCACGCAGCCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:3,2:0.5:2,2:20.4:1.0:30.6:1.0:1.0:2.41:60.0:10.0:0.5:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 420915 . GCCACGCAGCCACCCAC G 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCGCGCTGCACGCACGCA;RSEQ=CCACGCAGCCACCCACCCAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:3,2:8,2:0.3333:2,2:24.8:1.0:32.3:1.0:0.56044:2.48238:60.0:10.0:0.3333:0.1333:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 1255297 . C A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.04145;SOR=0.0;LSEQ=GGTTAAACCACTTCCTGATG;RSEQ=GAAAAGGGGTAAGAACTTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:13:13,0:149,5:0.0778:1,1:25.4:1.0:30.7:1.0:1.0:0.0:60.0:26.0:0.0802:0.0:1.1 0/0:53:0:0,0:50,3:0.0:2,0:22.4:1.0:32.2:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.0 -5 1260195 . T C 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGCCTGGGACCCCGTCTCA;RSEQ=CCTGTAAGGAGTGGCACTGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:31.2:1.0:28.8:1.0:1.0:0.0:60.0:5.0:0.7143:0.0:2.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 1264152 . A G 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GGCCCCAGGGTCTCGGGTTC;RSEQ=GAGGGACTCATGCCCAGCAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:0.7273:0,0:32.1:1.0:29.0:1.0:1.0:0.0:60.0:16.0:0.7273:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 1266310 . A G 127 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCAAAGAGCAGCAGGAGCC;RSEQ=GGTCACCGCCTGCACTCACC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:21,2:0,0:1.0:0,2:21.5:1.0:28.2:1.0:1.0:0.0:60.0:10.5:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 1272414 . G A 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03292;LSEQ=ACCTGCCGGCAGAGGAGAGG;RSEQ=CATGAGCCACAAATGTGGCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:906:205:73,132:240,461:0.2263:2,2:25.9:1.0:29.5:1.0:0.73867:1.06:60.0:67.333:0.2262:0.0:1.1 0/0:420:4:3,1:159,257:0.0095:2,2:3.3:1.0:23.0:1.0:0.16203:4.83:60.0:3.0:0.0073:0.0:1.0 -5 1279964 . G C 116 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTAAGCGGAAGCGCACGGAG;RSEQ=CTGCGCACCACAGCAGGACA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:9,3:7,3:0.5455:2,2:21.3:1.0:32.6:1.0:1.0:1.27:60.0:24.0:0.6:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 1280190 . G A 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTCCCGTGGCCCCTCCTCC;RSEQ=GGCCCTTCATCTAAGCTGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:107:94,13:329,40:0.2243:2,2:25.5:1.0:30.0:1.0:0.7276:1.13716:60.0:20.4:0.2189:0.0:1.4 0/0:192:0:0,0:158,34:0.0:2,0:23.1:1.0:28.9:1.0:1.0:0.0:60.0:37.4:1.0:0.0:0.2 -5 1280830 . G C 68 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=CAGCCACTGGGGTAGCCCAA;RSEQ=GCTGGCCCCAGGCAGGACCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:18.6:1.0:29.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:1:0:0,0:0,1:0.0:0,0:16.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -5 1284554 . TCTGGCGACCTCACCCCGGACCGGCACCATCCGGACTCCATACATCCAGCTCACCGAGGGC T 86 NM4 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=2.0;MSILEN=1.0;SSF=0.125;SOR=0.0;LSEQ=ATATCCAGCTCACAGCAGGG;RSEQ=CTGGCGACCTCACTCCAGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:4,3:0,0:1.0:0,2:34.9:1.0:30.8:1.0:1.0:0.0:44.3:14.0:1.0:1.0:4.3 0/0:1:0:0,0:1,0:0.0:0,0:5.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -5 1293389 . C G 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGAGCCCCTACTGCATTCAG;RSEQ=TCTGGGGCCTGGGCCCTCGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:154:127,27:235,48:0.3524:2,2:22.4:1.0:31.2:1.0:0.89484:1.04073:60.0:153.0:0.355:0.0:1.1 0/0:154:0:0,0:124,30:0.0:2,0:25.0:1.0:31.9:1.0:1.0:0.0:60.0:37.5:1.0:0.0:0.2 -5 1295250 . G A 234 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGCTGGGCCGGGGACCCGG;RSEQ=AGGGGTCGGGACGGGGCGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1241:290:175,115:570,377:0.2337:2,2:25.8:1.0:28.7:1.0:1.0:1.01:60.0:16.059:0.2306:0.0:1.3 0/0:602:0:0,0:332,267:0.0:2,0:25.5:1.0:29.7:1.0:1.0:0.0:60.0:25.043:0.9948:0.0:0.4 -5 1576000 . C G 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00125;SOR=0.0;LSEQ=AATAAACTGGCATTTACTTC;RSEQ=TGGTCATGCCACTCTAGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:19:17,2:170,10:0.0955:2,2:21.9:1.0:30.3:1.0:0.32066:1.99118:57.3:38.0:0.0969:0.0:1.0 0/0:86:0:0,0:72,14:0.0:2,0:24.2:1.0:30.0:1.0:1.0:0.0:58.9:20.5:1.0:0.0:0.1 -5 6624371 . C T 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.03162;SOR=0.0;LSEQ=ATCCAAGGTTTTGATTAAAG;RSEQ=ATTAAGTAAGATGGGGACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:15:15,0:5,0:0.75:0,1:25.5:1.0:29.9:1.0:1.0:0.0:60.0:14.0:0.7368:0.0:1.1 0/0:3:0:0,0:3,0:0.0:0,0:40.0:1.0:27.7:1.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -5 8453932 . CAT C 86 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=8.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CAGATACTGTATTTTATATA;RSEQ=ATATATATATATATAGAAGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:0,6:0,2:0.6667:0,0:37.2:1.0:33.5:1.0:1.0:0.0:60.0:12.0:0.6667:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 17464034 . C T 78 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCCCCACCCAGGGAGCTTC;RSEQ=GTGTTAGGCAGTTGCAAGTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:1.0:0,2:24.5:1.0:30.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 17491448 . T A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTCCTCTAGAGTGCAAGGT;RSEQ=TCCCAGGAGCGTGGGCTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:114:95,19:317,45:0.2395:2,2:23.0:1.0:28.4:1.0:0.27078:1.40781:60.0:113.0:0.2399:0.0:1.1 0/0:263:0:0,0:215,48:0.0:2,0:23.7:1.0:29.8:1.0:1.0:0.0:60.0:86.667:1.0:0.0:0.1 -5 17670396 . G T 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=TCAAAGAGGCGCACCAGGTA;RSEQ=GCCTTGCTGGGCTCCTGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:23:9,14:321,477:0.028:2,2:21.9:1.0:30.1:1.0:1.0:1.04677:60.0:46.0:0.0284:0.0:1.0 0/0:487:0:0,0:200,287:0.0:2,0:25.5:1.0:30.4:1.0:1.0:0.0:60.0:59.875:1.0:0.0:0.2 -5 17670600 . C A 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=8e-05;SOR=0.05177;LSEQ=TTCTTGATCCCTCCTGTAGG;RSEQ=GGCGCCCTCTTGCTGGCAGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:36:5,31:5,37:0.4615:2,2:22.4:1.0:31.2:1.0:1.0:1.19:60.0:17.0:0.4658:0.0:1.1 0/1:24:1:0,1:5,18:0.0417:2,0:44.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0417:0.0:1.0 -5 22934638 . G T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01471;SOR=0.0;LSEQ=ATACCAACCTCTGGAGTTGG;RSEQ=TGACATGGCTTCTCCCCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:10:4,6:63,66:0.0719:2,2:30.5:1.0:28.5:1.0:0.74633:1.42816:59.0:9.0:0.0667:0.0:1.7 0/0:84:0:0,0:36,48:0.0:2,0:28.4:1.0:30.1:1.0:1.0:0.0:60.0:83.0:1.0:0.0:0.5 -5 23146100 . G A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06912;SOR=0.0;LSEQ=AGGGTGTGTTTCGCTGGGGG;RSEQ=AAACCCACTTGTCTGTACTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:3,3:8,8:0.2727:2,2:29.7:1.0:31.0:1.0:1.0:1.0:60.0:12.0:0.2727:0.0:1.0 0/0:12:0:0,0:5,7:0.0:2,0:26.9:1.0:26.4:1.0:1.0:0.0:60.0:11.0:1.0:0.0:0.5 -5 23303757 . G A 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTCTGCACAGGGTGGCGTT;RSEQ=GAGTACAAGGCAGGAGGGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1168:93:42,51:476,597:0.0796:2,2:25.8:1.0:29.6:1.0:0.91359:1.03:60.0:92.0:0.0803:0.0:1.1 0/0:640:0:0,0:283,357:0.0:2,0:25.8:1.0:30.3:1.0:1.0:0.0:60.0:57.182:1.0:0.0:0.3 -5 23303943 . C A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATGCTTCTGTCTGGACCATC;RSEQ=CTGACCTCTGAGACCGCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1116:60:38,22:552,504:0.0538:2,2:24.6:1.0:30.2:1.0:0.11061:1.58:59.8:120.0:0.0543:0.0:1.2 0/0:619:0:0,0:320,299:0.0:2,0:25.8:1.0:30.2:1.0:1.0:0.0:59.9:60.9:1.0:0.0:0.1 -5 23304880 . TT CC 230 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTAATGTTCTTCAAGATCTG;RSEQ=AAAGAATCAAACCGTTCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:946:152:73,79:404,388:0.1607:2,2:27.4:1.0:31.8:1.0:0.53566:1.12667:59.6:304.0:0.162:0.0053:1.8 0/0:482:0:0,0:243,239:0.0:2,0:26.6:1.0:29.5:1.0:1.0:0.0:60.0:79.333:1.0:0.0:0.7 -5 26148813 . A G 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAGTGGGGAGGGGGTGGGGC;RSEQ=ACCAGCACTGCCTGCAGCTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:0,1:0.8571:0,2:28.7:1.0:30.8:1.0:0.28571:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 26149197 . C T 59 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.12797;SOR=0.0;LSEQ=CCCTTAGGAGTAGGGGTGGC;RSEQ=ACAGTCGCTGTGGACCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:1,4:2,6:0.3846:2,2:29.8:1.0:25.6:1.0:1.0:1.30472:60.0:4.0:0.3333:0.0:1.4 0/0:6:0:0,0:1,5:0.0:2,0:26.7:1.0:31.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 -5 26149350 . C T 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.19231;SOR=0.0;LSEQ=GGCCCTGCTCCCTATGACAC;RSEQ=CAACTGGGTGATATCTTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:3,4:2,2:0.6364:2,2:30.0:1.0:28.7:1.0:1.0:1.29868:60.0:6.0:0.6:0.0:1.4 0/0:3:0:0,0:2,1:0.0:2,0:15.0:1.0:28.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -5 26150118 . A T 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=2.0;SSF=0.00058;SOR=0.0;LSEQ=ATGAACAAAGCTTCCAAGAA;RSEQ=TATGGGACTTCATAAAAAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:14:8,6:8,8:0.4667:2,2:28.1:1.0:30.1:1.0:0.73001:1.32:54.4:28.0:0.4667:0.0:1.2 0/0:17:0:0,0:12,5:0.0:2,0:22.9:1.0:30.8:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.2 -5 26670194 . A C 105 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07548;SOR=0.0;LSEQ=AATAATATATCTTTAATTTT;RSEQ=CTTAGATTACAAAACAGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:12:0,12:0,196:0.0577:1,0:31.1:1.0:29.4:1.0:1.0:0.0:60.0:24.0:0.0583:0.0:1.1 0/0:65:0:0,0:1,64:0.0:1,0:23.6:1.0:29.8:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.0 -5 28499327 . T A 61 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGCTGCTCTTAAGAGTGAA;RSEQ=AAAAGCTCACAAGTGTTTGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:16.6:1.0:26.4:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 29955160 . GA G 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.24895;SOR=0.0;LSEQ=GATGTTTTAAGAATTTTTGG;RSEQ=AAGGAAAATAGAAAATGATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:0,8:0.3846:0,0:33.6:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.4167:0.0:1.2 0/0:5:0:0,0:0,5:0.0:0,0:17.0:1.0:30.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 -5 33997307 . A C 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00415;SOR=0.0;LSEQ=TACCCTATATGAGGGTTGAG;RSEQ=GCTGTCACCAGCATTAGCGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:16:6,10:113,148:0.0578:2,2:24.4:1.0:31.2:1.0:0.79658:1.27143:60.0:32.0:0.0597:0.0:1.0 0/0:119:0:0,0:53,66:0.0:2,0:23.6:1.0:30.1:1.0:1.0:0.0:60.0:58.5:1.0:0.0:0.1 -5 35860873 . C T 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATGTCTGCCACAGAGTCTG;RSEQ=TATTTTATTAAGGTCATGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:55:50,5:109,6:0.3235:2,2:22.4:1.0:29.6:1.0:0.33707:1.80989:60.0:54.0:0.3253:0.0:1.1 0/0:111:0:0,0:95,16:0.0:2,0:20.0:1.0:31.9:1.0:1.0:0.0:60.0:222.0:1.0:0.0:0.1 -5 35871291 . G A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01498;LSEQ=CACGATGTAGCTTACCGCCA;RSEQ=GAAAAGGATGAAAACAAATG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:78:30,48:218,411:0.1103:2,2:27.3:1.0:30.9:1.0:0.53041:1.18:60.0:156.0:0.1116:0.0:1.1 0/0:540:1:1,0:203,336:0.0019:2,0:3.0:0.0:27.0:0.0:0.37778:0.0:60.0:2.0:0.0019:0.0:1.0 -5 35875518 . C T 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTAGAGCCAAGACTAGAAAT;RSEQ=TGTTCTTCTGATTCCAAGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:35:33,2:131,9:0.2:2,2:23.1:1.0:29.8:1.0:1.0:1.13:60.0:34.0:0.1965:0.0:1.7 0/0:105:0:0,0:96,9:0.0:2,0:22.9:1.0:31.4:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.2 -5 36367987 . T G 123 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATTTGGGGAATATTCAAT;RSEQ=GTTCATGTTTGGATCTACTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:14,0:3,1:0.7778:2,1:25.9:1.0:32.4:1.0:0.22222:0.0:60.0:28.0:0.7778:0.0:1.7 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 37744444 . GA G 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGAGTCAACAAAAAAATGCT;RSEQ=AAACCCACAAGGCCAGAGTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:0.625:2,2:25.0:1.0:30.4:1.0:1.0:2.60168:60.0:10.0:0.625:0.125:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 38942090 . T C 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTATTGTTCCACTGTCATTA;RSEQ=GCTTTTAAAATGAAAGAAAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:24.1:1.0:30.1:1.0:1.0:0.0:60.0:7.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 38942628 . T C 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.17451;SOR=0.0;LSEQ=AATGTTGCCATCTTTGTTCA;RSEQ=TGCAACCTCTGAGTCCTGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:6:1,5:8,41:0.1091:2,2:17.2:1.0:32.0:1.0:1.0:1.02:60.0:12.0:0.1154:0.0:1.0 0/0:22:0:0,0:0,22:0.0:1,0:22.7:1.0:30.4:1.0:1.0:0.0:59.5:44.0:1.0:0.0:0.2 -5 38947185 . C G 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02056;SOR=0.0;LSEQ=AAGGACTAAATAAAAGAGTA;RSEQ=AGAGTAGTTGAAAAGGGCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:9,0:25,1:0.2571:1,0:17.1:1.0:31.6:1.0:1.0:0.0:60.0:18.0:0.2647:0.0:1.4 0/0:18:0:0,0:17,1:0.0:1,0:20.2:1.0:31.3:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.1 -5 38949632 . C T 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATAGGATTTTCTTCCCCCCT;RSEQ=GCAGCTGCAAGAATCCATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:36:9,27:34,83:0.2353:2,2:27.1:1.0:29.1:1.0:0.67842:1.22729:60.0:11.0:0.2245:0.0:1.1 0/0:70:0:0,0:13,57:0.0:2,0:24.9:1.0:30.2:1.0:1.0:0.0:60.0:140.0:1.0:0.0:0.1 -5 38958167 . A G 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGCCAACATGGTGAAACTCC;RSEQ=ACTCTACTAAAAATACAAAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:4,4:0,0:1.0:0,2:23.5:1.0:30.6:1.0:1.0:0.0:58.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 38962656 . T C 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00197;SOR=0.0;LSEQ=TGTTGAAGGACTTGGCTATC;RSEQ=CTAAGGTTAATTAAAAGAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:12:4,8:419,554:0.0122:2,2:19.2:1.0:29.3:1.0:0.57002:1.51202:60.0:11.0:0.0114:0.0:1.2 0/0:706:0:0,0:306,400:0.0:2,0:25.5:1.0:29.5:1.0:1.0:0.0:60.0:57.833:1.0:0.0:0.2 -5 38972335 . T C 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCATGAGTCTGACTGCCTGA;RSEQ=GAACTCTTCTCTGGGAGTAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:1.0:0,0:14.1:1.0:28.9:1.0:1.0:0.0:60.0:18.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 38990820 . G C 89 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATATCAGATATGATATATAT;RSEQ=ATATATATCATATATATGAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:0.7778:0,0:37.7:1.0:32.0:1.0:1.0:0.0:57.1:14.0:0.7778:0.0:4.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 38990930 . TATATGAGATATATG T 123 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00998;SOR=0.0;LSEQ=GAGATATATGAGATATATGA;RSEQ=AGATATATGATATATATATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:16:16,0:58,1:0.2133:1,1:7.4:1.0:30.9:1.0:1.0:0.0:59.7:32.0:0.2133:0.2133:2.0 0/0:26:0:0,0:25,1:0.0:1,0:21.7:1.0:28.9:1.0:1.0:0.0:60.0:52.0:1.0:0.0:2.2 -5 38997170 . G A 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.32415;SOR=0.0;LSEQ=ATCTCGAGGGATAAATATCT;RSEQ=TCATTTAAAAGACCAATTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:1,28:0.2162:1,0:16.1:1.0:30.1:1.0:1.0:0.0:60.0:16.0:0.2162:0.0:1.0 0/0:9:0:0,0:1,8:0.0:2,0:13.3:1.0:31.4:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 -5 39002519 . C T 157 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGTGTATATATATATATATA;RSEQ=ACACACACAAAATTCATCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:40:39,1:25,2:0.4878:2,1:25.2:1.0:29.6:1.0:0.56038:3.07:60.0:19.0:0.5938:0.0:1.4 0/0:32:0:0,0:9,0:0.0:0,0:17.4:1.0:30.1:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.3 -5 39021493 . G A 83 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACCACAAAATCTTAAATCTT;RSEQ=CTATTATTTGAATGTGTTCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:0.5385:0,0:13.3:1.0:29.6:1.0:1.0:0.0:60.0:14.0:0.5385:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 40457488 . G A 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04799;LSEQ=CAACAACACACTGCAGGACC;RSEQ=ATATATTTTCCTTGCCCAAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:30:15,15:240,299:0.0527:2,2:20.5:1.0:29.8:1.0:0.57653:1.25:60.0:60.0:0.0533:0.0:1.2 0/0:376:1:1,0:174,201:0.0027:2,0:1.0:0.0:26.0:0.0:0.46543:0.0:60.0:2.0:0.0027:0.0:1.0 -5 52665229 . GTCT AGAC 209 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACACATTATGAATAAAACAA;RSEQ=AGATGATGCAAGAGAATGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:108:71,37:110,56:0.3899:2,2:26.9:1.0:31.0:1.0:1.0:1.02356:60.0:216.0:0.3942:0.0939:1.4 0/0:329:0:0,0:203,125:0.0:2,0:24.5:1.0:31.6:1.0:1.0:0.0:60.0:108.333:0.9969:0.0:0.4 -5 52665368 . G T 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=AAGACATTAGACTTCCTATT;RSEQ=CAGTGGTTTATAACAAAACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:15:5,10:83,196:0.051:2,2:23.1:1.0:30.3:1.0:0.77606:1.18:60.0:30.0:0.0523:0.0:1.1 0/0:312:0:0,0:122,190:0.0:2,0:25.3:1.0:31.4:1.0:1.0:0.0:60.0:51.0:1.0:0.0:0.5 -5 56168571 . G A 215 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAATAATTTTGAAATGATAC;RSEQ=GATATGTTTAATTTTTAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:134:79,55:95,88:0.4227:2,2:21.1:1.0:30.5:1.0:0.25326:1.33:60.0:66.0:0.419:0.0:1.0 0/0:460:0:0,0:258,200:0.0:2,0:22.6:1.0:29.7:1.0:1.0:0.0:60.0:228.0:0.9956:0.0:0.1 -5 56183637 . G C 74 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAAACTCAAAGTGCACATAA;RSEQ=AAATTTTTAAAAATATTCTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:1.0:0,2:16.8:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 56183743 . T G 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.16667;SOR=0.0;LSEQ=ATTGTTCTTCTGACTCAGCT;RSEQ=CTTCTGTCGTGTTCATAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,1:0.7143:2,2:21.6:1.0:32.4:1.0:1.0:1.41418:60.0:10.0:0.7143:0.0:1.0 0/0:2:0:0,0:1,1:0.0:2,0:13.5:1.0:27.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -5 56184610 . C T 65 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GACTAAGCTATAATGTTTGG;RSEQ=AGGTTAGGTGTATTAACTGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:35.6:1.0:28.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 56188977 . G A 68 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCTTAATCTAAATAGCTCT;RSEQ=TATGCTGAAGAAATAGAAAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:27.2:1.0:29.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 57752811 . CA C 80 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.00888;SOR=0.0;LSEQ=TGCTTTGTCTTTTTTGCCAC;RSEQ=AAAAGAGCAGCAGCTGCTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:6:3,3:219,209:0.0138:2,2:30.8:1.0:31.2:1.0:1.0:1.04775:60.0:12.0:0.014:0.0:0.2 0/0:518:0:0,0:249,269:0.0:2,0:25.6:1.0:29.7:1.0:1.0:0.0:60.0:128.5:1.0:0.0:0.1 -5 57754489 . ACT A 231 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.05193;LSEQ=GCTAAAATCCCAGATAAAAT;RSEQ=CTTTGAATACCATGTTAATT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:145:108,37:127,68:0.4265:2,2:24.4:1.0:32.2:1.0:0.07517:1.56:60.0:290.0:0.4315:0.0618:0.1 0/1:324:12:7,5:205,107:0.037:2,2:20.2:1.0:29.8:1.0:0.75812:1.36706:60.0:24.0:0.0372:0.0123:0.2 -5 62835420 . G A 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03112;LSEQ=TATTTTTTTTTTTATTTTTC;RSEQ=GAAGAAATAGGTATGTTTAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:16:8,8:18,11:0.3556:2,2:18.7:1.0:30.1:1.0:0.53364:1.61817:60.0:32.0:0.3556:0.0:1.2 0/1:61:1:1,0:35,25:0.0164:2,0:38.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0167:0.0:1.0 -5 62836591 . T C 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03294;LSEQ=AGTGATATTACTTTTAAAAA;RSEQ=CACCAAGTGTAAGCACAACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:22:22,0:31,0:0.4151:1,1:27.8:1.0:31.8:1.0:1.0:0.0:60.0:21.0:0.4118:0.0:1.0 0/1:45:1:1,0:41,3:0.0222:2,0:12.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0227:0.0:1.0 -5 62836726 . T C 225 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03212;LSEQ=TTCCAAATCCACAGTGGCAC;RSEQ=GCAGATTCAAAGCACTTTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:182:110,72:118,92:0.4631:2,2:25.2:1.0:30.1:1.0:0.41285:1.19:60.0:59.667:0.4602:0.0:1.1 0/1:484:13:7,6:268,202:0.0269:2,2:22.5:1.0:30.5:1.0:1.0:1.13689:60.0:26.0:0.0272:0.0:1.8 -5 67569342 . T C 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTAGAGGGCATCAGTTCCT;RSEQ=TGTTCTACCCTTATTTCATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:19:6,13:75,277:0.0512:2,2:23.2:1.0:32.1:1.0:0.26864:1.7:60.0:38.0:0.0512:0.0:1.2 0/0:361:0:0,0:85,275:0.0:2,0:24.1:1.0:29.6:1.0:1.0:0.0:60.0:50.429:0.9972:0.0:0.2 -5 68390203 . C G 107 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00098;SOR=0.03358;LSEQ=AAGGCAGCGACCGGCCGGGT;RSEQ=GCTCAGGATGCACTTTCTCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:6,5:2,1:0.7857:2,2:18.1:1.0:31.1:1.0:1.0:1.60839:60.0:22.0:0.7857:0.0:1.4 0/1:11:1:0,1:7,3:0.0909:2,0:49.0:0.0:29.0:0.0:0.36364:0.0:60.0:2.0:0.0909:0.0:1.0 -5 79172158 . C T 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTCCAGGGTAGAGATTGTG;RSEQ=CTGATTCATGTAGCTTAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:25:11,14:88,134:0.1012:2,2:25.6:1.0:29.6:1.0:0.67307:1.2:60.0:50.0:0.1029:0.0:1.2 0/0:216:0:0,0:87,129:0.0:2,0:26.4:1.0:30.7:1.0:1.0:0.0:60.0:53.0:1.0:0.0:0.5 -5 86659159 . A T 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0129;SOR=0.0;LSEQ=AGAAAACAATTTTTTTTTTT;RSEQ=AACAGGCAAAGGAAAACGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:6:5,1:248,80:0.018:2,2:23.2:1.0:26.2:1.0:1.0:1.61:60.0:5.0:0.0155:0.0:2.0 0/0:353:0:0,0:259,94:0.0:2,0:24.4:1.0:28.2:1.0:1.0:0.0:60.0:69.6:1.0:0.0:0.2 -5 87899069 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.14144;SOR=0.0;LSEQ=TTCTCCCCGCCCGCCCCCTC;RSEQ=CCCGGCCCCATGGGGTCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:0,5:1,22:0.1786:1,0:26.4:1.0:30.6:1.0:1.0:0.0:60.0:10.0:0.1786:0.0:1.4 0/0:16:0:0,0:1,15:0.0:1,0:17.7:1.0:30.7:1.0:1.0:0.0:60.0:32.0:1.0:0.0:0.1 -5 112043282 . CG GT 103 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=7.0;MSILEN=1.0;SSF=0.00523;SOR=0.0;LSEQ=CCGGAAGCCTAGCCGCTGCT;RSEQ=GGGGGGACCTGCGGGCTCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:10:9,1:76,0:0.1163:1,2:26.3:1.0:31.2:1.0:0.11628:0.0:60.0:20.0:0.119:0.0:1.0 0/0:63:0:0,0:44,1:0.0:1,0:27.6:1.0:31.4:1.0:1.0:0.0:60.0:90.0:0.7258:0.0:0.1 -5 112164716 . C CT 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.08912;SOR=0.15067;LSEQ=AATATGAATTTCATGTTTGG;RSEQ=TTTTTTTTGCTGCCTTCTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:5:1,4:7,97:0.0459:2,2:29.4:1.0:30.4:1.0:0.32201:3.4:60.0:10.0:0.0467:0.0:0.0 0/0:140:1:0,1:27,112:0.0071:2,0:42.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0072:0.0:0.0 -5 112172930 . T C 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CAACATAGGATTTCATGATA;RSEQ=AGTTTTTAAATTGGGAAACT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:0.8571:0,2:16.5:1.0:31.5:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 112173849 . A T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.04776;SOR=0.1283;LSEQ=TGAAAAAGATAGAAGTTTGG;RSEQ=GAGAGAACGCGGAATTGGTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:6:0,6:211,227:0.0135:2,0:8.2:1.0:27.8:1.0:0.03134:0.0:60.0:12.0:0.0139:0.0:1.0 0/0:571:1:0,1:287,283:0.0018:2,0:1.0:0.0:24.0:0.0:0.49737:0.0:60.0:2.0:0.0018:0.0:1.0 -5 112175617 . T A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTAAAACACCTCCACCACC;RSEQ=CCTCAAACAGCTCAAACCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:881:93:48,45:391,394:0.1056:2,2:27.8:1.0:29.7:1.0:0.82651:1.07:60.0:30.0:0.1056:0.0:1.1 0/0:1272:0:0,0:617,653:0.0:2,0:23.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:4.0 -5 112177863 . G GA 69 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.01359;SOR=0.0;LSEQ=AAGTAAAGGAATCAAAGGAG;RSEQ=AAAAAAAGTTTATAAAAGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:474:5:3,2:262,206:0.0105:2,2:20.4:1.0:30.1:1.0:1.0:1.18:60.0:10.0:0.0107:0.0063:0.4 0/0:643:0:0,0:353,289:0.0:2,0:23.6:1.0:30.6:1.0:1.0:0.0:60.0:63.2:0.9984:0.0:0.1 -5 112213678 . CTGTGTGTG C 257 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=20.0;MSILEN=2.0;SSF=0.0;SOR=0.01801;LSEQ=ATTGAGAGTTACAGGTTACT;RSEQ=TGTGTGTGTGTGTGTGTGTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:283:153,130:184,179:0.3086:2,2:31.7:1.0:31.6:1.0:0.42748:1.14:59.3:93.333:0.3135:0.0142:0.4 0/0:1130:9:5,4:272,260:0.008:2,2:23.4:1.0:29.7:1.0:1.0:1.19:60.0:18.0:0.0082:0.0018:0.0 -5 112213906 . G A 51 q23;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06242;SOR=0.0;LSEQ=TTATTTAGTAGACCACACCA;RSEQ=CACAATGGTTCCTCCAGCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:5:3,2:94,323:0.0118:2,2:15.0:1.0:22.2:1.0:0.08221:5.13:60.0:1.5:0.0073:0.0:1.0 0/0:395:0:0,0:85,310:0.0:2,0:22.3:1.0:31.7:1.0:1.0:0.0:60.0:64.833:1.0:0.0:0.1 -5 112227998 . G A 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01064;LSEQ=TGGAATGGAGCAGTGCAGGA;RSEQ=GGATGACTATGACCCTGACG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1357:79:42,37:637,638:0.0582:2,2:23.3:1.0:30.2:1.0:0.64319:1.14:52.2:38.5:0.0575:0.0:1.2 0/0:1523:1:1,0:790,729:0.0007:2,0:1.0:0.0:22.0:0.0:1.0:0.0:60.0:2.0:0.0007:0.0:2.0 -5 131924374 . A T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00537;SOR=0.0;LSEQ=AATTATGAGATTTTTTTTTT;RSEQ=AAAGGTCGTCTACAGCTGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:7:3,4:175,48:0.0304:2,2:9.7:1.0:24.6:1.0:0.04787:4.81737:60.0:6.0:0.0271:0.0:1.0 0/0:252:0:0,0:181,70:0.0:2,0:21.7:1.0:27.9:1.0:1.0:0.0:59.9:49.2:0.996:0.0:0.2 -5 131925174 . A C 102 MAF0.05;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05485;SOR=0.12688;LSEQ=CACAATGATAAAATTGCCTA;RSEQ=TGATGCATTTCTTGGAATAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:13,0:0.4091:1,0:28.2:1.0:32.2:1.0:1.0:0.0:60.0:18.0:0.4091:0.0:2.0 0/1:13:1:1,0:12,0:0.0769:0,0:6.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0769:0.0:1.0 -5 131951996 . T C 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.26632;SOR=0.0;LSEQ=CATGGCCTTAAGAACTTTAT;RSEQ=ACTGAAGAAGTGATATAGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:0.3333:0,0:14.8:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.3333:0.0:1.4 0/0:5:0:0,0:0,5:0.0:0,0:18.8:1.0:29.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 -5 131952072 . C T 69 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCAGTATTGAACATGCTTAG;RSEQ=CCCCATACATCTGCTAGCCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:1.0:0,0:18.8:1.0:30.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 133478475 . C T 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=7e-05;SOR=0.0;LSEQ=CCAACCATCAAGAAGCCCCT;RSEQ=AATGCCTTCATGCTGTACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:10,2:2,0:0.8571:0,2:22.8:1.0:29.8:1.0:1.0:0.0:60.0:24.0:0.8571:0.0:1.2 0/0:10:0:0,0:6,4:0.0:2,0:20.6:1.0:31.3:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.0 -5 140256920 . G C 243 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCGGTCGGCGCGCACATCCC;RSEQ=TTCCACGTGGGGCTGTACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:218:85,133:58,102:0.5767:2,2:22.7:1.0:31.3:1.0:0.59361:1.12:60.0:71.667:0.5749:0.0:1.1 0/0:333:0:0,0:115,217:0.0:2,0:22.3:1.0:29.6:1.0:1.0:0.0:60.0:40.5:0.9969:0.0:0.1 -5 142329054 . C T 56 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03052;SOR=0.0;LSEQ=CAATATTAATGCATCAGAAT;RSEQ=AGTGTTTGGAAGTTCAGATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:5:2,3:195,118:0.0157:2,2:11.6:1.0:24.4:1.0:0.37254:2.47144:60.0:4.0:0.0128:0.0:1.0 0/0:319:0:0,0:216,103:0.0:2,0:25.2:1.0:31.0:1.0:1.0:0.0:60.0:78.75:1.0:0.0:0.2 -5 149434518 . C A 87 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCTATGATTGCACACATCA;RSEQ=TGCGCTCCAGCCCGGGCTAC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:4,1:0.6154:2,0:19.9:1.0:29.1:1.0:0.38462:0.0:60.0:7.0:0.5833:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 149436598 . A T 90 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCATACACTATTTAGTAAAA;RSEQ=CGAATGAAGAAAGCCTGGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:8,0:8,0:0.5:0,0:24.3:1.0:30.0:1.0:1.0:0.0:60.0:16.0:0.5:0.0:1.4 0/0:1:0:0,0:1,0:0.0:0,0:23.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -5 149460627 . G A 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=5e-05;SOR=0.0;LSEQ=GCAGACAGAAGTGAGGTCTA;RSEQ=GATGCGCCCCTTGGGCCGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:22:5,17:44,201:0.0824:2,2:23.5:1.0:31.0:1.0:0.56881:1.34:60.0:44.0:0.0827:0.0:1.2 0/0:152:0:0,0:34,118:0.0:2,0:22.8:1.0:30.8:1.0:1.0:0.0:60.0:151.0:1.0:0.0:0.4 -5 149495050 . T C 94 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATCAAGCCTAACTTTCCCAT;RSEQ=TTACATATGGGAAAACTGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:31.1:1.0:31.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 149497672 . C T 66 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCTAACTCTTCCCCCACTT;RSEQ=AGAGCAGACAGGCACAGGCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:0.625:0,0:16.0:1.0:28.6:1.0:1.0:0.0:60.0:10.0:0.625:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 149498064 . C G 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GCAGCAGGACAGACAGTGCT;RSEQ=TAGGCCCCCTCCCTGCATCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:6,1:12,0:0.3684:0,2:31.3:1.0:33.0:1.0:0.36842:0.0:60.0:14.0:0.3684:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 149502838 . G C 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAGGCCATGAGGCTAATCA;RSEQ=GGGCTGGATGTGGGAGAGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:220:121:11,110:6,93:0.55:2,2:24.4:1.0:30.2:1.0:0.45585:1.55:60.0:120.0:0.5556:0.0:1.1 0/0:104:0:0,0:16,88:0.0:2,0:21.8:1.0:30.4:1.0:1.0:0.0:60.0:208.0:1.0:0.0:0.1 -5 154505054 . CAGA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG 104 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.04625;SOR=0.0;LSEQ=GTGTGCGCATGTGAGTGAAT;RSEQ=TGTTAATCTGCTTTGAGTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:9:0,9:0,27:0.2308:1,0:21.2:1.0:32.9:1.0:1.0:0.0:60.0:18.0:0.2432:0.1026:1.4 0/0:16:0:0,0:1,12:0.0:1,0:17.4:1.0:30.4:1.0:1.0:0.0:60.0:26.0:0.8125:0.0:0.3 -5 170826687 . A ATT 71 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTTTCTATTTAGGTCTTTA;RSEQ=TTTTTTTTTTTAACACAAAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,0:0.7143:0,2:31.6:1.0:30.9:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:0.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 170827459 . C T 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.47619;SOR=0.0;LSEQ=CCAAGTGGTTGCTGCTTTTT;RSEQ=CTTCCTTTTTTTTTTTTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:1,10:2,6:0.55:2,2:22.1:1.0:27.1:1.0:0.54592:3.12168:59.1:4.5:0.5294:0.0:1.6 0/0:1:0:0,0:0,1:0.0:0,0:25.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -5 170827464 . CT C 76 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGTTGCTGCTTTTTCCTTC;RSEQ=TTTTTTTTTTTTTTTGAGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:0,6:0.3125:0,2:34.2:1.0:32.8:1.0:0.18182:0.0:58.0:10.0:0.3125:0.0:3.2 0/0:1:0:0,0:0,1:0.0:0,0:19.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -5 170832637 . C T 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATTTTCCATTATGCAAGGAA;RSEQ=GTAGTGCACTGGTTGCAAGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:26.0:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 170832767 . TACAA T 69 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTATGAGACTTCATTAAAAT;RSEQ=ACAGCTGGAAAAGTAGATGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:21.8:1.0:29.8:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 176516631 . G A 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0082;LSEQ=TGCTGCTGGCCCTGTTGGGG;RSEQ=TCCTGCTGAGTGTGCCTGGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:171:80,91:291,277:0.2311:2,2:23.0:1.0:30.6:1.0:0.33749:1.1947:60.0:170.0:0.2326:0.0:1.1 0/0:815:2:2,0:395,418:0.0025:2,0:13.0:1.0:29.0:1.0:0.23698:0.0:60.0:4.0:0.0025:0.0:1.0 -5 176517170 . G A 105 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGTGTGTCTTGGCCACTGTC;RSEQ=TGTGCACTAAATGCTGTGTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:1.0:0,2:29.5:1.0:29.4:1.0:1.0:0.0:59.2:11.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 176517801 . G A 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGTCCCATAGGGACCCCTC;RSEQ=AATAGGCACAGTTACCCCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1169:52:24,28:504,612:0.0445:2,2:26.3:1.0:30.2:1.0:0.88779:1.04:60.0:104.0:0.045:0.0:2.1 0/0:993:0:0,0:443,550:0.0:2,0:25.0:1.0:30.2:1.0:1.0:0.0:60.0:75.385:1.0:0.0:0.8 -5 176518426 . T C 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GCTGTCATGAGGCAACTGAG;RSEQ=CTCAGAGAAGGCAAGGGTTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:1.0:0,2:25.9:1.0:30.9:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 176524465 . C T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.05646;LSEQ=GGCCTCATCTGGCCTGACCG;RSEQ=GTGGACATGCGCCCCGTCCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:902:42:20,22:435,424:0.0466:2,2:26.7:1.0:29.4:1.0:0.75331:1.12839:60.0:41.0:0.0464:0.0:1.1 0/0:728:2:0,2:381,345:0.0027:2,0:4.5:1.0:26.5:1.0:0.22685:0.0:60.0:4.0:0.0028:0.0:1.0 -5 176636546 . G A 132 LongAT SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11281;LSEQ=TCTCAAAAAAAAAAAAAAAA;RSEQ=GAATAAAAAAAAAAGCTTCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:32:30,2:33,1:0.2909:1,2:9.4:1.0:26.4:1.0:0.60769:2.17462:56.9:3.571:0.3623:0.0:1.6 0/1:114:5:3,2:95,10:0.0439:2,2:20.6:1.0:17.8:1.0:0.09096:6.1479:60.0:0.667:0.0217:0.0:2.0 -5 176636882 . C T 251 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03834;LSEQ=GATGAGAAGGAAAAGCCTTG;RSEQ=GCTAAATCTCGAGCCAGAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:470:338:161,177:57,73:0.7191:2,2:24.8:1.0:29.9:1.0:0.47105:1.16:60.0:111.667:0.7267:0.0:1.1 0/1:438:39:15,24:193,205:0.089:2,2:20.4:1.0:29.4:1.0:0.24465:1.50494:60.0:78.0:0.0899:0.0:1.1 -5 176637149 . G A 239 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.01349;LSEQ=ACTGCAAAGAAAGAATTTGA;RSEQ=ACTTCAAATGGTGACTCTTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:254:134,120:68,56:0.672:2,2:25.9:1.0:30.0:1.0:0.74236:1.08718:60.0:30.75:0.6685:0.0:1.1 0/1:449:12:7,5:226,211:0.0267:2,2:22.5:1.0:29.2:1.0:0.77335:1.31:60.0:11.0:0.0249:0.0:1.3 -5 176637240 . G T 256 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.01739;LSEQ=ATAAACCCCAACGAAGCCTG;RSEQ=TGTGTGGTTCAAAAGTGAAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:613:390:200,190:107,114:0.6362:2,2:24.5:1.0:29.8:1.0:0.50189:1.12:60.0:77.0:0.6385:0.0:1.2 0/1:646:19:10,9:298,329:0.0294:2,2:28.4:1.0:29.7:1.0:0.81645:1.23:60.0:38.0:0.0296:0.0:1.1 -5 176637576 . T C 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.02042;LSEQ=CAGAGCCTGGAACCGAGACG;RSEQ=CTCAGGTTAATCTCTCTGAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:433:264:145,119:89,79:0.6097:2,2:23.5:1.0:31.8:1.0:0.69343:1.08:60.0:87.0:0.6185:0.0:1.1 0/1:455:14:7,7:251,190:0.0308:2,2:24.7:1.0:30.7:1.0:0.78526:1.32022:60.0:28.0:0.031:0.0:1.0 -5 178012712 . A T 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.55906;SOR=0.0;LSEQ=GTAATGCCCTACAGCCCTGG;RSEQ=TGGCGCTGGGGTAACACTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:4,3:11,10:0.25:2,2:25.3:1.0:29.0:1.0:1.0:1.2:37.6:14.0:0.28:0.0:3.6 0/0:5:0:0,0:2,3:0.0:2,0:19.6:1.0:30.0:1.0:1.0:0.0:55.6:10.0:1.0:0.0:1.6 -5 178012715 . GC AT 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ATGCCCTACAGCCCTGGATG;RSEQ=GCTGGGGTAACACTCCACAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:5:2,3:12,10:0.1852:2,2:28.2:1.0:30.7:1.0:0.64831:1.76109:36.8:10.0:0.1923:0.0:2.4 0/0:4:0:0,0:2,2:0.0:2,0:20.8:1.0:33.3:1.0:1.0:0.0:54.5:8.0:1.0:0.0:1.5 -5 178012719 . T TG 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTACAGCCCTGGATGGCGC;RSEQ=GGGGTAACACTCCACAGCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:2,3:12,9:0.1923:2,2:24.2:1.0:32.0:1.0:0.63478:1.94676:36.8:10.0:0.2083:0.0:3.4 0/0:4:0:0,0:2,2:0.0:2,0:16.8:1.0:31.5:1.0:1.0:0.0:54.5:8.0:1.0:0.0:1.5 -5 178996554 . G A 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACTGGTAGAGGACCCCAGG;RSEQ=ATGCAGCTGGGGAAGGTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:28:0,28:1,16:0.6222:1,1:23.1:1.0:30.5:1.0:0.37778:0.0:60.0:56.0:0.6222:0.0:1.0 0/0:28:0:0,0:2,26:0.0:2,0:19.8:1.0:31.1:1.0:1.0:0.0:60.0:27.0:1.0:0.0:0.1 -5 180056434 . G A 66 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.16266;SOR=0.0;LSEQ=TTACCCCGCTCTGCCTGCCC;RSEQ=CACCCAGGGAAGCCCCGCGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:5:3,2:122,333:0.0109:2,2:26.4:1.0:28.6:1.0:0.12658:4.08:60.0:10.0:0.0112:0.0:1.0 0/0:284:0:0,0:92,192:0.0:2,0:24.8:1.0:31.0:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.1 -5 180058008 . C A 95 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCCGGGGCTGGCCTGTGG;RSEQ=CAAGCACAGGCCTTGGATCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:1.0:0,2:24.3:1.0:28.6:1.0:1.0:0.0:60.0:9.0:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 180525845 . T G 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGACGGAGTCTTGCTTTGTT;RSEQ=CCAGGCTGGAGTGCAGTGGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:29.5:1.0:28.4:1.0:1.0:0.0:53.0:3.0:1.0:0.0:1.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -5 180525899 . C G 98 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACTGCAATCTCCGCCTCCCA;RSEQ=GTTCAAGCGATTCTTCTGCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:1.0:0,0:29.2:1.0:31.1:1.0:1.0:0.0:52.6:18.0:1.0:0.0:1.7 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 6728616 . G A 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAGCCTAGGCCTTCACAGCA;RSEQ=GGGGCAAGGGGGATGTCAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:20:5,15:2,10:0.625:2,2:23.0:1.0:30.8:1.0:0.68332:1.64:60.0:40.0:0.625:0.0:1.1 0/0:29:0:0,0:13,16:0.0:2,0:19.7:1.0:30.1:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.2 -6 7516674 . A ATATATACATATATATATATATATATG 129 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.0;MSILEN=2.0;SSF=4e-05;SOR=0.0;LSEQ=AACGGTGGCAATAACTGTAT;RSEQ=TATATATATGTCTATAAACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:18,0:21,0:0.4286:1,1:18.6:1.0:31.1:1.0:1.0:0.0:60.0:36.0:0.439:0.1905:1.1 0/0:26:0:0,0:21,1:0.0:1,0:17.7:1.0:28.6:1.0:1.0:0.0:60.0:44.0:0.8462:0.0:0.0 -6 8909371 . T C 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00023;SOR=0.0;LSEQ=TTTCTTAGTTTAGATTCCCC;RSEQ=TGAAATAGACCCTCAACCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:8,3:0,0:1.0:0,2:21.8:1.0:28.5:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.3 0/0:5:0:0,0:3,1:0.0:2,0:15.3:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -6 17729851 . C T 86 MAF0.05;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.05246;SOR=0.12258;LSEQ=TTGTGTTTTTTTGTTCTTTA;RSEQ=GTTAAAACTTGTTGCTGCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:7,7:0.3636:2,2:16.1:1.0:28.9:1.0:0.67492:1.62835:60.0:16.0:0.3636:0.0:1.9 0/1:16:1:1,0:4,10:0.0625:2,0:26.0:0.0:32.0:0.0:0.33333:0.0:60.0:2.0:0.0667:0.0:2.0 -6 20486794 . C T 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.04034;SOR=0.0;LSEQ=ATTACAGGTGTGAGCCACCG;RSEQ=GCCCGGCCACATATGCATAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:7:7,0:61,0:0.1029:1,0:26.9:1.0:28.3:1.0:1.0:0.0:60.0:6.0:0.0909:0.0:1.4 0/0:46:0:0,0:46,0:0.0:1,0:27.3:1.0:32.6:1.0:1.0:0.0:60.0:92.0:1.0:0.0:0.6 -6 23515364 . G A 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.29644;SOR=0.0;LSEQ=AAAACTTTAGTCAGGTTTCT;RSEQ=AACCTTCTCCTAGGTCCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:5,2:12,7:0.2692:2,2:22.7:1.0:27.0:1.0:1.0:1.44:60.0:14.0:0.2692:0.0:1.0 0/0:6:0:0,0:4,2:0.0:2,0:26.7:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -6 25261662 . A T 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCAAAACTGGAAGAGTCTAC;RSEQ=ATTTTACCCAGCATGCTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:84:38,46:64,76:0.375:2,2:26.6:1.0:29.4:1.0:1.0:1.01931:59.7:83.0:0.3739:0.0:1.1 0/0:227:0:0,0:106,121:0.0:2,0:28.3:1.0:29.4:1.0:1.0:0.0:60.0:74.667:1.0:0.0:0.1 -6 25606672 . C T 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.13043;LSEQ=GTGAAAGTGATGAGAGCTGA;RSEQ=GGATTCTTTTATTTAATGCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:128:55,73:127,121:0.3404:2,2:24.3:1.0:29.9:1.0:0.15679:1.39184:60.0:41.667:0.3369:0.0:1.9 0/1:302:19:9,10:131,150:0.0629:2,2:16.0:1.0:28.7:1.0:1.0:1.03:60.0:18.0:0.0608:0.0:2.0 -6 26031720 . C G 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00441;SOR=0.0;LSEQ=AAACCGTTATTTCTGTTAAT;RSEQ=AACTTTAAGACCATAGTCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:14:14,0:61,0:0.1842:1,1:22.7:1.0:31.2:1.0:1.0:0.0:60.0:13.0:0.1757:0.0:1.1 0/0:36:0:0,0:36,0:0.0:1,0:24.4:1.0:31.4:1.0:1.0:0.0:60.0:35.0:1.0:0.0:0.2 -6 26200050 . C G 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.05901;SOR=0.0;LSEQ=GCGCATTACAACAAGCGCTC;RSEQ=ACCATCACCTCCAGGGAGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:5:2,3:51,30:0.0581:2,2:25.0:1.0:31.8:1.0:0.36737:2.52106:49.2:10.0:0.0595:0.0:1.4 0/0:83:0:0,0:48,35:0.0:2,0:22.5:1.0:30.4:1.0:1.0:0.0:58.0:166.0:1.0:0.0:0.4 -6 26322501 . G A 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCCGGTCGATTTGCGGGCA;RSEQ=TCGGCTTTCTACGAGCCGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:57:22,35:76,93:0.2522:2,2:26.6:1.0:30.2:1.0:0.44195:1.2986:60.0:56.0:0.25:0.0:1.1 0/0:188:0:0,0:84,104:0.0:2,0:26.5:1.0:31.6:1.0:1.0:0.0:60.0:187.0:1.0:0.0:0.4 -6 27114488 . G C 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00134;SOR=0.0;LSEQ=CTCTCCTTGCGGCTGCGCTT;RSEQ=CGCTTCTTGCCGTCCTTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:11:3,8:83,112:0.0534:2,2:28.8:1.0:31.2:1.0:0.36604:1.97012:45.2:22.0:0.0537:0.0:1.1 0/0:169:0:0,0:77,92:0.0:2,0:27.5:1.0:31.2:1.0:1.0:0.0:45.9:27.167:1.0:0.0:0.3 -6 27840221 . C A 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00252;SOR=0.0;LSEQ=CGTCTCACACACGGAATTGG;RSEQ=TCCCAGTTTAATCTGCTAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:13:0,13:5,192:0.0619:1,1:23.9:1.0:31.2:1.0:1.0:0.0:60.0:26.0:0.0644:0.0:1.0 0/0:125:0:0,0:2,123:0.0:1,0:23.1:1.0:31.9:1.0:1.0:0.0:60.0:61.5:1.0:0.0:0.1 -6 29230520 . A C 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=2e-05;SOR=0.13102;LSEQ=TGGGAGTAACAATGGAGTAA;RSEQ=ATATATGGAGAAGTTTGCCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:37:36,1:72,0:0.3394:1,1:24.1:1.0:32.5:1.0:0.33945:0.0:60.0:74.0:0.3491:0.0:1.1 0/1:64:4:4,0:60,0:0.0625:1,0:14.3:1.0:30.8:1.0:1.0:0.0:60.0:8.0:0.0625:0.0:1.0 -6 29236588 . A G 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.12518;LSEQ=CAAGAACTATAATCAGGCAC;RSEQ=TGGCAAATGTGGTTACCTCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:36:1,35:6,78:0.3:2,1:25.5:1.0:32.3:1.0:0.67305:2.67444:60.0:72.0:0.3:0.0:1.1 0/1:99:5:1,4:11,83:0.0505:2,2:20.6:1.0:30.8:1.0:0.48339:1.87:60.0:10.0:0.051:0.0:1.0 -6 29693183 . G A 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGCAGGGTCAGGGCTGAG;RSEQ=CCTGGAGATCAGGGCCCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:394:116:62,54:166,111:0.2944:2,2:22.4:1.0:29.4:1.0:0.26288:1.30162:60.0:57.0:0.2992:0.0:1.2 0/0:326:0:0,0:192,132:0.0:2,0:21.5:1.0:31.0:1.0:1.0:0.0:60.0:63.8:0.9969:0.0:0.2 -6 29760132 . G T 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTGTGGGGAGTAGCTAGGG;RSEQ=CCTGCCCGGCGGGGGCGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:108:25,83:59,168:0.3224:2,2:25.2:1.0:29.6:1.0:0.5931:1.16541:60.0:53.0:0.3242:0.0:2.3 0/0:240:0:0,0:70,168:0.0:2,0:23.4:1.0:31.1:1.0:1.0:0.0:60.0:78.333:1.0:0.0:0.5 -6 29760317 . G C 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GACGACACGCAGTGCGTGCG;RSEQ=CTCGACAGCGACGCCACGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:40:12,28:74,54:0.2381:2,2:24.5:1.0:30.7:1.0:0.00342:3.17518:59.6:19.0:0.2331:0.0:1.1 0/0:141:0:0,0:80,61:0.0:2,0:25.4:1.0:29.9:1.0:1.0:0.0:60.0:14.667:1.0:0.0:0.2 -6 29760462 . T C 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=ACCTGCGGACCCTGAGCGGC;RSEQ=ACTACAACCAGAGTGAGGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:35:18,17:88,107:0.1522:2,2:30.7:1.0:31.0:1.0:0.58142:1.29:60.0:34.0:0.1491:0.0:1.5 0/0:244:0:0,0:107,137:0.0:2,0:29.7:1.0:29.0:1.0:1.0:0.0:60.0:60.0:1.0:0.0:0.4 -6 29760730 . AC A 210 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGCGGGGCCAGGGTCTCAC;RSEQ=CCATCTAGAGGATGTCTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:99:62,37:224,163:0.2037:2,2:27.7:1.0:31.8:1.0:0.42428:1.22:60.0:198.0:0.2054:0.0226:1.6 0/0:469:0:0,0:266,202:0.0:2,0:25.0:1.0:30.6:1.0:1.0:0.0:60.0:45.8:0.9978:0.0:0.3 -6 29760765 . C A 201 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTCTGTCTGCGACGTGGGGT;RSEQ=GGACGGGCGCCTACTCCGCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:118:64,54:228,251:0.1977:2,2:25.6:1.0:29.3:1.0:0.21769:1.3:60.0:236.0:0.2014:0.0:2.0 0/0:575:0:0,0:278,296:0.0:2,0:27.5:1.0:30.1:1.0:1.0:0.0:60.0:94.667:0.9982:0.0:0.3 -6 29760799 . T C 194 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCGCGGGTATCACCAGCT;RSEQ=GCTTACGATGGCAAGGATTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:93:45,48:119,204:0.2236:2,2:25.1:1.0:29.8:1.0:0.05385:1.61:60.0:30.0:0.2217:0.0:2.3 0/0:423:0:0,0:181,241:0.0:2,0:24.8:1.0:29.7:1.0:1.0:0.0:60.0:421.0:0.9976:0.0:0.3 -6 29760856 . C T 186 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GACCTGTGCTCCTTGACAGC;RSEQ=GCAGACACGGCGGCTCAGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:77:21,56:31,117:0.3422:2,2:23.9:1.0:29.7:1.0:0.31871:1.41:60.0:37.5:0.3363:0.0:1.7 0/0:153:0:0,0:38,115:0.0:2,0:24.8:1.0:29.0:1.0:1.0:0.0:60.0:37.25:1.0:0.0:0.3 -6 29768908 . T G 73 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00296;SOR=0.0;LSEQ=GATTATCCCAGGTGCCTGTG;RSEQ=CCAGAATGTTGTCTGGGTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:1,1:0.5556:2,2:13.6:1.0:31.8:1.0:1.0:3.16:43.8:10.0:0.5556:0.0:7.2 0/0:15:0:0,0:8,6:0.0:2,0:26.9:1.0:29.6:1.0:1.0:0.0:60.0:28.0:0.9333:0.0:0.6 -6 29768948 . CAGATGTCCCATCCAT AGGTTTCCCGTCCTA 67 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.00383;SOR=0.0;LSEQ=CTGTGCTCCCTTCCCCACCC;RSEQ=TCTCAGGATGGTCACATGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:4,1:4,1:0.5:2,2:49.0:1.0:29.0:1.0:1.0:1.0:40.8:4.0:0.4444:0.1:2.0 0/0:16:0:0,0:8,8:0.0:2,0:25.6:1.0:30.3:1.0:1.0:0.0:59.3:15.0:1.0:0.0:1.1 -6 29769246 . G A 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGCTGCAGTGGTGTCTTCTG;RSEQ=AGAGAAGCAGAGGTACACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:45:28,17:59,23:0.3543:2,2:22.0:1.0:29.4:1.0:0.31871:1.5518:60.0:90.0:0.3571:0.0:1.2 0/0:109:0:0,0:69,40:0.0:2,0:21.1:1.0:31.1:1.0:1.0:0.0:60.0:218.0:1.0:0.0:0.8 -6 29770158 . C G 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.20455;SOR=0.0;LSEQ=TGTTCCACCCCAAACAGGAA;RSEQ=AGTACCCAGGGCTCTGATGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:3,1:0.5556:2,2:22.0:1.0:30.8:1.0:0.52381:3.76419:60.0:10.0:0.5556:0.0:1.0 0/0:3:0:0,0:1,2:0.0:2,0:46.0:1.0:31.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:1.0 -6 29795253 . C A 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=TGAAAAGTGAAGGGAGAGGG;RSEQ=CAGGGACCTTGCCGAGGGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:2,0:0.7143:0,2:27.4:1.0:30.2:1.0:1.0:0.0:52.6:10.0:0.7143:0.0:2.8 0/0:1:0:0,0:0,1:0.0:0,0:47.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -6 29795566 . C T 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02273;LSEQ=CCAATCAGCGTCGCCGCGGT;RSEQ=CTGGTTCTAAAGTCCTCGCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:140:107,33:272,87:0.2806:2,2:21.4:1.0:29.3:1.0:0.90773:1.04:60.0:22.333:0.2746:0.0:1.1 0/0:342:3:1,2:243,96:0.0088:2,2:9.7:1.0:19.0:1.0:0.1985:5.03468:60.0:2.0:0.006:0.0:2.0 -6 29795913 . A T 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0077;LSEQ=CCATGGGCTACGTGGACGAC;RSEQ=CGCAGTTCGTGCGGTTCGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:516:142:90,52:217,157:0.2752:2,2:26.0:1.0:30.6:1.0:0.31538:1.25:60.0:46.333:0.2742:0.0:1.2 0/0:344:1:0,1:176,167:0.0029:2,0:1.0:0.0:24.0:0.0:0.48837:0.0:60.0:2.0:0.003:0.0:1.0 -6 29796106 . G T 220 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGAGGCCAGTGAGTAACTCC;RSEQ=GCCCAGGGAGCAGATCACGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:160:51,109:145,274:0.2754:2,2:25.9:1.0:30.1:1.0:0.55703:1.13077:60.0:79.0:0.2782:0.0:3.6 0/0:427:0:0,0:157,269:0.0:2,0:23.7:1.0:29.5:1.0:1.0:0.0:60.0:105.5:0.9976:0.0:1.0 -6 29796128 . C A 200 InIns SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCAGGGAGCAGATCACGAC;RSEQ=CCCACCTCCATGCCCCACGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:123:29,94:74,204:0.306:2,2:25.0:1.0:28.9:1.0:0.53854:1.17532:60.0:23.6:0.3041:0.0:3.9 0/0:275:0:0,0:84,191:0.0:2,0:20.8:1.0:29.7:1.0:1.0:0.0:59.9:33.375:1.0:0.0:1.1 -6 29796265 . G T 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACCAAAATCCCCGCGGGTG;RSEQ=GTCCGGGCGAGGGCGAGGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:41:32,9:65,49:0.2645:2,2:22.5:1.0:30.5:1.0:0.02328:2.66:60.0:82.0:0.268:0.0:1.9 0/0:59:0:0,0:46,13:0.0:2,0:23.8:1.0:30.8:1.0:1.0:0.0:60.0:118.0:1.0:0.0:0.8 -6 29796675 . G T 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00169;SOR=0.0;LSEQ=ACAAGGAGAGGAGGAAAATG;RSEQ=GACCAACACTAGAATATCGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:15:1,14:2,39:0.2679:1,1:23.5:1.0:29.9:1.0:1.0:1.38:60.0:30.0:0.2679:0.0:1.8 0/0:28:0:0,0:2,26:0.0:2,0:27.5:1.0:30.5:1.0:1.0:0.0:60.0:27.0:1.0:0.0:1.0 -6 29797155 . G C 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GCTGCTGGAGTGTCCCATGA;RSEQ=AGATGCAAAGTGCTTGAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:111:77,34:143,95:0.3171:2,2:22.4:1.0:31.6:1.0:0.0974:1.5:60.0:54.5:0.3178:0.0:2.7 0/0:237:0:0,0:143,94:0.0:2,0:23.6:1.0:30.9:1.0:1.0:0.0:60.0:38.5:1.0:0.0:0.5 -6 29797211 . C T 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGACCCCCCCAAGACACA;RSEQ=GTGACCCACCACCCTGTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:547:180:87,93:170,197:0.3291:2,2:27.9:1.0:30.6:1.0:0.71545:1.08:60.0:360.0:0.3321:0.0:2.2 0/0:385:0:0,0:173,210:0.0:2,0:27.5:1.0:30.1:1.0:1.0:0.0:59.9:94.75:0.9948:0.0:0.4 -6 29855296 . C T 84 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCTCTCAGGGTCTCAGGCCC;RSEQ=GAAGGCGGTGTATGGATTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:6:6,0:34,3:0.1395:2,0:25.5:1.0:32.8:1.0:1.0:0.0:34.7:12.0:0.1463:0.0:6.5 0/0:5:0:0,0:5,0:0.0:0,0:20.6:1.0:30.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.2 -6 29855325 . C A 72 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.57467;SOR=0.0;LSEQ=TGTATGGATTGGGGATGCCC;RSEQ=GCCTTAGGGATTCGCCACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:5:5,0:48,2:0.0909:1,0:36.2:1.0:31.4:1.0:1.0:0.0:33.8:10.0:0.0909:0.0:7.4 0/0:13:0:0,0:13,0:0.0:1,0:21.2:1.0:30.2:1.0:1.0:0.0:60.0:26.0:1.0:0.0:3.5 -6 29855328 . C G 71 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.5762;SOR=0.0;LSEQ=ATGGATTGGGGATGCCCCGC;RSEQ=TTAGGGATTCGCCACCTCCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:5:5,0:52,2:0.0847:1,0:34.4:1.0:30.6:1.0:1.0:0.0:33.8:10.0:0.0893:0.0:7.4 0/0:15:0:0,0:15,0:0.0:1,0:20.5:1.0:30.8:1.0:1.0:0.0:60.0:30.0:1.0:0.0:3.4 -6 29855571 . GGGGCCCT G 256 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.14468;LSEQ=CCCTCCTCCTGCTGCTCTCA;RSEQ=GGCCCTGACCCTGACCCAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1172:276:115,161:392,502:0.2355:2,2:29.9:1.0:31.6:1.0:0.53253:1.09312:59.7:275.0:0.2391:0.0316:1.1 0/1:821:35:17,18:354,427:0.0426:2,2:33.0:1.0:31.3:1.0:0.73124:1.14:58.7:70.0:0.044:0.0024:1.3 -6 29855999 . G A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00373;SOR=0.09055;LSEQ=CTACTACAACCAGAGCGAGG;RSEQ=CGGTGAGTGACCCCGGCCCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:12:5,7:48,160:0.0538:2,2:34.9:1.0:27.1:1.0:0.16644:2.37:36.2:5.0:0.0463:0.0:3.1 0/0:196:1:1,0:31,92:0.0051:2,0:1.0:0.0:24.0:0.0:0.25806:0.0:60.0:2.0:0.0053:0.0:2.0 -6 29856198 . C T 60 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08843;SOR=0.0;LSEQ=CCCCCGCGGGTTGGTCGGGG;RSEQ=AGGGCGGGGCTCGGGGGACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:6:3,3:344,105:0.0132:2,2:15.5:1.0:23.3:1.0:0.1486:3.26554:60.0:5.0:0.0112:0.0:1.2 0/0:276:0:0,0:204,72:0.0:2,0:23.5:1.0:31.3:1.0:1.0:0.0:59.3:45.0:1.0:0.0:1.0 -6 29856655 . G C 103 MAF0.05;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.05911;SOR=0.13365;LSEQ=GAGGGAGAAGAATCCTCCTG;RSEQ=GTTTCCAGAGAGTGACTCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:3,7:3,11:0.4167:2,2:20.5:1.0:31.3:1.0:0.66533:1.54:60.0:20.0:0.4167:0.0:1.0 0/1:12:1:0,1:2,8:0.0833:2,0:28.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0909:0.0:1.0 -6 29857971 . TG AC 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05573;SOR=0.0;LSEQ=CTTCTCTGGGGTCCGAGACT;RSEQ=GAGGTTCCTCTAGGACCTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:395:8:8,0:295,92:0.0203:2,0:6.0:1.0:31.0:1.0:0.20667:0.0:38.1:16.0:0.0205:0.0101:3.9 0/0:220:0:0,0:156,64:0.0:2,0:21.4:1.0:29.7:1.0:1.0:0.0:58.8:440.0:1.0:0.0:1.0 -6 29864379 . G A 77 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.25359;SOR=0.0;LSEQ=CACATGGGTGCTGCTGGAGT;RSEQ=TCCCATGAGGAATGCAAAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:6,2:5,5:0.4444:2,2:32.1:1.0:25.8:1.0:0.36652:2.82:30.9:7.0:0.4118:0.0:2.8 0/0:4:0:0,0:2,2:0.0:2,0:9.3:1.0:33.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:2.3 -6 29864413 . T G 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.25359;SOR=0.0;LSEQ=GCAAAGTGCCTGAATTTTCT;RSEQ=ACTCTTCCCCTCAGAATCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:6,2:7,3:0.4444:2,2:12.4:1.0:28.5:1.0:1.0:1.27:30.9:7.0:0.4118:0.0:2.8 0/0:4:0:0,0:3,1:0.0:2,0:31.8:1.0:30.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:4.0 -6 29864421 . C T 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.26749;SOR=0.0;LSEQ=CCTGAATTTTCTTACTCTTC;RSEQ=CCTCAGAATCCCAGAATACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:7,3:0.375:2,2:6.8:1.0:30.3:1.0:1.0:1.15538:32.0:12.0:0.375:0.0:3.0 0/0:4:0:0,0:3,1:0.0:2,0:35.5:1.0:27.0:1.0:1.0:0.0:60.0:3.0:1.0:0.0:4.0 -6 29893922 . A T 67 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ACTCAGGGAGACATTGAGAC;RSEQ=GAGCGCTTGGCACAGGAGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:0.3571:0,0:23.8:1.0:29.2:1.0:1.0:0.0:58.0:10.0:0.3571:0.0:4.2 0/0:1:0:0,0:1,0:0.0:0,0:38.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -6 29895837 . CC GCA 219 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.09793;LSEQ=CTTCCTGTTAGACCTCTCCC;RSEQ=AGACACATATGATCCACCAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:126:66,60:68,60:0.4884:2,2:32.0:1.0:31.5:1.0:1.0:1.0302:60.0:252.0:0.4961:0.0155:4.4 0/1:235:20:9,11:63,67:0.0851:2,2:34.9:1.0:31.6:1.0:0.8142:1.14819:60.0:40.0:0.1351:0.0:4.2 -6 29896636 . C T 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.22857;SOR=0.0;LSEQ=ACCTCAGGAGGGCAGTTGGT;RSEQ=CAGGACCCACACCTGCTTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:5,1:0.5:2,0:22.2:1.0:31.2:1.0:1.0:0.0:60.0:12.0:0.5:0.0:1.3 0/0:3:0:0,0:1,2:0.0:2,0:14.0:1.0:25.0:1.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -6 29896850 . TCC GATCT 177 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=TGAAGTGGGCTGATCCCTGA;RSEQ=TTGGGATATTGTGGTCGGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:49:30,19:48,33:0.35:2,2:30.7:1.0:31.6:1.0:0.85534:1.08:60.0:98.0:0.3525:0.0071:1.3 0/0:122:0:0,0:0,6:0.0:0,0:36.0:1.0:31.3:1.0:1.0:0.0:60.0:8.0:0.0449:0.0:-9.5 -6 29896852 . C T 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00072;SOR=0.0;LSEQ=AAGTGGGCTGATCCCTGATC;RSEQ=TTGGGATATTGTGGTCGGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:12:7,5:46,31:0.0876:2,2:17.2:1.0:27.4:1.0:1.0:1.0592:57.9:5.0:0.1163:0.0:1.9 0/0:110:0:0,0:38,39:0.0:2,0:26.1:1.0:30.5:1.0:1.0:0.0:60.0:37.5:1.0:0.0:0.4 -6 29897036 . G T 106 InIns SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.00058;SOR=0.0;LSEQ=ACACTGGGGGACCTGATGTG;RSEQ=GGGGGTGTTGGGGGCAATAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:12:6,6:65,96:0.0686:2,2:10.1:1.0:29.7:1.0:0.55346:1.47:60.0:24.0:0.0719:0.0:2.6 0/0:149:0:0,0:54,80:0.0:2,0:23.5:1.0:29.2:1.0:1.0:0.0:59.8:15.75:0.9921:0.0:2.1 -6 29902073 . GA AG 104 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05712;SOR=0.0;LSEQ=TGCAGCACACCTGTACCAGG;RSEQ=CCACGGGCGCCTCCCTGATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:9:0,9:12,74:0.0947:2,0:17.3:1.0:33.1:1.0:0.59717:0.0:24.4:18.0:0.0947:0.0:5.1 0/0:44:0:0,0:6,38:0.0:2,0:16.5:1.0:30.8:1.0:1.0:0.0:56.4:88.0:1.0:0.0:1.3 -6 29902078 . C CG 96 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.0555;SOR=0.0;LSEQ=CACACCTGTACCAGGGACCA;RSEQ=GGGCGCCTCCCTGATCGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:83:8:0,8:8,67:0.0964:2,0:13.8:1.0:32.0:1.0:1.0:0.0:22.5:16.0:0.0988:0.0:7.0 0/0:38:0:0,0:6,31:0.0:2,0:17.2:1.0:29.4:1.0:1.0:0.0:60.0:74.0:1.0:0.0:0.7 -6 29910444 . AAGCAAGGGGCCCTCCT GAGCGGGCTGCCCGCCC 190 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAACCGCCTCTGCGGGGAG;RSEQ=GGCGGGGGCGCAGGACCGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1015:76:27,49:388,483:0.0749:2,2:13.0:1.0:30.5:1.0:0.14816:1.45729:52.4:152.0:0.0764:0.0739:1.6 0/0:632:0:0,0:274,304:0.0:2,0:24.1:1.0:29.0:1.0:1.0:0.0:59.2:56.8:0.9147:0.0:2.3 -6 29910516 . G A 140 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00043;SOR=0.16277;LSEQ=CGAGGGTCGGGCAGGTCTCA;RSEQ=CCACTGCTCGCCCCCAGGCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1103:26:7,19:560,514:0.0236:2,2:34.5:1.0:29.9:1.0:0.01565:2.95447:32.1:52.0:0.0242:0.0:7.5 0/0:767:3:0,3:412,349:0.0039:2,0:36.0:1.0:31.7:1.0:0.09735:0.0:36.3:6.0:0.004:0.0:7.7 -6 29910519 . A C 155 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00011;SOR=0.17512;LSEQ=GGGTCGGGCAGGTCTCAGCC;RSEQ=CTGCTCGCCCCCAGGCTCCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1138:32:10,22:571,532:0.0281:2,2:30.7:1.0:31.1:1.0:0.02999:2.35957:32.8:64.0:0.0286:0.0:7.1 0/0:794:4:1,3:422,366:0.005:2,2:33.5:1.0:32.8:1.0:0.34348:3.454:35.0:8.0:0.0051:0.0:7.3 -6 29910856 . G A 224 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCCCTCATCCCCCACGGAC;RSEQ=GGCCAGGTCGCCCACAGTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:551:153:34,119:74,324:0.2777:2,2:23.3:1.0:30.9:1.0:0.33981:1.25:59.8:75.5:0.2761:0.0:4.8 0/0:309:0:0,0:61,248:0.0:2,0:22.1:1.0:29.9:1.0:1.0:0.0:58.8:102.0:1.0:0.0:2.2 -6 29911857 . G T 176 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.1765;LSEQ=GTGCTGGTGGAGTGTCCCAT;RSEQ=ACAGATGCAAAATGCCTGAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:66:42,24:389,237:0.0954:2,2:22.6:1.0:29.2:1.0:0.89404:1.07:36.2:132.0:0.0968:0.0:6.8 0/1:767:14:9,5:462,291:0.0183:2,2:22.4:1.0:25.4:1.0:1.0:1.13:42.7:6.0:0.016:0.0:5.1 -6 29911879 . T G 207 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.15621;LSEQ=CAGATGCAAAATGCCTGAAT;RSEQ=TTCTGACTCTTCCCGTCAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:950:90:51,39:487,372:0.0947:2,2:30.2:1.0:31.9:1.0:1.0:1.00111:38.3:44.0:0.094:0.0:7.3 0/1:1182:19:14,5:651,511:0.0161:2,2:25.7:1.0:29.7:1.0:0.16232:2.2:37.8:38.0:0.0162:0.0:7.5 -6 29911895 . T A 197 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.17377;LSEQ=GAATTTTCTGACTCTTCCCG;RSEQ=CAGACCCCCCCAAGACACAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1159:99:47,52:576,484:0.0854:2,2:26.9:1.0:29.8:1.0:0.20652:1.31636:39.7:98.0:0.0858:0.0:7.6 0/1:1441:23:11,12:772,644:0.016:2,2:21.7:1.0:27.3:1.0:0.53475:1.30748:39.9:46.0:0.0163:0.0:7.9 -6 29911912 . A G 206 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.1783;LSEQ=CCGTCAGACCCCCCCAAGAC;RSEQ=CATATGACCCACCACCCCAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1195:105:47,58:535,554:0.0879:2,2:23.9:1.0:30.7:1.0:0.41465:1.19154:39.3:51.5:0.0881:0.0:7.5 0/1:1422:24:10,14:688,710:0.0169:2,2:25.8:1.0:29.8:1.0:0.53944:1.35633:38.8:48.0:0.0172:0.0:7.8 -6 29911921 . C T 199 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.17872;LSEQ=CCCCCCAAGACACATATGAC;RSEQ=CACCACCCCATCTCTGACCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1131:95:37,58:495,539:0.084:2,2:24.2:1.0:30.3:1.0:0.10727:1.43914:40.8:94.0:0.0849:0.0:7.4 0/1:1303:21:7,14:617,662:0.0161:2,2:30.6:1.0:28.4:1.0:0.19315:1.86318:40.8:42.0:0.0164:0.0:7.8 -6 29912395 . T TGG 106 NM4 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.00019;SOR=0.0;LSEQ=TGGAGGAGGAAGAGCTCAGG;RSEQ=GGAGAAGGGGTGAAGGGTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1105:14:4,10:382,527:0.0127:2,2:15.1:1.0:27.9:1.0:0.41666:1.81105:51.2:28.0:0.0129:0.0072:6.4 0/0:944:0:0,0:380,502:0.0:2,0:24.7:1.0:29.2:1.0:1.0:0.0:59.5:66.846:0.9344:0.0:1.1 -6 29912918 . G A 157 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.13011;LSEQ=TCCTTGGGATATTGTGTTTG;RSEQ=GAGCCCATGGGGGAGCCCAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:942:38:34,4:461,443:0.0403:2,2:14.2:1.0:30.0:1.0:0.0:8.15:39.6:18.0:0.0388:0.0:6.2 0/0:736:4:3,1:357,375:0.0054:2,2:14.0:1.0:28.5:1.0:0.36343:3.15:40.0:8.0:0.0055:0.0:6.0 -6 29912923 . C A 166 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.17597;LSEQ=GGGATATTGTGTTTGGGAGC;RSEQ=CATGGGGGAGCCCACCCACC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:920:43:39,4:453,421:0.0467:2,2:17.3:1.0:30.6:1.0:0.0:9.05:39.7:86.0:0.0477:0.0:6.0 0/0:702:6:5,1:343,353:0.0085:2,2:13.2:1.0:30.2:1.0:0.12053:5.14:43.5:12.0:0.0087:0.0:5.0 -6 29912927 . G T 171 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.15942;LSEQ=TATTGTGTTTGGGAGCCCAT;RSEQ=GGGGAGCCCACCCACCTCAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:944:49:43,6:486,408:0.0519:2,2:19.0:1.0:30.6:1.0:0.0:6.01:40.9:48.0:0.0514:0.0:5.7 0/0:694:6:4,2:350,338:0.0086:2,2:16.5:1.0:29.7:1.0:0.68653:1.93:38.0:12.0:0.0087:0.0:5.5 -6 29913483 . T C 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.32275;SOR=0.0;LSEQ=CTGAGGTGTCTCCATCTCTG;RSEQ=CTCAACTTCATGGTGCACTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:9:1,8:0,30:0.2308:1,2:21.8:1.0:31.6:1.0:0.23077:0.0:60.0:18.0:0.2308:0.0:1.0 0/0:8:0:0,0:0,8:0.0:0,0:20.9:1.0:28.8:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.8 -6 29913518 . C A 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCACTGAGCTGTAACTTCTT;RSEQ=CTTCCCTATTAAAATTAGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:0,6:0,21:0.2222:1,0:17.0:1.0:30.5:1.0:1.0:0.0:42.3:12.0:0.24:0.0:3.5 0/0:1:0:0,0:0,1:0.0:0,0:34.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -6 29913526 . A G 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGTAACTTCTTCCTTCCCT;RSEQ=TTAAAATTAGAACCTTAGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:0,6:0,19:0.24:1,0:16.2:1.0:32.0:1.0:1.0:0.0:41.0:12.0:0.24:0.0:3.3 0/0:1:0:0,0:0,1:0.0:0,0:26.0:0.0:18.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:0.0 -6 29917801 . G A 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.14256;SOR=0.0;LSEQ=ACTCCTAGGTAATGTCCCAC;RSEQ=TCTCTGCTTCTGTGCTCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:4,1:21,0:0.1923:1,2:27.4:1.0:29.8:1.0:0.19231:0.0:59.4:10.0:0.2083:0.0:1.4 0/0:14:0:0,0:14,0:0.0:1,0:24.5:1.0:29.5:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.2 -6 29925209 . C T 90 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.07591;SOR=0.16541;LSEQ=CCTGAATTTTCTGACTCTTC;RSEQ=CCTCAGAACCCCAAAGACTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:635:7:7,0:342,284:0.011:2,0:34.1:1.0:32.1:1.0:0.01858:0.0:36.6:14.0:0.0112:0.0:5.7 0/0:544:1:1,0:298,245:0.0018:2,0:42.0:0.0:33.0:0.0:1.0:0.0:22.0:2.0:0.0019:0.0:6.0 -6 29925217 . A TC 93 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.04383;SOR=0.14547;LSEQ=TTCTGACTCTTCCCCTCAGA;RSEQ=CCCCAAAGACTCACATGACC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:645:8:6,2:327,310:0.0124:2,2:35.0:1.0:31.1:1.0:0.2881:2.84:30.5:16.0:0.0127:0.0031:6.8 0/0:549:1:1,0:287,261:0.0018:2,0:43.0:0.0:32.5:0.0:1.0:0.0:22.0:2.0:0.0018:0.0:6.0 -6 29925228 . T A 96 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0264;SOR=0.13261;LSEQ=CCCCTCAGAACCCCAAAGAC;RSEQ=CACATGACCCACCACCCCAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:673:9:6,3:313,348:0.0134:2,2:33.7:1.0:30.4:1.0:0.32168:2.22:32.1:18.0:0.0137:0.0:6.9 0/0:558:1:1,0:256,300:0.0018:2,0:31.0:0.0:32.0:0.0:0.4614:0.0:22.0:2.0:0.0019:0.0:6.0 -6 29925235 . A T 94 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.02802;SOR=0.12196;LSEQ=GAACCCCAAAGACTCACATG;RSEQ=CCCACCACCCCATCTCTGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:686:10:6,4:305,370:0.0146:2,2:29.6:1.0:28.5:1.0:0.52465:1.82:34.9:9.0:0.0134:0.0:6.3 0/0:556:1:1,0:242,309:0.0018:2,0:24.0:0.0:32.0:0.0:0.44022:0.0:22.0:2.0:0.0019:0.0:6.0 -6 29925438 . C T 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.08002;LSEQ=TCTGGAGAGGAGCAGAGATA;RSEQ=ACATGCCATGTGCAGCACGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:105:63,42:132,109:0.3035:2,2:24.1:1.0:29.1:1.0:0.4098:1.24:60.0:104.0:0.3023:0.0:1.2 0/1:268:9:6,3:149,110:0.0336:2,2:29.1:1.0:29.9:1.0:0.73788:1.47:60.0:18.0:0.0338:0.0:1.0 -6 29974083 . CG C 77 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCGTTTGTCACAGGAGGAG;RSEQ=GGGTCAGGGCGAAGTCCCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:5,1:7,1:0.4286:2,2:31.0:1.0:29.8:1.0:1.0:1.36624:59.5:5.0:0.4167:0.0:0.7 0/0:1:0:0,0:1,0:0.0:0,0:9.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -6 29975766 . G C 109 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.18947;SOR=0.0;LSEQ=CACTCAGATCAGGACCAGAA;RSEQ=TCCCTGCTACCCTGCTCAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:9,2:6,1:0.6111:2,2:24.3:1.0:31.6:1.0:1.0:1.3127:59.5:22.0:0.6471:0.0:2.5 0/0:2:0:0,0:1,1:0.0:2,0:10.5:1.0:32.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -6 29975775 . A C 103 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.18947;SOR=0.0;LSEQ=CAGGACCAGAAGTCCCTGCT;RSEQ=CCCTGCTCAGAGACTAGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:9,2:6,1:0.6111:2,2:26.5:1.0:29.8:1.0:1.0:1.3127:59.5:10.0:0.625:0.0:2.3 0/0:2:0:0,0:1,1:0.0:2,0:10.5:1.0:27.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -6 29976971 . C A 96 NM4;Bias SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01251;SOR=0.0;LSEQ=GCAAGTAAGTATGAAGGAGG;RSEQ=TGATCCCTGAGATCCTTGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:9:9,0:349,297:0.0137:2,0:25.0:1.0:30.4:1.0:0.00491:0.0:39.4:18.0:0.014:0.0:6.1 0/0:484:0:0,0:245,239:0.0:2,0:27.6:1.0:31.6:1.0:1.0:0.0:59.5:68.143:1.0:0.0:0.2 -6 29976978 . CT AA 86 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.02185;SOR=0.0;LSEQ=AGTATGAAGGAGGCTGATCC;RSEQ=GAGATCCTTGGGATATTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:638:7:7,0:335,296:0.011:2,0:32.3:1.0:30.9:1.0:0.01681:0.0:42.6:14.0:0.0111:0.0016:6.1 0/0:482:0:0,0:239,243:0.0:2,0:26.7:1.0:30.7:1.0:1.0:0.0:59.6:79.333:1.0:0.0:0.2 -6 29976982 . G A 82 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0236;SOR=0.0;LSEQ=TGAAGGAGGCTGATCCCTGA;RSEQ=ATCCTTGGGATATTGTGGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:629:7:7,0:329,293:0.0111:2,0:35.9:1.0:29.3:1.0:0.01663:0.0:42.6:6.0:0.0098:0.0:6.1 0/0:459:0:0,0:224,235:0.0:2,0:27.1:1.0:31.3:1.0:1.0:0.0:59.6:113.75:1.0:0.0:0.2 -6 29977004 . G A 91 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.05442;SOR=0.15879;LSEQ=TCCTTGGGATATTGTGGTTG;RSEQ=GAGCCCATGGGGGAGCTCAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:9:3,6:317,301:0.0144:2,2:8.3:1.0:29.0:1.0:0.33112:2.10388:43.2:18.0:0.0149:0.0:4.8 0/0:434:1:0,1:208,224:0.0023:2,0:17.0:0.0:25.0:0.0:1.0:0.0:40.0:2.0:0.0023:0.0:6.0 -6 29977047 . G T 135 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00309;SOR=0.19433;LSEQ=ACCCCACAATTCCTCCTCTA;RSEQ=CCACATCTCCTGTGGGATCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:607:22:5,17:267,318:0.0362:2,2:34.3:1.0:30.3:1.0:0.04735:2.85019:41.3:44.0:0.037:0.0:4.0 0/0:414:3:1,2:206,205:0.0072:2,2:34.0:1.0:30.3:1.0:1.0:2.00649:43.3:6.0:0.0074:0.0:3.7 -6 29977101 . CC TG 104 Bias SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00327;SOR=0.0;LSEQ=TTTTGTTCTACCCCAGGCAG;RSEQ=AAAGTGCCCAGGGCTCTGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:568:10:0,10:253,302:0.0176:2,0:6.8:1.0:31.4:1.0:0.00276:0.0:36.4:20.0:0.018:0.0141:3.9 0/0:443:0:0,0:219,218:0.0:2,0:25.0:1.0:31.0:1.0:1.0:0.0:60.0:47.556:0.9862:0.0:0.3 -6 29977402 . AAAGGCATCTGAATGTGTCTGTGTCCCTATAGGCATAATGTGAGGTGGTGGG A 89 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.04535;SOR=0.0;LSEQ=ACCCTGACTTCTCTTTCTGC;RSEQ=GAGACCAGCCCACACCCGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:7:0,7:110,253:0.0189:2,0:69.0:1.0:32.0:1.0:0.10904:0.0:58.7:14.0:0.0192:0.0189:2.1 0/0:263:0:0,0:79,184:0.0:2,0:20.7:1.0:29.6:1.0:1.0:0.0:57.8:86.667:1.0:0.0:0.6 -6 30228918 . TA GG 117 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.01149;SOR=0.11024;LSEQ=ATTCTCAGGATGGTCACATG;RSEQ=TGCTGCTGGAGTGTCCTATG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:14:9,5:128,24:0.0843:2,2:15.5:1.0:30.8:1.0:0.07264:2.93784:36.9:28.0:0.0843:0.0361:4.3 0/1:100:1:1,0:80,18:0.01:2,0:20.0:0.0:33.0:0.0:1.0:0.0:31.0:2.0:0.0101:0.0:6.0 -6 30228932 . G A 120 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00395;SOR=0.14588;LSEQ=CACATGTATGCTGCTGGAGT;RSEQ=TCCTATGAGGAATGCAAAGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:18:10,8:149,59:0.0796:2,2:19.7:1.0:29.0:1.0:0.17997:2.01345:39.6:36.0:0.08:0.0:4.1 0/1:161:2:1,1:106,52:0.0124:2,2:22.0:1.0:28.5:1.0:1.0:2.0287:38.0:4.0:0.0127:0.0:4.5 -6 30228974 . C T 133 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00028;SOR=0.11094;LSEQ=CCTGAATTTTCTGACTCTTC;RSEQ=CCTCAGATCCCCCAAAGGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:20:9,11:192,150:0.0552:2,2:23.6:1.0:31.0:1.0:0.36133:1.56246:37.0:40.0:0.0559:0.0:3.5 0/0:311:2:1,1:172,136:0.0064:2,2:23.5:1.0:20.5:1.0:1.0:1.26373:38.0:1.0:0.0033:0.0:4.5 -6 30228992 . G A 132 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00027;SOR=0.10835;LSEQ=TCCCCTCAGATCCCCCAAAG;RSEQ=CACATGTGACCCAGCACCCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:354:20:9,11:167,167:0.0565:2,2:6.9:1.0:30.6:1.0:0.81867:1.22153:37.0:40.0:0.0583:0.0:3.5 0/0:311:2:1,1:157,152:0.0064:2,2:5.5:1.0:19.0:1.0:1.0:1.0328:38.0:1.0:0.0034:0.0:4.5 -6 30458875 . AG GA 89 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.03191;SOR=0.13012;LSEQ=CTGCTGGAGTGTCCCATGAG;RSEQ=ATACAAAGTGCCTGAATTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:315:7:7,0:205,102:0.0222:2,0:36.6:1.0:31.8:1.0:0.10071:0.0:33.3:14.0:0.0233:0.0:5.3 0/0:340:1:1,0:206,133:0.0029:2,0:45.0:0.0:32.0:0.0:1.0:0.0:33.0:2.0:0.003:0.0:7.0 -6 30458879 . A G 92 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03285;SOR=0.13193;LSEQ=TGGAGTGTCCCATGAGAGAT;RSEQ=CAAAGTGCCTGAATTTTCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:7:7,0:215,124:0.0202:2,0:39.6:1.0:33.0:1.0:0.05287:0.0:33.3:14.0:0.0205:0.0:5.3 0/0:370:1:1,0:217,150:0.0027:2,0:48.0:0.0:34.0:0.0:1.0:0.0:33.0:2.0:0.0027:0.0:7.0 -6 30458907 . C T 90 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.01627;SOR=0.11214;LSEQ=CCTGAATTTTCTGACTCTTC;RSEQ=CCTCAGAGCCCCCAAAGACA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:8:7,1:235,202:0.018:2,2:24.0:1.0:30.3:1.0:0.07625:6.0:33.3:16.0:0.0182:0.0:5.6 0/0:489:1:1,0:254,234:0.002:2,0:25.0:0.0:33.0:0.0:1.0:0.0:33.0:2.0:0.0021:0.0:7.0 -6 30458915 . G T 89 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.01532;SOR=0.10923;LSEQ=TTCTGACTCTTCCCCTCAGA;RSEQ=CCCCCAAAGACACACGTGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:8:7,1:217,212:0.0183:2,2:18.0:1.0:29.8:1.0:0.0685:6.82:33.3:16.0:0.0189:0.0:5.6 0/0:494:1:1,0:244,249:0.002:2,0:17.0:0.0:32.0:0.0:0.49595:0.0:33.0:2.0:0.002:0.0:7.0 -6 30459165 . C T 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATGTGCAGCATGAGGGGCTA;RSEQ=CCGAGCCCGTCACCCTGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:481:46:24,22:247,188:0.0956:2,2:28.6:1.0:30.4:1.0:0.63953:1.20387:59.6:92.0:0.0973:0.0:1.2 0/0:501:0:0,0:264,237:0.0:2,0:27.9:1.0:30.6:1.0:1.0:0.0:59.2:82.5:1.0:0.0:0.2 -6 30670292 . C T 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07962;LSEQ=AGCCACCTCTTTAACTGCCA;RSEQ=TGCCACCTCACCCAGACCCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:744:28:17,11:466,250:0.0376:2,2:23.7:1.0:29.9:1.0:0.68773:1.20579:60.0:56.0:0.0379:0.0:1.0 0/0:645:2:0,2:382,261:0.0031:2,0:12.0:1.0:28.5:1.0:0.16589:0.0:60.0:4.0:0.0031:0.0:1.0 -6 30672326 . T C 279 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0983;LSEQ=TGGGCTCAGGGGTGACAGGT;RSEQ=GGTCTGTGGAGGTGGAAGGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1810:666:320,346:556,587:0.368:2,2:25.1:1.0:29.8:1.0:0.80757:1.02414:59.9:36.0:0.3686:0.0:2.0 0/1:1571:85:38,47:746,739:0.0541:2,2:24.1:1.0:29.4:1.0:0.37241:1.24838:59.6:41.5:0.0541:0.0:2.0 -6 30954245 . T C 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAACTCTGAGTTCAGCACAG;RSEQ=GTCCAGTGGGATCAGCATAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:2,0:0.7143:0,2:33.0:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 31053516 . G C 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGCCTCCTCCTGGGGCCATC;RSEQ=TCCCAGGGGTTATGCCTCGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:23.2:1.0:31.8:1.0:1.0:0.0:60.0:12.0:0.3529:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 31053521 . A G 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTCCTGGGGCCATCGTCCC;RSEQ=GGGGTTATGCCTCGCTGCTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:22.3:1.0:31.7:1.0:1.0:0.0:60.0:12.0:0.3333:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 31237955 . TAAGAGATGTGACCCCCCATT GAAGACACATCACCCCTCATC 201 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGACTTCTGCTTTCTCTGA;RSEQ=CCCCTCCTTACCCCAGCTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:71:90:29,61:0,0:1.0:0,2:18.8:1.0:31.0:1.0:1.0:0.0:55.7:180.0:0.75:1.0:2.0 0/0:75:0:0,0:16,12:0.0:2,0:24.7:1.0:30.2:1.0:1.0:0.0:60.0:56.0:0.3733:0.0:0.1 -6 31238027 . C A 120 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00014;SOR=0.05417;LSEQ=TCTTGCAGCCCCTCGTGCTG;RSEQ=ATATGGCACGTGTATCTCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:16:4,12:21,44:0.1975:2,2:28.9:1.0:30.1:1.0:0.76451:1.42576:41.8:32.0:0.2:0.0:4.5 0/1:77:1:0,1:32,44:0.013:2,0:31.0:0.0:32.0:0.0:1.0:0.0:37.0:2.0:0.0133:0.0:4.0 -6 31238068 . C T 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11383;LSEQ=CTCTTGTCCAGAAGGCACCA;RSEQ=CACAGCTGCCCACTTCTGGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:31:13,18:16,31:0.3974:2,2:26.7:1.0:30.2:1.0:0.63256:1.39:45.2:62.0:0.4133:0.0:3.6 0/1:87:6:2,4:28,53:0.069:2,2:30.0:1.0:30.2:1.0:1.0:1.05594:37.5:12.0:0.069:0.0:3.5 -6 31238267 . C T 172 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.1367;LSEQ=TGTGTCTTTGGGGGTTCTGA;RSEQ=GGGAAGAGTCAGAAAATTCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:271:55:27,28:105,111:0.203:2,2:32.1:1.0:29.8:1.0:1.0:1.02:55.2:17.333:0.197:0.0:5.2 0/1:328:11:6,5:147,170:0.0335:2,2:30.9:1.0:27.2:1.0:0.76065:1.39:58.7:4.5:0.0285:0.0:5.0 -6 31238492 . C A 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.05;SOR=0.0;LSEQ=CCTGACCTGAGTGGAGGCTG;RSEQ=AGGACTCAGAAAAGCTGGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:0,12:0,2:0.8571:0,0:27.3:1.0:31.0:1.0:1.0:0.0:60.0:24.0:0.8571:0.0:2.9 0/0:2:0:0,0:0,2:0.0:0,0:15.0:1.0:33.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -6 31238524 . G A 72 d7;NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGCTGGAATCAAACCTTCA;RSEQ=ACACATTGAGTGTGAGGCAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:19.8:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:4.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 31238815 . A G 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0124;SOR=0.0;LSEQ=GGCCATCCCGGGAGATCTAT;RSEQ=GGAGATGGGGAAGGCTCCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:9:7,2:96,8:0.0431:2,2:9.8:1.0:26.4:1.0:0.18136:3.37311:58.9:8.0:0.0727:0.0:3.3 0/0:143:0:0,0:104,16:0.0:2,0:20.2:1.0:29.2:1.0:1.0:0.0:57.1:59.0:1.0:0.0:1.8 -6 31239171 . GC AGT 204 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=AGTCCCCCGAGCCCCGCCCC;RSEQ=CCCGACCAACCCGCGGGGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:180:95:19,76:19,49:0.5278:2,2:23.5:1.0:31.1:1.0:0.2631:1.54671:51.9:190.0:0.5367:0.1:4.3 0/0:130:0:0,0:8,24:0.0:2,0:13.7:1.0:31.2:1.0:1.0:0.0:47.7:66.0:0.3113:0.0:3.3 -6 31239172 . C T 86 InIns SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0119;SOR=0.0;LSEQ=GTCCCCCGAGCCCCGCCCCG;RSEQ=CCCGACCAACCCGCGGGGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:9:4,5:17,53:0.0577:2,2:7.0:1.0:27.2:1.0:0.23607:2.46:56.7:8.0:0.1067:0.0:3.8 0/0:108:0:0,0:20,68:0.0:2,0:21.2:1.0:30.2:1.0:1.0:0.0:50.2:11.571:1.0:0.0:3.8 -6 31239279 . T C 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGGGTTCCGCAGATCCACCT;RSEQ=GGGGTGGATCTCAGACGGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:26:23,3:28,3:0.4483:2,2:12.1:1.0:28.3:1.0:1.0:1.21317:57.6:5.5:0.4231:0.0:3.9 0/0:28:0:0,0:15,3:0.0:2,0:24.0:1.0:30.4:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.6 -6 31239602 . G A 223 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.10766;LSEQ=AAGCGGGGCTCTCCGCGGCC;RSEQ=GGCCGGGACACGGCGGTGTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:165:84,81:135,165:0.3548:2,2:20.8:1.0:30.4:1.0:0.24434:1.27:48.6:54.0:0.3553:0.0:4.2 0/1:484:27:9,18:218,239:0.0558:2,2:20.8:1.0:30.4:1.0:0.16778:1.82208:48.4:54.0:0.0564:0.0:4.0 -6 31239607 . G A 178 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.12285;LSEQ=GGGCTCTCCGCGGCCGGGCC;RSEQ=GGACACGGCGGTGTCGAAAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:53:22,31:188,197:0.121:2,2:8.0:1.0:31.2:1.0:0.37932:1.34381:39.2:106.0:0.1241:0.0:5.2 0/1:482:8:2,6:226,247:0.0166:2,2:7.3:1.0:30.3:1.0:0.29031:2.73953:34.5:16.0:0.0168:0.0:4.6 -6 31239616 . CG AT 214 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08325;LSEQ=GCGGCCGGGCCGGGACACGG;RSEQ=GTGTCGAAATACCTCATGGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:358:121:70,51:107,126:0.338:2,2:31.3:1.0:31.0:1.0:0.04348:1.61:42.6:242.0:0.3428:0.0:5.7 0/1:492:20:8,12:220,248:0.0407:2,2:33.9:1.0:29.2:1.0:0.64941:1.32987:40.1:40.0:0.0412:0.0:5.7 -6 31239621 . TC AA 205 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.089;LSEQ=CGGGCCGGGACACGGCGGTG;RSEQ=GAAATACCTCATGGAGTGGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:100:54,46:113,126:0.2747:2,2:33.9:1.0:31.0:1.0:0.28462:1.31:43.7:200.0:0.2762:0.0:4.5 0/1:492:16:6,10:221,250:0.0325:2,2:34.5:1.0:30.2:1.0:0.61199:1.47218:42.6:32.0:0.0329:0.0:4.4 -6 31239630 . C T 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08443;LSEQ=ACACGGCGGTGTCGAAATAC;RSEQ=TCATGGAGTGGGAGCCTGGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:137:72,65:174,156:0.2934:2,2:26.6:1.0:30.9:1.0:1.0:1.00693:44.1:136.0:0.2944:0.0:3.9 0/1:503:17:7,10:228,258:0.0338:2,2:31.5:1.0:30.5:1.0:0.80576:1.26188:42.6:34.0:0.0344:0.0:4.2 -6 31239727 . C A 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.14491;LSEQ=TGCGCCCTCGCCGGGAGGGC;RSEQ=CCTCGCTCCTCTCCGCAGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:514:160:90,70:179,173:0.3113:2,2:25.3:1.0:30.0:1.0:0.29367:1.24:59.3:52.333:0.3178:0.0:4.6 0/1:326:20:12,8:181,125:0.0613:2,2:24.6:1.0:29.9:1.0:1.0:1.04:60.0:40.0:0.0631:0.0:4.7 -6 31322204 . C CCT 74 NM4 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.01617;SOR=0.0;LSEQ=CAGGCCTTTCCCCTCTGCCC;RSEQ=ACCCACCCCCAGACCCGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:7:7,0:46,5:0.0753:2,0:23.3:1.0:26.6:1.0:1.0:0.0:51.4:14.0:0.0795:0.0:5.9 0/0:78:0:0,0:65,13:0.0:2,0:12.9:1.0:28.9:1.0:1.0:0.0:59.1:18.5:1.0:0.0:2.3 -6 31322205 . A CTC 135 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=AGGCCTTTCCCCTCTGCCCC;RSEQ=CCCACCCCCAGACCCGCCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:25:19,6:46,5:0.2688:2,2:19.6:1.0:29.2:1.0:0.16212:2.86015:58.8:50.0:0.2841:0.1183:4.3 0/0:78:0:0,0:65,13:0.0:2,0:12.9:1.0:28.9:1.0:1.0:0.0:59.1:18.5:1.0:0.0:2.3 -6 31322767 . G A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.11808;SOR=0.0;LSEQ=CACACAGGGTCCCAGGCTGC;RSEQ=TTAGCCCCTGTGTGCATGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:4,1:9,1:0.3333:2,2:23.4:1.0:30.2:1.0:1.0:2.12136:53.4:10.0:0.3333:0.0:2.4 0/0:9:0:0,0:8,1:0.0:2,0:27.1:1.0:30.6:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.9 -6 31322920 . C T 78 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.04083;SOR=0.0;LSEQ=ACACATCACAGCAGCGACCA;RSEQ=AGCTCCGATGACCACAACTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:6:4,2:156,46:0.0287:2,2:5.5:1.0:30.3:1.0:0.62346:1.6908:32.2:12.0:0.0288:0.0:6.3 0/0:154:0:0,0:104,50:0.0:2,0:25.1:1.0:30.6:1.0:1.0:0.0:59.6:37.5:1.0:0.0:1.3 -6 31323020 . T C 248 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04685;LSEQ=TCTGGGAAAGGAGGGGAAGA;RSEQ=GAGGGGCCCTGACCCTGCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:384:282:143,139:45,56:0.7344:2,2:23.5:1.0:30.5:1.0:0.2989:1.28:59.9:55.4:0.7328:0.0:2.6 0/1:263:30:13,17:112,121:0.1141:2,2:22.1:1.0:30.2:1.0:0.69971:1.20955:59.8:60.0:0.1154:0.0:2.6 -6 31323025 . G GGCCCTGACCCTCCAAGCCTCA 79 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.08619;SOR=0.0;LSEQ=GAAAGGAGGGGAAGATGAGG;RSEQ=GCCCTGACCCTGCTGAAGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:6:3,3:184,192:0.0157:2,2:10.8:1.0:30.6:1.0:1.0:1.04:27.7:12.0:0.0164:0.0157:4.3 0/0:258:0:0,0:122,135:0.0:2,0:21.5:1.0:29.8:1.0:1.0:0.0:59.7:31.125:0.996:0.0:1.2 -6 31323041 . AAGGG TAGGGCTCCAGGA 91 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0157;SOR=0.0;LSEQ=GAGGGGCCCTGACCCTGCTG;RSEQ=CTCCTGCTTTCCCTGAGAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:439:9:4,5:218,211:0.0205:2,2:5.9:1.0:28.9:1.0:0.74836:1.29071:47.4:18.0:0.021:0.0205:6.9 0/0:268:0:0,0:139,129:0.0:2,0:18.8:1.0:31.2:1.0:1.0:0.0:58.8:66.0:1.0:0.0:1.2 -6 31323414 . G A 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01479;LSEQ=AGGCGCTTTGCATCTTTCAT;RSEQ=GGACACCCTAGGACCACCCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:161:55,106:125,245:0.3032:2,2:21.4:1.0:29.5:1.0:1.0:1.02:60.0:39.25:0.3025:0.0:2.1 0/0:471:3:3,0:195,273:0.0064:2,0:6.7:1.0:15.7:1.0:0.07364:0.0:60.0:0.5:0.0022:0.0:3.3 -6 31324143 . GT TA 201 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04971;LSEQ=TAATCCTTGCCGTCGTAGGC;RSEQ=ACTGGTCATGCCCGCGGAGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:118:71,47:100,127:0.3401:2,2:33.0:1.0:29.3:1.0:0.0047:1.91:41.8:117.0:0.3401:0.0115:4.3 0/1:482:12:8,4:230,239:0.0249:2,2:35.0:1.0:30.0:1.0:0.25644:2.08:46.7:24.0:0.0253:0.0:3.8 -6 31324176 . C G 145 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.16806;LSEQ=CCGCGGAGGAGGCGCCCGTC;RSEQ=GGCCCCACGTCGCAGCCGTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:30:23,7:144,145:0.094:2,2:25.1:1.0:29.6:1.0:0.00647:3.3:36.8:14.0:0.0897:0.0:6.2 0/1:526:9:0,9:255,262:0.0171:2,0:20.0:1.0:31.1:1.0:0.00377:0.0:34.1:18.0:0.0172:0.0:4.0 -6 31324184 . C G 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04548;LSEQ=GAGGCGCCCGTCCGGCCCCA;RSEQ=GTCGCAGCCGTACATGCTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:132:79,53:75,93:0.4385:2,2:16.2:1.0:31.2:1.0:0.01049:1.84:42.1:25.4:0.4349:0.0:4.8 0/1:527:18:8,10:243,266:0.0342:2,2:11.6:1.0:29.0:1.0:0.81519:1.14163:46.9:17.0:0.0328:0.0:4.6 -6 31324200 . GCTCTGGAGG CGTCTGCCAA 190 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCACGTCGCAGCCGTACAT;RSEQ=GTGTGAGACCCTGGCCCCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:96:41,55:18,33:0.4248:2,2:15.9:1.0:29.0:1.0:0.47985:1.36:44.8:47.0:0.4273:0.4248:3.3 0/0:429:0:0,0:70,98:0.0:2,0:27.2:1.0:31.3:1.0:1.0:0.0:60.0:41.0:0.3877:0.0:0.7 -6 31324295 . C A 73 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.15995;SOR=0.0;LSEQ=ACCCGCGGGGATTTTGGCCT;RSEQ=AACTGAAAATGAAACCGGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:5:0,5:29,110:0.0345:2,0:14.4:1.0:31.6:1.0:0.58319:0.0:37.0:10.0:0.0352:0.0:4.4 0/0:95:0:0,0:16,79:0.0:2,0:25.9:1.0:31.5:1.0:1.0:0.0:57.0:46.5:1.0:0.0:1.2 -6 31324719 . C T 109 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00106;SOR=0.0;LSEQ=ACACGGAGGTGTAGAAATAC;RSEQ=TCATGGAGTGGGAGCCTGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:620:13:7,6:280,326:0.021:2,2:34.3:1.0:29.5:1.0:0.58986:1.36:36.2:12.0:0.0197:0.0:5.7 0/0:443:0:0,0:195,248:0.0:2,0:25.5:1.0:31.0:1.0:1.0:0.0:51.5:146.667:1.0:0.0:2.4 -6 31324941 . C T 209 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02012;LSEQ=CGCCATGACCAGCATCTCGG;RSEQ=GTCTGAGGAGACTCTGAGTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:750:130:51,79:268,350:0.1733:2,2:26.9:1.0:29.8:1.0:0.4353:1.18584:55.5:260.0:0.1754:0.0:6.3 0/0:716:3:0,3:326,387:0.0042:2,0:17.7:1.0:31.0:1.0:0.25495:0.0:53.3:6.0:0.0042:0.0:3.0 -6 31325159 . GC AA 127 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0003;SOR=0.0;LSEQ=TGCGCCTCCCCATTGCAGAC;RSEQ=GGCCCTCGGAGCCTGAGACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:17:0,17:1,6:0.7083:2,1:21.1:1.0:31.2:1.0:0.29167:0.0:49.2:34.0:0.7083:0.1667:5.2 0/0:9:0:0,0:0,8:0.0:0,0:25.0:1.0:31.6:1.0:1.0:0.0:60.0:16.0:0.8889:0.0:0.9 -6 31325164 . C T 108 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00248;SOR=0.0;LSEQ=CTCCCCATTGCAGACGCGGC;RSEQ=CTCGGAGCCTGAGACCCTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:13:0,13:1,6:0.65:2,1:24.8:1.0:29.2:1.0:0.35:0.0:47.8:12.0:0.6316:0.0:5.2 0/0:8:0:0,0:0,8:0.0:0,0:24.1:1.0:30.3:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.9 -6 31325201 . C A 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.1235;SOR=0.0;LSEQ=CTGAGAGCCCCGTCCGGGAC;RSEQ=TGGGACTTCGTCCTGATCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:0.3571:0,0:18.2:1.0:32.0:1.0:1.0:0.0:51.0:10.0:0.3571:0.0:2.4 0/0:7:0:0,0:1,6:0.0:2,0:30.6:1.0:31.6:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.6 -6 31345484 . G A 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00023;SOR=0.04088;LSEQ=AAGGCCTGCTGCAGCCTCCC;RSEQ=CTGAGGTCTTGAAACCATCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:12,0:10,0:0.5455:0,0:21.8:1.0:31.2:1.0:1.0:0.0:60.0:24.0:0.5455:0.0:1.0 0/1:23:1:1,0:22,0:0.0435:1,0:41.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0455:0.0:1.0 -6 31349819 . C A 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.04762;SOR=0.0;LSEQ=AAGGGGCGGCATGAAGAAAT;RSEQ=CTGCATCTCAGTCCCTCACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:0.8333:0,0:22.8:1.0:28.4:1.0:1.0:0.0:59.4:10.0:0.8333:0.0:2.6 0/0:3:0:0,0:2,1:0.0:2,0:6.0:1.0:32.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -6 31456099 . T G 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACCAGAAATGCAGAGTTTT;RSEQ=GTATGTGCGGGTCCGGGGTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:1,4:1,4:0.5:2,2:33.6:1.0:32.6:1.0:1.0:1.0:46.8:10.0:0.5:0.0:3.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 31456104 . G A 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAAATGCAGAGTTTTTGTAT;RSEQ=TGCGGGTCCGGGGTCTTCAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:1,4:1,4:0.5:2,2:30.6:1.0:31.2:1.0:1.0:1.0:46.8:10.0:0.5:0.0:3.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 31456108 . G A 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCAGAGTTTTTGTATGTGC;RSEQ=GGTCCGGGGTCTTCAGGAGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:1,4:1,4:0.5:2,2:28.2:1.0:31.8:1.0:1.0:1.0:46.8:10.0:0.5556:0.0:3.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 32169795 . TTCC T 66 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.0;MSILEN=3.0;SSF=0.0428;SOR=0.0;LSEQ=ACTCAGAGCCATCTACGTCC;RSEQ=TCCTCCTCTCACCCACCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:6:1,5:418,113:0.0111:2,2:11.8:1.0:25.8:1.0:0.00237:18.36814:60.0:5.0:0.0094:0.0074:0.7 0/0:392:0:0,0:289,101:0.0:2,0:21.0:1.0:29.3:1.0:1.0:0.0:60.0:54.714:0.9974:0.0:0.1 -6 32182243 . G GAT 88 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=10.0;MSILEN=2.0;SSF=0.1591;SOR=0.0;LSEQ=CATCTATATATCTAGTTGGA;RSEQ=ATATATATATATATATATAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:0,8:0,19:0.2759:1,0:36.9:1.0:29.5:1.0:1.0:0.0:60.0:16.0:0.2759:0.0345:0.1 0/0:9:0:0,0:0,9:0.0:0,0:16.3:1.0:31.1:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.2 -6 32185246 . T G 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00743;SOR=0.0;LSEQ=TGTGACTTTGGGCAAGCTGG;RSEQ=CAACCCTCTAGGCCCCAGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:2,7:0,19:0.3214:1,2:29.1:1.0:32.4:1.0:0.09524:0.0:60.0:18.0:0.3333:0.0:1.3 0/0:18:0:0,0:1,17:0.0:1,0:27.5:1.0:27.7:1.0:1.0:0.0:60.0:17.0:1.0:0.0:0.3 -6 32188713 . C G 238 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACGGAGACATCCTGCCCTG;RSEQ=CCAGAGAGAGGGGCGGCCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:635:192:88,104:188,251:0.3024:2,2:22.0:1.0:31.5:1.0:0.48684:1.13:60.0:47.0:0.3042:0.0:1.1 0/0:443:0:0,0:213,227:0.0:2,0:23.7:1.0:31.2:1.0:1.0:0.0:60.0:54.0:0.9931:0.0:0.3 -6 32188823 . G A 246 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTGGCAGGTGCCCCCATTC;RSEQ=AACAGCCCCTAGGAGGGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:306:181,125:313,255:0.3493:2,2:25.1:1.0:29.9:1.0:0.25351:1.18:60.0:50.0:0.3497:0.0:1.1 0/0:680:0:0,0:361,319:0.0:2,0:25.4:1.0:30.1:1.0:1.0:0.0:60.0:96.143:1.0:0.0:0.2 -6 32189192 . G A 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCACTCTGGATTATCTCT;RSEQ=GGTCTCATTTTCATATTTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:36:0,36:2,101:0.259:1,1:22.1:1.0:31.8:1.0:1.0:0.0:60.0:72.0:0.2609:0.0:1.3 0/0:76:0:0,0:6,70:0.0:2,0:25.7:1.0:30.3:1.0:1.0:0.0:60.0:75.0:1.0:0.0:0.1 -6 32190028 . A G 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGGAGATTAAAGGGGCTAG;RSEQ=ACAGGCATCAGGATGGTGCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:25.6:1.0:29.5:1.0:1.0:0.0:60.0:7.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 32190484 . G A 283 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00067;LSEQ=CTGGGGAGCCCTAGGGGAGC;RSEQ=GGAAGCAGGGCTTGGCAGCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:954:626:297,329:154,174:0.6562:2,2:25.8:1.0:30.5:1.0:0.89162:1.02:60.0:77.25:0.6581:0.0:1.1 0/0:803:1:1,0:383,417:0.0012:2,0:1.0:0.0:26.0:0.0:0.4794:0.0:60.0:2.0:0.0013:0.0:1.0 -6 32877176 . C T 56 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06395;SOR=0.0;LSEQ=TCTTGAATATTCACTATAAG;RSEQ=CTGATGCTATGCGAGGTGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:5:0,5:226,206:0.0114:2,0:6.4:1.0:24.4:1.0:0.0256:0.0:60.0:4.0:0.0094:0.0:2.0 0/0:388:0:0,0:191,197:0.0:2,0:23.5:1.0:31.0:1.0:1.0:0.0:60.0:54.429:1.0:0.0:0.5 -6 33290827 . A T 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.15819;SOR=0.0;LSEQ=TTCCTGTGGCCGGAGGTGAC;RSEQ=GTAGGCCCGCCCCGCGAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:5:0,5:4,102:0.045:1,0:17.8:1.0:30.4:1.0:1.0:0.0:60.0:10.0:0.0459:0.0:1.0 0/0:68:0:0,0:2,66:0.0:1,0:25.4:1.0:31.1:1.0:1.0:0.0:60.0:33.0:1.0:0.0:0.7 -6 36648084 . C CGTGTGTGT 92 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=38;MSI=23.0;MSILEN=2.0;SSF=0.29123;SOR=0.0;LSEQ=CGCGTGCGTGTCTGCGCGGG;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:8,0:13,0:0.3077:1,0:13.8:1.0:30.7:1.0:1.0:0.0:59.9:16.0:0.32:0.2308:1.0 0/0:5:0:0,0:5,0:0.0:0,0:23.8:1.0:26.0:1.0:1.0:0.0:56.0:4.0:1.0:0.0:1.2 -6 36650547 . G A 224 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATGGGCAAACTCACTCTCC;RSEQ=TTTTCCCTCTCCTGAAGGGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1075:163:79,84:443,468:0.1516:2,2:26.1:1.0:30.5:1.0:1.0:1.00649:60.0:162.0:0.1523:0.0:1.1 0/0:938:0:0,0:470,465:0.0:2,0:25.4:1.0:30.2:1.0:1.0:0.0:60.0:132.571:0.9968:0.0:0.4 -6 42701641 . G A 68 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=GACAAAGAGATAAAGAGAAA;RSEQ=CAGCTGGGCCTGGGGGACCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1.0:0,2:16.0:1.0:29.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 43738977 . C T 310 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03614;LSEQ=GCCGGCCCCGGTCGGGCCTC;RSEQ=GAAACCATGAACTTTCTGCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1457:1163:631,532:157,135:0.7982:2,2:24.7:1.0:30.5:1.0:0.8956:1.02:60.0:76.533:0.7967:0.0:1.2 0/1:1097:137:70,67:509,451:0.1249:2,2:25.7:1.0:30.4:1.0:0.7147:1.08015:60.0:136.0:0.1244:0.0:1.3 -6 43746352 . CT C 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.09435;SOR=0.0;LSEQ=CCAGGGTTAAGCATGCTGTA;RSEQ=TTTTGGCCCCCGTCCAGCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:2,4:84,367:0.0131:2,2:25.7:1.0:32.0:1.0:0.31546:2.18:60.0:12.0:0.0133:0.0022:0.2 0/0:252:0:0,0:61,189:0.0:2,0:23.0:1.0:30.2:1.0:1.0:0.0:60.0:124.0:0.992:0.0:0.1 -6 43748328 . C G 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATGCCTCCCCAGAGACCA;RSEQ=CTGCCTCCTGACACTTCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:56:54,2:81,4:0.3916:1,1:23.6:1.0:32.0:1.0:1.0:1.33:60.0:27.0:0.383:0.0:1.2 0/0:65:0:0,0:63,2:0.0:1,0:23.0:1.0:30.7:1.0:1.0:0.0:60.0:31.5:1.0:0.0:0.2 -6 46910123 . C T 105 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATGAATCCCTAACGCAGCA;RSEQ=GCTATTAGAGATGCTTAAGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1.0:0,0:24.3:1.0:30.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 46910144 . G A 122 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCTATTAGAGATGCTTAAGA;RSEQ=GGTAAAAGCATGGGCTATGG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:1.0:0,1:29.1:1.0:30.5:1.0:1.0:0.0:60.0:32.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 54873784 . A G 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGGATTCCTCAGAACTACC;RSEQ=GGAGTAGAGGCTAAGTCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:5,1:7,10:0.2609:2,2:22.0:1.0:29.5:1.0:0.15495:6.57:60.0:12.0:0.2609:0.0:2.3 0/0:2:0:0,0:1,1:0.0:2,0:36.5:1.0:30.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.0 -6 54873908 . G A 86 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.48529;SOR=0.0;LSEQ=GAGTTATTGGAGATCCTGCA;RSEQ=GAAAGCCCCACCCACTGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:4,4:0.4667:2,2:25.1:1.0:30.9:1.0:0.60839:2.34872:60.0:14.0:0.4667:0.0:1.0 0/0:2:0:0,0:0,2:0.0:0,0:15.5:1.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -6 54874135 . A G 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTTAGGCAGTTGCAAGTCCC;RSEQ=GTGCTGGCTGCTACCCCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:0.4545:2,2:17.8:1.0:29.4:1.0:1.0:1.3:60.0:10.0:0.5:0.0:2.2 0/0:1:0:0,0:0,1:0.0:0,0:5.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -6 58776318 . AC GT 92 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00072;SOR=0.08345;LSEQ=AGAGTGCAACATTCCTCTTG;RSEQ=AGAGCAGTTGGGAAACACTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:9:5,4:3,4:0.5625:2,2:21.4:1.0:29.3:1.0:1.0:1.61:41.4:18.0:0.5625:0.125:1.6 0/1:33:3:2,1:17,13:0.0909:2,2:24.3:1.0:30.3:1.0:1.0:1.51:41.7:6.0:0.0938:0.0:1.3 -6 58777300 . T G 86 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.01396;SOR=0.0;LSEQ=TCAGAATCTGCTTTGTGATG;RSEQ=GTGCGTTCAACTCATAGAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:7:2,5:16,23:0.1522:2,2:24.3:1.0:30.9:1.0:0.68785:1.71934:60.0:14.0:0.1522:0.0:4.4 0/0:39:0:0,0:19,20:0.0:2,0:21.0:1.0:30.1:1.0:1.0:0.0:53.8:78.0:1.0:0.0:3.0 -6 58777419 . T C 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08768;LSEQ=GCCCACAGTAGAAAAGGAAA;RSEQ=AACTTCACCTAAAACCTAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:57:33:17,16:16,8:0.5789:2,2:21.4:1.0:31.3:1.0:0.2885:1.86149:59.6:15.5:0.5741:0.0:1.7 0/1:57:6:4,2:29,22:0.1053:2,2:23.5:1.0:31.8:1.0:1.0:1.51:55.5:12.0:0.1053:0.0:2.3 -6 58777508 . T G 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00934;SOR=0.0;LSEQ=GAGTGGAACTTTCCTCTTTA;RSEQ=AGAGCAGTGTTGAAACACTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:2,3:16,25:0.1087:2,2:26.8:1.0:32.4:1.0:1.0:1.04:57.8:10.0:0.1087:0.0:1.6 0/0:68:0:0,0:28,38:0.0:2,0:24.4:1.0:28.3:1.0:1.0:0.0:54.4:65.0:0.9701:0.0:1.1 -6 58777960 . T C 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.02372;SOR=0.0;LSEQ=TAAAAGGCAGACAGAAGTGT;RSEQ=CTCAGAAACTGCTTTGTGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:4,1:13,11:0.1724:2,2:11.4:1.0:31.8:1.0:0.37013:3.26:56.0:10.0:0.1786:0.0:3.0 0/0:30:0:0,0:16,14:0.0:2,0:21.6:1.0:29.1:1.0:1.0:0.0:45.3:29.0:1.0:0.0:2.1 -6 58778828 . T A 101 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00384;SOR=0.12262;LSEQ=CAATCTCAGAAACGACTTTG;RSEQ=GATGTCTGCATTCAACTCAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:10:4,6:18,22:0.1961:2,2:28.2:1.0:30.7:1.0:1.0:1.22229:60.0:20.0:0.2:0.0:1.9 0/1:70:2:1,1:33,35:0.0286:2,2:5.0:1.0:28.0:1.0:1.0:1.06:60.0:4.0:0.0286:0.0:2.0 -6 58779032 . T G 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06193;SOR=0.0;LSEQ=GTCACAGAGTGGAACCTTCC;RSEQ=TTGGATAGAGCAGTTTGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:2,3:31,24:0.0833:2,2:10.2:1.0:31.4:1.0:0.64935:1.91607:60.0:10.0:0.0862:0.0:2.6 0/0:50:0:0,0:25,25:0.0:2,0:24.1:1.0:30.0:1.0:1.0:0.0:60.0:49.0:1.0:0.0:2.1 -6 80564836 . C T 76 d7;MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00466;SOR=0.0;LSEQ=CAGTTTCCCAAGCAGGACTT;RSEQ=CCCTAAACCAGAAGAAACAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1.0:0,2:15.0:1.0:29.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.3 0/1:7:1:1,0:5,1:0.1429:2,0:22.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.1667:0.0:1.0 -6 82852407 . AAAATAAATAAAT A 116 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=10.0;MSILEN=4.0;SSF=0.00012;SOR=0.0;LSEQ=GTGAGACCCTGTCCCCCCAA;RSEQ=AAATAAATAAATAAATAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:13:12,1:42,2:0.2167:1,1:21.2:1.0:31.4:1.0:0.54737:1.73063:58.8:26.0:0.2241:0.05:0.4 0/0:57:0:0,0:17,1:0.0:1,0:15.6:1.0:30.1:1.0:1.0:0.0:60.0:36.0:0.3158:0.0:0.1 -6 89795551 . G C 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGACACCTTAGAAAGTAACA;RSEQ=TGAGTTGAGCTGGGCATGGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:0.5:0,0:15.0:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 90009220 . G A 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTGTAGGACAAAAAAGTTG;RSEQ=CAGCTGCAGGGCCTGTCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:21:12,9:150,68:0.0879:2,2:17.3:1.0:28.3:1.0:0.32887:1.65073:60.0:20.0:0.0858:0.0:1.7 0/0:217:0:0,0:142,75:0.0:2,0:25.5:1.0:30.8:1.0:1.0:0.0:60.0:71.333:1.0:0.0:0.8 -6 93968294 . A ACTGT 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAGAAGTTACGCTTTCCTAA;RSEQ=CTGTTAAACAGGCTACTATT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:0.3333:0,0:25.3:1.0:30.9:1.0:1.0:0.0:60.0:12.0:0.3333:0.1111:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 93973735 . T C 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACAACTTACTAGAGTTAAA;RSEQ=TTACTGTTCATAGTTATGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:43:1,42:8,239:0.1483:1,1:22.8:1.0:32.4:1.0:1.0:1.40438:60.0:86.0:0.1498:0.0:1.8 0/0:192:0:0,0:9,183:0.0:1,0:22.7:1.0:30.2:1.0:1.0:0.0:60.0:384.0:1.0:0.0:0.5 -6 93973784 . G T 64 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.1796;SOR=0.0;LSEQ=GTAATAATATAGCGATTCAC;RSEQ=ATTAAAATTGCAAAGAAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:6:0,6:3,126:0.0444:1,0:27.2:1.0:24.8:1.0:1.0:0.0:60.0:5.0:0.0379:0.0:1.5 0/0:61:0:0,0:1,60:0.0:1,0:21.9:1.0:32.1:1.0:1.0:0.0:60.0:122.0:1.0:0.0:0.1 -6 94066172 . C T 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.52632;SOR=0.0;LSEQ=ACCTTGTGATCTGCCCGCCT;RSEQ=GGCCTCCCAAAATGCTGGGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:0.3333:0,0:23.3:1.0:31.8:1.0:1.0:0.0:60.0:12.0:0.3333:0.0:1.0 0/0:3:0:0,0:3,0:0.0:0,0:21.7:1.0:30.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.7 -6 94066446 . G T 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02742;LSEQ=AAAACATACCTGCTTGACCA;RSEQ=TGGTGATACTGACAGCAGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1535:77:48,29:869,589:0.0502:2,2:24.5:1.0:30.2:1.0:0.72086:1.12:60.0:76.0:0.05:0.0:1.2 0/0:1384:2:1,1:822,560:0.0014:2,2:7.0:1.0:30.0:1.0:1.0:1.46741:60.0:4.0:0.0015:0.0:1.0 -6 94068208 . G C 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAATTGTATTATTTAGCAAG;RSEQ=AATCAAATATTAAATGTGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:359:28:6,22:32,299:0.078:2,2:25.7:1.0:32.0:1.0:0.0993:2.54:60.0:56.0:0.0791:0.0:1.1 0/0:259:0:0,0:22,237:0.0:2,0:23.8:1.0:31.1:1.0:1.0:0.0:60.0:50.8:1.0:0.0:0.1 -6 100498638 . G T 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0286;SOR=0.11955;LSEQ=CACCATCATCATCATCTTCG;RSEQ=CATTATCATCATCATCTTAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:11:4,7:29,57:0.1134:2,2:26.5:1.0:27.8:1.0:1.0:1.12:60.0:4.5:0.0947:0.0:1.5 0/1:67:1:0,1:31,35:0.0149:2,0:28.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0152:0.0:1.0 -6 100498976 . C T 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTGCTTCAACAATGTGCAA;RSEQ=TTATCCTTCGCACCAGCCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:33:17,16:93,73:0.1658:2,2:25.1:1.0:30.9:1.0:0.70296:1.19793:60.0:66.0:0.1667:0.0:1.3 0/0:226:0:0,0:114,112:0.0:2,0:27.7:1.0:31.6:1.0:1.0:0.0:60.0:452.0:1.0:0.0:0.1 -6 100977940 . T C 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00192;SOR=0.0;LSEQ=TATTCTGGTATAATTTGGTA;RSEQ=TTAACATACATTAATTCCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:16,0:11,0:0.5714:0,1:29.4:1.0:30.0:1.0:1.0:0.0:60.0:7.0:0.5385:0.0:1.3 0/0:10:0:0,0:10,0:0.0:0,0:10.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 -6 106051478 . G A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.10131;SOR=0.0;LSEQ=GCTGAAATATATCAGTAACA;RSEQ=TATTAAATAATGTGTGTATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:6,1:6,0:0.5385:0,2:28.1:1.0:31.6:1.0:1.0:0.0:60.0:14.0:0.5385:0.0:1.0 0/0:5:0:0,0:5,0:0.0:0,0:22.2:1.0:33.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 -6 106051695 . A G 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTTCAGAAGACTTTTGATC;RSEQ=TAATTTTGGGGTTAATAGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:136:74,62:116,98:0.3886:2,2:25.1:1.0:30.5:1.0:1.0:1.01:60.0:135.0:0.3879:0.0:1.7 0/0:390:0:0,0:205,183:0.0:2,0:25.7:1.0:29.7:1.0:1.0:0.0:60.0:76.6:0.9948:0.0:0.4 -6 106543620 . G A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01293;LSEQ=TTTTTGGAGGGTAAGTAAGG;RSEQ=AAATTTCTTCAGACCCATTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:61:19,42:88,183:0.1837:2,2:26.2:1.0:30.1:1.0:0.88068:1.0628:60.0:60.0:0.1835:0.0:1.2 0/0:346:1:1,0:134,211:0.0029:2,0:1.0:0.0:23.0:0.0:0.39017:0.0:60.0:2.0:0.0029:0.0:2.0 -6 106553096 . G A 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CAAGAGCTCCAGCCCTCACA;RSEQ=CAGCCCTGGGAATACGGTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:949:92:40,52:382,474:0.0969:2,2:27.8:1.0:29.3:1.0:0.91219:1.04764:60.0:29.667:0.0956:0.0:1.2 0/0:920:0:0,0:421,499:0.0:2,0:24.4:1.0:31.4:1.0:1.0:0.0:60.0:60.333:1.0:0.0:0.2 -6 110700229 . T C 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.01522;LSEQ=CGGGGCTACCCTGCAGGATC;RSEQ=CCAATAATGCCAGCCAGAGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:7,9:0,0:0.9412:0,2:24.6:1.0:29.1:1.0:1.0:0.0:60.0:15.0:0.9375:0.0:1.1 0/1:13:2:0,2:5,6:0.1538:2,0:22.0:1.0:29.5:1.0:0.48718:0.0:60.0:4.0:0.1538:0.0:1.0 -6 110700656 . A G 79 d7;MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.00466;SOR=0.0;LSEQ=ATGAATAGGGCCTGAAGTGA;RSEQ=CCCCCAGCAACCTGCAGCAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:1.0:0,2:27.8:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.2 0/1:7:1:1,0:4,2:0.1429:2,0:47.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.1429:0.0:1.0 -6 112029505 . G C 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.25;SOR=0.0;LSEQ=CTCTTGGTAGGGGGCATTTT;RSEQ=CTTGGTTAGTGTCCTTAACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:28.0:1.0:30.3:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:1:0:0,0:1,0:0.0:0,0:41.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -6 115553830 . C T 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00024;SOR=0.04802;LSEQ=AAGGGAGAGGCAATGTTGCC;RSEQ=AACTCCAGAGGTTGGTATAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:7,7:10,8:0.4375:2,2:30.9:1.0:29.4:1.0:1.0:1.24128:60.0:28.0:0.4375:0.0:1.1 0/1:29:1:1,0:15,13:0.0345:2,0:43.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.037:0.0:1.0 -6 117629650 . A T 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=2.0;SSF=0.33333;SOR=0.0;LSEQ=GTGTGTATACTCTCTCTCTC;RSEQ=CACACACACACATACACTCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:28.7:1.0:31.8:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.5 0/0:1:0:0,0:1,0:0.0:0,0:49.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -6 117629663 . T C 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCTCTCACACACACACACA;RSEQ=ACACTCGGAGTGCTTTTATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:0,0:0.5455:0,0:19.7:1.0:33.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.5 0/0:1:0:0,0:1,0:0.0:0,0:36.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -6 117631479 . T C 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=3.0;SSF=0.01228;SOR=0.0;LSEQ=ATATTTAATAATAATAATAA;RSEQ=AACAACAATAAAGTTCCAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:9:1,8:65,286:0.0249:2,2:17.1:1.0:32.9:1.0:1.0:1.81566:60.0:18.0:0.0264:0.0:1.3 0/0:273:0:0,0:61,204:0.0:2,0:28.4:1.0:27.3:1.0:1.0:0.0:59.9:23.091:0.9922:0.0:0.2 -6 117639262 . G A 131 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00018;SOR=0.10731;LSEQ=TGTTGTTTTAGTCATGATCC;RSEQ=TTAAGTCATGTCATTTTGGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:22:19,3:191,36:0.0884:2,2:28.9:1.0:29.6:1.0:1.0:1.19:60.0:44.0:0.0894:0.0:1.1 0/1:195:2:2,0:158,35:0.0103:2,0:27.0:1.0:29.5:1.0:1.0:0.0:60.0:4.0:0.0103:0.0:1.0 -6 117648215 . T C 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAAGGCAAGCTCAAGGTCT;RSEQ=CCATTATGTCTTCTCTAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1400:101:57,44:666,632:0.0721:2,2:24.4:1.0:30.7:1.0:0.35273:1.23:60.0:32.667:0.071:0.0:1.1 0/0:1205:0:0,0:639,564:0.0:2,0:23.8:1.0:29.4:1.0:1.0:0.0:60.0:91.538:0.9992:0.0:0.1 -6 117652187 . T C 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.07161;LSEQ=CAGAAGTAGGCTTCACAAGA;RSEQ=GGGTAGAAAAAACTATGATG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:48:21,27:26,60:0.3582:2,2:25.0:1.0:30.3:1.0:0.13333:1.79:60.0:47.0:0.3588:0.0:1.2 0/1:105:4:1,3:37,64:0.0381:2,2:20.3:1.0:27.3:1.0:1.0:1.72606:60.0:8.0:0.0396:0.0:1.0 -6 117653900 . G A 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATTGAACAACTTGCTCCT;RSEQ=AATGGCTCCTGGGTAAATAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:4,1:12,0:0.2941:0,2:27.2:1.0:28.4:1.0:0.29412:0.0:58.4:10.0:0.2941:0.0:1.2 0/0:1:0:0,0:1,0:0.0:0,0:2.0:0.0:28.0:0.0:1.0:0.0:56.0:2.0:1.0:0.0:4.0 -6 117657686 . A G 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.28007;SOR=0.0;LSEQ=TCATTCCTTTTTATGGCTGC;RSEQ=TAGTATGCCATGGTGTATAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:3,2:12,1:0.2778:1,2:25.2:1.0:30.0:1.0:0.17157:6.87863:60.0:10.0:0.2778:0.0:1.0 0/0:6:0:0,0:5,1:0.0:2,0:26.5:1.0:30.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 -6 117662453 . C T 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.033;LSEQ=ACTCTCTGTACACCACATTT;RSEQ=CTCAGAGTGGCAGGCAAGAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:945:103:53,50:386,456:0.109:2,2:30.0:1.0:29.8:1.0:0.29646:1.25:60.0:102.0:0.1093:0.0:1.1 0/0:747:3:0,3:356,388:0.004:2,0:1.0:0.0:23.7:1.0:0.25064:0.0:60.0:6.0:0.0041:0.0:1.0 -6 117665115 . G A 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06562;LSEQ=ATTAGCTGTAAAAAAGTTGC;RSEQ=TACTAGTCCATTTCAGAACA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:35:35,0:52,0:0.4023:1,1:21.8:1.0:30.6:1.0:1.0:0.0:60.0:34.0:0.3953:0.0:1.0 0/1:48:2:2,0:44,2:0.0417:1,0:37.5:1.0:29.5:1.0:1.0:0.0:60.0:4.0:0.0417:0.0:1.0 -6 117686918 . CA C 123 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.01096;SOR=0.10711;LSEQ=AAGTTCCCTACAGGATGAAA;RSEQ=AAAAAAAGAAATAGGAGAAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:13:3,10:184,382:0.0225:2,2:37.3:1.0:33.5:1.0:0.56332:1.60439:60.0:26.0:0.0226:0.0:0.1 0/0:408:1:1,0:134,273:0.0025:2,0:12.0:0.0:33.0:0.0:0.33088:0.0:60.0:2.0:0.0025:0.0:0.0 -6 117699988 . A G 77 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATACACTTCCTGGGCTCTTA;RSEQ=GCAGCATTCTCCTGAGTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,1:0.2:1,0:27.8:1.0:33.4:1.0:1.0:0.0:60.0:10.0:0.2:0.0:1.0 0/0:1:0:0,0:1,0:0.0:0,0:26.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -6 117707038 . G A 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01126;LSEQ=TCCATGTCTCAAAATAAAGT;RSEQ=AATGATTAGCAGTTATTTTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:506:152:42,110:88,265:0.3004:2,2:23.4:1.0:29.2:1.0:0.57917:1.15:60.0:37.0:0.299:0.0:1.1 0/0:417:2:2,0:119,296:0.0048:2,0:1.0:0.0:24.0:0.0:0.0837:0.0:60.0:4.0:0.0048:0.0:1.5 -6 117724207 . G A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0069;SOR=0.0;LSEQ=TTGAATGGATCGATTAATAG;RSEQ=AAGGAATAGATTTATTTCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:8:7,1:92,5:0.0762:2,2:11.1:1.0:31.0:1.0:0.38598:2.59429:60.0:16.0:0.0777:0.0:1.1 0/0:100:0:0,0:90,10:0.0:2,0:21.2:1.0:31.0:1.0:1.0:0.0:60.0:99.0:1.0:0.0:0.1 -6 131790227 . G T 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0142;SOR=0.0;LSEQ=CACAAAGGGAAAGAGGAGAG;RSEQ=CACCGATACGTGTTCTCTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:3,2:39,2:0.1087:1,2:22.0:1.0:28.2:1.0:0.05279:11.59891:60.0:10.0:0.1163:0.0:1.0 0/0:59:0:0,0:52,7:0.0:2,0:23.3:1.0:31.5:1.0:1.0:0.0:60.0:118.0:1.0:0.0:0.1 -6 137519780 . T C 210 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.04488;LSEQ=CTTCTTACCACAGAGATCTA;RSEQ=GGGGAGAAAAATTGATTAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:124:38,86:37,112:0.4542:2,2:25.5:1.0:30.2:1.0:0.34061:1.34:60.0:61.0:0.4569:0.0:1.2 0/1:307:11:3,8:106,190:0.0358:2,2:19.3:1.0:30.1:1.0:0.75207:1.48591:60.0:22.0:0.0364:0.0:1.0 -6 137519834 . C CA 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.06049;SOR=0.0;LSEQ=TAAGCTTAAGTGCCTACCCT;RSEQ=AAAAAAAACAAAGGTCTGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:0,5:15,94:0.0439:2,0:32.4:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.0446:0.0088:0.4 0/0:106:0:0,0:20,85:0.0:2,0:23.0:1.0:31.9:1.0:1.0:0.0:60.0:210.0:1.0:0.0:0.1 -6 137540536 . G A 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08232;LSEQ=CAGCACTGCCCTCCAGCCCC;RSEQ=GCCTTACGTCACTTCCGTCA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:67:5,62:22,125:0.3131:2,2:26.1:1.0:30.6:1.0:0.18184:2.17539:60.0:21.333:0.3048:0.0:2.1 0/1:139:5:0,5:14,120:0.036:2,0:20.6:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.0362:0.0:1.8 -6 138026354 . G A 60 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGAGAGGTCTAGCTACCCT;RSEQ=CCAGCCAGCCACTGAAAGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:1.0:0,2:30.0:1.0:26.2:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 138027910 . A G 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGTGCGCACAGAGAGAAC;RSEQ=AAATCTCCAGGGTGGCTCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:134:62,72:228,269:0.212:2,2:28.8:1.0:30.1:1.0:1.0:1.02:60.0:32.5:0.2107:0.0:1.1 0/0:594:0:0,0:285,308:0.0:2,0:26.5:1.0:29.8:1.0:1.0:0.0:60.0:147.25:0.9983:0.0:0.2 -6 138199768 . A T 254 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00198;LSEQ=CGCCCAACTGCCCCTTCTTC;RSEQ=TGTCTGTGAACACCCAGCCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1125:328:160,168:388,408:0.2916:2,2:25.3:1.0:30.5:1.0:1.0:1.0:60.0:45.857:0.2887:0.0:1.1 0/0:1240:1:0,1:621,617:0.0008:2,0:1.0:0.0:24.0:0.0:0.49879:0.0:60.0:2.0:0.0008:0.0:1.0 -6 147728117 . C T 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCAGGGGCAGGGCCCGCGGT;RSEQ=CAGACCAGGGCACCCGGCGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:21:11,10:44,29:0.2234:2,2:20.4:1.0:30.5:1.0:0.6172:1.3745:60.0:42.0:0.2234:0.0:1.2 0/0:69:0:0,0:42,27:0.0:2,0:15.4:1.0:31.7:1.0:1.0:0.0:60.0:68.0:1.0:0.0:0.1 -6 148266586 . C T 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01357;LSEQ=ACCCCCAAACGTTATTTATC;RSEQ=GTGTATAAATACATGTCAGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:35:35,0:20,0:0.6364:1,1:25.9:1.0:31.9:1.0:1.0:0.0:60.0:70.0:0.6364:0.0:2.1 0/1:45:1:1,0:41,2:0.0222:1,0:11.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0227:0.0:2.0 -6 148266965 . A G 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=GTTCCTACCTTGTGCCAGGC;RSEQ=CTAGGGTTATGCAAAAAAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:23:0,23:0,15:0.6053:1,1:24.5:1.0:31.3:1.0:1.0:0.0:60.0:22.0:0.5946:0.0:1.2 0/0:15:0:0,0:0,15:0.0:1,0:26.4:1.0:30.7:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.0 -6 151176771 . C T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0258;SOR=0.0;LSEQ=TTTGGGCCCTGTATTTTTAA;RSEQ=CTTCTTGTCAAATTTGTTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:3,5:3,7:0.4444:2,2:21.6:1.0:31.6:1.0:1.0:1.37:52.5:16.0:0.4444:0.0:1.0 0/0:9:0:0,0:2,7:0.0:2,0:34.9:1.0:31.0:1.0:1.0:0.0:53.9:18.0:1.0:0.0:0.1 -6 152129308 . G C 290 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03415;LSEQ=GGCCCCGGGTCTGAGGCTGC;RSEQ=GCGTTCGGCTCCAACGGCCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1053:801:355,446:111,136:0.7607:2,2:25.0:1.0:30.1:1.0:0.88369:1.02538:60.0:56.214:0.7663:0.0:1.2 0/1:870:85:37,48:357,423:0.0977:2,2:22.8:1.0:29.3:1.0:0.73168:1.09474:60.0:41.5:0.0971:0.0:1.2 -6 152164026 . A G 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00373;SOR=0.0;LSEQ=GAATCAGCCATTTGTACAAA;RSEQ=CATGAATCCCTAGTAGGTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:12:0,12:2,98:0.1071:1,0:25.8:1.0:32.2:1.0:1.0:0.0:60.0:24.0:0.1091:0.0:1.0 0/0:73:0:0,0:0,73:0.0:1,0:22.8:1.0:29.8:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 -6 152201853 . G T 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00799;SOR=0.0;LSEQ=TGATAAAAACAGGAGGAAGA;RSEQ=CTGCCAGGCCTGCCGGCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:589:8:4,4:287,293:0.0136:2,2:23.9:1.0:29.8:1.0:1.0:1.02:60.0:16.0:0.0137:0.0:1.8 0/0:542:0:0,0:254,288:0.0:2,0:24.6:1.0:31.5:1.0:1.0:0.0:60.0:48.273:1.0:0.0:0.9 -6 152332921 . C G 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGTTTGCTCCTAACTTGCT;RSEQ=TTGGACAGGTAAGTGACCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:50:16,34:167,370:0.085:2,2:25.1:1.0:31.8:1.0:0.87446:1.04:60.0:49.0:0.0848:0.0:1.1 0/0:529:0:0,0:180,347:0.0:2,0:25.0:1.0:31.6:1.0:1.0:0.0:60.0:262.5:0.9962:0.0:0.1 -6 152333032 . A G 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00353;SOR=0.0;LSEQ=GTGAAGCTTCAGAGAACTTT;RSEQ=TTAGGTATGTTTACTTAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:12:0,12:1,74:0.1379:1,0:23.6:1.0:32.6:1.0:1.0:0.0:60.0:24.0:0.1379:0.0:1.0 0/0:53:0:0,0:1,52:0.0:1,0:18.2:1.0:29.6:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.1 -6 155699472 . TA T 77 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.03278;SOR=0.0;LSEQ=AATAAGTAAAATGCAAATAT;RSEQ=AAAAAAAATCTGAAATCCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:5,1:75,1:0.0732:1,2:19.2:1.0:30.0:1.0:0.14182:13.78406:60.0:12.0:0.0741:0.0244:0.0 0/0:67:0:0,0:61,5:0.0:2,0:19.8:1.0:28.4:1.0:1.0:0.0:60.0:65.0:1.0:0.0:0.1 -6 157100255 . G T 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.02205;SOR=0.0;LSEQ=GCAAGGCGGCCGCCGGCTCG;RSEQ=CGGCGGGGGGCTTCCAGCGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:5:1,4:244,126:0.0133:2,2:14.6:1.0:27.2:1.0:0.05101:7.70377:60.0:10.0:0.0136:0.0:1.2 0/0:428:0:0,0:271,157:0.0:2,0:20.8:1.0:31.6:1.0:1.0:0.0:60.0:52.5:1.0:0.0:0.3 -6 157150230 . A G 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.08219;LSEQ=GTCTTGCTGGATGTTTTGTC;RSEQ=GGTCATTGTTTTTAATATTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:32:31,1:59,2:0.3441:1,1:23.4:1.0:29.8:1.0:1.0:1.05:60.0:64.0:0.3441:0.0:1.1 0/1:49:2:2,0:47,0:0.0408:1,0:23.5:1.0:28.0:1.0:1.0:0.0:60.0:4.0:0.0426:0.0:1.0 -6 157511319 . G A 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00016;SOR=0.10393;LSEQ=ATGCCCTATGAGCCCAACAA;RSEQ=GACCCCTTTGGGGGAATGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:18:5,13:135,329:0.0373:2,2:21.4:1.0:30.4:1.0:1.0:1.06673:60.0:36.0:0.0382:0.0:1.0 0/0:500:2:2,0:181,317:0.004:2,0:1.0:0.0:27.5:1.0:0.13349:0.0:60.0:4.0:0.004:0.0:1.0 -6 157527280 . TCTC T 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.0;MSILEN=3.0;SSF=0.11762;SOR=0.19136;LSEQ=TGTACCTGTTCTTTCTTTCT;RSEQ=CTCCTCCTCCTCTCCAGTTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:5:5,0:205,46:0.0196:2,0:25.2:1.0:32.2:1.0:0.58886:0.0:60.0:10.0:0.0199:0.0039:0.2 0/0:263:1:0,1:193,66:0.0038:2,0:15.0:0.0:34.0:0.0:0.25769:0.0:60.0:2.0:0.0038:0.0:0.0 -6 159215375 . G T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02277;SOR=0.0;LSEQ=ACCACCACCACCAGGCTTTG;RSEQ=CAATTGAGAAAACACATCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:14,14:0.1515:2,2:29.4:1.0:30.0:1.0:1.0:1.48182:60.0:10.0:0.1515:0.0:1.0 0/0:35:0:0,0:15,20:0.0:2,0:28.6:1.0:31.3:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.3 -6 160639744 . C TAATAATAGAAACAGCAACATAGCAGTAGCAGCAACAACAGCAGCAGCAACAGCAATGTCAGCAACAGGT 143 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=AGCAGCAGCAGCAACAGCAA;RSEQ=AGCAGCAGCAACAATAACAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:631:29:11,18:300,285:0.046:2,2:40.0:1.0:29.6:1.0:0.1851:1.72097:24.0:58.0:0.0481:0.046:0.0 0/0:622:0:0,0:302,305:0.0:2,0:21.5:1.0:29.8:1.0:1.0:0.0:48.9:74.875:0.982:0.0:1.4 -6 160639753 . CAACAATAACAAAAGCAACAGAAACAGT C 255 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=AGCAACAGCAACAGCAGCAG;RSEQ=AACAACAAAACCAACAATAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:629:329:175,154:150,150:0.5231:2,2:31.3:1.0:30.5:1.0:0.42589:1.14:44.6:658.0:0.5324:0.5231:2.0 0/0:622:0:0,0:309,313:0.0:2,0:14.1:1.0:29.8:1.0:1.0:0.0:47.6:68.111:1.0:0.0:1.4 -6 160639965 . GTAGCAGT ATAGC 71 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01876;SOR=0.0;LSEQ=CAGCAGCAGCAGCAACAGAA;RSEQ=AGTAATAGCAGCAACAGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:5:4,1:29,18:0.0862:2,2:16.6:1.0:30.8:1.0:0.64102:2.45:35.6:10.0:0.0877:0.0345:3.4 0/0:68:0:0,0:24,20:0.0:2,0:23.6:1.0:31.3:1.0:1.0:0.0:60.0:88.0:0.8148:0.0:0.2 -6 160639980 . G A 68 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.10447;SOR=0.17481;LSEQ=CAGAAGTAGCAGTAGTAATA;RSEQ=CAGCAACAGCAGCAGCAGCA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:2,3:37,23:0.0725:2,2:16.6:1.0:29.4:1.0:0.3815:2.37935:60.0:10.0:0.082:0.0145:4.8 0/1:75:1:0,1:23,20:0.0133:2,0:1.0:1.0:27.0:1.0:0.47727:0.0:60.0:2.0:0.0213:0.0133:0.0 -6 160639986 . A ACAGCAGCAGCAGCAGCAGCAGCAATCATTACCATAGTAGCAACAACAGTAGCAGCAACTAACAATGGAAGCATCGGCAACAACAATAGCAAGAGCATCACAGTCAACAACAGCAACAGCAGCAACAATAGCCACAGCAACAGCAACAGCAGCAGTAGCAACAGAAATCACAGTAATAACAGTAG 161 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAGCAGTAGTAATAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:42:27,15:64,54:0.2428:2,2:41.4:1.0:29.9:1.0:0.28155:1.51:52.8:84.0:0.25:0.2428:1.1 0/0:142:0:0,0:65,45:0.0:2,0:8.0:1.0:29.4:1.0:1.0:0.0:58.6:220.0:1.0:0.007:1.3 -6 160640080 . T TAGCAGCCACAGCATCAGTAGCAGCAGCAGCAACAAGAGCAACAATAACAAAAGCAACAATAGCAAC 183 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCAGCAATAGCAACAGTAA;RSEQ=AGTAGCAGCAACAGCAATAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:65:30,35:470,341:0.0721:2,2:34.7:1.0:30.5:1.0:0.06909:1.60709:42.0:130.0:0.0744:0.0721:0.1 0/0:883:0:0,0:404,302:0.0:2,0:19.9:1.0:28.3:1.0:1.0:0.0:58.0:43.125:0.8005:0.0:2.2 -6 160640085 . G GCAGCAACAGCAATAGCAACAGTAGCAGCATCAGCAACAATAACAGCAAGTAAAAACAGCAACAGCAGCAGCAACAACAACAGTAGCAGCAGCAGCAACAACAGCAACAATAACAAAAGCAACGATAGCAACAGTATCAGCAA 238 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=48;MSI=3.0;MSILEN=6.0;SSF=0.0;SOR=0.0;LSEQ=CAATAGCAACAGTAATAGTA;RSEQ=CAGCAACAGCAATAGCAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1101:246:122,124:474,372:0.2234:2,2:31.0:1.0:30.0:1.0:0.08089:1.29476:54.9:81.0:0.2263:0.2234:2.5 0/0:1031:0:0,0:473,393:0.0:2,0:20.9:1.0:31.4:1.0:1.0:0.0:55.7:36.652:0.8371:0.001:1.9 -6 160640124 . ATAACAGCAACAGAAGCAATAACAGC GCAATAGTATCACAATTAACAACAGCAACAATAGCCACAGCAACAGCAACAGCAGCAGTAGCAACAGCAATAGCAGTAATAGCAGCAGCAGCAGTAGCAGCAATAATTACAACAATAGCAGCAAT 201 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=CAGTAGCAGCATCAGCAACA;RSEQ=AGCAGCAACAACAGCAGTAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:934:98:32,66:420,407:0.1049:2,2:32.1:1.0:30.4:1.0:0.00085:2.1267:41.4:196.0:0.1063:0.1049:0.2 0/0:887:0:0,0:391,407:0.0:2,0:11.9:1.0:29.7:1.0:1.0:0.0:54.9:71.545:0.8984:0.0:2.4 -6 160640134 . CAGAAGCAATAACAGCAGCAGCAACAACAGCAGTACGAACACCAGCAGTAA TAATAACAGCAACAACAACAGCAACAGCAGCAACAACAGCAACAATAACAAAAGCAACGATAGCAACAGTATCAGCAACAG 88 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.00335;SOR=0.0;LSEQ=ATCAGCAACAATAACAGCAA;RSEQ=CAACAGCAGCAGCAACATCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:10:1,9:109,115:0.0179:2,2:49.7:1.0:26.7:1.0:0.02102:8.47271:39.8:20.0:0.0382:0.0179:2.8 0/0:433:0:0,0:97,97:0.0:2,0:4.5:1.0:29.4:1.0:1.0:0.0:56.1:96.0:0.4496:0.0:0.7 -6 160640163 . G A 182 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAACAGCAGCAGCAACAACA;RSEQ=CAGTACGAACACCAGCAGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:78:34,44:82,105:0.291:2,2:5.4:1.0:29.1:1.0:1.0:1.0106:46.8:77.0:0.295:0.0:5.5 0/0:253:0:0,0:87,100:0.0:2,0:18.3:1.0:31.5:1.0:1.0:0.0:55.8:45.75:0.9946:0.0:1.4 -6 160640193 . G T 91 Bias SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.0197;SOR=0.11966;LSEQ=CACCAGCAGTAACAACAGCA;RSEQ=CAGCAACATCAGCAACAACA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:169:8:0,8:83,78:0.0473:2,0:9.0:0.0:30.4:1.0:0.00663:0.0:38.5:16.0:0.0485:0.0:3.0 0/0:170:1:0,1:81,88:0.0059:2,0:9.0:0.0:30.0:0.0:1.0:0.0:40.0:2.0:0.006:0.0:3.0 -6 160640212 . C T 86 Bias SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.01968;SOR=0.10696;LSEQ=AGCAGCAACATCAGCAACAA;RSEQ=AGCAGCAACAACAGTAGCAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:9:0,9:76,83:0.0536:2,0:8.6:1.0:27.2:1.0:0.00428:0.0:40.9:8.0:0.0497:0.0:3.6 0/0:167:1:0,1:76,90:0.006:2,0:8.0:0.0:30.0:0.0:1.0:0.0:40.0:2.0:0.0061:0.0:3.0 -6 161771035 . CGTGT C 133 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=7.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGTGTGTGTGCGCGCGCGCG;RSEQ=GTGTGTGTGTTTGAAAAGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:20:14,6:158,29:0.093:2,2:8.3:1.0:30.8:1.0:0.11671:2.32321:60.0:40.0:0.0943:0.0419:0.1 0/0:262:0:0,0:203,39:0.0:2,0:22.7:1.0:29.7:1.0:1.0:0.0:60.0:79.0:0.9186:0.0:0.2 -6 161771037 . T C 173 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGTGTGTGCGCGCGCGCGCG;RSEQ=GTGTGTGTGTGTTTGAAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:52:46,6:117,25:0.2441:2,2:24.7:1.0:30.4:1.0:0.38024:1.63:60.0:12.0:0.2595:0.0:2.0 0/0:270:0:0,0:208,43:0.0:2,0:22.3:1.0:28.2:1.0:1.0:0.0:60.0:34.857:1.0:0.0:0.2 -6 161771039 . T C 177 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGTGTGCGCGCGCGCGCGTG;RSEQ=GTGTGTGTGTTTGAAAAGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:54:48,6:122,28:0.25:2,2:23.6:1.0:30.9:1.0:0.28658:1.83:60.0:26.0:0.268:0.0:2.0 0/0:273:0:0,0:223,49:0.0:2,0:23.1:1.0:28.1:1.0:1.0:0.0:60.0:26.2:1.0:0.0:0.3 -6 162137107 . C A 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01854;LSEQ=CTGTGCTGGGCCCATCTTAC;RSEQ=GACTCCTCTCCTGAATCCCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1196:99:47,52:604,491:0.0828:2,2:26.8:1.0:30.3:1.0:0.17043:1.36064:60.0:98.0:0.0829:0.0:1.1 0/0:1199:2:2,0:644,552:0.0017:2,0:1.0:0.0:25.5:1.0:0.50266:0.0:60.0:4.0:0.0017:0.0:1.0 -6 162206873 . A T 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATCATTGAGTCTTGTCACAC;RSEQ=GTATAAGTGGAAACAGTCTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:672:82:34,48:263,325:0.122:2,2:26.1:1.0:30.9:1.0:0.63563:1.14222:60.0:164.0:0.1237:0.0:1.1 0/0:795:0:0,0:360,435:0.0:2,0:23.9:1.0:30.2:1.0:1.0:0.0:60.0:87.333:1.0:0.0:0.2 -6 163092867 . C T 69 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAATCAGATGTCAAATTGTA;RSEQ=AGTCAAAGAATAAATGGAAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,1:0.8333:0,2:21.4:1.0:29.8:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -6 163528910 . C T 188 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTATAAATTTCTCCAAAAT;RSEQ=CTAACATGTTGTTTGAAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:76:41,35:183,171:0.1763:2,2:25.6:1.0:30.1:1.0:0.80042:1.09:60.0:152.0:0.178:0.0:1.8 0/0:543:0:0,0:271,271:0.0:2,0:27.2:1.0:30.7:1.0:1.0:0.0:60.0:66.75:0.9981:0.0:0.3 -6 163529226 . A G 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.25;SOR=0.0;LSEQ=TTCTTTCTGTTCTCATGATG;RSEQ=TGAGTGAGCTCTCACGAGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:0.8571:0,0:31.2:1.0:32.7:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:2.0 0/0:1:0:0,0:0,1:0.0:0,0:7.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -6 169643879 . T C 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=5e-05;SOR=0.08928;LSEQ=GCTCTGACAGGAATGTAGTT;RSEQ=TACCTGGTAGTAAAACCTTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:39:38,1:77,4:0.325:1,1:23.9:1.0:31.8:1.0:1.0:1.96:60.0:78.0:0.325:0.0:1.1 0/1:49:2:2,0:45,2:0.0408:1,0:37.0:1.0:33.0:0.0:1.0:0.0:60.0:4.0:0.0408:0.0:1.0 -7 58414 . C G 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGATCTGCATATAGGCCAG;RSEQ=CTTTCTGCATAGGGCACAGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:4,2:2,1:0.6667:2,2:20.3:1.0:31.8:1.0:1.0:1.0:60.0:12.0:0.6667:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 60033 . C T 99 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01562;SOR=0.09863;LSEQ=ACTCCAAGCTCCCCCAGACC;RSEQ=GGTGGAAACGCAGACTCCTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:4,6:9,8:0.3704:2,2:27.7:1.0:29.9:1.0:0.69458:1.65488:60.0:9.0:0.3462:0.0:1.6 0/1:19:1:0,1:11,7:0.0526:2,0:21.0:0.0:32.0:0.0:0.42105:0.0:60.0:2.0:0.0556:0.0:1.0 -7 60055 . G T 116 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00038;SOR=0.04495;LSEQ=GTGGAAACGCAGACTCCTTG;RSEQ=CTAACACTGCCATGGGAGTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:7,8:3,7:0.6:2,2:19.9:1.0:29.7:1.0:0.67846:1.98:60.0:30.0:0.6:0.0:1.9 0/1:17:1:0,1:8,8:0.0588:2,0:39.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0625:0.0:2.0 -7 2166580 . C T 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGTAGGGCATTTTAAACAA;RSEQ=GGCAGATTACAACTGAGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:56:20,36:73,166:0.1886:2,2:26.1:1.0:29.6:1.0:0.52294:1.26:60.0:27.0:0.1862:0.0:1.1 0/0:135:0:0,0:42,93:0.0:2,0:22.1:1.0:29.6:1.0:1.0:0.0:60.0:44.0:1.0:0.0:0.4 -7 2951934 . C T 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=ATCTCTTGTGACGATATCTG;RSEQ=AGAGAGAGGGGCCAGTCCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:22:5,17:255,426:0.0313:2,2:27.3:1.0:28.9:1.0:0.18408:2.03337:60.0:44.0:0.0318:0.0:1.0 0/0:477:0:0,0:161,315:0.0:2,0:24.0:1.0:31.4:1.0:1.0:0.0:59.9:78.333:0.9979:0.0:0.1 -7 2952802 . A AGAGGGAAGAGAAGAGGGGAG 169 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=5e-05;SOR=0.0;LSEQ=GAAAGAGGGAAGAGGAGGAA;RSEQ=GAGGGAAGAGAAGAGGGGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:49:49,0:70,2:0.405:1,1:15.1:1.0:30.2:1.0:0.51405:0.0:58.8:48.0:0.4103:0.314:0.2 0/0:23:0:0,0:18,1:0.0:1,0:13.3:1.0:31.6:1.0:1.0:0.0:60.0:38.0:0.8261:0.0:0.2 -7 2952915 . G A 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.00025;SOR=0.0;LSEQ=CCAGGTGGCCGTGGCTCGCC;RSEQ=CTCACCTGACTTGCAGATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:21:13,8:417,237:0.0311:2,2:29.7:1.0:28.9:1.0:0.82262:1.08264:60.0:20.0:0.0303:0.0:1.0 0/0:336:0:0,0:208,127:0.0:2,0:23.1:1.0:29.9:1.0:1.0:0.0:60.0:166.5:0.997:0.0:0.3 -7 2961909 . A C 100 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGAAGCCCGAGAGAGGAGG;RSEQ=AACTTCCACTTACCAGGGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:27.5:1.0:33.4:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 2962036 . C T 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.3248;SOR=0.0;LSEQ=GACACCTGGGCAGGTGAGTG;RSEQ=AGACGTGGCCAAAGAGCCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:8:8,0:31,0:0.2051:1,0:17.3:1.0:29.9:1.0:1.0:0.0:60.0:16.0:0.2162:0.0:1.0 0/0:7:0:0,0:7,0:0.0:0,0:28.3:1.0:33.6:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.3 -7 2962201 . A C 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGCTCTAGGCGGCGAGGTC;RSEQ=CTTGTCCAGGTCAGAGACTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:37:27,10:504,187:0.0508:2,2:25.1:1.0:31.3:1.0:1.0:1.0:60.0:74.0:0.0514:0.0:1.1 0/0:387:0:0,0:267,118:0.0:2,0:22.0:1.0:29.7:1.0:1.0:0.0:60.0:76.0:0.9948:0.0:0.2 -7 2963521 . G T 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCTGGGCTCAAGTGATCC;RSEQ=CCTGCCTCAGCCTCCTGAGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:27.3:1.0:29.2:1.0:1.0:0.0:50.0:5.0:0.8333:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 2963744 . T C 116 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.07528;SOR=0.0;LSEQ=CTGACTCGGGAATGCTACAA;RSEQ=TCTGGTTCTGGCTCTAGGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:12:12,0:181,2:0.0615:1,0:20.0:1.0:32.5:1.0:1.0:0.0:60.0:24.0:0.0625:0.0:1.2 0/0:53:0:0,0:53,0:0.0:1,0:24.2:1.0:30.3:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.0 -7 2968289 . T C 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TGGAGTCGTTTCCCGGGGGC;RSEQ=CGGCGGTGATTGACATGATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1598:26:8,18:662,906:0.0163:2,2:22.0:1.0:30.6:1.0:0.31709:1.64355:60.0:25.0:0.0162:0.0:1.3 0/0:937:0:0,0:418,517:0.0:2,0:23.9:1.0:29.3:1.0:1.0:0.0:60.0:45.75:0.9978:0.0:0.2 -7 2968548 . G A 110 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=CTCGCACATCTGCTCACAGG;RSEQ=AGGACGCAGGCGGGAGCCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:0,12:0,11:0.5217:0,0:21.2:1.0:30.9:1.0:1.0:0.0:60.0:24.0:0.5455:0.0:1.3 0/0:1:0:0,0:0,1:0.0:0,0:39.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 -7 2969660 . C A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTTGGTGATGGGCAGAGAT;RSEQ=CGCAGGAGCTAGGGCTGGCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1605:77:41,36:739,789:0.048:2,2:26.3:1.0:28.5:1.0:0.41571:1.22:60.0:76.0:0.0479:0.0:1.2 0/0:862:0:0,0:440,421:0.0:2,0:25.3:1.0:30.7:1.0:1.0:0.0:60.0:85.1:0.9988:0.0:0.4 -7 2969983 . C T 112 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AACCTCCTCTTGCTTTTTAT;RSEQ=AAATTTTTTATAGAGATGGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:15:0,15:0,4:0.7895:0,1:22.9:1.0:28.7:1.0:1.0:0.0:60.0:30.0:0.7895:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 2973685 . TTTTTC T 69 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACCACAATGCCTGGCTGTTT;RSEQ=TTTTCTTTTCTTTTCTTTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:34.8:1.0:26.8:1.0:1.0:0.0:60.0:5.0:1.0:0.1667:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 2977488 . C T 61 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.17127;SOR=0.0;LSEQ=GGAGCCGGTGGTCTGGGGTG;RSEQ=GGGCCCCGCTGTGCAGCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:5:3,2:383,99:0.0103:2,2:9.8:1.0:26.4:1.0:0.27756:2.57285:60.0:10.0:0.0104:0.0:1.0 0/0:254:0:0,0:187,67:0.0:2,0:21.6:1.0:30.9:1.0:1.0:0.0:60.0:41.333:1.0:0.0:0.2 -7 2977768 . G T 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.05018;SOR=0.0;LSEQ=CCCGCCAGCTGGCTGGAGCT;RSEQ=GCCTGTCCCTCCCTAAGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:7:0,7:2,147:0.0446:1,0:35.7:1.0:30.1:1.0:1.0:0.0:60.0:14.0:0.0467:0.0:1.0 0/0:90:0:0,0:0,90:0.0:1,0:21.1:1.0:29.9:1.0:1.0:0.0:60.0:21.5:1.0:0.0:0.2 -7 2985351 . C A 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05672;SOR=0.0;LSEQ=TCACAGCTTAAGAACCATGC;RSEQ=ACTACTGAGGACACACACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:246:8:8,0:233,5:0.0325:1,0:24.8:1.0:30.8:1.0:1.0:0.0:60.0:16.0:0.0342:0.0:1.3 0/0:121:0:0,0:114,5:0.0:1,0:22.4:1.0:30.0:1.0:1.0:0.0:60.0:28.75:0.9829:0.0:0.3 -7 2985391 . C G 76 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=2.0;SSF=0.08685;SOR=0.0;LSEQ=CACACACACACACACACAGA;RSEQ=ACACACACACACACGCCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:444:6:5,1:343,78:0.0135:2,2:6.8:1.0:29.5:1.0:1.0:1.14:60.0:5.0:0.012:0.0:1.5 0/0:283:0:0,0:211,59:0.0:2,0:22.7:1.0:30.4:1.0:1.0:0.0:59.9:44.0:1.0:0.0:0.4 -7 6026530 . C T 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTCGTTTAGCTAAAGAACT;RSEQ=ATAGAAAAGTCCAGGGGCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1618:85:37,48:752,779:0.0525:2,2:23.6:1.0:28.7:1.0:0.37263:1.25216:59.3:84.0:0.0526:0.0:1.0 0/0:1097:0:0,0:536,561:0.0:2,0:24.9:1.0:31.3:1.0:1.0:0.0:59.7:83.385:1.0:0.0:0.1 -7 6039129 . T C 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTCACTTCCCAATGTGCCA;RSEQ=GCATCCTGGTAAAACAACTA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:0.4:0,0:20.4:1.0:30.5:1.0:1.0:0.0:60.0:16.0:0.4444:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 6048510 . G T 49 q23;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.17444;SOR=0.0;LSEQ=GCCACTCCGGGGCCTCCAGG;RSEQ=GGCTGCCTCGCCACGCGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:5:3,2:235,43:0.0176:2,2:13.0:1.0:21.2:1.0:0.18038:3.61968:60.0:1.5:0.0109:0.0:2.8 0/0:142:0:0,0:113,29:0.0:2,0:22.7:1.0:30.5:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.3 -7 6426892 . C T 167 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTTACACAACCAATGCATTT;RSEQ=CTGGAGAATATATCCCTACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1095:51:20,31:474,569:0.0466:2,2:24.6:1.0:29.6:1.0:0.47157:1.29091:59.9:24.5:0.0456:0.0:1.1 0/0:759:0:0,0:373,385:0.0:2,0:24.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -7 6426908 . C G 189 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTTCCTGGAGAATATATCC;RSEQ=TACTGTGTAAGTATCTTAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:983:73:30,43:375,534:0.0743:2,2:26.3:1.0:30.6:1.0:1.0:1.00655:60.0:72.0:0.0744:0.0:2.0 0/0:712:0:0,0:320,391:0.0:2,0:25.2:1.0:30.8:1.0:1.0:0.0:59.6:70.1:1.0:0.0:0.5 -7 6431457 . C G 151 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00014;SOR=0.16965;LSEQ=GGTGTGGCAGCCTCCAGGCC;RSEQ=GTCCCCAGCCTTTTTCTTGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:35:33,2:160,10:0.1707:2,2:19.9:1.0:29.6:1.0:1.0:1.03:60.0:70.0:0.1716:0.0:1.4 0/1:119:4:4,0:105,10:0.0336:2,0:27.3:1.0:31.8:1.0:1.0:0.0:60.0:8.0:0.0339:0.0:1.5 -7 6431523 . C CT 135 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CAGTGACTTAGCTTCTACAC;RSEQ=TGTGACTAACCATTTTCATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:23:15,8:455,199:0.034:2,2:25.1:1.0:29.9:1.0:0.6498:1.21903:60.0:22.0:0.0329:0.0103:0.2 0/0:452:0:0,0:289,163:0.0:2,0:23.7:1.0:30.3:1.0:1.0:0.0:60.0:36.667:1.0:0.0:0.2 -7 6438388 . C T 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00013;SOR=0.0;LSEQ=CCACTTCAGTTTCAAGCTTT;RSEQ=TCTGTTCTCTCATTTCACTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:18:6,12:278,591:0.0202:2,2:26.9:1.0:30.7:1.0:1.0:1.06:60.0:36.0:0.0205:0.0:1.0 0/0:581:0:0,0:212,368:0.0:2,0:25.3:1.0:31.3:1.0:1.0:0.0:60.0:115.0:0.9983:0.0:0.1 -7 6441229 . T TC 111 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCTTTTGTTTCTCTTCCCT;RSEQ=CCCCCCTTCCCCTGCGGTTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:12,0:7,0:0.6316:0,0:31.0:1.0:31.1:1.0:1.0:0.0:60.0:24.0:0.6316:0.0:0.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 6441993 . C G 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCGCTCACACAGCGAGGCCT;RSEQ=AAGACAGTGTTTGACGAAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:897:23:12,11:426,447:0.0256:2,2:27.1:1.0:31.0:1.0:0.834:1.14:57.6:22.0:0.0252:0.0:1.2 0/0:731:0:0,0:364,365:0.0:2,0:24.9:1.0:30.9:1.0:1.0:0.0:56.9:51.071:0.9986:0.0:0.2 -7 6442156 . C A 168 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAAAAAACAAAAAAAAAAAA;RSEQ=AAAAAAAAAAAACAACGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:53:6,47:3,33:0.5761:2,2:18.7:1.0:29.4:1.0:0.73406:1.4:47.3:52.0:0.6118:0.0:2.5 0/0:41:0:0,0:1,22:0.0:1,0:24.5:1.0:27.7:1.0:1.0:0.0:57.1:4.75:0.8636:0.0:1.0 -7 6776825 . AGA G 119 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=2.0;MSILEN=2.0;SSF=0.00335;SOR=0.0;LSEQ=GTGTCCATTTCCAGACTGCG;RSEQ=GGCCTTTTCTCTTCGTCACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:14:7,7:522,436:0.0144:2,2:23.1:1.0:31.4:1.0:0.79142:1.19702:57.0:28.0:0.0146:0.0041:0.1 0/0:528:0:0,0:289,239:0.0:2,0:25.1:1.0:30.0:1.0:1.0:0.0:53.3:74.429:1.0:0.0:0.1 -7 11297507 . T G 71 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.27207;SOR=0.0;LSEQ=TTTTAGTTTTTTTTTTCCCT;RSEQ=TTTTTTTTTTTTGAGTGATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:2,3:4,6:0.2941:2,2:14.4:1.0:30.8:1.0:1.0:1.0:60.0:10.0:0.3571:0.0:1.0 0/0:7:0:0,0:2,3:0.0:2,0:25.8:1.0:27.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 -7 12462931 . G GCC 117 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.0;MSILEN=1.0;SSF=0.01147;SOR=0.0;LSEQ=TACCCAATAATCCTTCTGTG;RSEQ=CCCCCCCCTTATTTCATTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:13:13,0:99,3:0.1111:1,1:22.7:1.0:31.8:1.0:1.0:0.0:59.2:26.0:0.114:0.0256:1.4 0/0:48:0:0,0:43,0:0.0:1,0:25.2:1.0:31.0:1.0:1.0:0.0:60.0:20.5:0.8913:0.0:0.3 -7 13935307 . C T 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=7e-05;SOR=0.0;LSEQ=TTTAGATTACTCCCACCCAC;RSEQ=CTCAAATAAAGTGCACAGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:22:20,2:7,0:0.7586:0,2:22.9:1.0:29.9:1.0:1.0:0.0:60.0:10.0:0.7407:0.0:1.2 0/0:9:0:0,0:9,0:0.0:0,0:19.0:1.0:30.3:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.1 -7 13935468 . G T 52 q23;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.07499;SOR=0.0;LSEQ=AAAAGGAAAAGCGCAAAAAC;RSEQ=CCCTGCTTGACTGTCACTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:5:2,3:323,161:0.0102:2,2:17.4:1.0:22.4:1.0:0.34024:3.00192:60.0:1.5:0.0063:0.0:1.4 0/0:366:0:0,0:240,125:0.0:2,0:25.4:1.0:29.9:1.0:1.0:0.0:60.0:35.5:1.0:0.0:0.2 -7 14025528 . C A 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00015;SOR=0.03805;LSEQ=AAAAGATATAACAGATTGCA;RSEQ=CACAAAATTTTAACAAAAAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:31:31,0:11,0:0.7381:0,1:28.4:1.0:29.8:1.0:1.0:0.0:60.0:30.0:0.7317:0.0:1.1 0/1:11:1:1,0:9,1:0.0909:2,0:4.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0909:0.0:1.0 -7 14026421 . C T 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00589;SOR=0.0;LSEQ=ATAAATTTAATTTCAAGAGA;RSEQ=GCAGTCAACATAAAAATAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:15:0,15:0,100:0.1304:1,1:17.3:1.0:30.3:1.0:1.0:0.0:60.0:30.0:0.1339:0.0:1.9 0/0:49:0:0,0:1,48:0.0:1,0:19.9:1.0:29.2:1.0:1.0:0.0:60.0:98.0:1.0:0.0:0.6 -7 14028575 . C T 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.01282;LSEQ=TCCCTTCTCATTTTCTCCCT;RSEQ=TCCCCACCCCCGACGGAGTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:807:101:66,35:476,229:0.1252:2,2:23.4:1.0:29.9:1.0:0.65212:1.10215:60.0:202.0:0.13:0.0:1.1 0/0:547:1:0,1:342,204:0.0018:2,0:1.0:0.0:29.0:0.0:0.37477:0.0:60.0:2.0:0.0019:0.0:1.0 -7 32159902 . G A 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.48529;SOR=0.0;LSEQ=GGCCGCAGTCTCTGCAGACC;RSEQ=TCATACTTAGCCTTTCCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:5,2:6,2:0.4667:2,2:20.1:1.0:29.1:1.0:1.0:1.18545:60.0:14.0:0.4667:0.0:1.1 0/0:2:0:0,0:1,1:0.0:2,0:14.0:1.0:30.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -7 36858427 . G T 99 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.21842;SOR=0.0;LSEQ=TCCACGTGCAAAAGAATGAA;RSEQ=TTGGACCCCTGCCTCACAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:7,2:7,1:0.5294:2,2:14.3:1.0:31.3:1.0:1.0:1.9219:60.0:18.0:0.5294:0.0:1.1 0/0:3:0:0,0:3,0:0.0:0,0:27.0:1.0:31.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -7 36859286 . A G 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.01182;SOR=0.0;LSEQ=AAAATGCAAGCAAGTATACA;RSEQ=AAAGCATATTGAACAGTCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:10:2,8:13,34:0.1754:2,2:17.0:1.0:32.4:1.0:1.0:1.51882:55.6:20.0:0.1852:0.0:1.1 0/0:33:0:0,0:9,24:0.0:2,0:23.4:1.0:29.7:1.0:1.0:0.0:60.0:66.0:1.0:0.0:0.1 -7 39836727 . G T 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02459;SOR=0.0;LSEQ=ATCACCCCCTCCTCCTCATG;RSEQ=ATGACCATGTGCTCCTCGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:15:8,7:59,87:0.0932:2,2:19.7:1.0:29.7:1.0:0.41243:1.68:52.1:30.0:0.0943:0.0:1.1 0/0:52:0:0,0:24,28:0.0:2,0:25.1:1.0:30.9:1.0:1.0:0.0:51.3:51.0:1.0:0.0:0.0 -7 41729758 . CA AG 152 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTTTCTTCTTCTTCTTGCC;RSEQ=GGAGAACCAAGCTGGCGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2532:28:13,15:1249,1247:0.0111:2,2:25.9:1.0:31.8:1.0:0.84972:1.15563:60.0:56.0:0.0113:0.0004:1.1 0/0:1564:0:0,0:781,780:0.0:2,0:24.9:1.0:30.5:1.0:1.0:0.0:60.0:56.815:0.9987:0.0:0.1 -7 41730289 . G C 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACAGCCCATGGGCTGAAACT;RSEQ=TTTCTGTACTGCCTGCAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:44:0,44:0,157:0.2189:1,1:25.5:1.0:31.8:1.0:1.0:0.0:60.0:21.0:0.2121:0.0:1.2 0/0:71:0:0,0:1,70:0.0:1,0:25.2:1.0:31.6:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.1 -7 41739141 . G C 105 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCCATTCCACTCCAATCCT;RSEQ=GTACATTCACCCCTCTACCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:1.0:0,2:35.4:1.0:31.7:1.0:1.0:0.0:60.0:20.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 43288295 . TTCCTCC T 99 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=25;MSI=10.0;MSILEN=3.0;SSF=0.0441;SOR=0.0;LSEQ=TCCTCCTCCTCCTCCTCCTT;RSEQ=TCCTCCTCCTCCTCCTCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:8,1:14,0:0.25:1,2:10.0:1.0:31.4:1.0:0.3913:0.0:58.3:18.0:0.3:0.1111:1.1 0/0:15:0:0,0:5,0:0.0:0,0:12.6:1.0:27.4:1.0:1.0:0.0:59.4:10.0:0.3333:0.0:0.8 -7 43299616 . T C 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACCACACCCAGGCACATCA;RSEQ=AGTCAAACTTCTGAAAACCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:51:26:12,14:12,13:0.5098:2,2:30.5:1.0:32.6:1.0:1.0:1.07536:60.0:52.0:0.5098:0.0:1.1 0/0:68:0:0,0:32,36:0.0:2,0:30.0:1.0:28.3:1.0:1.0:0.0:60.0:33.0:1.0:0.0:0.1 -7 45551574 . A T 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.54067;SOR=0.0;LSEQ=CCTCTTGTGATTTTCCATCC;RSEQ=CTGACCCTTGCAACCTGCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:2,4:7,5:0.3333:2,2:26.2:1.0:29.7:1.0:0.61991:2.64037:60.0:12.0:0.3333:0.0:1.0 0/0:4:0:0,0:1,3:0.0:2,0:26.8:1.0:29.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -7 45856989 . T TAGG 129 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATCCCCAGGGGTGGGGGCCA;RSEQ=GGGCCCACTCTGCTGCCCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:20:7,13:7,11:0.5263:2,2:18.3:1.0:29.9:1.0:1.0:1.17662:41.3:19.0:0.5278:0.2105:0.4 0/0:27:0:0,0:9,18:0.0:2,0:24.0:1.0:29.2:1.0:1.0:0.0:59.3:54.0:1.0:0.0:0.2 -7 45857101 . C T 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGAGTGTGTAGGAGGAGGA;RSEQ=GGGGTGGGACCATAGACTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:3,3:4,5:0.4:2,2:22.5:1.0:30.5:1.0:1.0:1.23:38.8:12.0:0.4286:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 45857415 . G A 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.01952;SOR=0.0;LSEQ=CGGCCATGTGCTGGGAATGA;RSEQ=CAGCTCAGGTGGGCAGCAGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:13:6,7:42,40:0.1368:2,2:27.2:1.0:30.0:1.0:0.77345:1.22238:46.3:26.0:0.1398:0.0:1.1 0/0:35:0:0,0:22,13:0.0:2,0:30.3:1.0:32.2:1.0:1.0:0.0:37.3:70.0:1.0:0.0:0.1 -7 45858363 . G C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.03691;SOR=0.13187;LSEQ=AGGTGGCTCCAGGGGGCCGC;RSEQ=CAGGGTCAACACTCCCTGTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:8:7,1:30,21:0.1333:2,2:25.0:1.0:30.8:1.0:0.23723:4.8:40.0:16.0:0.1333:0.0:1.8 0/1:51:1:1,0:29,21:0.0196:2,0:1.0:0.0:29.0:0.0:1.0:0.0:40.0:2.0:0.0204:0.0:1.0 -7 47092291 . G T 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01556;SOR=0.0;LSEQ=CTCTCCCCCAGGTCTCTCCC;RSEQ=ACGTCCCCACGCGGGGCGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:18:18,0:164,2:0.0978:1,1:24.6:1.0:31.9:1.0:1.0:0.0:58.6:36.0:0.1:0.0:1.1 0/0:51:0:0,0:51,0:0.0:1,0:20.8:1.0:29.9:1.0:1.0:0.0:58.1:50.0:1.0:0.0:0.0 -7 47802771 . C T 76 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGCCTTGAGCTACCTGACT;RSEQ=TTCCCAGTTGGCCAGACACA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:1.0:0,0:19.0:1.0:29.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:2.7 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 50444040 . G A 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.13723;SOR=0.0;LSEQ=TGTAACCCCAGGTGCATCCC;RSEQ=AGGCCTGCCACCGAAGCCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:7,0:12,0:0.3684:0,0:31.7:1.0:28.4:1.0:1.0:0.0:60.0:6.0:0.3333:0.0:1.1 0/0:6:0:0,0:5,1:0.0:2,0:17.7:1.0:30.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 -7 50455179 . C A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.02674;SOR=0.0;LSEQ=CTGTACCCAGGTAAGCGCTG;RSEQ=TGCTCGGAGGCCAGCCTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:8:2,6:142,308:0.0175:2,2:20.3:1.0:31.6:1.0:1.0:1.38223:60.0:16.0:0.0177:0.0:1.1 0/0:284:0:0,0:89,193:0.0:2,0:24.0:1.0:32.2:1.0:1.0:0.0:60.0:564.0:0.993:0.0:0.1 -7 50739151 . G A 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.50877;SOR=0.0;LSEQ=GATCCAGCTAACTATCCCAC;RSEQ=TAGACCAGCAAATGATGCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:7,0:10,0:0.4118:0,0:23.3:1.0:31.4:1.0:1.0:0.0:60.0:14.0:0.4375:0.0:1.1 0/0:2:0:0,0:2,0:0.0:0,0:18.0:1.0:29.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -7 51451784 . C T 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCAGTCATCGTGGTCCCTC;RSEQ=CAACACTAAGGCTTTCCTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:41:10,31:12,32:0.4824:2,2:25.0:1.0:29.9:1.0:0.80832:1.16044:43.1:82.0:0.4881:0.0:1.5 0/0:29:0:0,0:13,16:0.0:2,0:24.1:1.0:30.1:1.0:1.0:0.0:38.8:58.0:1.0:0.0:0.6 -7 53854866 . G A 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=5e-05;SOR=0.0;LSEQ=TTAACTCAGTTAGGGATTTG;RSEQ=ATCCTGCTCCTAATCCACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:724:21:15,6:435,267:0.029:2,2:16.6:1.0:30.2:1.0:0.49506:1.53:60.0:42.0:0.0295:0.0:1.2 0/0:439:0:0,0:277,161:0.0:2,0:27.0:1.0:30.8:1.0:1.0:0.0:60.0:86.6:0.9977:0.0:0.1 -7 55210733 . G C 113 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGAGAGTGTTGAACCCCGT;RSEQ=AGGCATGAGAGCACAGTGTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:12,0:9,1:0.5455:2,0:20.2:1.0:31.7:1.0:0.45455:0.0:60.0:24.0:0.5455:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 55219290 . T C 137 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00106;SOR=0.03869;LSEQ=AAGTGAACATCAGCAGGGGC;RSEQ=GGGCGCGGTGGCTCACCCCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:35:29:0,29:0,6:0.8286:0,1:23.9:1.0:28.3:1.0:1.0:0.0:60.0:28.0:0.8235:0.0:1.8 0/1:7:1:0,1:0,6:0.1429:0,0:17.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.1429:0.0:1.0 -7 55219307 . C G 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.00769;SOR=0.0;LSEQ=GGCTGGGCGCGGTGGCTCAC;RSEQ=CCTATAATCCCAGCACTTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:20:0,20:0,3:0.8696:0,1:26.8:1.0:32.5:1.0:1.0:0.0:60.0:40.0:0.8696:0.0:2.0 0/0:3:0:0,0:0,3:0.0:0,0:16.7:1.0:32.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -7 55222593 . A C 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=4.0;MSILEN=1.0;SSF=0.00054;SOR=0.0;LSEQ=CAGATTTGTGTACATGAAAA;RSEQ=TTTTACATTCCGTATGGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:21:12,9:301,373:0.0301:2,2:20.3:1.0:30.9:1.0:0.27375:1.65:59.6:9.5:0.0278:0.0:1.2 0/0:308:0:0,0:135,172:0.0:2,0:23.2:1.0:29.9:1.0:1.0:0.0:60.0:75.75:1.0:0.0:0.2 -7 55228160 . T G 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00126;SOR=0.0;LSEQ=TTAAGAAGCAAATTAAAATC;RSEQ=TAAGATTCCTAACTGTGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:31:2,29:1,88:0.2583:1,2:22.2:1.0:32.2:1.0:0.16337:5.96:60.0:62.0:0.2583:0.0:1.7 0/0:28:0:0,0:2,26:0.0:2,0:22.9:1.0:30.9:1.0:1.0:0.0:60.0:56.0:1.0:0.0:0.5 -7 55805756 . G C 109 Bias;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.05346;SOR=0.14902;LSEQ=GTCATCCATGAGGAGGAGGG;RSEQ=GTGATGATGTCATTGCTGAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:10:10,0:57,54:0.0826:2,0:19.8:1.0:33.0:1.0:0.00215:0.0:38.3:20.0:0.0833:0.0:1.1 0/1:76:1:1,0:44,31:0.0132:2,0:7.0:0.0:33.0:0.0:1.0:0.0:40.0:2.0:0.0133:0.0:1.0 -7 55807008 . G A 142 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00048;SOR=0.11424;LSEQ=GCCGCTGCATGGGTCCCAGA;RSEQ=GCTGGACTGCGGCAGGTGCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:147:25:10,15:46,76:0.1701:2,2:31.9:1.0:30.6:1.0:0.82501:1.1:53.8:50.0:0.1712:0.0:1.1 0/1:88:2:1,1:39,47:0.0227:2,2:30.0:1.0:26.5:1.0:1.0:1.2:48.5:4.0:0.0227:0.0:1.0 -7 56430693 . C A 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.17241;SOR=0.0;LSEQ=TAAGAAGGATGGACACAGCC;RSEQ=CAACAAATGGGACAAGGACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:4,2:35,26:0.0896:2,2:34.3:1.0:30.5:1.0:1.0:1.48:60.0:12.0:0.0896:0.0:1.0 0/0:31:0:0,0:17,14:0.0:2,0:18.9:1.0:30.1:1.0:1.0:0.0:59.6:62.0:1.0:0.0:0.6 -7 56430843 . C T 91 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.05125;SOR=0.0;LSEQ=CCTGAGCAAGCGGTGGTACA;RSEQ=CCTGGGGCCCAATGAGACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:7:7,0:91,41:0.0504:2,0:32.3:1.0:32.6:1.0:0.10468:0.0:60.0:14.0:0.0511:0.0:1.1 0/0:78:0:0,0:50,28:0.0:2,0:21.1:1.0:30.5:1.0:1.0:0.0:58.7:38.0:1.0:0.0:0.3 -7 56431383 . C T 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03544;LSEQ=CATGGCCAGTGAGGACACAG;RSEQ=GAGTGACGAGGAGCCCATGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:59:35,24:11,4:0.7973:2,2:27.6:1.0:30.2:1.0:0.38342:1.8704:44.6:58.0:0.8169:0.0:1.1 0/1:34:4:2,2:21,9:0.1176:2,2:15.3:1.0:28.5:1.0:0.57993:2.27026:40.5:8.0:0.1176:0.0:1.0 -7 56431756 . G A 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0488;LSEQ=GGAGCCTTCAAAGCCCAGGA;RSEQ=TCTGGTCAGGGCAGCAGAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:42:30,12:8,9:0.7119:2,2:31.3:1.0:30.3:1.0:0.13177:2.76:46.5:41.0:0.7193:0.0:1.2 0/1:48:5:5,0:20,23:0.1042:2,0:26.4:1.0:29.6:1.0:0.05068:0.0:45.6:10.0:0.1042:0.0:1.0 -7 56439453 . T C 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.04216;LSEQ=GTGAGGCAAGGGGCTCACGC;RSEQ=GACCTCTCTCGGCGTGAGAG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:21:14,7:5,1:0.7778:2,2:33.0:1.0:30.3:1.0:0.63336:2.42585:26.3:42.0:0.7778:0.0:1.1 0/1:17:2:1,1:9,6:0.1176:2,2:15.5:1.0:27.5:1.0:1.0:1.46382:25.0:4.0:0.125:0.0:1.0 -7 56873374 . C T 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.08811;SOR=0.0;LSEQ=ACCTGGTAAGGGCCCACCTC;RSEQ=CACCATGGAGGAGGAGCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:4,2:28,14:0.125:2,2:6.8:1.0:29.7:1.0:1.0:1.0:34.3:12.0:0.125:0.0:1.3 0/0:25:0:0,0:12,13:0.0:2,0:31.4:1.0:29.8:1.0:1.0:0.0:43.7:50.0:1.0:0.0:0.1 -7 56873424 . G A 99 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05363;SOR=0.0;LSEQ=AGGGGAGTCCCTGCTGGACA;RSEQ=TGAGACAGAGAATGACCACG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:9:7,2:29,23:0.1475:2,2:25.8:1.0:31.4:1.0:0.2862:2.73:30.7:18.0:0.1475:0.0:1.0 0/0:25:0:0,0:11,14:0.0:2,0:25.1:1.0:31.6:1.0:1.0:0.0:47.1:50.0:1.0:0.0:0.1 -7 56874006 . C G 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00019;SOR=0.0;LSEQ=GAACGGCTGCATACAGGGAA;RSEQ=CTGGCTCAGCCTGGCCCAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:13:4,9:30,28:0.1831:2,2:29.5:1.0:32.9:1.0:0.22536:2.38166:37.2:26.0:0.1831:0.0:1.0 0/0:62:0:0,0:31,31:0.0:2,0:27.0:1.0:30.3:1.0:1.0:0.0:34.4:61.0:1.0:0.0:0.1 -7 56874457 . C T 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.09175;SOR=0.0;LSEQ=TTTGCACCTGTCATTCCTTC;RSEQ=TCCTTTACTCCTGCCGCCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:0,8:7,26:0.1951:2,0:27.6:1.0:31.0:1.0:0.31029:0.0:37.8:16.0:0.2:0.0:1.5 0/0:18:0:0,0:3,15:0.0:2,0:22.2:1.0:31.8:1.0:1.0:0.0:40.7:36.0:1.0:0.0:0.0 -7 61968966 . A C 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.04595;SOR=0.12372;LSEQ=TGTAAAGTCTGCAAGTGGAT;RSEQ=TATGGACCGCATTGAGGCCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:173:6:3,3:84,83:0.0347:2,2:19.7:1.0:31.5:1.0:1.0:1.01198:60.0:12.0:0.0353:0.0:1.5 0/0:227:1:1,0:110,116:0.0044:2,0:4.0:0.0:32.0:0.0:0.48899:0.0:60.0:2.0:0.0044:0.0:1.0 -7 61968975 . G A 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01504;SOR=0.0;LSEQ=TGCAAGTGGATATATGGACC;RSEQ=CATTGAGGCCTTCGTTGGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:5:3,2:79,78:0.0305:2,2:17.6:1.0:29.0:1.0:1.0:1.48:60.0:10.0:0.0314:0.0:1.2 0/0:213:0:0,0:107,105:0.0:2,0:24.8:1.0:30.7:1.0:1.0:0.0:59.6:69.667:0.9952:0.0:0.5 -7 61969240 . A C 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.00098;SOR=0.0;LSEQ=GATGTGTGCCTTCAACTCAC;RSEQ=GAGTTTAACCTTTCTTTTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:8:4,4:81,84:0.046:2,2:23.0:1.0:28.3:1.0:1.0:1.04:39.6:7.0:0.0405:0.0:3.4 0/0:235:0:0,0:119,114:0.0:2,0:25.2:1.0:30.5:1.0:1.0:0.0:50.8:115.5:0.9914:0.0:0.9 -7 61969422 . T C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00214;SOR=0.0;LSEQ=TCAACTCACAGAGTTGAACC;RSEQ=TGCTTTAGAGAGAGCAGATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:180:8:3,5:80,92:0.0444:2,2:30.4:1.0:30.9:1.0:0.72723:1.44635:52.8:16.0:0.0447:0.0:1.9 0/0:204:0:0,0:101,103:0.0:2,0:43.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 -7 61969454 . T C 110 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00262;SOR=0.16701;LSEQ=GAGCAGATTTGAAACACTCT;RSEQ=GCTGTGGCATTTTCAGGTGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:12:4,8:72,83:0.0719:2,2:20.6:1.0:30.9:1.0:0.54954:1.72942:45.8:24.0:0.0723:0.0:2.4 0/1:236:3:2,1:114,115:0.0127:2,2:23.7:1.0:30.3:1.0:1.0:2.01:46.0:6.0:0.0129:0.0:2.0 -7 61970454 . G C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.04809;SOR=0.13167;LSEQ=GTGGAACGTCCCTTTAGACA;RSEQ=AGCAGATTTGAAACACTCTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:6:0,6:21,62:0.0674:2,0:21.3:1.0:33.2:1.0:0.32899:0.0:51.3:12.0:0.0682:0.0:1.2 0/0:107:1:0,1:35,71:0.0093:2,0:33.0:0.0:33.0:0.0:1.0:0.0:25.0:2.0:0.0094:0.0:1.0 -7 63230653 . G A 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00388;SOR=0.0882;LSEQ=TGCTAGCCCCTGGCTTGTGG;RSEQ=CTTGGCCTCTGAGCTGTACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:13:7,6:43,41:0.134:2,2:28.4:1.0:27.8:1.0:1.0:1.11:60.0:5.5:0.1196:0.0:1.2 0/1:75:1:0,1:41,33:0.0133:2,0:2.0:0.0:29.0:0.0:0.45333:0.0:60.0:2.0:0.0141:0.0:1.0 -7 65970787 . T A 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCCTGCGGTCGTAGCACTCG;RSEQ=GGATGCCGGGGTCGTCCCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:823:40:23,17:426,357:0.0486:2,2:22.6:1.0:30.6:1.0:0.74686:1.13:60.0:39.0:0.0479:0.0:1.2 0/0:716:0:0,0:384,332:0.0:2,0:25.7:1.0:29.6:1.0:1.0:0.0:60.0:118.333:1.0:0.0:0.2 -7 66761667 . A T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.18182;SOR=0.0;LSEQ=AACTATCATTTATTACCTAT;RSEQ=TGTTATGTTAAAATTGAGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:0.625:0,0:18.2:1.0:30.8:1.0:1.0:0.0:46.6:10.0:0.625:0.0:1.0 0/0:3:0:0,0:2,1:0.0:2,0:13.7:1.0:29.0:1.0:1.0:0.0:55.3:6.0:1.0:0.0:0.0 -7 70859670 . C T 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.02797;SOR=0.0;LSEQ=GTGACCAGGATGGAGGAATT;RSEQ=GGGTGCACAGAGGTATCACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:1,5:0,33:0.1538:1,2:19.7:1.0:31.5:1.0:0.15385:0.0:60.0:12.0:0.1538:0.0:1.0 0/0:33:0:0,0:0,33:0.0:1,0:24.1:1.0:29.7:1.0:1.0:0.0:60.0:66.0:1.0:0.0:0.1 -7 74306708 . G GA 77 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.06061;SOR=0.0;LSEQ=GACCCTGCTGCGGGCGTTCG;RSEQ=AAAAAAAACGCAGTCCGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:5,1:2,0:0.75:0,2:12.8:1.0:29.9:1.0:1.0:0.0:29.7:12.0:0.75:0.375:0.3 0/0:4:0:0,0:1,3:0.0:2,0:28.5:1.0:31.3:1.0:1.0:0.0:25.0:8.0:1.0:0.0:0.0 -7 74312339 . CG TA 133 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=5e-05;SOR=0.09344;LSEQ=GGGGTAGAAGAAGAAAACTT;RSEQ=AAGGCTTAAGTAAGTTAACT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:48:26:22,4:14,8:0.5417:2,2:20.4:1.0:28.5:1.0:0.11066:3.07:23.3:25.0:0.5319:0.0625:0.9 0/1:31:3:3,0:26,2:0.0968:2,0:13.7:1.0:28.0:1.0:1.0:0.0:20.0:6.0:0.0968:0.0:1.7 -7 74712316 . C T 232 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02606;LSEQ=AGTTTCAACCCGAGTTAGGT;RSEQ=GGCAAACTCTCGAATCTTAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1398:221:109,112:534,643:0.1581:2,2:27.3:1.0:29.8:1.0:0.30325:1.17:29.6:109.5:0.1585:0.0:1.1 0/0:1232:6:2,4:549,677:0.0049:2,2:27.5:1.0:29.7:1.0:0.69712:1.62125:32.3:12.0:0.0049:0.0:1.5 -7 76641232 . G A 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGCCATCAAACCTATTGATC;RSEQ=GAAGTCAGTCCATCAGATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:87:85:64,21:2,0:0.977:0,2:24.2:1.0:29.5:1.0:1.0:0.0:36.0:84.0:0.9767:0.0:1.0 0/0:44:0:0,0:27,17:0.0:2,0:24.4:1.0:28.8:1.0:1.0:0.0:39.3:88.0:1.0:0.0:0.1 -7 81061460 . T C 81 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGCTCTTCCCCCCTTCGCT;RSEQ=GGCACTTCTCCTTCCTGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:5,5:0.375:2,2:20.7:1.0:31.7:1.0:1.0:1.0:60.0:12.0:0.4:0.0:1.5 0/0:1:0:0,0:0,1:0.0:0,0:41.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -7 81076550 . A G 99 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.38462;SOR=0.0;LSEQ=ATTTAATCAAACATTTTAAT;RSEQ=CTGTGAAAATTCTTAGGTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:0.6667:0,0:26.6:1.0:33.0:1.0:1.0:0.0:60.0:16.0:0.6667:0.0:1.8 0/0:1:0:0,0:1,0:0.0:0,0:27.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -7 81076607 . C T 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.02667;SOR=0.0;LSEQ=AAAACAAACTCAAAAATATA;RSEQ=GTGCCCTATGAACATAGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:9,0:9,0:0.5:0,0:17.6:1.0:30.0:1.0:1.0:0.0:60.0:18.0:0.5:0.0:1.7 0/0:7:0:0,0:7,0:0.0:0,0:28.4:1.0:31.9:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.0 -7 81336265 . C T 79 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGAAAGAAGTAGTGAGGA;RSEQ=TGAAAAAAGCCTATTGACAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:2,0:0.75:0,2:25.3:1.0:30.8:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 81336535 . C A 206 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.14271;LSEQ=AAAATGAATACATATTATAA;RSEQ=CTTAAGAGCAAAGTGGAAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:421:110:93,17:249,61:0.2613:2,2:25.7:1.0:30.4:1.0:0.39238:1.34:60.0:220.0:0.2619:0.0:1.0 0/1:292:14:11,3:217,60:0.0479:2,2:18.4:1.0:30.2:1.0:1.0:1.01:60.0:28.0:0.0486:0.0:1.0 -7 81340916 . C A 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00216;SOR=0.0;LSEQ=AACCAAATATATATTAAAAT;RSEQ=CAAGTATCAATGAATTCAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:12:1,11:16,163:0.0628:2,2:21.3:1.0:30.2:1.0:1.0:1.07934:60.0:24.0:0.0638:0.0:1.0 0/0:127:0:0,0:17,110:0.0:2,0:22.0:1.0:31.1:1.0:1.0:0.0:60.0:126.0:1.0:0.0:0.1 -7 81346925 . G A 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCATAATTGGCATATTAG;RSEQ=TTTTGTGATTTTGCCTCTAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:0,2:0.8:0,0:26.5:1.0:30.8:1.0:1.0:0.0:60.0:16.0:0.8:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 81388001 . C A 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCAATATTTAGGGAGAAGT;RSEQ=AGTTACCTTTGTTTTCATAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1085:58:41,17:600,425:0.0535:2,2:22.3:1.0:29.0:1.0:0.07451:1.71:60.0:116.0:0.0538:0.0:1.0 0/0:849:0:0,0:502,345:0.0:2,0:47.0:0.0:11.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:7.0 -7 91180083 . T C 97 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.30855;SOR=0.0;LSEQ=TCCATTCATCCTACTTCCTT;RSEQ=ACTAATTCTCCTTTCTATTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:0,8:1,20:0.2759:1,0:23.9:1.0:32.6:1.0:1.0:0.0:60.0:16.0:0.2759:0.0:1.0 0/0:5:0:0,0:0,5:0.0:0,0:30.0:1.0:27.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.4 -7 92404285 . A G 82 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.17683;SOR=0.0;LSEQ=TCTTGTGATCATATGTAAAG;RSEQ=TATCAAATGAGATCTGATAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:0,6:0,45:0.1154:1,0:19.8:1.0:32.0:1.0:1.0:0.0:60.0:12.0:0.1176:0.0:1.0 0/0:20:0:0,0:0,20:0.0:1,0:21.3:1.0:30.3:1.0:1.0:0.0:60.0:19.0:1.0:0.0:0.0 -7 101977547 . A G 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01753;SOR=0.0;LSEQ=ATGTTATAAATAATATCAAT;RSEQ=TAAAAGCTTATAGCATGGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:8,0:18,1:0.2963:1,0:27.1:1.0:32.5:1.0:1.0:0.0:31.4:16.0:0.2963:0.0:1.6 0/0:16:0:0,0:15,1:0.0:1,0:20.6:1.0:29.2:1.0:1.0:0.0:32.1:32.0:1.0:0.0:0.6 -7 103275947 . A C 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.04013;SOR=0.0;LSEQ=CATTATCATAAGAATAATGC;RSEQ=ACAAAACTCCTTCACCAGGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:0,7:0,53:0.1167:1,0:13.7:1.0:32.4:1.0:1.0:0.0:60.0:14.0:0.1273:0.0:1.1 0/0:39:0:0,0:3,36:0.0:2,0:23.9:1.0:30.9:1.0:1.0:0.0:60.0:78.0:1.0:0.0:0.0 -7 106522693 . G A 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01599;LSEQ=ATGAATAGACCTCTCAGCTC;RSEQ=TTTGAAAAGATTATAATTCC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:636:176:46,130:128,332:0.2767:2,2:23.7:1.0:30.5:1.0:0.6921:1.08945:60.0:57.667:0.2746:0.0:1.1 0/0:495:3:1,2:167,323:0.0061:2,2:4.0:1.0:25.7:1.0:1.0:1.03399:60.0:2.0:0.0041:0.0:1.0 -7 106524644 . CTG C 173 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GTTTATTCCTGTGCAGGCTA;RSEQ=TGTGGCAACCTTTGTTCTTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:44:21,23:319,323:0.064:2,2:29.3:1.0:31.8:1.0:0.87659:1.08153:60.0:88.0:0.0651:0.0029:0.8 0/0:593:0:0,0:289,304:0.0:2,0:25.6:1.0:30.1:1.0:1.0:0.0:60.0:83.714:1.0:0.0:0.2 -7 114270000 . G A 77 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=3.0;SSF=0.00303;SOR=0.0;LSEQ=CAACAACAGCAGCAACAACA;RSEQ=CAGCAGCAGCAGCAACAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:7:4,3:101,120:0.0303:2,2:34.1:1.0:27.7:1.0:0.7061:1.58:60.0:6.0:0.0275:0.0:1.4 0/0:294:0:0,0:135,142:0.0:2,0:24.7:1.0:31.2:1.0:1.0:0.0:60.0:26.7:0.9963:0.0:0.3 -7 114270077 . T G 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.11687;LSEQ=AGAGGTAGGATCCGGTTATC;RSEQ=CATTGATACATAACAGTTTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:48:11,37:12,43:0.466:2,2:22.4:1.0:31.4:1.0:1.0:1.06:60.0:96.0:0.4752:0.0:1.1 0/1:120:11:3,8:28,81:0.0917:2,2:15.6:1.0:30.8:1.0:1.0:1.08:60.0:22.0:0.0957:0.0:1.0 -7 116187106 . G A 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.08852;LSEQ=CTCTGCCTCCATCATTAATG;RSEQ=CCTTCTGCCTGAGTGTTTTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:25:6,19:6,10:0.6098:2,2:28.3:1.0:29.8:1.0:0.48495:1.86941:60.0:50.0:0.6098:0.0:1.0 0/1:34:4:1,3:9,21:0.1176:2,2:20.5:1.0:30.0:1.0:1.0:1.27668:60.0:8.0:0.1176:0.0:1.0 -7 116339672 . C T 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=4e-05;SOR=0.05451;LSEQ=TGTCCTGACTGTGTGGTGAG;RSEQ=GCCCTGGGAGCCAAAGTCCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:19:11,8:306,211:0.0354:2,2:24.0:1.0:28.2:1.0:1.0:1.05459:60.0:8.5:0.0323:0.0:1.4 0/0:501:1:0,1:280,220:0.002:2,0:1.0:0.0:25.0:0.0:0.44112:0.0:60.0:2.0:0.002:0.0:1.0 -7 116340531 . A AT 92 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.08669;SOR=0.0;LSEQ=AATTATATCTTTAAAATGTA;RSEQ=ATGGTAACTAAAAGAAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:0,9:0,6:0.6:0,0:21.1:1.0:29.1:1.0:1.0:0.0:60.0:18.0:0.6:0.2:0.4 0/0:4:0:0,0:0,4:0.0:0,0:20.0:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -7 116340582 . A C 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.22222;SOR=0.0;LSEQ=TTCAGATTTGCATGTTCGTG;RSEQ=CATTTCAGATTATATTAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:0.875:0,0:27.4:1.0:31.6:1.0:1.0:0.0:60.0:14.0:0.875:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:33.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -7 116397572 . A G 268 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04763;LSEQ=AATGGCCACGGGACAACACA;RSEQ=TACAGTACATTCTCCTATGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:336:176,160:339,333:0.3333:2,2:27.1:1.0:32.0:1.0:0.59302:1.08:60.0:111.0:0.3343:0.0:1.1 0/1:990:23:11,12:468,499:0.0232:2,2:23.8:1.0:30.8:1.0:1.0:1.02312:60.0:46.0:0.0235:0.0:1.2 -7 116403127 . A G 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00058;SOR=0.0;LSEQ=TGTCAACATCGCTCTAATTC;RSEQ=GAGATAATCTGTTGTACCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:12:9,3:253,184:0.0267:2,2:21.9:1.0:29.9:1.0:0.37428:2.18:60.0:24.0:0.0272:0.0:1.2 0/0:395:0:0,0:223,171:0.0:2,0:23.3:1.0:30.0:1.0:1.0:0.0:60.0:77.8:0.9974:0.0:0.1 -7 116411923 . C T 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02139;LSEQ=ATCTGGGCAGTGAATTAGTT;RSEQ=GCTACGATGCAAGAGTACAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:655:88:53,35:329,238:0.1344:2,2:27.7:1.0:30.2:1.0:0.72857:1.1:60.0:87.0:0.1343:0.0:1.0 0/0:606:2:0,2:348,256:0.0033:2,0:1.0:0.0:27.5:1.0:0.18085:0.0:60.0:4.0:0.0033:0.0:1.0 -7 116423161 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00628;SOR=0.0;LSEQ=TTTCCTCAGCCTGTTGAATT;RSEQ=GCAATGTCAATGTCAAGCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:9,0:19,0:0.3214:1,0:23.0:1.0:28.6:1.0:1.0:0.0:58.7:18.0:0.3214:0.0:1.8 0/0:21:0:0,0:18,3:0.0:2,0:26.0:1.0:31.4:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.0 -7 127153538 . C T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00223;SOR=0.05425;LSEQ=TAGCCCTGTTGTGCAAAGAA;RSEQ=AGTACCGCTGCTGCTGCCGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:4,5:0.5:2,2:33.0:1.0:29.9:1.0:0.63719:2.37:60.0:18.0:0.5:0.0:1.2 0/1:21:1:0,1:11,9:0.0476:2,0:47.0:0.0:27.0:0.0:0.47619:0.0:60.0:2.0:0.0476:0.0:1.0 -7 128296052 . T G 84 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATGGAGACCCCCCAGGTGTT;RSEQ=AGGCAGGGCTGGGGTGTCCC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1.0:0,2:31.2:1.0:32.8:1.0:1.0:0.0:28.3:12.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 128298370 . C G 134 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=6e-05;SOR=0.13085;LSEQ=CTGGGCCTGACATCATCTGG;RSEQ=TGGTAGAGGCAACTGGGTGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:18:1,17:34,46:0.1837:2,1:25.3:1.0:32.3:1.0:0.00243:12.33898:33.5:36.0:0.1837:0.0:1.1 0/1:141:4:0,4:67,70:0.0284:2,0:44.3:1.0:30.0:1.0:0.12151:0.0:37.0:8.0:0.0288:0.0:1.0 -7 128766971 . G A 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.03281;LSEQ=CGTACATCGTGGGCTTCTAC;RSEQ=GGGCCTTCTACTGTGACAGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:595:26:11,15:303,265:0.0437:2,2:20.4:1.0:30.3:1.0:0.31741:1.55799:60.0:52.0:0.0446:0.0:1.0 0/0:669:1:1,0:335,333:0.0015:2,0:1.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.0015:0.0:1.0 -7 128767250 . G A 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTCCATGGCCAACTCCTTC;RSEQ=TGGGCACGCGCTCCTACATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:182:77,105:357,377:0.1985:2,2:24.6:1.0:30.3:1.0:0.13581:1.29093:53.0:90.0:0.1985:0.0:1.1 0/0:810:0:0,0:384,423:0.0:2,0:27.0:1.0:30.2:1.0:1.0:0.0:54.1:114.286:0.9963:0.0:0.2 -7 128829066 . A G 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00024;SOR=0.0;LSEQ=GCTGCTGCTGCTGCTGGGGG;RSEQ=CCCGGGCCGGGGGGCGGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:9:4,5:39,39:0.1034:2,2:21.7:1.0:32.4:1.0:1.0:1.2468:60.0:18.0:0.1084:0.0:1.3 0/0:126:0:0,0:61,64:0.0:2,0:21.1:1.0:27.7:1.0:1.0:0.0:60.0:14.625:1.0:0.0:0.4 -7 128845223 . C T 192 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACATCGCGGCCTTCGGGGC;RSEQ=GTCACGGGCCTCTGCACGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:81:27,54:98,250:0.1888:2,2:27.1:1.0:30.4:1.0:0.4153:1.27:60.0:80.0:0.1891:0.0:1.4 0/0:379:0:0,0:124,255:0.0:2,0:23.6:1.0:29.4:1.0:1.0:0.0:60.0:74.8:1.0:0.0:0.4 -7 128846679 . GT G 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGCCCAGGGCTCACAGCTT;RSEQ=TTTTTTTGTTTGTTTTTGTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:0.4545:0,0:36.4:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.4545:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 128849078 . C A 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=AGACTCTCTCCTCCCCACTG;RSEQ=TGCTGCGGGACTGGGCTTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:607:70:50,20:352,183:0.1153:2,2:27.4:1.0:30.0:1.0:0.41954:1.3:60.0:69.0:0.1168:0.0:1.1 0/0:606:0:0,0:382,223:0.0:2,0:23.7:1.0:31.5:1.0:1.0:0.0:60.0:150.25:0.9983:0.0:0.1 -7 128850084 . T G 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01786;LSEQ=TGAGCCCAGGAGTTGGAAGC;RSEQ=GCAGTGGGTTGTGATCACGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:39:39,0:36,0:0.52:1,1:26.4:1.0:29.0:1.0:1.0:0.0:60.0:12.0:0.5:0.0:1.0 0/1:54:1:1,0:53,0:0.0185:1,0:8.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0185:0.0:1.0 -7 128850798 . G T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01047;SOR=0.0;LSEQ=GCTCCTTCCCTATCCCTTCT;RSEQ=CTCTCAGGTTGACTGGGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:499:6:3,3:309,184:0.012:2,2:9.5:1.0:29.3:1.0:0.67627:1.67745:60.0:12.0:0.0123:0.0:1.0 0/0:565:0:0,0:343,221:0.0:2,0:24.2:1.0:31.8:1.0:1.0:0.0:60.0:187.0:1.0:0.0:0.2 -7 128851674 . C G 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00147;SOR=0.0;LSEQ=GAGGCTGGGGGCTTCTGGGA;RSEQ=TGGAGTACAGGGGCTGTCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:11:5,6:71,201:0.0389:2,2:13.6:1.0:32.9:1.0:0.17202:2.35:60.0:22.0:0.04:0.0:1.0 0/0:229:0:0,0:67,161:0.0:2,0:23.8:1.0:30.8:1.0:1.0:0.0:60.0:24.333:0.9955:0.0:0.1 -7 128852381 . C T 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02664;LSEQ=AGCATGCTTCCCTAGGATCC;RSEQ=GTCTTCCAGAGAACCTGTGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:34:0,34:2,46:0.4146:1,1:24.3:1.0:30.1:1.0:0.50858:0.0:60.0:68.0:0.4198:0.0:1.1 0/1:55:1:0,1:2,52:0.0182:1,0:40.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0185:0.0:1.0 -7 135335822 . C T 157 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.10655;LSEQ=ATAATGCACTGGAATGAAAT;RSEQ=GTAGGGACCACATCAAAGGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:40:22,18:80,65:0.2162:2,2:30.2:1.0:29.6:1.0:1.0:1.00696:60.0:39.0:0.2155:0.0:1.2 0/1:176:5:2,3:89,82:0.0284:2,2:20.0:1.0:28.8:1.0:0.67364:1.62357:60.0:10.0:0.0289:0.0:1.2 -7 140434607 . G A 58 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.05896;SOR=0.0;LSEQ=AAAAAAAAAAGAAAAAAAAA;RSEQ=AAAAAAGAAAAAAAAAGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:5:3,2:1,81:0.0575:1,2:12.8:1.0:25.4:1.0:0.00037:92.94:60.0:4.0:0.0506:0.0:2.8 0/0:85:0:0,0:1,75:0.0:1,0:22.8:1.0:29.3:1.0:1.0:0.0:55.0:8.5:1.0:0.0:2.2 -7 140439319 . TG T 75 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATATAAACAAAAGCTCTTTG;RSEQ=GGGGGGGGGGTCTTCGATAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:0.7143:0,0:23.4:1.0:32.7:1.0:1.0:0.0:60.0:10.0:0.7143:0.1429:0.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 140453136 . A T 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCCACTCCATCGAGATTTC;RSEQ=CTGTAGCTAGACCAAAATCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:537:78:42,36:211,248:0.1453:2,2:26.2:1.0:30.5:1.0:0.22052:1.37:59.8:77.0:0.1442:0.0:1.1 0/0:640:0:0,0:303,337:0.0:2,0:25.8:1.0:29.5:1.0:1.0:0.0:60.0:63.0:1.0:0.0:0.1 -7 140482427 . T C 238 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07306;LSEQ=GAATGTGCAGGTTTGTTACA;RSEQ=ACGTATACATGTGCCATGGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:171:85,86:171,198:0.3167:2,2:26.5:1.0:32.2:1.0:0.51679:1.14:59.9:342.0:0.3184:0.0:1.1 0/1:459:15:4,11:193,251:0.0327:2,2:24.1:1.0:30.9:1.0:0.28923:2.11134:57.9:30.0:0.0328:0.0:1.1 -7 140483403 . C T 232 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.00391;LSEQ=TATTAAAAAAAAGGAAATCC;RSEQ=CAGATGGAAACATTTTCTAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:192:111,81:253,230:0.2844:2,2:26.7:1.0:30.6:1.0:0.23084:1.25:60.0:63.0:0.2868:0.0:2.1 0/0:646:1:0,1:337,307:0.0015:2,0:1.0:0.0:26.0:0.0:0.47752:0.0:60.0:2.0:0.0016:0.0:1.0 -7 140483605 . C T 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.09489;LSEQ=AAAGTTAATGTAAATAAAGC;RSEQ=GGGCATATTTCTCAAGACTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:560:157:72,85:187,216:0.2804:2,2:24.6:1.0:30.4:1.0:0.92507:1.02202:60.0:38.25:0.2777:0.0:1.1 0/1:534:19:8,11:242,271:0.0356:2,2:24.4:1.0:30.3:1.0:0.81589:1.22739:60.0:38.0:0.0359:0.0:1.1 -7 140486743 . T C 256 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08294;LSEQ=TGTAGTCTACGGCCATACCA;RSEQ=CCTGAACGTGTCCGATCTTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1040:275:117,158:355,409:0.2644:2,2:25.2:1.0:31.6:1.0:0.2895:1.17195:60.0:136.5:0.2679:0.0:1.1 0/1:1348:39:19,20:635,670:0.0289:2,2:24.5:1.0:30.8:1.0:1.0:1.0:60.0:38.0:0.0287:0.0:1.1 -7 140487494 . C T 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00792;LSEQ=AATTATTTTATTAATTAAAA;RSEQ=AATACATCTTATAACTATTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:111:51,60:293,365:0.1442:2,2:24.9:1.0:29.6:1.0:0.83663:1.06:60.0:110.0:0.1444:0.0:1.2 0/0:752:1:0,1:349,401:0.0013:2,0:1.0:0.0:22.0:0.0:1.0:0.0:60.0:2.0:0.0013:0.0:1.0 -7 140488156 . T G 237 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.11033;LSEQ=AAAAAGTTATAAATAATTAT;RSEQ=TCTCTATTATAGGCATTTTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:172:84,88:196,196:0.305:2,2:25.5:1.0:32.0:1.0:0.85492:1.04756:60.0:56.333:0.3056:0.0:1.1 0/1:564:26:13,13:271,266:0.0461:2,2:21.2:1.0:30.9:1.0:1.0:1.01877:60.0:52.0:0.0468:0.0:1.0 -7 140489173 . A G 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GAGGGATTGAATGGCCCCAA;RSEQ=TATCTCTGAATAGTCTCTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1276:62:27,35:508,706:0.0486:2,2:25.6:1.0:31.9:1.0:0.79335:1.07:60.0:61.0:0.0485:0.0:1.1 0/0:1334:0:0,0:604,727:0.0:2,0:26.0:1.0:29.8:1.0:1.0:0.0:60.0:82.188:0.9985:0.0:0.1 -7 140492039 . T C 247 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.06146;LSEQ=ATACTGTAAAAACCACATTA;RSEQ=TGACAGTCCTGCCTCTATGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:680:206:92,114:202,272:0.3029:2,2:25.8:1.0:32.2:1.0:0.67372:1.09:60.0:205.0:0.3042:0.0:1.1 0/1:616:16:5,11:272,328:0.026:2,2:26.3:1.0:32.3:1.0:0.31556:1.8227:60.0:32.0:0.0263:0.0:1.1 -7 140494413 . A C 205 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTAGCAGTAATGACTTTTAA;RSEQ=AGTATTAATTTAAAAATCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:86:46,40:286,276:0.1325:2,2:25.0:1.0:32.0:1.0:0.72844:1.11:60.0:172.0:0.1337:0.0:1.1 0/0:763:0:0,0:378,384:0.0:2,0:23.7:1.0:29.9:1.0:1.0:0.0:60.0:761.0:0.9987:0.0:0.1 -7 140496563 . T C 252 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.07216;LSEQ=GTGATCATAATCTGATGTCA;RSEQ=TGAATATCTCAGCCATGTCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:228:86,142:222,278:0.3128:2,2:24.8:1.0:32.2:1.0:0.10566:1.31805:60.0:227.0:0.314:0.0:1.1 0/1:630:20:12,8:266,344:0.0317:2,2:24.6:1.0:31.0:1.0:0.17237:1.94:60.0:40.0:0.0318:0.0:1.1 -7 140496901 . TC T 255 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGTCGGCAAACTGGCTTTC;RSEQ=CCAATGATACCTGTACCTAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:288:142,146:288,301:0.3265:2,2:26.6:1.0:31.3:1.0:0.9427:1.02:60.0:287.0:0.3269:0.0385:0.1 0/0:848:0:0,0:415,432:0.0:2,0:25.1:1.0:31.0:1.0:1.0:0.0:60.0:120.0:0.9988:0.0:0.1 -7 140497586 . A T 234 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.08833;LSEQ=GGACCTGCCATTAGAAAGGC;RSEQ=TCATGGTCTACAGAATCTGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:205:103,102:209,219:0.3239:2,2:25.6:1.0:30.6:1.0:0.79889:1.06:60.0:40.0:0.319:0.0:1.1 0/1:543:22:14,8:278,242:0.0405:2,2:22.2:1.0:29.1:1.0:0.3894:1.52:60.0:21.0:0.0393:0.0:1.1 -7 140507901 . C T 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCCTTTCTTGGTTATTACA;RSEQ=CTAAAAATATTCATATACCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:27:6,21:71,239:0.0799:2,2:23.1:1.0:30.6:1.0:1.0:1.03966:60.0:54.0:0.0811:0.0:1.1 0/0:338:0:0,0:92,245:0.0:2,0:23.0:1.0:30.8:1.0:1.0:0.0:60.0:66.4:0.997:0.0:0.1 -7 148505788 . T C 75 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATAAAGATATGCATAGTATA;RSEQ=TGTCAAGTAAAACCATGTTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:36.8:1.0:32.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 148505864 . G A 80 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGGAAAACGCTCCACGAGT;RSEQ=AGCATGCAGCATGCGGCATG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:0.7:0,0:24.1:1.0:28.7:1.0:1.0:0.0:60.0:14.0:0.7:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -7 151168756 . G A 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02179;LSEQ=AGTTTTTAAATGTATGTTAT;RSEQ=TTGCCAGCTGGAAAAATGTA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:93:19,74:92,322:0.1831:2,2:23.5:1.0:30.6:1.0:0.78221:1.11256:60.0:186.0:0.1849:0.0:1.2 0/0:413:2:1,1:98,312:0.0048:2,2:22.0:1.0:26.5:1.0:0.42329:3.17:60.0:4.0:0.0049:0.0:1.0 -7 151828793 . T C 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=CTGGAACGCTGTTCCCACCA;RSEQ=GTTGGGTTACGTTGTAGGTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:15:9,6:30,18:0.2381:2,2:25.1:1.0:30.3:1.0:1.0:1.10924:60.0:30.0:0.2459:0.0:1.1 0/0:54:0:0,0:27,27:0.0:2,0:24.2:1.0:29.0:1.0:1.0:0.0:60.0:108.0:1.0:0.0:0.1 -7 151836397 . T C 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00736;SOR=0.0;LSEQ=GTCGACCTGAAACTCCCCTC;RSEQ=GTGTTCCTATCCACACCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:8:3,5:66,146:0.0362:2,2:24.9:1.0:26.1:1.0:0.7081:1.33:60.0:7.0:0.0323:0.0:1.0 0/0:215:0:0,0:60,154:0.0:2,0:21.6:1.0:29.9:1.0:1.0:0.0:60.0:41.8:0.9952:0.0:0.1 -7 151859061 . T TAGAAATG 103 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=2.0;MSILEN=7.0;SSF=0.01309;SOR=0.0;LSEQ=AAACATGGGTTCCAGAGAGG;RSEQ=AGAAATGACAAAATAAAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:10:10,0:63,1:0.1333:1,0:22.5:1.0:31.1:1.0:1.0:0.0:60.0:20.0:0.137:0.0533:0.0 0/0:43:0:0,0:41,2:0.0:1,0:20.6:1.0:29.9:1.0:1.0:0.0:60.0:20.5:1.0:0.0:0.0 -7 151874581 . G C 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTGAAAATTCACCACCTA;RSEQ=TGGATGGTTCAGAGTCCTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:114:60,54:282,254:0.1746:2,2:23.6:1.0:31.8:1.0:1.0:1.0:60.0:56.0:0.1742:0.0:1.1 0/0:670:0:0,0:357,312:0.0:2,0:24.8:1.0:31.5:1.0:1.0:0.0:60.0:166.25:0.9985:0.0:0.1 -7 151875047 . G A 192 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.02849;LSEQ=TGCTGAGGAGGCACAAGGAA;RSEQ=CGCTCTTGACTCGGCATGGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:86:28,58:158,211:0.189:2,2:29.0:1.0:30.0:1.0:0.0889:1.54965:60.0:172.0:0.1982:0.0:1.2 0/0:456:3:0,3:190,262:0.0066:2,0:13.0:1.0:15.3:1.0:0.26877:0.0:60.0:0.0:0.0:0.0:6.3 -7 151891255 . G A 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00684;LSEQ=GTAACAAGATTAAAAGACTA;RSEQ=TAGGGTCCTGGTATGGGGAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:121:68,53:327,265:0.1685:2,2:26.6:1.0:30.3:1.0:0.92011:1.04:60.0:39.333:0.1676:0.0:1.1 0/0:724:1:1,0:391,329:0.0014:2,0:1.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0014:0.0:1.0 -7 151932694 . C CAAAGAGGAAGGTAAGA 85 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=22;MSI=4.0;MSILEN=1.0;SSF=0.03848;SOR=0.0;LSEQ=GGCATAGAAAGATAAGGAGT;RSEQ=AAAGAGGAAGGTAAGAAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:7:7,0:34,1:0.1667:1,0:26.1:1.0:30.6:1.0:1.0:0.0:35.6:14.0:0.1795:0.0952:2.7 0/0:26:0:0,0:19,6:0.0:2,0:24.6:1.0:29.7:1.0:1.0:0.0:45.2:11.5:0.9583:0.0:0.7 -7 151932748 . A G 76 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.08358;SOR=0.0;LSEQ=AAGTAAATATACAAGAAAAC;RSEQ=TAACCAGAGGCTCAAAAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:6:5,1:72,11:0.0465:2,2:26.8:1.0:29.5:1.0:1.0:1.30479:37.0:12.0:0.0674:0.0:2.8 0/0:89:0:0,0:49,9:0.0:2,0:25.0:1.0:30.3:1.0:1.0:0.0:58.9:116.0:1.0:0.0:0.1 -7 151935768 . G T 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02322;SOR=0.12401;LSEQ=ATCAGACAGAAATGATATAT;RSEQ=AATGTAAATGCAATTTTATT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:660:9:6,3:422,229:0.0136:2,2:35.0:1.0:28.2:1.0:1.0:1.09:35.4:18.0:0.0138:0.0:1.1 0/0:585:1:0,1:376,208:0.0017:2,0:1.0:0.0:27.0:0.0:0.35726:0.0:50.0:2.0:0.0017:0.0:1.0 -7 151944908 . C A 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0188;SOR=0.0;LSEQ=AGAAAAAGTTGCCATCCACA;RSEQ=CAAAGCTACACATATACCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:7:7,0:159,5:0.0409:1,0:26.7:1.0:31.0:1.0:1.0:0.0:26.1:14.0:0.0412:0.0:1.4 0/0:136:0:0,0:133,3:0.0:1,0:23.3:1.0:31.3:1.0:1.0:0.0:36.8:272.0:1.0:0.0:0.3 -7 151945252 . C T 107 Bias SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00051;SOR=0.0;LSEQ=ATAACTTTATAGATTTGCCT;RSEQ=CTTGGTATGAAACATCTTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:12:0,12:204,268:0.0248:2,0:26.1:1.0:30.1:1.0:0.00175:0.0:37.0:24.0:0.0253:0.0:3.0 0/0:444:0:0,0:180,263:0.0:2,0:23.1:1.0:30.8:1.0:1.0:0.0:42.3:39.273:0.9977:0.0:0.2 -7 151945313 . A G 98 Bias SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0083;SOR=0.0;LSEQ=AGTCATTTCAGAGTCCATCA;RSEQ=TCCAGTAGAAAGTTCAGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:8:0,8:254,268:0.0151:2,0:21.5:1.0:32.9:1.0:0.00777:0.0:35.0:16.0:0.0153:0.0:2.5 0/0:473:0:0,0:237,235:0.0:2,0:23.6:1.0:29.8:1.0:1.0:0.0:45.8:77.667:0.9979:0.0:0.1 -7 151946985 . C G 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATAAGAAGACTATCTGTGT;RSEQ=AAGACTTTCTGAGGGATGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:24:13,11:333,312:0.0358:2,2:26.0:1.0:31.0:1.0:0.83824:1.11:60.0:48.0:0.036:0.0:1.0 0/0:797:0:0,0:414,383:0.0:2,0:25.8:1.0:31.2:1.0:1.0:0.0:59.9:131.833:1.0:0.0:0.1 -7 151948998 . TA T 96 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.0009;SOR=0.0;LSEQ=CATTACAAAAACAAAAAATT;RSEQ=AAAAAAAATCATTCTCAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:11:4,7:248,85:0.032:2,2:16.5:1.0:28.0:1.0:0.01006:5.07646:60.0:22.0:0.0324:0.0145:0.7 0/0:339:0:0,0:248,90:0.0:2,0:23.0:1.0:28.1:1.0:1.0:0.0:60.0:111.667:0.997:0.0:0.1 -7 151949735 . T C 262 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTTGGTAACAATTGTCACA;RSEQ=ATCAGGCAATTGTGGTGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:829:308:129,179:206,314:0.3715:2,2:24.9:1.0:31.8:1.0:0.55796:1.1:60.0:76.0:0.3712:0.0:1.1 0/0:835:0:0,0:354,478:0.0:2,0:24.0:1.0:28.4:1.0:1.0:0.0:60.0:137.667:0.9964:0.0:0.1 -7 151962294 . G A 97 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00081;SOR=0.0;LSEQ=CACAGTTTGCATCTTCCTTC;RSEQ=CTATAATTAACAGTGAAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:209:9:1,8:40,160:0.0431:2,2:13.7:1.0:30.9:1.0:1.0:1.99454:31.4:18.0:0.0446:0.0:2.4 0/0:247:0:0,0:61,186:0.0:2,0:9.0:0.0:14.0:0.0:1.0:0.0:40.0:0.0:0.0:0.0:1.0 -7 151962296 . T C 77 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01862;SOR=0.0;LSEQ=CAGTTTGCATCTTCCTTCGC;RSEQ=ATAATTAACAGTGAAACAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:5:0,5:41,153:0.0251:2,0:8.4:1.0:33.4:1.0:0.58553:0.0:25.8:10.0:0.0255:0.0:3.0 0/0:240:0:0,0:59,181:0.0:2,0:22.8:1.0:28.8:1.0:1.0:0.0:41.5:119.0:1.0:0.0:0.2 -7 151971015 . G A 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01126;SOR=0.0;LSEQ=AAAGGAATATTCAAATATAA;RSEQ=CTGGGAAGGTATAAAAAACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:9:0,9:13,109:0.0687:2,0:29.8:1.0:30.3:1.0:0.59774:0.0:42.8:18.0:0.0709:0.0:2.1 0/0:98:0:0,0:18,80:0.0:2,0:28.4:1.0:32.3:1.0:1.0:0.0:43.6:97.0:1.0:0.0:0.9 -7 151971078 . TAAAC T 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.17278;SOR=0.0;LSEQ=AAATTGAACCTGCAAAATAT;RSEQ=AAAGGATTCGTTAAAAATAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:5:0,5:0,45:0.1:1,0:28.0:1.0:31.7:1.0:1.0:0.0:45.2:10.0:0.102:0.02:2.0 0/0:23:0:0,0:3,20:0.0:2,0:24.0:1.0:30.1:1.0:1.0:0.0:46.4:46.0:1.0:0.0:1.7 -7 152357777 . A AT 171 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTATTTATATAAAGGTTGT;RSEQ=TTTTTTACCATGCACAGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:51:28,23:420,214:0.0745:2,2:26.9:1.0:30.3:1.0:0.12526:1.61102:60.0:102.0:0.0752:0.0117:0.2 0/0:782:0:0,0:483,294:0.0:2,0:25.4:1.0:28.5:1.0:1.0:0.0:60.0:76.7:0.9935:0.0:0.1 -7 153622478 . CG AA 159 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAGGGAGATCATCCCGCAT;RSEQ=TGGAGGGTCCCTGAGGTTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:469:41:17,24:186,241:0.0874:2,2:27.5:1.0:29.8:1.0:0.8697:1.08941:60.0:40.0:0.0895:0.0064:2.1 0/0:371:0:0,0:160,210:0.0:2,0:22.9:1.0:29.5:1.0:1.0:0.0:60.0:51.857:1.0:0.0:1.0 -7 153622749 . G T 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0001;SOR=0.0;LSEQ=GGAGATCATCCCACATGGTG;RSEQ=AGGGTCCCTGAGGTTCTGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:14:5,9:96,123:0.0601:2,2:22.8:1.0:27.2:1.0:0.59265:1.40288:60.0:6.0:0.0522:0.0:1.6 0/0:230:0:0,0:112,118:0.0:2,0:23.6:1.0:30.6:1.0:1.0:0.0:60.0:56.5:1.0:0.0:0.5 -7 154594008 . G T 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00061;SOR=0.0;LSEQ=CCTCAAAGGCAATTTCAAAA;RSEQ=AAAATCCAAGAACATCCGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:153:12:8,4:91,50:0.0784:2,2:29.5:1.0:30.1:1.0:1.0:1.1:60.0:24.0:0.0789:0.0:1.5 0/0:128:0:0,0:70,58:0.0:2,0:27.1:1.0:31.2:1.0:1.0:0.0:60.0:256.0:1.0:0.0:0.3 -7 154594127 . C T 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGGATGGAAATGGCGTCT;RSEQ=TTGGAGGTTCAGGTGCAATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:182:35:12,23:60,87:0.1923:2,2:27.7:1.0:29.3:1.0:0.56563:1.31985:57.8:16.5:0.1864:0.0:1.2 0/0:149:0:0,0:71,78:0.0:2,0:28.6:1.0:31.2:1.0:1.0:0.0:59.9:73.5:1.0:0.0:0.2 -7 155835626 . C G 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01213;SOR=0.0;LSEQ=GCTGAACAATGATATTTTGC;RSEQ=CAAAGCCTTCTTTCTGTGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:9:0,9:78,200:0.0314:2,0:22.8:1.0:32.4:1.0:0.1197:0.0:59.4:18.0:0.0321:0.0:1.1 0/0:209:0:0,0:69,139:0.0:2,0:26.6:1.0:30.7:1.0:1.0:0.0:60.0:68.333:1.0:0.0:0.3 -7 157745089 . C G 123 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=CAAGGGTGGGTAGTGTGCAT;RSEQ=CCTGAGACGGGGTGGGGGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:15:15,0:7,0:0.6818:0,1:19.1:1.0:31.5:1.0:1.0:0.0:60.0:14.0:0.6667:0.0:2.3 0/0:15:0:0,0:7,0:0.0:0,0:28.6:1.0:29.1:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.1 -7 158451102 . T C 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.01229;SOR=0.0;LSEQ=GGATCTTGCAGCGATCATCC;RSEQ=AAAAGCGAAAAAAGAAAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:9:0,9:2,48:0.1525:1,0:18.8:1.0:33.3:1.0:1.0:0.0:60.0:18.0:0.1579:0.0:1.1 0/0:36:0:0,0:2,34:0.0:2,0:25.1:1.0:27.7:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 -7 158628009 . A G 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04443;LSEQ=CCTTCTTACCCTGCCCCCTT;RSEQ=TCTTGTATGCAATAAATATC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:20:10,10:6,11:0.5405:2,2:22.2:1.0:31.3:1.0:0.50847:1.8:60.0:40.0:0.5556:0.0:1.1 0/1:42:2:1,1:16,24:0.0476:2,2:5.0:0.0:28.0:1.0:1.0:1.49:60.0:4.0:0.0476:0.0:0.5 -8 2387994 . T C 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TCATCCTATTTGCTGAAGAG;RSEQ=GTGATTAATGCTCTCTCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:49:20,29:57,70:0.2784:2,2:23.9:1.0:29.6:1.0:0.73494:1.1796:60.0:48.0:0.2775:0.0:2.1 0/0:278:0:0,0:123,155:0.0:2,0:24.1:1.0:29.6:1.0:1.0:0.0:60.0:277.0:1.0:0.0:0.7 -8 3489674 . G A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.11554;LSEQ=CATTCCTGCTAGAGAAAAGG;RSEQ=ATTTATTTTAAAAAATTCAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:27:23,4:60,21:0.2477:2,2:20.4:1.0:29.7:1.0:0.29868:2.0:60.0:54.0:0.25:0.0:2.0 0/1:165:6:5,1:109,50:0.0364:2,2:22.0:1.0:29.5:1.0:0.6672:2.28:60.0:12.0:0.0368:0.0:2.0 -8 3489677 . T C 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.09725;LSEQ=TCCTGCTAGAGAAAAGGGAT;RSEQ=TATTTTAAAAAATTCAAAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:30:25,5:60,21:0.2703:2,2:19.4:1.0:31.3:1.0:0.44943:1.74:60.0:60.0:0.2778:0.0:2.0 0/1:174:6:5,1:113,55:0.0345:2,2:25.0:1.0:31.8:1.0:0.66549:2.42:60.0:12.0:0.0347:0.0:2.0 -8 3489842 . C T 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0476;LSEQ=CTCATAGGTAAAGCCCCGTT;RSEQ=GCCTTCTTGGACCTTCAGCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:43:15,28:24,54:0.3554:2,2:24.6:1.0:28.6:1.0:0.68711:1.2:60.0:9.75:0.3362:0.0:1.3 0/1:158:4:0,4:54,100:0.0253:2,0:10.3:1.0:28.0:1.0:0.29986:0.0:60.0:8.0:0.026:0.0:1.5 -8 3489935 . G T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00439;SOR=0.07133;LSEQ=AAAGACTACCCCTGGGATAT;RSEQ=TCCATGTTATAGGAGATTAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:0.3913:1,0:15.3:1.0:29.8:1.0:1.0:0.0:60.0:18.0:0.4091:0.0:1.3 0/1:24:1:0,1:2,21:0.0417:2,0:6.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0417:0.0:2.0 -8 4166516 . A T 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATGTTGAACTAATTCCTAA;RSEQ=ACTAGGTGAGAAAATGCATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:16:4,12:17,62:0.1684:2,2:26.1:1.0:28.9:1.0:0.74778:1.21:60.0:32.0:0.1702:0.0:3.7 0/0:114:0:0,0:31,83:0.0:2,0:23.2:1.0:29.0:1.0:1.0:0.0:60.0:56.0:1.0:0.0:2.1 -8 11096119 . A G 57 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00855;SOR=0.0;LSEQ=AAAAAGATGGAAAAGCAAAA;RSEQ=GGCGAGGAGGGGTGGGATTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:5:2,3:211,172:0.0129:2,2:17.2:1.0:24.8:1.0:0.66142:1.8372:60.0:10.0:0.0132:0.0:2.0 0/0:616:0:0,0:317,298:0.0:2,0:26.3:1.0:30.3:1.0:1.0:0.0:60.0:152.75:1.0:0.0:0.7 -8 11587234 . G T 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06944;LSEQ=CATGATGCAAAATTGTGTTC;RSEQ=CTGAAAAGCAGGGGTTAAGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:56:25,31:47,64:0.3353:2,2:24.0:1.0:30.2:1.0:0.86877:1.1:60.0:27.0:0.3313:0.0:1.1 0/1:327:11:5,6:144,171:0.0336:2,2:24.7:1.0:29.2:1.0:1.0:1.01049:60.0:22.0:0.0342:0.0:1.0 -8 14166825 . G A 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CTTTTTAAGGATGGTATTGA;RSEQ=ACTATGTGGGAAGATGAGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:162:95,67:167,126:0.356:2,2:23.3:1.0:29.8:1.0:0.76681:1.07:57.9:53.0:0.3549:0.0:1.1 0/0:713:0:0,0:410,302:0.0:2,0:22.7:1.0:31.2:1.0:1.0:0.0:58.9:46.467:0.9986:0.0:0.1 -8 18917162 . A C 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.0;MSILEN=1.0;SSF=0.06846;SOR=0.0;LSEQ=GTTAGTCAAGAAATTTAAAA;RSEQ=ATTTCTACGTCTGTAAAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:0,21:0.1923:1,0:17.6:1.0:32.6:1.0:1.0:0.0:60.0:10.0:0.1923:0.0:1.2 0/0:18:0:0,0:0,18:0.0:1,0:20.4:1.0:30.3:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.2 -8 22438859 . C G 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00152;SOR=0.0;LSEQ=TCCCTTCTCCAGCTGGGCCA;RSEQ=GGTCTGAGCATGCCAGCTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:5,1:9,2:0.3529:2,2:28.0:1.0:32.5:1.0:1.0:1.1:60.0:12.0:0.3529:0.0:1.0 0/0:28:0:0,0:14,13:0.0:2,0:14.9:1.0:29.6:1.0:1.0:0.0:60.0:54.0:0.9643:0.0:0.2 -8 23548530 . T C 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCCTCCATGGCTGCCGGCT;RSEQ=CTGGAGAGCCCCAGGCTGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1168:111:62,49:542,513:0.095:2,2:24.8:1.0:30.8:1.0:0.42452:1.2:60.0:36.0:0.0938:0.0:1.1 0/0:1629:0:0,0:833,794:0.0:2,0:25.4:1.0:29.2:1.0:1.0:0.0:60.0:59.259:0.9988:0.0:0.2 -8 28157994 . C G 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00027;SOR=0.12258;LSEQ=TTAAAAAGAAGAGGTGGAAC;RSEQ=ATCCCAAAATGTCCCTCACT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:14:8,6:16,13:0.3256:2,2:25.7:1.0:30.4:1.0:1.0:1.08:60.0:28.0:0.3256:0.0:1.1 0/1:73:4:3,1:40,29:0.0548:2,2:25.5:1.0:29.8:1.0:0.63911:2.15:60.0:8.0:0.0548:0.0:1.0 -8 29496868 . T C 129 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TGATGGTTAAGAACATAGTC;RSEQ=ATGGGGTCAGACATGCATGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:17:2,15:11,117:0.1172:2,2:16.1:1.0:31.6:1.0:0.65101:1.41:60.0:34.0:0.1172:0.0:1.0 0/0:129:0:0,0:13,116:0.0:2,0:23.1:1.0:28.7:1.0:1.0:0.0:60.0:258.0:1.0:0.0:0.0 -8 38279065 . G A 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00254;SOR=0.0;LSEQ=CCAGATCCCGGGCATGCATT;RSEQ=CAATGGCCAGGGGGAGAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:13:13,0:30,0:0.3023:1,1:18.2:1.0:28.1:1.0:1.0:0.0:60.0:26.0:0.3023:0.0:1.2 0/0:23:0:0,0:22,1:0.0:1,0:24.3:1.0:32.8:1.0:1.0:0.0:60.0:46.0:1.0:0.0:0.0 -8 38283759 . C T 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGATGCTCCAGGTGGCATAA;RSEQ=GGACCTGAGGGGAAATGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:45:13,32:165,272:0.093:2,2:25.9:1.0:30.4:1.0:0.26071:1.49203:60.0:90.0:0.0943:0.0:1.0 0/0:648:0:0,0:228,420:0.0:2,0:23.9:1.0:29.7:1.0:1.0:0.0:60.0:91.571:1.0:0.0:0.2 -8 38285934 . C A 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00266;SOR=0.0;LSEQ=TCATCATCATCATCATCATC;RSEQ=TCCGAGGAGGGGAGAGCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:578:7:2,5:208,362:0.0121:2,2:32.7:1.0:27.6:1.0:1.0:1.43561:59.3:6.0:0.0106:0.0:1.6 0/0:766:0:0,0:313,451:0.0:2,0:22.6:1.0:30.6:1.0:1.0:0.0:60.0:75.4:1.0:0.0:0.2 -8 38287486 . G A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.04578;SOR=0.1198;LSEQ=GCTGCAGCCACCACGGGGCC;RSEQ=GGAAGGGAAGCCAAGGGGCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:6:4,2:102,202:0.0194:2,2:23.0:1.0:27.3:1.0:0.18583:3.94:60.0:5.0:0.0162:0.0:1.2 0/0:425:1:1,0:157,267:0.0024:2,0:1.0:0.0:25.0:0.0:0.37176:0.0:60.0:2.0:0.0024:0.0:1.0 -8 38297776 . G C 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCGGGGGCCCTCTGCAGA;RSEQ=GTTTTTTTATTACGTATTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:29:18,11:167,90:0.1003:2,2:25.8:1.0:31.7:1.0:0.8381:1.13344:60.0:58.0:0.101:0.0:1.0 0/0:507:0:0,0:302,202:0.0:2,0:26.2:1.0:30.9:1.0:1.0:0.0:60.0:83.0:0.994:0.0:0.2 -8 43092933 . C G 76 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00536;SOR=0.10259;LSEQ=GTACTTTGATATTTTATGTA;RSEQ=AGTATATAATAAGTATTTGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:5:3,2:88,85:0.0281:2,2:14.8:1.0:33.0:1.0:1.0:1.45:37.0:10.0:0.0284:0.0:5.0 0/0:679:2:1,1:341,322:0.0029:2,2:24.0:1.0:30.0:1.0:1.0:1.05894:24.0:4.0:0.003:0.0:5.0 -8 43092940 . T G 186 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GATATTTTATGTACAGTATA;RSEQ=AATAAGTATTTGGTGTACTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:61:33,28:27,32:0.4519:2,2:10.6:1.0:31.5:1.0:0.46531:1.39:44.3:122.0:0.4552:0.0:4.4 0/0:530:0:0,0:135,133:0.0:2,0:13.0:1.0:29.0:1.0:1.0:0.0:39.6:267.0:0.8266:0.0:4.6 -8 43094789 . A ATATTATATACTGTACATAAAATATCAAAGTACCCCAAGGTATATATTCAATACTGTACAAAAAATATCAAAGTACCCAAAGCATG 90 NM4 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=1e-05;SOR=0.0;LSEQ=TACCAAAGTACACAAAATAT;RSEQ=TATTATATACTGTACATAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:8:3,5:29,29:0.1159:2,2:28.1:1.0:30.3:1.0:0.70964:1.65399:33.6:16.0:0.1159:0.1159:5.3 0/0:224:0:0,0:115,106:0.0:2,0:11.6:1.0:28.6:1.0:1.0:0.0:33.8:109.5:0.9865:0.0:6.4 -8 54049868 . T A 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=2e-05;SOR=0.03761;LSEQ=TGTCTGATTTCAGAAGCCTT;RSEQ=TCCTGTAAATGCTGGGTGGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:14:7,7:8,18:0.35:2,2:20.3:1.0:28.8:1.0:0.31011:2.2:60.0:28.0:0.35:0.0:1.9 0/1:52:1:0,1:18,33:0.0192:2,0:27.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0196:0.0:3.0 -8 54445600 . T C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03778;SOR=0.0;LSEQ=GAGAGGCCGAGGCAGGAGGA;RSEQ=TGCCTGAGCTCAGGAGTTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:0,7:0,17:0.2917:1,0:33.0:1.0:33.0:1.0:1.0:0.0:60.0:14.0:0.2917:0.0:1.0 0/0:13:0:0,0:0,13:0.0:1,0:29.8:1.0:29.2:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.1 -8 55367460 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.12284;SOR=0.19734;LSEQ=AAAGCAAGGCTTGCAGGAAG;RSEQ=CACTCCGGATGTTTGCTGCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:5:2,3:307,161:0.0106:2,2:31.0:1.0:30.8:1.0:0.34674:2.85341:60.0:10.0:0.0109:0.0:1.2 0/0:476:1:0,1:309,164:0.0021:2,0:1.0:0.0:24.0:0.0:0.3481:0.0:60.0:2.0:0.0021:0.0:1.0 -8 55371474 . C A 68 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0628;SOR=0.0;LSEQ=GGGCTCGGACTCAGGAGTCC;RSEQ=AGATCTCCCTCTTTAACTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:5:5,0:37,1:0.1163:1,0:20.2:1.0:29.4:1.0:1.0:0.0:60.0:10.0:0.1163:0.0:2.0 0/0:34:0:0,0:34,0:0.0:1,0:21.1:1.0:30.7:1.0:1.0:0.0:60.0:33.0:1.0:0.0:1.4 -8 55374948 . A G 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTGGTAGTTTTAAATTACCA;RSEQ=AACATTTGGTATCCTTAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:26:20,6:238,75:0.0767:2,2:23.3:1.0:29.5:1.0:1.0:1.05:60.0:7.667:0.0695:0.0:1.1 0/0:330:0:0,0:251,79:0.0:2,0:18.6:1.0:29.5:1.0:1.0:0.0:59.8:81.5:1.0:0.0:0.3 -8 59337497 . G C 203 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAACACCTTTCTCTCTGTT;RSEQ=ATGTCAGTCAGAATATCAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:287:85:40,45:70,105:0.2962:2,2:22.8:1.0:31.7:1.0:0.2878:1.33:60.0:84.0:0.3281:0.0:1.2 0/0:278:0:0,0:73,107:0.0:2,0:23.7:1.0:31.0:1.0:1.0:0.0:60.0:89.0:1.0:0.0:0.1 -8 59339186 . A G 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTCAGCTCCTCTTATCAAC;RSEQ=GTGGGTTTTCTGCCTCCACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:109:63,46:234,218:0.194:2,2:26.4:1.0:29.5:1.0:0.28558:1.28:60.0:26.25:0.1909:0.0:1.2 0/0:592:0:0,0:313,277:0.0:2,0:25.8:1.0:30.1:1.0:1.0:0.0:60.0:72.75:1.0:0.0:0.2 -8 59790418 . A T 68 MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=13.0;MSILEN=1.0;SSF=0.25654;SOR=0.0;LSEQ=TTGGAGAAAGCCTACATATT;RSEQ=AAAAAAAAAAAAGCCTCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,6:0.3571:0,0:22.6:1.0:29.4:1.0:1.0:0.0:60.0:10.0:0.3571:0.0:1.0 0/0:5:0:0,0:0,2:0.0:0,0:11.0:1.0:26.5:1.0:1.0:0.0:60.0:4.0:0.4:0.0:0.5 -8 62115431 . AGAT A 141 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=GAAGAAGATGATGATGATGA;RSEQ=GATGATGATGATTTTAATGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:23:11,12:37,34:0.2447:2,2:28.9:1.0:31.2:1.0:0.81207:1.18499:58.2:22.0:0.2418:0.0213:0.3 0/0:107:0:0,0:51,56:0.0:2,0:22.6:1.0:31.0:1.0:1.0:0.0:59.9:34.667:1.0:0.0:0.2 -8 70250559 . G A 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05839;SOR=0.0;LSEQ=GGGAGAGCTCAGTGGGAATC;RSEQ=ATGGAGAGGAGGACTCAGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:0,5:2,24:0.1613:2,0:30.0:1.0:30.6:1.0:1.0:0.0:60.0:10.0:0.1613:0.0:1.2 0/0:25:0:0,0:0,25:0.0:1,0:21.8:1.0:31.8:1.0:1.0:0.0:60.0:50.0:1.0:0.0:0.3 -8 74885277 . G A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03794;SOR=0.0;LSEQ=GGCTGAAACAGCTAAATAAA;RSEQ=TTCACCTTCTACTGTTTTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:6:0,6:1,43:0.12:1,0:15.8:1.0:31.2:1.0:1.0:0.0:60.0:12.0:0.1224:0.0:1.0 0/0:36:0:0,0:2,34:0.0:2,0:21.4:1.0:31.5:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.0 -8 77776848 . TA T 113 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.23529;SOR=0.0;LSEQ=AAAAATAAAAAATAAAAAAA;RSEQ=AAAAAAAAATAAGACTTTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:0,13:0,3:0.8125:0,1:30.6:1.0:30.7:1.0:1.0:0.0:60.0:26.0:0.8125:0.0:0.0 0/0:1:0:0,0:0,1:0.0:0,0:23.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -8 90949097 . T C 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02586;SOR=0.0;LSEQ=GCTATAGCCAATAAACCCAA;RSEQ=TGAGAGGTGCTTAAGTAATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:10:10,0:31,0:0.2439:1,0:24.9:1.0:32.7:1.0:1.0:0.0:60.0:20.0:0.25:0.0:1.1 0/0:17:0:0,0:16,1:0.0:1,0:21.9:1.0:30.9:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.0 -8 90955253 . T G 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06218;SOR=0.0;LSEQ=ATTAGGATGTAAACTGAATT;RSEQ=CTTAGGTCTCACCTTTTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:11,0:0.4211:0,0:20.1:1.0:31.3:1.0:1.0:0.0:60.0:16.0:0.4211:0.0:2.9 0/0:7:0:0,0:7,0:0.0:0,0:15.7:1.0:30.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 -8 90958341 . C A 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAAACATTTCAAACACTGAC;RSEQ=TCTTGTGATACAGTTGAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:31:24,7:246,114:0.0791:2,2:26.3:1.0:28.9:1.0:0.41782:1.59:60.0:9.333:0.0727:0.0:1.0 0/0:346:0:0,0:236,110:0.0:2,0:24.3:1.0:30.4:1.0:1.0:0.0:60.0:114.333:1.0:0.0:0.2 -8 90993395 . C T 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.2451;SOR=0.0;LSEQ=GAGGAATCGAAGAAATGTAA;RSEQ=TTCCCATGAAGTCCCTCAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:0.4667:0,0:23.1:1.0:31.7:1.0:1.0:0.0:60.0:14.0:0.4667:0.0:1.0 0/0:3:0:0,0:3,0:0.0:0,0:17.0:1.0:29.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -8 91434037 . C A 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0435;SOR=0.0;LSEQ=GCCAGAAAGACTATGGGATC;RSEQ=CAGGAGTTTGTTCTAGCATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:7:1,6:12,115:0.0522:2,2:24.1:1.0:30.0:1.0:0.51895:1.59:60.0:14.0:0.0534:0.0:2.0 0/0:90:0:0,0:6,84:0.0:2,0:22.3:1.0:31.1:1.0:1.0:0.0:60.0:180.0:1.0:0.0:0.6 -8 98382341 . C G 104 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAAAGGTCCTGCTACGTCCA;RSEQ=TGTTGTCTTAGATCTAACGA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:0.9091:0,0:35.5:1.0:31.6:1.0:1.0:0.0:60.0:20.0:0.9091:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -8 109144095 . CCCAGGGGACGC T 81 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01494;SOR=0.0;LSEQ=CATGTACAAACTTGTCTTTG;RSEQ=CCAGTCTCAAGGTCGTCGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:2,5:10,36:0.1296:2,2:19.4:1.0:28.9:1.0:0.64996:1.43:60.0:14.0:0.1346:0.0556:0.6 0/0:45:0:0,0:13,32:0.0:2,0:21.4:1.0:32.1:1.0:1.0:0.0:60.0:90.0:1.0:0.0:0.2 -8 109735723 . T C 165 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.134;LSEQ=ATGAATATGTTTCACTAAAA;RSEQ=AGGCAAGGCAGCAATCATTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:34:28,6:92,23:0.2282:2,2:21.6:1.0:32.6:1.0:1.0:1.17:59.9:68.0:0.2313:0.0:1.0 0/1:132:5:3,2:96,31:0.0379:2,2:25.6:1.0:30.8:1.0:0.59839:2.05154:60.0:10.0:0.0382:0.0:1.0 -8 117352461 . G A 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06769;SOR=0.0;LSEQ=GCGCTCTTGGCATGGATAGG;RSEQ=CCCTCGGTGTTCACATCCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:4,5:7,7:0.3913:2,2:34.0:1.0:30.1:1.0:1.0:1.23792:60.0:18.0:0.4091:0.0:1.0 0/0:8:0:0,0:3,5:0.0:2,0:22.3:1.0:31.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.3 -8 117864369 . C G 205 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATGAAGAGAAAACATAGGT;RSEQ=ATACAGTTTTGAACAGTATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:774:93:16,77:161,520:0.1202:2,2:25.9:1.0:31.4:1.0:0.18888:1.48935:60.0:45.5:0.1185:0.0:1.1 0/0:480:0:0,0:121,358:0.0:2,0:24.8:1.0:31.5:1.0:1.0:0.0:60.0:94.8:0.9979:0.0:0.2 -8 117870036 . TATA T 106 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACAGCTGAAACTTTCCCGT;RSEQ=ATGTGTTTCATCAAGAAAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:1.0:0,2:27.5:1.0:32.0:1.0:1.0:0.0:60.0:20.0:1.0:0.2:0.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -8 117870196 . A C 84 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGAGCCACGGCACTCCAGC;RSEQ=TGGATAACACAGCAGAGACC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:5,4:1,1:0.8182:2,2:27.6:1.0:26.6:1.0:1.0:1.22:60.0:3.5:0.7778:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -8 117874055 . A AT 92 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.01364;SOR=0.0;LSEQ=TATTGCAGACCAAGTCAACA;RSEQ=TTTTTTTTAAAAGAAGACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:896:9:5,4:634,253:0.01:2,2:19.2:1.0:29.1:1.0:0.2869:2.00308:60.0:18.0:0.0102:0.0045:0.4 0/0:597:0:0,0:400,196:0.0:2,0:24.1:1.0:29.4:1.0:1.0:0.0:60.0:58.6:0.9983:0.0:0.1 -8 120428447 . G A 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00191;SOR=0.03302;LSEQ=GAGCCCTGGGTCCTGGCCTC;RSEQ=GAACTCCACCCAGCCCCTCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:6,2:1,0:0.8889:0,2:19.5:1.0:29.8:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.1 0/1:12:2:1,1:6,4:0.1667:2,2:22.5:1.0:30.0:1.0:1.0:1.4491:60.0:4.0:0.1667:0.0:1.0 -8 125875063 . G A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAGACCCAAATACTAGTAAT;RSEQ=AGATGCCAAAGTGAACATGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:60:11,49:39,190:0.2076:2,2:21.0:1.0:30.3:1.0:0.84836:1.09:60.0:120.0:0.2091:0.0:1.1 0/0:121:0:0,0:22,99:0.0:2,0:22.7:1.0:30.8:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.0 -8 128747953 . G T 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGGCGCGCAGTGCGTTCTC;RSEQ=GTGTGGAGGGCAGCTGTTCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:43:40,3:237,46:0.1319:2,2:28.0:1.0:31.3:1.0:0.16671:2.58:60.0:42.0:0.1304:0.0:1.0 0/0:181:0:0,0:142,39:0.0:2,0:24.2:1.0:29.4:1.0:1.0:0.0:60.0:44.25:1.0:0.0:0.1 -8 128751201 . G A 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03363;LSEQ=TCCTCGACGGAGTCCTCCCC;RSEQ=CAGGGCAGCCCCGAGCCCCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:108:37,71:221,374:0.1534:2,2:26.9:1.0:29.1:1.0:0.58932:1.13367:60.0:53.0:0.153:0.0:1.1 0/0:496:3:3,0:185,308:0.006:2,0:13.7:1.0:22.3:1.0:0.05391:0.0:60.0:2.0:0.0041:0.0:1.0 -8 139766211 . G C 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.06667;SOR=0.0;LSEQ=ATACTCCGTGGTGAAAACAG;RSEQ=AGAGGCTGCACAGTCAGATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:1.0:0,1:21.9:1.0:31.7:1.0:1.0:0.0:60.0:13.0:1.0:0.0:1.6 0/0:1:0:0,0:1,0:0.0:0,0:15.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -8 143164976 . G A 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGTGGGCTCTCCCAGGGTCA;RSEQ=TGTGGAATACAACAAGAGAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:2,5:3,3:0.5385:2,2:37.6:1.0:31.9:1.0:0.59207:2.32357:60.0:14.0:0.5385:0.0:1.1 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -8 143445733 . A G 78 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.30769;SOR=0.0;LSEQ=TTTTTAAGATGCACAGAGAA;RSEQ=TACAGATATAGATGTGTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:2,3:15,16:0.1389:2,2:25.2:1.0:34.0:1.0:1.0:1.39312:60.0:10.0:0.1389:0.0:1.4 0/0:16:0:0,0:6,10:0.0:2,0:25.8:1.0:28.3:1.0:1.0:0.0:60.0:15.0:1.0:0.0:0.0 -8 144227728 . A G 78 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCAGCCCCCTCCCCTTTCCA;RSEQ=CTGCGGAACCTGGAGCAACT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1.0:0,2:25.0:1.0:34.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -8 144343986 . TGCACCTGCCACGCCTGTCTCCGGCAGCCCCTGCCCGCACCCGCACCCCTGCACCTGCCACGCCCGTCTCCGGCAGCACCTGCCACGCCCGTCTCCGGCA T 63 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=2.0;MSILEN=3.0;SSF=0.15237;SOR=0.0;LSEQ=CCTGCCCCCACCCGCACCCC;RSEQ=GCACCTGCCACGCCCGTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:2,3:19,21:0.1111:2,2:15.4:1.0:27.5:1.0:1.0:1.34807:51.6:10.0:0.1316:0.1111:1.4 0/0:25:0:0,0:13,12:0.0:2,0:25.2:1.0:29.5:1.0:1.0:0.0:58.5:11.5:1.0:0.0:1.1 -8 144344100 . C T 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0095;SOR=0.0;LSEQ=CCGGCAGCACCTGCCACGCC;RSEQ=GTCTCCGGCAGCACCTGCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:5,5:3,5:0.5556:2,2:12.8:1.0:28.2:1.0:0.66406:1.62:55.4:4.0:0.5714:0.0:1.6 0/0:8:0:0,0:4,4:0.0:2,0:19.3:1.0:26.8:1.0:1.0:0.0:46.3:7.0:1.0:0.0:0.5 -8 144351029 . C CTGCTGCTGCTGCTGT 113 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.0;MSILEN=3.0;SSF=0.02718;SOR=0.0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGTTTGAGTCTTGCTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:5,9:1,0:0.5:0,2:25.1:1.0:29.8:1.0:0.4:0.0:57.8:28.0:0.5185:0.3214:0.9 0/0:7:0:0,0:2,0:0.0:0,0:3.0:0.0:28.5:1.0:1.0:0.0:60.0:4.0:0.2857:0.0:0.0 -8 144999077 . G A 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.15284;SOR=0.0;LSEQ=CTCCGCCTTGCCGCGCCGCC;RSEQ=CGCCTCGCGCTCCGCCTCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:2,3:8,7:0.25:2,2:33.6:1.0:28.4:1.0:1.0:1.66859:60.0:10.0:0.25:0.0:1.0 0/0:9:0:0,0:5,4:0.0:2,0:29.6:1.0:29.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.2 -8 145736791 . C T 279 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGACAACCCCAGCTCTACC;RSEQ=GACATCCCCCAATGCAGTGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1275:575:381,194:442,253:0.451:2,2:24.5:1.0:30.5:1.0:0.34507:1.12:60.0:51.273:0.4498:0.0:1.1 0/0:472:0:0,0:291,181:0.0:2,0:23.2:1.0:29.5:1.0:1.0:0.0:60.0:66.429:1.0:0.0:0.2 -8 145738441 . G A 277 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CAGGTGCAGGCTGGGAACAC;RSEQ=CGCTGTACCAGCCTCTTCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1342:675:264,411:250,415:0.503:2,2:24.8:1.0:29.5:1.0:0.57469:1.07:60.0:47.214:0.5015:0.0:1.2 0/0:492:0:0,0:201,291:0.0:2,0:23.5:1.0:30.3:1.0:1.0:0.0:60.0:36.846:1.0:0.0:0.2 -8 145739175 . C G 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01004;SOR=0.0;LSEQ=GGGGAGTGAGGAGGGGTCGG;RSEQ=GTGGGGAGTGAGGAGGGGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:20:16,4:13,193:0.0826:2,2:5.6:1.0:27.4:1.0:0.0:56.63:54.3:5.667:0.0885:0.0:3.9 0/0:71:0:0,0:2,43:0.0:1,0:16.9:1.0:26.6:1.0:1.0:0.0:59.2:5.429:0.6129:0.0141:0.6 -8 145743081 . G A 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.18843;SOR=0.0;LSEQ=CCTCGGCCCCTGGGCAGCCC;RSEQ=CACCTGGCTCGGTCGCCGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:6:5,1:129,188:0.0186:2,2:9.7:1.0:27.7:1.0:0.08551:7.25:60.0:12.0:0.0189:0.0:1.3 0/0:131:0:0,0:53,78:0.0:2,0:16.5:1.0:30.9:1.0:1.0:0.0:60.0:130.0:1.0:0.0:0.3 -8 145745182 . T C 74 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGCCTGCCAGGCCCTGCCC;RSEQ=TGCTGCCACGCGAACTCTTC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1.0:0,2:29.8:1.0:32.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 1011564 . A AT 82 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=TGCGCCATCACACCAGGCTA;RSEQ=TTTTTTTTTTTTGTATTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:1,0:0.75:0,0:21.5:1.0:32.0:1.0:1.0:0.0:53.3:12.0:0.75:0.0:1.2 0/0:2:0:0,0:1,0:0.0:0,0:32.0:1.0:31.0:1.0:1.0:0.0:60.0:2.0:0.5:0.0:5.0 -9 2039827 . G A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGCAGCAACAGCAGCC;RSEQ=CAGCAGCAGCCGCCGCAACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:11,13:9,13:0.5217:2,2:22.8:1.0:30.9:1.0:0.77386:1.22:60.0:48.0:0.5333:0.0:1.0 0/0:37:0:0,0:17,20:0.0:2,0:25.5:1.0:31.1:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.4 -9 3776612 . C G 121 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00492;SOR=0.06465;LSEQ=TTTAGGGCTTTAGGGCAAGG;RSEQ=TCACTCACTCGCATTCATTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:11,2:11,0:0.5417:0,2:27.7:1.0:32.8:1.0:0.48188:0.0:60.0:26.0:0.5417:0.0:1.4 0/1:15:1:1,0:14,0:0.0667:1,0:41.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0667:0.0:2.0 -9 4804901 . A G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.03509;SOR=0.0;LSEQ=CAAGTCTGTCACCAGGTCAT;RSEQ=GGGTGGCTGGGAAGCACCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:1,5:0.4545:2,0:37.4:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.4545:0.0:1.2 0/0:10:0:0,0:2,8:0.0:2,0:24.0:1.0:31.8:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 -9 5072798 . T C 75 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.2908;SOR=0.0;LSEQ=AGAATTACAGGGTTTGAAAA;RSEQ=TACCGGATTAAAAAAATTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:0.2083:1,0:21.2:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.2083:0.0:1.0 0/0:10:0:0,0:2,8:0.0:2,0:25.6:1.0:30.4:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.4 -9 5126742 . G T 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAATCAACGCCCCTCCTTTA;RSEQ=GGATCTAGCTCTTCGAGTGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:57:30,27:242,247:0.1044:2,2:30.3:1.0:30.5:1.0:0.67672:1.13:60.0:56.0:0.1047:0.0:1.2 0/0:670:0:0,0:355,315:0.0:2,0:26.1:1.0:30.7:1.0:1.0:0.0:60.0:50.538:1.0:0.0:0.2 -9 5456083 . G A 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGTGAAGCAGTCTTCTTTTC;RSEQ=TGTTTTCCATAATTAGGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:30:18,12:232,156:0.0716:2,2:24.7:1.0:30.8:1.0:1.0:1.01:60.0:60.0:0.0719:0.0:1.1 0/0:529:0:0,0:321,207:0.0:2,0:24.9:1.0:30.0:1.0:1.0:0.0:60.0:131.0:0.9981:0.0:0.1 -9 5456775 . C G 71 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GGATGTCTACATGAAACCAA;RSEQ=TCTCCCTGGTTGTAAGGACT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:1.0:0,0:15.4:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 5467807 . C T 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01762;SOR=0.0;LSEQ=CTTTTTCCCCAGACCACTTC;RSEQ=CATGAAATTAATATACTATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:5:1,4:215,164:0.013:2,2:11.4:1.0:27.2:1.0:0.1727:5.22396:60.0:10.0:0.0132:0.0:1.2 0/0:476:0:0,0:276,200:0.0:2,0:25.0:1.0:30.2:1.0:1.0:0.0:60.0:118.0:1.0:0.0:0.2 -9 8331548 . C T 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01759;LSEQ=ACAATGAAGAAACACCACCA;RSEQ=TTATCACTGCTTTATTCACA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:41:32,9:350,180:0.0718:2,2:22.3:1.0:31.2:1.0:0.12444:1.83:59.8:82.0:0.0722:0.0:1.1 0/0:738:1:0,1:455,282:0.0014:2,0:1.0:0.0:25.0:0.0:0.38347:0.0:60.0:2.0:0.0014:0.0:1.0 -9 8331574 . A AAACTTACCATTCTTGAACTGT 236 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.10866;LSEQ=ACTGCTTTATTCACAAATGG;RSEQ=AACTTACCTGCAATGGACTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:215:128,87:288,195:0.2894:2,2:30.7:1.0:30.5:1.0:1.0:1.00384:59.8:430.0:0.2925:0.0175:0.1 0/1:1087:46:28,18:444,374:0.0423:2,2:31.9:1.0:29.7:1.0:0.44757:1.31:59.8:92.0:0.0428:0.0:0.0 -9 8332033 . A G 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=TCCACATAGTTCCCCCATTA;RSEQ=CAAATGTTTCTGAGACCCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:0.75:0,0:17.3:1.0:31.0:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.0 0/0:2:0:0,0:1,1:0.0:2,0:8.0:0.0:31.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -9 8376899 . T C 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.1032;SOR=0.0;LSEQ=AATTACTGCTCTGATGCCAA;RSEQ=ATAAACCACATTTTTCAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:0,7:0.5333:0,0:25.9:1.0:33.5:1.0:1.0:0.0:60.0:16.0:0.5333:0.0:1.0 0/0:4:0:0,0:0,4:0.0:0,0:11.0:1.0:29.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 -9 8449993 . C A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=1.0;SSF=0.02019;SOR=0.0;LSEQ=ACCCAGTTCGGGTTGCTTTT;RSEQ=CCCCCTGGCCTAATTGTTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:1,9:0,8:0.5556:0,2:21.3:1.0:29.5:1.0:1.0:0.0:60.0:20.0:0.5556:0.0:1.1 0/0:7:0:0,0:0,7:0.0:0,0:20.1:1.0:31.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.0 -9 8454265 . G T 102 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTTTATGAGACACCTCACAT;RSEQ=TCTGCTCTGTAAACACATCA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:1.0:0,0:19.9:1.0:29.7:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 8504387 . G A 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.01803;SOR=0.0;LSEQ=CAGCCTATATGATGTCCCTG;RSEQ=CTCAATGGTAATTCGTTGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:5:4,1:153,287:0.0112:2,2:12.8:1.0:28.4:1.0:0.05459:7.47:60.0:10.0:0.0113:0.0:1.0 0/0:546:0:0,0:221,324:0.0:2,0:26.0:1.0:31.2:1.0:1.0:0.0:60.0:59.556:0.9981:0.0:0.1 -9 16181267 . G C 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.1071;LSEQ=TTTGGAGGGCAAGAGTTTCA;RSEQ=AAAGACACTAGAAAGGCAGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:23,0:26,0:0.4694:1,1:24.2:1.0:32.5:1.0:1.0:0.0:60.0:46.0:0.4694:0.0:1.1 0/1:59:5:5,0:54,0:0.0847:1,0:26.6:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.0877:0.0:1.0 -9 16206756 . T G 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02041;LSEQ=CATTTCCACAACTGGTTATT;RSEQ=CAGTTGACAATTAACAGGAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:108:53,55:73,75:0.4202:2,2:26.7:1.0:31.6:1.0:1.0:1.01002:60.0:26.0:0.416:0.0:2.2 0/1:345:5:3,2:175,164:0.0145:2,2:10.6:1.0:30.4:1.0:1.0:1.4:60.0:10.0:0.0147:0.0:2.2 -9 20777008 . A G 75 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCGACTGTATTTCAAAACA;RSEQ=TGAACACATATATTCCTAAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:13.2:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 21993964 . T C 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAGGGAGGTCCAGGTTCAA;RSEQ=GGTACTGCGAGAACCACATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:39:39,0:39,0:0.5:1,1:21.8:1.0:31.2:1.0:1.0:0.0:60.0:12.0:0.48:0.0:1.2 0/0:65:0:0,0:65,0:0.0:1,0:18.3:1.0:30.3:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.1 -9 22012051 . T C 233 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10719;LSEQ=CTAGTAATAATATTTTTATA;RSEQ=TCTAGTTGGTGAAATTGTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:166:73,93:142,169:0.348:2,2:24.0:1.0:31.6:1.0:0.77219:1.07026:60.0:82.0:0.346:0.0:1.1 0/1:611:33:15,18:264,313:0.054:2,2:24.9:1.0:31.9:1.0:1.0:1.01212:60.0:66.0:0.0545:0.0:1.1 -9 33676618 . C T 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTGATATCTCCTTTTGTTT;RSEQ=TGCTAACGATCTCTTTGATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:438:28:11,17:164,245:0.0639:2,2:27.8:1.0:30.2:1.0:1.0:1.03443:53.6:56.0:0.0648:0.0:1.0 0/0:543:0:0,0:244,298:0.0:2,0:18.0:0.0:18.0:0.0:1.0:0.0:49.0:0.0:0.0:0.0:1.0 -9 36881930 . T TG 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.08325;SOR=0.0;LSEQ=TAGAGGTCACCCAGGCTGTT;RSEQ=GGGGGGGGATGTCCCCCCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:5:4,1:159,20:0.027:2,2:20.0:1.0:30.0:1.0:0.45831:1.97811:60.0:10.0:0.0278:0.0:0.0 0/0:126:0:0,0:103,23:0.0:2,0:23.6:1.0:29.7:1.0:1.0:0.0:60.0:62.0:1.0:0.0:0.1 -9 36930460 . T G 94 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTTGAACTGCTGAGCTCAA;RSEQ=TGATCCACCCACCCCAACCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:1.0:0,0:25.3:1.0:31.6:1.0:1.0:0.0:58.8:16.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 37015450 . G A 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAATAATTTTGATATTAGTT;RSEQ=TATGTTGAAATAACAATTTT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1.0:0,0:21.5:1.0:29.4:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 66458606 . G A 69 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.04396;SOR=0.0;LSEQ=CGGGAGCTCCGGAGCTCCGG;RSEQ=GCTTCCACCACATCTGCCGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:2,3:0,2:0.5556:0,2:23.2:1.0:30.0:1.0:1.0:0.0:40.4:10.0:0.7143:0.0:6.4 0/0:6:0:0,0:2,3:0.0:2,0:36.6:1.0:29.6:1.0:1.0:0.0:40.6:10.0:1.0:0.0:1.0 -9 66833834 . TG CT 75 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00028;SOR=0.0;LSEQ=AGCATTCTCAGAAACTTGTT;RSEQ=TGATGTGTGTACTCAACTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:3,2:8,1:0.2778:2,2:29.0:1.0:32.6:1.0:0.50549:4.64888:41.8:10.0:0.2778:0.0:4.8 0/0:66:0:0,0:27,17:0.0:2,0:23.9:1.0:29.4:1.0:1.0:0.0:36.2:88.0:0.6667:0.0:4.8 -9 68413168 . G T 75 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03571;SOR=0.0;LSEQ=GAACGCGGGGGGGAAAGGGA;RSEQ=GAGAGCTCCGCCTGGGCTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:1.0:0,2:23.3:1.0:29.3:1.0:1.0:0.0:44.8:12.0:1.0:0.0:5.2 0/0:2:0:0,0:1,1:0.0:2,0:18.5:1.0:29.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -9 68414161 . CAGGAAGCGACGTTCCCCACGCCCCGGTGTAGGTGAACCCG TGGGAAGCGCAATTCCCGGGCGAACTCA 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.23077;SOR=0.0;LSEQ=AGCGCAGGGCATGTGGGGTG;RSEQ=ATAGAGGAGGGAGGAGGGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:1,4:2,3:0.4545:2,2:25.8:1.0:28.0:1.0:1.0:2.41422:52.6:10.0:0.4545:0.4545:3.8 0/0:4:0:0,0:1,2:0.0:2,0:8.3:1.0:28.7:1.0:1.0:0.0:53.3:6.0:0.75:0.0:5.3 -9 68414170 . A C 72 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CATGTGGGGTGCAGGAAGCG;RSEQ=CGTTCCCCACGCCCCGGTGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:1,1:0.7143:2,2:26.4:1.0:31.2:1.0:1.0:3.1622:40.4:10.0:0.7143:0.0:5.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 75155834 . G A 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00049;SOR=0.0;LSEQ=GGATGTTGTGAAGCTTCAGT;RSEQ=AGTTAATACAGATATAATGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:14,1:14,0:0.5172:1,1:22.8:1.0:27.7:1.0:1.0:0.0:60.0:14.0:0.5:0.0:1.0 0/0:15:0:0,0:15,0:0.0:1,0:23.1:1.0:31.1:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 -9 75794996 . A T 70 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAGAAACTTTCCTTTAACA;RSEQ=GATAATGCATTATGAAATAT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:0.8333:0,0:20.4:1.0:30.4:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 80409358 . G T 59 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02892;SOR=0.0;LSEQ=TAATAAAATGATAATCCATT;RSEQ=CCTGTCTAAAGAACACTTAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:5:3,2:356,121:0.0104:2,2:23.8:1.0:25.6:1.0:0.60575:1.9584:60.0:4.0:0.0085:0.0:1.8 0/0:496:0:0,0:325,168:0.0:2,0:24.4:1.0:31.4:1.0:1.0:0.0:60.0:48.3:0.9938:0.0:0.5 -9 80646091 . T A 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCGCTCGATCTCGTCGTTGA;RSEQ=CCGCCGGGCTTCCTTGGCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:893:52:27,25:423,418:0.0582:2,2:26.6:1.0:29.2:1.0:0.88672:1.07:45.9:51.0:0.0582:0.0:1.1 0/0:1043:0:0,0:531,511:0.0:2,0:25.2:1.0:28.9:1.0:1.0:0.0:48.6:79.154:1.0:0.0:0.1 -9 80801556 . G A 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.24451;SOR=0.0;LSEQ=CCCCACTCCTGCCCGCCAGA;RSEQ=AACAATACCCCTTTGACTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:20.2:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.4167:0.0:1.6 0/0:5:0:0,0:4,1:0.0:2,0:17.2:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.6 -9 87342854 . G A 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0624;SOR=0.0;LSEQ=GATTTCTGCTCACTTCATGG;RSEQ=CTGGCCTGGAATTGACGATG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:5:3,2:143,286:0.0115:2,2:15.0:1.0:31.2:1.0:0.34049:2.99:60.0:10.0:0.012:0.0:1.2 0/0:407:0:0,0:156,251:0.0:2,0:25.1:1.0:31.2:1.0:1.0:0.0:60.0:57.143:1.0:0.0:0.1 -9 87570478 . C A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02723;LSEQ=CCCAGGGACCTCTTTCCCTG;RSEQ=GGGACCCCTGCTGTATTTGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:84:28,56:167,367:0.1357:2,2:26.2:1.0:31.1:1.0:0.70615:1.1:60.0:168.0:0.1375:0.0:1.1 0/0:706:3:2,1:273,428:0.0042:2,2:32.3:1.0:27.7:1.0:0.564:3.13:60.0:6.0:0.0043:0.0:1.3 -9 93607915 . G A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCTCACCTCCTGCCACCAG;RSEQ=CCTGTGTGGACAATTGGGAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:63:19,44:126,242:0.1462:2,2:25.5:1.0:29.8:1.0:0.56667:1.2052:60.0:62.0:0.1473:0.0:1.1 0/0:346:0:0,0:112,233:0.0:2,0:23.1:1.0:31.3:1.0:1.0:0.0:60.0:56.5:1.0:0.0:0.1 -9 93608130 . G A 92 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.47712;SOR=0.0;LSEQ=CGAGGGATGTAATATTTAAA;RSEQ=AAAATGTGATTCAGCCCCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:0.5:0,0:18.8:1.0:30.9:1.0:1.0:0.0:60.0:16.0:0.5333:0.0:1.3 0/0:2:0:0,0:0,2:0.0:0,0:22.5:1.0:32.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 -9 93636431 . A G 264 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08092;LSEQ=AAAAATAATTATGCAGATCA;RSEQ=CTTAACAGTTTTGTGGATGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:731:315:207,108:275,140:0.4309:2,2:24.3:1.0:31.9:1.0:0.87502:1.02482:60.0:77.75:0.4302:0.0:1.1 0/1:798:46:25,21:454,295:0.0576:2,2:27.8:1.0:31.8:1.0:0.43891:1.2923:60.0:92.0:0.0582:0.0:1.3 -9 93637282 . G T 110 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00185;SOR=0.06592;LSEQ=GGTACTATTATAATGAAAGC;RSEQ=TCCATTACCTTTAATGGCAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:0,15:0,17:0.4688:1,1:20.1:1.0:28.3:1.0:1.0:0.0:60.0:6.5:0.4483:0.0:1.3 0/1:19:1:0,1:0,18:0.0526:1,0:15.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0526:0.0:1.0 -9 93639590 . A G 83 d7;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCCTTTCAACCTCCCAAAGT;RSEQ=TGGGGATTGTCAGCATGAGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:1.0:0,0:32.5:1.0:32.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 93639640 . T C 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.50549;SOR=0.0;LSEQ=CAGCCCCCACCATTCTTTTT;RSEQ=AGTAATGGAGTATTACTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:0.4167:0,0:21.0:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.4167:0.0:2.0 0/0:3:0:0,0:3,0:0.0:0,0:27.0:1.0:32.0:0.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -9 93639679 . G A 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.02041;SOR=0.08518;LSEQ=TCATTGTCTATAAAATAAGG;RSEQ=AATATAGGTTGGAAGGCCAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:14,0:10,0:0.5833:0,1:23.5:1.0:31.1:1.0:1.0:0.0:60.0:28.0:0.6087:0.0:1.2 0/1:10:1:1,0:9,0:0.1:0,0:33.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -9 93640895 . G A 114 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00387;SOR=0.07411;LSEQ=TGAGTCCTGAAGAGCTATAT;RSEQ=CTAACAAAGTTATTTGTCAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:15,0:17,0:0.4688:1,1:21.5:1.0:29.3:1.0:1.0:0.0:60.0:30.0:0.4688:0.0:1.6 0/1:17:1:1,0:16,0:0.0588:1,0:39.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0588:0.0:2.0 -9 93641193 . C T 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACGCCAAGATCAGTGATTT;RSEQ=GGACTTTCCAAAGCACTGCG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:610:38:14,24:252,319:0.0623:2,2:20.6:1.0:29.5:1.0:0.40394:1.35357:60.0:37.0:0.0615:0.0:1.1 0/0:617:0:0,0:270,346:0.0:2,0:24.7:1.0:29.8:1.0:1.0:0.0:60.0:40.067:0.9983:0.0:0.3 -9 93641199 . T C 245 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.08109;LSEQ=AAGATCAGTGATTTCGGACT;RSEQ=TCCAAAGCACTGCGTGCTGA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:221:92,129:165,199:0.3778:2,2:24.7:1.0:31.5:1.0:0.39154:1.16231:60.0:72.667:0.3759:0.0:2.0 0/1:598:28:11,17:241,328:0.0468:2,2:21.0:1.0:31.2:1.0:0.84575:1.13526:60.0:56.0:0.0469:0.0:1.9 -9 93650322 . G A 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00965;SOR=0.0;LSEQ=CCCTCAGTCTATTCCAAACT;RSEQ=AGAATGAAATATCTGATGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:13:0,13:3,18:0.3824:2,1:20.3:1.0:28.8:1.0:0.27005:0.0:60.0:12.0:0.3636:0.0:1.0 0/0:14:0:0,0:0,14:0.0:1,0:29.7:1.0:30.5:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.2 -9 94768176 . T A 73 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=3.0;SSF=0.14402;SOR=0.0;LSEQ=TCTCAAAAAAAAAAAAAAAA;RSEQ=AATAATAATAAATAAATTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:18,1:0.2:1,0:17.2:1.0:31.6:1.0:1.0:0.0:52.0:10.0:0.2:0.0:2.8 0/0:13:0:0,0:13,0:0.0:1,0:20.0:0.0:12.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 -9 95439427 . A G 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0515;SOR=0.0;LSEQ=GAGCTTAATGTGCTCAATAC;RSEQ=CACGTTAATTCTCTTGGCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:4,2:6,1:0.4615:2,2:28.2:1.0:31.7:1.0:0.55944:2.75172:60.0:12.0:0.4615:0.0:1.3 0/0:7:0:0,0:6,1:0.0:2,0:25.1:1.0:31.4:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.1 -9 97873931 . G A 62 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.11964;SOR=0.19385;LSEQ=CCGCAGGACCTGGAACAGAG;RSEQ=CAGAACACATGGCAGTTGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:5:4,1:123,327:0.011:2,2:8.6:1.0:27.0:1.0:0.02292:10.57:60.0:4.0:0.0089:0.0:1.2 0/0:466:1:1,0:148,317:0.0021:2,0:1.0:0.0:24.0:0.0:0.31974:0.0:60.0:2.0:0.0022:0.0:1.0 -9 98009794 . G C 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATCTTTCAATGACTGTATTA;RSEQ=AATCCTGTGAAAGAAAAATA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:28:11,17:215,361:0.0461:2,2:26.2:1.0:32.2:1.0:0.84344:1.09:60.0:56.0:0.0467:0.0:1.1 0/0:603:0:0,0:221,380:0.0:2,0:23.7:1.0:31.0:1.0:1.0:0.0:60.0:199.333:0.9967:0.0:0.1 -9 98278972 . TCTC T 129 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=4.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CTCCGTTTTCTTCTTCTTCT;RSEQ=CTCCTCCTCCGTCTTTACAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1066:19:7,12:413,635:0.0178:2,2:19.9:1.0:30.6:1.0:1.0:1.11487:58.4:38.0:0.0179:0.0084:0.6 0/0:1169:0:0,0:496,669:0.0:2,0:23.1:1.0:31.2:1.0:1.0:0.0:60.0:96.083:0.9965:0.0:0.2 -9 107068085 . G C 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00444;SOR=0.03977;LSEQ=GCAAAAGCCCTACAGAAGAG;RSEQ=GACTGGACTATTGAAAGAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:0.8571:0,2:25.2:1.0:28.0:1.0:1.0:0.0:60.0:5.0:0.8333:0.0:1.2 0/1:13:2:2,0:8,3:0.1538:2,0:34.5:1.0:29.5:1.0:1.0:0.0:60.0:4.0:0.1538:0.0:1.5 -9 109484504 . A G 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATAAAAATGAGAATTACAGT;RSEQ=AAATTCAGCTTGTCTAATCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:24:24,0:16,0:0.6:1,1:23.1:1.0:32.5:1.0:1.0:0.0:60.0:48.0:0.6:0.0:1.0 0/0:24:0:0,0:23,1:0.0:1,0:22.1:1.0:28.6:1.0:1.0:0.0:60.0:48.0:1.0:0.0:0.0 -9 110248177 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.08752;SOR=0.14164;LSEQ=GGGCGAATTTCCATCCACAG;RSEQ=CGTCCCAGTCACAGTGGTAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:5:2,3:124,217:0.0144:2,2:22.2:1.0:30.8:1.0:1.0:1.17:60.0:10.0:0.0146:0.0:1.2 0/0:485:1:0,1:195,289:0.0021:2,0:1.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0021:0.0:1.0 -9 127952210 . G T 88 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.42857;SOR=0.0;LSEQ=CGACTGCAGGCCCCAAGAGA;RSEQ=CCCGCTTCGGTCCACCCCGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:0.6154:0,0:27.1:1.0:29.4:1.0:1.0:0.0:60.0:16.0:0.6154:0.0:1.0 0/0:1:0:0,0:0,1:0.0:0,0:2.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -9 133711140 . TTCTC T 70 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=5.0;MSILEN=2.0;SSF=0.04784;SOR=0.0;LSEQ=CTTCTCTTGTCTCTCTCTTT;RSEQ=TCTCTCTGTCTCTTTCTCTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:0,5:0,16:0.2381:1,0:26.6:1.0:30.4:1.0:1.0:0.0:60.0:10.0:0.25:0.0476:0.0 0/0:20:0:0,0:2,18:0.0:2,0:20.2:1.0:28.8:1.0:1.0:0.0:59.0:19.0:1.0:0.0:0.4 -9 133750550 . A G 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03651;LSEQ=TTTCTTTTTGTTTTTTTGAG;RSEQ=CGGAGTCTCACTCTGTCACC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:39:0,39:0,80:0.325:1,1:20.3:1.0:32.2:1.0:1.0:0.0:60.0:78.0:0.3305:0.0:1.1 0/1:117:2:0,2:0,115:0.0171:1,0:36.5:1.0:31.0:1.0:1.0:0.0:60.0:4.0:0.0179:0.0:1.0 -9 133754099 . C A 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=5e-05;SOR=0.07063;LSEQ=GCAGCTAATGTAGCCATTTG;RSEQ=TACCTATTGACCTTTATTTA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:28:0,28:0,22:0.56:1,1:26.9:1.0:32.1:1.0:1.0:0.0:60.0:56.0:0.5714:0.0:1.6 0/1:25:2:0,2:1,22:0.08:1,0:10.5:1.0:29.5:1.0:1.0:0.0:60.0:4.0:0.08:0.0:2.0 -9 133754220 . T C 110 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TACAGATTCCTGGGCCCTGC;RSEQ=TTCACAGACATTCTGCTATA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:13:0,13:0,2:0.8667:0,1:27.5:1.0:29.9:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.4 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 133755282 . T G 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.05681;LSEQ=CATCTAACGTCTTTTCAAAT;RSEQ=CTTAATGTCTATAACAGGAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:25:24,1:17,0:0.5952:1,1:23.7:1.0:32.8:1.0:1.0:0.0:60.0:50.0:0.5952:0.0:1.2 0/1:27:2:2,0:22,3:0.0741:2,0:6.0:1.0:29.0:1.0:1.0:0.0:60.0:4.0:0.0741:0.0:1.0 -9 133759957 . G T 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01724;LSEQ=GGGCACAAAAGTGAGAAGCC;RSEQ=GCTCTGCCTCGGAAGAGGGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:924:54:23,31:424,444:0.0584:2,2:27.7:1.0:30.2:1.0:0.40206:1.28676:60.0:53.0:0.0582:0.0:1.3 0/0:937:1:0,1:472,463:0.0011:2,0:1.0:0.0:31.0:0.0:0.49573:0.0:60.0:2.0:0.0011:0.0:1.0 -9 135771515 . A G 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02251;LSEQ=CCTCCGTCCCATTTCCACAC;RSEQ=TGAACTTGCACTCAGACCCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:39:39,0:50,0:0.4382:1,1:24.0:1.0:29.9:1.0:1.0:0.0:60.0:78.0:0.4382:0.0:1.1 0/1:59:1:1,0:54,4:0.0169:2,0:11.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0169:0.0:1.0 -9 135773164 . C T 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.13116;SOR=0.0;LSEQ=AAGTAAGCTGGTAGTATTAT;RSEQ=CTAGTAACCCTTCCTTGAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:0,8:0,9:0.4706:0,0:26.5:1.0:29.3:1.0:1.0:0.0:60.0:16.0:0.4706:0.0:2.4 0/0:4:0:0,0:0,4:0.0:0,0:25.5:1.0:31.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 -9 135778867 . T C 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01637;SOR=0.0;LSEQ=CCCACGGTTTCTGAGAATTA;RSEQ=GAGGGAATTCCGAGGTGTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:8,1:19,0:0.3214:1,2:21.9:1.0:32.9:1.0:0.32143:0.0:60.0:18.0:0.3333:0.0:1.0 0/0:16:0:0,0:16,0:0.0:1,0:26.1:1.0:30.8:1.0:1.0:0.0:60.0:32.0:1.0:0.0:0.1 -9 135781709 . G C 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.10164;LSEQ=TTGGGAGGCTGAGGAGGGAG;RSEQ=ATCACTTGAGCCCAGGAGTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:80:0,80:1,102:0.4348:1,1:25.3:1.0:31.8:1.0:1.0:0.0:59.8:39.0:0.4333:0.0:1.1 0/1:111:8:0,8:2,100:0.0721:1,0:27.4:1.0:33.4:1.0:1.0:0.0:60.0:16.0:0.0727:0.0:1.0 -9 135782026 . C A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07535;LSEQ=ACCTCAAGAGAAGAAAAATC;RSEQ=AGCAAGCCTGTGAGCAATGG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:94:84,10:113,22:0.4069:2,2:21.5:1.0:30.3:1.0:0.25038:1.63:60.0:93.0:0.4097:0.0:1.1 0/1:225:11:9,2:184,30:0.0489:2,2:11.5:1.0:29.0:1.0:0.65881:1.36089:60.0:22.0:0.0502:0.0:1.8 -9 135782221 . T C 249 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0824;LSEQ=CCTTTGCTGCCAGGTGGCTC;RSEQ=TCTGAAGAGAAACAAAGACA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:239:83,156:94,187:0.4587:2,2:22.9:1.0:31.6:1.0:0.78106:1.06:60.0:118.5:0.4584:0.0:1.1 0/1:476:31:9,22:146,299:0.0651:2,2:20.7:1.0:31.0:1.0:0.84313:1.19321:60.0:30.0:0.0638:0.0:1.1 -9 135782396 . A G 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.07054;SOR=0.0;LSEQ=ACTGAAATATTAAAAATAAT;RSEQ=TAACTAAAAGTACCAAAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:4,10:7,12:0.4242:2,2:21.6:1.0:31.2:1.0:0.71934:1.44185:60.0:13.0:0.4063:0.0:1.1 0/0:6:0:0,0:1,5:0.0:2,0:30.3:1.0:30.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 -9 135786112 . T C 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.12691;LSEQ=GGCAGAACATATATGAACAC;RSEQ=GAGCCCAACTATTAGAAAAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:195:58,137:98,228:0.3743:2,2:23.0:1.0:29.8:1.0:1.0:1.01525:60.0:96.5:0.3755:0.0:1.1 0/1:426:30:11,19:146,250:0.0704:2,2:23.4:1.0:29.6:1.0:1.0:1.00871:60.0:60.0:0.0709:0.0:1.1 -9 135796608 . A C 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03184;LSEQ=TTTAAACTCACACAAATTTT;RSEQ=GCTGTATGAGTGCTTCCAAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:28:28,0:40,1:0.4058:1,1:26.3:1.0:31.7:1.0:1.0:0.0:60.0:56.0:0.4058:0.0:1.0 0/1:48:1:1,0:46,1:0.0208:1,0:9.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0208:0.0:1.0 -9 136206057 . CAAGT C 114 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.00164;SOR=0.0;LSEQ=GCTGTTGGCACTGTTGTAAA;RSEQ=AAGGGCAAGATTCTTGCCAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:5,7:5,4:0.5714:2,2:19.9:1.0:31.8:1.0:0.66992:1.70337:60.0:24.0:0.6:0.0952:0.1 0/0:11:0:0,0:5,6:0.0:2,0:17.5:1.0:29.9:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.0 -9 139391461 . T C 186 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGCCACGTTCAGGTGCCCGA;RSEQ=GCCCAGGTGGGTGTCGGGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:62:31,31:393,339:0.0781:2,2:22.2:1.0:31.3:1.0:0.59792:1.15907:59.9:61.0:0.078:0.0:1.1 0/0:643:0:0,0:336,306:0.0:2,0:22.6:1.0:29.4:1.0:1.0:0.0:60.0:57.364:0.9984:0.0:0.2 -9 139396113 . T A 192 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08135;LSEQ=CCAATTCTAAGTTTCCAGAG;RSEQ=ATCAACTGTACCCCAGCCTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:90:83,7:98,10:0.4545:2,2:22.3:1.0:29.7:1.0:0.80211:1.21:60.0:29.0:0.4531:0.0:1.1 0/1:111:7:7,0:88,16:0.0631:2,0:24.0:1.0:27.9:1.0:0.59057:0.0:60.0:14.0:0.0631:0.0:1.3 -9 139397557 . C G 272 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.09575;LSEQ=TGGGTAGCAACTGGCACAAA;RSEQ=AGCCAGCGTGTCTGGGGCAC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:417:209,208:300,288:0.4145:2,2:24.6:1.0:31.3:1.0:0.79803:1.03666:60.0:40.7:0.4136:0.0:1.1 0/1:820:52:26,26:377,390:0.0634:2,2:27.6:1.0:30.7:1.0:1.0:1.03:60.0:104.0:0.0644:0.0:1.1 -9 139399641 . G A 192 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07538;LSEQ=CTCCAGCCCACTGGCCAGCC;RSEQ=CGGGGGACGTCCCTGCACCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:77:30,47:47,59:0.4208:2,2:22.5:1.0:30.7:1.0:0.54449:1.24651:60.0:154.0:0.4254:0.0:1.1 0/1:97:5:2,3:51,41:0.0515:2,2:37.2:1.0:30.6:1.0:0.65613:1.85383:60.0:10.0:0.0521:0.0:1.0 -9 139401565 . A G 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00024;SOR=0.06112;LSEQ=AGGTGTCAAGGGTGCCGTGG;RSEQ=GACGCCCTTCCCACTGGGAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:32:17,15:24,26:0.3902:2,2:18.6:1.0:31.3:1.0:0.82113:1.22:60.0:64.0:0.3902:0.0:1.7 0/1:27:1:0,1:15,11:0.037:2,0:40.0:0.0:32.0:0.0:0.44444:0.0:60.0:2.0:0.0385:0.0:1.0 -9 139401646 . T C 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.06763;LSEQ=CTTGGCCTCACACAGGAAAA;RSEQ=GGGAGTTTCTGGCTGGTTCC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:69:66,3:100,10:0.3855:2,1:24.7:1.0:32.2:1.0:0.37542:2.19:60.0:138.0:0.3855:0.0:1.1 0/1:99:4:4,0:89,6:0.0404:2,0:21.8:1.0:32.3:1.0:1.0:0.0:60.0:8.0:0.0408:0.0:1.0 -9 139405093 . G A 271 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.08571;LSEQ=CTGGAGGAGGCCAGAGCCGC;RSEQ=GGGCTACTCACTGGGCCGGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:876:478:282,196:226,168:0.5457:2,2:27.3:1.0:30.5:1.0:0.62985:1.07:60.0:118.5:0.5499:0.0:1.1 0/1:719:67:39,28:361,290:0.0932:2,2:27.9:1.0:29.2:1.0:0.69997:1.12:60.0:15.75:0.0894:0.0:1.1 -9 139408892 . C T 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00379;LSEQ=TCTCAAGCTCTGTGCAGGTG;RSEQ=CACCCTCCTGGCAGCAGAGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:150:139:124,15:11,0:0.9267:0,2:24.8:1.0:29.8:1.0:0.60315:0.0:60.0:45.333:0.9252:0.0:1.1 0/1:70:3:2,1:55,12:0.0429:2,2:16.7:1.0:29.7:1.0:0.46547:2.25824:60.0:6.0:0.0429:0.0:1.0 -9 139409676 . G T 60 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.07782;SOR=0.0;LSEQ=CCAACCCCTCAGCAGCCCCA;RSEQ=GGCAGAGTGGCTGACCTTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:5:3,2:134,29:0.0298:2,2:15.0:1.0:26.0:1.0:0.22975:3.05342:60.0:4.0:0.0247:0.0:2.4 0/0:120:0:0,0:92,28:0.0:2,0:23.9:1.0:31.3:1.0:1.0:0.0:60.0:119.0:1.0:0.0:0.2 -9 139412182 . G A 233 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCCTCGACTCGGTTTCCC;RSEQ=CCCTGGCCCCGGCCGACGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:554:228:163,65:219,106:0.4116:2,2:23.7:1.0:29.8:1.0:0.35002:1.21:60.0:56.0:0.4118:0.0:2.0 0/0:447:0:0,0:293,154:0.0:2,0:26.1:1.0:30.2:1.0:1.0:0.0:60.0:48.667:1.0:0.0:0.6 -9 139413539 . C T 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTAATTCCCGAACACAGGGC;RSEQ=TGTCTGTTCATCCAGGCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:1,6:0.4667:2,2:30.9:1.0:30.3:1.0:1.0:2.26:60.0:14.0:0.5833:0.0:1.1 0/0:1:0:0,0:0,1:0.0:0,0:19.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -9 139413908 . C T 257 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01123;LSEQ=TACGCGCCTGTCCACTCTGG;RSEQ=GGGCAGCGGCAGTTGTAGGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:996:412:248,164:336,247:0.4137:2,2:25.9:1.0:29.6:1.0:0.43331:1.11:60.0:136.333:0.4148:0.0:1.1 0/0:766:6:2,4:437,323:0.0078:2,2:9.7:1.0:25.8:1.0:0.41032:2.7024:60.0:5.0:0.0066:0.0:1.3 -9 139565475 . TTGG T 132 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08784;LSEQ=CTGCTGGAGGAGGTGAGGCA;RSEQ=TGGGGGGGGGGGGGGGCAGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:939:32:5,27:468,388:0.0341:2,2:31.3:1.0:26.5:1.0:1e-05:6.50104:59.0:5.4:0.0372:0.0:3.7 0/0:972:3:1,2:461,474:0.0031:2,2:38.3:1.0:23.3:1.0:1.0:1.94381:60.0:2.0:0.0025:0.0:3.3 -9 139565987 . A AC 93 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.27273;SOR=0.0;LSEQ=GCAGCTGGACACTGACCAGG;RSEQ=CCCCCCAGGGCCGGAGGAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:1,1:0.8:2,0:29.6:1.0:31.3:1.0:0.2:0.0:60.0:16.0:0.8:0.1:0.0 0/0:1:0:0,0:0,1:0.0:0,0:28.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 -9 139566996 . G A 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.01129;SOR=0.0;LSEQ=GGCATCCCAAGGCCAGGTGG;RSEQ=CCCTCAGCTGAGGGAAGGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:0,3:0.85:0,1:22.9:1.0:28.8:1.0:1.0:0.0:60.0:16.0:0.8889:0.0:1.1 0/0:3:0:0,0:0,3:0.0:0,0:6.0:1.0:32.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 -9 139794638 . T A 72 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTTTAAAAAAAAAAAAAGAA;RSEQ=AAAGGGCCGCCAGAAGTTGT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:0.3846:0,0:10.0:1.0:31.2:1.0:1.0:0.0:56.0:10.0:0.4167:0.0:2.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 139810652 . G A 65 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCAGTGGGCGTTTGATTCT;RSEQ=GGTTTTGAACCCAGGCCCTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:0.5556:0,0:32.4:1.0:28.2:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.2 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -9 139815960 . A G 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01515;SOR=0.0;LSEQ=AGCCTGGTCCTCTGGCACAC;RSEQ=GCCCTAAAGCAGACATTACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:1.0:0,0:23.1:1.0:30.4:1.0:1.0:0.0:60.0:20.0:1.0:0.0:1.4 0/0:2:0:0,0:1,1:0.0:2,0:3.0:0.0:24.0:1.0:1.0:0.0:60.0:1.0:1.0:0.0:2.0 -GL000199.1 72929 . A C 82 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00947;SOR=0.15011;LSEQ=TGAGTACACACATCACAAGG;RSEQ=AGTTTCTGAGAATGCTTCTG;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:3,3:11,14:0.1935:2,2:25.2:1.0:31.8:1.0:1.0:1.26:40.7:12.0:0.1935:0.0:6.3 0/1:88:3:2,1:40,43:0.0341:2,2:32.3:1.0:27.0:1.0:0.61176:2.13:42.3:2.0:0.023:0.0:6.0 -GL000212.1 246 . A G 84 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=4.0;SSF=0.01539;SOR=0.15011;LSEQ=TGTGGTCAGTGTTACCATCC;RSEQ=TAGTTTGTCAGTATTAAGGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:8:3,5:30,57:0.0842:2,2:32.1:1.0:28.0:1.0:1.0:1.14:29.8:7.0:0.0761:0.0:2.4 0/1:148:2:1,1:45,101:0.0135:2,2:32.0:1.0:30.5:1.0:0.52648:2.23:23.0:4.0:0.0135:0.0:2.0 -GL000212.1 40744 . T G 84 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0101;SOR=0.0367;LSEQ=TTTTCAAAGGTCAGAGCAGA;RSEQ=TGAACCTTTGTGGTTTCATT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:3,3:0,1:0.8571:0,2:31.5:1.0:32.5:1.0:1.0:0.0:45.7:12.0:0.8571:0.0:7.3 0/1:8:1:1,0:3,4:0.125:2,0:32.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.125:0.0:7.0 -GL000212.1 40827 . T G 74 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00034;SOR=0.0;LSEQ=CATTCAAGGTATGTTCATAC;RSEQ=GGCCTGTCAAATGCGAACTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:6,5:0.3125:2,2:28.2:1.0:32.0:1.0:1.0:1.73457:47.6:10.0:0.3125:0.0:6.6 0/0:55:0:0,0:27,28:0.0:2,0:21.8:1.0:30.1:1.0:1.0:0.0:56.8:110.0:1.0:0.0:5.7 -GL000212.1 40875 . A G 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00022;SOR=0.05777;LSEQ=TACTAGTTAATGCTTTCAAA;RSEQ=TATGTTATTTAAAAAATTAT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:4,2:1,4:0.5455:2,2:40.2:1.0:33.2:1.0:0.24242:6.44:52.8:12.0:0.5455:0.0:5.2 0/1:82:5:2,3:37,40:0.061:2,2:22.0:1.0:31.6:1.0:1.0:1.38204:55.6:10.0:0.0625:0.0:6.8 -GL000212.1 40886 . A C 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=1.0;SSF=6e-05;SOR=0.03884;LSEQ=GCTTTCAAAATATGTTATTT;RSEQ=AAAAATTATCCTCTGTATTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:3,3:1,3:0.6:2,2:28.2:1.0:31.7:1.0:0.57143:2.69:49.5:12.0:0.6:0.0:5.5 0/1:79:4:2,2:37,36:0.0506:2,2:14.0:1.0:30.0:1.0:1.0:1.02742:54.5:8.0:0.0506:0.0:6.5 -GL000212.1 163535 . T A 88 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01031;SOR=0.17632;LSEQ=TTAAAAATTATTTTGGGCTG;RSEQ=CACAGAATGTTGACTTTTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:9:1,8:83,37:0.0698:2,2:24.6:1.0:28.0:1.0:0.00093:17.56221:25.6:18.0:0.0714:0.0:3.2 0/1:231:3:0,3:160,68:0.013:2,0:25.7:1.0:32.0:0.0:0.02819:0.0:23.3:6.0:0.013:0.0:3.0 -GL000212.1 163555 . T C 92 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00926;SOR=0.18583;LSEQ=TCACAGAATGTTGACTTTTC;RSEQ=TAATCTGTTACATAGGGCTG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:8:1,7:100,57:0.0485:2,2:37.9:1.0:30.9:1.0:0.00586:12.11486:25.6:16.0:0.0488:0.0:3.5 0/0:321:3:0,3:203,115:0.0093:2,0:45.7:1.0:34.0:0.0:0.04887:0.0:23.3:6.0:0.0095:0.0:3.0 -GL000212.1 163574 . T C 109 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00026;SOR=0.14484;LSEQ=CTTAATCTGTTACATAGGGC;RSEQ=GTGGGTCTGGATTTCCAGGA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:13:4,9:124,74:0.0616:2,2:28.3:1.0:29.6:1.0:0.03681:3.74592:26.7:12.0:0.0585:0.0:3.2 0/0:426:4:1,3:253,169:0.0094:2,2:28.3:1.0:31.5:1.0:0.30764:4.47577:24.8:8.0:0.0096:0.0:3.0 -GL000212.1 163644 . G A 97 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00108;SOR=0.10497;LSEQ=GGGGTGAGGTGGCCGAGGCA;RSEQ=GTCAAAGCTGAAAAGTGGAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:295:9:6,3:138,148:0.0305:2,2:13.4:1.0:30.8:1.0:0.32613:2.14:33.1:18.0:0.0308:0.0:3.2 0/0:609:2:0,2:304,303:0.0033:2,0:34.5:1.0:24.0:1.0:0.49918:0.0:41.5:1.0:0.0017:0.0:2.0 -GL000212.1 175100 . A T 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00057;SOR=0.0;LSEQ=CTTAGGGCTTTTAAGTTTGA;RSEQ=GACTCAGTGTTACAGGTTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:11:11,0:45,0:0.1964:1,0:23.9:1.0:32.3:1.0:1.0:0.0:23.9:22.0:0.2037:0.0:1.0 0/0:55:0:0,0:54,1:0.0:1,0:22.3:1.0:30.6:1.0:1.0:0.0:25.3:110.0:1.0:0.0:0.3 -GL000220.1 119178 . T C 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00299;SOR=0.0761;LSEQ=GCGCACCGACGCGAGGGCGC;RSEQ=GATTCCCGTTCACGCGCCCG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:10:7,3:15,9:0.2083:2,2:23.5:1.0:31.9:1.0:1.0:1.39:53.7:20.0:0.2941:0.0:2.1 0/1:52:1:1,0:16,13:0.0192:2,0:8.0:0.0:31.0:0.0:1.0:0.0:24.0:2.0:0.0333:0.0:2.0 -GL000220.1 119477 . TTCTTTCTCTTTCTCTTTCTCTCTCTC T 190 NM4;MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=16.0;MSILEN=2.0;SSF=0.0;SOR=0.04223;LSEQ=CGCTCTCTCCCTCGCTCGTT;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:77:37,40:58,50:0.3909:2,2:14.0:1.0:30.4:1.0:0.45993:1.25251:43.2:10.0:0.3627:0.3909:4.5 0/1:267:7:3,4:117,127:0.0262:2,2:29.7:1.0:30.4:1.0:1.0:1.22735:34.0:14.0:0.0266:0.0225:1.6 -GL000220.1 119479 . CTTTCTCTTTCTCTTTCTCTCTC ATCTCTCTCTCGCTCTTGCCCTCTCGCTCTCTCCCTCGCTCGTTT 81 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.00097;SOR=0.0;LSEQ=CTCTCTCCCTCGCTCGTTTT;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:197:8:3,5:58,50:0.0406:2,2:25.9:1.0:27.2:1.0:0.47417:1.92244:35.6:7.0:0.0363:0.0406:2.1 0/0:267:0:0,0:117,127:0.0:2,0:22.2:1.0:29.4:1.0:1.0:0.0:52.1:243.0:0.924:0.0:1.6 -GL000220.1 119493 . T C 83 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.00039;SOR=0.0;LSEQ=CGTTTTCTTTCTCTTTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:140:9:4,5:58,42:0.0643:2,2:11.3:1.0:26.4:1.0:0.49547:1.71737:29.4:3.5:0.0693:0.0:4.6 0/0:189:0:0,0:64,70:0.0:2,0:26.9:1.0:27.6:1.0:1.0:0.0:57.7:9.308:0.9528:0.0:0.7 -GL000220.1 119595 . CTC GTCGCTCTCGCCCTCTCGCTCTCTCTCTGTCTCTGTCTGTG 94 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.00146;SOR=0.0;LSEQ=CTGTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCTCTCCCTCCCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:9:3,6:47,56:0.0804:2,2:25.3:1.0:29.9:1.0:0.72877:1.67109:35.9:18.0:0.0833:0.0804:2.6 0/0:115:0:0,0:54,60:0.0:2,0:18.4:1.0:28.4:1.0:1.0:0.0:52.1:11.667:0.9906:0.0:1.9 -GL000220.1 119610 . C T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=8e-05;SOR=0.0;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CTCCCCCTCCCTCCCTCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:14:9,5:35,48:0.1373:2,2:8.9:1.0:24.8:1.0:0.15282:2.45:57.6:1.8:0.1084:0.0:1.8 0/0:96:0:0,0:42,47:0.0:2,0:21.4:1.0:28.1:1.0:1.0:0.0:53.2:8.889:1.0:0.0:2.2 -GL000220.1 119911 . C T 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00015;SOR=0.0;LSEQ=CGTCGATTCCGGTTCACGCG;RSEQ=CGGCGACCTCCACCGGCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:8:5,3:14,10:0.25:2,2:16.1:1.0:27.0:1.0:1.0:1.18:60.0:7.0:0.2333:0.0:2.1 0/0:57:0:0,0:30,25:0.0:2,0:25.7:1.0:30.3:1.0:1.0:0.0:59.7:17.333:0.963:0.0:0.5 -GL000220.1 119967 . T C 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00832;SOR=0.0;LSEQ=TGGGACCACGCGGAACTCCC;RSEQ=CTCCTACATTTTTTTCAGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:3,2:23,17:0.1111:2,2:30.4:1.0:31.8:1.0:1.0:1.11:55.8:10.0:0.1111:0.0:1.6 0/0:69:0:0,0:37,32:0.0:2,0:6.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 -GL000220.1 120161 . G C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00784;SOR=0.0;LSEQ=CTCTCTCTCTCTCTCTCTCT;RSEQ=TCTCTCTCCCCTCCCTCCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:6:4,2:36,53:0.0632:2,2:9.5:1.0:29.2:1.0:0.23557:2.91:40.7:5.0:0.0581:0.0:2.7 0/0:115:0:0,0:52,54:0.0:2,0:20.6:1.0:28.7:1.0:1.0:0.0:58.3:6.067:1.0:0.0:0.8 -GL000220.1 121453 . TTGCCTGCCTGCC T 86 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=37;MSI=12.0;MSILEN=4.0;SSF=0.0104;SOR=0.0;LSEQ=GCGCCTGGCTCCTTCTACAT;RSEQ=TGCCTGCCTGCCTGCCTGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:7:3,4:8,8:0.25:2,2:36.0:1.0:30.9:1.0:1.0:1.31677:60.0:14.0:0.2593:0.0:0.3 0/0:26:0:0,0:10,9:0.0:2,0:24.2:1.0:30.1:1.0:1.0:0.0:57.4:38.0:0.7308:0.0:0.5 -GL000220.1 123214 . G C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01904;SOR=0.09556;LSEQ=ACACACAATTTCCATATCTA;RSEQ=TTCACAGAGCACACTCACTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:3,4:13,15:0.2:2,2:26.9:1.0:33.0:1.0:1.0:1.15081:60.0:14.0:0.2059:0.0:1.0 0/1:44:1:0,1:20,23:0.0227:2,0:43.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.0233:0.0:1.0 -GL000220.1 125098 . C G 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02061;SOR=0.09924;LSEQ=CTGAGATCCCCCGCCTCCAC;RSEQ=GCCTTGCAGGCTCACCTCTT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:2,3:20,14:0.1282:2,2:22.6:1.0:31.8:1.0:0.63624:2.10061:60.0:10.0:0.1351:0.0:1.2 0/1:71:1:0,1:33,37:0.0141:2,0:14.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0143:0.0:1.0 -GL000220.1 126307 . G A 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00248;SOR=0.0;LSEQ=AAGAAATGGCACTGTACACT;RSEQ=AACGCAGTGGCTCACGTCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:5,4:6,9:0.375:2,2:32.3:1.0:29.3:1.0:0.67517:1.83:52.7:18.0:0.375:0.0:1.2 0/0:19:0:0,0:9,10:0.0:2,0:21.3:1.0:31.1:1.0:1.0:0.0:52.8:38.0:1.0:0.0:0.2 -GL000220.1 127312 . G C 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=4.0;SSF=0.0;SOR=0.0;LSEQ=TTCGTTCTCTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:34:11,23:24,28:0.272:2,2:18.4:1.0:31.9:1.0:0.26305:1.78013:58.8:68.0:0.281:0.0:1.9 0/0:108:0:0,0:31,38:0.0:2,0:22.9:1.0:30.0:1.0:1.0:0.0:59.4:68.0:0.7083:0.0:0.6 -GL000220.1 127757 . T TCTGC 85 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.03217;SOR=0.18106;LSEQ=TCTCTGTCTTTTTCTGTCTG;RSEQ=CTCTCTCTTTCTTTCTGTCT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:7:3,4:51,39:0.0722:2,2:28.0:1.0:30.4:1.0:0.69619:1.73348:41.3:6.0:0.0659:0.0103:1.9 0/1:145:2:1,1:69,62:0.0138:2,2:46.0:0.0:32.0:1.0:1.0:1.11201:37.0:4.0:0.0144:0.0:3.0 -GL000220.1 127790 . G CTCTCTCTGTC 103 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.00017;SOR=0.0;LSEQ=TTCTGTCTGTCTCTGTCTCT;RSEQ=TCTCTCTCTCTCTCTCTGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:11:5,6:58,42:0.0982:2,2:20.4:1.0:29.9:1.0:0.52667:1.64945:45.9:10.0:0.0935:0.0804:2.3 0/0:129:0:0,0:66,60:0.0:2,0:23.1:1.0:30.5:1.0:1.0:0.0:58.0:41.0:0.9919:0.0:0.4 -GL000220.1 128282 . CCTGT C 70 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=4.0;MSILEN=4.0;SSF=0.01804;SOR=0.0;LSEQ=TTACTCTGTTTCTCTGCCTG;RSEQ=CTGTCTGTCTGTCTCTCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:2,3:58,52:0.0439:2,2:26.2:1.0:30.4:1.0:0.6689:1.66564:59.2:10.0:0.0442:0.0175:1.2 0/0:138:0:0,0:68,69:0.0:2,0:23.9:1.0:30.3:1.0:1.0:0.0:59.6:21.833:1.0:0.0:0.3 -GL000220.1 128928 . C CCTGTCTCCTCTCTCTCTCA 69 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06257;SOR=0.0;LSEQ=CCTGTCTCCGTCCCTCCCTC;RSEQ=CTGTCTGTCTGTTTCTCTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:2,3:60,63:0.0379:2,2:14.0:1.0:29.8:1.0:1.0:1.42464:46.8:10.0:0.041:0.0379:1.6 0/0:116:0:0,0:54,60:0.0:2,0:21.1:1.0:29.5:1.0:1.0:0.0:58.6:21.8:1.0:0.0:0.6 -GL000220.1 128957 . TTCTG T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.06031;SOR=0.0;LSEQ=CTGTTTCTCTCTCTGTCCAT;RSEQ=TCTGTCTCTTTCTCTTTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:131:5:3,2:62,64:0.0382:2,2:19.6:1.0:31.0:0.0:0.68017:1.54:60.0:10.0:0.0388:0.0:0.0 0/0:126:0:0,0:63,63:0.0:2,0:24.5:1.0:29.2:1.0:1.0:0.0:59.1:41.0:1.0:0.0:0.7 -GL000220.1 129019 . G C 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00164;SOR=0.0;LSEQ=GTCTCTCTCTGTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:10:3,7:56,44:0.0877:2,2:18.4:1.0:29.4:1.0:0.18288:2.94101:57.6:4.0:0.087:0.0:2.3 0/0:108:0:0,0:48,33:0.0:2,0:24.1:1.0:28.0:1.0:1.0:0.0:58.1:5.75:0.9324:0.0:0.6 -GL000220.1 130027 . GGGGGGA TGGG 63 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=6.0;MSILEN=1.0;SSF=0.00256;SOR=0.0;LSEQ=GAGAGAGAGACGGGGAGAGA;RSEQ=GAGGGGGGGGGAGAGAGAGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:2,4:13,7:0.2069:2,2:16.7:1.0:24.5:1.0:0.34783:3.52018:56.2:5.0:0.25:0.1379:1.2 0/0:45:0:0,0:28,16:0.0:2,0:19.3:1.0:30.4:1.0:1.0:0.0:56.7:88.0:1.0:0.0:1.5 -GL000220.1 130109 . C A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=3.0;SSF=0.01014;SOR=0.08689;LSEQ=AGAAAGAGAAGTAAAACCAA;RSEQ=CACCACCTCCTTGACCTGAG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:8:4,4:19,24:0.1569:2,2:29.1:1.0:26.9:1.0:1.0:1.26:56.4:3.0:0.1364:0.0:2.5 0/1:64:1:0,1:31,32:0.0156:2,0:2.0:0.0:25.0:0.0:1.0:0.0:40.0:2.0:0.0172:0.0:2.0 -GL000220.1 132352 . CTCTCTG C 84 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=3.0;MSILEN=6.0;SSF=0.00957;SOR=0.09564;LSEQ=CTCTGTCTGTCTGTCTCTTT;RSEQ=TCTCTGTCTCTGTCTCTCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:7:1,6:60,47:0.0614:2,2:17.6:1.0:30.1:1.0:0.04838:7.54265:60.0:6.0:0.0541:0.0439:1.1 0/0:162:1:0,1:76,85:0.0062:2,0:14.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.0062:0.0:0.0 -GL000220.1 132475 . T C 80 DIFF0.2 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=15;MSI=5.0;MSILEN=1.0;SSF=0.03176;SOR=0.17978;LSEQ=CTCTCCTTTCCTGTCTGTTT;RSEQ=TCTCTCTCTCTCTCTCTTTC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:7:2,5:32,37:0.0875:2,2:26.0:1.0:28.7:1.0:0.4501:2.14158:60.0:2.5:0.0667:0.0:2.3 0/1:119:2:1,1:52,45:0.0168:2,2:5.0:1.0:33.5:1.0:1.0:1.15386:24.5:4.0:0.02:0.0168:0.5 -GL000220.1 133311 . A ACGTC 76 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02974;SOR=0.0;LSEQ=CTGTCTGTCTCTCTCCCTCC;RSEQ=TGTCTCTCTCTCTCTCTCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:6:2,4:66,62:0.0438:2,2:14.8:1.0:29.5:1.0:0.43714:2.11743:55.3:12.0:0.0462:0.0219:2.3 0/0:131:0:0,0:62,62:0.0:2,0:24.5:1.0:29.3:1.0:1.0:0.0:57.9:40.333:0.9528:0.0:0.3 -GL000220.1 133431 . G A 62 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=12;MSI=1.0;MSILEN=1.0;SSF=0.01118;SOR=0.0;LSEQ=CTCTCACTCACTCTCTCTCC;RSEQ=TCTCTCTCTCTCTTTCTGTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:5:2,3:46,53:0.0476:2,2:13.0:1.0:26.8:1.0:1.0:1.29863:34.4:4.0:0.044:0.0:1.8 0/0:150:0:0,0:67,73:0.0:2,0:23.1:1.0:28.2:1.0:1.0:0.0:46.3:13.0:0.9848:0.0:0.4 -GL000220.1 133549 . G C 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=4.0;SSF=0.00011;SOR=0.0;LSEQ=CTCTTTCTGTCTGTTTCTCT;RSEQ=TCTGTCTGTCTGTCTGTCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:10:4,6:46,51:0.0926:2,2:27.3:1.0:28.6:1.0:0.74752:1.34917:50.9:4.0:0.0851:0.0:2.2 0/0:153:0:0,0:66,68:0.0:2,0:23.7:1.0:30.0:1.0:1.0:0.0:56.5:11.182:1.0:0.0:0.5 -GL000220.1 133613 . T A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.00034;SOR=0.0;LSEQ=CTCTCTCTCTCTGTTTGTCT;RSEQ=TCTCCCTCCCTGTCTGTCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:9:4,5:44,47:0.0882:2,2:20.3:1.0:26.2:1.0:1.0:1.16838:60.0:8.0:0.0889:0.0:1.0 0/0:140:0:0,0:60,78:0.0:2,0:24.0:1.0:29.3:1.0:1.0:0.0:58.8:33.5:0.9853:0.0:0.5 -GL000220.1 137741 . G A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00631;SOR=0.0;LSEQ=CGCCCCACGCCCCACGTCCC;RSEQ=GGCACCCGCGGGACACCGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:7:4,3:55,54:0.0603:2,2:18.3:1.0:29.6:1.0:1.0:1.31:60.0:6.0:0.0561:0.0:1.6 0/0:120:0:0,0:60,60:0.0:2,0:23.3:1.0:28.0:1.0:1.0:0.0:60.0:16.143:1.0:0.0:0.7 -GL000220.1 146098 . CTT C 90 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=23.0;MSILEN=3.0;SSF=0.00213;SOR=0.0;LSEQ=TTCTTCTTCTTCTTCTTCTT;RSEQ=TTTTTTTTGAGACAGAGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:4,3:5,4:0.4375:2,2:31.4:1.0:32.4:1.0:1.0:1.06:33.1:14.0:0.4375:0.0:0.1 0/0:18:0:0,0:8,7:0.0:2,0:25.8:1.0:29.3:1.0:1.0:0.0:41.3:30.0:0.8333:0.0:0.5 -GL000224.1 4495 . G T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05683;SOR=0.0;LSEQ=GGGAGTGCCTGAGTGTAAGT;RSEQ=GAGATGGGTTTGGGGTCACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:3,3:5,7:0.3333:2,2:25.0:1.0:30.5:1.0:1.0:1.37:42.2:12.0:0.3333:0.0:1.3 0/0:12:0:0,0:7,5:0.0:2,0:29.3:1.0:30.4:1.0:1.0:0.0:32.5:24.0:1.0:0.0:0.5 -GL000225.1 44342 . T C 73 MAF0.05;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.05573;SOR=0.10246;LSEQ=CGCGCGGGTTTGCGGGCAGC;RSEQ=GCCTGGGCTGTGGGAGCAGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:3,2:3,2:0.5:2,2:27.4:1.0:31.6:1.0:1.0:1.0:47.6:10.0:0.5:0.0:3.6 0/1:12:1:0,1:3,3:0.0833:2,0:42.0:0.0:32.0:0.0:1.0:0.0:40.0:2.0:0.0833:0.0:3.0 -GL000225.1 44344 . C A 70 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00957;SOR=0.0;LSEQ=CGCGGGTTTGCGGGCAGCTG;RSEQ=CTGGGCTGTGGGAGCAGCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:3,2:3,2:0.5:2,2:44.2:1.0:30.2:1.0:1.0:1.0:48.4:10.0:0.5:0.0:4.8 0/0:12:0:0,0:5,7:0.0:2,0:30.8:1.0:30.8:1.0:1.0:0.0:41.3:24.0:1.0:0.0:5.0 -GL000225.1 44549 . A G 78 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=7e-05;SOR=0.0;LSEQ=CTCGCCTCCTCTGTGCCACC;RSEQ=CGCCACCGTCGCCGGCCCGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:2,4:1,0:0.8571:0,2:32.8:1.0:30.3:1.0:0.42857:0.0:45.2:12.0:0.8571:0.0:6.7 0/0:16:0:0,0:9,5:0.0:2,0:23.5:1.0:28.9:1.0:1.0:0.0:44.3:13.0:1.0:0.0:6.6 -GL000225.1 65091 . A G 102 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00203;SOR=0.0;LSEQ=AGCGGCTCTTATAAAGGCCC;RSEQ=CAGGCAGGCAGGCTCCACCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:6,4:4,5:0.4348:2,2:26.0:1.0:30.8:1.0:0.65628:1.81:42.4:20.0:0.4348:0.0:4.0 0/0:17:0:0,0:7,8:0.0:2,0:25.2:1.0:29.7:1.0:1.0:0.0:45.3:30.0:1.0:0.0:5.1 -GL000225.1 78924 . C T 74 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.12845;SOR=0.0;LSEQ=TGTGCCTGCTGCAGAAACTC;RSEQ=GGGCTCGCCAGGAGCTCATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:3,2:10,4:0.2632:2,2:30.0:1.0:32.0:1.0:1.0:1.62034:48.4:10.0:0.2632:0.0:7.0 0/0:12:0:0,0:9,3:0.0:2,0:26.3:1.0:30.1:1.0:1.0:0.0:37.8:11.0:1.0:0.0:5.3 -GL000225.1 91008 . T A 68 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.12855;SOR=0.0;LSEQ=ACCTCCGTGGGAGTCTTGAG;RSEQ=GTTCCAGGCCCTCTCCGTGA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:3,2:4,8:0.2941:2,2:24.2:1.0:29.6:1.0:0.59276:2.8:32.0:10.0:0.3125:0.0:6.4 0/0:9:0:0,0:4,5:0.0:2,0:18.9:1.0:30.0:1.0:1.0:0.0:42.0:18.0:1.0:0.0:4.4 -GL000225.1 131540 . T A 74 d7;NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGATCACCCAAGTGATGTA;RSEQ=CCATTGTCCAGGCTTTGCCT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:1.0:0,2:18.6:1.0:32.0:0.0:1.0:0.0:45.2:10.0:1.0:0.0:5.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -GL000225.1 131568 . T G 76 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=CCAGGCTTTGCCTACAGGGG;RSEQ=CTTTGTGACATAGCTTTGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:0,0:0.7143:0,2:37.2:1.0:32.8:1.0:1.0:0.0:38.8:10.0:0.7143:0.0:5.8 0/0:1:0:0,0:1,0:0.0:0,0:21.0:0.0:26.0:0.0:1.0:0.0:41.0:2.0:1.0:0.0:8.0 -GL000229.1 7982 . T C 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=TGCTGCTGCTGCTGCTCTTG;RSEQ=TGCTGTTGTTGTTGTTGTTT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:11:6,5:6,10:0.4074:2,2:16.5:1.0:30.5:1.0:0.45165:1.95:52.2:10.0:0.3846:0.0:1.5 0/0:36:0:0,0:12,16:0.0:2,0:26.9:1.0:29.7:1.0:1.0:0.0:56.8:56.0:1.0:0.0:1.1 -GL000229.1 8042 . C G 76 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04396;SOR=0.0;LSEQ=CCGTTTATGGGATCAAAAGC;RSEQ=TTATAAAATATGTGTAATTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:1,4:2,2:0.5556:2,2:18.4:1.0:32.8:1.0:0.52381:3.38757:33.0:10.0:0.5556:0.0:4.0 0/0:6:0:0,0:2,4:0.0:2,0:22.2:1.0:31.0:1.0:1.0:0.0:59.0:12.0:1.0:0.0:0.2 -GL000231.1 24616 . C T 88 InIns SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=3.0;SSF=0.01327;SOR=0.0;LSEQ=CTTCTGTTCTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGGTGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:4,3:23,17:0.1296:2,2:25.3:1.0:31.7:1.0:1.0:1.01439:41.6:14.0:0.1489:0.0:3.9 0/0:49:0:0,0:19,17:0.0:2,0:20.1:1.0:31.8:1.0:1.0:0.0:57.9:72.0:1.0:0.0:0.4 -MT 152 . T C 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=5e-05;SOR=0.06779;LSEQ=CTTTGATTCCTGCCTCATCC;RSEQ=ATTATTTATCGCACCTACGT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:36:18,18:15,5:0.6429:2,2:21.8:1.0:31.2:1.0:0.09199:2.94184:60.0:72.0:0.6429:0.0:2.6 0/1:19:2:1,1:8,9:0.1053:2,2:38.5:1.0:30.5:1.0:1.0:1.12:60.0:4.0:0.1053:0.0:1.5 -MT 178 . A G 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TTATCGCACCTACGTTCAAT;RSEQ=TTACAGGCGAACATACTTAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:33:19,14:20,9:0.5323:2,2:23.7:1.0:32.1:1.0:0.43363:1.62437:60.0:66.0:0.5323:0.0:2.8 0/0:19:0:0,0:10,9:0.0:2,0:22.8:1.0:29.3:1.0:1.0:0.0:60.0:38.0:1.0:0.0:1.9 -MT 477 . T C 148 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCTCCCACTCCCATACTAC;RSEQ=AATCTCATCAATACAACCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:26:13,13:16,16:0.4483:2,2:21.4:1.0:31.6:1.0:1.0:1.0:60.0:52.0:0.4643:0.0:1.3 0/0:49:0:0,0:24,25:0.0:2,0:23.3:1.0:28.7:1.0:1.0:0.0:60.0:23.5:1.0:0.0:0.6 -MT 533 . A G 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0047;SOR=0.0;LSEQ=GCACACACACACCGCTGCTA;RSEQ=CCCCATACCCCGAACCAACC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:9:4,5:20,27:0.1607:2,2:26.2:1.0:32.8:1.0:1.0:1.08:60.0:18.0:0.1607:0.0:1.9 0/0:43:0:0,0:19,24:0.0:2,0:28.3:1.0:29.6:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.5 -MT 1888 . G A 115 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00043;SOR=0.04706;LSEQ=GAAATAACTTTGCAAGGAGA;RSEQ=CCAAAGCTAAGACCCCCGAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:9,7:7,5:0.5714:2,2:31.1:1.0:28.9:1.0:1.0:1.08558:40.9:15.0:0.5769:0.0:1.0 0/1:18:1:1,0:7,10:0.0556:2,0:44.0:0.0:32.0:0.0:0.44444:0.0:40.0:2.0:0.0556:0.0:1.0 -MT 1990 . G A 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00265;SOR=0.0;LSEQ=GAAGATTTATAGGTAGAGGC;RSEQ=ACAAACCTACCGAGCCTGGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:7,5:5,6:0.5217:2,2:24.2:1.0:30.6:1.0:0.68427:1.64:51.5:24.0:0.5217:0.0:1.2 0/0:11:0:0,0:5,6:0.0:2,0:20.6:1.0:28.2:1.0:1.0:0.0:51.5:10.0:1.0:0.0:0.0 -MT 4917 . A G 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCAAATCTCTCCCTCACTA;RSEQ=ACGTAAGCCTTCTCCTCACT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:20:9,11:11,15:0.4348:2,2:26.0:1.0:31.8:1.0:1.0:1.11:59.5:40.0:0.4348:0.0:1.1 0/0:43:0:0,0:22,21:0.0:2,0:18.3:1.0:29.4:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.2 -MT 5007 . G A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.04236;SOR=0.0;LSEQ=CCCAGCTACGCAAAATCTTA;RSEQ=CATACTCCTCAATTACCCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:4,4:16,17:0.1951:2,2:24.0:1.0:31.4:1.0:1.0:1.06:59.8:16.0:0.1951:0.0:1.0 0/0:22:0:0,0:9,13:0.0:2,0:22.7:1.0:31.6:1.0:1.0:0.0:57.5:44.0:1.0:0.0:0.2 -MT 7051 . T C 74 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.23077;SOR=0.0;LSEQ=CTTCCACTATGTCCTATCAA;RSEQ=AGGAGCTGTATTTGCCATCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:4,1:4,2:0.4545:2,2:31.4:1.0:32.2:1.0:1.0:1.88:32.2:10.0:0.4545:0.0:1.0 0/0:4:0:0,0:3,1:0.0:2,0:28.5:1.0:29.8:1.0:1.0:0.0:35.3:8.0:1.0:0.0:0.8 -MT 8697 . G A 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00114;SOR=0.10232;LSEQ=AAACTAACCTCAAAACAAAT;RSEQ=ATAACCATACACAACACTAA;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:21:10,11:10,14:0.4667:2,2:23.2:1.0:28.7:1.0:0.76854:1.27:59.3:42.0:0.4667:0.0:1.2 0/1:25:2:2,0:13,10:0.08:2,0:19.5:1.0:30.0:0.0:0.5:0.0:42.0:4.0:0.0833:0.0:1.0 -MT 9150 . A G 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01536;SOR=0.0;LSEQ=CTAGAAATCGCTGTCGCCTT;RSEQ=ATCCAAGCCTACGTTTTCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:8:6,2:12,11:0.2581:2,2:20.5:1.0:32.4:1.0:0.41203:2.66:49.3:16.0:0.2667:0.0:1.0 0/0:23:0:0,0:13,10:0.0:2,0:27.8:1.0:27.7:1.0:1.0:0.0:50.7:22.0:1.0:0.0:0.3 -MT 9899 . T C 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00414;SOR=0.0;LSEQ=TTTCACTTTACATCCAAACA;RSEQ=CACTTTGGCTTCGAAGCCGC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:7,7:0.3636:2,2:27.9:1.0:29.8:1.0:0.67492:1.62835:60.0:7.0:0.3333:0.0:1.0 0/0:19:0:0,0:9,10:0.0:2,0:24.7:1.0:29.1:1.0:1.0:0.0:60.0:38.0:1.0:0.0:0.3 -MT 10463 . T C 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00035;SOR=0.0;LSEQ=TTAAATTATGATAATCATAT;RSEQ=TACCAAATGCCCCTCATTTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:6,8:7,3:0.5833:2,2:30.1:1.0:32.3:1.0:0.23967:2.96235:60.0:28.0:0.5833:0.0:1.2 0/0:13:0:0,0:7,6:0.0:2,0:17.5:1.0:28.2:1.0:1.0:0.0:53.2:26.0:1.0:0.0:0.3 -MT 10601 . T C 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0491;SOR=0.0;LSEQ=CTATCGCTGTTCATTATAGC;RSEQ=ACTCTCATAACCCTCAACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:3,2:11,7:0.2174:2,2:30.2:1.0:30.6:1.0:1.0:1.04547:60.0:10.0:0.2174:0.0:1.0 0/0:23:0:0,0:13,10:0.0:2,0:22.8:1.0:29.7:1.0:1.0:0.0:60.0:46.0:1.0:0.0:0.3 -MT 12633 . C A 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATTGTTCGTTACATGGTC;RSEQ=ATCATAGAATTCTCACTGTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:24:12,12:4,5:0.7273:2,2:20.9:1.0:30.0:1.0:1.0:1.24:60.0:48.0:0.7273:0.0:1.1 0/0:14:0:0,0:7,7:0.0:2,0:25.9:1.0:30.5:1.0:1.0:0.0:60.0:13.0:1.0:0.0:0.9 -MT 13368 . G A 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATACTATTTATGTGCTCCGG;RSEQ=TCCATCATCCACAACCTTAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:18:7,11:6,6:0.6:2,2:23.9:1.0:30.8:1.0:0.71062:1.54757:46.5:36.0:0.6207:0.0:1.0 0/0:22:0:0,0:11,11:0.0:2,0:24.8:1.0:30.9:1.0:1.0:0.0:60.0:44.0:1.0:0.0:0.1 -MT 14905 . G A 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0001;SOR=0.07795;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC;STATUS=AFDiff GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:21:11,10:9,14:0.4773:2,2:27.4:1.0:29.1:1.0:0.54519:1.69:60.0:42.0:0.4773:0.0:1.3 0/1:31:2:1,1:13,16:0.0645:2,2:2.5:1.0:24.5:1.0:1.0:1.22:60.0:4.0:0.0645:0.0:1.0 -MT 15607 . A G 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0006;SOR=0.0527;LSEQ=CTCCGATCCGTCCCTAACAA;RSEQ=CTAGGAGGCGTCCTTGCCCT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:15:6,9:6,9:0.5:2,2:22.0:1.0:31.1:1.0:1.0:1.0:60.0:30.0:0.5357:0.0:1.1 0/1:21:1:0,1:11,9:0.0476:2,0:26.0:0.0:34.0:0.0:0.47619:0.0:60.0:2.0:0.0476:0.0:1.0 -MT 16019 . C T 71 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.14485;SOR=0.0;LSEQ=AGATTCTAATTTAAACTATT;RSEQ=TCTGTTCTTTCATGGGGAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:2,3:16,13:0.1471:2,2:28.0:1.0:31.0:1.0:0.64809:1.813:60.0:10.0:0.1563:0.0:1.8 0/0:22:0:0,0:13,9:0.0:2,0:21.4:1.0:30.6:1.0:1.0:0.0:60.0:21.0:1.0:0.0:0.3 -MT 16163 . A G 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTGACCACCTGTAGTACATA;RSEQ=AAACCCAATCCACATCAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:21:12,9:17,9:0.4468:2,2:29.0:1.0:32.1:1.0:0.76341:1.40609:60.0:42.0:0.4468:0.0:3.4 0/0:43:0:0,0:24,19:0.0:2,0:26.5:1.0:30.3:1.0:1.0:0.0:60.0:86.0:1.0:0.0:1.1 -MT 16186 . C T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCCAATCCACATCAAAACC;RSEQ=CCTCCCCATGCTTACAAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:25:14,11:21,11:0.4386:2,2:24.4:1.0:29.9:1.0:0.5851:1.48921:60.0:24.0:0.4286:0.0:3.2 0/0:40:0:0,0:19,20:0.0:2,0:25.6:1.0:30.4:1.0:1.0:0.0:60.0:38.0:1.0:0.0:1.4 -MT 16263 . T C 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCAACTCCAAAGCCACCCC;RSEQ=CACCCACTAGGATACCAACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:37:17,20:15,18:0.5286:2,2:27.7:1.0:31.3:1.0:1.0:1.02:60.0:74.0:0.5286:0.0:1.6 0/0:30:0:0,0:15,15:0.0:2,0:22.3:1.0:30.2:1.0:1.0:0.0:60.0:60.0:1.0:0.0:1.5 -MT 16294 . C T 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GATACCAACAAACCTACCCA;RSEQ=CCTTAACAGTACATAGTACA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:26:13,13:12,21:0.4407:2,2:21.8:1.0:30.1:1.0:0.4264:1.73:60.0:25.0:0.431:0.0:1.0 0/0:29:0:0,0:17,12:0.0:2,0:23.9:1.0:30.8:1.0:1.0:0.0:60.0:58.0:1.0:0.0:1.2 -MT 16316 . A G 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTAACAGTACATAGTACAT;RSEQ=AAGCCATTTACCGTACATAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:29:12,17:10,13:0.5577:2,2:20.2:1.0:31.1:1.0:1.0:1.08794:60.0:28.0:0.549:0.0:1.9 0/0:31:0:0,0:16,15:0.0:2,0:21.5:1.0:27.4:1.0:1.0:0.0:60.0:14.5:1.0:0.0:1.1 -MT 16390 . G A 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00012;SOR=0.05048;LSEQ=GATGACCCCCCTCAGATAGG;RSEQ=GTCCCTTGACCACCATCCTC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:10,12:20,18:0.3667:2,2:20.4:1.0:30.0:1.0:0.78917:1.32692:60.0:21.0:0.3621:0.0:1.5 0/1:36:1:0,1:19,16:0.0278:2,0:13.0:0.0:33.0:0.0:0.47222:0.0:60.0:2.0:0.0286:0.0:2.0 -X 1314857 . GG AT 192 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.1438;LSEQ=TCACAGACATTGTGCAAGCA;RSEQ=TCCCTCCACCCACGGGCGGC;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:79:58,21:126,50:0.3062:2,2:24.1:1.0:30.5:1.0:0.88004:1.1:60.0:158.0:0.3123:0.0349:1.0 0/1:353:21:15,6:220,112:0.0595:2,2:26.3:1.0:29.9:1.0:0.81223:1.27:60.0:42.0:0.06:0.0085:1.1 -X 1317599 . T C 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGACTGGAGAAACATACACA;RSEQ=ACACACACACACACACACAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:31:16,15:38,105:0.1455:2,2:17.4:1.0:29.6:1.0:0.00962:2.93:59.6:9.333:0.1854:0.0:1.5 0/0:355:0:0,0:86,164:0.0:2,0:21.6:1.0:24.8:1.0:1.0:0.0:59.3:3.902:0.9343:0.0:0.4 -X 1325301 . G T 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00011;SOR=0.053;LSEQ=AAGGAAGTACTGAAAAGCAT;RSEQ=GTGAGCTGGCTTTACAATAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:12:10,2:167,91:0.0444:2,2:20.0:1.0:30.9:1.0:0.22848:2.72:60.0:24.0:0.0446:0.0:1.1 0/0:408:1:0,1:257,150:0.0025:2,0:1.0:0.0:25.0:0.0:0.3701:0.0:60.0:2.0:0.0025:0.0:1.0 -X 1325426 . C T 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCTCTGCGTCTAGGAGGCA;RSEQ=CCCGAAGTGTGACCTTCCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:451:148:65,83:143,160:0.3282:2,2:25.8:1.0:30.4:1.0:0.54676:1.14091:60.0:296.0:0.3311:0.0:1.1 0/0:697:0:0,0:311,386:0.0:2,0:26.3:1.0:30.6:1.0:1.0:0.0:60.0:48.786:1.0:0.0:0.2 -X 15822104 . TA T 115 MSI6 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.0188;SOR=0.12165;LSEQ=AGAGTTGCCTATCTTGAACT;RSEQ=AAAAAAAAAAACAAAAAACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:13:9,4:61,21:0.1354:2,2:29.7:1.0:31.2:1.0:0.73854:1.28741:60.0:26.0:0.1368:0.0208:1.0 0/1:54:1:0,1:41,8:0.0185:2,0:23.0:0.0:32.0:0.0:0.18:0.0:60.0:2.0:0.0204:0.0:0.0 -X 15822401 . C T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01573;SOR=0.0;LSEQ=AGAGTTTGGGTTTTTTTTTT;RSEQ=TCTTTTTCTTGTCATTTCAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:7:2,5:36,162:0.0341:2,2:6.7:1.0:26.9:1.0:0.61592:1.79:57.1:6.0:0.0305:0.0:2.4 0/0:184:0:0,0:29,154:0.0:2,0:21.4:1.0:31.6:1.0:1.0:0.0:60.0:29.5:1.0:0.0:0.2 -X 22516183 . G A 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00088;SOR=0.0;LSEQ=ATCACATATTGCTGATCTTT;RSEQ=CTTCTACTGAGCACTATTCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:12,0:35,0:0.2553:1,0:27.4:1.0:27.7:1.0:1.0:0.0:60.0:11.0:0.2444:0.0:1.0 0/0:35:0:0,0:35,0:0.0:1,0:22.1:1.0:31.7:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.1 -X 39911835 . G T 83 InGap;LongAT SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0031;SOR=0.0;LSEQ=TTTTTTTTTTTTTTTTTTTT;RSEQ=GAGACGGAATCTCGCTCTGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:0.7:0,0:19.3:1.0:29.7:1.0:1.0:0.0:43.6:14.0:0.7:0.0:1.1 0/0:9:0:0,0:0,1:0.0:0,0:1.0:0.0:30.0:0.0:1.0:0.0:40.0:2.0:1.0:0.0:0.0 -X 39930099 . C G 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00544;SOR=0.0;LSEQ=TCTTTCACAGACGCCTCGTT;RSEQ=CTGGTTGCCACCATTCATAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:9:9,0:140,3:0.0592:1,0:21.7:1.0:30.9:1.0:1.0:0.0:60.0:8.0:0.0541:0.0:1.1 0/0:119:0:0,0:119,0:0.0:1,0:22.6:1.0:30.8:1.0:1.0:0.0:60.0:22.8:1.0:0.0:0.1 -X 44896832 . C G 235 Cluster75bp SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0083;LSEQ=ATGTTTGATGCTTTGTTATT;RSEQ=TTACTTAATTTGCCCCAAAT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:160:105,55:176,88:0.3765:2,2:25.9:1.0:32.2:1.0:0.83288:1.04748:60.0:320.0:0.3791:0.0:1.7 0/0:606:3:2,1:396,206:0.005:2,2:26.0:1.0:27.0:1.0:1.0:1.04:60.0:2.0:0.0034:0.0:1.7 -X 44896888 . C T 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGATTTTTTTGTCTTTCCT;RSEQ=ATCCTTTGCAGTTCAATTTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:233:106,127:207,233:0.3447:2,2:26.8:1.0:29.0:1.0:0.74538:1.06429:60.0:115.5:0.3463:0.0:1.5 0/0:1036:0:0,0:511,524:0.0:2,0:25.6:1.0:31.2:1.0:1.0:0.0:60.0:128.375:0.999:0.0:0.2 -X 47425058 . G A 94 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTAAATAATCAATTTTTTT;RSEQ=TTATTAATTATAAATATATT;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:0,8:0,1:0.8889:0,0:28.3:1.0:31.5:1.0:1.0:0.0:60.0:16.0:0.8889:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -X 47430509 . A AGTGT 140 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=18.0;MSILEN=2.0;SSF=0.0;SOR=0.06409;LSEQ=ATATGAAAGCTCAGAGGTAT;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:24:11,13:10,53:0.2474:2,2:27.8:1.0:30.6:1.0:0.00556:4.39:60.0:48.0:0.25:0.0309:0.5 0/1:98:2:1,1:13,81:0.0204:2,2:24.5:1.0:29.9:1.0:0.27171:6.04:60.0:4.0:0.0208:0.0102:0.5 -X 50648296 . A AAAATAAAT 80 MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=41;MSI=12.0;MSILEN=4.0;SSF=0.02098;SOR=0.0;LSEQ=AGCGAAACTTCGTCTCAAAT;RSEQ=AAATAAATAAATAAATAAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:0.75:0,0:17.2:1.0:31.1:1.0:1.0:0.0:60.0:12.0:0.75:0.375:0.2 0/0:5:0:0,0:3,0:0.0:0,0:20.3:1.0:28.3:1.0:1.0:0.0:60.0:6.0:0.6:0.0:0.0 -X 53223092 . C A 60 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.11139;SOR=0.1842;LSEQ=TGAAGAACCAGGCCCTATTC;RSEQ=TCCTCCGCCAACCCCAAACT;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:5:3,2:64,207:0.0181:2,2:8.0:1.0:26.2:1.0:0.09411:4.82:60.0:4.0:0.0148:0.0:1.8 0/0:296:1:1,0:68,227:0.0034:2,0:1.0:0.0:27.0:0.0:0.23311:0.0:60.0:2.0:0.0034:0.0:1.0 -X 53224366 . C T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00839;SOR=0.0;LSEQ=ATGAGCCATCTCACAGAAGC;RSEQ=AGGGCAGGCGTTAAGAGACG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:6:1,5:214,142:0.0166:2,2:14.8:1.0:26.8:1.0:0.04251:7.49592:60.0:12.0:0.0169:0.0:1.2 0/0:438:0:0,0:270,168:0.0:2,0:24.8:1.0:30.4:1.0:1.0:0.0:60.0:61.571:1.0:0.0:0.1 -X 53225501 . T C 89 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GCCTGCTAGCAATGCCTACA;RSEQ=ATACAACCTGTATTGTGTAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:1.0:0,0:17.7:1.0:32.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -X 53246599 . C G 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00013;SOR=0.0;LSEQ=ACAGCCCCTGTTCCACTGGT;RSEQ=TTTAGCACTGACACCAGCAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:13:0,13:3,31:0.2766:2,1:16.5:1.0:32.5:1.0:0.55023:0.0:60.0:26.0:0.2826:0.0:1.0 0/0:41:0:0,0:0,41:0.0:1,0:22.1:1.0:32.6:1.0:1.0:0.0:60.0:82.0:1.0:0.0:0.0 -X 63415940 . C T 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.00136;SOR=0.0;LSEQ=TGCTTTCCAGAGCCTTGACG;RSEQ=CCCAGTTAGAAGACAGTCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:16:0,16:1,63:0.2:1,1:27.7:1.0:30.0:1.0:1.0:0.0:60.0:15.0:0.1899:0.0:1.3 0/0:38:0:0,0:0,37:0.0:1,0:22.1:1.0:31.4:1.0:1.0:0.0:60.0:74.0:1.0:0.0:0.1 -X 63425821 . G A 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTGCGGAACCACTGGCTGG;RSEQ=GCTCCCCACTCCCGCCCCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:43:0,43:5,126:0.2457:1,1:25.6:1.0:30.0:1.0:0.33471:0.0:60.0:13.333:0.2395:0.0:1.2 0/0:149:0:0,0:5,142:0.0:1,0:23.7:1.0:30.4:1.0:1.0:0.0:60.0:146.0:0.9932:0.0:0.1 -X 66766359 . C T 142 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.0;MSILEN=3.0;SSF=0.0;SOR=0.08815;LSEQ=GGTGGTGGTGGGGGTGGTGG;RSEQ=GGCGGCGGCGGCGGCGGCGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:31:5,26:14,55:0.2981:2,2:10.4:1.0:28.8:1.0:0.78497:1.32005:60.0:6.75:0.2872:0.0:1.5 0/1:84:3:1,2:25,49:0.0357:2,2:20.0:1.0:19.3:1.0:1.0:1.02014:60.0:0.5:0.0141:0.0:2.0 -X 66789057 . G T 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.0;MSILEN=1.0;SSF=0.00727;SOR=0.0;LSEQ=GTGGGGGATTTTGTGTGTGG;RSEQ=GGGGGGTTGGGGGTTGAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:15:0,15:1,31:0.3191:1,1:23.9:1.0:25.9:1.0:1.0:0.0:60.0:2.75:0.2619:0.0:1.4 0/0:16:0:0,0:2,14:0.0:2,0:17.6:1.0:29.6:1.0:1.0:0.0:58.8:32.0:1.0:0.0:2.5 -X 66937707 . A G 114 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAGAACCAATCCTAGTCAT;RSEQ=TTTCTGGTCTGCTTTGCAGC;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:0,6:0.6471:0,0:31.7:1.0:33.1:1.0:1.0:0.0:60.0:22.0:0.6875:0.0:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -X 66942476 . A G 85 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.31495;SOR=0.0;LSEQ=ACTCCTTTCAGATCGGATCC;RSEQ=GCTATCCTTTCCCCTGAGAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:8:8,0:28,0:0.2222:1,0:29.3:1.0:28.5:1.0:1.0:0.0:60.0:16.0:0.2286:0.0:1.1 0/0:7:0:0,0:7,0:0.0:0,0:26.0:1.0:30.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.0 -X 66943154 . C CTCTGTGTGTGTG 76 d7;MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=25.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GTTCATGTGAGTTTGTCTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,0:0.8333:0,2:13.0:1.0:33.0:1.0:1.0:0.0:56.0:10.0:0.8333:0.6667:1.0 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -X 66943769 . C A 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0041;SOR=0.0;LSEQ=AACTCTGCACTACTCCTCTG;RSEQ=AGTGCCTTGGGGAATTTCCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:163:12:0,12:6,145:0.0736:1,0:24.2:1.0:29.3:1.0:1.0:0.0:60.0:11.0:0.0679:0.0:1.3 0/0:107:0:0,0:1,106:0.0:1,0:22.3:1.0:31.5:1.0:1.0:0.0:59.8:34.667:1.0:0.0:0.2 -X 70344763 . G T 248 InGap SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTATGCCTGCTTTTGGCAT;RSEQ=TTTTTTTGCCCCCTCATCCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:486:294:161,133:101,75:0.6049:2,2:22.2:1.0:30.3:1.0:0.6316:1.11221:60.0:97.0:0.6113:0.0:1.1 0/0:508:0:0,0:143,119:0.0:2,0:23.3:1.0:31.8:1.0:1.0:0.0:60.0:261.0:0.9703:0.0:0.1 -X 70347614 . C T 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.0;MSILEN=1.0;SSF=0.00015;SOR=0.0;LSEQ=CAGTCTGTTTTGTCCCATCT;RSEQ=CCTTTTCTTGTCTCAAGATC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:15:15,0:69,1:0.1765:1,1:27.5:1.0:30.6:1.0:1.0:0.0:60.0:30.0:0.1765:0.0:1.1 0/0:64:0:0,0:63,1:0.0:1,0:28.0:1.0:31.4:1.0:1.0:0.0:60.0:128.0:1.0:0.0:0.1 -X 70352491 . G A 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGAAGCATCATAGGAAAGT;RSEQ=GAAAATCAGAGGATAAGAGT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:53:12,41:15,108:0.3011:2,2:21.1:1.0:30.9:1.0:0.10886:2.1:60.0:106.0:0.3046:0.0:2.1 0/0:71:0:0,0:6,65:0.0:2,0:25.9:1.0:29.8:1.0:1.0:0.0:60.0:22.667:1.0:0.0:0.6 -X 70356829 . A G 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTATAACACACCTTAACT;RSEQ=CAGGCAAGGCTCCATAGGCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:976:130:57,73:390,454:0.1332:2,2:23.4:1.0:30.9:1.0:0.63737:1.10004:60.0:25.0:0.1297:0.0:1.1 0/0:922:0:0,0:447,474:0.0:2,0:24.0:1.0:28.5:1.0:1.0:0.0:60.0:130.571:1.0:0.0:0.2 -X 72744762 . C CT 75 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.01167;SOR=0.0;LSEQ=CCTTTTGCTTCCTCTCAGCC;RSEQ=TTTTTTTTAGTCTGATGTAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:6:3,3:107,35:0.0405:2,2:24.7:1.0:29.2:1.0:0.17621:3.02932:60.0:12.0:0.0414:0.0068:0.5 0/0:160:0:0,0:118,40:0.0:2,0:23.7:1.0:30.3:1.0:1.0:0.0:60.0:51.667:0.9936:0.0:0.2 -X 74803898 . T C 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGAAATCTCCAGGACTTCAG;RSEQ=GAGAAAGGAAGTCATCTTCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:54:36,18:110,61:0.24:2,2:27.5:1.0:31.0:1.0:0.87032:1.11:60.0:53.0:0.2366:0.0:1.1 0/0:256:0:0,0:160,96:0.0:2,0:25.9:1.0:29.4:1.0:1.0:0.0:59.9:84.333:1.0:0.0:0.1 -X 76814401 . GT G 81 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.03494;SOR=0.0;LSEQ=ATATGACTTTTTGATACTTA;RSEQ=TTTTTTTTAACTATCAAGAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:6:0,6:4,67:0.0779:2,0:24.7:1.0:31.6:1.0:1.0:0.0:60.0:12.0:0.08:0.026:0.2 0/0:60:0:0,0:2,58:0.0:1,0:26.2:1.0:30.2:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.0 -X 76939830 . A G 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GATGTATGTTCATATACTTT;RSEQ=TTACTCTTTTCACTGTCAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:703:62:29,33:326,315:0.0882:2,2:25.0:1.0:32.2:1.0:0.59547:1.17739:60.0:61.0:0.0879:0.0:1.1 0/0:896:0:0,0:452,444:0.0:2,0:24.1:1.0:28.7:1.0:1.0:0.0:60.0:111.0:1.0:0.0:0.1 -X 100057572 . C T 225 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCTATGCCTCCACCACCAC;RSEQ=TCAGGGAGTTAAGTGAAAAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:665:178:96,82:263,224:0.2677:2,2:27.0:1.0:30.1:1.0:1.0:1.00288:60.0:88.0:0.2687:0.0:1.1 0/0:787:0:0,0:406,380:0.0:2,0:24.6:1.0:30.4:1.0:1.0:0.0:59.9:28.111:1.0:0.0:0.2 -X 100609517 . G GA 70 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.0291;SOR=0.0;LSEQ=GGCAGAAAACGCTAGAATGA;RSEQ=AAAAAAAAGAAAAGGAGAGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:5:4,1:158,13:0.0284:2,2:21.2:1.0:30.4:1.0:0.34258:3.00912:60.0:10.0:0.0286:0.017:0.4 0/0:179:0:0,0:161,18:0.0:2,0:20.8:1.0:31.8:1.0:1.0:0.0:60.0:88.5:1.0:0.0:0.8 -X 100615505 . G T 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0189;LSEQ=TATGCCGCAGCACTTTTTGC;RSEQ=TGTAGGGAGTGGGCAGGCAC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:44:37,7:209,55:0.1429:2,2:25.5:1.0:31.4:1.0:0.54558:1.39:60.0:88.0:0.1443:0.0:1.0 0/0:320:1:0,1:224,95:0.0031:2,0:1.0:0.0:28.0:0.0:0.3:0.0:60.0:2.0:0.0031:0.0:1.0 -X 106846430 . C CAACAACAACAGCAGCAGCAGCAACAACAACAGCAGCAGCAACAACAACAGCAGACAATAACAAAAGCAACGATAGCAACAGTATCAGCAACAGCAACAGCATCAGCAACAACAGCAACAATAGCAGCAGTAAA 177 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=53;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCTTAACCAGCAGCAGCAG;RSEQ=AACAACAACAGCAGCAGCAG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:64:24,40:96,81:0.2656:2,2:21.8:1.0:29.6:1.0:0.02835:1.96973:41.1:128.0:0.2723:0.2656:3.2 0/0:293:0:0,0:148,145:0.0:2,0:13.5:1.0:31.6:1.0:1.0:0.0:39.7:47.833:1.0:0.0034:2.7 -X 106846447 . G GCAGCAACAACAACAGCAGACAATAACAAAAGCAACGATAGCAACAGTAT 188 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAACAACAACAGCAGCA;RSEQ=CAGCAACAACAACAGCAGCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:77:28,49:96,84:0.2996:2,2:35.6:1.0:30.0:1.0:0.01432:1.99461:34.7:154.0:0.3056:0.2996:2.0 0/0:313:0:0,0:154,157:0.0:2,0:22.8:1.0:31.5:1.0:1.0:0.0:40.3:43.429:0.9935:0.0:2.6 -X 122035670 . C T 68 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=3.0;SSF=0.0202;SOR=0.0;LSEQ=AACTGTTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGCTGCTG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:3,2:7,7:0.2632:2,2:30.4:1.0:29.6:1.0:1.0:1.47:60.0:10.0:0.2632:0.0:1.2 0/0:20:0:0,0:9,11:0.0:2,0:31.4:1.0:32.4:1.0:1.0:0.0:58.0:19.0:1.0:0.0:0.3 -X 122035688 . C T 71 MSI6 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=3.0;SSF=0.01707;SOR=0.0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGTTGTTTTGTATCCTC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:6,7:0.2778:2,2:20.8:1.0:30.6:1.0:1.0:1.26799:50.8:10.0:0.2778:0.0:1.8 0/0:20:0:0,0:9,11:0.0:2,0:31.6:1.0:30.9:1.0:1.0:0.0:58.0:9.0:1.0:0.0:0.3 -X 123041111 . G C 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAACTGACTTTAAGTAATCA;RSEQ=GATTGAATTCCATTAGCATT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:37:4,33:2,43:0.4512:1,2:21.3:1.0:29.4:1.0:0.40174:2.58:43.5:36.0:0.4557:0.0:1.0 0/0:63:0:0,0:4,51:0.0:2,0:25.2:1.0:30.8:1.0:1.0:0.0:56.3:110.0:0.8871:0.0:0.1 -X 123159533 . A G 98 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.10123;SOR=0.0;LSEQ=TGTGTTTGGTAACGTGCTAT;RSEQ=GTATGATGTTTTGGGGAAAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:8,0:57,1:0.1212:1,0:28.6:1.0:32.9:1.0:1.0:0.0:60.0:16.0:0.1231:0.0:1.4 0/0:29:0:0,0:29,0:0.0:1,0:28.8:1.0:28.7:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.1 -X 123184027 . C T 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0195;LSEQ=TATGCATCGTTTTTCCTTCC;RSEQ=CCATTCAGTGATGCGATAGC;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:51:33,18:337,165:0.0922:2,2:20.4:1.0:30.2:1.0:0.75562:1.11382:60.0:50.0:0.0921:0.0:1.1 0/0:507:1:0,1:308,196:0.002:2,0:1.0:0.0:23.0:0.0:0.3901:0.0:60.0:2.0:0.002:0.0:1.0 -X 123184284 . T A 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00697;SOR=0.0;LSEQ=TGGAAGCCTCCCCTTTATTC;RSEQ=TTTCTATCTTCTCTGTAAAA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:11:1,10:2,72:0.1294:1,2:24.8:1.0:31.3:1.0:0.34369:3.52:60.0:22.0:0.131:0.0:1.0 0/0:50:0:0,0:1,49:0.0:1,0:23.4:1.0:29.7:1.0:1.0:0.0:60.0:49.0:1.0:0.0:0.0 -X 123191922 . A G 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00131;SOR=0.0;LSEQ=AAAAATATTCCTTGTAGCAC;RSEQ=GTAAATTGTGAATAGAATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:15:0,15:0,109:0.121:1,1:21.8:1.0:29.9:1.0:1.0:0.0:60.0:14.0:0.1176:0.0:1.0 0/0:69:0:0,0:1,68:0.0:1,0:24.8:1.0:31.5:1.0:1.0:0.0:59.9:138.0:1.0:0.0:0.1 -X 123202318 . C CTATA 112 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.0;MSILEN=2.0;SSF=0.00108;SOR=0.0;LSEQ=CAGAAGTAGAGTTAATAAAG;RSEQ=TATGAGATAATGTTTTACAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:14:13,1:98,0:0.125:1,1:28.2:1.0:29.5:1.0:0.125:0.0:60.0:28.0:0.1308:0.0268:0.0 0/0:69:0:0,0:68,1:0.0:1,0:21.6:1.0:32.7:1.0:1.0:0.0:60.0:138.0:1.0:0.0:0.1 -X 123217527 . A G 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03469;SOR=0.0;LSEQ=ATTAATACACAAAAAAGTTT;RSEQ=TACTTCAGCAACTTTATAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:12:0,12:1,75:0.1364:1,0:22.6:1.0:32.3:1.0:1.0:0.0:60.0:24.0:0.1463:0.0:1.1 0/0:31:0:0,0:0,31:0.0:1,0:23.3:1.0:30.2:1.0:1.0:0.0:60.0:62.0:1.0:0.0:0.0 -X 123499949 . T TAGAA 97 P0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTAGTGACTATGTGAAATCT;RSEQ=AGCATATCAAAAGTAGGTAA;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:0,2:0.8182:0,0:30.6:1.0:30.9:1.0:1.0:0.0:60.0:18.0:0.8182:0.0:0.6 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -X 123499991 . T G 94 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATAATTAAATGAACAATTAT;RSEQ=TACCAAATGATACCAATATG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:1.0:0,0:19.4:1.0:31.4:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 -X 136524003 . G A 62 P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0794;SOR=0.0;LSEQ=TGATGGCCTGCATCTGGGCC;RSEQ=CTCGCTGGGCCGCAGCTGCT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:311:5:3,2:85,221:0.0161:2,2:22.0:1.0:26.8:1.0:0.13954:3.88:60.0:10.0:0.0163:0.0:1.0 0/0:221:0:0,0:77,144:0.0:2,0:26.6:1.0:30.5:1.0:1.0:0.0:59.1:43.2:1.0:0.0:0.3 -X 139479797 . C T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTAGAGATCCAAATCTACT;RSEQ=CTATCAGTAAGTAAAGATCA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:25:15,10:64,59:0.1689:2,2:24.6:1.0:29.8:1.0:0.51541:1.38:60.0:24.0:0.1678:0.0:1.0 0/0:98:0:0,0:56,42:0.0:2,0:24.7:1.0:30.8:1.0:1.0:0.0:60.0:97.0:1.0:0.0:0.2 -X 145042124 . TA T 70 P0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.0686;SOR=0.0;LSEQ=CATGCAAAAAAGACATAGGT;RSEQ=AAAAAAATAGTTTCTATGTA;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:5:2,3:87,101:0.0259:2,2:21.2:1.0:30.4:1.0:1.0:1.29039:60.0:10.0:0.0265:0.0:0.4 0/0:154:0:0,0:70,84:0.0:2,0:25.8:1.0:28.1:1.0:1.0:0.0:60.0:50.333:1.0:0.0:0.8 -Y 13489086 . G A 68 NM4;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.14005;SOR=0.0;LSEQ=TCCAAGGCGCTTCAGGAGCC;RSEQ=GGGCGCTCGTCTGCACTCCC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:3,2:13,10:0.1786:2,2:18.0:1.0:29.4:1.0:1.0:1.15:43.2:10.0:0.1786:0.0:5.0 0/0:17:0:0,0:12,5:0.0:2,0:18.5:1.0:30.3:1.0:1.0:0.0:36.6:34.0:1.0:0.0:4.9 -Y 13573061 . A G 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00079;SOR=0.0;LSEQ=CACAGCTACTTATGTTTTTA;RSEQ=TTCCCTCACAGGATGAAGAC;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:7:6,1:73,56:0.0515:2,2:23.4:1.0:30.9:1.0:0.23827:4.56:30.1:14.0:0.053:0.0:2.6 0/0:236:0:0,0:149,87:0.0:2,0:24.1:1.0:29.6:1.0:1.0:0.0:40.0:58.0:1.0:0.0:0.8 -Y 13573216 . G A 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=2e-05;SOR=0.08602;LSEQ=AGGAGCTGATAAGCAAAGAT;RSEQ=ATGAAATTCAAGATTTTCCT;STATUS=AFDiff GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:0,11:2,7:0.55:2,0:16.7:1.0:31.0:1.0:0.18947:0.0:24.2:22.0:0.55:0.0:2.1 0/1:87:8:0,8:18,61:0.092:2,0:4.5:1.0:29.3:1.0:0.19683:0.0:25.9:16.0:0.0941:0.0:2.0 -Y 13573240 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.00078;SOR=0.07082;LSEQ=AAATTCAAGATTTTCCTGAG;RSEQ=AGCAATTGCTTAACATTGTT;STATUS=Germline GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:2,4:1,7:0.4286:2,2:11.3:1.0:29.8:1.0:0.53846:3.19:27.8:12.0:0.4286:0.0:2.2 0/1:63:3:2,1:12,48:0.0476:2,2:8.7:1.0:28.7:1.0:0.12145:7.65:23.0:6.0:0.0484:0.0:2.0 -Y 13801134 . G GAATGTGCTCGAATGGAATGGAATCGTATGGATTGATATCA 88 NM4;MSI6 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=11.0;MSILEN=5.0;SSF=6e-05;SOR=0.0;LSEQ=GAATGGAATGGAATGGAATG;RSEQ=AATGGAATGGAATGGAATGG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:5,3:8,17:0.2286:2,2:11.6:1.0:29.4:1.0:0.21338:3.4:53.5:16.0:0.2286:0.2286:4.1 0/0:75:0:0,0:37,38:0.0:2,0:20.9:1.0:31.2:1.0:1.0:0.0:43.6:150.0:1.0:0.0:4.1 -Y 13801161 . AT TTGATATCAAGTGGAAA 102 NM4 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=ATGGAATGGAATGGAATGGA;RSEQ=GGAATGGAATGAACTCGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:3,7:3,0:0.7692:0,2:9.0:1.0:30.8:1.0:0.06993:0.0:47.1:20.0:0.7692:0.7692:5.0 0/0:24:0:0,0:10,14:0.0:2,0:5.8:1.0:29.0:1.0:1.0:0.0:39.3:23.0:1.0:0.0417:4.0 -Y 13842723 . G C 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00468;SOR=0.06477;LSEQ=GAATCAACCCGAGTGGAATG;RSEQ=AATGGAGTGGAATGGAATGG;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:3,2:32,29:0.0725:2,2:19.2:1.0:33.0:1.0:1.0:1.35:31.0:10.0:0.0735:0.0145:2.2 0/0:201:1:1,0:94,96:0.005:2,0:44.0:0.0:27.0:0.0:0.49738:0.0:22.0:2.0:0.0052:0.0:3.0 -Y 13842730 . G A 97 NM4 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.03094;LSEQ=CCCGAGTGGAATGGAATGGA;RSEQ=TGGAATGGAATGGAATGGAA;STATUS=LikelySomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:10:6,4:28,26:0.1493:2,2:17.1:1.0:29.4:1.0:0.73822:1.39:34.7:20.0:0.1515:0.0149:4.8 0/0:188:1:1,0:77,79:0.0053:2,0:4.0:1.0:32.0:1.0:0.49682:0.0:37.0:2.0:0.0062:0.0053:0.0 -Y 13868369 . T TCGAATGGAATGGAATGGAATGGAACGGAACTACGGAATAGAATGGAATGGAATTAACC 74 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=3.0;MSILEN=1.0;SSF=0.02098;SOR=0.0;LSEQ=TAGAATCGAATTGTATGGCA;RSEQ=CGAATGGAATGGAATGGAAT;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:3,3:1,1:0.75:2,2:15.2:1.0:29.0:1.0:1.0:1.0:43.3:12.0:0.75:0.75:3.3 0/0:5:0:0,0:3,2:0.0:2,0:6.8:1.0:27.4:1.0:1.0:0.0:37.0:4.0:1.0:0.0:3.4 -Y 13868375 . G A 68 InIns SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=5.0;SSF=0.00145;SOR=0.0;LSEQ=CGAATTGTATGGCATCGAAT;RSEQ=GAATGGAATGGAATGGAACG;STATUS=StrongSomatic GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:3,2:10,6:0.2381:2,2:5.6:1.0:29.6:1.0:1.0:1.10551:33.8:10.0:0.2381:0.0:3.2 0/0:51:0:0,0:11,15:0.0:2,0:2.4:1.0:29.6:1.0:1.0:0.0:40.3:25.0:0.5:0.0:2.4 -Y 13869847 . T A 73 d7;MSI6;P0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.0;MSILEN=5.0;SSF=1.0;SOR=0.0;LSEQ=TGGAATGGAATGGAATGGAA;RSEQ=GGAATGGAATGGAATGGAAG;STATUS=SampleSpecific GT:DP:VD:AD:RD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:1.0:0,2:21.4:1.0:31.8:1.0:1.0:0.0:39.2:10.0:1.0:0.0:3.8 0/0:0:0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 4955833 . A T 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAGCGGCAGATAAAAAAAC;RSEQ=GACAAACCGGAGAGCACGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:18:9,9:90,91:181,18:0.0905:2,2:26.8:1.0:30.4:1.0:1.0:1.01:60.0:36.0:0.0914:0.0:1.2 0/0:278:0:0,0:147,131:278,0:0.0:2,0:27.0:1.0:29.7:1.0:1.0:0.0:59.9:68.5:1.0:0.0:0.5 +1 9780743 . TG T 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.03061;SOR=0.0;LSEQ=AGTGGGGTGGGGGTGTGGGG;RSEQ=GGGGGCATGGAGCCGGCGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:5:3,2:226,255:481,5:0.0103:2,2:30.2:1.0:30.8:1.0:0.67019:1.69:60.0:10.0:0.0105:0.0:0.2 0/0:489:0:0,0:225,257:482,0:0.0:2,0:23.0:1.0:30.2:1.0:1.0:0.0:59.6:39.167:0.9874:0.0:0.8 +1 9781880 . A G 48 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.02779;SOR=0.0;LSEQ=TCATCCTGGAGGCCTACTGC;RSEQ=GGGGCAGCACCCACCACATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:5:2,3:228,253:481,5:0.0103:2,2:33.4:1.0:21.0:1.0:1.0:1.35095:60.0:1.5:0.0063:0.0:2.0 0/0:507:0:0,0:212,294:506,0:0.0:2,0:23.6:1.0:29.6:1.0:1.0:0.0:60.0:55.222:0.998:0.0:0.2 +1 11181985 . G A 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ATGAGAAAAGCAGCGCTACG;RSEQ=AGATTCCCTGCCACGGAAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:40:30,10:156,47:203,40:0.1646:2,2:22.5:1.0:30.4:1.0:0.83885:1.10591:60.0:39.0:0.1632:0.0:1.1 0/0:210:0:0,0:161,49:210,0:0.0:2,0:23.0:1.0:30.4:1.0:1.0:0.0:60.0:51.5:1.0:0.0:0.2 +1 11291380 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01272;SOR=0.09544;LSEQ=TCTGCGTGTACCCTGGTTCT;RSEQ=CTCAGTCTTCAGAAAATTCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:689:8:6,2:387,294:681,8:0.0116:2,2:15.6:1.0:26.1:1.0:0.47686:2.28:60.0:16.0:0.0118:0.0:1.0 0/0:894:1:1,0:457,436:893,1:0.0011:2,0:1.0:0.0:22.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 +1 11303131 . C T 60 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.06251;SOR=0.0;LSEQ=GAGCGTCCTTCCTCTCCAAC;RSEQ=AAATGGAGTGGAAGGTGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:5:1,4:204,64:268,5:0.0183:2,2:11.4:1.0:26.2:1.0:0.01456:12.60622:60.0:10.0:0.0187:0.0:1.0 0/0:250:0:0,0:185,65:250,0:0.0:2,0:23.4:1.0:30.1:1.0:1.0:0.0:60.0:40.667:1.0:0.0:0.1 +1 14192818 . G T 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.00554;SOR=0.0;LSEQ=CTGTTCATGGCTAATTCTTG;RSEQ=GTGGCTTCCATCACAGCTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:8:0,8:1,32:33,8:0.1951:1,0:11.1:1.0:31.3:1.0:1.0:0.0:60.0:16.0:0.1951:0.0:1.0 0/0:38:0:0,0:2,35:37,0:0.0:2,0:25.9:1.0:30.3:1.0:1.0:0.0:60.0:17.5:1.0:0.0:0.1 +1 16245610 . GT G 191 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.0;SOR=0.06659;LSEQ=TGTTTTTTAAGACTTGAAGG;RSEQ=TTTTTTTTTGCATATGCCTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:60:5,55:15,95:110,60:0.3529:2,2:30.1:1.0:32.4:1.0:0.45534:1.7316:60.0:120.0:0.3571:0.0:0.0 0/1:201:7:0,7:37,157:194,7:0.0348:2,0:26.6:1.0:31.9:1.0:0.35315:0.0:60.0:14.0:0.0354:0.0:0.0 +1 16258302 . A G 264 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04698;LSEQ=GGAAAAACTCAAGCGGTCCA;RSEQ=TTCTCCTCGGGGAGAAGCAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:273:126,147:159,188:347,273:0.4389:2,2:23.1:1.0:32.7:1.0:0.93552:1.01:60.0:135.5:0.4407:0.0:1.1 0/1:763:27:15,12:351,385:736,27:0.0354:2,2:22.5:1.0:31.1:1.0:0.43996:1.37:60.0:54.0:0.0358:0.0:1.0 +1 16262650 . G A 63 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02732;SOR=0.0;LSEQ=AGCGGGGAGCTGTTTCAAGA;RSEQ=TACCGGTACGGCGACATCCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:5:4,1:185,271:456,5:0.0108:2,2:6.8:1.0:27.2:1.0:0.16415:5.84:60.0:10.0:0.011:0.0:1.0 0/0:484:0:0,0:222,262:484,0:0.0:2,0:24.4:1.0:31.0:1.0:1.0:0.0:60.0:59.5:1.0:0.0:0.2 +1 16971804 . A T 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.47253;SOR=0.0;LSEQ=CTGGCAGCTGTCACTTTCAC;RSEQ=ATGCCCTTGGGCTGACTAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:5,1:6,6:0.5:2,0:28.2:1.0:32.2:1.0:1.0:0.0:28.2:12.0:0.5:0.0:1.0 0/0:2:0:0,0:2,0:2,0:0.0:0,0:31.0:1.0:31.0:0.0:1.0:0.0:21.0:4.0:1.0:0.0:0.0 +1 16972790 . GAAT AA 106 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00035;SOR=0.0;LSEQ=CCTTGTAGCTTTGATCCCCT;RSEQ=GAACAAACTGTGGACATGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:11:10,1:104,22:126,11:0.0791:2,2:12.0:1.0:30.9:1.0:0.69024:2.11:34.7:22.0:0.0815:0.0288:0.6 0/0:142:0:0,0:99,42:141,0:0.0:2,0:11.1:1.0:31.0:1.0:1.0:0.0:28.2:69.5:0.9929:0.0:0.1 +1 16974817 . C G 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=7e-05;SOR=0.04067;LSEQ=GCTACCACGGCGCGGGGGAG;RSEQ=AGTACCGCGGCACGGTCAGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:11:6,5:17,9:26,11:0.2973:2,2:12.1:1.0:31.6:1.0:0.71298:1.55431:21.4:22.0:0.3056:0.0:2.0 0/1:61:1:0,1:21,38:59,1:0.0164:2,0:13.0:0.0:32.0:0.0:1.0:0.0:21.0:2.0:0.0164:0.0:2.0 +1 16975228 . C T 188 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCAAAGGCTGGCTCCCTTAA;RSEQ=CGCAGTGAACTTTGTCTTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:200:76:34,42:62,61:123,76:0.38:2,2:30.3:1.0:30.1:1.0:0.46771:1.2541:21.8:37.0:0.3776:0.0:1.1 0/0:198:0:0,0:108,90:198,0:0.0:2,0:28.9:1.0:30.8:1.0:1.0:0.0:30.2:197.0:1.0:0.0:0.1 +1 17087395 . G A 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.01208;SOR=0.11666;LSEQ=AGAAGAAGGCACAGGGTAAC;RSEQ=CCACGGCCCAGGCTCCCCTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:13:6,7:521,459:980,13:0.0131:2,2:18.3:1.0:28.8:1.0:0.78122:1.32387:21.8:26.0:0.0133:0.0:1.9 0/0:649:1:0,1:356,290:646,1:0.0015:2,0:26.0:0.0:25.0:0.0:0.44977:0.0:23.0:2.0:0.0016:0.0:2.0 +1 17345073 . G GC 71 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGAACAAGCTGCAGGCCCT;RSEQ=CTGATGTCAGTTCCACGGCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:17.0:1.0:30.9:1.0:1.0:0.0:60.0:10.0:0.5:0.3:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 17380195 . TC T 95 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.1032;SOR=0.0;LSEQ=TCAAGTCCCCTTTCTGAACG;RSEQ=CCCCCCCCCCGCACCCTTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:8,0:7,0:7,8:0.5333:0,0:34.3:1.0:31.9:1.0:1.0:0.0:60.0:16.0:0.5333:0.0:0.6 0/0:4:0:0,0:4,0:4,0:0.0:0,0:15.5:1.0:29.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:3.5 +1 17380653 . C A 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11654;LSEQ=ACCAAGTGGGAGGCGGCTTC;RSEQ=GGTTTCCCGGGTGGGCGGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:45:0,45:0,57:57,45:0.4412:1,1:23.6:1.0:33.2:1.0:1.0:0.0:60.0:90.0:0.4455:0.0:1.0 0/1:60:5:1,4:2,53:55,5:0.0833:1,2:28.4:1.0:31.2:1.0:0.23334:6.24:60.0:10.0:0.0862:0.0:1.0 +1 23111036 . C T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00216;SOR=0.0;LSEQ=CCACGTGGAGATGAAGTTTT;RSEQ=GGTGCGTGACTGCAGCAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1.0:0,2:24.7:1.0:30.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:5:0:0,0:2,3:5,0:0.0:2,0:17.8:1.0:31.6:1.0:1.0:0.0:52.2:10.0:1.0:0.0:0.2 +1 23880912 . G A 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01501;LSEQ=TGCCACTGACTGACCCCTAA;RSEQ=AGGAGAACTAATCAGAGAAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:253:181:164,17:61,10:71,181:0.7154:2,2:23.4:1.0:30.2:1.0:0.36446:1.58:60.0:35.2:0.7126:0.0:1.2 0/1:334:12:8,4:279,43:322,12:0.0359:2,2:18.5:1.0:29.3:1.0:0.07251:3.22799:60.0:24.0:0.0366:0.0:1.3 +1 23881005 . G A 301 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00735;LSEQ=GTGGGGAAGGACTTCGAGAG;RSEQ=GCAGAGGCTTCCCGGAGGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1198:904:507,397:165,128:293,904:0.7546:2,2:25.4:1.0:30.7:1.0:1.0:1.00938:59.9:44.2:0.7543:0.0:1.2 0/1:1541:34:16,18:788,717:1505,34:0.0221:2,2:25.4:1.0:29.2:1.0:0.60418:1.23623:60.0:68.0:0.0225:0.0:1.2 +1 23885230 . C G 126 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.00505;SOR=0.06954;LSEQ=GCCACTGCGGGAGGGCAGGG;RSEQ=CCAGGCGCATTTAAGGCTTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:31:18:18,0:13,0:13,18:0.5806:1,1:26.2:1.0:30.4:1.0:1.0:0.0:58.3:17.0:0.6071:0.0:1.1 0/1:12:1:1,0:11,0:11,1:0.0833:0,0:47.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0833:0.0:1.0 +1 23886338 . G GC 72 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTAGCCCAACACTGGTTCGA;RSEQ=CCACAGCTCCTCCGAGGTCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,1:1,5:0.8333:0,2:33.4:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 27023140 . TGGC T 83 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.0;MSILEN=3.0;SSF=0.00651;SOR=0.08781;LSEQ=GGGGCCGAGAGCAATGGGGG;RSEQ=GGCGGCGGCGGAGCCGGCAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:7:3,4:93,125:218,7:0.0311:2,2:20.7:1.0:29.6:1.0:1.0:1.01:60.0:6.0:0.0271:0.0089:0.1 0/0:357:1:1,0:169,182:351,1:0.0028:2,0:11.0:0.0:34.0:0.0:0.48295:0.0:60.0:2.0:0.0028:0.0:0.0 +1 27106967 . G A 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.10033;SOR=0.1695;LSEQ=AGTGCAGAAGGGCAGTATCG;RSEQ=CAACCTCCTGGGCTTCCTAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:5:2,3:229,233:462,5:0.0107:2,2:19.8:1.0:29.6:1.0:1.0:1.47303:60.0:10.0:0.0109:0.0:1.2 0/0:547:1:1,0:268,278:546,1:0.0018:2,0:1.0:0.0:23.0:0.0:0.49177:0.0:60.0:2.0:0.0018:0.0:1.0 +1 27533368 . G T 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02011;LSEQ=CGGCTGTTCTCTTGAGCAGC;RSEQ=TTCATTTATCTCCGTCTGCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:31:17,14:135,83:218,31:0.1245:2,2:26.1:1.0:30.1:1.0:0.55535:1.33784:59.7:30.0:0.1215:0.0:1.1 0/0:352:1:0,1:203,148:351,1:0.0028:2,0:1.0:0.0:26.0:0.0:0.4233:0.0:60.0:2.0:0.0029:0.0:1.0 +1 28637962 . AT A 93 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=13.0;MSILEN=1.0;SSF=0.33333;SOR=0.0;LSEQ=AAAAAAAATTAAAAAAAAAA;RSEQ=AATAATAATAATAATATGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:0,0:0,8:0.7273:0,0:13.4:1.0:31.0:1.0:1.0:0.0:60.0:16.0:0.7273:0.2727:0.1 0/0:1:0:0,0:1,0:1,0:0.0:0,0:22.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +1 29644328 . C T 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00048;SOR=0.0;LSEQ=GCCCTGTTGCCCCGGAACCG;RSEQ=GACAAGAACCGCAGCATGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:10:6,4:7,3:10,10:0.5:2,2:26.0:1.0:30.5:1.0:1.0:1.52135:60.0:20.0:0.5:0.0:1.2 0/0:18:0:0,0:11,7:18,0:0.0:2,0:25.2:1.0:30.0:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.1 +1 34805896 . G A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04805;SOR=0.0;LSEQ=CCTGGGAACCAGTGAATCCT;RSEQ=CCTCCACCCCATGTCTGACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:24.2:1.0:28.0:1.0:1.0:0.0:60.0:12.0:0.4286:0.0:1.7 0/0:9:0:0,0:9,0:9,0:0.0:0,0:21.3:1.0:31.8:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 +1 36824305 . C T 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTGGCATGACAGGCCCTGTT;RSEQ=CTGAGGCACCCTCACCCCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:692:104:57,47:342,246:588,104:0.1503:2,2:25.5:1.0:29.9:1.0:0.52078:1.14611:60.0:208.0:0.1529:0.0:2.1 0/0:690:0:0,0:408,281:689,0:0.0:2,0:25.9:1.0:30.3:1.0:1.0:0.0:60.0:67.9:1.0:0.0:0.4 +1 36941539 . G GT 105 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03612;SOR=0.0;LSEQ=AGTGTGTGCCTTTCCGCGGT;RSEQ=TAAGTGCTCTCACTGTAGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:0,12:1,3:4,12:0.75:2,0:19.0:1.0:29.4:1.0:0.25:0.0:60.0:24.0:0.75:0.3125:0.3 0/0:3:0:0,0:1,2:3,0:0.0:2,0:42.0:1.0:32.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +1 45798981 . C A 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02822;LSEQ=ATATGCCCGCCTGTCCAGGT;RSEQ=CATCTCATCTTCTGCCTGTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:879:32:21,11:438,408:846,32:0.0364:2,2:21.5:1.0:29.0:1.0:0.14967:1.78:60.0:64.0:0.037:0.0:1.3 0/0:939:1:1,0:486,452:938,1:0.0011:2,0:1.0:0.0:21.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 +1 45805566 . G C 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=7.0;SSF=1.0;SOR=0.0;LSEQ=ACCCAGCCACCCCACTACCC;RSEQ=CTACCCGCGGCCCACGCTGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:18.4:1.0:32.6:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 46509146 . G A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01087;SOR=0.0;LSEQ=GCTTAGTATGTCAGTGCAGC;RSEQ=GCATGGCTGAGTCCTAGAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:31.2:1.0:31.2:1.0:1.0:0.0:55.0:10.0:0.4545:0.0:1.0 0/0:13:0:0,0:12,1:13,0:0.0:1,0:23.5:1.0:30.2:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.2 +1 46740500 . A G 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00714;SOR=0.0;LSEQ=TCTGCCTCTAGCAGTAGCCA;RSEQ=GCTATGGGCCCAGAAGTGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:8:0,8:0,78:78,8:0.093:1,0:32.8:1.0:32.8:1.0:1.0:0.0:60.0:16.0:0.0941:0.0:1.0 0/0:77:0:0,0:0,77:77,0:0.0:1,0:23.5:1.0:31.6:1.0:1.0:0.0:59.9:154.0:1.0:0.0:0.0 +1 51436157 . G T 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=GCACAAAATGGATTTGGAAG;RSEQ=ACTGCGCTGCAGGTTGGTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:14:5,9:170,265:435,14:0.0312:2,2:22.3:1.0:29.4:1.0:1.0:1.15439:60.0:28.0:0.0314:0.0:1.0 0/0:530:0:0,0:210,320:530,0:0.0:2,0:26.6:1.0:30.4:1.0:1.0:0.0:60.0:105.0:1.0:0.0:0.2 +1 51439777 . C T 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11593;LSEQ=CACTTGGCTGCCAAAGAAGG;RSEQ=CACCTCCGGGTGGTGGAGTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:80:32,48:167,202:369,80:0.1782:2,2:22.0:1.0:30.0:1.0:0.45661:1.23951:60.0:79.0:0.1779:0.0:1.1 0/1:572:14:9,5:237,320:557,14:0.0245:2,2:33.3:1.0:27.2:1.0:0.16968:2.43:60.0:13.0:0.0232:0.0:1.2 +1 51441409 . A G 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03054;SOR=0.0;LSEQ=TTTTCAATAATTTATTTTCC;RSEQ=TGATAGTATAAAAGAATATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:5:2,3:100,222:322,5:0.0153:2,2:34.6:1.0:32.4:1.0:0.64904:1.48:60.0:10.0:0.0154:0.0:1.0 0/0:328:0:0,0:129,199:328,0:0.0:2,0:24.5:1.0:29.6:1.0:1.0:0.0:60.0:108.333:1.0:0.0:0.1 +1 58158647 . C G 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02391;SOR=0.0;LSEQ=CCCCTTTCTAGGTCCCATAA;RSEQ=AGCCATCTTGCTATTACTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:6:1,5:8,13:21,6:0.2222:2,2:32.3:1.0:32.7:1.0:0.62785:2.96583:50.0:12.0:0.2222:0.0:1.0 0/0:24:0:0,0:10,13:23,0:0.0:2,0:19.6:1.0:30.3:1.0:1.0:0.0:55.4:46.0:0.9583:0.0:0.3 +1 59250675 . C G 265 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10766;LSEQ=TAACAGGGTCCAGATGGGAA;RSEQ=AAGCGTGTAGGCGATCCGAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1544:274:158,116:676,592:1268,274:0.1775:2,2:28.3:1.0:32.8:1.0:0.20419:1.19:60.0:273.0:0.1796:0.0:1.1 0/1:1631:37:22,15:844,747:1591,37:0.0227:2,2:25.7:1.0:30.9:1.0:0.5066:1.3:60.0:36.0:0.0224:0.0:1.2 +1 65312100 . TG T 66 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.54404;SOR=0.0;LSEQ=CTAGCACAGTGTAGGGTTCT;RSEQ=GCCAGCGTTGACAAGAAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:5,0:14,1:15,5:0.25:1,0:26.0:1.0:28.8:1.0:1.0:0.0:60.0:4.0:0.2:0.1:0.2 0/0:4:0:0,0:4,0:4,0:0.0:0,0:32.3:1.0:32.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +1 65332766 . T C 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATGCGTGGACACGCTGCTG;RSEQ=CACAAATGGTCTTGTTGTTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:25:10,15:271,336:607,25:0.0394:2,2:21.6:1.0:31.0:1.0:0.68672:1.20946:60.0:24.0:0.0385:0.0:1.0 0/0:658:0:0,0:317,341:658,0:0.0:2,0:24.1:1.0:28.7:1.0:1.0:0.0:60.0:218.333:1.0:0.0:0.1 +1 65349304 . G A 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00228;SOR=0.0;LSEQ=CCCTGCCCCTTCCCTTCCTG;RSEQ=AAACCAAACATGTCAGATCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:11:1,10:1,35:36,11:0.234:1,2:29.2:1.0:31.9:1.0:0.41721:3.38:60.0:22.0:0.2444:0.0:1.3 0/0:32:0:0,0:0,32:32,0:0.0:1,0:25.6:1.0:30.9:1.0:1.0:0.0:60.0:15.0:1.0:0.0:0.1 +1 65351748 . C T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01358;SOR=0.0;LSEQ=CAAGGGAAGTTTAACTTTTA;RSEQ=TCTGTACCTCCTATACTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:7,0:47,0:47,7:0.1296:1,0:21.0:1.0:31.6:1.0:1.0:0.0:60.0:14.0:0.1321:0.0:1.0 0/0:48:0:0,0:47,1:48,0:0.0:1,0:24.5:1.0:31.9:1.0:1.0:0.0:60.0:47.0:1.0:0.0:0.0 +1 69777307 . A G 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01767;SOR=0.0;LSEQ=ATTGATTCTTTCTCGTCATG;RSEQ=GTTTGTCTACTTTCAGTCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:8,6:14,5:0.2632:2,2:28.2:1.0:30.6:1.0:0.62848:1.92739:60.0:10.0:0.2632:0.0:1.4 0/0:21:0:0,0:12,9:21,0:0.0:2,0:20.8:1.0:29.1:1.0:1.0:0.0:57.3:42.0:1.0:0.0:0.0 +1 72058827 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03643;SOR=0.0;LSEQ=TTAGTAGATTTGGGGGAGGT;RSEQ=AGGTTGCATGTCAGCTGTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:6:0,6:1,42:43,6:0.1224:1,0:20.0:1.0:31.7:1.0:1.0:0.0:60.0:12.0:0.125:0.0:2.0 0/0:36:0:0,0:2,34:36,0:0.0:2,0:23.9:1.0:31.0:1.0:1.0:0.0:60.0:35.0:1.0:0.0:0.6 +1 78414402 . GT G 81 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.00598;SOR=0.0;LSEQ=CATCCATATATTTAACAAAG;RSEQ=TTTTTTCCCCCACACAATGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:6:3,3:252,206:458,6:0.0129:2,2:29.7:1.0:31.5:1.0:1.0:1.22276:60.0:12.0:0.0132:0.0:0.2 0/0:623:0:0,0:348,275:623,0:0.0:2,0:27.0:1.0:28.3:1.0:1.0:0.0:59.9:33.611:1.0:0.0:0.2 +1 78432659 . T A 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTAGTTAGAAAAAAAAAAA;RSEQ=TTTTTTTTTGGTTGAAAGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:301:18:6,12:128,143:271,18:0.0598:2,2:13.7:1.0:30.3:1.0:0.33096:1.78673:60.0:36.0:0.061:0.0:1.1 0/0:359:0:0,0:136,159:295,0:0.0:2,0:22.6:1.0:29.3:1.0:1.0:0.0:59.7:48.167:0.8257:0.0:0.3 +1 84971819 . G A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.0087;SOR=0.0;LSEQ=TCGTGGGTCGGTGGGTCGTG;RSEQ=GCCGTGGGTCGGCGGGGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:6:1,5:6,13:19,6:0.24:2,2:24.0:1.0:29.5:1.0:0.63715:2.23947:56.7:5.0:0.2083:0.0:2.0 0/0:27:0:0,0:5,22:27,0:0.0:2,0:19.1:1.0:29.4:1.0:1.0:0.0:54.8:26.0:1.0:0.0:0.2 +1 85733704 . TA T 72 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.06218;SOR=0.0;LSEQ=GATGTAAATGAAAAAGTAAC;RSEQ=AAAAAATGGAGTCACTGTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:5:2,3:100,338:438,5:0.0113:2,2:35.6:1.0:31.4:1.0:0.32539:2.25:60.0:10.0:0.0115:0.0:0.0 0/0:421:0:0,0:97,324:421,0:0.0:2,0:22.0:1.0:29.0:1.0:1.0:0.0:60.0:59.143:1.0:0.0:0.1 +1 85739751 . T C 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.2719;SOR=0.0;LSEQ=ATGCTCTTCCCTCAGTTCTG;RSEQ=CAAATCTTTCAGGAATCAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:7,0:10,1:11,7:0.3889:2,0:22.4:1.0:32.1:1.0:1.0:0.0:60.0:14.0:0.3889:0.0:1.3 0/0:5:0:0,0:5,0:5,0:0.0:0,0:26.0:1.0:29.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 +1 85739778 . A G 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01124;SOR=0.0;LSEQ=TTTCAGGAATCAGTTTAAAT;RSEQ=TAACCTCTCCTGACCATCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:10,1:23,0:23,11:0.3235:1,2:22.6:1.0:33.2:1.0:0.32353:0.0:60.0:22.0:0.3235:0.0:1.7 0/0:15:0:0,0:15,0:15,0:0.0:1,0:18.9:1.0:28.1:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 +1 85739861 . A G 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=4e-05;SOR=0.13736;LSEQ=ATTCCTTCATAGTAATTGCA;RSEQ=TAATGAAAACAAAATTTATT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:31:31,0:77,0:77,31:0.287:1,1:23.2:1.0:33.3:1.0:1.0:0.0:60.0:62.0:0.2897:0.0:1.2 0/1:77:4:4,0:73,0:73,4:0.0519:1,0:19.0:1.0:29.5:1.0:1.0:0.0:60.0:8.0:0.0526:0.0:1.0 +1 85741968 . G C 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGCCCGCCCTGGGCACAGCT;RSEQ=CGTTACTCACGTCCTTCTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1483:70:39,31:713,695:1408,70:0.0472:2,2:26.2:1.0:31.9:1.0:0.46286:1.23:60.0:140.0:0.0483:0.0:1.6 0/0:1926:0:0,0:969,953:1922,0:0.0:2,0:24.9:1.0:31.2:1.0:1.0:0.0:60.0:67.643:0.9984:0.0:0.8 +1 85742157 . G C 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.00183;SOR=0.0;LSEQ=GAGGAGGCGGAGCGGGTCGG;RSEQ=AGAAAGACGGCCGCCCCTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:248:10:0,10:14,221:235,10:0.0403:2,0:27.9:1.0:31.0:1.0:1.0:0.0:60.0:9.0:0.0378:0.0:1.1 0/0:236:0:0,0:13,223:236,0:0.0:2,0:24.1:1.0:31.1:1.0:1.0:0.0:60.0:77.667:1.0:0.0:0.2 +1 90228304 . TCT GAAAAACGTAA 78 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.06061;SOR=0.0;LSEQ=CATTTCAGACCTGGGACTGG;RSEQ=GAAACTGTATAATGGAATGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:1,5:0,2:2,6:0.75:0,2:18.7:1.0:30.3:1.0:1.0:0.0:59.2:12.0:0.75:0.375:1.3 0/0:3:0:0,0:1,2:3,0:0.0:2,0:13.0:1.0:29.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 +1 101971074 . T C 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CTTATACTGACCACTGGAGT;RSEQ=GGGCGACATGGCTTCTCCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:13:3,10:26,23:49,13:0.2097:2,2:27.9:1.0:30.8:1.0:0.06704:3.69123:45.1:26.0:0.2167:0.0:1.0 0/0:84:0:0,0:38,46:84,0:0.0:2,0:30.1:1.0:29.8:1.0:1.0:0.0:41.8:168.0:1.0:0.0:0.3 +1 117753543 . G A 174 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGCCGCTGCCTTCCTTGGT;RSEQ=ACTCACAACCAGCTCCCGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:401:48:9,39:98,255:353,48:0.1197:2,2:25.4:1.0:31.2:1.0:0.22468:1.66344:60.0:96.0:0.1228:0.0:1.0 0/0:337:0:0,0:108,229:337,0:0.0:2,0:22.4:1.0:30.2:1.0:1.0:0.0:60.0:47.143:1.0:0.0:0.1 +1 118156191 . T A 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.16973;LSEQ=CTGTGTGTTGGCTTCTCACT;RSEQ=CTTAGTGGGAAGTGAGAATT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:53:12,41:52,257:309,53:0.1464:2,2:22.5:1.0:29.7:1.0:0.33012:1.44:60.0:106.0:0.1489:0.0:1.1 0/1:248:7:0,7:50,191:241,7:0.0282:2,0:15.4:1.0:29.7:1.0:0.35031:0.0:60.0:14.0:0.0287:0.0:1.3 +1 118161094 . GTC G 232 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.11196;LSEQ=AGGCATTCTAAAGGAAAAGA;RSEQ=TCTCTTCCTCTGTTCATCCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:137:78,59:311,237:548,137:0.2:2,2:27.7:1.0:32.7:1.0:1.0:1.01:59.8:274.0:0.2024:0.019:0.3 0/1:662:18:9,9:349,294:643,18:0.0272:2,2:21.1:1.0:31.0:1.0:0.81221:1.18676:59.7:36.0:0.0275:0.0045:0.4 +1 118166096 . C T 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.14709;LSEQ=GACTGTTCCAATAATCCCAT;RSEQ=TCTGAGCACTTCCACCCCAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1143:189:86,103:455,499:954,189:0.1654:2,2:25.0:1.0:30.3:1.0:0.63246:1.09197:59.9:36.8:0.1636:0.0:1.1 0/1:1025:29:17,12:497,497:994,29:0.0283:2,2:24.4:1.0:29.8:1.0:0.45188:1.42:60.0:58.0:0.0286:0.0:1.1 +1 118166750 . A G 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00016;SOR=0.0;LSEQ=GCCTCCTTCTAGATGTAGGC;RSEQ=TTTGGCTTTTAAAGGGGAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:20:1,19:0,32:32,20:0.3846:1,1:25.7:1.0:30.6:1.0:0.38462:0.0:58.0:9.0:0.3913:0.0:1.4 0/0:24:0:0,0:1,23:24,0:0.0:1,0:29.3:1.0:30.4:1.0:1.0:0.0:60.0:48.0:1.0:0.0:0.2 +1 120429402 . A G 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07847;SOR=0.0;LSEQ=CTCTCTTCTAGTTAGAGGGT;RSEQ=GAATTGGAAATTAAGAATTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:5:5,0:70,3:73,5:0.0641:1,0:27.0:1.0:33.6:1.0:1.0:0.0:60.0:10.0:0.0641:0.0:1.0 0/0:54:0:0,0:51,3:54,0:0.0:2,0:26.4:1.0:27.8:1.0:1.0:0.0:60.0:108.0:1.0:0.0:0.0 +1 120468134 . C T 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCCTCATCACAGACGCCATC;RSEQ=CGAGCTTTGTCGGCACAATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:967:176:80,96:352,438:790,176:0.182:2,2:22.2:1.0:30.6:1.0:0.86696:1.04:60.0:34.2:0.1806:0.0:1.1 0/0:804:0:0,0:358,446:804,0:0.0:2,0:24.8:1.0:30.0:1.0:1.0:0.0:60.0:72.091:1.0:0.0:0.2 +1 120468487 . T C 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGTAGGAAAACAGTCATAT;RSEQ=GGAAGTTTGAGGTTTCTAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:32:3,29:14,95:109,32:0.227:2,2:26.6:1.0:29.3:1.0:0.7627:1.42131:60.0:31.0:0.223:0.0:1.2 0/0:154:0:0,0:34,119:153,0:0.0:2,0:22.0:1.0:29.5:1.0:1.0:0.0:60.0:152.0:0.9935:0.0:0.1 +1 120469388 . ACACT A 75 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.15209;SOR=0.0;LSEQ=AATCTGAGCATAGAAAGAAA;RSEQ=CACTGCATCTCAACATGATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:0,5:0,20:20,5:0.2:1,0:20.6:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.2:0.0:0.2 0/0:12:0:0,0:0,12:12,0:0.0:0,0:28.0:1.0:32.9:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.2 +1 120611715 . A G 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.48571;SOR=0.0;LSEQ=CTCCTGCCGAGGAGGCGTGT;RSEQ=AGGGGTCCCGGGCCGCGGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:7,0:7,6:0.4615:0,0:10.7:1.0:31.0:1.0:1.0:0.0:39.2:5.0:0.4167:0.0:2.3 0/0:2:0:0,0:2,0:2,0:0.0:0,0:9.5:1.0:29.0:0.0:1.0:0.0:51.0:4.0:1.0:0.0:0.0 +1 121484636 . T G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=5.0;SSF=0.01052;SOR=0.08308;LSEQ=AACTCTCAGAGTTTAACTTT;RSEQ=CTTTTCATTCAGCAGTTTGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:5:3,2:48,53:101,5:0.0472:2,2:31.2:1.0:32.8:1.0:0.66993:1.65:31.2:10.0:0.0476:0.0:2.4 0/0:246:1:1,0:115,129:244,1:0.0041:2,0:40.0:0.0:29.0:0.0:0.47347:0.0:23.0:2.0:0.0041:0.0:3.0 +1 121484973 . C T 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00044;SOR=0.0;LSEQ=TTCAACTCACAGAGTTTAAC;RSEQ=TTTCTGTTCATAGAGCAGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:6:3,3:47,41:88,6:0.0625:2,2:19.2:1.0:32.2:1.0:1.0:1.14467:28.2:12.0:0.0625:0.0:4.5 0/0:246:0:0,0:119,125:244,0:0.0:2,0:36.0:0.0:18.0:0.0:1.0:0.0:34.0:0.0:0.0:0.0:4.0 +1 121485011 . T A 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00612;SOR=0.12888;LSEQ=GTTAGGAAACGCTCTGTTTG;RSEQ=AAAGTCTGTAAGTGGATATT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:7:3,4:44,46:90,7:0.0722:2,2:15.1:1.0:32.0:1.0:1.0:1.27219:40.7:14.0:0.0722:0.0:3.9 0/0:203:2:2,0:90,111:201,2:0.0099:2,0:25.0:1.0:25.0:1.0:0.20417:0.0:30.0:4.0:0.0099:0.0:4.0 +1 121485204 . C A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00996;SOR=0.137;LSEQ=TTTGCAAGTGGAGATTTCAG;RSEQ=CGCTTTGAGGTCAATGGTAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:6:2,4:132,150:282,6:0.0206:2,2:38.3:1.0:29.7:1.0:0.68881:1.75668:30.7:12.0:0.0208:0.0:4.0 0/0:697:2:1,1:333,360:693,2:0.0029:2,2:26.5:1.0:30.5:1.0:1.0:1.08:22.5:4.0:0.0029:0.0:4.5 +1 149857797 . T C 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCGAGCGAGCGAGCGCCAGG;RSEQ=CCCGGCAGGGACTCACTTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:23:14,9:35,23:58,23:0.284:2,2:22.4:1.0:30.9:1.0:1.0:1.02:50.0:22.0:0.275:0.0:1.1 0/0:56:0:0,0:35,21:56,0:0.0:2,0:27.2:1.0:28.7:1.0:1.0:0.0:53.9:112.0:1.0:0.0:0.1 +1 150552042 . G A 261 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.08189;LSEQ=CCGCCTGGCTGAGAAAACTG;RSEQ=GGAAGACCCCGACTCCTTAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:571:337:106,231:75,157:232,337:0.5902:2,2:22.1:1.0:31.2:1.0:0.85487:1.041:60.0:32.7:0.586:0.0:1.2 0/1:532:56:15,41:157,317:474,56:0.1053:2,2:20.4:1.0:29.7:1.0:0.36905:1.35298:60.0:55.0:0.1048:0.0:1.2 +1 152330829 . G T 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTAGATGGAATAAAATGCT;RSEQ=GCATTTTATTTTTGATTCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:256:79:56,23:134,43:177,79:0.3086:2,2:21.9:1.0:30.7:1.0:0.44125:1.2786:59.9:158.0:0.3123:0.0:1.1 0/0:145:0:0,0:105,40:145,0:0.0:2,0:21.2:1.0:31.0:1.0:1.0:0.0:60.0:144.0:1.0:0.0:0.1 +1 152331013 . G A 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0001;SOR=0.06305;LSEQ=AAAGTCTGAGAGTCTATGAG;RSEQ=TAGGAGTGCATAGGTGGAAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:212:26:7,19:46,140:186,26:0.1226:2,2:22.5:1.0:30.6:1.0:0.81109:1.12:60.0:52.0:0.125:0.0:1.1 0/0:115:1:1,0:28,86:114,1:0.0087:2,0:1.0:0.0:25.0:0.0:0.25217:0.0:60.0:2.0:0.0087:0.0:1.0 +1 154842199 . G GGCTGCTGCT 94 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=43;MSI=17.0;MSILEN=3.0;SSF=0.01771;SOR=0.0;LSEQ=GCTGAGACAGGGGATGCGGT;RSEQ=GCTGCTGCTGCTGCTGCTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:7,1:2,3:5,8:0.5714:2,2:31.6:1.0:31.6:1.0:0.21678:8.37:50.6:16.0:0.5714:0.1429:1.0 0/0:8:0:0,0:3,1:4,0:0.0:2,0:43.0:1.0:27.5:1.0:1.0:0.0:60.0:8.0:0.5:0.0:0.0 +1 156785653 . C G 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ACTCCTCATTTTCGTTCTCT;RSEQ=TCTCTGTGCCCCAGCCCGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1266:43:17,26:547,672:1219,43:0.034:2,2:28.6:1.0:32.6:1.0:0.53505:1.24471:59.5:86.0:0.0343:0.0:1.9 0/0:988:0:0,0:463,524:987,0:0.0:2,0:25.7:1.0:31.0:1.0:1.0:0.0:60.0:108.667:0.999:0.0:0.7 +1 156838809 . TC T 68 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCGTACATCACTTTTCTCTC;RSEQ=CCTTCCTTCCTTCCTTCCTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1.0:0,2:29.0:1.0:29.6:1.0:1.0:0.0:49.8:10.0:1.0:0.2:0.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 156848778 . C T 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.004;SOR=0.0;LSEQ=ACCCCTCTGGACAGCTGCCT;RSEQ=TACTGTTCTCTCAATCCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:20:20,0:92,1:93,20:0.177:1,1:25.5:1.0:30.4:1.0:1.0:0.0:58.9:19.0:0.1712:0.0:3.1 0/0:38:0:0,0:37,1:38,0:0.0:1,0:26.5:1.0:30.6:1.0:1.0:0.0:60.0:37.0:1.0:0.0:1.6 +1 156849047 . G T 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=ACCTGGCGGGTCTGCATTTT;RSEQ=TGCACCGGGACCTGGCCACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1254:27:14,13:655,570:1225,27:0.0215:2,2:21.8:1.0:30.3:1.0:1.0:1.06696:59.3:26.0:0.021:0.0:1.4 0/0:678:0:0,0:369,308:677,0:0.0:2,0:23.4:1.0:31.3:1.0:1.0:0.0:60.0:60.545:0.9985:0.0:0.4 +1 156849505 . G A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTGACTCCCTGGTTCAAGC;RSEQ=ATTCTCCTGCTTCAGCCTCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:4,1:6,3:9,5:0.3571:2,2:12.4:1.0:30.4:1.0:1.0:1.91:35.6:10.0:0.3571:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 156849658 . C T 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.1144;SOR=0.0;LSEQ=TGATTGCCCACCTCGGCCTC;RSEQ=CAAAGTGCTGGGATTACAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:10:9,1:74,0:74,10:0.119:1,2:31.7:1.0:31.6:1.0:0.11905:0.0:51.2:20.0:0.1266:0.0:1.1 0/0:23:0:0,0:22,1:23,0:0.0:1,0:29.4:1.0:31.0:1.0:1.0:0.0:52.0:46.0:1.0:0.0:0.2 +1 157599882 . C A 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAGCAGAACTGGAGCTGGA;RSEQ=TTCTGATCTCTCTAGAGAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:32:18,14:115,87:202,32:0.1368:2,2:26.6:1.0:31.2:1.0:1.0:1.02799:53.5:64.0:0.1379:0.0:3.0 0/0:204:0:0,0:114,87:201,0:0.0:2,0:26.6:1.0:31.4:1.0:1.0:0.0:58.3:99.5:0.9851:0.0:0.9 +1 162736690 . C T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATTAGCCGGGCGTAGTGG;RSEQ=GCATGCCTGTAATCCCAGCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:21.2:1.0:29.0:1.0:1.0:0.0:29.5:12.0:0.8571:0.0:1.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 162737241 . A G 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00219;SOR=0.0;LSEQ=GTAAAAGGCAAATTGCAAAC;RSEQ=TTTATTAATGGTTGGAATTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:171:18:0,18:7,146:153,18:0.1053:1,1:25.9:1.0:29.2:1.0:1.0:0.0:60.0:8.0:0.0988:0.0:1.2 0/0:71:0:0,0:3,68:71,0:0.0:1,0:20.3:1.0:30.4:1.0:1.0:0.0:60.0:142.0:1.0:0.0:0.0 +1 162740121 . G A 234 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.14707;LSEQ=AGGATGCTGGATGATGAAAT;RSEQ=ACAGTCAGCCTTTCCCTGCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1055:262:179,83:476,316:792,262:0.2483:2,2:24.5:1.0:29.2:1.0:0.01869:1.43:60.0:130.0:0.249:0.0:1.1 0/1:756:35:21,14:420,301:721,35:0.0463:2,2:27.5:1.0:28.0:1.0:0.86293:1.07:60.0:34.0:0.0452:0.0:1.2 +1 162750208 . C T 104 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00101;SOR=0.0;LSEQ=CCCTACCCCTGACTCATATA;RSEQ=ACTTTTTTTTTTTTTTACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:20:0,20:0,0:0,20:0.4545:0,1:13.3:1.0:24.1:1.0:1.0:0.0:60.0:2.333:0.4:0.0:1.9 0/0:15:0:0,0:0,1:1,0:0.0:0,0:11.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.0667:0.0:0.0 +1 162830985 . CCCTCCCTA C 86 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACTTGAAAGCTCTCTTCGT;RSEQ=CCTCCCCTGGTCAGGAATGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:25.5:1.0:33.3:1.0:1.0:0.0:60.0:12.0:0.6667:0.1111:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 165044147 . G A 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTGTTTGTTTATTTTTTGG;RSEQ=AATAGCGCAAATGTTCTACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:108:62:11,51:8,38:46,62:0.5741:2,2:22.3:1.0:31.5:1.0:1.0:1.02:60.0:124.0:0.5741:0.0:1.1 0/0:74:0:0,0:17,57:74,0:0.0:2,0:25.2:1.0:30.4:1.0:1.0:0.0:60.0:73.0:1.0:0.0:0.2 +1 168652905 . G C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00445;SOR=0.0;LSEQ=TGTATAGGGTGTCTGACAAC;RSEQ=CCTGTTGGAGGGTCTCACCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:5,3:5,5:10,8:0.4444:2,2:24.1:1.0:29.0:1.0:0.66406:1.62:46.1:7.0:0.4118:0.0:1.5 0/0:14:0:0,0:9,5:14,0:0.0:2,0:12.5:1.0:28.9:1.0:1.0:0.0:59.3:28.0:1.0:0.0:0.4 +1 171207335 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00749;SOR=0.0;LSEQ=GATATCTCCAGGCACAGGAG;RSEQ=GAATCAGATGAATAAGACCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:4,3:4,2:6,7:0.5385:2,2:24.4:1.0:27.7:1.0:1.0:1.45385:38.1:14.0:0.5385:0.0:1.9 0/0:10:0:0,0:4,6:10,0:0.0:2,0:32.0:1.0:30.7:1.0:1.0:0.0:54.2:20.0:1.0:0.0:0.7 +1 173485336 . C T 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTTGTCCCTTGGTCTTTGG;RSEQ=TCATTTCTATTTGAATTCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:19:7,12:7,4:11,19:0.6333:2,2:23.4:1.0:29.9:1.0:0.25677:2.88672:60.0:38.0:0.6333:0.0:1.1 0/0:27:0:0,0:14,13:27,0:0.0:2,0:27.9:1.0:31.0:1.0:1.0:0.0:60.0:54.0:1.0:0.0:0.1 +1 175869807 . C G 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06479;SOR=0.0;LSEQ=ACATTGTGCAACTCAGTGAG;RSEQ=CCTCACACATTGAACACATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:10,7:0.4118:0,0:22.1:1.0:29.6:1.0:1.0:0.0:60.0:6.0:0.375:0.0:1.3 0/0:7:0:0,0:0,7:7,0:0.0:0,0:19.9:1.0:31.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.1 +1 175958637 . T A 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00047;SOR=0.0;LSEQ=TAAAACAAAACAAAATTAGA;RSEQ=AAATGTAGTAAATGCAGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:17:4,13:85,371:456,17:0.0359:2,2:19.3:1.0:29.1:1.0:0.53931:1.34:60.0:7.5:0.0326:0.0:1.3 0/0:293:0:0,0:59,233:292,0:0.0:2,0:23.1:1.0:27.7:1.0:1.0:0.0:59.9:72.0:1.0:0.0:0.1 +1 176050676 . A T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCAATAATTCCTTGGAAAAA;RSEQ=AATAATAACAATAATAATAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:17.3:1.0:29.2:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 176085412 . C G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCATAGGGCCAGCTACTTGA;RSEQ=AGGCTGAGGTAGGAGAATTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:13.2:1.0:32.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 176103954 . C T 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.57425;SOR=0.0;LSEQ=TAACATTATAGTATTCTACT;RSEQ=GCTAACTCTTCCTGGCATGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:8:8,0:38,1:39,8:0.1702:1,0:25.5:1.0:31.0:1.0:1.0:0.0:60.0:16.0:0.1778:0.0:1.0 0/0:6:0:0,0:6,0:6,0:0.0:0,0:22.3:1.0:32.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 +1 176175885 . C A 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00227;SOR=0.0;LSEQ=TGGACACCGCCCCGCCGCCG;RSEQ=TACCCGATACGGCGGGCGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:13:5,8:49,176:225,13:0.0546:2,2:24.8:1.0:31.4:1.0:0.17753:2.24:59.6:26.0:0.0563:0.0:1.3 0/0:153:0:0,0:51,102:153,0:0.0:2,0:20.3:1.0:32.1:1.0:1.0:0.0:60.0:152.0:1.0:0.0:0.3 +1 177294353 . G A 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.13364;SOR=0.0;LSEQ=AATTTGTTTCCTCTAGGATC;RSEQ=AGGCCATCGAGCTACAGATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:1,4:3,11:14,5:0.2632:2,2:24.8:1.0:30.0:1.0:1.0:1.086:26.0:10.0:0.2632:0.0:1.2 0/0:10:0:0,0:5,5:10,0:0.0:2,0:25.3:1.0:29.3:1.0:1.0:0.0:52.0:20.0:1.0:0.0:0.2 +1 181819068 . G A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.28871;SOR=0.0;LSEQ=ACATTTCCAGGCATGGAAGC;RSEQ=AATCAGATGAATAGGGCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:3,3:6,8:14,6:0.3:2,2:33.7:1.0:31.2:1.0:1.0:1.31:60.0:12.0:0.3:0.0:1.0 0/0:5:0:0,0:3,2:5,0:0.0:2,0:17.0:1.0:33.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.6 +1 181819202 . C T 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=AAAAATAACAACAAAACGGG;RSEQ=CCCCACAAAAACCCCATCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:22:11,11:39,35:74,22:0.2292:2,2:27.7:1.0:29.3:1.0:1.0:1.11303:54.9:44.0:0.2316:0.0:2.6 0/0:51:0:0,0:25,26:51,0:0.0:2,0:29.2:1.0:29.5:1.0:1.0:0.0:53.2:50.0:1.0:0.0:1.6 +1 184327323 . T G 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAAGAAAAAGTAAGAATATA;RSEQ=TCTTCTTAATAACCTTCACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:76:28,48:71,145:216,76:0.2603:2,2:25.8:1.0:31.5:1.0:0.57385:1.19:60.0:24.333:0.2544:0.0:1.1 0/0:150:0:0,0:48,101:149,0:0.0:2,0:22.5:1.0:29.2:1.0:1.0:0.0:60.0:48.667:0.9932:0.0:0.3 +1 185520654 . C G 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00031;SOR=0.0;LSEQ=TGTGAAGTTTCTGCAACAGT;RSEQ=CTATGGTCTTTCACCTTCGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:613:23:6,17:172,417:589,23:0.0375:2,2:22.9:1.0:30.3:1.0:1.0:1.16837:60.0:10.5:0.0347:0.0:1.0 0/0:281:0:0,0:89,192:281,0:0.0:2,0:23.2:1.0:30.4:1.0:1.0:0.0:60.0:139.5:1.0:0.0:0.4 +1 193091490 . G T 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00011;SOR=0.0;LSEQ=GGCATGGCTGTGGCCCAGGG;RSEQ=TGGCAGGGCAGAGTTGGGCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:767:21:6,15:224,521:745,21:0.0274:2,2:22.0:1.0:30.0:1.0:1.0:1.07476:60.0:42.0:0.0276:0.0:1.2 0/0:421:0:0,0:131,290:421,0:0.0:2,0:22.8:1.0:30.7:1.0:1.0:0.0:60.0:139.333:1.0:0.0:0.1 +1 193104712 . G A 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCAGAAGCAAAGAAACCAC;RSEQ=AATTGAGGTAAAGAAACTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:815:134:45,89:268,413:681,134:0.1644:2,2:28.6:1.0:30.8:1.0:0.24362:1.28301:60.0:66.0:0.1632:0.0:1.1 0/0:525:0:0,0:219,306:525,0:0.0:2,0:26.5:1.0:29.7:1.0:1.0:0.0:60.0:74.0:1.0:0.0:0.1 +1 193105216 . A G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTTTCCGTGTTGGCCAGGCT;RSEQ=CAGAATTCTTTCTTTATGAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:32.8:1.0:32.2:1.0:1.0:0.0:55.2:10.0:1.0:0.0:2.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 193173335 . GTGTATATATA G 68 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=4.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ACACACACACATATATATAC;RSEQ=TGTATATATATGTATATATA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:30.6:1.0:29.5:1.0:1.0:0.0:47.2:10.0:0.7143:0.1429:2.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 193173356 . TG CA 75 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=9;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTATATATATGTATATATA;RSEQ=TATATATACACGTATATATA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:35.4:1.0:32.7:1.0:1.0:0.0:47.2:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 193202953 . G A 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=AACACTTTTATTGAATTTAA;RSEQ=TGTCCTTTAACAAAATATTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:0,7:1.0:0,2:14.6:1.0:30.9:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 193203035 . C T 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.25;SOR=0.0;LSEQ=AATTACCTTATTTCTTTAAC;RSEQ=GGGAGTAAAAGTTGAGTATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:9,1:12,0:12,10:0.4545:0,2:28.5:1.0:32.9:1.0:0.45455:0.0:60.0:20.0:0.4545:0.0:1.2 0/0:3:0:0,0:3,0:3,0:0.0:0,0:23.3:1.0:29.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 +1 193203268 . C T 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=5e-05;SOR=0.0;LSEQ=CTTAAACTTATGCCTCAAGA;RSEQ=TGGTAGGATAATTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:22:7,15:221,282:503,22:0.0418:2,2:18.1:1.0:30.7:1.0:0.28227:1.67775:56.4:44.0:0.0437:0.0:1.0 0/0:304:0:0,0:128,176:304,0:0.0:2,0:24.1:1.0:30.5:1.0:1.0:0.0:54.1:20.714:1.0:0.0:0.4 +1 193203305 . TCACACACACACACA T 176 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=23.0;MSILEN=2.0;SSF=0.0;SOR=0.13907;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CACACACACACACACACACA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:53:9,44:55,55:110,53:0.2524:2,2:29.8:1.0:30.9:1.0:4e-05:4.84294:46.0:52.0:0.2723:0.0905:0.5 0/1:112:5:0,5:36,54:90,5:0.0446:2,0:25.6:1.0:31.0:1.0:0.15289:0.0:40.8:10.0:0.0467:0.0089:0.6 +1 193203397 . T TTATAATATATATAATTTATTATATATATATTATA 115 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=15;MSI=4.0;MSILEN=2.0;SSF=0.00025;SOR=0.0;LSEQ=TATTTATATATATAATTTAA;RSEQ=TATAATATATATAATATACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:15:1,14:0,16:16,15:0.4839:1,1:20.9:1.0:29.5:1.0:0.48387:0.0:57.3:30.0:0.5357:0.3226:0.4 0/0:18:0:0,0:0,18:18,0:0.0:1,0:16.9:1.0:30.1:1.0:1.0:0.0:57.6:36.0:1.0:0.0:0.4 +1 198167287 . T C 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01067;SOR=0.0;LSEQ=GTGGGGGGATATGGATTTGG;RSEQ=CCTGGCTGGCCGGCATTGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:12:2,10:9,16:25,12:0.3243:2,2:21.9:1.0:30.4:1.0:0.27934:2.74057:42.4:11.0:0.3235:0.0:1.0 0/0:17:0:0,0:7,10:17,0:0.0:2,0:23.8:1.0:29.1:1.0:1.0:0.0:57.8:34.0:1.0:0.0:0.1 +1 202188932 . A G 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTCATTCTATACTAATAATT;RSEQ=TAATTCAGTTAGATGAGTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:1,3:4,5:0.5556:2,0:28.8:1.0:31.8:1.0:0.44444:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:44.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +1 203224985 . G T 60 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0614;SOR=0.0;LSEQ=ACCAGTTATCTTTAATAACG;RSEQ=CCAGTTTAGGGGCTGCTACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:5:3,2:36,28:64,5:0.0725:2,2:21.8:1.0:26.2:1.0:1.0:1.16:40.4:4.0:0.0597:0.0:1.0 0/0:59:0:0,0:26,33:59,0:0.0:2,0:27.3:1.0:30.5:1.0:1.0:0.0:54.8:118.0:1.0:0.0:0.1 +1 204495610 . G T 86 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00084;SOR=0.0;LSEQ=TTTTTGTTTTTTTTTTTTTT;RSEQ=AGATGGAGTCTCCCTCTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:11:6,5:35,146:181,11:0.057:2,2:6.5:1.0:25.1:1.0:0.0134:4.95:58.2:2.667:0.0485:0.0:1.6 0/0:192:0:0,0:43,143:186,0:0.0:2,0:18.2:1.0:29.0:1.0:1.0:0.0:55.3:7.857:0.9821:0.0:1.0 +1 204511602 . C A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CCATTTAGAAATTCTTTTAG;RSEQ=ACAAGGTCATTGTTCAGATG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:9.0:1.0:31.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 206648147 . T G 210 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11928;LSEQ=GCTCCAGGCTGAGCCACTTC;RSEQ=TCCTGGTGGGTGGGGAGGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:119:89,30:213,73:286,119:0.2931:2,2:24.8:1.0:30.5:1.0:1.0:1.02:60.0:118.0:0.2943:0.0:1.1 0/1:234:11:8,3:157,66:223,11:0.047:2,2:27.8:1.0:29.7:1.0:1.0:1.12:60.0:10.0:0.0439:0.0:1.2 +1 206650065 . A G 265 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTGCTTCGAAAGCCCCAGCA;RSEQ=AAAGCGTTCGGGGTGACTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1088:277:161,116:447,364:811,277:0.2546:2,2:25.7:1.0:32.7:1.0:0.40086:1.13:60.0:91.333:0.2537:0.0:1.1 0/0:817:0:0,0:422,395:817,0:0.0:2,0:25.1:1.0:29.6:1.0:1.0:0.0:60.0:101.125:1.0:0.0:0.2 +1 206669136 . C A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATCCATTTAAACTCCTTTC;RSEQ=CCTCCTAAACCTTGGCTACA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:24.4:1.0:30.6:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 206944952 . T G 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.18019;SOR=0.0;LSEQ=TCACTTAAATCAGGTCCTCC;RSEQ=CCTCAGAGTCAAGTTATTTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:8:0,8:1,30:31,8:0.2051:1,0:27.9:1.0:33.8:1.0:1.0:0.0:60.0:16.0:0.2105:0.0:1.3 0/0:10:0:0,0:1,9:10,0:0.0:2,0:22.2:1.0:29.6:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 +1 219991332 . A ATGG 106 p8 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00131;SOR=0.0;LSEQ=TTTTGTGCCTTAATCAGAAG;RSEQ=AGGAGGAGGAGGAGAAAGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:13:7,6:374,340:714,13:0.0178:2,2:5.2:1.0:28.7:1.0:1.0:1.06:58.0:12.0:0.0168:0.0165:0.8 0/0:492:0:0,0:243,241:484,0:0.0:2,0:23.5:1.0:28.7:1.0:1.0:0.0:59.7:47.4:0.9854:0.0:0.1 +1 221053574 . A C 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.03088;SOR=0.0;LSEQ=TACCACCACCATCACCCGCA;RSEQ=CAACAACAGCAGCAGCAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:6:5,1:54,46:100,6:0.0566:2,2:25.2:1.0:33.3:1.0:0.22369:4.21:60.0:12.0:0.0577:0.0:1.0 0/0:93:0:0,0:57,36:93,0:0.0:2,0:24.2:1.0:28.9:1.0:1.0:0.0:59.9:186.0:1.0:0.0:0.3 +1 224137928 . T C 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAAGATGTGTGCATAGCGGG;RSEQ=CCACTGCTGCTGCCCCTGCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:0,2:2,5:0.7143:0,2:36.0:1.0:32.2:1.0:1.0:0.0:20.2:10.0:0.8333:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 226253926 . T C 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CTTCAGGTCCTGAAGAAACA;RSEQ=ATAGGTAGAGAGAGCTTAAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:18.6:1.0:33.4:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 226254036 . T C 60 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAGGATTGGATTGGCAAGAT;RSEQ=GGGGGAACGGTGCTTAAAGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:23.8:1.0:26.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 226554736 . G C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCACCAGAGAAAAATGAAC;RSEQ=CAAGCATTGTGTTTTTATTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:24.0:1.0:31.1:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +1 226554951 . T C 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCAAGCTGAGGTGCTGGCT;RSEQ=GGAAGGCTGCCTTGCAAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:6:6,0:29,0:29,6:0.1714:1,0:23.7:1.0:31.3:1.0:1.0:0.0:60.0:12.0:0.1765:0.0:1.0 0/0:4:0:0,0:4,0:4,0:0.0:0,0:25.0:1.0:29.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +1 226567172 . A C 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.14745;LSEQ=GTGAGGACAAAGGCACGACC;RSEQ=CACTGCCCCAGGTATGCTGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:244:58:47,11:138,47:185,58:0.2377:2,2:22.3:1.0:30.7:1.0:0.37922:1.45:60.0:18.333:0.2311:0.0:1.0 0/1:137:6:6,0:111,19:130,6:0.0438:2,0:28.5:1.0:31.5:1.0:0.59491:0.0:60.0:12.0:0.0451:0.0:1.0 +1 226595403 . A AGGGCCC 102 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=13;MSI=3.0;MSILEN=1.0;SSF=0.14987;SOR=0.0;LSEQ=AGGCCCCAAGTGCCGCTCCG;RSEQ=GGGCCCGGGCCCGCTCGCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:8,1:17,0:17,9:0.3462:1,2:15.0:1.0:32.4:1.0:0.34615:0.0:60.0:18.0:0.3462:0.0769:0.2 0/0:6:0:0,0:6,0:6,0:0.0:0,0:8.3:1.0:30.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 +1 228617397 . G A 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGAGATTTCCTCTGCAAACT;RSEQ=AAGAGAATGTGAGATACAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:46:45,1:301,8:309,46:0.1296:1,1:20.8:1.0:28.8:1.0:1.0:1.2:59.7:92.0:0.1311:0.0:1.2 0/0:120:0:0,0:119,1:120,0:0.0:1,0:23.6:1.0:31.6:1.0:1.0:0.0:60.0:39.0:1.0:0.0:0.3 +1 229106423 . C CTG 140 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.00297;SOR=0.1238;LSEQ=CAGCTGGTGAAGTAAGTACT;RSEQ=TGGATGGTGGCGACTCTGGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:20:9,11:14,15:29,20:0.4082:2,2:27.1:1.0:32.6:1.0:1.0:1.13768:59.8:40.0:0.4082:0.0408:0.2 0/1:26:2:1,1:15,8:23,2:0.0769:2,2:26.0:0.0:32.5:1.0:1.0:1.82581:60.0:4.0:0.0769:0.0:0.5 +1 229223719 . G C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.36364;SOR=0.0;LSEQ=GGGGTTTCAAGAAAGGCTCA;RSEQ=AGTCAGCCTCACTTCAGGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,1:3,7:0.7:2,0:39.7:1.0:33.1:1.0:0.3:0.0:60.0:14.0:0.7:0.0:1.0 0/0:1:0:0,0:1,0:1,0:0.0:0,0:24.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +1 230355441 . G A 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTCTTGAGACTTCTGACGT;RSEQ=GATGCATTCCAGATGTGGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:430:114:56,58:154,162:316,114:0.2651:2,2:26.5:1.0:29.9:1.0:1.0:1.02:60.0:56.0:0.2623:0.0:2.1 0/0:304:0:0,0:143,161:304,0:0.0:2,0:25.8:1.0:30.4:1.0:1.0:0.0:60.0:75.0:1.0:0.0:0.4 +1 230355471 . G A 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07843;SOR=0.0;LSEQ=CAGATGTGGGGGCATTCTTT;RSEQ=CAAAGTGCTTGTGGCTGTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:388:5:3,2:162,221:383,5:0.0129:2,2:24.2:1.0:27.4:1.0:0.65449:2.04:60.0:10.0:0.0129:0.0:1.8 0/0:279:0:0,0:120,159:279,0:0.0:2,0:26.2:1.0:31.0:1.0:1.0:0.0:60.0:68.75:1.0:0.0:0.3 +1 230724588 . G GGTAGGTGTGCAGGTAAGTAGGTAGGTGTGTAGGTAAGCAGGTAGGTGTGTGGATAAGTA 167 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=37;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=AGTAGGTAGGTGTGTGGATA;RSEQ=GTAGGTGTGCAGGTAAGTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:47:13,34:33,30:63,47:0.4234:2,2:22.7:1.0:30.2:1.0:0.01137:2.84876:59.7:94.0:0.4312:0.3333:0.1 0/0:64:0:0,0:25,30:55,0:0.0:2,0:21.4:1.0:30.4:1.0:1.0:0.0:54.1:17.333:1.0:0.0:0.7 +1 241663893 . T TTGAG 76 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=4.0;MSILEN=4.0;SSF=0.09201;SOR=0.0;LSEQ=GTGTAACACATTTTTAATCT;RSEQ=TGAGTGAGTGAGAGAGAGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:426:6:0,6:128,287:415,6:0.0141:2,0:33.7:1.0:29.5:1.0:0.18414:0.0:57.5:12.0:0.0157:0.0:0.0 0/0:242:0:0,0:76,166:242,0:0.0:2,0:26.0:1.0:28.1:1.0:1.0:0.0:50.2:10.0:1.0:0.0:0.4 +1 241669668 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTTTATAGAACCATAAGGTA;RSEQ=GACAATGCCACTGATAACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:1,20:21,5:0.1923:1,0:18.4:1.0:30.6:1.0:1.0:0.0:60.0:10.0:0.1923:0.0:2.2 0/0:3:0:0,0:0,3:3,0:0.0:0,0:18.7:1.0:29.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 +1 243809488 . C T 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.06046;SOR=0.0;LSEQ=CATACACTCTCACCATCACC;RSEQ=CAAAGTGAAAATAATCCTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:12:1,11:0,53:53,12:0.1846:1,2:25.9:1.0:30.8:1.0:0.18462:0.0:60.0:24.0:0.1905:0.0:1.3 0/0:18:0:0,0:0,18:18,0:0.0:1,0:24.8:1.0:30.1:1.0:1.0:0.0:60.0:17.0:1.0:0.0:0.1 +1 247555079 . A G 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00059;SOR=0.0;LSEQ=CCTTATAAAATCCAGCTTTA;RSEQ=CAAGAATCCTGCTAAGTCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:15:6,9:9,24:33,15:0.3125:2,2:23.9:1.0:32.9:1.0:0.50411:1.76:55.1:30.0:0.3125:0.0:1.1 0/0:28:0:0,0:9,19:28,0:0.0:2,0:21.4:1.0:28.9:1.0:1.0:0.0:60.0:56.0:1.0:0.0:0.1 +1 248567502 . T TGTGTGTGGCAGAGGCCGCTATTACATGTAC 70 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=8.0;MSILEN=2.0;SSF=0.54067;SOR=0.0;LSEQ=TGCTATTACATATACGTGTG;RSEQ=GTGTGTGTGTATAAAATGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:2,4:4,3:7,6:0.3333:2,2:24.8:1.0:27.2:1.0:0.59207:2.46629:40.3:5.0:0.4167:0.3333:1.3 0/0:4:0:0,0:2,2:4,0:0.0:2,0:8.3:1.0:30.3:1.0:1.0:0.0:34.5:8.0:1.0:0.0:1.8 +10 3280619 . T C 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0125;SOR=0.0;LSEQ=GTGCTAGTCTGGAAGTGGAG;RSEQ=CTGGAGCTTAGATTAGAAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:4,2:237,213:450,6:0.0131:2,2:18.3:1.0:32.2:1.0:0.68851:1.8:60.0:12.0:0.0135:0.0:1.2 0/0:489:0:0,0:252,237:489,0:0.0:2,0:23.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 +10 8100647 . C T 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02231;LSEQ=TCCCGTGGCAGCATGACCGC;RSEQ=CTGGGTGGAGCCTCCTCGTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:949:39:19,20:445,465:910,39:0.0411:2,2:27.3:1.0:30.8:1.0:1.0:1.00735:60.0:38.0:0.0409:0.0:1.1 0/0:1049:1:0,1:529,518:1047,1:0.001:2,0:1.0:0.0:25.0:0.0:0.49523:0.0:60.0:2.0:0.001:0.0:1.0 +10 8106274 . C T 101 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=17.0;MSILEN=1.0;SSF=0.00151;SOR=0.0;LSEQ=TTCTTTCTTTTCTTCTTCTT;RSEQ=TTTTTTTTTTTTTTTTTCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:10:0,10:0,0:0,10:0.8333:0,0:13.8:1.0:30.5:1.0:1.0:0.0:49.5:20.0:1.0:0.0:3.5 0/0:6:0:0,0:0,1:1,0:0.0:0,0:12.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:4.0 +10 8111850 . GA G 79 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.03333;SOR=0.0;LSEQ=GGGCCTGTGTGGTTTATAAG;RSEQ=AAAAAAAAAAATCTTCCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,0:0,6:0.8571:0,0:31.3:1.0:30.7:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:0.7 0/0:3:0:0,0:1,2:3,0:0.0:2,0:24.0:1.0:29.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:1.7 +10 8116079 . C T 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GCAGTATCATGAAGCCTAAA;RSEQ=GCGATGGATATATGTTTTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:59:40:0,40:0,19:19,40:0.678:1,1:17.7:1.0:30.5:1.0:1.0:0.0:60.0:19.0:0.6667:0.0:1.1 0/0:29:0:0,0:3,26:29,0:0.0:2,0:23.0:1.0:29.0:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.2 +10 9959556 . C T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.0;MSILEN=1.0;SSF=0.02718;SOR=0.0;LSEQ=ATGTTTTAAATATATCCTGT;RSEQ=TAAAATAGAAATCAAAAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:7:6,1:13,1:14,7:0.3333:1,2:15.1:1.0:32.3:1.0:1.0:2.08171:60.0:14.0:0.35:0.0:1.0 0/0:14:0:0,0:13,0:13,0:0.0:1,0:19.5:1.0:31.8:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.0 +10 10923431 . T A 250 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0088;LSEQ=GCTGTTAGTAAAATATGAGA;RSEQ=ACTTCAAACTTAATGCCTCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:347:326:180,146:10,11:21,326:0.9395:2,2:25.0:1.0:30.0:1.0:0.50759:1.35:60.0:39.75:0.9381:0.0:1.2 0/1:445:53:27,26:192,200:392,53:0.1191:2,2:29.5:1.0:29.2:1.0:0.8838:1.08:60.0:52.0:0.119:0.0:1.3 +10 15009109 . T C 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.01099;SOR=0.0;LSEQ=TGGGAGAAGAGGTGGTCGTT;RSEQ=AGCTGGGCACATTCAGAATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:10,0:1,0:1,10:0.9091:0,0:28.9:1.0:32.5:1.0:1.0:0.0:57.8:20.0:0.9091:0.0:2.3 0/0:3:0:0,0:2,1:3,0:0.0:2,0:39.3:1.0:29.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +10 19229864 . GC AT 70 p8 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01213;SOR=0.0;LSEQ=AGACCAATAATGCTGTTTCT;RSEQ=ATCATCTTCCAACTTTACCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:242:5:2,3:101,136:237,5:0.0207:2,2:6.4:1.0:30.4:1.0:1.0:1.11351:60.0:10.0:0.0209:0.0124:0.8 0/0:340:0:0,0:152,188:340,0:0.0:2,0:24.4:1.0:31.2:1.0:1.0:0.0:59.9:67.0:1.0:0.0:0.3 +10 20007127 . A C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=3.0;MSILEN=3.0;SSF=0.01806;SOR=0.0;LSEQ=AAGGAAAAAGAAGACGAAGA;RSEQ=GAAGAGGAAGAAGAAGAAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:5,3:3,2:5,8:0.6154:2,2:11.5:1.0:30.8:1.0:1.0:1.1:57.9:16.0:0.6154:0.0:1.0 0/0:6:0:0,0:3,3:6,0:0.0:2,0:25.8:1.0:28.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 +10 36853842 . G A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ATGGAAGTTGTAGCTGAAAC;RSEQ=TGTCCTCTGAGAGAGGCTGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1.0:0,1:24.3:1.0:30.7:1.0:1.0:0.0:60.0:26.0:1.0:0.0:2.5 0/1:16:2:2,0:14,0:14,2:0.125:1,0:7.5:1.0:31.0:0.0:1.0:0.0:60.0:4.0:0.125:0.0:2.0 +10 36853858 . G C 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAACGTGTCCTCTGAGAGAG;RSEQ=CTGGCGCTCTCTCCGCCCGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:24:24:24,0:0,0:0,24:1.0:0,1:21.0:1.0:32.7:1.0:1.0:0.0:60.0:48.0:1.0:0.0:2.4 0/1:22:3:3,0:19,0:19,3:0.1364:1,0:10.7:1.0:33.3:1.0:1.0:0.0:60.0:6.0:0.15:0.0:2.3 +10 43596179 . G A 262 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02168;LSEQ=TCAGTGTCCGCAGTAAGGGA;RSEQ=CCGCCCCAACACCCACCCCG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:544:491:176,315:18,34:52,491:0.9026:2,2:26.9:1.0:29.4:1.0:1.0:1.06:60.0:34.071:0.9034:0.0:1.3 0/1:481:80:34,46:159,242:401,80:0.1663:2,2:24.0:1.0:28.3:1.0:0.70804:1.12:60.0:79.0:0.1667:0.0:1.3 +10 43596241 . C T 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAGCCGCCCTTATCACAGC;RSEQ=GCTGACACTGAAGCTTGGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:87:7,80:9,79:88,87:0.4943:2,2:25.8:1.0:29.5:1.0:0.79406:1.30003:59.8:16.4:0.4881:0.0:1.9 0/0:136:0:0,0:16,120:136,0:0.0:2,0:22.2:1.0:29.2:1.0:1.0:0.0:60.0:44.333:1.0:0.0:0.5 +10 43600210 . AGCACAGTCAT A 141 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00014;SOR=0.0;LSEQ=CTGCAAACTGCAAACTCGTA;RSEQ=CGCTGCAAACTGCAAACTCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:22:21,1:19,1:20,22:0.5238:1,1:21.7:1.0:31.7:1.0:1.0:1.1:58.6:44.0:0.5238:0.0952:0.3 0/0:16:0:0,0:14,2:16,0:0.0:2,0:20.9:1.0:32.4:1.0:1.0:0.0:58.1:32.0:1.0:0.0:0.2 +10 43604148 . A C 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTATGCACAGACACCACACA;RSEQ=ATGCATACTACACACTTACA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:2,0:2,6:0.6667:0,0:24.0:1.0:33.5:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +10 43604950 . A G 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCAAAAATGCAAGAGCAAT;RSEQ=CTGGGTAAATCTGCATATGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:19.1:1.0:32.1:1.0:1.0:0.0:60.0:14.0:0.875:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +10 43607471 . T G 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00041;SOR=0.0;LSEQ=GGGCAGCTCAGCTGGTGCTG;RSEQ=TCCCTGTCCTTGGGCACTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:14:11,3:111,4:115,14:0.1085:1,2:27.8:1.0:31.3:1.0:0.02778:7.35353:60.0:28.0:0.1085:0.0:1.1 0/0:94:0:0,0:85,9:94,0:0.0:2,0:21.1:1.0:29.2:1.0:1.0:0.0:60.0:188.0:1.0:0.0:0.2 +10 43610119 . G A 317 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02021;LSEQ=CGGTCAGCTACTCCTCTTCC;RSEQ=GTGCCCGCCGGCCCTCGCTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1333:1222:611,611:56,53:109,1222:0.9167:2,2:24.2:1.0:31.0:1.0:0.84168:1.05658:60.0:33.914:0.9173:0.0:1.1 0/1:1008:183:97,86:449,373:822,183:0.1815:2,2:23.9:1.0:29.6:1.0:0.74285:1.06716:60.0:60.0:0.1816:0.0:1.2 +10 43615382 . C T 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=11;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0035;LSEQ=GTCACACCCTGACTCCACCA;RSEQ=GCCCCTGCCATGCCACACCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:80:76:56,20:3,1:4,76:0.95:2,2:28.6:1.0:30.6:1.0:1.0:1.07052:59.8:14.2:0.9467:0.0:1.3 0/1:37:2:1,1:24,11:35,2:0.0541:2,2:34.5:1.0:31.0:0.0:1.0:2.13205:60.0:4.0:0.0556:0.0:1.5 +10 43618751 . G A 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGTGGCCTGCATTCTCACC;RSEQ=CTTTAAGTGTGAGAATCTTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:13.2:1.0:29.0:1.0:1.0:0.0:56.4:10.0:0.8333:0.0:2.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +10 43620134 . C T 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.09804;SOR=0.0;LSEQ=GACCTGAGCACAGTGGCCCA;RSEQ=GGGCTGGGATCCTGCAACAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:11,1:4,0:4,12:0.75:0,2:36.1:1.0:32.7:1.0:1.0:0.0:60.0:24.0:0.75:0.0:1.1 0/0:2:0:0,0:2,0:2,0:0.0:0,0:32.5:1.0:29.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +10 52388952 . G A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATAAAAGGTACAGTATTTGC;RSEQ=TATAACCTCCCCATATCCTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:23.3:1.0:31.0:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +10 52389659 . G A 222 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.09488;LSEQ=TCTGAATCACCTGCCTCAGA;RSEQ=CTGCAGCAAAGTTTCTGCTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:315:173:83,90:66,76:142,173:0.5492:2,2:22.9:1.0:29.9:1.0:0.82113:1.06:57.3:56.667:0.5502:0.0:1.1 0/1:281:29:15,14:124,127:251,29:0.1032:2,2:19.4:1.0:29.1:1.0:0.84665:1.1:56.1:58.0:0.1074:0.0:1.2 +10 54611395 . A G 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.04762;SOR=0.0;LSEQ=AGCCACAGCCAGTGCTGGTC;RSEQ=CCCCTCACCTCAGGAGTTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1.0:0,2:24.8:1.0:28.6:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.2 0/0:2:0:0,0:2,0:2,0:0.0:0,0:27.0:1.0:27.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +10 70404938 . G T 64 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.06191;SOR=0.0;LSEQ=TGAGTTGTGATCATCTCAAG;RSEQ=GGAGAAGTAACGTTTTAGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:5:0,5:245,199:444,5:0.0111:2,0:7.2:1.0:27.6:1.0:0.01884:0.0:60.0:10.0:0.0113:0.0:1.0 0/0:437:0:0,0:215,221:436,0:0.0:2,0:24.5:1.0:30.2:1.0:1.0:0.0:60.0:47.444:0.9977:0.0:0.1 +10 70405237 . G A 233 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.09301;LSEQ=TCAAAGTCAGAGAAGGATGA;RSEQ=GAATCAGAGCAGAGAACAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:330:181:94,87:79,70:149,181:0.5485:2,2:23.7:1.0:31.1:1.0:0.91187:1.04442:54.8:362.0:0.5502:0.0:1.0 0/1:435:44:19,25:203,188:391,44:0.1011:2,2:23.3:1.0:30.0:1.0:0.34007:1.41962:53.6:88.0:0.1021:0.0:1.2 +10 70406345 . C T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00873;SOR=0.0;LSEQ=AAGCTTATAATTCTCAGGTA;RSEQ=AGTTAACGGTGAATGCCAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:545:6:2,4:277,262:539,6:0.011:2,2:21.8:1.0:28.7:1.0:0.44034:2.11168:59.5:12.0:0.0111:0.0:1.2 0/0:653:0:0,0:324,329:653,0:0.0:2,0:1.0:0.0:13.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 +10 70406518 . A T 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00444;LSEQ=CCTGGTATCTCTCATGAAAC;RSEQ=CCCTTACCGGAGTCAGCACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:662:305:172,133:190,167:357,305:0.4607:2,2:24.5:1.0:30.9:1.0:0.43401:1.14:60.0:37.125:0.4562:0.0:1.1 0/0:797:3:0,3:411,381:792,3:0.0038:2,0:1.0:0.0:23.7:1.0:0.11224:0.0:60.0:6.0:0.0038:0.0:1.0 +10 70406864 . C T 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.05677;LSEQ=TTTTGTGTGATATTTTTTCC;RSEQ=CATTCTTATTCTAACTAAGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:49:28:0,28:0,21:21,28:0.5714:1,1:21.9:1.0:30.6:1.0:1.0:0.0:60.0:56.0:0.5714:0.0:1.1 0/1:44:3:0,3:0,41:41,3:0.0682:1,0:28.7:1.0:27.7:1.0:1.0:0.0:60.0:6.0:0.0682:0.0:1.3 +10 70412132 . AAG A 172 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.05586;LSEQ=TTTAACAAGAGTAAATTACG;RSEQ=AGTGTCTAATTTTTGAACTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:80:48:48,0:32,0:32,48:0.6:1,1:21.9:1.0:30.9:1.0:1.0:0.0:60.0:96.0:0.6076:0.1875:0.0 0/1:66:5:5,0:61,0:61,5:0.0758:1,0:25.0:1.0:28.6:1.0:1.0:0.0:60.0:10.0:0.0769:0.0:0.2 +10 70451383 . A T 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTGAGGCTAAAGAAGCTAAG;RSEQ=ATAAGAAAATGAAGGCCTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:131:61,70:435,407:842,131:0.1345:2,2:24.6:1.0:28.5:1.0:0.30183:1.22623:59.4:31.75:0.1333:0.0:1.1 0/0:1342:0:0,0:648,694:1342,0:0.0:2,0:25.2:1.0:29.1:1.0:1.0:0.0:60.0:77.941:1.0:0.0:0.1 +10 74677784 . GTCA G 93 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=20;MSI=7.0;MSILEN=3.0;SSF=0.01821;SOR=0.11548;LSEQ=TCATCTTCATCTTCTTCATC;RSEQ=TCATCATCATCATCATCATC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:8:5,3:53,45:98,8:0.0748:2,2:21.1:1.0:31.2:1.0:0.72626:1.41:44.1:16.0:0.0762:0.0187:0.0 0/0:109:1:1,0:61,47:108,1:0.0092:2,0:29.0:0.0:32.0:0.0:1.0:0.0:32.0:2.0:0.0093:0.0:0.0 +10 86331960 . A G 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00776;SOR=0.10947;LSEQ=GGGTCCTTTTCCACACTGGG;RSEQ=AAAGTTTGTTCTTTTGCTCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:4,5:9,7:0.4375:2,2:26.1:1.0:33.6:1.0:1.0:1.06235:49.7:14.0:0.4375:0.0:2.1 0/1:27:2:0,2:12,13:25,2:0.0741:2,0:26.5:1.0:25.5:1.0:0.48718:0.0:60.0:4.0:0.0769:0.0:3.0 +10 88866085 . TCA T 138 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGGAATAATTGTTAGACAAC;RSEQ=CAGTGTCTGCCATATTTGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:18:11,7:69,46:115,18:0.1353:2,2:29.6:1.0:33.2:1.0:1.0:1.05:59.4:36.0:0.1374:0.0:0.3 0/0:233:0:0,0:127,105:232,0:0.0:2,0:25.6:1.0:30.7:1.0:1.0:0.0:59.9:76.333:0.9957:0.0:0.3 +10 89692844 . C T 190 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTTTTGTGAAGATCTTGAC;RSEQ=AATGGCTAAGTGAAGATGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:85:49,36:55,53:108,85:0.4404:2,2:7.6:1.0:29.7:1.0:0.38482:1.31:26.5:84.0:0.4421:0.0:1.1 0/0:194:0:0,0:101,92:193,0:0.0:2,0:6.8:1.0:29.4:1.0:1.0:0.0:26.0:63.333:0.9948:0.0:0.0 +10 89717709 . AGCCGT A 238 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATGTACTTTGAGTTCCCTC;RSEQ=TACCTGTGTGTGGTGATATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:467:209:90,119:114,144:258,209:0.4475:2,2:25.8:1.0:31.0:1.0:0.85131:1.04668:35.3:418.0:0.4553:0.0771:0.0 0/0:579:0:0,0:271,307:578,0:0.0:2,0:25.0:1.0:31.4:1.0:1.0:0.0:38.7:191.667:0.9983:0.0:0.2 +10 99804144 . G GCAGCAAAA 229 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.01271;LSEQ=CAACAGTAGTGTCAACAGCA;RSEQ=CAGCGACAGCAGCAACAACA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:226:171:87,84:15,37:52,171:0.7566:2,2:26.1:1.0:31.0:1.0:0.00663:2.54:56.8:342.0:0.7703:0.1947:2.1 0/1:320:12:1,11:156,152:308,12:0.0375:2,2:30.8:1.0:28.8:1.0:0.00557:11.22732:49.1:24.0:0.0382:0.0031:3.5 +10 99804159 . A G 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGCAGCGACAGCAGCA;RSEQ=CAACAGCAGCAGCGACAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:96:45,51:9,23:32,96:0.7273:2,2:22.6:1.0:32.2:1.0:0.06741:2.24:54.8:18.2:0.7165:0.0:3.5 0/0:279:0:0,0:69,83:152,0:0.0:2,0:21.5:1.0:29.0:1.0:1.0:0.0:54.4:151.0:0.9869:0.0:0.8 +10 99804161 . A G 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04429;LSEQ=GCAGCAGCGACAGCAGCAAC;RSEQ=ACAGCAGCAGCGACAGCAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:153:94:45,49:34,24:58,94:0.6144:2,2:21.5:1.0:30.1:1.0:0.24258:1.53815:53.9:22.5:0.625:0.0:3.6 0/1:291:19:4,15:93,95:188,19:0.0653:2,2:31.5:1.0:26.8:1.0:0.02777:3.6504:48.6:3.75:0.0769:0.0:4.5 +10 99804170 . AG GA 81 Bias SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.00125;SOR=0.0;LSEQ=ACAGCAGCAACAACAGCAGC;RSEQ=CGACAGCAGCAACAACAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:6:0,6:65,40:105,6:0.0448:2,0:35.8:1.0:31.6:1.0:0.00414:0.0:47.2:12.0:0.055:0.0:7.0 0/0:269:0:0,0:133,132:265,0:0.0:2,0:22.5:1.0:29.6:1.0:1.0:0.0:53.0:87.333:1.0:0.0:2.4 +10 99804171 . G A 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.03749;LSEQ=CAGCAGCAACAACAGCAGCA;RSEQ=CGACAGCAGCAACAACAGCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:132:74:38,36:26,3:29,74:0.5606:2,2:18.1:1.0:30.2:1.0:0.00025:8.06537:50.4:148.0:0.74:0.0:4.1 0/1:266:12:1,11:130,120:250,12:0.0451:2,2:30.0:1.0:30.1:1.0:0.00529:11.83475:47.8:24.0:0.0474:0.0:4.2 +10 99804173 . G A 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04197;LSEQ=GCAGCAACAACAGCAGCAGC;RSEQ=ACAGCAGCAACAACAGCAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:139:85:43,42:27,3:30,85:0.6115:2,2:17.1:1.0:30.6:1.0:0.00015:8.6458:47.6:170.0:0.7522:0.0:4.6 0/1:261:16:2,14:127,112:239,16:0.0613:2,2:22.9:1.0:28.9:1.0:0.00156:7.88477:45.6:7.0:0.0576:0.0:5.5 +10 99804184 . C T 74 q25;Bias SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00033;SOR=0.0;LSEQ=AGCAGCAGCGACAGCAGCAA;RSEQ=AACAGCAGCAATAGCAGCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:8:0,8:97,73:170,8:0.0449:2,0:27.0:1.0:24.9:1.0:0.00151:0.0:41.6:3.0:0.0349:0.0:7.0 0/0:301:0:0,0:151,150:301,0:0.0:2,0:18.3:1.0:30.9:1.0:1.0:0.0:48.5:74.25:1.0:0.0:2.8 +10 99804192 . G A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.00369;SOR=0.0;LSEQ=CGACAGCAGCAACAACAGCA;RSEQ=CAATAGCAGCAACAACAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:6:0,6:85,77:162,6:0.0311:2,0:27.7:1.0:32.0:0.0:0.01323:0.0:47.2:12.0:0.0339:0.0:7.0 0/0:294:0:0,0:127,145:272,0:0.0:2,0:18.2:1.0:30.6:1.0:1.0:0.0:47.9:23.727:0.9812:0.0:3.0 +10 99804194 . AAT GACAAC 118 Bias SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=4e-05;SOR=0.08164;LSEQ=GACAGCAGCAACAACAGCAG;RSEQ=AGCAGCAACAACAGCAGCAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:15:15,0:85,77:162,15:0.0777:2,1:34.4:1.0:30.4:1.0:0.00016:0.0:33.2:30.0:0.0847:0.0:5.3 0/0:294:2:2,0:127,145:272,2:0.0068:2,0:34.0:0.0:29.4:1.0:0.22074:0.0:36.5:4.0:0.0075:0.0:5.0 +10 99804205 . C T 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00094;SOR=0.1443;LSEQ=AACAGCAGCAATAGCAGCAA;RSEQ=AACAGCAGCAATAGCAGCGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:15:15,0:105,96:201,15:0.0691:2,1:28.1:1.0:27.7:1.0:0.00016:0.0:33.2:6.5:0.0613:0.0:5.3 0/1:284:3:2,1:124,128:252,3:0.0106:2,2:17.7:1.0:27.7:1.0:0.61911:2.06:37.3:6.0:0.012:0.0:5.7 +10 99804211 . CAGCAAT C 124 p8 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=AGCAATAGCAGCAACAACAG;RSEQ=AGCAGCGACAACAGCAATAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:18:9,9:120,85:205,18:0.0789:2,2:5.3:1.0:29.8:1.0:0.61967:1.40952:41.9:36.0:0.0829:0.0789:5.3 0/0:273:0:0,0:112,109:221,0:0.0:2,0:21.8:1.0:29.0:1.0:1.0:0.0:48.3:21.1:1.0:0.0037:3.1 +10 99804215 . A G 62 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00556;SOR=0.0;LSEQ=ATAGCAGCAACAACAGCAGC;RSEQ=ATAGCAGCGACAACAGCAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:6:2,4:105,67:172,6:0.0291:2,2:15.2:1.0:24.0:1.0:0.21823:3.11385:22.5:2.0:0.023:0.0:5.7 0/0:280:0:0,0:110,102:212,0:0.0:2,0:23.1:1.0:28.8:1.0:1.0:0.0:48.8:20.2:1.0:0.0036:3.1 +10 99804216 . A ACAG 76 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02039;SOR=0.17616;LSEQ=TAGCAGCAACAACAGCAGCA;RSEQ=TAGCAGCGACAACAGCAATA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:8:3,5:31,17:48,8:0.0379:2,2:8.5:1.0:25.5:1.0:0.24081:2.97594:42.5:3.0:0.0335:0.0237:5.9 0/0:291:2:0,2:68,70:138,2:0.0069:2,0:22.5:1.0:20.5:1.0:0.49681:0.0:44.5:4.0:0.0091:0.0:7.5 +10 99804224 . G A 108 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACAACAGCAGCAATAGCAGC;RSEQ=ACAACAGCAATAGCAGCAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:15:11,4:115,83:198,15:0.067:2,2:6.7:1.0:27.7:1.0:0.28796:1.98:37.1:14.0:0.0707:0.0:2.9 0/0:314:0:0,0:106,102:208,0:0.0:2,0:26.3:1.0:28.7:1.0:1.0:0.0:52.0:9.947:0.913:0.0:3.0 +10 99804243 . GCAACAA G 174 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.16115;LSEQ=CGACAACAGCAATAGCAGCA;RSEQ=CAACAGCAGCAGCAACAGCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:263:49:22,27:15,5:20,49:0.1863:2,2:16.6:1.0:31.1:1.0:0.03307:3.61251:42.2:48.0:0.1846:0.0913:3.4 0/1:310:11:4,7:85,84:169,11:0.0355:2,2:29.9:1.0:29.1:1.0:0.53609:1.76532:42.4:10.0:0.0348:0.0:5.4 +10 99804253 . C T 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.04976;LSEQ=AATAGCAGCAGCAACAACAA;RSEQ=AGCAGCAGCAACAGCAGCAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:85:66:31,35:10,9:19,66:0.7765:2,2:12.6:1.0:24.8:1.0:0.79567:1.25112:44.7:2.474:0.7705:0.0:2.7 0/1:213:31:8,23:88,91:179,31:0.1455:2,2:13.3:1.0:21.9:1.0:0.01888:2.76745:48.0:2.1:0.1066:0.0:3.0 +10 104378688 . CGT C 167 MSI12;MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=46;MSI=24.0;MSILEN=2.0;SSF=0.0;SOR=0.14335;LSEQ=TCCCAAGTGTCCTCAGGTAG;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:34:30,4:76,1:77,34:0.2378:1,2:24.3:1.0:32.9:1.0:0.03003:9.90233:55.4:33.0:0.2391:0.035:0.7 0/1:141:6:6,0:93,3:96,6:0.0426:1,0:27.7:1.0:33.0:1.0:1.0:0.0:56.7:12.0:0.0441:0.0:0.3 +10 110550348 . A C 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0079;SOR=0.07215;LSEQ=TAGTCCCAGGAAAAGTCAGC;RSEQ=AGGTCATCTGTGAGTTCTTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:8,1:9,9:0.5:2,2:16.8:1.0:31.3:1.0:0.57647:3.70691:60.0:18.0:0.5294:0.0:1.0 0/1:16:1:1,0:13,2:15,1:0.0625:2,0:7.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0625:0.0:1.0 +10 114911035 . AAG A 78 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.0;MSILEN=2.0;SSF=0.07979;SOR=0.0;LSEQ=GGGCTCTTCACTCCCTTACA;RSEQ=AGAGAGAGAGTGCACAGTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:5:0,5:2,125:127,5:0.0379:1,0:30.0:1.0:34.0:0.0:1.0:0.0:57.2:10.0:0.0394:0.0:0.4 0/0:92:0:0,0:1,91:92,0:0.0:1,0:24.4:1.0:30.8:1.0:1.0:0.0:59.9:91.0:1.0:0.0:0.4 +10 114912534 . C T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.44444;SOR=0.0;LSEQ=ACCCAAAGGACCTTATGTTC;RSEQ=GGATTAGGTTCCGCAGGCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:22.6:1.0:31.4:1.0:1.0:0.0:54.4:10.0:0.625:0.0:1.0 0/0:2:0:0,0:0,2:2,0:0.0:0,0:3.5:1.0:26.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +10 114919608 . T C 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00041;SOR=0.0;LSEQ=TTCCCCCCCCCCCCCCCTCT;RSEQ=TCTCTCTCTCTCTCTCTCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:12:6,6:130,39:169,12:0.0642:2,2:17.2:1.0:29.2:1.0:0.07558:3.30618:53.3:5.0:0.0654:0.0:3.7 0/0:187:0:0,0:118,59:177,0:0.0:2,0:11.0:1.0:27.6:1.0:1.0:0.0:57.6:8.316:1.0:0.0:1.3 +10 114920089 . A G 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08669;SOR=0.0;LSEQ=CCTAGGTAGAAGCAAATGAC;RSEQ=TCACCTTCTCCCCTCCTCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:8,2:3,3:6,10:0.625:2,2:27.4:1.0:30.7:1.0:0.29945:3.63:60.0:20.0:0.625:0.0:1.2 0/0:3:0:0,0:1,2:3,0:0.0:2,0:34.7:1.0:30.7:1.0:1.0:0.0:51.7:6.0:1.0:0.0:0.7 +10 123240645 . C T 263 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.08496;LSEQ=AAAGCTGAAAATATTTACTC;RSEQ=CTGGCCCTTTACAGAAAGCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:795:365:168,197:189,240:429,365:0.4591:2,2:24.9:1.0:30.9:1.0:0.61643:1.08:59.8:72.0:0.4615:0.0:1.9 0/1:938:63:31,32:402,472:874,63:0.0672:2,2:24.3:1.0:29.1:1.0:0.69505:1.14:59.5:14.75:0.0638:0.0:1.9 +10 123241323 . G A 263 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04387;LSEQ=CATTAAAATAGAACTTTAGT;RSEQ=CTTTTCCCGGTTTCTTTCTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:924:484:185,299:236,203:439,484:0.5238:2,2:26.9:1.0:29.5:1.0:0.0:1.87766:55.1:160.333:0.5286:0.0:3.4 0/1:1632:75:38,37:781,774:1555,75:0.046:2,2:26.9:1.0:27.7:1.0:1.0:1.02:53.2:36.5:0.0473:0.0:3.6 +10 123241354 . AT TA 240 MSI12 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.0;SOR=0.03789;LSEQ=TTTCTTTCTTTTTTATTTTT;RSEQ=TTTTTTTTTTTTTGAGACGG;STATUS=AFDiff GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:404:266:80,186:10,15:25,266:0.6584:2,2:22.7:1.0:29.8:1.0:0.36541:1.54753:48.5:265.0:0.9075:0.0:3.8 0/1:929:63:19,44:237,343:580,63:0.0678:2,2:21.7:1.0:28.6:1.0:0.10559:1.599:48.9:126.0:0.0903:0.0:3.4 +10 123241361 . T A 241 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.0;SOR=0.02779;LSEQ=CTTTTTTATTTTTATTTTTT;RSEQ=TTTTTTTGAGACGGAGTCTC;STATUS=AFDiff GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:369:253:73,180:89,27:116,253:0.6856:2,2:20.3:1.0:30.3:1.0:0.0:8.0761:47.1:125.5:0.6858:0.0:3.8 0/1:826:47:16,31:372,407:779,47:0.0569:2,2:19.7:1.0:28.7:1.0:0.07222:1.76969:45.7:94.0:0.057:0.0:3.7 +10 123242589 . G A 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06636;LSEQ=CCAAAATGCTGGGATTACAG;RSEQ=CGAGAGCATAAATATTTTAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:154:105,49:137,59:196,154:0.44:2,2:23.8:1.0:30.1:1.0:0.72842:1.08337:58.5:153.0:0.4435:0.0:1.1 0/1:405:20:11,9:258,127:385,20:0.0494:2,2:22.9:1.0:27.7:1.0:0.33139:1.65996:57.9:40.0:0.05:0.0:1.1 +10 123274653 . A G 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTACCTGTCTCCGCAGGGGG;RSEQ=TACGTTTGGTCAGCTTGTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:37:23,14:341,160:501,37:0.0688:2,2:25.9:1.0:32.0:1.0:0.46971:1.29658:60.0:74.0:0.0703:0.0:1.1 0/0:673:0:0,0:410,262:672,0:0.0:2,0:24.0:1.0:28.5:1.0:1.0:0.0:59.9:28.217:0.9985:0.0:0.2 +10 123279795 . C T 134 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01553;LSEQ=CATGCCAGAAAAGCCTCAAG;RSEQ=CTGCTGGCTGACACCTTTGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:25:23:0,23:0,2:2,23:0.92:0,1:21.5:1.0:29.7:1.0:1.0:0.0:60.0:10.5:0.913:0.0:1.9 0/1:16:2:0,2:0,14:14,2:0.125:1,0:11.0:1.0:26.0:1.0:1.0:0.0:60.0:4.0:0.1333:0.0:2.0 +10 123488416 . A G 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=8e-05;SOR=0.0;LSEQ=AGCACGCTGCCTCCTTCTTA;RSEQ=CCAAGCTGGCCACTGTGTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:10:4,6:4,5:9,10:0.5263:2,2:30.3:1.0:30.8:1.0:1.0:1.18851:60.0:9.0:0.5:0.0:2.4 0/0:22:0:0,0:12,10:22,0:0.0:2,0:26.0:1.0:27.4:1.0:1.0:0.0:58.2:21.0:1.0:0.0:1.0 +10 124403674 . G T 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=4.0;MSILEN=8.0;SSF=0.00049;SOR=0.0;LSEQ=GTGCGGCTGTGCGGCTGTGC;RSEQ=GCTGTGCTGCTGTGTTGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:3,4:2,1:3,7:0.7:2,2:11.0:1.0:30.9:1.0:1.0:2.41422:60.0:14.0:0.7:0.0:4.1 0/0:13:0:0,0:6,7:13,0:0.0:2,0:32.4:1.0:28.6:1.0:1.0:0.0:51.2:12.0:1.0:0.0:0.5 +10 124403681 . C T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.0;MSILEN=3.0;SSF=0.00022;SOR=0.0;LSEQ=TGTGCGGCTGTGCGGCTGTG;RSEQ=TGCTGTGTTGCTGTGCGGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:3,5:2,1:3,8:0.7273:2,2:16.1:1.0:29.6:1.0:0.54545:2.97405:60.0:16.0:0.8:0.0:4.1 0/0:13:0:0,0:6,7:13,0:0.0:2,0:33.5:1.0:31.6:1.0:1.0:0.0:51.2:26.0:1.0:0.0:0.5 +10 124403689 . T C 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=15;MSI=2.0;MSILEN=1.0;SSF=0.00011;SOR=0.0;LSEQ=TGTGCGGCTGTGCTGCTGTG;RSEQ=TGCTGTGCGGCTGTGCTGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:9:4,5:2,1:3,9:0.75:2,2:22.3:1.0:33.2:1.0:1.0:2.31595:60.0:18.0:0.8182:0.0:4.0 0/0:13:0:0,0:6,7:13,0:0.0:2,0:23.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 +10 134913291 . C T 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04556;SOR=0.0;LSEQ=ACAGCCCAGTACAGTCACCT;RSEQ=CAGGGCCCAGACACAGCCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:3,4:7,8:0.5333:2,2:19.0:1.0:27.3:1.0:1.0:1.23147:60.0:7.0:0.5:0.0:1.0 0/0:6:0:0,0:3,3:6,0:0.0:2,0:17.8:1.0:31.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.2 +11 2156741 . T G 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACCAGCATCGACTTCCCCA;RSEQ=TGGGATTCCCATTGGTGTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1040:130:55,75:420,490:910,130:0.125:2,2:24.2:1.0:32.6:1.0:0.45178:1.16866:60.0:129.0:0.1261:0.0:1.1 0/0:1037:0:0,0:485,552:1037,0:0.0:2,0:24.9:1.0:29.3:1.0:1.0:0.0:59.9:44.087:1.0:0.0:0.2 +11 8246137 . C T 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.02427;SOR=0.0;LSEQ=CAGGCGGGCAGATGGACAGA;RSEQ=GGGCCTGGAGGCCAGGCGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:5:1,4:295,194:489,5:0.0101:2,2:9.0:1.0:28.6:1.0:0.16276:6.06174:60.0:10.0:0.0102:0.0:1.2 0/0:543:0:0,0:315,227:542,0:0.0:2,0:23.7:1.0:30.2:1.0:1.0:0.0:60.0:179.667:0.9981:0.0:0.3 +11 8248574 . G T 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGGTGATACACGTTGTCCC;RSEQ=GGCCCGCATCACCATCTCGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:882:74:38,36:408,400:808,74:0.0839:2,2:26.6:1.0:31.4:1.0:0.90392:1.03:59.9:148.0:0.0846:0.0:1.2 0/0:1008:0:0,0:508,496:1004,0:0.0:2,0:24.8:1.0:29.5:1.0:1.0:0.0:60.0:76.231:0.997:0.0:0.2 +11 17746976 . G T 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01879;LSEQ=CAAGAGGGAAGGGAACAGCT;RSEQ=GAGACTGGATCACACCATCG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1193:50:27,23:634,509:1143,50:0.0419:2,2:23.4:1.0:30.7:1.0:0.88491:1.06097:60.0:100.0:0.0427:0.0:1.2 0/0:1219:1:0,1:651,567:1218,1:0.0008:2,0:1.0:0.0:24.0:0.0:0.46596:0.0:60.0:2.0:0.0008:0.0:1.0 +11 20246743 . C A 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.06372;SOR=0.0;LSEQ=AGATTGATACTAGTGGGAAC;RSEQ=CCTTGGAGATTACTTAGATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:10:0,10:0,13:13,10:0.4348:1,0:22.7:1.0:32.0:0.0:1.0:0.0:60.0:20.0:0.4348:0.0:1.0 0/0:7:0:0,0:1,6:7,0:0.0:2,0:20.4:1.0:31.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.0 +11 20575654 . G C 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01919;LSEQ=GTGCTAGGTGTGGGGTTAGA;RSEQ=TGGGGAGCAAGATGGAGATG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:84:33:32,1:48,3:51,33:0.3929:2,1:30.2:1.0:31.2:1.0:1.0:1.99:60.0:10.0:0.3704:0.0:1.1 0/1:83:1:1,0:72,10:82,1:0.012:2,0:16.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.012:0.0:1.0 +11 21635295 . T G 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAATCAGCGGTAATGGGAGC;RSEQ=GCTAGACAGGAGGGAAGACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:94:47,47:88,102:190,94:0.3298:2,2:27.1:1.0:30.7:1.0:0.61402:1.16:59.6:188.0:0.3333:0.0:2.3 0/0:304:0:0,0:141,163:304,0:0.0:2,0:25.0:1.0:29.5:1.0:1.0:0.0:59.9:59.8:1.0:0.0:0.8 +11 23122852 . A C 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGATTCTCAGCAATAAATA;RSEQ=TTTTCCCAAATGTTTGCATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:27.6:1.0:34.0:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:29.0:0.0:18.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 +11 25022172 . T C 80 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.09848;SOR=0.15357;LSEQ=CTTAGAAAGGGGAGAAGCCA;RSEQ=GTTGCCCAACTCCAGAGGTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:8,7:15,6:0.2857:2,2:35.0:1.0:31.3:1.0:0.65944:1.7:41.3:12.0:0.2857:0.0:1.7 0/1:18:1:1,0:10,7:17,1:0.0556:2,0:31.0:0.0:34.0:0.0:1.0:0.0:31.0:2.0:0.0556:0.0:2.0 +11 30098849 . G T 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0033;SOR=0.0;LSEQ=AGACTAAAAATTGTGTAAAT;RSEQ=TAGACAGCATATACCTCTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:8,8:0.5:0,0:22.6:1.0:31.3:1.0:1.0:0.0:60.0:16.0:0.5:0.0:1.0 0/0:13:0:0,0:0,13:13,0:0.0:1,0:22.2:1.0:32.8:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.4 +11 30254268 . T G 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.45455;SOR=0.0;LSEQ=GAAATAGTTTCCATGGTGCT;RSEQ=TCTTTTTTCTCTGCAGCACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:27.6:1.0:32.6:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:2:0:0,0:2,0:2,0:0.0:0,0:8.0:1.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +11 32437699 . T C 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCAAGTTAAGACTGAAAGC;RSEQ=TTGACTGATCTAACAGGAAC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:12.0:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 32437841 . A C 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0001;SOR=0.0;LSEQ=TCCAGGGGCATGTTGATGAG;RSEQ=AATGCTACTCCCTCCATTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:14,0:19,0:19,14:0.4242:1,1:17.6:1.0:31.9:1.0:1.0:0.0:60.0:13.0:0.4063:0.0:1.1 0/0:25:0:0,0:25,0:25,0:0.0:1,0:26.9:1.0:28.8:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.2 +11 32439001 . T C 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGAGGAAAGCGTTCTAATG;RSEQ=CACAGAGAGCTTTGCCCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:41:40,1:67,0:67,41:0.3796:1,1:27.2:1.0:32.1:1.0:0.37963:0.0:60.0:19.5:0.3679:0.0:1.0 0/0:85:0:0,0:85,0:85,0:0.0:1,0:24.4:1.0:29.8:1.0:1.0:0.0:60.0:170.0:1.0:0.0:0.1 +11 32450244 . CG C 171 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGTCTGAACCAGCCACGGG;RSEQ=GGGGGGGTGTGCGCTGAACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:40:3,37:8,47:55,40:0.4211:2,2:26.5:1.0:32.2:1.0:0.34719:2.08397:60.0:80.0:0.4255:0.0105:0.1 0/0:67:0:0,0:8,59:67,0:0.0:2,0:17.3:1.0:29.7:1.0:1.0:0.0:59.9:32.5:1.0:0.0:0.3 +11 35242653 . C T 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04608;SOR=0.0;LSEQ=TATACCAAAATGTGATTACA;RSEQ=CTTACACGGTGTTTAGCAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:6,0:7,0:7,6:0.4615:0,0:26.5:1.0:31.7:1.0:1.0:0.0:60.0:12.0:0.4615:0.0:2.2 0/0:9:0:0,0:9,0:9,0:0.0:0,0:17.4:1.0:31.7:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.9 +11 39894274 . C T 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCTGTTATTTCACTAACCC;RSEQ=CTCTACTCACAAAAATTTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:49:37,12:67,25:92,49:0.3475:2,2:24.2:1.0:31.6:1.0:0.84148:1.15:60.0:98.0:0.3475:0.0:1.1 0/0:166:0:0,0:118,47:165,0:0.0:2,0:25.2:1.0:30.4:1.0:1.0:0.0:60.0:330.0:1.0:0.0:0.1 +11 42138434 . C T 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01073;LSEQ=AACATATGTACAATCCTGTG;RSEQ=CTTTAGTACCCTTTTGATTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:109:55:34,21:34,20:54,55:0.5046:2,2:23.7:1.0:29.6:1.0:1.0:1.04956:60.0:110.0:0.514:0.0:1.0 0/1:94:1:0,1:59,34:93,1:0.0106:2,0:1.0:0.0:22.0:0.0:0.37234:0.0:60.0:2.0:0.0108:0.0:2.0 +11 44368605 . T C 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.10294;SOR=0.0;LSEQ=TTTGTTGGCTGGCTTTGCCT;RSEQ=CGGGAGGTGTGAGCCTCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:6,7:0.5385:0,0:32.1:1.0:31.6:1.0:1.0:0.0:60.0:14.0:0.5385:0.0:1.0 0/0:4:0:0,0:0,4:4,0:0.0:0,0:20.5:1.0:29.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +11 62098295 . T A 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00223;SOR=0.05206;LSEQ=GGAATTGTGGGTGTATACAT;RSEQ=TATCTGTAAAAGATGTGGTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:9:9,0:10,0:10,9:0.4737:0,0:15.1:1.0:29.0:1.0:1.0:0.0:60.0:18.0:0.4737:0.0:1.3 0/1:24:1:1,0:23,0:23,1:0.0417:1,0:41.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0417:0.0:1.0 +11 64571710 . C T 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01649;SOR=0.0;LSEQ=GGTTTGGGTAGAGGTGAGGC;RSEQ=TGTCCCCTTTGGGCTGGGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:415:7:6,1:365,43:408,7:0.0169:2,2:19.7:1.0:29.6:1.0:0.54643:1.41338:60.0:6.0:0.0147:0.0:1.0 0/0:366:0:0,0:328,38:366,0:0.0:2,0:23.3:1.0:30.6:1.0:1.0:0.0:59.9:90.5:1.0:0.0:0.1 +11 64575505 . C T 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04041;LSEQ=ACAGGGCGAGGTGGACATCC;RSEQ=GGAGACCCAGGGCCTGGCAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:862:94:44,50:311,456:767,94:0.109:2,2:23.5:1.0:30.8:1.0:0.26743:1.29:60.0:30.333:0.1067:0.0:1.1 0/0:1017:5:1,4:474,535:1009,5:0.0049:2,2:8.6:1.0:29.8:1.0:0.37875:3.53998:57.0:10.0:0.005:0.0:1.0 +11 68132731 . A G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.10714;SOR=0.0;LSEQ=CATAGGAGCTTGGTGGGAGG;RSEQ=AGCAGATGGGGAGATGTCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:28.4:1.0:32.2:1.0:1.0:0.0:46.2:10.0:0.8333:0.0:1.0 0/0:2:0:0,0:0,2:2,0:0.0:0,0:31.0:1.0:32.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +11 69069783 . T C 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCGTGTCCTCGTCTGTAG;RSEQ=CGGGCTGTCGGCAGGCACCG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:23.8:1.0:31.6:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 69515423 . G A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTGCCTTTATCATTCTAAG;RSEQ=CCTTCTGGTCTGCAGCAGTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:32.4:1.0:27.4:1.0:1.0:0.0:60.0:6.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 81185242 . G T 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=6e-05;SOR=0.0;LSEQ=CTTTCCTTTTCTCCTTCCAT;RSEQ=TTTCCTTTACTAAAAATTAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:150:11:6,5:92,47:139,11:0.0733:2,2:27.9:1.0:30.7:1.0:0.51475:1.62566:60.0:22.0:0.0743:0.0:1.1 0/0:208:0:0,0:134,74:208,0:0.0:2,0:22.9:1.0:31.2:1.0:1.0:0.0:60.0:416.0:1.0:0.0:0.2 +11 81185452 . TC T 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.05466;SOR=0.0;LSEQ=CTCAAACATCCCAAAAGTCA;RSEQ=TTTGAAAGAGATCTCACTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:0,5:1,30:31,5:0.1389:1,0:34.6:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.1389:0.0:0.0 0/0:33:0:0,0:1,32:33,0:0.0:1,0:28.3:1.0:31.8:1.0:1.0:0.0:60.0:66.0:1.0:0.0:0.0 +11 85961166 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.2605;SOR=0.0;LSEQ=AATATAAAATATCTACAAAC;RSEQ=TTCTAACCTGTAGCTGGATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:7,1:8,5:0.3846:2,0:20.8:1.0:33.4:1.0:1.0:0.0:60.0:10.0:0.3846:0.0:1.0 0/0:4:0:0,0:4,0:4,0:0.0:0,0:38.3:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +11 85963619 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGTATTTATCATTCAAATAG;RSEQ=GTAAGAACTGGCTGTGATTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:4,6:0.6:0,2:30.3:1.0:29.8:1.0:1.0:0.0:60.0:12.0:0.6:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 85963632 . T C 59 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CAAATAGCGTAAGAACTGGC;RSEQ=GTGATTTTTTTAAAATTAAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:3,5:0.625:0,2:31.8:1.0:25.6:1.0:1.0:0.0:60.0:10.0:0.625:0.0:2.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 85980945 . G T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06833;SOR=0.0;LSEQ=TTATGTAACTATCTATGGTA;RSEQ=GAGGTTTTGGTCATTTCCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:5:5,0:62,1:63,5:0.0735:1,0:18.2:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.0746:0.0:2.0 0/0:52:0:0,0:52,0:52,0:0.0:1,0:23.8:1.0:32.3:1.0:1.0:0.0:60.0:104.0:1.0:0.0:1.0 +11 86333429 . TA T 196 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.0;SOR=0.11922;LSEQ=CAGGGATTGTGGGAGGGCAT;RSEQ=AAAAAAAAAAAGTTGTTTGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:300:83:33,50:104,99:203,83:0.2767:2,2:28.5:1.0:30.8:1.0:0.09035:1.58906:59.6:82.0:0.2742:0.0:0.3 0/1:322:14:7,7:149,156:305,14:0.0435:2,2:28.7:1.0:29.9:1.0:1.0:1.05:60.0:28.0:0.0439:0.0:0.4 +11 86807219 . A AA 72 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=5.0;MSILEN=1.0;SSF=0.09687;SOR=0.16397;LSEQ=TACTACTTGGAAAACTAGCA;RSEQ=AAGTTTTTTATCCGTTAAAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:456:5:3,2:236,214:450,5:0.011:2,2:18.0:0.0:31.2:1.0:1.0:1.36:60.0:10.0:0.0111:0.0:1.4 0/0:552:1:1,0:284,265:549,1:0.0018:2,0:18.0:0.0:24.0:0.0:1.0:0.0:55.0:2.0:0.0018:0.0:1.0 +11 88359287 . AT GG 85 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATTGAGAGCAGCCTTTACA;RSEQ=TTACACCAAATATAGAGAGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:23.8:1.0:32.9:1.0:1.0:0.0:60.0:12.0:1.0:0.3333:0.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 94153641 . C G 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGTAAGCCAGAAAAATAATT;RSEQ=AAGTCATTTTATATTTGGTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:24.6:1.0:30.4:1.0:1.0:0.0:60.0:4.0:0.8:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 94203801 . C A 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04473;LSEQ=CCCTTTAATACGCAGCAAAC;RSEQ=AACATGTCTGAAGTGGAGAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:37:15,22:145,252:397,37:0.0851:2,2:27.9:1.0:30.8:1.0:0.72199:1.18:60.0:36.0:0.0845:0.0:1.1 0/0:484:2:2,0:197,285:482,2:0.0041:2,0:1.0:0.0:24.0:0.0:0.16855:0.0:60.0:4.0:0.0041:0.0:1.0 +11 94770943 . G T 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00067;SOR=0.0;LSEQ=TCGCCTTCGTCCGCTTTCAC;RSEQ=ACCGGAGCGACGCGCAAGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:12:1,11:150,314:464,12:0.0252:2,2:15.9:1.0:25.8:1.0:0.1145:5.243:28.3:11.0:0.0237:0.0:1.3 0/0:404:0:0,0:168,236:404,0:0.0:2,0:26.3:1.0:29.8:1.0:1.0:0.0:48.1:79.8:1.0:0.0:0.2 +11 99322049 . T C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GATGACCCCATGTTACATTA;RSEQ=ACAAAAGTTATGAGATGAAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:16.0:1.0:33.0:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 100913165 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TACATGCTTCTTAAATACTT;RSEQ=GTTTGACTTAGTTTACAGCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:17.6:1.0:33.8:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 100999043 . G T 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01018;LSEQ=GCCCCCGGCGGGACAGCCGC;RSEQ=GCTCCTCCTCCAGCCGCCGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1549:112:56,56:765,669:1434,112:0.0723:2,2:23.7:1.0:31.3:1.0:0.55548:1.1434:60.0:55.0:0.0718:0.0:1.1 0/0:1262:1:0,1:657,603:1260,1:0.0008:2,0:1.0:0.0:25.0:0.0:0.47898:0.0:60.0:2.0:0.0008:0.0:1.0 +11 100999194 . G T 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGGGCCCCGGACCAGTGA;RSEQ=GGCTCTCAGAGGCCGGGAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1510:120:60,60:700,688:1388,120:0.0795:2,2:27.6:1.0:30.2:1.0:1.0:1.01743:60.0:16.143:0.0766:0.0:1.3 0/0:1234:0:0,0:605,628:1233,0:0.0:2,0:23.2:1.0:30.5:1.0:1.0:0.0:60.0:55.045:0.9992:0.0:0.3 +11 102057068 . C A 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00188;SOR=0.07796;LSEQ=GAATCAGATTTTTAGGGCTC;RSEQ=TCAGGTTGGGGTGGGGGAAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:0,13:0,6:6,13:0.6842:0,1:23.6:1.0:32.8:1.0:1.0:0.0:58.2:26.0:0.7222:0.0:1.2 0/1:15:2:0,2:1,12:13,2:0.1333:1,0:7.0:1.0:30.0:1.0:1.0:0.0:60.0:4.0:0.1333:0.0:1.0 +11 102077200 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.11111;SOR=0.0;LSEQ=TTATTAATAACTTACGTGGC;RSEQ=GGATACACCAATATGACATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1.0:0,0:19.9:1.0:30.0:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.1 0/0:1:0:0,0:0,1:1,0:0.0:0,0:44.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +11 102098001 . G C 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.2;SOR=0.0;LSEQ=GAGCTGCCAGCTTCAATTAG;RSEQ=ATTAACTTGTCTATTTCACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:5,0:5,8:0.6154:0,0:25.0:1.0:33.9:1.0:1.0:0.0:60.0:16.0:0.6154:0.0:1.0 0/0:2:0:0,0:2,0:2,0:0.0:0,0:21.5:1.0:32.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +11 102098343 . G A 55 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07045;SOR=0.0;LSEQ=TTTATTCCTCTTAGTAACCT;RSEQ=ACTTAACAGTGGGATATGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:490:5:4,1:143,341:484,5:0.0102:2,2:11.2:1.0:23.8:1.0:0.03031:9.49:60.0:4.0:0.0083:0.0:1.8 0/0:387:0:0,0:127,260:387,0:0.0:2,0:23.0:1.0:30.5:1.0:1.0:0.0:60.0:76.4:1.0:0.0:0.3 +11 102206417 . T C 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.44444;SOR=0.0;LSEQ=AAGACAGGGTATTGCTATGT;RSEQ=GCCCAGTCTGGTCTCTGACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:34.8:1.0:32.8:1.0:1.0:0.0:60.0:10.0:0.625:0.0:1.0 0/0:2:0:0,0:2,0:2,0:0.0:0,0:29.0:1.0:31.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +11 108115594 . C T 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.05218;LSEQ=AGACTTTGGCTGTCAACTTT;RSEQ=GAATTCGAGTGTGTGAATTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:856:18:11,7:411,427:838,18:0.021:2,2:25.4:1.0:30.8:1.0:0.34829:1.63:58.7:17.0:0.0201:0.0:1.0 0/0:894:1:0,1:444,448:892,1:0.0011:2,0:1.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 +11 108124299 . G A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGAATTTGCCTTTGAGATT;RSEQ=TAACTTGTATTTTTTCTCTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:12,0:0,0:0,12:1.0:0,0:23.6:1.0:27.1:1.0:1.0:0.0:58.2:11.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 108127288 . T C 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGTTCTGGGGTACATGATG;RSEQ=AGAGCATGCAGGTTTGTTAC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:0,13:0,0:0,13:1.0:0,1:18.5:1.0:31.5:1.0:1.0:0.0:56.9:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 108143456 . C G 256 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTTTTCCCGTAGGCTGATC;RSEQ=TTATTCAAAATGGGCCATTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1029:305:172,133:394,327:721,305:0.2964:2,2:25.3:1.0:31.1:1.0:0.631:1.07:59.8:100.667:0.2967:0.0:1.1 0/0:925:0:0,0:500,423:923,0:0.0:2,0:8.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 +11 108160632 . C T 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGACAAAGACTCACTCTGTC;RSEQ=GCCCAGGCTGGGTGCAGTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:29:0,29:1,25:26,29:0.5273:1,1:25.1:1.0:31.0:1.0:0.47273:0.0:59.3:58.0:0.537:0.0:1.1 0/0:46:0:0,0:0,46:46,0:0.0:1,0:9.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 +11 108188342 . TTATATA T 103 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=32;MSI=19.0;MSILEN=2.0;SSF=0.0315;SOR=0.0;LSEQ=TGAATATAACAGGAGTTGTT;RSEQ=TATATATATATATATATATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:12:0,12:0,36:36,12:0.2069:1,0:37.5:1.0:28.9:1.0:1.0:0.0:42.3:24.0:0.2069:0.0172:1.1 0/0:19:0:0,0:0,12:12,0:0.0:0,0:15.1:1.0:26.8:1.0:1.0:0.0:53.8:11.0:0.6111:0.0:0.8 +11 108188462 . T A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.06061;SOR=0.0;LSEQ=TATATATATATAAAAAAATA;RSEQ=ATAGTAGATGTTGCAAGCTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:24.2:1.0:32.0:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.5 0/0:3:0:0,0:0,3:3,0:0.0:0,0:19.0:1.0:29.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.7 +11 108206868 . TA T 75 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=15.0;MSILEN=1.0;SSF=0.26213;SOR=0.0;LSEQ=ACCCCATCTTGACAAAAAGT;RSEQ=AAAAAAAAAAAAAAGCCAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:10,6:0.375:0,0:21.7:1.0:29.2:1.0:1.0:0.0:59.3:12.0:0.375:0.0625:0.5 0/0:5:0:0,0:1,4:5,0:0.0:2,0:20.8:1.0:28.4:1.0:1.0:0.0:57.6:10.0:1.0:0.0:0.2 +11 108224757 . A T 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00094;SOR=0.0;LSEQ=GTTTGAGTCCAGCCTAGGCA;RSEQ=TACAGCAAGACCCTGTATCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:1,12:0,12:12,13:0.52:0,1:20.6:1.0:31.7:1.0:1.0:0.0:59.5:26.0:0.52:0.0:2.0 0/0:14:0:0,0:0,14:14,0:0.0:1,0:15.4:1.0:31.3:1.0:1.0:0.0:58.5:28.0:1.0:0.0:1.0 +11 108224791 . CACACAA C 86 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=21.0;MSILEN=2.0;SSF=0.00126;SOR=0.0;LSEQ=TGTATCTAAAAAAATACACA;RSEQ=ACACACACACACACACACAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:7:1,6:0,0:0,7:1.0:0,2:19.4:1.0:30.7:1.0:1.0:0.0:50.3:14.0:1.0:0.7143:1.7 0/0:5:0:0,0:0,5:5,0:0.0:0,0:26.2:1.0:30.8:1.0:1.0:0.0:49.4:10.0:1.0:0.0:1.4 +11 108225473 . G A 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00025;SOR=0.0;LSEQ=ACTACACATGAGAGTATACA;RSEQ=ATAAAGATACGTTGACAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:13:9,4:218,58:276,13:0.0447:2,2:18.7:1.0:30.4:1.0:0.48654:1.66714:60.0:26.0:0.045:0.0:2.1 0/0:266:0:0,0:192,73:265,0:0.0:2,0:22.0:1.0:31.1:1.0:1.0:0.0:60.0:87.333:1.0:0.0:0.8 +11 118342819 . T G 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=ACAGAAAGGATAAAGACCCC;RSEQ=TCGGGTCTCCTCATTAATTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:888:18:10,8:431,437:868,18:0.0203:2,2:25.1:1.0:31.4:1.0:0.64287:1.27:60.0:36.0:0.0206:0.0:1.0 0/0:710:0:0,0:347,361:708,0:0.0:2,0:23.9:1.0:29.6:1.0:1.0:0.0:60.0:63.364:0.9986:0.0:0.2 +11 118370615 . C G 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=ACTGTGAAGATAAGCTCTTT;RSEQ=CTATTGGATATCAGTAAGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:512:15:8,7:208,288:496,15:0.0293:2,2:28.2:1.0:32.3:1.0:0.43201:1.58:60.0:30.0:0.0299:0.0:1.1 0/0:530:0:0,0:229,301:530,0:0.0:2,0:24.9:1.0:30.2:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.1 +11 118372452 . C G 222 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCATCACCAGACCGACCT;RSEQ=CTCATTCACAAACCTCTGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1401:119:69,50:677,600:1277,119:0.0849:2,2:25.4:1.0:32.2:1.0:0.33682:1.22:59.9:118.0:0.0856:0.0:1.1 0/0:1404:0:0,0:737,664:1401,0:0.0:2,0:24.8:1.0:30.4:1.0:1.0:0.0:60.0:86.563:0.9978:0.0:0.2 +11 119077003 . C T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=10.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=CCCTCCGCCCGGATAGCCGG;RSEQ=GGCGGCGGCGGCGGCGGCGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:5,1:2,1:3,6:0.6667:2,2:29.3:1.0:28.8:1.0:1.0:2.24:60.0:5.0:0.625:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +11 119145274 . A G 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=TTTCAGTTTGTTGTTGTTCA;RSEQ=CCCCACTACTGTTAATTAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:13:11,2:6,0:6,13:0.6842:0,2:29.2:1.0:30.0:1.0:1.0:0.0:60.0:5.5:0.6471:0.0:1.8 0/0:2:0:0,0:2,0:2,0:0.0:0,0:15.5:1.0:30.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +11 121232811 . A G 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGCAATTGGTACTCTTCCAC;RSEQ=ATCCCTCCTGTGATACAACG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:33:33:12,21:0,0:0,33:1.0:0,2:28.7:1.0:32.2:1.0:1.0:0.0:32.6:66.0:1.0:0.0:1.2 0/1:164:29:9,20:68,67:135,29:0.1768:2,2:29.3:1.0:30.4:1.0:0.06702:2.24452:33.0:28.0:0.175:0.0:1.3 +11 121779664 . T C 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.00588;SOR=0.0;LSEQ=GGCTTTATGCATTTATCTCT;RSEQ=GGTTCCAGGCACAGCTTTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:13:0,13:0,1:1,13:0.9286:0,1:17.0:1.0:31.1:1.0:1.0:0.0:60.0:26.0:0.9286:0.0:1.4 0/0:3:0:0,0:0,3:3,0:0.0:0,0:32.3:1.0:26.3:1.0:1.0:0.0:60.0:2.0:1.0:0.0:0.7 +11 123606029 . A C 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08647;LSEQ=ATCCTACAACGTATGCATTG;RSEQ=CAGAAGAGTTCCTGCTCTCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:83:18,65:27,71:98,83:0.4586:2,2:24.5:1.0:32.1:1.0:0.39244:1.37084:60.0:166.0:0.4611:0.0:1.0 0/1:177:12:3,9:42,123:165,12:0.0678:2,2:19.1:1.0:31.2:1.0:1.0:1.02426:60.0:24.0:0.0686:0.0:1.2 +11 132534934 . G A 64 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.07302;SOR=0.0;LSEQ=ACAGTGCCACACTAACACCA;RSEQ=CTGGAGGGGAGATGTCACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:278:5:4,1:71,202:273,5:0.018:2,2:17.0:1.0:27.8:1.0:0.01978:11.27:60.0:10.0:0.0184:0.0:1.2 0/0:211:0:0,0:72,139:211,0:0.0:2,0:22.4:1.0:31.1:1.0:1.0:0.0:60.0:104.5:1.0:0.0:0.5 +12 401969 . C A 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTTCTGTGCTGCGCACACAG;RSEQ=ATTCTCATCATCAGACTCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1678:41:19,22:795,839:1634,41:0.0244:2,2:27.0:1.0:29.0:1.0:0.8746:1.09709:60.0:9.25:0.0222:0.0:1.2 0/0:1130:0:0,0:552,577:1129,0:0.0:2,0:24.8:1.0:31.3:1.0:1.0:0.0:60.0:111.9:0.9991:0.0:0.1 +12 406427 . G C 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TTTAACTTATTTTATGACAA;RSEQ=GCCCAAAATGGAGGCTTTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:29:2,27:17,231:248,29:0.1047:2,2:24.0:1.0:30.3:1.0:1.0:1.01:60.0:58.0:0.1062:0.0:1.1 0/0:135:0:0,0:16,119:135,0:0.0:2,0:25.0:1.0:30.2:1.0:1.0:0.0:60.0:44.0:1.0:0.0:0.1 +12 416764 . C A 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTTCATCTGTGGCTAGAGC;RSEQ=TGCCGCGCTCTATCTTGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1193:85:45,40:607,500:1107,85:0.0712:2,2:25.2:1.0:30.5:1.0:0.7361:1.07904:60.0:41.5:0.0709:0.0:1.1 0/0:806:0:0,0:427,379:806,0:0.0:2,0:24.2:1.0:30.8:1.0:1.0:0.0:60.0:114.143:1.0:0.0:0.1 +12 427077 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.53924;SOR=0.0;LSEQ=GGGAGAGAGGAGAATCTCCC;RSEQ=GTTTCCTTCAGGCCCTGGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:6,0:14,0:14,6:0.3:1,0:19.7:1.0:30.2:1.0:1.0:0.0:60.0:12.0:0.3:0.0:2.0 0/0:3:0:0,0:3,0:3,0:0.0:0,0:19.7:1.0:28.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +12 459805 . C A 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=ACCTCTTCTTCTGGCAGAAT;RSEQ=TTTCTCCGCCCATCCTTCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1657:24:15,9:872,759:1631,24:0.0145:2,2:22.8:1.0:29.5:1.0:0.41612:1.45:58.9:48.0:0.0146:0.0:1.1 0/0:1086:0:0,0:574,512:1086,0:0.0:2,0:25.5:1.0:30.9:1.0:1.0:0.0:60.0:82.538:1.0:0.0:0.2 +12 461807 . A G 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CATGCCTAGGGATGCCTAAC;RSEQ=TTCTTGGCATACCCAGTGGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:36.2:1.0:30.3:1.0:1.0:0.0:55.5:5.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 465673 . C G 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATCTGAAGTTTCTTCAGTT;RSEQ=CGTGTTTCTACTCACATCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1195:98:38,60:436,661:1097,98:0.082:2,2:27.0:1.0:32.3:1.0:0.91433:1.04145:60.0:196.0:0.0832:0.0:1.2 0/0:932:0:0,0:384,547:931,0:0.0:2,0:25.2:1.0:30.1:1.0:1.0:0.0:60.0:83.636:0.9989:0.0:0.1 +12 1022352 . A G 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00034;SOR=0.05909;LSEQ=TCTGTCCAGAGCCTCTCCCT;RSEQ=CTAGAGTGATGGACAAGCTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:25:25,0:42,0:42,25:0.3731:1,1:23.1:1.0:33.7:1.0:1.0:0.0:57.4:50.0:0.3731:0.0:1.0 0/1:30:1:1,0:29,0:29,1:0.0333:1,0:21.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.0333:0.0:1.0 +12 1034943 . C T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGATGAGTATGAAAAGATTA;RSEQ=GGCGCCATTCACAAAACCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:14,5:0.2632:1,0:22.0:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.0 0/0:2:0:0,0:0,2:2,0:0.0:0,0:23.5:1.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +12 1036562 . AG A 144 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00135;SOR=0.0;LSEQ=GCTACAGGGGCACGGGCAGA;RSEQ=GCTGGGTGAGAATCCATCGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:21:0,21:0,52:52,21:0.2877:1,1:22.7:1.0:32.8:1.0:1.0:0.0:60.0:42.0:0.2877:0.0685:0.2 0/0:26:0:0,0:0,26:26,0:0.0:1,0:20.9:1.0:29.8:1.0:1.0:0.0:60.0:25.0:1.0:0.0:0.3 +12 1038602 . AT CA 71 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=AAACAACTTATTAACAAAAC;RSEQ=ATTTTTGTTTTCATCAATGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:0,0:0,5:0.8333:0,0:20.6:1.0:30.9:1.0:1.0:0.0:56.6:10.0:1.0:0.1667:0.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 1038742 . A G 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.47826;SOR=0.0;LSEQ=CCAAAAAATACATCCTTTGC;RSEQ=ACAATTTTTATATATGGTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:11,0:10,0:10,11:0.5238:0,0:21.7:1.0:30.3:1.0:1.0:0.0:60.0:22.0:0.5238:0.0:1.1 0/0:2:0:0,0:2,0:2,0:0.0:0,0:39.0:1.0:29.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +12 1038766 . C G 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.53613;SOR=0.0;LSEQ=ATTTTTATATATGGTGAAAA;RSEQ=TTTTAGGTGTCAGCTTGAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:12:12,0:21,0:21,12:0.3636:1,0:19.6:1.0:32.8:1.0:1.0:0.0:60.0:24.0:0.3636:0.0:1.2 0/0:3:0:0,0:3,0:3,0:0.0:0,0:27.3:1.0:31.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +12 1038854 . C T 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.00159;SOR=0.0;LSEQ=AGAGTATTTGAATTCCACCA;RSEQ=TCTAGGGAACGCTGGCTGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:24:24,0:140,2:142,24:0.1446:1,1:24.3:1.0:31.4:1.0:1.0:0.0:60.0:48.0:0.1463:0.0:1.1 0/0:51:0:0,0:48,3:51,0:0.0:2,0:22.0:1.0:32.0:1.0:1.0:0.0:60.0:102.0:1.0:0.0:0.1 +12 1040143 . TA T 92 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.0;MSILEN=1.0;SSF=0.52273;SOR=0.0;LSEQ=CAAGACCCTGTCTTTAAAAA;RSEQ=AAAAAAAAAAAAGATGATGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:7,0:10,0:10,7:0.3684:0,0:27.0:1.0:32.8:1.0:1.0:0.0:60.0:14.0:0.3684:0.0526:0.0 0/0:3:0:0,0:3,0:3,0:0.0:0,0:11.7:1.0:29.0:1.0:1.0:0.0:56.7:6.0:1.0:0.0:0.0 +12 9848439 . T TTGCTGC 164 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=14;MSI=6.0;MSILEN=3.0;SSF=0.0;SOR=0.03995;LSEQ=TGGGCAGAAAAAAGTAAAAC;RSEQ=TGCTGCTGCTGCTGATGATG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:34:25,9:22,16:38,34:0.2519:2,2:34.0:1.0:32.3:1.0:0.21701:2.0:59.6:68.0:0.2519:0.0074:1.8 0/1:152:2:2,0:49,32:81,2:0.0132:2,0:29.0:1.0:32.7:0.0:0.52042:0.0:60.0:4.0:0.0133:0.0:2.0 +12 9848467 . T A 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=3.0;SSF=0.0;SOR=0.10783;LSEQ=GCTGCTGATGATGATGATGA;RSEQ=GAAGATGATGATGATGATGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:31:23,8:84,45:129,31:0.1938:2,2:26.3:1.0:29.8:1.0:0.39944:1.54:58.2:30.0:0.1923:0.0:2.1 0/1:199:5:4,1:125,69:194,5:0.0251:2,2:39.4:1.0:29.4:1.0:0.65859:2.2:52.0:10.0:0.0256:0.0:2.6 +12 9848470 . A T 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTGATGATGATGATGATGA;RSEQ=GATGATGATGATGATGATGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:32:24,8:85,49:134,32:0.1928:2,2:23.4:1.0:30.0:1.0:0.30017:1.72:58.9:15.0:0.1899:0.0:2.2 0/0:201:0:0,0:124,70:194,0:0.0:2,0:23.4:1.0:29.6:1.0:1.0:0.0:46.3:63.667:1.0:0.0:0.8 +12 9848648 . A G 99 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.02683;SOR=0.10923;LSEQ=AAAAACAGGAAAAATCTCCT;RSEQ=AAACACCAAAAGGATCTAGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:2,6:0,15:15,8:0.3478:1,2:20.8:1.0:33.1:1.0:0.11067:0.0:24.1:16.0:0.3478:0.0:1.0 0/1:19:1:0,1:1,17:18,1:0.0526:1,0:30.0:0.0:32.0:0.0:1.0:0.0:22.0:2.0:0.0526:0.0:1.0 +12 12006544 . G A 231 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01033;LSEQ=CTGAGGTTTAGACAAATCCA;RSEQ=GAAGTTTAATTGTTAACTTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:999:170:83,87:421,406:827,170:0.1702:2,2:21.5:1.0:31.2:1.0:0.6738:1.08682:60.0:41.5:0.1692:0.0:1.1 0/0:948:2:2,0:476,469:945,2:0.0021:2,0:16.5:1.0:27.5:1.0:0.49952:0.0:60.0:4.0:0.0021:0.0:1.0 +12 12007893 . C G 322 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04372;LSEQ=ATTTAATTTAGGCCCTGGAC;RSEQ=TAGTTCCAGAATAGGTGTTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1515:1234:489,745:116,161:277,1234:0.8145:2,2:26.7:1.0:31.4:1.0:0.49802:1.09762:59.9:175.286:0.8169:0.0:1.1 0/1:1635:263:115,148:612,755:1367,263:0.1609:2,2:23.8:1.0:30.4:1.0:0.7866:1.04319:60.0:64.75:0.1607:0.0:1.2 +12 12009741 . A G 254 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATATGTTAACATACAGAAAG;RSEQ=TCTGGTTCTGAAAAAAAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1523:267:132,135:647,604:1251,267:0.1753:2,2:26.2:1.0:31.6:1.0:0.501:1.09547:60.0:43.5:0.1765:0.0:1.1 0/0:1380:0:0,0:698,682:1380,0:0.0:2,0:24.9:1.0:29.0:1.0:1.0:0.0:60.0:54.2:1.0:0.0:0.1 +12 12010056 . G A 315 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.08008;LSEQ=CCTTGTGATTTCACCTCGTC;RSEQ=TGGCCACAAACTTAACCAGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1885:1210:599,611:333,339:672,1210:0.6419:2,2:24.4:1.0:30.8:1.0:1.0:1.00198:59.9:92.077:0.6432:0.0:1.1 0/1:1626:204:107,97:701,721:1422,204:0.1255:2,2:24.7:1.0:29.8:1.0:0.41096:1.13:60.0:101.0:0.1252:0.0:1.1 +12 12013626 . T TC 260 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.0077;LSEQ=CTGGCTGTTATTTGGTTGTT;RSEQ=CCCCCCCTCTGTTTGTGTAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1777:308:155,153:763,702:1465,308:0.1733:2,2:27.2:1.0:31.5:1.0:0.61586:1.07281:59.8:50.333:0.1729:0.0214:1.0 0/0:1863:3:3,0:925,932:1857,3:0.0016:2,0:42.3:1.0:31.7:1.0:0.12399:0.0:60.0:6.0:0.0016:0.0:0.3 +12 12016089 . C T 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00641;LSEQ=TGGAAACTTATCGGTCAAAA;RSEQ=TTTCACTAAAGGCAGTTTTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1859:138:66,72:822,897:1719,138:0.0742:2,2:25.1:1.0:31.2:1.0:1.0:1.0:59.9:276.0:0.075:0.0:1.3 0/0:1949:1:0,1:934,1011:1945,1:0.0005:2,0:1.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0005:0.0:2.0 +12 12018392 . C T 242 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01442;LSEQ=TATACATTGCAGATGGTTAA;RSEQ=GTATCTCTTAAGTTTTTTTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1444:242:120,122:576,626:1202,242:0.1676:2,2:23.4:1.0:30.6:1.0:0.6724:1.07:60.0:79.667:0.1678:0.0:1.1 0/0:1384:4:0,4:634,746:1380,4:0.0029:2,0:1.0:0.0:24.8:1.0:0.12973:0.0:60.0:8.0:0.0029:0.0:1.0 +12 12018911 . T C 207 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTATTCTACTCTGTTTTTT;RSEQ=CTATATTCTCCTTCTTGGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1759:90:45,45:888,781:1669,90:0.0512:2,2:22.9:1.0:31.9:1.0:0.58848:1.13692:59.7:180.0:0.0517:0.0:1.1 0/0:1565:0:0,0:804,760:1564,0:0.0:2,0:23.1:1.0:29.2:1.0:1.0:0.0:60.0:119.308:0.9994:0.0:0.1 +12 12022533 . C T 271 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACATGATCCGCCGCCTCTC;RSEQ=CCGGCTGAGAGAGCTCAGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1239:474:201,273:334,430:764,474:0.3826:2,2:23.7:1.0:30.6:1.0:0.67962:1.05496:60.0:58.25:0.3835:0.0:1.2 0/0:1147:0:0,0:526,619:1145,0:0.0:2,0:23.8:1.0:30.1:1.0:1.0:0.0:60.0:70.563:0.9982:0.0:0.2 +12 12027431 . TATGTGTA CGTGTG 69 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.01515;SOR=0.0;LSEQ=TATGTGCGTGTGTACACACA;RSEQ=TGTGCGTGTGTACACACATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:4,1:1,0:1,5:0.8333:0,2:23.4:1.0:29.9:1.0:1.0:0.0:29.2:10.0:0.8333:0.1667:3.0 0/0:5:0:0,0:5,0:5,0:0.0:0,0:1.0:0.0:27.4:1.0:1.0:0.0:32.4:10.0:1.0:0.0:2.0 +12 12027664 . GTA G 75 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.0;MSILEN=2.0;SSF=0.1613;SOR=0.0;LSEQ=GTATATGTGTATATATATGT;RSEQ=TATATATATGAAATTTTTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:5:3,2:152,82:234,5:0.0209:2,2:28.6:1.0:32.4:1.0:1.0:1.23463:59.0:10.0:0.021:0.0:0.2 0/0:148:0:0,0:93,55:148,0:0.0:2,0:25.4:1.0:28.4:1.0:1.0:0.0:57.7:73.0:1.0:0.0:0.2 +12 12029765 . A G 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGTTGGGTCATTAATCCT;RSEQ=CAGCAGGCAAGACACAGAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:78:45,33:251,203:454,78:0.1463:2,2:21.7:1.0:32.1:1.0:0.7131:1.1:60.0:156.0:0.1477:0.0:1.8 0/0:431:0:0,0:232,199:431,0:0.0:2,0:22.8:1.0:27.8:1.0:1.0:0.0:59.9:70.833:1.0:0.0:0.8 +12 12030834 . TC T 95 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.00757;SOR=0.0;LSEQ=TTAATTGCTACGTGTCACTG;RSEQ=CCCCCCTGCCTCACTGCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:384:8:3,5:167,209:376,8:0.0208:2,2:30.6:1.0:31.9:1.0:1.0:1.33076:60.0:16.0:0.0213:0.0:0.1 0/0:373:0:0,0:168,203:371,0:0.0:2,0:23.6:1.0:30.3:1.0:1.0:0.0:59.8:52.0:0.9945:0.0:0.2 +12 12031265 . G A 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGAGTGGAAAATAATAGAA;RSEQ=GGGCTTGAGGAGACTGGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:61:35,26:187,134:321,61:0.1597:2,2:27.9:1.0:30.2:1.0:0.88862:1.0366:60.0:19.333:0.1538:0.0:1.1 0/0:396:0:0,0:214,182:396,0:0.0:2,0:24.6:1.0:30.6:1.0:1.0:0.0:60.0:78.2:1.0:0.0:0.2 +12 12308074 . G A 111 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00288;SOR=0.066;LSEQ=TGGGAGGCGGATGTTGCAGT;RSEQ=AGCCAAGATCACGCCACTTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:14:14,0:14,0:14,14:0.5:1,1:19.1:1.0:29.4:1.0:1.0:0.0:42.4:28.0:0.5:0.0:2.1 0/1:17:1:1,0:16,0:16,1:0.0588:1,0:13.0:0.0:29.0:0.0:1.0:0.0:49.0:2.0:0.0588:0.0:2.0 +12 12308087 . G A 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00064;SOR=0.08927;LSEQ=TTGCAGTGAGCCAAGATCAC;RSEQ=CCACTTTACTCCAGCCTGGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:17:17,0:16,0:16,17:0.5152:1,1:25.5:1.0:31.5:1.0:1.0:0.0:47.2:34.0:0.5152:0.0:1.8 0/1:24:2:2,0:22,0:22,2:0.0833:1,0:17.0:1.0:31.0:0.0:1.0:0.0:51.5:4.0:0.0833:0.0:2.0 +12 12767856 . A G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=GGCTGGAGTGCAGTGGCACG;RSEQ=TCTCAGCTCACTGCAATCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1.0:0,2:32.0:1.0:32.2:1.0:1.0:0.0:44.6:10.0:1.0:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:41.0:0.0:33.0:0.0:1.0:0.0:59.0:2.0:1.0:0.0:0.0 +12 12873211 . A T 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.02984;SOR=0.0;LSEQ=TTTGATCTGGCCCTGTTCTG;RSEQ=CATGCAATGAGGCATTTGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:6:1,5:1,65:66,6:0.0833:1,2:23.2:1.0:30.8:1.0:0.1608:11.96:60.0:12.0:0.0833:0.0:1.7 0/0:63:0:0,0:4,59:63,0:0.0:2,0:23.0:1.0:29.3:1.0:1.0:0.0:60.0:62.0:1.0:0.0:0.4 +12 16753747 . G A 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGGTCCTTGATCTTTCGGTT;RSEQ=CAGCCAGCACAACCTTTCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:25:7,18:17,112:129,25:0.1623:2,2:22.4:1.0:29.2:1.0:0.07376:2.54:60.0:50.0:0.1689:0.0:1.0 0/0:112:0:0,0:22,89:111,0:0.0:2,0:23.1:1.0:31.6:1.0:1.0:0.0:60.0:222.0:1.0:0.0:0.1 +12 18467122 . T C 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AATACATGTTTATTTAAATA;RSEQ=ATTCATTGAAACATGATGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:67:1,66:0,36:36,67:0.6505:1,1:23.4:1.0:33.0:1.0:1.0:0.0:59.4:134.0:0.6505:0.0:1.0 0/0:51:0:0,0:0,51:51,0:0.0:1,0:20.8:1.0:28.5:1.0:1.0:0.0:60.0:102.0:1.0:0.0:0.2 +12 18473881 . T G 287 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03952;LSEQ=ACTCAATAAATATTAATATA;RSEQ=TCTGCTGTCTACAGCATGAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:659:444:289,155:136,79:215,444:0.6737:2,2:24.4:1.0:32.7:1.0:0.66471:1.08:60.0:110.0:0.6728:0.0:1.1 0/1:452:34:22,12:264,154:418,34:0.0752:2,2:25.0:1.0:31.1:1.0:1.0:1.07:60.0:68.0:0.0754:0.0:1.1 +12 18524061 . T G 148 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATTATAAGAACATTTTCAT;RSEQ=AAAATATCAGTACAATTGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:371:24:17,7:262,85:347,24:0.0647:2,2:26.5:1.0:32.4:1.0:0.62703:1.26836:60.0:48.0:0.0652:0.0:1.0 0/0:303:0:0,0:217,86:303,0:0.0:2,0:24.1:1.0:29.1:1.0:1.0:0.0:60.0:74.75:1.0:0.0:0.1 +12 18690977 . A G 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00011;SOR=0.0;LSEQ=GAAGGAAATTTATCTATTAC;RSEQ=GTAGAGAAAAAAAAAAGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:13:13,0:41,0:41,13:0.2407:1,1:24.9:1.0:29.0:1.0:1.0:0.0:60.0:12.0:0.2264:0.0:1.3 0/0:51:0:0,0:51,0:51,0:0.0:1,0:18.1:1.0:29.7:1.0:1.0:0.0:60.0:102.0:1.0:0.0:0.1 +12 18715728 . T G 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCCATAAGCCCTGCCAAA;RSEQ=CTACTTCACAGACTTTTCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:531:45:21,24:238,247:485,45:0.0847:2,2:27.7:1.0:32.5:1.0:0.87633:1.10101:60.0:90.0:0.0856:0.0:1.0 0/0:945:0:0,0:468,476:944,0:0.0:2,0:25.0:1.0:29.0:1.0:1.0:0.0:60.0:71.615:0.9989:0.0:0.1 +12 18719938 . G T 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.00853;SOR=0.0;LSEQ=CAGATCACAGAAGATTCAGA;RSEQ=ATCTAAATCATTACATGGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:5:2,3:203,270:473,5:0.0104:2,2:14.8:1.0:27.4:1.0:1.0:1.12746:60.0:10.0:0.0106:0.0:1.0 0/0:760:0:0,0:337,420:757,0:0.0:2,0:26.4:1.0:30.6:1.0:1.0:0.0:60.0:74.7:0.9973:0.0:0.2 +12 21600952 . CG TA 80 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00039;SOR=0.0;LSEQ=CATGCGTACTTTTGATAGCA;RSEQ=TGTGAAGGTATCTCTCTAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:7:5,2:21,16:37,7:0.1522:2,2:29.0:1.0:28.8:1.0:0.68165:1.88:51.6:6.0:0.1622:0.0:1.3 0/0:89:0:0,0:44,43:87,0:0.0:2,0:26.3:1.0:29.3:1.0:1.0:0.0:45.2:8.667:1.0:0.0:1.3 +12 23618113 . G A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02778;SOR=0.0;LSEQ=AAGAAAAACAAGCAGAAAGT;RSEQ=ACAACAACAGCATCAACAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:1,6:0,0:0,7:1.0:0,2:26.3:1.0:29.9:1.0:1.0:0.0:57.0:14.0:1.0:0.0:1.0 0/0:2:0:0,0:1,1:2,0:0.0:2,0:25.0:1.0:21.5:1.0:1.0:0.0:54.5:1.0:1.0:0.0:1.5 +12 25368084 . T C 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAAACTTTTCCCTTAAAAA;RSEQ=AAAGGTAAATATCAGTTTCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:28.6:1.0:34.1:1.0:1.0:0.0:56.4:14.0:1.0:0.0:1.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 25378224 . ATATATATATATATATATATATATA T 80 MSI12 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=22;MSI=24.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TTTGTTGCCCTGTTCTTTAT;RSEQ=TATATATATATATATATATA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:0,0:0,6:0.6667:0,0:17.7:1.0:31.0:1.0:1.0:0.0:60.0:12.0:0.6667:0.6667:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 25398285 . C A 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=GGCACTCTTGCCTACGCCAC;RSEQ=AGCTCCAACTACCACAAGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:113:49,64:384,490:874,113:0.1144:2,2:25.5:1.0:30.5:1.0:0.92017:1.02355:49.3:36.667:0.1125:0.0:1.1 0/0:664:0:0,0:288,376:664,0:0.0:2,0:24.7:1.0:30.7:1.0:1.0:0.0:59.3:220.333:1.0:0.0:0.1 +12 27578740 . G A 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00256;SOR=0.0;LSEQ=TCTAGAGAGTCAACCATCAT;RSEQ=AATTATAAGGTTCTATTGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:13,0:12,0:12,13:0.52:0,1:30.8:1.0:29.2:1.0:1.0:0.0:60.0:26.0:0.52:0.0:1.0 0/0:11:0:0,0:11,0:11,0:0.0:0,0:17.6:1.0:31.3:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.1 +12 30848675 . C T 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.17222;SOR=0.0;LSEQ=CAGCCTCCTCTTCCGCGACC;RSEQ=CTGGATTACCTCACACCCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:6,3:14,13:27,9:0.25:2,2:18.8:1.0:31.8:1.0:0.70027:1.83:60.0:18.0:0.25:0.0:1.7 0/0:10:0:0,0:5,5:10,0:0.0:2,0:20.7:1.0:30.1:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 +12 31932814 . A C 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01992;SOR=0.10853;LSEQ=ATCCCCTCGGAGGGTTTTAC;RSEQ=AACATTTACAATTTTCTTCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:14,0:19,0:19,14:0.4242:1,1:12.4:1.0:31.5:1.0:1.0:0.0:60.0:28.0:0.4242:0.0:1.0 0/1:14:1:1,0:12,1:13,1:0.0714:1,0:6.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0769:0.0:1.0 +12 32411481 . C T 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0419;SOR=0.0;LSEQ=GGGGACCACTACCACCAAGA;RSEQ=GCAGAGACCAGTAATGGCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:8,0:5,1:6,8:0.5714:2,0:24.8:1.0:32.4:1.0:0.42857:0.0:48.5:16.0:0.5714:0.0:2.3 0/0:6:0:0,0:6,0:6,0:0.0:0,0:27.3:1.0:32.3:1.0:1.0:0.0:48.0:12.0:1.0:0.0:1.3 +12 38601111 . A T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.03471;SOR=0.0;LSEQ=TACAAGAAATGTAAAAAAAC;RSEQ=CATTAAAATCAACCCCAAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:7:0,7:0,28:28,7:0.2:1,0:33.3:1.0:26.9:1.0:1.0:0.0:54.7:6.0:0.1765:0.0:1.1 0/0:25:0:0,0:2,23:25,0:0.0:2,0:25.5:1.0:29.1:1.0:1.0:0.0:55.7:50.0:1.0:0.0:0.0 +12 43130905 . G A 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.25359;SOR=0.0;LSEQ=GTTTTCTGGCATGAAACATA;RSEQ=TTTTATTTGTTTTCAGACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:8:8,0:10,0:10,8:0.4444:0,0:32.4:1.0:30.4:1.0:1.0:0.0:60.0:16.0:0.4444:0.0:1.0 0/0:4:0:0,0:4,0:4,0:0.0:0,0:10.3:1.0:32.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 +12 43131208 . T C 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0116;LSEQ=TAGATCGGGTATGTATTCTT;RSEQ=TGGAGTTATCAAATATAGCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:24:4,20:0,10:10,24:0.7059:0,2:22.1:1.0:32.5:1.0:0.29576:0.0:60.0:23.0:0.697:0.0:1.2 0/1:40:1:0,1:3,36:39,1:0.025:2,0:19.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.025:0.0:2.0 +12 46208438 . A G 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0063;SOR=0.0;LSEQ=CAAAACTCCATCTCAAAAAA;RSEQ=TAATAAACTTCCCTCCTCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:11,0:2,0:2,11:0.8462:0,0:28.4:1.0:33.6:1.0:1.0:0.0:60.0:22.0:0.8462:0.0:1.1 0/0:4:0:0,0:4,0:4,0:0.0:0,0:10.3:1.0:30.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 +12 46254505 . C G 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=GAAATGTATAACAACATAAT;RSEQ=AAATTTATAAGACTATACTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:11:11,0:98,10:108,11:0.0924:2,0:29.1:1.0:32.8:1.0:0.59561:0.0:59.1:22.0:0.0932:0.0:1.1 0/0:177:0:0,0:157,19:176,0:0.0:2,0:21.8:1.0:30.3:1.0:1.0:0.0:59.9:24.143:1.0:0.0:0.1 +12 46287550 . A G 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGTGAATTTAGTTTATTTT;RSEQ=TTTTTACATATAAGTTAATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:126:13:3,10:25,88:113,13:0.1032:2,2:29.5:1.0:29.3:1.0:1.0:1.06:59.0:5.5:0.0894:0.0:1.2 0/0:210:0:0,0:61,149:210,0:0.0:2,0:22.5:1.0:29.2:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.1 +12 49421368 . G A 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.04564;SOR=0.0;LSEQ=TCAGCCTTTCGAGTAGCTGG;RSEQ=ATTACAGGCACGCACCATCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:27:15:12,3:9,3:12,15:0.5556:2,2:30.5:1.0:31.1:1.0:1.0:1.32:59.4:30.0:0.5556:0.0:1.1 0/0:5:0:0,0:4,1:5,0:0.0:2,0:28.0:1.0:32.6:1.0:1.0:0.0:56.4:10.0:1.0:0.0:0.0 +12 49428717 . G A 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01971;LSEQ=TCTGCAGCAAATTTGTCCAG;RSEQ=TCTGGAGAGGGGAGAACCAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:747:57:23,34:229,461:690,57:0.0763:2,2:28.5:1.0:29.8:1.0:0.30771:1.36:60.0:13.25:0.0724:0.0:1.3 0/0:616:1:1,0:238,377:615,1:0.0016:2,0:1.0:0.0:23.0:0.0:0.38799:0.0:60.0:2.0:0.0017:0.0:1.0 +12 49431654 . C T 215 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01494;LSEQ=CCATCCGGGTATCCCGGCTG;RSEQ=CCATCATGCTCTGTCCTGGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:914:148:81,67:411,355:766,148:0.1619:2,2:24.8:1.0:29.9:1.0:0.85721:1.04:59.9:36.0:0.1609:0.0:1.2 0/0:696:2:0,2:370,323:693,2:0.0029:2,0:1.0:0.0:23.5:1.0:0.21832:0.0:60.0:4.0:0.0029:0.0:1.0 +12 49436248 . G A 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGAATGGGGAGGAGCAGGG;RSEQ=AAGTGCTGCAGGAGTCCGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:46:41,5:226,54:280,46:0.1411:2,2:23.7:1.0:29.9:1.0:0.21623:1.96:60.0:22.0:0.1406:0.0:1.1 0/0:239:0:0,0:198,41:239,0:0.0:2,0:22.3:1.0:30.6:1.0:1.0:0.0:60.0:78.667:1.0:0.0:0.1 +12 49438490 . C A 222 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACTCCCAGAGTCACGCTCC;RSEQ=CCTACTCTGCCGCTCCCTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:611:181:127,54:281,148:429,181:0.2962:2,2:25.7:1.0:29.7:1.0:0.30034:1.24:60.0:44.25:0.2945:0.0:1.1 0/0:556:0:0,0:359,196:555,0:0.0:2,0:23.3:1.0:29.9:1.0:1.0:0.0:60.0:38.643:0.9982:0.0:0.2 +12 49439376 . A G 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGCAAAGCTTGCAATGTGCC;RSEQ=AGCTTGTGCCACTGCACTCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:31.2:1.0:30.8:1.0:1.0:0.0:29.6:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 49441376 . AT A 100 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACACTCAGCTAATTTTTGTT;RSEQ=TTTTTAGAAGAGACGGGGTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:1,9:0.9:0,0:22.0:1.0:31.8:1.0:1.0:0.0:56.8:18.0:0.9:0.3:0.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 50413034 . C A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01599;SOR=0.1107;LSEQ=TTCCTCCAGTCCTTCCCCTA;RSEQ=TGCTTCAGGCAGTTGCCACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:156:8:0,8:19,129:148,8:0.0513:2,0:24.0:1.0:32.4:1.0:0.59685:0.0:60.0:16.0:0.0513:0.0:2.1 0/0:169:1:1,0:29,139:168,1:0.0059:2,0:1.0:0.0:24.0:0.0:0.17751:0.0:60.0:2.0:0.0059:0.0:2.0 +12 50484405 . C T 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTGGGAGGCAGTGCTGTGC;RSEQ=GGAGCTGCCTTGTGCCGATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:72:15,57:56,206:262,72:0.2149:2,2:26.2:1.0:30.8:1.0:1.0:1.03291:59.9:35.0:0.2121:0.0:1.2 0/0:352:0:0,0:112,239:351,0:0.0:2,0:21.3:1.0:28.9:1.0:1.0:0.0:59.9:57.5:0.9971:0.0:0.1 +12 52906415 . C A 98 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00109;SOR=0.02184;LSEQ=TTACTCTCCAGCCTGGGCAA;RSEQ=AATAGCAAAACTCTGTAGGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:9,0:1,0:1,9:0.9:0,0:26.3:1.0:31.0:1.0:1.0:0.0:41.1:18.0:0.9:0.0:2.4 0/1:9:1:1,0:8,0:8,1:0.1111:0,0:18.0:0.0:31.0:0.0:1.0:0.0:22.0:2.0:0.125:0.0:2.0 +12 52906545 . C T 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.16033;SOR=0.0;LSEQ=ACCGCTGCCGCTGCCTATGC;RSEQ=TCTGTTACCAGAAAAGATCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:5:1,4:53,70:123,5:0.0388:2,2:31.0:1.0:31.6:1.0:0.39615:3.00602:60.0:10.0:0.0394:0.0:1.0 0/0:75:0:0,0:30,45:75,0:0.0:2,0:24.3:1.0:31.1:1.0:1.0:0.0:59.8:150.0:1.0:0.0:1.2 +12 52921297 . C A 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATAACATCTTCCAGCAGCC;RSEQ=CAAGAGAGAGGGACCCCTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:408:34:12,22:155,219:374,34:0.0833:2,2:29.7:1.0:30.2:1.0:0.58583:1.29675:60.0:68.0:0.0848:0.0:1.2 0/0:272:0:0,0:121,151:272,0:0.0:2,0:26.6:1.0:30.1:1.0:1.0:0.0:59.8:67.0:1.0:0.0:1.8 +12 53030489 . C T 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CACGGGTATCATGTATTGCC;RSEQ=GATTATTGTGTTTCACAACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:107:18:7,11:35,54:89,18:0.1682:2,2:27.6:1.0:29.8:1.0:1.0:1.01835:60.0:17.0:0.1635:0.0:1.0 0/0:92:0:0,0:39,53:92,0:0.0:2,0:26.6:1.0:29.5:1.0:1.0:0.0:60.0:91.0:1.0:0.0:0.3 +12 53130533 . G A 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCACTGCGGTGGGGTCCTC;RSEQ=GGATGCAGGGGCCATCAAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:0,5:1,33:34,5:0.1282:1,0:34.2:1.0:33.4:1.0:1.0:0.0:60.0:10.0:0.1282:0.0:1.0 0/0:7:0:0,0:0,7:7,0:0.0:0,0:19.6:1.0:32.1:1.0:1.0:0.0:58.6:14.0:1.0:0.0:0.9 +12 55427158 . A C 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.05131;SOR=0.0;LSEQ=AGTGATTGAGTAAAAGCTAA;RSEQ=AGATGAGGCAAAAATCGACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:7:7,0:95,3:98,7:0.0667:1,0:24.4:1.0:31.4:1.0:1.0:0.0:60.0:14.0:0.068:0.0:1.0 0/0:58:0:0,0:55,3:58,0:0.0:2,0:21.6:1.0:29.3:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 +12 56474480 . A G 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.22222;SOR=0.0;LSEQ=TGCAGGGAGGGGAGCAGGGA;RSEQ=CTTCATTCTGTAAACAGGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:23.9:1.0:31.1:1.0:1.0:0.0:59.4:6.0:0.8571:0.0:1.3 0/0:1:0:0,0:1,0:1,0:0.0:0,0:8.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +12 56478002 . A C 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGATGAGGAAGGGGCCCT;RSEQ=CTGGTATGAGGCACTTTGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:12.4:1.0:31.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 56489613 . T C 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGTACTTAGCTTACTTTTG;RSEQ=TTTTTCTTTTCTTTTTTTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:97:33,64:119,211:330,97:0.2272:2,2:24.2:1.0:33.0:1.0:0.80948:1.09358:60.0:96.0:0.227:0.0:1.1 0/0:444:0:0,0:156,288:444,0:0.0:2,0:25.6:1.0:29.1:1.0:1.0:0.0:60.0:73.0:1.0:0.0:0.2 +12 57860293 . T C 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.015;SOR=0.0;LSEQ=CCATAAACAAATATTAAAAA;RSEQ=AATGTTTGTGTGACTGTGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:10:0,10:3,144:147,10:0.0637:1,0:14.1:1.0:32.8:1.0:1.0:0.0:60.0:20.0:0.0645:0.0:1.0 0/0:96:0:0,0:4,92:96,0:0.0:1,0:22.2:1.0:28.0:1.0:1.0:0.0:60.0:47.0:1.0:0.0:0.1 +12 57860826 . T C 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AACAGCCCGTTCCCCCAAGA;RSEQ=GACCCCATCTTGGGACAGCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:13,0:3,0:3,13:0.8125:0,1:30.9:1.0:29.6:1.0:1.0:0.0:60.0:12.0:0.8:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 57865284 . C T 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01996;LSEQ=GCAGGGAAGATGCCCCCGCC;RSEQ=AGGAACCTTCCTACCAGAGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1566:93:45,48:759,713:1472,93:0.0594:2,2:24.1:1.0:30.3:1.0:0.59337:1.13539:60.0:92.0:0.0596:0.0:1.1 0/0:1591:2:0,2:815,773:1588,2:0.0013:2,0:1.0:0.0:23.0:1.0:0.23742:0.0:53.5:4.0:0.0013:0.0:1.5 +12 58144359 . G T 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCCCTGGTCTCAAAAAAAAA;RSEQ=AATGGGCAAGGTATGGATGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:253:91:74,17:135,27:162,91:0.3597:2,2:22.8:1.0:29.2:1.0:0.73074:1.14801:60.0:12.0:0.3457:0.0:1.1 0/0:198:0:0,0:151,46:197,0:0.0:2,0:20.7:1.0:30.9:1.0:1.0:0.0:60.0:196.0:1.0:0.0:0.1 +12 61873046 . G A 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CCACAACTAATATAAGTCAC;RSEQ=TCTTCACATAGTAAATATCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:18:9,9:165,159:324,18:0.0525:2,2:21.3:1.0:30.9:1.0:1.0:1.03764:60.0:36.0:0.0529:0.0:2.7 0/0:332:0:0,0:183,149:332,0:0.0:2,0:27.3:1.0:29.9:1.0:1.0:0.0:60.0:109.667:1.0:0.0:1.5 +12 62290651 . C G 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.07004;SOR=0.0;LSEQ=ATGATGTTTCCTTTCTTTTG;RSEQ=CTGCCATCAAGCTATTTGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:213:5:2,3:86,122:208,5:0.0235:2,2:18.4:1.0:31.0:1.0:1.0:1.05711:60.0:10.0:0.0236:0.0:3.6 0/0:167:0:0,0:70,97:167,0:0.0:2,0:26.7:1.0:30.7:1.0:1.0:0.0:60.0:82.5:1.0:0.0:1.2 +12 62290742 . T C 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00021;SOR=0.08292;LSEQ=TAGATAATATCTTATCTCTA;RSEQ=TGAGGGTCCAGATGATCTCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:20:3,17:0,20:20,20:0.5:1,2:22.3:1.0:32.9:1.0:0.23077:0.0:60.0:40.0:0.5:0.0:1.3 0/1:27:2:0,2:4,21:25,2:0.0741:2,0:16.5:1.0:33.0:0.0:1.0:0.0:60.0:4.0:0.0741:0.0:1.0 +12 63295001 . T C 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00562;SOR=0.09488;LSEQ=CTGATACCATATGTTCCCAG;RSEQ=GGGCAACAGCCAATCACTTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:23:1,22:1,44:45,23:0.3382:1,1:26.3:1.0:30.7:1.0:1.0:1.98:60.0:46.0:0.3382:0.0:1.0 0/1:22:1:0,1:1,20:21,1:0.0455:1,0:3.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0455:0.0:1.0 +12 66943230 . T A 57 p8;q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06283;SOR=0.0;LSEQ=TACTACTATTGAAAAAAATA;RSEQ=TATTGCTCATACTACAGTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:5:4,1:90,199:289,5:0.017:2,2:6.0:1.0:24.8:1.0:0.03758:8.78:60.0:4.0:0.0138:0.0:1.8 0/0:267:0:0,0:87,180:267,0:0.0:2,0:24.4:1.0:29.4:1.0:1.0:0.0:60.0:88.0:1.0:0.0:0.3 +12 69202867 . G C 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00483;SOR=0.0;LSEQ=CTTTTTCTCTGCTGATCCAG;RSEQ=TAAGCACCGACTTGCTTGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:13:13,0:118,2:120,13:0.0977:1,1:27.7:1.0:30.9:1.0:1.0:0.0:60.0:12.0:0.0923:0.0:1.0 0/0:75:0:0,0:73,2:75,0:0.0:1,0:21.9:1.0:31.3:1.0:1.0:0.0:60.0:150.0:1.0:0.0:0.1 +12 69203524 . T A 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTGTGCGTACCCACATATA;RSEQ=TTACATTTGAATTTAAATCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:23.3:1.0:30.0:1.0:1.0:0.0:58.7:5.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 72825422 . GT G 98 MAF0.05;MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=13.0;MSILEN=1.0;SSF=0.04952;SOR=0.1084;LSEQ=GCCAATAACAGGAAGAAGAG;RSEQ=TTTTTTTTTTTTGAGAATGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:9:5,4:6,5:11,9:0.45:2,2:14.9:1.0:31.1:1.0:1.0:1.04:55.2:18.0:0.45:0.25:0.2 0/1:13:1:0,1:7,5:12,1:0.0769:2,0:34.0:0.0:30.0:0.0:0.46154:0.0:39.0:2.0:0.0769:0.0:4.0 +12 77054235 . G T 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0368;LSEQ=ACCCCATATATGTTCTCTAG;RSEQ=CCTTTTAGAAAACATGGAGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:44:25:11,14:9,10:19,25:0.5682:2,2:39.8:1.0:31.2:1.0:1.0:1.14192:22.3:50.0:0.5682:0.0:1.1 0/1:45:2:1,1:16,27:43,2:0.0444:2,2:34.5:1.0:29.5:1.0:1.0:1.67:20.0:4.0:0.0444:0.0:1.0 +12 78288910 . GA G 85 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.02947;SOR=0.0;LSEQ=AAAGGACAGGAGTGTTTCTT;RSEQ=AAAAAAAAATTCTCACAGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:6:2,4:9,66:75,6:0.0741:2,2:19.2:1.0:33.1:1.0:0.18577:3.58:60.0:12.0:0.075:0.0123:0.2 0/0:73:0:0,0:15,58:73,0:0.0:2,0:24.2:1.0:30.0:1.0:1.0:0.0:60.0:146.0:1.0:0.0:0.2 +12 82298589 . G GC 111 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=6e-05;SOR=0.0;LSEQ=CCCAGCGTTTACAGGAAAAG;RSEQ=CTTGTGAAATCAGACAACGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:11:6,5:28,10:38,11:0.2245:2,2:27.7:1.0:32.1:1.0:0.27541:2.28948:34.6:22.0:0.2245:0.0204:0.8 0/0:62:0:0,0:37,24:61,0:0.0:2,0:19.6:1.0:30.7:1.0:1.0:0.0:43.9:122.0:0.9839:0.0:0.2 +12 87756834 . G A 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00028;SOR=0.0;LSEQ=CACCTGCTCCTTCTTCTGGG;RSEQ=ACTTCTGACCTCTAGGGGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:3,3:1,2:3,6:0.6667:2,2:28.0:1.0:30.0:1.0:1.0:1.85:60.0:12.0:0.6667:0.0:1.2 0/0:18:0:0,0:7,11:18,0:0.0:2,0:18.2:1.0:29.8:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.2 +12 91238015 . G A 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAAAAAAATACATCATAAG;RSEQ=ATATGAGCTAACTGTTGGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:18:5,13:9,44:53,18:0.2535:2,2:20.1:1.0:30.5:1.0:0.32418:1.86:60.0:36.0:0.2535:0.0:1.1 0/0:88:0:0,0:26,62:88,0:0.0:2,0:24.4:1.0:30.6:1.0:1.0:0.0:60.0:176.0:1.0:0.0:0.1 +12 97487829 . TTG GT 122 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGGATACGTGTTTTTTTTT;RSEQ=TTTTTTTTTTGTAACTTTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:20:9,11:203,262:465,20:0.0407:2,2:8.2:1.0:28.4:1.0:1.0:1.06:60.0:40.0:0.041:0.0367:0.2 0/0:494:0:0,0:206,275:481,0:0.0:2,0:21.4:1.0:29.1:1.0:1.0:0.0:58.3:67.714:0.9793:0.0:1.0 +12 97487836 . T TG 199 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.0;MSILEN=1.0;SSF=0.0;SOR=0.09837;LSEQ=CGTGTTTTTTTTTTTGTTTT;RSEQ=TTTTTGTAACTTTAACTTTA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:126:41,85:145,177:322,126:0.2775:2,2:22.5:1.0:28.6:1.0:0.01884:1.69637:54.2:3.667:0.2357:0.0529:1.3 0/1:468:17:6,11:188,262:450,17:0.0363:2,2:24.3:1.0:32.5:1.0:0.80288:1.31477:60.0:34.0:0.0366:0.0064:0.3 +12 108602855 . C G 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.05095;LSEQ=AGGTTTTGTCCTTCCTACTC;RSEQ=CAGAGCCAGAGCAAGCAATG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:92:69:62,7:20,3:23,69:0.75:2,2:26.0:1.0:29.8:1.0:0.70662:1.32:60.0:68.0:0.764:0.0:1.1 0/1:77:10:10,0:50,17:67,10:0.1299:2,0:30.6:1.0:30.3:1.0:0.10568:0.0:60.0:20.0:0.1316:0.0:1.0 +12 115109672 . C A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02338;LSEQ=GGACGCGCTGCGGGACCTGT;RSEQ=CGGCTTGGCTTCCAAGCCGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:37:21,16:400,362:762,37:0.0463:2,2:23.2:1.0:27.2:1.0:0.73647:1.19:60.0:17.5:0.0446:0.0:1.2 0/0:885:1:1,0:463,421:884,1:0.0011:2,0:1.0:0.0:21.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 +12 115110038 . C T 61 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.06263;SOR=0.0;LSEQ=GGAGGCTGCCGCAGAGGAGG;RSEQ=GGCCGCCGCTGCGGCCATGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:5:2,3:219,248:467,5:0.0106:2,2:15.0:1.0:26.4:1.0:1.0:1.32382:60.0:4.0:0.0087:0.0:1.4 0/0:439:0:0,0:218,220:438,0:0.0:2,0:24.3:1.0:29.5:1.0:1.0:0.0:60.0:61.571:0.9977:0.0:0.2 +12 115110078 . C T 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00016;SOR=0.0;LSEQ=TACGTGTAGGGGTAAGGGAA;RSEQ=AGGCTTCCGAAAGGGGACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:14:7,7:156,241:397,14:0.0341:2,2:20.3:1.0:30.5:1.0:0.42078:1.54:60.0:28.0:0.0347:0.0:1.2 0/0:357:0:0,0:141,216:357,0:0.0:2,0:26.3:1.0:31.0:1.0:1.0:0.0:60.0:38.667:1.0:0.0:0.2 +12 115117337 . G A 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTGGTATGCAGTCACAGC;RSEQ=ATGAATTCAGTTTCGGGGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:152:89,63:407,344:751,152:0.1683:2,2:25.2:1.0:30.3:1.0:0.37148:1.19:60.0:304.0:0.1698:0.0:1.1 0/0:1097:0:0,0:586,510:1096,0:0.0:2,0:26.0:1.0:29.8:1.0:1.0:0.0:60.0:77.286:0.9991:0.0:0.2 +12 115118589 . G A 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATGCTTAGGGAGAAGCAAA;RSEQ=GAGAAGTCTGGGCTGAAACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:35:26,9:152,38:190,35:0.1556:2,2:25.7:1.0:31.1:1.0:0.49752:1.38248:60.0:70.0:0.157:0.0:1.0 0/0:203:0:0,0:158,45:203,0:0.0:2,0:24.3:1.0:31.6:1.0:1.0:0.0:60.0:100.5:1.0:0.0:0.1 +12 120541570 . G A 224 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01219;LSEQ=ACCATGACCAGGCACCGGTC;RSEQ=CTCAACTGTGTCCACAGGTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:184:141,43:455,198:653,184:0.2196:2,2:22.3:1.0:29.8:1.0:0.07962:1.43:60.0:25.286:0.2153:0.0:2.0 0/0:586:2:1,1:401,181:582,2:0.0034:2,2:17.0:1.0:31.5:1.0:0.52653:2.21217:60.0:4.0:0.0035:0.0:1.0 +12 120541597 . G A 239 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00704;LSEQ=TGTGTCCACAGGTCAGTGGC;RSEQ=CGGGTTGGGTGGGAGTGGGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1232:276:178,98:578,374:952,276:0.224:2,2:25.4:1.0:29.5:1.0:0.26181:1.18:60.0:22.0:0.2198:0.0:1.7 0/0:987:2:2,0:594,388:982,2:0.002:2,0:11.0:1.0:23.0:1.0:0.52186:0.0:60.0:1.0:0.001:0.0:1.5 +12 120554466 . G A 240 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00243;LSEQ=CCGGGCCATGGCGGGCGGGG;RSEQ=CGGTGCGCGCGGGCGGGCGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:688:291:170,121:224,169:393,291:0.423:2,2:27.1:1.0:29.4:1.0:0.75437:1.06:60.0:35.375:0.4268:0.0:1.2 0/0:560:1:1,0:299,257:556,1:0.0018:2,0:1.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0018:0.0:1.0 +12 121435778 . C T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03945;SOR=0.0;LSEQ=ATGAATTTCTAAAATCTATT;RSEQ=AGATTTTAGAAAGGTAATCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:0,7:0,53:53,7:0.1167:1,0:20.1:1.0:27.4:1.0:1.0:0.0:58.9:6.0:0.1053:0.0:1.6 0/0:41:0:0,0:0,41:41,0:0.0:1,0:21.9:1.0:32.4:1.0:1.0:0.0:59.6:82.0:1.0:0.0:0.1 +12 131945101 . C T 60 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.02628;SOR=0.0;LSEQ=AGCGAACCTAAGTGTGGGTG;RSEQ=ACAGAGTGTCACCATATTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:5:2,3:203,149:352,5:0.014:2,2:20.0:1.0:26.0:1.0:0.6544:2.03951:60.0:4.0:0.0113:0.0:1.2 0/0:380:0:0,0:214,166:380,0:0.0:2,0:23.5:1.0:31.1:1.0:1.0:0.0:60.0:94.0:1.0:0.0:0.8 +12 131945403 . A G 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATAATGACAGGCAAAGAAA;RSEQ=TAAACCCTATAAATTTGTAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:0,6:0,1:1,6:0.8571:0,0:22.7:1.0:31.7:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 132547162 . G A 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.00292;SOR=0.06371;LSEQ=CAGCAGCAGCAACAGACGAC;RSEQ=ACGACCTCTCAGGTGCAAGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:5,3:6,7:13,8:0.381:2,2:27.8:1.0:30.5:1.0:0.65944:1.88:57.4:16.0:0.381:0.0:1.0 0/1:28:1:0,1:10,17:27,1:0.0357:2,0:9.0:0.0:32.0:0.0:1.0:0.0:45.0:2.0:0.0357:0.0:3.0 +12 133208752 . T A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.077;SOR=0.0;LSEQ=ATTCATTAACATCCTTACCA;RSEQ=GCACAGGTATGTCGGTGTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:5:5,0:41,1:42,5:0.1064:1,0:23.0:1.0:30.2:1.0:1.0:0.0:60.0:10.0:0.1087:0.0:1.0 0/0:32:0:0,0:31,1:32,0:0.0:1,0:20.0:1.0:31.0:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.4 +12 133211059 . T C 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCCTCCAACCTGGGTCCA;RSEQ=CTGCCCCGTTTGACCAGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:31:0,31:0,61:61,31:0.337:1,1:23.9:1.0:31.7:1.0:1.0:0.0:60.0:30.0:0.3333:0.0:1.5 0/0:71:0:0,0:1,70:71,0:0.0:1,0:22.2:1.0:29.2:1.0:1.0:0.0:60.0:142.0:1.0:0.0:0.4 +12 133226249 . G T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03696;SOR=0.1392;LSEQ=CAGAGACAGACAGTATCACA;RSEQ=CTGTGTGCCTTACCTGGCTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:624:7:1,6:378,239:617,7:0.0112:2,2:11.3:1.0:26.9:1.0:0.01651:9.45822:60.0:14.0:0.0116:0.0:1.1 0/0:635:1:0,1:402,232:634,1:0.0016:2,0:1.0:0.0:23.0:0.0:0.36693:0.0:60.0:2.0:0.0016:0.0:1.0 +12 133240781 . CACCCAGTGTGTGGCCTCCAGCCTTCCCTCCTTCCTTCCT C 90 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.0;MSILEN=4.0;SSF=0.04738;SOR=0.0;LSEQ=GTGAGTTCCCCTTTCCTTTT;RSEQ=GCCCAGTGTGTGGCCTCCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:7:2,5:43,64:107,7:0.0262:2,2:43.6:1.0:32.4:1.0:0.70187:1.67252:24.9:14.0:0.027:0.0:0.0 0/0:165:0:0,0:26,60:86,0:0.0:2,0:22.3:1.0:29.1:1.0:1.0:0.0:54.5:85.0:0.528:0.0:0.1 +12 133243788 . T A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAAACAATAGGCGAAGGCAG;RSEQ=TGGGTTCGTAAAACTTGATG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:14.2:1.0:29.7:1.0:1.0:0.0:57.0:12.0:0.8571:0.0:1.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +12 133244668 . CA C 74 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.23077;SOR=0.0;LSEQ=GACAGAGTGAGACCTCATTT;RSEQ=AAAAAAAAAAGAAAGAAATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:3,0:3,5:0.5:0,0:28.0:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:0.0 0/0:3:0:0,0:3,0:3,0:0.0:0,0:16.7:1.0:30.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 +12 133257837 . C A 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02545;LSEQ=CCGTTCCAGGCGCTTGAGTG;RSEQ=CGAAACTGAGGAAGTGGCGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:28:10,18:203,251:454,28:0.0579:2,2:22.7:1.0:29.7:1.0:0.43438:1.45467:60.0:56.0:0.0587:0.0:1.0 0/0:642:1:1,0:283,357:640,1:0.0016:2,0:1.0:0.0:22.0:0.0:0.44306:0.0:60.0:2.0:0.0016:0.0:1.0 +13 21004758 . T C 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGCTCTTGCAATGGAGAGT;RSEQ=CTTTGTGTACACCTCCCACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:321:18:8,10:147,156:303,18:0.0561:2,2:24.4:1.0:31.7:1.0:0.81122:1.17729:60.0:36.0:0.057:0.0:1.7 0/0:359:0:0,0:168,191:359,0:0.0:2,0:26.1:1.0:28.9:1.0:1.0:0.0:59.9:70.8:1.0:0.0:1.1 +13 21554217 . A T 64 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATTGTTAGCAAATAGTTACT;RSEQ=GCCAGAATTTTATGTTCTTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:22.6:1.0:27.6:1.0:1.0:0.0:60.0:4.0:0.6667:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +13 21563715 . C T 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGAAGACTGCGTCCACATCC;RSEQ=GAGGTGCGTCCCTGCCCCCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:7:0,7:0,5:5,7:0.5833:0,0:19.1:1.0:26.1:1.0:1.0:0.0:60.0:2.5:0.5:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +13 28601389 . TAC T 207 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAAATTGGTCCTGAAATAGT;RSEQ=AGTTTCAATTATAGGCATAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:305:93:23,70:64,148:212,93:0.3049:2,2:25.6:1.0:31.7:1.0:0.40864:1.31494:59.9:186.0:0.3079:0.0525:0.1 0/0:397:0:0,0:132,265:397,0:0.0:2,0:24.8:1.0:28.3:1.0:1.0:0.0:60.0:78.4:1.0:0.0:0.1 +13 28608709 . G A 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02795;SOR=0.0;LSEQ=CCCACAGACAATCAGGCAAT;RSEQ=TCCCTGTAAAGGATACATTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:0,11:0,12:12,11:0.4783:0,0:22.4:1.0:31.0:1.0:1.0:0.0:60.0:22.0:0.4783:0.0:1.0 0/0:8:0:0,0:0,8:8,0:0.0:0,0:20.6:1.0:32.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.3 +13 28611186 . G C 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02753;LSEQ=CCAGTAGATATGAGAGTAAA;RSEQ=TTTCAAAACACTTCAGCGTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:20:20,0:25,0:25,20:0.4444:1,1:23.9:1.0:32.0:1.0:1.0:0.0:60.0:19.0:0.4318:0.0:2.0 0/1:48:1:1,0:47,0:47,1:0.0208:1,0:19.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.0208:0.0:3.0 +13 28611219 . TGT GC 156 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGCGTACAAAAACAGTTT;RSEQ=AGTAGCCCTTCTAAGCCATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:31:31,0:33,0:33,31:0.4306:1,1:26.8:1.0:31.5:1.0:1.0:0.0:60.0:30.0:0.4478:0.0972:0.8 0/0:80:0:0,0:41,1:42,0:0.0:1,0:25.3:1.0:28.2:1.0:1.0:0.0:60.0:20.0:0.5195:0.0:0.2 +13 28636446 . G A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGTACGGACTGTCATGGCGT;RSEQ=TGTCCCCCTACCTCTGCAAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1.0:0,0:19.4:1.0:29.9:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +13 28644610 . A C 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAAAACAGCTAAAGGTATA;RSEQ=TTTTAATGTTACTTTACCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:398:39:24,15:234,125:359,39:0.098:2,2:24.8:1.0:32.5:1.0:0.72449:1.16952:60.0:38.0:0.0964:0.0:1.1 0/0:513:0:0,0:311,201:512,0:0.0:2,0:25.1:1.0:29.4:1.0:1.0:0.0:60.0:127.0:0.998:0.0:0.1 +13 28885593 . TTCTTTCTTTCTTTCTC T 102 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=4.0;SSF=0.0029;SOR=0.0;LSEQ=GGTGGTGATCAACATAATCT;RSEQ=TCTTTCTTTCTTTCTCTCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:9:9,0:42,0:42,9:0.1765:1,0:29.2:1.0:32.3:1.0:1.0:0.0:46.7:18.0:0.1765:0.0196:1.0 0/0:46:0:0,0:46,0:46,0:0.0:1,0:23.2:1.0:31.4:1.0:1.0:0.0:58.3:92.0:1.0:0.0:0.5 +13 28964198 . C T 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00028;SOR=0.14334;LSEQ=AGTTTCAGGTCCTCTCCTTC;RSEQ=GTCGGCATTTTTTCCAAGTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:492:18:6,12:179,295:474,18:0.0366:2,2:28.1:1.0:30.7:1.0:0.8076:1.21306:60.0:36.0:0.0369:0.0:1.2 0/0:555:3:1,2:238,314:552,3:0.0054:2,2:22.7:1.0:25.7:1.0:1.0:1.51483:60.0:6.0:0.0055:0.0:1.0 +13 28971220 . G A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02893;LSEQ=AGCCATCTGCAAAAGAAAAG;RSEQ=AAACTTTAGCTAGCAACAGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:281:76:17,59:43,162:205,76:0.2705:2,2:24.0:1.0:31.1:1.0:0.86998:1.09:60.0:152.0:0.2714:0.0:1.1 0/1:284:3:3,0:78,202:280,3:0.0106:2,0:1.0:0.0:24.0:1.0:0.02283:0.0:60.0:6.0:0.0107:0.0:1.0 +13 29069039 . G A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02556;SOR=0.17709;LSEQ=TCCCCGCGGCCAACGACCCG;RSEQ=CCGCCAGAGTCCGTCCTCTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:9:3,6:18,73:91,9:0.09:2,2:15.8:1.0:29.7:1.0:0.39198:2.01:60.0:18.0:0.0909:0.0:1.1 0/1:117:2:1,1:30,85:115,2:0.0171:2,2:7.5:1.0:26.5:1.0:0.46139:2.8:60.0:4.0:0.0175:0.0:1.0 +13 32747212 . C G 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0632;LSEQ=GTGTAATACCAAGTGGTATA;RSEQ=ATGAAAGGAGTTGTGTTTTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:50:9,41:18,56:74,50:0.4032:2,2:23.9:1.0:32.3:1.0:0.50735:1.45988:60.0:100.0:0.4032:0.0:1.0 0/1:148:6:2,4:34,108:142,6:0.0405:2,2:20.3:1.0:31.0:1.0:0.63336:1.58:60.0:12.0:0.0411:0.0:1.0 +13 32893791 . A G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AACTAAACTATATTTCTGCA;RSEQ=GCTATCACAGAGGACAGAGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1.0:0,2:22.2:1.0:32.8:1.0:1.0:0.0:52.6:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +13 32899388 . A C 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0674;LSEQ=TACATATATTTGTTCTATAA;RSEQ=GATGAATCTGATTTTTATGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:49:3,46:3,51:54,49:0.4757:2,2:25.1:1.0:30.1:1.0:1.0:1.11:59.9:98.0:0.4757:0.0:1.2 0/1:158:9:1,8:12,137:149,9:0.057:2,2:21.6:1.0:30.3:1.0:0.54796:1.42:60.0:18.0:0.057:0.0:1.0 +13 32900149 . T C 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08577;LSEQ=TAGTATTCCAACAATTTATA;RSEQ=GAATGAGAATCTTCTTTTAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:63:52,11:61,11:72,63:0.4599:2,2:21.5:1.0:32.0:1.0:0.81698:1.17168:60.0:62.0:0.4627:0.0:1.1 0/1:163:11:10,1:122,30:152,11:0.0675:2,2:18.4:1.0:30.9:1.0:0.69192:2.45:60.0:22.0:0.0692:0.0:1.0 +13 32900933 . T A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02754;SOR=0.0;LSEQ=GGAATAAATACAAATACATT;RSEQ=AGTGGTAGTCCAGTGGTGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:13:1,12:0,12:12,13:0.52:0,1:28.0:1.0:30.8:1.0:1.0:0.0:60.0:26.0:0.52:0.0:1.0 0/0:6:0:0,0:0,6:6,0:0.0:0,0:31.2:1.0:27.8:1.0:1.0:0.0:53.7:12.0:1.0:0.0:0.0 +13 32906480 . A C 259 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.08838;LSEQ=ACATTGGAAAGTCAATGCCA;RSEQ=ATGTCCTAGAAGATGAAGTA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:274:134,140:201,195:396,274:0.409:2,2:24.6:1.0:32.0:1.0:0.69443:1.0768:59.9:90.333:0.4087:0.0:1.1 0/1:730:42:18,24:334,353:687,42:0.0575:2,2:25.2:1.0:31.6:1.0:0.52625:1.26117:60.0:84.0:0.0583:0.0:1.1 +13 32906980 . A G 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.11044;LSEQ=ATTTCTAGCCTACCAAAATC;RSEQ=GAGAAGCCATTAAATGAGGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:309:117:58,59:109,83:192,117:0.3786:2,2:25.1:1.0:30.8:1.0:0.24015:1.33462:59.8:116.0:0.3803:0.0:1.1 0/1:350:22:12,10:172,156:328,22:0.0629:2,2:23.3:1.0:29.2:1.0:1.0:1.09:60.0:44.0:0.063:0.0:1.1 +13 32910351 . G T 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10265;LSEQ=CTTAGTGAAAAATATTTAGT;RSEQ=AATGTGATTGATGGTACTTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:182:151,31:172,25:197,182:0.4802:2,2:23.3:1.0:30.6:1.0:0.24924:1.41115:60.0:90.0:0.4813:0.0:1.1 0/1:440:38:27,11:306,96:402,38:0.0864:2,2:22.0:1.0:28.7:1.0:0.55259:1.2978:60.0:76.0:0.087:0.0:1.1 +13 32910721 . T C 307 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.09989;LSEQ=GCATGTCACCCAGTACAACA;RSEQ=TCAAAAGTGGAATACAGTGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1597:675:340,335:462,459:921,675:0.4227:2,2:26.9:1.0:32.7:1.0:0.9596:1.01:60.0:83.375:0.4243:0.0:1.1 0/1:1865:127:65,62:842,895:1737,127:0.0681:2,2:24.8:1.0:31.3:1.0:0.58181:1.11:60.0:41.333:0.0673:0.0:1.1 +13 32911463 . A G 299 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0883;LSEQ=AAAAAAATAATGATTACATG;RSEQ=ACAAATGGGCAGGACTCTTA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1553:689:353,336:472,390:862,689:0.4437:2,2:23.5:1.0:31.8:1.0:0.18304:1.15186:60.0:75.556:0.4442:0.0:1.1 0/1:1780:117:62,55:859,801:1660,117:0.0657:2,2:21.5:1.0:30.2:1.0:0.84834:1.05:60.0:116.0:0.0661:0.0:1.2 +13 32912885 . G A 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.08569;LSEQ=ATAACTTTTCCTTAAATTCT;RSEQ=AATTACATTCTGACATAAGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1573:21:10,11:763,788:1551,21:0.0134:2,2:21.0:1.0:29.0:1.0:1.0:1.06509:60.0:20.0:0.0128:0.0:1.1 0/0:1728:2:1,1:855,869:1724,2:0.0012:2,2:16.0:1.0:27.0:1.0:1.0:1.02:60.0:4.0:0.0012:0.0:1.0 +13 32929478 . C T 286 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06881;LSEQ=GCCTTTCAGTTAGATATTTC;RSEQ=GTTGTTAAATAATGTCCTGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1177:589:229,360:238,348:586,589:0.5004:2,2:26.8:1.0:31.1:1.0:0.55157:1.07507:59.9:146.25:0.5004:0.0:1.2 0/1:1444:93:38,55:582,766:1348,93:0.0644:2,2:27.4:1.0:29.2:1.0:0.7455:1.09966:60.0:45.5:0.0634:0.0:1.2 +13 32930673 . C T 209 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00967;LSEQ=CAGTCTGTATCTTGCAAAAA;RSEQ=ATCCACTCTGCCTCGAATCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:573:133:64,69:205,235:440,133:0.2321:2,2:26.3:1.0:29.7:1.0:0.76702:1.06:60.0:132.0:0.2316:0.0:1.1 0/0:688:2:1,1:331,355:686,2:0.0029:2,2:15.0:0.0:24.0:1.0:1.0:1.07:60.0:4.0:0.003:0.0:1.5 +13 32968793 . T C 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAATTCATCTAACACATCTA;RSEQ=AATAACATTCTTTTCTTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:18:13,5:137,28:165,18:0.0984:2,2:22.9:1.0:32.7:1.0:0.32836:1.87439:57.9:36.0:0.0994:0.0:1.1 0/0:205:0:0,0:166,39:205,0:0.0:2,0:23.0:1.0:29.2:1.0:1.0:0.0:60.0:101.5:1.0:0.0:0.2 +13 41032432 . G C 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCACTGGGACAGTCGCCCAG;RSEQ=GGACACGAGACATATACAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:56:31,25:61,52:113,56:0.3294:2,2:31.9:1.0:30.9:1.0:1.0:1.06:60.0:55.0:0.3293:0.0:2.0 0/0:191:0:0,0:101,89:190,0:0.0:2,0:27.3:1.0:29.8:1.0:1.0:0.0:60.0:46.5:0.9947:0.0:0.4 +13 41161770 . G A 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.12884;SOR=0.0;LSEQ=TCCATCTATACCTAAAGCAC;RSEQ=GCTCAAGTGCTTGGAGAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:10,1:14,0:14,11:0.44:1,2:23.6:1.0:30.2:1.0:0.44:0.0:60.0:22.0:0.44:0.0:1.6 0/0:5:0:0,0:5,0:5,0:0.0:0,0:25.8:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 +13 41161979 . C G 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGTGTTCACAGTAGCCTCT;RSEQ=CCCACCTTTTAAAAGGGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1029:68:48,20:647,313:960,68:0.0661:2,2:26.9:1.0:32.0:1.0:0.68778:1.16:60.0:67.0:0.0654:0.0:1.1 0/0:1138:0:0,0:712,426:1138,0:0.0:2,0:25.4:1.0:30.1:1.0:1.0:0.0:60.0:102.455:1.0:0.0:0.2 +13 43549921 . AAC A 95 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=13;MSI=7.0;MSILEN=2.0;SSF=0.02926;SOR=0.19329;LSEQ=ATGATGTATTTCTTCACTTA;RSEQ=ACACACACACACATAAGTAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:9:5,4:166,76:242,9:0.0359:2,2:15.9:1.0:30.2:1.0:0.47185:1.74321:59.4:18.0:0.036:0.0159:0.1 0/0:281:2:0,2:183,90:273,2:0.0071:2,0:23.0:1.0:32.0:0.0:0.11111:0.0:60.0:4.0:0.0071:0.0:0.0 +13 43550043 . CA C 76 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.10567;SOR=0.17702;LSEQ=ACTCACCATCTTTAAGAGGC;RSEQ=AAAACCAATGATGGGACCAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:5:2,3:112,190:302,5:0.0163:2,2:30.0:1.0:32.8:1.0:1.0:1.13:60.0:10.0:0.0164:0.0033:0.8 0/0:343:1:0,1:125,217:342,1:0.0029:2,0:50.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0029:0.0:0.0 +13 43550243 . A G 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.26316;SOR=0.0;LSEQ=ACTGTTTCACAGACACTGGC;RSEQ=GAAGACATGAAATTCCTGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:0,7:0,9:9,7:0.4375:0,0:29.3:1.0:31.4:1.0:1.0:0.0:60.0:14.0:0.4375:0.0:2.0 0/0:3:0:0,0:1,2:3,0:0.0:2,0:18.0:1.0:31.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +13 43550270 . T A 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATGAAATTCCTGGATCAGAG;RSEQ=CAAAGACTTTATTACTGATG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1.0:0,0:26.2:1.0:31.4:1.0:1.0:0.0:60.0:20.0:1.0:0.0:1.9 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +13 48939018 . C T 51 p8;q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01465;SOR=0.0;LSEQ=TAATGATCATGTTGTAACTT;RSEQ=ATCTTTTTCAGGTGAAAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:372:5:1,4:217,150:367,5:0.0134:2,2:5.0:1.0:22.0:1.0:0.16451:5.76167:60.0:4.0:0.011:0.0:1.8 0/0:491:0:0,0:280,211:491,0:0.0:2,0:24.2:1.0:30.9:1.0:1.0:0.0:60.0:162.667:1.0:0.0:0.1 +13 49037825 . G T 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02587;LSEQ=TTTTTTAAGAACAAAACCAT;RSEQ=TAATAAAATTCTGACTACTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:34:25,9:199,58:257,34:0.1168:2,2:20.8:1.0:30.3:1.0:0.66496:1.23426:60.0:33.0:0.1158:0.0:1.0 0/0:294:1:1,0:216,77:293,1:0.0034:2,0:27.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0034:0.0:1.0 +13 49047529 . G C 236 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTGGTGAATCATTCGGGGT;RSEQ=AGTATTTTCTTTCTATGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:389:158:63,95:89,140:229,158:0.4062:2,2:27.3:1.0:32.4:1.0:0.9157:1.04:60.0:157.0:0.4067:0.0:1.1 0/0:508:0:0,0:217,290:507,0:0.0:2,0:25.9:1.0:30.7:1.0:1.0:0.0:60.0:100.4:0.998:0.0:0.1 +13 49051848 . G A 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAGCAGAACTACAAAGAGGA;RSEQ=CTATTTGGGAGTGTTAGATA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:25.3:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +13 67591561 . CA TG 163 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGGCATTGATATTCCCTAA;RSEQ=GTTTAAAATACCCCTGTTTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:35:35,0:68,1:69,35:0.3365:1,1:23.3:1.0:31.8:1.0:1.0:0.0:60.0:70.0:0.3365:0.0385:1.4 0/0:64:0:0,0:63,1:64,0:0.0:1,0:25.8:1.0:31.7:1.0:1.0:0.0:60.0:128.0:1.0:0.0:0.2 +13 68406205 . T A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=1.0;SSF=0.00044;SOR=0.0;LSEQ=TTAGGAGTTCTTTCCCGTTT;RSEQ=TTGTAGGATTTTTGTTCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:10:8,2:37,16:53,10:0.1587:2,2:28.5:1.0:28.2:1.0:0.71026:1.72:60.0:20.0:0.1724:0.0:1.0 0/0:68:0:0,0:49,19:68,0:0.0:2,0:23.0:1.0:29.7:1.0:1.0:0.0:59.9:33.0:1.0:0.0:0.2 +13 71158400 . G A 61 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01589;SOR=0.0;LSEQ=CAGACCACCGTGTTCAGTTT;RSEQ=TATTTTCGATTGAGAATGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:5:3,2:118,200:318,5:0.0155:2,2:11.6:1.0:26.6:1.0:0.36716:2.53:36.0:10.0:0.0157:0.0:1.0 0/0:414:0:0,0:151,263:414,0:0.0:2,0:23.3:1.0:31.0:1.0:1.0:0.0:49.4:102.5:1.0:0.0:0.2 +13 72248871 . T TAATAGAGTGCTCCATTCAAGTTTGAAAACTA 83 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTACGGCAGGCACAGGAAAC;RSEQ=AATAAATTGCATGATGAAGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:41.3:1.0:29.7:1.0:1.0:0.0:54.0:14.0:1.0:1.0:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +13 103508378 . C T 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01699;LSEQ=TCCTTAAAAATCATAGATAT;RSEQ=GTAAAAGTATGTTTGACTTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:312:46:30,16:157,108:265,46:0.1474:2,2:25.8:1.0:30.6:1.0:0.51548:1.29:60.0:92.0:0.1498:0.0:1.1 0/0:343:1:1,0:206,136:342,1:0.0029:2,0:16.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0029:0.0:1.0 +13 104378382 . A G 131 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00174;SOR=0.03601;LSEQ=TAGGTAGTGTCCACATGCAG;RSEQ=TATTGATATAATGTATATTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:0,3:3,17:0.85:0,1:22.1:1.0:32.1:1.0:1.0:0.0:60.0:34.0:0.85:0.0:1.3 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:33.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.1429:0.0:2.0 +13 106826430 . G T 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.09997;LSEQ=ACAATTGTGGGTTGTTTCAC;RSEQ=TTTCAGTGAAAGGAGAGAAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:61:20,41:84,130:214,61:0.2218:2,2:27.4:1.0:30.7:1.0:0.37419:1.32329:60.0:122.0:0.2243:0.0:1.5 0/1:326:9:4,5:123,194:317,9:0.0276:2,2:32.2:1.0:29.6:1.0:0.74007:1.26:60.0:18.0:0.0278:0.0:1.2 +13 110414685 . A G 184 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.12803;LSEQ=GGGTGGACCCTTTCTTTTAA;RSEQ=TTATGAAATGTTAGACCCTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:56:3,53:3,80:83,56:0.4029:1,2:23.3:1.0:31.7:1.0:0.68485:1.5:60.0:27.0:0.3971:0.0:1.1 0/1:114:9:2,7:10,95:105,9:0.0789:2,2:18.3:1.0:32.4:1.0:0.24065:2.68:60.0:18.0:0.0804:0.0:1.1 +13 110419404 . C T 247 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00977;LSEQ=CACCAGAGGACCCAGATCTG;RSEQ=GAAATGCTTTGGTCAGGGAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:322:309:277,32:12,1:13,309:0.9596:1,2:23.8:1.0:29.9:1.0:1.0:1.38503:60.0:37.625:0.9586:0.0:1.1 0/1:274:51:43,8:190,33:223,51:0.1861:2,2:23.4:1.0:28.0:1.0:0.83032:1.07091:60.0:16.0:0.1798:0.0:1.2 +13 110428702 . A G 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0119;SOR=0.0;LSEQ=GACAGAGTTTCCAAGGCTTC;RSEQ=CCTTTACCCATTCAAGTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:27.0:1.0:27.2:1.0:1.0:0.0:54.7:5.0:1.0:0.0:2.2 0/0:3:0:0,0:2,1:3,0:0.0:2,0:35.3:1.0:28.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 +13 110428923 . G A 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01497;LSEQ=ATAACACACAGAAGCATCTT;RSEQ=CATTATTTGCACCTACAGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:231:170:155,15:49,12:61,170:0.7359:2,2:25.6:1.0:28.8:1.0:0.03485:2.52:59.7:84.0:0.7336:0.0:1.1 0/1:177:7:7,0:151,19:170,7:0.0395:2,0:26.7:1.0:28.6:1.0:1.0:0.0:60.0:14.0:0.0407:0.0:1.1 +13 110435914 . G A 223 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.00738;LSEQ=TCCTCCAGGATGCGCCCCAC;RSEQ=GGGGAGCTCATGAGCACGTA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:224:170:104,66:33,20:53,170:0.7589:2,2:26.9:1.0:30.2:1.0:1.0:1.04691:59.9:20.25:0.7535:0.0:1.2 0/1:179:4:3,1:97,78:175,4:0.0223:2,2:20.0:1.0:28.0:1.0:0.63124:2.4:60.0:3.0:0.0172:0.0:1.0 +13 110436790 . ACCG A 100 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.0;MSILEN=3.0;SSF=0.02451;SOR=0.12788;LSEQ=GTCATGTACCCGTAGAACTC;RSEQ=CCGCCGCCGCCGTCTCGGGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:838:9:4,5:367,461:828,9:0.0107:2,2:20.4:1.0:31.8:1.0:1.0:1.0:60.0:18.0:0.0109:0.0036:0.3 0/0:722:1:1,0:336,379:715,1:0.0014:2,0:25.0:0.0:27.0:0.0:0.47067:0.0:60.0:2.0:0.0014:0.0:0.0 +13 111588868 . C T 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTTACAGACCGAATGAAAA;RSEQ=ATCCAGGAGAAAGAGTTTAC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:22.9:1.0:31.3:1.0:1.0:0.0:57.4:14.0:0.7778:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +13 111590803 . T A 58 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02885;SOR=0.0;LSEQ=TCGTTAAAGGAACCAACTCC;RSEQ=ATTACAAGCTGAAGTTGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:3,2:205,288:493,5:0.01:2,2:9.0:1.0:25.2:1.0:0.6538:2.1:59.0:4.0:0.0081:0.0:1.0 0/0:512:0:0,0:224,286:510,0:0.0:2,0:24.7:1.0:28.6:1.0:1.0:0.0:59.9:71.857:1.0:0.0:0.1 +14 20893115 . T A 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TAGGCACAGGAGACAAGTGA;RSEQ=ACCTAGAGTCCCACACACTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:383:27:17,10:239,117:356,27:0.0705:2,2:22.2:1.0:30.2:1.0:0.67461:1.201:60.0:54.0:0.0712:0.0:1.2 0/0:213:0:0,0:143,70:213,0:0.0:2,0:25.1:1.0:28.6:1.0:1.0:0.0:60.0:41.6:1.0:0.0:0.1 +14 20969716 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATATTCCATGGTACATGTAC;RSEQ=ATGGTTTGCTTAATGCATCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,1:2,5:0.7143:2,0:18.8:1.0:33.4:1.0:0.28571:0.0:60.0:10.0:0.8333:0.0:2.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 21336860 . A AT 77 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=CATGCCTGGCTTATTTTTGT;RSEQ=TTTTTAGTACAGACGGGGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:25.8:1.0:33.2:1.0:1.0:0.0:36.2:10.0:1.0:0.0:0.0 0/0:1:0:0,0:1,0:1,0:0.0:0,0:2.0:0.0:24.0:0.0:1.0:0.0:22.0:2.0:1.0:0.0:0.0 +14 22395405 . A T 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.33085;SOR=0.0;LSEQ=AAATTATCTTTTATATATTC;RSEQ=TTTTTACTGATATTCCCAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:7:0,7:0,36:36,7:0.1628:1,0:18.0:1.0:31.0:1.0:1.0:0.0:54.4:14.0:0.1628:0.0:1.6 0/0:9:0:0,0:0,9:9,0:0.0:0,0:26.9:1.0:31.9:1.0:1.0:0.0:60.0:18.0:1.0:0.0:1.6 +14 22395437 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATTCCCAGTACAAACAAATG;RSEQ=TATTTAAAAATCATCTTGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,19:19,5:0.2083:1,0:28.6:1.0:31.0:1.0:1.0:0.0:52.2:10.0:0.2083:0.0:1.8 0/0:4:0:0,0:0,4:4,0:0.0:0,0:17.0:1.0:32.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:1.0 +14 22592304 . G A 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00068;SOR=0.056;LSEQ=CTGGTGGCAAGTGAGGAGGA;RSEQ=GGTAGCATTCACCTAGAGCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:4,10:6,12:18,14:0.4375:2,2:17.9:1.0:30.6:1.0:1.0:1.24135:60.0:28.0:0.4375:0.0:1.0 0/1:25:1:1,0:10,14:24,1:0.04:2,0:9.0:0.0:31.0:0.0:0.44:0.0:60.0:2.0:0.04:0.0:1.0 +14 23587046 . A C 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01173;SOR=0.10491;LSEQ=AGGGGCCTGGAGGGGAAGGC;RSEQ=CGGAGAGACGGAGAGGTGAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:19:0,19:1,58:59,19:0.2436:1,1:20.2:1.0:31.4:1.0:1.0:0.0:60.0:18.0:0.2368:0.0:1.2 0/1:31:1:0,1:3,27:30,1:0.0323:2,0:8.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0323:0.0:1.0 +14 23652305 . A C 282 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.06001;LSEQ=TATTCCTACTCCGCATTCAC;RSEQ=CTTTCTGGTCACTCGCGTTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1339:523:258,265:413,403:816,523:0.3906:2,2:26.9:1.0:31.3:1.0:0.65444:1.05255:59.6:36.357:0.3943:0.0:1.2 0/1:1189:44:22,22:591,554:1145,44:0.037:2,2:20.7:1.0:27.9:1.0:0.87857:1.0667:57.0:6.333:0.0333:0.0:2.0 +14 23764770 . C G 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=8e-05;SOR=0.0;LSEQ=GCTTCCTGTCATTGGTAGTT;RSEQ=TGAATGTTAGATATTTTTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:20:2,18:3,69:72,20:0.2174:1,2:31.3:1.0:33.5:1.0:0.29708:2.52:59.8:40.0:0.2198:0.0:1.2 0/0:52:0:0,0:6,46:52,0:0.0:2,0:24.8:1.0:31.2:1.0:1.0:0.0:60.0:16.333:1.0:0.0:0.3 +14 25438196 . T C 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAGAACCAGGCCATCTGTAC;RSEQ=TTGAGAAATTCTAGAGGGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:472:40:24,16:253,179:432,40:0.0847:2,2:31.8:1.0:31.9:1.0:1.0:1.06:60.0:80.0:0.0862:0.0:1.6 0/0:264:0:0,0:146,118:264,0:0.0:2,0:25.3:1.0:29.7:1.0:1.0:0.0:59.9:65.0:1.0:0.0:0.5 +14 33960172 . TGCA T 75 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=18;MSI=7.0;MSILEN=3.0;SSF=0.15749;SOR=0.0;LSEQ=GCAAAAATACAATTTTTCAC;RSEQ=GCAGCAGCAGCAGCAGCAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:5:3,2:29,17:46,5:0.098:2,2:31.4:1.0:32.6:1.0:1.0:1.13435:60.0:10.0:0.098:0.0:0.0 0/0:27:0:0,0:17,10:27,0:0.0:2,0:28.0:1.0:31.5:1.0:1.0:0.0:60.0:54.0:1.0:0.0:0.1 +14 34771783 . G T 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCTCTCAGTCTGGTTTCCTG;RSEQ=GACGCTTGTCACCACTGGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:5,3:2,1:3,8:0.7273:2,2:26.4:1.0:30.5:1.0:1.0:1.18052:60.0:16.0:0.7273:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 35871430 . T TTTAAAAAAGAGTAAGCTA 185 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00012;SOR=0.0;LSEQ=GTTTGCCTTTAATGCTTCTC;RSEQ=TTAAAAAAAGAGGGGGGGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:72:54,18:139,321:460,72:0.1351:2,2:9.1:1.0:30.1:1.0:0.0:6.9:58.4:71.0:0.1365:0.1351:0.3 0/0:70:0:0,0:19,51:70,0:0.0:2,0:17.6:1.0:30.2:1.0:1.0:0.0:59.6:69.0:1.0:0.0:0.8 +14 35872920 . G T 233 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01114;LSEQ=TGCAGGTTGTTCTGGAAGTT;RSEQ=AGGAAGGCCAGGTCTCCCTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:5599:257:124,133:2686,2653:5339,257:0.0459:2,2:24.3:1.0:29.2:1.0:0.52382:1.08589:60.0:84.667:0.0458:0.0:1.2 0/0:1870:1:0,1:969,900:1869,1:0.0005:2,0:1.0:0.0:22.0:0.0:0.48182:0.0:60.0:2.0:0.0005:0.0:1.0 +14 36983065 . A C 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGGGGCCAGGGTGGGGAGC;RSEQ=GCTTTGGGATGCTAAACATC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1.0:0,2:25.6:1.0:30.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 36983623 . A G 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGCGGATGGAGCCAGCGT;RSEQ=ATTGATGGCAAGAAAGAGGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:21:20,1:0,0:0,21:1.0:0,1:25.3:1.0:31.3:1.0:1.0:0.0:60.0:20.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 36986190 . A AC 179 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.03704;SOR=0.0;LSEQ=TTGAATCACCAAAAAAAGAC;RSEQ=CCCCAAAGCTGTTTTATGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:53:44:39,5:9,0:9,44:0.8302:0,2:23.2:1.0:32.8:1.0:0.57425:0.0:59.1:88.0:0.8302:0.1132:0.4 0/0:2:0:0,0:2,0:2,0:0.0:0,0:31.0:1.0:31.5:1.0:1.0:0.0:41.0:4.0:1.0:0.0:0.0 +14 36986272 . T TTA 147 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=12.0;MSILEN=1.0;SSF=0.37433;SOR=0.0;LSEQ=TGTTTTTCATTTTCTTTTTT;RSEQ=AAAAAAAAAAACCCACAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:266:30:30,0:228,7:235,30:0.1128:1,1:19.1:1.0:30.0:1.0:1.0:0.0:57.2:60.0:0.1163:0.0301:0.6 0/0:12:0:0,0:12,0:12,0:0.0:0,0:28.3:1.0:30.9:1.0:1.0:0.0:58.6:24.0:1.0:0.0:0.7 +14 36986304 . AAAA GGGGGG 73 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCCACAAATTTTAGGGGGGG;RSEQ=AAAGAAAGACGTCCAGCAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:6:6,0:103,3:106,6:0.0162:1,0:40.5:1.0:28.4:1.0:1.0:0.0:48.5:12.0:0.0169:0.0:1.8 0/0:28:0:0,0:15,0:15,0:0.0:1,0:21.3:1.0:32.0:1.0:1.0:0.0:58.9:30.0:0.5357:0.0:0.5 +14 36988175 . G A 313 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCCCGCGGCCCCGCAGTGG;RSEQ=GCGGCCTCACTTACTGGCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1726:1414:960,454:211,99:310,1414:0.8192:2,2:23.8:1.0:30.0:1.0:1.0:1.00793:60.0:25.679:0.8159:0.0:1.3 0/0:235:0:0,0:143,92:235,0:0.0:2,0:24.1:1.0:29.4:1.0:1.0:0.0:59.9:38.167:1.0:0.0:0.3 +14 36989638 . A C 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCCGCTAACACGCCTCCCCC;RSEQ=AGGTCTTCCCCCCCCCCCCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:40:32:1,31:0,2:2,32:0.8:0,1:18.8:1.0:31.7:1.0:1.0:0.0:58.1:31.0:0.8611:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 36989645 . TCCCC T 127 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=14.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACACGCCTCCCCCAAGGTCT;RSEQ=CCCCCCCCCCACCCCCGGCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:18:0,18:2,7:9,18:0.6207:2,1:29.8:1.0:30.5:1.0:0.10256:0.0:56.6:36.0:0.7826:0.1379:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 38055445 . C T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGCAAGGGGGAGGAGTGCT;RSEQ=ACTCTCACCATGTGCTTTGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:21.6:1.0:27.0:1.0:1.0:0.0:56.4:14.0:0.875:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 38060768 . G A 232 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.05847;LSEQ=TTATGCTGCTGCTCCGAGGA;RSEQ=GACATGAGGTTGTTGATGGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:7224:172:93,79:3566,3481:7047,172:0.0238:2,2:25.2:1.0:31.3:1.0:0.39614:1.15:59.3:85.0:0.0238:0.0:1.1 0/0:2107:3:3,0:1062,1039:2101,3:0.0014:2,0:1.0:0.0:26.7:1.0:0.24976:0.0:53.3:6.0:0.0014:0.0:1.0 +14 38061106 . T A 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00869;SOR=0.0;LSEQ=AGAGGCGCCAGAGGGGTCCT;RSEQ=GCGGCTCTCAGGGCCGCCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:753:28:20,8:378,346:724,28:0.0372:2,2:22.0:1.0:30.1:1.0:0.05362:2.29:60.0:56.0:0.0377:0.0:1.3 0/0:155:0:0,0:81,74:155,0:0.0:2,0:19.5:1.0:29.7:1.0:1.0:0.0:60.0:50.667:1.0:0.0:0.1 +14 38882673 . T A 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.15441;SOR=0.0;LSEQ=AAAGACCTCATCCAAAGGTC;RSEQ=GCATCCTCAAAGACTGAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:10:7,3:2,3:5,10:0.6667:2,2:27.6:1.0:31.9:1.0:0.32867:3.2:41.3:20.0:0.6667:0.0:1.1 0/0:2:0:0,0:1,1:2,0:0.0:2,0:35.0:0.0:32.0:0.0:1.0:0.0:46.0:4.0:1.0:0.0:0.5 +14 38910644 . G C 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=TAAGAGTCTATGCCATAGGA;RSEQ=GTACCATGGGAGTTTTTTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:12.8:1.0:33.4:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:1:0:0,0:1,0:1,0:0.0:0,0:3.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +14 38910766 . TAG T 126 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.03652;SOR=0.0;LSEQ=CAGAGCCATCTTAAGGTTTA;RSEQ=AGTCTCAGTGAGCTCTCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:16:7,9:1,5:6,16:0.7273:2,2:21.6:1.0:31.7:1.0:0.35116:3.68:60.0:32.0:0.7273:0.1364:0.0 0/0:3:0:0,0:1,2:3,0:0.0:2,0:14.7:1.0:30.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +14 52640760 . ACTA T 111 MAF0.05;MSI12 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=42;MSI=15.0;MSILEN=3.0;SSF=0.01294;SOR=0.08388;LSEQ=CAGAGCTAGCCAAAATGCTT;RSEQ=CTACTACTACTACTACTACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:0,11:0,10:10,11:0.44:0,0:22.7:1.0:32.2:1.0:1.0:0.0:60.0:22.0:0.4583:0.12:0.6 0/1:17:1:0,1:0,16:16,1:0.0588:1,0:44.0:0.0:32.8:0.0:1.0:0.0:60.0:2.0:0.0588:0.0:1.0 +14 57141401 . G A 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.31484;SOR=0.0;LSEQ=AGGAACAGGTGAAGGAAACA;RSEQ=CTTTCAGACACAAGTGAGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:11:11,0:32,0:32,11:0.2558:1,0:23.3:1.0:30.0:1.0:1.0:0.0:60.0:10.0:0.2439:0.0:1.1 0/0:6:0:0,0:5,1:6,0:0.0:2,0:27.5:1.0:31.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 +14 61799782 . G T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.06918;SOR=0.0;LSEQ=TTTGGGAAGCGCACCCAAAA;RSEQ=TCATACGTGTATTAGCCTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:5:2,3:195,252:447,5:0.011:2,2:19.4:1.0:29.8:1.0:1.0:1.16032:60.0:10.0:0.0111:0.0:1.8 0/0:364:0:0,0:161,203:364,0:0.0:2,0:24.5:1.0:31.4:1.0:1.0:0.0:60.0:728.0:1.0:0.0:0.7 +14 61799788 . C T 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGCGCACCCAAAAGTCATA;RSEQ=GTGTATTAGCCTAATTCCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:58:20,38:159,224:383,58:0.1315:2,2:25.7:1.0:30.5:1.0:0.38945:1.34776:60.0:57.0:0.1323:0.0:1.1 0/0:352:0:0,0:155,197:352,0:0.0:2,0:24.6:1.0:30.0:1.0:1.0:0.0:60.0:87.0:1.0:0.0:0.7 +14 65544815 . G A 186 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCCAATCCAGGCAGTGAGG;RSEQ=AACCTGGCCTGCAGCAACTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:208:72:7,65:15,120:135,72:0.3462:2,2:23.4:1.0:30.3:1.0:0.81758:1.15993:60.0:144.0:0.3478:0.0:1.1 0/0:121:0:0,0:21,100:121,0:0.0:2,0:22.8:1.0:30.1:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.1 +14 65544917 . ATTTATTTT A 75 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=7.0;MSILEN=1.0;SSF=0.57728;SOR=0.0;LSEQ=ACTGTAGGCTTTATTTATTT;RSEQ=TTTATTTTTTTGAGACAGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:1,4:0,40:40,5:0.1111:1,2:27.8:1.0:32.6:1.0:0.11111:0.0:59.2:10.0:0.1111:0.0:0.0 0/0:13:0:0,0:0,13:13,0:0.0:1,0:22.2:1.0:30.5:1.0:1.0:0.0:59.1:26.0:1.0:0.0:0.2 +14 65568285 . C A 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GCAGATTGAAACCTCGGTTG;RSEQ=TCTTCCTGGAATAAGAGAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:424:29:12,17:145,250:395,29:0.0684:2,2:21.0:1.0:29.9:1.0:0.69118:1.22:60.0:28.0:0.068:0.0:1.2 0/0:432:0:0,0:160,270:430,0:0.0:2,0:23.0:1.0:30.7:1.0:1.0:0.0:59.8:22.889:1.0:0.0:0.3 +14 65568563 . C T 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTCCTCCCTGCAGACCCAG;RSEQ=TCGGGCATCTAGGCACCCCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:3,5:0.625:2,2:13.6:1.0:29.6:1.0:1.0:2.60168:58.2:10.0:0.625:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 69061259 . C G 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGGCTCCAGAAATCCTCC;RSEQ=ACCTCAGCCTCCTGAGCAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:227:76:0,76:1,150:151,76:0.3348:1,1:26.0:1.0:32.8:1.0:1.0:0.0:60.0:152.0:0.3393:0.0:1.1 0/0:143:0:0,0:2,141:143,0:0.0:1,0:24.7:1.0:31.8:1.0:1.0:0.0:59.9:70.5:1.0:0.0:0.1 +14 69117298 . G A 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.08954;SOR=0.0;LSEQ=TAAAATCAGACCAGAACCTG;RSEQ=GGATGAGCCAAGAAATGTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:7:7,0:48,1:49,7:0.125:1,0:31.7:1.0:30.1:1.0:1.0:0.0:60.0:14.0:0.1273:0.0:1.0 0/0:28:0:0,0:28,0:28,0:0.0:1,0:24.5:1.0:30.6:1.0:1.0:0.0:60.0:27.0:1.0:0.0:0.4 +14 69117450 . T C 207 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGATGAATCCTCTCAAAA;RSEQ=AGGAAAAGCTAGGTTCCTTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:733:88:60,28:412,233:645,88:0.1201:2,2:23.7:1.0:32.1:1.0:0.47737:1.21:60.0:87.0:0.1202:0.0:1.8 0/0:526:0:0,0:332,194:526,0:0.0:2,0:23.6:1.0:29.0:1.0:1.0:0.0:60.0:525.0:1.0:0.0:0.4 +14 70439776 . A G 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06213;SOR=0.0;LSEQ=TTCCCCAGAGGTGATTATTG;RSEQ=CCAAGGAGGAGAGAGCAGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:2,5:6,6:12,7:0.3684:2,2:22.4:1.0:31.1:1.0:0.63325:2.38223:60.0:14.0:0.3889:0.0:1.3 0/0:9:0:0,0:4,5:9,0:0.0:2,0:27.8:1.0:28.8:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 +14 77493815 . T C 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=6.0;SSF=0.02074;SOR=0.0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGCTGTTGCTGTTGCGCGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:3,2:19,25:44,5:0.102:2,2:19.2:1.0:33.6:1.0:0.64567:1.95:40.0:10.0:0.102:0.0:2.0 0/0:55:0:0,0:20,35:55,0:0.0:2,0:22.7:1.0:29.1:1.0:1.0:0.0:53.4:26.5:1.0:0.0:0.7 +14 78150336 . C T 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01238;SOR=0.0;LSEQ=CCCTTTGTCTTCGTCATTTT;RSEQ=GCAAATTACTGGAAGATGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:11:7,4:3,2:5,11:0.6875:2,2:24.7:1.0:30.7:1.0:1.0:1.16:55.1:22.0:0.6875:0.0:1.2 0/0:6:0:0,0:3,3:6,0:0.0:2,0:31.3:1.0:29.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 +14 80471852 . A G 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTTTCTACTCAAACATTCC;RSEQ=TGAACTCACTCCCCAGTGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:403:55:27,28:184,164:348,55:0.1365:2,2:28.9:1.0:30.8:1.0:0.66375:1.16306:60.0:110.0:0.1389:0.0:1.5 0/0:333:0:0,0:168,165:333,0:0.0:2,0:25.9:1.0:29.4:1.0:1.0:0.0:60.0:46.571:1.0:0.0:0.7 +14 81557084 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ATAATTTTTTCCAATTAAAC;RSEQ=AGAAAATCACACACACACAC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:24.7:1.0:30.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 81563195 . G A 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01278;SOR=0.0;LSEQ=AACATGGAAATGAGGTCAAG;RSEQ=AACTTGGCAGGGGCCCACTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:0,20:1,82:83,20:0.1942:1,1:19.8:1.0:32.2:1.0:1.0:0.0:60.0:40.0:0.198:0.0:1.1 0/0:25:0:0,0:0,25:25,0:0.0:1,0:26.2:1.0:31.3:1.0:1.0:0.0:60.0:50.0:1.0:0.0:0.0 +14 81563267 . G GGTGT 69 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=30;MSI=17.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GTTCCAAAGCTTTTCTCCCT;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:5:0,5:0,14:14,5:0.2083:1,0:45.0:1.0:30.0:1.0:1.0:0.0:57.0:10.0:0.2174:0.0:0.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 81574429 . G A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.33333;SOR=0.0;LSEQ=AAAAAATACAGTTGCCACTG;RSEQ=CCTGAAAAATAGGGAATTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:3,8:0.7273:0,0:18.6:1.0:27.5:1.0:1.0:0.0:60.0:3.0:0.6667:0.0:1.4 0/0:1:0:0,0:0,1:1,0:0.0:0,0:22.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +14 81575419 . T C 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCCCTTGGTTTTGCCTCAG;RSEQ=TTAGAATCTCATCATTGAGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:24.0:1.0:32.8:1.0:1.0:0.0:53.0:10.0:0.8333:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +14 84782145 . C G 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05359;SOR=0.0;LSEQ=AGAGGGGTGGACATGACAAA;RSEQ=GGCTGCCTCACCTGCAGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:6,3:9,6:0.375:2,2:24.5:1.0:30.8:1.0:1.0:1.0:60.0:5.0:0.3333:0.0:1.2 0/0:11:0:0,0:6,5:11,0:0.0:2,0:19.0:1.0:30.4:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.1 +14 87813148 . T A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04426;SOR=0.0;LSEQ=TACAGAAAGCCCTAGGTCTC;RSEQ=GGTTTGGGGCTTTCCTAACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:125:7:1,6:13,105:118,7:0.056:2,2:21.9:1.0:33.3:1.0:0.57407:1.34:60.0:14.0:0.0588:0.0:1.1 0/0:80:0:0,0:14,66:80,0:0.0:2,0:21.2:1.0:29.9:1.0:1.0:0.0:60.0:160.0:1.0:0.0:0.2 +14 87813214 . G A 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.08817;SOR=0.0;LSEQ=CTGCATAACCTACCAATTCA;RSEQ=GAATGCCTCTTTGGCATTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:7:0,7:0,37:37,7:0.1591:1,0:18.7:1.0:32.0:1.0:1.0:0.0:60.0:14.0:0.1591:0.0:1.6 0/0:20:0:0,0:0,20:20,0:0.0:1,0:20.7:1.0:29.8:1.0:1.0:0.0:60.0:19.0:1.0:0.0:0.1 +14 87813312 . A C 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=CTTGTAGTATCATCCATCCA;RSEQ=GTTCTTGCCATGGGCTCAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:15.0:1.0:29.2:1.0:1.0:0.0:57.2:10.0:0.7143:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:12.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +14 88360375 . C T 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00019;SOR=0.0;LSEQ=GCTGACTCCCCCAAGTCTAC;RSEQ=GTGTTTTGTTCCTGGGTTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:3,9:10,12:22,12:0.3529:2,2:27.8:1.0:30.3:1.0:0.29195:2.43465:60.0:24.0:0.3529:0.0:2.0 0/0:30:0:0,0:13,17:30,0:0.0:2,0:30.3:1.0:29.6:1.0:1.0:0.0:60.0:60.0:1.0:0.0:0.1 +14 88360384 . T A 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=7e-05;SOR=0.0;LSEQ=CCCAAGTCTACCGTGTTTTG;RSEQ=TCCTGGGTTATCTTTGCTTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:11:2,9:6,7:13,11:0.4583:2,2:24.2:1.0:29.2:1.0:0.2108:3.64266:60.0:22.0:0.4583:0.0:2.1 0/0:26:0:0,0:12,14:26,0:0.0:2,0:28.6:1.0:28.8:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.0 +14 95556644 . A C 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.15053;SOR=0.0;LSEQ=GCGCAAAAAACTAAAACTAC;RSEQ=ATTAGTTCCAAAATTTTATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:6:6,0:20,0:20,6:0.2308:1,0:31.3:1.0:32.3:1.0:1.0:0.0:55.7:12.0:0.24:0.0:1.0 0/0:11:0:0,0:11,0:11,0:0.0:0,0:14.9:1.0:29.8:1.0:1.0:0.0:58.3:22.0:1.0:0.0:0.0 +14 95560444 . G A 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCATAAAGGTGCTTGGTTAT;RSEQ=AGGTAGTCCAAAATCGCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:462:26:9,17:168,268:436,26:0.0563:2,2:18.0:1.0:29.8:1.0:0.83618:1.18362:60.0:52.0:0.057:0.0:1.0 0/0:385:0:0,0:157,226:383,0:0.0:2,0:24.5:1.0:30.8:1.0:1.0:0.0:60.0:382.0:0.9948:0.0:0.1 +14 95562999 . C A 181 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=GCTCTCCTCCTCCTCATCCT;RSEQ=CTCCTCGTAATCCTCATCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1043:82:36,46:417,543:960,82:0.0786:2,2:25.2:1.0:28.6:1.0:1.0:1.02:60.0:164.0:0.0795:0.0:1.1 0/0:796:0:0,0:352,442:794,0:0.0:2,0:25.1:1.0:30.2:1.0:1.0:0.0:59.8:55.714:0.9987:0.0:0.2 +14 95566068 . TACACACACACAC T 199 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=29;MSI=20.0;MSILEN=2.0;SSF=0.0;SOR=0.0864;LSEQ=GAAAAGTAAATCCCTCCAGT;RSEQ=ACACACACACACACACACAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:292:86:75,11:48,0:48,86:0.2945:1,2:29.8:1.0:31.1:1.0:0.00759:0.0:58.7:85.0:0.2972:0.0308:1.3 0/1:173:6:6,0:39,0:39,6:0.0347:1,0:29.3:1.0:31.7:1.0:1.0:0.0:60.0:12.0:0.0357:0.0:1.0 +14 95569500 . C T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.57302;SOR=0.0;LSEQ=TGTAAAGCAATACTCATCAA;RSEQ=TGCCAGGTAGTTCTGCCACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:5,0:35,0:35,5:0.125:1,0:28.0:1.0:32.8:1.0:1.0:0.0:60.0:10.0:0.125:0.0:1.0 0/0:8:0:0,0:8,0:8,0:0.0:0,0:22.6:1.0:31.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.1 +14 95578448 . CT C 95 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.02599;SOR=0.0;LSEQ=TCTATAAAGTCCTCTATATG;RSEQ=TTTTTTTTACAATGGTTGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:328:8:8,0:243,76:319,8:0.0244:2,0:21.5:1.0:31.7:1.0:0.20568:0.0:59.4:16.0:0.0246:0.0091:0.1 0/0:206:0:0,0:151,55:206,0:0.0:2,0:21.2:1.0:29.9:1.0:1.0:0.0:60.0:412.0:1.0:0.0:0.2 +14 95578675 . T C 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.09131;LSEQ=TGAAACCACTGCCCCAACAT;RSEQ=TTTAAAGTTCAATTTACCAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:95:8,87:12,113:125,95:0.4318:2,2:21.4:1.0:33.0:1.0:0.81696:1.15412:60.0:46.5:0.4306:0.0:1.1 0/1:93:6:1,5:18,69:87,6:0.0645:2,2:27.3:1.0:31.3:1.0:1.0:1.30087:60.0:12.0:0.0645:0.0:1.0 +14 95582395 . GAC G 78 MSI12;MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=30;MSI=16.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TACTGTACCGTGCCTACACA;RSEQ=ACACACACACACACACACAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:1,5:4,11:15,6:0.2857:2,2:18.2:1.0:30.5:1.0:1.0:1.77078:53.2:12.0:0.2857:0.1429:1.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:9.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +14 95583900 . C T 62 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0804;SOR=0.0;LSEQ=AAAAAGGGAGACCCTATGGG;RSEQ=ACTTTGTCTGTATATGTCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:5:2,3:230,48:278,5:0.0177:2,2:12.0:1.0:27.0:1.0:0.04236:7.11288:60.0:10.0:0.0179:0.0:1.0 0/0:199:0:0,0:150,49:199,0:0.0:2,0:23.5:1.0:31.3:1.0:1.0:0.0:60.0:65.333:1.0:0.0:0.1 +14 95591070 . G A 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATGTAGCATTTTCATGTGGG;RSEQ=TTTAACTGGGATTTCAGTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:33:1,32:1,46:47,33:0.4125:1,1:26.8:1.0:31.4:1.0:1.0:1.43:60.0:66.0:0.4177:0.0:1.3 0/0:48:0:0,0:3,45:48,0:0.0:2,0:22.4:1.0:31.4:1.0:1.0:0.0:60.0:96.0:1.0:0.0:0.1 +14 103707780 . G A 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01372;SOR=0.14574;LSEQ=TACATTGGTTCTTTAAAATG;RSEQ=CATCAGTGCCTTTTGGCCAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:11:8,3:22,11:33,11:0.25:2,2:28.4:1.0:31.2:1.0:1.0:1.32:60.0:22.0:0.25:0.0:1.1 0/1:44:2:1,1:25,17:42,2:0.0455:2,2:22.5:1.0:27.5:1.0:1.0:1.45743:60.0:4.0:0.0455:0.0:1.0 +14 104146611 . AT A 67 MSI12;MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=16;MSI=17.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGAATTTTTTAGCACATGG;RSEQ=TTTTTTTTTTTTTTTTGATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,8:8,5:0.3125:0,0:22.2:1.0:29.0:1.0:1.0:0.0:60.0:4.0:0.2857:0.0625:0.0 0/0:2:0:0,0:0,1:1,0:0.0:0,0:6.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.5:0.0:0.0 +14 104540796 . G T 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08474;SOR=0.0;LSEQ=GCATGTGGTCGTGTATATTT;RSEQ=CTTCCAGGCTATTTATTCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:5:2,3:277,155:432,5:0.0114:2,2:24.8:1.0:29.0:1.0:0.35706:2.67423:60.0:10.0:0.0116:0.0:1.2 0/0:297:0:0,0:179,118:297,0:0.0:2,0:25.8:1.0:31.2:1.0:1.0:0.0:60.0:73.25:1.0:0.0:0.3 +14 105238820 . G C 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAACAAGGCCACAGTGTCG;RSEQ=TACCGCCACCTGCCCAGGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:622:48:13,35:170,403:573,48:0.0772:2,2:23.4:1.0:32.8:1.0:0.86918:1.13548:60.0:96.0:0.0782:0.0:1.1 0/0:343:0:0,0:111,231:342,0:0.0:2,0:25.9:1.0:30.9:1.0:1.0:0.0:60.0:170.0:0.9971:0.0:0.2 +14 105241378 . C T 267 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07752;LSEQ=GTGAGCTGCCACCCCGCACC;RSEQ=TCATCTCCACCCTGCCCCAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1568:399:193,206:605,562:1167,399:0.2545:2,2:23.3:1.0:31.0:1.0:0.2461:1.14892:59.9:48.875:0.2534:0.0:1.1 0/1:815:21:9,12:398,392:790,21:0.0258:2,2:22.4:1.0:28.3:1.0:0.51665:1.35323:60.0:42.0:0.0262:0.0:1.0 +14 105241607 . G A 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCCCAGCTGGTCGGCATGC;RSEQ=TGGGGTGGCATGAGGGGCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:465:128:26,102:64,273:337,128:0.2753:2,2:22.6:1.0:30.9:1.0:0.7929:1.09:60.0:41.667:0.2717:0.0:1.1 0/0:225:0:0,0:45,179:224,0:0.0:2,0:21.0:1.0:30.5:1.0:1.0:0.0:60.0:31.0:0.9954:0.0:0.2 +14 105242374 . G A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.53924;SOR=0.0;LSEQ=AGGACTCTGTCCCCACAACC;RSEQ=GACTCCAACCCCCAGCAGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:14,5:0.2632:1,0:26.8:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.2 0/0:4:0:0,0:1,3:4,0:0.0:2,0:26.0:1.0:30.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.5 +14 105242826 . C T 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.05819;SOR=0.0;LSEQ=CCTCAGTTTCCCCACCCAAA;RSEQ=CCCACAGGCAGGACTGGGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:11:10,1:47,1:48,11:0.1864:1,2:30.3:1.0:31.5:1.0:0.34074:4.52871:60.0:22.0:0.1864:0.0:1.0 0/0:18:0:0,0:16,2:18,0:0.0:2,0:24.1:1.0:32.6:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.5 +15 20489987 . A G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=5.0;SSF=1.0;SOR=0.0;LSEQ=AAAATTAAATGTCAAATAAC;RSEQ=TAACATAGGTAATTGTGTTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:3,2:5,5:0.5:2,0:24.8:1.0:32.2:1.0:0.16667:0.0:53.8:10.0:0.5:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 20495202 . A AG 107 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.04316;SOR=0.12157;LSEQ=GGACTCCTGTGGGAAGGTAG;RSEQ=GGGGGGCAACACATAATGCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:11:9,2:20,1:21,11:0.2683:1,2:26.6:1.0:31.2:1.0:0.26613:4.22133:32.1:22.0:0.275:0.0732:0.2 0/1:24:1:1,0:17,0:17,1:0.0417:1,0:32.0:0.0:33.0:0.0:1.0:0.0:26.0:2.0:0.05:0.0:0.0 +15 33027179 . T A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATCACACAGAAATGATAATA;RSEQ=CTTCATTTCAGGGTGTTCCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:30.2:1.0:30.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 35385071 . C T 250 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.07123;LSEQ=GCTGTGATTGACTTGAACAA;RSEQ=CGTTGGTTTAACGGACAGCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:699:283:145,138:197,214:411,283:0.4049:2,2:26.5:1.0:30.7:1.0:0.39666:1.14:47.8:93.333:0.4058:0.0:1.1 0/1:802:37:17,20:359,405:764,37:0.0461:2,2:26.7:1.0:29.0:1.0:1.0:1.0428:46.7:36.0:0.0453:0.0:1.1 +15 35385596 . T C 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01875;SOR=0.0;LSEQ=AAAGATTCTCCATAAATAGG;RSEQ=CGGGCGCGGTGCCTCACGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:10:0,10:0,21:21,10:0.3226:1,0:15.2:1.0:30.6:1.0:1.0:0.0:55.9:9.0:0.3103:0.0:1.0 0/0:15:0:0,0:0,15:15,0:0.0:1,0:20.2:1.0:27.6:1.0:1.0:0.0:58.5:14.0:1.0:0.0:0.4 +15 38457041 . G A 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.01832;SOR=0.0;LSEQ=AATTCCAGCATAAAAAAAGA;RSEQ=CACAAATCAGAAACACAGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:12:0,12:1,18:19,12:0.3871:1,0:24.3:1.0:29.9:1.0:1.0:0.0:60.0:11.0:0.3667:0.0:2.0 0/0:11:0:0,0:0,11:11,0:0.0:0,0:21.7:1.0:31.0:1.0:1.0:0.0:60.0:22.0:1.0:0.0:1.5 +15 40328575 . G C 288 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTTGTTGCTGCTGTTGTTG;RSEQ=TGCTGTTGCTGCTGCGGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:486:482:214,268:1,1:2,482:0.9918:2,2:25.7:1.0:32.4:1.0:1.0:1.25174:53.4:39.167:0.9937:0.0:1.2 0/0:609:0:0,0:10,14:24,0:0.0:2,0:24.0:1.0:30.7:1.0:1.0:0.0:57.0:23.0:0.8846:0.0:0.1 +15 42004962 . G C 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.1;SOR=0.0;LSEQ=AGACCATACACTCTCTATAG;RSEQ=AGTTACTGAACTCTGCTGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:9,0:0,0:0,9:1.0:0,0:21.8:1.0:32.7:1.0:1.0:0.0:54.4:18.0:1.0:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:41.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +15 42026363 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGATCTTCCCACCTCGGCCT;RSEQ=TCGGAATGCTGGGATTGCAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:28.6:1.0:30.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 42032655 . T C 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.04348;SOR=0.0;LSEQ=TATTTTTTAATAACACTGAC;RSEQ=TGAAGGCAAGTTTTATAGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:22:3,19:0,0:0,22:1.0:0,2:25.3:1.0:32.9:1.0:1.0:0.0:60.0:44.0:1.0:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:29.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +15 42035713 . C A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAAATACTAAAAAACATTA;RSEQ=AATGGAAGTGGTGGCTGAAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:30.8:1.0:30.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 42046575 . A T 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.00081;SOR=0.0;LSEQ=ATAAGGGGAACAAACATTTG;RSEQ=AAAGTTTAGGTGTGCTTGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:13:11,2:235,17:252,13:0.0491:2,2:18.3:1.0:30.4:1.0:0.23672:2.50094:60.0:26.0:0.0504:0.0:2.2 0/0:214:0:0,0:194,20:214,0:0.0:2,0:23.0:1.0:28.9:1.0:1.0:0.0:60.0:213.0:1.0:0.0:0.7 +15 42049890 . A AC 179 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCACACCTTGGGAAAAAGAA;RSEQ=CTGGTTGTAATTTGGAATGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:46:43,3:174,17:191,46:0.1933:2,2:26.4:1.0:32.5:1.0:0.77232:1.4:59.9:45.0:0.1923:0.0336:0.2 0/0:215:0:0,0:182,33:215,0:0.0:2,0:23.3:1.0:29.7:1.0:1.0:0.0:60.0:430.0:1.0:0.0:0.1 +15 50245089 . C CTTTTGT 101 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=5.0;MSILEN=1.0;SSF=0.07212;SOR=0.14667;LSEQ=GATGGGGTTTTTGTGGGGGC;RSEQ=TTTTGTTGTTGTTGTTGTTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:9:3,6:13,14:27,9:0.25:2,2:29.2:1.0:32.1:1.0:0.70027:1.82595:54.7:18.0:0.25:0.0:0.0 0/1:22:1:1,0:10,11:21,1:0.0455:2,0:34.0:0.0:31.2:0.0:1.0:0.0:42.0:2.0:0.0476:0.0:0.0 +15 50245685 . C T 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00521;SOR=0.0;LSEQ=ACCTGAAGAGGCCCTCTGGC;RSEQ=GCAGACTACCACAGCCAGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:6:2,4:10,8:18,6:0.25:2,2:22.8:1.0:31.3:1.0:0.64041:2.40592:60.0:12.0:0.25:0.0:1.2 0/0:30:0:0,0:14,16:30,0:0.0:2,0:31.0:1.0:29.8:1.0:1.0:0.0:59.5:60.0:1.0:0.0:0.6 +15 59502492 . TTGTACATTGAC T 204 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATTCAATAACAACTTCCAT;RSEQ=ATTTTACTCATATCCACATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:314:96:45,51:105,113:218,96:0.3057:2,2:27.2:1.0:31.0:1.0:0.90252:1.05295:59.7:192.0:0.3097:0.0446:0.2 0/0:484:0:0,0:242,242:484,0:0.0:2,0:24.8:1.0:29.4:1.0:1.0:0.0:59.9:95.8:1.0:0.0:0.3 +15 66679684 . A G 206 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGCGCGTTACCCGGGTCCA;RSEQ=AATGCCCAAGAAGAAGCCGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1040:76:46,30:551,412:963,76:0.0731:2,2:27.6:1.0:33.0:1.0:0.63056:1.15:51.9:75.0:0.0734:0.0:1.1 0/0:1239:0:0,0:663,575:1238,0:0.0:2,0:24.4:1.0:29.5:1.0:1.0:0.0:58.2:60.9:0.9992:0.0:0.3 +15 66735925 . C CAG 95 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATCTGTGTGTCTTGAAAAA;RSEQ=GGGCCAGGCACAGTGGCTCG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1.0:0,0:27.4:1.0:31.7:1.0:1.0:0.0:55.8:16.0:1.0:0.25:0.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 66779698 . C T 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAAGAAAACACCCAGGTGGC;RSEQ=GGGTGCAGTGGTTCACGCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:52:12,40:33,150:183,52:0.2203:2,2:21.4:1.0:30.3:1.0:0.42772:1.36:56.6:51.0:0.2237:0.0:1.2 0/0:248:0:0,0:57,190:247,0:0.0:2,0:21.6:1.0:29.3:1.0:1.0:0.0:58.5:122.5:0.9959:0.0:0.1 +15 66782048 . C T 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCTTACCTTGTCTTTCTT;RSEQ=CTTTAAGCTTAATAAAAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:644:110:60,50:288,246:534,110:0.1708:2,2:23.7:1.0:30.2:1.0:0.91678:1.02:60.0:35.667:0.1709:0.0:1.2 0/0:819:0:0,0:431,388:819,0:0.0:2,0:25.1:1.0:30.2:1.0:1.0:0.0:60.0:57.5:1.0:0.0:0.2 +15 67430733 . T C 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCTTGCCATCGCAGTGGAT;RSEQ=TGCGGAAGAGGGTTCCAGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1.0:0,0:17.3:1.0:33.3:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 67457480 . T TC 153 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTGCCAGGGGTCATCACCTC;RSEQ=CCCCGGCTCCCCATCCCCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:39:25,14:42,89:131,39:0.0975:2,2:10.6:1.0:29.1:1.0:0.00064:3.75:58.7:12.0:0.0916:0.07:1.3 0/0:217:0:0,0:82,135:217,0:0.0:2,0:21.0:1.0:28.9:1.0:1.0:0.0:59.8:30.0:1.0:0.0:0.7 +15 67457485 . G CC 247 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=AGGGGTCATCACCTCTCCCC;RSEQ=GCTCCCCATCCCCCCGAGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:400:230:74,156:42,89:131,230:0.575:2,2:28.3:1.0:31.6:1.0:1.0:1.01:59.8:229.0:0.5827:0.0375:1.1 0/0:217:0:0,0:82,135:217,0:0.0:2,0:21.0:1.0:28.9:1.0:1.0:0.0:59.8:30.0:1.0:0.0:0.7 +15 67458805 . G A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTGGACGCCTCCCTGGAGG;RSEQ=GGTGGGGCTTAACCCTCACC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:7,0:0,0:0,7:0.875:0,0:29.6:1.0:28.7:1.0:1.0:0.0:56.1:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 67473790 . C T 245 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGCTGACACGGAGACACAT;RSEQ=GGTATGGGGTGGCTCCATTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:632:259:95,164:137,236:373,259:0.4098:2,2:24.1:1.0:30.6:1.0:1.0:1.00214:59.5:63.75:0.414:0.0:1.3 0/0:586:0:0,0:237,346:583,0:0.0:2,0:24.0:1.0:29.6:1.0:1.0:0.0:59.6:63.778:0.9948:0.0:0.4 +15 67479678 . A AG 216 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGCCACTTCCATCCCCAC;RSEQ=GCCCTGTTTCTGTGTTTTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:787:99:66,33:418,265:683,99:0.1258:2,2:29.6:1.0:32.6:1.0:0.32028:1.27:60.0:98.0:0.1284:0.0038:0.1 0/0:708:0:0,0:419,288:707,0:0.0:2,0:25.1:1.0:29.7:1.0:1.0:0.0:59.9:77.556:0.9986:0.0:0.2 +15 88126117 . G T 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00403;LSEQ=AATGCTACCTCTGGGAATCG;RSEQ=ATCATTCAGGAAAAGACACC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:327:130:66,64:94,100:194,130:0.3976:2,2:25.9:1.0:28.8:1.0:0.73413:1.1:59.7:64.0:0.4:0.0:1.2 0/0:379:1:0,1:173,204:377,1:0.0026:2,0:44.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0027:0.0:1.0 +15 88472228 . G T 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.16588;SOR=0.0;LSEQ=TGTCCAAGAAGAAAGAAGGA;RSEQ=TGGGCAATTGAGAACATAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:6:6,0:35,0:35,6:0.1463:1,0:27.7:1.0:32.5:1.0:1.0:0.0:60.0:12.0:0.15:0.0:1.0 0/0:17:0:0,0:17,0:17,0:0.0:1,0:16.6:1.0:32.5:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.1 +15 88472655 . G T 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACAAGGATCATTGCATCTG;RSEQ=CCCATGGGCCCTGCAAGAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:494:195:52,143:91,208:299,195:0.3947:2,2:23.7:1.0:29.8:1.0:0.41699:1.20268:60.0:47.75:0.3979:0.0:1.1 0/0:375:0:0,0:112,262:374,0:0.0:2,0:24.1:1.0:31.0:1.0:1.0:0.0:59.9:40.556:0.9973:0.0:0.2 +15 88524788 . A G 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.03324;SOR=0.0;LSEQ=ATCTAGATCCTAAGAATCTC;RSEQ=CCCTGGCATTATAGAAATGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:12,8:0.4:0,0:23.1:1.0:33.9:1.0:1.0:0.0:60.0:16.0:0.4:0.0:1.0 0/0:9:0:0,0:0,9:9,0:0.0:0,0:29.6:1.0:30.2:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 +15 88576408 . TATATATATATATATAT C 104 MSI12 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=24;MSI=20.0;MSILEN=2.0;SSF=0.0129;SOR=0.0;LSEQ=TTTACTTTTGGGGGGTGTGT;RSEQ=ATATATATATATATATATAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:0,11:0,7:7,11:0.4783:0,0:15.6:1.0:30.3:1.0:1.0:0.0:54.2:10.0:0.4762:0.3043:0.7 0/0:10:0:0,0:0,6:6,0:0.0:0,0:7.0:1.0:28.8:1.0:1.0:0.0:60.0:12.0:0.6:0.0:0.0 +15 88669163 . T C 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAACTAGGAGTCCCTTTAC;RSEQ=CACCCGTAATGAAAATAAAC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:23.4:1.0:31.8:1.0:1.0:0.0:59.6:10.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 88726405 . G A 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.12797;SOR=0.0;LSEQ=GAAAGTGAACACACTTGGGT;RSEQ=TCAGGAGACTGACTCTCCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:6,0:8,0:8,6:0.4286:0,0:23.2:1.0:26.8:1.0:1.0:0.0:60.0:12.0:0.4286:0.0:1.0 0/0:5:0:0,0:5,0:5,0:0.0:0,0:27.8:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 +15 90631255 . G A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=GCTGGAACTGGGGATAAAGA;RSEQ=GCATTCTCTTCTGATAGGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:0,2:2,6:0.75:0,2:22.8:1.0:27.3:1.0:0.42857:0.0:60.0:5.0:0.7143:0.0:2.2 0/0:2:0:0,0:1,1:2,0:0.0:2,0:26.5:1.0:29.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.0 +15 90633416 . A G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.36364;SOR=0.0;LSEQ=TGGCCTGGGAGATGGAAGAC;RSEQ=TGGATTCTGTTCTCAGCTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:3,7:0.7:0,0:16.3:1.0:27.4:1.0:1.0:0.0:60.0:14.0:0.7:0.0:1.4 0/0:1:0:0,0:1,0:1,0:0.0:0,0:6.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +15 91292969 . G A 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATCAATGATTGGGATGATAT;RSEQ=GATGACTTTGATACTTCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:26:15,11:238,254:492,26:0.0502:2,2:21.3:1.0:30.7:1.0:0.42263:1.45:60.0:52.0:0.051:0.0:1.2 0/0:541:0:0,0:275,264:539,0:0.0:2,0:25.0:1.0:30.7:1.0:1.0:0.0:60.0:133.75:0.9963:0.0:0.1 +15 91295363 . C T 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.54629;SOR=0.0;LSEQ=TTGCATTCTAAAGATGAAGT;RSEQ=CCATTATGATTAATTACATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:0,7:1,14:15,7:0.3182:1,0:27.4:1.0:30.6:1.0:1.0:0.0:58.3:14.0:0.3182:0.0:1.9 0/0:4:0:0,0:0,4:4,0:0.0:0,0:16.5:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +15 91352774 . A G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGGGATCAGAGCCCTGGGT;RSEQ=CCAGTTCCAGATCTGCCACC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:38.2:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 91792303 . C T 84 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=20.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CATACATCTACGTTTTCACA;RSEQ=ACACACACACACACACACAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:3,4:5,4:9,7:0.35:2,2:23.3:1.0:30.0:1.0:1.0:1.61372:59.9:14.0:0.4375:0.0:1.1 0/0:2:0:0,0:1,0:1,0:0.0:0,0:28.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +15 92829452 . G A 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.09258;LSEQ=GAGTCAGAAGACGAAGAGGA;RSEQ=GAGGATGTGAGACTCTTAAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:67:27,40:39,51:90,67:0.4268:2,2:25.2:1.0:31.2:1.0:0.74546:1.132:39.6:32.5:0.4194:0.0:1.1 0/1:125:8:5,3:51,66:117,8:0.064:2,2:18.6:1.0:30.0:1.0:0.46517:2.14:45.0:16.0:0.064:0.0:1.0 +15 99434357 . G A 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.28007;SOR=0.0;LSEQ=GACTGAACTTTAAAGATATC;RSEQ=ACTCTCTGCAGGTCTAAGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:13,0:13,6:0.3158:1,0:15.8:1.0:28.5:1.0:1.0:0.0:60.0:5.0:0.2778:0.0:1.5 0/0:5:0:0,0:5,0:5,0:0.0:0,0:18.8:1.0:30.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 +15 99460184 . G T 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GCCTTTCTCCCCACCAGGTA;RSEQ=TGTGTAAGTCAGCAGCTGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:154:35:2,33:8,111:119,35:0.2273:2,2:25.0:1.0:30.5:1.0:1.0:1.1879:60.0:34.0:0.2267:0.0:1.1 0/0:121:0:0,0:4,117:121,0:0.0:1,0:23.7:1.0:31.5:1.0:1.0:0.0:60.0:59.5:1.0:0.0:0.2 +15 99467930 . G A 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00961;LSEQ=AAAAGTAAGGCTTGTGGAGG;RSEQ=AGAAGAAACGTGGTAAAACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:507:99:29,70:115,292:407,99:0.1953:2,2:25.2:1.0:30.6:1.0:0.90121:1.05:60.0:32.0:0.1932:0.0:1.1 0/0:431:1:1,0:144,286:430,1:0.0023:2,0:1.0:0.0:22.0:0.0:0.33643:0.0:60.0:2.0:0.0024:0.0:1.0 +15 99478966 . C T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACCTGCCAAGCCAGGCCAG;RSEQ=GCCACTCCCTCCCCGAAGCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:21.4:1.0:31.4:1.0:1.0:0.0:59.6:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +15 99485931 . T A 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.09023;SOR=0.0;LSEQ=GAATCAAATTGTAAATATAT;RSEQ=AAAAGTGGAGATTGCTTGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:10:10,0:7,0:7,10:0.5882:0,0:24.5:1.0:28.6:1.0:1.0:0.0:60.0:20.0:0.5882:0.0:1.1 0/0:4:0:0,0:3,1:4,0:0.0:2,0:30.0:1.0:31.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 +15 99861641 . T G 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGAGACTGGGGCTATTTAGC;RSEQ=TGTGGGCAGCTGGCGTTCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:77:35,42:155,203:358,77:0.177:2,2:25.4:1.0:30.9:1.0:0.80025:1.09:60.0:154.0:0.182:0.0:1.1 0/0:493:0:0,0:233,260:493,0:0.0:2,0:26.3:1.0:29.6:1.0:1.0:0.0:60.0:81.167:1.0:0.0:0.6 +15 99945673 . C G 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00041;SOR=0.0;LSEQ=GAGAAGGCCCAGGAATCTGA;RSEQ=TAAAGTTTGGTCAAGCAAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:9:4,5:1,0:1,9:0.9:0,2:17.1:1.0:31.4:1.0:1.0:0.0:60.0:18.0:0.9:0.0:1.2 0/0:8:0:0,0:3,5:8,0:0.0:2,0:26.3:1.0:30.6:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.1 +16 337871 . T C 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAGCAGGGACCTCGGCTGCC;RSEQ=CACTTGGGCTGGGCCCTCCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:12,6:0.3333:0,0:31.0:1.0:32.2:1.0:1.0:0.0:60.0:12.0:0.3333:0.0:1.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +16 339415 . G T 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.12714;LSEQ=CCACATACTCGTGCGGGGAG;RSEQ=GGGCACCCCAGCCCTCACAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:667:214:148,66:312,138:450,214:0.3208:2,2:25.1:1.0:29.6:1.0:1.0:1.00821:60.0:34.667:0.318:0.0:1.1 0/1:495:28:14,14:294,173:467,28:0.0566:2,2:22.4:1.0:28.4:1.0:0.22776:1.69745:60.0:27.0:0.0556:0.0:1.1 +16 339727 . C T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCAGGGGTGAGCAGCACCC;RSEQ=ATTCAAACACCTGGGGCCCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:30:1,29:0,63:63,30:0.3226:1,1:21.8:1.0:28.3:1.0:0.32258:0.0:59.9:14.0:0.3146:0.0:1.7 0/0:43:0:0,0:0,43:43,0:0.0:1,0:20.1:1.0:31.9:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.3 +16 347184 . A G 241 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07881;LSEQ=CTGGCGCTCTTCCCCGACTC;RSEQ=GCCTTCTTGGCATTTCTTTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:244:96,148:265,407:672,244:0.2661:2,2:25.7:1.0:30.5:1.0:1.0:1.00378:60.0:243.0:0.2703:0.0:1.1 0/1:829:23:9,14:347,457:804,23:0.0277:2,2:24.5:1.0:29.4:1.0:0.83184:1.1809:60.0:46.0:0.0282:0.0:1.2 +16 347326 . G A 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGCATCTGTAAGGCTCCC;RSEQ=TGGTGCAGCCGCCGCCCGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:36:0,36:2,71:73,36:0.3303:1,1:21.3:1.0:30.7:1.0:1.0:0.0:60.0:17.0:0.3208:0.0:1.2 0/0:43:0:0,0:1,42:43,0:0.0:1,0:17.8:1.0:31.4:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.2 +16 360149 . G A 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01556;SOR=0.0;LSEQ=CCAATAGAGCTCCTGGCCCC;RSEQ=ACCGCCGGTCAGCAGGCAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:10:1,9:23,187:210,10:0.0455:2,2:18.4:1.0:30.9:1.0:1.0:1.10648:60.0:20.0:0.0457:0.0:1.0 0/0:129:0:0,0:17,112:129,0:0.0:2,0:23.2:1.0:30.3:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.1 +16 396234 . G A 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCTTCTGAGGGAGTCTTCC;RSEQ=GGGGGAGCAGCGTCTCTGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:794:32:17,15:450,310:760,32:0.0403:2,2:26.1:1.0:30.3:1.0:0.58275:1.28041:60.0:31.0:0.0394:0.0:1.9 0/0:707:0:0,0:391,316:707,0:0.0:2,0:23.6:1.0:29.6:1.0:1.0:0.0:60.0:234.667:1.0:0.0:0.6 +16 1987179 . C T 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00675;SOR=0.0;LSEQ=ATCCACTCCCACATGCTCCC;RSEQ=GGATTTCTGTGGGTATAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:8:1,7:1,31:32,8:0.2:1,2:24.9:1.0:29.0:1.0:0.3641:4.21:60.0:7.0:0.1795:0.0:1.3 0/0:33:0:0,0:3,30:33,0:0.0:2,0:20.4:1.0:29.5:1.0:1.0:0.0:60.0:66.0:1.0:0.0:0.1 +16 2105055 . A G 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCACACGTCTCCTCCGAGCC;RSEQ=CTCTCTGCTGGGGGTGGGGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:4,1:3,0:3,5:0.625:0,2:33.8:1.0:31.2:1.0:1.0:0.0:48.4:10.0:0.7143:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +16 2110795 . G A 231 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00592;LSEQ=TCTGCTGAACATCATCGAAC;RSEQ=GCTCCTTCAGCAGCTCCAGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:904:173:71,102:331,400:731,173:0.1914:2,2:26.3:1.0:31.2:1.0:0.34947:1.18858:60.0:85.5:0.1926:0.0:1.1 0/0:716:1:1,0:318,397:715,1:0.0014:2,0:37.0:0.0:25.0:0.0:0.44553:0.0:60.0:2.0:0.0014:0.0:1.0 +16 2132583 . G A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGTGCTCGTCGCCTCATCC;RSEQ=CCCACCCCCATGGTCCGTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:251:94:16,78:20,136:156,94:0.3745:2,2:25.6:1.0:30.3:1.0:0.35981:1.39:60.0:188.0:0.379:0.0:1.1 0/0:152:0:0,0:29,122:151,0:0.0:2,0:20.7:1.0:30.4:1.0:1.0:0.0:60.0:24.167:1.0:0.0:0.1 +16 2134852 . G A 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTGGAACCCCTGGGAGGGC;RSEQ=GTGGAGTGGGAGATGGCCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:112:100,12:193,35:228,112:0.3294:2,2:23.6:1.0:30.6:1.0:0.31586:1.51:60.0:36.333:0.3313:0.0:1.1 0/0:170:0:0,0:140,29:169,0:0.0:2,0:22.1:1.0:30.0:1.0:1.0:0.0:60.0:338.0:1.0:0.0:0.2 +16 2136455 . C T 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATCCAGTCCTGCTACCCCA;RSEQ=GCCCTGGGGCATGGCCCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:38:4,34:28,158:186,38:0.1696:2,2:25.6:1.0:29.8:1.0:0.61401:1.50378:60.0:76.0:0.1704:0.0:1.1 0/0:118:0:0,0:14,104:118,0:0.0:2,0:23.3:1.0:29.3:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.1 +16 2215659 . CT GC 111 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=5.0;SSF=0.0506;SOR=0.0;LSEQ=GCGTGTGAGTGCTGCGTGGC;RSEQ=GGCCTGGTCGCATGGTTAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:11:11,0:30,1:31,11:0.2619:1,0:8.8:1.0:32.1:1.0:1.0:0.0:42.2:22.0:0.2619:0.0714:1.3 0/0:15:0:0,0:14,1:15,0:0.0:1,0:22.0:1.0:31.3:1.0:1.0:0.0:42.5:30.0:1.0:0.0:0.2 +16 2226763 . C G 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.18678;SOR=0.0;LSEQ=TCTACTCGGCACTGTCCTTG;RSEQ=TGCCCAGCCCCTCTCTGGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:7:0,7:0,58:58,7:0.1077:1,0:29.7:1.0:33.1:1.0:1.0:0.0:60.0:14.0:0.1077:0.0:1.0 0/0:21:0:0,0:0,21:21,0:0.0:1,0:19.1:1.0:31.7:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.1 +16 3777496 . C A 62 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.23077;SOR=0.0;LSEQ=GGAAAAAAAAGAACCCCCCC;RSEQ=ACCCCCCCGCCAAAAAAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:20.4:1.0:26.8:1.0:1.0:0.0:60.0:4.0:0.5714:0.0:2.6 0/0:3:0:0,0:3,0:3,0:0.0:0,0:7.3:1.0:32.0:0.0:1.0:0.0:43.3:6.0:1.0:0.0:0.3 +16 3786594 . C G 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAATGCAAGAAAAAGGCACA;RSEQ=AAATATCCTCCCCTCAGTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:51:40,11:330,70:400,51:0.1126:2,2:26.9:1.0:32.1:1.0:0.44449:1.29563:60.0:50.0:0.1126:0.0:1.1 0/0:367:0:0,0:286,81:367,0:0.0:2,0:23.6:1.0:31.3:1.0:1.0:0.0:60.0:72.4:1.0:0.0:0.1 +16 3794705 . T G 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00073;SOR=0.0;LSEQ=ACATTCTTGCATTCTTACCC;RSEQ=CATGACTGGCCTGGCTCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:14:13,1:53,0:53,14:0.209:1,1:19.6:1.0:30.3:1.0:0.20896:0.0:60.0:28.0:0.209:0.0:1.0 0/0:43:0:0,0:41,2:43,0:0.0:1,0:17.5:1.0:31.2:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.1 +16 3807171 . G A 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGCGTGAGCCACCACACCC;RSEQ=GCCTGAAATTGGGCCACTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:16,0:28,0:28,16:0.3636:1,1:29.4:1.0:30.6:1.0:1.0:0.0:52.6:32.0:0.3636:0.0:1.1 0/0:63:0:0,0:58,4:62,0:0.0:2,0:24.0:1.0:29.0:1.0:1.0:0.0:57.9:61.0:1.0:0.0:0.0 +16 3807946 . C T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0202;LSEQ=AGGCATTGTTGAACATGAGC;RSEQ=AGACGTCGTCCACGTACTGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:570:39:16,23:247,284:531,39:0.0684:2,2:24.9:1.0:29.9:1.0:0.61816:1.24973:60.0:78.0:0.0693:0.0:1.2 0/0:677:1:0,1:329,347:676,1:0.0015:2,0:2.0:0.0:22.0:0.0:1.0:0.0:60.0:2.0:0.0015:0.0:1.0 +16 3860554 . C T 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAATGGTAAAAATCCACAGA;RSEQ=CACAGCACCCACCGGAGAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:130:93,37:181,67:248,130:0.3439:2,2:23.0:1.0:31.1:1.0:0.80872:1.07458:60.0:260.0:0.3476:0.0:1.1 0/0:322:0:0,0:222,100:322,0:0.0:2,0:1.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 +16 8382667 . T A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=8.0;MSILEN=1.0;SSF=0.02375;SOR=0.0;LSEQ=AGTTTTATGTGCCTGCTCCA;RSEQ=AAAAAAAAGAAATGCGCTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:6,0:9,0:9,6:0.4:0,0:11.5:1.0:31.3:1.0:1.0:0.0:60.0:12.0:0.4:0.0:2.0 0/0:11:0:0,0:11,0:11,0:0.0:0,0:22.9:1.0:31.3:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.2 +16 9944017 . G A 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.53044;SOR=0.0;LSEQ=GGCAGTTCTCCATCCCAGCC;RSEQ=CCCTCATCCCCAGAGGAATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,11:11,5:0.3125:0,0:17.2:1.0:29.8:1.0:1.0:0.0:60.0:10.0:0.3125:0.0:1.0 0/0:3:0:0,0:0,3:3,0:0.0:0,0:27.3:1.0:31.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:1.0 +16 10273656 . C T 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.25824;SOR=0.0;LSEQ=GTGTACACCATTTTCAGAAA;RSEQ=AAGGCAAAAGGCATTTCCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:10.8:1.0:28.8:1.0:1.0:0.0:60.0:4.0:0.4:0.0:1.8 0/0:3:0:0,0:2,1:3,0:0.0:2,0:11.3:1.0:33.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 +16 10273821 . C T 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CCATGCAGCTGGTGGCTTCC;RSEQ=AGGTCCTGGCAGGGCATCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:20:16,4:254,62:316,20:0.0595:2,2:23.5:1.0:31.3:1.0:1.0:1.02412:60.0:19.0:0.0572:0.0:1.2 0/0:268:0:0,0:191,77:268,0:0.0:2,0:23.9:1.0:30.6:1.0:1.0:0.0:60.0:88.333:1.0:0.0:0.2 +16 11345660 . AAAG A 76 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=11.0;MSILEN=1.0;SSF=0.17243;SOR=0.0;LSEQ=AGACTCTGTCTTAAAAAAAA;RSEQ=AAGAAGAAACCTGTCTTGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:6:6,0:26,0:26,6:0.1935:1,0:12.8:1.0:29.5:1.0:1.0:0.0:60.0:12.0:0.1935:0.129:0.8 0/0:11:0:0,0:10,1:11,0:0.0:2,0:25.4:1.0:29.1:1.0:1.0:0.0:58.5:22.0:1.0:0.0:0.5 +16 11349302 . C T 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.09072;SOR=0.15169;LSEQ=CTCTGCTGCTGTGGAGACTG;RSEQ=ATTGTCGGCTGCCACCTGGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:407:5:2,3:232,169:401,5:0.0123:2,2:21.0:1.0:27.4:1.0:0.65431:2.05549:60.0:10.0:0.0126:0.0:1.0 0/0:532:1:0,1:299,232:531,1:0.0019:2,0:1.0:0.0:23.0:0.0:0.43797:0.0:60.0:2.0:0.0019:0.0:2.0 +16 11352930 . G A 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0004;SOR=0.12796;LSEQ=GCAAGTGACCTGTCCTCTTG;RSEQ=GACCTGATTTGCCCCAACTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:21:0,21:0,45:45,21:0.3182:1,1:28.6:1.0:32.9:1.0:1.0:0.0:60.0:42.0:0.3387:0.0:2.0 0/1:54:3:0,3:5,46:51,3:0.0556:2,0:18.7:1.0:32.0:0.0:1.0:0.0:60.0:6.0:0.0556:0.0:2.0 +16 14028861 . C T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.03594;SOR=0.0;LSEQ=ATTTGATCAATACCTAAGAC;RSEQ=CTTTTTAAATAGTTTGTAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:7:7,0:32,0:32,7:0.1795:1,0:30.4:1.0:32.4:1.0:1.0:0.0:60.0:14.0:0.1795:0.0:1.6 0/0:28:0:0,0:28,0:28,0:0.0:1,0:22.3:1.0:31.0:1.0:1.0:0.0:60.0:56.0:1.0:0.0:0.0 +16 14041760 . C A 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTAGCAAGCCTTTCTCTCT;RSEQ=ACTTCCCGAGGTGCCTTGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:19:9,10:290,350:640,19:0.0288:2,2:28.8:1.0:29.1:1.0:1.0:1.09:60.0:38.0:0.0288:0.0:1.1 0/0:751:0:0,0:357,392:749,0:0.0:2,0:24.6:1.0:30.9:1.0:1.0:0.0:59.9:123.833:0.9973:0.0:0.1 +16 14042077 . A G 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCACGTTAAGAACATCGCAG;RSEQ=ATTAGCAGCCCTGTCACAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:61:26,35:269,323:592,61:0.0934:2,2:26.2:1.0:31.9:1.0:0.688:1.12089:59.5:122.0:0.0953:0.0:1.2 0/0:727:0:0,0:358,369:727,0:0.0:2,0:24.8:1.0:29.2:1.0:1.0:0.0:59.9:144.4:1.0:0.0:0.2 +16 17380507 . T TATCATCATCATCCTC 88 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=39;MSI=2.6;MSILEN=1.0;SSF=0.00968;SOR=0.0;LSEQ=CAACAATCCCCATGGATAGG;RSEQ=ATCATCATCATCCTCATCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:4,4:6,3:9,8:0.4706:2,2:12.1:1.0:29.5:1.0:0.63719:1.91839:38.6:16.0:0.4706:0.4706:0.1 0/0:11:0:0,0:7,4:11,0:0.0:2,0:30.5:1.0:29.1:1.0:1.0:0.0:52.9:22.0:1.0:0.0:0.1 +16 24788422 . AGCAGCCACAGCC A 72 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=2.0;MSILEN=1.0;SSF=0.0277;SOR=0.14918;LSEQ=GCAGCAGCAGCAGCCACAGC;RSEQ=GCAGCCGCAGCAGCAGCAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:2,3:7,7:14,5:0.2632:2,2:35.4:1.0:31.2:1.0:1.0:1.46843:45.2:10.0:0.2632:0.0:0.0 0/1:41:2:2,0:14,25:39,2:0.0488:2,0:32.5:1.0:31.0:1.0:0.14634:0.0:43.5:4.0:0.05:0.0:0.5 +16 27356584 . T G 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTGTTTCCACCCCTGAACT;RSEQ=AAGTGCCCAGGAAGGCGTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:56:43,13:70,40:110,56:0.3373:2,2:24.1:1.0:32.0:1.0:0.11282:1.88:60.0:27.0:0.3293:0.0:1.3 0/0:150:0:0,0:100,50:150,0:0.0:2,0:23.6:1.0:28.7:1.0:1.0:0.0:60.0:49.0:1.0:0.0:0.3 +16 30129936 . C T 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00817;LSEQ=AGGAAAACAGGCTCTGAAGG;RSEQ=GAGGCTGCACACCTCCTCCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:91:7,84:14,150:164,91:0.3569:2,2:22.5:1.0:30.4:1.0:1.0:1.11953:60.0:90.0:0.3571:0.0:1.1 0/0:223:1:0,1:30,192:222,1:0.0045:2,0:21.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0045:0.0:1.0 +16 33371341 . CG C 76 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.48718;SOR=0.0;LSEQ=GCAGGAGGATCACTTGAACC;RSEQ=GGGGGCAGAGGTTGCAGTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:28.2:1.0:32.8:1.0:1.0:0.0:41.4:10.0:0.4545:0.0:0.0 0/0:2:0:0,0:0,1:1,0:0.0:0,0:14.0:0.0:32.0:0.0:1.0:0.0:20.0:2.0:0.5:0.0:1.0 +16 33373312 . G T 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGTCCAACACAAACAA;RSEQ=AACTTCAGGAGCCAAGCAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:587:22:11,11:345,220:565,22:0.0375:2,2:26.3:1.0:29.2:1.0:0.37409:1.56689:50.3:44.0:0.0382:0.0:1.1 0/0:1114:0:0,0:628,486:1114,0:0.0:2,0:26.7:1.0:30.8:1.0:1.0:0.0:50.3:60.889:1.0:0.0:0.2 +16 33948696 . G C 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTGTTGTTGTTGTTGTTG;RSEQ=TGCTGCTGCTGCTGTTGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:21:9,12:21,21:42,21:0.2877:2,2:35.2:1.0:33.1:1.0:0.78947:1.32725:44.4:20.0:0.3279:0.0:4.0 0/0:85:0:0,0:24,28:52,0:0.0:2,0:25.7:1.0:31.0:1.0:1.0:0.0:57.5:104.0:1.0:0.0:0.2 +16 33948711 . T C 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTTGGTGCTGCTGCTGCTG;RSEQ=TGCTGCTGCTGCTGGTGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:21:11,10:23,27:50,21:0.2958:2,2:31.5:1.0:33.2:1.0:0.79516:1.29:43.3:20.0:0.2899:0.0:4.1 0/0:88:0:0,0:26,32:58,0:0.0:2,0:29.4:1.0:29.7:1.0:1.0:0.0:53.8:116.0:1.0:0.0:0.2 +16 52085593 . A G 253 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.04744;LSEQ=CTCCTTTTTCTATGGGGAGA;RSEQ=AATTAATATCCAGGCAGTGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:271:212:98,114:25,34:59,212:0.7823:2,2:25.3:1.0:32.8:1.0:0.6585:1.17:60.0:211.0:0.7815:0.0:1.1 0/1:311:45:23,22:125,141:266,45:0.1447:2,2:27.5:1.0:31.2:1.0:0.63148:1.18:60.0:90.0:0.1456:0.0:1.0 +16 56863229 . T C 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03858;SOR=0.0;LSEQ=CAGCTCCGGGTGGAGAAGAG;RSEQ=GCATGGAGAAGATGTCATTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:0,7:0,23:23,7:0.2333:1,0:22.7:1.0:32.0:0.0:1.0:0.0:60.0:14.0:0.2333:0.0:1.0 0/0:17:0:0,0:0,17:17,0:0.0:1,0:17.7:1.0:29.5:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.3 +16 56866054 . A AT 174 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.02565;LSEQ=GTTCCTCGTCTCCTGTCCCC;RSEQ=TTTTTTGTTGTGTAATTCCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:224:49:20,29:88,87:175,49:0.2188:2,2:28.3:1.0:31.0:1.0:0.26107:1.46415:58.7:48.0:0.2192:0.0268:0.1 0/0:141:1:0,1:71,69:140,1:0.0071:2,0:12.0:0.0:31.0:0.0:0.49645:0.0:60.0:2.0:0.0072:0.0:0.0 +16 56866196 . T C 241 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.11893;LSEQ=ACCAATGCATGTGTTTCTCT;RSEQ=GGGGATTTAGTTGAACCAAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1123:221:130,91:526,376:902,221:0.1968:2,2:24.8:1.0:31.0:1.0:0.93934:1.02:60.0:220.0:0.1984:0.0:1.2 0/1:1202:34:24,10:675,493:1168,34:0.0283:2,2:23.6:1.0:29.2:1.0:0.15959:1.75:60.0:33.0:0.0277:0.0:1.1 +16 56866801 . G T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCTTGAGTGACTTAACAGG;RSEQ=TAAAGGAGATAAACACTCTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:7,1:0,0:0,8:1.0:0,2:21.5:1.0:29.6:1.0:1.0:0.0:56.5:16.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +16 56871762 . T C 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.00044;SOR=0.0;LSEQ=ACAGCTTTCCAAAGTGGTTC;RSEQ=ACTAACTCACCATGCCACCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:15:0,15:2,70:72,15:0.1724:1,1:26.3:1.0:32.3:1.0:1.0:0.0:60.0:30.0:0.1744:0.0:1.0 0/0:56:0:0,0:0,56:56,0:0.0:1,0:23.1:1.0:28.4:1.0:1.0:0.0:60.0:112.0:1.0:0.0:0.0 +16 56872824 . G A 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.15683;LSEQ=CGGATTACACAGAAATTCCT;RSEQ=ATACACTCTTACTACCCCCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:736:169:106,63:383,184:567,169:0.2296:2,2:25.3:1.0:29.4:1.0:0.26558:1.23674:60.0:338.0:0.2312:0.0:1.1 0/1:807:36:24,12:485,285:770,36:0.0446:2,2:19.6:1.0:28.4:1.0:0.72609:1.18:60.0:72.0:0.0454:0.0:1.1 +16 56873613 . T TA 176 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.103;LSEQ=ACAGCTTTAAGAATTCTAGT;RSEQ=ACAGTAACTATCCAGACTGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:240:49:1,48:8,183:191,49:0.2042:1,1:23.0:1.0:31.5:1.0:0.69047:2.09308:60.0:98.0:0.2059:0.0458:0.0 0/1:195:5:1,4:10,180:190,5:0.0256:2,2:13.4:1.0:28.1:1.0:0.2543:4.44:60.0:10.0:0.0259:0.0051:0.0 +16 56873789 . T C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ACAGGTTTCTGGTTGATCTG;RSEQ=GAAGTCTGGTTTAATTCTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:8,7:0.4667:0,0:23.6:1.0:30.3:1.0:1.0:0.0:60.0:14.0:0.4667:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:33.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +16 58032026 . G A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01686;SOR=0.0;LSEQ=TGCAGGAGGATGCCATAGAC;RSEQ=GCACAGCCCAGGGGGTTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:6:5,1:7,2:9,6:0.4:2,2:32.3:1.0:29.5:1.0:1.0:1.4:60.0:5.0:0.3571:0.0:1.2 0/0:14:0:0,0:10,4:14,0:0.0:2,0:22.9:1.0:30.0:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 +16 58960831 . G A 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATACAGTAATTGACCAAGG;RSEQ=TACCAACTATTGTGCTTTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:24:24,0:39,1:40,24:0.375:1,1:21.5:1.0:30.3:1.0:1.0:0.0:57.1:48.0:0.375:0.0:1.2 0/0:45:0:0,0:44,1:45,0:0.0:1,0:22.5:1.0:31.0:1.0:1.0:0.0:58.1:90.0:1.0:0.0:0.0 +16 59584343 . G A 148 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.10373;LSEQ=TTACAAGGAAATGCACAGAT;RSEQ=AGCCTAGGTGAAGATTCGAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:31:15,16:18,18:36,31:0.4627:2,2:26.0:1.0:29.9:1.0:1.0:1.06563:58.5:62.0:0.4627:0.0:1.9 0/1:99:8:4,4:42,49:91,8:0.0808:2,2:24.4:1.0:29.3:1.0:1.0:1.16:60.0:16.0:0.0808:0.0:1.8 +16 59584360 . C T 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0833;LSEQ=GATGAGCCTAGGTGAAGATT;RSEQ=GATCTAAGGTTTTGACTGAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:25:10,15:13,18:31,25:0.4464:2,2:22.3:1.0:30.2:1.0:1.0:1.08178:58.8:24.0:0.4364:0.0:2.0 0/1:81:5:2,3:30,46:76,5:0.0617:2,2:32.4:1.0:30.0:1.0:1.0:1.02:60.0:10.0:0.0625:0.0:2.0 +16 67450281 . T TGGCTCC 86 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=42;MSI=8.0;MSILEN=6.0;SSF=0.01522;SOR=0.15118;LSEQ=GAGTCCTCGAGCTCTGGCTC;RSEQ=GGCTCCGGCTCCGGCTCCGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:5,3:13,16:29,8:0.2162:2,2:14.5:1.0:28.9:1.0:0.44703:2.01:60.0:7.0:0.1944:0.1351:0.0 0/1:51:2:1,1:27,22:49,2:0.0392:2,2:31.5:1.0:30.3:1.0:1.0:1.22232:60.0:4.0:0.0392:0.0:0.0 +16 67645883 . TGCAGTTACA T 214 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGACATTCCAGTGTGAGCTT;RSEQ=CGTGTCCACGGCGTTCAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:111:66,45:227,170:397,111:0.2185:2,2:27.9:1.0:31.6:1.0:0.74457:1.1:59.9:110.0:0.2187:0.0177:0.1 0/0:723:0:0,0:406,317:723,0:0.0:2,0:25.0:1.0:31.5:1.0:1.0:0.0:60.0:102.286:1.0:0.0:0.1 +16 68862182 . A G 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAACGTTTATTACTATGATG;RSEQ=AGAAGGAGGCGGAGAAGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:479:18:8,10:177,283:460,18:0.0376:2,2:31.1:1.0:31.7:1.0:0.62828:1.28:60.0:36.0:0.0385:0.0:1.0 0/0:622:0:0,0:281,341:622,0:0.0:2,0:24.6:1.0:29.1:1.0:1.0:0.0:60.0:50.833:1.0:0.0:0.2 +16 68867456 . C T 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.15792;LSEQ=GCTGGGAAATGCAGAAATCA;RSEQ=GTTGCTGGTGGTTTTTCAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:23:4,19:16,76:92,23:0.2:2,2:20.0:1.0:31.1:1.0:1.0:1.0:60.0:46.0:0.2018:0.0:1.1 0/1:159:6:1,5:29,124:153,6:0.0377:2,2:22.2:1.0:31.2:1.0:1.0:1.16826:60.0:12.0:0.0387:0.0:1.2 +16 72822296 . G A 258 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.15814;LSEQ=GTGGGGTCCGAAGTCAACGC;RSEQ=GCCTGCAGGGCCTGCAGCTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1798:337:185,152:774,684:1458,337:0.1874:2,2:24.5:1.0:30.8:1.0:0.58563:1.08:60.0:36.444:0.185:0.0:1.1 0/1:2132:75:39,36:1077,977:2054,75:0.0352:2,2:25.5:1.0:29.9:1.0:1.0:1.01755:60.0:150.0:0.0356:0.0:1.2 +16 72828383 . C T 246 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01444;LSEQ=TCTTGGCTTCATGCCAGTGA;RSEQ=GGGACCGGATATGAGCCTCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:269:133,136:530,562:1092,269:0.1974:2,2:23.8:1.0:30.5:1.0:0.83817:1.04:60.0:37.429:0.1948:0.0:1.1 0/0:1416:5:2,3:720,690:1410,5:0.0035:2,2:19.2:1.0:28.8:1.0:0.68089:1.56472:60.0:10.0:0.0036:0.0:1.0 +16 72830539 . C G 258 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.16959;LSEQ=TGTTTGGCAAACCTCTCGAG;RSEQ=TGTTTGAAAGGAAAGTAATT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1827:283:140,143:747,793:1540,283:0.1549:2,2:24.2:1.0:31.7:1.0:0.79589:1.04:59.9:55.6:0.1543:0.0:1.2 0/1:1991:60:28,32:939,988:1927,60:0.0301:2,2:30.2:1.0:31.1:1.0:0.79403:1.0861:60.0:120.0:0.0307:0.0:1.2 +16 72832377 . G A 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04323;LSEQ=CAGGCTACACTGATTACAGC;RSEQ=GTACTTGTACACATGGCGAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1538:64:29,35:725,749:1474,64:0.0416:2,2:27.5:1.0:31.6:1.0:0.60999:1.16811:60.0:128.0:0.0421:0.0:1.1 0/0:1602:3:3,0:804,792:1596,3:0.0019:2,0:1.0:0.0:27.7:1.0:0.2496:0.0:60.0:6.0:0.0019:0.0:1.0 +16 72924122 . T C 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATATGGGGGTGGTTCCCCCA;RSEQ=GCTGTTCTTGTGATACTGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:9,5:0.3571:0,0:24.8:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.3846:0.0:1.0 0/0:2:0:0,0:0,2:2,0:0.0:0,0:9.5:1.0:31.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +16 72991696 . TGCC T 119 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=4.0;MSILEN=3.0;SSF=0.00719;SOR=0.15522;LSEQ=CAGGAGCTACTGATATTGGC;RSEQ=GCCGCCGCCGCAGCCACCGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:886:13:8,5:394,477:871,13:0.0147:2,2:22.4:1.0:32.2:1.0:0.2721:1.94:60.0:26.0:0.0149:0.0023:1.4 0/0:868:2:0,2:407,451:858,2:0.0023:2,0:18.5:1.0:27.0:1.0:0.50085:0.0:60.0:4.0:0.0023:0.0012:0.5 +16 72991715 . A G 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGCCGCCGCCGCCGCAGCC;RSEQ=CCGCCGCCGCCGCCGCCCCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:853:294:153,141:268,282:550,294:0.3447:2,2:22.1:1.0:31.1:1.0:0.38609:1.14:60.0:97.0:0.346:0.0:1.6 0/0:806:0:0,0:83,79:162,0:0.0:2,0:22.9:1.0:28.5:1.0:1.0:0.0:60.0:39.5:0.9814:0.0:0.2 +16 72993622 . C T 233 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.14556;LSEQ=CTCAGGCTCTCCACAATGTA;RSEQ=GCGGAGCCGTCCGGCTGGTA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1275:196:88,108:492,586:1078,196:0.1537:2,2:24.4:1.0:30.7:1.0:0.87626:1.03039:60.0:97.0:0.1546:0.0:1.3 0/1:1437:37:16,21:684,711:1395,37:0.0257:2,2:19.5:1.0:29.1:1.0:0.50983:1.26245:60.0:36.0:0.0255:0.0:1.3 +16 72993706 . G A 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.1477;LSEQ=CCCTCCTCACCGGTGTCGCT;RSEQ=GCGCTCTCCTCTCTCAGGGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:193:92,101:586,551:1137,193:0.1449:2,2:22.8:1.0:30.2:1.0:0.35019:1.16742:60.0:63.333:0.1454:0.0:1.3 0/1:1516:37:17,20:716,763:1479,37:0.0244:2,2:22.1:1.0:28.5:1.0:0.86813:1.10391:60.0:74.0:0.0248:0.0:1.3 +16 79167945 . A G 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01786;SOR=0.0;LSEQ=AGAGTTTGTTTCTTCCTGCT;RSEQ=TGGCCATAGAGGTTTGGTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:20.2:1.0:33.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:3:0:0,0:0,3:3,0:0.0:0,0:19.0:1.0:30.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +16 81887820 . C T 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.28327;SOR=0.0;LSEQ=GGGTGAGCGGAAACCCCAAA;RSEQ=TCTTCAGACTCCAGGGGTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:12,1:13,7:0.35:1,0:30.1:1.0:30.1:1.0:1.0:0.0:60.0:14.0:0.35:0.0:1.1 0/0:4:0:0,0:4,0:4,0:0.0:0,0:29.0:1.0:31.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 +16 81887903 . A G 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00101;SOR=0.11808;LSEQ=TCCATTTCCAGAAGGAGGGG;RSEQ=CACTGAGTCCAGACGCAGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:24:24,0:61,2:63,24:0.2759:1,1:29.5:1.0:30.4:1.0:1.0:0.0:60.0:11.0:0.2619:0.0:3.1 0/1:47:2:2,0:43,2:45,2:0.0426:1,0:16.5:1.0:32.0:1.0:1.0:0.0:60.0:4.0:0.0444:0.0:2.0 +16 81887977 . G C 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.05421;LSEQ=AGCCAGGCTGTGCCTGGGCT;RSEQ=CAGTTGTGTGGCTGCATCCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:265:107:96,11:141,17:158,107:0.4038:2,2:24.3:1.0:32.2:1.0:1.0:1.05:60.0:106.0:0.403:0.0:2.2 0/1:227:8:7,1:194,25:219,8:0.0352:2,2:24.1:1.0:31.0:1.0:1.0:1.10801:60.0:16.0:0.0357:0.0:2.0 +16 81888274 . C A 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.07271;LSEQ=CGCTAATAGCAGAATGCTCA;RSEQ=CCCTGCCTGCTCACTGATGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:264:105:10,95:21,138:159,105:0.3977:2,2:26.4:1.0:29.8:1.0:0.43685:1.4437:60.0:34.0:0.3969:0.0:2.0 0/1:263:12:1,11:39,212:251,12:0.0456:2,2:21.2:1.0:29.6:1.0:0.69943:2.01927:60.0:24.0:0.0463:0.0:1.9 +16 81891432 . C G 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCTTGGACACATGACTGAA;RSEQ=CTGTCTTAGGTTCAGTGGTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:33.0:1.0:33.0:1.0:1.0:0.0:57.7:14.0:0.7:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +16 81891790 . C G 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06394;LSEQ=GCTTCTCCCATCTTCGTGAT;RSEQ=TGTATGGGGCAGGGCTTTGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:86:80,6:182,12:194,86:0.3071:2,2:24.7:1.0:32.5:1.0:0.7956:1.13696:60.0:85.0:0.308:0.0:1.2 0/1:255:7:7,0:225,23:248,7:0.0275:2,0:28.1:1.0:30.9:1.0:1.0:0.0:60.0:14.0:0.028:0.0:1.0 +16 81892498 . A T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACTATCATCAGAAGGAATTG;RSEQ=CAATGTAAAGAAACCTGGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:10,1:11,5:0.3125:2,0:27.8:1.0:30.0:1.0:1.0:0.0:60.0:10.0:0.3125:0.0:1.0 0/0:1:0:0,0:1,0:1,0:0.0:0,0:47.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +16 81892913 . C T 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.10021;LSEQ=TGCGGATGCCATGTTGGGTC;RSEQ=TGGGGTTGAGGATGACAAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:37:0,37:0,91:91,37:0.2891:1,1:23.5:1.0:31.5:1.0:1.0:0.0:59.1:74.0:0.296:0.0:1.1 0/1:103:4:0,4:2,97:99,4:0.0388:1,0:26.8:1.0:29.5:1.0:1.0:0.0:60.0:8.0:0.0392:0.0:1.3 +16 81914851 . G GT 88 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.46667;SOR=0.0;LSEQ=TGAGATGTGACAGGTTAATA;RSEQ=TTTTTTTTTTTAATTACAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:8:0,8:0,5:5,8:0.5714:0,0:22.3:1.0:29.5:1.0:1.0:0.0:58.3:16.0:0.5714:0.0:0.1 0/0:2:0:0,0:0,2:2,0:0.0:0,0:18.0:1.0:33.5:1.0:1.0:0.0:41.0:4.0:1.0:0.0:0.0 +16 81917099 . G T 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=6e-05;SOR=0.11666;LSEQ=GTCTTCATGGAACGATTGCA;RSEQ=TCTGCCAGATGCCAGAGACT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:26:0,26:2,65:67,26:0.2796:1,1:20.9:1.0:30.4:1.0:1.0:0.0:60.0:52.0:0.2889:0.0:1.2 0/1:70:3:0,3:2,65:67,3:0.0429:1,0:13.7:1.0:31.7:1.0:1.0:0.0:60.0:6.0:0.0441:0.0:1.0 +16 81941530 . CCTGGCTGGCTTGTCTCTGATTGG C 83 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.0;MSILEN=1.0;SSF=0.32451;SOR=0.0;LSEQ=TGATACTCTGGGTACCATGT;RSEQ=CTGGCTGCCCCAGGTGCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:0,6:3,43:46,6:0.1154:2,0:26.5:1.0:32.3:1.0:1.0:0.0:60.0:12.0:0.1176:0.0192:0.3 0/0:15:0:0,0:3,12:15,0:0.0:2,0:23.1:1.0:30.5:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.3 +16 81946328 . G A 254 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00466;LSEQ=GCCATCACCTTCAGGTGGGT;RSEQ=CGAGGGTGGGAGGCACATGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1285:440:182,258:367,476:843,440:0.3424:2,2:25.0:1.0:29.0:1.0:0.47592:1.09289:60.0:72.333:0.3439:0.0:1.2 0/0:1240:3:3,0:556,681:1237,3:0.0024:2,0:1.0:0.0:23.3:1.0:0.09135:0.0:60.0:6.0:0.0025:0.0:1.0 +16 81955238 . A G 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCTTGCAGTGCAAATGCT;RSEQ=TCTCATATTCCCACCCTGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:0,8:8,7:0.4667:0,0:26.0:1.0:33.6:1.0:1.0:0.0:60.0:14.0:0.4667:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:10.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 +16 81956810 . G C 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.53044;SOR=0.0;LSEQ=AGCCTAACCCTAACCCCAGC;RSEQ=CTAAACCCTAGCCCCAAACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:5,0:11,0:11,5:0.3125:0,0:20.6:1.0:30.2:1.0:1.0:0.0:60.0:10.0:0.3333:0.0:1.4 0/0:3:0:0,0:3,0:3,0:0.0:0,0:26.0:1.0:28.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.3 +16 81957227 . C T 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGAGTGGAGGCTGGGCTGCT;RSEQ=GGCAGGTGGGCTTGACTTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:133:44,89:224,392:616,133:0.1776:2,2:27.2:1.0:30.2:1.0:0.48721:1.1556:60.0:266.0:0.1807:0.0:1.1 0/0:774:0:0,0:284,490:774,0:0.0:2,0:24.8:1.0:29.4:1.0:1.0:0.0:60.0:63.5:1.0:0.0:0.2 +16 81957349 . G T 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00978;SOR=0.0;LSEQ=AGTCCCTTCTTAGGAAGGTG;RSEQ=CTTGGTGCATGCTCTATTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:13:0,13:1,84:85,13:0.1327:1,1:21.6:1.0:29.8:1.0:1.0:0.0:59.8:12.0:0.1237:0.0:1.5 0/0:43:0:0,0:1,42:43,0:0.0:1,0:25.5:1.0:32.0:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.9 +16 81961002 . T C 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.24;SOR=0.0;LSEQ=CGTGTTTTAATCAGGTTGTG;RSEQ=TGGGCTTGGAAGGATTTCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:19:1,18:0,5:5,19:0.7917:0,1:28.6:1.0:32.8:1.0:1.0:0.0:58.6:18.0:0.7826:0.0:2.9 0/0:1:0:0,0:0,1:1,0:0.0:0,0:14.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +16 81961020 . C G 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTTGGGCTTGGAAGGATTT;RSEQ=ATTATGCAGGAGAATTCCCG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:1,16:0,3:3,17:0.85:0,1:29.6:1.0:32.6:1.0:1.0:0.0:59.0:34.0:0.85:0.0:3.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +16 81961022 . T A 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGGGCTTGGAAGGATTTCA;RSEQ=TATGCAGGAGAATTCCCGCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:18:1,17:0,2:2,18:0.9:0,1:27.4:1.0:30.4:1.0:1.0:0.0:59.1:17.0:0.8947:0.0:3.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +16 81961873 . G T 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATAGTCTAGGATGTGTTT;RSEQ=GAAACCAGATCTGAGGAAGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:21:17:17,0:4,0:4,17:0.8095:0,1:29.6:1.0:30.5:1.0:1.0:0.0:58.8:16.0:0.8:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +16 81962531 . T C 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.53602;SOR=0.0;LSEQ=GGATCCATCTGTGTTTCCCA;RSEQ=GCGTTGCGAAGGAAAGCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:8:0,8:0,17:17,8:0.32:1,0:18.8:1.0:31.4:1.0:1.0:0.0:54.0:16.0:0.32:0.0:1.5 0/0:3:0:0,0:0,3:3,0:0.0:0,0:38.7:1.0:29.3:1.0:1.0:0.0:47.3:6.0:1.0:0.0:0.0 +16 81962574 . A C 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTCAGCCTGGCTGAAATGC;RSEQ=GCGTGGAGTTGGGAGTCTTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:0,6:0,4:4,6:0.6:0,0:45.3:1.0:31.0:1.0:1.0:0.0:52.0:12.0:0.6:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +16 81973841 . G C 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00118;SOR=0.0;LSEQ=GTGTAGCACACAGGTGGGAG;RSEQ=AAGTGGGTGACAGGGGAGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:18:0,18:0,26:26,18:0.4091:1,1:22.1:1.0:31.6:1.0:1.0:0.0:60.0:17.0:0.3953:0.0:1.2 0/0:17:0:0,0:1,16:17,0:0.0:1,0:19.7:1.0:31.2:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.6 +16 81990505 . G T 249 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTAGGTCAGCCCCTCCACCT;RSEQ=CAAAAACTTTTGGGGGGTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:959:316:114,202:238,403:641,316:0.3295:2,2:25.2:1.0:30.0:1.0:0.77583:1.04641:60.0:34.111:0.3273:0.0:1.1 0/0:1027:0:0,0:406,618:1024,0:0.0:2,0:25.4:1.0:31.3:1.0:1.0:0.0:60.0:77.769:0.997:0.0:0.2 +16 85490399 . T C 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01947;SOR=0.0;LSEQ=GCTGTGGCGACTCAGGGTCC;RSEQ=GGCGGGGAGAACCTGCCCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:4,5:8,10:18,9:0.3333:2,2:20.0:1.0:27.4:1.0:1.0:1.0:60.0:8.0:0.32:0.0:1.1 0/0:13:0:0,0:4,9:13,0:0.0:2,0:28.2:1.0:29.7:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.1 +16 86601049 . C T 64 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.23077;SOR=0.0;LSEQ=AGCTACGGCGGCATGGCCAG;RSEQ=CCCATGGGCGTCTATTCCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:5,0:6,0:6,5:0.4545:0,0:22.6:1.0:27.8:1.0:1.0:0.0:55.8:4.0:0.4:0.0:1.0 0/0:4:0:0,0:4,0:4,0:0.0:0,0:20.8:1.0:31.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +16 89337526 . G A 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00619;SOR=0.0;LSEQ=CTCCCTAAAATGCGCGTGGA;RSEQ=GCAGCTGGGCCTTTGTCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:19:0,19:1,17:18,19:0.5135:1,1:26.6:1.0:32.3:1.0:0.48649:0.0:59.7:18.0:0.5:0.0:1.2 0/0:9:0:0,0:0,9:9,0:0.0:0,0:20.3:1.0:29.2:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.8 +16 89350597 . C G 246 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTCTCTTTTGAAATTTTGT;RSEQ=CTCTTTTAAATCATTCTTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1731:191:105,86:786,751:1537,191:0.1103:2,2:28.3:1.0:32.5:1.0:0.31973:1.17:48.7:382.0:0.1118:0.0:1.1 0/0:1937:0:0,0:1010,925:1935,0:0.0:2,0:27.0:1.0:30.5:1.0:1.0:0.0:56.7:128.0:0.999:0.0:0.2 +16 89356864 . T G 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00833;SOR=0.0;LSEQ=GGCTCAGGGCTCCAATGGGG;RSEQ=GAGGCTCAGGGCTCCAGCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:38.3:1.0:29.4:1.0:1.0:0.0:22.7:14.0:1.0:0.0:2.0 0/0:3:0:0,0:3,0:3,0:0.0:0,0:11.7:1.0:28.7:1.0:1.0:0.0:35.0:6.0:1.0:0.0:0.0 +16 89809061 . CA C 75 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=22;MSI=23.0;MSILEN=1.0;SSF=0.1235;SOR=0.0;LSEQ=CCCCGTCTCTACTAAAAATA;RSEQ=AAAAAAAAAAAAAAAAAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:7,0:7,5:0.3571:0,0:11.4:1.0:32.7:1.0:1.0:0.0:43.8:10.0:0.3571:0.2143:2.6 0/0:7:0:0,0:7,0:7,0:0.0:0,0:3.4:1.0:29.9:1.0:1.0:0.0:53.1:14.0:1.0:0.0:3.6 +16 89839915 . G A 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0312;SOR=0.0;LSEQ=AGCTGCTGTGTGTGGCAGAC;RSEQ=GAGGGACTGGGAGTCTCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:6:0,6:2,69:71,6:0.0769:1,0:33.0:1.0:32.7:1.0:1.0:0.0:60.0:12.0:0.0769:0.0:1.0 0/0:66:0:0,0:2,64:66,0:0.0:1,0:23.5:1.0:30.6:1.0:1.0:0.0:60.0:65.0:1.0:0.0:0.2 +16 89877720 . C T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.50549;SOR=0.0;LSEQ=TTATACATTGGTATTTGTTA;RSEQ=GTTTCCCATGACACAAAAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:1,4:0,7:7,5:0.4167:0,2:19.4:1.0:31.4:1.0:0.41667:0.0:59.4:10.0:0.4167:0.0:1.0 0/0:2:0:0,0:0,2:2,0:0.0:0,0:10.0:1.0:31.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +17 3568401 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00404;SOR=0.0;LSEQ=TGCTGTGGCTTCTGTAGGTG;RSEQ=GAAGCCCGTCTCACAGGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:8:8,0:16,0:16,8:0.3333:1,0:29.3:1.0:30.1:1.0:1.0:0.0:60.0:16.0:0.3478:0.0:1.1 0/0:22:0:0,0:22,0:22,0:0.0:1,0:24.4:1.0:30.6:1.0:1.0:0.0:60.0:44.0:1.0:0.0:0.1 +17 4540268 . G C 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=5e-05;SOR=0.0;LSEQ=CACTGCAAGGCCTTCGAATA;RSEQ=AGACTTGGCGCATTTCCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:13:7,6:84,80:164,13:0.073:2,2:27.8:1.0:32.8:1.0:1.0:1.11:51.2:26.0:0.0743:0.0:2.0 0/0:195:0:0,0:93,102:195,0:0.0:2,0:27.1:1.0:30.4:1.0:1.0:0.0:45.0:31.5:1.0:0.0:0.5 +17 7577407 . A C 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03318;LSEQ=GTGGATGGGTAGTAGTATGG;RSEQ=AGAAATCGGTAAGAGGTGGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:121:70:56,14:47,4:51,70:0.5785:2,2:22.3:1.0:33.1:1.0:0.07431:2.91375:60.0:140.0:0.5983:0.0:2.0 0/1:163:7:6,1:137,18:155,7:0.0429:2,2:22.7:1.0:31.3:1.0:0.58975:1.2665:60.0:14.0:0.0449:0.0:2.0 +17 7577427 . G A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.03018;LSEQ=AAGAAATCGGTAAGAGGTGG;RSEQ=CCCAGGGGTCAGAGGCAAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:154:93:77,16:54,7:61,93:0.6039:2,2:24.0:1.0:30.3:1.0:0.36527:1.59825:60.0:92.0:0.6053:0.0:1.8 0/1:230:10:8,2:179,38:217,10:0.0435:2,2:25.2:1.0:28.3:1.0:0.69041:1.1767:60.0:20.0:0.0452:0.0:1.7 +17 7578461 . C A 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GTAGATGGCCATGGCGCGGA;RSEQ=GCGGGTGCCGGGCGGGGGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:417:145:79,66:142,130:272,145:0.3477:2,2:20.9:1.0:30.9:1.0:0.68119:1.1:59.9:35.25:0.3447:0.0:1.2 0/0:626:0:0,0:343,281:624,0:0.0:2,0:23.5:1.0:30.0:1.0:1.0:0.0:59.9:61.4:0.9968:0.0:0.2 +17 7580500 . C T 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01571;LSEQ=CTTACTTCAGGTGATCGGCC;RSEQ=GCCTCAGCCTCCTAAAGTGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:64:64,0:30,0:30,64:0.6737:1,1:27.1:1.0:32.9:1.0:1.0:0.0:59.1:128.0:0.6809:0.0:1.0 0/1:98:3:3,0:94,1:95,3:0.0306:1,0:18.7:1.0:30.3:1.0:1.0:0.0:53.0:6.0:0.0319:0.0:1.3 +17 7976917 . A T 184 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTTTGAGGTTGGGGCATGG;RSEQ=CGAAATTTAGAAGGTCTGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:276:87:58,29:145,44:189,87:0.3152:2,2:24.0:1.0:28.7:1.0:0.10561:1.64468:59.9:28.0:0.3111:0.0:1.2 0/0:260:0:0,0:192,67:259,0:0.0:2,0:23.1:1.0:27.8:1.0:1.0:0.0:60.0:22.545:1.0:0.0:0.1 +17 7979468 . C T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01276;SOR=0.0;LSEQ=CAGGTTGTCCACCCTAAGAG;RSEQ=CACCCACTGCTGTCCTGAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:6:3,3:348,209:557,6:0.0107:2,2:20.3:1.0:29.2:1.0:0.67712:1.66343:60.0:12.0:0.0108:0.0:1.7 0/0:599:0:0,0:381,218:599,0:0.0:2,0:25.1:1.0:30.8:1.0:1.0:0.0:60.0:58.9:1.0:0.0:0.7 +17 7983681 . G A 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGATGGGATTCCAGGAAGA;RSEQ=GCCTTCAGAGGGGCTGCCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:40:16,24:105,247:352,40:0.102:2,2:21.6:1.0:30.5:1.0:0.20731:1.57:60.0:39.0:0.101:0.0:1.1 0/0:359:0:0,0:116,243:359,0:0.0:2,0:23.6:1.0:30.5:1.0:1.0:0.0:60.0:88.75:1.0:0.0:0.2 +17 7984157 . A C 224 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.10576;LSEQ=CGGGGAGGAGGCAGGCGCCC;RSEQ=GGGGAAAACCATGGGCGGGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:682:157:91,66:301,224:525,157:0.2302:2,2:25.7:1.0:30.8:1.0:0.92682:1.03:60.0:156.0:0.2332:0.0:1.1 0/1:588:18:10,8:304,263:567,18:0.0306:2,2:21.0:1.0:27.8:1.0:1.0:1.08:60.0:8.0:0.0278:0.0:1.2 +17 7984552 . G A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.07294;SOR=0.1595;LSEQ=AAGGGCTGACCCTTGCCCCT;RSEQ=CCCACTTCAGGAAGCAGGAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:7:5,2:116,245:361,7:0.019:2,2:12.3:1.0:26.0:1.0:0.04118:5.25:60.0:14.0:0.0194:0.0:1.0 0/0:325:1:1,0:116,207:323,1:0.0031:2,0:1.0:0.0:22.0:0.0:0.36111:0.0:60.0:2.0:0.0032:0.0:1.0 +17 12043531 . A AG 74 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAAGAAAAAAATTAGTGAAA;RSEQ=TTTGTGTTTATTCTGCCTTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:20.6:1.0:32.1:1.0:1.0:0.0:60.0:10.0:1.0:0.2:0.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 15977132 . T C 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.44444;SOR=0.0;LSEQ=AAATTAAGTCCCTTTCTGCA;RSEQ=GAAACTTACACAATAATGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:16.4:1.0:30.8:1.0:1.0:0.0:59.2:10.0:0.625:0.0:1.4 0/0:1:0:0,0:0,1:1,0:0.0:0,0:13.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +17 15983458 . G A 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAAACAGCCCCTACTTGGGA;RSEQ=AGTACTCAACTAAGAAGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:82:10,72:6,113:119,82:0.408:2,2:24.8:1.0:31.0:1.0:0.10896:2.6:60.0:81.0:0.4091:0.0:1.1 0/0:190:0:0,0:17,173:190,0:0.0:2,0:24.7:1.0:30.9:1.0:1.0:0.0:60.0:380.0:1.0:0.0:0.0 +17 16041777 . C T 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=GGGATGGTGGCACATGCCTG;RSEQ=AGTCCCACCTACTCAGGAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:26.8:1.0:28.4:1.0:1.0:0.0:30.2:10.0:0.7143:0.0:2.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:13.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +17 16041792 . A G 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCTGCAGTCCCACCTACTC;RSEQ=GGAAGCTGAGGCAGGAGAAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:17.8:1.0:31.4:1.0:1.0:0.0:30.2:10.0:0.7143:0.0:2.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 16049563 . C A 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00372;SOR=0.0;LSEQ=CTCCACTATTGTCCTATGAC;RSEQ=CTGCCAAATCCCCCTCTCCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:9:9,0:51,0:51,9:0.15:1,0:15.0:1.0:31.9:1.0:1.0:0.0:46.3:18.0:0.15:0.0:1.9 0/0:50:0:0,0:50,0:50,0:0.0:1,0:15.2:1.0:31.6:1.0:1.0:0.0:48.8:100.0:1.0:0.0:0.6 +17 16049641 . TA T 68 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.01289;SOR=0.0;LSEQ=TTTTTAAAAAAAAGAAACAA;RSEQ=AATATTTGAAGAAAAATATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:5:2,3:348,134:482,5:0.0103:2,2:20.2:1.0:29.4:1.0:0.13815:3.88273:60.0:10.0:0.0104:0.0041:0.6 0/0:673:0:0,0:468,205:673,0:0.0:2,0:23.4:1.0:28.0:1.0:1.0:0.0:59.7:167.25:1.0:0.0:0.5 +17 17125595 . A G 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00179;SOR=0.0;LSEQ=CAGGAAGAAGTGAGTTCCAC;RSEQ=TCAATATGTTTTCAGCACAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:13:13,0:0,0:0,13:1.0:0,1:23.3:1.0:30.1:1.0:1.0:0.0:57.5:26.0:1.0:0.0:1.1 0/0:3:0:0,0:3,0:3,0:0.0:0,0:19.3:1.0:30.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +17 21544599 . A G 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.09779;LSEQ=AAACTGAAAAAGAAACAAGT;RSEQ=AAAGTCTTTGCTTATAATAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:355:115:31,84:84,156:240,115:0.3239:2,2:33.1:1.0:32.0:1.0:0.1465:1.45753:39.5:37.333:0.3191:0.0:1.0 0/1:336:15:6,9:116,205:321,15:0.0446:2,2:31.3:1.0:30.7:1.0:0.7875:1.18:39.6:30.0:0.0453:0.0:1.1 +17 29482701 . C T 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATAGTGCTGGATAAAGAATT;RSEQ=TATTTTGTAGATAGAGATTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1.0:0,2:23.0:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 29533685 . CTTTTGAACAAAAATA C 82 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGTTTTTTTTCTCCTTAAAA;RSEQ=TTTTGATTAGCCTCTCACGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1.0:0,2:20.0:1.0:31.9:1.0:1.0:0.0:59.0:12.0:1.0:0.5:0.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 29553719 . GT G 73 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.02233;SOR=0.0;LSEQ=ACAGGTAAATGTGAATAGTG;RSEQ=TTTTTTTACTCAGTCTGCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:304:5:2,3:69,229:298,5:0.0164:2,2:31.2:1.0:31.6:1.0:0.33392:2.21:44.2:10.0:0.0167:0.0:1.0 0/0:344:0:0,0:117,227:344,0:0.0:2,0:25.6:1.0:28.7:1.0:1.0:0.0:58.5:56.333:1.0:0.0:0.1 +17 29585907 . T C 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.17994;SOR=0.0;LSEQ=AGAAACACTACCTAAAATAA;RSEQ=TTATAGAATGAGGAATGTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:8:8,0:33,5:38,8:0.1739:2,0:25.1:1.0:31.0:1.0:0.5692:0.0:60.0:16.0:0.1739:0.0:1.0 0/0:13:0:0,0:13,0:13,0:0.0:1,0:31.1:1.0:29.4:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 +17 29587341 . G C 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTAATTCAAACATAAGTCT;RSEQ=GGTGTATCTGGTGTTGAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:404:69:44,25:235,100:335,69:0.1708:2,2:23.2:1.0:29.8:1.0:0.31797:1.33429:59.8:22.0:0.1654:0.0:1.2 0/0:442:0:0,0:278,164:442,0:0.0:2,0:24.6:1.0:30.6:1.0:1.0:0.0:59.9:43.2:1.0:0.0:0.1 +17 29663623 . TTT AAA 62 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=11.0;MSILEN=1.0;SSF=0.06469;SOR=0.0;LSEQ=TTGAGTCCCATGTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:453:5:3,2:293,130:423,5:0.011:2,2:26.4:1.0:26.9:1.0:0.64614:1.50104:56.0:10.0:0.0111:0.0:2.0 0/0:395:0:0,0:249,137:386,0:0.0:2,0:23.3:1.0:29.1:1.0:1.0:0.0:59.0:76.2:0.9769:0.0:1.1 +17 29663625 . T A 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=11.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGTCCCATGTTTTTTTTTT;RSEQ=AAAAAAAAAAATCCTGCTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:463:125:74,51:39,19:58,125:0.27:2,2:19.5:1.0:28.9:1.0:0.32978:1.412:59.9:40.667:0.5351:0.0:1.4 0/0:422:0:0,0:61,36:97,0:0.0:2,0:22.8:1.0:27.4:1.0:1.0:0.0:59.2:15.167:0.3033:0.0:0.6 +17 29665081 . C T 54 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.12177;SOR=0.1962;LSEQ=TCCATCCCTGCAACCAAGAG;RSEQ=TCTTGTTGTCTTTGGGTGTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:5:0,5:274,206:480,5:0.0103:2,0:9.2:1.0:23.6:1.0:0.01517:0.0:60.0:4.0:0.0084:0.0:2.0 0/0:491:1:0,1:260,229:489,1:0.002:2,0:1.0:0.0:23.0:0.0:0.46939:0.0:60.0:2.0:0.0021:0.0:1.0 +17 30315470 . C T 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTAGAAATTCAGAGAGTCT;RSEQ=CATCAGGAAAACAAGCCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:179:85,94:368,400:768,179:0.1888:2,2:26.4:1.0:30.7:1.0:0.93395:1.0174:60.0:358.0:0.191:0.0:1.1 0/0:1115:0:0,0:542,572:1114,0:0.0:2,0:26.1:1.0:30.4:1.0:1.0:0.0:60.0:84.692:1.0:0.0:0.1 +17 33430327 . C A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02951;LSEQ=TTCAGCTCTCGGGCCAGCTG;RSEQ=ATCATCAAGGCCAAGCCTGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:977:89:41,48:420,467:887,89:0.0911:2,2:26.6:1.0:30.1:1.0:0.82488:1.05287:60.0:21.25:0.0892:0.0:1.2 0/0:1018:3:3,0:442,572:1014,3:0.0029:2,0:1.0:0.0:23.0:1.0:0.08346:0.0:60.0:6.0:0.003:0.0:1.3 +17 37618220 . C T 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00227;SOR=0.0;LSEQ=TGCCCTCCCCACCCCCTTCC;RSEQ=GGGGCGCTTTGGTGGGCGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:14:14,0:85,4:89,14:0.1359:1,1:21.7:1.0:32.6:1.0:1.0:0.0:60.0:28.0:0.1414:0.0:1.0 0/0:60:0:0,0:57,3:60,0:0.0:2,0:24.2:1.0:30.0:1.0:1.0:0.0:60.0:29.0:1.0:0.0:0.3 +17 37646947 . C T 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03014;LSEQ=AGACTCTCCAGAACCAAAGG;RSEQ=AATCACACCACCTCAGCAAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:876:32:17,15:362,482:844,32:0.0365:2,2:27.3:1.0:29.1:1.0:0.27817:1.51:60.0:64.0:0.0369:0.0:1.1 0/0:877:1:0,1:395,481:876,1:0.0011:2,0:1.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0012:0.0:1.0 +17 37657481 . AT A 72 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.06456;SOR=0.0;LSEQ=TTTTTTTTTTCTTGCTTTTA;RSEQ=TTTTTTTCGTCTTTATGTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:491:5:3,2:330,155:485,5:0.0102:2,2:35.2:1.0:31.4:1.0:0.65747:1.41832:60.0:10.0:0.0104:0.002:0.0 0/0:430:0:0,0:269,159:428,0:0.0:2,0:25.9:1.0:29.4:1.0:1.0:0.0:59.7:106.0:0.9953:0.0:0.3 +17 37687968 . A G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTAAAGTTTTGGGGTGGGGG;RSEQ=TTGTGTGTGGTTTCTTTCTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:38.2:1.0:32.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 37866797 . G T 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGTTTGTTTCTGTAAATGG;RSEQ=AGCATATGGGGAGCACTGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:34:5,29:35,155:190,34:0.1504:2,2:24.6:1.0:27.5:1.0:0.80826:1.30817:60.0:33.0:0.15:0.0:1.0 0/0:149:0:0,0:27,122:149,0:0.0:2,0:20.8:1.0:30.4:1.0:1.0:0.0:60.0:148.0:1.0:0.0:0.2 +17 37871848 . G A 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCAGGGAGGAGTCCCTGTG;RSEQ=GAAGCTTTGGGCCTGAGGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:405:49:19,30:134,222:356,49:0.121:2,2:26.1:1.0:31.2:1.0:0.87633:1.05:60.0:48.0:0.1209:0.0:1.0 0/0:228:0:0,0:64,164:228,0:0.0:2,0:24.1:1.0:30.2:1.0:1.0:0.0:60.0:31.571:1.0:0.0:0.2 +17 37880997 . G GTGT 286 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=4.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGGAAGCATACGTGATGGCT;RSEQ=GTGTGGGCTCCCCATATGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1440:624:314,310:419,389:808,624:0.4333:2,2:25.4:1.0:30.9:1.0:0.59401:1.06334:59.7:623.0:0.436:0.0778:0.2 0/0:1125:0:0,0:580,543:1123,0:0.0:2,0:26.2:1.0:30.8:1.0:1.0:0.0:59.9:79.214:0.9991:0.0:0.2 +17 38497450 . G A 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.20164;SOR=0.0;LSEQ=TAGTCCACTGGAAGGCACCA;RSEQ=CTCTTCCTTTTATCTCTCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:9,0:78,1:79,9:0.1023:1,0:27.6:1.0:30.6:1.0:1.0:0.0:60.0:18.0:0.1023:0.0:1.1 0/0:21:0:0,0:20,1:21,0:0.0:1,0:24.5:1.0:31.8:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.1 +17 38497833 . G A 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02798;LSEQ=GCTGGCGGGCGAGCCCCGCG;RSEQ=GCGGGCTGGCGAGCGGGTGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:693:38:21,17:427,227:654,38:0.0548:2,2:28.3:1.0:29.7:1.0:0.22381:1.52185:60.0:11.667:0.0515:0.0:1.2 0/0:618:1:1,0:377,239:616,1:0.0016:2,0:1.0:0.0:27.0:0.0:1.0:0.0:57.0:2.0:0.0016:0.0:1.0 +17 38497884 . G A 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00818;LSEQ=AGCGGTGGGTGGGTCACTCG;RSEQ=AGGTGAGGCGCCGCCAGGCG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:109:55,54:356,275:631,109:0.1467:2,2:24.7:1.0:29.6:1.0:0.25284:1.27058:60.0:26.25:0.1446:0.0:1.1 0/0:713:1:1,0:371,341:712,1:0.0014:2,0:1.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.0014:0.0:1.0 +17 38512197 . T C 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08565;LSEQ=TTCCCACCTCGAGCCAGGCT;RSEQ=GCTGGGGCTGGGGGTGGGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:341:145:119,26:162,34:196,145:0.4252:2,2:24.4:1.0:31.7:1.0:0.88674:1.04093:60.0:71.5:0.4231:0.0:1.1 0/1:219:13:11,2:164,42:206,13:0.0594:2,2:28.1:1.0:28.5:1.0:1.0:1.41:60.0:12.0:0.0556:0.0:1.5 +17 38512457 . C G 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCAGCTCCAACAGAAGCAG;RSEQ=CCGGCCACCCACTCCCCGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1138:41:15,26:488,606:1094,41:0.036:2,2:24.3:1.0:31.1:1.0:0.34009:1.39542:60.0:19.5:0.0349:0.0:2.2 0/0:857:0:0,0:396,458:854,0:0.0:2,0:25.3:1.0:30.5:1.0:1.0:0.0:59.9:36.13:0.9964:0.0:0.3 +17 38512461 . G T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03168;LSEQ=GCTCCAACAGAAGCAGCCCG;RSEQ=CCACCCACTCCCCGTGACCG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1134:40:14,26:495,597:1092,40:0.0353:2,2:25.8:1.0:29.7:1.0:0.25713:1.53927:60.0:39.0:0.0357:0.0:2.2 0/0:865:1:0,1:404,457:861,1:0.0012:2,0:6.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0012:0.0:1.0 +17 39874283 . T A 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.16667;SOR=0.0;LSEQ=GTCCTCGGCTGGGGCTCTGT;RSEQ=ATAAAAGACAGATTACAAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:24.8:1.0:29.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.6 0/0:1:0:0,0:1,0:1,0:0.0:0,0:27.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +17 40458193 . TTG T 92 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.0;MSILEN=2.0;SSF=0.01301;SOR=0.0;LSEQ=TCTCTAGGTGTCTGTGTATC;RSEQ=TGTGTGTGTGAATATTTCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:758:9:4,5:622,126:748,9:0.0119:2,2:19.7:1.0:29.1:1.0:0.01009:6.1484:60.0:8.0:0.0108:0.0026:0.2 0/0:524:0:0,0:432,92:524,0:0.0:2,0:21.7:1.0:29.7:1.0:1.0:0.0:60.0:64.5:1.0:0.0:0.1 +17 40458742 . CT C 89 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAGATGTGTTTGCTAATTTT;RSEQ=TTTTTTTTTTTAGAGACAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:7:0,7:0,26:26,7:0.2121:1,0:31.7:1.0:32.0:1.0:1.0:0.0:54.3:14.0:0.2121:0.0:0.4 0/0:3:0:0,0:0,3:3,0:0.0:0,0:11.3:1.0:30.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +17 40467934 . C T 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.03784;SOR=0.1384;LSEQ=CACTGCTATCCAATCTCCTG;RSEQ=CCCTTAAGGCCCAGGGATGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:12:0,12:15,343:358,12:0.0324:1,0:30.5:1.0:31.1:1.0:1.0:0.0:60.0:24.0:0.0335:0.0:1.0 0/0:217:1:0,1:12,204:216,1:0.0046:2,0:1.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0047:0.0:1.0 +17 40489660 . C T 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CCTCAGACTGTCTCTAACCA;RSEQ=ATTCTTTAGTCAACTCCAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:774:37:13,24:299,436:735,37:0.0478:2,2:24.6:1.0:29.8:1.0:0.60735:1.26568:60.0:74.0:0.0485:0.0:1.1 0/0:697:0:0,0:266,429:695,0:0.0:2,0:21.8:1.0:31.4:1.0:1.0:0.0:60.0:172.75:0.9971:0.0:0.1 +17 41231216 . C CA 79 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.06589;SOR=0.16068;LSEQ=AAAAACAAAACAAAACAAAA;RSEQ=AAAAAAAATGAAAGGCAGAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:442:6:4,2:365,70:435,6:0.0136:2,2:21.2:1.0:30.7:1.0:0.25453:2.59966:60.0:12.0:0.0137:0.0068:0.0 0/0:454:1:1,0:348,103:451,1:0.0022:2,0:30.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0022:0.0:0.0 +17 41244880 . C G 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTTTGTTTCTTTAAGGACC;RSEQ=AGAGTGGGCAGAGAATGTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:604:56:33,23:277,269:546,56:0.0927:2,2:24.8:1.0:31.5:1.0:0.26351:1.39:60.0:112.0:0.0952:0.0:1.1 0/0:502:0:0,0:259,241:500,0:0.0:2,0:23.9:1.0:30.7:1.0:1.0:0.0:59.9:82.333:0.996:0.0:0.2 +17 41245586 . C CT 116 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.00106;SOR=0.07657;LSEQ=CTGACTGGCATTTGGTTGTA;RSEQ=TTTTTTTTCTTTATCTCTTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1020:14:4,10:426,577:1003,14:0.0137:2,2:23.3:1.0:30.6:1.0:0.41611:1.84471:60.0:28.0:0.0139:0.0029:0.0 0/0:940:1:1,0:392,543:935,1:0.0011:2,0:28.0:0.0:33.0:0.0:0.41987:0.0:60.0:2.0:0.0011:0.0:1.0 +17 41267608 . G C 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03751;SOR=0.0;LSEQ=ACTATATACTCTCTGAGAAA;RSEQ=AATGAAATGGAGTTGGATTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:161:6:6,0:152,2:154,6:0.0373:1,0:18.5:1.0:32.5:1.0:1.0:0.0:60.0:12.0:0.0387:0.0:1.0 0/0:124:0:0,0:121,3:124,0:0.0:1,0:25.1:1.0:31.5:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 +17 43344458 . C A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCGGGGCCACAACCGACTCA;RSEQ=CTTCTCACTGTCATCCGACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:576:28:19,9:367,181:548,28:0.0486:2,2:24.8:1.0:29.5:1.0:1.0:1.04:60.0:56.0:0.0494:0.0:1.2 0/0:498:0:0,0:324,173:497,0:0.0:2,0:22.7:1.0:31.1:1.0:1.0:0.0:60.0:123.25:0.998:0.0:0.1 +17 43347610 . C T 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01996;LSEQ=GCGCTGCCTCTGGGTCCAGG;RSEQ=GTGGCACTGTCGCAATCTCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:127:109:109,0:17,0:17,109:0.8583:1,1:26.5:1.0:30.1:1.0:1.0:0.0:59.7:108.0:0.864:0.0:1.1 0/1:48:5:5,0:42,1:43,5:0.1042:1,0:27.6:1.0:29.2:1.0:1.0:0.0:60.0:10.0:0.1042:0.0:1.2 +17 43348887 . G A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CATGCCCAGCTAATTTTTAT;RSEQ=TTTTTGTAGAGATGGGGTTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1.0:0,0:25.4:1.0:32.5:1.0:1.0:0.0:31.4:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 43350514 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACTGTGCTTCCAGCCAACC;RSEQ=TGCTCAGAGGCGCAGGAGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:15.4:1.0:31.0:1.0:1.0:0.0:59.4:10.0:0.8333:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 43352049 . C T 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=2.0;SSF=0.0;SOR=0.00891;LSEQ=CAGCACCCTAGTGCTCCACA;RSEQ=ACAGAGGCTGCTGCTGTTTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:297:267:14,253:1,28:29,267:0.899:1,2:24.4:1.0:28.4:1.0:1.0:1.55:60.0:52.4:0.8973:0.0:1.1 0/1:125:9:0,9:7,109:116,9:0.072:2,0:15.3:1.0:26.6:1.0:1.0:0.0:60.0:8.0:0.0656:0.0:1.1 +17 46801231 . G C 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01686;SOR=0.0;LSEQ=GAAATTATTTCGGGCCTGGA;RSEQ=CCCGCGTAGACGCGACCCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:10:0,10:3,191:194,10:0.049:1,0:28.6:1.0:30.1:1.0:1.0:0.0:60.0:9.0:0.0446:0.0:1.0 0/0:109:0:0,0:3,106:109,0:0.0:1,0:26.1:1.0:31.7:1.0:1.0:0.0:60.0:35.333:1.0:0.0:0.0 +17 47685477 . AATAC A 113 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02254;SOR=0.0;LSEQ=AACAATAAGTAACTAATTAT;RSEQ=ATAAAGGAAAATAAGAAACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:12:0,12:0,22:22,12:0.3529:1,0:26.4:1.0:31.7:1.0:1.0:0.0:60.0:24.0:0.375:0.0294:0.0 0/0:11:0:0,0:0,11:11,0:0.0:0,0:21.8:1.0:31.1:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.0 +17 51931075 . C T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01373;SOR=0.0;LSEQ=ATCATCAGCATCATCAACAA;RSEQ=GACAACAACAACAACAAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:3,2:4,2:6,5:0.4545:2,2:35.4:1.0:30.0:1.0:1.0:1.29868:60.0:10.0:0.4545:0.0:1.6 0/0:12:0:0,0:6,6:12,0:0.0:2,0:10.6:1.0:30.2:1.0:1.0:0.0:56.3:24.0:1.0:0.0:0.6 +17 56440474 . G A 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.00013;SOR=0.0;LSEQ=GTAGGTGAGGCCCAAAGACG;RSEQ=GGGAAAACTTGCCCAGAGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:27:27,0:131,4:135,27:0.1667:1,1:19.3:1.0:30.7:1.0:1.0:0.0:60.0:26.0:0.1635:0.0:2.7 0/0:61:0:0,0:60,1:61,0:0.0:1,0:26.8:1.0:31.3:1.0:1.0:0.0:60.0:122.0:1.0:0.0:0.3 +17 56440642 . C T 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.03394;LSEQ=TCTAGTGTGCTTACCCAGGC;RSEQ=GGGGGCTCCTTCAGCTCAAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1696:78:43,35:857,761:1618,78:0.046:2,2:24.0:1.0:30.1:1.0:0.72897:1.09:60.0:12.0:0.0434:0.0:1.1 0/0:1225:2:0,2:649,572:1221,2:0.0016:2,0:1.0:0.0:28.5:1.0:0.22007:0.0:60.0:4.0:0.0017:0.0:1.0 +17 58678009 . T A 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00606;LSEQ=GCCCGAGAGGCTCGCGACCC;RSEQ=CTCCCGGACGCCGGGGCCTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:853:145:79,66:375,329:704,145:0.17:2,2:23.2:1.0:30.6:1.0:0.85499:1.05:60.0:144.0:0.1735:0.0:1.1 0/0:808:1:1,0:440,366:806,1:0.0012:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0013:0.0:1.0 +17 59761706 . A G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCTAATGTTTCCTAGCCCA;RSEQ=GTTATAATGCTGTCTGGTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:25.8:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:32.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 +17 59924512 . C T 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02023;LSEQ=CAGTGGAGAGTTGAGTTTTA;RSEQ=AGTCTTTCCTGAATCAACTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1267:56:26,30:616,593:1209,56:0.0442:2,2:21.6:1.0:29.1:1.0:0.58495:1.19843:60.0:112.0:0.0446:0.0:1.1 0/0:1071:1:0,1:520,550:1070,1:0.0009:2,0:1.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.0009:0.0:1.0 +17 59926645 . C T 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGTAATTTAAAAAAAACAG;RSEQ=ATAAATAACTTACAGGTAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:138:32,106:47,146:193,138:0.4157:2,2:20.4:1.0:28.8:1.0:0.89607:1.06617:59.9:276.0:0.4169:0.0:1.1 0/0:210:0:0,0:54,156:210,0:0.0:2,0:23.0:1.0:31.2:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.1 +17 59926837 . A AT 78 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATAGGAAAAGTCCAATTTG;RSEQ=TTTTTTAAATCGCCTTATGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:0,6:0,8:8,6:0.4286:0,0:34.3:1.0:30.2:1.0:1.0:0.0:57.0:12.0:0.4286:0.0:0.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:42.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +17 61878535 . G A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00699;SOR=0.0;LSEQ=TCTGCCTGCCTCAGCCTCCT;RSEQ=GGTAACTGGGATTACAGGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:3,5:0,1:1,8:0.8889:0,2:38.1:1.0:29.6:1.0:1.0:0.0:60.0:7.0:0.875:0.0:1.4 0/0:4:0:0,0:1,3:4,0:0.0:2,0:25.5:1.0:29.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +17 62008760 . G A 248 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCAGCTGCTGGGTGGGAG;RSEQ=AAGTGGGCGGGGCCAGTCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:290:113,177:282,396:678,290:0.299:2,2:26.7:1.0:30.4:1.0:0.47553:1.11532:60.0:47.333:0.298:0.0:1.2 0/0:713:0:0,0:294,419:713,0:0.0:2,0:25.1:1.0:30.1:1.0:1.0:0.0:60.0:46.533:1.0:0.0:0.2 +17 63313715 . A T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAATCATTACATCAGCTCTG;RSEQ=GTGGCAGGTTCTTTGATTGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:1,0:1,5:0.7143:0,0:32.4:1.0:31.2:1.0:1.0:0.0:59.4:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 63532779 . T TA 88 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.06011;SOR=0.0;LSEQ=ATTCTGCTCAGAGAGAGAGT;RSEQ=AAAAAAAAAACTACCATAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:9:2,7:40,47:87,9:0.0938:2,2:34.1:1.0:28.0:1.0:0.29081:2.94815:60.0:8.0:0.087:0.0:1.0 0/0:38:0:0,0:7,31:38,0:0.0:2,0:25.0:1.0:27.7:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.9 +17 64938402 . GG TT 104 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0033;SOR=0.0;LSEQ=CTCCTGTGACCATTATTTCA;RSEQ=AAACAAACTCCTTTAAACCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:11:1,10:58,124:182,11:0.057:2,2:18.7:1.0:30.1:1.0:0.17751:4.65062:60.0:22.0:0.0576:0.0052:0.9 0/0:137:0:0,0:43,94:137,0:0.0:2,0:24.2:1.0:30.5:1.0:1.0:0.0:60.0:44.667:1.0:0.0:0.3 +17 70120111 . G A 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00271;SOR=0.0;LSEQ=GCGCCCCCACAGCAGCCGGC;RSEQ=GCACCCCCGCAGCAGCCACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:20:18,2:173,13:186,20:0.0971:2,2:22.1:1.0:31.3:1.0:0.64418:1.47542:60.0:40.0:0.0995:0.0:1.1 0/0:74:0:0,0:66,8:74,0:0.0:2,0:20.4:1.0:30.3:1.0:1.0:0.0:59.8:148.0:1.0:0.0:0.1 +17 72843378 . C T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.50549;SOR=0.0;LSEQ=CCAGACTCGACTGTCCAGGG;RSEQ=CTGCCCACTCACGGCCTGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:6,0:6,5:0.4167:0,0:17.6:1.0:32.0:0.0:1.0:0.0:60.0:10.0:0.4545:0.0:2.0 0/0:2:0:0,0:1,1:2,0:0.0:2,0:38.5:1.0:31.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.0 +17 72843411 . GC G 95 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.28327;SOR=0.0;LSEQ=GGCCTGTCCCCACCCTCAGT;RSEQ=CCCCCCCCACCCCCAGCAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:7,0:13,0:13,7:0.35:1,0:36.4:1.0:34.0:1.0:1.0:0.0:60.0:14.0:0.3684:0.0:1.4 0/0:4:0:0,0:3,1:4,0:0.0:2,0:19.0:1.0:32.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.8 +17 72904115 . G A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.27778;SOR=0.0;LSEQ=AGCCTTTTCCTGTAAACGCC;RSEQ=GGTGGCATCTCTTACTATCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:1,4:5,4:9,5:0.3571:2,2:39.2:1.0:33.0:1.0:0.3007:4.45211:43.4:10.0:0.3571:0.0:1.0 0/0:4:0:0,0:1,3:4,0:0.0:2,0:33.8:1.0:26.0:1.0:1.0:0.0:46.0:3.0:1.0:0.0:0.0 +17 77280452 . A G 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTTTCTTCAATGTTTTGTT;RSEQ=TTCCAAATCCACAACCCAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:37:1,36:1,24:25,37:0.5968:1,1:28.1:1.0:33.1:1.0:1.0:1.48993:59.4:74.0:0.5968:0.0:1.0 0/0:27:0:0,0:1,26:27,0:0.0:1,0:24.0:1.0:31.1:1.0:1.0:0.0:60.0:54.0:1.0:0.0:0.4 +17 77386106 . T G 76 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00782;SOR=0.0;LSEQ=GCCTCCAGGTCTCCGCAGCC;RSEQ=CCAGGTCTCCGTAGCCTCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:8:7,1:16,18:34,8:0.1905:2,2:7.4:1.0:25.4:1.0:0.05408:7.54:37.1:7.0:0.1795:0.0:2.0 0/0:33:0:0,0:23,10:33,0:0.0:2,0:23.7:1.0:28.1:1.0:1.0:0.0:38.3:7.25:1.0:0.0:1.0 +17 77386109 . A G 62 p8;q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03005;SOR=0.0;LSEQ=TCCAGGTCTCCGCAGCCTCC;RSEQ=GGTCTCCGTAGCCTCCAGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:6:6,0:17,20:37,6:0.1395:2,0:6.2:1.0:24.0:1.0:0.02292:0.0:33.0:5.0:0.125:0.0:2.3 0/0:35:0:0,0:24,11:35,0:0.0:2,0:24.5:1.0:29.3:1.0:1.0:0.0:39.5:34.0:1.0:0.0:0.9 +17 77386118 . T C 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06595;LSEQ=CCGCAGCCTCCAGGTCTCCG;RSEQ=AGCCTCCAGGTCTCCGCAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:34:15,19:10,6:16,34:0.68:2,2:17.1:1.0:31.9:1.0:0.3635:2.0794:45.2:33.0:0.6875:0.0:1.4 0/1:42:5:4,1:23,14:37,5:0.119:2,2:5.4:1.0:31.0:1.0:0.63896:2.39:34.6:10.0:0.1282:0.0:1.6 +17 78765080 . A C 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00097;SOR=0.0996;LSEQ=GCCTTGACAGAATGGCAATG;RSEQ=GATTTTCTTTACAAATCTAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:19:19,0:22,0:22,19:0.4634:1,1:21.6:1.0:32.8:1.0:1.0:0.0:60.0:38.0:0.4872:0.0:1.1 0/1:26:2:2,0:22,2:24,2:0.0769:2,0:9.5:1.0:32.0:1.0:1.0:0.0:60.0:4.0:0.0769:0.0:1.0 +17 78796361 . T A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GACCGGTGCACAGCCCTTAC;RSEQ=GCGCACCGGCGGCTTATCTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:30.0:1.0:31.2:1.0:1.0:0.0:59.6:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 78796907 . C G 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAAAGCTCTTCAGACAGGA;RSEQ=TTGCTGGTGGCTAGTCTGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:37:22,15:385,304:689,37:0.0508:2,2:25.6:1.0:32.6:1.0:0.73556:1.16:60.0:74.0:0.0514:0.0:1.1 0/0:620:0:0,0:336,283:619,0:0.0:2,0:25.3:1.0:31.1:1.0:1.0:0.0:60.0:87.429:1.0:0.0:0.2 +17 78829114 . G C 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.15805;SOR=0.0;LSEQ=CTAAAAGCATGAACTTGTAA;RSEQ=GAAAGGAGCACCAGCTCTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:5:5,0:85,1:86,5:0.0549:1,0:29.0:1.0:33.2:1.0:1.0:0.0:55.8:10.0:0.0562:0.0:1.0 0/0:53:0:0,0:52,1:53,0:0.0:1,0:24.5:1.0:31.7:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.1 +17 78857631 . C T 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03123;LSEQ=ATCTGCCTGGAGCAGCTCAA;RSEQ=GACCCGCACCCCTTGCTGCG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:861:40:17,23:397,424:821,40:0.0465:2,2:27.5:1.0:30.5:1.0:0.5191:1.26644:60.0:39.0:0.0461:0.0:1.1 0/0:659:1:0,1:342,316:658,1:0.0015:2,0:1.0:0.0:23.0:0.0:0.48103:0.0:60.0:2.0:0.0015:0.0:1.0 +17 78882329 . G A 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.125;SOR=0.0;LSEQ=GTGGTCATGCCCTCCGATCC;RSEQ=CTGAGGCATTTCAAGGAAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:31.4:1.0:30.4:1.0:1.0:0.0:59.3:14.0:1.0:0.0:1.1 0/0:1:0:0,0:1,0:1,0:0.0:0,0:49.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +17 78897732 . CT TA 116 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00735;SOR=0.0;LSEQ=TGCACTCTTTAGGAGCACTG;RSEQ=GGGTGTGTCCCGGTTCTCCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:15:0,15:0,0:0,15:1.0:0,1:26.0:1.0:29.9:1.0:1.0:0.0:60.0:30.0:1.0:0.0:1.4 0/0:2:0:0,0:1,1:2,0:0.0:2,0:9.0:0.0:33.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 +17 78919466 . G T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTGTGTGTTTCTTTTGACA;RSEQ=GCATTACGAGATTGGACGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1178:37:21,16:631,510:1141,37:0.0314:2,2:29.2:1.0:30.4:1.0:1.0:1.06:60.0:74.0:0.0321:0.0:1.4 0/0:966:0:0,0:521,444:965,0:0.0:2,0:26.6:1.0:30.5:1.0:1.0:0.0:60.0:40.957:1.0:0.0:0.2 +17 78922952 . C G 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGAGGAAGGGCAGCCCCGG;RSEQ=TCCCAGGGCAGCCAAACCTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:10,0:0,0:0,10:1.0:0,0:20.4:1.0:30.1:1.0:1.0:0.0:56.8:9.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +17 78923126 . T G 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.11713;LSEQ=CCACGGGTAGTGAGTCAGGC;RSEQ=GGCCGCCCAGGGTCACTGCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:146:54:53,1:92,0:92,54:0.3699:1,1:22.1:1.0:29.9:1.0:0.36986:0.0:60.0:26.0:0.3611:0.0:1.1 0/1:47:3:3,0:43,1:44,3:0.0638:1,0:21.0:1.0:31.0:0.0:1.0:0.0:60.0:6.0:0.0652:0.0:1.0 +17 78934088 . G A 200 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGTGTCACTGCCATTTGGTT;RSEQ=GGTCCAGGTTTCTCAGTGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:68:2,66:6,88:94,68:0.4198:2,1:24.3:1.0:32.9:1.0:0.46971:2.23975:60.0:136.0:0.4198:0.0:1.1 0/0:89:0:0,0:5,84:89,0:0.0:2,0:23.9:1.0:30.6:1.0:1.0:0.0:60.0:178.0:1.0:0.0:0.1 +17 79996915 . T C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACATTTCTTGTCCACTTCCA;RSEQ=GTTCCTCCCGTACTCCTGGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1.0:0,2:44.0:1.0:32.6:1.0:1.0:0.0:50.6:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +18 4131501 . C G 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=CTTTTCTAGAACAAAAGCAG;RSEQ=CACAGACAATACATAAGAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:20.8:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:2:0:0,0:2,0:2,0:0.0:0,0:24.0:1.0:30.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +18 8413657 . G A 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=GTCTAACAGGAGCGTGAGAA;RSEQ=AGGTGTTGAAGTGTTTCATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:646:39:21,18:266,341:607,39:0.0604:2,2:20.4:1.0:30.4:1.0:0.24658:1.49:59.3:38.0:0.0599:0.0:1.1 0/0:485:0:0,0:215,270:485,0:0.0:2,0:23.1:1.0:30.8:1.0:1.0:0.0:59.6:120.25:1.0:0.0:0.1 +18 12912750 . C T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01884;SOR=0.0;LSEQ=TGTTGGATCAGGAACTGTGT;RSEQ=TGCTCTTAAGTGCTTGTGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:7:7,0:95,2:97,7:0.0673:1,0:25.6:1.0:31.4:1.0:1.0:0.0:51.3:14.0:0.0686:0.0:1.4 0/0:81:0:0,0:80,1:81,0:0.0:1,0:24.0:1.0:31.0:1.0:1.0:0.0:60.0:80.0:1.0:0.0:0.0 +18 12912821 . G C 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTCTTTTCAGTTGGGTGTT;RSEQ=AGTGGTTTTCCAGATCACGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:418:22:18,4:306,90:396,22:0.0526:2,2:22.7:1.0:32.0:1.0:0.79519:1.32:60.0:44.0:0.0534:0.0:1.3 0/0:399:0:0,0:293,105:398,0:0.0:2,0:22.4:1.0:30.8:1.0:1.0:0.0:60.0:78.6:0.9975:0.0:0.1 +18 23784839 . A G 111 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00205;SOR=0.04814;LSEQ=CACGCCTCCACCCCATGGGA;RSEQ=ATTCGATGGACATGGACATA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:8,2:5,1:6,10:0.625:2,2:22.4:1.0:33.7:1.0:1.0:1.23302:54.8:20.0:0.625:0.0:1.0 0/1:15:1:1,0:9,5:14,1:0.0667:2,0:15.0:0.0:34.0:0.0:1.0:0.0:56.0:2.0:0.0667:0.0:1.0 +18 28787355 . T A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.00307;SOR=0.11065;LSEQ=TCATTTTATAAATTCTTTCC;RSEQ=AATTACCTCAAATCACAAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:14:14,0:21,0:21,14:0.4:1,1:28.0:1.0:29.9:1.0:1.0:0.0:60.0:13.0:0.3939:0.0:1.1 0/1:30:2:2,0:26,2:28,2:0.0667:2,0:28.5:1.0:28.0:1.0:1.0:0.0:60.0:4.0:0.0667:0.0:1.0 +18 28787634 . G T 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00016;SOR=0.0;LSEQ=ATAATAACTTCCATTTATTG;RSEQ=TCTAGAAATCACTGTGTGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:11:2,9:9,37:46,11:0.193:2,2:24.7:1.0:30.0:1.0:1.0:1.09289:60.0:22.0:0.193:0.0:1.1 0/0:63:0:0,0:14,49:63,0:0.0:2,0:13.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 +18 34883082 . T G 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.10526;SOR=0.0;LSEQ=GTACCATTGTTCTCAGCACT;RSEQ=CCTTTGGCTCATTTGAACCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:18:17:0,17:0,1:1,17:0.9444:0,1:21.6:1.0:32.5:1.0:1.0:0.0:60.0:34.0:0.9444:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:19.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +18 35069156 . C T 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01767;SOR=0.0;LSEQ=ATCCGATGCAGCGGCTGACA;RSEQ=GCCAGCATGGCAGATTAGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:8,2:10,6:0.375:2,0:20.3:1.0:32.2:1.0:0.5:0.0:60.0:12.0:0.375:0.0:1.0 0/0:16:0:0,0:12,4:16,0:0.0:2,0:28.1:1.0:30.6:1.0:1.0:0.0:60.0:32.0:1.0:0.0:0.2 +18 39537688 . G C 249 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAGCCTTTGGCCTTGCCAGT;RSEQ=AGAACATCCTACAAAGCATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:220:90,130:117,163:280,220:0.44:2,2:24.5:1.0:32.0:1.0:0.85534:1.03675:60.0:109.0:0.4404:0.0:1.1 0/0:622:0:0,0:268,354:622,0:0.0:2,0:25.4:1.0:30.6:1.0:1.0:0.0:60.0:61.2:1.0:0.0:0.1 +18 39593388 . CT C 86 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.00858;SOR=0.0;LSEQ=CTTTTCCTAATATTACTTTA;RSEQ=TTTTTTTGTTTTCCAGGATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:6:5,1:171,42:213,6:0.0274:2,2:30.8:1.0:33.5:1.0:1.0:1.23:60.0:12.0:0.0274:0.0:0.0 0/0:262:0:0,0:202,60:262,0:0.0:2,0:24.1:1.0:30.2:1.0:1.0:0.0:60.0:261.0:1.0:0.0:0.1 +18 46996404 . A G 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00281;SOR=0.0;LSEQ=GGGTCCCTACCTTCCTCCAT;RSEQ=CCCACCACCTGCCCCTGGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:6:1,5:0,4:4,6:0.6:0,2:21.7:1.0:33.3:1.0:1.0:0.0:60.0:12.0:0.6:0.0:1.3 0/0:12:0:0,0:3,9:12,0:0.0:2,0:21.8:1.0:28.2:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.8 +18 48190817 . G A 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.10694;LSEQ=ATCAGCACAGAGGACCTCGT;RSEQ=CTCAAGATTGGGGATTTCGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:165:80:22,58:26,59:85,80:0.4848:2,2:18.6:1.0:28.9:1.0:0.73266:1.16073:60.0:25.667:0.4753:0.0:1.2 0/1:209:19:8,11:56,134:190,19:0.0909:2,2:17.5:1.0:28.4:1.0:0.29807:1.74:60.0:38.0:0.0927:0.0:1.2 +18 48584855 . A TTT 97 q25;Bias SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=1e-05;SOR=0.09986;LSEQ=CTTGTTTTTGTTGTAAGGGC;RSEQ=TTTTTTTTTTTTTTTTGGTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:20:0,20:138,218:356,20:0.0498:2,1:27.5:1.0:22.6:1.0:0.00014:0.0:48.0:4.0:0.0494:0.0:3.0 0/0:578:3:0,3:201,360:561,3:0.0052:2,0:36.7:1.0:23.0:1.0:0.55597:0.0:47.7:2.0:0.0043:0.0:3.0 +18 55466751 . G GTA 96 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0054;SOR=0.0;LSEQ=CAGGAGTTTGAGACTAGCCT;RSEQ=GCCAACATGGTGAAACCCGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:0,9:0,14:14,9:0.375:1,0:25.8:1.0:30.5:1.0:1.0:0.0:54.2:18.0:0.375:0.0417:0.4 0/0:18:0:0,0:0,18:18,0:0.0:1,0:26.2:1.0:31.1:1.0:1.0:0.0:53.2:36.0:1.0:0.0:0.2 +18 56378529 . C T 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTAAGAAAGATAGGTGGCTA;RSEQ=GTGATCATGGATATTTGTTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:16.2:1.0:28.6:1.0:1.0:0.0:53.4:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +18 56412894 . A T 47 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01399;SOR=0.0;LSEQ=AGTCCCTAATTTTTTTTTTT;RSEQ=CAGGATCTAGATATTGATCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:5:3,2:341,151:492,5:0.01:2,2:10.6:1.0:20.6:1.0:0.64578:1.5042:60.0:1.5:0.0062:0.0:1.8 0/0:669:0:0,0:458,211:669,0:0.0:2,0:23.4:1.0:27.2:1.0:1.0:0.0:59.9:38.353:1.0:0.0:0.1 +18 60910366 . G A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCAGTGATAGACTGGATAAA;RSEQ=AAAATTTGGTACATATACAC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:22.8:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +18 66534393 . CCCC ACCCT 82 NM7.25 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.14475;SOR=0.0;LSEQ=ATCCTTTTGGGCTTTCAGAT;RSEQ=TGGAGCTCAGTAGCAGTAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:6:3,3:1,15:16,6:0.2727:1,2:25.0:0.0:31.9:1.0:0.0458:12.57:23.8:12.0:0.2727:0.0:7.8 0/0:9:0:0,0:3,5:8,0:0.0:2,0:18.5:1.0:28.9:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.3 +18 69372730 . A G 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=TGGCATTTAAAAAAATTATT;RSEQ=TCTATGCCTAGTTTCCTTTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:25.7:1.0:32.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +19 1221161 . C T 230 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.09565;LSEQ=TAGAGCTGGGGCTCCTAGGG;RSEQ=GTCAACCACCTTGACTGACC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:605:207:133,74:257,141:398,207:0.3421:2,2:24.4:1.0:29.9:1.0:1.0:1.01411:60.0:68.0:0.3406:0.0:1.1 0/1:613:29:18,11:346,238:584,29:0.0473:2,2:23.2:1.0:28.4:1.0:0.84781:1.13:60.0:28.0:0.0462:0.0:1.1 +19 1221991 . G A 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02268;SOR=0.1909;LSEQ=AAGAGGTTCTCCATCCGGCA;RSEQ=ATCCGGCAGCACAGGTGAGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:908:11:6,5:365,531:896,11:0.0121:2,2:17.9:1.0:30.6:1.0:0.37158:1.74:60.0:22.0:0.0123:0.0:1.3 0/0:857:2:1,1:366,489:855,2:0.0023:2,2:9.0:1.0:19.0:1.0:1.0:1.34:60.0:1.0:0.0012:0.0:3.5 +19 1611856 . G A 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01687;LSEQ=TTCAGGTTCCGCTCTGGAGG;RSEQ=AGGGGGGAGAGCTCTGTGGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:49:17,32:386,560:946,49:0.0492:2,2:24.9:1.0:30.2:1.0:0.45682:1.29715:58.2:23.5:0.0484:0.0:1.2 0/0:1147:1:1,0:490,656:1146,1:0.0009:2,0:1.0:0.0:22.0:0.0:0.42807:0.0:60.0:2.0:0.0009:0.0:3.0 +19 1622115 . C T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCCACTGCTGCCCACCGGGC;RSEQ=GCTACCGGGCGGGAGGGGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1121:33:14,19:523,565:1088,33:0.0294:2,2:23.5:1.0:31.4:1.0:0.59738:1.256:60.0:32.0:0.0291:0.0:1.1 0/0:950:0:0,0:466,482:948,0:0.0:2,0:24.9:1.0:29.9:1.0:1.0:0.0:59.9:93.8:0.9989:0.0:0.5 +19 2194896 . T C 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03571;SOR=0.0;LSEQ=GGACAGGCTGGGTTCTGGGC;RSEQ=GGCTGCGGCATCCTTGGGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1.0:0,2:20.5:1.0:29.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.3 0/0:2:0:0,0:1,1:2,0:0.0:2,0:1.0:0.0:31.0:0.0:1.0:0.0:57.5:4.0:1.0:0.0:0.5 +19 2207386 . G C 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.16227;SOR=0.0;LSEQ=GGTTGGAGGGGCCCAGGCCA;RSEQ=GTGGTGTTGAATGGTGCACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:11,0:23,0:23,11:0.3235:1,0:26.2:1.0:31.8:1.0:1.0:0.0:60.0:22.0:0.3235:0.0:1.5 0/0:6:0:0,0:6,0:6,0:0.0:0,0:18.5:1.0:33.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 +19 2211220 . G T 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGAAGCTTCTAGGTGAGCCC;RSEQ=TGTGAGGCGTCCGGCGAAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:24:7,17:182,344:526,24:0.0434:2,2:21.7:1.0:30.7:1.0:0.6653:1.28434:60.0:48.0:0.0442:0.0:1.1 0/0:535:0:0,0:195,340:535,0:0.0:2,0:22.5:1.0:30.4:1.0:1.0:0.0:60.0:88.167:1.0:0.0:0.2 +19 2214242 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCGAGGTGTGGGGTCATGC;RSEQ=AGCATCCCACCATCGTGGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:5,1:6,5:11,6:0.3529:2,2:20.8:1.0:27.8:1.0:0.33339:3.85:60.0:5.0:0.3333:0.0:2.0 0/0:1:0:0,0:1,0:1,0:0.0:0,0:9.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +19 2217203 . G A 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.04334;SOR=0.0;LSEQ=TTGGGGCACGGTGAGGTACT;RSEQ=GGGCTGACCTGGAGTAGGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:7:1,6:1,51:52,7:0.1186:1,2:24.9:1.0:31.1:1.0:0.22501:7.95:60.0:14.0:0.1207:0.0:1.0 0/0:35:0:0,0:2,33:35,0:0.0:2,0:18.3:1.0:31.1:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.2 +19 3110361 . C T 192 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07767;LSEQ=CGGGCGCCTGGGGAGGGGAG;RSEQ=GCCTGGGCAGCTGTGGGCTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:293:86:19,67:43,164:207,86:0.2935:2,2:25.6:1.0:30.0:1.0:0.87532:1.08:60.0:85.0:0.2951:0.0:2.1 0/1:321:10:2,8:82,228:310,10:0.0312:2,2:21.9:1.0:28.7:1.0:1.0:1.43705:60.0:20.0:0.0321:0.0:2.0 +19 3110585 . A G 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.14286;SOR=0.0;LSEQ=CCAAGTAGCTGTGGGCGCCC;RSEQ=CATCCTGTGGGTGGGGAAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1.0:0,2:39.7:1.0:33.0:1.0:1.0:0.0:56.0:12.0:1.0:0.0:1.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:14.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +19 3114864 . C T 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.14971;LSEQ=CTGGTGGCTTTCCGTCCTCC;RSEQ=GCTGGTTTGGGTGCTGTGTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:47:40,7:117,19:136,47:0.2568:2,2:23.2:1.0:32.0:1.0:1.0:1.07718:60.0:94.0:0.2626:0.0:1.1 0/1:143:7:5,2:117,19:136,7:0.049:2,2:19.7:1.0:30.4:1.0:0.27337:2.44297:60.0:14.0:0.0493:0.0:1.0 +19 3118851 . G T 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00014;SOR=0.0;LSEQ=GGCAGGAGGGGCTTGGGTGG;RSEQ=AGCCGTCCTGGGATTGCAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:20:18,2:208,19:227,20:0.081:2,2:27.9:1.0:29.3:1.0:0.68184:1.21534:60.0:40.0:0.0823:0.0:1.3 0/0:143:0:0,0:125,18:143,0:0.0:2,0:20.9:1.0:30.5:1.0:1.0:0.0:60.0:142.0:1.0:0.0:0.2 +19 3121609 . T C 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GCCCCCACACCGCAGCCCCC;RSEQ=GTGGCTGTCCTTCCAACCCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:30.2:1.0:29.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +19 4094775 . G A 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=1.0;MSILEN=1.0;SSF=0.44444;SOR=0.0;LSEQ=GGTGGGTCAGAAGCCTGGAC;RSEQ=CAACCCCAGCTAACTGTCTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:1,4:0,3:3,5:0.625:0,2:22.0:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.625:0.0:1.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:47.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +19 4102132 . A C 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06061;SOR=0.0;LSEQ=GGGACCAGTGTGGCAAACAG;RSEQ=GGATACTAAGAGTGAAGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:24.2:1.0:29.0:1.0:1.0:0.0:59.5:5.0:0.7143:0.0:2.2 0/0:4:0:0,0:4,0:4,0:0.0:0,0:25.5:1.0:28.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +19 4102449 . G A 261 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04035;LSEQ=ACCTGGTCCAGGGAGCCGCC;RSEQ=TCCTAGAGGGCACACAAGGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:626:384:164,220:109,132:241,384:0.6134:2,2:26.8:1.0:30.5:1.0:0.56237:1.10754:51.5:53.857:0.619:0.0:1.1 0/1:700:42:17,25:288,370:658,42:0.06:2,2:29.7:1.0:29.0:1.0:0.74941:1.14444:52.2:20.0:0.0581:0.0:1.2 +19 5174304 . G A 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0069;SOR=0.0;LSEQ=TTTGCTGAATAAAGCAGTGT;RSEQ=GGATTTGTGGTTCCCGAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:9:0,9:0,22:22,9:0.2903:1,0:28.3:1.0:29.2:1.0:1.0:0.0:60.0:8.0:0.2667:0.0:1.7 0/0:22:0:0,0:2,20:22,0:0.0:2,0:19.5:1.0:29.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.1 +19 5206724 . C A 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTCCAGGCCTCAGGAGGTC;RSEQ=GCCCGGGAGGGGCAGAGGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:101:77,24:180,36:216,101:0.3186:2,2:24.0:1.0:30.6:1.0:0.1656:1.55619:59.9:202.0:0.3248:0.0:1.7 0/0:303:0:0,0:233,70:303,0:0.0:2,0:24.0:1.0:29.6:1.0:1.0:0.0:60.0:49.5:1.0:0.0:0.7 +19 5207183 . T C 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TTGGCTCCCTGCAACCTCTG;RSEQ=CTCCTGGGTTCAAGTGATTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1.0:0,0:26.8:1.0:31.8:1.0:1.0:0.0:34.2:18.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +19 5208216 . G A 241 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.07001;LSEQ=GGCCTCAGTTTCCCCAGCAG;RSEQ=GCCAAAAGCTGGGACACTCG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:486:249:151,98:139,94:233,249:0.5123:2,2:24.8:1.0:30.4:1.0:0.85257:1.04:59.8:40.5:0.5137:0.0:2.0 0/1:483:33:21,12:284,164:448,33:0.0683:2,2:23.2:1.0:27.7:1.0:1.0:1.01:60.0:66.0:0.0689:0.0:1.8 +19 5208257 . A T 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01616;LSEQ=AGGGAGCTCACCTGCAGTGG;RSEQ=CAGAGATGGGGCCGTCCTGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:796:54:33,21:395,347:742,54:0.0678:2,2:25.8:1.0:29.7:1.0:0.32252:1.38:60.0:108.0:0.0693:0.0:1.1 0/0:853:1:0,1:458,394:852,1:0.0012:2,0:1.0:0.0:25.0:0.0:0.46307:0.0:60.0:2.0:0.0012:0.0:1.0 +19 5208514 . TG T 176 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.1036;LSEQ=TTGTTTGTTTGTTTTTGAGA;RSEQ=GAGTTTCACTCTTGTCGCCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:98:44:0,44:1,53:54,44:0.449:1,1:26.8:1.0:32.3:1.0:1.0:0.0:55.2:88.0:0.4536:0.0816:0.2 0/1:65:5:1,4:0,60:60,5:0.0769:1,2:28.4:1.0:31.6:1.0:0.07692:0.0:60.0:10.0:0.0769:0.0154:0.2 +19 5212482 . G A 262 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03134;LSEQ=AACTGGAACTGGCGGACCTC;RSEQ=CGTTTCTCACTGGAGCCATT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:720:419:194,225:145,156:301,419:0.5819:2,2:25.9:1.0:30.1:1.0:0.64995:1.0779:60.0:68.833:0.5817:0.0:1.2 0/1:767:32:16,16:343,392:735,32:0.0417:2,2:25.3:1.0:28.9:1.0:0.72149:1.14:60.0:64.0:0.0422:0.0:1.2 +19 5212586 . G T 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.05347;LSEQ=CCCAAGTGGCCGGGTGTGGT;RSEQ=GCTCATGCCTGTTATCCCAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:153:78:4,74:5,70:75,78:0.5098:2,2:23.5:1.0:31.2:1.0:0.74241:1.31902:55.7:156.0:0.5132:0.0:1.1 0/1:115:6:1,5:8,101:109,6:0.0522:2,2:21.0:1.0:30.5:1.0:0.39372:2.5:59.8:12.0:0.0536:0.0:1.3 +19 5212680 . C T 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.51471;SOR=0.0;LSEQ=GCCTGACCAACATGGAGAAA;RSEQ=CTCGTCTCAACTAAAAATAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,9:9,5:0.3571:0,0:24.4:1.0:29.2:1.0:1.0:0.0:24.6:10.0:0.3571:0.0:1.0 0/0:3:0:0,0:0,3:3,0:0.0:0,0:26.7:1.0:31.3:1.0:1.0:0.0:26.0:6.0:1.0:0.0:0.0 +19 5214116 . A G 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.11111;SOR=0.0;LSEQ=GGGCATGAGTAAAGGCAAGA;RSEQ=GAAATCAGGCTCATTGCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1.0:0,0:23.9:1.0:34.0:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.8 0/0:1:0:0,0:0,1:1,0:0.0:0,0:10.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +19 5214904 . C T 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00042;SOR=0.0;LSEQ=CAGTTTCTCCCCCTCAGCGC;RSEQ=ATCACCATTTGGGGCCAGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:19:1,18:1,19:20,19:0.4872:1,1:19.1:1.0:28.9:1.0:1.0:1.05:60.0:38.0:0.5:0.0:1.1 0/0:15:0:0,0:0,15:15,0:0.0:1,0:27.3:1.0:31.9:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.2 +19 5214986 . G A 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.03251;SOR=0.0;LSEQ=GAGCAGCATCCCTGGCCTCC;RSEQ=CCCACTCCACGCCAGCAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:5,4:1,4:5,9:0.6429:2,2:30.2:1.0:30.2:1.0:0.3007:4.45:60.0:18.0:0.75:0.0:1.1 0/0:5:0:0,0:1,4:5,0:0.0:2,0:26.0:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.4 +19 5215474 . G A 246 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07902;LSEQ=GGGTAGGTGCCTGTGAGGCC;RSEQ=AGGTGATGAGGGTGGGAGGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:554:284:142,142:138,132:270,284:0.5126:2,2:24.3:1.0:30.3:1.0:0.79935:1.0454:59.9:34.5:0.5102:0.0:1.1 0/1:627:48:28,20:313,265:578,48:0.0766:2,2:25.9:1.0:30.3:1.0:0.65182:1.18:58.7:47.0:0.0768:0.0:1.1 +19 5218213 . T TA 67 MSI12;MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CATTGGTTAAATGTTAACTT;RSEQ=AAAAAAAAAAAAGCCTCACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:5,0:10,0:10,5:0.2941:0,0:19.6:1.0:29.2:1.0:1.0:0.0:60.0:10.0:0.2941:0.1176:0.8 0/0:2:0:0,0:2,0:2,0:0.0:0,0:17.5:1.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 +19 5218684 . G A 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CCAGGACCAAGTACAGCTAC;RSEQ=TGTACAAGCTGTGGGGGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:88:60,28:132,67:199,88:0.3056:2,2:28.3:1.0:30.9:1.0:0.78714:1.09:60.0:176.0:0.3088:0.0:1.0 0/0:194:0:0,0:137,57:194,0:0.0:2,0:22.5:1.0:29.5:1.0:1.0:0.0:60.0:193.0:1.0:0.0:0.1 +19 5220134 . C T 57 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01908;SOR=0.0;LSEQ=GACGCGAGTGCCGCAGGCTG;RSEQ=GCCTCTGTAGCCGTGAGATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:5:2,3:146,174:320,5:0.0154:2,2:19.6:1.0:24.6:1.0:1.0:1.25774:60.0:4.0:0.0125:0.0:1.0 0/0:390:0:0,0:177,213:390,0:0.0:2,0:24.8:1.0:30.0:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.1 +19 5222088 . C G 231 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAAGCCCTGCTGAACTACAA;RSEQ=CCCTGACCCTGCCTGCCTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:246:128:108,20:98,19:117,128:0.5203:2,2:21.9:1.0:33.1:1.0:1.0:1.05:60.0:127.0:0.5205:0.0:1.7 0/0:216:0:0,0:182,34:216,0:0.0:2,0:22.7:1.0:31.1:1.0:1.0:0.0:60.0:107.0:1.0:0.0:0.7 +19 5225558 . G C 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=0.00119;SOR=0.0;LSEQ=AAAGGAGGAGGCAGGGGCGG;RSEQ=GGGGGCCAAGCTGGGCCCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:20:20,0:25,1:26,20:0.4348:1,1:26.8:1.0:33.0:1.0:1.0:0.0:60.0:40.0:0.4348:0.0:1.0 0/0:16:0:0,0:15,1:16,0:0.0:1,0:19.4:1.0:30.3:1.0:1.0:0.0:60.0:15.0:1.0:0.0:0.3 +19 5229728 . G A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00199;SOR=0.0;LSEQ=AGGGGAGGGGAGGGGCGGGC;RSEQ=GAGCCGTTACCAGGGCGCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:7:5,2:8,7:15,7:0.3182:2,2:22.7:1.0:29.7:1.0:0.64783:2.11:60.0:14.0:0.3684:0.0:1.1 0/0:27:0:0,0:15,12:27,0:0.0:2,0:14.2:1.0:28.7:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.4 +19 5238944 . C T 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.06435;SOR=0.0;LSEQ=ACCTACTGGACTGCAGCGTG;RSEQ=GCTGCCGCACCACGGGGGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:5:3,2:356,94:450,5:0.011:2,2:31.0:1.0:29.6:1.0:0.28501:2.51844:60.0:10.0:0.0112:0.0:1.2 0/0:400:0:0,0:277,122:399,0:0.0:2,0:24.0:1.0:30.5:1.0:1.0:0.0:59.9:38.9:1.0:0.0:0.1 +19 5240392 . C T 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.06494;LSEQ=GTCGGGGAGCGTCCACCCCA;RSEQ=AAAGGGGGCCCCACCTGCTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:284:115:32,83:37,132:169,115:0.4049:2,2:25.3:1.0:28.7:1.0:0.26262:1.37:60.0:56.5:0.4036:0.0:1.1 0/1:261:11:3,8:70,180:250,11:0.0421:2,2:21.3:1.0:26.6:1.0:1.0:1.03686:60.0:22.0:0.0423:0.0:1.2 +19 7116778 . TG T 91 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.125;SOR=0.0;LSEQ=TTCCATCTGCTGGGGGCGGG;RSEQ=GGGGGAACGAAAAAACACAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:30.6:1.0:32.7:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.1 0/0:1:0:0,0:1,0:1,0:0.0:0,0:38.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +19 7116843 . G A 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.24451;SOR=0.0;LSEQ=GCCCCAAAGGAGCAGCAACT;RSEQ=TGGAAACCCCTTGCCCTCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:17.8:1.0:28.6:1.0:1.0:0.0:60.0:10.0:0.4167:0.0:1.0 0/0:5:0:0,0:5,0:5,0:0.0:0,0:14.2:1.0:32.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 +19 7119651 . G A 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ATTTAGACACACACACACAC;RSEQ=CGCGCGCGCAAACACACACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:18:3,15:33,169:202,18:0.0818:2,2:20.9:1.0:29.9:1.0:1.0:1.02:56.6:36.0:0.0841:0.0:2.2 0/0:247:0:0,0:40,156:196,0:0.0:2,0:23.1:1.0:30.3:1.0:1.0:0.0:60.0:27.0:1.0:0.0:0.1 +19 7123031 . G A 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.06548;LSEQ=AGCAACCAGGGTTCTTGGAG;RSEQ=AGGGTCCGTGATTCGACTCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:511:179:52,127:119,211:330,179:0.3503:2,2:25.5:1.0:30.5:1.0:0.11669:1.37655:60.0:43.75:0.3507:0.0:1.1 0/1:529:18:5,13:196,315:511,18:0.034:2,2:21.8:1.0:29.7:1.0:0.46269:1.6164:60.0:36.0:0.0342:0.0:1.3 +19 7132343 . G A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCTCCTGGGAGGAAGAGA;RSEQ=GAGGAGAAGGAGGGTGGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:238:82:21,61:31,125:156,82:0.3445:2,2:24.4:1.0:31.2:1.0:0.32524:1.39:60.0:40.0:0.3448:0.0:1.1 0/0:241:0:0,0:56,185:241,0:0.0:2,0:24.2:1.0:30.8:1.0:1.0:0.0:60.0:59.25:1.0:0.0:0.2 +19 7162789 . T C 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCGATGAGCCAAGGTCGCG;RSEQ=CATTGCACTCCAGCCTGGGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:11.7:1.0:31.8:1.0:1.0:0.0:42.7:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +19 7162968 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.10488;SOR=0.17588;LSEQ=CAGGAAGAGATAGCTGCTTC;RSEQ=CTAGAGGTGAAGCAAAGTGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:5:5,0:144,18:162,5:0.0299:2,0:31.2:1.0:33.4:1.0:1.0:0.0:60.0:10.0:0.0299:0.0:1.0 0/0:186:1:0,1:153,32:185,1:0.0054:2,0:1.0:0.0:24.0:0.0:0.17742:0.0:60.0:2.0:0.0056:0.0:1.0 +19 7168240 . C G 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.03778;SOR=0.0;LSEQ=ATTCCCTTAAGGGTCTCCTC;RSEQ=CCATGTGCCTGGCTGAGTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:9:0,9:0,18:18,9:0.3333:1,0:27.4:1.0:33.8:1.0:1.0:0.0:60.0:18.0:0.3462:0.0:1.0 0/0:11:0:0,0:0,11:11,0:0.0:0,0:26.5:1.0:31.4:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.3 +19 7172526 . C A 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTCCATGGTGAGAAGATAA;RSEQ=CCTCAGGCTGCAAATGACTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:26:0,26:0,40:40,26:0.3939:1,1:27.0:1.0:31.2:1.0:1.0:0.0:60.0:52.0:0.4:0.0:1.1 0/0:68:0:0,0:3,65:68,0:0.0:1,0:23.5:1.0:31.1:1.0:1.0:0.0:60.0:67.0:1.0:0.0:0.1 +19 7184238 . G A 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06736;LSEQ=AGCCAATTAACCCTGGGTTT;RSEQ=CACACAGTTTTAACAAGCGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:163:84:74,10:67,12:79,84:0.5153:2,2:23.4:1.0:28.7:1.0:0.64806:1.32:60.0:168.0:0.5217:0.0:2.2 0/1:181:12:9,3:144,23:167,12:0.0663:2,2:19.5:1.0:27.4:1.0:0.38627:2.07638:60.0:24.0:0.0678:0.0:2.0 +19 7184243 . C G 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.04819;LSEQ=ATTAACCCTGGGTTTGCACA;RSEQ=AGTTTTAACAAGCGGCATCG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:89:76,13:76,18:94,89:0.4863:2,2:24.3:1.0:33.4:1.0:0.43729:1.38:60.0:178.0:0.4863:0.0:2.1 0/1:208:9:6,3:164,35:199,9:0.0433:2,2:20.4:1.0:30.8:1.0:0.2138:2.33092:60.0:18.0:0.0433:0.0:2.3 +19 7184490 . G A 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.00534;LSEQ=GTCCTGGAAGTGGTAGTACG;RSEQ=GGGCGGGCAGGTCTCCACAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:174:65,109:122,190:312,174:0.3573:2,2:25.0:1.0:30.9:1.0:0.7706:1.07657:60.0:57.0:0.357:0.0:1.1 0/0:679:2:2,0:290,387:677,2:0.0029:2,0:1.0:0.0:24.5:1.0:0.18458:0.0:60.0:4.0:0.003:0.0:1.0 +19 7184651 . GGA G 144 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=10.0;MSILEN=2.0;SSF=0.00037;SOR=0.15829;LSEQ=TACAGATGGTCGGGCAAACT;RSEQ=GAGAGAGAGAGAGAGAGAGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:21:5,16:9,52:61,21:0.2442:2,2:27.3:1.0:33.0:1.0:0.33523:1.79:58.5:42.0:0.2471:0.0116:0.5 0/1:83:4:0,4:19,60:79,4:0.0482:2,0:16.5:1.0:26.5:1.0:0.56922:0.0:60.0:8.0:0.0494:0.0241:0.3 +19 7805951 . A T 303 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0047;LSEQ=CATGTTTACAGTGTTTGGAA;RSEQ=GGAGCAGTGCAGGAGGGATG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:993:933:489,444:36,24:60,933:0.9396:2,2:25.4:1.0:30.8:1.0:0.28675:1.36154:38.6:76.75:0.9398:0.0:1.1 0/1:1230:83:46,37:582,565:1147,83:0.0675:2,2:23.7:1.0:30.3:1.0:0.42804:1.21:38.2:82.0:0.0673:0.0:1.1 +19 7815587 . G C 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.07604;LSEQ=AAAATGATGAACGCAAAGGG;RSEQ=AAGAGGAGAGGCACCCAATA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:36:12,24:11,15:26,36:0.5806:2,2:22.0:1.0:32.8:1.0:0.59556:1.45748:49.6:72.0:0.5902:0.0:1.3 0/1:75:7:3,4:31,37:68,7:0.0933:2,2:26.3:1.0:32.1:1.0:1.0:1.11546:42.7:14.0:0.0933:0.0:1.1 +19 7815690 . G T 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=GTAAGAAAGGTGATATTGTA;RSEQ=ACATCAAGGGAATGGGTACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:15:11,4:30,14:44,15:0.2542:2,2:28.5:1.0:31.7:1.0:1.0:1.28:47.9:30.0:0.2632:0.0:1.0 0/0:54:0:0,0:37,17:54,0:0.0:2,0:22.5:1.0:31.3:1.0:1.0:0.0:42.6:53.0:1.0:0.0:0.1 +19 10260400 . T C 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01473;SOR=0.0;LSEQ=CAGATATGTGACCAAGTCTA;RSEQ=GCAGGAGCACTCGTCCTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:7:2,5:43,105:148,7:0.0452:2,2:25.0:1.0:30.7:1.0:1.0:1.02367:60.0:14.0:0.0467:0.0:1.0 0/0:148:0:0,0:60,88:148,0:0.0:2,0:23.8:1.0:29.7:1.0:1.0:0.0:60.0:73.0:1.0:0.0:0.1 +19 10278953 . T G 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTATTTTACCAAGATACTTA;RSEQ=GTTAGCAATTCAGTTTCACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:471:93:64,29:228,150:378,93:0.1975:2,2:26.5:1.0:32.8:1.0:0.15254:1.45:60.0:186.0:0.2009:0.0:1.1 0/0:585:0:0,0:357,227:584,0:0.0:2,0:22.6:1.0:29.3:1.0:1.0:0.0:60.0:63.889:1.0:0.0:0.1 +19 10287635 . A T 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=2.0;SSF=0.44444;SOR=0.0;LSEQ=CTAGAAATATACTAAACTAT;RSEQ=TATGGACAAAGTAATCCAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:18.2:1.0:30.4:1.0:1.0:0.0:58.2:10.0:0.625:0.0:1.0 0/0:2:0:0,0:1,1:2,0:0.0:2,0:8.5:1.0:30.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +19 10292608 . C A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00478;SOR=0.0;LSEQ=TCCAAATTATCTTTGAAACT;RSEQ=CATGGGAAAAAATGCAAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:7:7,0:68,4:72,7:0.0886:2,0:25.9:1.0:27.9:1.0:1.0:0.0:60.0:14.0:0.0886:0.0:1.0 0/0:87:0:0,0:79,8:87,0:0.0:2,0:23.1:1.0:30.1:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.1 +19 10292901 . C T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06512;SOR=0.15027;LSEQ=TAAGCTGGCTTTTGTCTCCC;RSEQ=GCAAGAGTCTAGAGTGTCCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:7:0,7:1,33:34,7:0.1707:1,0:23.4:1.0:31.6:1.0:1.0:0.0:60.0:14.0:0.175:0.0:1.0 0/1:34:1:0,1:1,32:33,1:0.0294:1,0:50.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0294:0.0:1.0 +19 10305434 . C T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00435;SOR=0.0;LSEQ=CCGGCCACCCCGAGGGGAAG;RSEQ=GACCCCCCACCCAGCGCCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:485:7:1,6:325,151:476,7:0.0144:2,2:8.0:1.0:27.3:1.0:0.00563:12.84973:60.0:14.0:0.0147:0.0:1.1 0/0:566:0:0,0:371,195:566,0:0.0:2,0:23.1:1.0:29.9:1.0:1.0:0.0:60.0:25.952:1.0:0.0:0.4 +19 10600615 . C CT 78 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.03983;SOR=0.0;LSEQ=GCCAGATACTCTTTTTTTTC;RSEQ=TTTTTTTTTTCCCCCTTAAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:0,6:1,60:61,6:0.0896:1,0:18.0:1.0:30.3:1.0:1.0:0.0:60.0:12.0:0.0909:0.0299:0.7 0/0:48:0:0,0:1,47:48,0:0.0:1,0:17.0:0.0:12.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 +19 10600654 . G A 89 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.02631;SOR=0.10715;LSEQ=AAGAGACAGGTTCATCCGGC;RSEQ=CGATGGCTCATGCCTGTAAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:8:0,8:0,13:13,8:0.381:1,0:19.1:1.0:29.9:1.0:1.0:0.0:42.3:16.0:0.381:0.0:1.1 0/1:17:1:0,1:0,16:16,1:0.0588:1,0:44.0:0.0:27.0:0.0:1.0:0.0:58.0:2.0:0.0667:0.0:1.0 +19 10610017 . G C 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07214;LSEQ=GGAGACAGTGATGAGCACTC;RSEQ=TCCATCCCTGGTCCTTCTCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:283:119:80,39:118,46:164,119:0.4205:2,2:21.9:1.0:31.0:1.0:0.43149:1.24953:59.9:28.75:0.4152:0.0:1.1 0/1:323:16:10,6:211,96:307,16:0.0495:2,2:20.6:1.0:30.4:1.0:0.59035:1.31762:60.0:32.0:0.0497:0.0:1.2 +19 11096829 . C T 64 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.06259;SOR=0.0;LSEQ=GTAAAAATCACAGACATATG;RSEQ=TGCCGAGTGACCAGTGGGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:5:1,4:341,151:492,5:0.0101:2,2:15.6:1.0:27.6:1.0:0.03476:8.99098:60.0:10.0:0.0102:0.0:1.2 0/0:464:0:0,0:301,163:464,0:0.0:2,0:24.7:1.0:31.3:1.0:1.0:0.0:60.0:76.333:1.0:0.0:0.2 +19 11098455 . G A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00661;SOR=0.0;LSEQ=TCCCACCCGCCGCCTCGCCC;RSEQ=TGATGCCACCGCAGACCCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:7:4,3:305,331:636,7:0.0109:2,2:17.6:1.0:26.0:1.0:0.7158:1.45:60.0:2.5:0.0079:0.0:1.7 0/0:671:0:0,0:315,353:668,0:0.0:2,0:1.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 +19 11130431 . G A 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00555;LSEQ=GGCCGAGTGCTCACACGTGG;RSEQ=TCACGCTGCCCGTCTCCTCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:114:29,85:82,213:295,114:0.2787:2,2:24.2:1.0:31.0:1.0:0.7102:1.12801:60.0:113.0:0.279:0.0:1.1 0/0:469:1:1,0:142,326:468,1:0.0021:2,0:1.0:0.0:23.0:0.0:0.3049:0.0:60.0:2.0:0.0022:0.0:1.0 +19 11138292 . A G 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00107;SOR=0.0;LSEQ=GCTTATTTCAGTTGGGGGAA;RSEQ=TGGCTTTGCTGAAGCTTTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:19:19,0:24,0:24,19:0.4419:1,1:22.1:1.0:34.3:1.0:1.0:0.0:60.0:38.0:0.4524:0.0:1.1 0/0:15:0:0,0:13,2:15,0:0.0:2,0:19.5:1.0:29.1:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.4 +19 11144287 . AT A 73 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.07859;SOR=0.0;LSEQ=TTTACCTTTTTTGCACTCTT;RSEQ=TTTTTTTGCATCCCTTTGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:5:4,1:64,74:138,5:0.035:2,2:31.0:1.0:31.8:1.0:0.19117:4.58:60.0:10.0:0.0355:0.0:0.0 0/0:101:0:0,0:47,54:101,0:0.0:2,0:20.9:1.0:30.0:1.0:1.0:0.0:60.0:100.0:1.0:0.0:0.2 +19 11169305 . T C 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.08133;LSEQ=GCTGGGCCTCAGTCATGCAG;RSEQ=TCCCATGCCTAGTGAGCCAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:78:30:26,4:37,11:48,30:0.3846:2,2:26.9:1.0:32.8:1.0:0.38274:1.92:60.0:60.0:0.3846:0.0:1.4 0/1:42:2:2,0:36,3:39,2:0.0476:2,0:21.5:1.0:26.5:1.0:1.0:0.0:60.0:4.0:0.0488:0.0:1.0 +19 11172439 . C T 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.02795;SOR=0.12147;LSEQ=GGGTGGCCAACGCACACTCT;RSEQ=TCCTCCTGTCCCCTCTCCAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:621:7:3,4:373,241:614,7:0.0113:2,2:21.6:1.0:28.4:1.0:0.4427:2.06117:60.0:14.0:0.0114:0.0:1.1 0/0:724:1:0,1:423,300:723,1:0.0014:2,0:1.0:0.0:25.0:0.0:0.41575:0.0:60.0:2.0:0.0014:0.0:1.0 +19 13051554 . G T 265 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00312;LSEQ=TCGGTTTCCTTCTCCCTTCT;RSEQ=CAGGGTGAGTGGAAGCCCCG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1332:418:204,214:447,467:914,418:0.3138:2,2:23.5:1.0:30.5:1.0:1.0:1.00409:60.0:51.25:0.3125:0.0:1.1 0/0:1401:2:0,2:733,660:1393,2:0.0014:2,0:1.0:0.0:26.5:1.0:0.22502:0.0:60.0:4.0:0.0014:0.0:1.0 +19 14627140 . C T 265 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00126;LSEQ=ACGAAAGCTCCACAACAGCG;RSEQ=CCTGGTCAGTCCTGTTCACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1566:464:243,221:587,513:1100,464:0.2963:2,2:23.0:1.0:30.0:1.0:0.73943:1.04065:60.0:153.667:0.2988:0.0:1.2 0/0:1895:1:1,0:978,915:1893,1:0.0005:2,0:2.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0005:0.0:1.0 +19 14629336 . G A 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00404;SOR=0.0;LSEQ=ATCGCCGCCGCCCTTTCAGC;RSEQ=ACACGCGACATCCGGGGCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:11:0,11:0,23:23,11:0.3235:1,0:11.5:1.0:32.2:1.0:1.0:0.0:60.0:22.0:0.3333:0.0:2.0 0/0:20:0:0,0:0,20:20,0:0.0:1,0:14.2:1.0:31.5:1.0:1.0:0.0:60.0:40.0:1.0:0.0:1.5 +19 15271135 . T G 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTAAAAAAAAAAAGAAAAA;RSEQ=AAAAATAATAATAATTCATT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:23.5:1.0:30.7:1.0:1.0:0.0:53.2:5.0:0.8333:0.0:1.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +19 15273576 . GTGTGTGTT G 119 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=13.0;MSILEN=2.0;SSF=0.05882;SOR=0.0;LSEQ=GAAGCACTTTGTGTCTGTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:0,13:0,11:11,13:0.5:0,1:23.2:1.0:32.3:1.0:1.0:0.0:53.9:26.0:0.5417:0.0769:1.3 0/0:6:0:0,0:0,6:6,0:0.0:0,0:12.8:1.0:27.0:1.0:1.0:0.0:59.8:5.0:1.0:0.0:1.5 +19 15288062 . G GGA 100 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=15.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGAGCAAGACTCCATCTCGG;RSEQ=AAAAAAAAAAAAAAGTAATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:9,0:8,0:8,9:0.5:0,0:22.2:1.0:31.6:1.0:1.0:0.0:58.8:18.0:0.5:0.1667:1.2 0/0:1:0:0,0:1,0:1,0:0.0:0,0:7.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:5.0 +19 15288072 . A T 101 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=14.0;MSILEN=1.0;SSF=0.13364;SOR=0.0;LSEQ=TCCATCTCGGGAAAAAAAAA;RSEQ=AAAAGTAATTATTGGATGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:10,0:12,0:12,10:0.4167:0,0:23.9:1.0:30.7:1.0:1.0:0.0:58.9:9.0:0.3913:0.0:1.2 0/0:5:0:0,0:5,0:5,0:0.0:0,0:7.8:1.0:29.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 +19 15290491 . G A 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.02019;SOR=0.0;LSEQ=TCACCTGAGATCAGGAGTTC;RSEQ=AGACCAGCCTGGCCAACATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:2,8:2,6:8,10:0.5556:2,2:19.9:1.0:29.8:1.0:1.0:1.31198:30.1:9.0:0.5294:0.0:2.1 0/0:7:0:0,0:0,7:7,0:0.0:0,0:18.4:1.0:30.1:1.0:1.0:0.0:35.7:14.0:1.0:0.0:1.1 +19 15290648 . C T 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.28083;SOR=0.0;LSEQ=AGGTTGCAGTGAGCTGAGAT;RSEQ=GCGCCACTGCACTCGTCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:8:7,1:14,1:15,8:0.3478:1,2:30.1:1.0:32.3:1.0:1.0:1.93655:58.1:16.0:0.3478:0.0:1.0 0/0:5:0:0,0:4,1:5,0:0.0:2,0:11.6:1.0:29.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 +19 15291576 . C G 258 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGGGGACAAAGGCAATAGG;RSEQ=CCCAGTCTGGACGCAGCGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:854:284:139,145:286,282:568,284:0.3326:2,2:25.7:1.0:31.7:1.0:0.71668:1.05786:60.0:46.333:0.3337:0.0:1.1 0/0:808:0:0,0:416,388:804,0:0.0:2,0:23.8:1.0:30.7:1.0:1.0:0.0:59.9:66.0:0.9975:0.0:0.2 +19 15291675 . TG T 84 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.03664;SOR=0.0;LSEQ=TCAGAGTCAGTACTGTGGGG;RSEQ=GGGGGTAGTCTGGGAGAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:6:2,4:159,253:412,6:0.0143:2,2:36.8:1.0:32.5:1.0:1.0:1.25623:55.8:12.0:0.0146:0.0:1.3 0/0:334:0:0,0:116,215:331,0:0.0:2,0:22.4:1.0:30.3:1.0:1.0:0.0:60.0:40.375:0.9908:0.0:0.2 +19 15291699 . T C 210 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GGGTAGTCTGGGAGAAACTG;RSEQ=GCCCCGACTTGGCTTCTCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:108:55,53:108,152:260,108:0.2935:2,2:18.7:1.0:31.1:1.0:0.10749:1.46:60.0:107.0:0.2972:0.0:1.1 0/0:250:0:0,0:106,143:249,0:0.0:2,0:22.3:1.0:29.5:1.0:1.0:0.0:60.0:248.0:1.0:0.0:0.1 +19 15296513 . C T 206 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=5.0;SSF=0.0;SOR=0.0;LSEQ=GGGGAGTACACAAGCAATCT;RSEQ=ATCTCAGAACAAAGTCAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:153:48,105:101,245:346,153:0.306:2,2:24.8:1.0:28.5:1.0:0.67151:1.11:60.0:37.25:0.3028:0.0:1.1 0/0:434:0:0,0:135,298:433,0:0.0:2,0:23.3:1.0:30.7:1.0:1.0:0.0:60.0:85.6:1.0:0.0:0.1 +19 15299048 . G A 241 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCTCCTGAGGTCCTCACCC;RSEQ=AGGGGCAGGTGCAGCTGAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:779:254:151,103:320,205:525,254:0.3261:2,2:23.9:1.0:30.2:1.0:0.69652:1.06468:59.9:62.5:0.3255:0.0:1.1 0/0:718:0:0,0:403,315:718,0:0.0:2,0:24.4:1.0:29.5:1.0:1.0:0.0:60.0:78.778:1.0:0.0:0.2 +19 15308287 . G C 232 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCCACACACAGGGCCCACT;RSEQ=GTGGCTCTGAGCCAGGCACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:753:230:134,96:297,222:519,230:0.3054:2,2:26.1:1.0:29.6:1.0:0.8104:1.04:59.8:16.692:0.3113:0.0:1.5 0/0:694:0:0,0:391,303:694,0:0.0:2,0:24.4:1.0:29.2:1.0:1.0:0.0:59.8:10.966:1.0:0.0:0.5 +19 15308545 . G A 119 q25;MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.0001;SOR=0.0489;LSEQ=CCCCCATCCACAGTTCCCAC;RSEQ=CCCCCCCCCCCCCCGCCCCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:28:0,28:1,21:22,28:0.4667:1,1:19.3:1.0:24.9:1.0:0.44:0.0:59.2:2.5:0.5405:0.0:1.9 0/1:25:1:0,1:0,23:23,1:0.04:1,0:42.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0455:0.0:1.0 +19 15311604 . GC G 77 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.06948;SOR=0.0;LSEQ=GTCCCGGCCCCTCACCTGCA;RSEQ=CCCCGGCCCCGCTAGCAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:5:2,3:86,139:225,5:0.0217:2,2:30.0:1.0:33.2:1.0:1.0:1.08:60.0:10.0:0.0221:0.0:0.0 0/0:182:0:0,0:66,116:182,0:0.0:2,0:26.8:1.0:30.6:1.0:1.0:0.0:60.0:90.0:1.0:0.0:0.2 +19 15366010 . A AG 204 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.0;SOR=0.10989;LSEQ=ATTATAATTGGAAAAAAAAA;RSEQ=GGGGGGGGGCGCAGAAAGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:75:73,2:61,0:61,75:0.4967:1,1:24.3:1.0:32.8:1.0:0.50163:0.0:59.6:24.0:0.518:0.1457:0.7 0/1:103:10:9,1:65,9:74,10:0.0971:2,2:27.4:1.0:31.9:1.0:1.0:1.24:60.0:20.0:0.1053:0.0:0.8 +19 15366663 . G A 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01247;SOR=0.0;LSEQ=ATCCTCCCCAACCAAACATG;RSEQ=TGAGCTCCGAAGGCTCATCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:17:15,2:27,4:31,17:0.3542:2,2:26.9:1.0:29.9:1.0:1.0:1.11:58.2:16.0:0.3404:0.0:1.2 0/0:13:0:0,0:11,2:13,0:0.0:2,0:25.6:1.0:30.7:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.0 +19 15890625 . CG GA 198 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01285;LSEQ=ATAGGTCCAGGCCAGGAAGC;RSEQ=GCCAGGAGCCGGGAGGCCCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:131:80:24,56:0,1:1,80:0.6107:0,2:21.8:1.0:31.4:1.0:1.0:0.0:59.4:79.0:0.627:0.0763:1.0 0/1:103:2:1,1:10,19:29,2:0.0194:2,2:17.0:1.0:26.8:1.0:1.0:1.86:60.0:4.0:0.0198:0.0097:0.5 +19 15890725 . G T 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00255;SOR=0.0;LSEQ=AGGCTCAGCTGCGGCATCCT;RSEQ=CAGGGCAGACAGGATGGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:10:0,10:0,6:6,10:0.625:0,0:17.3:1.0:30.2:1.0:1.0:0.0:50.7:20.0:0.625:0.0:1.0 0/0:10:0:0,0:0,10:10,0:0.0:0,0:26.3:1.0:30.8:1.0:1.0:0.0:44.6:20.0:1.0:0.0:0.6 +19 17953950 . G C 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTTGAGACTGAGGCCCACG;RSEQ=GGAGGCGCCCACTCACCAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:35:11,24:203,317:520,35:0.0631:2,2:24.0:1.0:30.1:1.0:0.47356:1.39638:60.0:34.0:0.0622:0.0:1.1 0/0:585:0:0,0:251,333:584,0:0.0:2,0:29.0:0.0:12.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 +19 18266882 . C T 58 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0294;SOR=0.0;LSEQ=CCGGCCTCAACGAGCGCACA;RSEQ=GGCAGCGAGGTGACTTCCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:449:5:1,4:186,257:443,5:0.0111:2,2:9.6:1.0:25.4:1.0:0.40613:2.88904:60.0:4.0:0.009:0.0:1.0 0/0:458:0:0,0:204,254:458,0:0.0:2,0:25.4:1.0:30.0:1.0:1.0:0.0:59.9:90.6:1.0:0.0:0.3 +19 18271576 . C T 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=8e-05;SOR=0.0;LSEQ=TGACCAGGCCACTGCATGTG;RSEQ=TGTGCCCTCTCCCAGTTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:17:12,5:37,13:50,17:0.2537:2,2:32.5:1.0:31.3:1.0:0.76166:1.1828:60.0:34.0:0.2615:0.0:1.0 0/0:45:0:0,0:37,8:45,0:0.0:2,0:21.3:1.0:31.7:1.0:1.0:0.0:60.0:90.0:1.0:0.0:0.2 +19 18277820 . C G 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0028;SOR=0.0;LSEQ=GCCAGACATGGTGGTGCACA;RSEQ=CTGTGGTCCCAGCTACTCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:11:10,1:90,0:90,11:0.1089:1,2:23.3:1.0:34.3:1.0:0.10891:0.0:59.3:22.0:0.11:0.0:1.1 0/0:73:0:0,0:72,1:73,0:0.0:1,0:26.6:1.0:31.8:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 +19 18279861 . C T 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00691;SOR=0.09972;LSEQ=GGAAAGCTTGGCGGGGAGGC;RSEQ=AGCCTTCCGACTCCCCCTCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:11:6,5:221,104:325,11:0.0326:2,2:19.3:1.0:28.6:1.0:0.34471:1.7675:60.0:22.0:0.0328:0.0:1.2 0/0:299:1:0,1:192,106:298,1:0.0033:2,0:1.0:0.0:23.0:0.0:0.35786:0.0:60.0:2.0:0.0034:0.0:1.0 +19 18280096 . G A 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.05158;LSEQ=GCCCCGGCCCGCCGCCTGCC;RSEQ=CCCGCTGAGCACCGAGGACC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:72:23:7,16:14,35:49,23:0.3194:2,2:19.3:1.0:29.9:1.0:1.0:1.09:60.0:22.0:0.3099:0.0:1.5 0/1:86:2:0,2:30,54:84,2:0.0233:2,0:11.0:1.0:30.5:1.0:0.54036:0.0:60.0:4.0:0.0238:0.0:1.0 +19 19256768 . TG T 73 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.06176;SOR=0.0;LSEQ=CGCTCAGACTTGATGCTGAC;RSEQ=GGGGGGTCGGCGGGGAGGCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:409:5:2,3:156,247:403,5:0.0122:2,2:30.6:1.0:31.6:1.0:1.0:1.06:60.0:10.0:0.0123:0.0:0.0 0/0:404:0:0,0:180,224:404,0:0.0:2,0:23.6:1.0:30.8:1.0:1.0:0.0:60.0:201.0:1.0:0.0:0.3 +19 19260105 . T C 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTACTTCAGCAGCACACGG;RSEQ=CCATGTCCGTGCTGGCATAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:24:9,15:333,321:654,24:0.0353:2,2:27.2:1.0:32.0:1.0:0.21768:1.72759:60.0:48.0:0.036:0.0:1.1 0/0:641:0:0,0:332,309:641,0:0.0:2,0:23.2:1.0:28.4:1.0:1.0:0.0:60.0:52.417:1.0:0.0:0.2 +19 30311555 . CCCCT TC 117 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=12.0;MSILEN=1.0;SSF=0.00041;SOR=0.0;LSEQ=ATTACAAGTTTTTTTTTTTT;RSEQ=CCCTCAAGTAAAACTTACTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:17:15,2:187,30:217,17:0.0717:2,2:18.5:1.0:28.7:1.0:1.0:1.2:59.1:16.0:0.0727:0.0338:1.2 0/0:148:0:0,0:124,23:147,0:0.0:2,0:21.9:1.0:29.4:1.0:1.0:0.0:59.7:13.7:1.0:0.0:0.3 +19 30312874 . C T 251 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00499;LSEQ=GAACTTCTTTTCTCAATCAT;RSEQ=GGTCTCTTTTCTCTCTGTTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:788:296:187,109:299,193:492,296:0.3756:2,2:24.5:1.0:30.6:1.0:0.54512:1.11:60.0:58.2:0.3755:0.0:1.1 0/0:670:2:0,2:406,262:668,2:0.003:2,0:1.0:0.0:24.5:1.0:0.1549:0.0:60.0:4.0:0.003:0.0:1.0 +19 30313622 . G T 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01107;SOR=0.0;LSEQ=GCACTTTGGGAGGCCGAGGT;RSEQ=GGCCGATCACTTGAGGCCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:9:0,9:1,78:79,9:0.1023:1,0:26.7:1.0:30.4:1.0:1.0:0.0:48.6:18.0:0.1059:0.0:1.2 0/0:60:0:0,0:0,60:60,0:0.0:1,0:27.7:1.0:30.9:1.0:1.0:0.0:49.5:120.0:1.0:0.0:0.6 +19 33792520 . G A 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.04964;SOR=0.14019;LSEQ=GCCTTGCCCGCGCCGCTGCC;RSEQ=CCACTCGCGCGGAGGTCGGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:793:9:6,3:240,544:784,9:0.0113:2,2:17.1:1.0:30.1:1.0:0.02911:4.52:60.0:18.0:0.0116:0.0:1.3 0/0:623:1:1,0:215,407:622,1:0.0016:2,0:1.0:0.0:24.0:0.0:0.34671:0.0:60.0:2.0:0.0016:0.0:1.0 +19 33792751 . C T 65 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=6.0;SSF=0.07836;SOR=0.0;LSEQ=GGCGGGTGCGGGTGCGGGTG;RSEQ=GAGGGCGGCGGCGGCGGCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:268:5:2,3:145,115:260,5:0.0187:2,2:6.0:1.0:28.0:1.0:0.65853:1.88672:60.0:10.0:0.019:0.0:1.2 0/0:192:0:0,0:104,86:190,0:0.0:2,0:13.5:1.0:30.0:1.0:1.0:0.0:59.8:30.667:0.9892:0.0:0.3 +19 33905969 . G A 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00832;SOR=0.0;LSEQ=CCACATGGCAAGCCCTGTGC;RSEQ=CCAGGCCAGACAGGCAGCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:8,1:24,2:26,9:0.2571:2,2:27.4:1.0:31.1:1.0:1.0:1.48133:60.0:18.0:0.2571:0.0:1.1 0/0:23:0:0,0:19,4:23,0:0.0:2,0:25.0:1.0:28.3:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.6 +19 34080443 . CC TT 163 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTGACACTTGTGAGGCATT;RSEQ=TTTTTGAACAGTGCCCATTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:38:14,24:24,38:62,38:0.3725:2,2:27.9:1.0:31.1:1.0:1.0:1.08183:38.2:76.0:0.3838:0.0:1.3 0/0:70:0:0,0:32,38:70,0:0.0:2,0:22.7:1.0:30.3:1.0:1.0:0.0:42.6:140.0:1.0:0.0:0.2 +19 39538680 . G A 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGATTTGAGGGTGCCCACAG;RSEQ=ATTTGCTGAAGAATTGGGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:132:21:6,15:18,93:111,21:0.1591:2,2:22.3:1.0:30.8:1.0:0.21631:2.05:60.0:42.0:0.1603:0.0:2.1 0/0:108:0:0,0:28,80:108,0:0.0:2,0:23.2:1.0:30.6:1.0:1.0:0.0:60.0:216.0:1.0:0.0:0.7 +19 40739513 . A G 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00303;SOR=0.0;LSEQ=TTGTGTGGATTAAAACCTGA;RSEQ=TCTCCAACCGCCCAACAGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:29.7:1.0:31.9:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 0/0:4:0:0,0:3,1:4,0:0.0:2,0:27.5:1.0:31.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +19 41173904 . TTGC T 72 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=6.0;MSILEN=3.0;SSF=0.16149;SOR=0.0;LSEQ=TGCTGCTGCTGCTGTTGCTG;RSEQ=TGCTGCTGCTGCTGCTGGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:5:1,4:50,53:103,5:0.0463:2,2:34.2:1.0:31.4:1.0:0.36715:3.733:60.0:10.0:0.0476:0.0:0.0 0/0:60:0:0,0:26,34:60,0:0.0:2,0:26.0:1.0:29.4:1.0:1.0:0.0:53.4:29.0:1.0:0.0:0.8 +19 41727143 . G C 223 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTCCCAGCCTGGCTATGTTG;RSEQ=GCTGGAGGGTGAGCTCTGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:845:154:63,91:276,415:691,154:0.1822:2,2:26.8:1.0:30.8:1.0:0.8559:1.04:59.9:153.0:0.1841:0.0:1.1 0/0:748:0:0,0:312,432:744,0:0.0:2,0:25.1:1.0:30.0:1.0:1.0:0.0:59.9:42.765:0.9945:0.0:0.2 +19 41727197 . C T 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGGGTCAGAGGACATGTGG;RSEQ=GCTCATAGGTTGTGGGAAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:87:16,71:46,240:286,87:0.2332:2,2:22.7:1.0:30.3:1.0:0.62336:1.18:59.8:86.0:0.2356:0.0:1.1 0/0:274:0:0,0:65,209:274,0:0.0:2,0:23.3:1.0:29.2:1.0:1.0:0.0:60.0:29.444:1.0:0.0:0.1 +19 41727231 . GGGTCAA G 167 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGAAGTCAGGAATCCTGAG;RSEQ=GGTCAAAGGGTGCTGGAGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:188:39:3,36:6,142:148,39:0.2074:1,2:27.5:1.0:31.7:1.0:0.39773:1.96:59.9:38.0:0.2077:0.0213:1.0 0/0:119:0:0,0:8,111:119,0:0.0:2,0:21.1:1.0:30.2:1.0:1.0:0.0:60.0:58.5:1.0:0.0:0.1 +19 41748982 . G A 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.07553;SOR=0.0;LSEQ=GAGAGGCTGGAGGCAGGGAG;RSEQ=CCAGTGAGGAGGCTGGTGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:5:3,2:73,304:377,5:0.0131:2,2:16.0:1.0:28.8:1.0:0.05591:6.2:60.0:10.0:0.0134:0.0:1.0 0/0:283:0:0,0:58,225:283,0:0.0:2,0:22.4:1.0:31.2:1.0:1.0:0.0:60.0:93.333:1.0:0.0:0.1 +19 41749397 . C T 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00042;SOR=0.0;LSEQ=GTAGCTGCCCAAGGCATGCT;RSEQ=AGCAAATGTTAGCACAGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:241:17:17,0:219,5:224,17:0.0705:1,1:25.9:1.0:31.9:1.0:1.0:0.0:59.6:34.0:0.0723:0.0:1.1 0/0:146:0:0,0:141,5:146,0:0.0:1,0:26.8:1.0:31.2:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 +19 41749511 . TC T 117 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.00022;SOR=0.0;LSEQ=CTGCCCTCACCTACTCCCCC;RSEQ=CCCCCCAGAGAAGTGTTTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1346:14:9,5:706,625:1331,14:0.0104:2,2:20.6:1.0:30.8:1.0:0.43468:1.59:60.0:28.0:0.0106:0.0015:0.1 0/0:1118:0:0,0:594,523:1117,0:0.0:2,0:24.6:1.0:30.2:1.0:1.0:0.0:60.0:43.68:1.0:0.0:0.2 +19 41759474 . C T 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGCATCAAGGACTCTGTTGA;RSEQ=CTCTCCTCCCACCTGCCTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:642:55:38,17:406,181:587,55:0.0857:2,2:21.6:1.0:30.5:1.0:1.0:1.00348:60.0:26.5:0.0841:0.0:1.1 0/0:515:0:0,0:327,188:515,0:0.0:2,0:23.2:1.0:30.9:1.0:1.0:0.0:60.0:127.75:1.0:0.0:0.2 +19 41763269 . A T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.15993;SOR=0.0;LSEQ=AAAGTATTATGTTTCTATGA;RSEQ=TACTTGTGATGCTCCCAGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:158:5:5,0:152,1:153,5:0.0316:1,0:26.2:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.0318:0.0:1.0 0/0:101:0:0,0:99,2:101,0:0.0:1,0:19.0:1.0:30.1:1.0:1.0:0.0:60.0:100.0:1.0:0.0:0.2 +19 42382729 . C G 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAGGGCCAGAGTACAAAGTG;RSEQ=GTATGCGGGAGGGGGACAAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:15.0:1.0:32.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +19 42382745 . A G 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGTGCGTATGCGGGAGGGGG;RSEQ=CAAGAGATGGCGCTGCAGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:3,0:3,5:0.625:0,0:26.2:1.0:28.6:1.0:1.0:0.0:60.0:4.0:0.5714:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +19 42790821 . G C 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00123;SOR=0.0;LSEQ=GGTGTTGGGGGTGGGGGGTA;RSEQ=ACAAAAGGGGTGGGGCTACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:334:13:13,0:309,10:319,13:0.0389:1,1:17.5:1.0:31.8:1.0:1.0:0.0:60.0:26.0:0.0406:0.0:1.0 0/0:226:0:0,0:213,12:225,0:0.0:2,0:17.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:8.0 +19 42791015 . C A 174 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.05001;LSEQ=GCCAGCCTGACCCCTCCGTG;RSEQ=AGCCGAGCGAGGCCCAGCAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1159:54:23,31:472,633:1105,54:0.0466:2,2:23.2:1.0:30.4:1.0:1.0:1.00501:60.0:53.0:0.0462:0.0:1.1 0/0:821:2:2,0:345,472:817,2:0.0024:2,0:1.0:0.0:24.5:1.0:0.17921:0.0:60.0:4.0:0.0024:0.0:1.0 +19 42795554 . T C 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCAACGGCAAAGTCCTGGC;RSEQ=GCCACTGCACCCACTCCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1331:198:109,89:583,549:1132,198:0.1488:2,2:25.9:1.0:29.9:1.0:0.39646:1.15:60.0:32.0:0.1469:0.0:1.1 0/0:1079:0:0,0:549,528:1077,0:0.0:2,0:23.0:0.0:9.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:7.0 +19 42797603 . C T 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0229;SOR=0.0;LSEQ=CTCCTCTCCCATCTGAGGCC;RSEQ=CTGTCTTGGCCTTCCTGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:104:15:7,8:56,33:89,15:0.1442:2,2:28.2:1.0:31.8:1.0:0.26298:1.92661:60.0:30.0:0.1456:0.0:1.2 0/0:30:0:0,0:23,7:30,0:0.0:2,0:23.9:1.0:30.7:1.0:1.0:0.0:60.0:60.0:1.0:0.0:0.0 +19 45856260 . G A 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGGGGTGGGTGGTTCCCC;RSEQ=CGGGAGCAGACAGCAGAGCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:27:19,8:249,94:343,27:0.073:2,2:22.3:1.0:30.3:1.0:0.82419:1.115:60.0:54.0:0.074:0.0:1.3 0/0:276:0:0,0:196,80:276,0:0.0:2,0:23.6:1.0:29.5:1.0:1.0:0.0:59.9:68.0:1.0:0.0:0.2 +19 45868647 . G A 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00481;SOR=0.0;LSEQ=CACTTTGTGAGGCTGAGGTG;RSEQ=GCAGATCACGAGGTCAGGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:0,2:2,9:0.8182:0,0:26.8:1.0:32.4:1.0:1.0:0.0:41.1:18.0:0.8182:0.0:2.0 0/0:5:0:0,0:0,5:5,0:0.0:0,0:19.6:1.0:31.8:1.0:1.0:0.0:48.6:10.0:1.0:0.0:0.4 +19 46376217 . C A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06619;SOR=0.0;LSEQ=GAACAGACACCAGCACCTCC;RSEQ=AAACTGGACGTGGGGTTTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:2,3:10,19:29,5:0.1471:2,2:24.8:1.0:30.2:1.0:1.0:1.26:60.0:10.0:0.1471:0.0:1.0 0/0:25:0:0,0:11,14:25,0:0.0:2,0:25.7:1.0:28.9:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.1 +19 50906507 . C T 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCACGCCCCACACCATTT;RSEQ=CCGGGGTCCCCGCCAGCCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:716:63:20,43:273,380:653,63:0.088:2,2:24.1:1.0:30.1:1.0:0.14026:1.5437:59.7:62.0:0.0883:0.0:1.1 0/0:692:0:0,0:272,419:691,0:0.0:2,0:21.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:7.0 +19 50910196 . A G 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.02125;LSEQ=CTTCTCCTGCTCCACCTCCC;RSEQ=CCCCCAACCCCTGGTCCCTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:791:81:60,21:469,239:708,81:0.1024:2,2:26.8:1.0:28.1:1.0:0.17109:1.46:60.0:12.5:0.1019:0.0:1.1 0/0:829:2:1,1:513,307:820,2:0.0024:2,2:25.5:1.0:11.5:1.0:1.0:1.66985:49.5:0.0:0.0:0.0:4.0 +19 50912821 . G C 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACAGACCCCCTCCGGCGCCA;RSEQ=GTCCTGGATGGACGGCAGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1184:136:68,68:545,502:1047,136:0.1149:2,2:25.0:1.0:31.3:1.0:0.71535:1.08558:60.0:135.0:0.1152:0.0:1.1 0/0:1115:0:0,0:544,566:1110,0:0.0:2,0:23.5:1.0:30.8:1.0:1.0:0.0:60.0:68.375:0.9955:0.0:0.2 +19 50920581 . T C 53 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.06382;SOR=0.0;LSEQ=CCCTTCCCAGCTCCCAGGCC;RSEQ=GTGGGTTGTGGACCCAACCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:5:3,2:126,286:412,5:0.0119:2,2:13.6:1.0:23.2:1.0:0.17441:3.39:60.0:1.5:0.0074:0.0:1.6 0/0:373:0:0,0:142,227:369,0:0.0:2,0:24.4:1.0:29.3:1.0:1.0:0.0:60.0:40.0:0.989:0.0:0.2 +19 52693297 . C CT 177 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTCCCAGCATTGCCCCCCC;RSEQ=ACGTTTCAGCACAGCGCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:55:39,16:98,41:139,55:0.2821:2,2:24.4:1.0:30.7:1.0:1.0:1.02:60.0:110.0:0.288:0.0564:0.3 0/0:164:0:0,0:126,38:164,0:0.0:2,0:23.1:1.0:30.0:1.0:1.0:0.0:59.8:40.0:1.0:0.0:0.3 +19 52714917 . G A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.0;MSILEN=1.0;SSF=0.06636;SOR=0.0;LSEQ=GAGAGTTGGTCTCTGGACAC;RSEQ=GCCACGTGTCAGTTTACCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:0,6:0,10:10,6:0.375:0,0:15.3:1.0:32.3:1.0:1.0:0.0:59.8:12.0:0.375:0.0:2.3 0/0:8:0:0,0:0,8:8,0:0.0:0,0:23.5:1.0:29.3:1.0:1.0:0.0:52.9:16.0:1.0:0.0:0.0 +19 53081735 . C T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01409;SOR=0.0;LSEQ=TTTGGGGCCACTACCTGTCT;RSEQ=CGCGTCTTGATGGTAGTGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:1,5:1,4:5,6:0.5455:2,2:27.8:1.0:29.7:1.0:1.0:1.22474:46.0:12.0:0.5455:0.0:1.0 0/0:9:0:0,0:3,6:9,0:0.0:2,0:24.1:1.0:30.8:1.0:1.0:0.0:46.7:18.0:1.0:0.0:0.1 +2 6636119 . T A 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06798;LSEQ=AGTGCTTCGTTAAACTTCAC;RSEQ=CGGAAGTGCTTCGTTAAACT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:815:106:46,60:363,345:708,106:0.1301:2,2:21.8:1.0:30.4:1.0:0.14505:1.37186:51.3:105.0:0.1316:0.0:1.8 0/1:597:6:3,3:301,290:591,6:0.0101:2,2:21.2:1.0:27.5:1.0:1.0:1.03788:53.3:12.0:0.0103:0.0:1.5 +2 6636414 . G A 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATGGGACACGCTGACGGTT;RSEQ=ATTCCAAACGTGGTCTTGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:974:54:22,32:443,477:920,54:0.0554:2,2:25.3:1.0:30.0:1.0:0.32759:1.35045:44.5:108.0:0.0562:0.0:2.0 0/0:695:0:0,0:344,350:694,0:0.0:2,0:24.9:1.0:30.8:1.0:1.0:0.0:50.5:85.75:0.9985:0.0:0.5 +2 6636735 . G A 132 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=CCACAGGACGTCCATGAGCC;RSEQ=GATCGTCTGCATGGTCAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:648:20:10,10:305,322:627,20:0.0309:2,2:31.2:1.0:30.6:1.0:1.0:1.06:57.9:19.0:0.0299:0.0:2.1 0/0:443:0:0,0:217,226:443,0:0.0:2,0:26.5:1.0:29.7:1.0:1.0:0.0:59.5:62.286:1.0:0.0:1.0 +2 7541706 . TA T 175 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.0;SOR=0.13436;LSEQ=TTATAAAATTCACAGATTCA;RSEQ=AAAAAAAAAGCAAAATGTTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:47:40,7:93,18:111,47:0.2938:2,2:27.0:1.0:31.6:1.0:1.0:1.11:59.8:94.0:0.2994:0.0563:2.4 0/1:152:8:7,1:115,29:144,8:0.0526:2,2:22.6:1.0:31.2:1.0:1.0:1.76:60.0:16.0:0.0533:0.0132:1.4 +2 7541718 . C G 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGATTCATAAAAAAAAAAG;RSEQ=AAAATGTTCTCTCTTTTCTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:195:59:49,10:104,29:133,59:0.3026:2,2:24.4:1.0:31.1:1.0:0.56038:1.36:59.9:28.5:0.3167:0.0:3.0 0/0:192:0:0,0:146,45:191,0:0.0:2,0:23.4:1.0:30.9:1.0:1.0:0.0:60.0:22.875:1.0:0.0:1.3 +2 14528089 . C T 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TCATCCTCCTTTCTCTTTCC;RSEQ=TCTCTTTCTCTCATCTCTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:412:42:13,29:119,250:369,42:0.1019:2,2:24.9:1.0:30.0:1.0:1.0:1.0617:60.0:20.0:0.1003:0.0:1.2 0/0:308:0:0,0:106,201:307,0:0.0:2,0:23.8:1.0:31.0:1.0:1.0:0.0:58.3:152.5:0.9967:0.0:0.7 +2 16085519 . C T 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.10683;SOR=0.0;LSEQ=AGCAGTCTGCCAGGGTCTGC;RSEQ=GGAAGAGACAGATAAGCATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:8:8,0:83,1:84,8:0.087:1,0:19.0:1.0:33.1:1.0:1.0:0.0:60.0:16.0:0.0879:0.0:1.1 0/0:34:0:0,0:34,0:34,0:0.0:1,0:22.4:1.0:30.4:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.2 +2 16086469 . C T 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACAGCGCTAAACGTTGGTGA;RSEQ=GGTTGGGAGCCTCTGGGGCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:30.8:1.0:31.8:1.0:1.0:0.0:58.0:10.0:0.8333:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 17675655 . TTTTCA T 83 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.03507;SOR=0.0;LSEQ=GGCCAGTGATGATGACCATT;RSEQ=TGCCTGACACCCTATTCTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:141:6:4,2:90,44:134,6:0.0426:2,2:32.5:1.0:32.3:1.0:1.0:1.02258:60.0:12.0:0.0426:0.0:0.0 0/0:113:0:0,0:66,47:113,0:0.0:2,0:23.1:1.0:29.7:1.0:1.0:0.0:57.7:112.0:1.0:0.0:0.5 +2 25466810 . C T 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02818;LSEQ=GACAGCACCCGGATGGGCTT;RSEQ=CTCTTCTCAGCTGGGACAGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1076:40:18,22:479,556:1035,40:0.0372:2,2:26.1:1.0:30.5:1.0:1.0:1.05292:60.0:80.0:0.0384:0.0:1.2 0/0:921:1:0,1:425,492:917,1:0.0011:2,0:1.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 +2 25469945 . C T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02584;SOR=0.13132;LSEQ=GGACCTCGTAGATGGCTTTG;RSEQ=GGTACATGGGCTGCTTGTTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:871:9:2,7:465,396:861,9:0.0103:2,2:11.0:1.0:28.4:1.0:0.08951:4.10401:59.4:18.0:0.0105:0.0:1.2 0/0:731:1:1,0:391,336:727,1:0.0014:2,0:47.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0014:0.0:2.0 +2 25471169 . GC G 221 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.1406;LSEQ=CTTGACCTCTCCAGGAATTA;RSEQ=AAGGCCACCTGACACTCAAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:118:18,100:33,208:241,118:0.3278:2,2:20.1:1.0:32.2:1.0:0.74801:1.13:60.0:117.0:0.3296:0.0694:0.2 0/1:250:16:4,12:40,194:234,16:0.064:2,2:18.4:1.0:30.6:1.0:0.4938:1.61:60.0:32.0:0.0643:0.012:0.4 +2 25972936 . C T 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTCTCAGATTCCTGTTCAG;RSEQ=AGAGGTGACTGGCTTCTGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:72:33,39:466,447:913,72:0.0729:2,2:22.0:1.0:28.7:1.0:0.46285:1.23179:60.0:71.0:0.0727:0.0:1.1 0/0:784:0:0,0:374,408:782,0:0.0:2,0:24.1:1.0:31.3:1.0:1.0:0.0:60.0:77.2:0.9974:0.0:0.1 +2 27014885 . G A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01526;SOR=0.0;LSEQ=TAAAACAGACAAAAATCCCT;RSEQ=CTCTGTGGAGGGTAGGCACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:10:10,0:162,3:165,10:0.0571:1,0:30.8:1.0:28.0:1.0:1.0:0.0:60.0:20.0:0.0578:0.0:1.6 0/0:108:0:0,0:107,1:108,0:0.0:1,0:20.5:1.0:31.2:1.0:1.0:0.0:60.0:35.0:1.0:0.0:0.2 +2 29415792 . G A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGCAGAGCACACACAATTT;RSEQ=AAAGAAGCATAAGGAAGTAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1.0:0,0:26.0:1.0:26.9:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 29429741 . C CTT 72 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGGCTGTTAATGTGTGGTC;RSEQ=CAGCCAGCAATGGCAGCATC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:28.8:1.0:31.4:1.0:1.0:0.0:60.0:10.0:0.8333:0.1667:0.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 29429948 . C T 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02378;LSEQ=TTTCCCTCCCTACTAACACA;RSEQ=GGGCTCCCGGCTTAGAGTAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:57:48,9:267,37:304,57:0.1579:2,2:24.1:1.0:30.6:1.0:0.51498:1.35182:59.1:56.0:0.1569:0.0:1.1 0/0:226:1:1,0:180,45:225,1:0.0044:2,0:2.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0045:0.0:1.0 +2 29437182 . T C 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05495;SOR=0.0;LSEQ=GTATTTGTACATTTGAAGTC;RSEQ=TCCCAGGTAATATGATGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:1,7:0,3:3,8:0.7273:0,2:22.3:1.0:32.6:1.0:1.0:0.0:58.8:16.0:0.7273:0.0:1.4 0/0:3:0:0,0:0,3:3,0:0.0:0,0:14.0:1.0:31.0:0.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +2 29445798 . T C 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGCTTTTCCCCGGGGGAGG;RSEQ=TCATGCTCCTTGGGGAGAGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:6,6:0,0:0,12:1.0:0,2:25.1:1.0:30.3:1.0:1.0:0.0:58.9:11.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 29449423 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCACATGCACAGCTGCTGCT;RSEQ=TAAGGAAACCTAGGAGAGGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:9:9,0:5,0:5,9:0.6429:0,0:21.3:1.0:25.6:1.0:1.0:0.0:54.2:8.0:0.6154:0.0:1.9 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 29451354 . A G 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCAGGAAGCTGGTGGGCTG;RSEQ=GGTAGGGAGCAGGAGTAAGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:6,1:0,0:0,7:1.0:0,2:16.4:1.0:32.4:1.0:1.0:0.0:54.6:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 29451557 . GAGGCAGGGTGCTGGCTCGAAAGCCAGCACCCTGCCTCTGGCTGGTCC G 78 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=2.0;MSILEN=1.0;SSF=0.33914;SOR=0.0;LSEQ=GCTGTCGCTGAGGAAGCCTG;RSEQ=AGGCAGGTCGAGAGGGAGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:6:6,0:64,0:64,6:0.0857:1,0:28.8:1.0:30.4:1.0:1.0:0.0:56.8:12.0:0.0896:0.0857:0.5 0/0:18:0:0,0:18,0:18,0:0.0:1,0:26.3:1.0:28.9:1.0:1.0:0.0:60.0:17.0:1.0:0.0:0.4 +2 29451675 . A AGGGCG 160 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=4;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGCCAGGGGAGGGCAGGGG;RSEQ=GGGCAGGGCAGGGAGGTGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:598:35:29,6:428,128:556,35:0.0585:2,2:20.9:1.0:31.2:1.0:0.53437:1.44:59.9:70.0:0.0609:0.0217:0.1 0/0:300:0:0,0:218,81:299,0:0.0:2,0:22.3:1.0:28.2:1.0:1.0:0.0:59.9:32.222:1.0:0.0:0.1 +2 29451986 . C T 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00036;SOR=0.0;LSEQ=GCTGGCAAGGTTCAATTAGC;RSEQ=ATGCTGGCCAGAGAAGCAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:363:19:2,17:45,299:344,19:0.0523:2,2:24.5:1.0:28.6:1.0:1.0:1.27846:60.0:38.0:0.0532:0.0:1.1 0/0:189:0:0,0:29,160:189,0:0.0:2,0:21.0:1.0:31.3:1.0:1.0:0.0:60.0:62.0:1.0:0.0:0.2 +2 29454901 . G GCAAGTTGGTAAAACC 103 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGGGGAGGCTCTAACAATT;RSEQ=CAGGGAGGGCCAGCTGGCTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:11,0:6,1:7,11:0.6111:2,0:18.3:1.0:30.0:1.0:0.38889:0.0:56.5:22.0:0.6471:0.5:0.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 29456384 . T C 267 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGTCATGAGGCTCTGACAT;RSEQ=GCAGATGCACAGGAACCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1304:370:240,130:602,332:934,370:0.2837:2,2:24.8:1.0:31.3:1.0:0.89801:1.02:60.0:369.0:0.2856:0.0:1.1 0/0:813:0:0,0:437,297:734,0:0.0:2,0:37.0:0.0:18.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 +2 29456865 . T TG 72 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=9.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGAAGGATAGGGAGTTTTT;RSEQ=TTTGTTTGTTTTTGTTTTTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:0,6:6,5:0.4545:0,0:29.2:1.0:31.4:1.0:1.0:0.0:59.0:10.0:0.4545:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 29456882 . T C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTTTTTTGTTTGTTTTTGTT;RSEQ=TTTTCACAGAGAGTGGGGCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:32.6:1.0:32.4:1.0:1.0:0.0:59.0:10.0:0.5556:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 29519851 . C A 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02257;LSEQ=CATCCTGCCTTGCTCCTTCC;RSEQ=GGTTTTGTTCTCCACTAGCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1147:51:22,29:523,573:1096,51:0.0445:2,2:25.6:1.0:30.9:1.0:0.56788:1.20296:59.6:50.0:0.0439:0.0:1.1 0/0:954:1:1,0:439,512:951,1:0.001:2,0:1.0:0.0:25.0:0.0:0.46218:0.0:60.0:2.0:0.0011:0.0:1.0 +2 29940332 . A G 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00845;SOR=0.0;LSEQ=GAAAGACTTCTTTTGCATAT;RSEQ=GGGAGCTGAGGGAATGCCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:12:12,0:82,1:83,12:0.1263:1,0:27.6:1.0:31.7:1.0:1.0:0.0:60.0:11.0:0.1222:0.0:1.2 0/0:52:0:0,0:51,1:52,0:0.0:1,0:18.7:1.0:28.7:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.1 +2 29940820 . C T 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAGGATCTCTGGGAGATGAA;RSEQ=TAGAAGCCAGGGCACTTAAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:0,12:0,1:1,12:0.9231:0,0:26.9:1.0:30.4:1.0:1.0:0.0:57.6:24.0:0.9231:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 30433204 . T G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.12131;SOR=0.0;LSEQ=TTATGATGGGGAACATTTCA;RSEQ=TCTCAAAAAAAAAAAAAATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:3,2:7,4:11,5:0.3125:2,2:40.8:1.0:33.0:1.0:1.0:1.15538:60.0:10.0:0.3333:0.0:1.6 0/0:10:0:0,0:6,4:10,0:0.0:2,0:24.1:1.0:29.4:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.1 +2 43081218 . CGT C 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=6.0;MSILEN=2.0;SSF=0.15097;SOR=0.0;LSEQ=TGTGTGTTTACATGTGTCTG;RSEQ=GTGTGTGTGTTGTGCCTGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:40:5:3,2:20,15:35,5:0.125:2,2:37.0:1.0:30.8:1.0:1.0:1.12:60.0:10.0:0.125:0.0:0.2 0/0:22:0:0,0:13,9:22,0:0.0:2,0:32.1:1.0:30.0:1.0:1.0:0.0:59.9:44.0:1.0:0.0:0.1 +2 43952068 . G A 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0017;SOR=0.0;LSEQ=TTCTTGTTCTCAAGGACAAG;RSEQ=AGATCTGGGTCATGGACACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:10:1,9:1,51:52,10:0.1613:1,2:18.2:1.0:30.5:1.0:0.29878:5.43:60.0:20.0:0.1639:0.0:1.0 0/0:53:0:0,0:2,51:53,0:0.0:1,0:20.4:1.0:30.7:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.1 +2 44311676 . C A 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.26749;SOR=0.0;LSEQ=ATTCTCTGCTTGGCCAAACT;RSEQ=TAGTCAGCCTTCTGAACTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:4,2:8,2:10,6:0.375:2,2:22.5:1.0:28.8:1.0:0.6044:1.91107:60.0:12.0:0.375:0.0:1.0 0/0:4:0:0,0:2,2:4,0:0.0:2,0:19.8:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 +2 44561591 . C CA 69 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.11433;SOR=0.18755;LSEQ=ATCATAACTTCTTTTTGTGA;RSEQ=AAAAAAAAATACTTCCAGAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:5:1,4:68,147:215,5:0.0227:2,2:24.0:1.0:29.8:1.0:1.0:1.8458:60.0:10.0:0.0236:0.0045:1.0 0/0:231:1:1,0:82,146:228,1:0.0043:2,0:49.0:0.0:32.0:0.0:0.36245:0.0:60.0:2.0:0.0044:0.0:0.0 +2 46128526 . C A 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GTAAGGTATTAGCCTGTTCA;RSEQ=ATATTTCTCATGTAATATTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:411:40:10,30:115,256:371,40:0.0973:2,2:24.2:1.0:31.5:1.0:0.47553:1.34673:60.0:80.0:0.0978:0.0:1.0 0/0:240:0:0,0:79,160:239,0:0.0:2,0:24.8:1.0:31.5:1.0:1.0:0.0:60.0:78.667:1.0:0.0:0.3 +2 47602178 . A T 139 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00252;SOR=0.10309;LSEQ=TGTCCAGAGAACAGAGGGTC;RSEQ=ATATTAGAAAAGGTGTTCCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:34:19:19,0:15,0:15,19:0.5588:1,1:25.5:1.0:32.9:1.0:1.0:0.0:58.9:38.0:0.5588:0.0:1.0 0/1:18:2:2,0:16,0:16,2:0.1111:1,0:10.5:1.0:32.0:0.0:1.0:0.0:60.0:4.0:0.1111:0.0:1.0 +2 47613870 . T C 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.05601;LSEQ=TTTGTTAGTTTAACATCATA;RSEQ=ATTTGTAATAGTGAAACCTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:71:33:3,30:1,37:38,33:0.4648:1,2:22.5:1.0:32.8:1.0:0.33147:3.64:59.5:66.0:0.4714:0.0:1.2 0/1:44:2:0,2:1,41:42,2:0.0455:1,0:27.0:1.0:33.5:1.0:1.0:0.0:60.0:4.0:0.0455:0.0:1.0 +2 47630213 . T C 184 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.06602;LSEQ=AACGCAGCCCTGGAAGCTGA;RSEQ=TGGGTGTGGTCGCCGTGGCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:128:53:51,2:70,4:74,53:0.4141:2,1:24.2:1.0:32.2:1.0:1.0:1.45:60.0:52.0:0.4228:0.0:1.1 0/1:68:3:2,1:61,3:64,3:0.0441:1,2:25.0:1.0:30.3:1.0:0.17105:9.36402:60.0:6.0:0.0448:0.0:1.0 +2 47630314 . G T 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGCATTTTCTTCAACCAGGA;RSEQ=GTGAGGAGGTTTCGACATGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:38:19,19:302,266:568,38:0.0627:2,2:25.8:1.0:31.3:1.0:0.73921:1.1351:60.0:76.0:0.0638:0.0:1.1 0/0:492:0:0,0:274,218:492,0:0.0:2,0:26.4:1.0:30.8:1.0:1.0:0.0:60.0:43.727:1.0:0.0:0.2 +2 47630371 . C T 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03863;SOR=0.0;LSEQ=GACGCTGCAGTTGGAGAGCG;RSEQ=GGCCGAGGTCGGCTTCGTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:6:2,4:262,307:569,6:0.0104:2,2:26.3:1.0:28.7:1.0:0.69216:1.70532:60.0:12.0:0.0106:0.0:1.0 0/0:444:0:0,0:210,233:443,0:0.0:2,0:24.7:1.0:29.8:1.0:1.0:0.0:60.0:109.75:0.9977:0.0:0.2 +2 47637065 . C T 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGTTGCAGTGAGTTGAGAT;RSEQ=GCACCATTGCACTCTAGCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:6:6,0:13,0:13,6:0.3158:1,0:30.7:1.0:31.8:1.0:1.0:0.0:48.5:12.0:0.3158:0.0:1.0 0/0:2:0:0,0:2,0:2,0:0.0:0,0:12.0:1.0:31.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 +2 47693788 . A T 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10365;LSEQ=TACTTTTTCTTTTCTTCTTG;RSEQ=TTATCAAGGCTTGGACCCTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:210:150,60:248,97:345,210:0.3784:2,2:21.0:1.0:29.5:1.0:0.9228:1.02265:60.0:51.5:0.378:0.0:1.2 0/1:422:25:19,6:276,121:397,25:0.0592:2,2:19.0:1.0:29.5:1.0:0.65389:1.39:60.0:50.0:0.0601:0.0:1.1 +2 47703241 . A G 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTCTTTCTAGGCCACAGTCA;RSEQ=ATTACAGGTATATTTGTCAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:12:12,0:4,0:4,12:0.75:0,0:29.2:1.0:31.4:1.0:1.0:0.0:54.9:11.0:0.7333:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 47703290 . G A 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGATGAAAGGCCCAGTATC;RSEQ=GTTTGTCTGAAGATATATAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:7,0:9,0:9,7:0.4375:0,0:21.7:1.0:32.0:1.0:1.0:0.0:60.0:14.0:0.4375:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 47704027 . G C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGGAATGGTCCTTCTTGCC;RSEQ=TTTATCCAACTTCTTTCTAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1.0:0,0:17.4:1.0:31.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:2.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 47888014 . A G 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03158;LSEQ=CTTCAAAGAATGTATCTCTC;RSEQ=TCCTGTAGAGATATTAAATG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:124:100:55,45:14,9:23,100:0.8065:2,2:26.7:1.0:30.7:1.0:0.64867:1.27026:60.0:99.0:0.8049:0.0:1.1 0/1:114:13:6,7:53,48:101,13:0.114:2,2:26.2:1.0:31.4:1.0:0.77178:1.28533:60.0:26.0:0.1161:0.0:1.1 +2 47905398 . C A 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00473;LSEQ=CATTTCCTAGGCCTGAAATT;RSEQ=ATTGCTTGTGTACCCAGAAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:808:170:79,91:308,330:638,170:0.2104:2,2:26.3:1.0:29.6:1.0:0.72978:1.07498:60.0:41.5:0.2083:0.0:1.1 0/0:795:1:1,0:394,400:794,1:0.0013:2,0:1.0:0.0:25.0:0.0:0.49686:0.0:60.0:2.0:0.0013:0.0:2.0 +2 48010214 . C T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.54404;SOR=0.0;LSEQ=GGGGCCTGGCGCGCACCGCC;RSEQ=GCGCACGGCGAGGCGCCTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:14,5:0.2632:1,0:21.8:1.0:34.0:0.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.0 0/0:5:0:0,0:5,0:5,0:0.0:0,0:18.0:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 +2 48025764 . C T 213 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.13647;LSEQ=TGGCAGGTAGGCACAACTTA;RSEQ=GTAACAGATAAGAGTGAAGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:122:86,36:231,102:333,122:0.2681:2,2:23.6:1.0:30.8:1.0:0.90841:1.05:60.0:121.0:0.2695:0.0:1.3 0/1:526:25:17,8:321,180:501,25:0.0475:2,2:21.5:1.0:28.9:1.0:0.83162:1.19:60.0:24.0:0.046:0.0:1.4 +2 48028465 . C T 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.14877;SOR=0.0;LSEQ=AATTTAAGTTACTTGAAACT;RSEQ=GCTTTTATCTTAGTAGCCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:0,21:21,5:0.1923:1,0:23.4:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.1923:0.0:1.0 0/0:13:0:0,0:0,13:13,0:0.0:1,0:28.6:1.0:29.1:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 +2 48030629 . G T 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTCGCCCAGTAATTCTGTT;RSEQ=CCGGAAGATACCCCCCCCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:73:30,43:599,691:1290,73:0.0536:2,2:24.7:1.0:29.6:1.0:0.4:1.2423:60.0:23.333:0.0524:0.0:1.1 0/0:1438:0:0,0:678,759:1437,0:0.0:2,0:25.4:1.0:31.1:1.0:1.0:0.0:60.0:48.552:1.0:0.0:0.2 +2 48032572 . C T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.02696;SOR=0.0;LSEQ=GGTGATCTGCTTGCCTCGGC;RSEQ=TCCCAAAGTGCTGGGATTAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:5,1:11,3:14,6:0.3:2,2:22.0:1.0:29.3:1.0:1.0:1.34:40.2:5.0:0.2632:0.0:2.0 0/0:15:0:0,0:14,1:15,0:0.0:1,0:22.7:1.0:31.0:1.0:1.0:0.0:41.9:30.0:1.0:0.0:0.8 +2 48033272 . ATTTTTGTTTTAATTCCT A 170 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=19;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.01883;LSEQ=TGTTGCTTTTCTGTCCTAGC;RSEQ=TTTTTGTTTTAATTCCTTTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:179:45:39,6:119,14:133,45:0.2514:2,2:24.5:1.0:31.1:1.0:0.59258:1.30563:60.0:44.0:0.2472:0.0559:0.1 0/0:160:1:1,0:135,24:159,1:0.0063:2,0:48.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0063:0.0:0.0 +2 48033546 . C CT 98 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.01589;SOR=0.0;LSEQ=TTCGGTTTTTTGAGAGGGCA;RSEQ=TTCTCTTGCTAGCACATGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:10:5,5:78,128:206,10:0.0338:2,2:13.3:1.0:29.7:1.0:0.51269:1.64:60.0:20.0:0.0345:0.027:1.1 0/0:175:0:0,0:73,98:171,0:0.0:2,0:26.1:1.0:31.3:1.0:1.0:0.0:60.0:27.5:0.9763:0.0:0.8 +2 48033549 . CTC TCTG 199 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.06448;LSEQ=TCGGTTTTTTGAGAGGGCAC;RSEQ=TTGCTAGCACATGTATCGCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:296:79:35,44:78,128:206,79:0.2669:2,2:24.4:1.0:31.6:1.0:0.34521:1.3:59.8:78.0:0.269:0.0608:1.1 0/1:175:4:1,3:73,98:171,4:0.0229:2,2:17.0:1.0:31.5:1.0:0.6387:2.22541:60.0:8.0:0.0237:0.0057:1.0 +2 48033846 . CAGTAAA C 217 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GACCTTAAGTTTCAAAGAAA;RSEQ=AGGGGAAGGGATGATGCACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:303:107:42,65:67,128:195,107:0.3531:2,2:24.7:1.0:32.2:1.0:0.45254:1.23:59.5:52.5:0.3559:0.0462:0.3 0/0:206:0:0,0:84,122:206,0:0.0:2,0:25.1:1.0:30.1:1.0:1.0:0.0:59.9:40.2:1.0:0.0:0.3 +2 51288710 . A C 289 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10562;LSEQ=GCAAAGTTGCGGGGTACAAG;RSEQ=TTGATACTCAAAAATCAGTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1204:487:153,334:222,494:716,487:0.4045:2,2:25.6:1.0:32.4:1.0:0.89916:1.02:60.0:47.7:0.4032:0.0:1.1 0/1:957:64:22,42:315,578:893,64:0.0669:2,2:24.2:1.0:31.0:1.0:1.0:1.04038:60.0:63.0:0.0669:0.0:1.2 +2 54660484 . G A 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.03495;LSEQ=GTATGATGTTAGGGATCTGC;RSEQ=TGTTCATAGGCTTCACTGCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:367:31:22,9:241,95:336,31:0.0845:2,2:26.1:1.0:30.3:1.0:1.0:1.03769:60.0:30.0:0.0845:0.0:1.3 0/0:312:1:1,0:194,117:311,1:0.0032:2,0:36.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0033:0.0:1.0 +2 61108926 . C G 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGACTGACTGCGGCCGCCT;RSEQ=CGGCCAGGACGCTGGGAGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:325:122:71,51:133,68:201,122:0.3754:2,2:24.7:1.0:31.5:1.0:0.15547:1.40339:60.0:60.0:0.3727:0.0:1.1 0/0:381:0:0,0:231,150:381,0:0.0:2,0:23.4:1.0:30.0:1.0:1.0:0.0:60.0:33.636:1.0:0.0:0.3 +2 61710320 . T A 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0396;SOR=0.0;LSEQ=AAGTATTCTGAATCTAACCC;RSEQ=GTTCTCCCTTTTTTTTGGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:6:0,6:1,86:87,6:0.0645:1,0:26.7:1.0:33.7:1.0:1.0:0.0:60.0:12.0:0.0659:0.0:1.0 0/0:68:0:0,0:0,68:68,0:0.0:1,0:24.0:1.0:29.6:1.0:1.0:0.0:60.0:136.0:1.0:0.0:0.1 +2 61713110 . GA G 72 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.06469;SOR=0.0;LSEQ=TCAGCGACCTGTTGGGGAGG;RSEQ=AAAAAAAGTTATGTTTTAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:5:1,4:66,293:359,5:0.0137:2,2:25.6:1.0:31.3:1.0:1.0:1.11:60.0:10.0:0.0139:0.0027:0.6 0/0:316:0:0,0:89,227:316,0:0.0:2,0:22.2:1.0:29.5:1.0:1.0:0.0:60.0:157.0:1.0:0.0:0.1 +2 61760814 . C T 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAATGCAAACTATGGAATAT;RSEQ=TTTTTTAAAGGTGATAATTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:207:27:23,4:172,8:180,27:0.1304:1,2:22.3:1.0:31.0:1.0:0.05474:3.70438:60.0:54.0:0.1311:0.0:1.0 0/0:150:0:0,0:138,12:150,0:0.0:2,0:22.7:1.0:31.1:1.0:1.0:0.0:60.0:149.0:1.0:0.0:0.1 +2 66352599 . G A 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.04341;LSEQ=CAAAGCTGGAATTTGTTTGT;RSEQ=TGGTTCCTCCACAGCTGTCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:74:55:55,0:19,0:19,55:0.7432:1,1:26.2:1.0:29.1:1.0:1.0:0.0:60.0:110.0:0.7432:0.0:1.0 0/1:37:4:4,0:33,0:33,4:0.1081:1,0:19.5:1.0:28.5:1.0:1.0:0.0:60.0:8.0:0.1081:0.0:1.0 +2 67049381 . T C 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCAAGCCACATGACACAG;RSEQ=GGGTGCCTTCAGCTGCTCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:71:46,25:198,165:363,71:0.1636:2,2:27.0:1.0:31.2:1.0:0.11836:1.53:58.9:70.0:0.1624:0.0:1.1 0/0:277:0:0,0:155,122:277,0:0.0:2,0:23.8:1.0:28.8:1.0:1.0:0.0:59.8:45.167:1.0:0.0:0.1 +2 67977367 . G GT 118 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.00028;SOR=0.0802;LSEQ=ATCAAGGAGTCAATAGGGTT;RSEQ=TTTTTTTTTTTCCTAGGGCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:16:13,3:15,4:19,16:0.4103:2,2:22.6:1.0:29.6:1.0:1.0:1.15:60.0:32.0:0.4324:0.1538:0.6 0/1:39:2:2,0:27,10:37,2:0.0513:2,0:12.0:1.0:31.0:0.0:1.0:0.0:60.0:4.0:0.0526:0.0:0.0 +2 75660834 . G T 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00866;SOR=0.0;LSEQ=TGCTTTGTTAAATGGGTCCT;RSEQ=CTCCCCGTGCCACCCAACTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:7:4,3:5,8:13,7:0.35:2,2:21.3:1.0:31.3:1.0:0.64241:2.05:58.3:14.0:0.35:0.0:1.0 0/0:18:0:0,0:9,9:18,0:0.0:2,0:24.7:1.0:31.1:1.0:1.0:0.0:59.9:36.0:1.0:0.0:0.6 +2 79228890 . G A 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00699;SOR=0.0;LSEQ=TATTGGATGCCATCCACATG;RSEQ=CAAATGAGTAGGCTAAACGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,1:2,5:0.7143:2,2:22.4:1.0:27.4:1.0:1.0:3.16:60.0:4.0:0.6667:0.0:3.2 0/0:8:0:0,0:5,3:8,0:0.0:2,0:22.6:1.0:30.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.0 +2 79228925 . T A 90 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00191;SOR=0.03262;LSEQ=AAACGGAAGGTAGCACAGAA;RSEQ=TGTCTCTGTCCTCAACAATG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:6,3:1,1:2,9:0.8182:2,2:23.8:1.0:28.7:1.0:1.0:1.87:60.0:8.0:0.8:0.0:2.6 0/1:10:1:1,0:4,5:9,1:0.1:2,0:18.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.1:0.0:2.0 +2 79423062 . TTTTG T 107 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.03318;SOR=0.1254;LSEQ=GTAGGGGGATGAACTCAGTT;RSEQ=TTTGTTTGTTTTATGAGATG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:12:4,8:17,79:96,12:0.1101:2,2:25.3:1.0:29.9:1.0:0.2432:2.3:59.0:24.0:0.1121:0.0092:0.0 0/1:66:1:0,1:14,51:65,1:0.0152:2,0:48.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0152:0.0:0.0 +2 79524994 . C T 233 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAATTCTGAGGCAGATTATC;RSEQ=ACACTCATTGGAAACAAATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:209:125,84:104,65:169,209:0.5529:2,2:27.7:1.0:30.3:1.0:0.75173:1.07498:60.0:103.5:0.5535:0.0:1.1 0/0:315:0:0,0:172,143:315,0:0.0:2,0:25.9:1.0:31.0:1.0:1.0:0.0:60.0:314.0:1.0:0.0:0.5 +2 79524996 . C T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.03483;SOR=0.0;LSEQ=ATTCTGAGGCAGATTATCCA;RSEQ=ACTCATTGGAAACAAATAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:6:3,3:226,154:380,6:0.0155:2,2:38.2:1.0:26.8:1.0:0.69065:1.46601:60.0:5.0:0.0131:0.0:2.0 0/0:319:0:0,0:174,145:319,0:0.0:2,0:26.0:1.0:31.7:1.0:1.0:0.0:60.0:158.5:1.0:0.0:0.5 +2 81424759 . C T 237 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.01716;LSEQ=CTCATCTTCACAGAGTCGTC;RSEQ=TTTTCTTTTTCTGCACTGTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1860:203:106,97:825,832:1657,203:0.1091:2,2:26.9:1.0:31.0:1.0:0.55205:1.1:60.0:39.6:0.1081:0.0:1.2 0/0:1431:3:0,3:724,704:1428,3:0.0021:2,0:1.0:0.0:26.0:1.0:0.12034:0.0:47.3:6.0:0.0021:0.0:1.0 +2 81425558 . C T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00018;SOR=0.11197;LSEQ=ACTTCTCAAGGACTTCCTCT;RSEQ=CTTGGAATATTCTTTATCTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2039:24:16,8:1008,1005:2013,24:0.0118:2,2:21.5:1.0:30.3:1.0:0.14932:1.99:59.6:48.0:0.012:0.0:1.1 0/0:1502:2:0,2:763,735:1498,2:0.0013:2,0:1.0:0.0:23.0:0.0:0.24124:0.0:60.0:4.0:0.0013:0.0:1.0 +2 81425585 . C T 282 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.11141;LSEQ=ATATTCTTTATCTGACTTCT;RSEQ=TTTGTGTTTGCTGTTAGCCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1954:595:302,293:676,675:1351,595:0.3045:2,2:24.5:1.0:30.6:1.0:0.80568:1.03:59.9:73.375:0.3051:0.0:1.1 0/1:1463:68:39,29:713,681:1394,68:0.0465:2,2:22.6:1.0:29.3:1.0:0.32378:1.28:60.0:67.0:0.0463:0.0:1.1 +2 81426909 . C T 273 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CTGATTTTTATTAAAATATT;RSEQ=ATCAAAAGCAGAATCTTCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2197:558:301,257:822,815:1637,558:0.254:2,2:26.4:1.0:30.0:1.0:0.12889:1.16:37.7:185.0:0.2549:0.0:1.1 0/0:1644:0:0,0:832,809:1641,0:0.0:2,0:26.1:1.0:31.0:1.0:1.0:0.0:41.4:163.1:0.9988:0.0:0.1 +2 81427308 . G A 265 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTTTTTTAAAGTGGTCTC;RSEQ=ATCAAGCTATAACACTTTTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1281:379:181,198:460,441:901,379:0.2959:2,2:24.0:1.0:31.0:1.0:0.29811:1.14093:58.8:188.5:0.2964:0.0:1.1 0/0:961:0:0,0:471,489:960,0:0.0:2,0:25.0:1.0:29.9:1.0:1.0:0.0:59.3:67.571:0.9989:0.0:0.1 +2 91884897 . T A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.14286;SOR=0.0;LSEQ=CCTTGGATTATAGGCAGAAA;RSEQ=GTTACATGTTTTTAAAAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1.0:0,2:16.0:1.0:31.7:1.0:1.0:0.0:26.2:12.0:1.0:0.0:2.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:18.0:0.0:27.0:0.0:1.0:0.0:21.0:2.0:1.0:0.0:0.0 +2 91884911 . A T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.11111;SOR=0.0;LSEQ=CAGAAATGTTACATGTTTTT;RSEQ=AAAAATGGTCTTCCTGGGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:2,6:0,0:0,8:1.0:0,2:23.8:1.0:29.4:1.0:1.0:0.0:34.6:16.0:1.0:0.0:1.9 0/0:1:0:0,0:0,1:1,0:0.0:0,0:32.0:0.0:32.0:0.0:1.0:0.0:21.0:2.0:1.0:0.0:0.0 +2 95849653 . T C 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCTGGGATTACAGACGTAAG;RSEQ=CACCGTGCCCGGCCTATATT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1.0:0,2:30.0:1.0:30.7:1.0:1.0:0.0:45.8:12.0:1.0:0.0:1.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 99160361 . G C 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTGTGTGAGCTGGAGGAGCT;RSEQ=GGAGAGCTGTCCCCTTGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:901:55:34,21:485,361:846,55:0.061:2,2:25.7:1.0:30.9:1.0:0.57452:1.2:60.0:54.0:0.0609:0.0:1.2 0/0:785:0:0,0:440,339:779,0:0.0:2,0:24.8:1.0:30.7:1.0:1.0:0.0:60.0:40.0:0.9922:0.0:0.2 +2 99168953 . T C 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TACGATCATTTGGGTGATTA;RSEQ=GGGATATGATTGTTCAATAC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1.0:0,0:22.6:1.0:33.4:1.0:1.0:0.0:60.0:22.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 99185423 . C G 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGGCATGCATTGTGCACCT;RSEQ=CTGGTAGGACTTGGGGGAAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1.0:0,2:24.0:1.0:32.2:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 99193007 . A G 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CCTACCTTCCAGGGAGACCT;RSEQ=GAGACCTGGCCCAGGACTGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1.0:0,2:26.8:1.0:32.7:1.0:1.0:0.0:54.2:12.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 106021437 . C T 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCGTCGGATACAGTTTCCA;RSEQ=TGTGGCTTTGATACCTCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:47:33,14:185,111:296,47:0.137:2,2:26.8:1.0:30.4:1.0:0.3325:1.41:60.0:22.5:0.1335:0.0:1.1 0/0:310:0:0,0:186,124:310,0:0.0:2,0:24.6:1.0:31.4:1.0:1.0:0.0:60.0:61.0:1.0:0.0:0.4 +2 106021465 . ACT A 144 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TTGATACCTCTTTAAGAAAG;RSEQ=CTGTTTGGTACATTAATGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:22:12,10:230,176:406,22:0.0514:2,2:21.7:1.0:32.3:1.0:1.0:1.0888:60.0:44.0:0.0518:0.0093:1.0 0/0:410:0:0,0:231,176:407,0:0.0:2,0:25.4:1.0:31.4:1.0:1.0:0.0:60.0:100.75:0.9975:0.0:0.6 +2 108622946 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCGGTCTCCCAAAGTGCTGG;RSEQ=ATTATAGGTGTGAGCTACTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1.0:0,2:17.2:1.0:30.3:1.0:1.0:0.0:44.0:12.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 111885565 . C T 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCATCTGAACCATTTATTT;RSEQ=TAAGTGTACTGTTCAGTAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:237:47:27,20:108,82:190,47:0.1983:2,2:26.4:1.0:30.9:1.0:1.0:1.02:59.8:94.0:0.2009:0.0:1.1 0/0:218:0:0,0:133,85:218,0:0.0:2,0:24.9:1.0:30.3:1.0:1.0:0.0:60.0:26.25:1.0:0.0:0.1 +2 111901935 . GGT G 90 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=7.0;MSILEN=2.0;SSF=0.14474;SOR=0.18843;LSEQ=GAGAAATAGACCTGGAGGGA;RSEQ=GTGTGTGTGTGTTGTTGGTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:7:5,2:166,14:180,7:0.0374:2,2:25.4:1.0:32.2:1.0:0.11203:4.67441:60.0:14.0:0.0378:0.0053:0.1 0/0:138:1:1,0:121,14:135,1:0.0072:2,0:20.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0075:0.0:0.0 +2 111911182 . ATCC A 144 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.00038;SOR=0.0;LSEQ=GCTGTCTTCACAAGGGAATT;RSEQ=TCTCTTGGCAAGCGAGTGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:22:22,0:32,2:34,22:0.3929:2,1:27.1:1.0:32.3:1.0:0.51429:0.0:60.0:44.0:0.4:0.0179:0.0 0/0:20:0:0,0:19,1:20,0:0.0:1,0:26.3:1.0:30.6:1.0:1.0:0.0:59.9:40.0:1.0:0.0:0.4 +2 113688949 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.04516;SOR=0.0;LSEQ=GGCCATGAAAAGTCCACCTG;RSEQ=AGTAGTGGTAGGAGGAACAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:497:6:2,4:308,183:491,6:0.0121:2,2:22.0:1.0:27.5:1.0:0.20443:3.35761:54.3:12.0:0.0122:0.0:1.7 0/0:350:0:0,0:218,132:350,0:0.0:2,0:24.4:1.0:31.0:1.0:1.0:0.0:59.7:69.0:1.0:0.0:0.6 +2 113978894 . G A 232 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00427;LSEQ=AATGTCCACCCAGCCTTTCA;RSEQ=AAACTCACCTACGATTGGGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:567:190:102,88:187,188:375,190:0.3351:2,2:24.5:1.0:30.7:1.0:0.42305:1.16:59.9:189.0:0.3357:0.0:1.1 0/0:467:1:1,0:230,236:466,1:0.0021:2,0:1.0:0.0:25.0:0.0:0.49465:0.0:60.0:2.0:0.0022:0.0:1.0 +2 113979364 . G A 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.12278;LSEQ=GCATTTATACAGGAAGAAGA;RSEQ=AGATGAAGAGGAGCAGCCTA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:70:34,36:209,198:407,70:0.1468:2,2:24.6:1.0:31.0:1.0:0.69911:1.11739:60.0:140.0:0.1471:0.0:1.1 0/1:436:9:5,4:233,194:427,9:0.0206:2,2:15.0:1.0:28.3:1.0:1.0:1.04:60.0:18.0:0.0207:0.0:1.1 +2 113981691 . T A 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.06931;LSEQ=ATGGATGATGAAAGGATAGA;RSEQ=GGAAAGACAGATTAAAGGAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:686:27:14,13:328,331:659,27:0.0394:2,2:30.6:1.0:31.7:1.0:0.8472:1.09:60.0:54.0:0.0398:0.0:1.0 0/0:707:2:1,1:380,325:705,2:0.0028:2,2:24.5:1.0:15.5:1.0:1.0:1.16897:60.0:0.0:0.0:0.0:1.0 +2 121735983 . C T 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGCCTCTGGCCCTGCTTAC;RSEQ=CTCTTCTGGGCATGTCCCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:302:19:13,6:187,96:283,19:0.0629:2,2:23.5:1.0:30.0:1.0:1.0:1.11:60.0:18.0:0.061:0.0:1.2 0/0:268:0:0,0:177,91:268,0:0.0:2,0:22.2:1.0:30.1:1.0:1.0:0.0:59.8:133.0:1.0:0.0:0.2 +2 125301742 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.36364;SOR=0.0;LSEQ=AAGTTAAACTAACCATCTAA;RSEQ=AGGTCTTAAGGGATCATCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:1,6:0,3:3,7:0.7:0,2:17.7:1.0:27.6:1.0:1.0:0.0:60.0:6.0:0.6667:0.0:1.6 0/0:1:0:0,0:0,1:1,0:0.0:0,0:33.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +2 128014913 . C T 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.38462;SOR=0.0;LSEQ=TCAGAACGGTAACATAAATA;RSEQ=ACCTTAAATATTAACATTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:27.5:1.0:27.9:1.0:1.0:0.0:56.1:7.0:0.6364:0.0:1.3 0/0:1:0:0,0:1,0:1,0:0.0:0,0:40.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +2 128036701 . G T 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.06563;SOR=0.0;LSEQ=CCACCTTCTGCACTCTCAAT;RSEQ=GGGAAGAGAAACTGGCCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:5:3,2:294,93:387,5:0.0128:2,2:9.6:1.0:29.4:1.0:0.59858:2.1029:60.0:10.0:0.0128:0.0:1.0 0/0:334:0:0,0:232,102:334,0:0.0:2,0:23.2:1.0:30.8:1.0:1.0:0.0:60.0:54.667:1.0:0.0:0.1 +2 128038005 . C A 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGCCCTTTCCCAGACGCCCC;RSEQ=AGCCCAGGCCCAGCTACCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:25:19,6:325,168:493,25:0.0483:2,2:21.2:1.0:29.7:1.0:0.38715:1.64:58.2:11.5:0.0451:0.0:1.3 0/0:511:0:0,0:326,184:510,0:0.0:2,0:25.5:1.0:30.2:1.0:1.0:0.0:60.0:38.231:0.998:0.0:0.3 +2 131947526 . AT A 68 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.01804;SOR=0.0;LSEQ=GAAAAGAGAAACAGCAAACA;RSEQ=TTTTTTGAAGTCACACCTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:5:1,4:87,134:221,5:0.0221:2,2:31.8:1.0:29.6:1.0:0.6509:2.58763:38.4:10.0:0.0227:0.0:0.2 0/0:276:0:0,0:112,164:276,0:0.0:2,0:33.0:1.0:29.5:1.0:1.0:0.0:42.2:137.0:1.0:0.0:0.2 +2 131950767 . A G 184 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGACAAAAGGCAACTTTACA;RSEQ=ACTTACCTGGCCATCTTCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:49:46,3:155,54:209,49:0.1899:2,2:33.2:1.0:32.9:1.0:0.0019:5.32:32.1:98.0:0.1922:0.0:1.0 0/0:267:0:0,0:189,78:267,0:0.0:2,0:28.9:1.0:29.5:1.0:1.0:0.0:37.7:132.5:1.0:0.0:0.1 +2 133919631 . G A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01806;SOR=0.0;LSEQ=ATTTGCACTTACTCATTCTT;RSEQ=GCCTTTTCTGTGCCCTCTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:5,8:0.6154:0,0:27.0:1.0:31.3:1.0:1.0:0.0:60.0:7.0:0.5833:0.0:1.5 0/0:6:0:0,0:1,5:6,0:0.0:2,0:30.5:1.0:28.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.5 +2 139308127 . G A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0094;SOR=0.0;LSEQ=CGAGAGGAAATGGGTGAAGT;RSEQ=TTAAAAAGTTCAACATTTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:5,4:4,4:8,9:0.5294:2,2:22.9:1.0:29.7:1.0:1.0:1.23:60.0:18.0:0.5294:0.0:1.0 0/0:9:0:0,0:5,4:9,0:0.0:2,0:29.6:1.0:32.1:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 +2 158617379 . A G 252 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTAAGACAATATTATATTAG;RSEQ=TTAGATACCTACCATTGCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1395:265:162,103:683,445:1128,265:0.19:2,2:25.2:1.0:31.4:1.0:0.88899:1.02:60.0:52.0:0.1898:0.0:1.1 0/0:1333:0:0,0:791,540:1331,0:0.0:2,0:24.2:1.0:29.0:1.0:1.0:0.0:60.0:109.917:0.9985:0.0:0.1 +2 158622572 . C A 223 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00711;LSEQ=AGACCACTAGCTATGGACAG;RSEQ=ACTATTCGAAGGCAGCTAAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1923:157:72,85:848,917:1765,157:0.0816:2,2:26.0:1.0:30.7:1.0:0.61774:1.09165:60.0:77.5:0.0818:0.0:1.2 0/0:1581:1:1,0:756,819:1575,1:0.0006:2,0:1.0:0.0:23.0:0.0:0.48033:0.0:60.0:2.0:0.0006:0.0:1.0 +2 158634289 . G A 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCAAAAGGTGCCTTTTTAAA;RSEQ=GAGCACTTTTATGGCTAAAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1.0:0,0:26.5:1.0:30.8:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 158636320 . C T 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAAAACTACAGGGTTTGTG;RSEQ=GAAATCTCATCCTGCTTCAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:25.8:1.0:29.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 158636341 . A G 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAAATCTCATCCTGCTTCAA;RSEQ=TTTCAGTGATAGGGTCACTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:21.6:1.0:31.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 158637137 . A G 293 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAAGGAGAGAAAGGAAGGGG;RSEQ=AAAAAAAAAAAAAGAGGAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1173:760:292,468:76,138:214,760:0.6479:2,2:21.0:1.0:30.7:1.0:0.47287:1.13:59.8:22.03:0.6462:0.0:1.4 0/0:1213:0:0,0:117,167:284,0:0.0:2,0:26.3:1.0:28.2:1.0:1.0:0.0:59.2:16.75:0.5403:0.0:0.8 +2 158637445 . A C 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTTCAGCGTGATTGGCTCT;RSEQ=AGATCCCAATTACTGCATCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1.0:0,0:29.2:1.0:33.3:1.0:1.0:0.0:58.9:22.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 158655838 . G C 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=CCAAATATTTATTATAAAAA;RSEQ=AGTGTTTTAAGTTTGATAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:261:20:20,0:230,11:241,20:0.0766:1,1:26.2:1.0:33.1:1.0:1.0:0.0:58.8:40.0:0.0797:0.0:1.4 0/0:182:0:0,0:174,8:182,0:0.0:1,0:22.7:1.0:31.6:1.0:1.0:0.0:59.3:44.5:1.0:0.0:0.4 +2 178883104 . A ACTTGACTTTAACTTGGCACG 151 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CAAGGCAGGCCTTTTGGCAC;RSEQ=CTTGACTTTAACCTTTGCCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:33:3,30:1,18:19,33:0.6346:1,2:25.4:1.0:30.1:1.0:1.0:1.78:56.5:32.0:0.6275:0.2308:0.2 0/0:31:0:0,0:2,22:24,0:0.0:2,0:13.1:1.0:30.7:1.0:1.0:0.0:59.5:48.0:0.7742:0.0:0.2 +2 180265135 . C T 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00986;LSEQ=TACAATTTCCAAGTGCGTTC;RSEQ=GAAAACTCCTGGGGGCTTGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:84:47,37:287,198:485,84:0.1476:2,2:24.6:1.0:31.2:1.0:0.63155:1.14082:56.3:168.0:0.1495:0.0:1.9 0/0:588:1:0,1:349,238:587,1:0.0017:2,0:1.0:0.0:24.0:0.0:0.40646:0.0:47.0:2.0:0.0017:0.0:2.0 +2 180265174 . G A 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01165;LSEQ=GCTTTAGCCCGTCTGTCACC;RSEQ=CCTCCTTCCTTGCCTTCTCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:768:129:64,65:348,291:639,129:0.168:2,2:23.8:1.0:30.3:1.0:0.33386:1.21425:55.4:128.0:0.1684:0.0:1.8 0/0:854:2:1,1:440,411:851,2:0.0023:2,2:35.5:1.0:30.0:1.0:1.0:1.07044:34.0:4.0:0.0024:0.0:2.5 +2 183484981 . T C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0634;SOR=0.0;LSEQ=CAACTATTAACACATTTCTA;RSEQ=ATTAATATGAATTTCAGTTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:6:6,0:17,0:17,6:0.2609:1,0:27.5:1.0:33.7:1.0:1.0:0.0:60.0:12.0:0.2727:0.0:1.0 0/0:15:0:0,0:15,0:15,0:0.0:1,0:17.1:1.0:31.1:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.0 +2 187558960 . G A 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.20455;SOR=0.0;LSEQ=CTCGGCCTGGCCGTGGTGCT;RSEQ=CTGAAAGCGCGGCTGGTCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:3,1:4,5:0.5556:2,0:34.6:1.0:29.0:1.0:0.44444:0.0:60.0:10.0:0.5556:0.0:1.0 0/0:3:0:0,0:3,0:3,0:0.0:0,0:43.0:1.0:31.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +2 189541807 . C G 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00039;SOR=0.0;LSEQ=CATAAAACATTCAAAATTAT;RSEQ=TTGATTATTTGCTTTATTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:13:0,13:2,34:36,13:0.2653:2,1:24.8:1.0:33.1:1.0:1.0:0.0:60.0:26.0:0.2708:0.0:1.2 0/0:39:0:0,0:0,39:39,0:0.0:1,0:22.1:1.0:31.8:1.0:1.0:0.0:60.0:38.0:1.0:0.0:0.0 +2 190708712 . G A 225 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTTATTTGGCAGAAAAGCA;RSEQ=AGTATCAGATCACAAGATGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1000:171:99,72:475,353:828,171:0.171:2,2:27.5:1.0:30.4:1.0:0.93241:1.02:60.0:56.0:0.169:0.0:1.1 0/0:837:0:0,0:453,383:836,0:0.0:2,0:26.1:1.0:30.9:1.0:1.0:0.0:60.0:118.429:0.9988:0.0:0.1 +2 190718940 . A C 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTATTTTCATAATTTCCCCT;RSEQ=ACATTTGTTAATTTGTATTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:234:70:48,22:109,55:164,70:0.2991:2,2:24.4:1.0:32.3:1.0:0.87934:1.1:60.0:140.0:0.3004:0.0:1.0 0/0:228:0:0,0:160,68:228,0:0.0:2,0:23.3:1.0:28.1:1.0:1.0:0.0:60.0:113.0:1.0:0.0:0.1 +2 196860410 . G T 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.09;LSEQ=ACTAGGGAGAGAAGATAAAG;RSEQ=GTGGTGGTGCTGGGCAGATG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:34:2,32:1,35:36,34:0.4857:1,2:25.4:1.0:30.8:1.0:0.6087:2.16:60.0:33.0:0.4783:0.0:1.1 0/1:39:3:0,3:1,35:36,3:0.0769:1,0:26.3:1.0:27.3:1.0:1.0:0.0:60.0:6.0:0.0769:0.0:1.3 +2 198257008 . C G 222 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGAAGTAGCTGTGCATTAAA;RSEQ=ACAAAATAAACAATAAAATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:110:80,30:118,54:172,110:0.3901:2,2:25.2:1.0:32.8:1.0:0.50577:1.22:60.0:220.0:0.3901:0.0:1.2 0/0:247:0:0,0:164,83:247,0:0.0:2,0:24.4:1.0:31.5:1.0:1.0:0.0:60.0:494.0:1.0:0.0:0.1 +2 198265952 . CA C 75 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.14086;SOR=0.0;LSEQ=TAAGTATTAATCCTCGAATC;RSEQ=AAATCAAAATGGAAGTTAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:5:5,0:17,7:24,5:0.1724:2,0:34.2:1.0:32.4:1.0:0.29649:0.0:60.0:10.0:0.1724:0.0:0.0 0/0:18:0:0,0:17,1:18,0:0.0:1,0:22.2:1.0:30.8:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.2 +2 198266602 . G A 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=ACCCAATAGCCTTCAAGAAA;RSEQ=CAGCCAAACCCTATTTTTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:38:18,20:201,279:480,38:0.0731:2,2:22.4:1.0:30.4:1.0:0.60933:1.25:60.0:76.0:0.0738:0.0:1.1 0/0:506:0:0,0:230,275:505,0:0.0:2,0:24.1:1.0:31.4:1.0:1.0:0.0:59.8:100.0:1.0:0.0:0.1 +2 202149589 . G C 207 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.15569;LSEQ=ATTTTGAGATCAAGCCCCAC;RSEQ=ATGACTGCACAGTAGAGCAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:90:38,52:263,264:527,90:0.1454:2,2:25.7:1.0:32.0:1.0:0.20943:1.36255:60.0:180.0:0.1461:0.0:1.1 0/1:776:20:11,9:389,365:754,20:0.0258:2,2:21.2:1.0:30.8:1.0:0.82353:1.15:60.0:40.0:0.026:0.0:1.1 +2 204637705 . TTCATCATCATCA T 162 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=23;MSI=11.0;MSILEN=3.0;SSF=0.0;SOR=0.07412;LSEQ=TCATCAAAATCATTATCATT;RSEQ=TCATCATCATCATCATCATC;STATUS=AFDiff GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:76:38:21,17:8,11:19,38:0.5:2,2:28.5:1.0:30.9:1.0:0.40767:1.68:33.5:76.0:0.5:0.1316:0.2 0/1:59:4:4,0:5,7:12,4:0.0678:2,0:30.8:1.0:31.5:1.0:0.08846:0.0:28.8:8.0:0.0678:0.0169:0.5 +2 209102117 . A ACT 106 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CTAGGCAACCGGCAGTAGAG;RSEQ=CAGCCATACATACTCAGTTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1.0:0,2:24.1:1.0:32.1:1.0:1.0:0.0:60.0:20.0:1.0:0.2:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +2 209103969 . G GA 100 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.00398;SOR=0.0;LSEQ=AAATGGAAGCTAAAAGAGGG;RSEQ=AAAAAAAACACAACACTCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:9:3,6:99,238:337,9:0.0259:2,2:28.4:1.0:31.6:1.0:0.7264:1.2:60.0:18.0:0.0264:0.0:0.2 0/0:317:0:0,0:107,210:317,0:0.0:2,0:23.8:1.0:30.3:1.0:1.0:0.0:60.0:104.667:1.0:0.0:0.1 +2 212251910 . G A 180 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.15394;LSEQ=AACATATGTGGAGAGAAGGC;RSEQ=TTGTTAGAAATAGTTTAAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:216:55:13,42:29,132:161,55:0.2546:2,2:21.7:1.0:31.2:1.0:0.42992:1.41:60.0:110.0:0.2558:0.0:1.1 0/1:221:11:2,9:53,157:210,11:0.0498:2,2:19.0:1.0:30.9:1.0:0.73544:1.51644:60.0:22.0:0.0505:0.0:1.1 +2 212292936 . T TTAAAATAAAA 78 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=8.0;MSILEN=5.0;SSF=0.26749;SOR=0.0;LSEQ=CTGCATGTGTATCGCAGAAC;RSEQ=TAAAATAAAATAAAATAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:6,0:10,0:10,6:0.375:0,0:8.0:1.0:30.5:1.0:1.0:0.0:54.2:12.0:0.375:0.375:0.2 0/0:4:0:0,0:4,0:4,0:0.0:0,0:34.0:1.0:31.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +2 212292968 . AT A 112 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.03504;SOR=0.11962;LSEQ=AAAATAAAATAAAATAAAAT;RSEQ=TTTTTTTTCATTGAGAAAGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:11:11,0:19,0:19,11:0.3667:1,0:23.2:1.0:32.4:1.0:1.0:0.0:58.0:22.0:0.3667:0.0333:0.0 0/1:16:1:1,0:15,0:15,1:0.0625:1,0:13.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0667:0.0:1.0 +2 212295468 . GTA G 119 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=5.0;MSILEN=2.0;SSF=0.00585;SOR=0.0;LSEQ=ACGGAAGCTGGTAATATATG;RSEQ=TATATATATGTGTGTGTATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:13:13,0:13,0:13,13:0.5:1,1:26.8:1.0:32.2:1.0:1.0:0.0:43.5:26.0:0.5:0.0769:0.0 0/0:10:0:0,0:10,0:10,0:0.0:0,0:23.0:1.0:29.9:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 +2 212295492 . GATATAT ATATATC 140 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=2e-05;SOR=0.0;LSEQ=ATATATATGTGTGTGTATAT;RSEQ=ATATACACACACATATATAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:43:24:24,0:19,0:19,24:0.5581:1,1:23.5:1.0:30.7:1.0:1.0:0.0:50.3:48.0:0.5714:0.186:0.1 0/0:17:0:0,0:17,0:17,0:0.0:1,0:23.6:1.0:32.3:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.2 +2 212426588 . C T 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01849;LSEQ=TCCAGGTTAGGAAATATTAA;RSEQ=CTAAAAATGTAATTTCCATA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:41:31,10:271,146:417,41:0.0895:2,2:25.6:1.0:30.7:1.0:0.22631:1.67:60.0:40.0:0.0879:0.0:1.0 0/0:553:1:0,1:351,200:551,1:0.0018:2,0:1.0:0.0:24.0:0.0:0.36413:0.0:60.0:2.0:0.0018:0.0:1.0 +2 212522450 . C T 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00299;LSEQ=TAACTAGGAAAGGATTTGAG;RSEQ=GACAAAATGGAAACATGGTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:379:143:94,49:154,81:235,143:0.3773:2,2:24.3:1.0:29.7:1.0:1.0:1.01:60.0:46.667:0.3794:0.0:1.1 0/0:556:1:0,1:324,230:554,1:0.0018:2,0:1.0:0.0:24.0:0.0:0.41622:0.0:60.0:2.0:0.0018:0.0:1.0 +2 212522651 . A G 234 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGAGCCTTGGAGGAAGAAC;RSEQ=TGGGAAGCAAGCACACCAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:187:99,88:225,242:467,187:0.2859:2,2:26.4:1.0:31.1:1.0:0.29917:1.21:60.0:92.5:0.2864:0.0:1.1 0/0:808:0:0,0:391,415:806,0:0.0:2,0:26.4:1.0:29.8:1.0:1.0:0.0:60.0:200.5:0.9975:0.0:0.1 +2 212544080 . T C 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00814;SOR=0.0;LSEQ=TACCCACAACTTCTTCTATA;RSEQ=TGCAGAGTCCTAGTAGCTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:0,7:1,7:8,7:0.4667:2,0:26.6:1.0:34.7:1.0:1.0:0.0:60.0:14.0:0.4667:0.0:1.0 0/0:12:0:0,0:1,11:12,0:0.0:2,0:31.3:1.0:30.1:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.3 +2 212578523 . C T 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03386;SOR=0.0;LSEQ=ACAACTCTTTGTTTAAATAT;RSEQ=TCAACCTGAAATTGTATTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:6:0,6:0,22:22,6:0.2143:1,0:21.5:1.0:31.0:1.0:1.0:0.0:60.0:12.0:0.2222:0.0:1.0 0/0:20:0:0,0:1,19:20,0:0.0:1,0:20.9:1.0:32.4:1.0:1.0:0.0:60.0:40.0:1.0:0.0:0.1 +2 212589774 . A G 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAGGAAAGGAGAGCAGGAT;RSEQ=ATAAAAGAGAGAAATCACAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:21:17,4:194,76:270,21:0.0722:2,2:30.2:1.0:33.0:1.0:0.45452:1.66:60.0:42.0:0.0724:0.0:1.1 0/0:346:0:0,0:243,103:346,0:0.0:2,0:24.0:1.0:28.0:1.0:1.0:0.0:60.0:85.5:1.0:0.0:0.1 +2 212698775 . T A 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0616;LSEQ=TAATTTTATGTCTATGAAAC;RSEQ=GACAATATGTCATCCTTCCG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:248:129:46,83:45,74:119,129:0.5202:2,2:25.8:1.0:31.0:1.0:0.79226:1.09683:60.0:42.0:0.5207:0.0:1.7 0/1:241:15:7,8:82,144:226,15:0.0622:2,2:20.6:1.0:29.1:1.0:0.42147:1.53:60.0:30.0:0.0622:0.0:1.3 +2 212812057 . G A 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00015;SOR=0.0;LSEQ=TGATATTTAAATGCCTTAGA;RSEQ=TGTTCCTCAATGTAACAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:17:17,0:117,1:118,17:0.1259:1,1:22.2:1.0:29.9:1.0:1.0:0.0:60.0:16.0:0.1203:0.0:1.0 0/0:88:0:0,0:84,4:88,0:0.0:1,0:25.2:1.0:32.0:1.0:1.0:0.0:60.0:176.0:1.0:0.0:0.4 +2 213402964 . A AC 106 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01457;SOR=0.0;LSEQ=AGGAGAGAAAAGAGGGACTC;RSEQ=GAGTGATTTTTCACGATAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:9:9,0:15,0:15,9:0.375:1,0:18.8:1.0:33.5:1.0:1.0:0.0:60.0:18.0:0.375:0.0833:0.0 0/0:13:0:0,0:11,2:13,0:0.0:2,0:24.8:1.0:30.5:1.0:1.0:0.0:60.0:26.0:1.0:0.0:0.1 +2 225069340 . C A 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTCAAAGGATTTTTCAGTT;RSEQ=CATTTTTCTTATAGGAAAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:19:8,11:97,102:199,19:0.0872:2,2:23.3:1.0:29.5:1.0:0.63691:1.306:58.2:38.0:0.0884:0.0:1.1 0/0:224:0:0,0:116,108:224,0:0.0:2,0:26.7:1.0:30.4:1.0:1.0:0.0:60.0:55.0:1.0:0.0:0.4 +2 226701540 . A C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.0;MSILEN=1.0;SSF=0.00756;SOR=0.0;LSEQ=ACAAAAAAAAACTGTAAAAC;RSEQ=AAAAGGTCATTATGTCATAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:6:0,6:0,26:26,6:0.1875:1,0:30.0:1.0:34.0:0.0:1.0:0.0:60.0:12.0:0.1875:0.0:1.0 0/0:37:0:0,0:0,37:37,0:0.0:1,0:25.2:1.0:31.2:1.0:1.0:0.0:60.0:74.0:1.0:0.0:0.1 +2 237242244 . T C 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03571;SOR=0.0;LSEQ=GGGTTTCATGCTTGCGGACT;RSEQ=GGTTCTGGGCACGCATGAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:21.7:1.0:29.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:2:0:0,0:0,2:2,0:0.0:0,0:38.0:1.0:31.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +20 61098 . C T 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06342;SOR=0.0;LSEQ=CTGCCAAGCACAGACAACCA;RSEQ=TGGGCCCCAGGGGAGCTGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:2,4:5,6:11,6:0.3529:2,2:20.7:1.0:32.3:1.0:1.0:1.6177:60.0:12.0:0.3529:0.0:1.3 0/0:9:0:0,0:5,4:9,0:0.0:2,0:25.3:1.0:31.2:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.2 +20 1421974 . T C 171 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACAGGGTTGCTGGGCATGA;RSEQ=TGTTAACAAGATCAAACAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:36:14,22:63,124:187,36:0.1614:2,2:26.2:1.0:33.1:1.0:0.5693:1.25:60.0:72.0:0.1644:0.0:1.9 0/0:152:0:0,0:57,95:152,0:0.0:2,0:23.6:1.0:28.8:1.0:1.0:0.0:60.0:29.4:1.0:0.0:0.7 +20 9624587 . C T 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.0;MSILEN=1.0;SSF=0.00202;SOR=0.0;LSEQ=ACATCTAAAGCCAAAGTTCC;RSEQ=TTTCATGGGCTGCAATTTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:30:30:30,0:0,0:0,30:1.0:0,1:26.0:1.0:32.0:1.0:1.0:0.0:59.8:29.0:1.0:0.0:1.2 0/0:2:0:0,0:2,0:2,0:0.0:0,0:18.0:1.0:30.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +20 11361032 . G A 56 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGCAAATCAGATTAATAG;RSEQ=GCCTGAACTGAACCCCCAGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:1,5:0.8333:0,2:24.6:1.0:24.4:1.0:1.0:0.0:57.8:1.5:0.75:0.0:2.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +20 16142333 . A C 259 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0839;LSEQ=ATTTTCCTACAGACGACAAC;RSEQ=TCTGAGCAACAGAATAGGCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:464:279:139,140:93,92:185,279:0.6013:2,2:25.7:1.0:31.9:1.0:1.0:1.01811:59.9:54.8:0.6009:0.0:1.1 0/1:366:41:17,24:160,165:325,41:0.112:2,2:22.4:1.0:30.1:1.0:0.40816:1.36781:59.6:82.0:0.1142:0.0:1.2 +20 22563356 . G T 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02918;SOR=0.0;LSEQ=GGCTCTGCTGGATGGCCATG;RSEQ=TGATGAGCGAGATGTACGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:8:3,5:245,465:710,8:0.0111:2,2:12.8:1.0:27.6:1.0:1.0:1.14:50.0:7.0:0.0099:0.0:1.8 0/0:424:0:0,0:187,237:424,0:0.0:2,0:26.6:1.0:31.0:1.0:1.0:0.0:55.8:211.0:1.0:0.0:0.2 +20 25733062 . T G 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.31484;SOR=0.0;LSEQ=CTTTAACCATACCCAAAGTC;RSEQ=ATTTTTATTTCTTGACAGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:6:6,0:31,1:32,6:0.1579:1,0:13.8:1.0:26.2:1.0:1.0:0.0:54.8:5.0:0.1351:0.0:1.0 0/0:11:0:0,0:10,1:11,0:0.0:2,0:30.2:1.0:30.9:1.0:1.0:0.0:59.5:22.0:1.0:0.0:0.0 +20 26084383 . GT G 83 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.09106;SOR=0.0;LSEQ=TGCCTTAAATGAAAAAGTCA;RSEQ=TTTAAACCACAGCAGAGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:6:0,6:1,58:59,6:0.0923:1,0:39.5:1.0:32.3:1.0:1.0:0.0:28.5:12.0:0.0938:0.0:0.0 0/0:34:0:0,0:2,32:34,0:0.0:2,0:20.7:1.0:27.4:1.0:1.0:0.0:26.4:68.0:1.0:0.0:2.2 +20 30296422 . C T 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCCAAACTGACCCCTCCC;RSEQ=CCAGCTGAGCCCAGCTGTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:340:118:97,21:188,32:220,118:0.3471:2,2:23.9:1.0:31.5:1.0:0.43676:1.27095:60.0:117.0:0.3514:0.0:1.1 0/0:248:0:0,0:200,48:248,0:0.0:2,0:22.7:1.0:30.4:1.0:1.0:0.0:60.0:247.0:1.0:0.0:0.1 +20 30296428 . T C 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACTGACCCCTCCCCCCAGC;RSEQ=GAGCCCAGCTGTCAACGGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:78:63,15:251,57:308,78:0.2021:2,2:22.8:1.0:30.5:1.0:0.87164:1.04833:60.0:25.0:0.1979:0.0:1.2 0/0:267:0:0,0:210,57:267,0:0.0:2,0:23.5:1.0:29.9:1.0:1.0:0.0:60.0:52.4:1.0:0.0:0.1 +20 30296664 . G C 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05439;SOR=0.0;LSEQ=CTGGCATTGTCACTGCAGGT;RSEQ=GCAGGAGACAGGTGATGTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:8:1,7:16,199:215,8:0.0359:2,2:22.6:1.0:29.5:1.0:0.47532:1.77:60.0:16.0:0.0369:0.0:1.0 0/0:121:0:0,0:9,112:121,0:0.0:2,0:22.2:1.0:30.9:1.0:1.0:0.0:60.0:242.0:1.0:0.0:0.1 +20 30309960 . C G 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAAACTGACTCCAGCTGTAT;RSEQ=CTTTCTGGGAAAGCTTGTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:670:29:7,22:232,409:641,29:0.0433:2,2:26.9:1.0:33.0:1.0:0.23537:1.78134:60.0:58.0:0.0438:0.0:1.1 0/0:574:0:0,0:238,336:574,0:0.0:2,0:24.9:1.0:30.2:1.0:1.0:0.0:60.0:70.75:1.0:0.0:0.1 +20 31016119 . C T 235 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.01054;LSEQ=GGACTAACCTTTATTTTCCT;RSEQ=TCTTCCAGTATCTCTTGATG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1680:206:109,97:720,754:1474,206:0.1226:2,2:24.4:1.0:30.7:1.0:0.29777:1.18:60.0:205.0:0.123:0.0:1.1 0/0:1361:2:1,1:708,651:1359,2:0.0015:2,2:3.5:1.0:27.5:1.0:1.0:1.08748:60.0:4.0:0.0015:0.0:1.0 +20 31019299 . C T 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03248;LSEQ=GACAGACAGGTGCACATGGG;RSEQ=AGCCTCCCCTTTGCCTCTCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:900:82:29,53:332,486:818,82:0.0911:2,2:27.8:1.0:29.1:1.0:0.40859:1.24817:60.0:164.0:0.0927:0.0:1.1 0/0:617:2:1,1:252,362:614,2:0.0032:2,2:37.0:1.0:27.5:1.0:1.0:1.44:60.0:4.0:0.0033:0.0:1.0 +20 36030658 . C T 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.28003;SOR=0.0;LSEQ=GTGCCCTGTGCTCCCTACTC;RSEQ=CGCAGAGCACTGCTCCTGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:9:5,4:14,2:16,9:0.36:2,2:26.2:1.0:30.2:1.0:0.14245:5.16859:60.0:8.0:0.381:0.0:1.3 0/0:4:0:0,0:3,1:4,0:0.0:2,0:32.0:1.0:30.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +20 36970823 . C A 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.0;MSILEN=1.0;SSF=0.22078;SOR=0.0;LSEQ=CAAGATCCCTGGGGGACTTG;RSEQ=CTGCACGTCTTTGTTTCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:5,0:5,5:0.5:0,0:15.6:1.0:32.0:0.0:1.0:0.0:55.6:10.0:0.5:0.0:1.0 0/0:4:0:0,0:3,1:4,0:0.0:2,0:26.0:1.0:31.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +20 36971052 . G A 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0412;SOR=0.0;LSEQ=CAGAAGAAATGCTCAGTGTT;RSEQ=CTAATTGTGTCCAACAGGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:515:6:3,3:334,174:508,6:0.0117:2,2:25.0:1.0:28.5:1.0:0.41923:1.917:60.0:12.0:0.0119:0.0:1.0 0/0:382:0:0,0:228,153:381,0:0.0:2,0:25.1:1.0:31.2:1.0:1.0:0.0:60.0:75.2:0.9973:0.0:0.3 +20 39704995 . G A 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTTTTGTTTACCTTTGAAA;RSEQ=CAGATATCTTAATTGCATAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:29:3,26:26,130:156,29:0.1568:2,2:22.3:1.0:30.1:1.0:0.57872:1.7289:60.0:28.0:0.1547:0.0:1.0 0/0:159:0:0,0:27,132:159,0:0.0:2,0:22.3:1.0:31.5:1.0:1.0:0.0:60.0:158.0:1.0:0.0:0.1 +20 39743905 . G A 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00012;SOR=0.0;LSEQ=TCTCGGTGACGGATGTATGC;RSEQ=TGTTCCTTGTGCCTTTTTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:185:24:22,2:153,8:161,24:0.1297:1,2:22.3:1.0:30.8:1.0:0.62107:1.73244:60.0:48.0:0.1311:0.0:1.2 0/0:82:0:0,0:78,4:82,0:0.0:1,0:25.1:1.0:29.6:1.0:1.0:0.0:59.9:81.0:1.0:0.0:0.4 +20 39751809 . C T 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.02774;LSEQ=TTGCTGAGTCACCCTAATCC;RSEQ=CCCCTTATTTCTCCTTTGTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:970:52:32,20:545,373:918,52:0.0536:2,2:25.6:1.0:30.8:1.0:0.88471:1.09:58.1:104.0:0.0541:0.0:1.1 0/0:638:1:0,1:386,251:637,1:0.0016:2,0:1.0:0.0:22.0:0.0:0.39498:0.0:51.0:2.0:0.0016:0.0:1.0 +20 40709305 . G A 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.5743;SOR=0.0;LSEQ=TGGCTGGTTAGGTTGAAAAG;RSEQ=AAGCCTGGGCCTTTTGGAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:5:5,0:38,0:38,5:0.1163:1,0:22.4:1.0:29.6:1.0:1.0:0.0:60.0:10.0:0.119:0.0:1.0 0/0:12:0:0,0:12,0:12,0:0.0:0,0:23.9:1.0:31.1:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.1 +20 40710486 . C T 57 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.1631;SOR=0.0;LSEQ=AGGTCAAGGGAACTAGTCAG;RSEQ=CCTGGCTGTTGGAGAACAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:5:2,3:335,146:481,5:0.0103:2,2:11.6:1.0:24.6:1.0:0.17081:3.43182:60.0:4.0:0.0084:0.0:1.0 0/0:293:0:0,0:192,101:293,0:0.0:2,0:25.2:1.0:30.6:1.0:1.0:0.0:60.0:57.6:1.0:0.0:0.1 +20 40714218 . G A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.18296;SOR=0.0;LSEQ=TCATTGCTGAGTCTGGAGCC;RSEQ=GAATCAGCACAGGCATCACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:6:6,0:73,1:74,6:0.075:1,0:31.2:1.0:31.0:1.0:1.0:0.0:60.0:12.0:0.0779:0.0:1.0 0/0:31:0:0,0:30,1:31,0:0.0:1,0:19.8:1.0:29.5:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 +20 40714305 . T C 192 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGGCTCAGCGGGATCCTCTC;RSEQ=CGGCAGCCTCCATCTGTCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:382:66:56,10:254,62:316,66:0.1728:2,2:25.0:1.0:31.9:1.0:0.48988:1.37:60.0:132.0:0.1769:0.0:2.1 0/0:205:0:0,0:149,56:205,0:0.0:2,0:23.6:1.0:29.6:1.0:1.0:0.0:60.0:40.0:1.0:0.0:0.1 +20 40714307 . G A 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCAGCGGGATCCTCTCTC;RSEQ=GCAGCCTCCATCTGTCTTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:406:121:97,24:220,64:284,121:0.298:2,2:25.3:1.0:30.6:1.0:0.59987:1.18:60.0:59.5:0.3013:0.0:1.7 0/0:224:0:0,0:159,65:224,0:0.0:2,0:22.6:1.0:29.3:1.0:1.0:0.0:60.0:55.0:1.0:0.0:0.1 +20 40730515 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTAGACTTGCCATGGTGACA;RSEQ=GGGAGCCACCTTACGCTTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:5,0:5,6:0.5455:0,0:28.8:1.0:30.0:1.0:1.0:0.0:58.5:12.0:0.5455:0.0:1.0 0/0:1:0:0,0:1,0:1,0:0.0:0,0:2.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 +20 40738926 . G A 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTCTCGAACTCCTGACCTC;RSEQ=TGATCTGCCCGCCTCGGCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:443:54:42,12:297,90:387,54:0.1219:2,2:23.0:1.0:30.2:1.0:1.0:1.06:49.4:53.0:0.1221:0.0:1.1 0/0:241:0:0,0:179,61:240,0:0.0:2,0:23.6:1.0:29.7:1.0:1.0:0.0:53.3:119.0:0.9958:0.0:0.1 +20 40746918 . C T 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.00068;SOR=0.0;LSEQ=AATAGGAGTGATGACACCTC;RSEQ=CTTGTAGGTTGCCGTGAGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:25:25,0:92,2:94,25:0.2083:1,1:27.1:1.0:31.4:1.0:1.0:0.0:60.0:11.5:0.2054:0.0:1.2 0/0:41:0:0,0:41,0:41,0:0.0:1,0:20.8:1.0:30.5:1.0:1.0:0.0:60.0:40.0:1.0:0.0:0.0 +20 40748532 . C A 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGCCCTTTCCCCTGGGACC;RSEQ=CTGAAGCCTCTCTGAGGCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:581:27:20,7:368,185:553,27:0.0465:2,2:19.0:1.0:29.9:1.0:0.53145:1.44:60.0:54.0:0.0469:0.0:1.1 0/0:369:0:0,0:240,129:369,0:0.0:2,0:23.6:1.0:30.0:1.0:1.0:0.0:60.0:91.25:1.0:0.0:0.1 +20 40748802 . C A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.31714;SOR=0.0;LSEQ=GTGTAGTAAGTCACTAAATG;RSEQ=TAGCTATTTTTATAGTTACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:62:5:0,5:0,57:57,5:0.0806:1,0:25.6:1.0:32.8:1.0:1.0:0.0:60.0:10.0:0.0806:0.0:1.0 0/0:23:0:0,0:0,23:23,0:0.0:1,0:22.0:1.0:32.0:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.1 +20 40944069 . A G 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.18182;SOR=0.0;LSEQ=TCTCTTTACTTTAATACAGG;RSEQ=GTGTGCAAAGGTTTTATGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:6,0:3,0:3,6:0.6667:0,0:34.2:1.0:33.0:0.0:1.0:0.0:60.0:12.0:0.6667:0.0:1.5 0/0:2:0:0,0:2,0:2,0:0.0:0,0:24.0:1.0:22.5:1.0:1.0:0.0:40.5:1.0:1.0:0.0:1.0 +20 40944812 . C T 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACGTTGTAGAACTTTACCTC;RSEQ=ACTTAGCTGTCTCAGAGCCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:0,7:0,10:10,7:0.4118:0,0:25.7:1.0:28.6:1.0:1.0:0.0:60.0:14.0:0.4118:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +20 40979469 . A T 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=9e-05;SOR=0.0;LSEQ=TAAAGACACAGCATGGATAG;RSEQ=GGGAGGACGTTTAGGAAAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:20:0,20:2,81:83,20:0.1942:1,1:23.4:1.0:30.9:1.0:1.0:0.0:60.0:40.0:0.198:0.0:1.5 0/0:57:0:0,0:1,56:57,0:0.0:1,0:22.2:1.0:30.7:1.0:1.0:0.0:60.0:56.0:1.0:0.0:0.3 +20 40980486 . G C 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACGTGTACTATTTAATGCAA;RSEQ=CCTGTGGGAAAATTATTTAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:7,0:4,0:4,7:0.6364:0,0:38.3:1.0:32.7:1.0:1.0:0.0:58.4:14.0:0.6364:0.0:2.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +20 40980495 . A C 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATTTAATGCAAGCCTGTGGG;RSEQ=AAATTATTTAGTGGCTTGCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:10:10,0:4,0:4,10:0.7143:0,0:25.4:1.0:31.1:1.0:1.0:0.0:58.9:9.0:0.6923:0.0:1.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +20 40980987 . G A 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.09613;LSEQ=CACTCAGGAAGCTGGATGGA;RSEQ=CTCCTTTAGAGGAACCTTAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:180:98:3,95:7,74:81,98:0.5444:2,1:25.3:1.0:29.7:1.0:0.18885:2.9776:60.0:18.6:0.5376:0.0:1.1 0/1:88:9:0,9:7,72:79,9:0.1023:2,0:19.8:1.0:29.6:1.0:1.0:0.0:60.0:18.0:0.1023:0.0:1.0 +20 41101067 . A T 186 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCTCGTACTGCTGCTGGTTG;RSEQ=ACACATACTGGTACTGCACG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1062:90:43,47:455,516:971,90:0.0847:2,2:24.3:1.0:28.8:1.0:0.91227:1.04:60.0:89.0:0.0849:0.0:1.1 0/0:685:0:0,0:327,358:685,0:0.0:2,0:25.9:1.0:29.3:1.0:1.0:0.0:60.0:61.273:1.0:0.0:0.2 +20 41759593 . G A 63 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06842;SOR=0.0;LSEQ=CAACTGGTGCAGAGACAGCT;RSEQ=GCTAAGCATCTAAATACAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:364:5:4,1:133,226:359,5:0.0137:2,2:5.0:1.0:27.4:1.0:0.06875:6.76:60.0:10.0:0.0138:0.0:1.2 0/0:295:0:0,0:114,181:295,0:0.0:2,0:24.1:1.0:30.3:1.0:1.0:0.0:59.9:97.333:1.0:0.0:0.8 +20 46256424 . C T 268 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00226;LSEQ=TAAACGCCAGTCCTGAAATG;RSEQ=GCCAGAGATATGAAACAATG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1969:475:212,263:659,832:1491,475:0.2412:2,2:24.3:1.0:30.2:1.0:0.87372:1.02:59.8:157.333:0.2425:0.0:1.1 0/0:1401:1:0,1:663,734:1397,1:0.0007:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0007:0.0:1.0 +20 46271008 . G A 243 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02359;LSEQ=GTTGGGCCACCTTCCAACCT;RSEQ=GAAGGCCAGAGTGACGAAAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2364:286:145,141:1061,1014:2075,286:0.121:2,2:25.2:1.0:29.9:1.0:0.89974:1.01748:60.0:56.2:0.121:0.0:1.1 0/0:1546:5:4,1:790,749:1539,5:0.0032:2,2:11.8:1.0:24.4:1.0:0.37521:3.79:60.0:10.0:0.0033:0.0:1.0 +20 46275917 . A C 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGACAGACATACCCAGCAC;RSEQ=GGGGCCTCCAATGCAAGGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2347:145:71,74:1091,1108:2199,145:0.0618:2,2:24.3:1.0:30.3:1.0:0.93172:1.02626:59.9:28.0:0.0603:0.0:1.2 0/0:1521:0:0,0:777,743:1520,0:0.0:2,0:24.0:1.0:29.9:1.0:1.0:0.0:60.0:107.571:0.9993:0.0:0.1 +20 46277834 . A T 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01105;LSEQ=GGTGATGAGGCCTATGATGC;RSEQ=GCCCCAGGTGAGCTCCCAGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1669:114:50,64:743,810:1553,114:0.0683:2,2:27.4:1.0:31.1:1.0:0.43787:1.17401:60.0:113.0:0.0686:0.0:1.2 0/0:1236:1:0,1:576,658:1234,1:0.0008:2,0:1.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.0008:0.0:1.0 +20 48450891 . ATATATATATACTGTG A 72 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=9.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TATATATATATATACTGTAT;RSEQ=TATATATATATATACTGTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:5,0:4,1:5,5:0.5:2,0:26.6:1.0:31.2:1.0:1.0:0.0:53.0:10.0:0.625:0.0:0.2 0/0:1:0:0,0:1,0:1,0:0.0:0,0:1.0:0.0:31.0:0.0:1.0:0.0:39.0:2.0:1.0:0.0:1.0 +20 48450944 . ATATATATATACTGTATATATATACTGTATATATATATATATACTGTATATATATATACTGTG A 75 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=8.0;MSILEN=2.0;SSF=0.01515;SOR=0.0;LSEQ=TGTATATATATATACTGTGT;RSEQ=TATATATATATATACTGTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:1,6:0.8571:0,2:20.0:1.0:29.2:1.0:1.0:0.0:59.2:12.0:0.8571:0.4286:0.5 0/0:4:0:0,0:4,0:4,0:0.0:0,0:23.3:1.0:31.3:1.0:1.0:0.0:48.3:8.0:1.0:0.0:0.8 +20 48450987 . C CTG 105 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=2.0;MSILEN=2.0;SSF=0.04482;SOR=0.0;LSEQ=ACTGTATATATATATATATA;RSEQ=TGTATATATATATACTGTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:10:9,1:23,0:23,10:0.2778:1,2:9.1:1.0:31.7:1.0:0.30303:0.0:55.6:20.0:0.303:0.1944:0.2 0/0:13:0:0,0:13,0:13,0:0.0:1,0:25.5:1.0:31.2:1.0:1.0:0.0:51.6:12.0:1.0:0.0:0.5 +20 52777119 . G A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTCAGAGGACTGGCAGCCTC;RSEQ=GCTGCAAATAAACTGTAGAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:23.0:1.0:32.8:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +20 54945145 . C T 210 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCAGTCAATGGTAAAATAAA;RSEQ=TTCAGTAGCATGTTCCTGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:110:88,22:320,69:389,110:0.22:2,2:24.4:1.0:31.0:1.0:0.57824:1.15904:45.4:54.0:0.2204:0.0:1.1 0/0:257:0:0,0:204,53:257,0:0.0:2,0:21.4:1.0:31.6:1.0:1.0:0.0:58.3:127.5:1.0:0.0:0.1 +20 55178239 . C G 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=4e-05;SOR=0.06653;LSEQ=ACCCACCACTCACCTGCCTT;RSEQ=CCCACTTCCAGGCAGCCACC;STATUS=AFDiff GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:26:0,26:0,20:20,26:0.5652:1,1:29.3:1.0:32.0:1.0:1.0:0.0:60.0:52.0:0.5778:0.0:1.2 0/1:26:2:0,2:0,24:24,2:0.0769:1,0:10.5:1.0:24.0:1.0:1.0:0.0:60.0:1.0:0.0417:0.0:3.0 +20 57428287 . C G 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGTGCTCCATCTTACGGAG;RSEQ=CCCAAACTTATTTTGAGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1035:76:56,20:701,258:959,76:0.0734:2,2:27.9:1.0:31.3:1.0:1.0:1.03:60.0:24.333:0.0719:0.0:1.1 0/0:572:0:0,0:358,212:570,0:0.0:2,0:25.5:1.0:30.7:1.0:1.0:0.0:60.0:80.429:0.9982:0.0:0.2 +20 59632034 . C T 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.02876;SOR=0.0;LSEQ=TCAGGATTTGAAGTTTCACG;RSEQ=CCAGCAGCAGCCCAGCCTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:10:7,3:8,4:12,10:0.4545:2,2:26.7:1.0:30.6:1.0:1.0:1.16:57.9:20.0:0.4545:0.0:1.1 0/0:8:0:0,0:5,3:8,0:0.0:2,0:24.6:1.0:32.8:1.0:1.0:0.0:58.3:16.0:1.0:0.0:0.3 +20 59928237 . T C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.41667;SOR=0.0;LSEQ=GTTTCCACCTGTGGAAAGCA;RSEQ=ATACATGATGAATGTGCTAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:1,6:0,4:4,7:0.6364:0,2:16.6:1.0:33.0:1.0:1.0:0.0:60.0:14.0:0.6364:0.0:1.3 0/0:1:0:0,0:0,1:1,0:0.0:0,0:19.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +20 61041333 . C T 136 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00042;SOR=0.02774;LSEQ=CCCGGGGGTGGTGCCGCAGT;RSEQ=GGCCGGCCGGGACATGTGTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:22:19:19,0:3,0:3,19:0.8636:0,1:25.1:1.0:32.2:1.0:1.0:0.0:60.0:38.0:0.8636:0.0:1.1 0/1:8:1:1,0:7,0:7,1:0.125:0,0:33.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.125:0.0:1.0 +20 62173029 . A G 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGCCAACGGCCGGTGAGGCC;RSEQ=GCGTCCACCCACGTCACCTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:1,1:2,5:0.7143:2,0:28.6:1.0:31.4:1.0:0.28571:0.0:60.0:10.0:0.7143:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +21 11021107 . A T 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02658;LSEQ=ACAGTAAATTGTCAAGTTCA;RSEQ=ACCTGATTCAAAGTGAACTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:32:13,19:178,245:423,32:0.0703:2,2:17.0:1.0:29.8:1.0:1.0:1.06173:36.1:64.0:0.0716:0.0:1.1 0/0:499:1:0,1:204,294:498,1:0.002:2,0:1.0:0.0:25.0:0.0:1.0:0.0:20.0:2.0:0.002:0.0:1.0 +21 11021189 . G A 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.1119;LSEQ=TTTCTTCATCATCCTTATTT;RSEQ=ATGAAATATCTGCAGTAGAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:563:34:11,23:177,352:529,34:0.0604:2,2:25.5:1.0:30.1:1.0:1.0:1.05131:31.7:33.0:0.0591:0.0:1.2 0/0:561:4:4,0:186,371:557,4:0.0071:2,0:1.0:0.0:19.5:1.0:0.01288:0.0:37.0:3.0:0.0054:0.0:1.3 +21 11029526 . A G 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00226;SOR=0.0;LSEQ=ATCTAGAAAAGAAAGATTTA;RSEQ=TTCTTAACATCCAGTAGGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:8:6,2:49,7:56,8:0.125:2,2:13.6:1.0:33.1:1.0:0.31229:2.29528:42.5:16.0:0.125:0.0:1.0 0/0:69:0:0,0:56,12:68,0:0.0:2,0:16.8:1.0:29.9:1.0:1.0:0.0:28.7:33.0:0.9851:0.0:0.3 +21 11047650 . C T 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00218;SOR=0.0;LSEQ=TTTAAACTTATGTTTTGCAA;RSEQ=ATAAGTAATCATGAAAATCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:921:10:1,9:81,830:911,10:0.0109:2,2:28.8:1.0:28.6:1.0:0.60832:1.14:39.1:20.0:0.0109:0.0:1.0 0/0:823:0:0,0:100,722:822,0:0.0:2,0:23.8:1.0:31.6:1.0:1.0:0.0:35.9:116.429:0.9988:0.0:0.2 +21 11047979 . CA TG 74 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=TTGAAAAGACTGTCATATAA;RSEQ=TAAAGAGGATCAAATTTGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:24.8:1.0:32.1:1.0:1.0:0.0:49.2:10.0:0.7143:0.1429:1.8 0/0:1:0:0,0:1,0:1,0:0.0:0,0:42.0:0.0:34.0:0.0:1.0:0.0:22.0:2.0:1.0:0.0:3.0 +21 11049346 . C T 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02159;SOR=0.11923;LSEQ=GTCACTCTGAATGAATACAG;RSEQ=CAAAATATGAACAACCTCTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:9:9,0:182,5:187,9:0.0459:1,0:33.8:1.0:31.1:1.0:1.0:0.0:45.0:18.0:0.0466:0.0:1.9 0/0:176:1:1,0:156,19:175,1:0.0057:2,0:45.0:0.0:31.0:0.0:1.0:0.0:44.0:2.0:0.0057:0.0:2.0 +21 11057701 . C A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCACACCTATCAGGGATACA;RSEQ=AATTTCCAAGAATTTCAGAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:4,1:2,1:3,5:0.5556:2,2:9.4:1.0:30.4:1.0:1.0:1.83:32.8:10.0:0.5556:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +21 11057983 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.04259;SOR=0.0;LSEQ=TTTTTGGATTTAATTTCAAT;RSEQ=AAACCGTTGATAACATTTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:7:7,0:94,9:103,7:0.0636:2,0:34.0:1.0:29.1:1.0:1.0:0.0:23.6:14.0:0.0642:0.0:3.3 0/0:76:0:0,0:60,16:76,0:0.0:2,0:22.3:1.0:31.1:1.0:1.0:0.0:26.0:37.0:1.0:0.0:2.5 +21 21056234 . C T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01658;SOR=0.11888;LSEQ=AACGAAGCACTTTGGCTGTC;RSEQ=TTTGGTGGCGGGGCTGTGCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:7:3,4:3,6:9,7:0.4375:2,2:23.9:1.0:31.4:1.0:1.0:1.46:60.0:14.0:0.4375:0.0:1.6 0/1:25:2:1,1:9,14:23,2:0.08:2,2:5.5:1.0:29.5:1.0:1.0:1.53:47.0:4.0:0.08:0.0:1.5 +21 27340191 . C T 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.11905;SOR=0.19265;LSEQ=GTATTTAATCTGGTAGCTTG;RSEQ=AGGCCTCCAAAGGTGGTAGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:5:3,2:132,32:164,5:0.0294:2,2:19.2:1.0:29.2:1.0:0.26392:2.72924:60.0:10.0:0.0299:0.0:1.0 0/0:173:1:1,0:136,36:172,1:0.0058:2,0:15.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0058:0.0:1.0 +21 28978250 . G A 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.03036;SOR=0.0;LSEQ=GAGCTGTCCCTTTTTGGAGG;RSEQ=GGTGTGCTACGTTGGGGAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:6,8:14,8:0.3636:2,2:27.3:1.0:32.3:1.0:1.0:1.23744:60.0:16.0:0.3636:0.0:1.0 0/0:12:0:0,0:4,8:12,0:0.0:2,0:25.0:1.0:30.4:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.0 +21 31384240 . C T 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00166;SOR=0.16797;LSEQ=GCCTTTTGACCCAAAAAGAC;RSEQ=GCATAGCCTCCAATTTGAAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:347:19:8,11:187,141:328,19:0.0548:2,2:32.2:1.0:32.1:1.0:0.23816:1.82035:60.0:38.0:0.0556:0.0:1.5 0/0:312:3:1,2:170,139:309,3:0.0096:2,2:29.0:1.0:29.0:1.0:0.5912:2.43919:60.0:6.0:0.0098:0.0:1.3 +21 36164388 . G C 102 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00713;SOR=0.0;LSEQ=AGGCCCGCGCGCCCGGAGGC;RSEQ=AAGGCGGCGGCCCGCGGGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:9:9,0:23,0:23,9:0.2727:1,0:7.0:1.0:32.2:1.0:1.0:0.0:60.0:18.0:0.3:0.0:1.0 0/0:24:0:0,0:21,3:24,0:0.0:2,0:9.5:1.0:27.9:1.0:1.0:0.0:58.7:11.0:1.0:0.0:1.0 +21 36971853 . G A 122 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.04101;SOR=0.12689;LSEQ=CCCTGATCCTCGGTCAGAGC;RSEQ=AGCGCTTAGGTTCCCGCTGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:15,0:24,0:24,15:0.3846:1,1:20.2:1.0:31.3:1.0:1.0:0.0:60.0:30.0:0.3846:0.0:1.1 0/1:14:1:1,0:13,0:13,1:0.0714:1,0:33.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.0714:0.0:2.0 +21 37954734 . T A 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.06191;SOR=0.0;LSEQ=TATCTCCAACAAACCAGCTG;RSEQ=CAGGAAATGGTCTCAAATCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:466:5:3,2:188,273:461,5:0.0107:2,2:32.4:1.0:27.4:1.0:0.40445:2.17:60.0:10.0:0.011:0.0:1.6 0/0:455:0:0,0:209,246:455,0:0.0:2,0:26.5:1.0:28.4:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.9 +21 39755976 . T A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.13002;SOR=0.0;LSEQ=TCACCAGGCCTGTCCGTCCA;RSEQ=CCCTCAGCTGCAGGGGTGCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:0,7:0,11:11,7:0.3889:0,0:33.1:1.0:29.6:1.0:1.0:0.0:60.0:14.0:0.4118:0.0:1.0 0/0:6:0:0,0:1,5:6,0:0.0:2,0:33.8:1.0:27.7:1.0:1.0:0.0:60.0:5.0:1.0:0.0:0.0 +21 39764016 . A T 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CATGGCCAAGATTCAGGAAA;RSEQ=CACCGATTATTTAATGTGTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:7:3,4:6,1:7,7:0.5:2,2:30.0:1.0:29.4:1.0:0.26573:6.78852:58.0:14.0:0.5385:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +21 39764588 . G A 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.375;SOR=0.0;LSEQ=TTGTCTGAAAACTTCCATTG;RSEQ=CAGATTCTCCCAGAGCTTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:12.8:1.0:27.2:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:20.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +21 39794880 . T G 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAACAATAATCTCCAAGAAG;RSEQ=GGCAATTCCTCCCTAGAAAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:24.0:1.0:29.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +21 39795279 . A T 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCTCCCTGAGGCTCAGCCT;RSEQ=GCCTTGGGGAAGTTGCGATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:489:35:27,8:361,93:454,35:0.0716:2,2:21.6:1.0:31.6:1.0:0.67112:1.14977:60.0:70.0:0.0725:0.0:1.1 0/0:359:0:0,0:275,84:359,0:0.0:2,0:22.5:1.0:28.0:1.0:1.0:0.0:60.0:118.667:1.0:0.0:0.1 +21 42842591 . C T 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=0.0;SOR=0.06689;LSEQ=TCACCTTTCTCCTCGGTGGC;RSEQ=CCCCACCCGGAAATCCAGCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:988:33:19,14:529,423:952,33:0.0334:2,2:25.9:1.0:30.5:1.0:0.86035:1.09:60.0:32.0:0.0331:0.0:1.2 0/0:868:2:1,1:475,391:866,2:0.0023:2,2:22.0:1.0:27.0:1.0:1.0:1.21456:60.0:4.0:0.0023:0.0:1.0 +21 42842949 . T C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATTACATATCTCCAGGTGA;RSEQ=CAAGACGGGAAAGACACACA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:0,8:1.0:0,2:23.1:1.0:29.1:1.0:1.0:0.0:59.3:7.0:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +21 42847036 . A G 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GAGTGAGGGGATGAGGGAGT;RSEQ=ATTCAGAGGGTGAAGGGGTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1.0:0,2:26.0:1.0:33.4:1.0:1.0:0.0:58.4:10.0:1.0:0.0:2.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +21 42848187 . C T 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCCAGGGCTCACTAACGCCA;RSEQ=CCCCCTTTGCTTTCTGGAGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:5,1:0,0:0,6:1.0:0,2:19.7:1.0:30.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +21 42848747 . C T 67 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.56914;SOR=0.0;LSEQ=AGACACTGAGCCAAGGTACG;RSEQ=GGCTCACATCCCCACAGTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:5:0,5:2,28:30,5:0.1429:2,0:36.8:1.0:29.2:1.0:1.0:0.0:60.0:10.0:0.1471:0.0:1.2 0/0:7:0:0,0:0,7:7,0:0.0:0,0:15.3:1.0:30.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.7 +21 42848835 . T C 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=AGGACGGTTGTGAGGGTAAG;RSEQ=ATACAATAATGCTAGTTTTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:1,7:0,0:0,8:1.0:0,2:15.3:1.0:32.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +21 42850911 . C T 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02206;SOR=0.0;LSEQ=TAGCAGAGAAACCTCAGCCA;RSEQ=TTCCTATGAATAAACCAAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:15:14:14,0:1,0:1,14:0.9333:0,1:21.4:1.0:32.4:1.0:1.0:0.0:60.0:28.0:0.9333:0.0:2.1 0/0:2:0:0,0:2,0:2,0:0.0:0,0:21.5:1.0:33.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.5 +21 42860532 . G A 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05303;SOR=0.0;LSEQ=CCGTGGCATTACTGTAGCTC;RSEQ=CTGCAGCCTCCAACTCCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:136:8:0,8:4,124:128,8:0.0588:1,0:23.5:1.0:30.4:1.0:1.0:0.0:60.0:16.0:0.0593:0.0:1.8 0/0:77:0:0,0:6,70:76,0:0.0:2,0:25.8:1.0:31.5:1.0:1.0:0.0:60.0:75.0:0.9868:0.0:0.9 +21 42866296 . TG CA 124 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=6e-05;SOR=0.0;LSEQ=ATCCTACTTGAGGTGCACAC;RSEQ=TCCCGGATGGGGATTTGGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:539:16:13,3:330,192:522,16:0.0297:2,2:23.3:1.0:31.0:1.0:0.18865:2.52:60.0:32.0:0.0303:0.0074:0.9 0/0:453:0:0,0:230,172:402,0:0.0:2,0:25.4:1.0:29.9:1.0:1.0:0.0:60.0:200.0:0.8909:0.0:0.2 +21 42867003 . A T 218 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=16.0;MSILEN=1.0;SSF=0.0;SOR=0.00552;LSEQ=AGACTATGTCTCAAAAAAAA;RSEQ=AAAAAAAGTAATAGAAAAGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:446:142:109,33:225,79:304,142:0.3184:2,2:18.7:1.0:30.6:1.0:0.55988:1.16:59.5:141.0:0.3183:0.0:1.0 0/0:390:1:0,1:271,118:389,1:0.0026:2,0:1.0:0.0:22.0:0.0:0.30513:0.0:60.0:2.0:0.0026:0.0:1.0 +21 42872398 . C T 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01192;LSEQ=TTCAGTACACCATCGCTTTC;RSEQ=TGTGTCCTAAGCAGAACTGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1052:93:45,48:452,507:959,93:0.0884:2,2:22.7:1.0:31.2:1.0:0.82859:1.05:60.0:186.0:0.089:0.0:1.1 0/0:867:1:0,1:410,455:865,1:0.0012:2,0:1.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.0012:0.0:1.0 +21 42878126 . A C 275 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0757;LSEQ=CCTGAGGCTCCAGCAACAGC;RSEQ=CAAGCTTGTTGTTAGAAGGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:801:488:251,237:167,146:313,488:0.6092:2,2:25.5:1.0:30.8:1.0:0.61235:1.07993:59.9:39.667:0.6087:0.0:1.1 0/1:655:69:44,25:304,280:584,69:0.1053:2,2:24.9:1.0:29.9:1.0:0.07416:1.62:60.0:33.5:0.1039:0.0:1.1 +21 42878780 . T G 181 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTCGCGGCTGGGAGCTCCG;RSEQ=GAGGTCAGGCATTGCCTTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:52:19,33:236,369:605,52:0.0789:2,2:26.6:1.0:31.8:1.0:0.7687:1.11068:60.0:104.0:0.0804:0.0:1.2 0/0:528:0:0,0:219,309:528,0:0.0:2,0:23.8:1.0:28.8:1.0:1.0:0.0:60.0:51.8:1.0:0.0:0.2 +21 43124132 . T C 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=GGGAGTGGGGGGAGCCAAGG;RSEQ=CCGGGAGACGGAGGCTCACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:73:22:18,4:35,16:51,22:0.3014:2,2:28.6:1.0:31.8:1.0:0.39124:2.04:60.0:44.0:0.3099:0.0:2.5 0/0:45:0:0,0:26,19:45,0:0.0:2,0:19.6:1.0:28.7:1.0:1.0:0.0:60.0:90.0:1.0:0.0:1.7 +21 43124280 . CAT TGC 111 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.02756;SOR=0.0;LSEQ=CCCAACTCCCCCCACCCCAC;RSEQ=GCCCCCGCCCAGCCTGGCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:11:0,11:2,31:33,11:0.2292:2,0:17.2:1.0:32.2:1.0:1.0:0.0:60.0:22.0:0.2391:0.0625:1.4 0/0:18:0:0,0:2,16:18,0:0.0:2,0:22.1:1.0:31.2:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.7 +21 44524290 . A C 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0001;SOR=0.08199;LSEQ=GCCTCACTATTATTTAAATA;RSEQ=AAGAACACACTTATGAACAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:22,0:37,1:38,22:0.3667:1,1:22.2:1.0:32.3:1.0:1.0:0.0:60.0:44.0:0.3667:0.0:1.1 0/1:45:2:2,0:42,1:43,2:0.0444:1,0:10.0:1.0:29.5:1.0:1.0:0.0:60.0:4.0:0.0444:0.0:1.0 +21 45649498 . C T 106 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.002;SOR=0.0;LSEQ=GGCGGTGCCCGGACCCACTC;RSEQ=GGACACCCCACAGGGGCTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:274:10:8,2:125,137:262,10:0.0365:2,2:5.1:1.0:32.2:1.0:0.05592:4.36:35.9:20.0:0.037:0.0:3.0 0/0:248:0:0,0:133,115:248,0:0.0:2,0:23.5:1.0:29.9:1.0:1.0:0.0:56.4:247.0:1.0:0.0:1.5 +21 45649748 . C T 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTGCACACCAGGATGCCATC;RSEQ=CATGCCAAGGGGAGGCTGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:800:88:43,45:334,377:711,88:0.11:2,2:24.4:1.0:30.8:1.0:0.82104:1.08:60.0:43.0:0.1101:0.0:1.9 0/0:770:0:0,0:363,407:770,0:0.0:2,0:23.1:1.0:30.0:1.0:1.0:0.0:60.0:50.333:1.0:0.0:0.5 +21 45651275 . G A 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02519;LSEQ=CACGTGGCCGCGTTTTTCTC;RSEQ=CCGGTACTGACTGGATTCTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1140:151:71,80:454,532:986,151:0.1325:2,2:25.1:1.0:29.6:1.0:0.86099:1.04:60.0:29.2:0.1305:0.0:1.2 0/0:1044:4:3,1:523,516:1039,4:0.0038:2,2:8.8:1.0:26.3:1.0:0.62434:2.96:60.0:8.0:0.0039:0.0:1.0 +22 17519579 . A G 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.04461;LSEQ=GCCTGAGTACCTAAGATGCA;RSEQ=TTATATGAACTCTACTCTGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:54:25,29:63,59:122,54:0.3068:2,2:24.6:1.0:33.3:1.0:0.62412:1.23713:56.1:108.0:0.3086:0.0:1.0 0/1:156:3:1,2:75,78:153,3:0.0192:2,2:23.0:1.0:30.7:1.0:1.0:1.91533:57.7:6.0:0.0194:0.0:1.3 +22 20918896 . TGCA T 76 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=14;MSI=5.0;MSILEN=3.0;SSF=0.06973;SOR=0.0;LSEQ=GCAGCAGTTCCAAGCAGTAG;RSEQ=GCAGCAGCAGCAGCTCCAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:2,3:6,14:20,5:0.2:2,2:29.4:1.0:32.8:1.0:1.0:1.53:60.0:10.0:0.2:0.0:0.2 0/0:17:0:0,0:7,10:17,0:0.0:2,0:17.1:1.0:29.4:1.0:1.0:0.0:60.0:7.5:1.0:0.0:0.2 +22 21135741 . G A 62 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.11151;SOR=0.18445;LSEQ=GCTCCCGTGGTTTTATAGCA;RSEQ=CCCAGGCGAAGGAAGGAGAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:5:4,1:221,207:428,5:0.0115:2,2:6.2:1.0:26.8:1.0:0.37404:3.74:60.0:10.0:0.0118:0.0:1.0 0/0:468:1:1,0:211,256:467,1:0.0021:2,0:1.0:0.0:24.0:0.0:0.45299:0.0:60.0:2.0:0.0022:0.0:1.0 +22 21272198 . G A 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.13301;SOR=0.19597;LSEQ=GGACAGCCGCCGCCCCTACC;RSEQ=CCGCAGAGTCCCCGGTCCAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:6:4,2:288,164:452,6:0.0131:2,2:33.3:1.0:29.3:1.0:1.0:1.14:60.0:12.0:0.0133:0.0:1.3 0/0:386:1:1,0:228,157:385,1:0.0026:2,0:3.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0026:0.0:1.0 +22 21272752 . C T 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.26632;SOR=0.0;LSEQ=CCTCTCACGAGGCTGTTTCT;RSEQ=AATGTGAAGAGGATGCGTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:10,5:0.3333:0,0:25.2:1.0:28.8:1.0:1.0:0.0:60.0:10.0:0.3333:0.0:2.2 0/0:5:0:0,0:1,4:5,0:0.0:2,0:16.8:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.4 +22 21288518 . G A 59 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06543;SOR=0.0;LSEQ=CCTGTGCTTATGACAAGACT;RSEQ=CCTTGGCATTAGAGGTAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:5:4,1:122,260:382,5:0.0129:2,2:6.8:1.0:25.6:1.0:0.04053:8.48:60.0:10.0:0.0131:0.0:1.0 0/0:331:0:0,0:124,207:331,0:0.0:2,0:42.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:6.0 +22 21304408 . A G 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACAAGTGGAGAGAAGTTGAC;RSEQ=TGGAAAGGGTCTTCCTTCTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:0,11:0,0:0,11:1.0:0,0:19.9:1.0:32.1:1.0:1.0:0.0:60.0:22.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +22 22127490 . C T 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.27761;SOR=0.0;LSEQ=ACCGCAAACAAAAACACTGG;RSEQ=ACTACTTAATGAAGCGTCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:1,10:11,5:0.3125:2,0:30.0:1.0:28.2:1.0:1.0:0.0:60.0:10.0:0.3333:0.0:1.2 0/0:5:0:0,0:0,5:5,0:0.0:0,0:26.2:1.0:32.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 +22 24134394 . T C 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGCGATGCTCTGCCATCTG;RSEQ=CGTGGGTGTGTCGCCATAAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:23.8:1.0:30.8:1.0:1.0:0.0:56.3:12.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +22 24159437 . G T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCAGGCTGAGTGCTCCAGGG;RSEQ=GGCCTAGTAACCCAATAAGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1.0:0,0:28.1:1.0:31.4:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +22 24176232 . C T 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCACATCCTGCCTCTGTTCC;RSEQ=ACCCCTACACTTGGCTGCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:25:19,6:264,46:310,25:0.0746:2,2:19.7:1.0:31.7:1.0:0.24802:1.80851:59.0:50.0:0.0755:0.0:1.0 0/0:226:0:0,0:181,45:226,0:0.0:2,0:22.0:1.0:30.5:1.0:1.0:0.0:60.0:112.0:1.0:0.0:0.2 +22 24176677 . GCAACAGGTCATGTTCAATTTCTT G 214 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=26;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.13205;LSEQ=TAACAGTTTTTAAATAAAAG;RSEQ=CAACAGGTCATGTTCAATTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:556:97:40,57:204,254:458,97:0.1745:2,2:31.0:1.0:32.5:1.0:0.57508:1.14421:59.8:194.0:0.177:0.0144:0.1 0/1:627:17:11,6:276,333:609,17:0.0271:2,2:34.1:1.0:31.7:1.0:0.14042:2.21:59.7:34.0:0.0276:0.0032:0.1 +22 24176959 . CA C 77 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGTAGCTGTGAGGCTCAGGG;RSEQ=AGAGGCTCTCTGCCTTTCAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:1,0:1,5:0.8333:0,0:16.0:1.0:33.3:1.0:0.16667:0.0:60.0:10.0:0.8333:0.1667:2.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +22 26388019 . G T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02006;SOR=0.0;LSEQ=AGATGGGCTGAGTATCCACT;RSEQ=TGCGTGGTGGTGCAGATTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:7,1:52,6:58,8:0.1212:2,2:25.8:1.0:31.5:1.0:1.0:1.23383:60.0:16.0:0.1231:0.0:1.1 0/0:46:0:0,0:39,7:46,0:0.0:2,0:20.1:1.0:31.5:1.0:1.0:0.0:60.0:92.0:1.0:0.0:0.0 +22 29090363 . G A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.44444;SOR=0.0;LSEQ=CACTGCCTGTTCCCTCTCTT;RSEQ=TTGCTAGACTCAAGGTCGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:0,5:0,3:3,5:0.625:0,0:16.8:1.0:30.2:1.0:1.0:0.0:28.6:10.0:0.625:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:10.0:0.0:34.0:0.0:1.0:0.0:28.0:2.0:1.0:0.0:0.0 +22 29093239 . A G 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=TAATAAACAACTCTTCACAC;RSEQ=GCAGAAATGTAAGGTGTCAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:0,7:0,0:0,7:1.0:0,0:19.0:1.0:32.0:1.0:1.0:0.0:56.4:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +22 29120915 . T A 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGGACAAATTTTCCTCCTA;RSEQ=GAGAGAGTGGAAAAAAAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:280:33:27,6:185,62:247,33:0.1179:2,2:24.0:1.0:30.5:1.0:0.51734:1.51:60.0:66.0:0.1209:0.0:1.1 0/0:271:0:0,0:193,78:271,0:0.0:2,0:5.0:0.0:17.0:0.0:1.0:0.0:35.0:0.0:0.0:0.0:5.0 +22 29682881 . CT C 76 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.56028;SOR=0.0;LSEQ=CAAGCCTCTTTCTAAAAAAG;RSEQ=TTTTTTTTTTTCTCTTCTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,0:19,5:0.2:1,0:24.2:1.0:32.8:1.0:1.0:0.0:60.0:10.0:0.2:0.04:0.2 0/0:7:0:0,0:6,1:7,0:0.0:2,0:31.4:1.0:30.4:1.0:1.0:0.0:56.9:14.0:1.0:0.0:1.3 +22 29689837 . A G 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAAGTTTTGTGATTGCAGAC;RSEQ=TGAGCCACTGTGCCTGGCCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:0,6:1.0:0,2:26.8:1.0:30.2:1.0:1.0:0.0:57.2:12.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +22 29689868 . G A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCCTGGCCTGTCTCTATTT;RSEQ=TTATTTTATTTTACTTTGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:5,2:0,0:0,7:1.0:0,2:15.9:1.0:29.4:1.0:1.0:0.0:58.4:14.0:1.0:0.0:2.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +22 29691910 . C T 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAAAGTCTGACTACCCCTA;RSEQ=GAGGTGGCTGTGCTCAGTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:60:36,24:193,160:353,60:0.1449:2,2:30.0:1.0:31.1:1.0:0.48422:1.24:60.0:120.0:0.146:0.0:1.1 0/0:366:0:0,0:194,170:364,0:0.0:2,0:24.0:1.0:30.1:1.0:1.0:0.0:59.9:71.8:0.9945:0.0:0.2 +22 30053939 . C A 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.54941;SOR=0.0;LSEQ=GAAACTAAGGCCAAGAAACT;RSEQ=CGTGATGAGTCTGTTCTCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:5:5,0:15,1:16,5:0.2381:1,0:14.0:1.0:28.4:1.0:1.0:0.0:60.0:10.0:0.2381:0.0:1.6 0/0:4:0:0,0:4,0:4,0:0.0:0,0:24.8:1.0:31.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +22 37903975 . G A 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.23077;SOR=0.0;LSEQ=GCAGGTACTGAGGGTGGCAC;RSEQ=GGGCGGGGTCAGACCACAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:6,5:0.4545:2,2:10.2:1.0:31.8:1.0:1.0:1.3:60.0:10.0:0.4545:0.0:1.0 0/0:4:0:0,0:1,3:4,0:0.0:2,0:20.5:1.0:30.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 +22 41525892 . A G 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAATATGTTTTCTTCTCTTT;RSEQ=GTGGCACACTGTGCATCTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:28:17,11:314,166:480,28:0.0551:2,2:23.9:1.0:32.2:1.0:0.68406:1.22344:60.0:56.0:0.0561:0.0:1.1 0/0:484:0:0,0:298,184:482,0:0.0:2,0:24.6:1.0:28.2:1.0:1.0:0.0:60.0:42.818:0.9958:0.0:0.1 +22 41542838 . T A 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGTAAATAGTGAAAAAAA;RSEQ=TTTTTTATTTTAAAAGAATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:30:5,25:53,228:281,30:0.0958:2,2:20.5:1.0:30.5:1.0:1.0:1.16174:60.0:29.0:0.0935:0.0:1.2 0/0:351:0:0,0:94,256:350,0:0.0:2,0:22.8:1.0:29.5:1.0:1.0:0.0:60.0:115.667:0.9971:0.0:0.1 +22 41562785 . A G 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.00061;SOR=0.0;LSEQ=TAATAGAGTAAAAATAAAAT;RSEQ=ATTCTATAATCTCCTTATAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:9:0,9:1,31:32,9:0.2195:1,0:24.2:1.0:33.2:1.0:1.0:0.0:60.0:18.0:0.2195:0.0:1.2 0/0:47:0:0,0:0,47:47,0:0.0:1,0:23.9:1.0:29.9:1.0:1.0:0.0:60.0:22.5:1.0:0.0:0.1 +22 41568804 . TAGAG T 133 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=2.0;SSF=0.00065;SOR=0.0;LSEQ=TTGGACAAGAAATATTGGCT;RSEQ=AGGTTATTAGGGTTCTGTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:17:0,17:0,29:29,17:0.3696:1,1:23.6:1.0:32.7:1.0:1.0:0.0:60.0:34.0:0.3778:0.087:0.1 0/0:21:0:0,0:0,21:21,0:0.0:1,0:19.1:1.0:31.4:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.0 +22 41574383 . A C 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=AGTTGGCTACCCACCACAGC;RSEQ=GCAGCAGCGGATGCAGCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:986:96:46,50:403,487:890,96:0.0974:2,2:24.1:1.0:30.9:1.0:0.66658:1.11:60.0:192.0:0.0986:0.0:1.1 0/0:1042:0:0,0:470,571:1041,0:0.0:2,0:25.7:1.0:29.9:1.0:1.0:0.0:59.9:68.4:0.999:0.0:0.2 +22 47217677 . C T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCCGAATTTACATGTTGGC;RSEQ=CGTCTTGCTAGGTTGGGGAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1.0:0,2:20.0:1.0:31.4:1.0:1.0:0.0:56.8:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 10191219 . C G 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ATTGCCAGTGTCGCTTCATC;RSEQ=ACATTCAGTTAGTTAAAGCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:9,0:2,0:2,9:0.8182:0,0:18.8:1.0:30.4:1.0:1.0:0.0:60.0:18.0:0.8182:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 14387169 . A AG 115 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0007;SOR=0.0;LSEQ=GACTTTTCCTGATGCCCTTT;RSEQ=GTAGCCGAGCTGGCTCCAAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:0,12:0,0:0,12:1.0:0,0:27.1:1.0:32.3:1.0:1.0:0.0:60.0:24.0:1.0:0.0833:1.3 0/1:6:1:0,1:1,4:5,1:0.1667:2,0:36.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.1667:0.0:0.0 +3 25482579 . C T 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.00031;SOR=0.07023;LSEQ=AGGAAGAAGAAATTTTTTTT;RSEQ=GGGGGGGTGGGTGGGAATGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:15:15,0:11,0:11,15:0.5357:0,1:31.9:1.0:30.1:1.0:1.0:0.0:60.0:14.0:0.5385:0.0:1.0 0/1:28:2:1,1:23,1:24,2:0.0714:1,2:23.0:1.0:28.5:1.0:0.15077:16.61257:60.0:4.0:0.08:0.0:2.5 +3 25502851 . G A 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.07228;SOR=0.0;LSEQ=AGGTGAGTATTCACACTTCT;RSEQ=TGCCTGATGAACTCTCATTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:5:2,3:15,29:44,5:0.102:2,2:20.0:1.0:28.0:1.0:1.0:1.28:60.0:10.0:0.102:0.0:1.0 0/0:35:0:0,0:13,22:35,0:0.0:2,0:26.4:1.0:31.5:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.2 +3 25569630 . G T 173 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=4.0;SSF=0.0;SOR=0.0;LSEQ=TTGAGGAAGGAAGACAGACA;RSEQ=ACTTGAAGCCAAGCCTCGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:56:18,38:32,60:92,56:0.3784:2,2:24.4:1.0:29.8:1.0:0.85806:1.12503:60.0:112.0:0.3784:0.0:1.7 0/0:232:0:0,0:94,138:232,0:0.0:2,0:23.3:1.0:30.6:1.0:1.0:0.0:60.0:76.333:1.0:0.0:0.3 +3 29047705 . C A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=2e-05;SOR=0.0;LSEQ=ATAAGAAAATATTTAAGACT;RSEQ=TAAGAAACAAGATTAAAGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:143:12:4,8:57,74:131,12:0.0839:2,2:29.8:1.0:31.6:1.0:0.55719:1.53605:60.0:24.0:0.0857:0.0:2.3 0/0:203:0:0,0:87,116:203,0:0.0:2,0:25.9:1.0:31.1:1.0:1.0:0.0:60.0:66.667:1.0:0.0:0.4 +3 30692219 . T C 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGTTTCTCAAAGTGCGGCC;RSEQ=CTTGAGCAGCCAGCATCAGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:14.2:1.0:31.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 30713834 . G A 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02023;LSEQ=TCAAGAGCTCCAATATCCTC;RSEQ=TGAAGAACGACCTAACCTGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:727:37:23,14:363,327:690,37:0.0509:2,2:22.5:1.0:30.5:1.0:0.3111:1.48:60.0:36.0:0.0504:0.0:1.1 0/0:925:1:1,0:494,429:923,1:0.0011:2,0:1.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 +3 32670533 . G C 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=4e-05;SOR=0.06423;LSEQ=AGGCCAAGGCAGGTGGATTG;RSEQ=TTGAGTCCAGGCGTTTGAGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:0,16:0,9:9,16:0.64:0,1:26.2:1.0:34.4:1.0:1.0:0.0:49.3:32.0:0.64:0.0:1.4 0/1:31:3:0,3:1,27:28,3:0.0968:1,0:19.3:1.0:32.7:1.0:1.0:0.0:58.3:6.0:0.1:0.0:1.0 +3 37034946 . G A 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03755;LSEQ=GGATGGCGTAAGCTACAGCT;RSEQ=AAGGAAGAACGTGAGCACGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:103:55:54,1:44,4:48,55:0.534:2,1:23.3:1.0:27.3:1.0:0.18155:4.84:60.0:17.333:0.5253:0.0:1.1 0/1:123:5:5,0:110,8:118,5:0.0407:2,0:19.4:1.0:27.2:1.0:1.0:0.0:60.0:10.0:0.041:0.0:1.4 +3 37050254 . T C 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.049;LSEQ=TGCCAGGACATCTTGGGTTT;RSEQ=ATTTTCAAGTACTTCTATGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:187:67:59,8:98,22:120,67:0.3583:2,2:23.0:1.0:32.3:1.0:0.30266:1.65:60.0:66.0:0.3568:0.0:1.1 0/1:189:5:5,0:144,40:184,5:0.0265:2,0:23.2:1.0:30.6:1.0:0.586:0.0:60.0:10.0:0.0266:0.0:1.0 +3 37061720 . G C 181 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11316;LSEQ=CATCTGGCCTCAAATCTTCT;RSEQ=GCCACCACATACACCATATG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:56:45,11:99,12:111,56:0.3353:2,2:22.7:1.0:31.3:1.0:0.15316:2.00761:59.8:55.0:0.3333:0.0:1.1 0/1:149:8:6,2:119,22:141,8:0.0537:2,2:28.5:1.0:29.6:1.0:0.61546:1.79459:60.0:16.0:0.0552:0.0:1.0 +3 37067097 . A T 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=12.0;MSILEN=2.0;SSF=0.00017;SOR=0.14822;LSEQ=ATATATATATATATATATAT;RSEQ=TATTTTTTTTTTTTTTTTTT;STATUS=AFDiff GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:16:16,0:17,2:19,16:0.2667:2,1:21.4:1.0:30.4:1.0:0.48908:0.0:40.8:32.0:0.3478:0.0:3.6 0/1:99:5:3,2:43,6:49,5:0.0505:2,2:23.4:1.0:22.2:1.0:0.15376:4.57627:43.4:1.5:0.0588:0.0:3.4 +3 37067099 . A T 139 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=21.0;MSILEN=1.0;SSF=0.0;SOR=0.09661;LSEQ=ATATATATATATATATATAT;RSEQ=TTTTTTTTTTTTTTTTTTTT;STATUS=AFDiff GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:51:24:22,2:9,1:10,24:0.4706:2,2:19.6:1.0:30.4:1.0:1.0:1.21:43.4:48.0:0.6667:0.0:3.0 0/1:103:8:5,3:39,7:46,8:0.0777:2,2:16.1:1.0:22.4:1.0:0.15606:3.24857:45.5:3.0:0.1132:0.0:2.3 +3 37092173 . GTTC G 232 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.11715;LSEQ=ATTTATGCACTGTGGGATGT;RSEQ=TTCTTTCTCTGTATTCCGAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:440:148:47,101:97,194:291,148:0.3364:2,2:25.0:1.0:32.3:1.0:0.82979:1.07432:59.9:296.0:0.3379:0.0341:0.1 0/1:447:25:8,17:145,277:422,25:0.0559:2,2:24.2:1.0:31.7:1.0:1.0:1.11212:60.0:50.0:0.0566:0.0045:0.1 +3 41266226 . A G 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGGATTTTCTCAGTCCTTC;RSEQ=CTCAAGAACAAGTAGCTGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:575:34:14,20:221,319:540,34:0.0591:2,2:25.7:1.0:31.1:1.0:1.0:1.01:60.0:68.0:0.0599:0.0:1.1 0/0:638:0:0,0:293,344:637,0:0.0:2,0:26.6:1.0:29.0:1.0:1.0:0.0:60.0:158.25:1.0:0.0:0.2 +3 41275350 . C T 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ACCCACCATCCCACTGGCCT;RSEQ=TGATAAAGGTAAATTGTCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:168:56,112:74,130:204,168:0.4492:2,2:26.2:1.0:30.8:1.0:0.58579:1.13806:60.0:167.0:0.4514:0.0:1.1 0/0:424:0:0,0:178,245:423,0:0.0:2,0:24.7:1.0:30.5:1.0:1.0:0.0:60.0:37.455:0.9976:0.0:0.1 +3 41443220 . C A 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCCACTCAATACTTCCACC;RSEQ=CAATTTCTCAATTTCAGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:19:9,10:168,174:342,19:0.0526:2,2:19.8:1.0:30.2:1.0:1.0:1.07262:60.0:38.0:0.0534:0.0:1.2 0/0:450:0:0,0:234,216:450,0:0.0:2,0:25.6:1.0:30.3:1.0:1.0:0.0:59.5:149.0:1.0:0.0:0.3 +3 47061453 . C T 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGATTCTTGGTATTAGAATC;RSEQ=GTTTAGAGGCCCTGACTCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:31:0,31:0,37:37,31:0.4559:1,1:23.4:1.0:29.8:1.0:1.0:0.0:60.0:30.0:0.4688:0.0:1.1 0/0:65:0:0,0:1,64:65,0:0.0:1,0:20.6:1.0:28.8:1.0:1.0:0.0:60.0:15.25:1.0:0.0:0.3 +3 47098278 . A G 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACATCCCATGAACAGACCAT;RSEQ=AAGCAGAAAAGAAAAGTTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:70:53,17:166,49:215,70:0.2456:2,2:23.4:1.0:32.5:1.0:0.87054:1.08631:59.6:140.0:0.2491:0.0:1.1 0/0:308:0:0,0:203,103:306,0:0.0:2,0:13.0:0.0:16.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 +3 48515221 . G A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=GGCTCACACCTGCAATCCCA;RSEQ=CACTTTGGGAGGCCGAGGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:0,9:1,8:9,9:0.5:2,0:33.2:1.0:30.9:1.0:1.0:0.0:60.0:18.0:0.5:0.0:1.0 0/0:29:0:0,0:1,28:29,0:0.0:1,0:18.8:1.0:31.7:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.0 +3 49725284 . CT C 149 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATGTAGCAGGTGCTGTAG;RSEQ=CTGTGCCCCGGAGCACTTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:480:25:6,19:209,245:454,25:0.0521:2,2:27.9:1.0:32.1:1.0:0.03805:2.69613:33.4:50.0:0.0527:0.0:0.1 0/0:485:0:0,0:228,257:485,0:0.0:2,0:19.6:1.0:28.8:1.0:1.0:0.0:36.1:59.625:1.0:0.0:0.1 +3 49934678 . C T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00702;SOR=0.0;LSEQ=GGTCCCCACCTGGATAGAAC;RSEQ=CTGCGGCCTCCCATGCCTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:526:7:1,6:352,167:519,7:0.0133:2,2:11.6:1.0:27.3:1.0:0.00605:12.59002:60.0:14.0:0.0136:0.0:1.0 0/0:539:0:0,0:366,172:538,0:0.0:2,0:23.3:1.0:30.0:1.0:1.0:0.0:60.0:88.667:0.9981:0.0:0.2 +3 52436441 . C A 236 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAGGTTGGCCAGCATGCCTG;RSEQ=GAAGAGGTAGAGACCCTTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:188:73,115:85,163:248,188:0.4302:2,2:24.8:1.0:31.3:1.0:0.36546:1.22:59.8:61.667:0.4282:0.0:1.1 0/0:333:0:0,0:116,217:333,0:0.0:2,0:21.9:1.0:29.9:1.0:1.0:0.0:60.0:110.0:1.0:0.0:0.1 +3 52584477 . C T 87 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01458;SOR=0.10659;LSEQ=TTGCTAATGCTGTTGGACTC;RSEQ=GCACTGAGTCCTTCAATGTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:703:8:2,6:399,296:695,8:0.0114:2,2:7.5:1.0:29.0:1.0:0.08048:4.03628:60.0:16.0:0.0115:0.0:1.0 0/0:817:1:0,1:456,359:815,1:0.0012:2,0:1.0:0.0:24.0:0.0:0.44118:0.0:60.0:2.0:0.0012:0.0:2.0 +3 52597664 . G A 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.00055;SOR=0.0;LSEQ=GAGTTTAAATGTGTATTTAT;RSEQ=AAATTACTTGTACTTAGAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:16:3,13:1,8:9,16:0.64:2,2:22.6:1.0:30.2:1.0:1.0:1.8:60.0:32.0:0.64:0.0:1.0 0/0:10:0:0,0:0,10:10,0:0.0:0,0:16.7:1.0:31.4:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.0 +3 52620628 . GT G 82 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.00523;SOR=0.0;LSEQ=TAATTTTCTTAAAAGATTTG;RSEQ=TTTGGCAGAATACCGTGATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:518:6:2,4:197,310:507,6:0.0116:2,2:24.2:1.0:32.0:1.0:1.0:1.27038:60.0:12.0:0.0121:0.0:0.2 0/0:722:0:0,0:309,410:719,0:0.0:2,0:25.8:1.0:28.7:1.0:1.0:0.0:60.0:30.261:1.0:0.0:0.2 +3 52663084 . T A 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGAAATTGCTAGAATTTTC;RSEQ=GTCATGAAAATTATGAAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:15:2,13:24,118:142,15:0.0955:2,2:22.4:1.0:32.3:1.0:1.0:1.31985:60.0:30.0:0.0962:0.0:1.3 0/0:215:0:0,0:51,164:215,0:0.0:2,0:22.2:1.0:29.7:1.0:1.0:0.0:59.9:430.0:1.0:0.0:0.1 +3 52676079 . G A 52 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06171;SOR=0.0;LSEQ=TTACTACAAAAAAAAAAAAA;RSEQ=CAATTAGACAGGGAAGGATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:307:5:3,2:64,235:299,5:0.0163:2,2:13.8:1.0:22.4:1.0:0.07314:5.47:60.0:1.5:0.0118:0.0:2.0 0/0:295:0:0,0:68,226:294,0:0.0:2,0:7.0:0.0:11.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:2.0 +3 52685397 . A G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATAAACAACAGGTTACCCC;RSEQ=TCTACCCTGATGTGATTATT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:28.0:1.0:29.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 52695835 . T C 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.02098;SOR=0.0;LSEQ=CAACACTGCCTTTCCTTACA;RSEQ=GATGTCTCAATGTAGCAATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:7:7,0:2,0:2,7:0.7778:0,0:22.3:1.0:31.7:1.0:1.0:0.0:58.0:14.0:0.7778:0.0:1.0 0/0:4:0:0,0:3,1:4,0:0.0:2,0:5.0:1.0:28.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +3 55487222 . A T 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00415;SOR=0.08753;LSEQ=CAATGGTCTCTTGCTCTTGC;RSEQ=GCCCCAGGTCAGAAATCTAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:228:10:6,4:156,62:218,10:0.0439:2,2:29.5:1.0:30.3:1.0:0.48052:1.67328:60.0:20.0:0.0441:0.0:1.0 0/0:251:1:0,1:169,81:250,1:0.004:2,0:1.0:0.0:22.0:0.0:0.32669:0.0:60.0:2.0:0.004:0.0:1.0 +3 55487515 . C T 131 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=2e-05;SOR=0.00943;LSEQ=GTGCTATGATTCCAAACTGC;RSEQ=AAACTGCTGAGCAATCCTAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:29:28:0,28:0,1:1,28:0.9655:0,1:24.5:1.0:27.4:1.0:1.0:0.0:57.6:27.0:0.9643:0.0:1.3 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:39.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.1429:0.0:1.0 +3 69986144 . A G 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.2125;SOR=0.0;LSEQ=TGTGTGGCTAAACTATCTTC;RSEQ=TCAGCTCCTGTTCATTGCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:6,7:0.5385:0,0:20.6:1.0:32.1:1.0:1.0:0.0:51.0:14.0:0.5833:0.0:1.7 0/0:3:0:0,0:0,3:3,0:0.0:0,0:14.7:1.0:28.0:1.0:1.0:0.0:60.0:6.0:1.0:0.0:2.7 +3 70005712 . T C 145 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TCGCGTGTTAATCTGCATCA;RSEQ=ATATTTTTCGTACCTGAATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:24:8,16:136,274:410,24:0.0552:2,2:24.7:1.0:31.8:1.0:1.0:1.01:60.0:23.0:0.0537:0.0:1.4 0/0:449:0:0,0:162,287:449,0:0.0:2,0:6.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 +3 70014447 . T C 312 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01904;LSEQ=AAACTGCTTCCTTTCTTGAT;RSEQ=CGTAGATTTAATAACTTACC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1158:992:376,616:62,101:163,992:0.8566:2,2:25.1:1.0:31.4:1.0:1.0:1.00568:60.0:75.308:0.8573:0.0:1.1 0/1:1374:140:61,79:511,723:1234,140:0.1019:2,2:25.3:1.0:30.3:1.0:0.65143:1.09:60.0:280.0:0.1025:0.0:1.1 +3 70348641 . A C 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01136;SOR=0.0;LSEQ=CCCCTAGAGACATATTAAAA;RSEQ=TTCCCATTGAATCCAGAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:2,1:3,7:0.7:2,0:22.6:1.0:32.4:1.0:0.3:0.0:60.0:14.0:0.7778:0.0:1.3 0/0:6:0:0,0:6,0:6,0:0.0:0,0:36.5:1.0:29.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 +3 71019797 . A T 180 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00915;LSEQ=TTTAACGGAATTAAAATTTA;RSEQ=TATCTAATTAGAGCAAGGCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:55:49,6:89,13:102,55:0.3503:2,2:23.8:1.0:31.2:1.0:0.80331:1.19:60.0:110.0:0.3503:0.0:1.5 0/0:206:1:0,1:175,30:205,1:0.0049:2,0:1.0:0.0:25.0:0.0:0.15049:0.0:60.0:2.0:0.0049:0.0:1.0 +3 71096086 . C T 61 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.09442;SOR=0.15965;LSEQ=TATGCCTTCTGTAAAATCAA;RSEQ=GCATACCTTGAGCAAGAGGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:397:5:2,3:240,151:391,5:0.0126:2,2:28.8:1.0:26.4:1.0:0.38132:2.3787:60.0:1.5:0.0077:0.0:1.2 0/0:493:1:0,1:276,216:492,1:0.002:2,0:1.0:0.0:27.0:0.0:0.44016:0.0:60.0:2.0:0.002:0.0:1.0 +3 71103136 . T C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.02424;SOR=0.0;LSEQ=GTAAAATCTTGCAGTACTGA;RSEQ=GGGGGTTCCAGGCAGCCTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:14.7:1.0:30.3:1.0:1.0:0.0:60.0:14.0:0.875:0.0:1.0 0/0:3:0:0,0:0,3:3,0:0.0:0,0:14.3:1.0:31.0:0.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +3 71246918 . C T 126 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATGTATTTATTTCAACTCT;RSEQ=CTTACTCATCTACTCTTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:16:15,1:16,0:16,16:0.5:1,1:26.1:1.0:31.5:1.0:1.0:0.0:60.0:32.0:0.5:0.0:1.1 0/0:35:0:0,0:34,1:35,0:0.0:1,0:20.1:1.0:29.5:1.0:1.0:0.0:60.0:16.5:1.0:0.0:0.3 +3 71247014 . A T 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00055;SOR=0.0;LSEQ=CGTTTAATTTTTATTTTTGC;RSEQ=TGAAAGCAGTGGGAACCATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:221:9:7,2:177,35:212,9:0.0407:2,2:24.2:1.0:32.7:1.0:0.64834:1.44222:60.0:18.0:0.0413:0.0:1.0 0/0:283:0:0,0:199,84:283,0:0.0:2,0:22.5:1.0:29.0:1.0:1.0:0.0:60.0:39.429:1.0:0.0:0.1 +3 71247304 . A G 222 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.11115;LSEQ=TAAGTGTAAAATTCAGCAGT;RSEQ=AAATTCGCACCCACCACCTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:313:118:81,37:130,64:194,118:0.377:2,2:22.8:1.0:32.3:1.0:0.80375:1.08:59.9:38.333:0.3758:0.0:1.1 0/1:382:24:14,10:241,117:358,24:0.0628:2,2:26.0:1.0:30.8:1.0:0.37673:1.46978:60.0:48.0:0.0632:0.0:1.1 +3 71247572 . A T 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.07284;LSEQ=AGGATTTCCAAGATGGGGGG;RSEQ=GGGAGGGGGGGAGAAAAAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:219:129:70,59:11,11:22,129:0.589:2,2:14.7:1.0:27.2:1.0:0.81816:1.19:59.5:8.214:0.6216:0.0:1.3 0/1:266:25:15,10:117,60:177,25:0.094:2,2:13.5:1.0:26.2:1.0:0.65401:1.29823:59.8:7.333:0.0978:0.0:1.2 +3 72323080 . G A 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGGAACTCCAGAACTTCCC;RSEQ=AGCACCTTGTCTGGTGGTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:21:15,6:117,40:157,21:0.118:2,2:22.9:1.0:30.0:1.0:0.79248:1.16891:60.0:20.0:0.113:0.0:1.4 0/0:242:0:0,0:177,65:242,0:0.0:2,0:26.3:1.0:29.1:1.0:1.0:0.0:60.0:25.889:1.0:0.0:0.1 +3 72323287 . A G 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.08131;LSEQ=ACTTCGGGTTTCCCCAAGAC;RSEQ=CTCAGGGTTCCCCAGGGCAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:164:68:9,59:11,85:96,68:0.4146:2,2:25.0:1.0:31.5:1.0:0.81032:1.18:60.0:33.0:0.4074:0.0:1.1 0/1:148:8:0,8:15,125:140,8:0.0541:2,0:34.3:1.0:32.1:1.0:1.0:0.0:60.0:16.0:0.0541:0.0:1.0 +3 72455797 . A C 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00164;SOR=0.0;LSEQ=AACAAAGGTATTTTAAATAG;RSEQ=TCCCCCGAGGAGATTCTAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:11,0:9,0:9,11:0.55:0,0:24.3:1.0:33.3:1.0:1.0:0.0:60.0:22.0:0.55:0.0:1.0 0/0:12:0:0,0:12,0:12,0:0.0:0,0:14.7:1.0:28.0:1.0:1.0:0.0:60.0:24.0:1.0:0.0:0.1 +3 75164938 . A T 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATGCCCCATAATTTGAATA;RSEQ=ATAATCAAGAAAATGAGAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:44:8,36:16,35:51,44:0.4632:2,2:24.0:1.0:28.5:1.0:0.16173:2.04174:60.0:43.0:0.4574:0.0:1.1 0/0:137:0:0,0:41,96:137,0:0.0:2,0:22.1:1.0:29.7:1.0:1.0:0.0:60.0:274.0:1.0:0.0:0.1 +3 87348307 . A ATTTG 89 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=2.0;MSILEN=4.0;SSF=0.00466;SOR=0.0;LSEQ=GAACGTAGCTATGTATGTTC;RSEQ=TTTGTGTATTGTCTATGAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:33.7:1.0:32.0:1.0:1.0:0.0:60.0:14.0:0.875:0.0:0.1 0/0:5:0:0,0:0,5:5,0:0.0:0,0:10.4:1.0:30.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.6 +3 89156692 . A G 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=1.0;MSILEN=1.0;SSF=0.01538;SOR=0.0;LSEQ=ATCCCGCTCTGCTTCAGCGC;RSEQ=CGCTGAAGACGGCACTAGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:9:8,1:17,0:17,9:0.3462:1,2:33.3:1.0:31.3:1.0:0.34615:0.0:60.0:18.0:0.3462:0.0:1.3 0/0:15:0:0,0:15,0:15,0:0.0:1,0:27.2:1.0:29.8:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 +3 89905902 . C G 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTATAGGTGAGGTGAAAAT;RSEQ=CAGTGGTTGAGATTCTAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:36:0,36:0,63:63,36:0.3636:1,1:29.0:1.0:32.1:1.0:1.0:0.0:60.0:17.0:0.3542:0.0:1.2 0/0:86:0:0,0:3,83:86,0:0.0:1,0:23.2:1.0:31.3:1.0:1.0:0.0:60.0:172.0:1.0:0.0:0.2 +3 94429115 . A G 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=ATTCTTAGTGGGGAACAACA;RSEQ=CCACGGAAATTAGAACTAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:54:33,21:386,267:653,54:0.0764:2,2:27.7:1.0:33.2:1.0:0.88559:1.09:60.0:108.0:0.0771:0.0:1.1 0/0:662:0:0,0:376,285:661,0:0.0:2,0:26.2:1.0:28.9:1.0:1.0:0.0:60.0:164.25:1.0:0.0:0.5 +3 106824274 . G A 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.06057;LSEQ=GGCACTCCGTGGTACAGCCA;RSEQ=GTCCACAAGTGGTATTGCCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:236:91:52,39:78,67:145,91:0.3856:2,2:23.9:1.0:31.2:1.0:0.68704:1.14:58.2:182.0:0.3872:0.0:1.8 0/1:247:9:5,4:127,111:238,9:0.0364:2,2:24.0:1.0:29.8:1.0:1.0:1.09:59.1:18.0:0.0366:0.0:1.7 +3 106824304 . C T 207 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0928;LSEQ=TGGTATTGCCAGACCATTCT;RSEQ=TCCATATTCCCTTGTCCAAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:269:106:62,44:80,83:163,106:0.3941:2,2:23.1:1.0:30.9:1.0:0.13607:1.46:58.4:212.0:0.3985:0.0:1.7 0/1:247:14:10,4:121,110:231,14:0.0567:2,2:20.2:1.0:29.0:1.0:0.18195:2.27:59.2:13.0:0.0535:0.0:1.6 +3 106825018 . A AT 65 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=5;MSI=6.0;MSILEN=1.0;SSF=0.06151;SOR=0.0;LSEQ=CGCGCCCGGCCTTTATATCT;RSEQ=TTTTTGGTTTTGTTTTCTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:5:1,4:232,73:305,5:0.0161:2,2:12.8:1.0:28.2:1.0:0.01451:12.58625:48.8:10.0:0.0165:0.0097:0.6 0/0:306:0:0,0:221,85:306,0:0.0:2,0:21.2:1.0:28.1:1.0:1.0:0.0:56.5:152.0:1.0:0.0:0.3 +3 106825024 . G C 235 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08712;LSEQ=CGGCCTTTATATCTATTTTT;RSEQ=GTTTTGTTTTCTTGCCTTCG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:344:176:130,46:124,42:166,176:0.5116:2,2:21.6:1.0:31.6:1.0:0.90183:1.04457:51.0:87.0:0.5133:0.0:1.3 0/1:336:28:20,8:218,90:308,28:0.0833:2,2:25.7:1.0:30.3:1.0:1.0:1.03:52.6:56.0:0.0843:0.0:1.3 +3 106825180 . A T 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=ACTCTGCTTTCTATTTCAGC;RSEQ=GCATTTGTACAAGTCGTGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:28:17,11:289,268:557,28:0.0479:2,2:24.6:1.0:32.1:1.0:0.43949:1.43:36.4:56.0:0.0483:0.0:1.1 0/0:550:0:0,0:240,310:550,0:0.0:2,0:30.3:1.0:30.1:1.0:1.0:0.0:37.4:109.0:1.0:0.0:0.1 +3 117078556 . C G 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.00032;SOR=0.0;LSEQ=AAAAAGGCCTCCACAAAAAA;RSEQ=CCATCCAAGGGTCAGCAGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:9:5,4:19,17:36,9:0.2:2,2:22.6:1.0:32.8:1.0:1.0:1.12:47.2:18.0:0.2045:0.0:1.1 0/0:59:0:0,0:30,29:59,0:0.0:2,0:26.8:1.0:31.0:1.0:1.0:0.0:54.0:58.0:1.0:0.0:0.3 +3 117078561 . C T 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGCCTCCACAAAAAACCCAT;RSEQ=CAAGGGTCAGCAGCCTCAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:21:10,11:13,10:23,21:0.4565:2,2:26.3:1.0:30.3:1.0:0.76304:1.41833:53.7:20.0:0.4651:0.0:1.2 0/0:60:0:0,0:30,30:60,0:0.0:2,0:25.2:1.0:30.3:1.0:1.0:0.0:52.5:29.0:1.0:0.0:0.4 +3 117863221 . C A 84 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.03518;SOR=0.08879;LSEQ=ATTTCTGCTGGTTTGTTTTT;RSEQ=TTTCAATAGTCAGGTCCCTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:3,5:8,7:0.4667:2,2:29.6:1.0:30.1:1.0:1.0:1.46001:56.6:14.0:0.4667:0.0:2.1 0/1:15:1:0,1:6,8:14,1:0.0667:2,0:19.0:0.0:32.0:0.0:1.0:0.0:52.0:2.0:0.0667:0.0:2.0 +3 118845663 . T C 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02424;SOR=0.0;LSEQ=AAAGAAAAACAAGCAGAAAG;RSEQ=GACAACAACAGCATCAACAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:2,5:1,0:1,7:0.875:0,2:24.4:1.0:31.7:1.0:0.375:0.0:51.1:14.0:0.875:0.0:1.0 0/0:3:0:0,0:1,2:3,0:0.0:2,0:11.0:1.0:30.3:1.0:1.0:0.0:32.7:6.0:1.0:0.0:0.3 +3 128199913 . G T 230 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00485;LSEQ=TGGGGGTGGCCGAAGGAGAG;RSEQ=CTGGAGGAGGGGTGGATGGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:895:223:129,94:374,296:670,223:0.2492:2,2:24.5:1.0:29.6:1.0:0.64019:1.09:59.9:43.6:0.2489:0.0:1.2 0/0:621:1:0,1:326,294:620,1:0.0016:2,0:1.0:0.0:22.0:0.0:0.47504:0.0:60.0:2.0:0.0016:0.0:1.0 +3 134670080 . A C 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00097;SOR=0.0;LSEQ=CTTAGATGTGTTCATTTCTC;RSEQ=AGTCAATCTGCTGGACTGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:20:19,1:88,1:89,20:0.1835:1,1:25.1:1.0:31.5:1.0:0.33469:4.5399:60.0:19.0:0.1776:0.0:1.1 0/0:45:0:0,0:44,0:44,0:0.0:1,0:20.9:1.0:29.7:1.0:1.0:0.0:60.0:43.0:0.9773:0.0:0.1 +3 134851577 . A T 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGTCCCATCAGGTCCCCGCA;RSEQ=TGTTATCTCCATCGTCAATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:840:95:56,39:411,334:745,95:0.1131:2,2:25.4:1.0:30.6:1.0:0.51209:1.17:60.0:46.5:0.1122:0.0:1.2 0/0:707:0:0,0:388,319:707,0:0.0:2,0:24.7:1.0:29.5:1.0:1.0:0.0:60.0:87.375:1.0:0.0:0.2 +3 134884695 . G C 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=ACTTACAACTCTGACACATA;RSEQ=AAACTATCCTCTACATATAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:25:24,1:93,3:96,25:0.2066:1,1:22.4:1.0:32.5:1.0:1.0:1.28874:60.0:50.0:0.2083:0.0:1.1 0/0:67:0:0,0:65,2:67,0:0.0:1,0:23.1:1.0:31.4:1.0:1.0:0.0:60.0:32.5:1.0:0.0:0.2 +3 134885042 . A C 174 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACAATCATCACTCCATCTC;RSEQ=ATCCAAGAGCAGCCTAGAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:130:40:0,40:0,90:90,40:0.3077:1,1:22.4:1.0:32.7:1.0:1.0:0.0:60.0:80.0:0.315:0.0:1.1 0/0:58:0:0,0:1,57:58,0:0.0:1,0:21.2:1.0:30.9:1.0:1.0:0.0:60.0:57.0:1.0:0.0:0.1 +3 134911143 . A AAAAACAAACTCACATATATTCTGAAATTCCACTT 111 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGAAAAATTAAGTGTGGGG;RSEQ=AAAACAAACTCACATATATT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:12,0:2,0:2,12:0.8571:0,0:18.8:1.0:31.0:1.0:1.0:0.0:57.5:24.0:0.8571:0.6429:0.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 134967265 . G A 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0907;LSEQ=CAGAAGGACCGGAACAGCCG;RSEQ=CCCCGGTTTGCGGAGATTGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:918:33:19,14:463,421:884,33:0.0359:2,2:25.7:1.0:30.1:1.0:0.59805:1.23:60.0:66.0:0.037:0.0:1.1 0/0:891:3:2,1:456,432:888,3:0.0034:2,2:23.0:1.0:28.7:1.0:1.0:1.89:56.0:6.0:0.0034:0.0:1.0 +3 135644964 . C T 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAATCCAGGGAAGGCTACTG;RSEQ=GGAAATCAAGAAAATGTTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:32:8,24:52,121:173,32:0.1561:2,2:23.0:1.0:30.3:1.0:0.67456:1.28769:60.0:31.0:0.1535:0.0:1.2 0/0:193:0:0,0:60,133:193,0:0.0:2,0:23.0:1.0:29.9:1.0:1.0:0.0:60.0:95.5:1.0:0.0:0.1 +3 137443260 . G A 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.01206;SOR=0.0;LSEQ=GCTGATGAAGATGATGATAT;RSEQ=ATGATGCAGATGATGATGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:45:5:2,3:18,22:40,5:0.1111:2,2:29.6:1.0:28.2:1.0:1.0:1.22176:52.2:4.0:0.093:0.0:1.0 0/0:61:0:0,0:28,33:61,0:0.0:2,0:25.3:1.0:30.7:1.0:1.0:0.0:54.7:19.333:1.0:0.0:0.3 +3 137483362 . G T 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTTGGGTCCCAGCCCCTGGT;RSEQ=CCTGAAGCCCCCCGGCCGAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:18.0:1.0:29.4:1.0:1.0:0.0:58.2:10.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 138374293 . C T 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01847;LSEQ=CACTTTAGTAGTCCAGCTTT;RSEQ=CCTGAGCGCCTCATCAAATT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:890:50:20,30:406,432:838,50:0.0562:2,2:24.2:1.0:30.1:1.0:0.30778:1.40918:60.0:100.0:0.0574:0.0:1.0 0/0:912:1:0,1:424,486:910,1:0.0011:2,0:1.0:0.0:30.0:0.0:1.0:0.0:47.0:2.0:0.0011:0.0:1.0 +3 138383144 . A C 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGTGGGGCTGTGAGTAGACT;RSEQ=ATGTTCACAGTACTTAGAAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:1,2:3,7:0.7:2,0:23.3:1.0:33.9:1.0:0.3:0.0:56.3:14.0:0.7:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 138423181 . CAT C 162 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=ACACTCACAGACTGTTCTTG;RSEQ=ATGAGTTACGGTCTTCTGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:223:34:28,6:159,30:189,34:0.1525:2,2:24.8:1.0:31.9:1.0:0.80141:1.13502:59.4:33.0:0.1493:0.0269:0.3 0/0:204:0:0,0:153,51:204,0:0.0:2,0:22.7:1.0:29.7:1.0:1.0:0.0:60.0:101.0:1.0:0.0:0.1 +3 138661770 . CACAA C 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.29151;SOR=0.0;LSEQ=AATTTTCACGCTAGACAAAG;RSEQ=ACAGACATGCACACAGCAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:4,1:18,2:20,5:0.2:2,2:17.4:1.0:30.8:1.0:0.50435:2.16466:60.0:10.0:0.2:0.04:0.2 0/0:10:0:0,0:10,0:10,0:0.0:0,0:13.0:1.0:29.3:1.0:1.0:0.0:60.0:9.0:1.0:0.0:0.0 +3 138662227 . G GGGGGGGGGGGGT 78 q25 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=10.0;MSILEN=1.0;SSF=0.02782;SOR=0.0;LSEQ=GGCCAGGCCCCGAGATAGAC;RSEQ=GGGGGGGGGCAGTGAGGGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:9:0,9:1,99:100,9:0.0796:1,0:34.3:1.0:24.7:1.0:1.0:0.0:57.4:18.0:0.0857:0.0708:0.1 0/0:61:0:0,0:0,59:59,0:0.0:1,0:19.5:1.0:29.9:1.0:1.0:0.0:59.5:58.0:0.9667:0.0:0.5 +3 138663179 . A G 259 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=TAGAAAATTTGGTCCCCCAA;RSEQ=CAACAAGCTACAGTACAACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:791:243:149,94:314,232:546,243:0.3072:2,2:28.4:1.0:32.8:1.0:0.34749:1.17:60.0:120.5:0.3082:0.0:1.1 0/0:788:0:0,0:426,361:787,0:0.0:2,0:26.5:1.0:29.0:1.0:1.0:0.0:60.0:97.375:1.0:0.0:0.2 +3 142188172 . C A 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATATAAAAAGGTAAAAGACC;RSEQ=TTTTACCTTTGACACAGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:47:29,18:214,101:315,47:0.1298:2,2:22.0:1.0:30.1:1.0:0.40842:1.31405:60.0:46.0:0.1281:0.0:1.2 0/0:352:0:0,0:218,133:351,0:0.0:2,0:24.9:1.0:30.6:1.0:1.0:0.0:60.0:174.5:0.9971:0.0:0.1 +3 142188373 . C A 52 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06186;SOR=0.0;LSEQ=GATAACCTTGTTTATTTTAC;RSEQ=CAAATCATTCCTCATTTGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:5:3,2:187,283:470,5:0.0105:2,2:20.0:1.0:22.4:1.0:0.39337:2.27:60.0:1.5:0.0065:0.0:2.0 0/0:470:0:0,0:188,282:470,0:0.0:2,0:26.9:1.0:30.1:1.0:1.0:0.0:60.0:66.143:1.0:0.0:0.1 +3 142215149 . T C 169 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=29.0;MSILEN=2.0;SSF=2e-05;SOR=0.08786;LSEQ=TATATATATATATATATATA;RSEQ=ATATATATATATATATATAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:40:29,11:107,30:137,40:0.2247:2,2:24.1:1.0:31.9:1.0:0.5235:1.35047:53.0:39.0:0.2241:0.0:2.2 0/1:81:2:2,0:50,21:71,2:0.0247:2,0:15.0:1.0:33.0:0.0:1.0:0.0:50.0:4.0:0.0278:0.0:3.0 +3 142218675 . T A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01009;SOR=0.0;LSEQ=ATTGAATTTGCATTATATTG;RSEQ=ATTTTGTTCTTAGATATAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:8:0,8:1,71:72,8:0.1:1,0:11.3:1.0:30.1:1.0:1.0:0.0:60.0:7.0:0.0933:0.0:1.3 0/0:61:0:0,0:3,58:61,0:0.0:1,0:24.3:1.0:28.1:1.0:1.0:0.0:60.0:122.0:1.0:0.0:0.1 +3 142234589 . C A 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.36364;SOR=0.0;LSEQ=CCTCAGATCCTTCCAACTCT;RSEQ=TTCTTATATAAGAAAAACCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:0,7:0,3:3,7:0.7:0,0:23.4:1.0:31.3:1.0:1.0:0.0:60.0:14.0:0.7:0.0:2.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:1.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +3 142241690 . C CA 66 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.03087;SOR=0.0;LSEQ=TCTTCTACTCCAGTCTCAAT;RSEQ=AGAAAAAAAAAAAAGAAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:538:6:1,5:170,360:530,6:0.0112:2,2:26.8:1.0:25.6:1.0:0.66982:2.35799:60.0:5.0:0.01:0.0056:1.7 0/0:526:0:0,0:185,340:525,0:0.0:2,0:22.6:1.0:30.0:1.0:1.0:0.0:59.9:17.75:0.998:0.0:0.3 +3 142266439 . C T 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCCTTTTCAAAATAAAAATA;RSEQ=CAACTTAAAATTTAAACAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:53:30:30,0:23,0:23,30:0.566:1,1:25.9:1.0:30.7:1.0:1.0:0.0:60.0:9.0:0.54:0.0:1.0 0/0:29:0:0,0:28,1:29,0:0.0:1,0:18.8:1.0:31.9:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.2 +3 142278101 . T C 236 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTTGTACTCACCTTGCATA;RSEQ=AAATCAAAGCATCATAAATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:643:164:100,64:270,209:479,164:0.2551:2,2:26.7:1.0:32.2:1.0:0.31532:1.21:60.0:53.667:0.2552:0.0:1.1 0/0:656:0:0,0:375,281:656,0:0.0:2,0:25.6:1.0:28.8:1.0:1.0:0.0:60.0:130.2:1.0:0.0:0.1 +3 142297576 . G A 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.1238;SOR=0.16567;LSEQ=GCGAGGCACTAGTCAACCAC;RSEQ=CCAACGCGGGTTCCCGGCGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:548:6:4,2:187,355:542,6:0.0109:2,2:14.5:1.0:29.3:1.0:0.18992:3.79:60.0:12.0:0.0112:0.0:1.0 0/0:547:1:1,0:221,325:546,1:0.0018:2,0:1.0:0.0:24.0:0.0:0.40585:0.0:60.0:2.0:0.0019:0.0:1.0 +3 166229248 . C T 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00427;SOR=0.0;LSEQ=AAAGGCCCCCACAAAAGCCC;RSEQ=ATCCAAGGGTCAGCAACCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:11:6,5:9,11:20,11:0.3548:2,2:27.9:1.0:30.3:1.0:0.71599:1.45:44.0:22.0:0.3548:0.0:1.2 0/0:17:0:0,0:8,9:17,0:0.0:2,0:26.5:1.0:30.6:1.0:1.0:0.0:56.0:34.0:1.0:0.0:0.2 +3 168576884 . T C 102 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02973;SOR=0.0;LSEQ=TAAAAGGCCTAGAGAACACG;RSEQ=ATCAAGTGCCTCTCCTCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:9:4,5:5,7:12,9:0.4286:2,2:21.4:1.0:32.3:1.0:1.0:1.11:60.0:18.0:0.4286:0.0:1.2 0/0:10:0:0,0:1,9:10,0:0.0:2,0:18.7:1.0:28.3:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.1 +3 178511531 . C A 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=GGCATGGGGCTATCAGGGAT;RSEQ=CAAGCCAGCTACCTCATCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:324:16:7,9:155,153:308,16:0.0494:2,2:23.3:1.0:30.0:1.0:0.79859:1.30146:59.6:32.0:0.0502:0.0:1.1 0/0:283:0:0,0:144,139:283,0:0.0:2,0:24.2:1.0:30.4:1.0:1.0:0.0:60.0:140.5:1.0:0.0:0.1 +3 178921158 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.16724;SOR=0.0;LSEQ=GATTGATCTTGTGCTTCAAC;RSEQ=TAAATCCTAAATGTTAGTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:6:6,0:32,0:32,6:0.1579:1,0:15.0:1.0:30.2:1.0:1.0:0.0:60.0:12.0:0.1622:0.0:1.2 0/0:15:0:0,0:12,3:15,0:0.0:2,0:21.6:1.0:30.1:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.0 +3 178927345 . T C 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00597;SOR=0.09725;LSEQ=ATATACTTTGATGAAGACTT;RSEQ=TCTTGATGTATTATTTTTGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:374:14:11,3:273,87:360,14:0.0374:2,2:22.0:1.0:32.5:1.0:1.0:1.17:60.0:28.0:0.0376:0.0:1.0 0/0:266:1:1,0:196,69:265,1:0.0038:2,0:16.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0038:0.0:1.0 +3 178927645 . C T 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00063;SOR=0.08553;LSEQ=AATGTATCATGGAAGAATAC;RSEQ=TTGGGAGAGCTTCAGGAATT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:23:3,20:3,14:17,23:0.575:2,2:24.4:1.0:30.6:1.0:1.0:1.41565:58.3:22.0:0.5641:0.0:1.0 0/1:20:2:0,2:1,17:18,2:0.1:1,0:15.5:1.0:31.0:0.0:1.0:0.0:60.0:4.0:0.1:0.0:1.0 +3 184298663 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.14055;SOR=0.0;LSEQ=TACTGGGACATGAGCAACCA;RSEQ=GATGTGAGTGAGGCTACGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:21:6:4,2:6,9:15,6:0.2857:2,2:21.3:1.0:30.2:1.0:0.36146:2.84:60.0:12.0:0.2857:0.0:1.0 0/0:9:0:0,0:5,4:9,0:0.0:2,0:27.1:1.0:30.3:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.1 +3 185155807 . G A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CAAAACAAAGTTGGCCGGGC;RSEQ=CAGTGGCTCATGTCTGTAAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:22.0:1.0:30.2:1.0:1.0:0.0:47.8:10.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 185183491 . C T 215 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01122;LSEQ=CATCAAGCGGACTTTTTTCT;RSEQ=CCGAAGTTGGTTGGCTGGGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:129:85,44:192,99:291,129:0.3071:2,2:26.8:1.0:30.8:1.0:1.0:1.00391:60.0:128.0:0.3107:0.0:1.2 0/0:406:2:0,2:254,150:404,2:0.0049:2,0:1.0:0.0:24.5:1.0:0.13959:0.0:60.0:4.0:0.0051:0.0:1.0 +3 185183656 . G A 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00404;LSEQ=AGAAGGAGCTCATTAAGTAT;RSEQ=TATCCAGACTAGTGTCTGTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:493:162:55,107:133,198:331,162:0.3286:2,2:25.9:1.0:29.9:1.0:0.19985:1.30609:60.0:39.5:0.3258:0.0:1.1 0/0:508:1:1,0:198,309:507,1:0.002:2,0:1.0:0.0:22.0:0.0:0.39173:0.0:60.0:2.0:0.002:0.0:1.0 +3 186504406 . A C 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTGACCCTTGAAGGAATCA;RSEQ=ACAGTTTTATATTAATGTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1147:73:34,39:492,580:1072,73:0.0636:2,2:31.3:1.0:32.9:1.0:1.0:1.03:49.8:72.0:0.0635:0.0:1.1 0/0:1282:0:0,0:618,661:1279,0:0.0:2,0:27.0:1.0:29.8:1.0:1.0:0.0:55.4:126.9:0.9984:0.0:0.1 +3 187440126 . G C 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08579;SOR=0.0;LSEQ=CACCCCCAACCCCCAGCTAT;RSEQ=ATTTGCACTAGTGGATGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:68:6:6,0:62,0:62,6:0.0882:1,0:18.8:1.0:26.8:1.0:1.0:0.0:60.0:2.0:0.0784:0.0:1.3 0/0:38:0:0,0:36,2:38,0:0.0:2,0:20.5:1.0:27.9:1.0:1.0:0.0:60.0:3.222:1.0:0.0:1.0 +3 187451349 . C A 148 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CATGAGGACCGTTTTATGGG;RSEQ=TCTAAACTGCTCACGGCTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:961:29:14,15:460,470:930,29:0.0302:2,2:25.1:1.0:30.6:1.0:1.0:1.0486:60.0:28.0:0.0297:0.0:1.1 0/0:857:0:0,0:445,412:857,0:0.0:2,0:25.3:1.0:31.1:1.0:1.0:0.0:60.0:49.412:1.0:0.0:0.2 +3 189349501 . G A 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01506;LSEQ=TATTATTTTGGACTTTCTGT;RSEQ=GACTTAAAGTGGTCTGTGGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:54:0,54:0,56:56,54:0.4909:1,1:26.0:1.0:32.2:1.0:1.0:0.0:60.0:108.0:0.5094:0.0:1.0 0/1:71:1:0,1:0,70:70,1:0.0141:1,0:2.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0143:0.0:1.0 +3 189525713 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AACAACCTCAAAATGGAATA;RSEQ=CAGGCAGTATTTATTTAAAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:24.4:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 189584420 . C T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.03103;LSEQ=ATGCAATTTCATTTTATTTT;RSEQ=TTTATTTTTAAGGTAAAGAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:243:34:29,5:180,29:209,34:0.1399:2,2:23.1:1.0:31.1:1.0:1.0:1.06986:60.0:68.0:0.1405:0.0:1.1 0/0:200:1:0,1:158,41:199,1:0.005:2,0:1.0:0.0:23.0:0.0:0.21:0.0:60.0:2.0:0.005:0.0:1.0 +3 189585692 . G A 82 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00821;SOR=0.0;LSEQ=TTGTGTTGGAGGGATGAACC;RSEQ=CCGTCCAATTTTAATCATTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:8:6,2:331,450:781,8:0.0101:2,2:7.0:1.0:27.4:1.0:0.07908:4.07:60.0:7.0:0.009:0.0:1.3 0/0:714:0:0,0:323,390:713,0:0.0:2,0:25.3:1.0:29.9:1.0:1.0:0.0:60.0:49.929:1.0:0.0:0.1 +3 189586466 . G A 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATAGCATCAGAAAGCAGCAA;RSEQ=TTTCGGACAGTACAAAGAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:525:25:13,12:237,263:500,25:0.0476:2,2:22.9:1.0:29.7:1.0:0.68599:1.2:60.0:24.0:0.0462:0.0:1.1 0/0:492:0:0,0:252,239:491,0:0.0:2,0:25.1:1.0:31.3:1.0:1.0:0.0:60.0:97.2:0.9979:0.0:0.2 +3 189586470 . C T 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATCAGAAAGCAGCAAGTTT;RSEQ=GGACAGTACAAAGAACGGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:519:150:69,81:178,191:369,150:0.289:2,2:27.0:1.0:30.3:1.0:0.69833:1.09382:59.9:49.0:0.2899:0.0:1.1 0/0:484:0:0,0:244,239:483,0:0.0:2,0:25.8:1.0:29.8:1.0:1.0:0.0:60.0:68.0:0.9979:0.0:0.2 +3 189590871 . G A 181 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTGATTGATGAGCAATGTG;RSEQ=AACATAATGGGAGATAGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:57:6,51:8,145:153,57:0.2714:2,2:20.7:1.0:31.2:1.0:0.21256:2.12:60.0:114.0:0.2754:0.0:1.1 0/0:134:0:0,0:14,119:133,0:0.0:2,0:23.2:1.0:30.8:1.0:1.0:0.0:59.7:43.333:1.0:0.0:0.5 +3 189597951 . G A 245 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00873;LSEQ=ACATTCCAAGCCCCCAAACC;RSEQ=ATCAGTGTACCCATAGAGCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1065:266:110,156:331,464:795,266:0.2498:2,2:26.7:1.0:30.5:1.0:0.94286:1.01167:59.9:32.25:0.2481:0.0:1.2 0/0:1037:3:3,0:441,593:1034,3:0.0029:2,0:1.0:0.0:25.0:1.0:0.07819:0.0:60.0:6.0:0.003:0.0:1.0 +3 189598095 . G A 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01133;SOR=0.0;LSEQ=TGAAGACACTTTGGCTCAGA;RSEQ=ACCCAACTGCTCAAAGGCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:101:14:1,13:2,85:87,14:0.1386:1,1:24.0:1.0:30.8:1.0:0.36397:3.21:60.0:13.0:0.1383:0.0:1.5 0/0:38:0:0,0:1,37:38,0:0.0:1,0:23.6:1.0:30.9:1.0:1.0:0.0:59.9:37.0:1.0:0.0:0.1 +3 195395145 . T TA 98 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=5.0;MSILEN=4.0;SSF=0.01282;SOR=0.0;LSEQ=TCTCAAAATAAATAAATAAA;RSEQ=AAATAAAATATAAATGGAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:10,1:0,0:0,11:1.0:0,2:29.4:1.0:28.6:1.0:1.0:0.0:22.9:22.0:1.0:0.0:0.1 0/0:2:0:0,0:2,0:2,0:0.0:0,0:25.5:1.0:31.5:1.0:1.0:0.0:25.5:4.0:1.0:0.0:0.0 +3 195399620 . C G 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GGGGCCCATCTCGCAGTTGT;RSEQ=TCTTTAGATCTTAGAGGAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:38:2,36:4,74:78,38:0.3276:2,2:40.7:1.0:31.7:1.0:1.0:1.03:25.7:37.0:0.3246:0.0:1.6 0/0:46:0:0,0:3,43:46,0:0.0:2,0:32.5:1.0:30.6:1.0:1.0:0.0:30.0:45.0:1.0:0.0:0.0 +3 195410875 . A T 122 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.00537;SOR=0.0;LSEQ=ACAGATTTGAGGCACCGCTG;RSEQ=AAAAGGCACTCTGACAGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:17:1,16:3,59:62,17:0.2152:1,1:26.1:1.0:30.0:1.0:1.0:1.23:23.1:34.0:0.2152:0.0:1.0 0/0:28:0:0,0:3,25:28,0:0.0:2,0:21.1:1.0:30.3:1.0:1.0:0.0:22.9:56.0:1.0:0.0:0.5 +3 195412960 . T C 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TTTGTCCCTTGCTTCATTCT;RSEQ=GTGACAAGATAAAACTGGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:1,4:3,31:34,5:0.1282:2,2:10.0:1.0:32.2:1.0:0.43616:2.5:23.8:10.0:0.1282:0.0:2.4 0/0:7:0:0,0:3,4:7,0:0.0:2,0:26.4:1.0:28.6:1.0:1.0:0.0:25.3:14.0:1.0:0.0:1.1 +3 195692069 . A G 62 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GTCCATCTGGCCCACACCAC;RSEQ=GAGCAACCCTTCCTTAAGGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:9.6:1.0:27.0:1.0:1.0:0.0:29.6:10.0:0.7143:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +3 195701198 . CA C 79 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.18265;SOR=0.0;LSEQ=AGGGCACTAAGACCCTGTCT;RSEQ=AAAAAAAAGAAAAAAGACTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:219:6:6,0:204,9:213,6:0.0274:1,0:31.0:1.0:30.7:1.0:1.0:0.0:54.7:12.0:0.0276:0.0:0.0 0/0:97:0:0,0:90,7:97,0:0.0:2,0:33.4:1.0:29.2:1.0:1.0:0.0:47.3:47.5:1.0:0.0:0.2 +4 1795701 . G T 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.077;SOR=0.0;LSEQ=CCCTCGCGCTCTGCGTGGCC;RSEQ=TGGCCATCGTGGCCGGCGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:373:5:2,3:257,111:368,5:0.0134:2,2:21.8:1.0:28.6:1.0:0.16919:3.45983:60.0:10.0:0.0139:0.0:1.0 0/0:272:0:0,0:180,92:272,0:0.0:2,0:23.8:1.0:30.0:1.0:1.0:0.0:60.0:53.4:1.0:0.0:0.2 +4 1795719 . G A 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.04255;SOR=0.0;LSEQ=CCGTGGCCATCGTGGCCGGC;RSEQ=CCTCCTCGGAGTCCTTGGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:500:6:3,3:336,157:493,6:0.012:2,2:20.5:1.0:30.7:1.0:0.39093:2.13659:60.0:12.0:0.0124:0.0:1.2 0/0:364:0:0,0:231,131:362,0:0.0:2,0:27.7:1.0:29.6:1.0:1.0:0.0:60.0:50.714:0.9972:0.0:0.2 +4 1795762 . G A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01973;LSEQ=GGAGCAGCGCGTCGTGGGGC;RSEQ=AGCGGCAGGTAAGAAGGGAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:740:65:37,28:394,281:675,65:0.0878:2,2:27.0:1.0:29.6:1.0:0.89537:1.06098:60.0:20.667:0.0854:0.0:1.2 0/0:528:1:1,0:277,250:527,1:0.0019:2,0:1.0:0.0:26.0:0.0:1.0:0.0:60.0:2.0:0.002:0.0:1.0 +4 1806937 . C T 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00213;SOR=0.0;LSEQ=GGTGACACTCTTCGTCCTTA;RSEQ=GAGCAGGCTGTAGGGGGAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:22:19,3:77,9:86,22:0.2018:2,2:23.0:1.0:31.4:1.0:0.70669:1.34686:58.6:21.0:0.2:0.0:1.4 0/0:36:0:0,0:30,6:36,0:0.0:2,0:18.7:1.0:31.4:1.0:1.0:0.0:60.0:17.0:1.0:0.0:0.3 +4 1807244 . GCGC G 101 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.09958;SOR=0.17866;LSEQ=GGTGCAGAGCAGGGCTGGGG;RSEQ=CGCCGCCGCCTGACACAGGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:743:9:4,5:375,358:733,9:0.0121:2,2:23.1:1.0:32.1:1.0:0.74765:1.30888:60.0:18.0:0.0123:0.0027:0.1 0/0:458:1:1,0:247,208:455,1:0.0022:2,0:14.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0022:0.0:0.0 +4 1809127 . CGTGT C 116 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=9.0;MSILEN=2.0;SSF=0.01287;SOR=0.0;LSEQ=GGTCTGTGTGTGTGTGTGTG;RSEQ=GTGTGTGTGTGTGTGCACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:1,11:1,21:22,12:0.2553:1,2:35.0:1.0:32.5:1.0:1.0:1.87:60.0:24.0:0.2727:0.0426:0.3 0/0:21:0:0,0:0,12:12,0:0.0:0,0:11.3:1.0:30.7:1.0:1.0:0.0:56.2:11.0:0.5789:0.0:1.3 +4 6113451 . C G 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=CCCGTGCTTTAATTAGACTG;RSEQ=CAGCACCCAACCAGGCACTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:172:18:14,4:111,43:154,18:0.1047:2,2:22.2:1.0:31.3:1.0:0.78233:1.35:60.0:36.0:0.1078:0.0:1.0 0/0:128:0:0,0:85,42:127,0:0.0:2,0:24.3:1.0:31.0:1.0:1.0:0.0:60.0:254.0:1.0:0.0:0.1 +4 6927471 . T G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GATCTTGTCACTATCCCTTC;RSEQ=GAGGCTGTAGCCATATCGCG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:29.0:1.0:32.0:1.0:1.0:0.0:55.8:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +4 8043703 . G A 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=TGCAGGTTCCAACAACAACA;RSEQ=CAGCAACAACAGCAACAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:86:48:25,23:25,12:37,48:0.5581:2,2:27.3:1.0:29.6:1.0:0.18513:1.90197:59.3:47.0:0.5663:0.0:2.2 0/0:135:0:0,0:7,7:14,0:0.0:2,0:28.4:1.0:31.7:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 +4 28400060 . A G 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=AATACATGCTTCTGTTTCTC;RSEQ=AGTGTGAAAAATCTGTTTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:13.6:1.0:31.2:1.0:1.0:0.0:57.8:10.0:1.0:0.0:2.4 0/0:1:0:0,0:1,0:1,0:0.0:0,0:40.0:0.0:27.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +4 28400468 . C T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCACCTTGAGCATGCATAGC;RSEQ=TTGTCCTCATCATCCTTAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:33:7,26:20,122:142,33:0.1886:2,2:22.8:1.0:31.5:1.0:0.29599:1.64:60.0:66.0:0.1897:0.0:1.1 0/0:139:0:0,0:30,109:139,0:0.0:2,0:21.7:1.0:31.5:1.0:1.0:0.0:60.0:278.0:1.0:0.0:0.2 +4 37822923 . G A 72 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=12.0;MSILEN=1.0;SSF=0.00032;SOR=0.0;LSEQ=ATGATCAATAAAAAAAAAAA;RSEQ=AAAAAAAAAAAAGATTTAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:8:1,7:24,10:34,8:0.1538:2,2:13.1:1.0:24.1:1.0:0.00433:15.63485:59.5:3.0:0.1622:0.0:1.3 0/0:84:0:0,0:34,33:67,0:0.0:2,0:12.0:0.0:10.0:0.0:1.0:0.0:58.0:0.0:0.0:0.0:1.0 +4 41747691 . C G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06291;SOR=0.0;LSEQ=CTTTATTCTTAGCGCGATTA;RSEQ=TTTAGGCCCTCAATGAAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:4,1:13,2:15,5:0.25:2,2:8.2:1.0:32.8:1.0:1.0:1.58265:60.0:10.0:0.25:0.0:1.2 0/0:14:0:0,0:13,1:14,0:0.0:1,0:19.7:1.0:29.8:1.0:1.0:0.0:60.0:13.0:1.0:0.0:0.0 +4 41748217 . G A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03018;LSEQ=TCAGTGCTCTTGGCCTCTTT;RSEQ=CTCTCGTCGTCCCTGGAAGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1221:118:60,58:606,497:1103,118:0.0966:2,2:25.4:1.0:28.8:1.0:0.43672:1.17851:60.0:38.333:0.0961:0.0:1.1 0/0:1555:5:5,0:844,704:1548,5:0.0032:2,0:1.0:0.0:23.8:1.0:0.06756:0.0:60.0:10.0:0.0033:0.0:1.0 +4 46726267 . C T 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCAGCTGTATCCCATAAGCC;RSEQ=AGATTCACCGGTTTTCCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:196:31:14,17:71,94:165,31:0.1582:2,2:20.2:1.0:30.2:1.0:0.8456:1.09:28.1:62.0:0.159:0.0:1.0 0/0:204:0:0,0:105,99:204,0:0.0:2,0:11.0:0.0:17.0:0.0:1.0:0.0:32.0:0.0:0.0:0.0:2.0 +4 54245372 . T A 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01468;SOR=0.0;LSEQ=TTGTTTGCTTATTTATTTAT;RSEQ=TGTTTATTTTACTTGGTAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:428:5:2,3:202,221:423,5:0.0117:2,2:23.0:1.0:31.8:1.0:1.0:1.37004:60.0:10.0:0.0118:0.0:1.0 0/0:565:0:0,0:285,279:564,0:0.0:2,0:23.1:1.0:29.6:1.0:1.0:0.0:60.0:93.0:0.9982:0.0:0.1 +4 55129831 . C T 241 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CTTCATTCTTTTTTAAACCA;RSEQ=AGACCCAGATGTAGCCTTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:258:172,86:238,130:368,258:0.4115:2,2:24.3:1.0:30.1:1.0:0.66942:1.09:60.0:257.0:0.4119:0.0:1.1 0/0:685:0:0,0:411,274:685,0:0.0:2,0:24.8:1.0:31.4:1.0:1.0:0.0:60.0:227.333:1.0:0.0:0.1 +4 55161516 . CA TG 73 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03112;SOR=0.0;LSEQ=AAAACCACTTTATTGCAATG;RSEQ=GAGGTTGAGAGGAGGACTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:211:6:2,4:31,174:205,6:0.0284:2,2:18.7:1.0:28.3:1.0:0.23736:2.79:60.0:12.0:0.0288:0.0047:0.8 0/0:192:0:0,0:32,160:192,0:0.0:2,0:21.2:1.0:29.7:1.0:1.0:0.0:60.0:95.0:1.0:0.0:1.1 +4 55955737 . A AT 214 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=0.0;SOR=0.09951;LSEQ=TCCTCATCACCTATGTATCT;RSEQ=TTTTTTTTTTCAAAGCTTCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:223:118:54,64:33,65:98,118:0.5291:2,2:27.5:1.0:31.2:1.0:0.09427:1.66:60.0:117.0:0.5318:0.0628:0.2 0/1:120:12:4,8:45,60:105,12:0.1:2,2:25.6:1.0:29.9:1.0:0.7588:1.49497:58.6:24.0:0.1008:0.0:0.8 +4 55962165 . AC TT 104 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.12475;SOR=0.0;LSEQ=CTTCTCTGGACATCTGTTAC;RSEQ=AAGTAACAAACTGTATCATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:11:10,1:10,2:12,11:0.4783:2,2:16.5:1.0:30.3:1.0:1.0:1.94:58.9:22.0:0.4783:0.0435:1.1 0/0:5:0:0,0:5,0:5,0:0.0:0,0:22.4:1.0:30.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 +4 55965031 . AT A 120 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00017;SOR=0.0;LSEQ=TTATACTTTTTGTTTGTAAG;RSEQ=GACAAATTTTAGCACTAAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:13:2,11:5,94:99,13:0.1161:2,2:24.0:1.0:32.6:1.0:0.18698:3.36:60.0:26.0:0.1161:0.0268:0.2 0/0:109:0:0,0:9,100:109,0:0.0:2,0:23.9:1.0:29.8:1.0:1.0:0.0:60.0:218.0:1.0:0.0:0.1 +4 55979609 . G A 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02748;LSEQ=CTTCATCTCACTCCCAGACT;RSEQ=GGTTTTTAGGTCTCGGTTTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:780:57:26,31:298,425:723,57:0.0731:2,2:24.9:1.0:30.3:1.0:0.57708:1.2:60.0:114.0:0.0736:0.0:1.1 0/0:926:2:2,0:400,524:924,2:0.0022:2,0:1.0:0.0:23.5:1.0:0.1882:0.0:60.0:4.0:0.0022:0.0:1.0 +4 55985209 . C G 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.4697;SOR=0.0;LSEQ=AACATGGTAAAACCCTGTCT;RSEQ=TACTAAAAATACAAAAATGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:36.8:1.0:32.6:1.0:1.0:0.0:42.0:10.0:0.5:0.0:1.6 0/0:2:0:0,0:0,2:2,0:0.0:0,0:16.5:1.0:33.0:0.0:1.0:0.0:42.5:4.0:1.0:0.0:1.0 +4 55991731 . T C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.22222;SOR=0.0;LSEQ=GGAAACGCAGCGACCACACA;RSEQ=TGACCGCTCTCCCGGGGTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:1,6:0,0:0,7:0.875:0,2:25.3:1.0:33.1:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.6 0/0:1:0:0,0:0,1:1,0:0.0:0,0:5.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +4 65604620 . C T 170 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01172;LSEQ=TTTACAAGAACCTTTAATAT;RSEQ=AATACAATAATGCCATGAGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:177:60:27,33:51,66:117,60:0.339:2,2:25.1:1.0:28.9:1.0:0.87417:1.06:59.8:120.0:0.3468:0.0:2.9 0/0:169:1:0,1:79,89:168,1:0.0059:2,0:1.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.006:0.0:1.0 +4 65604632 . G GA 63 q25 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.12123;SOR=0.16637;LSEQ=TTTAATATCAATACAATAAT;RSEQ=CCATGAGCTAGACTTCTACA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:6:4,2:14,21:35,6:0.0357:2,2:26.0:1.0:24.7:1.0:0.37729:2.92:60.0:2.0:0.0238:0.006:2.8 0/0:164:1:1,0:49,54:103,1:0.0061:2,0:10.0:0.0:30.0:0.0:0.48077:0.0:60.0:2.0:0.0061:0.0:2.0 +4 66189753 . C CT 195 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.14857;LSEQ=CACTGTTTTCCCTTTTCCCC;RSEQ=TTTTTTTGTTAAAATAAATC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:64:57,7:185,38:223,64:0.2078:2,2:28.5:1.0:32.6:1.0:0.32898:1.67:60.0:128.0:0.2254:0.0:0.1 0/1:294:11:11,0:225,55:280,11:0.0374:2,0:25.6:1.0:30.4:1.0:0.13281:0.0:60.0:22.0:0.0375:0.0068:0.5 +4 66216523 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCAATTTTCCATAGTGTAGA;RSEQ=GTAACAGTTTTTAAATAGCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1.0:0,2:21.8:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +4 66218527 . A T 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.17194;SOR=0.0;LSEQ=TTTTTTTTTCAAATTAAGAC;RSEQ=TACTTAAATAAAACTTTAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:38:10:10,0:28,0:28,10:0.2632:1,0:29.6:1.0:32.1:1.0:1.0:0.0:60.0:20.0:0.2632:0.0:1.1 0/0:9:0:0,0:9,0:9,0:0.0:0,0:25.4:1.0:29.7:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 +4 66218677 . C T 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGTGGCCCAAATTCAACTT;RSEQ=AACATCACAGCATCATCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:427:28:21,7:306,93:399,28:0.0656:2,2:23.0:1.0:30.1:1.0:0.81929:1.09654:60.0:56.0:0.0671:0.0:1.9 0/0:363:0:0,0:272,91:363,0:0.0:2,0:24.8:1.0:30.4:1.0:1.0:0.0:60.0:71.6:1.0:0.0:0.6 +4 66270345 . G A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.17387;SOR=0.0;LSEQ=CCTAATATCCTTTCTTAAAA;RSEQ=TGTGTAATTGAAAAGTCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:7:0,7:0,35:35,7:0.1667:1,0:24.9:1.0:31.7:1.0:1.0:0.0:60.0:14.0:0.1707:0.0:1.0 0/0:14:0:0,0:0,14:14,0:0.0:1,0:19.1:1.0:33.1:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 +4 66286376 . G A 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05177;SOR=0.15512;LSEQ=TATATTGGCATTTTGAGAAC;RSEQ=TAGCAATATAAAAAAAATCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:99:9:0,9:1,89:90,9:0.0909:1,0:21.8:1.0:30.0:1.0:1.0:0.0:60.0:18.0:0.0928:0.0:1.7 0/1:66:1:0,1:1,64:65,1:0.0152:1,0:23.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0154:0.0:1.0 +4 69761131 . T C 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05249;SOR=0.0;LSEQ=AAAATGTCACATTTGTAGTT;RSEQ=CCATTTTCTTGTCTCTATAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:5:2,3:3,10:13,5:0.2778:2,2:18.0:1.0:32.0:1.0:0.58275:2.12:55.2:10.0:0.2778:0.0:1.2 0/0:14:0:0,0:7,7:14,0:0.0:2,0:14.3:1.0:29.6:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.1 +4 78271554 . C G 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00014;SOR=0.0;LSEQ=TCCCTTTCATCTTCATTTCT;RSEQ=TTAGCAAATTCAGGGCATAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:250:11:9,2:145,92:237,11:0.044:2,2:24.3:1.0:33.0:1.0:0.21479:2.84:59.3:22.0:0.0444:0.0:1.0 0/0:305:0:0,0:177,126:303,0:0.0:2,0:23.5:1.0:31.0:1.0:1.0:0.0:60.0:150.5:0.9934:0.0:0.5 +4 87163541 . G T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.02707;SOR=0.0;LSEQ=TTTGTCCCTTGATGGAGAGG;RSEQ=TGTGCTTTGCTGAGGGAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:2,4:17,16:33,6:0.1538:2,2:13.7:1.0:28.2:1.0:0.66142:2.08513:47.2:5.0:0.1316:0.0:2.0 0/0:34:0:0,0:16,18:34,0:0.0:2,0:27.9:1.0:30.8:1.0:1.0:0.0:56.6:68.0:1.0:0.0:0.2 +4 99808693 . T C 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTTAATGAATGTCCCGTCCC;RSEQ=CTACCAACTGACAAAGCCCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:3,5:0,0:0,8:1.0:0,2:22.3:1.0:32.8:1.0:1.0:0.0:54.4:16.0:1.0:0.0:1.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +4 120324304 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01989;SOR=0.0;LSEQ=GGAGGAGGGGGTGATGATGT;RSEQ=ATTGCTGATGACGGCTTTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:5,0:19,10:29,5:0.1471:2,0:17.2:1.0:31.0:1.0:0.2908:0.0:30.0:10.0:0.1471:0.0:1.2 0/0:38:0:0,0:21,17:38,0:0.0:2,0:14.8:1.0:30.4:1.0:1.0:0.0:28.9:76.0:1.0:0.0:0.2 +4 124344819 . G A 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10798;LSEQ=TCTTCAACCAAAGGCTGCTA;RSEQ=GATTGTTTCTGTAATCTCCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:167:85:11,74:14,68:82,85:0.509:2,2:24.0:1.0:31.5:1.0:0.51868:1.38232:60.0:84.0:0.506:0.0:1.1 0/1:160:16:3,13:38,106:144,16:0.1:2,2:25.9:1.0:29.9:1.0:0.76332:1.54956:60.0:32.0:0.1006:0.0:1.1 +4 136777565 . CT C 147 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTCATCCCTCTTTACAATT;RSEQ=TTTCCTTGGGTATCTAAATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:24:20,4:55,7:62,24:0.2791:2,2:25.4:1.0:32.2:1.0:0.49141:1.56259:60.0:48.0:0.2791:0.0465:0.0 0/0:102:0:0,0:86,16:102,0:0.0:2,0:25.8:1.0:30.3:1.0:1.0:0.0:60.0:101.0:1.0:0.0:0.0 +4 143043397 . G A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.11475;LSEQ=TCTAGCATTCCAATTTCATC;RSEQ=CCTAAACAATAGAAAAGGCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:93:28,65:119,219:338,93:0.2158:2,2:26.8:1.0:29.8:1.0:0.38907:1.26075:60.0:45.5:0.2156:0.0:1.2 0/1:491:15:7,8:172,303:475,15:0.0305:2,2:15.5:1.0:28.1:1.0:0.42376:1.54:60.0:30.0:0.0311:0.0:1.3 +4 143043464 . C T 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.12966;LSEQ=AAATGTCACTAGCTACTATG;RSEQ=CTCCCTGCTGGAATTTGTTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:35:1,34:12,98:110,35:0.2414:2,1:26.4:1.0:30.6:1.0:0.18949:4.13508:60.0:70.0:0.2448:0.0:1.4 0/1:127:5:0,5:17,104:121,5:0.0394:2,0:22.6:1.0:29.2:1.0:1.0:0.0:60.0:10.0:0.04:0.0:1.8 +4 143066973 . G GA 62 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.10249;SOR=0.17267;LSEQ=TTTACTCAGTAAATGATTGG;RSEQ=AAAAAAAATTATTTCTTACC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:461:5:4,1:311,145:456,5:0.0108:2,2:14.6:1.0:27.0:1.0:1.0:1.86:60.0:4.0:0.0088:0.0022:0.2 0/0:530:1:1,0:352,177:529,1:0.0019:2,0:39.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0019:0.0:0.0 +4 143095139 . C T 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=5.0;MSILEN=1.0;SSF=0.05699;SOR=0.0;LSEQ=TATGTAAGGTGACGAAAATG;RSEQ=TTTTTAAAACTAGGTAATCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:11,6:0.3529:0,0:19.5:1.0:31.0:1.0:1.0:0.0:60.0:12.0:0.375:0.0:1.0 0/0:10:0:0,0:0,10:10,0:0.0:0,0:26.4:1.0:33.3:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 +4 143158979 . A C 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.03099;LSEQ=AAAATTTTTAAATGGTATAA;RSEQ=ATAATTAATATGAGAGAAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:98:77,21:98,22:120,98:0.4495:2,2:20.8:1.0:32.0:1.0:0.61003:1.21378:60.0:48.0:0.4486:0.0:1.1 0/1:204:5:3,2:152,46:198,5:0.0245:2,2:30.2:1.0:31.0:1.0:0.33834:2.19283:60.0:10.0:0.0249:0.0:1.0 +4 143326714 . T G 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.33333;SOR=0.0;LSEQ=TTGCAGTTCATGCAAGTCTT;RSEQ=ACTGGTCTGAGATCCCAGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:24.3:1.0:32.7:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.3 0/0:1:0:0,0:0,1:1,0:0.0:0,0:19.0:0.0:12.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:0.0 +4 147770229 . T G 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTGCTGCCCTCAGTATGCC;RSEQ=GAGTCAGCAGTCTCACCCTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:54:54:28,26:0,0:0,54:1.0:0,2:26.5:1.0:29.4:1.0:1.0:0.0:60.0:17.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +4 153245521 . C G 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00093;SOR=0.0;LSEQ=GGATTGATGTATCAAGAGAT;RSEQ=CACTCACCACATGGATACCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:555:11:4,7:190,351:541,11:0.0198:2,2:30.8:1.0:32.0:1.0:1.0:1.06:60.0:22.0:0.0203:0.0:1.1 0/0:550:0:0,0:214,334:548,0:0.0:2,0:24.8:1.0:30.4:1.0:1.0:0.0:60.0:77.286:0.9963:0.0:0.1 +4 153253991 . TA T 91 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.03581;SOR=0.0;LSEQ=TAATTCTGCACTCTGATTTC;RSEQ=AAATTATGAAAGGCAGTAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:7:0,7:0,29:29,7:0.1892:1,0:28.6:1.0:32.7:1.0:1.0:0.0:60.0:14.0:0.1892:0.0:0.0 0/0:24:0:0,0:0,24:24,0:0.0:1,0:21.9:1.0:31.4:1.0:1.0:0.0:60.0:48.0:1.0:0.0:0.1 +4 153270964 . A G 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.27778;SOR=0.0;LSEQ=TTTAAATTTTTGTTCACAAG;RSEQ=TAATTTCTGCTTGTGTCCTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:5,0:9,0:9,5:0.3571:0,0:28.6:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.3571:0.0:1.0 0/0:4:0:0,0:4,0:4,0:0.0:0,0:27.8:1.0:30.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +4 166144830 . A G 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CTTTTGAGAAACGGAGCATC;RSEQ=TGCTAAGATTAATGATGTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:19:6,13:100,138:238,19:0.0739:2,2:28.6:1.0:31.8:1.0:0.47096:1.56741:22.0:38.0:0.0742:0.0:1.5 0/0:319:0:0,0:144,175:319,0:0.0:2,0:28.4:1.0:29.5:1.0:1.0:0.0:33.0:105.333:1.0:0.0:0.3 +4 168210641 . C A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.01282;SOR=0.0;LSEQ=GGCTTTTGTGGGGACTTTTT;RSEQ=TTTTTGTTGTTGTTGATGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:5,2:2,2:4,7:0.6364:2,2:25.4:1.0:27.3:1.0:0.57576:2.29:55.3:14.0:0.6364:0.0:1.0 0/0:7:0:0,0:5,2:7,0:0.0:2,0:7.7:1.0:28.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +4 171735386 . C T 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.27982;SOR=0.0;LSEQ=AAACTCTTGGATTTTATAGC;RSEQ=TAGGCAATTTGAAGTCAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:14,0:14,5:0.2632:1,0:21.4:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.2632:0.0:1.0 0/0:8:0:0,0:8,0:8,0:0.0:0,0:28.1:1.0:28.5:1.0:1.0:0.0:60.0:7.0:1.0:0.0:0.0 +4 175047618 . G A 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.11129;LSEQ=CACCAGGGCCTGATAGAACC;RSEQ=TAAAAATGAGTTTTGCAGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:97:48,49:72,88:160,97:0.3774:2,2:24.1:1.0:30.7:1.0:0.52027:1.2:60.0:96.0:0.381:0.0:1.1 0/1:270:17:9,8:119,134:253,17:0.063:2,2:26.4:1.0:30.2:1.0:0.80278:1.27:60.0:34.0:0.063:0.0:1.2 +4 182443933 . G C 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGTAAATGGAGAACAACTG;RSEQ=ATCTGGATCCTGGTCAAACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:40:23,17:148,122:270,40:0.129:2,2:30.6:1.0:32.5:1.0:0.86504:1.11:43.4:80.0:0.1294:0.0:1.1 0/0:491:0:0,0:273,217:490,0:0.0:2,0:24.3:1.0:30.2:1.0:1.0:0.0:57.6:60.25:0.9979:0.0:0.1 +4 182444093 . T A 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATTTCCAGAAAGAAGAGAA;RSEQ=GGCAAAGTATGAGAAGGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:361:37:13,24:125,198:323,37:0.1025:2,2:26.5:1.0:31.7:1.0:0.72423:1.16499:60.0:74.0:0.1048:0.0:1.0 0/0:703:0:0,0:301,402:703,0:0.0:2,0:24.5:1.0:29.5:1.0:1.0:0.0:58.4:99.429:1.0:0.0:0.4 +4 182444132 . G T 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGAGATAAAGGAGATGGGTA;RSEQ=GATGCATAGGGAACTCAATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:95:32,63:51,111:162,95:0.3682:2,2:26.2:1.0:31.0:1.0:0.78254:1.11:59.1:94.0:0.3715:0.0:1.1 0/0:463:0:0,0:157,305:462,0:0.0:2,0:12.0:0.0:16.0:0.0:1.0:0.0:57.0:0.0:0.0:0.0:2.0 +4 183806854 . G T 57 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02106;SOR=0.0;LSEQ=GAATGCCCATTTAAAACCTG;RSEQ=ACCAAATGGCATGTTTAAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:343:5:2,3:182,155:337,5:0.0146:2,2:21.8:1.0:24.6:1.0:0.6654:1.75837:60.0:4.0:0.0119:0.0:1.4 0/0:397:0:0,0:228,169:397,0:0.0:2,0:26.0:1.0:30.3:1.0:1.0:0.0:60.0:65.167:1.0:0.0:0.4 +4 187509875 . G A 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGGCTGACACGTCAGA;RSEQ=CAGGAGGCGGTGGAGGCGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:414:56:32,24:206,150:356,56:0.1353:2,2:27.4:1.0:29.7:1.0:1.0:1.02994:59.4:55.0:0.1361:0.0:1.4 0/0:611:0:0,0:320,289:609,0:0.0:2,0:26.4:1.0:31.2:1.0:1.0:0.0:60.0:120.8:0.9967:0.0:0.2 +4 187525910 . A T 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.27761;SOR=0.0;LSEQ=GTGAGGAGGAGGGAAAGGAG;RSEQ=AGGGGTGTAGCGAAAAGGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:0,11:11,5:0.3125:0,0:23.6:1.0:29.6:1.0:1.0:0.0:60.0:10.0:0.3125:0.0:1.8 0/0:5:0:0,0:0,5:5,0:0.0:0,0:25.8:1.0:31.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.4 +4 187527089 . T C 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=AAATGCTCATCTTTTAATAC;RSEQ=GATAGCGACTTCTTGAATTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:13:13,0:35,2:37,13:0.26:2,1:30.6:1.0:32.0:1.0:1.0:0.0:60.0:26.0:0.26:0.0:1.4 0/0:60:0:0,0:58,2:60,0:0.0:1,0:23.8:1.0:30.8:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.2 +4 187530731 . T C 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.05371;SOR=0.0;LSEQ=CAGGCGCCCGCCACCACGCC;RSEQ=GGCTAATTTTTTTTTGTATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:5,1:2,4:6,6:0.5:2,2:9.7:1.0:31.8:1.0:0.24242:7.96:51.0:12.0:0.5:0.0:1.0 0/0:6:0:0,0:4,2:6,0:0.0:2,0:25.8:1.0:29.3:1.0:1.0:0.0:40.5:5.0:1.0:0.0:0.2 +4 187531022 . A G 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0045;LSEQ=TGTAGGTGTCTTGGCTGAAC;RSEQ=CAGGGGTATTATCGTTGATA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:590:133:77,56:242,215:457,133:0.2254:2,2:24.6:1.0:30.8:1.0:0.32461:1.22:60.0:43.333:0.2241:0.0:1.1 0/0:767:1:1,0:399,366:765,1:0.0013:2,0:18.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0013:0.0:1.0 +4 187534689 . G T 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00606;SOR=0.0;LSEQ=AGGTCTCCAACCCTGCCAGG;RSEQ=GCTAGCTCTTTAAGTCCTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1.0:0,0:18.6:1.0:31.3:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:3:0:0,0:0,3:3,0:0.0:0,0:17.3:1.0:30.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +4 187535063 . T C 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.03333;SOR=0.0;LSEQ=AAGCTTGAGTTATATTTTAA;RSEQ=TTCTGAGGGTTGTTTTTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:6,0:1,0:1,6:0.8571:0,0:26.3:1.0:30.8:1.0:1.0:0.0:60.0:5.0:0.8333:0.0:1.2 0/0:3:0:0,0:3,0:3,0:0.0:0,0:28.0:1.0:31.7:1.0:1.0:0.0:49.3:6.0:1.0:0.0:0.0 +4 187535765 . T C 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.375;SOR=0.0;LSEQ=TACAAAATGCTATTATATGT;RSEQ=ATTAAGCTGATTTCATATTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:0,5:0,2:2,5:0.7143:0,0:24.6:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:8.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +4 187540042 . G A 188 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATCCTTAGCCATTAAACG;RSEQ=ACTGAGATCACTTTCTCCGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:706:74:36,38:313,319:632,74:0.1048:2,2:27.1:1.0:30.4:1.0:0.90282:1.03566:53.3:36.0:0.1047:0.0:1.1 0/0:916:0:0,0:474,442:916,0:0.0:2,0:26.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:4.0 +4 187541598 . C G 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=TGTCACTTCTACAACCACAT;RSEQ=AAACGCCTCCTGCTGCTCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:495:14:5,9:208,273:481,14:0.0283:2,2:24.6:1.0:30.4:1.0:0.78543:1.37058:60.0:13.0:0.0269:0.0:1.1 0/0:555:0:0,0:267,288:555,0:0.0:2,0:23.8:1.0:31.1:1.0:1.0:0.0:60.0:68.375:1.0:0.0:0.1 +4 187542755 . T C 244 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00368;LSEQ=ATGTAAACTTCGGAGAGGCG;RSEQ=TGTCAGCAATTGTGACAAAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:789:180:90,90:289,318:607,180:0.2281:2,2:26.0:1.0:32.7:1.0:0.61059:1.1:59.8:59.0:0.2275:0.0:1.1 0/0:919:1:0,1:442,476:918,1:0.0011:2,0:17.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0011:0.0:1.0 +4 187542922 . A G 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAATCATAAAAGAATTTCC;RSEQ=ATATTTCCTGGAAGGAGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:368:42:16,26:112,214:326,42:0.1141:2,2:23.7:1.0:30.7:1.0:0.73094:1.18:60.0:41.0:0.1139:0.0:1.1 0/0:402:0:0,0:147,255:402,0:0.0:2,0:24.5:1.0:29.4:1.0:1.0:0.0:60.0:99.5:1.0:0.0:0.2 +4 187542986 . G C 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CACAAGGGGCAGTAGTAGTA;RSEQ=TAGTTAGAGAAACAGAAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:129:36:2,34:9,84:93,36:0.2791:2,2:27.8:1.0:33.4:1.0:0.72667:1.81396:60.0:72.0:0.2835:0.0:1.1 0/0:119:0:0,0:15,104:119,0:0.0:2,0:22.3:1.0:31.8:1.0:1.0:0.0:60.0:118.0:1.0:0.0:0.1 +4 187557113 . C G 129 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=GACTTGTGCCCAAAACTCAT;RSEQ=AAACCGTATGCAGGTTCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:18:12,6:161,31:192,18:0.0857:2,2:20.6:1.0:31.1:1.0:0.09839:2.58191:60.0:36.0:0.0865:0.0:2.0 0/0:193:0:0,0:151,42:193,0:0.0:2,0:22.8:1.0:30.6:1.0:1.0:0.0:60.0:63.333:1.0:0.0:0.1 +4 187558187 . CA C 120 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00051;SOR=0.07257;LSEQ=CATTTTGCAGGGCACGATGA;RSEQ=ACATACACAGCAGATCTTCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:14:1,13:0,9:9,14:0.6087:0,1:25.6:1.0:31.7:1.0:1.0:0.0:60.0:28.0:0.6087:0.0435:0.4 0/1:21:2:0,2:0,19:19,2:0.0952:1,0:34.0:1.0:28.0:1.0:1.0:0.0:60.0:4.0:0.0952:0.0:0.0 +4 187584530 . G A 185 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01325;LSEQ=TGAGCTTGTCATTAGAGCTC;RSEQ=AATCTGGATCAAATGCCTCG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:649:66:37,29:347,236:583,66:0.1017:2,2:26.9:1.0:30.7:1.0:0.59928:1.15217:60.0:65.0:0.1011:0.0:1.1 0/0:669:1:1,0:376,290:666,1:0.0015:2,0:1.0:0.0:24.0:0.0:1.0:0.0:60.0:2.0:0.0015:0.0:1.0 +4 187628352 . A T 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CCAGAGGGCGTGCGATGTTA;RSEQ=CAACACCCGTCACGCTGTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:319:96:55,41:123,100:223,96:0.3009:2,2:24.5:1.0:30.2:1.0:0.80597:1.09:60.0:31.0:0.2971:0.0:1.7 0/0:411:0:0,0:216,194:410,0:0.0:2,0:23.0:1.0:29.4:1.0:1.0:0.0:59.9:204.0:1.0:0.0:0.6 +4 190093234 . C T 239 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01137;LSEQ=TAACGGGAGAAAAAATTCCC;RSEQ=GAAGCTGACACTCATCCAGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:323:206:98,108:58,59:117,206:0.6378:2,2:25.3:1.0:31.1:1.0:0.81686:1.08309:60.0:412.0:0.6398:0.0:1.1 0/1:462:9:4,5:214,236:450,9:0.0195:2,2:24.3:1.0:28.1:1.0:1.0:1.13317:60.0:8.0:0.0175:0.0:1.3 +5 223890 . G C 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTACATTTTTACTTGTATCT;RSEQ=TTATGTATCTATAAACTAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:0,6:0,23:23,6:0.2069:1,0:31.5:1.0:29.8:1.0:1.0:0.0:35.3:5.0:0.1852:0.0:2.5 0/0:1:0:0,0:0,1:1,0:0.0:0,0:42.0:0.0:33.0:0.0:1.0:0.0:23.0:2.0:1.0:0.0:0.0 +5 223909 . GATTTAA G 84 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=5;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTTATGTATCTATAAACTA;RSEQ=ATTTAGATCAAGTAAAGCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:6:0,6:1,26:27,6:0.1818:1,0:29.3:1.0:32.6:1.0:1.0:0.0:33.8:12.0:0.1875:0.0303:1.7 0/0:1:0:0,0:0,1:1,0:0.0:0,0:39.0:0.0:33.0:0.0:1.0:0.0:23.0:2.0:1.0:0.0:0.0 +5 223958 . T C 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATTAAAATAAAATGAACAG;RSEQ=GTCTGCTGTGATAGATGATA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:0,5:4,14:18,5:0.2174:2,0:17.4:1.0:28.2:1.0:0.53924:0.0:48.4:10.0:0.2174:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 225267 . C A 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.56006;SOR=0.0;LSEQ=GTAGCCTTTCACTCACTGCT;RSEQ=CAGTCAGCCCTTCCTGGAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:5,0:21,0:21,5:0.1923:1,0:36.4:1.0:28.0:1.0:1.0:0.0:33.8:10.0:0.1923:0.0:1.0 0/0:5:0:0,0:5,0:5,0:0.0:0,0:16.6:1.0:32.2:1.0:1.0:0.0:52.6:10.0:1.0:0.0:0.0 +5 228279 . T C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.0;MSILEN=1.0;SSF=0.10206;SOR=0.0;LSEQ=TGGCTTAACACTTCTTGCCC;RSEQ=TTTTTTTTCCTTTCTTTTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:400:7:5,2:293,82:375,7:0.0175:2,2:8.6:1.0:31.1:1.0:0.65146:1.4278:50.0:14.0:0.0175:0.0:1.7 0/0:210:0:0,0:143,49:192,0:0.0:2,0:29.6:1.0:30.6:1.0:1.0:0.0:48.6:191.0:0.9139:0.0:0.2 +5 230778 . T C 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.33864;SOR=0.0;LSEQ=TACAAATGGAAGTCCTTTCT;RSEQ=TGATCCCAGGCTTCTATCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:8,0:56,2:58,8:0.1212:1,0:23.5:1.0:32.4:1.0:1.0:0.0:32.8:16.0:0.1212:0.0:2.6 0/0:14:0:0,0:14,0:14,0:0.0:1,0:21.1:1.0:31.4:1.0:1.0:0.0:59.6:28.0:1.0:0.0:0.1 +5 233325 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TACACTGGGCTGTAATCAGA;RSEQ=TATTGGCCAGAGGTCTGTGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:28.2:1.0:31.5:1.0:1.0:0.0:22.8:12.0:1.0:0.0:2.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 233362 . T G 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GTGGGCCGGCCTTTCTCCTC;RSEQ=CTGGGGACACCGCTCTGCCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1.0:0,0:28.1:1.0:29.8:1.0:1.0:0.0:22.1:16.0:1.0:0.0:1.9 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 236932 . T A 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=7.0;MSILEN=1.0;SSF=0.083;SOR=0.0;LSEQ=CACCACACCTGGCTAATTTT;RSEQ=AAAAAAATTTATTTTGTAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:16:0,16:0,5:5,16:0.7619:0,1:28.3:1.0:29.6:1.0:1.0:0.0:23.3:7.0:0.7368:0.0:1.4 0/0:2:0:0,0:0,2:2,0:0.0:0,0:24.0:1.0:29.0:0.0:1.0:0.0:29.0:4.0:1.0:0.0:0.0 +5 240664 . A C 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.04338;SOR=0.0;LSEQ=TGCACTGGTTTTGTTTTTTA;RSEQ=AAACTAGATCTAGGGGGATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:0,5:1,10:11,5:0.3125:2,0:10.2:1.0:28.4:1.0:1.0:0.0:20.4:10.0:0.3125:0.0:1.2 0/0:16:0:0,0:2,14:16,0:0.0:2,0:31.4:1.0:30.8:1.0:1.0:0.0:46.1:15.0:1.0:0.0:0.1 +5 1255297 . C A 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.04139;SOR=0.0;LSEQ=GGTTAAACCACTTCCTGATG;RSEQ=GAAAAGGGGTAAGAACTTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:13:13,0:148,5:153,13:0.0783:1,1:25.4:1.0:31.0:1.0:1.0:0.0:60.0:26.0:0.0807:0.0:1.1 0/0:53:0:0,0:50,3:53,0:0.0:2,0:22.4:1.0:31.8:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.0 +5 1260195 . T C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGCCTGGGACCCCGTCTCA;RSEQ=CCTGTAAGGAGTGGCACTGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:31.2:1.0:29.3:1.0:1.0:0.0:58.7:5.0:0.7143:0.0:2.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 1264152 . A G 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GGCCCCAGGGTCTCGGGTTC;RSEQ=GAGGGACTCATGCCCAGCAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:8:8,0:3,0:3,8:0.7273:0,0:32.1:1.0:29.1:1.0:1.0:0.0:59.6:16.0:0.7273:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 1266310 . A G 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCAAAGAGCAGCAGGAGCC;RSEQ=GGTCACCGCCTGCACTCACC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:23:23:21,2:0,0:0,23:1.0:0,2:21.5:1.0:28.5:1.0:1.0:0.0:60.0:10.5:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 1272414 . G A 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03278;LSEQ=ACCTGCCGGCAGAGGAGAGG;RSEQ=CATGAGCCACAAATGTGGCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:903:205:73,132:238,460:698,205:0.227:2,2:25.9:1.0:29.5:1.0:0.73816:1.07:60.0:67.333:0.2267:0.0:1.1 0/0:420:4:3,1:159,257:416,4:0.0095:2,2:3.3:1.0:23.3:1.0:0.16203:4.83:60.0:3.0:0.0073:0.0:1.0 +5 1279964 . G C 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTAAGCGGAAGCGCACGGAG;RSEQ=CTGCGCACCACAGCAGGACA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:12:9,3:6,2:8,12:0.6:2,2:21.3:1.0:32.8:1.0:1.0:1.0:58.9:24.0:0.6667:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 1280190 . G A 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTCCCGTGGCCCCTCCTCC;RSEQ=GGCCCTTCATCTAAGCTGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:107:94,13:329,40:369,107:0.2243:2,2:25.5:1.0:30.4:1.0:0.7276:1.13716:60.0:20.4:0.2189:0.0:1.4 0/0:192:0:0,0:158,34:192,0:0.0:2,0:23.1:1.0:28.8:1.0:1.0:0.0:60.0:37.4:1.0:0.0:0.2 +5 1280830 . G C 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=CAGCCACTGGGGTAGCCCAA;RSEQ=GCTGGCCCCAGGCAGGACCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:18.6:1.0:30.0:1.0:1.0:0.0:57.6:10.0:1.0:0.0:1.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:16.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +5 1293389 . C G 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGAGCCCCTACTGCATTCAG;RSEQ=TCTGGGGCCTGGGCCCTCGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:437:154:127,27:235,48:283,154:0.3524:2,2:22.4:1.0:31.4:1.0:0.89484:1.04073:59.9:153.0:0.355:0.0:1.1 0/0:154:0:0,0:124,30:154,0:0.0:2,0:25.0:1.0:31.5:1.0:1.0:0.0:60.0:37.5:1.0:0.0:0.2 +5 1295250 . G A 236 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGCTGGGCCGGGGACCCGG;RSEQ=AGGGGTCGGGACGGGGCGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1239:290:175,115:569,376:945,290:0.2341:2,2:25.8:1.0:28.9:1.0:1.0:1.01:60.0:17.125:0.2314:0.0:1.3 0/0:602:0:0,0:332,267:599,0:0.0:2,0:25.5:1.0:29.4:1.0:1.0:0.0:60.0:25.043:0.9948:0.0:0.4 +5 1576000 . C G 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0923;SOR=0.0;LSEQ=AATAAACTGGCATTTACTTC;RSEQ=TGGTCATGCCACTCTAGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:65:7:6,1:53,5:58,7:0.1077:2,2:35.4:1.0:29.9:1.0:0.50998:1.74827:50.7:14.0:0.1094:0.0:1.0 0/0:31:0:0,0:27,4:31,0:0.0:2,0:35.6:1.0:29.9:1.0:1.0:0.0:46.6:14.5:1.0:0.0:0.0 +5 6624371 . C T 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.03162;SOR=0.0;LSEQ=ATCCAAGGTTTTGATTAAAG;RSEQ=ATTAAGTAAGATGGGGACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:15:15,0:5,0:5,15:0.75:0,1:25.5:1.0:30.3:1.0:1.0:0.0:60.0:14.0:0.7368:0.0:1.1 0/0:3:0:0,0:3,0:3,0:0.0:0,0:40.0:1.0:27.3:1.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +5 8453932 . CAT C 87 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=8.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CAGATACTGTATTTTATATA;RSEQ=ATATATATATATATAGAAGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:37.2:1.0:33.8:1.0:1.0:0.0:57.8:12.0:0.75:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 17464034 . C T 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCCCCACCCAGGGAGCTTC;RSEQ=GTGTTAGGCAGTTGCAAGTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:1,5:0,0:0,6:1.0:0,2:24.5:1.0:30.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 17491448 . T A 195 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTCCTCTAGAGTGCAAGGT;RSEQ=TCCCAGGAGCGTGGGCTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:476:114:95,19:317,45:362,114:0.2395:2,2:23.0:1.0:28.6:1.0:0.27078:1.40781:58.0:113.0:0.2399:0.0:1.1 0/0:263:0:0,0:215,48:263,0:0.0:2,0:23.7:1.0:29.9:1.0:1.0:0.0:59.0:262.0:1.0:0.0:0.1 +5 17670396 . G T 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=TCAAAGAGGCGCACCAGGTA;RSEQ=GCCTTGCTGGGCTCCTGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:23:9,14:321,477:798,23:0.028:2,2:21.9:1.0:30.5:1.0:1.0:1.04677:58.8:46.0:0.0284:0.0:1.0 0/0:487:0:0,0:200,287:487,0:0.0:2,0:25.5:1.0:30.4:1.0:1.0:0.0:58.9:59.875:1.0:0.0:0.2 +5 17670600 . C A 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=7e-05;SOR=0.05057;LSEQ=TTCTTGATCCCTCCTGTAGG;RSEQ=GGCGCCCTCTTGCTGGCAGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:36:5,31:5,36:41,36:0.4675:2,2:22.4:1.0:32.2:1.0:1.0:1.16:59.6:17.0:0.4722:0.0:1.1 0/1:24:1:0,1:5,18:23,1:0.0417:2,0:44.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0417:0.0:1.0 +5 22934638 . G T 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02358;SOR=0.0;LSEQ=ATACCAACCTCTGGAGTTGG;RSEQ=TGACATGGCTTCTCCCCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:8:3,5:58,61:119,8:0.063:2,2:30.5:1.0:28.5:1.0:0.71939:1.57907:31.8:7.0:0.0569:0.0:1.8 0/0:82:0:0,0:35,47:82,0:0.0:2,0:28.2:1.0:30.1:1.0:1.0:0.0:35.2:81.0:1.0:0.0:0.5 +5 23146100 . G A 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06127;SOR=0.0;LSEQ=AGGGTGTGTTTCGCTGGGGG;RSEQ=AAACCCACTTGTCTGTACTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:6:3,3:7,7:14,6:0.3:2,2:29.7:1.0:31.8:1.0:1.0:1.0:56.3:12.0:0.3:0.0:1.0 0/0:12:0:0,0:5,7:12,0:0.0:2,0:26.9:1.0:26.3:1.0:1.0:0.0:58.8:11.0:1.0:0.0:0.5 +5 23303757 . G A 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTCTGCACAGGGTGGCGTT;RSEQ=GAGTACAAGGCAGGAGGGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1167:92:41,51:476,597:1073,92:0.0788:2,2:26.1:1.0:30.1:1.0:1.0:1.01:58.7:91.0:0.0795:0.0:1.1 0/0:640:0:0,0:283,357:640,0:0.0:2,0:25.8:1.0:30.4:1.0:1.0:0.0:58.9:57.182:1.0:0.0:0.3 +5 23303943 . C A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATGCTTCTGTCTGGACCATC;RSEQ=CTGACCTCTGAGACCGCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1092:59:37,22:540,493:1033,59:0.054:2,2:24.3:1.0:30.4:1.0:0.14015:1.53:53.1:118.0:0.0546:0.0:1.1 0/0:601:0:0,0:311,290:601,0:0.0:2,0:25.9:1.0:30.1:1.0:1.0:0.0:58.7:65.778:1.0:0.0:0.1 +5 23304880 . TT CC 229 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTAATGTTCTTCAAGATCTG;RSEQ=AAAGAATCAAACCGTTCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:931:145:70,75:401,383:784,145:0.1557:2,2:27.8:1.0:32.0:1.0:0.52849:1.12164:51.7:290.0:0.1569:0.0054:1.7 0/0:480:0:0,0:242,238:480,0:0.0:2,0:26.6:1.0:29.1:1.0:1.0:0.0:55.6:79.0:1.0:0.0:0.7 +5 26148813 . A G 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAGTGGGGAGGGGGTGGGGC;RSEQ=ACCAGCACTGCCTGCAGCTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:0,1:1,6:0.8571:0,2:28.7:1.0:31.3:1.0:0.28571:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 26149197 . C T 60 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.12797;SOR=0.0;LSEQ=CCCTTAGGAGTAGGGGTGGC;RSEQ=ACAGTCGCTGTGGACCAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:1,4:2,6:8,5:0.3846:2,2:29.8:1.0:26.0:1.0:1.0:1.30472:55.6:4.0:0.3333:0.0:1.4 0/0:6:0:0,0:1,5:6,0:0.0:2,0:26.7:1.0:31.0:1.0:1.0:0.0:58.0:12.0:1.0:0.0:0.2 +5 26149350 . C T 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.19231;SOR=0.0;LSEQ=GGCCCTGCTCCCTATGACAC;RSEQ=CAACTGGGTGATATCTTCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:7:3,4:2,2:4,7:0.6364:2,2:30.0:1.0:28.9:1.0:1.0:1.29868:60.0:6.0:0.6:0.0:1.4 0/0:3:0:0,0:2,1:3,0:0.0:2,0:15.0:1.0:27.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +5 26150118 . A T 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=2.0;SSF=0.00261;SOR=0.0;LSEQ=ATGAACAAAGCTTCCAAGAA;RSEQ=TATGGGACTTCATAAAAAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:11:6,5:7,7:14,11:0.44:2,2:33.5:1.0:30.5:1.0:1.0:1.19:35.6:22.0:0.44:0.0:1.1 0/0:15:0:0,0:11,4:15,0:0.0:2,0:21.9:1.0:30.1:1.0:1.0:0.0:32.9:30.0:1.0:0.0:0.1 +5 26670194 . A C 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0714;SOR=0.0;LSEQ=AATAATATATCTTTAATTTT;RSEQ=CTTAGATTACAAAACAGTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:11:0,11:0,195:195,11:0.0534:1,0:31.7:1.0:29.2:1.0:1.0:0.0:60.0:22.0:0.0539:0.0:1.1 0/0:65:0:0,0:1,64:65,0:0.0:1,0:23.6:1.0:29.5:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.0 +5 28499327 . T A 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTGCTGCTCTTAAGAGTGAA;RSEQ=AAAAGCTCACAAGTGTTTGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:16.6:1.0:27.4:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 29955160 . GA G 73 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.24895;SOR=0.0;LSEQ=GATGTTTTAAGAATTTTTGG;RSEQ=AAGGAAAATAGAAAATGATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:0,5:0,8:8,5:0.3846:0,0:33.6:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.4167:0.0:1.2 0/0:5:0:0,0:0,5:5,0:0.0:0,0:17.0:1.0:30.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 +5 33997307 . A C 125 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00415;SOR=0.0;LSEQ=TACCCTATATGAGGGTTGAG;RSEQ=GCTGTCACCAGCATTAGCGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:16:6,10:113,148:261,16:0.0578:2,2:24.4:1.0:31.4:1.0:0.79658:1.27143:60.0:32.0:0.0597:0.0:1.0 0/0:119:0:0,0:53,66:119,0:0.0:2,0:23.6:1.0:29.5:1.0:1.0:0.0:60.0:58.5:1.0:0.0:0.1 +5 35860873 . C T 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATGTCTGCCACAGAGTCTG;RSEQ=TATTTTATTAAGGTCATGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:170:55:50,5:109,6:115,55:0.3235:2,2:22.4:1.0:29.9:1.0:0.33707:1.80989:60.0:54.0:0.3253:0.0:1.1 0/0:111:0:0,0:95,16:111,0:0.0:2,0:20.0:1.0:31.5:1.0:1.0:0.0:60.0:222.0:1.0:0.0:0.1 +5 35871291 . G A 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01498;LSEQ=CACGATGTAGCTTACCGCCA;RSEQ=GAAAAGGATGAAAACAAATG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:707:78:30,48:218,411:629,78:0.1103:2,2:27.3:1.0:31.6:1.0:0.53041:1.18:60.0:156.0:0.1116:0.0:1.1 0/0:540:1:1,0:203,336:539,1:0.0019:2,0:3.0:0.0:26.0:0.0:0.37778:0.0:60.0:2.0:0.0019:0.0:1.0 +5 35875518 . C T 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTAGAGCCAAGACTAGAAAT;RSEQ=TGTTCTTCTGATTCCAAGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:35:33,2:131,9:140,35:0.2:2,2:23.1:1.0:30.5:1.0:1.0:1.13:60.0:34.0:0.1965:0.0:1.7 0/0:105:0:0,0:96,9:105,0:0.0:2,0:22.9:1.0:30.9:1.0:1.0:0.0:60.0:104.0:1.0:0.0:0.2 +5 36367987 . T G 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATTTGGGGAATATTCAAT;RSEQ=GTTCATGTTTGGATCTACTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:14,0:3,1:4,14:0.7778:2,1:25.9:1.0:32.6:1.0:0.22222:0.0:60.0:28.0:0.7778:0.0:1.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 37744444 . GA G 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGAGTCAACAAAAAAATGCT;RSEQ=AAACCCACAAGGCCAGAGTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:2,3:2,1:3,5:0.625:2,2:25.0:1.0:31.0:1.0:1.0:2.60168:57.6:10.0:0.625:0.125:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 38942090 . T C 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTATTGTTCCACTGTCATTA;RSEQ=GCTTTTAAAATGAAAGAAAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1.0:0,0:24.1:1.0:30.4:1.0:1.0:0.0:57.6:7.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 38942628 . T C 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.17863;SOR=0.0;LSEQ=AATGTTGCCATCTTTGTTCA;RSEQ=TGCAACCTCTGAGTCCTGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:55:6:1,5:8,41:49,6:0.1091:2,2:17.2:1.0:32.7:1.0:1.0:1.02:60.0:12.0:0.1154:0.0:1.0 0/0:21:0:0,0:0,21:21,0:0.0:1,0:22.2:1.0:30.1:1.0:1.0:0.0:59.5:42.0:1.0:0.0:0.2 +5 38947185 . C G 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02056;SOR=0.0;LSEQ=AAGGACTAAATAAAAGAGTA;RSEQ=AGAGTAGTTGAAAAGGGCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:9:9,0:25,1:26,9:0.2571:1,0:17.1:1.0:32.7:1.0:1.0:0.0:60.0:18.0:0.2647:0.0:1.4 0/0:18:0:0,0:17,1:18,0:0.0:1,0:20.2:1.0:31.7:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.1 +5 38949632 . C T 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATAGGATTTTCTTCCCCCCT;RSEQ=GCAGCTGCAAGAATCCATTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:35:8,27:33,83:116,35:0.2318:2,2:27.9:1.0:29.6:1.0:0.66521:1.33935:60.0:10.667:0.2207:0.0:1.1 0/0:70:0:0,0:13,57:70,0:0.0:2,0:24.9:1.0:30.1:1.0:1.0:0.0:60.0:140.0:1.0:0.0:0.1 +5 38958167 . A G 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGCCAACATGGTGAAACTCC;RSEQ=ACTCTACTAAAAATACAAAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:3,4:0,0:0,7:1.0:0,2:23.4:1.0:31.1:1.0:1.0:0.0:38.4:14.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 38962656 . T C 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00196;SOR=0.0;LSEQ=TGTTGAAGGACTTGGCTATC;RSEQ=CTAAGGTTAATTAAAAGAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:984:12:4,8:417,554:971,12:0.0122:2,2:19.2:1.0:29.6:1.0:0.57067:1.50481:60.0:11.0:0.0114:0.0:1.2 0/0:706:0:0,0:306,400:706,0:0.0:2,0:25.5:1.0:29.1:1.0:1.0:0.0:60.0:57.833:1.0:0.0:0.2 +5 38972335 . T C 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCATGAGTCTGACTGCCTGA;RSEQ=GAACTCTTCTCTGGGAGTAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:0,9:0,0:0,9:1.0:0,0:14.1:1.0:28.9:1.0:1.0:0.0:57.8:18.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 38990820 . G C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATATCAGATATGATATATAT;RSEQ=ATATATATCATATATATGAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:40.5:1.0:33.0:1.0:1.0:0.0:39.7:12.0:0.75:0.0:3.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 38997170 . G A 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.32415;SOR=0.0;LSEQ=ATCTCGAGGGATAAATATCT;RSEQ=TCATTTAAAAGACCAATTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:8:0,8:1,28:29,8:0.2162:1,0:16.1:1.0:30.6:1.0:1.0:0.0:60.0:16.0:0.2162:0.0:1.0 0/0:9:0:0,0:1,8:9,0:0.0:2,0:13.3:1.0:32.2:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.0 +5 39002519 . C T 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGTGTATATATATATATATA;RSEQ=ACACACACAAAATTCATCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:32:31,1:23,2:25,32:0.4324:2,1:23.8:1.0:29.8:1.0:0.57621:2.65:60.0:15.0:0.5556:0.0:1.5 0/0:31:0:0,0:9,0:9,0:0.0:0,0:17.4:1.0:30.6:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.3 +5 39021493 . G A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACCACAAAATCTTAAATCTT;RSEQ=CTATTATTTGAATGTGTTCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:0,6:6,7:0.5385:0,0:13.3:1.0:29.7:1.0:1.0:0.0:55.6:14.0:0.5385:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 40457488 . G A 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04799;LSEQ=CAACAACACACTGCAGGACC;RSEQ=ATATATTTTCCTTGCCCAAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:569:30:15,15:240,299:539,30:0.0527:2,2:20.5:1.0:30.5:1.0:0.57653:1.25:60.0:60.0:0.0533:0.0:1.2 0/0:376:1:1,0:174,201:375,1:0.0027:2,0:1.0:0.0:25.0:0.0:0.46543:0.0:60.0:2.0:0.0027:0.0:1.0 +5 52665229 . GTCT AGAC 212 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACACATTATGAATAAAACAA;RSEQ=AGATGATGCAAGAGAATGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:277:108:71,37:110,56:166,108:0.3899:2,2:26.9:1.0:31.5:1.0:1.0:1.02356:60.0:216.0:0.3942:0.0939:1.4 0/0:329:0:0,0:203,125:328,0:0.0:2,0:24.5:1.0:31.5:1.0:1.0:0.0:60.0:108.333:0.9969:0.0:0.4 +5 52665368 . G T 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=AAGACATTAGACTTCCTATT;RSEQ=CAGTGGTTTATAACAAAACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:294:15:5,10:83,196:279,15:0.051:2,2:23.1:1.0:30.5:1.0:0.77606:1.18:59.6:30.0:0.0523:0.0:1.1 0/0:312:0:0,0:122,190:312,0:0.0:2,0:25.3:1.0:31.0:1.0:1.0:0.0:60.0:51.0:1.0:0.0:0.5 +5 56168571 . G A 219 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAATAATTTTGAAATGATAC;RSEQ=GATATGTTTAATTTTTAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:317:134:79,55:95,88:183,134:0.4227:2,2:21.1:1.0:31.1:1.0:0.25326:1.33:60.0:66.0:0.419:0.0:1.0 0/0:459:0:0,0:257,200:457,0:0.0:2,0:22.6:1.0:29.6:1.0:1.0:0.0:59.8:227.5:0.9956:0.0:0.1 +5 56183637 . G C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAAACTCAAAGTGCACATAA;RSEQ=AAATTTTTAAAAATATTCTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1.0:0,2:16.8:1.0:32.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 56183743 . T G 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.16667;SOR=0.0;LSEQ=ATTGTTCTTCTGACTCAGCT;RSEQ=CTTCTGTCGTGTTCATAATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:2,3:1,1:2,5:0.7143:2,2:21.6:1.0:32.6:1.0:1.0:1.41418:52.2:10.0:0.7143:0.0:1.0 0/0:2:0:0,0:1,1:2,0:0.0:2,0:13.5:1.0:27.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +5 56184610 . C T 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GACTAAGCTATAATGTTTGG;RSEQ=AGGTTAGGTGTATTAACTGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:35.6:1.0:28.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 57752811 . CA C 81 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.00893;SOR=0.0;LSEQ=TGCTTTGTCTTTTTTGCCAC;RSEQ=AAAAGAGCAGCAGCTGCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:6:3,3:219,209:428,6:0.0138:2,2:30.8:1.0:31.7:1.0:1.0:1.04775:60.0:12.0:0.014:0.0:0.2 0/0:517:0:0,0:248,269:517,0:0.0:2,0:25.6:1.0:29.6:1.0:1.0:0.0:60.0:128.25:1.0:0.0:0.1 +5 57754489 . ACT A 234 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.05166;LSEQ=GCTAAAATCCCAGATAAAAT;RSEQ=CTTTGAATACCATGTTAATT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:339:145:108,37:127,67:194,145:0.4277:2,2:24.4:1.0:32.6:1.0:0.09539:1.54:59.6:290.0:0.4328:0.0619:0.1 0/1:324:12:7,5:205,107:312,12:0.037:2,2:20.2:1.0:29.6:1.0:0.75812:1.36706:59.6:24.0:0.0372:0.0123:0.3 +5 62835420 . G A 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03008;LSEQ=TATTTTTTTTTTTATTTTTC;RSEQ=GAAGAAATAGGTATGTTTAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:16:8,8:18,10:28,16:0.3636:2,2:18.7:1.0:30.8:1.0:0.52475:1.77554:60.0:32.0:0.3636:0.0:1.2 0/1:61:1:1,0:35,25:60,1:0.0164:2,0:38.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0167:0.0:1.0 +5 62836591 . T C 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03294;LSEQ=AGTGATATTACTTTTAAAAA;RSEQ=CACCAAGTGTAAGCACAACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:22:22,0:31,0:31,22:0.4151:1,1:27.8:1.0:32.1:1.0:1.0:0.0:60.0:21.0:0.4118:0.0:1.0 0/1:45:1:1,0:41,3:44,1:0.0222:2,0:12.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0227:0.0:1.0 +5 62836726 . T C 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03219;LSEQ=TTCCAAATCCACAGTGGCAC;RSEQ=GCAGATTCAAAGCACTTTCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:182:110,72:118,92:210,182:0.4631:2,2:25.2:1.0:30.4:1.0:0.41285:1.19:58.1:59.667:0.4602:0.0:1.1 0/1:483:13:7,6:268,201:469,13:0.0269:2,2:22.5:1.0:30.4:1.0:1.0:1.14254:57.6:26.0:0.0273:0.0:1.8 +5 67569342 . T C 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTAGAGGGCATCAGTTCCT;RSEQ=TGTTCTACCCTTATTTCATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:370:19:6,13:75,276:351,19:0.0514:2,2:23.2:1.0:33.1:1.0:0.39012:1.7:60.0:38.0:0.0514:0.0:1.2 0/0:361:0:0,0:85,275:360,0:0.0:2,0:24.1:1.0:29.4:1.0:1.0:0.0:60.0:50.429:0.9972:0.0:0.2 +5 68390203 . C G 108 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00098;SOR=0.03358;LSEQ=AAGGCAGCGACCGGCCGGGT;RSEQ=GCTCAGGATGCACTTTCTCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:14:11:6,5:2,1:3,11:0.7857:2,2:18.1:1.0:31.4:1.0:1.0:1.60839:60.0:22.0:0.7857:0.0:1.4 0/1:11:1:0,1:7,3:10,1:0.0909:2,0:49.0:0.0:29.0:0.0:0.36364:0.0:60.0:2.0:0.0909:0.0:1.0 +5 79172158 . C T 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTCCAGGGTAGAGATTGTG;RSEQ=CTGATTCATGTAGCTTAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:247:25:11,14:88,134:222,25:0.1012:2,2:25.6:1.0:29.7:1.0:0.67307:1.2:60.0:50.0:0.1029:0.0:1.2 0/0:216:0:0,0:87,129:216,0:0.0:2,0:26.4:1.0:30.2:1.0:1.0:0.0:60.0:53.0:1.0:0.0:0.5 +5 86659159 . A T 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01266;SOR=0.0;LSEQ=AGAAAACAATTTTTTTTTTT;RSEQ=AACAGGCAAAGGAAAACGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:6:5,1:247,79:326,6:0.0181:2,2:23.2:1.0:27.2:1.0:1.0:1.6:59.7:5.0:0.0156:0.0:2.0 0/0:353:0:0,0:259,94:353,0:0.0:2,0:24.4:1.0:27.9:1.0:1.0:0.0:59.9:69.6:1.0:0.0:0.2 +5 87899069 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.14144;SOR=0.0;LSEQ=TTCTCCCCGCCCGCCCCCTC;RSEQ=CCCGGCCCCATGGGGTCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:5:0,5:1,22:23,5:0.1786:1,0:26.4:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.1786:0.0:1.4 0/0:16:0:0,0:1,15:16,0:0.0:1,0:17.7:1.0:30.3:1.0:1.0:0.0:60.0:32.0:1.0:0.0:0.1 +5 112043282 . CG GT 105 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=2;MSI=7.0;MSILEN=1.0;SSF=0.00523;SOR=0.0;LSEQ=CCGGAAGCCTAGCCGCTGCT;RSEQ=GGGGGGACCTGCGGGCTCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:86:10:9,1:76,0:76,10:0.1163:1,2:26.3:1.0:31.7:1.0:0.11628:0.0:60.0:20.0:0.119:0.0:1.0 0/0:63:0:0,0:44,1:45,0:0.0:1,0:27.6:1.0:30.9:1.0:1.0:0.0:60.0:90.0:0.7258:0.0:0.1 +5 112164716 . C CT 71 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.08912;SOR=0.15067;LSEQ=AATATGAATTTCATGTTTGG;RSEQ=TTTTTTTTGCTGCCTTCTTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:5:1,4:7,97:104,5:0.0459:2,2:29.4:1.0:30.6:1.0:0.32201:3.4:57.6:10.0:0.0467:0.0:0.0 0/0:140:1:0,1:27,112:139,1:0.0071:2,0:42.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0072:0.0:0.0 +5 112172930 . T C 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=CAACATAGGATTTCATGATA;RSEQ=AGTTTTTAAATTGGGAAACT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:5,1:1,0:1,6:0.8571:0,2:16.5:1.0:32.0:1.0:1.0:0.0:60.0:12.0:0.8571:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 112173849 . A T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.04763;SOR=0.12787;LSEQ=TGAAAAAGATAGAAGTTTGG;RSEQ=GAGAGAACGCGGAATTGGTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:441:6:0,6:209,226:435,6:0.0136:2,0:8.2:1.0:28.0:1.0:0.03146:0.0:60.0:12.0:0.014:0.0:1.0 0/0:569:1:0,1:286,282:568,1:0.0018:2,0:1.0:0.0:23.0:0.0:0.49736:0.0:60.0:2.0:0.0018:0.0:1.0 +5 112175617 . T A 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTAAAACACCTCCACCACC;RSEQ=CCTCAAACAGCTCAAACCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:881:93:48,45:391,394:785,93:0.1056:2,2:27.8:1.0:30.0:1.0:0.82651:1.07:60.0:30.0:0.1056:0.0:1.1 0/0:1271:0:0,0:617,652:1269,0:0.0:2,0:23.0:0.0:14.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:4.0 +5 112177863 . G GA 71 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.01351;SOR=0.0;LSEQ=AAGTAAAGGAATCAAAGGAG;RSEQ=AAAAAAAGTTTATAAAAGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:5:3,2:262,205:467,5:0.0106:2,2:20.4:1.0:30.6:1.0:1.0:1.17:60.0:10.0:0.0107:0.0063:0.4 0/0:643:0:0,0:353,289:642,0:0.0:2,0:23.6:1.0:30.1:1.0:1.0:0.0:60.0:63.2:0.9984:0.0:0.1 +5 112213678 . CTGTGTGTG C 253 MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=33;MSI=20.0;MSILEN=2.0;SSF=0.0;SOR=0.00814;LSEQ=ATTGAGAGTTACAGGTTACT;RSEQ=TGTGTGTGTGTGTGTGTGTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:764:224:124,100:172,172:344,224:0.2932:2,2:32.4:1.0:32.5:1.0:0.2293:1.24:58.3:73.667:0.2982:0.017:0.5 0/0:894:3:3,0:265,255:520,3:0.0034:2,0:29.0:1.0:32.0:1.0:0.24903:0.0:60.0:6.0:0.0034:0.0:0.0 +5 112213906 . G A 51 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.06242;SOR=0.0;LSEQ=TTATTTAGTAGACCACACCA;RSEQ=CACAATGGTTCCTCCAGCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:422:5:3,2:94,323:417,5:0.0118:2,2:15.0:1.0:22.2:1.0:0.08221:5.13:60.0:1.5:0.0073:0.0:1.0 0/0:395:0:0,0:85,310:395,0:0.0:2,0:22.3:1.0:31.3:1.0:1.0:0.0:60.0:64.833:1.0:0.0:0.1 +5 112227998 . G A 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=TGGAATGGAGCAGTGCAGGA;RSEQ=GGATGACTATGACCCTGACG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:167:18:8,10:45,104:149,18:0.1078:2,2:9.6:1.0:30.7:1.0:0.28334:1.84:57.9:17.0:0.1024:0.0:1.1 0/0:140:0:0,0:48,92:140,0:0.0:2,0:10.8:1.0:30.4:1.0:1.0:0.0:58.4:139.0:1.0:0.0:0.2 +5 131924374 . A T 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00545;SOR=0.0;LSEQ=AATTATGAGATTTTTTTTTT;RSEQ=AAAGGTCGTCTACAGCTGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:7:3,4:175,48:223,7:0.0304:2,2:9.7:1.0:25.0:1.0:0.04787:4.81737:60.0:6.0:0.0271:0.0:1.0 0/0:251:0:0,0:180,70:250,0:0.0:2,0:21.7:1.0:27.8:1.0:1.0:0.0:60.0:61.5:0.996:0.0:0.2 +5 131925174 . A C 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05485;SOR=0.12688;LSEQ=CACAATGATAAAATTGCCTA;RSEQ=TGATGCATTTCTTGGAATAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:9,0:13,0:13,9:0.4091:1,0:28.2:1.0:32.6:1.0:1.0:0.0:60.0:18.0:0.4091:0.0:2.0 0/1:13:1:1,0:12,0:12,1:0.0769:0,0:6.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0769:0.0:1.0 +5 131951996 . T C 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.26632;SOR=0.0;LSEQ=CATGGCCTTAAGAACTTTAT;RSEQ=ACTGAAGAAGTGATATAGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:5:0,5:0,10:10,5:0.3333:0,0:14.8:1.0:32.2:1.0:1.0:0.0:60.0:10.0:0.3333:0.0:1.4 0/0:5:0:0,0:0,5:5,0:0.0:0,0:18.8:1.0:29.0:0.0:1.0:0.0:60.0:10.0:1.0:0.0:0.2 +5 131952072 . C T 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=5.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCAGTATTGAACATGCTTAG;RSEQ=CCCCATACATCTGCTAGCCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:18.8:1.0:30.4:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 133478475 . C T 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=7e-05;SOR=0.0;LSEQ=CCAACCATCAAGAAGCCCCT;RSEQ=AATGCCTTCATGCTGTACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:10,2:2,0:2,12:0.8571:0,2:22.8:1.0:30.2:1.0:1.0:0.0:60.0:24.0:0.8571:0.0:1.2 0/0:10:0:0,0:6,4:10,0:0.0:2,0:20.6:1.0:31.3:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.0 +5 140256920 . G C 247 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCGGTCGGCGCGCACATCCC;RSEQ=TTCCACGTGGGGCTGTACAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:218:85,133:58,102:160,218:0.5767:2,2:22.7:1.0:31.9:1.0:0.59361:1.12:59.9:71.667:0.5749:0.0:1.1 0/0:333:0:0,0:115,217:332,0:0.0:2,0:22.3:1.0:29.8:1.0:1.0:0.0:60.0:40.5:0.9969:0.0:0.1 +5 142329054 . C T 58 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03052;SOR=0.0;LSEQ=CAATATTAATGCATCAGAAT;RSEQ=AGTGTTTGGAAGTTCAGATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:318:5:2,3:195,118:313,5:0.0157:2,2:11.6:1.0:25.2:1.0:0.37254:2.47144:60.0:4.0:0.0128:0.0:1.0 0/0:319:0:0,0:216,103:319,0:0.0:2,0:25.2:1.0:30.6:1.0:1.0:0.0:60.0:78.75:1.0:0.0:0.2 +5 149434518 . C A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCTATGATTGCACACATCA;RSEQ=TGCGCTCCAGCCCGGGCTAC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:8,0:4,1:5,8:0.6154:2,0:19.9:1.0:29.4:1.0:0.38462:0.0:49.1:7.0:0.5833:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 149436598 . A T 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCATACACTATTTAGTAAAA;RSEQ=CGAATGAAGAAAGCCTGGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:8,0:8,0:8,8:0.5:0,0:24.3:1.0:30.5:1.0:1.0:0.0:60.0:16.0:0.5:0.0:1.4 0/0:1:0:0,0:1,0:1,0:0.0:0,0:23.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +5 149460627 . G A 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=5e-05;SOR=0.0;LSEQ=GCAGACAGAAGTGAGGTCTA;RSEQ=GATGCGCCCCTTGGGCCGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:267:22:5,17:44,201:245,22:0.0824:2,2:23.5:1.0:32.0:1.0:0.56881:1.34:60.0:44.0:0.0827:0.0:1.2 0/0:152:0:0,0:34,118:152,0:0.0:2,0:22.8:1.0:30.9:1.0:1.0:0.0:60.0:151.0:1.0:0.0:0.4 +5 149495050 . T C 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATCAAGCCTAACTTTCCCAT;RSEQ=TTACATATGGGAAAACTGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1.0:0,0:31.1:1.0:32.5:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 149498064 . C G 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GCAGCAGGACAGACAGTGCT;RSEQ=TAGGCCCCCTCCCTGCATCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:7:6,1:12,0:12,7:0.3684:0,2:31.3:1.0:33.3:1.0:0.36842:0.0:60.0:14.0:0.3684:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 149502838 . G C 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAGGCCATGAGGCTAATCA;RSEQ=GGGCTGGATGTGGGAGAGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:220:121:11,110:6,93:99,121:0.55:2,2:24.4:1.0:30.5:1.0:0.45585:1.55:60.0:120.0:0.5556:0.0:1.1 0/0:104:0:0,0:16,88:104,0:0.0:2,0:21.8:1.0:30.5:1.0:1.0:0.0:60.0:208.0:1.0:0.0:0.1 +5 154505054 . CAGA GTGTGTGTGTGTGTGTGTGTATCACACACACACACATACACAGG 105 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0494;SOR=0.0;LSEQ=GTGTGCGCATGTGAGTGAAT;RSEQ=TGTTAATCTGCTTTGAGTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:9:0,9:0,27:27,9:0.2308:1,0:21.2:1.0:33.3:1.0:1.0:0.0:60.0:18.0:0.2432:0.1026:1.4 0/0:15:0:0,0:1,14:15,0:0.0:1,0:15.3:1.0:30.1:1.0:1.0:0.0:58.5:30.0:1.0:0.0:0.3 +5 170826687 . A ATT 72 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=11;MSI=13.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTTTCTATTTAGGTCTTTA;RSEQ=TTTTTTTTTTTAACACAAAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:1,0:1,5:0.7143:0,2:31.6:1.0:31.3:1.0:1.0:0.0:60.0:10.0:0.7143:0.0:0.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 170827459 . C T 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.47619;SOR=0.0;LSEQ=CCAAGTGGTTGCTGCTTTTT;RSEQ=CTTCCTTTTTTTTTTTTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:20:11:1,10:2,6:8,11:0.55:2,2:22.1:1.0:27.5:1.0:0.54592:3.12168:57.8:4.5:0.5294:0.0:1.6 0/0:1:0:0,0:0,1:1,0:0.0:0,0:25.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +5 170827464 . CT C 76 MSI12;MSI12 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=15;MSI=16.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGTTGCTGCTTTTTCCTTC;RSEQ=TTTTTTTTTTTTTTTGAGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:2,3:0,6:6,5:0.3125:0,2:34.2:1.0:33.0:1.0:0.18182:0.0:48.0:10.0:0.3125:0.0:3.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:19.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +5 170832637 . C T 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATTTTCCATTATGCAAGGAA;RSEQ=GTAGTGCACTGGTTGCAAGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:26.0:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 170832767 . TACAA T 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTATGAGACTTCATTAAAAT;RSEQ=ACAGCTGGAAAAGTAGATGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:21.8:1.0:30.6:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 176516631 . G A 227 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00819;LSEQ=TGCTGCTGGCCCTGTTGGGG;RSEQ=TCCTGCTGAGTGTGCCTGGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:739:171:80,91:291,277:568,171:0.2314:2,2:23.0:1.0:30.7:1.0:0.33749:1.1947:60.0:170.0:0.2326:0.0:1.1 0/0:815:2:2,0:395,418:813,2:0.0025:2,0:13.0:1.0:28.0:1.0:0.23698:0.0:60.0:4.0:0.0025:0.0:1.0 +5 176517170 . G A 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGTGTGTCTTGGCCACTGTC;RSEQ=TGTGCACTAAATGCTGTGTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:12:12:11,1:0,0:0,12:1.0:0,2:29.5:1.0:30.3:1.0:1.0:0.0:58.8:11.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 176517801 . G A 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAGTCCCATAGGGACCCCTC;RSEQ=AATAGGCACAGTTACCCCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1169:52:24,28:504,612:1116,52:0.0445:2,2:26.3:1.0:30.9:1.0:0.88779:1.04:60.0:104.0:0.045:0.0:2.1 0/0:993:0:0,0:443,550:993,0:0.0:2,0:25.0:1.0:29.8:1.0:1.0:0.0:60.0:75.385:1.0:0.0:0.8 +5 176518426 . T C 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GCTGTCATGAGGCAACTGAG;RSEQ=CTCAGAGAAGGCAAGGGTTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:0,8:1.0:0,2:25.9:1.0:31.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 176524465 . C T 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.05654;LSEQ=GGCCTCATCTGGCCTGACCG;RSEQ=GTGGACATGCGCCCCGTCCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:902:42:20,22:435,424:859,42:0.0466:2,2:26.7:1.0:29.7:1.0:0.75331:1.12839:60.0:41.0:0.0464:0.0:1.1 0/0:727:2:0,2:381,344:725,2:0.0028:2,0:4.5:1.0:25.5:1.0:0.22616:0.0:60.0:4.0:0.0028:0.0:1.0 +5 176636546 . G A 133 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.09246;LSEQ=TCTCAAAAAAAAAAAAAAAA;RSEQ=GAATAAAAAAAAAAGCTTCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:92:28:26,2:30,1:31,28:0.3043:1,2:8.6:1.0:27.7:1.0:0.5995:2.27599:56.1:4.6:0.3651:0.0:1.3 0/1:104:4:2,2:87,10:97,4:0.0385:2,2:22.0:1.0:19.8:1.0:0.06822:8.35858:40.5:1.0:0.0225:0.0:2.3 +5 176636882 . C T 252 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03826;LSEQ=GATGAGAAGGAAAAGCCTTG;RSEQ=GCTAAATCTCGAGCCAGAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:468:337:160,177:57,72:129,337:0.7201:2,2:24.8:1.0:30.1:1.0:0.53531:1.14:60.0:111.333:0.7277:0.0:1.1 0/1:437:39:15,24:192,205:397,39:0.0892:2,2:20.4:1.0:28.9:1.0:0.24572:1.49716:60.0:78.0:0.0901:0.0:1.1 +5 176637149 . G A 244 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.01352;LSEQ=ACTGCAAAGAAAGAATTTGA;RSEQ=ACTTCAAATGGTGACTCTTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:378:254:134,120:68,56:124,254:0.672:2,2:25.9:1.0:30.6:1.0:0.74236:1.08718:60.0:30.75:0.6685:0.0:1.1 0/1:448:12:7,5:226,210:436,12:0.0268:2,2:22.5:1.0:28.8:1.0:0.77359:1.3:60.0:11.0:0.0249:0.0:1.3 +5 176637240 . G T 257 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.01743;LSEQ=ATAAACCCCAACGAAGCCTG;RSEQ=TGTGTGGTTCAAAAGTGAAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:612:389:199,190:107,114:221,389:0.6356:2,2:24.5:1.0:29.9:1.0:0.55558:1.12:59.9:76.8:0.6379:0.0:1.2 0/1:646:19:10,9:298,329:627,19:0.0294:2,2:28.4:1.0:29.5:1.0:0.81645:1.23:60.0:38.0:0.0296:0.0:1.1 +5 176637576 . T C 258 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.02042;LSEQ=CAGAGCCTGGAACCGAGACG;RSEQ=CTCAGGTTAATCTCTCTGAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:431:263:145,118:88,79:167,263:0.6102:2,2:23.4:1.0:32.1:1.0:0.6913:1.1:59.8:86.667:0.6176:0.0:1.1 0/1:454:14:7,7:250,190:440,14:0.0308:2,2:24.7:1.0:30.2:1.0:0.78532:1.31497:60.0:28.0:0.031:0.0:1.0 +5 178996554 . G A 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CACTGGTAGAGGACCCCAGG;RSEQ=ATGCAGCTGGGGAAGGTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:45:28:0,28:1,16:17,28:0.6222:1,1:23.1:1.0:31.6:1.0:0.37778:0.0:60.0:56.0:0.6222:0.0:1.0 0/0:28:0:0,0:2,26:28,0:0.0:2,0:19.8:1.0:30.9:1.0:1.0:0.0:60.0:27.0:1.0:0.0:0.1 +5 180056434 . G A 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.16266;SOR=0.0;LSEQ=TTACCCCGCTCTGCCTGCCC;RSEQ=CACCCAGGGAAGCCCCGCGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:460:5:3,2:122,333:455,5:0.0109:2,2:26.4:1.0:28.8:1.0:0.12658:4.08:60.0:10.0:0.0112:0.0:1.0 0/0:284:0:0,0:92,192:284,0:0.0:2,0:24.8:1.0:30.5:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.1 +5 180058008 . C A 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCCGGGGCTGGCCTGTGG;RSEQ=CAAGCACAGGCCTTGGATCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1.0:0,2:24.3:1.0:29.3:1.0:1.0:0.0:60.0:9.0:1.0:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 180058451 . T C 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCACTGCACTCCAGCCTGGG;RSEQ=GACAGAGTGAGACTCCATCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:31.7:1.0:33.9:1.0:1.0:0.0:37.3:14.0:1.0:0.0:1.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 180525845 . T G 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGACGGAGTCTTGCTTTGTT;RSEQ=CCAGGCTGGAGTGCAGTGGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:32.0:1.0:27.9:1.0:1.0:0.0:36.6:2.5:1.0:0.0:1.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 180525899 . C G 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACTGCAATCTCCGCCTCCCA;RSEQ=GTTCAAGCGATTCTTCTGCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1.0:0,0:28.5:1.0:32.4:1.0:1.0:0.0:31.6:16.0:1.0:0.0:1.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +5 180527792 . C CGCGGAGCTCCCGCCCGGGCG 103 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGAGGTGGCCGCGTGGGACC;RSEQ=GCGACTGGAAATCCGGGTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:10:3,7:0,1:1,10:0.7692:0,2:15.6:1.0:31.2:1.0:1.0:0.0:60.0:20.0:0.7692:0.6923:1.4 0/0:24:0:0,0:5,8:13,0:0.0:2,0:12.7:1.0:29.9:1.0:1.0:0.0:60.0:26.0:0.5417:0.0:0.3 +6 6728616 . G A 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TAGCCTAGGCCTTCACAGCA;RSEQ=GGGGCAAGGGGGATGTCAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:32:20:5,15:2,10:12,20:0.625:2,2:23.0:1.0:31.4:1.0:0.68332:1.64:60.0:40.0:0.625:0.0:1.1 0/0:29:0:0,0:13,16:29,0:0.0:2,0:19.7:1.0:29.9:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.2 +6 7516674 . A ATATATACATATATATATATATATATG 130 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=6.0;MSILEN=2.0;SSF=4e-05;SOR=0.0;LSEQ=AACGGTGGCAATAACTGTAT;RSEQ=TATATATATGTCTATAAACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:18:18,0:21,0:21,18:0.4286:1,1:18.6:1.0:31.3:1.0:1.0:0.0:60.0:36.0:0.439:0.1905:1.1 0/0:26:0:0,0:21,1:22,0:0.0:1,0:17.7:1.0:28.0:1.0:1.0:0.0:59.9:44.0:0.8462:0.0:0.0 +6 8909371 . T C 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00023;SOR=0.0;LSEQ=TTTCTTAGTTTAGATTCCCC;RSEQ=TGAAATAGACCCTCAACCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:8,3:0,0:0,11:1.0:0,2:21.8:1.0:28.5:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.3 0/0:5:0:0,0:3,1:4,0:0.0:2,0:15.3:1.0:31.3:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 +6 17729851 . C T 88 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.05246;SOR=0.12258;LSEQ=TTGTGTTTTTTTGTTCTTTA;RSEQ=GTTAAAACTTGTTGCTGCTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:7,7:14,8:0.3636:2,2:16.1:1.0:29.6:1.0:0.67492:1.62835:60.0:16.0:0.3636:0.0:1.9 0/1:16:1:1,0:4,10:14,1:0.0625:2,0:26.0:0.0:32.0:0.0:0.33333:0.0:60.0:2.0:0.0667:0.0:2.0 +6 20486794 . C T 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.04032;SOR=0.0;LSEQ=ATTACAGGTGTGAGCCACCG;RSEQ=GCCCGGCCACATATGCATAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:7:7,0:60,0:60,7:0.1045:1,0:26.9:1.0:28.3:1.0:1.0:0.0:45.7:6.0:0.0923:0.0:1.4 0/0:45:0:0,0:45,0:45,0:0.0:1,0:27.9:1.0:32.2:1.0:1.0:0.0:51.8:90.0:1.0:0.0:0.6 +6 23515364 . G A 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.29644;SOR=0.0;LSEQ=AAAACTTTAGTCAGGTTTCT;RSEQ=AACCTTCTCCTAGGTCCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:7:5,2:12,7:19,7:0.2692:2,2:22.7:1.0:27.4:1.0:1.0:1.44:60.0:14.0:0.2692:0.0:1.0 0/0:6:0:0,0:4,2:6,0:0.0:2,0:26.7:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 +6 25261662 . A T 189 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCAAAACTGGAAGAGTCTAC;RSEQ=ATTTTACCCAGCATGCTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:218:80:36,44:63,75:138,80:0.367:2,2:27.5:1.0:29.9:1.0:1.0:1.02655:43.6:79.0:0.3657:0.0:1.1 0/0:224:0:0,0:104,120:224,0:0.0:2,0:28.5:1.0:29.4:1.0:1.0:0.0:56.8:73.667:1.0:0.0:0.1 +6 25606672 . C T 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.13043;LSEQ=GTGAAAGTGATGAGAGCTGA;RSEQ=GGATTCTTTTATTTAATGCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:376:128:55,73:127,121:248,128:0.3404:2,2:24.3:1.0:30.2:1.0:0.15679:1.39184:60.0:41.667:0.3369:0.0:1.9 0/1:302:19:9,10:131,150:281,19:0.0629:2,2:16.0:1.0:28.6:1.0:1.0:1.03:60.0:18.0:0.0608:0.0:2.0 +6 26031720 . C G 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00441;SOR=0.0;LSEQ=AAACCGTTATTTCTGTTAAT;RSEQ=AACTTTAAGACCATAGTCTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:76:14:14,0:61,0:61,14:0.1842:1,1:22.7:1.0:31.6:1.0:1.0:0.0:60.0:13.0:0.1757:0.0:1.1 0/0:36:0:0,0:36,0:36,0:0.0:1,0:24.4:1.0:30.9:1.0:1.0:0.0:59.1:35.0:1.0:0.0:0.2 +6 26322501 . G A 177 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCCGGTCGATTTGCGGGCA;RSEQ=TCGGCTTTCTACGAGCCGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:57:22,35:76,93:169,57:0.2522:2,2:26.6:1.0:30.5:1.0:0.44195:1.2986:60.0:56.0:0.25:0.0:1.1 0/0:188:0:0,0:84,104:188,0:0.0:2,0:26.5:1.0:31.7:1.0:1.0:0.0:59.7:187.0:1.0:0.0:0.4 +6 27840221 . C A 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00252;SOR=0.0;LSEQ=CGTCTCACACACGGAATTGG;RSEQ=TCCCAGTTTAATCTGCTAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:210:13:0,13:5,192:197,13:0.0619:1,1:23.9:1.0:31.8:1.0:1.0:0.0:60.0:26.0:0.0644:0.0:1.0 0/0:125:0:0,0:2,123:125,0:0.0:1,0:23.1:1.0:31.6:1.0:1.0:0.0:60.0:61.5:1.0:0.0:0.1 +6 29230520 . A C 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=3e-05;SOR=0.13465;LSEQ=TGGGAGTAACAATGGAGTAA;RSEQ=ATATATGGAGAAGTTTGCCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:36:35,1:72,0:72,36:0.3333:1,1:24.3:1.0:32.8:1.0:0.33333:0.0:60.0:72.0:0.3429:0.0:1.1 0/1:64:4:4,0:60,0:60,4:0.0625:1,0:14.3:1.0:30.8:1.0:1.0:0.0:60.0:8.0:0.0625:0.0:1.0 +6 29236588 . A G 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.12518;LSEQ=CAAGAACTATAATCAGGCAC;RSEQ=TGGCAAATGTGGTTACCTCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:36:1,35:6,78:84,36:0.3:2,1:25.5:1.0:32.5:1.0:0.67305:2.67444:60.0:72.0:0.3:0.0:1.1 0/1:99:5:1,4:11,83:94,5:0.0505:2,2:20.6:1.0:31.2:1.0:0.48339:1.87:60.0:10.0:0.051:0.0:1.0 +6 29693183 . G A 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=6;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGCAGGGTCAGGGCTGAG;RSEQ=CCTGGAGATCAGGGCCCCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:393:115:62,53:166,111:277,115:0.2926:2,2:22.5:1.0:29.7:1.0:0.31164:1.27758:59.8:56.5:0.2974:0.0:1.2 0/0:326:0:0,0:192,132:324,0:0.0:2,0:21.5:1.0:30.5:1.0:1.0:0.0:59.9:63.8:0.9969:0.0:0.2 +6 29760132 . G T 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTGTGGGGAGTAGCTAGGG;RSEQ=CCTGCCCGGCGGGGGCGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:335:108:25,83:59,168:227,108:0.3224:2,2:25.2:1.0:29.9:1.0:0.5931:1.16541:59.6:53.0:0.3242:0.0:2.3 0/0:239:0:0,0:69,168:237,0:0.0:2,0:23.4:1.0:30.6:1.0:1.0:0.0:59.9:78.0:1.0:0.0:0.5 +6 29760317 . G C 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GACGACACGCAGTGCGTGCG;RSEQ=CTCGACAGCGACGCCACGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:39:12,27:74,53:127,39:0.2349:2,2:24.4:1.0:30.7:1.0:0.00327:3.11956:59.6:18.5:0.2298:0.0:1.1 0/0:141:0:0,0:80,61:141,0:0.0:2,0:25.4:1.0:29.6:1.0:1.0:0.0:60.0:14.667:1.0:0.0:0.2 +6 29760462 . T C 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=ACCTGCGGACCCTGAGCGGC;RSEQ=ACTACAACCAGAGTGAGGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:230:35:18,17:88,107:195,35:0.1522:2,2:30.7:1.0:31.3:1.0:0.58142:1.29:60.0:34.0:0.1491:0.0:1.5 0/0:243:0:0,0:107,136:243,0:0.0:2,0:29.8:1.0:28.5:1.0:1.0:0.0:60.0:59.75:1.0:0.0:0.4 +6 29760730 . AC A 212 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGGCGGGGCCAGGGTCTCAC;RSEQ=CCATCTAGAGGATGTCTGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:486:99:62,37:224,163:387,99:0.2037:2,2:27.7:1.0:32.0:1.0:0.42428:1.22:57.8:198.0:0.2054:0.0226:1.6 0/0:469:0:0,0:266,202:468,0:0.0:2,0:25.0:1.0:30.7:1.0:1.0:0.0:59.7:45.8:0.9978:0.0:0.3 +6 29760765 . C A 205 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTCTGTCTGCGACGTGGGGT;RSEQ=GGACGGGCGCCTACTCCGCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:597:118:64,54:228,251:479,118:0.1977:2,2:25.6:1.0:29.8:1.0:0.21769:1.3:58.9:236.0:0.2014:0.0:2.0 0/0:573:0:0,0:277,295:572,0:0.0:2,0:27.6:1.0:29.7:1.0:1.0:0.0:59.9:94.333:0.9982:0.0:0.3 +6 29760799 . T C 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCGCGGGTATCACCAGCT;RSEQ=GCTTACGATGGCAAGGATTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:416:93:45,48:119,204:323,93:0.2236:2,2:25.1:1.0:30.3:1.0:0.05385:1.61:59.9:30.0:0.2217:0.0:2.3 0/0:423:0:0,0:181,241:422,0:0.0:2,0:24.8:1.0:29.5:1.0:1.0:0.0:60.0:421.0:0.9976:0.0:0.3 +6 29760856 . C T 188 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GACCTGTGCTCCTTGACAGC;RSEQ=GCAGACACGGCGGCTCAGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:77:21,56:31,117:148,77:0.3422:2,2:23.9:1.0:30.1:1.0:0.31871:1.41:58.8:37.5:0.3363:0.0:1.7 0/0:153:0:0,0:38,115:153,0:0.0:2,0:24.8:1.0:29.0:1.0:1.0:0.0:59.9:37.25:1.0:0.0:0.3 +6 29769246 . G A 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGCTGCAGTGGTGTCTTCTG;RSEQ=AGAGAAGCAGAGGTACACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:127:45:28,17:59,23:82,45:0.3543:2,2:22.0:1.0:29.9:1.0:0.31871:1.5518:57.8:90.0:0.3571:0.0:1.2 0/0:109:0:0,0:69,40:109,0:0.0:2,0:21.1:1.0:30.6:1.0:1.0:0.0:60.0:218.0:1.0:0.0:0.8 +6 29795566 . C T 212 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01514;LSEQ=CCAATCAGCGTCGCCGCGGT;RSEQ=CTGGTTCTAAAGTCCTCGCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:140:107,33:271,87:358,140:0.2811:2,2:21.4:1.0:29.8:1.0:0.90761:1.04:59.7:22.333:0.2752:0.0:1.1 0/0:341:2:0,2:243,96:339,2:0.0059:2,0:1.0:0.0:23.0:0.0:0.08199:0.0:60.0:4.0:0.006:0.0:2.0 +6 29795913 . A T 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.00782;LSEQ=CCATGGGCTACGTGGACGAC;RSEQ=CGCAGTTCGTGCGGTTCGAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:140:89,51:215,153:368,140:0.2756:2,2:25.9:1.0:31.1:1.0:0.31208:1.24:46.6:45.667:0.2745:0.0:1.2 0/0:338:1:0,1:173,164:337,1:0.003:2,0:1.0:0.0:23.0:0.0:0.48817:0.0:60.0:2.0:0.003:0.0:1.0 +6 29796106 . G T 224 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGAGGCCAGTGAGTAACTCC;RSEQ=GCCCAGGGAGCAGATCACGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:580:160:51,109:145,273:418,160:0.2759:2,2:25.9:1.0:30.7:1.0:0.55656:1.13491:59.2:79.0:0.2787:0.0:3.6 0/0:427:0:0,0:157,269:426,0:0.0:2,0:23.7:1.0:29.6:1.0:1.0:0.0:59.0:105.5:0.9976:0.0:1.0 +6 29796128 . C A 202 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCAGGGAGCAGATCACGAC;RSEQ=CCCACCTCCATGCCCCACGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:402:123:29,94:74,204:278,123:0.306:2,2:25.0:1.0:29.2:1.0:0.53854:1.17532:59.4:23.6:0.3041:0.0:3.9 0/0:275:0:0,0:84,191:275,0:0.0:2,0:20.8:1.0:29.5:1.0:1.0:0.0:59.2:33.375:1.0:0.0:1.1 +6 29796265 . G T 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACCAAAATCCCCGCGGGTG;RSEQ=GTCCGGGCGAGGGCGAGGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:41:32,9:65,49:114,41:0.2645:2,2:22.5:1.0:30.7:1.0:0.02328:2.66:60.0:82.0:0.268:0.0:1.9 0/0:59:0:0,0:46,13:59,0:0.0:2,0:23.8:1.0:30.5:1.0:1.0:0.0:60.0:118.0:1.0:0.0:0.8 +6 29796675 . G T 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00169;SOR=0.0;LSEQ=ACAAGGAGAGGAGGAAAATG;RSEQ=GACCAACACTAGAATATCGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:15:1,14:2,39:41,15:0.2679:1,1:23.5:1.0:30.1:1.0:1.0:1.38:54.9:30.0:0.2679:0.0:1.8 0/0:28:0:0,0:2,26:28,0:0.0:2,0:27.5:1.0:30.6:1.0:1.0:0.0:60.0:27.0:1.0:0.0:1.0 +6 29797155 . G C 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GCTGCTGGAGTGTCCCATGA;RSEQ=AGATGCAAAGTGCTTGAATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:349:111:77,34:142,95:237,111:0.3181:2,2:22.4:1.0:32.0:1.0:0.09645:1.51:51.7:54.5:0.3187:0.0:2.7 0/0:237:0:0,0:143,94:237,0:0.0:2,0:23.6:1.0:30.4:1.0:1.0:0.0:59.5:38.5:1.0:0.0:0.5 +6 29797211 . C T 232 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAGACCCCCCCAAGACACA;RSEQ=GTGACCCACCACCCTGTCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:542:180:87,93:166,196:362,180:0.3321:2,2:27.9:1.0:31.0:1.0:0.64772:1.1:46.4:360.0:0.3352:0.0:2.2 0/0:384:0:0,0:171,211:382,0:0.0:2,0:27.5:1.0:30.1:1.0:1.0:0.0:57.3:94.5:0.9947:0.0:0.4 +6 29855571 . GGGGCCCT G 259 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.1525;LSEQ=CCCTCCTCCTGCTGCTCTCA;RSEQ=GGCCCTGACCCTGACCCAGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1157:271:114,157:389,495:884,271:0.2342:2,2:29.9:1.0:32.1:1.0:0.62408:1.08218:51.3:270.0:0.2377:0.032:1.1 0/1:786:35:16,19:336,410:746,35:0.0445:2,2:30.2:1.0:31.1:1.0:1.0:1.03:48.1:70.0:0.0461:0.0064:1.3 +6 29856198 . C T 59 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.09148;SOR=0.0;LSEQ=CCCCCGCGGGTTGGTCGGGG;RSEQ=AGGGCGGGGCTCGGGGGACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:6:3,3:337,102:439,6:0.0135:2,2:15.5:1.0:23.2:1.0:0.14647:3.29283:50.5:5.0:0.0115:0.0:1.2 0/0:255:0:0,0:186,69:255,0:0.0:2,0:22.8:1.0:31.0:1.0:1.0:0.0:52.5:41.5:1.0:0.0:0.8 +6 29856655 . G C 103 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.05911;SOR=0.13365;LSEQ=GAGGGAGAAGAATCCTCCTG;RSEQ=GTTTCCAGAGAGTGACTCTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:10:3,7:3,11:14,10:0.4167:2,2:20.5:1.0:31.2:1.0:0.66533:1.54:56.5:20.0:0.4167:0.0:1.0 0/1:12:1:0,1:2,8:10,1:0.0833:2,0:28.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0909:0.0:1.0 +6 29893922 . A T 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=ACTCAGGGAGACATTGAGAC;RSEQ=GAGCGCTTGGCACAGGAGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:5:5,0:8,0:8,5:0.3846:0,0:23.8:1.0:30.2:1.0:1.0:0.0:41.8:10.0:0.3846:0.0:4.2 0/0:1:0:0,0:1,0:1,0:0.0:0,0:38.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +6 29895837 . CC GCA 222 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.09635;LSEQ=CTTCCTGTTAGACCTCTCCC;RSEQ=AGACACATATGATCCACCAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:255:128:67,61:64,60:124,128:0.502:2,2:31.9:1.0:31.8:1.0:1.0:1.03:50.9:256.0:0.51:0.0157:4.4 0/1:227:20:9,11:61,67:128,20:0.0881:2,2:34.9:1.0:31.3:1.0:1.0:1.11197:56.5:40.0:0.137:0.0:4.2 +6 29896636 . C T 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.22857;SOR=0.0;LSEQ=ACCTCAGGAGGGCAGTTGGT;RSEQ=CAGGACCCACACCTGCTTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:6:6,0:5,1:6,6:0.5:2,0:22.2:1.0:32.0:1.0:1.0:0.0:56.8:12.0:0.5:0.0:1.3 0/0:3:0:0,0:1,2:3,0:0.0:2,0:14.0:1.0:25.0:1.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +6 29896850 . TCC GATCT 181 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=TGAAGTGGGCTGATCCCTGA;RSEQ=TTGGGATATTGTGGTCGGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:137:49:30,19:46,33:79,49:0.3577:2,2:30.7:1.0:32.3:1.0:0.85339:1.13:57.0:98.0:0.3603:0.0073:1.3 0/0:122:0:0,0:0,6:6,0:0.0:0,0:36.0:1.0:27.5:1.0:1.0:0.0:99.8:8.0:0.0449:0.0:-9.5 +6 29896852 . C T 97 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00125;SOR=0.0;LSEQ=AAGTGGGCTGATCCCTGATC;RSEQ=TTGGGATATTGTGGTCGGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:11:7,4:44,31:75,11:0.0821:2,2:18.3:1.0:28.2:1.0:1.0:1.23:54.5:4.5:0.1084:0.0:1.9 0/0:110:0:0,0:38,39:77,0:0.0:2,0:26.1:1.0:30.3:1.0:1.0:0.0:53.0:37.5:1.0:0.0:0.4 +6 29897036 . G T 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.00057;SOR=0.0;LSEQ=ACACTGGGGGACCTGATGTG;RSEQ=GGGGGTGTTGGGGGCAATAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:174:12:6,6:65,95:160,12:0.069:2,2:10.1:1.0:29.7:1.0:0.55532:1.46:57.8:24.0:0.0719:0.0:2.6 0/0:149:0:0,0:54,80:134,0:0.0:2,0:23.5:1.0:29.4:1.0:1.0:0.0:57.8:15.75:0.9921:0.0:2.1 +6 29902040 . A G 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.07176;SOR=0.17187;LSEQ=TCCGCAGATACCTGGAGAAC;RSEQ=GGAAGGAGACACTGCAGCAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:13:5,8:44,134:178,13:0.0681:2,2:14.0:1.0:31.5:1.0:0.32398:1.9:21.6:26.0:0.0688:0.0:3.1 0/1:81:1:0,1:21,59:80,1:0.0123:2,0:2.0:0.0:30.0:0.0:1.0:0.0:24.0:2.0:0.0127:0.0:2.0 +6 29910507 . CA TG 99 p8 SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00887;SOR=0.0;LSEQ=GCGCCGGGACGAGGGTCGGG;RSEQ=GGTCTCAGCCACTGCTCGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:776:11:7,4:371,389:760,11:0.0142:2,2:7.7:1.0:28.9:1.0:0.37594:1.83:27.0:22.0:0.0144:0.0052:6.7 0/0:475:0:0,0:253,221:474,0:0.0:2,0:24.2:1.0:31.0:1.0:1.0:0.0:51.8:51.667:0.9979:0.0:1.2 +6 29910856 . G A 222 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCCCTCATCCCCCACGGAC;RSEQ=GGCCAGGTCGCCCACAGTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:517:129:28,101:71,317:388,129:0.2495:2,2:24.9:1.0:31.7:1.0:0.43838:1.24:45.3:128.0:0.2485:0.0:4.6 0/0:263:0:0,0:52,211:263,0:0.0:2,0:23.7:1.0:29.9:1.0:1.0:0.0:48.1:86.667:1.0:0.0:2.0 +6 29911272 . T A 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.12402;SOR=0.18877;LSEQ=TGGATGGCACGTGCGTGGAG;RSEQ=GGCTCCGCAGATACCTGGAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:12:3,9:273,389:662,12:0.0178:2,2:8.3:1.0:28.3:1.0:0.37683:2.10328:31.0:11.0:0.0166:0.0:4.3 0/0:294:1:0,1:108,179:287,1:0.0034:2,0:17.0:0.0:26.0:0.0:1.0:0.0:25.0:2.0:0.0035:0.0:6.0 +6 29911329 . G A 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00152;SOR=0.1859;LSEQ=TGCAGCGCACGGGTACCAGG;RSEQ=GCCACGGGGCGCCTCCCTGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:386:27:3,24:70,289:359,27:0.0699:2,2:37.3:1.0:32.1:1.0:0.44312:1.93488:37.4:54.0:0.0714:0.0:3.9 0/1:218:3:0,3:46,169:215,3:0.0138:2,0:39.0:1.0:27.3:1.0:1.0:0.0:40.3:2.0:0.0093:0.0:4.0 +6 29912149 . G C 143 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=4e-05;SOR=0.14251;LSEQ=CATGTGCAGCATGAGGGTCT;RSEQ=CCCAAGCCCCTCACCCTGAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:28:12,16:58,55:113,28:0.1972:2,2:5.1:1.0:29.8:1.0:0.52743:1.40266:22.7:56.0:0.1986:0.0:2.1 0/1:119:4:2,2:51,64:115,4:0.0336:2,2:3.0:1.0:30.0:1.0:1.0:1.25:22.3:8.0:0.0339:0.0:2.0 +6 29912345 . A T 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.17435;LSEQ=TGGTTCTCCTTGGAGCTGTG;RSEQ=TCACTGGAGCTGTGGTCGCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:887:70:27,43:368,449:817,70:0.0789:2,2:8.2:1.0:28.8:1.0:0.31812:1.3049:26.7:34.0:0.0781:0.0:4.9 0/1:816:12:6,6:390,413:803,12:0.0147:2,2:10.4:1.0:27.8:1.0:1.0:1.06:25.3:24.0:0.0149:0.0:4.8 +6 29912652 . CAGA C 95 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.11284;SOR=0.0;LSEQ=CAGGGGAAGGTCCCTGAGGA;RSEQ=CCTCAGGAGGGCTATTGGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:100:9:8,1:47,9:56,9:0.09:2,2:8.3:1.0:30.0:1.0:1.0:1.52:43.2:18.0:0.0909:0.08:3.1 0/0:37:0:0,0:22,2:24,0:0.0:2,0:20.6:1.0:30.2:1.0:1.0:0.0:55.0:48.0:0.6486:0.0:1.2 +6 29913483 . T C 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.17924;SOR=0.0;LSEQ=CTGAGGTGTCTCCATCTCTG;RSEQ=CTCAACTTCATGGTGCACTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:37:9:1,8:0,28:28,9:0.2432:1,2:21.8:1.0:31.8:1.0:0.24324:0.0:55.0:18.0:0.2432:0.0:1.0 0/0:8:0:0,0:0,8:8,0:0.0:0,0:20.9:1.0:29.1:1.0:1.0:0.0:57.0:16.0:1.0:0.0:1.8 +6 29917801 . G A 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.14256;SOR=0.0;LSEQ=ACTCCTAGGTAATGTCCCAC;RSEQ=TCTCTGCTTCTGTGCTCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:4,1:21,0:21,5:0.1923:1,2:27.4:1.0:30.0:1.0:0.19231:0.0:49.2:10.0:0.2083:0.0:1.4 0/0:14:0:0,0:14,0:14,0:0.0:1,0:24.5:1.0:29.6:1.0:1.0:0.0:59.4:28.0:1.0:0.0:0.2 +6 29925438 . C T 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.08012;LSEQ=TCTGGAGAGGAGCAGAGATA;RSEQ=ACATGCCATGTGCAGCACGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:336:105:63,42:131,100:231,105:0.3125:2,2:24.1:1.0:29.3:1.0:0.63403:1.14:58.7:104.0:0.3114:0.0:1.2 0/1:257:9:6,3:144,104:248,9:0.035:2,2:29.1:1.0:30.0:1.0:0.73902:1.44:56.0:18.0:0.0353:0.0:1.0 +6 29974083 . CG C 76 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCGTTTGTCACAGGAGGAG;RSEQ=GGGTCAGGGCGAAGTCCCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:5,1:6,1:7,6:0.4615:2,2:31.0:1.0:29.7:1.0:1.0:1.18321:53.5:5.0:0.4545:0.0:0.7 0/0:1:0:0,0:1,0:1,0:0.0:0,0:9.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 +6 29975766 . G C 111 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.18947;SOR=0.0;LSEQ=CACTCAGATCAGGACCAGAA;RSEQ=TCCCTGCTACCCTGCTCAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:9,2:6,1:7,11:0.6111:2,2:24.3:1.0:32.1:1.0:1.0:1.3127:38.5:22.0:0.6471:0.0:2.5 0/0:2:0:0,0:1,1:2,0:0.0:2,0:10.5:1.0:33.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +6 29975775 . A C 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.18947;SOR=0.0;LSEQ=CAGGACCAGAAGTCCCTGCT;RSEQ=CCCTGCTCAGAGACTAGAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:11:9,2:6,1:7,11:0.6111:2,2:26.5:1.0:30.7:1.0:1.0:1.3127:38.5:10.0:0.625:0.0:2.3 0/0:2:0:0,0:1,1:2,0:0.0:2,0:10.5:1.0:27.0:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +6 30459165 . C T 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATGTGCAGCATGAGGGGCTA;RSEQ=CCGAGCCCGTCACCCTGAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:435:42:21,21:218,175:393,42:0.0966:2,2:30.1:1.0:30.6:1.0:0.51779:1.24507:53.3:84.0:0.0981:0.0:1.2 0/0:457:0:0,0:236,221:457,0:0.0:2,0:29.8:1.0:30.7:1.0:1.0:0.0:50.7:75.167:1.0:0.0:0.2 +6 30670292 . C T 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07962;LSEQ=AGCCACCTCTTTAACTGCCA;RSEQ=TGCCACCTCACCCAGACCCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:744:28:17,11:466,250:716,28:0.0376:2,2:23.7:1.0:30.1:1.0:0.68773:1.20579:60.0:56.0:0.0379:0.0:1.0 0/0:645:2:0,2:382,261:643,2:0.0031:2,0:12.0:1.0:27.5:1.0:0.16589:0.0:60.0:4.0:0.0031:0.0:1.0 +6 30672326 . T C 282 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0968;LSEQ=TGGGCTCAGGGGTGACAGGT;RSEQ=GGTCTGTGGAGGTGGAAGGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1793:654:313,341:553,584:1137,654:0.3648:2,2:25.3:1.0:30.2:1.0:0.76838:1.03162:45.4:35.333:0.3653:0.0:2.0 0/1:1558:82:37,45:741,734:1475,82:0.0526:2,2:24.5:1.0:29.5:1.0:0.42724:1.22765:44.6:81.0:0.0532:0.0:2.0 +6 30954245 . T C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAACTCTGAGTTCAGCACAG;RSEQ=GTCCAGTGGGATCAGCATAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:4,1:2,0:2,5:0.7143:0,2:33.0:1.0:32.4:1.0:1.0:0.0:55.4:10.0:0.7143:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 31053516 . G C 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGCCTCCTCCTGGGGCCATC;RSEQ=TCCCAGGGGTTATGCCTCGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:11,6:0.3529:0,0:23.2:1.0:32.8:1.0:1.0:0.0:60.0:12.0:0.375:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 31053521 . A G 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCTCCTGGGGCCATCGTCCC;RSEQ=GGGGTTATGCCTCGCTGCTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:0,6:0,11:11,6:0.3529:0,0:22.3:1.0:31.8:1.0:1.0:0.0:60.0:12.0:0.3529:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 31237802 . A G 254 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCAAGGACAGCTAGGACA;RSEQ=CCAGGACAGCCAGGCCAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:259:215:152,63:33,11:44,215:0.8301:2,2:25.7:1.0:32.9:1.0:0.7144:1.24237:34.1:42.0:0.83:0.0:4.8 0/0:199:0:0,0:37,19:56,0:0.0:2,0:26.0:1.0:28.5:1.0:1.0:0.0:60.0:112.0:0.9825:0.0:0.1 +6 31238492 . C A 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.05;SOR=0.0;LSEQ=CCTGACCTGAGTGGAGGCTG;RSEQ=AGGACTCAGAAAAGCTGGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:12:0,12:0,2:2,12:0.8571:0,0:27.3:1.0:32.0:1.0:1.0:0.0:58.2:24.0:0.8571:0.0:2.9 0/0:2:0:0,0:0,2:2,0:0.0:0,0:15.0:1.0:33.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +6 31238524 . G A 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGCTGGAATCAAACCTTCA;RSEQ=ACACATTGAGTGTGAGGCAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:19.8:1.0:32.0:1.0:1.0:0.0:59.8:10.0:0.8333:0.0:4.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 31238801 . C G 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0001;SOR=0.15308;LSEQ=CCCTCCTCGTGGGAGGCCAT;RSEQ=CCGGGAGATCTATAGGAGAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:120:30:29,1:82,7:89,30:0.25:2,1:22.1:1.0:32.2:1.0:0.67768:2.46:42.5:29.0:0.25:0.0:4.3 0/1:83:4:4,0:72,7:79,4:0.0482:2,0:28.0:1.0:32.0:1.0:1.0:0.0:41.8:8.0:0.0488:0.0:4.5 +6 31238815 . A G 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00625;SOR=0.0;LSEQ=GGCCATCCCGGGAGATCTAT;RSEQ=GGAGATGGGGAAGGCTCCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:10:8,2:70,7:77,10:0.0543:2,2:8.9:1.0:27.1:1.0:0.27524:2.46602:34.5:9.0:0.1059:0.0:3.2 0/0:130:0:0,0:90,17:107,0:0.0:2,0:20.6:1.0:28.6:1.0:1.0:0.0:43.7:52.5:1.0:0.0:1.6 +6 31239171 . GC AGT 179 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=AGTCCCCCGAGCCCCGCCCC;RSEQ=CCCGACCAACCCGCGGGGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:95:58:13,45:8,18:26,58:0.6105:2,2:10.8:1.0:30.6:1.0:0.42597:1.53029:31.3:57.0:0.6196:0.2842:4.0 0/0:41:0:0,0:0,3:3,0:0.0:0,0:9.0:1.0:34.9:1.0:1.0:0.0:42.7:6.0:0.0909:0.0:-6.7 +6 31239279 . T C 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGGGTTCCGCAGATCCACCT;RSEQ=GGGGTGGATCTCAGACGGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:57:26:23,3:27,3:30,26:0.4561:2,2:12.1:1.0:28.8:1.0:1.0:1.17054:43.2:5.5:0.4314:0.0:3.9 0/0:28:0:0,0:15,3:18,0:0.0:2,0:24.0:1.0:30.8:1.0:1.0:0.0:59.8:36.0:1.0:0.0:0.6 +6 31239602 . G A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.08253;LSEQ=AAGCGGGGCTCTCCGCGGCC;RSEQ=GGCCGGGACACGGCGGTGTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:272:80:41,39:87,105:192,80:0.2941:2,2:16.8:1.0:30.7:1.0:0.42422:1.27:35.8:79.0:0.2959:0.0:3.3 0/1:332:11:5,6:156,165:321,11:0.0331:2,2:20.0:1.0:29.7:1.0:1.0:1.13411:39.9:22.0:0.0333:0.0:3.4 +6 31239616 . CG AT 163 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.09495;LSEQ=GCGGCCGGGCCGGGACACGG;RSEQ=GTGTCGAAATACCTCATGGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:232:39:21,18:90,103:193,39:0.1681:2,2:39.2:1.0:31.0:1.0:0.48306:1.33:36.6:78.0:0.1696:0.0172:4.8 0/1:320:6:2,4:149,164:313,6:0.0188:2,2:39.2:1.0:29.2:1.0:0.68724:1.8138:43.8:12.0:0.0189:0.0031:4.5 +6 31239621 . TC AA 160 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08866;LSEQ=CGGGCCGGGACACGGCGGTG;RSEQ=GAAATACCTCATGGAGTGGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:235:36:21,15:95,104:199,36:0.1532:2,2:44.0:1.0:31.0:1.0:0.27927:1.53:38.8:72.0:0.1538:0.0043:4.2 0/1:318:5:1,4:146,167:313,5:0.0157:2,2:45.2:1.0:31.0:1.0:0.37823:3.48504:47.2:10.0:0.0159:0.0:4.0 +6 31239630 . C T 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08925;LSEQ=ACACGGCGGTGTCGAAATAC;RSEQ=TCATGGAGTGGGAGCCTGGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:35:20,15:92,99:191,35:0.1549:2,2:42.9:1.0:31.4:1.0:0.36186:1.43:38.2:34.0:0.1532:0.0:4.3 0/1:312:5:1,4:139,168:307,5:0.016:2,2:38.6:1.0:31.0:1.0:0.38421:3.29855:47.2:10.0:0.0162:0.0:4.0 +6 31239727 . C A 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.14492;LSEQ=TGCGCCCTCGCCGGGAGGGC;RSEQ=CCTCGCTCCTCTCCGCAGAG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:475:143:85,58:171,159:330,143:0.3011:2,2:27.0:1.0:30.2:1.0:0.13293:1.36:45.9:46.667:0.307:0.0:4.7 0/1:307:18:12,6:177,112:289,18:0.0586:2,2:25.9:1.0:29.2:1.0:0.80427:1.26:45.4:36.0:0.06:0.0:4.8 +6 31322204 . C CCT 70 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.0399;SOR=0.0;LSEQ=CAGGCCTTTCCCCTCTGCCC;RSEQ=ACCCACCCCCAGACCCGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:6:6,0:41,5:46,6:0.0625:2,0:23.7:1.0:27.1:1.0:1.0:0.0:51.2:12.0:0.0659:0.0:5.5 0/0:70:0:0,0:57,13:70,0:0.0:2,0:13.8:1.0:29.0:1.0:1.0:0.0:56.8:22.333:1.0:0.0:2.4 +6 31322205 . A CTC 136 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=0.0;SOR=0.0;LSEQ=AGGCCTTTCCCCTCTGCCCC;RSEQ=CCCACCCCCAGACCCGCCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:26:19,7:41,5:46,26:0.2708:2,2:19.2:1.0:29.1:1.0:0.10386:2.97087:58.0:52.0:0.2857:0.125:4.3 0/0:70:0:0,0:57,13:70,0:0.0:2,0:13.8:1.0:29.0:1.0:1.0:0.0:56.8:22.333:1.0:0.0:2.4 +6 31323020 . T C 247 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04878;LSEQ=TCTGGGAAAGGAGGGGAAGA;RSEQ=GAGGGGCCCTGACCCTGCTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:364:266:129,137:41,56:97,266:0.7308:2,2:23.2:1.0:30.7:1.0:0.34183:1.29:39.8:52.2:0.7291:0.0:2.7 0/1:258:30:13,17:109,119:228,30:0.1163:2,2:20.8:1.0:30.1:1.0:0.70021:1.19697:38.0:60.0:0.1176:0.0:2.6 +6 31323414 . G A 220 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01492;LSEQ=AGGCGCTTTGCATCTTTCAT;RSEQ=GGACACCCTAGGACCACCCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:530:160:55,105:125,245:370,160:0.3019:2,2:21.5:1.0:30.1:1.0:0.92057:1.03:57.2:39.0:0.3012:0.0:2.1 0/0:470:3:3,0:194,273:467,3:0.0064:2,0:6.7:1.0:15.7:1.0:0.07299:0.0:48.3:0.5:0.0022:0.0:3.3 +6 31324143 . GT TA 78 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00058;SOR=0.0;LSEQ=TAATCCTTGCCGTCGTAGGC;RSEQ=ACTGGTCATGCCCGCGGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:113:6:3,3:53,53:106,6:0.0531:2,2:14.0:1.0:30.4:1.0:1.0:1.0:39.8:12.0:0.0536:0.0:4.7 0/0:272:0:0,0:142,130:272,0:0.0:2,0:26.4:1.0:30.0:1.0:1.0:0.0:38.6:135.0:1.0:0.0:2.2 +6 31324941 . C T 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01918;LSEQ=CGCCATGACCAGCATCTCGG;RSEQ=GTCTGAGGAGACTCTGAGTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:678:92:29,63:244,340:584,92:0.1357:2,2:32.4:1.0:30.1:1.0:0.06776:1.55803:42.2:184.0:0.1375:0.0:5.9 0/0:668:2:0,2:304,362:666,2:0.003:2,0:25.5:1.0:30.5:1.0:0.50329:0.0:48.5:4.0:0.003:0.0:1.0 +6 31325159 . GC AA 111 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00241;SOR=0.0;LSEQ=TGCGCCTCCCCATTGCAGAC;RSEQ=GGCCCTCGGAGCCTGAGACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:1,5:6,11:0.6471:2,0:14.2:1.0:32.3:1.0:0.35294:0.0:32.0:22.0:0.6471:0.2353:5.4 0/0:9:0:0,0:0,8:8,0:0.0:0,0:25.0:1.0:31.0:1.0:1.0:0.0:52.0:16.0:0.8889:0.0:0.9 +6 31325164 . C T 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01796;SOR=0.0;LSEQ=CTCCCCATTGCAGACGCGGC;RSEQ=CTCGGAGCCTGAGACCCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:0,7:1,5:6,7:0.5385:2,0:13.9:1.0:31.3:1.0:0.46154:0.0:28.4:14.0:0.5385:0.0:5.4 0/0:8:0:0,0:0,8:8,0:0.0:0,0:24.1:1.0:29.8:1.0:1.0:0.0:52.0:16.0:1.0:0.0:0.9 +6 31345484 . G A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00023;SOR=0.04088;LSEQ=AAGGCCTGCTGCAGCCTCCC;RSEQ=CTGAGGTCTTGAAACCATCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:12:12,0:10,0:10,12:0.5455:0,0:21.8:1.0:31.7:1.0:1.0:0.0:60.0:24.0:0.5455:0.0:1.0 0/1:23:1:1,0:22,0:22,1:0.0435:1,0:41.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0455:0.0:1.0 +6 31349819 . C A 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.04762;SOR=0.0;LSEQ=AAGGGGCGGCATGAAGAAAT;RSEQ=CTGCATCTCAGTCCCTCACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:22.8:1.0:28.8:1.0:1.0:0.0:52.4:10.0:0.8333:0.0:2.6 0/0:3:0:0,0:2,1:3,0:0.0:2,0:6.0:1.0:31.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +6 32169795 . TTCC T 67 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=3.0;MSILEN=3.0;SSF=0.043;SOR=0.0;LSEQ=ACTCAGAGCCATCTACGTCC;RSEQ=TCCTCCTCTCACCCACCCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:540:6:1,5:418,113:531,6:0.0111:2,2:11.8:1.0:26.0:1.0:0.00237:18.36814:60.0:5.0:0.0094:0.0074:0.7 0/0:391:0:0,0:288,101:389,0:0.0:2,0:21.1:1.0:29.3:1.0:1.0:0.0:59.9:63.833:0.9974:0.0:0.1 +6 32182243 . G GAT 89 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=19;MSI=10.0;MSILEN=2.0;SSF=0.1591;SOR=0.0;LSEQ=CATCTATATATCTAGTTGGA;RSEQ=ATATATATATATATATATAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:0,8:0,19:19,8:0.2759:1,0:36.9:1.0:29.7:1.0:1.0:0.0:60.0:16.0:0.2759:0.0345:0.1 0/0:9:0:0,0:0,9:9,0:0.0:0,0:16.3:1.0:31.1:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.2 +6 32185246 . T G 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00743;SOR=0.0;LSEQ=TGTGACTTTGGGCAAGCTGG;RSEQ=CAACCCTCTAGGCCCCAGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:2,7:0,19:19,9:0.3214:1,2:29.1:1.0:32.9:1.0:0.09524:0.0:60.0:18.0:0.3333:0.0:1.3 0/0:18:0:0,0:1,17:18,0:0.0:1,0:27.5:1.0:27.5:1.0:1.0:0.0:59.2:17.0:1.0:0.0:0.3 +6 32188713 . C G 240 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACGGAGACATCCTGCCCTG;RSEQ=CCAGAGAGAGGGGCGGCCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:191:88,103:188,251:439,191:0.3013:2,2:22.0:1.0:31.8:1.0:0.48488:1.14:59.8:46.75:0.3031:0.0:1.1 0/0:443:0:0,0:213,227:440,0:0.0:2,0:23.7:1.0:30.7:1.0:1.0:0.0:60.0:54.0:0.9931:0.0:0.3 +6 32188823 . G A 251 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTGGCAGGTGCCCCCATTC;RSEQ=AACAGCCCCTAGGAGGGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:873:306:181,125:311,254:565,306:0.3505:2,2:25.1:1.0:30.5:1.0:0.25268:1.18:60.0:50.0:0.3509:0.0:1.1 0/0:680:0:0,0:361,319:680,0:0.0:2,0:25.4:1.0:29.7:1.0:1.0:0.0:60.0:96.143:1.0:0.0:0.2 +6 32189192 . G A 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCTCACTCTGGATTATCTCT;RSEQ=GGTCTCATTTTCATATTTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:139:36:0,36:2,101:103,36:0.259:1,1:22.1:1.0:32.8:1.0:1.0:0.0:58.9:72.0:0.2609:0.0:1.3 0/0:76:0:0,0:6,70:76,0:0.0:2,0:25.7:1.0:30.4:1.0:1.0:0.0:60.0:75.0:1.0:0.0:0.1 +6 32190028 . A G 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGGAGATTAAAGGGGCTAG;RSEQ=ACAGGCATCAGGATGGTGCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1.0:0,0:25.6:1.0:29.9:1.0:1.0:0.0:55.5:7.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 32190484 . G A 288 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.00067;LSEQ=CTGGGGAGCCCTAGGGGAGC;RSEQ=GGAAGCAGGGCTTGGCAGCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:954:626:297,329:154,174:328,626:0.6562:2,2:25.8:1.0:31.1:1.0:0.89162:1.02:59.9:77.25:0.6581:0.0:1.1 0/0:803:1:1,0:383,417:800,1:0.0012:2,0:1.0:0.0:25.0:0.0:0.4794:0.0:60.0:2.0:0.0013:0.0:1.0 +6 32877176 . C T 57 p8;q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.06386;SOR=0.0;LSEQ=TCTTGAATATTCACTATAAG;RSEQ=CTGATGCTATGCGAGGTGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:436:5:0,5:225,206:431,5:0.0115:2,0:6.4:1.0:24.6:1.0:0.0259:0.0:60.0:4.0:0.0094:0.0:2.0 0/0:388:0:0,0:191,197:388,0:0.0:2,0:23.5:1.0:30.5:1.0:1.0:0.0:60.0:54.429:1.0:0.0:0.5 +6 33290827 . A T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.15806;SOR=0.0;LSEQ=TTCCTGTGGCCGGAGGTGAC;RSEQ=GTAGGCCCGCCCCGCGAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:110:5:0,5:4,101:105,5:0.0455:1,0:17.8:1.0:31.2:1.0:1.0:0.0:60.0:10.0:0.0463:0.0:1.0 0/0:68:0:0,0:2,66:68,0:0.0:1,0:25.4:1.0:30.7:1.0:1.0:0.0:60.0:33.0:1.0:0.0:0.7 +6 36648084 . C CGTGT 92 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=38;MSI=21.0;MSILEN=2.0;SSF=0.55045;SOR=0.0;LSEQ=CGCGTGCGTGTCTGCGCGGG;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:8:8,0:13,0:13,8:0.3077:1,0:11.0:1.0:30.9:1.0:1.0:0.0:52.9:16.0:0.32:0.2308:1.3 0/0:4:0:0,0:4,0:4,0:0.0:0,0:25.0:1.0:29.3:1.0:1.0:0.0:51.8:8.0:1.0:0.0:0.8 +6 36650547 . G A 226 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CATGGGCAAACTCACTCTCC;RSEQ=TTTTCCCTCTCCTGAAGGGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1074:163:79,84:442,468:910,163:0.1518:2,2:26.1:1.0:30.8:1.0:1.0:1.00422:60.0:162.0:0.1524:0.0:1.1 0/0:938:0:0,0:470,465:935,0:0.0:2,0:25.4:1.0:30.3:1.0:1.0:0.0:60.0:132.571:0.9968:0.0:0.4 +6 42701641 . G A 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=GACAAAGAGATAAAGAGAAA;RSEQ=CAGCTGGGCCTGGGGGACCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1.0:0,2:16.0:1.0:30.0:1.0:1.0:0.0:30.0:10.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 43738977 . C T 317 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03614;LSEQ=GCCGGCCCCGGTCGGGCCTC;RSEQ=GAAACCATGAACTTTCTGCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1457:1163:631,532:157,135:292,1163:0.7982:2,2:24.7:1.0:31.2:1.0:0.8956:1.02:60.0:76.533:0.7967:0.0:1.2 0/1:1097:137:70,67:509,451:960,137:0.1249:2,2:25.7:1.0:29.9:1.0:0.7147:1.08015:59.9:136.0:0.1244:0.0:1.3 +6 43746352 . CT C 85 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=5.0;MSILEN=1.0;SSF=0.09435;SOR=0.0;LSEQ=CCAGGGTTAAGCATGCTGTA;RSEQ=TTTTGGCCCCCGTCCAGCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:457:6:2,4:84,367:451,6:0.0131:2,2:25.7:1.0:33.0:1.0:0.31546:2.18:60.0:12.0:0.0133:0.0022:0.2 0/0:252:0:0,0:61,189:250,0:0.0:2,0:23.0:1.0:29.7:1.0:1.0:0.0:60.0:124.0:0.992:0.0:0.1 +6 43748328 . C G 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATGCCTCCCCAGAGACCA;RSEQ=CTGCCTCCTGACACTTCCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:142:56:54,2:81,4:85,56:0.3944:1,1:23.6:1.0:32.9:1.0:1.0:1.33:59.8:27.0:0.3857:0.0:1.2 0/0:65:0:0,0:63,2:65,0:0.0:1,0:23.0:1.0:31.3:1.0:1.0:0.0:60.0:31.5:1.0:0.0:0.2 +6 46910123 . C T 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AATGAATCCCTAACGCAGCA;RSEQ=GCTATTAGAGATGCTTAAGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1.0:0,0:24.3:1.0:31.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:2.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 46910144 . G A 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCTATTAGAGATGCTTAAGA;RSEQ=GGTAAAAGCATGGGCTATGG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:16:16,0:0,0:0,16:1.0:0,1:29.1:1.0:30.8:1.0:1.0:0.0:60.0:32.0:1.0:0.0:1.8 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 54635613 . G C 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=16.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATGAGGACTGGGCGGGGGGG;RSEQ=GGGGGGGGCTTTCTTTGTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:160:47:19,28:58,54:112,47:0.2938:2,2:12.9:1.0:26.1:1.0:0.22499:1.57825:55.8:3.7:0.2552:0.0:1.4 0/0:254:0:0,0:131,107:238,0:0.0:2,0:16.7:1.0:28.8:1.0:1.0:0.0:48.4:18.833:1.0:0.0:0.9 +6 54873784 . A G 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGGATTCCTCAGAACTACC;RSEQ=GGAGTAGAGGCTAAGTCTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:5,0:6,8:14,5:0.2632:2,0:18.8:1.0:28.8:1.0:0.04455:0.0:31.2:10.0:0.2632:0.0:2.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:28.0:0.0:32.0:0.0:1.0:0.0:31.0:2.0:1.0:0.0:1.0 +6 54873908 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.5;SOR=0.0;LSEQ=GAGTTATTGGAGATCCTGCA;RSEQ=GAAAGCCCCACCCACTGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:6:2,4:4,4:8,6:0.4286:2,2:29.2:1.0:31.7:1.0:0.62704:1.90258:59.5:12.0:0.4286:0.0:1.0 0/0:2:0:0,0:0,2:2,0:0.0:0,0:15.5:1.0:32.0:0.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +6 54874135 . A G 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTTAGGCAGTTGCAAGTCCC;RSEQ=GTGCTGGCTGCTACCCCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:2,3:2,4:6,5:0.4545:2,2:17.8:1.0:29.6:1.0:1.0:1.3:43.8:10.0:0.5:0.0:2.2 0/0:1:0:0,0:0,1:1,0:0.0:0,0:5.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +6 58777300 . T G 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.00723;SOR=0.0;LSEQ=TCAGAATCTGCTTTGTGATG;RSEQ=GTGCGTTCAACTCATAGAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:2,5:5,5:10,7:0.4118:2,2:24.3:1.0:30.9:1.0:0.62207:2.36758:44.6:14.0:0.4118:0.0:4.4 0/0:16:0:0,0:8,8:16,0:0.0:2,0:9.1:1.0:29.0:1.0:1.0:0.0:32.6:32.0:1.0:0.0:2.6 +6 58777419 . T C 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.09406;LSEQ=GCCCACAGTAGAAAAGGAAA;RSEQ=AACTTCACCTAAAACCTAGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:32:16,16:16,8:24,32:0.5714:2,2:21.5:1.0:32.3:1.0:0.27854:1.97518:45.9:31.0:0.5741:0.0:1.7 0/1:55:6:4,2:28,21:49,6:0.1091:2,2:23.5:1.0:32.2:1.0:1.0:1.49:37.5:12.0:0.1091:0.0:2.3 +6 58778828 . T A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.01528;SOR=0.15247;LSEQ=CAATCTCAGAAACGACTTTG;RSEQ=GATGTCTGCATTCAACTCAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:8:3,5:17,21:38,8:0.1702:2,2:30.1:1.0:31.3:1.0:1.0:1.34057:47.4:16.0:0.1739:0.0:1.8 0/1:67:2:1,1:31,34:65,2:0.0299:2,2:5.0:1.0:27.5:1.0:1.0:1.1:35.0:4.0:0.0299:0.0:2.0 +6 58779032 . T G 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06193;SOR=0.0;LSEQ=GTCACAGAGTGGAACCTTCC;RSEQ=TTGGATAGAGCAGTTTGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:5:2,3:31,24:55,5:0.0833:2,2:10.2:1.0:31.8:1.0:0.64935:1.91607:53.2:10.0:0.0862:0.0:2.6 0/0:50:0:0,0:25,25:50,0:0.0:2,0:24.1:1.0:29.6:1.0:1.0:0.0:54.2:49.0:1.0:0.0:2.1 +6 80564836 . C T 79 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00466;SOR=0.0;LSEQ=CAGTTTCCCAAGCAGGACTT;RSEQ=CCCTAAACCAGAAGAAACAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:4,2:0,0:0,6:1.0:0,2:15.0:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.3 0/1:7:1:1,0:5,1:6,1:0.1429:2,0:22.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.1667:0.0:1.0 +6 89795551 . G C 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGACACCTTAGAAAGTAACA;RSEQ=TGAGTTGAGCTGGGCATGGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:5:0,5:0,5:5,5:0.5:0,0:15.0:1.0:33.6:1.0:1.0:0.0:60.0:10.0:0.5:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 90009220 . G A 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTGTAGGACAAAAAAGTTG;RSEQ=CAGCTGCAGGGCCTGTCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:239:21:12,9:150,68:218,21:0.0879:2,2:17.3:1.0:28.4:1.0:0.32887:1.65073:60.0:20.0:0.0858:0.0:1.7 0/0:217:0:0,0:142,75:217,0:0.0:2,0:25.5:1.0:30.4:1.0:1.0:0.0:60.0:71.333:1.0:0.0:0.8 +6 93968294 . A ACTGT 80 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAGAAGTTACGCTTTCCTAA;RSEQ=CTGTTAAACAGGCTACTATT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:0,6:0,12:12,6:0.3333:0,0:25.3:1.0:31.1:1.0:1.0:0.0:58.0:12.0:0.3333:0.1111:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 93973735 . T C 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACAACTTACTAGAGTTAAA;RSEQ=TTACTGTTCATAGTTATGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:290:43:1,42:8,239:247,43:0.1483:1,1:22.8:1.0:33.1:1.0:1.0:1.40438:59.2:86.0:0.1498:0.0:1.8 0/0:192:0:0,0:9,183:192,0:0.0:1,0:22.7:1.0:29.8:1.0:1.0:0.0:60.0:384.0:1.0:0.0:0.5 +6 93973784 . G T 64 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.1796;SOR=0.0;LSEQ=GTAATAATATAGCGATTCAC;RSEQ=ATTAAAATTGCAAAGAAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:135:6:0,6:3,126:129,6:0.0444:1,0:27.2:1.0:25.0:1.0:1.0:0.0:60.0:5.0:0.0379:0.0:1.5 0/0:61:0:0,0:1,60:61,0:0.0:1,0:21.9:1.0:31.7:1.0:1.0:0.0:60.0:122.0:1.0:0.0:0.1 +6 94066172 . C T 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.52632;SOR=0.0;LSEQ=ACCTTGTGATCTGCCCGCCT;RSEQ=GGCCTCCCAAAATGCTGGGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:6,0:12,0:12,6:0.3333:0,0:23.3:1.0:33.0:0.0:1.0:0.0:46.7:12.0:0.3333:0.0:1.0 0/0:3:0:0,0:3,0:3,0:0.0:0,0:21.7:1.0:30.7:1.0:1.0:0.0:58.7:6.0:1.0:0.0:0.7 +6 94066446 . G T 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0274;LSEQ=AAAACATACCTGCTTGACCA;RSEQ=TGGTGATACTGACAGCAGCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1532:77:48,29:866,589:1455,77:0.0503:2,2:24.5:1.0:30.6:1.0:0.72088:1.13:60.0:76.0:0.0501:0.0:1.2 0/0:1382:2:1,1:820,560:1380,2:0.0014:2,2:7.0:1.0:29.5:1.0:1.0:1.46384:60.0:4.0:0.0015:0.0:1.0 +6 94068208 . G C 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAATTGTATTATTTAGCAAG;RSEQ=AATCAAATATTAAATGTGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:357:28:6,22:32,297:329,28:0.0784:2,2:25.7:1.0:32.3:1.0:0.09997:2.52:60.0:56.0:0.0795:0.0:1.1 0/0:259:0:0,0:22,237:259,0:0.0:2,0:23.8:1.0:30.7:1.0:1.0:0.0:60.0:50.8:1.0:0.0:0.1 +6 100498638 . G T 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0286;SOR=0.11955;LSEQ=CACCATCATCATCATCTTCG;RSEQ=CATTATCATCATCATCTTAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:97:11:4,7:29,57:86,11:0.1134:2,2:26.5:1.0:27.7:1.0:1.0:1.12:59.6:4.5:0.0947:0.0:1.5 0/1:67:1:0,1:31,35:66,1:0.0149:2,0:28.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0152:0.0:1.0 +6 100498976 . C T 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTGCTTCAACAATGTGCAA;RSEQ=TTATCCTTCGCACCAGCCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:199:33:17,16:93,73:166,33:0.1658:2,2:25.1:1.0:31.3:1.0:0.70296:1.19793:44.4:66.0:0.1667:0.0:1.3 0/0:226:0:0,0:114,112:226,0:0.0:2,0:27.7:1.0:31.6:1.0:1.0:0.0:56.2:452.0:1.0:0.0:0.1 +6 100977940 . T C 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00192;SOR=0.0;LSEQ=TATTCTGGTATAATTTGGTA;RSEQ=TTAACATACATTAATTCCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:28:16:16,0:11,0:11,16:0.5714:0,1:29.4:1.0:30.4:1.0:1.0:0.0:60.0:7.0:0.5385:0.0:1.3 0/0:10:0:0,0:10,0:10,0:0.0:0,0:10.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:5.0 +6 106051478 . G A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.10131;SOR=0.0;LSEQ=GCTGAAATATATCAGTAACA;RSEQ=TATTAAATAATGTGTGTATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:6,1:6,0:6,7:0.5385:0,2:28.1:1.0:31.6:1.0:1.0:0.0:60.0:14.0:0.5385:0.0:1.0 0/0:5:0:0,0:5,0:5,0:0.0:0,0:22.2:1.0:33.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.0 +6 106051695 . A G 217 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTTCAGAAGACTTTTGATC;RSEQ=TAATTTTGGGGTTAATAGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:350:136:74,62:116,98:214,136:0.3886:2,2:25.1:1.0:30.7:1.0:1.0:1.01:60.0:135.0:0.3879:0.0:1.7 0/0:390:0:0,0:205,183:388,0:0.0:2,0:25.7:1.0:29.5:1.0:1.0:0.0:60.0:76.6:0.9948:0.0:0.4 +6 106543620 . G A 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01293;LSEQ=TTTTTGGAGGGTAAGTAAGG;RSEQ=AAATTTCTTCAGACCCATTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:332:61:19,42:88,183:271,61:0.1837:2,2:26.2:1.0:30.8:1.0:0.88068:1.0628:60.0:60.0:0.1835:0.0:1.2 0/0:346:1:1,0:134,211:345,1:0.0029:2,0:1.0:0.0:22.0:0.0:0.39017:0.0:60.0:2.0:0.0029:0.0:2.0 +6 106553096 . G A 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=CAAGAGCTCCAGCCCTCACA;RSEQ=CAGCCCTGGGAATACGGTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:948:92:40,52:381,474:855,92:0.097:2,2:27.8:1.0:29.6:1.0:0.9122:1.0449:60.0:29.667:0.0957:0.0:1.2 0/0:919:0:0,0:421,498:919,0:0.0:2,0:24.4:1.0:31.0:1.0:1.0:0.0:60.0:60.267:1.0:0.0:0.2 +6 110700229 . T C 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.01522;LSEQ=CGGGGCTACCCTGCAGGATC;RSEQ=CCAATAATGCCAGCCAGAGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:17:16:7,9:0,0:0,16:0.9412:0,2:24.6:1.0:29.4:1.0:1.0:0.0:60.0:15.0:0.9375:0.0:1.1 0/1:13:2:0,2:5,6:11,2:0.1538:2,0:22.0:1.0:28.5:1.0:0.48718:0.0:60.0:4.0:0.1538:0.0:1.0 +6 110700656 . A G 80 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.00466;SOR=0.0;LSEQ=ATGAATAGGGCCTGAAGTGA;RSEQ=CCCCCAGCAACCTGCAGCAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:2,4:0,0:0,6:1.0:0,2:27.8:1.0:31.3:1.0:1.0:0.0:45.5:12.0:1.0:0.0:1.2 0/1:7:1:1,0:4,2:6,1:0.1429:2,0:47.0:0.0:34.0:0.0:1.0:0.0:36.0:2.0:0.1429:0.0:1.0 +6 112029505 . G C 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.28571;SOR=0.0;LSEQ=CTCTTGGTAGGGGGCATTTT;RSEQ=CTTGGTTAGTGTCCTTAACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:24.0:1.0:30.4:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.0 0/0:1:0:0,0:1,0:1,0:0.0:0,0:41.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +6 115553830 . C T 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00062;SOR=0.05376;LSEQ=AAGGGAGAGGCAATGTTGCC;RSEQ=AACTCCAGAGGTTGGTATAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:14:7,7:10,8:18,14:0.4375:2,2:30.9:1.0:30.1:1.0:1.0:1.24128:29.7:28.0:0.4375:0.0:1.1 0/1:26:1:1,0:14,11:25,1:0.0385:2,0:43.0:0.0:30.0:0.0:1.0:0.0:44.0:2.0:0.04:0.0:1.0 +6 117629650 . A T 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GTGTGTATACTCTCTCTCTC;RSEQ=CACACACACACATACACTCG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:2,0:2,6:0.75:0,0:28.7:1.0:32.8:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 117629663 . T C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCTCTCACACACACACACA;RSEQ=ACACTCGGAGTGCTTTTATT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:11:6:6,0:0,0:0,6:0.5455:0,0:19.7:1.0:33.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 117631479 . T C 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=3.0;SSF=0.01225;SOR=0.0;LSEQ=ATATTTAATAATAATAATAA;RSEQ=AACAACAATAAAGTTCCAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:360:9:1,8:64,286:350,9:0.025:2,2:17.1:1.0:32.9:1.0:1.0:1.78778:60.0:18.0:0.0265:0.0:1.3 0/0:270:0:0,0:60,202:262,0:0.0:2,0:28.6:1.0:27.1:1.0:1.0:0.0:59.8:22.818:0.9921:0.0:0.2 +6 117639262 . G A 131 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00019;SOR=0.10787;LSEQ=TGTTGTTTTAGTCATGATCC;RSEQ=TTAAGTCATGTCATTTTGGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:249:22:19,3:191,36:227,22:0.0884:2,2:28.9:1.0:29.6:1.0:1.0:1.19:60.0:44.0:0.0894:0.0:1.1 0/1:194:2:2,0:157,35:192,2:0.0103:2,0:27.0:1.0:28.5:1.0:1.0:0.0:60.0:4.0:0.0103:0.0:1.0 +6 117648215 . T C 208 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAAAGGCAAGCTCAAGGTCT;RSEQ=CCATTATGTCTTCTCTAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1399:101:57,44:665,632:1297,101:0.0722:2,2:24.4:1.0:31.3:1.0:0.35259:1.23:60.0:32.667:0.071:0.0:1.1 0/0:1205:0:0,0:639,564:1203,0:0.0:2,0:23.8:1.0:29.3:1.0:1.0:0.0:59.9:91.538:0.9992:0.0:0.1 +6 117652187 . T C 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.07161;LSEQ=CAGAAGTAGGCTTCACAAGA;RSEQ=GGGTAGAAAAAACTATGATG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:134:48:21,27:26,60:86,48:0.3582:2,2:25.0:1.0:30.4:1.0:0.13333:1.79:59.0:47.0:0.3588:0.0:1.2 0/1:105:4:1,3:37,64:101,4:0.0381:2,2:20.3:1.0:27.0:1.0:1.0:1.72606:60.0:8.0:0.0396:0.0:1.0 +6 117653900 . G A 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAATTGAACAACTTGCTCCT;RSEQ=AATGGCTCCTGGGTAAATAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:5:4,1:11,0:11,5:0.3125:0,2:27.2:1.0:28.6:1.0:0.3125:0.0:36.2:10.0:0.3125:0.0:1.2 0/0:1:0:0,0:1,0:1,0:0.0:0,0:2.0:0.0:28.0:0.0:1.0:0.0:41.0:2.0:1.0:0.0:4.0 +6 117657686 . A G 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.27249;SOR=0.0;LSEQ=TCATTCCTTTTTATGGCTGC;RSEQ=TAGTATGCCATGGTGTATAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:3,2:11,1:12,5:0.2941:2,2:25.2:1.0:29.8:1.0:0.19118:6.32143:52.4:10.0:0.2941:0.0:1.0 0/0:6:0:0,0:5,1:6,0:0.0:2,0:26.5:1.0:30.2:1.0:1.0:0.0:54.7:12.0:1.0:0.0:0.2 +6 117662453 . C T 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03304;LSEQ=ACTCTCTGTACACCACATTT;RSEQ=CTCAGAGTGGCAGGCAAGAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:945:103:53,50:386,456:842,103:0.109:2,2:30.0:1.0:30.4:1.0:0.29646:1.25:60.0:102.0:0.1093:0.0:1.1 0/0:746:3:0,3:355,388:743,3:0.004:2,0:1.0:0.0:23.0:1.0:0.25074:0.0:60.0:6.0:0.0041:0.0:1.0 +6 117665115 . G A 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06562;LSEQ=ATTAGCTGTAAAAAAGTTGC;RSEQ=TACTAGTCCATTTCAGAACA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:35:35,0:52,0:52,35:0.4023:1,1:21.8:1.0:31.0:1.0:1.0:0.0:60.0:34.0:0.3953:0.0:1.0 0/1:48:2:2,0:44,2:46,2:0.0417:1,0:37.5:1.0:29.5:1.0:1.0:0.0:60.0:4.0:0.0417:0.0:1.0 +6 117686918 . CA C 124 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.01096;SOR=0.10738;LSEQ=AAGTTCCCTACAGGATGAAA;RSEQ=AAAAAAAGAAATAGGAGAAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:579:13:3,10:184,382:566,13:0.0225:2,2:37.3:1.0:33.7:1.0:0.56332:1.60439:57.0:26.0:0.0226:0.0:0.1 0/0:407:1:1,0:134,272:406,1:0.0025:2,0:12.0:0.0:33.0:0.0:0.3317:0.0:60.0:2.0:0.0025:0.0:0.0 +6 117699988 . A G 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATACACTTCCTGGGCTCTTA;RSEQ=GCAGCATTCTCCTGAGTGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:25:5:5,0:19,1:20,5:0.2:1,0:27.8:1.0:34.2:1.0:1.0:0.0:60.0:10.0:0.2:0.0:1.0 0/0:1:0:0,0:1,0:1,0:0.0:0,0:26.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +6 117707038 . G A 215 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01123;LSEQ=TCCATGTCTCAAAATAAAGT;RSEQ=AATGATTAGCAGTTATTTTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:152:42,110:88,264:352,152:0.301:2,2:23.4:1.0:29.8:1.0:0.57937:1.15:60.0:37.0:0.2996:0.0:1.1 0/0:417:2:2,0:119,296:415,2:0.0048:2,0:1.0:0.0:23.5:1.0:0.0837:0.0:60.0:4.0:0.0048:0.0:1.5 +6 117724207 . G A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0069;SOR=0.0;LSEQ=TTGAATGGATCGATTAATAG;RSEQ=AAGGAATAGATTTATTTCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:105:8:7,1:92,5:97,8:0.0762:2,2:11.1:1.0:31.1:1.0:0.38598:2.59429:60.0:16.0:0.0777:0.0:1.1 0/0:100:0:0,0:90,10:100,0:0.0:2,0:21.2:1.0:30.6:1.0:1.0:0.0:60.0:99.0:1.0:0.0:0.1 +6 131790227 . G T 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0142;SOR=0.0;LSEQ=CACAAAGGGAAAGAGGAGAG;RSEQ=CACCGATACGTGTTCTCTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:5:3,2:39,2:41,5:0.1087:1,2:22.0:1.0:28.4:1.0:0.05279:11.59891:59.2:10.0:0.1163:0.0:1.0 0/0:59:0:0,0:52,7:59,0:0.0:2,0:23.3:1.0:31.0:1.0:1.0:0.0:59.0:118.0:1.0:0.0:0.1 +6 137519780 . T C 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.04488;LSEQ=CTTCTTACCACAGAGATCTA;RSEQ=GGGGAGAAAAATTGATTAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:273:124:38,86:37,112:149,124:0.4542:2,2:25.5:1.0:30.4:1.0:0.34061:1.34:60.0:61.0:0.4569:0.0:1.2 0/1:307:11:3,8:106,190:296,11:0.0358:2,2:19.3:1.0:30.0:1.0:0.75207:1.48591:60.0:22.0:0.0364:0.0:1.0 +6 137519834 . C CA 73 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.06049;SOR=0.0;LSEQ=TAAGCTTAAGTGCCTACCCT;RSEQ=AAAAAAAACAAAGGTCTGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:5:0,5:15,94:109,5:0.0439:2,0:32.4:1.0:31.8:1.0:1.0:0.0:60.0:10.0:0.0446:0.0088:0.4 0/0:106:0:0,0:20,85:105,0:0.0:2,0:23.0:1.0:31.5:1.0:1.0:0.0:60.0:210.0:1.0:0.0:0.1 +6 137540536 . G A 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08232;LSEQ=CAGCACTGCCCTCCAGCCCC;RSEQ=GCCTTACGTCACTTCCGTCA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:67:5,62:22,125:147,67:0.3131:2,2:26.1:1.0:31.4:1.0:0.18184:2.17539:60.0:21.333:0.3048:0.0:2.1 0/1:139:5:0,5:14,120:134,5:0.036:2,0:20.6:1.0:31.0:1.0:1.0:0.0:60.0:10.0:0.0362:0.0:1.8 +6 138026354 . G A 61 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTGAGAGGTCTAGCTACCCT;RSEQ=CCAGCCAGCCACTGAAAGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:4,1:0,0:0,5:1.0:0,2:30.0:1.0:26.6:1.0:1.0:0.0:60.0:4.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 138027910 . A G 216 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGTGCGCACAGAGAGAAC;RSEQ=AAATCTCCAGGGTGGCTCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:627:134:62,72:226,266:492,134:0.2137:2,2:28.8:1.0:30.7:1.0:1.0:1.01:54.6:32.5:0.2124:0.0:1.1 0/0:586:0:0,0:281,304:585,0:0.0:2,0:26.7:1.0:29.7:1.0:1.0:0.0:58.1:145.25:0.9983:0.0:0.2 +6 138199768 . A T 259 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00198;LSEQ=CGCCCAACTGCCCCTTCTTC;RSEQ=TGTCTGTGAACACCCAGCCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1125:328:160,168:388,408:796,328:0.2916:2,2:25.3:1.0:31.1:1.0:1.0:1.0:60.0:45.857:0.2887:0.0:1.1 0/0:1240:1:0,1:621,617:1238,1:0.0008:2,0:1.0:0.0:24.0:0.0:0.49879:0.0:60.0:2.0:0.0008:0.0:1.0 +6 147728117 . C T 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCAGGGGCAGGGCCCGCGGT;RSEQ=CAGACCAGGGCACCCGGCGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:21:11,10:44,29:73,21:0.2234:2,2:20.4:1.0:31.0:1.0:0.6172:1.3745:60.0:42.0:0.2234:0.0:1.2 0/0:69:0:0,0:42,27:69,0:0.0:2,0:15.4:1.0:31.1:1.0:1.0:0.0:60.0:68.0:1.0:0.0:0.1 +6 148266586 . C T 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01357;LSEQ=ACCCCCAAACGTTATTTATC;RSEQ=GTGTATAAATACATGTCAGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:55:35:35,0:20,0:20,35:0.6364:1,1:25.9:1.0:33.1:1.0:1.0:0.0:60.0:70.0:0.6364:0.0:2.1 0/1:45:1:1,0:41,2:43,1:0.0222:1,0:11.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0227:0.0:2.0 +6 148266965 . A G 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=3e-05;SOR=0.0;LSEQ=GTTCCTACCTTGTGCCAGGC;RSEQ=CTAGGGTTATGCAAAAAAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:38:23:0,23:0,15:15,23:0.6053:1,1:24.5:1.0:31.8:1.0:1.0:0.0:60.0:22.0:0.5946:0.0:1.2 0/0:15:0:0,0:0,15:15,0:0.0:1,0:26.4:1.0:30.2:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.0 +6 151176771 . C T 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.10714;SOR=0.0;LSEQ=TTTGGGCCCTGTATTTTTAA;RSEQ=CTTCTTGTCAAATTTGTTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:3,2:0,1:1,5:0.8333:0,2:25.0:1.0:31.8:1.0:1.0:0.0:42.6:10.0:0.8333:0.0:1.0 0/0:2:0:0,0:0,2:2,0:0.0:0,0:46.5:1.0:31.0:1.0:1.0:0.0:21.0:4.0:1.0:0.0:0.0 +6 152129308 . G C 292 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.03415;LSEQ=GGCCCCGGGTCTGAGGCTGC;RSEQ=GCGTTCGGCTCCAACGGCCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1053:801:355,446:111,136:247,801:0.7607:2,2:25.0:1.0:30.3:1.0:0.88369:1.02538:60.0:56.214:0.7663:0.0:1.2 0/1:870:85:37,48:357,423:780,85:0.0977:2,2:22.8:1.0:29.2:1.0:0.73168:1.09474:60.0:41.5:0.0971:0.0:1.2 +6 152164026 . A G 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00374;SOR=0.0;LSEQ=GAATCAGCCATTTGTACAAA;RSEQ=CATGAATCCCTAGTAGGTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:12:0,12:2,97:99,12:0.1081:1,0:25.8:1.0:32.5:1.0:1.0:0.0:60.0:24.0:0.1101:0.0:1.0 0/0:73:0:0,0:0,73:73,0:0.0:1,0:22.8:1.0:29.5:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 +6 152201853 . G T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00799;SOR=0.0;LSEQ=TGATAAAAACAGGAGGAAGA;RSEQ=CTGCCAGGCCTGCCGGCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:589:8:4,4:287,293:580,8:0.0136:2,2:23.9:1.0:30.0:1.0:1.0:1.02:60.0:16.0:0.0137:0.0:1.8 0/0:542:0:0,0:254,288:542,0:0.0:2,0:24.6:1.0:31.1:1.0:1.0:0.0:59.9:53.2:1.0:0.0:0.9 +6 152332921 . C G 180 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGTTTGCTCCTAACTTGCT;RSEQ=TTGGACAGGTAAGTGACCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:588:50:16,34:167,370:537,50:0.085:2,2:25.1:1.0:31.9:1.0:0.87446:1.04:60.0:49.0:0.0848:0.0:1.1 0/0:528:0:0,0:179,347:526,0:0.0:2,0:25.0:1.0:31.2:1.0:1.0:0.0:60.0:525.0:0.9962:0.0:0.1 +6 152333032 . A G 118 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00353;SOR=0.0;LSEQ=GTGAAGCTTCAGAGAACTTT;RSEQ=TTAGGTATGTTTACTTAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:12:0,12:1,74:75,12:0.1379:1,0:23.6:1.0:33.0:1.0:1.0:0.0:60.0:24.0:0.1379:0.0:1.0 0/0:53:0:0,0:1,52:53,0:0.0:1,0:18.2:1.0:29.8:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.1 +6 155699472 . TA T 79 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.03278;SOR=0.0;LSEQ=AATAAGTAAAATGCAAATAT;RSEQ=AAAAAAAATCTGAAATCCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:6:5,1:75,1:76,6:0.0732:1,2:19.2:1.0:30.6:1.0:0.14182:13.78406:60.0:12.0:0.0741:0.0244:0.0 0/0:67:0:0,0:61,5:66,0:0.0:2,0:19.8:1.0:28.0:1.0:1.0:0.0:60.0:65.0:1.0:0.0:0.1 +6 157100255 . G T 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.02237;SOR=0.0;LSEQ=GCAAGGCGGCCGCCGGCTCG;RSEQ=CGGCGGGGGGCTTCCAGCGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:378:5:1,4:245,127:372,5:0.0132:2,2:14.6:1.0:27.2:1.0:0.05146:7.67479:60.0:10.0:0.0135:0.0:1.2 0/0:428:0:0,0:271,157:428,0:0.0:2,0:20.8:1.0:31.2:1.0:1.0:0.0:59.9:52.5:1.0:0.0:0.3 +6 157150230 . A G 150 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=2e-05;SOR=0.08219;LSEQ=GTCTTGCTGGATGTTTTGTC;RSEQ=GGTCATTGTTTTTAATATTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:93:32:31,1:59,2:61,32:0.3441:1,1:23.4:1.0:30.0:1.0:1.0:1.05:60.0:64.0:0.3441:0.0:1.1 0/1:49:2:2,0:47,0:47,2:0.0408:1,0:23.5:1.0:28.0:1.0:1.0:0.0:60.0:4.0:0.0426:0.0:1.0 +6 157511319 . G A 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00016;SOR=0.10393;LSEQ=ATGCCCTATGAGCCCAACAA;RSEQ=GACCCCTTTGGGGGAATGAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:18:5,13:135,329:464,18:0.0373:2,2:21.4:1.0:31.2:1.0:1.0:1.06673:60.0:36.0:0.0382:0.0:1.0 0/0:500:2:2,0:181,317:498,2:0.004:2,0:1.0:0.0:26.5:1.0:0.13349:0.0:56.5:4.0:0.004:0.0:1.0 +6 157527280 . TCTC T 76 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.0;MSILEN=3.0;SSF=0.11762;SOR=0.19136;LSEQ=TGTACCTGTTCTTTCTTTCT;RSEQ=CTCCTCCTCCTCTCCAGTTG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:255:5:5,0:205,46:251,5:0.0196:2,0:25.2:1.0:32.8:1.0:0.58886:0.0:60.0:10.0:0.0199:0.0039:0.2 0/0:263:1:0,1:193,66:259,1:0.0038:2,0:15.0:0.0:33.0:0.0:0.25769:0.0:60.0:2.0:0.0038:0.0:0.0 +6 159215375 . G T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02277;SOR=0.0;LSEQ=ACCACCACCACCAGGCTTTG;RSEQ=CAATTGAGAAAACACATCTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:5:2,3:14,14:28,5:0.1515:2,2:29.4:1.0:30.0:1.0:1.0:1.48182:60.0:10.0:0.1515:0.0:1.0 0/0:35:0:0,0:15,20:35,0:0.0:2,0:28.6:1.0:30.9:1.0:1.0:0.0:57.2:34.0:1.0:0.0:0.3 +6 160639986 . A G 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03135;SOR=0.0;LSEQ=TAGCAGTAGTAATAGCAGCA;RSEQ=CAGCAGCAGCAGCAGCAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:6:2,4:68,38:106,6:0.0526:2,2:21.2:1.0:32.2:1.0:0.19487:3.53638:56.3:12.0:0.0541:0.0:5.3 0/0:99:0:0,0:56,34:90,0:0.0:2,0:9.2:1.0:29.0:1.0:1.0:0.0:56.8:180.0:1.0:0.0:1.3 +6 160640146 . C G 213 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACAGCAACAGAAGCAATAA;RSEQ=AGCAGCAGCAACAACAGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:88:42,46:110,83:193,88:0.2604:2,2:7.7:1.0:33.0:1.0:0.15763:1.44955:56.7:176.0:0.3154:0.0:4.9 0/0:387:0:0,0:117,90:207,0:0.0:2,0:15.8:1.0:31.2:1.0:1.0:0.0:51.0:102.5:1.0:0.0:2.7 +6 160640164 . CAGTACGAACACCAGCAGT C 122 NM7.25 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=AACAGCAGCAGCAACAACAG;RSEQ=AACAACAGCAGCAGCAACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:206:17:6,11:103,83:186,17:0.0825:2,2:24.7:1.0:30.0:1.0:0.13193:2.26597:23.4:34.0:0.0837:0.0825:7.8 0/0:188:0:0,0:101,87:188,0:0.0:2,0:17.0:1.0:29.6:1.0:1.0:0.0:53.1:187.0:1.0:0.0:2.5 +6 161771035 . CGTGT C 134 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=7.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGTGTGTGTGCGCGCGCGCG;RSEQ=GTGTGTGTGTTTGAAAAGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:215:19:14,5:158,30:188,19:0.0884:2,2:8.4:1.0:31.6:1.0:0.33012:1.87431:60.0:38.0:0.0896:0.0372:0.1 0/0:261:0:0,0:202,39:241,0:0.0:2,0:22.7:1.0:29.6:1.0:1.0:0.0:60.0:78.667:0.9183:0.0:0.2 +6 161771037 . T C 175 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=6.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGTGTGTGCGCGCGCGCGCG;RSEQ=GTGTGTGTGTGTTTGAAAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:214:53:46,7:117,25:142,53:0.2477:2,2:24.3:1.0:30.6:1.0:0.52185:1.4:59.9:12.25:0.2649:0.0:2.0 0/0:269:0:0,0:207,43:250,0:0.0:2,0:22.3:1.0:28.3:1.0:1.0:0.0:60.0:34.714:1.0:0.0:0.2 +6 161771039 . T C 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TGTGTGCGCGCGCGCGCGTG;RSEQ=GTGTGTGTGTTTGAAAAGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:217:55:48,7:122,28:150,55:0.2535:2,2:23.3:1.0:31.0:1.0:0.40392:1.57:59.9:26.5:0.2718:0.0:2.0 0/0:272:0:0,0:222,49:271,0:0.0:2,0:23.1:1.0:28.2:1.0:1.0:0.0:60.0:26.1:1.0:0.0:0.3 +6 162137107 . C A 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01856;LSEQ=CTGTGCTGGGCCCATCTTAC;RSEQ=GACTCCTCTCCTGAATCCCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1196:99:47,52:604,491:1095,99:0.0828:2,2:26.8:1.0:30.8:1.0:0.17043:1.36064:60.0:98.0:0.0829:0.0:1.1 0/0:1198:2:2,0:643,552:1195,2:0.0017:2,0:1.0:0.0:25.5:1.0:0.5026:0.0:60.0:4.0:0.0017:0.0:1.0 +6 162206873 . A T 199 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATCATTGAGTCTTGTCACAC;RSEQ=GTATAAGTGGAAACAGTCTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:671:82:34,48:262,325:587,82:0.1222:2,2:26.1:1.0:31.4:1.0:0.63582:1.13788:60.0:164.0:0.1239:0.0:1.1 0/0:795:0:0,0:360,435:795,0:0.0:2,0:23.9:1.0:29.7:1.0:1.0:0.0:60.0:87.333:1.0:0.0:0.2 +6 163092867 . C T 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TAATCAGATGTCAAATTGTA;RSEQ=AGTCAAAGAATAAATGGAAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:1,4:0,1:1,5:0.8333:0,2:21.4:1.0:30.0:0.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +6 163528910 . C T 191 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTATAAATTTCTCCAAAAT;RSEQ=CTAACATGTTGTTTGAAATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:76:41,35:183,171:354,76:0.1763:2,2:25.6:1.0:30.7:1.0:0.80042:1.09:59.8:152.0:0.178:0.0:1.8 0/0:543:0:0,0:271,271:542,0:0.0:2,0:27.2:1.0:30.2:1.0:1.0:0.0:59.9:66.75:0.9981:0.0:0.3 +6 163529226 . A G 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.28571;SOR=0.0;LSEQ=TTCTTTCTGTTCTCATGATG;RSEQ=TGAGTGAGCTCTCACGAGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:28.4:1.0:32.8:1.0:1.0:0.0:52.0:10.0:0.8333:0.0:2.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:7.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:1.0 +6 169643879 . T C 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=2e-05;SOR=0.08819;LSEQ=GCTCTGACAGGAATGTAGTT;RSEQ=TACCTGGTAGTAAAACCTTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:39:38,1:76,4:80,39:0.3277:2,1:23.9:1.0:32.6:1.0:1.0:1.99:60.0:78.0:0.3277:0.0:1.1 0/1:49:2:2,0:45,2:47,2:0.0408:1,0:37.0:1.0:33.0:0.0:1.0:0.0:60.0:4.0:0.0408:0.0:1.0 +7 58414 . C G 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGATCTGCATATAGGCCAG;RSEQ=CTTTCTGCATAGGGCACAGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:6:4,2:2,1:3,6:0.6667:2,2:20.3:1.0:32.2:1.0:1.0:1.0:60.0:12.0:0.6667:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 60033 . C T 101 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01562;SOR=0.09863;LSEQ=ACTCCAAGCTCCCCCAGACC;RSEQ=GGTGGAAACGCAGACTCCTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:10:4,6:9,8:17,10:0.3704:2,2:27.7:1.0:30.6:1.0:0.69458:1.65488:60.0:9.0:0.3462:0.0:1.6 0/1:19:1:0,1:11,7:18,1:0.0526:2,0:21.0:0.0:31.0:0.0:0.42105:0.0:60.0:2.0:0.0556:0.0:1.0 +7 60055 . G T 117 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00038;SOR=0.04495;LSEQ=GTGGAAACGCAGACTCCTTG;RSEQ=CTAACACTGCCATGGGAGTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:25:15:7,8:3,7:10,15:0.6:2,2:19.9:1.0:30.1:1.0:0.67846:1.98:60.0:30.0:0.6:0.0:1.9 0/1:17:1:0,1:8,8:16,1:0.0588:2,0:39.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0625:0.0:2.0 +7 2166580 . C T 174 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGTAGGGCATTTTAAACAA;RSEQ=GGCAGATTACAACTGAGAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:297:56:20,36:73,166:239,56:0.1886:2,2:26.1:1.0:30.0:1.0:0.52294:1.26:60.0:27.0:0.1862:0.0:1.1 0/0:135:0:0,0:42,93:135,0:0.0:2,0:22.1:1.0:29.5:1.0:1.0:0.0:60.0:44.0:1.0:0.0:0.4 +7 2951934 . C T 129 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=2e-05;SOR=0.0;LSEQ=ATCTCTTGTGACGATATCTG;RSEQ=AGAGAGAGGGGCCAGTCCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:22:5,17:255,426:681,22:0.0313:2,2:27.3:1.0:29.0:1.0:0.18408:2.03337:60.0:44.0:0.0318:0.0:1.0 0/0:477:0:0,0:161,315:476,0:0.0:2,0:24.0:1.0:31.1:1.0:1.0:0.0:59.9:78.333:0.9979:0.0:0.1 +7 2952796 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=GGAAAGGAAAGAGGGAAGAG;RSEQ=AGGAAAGAGGGAAGAGAAGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:5:5,0:75,0:75,5:0.0625:1,0:14.8:1.0:30.6:1.0:1.0:0.0:26.0:10.0:0.0676:0.0:3.0 0/0:14:0:0,0:13,1:14,0:0.0:1,0:13.6:1.0:30.9:1.0:1.0:0.0:58.4:28.0:1.0:0.0:0.1 +7 2952799 . GAAA AGGGGAG 76 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=0.0;MSILEN=0.0;SSF=1.0;SOR=0.0;LSEQ=AAGGAAAGAGGGAAGAGGAG;RSEQ=GAGGGAAGAGAAGAGGGGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:5:5,0:76,0:76,5:0.0617:1,0:16.8:1.0:33.0:1.0:1.0:0.0:26.0:10.0:0.0676:0.0:3.0 0/0:14:0:0,0:13,1:14,0:0.0:1,0:14.6:1.0:29.4:1.0:1.0:0.0:58.4:28.0:1.0:0.0:0.1 +7 2952802 . A AGAGGGAAGAGAAGAGGGGAG 162 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00045;SOR=0.0;LSEQ=GAAAGAGGGAAGAGGAGGAA;RSEQ=GAGGGAAGAGAAGAGGGGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:117:41:41,0:70,1:71,41:0.3504:1,1:13.6:1.0:30.4:1.0:1.0:0.0:58.1:40.0:0.3704:0.2735:0.2 0/0:21:0:0,0:18,1:19,0:0.0:1,0:14.4:1.0:30.7:1.0:1.0:0.0:60.0:38.0:0.9048:0.0:0.2 +7 2952915 . G A 127 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.00025;SOR=0.0;LSEQ=CCAGGTGGCCGTGGCTCGCC;RSEQ=CTCACCTGACTTGCAGATGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:676:21:13,8:417,237:654,21:0.0311:2,2:29.7:1.0:29.0:1.0:0.82262:1.08264:60.0:20.0:0.0303:0.0:1.0 0/0:336:0:0,0:208,127:335,0:0.0:2,0:23.1:1.0:29.6:1.0:1.0:0.0:59.6:166.5:0.997:0.0:0.3 +7 2961909 . A C 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGAAGCCCGAGAGAGGAGG;RSEQ=AACTTCCACTTACCAGGGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:8,0:0,0:0,8:1.0:0,0:27.5:1.0:33.5:1.0:1.0:0.0:59.3:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 2962036 . C T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.57187;SOR=0.0;LSEQ=GACACCTGGGCAGGTGAGTG;RSEQ=AGACGTGGCCAAAGAGCCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:8:8,0:31,0:31,8:0.2051:1,0:17.3:1.0:30.0:1.0:1.0:0.0:60.0:16.0:0.2162:0.0:1.0 0/0:6:0:0,0:6,0:6,0:0.0:0,0:31.7:1.0:33.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.3 +7 2962201 . A C 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGGCTCTAGGCGGCGAGGTC;RSEQ=CTTGTCCAGGTCAGAGACTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:729:37:27,10:504,187:691,37:0.0508:2,2:25.1:1.0:31.6:1.0:1.0:1.0:60.0:74.0:0.0515:0.0:1.1 0/0:387:0:0,0:267,118:385,0:0.0:2,0:22.0:1.0:29.2:1.0:1.0:0.0:60.0:76.0:0.9948:0.0:0.2 +7 2963744 . T C 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.07503;SOR=0.0;LSEQ=CTGACTCGGGAATGCTACAA;RSEQ=TCTGGTTCTGGCTCTAGGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:194:12:12,0:180,2:182,12:0.0619:1,0:20.0:1.0:32.7:1.0:1.0:0.0:60.0:24.0:0.0628:0.0:1.2 0/0:53:0:0,0:53,0:53,0:0.0:1,0:24.2:1.0:30.7:1.0:1.0:0.0:60.0:52.0:1.0:0.0:0.0 +7 2968289 . T C 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TGGAGTCGTTTCCCGGGGGC;RSEQ=CGGCGGTGATTGACATGATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1596:26:8,18:661,905:1566,26:0.0163:2,2:22.0:1.0:30.7:1.0:0.3171:1.64288:60.0:25.0:0.0162:0.0:1.3 0/0:937:0:0,0:418,517:935,0:0.0:2,0:23.9:1.0:28.9:1.0:1.0:0.0:59.9:45.75:0.9978:0.0:0.2 +7 2968548 . G A 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=1.0;SOR=0.0;LSEQ=CTCGCACATCTGCTCACAGG;RSEQ=AGGACGCAGGCGGGAGCCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:23:12:0,12:0,11:11,12:0.5217:0,0:21.2:1.0:31.3:1.0:1.0:0.0:60.0:24.0:0.5455:0.0:1.3 0/0:1:0:0,0:0,1:1,0:0.0:0,0:39.0:0.0:32.0:0.0:1.0:0.0:23.0:2.0:1.0:0.0:1.0 +7 2969660 . C A 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGTTGGTGATGGGCAGAGAT;RSEQ=CGCAGGAGCTAGGGCTGGCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1601:76:41,35:738,787:1525,76:0.0475:2,2:26.5:1.0:28.7:1.0:0.34992:1.25:60.0:75.0:0.0474:0.0:1.2 0/0:862:0:0,0:440,421:861,0:0.0:2,0:25.3:1.0:30.3:1.0:1.0:0.0:60.0:85.1:0.9988:0.0:0.4 +7 2969983 . C T 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AACCTCCTCTTGCTTTTTAT;RSEQ=AAATTTTTTATAGAGATGGT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:14:0,14:0,4:4,14:0.7778:0,1:22.8:1.0:29.1:1.0:1.0:0.0:57.9:28.0:0.7778:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 2973685 . TTTTTC T 69 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ACCACAATGCCTGGCTGTTT;RSEQ=TTTTCTTTTCTTTTCTTTTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:37.6:1.0:29.8:1.0:1.0:0.0:57.0:10.0:1.0:0.1667:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 2977488 . C T 60 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.17127;SOR=0.0;LSEQ=GGAGCCGGTGGTCTGGGGTG;RSEQ=GGGCCCCGCTGTGCAGCCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:487:5:3,2:383,99:482,5:0.0103:2,2:9.8:1.0:26.2:1.0:0.27756:2.57285:60.0:10.0:0.0104:0.0:1.0 0/0:254:0:0,0:187,67:254,0:0.0:2,0:21.6:1.0:30.5:1.0:1.0:0.0:60.0:41.333:1.0:0.0:0.2 +7 2977768 . G T 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.05018;SOR=0.0;LSEQ=CCCGCCAGCTGGCTGGAGCT;RSEQ=GCCTGTCCCTCCCTAAGCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:157:7:0,7:2,147:149,7:0.0446:1,0:35.7:1.0:30.7:1.0:1.0:0.0:60.0:14.0:0.0467:0.0:1.0 0/0:90:0:0,0:0,90:90,0:0.0:1,0:21.1:1.0:30.2:1.0:1.0:0.0:60.0:21.5:1.0:0.0:0.2 +7 2985351 . C A 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05689;SOR=0.0;LSEQ=TCACAGCTTAAGAACCATGC;RSEQ=ACTACTGAGGACACACACAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:245:8:8,0:232,5:237,8:0.0327:1,0:24.8:1.0:31.4:1.0:1.0:0.0:60.0:16.0:0.0343:0.0:1.3 0/0:120:0:0,0:113,5:118,0:0.0:1,0:22.4:1.0:30.4:1.0:1.0:0.0:59.8:28.5:0.9828:0.0:0.3 +7 2985391 . C G 75 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=2.0;SSF=0.08684;SOR=0.0;LSEQ=CACACACACACACACACAGA;RSEQ=ACACACACACACACGCCCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:6:5,1:331,78:409,6:0.014:2,2:6.8:1.0:29.3:1.0:1.0:1.18:60.0:5.0:0.0123:0.0:1.5 0/0:273:0:0,0:203,60:263,0:0.0:2,0:22.6:1.0:30.9:1.0:1.0:0.0:59.7:51.6:1.0:0.0:0.4 +7 6026530 . C T 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTCGTTTAGCTAAAGAACT;RSEQ=ATAGAAAAGTCCAGGGGCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1363:70:27,43:653,639:1292,70:0.0514:2,2:26.1:1.0:29.2:1.0:0.06498:1.6269:30.2:69.0:0.0513:0.0:1.0 0/0:949:0:0,0:475,474:949,0:0.0:2,0:27.3:1.0:31.1:1.0:1.0:0.0:36.3:85.273:1.0:0.0:0.1 +7 6039129 . T C 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTCACTTCCCAATGTGCCA;RSEQ=GCATCCTGGTAAAACAACTA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:8:0,8:0,12:12,8:0.4:0,0:20.4:1.0:31.0:1.0:1.0:0.0:57.6:16.0:0.4444:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 6048510 . G T 49 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.17366;SOR=0.0;LSEQ=GCCACTCCGGGGCCTCCAGG;RSEQ=GGCTGCCTCGCCACGCGCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:5:3,2:234,42:276,5:0.0177:2,2:13.0:1.0:21.4:1.0:0.17577:3.68937:40.8:1.5:0.011:0.0:2.8 0/0:142:0:0,0:113,29:142,0:0.0:2,0:22.7:1.0:30.2:1.0:1.0:0.0:53.4:70.0:1.0:0.0:0.3 +7 6426892 . C T 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GTTACACAACCAATGCATTT;RSEQ=CTGGAGAATATATCCCTACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1063:49:19,30:460,553:1013,49:0.0461:2,2:25.2:1.0:30.1:1.0:0.38183:1.31308:48.3:23.5:0.0451:0.0:1.1 0/0:724:0:0,0:355,368:723,0:0.0:2,0:24.0:0.0:15.0:0.0:1.0:0.0:39.0:0.0:0.0:0.0:1.0 +7 6426908 . C G 190 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTTCCTGGAGAATATATCC;RSEQ=TACTGTGTAAGTATCTTAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:962:73:30,43:366,523:889,73:0.0759:2,2:26.3:1.0:30.8:1.0:1.0:1.00306:46.8:72.0:0.076:0.0:2.0 0/0:683:0:0,0:305,377:682,0:0.0:2,0:25.8:1.0:30.8:1.0:1.0:0.0:46.7:84.25:1.0:0.0:0.5 +7 6431457 . C G 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00015;SOR=0.17114;LSEQ=GGTGTGGCAGCCTCCAGGCC;RSEQ=GTCCCCAGCCTTTTTCTTGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:205:35:33,2:160,10:170,35:0.1707:2,2:19.9:1.0:29.9:1.0:1.0:1.03:60.0:70.0:0.1716:0.0:1.4 0/1:118:4:4,0:104,10:114,4:0.0339:2,0:27.3:1.0:31.5:1.0:1.0:0.0:60.0:8.0:0.0342:0.0:1.5 +7 6431523 . C CT 137 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=CAGTGACTTAGCTTCTACAC;RSEQ=TGTGACTAACCATTTTCATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:677:23:15,8:455,199:654,23:0.034:2,2:25.1:1.0:30.5:1.0:0.6498:1.21903:55.9:22.0:0.0329:0.0103:0.2 0/0:452:0:0,0:289,163:452,0:0.0:2,0:23.7:1.0:30.3:1.0:1.0:0.0:58.3:36.667:1.0:0.0:0.2 +7 6438388 . C T 129 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00013;SOR=0.0;LSEQ=CCACTTCAGTTTCAAGCTTT;RSEQ=TCTGTTCTCTCATTTCACTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:886:18:6,12:278,588:866,18:0.0203:2,2:26.9:1.0:31.1:1.0:1.0:1.06:60.0:36.0:0.0206:0.0:1.0 0/0:581:0:0,0:212,368:580,0:0.0:2,0:25.3:1.0:30.9:1.0:1.0:0.0:60.0:115.0:0.9983:0.0:0.1 +7 6441229 . T TC 114 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCCTTTTGTTTCTCTTCCCT;RSEQ=CCCCCCTTCCCCTGCGGTTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:19:12:12,0:7,0:7,12:0.6316:0,0:31.0:1.0:32.0:1.0:1.0:0.0:60.0:24.0:0.6316:0.0:0.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 6441993 . C G 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00044;SOR=0.0;LSEQ=GCGCTCACACAGCGAGGCCT;RSEQ=AAGACAGTGTTTGACGAAGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:505:13:7,6:279,212:491,13:0.0257:2,2:26.6:1.0:30.7:1.0:1.0:1.12776:45.6:12.0:0.0243:0.0:1.2 0/0:410:0:0,0:225,183:408,0:0.0:2,0:21.7:1.0:30.5:1.0:1.0:0.0:55.8:39.8:0.9975:0.0:0.2 +7 11297507 . T G 72 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=14.0;MSILEN=1.0;SSF=0.27207;SOR=0.0;LSEQ=TTTTAGTTTTTTTTTTCCCT;RSEQ=TTTTTTTTTTTTGAGTGATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:5:2,3:4,6:10,5:0.2941:2,2:14.4:1.0:31.4:1.0:1.0:1.0:60.0:10.0:0.3571:0.0:1.0 0/0:7:0:0,0:2,3:5,0:0.0:2,0:25.8:1.0:27.8:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 +7 12462931 . G GCC 119 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=10.0;MSILEN=1.0;SSF=0.01125;SOR=0.0;LSEQ=TACCCAATAATCCTTCTGTG;RSEQ=CCCCCCCCTTATTTCATTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:116:13:13,0:98,3:101,13:0.1121:1,1:22.7:1.0:32.3:1.0:1.0:0.0:59.2:26.0:0.115:0.0259:1.4 0/0:48:0:0,0:43,0:43,0:0.0:1,0:25.2:1.0:30.6:1.0:1.0:0.0:60.0:20.5:0.8913:0.0:0.3 +7 13935307 . C T 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=7e-05;SOR=0.0;LSEQ=TTTAGATTACTCCCACCCAC;RSEQ=CTCAAATAAAGTGCACAGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:22:20,2:7,0:7,22:0.7586:0,2:22.9:1.0:30.7:1.0:1.0:0.0:58.5:10.0:0.7407:0.0:1.2 0/0:9:0:0,0:9,0:9,0:0.0:0,0:19.0:1.0:30.7:1.0:1.0:0.0:60.0:18.0:1.0:0.0:0.1 +7 13935468 . G T 52 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.07462;SOR=0.0;LSEQ=AAAAGGAAAAGCGCAAAAAC;RSEQ=CCCTGCTTGACTGTCACTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:488:5:2,3:321,161:482,5:0.0102:2,2:17.4:1.0:22.6:1.0:0.34096:2.98336:60.0:1.5:0.0063:0.0:1.4 0/0:366:0:0,0:240,125:365,0:0.0:2,0:25.4:1.0:29.5:1.0:1.0:0.0:60.0:35.5:1.0:0.0:0.2 +7 14025528 . C A 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00019;SOR=0.03931;LSEQ=AAAAGATATAACAGATTGCA;RSEQ=CACAAAATTTTAACAAAAAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:30:30,0:11,0:11,30:0.7317:0,1:28.5:1.0:30.0:1.0:1.0:0.0:60.0:29.0:0.725:0.0:1.1 0/1:11:1:1,0:9,1:10,1:0.0909:2,0:4.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:0.0909:0.0:1.0 +7 14026421 . C T 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00585;SOR=0.0;LSEQ=ATAAATTTAATTTCAAGAGA;RSEQ=GCAGTCAACATAAAAATAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:114:15:0,15:0,99:99,15:0.1316:1,1:17.3:1.0:31.0:1.0:1.0:0.0:60.0:30.0:0.1351:0.0:1.9 0/0:49:0:0,0:1,48:49,0:0.0:1,0:19.9:1.0:29.1:1.0:1.0:0.0:60.0:98.0:1.0:0.0:0.6 +7 14028575 . C T 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.01291;LSEQ=TCCCTTCTCATTTTCTCCCT;RSEQ=TCCCCACCCCCGACGGAGTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:804:100:65,35:475,228:703,100:0.1244:2,2:23.3:1.0:30.4:1.0:0.64901:1.12163:60.0:200.0:0.1292:0.0:1.1 0/0:547:1:0,1:342,204:546,1:0.0018:2,0:1.0:0.0:28.0:0.0:0.37477:0.0:60.0:2.0:0.0019:0.0:1.0 +7 32159902 . G A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.48529;SOR=0.0;LSEQ=GGCCGCAGTCTCTGCAGACC;RSEQ=TCATACTTAGCCTTTCCTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:5,2:6,2:8,7:0.4667:2,2:20.1:1.0:29.7:1.0:1.0:1.18545:47.9:14.0:0.4667:0.0:1.1 0/0:2:0:0,0:1,1:2,0:0.0:2,0:14.0:1.0:30.0:1.0:1.0:0.0:54.0:4.0:1.0:0.0:0.0 +7 34959604 . C T 119 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0762;SOR=0.14039;LSEQ=TTTTAGTCTCCCCTGGTTCC;RSEQ=AGTCTGAGGAGTCTGAGTCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:13:11,2:23,0:23,13:0.3611:1,2:12.8:1.0:32.4:1.0:0.12381:0.0:51.2:26.0:0.3611:0.0:2.1 0/1:14:1:1,0:11,2:13,1:0.0714:2,0:10.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0833:0.0:3.0 +7 36858427 . G T 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.21842;SOR=0.0;LSEQ=TCCACGTGCAAAAGAATGAA;RSEQ=TTGGACCCCTGCCTCACAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:7,2:7,1:8,9:0.5294:2,2:14.3:1.0:31.7:1.0:1.0:1.9219:60.0:18.0:0.5294:0.0:1.1 0/0:3:0:0,0:3,0:3,0:0.0:0,0:27.0:1.0:31.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +7 36859286 . A G 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.04323;SOR=0.0;LSEQ=AAAATGCAAGCAAGTATACA;RSEQ=AAAGCATATTGAACAGTCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:7:1,6:13,33:46,7:0.1321:2,2:23.4:1.0:33.4:1.0:0.6601:2.33155:46.9:14.0:0.14:0.0:1.0 0/0:31:0:0,0:7,24:31,0:0.0:2,0:24.8:1.0:30.0:1.0:1.0:0.0:51.8:62.0:1.0:0.0:0.1 +7 39836727 . G T 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.34121;SOR=0.0;LSEQ=ATCACCCCCTCCTCCTCATG;RSEQ=ATGACCATGTGCTCCTCGTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:61:7:5,2:22,32:54,7:0.1148:2,2:19.9:1.0:29.9:1.0:0.22448:3.56:27.4:14.0:0.1167:0.0:1.0 0/0:18:0:0,0:11,7:18,0:0.0:2,0:23.7:1.0:29.4:1.0:1.0:0.0:25.7:17.0:1.0:0.0:0.1 +7 41729758 . CA AG 155 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCTTTCTTCTTCTTCTTGCC;RSEQ=GGAGAACCAAGCTGGCGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:2531:28:13,15:1250,1245:2495,28:0.0111:2,2:25.9:1.0:32.4:1.0:0.70924:1.15841:60.0:56.0:0.0113:0.0004:1.1 0/0:1565:0:0,0:781,781:1562,0:0.0:2,0:24.8:1.0:30.5:1.0:1.0:0.0:60.0:56.852:0.9987:0.0:0.1 +7 41730289 . G C 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACAGCCCATGGGCTGAAACT;RSEQ=TTTCTGTACTGCCTGCAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:201:44:0,44:0,157:157,44:0.2189:1,1:25.5:1.0:32.8:1.0:1.0:0.0:60.0:21.0:0.2121:0.0:1.2 0/0:71:0:0,0:1,70:71,0:0.0:1,0:25.2:1.0:32.0:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.1 +7 41739141 . G C 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGCCATTCCACTCCAATCCT;RSEQ=GTACATTCACCCCTCTACCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:9,1:0,0:0,10:1.0:0,2:35.4:1.0:32.7:1.0:1.0:0.0:60.0:20.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 41740079 . G T 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.18526;SOR=0.0;LSEQ=ATTTTTTTATTTTTTTTTTT;RSEQ=GTGTTTTTTTTTTCCTTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:6:0,6:14,462:476,6:0.0124:1,0:9.0:1.0:25.8:1.0:1.0:0.0:60.0:2.0:0.009:0.0:1.7 0/0:212:0:0,0:6,201:207,0:0.0:1,0:21.8:1.0:29.9:1.0:1.0:0.0:59.2:16.25:1.0:0.0:0.6 +7 43299616 . T C 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AACCACACCCAGGCACATCA;RSEQ=AGTCAAACTTCTGAAAACCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:51:26:12,14:12,13:25,26:0.5098:2,2:30.5:1.0:32.9:1.0:1.0:1.07536:60.0:52.0:0.5098:0.0:1.1 0/0:68:0:0,0:32,36:68,0:0.0:2,0:30.0:1.0:28.3:1.0:1.0:0.0:60.0:33.0:1.0:0.0:0.1 +7 45551574 . A T 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.54067;SOR=0.0;LSEQ=CCTCTTGTGATTTTCCATCC;RSEQ=CTGACCCTTGCAACCTGCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:6:2,4:7,5:12,6:0.3333:2,2:26.2:1.0:29.7:1.0:0.61991:2.64037:60.0:12.0:0.3333:0.0:1.0 0/0:4:0:0,0:1,3:4,0:0.0:2,0:26.8:1.0:29.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +7 47092258 . G GC 81 p8 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTAGAGCGCTCCCTGCGGA;RSEQ=TCGGCCGCCCGCCTCTCCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:67:6:6,0:59,2:61,6:0.0896:1,0:6.3:1.0:31.7:1.0:1.0:0.0:23.7:12.0:0.0909:0.0746:0.8 0/0:6:0:0,0:6,0:6,0:0.0:0,0:26.0:1.0:30.3:1.0:1.0:0.0:29.8:5.0:1.0:0.0:0.5 +7 47092291 . G T 134 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.04674;SOR=0.0;LSEQ=CTCTCCCCCAGGTCTCTCCC;RSEQ=ACGTCCCCACGCGGGGCGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:16:16,0:144,2:146,16:0.0988:1,1:23.8:1.0:33.5:1.0:1.0:0.0:35.3:32.0:0.1:0.0:1.1 0/0:42:0:0,0:42,0:42,0:0.0:1,0:18.5:1.0:29.6:1.0:1.0:0.0:40.6:41.0:1.0:0.0:0.1 +7 47802771 . C T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGGCCTTGAGCTACCTGACT;RSEQ=TTCCCAGTTGGCCAGACACA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:19.0:1.0:29.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:2.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 50444040 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.13002;SOR=0.0;LSEQ=TGTAACCCCAGGTGCATCCC;RSEQ=AGGCCTGCCACCGAAGCCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:7,0:11,0:11,7:0.3889:0,0:31.7:1.0:29.1:1.0:1.0:0.0:55.0:6.0:0.3529:0.0:1.1 0/0:6:0:0,0:5,1:6,0:0.0:2,0:17.7:1.0:30.8:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.0 +7 50455179 . C A 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.02674;SOR=0.0;LSEQ=CTGTACCCAGGTAAGCGCTG;RSEQ=TGCTCGGAGGCCAGCCTGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:458:8:2,6:142,308:450,8:0.0175:2,2:20.3:1.0:32.0:1.0:1.0:1.38223:60.0:16.0:0.0177:0.0:1.1 0/0:284:0:0,0:89,193:282,0:0.0:2,0:24.0:1.0:31.8:1.0:1.0:0.0:60.0:564.0:0.993:0.0:0.1 +7 50739151 . G A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.50877;SOR=0.0;LSEQ=GATCCAGCTAACTATCCCAC;RSEQ=TAGACCAGCAAATGATGCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:7:7,0:10,0:10,7:0.4118:0,0:23.3:1.0:31.4:1.0:1.0:0.0:57.9:14.0:0.4375:0.0:1.1 0/0:2:0:0,0:2,0:2,0:0.0:0,0:18.0:1.0:29.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +7 53854866 . G A 134 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=5e-05;SOR=0.0;LSEQ=TTAACTCAGTTAGGGATTTG;RSEQ=ATCCTGCTCCTAATCCACCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:723:21:15,6:436,265:701,21:0.029:2,2:16.6:1.0:30.7:1.0:0.49538:1.52:39.7:42.0:0.0295:0.0:1.2 0/0:439:0:0,0:277,161:438,0:0.0:2,0:27.0:1.0:30.4:1.0:1.0:0.0:49.4:86.6:0.9977:0.0:0.1 +7 55210733 . G C 112 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGAGAGTGTTGAACCCCGT;RSEQ=AGGCATGAGAGCACAGTGTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:11:11,0:9,1:10,11:0.5238:2,0:21.0:1.0:32.6:1.0:0.47619:0.0:60.0:22.0:0.5238:0.0:1.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 55219290 . T C 135 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00167;SOR=0.04312;LSEQ=AAGTGAACATCAGCAGGGGC;RSEQ=GGGCGCGGTGGCTCACCCCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:32:26:0,26:0,6:6,26:0.8125:0,1:25.0:1.0:28.9:1.0:1.0:0.0:53.4:25.0:0.8065:0.0:1.7 0/1:7:1:0,1:0,6:6,1:0.1429:0,0:17.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.1429:0.0:1.0 +7 55219307 . C G 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.01129;SOR=0.0;LSEQ=GGCTGGGCGCGGTGGCTCAC;RSEQ=CCTATAATCCCAGCACTTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:17:0,17:0,3:3,17:0.85:0,1:25.9:1.0:33.2:1.0:1.0:0.0:48.6:34.0:0.85:0.0:1.9 0/0:3:0:0,0:0,3:3,0:0.0:0,0:16.7:1.0:31.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +7 55222593 . A C 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=5;MSI=4.0;MSILEN=1.0;SSF=0.00054;SOR=0.0;LSEQ=CAGATTTGTGTACATGAAAA;RSEQ=TTTTACATTCCGTATGGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:697:21:12,9:301,373:674,21:0.0301:2,2:20.3:1.0:31.2:1.0:0.27375:1.65:59.0:9.5:0.0278:0.0:1.2 0/0:308:0:0,0:135,172:307,0:0.0:2,0:23.2:1.0:29.8:1.0:1.0:0.0:59.9:75.75:1.0:0.0:0.3 +7 55228160 . T G 161 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00127;SOR=0.0;LSEQ=TTAAGAAGCAAATTAAAATC;RSEQ=TAAGATTCCTAACTGTGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:31:2,29:1,87:88,31:0.2605:1,2:22.2:1.0:32.5:1.0:0.16586:5.89:60.0:62.0:0.2605:0.0:1.7 0/0:28:0:0,0:2,26:28,0:0.0:2,0:22.9:1.0:30.4:1.0:1.0:0.0:60.0:56.0:1.0:0.0:0.5 +7 55807008 . G A 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.05641;SOR=0.14746;LSEQ=GCCGCTGCATGGGTCCCAGA;RSEQ=GCTGGACTGCGGCAGGTGCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:64:13:3,10:11,40:51,13:0.2031:2,2:38.5:1.0:32.5:1.0:1.0:1.09:28.5:26.0:0.2063:0.0:1.1 0/1:28:1:0,1:8,19:27,1:0.0357:2,0:31.0:0.0:26.0:0.0:1.0:0.0:22.0:2.0:0.0357:0.0:1.0 +7 56430693 . C A 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.32315;SOR=0.0;LSEQ=TAAGAAGGATGGACACAGCC;RSEQ=CAACAAATGGGACAAGGACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:48:6:4,2:25,17:42,6:0.125:2,2:34.3:1.0:30.7:1.0:1.0:1.35:27.8:12.0:0.125:0.0:1.0 0/0:16:0:0,0:8,8:16,0:0.0:2,0:26.4:1.0:30.4:1.0:1.0:0.0:23.9:32.0:1.0:0.0:0.4 +7 56430843 . C T 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.09642;SOR=0.0;LSEQ=CCTGAGCAAGCGGTGGTACA;RSEQ=CCTGGGGCCCAATGAGACAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:7:7,0:70,31:101,7:0.0648:2,0:32.3:1.0:33.0:0.0:0.18875:0.0:22.7:14.0:0.066:0.0:1.1 0/0:54:0:0,0:31,23:54,0:0.0:2,0:24.7:1.0:30.8:1.0:1.0:0.0:25.8:53.0:1.0:0.0:0.2 +7 56432708 . T C 135 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCAGGGGCCAACTGAAGCTG;RSEQ=TGGGGCAGCATGAGCAGGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:16:1,15:1,3:4,16:0.8:2,1:42.7:1.0:33.9:1.0:0.36842:4.47215:23.9:32.0:0.8:0.0:2.1 0/0:31:0:0,0:8,23:31,0:0.0:2,0:22.3:1.0:28.6:1.0:1.0:0.0:31.7:62.0:1.0:0.0:0.1 +7 56432714 . C A 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=GCCAACTGAAGCTGTTGGGG;RSEQ=AGCATGAGCAGGATGTTCTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:20:16:1,15:1,3:4,16:0.8:2,1:46.4:1.0:32.1:1.0:0.36842:4.47215:23.9:32.0:0.8:0.0:2.1 0/0:27:0:0,0:7,20:27,0:0.0:2,0:24.1:1.0:31.1:1.0:1.0:0.0:33.0:54.0:1.0:0.0:0.0 +7 61968966 . A C 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=2.0;SSF=0.09173;SOR=0.15538;LSEQ=TGTAAAGTCTGCAAGTGGAT;RSEQ=TATGGACCGCATTGAGGCCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:155:5:2,3:76,74:150,5:0.0323:2,2:22.2:1.0:34.0:1.0:0.68133:1.53629:24.0:10.0:0.0329:0.0:1.6 0/0:195:1:1,0:95,99:194,1:0.0051:2,0:4.0:0.0:31.0:0.0:0.49231:0.0:29.0:2.0:0.0052:0.0:1.0 +7 63230653 . G A 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0203;SOR=0.11634;LSEQ=TGCTAGCCCCTGGCTTGTGG;RSEQ=CTTGGCCTCTGAGCTGTACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:70:9:5,4:30,31:61,9:0.1286:2,2:34.8:1.0:28.1:1.0:1.0:1.29:39.1:3.5:0.1045:0.0:1.0 0/1:60:1:0,1:33,26:59,1:0.0167:2,0:2.0:0.0:29.0:0.0:0.45:0.0:21.0:2.0:0.0175:0.0:1.0 +7 65970787 . T A 165 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCCTGCGGTCGTAGCACTCG;RSEQ=GGATGCCGGGGTCGTCCCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:822:40:23,17:426,356:782,40:0.0487:2,2:22.6:1.0:31.1:1.0:0.74709:1.13:58.7:39.0:0.048:0.0:1.2 0/0:716:0:0,0:384,332:716,0:0.0:2,0:25.7:1.0:29.2:1.0:1.0:0.0:59.5:118.333:1.0:0.0:0.2 +7 70859670 . C T 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.02797;SOR=0.0;LSEQ=GTGACCAGGATGGAGGAATT;RSEQ=GGGTGCACAGAGGTATCACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:6:1,5:0,33:33,6:0.1538:1,2:19.7:1.0:32.3:1.0:0.15385:0.0:54.0:12.0:0.1538:0.0:1.0 0/0:33:0:0,0:0,33:33,0:0.0:1,0:24.1:1.0:29.6:1.0:1.0:0.0:60.0:66.0:1.0:0.0:0.1 +7 81061460 . T C 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGGCTCTTCCCCCCTTCGCT;RSEQ=GGCACTTCTCCTTCCTGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:16:6:3,3:5,5:10,6:0.375:2,2:20.7:1.0:32.3:1.0:1.0:1.0:54.7:12.0:0.4:0.0:1.5 0/0:1:0:0,0:0,1:1,0:0.0:0,0:41.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +7 81076550 . A G 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.38462;SOR=0.0;LSEQ=ATTTAATCAAACATTTTAAT;RSEQ=CTGTGAAAATTCTTAGGTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:12:8:8,0:4,0:4,8:0.6667:0,0:26.6:1.0:33.3:1.0:1.0:0.0:60.0:16.0:0.6667:0.0:1.8 0/0:1:0:0,0:1,0:1,0:0.0:0,0:27.0:0.0:29.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +7 81076607 . C T 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.02667;SOR=0.0;LSEQ=AAAACAAACTCAAAAATATA;RSEQ=GTGCCCTATGAACATAGTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:9,0:9,0:9,9:0.5:0,0:17.6:1.0:30.3:1.0:1.0:0.0:60.0:18.0:0.5:0.0:1.7 0/0:7:0:0,0:7,0:7,0:0.0:0,0:28.4:1.0:32.4:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.0 +7 81336265 . C T 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGAAAGAAGTAGTGAGGA;RSEQ=TGAAAAAAGCCTATTGACAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:4,2:2,0:2,6:0.75:0,2:25.3:1.0:31.8:1.0:1.0:0.0:52.3:12.0:0.75:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 81336535 . C A 207 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.14226;LSEQ=AAAATGAATACATATTATAA;RSEQ=CTTAAGAGCAAAGTGGAAGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:420:110:93,17:248,61:309,110:0.2619:2,2:25.7:1.0:30.6:1.0:0.39232:1.34:60.0:220.0:0.2625:0.0:1.0 0/1:292:14:11,3:217,60:277,14:0.0479:2,2:18.4:1.0:29.9:1.0:1.0:1.01:60.0:28.0:0.0486:0.0:1.0 +7 81340916 . C A 108 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00216;SOR=0.0;LSEQ=AACCAAATATATATTAAAAT;RSEQ=CAAGTATCAATGAATTCAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:191:12:1,11:16,163:179,12:0.0628:2,2:21.3:1.0:30.3:1.0:1.0:1.07934:60.0:24.0:0.0638:0.0:1.0 0/0:127:0:0,0:17,110:127,0:0.0:2,0:22.0:1.0:30.6:1.0:1.0:0.0:60.0:126.0:1.0:0.0:0.1 +7 81346925 . G A 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTCCATAATTGGCATATTAG;RSEQ=TTTTGTGATTTTGCCTCTAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:0,2:2,8:0.8:0,0:26.5:1.0:31.0:1.0:1.0:0.0:57.0:16.0:0.8:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 81388001 . C A 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCAATATTTAGGGAGAAGT;RSEQ=AGTTACCTTTGTTTTCATAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1085:58:41,17:600,425:1025,58:0.0535:2,2:22.3:1.0:29.4:1.0:0.07451:1.71:60.0:116.0:0.0538:0.0:1.0 0/0:847:0:0,0:501,344:845,0:0.0:2,0:47.0:0.0:12.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:7.0 +7 91180083 . T C 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.30855;SOR=0.0;LSEQ=TCCATTCATCCTACTTCCTT;RSEQ=ACTAATTCTCCTTTCTATTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:8:0,8:1,20:21,8:0.2759:1,0:23.9:1.0:33.0:1.0:1.0:0.0:60.0:16.0:0.2759:0.0:1.0 0/0:5:0:0,0:0,5:5,0:0.0:0,0:30.0:1.0:27.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:0.4 +7 92404285 . A G 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.17683;SOR=0.0;LSEQ=TCTTGTGATCATATGTAAAG;RSEQ=TATCAAATGAGATCTGATAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:52:6:0,6:0,45:45,6:0.1154:1,0:19.8:1.0:32.2:1.0:1.0:0.0:58.7:12.0:0.1176:0.0:1.0 0/0:20:0:0,0:0,20:20,0:0.0:1,0:21.3:1.0:30.7:1.0:1.0:0.0:60.0:19.0:1.0:0.0:0.0 +7 103275947 . A C 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.04013;SOR=0.0;LSEQ=CATTATCATAAGAATAATGC;RSEQ=ACAAAACTCCTTCACCAGGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:7:0,7:0,53:53,7:0.1167:1,0:13.7:1.0:33.1:1.0:1.0:0.0:60.0:14.0:0.1273:0.0:1.1 0/0:39:0:0,0:3,36:39,0:0.0:2,0:23.9:1.0:31.1:1.0:1.0:0.0:60.0:78.0:1.0:0.0:0.0 +7 106522693 . G A 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01592;LSEQ=ATGAATAGACCTCTCAGCTC;RSEQ=TTTGAAAAGATTATAATTCC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:634:176:46,130:128,330:458,176:0.2776:2,2:23.7:1.0:30.8:1.0:0.69156:1.09605:59.9:57.667:0.2755:0.0:1.1 0/0:495:3:1,2:167,323:490,3:0.0061:2,2:4.0:1.0:25.3:1.0:1.0:1.03399:60.0:2.0:0.0041:0.0:1.0 +7 106524644 . CTG C 177 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=4;MSI=3.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GTTTATTCCTGTGCAGGCTA;RSEQ=TGTGGCAACCTTTGTTCTTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:687:44:21,23:319,323:642,44:0.064:2,2:29.3:1.0:32.5:1.0:0.87659:1.08153:60.0:88.0:0.0651:0.0029:0.8 0/0:593:0:0,0:289,304:593,0:0.0:2,0:25.6:1.0:29.7:1.0:1.0:0.0:60.0:83.714:1.0:0.0:0.2 +7 114270000 . G A 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=3.0;SSF=0.00306;SOR=0.0;LSEQ=CAACAACAGCAGCAACAACA;RSEQ=CAGCAGCAGCAGCAACAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:226:7:4,3:99,118:217,7:0.031:2,2:34.1:1.0:28.1:1.0:0.70583:1.59:58.3:6.0:0.0279:0.0:1.4 0/0:287:0:0,0:132,138:270,0:0.0:2,0:24.8:1.0:30.9:1.0:1.0:0.0:58.4:26.0:0.9962:0.0:0.3 +7 114270077 . T G 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.11935;LSEQ=AGAGGTAGGATCCGGTTATC;RSEQ=CATTGATACATAACAGTTTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:102:47:11,36:12,43:55,47:0.4608:2,2:22.4:1.0:31.7:1.0:1.0:1.09:60.0:94.0:0.47:0.0:1.1 0/1:120:11:3,8:28,81:109,11:0.0917:2,2:15.6:1.0:30.3:1.0:1.0:1.08:60.0:22.0:0.0957:0.0:1.0 +7 116187106 . G A 138 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.08852;LSEQ=CTCTGCCTCCATCATTAATG;RSEQ=CCTTCTGCCTGAGTGTTTTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:41:25:6,19:6,10:16,25:0.6098:2,2:28.3:1.0:29.8:1.0:0.48495:1.86941:60.0:50.0:0.6098:0.0:1.0 0/1:34:4:1,3:9,21:30,4:0.1176:2,2:20.5:1.0:29.5:1.0:1.0:1.27668:60.0:8.0:0.1176:0.0:1.0 +7 116339672 . C T 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=4e-05;SOR=0.05462;LSEQ=TGTCCTGACTGTGTGGTGAG;RSEQ=GCCCTGGGAGCCAAAGTCCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:536:19:11,8:306,211:517,19:0.0354:2,2:24.0:1.0:28.3:1.0:1.0:1.05459:60.0:8.5:0.0323:0.0:1.4 0/0:500:1:0,1:279,220:499,1:0.002:2,0:1.0:0.0:24.0:0.0:0.442:0.0:60.0:2.0:0.002:0.0:1.0 +7 116340531 . A AT 92 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.08669;SOR=0.0;LSEQ=AATTATATCTTTAAAATGTA;RSEQ=ATGGTAACTAAAAGAAAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:9:0,9:0,6:6,9:0.6:0,0:21.1:1.0:29.3:1.0:1.0:0.0:58.3:18.0:0.6:0.2:0.4 0/0:4:0:0,0:0,4:4,0:0.0:0,0:20.0:1.0:31.5:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +7 116340582 . A C 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.22222;SOR=0.0;LSEQ=TTCAGATTTGCATGTTCGTG;RSEQ=CATTTCAGATTATATTAAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:27.4:1.0:31.7:1.0:1.0:0.0:60.0:14.0:0.875:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:33.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +7 116397572 . A G 274 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04763;LSEQ=AATGGCCACGGGACAACACA;RSEQ=TACAGTACATTCTCCTATGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1008:336:176,160:339,333:672,336:0.3333:2,2:27.1:1.0:32.7:1.0:0.59302:1.08:60.0:111.0:0.3343:0.0:1.1 0/1:990:23:11,12:468,499:967,23:0.0232:2,2:23.8:1.0:31.0:1.0:1.0:1.02312:60.0:46.0:0.0235:0.0:1.2 +7 116403127 . A G 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00058;SOR=0.0;LSEQ=TGTCAACATCGCTCTAATTC;RSEQ=GAGATAATCTGTTGTACCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:448:12:9,3:252,184:436,12:0.0268:2,2:21.9:1.0:29.9:1.0:0.37431:2.19:60.0:24.0:0.0273:0.0:1.2 0/0:395:0:0,0:223,171:394,0:0.0:2,0:23.3:1.0:29.5:1.0:1.0:0.0:60.0:77.8:0.9974:0.0:0.1 +7 116411923 . C T 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02135;LSEQ=ATCTGGGCAGTGAATTAGTT;RSEQ=GCTACGATGCAAGAGTACAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:654:88:53,35:329,237:566,88:0.1346:2,2:27.7:1.0:30.8:1.0:0.72893:1.09:60.0:87.0:0.1345:0.0:1.0 0/0:606:2:0,2:348,256:604,2:0.0033:2,0:1.0:0.0:26.5:1.0:0.18085:0.0:60.0:4.0:0.0033:0.0:1.0 +7 116423161 . G A 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00642;SOR=0.0;LSEQ=TTTCCTCAGCCTGTTGAATT;RSEQ=GCAATGTCAATGTCAAGCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:8,0:19,0:19,8:0.2963:1,0:24.3:1.0:29.4:1.0:1.0:0.0:59.6:16.0:0.2963:0.0:1.0 0/0:21:0:0,0:18,3:21,0:0.0:2,0:26.0:1.0:31.1:1.0:1.0:0.0:60.0:42.0:1.0:0.0:0.0 +7 127153538 . C T 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.00223;SOR=0.05425;LSEQ=TAGCCCTGTTGTGCAAAGAA;RSEQ=AGTACCGCTGCTGCTGCCGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:9:6,3:4,5:9,9:0.5:2,2:33.0:1.0:30.0:1.0:0.63719:2.37:60.0:18.0:0.5:0.0:1.2 0/1:21:1:0,1:11,9:20,1:0.0476:2,0:47.0:0.0:27.0:0.0:0.47619:0.0:60.0:2.0:0.0476:0.0:1.0 +7 128766971 . G A 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.03264;LSEQ=CGTACATCGTGGGCTTCTAC;RSEQ=GGGCCTTCTACTGTGACAGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:592:26:11,15:302,263:565,26:0.0439:2,2:20.4:1.0:31.1:1.0:0.31684:1.56464:55.0:52.0:0.0448:0.0:1.0 0/0:669:1:1,0:335,333:668,1:0.0015:2,0:1.0:0.0:23.0:0.0:1.0:0.0:60.0:2.0:0.0015:0.0:1.0 +7 128767250 . G A 205 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACTCCATGGCCAACTCCTTC;RSEQ=TGGGCACGCGCTCCTACATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:544:104:43,61:201,238:439,104:0.1912:2,2:29.8:1.0:30.7:1.0:0.44391:1.19767:49.9:103.0:0.1911:0.0:1.1 0/0:499:0:0,0:228,268:496,0:0.0:2,0:30.3:1.0:30.4:1.0:1.0:0.0:48.8:164.333:0.994:0.0:0.2 +7 128829066 . A G 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00026;SOR=0.0;LSEQ=GCTGCTGCTGCTGCTGGGGG;RSEQ=CCCGGGCCGGGGGGCGGCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:87:9:4,5:39,39:78,9:0.1034:2,2:21.7:1.0:33.0:1.0:1.0:1.2468:60.0:18.0:0.1084:0.0:1.3 0/0:125:0:0,0:61,64:125,0:0.0:2,0:21.1:1.0:27.5:1.0:1.0:0.0:60.0:14.625:1.0:0.0:0.4 +7 128845223 . C T 196 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACATCGCGGCCTTCGGGGC;RSEQ=GTCACGGGCCTCTGCACGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:429:81:27,54:98,250:348,81:0.1888:2,2:27.1:1.0:31.0:1.0:0.4153:1.27:60.0:80.0:0.1891:0.0:1.4 0/0:379:0:0,0:124,255:379,0:0.0:2,0:23.6:1.0:29.4:1.0:1.0:0.0:60.0:74.8:1.0:0.0:0.4 +7 128846679 . GT G 74 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGCCCAGGGCTCACAGCTT;RSEQ=TTTTTTTGTTTGTTTTTGTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:0,5:0,4:4,5:0.5556:0,0:36.4:1.0:32.2:1.0:1.0:0.0:55.2:10.0:0.5556:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 128849078 . C A 184 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.0;LSEQ=AGACTCTCTCCTCCCCACTG;RSEQ=TGCTGCGGGACTGGGCTTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:606:70:50,20:351,183:534,70:0.1155:2,2:27.4:1.0:30.1:1.0:0.41956:1.3:60.0:69.0:0.1169:0.0:1.1 0/0:606:0:0,0:382,223:605,0:0.0:2,0:23.7:1.0:31.0:1.0:1.0:0.0:60.0:150.25:0.9983:0.0:0.1 +7 128850084 . T G 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.01786;LSEQ=TGAGCCCAGGAGTTGGAAGC;RSEQ=GCAGTGGGTTGTGATCACGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:75:39:39,0:36,0:36,39:0.52:1,1:26.4:1.0:29.3:1.0:1.0:0.0:59.4:12.0:0.5:0.0:1.0 0/1:54:1:1,0:53,0:53,1:0.0185:1,0:8.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0185:0.0:1.0 +7 128850798 . G T 77 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.01052;SOR=0.0;LSEQ=GCTCCTTCCCTATCCCTTCT;RSEQ=CTCTCAGGTTGACTGGGCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:498:6:3,3:309,183:492,6:0.012:2,2:9.5:1.0:29.8:1.0:0.67584:1.68659:60.0:12.0:0.0123:0.0:1.0 0/0:563:0:0,0:342,220:562,0:0.0:2,0:24.2:1.0:31.4:1.0:1.0:0.0:60.0:186.333:1.0:0.0:0.2 +7 128851674 . C G 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00145;SOR=0.0;LSEQ=GAGGCTGGGGGCTTCTGGGA;RSEQ=TGGAGTACAGGGGCTGTCGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:282:11:5,6:70,201:271,11:0.039:2,2:13.6:1.0:33.5:1.0:0.16847:2.38:60.0:22.0:0.0401:0.0:1.0 0/0:229:0:0,0:67,161:228,0:0.0:2,0:23.8:1.0:30.7:1.0:1.0:0.0:60.0:24.333:0.9955:0.0:0.1 +7 128852381 . C T 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02664;LSEQ=AGCATGCTTCCCTAGGATCC;RSEQ=GTCTTCCAGAGAACCTGTGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:34:0,34:2,46:48,34:0.4146:1,1:24.3:1.0:30.6:1.0:0.50858:0.0:60.0:68.0:0.4198:0.0:1.1 0/1:55:1:0,1:2,52:54,1:0.0182:1,0:40.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0185:0.0:1.0 +7 135335822 . C T 160 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.10582;LSEQ=ATAATGCACTGGAATGAAAT;RSEQ=GTAGGGACCACATCAAAGGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:40:22,18:80,64:144,40:0.2174:2,2:30.2:1.0:30.2:1.0:1.0:1.02261:60.0:39.0:0.2167:0.0:1.2 0/1:176:5:2,3:89,82:171,5:0.0284:2,2:20.0:1.0:28.4:1.0:0.67364:1.62357:60.0:10.0:0.0289:0.0:1.2 +7 140439319 . TG T 77 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=10;MSI=11.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATATAAACAAAAGCTCTTTG;RSEQ=GGGGGGGGGGTCTTCGATAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:5,0:2,0:2,5:0.7143:0,0:23.4:1.0:33.3:1.0:1.0:0.0:60.0:10.0:0.7143:0.1429:0.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 140453136 . A T 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCCACTCCATCGAGATTTC;RSEQ=CTGTAGCTAGACCAAAATCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:533:76:41,35:210,247:457,76:0.1426:2,2:26.8:1.0:31.1:1.0:0.21555:1.38:49.9:75.0:0.1415:0.0:1.1 0/0:639:0:0,0:303,336:639,0:0.0:2,0:25.8:1.0:29.0:1.0:1.0:0.0:58.6:62.9:1.0:0.0:0.1 +7 140482427 . T C 240 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06837;LSEQ=GAATGTGCAGGTTTGTTACA;RSEQ=ACGTATACATGTGCCATGGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:537:170:85,85:171,196:367,170:0.3166:2,2:26.5:1.0:32.4:1.0:0.51568:1.15:44.5:340.0:0.3184:0.0:1.1 0/1:457:14:4,10:192,251:443,14:0.0306:2,2:24.5:1.0:30.6:1.0:0.41175:1.9098:44.1:28.0:0.0308:0.0:1.1 +7 140483403 . C T 237 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0039;LSEQ=TATTAAAAAAAAGGAAATCC;RSEQ=CAGATGGAAACATTTTCTAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:674:192:111,81:253,229:482,192:0.2849:2,2:26.7:1.0:31.3:1.0:0.2309:1.24:60.0:63.0:0.2872:0.0:2.1 0/0:646:1:0,1:337,307:644,1:0.0015:2,0:1.0:0.0:26.0:0.0:0.47752:0.0:60.0:2.0:0.0016:0.0:1.0 +7 140483605 . C T 225 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.09569;LSEQ=AAAGTTAATGTAAATAAAGC;RSEQ=GGGCATATTTCTCAAGACTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:559:156:72,84:187,216:403,156:0.2791:2,2:24.7:1.0:31.0:1.0:1.0:1.01001:60.0:38.0:0.2764:0.0:1.1 0/1:533:19:8,11:242,270:512,19:0.0356:2,2:24.4:1.0:29.7:1.0:0.81584:1.23193:60.0:38.0:0.036:0.0:1.1 +7 140486743 . T C 258 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08283;LSEQ=TGTAGTCTACGGCCATACCA;RSEQ=CCTGAACGTGTCCGATCTTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1039:275:117,158:355,408:763,275:0.2647:2,2:25.3:1.0:31.9:1.0:0.25947:1.17482:59.6:136.5:0.2682:0.0:1.1 0/1:1348:39:19,20:635,670:1305,39:0.0289:2,2:24.5:1.0:30.9:1.0:1.0:1.0:57.4:38.0:0.0287:0.0:1.1 +7 140487494 . C T 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00793;LSEQ=AATTATTTTATTAATTAAAA;RSEQ=AATACATCTTATAACTATTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:770:111:51,60:292,366:658,111:0.1442:2,2:24.9:1.0:29.9:1.0:0.75806:1.07:60.0:110.0:0.1444:0.0:1.2 0/0:751:1:0,1:348,401:749,1:0.0013:2,0:1.0:0.0:22.0:0.0:1.0:0.0:60.0:2.0:0.0013:0.0:1.0 +7 140488156 . T G 239 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.11033;LSEQ=AAAAAGTTATAAATAATTAT;RSEQ=TCTCTATTATAGGCATTTTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:564:172:84,88:196,196:392,172:0.305:2,2:25.5:1.0:32.2:1.0:0.85492:1.04756:60.0:56.333:0.3056:0.0:1.1 0/1:564:26:13,13:271,266:537,26:0.0461:2,2:21.2:1.0:30.9:1.0:1.0:1.01877:60.0:52.0:0.0468:0.0:1.0 +7 140489173 . A G 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=GAGGGATTGAATGGCCCCAA;RSEQ=TATCTCTGAATAGTCTCTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1275:62:27,35:508,705:1213,62:0.0486:2,2:25.6:1.0:32.6:1.0:0.79349:1.07:60.0:61.0:0.0485:0.0:1.1 0/0:1333:0:0,0:603,727:1330,0:0.0:2,0:26.0:1.0:29.8:1.0:1.0:0.0:60.0:82.125:0.9985:0.0:0.1 +7 140492039 . T C 252 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.06144;LSEQ=ATACTGTAAAAACCACATTA;RSEQ=TGACAGTCCTGCCTCTATGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:679:206:92,114:201,272:473,206:0.3034:2,2:25.8:1.0:32.9:1.0:0.61385:1.09:60.0:205.0:0.3046:0.0:1.1 0/1:615:16:5,11:271,328:599,16:0.026:2,2:26.3:1.0:32.3:1.0:0.31609:1.816:60.0:32.0:0.0264:0.0:1.1 +7 140494413 . A C 206 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTAGCAGTAATGACTTTTAA;RSEQ=AGTATTAATTTAAAAATCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:647:86:46,40:286,274:560,86:0.1329:2,2:25.0:1.0:32.2:1.0:0.72862:1.1:59.9:172.0:0.1342:0.0:1.1 0/0:763:0:0,0:378,384:762,0:0.0:2,0:23.7:1.0:29.7:1.0:1.0:0.0:60.0:761.0:0.9987:0.0:0.1 +7 140496563 . T C 258 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.07259;LSEQ=GTGATCATAATCTGATGTCA;RSEQ=TGAATATCTCAGCCATGTCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:728:227:85,142:222,278:500,227:0.3118:2,2:24.8:1.0:33.0:1.0:0.08883:1.33353:60.0:226.0:0.313:0.0:1.1 0/1:629:20:12,8:266,343:609,20:0.0318:2,2:24.6:1.0:31.2:1.0:0.17284:1.93:60.0:40.0:0.0319:0.0:1.1 +7 140496901 . TC T 259 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGTCGGCAAACTGGCTTTC;RSEQ=CCAATGATACCTGTACCTAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:881:288:142,146:287,301:588,288:0.3269:2,2:26.6:1.0:31.8:1.0:0.94266:1.02:59.9:576.0:0.328:0.0375:0.1 0/0:847:0:0,0:415,431:846,0:0.0:2,0:25.1:1.0:30.5:1.0:1.0:0.0:60.0:119.857:0.9988:0.0:0.1 +7 140497586 . A T 239 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.08833;LSEQ=GGACCTGCCATTAGAAAGGC;RSEQ=TCATGGTCTACAGAATCTGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:633:205:103,102:209,219:428,205:0.3239:2,2:25.6:1.0:31.2:1.0:0.79889:1.06:59.9:40.0:0.319:0.0:1.1 0/1:543:22:14,8:278,242:520,22:0.0405:2,2:22.2:1.0:28.7:1.0:0.3894:1.52:60.0:21.0:0.0393:0.0:1.1 +7 140498072 . C T 124 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=8.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTATGGGGACTTTTTTTTT;RSEQ=TTTTTTTTGAGACGGAGTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:561:38:3,35:259,243:502,38:0.0677:2,2:8.7:1.0:23.8:1.0:0.0:12.39247:37.8:1.714:0.0521:0.0:2.7 0/0:685:0:0,0:268,258:526,0:0.0:2,0:11.9:1.0:28.4:1.0:1.0:0.0:57.9:6.306:0.7605:0.0:0.3 +7 140507901 . C T 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCCTTTCTTGGTTATTACA;RSEQ=CTAAAAATATTCATATACCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:338:27:6,21:71,239:310,27:0.0799:2,2:23.1:1.0:30.8:1.0:1.0:1.03966:60.0:54.0:0.0811:0.0:1.1 0/0:338:0:0,0:92,245:337,0:0.0:2,0:23.0:1.0:30.6:1.0:1.0:0.0:60.0:66.4:0.997:0.0:0.1 +7 148505788 . T C 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATAAAGATATGCATAGTATA;RSEQ=TGTCAAGTAAAACCATGTTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:36.8:1.0:33.0:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 148505864 . G A 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGGAAAACGCTCCACGAGT;RSEQ=AGCATGCAGCATGCGGCATG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:10:7:7,0:3,0:3,7:0.7:0,0:24.1:1.0:28.7:1.0:1.0:0.0:60.0:14.0:0.7:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +7 151168756 . G A 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.02179;LSEQ=AGTTTTTAAATGTATGTTAT;RSEQ=TTGCCAGCTGGAAAAATGTA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:508:93:19,74:92,322:414,93:0.1831:2,2:23.5:1.0:30.8:1.0:0.78221:1.11256:60.0:186.0:0.1849:0.0:1.2 0/0:413:2:1,1:98,312:410,2:0.0048:2,2:22.0:1.0:26.0:1.0:0.42329:3.17:60.0:4.0:0.0049:0.0:1.0 +7 151828793 . T C 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=CTGGAACGCTGTTCCCACCA;RSEQ=GTTGGGTTACGTTGTAGGTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:63:15:9,6:30,18:48,15:0.2381:2,2:25.1:1.0:30.6:1.0:1.0:1.10924:60.0:30.0:0.2459:0.0:1.1 0/0:54:0:0,0:27,27:54,0:0.0:2,0:24.2:1.0:28.8:1.0:1.0:0.0:60.0:108.0:1.0:0.0:0.1 +7 151836397 . T C 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00735;SOR=0.0;LSEQ=GTCGACCTGAAACTCCCCTC;RSEQ=GTGTTCCTATCCACACCAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:220:8:3,5:65,146:211,8:0.0364:2,2:24.9:1.0:26.1:1.0:0.70587:1.35:60.0:7.0:0.0324:0.0:1.0 0/0:215:0:0,0:60,154:214,0:0.0:2,0:21.6:1.0:29.4:1.0:1.0:0.0:60.0:41.8:0.9952:0.0:0.1 +7 151859061 . T TAGAAATG 103 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=2.0;MSILEN=7.0;SSF=0.01293;SOR=0.0;LSEQ=AAACATGGGTTCCAGAGAGG;RSEQ=AGAAATGACAAAATAAAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:74:10:10,0:62,1:63,10:0.1351:1,0:22.5:1.0:31.3:1.0:1.0:0.0:60.0:20.0:0.1389:0.0541:0.0 0/0:43:0:0,0:41,2:43,0:0.0:1,0:20.6:1.0:29.5:1.0:1.0:0.0:60.0:20.5:1.0:0.0:0.0 +7 151874581 . G C 221 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTGAAAATTCACCACCTA;RSEQ=TGGATGGTTCAGAGTCCTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:653:114:60,54:282,254:536,114:0.1746:2,2:23.6:1.0:32.4:1.0:1.0:1.0:60.0:56.0:0.1742:0.0:1.1 0/0:670:0:0,0:357,312:669,0:0.0:2,0:24.8:1.0:31.5:1.0:1.0:0.0:60.0:166.25:0.9985:0.0:0.1 +7 151875047 . G A 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.02842;LSEQ=TGCTGAGGAGGCACAAGGAA;RSEQ=CGCTCTTGACTCGGCATGGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:455:86:28,58:159,210:369,86:0.189:2,2:29.0:1.0:30.1:1.0:0.08826:1.56685:59.9:172.0:0.1982:0.0:1.2 0/0:457:3:0,3:191,262:453,3:0.0066:2,0:13.0:1.0:15.3:1.0:0.26815:0.0:43.0:0.0:0.0:0.0:6.3 +7 151891255 . G A 211 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.00685;LSEQ=GTAACAAGATTAAAAGACTA;RSEQ=TAGGGTCCTGGTATGGGGAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:718:121:68,53:327,265:592,121:0.1685:2,2:26.6:1.0:30.5:1.0:0.92011:1.04:60.0:39.333:0.1676:0.0:1.1 0/0:723:1:1,0:391,328:719,1:0.0014:2,0:1.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0014:0.0:1.0 +7 151946985 . C G 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATAAGAAGACTATCTGTGT;RSEQ=AAGACTTTCTGAGGGATGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:669:24:13,11:332,311:643,24:0.0359:2,2:26.0:1.0:31.5:1.0:0.83825:1.11:58.7:48.0:0.0361:0.0:1.0 0/0:795:0:0,0:413,382:795,0:0.0:2,0:25.9:1.0:30.8:1.0:1.0:0.0:59.8:131.5:1.0:0.0:0.1 +7 151948998 . TA T 98 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.0009;SOR=0.0;LSEQ=CATTACAAAAACAAAAAATT;RSEQ=AAAAAAAATCATTCTCAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:344:11:4,7:248,85:333,11:0.032:2,2:16.5:1.0:28.5:1.0:0.01006:5.07646:60.0:22.0:0.0324:0.0145:0.7 0/0:339:0:0,0:248,90:338,0:0.0:2,0:23.0:1.0:27.8:1.0:1.0:0.0:60.0:111.667:0.997:0.0:0.1 +7 151949735 . T C 264 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTTGGTAACAATTGTCACA;RSEQ=ATCAGGCAATTGTGGTGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:829:308:129,179:206,314:520,308:0.3715:2,2:24.9:1.0:32.0:1.0:0.55796:1.1:60.0:101.667:0.372:0.0:1.1 0/0:835:0:0,0:354,478:832,0:0.0:2,0:24.0:1.0:28.2:1.0:1.0:0.0:60.0:137.667:0.9964:0.0:0.1 +7 152357777 . A AT 173 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTTATTTATATAAAGGTTGT;RSEQ=TTTTTTACCATGCACAGGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:685:51:28,23:420,214:634,51:0.0745:2,2:26.9:1.0:30.5:1.0:0.12526:1.61102:60.0:102.0:0.0752:0.0117:0.2 0/0:782:0:0,0:483,294:777,0:0.0:2,0:25.4:1.0:28.4:1.0:1.0:0.0:60.0:76.7:0.9935:0.0:0.1 +7 153622478 . CG AA 162 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAGGGAGATCATCCCGCAT;RSEQ=TGGAGGGTCCCTGAGGTTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:468:41:17,24:185,241:426,41:0.0876:2,2:27.5:1.0:30.3:1.0:0.86985:1.08356:57.5:40.0:0.0897:0.0064:2.1 0/0:371:0:0,0:160,210:370,0:0.0:2,0:22.9:1.0:29.2:1.0:1.0:0.0:59.4:51.857:1.0:0.0:1.0 +7 153622749 . G T 103 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0001;SOR=0.0;LSEQ=GGAGATCATCCCACATGGTG;RSEQ=AGGGTCCCTGAGGTTCTGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:233:14:5,9:96,123:219,14:0.0601:2,2:22.8:1.0:27.2:1.0:0.59265:1.40288:58.9:6.0:0.0522:0.0:1.6 0/0:230:0:0,0:112,118:230,0:0.0:2,0:23.6:1.0:30.1:1.0:1.0:0.0:59.2:56.5:1.0:0.0:0.5 +7 154594008 . G T 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00064;SOR=0.0;LSEQ=CCTCAAAGGCAATTTCAAAA;RSEQ=AAAATCCAAGAACATCCGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:152:12:8,4:91,49:140,12:0.0789:2,2:29.5:1.0:30.5:1.0:1.0:1.08:59.6:24.0:0.0795:0.0:1.2 0/0:126:0:0,0:69,57:126,0:0.0:2,0:27.5:1.0:30.7:1.0:1.0:0.0:57.9:252.0:1.0:0.0:0.4 +7 154594127 . C T 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGGGATGGAAATGGCGTCT;RSEQ=TTGGAGGTTCAGGTGCAATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:35:12,23:46,80:126,35:0.216:2,2:26.1:1.0:29.6:1.0:0.84513:1.10146:57.5:16.5:0.2089:0.0:1.3 0/0:137:0:0,0:64,73:137,0:0.0:2,0:29.7:1.0:30.9:1.0:1.0:0.0:57.9:67.5:1.0:0.0:0.3 +7 155835626 . C G 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0234;SOR=0.0;LSEQ=GCTGAACAATGATATTTTGC;RSEQ=CAAAGCCTTCTTTCTGTGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:286:8:0,8:78,200:278,8:0.028:2,0:19.9:1.0:32.9:1.0:0.11248:0.0:59.4:16.0:0.0287:0.0:1.1 0/0:208:0:0,0:69,138:207,0:0.0:2,0:26.6:1.0:30.5:1.0:1.0:0.0:60.0:68.0:1.0:0.0:0.3 +7 157745089 . C G 124 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00014;SOR=0.0;LSEQ=CAAGGGTGGGTAGTGTGCAT;RSEQ=CCTGAGACGGGGTGGGGGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:22:15:15,0:7,0:7,15:0.6818:0,1:19.1:1.0:31.8:1.0:1.0:0.0:55.5:14.0:0.6667:0.0:2.3 0/0:12:0:0,0:7,0:7,0:0.0:0,0:28.6:1.0:29.1:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.1 +7 158451102 . T C 107 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.02427;SOR=0.0;LSEQ=GGATCTTGCAGCGATCATCC;RSEQ=AAAAGCGAAAAAAGAAAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:9:0,9:2,49:51,9:0.15:1,0:18.8:1.0:33.8:1.0:1.0:0.0:60.0:18.0:0.1552:0.0:1.1 0/0:36:0:0,0:2,34:36,0:0.0:2,0:25.1:1.0:27.4:1.0:1.0:0.0:60.0:72.0:1.0:0.0:0.1 +7 158628009 . A G 136 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.04443;LSEQ=CCTTCTTACCCTGCCCCCTT;RSEQ=TCTTGTATGCAATAAATATC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:37:20:10,10:6,11:17,20:0.5405:2,2:22.2:1.0:31.5:1.0:0.50847:1.8:50.8:40.0:0.5556:0.0:1.1 0/1:42:2:1,1:16,24:40,2:0.0476:2,2:5.0:0.0:28.5:1.0:1.0:1.49:60.0:4.0:0.0476:0.0:0.5 +8 2387994 . T C 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=TCATCCTATTTGCTGAAGAG;RSEQ=GTGATTAATGCTCTCTCCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:49:20,29:57,70:127,49:0.2784:2,2:23.9:1.0:29.8:1.0:0.73494:1.1796:60.0:48.0:0.2775:0.0:2.1 0/0:278:0:0,0:123,155:278,0:0.0:2,0:24.1:1.0:29.1:1.0:1.0:0.0:60.0:277.0:1.0:0.0:0.7 +8 3489674 . G A 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.11627;LSEQ=CATTCCTGCTAGAGAAAAGG;RSEQ=ATTTATTTTAAAAAATTCAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:109:27:23,4:60,21:81,27:0.2477:2,2:20.4:1.0:30.0:1.0:0.29868:2.0:60.0:54.0:0.25:0.0:2.0 0/1:164:6:5,1:109,49:158,6:0.0366:2,2:22.0:1.0:29.0:1.0:0.66819:2.24:60.0:12.0:0.037:0.0:2.0 +8 3489677 . T C 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.09784;LSEQ=TCCTGCTAGAGAAAAGGGAT;RSEQ=TATTTTAAAAAATTCAAAGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:111:30:25,5:60,21:81,30:0.2703:2,2:19.4:1.0:32.3:1.0:0.44943:1.74:60.0:60.0:0.2778:0.0:2.0 0/1:173:6:5,1:113,54:167,6:0.0347:2,2:25.0:1.0:31.3:1.0:0.66592:2.38:60.0:12.0:0.0349:0.0:2.0 +8 3489842 . C T 158 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0476;LSEQ=CTCATAGGTAAAGCCCCGTT;RSEQ=GCCTTCTTGGACCTTCAGCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:121:43:15,28:24,54:78,43:0.3554:2,2:24.6:1.0:29.2:1.0:0.68711:1.2:60.0:9.75:0.3362:0.0:1.3 0/1:158:4:0,4:54,100:154,4:0.0253:2,0:10.3:1.0:28.3:1.0:0.29986:0.0:60.0:8.0:0.026:0.0:1.5 +8 3489935 . G T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00439;SOR=0.07133;LSEQ=AAAGACTACCCCTGGGATAT;RSEQ=TCCATGTTATAGGAGATTAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:0,9:0,14:14,9:0.3913:1,0:15.3:1.0:29.9:1.0:1.0:0.0:60.0:18.0:0.4091:0.0:1.3 0/1:24:1:0,1:2,21:23,1:0.0417:2,0:6.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0417:0.0:2.0 +8 4166516 . A T 116 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AATGTTGAACTAATTCCTAA;RSEQ=ACTAGGTGAGAAAATGCATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:16:4,12:17,62:79,16:0.1684:2,2:26.1:1.0:29.1:1.0:0.74778:1.21:60.0:32.0:0.1702:0.0:3.7 0/0:114:0:0,0:31,83:114,0:0.0:2,0:23.2:1.0:29.2:1.0:1.0:0.0:60.0:56.0:1.0:0.0:2.1 +8 11096119 . A G 58 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00842;SOR=0.0;LSEQ=AAAAAGATGGAAAAGCAAAA;RSEQ=GGCGAGGAGGGGTGGGATTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:387:5:2,3:209,172:381,5:0.0129:2,2:17.2:1.0:25.2:1.0:0.66225:1.81982:60.0:10.0:0.0132:0.0:2.0 0/0:616:0:0,0:317,298:615,0:0.0:2,0:26.3:1.0:29.8:1.0:1.0:0.0:60.0:152.75:1.0:0.0:0.7 +8 11587234 . G T 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.06882;LSEQ=CATGATGCAAAATTGTGTTC;RSEQ=CTGAAAAGCAGGGGTTAAGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:166:56:25,31:46,64:110,56:0.3373:2,2:24.0:1.0:30.8:1.0:0.74273:1.12:60.0:27.0:0.3333:0.0:1.1 0/1:327:11:5,6:144,171:315,11:0.0336:2,2:24.7:1.0:28.7:1.0:1.0:1.01049:60.0:22.0:0.0342:0.0:1.0 +8 14166825 . G A 193 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CTTTTTAAGGATGGTATTGA;RSEQ=ACTATGTGGGAAGATGAGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:259:85:46,39:108,66:174,85:0.3282:2,2:17.4:1.0:30.2:1.0:0.22834:1.38554:38.0:84.0:0.3281:0.0:1.1 0/0:423:0:0,0:259,164:423,0:0.0:2,0:18.7:1.0:30.8:1.0:1.0:0.0:51.4:46.0:1.0:0.0:0.2 +8 14167258 . T G 89 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GGAGCTGAACCAAAGCCTCT;RSEQ=CAAAAAGCAGAGTGGACTGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:15.8:1.0:34.5:1.0:1.0:0.0:41.8:12.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +8 18917162 . A C 76 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=6.0;MSILEN=1.0;SSF=0.06846;SOR=0.0;LSEQ=GTTAGTCAAGAAATTTAAAA;RSEQ=ATTTCTACGTCTGTAAAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:26:5:0,5:0,21:21,5:0.1923:1,0:17.6:1.0:33.0:1.0:1.0:0.0:60.0:10.0:0.1923:0.0:1.2 0/0:18:0:0,0:0,18:18,0:0.0:1,0:20.4:1.0:30.7:1.0:1.0:0.0:60.0:36.0:1.0:0.0:0.2 +8 22438859 . C G 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00152;SOR=0.0;LSEQ=TCCCTTCTCCAGCTGGGCCA;RSEQ=GGTCTGAGCATGCCAGCTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:6:5,1:9,2:11,6:0.3529:2,2:28.0:1.0:33.5:1.0:1.0:1.1:60.0:12.0:0.3529:0.0:1.0 0/0:28:0:0,0:14,13:27,0:0.0:2,0:14.9:1.0:29.3:1.0:1.0:0.0:60.0:54.0:0.9643:0.0:0.2 +8 23548530 . T C 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCCTCCATGGCTGCCGGCT;RSEQ=CTGGAGAGCCCCAGGCTGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1168:111:62,49:542,513:1055,111:0.095:2,2:24.8:1.0:31.5:1.0:0.42452:1.2:60.0:36.0:0.0938:0.0:1.1 0/0:1629:0:0,0:833,794:1627,0:0.0:2,0:25.4:1.0:29.1:1.0:1.0:0.0:59.9:59.259:0.9988:0.0:0.2 +8 28157994 . C G 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00027;SOR=0.12258;LSEQ=TTAAAAAGAAGAGGTGGAAC;RSEQ=ATCCCAAAATGTCCCTCACT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:14:8,6:16,13:29,14:0.3256:2,2:25.7:1.0:30.9:1.0:1.0:1.08:49.6:28.0:0.3256:0.0:1.1 0/1:73:4:3,1:40,29:69,4:0.0548:2,2:25.5:1.0:29.0:1.0:0.63911:2.15:50.8:8.0:0.0548:0.0:1.0 +8 29496868 . T C 130 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TGATGGTTAAGAACATAGTC;RSEQ=ATGGGGTCAGACATGCATGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:145:17:2,15:11,117:128,17:0.1172:2,2:16.1:1.0:31.9:1.0:0.65101:1.41:60.0:34.0:0.1172:0.0:1.0 0/0:129:0:0,0:13,116:129,0:0.0:2,0:23.1:1.0:28.1:1.0:1.0:0.0:60.0:258.0:1.0:0.0:0.0 +8 38279065 . G A 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00243;SOR=0.0;LSEQ=CCAGATCCCGGGCATGCATT;RSEQ=CAATGGCCAGGGGGAGAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:42:13:13,0:29,0:29,13:0.3095:1,1:18.2:1.0:28.2:1.0:1.0:0.0:60.0:26.0:0.3095:0.0:1.2 0/0:23:0:0,0:22,1:23,0:0.0:1,0:24.3:1.0:32.6:1.0:1.0:0.0:60.0:46.0:1.0:0.0:0.0 +8 38283759 . C T 168 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGATGCTCCAGGTGGCATAA;RSEQ=GGACCTGAGGGGAAATGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:484:45:13,32:165,272:437,45:0.093:2,2:25.9:1.0:30.6:1.0:0.26071:1.49203:60.0:90.0:0.0943:0.0:1.0 0/0:648:0:0,0:228,420:648,0:0.0:2,0:23.9:1.0:29.8:1.0:1.0:0.0:60.0:91.571:1.0:0.0:0.2 +8 38285934 . C A 79 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00267;SOR=0.0;LSEQ=TCATCATCATCATCATCATC;RSEQ=TCCGAGGAGGGGAGAGCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:574:7:2,5:205,361:566,7:0.0122:2,2:32.7:1.0:28.3:1.0:1.0:1.41885:59.3:6.0:0.0106:0.0:1.6 0/0:760:0:0,0:310,448:758,0:0.0:2,0:22.6:1.0:30.7:1.0:1.0:0.0:59.9:74.8:1.0:0.0:0.2 +8 38287486 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.04578;SOR=0.1198;LSEQ=GCTGCAGCCACCACGGGGCC;RSEQ=GGAAGGGAAGCCAAGGGGCG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:310:6:4,2:102,202:304,6:0.0194:2,2:23.0:1.0:27.5:1.0:0.18583:3.94:60.0:5.0:0.0162:0.0:1.2 0/0:425:1:1,0:157,267:424,1:0.0024:2,0:1.0:0.0:24.0:0.0:0.37176:0.0:60.0:2.0:0.0024:0.0:1.0 +8 38297776 . G C 154 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTCCGGGGGCCCTCTGCAGA;RSEQ=GTTTTTTTATTACGTATTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:288:29:18,11:166,90:256,29:0.1007:2,2:25.8:1.0:31.8:1.0:0.83834:1.12668:59.2:58.0:0.1014:0.0:1.0 0/0:507:0:0,0:302,202:504,0:0.0:2,0:26.2:1.0:30.8:1.0:1.0:0.0:60.0:83.0:0.994:0.0:0.2 +8 54049868 . T A 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00118;SOR=0.05468;LSEQ=TGTCTGATTTCAGAAGCCTT;RSEQ=TCCTGTAAATGCTGGGTGGA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:9:4,5:3,10:13,9:0.4091:2,2:16.9:1.0:28.8:1.0:0.37616:2.54:23.2:18.0:0.4091:0.0:1.9 0/1:29:1:0,1:12,16:28,1:0.0345:2,0:27.0:0.0:32.0:0.0:1.0:0.0:22.0:2.0:0.0345:0.0:3.0 +8 54445600 . T C 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03778;SOR=0.0;LSEQ=GAGAGGCCGAGGCAGGAGGA;RSEQ=TGCCTGAGCTCAGGAGTTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:24:7:0,7:0,17:17,7:0.2917:1,0:33.0:1.0:34.3:1.0:1.0:0.0:56.1:14.0:0.2917:0.0:1.0 0/0:13:0:0,0:0,13:13,0:0.0:1,0:29.8:1.0:28.8:1.0:1.0:0.0:50.0:26.0:1.0:0.0:0.1 +8 55367460 . C T 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.12322;SOR=0.19776;LSEQ=AAAGCAAGGCTTGCAGGAAG;RSEQ=CACTCCGGATGTTTGCTGCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:473:5:2,3:307,161:468,5:0.0106:2,2:31.0:1.0:30.8:1.0:0.34674:2.85341:60.0:10.0:0.0109:0.0:1.2 0/0:475:1:0,1:308,164:472,1:0.0021:2,0:1.0:0.0:23.0:0.0:0.34884:0.0:60.0:2.0:0.0021:0.0:1.0 +8 55371474 . C A 69 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0628;SOR=0.0;LSEQ=GGGCTCGGACTCAGGAGTCC;RSEQ=AGATCTCCCTCTTTAACTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:43:5:5,0:37,1:38,5:0.1163:1,0:20.2:1.0:30.0:1.0:1.0:0.0:60.0:10.0:0.1163:0.0:2.0 0/0:34:0:0,0:34,0:34,0:0.0:1,0:21.1:1.0:30.9:1.0:1.0:0.0:60.0:33.0:1.0:0.0:1.4 +8 55374948 . A G 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTGGTAGTTTTAAATTACCA;RSEQ=AACATTTGGTATCCTTAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:337:26:20,6:236,75:311,26:0.0772:2,2:23.3:1.0:29.8:1.0:1.0:1.06:60.0:7.667:0.0699:0.0:1.1 0/0:330:0:0,0:251,79:330,0:0.0:2,0:18.6:1.0:29.2:1.0:1.0:0.0:59.2:81.5:1.0:0.0:0.3 +8 59337497 . G C 204 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TCAACACCTTTCTCTCTGTT;RSEQ=ATGTCAGTCAGAATATCAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:285:83:38,45:70,105:175,83:0.2912:2,2:22.5:1.0:32.1:1.0:0.41859:1.27:59.2:82.0:0.3228:0.0:1.2 0/0:282:0:0,0:73,107:180,0:0.0:2,0:23.7:1.0:30.6:1.0:1.0:0.0:59.9:89.0:1.0:0.0:0.1 +8 59339186 . A G 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGTCAGCTCCTCTTATCAAC;RSEQ=GTGGGTTTTCTGCCTCCACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:562:109:63,46:234,218:452,109:0.194:2,2:26.4:1.0:29.8:1.0:0.28558:1.28:53.2:26.25:0.1909:0.0:1.2 0/0:592:0:0,0:313,277:590,0:0.0:2,0:25.8:1.0:29.6:1.0:1.0:0.0:57.1:72.75:1.0:0.0:0.2 +8 59790418 . A T 68 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=13.0;MSILEN=1.0;SSF=0.25654;SOR=0.0;LSEQ=TTGGAGAAAGCCTACATATT;RSEQ=AAAAAAAAAAAAGCCTCAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:14:5:0,5:0,6:6,5:0.3571:0,0:22.6:1.0:29.6:1.0:1.0:0.0:60.0:10.0:0.3571:0.0:1.0 0/0:5:0:0,0:0,2:2,0:0.0:0,0:11.0:1.0:26.0:1.0:1.0:0.0:60.0:4.0:0.4:0.0:0.5 +8 62115431 . AGAT A 117 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=5.0;MSILEN=3.0;SSF=3e-05;SOR=0.0;LSEQ=GAAGAAGATGATGATGATGA;RSEQ=GATGATGATGATTTTAATGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:12:8,4:38,33:71,12:0.1463:2,2:33.0:1.0:32.8:1.0:0.53426:1.73:31.9:24.0:0.15:0.0244:0.2 0/0:105:0:0,0:50,55:105,0:0.0:2,0:22.9:1.0:30.7:1.0:1.0:0.0:40.4:34.0:1.0:0.0:0.2 +8 70250559 . G A 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.05839;SOR=0.0;LSEQ=GGGAGAGCTCAGTGGGAATC;RSEQ=ATGGAGAGGAGGACTCAGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:5:0,5:2,24:26,5:0.1613:2,0:30.0:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.1613:0.0:1.2 0/0:25:0:0,0:0,25:25,0:0.0:1,0:21.8:1.0:31.4:1.0:1.0:0.0:60.0:50.0:1.0:0.0:0.3 +8 74885277 . G A 81 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.04005;SOR=0.0;LSEQ=GGCTGAAACAGCTAAATAAA;RSEQ=TTCACCTTCTACTGTTTTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:50:6:0,6:1,43:44,6:0.12:1,0:15.8:1.0:31.5:1.0:1.0:0.0:60.0:12.0:0.1224:0.0:1.0 0/0:35:0:0,0:2,33:35,0:0.0:2,0:21.6:1.0:31.9:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.0 +8 77776848 . TA T 116 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=9;MSI=10.0;MSILEN=1.0;SSF=0.23529;SOR=0.0;LSEQ=AAAAATAAAAAATAAAAAAA;RSEQ=AAAAAAAAATAAGACTTTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:16:13:0,13:0,3:3,13:0.8125:0,1:30.6:1.0:31.5:1.0:1.0:0.0:60.0:26.0:0.8125:0.0:0.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:23.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +8 90949097 . T C 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02586;SOR=0.0;LSEQ=GCTATAGCCAATAAACCCAA;RSEQ=TGAGAGGTGCTTAAGTAATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:10:10,0:31,0:31,10:0.2439:1,0:24.9:1.0:33.1:1.0:1.0:0.0:59.1:20.0:0.25:0.0:1.1 0/0:17:0:0,0:16,1:17,0:0.0:1,0:21.9:1.0:31.2:1.0:1.0:0.0:60.0:34.0:1.0:0.0:0.0 +8 90955253 . T G 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.13257;SOR=0.0;LSEQ=ATTAGGATGTAAACTGAATT;RSEQ=CTTAGGTCTCACCTTTTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:18:7:7,0:11,0:11,7:0.3889:0,0:19.9:1.0:31.7:1.0:1.0:0.0:58.6:14.0:0.3889:0.0:3.1 0/0:7:0:0,0:7,0:7,0:0.0:0,0:15.7:1.0:31.0:1.0:1.0:0.0:60.0:14.0:1.0:0.0:1.0 +8 90958341 . C A 144 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAAACATTTCAAACACTGAC;RSEQ=TCTTGTGATACAGTTGAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:392:31:24,7:246,114:360,31:0.0791:2,2:26.3:1.0:29.2:1.0:0.41782:1.59:60.0:9.333:0.0727:0.0:1.0 0/0:346:0:0,0:236,110:346,0:0.0:2,0:24.3:1.0:30.5:1.0:1.0:0.0:60.0:114.333:1.0:0.0:0.2 +8 90993395 . C T 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.2451;SOR=0.0;LSEQ=GAGGAATCGAAGAAATGTAA;RSEQ=TTCCCATGAAGTCCCTCAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:7,0:8,0:8,7:0.4667:0,0:23.1:1.0:32.1:1.0:1.0:0.0:55.7:14.0:0.4667:0.0:1.0 0/0:3:0:0,0:3,0:3,0:0.0:0,0:17.0:1.0:29.7:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +8 91434037 . C A 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.04339;SOR=0.0;LSEQ=GCCAGAAAGACTATGGGATC;RSEQ=CAGGAGTTTGTTCTAGCATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:7:1,6:12,114:126,7:0.0526:2,2:24.1:1.0:30.3:1.0:0.5218:1.58:60.0:14.0:0.0538:0.0:2.0 0/0:90:0:0,0:6,84:90,0:0.0:2,0:22.3:1.0:30.7:1.0:1.0:0.0:60.0:180.0:1.0:0.0:0.6 +8 98382341 . C G 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAAAGGTCCTGCTACGTCCA;RSEQ=TGTTGTCTTAGATCTAACGA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:10:0,10:0,1:1,10:0.9091:0,0:35.5:1.0:32.0:1.0:1.0:0.0:52.4:20.0:0.9091:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +8 109144095 . CCCAGGGGACGC T 81 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01494;SOR=0.0;LSEQ=CATGTACAAACTTGTCTTTG;RSEQ=CCAGTCTCAAGGTCGTCGAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:54:7:2,5:10,36:46,7:0.1296:2,2:19.4:1.0:29.0:1.0:0.64996:1.43:60.0:14.0:0.1346:0.0556:0.6 0/0:45:0:0,0:13,32:45,0:0.0:2,0:21.4:1.0:31.6:1.0:1.0:0.0:60.0:90.0:1.0:0.0:0.2 +8 109735723 . T C 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.134;LSEQ=ATGAATATGTTTCACTAAAA;RSEQ=AGGCAAGGCAGCAATCATTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:149:34:28,6:92,23:115,34:0.2282:2,2:21.6:1.0:33.0:1.0:1.0:1.17:59.9:68.0:0.2313:0.0:1.0 0/1:132:5:3,2:96,31:127,5:0.0379:2,2:25.6:1.0:31.0:1.0:0.59839:2.05154:58.8:10.0:0.0382:0.0:1.0 +8 117352461 . G A 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.06769;SOR=0.0;LSEQ=GCGCTCTTGGCATGGATAGG;RSEQ=CCCTCGGTGTTCACATCCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:9:4,5:7,7:14,9:0.3913:2,2:34.0:1.0:30.1:1.0:1.0:1.23792:60.0:18.0:0.4091:0.0:1.0 0/0:8:0:0,0:3,5:8,0:0.0:2,0:22.3:1.0:31.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:0.3 +8 117864369 . C G 210 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TATGAAGAGAAAACATAGGT;RSEQ=ATACAGTTTTGAACAGTATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:772:93:16,77:161,518:679,93:0.1205:2,2:25.9:1.0:32.2:1.0:0.18871:1.49508:60.0:45.5:0.1186:0.0:1.1 0/0:480:0:0,0:121,358:479,0:0.0:2,0:24.8:1.0:31.2:1.0:1.0:0.0:60.0:94.8:0.9979:0.0:0.2 +8 117868529 . T A 78 p8;q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03408;SOR=0.14577;LSEQ=GGACTATCAGGCCCACCCAC;RSEQ=GTAAAAAAAAAAAAAAAAAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:907:10:7,3:300,581:881,10:0.011:2,2:6.3:1.0:23.7:1.0:0.0374:4.51:55.5:2.333:0.0092:0.0:1.7 0/0:617:1:0,1:227,380:607,1:0.0016:2,0:26.0:0.0:20.0:0.0:1.0:0.0:33.0:2.0:0.0019:0.0:6.0 +8 117870036 . TATA T 108 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CACAGCTGAAACTTTCCCGT;RSEQ=ATGTGTTTCATCAAGAAAAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:1,9:0,0:0,10:1.0:0,2:27.5:1.0:32.6:1.0:1.0:0.0:57.1:20.0:1.0:0.2:0.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +8 117870196 . A C 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AAGAGCCACGGCACTCCAGC;RSEQ=TGGATAACACAGCAGAGACC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:5,4:1,1:2,9:0.8182:2,2:27.6:1.0:27.0:1.0:1.0:1.22:57.7:3.5:0.7778:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +8 117874055 . A AT 94 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.01367;SOR=0.0;LSEQ=TATTGCAGACCAAGTCAACA;RSEQ=TTTTTTTTAAAAGAAGACAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:896:9:5,4:634,253:887,9:0.01:2,2:19.2:1.0:29.8:1.0:0.2869:2.00308:59.0:18.0:0.0102:0.0045:0.4 0/0:596:0:0,0:400,195:595,0:0.0:2,0:24.1:1.0:29.2:1.0:1.0:0.0:59.9:58.5:0.9983:0.0:0.1 +8 120428447 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00191;SOR=0.03302;LSEQ=GAGCCCTGGGTCCTGGCCTC;RSEQ=GAACTCCACCCAGCCCCTCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:6,2:1,0:1,8:0.8889:0,2:19.5:1.0:30.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.1 0/1:12:2:1,1:6,4:10,2:0.1667:2,2:22.5:1.0:30.0:1.0:1.0:1.4491:60.0:4.0:0.1667:0.0:1.0 +8 125875063 . G A 183 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AAGACCCAAATACTAGTAAT;RSEQ=AGATGCCAAAGTGAACATGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:289:60:11,49:39,190:229,60:0.2076:2,2:21.0:1.0:31.1:1.0:0.84836:1.09:60.0:120.0:0.2091:0.0:1.1 0/0:121:0:0,0:22,99:121,0:0.0:2,0:22.7:1.0:30.4:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.0 +8 128747953 . G T 174 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGGGCGCGCAGTGCGTTCTC;RSEQ=GTGTGGAGGGCAGCTGTTCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:326:43:40,3:237,46:283,43:0.1319:2,2:28.0:1.0:32.1:1.0:0.16671:2.58:59.1:42.0:0.1304:0.0:1.0 0/0:181:0:0,0:142,39:181,0:0.0:2,0:24.2:1.0:29.2:1.0:1.0:0.0:60.0:44.25:1.0:0.0:0.1 +8 128751201 . G A 197 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03363;LSEQ=TCCTCGACGGAGTCCTCCCC;RSEQ=CAGGGCAGCCCCGAGCCCCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:704:108:37,71:221,374:595,108:0.1534:2,2:26.9:1.0:29.3:1.0:0.58932:1.13367:60.0:53.0:0.153:0.0:1.1 0/0:496:3:3,0:185,308:493,3:0.006:2,0:13.7:1.0:21.7:1.0:0.05391:0.0:60.0:2.0:0.0041:0.0:1.0 +8 131759339 . C T 94 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.13043;SOR=0.0;LSEQ=AATAGTGAAAGTCTTAAAGT;RSEQ=TTTGATCTTTCTTACAAGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:8:8,0:10,1:11,8:0.4211:2,0:26.4:1.0:31.5:1.0:1.0:0.0:27.6:16.0:0.4211:0.0:1.5 0/0:5:0:0,0:4,1:5,0:0.0:2,0:14.2:1.0:29.8:1.0:1.0:0.0:23.0:10.0:1.0:0.0:0.0 +8 139766211 . G C 121 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=2.0;SSF=0.06667;SOR=0.0;LSEQ=ATACTCCGTGGTGAAAACAG;RSEQ=AGAGGCTGCACAGTCAGATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:14:14:14,0:0,0:0,14:1.0:0,1:21.9:1.0:32.0:1.0:1.0:0.0:59.9:13.0:1.0:0.0:1.6 0/0:1:0:0,0:1,0:1,0:0.0:0,0:15.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +8 143164976 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGTGGGCTCTCCCAGGGTCA;RSEQ=TGTGGAATACAACAAGAGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:7:2,5:3,3:6,7:0.5385:2,2:37.6:1.0:32.3:1.0:0.59207:2.32357:60.0:14.0:0.5385:0.0:1.1 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +8 143445733 . A G 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.30769;SOR=0.0;LSEQ=TTTTTAAGATGCACAGAGAA;RSEQ=TACAGATATAGATGTGTGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:36:5:2,3:15,16:31,5:0.1389:2,2:25.2:1.0:34.6:1.0:1.0:1.39312:60.0:10.0:0.1389:0.0:1.4 0/0:16:0:0,0:6,10:16,0:0.0:2,0:25.8:1.0:28.3:1.0:1.0:0.0:60.0:15.0:1.0:0.0:0.0 +8 144227728 . A G 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCAGCCCCCTCCCCTTTCCA;RSEQ=CTGCGGAACCTGGAGCAACT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1.0:0,2:25.0:1.0:34.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +8 144344100 . C T 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.10376;SOR=0.0;LSEQ=CCGGCAGCACCTGCCACGCC;RSEQ=GTCTCCGGCAGCACCTGCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:9:5,4:3,5:8,9:0.5294:2,2:12.6:1.0:29.1:1.0:0.63719:1.99:40.1:3.5:0.5385:0.0:1.7 0/0:4:0:0,0:2,2:4,0:0.0:2,0:16.3:1.0:22.3:1.0:1.0:0.0:29.8:3.0:1.0:0.0:0.8 +8 144351029 . C CTGCTGCTGCTGCTGT 119 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=7.0;MSILEN=3.0;SSF=0.00896;SOR=0.0;LSEQ=TGCTGCTGCTGCTGCTGCTG;RSEQ=TGTTGTTTGAGTCTTGCTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:26:15:5,10:0,0:0,15:0.5769:0,2:24.5:1.0:30.7:1.0:1.0:0.0:48.3:30.0:0.5769:0.2692:0.7 0/0:7:0:0,0:2,0:2,0:0.0:0,0:3.0:0.0:27.5:1.0:1.0:0.0:51.0:4.0:0.2857:0.0:0.0 +8 144999077 . G A 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=3.0;SSF=0.15284;SOR=0.0;LSEQ=CTCCGCCTTGCCGCGCCGCC;RSEQ=CGCCTCGCGCTCCGCCTCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:20:5:2,3:8,7:15,5:0.25:2,2:33.6:1.0:28.6:1.0:1.0:1.66859:60.0:10.0:0.25:0.0:1.0 0/0:9:0:0,0:5,4:9,0:0.0:2,0:29.6:1.0:29.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.2 +8 145736791 . C T 286 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGACAACCCCAGCTCTACC;RSEQ=GACATCCCCCAATGCAGTGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1275:575:381,194:442,253:695,575:0.451:2,2:24.5:1.0:31.2:1.0:0.34507:1.12:60.0:51.273:0.4498:0.0:1.1 0/0:472:0:0,0:291,181:472,0:0.0:2,0:23.2:1.0:29.6:1.0:1.0:0.0:59.9:66.429:1.0:0.0:0.2 +8 145738441 . G A 279 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=CAGGTGCAGGCTGGGAACAC;RSEQ=CGCTGTACCAGCCTCTTCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:1334:668:257,411:249,415:664,668:0.5007:2,2:24.8:1.0:29.8:1.0:0.73495:1.04:60.0:46.714:0.4992:0.0:1.2 0/0:487:0:0,0:196,291:487,0:0.0:2,0:23.5:1.0:29.9:1.0:1.0:0.0:59.8:36.462:1.0:0.0:0.2 +8 145743081 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.18843;SOR=0.0;LSEQ=CCTCGGCCCCTGGGCAGCCC;RSEQ=CACCTGGCTCGGTCGCCGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:323:6:5,1:129,188:317,6:0.0186:2,2:9.7:1.0:27.8:1.0:0.08551:7.25:60.0:12.0:0.019:0.0:1.3 0/0:131:0:0,0:53,78:131,0:0.0:2,0:16.5:1.0:30.7:1.0:1.0:0.0:59.9:130.0:1.0:0.0:0.3 +8 145745182 . T C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CTGCCTGCCAGGCCCTGCCC;RSEQ=TGCTGCCACGCGAACTCTTC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:2,3:0,0:0,5:1.0:0,2:29.8:1.0:32.6:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 1011564 . A AT 84 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=12;MSI=13.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=TGCGCCATCACACCAGGCTA;RSEQ=TTTTTTTTTTTTGTATTTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:6,0:1,0:1,6:0.75:0,0:21.5:1.0:32.8:1.0:1.0:0.0:34.3:12.0:0.75:0.0:1.2 0/0:2:0:0,0:1,0:1,0:0.0:0,0:32.0:1.0:31.0:1.0:1.0:0.0:52.0:2.0:0.5:0.0:5.0 +9 2039827 . G A 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCAGCAGCAACAGCAGCC;RSEQ=CAGCAGCAGCCGCCGCAACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:46:24:11,13:9,13:22,24:0.5217:2,2:22.8:1.0:31.0:1.0:0.77386:1.22:56.4:48.0:0.5333:0.0:1.0 0/0:33:0:0,0:15,18:33,0:0.0:2,0:22.9:1.0:30.5:1.0:1.0:0.0:52.4:32.0:1.0:0.0:0.3 +9 3776612 . C G 122 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00492;SOR=0.06465;LSEQ=TTTAGGGCTTTAGGGCAAGG;RSEQ=TCACTCACTCGCATTCATTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:13:11,2:11,0:11,13:0.5417:0,2:27.7:1.0:33.0:1.0:0.48188:0.0:60.0:26.0:0.5417:0.0:1.4 0/1:15:1:1,0:14,0:14,1:0.0667:1,0:41.0:0.0:28.0:0.0:1.0:0.0:60.0:2.0:0.0667:0.0:2.0 +9 4804901 . A G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.03509;SOR=0.0;LSEQ=CAAGTCTGTCACCAGGTCAT;RSEQ=GGGTGGCTGGGAAGCACCAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:11:5:0,5:1,5:6,5:0.4545:2,0:37.4:1.0:32.0:1.0:1.0:0.0:60.0:10.0:0.4545:0.0:1.2 0/0:10:0:0,0:2,8:10,0:0.0:2,0:24.0:1.0:31.1:1.0:1.0:0.0:60.0:20.0:1.0:0.0:0.3 +9 5126742 . G T 179 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AAATCAACGCCCCTCCTTTA;RSEQ=GGATCTAGCTCTTCGAGTGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:546:57:30,27:242,247:489,57:0.1044:2,2:30.3:1.0:30.8:1.0:0.67672:1.13:60.0:56.0:0.1047:0.0:1.2 0/0:670:0:0,0:355,315:670,0:0.0:2,0:26.1:1.0:30.6:1.0:1.0:0.0:60.0:50.538:1.0:0.0:0.2 +9 5456083 . G A 152 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0;LSEQ=AGTGAAGCAGTCTTCTTTTC;RSEQ=TGTTTTCCATAATTAGGGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:419:30:18,12:232,156:388,30:0.0716:2,2:24.7:1.0:31.1:1.0:1.0:1.01:60.0:60.0:0.0719:0.0:1.1 0/0:528:0:0,0:321,206:527,0:0.0:2,0:24.9:1.0:30.0:1.0:1.0:0.0:60.0:130.75:0.9981:0.0:0.1 +9 5456775 . C G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GGATGTCTACATGAAACCAA;RSEQ=TCTCCCTGGTTGTAAGGACT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:15.4:1.0:32.2:1.0:1.0:0.0:60.0:10.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 5467807 . C T 63 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01772;SOR=0.0;LSEQ=CTTTTTCCCCAGACCACTTC;RSEQ=CATGAAATTAATATACTATT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:385:5:1,4:215,164:379,5:0.013:2,2:11.4:1.0:27.4:1.0:0.1727:5.22396:60.0:10.0:0.0132:0.0:1.2 0/0:475:0:0,0:275,200:475,0:0.0:2,0:25.0:1.0:30.1:1.0:1.0:0.0:60.0:117.75:1.0:0.0:0.2 +9 8331406 . ATTATTTTCAC A 126 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=12;MSI=1.2;MSILEN=1.0;SSF=0.00572;SOR=0.08486;LSEQ=GGGCTAAACATTTTCCTCTG;RSEQ=TTATTTTCACTTTATGAAAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:41:16:16,0:25,0:25,16:0.3902:1,1:27.6:1.0:31.7:1.0:1.0:0.0:59.8:32.0:0.3902:0.0976:0.0 0/1:20:1:1,0:19,0:19,1:0.05:1,0:41.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.05:0.0:0.0 +9 8331548 . C T 169 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.01714;LSEQ=ACAATGAAGAAACACCACCA;RSEQ=TTATCACTGCTTTATTCACA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:571:42:31,11:349,180:529,42:0.0736:2,2:21.6:1.0:31.4:1.0:0.3956:1.45:59.3:84.0:0.0739:0.0:1.1 0/0:738:1:0,1:456,281:737,1:0.0014:2,0:1.0:0.0:24.0:0.0:0.38211:0.0:60.0:2.0:0.0014:0.0:1.0 +9 8331574 . A AAACTTACCATTCTTGAACTGT 249 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.09084;LSEQ=ACTGCTTTATTCACAAATGG;RSEQ=AACTTACCTGCAATGGACTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:749:284:174,110:239,177:416,284:0.3792:2,2:26.5:1.0:30.6:1.0:0.34776:1.17:59.5:568.0:0.3833:0.0948:0.2 0/1:1086:57:33,24:444,374:818,57:0.0525:2,2:31.7:1.0:29.7:1.0:0.68032:1.16:59.5:114.0:0.053:0.0:0.1 +9 8332033 . A G 80 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.13333;SOR=0.0;LSEQ=TCCACATAGTTCCCCCATTA;RSEQ=CAAATGTTTCTGAGACCCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:6:0,6:0,2:2,6:0.75:0,0:17.3:1.0:31.2:1.0:1.0:0.0:60.0:12.0:0.75:0.0:1.0 0/0:2:0:0,0:1,1:2,0:0.0:2,0:8.0:0.0:31.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +9 8376899 . T C 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.1032;SOR=0.0;LSEQ=AATTACTGCTCTGATGCCAA;RSEQ=ATAAACCACATTTTTCAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:0,8:0,7:7,8:0.5333:0,0:25.9:1.0:33.9:1.0:1.0:0.0:56.1:16.0:0.5333:0.0:1.0 0/0:4:0:0,0:0,4:4,0:0.0:0,0:11.0:1.0:28.8:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.3 +9 8449993 . C A 98 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=6.0;MSILEN=1.0;SSF=0.02019;SOR=0.0;LSEQ=ACCCAGTTCGGGTTGCTTTT;RSEQ=CCCCCTGGCCTAATTGTTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:18:10:1,9:0,8:8,10:0.5556:0,2:21.3:1.0:29.6:1.0:1.0:0.0:60.0:20.0:0.5556:0.0:1.1 0/0:7:0:0,0:0,7:7,0:0.0:0,0:20.1:1.0:31.1:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.0 +9 8454265 . G T 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTTTATGAGACACCTCACAT;RSEQ=TCTGCTCTGTAAACACATCA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:11:11,0:0,0:0,11:1.0:0,0:19.9:1.0:30.6:1.0:1.0:0.0:58.6:10.0:1.0:0.0:1.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 8504387 . G A 66 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.01803;SOR=0.0;LSEQ=CAGCCTATATGATGTCCCTG;RSEQ=CTCAATGGTAATTCGTTGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:445:5:4,1:153,287:440,5:0.0112:2,2:12.8:1.0:28.6:1.0:0.05459:7.47:60.0:10.0:0.0113:0.0:1.0 0/0:546:0:0,0:221,324:545,0:0.0:2,0:26.0:1.0:30.7:1.0:1.0:0.0:60.0:59.556:0.9981:0.0:0.1 +9 16181267 . G C 147 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1e-05;SOR=0.1071;LSEQ=TTTGGAGGGCAAGAGTTTCA;RSEQ=AAAGACACTAGAAAGGCAGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:23:23,0:26,0:26,23:0.4694:1,1:24.2:1.0:32.7:1.0:1.0:0.0:60.0:46.0:0.4694:0.0:1.1 0/1:59:5:5,0:54,0:54,5:0.0847:1,0:26.6:1.0:33.4:1.0:1.0:0.0:60.0:10.0:0.0877:0.0:1.0 +9 16206756 . T G 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02047;LSEQ=CATTTCCACAACTGGTTATT;RSEQ=CAGTTGACAATTAACAGGAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:257:108:53,55:73,75:148,108:0.4202:2,2:26.7:1.0:31.8:1.0:1.0:1.01002:59.9:26.0:0.416:0.0:2.2 0/1:344:5:3,2:174,164:338,5:0.0145:2,2:10.6:1.0:29.8:1.0:1.0:1.41:60.0:10.0:0.0148:0.0:2.2 +9 20777008 . A G 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTCGACTGTATTTCAAAACA;RSEQ=TGAACACATATATTCCTAAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:13.2:1.0:32.6:1.0:1.0:0.0:60.0:10.0:0.8333:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 21993964 . T C 167 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAAGGGAGGTCCAGGTTCAA;RSEQ=GGTACTGCGAGAACCACATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:78:39:39,0:39,0:39,39:0.5:1,1:21.8:1.0:31.6:1.0:1.0:0.0:60.0:12.0:0.48:0.0:1.2 0/0:65:0:0,0:65,0:65,0:0.0:1,0:18.3:1.0:30.5:1.0:1.0:0.0:60.0:64.0:1.0:0.0:0.1 +9 22012051 . T C 238 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.10719;LSEQ=CTAGTAATAATATTTTTATA;RSEQ=TCTAGTTGGTGAAATTGTCT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:477:166:73,93:142,169:311,166:0.348:2,2:24.0:1.0:32.3:1.0:0.77219:1.07026:60.0:82.0:0.346:0.0:1.1 0/1:611:33:15,18:264,313:577,33:0.054:2,2:24.9:1.0:31.9:1.0:1.0:1.01212:60.0:66.0:0.0545:0.0:1.1 +9 25247018 . C T 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.04762;SOR=0.0;LSEQ=TAGGGGAAGAGTGTTGTTTT;RSEQ=ACACTAACCAGTCAGGGATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:5,0:0,0:0,5:1.0:0,0:8.0:1.0:31.8:1.0:1.0:0.0:24.4:10.0:1.0:0.0:1.0 0/0:2:0:0,0:1,1:2,0:0.0:2,0:38.5:1.0:25.0:1.0:1.0:0.0:38.0:1.0:1.0:0.0:0.5 +9 33676618 . C T 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00025;SOR=0.0;LSEQ=CTTGATATCTCCTTTTGTTT;RSEQ=TGCTAACGATCTCTTTGATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:189:10:5,5:75,103:178,10:0.0529:2,2:24.5:1.0:32.0:1.0:0.74598:1.37:41.4:20.0:0.0538:0.0:1.0 0/0:238:0:0,0:102,135:237,0:0.0:2,0:21.0:1.0:31.0:1.0:1.0:0.0:42.5:117.5:0.9958:0.0:0.1 +9 36881930 . T TG 70 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.08261;SOR=0.0;LSEQ=TAGAGGTCACCCAGGCTGTT;RSEQ=GGGGGGGGATGTCCCCCCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:184:5:4,1:158,20:178,5:0.0272:2,2:20.0:1.0:30.2:1.0:0.46026:1.96573:60.0:10.0:0.0279:0.0:0.0 0/0:126:0:0,0:103,23:126,0:0.0:2,0:23.6:1.0:29.7:1.0:1.0:0.0:59.8:62.0:1.0:0.0:0.1 +9 36930460 . T G 92 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TCTTGAACTGCTGAGCTCAA;RSEQ=TGATCCACCCACCCCAACCT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:7:7,0:0,0:0,7:1.0:0,0:28.7:1.0:33.0:1.0:1.0:0.0:41.6:14.0:1.0:0.0:1.9 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 37015450 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAATAATTTTGATATTAGTT;RSEQ=TATGTTGAAATAACAATTTT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1.0:0,0:21.5:1.0:30.1:1.0:1.0:0.0:60.0:16.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 37490859 . G A 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0086;SOR=0.06436;LSEQ=GTCTAGAGAACATATATTGG;RSEQ=TGCCTCTCCTCTTTCCCTTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:24.6:1.0:30.4:1.0:1.0:0.0:54.0:10.0:0.7143:0.0:2.8 0/1:17:2:0,2:5,9:14,2:0.1176:2,0:28.5:1.0:32.0:0.0:1.0:0.0:41.5:4.0:0.125:0.0:2.5 +9 37490862 . C A 68 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.01355;SOR=0.074;LSEQ=TAGAGAACATATATTGGGTG;RSEQ=CTCTCCTCTTTCCCTTTGTG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:1,4:0,2:2,5:0.7143:0,2:26.4:1.0:29.4:1.0:1.0:0.0:54.0:10.0:0.7143:0.0:2.8 0/1:15:2:0,2:4,9:13,2:0.1333:2,0:28.5:1.0:31.0:0.0:1.0:0.0:41.5:4.0:0.1429:0.0:2.5 +9 68414063 . T C 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=TGGGAGAGTCCTTCTGCCTG;RSEQ=GCAGCCTGGCTGGGCTGGAG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:11:7,4:0,0:0,11:0.8462:0,2:24.3:1.0:30.5:1.0:1.0:0.0:30.5:22.0:1.0:0.0:4.7 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 68414094 . A G 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGGGCTGGAGCAGGGGGATG;RSEQ=CCCTTGCTTCCTGGCTCACG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:6,4:0,0:0,10:1.0:0,2:24.5:1.0:30.5:1.0:1.0:0.0:29.1:20.0:1.0:0.0:4.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 68414103 . T G 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GCAGGGGGATGACCCTTGCT;RSEQ=CCTGGCTCACGAAAGCCCCC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:8:4,4:0,0:0,8:0.8889:0,2:27.0:1.0:31.9:1.0:1.0:0.0:29.5:16.0:0.8889:0.0:4.5 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 75155834 . G A 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00049;SOR=0.0;LSEQ=GGATGTTGTGAAGCTTCAGT;RSEQ=AGTTAATACAGATATAATGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:29:15:14,1:14,0:14,15:0.5172:1,1:22.8:1.0:28.1:1.0:1.0:0.0:60.0:14.0:0.5:0.0:1.0 0/0:15:0:0,0:15,0:15,0:0.0:1,0:23.1:1.0:30.9:1.0:1.0:0.0:60.0:30.0:1.0:0.0:0.1 +9 75794996 . A T 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAGAAACTTTCCTTTAACA;RSEQ=GATAATGCATTATGAAATAT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:5:0,5:0,1:1,5:0.8333:0,0:20.4:1.0:30.4:1.0:1.0:0.0:56.2:10.0:0.8333:0.0:1.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 80409358 . G T 60 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.02892;SOR=0.0;LSEQ=TAATAAAATGATAATCCATT;RSEQ=CCTGTCTAAAGAACACTTAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:483:5:3,2:356,121:477,5:0.0104:2,2:23.8:1.0:26.2:1.0:0.60575:1.9584:60.0:4.0:0.0084:0.0:1.8 0/0:496:0:0,0:325,168:493,0:0.0:2,0:24.4:1.0:31.0:1.0:1.0:0.0:58.1:48.3:0.9938:0.0:0.5 +9 80646091 . T A 78 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00514;SOR=0.0;LSEQ=CCGCTCGATCTCGTCGTTGA;RSEQ=CCGCCGGGCTTCCTTGGCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:133:7:6,1:84,42:126,7:0.0526:2,2:7.6:1.0:28.1:1.0:0.42748:2.98:45.3:14.0:0.0538:0.0:1.1 0/0:146:0:0,0:87,58:145,0:0.0:2,0:8.7:1.0:28.2:1.0:1.0:0.0:34.8:71.5:1.0:0.0:0.1 +9 80801556 . G A 73 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.50549;SOR=0.0;LSEQ=CCCCACTCCTGCCCGCCAGA;RSEQ=AACAATACCCCTTTGACTGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:20.2:1.0:31.8:1.0:1.0:0.0:28.4:10.0:0.4167:0.0:1.6 0/0:2:0:0,0:2,0:2,0:0.0:0,0:17.0:1.0:32.5:1.0:1.0:0.0:27.5:4.0:1.0:0.0:0.0 +9 87342854 . G A 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0624;SOR=0.0;LSEQ=GATTTCTGCTCACTTCATGG;RSEQ=CTGGCCTGGAATTGACGATG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:434:5:3,2:143,286:429,5:0.0115:2,2:15.0:1.0:31.2:1.0:0.34049:2.99:60.0:10.0:0.012:0.0:1.2 0/0:407:0:0,0:156,251:407,0:0.0:2,0:25.1:1.0:30.7:1.0:1.0:0.0:60.0:57.143:1.0:0.0:0.1 +9 87570478 . C A 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.02727;LSEQ=CCCAGGGACCTCTTTCCCTG;RSEQ=GGGACCCCTGCTGTATTTGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:619:84:28,56:167,367:534,84:0.1357:2,2:26.2:1.0:31.8:1.0:0.70615:1.1:60.0:168.0:0.1375:0.0:1.1 0/0:705:3:2,1:273,427:700,3:0.0043:2,2:32.3:1.0:27.3:1.0:0.56417:3.12:60.0:6.0:0.0043:0.0:1.3 +9 93607915 . G A 178 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCTCACCTCCTGCCACCAG;RSEQ=CCTGTGTGGACAATTGGGAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:431:63:19,44:126,242:368,63:0.1462:2,2:25.5:1.0:29.9:1.0:0.56667:1.2052:60.0:62.0:0.1473:0.0:1.1 0/0:346:0:0,0:112,233:345,0:0.0:2,0:23.1:1.0:30.7:1.0:1.0:0.0:60.0:56.5:1.0:0.0:0.1 +9 93608130 . G A 95 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.47712;SOR=0.0;LSEQ=CGAGGGATGTAATATTTAAA;RSEQ=AAAATGTGATTCAGCCCCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:16:8:0,8:0,8:8,8:0.5:0,0:18.8:1.0:31.9:1.0:1.0:0.0:55.1:16.0:0.5333:0.0:1.3 0/0:2:0:0,0:0,2:2,0:0.0:0,0:22.5:1.0:32.5:1.0:1.0:0.0:60.0:4.0:1.0:0.0:0.0 +9 93636431 . A G 271 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08114;LSEQ=AAAAATAATTATGCAGATCA;RSEQ=CTTAACAGTTTTGTGGATGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:731:315:207,108:275,140:415,315:0.4309:2,2:24.3:1.0:32.7:1.0:0.87502:1.02482:60.0:77.75:0.4302:0.0:1.1 0/1:796:46:25,21:453,294:747,46:0.0578:2,2:27.8:1.0:31.3:1.0:0.43872:1.29384:59.8:92.0:0.0582:0.0:1.3 +9 93637282 . G T 111 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00185;SOR=0.06592;LSEQ=GGTACTATTATAATGAAAGC;RSEQ=TCCATTACCTTTAATGGCAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:0,15:0,17:17,15:0.4688:1,1:20.1:1.0:28.6:1.0:1.0:0.0:60.0:6.5:0.4483:0.0:1.3 0/1:19:1:0,1:0,18:18,1:0.0526:1,0:15.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0526:0.0:1.0 +9 93639590 . A G 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CCCTTTCAACCTCCCAAAGT;RSEQ=TGGGGATTGTCAGCATGAGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:6,0:0,0:0,6:1.0:0,0:32.5:1.0:32.5:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 93639640 . T C 75 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.50549;SOR=0.0;LSEQ=CAGCCCCCACCATTCTTTTT;RSEQ=AGTAATGGAGTATTACTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:12:5:5,0:7,0:7,5:0.4167:0,0:21.0:1.0:32.4:1.0:1.0:0.0:60.0:10.0:0.4167:0.0:2.0 0/0:3:0:0,0:3,0:3,0:0.0:0,0:27.0:1.0:32.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +9 93639679 . G A 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.02041;SOR=0.08518;LSEQ=TCATTGTCTATAAAATAAGG;RSEQ=AATATAGGTTGGAAGGCCAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:24:14:14,0:10,0:10,14:0.5833:0,1:23.5:1.0:31.4:1.0:1.0:0.0:60.0:28.0:0.6087:0.0:1.2 0/1:10:1:1,0:9,0:9,1:0.1:0,0:33.0:0.0:15.0:0.0:1.0:0.0:60.0:0.0:0.0:0.0:1.0 +9 93640895 . G A 115 MAF0.05 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00387;SOR=0.07411;LSEQ=TGAGTCCTGAAGAGCTATAT;RSEQ=CTAACAAAGTTATTTGTCAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:32:15:15,0:17,0:17,15:0.4688:1,1:21.5:1.0:29.5:1.0:1.0:0.0:60.0:30.0:0.4688:0.0:1.6 0/1:17:1:1,0:16,0:16,1:0.0588:1,0:39.0:0.0:30.0:0.0:1.0:0.0:60.0:2.0:0.0588:0.0:2.0 +9 93641193 . C T 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TACGCCAAGATCAGTGATTT;RSEQ=GGACTTTCCAAAGCACTGCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:610:38:14,24:252,319:571,38:0.0623:2,2:20.6:1.0:30.1:1.0:0.40394:1.35357:60.0:37.0:0.0615:0.0:1.1 0/0:617:0:0,0:270,346:616,0:0.0:2,0:24.7:1.0:29.5:1.0:1.0:0.0:60.0:40.067:0.9983:0.0:0.3 +9 93641199 . T C 252 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.08109;LSEQ=AAGATCAGTGATTTCGGACT;RSEQ=TCCAAAGCACTGCGTGCTGA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:585:221:92,129:165,199:364,221:0.3778:2,2:24.7:1.0:32.4:1.0:0.39154:1.16231:59.9:72.667:0.3759:0.0:2.0 0/1:598:28:11,17:241,328:569,28:0.0468:2,2:21.0:1.0:30.7:1.0:0.84575:1.13526:60.0:56.0:0.0469:0.0:1.9 +9 93650322 . G A 109 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00965;SOR=0.0;LSEQ=CCCTCAGTCTATTCCAAACT;RSEQ=AGAATGAAATATCTGATGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:13:0,13:3,18:21,13:0.3824:2,1:20.3:1.0:29.6:1.0:0.27005:0.0:60.0:12.0:0.3636:0.0:1.0 0/0:14:0:0,0:0,14:14,0:0.0:1,0:29.7:1.0:30.3:1.0:1.0:0.0:60.0:28.0:1.0:0.0:0.2 +9 95439427 . A G 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=2.0;SSF=0.0515;SOR=0.0;LSEQ=GAGCTTAATGTGCTCAATAC;RSEQ=CACGTTAATTCTCTTGGCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:13:6:4,2:6,1:7,6:0.4615:2,2:28.2:1.0:31.8:1.0:0.55944:2.75172:44.5:12.0:0.4615:0.0:1.3 0/0:7:0:0,0:6,1:7,0:0.0:2,0:25.1:1.0:30.7:1.0:1.0:0.0:59.4:14.0:1.0:0.0:0.1 +9 97873931 . G A 62 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.11925;SOR=0.19342;LSEQ=CCGCAGGACCTGGAACAGAG;RSEQ=CAGAACACATGGCAGTTGAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:454:5:4,1:122,327:449,5:0.011:2,2:8.6:1.0:27.0:1.0:0.02244:10.66:60.0:4.0:0.009:0.0:1.2 0/0:466:1:1,0:148,317:465,1:0.0021:2,0:1.0:0.0:23.0:0.0:0.31974:0.0:60.0:2.0:0.0022:0.0:1.0 +9 98009794 . G C 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATCTTTCAATGACTGTATTA;RSEQ=AATCCTGTGAAAGAAAAATA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:608:28:11,17:215,361:576,28:0.0461:2,2:26.2:1.0:32.5:1.0:0.84344:1.09:60.0:56.0:0.0467:0.0:1.1 0/0:603:0:0,0:221,380:601,0:0.0:2,0:23.7:1.0:30.5:1.0:1.0:0.0:60.0:199.333:0.9967:0.0:0.1 +9 107068085 . G C 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00444;SOR=0.03977;LSEQ=GCAAAAGCCCTACAGAAGAG;RSEQ=GACTGGACTATTGAAAGAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:7:6:4,2:1,0:1,6:0.8571:0,2:25.2:1.0:28.7:1.0:1.0:0.0:60.0:5.0:0.8333:0.0:1.2 0/1:13:2:2,0:8,3:11,2:0.1538:2,0:34.5:1.0:29.5:1.0:1.0:0.0:60.0:4.0:0.1538:0.0:1.5 +9 109484504 . A G 149 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATAAAAATGAGAATTACAGT;RSEQ=AAATTCAGCTTGTCTAATCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:40:24:24,0:16,0:16,24:0.6:1,1:23.1:1.0:32.7:1.0:1.0:0.0:60.0:48.0:0.6:0.0:1.0 0/0:24:0:0,0:23,1:24,0:0.0:1,0:22.1:1.0:28.3:1.0:1.0:0.0:60.0:48.0:1.0:0.0:0.0 +9 110248177 . C T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.08744;SOR=0.14122;LSEQ=GGGCGAATTTCCATCCACAG;RSEQ=CGTCCCAGTCACAGTGGTAA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:346:5:2,3:124,216:340,5:0.0145:2,2:22.2:1.0:31.2:1.0:1.0:1.16:60.0:10.0:0.0147:0.0:1.2 0/0:485:1:0,1:195,289:484,1:0.0021:2,0:1.0:0.0:25.0:0.0:1.0:0.0:60.0:2.0:0.0021:0.0:1.0 +9 127952210 . G T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.42857;SOR=0.0;LSEQ=CGACTGCAGGCCCCAAGAGA;RSEQ=CCCGCTTCGGTCCACCCCGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:13:8:0,8:0,5:5,8:0.6154:0,0:27.1:1.0:29.5:1.0:1.0:0.0:60.0:16.0:0.6154:0.0:1.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:2.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +9 133711140 . TTCTC T 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=5.0;MSILEN=2.0;SSF=0.05743;SOR=0.0;LSEQ=CTTCTCTTGTCTCTCTCTTT;RSEQ=TCTCTCTGTCTCTTTCTCTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:19:5:0,5:0,14:14,5:0.2632:1,0:25.2:1.0:30.7:1.0:1.0:0.0:60.0:10.0:0.2778:0.1053:0.0 0/0:14:0:0,0:2,12:14,0:0.0:2,0:26.9:1.0:28.5:1.0:1.0:0.0:58.6:13.0:1.0:0.0:0.5 +9 133750550 . A G 172 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03607;LSEQ=TTTCTTTTTGTTTTTTTGAG;RSEQ=CGGAGTCTCACTCTGTCACC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:119:39:0,39:0,79:79,39:0.3277:1,1:20.3:1.0:32.6:1.0:1.0:0.0:53.2:78.0:0.3362:0.0:1.1 0/1:117:2:0,2:0,115:115,2:0.0171:1,0:36.5:1.0:30.0:1.0:1.0:0.0:54.5:4.0:0.0179:0.0:1.0 +9 133754099 . C A 156 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=5e-05;SOR=0.07063;LSEQ=GCAGCTAATGTAGCCATTTG;RSEQ=TACCTATTGACCTTTATTTA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:50:28:0,28:0,22:22,28:0.56:1,1:26.9:1.0:32.6:1.0:1.0:0.0:59.0:56.0:0.5714:0.0:1.6 0/1:25:2:0,2:1,22:23,2:0.08:1,0:10.5:1.0:30.0:1.0:1.0:0.0:60.0:4.0:0.08:0.0:2.0 +9 133754220 . T C 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TACAGATTCCTGGGCCCTGC;RSEQ=TTCACAGACATTCTGCTATA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:13:12:0,12:0,1:1,12:0.9231:0,0:28.8:1.0:30.8:1.0:1.0:0.0:58.2:11.0:0.9167:0.0:1.4 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 133755282 . T G 153 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=1e-05;SOR=0.05681;LSEQ=CATCTAACGTCTTTTCAAAT;RSEQ=CTTAATGTCTATAACAGGAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:25:24,1:17,0:17,25:0.5952:1,1:23.7:1.0:33.1:1.0:1.0:0.0:60.0:50.0:0.5952:0.0:1.2 0/1:27:2:2,0:22,3:25,2:0.0741:2,0:6.0:1.0:28.5:1.0:1.0:0.0:60.0:4.0:0.0741:0.0:1.0 +9 133759957 . G T 176 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0172;LSEQ=GGGCACAAAAGTGAGAAGCC;RSEQ=GCTCTGCCTCGGAAGAGGGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:922:54:23,31:422,444:866,54:0.0586:2,2:27.7:1.0:30.6:1.0:0.40281:1.2807:60.0:53.0:0.0584:0.0:1.3 0/0:937:1:0,1:472,463:935,1:0.0011:2,0:1.0:0.0:31.0:0.0:0.49573:0.0:37.0:2.0:0.0011:0.0:1.0 +9 135771515 . A G 159 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.02251;LSEQ=CCTCCGTCCCATTTCCACAC;RSEQ=TGAACTTGCACTCAGACCCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:39:39,0:50,0:50,39:0.4382:1,1:24.0:1.0:30.2:1.0:1.0:0.0:60.0:78.0:0.4382:0.0:1.1 0/1:59:1:1,0:54,4:58,1:0.0169:2,0:11.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:0.0169:0.0:1.0 +9 135773164 . C T 88 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.13116;SOR=0.0;LSEQ=AAGTAAGCTGGTAGTATTAT;RSEQ=CTAGTAACCCTTCCTTGAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:17:8:0,8:0,9:9,8:0.4706:0,0:26.5:1.0:29.6:1.0:1.0:0.0:60.0:16.0:0.4706:0.0:2.4 0/0:4:0:0,0:0,4:4,0:0.0:0,0:25.5:1.0:31.0:1.0:1.0:0.0:60.0:8.0:1.0:0.0:0.0 +9 135778867 . T C 104 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01637;SOR=0.0;LSEQ=CCCACGGTTTCTGAGAATTA;RSEQ=GAGGGAATTCCGAGGTGTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:28:9:8,1:19,0:19,9:0.3214:1,2:21.9:1.0:33.1:1.0:0.32143:0.0:60.0:18.0:0.3333:0.0:1.0 0/0:16:0:0,0:16,0:16,0:0.0:1,0:26.1:1.0:31.1:1.0:1.0:0.0:60.0:32.0:1.0:0.0:0.1 +9 135781709 . G C 203 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=3.0;SSF=0.0;SOR=0.10096;LSEQ=TTGGGAGGCTGAGGAGGGAG;RSEQ=ATCACTTGAGCCCAGGAGTT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:181:79:0,79:1,100:101,79:0.4365:1,1:25.4:1.0:32.3:1.0:1.0:0.0:57.4:78.0:0.4382:0.0:1.0 0/1:111:8:0,8:2,100:102,8:0.0721:1,0:27.4:1.0:33.1:1.0:1.0:0.0:57.8:16.0:0.0727:0.0:1.0 +9 135782026 . C A 201 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0757;LSEQ=ACCTCAAGAGAAGAAAAATC;RSEQ=AGCAAGCCTGTGAGCAATGG;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:231:94:84,10:113,22:135,94:0.4069:2,2:21.5:1.0:30.7:1.0:0.25038:1.63:60.0:93.0:0.4097:0.0:1.1 0/1:224:11:9,2:183,30:213,11:0.0491:2,2:11.5:1.0:28.5:1.0:0.65986:1.35353:60.0:22.0:0.0505:0.0:1.8 +9 135782221 . T C 255 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08256;LSEQ=CCTTTGCTGCCAGGTGGCTC;RSEQ=TCTGAAGAGAAACAAAGACA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:520:238:83,155:94,187:281,238:0.4577:2,2:23.0:1.0:32.4:1.0:0.78058:1.07:60.0:118.0:0.4574:0.0:1.1 0/1:477:31:9,22:146,300:446,31:0.065:2,2:20.7:1.0:30.8:1.0:0.84309:1.18924:60.0:30.0:0.0637:0.0:1.1 +9 135782396 . A G 119 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.07054;SOR=0.0;LSEQ=ACTGAAATATTAAAAATAAT;RSEQ=TAACTAAAAGTACCAAAAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:4,10:7,12:19,14:0.4242:2,2:21.6:1.0:31.4:1.0:0.71934:1.44185:59.6:13.0:0.4063:0.0:1.1 0/0:6:0:0,0:1,5:6,0:0.0:2,0:30.3:1.0:30.7:1.0:1.0:0.0:60.0:12.0:1.0:0.0:0.2 +9 135786112 . T C 228 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.12723;LSEQ=GGCAGAACATATATGAACAC;RSEQ=GAGCCCAACTATTAGAAAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:521:195:58,137:98,228:326,195:0.3743:2,2:23.0:1.0:30.1:1.0:1.0:1.01525:60.0:96.5:0.3755:0.0:1.1 0/1:425:30:11,19:146,249:395,30:0.0706:2,2:23.4:1.0:29.6:1.0:1.0:1.01275:60.0:60.0:0.0711:0.0:1.1 +9 135796608 . A C 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.03184;LSEQ=TTTAAACTCACACAAATTTT;RSEQ=GCTGTATGAGTGCTTCCAAG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:69:28:28,0:40,1:41,28:0.4058:1,1:26.3:1.0:32.8:1.0:1.0:0.0:60.0:56.0:0.4058:0.0:1.0 0/1:48:1:1,0:46,1:47,1:0.0208:1,0:9.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0208:0.0:1.0 +9 136206057 . CAAGT C 114 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=1.0;MSILEN=1.0;SSF=0.00164;SOR=0.0;LSEQ=GCTGTTGGCACTGTTGTAAA;RSEQ=AAGGGCAAGATTCTTGCCAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:21:12:5,7:5,4:9,12:0.5714:2,2:19.9:1.0:31.9:1.0:0.66992:1.70337:52.3:24.0:0.6:0.0952:0.1 0/0:11:0:0,0:5,6:11,0:0.0:2,0:17.5:1.0:29.5:1.0:1.0:0.0:60.0:22.0:1.0:0.0:0.0 +9 139391461 . T C 187 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CGCCACGTTCAGGTGCCCGA;RSEQ=GCCCAGGTGGGTGTCGGGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:792:62:31,31:391,339:730,62:0.0783:2,2:22.2:1.0:31.5:1.0:0.59869:1.15318:59.9:61.0:0.0782:0.0:1.1 0/0:643:0:0,0:336,306:642,0:0.0:2,0:22.6:1.0:29.2:1.0:1.0:0.0:59.9:57.364:0.9984:0.0:0.2 +9 139396113 . T A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.08135;LSEQ=CCAATTCTAAGTTTCCAGAG;RSEQ=ATCAACTGTACCCCAGCCTC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:198:90:83,7:98,10:108,90:0.4545:2,2:22.3:1.0:30.0:1.0:0.80211:1.21:59.8:29.0:0.4531:0.0:1.1 0/1:111:7:7,0:88,16:104,7:0.0631:2,0:24.0:1.0:27.7:1.0:0.59057:0.0:60.0:14.0:0.0631:0.0:1.3 +9 139397557 . C G 280 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.09588;LSEQ=TGGGTAGCAACTGGCACAAA;RSEQ=AGCCAGCGTGTCTGGGGCAC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:1006:417:209,208:300,288:588,417:0.4145:2,2:24.6:1.0:32.2:1.0:0.79803:1.03666:60.0:40.7:0.4136:0.0:1.1 0/1:819:52:26,26:376,390:766,52:0.0635:2,2:27.6:1.0:30.3:1.0:1.0:1.04:60.0:104.0:0.0644:0.0:1.1 +9 139399641 . G A 194 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.07538;LSEQ=CTCCAGCCCACTGGCCAGCC;RSEQ=CGGGGGACGTCCCTGCACCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:183:77:30,47:47,59:106,77:0.4208:2,2:22.5:1.0:31.0:1.0:0.54449:1.24651:60.0:154.0:0.4254:0.0:1.1 0/1:97:5:2,3:51,41:92,5:0.0515:2,2:37.2:1.0:30.0:1.0:0.65613:1.85383:60.0:10.0:0.0521:0.0:1.0 +9 139401565 . A G 157 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00024;SOR=0.06112;LSEQ=AGGTGTCAAGGGTGCCGTGG;RSEQ=GACGCCCTTCCCACTGGGAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:32:17,15:24,26:50,32:0.3902:2,2:18.6:1.0:31.5:1.0:0.82113:1.22:60.0:64.0:0.3902:0.0:1.7 0/1:27:1:0,1:15,11:26,1:0.037:2,0:40.0:0.0:33.0:0.0:0.44444:0.0:60.0:2.0:0.0385:0.0:1.0 +9 139401646 . T C 198 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.06702;LSEQ=CTTGGCCTCACACAGGAAAA;RSEQ=GGGAGTTTCTGGCTGGTTCC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:178:69:66,3:100,9:109,69:0.3876:2,1:24.7:1.0:32.5:1.0:0.37329:1.97:60.0:138.0:0.3876:0.0:1.1 0/1:99:4:4,0:89,6:95,4:0.0404:2,0:21.8:1.0:32.8:1.0:1.0:0.0:60.0:8.0:0.0408:0.0:1.0 +9 139405093 . G A 274 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.08625;LSEQ=CTGGAGGAGGCCAGAGCCGC;RSEQ=GGGCTACTCACTGGGCCGGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:873:475:281,194:226,168:394,475:0.5441:2,2:27.3:1.0:30.9:1.0:0.62862:1.08:60.0:117.75:0.5483:0.0:1.1 0/1:719:67:39,28:361,290:651,67:0.0932:2,2:27.9:1.0:28.7:1.0:0.69997:1.12:60.0:15.75:0.0894:0.0:1.1 +9 139408892 . C T 214 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.00379;LSEQ=TCTCAAGCTCTGTGCAGGTG;RSEQ=CACCCTCCTGGCAGCAGAGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:150:139:124,15:11,0:11,139:0.9267:0,2:24.8:1.0:30.1:1.0:0.60315:0.0:60.0:45.333:0.9252:0.0:1.1 0/1:70:3:2,1:55,12:67,3:0.0429:2,2:16.7:1.0:28.7:1.0:0.46547:2.25824:60.0:6.0:0.0429:0.0:1.0 +9 139409676 . G T 59 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.07782;SOR=0.0;LSEQ=CCAACCCCTCAGCAGCCCCA;RSEQ=GGCAGAGTGGCTGACCTTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:168:5:3,2:134,29:163,5:0.0298:2,2:15.0:1.0:25.8:1.0:0.22975:3.05342:60.0:4.0:0.0247:0.0:2.4 0/0:120:0:0,0:92,28:120,0:0.0:2,0:23.9:1.0:31.2:1.0:1.0:0.0:60.0:119.0:1.0:0.0:0.2 +9 139412182 . G A 235 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CAGCCTCGACTCGGTTTCCC;RSEQ=CCCTGGCCCCGGCCGACGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:228:163,65:218,106:324,228:0.4123:2,2:23.7:1.0:30.1:1.0:0.30514:1.22:60.0:56.0:0.4125:0.0:2.0 0/0:447:0:0,0:293,154:447,0:0.0:2,0:26.1:1.0:29.8:1.0:1.0:0.0:60.0:48.667:1.0:0.0:0.6 +9 139413539 . C T 85 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=GTAATTCCCGAACACAGGGC;RSEQ=TGTCTGTTCATCCAGGCATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:15:7:2,5:1,6:7,7:0.4667:2,2:30.9:1.0:30.4:1.0:1.0:2.26:60.0:14.0:0.5833:0.0:1.1 0/0:1:0:0,0:0,1:1,0:0.0:0,0:19.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +9 139413908 . C T 258 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.01126;LSEQ=TACGCGCCTGTCCACTCTGG;RSEQ=GGGCAGCGGCAGTTGTAGGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:995:411:247,164:336,247:583,411:0.4131:2,2:25.9:1.0:29.8:1.0:0.47198:1.11:59.9:136.0:0.4142:0.0:1.1 0/0:766:6:2,4:437,323:760,6:0.0078:2,2:9.7:1.0:25.2:1.0:0.41032:2.7024:60.0:5.0:0.0066:0.0:1.3 +9 139565474 . ATTGG A 79 q25 SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.01908;SOR=0.18774;LSEQ=CCTGCTGGAGGAGGTGAGGC;RSEQ=TGGGGGGGGGGGGGGGCAGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:917:10:6,4:484,410:894,10:0.0109:2,2:14.8:1.0:23.9:1.0:0.76123:1.27:56.8:2.333:0.0089:0.0065:1.7 0/0:969:2:1,1:481,469:950,2:0.0021:2,2:45.0:1.0:29.0:1.0:1.0:1.02556:46.0:4.0:0.0023:0.0:3.5 +9 139565475 . TTGG T 131 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.08861;LSEQ=CTGCTGGAGGAGGTGAGGCA;RSEQ=TGGGGGGGGGGGGGGGCAGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:889:31:5,26:437,376:813,31:0.0349:2,2:31.2:1.0:26.6:1.0:3e-05:6.03204:46.7:5.2:0.0377:0.0:3.6 0/0:941:3:1,2:443,463:906,3:0.0032:2,2:38.3:1.0:23.3:1.0:1.0:1.91229:51.7:2.0:0.0026:0.0:3.3 +9 139565987 . A AC 94 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=6;MSI=7.0;MSILEN=1.0;SSF=0.27273;SOR=0.0;LSEQ=GCAGCTGGACACTGACCAGG;RSEQ=CCCCCCAGGGCCGGAGGAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:8:0,8:1,1:2,8:0.8:2,0:29.6:1.0:31.6:1.0:0.2:0.0:60.0:16.0:0.8:0.1:0.0 0/0:1:0:0,0:0,1:1,0:0.0:0,0:28.0:0.0:31.0:0.0:1.0:0.0:60.0:2.0:1.0:0.0:0.0 +9 139566996 . G A 115 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.01299;SOR=0.0;LSEQ=GGCATCCCAAGGCCAGGTGG;RSEQ=CCCTCAGCTGAGGGAAGGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:19:16:0,16:0,3:3,16:0.8421:0,1:22.2:1.0:28.9:1.0:1.0:0.0:57.6:7.0:0.875:0.0:1.1 0/0:3:0:0,0:0,3:3,0:0.0:0,0:6.0:1.0:31.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +9 139810652 . G A 65 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=AGCAGTGGGCGTTTGATTCT;RSEQ=GGTTTTGAACCCAGGCCCTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:9:5:5,0:4,0:4,5:0.5556:0,0:32.4:1.0:28.4:1.0:1.0:0.0:60.0:10.0:0.5556:0.0:1.2 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +9 139815960 . A G 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.01515;SOR=0.0;LSEQ=AGCCTGGTCCTCTGGCACAC;RSEQ=GCCCTAAAGCAGACATTACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:0,10:0,0:0,10:1.0:0,0:23.1:1.0:30.7:1.0:1.0:0.0:56.3:20.0:1.0:0.0:1.4 0/0:2:0:0,0:1,1:2,0:0.0:2,0:3.0:0.0:24.0:1.0:1.0:0.0:60.0:1.0:1.0:0.0:2.0 +GL000212.1 40875 . A G 78 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.00211;SOR=0.05956;LSEQ=TACTAGTTAATGCTTTCAAA;RSEQ=TATGTTATTTAAAAAATTAT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:3,2:1,2:3,5:0.625:2,2:39.4:1.0:33.6:1.0:1.0:2.6:24.6:10.0:0.625:0.0:5.0 0/1:37:3:0,3:19,15:34,3:0.0811:2,0:23.7:1.0:33.3:1.0:0.10502:0.0:21.7:6.0:0.0857:0.0:6.3 +GL000220.1 119178 . T C 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02525;SOR=0.0;LSEQ=GCGCACCGACGCGAGGGCGC;RSEQ=GATTCCCGTTCACGCGCCCG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:29:6:4,2:13,9:22,6:0.2069:2,2:30.0:1.0:32.0:1.0:1.0:1.37:29.8:12.0:0.2143:0.0:1.2 0/0:25:0:0,0:14,10:24,0:0.0:2,0:28.6:1.0:29.5:1.0:1.0:0.0:41.1:23.0:1.0:0.0:0.8 +GL000220.1 119610 . C T 89 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=0.00031;SOR=0.0;LSEQ=TCTCTCTCTCTCTCTCTCTC;RSEQ=CTCCCCCTCCCTCCCTCTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:75:12:7,5:22,36:58,12:0.16:2,2:7.6:1.0:25.0:1.0:0.21465:2.26:52.1:2.0:0.125:0.0:1.7 0/0:72:0:0,0:29,35:64,0:0.0:2,0:20.3:1.0:28.9:1.0:1.0:0.0:49.6:15.0:1.0:0.0:2.1 +GL000220.1 119911 . C T 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00012;SOR=0.0;LSEQ=CGTCGATTCCGGTTCACGCG;RSEQ=CGGCGACCTCCACCGGCCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:8:5,3:13,9:22,8:0.2667:2,2:16.1:1.0:27.5:1.0:1.0:1.15:40.4:7.0:0.25:0.0:2.1 0/0:55:0:0,0:29,24:53,0:0.0:2,0:26.1:1.0:30.0:1.0:1.0:0.0:46.9:16.667:0.9615:0.0:0.5 +GL000220.1 119970 . C T 91 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00818;SOR=0.07621;LSEQ=GACCACGCGGAACTCCCTCT;RSEQ=CTACATTTTTTTCAGCCCCA;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:31:8:5,3:13,10:23,8:0.2581:2,2:35.8:1.0:30.5:1.0:1.0:1.27:34.9:16.0:0.2581:0.0:1.5 0/1:40:1:0,1:21,17:38,1:0.025:2,0:4.0:0.0:27.0:0.0:0.46154:0.0:60.0:2.0:0.0256:0.0:1.0 +GL000220.1 121453 . TTGCCTGCCTGCC T 73 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=37;MSI=12.0;MSILEN=4.0;SSF=0.05323;SOR=0.0;LSEQ=GCGCCTGGCTCCTTCTACAT;RSEQ=TGCCTGCCTGCCTGCCTGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:23:5:2,3:8,7:15,5:0.2174:2,2:25.0:1.0:31.6:1.0:1.0:1.66859:49.6:10.0:0.2273:0.0435:0.4 0/0:19:0:0,0:8,8:16,0:0.0:2,0:25.3:1.0:29.9:1.0:1.0:0.0:55.7:32.0:0.8421:0.0:0.6 +GL000220.1 123139 . G GTCTCTCTCTCTCTC 86 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=23.0;MSILEN=2.0;SSF=0.001;SOR=0.0;LSEQ=GGGTCCTCGTGGTGGGATTG;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:27:8:4,4:9,7:16,8:0.2963:2,2:13.5:1.0:28.8:1.0:1.0:1.27224:50.8:7.0:0.28:0.2593:0.4 0/0:32:0:0,0:10,11:21,0:0.0:2,0:24.5:1.0:28.0:1.0:1.0:0.0:54.5:6.0:0.6207:0.0:0.6 +GL000220.1 123214 . G C 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.03968;SOR=0.11403;LSEQ=ACACACAATTTCCATATCTA;RSEQ=TTCACAGAGCACACTCACTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:6:3,3:13,15:28,6:0.1765:2,2:30.2:1.0:34.0:1.0:1.0:1.15:59.2:12.0:0.1818:0.0:1.0 0/1:43:1:0,1:20,22:42,1:0.0233:2,0:43.0:0.0:34.0:0.0:1.0:0.0:60.0:2.0:0.0238:0.0:1.0 +GL000220.1 124694 . C CCTTTCTTTCTTTCTTCTTTCTTTCTTTCTGT 108 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=2.0;MSILEN=1.0;SSF=4e-05;SOR=0.0;LSEQ=ACCACCATCGCTCTACTGAT;RSEQ=CTTTCTTTCTTTCTTTCTTT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:53:13:4,9:13,15:28,13:0.2453:2,2:14.1:1.0:29.2:1.0:0.49861:1.91893:32.7:26.0:0.2653:0.2453:0.6 0/0:55:0:0,0:16,16:32,0:0.0:2,0:24.8:1.0:30.7:1.0:1.0:0.0:57.0:64.0:0.5926:0.0:0.3 +GL000220.1 125098 . C G 74 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.02061;SOR=0.09924;LSEQ=CTGAGATCCCCCGCCTCCAC;RSEQ=GCCTTGCAGGCTCACCTCTT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:5:2,3:20,14:34,5:0.1282:2,2:22.6:1.0:32.0:1.0:0.63624:2.10061:60.0:10.0:0.1351:0.0:1.2 0/1:71:1:0,1:33,37:70,1:0.0141:2,0:14.0:0.0:32.0:0.0:1.0:0.0:60.0:2.0:0.0143:0.0:1.0 +GL000220.1 126947 . TTC T 74 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=6.0;MSILEN=2.0;SSF=0.00461;SOR=0.0;LSEQ=CTCTCTCCCTCCCTGTCTGT;RSEQ=TCTCTCTCTCTTTCTGTCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:79:6:2,4:41,32:73,6:0.0759:2,2:23.8:1.0:28.8:1.0:0.40329:2.53243:54.5:12.0:0.0759:0.0127:2.0 0/0:111:0:0,0:57,54:111,0:0.0:2,0:22.1:1.0:28.8:1.0:1.0:0.0:54.8:36.0:1.0:0.0:0.5 +GL000220.1 127312 . G C 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=4.0;SSF=0.0;SOR=0.0;LSEQ=TTCGTTCTCTCTGTCTGTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:32:11,21:23,28:51,32:0.2857:2,2:18.1:1.0:33.2:1.0:0.36747:1.55971:47.8:64.0:0.2936:0.0:1.8 0/0:100:0:0,0:29,36:65,0:0.0:2,0:23.0:1.0:30.2:1.0:1.0:0.0:57.6:64.0:0.7033:0.0:0.6 +GL000220.1 128203 . CCTCTCTCTT TCTGCCTC 79 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00935;SOR=0.0;LSEQ=TCTCCGTCTTTCTCTGTCTG;RSEQ=TCTTTTTCTGCGTCTCTCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:95:6:2,4:49,40:89,6:0.0632:2,2:14.2:1.0:30.6:1.0:0.41065:2.42736:31.2:12.0:0.0667:0.0421:0.8 0/0:109:0:0,0:52,53:105,0:0.0:2,0:24.1:1.0:30.7:1.0:1.0:0.0:51.9:25.25:0.9806:0.0:0.3 +GL000220.1 128957 . TTCTG T 84 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.02951;SOR=0.0;LSEQ=CTGTTTCTCTCTCTGTCCAT;RSEQ=TCTGTCTCTTTCTCTTTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:122:6:4,2:58,57:115,6:0.0492:2,2:18.3:1.0:32.5:1.0:0.6801:1.95:47.8:12.0:0.0504:0.0:0.0 0/0:117:0:0,0:60,57:117,0:0.0:2,0:25.7:1.0:29.2:1.0:1.0:0.0:51.6:38.0:1.0:0.0:0.7 +GL000220.1 129019 . G C 93 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0032;SOR=0.0;LSEQ=GTCTCTCTCTGTCTCTCTCT;RSEQ=TCTCTCTCTCTCTCTCTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:82:9:3,6:42,28:70,9:0.1098:2,2:16.3:1.0:29.6:1.0:0.16274:2.95782:42.8:3.5:0.0986:0.0:2.0 0/0:77:0:0,0:37,22:59,0:0.0:2,0:21.3:1.0:29.6:1.0:1.0:0.0:47.0:10.8:0.9818:0.0:0.4 +GL000220.1 130109 . C A 56 q25 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=3.0;SSF=0.05544;SOR=0.0;LSEQ=AGAAAGAGAAGTAAAACCAA;RSEQ=CACCACCTCCTTGACCTGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:44:5:3,2:19,20:39,5:0.1136:2,2:38.4:1.0:24.4:1.0:1.0:1.56:32.8:1.5:0.0789:0.0:2.8 0/0:44:0:0,0:24,20:44,0:0.0:2,0:27.0:1.0:29.4:1.0:1.0:0.0:46.7:7.8:1.0:0.0:0.7 +GL000220.1 132352 . CTCTCTG C 85 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=17;MSI=3.0;MSILEN=6.0;SSF=0.05474;SOR=0.14388;LSEQ=CTCTGTCTGTCTGTCTCTTT;RSEQ=TCTCTGTCTCTGTCTCTCTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:108:6:1,5:58,44:102,6:0.0556:2,2:16.0:1.0:33.2:1.0:0.08965:6.48853:49.2:12.0:0.0571:0.037:0.7 0/0:120:1:0,1:57,62:119,1:0.0083:2,0:14.0:0.0:33.0:0.0:1.0:0.0:60.0:2.0:0.0084:0.0:0.0 +GL000220.1 132475 . T C 82 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=15;MSI=5.0;MSILEN=1.0;SSF=0.00525;SOR=0.0;LSEQ=CTCTCCTTTCCTGTCTGTTT;RSEQ=TCTCTCTCTCTCTCTCTTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:89:7:2,5:35,44:79,7:0.0787:2,2:26.0:1.0:29.4:1.0:0.69361:1.97375:50.3:2.5:0.0588:0.0:2.3 0/0:96:0:0,0:45,41:86,0:0.0:2,0:22.8:1.0:29.6:1.0:1.0:0.0:58.5:85.0:0.977:0.0:0.6 +GL000220.1 133613 . T A 84 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=3;MSI=3.0;MSILEN=1.0;SSF=0.00031;SOR=0.0;LSEQ=CTCTCTCTCTCTGTTTGTCT;RSEQ=TCTCCCTCCCTGTCTGTCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:81:9:4,5:35,35:70,9:0.1111:2,2:20.3:1.0:26.6:1.0:1.0:1.24648:55.9:8.0:0.1111:0.0:1.0 0/0:112:0:0,0:48,63:111,0:0.0:2,0:24.2:1.0:29.2:1.0:1.0:0.0:51.4:26.75:1.0:0.0:0.4 +GL000220.1 137741 . G A 83 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.01283;SOR=0.0;LSEQ=CGCCCCACGCCCCACGTCCC;RSEQ=GGCACCCGCGGGACACCGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:115:6:3,3:55,54:109,6:0.0522:2,2:21.0:1.0:32.3:1.0:1.0:1.01836:60.0:12.0:0.0561:0.0:1.2 0/0:120:0:0,0:60,60:120,0:0.0:2,0:23.3:1.0:28.2:1.0:1.0:0.0:59.2:16.143:1.0:0.0:0.7 +GL000231.1 24498 . T A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.18182;SOR=0.0;LSEQ=TCTGCTGTTTTCTTTTTTAA;RSEQ=CCCGAGGGGACTGAGCCTGA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:8:5:5,0:1,2:3,5:0.625:2,0:27.2:1.0:31.0:1.0:0.10714:0.0:22.4:10.0:0.625:0.0:3.6 0/0:3:0:0,0:2,1:3,0:0.0:2,0:3.0:1.0:27.3:1.0:1.0:0.0:60.0:6.0:1.0:0.0:0.0 +MT 152 . T C 163 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=5e-05;SOR=0.06779;LSEQ=CTTTGATTCCTGCCTCATCC;RSEQ=ATTATTTATCGCACCTACGT;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:56:36:18,18:15,5:20,36:0.6429:2,2:21.8:1.0:31.6:1.0:0.09199:2.94184:57.6:72.0:0.6429:0.0:2.6 0/1:19:2:1,1:8,9:17,2:0.1053:2,2:38.5:1.0:30.5:1.0:1.0:1.12:60.0:4.0:0.1053:0.0:1.5 +MT 178 . A G 162 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=1e-05;SOR=0.0;LSEQ=TTATCGCACCTACGTTCAAT;RSEQ=TTACAGGCGAACATACTTAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:62:33:19,14:20,9:29,33:0.5323:2,2:23.7:1.0:32.3:1.0:0.43363:1.62437:60.0:66.0:0.5323:0.0:2.8 0/0:19:0:0,0:10,9:19,0:0.0:2,0:22.8:1.0:29.2:1.0:1.0:0.0:60.0:38.0:1.0:0.0:1.9 +MT 477 . T C 151 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CCCTCCCACTCCCATACTAC;RSEQ=AATCTCATCAATACAACCCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:26:13,13:16,16:32,26:0.4483:2,2:21.4:1.0:32.2:1.0:1.0:1.0:59.3:52.0:0.4643:0.0:1.3 0/0:49:0:0,0:24,25:49,0:0.0:2,0:23.3:1.0:28.4:1.0:1.0:0.0:60.0:23.5:1.0:0.0:0.6 +MT 533 . A G 105 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0047;SOR=0.0;LSEQ=GCACACACACACCGCTGCTA;RSEQ=CCCCATACCCCGAACCAACC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:56:9:4,5:20,27:47,9:0.1607:2,2:26.2:1.0:33.2:1.0:1.0:1.08:45.2:18.0:0.1607:0.0:1.9 0/0:43:0:0,0:19,24:43,0:0.0:2,0:28.3:1.0:29.4:1.0:1.0:0.0:60.0:86.0:1.0:0.0:0.5 +MT 1990 . G A 71 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.16667;SOR=0.0;LSEQ=GAAGATTTATAGGTAGAGGC;RSEQ=ACAAACCTACCGAGCCTGGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:7:5:3,2:1,1:2,5:0.7143:2,2:17.6:1.0:30.8:1.0:1.0:1.41:30.8:10.0:0.7143:0.0:1.2 0/0:3:0:0,0:1,2:3,0:0.0:2,0:8.7:1.0:29.0:1.0:1.0:0.0:42.0:6.0:1.0:0.0:0.0 +MT 4917 . A G 141 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCAAATCTCTCCCTCACTA;RSEQ=ACGTAAGCCTTCTCCTCACT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:46:20:9,11:11,15:26,20:0.4348:2,2:26.0:1.0:32.8:1.0:1.0:1.11:28.3:40.0:0.4348:0.0:1.1 0/0:43:0:0,0:22,21:43,0:0.0:2,0:18.3:1.0:29.3:1.0:1.0:0.0:48.1:42.0:1.0:0.0:0.2 +MT 8697 . G A 113 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0018;SOR=0.0;LSEQ=AAACTAACCTCAAAACAAAT;RSEQ=ATAACCATACACAACACTAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:33:14:6,8:9,10:19,14:0.4242:2,2:30.4:1.0:29.8:1.0:1.0:1.19338:29.4:28.0:0.4242:0.0:1.2 0/0:17:0:0,0:10,7:17,0:0.0:2,0:24.2:1.0:30.8:1.0:1.0:0.0:43.2:16.0:1.0:0.0:0.3 +MT 9899 . T C 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00414;SOR=0.0;LSEQ=TTTCACTTTACATCCAAACA;RSEQ=CACTTTGGCTTCGAAGCCGC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:22:8:3,5:7,7:14,8:0.3636:2,2:27.9:1.0:30.1:1.0:0.67492:1.62835:60.0:7.0:0.3333:0.0:1.0 0/0:19:0:0,0:9,10:19,0:0.0:2,0:24.7:1.0:29.3:1.0:1.0:0.0:60.0:38.0:1.0:0.0:0.3 +MT 10463 . T C 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00766;SOR=0.0;LSEQ=TTAAATTATGATAATCATAT;RSEQ=TACCAAATGCCCCTCATTTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:15:8:3,5:6,1:7,8:0.5333:2,2:27.9:1.0:33.4:1.0:0.11888:8.40708:33.9:16.0:0.5333:0.0:1.3 0/0:10:0:0,0:5,5:10,0:0.0:2,0:17.3:1.0:27.3:1.0:1.0:0.0:48.9:20.0:1.0:0.0:0.1 +MT 12633 . C A 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GCATTGTTCGTTACATGGTC;RSEQ=ATCATAGAATTCTCACTGTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:33:24:12,12:4,5:9,24:0.7273:2,2:20.9:1.0:30.7:1.0:1.0:1.24:60.0:48.0:0.7273:0.0:1.1 0/0:14:0:0,0:7,7:14,0:0.0:2,0:25.9:1.0:30.4:1.0:1.0:0.0:58.4:13.0:1.0:0.0:0.9 +MT 14905 . G A 128 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0001;SOR=0.0767;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC;STATUS=AFDiff GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:42:21:11,10:8,13:21,21:0.5:2,2:27.4:1.0:29.3:1.0:0.5359:1.76:32.5:42.0:0.5:0.0:1.3 0/1:29:2:1,1:12,15:27,2:0.069:2,2:2.5:1.0:24.5:1.0:1.0:1.24:42.5:4.0:0.069:0.0:1.0 +MT 15607 . A G 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0006;SOR=0.0527;LSEQ=CTCCGATCCGTCCCTAACAA;RSEQ=CTAGGAGGCGTCCTTGCCCT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:30:15:6,9:6,9:15,15:0.5:2,2:22.0:1.0:31.5:1.0:1.0:1.0:60.0:30.0:0.5357:0.0:1.1 0/1:21:1:0,1:11,9:20,1:0.0476:2,0:26.0:0.0:34.0:0.0:0.47619:0.0:60.0:2.0:0.0476:0.0:1.0 +MT 16019 . C T 72 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=2.0;SSF=0.14485;SOR=0.0;LSEQ=AGATTCTAATTTAAACTATT;RSEQ=TCTGTTCTTTCATGGGGAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:34:5:2,3:16,13:29,5:0.1471:2,2:28.0:1.0:31.2:1.0:0.64809:1.813:60.0:10.0:0.1563:0.0:1.8 0/0:22:0:0,0:13,9:22,0:0.0:2,0:21.4:1.0:30.2:1.0:1.0:0.0:60.0:21.0:1.0:0.0:0.3 +MT 16163 . A G 146 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTGACCACCTGTAGTACATA;RSEQ=AAACCCAATCCACATCAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:21:12,9:17,9:26,21:0.4468:2,2:29.0:1.0:33.3:1.0:0.76341:1.40609:60.0:42.0:0.4468:0.0:3.4 0/0:43:0:0,0:24,19:43,0:0.0:2,0:26.5:1.0:30.1:1.0:1.0:0.0:60.0:86.0:1.0:0.0:1.1 +MT 16186 . C T 142 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ACCCAATCCACATCAAAACC;RSEQ=CCTCCCCATGCTTACAAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:58:25:14,11:21,12:33,25:0.431:2,2:24.4:1.0:30.6:1.0:0.59697:1.36738:60.0:24.0:0.4211:0.0:3.2 0/0:40:0:0,0:19,20:39,0:0.0:2,0:25.6:1.0:30.3:1.0:1.0:0.0:59.8:38.0:1.0:0.0:1.4 +MT 16263 . T C 164 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCAACTCCAAAGCCACCCC;RSEQ=CACCCACTAGGATACCAACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:70:37:17,20:15,18:33,37:0.5286:2,2:27.7:1.0:31.6:1.0:1.0:1.02:60.0:74.0:0.5286:0.0:1.6 0/0:30:0:0,0:15,15:30,0:0.0:2,0:22.3:1.0:29.9:1.0:1.0:0.0:60.0:60.0:1.0:0.0:1.5 +MT 16294 . C T 143 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GATACCAACAAACCTACCCA;RSEQ=CCTTAACAGTACATAGTACA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:59:26:13,13:12,21:33,26:0.4407:2,2:21.8:1.0:30.5:1.0:0.4264:1.73:60.0:25.0:0.431:0.0:1.0 0/0:29:0:0,0:17,12:29,0:0.0:2,0:23.9:1.0:30.8:1.0:1.0:0.0:60.0:58.0:1.0:0.0:1.2 +MT 16316 . A G 155 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTAACAGTACATAGTACAT;RSEQ=AAGCCATTTACCGTACATAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:52:29:12,17:10,13:23,29:0.5577:2,2:20.2:1.0:32.0:1.0:1.0:1.08794:60.0:28.0:0.549:0.0:1.9 0/0:31:0:0,0:16,15:31,0:0.0:2,0:21.5:1.0:27.3:1.0:1.0:0.0:59.8:14.5:1.0:0.0:1.1 +MT 16390 . G A 137 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00012;SOR=0.05048;LSEQ=GATGACCCCCCTCAGATAGG;RSEQ=GTCCCTTGACCACCATCCTC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:60:22:10,12:20,18:38,22:0.3667:2,2:20.4:1.0:30.8:1.0:0.78917:1.32692:60.0:21.0:0.3621:0.0:1.5 0/1:36:1:0,1:19,16:35,1:0.0278:2,0:13.0:0.0:32.0:0.0:0.47222:0.0:60.0:2.0:0.0286:0.0:2.0 +X 1314857 . GG AT 194 PASS SAMPLE=PoolTumor2-T;TYPE=Complex;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.1438;LSEQ=TCACAGACATTGTGCAAGCA;RSEQ=TCCCTCCACCCACGGGCGGC;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:258:79:58,21:126,50:176,79:0.3062:2,2:24.1:1.0:30.8:1.0:0.88004:1.1:60.0:158.0:0.3123:0.0349:1.0 0/1:353:21:15,6:220,112:332,21:0.0595:2,2:26.3:1.0:29.8:1.0:0.81223:1.27:60.0:42.0:0.06:0.0085:1.1 +X 1325301 . G T 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.00011;SOR=0.053;LSEQ=AAGGAAGTACTGAAAAGCAT;RSEQ=GTGAGCTGGCTTTACAATAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:270:12:10,2:167,91:258,12:0.0444:2,2:20.0:1.0:31.8:1.0:0.22848:2.72:60.0:24.0:0.0446:0.0:1.1 0/0:408:1:0,1:257,150:407,1:0.0025:2,0:1.0:0.0:24.0:0.0:0.3701:0.0:60.0:2.0:0.0025:0.0:1.0 +X 1325426 . C T 220 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TGCTCTGCGTCTAGGAGGCA;RSEQ=CCCGAAGTGTGACCTTCCTG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:450:147:65,82:143,160:303,147:0.3267:2,2:25.8:1.0:30.6:1.0:0.61436:1.1272:60.0:294.0:0.3296:0.0:1.1 0/0:697:0:0,0:311,386:697,0:0.0:2,0:26.3:1.0:30.5:1.0:1.0:0.0:60.0:48.786:1.0:0.0:0.2 +X 1331309 . C CAG 84 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.02308;SOR=0.14355;LSEQ=GCAGGAGAATTGCTTGAACC;RSEQ=GGAAAAAAAAAAAAAAAAAA;STATUS=Germline GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:30:7:7,0:21,0:21,7:0.2333:1,0:26.1:1.0:30.2:1.0:1.0:0.0:40.6:14.0:0.2414:0.0:0.3 0/1:49:2:2,0:46,1:47,2:0.0408:1,0:23.5:1.0:32.5:1.0:1.0:0.0:29.0:4.0:0.0444:0.0:0.0 +X 15822104 . TA T 118 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=11;MSI=12.0;MSILEN=1.0;SSF=0.02012;SOR=0.12641;LSEQ=AGAGTTGCCTATCTTGAACT;RSEQ=AAAAAAAAAAACAAAAAACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:96:13:9,4:61,21:82,13:0.1354:2,2:29.7:1.0:32.0:1.0:0.73854:1.28741:60.0:26.0:0.1368:0.0208:1.0 0/1:52:1:0,1:40,7:47,1:0.0192:2,0:23.0:0.0:32.0:0.0:0.16667:0.0:60.0:2.0:0.0213:0.0:0.0 +X 15822401 . C T 71 p8 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.03141;SOR=0.0;LSEQ=AGAGTTTGGGTTTTTTTTTT;RSEQ=TCTTTTTCTTGTCATTTCAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:204:6:2,4:36,162:198,6:0.0294:2,2:6.0:1.0:27.8:1.0:0.3105:2.24:60.0:5.0:0.0255:0.0:1.8 0/0:183:0:0,0:29,153:182,0:0.0:2,0:21.3:1.0:31.3:1.0:1.0:0.0:60.0:29.333:1.0:0.0:0.2 +X 22516183 . G A 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=2;MSI=1.0;MSILEN=1.0;SSF=0.00088;SOR=0.0;LSEQ=ATCACATATTGCTGATCTTT;RSEQ=CTTCTACTGAGCACTATTCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:12:12,0:35,0:35,12:0.2553:1,0:27.4:1.0:28.0:1.0:1.0:0.0:60.0:11.0:0.2444:0.0:1.0 0/0:35:0:0,0:35,0:35,0:0.0:1,0:22.1:1.0:31.6:1.0:1.0:0.0:60.0:70.0:1.0:0.0:0.1 +X 39930099 . C G 99 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.00533;SOR=0.0;LSEQ=TCTTTCACAGACGCCTCGTT;RSEQ=CTGGTTGCCACCATTCATAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:151:9:9,0:139,3:142,9:0.0596:1,0:21.7:1.0:31.3:1.0:1.0:0.0:60.0:8.0:0.0544:0.0:1.1 0/0:119:0:0,0:119,0:119,0:0.0:1,0:22.6:1.0:30.4:1.0:1.0:0.0:59.7:22.8:1.0:0.0:0.1 +X 44896832 . C G 237 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0083;LSEQ=ATGTTTGATGCTTTGTTATT;RSEQ=TTACTTAATTTGCCCCAAAT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:425:160:105,55:176,88:264,160:0.3765:2,2:25.9:1.0:32.4:1.0:0.83288:1.04748:60.0:320.0:0.3791:0.0:1.7 0/0:606:3:2,1:396,206:602,3:0.005:2,2:26.0:1.0:28.0:1.0:1.0:1.04:60.0:2.0:0.0034:0.0:1.7 +X 44896888 . C T 231 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTGATTTTTTTGTCTTTCCT;RSEQ=ATCCTTTGCAGTTCAATTTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:675:233:106,127:207,232:439,233:0.3452:2,2:26.8:1.0:29.5:1.0:0.68555:1.06888:59.8:115.5:0.3468:0.0:1.5 0/0:1036:0:0,0:511,524:1035,0:0.0:2,0:25.6:1.0:31.0:1.0:1.0:0.0:60.0:128.375:0.999:0.0:0.2 +X 47425058 . G A 90 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TGTAAATAATCAATTTTTTT;RSEQ=TTATTAATTATAAATATATT;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:7:0,7:0,1:1,7:0.875:0,0:25.1:1.0:32.3:1.0:1.0:0.0:60.0:14.0:0.875:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +X 47430509 . A AGTGT 138 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=32;MSI=18.0;MSILEN=2.0;SSF=0.0;SOR=0.06968;LSEQ=ATATGAAAGCTCAGAGGTAT;RSEQ=GTGTGTGTGTGTGTGTGTGT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:94:22:10,12:10,52:62,22:0.234:2,2:27.6:1.0:31.1:1.0:0.00889:4.24:59.4:44.0:0.2366:0.0319:0.5 0/1:97:2:1,1:12,81:93,2:0.0206:2,2:24.5:1.0:30.1:1.0:0.25622:6.53:60.0:4.0:0.0211:0.0103:0.5 +X 53223092 . C A 61 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=3.0;SSF=0.11083;SOR=0.18352;LSEQ=TGAAGAACCAGGCCCTATTC;RSEQ=TCCTCCGCCAACCCCAAACT;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:275:5:3,2:63,207:270,5:0.0182:2,2:8.0:1.0:26.6:1.0:0.09134:4.89:60.0:4.0:0.0149:0.0:1.8 0/0:296:1:1,0:68,227:295,1:0.0034:2,0:1.0:0.0:27.0:0.0:0.23311:0.0:60.0:2.0:0.0034:0.0:1.0 +X 53224366 . C T 70 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00839;SOR=0.0;LSEQ=ATGAGCCATCTCACAGAAGC;RSEQ=AGGGCAGGCGTTAAGAGACG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:362:6:1,5:214,142:356,6:0.0166:2,2:14.8:1.0:27.2:1.0:0.04251:7.49592:60.0:12.0:0.0169:0.0:1.2 0/0:438:0:0,0:270,168:438,0:0.0:2,0:24.8:1.0:30.4:1.0:1.0:0.0:60.0:61.571:1.0:0.0:0.1 +X 53225501 . T C 86 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GCCTGCTAGCAATGCCTACA;RSEQ=ATACAACCTGTATTGTGTAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:6:6:0,6:0,0:0,6:1.0:0,0:17.8:1.0:33.3:1.0:1.0:0.0:60.0:12.0:1.0:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +X 53246599 . C G 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=0.00013;SOR=0.0;LSEQ=ACAGCCCCTGTTCCACTGGT;RSEQ=TTTAGCACTGACACCAGCAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:47:13:0,13:3,31:34,13:0.2766:2,1:16.5:1.0:32.5:1.0:0.55023:0.0:60.0:26.0:0.2826:0.0:1.0 0/0:41:0:0,0:0,41:41,0:0.0:1,0:22.1:1.0:32.4:1.0:1.0:0.0:60.0:82.0:1.0:0.0:0.0 +X 63415940 . C T 120 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=4.0;MSILEN=1.0;SSF=0.00136;SOR=0.0;LSEQ=TGCTTTCCAGAGCCTTGACG;RSEQ=CCCAGTTAGAAGACAGTCTC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:80:16:0,16:1,63:64,16:0.2:1,1:27.7:1.0:30.1:1.0:1.0:0.0:60.0:15.0:0.1899:0.0:1.3 0/0:38:0:0,0:0,37:37,0:0.0:1,0:22.1:1.0:31.1:1.0:1.0:0.0:59.0:74.0:1.0:0.0:0.1 +X 63425821 . G A 166 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GGTGCGGAACCACTGGCTGG;RSEQ=GCTCCCCACTCCCGCCCCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:175:43:0,43:5,126:131,43:0.2457:1,1:25.6:1.0:30.7:1.0:0.33471:0.0:60.0:13.333:0.2395:0.0:1.2 0/0:149:0:0,0:5,142:147,0:0.0:1,0:23.7:1.0:30.6:1.0:1.0:0.0:60.0:146.0:0.9932:0.0:0.1 +X 66766359 . C T 145 MSI12 SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=17.0;MSILEN=3.0;SSF=0.0;SOR=0.08916;LSEQ=GGTGGTGGTGGGGGTGGTGG;RSEQ=GGCGGCGGCGGCGGCGGCGG;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:103:31:5,26:14,54:68,31:0.301:2,2:10.4:1.0:29.3:1.0:0.78454:1.34423:59.7:6.75:0.2903:0.0:1.5 0/1:82:3:1,2:25,48:73,3:0.0366:2,2:20.0:1.0:19.3:1.0:1.0:1.04111:60.0:0.5:0.0141:0.0:2.0 +X 66789057 . G T 101 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=9.0;MSILEN=1.0;SSF=0.00516;SOR=0.0;LSEQ=GTGGGGGATTTTGTGTGTGG;RSEQ=GGGGGGTTGGGGGTTGAGCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:39:15:0,15:1,23:24,15:0.3846:1,1:23.9:1.0:26.1:1.0:1.0:0.0:58.4:2.75:0.3235:0.0:1.4 0/0:14:0:0,0:2,12:14,0:0.0:2,0:17.6:1.0:29.5:1.0:1.0:0.0:51.7:28.0:1.0:0.0:2.1 +X 66937707 . A G 114 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=CAAGAACCAATCCTAGTCAT;RSEQ=TTTCTGGTCTGCTTTGCAGC;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:17:11:0,11:0,6:6,11:0.6471:0,0:31.7:1.0:33.2:1.0:1.0:0.0:60.0:22.0:0.6875:0.0:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +X 66942476 . A G 87 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.3124;SOR=0.0;LSEQ=ACTCCTTTCAGATCGGATCC;RSEQ=GCTATCCTTTCCCCTGAGAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:35:8:8,0:27,0:27,8:0.2286:1,0:29.3:1.0:29.3:1.0:1.0:0.0:60.0:16.0:0.2353:0.0:1.1 0/0:7:0:0,0:7,0:7,0:0.0:0,0:26.0:1.0:30.1:1.0:1.0:0.0:60.0:14.0:1.0:0.0:0.0 +X 66943154 . C CTCTGTG 79 MSI12 SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=1;MSI=22.0;MSILEN=2.0;SSF=1.0;SOR=0.0;LSEQ=GTTCATGTGAGTTTGTCTGT;RSEQ=TGTGTGTGTGTGTGTGTGTG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:0,5:0,0:0,5:1.0:0,0:15.4:1.0:34.2:1.0:1.0:0.0:54.6:10.0:1.0:0.8:1.0 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +X 66943769 . C A 106 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00215;SOR=0.0;LSEQ=AACTCTGCACTACTCCTCTG;RSEQ=AGTGCCTTGGGGAATTTCCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:162:12:0,12:6,144:150,12:0.0741:1,0:24.2:1.0:29.6:1.0:1.0:0.0:60.0:11.0:0.0683:0.0:1.3 0/0:107:0:0,0:1,106:107,0:0.0:1,0:22.3:1.0:31.1:1.0:1.0:0.0:59.8:34.667:1.0:0.0:0.2 +X 70344763 . G T 252 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=7.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=ATTATGCCTGCTTTTGGCAT;RSEQ=TTTTTTTGCCCCCTCATCCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:485:293:161,132:101,75:176,293:0.6041:2,2:22.2:1.0:30.8:1.0:0.63188:1.10387:60.0:96.667:0.6105:0.0:1.1 0/0:508:0:0,0:143,119:262,0:0.0:2,0:23.3:1.0:31.8:1.0:1.0:0.0:60.0:261.0:0.9703:0.0:0.1 +X 70347614 . C T 123 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=4;MSI=3.0;MSILEN=1.0;SSF=0.00015;SOR=0.0;LSEQ=CAGTCTGTTTTGTCCCATCT;RSEQ=CCTTTTCTTGTCTCAAGATC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:15:15,0:69,1:70,15:0.1765:1,1:27.5:1.0:31.5:1.0:1.0:0.0:60.0:30.0:0.1765:0.0:1.1 0/0:64:0:0,0:63,1:64,0:0.0:1,0:28.0:1.0:31.0:1.0:1.0:0.0:59.6:128.0:1.0:0.0:0.1 +X 70352491 . G A 182 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GAGAAGCATCATAGGAAAGT;RSEQ=GAAAATCAGAGGATAAGAGT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:53:12,41:15,108:123,53:0.3011:2,2:21.1:1.0:31.8:1.0:0.10886:2.1:60.0:106.0:0.3046:0.0:2.1 0/0:71:0:0,0:6,65:71,0:0.0:2,0:25.9:1.0:29.9:1.0:1.0:0.0:60.0:22.667:1.0:0.0:0.6 +X 70356829 . A G 218 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=TTCTATAACACACCTTAACT;RSEQ=CAGGCAAGGCTCCATAGGCC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:975:129:57,72:390,454:844,129:0.1323:2,2:23.4:1.0:31.2:1.0:0.70487:1.08497:59.9:24.8:0.1288:0.0:1.1 0/0:922:0:0,0:447,474:921,0:0.0:2,0:24.0:1.0:28.1:1.0:1.0:0.0:59.9:130.571:1.0:0.0:0.2 +X 72744762 . C CT 75 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.01167;SOR=0.0;LSEQ=CCTTTTGCTTCCTCTCAGCC;RSEQ=TTTTTTTTAGTCTGATGTAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:6:3,3:107,35:142,6:0.0405:2,2:24.7:1.0:29.3:1.0:0.17621:3.02932:56.7:12.0:0.0414:0.0068:0.5 0/0:160:0:0,0:118,40:158,0:0.0:2,0:23.7:1.0:30.4:1.0:1.0:0.0:60.0:51.667:0.9936:0.0:0.2 +X 74803898 . T C 180 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGAAATCTCCAGGACTTCAG;RSEQ=GAGAAAGGAAGTCATCTTCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:225:54:36,18:110,61:171,54:0.24:2,2:27.5:1.0:31.4:1.0:0.87032:1.11:45.9:53.0:0.2366:0.0:1.1 0/0:254:0:0,0:159,95:254,0:0.0:2,0:26.1:1.0:29.1:1.0:1.0:0.0:58.3:83.667:1.0:0.0:0.1 +X 76814401 . GT G 82 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.03494;SOR=0.0;LSEQ=ATATGACTTTTTGATACTTA;RSEQ=TTTTTTTTAACTATCAAGAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:77:6:0,6:4,67:71,6:0.0779:2,0:24.7:1.0:32.0:1.0:1.0:0.0:60.0:12.0:0.08:0.026:0.2 0/0:60:0:0,0:2,58:60,0:0.0:1,0:26.2:1.0:29.8:1.0:1.0:0.0:60.0:120.0:1.0:0.0:0.0 +X 76939830 . A G 192 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=GATGTATGTTCATATACTTT;RSEQ=TTACTCTTTTCACTGTCAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:702:61:29,32:326,315:641,61:0.0869:2,2:25.0:1.0:32.4:1.0:0.68821:1.14176:59.7:60.0:0.0866:0.0:1.1 0/0:896:0:0,0:452,444:896,0:0.0:2,0:24.1:1.0:28.5:1.0:1.0:0.0:60.0:111.0:1.0:0.0:0.1 +X 100057572 . C T 229 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=AGCTATGCCTCCACCACCAC;RSEQ=TCAGGGAGTTAAGTGAAAAG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:659:176:95,81:262,221:483,176:0.2671:2,2:27.0:1.0:30.7:1.0:1.0:1.0108:52.7:87.0:0.2681:0.0:1.1 0/0:766:0:0,0:395,370:765,0:0.0:2,0:24.7:1.0:30.4:1.0:1.0:0.0:57.2:28.423:1.0:0.0:0.2 +X 100609517 . G GA 70 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=8;MSI=9.0;MSILEN=1.0;SSF=0.0291;SOR=0.0;LSEQ=GGCAGAAAACGCTAGAATGA;RSEQ=AAAAAAAAGAAAAGGAGAGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:176:5:4,1:158,13:171,5:0.0284:2,2:21.2:1.0:30.5:1.0:0.34258:3.00912:60.0:10.0:0.0286:0.017:0.4 0/0:179:0:0,0:161,18:179,0:0.0:2,0:20.8:1.0:31.5:1.0:1.0:0.0:60.0:88.5:1.0:0.0:0.8 +X 100615505 . G T 174 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=2.0;SSF=0.0;SOR=0.0189;LSEQ=TATGCCGCAGCACTTTTTGC;RSEQ=TGTAGGGAGTGGGCAGGCAC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:308:44:37,7:209,55:264,44:0.1429:2,2:25.5:1.0:32.0:1.0:0.54558:1.39:60.0:88.0:0.1443:0.0:1.0 0/0:320:1:0,1:224,95:319,1:0.0031:2,0:1.0:0.0:27.0:0.0:0.3:0.0:60.0:2.0:0.0031:0.0:1.0 +X 123159533 . A G 100 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=1.0;MSILEN=1.0;SSF=0.10123;SOR=0.0;LSEQ=TGTGTTTGGTAACGTGCTAT;RSEQ=GTATGATGTTTTGGGGAAAC;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:66:8:8,0:57,1:58,8:0.1212:1,0:28.6:1.0:33.4:1.0:1.0:0.0:60.0:16.0:0.1231:0.0:1.4 0/0:29:0:0,0:29,0:29,0:0.0:1,0:28.8:1.0:28.1:1.0:1.0:0.0:60.0:58.0:1.0:0.0:0.1 +X 123184027 . C T 174 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=5.0;MSILEN=1.0;SSF=0.0;SOR=0.0195;LSEQ=TATGCATCGTTTTTCCTTCC;RSEQ=CCATTCAGTGATGCGATAGC;STATUS=LikelySomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:553:51:33,18:337,165:502,51:0.0922:2,2:20.4:1.0:30.8:1.0:0.75562:1.11382:60.0:50.0:0.0921:0.0:1.1 0/0:507:1:0,1:308,196:504,1:0.002:2,0:1.0:0.0:22.0:0.0:0.3901:0.0:60.0:2.0:0.002:0.0:1.0 +X 123184284 . T A 110 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=4.0;MSILEN=1.0;SSF=0.00697;SOR=0.0;LSEQ=TGGAAGCCTCCCCTTTATTC;RSEQ=TTTCTATCTTCTCTGTAAAA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:85:11:1,10:2,72:74,11:0.1294:1,2:24.8:1.0:31.8:1.0:0.34369:3.52:60.0:22.0:0.131:0.0:1.0 0/0:50:0:0,0:1,49:50,0:0.0:1,0:23.4:1.0:29.2:1.0:1.0:0.0:60.0:49.0:1.0:0.0:0.0 +X 123191922 . A G 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.00141;SOR=0.0;LSEQ=AAAAATATTCCTTGTAGCAC;RSEQ=GTAAATTGTGAATAGAATGG;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:15:0,15:0,109:109,15:0.121:1,1:21.8:1.0:30.1:1.0:1.0:0.0:60.0:14.0:0.1176:0.0:1.0 0/0:67:0:0,0:1,66:67,0:0.0:1,0:24.6:1.0:31.0:1.0:1.0:0.0:60.0:134.0:1.0:0.0:0.1 +X 123202318 . C CTATA 113 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=3;MSI=3.0;MSILEN=2.0;SSF=0.00108;SOR=0.0;LSEQ=CAGAAGTAGAGTTAATAAAG;RSEQ=TATGAGATAATGTTTTACAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:112:14:13,1:98,0:98,14:0.125:1,1:28.2:1.0:29.8:1.0:0.125:0.0:60.0:28.0:0.1308:0.0268:0.0 0/0:69:0:0,0:68,1:69,0:0.0:1,0:21.6:1.0:32.2:1.0:1.0:0.0:59.8:138.0:1.0:0.0:0.1 +X 123217527 . A G 117 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.03469;SOR=0.0;LSEQ=ATTAATACACAAAAAAGTTT;RSEQ=TACTTCAGCAACTTTATAAT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:88:12:0,12:1,75:76,12:0.1364:1,0:22.6:1.0:32.8:1.0:1.0:0.0:60.0:24.0:0.1463:0.0:1.1 0/0:31:0:0,0:0,31:31,0:0.0:1,0:23.3:1.0:30.6:1.0:1.0:0.0:60.0:62.0:1.0:0.0:0.0 +X 123499949 . T TAGAA 101 PASS SAMPLE=PoolTumor2-T;TYPE=Insertion;SHIFT3=2;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=TTAGTGACTATGTGAAATCT;RSEQ=AGCATATCAAAAGTAGGTAA;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:11:9:0,9:0,2:2,9:0.8182:0,0:30.6:1.0:31.9:1.0:1.0:0.0:57.4:18.0:0.8182:0.0:0.6 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +X 123499991 . T G 96 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=1;MSI=3.0;MSILEN=1.0;SSF=1.0;SOR=0.0;LSEQ=ATAATTAAATGAACAATTAT;RSEQ=TACCAAATGATACCAATATG;STATUS=SampleSpecific GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:0,8:0,0:0,8:1.0:0,0:19.4:1.0:32.1:1.0:1.0:0.0:58.8:16.0:1.0:0.0:1.3 0/0:0:0:0,0:0,0:0,0:0.0:0:0.0:0.0:0.0:0.0:1.0:0.0:0.0:0.0:0.0:0.0:0.0 +X 136524003 . G A 61 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=1.0;MSILEN=1.0;SSF=0.08356;SOR=0.0;LSEQ=TGATGGCCTGCATCTGGGCC;RSEQ=CTCGCTGGGCCGCAGCTGCT;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:291:5:3,2:76,210:286,5:0.0172:2,2:22.0:1.0:26.6:1.0:0.12559:4.12:35.6:10.0:0.0175:0.0:1.0 0/0:199:0:0,0:65,134:199,0:0.0:2,0:28.0:1.0:30.3:1.0:1.0:0.0:38.7:48.75:1.0:0.0:0.3 +X 139479797 . C T 140 PASS SAMPLE=PoolTumor2-T;TYPE=SNV;SHIFT3=0;MSI=2.0;MSILEN=1.0;SSF=0.0;SOR=0.0;LSEQ=CTTAGAGATCCAAATCTACT;RSEQ=CTATCAGTAAGTAAAGATCA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:148:25:15,10:64,59:123,25:0.1689:2,2:24.6:1.0:30.3:1.0:0.51541:1.38:60.0:24.0:0.1678:0.0:1.0 0/0:98:0:0,0:56,42:98,0:0.0:2,0:24.7:1.0:30.3:1.0:1.0:0.0:60.0:97.0:1.0:0.0:0.2 +X 145042124 . TA T 71 PASS SAMPLE=PoolTumor2-T;TYPE=Deletion;SHIFT3=7;MSI=8.0;MSILEN=1.0;SSF=0.0686;SOR=0.0;LSEQ=CATGCAAAAAAGACATAGGT;RSEQ=AAAAAAATAGTTTCTATGTA;STATUS=StrongSomatic GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:193:5:2,3:87,101:188,5:0.0259:2,2:21.2:1.0:31.0:1.0:1.0:1.29039:60.0:10.0:0.0265:0.0:0.4 0/0:154:0:0,0:70,84:154,0:0.0:2,0:25.8:1.0:28.1:1.0:1.0:0.0:60.0:50.333:1.0:0.0:0.8